Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009566.1 Hibiscus syriacus cultivar Beakdansim tig00116925_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: 439029
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:206352 original size:28 final size:28
Alignment explanation
Indices: 206298--206353 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
206288 GAGGTAAGGG
* * *
206298 TTAGAGTTTATGGTTTAAGATTAATGAT
1 TTAGAGTTTAGGGCTTAAGAGTAATGAT
206326 TTAGAGTTTAGGGCTT-AGAGTACATGAT
1 TTAGAGTTTAGGGCTTAAGAGTA-ATGAT
206354 GCGATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 5 0.21
28 19 0.79
ACGTcount: A:0.30, C:0.04, G:0.25, T:0.41
Consensus pattern (28 bp):
TTAGAGTTTAGGGCTTAAGAGTAATGAT
Found at i:215660 original size:51 final size:50
Alignment explanation
Indices: 215550--215660 Score: 136
Period size: 49 Copynumber: 2.2 Consensus size: 50
215540 GTATTAAGAG
* * * *
215550 CTACATTTTTTTATTTTATTCACTTATATTGGTGTGTATGTGTTAAGTGT
1 CTACATTTTTTTATTTTATTCACTTACATTGATGTATATGAGTTAAGTGT
* *
215600 -TACAATTTTTTATTTTATTTACTTACATTGATGTAAATATGAGTTAAGT-T
1 CTACATTTTTTTATTTTATTCACTTACATTGATGT--ATATGAGTTAAGTGT
215650 CTACATTTTTT
1 CTACATTTTTT
215661 GCAGTATGAA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
49 30 0.59
50 1 0.02
51 20 0.39
ACGTcount: A:0.25, C:0.08, G:0.12, T:0.55
Consensus pattern (50 bp):
CTACATTTTTTTATTTTATTCACTTACATTGATGTATATGAGTTAAGTGT
Found at i:217959 original size:20 final size:20
Alignment explanation
Indices: 217934--217971 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
217924 TTTGGTTCAC
217934 GGAATGTAAGATTACCAGTT
1 GGAATGTAAGATTACCAGTT
217954 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
217972 GGAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTT
Found at i:217981 original size:16 final size:18
Alignment explanation
Indices: 217934--217983 Score: 59
Period size: 20 Copynumber: 2.7 Consensus size: 18
217924 TTTGGTTCAC
217934 GGAATGTAAGATTACCAGTT
1 GGAA-GTAAGATTACCAG-T
217954 GGAATGTAAGATTACCAG-
1 GGAA-GTAAGATTACCAGT
217972 GGAA-TAAGATTA
1 GGAAGTAAGATTA
217984 ATGTGAATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
16 8 0.27
18 4 0.13
20 18 0.60
ACGTcount: A:0.40, C:0.08, G:0.26, T:0.26
Consensus pattern (18 bp):
GGAAGTAAGATTACCAGT
Found at i:218163 original size:2 final size:2
Alignment explanation
Indices: 218158--218193 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
218148 TAAATTCATA
218158 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
218194 AAATTAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:223226 original size:21 final size:22
Alignment explanation
Indices: 223187--223229 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
223177 TTTAATATCT
223187 AATTTATTTATTAATTAATTTA
1 AATTTATTTATTAATTAATTTA
223209 AATTTA-TT-TTATATTAATTTA
1 AATTTATTTATTA-ATTAATTTA
223230 TTATAGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 3 0.15
21 11 0.55
22 6 0.30
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
AATTTATTTATTAATTAATTTA
Found at i:223679 original size:36 final size:39
Alignment explanation
Indices: 223641--223723 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 39
223631 TTTTTGCATT
223641 AAAATAATATTAATTAA-TAATA-TTTTATTATTTATTAA
1 AAAATAATA-TAATTAACTAATATTTTTATTATTTATTAA
* *
223679 AAAATAATATAGTTAACTTATTATTTTTATTATTTATTAA
1 AAAATAATATAATTAAC-TAATATTTTTATTATTTATTAA
*
223719 TAAAT
1 AAAAT
223724 TAAAATTATT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
37 6 0.15
38 9 0.23
39 4 0.10
40 20 0.51
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (39 bp):
AAAATAATATAATTAACTAATATTTTTATTATTTATTAA
Found at i:229361 original size:239 final size:230
Alignment explanation
Indices: 228919--229387 Score: 857
Period size: 239 Copynumber: 2.0 Consensus size: 230
228909 CTATATAATG
228919 TAATTATATAAAATATGTTATTATTATTATTTTTTGAATGAAAGAAAGAAACAAATACTACAGAG
1 TAATTATATAAAATATGTTATTATTATTATTTTTTGAATGAAAGAAAGAAACAAATACTACAGAG
228984 CTACTCCATTTGTTGCCAGTATCCAGCAGCCACCAGATTACCGTCGTGGTTATCATCAGTGGTGG
66 CTACTCCATTTGTTGCCAGTATCCAGCAGCCACCAGATTACCGTCGTGGTTATCATCAGTGGTGG
229049 TGCTGGAAAATTTGGACACCGAATCTGCCGATCGAGCCAACTTAGCCATTTCATCTGCTATTGTG
131 TGCTGGAAAATTTGGACACCGAATCTGCCGATCGAGCCAACTTAGCCATTTCATCTGCTATTGTG
229114 TTATCCCTCCTCGATACTTTTCTGAACTATACCCT
196 TTATCCCTCCTCGATACTTTTCTGAACTATACCCT
229149 TAATTATATAAAATTATATGTTATTATTATTATTTTTTGAATGAAAAGAAAGAAACCAAACTACT
1 TAATTATAT-AAA--ATATGTTATTATTATTATTTTTTGAATG-AAAGAAAGAAA-CAAA-TACT
229214 ACAGAGCTACTCCATTTGTTGCCAGTATCCAGCAGCCACCAGATTAACCGTCGTGGTTATCATCA
60 ACAGAGCTACTCCATTTGTTGCCAGTATCCAGCAGCCACCAGATT-ACCGTCGTGGTTATCATCA
229279 GTGGTGGTTGCTGGAAAATTTGGACACCGAAATCTGCCGATCGAGCCAACTTAGCCATTTCATCT
124 GTGGTGG-TGCTGGAAAATTTGGACACCG-AATCTGCCGATCGAGCCAACTTAGCCATTTCATCT
229344 GCTATTGTGTTATCCCTCCTCGATACTTTTCTGAACTATACCCT
187 GCTATTGTGTTATCCCTCCTCGATACTTTTCTGAACTATACCCT
229388 CCAATTCTGC
Statistics
Matches: 230, Mismatches: 0, Indels: 9
0.96 0.00 0.04
Matches are distributed among these distances:
230 9 0.04
231 3 0.01
233 28 0.12
234 11 0.05
235 4 0.02
236 49 0.21
237 26 0.11
238 21 0.09
239 79 0.34
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.33
Consensus pattern (230 bp):
TAATTATATAAAATATGTTATTATTATTATTTTTTGAATGAAAGAAAGAAACAAATACTACAGAG
CTACTCCATTTGTTGCCAGTATCCAGCAGCCACCAGATTACCGTCGTGGTTATCATCAGTGGTGG
TGCTGGAAAATTTGGACACCGAATCTGCCGATCGAGCCAACTTAGCCATTTCATCTGCTATTGTG
TTATCCCTCCTCGATACTTTTCTGAACTATACCCT
Found at i:229910 original size:40 final size:40
Alignment explanation
Indices: 229856--229934 Score: 149
Period size: 40 Copynumber: 2.0 Consensus size: 40
229846 ATTCGTCATC
*
229856 AAAAAGTAAACTATTCCTCCTTGCTCAAAGACTCCAAATA
1 AAAAAGTAAACTATTCCTCCTTGCCCAAAGACTCCAAATA
229896 AAAAAGTAAACTATTCCTCCTTGCCCAAAGACTCCAAAT
1 AAAAAGTAAACTATTCCTCCTTGCCCAAAGACTCCAAAT
229935 GATGGCGCCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.42, C:0.27, G:0.08, T:0.24
Consensus pattern (40 bp):
AAAAAGTAAACTATTCCTCCTTGCCCAAAGACTCCAAATA
Found at i:230598 original size:28 final size:29
Alignment explanation
Indices: 230566--230622 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
230556 AAAGTTGTAA
230566 TAATTAAT-TTATTAATTGTTTAAAAAAT
1 TAATTAATATTATTAATTGTTTAAAAAAT
* * *
230594 TAATTATTATTATTATTTTTTTAAAAAAT
1 TAATTAATATTATTAATTGTTTAAAAAAT
230623 AACATGAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 7 0.28
29 18 0.72
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
TAATTAATATTATTAATTGTTTAAAAAAT
Found at i:234500 original size:36 final size:36
Alignment explanation
Indices: 234436--234739 Score: 491
Period size: 36 Copynumber: 8.4 Consensus size: 36
234426 TAAGGTGAAT
* *
234436 AAGTCGAACGGAAGGAAGCATTGACACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
* *
234472 AAGTTGAACGGAAGGATGCATCGGCACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
* *
234508 AAGTCGAACGGAAGGAGGCATCGACACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
234544 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
* *
234580 AAGTCGAACGGAAGGAAGCATCGACACTTTCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
*
234616 AAGTCGAACGGAAGGAAGCATCGGCACATCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
* *
234652 AAGTCGAACGGAATGAACCATCGGCACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
**
234688 AAGTCGAACGGAAGGAAGCATTAGCACTTCCGATTC
1 AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
234724 AAGTCGAACGGAAGGA
1 AAGTCGAACGGAAGGA
234740 TGTATTGCAC
Statistics
Matches: 247, Mismatches: 21, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 247 1.00
ACGTcount: A:0.32, C:0.23, G:0.27, T:0.18
Consensus pattern (36 bp):
AAGTCGAACGGAAGGAAGCATCGGCACTTCCGATTC
Found at i:239854 original size:18 final size:17
Alignment explanation
Indices: 239822--239863 Score: 66
Period size: 18 Copynumber: 2.4 Consensus size: 17
239812 AAAATATATT
*
239822 TTGATGATCAAAACGAA
1 TTGATGCTCAAAACGAA
239839 TTGATGCTCAAAAACGAA
1 TTGATGCTC-AAAACGAA
239857 TTGATGC
1 TTGATGC
239864 AAAGCGAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 8 0.35
18 15 0.65
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.26
Consensus pattern (17 bp):
TTGATGCTCAAAACGAA
Found at i:241909 original size:16 final size:14
Alignment explanation
Indices: 241881--241923 Score: 54
Period size: 15 Copynumber: 3.1 Consensus size: 14
241871 TATGTGCAAC
241881 TTAAAAAAGACAAA
1 TTAAAAAAGACAAA
241895 GTTAAAAAAGAACAAA
1 -TTAAAAAAG-ACAAA
241911 -TAAAAAAG-CAAA
1 TTAAAAAAGACAAA
241923 T
1 T
241924 AAATTGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 4 0.15
14 8 0.31
15 9 0.35
16 5 0.19
ACGTcount: A:0.70, C:0.07, G:0.09, T:0.14
Consensus pattern (14 bp):
TTAAAAAAGACAAA
Found at i:241922 original size:12 final size:13
Alignment explanation
Indices: 241882--241926 Score: 56
Period size: 12 Copynumber: 3.3 Consensus size: 13
241872 ATGTGCAACT
241882 TAAAAAAGACAAA
1 TAAAAAAGACAAA
241895 GTTAAAAAAGAACAAA
1 --TAAAAAAG-ACAAA
241911 TAAAAAAG-CAAA
1 TAAAAAAGACAAA
241923 TAAA
1 TAAA
241927 TTGAATAGTG
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 8 0.28
14 8 0.28
15 8 0.28
16 5 0.17
ACGTcount: A:0.73, C:0.07, G:0.09, T:0.11
Consensus pattern (13 bp):
TAAAAAAGACAAA
Found at i:242033 original size:19 final size:19
Alignment explanation
Indices: 241995--242039 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
241985 GTAATAAAAA
* *
241995 TTATTTAAAAAATTATTAT
1 TTATTTAAAAAATCAATAT
*
242014 TTATTTAAAATATCAATAT
1 TTATTTAAAAAATCAATAT
242033 TT-TTTAA
1 TTATTTAA
242040 TATTTTTGAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTTAAAAAATCAATAT
Found at i:242562 original size:38 final size:40
Alignment explanation
Indices: 242508--242591 Score: 111
Period size: 41 Copynumber: 2.1 Consensus size: 40
242498 AAACTACAAA
* **
242508 ATTTAATAAATAAAAT-AATTTTTGATTT-AT-CTAAATT
1 ATTTAATAAATAAAATAAATATTAAATTTGATCCTAAATT
242545 ATTTAATAAAATAAAATAAATATTAAATTTGATCCTAAATT
1 ATTTAAT-AAATAAAATAAATATTAAATTTGATCCTAAATT
242586 ATTTAA
1 ATTTAA
242592 AATACTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
37 7 0.17
38 9 0.22
39 9 0.22
40 2 0.05
41 13 0.32
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (40 bp):
ATTTAATAAATAAAATAAATATTAAATTTGATCCTAAATT
Found at i:246392 original size:16 final size:16
Alignment explanation
Indices: 246368--246405 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
246358 CATAAACTCT
* *
246368 AAATCTAAAAAAAGTA
1 AAATATAAAAAAACTA
246384 AAATATAAAAAAACTA
1 AAATATAAAAAAACTA
246400 AAATAT
1 AAATAT
246406 GAAGACGTAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.71, C:0.05, G:0.03, T:0.21
Consensus pattern (16 bp):
AAATATAAAAAAACTA
Found at i:246847 original size:28 final size:28
Alignment explanation
Indices: 246807--246878 Score: 112
Period size: 28 Copynumber: 2.6 Consensus size: 28
246797 CGTTGTTTAA
246807 ACGAGCCAAATCGAACTCGAGTATTGCT
1 ACGAGCCAAATCGAACTCGAGTATTGCT
246835 ACGAGCCAAATCGAACTCGAGTATTGCT
1 ACGAGCCAAATCGAACTCGAGTATTGCT
*
246863 --GAGCTCAACTCGAACT
1 ACGAGC-CAAATCGAACT
246879 TGAAAACTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 4 0.10
27 10 0.24
28 28 0.67
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (28 bp):
ACGAGCCAAATCGAACTCGAGTATTGCT
Found at i:264878 original size:22 final size:22
Alignment explanation
Indices: 264859--264931 Score: 73
Period size: 23 Copynumber: 3.5 Consensus size: 22
264849 AGAGGGAATT
264859 GATACCCCCTTGAAGGGGAACC
1 GATACCCCCTTGAAGGGGAACC
* *
264881 GATTCCCCCTTTGAAGGGGAACT
1 GATACCCCC-TTGAAGGGGAACC
* *
264904 GAT-TCCCC-T--AGGGGAATC
1 GATACCCCCTTGAAGGGGAACC
264922 GATACCCCCT
1 GATACCCCCT
264932 GGGGTTCTGG
Statistics
Matches: 42, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
18 10 0.24
19 4 0.10
20 1 0.02
22 12 0.29
23 15 0.36
ACGTcount: A:0.23, C:0.32, G:0.25, T:0.21
Consensus pattern (22 bp):
GATACCCCCTTGAAGGGGAACC
Found at i:264894 original size:23 final size:22
Alignment explanation
Indices: 264863--264911 Score: 80
Period size: 23 Copynumber: 2.2 Consensus size: 22
264853 GGAATTGATA
264863 CCCCCTTGAAGGGGAACCGATT
1 CCCCCTTGAAGGGGAACCGATT
*
264885 CCCCCTTTGAAGGGGAACTGATT
1 CCCCC-TTGAAGGGGAACCGATT
264908 CCCC
1 CCCC
264912 TAGGGGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 5 0.20
23 20 0.80
ACGTcount: A:0.20, C:0.35, G:0.24, T:0.20
Consensus pattern (22 bp):
CCCCCTTGAAGGGGAACCGATT
Found at i:268449 original size:17 final size:18
Alignment explanation
Indices: 268412--268449 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
268402 TGAAAAAATG
*
268412 TATAATTTAGACTTATTT
1 TATAATTAAGACTTATTT
*
268430 TATAATTAAGCCTT-TTT
1 TATAATTAAGACTTATTT
268447 TAT
1 TAT
268450 TAAATGGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 6 0.33
18 12 0.67
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (18 bp):
TATAATTAAGACTTATTT
Found at i:268899 original size:27 final size:27
Alignment explanation
Indices: 268869--268929 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
268859 TTCATTCACT
268869 CTCCGCCTCCAAATCTCTTAACTCGGC
1 CTCCGCCTCCAAATCTCTTAACTCGGC
*
268896 CTCCGCCTCCAAATCTCTTAACTTGGC
1 CTCCGCCTCCAAATCTCTTAACTCGGC
268923 CTCCGCC
1 CTCCGCC
268930 ACTCTCATCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.16, C:0.46, G:0.11, T:0.26
Consensus pattern (27 bp):
CTCCGCCTCCAAATCTCTTAACTCGGC
Found at i:281236 original size:172 final size:172
Alignment explanation
Indices: 280941--281287 Score: 559
Period size: 172 Copynumber: 2.0 Consensus size: 172
280931 CAACAACTCA
* * * *
280941 GTTGACAGATGCATGGATTCTTGATTCAGGATGCTCTTATTATATAACGCCTAACAAAGAGTGGT
1 GTTGACAAATGCATGGATTCTTGATTCAAGATGCTCTTATCATATAACACCTAACAAAGAGTGGT
* * *
281006 TTTCGACATACATGTCAGTTAATTATGGTTCTGTCTATTTAAGTGATGAAAGATGTTGCAATATT
66 TTTCGACATACAAGTCAGTTAATTATAGTTCTGTCTATTTAAGTGACGAAAGATGTTGCAATATT
* *
281071 GTTTGTATTGGTGAAGTCAGAATTAAGATGTATGATAGTATT
131 GTTGGTATTGGTGAAGTCAAAATTAAGATGTATGATAGTATT
**
281113 GTTGACAAATGCATGGATTCTTGATTCAAGATGCTCTTATCATATAACACCTAACATGGAGTGGT
1 GTTGACAAATGCATGGATTCTTGATTCAAGATGCTCTTATCATATAACACCTAACAAAGAGTGGT
* * *
281178 TTTCGACATACAAGTCAGTTAATTTTAGTTCTGTCTATTTAAGTGACGACATATGTTGCAATATT
66 TTTCGACATACAAGTCAGTTAATTATAGTTCTGTCTATTTAAGTGACGAAAGATGTTGCAATATT
*
281243 GTTGGTATTGGTGAAGTCAAAATTAAGATGTATGATGGTATT
131 GTTGGTATTGGTGAAGTCAAAATTAAGATGTATGATAGTATT
281285 GTT
1 GTT
281288 AGGACATTCT
Statistics
Matches: 160, Mismatches: 15, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
172 160 1.00
ACGTcount: A:0.30, C:0.11, G:0.21, T:0.38
Consensus pattern (172 bp):
GTTGACAAATGCATGGATTCTTGATTCAAGATGCTCTTATCATATAACACCTAACAAAGAGTGGT
TTTCGACATACAAGTCAGTTAATTATAGTTCTGTCTATTTAAGTGACGAAAGATGTTGCAATATT
GTTGGTATTGGTGAAGTCAAAATTAAGATGTATGATAGTATT
Found at i:285858 original size:23 final size:23
Alignment explanation
Indices: 285814--285862 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
285804 ATAAAGAACC
*
285814 AAAATAAACTTAAATATACCATT
1 AAAATAAACTTAAACATACCATT
*
285837 AAAATAAAGTTAAAACAT-CCATT
1 AAAATAAACTT-AAACATACCATT
285860 AAA
1 AAA
285863 CCAACACCAC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.59, C:0.12, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTTAAACATACCATT
Found at i:287683 original size:25 final size:25
Alignment explanation
Indices: 287649--287703 Score: 110
Period size: 25 Copynumber: 2.2 Consensus size: 25
287639 AACTAGACTA
287649 CATGCTATGTGATGCGATGCAATTC
1 CATGCTATGTGATGCGATGCAATTC
287674 CATGCTATGTGATGCGATGCAATTC
1 CATGCTATGTGATGCGATGCAATTC
287699 CATGC
1 CATGC
287704 AAGGTACCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.31
Consensus pattern (25 bp):
CATGCTATGTGATGCGATGCAATTC
Found at i:288231 original size:15 final size:15
Alignment explanation
Indices: 288198--288240 Score: 54
Period size: 14 Copynumber: 3.0 Consensus size: 15
288188 AAAATAATAT
* *
288198 TAAAATTAAAACTAA
1 TAAAAATAAAACAAA
288213 -AAAAATAAAACAAA
1 TAAAAATAAAACAAA
288227 TAAAAAT-AAACAAA
1 TAAAAATAAAACAAA
288241 CAAACACTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
14 19 0.76
15 6 0.24
ACGTcount: A:0.77, C:0.07, G:0.00, T:0.16
Consensus pattern (15 bp):
TAAAAATAAAACAAA
Found at i:291497 original size:23 final size:23
Alignment explanation
Indices: 291471--291519 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
291461 ATAAAGAACC
291471 AAAATAAACTT-AAATATACCATT
1 AAAATAAACTTAAAATAT-CCATT
*
291494 AAAATAAAGTTAAAATATCCATT
1 AAAATAAACTTAAAATATCCATT
291517 AAA
1 AAA
291520 CCAACACCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 18 0.75
24 6 0.25
ACGTcount: A:0.59, C:0.10, G:0.02, T:0.29
Consensus pattern (23 bp):
AAAATAAACTTAAAATATCCATT
Found at i:294861 original size:65 final size:65
Alignment explanation
Indices: 294728--294887 Score: 188
Period size: 65 Copynumber: 2.5 Consensus size: 65
294718 TGCACTAAGA
*
294728 GTGCAACGATGCATAAAATGCATTCGATG-TTTCAAAATAGCCGTAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCGTAGTGCATCGATGCATGACTG
* *
294792 GTGCATCGATACATCAAATGCATTCGATGTTTTCATAAA-A-CTC-TGAGTGCATCGATGCATAG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTTCA-AAATAGC-CGT-AGTGCATCGATGCAT-G
294854 TA-T-
62 -ACTG
* *
294857 GTGCATCGATGCATGAAATGCATTCAATGTT
1 GTGCATCGATGCATAAAATGCATTCGATGTT
294888 CAATTTATTT
Statistics
Matches: 84, Mismatches: 6, Indels: 11
0.83 0.06 0.11
Matches are distributed among these distances:
64 28 0.33
65 50 0.60
66 5 0.06
67 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTTCAAAATAGCCGTAGTGCATCGATGCATGACTG
Found at i:297567 original size:44 final size:44
Alignment explanation
Indices: 297518--297614 Score: 135
Period size: 44 Copynumber: 2.2 Consensus size: 44
297508 GGCCTTGTGC
* *
297518 ATCGATGCACATTC-AAGGCATGCATCGGTGCACCT-TTATGGTGT
1 ATCGATGCACATTCAAAGGCATGCATCGATGCA-CTGTTA-AGTGT
*
297562 ATCGATGCACATTCAAAGGGATGCATCGATGCACTGTTAAGTGT
1 ATCGATGCACATTCAAAGGCATGCATCGATGCACTGTTAAGTGT
297606 ATCGATGCA
1 ATCGATGCA
297615 TTAAGCACAA
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
44 29 0.60
45 19 0.40
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.28
Consensus pattern (44 bp):
ATCGATGCACATTCAAAGGCATGCATCGATGCACTGTTAAGTGT
Found at i:301717 original size:117 final size:117
Alignment explanation
Indices: 301497--301717 Score: 259
Period size: 117 Copynumber: 1.9 Consensus size: 117
301487 ATTTCAAATC
* * *
301497 GAAATTTTCTTTTGCAATATTTTTAAATTTTATTTTTGAAAGCTCTAAATCCTTCTTAACGATTT
1 GAAAATTTCTTTTGCAATATTTTCAAATTTTATTTTTGAAAGCTCTAAATCCTTCTCAACGATTT
* * *
301562 CATTTTGTTTTTCAAAATCCATTTTCGTTTCTAGAAGAATTTTGTTTAATTT
66 CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAATTTTGTTTAATTT
* * * * *
301614 GAAAATTTCTTTTTCAA-AGTTTTCAGATTTTATTTTTGAAAGCTCTAACTCATTTCTCAA-TAT
1 GAAAATTTCTTTTGCAATA-TTTTCAAATTTTATTTTTGAAAGCTCTAAATC-CTTCTCAACGAT
* * **
301677 TTCATTTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAA
64 TTCATTTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
301718 GATCATTTTT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
116 1 0.01
117 75 0.87
118 10 0.12
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.50
Consensus pattern (117 bp):
GAAAATTTCTTTTGCAATATTTTCAAATTTTATTTTTGAAAGCTCTAAATCCTTCTCAACGATTT
CATTTTGATTTTCAAAATCCATTTTAGTTTCTAAAAGAATTTTGTTTAATTT
Found at i:303074 original size:64 final size:64
Alignment explanation
Indices: 302989--303198 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
302979 TGCACTAAGA
* * *
302989 GTGCAACGATGCATAAAATGCATTCGATGTTTCAAAATAACCTGAGTACATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAACCTGAGTGCATCGATGCATGGTTG
* * * *
303053 GTGCATCGATGCATCAAATGCATTCGACGTTTTCATAA-AACTCTGAGTGTATCGATGCATAGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAAAATAAC-CTGAGTGCATCGATGCATGGT-
303117 T-
63 TG
* * ** *
303118 GTGCATCGATACATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATA-ACC-TGAGTGCATCGATGCATGG-T
303181 TG
63 TG
*
303183 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
303199 CTTTGAAAAT
Statistics
Matches: 119, Mismatches: 19, Indels: 15
0.78 0.12 0.10
Matches are distributed among these distances:
63 4 0.03
64 46 0.39
65 68 0.57
66 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAACCTGAGTGCATCGATGCATGGTTG
Found at i:308377 original size:13 final size:13
Alignment explanation
Indices: 308346--308371 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
308336 AAAGATATAA
308346 ATAAATTTGAGGG
1 ATAAATTTGAGGG
308359 ATAAATTTGAGGG
1 ATAAATTTGAGGG
308372 GAAAATATCC
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:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (13 bp):
ATAAATTTGAGGG
Found at i:317910 original size:4 final size:4
Alignment explanation
Indices: 317895--317937 Score: 50
Period size: 4 Copynumber: 10.8 Consensus size: 4
317885 ATCTATCTAT
* * * *
317895 ATAG ATAT ATAG ATAG ATAG ATAC ATAA ATAA ATAG ATAG ATA
1 ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATAG ATA
317938 AGTAGTAGAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.56, C:0.02, G:0.14, T:0.28
Consensus pattern (4 bp):
ATAG
Found at i:317910 original size:12 final size:12
Alignment explanation
Indices: 317895--317949 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
317885 ATCTATCTAT
317895 ATAGATATATAG
1 ATAGATATATAG
* *
317907 ATAGATAGATAC
1 ATAGATATATAG
* *
317919 ATAAATAAATAG
1 ATAGATATATAG
317931 ATAGATA-AGTAG
1 ATAGATATA-TAG
317943 -TAGATAT
1 ATAGATAT
317950 GTCCATCTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
11 7 0.20
12 28 0.80
ACGTcount: A:0.53, C:0.02, G:0.16, T:0.29
Consensus pattern (12 bp):
ATAGATATATAG
Found at i:321644 original size:20 final size:20
Alignment explanation
Indices: 321619--321662 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
321609 ACCATAGTTA
321619 ACCAACAGTTGACATCTCTT
1 ACCAACAGTTGACATCTCTT
321639 ACCAACAGTTGACATCTCTT
1 ACCAACAGTTGACATCTCTT
321659 ACCA
1 ACCA
321663 TTACTATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.32, G:0.09, T:0.27
Consensus pattern (20 bp):
ACCAACAGTTGACATCTCTT
Found at i:322672 original size:17 final size:19
Alignment explanation
Indices: 322637--322673 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
322627 CGATATAAGA
*
322637 TATATAAAAATATTTAAAT
1 TATATAAAAATATTAAAAT
322656 TATAT-AAAAT-TTAAAAT
1 TATATAAAAATATTAAAAT
322673 T
1 T
322674 TTCAGATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 7 0.41
18 5 0.29
19 5 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (19 bp):
TATATAAAAATATTAAAAT
Found at i:323325 original size:3 final size:3
Alignment explanation
Indices: 323319--323344 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
323309 AAAAATATAC
323319 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
323345 ATAAAATTAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:323383 original size:87 final size:84
Alignment explanation
Indices: 323282--323453 Score: 308
Period size: 84 Copynumber: 2.0 Consensus size: 84
323272 TTTAAATATT
323282 GTAGATACTCGTTTTTGTCCGGATCAAAAAAATATACTATTATTATTATTATTATTATTATTAAT
1 GTAGATACTCGTTTTTGTCCGGATCAAAAAAATATAC---TATTATTATTATTATTATTATTAAT
323347 AAAATTAAATTACATTTTGCAG
63 AAAATTAAATTACATTTTGCAG
*
323369 GTAGATACTCGTTTTTGTCCGGATCAAAAAAATATACTATTATTATTATTATTATTATTAATTAA
1 GTAGATACTCGTTTTTGTCCGGATCAAAAAAATATACTATTATTATTATTATTATTATTAATAAA
323434 ATTAAATTACATTTTGCAG
66 ATTAAATTACATTTTGCAG
323453 G
1 G
323454 CCTACTCCCA
Statistics
Matches: 84, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
84 47 0.56
87 37 0.44
ACGTcount: A:0.37, C:0.09, G:0.10, T:0.44
Consensus pattern (84 bp):
GTAGATACTCGTTTTTGTCCGGATCAAAAAAATATACTATTATTATTATTATTATTATTAATAAA
ATTAAATTACATTTTGCAG
Found at i:326886 original size:2 final size:2
Alignment explanation
Indices: 326879--326905 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
326869 TCATTGTTAG
326879 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 T
326906 TATTTGATAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:327268 original size:2 final size:2
Alignment explanation
Indices: 327263--327306 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
327253 GCATATTCGA
*
327263 AT AT AT AT AT AT AT AT AT AG AT AT A- 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
327304 AT A
1 AT A
327307 ATGTCTTTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (2 bp):
AT
Found at i:330525 original size:25 final size:25
Alignment explanation
Indices: 330487--330536 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
330477 TCAATACTTC
* * *
330487 ATCTGCTAATGCTAGATGAAAGTTT
1 ATCTACTAACGCTAGAGGAAAGTTT
330512 ATCTACTAACGCTAGAGGAAAGTTT
1 ATCTACTAACGCTAGAGGAAAGTTT
330537 GCCATAACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (25 bp):
ATCTACTAACGCTAGAGGAAAGTTT
Found at i:334730 original size:14 final size:13
Alignment explanation
Indices: 334713--334761 Score: 62
Period size: 14 Copynumber: 3.5 Consensus size: 13
334703 GATTGGGTTA
*
334713 AACATACATAAACG
1 AACATA-ATGAACG
334727 AACATAATCGAACG
1 AACATAAT-GAACG
334741 AACATAACTGAACG
1 AACATAA-TGAACG
334755 AACATAA
1 AACATAA
334762 CCGAACGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 2 0.06
14 29 0.91
15 1 0.03
ACGTcount: A:0.55, C:0.20, G:0.10, T:0.14
Consensus pattern (13 bp):
AACATAATGAACG
Found at i:334762 original size:14 final size:14
Alignment explanation
Indices: 334723--334768 Score: 67
Period size: 14 Copynumber: 3.3 Consensus size: 14
334713 AACATACATA
334723 AACGAACATAA-TCG
1 AACGAACATAACT-G
334737 AACGAACATAACTG
1 AACGAACATAACTG
*
334751 AACGAACATAACCG
1 AACGAACATAACTG
334765 AACG
1 AACG
334769 TTCACGAACG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 29 0.97
15 1 0.03
ACGTcount: A:0.50, C:0.24, G:0.15, T:0.11
Consensus pattern (14 bp):
AACGAACATAACTG
Found at i:335340 original size:21 final size:21
Alignment explanation
Indices: 335314--335353 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
335304 AAGTTCAGTG
*
335314 AGTAAATTGAAAAAAATAAAA
1 AGTAAAGTGAAAAAAATAAAA
*
335335 AGTAAAGTGAATAAAATAA
1 AGTAAAGTGAAAAAAATAA
335354 GAGAGAGAGT
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:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (21 bp):
AGTAAAGTGAAAAAAATAAAA
Found at i:335905 original size:37 final size:37
Alignment explanation
Indices: 335855--335928 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
335845 TGCAATTAAA
335855 ATTTTCTTAGATTTTAATCTTATATTAAATATATTTT
1 ATTTTCTTAGATTTTAATCTTATATTAAATATATTTT
335892 ATTTTCTTAGATTTTAATCTTATATTAAATATATTTT
1 ATTTTCTTAGATTTTAATCTTATATTAAATATATTTT
335929 CTGGTGAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.59
Consensus pattern (37 bp):
ATTTTCTTAGATTTTAATCTTATATTAAATATATTTT
Found at i:341625 original size:397 final size:397
Alignment explanation
Indices: 341123--342312 Score: 2070
Period size: 397 Copynumber: 3.0 Consensus size: 397
341113 CAAGTTAGGT
*
341123 GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGTGGGTAGGATAGTCACTCTTAAAATTTTAAAA
1 GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGTGGGTAGGGTAGTCACTCTTAAAATTTTAAAA
* *
341188 TTATTATATATTTAAAAAATTTTCTATTTATTTTTTATTGAAAATATACTTTCGTCTCTCTAGAA
66 TTATTATATATTTCAAAAATTTTCTATTTATTTTTTATTGAAAATATACTTTCGTCTCTCTAAAA
* * * *
341253 TTTTATAAGTTTAAGTTCACACACCTGAAATTTTATAAGTTCAAGTTCACACCTTCGACATAAAA
131 TTGTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAGTTCATGTTCACACCTT-AACATAAAA
* *
341318 TCATGCATTCCTCCCTGTGTTTGTTTCTTATAATATATTTCAATATGAGCCTTTCAAAACGATAT
195 TCATGCATTCCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGATAT
*
341383 TGTTTTGGAAAGATTGTTCGTATTCT-AAACAACATCGTTTTGATTATCTAGTATGATATTCGAC
260 TGTTTTGGAAAGATTGTTCGTATTCTAAAACAACATCGTTTTGATTATCTAGTATGATGTTCGAC
*
341447 CCATACGTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTTTG
325 CCATACCTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTTTG
*
341512 GTCTTTCC
390 GTCCTTCC
*
341520 GCTCTTGTTCCCAACGATGGACCTAAGCAGGGGTGGGTAGGGTAGTCACTCTTAAAATTTTAAAA
1 GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGTGGGTAGGGTAGTCACTCTTAAAATTTTAAAA
341585 TTATTATATATTTCAAAAATTTTCTATTTATTTTTTATTGAAAATATACTTTCGTCTCTCTAAAA
66 TTATTATATATTTCAAAAATTTTCTATTTATTTTTTATTGAAAATATACTTTCGTCTCTCTAAAA
341650 TTGTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAGTTCATGTTCACACTCTTAACATAAAA
131 TTGTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAGTTCATGTTCACAC-CTTAACATAAAA
341715 TCATGCATTCCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGATAT
195 TCATGCATTCCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGATAT
* *
341780 TGTTTTGGAAAGATTGTTCGTATTCTAAAACAGCATCGTTTTGATTATCTAGTTTGATGTTCG--
260 TGTTTTGGAAAGATTGTTCGTATTCTAAAACAACATCGTTTTGATTATCTAGTATGATGTTCGAC
341843 --ATACCTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTTTG
325 CCATACCTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTTTG
341906 GTCCTTCC
390 GTCCTTCC
*
341914 GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGTGGGTAGGGCAGTCACTCTTAAAATTTTAAAA
1 GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGTGGGTAGGGTAGTCACTCTTAAAATTTTAAAA
** * *
341979 TTATTATATATTTCAAATTTTTTCTATTTATTTTTTATTGAAAATATATTTTCGTCTCTCTATAA
66 TTATTATATATTTCAAAAATTTTCTATTTATTTTTTATTGAAAATATACTTTCGTCTCTCTAAAA
342044 TTGTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAGTTCATGTTCACACCCTTAACATAAAA
131 TTGTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAGTTCATGTTCACA-CCTTAACAT-AAA
* *
342109 ATCATGTATTTCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGATA
194 ATCATGCATTCCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGATA
*
342174 TTGTTTTGGAAAGATTGTTCGTATTCTAAAACAACATCGTTTTGATTATCAAGTATGATGTTCGA
259 TTGTTTTGGAAAGATTGTTCGTATTCTAAAACAACATCGTTTTGATTATCTAGTATGATGTTCGA
* *
342239 CCCATACCTAAACTAGATCCACAACCAAGA--TGTGTTTGAAATCTTTGGATAAATTTTAATTTT
324 CCCATACCTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTTT
342302 GGTCCTTCC
389 GGTCCTTCC
342311 GC
1 GC
342313 CTTTCTAACT
Statistics
Matches: 757, Mismatches: 28, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
394 252 0.33
395 128 0.17
397 315 0.42
398 36 0.05
399 26 0.03
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (397 bp):
GCTCTTGTTCCCAGCGATGGACCTAAGCAGGGGTGGGTAGGGTAGTCACTCTTAAAATTTTAAAA
TTATTATATATTTCAAAAATTTTCTATTTATTTTTTATTGAAAATATACTTTCGTCTCTCTAAAA
TTGTATAAGTTTAAGTTCACCCACCTGAAATTTTATAAGTTCATGTTCACACCTTAACATAAAAT
CATGCATTCCTCCCTGTGTTTGTTCCTTATGATATATTTCAATATGAGCCTTTCAAAACGATATT
GTTTTGGAAAGATTGTTCGTATTCTAAAACAACATCGTTTTGATTATCTAGTATGATGTTCGACC
CATACCTGAACTAGATCCACAACCAAGATCTGTGTTTGAAATCTTTGGATAAATTTCAATTTTGG
TCCTTCC
Found at i:347515 original size:16 final size:16
Alignment explanation
Indices: 347496--347535 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
347486 CATCGATTTA
347496 CTCTTACAGCCGACAC
1 CTCTTACAGCCGACAC
**
347512 CTCTTACAGTGGACAC
1 CTCTTACAGCCGACAC
*
347528 CTCCTACA
1 CTCTTACA
347536 CCCCATTGTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (16 bp):
CTCTTACAGCCGACAC
Found at i:347784 original size:28 final size:29
Alignment explanation
Indices: 347743--347815 Score: 80
Period size: 28 Copynumber: 2.6 Consensus size: 29
347733 CTTTATAAAG
* *
347743 TTTAATTTAATTAAATTGAGTT-AAAAAA
1 TTTAAATTATTTAAATTGAGTTAAAAAAA
*
347771 TTTAAGTTATTTAAA--GAGTTAAAAAAA
1 TTTAAATTATTTAAATTGAGTTAAAAAAA
*
347798 TTCTAAATTATTTGAATT
1 TT-TAAATTATTTAAATT
347816 AACAAGTCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
26 5 0.14
27 8 0.22
28 24 0.65
ACGTcount: A:0.47, C:0.01, G:0.08, T:0.44
Consensus pattern (29 bp):
TTTAAATTATTTAAATTGAGTTAAAAAAA
Found at i:349243 original size:29 final size:31
Alignment explanation
Indices: 349166--349243 Score: 81
Period size: 29 Copynumber: 2.6 Consensus size: 31
349156 AGAGAAAAAC
* *
349166 AAAAACTTAAGGGATT-AAATAGCAAAAGAA
1 AAAAAATTAAAGGATTAAAATAGCAAAAGAA
* * *
349196 AAAAAATTAAAGTACTAAAATAGC-ATA-AA
1 AAAAAATTAAAGGATTAAAATAGCAAAAGAA
*
349225 TAAAAATTAAAGGATTAAA
1 AAAAAATTAAAGGATTAAA
349244 GTAGAAAGAT
Statistics
Matches: 39, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
29 18 0.46
30 14 0.36
31 7 0.18
ACGTcount: A:0.63, C:0.05, G:0.12, T:0.21
Consensus pattern (31 bp):
AAAAAATTAAAGGATTAAAATAGCAAAAGAA
Found at i:350499 original size:17 final size:17
Alignment explanation
Indices: 350477--350509 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
350467 AATTGCAATC
350477 AAAATACTAA-ATTAAGT
1 AAAATAC-AATATTAAGT
350494 AAAATACAATATTAAG
1 AAAATACAATATTAAG
350510 AGTCTAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 2 0.13
17 13 0.87
ACGTcount: A:0.61, C:0.06, G:0.06, T:0.27
Consensus pattern (17 bp):
AAAATACAATATTAAGT
Found at i:353843 original size:2 final size:2
Alignment explanation
Indices: 353836--353890 Score: 78
Period size: 2 Copynumber: 28.5 Consensus size: 2
353826 AATACTTTAC
*
353836 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
353877 A- AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT A
353891 CGTTAAAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:353896 original size:22 final size:22
Alignment explanation
Indices: 353836--353897 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
353826 AATACTTTAC
* *
353836 ATATATATATATATA-TATAT-
1 ATATATATATATACATTAAATA
*
353856 ATATATATATATATATTAAATA
1 ATATATATATATACATTAAATA
* *
353878 ATATATATTTATACGTTAAA
1 ATATATATATATACATTAAA
353898 AGTTGTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
20 15 0.42
21 4 0.11
22 17 0.47
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
ATATATATATATACATTAAATA
Found at i:355699 original size:22 final size:22
Alignment explanation
Indices: 355667--355732 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
355657 CCTTTCAATT
355667 AAATACATATTTTTATTGAATAA
1 AAATA-ATATTTTTATTGAATAA
355690 AAATAATATTTTTATTGAATAA
1 AAATAATATTTTTATTGAATAA
355712 AAATAATATTTTTATTGAATA
1 AAATAATATTTTTATTGAATA
355733 TATCATTTCG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 38 0.88
23 5 0.12
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (22 bp):
AAATAATATTTTTATTGAATAA
Found at i:357490 original size:60 final size:59
Alignment explanation
Indices: 357418--357595 Score: 169
Period size: 60 Copynumber: 3.0 Consensus size: 59
357408 GTACGTCCTC
* *
357418 AAACTATAACTCTTATTTTAAATTAATCCTTAAACTTTTGAATATTTTAATTTTATCGC-T
1 AAACTAT-ACTCTTATTTTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATC-CAT
** * * * *
357478 AAACTATGACTCTCGTTCTAAATCAATCCTTAAAGTTTTGAACATTCTAATTTCATCCAT
1 AAACTAT-ACTCTTATTTTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCCAT
* * * ** * **
357538 AAACTATATTCCTCTTTCTAAATTAGCCCTCAAACTTTTGAATATTCCCATTTCATCC
1 AAACTATACTCTTATTT-TAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCC
357596 CCAGTTTCAT
Statistics
Matches: 94, Mismatches: 22, Indels: 4
0.78 0.18 0.03
Matches are distributed among these distances:
59 6 0.06
60 88 0.94
ACGTcount: A:0.33, C:0.21, G:0.04, T:0.42
Consensus pattern (59 bp):
AAACTATACTCTTATTTTAAATTAATCCTTAAACTTTTGAATATTCTAATTTCATCCAT
Found at i:357815 original size:60 final size:58
Alignment explanation
Indices: 357722--357890 Score: 155
Period size: 60 Copynumber: 2.8 Consensus size: 58
357712 AGTATATATG
* ** *
357722 TATAGTTTGGGATGAAGTCAAAATGTTAAAAAAGTTTAGGGGTCAATTTAGGAT-AAAGGT
1 TATAGTTTGGGATGAAATTGAAATGTT--AAAAGTTTAGGGATCAATTTAGGATGAAA-GT
* * **
357782 TATAGTTTGGGGATGAAATTGAAATGTTCAAAAGTCT-GAGGATTAATTTAGGATGGTAGT
1 TATAGTTT-GGGATGAAATTGAAATGTT-AAAAGTTTAG-GGATCAATTTAGGATGAAAGT
* *
357842 CATAGTTAGGGATGAAATTAGAATAT-TTAAAAGTTTAGGGATCAATTTA
1 TATAGTTTGGGATGAAATT-GAA-ATGTTAAAAGTTTAGGGATCAATTTA
357891 AAATAAAAAA
Statistics
Matches: 90, Mismatches: 13, Indels: 13
0.78 0.11 0.11
Matches are distributed among these distances:
59 29 0.32
60 42 0.47
61 19 0.21
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.34
Consensus pattern (58 bp):
TATAGTTTGGGATGAAATTGAAATGTTAAAAGTTTAGGGATCAATTTAGGATGAAAGT
Found at i:362218 original size:7 final size:7
Alignment explanation
Indices: 362208--362267 Score: 52
Period size: 7 Copynumber: 8.7 Consensus size: 7
362198 CTAAATTATA
*
362208 AAACCAT
1 AAACCTT
362215 AAACCTT
1 AAACCTT
*
362222 AAGCCTT
1 AAACCTT
362229 AAACC-T
1 AAACCTT
*
362235 AAGCCTT
1 AAACCTT
* *
362242 AAACATC
1 AAACCTT
362249 AAATCC-T
1 AAA-CCTT
362256 AAACCTT
1 AAACCTT
362263 AAACC
1 AAACC
362268 CTAAGGCCTA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
6 7 0.17
7 33 0.80
8 1 0.02
ACGTcount: A:0.45, C:0.30, G:0.03, T:0.22
Consensus pattern (7 bp):
AAACCTT
Found at i:362239 original size:13 final size:14
Alignment explanation
Indices: 362214--362245 Score: 57
Period size: 13 Copynumber: 2.4 Consensus size: 14
362204 TATAAAACCA
362214 TAAACCTTAAGCCT
1 TAAACCTTAAGCCT
362228 TAAACC-TAAGCCT
1 TAAACCTTAAGCCT
362241 TAAAC
1 TAAAC
362246 ATCAAATCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.41, C:0.28, G:0.06, T:0.25
Consensus pattern (14 bp):
TAAACCTTAAGCCT
Found at i:362270 original size:14 final size:14
Alignment explanation
Indices: 362177--362271 Score: 59
Period size: 14 Copynumber: 6.8 Consensus size: 14
362167 TTCATTTTCA
362177 TTAAACCCTAAACC
1 TTAAACCCTAAACC
* * *
362191 CTAAATCCTAAA-T
1 TTAAACCCTAAACC
*
362204 TATAAAACCATAAACC
1 T-T-AAACCCTAAACC
* *
362220 TTAAGCCTTAAACC
1 TTAAACCCTAAACC
* * *
362234 -TAAGCCTTAAACA
1 TTAAACCCTAAACC
* *
362247 TCAAATCCTAAACC
1 TTAAACCCTAAACC
362261 TTAAACCCTAA
1 TTAAACCCTAA
362272 GGCCTAAAAC
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
13 12 0.20
14 38 0.63
15 9 0.15
16 1 0.02
ACGTcount: A:0.45, C:0.28, G:0.02, T:0.24
Consensus pattern (14 bp):
TTAAACCCTAAACC
Found at i:362326 original size:7 final size:7
Alignment explanation
Indices: 362316--362341 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
362306 CTTAAAACAC
362316 TAAACTA
1 TAAACTA
362323 TAAACTA
1 TAAACTA
362330 TAAACTA
1 TAAACTA
362337 TAAAC
1 TAAAC
362342 CCCAAACCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAACTA
Found at i:362398 original size:49 final size:49
Alignment explanation
Indices: 362345--362439 Score: 113
Period size: 49 Copynumber: 1.9 Consensus size: 49
362335 TATAAACCCC
*
362345 AAACCCCAAACCCTAAATTATAAA-C-TATAAACCTTAAACCCTAAATACT
1 AAACCCCAAA-CATAAATTATAAATCATA-AAACCTTAAACCCTAAATACT
*** *
362394 AAACCTTGAACATAAATTTTAAATCATAAAACCTTAAACCCTAAAT
1 AAACCCCAAACATAAATTATAAATCATAAAACCTTAAACCCTAAAT
362440 CCCTAAACTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
48 11 0.28
49 26 0.67
50 2 0.05
ACGTcount: A:0.49, C:0.24, G:0.01, T:0.25
Consensus pattern (49 bp):
AAACCCCAAACATAAATTATAAATCATAAAACCTTAAACCCTAAATACT
Found at i:365072 original size:17 final size:17
Alignment explanation
Indices: 365050--365105 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
365040 AGGTTCAAAT
365050 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
*
365067 TCGAGTTCGAGTTTGAA
1 TCGAGTTCGAGCTTGAA
365084 TCGAGTTCGAGCTTGAA
1 TCGAGTTCGAGCTTGAA
365101 TCGAG
1 TCGAG
365106 CTCAAATTCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.30
Consensus pattern (17 bp):
TCGAGTTCGAGCTTGAA
Found at i:365104 original size:11 final size:11
Alignment explanation
Indices: 365090--365177 Score: 68
Period size: 11 Copynumber: 7.6 Consensus size: 11
365080 TGAATCGAGT
365090 TCGAGCTTGAA
1 TCGAGCTTGAA
**
365101 TCGAGCTCAAA
1 TCGAGCTTGAA
365112 TTCGAGCTTGAA
1 -TCGAGCTTGAA
**
365124 TCGAGCTCAAAA
1 TCGAGCT-TGAA
*
365136 TCGAGCTTCAA
1 TCGAGCTTGAA
* *
365147 TCGAGCTCGAGTC
1 TCGAGCTTGA--A
*
365160 TCGAGCTTCAA
1 TCGAGCTTGAA
365171 TCGAGCT
1 TCGAGCT
365178 CCTGATTTTT
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
11 33 0.56
12 18 0.31
13 8 0.14
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:365115 original size:23 final size:23
Alignment explanation
Indices: 365089--365178 Score: 126
Period size: 23 Copynumber: 3.9 Consensus size: 23
365079 TTGAATCGAG
*
365089 TTCGAGCTTGAATCGAGCTCAAA
1 TTCGAGCTTCAATCGAGCTCAAA
*
365112 TTCGAGCTTGAATCGAGCTCAAA
1 TTCGAGCTTCAATCGAGCTCAAA
* * *
365135 ATCGAGCTTCAATCGAGCTCGAG
1 TTCGAGCTTCAATCGAGCTCAAA
365158 TCTCGAGCTTCAATCGAGCTC
1 T-TCGAGCTTCAATCGAGCTC
365179 CTGATTTTTT
Statistics
Matches: 61, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
23 42 0.69
24 19 0.31
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.26
Consensus pattern (23 bp):
TTCGAGCTTCAATCGAGCTCAAA
Found at i:365265 original size:72 final size:71
Alignment explanation
Indices: 365189--365326 Score: 165
Period size: 72 Copynumber: 1.9 Consensus size: 71
365179 CTGATTTTTT
* * *
365189 TTTTAGTTCGAGCCTTTTCGAGTTCGAGTCGAGT-TTCTATATT-A-TCTTTCGAGTTCGAGTCG
1 TTTTAGGTCGAGACTTTTCGAG-TCGAGTCGAGTCTAC-AT-TTAAGT-TTTCGAGTTCGAGTCG
365251 AGCTTGAAAA
62 AGCTTGAAAA
* *
365261 TTTTAGGTCGCGAGTTTTCGAGTCGAGTCGAGTCTACATTTAAAGTTTTCGAGTTCGAGTCGAGC
1 TTTTAGGTCGAGACTTTTCGAGTCGAGTCGAGTCTACATTT-AAGTTTTCGAGTTCGAGTCGAGC
365326 T
65 T
365327 CGGCAATACT
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
70 2 0.04
71 13 0.23
72 41 0.72
73 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (71 bp):
TTTTAGGTCGAGACTTTTCGAGTCGAGTCGAGTCTACATTTAAGTTTTCGAGTTCGAGTCGAGCT
TGAAAA
Found at i:365765 original size:29 final size:30
Alignment explanation
Indices: 365708--365782 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
365698 TAGAACTTGA
* * * *
365708 TTTTTTTAGAATTTTAGGATTTTAGGAGTT
1 TTTTTTTGGAATTTTAGAAATTTAGGAGTG
*
365738 TTTTTTTGGAATTTTTGAAATTTA-GAGTG
1 TTTTTTTGGAATTTTAGAAATTTAGGAGTG
* *
365767 TTATTTAGGAATTTTA
1 TTTTTTTGGAATTTTA
365783 ATAATTTCAT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
29 17 0.46
30 20 0.54
ACGTcount: A:0.25, C:0.00, G:0.19, T:0.56
Consensus pattern (30 bp):
TTTTTTTGGAATTTTAGAAATTTAGGAGTG
Found at i:366399 original size:21 final size:22
Alignment explanation
Indices: 366367--366407 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
366357 AGTGTCTATT
366367 CAAATAAAATAATA-AAAAATA
1 CAAATAAAATAATAGAAAAATA
366388 CAAA-AAATATAATAGAAAAA
1 CAAATAAA-ATAATAGAAAAA
366408 CTAAAATGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.17
21 10 0.56
22 5 0.28
ACGTcount: A:0.76, C:0.05, G:0.02, T:0.17
Consensus pattern (22 bp):
CAAATAAAATAATAGAAAAATA
Found at i:375713 original size:11 final size:11
Alignment explanation
Indices: 375697--375729 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
375687 GGAATGGCAA
375697 CGGGTCGGGTT
1 CGGGTCGGGTT
375708 CGGGTCGGGTT
1 CGGGTCGGGTT
375719 CGGGTCGGGTT
1 CGGGTCGGGTT
375730 TTACTCGTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.18, G:0.55, T:0.27
Consensus pattern (11 bp):
CGGGTCGGGTT
Found at i:375929 original size:34 final size:34
Alignment explanation
Indices: 375877--375962 Score: 154
Period size: 34 Copynumber: 2.5 Consensus size: 34
375867 CCCGAACCCG
*
375877 AAAATATTTTTATATATAATTAATATAAAAAATAT
1 AAAATA-TTATATATATAATTAATATAAAAAATAT
375912 AAAATATTATATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
375946 AAAATATTATATATATA
1 AAAATATTATATATATA
375963 TATAATCGGG
Statistics
Matches: 50, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 44 0.88
35 6 0.12
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:377951 original size:30 final size:30
Alignment explanation
Indices: 377917--378050 Score: 139
Period size: 30 Copynumber: 4.5 Consensus size: 30
377907 TCAAGGTAAG
* *
377917 TCCGTCACCGCACCTGCGGTTCAGGGAAGT
1 TCCGTCACTGCACCGGCGGTTCAGGGAAGT
* *
377947 TCCGTCACTGCACCGGCGGTTCAGGGGAGC
1 TCCGTCACTGCACCGGCGGTTCAGGGAAGT
***
377977 TCAACCACTGCACCGGCGGTTCAGGGAAGT
1 TCCGTCACTGCACCGGCGGTTCAGGGAAGT
* *
378007 TCC-TCCACTGCACCCGG-GATTCAAGGAAGT
1 TCCGT-CACTGCA-CCGGCGGTTCAGGGAAGT
378037 TCC-TCCACTGCACC
1 TCCGT-CACTGCACC
378051 CGGTTTAGAT
Statistics
Matches: 89, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
29 2 0.02
30 83 0.93
31 4 0.04
ACGTcount: A:0.19, C:0.35, G:0.28, T:0.19
Consensus pattern (30 bp):
TCCGTCACTGCACCGGCGGTTCAGGGAAGT
Found at i:378045 original size:60 final size:58
Alignment explanation
Indices: 377902--378050 Score: 158
Period size: 60 Copynumber: 2.5 Consensus size: 58
377892 CAATGTACGT
* *
377902 GGGATTCAAGGTAAGTCCGT-CACCGCACCTGCGGTTCAGGGAAGTTCCGTCACTGCACC
1 GGGATTCAAGG-AAGTCC-TCCACTGCACCGGCGGTTCAGGGAAGTTCCGTCACTGCACC
* * * **
377961 GGCGGTTCAGGGGAGCTCAACCACTGCACCGGCGGTTCAGGGAAGTTCC-TCCACTGCACCC
1 GG-GATTCAAGGAAG-TCCTCCACTGCACCGGCGGTTCAGGGAAGTTCCGT-CACTGCA-CC
378022 GGGATTCAAGGAAGTTCCTCCACTGCACC
1 GGGATTCAAGGAAG-TCCTCCACTGCACC
378051 CGGTTTAGAT
Statistics
Matches: 72, Mismatches: 13, Indels: 9
0.77 0.14 0.10
Matches are distributed among these distances:
59 5 0.07
60 63 0.88
61 4 0.06
ACGTcount: A:0.20, C:0.32, G:0.29, T:0.19
Consensus pattern (58 bp):
GGGATTCAAGGAAGTCCTCCACTGCACCGGCGGTTCAGGGAAGTTCCGTCACTGCACC
Found at i:381407 original size:14 final size:14
Alignment explanation
Indices: 381388--381416 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
381378 ATTTGAGAAA
381388 ATAAAAATGAAGAT
1 ATAAAAATGAAGAT
381402 ATAAAAATGAAGAT
1 ATAAAAATGAAGAT
381416 A
1 A
381417 AAAGAGACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.21
Consensus pattern (14 bp):
ATAAAAATGAAGAT
Found at i:381419 original size:12 final size:13
Alignment explanation
Indices: 381387--381419 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
381377 AATTTGAGAA
381387 AATAAAAATGAAG
1 AATAAAAATGAAG
381400 ATATAAAAATGAAG
1 A-ATAAAAATGAAG
381414 -ATAAAA
1 AATAAAA
381420 GAGACACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 1 0.05
14 12 0.63
ACGTcount: A:0.70, C:0.00, G:0.12, T:0.18
Consensus pattern (13 bp):
AATAAAAATGAAG
Found at i:382987 original size:15 final size:13
Alignment explanation
Indices: 382943--382989 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 13
382933 TGTTAGATAG
382943 AAAAATAAATA-AA
1 AAAAATAAA-AGAA
382956 TAAAAATAAAAGAA
1 -AAAAATAAAAGAA
382970 AAAACATAAAATGAA
1 AAAA-ATAAAA-GAA
382985 AAAAA
1 AAAAA
382990 AACATAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
13 5 0.17
14 18 0.60
15 7 0.23
ACGTcount: A:0.81, C:0.02, G:0.04, T:0.13
Consensus pattern (13 bp):
AAAAATAAAAGAA
Found at i:383007 original size:20 final size:18
Alignment explanation
Indices: 382958--383008 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
382948 TAAATAAATA
382958 AAAATAAAAGAAAAAACAT
1 AAAATAAAA-AAAAAACAT
*
382977 AAAATGAAAAAAAAACAT
1 AAAATAAAAAAAAAACAT
382995 AATAATAATAAAAA
1 AA-AATAA-AAAAA
383009 TAAATCAAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 11 0.39
19 12 0.43
20 5 0.18
ACGTcount: A:0.78, C:0.04, G:0.04, T:0.14
Consensus pattern (18 bp):
AAAATAAAAAAAAAACAT
Found at i:383008 original size:18 final size:18
Alignment explanation
Indices: 382958--382996 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
382948 TAAATAAATA
*
382958 AAAATAAAAGAAAAAACAT
1 AAAATGAAA-AAAAAACAT
382977 AAAATGAAAAAAAAACAT
1 AAAATGAAAAAAAAACAT
382995 AA
1 AA
382997 TAATAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.79, C:0.05, G:0.05, T:0.10
Consensus pattern (18 bp):
AAAATGAAAAAAAAACAT
Found at i:383137 original size:26 final size:26
Alignment explanation
Indices: 383108--383157 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
383098 AAAATGGAAA
*
383108 CAATATGAAGTAAAATA-AATAATACT
1 CAATAT-AAGTAAAACATAATAATACT
*
383134 CAATATAATTAAAACATAATAATA
1 CAATATAAGTAAAACATAATAATA
383158 ATAATAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.60, C:0.08, G:0.04, T:0.28
Consensus pattern (26 bp):
CAATATAAGTAAAACATAATAATACT
Found at i:384349 original size:12 final size:12
Alignment explanation
Indices: 384332--384378 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
384322 AAATGAAAAA
384332 AATAAAATAAAT
1 AATAAAATAAAT
**
384344 AATAAACGAAAT
1 AATAAAATAAAT
384356 AATAAAA-AAAT
1 AATAAAATAAAT
384367 AGATAAATATAA
1 A-ATAAA-ATAA
384379 CAAAAAACAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
11 5 0.17
12 21 0.72
13 1 0.03
14 2 0.07
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (12 bp):
AATAAAATAAAT
Found at i:384429 original size:28 final size:28
Alignment explanation
Indices: 384389--384443 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
384379 CAAAAAACAT
*
384389 TTTTTAAAACCATACAATATATGTTTTG
1 TTTTTAAAACCATACAATATATATTTTG
*
384417 TTTTTAAAACCATATAATATATATTTT
1 TTTTTAAAACCATACAATATATATTTT
384444 TAAAAATATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (28 bp):
TTTTTAAAACCATACAATATATATTTTG
Found at i:384480 original size:36 final size:35
Alignment explanation
Indices: 384418--384792 Score: 123
Period size: 37 Copynumber: 10.6 Consensus size: 35
384408 TATGTTTTGT
**
384418 TTTTAAAACCATATAATATATATTTTT-AAAAATA
1 TTTTAAAATTATATAATATATATTTTTAAAAAATA
*
384452 TTTTAAAATTATATATTATATACTTTTTTAAAAAA-A
1 TTTTAAAATTATATAATATATA--TTTTTAAAAAATA
** * * *
384488 TGTTTTCAA--A-AT--TATATAGTTTTCAAAAATGT
1 T-TTTAAAATTATATAATATATATTTTTAAAAAAT-A
* * * *
384520 TTTTAAAACTATATATTATATGTTTTTAAAAGGAT-
1 TTTTAAAATTATATAATATATATTTTTAAAA-AATA
** * ** *
384555 TTCAAAAACTATATAATATATATATGTTTTCAAAATGTT
1 TTTTAAAATTATAT-A-ATATATAT-TTTT-AAAAAATA
* *
384594 TTTTAAAA--A-CT-ATATATATTTTT--AAAATG
1 TTTTAAAATTATATAATATATATTTTTAAAAAATA
* * * *
384623 TTTTAAAAACTATATAATATATGTATTTTCAAAAATG
1 TTTT-AAAATTATATAATATATAT-TTTTAAAAAATA
* * * ** *
384660 TTTTAAAAACTATATATTATATTATTTTTCAAATTTT
1 TTTT-AAAATTATATAATATA-TATTTTTAAAAAATA
* * *
384697 TTTTAAAAACTATATAATATATATATTTTCAAAAATG
1 TTTT-AAAATTATATAATATATAT-TTTTAAAAAATA
* * * * *
384734 TTTTGAAAACTATATATTATATTAATTTT-CAAAATG
1 TTTT-AAAATTATATAATATA-TATTTTTAAAAAATA
* *
384770 TCTTAAGAACTATATAATATATA
1 TTTTAA-AATTATATAATATATA
384793 AATGTTTTGA
Statistics
Matches: 269, Mismatches: 43, Indels: 57
0.73 0.12 0.15
Matches are distributed among these distances:
29 7 0.03
30 13 0.05
31 5 0.02
32 12 0.04
33 10 0.04
34 30 0.11
35 21 0.08
36 46 0.17
37 106 0.39
38 9 0.03
39 10 0.04
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (35 bp):
TTTTAAAATTATATAATATATATTTTTAAAAAATA
Found at i:384521 original size:102 final size:101
Alignment explanation
Indices: 384415--384825 Score: 310
Period size: 104 Copynumber: 3.9 Consensus size: 101
384405 ATATATGTTT
* * *
384415 TGTTTTTAAAACCATATAATATATATTTTTAAAAATATTTTAAAATTATATATTATATACTTTTT
1 TGTTTTTAAAACTATATAATATATATTTTTAAAAATATTTTAAAACTATATATTATATA-TGTTT
*
384480 TAAAAAAATGTTTTCAAAA-T-TATATAGTTTTCAAAAA
65 TAAAAAAATGTTTTAAAAACTATATATA-TTTT-AAAAA
* * ** *
384517 TGTTTTTAAAACTATATATTATATGTTTTTAAAAGGATTTCAAAAACTATATAATATATATATGT
1 TGTTTTTAAAACTATATAATATATATTTTTAAAAATATTT-TAAAACTATAT-AT-TATATATGT
* ** * *
384582 TTTCAAAATGTTTTTTAAAAACTATATATATTTTTAAAA
63 TTTAAAAAAATGTTTTAAAAACTATATATATTTTAAAAA
* * *
384621 TGTTTTAAAAACTATATAATATATGTATTTTCAAAAATGTTTTAAAAACTATATATTATATTAT-
1 TGTTTTTAAAACTATATAATATA--TATTTTTAAAAATATTTT-AAAACTATATATTATA-TATG
* ** *
384685 TTTT-CAAATTTTTTTTAAAAACTATATAATATATATATTTTCAAAAA
62 TTTTAAAAAAATGTTTTAAAAAC-------TATATATATTTT-AAAAA
* * * * * * *
384732 TGTTTTGAAAACTATATATTATATTAATTTTCAAAATGTCTTAAGAACTATATAATATATAAATG
1 TGTTTTTAAAACTATATAATATA-TATTTTTAAAAATATTTTAA-AACTATAT-AT-TATATATG
* * *
384797 TTTT-GAAATATGTTTTCAAAACTATATAT
62 TTTTAAAAAAATGTTTTAAAAACTATATAT
384826 TATATATACA
Statistics
Matches: 251, Mismatches: 37, Indels: 39
0.77 0.11 0.12
Matches are distributed among these distances:
102 35 0.14
103 25 0.10
104 53 0.21
105 23 0.09
106 28 0.11
109 2 0.01
110 34 0.14
111 29 0.12
112 22 0.09
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (101 bp):
TGTTTTTAAAACTATATAATATATATTTTTAAAAATATTTTAAAACTATATATTATATATGTTTT
AAAAAAATGTTTTAAAAACTATATATATTTTAAAAA
Found at i:384611 original size:37 final size:35
Alignment explanation
Indices: 384500--384849 Score: 274
Period size: 37 Copynumber: 9.7 Consensus size: 35
384490 TTTTCAAAAT
*
384500 TATATA-GTTTTCAAAAATGTTTTTAAAACTATATA
1 TATATATGTTTTC-AAAATGTTTTAAAAACTATATA
* * *
384535 T-TATATGTTTTTAAAAGGATTTCAAAAACTATATAATA
1 TATATATGTTTTCAAAATG-TTTTAAAAAC--TAT-ATA
384573 TATATATGTTTTCAAAATGTTTTTTAAAAAC----TA
1 TATATATGTTTTCAAAATG--TTTTAAAAACTATATA
384606 TATATAT-TTTT-AAAATGTTTTAAAAACTATATA
1 TATATATGTTTTCAAAATGTTTTAAAAACTATATA
384639 -ATATATGTATTTTCAAAAATGTTTTAAAAACTATATA
1 TATATATG--TTTTC-AAAATGTTTTAAAAACTATATA
* *
384676 TTATATTAT-TTTTCAAATTTTTTTTAAAAACTATATAA
1 -TATA-TATGTTTTCAAA-ATGTTTTAAAAACTATAT-A
* *
384714 TATATATATTTTCAAAAATGTTTTGAAAACTATATA
1 TATATATGTTTTC-AAAATGTTTTAAAAACTATATA
* * *
384750 T-TATATTAATTTTCAAAATGTCTTAAGAACTATATAA
1 TATATA-T-GTTTTCAAAATGTTTTAAAAACTATAT-A
* *
384787 TATATAAATGTTTTGAAATATGTTTTCAAAACTATATA
1 TATAT--ATGTTTTCAAA-ATGTTTTAAAAACTATATA
*
384825 TTATATATACATTTT-AAAATGTTTT
1 -TATATAT--GTTTTCAAAATGTTTT
384850 CAAACTGCAT
Statistics
Matches: 260, Mismatches: 22, Indels: 64
0.75 0.06 0.18
Matches are distributed among these distances:
29 10 0.04
31 6 0.02
32 10 0.04
33 11 0.04
34 9 0.03
35 22 0.08
36 27 0.10
37 87 0.33
38 22 0.08
39 43 0.17
40 13 0.05
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (35 bp):
TATATATGTTTTCAAAATGTTTTAAAAACTATATA
Found at i:384713 original size:74 final size:72
Alignment explanation
Indices: 384500--384849 Score: 383
Period size: 74 Copynumber: 4.8 Consensus size: 72
384490 TTTTCAAAAT
* * * *
384500 TATATAGTTTTCAAAAATGTTTTTAAAACTATATATTATA-TGTTTTTAAAAGGATTTCAAAAAC
1 TATATA-TTTTCAAAAATGTTTTAAAAACTATATATTATATTATTTTTAAAATG-TTTTAAAAAC
384564 TATATAATA
64 TATATAATA
384573 TATATATGTTTTC-AAAATGTTTTTTAAAAAC----TA-TATA-TATTTTTAAAATGTTTTAAAA
1 TATATA--TTTTCAAAAATG--TTTTAAAAACTATATATTATATTATTTTTAAAATGTTTTAAAA
384631 ACTATATAATA
62 ACTATATAATA
* * *
384642 TATGTATTTTCAAAAATGTTTTAAAAACTATATATTATATTATTTTTCAAATTTTTTTTAAAAAC
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTATATTATTTTT-AAA-ATGTTTTAAAAAC
384707 TATATAATA
64 TATATAATA
* * * *
384716 TATATATTTTCAAAAATGTTTTGAAAACTATATATTATATTAATTTTCAAAATGTCTTAAGAACT
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTATATT-ATTTTTAAAATGTTTTAAAAACT
384781 ATATAATA
65 ATATAATA
* * * * *
384789 TATAAATGTTTTGAAATATGTTTTCAAAACTATATATTATATATACATTTTAAAATGTTTT
1 TAT--ATATTTTCAAAAATGTTTTAAAAACTATATATTATAT-TA-TTTTTAAAATGTTTT
384850 CAAACTGCAT
Statistics
Matches: 239, Mismatches: 21, Indels: 31
0.82 0.07 0.11
Matches are distributed among these distances:
66 10 0.04
67 5 0.02
68 6 0.03
69 23 0.10
70 17 0.07
71 6 0.03
72 7 0.03
73 36 0.15
74 68 0.28
75 48 0.20
76 13 0.05
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.47
Consensus pattern (72 bp):
TATATATTTTCAAAAATGTTTTAAAAACTATATATTATATTATTTTTAAAATGTTTTAAAAACTA
TATAATA
Found at i:398689 original size:30 final size:30
Alignment explanation
Indices: 398562--398686 Score: 173
Period size: 30 Copynumber: 4.2 Consensus size: 30
398552 GTCCGTCACC
*
398562 GCACCTGCGGTTCAGGGAAGTTCCGT-CACT
1 GCACCGGCGGTTCAGGGAAGTTCC-TCCACT
* * *
398592 GCACCGGCGGTTCAGGGTAGCTCCACCACT
1 GCACCGGCGGTTCAGGGAAGTTCCTCCACT
398622 GCACCGGCGGTTCAGGGAAGTTCCTCCACT
1 GCACCGGCGGTTCAGGGAAGTTCCTCCACT
*
398652 GCACCCGG-GGTTCAAGGAAGTTCCTCCACT
1 GCA-CCGGCGGTTCAGGGAAGTTCCTCCACT
398682 GCACC
1 GCACC
398687 CGGTTTAGAT
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
29 2 0.02
30 79 0.93
31 4 0.05
ACGTcount: A:0.18, C:0.34, G:0.29, T:0.19
Consensus pattern (30 bp):
GCACCGGCGGTTCAGGGAAGTTCCTCCACT
Found at i:403384 original size:41 final size:42
Alignment explanation
Indices: 403294--403574 Score: 171
Period size: 42 Copynumber: 6.8 Consensus size: 42
403284 AATTGATACT
* * * * *
403294 TTAGCGGCGTTTTTAGTAAAAACGCTGCAATATAATTGACATA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATA-GAGTGATAAA
*
403337 TT-GCGGCGTTTTTA-TAAAAACGCCGCAATAGGGTGATAAA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* * ** *
403377 TTAGCGGCGTTTATA-TCACAAACGCTTCAATAGA-TTATAAA
1 TTAGCGGCGTTTTTAGT-AAAAACGCCGCAATAGAGTGATAAA
* * ** * *
403418 TTTTGCGGCG-ATTTAGCCAAAACGCCGCAATATAGTGGTAAA
1 -TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* * * ** * * *
403460 CTGGCAGCGTTTTTACCACAAACGCCACAATAGAAT-ATAAA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* * * * * *
403501 TTTTGCAGCG-ATTGAGTAAAAACGCCGCAATAGAGCGGTAAA
1 -TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
* **
403543 TTGGCGGCGTTTTTACAAAAAACGCCGCAATA
1 TTAGCGGCGTTTTTAGTAAAAACGCCGCAATA
403575 TATACACATA
Statistics
Matches: 178, Mismatches: 51, Indels: 19
0.72 0.21 0.08
Matches are distributed among these distances:
40 7 0.04
41 83 0.47
42 86 0.48
43 2 0.01
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.27
Consensus pattern (42 bp):
TTAGCGGCGTTTTTAGTAAAAACGCCGCAATAGAGTGATAAA
Found at i:403426 original size:42 final size:41
Alignment explanation
Indices: 403297--403574 Score: 102
Period size: 41 Copynumber: 6.7 Consensus size: 41
403287 TGATACTTTA
* * ** * *
403297 GCGGCGTTTTTAGTAAAAACGCTGCAATATAATTGACATA-TT
1 GCGGCGTTTATA-TAAAAACGCCGCAATAGGA-TGATAAATTT
* * *
403339 GCGGCGTTTTTATAAAAACGCCGCAATAGGGTGATAAATTA
1 GCGGCGTTTATATAAAAACGCCGCAATAGGATGATAAATTT
* ** *
403380 GCGGCGTTTATATCACAAACGCTTCAATA-GATTATAAATTTT
1 GCGGCGTTTATAT-AAAAACGCCGCAATAGGATGATAAA-TTT
*** * * * *
403422 GCGGCGATTTA-GCCAAAACGCCGCAATA-TAGTGGTAAACTG
1 GCGGCG-TTTATATAAAAACGCCGCAATAGGA-TGATAAATTT
* * * * * *
403463 GCAGCGTTTTTACCACAAACGCCACAATAGAAT-ATAAATTTT
1 GCGGCGTTTATA-TAAAAACGCCGCAATAGGATGATAAA-TTT
* * * * * *
403505 GCAGCGATTGA-GTAAAAACGCCGCAATA-GAGCGGTAAATTG
1 GCGGCG-TTTATATAAAAACGCCGCAATAGGA-TGATAAATTT
* *
403546 GCGGCGTTTTTACAAAAAACGCCGCAATA
1 GCGGCGTTTATA-TAAAAACGCCGCAATA
403575 TATACACATA
Statistics
Matches: 172, Mismatches: 50, Indels: 28
0.69 0.20 0.11
Matches are distributed among these distances:
40 11 0.06
41 77 0.45
42 77 0.45
43 7 0.04
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (41 bp):
GCGGCGTTTATATAAAAACGCCGCAATAGGATGATAAATTT
Found at i:403426 original size:83 final size:83
Alignment explanation
Indices: 403337--403574 Score: 271
Period size: 83 Copynumber: 2.9 Consensus size: 83
403327 AATTGACATA
* * * * *
403337 TTGCGGCGTTTTTA-TAAAAACGCCGCAATAGGGTGATAAATTAGCGGCGTTTATATCACAAACG
1 TTGCGGCG-ATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACG
** *
403401 CTTCAATAGATTATAAATT
65 CCACAATAGAATATAAATT
** * * * *
403420 TTGCGGCGATTTAGCCAAAACGCCGCAATATAGTGGTAAACTGGCAGCGTTTTTACCACAAACGC
1 TTGCGGCGATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACGC
403485 CACAATAGAATATAAATT
66 CACAATAGAATATAAATT
* * * * * *
403503 TTGCAGCGATTGAGTAAAAACGCCGCAATAGAGCGGTAAATTGGCGGCGTTTTTACAAAAAACGC
1 TTGCGGCGATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACGC
*
403568 CGCAATA
66 CACAATA
403575 TATACACATA
Statistics
Matches: 129, Mismatches: 25, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
82 4 0.03
83 125 0.97
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (83 bp):
TTGCGGCGATTTAGTAAAAACGCCGCAATAGAGTGGTAAATTGGCGGCGTTTATACCACAAACGC
CACAATAGAATATAAATT
Found at i:405249 original size:2 final size:2
Alignment explanation
Indices: 405242--405272 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
405232 TATTTATAGG
405242 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 A
405273 ATTAAGTGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:411875 original size:21 final size:21
Alignment explanation
Indices: 411857--411942 Score: 102
Period size: 21 Copynumber: 4.1 Consensus size: 21
411847 ATGAAGCAAG
*
411857 GGAAACAGAGAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
**
411878 GGAAGCAGCTAGAGCAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
*
411899 GGAAGCAGAGAGAGAAGCAGC
1 GGAAGCAGAGAGAGCAGCAGC
* *
411920 GGCAGCACAGAGAG-AGGCAGC
1 GGAAGCAGAGAGAGCA-GCAGC
411941 GG
1 GG
411943 CAGAACAGAG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 1 0.02
21 55 0.98
ACGTcount: A:0.37, C:0.20, G:0.42, T:0.01
Consensus pattern (21 bp):
GGAAGCAGAGAGAGCAGCAGC
Found at i:411943 original size:21 final size:21
Alignment explanation
Indices: 411865--411957 Score: 98
Period size: 21 Copynumber: 4.4 Consensus size: 21
411855 AGGGAAACAG
* *
411865 AGAGAGCAGCAGCGGAAGCAGC
1 AGAGAGAAGCAGCGGCAGCA-C
* * * *
411887 -TAGAGCAGCAGCGGAAGCAG
1 AGAGAGAAGCAGCGGCAGCAC
411907 AGAGAGAAGCAGCGGCAGCAC
1 AGAGAGAAGCAGCGGCAGCAC
* *
411928 AGAGAGAGGCAGCGGCAGAAC
1 AGAGAGAAGCAGCGGCAGCAC
411949 AGAGAGAAG
1 AGAGAGAAG
411958 TAATATATCA
Statistics
Matches: 61, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
21 61 1.00
ACGTcount: A:0.39, C:0.19, G:0.41, T:0.01
Consensus pattern (21 bp):
AGAGAGAAGCAGCGGCAGCAC
Found at i:412425 original size:43 final size:43
Alignment explanation
Indices: 412293--412516 Score: 158
Period size: 43 Copynumber: 5.2 Consensus size: 43
412283 CATACATTTA
* * * *
412293 GCGGCGTTTTTGATA-AAAACGCCGCAAAATCTCAATACATATT
1 GCGGCGTTTTTG-TAGAAAACGCCGCTAAATATCAACACCTATT
* * * * * *
412336 CGCAGCG--TTTGTAAGAAAACGCCAG-TAAAAATAAAAATCTACT
1 -GCGGCGTTTTTGT-AGAAAACGCC-GCTAAATATCAACACCTATT
*
412379 GCGGCGTTTTTGTAGAAAACGCCGCTAAACATCAACGA-CTATT
1 GCGGCGTTTTTGTAGAAAACGCCGCTAAATATCAAC-ACCTATT
* * *
412422 GCGGCG--TTTGTATGCCAAATGCCGTTAAATATCAACACCTATT
1 GCGGCGTTTTTGTA-G-AAAACGCCGCTAAATATCAACACCTATT
** * *
412465 GCGGCGTTTTAAT-GATAAACGCCGCTAAATATCAATACCTTTT
1 GCGGCGTTTTTGTAGA-AAACGCCGCTAAATATCAACACCTATT
412508 GCGGCGTTT
1 GCGGCGTTT
412517 GTTGAACTAT
Statistics
Matches: 142, Mismatches: 25, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
41 7 0.05
42 13 0.09
43 107 0.75
44 12 0.08
45 3 0.02
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (43 bp):
GCGGCGTTTTTGTAGAAAACGCCGCTAAATATCAACACCTATT
Found at i:412626 original size:15 final size:15
Alignment explanation
Indices: 412582--412653 Score: 53
Period size: 15 Copynumber: 4.9 Consensus size: 15
412572 CGCCGCAAAC
* *
412582 TTTAGCGGCGCTATT
1 TTTAGCGGCGTTTTT
*
412597 TTTAGCGGCG---CT
1 TTTAGCGGCGTTTTT
412609 TTTAGCGGCGTTTTT
1 TTTAGCGGCGTTTTT
*
412624 TTTA-CGCCGTATGTGTT
1 TTTAGCGGCGT-T-T-TT
412641 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
412654 AAAAACGCCG
Statistics
Matches: 46, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
12 11 0.24
14 5 0.11
15 16 0.35
16 2 0.04
17 7 0.15
18 5 0.11
ACGTcount: A:0.10, C:0.18, G:0.28, T:0.44
Consensus pattern (15 bp):
TTTAGCGGCGTTTTT
Found at i:414415 original size:17 final size:17
Alignment explanation
Indices: 414393--414425 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
414383 GTTTAGTTGT
414393 TTTTTTTTCTTTCTCTG
1 TTTTTTTTCTTTCTCTG
414410 TTTTTTTTCTTTCTCT
1 TTTTTTTTCTTTCTCT
414426 CCGGTTCTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (17 bp):
TTTTTTTTCTTTCTCTG
Found at i:414927 original size:3 final size:3
Alignment explanation
Indices: 414919--414966 Score: 89
Period size: 3 Copynumber: 16.3 Consensus size: 3
414909 AATATATATT
414919 TAA TAA TAA TAA TAA TAA T-A 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
414966 T
1 T
414967 TTATTAGTAT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:415298 original size:116 final size:116
Alignment explanation
Indices: 415094--415942 Score: 1328
Period size: 116 Copynumber: 7.4 Consensus size: 116
415084 ATTGAATAAA
* * ** * *
415094 TTCTTC-TCTTTCTTCAGAT---GAGTTCTTCTCATTATGAACTTTCT-GCTGGGGATGATGATC
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAAC--TCTACCTGGCAAAGATAATC
415154 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
64 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* *
415207 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
415272 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* *
415323 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGTTGATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
415388 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* *
415439 TTCTTCTTCCTTCTTCAGATGGCGAGTTCTTCTCATTATGAACTCTTCCTGGCAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
415504 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
415555 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
*
415620 TCAAATGATGAATTCAAGAAAAAGATTGAACAAGTTCTTCTCATTATGAAC
66 TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
415671 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
* * * *
415736 TCAACTTGATGAATTC-AGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 TCAA-ATGATGAATTCAAG-CAAAAGATTGAACAAGTTCTTCTCATTATGAAC
* * *
415788 TTCTTCTTCCTTCTTCAGAT-A--AGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGACTGATC
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAAAGA-TAATC
* ** * *
415849 CATCAAATGATGGATTCGGGTAAAAGATTGAACAAATTCTTCTCATTATGAAC
64 CATCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
415902 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACT
1 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACT
415943 TTCTCTGGAA
Statistics
Matches: 701, Mismatches: 24, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
113 8 0.01
114 121 0.17
115 14 0.02
116 477 0.68
117 81 0.12
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.36
Consensus pattern (116 bp):
TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAAAGATAATCCA
TCAAATGATGAATTCAAGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
Found at i:416842 original size:83 final size:83
Alignment explanation
Indices: 416703--417177 Score: 812
Period size: 83 Copynumber: 5.7 Consensus size: 83
416693 GTAGTTCTTA
*
416703 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
416768 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
416786 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
416851 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
416869 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCC-A
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
416933 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* *
416951 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
417016 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
* * * *
417034 CTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
417099 ATTCAATGATTGGTTCTG
66 ATTCAATGATTGGTTCTG
417117 TCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTT
1 -CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTT
417178 TCATTTAATG
Statistics
Matches: 371, Mismatches: 18, Indels: 6
0.94 0.05 0.02
Matches are distributed among these distances:
82 79 0.21
83 290 0.78
84 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (83 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
ATTCAATGATTGGTTCTG
Found at i:416994 original size:165 final size:165
Alignment explanation
Indices: 416705--417177 Score: 869
Period size: 165 Copynumber: 2.9 Consensus size: 165
416695 AGTTCTTACC
416705 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCC-AAT
416770 TCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
65 TCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAG
416835 CATATTCATCTTCCCAATTCAATGATTGGTTCTGCT
130 CATATTCATCTTCCCAATTCAATGATTGGTTCTGCT
416871 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAATT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAATT
416936 CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
66 CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
417001 ATATTCATCTTCCCAATTCAATGATTGGTTCTGCT
131 ATATTCATCTTCCCAATTCAATGATTGGTTCTGCT
* *
417036 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAACAAATTCATCTTCTAAAT
1 AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTC-CAAT
417101 TCAATGATTGGTTCTGTCC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG
65 TCAATGATTGGTTCTG-CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TG
*
417165 -GCAAATTCATCTT
128 AGCATATTCATCTT
417178 TCATTTAATG
Statistics
Matches: 301, Mismatches: 3, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
165 163 0.54
166 134 0.45
167 4 0.01
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.27
Consensus pattern (165 bp):
AAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAATT
CAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGC
ATATTCATCTTCCCAATTCAATGATTGGTTCTGCT
Found at i:417141 original size:248 final size:248
Alignment explanation
Indices: 416703--417177 Score: 835
Period size: 248 Copynumber: 1.9 Consensus size: 248
416693 GTAGTTCTTA
*
416703 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
416768 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
66 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
* * *
416833 AGCATATTCATCTTCCCAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACA
131 AACAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACA
416898 CTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAATTCAATGATTGGTTCTG
196 CTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAATTCAATGATTGGTTCTG
* *
416951 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCCA
1 CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
* *
417016 ATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
66 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
* *
417081 AACAAATTCATCTTCTAAATTCAATGATTGGTTCTG-TCCAACCAGATCAGATAACTCAAAGAAC
131 AACAAATTCATCTTCCAAATTCAATGATTGGTTCTGCT-AAACCAGATCAGATAACTCAAAGAAC
*
417145 ACTTCCAGAAGATGCTATTGGCAAATTCATCTT
195 ACTTCCAGAAGATGCTATTAGCAAATTCATCTT
417178 TCATTTAATG
Statistics
Matches: 215, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
247 1 0.00
248 214 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.27
Consensus pattern (248 bp):
CCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCCAA
ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
AACAAATTCATCTTCCAAATTCAATGATTGGTTCTGCTAAACCAGATCAGATAACTCAAAGAACA
CTTCCAGAAGATGCTATTAGCAAATTCATCTTCCAATTCAATGATTGGTTCTG
Found at i:418218 original size:8 final size:8
Alignment explanation
Indices: 418207--418270 Score: 80
Period size: 8 Copynumber: 8.2 Consensus size: 8
418197 CCTTGACCCC
418207 TTTTTCTT
1 TTTTTCTT
*
418215 TTTTTCCT
1 TTTTTCTT
*
418223 CTTTTCTT
1 TTTTTCTT
418231 TTTTTCTT
1 TTTTTCTT
418239 TTTTT-TT
1 TTTTTCTT
418246 CTTTTTC-T
1 -TTTTTCTT
418254 TTTTT-TT
1 TTTTTCTT
418261 TTTTTCTT
1 TTTTTCTT
418269 TT
1 TT
418271 CTTCAAGCAT
Statistics
Matches: 48, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
7 13 0.27
8 35 0.73
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (8 bp):
TTTTTCTT
Found at i:418227 original size:16 final size:15
Alignment explanation
Indices: 418208--418273 Score: 75
Period size: 14 Copynumber: 4.5 Consensus size: 15
418198 CTTGACCCCT
418208 TTTTCTTTTTTTCCTC
1 TTTTCTTTTTTT-CTC
418224 TTTTCTTTTTTTCT-
1 TTTTCTTTTTTTCTC
*
418238 TTTT-TTTTCTTTTTC
1 TTTTCTTTT-TTTCTC
*
418253 TTTT-TTTTTTTTTC
1 TTTTCTTTTTTTCTC
418267 TTTTCTT
1 TTTTCTT
418274 CAAGCATAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
13 4 0.09
14 18 0.39
15 12 0.26
16 12 0.26
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTCTTTTTTTCTC
Found at i:418242 original size:10 final size:10
Alignment explanation
Indices: 418229--418270 Score: 68
Period size: 10 Copynumber: 4.2 Consensus size: 10
418219 TCCTCTTTTC
418229 TTTTTTTCTT
1 TTTTTTTCTT
418239 TTTTTTTCTT
1 TTTTTTTCTT
418249 TTTCTTTT-TT
1 TTT-TTTTCTT
418259 TTTTTTTCTT
1 TTTTTTTCTT
418269 TT
1 TT
418271 CTTCAAGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 4 0.13
10 22 0.73
11 4 0.13
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (10 bp):
TTTTTTTCTT
Found at i:418270 original size:25 final size:24
Alignment explanation
Indices: 418207--418273 Score: 89
Period size: 25 Copynumber: 2.7 Consensus size: 24
418197 CCTTGACCCC
* *
418207 TTTTTCTTTTTTTCCTCTTTTCTTT
1 TTTTTTTTTTTTTTCT-TTTTCTTT
*
418232 TTTTCTTTTTTTTTCTTTTTCTTT
1 TTTTTTTTTTTTTTCTTTTTCTTT
418256 TTTTTTTTTTCTTTTCTT
1 TTTTTTTTTT-TTTTCTT
418274 CAAGCATAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 17 0.46
25 20 0.54
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (24 bp):
TTTTTTTTTTTTTTCTTTTTCTTT
Found at i:430524 original size:16 final size:16
Alignment explanation
Indices: 430503--430533 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
430493 TTTAGTTGTT
430503 TTTTTTTCTTTCTCTG
1 TTTTTTTCTTTCTCTG
*
430519 TTTTTTTTTTTCTCT
1 TTTTTTTCTTTCTCT
430534 CCGGTTCTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.16, G:0.03, T:0.81
Consensus pattern (16 bp):
TTTTTTTCTTTCTCTG
Found at i:431037 original size:3 final size:3
Alignment explanation
Indices: 431029--431081 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
431019 AATATATATT
*
431029 TAA TAA TAA TAA TAA TAA TGA 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
431077 TAA TA
1 TAA TA
431082 TGGGTAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:437378 original size:30 final size:30
Alignment explanation
Indices: 437294--437416 Score: 124
Period size: 30 Copynumber: 4.1 Consensus size: 30
437284 TCAAGGTAAG
* * * *
437294 TCCGTCACCGCACCTGCGGTTCAGAGAAGA
1 TCCGTCACTGCACCGGCGGTTCAGGGAAGT
*
437324 TCCGTCA-TCGCACCTGCGGTTCAGGGAAGT
1 TCCGTCACT-GCACCGGCGGTTCAGGGAAGT
* *
437354 TCCGTCACTGCACCGGCGGTTCAGGTAGGT
1 TCCGTCACTGCACCGGCGGTTCAGGGAAGT
* * *
437384 TCCATCACTGCACCAGG-GATTCAGGGAAAT
1 TCCGTCACTGCACC-GGCGGTTCAGGGAAGT
437414 TCC
1 TCC
437417 TCCACTGTGC
Statistics
Matches: 79, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
30 76 0.96
31 3 0.04
ACGTcount: A:0.20, C:0.31, G:0.28, T:0.21
Consensus pattern (30 bp):
TCCGTCACTGCACCGGCGGTTCAGGGAAGT
Found at i:437397 original size:60 final size:60
Alignment explanation
Indices: 437279--437416 Score: 138
Period size: 60 Copynumber: 2.3 Consensus size: 60
437269 CTATGTACGT
* * * * * *
437279 GGGATTCAAGGTAAGTCCGTCACCGCACCTGCGGTTCAGAGAAGATCCGTCATCGCACCT
1 GGGATTCAGGGAAATTCCGTCACCGCACCGGCGGTTCAGAGAAGATCCATCATCGCACCA
* * * *
437339 GCGG-TTCAGGGAAGTTCCGTCACTGCACCGGCGGTTCAG-GTAGGTTCCATCA-CTGCACCA
1 G-GGATTCAGGGAAATTCCGTCACCGCACCGGCGGTTCAGAG-AAGATCCATCATC-GCACCA
437399 GGGATTCAGGGAAATTCC
1 GGGATTCAGGGAAATTCC
437417 TCCACTGTGC
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
59 4 0.06
60 57 0.90
61 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.29, T:0.21
Consensus pattern (60 bp):
GGGATTCAGGGAAATTCCGTCACCGCACCGGCGGTTCAGAGAAGATCCATCATCGCACCA
Found at i:438596 original size:30 final size:30
Alignment explanation
Indices: 438560--438681 Score: 131
Period size: 30 Copynumber: 4.1 Consensus size: 30
438550 TTCAAGGACA
*
438560 TTCCGTCACCACACCTCCGGTTCAGGGAAG
1 TTCCGTCACCGCACCTCCGGTTCAGGGAAG
*
438590 TTCCGTCACTGCACCTCCGGTTCAGGGAAG
1 TTCCGTCACCGCACCTCCGGTTCAGGGAAG
* ** *
438620 CTCCGTCA-CGCACCGGCGGTTCAGGGAGG
1 TTCCGTCACCGCACCTCCGGTTCAGGGAAG
* ** *
438649 TTCCAG-CACTGCACCTGGGGTTCTGGGAAG
1 TTCC-GTCACCGCACCTCCGGTTCAGGGAAG
438679 TTC
1 TTC
438682 TTCCACCGCA
Statistics
Matches: 77, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
29 22 0.29
30 55 0.71
ACGTcount: A:0.16, C:0.33, G:0.30, T:0.21
Consensus pattern (30 bp):
TTCCGTCACCGCACCTCCGGTTCAGGGAAG
Done.