Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000251.1 Hibiscus syriacus cultivar Beakdansim tig00000453_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: 648719
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:167044 original size:20 final size:19
Alignment explanation
Indices: 167017--167074 Score: 82
Period size: 19 Copynumber: 3.0 Consensus size: 19
167007 CGTTTAATGA
167017 AAAAGATACTAATTGTTAC
1 AAAAGATACTAATTGTTAC
167036 AAAAGGATACTAATTGTTA-
1 AAAA-GATACTAATTGTTAC
*
167055 AAAAGATAACCAATTGTTAC
1 AAAAGAT-ACTAATTGTTAC
167075 CAATTGTTGG
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
18 3 0.09
19 18 0.51
20 14 0.40
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.29
Consensus pattern (19 bp):
AAAAGATACTAATTGTTAC
Found at i:168264 original size:19 final size:21
Alignment explanation
Indices: 168217--168264 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
168207 TCTAAATCTT
* *
168217 TTTTCAAAATTTCATTTTGGC
1 TTTTCAAAATCTCATTTTAGC
168238 TTTT-AAAATCT-ATTTTAG-
1 TTTTCAAAATCTCATTTTAGC
168256 TTTTCAAAA
1 TTTTCAAAA
168265 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.17
19 10 0.42
20 6 0.25
21 4 0.17
ACGTcount: A:0.31, C:0.10, G:0.06, T:0.52
Consensus pattern (21 bp):
TTTTCAAAATCTCATTTTAGC
Found at i:169744 original size:29 final size:31
Alignment explanation
Indices: 169712--169770 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
169702 AAACTTTGAA
*
169712 TAAATCCAATT-AAGTCCAAAAA-CATTTTT
1 TAAATCCAATTCAAGTCAAAAAACCATTTTT
*
169741 TAAATTCAATTCAAGTCAAAAAACCATTTT
1 TAAATCCAATTCAAGTCAAAAAACCATTTT
169771 GCCTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 10 0.38
30 10 0.38
31 6 0.23
ACGTcount: A:0.46, C:0.17, G:0.03, T:0.34
Consensus pattern (31 bp):
TAAATCCAATTCAAGTCAAAAAACCATTTTT
Found at i:173521 original size:19 final size:19
Alignment explanation
Indices: 173494--173543 Score: 68
Period size: 18 Copynumber: 2.7 Consensus size: 19
173484 AATGGCAGTG
*
173494 AGAGTGAAATAAAA-AAAGA
1 AGAGAGAAA-AAAAGAAAGA
173513 AGAGAGAAAAAAAGAAAGA
1 AGAGAGAAAAAAAGAAAGA
173532 A-AGAGAAAAAAA
1 AGAGAGAAAAAAA
173544 TAATAAGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 15 0.52
19 14 0.48
ACGTcount: A:0.74, C:0.00, G:0.22, T:0.04
Consensus pattern (19 bp):
AGAGAGAAAAAAAGAAAGA
Found at i:179234 original size:26 final size:26
Alignment explanation
Indices: 179205--179257 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 26
179195 TTTTATTTTG
179205 ATAACTTAAT-TATTCTTTTTT-AAGAA
1 ATAA-TTAATCTATT-TTTTTTAAAGAA
*
179231 ATAATTATTCTATTTTTTTTAAAGAA
1 ATAATTAATCTATTTTTTTTAAAGAA
179257 A
1 A
179258 GATAGGTCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.51
Consensus pattern (26 bp):
ATAATTAATCTATTTTTTTTAAAGAA
Found at i:181950 original size:20 final size:20
Alignment explanation
Indices: 181925--181966 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
181915 TTATTTCAAT
181925 TATGGAAAGTATACCAAATA
1 TATGGAAAGTATACCAAATA
181945 TATGGAAAGTATACCAAATA
1 TATGGAAAGTATACCAAATA
181965 TA
1 TA
181967 CAAATCAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.26
Consensus pattern (20 bp):
TATGGAAAGTATACCAAATA
Found at i:183078 original size:32 final size:32
Alignment explanation
Indices: 183042--183141 Score: 78
Period size: 32 Copynumber: 3.3 Consensus size: 32
183032 TTTATTTATT
183042 ATTTATATTTTTATTAACTCTCTTTTCATGAC
1 ATTTATATTTTTATTAACTCTCTTTTCATGAC
183074 ATTTAT-TTTTCT-TT-A-T-T-TTATT-AT---
1 ATTTATATTTT-TATTAACTCTCTT-TTCATGAC
183098 A-TTATATTTTTTATTAACTCTCTTTTCATGAC
1 ATTTATA-TTTTTATTAACTCTCTTTTCATGAC
*
183130 ATATTTTATTTT
1 AT-TTATATTTT
183142 GCATTTATGT
Statistics
Matches: 52, Mismatches: 1, Indels: 29
0.63 0.01 0.35
Matches are distributed among these distances:
23 4 0.08
24 2 0.04
25 6 0.12
26 1 0.02
27 5 0.10
28 6 0.12
29 5 0.10
30 1 0.02
31 6 0.12
32 8 0.15
33 4 0.08
34 4 0.08
ACGTcount: A:0.24, C:0.11, G:0.02, T:0.63
Consensus pattern (32 bp):
ATTTATATTTTTATTAACTCTCTTTTCATGAC
Found at i:183080 original size:53 final size:56
Alignment explanation
Indices: 183023--183131 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
183013 TAGGTATTCA
183023 TTATTTTTCTTTA-TTTATTAT-TTATA-TTTTTATTAACTCTCTTTTCATGACAT
1 TTATTTTTCTTTATTTTATTATATTATATTTTTTATTAACTCTCTTTTCATGACAT
183076 TTATTTTTCTTTATTTTATTATATTATATTTTTTATTAACTCTCTTTTCATGACAT
1 TTATTTTTCTTTATTTTATTATATTATATTTTTTATTAACTCTCTTTTCATGACAT
183132 ATTTTATTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
53 13 0.25
54 8 0.15
55 5 0.09
56 27 0.51
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.64
Consensus pattern (56 bp):
TTATTTTTCTTTATTTTATTATATTATATTTTTTATTAACTCTCTTTTCATGACAT
Found at i:184029 original size:438 final size:447
Alignment explanation
Indices: 183152--184035 Score: 1504
Period size: 438 Copynumber: 2.0 Consensus size: 447
183142 GCATTTATGT
* *
183152 CACATTTCTTTCTATGTTTTGACATATTTTTTGTCGTTTGGTCGTTATTTTTATTTTTTTATCAA
1 CACATTTCTTTCTATGTTTTGACACATTTTTTGTCGTTTGGTCGTTA-TTTTATGTTTTTATCAA
* *
183217 GATTGGATTTGATATTACTACTAATGATCGAGATAGCTCTGATTTGTTATCATGCTTATTTCTCT
65 GATTGGATTTGACATTACTACTAATGATC-AGATAGCTCTGATTTGTTATCAAGCTTATTTCTCT
*
183282 TGCTTTGGACCTTCAAATTAAATTTGGATACGCAATTTGCGTTCGTGAATATTTTTATCATGTCA
129 TGCTTTGGACCTTCAAATTAAATTTGGATACACAATTTGCGTTCGTGAATATTTTTATCATGTCA
*
183347 CTTGATTCTGATTTACGATTTTCAATGGTAGCTTGATCTCTTTGTGGTTTATTTTTCGATGCGGT
194 CTTGATTCTGATTTACGATTTTCAATGGTAGCTTGATCTCTTTGTGGTTTATTTGTCGATGCGGT
183412 CATATCTGTTTGTATATACCTTTAAGTTTATTTTAAGTGACTAGTTTTTTGTATTAATGATTATA
259 CATATCTGTTTGTATATACCTTTAAGTTTATTTTAAGTGACTAG-TTTTTGTATTAATGATTATA
183477 AGAAAAAAAATTAGTTGACCCTATTCCCATATATGTAATGGGGAGGGGGAGGTAAGGTAGTAGGC
323 AGAAAAAAAATTAGTTGACCCTATTCCCATATATGTAATGGGGAGGGGGAGGTAAGGTAGTAGGC
183542 TGACCCAACGCCAGGTTGAGAGCAGCTTCCGTCGAAGACCTCCGGCAATCAGAATTATTA
388 TGACCCAACGCCAGGTTGAGAGCAGCTTCCGTCGAAGACCTCCGGCAATCAGAATTATTA
* *
183602 CACATTTCTTTCTATGTTTTGGCACATTTTTTGTCGTTTGGTCGTTA-TTT-TGTTTTTATCAGG
1 CACATTTCTTTCTATGTTTTGACACATTTTTTGTCGTTTGGTCGTTATTTTATGTTTTTATCAAG
183665 ATTGGATTTGACATTACTACTAATGATC-GATAGCTCTGATTTGTTATCAAGCTTATTTCTCTTG
66 ATTGGATTTGACATTACTACTAATGATCAGATAGCTCTGATTTGTTATCAAGCTTATTTCTCTTG
* *
183729 CTTTGGACCTTCAAATTAAATTTGGATACACAATTTGCGTTCGTGGATA-TTTTATCATGTC-GT
131 CTTTGGACCTTCAAATTAAATTTGGATACACAATTTGCGTTCGTGAATATTTTTATCATGTCACT
*
183792 TGATTTTGATTTACGA-TTTCAATGGTAGCTTGATCTCCTTTGTGGTTTATTTGTCGATGCGGTC
196 TGATTCTGATTTACGATTTTCAATGGTAGCTTGATCT-CTTTGTGGTTTATTTGTCGATGCGGTC
*
183856 ATATC-GTTTGTATCTACCTTTAAGTTTATTTTAAGTG-CTA-TTTTTGTATTAATGATTATAA-
260 ATATCTGTTTGTATATACCTTTAAGTTTATTTTAAGTGACTAGTTTTTGTATTAATGATTATAAG
183917 AAAAAAAATTAGTTGACCCTATTCCCATATATGTAATGGGTGA-GGGGA-GTAAGGTAGTAGGCT
325 AAAAAAAATTAGTTGACCCTATTCCCATATATGTAATGGG-GAGGGGGAGGTAAGGTAGTAGGCT
* *
183980 GCCCCCAACGCCAGGTTGAGAGCAGCTTCCGTGGAAGACCTCCGGCAATCAGAATT
389 G-ACCCAACGCCAGGTTGAGAGCAGCTTCCGTCGAAGACCTCCGGCAATCAGAATT
184036 TGAATTGCCC
Statistics
Matches: 417, Mismatches: 14, Indels: 18
0.93 0.03 0.04
Matches are distributed among these distances:
437 16 0.04
438 97 0.23
439 23 0.06
441 3 0.01
442 51 0.12
443 47 0.11
444 12 0.03
445 82 0.20
447 38 0.09
448 3 0.01
450 45 0.11
ACGTcount: A:0.24, C:0.15, G:0.19, T:0.41
Consensus pattern (447 bp):
CACATTTCTTTCTATGTTTTGACACATTTTTTGTCGTTTGGTCGTTATTTTATGTTTTTATCAAG
ATTGGATTTGACATTACTACTAATGATCAGATAGCTCTGATTTGTTATCAAGCTTATTTCTCTTG
CTTTGGACCTTCAAATTAAATTTGGATACACAATTTGCGTTCGTGAATATTTTTATCATGTCACT
TGATTCTGATTTACGATTTTCAATGGTAGCTTGATCTCTTTGTGGTTTATTTGTCGATGCGGTCA
TATCTGTTTGTATATACCTTTAAGTTTATTTTAAGTGACTAGTTTTTGTATTAATGATTATAAGA
AAAAAAATTAGTTGACCCTATTCCCATATATGTAATGGGGAGGGGGAGGTAAGGTAGTAGGCTGA
CCCAACGCCAGGTTGAGAGCAGCTTCCGTCGAAGACCTCCGGCAATCAGAATTATTA
Found at i:184829 original size:45 final size:45
Alignment explanation
Indices: 184731--184834 Score: 115
Period size: 45 Copynumber: 2.3 Consensus size: 45
184721 GAATATTTTA
* *
184731 AATTAAAAGATATTTATTATATTTTTAAATTTAAATATTAAAGAT
1 AATTAAAAGATATTCAATATATTTTTAAATTTAAATATTAAAGAT
* *
184776 -ATTAAAAAGATA-TCAATATCTTTTTAAATATTTTAA-ATTAAAGAT
1 AATT-AAAAGATATTCAATATATTTTT-AA-ATTTAAATATTAAAGAT
*
184821 AATTAAAAGGTATT
1 AATTAAAAGATATT
184835 ATTTTTTAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
44 13 0.27
45 26 0.53
46 10 0.20
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (45 bp):
AATTAAAAGATATTCAATATATTTTTAAATTTAAATATTAAAGAT
Found at i:187541 original size:2 final size:2
Alignment explanation
Indices: 187534--187609 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
187524 GTTGGTAAGA
187534 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
187576 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
187610 TGCAACACAG
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:187797 original size:3 final size:3
Alignment explanation
Indices: 187789--187839 Score: 57
Period size: 3 Copynumber: 16.7 Consensus size: 3
187779 TCATTTCGTT
** **
187789 TTA TTA TTA TTA TTA TTA AAA TTA AAA TTA TTA TATA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
187835 TTA TT
1 TTA TT
187840 TAATAAAAAT
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:189626 original size:39 final size:39
Alignment explanation
Indices: 189577--189651 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
189567 TTCTGATATA
*
189577 TTTTAAATAAATATTTTTTTATA-AGTATATATATATTAT
1 TTTTAAATAAATATTTTATTATATA-TATATATATATTAT
*
189616 TTTTACATAAATATTTTATTATATATATATATATAT
1 TTTTAAATAAATATTTTATTATATATATATATATAT
189652 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 32 0.97
40 1 0.03
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (39 bp):
TTTTAAATAAATATTTTATTATATATATATATATATTAT
Found at i:189642 original size:2 final size:2
Alignment explanation
Indices: 189635--189666 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
189625 AATATTTTAT
189635 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
189667 TATTTTAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:189680 original size:16 final size:16
Alignment explanation
Indices: 189632--189695 Score: 51
Period size: 16 Copynumber: 4.0 Consensus size: 16
189622 ATAAATATTT
* *
189632 TATTATATATA-TATA
1 TATTATATTTATTTTA
* *
189647 TATATATATATATATTA
1 TAT-TATATTTATTTTA
189664 TATTAT-TTTAGTTTTA
1 TATTATATTTA-TTTTA
*
189680 TTTTATATTTATTTTA
1 TATTATATTTATTTTA
189696 ATGTTAAGAA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
15 6 0.15
16 25 0.62
17 9 0.22
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
TATTATATTTATTTTA
Found at i:190927 original size:17 final size:18
Alignment explanation
Indices: 190907--190942 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 18
190897 TTTTGTTTTT
190907 TTTTTAATTTTTT-TTAA
1 TTTTTAATTTTTTCTTAA
190924 TTTTTAATTTTTTCTTAA
1 TTTTTAATTTTTTCTTAA
190942 T
1 T
190943 AAATGCATGC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (18 bp):
TTTTTAATTTTTTCTTAA
Found at i:190942 original size:11 final size:10
Alignment explanation
Indices: 190904--190928 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
190894 ACTTTTTGTT
190904 TTTTTTTTAA
1 TTTTTTTTAA
190914 TTTTTTTTAA
1 TTTTTTTTAA
190924 TTTTT
1 TTTTT
190929 AATTTTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTTTTAA
Found at i:192700 original size:18 final size:17
Alignment explanation
Indices: 192665--192703 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
192655 TTGTATTCTT
*
192665 ATTTTTACATTTATTAC
1 ATTTTTACATTTAATAC
*
192682 ATTTTTGCATTTACATAC
1 ATTTTTACATTTA-ATAC
192700 ATTT
1 ATTT
192704 ATTATTGTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.28, C:0.13, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTTTACATTTAATAC
Found at i:194250 original size:28 final size:28
Alignment explanation
Indices: 194215--194273 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
194205 GTGTTGCTTT
194215 TAAGGTTATGAGCATTGAATCAATTTTG
1 TAAGGTTATGAGCATTGAATCAATTTTG
194243 TAAGGTTATGAGCATTGAATCAATTTTG
1 TAAGGTTATGAGCATTGAATCAATTTTG
194271 TAA
1 TAA
194274 TCTTACAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (28 bp):
TAAGGTTATGAGCATTGAATCAATTTTG
Found at i:194819 original size:72 final size:72
Alignment explanation
Indices: 194729--194862 Score: 171
Period size: 72 Copynumber: 1.9 Consensus size: 72
194719 TACAATAAAG
* * **
194729 CTTGAGTTATCCCCCTAAAACAATTGGTTAAT-AGCCATGGTTTTATGGATAATATTCAGCTAGT
1 CTTGAGTTATCCCCCTAAAACAATTAGTTAATCA-CCACGACTTTATGGATAATATTCAGCTAGT
194793 CTGTTATT
65 CTGTTATT
* * ** *
194801 CTTGAGTTGTCCCTCTAAAGTAATTAGTTAATCACCCCGACTTTATGGATAATATTCAGCTA
1 CTTGAGTTATCCCCCTAAAACAATTAGTTAATCACCACGACTTTATGGATAATATTCAGCTA
194863 ACCCATTATA
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
72 51 0.98
73 1 0.02
ACGTcount: A:0.28, C:0.19, G:0.16, T:0.37
Consensus pattern (72 bp):
CTTGAGTTATCCCCCTAAAACAATTAGTTAATCACCACGACTTTATGGATAATATTCAGCTAGTC
TGTTATT
Found at i:198911 original size:22 final size:22
Alignment explanation
Indices: 198881--198957 Score: 118
Period size: 22 Copynumber: 3.5 Consensus size: 22
198871 ACATCTACAT
198881 TTTTCAAAGATGATAGATTCTC
1 TTTTCAAAGATGATAGATTCTC
* *
198903 TCTTCAAAGATGATATATTCTC
1 TTTTCAAAGATGATAGATTCTC
* *
198925 TTTTTAAATATGATAGATTCTC
1 TTTTCAAAGATGATAGATTCTC
198947 TTTTCAAAGAT
1 TTTTCAAAGAT
198958 TAAAGCTTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.32, C:0.13, G:0.10, T:0.44
Consensus pattern (22 bp):
TTTTCAAAGATGATAGATTCTC
Found at i:199806 original size:76 final size:76
Alignment explanation
Indices: 199639--200502 Score: 1498
Period size: 76 Copynumber: 11.4 Consensus size: 76
199629 CTATTTCCCA
* *
199639 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGGAGATTTTTGATGTTTTTA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC-GGGAGCTTTTTGATGTTTTCA
199704 AAGCCTTAGGGT
65 AAGCCTTAGGGT
*
199716 CATCTGTAAGTCCTAAAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
199781 AGCCTTAGGTT
66 AGCCTTAGGGT
199792 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
199857 AGCCTTAGGGT
66 AGCCTTAGGGT
*
199868 CATCTGTAAGTTCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
199932 AGCCTTAGGGT
66 AGCCTTAGGGT
199943 CATCTGTAAGTCCTACAGTGCATGATG-TTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
200007 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
200018 CATCTGTAAGTCCTACAGTGCATGATGTTCCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
200083 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
200094 CATCTGTAAGTCCTACAGTGCATAATGTTTCCAAAAACCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
200159 AGCCTTAGAGT
66 AGCCTTAGGGT
*
200170 CATCTGTAAGTCCTACAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
200235 AGCTTTAGGGT
66 AGCCTTAGGGT
* * *
200246 CATCTTTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
200311 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
200322 CATCTGTAAGTTCTGCAGTGCATGATGTTTTCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
200387 AGTCTTAGGGT
66 AGCCTTAGGGT
* **
200398 CATCTATAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
200463 AGCCTTAGGGT
66 AGCCTTAGGGT
*
200474 CATCTGTAAGTCCTGCAGTGCATGATGTT
1 CATCTGTAAGTCCTACAGTGCATGATGTT
200503 CTTAGGACCT
Statistics
Matches: 748, Mismatches: 37, Indels: 5
0.95 0.05 0.01
Matches are distributed among these distances:
74 21 0.03
75 105 0.14
76 580 0.78
77 42 0.06
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:200665 original size:3 final size:3
Alignment explanation
Indices: 200657--200722 Score: 78
Period size: 3 Copynumber: 21.7 Consensus size: 3
200647 TCATTTCGTT
** * **
200657 TTA TTA TTA TTA TTA TTA TTA AAA TCA AAA TTA TTA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
200703 TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
200723 TAATAAAAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
3 51 0.94
4 3 0.06
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:202512 original size:43 final size:38
Alignment explanation
Indices: 202455--202538 Score: 96
Period size: 39 Copynumber: 2.1 Consensus size: 38
202445 TTCTGATATA
**
202455 TTTTAAATAATATTTTATTGTTATAAGTTATATATATATTAT
1 TTTTAAATAATATTTTA-AATTAT-A--TATATATATATTAT
*
202497 TTTTACATAAATATTTTAAATTATATATATATATATTAT
1 TTTTAAAT-AATATTTTAAATTATATATATATATATTAT
202536 TTT
1 TTT
202539 AGTTTTATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
39 17 0.45
41 1 0.03
42 11 0.29
43 9 0.24
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.57
Consensus pattern (38 bp):
TTTTAAATAATATTTTAAATTATATATATATATATTAT
Found at i:202765 original size:123 final size:120
Alignment explanation
Indices: 202552--202772 Score: 275
Period size: 123 Copynumber: 1.8 Consensus size: 120
202542 TTTATTTTAA
* * * * * *
202552 TATTTATTTTTAATGTTAAGAAAGAGCAGTCTTAAACAACTGGATGTCCATTTTTTGATATTTTT
1 TATTTATTTTTAATATTAAAAAAGAGCAGTCTTAAACAACTAGAAGTCCATTTTCTGATATTTCT
**
202617 AAATAAATATTTACTTTTATCAATTATATATATTAGTAGAAATGTTTTATTAATATT
66 AAATAAATAAATACTTTTA-CAATTA-ATATATTAGTAGAAATGTTTTATTAATATT
* * *
202674 TATTTATTTTTAATATTAAAAAAGGAGCTGTTTTAAAGCACCTAGAAG-CCATTTTCTGATATTT
1 TATTTATTTTTAATATTAAAAAA-GAGCAGTCTTAAA-CAACTAGAAGTCCATTTTCTGATATTT
202738 CTAAATAAATAAATATCTTATTA-AATTAATATATT
64 CTAAATAAATAAATA-CTT-TTACAATTAATATATT
202773 TTCTTAAAAT
Statistics
Matches: 84, Mismatches: 11, Indels: 8
0.82 0.11 0.08
Matches are distributed among these distances:
122 28 0.33
123 43 0.51
124 10 0.12
125 3 0.04
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (120 bp):
TATTTATTTTTAATATTAAAAAAGAGCAGTCTTAAACAACTAGAAGTCCATTTTCTGATATTTCT
AAATAAATAAATACTTTTACAATTAATATATTAGTAGAAATGTTTTATTAATATT
Found at i:204565 original size:36 final size:36
Alignment explanation
Indices: 204518--204590 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
204508 GAAGCCCTAC
*
204518 TTTGAATTGACAAATGTGAGTAAAAAGTGTTTTTCA
1 TTTGAATTGACAAATGTGAGTAAAAAGAGTTTTTCA
204554 TTTGAATTGACAAATGTGAGTAAAAAGAGTTTTTCA
1 TTTGAATTGACAAATGTGAGTAAAAAGAGTTTTTCA
204590 T
1 T
204591 ACTTAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.38
Consensus pattern (36 bp):
TTTGAATTGACAAATGTGAGTAAAAAGAGTTTTTCA
Found at i:205021 original size:2 final size:2
Alignment explanation
Indices: 204961--205009 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
204951 TCAATCTACA
204961 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
205003 AT AT AT A
1 AT AT AT A
205010 ATTTACTATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:205176 original size:13 final size:13
Alignment explanation
Indices: 205158--205196 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
205148 AACGACTCGC
205158 AATGCGCATCATA
1 AATGCGCATCATA
**
205171 AATGCGTGTCATA
1 AATGCGCATCATA
205184 AATGCGCATCATA
1 AATGCGCATCATA
205197 GATTTATGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (13 bp):
AATGCGCATCATA
Found at i:206570 original size:2 final size:2
Alignment explanation
Indices: 206559--206596 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
206549 TAAAGGCGAT
206559 TA TA -A TA TA TA TA TA TA TA T- 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 TA
206597 CAATAAAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:206582 original size:15 final size:15
Alignment explanation
Indices: 206559--206593 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
206549 TAAAGGCGAT
*
206559 TATAATATATATATA
1 TATATTATATATATA
206574 TATATTATATATATA
1 TATATTATATATATA
206589 TATAT
1 TATAT
206594 ATACAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TATATTATATATATA
Found at i:206585 original size:17 final size:17
Alignment explanation
Indices: 206563--206595 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
206553 GGCGATTATA
206563 ATATATATATATATATT
1 ATATATATATATATATT
206580 ATATATATATATATAT
1 ATATATATATATATAT
206596 ACAATAAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
ATATATATATATATATT
Found at i:208654 original size:135 final size:134
Alignment explanation
Indices: 208246--209006 Score: 766
Period size: 135 Copynumber: 5.6 Consensus size: 134
208236 ATCGGGTACG
* * * * *
208246 GAGAAGTGGATCAAAGTTTTTCTCGAGTCTAACCTCCCCTAAAGAGTAGTGGAGGAGATTCTTTC
1 GAGAAGTGGATC-AAGATTTCCTTGAGTCTAACCTCCCCTAAAGAGTAGCGGAGCAGATTC-TTC
* ** * * * **
208311 TTCTTTCAGATTTGATCTTCCTGAAAATTAGTGAAGCAAATCACATCCGATTTAATCTTCATTGA
64 TTCTTTCAGATTTGATCTTCCTGAAGAGAAGCGAAGCAAATCACATCTGATTCAATCTTCCCTGA
*
208376 AGAACAA
129 A-AAGAA
* ** * *
208383 -AAAAGTGGATCAA-AGTTTTTTTAGAGTCTGACCTCCCCTAAAGAGTAGCAGAGCAGATTCTTT
1 GAGAAGTGGATCAAGA-TTTCCTT-GAGTCTAACCTCCCCTAAAGAGTAGCGGAGCAGATTC-TT
* * * * * * * *
208446 CTTCTTTCATATTTTATCTTCTTTAATAGCAGCAAAGCAAATCAAAATCT-ATT-AATTCTTCCC
63 CTTCTTTCAGATTTGATCTTCCTGAAGAGAAGCGAAGCAAATC-ACATCTGATTCAA-TCTTCCC
*
208509 TGAAGAGAA
126 TGAAAAGAA
*
208518 GAGAAAGTGGATCAAGATTTCCTTGAGTCTAACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTTT
1 GAG-AAGTGGATCAAGATTTCCTTGAGTCTAACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCT
* * * * * *
208583 TCCTTCATATATGATCTTCTTGAAGAGAAGCGAAGTAAATCACATTTGATTCAATCTTCCCTGAA
65 TCTTTCAGATTTGATCTTCCTGAAGAGAAGCGAAGCAAATCACATCTGATTCAATCTTCCCTGAA
208648 AAGAA
130 AAGAA
** *
208653 GAGAAGTGGATCAAAGA-TTCCTTGAGTCTGGCCTCCCCTAAAGAGTAGCGGAGCATATTCTTCT
1 GAGAAGTGGATC-AAGATTTCCTTGAGTCTAACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCT
* *
208717 TCTTTC-GAATTTGGTCTTCCTGAAGAGCAA-CGAAGCAAATCACATTATGATTCAATCTTCCCT
65 TCTTTCAG-ATTTGATCTTCCTGAAGAG-AAGCGAAGCAAATCACA-TCTGATTCAATCTTCCCT
*
208780 GAAAAGCA
127 GAAAAGAA
* * ** * *
208788 GAGAAGTGGATCAA-AGTTTCCTTGAGTCTGACCTCCCCTAAATAGTAGCGGAATAGATTGTACT
1 GAGAAGTGGATCAAGA-TTTCCTTGAGTCTAACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCT
* * * * *
208852 TCTTTCAGATTTGGTATTCCTGAAGAGCAGTGAAGTAAATCACAGTCTGATTCAATCTTCCCTGA
65 TCTTTCAGATTTGATCTTCCTGAAGAGAAGCGAAGCAAATCACA-TCTGATTCAATCTTCCCTGA
* *
208917 AGAGCA
129 AAAGAA
* * * * * * *
208923 GCGAAGTGAATCAAAATTTTCTCGAGTCTAACCTCCCCTAAAGAGCAGTGGAGCAGATTCTTCTT
1 GAGAAGTGGATCAAGATTTCCTTGAGTCTAACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTT
208988 CTTTCAGATTT-ATTCTTCC
66 CTTTCAGATTTGA-TCTTCC
209007 CAAAAAAAGA
Statistics
Matches: 525, Mismatches: 80, Indels: 40
0.81 0.12 0.06
Matches are distributed among these distances:
133 1 0.00
134 93 0.18
135 278 0.53
136 132 0.25
137 20 0.04
138 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (134 bp):
GAGAAGTGGATCAAGATTTCCTTGAGTCTAACCTCCCCTAAAGAGTAGCGGAGCAGATTCTTCTT
CTTTCAGATTTGATCTTCCTGAAGAGAAGCGAAGCAAATCACATCTGATTCAATCTTCCCTGAAA
AGAA
Found at i:209289 original size:2 final size:2
Alignment explanation
Indices: 209282--209347 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
209272 ATGTAACTAT
209282 TA TA 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 TA TA
209324 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
209348 AAATATGTAA
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:214917 original size:72 final size:72
Alignment explanation
Indices: 214816--215587 Score: 272
Period size: 72 Copynumber: 11.0 Consensus size: 72
214806 AACAGAATTA
* * * *
214816 ATAACTAAAATGCATGAACGGGTGCATTAAGACATGAAAGTATGCCATAATTAAAATGCATGAAA
1 ATAACTAAAATGCATGAAAGGATACATTAAGACATGAAAGGATGCCATAATTAAAATGCATGAAA
214881 GGATGAC
66 GGATGAC
* * * *
214888 ATAATTAAAATGCATGAAATGATACATTAAGGCATGAAAGGATGCCATAATTAAAATGCATGAAC
1 ATAACTAAAATGCATGAAAGGATACATTAAGACATGAAAGGATGCCATAATTAAAATGCATGAAA
214953 GGATG-C
66 GGATGAC
* * * * * *
214959 AT---T--AAGGCAAGAAAAGATGTCATAACTAAAATACATGAAAGGATG-C---ATT--AAGGC
1 ATAACTAAAATGCATGAAAGGAT-ACAT---T--AAGACATGAAAGGATGCCATAATTAAAATGC
215013 ATGAAAGGATG-C
60 ATGAAAGGATGAC
* * * * *
215025 AT---T--AAGGCATGAAAGGATGTCATAATTAAAATGCATGAAAGGATG-C---ATT--AAGGA
1 ATAACTAAAATGCATGAAAGGA--T-A-CATTAAGA--CATGAAAGGATGCCATAATTAAAATGC
*
215079 ATGAAAGGATGTC
60 ATGAAAGGATGAC
* * * * *
215092 AAAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAATTAAAATGCATGAAC
1 ATAACTAAAATGCATGAAAGGATACATTAAGACATGAAAGGATGCCATAATTAAAATGCATGAA-
215157 A-GATG-C
65 AGGATGAC
* * * *
215163 AT---T--AAGGCATGAAAGGATGCCATAACTAAAATTCATGAAAGGATG-C---ATT--AAGGC
1 ATAACTAAAATGCATGAAAGGAT-ACAT---TAAGA--CATGAAAGGATGCCATAATTAAAATGC
*
215217 ATGAAAGGATGTC
60 ATGAAAGGATGAC
* * * *
215230 ATAATTAAAAGGCATGAAATGATGCCATA-ATTAAATGGCATGAACGGATGCCATAATTAAAATG
1 ATAACTAAAATGCATGAAA-G--G--ATACATT-AA-GACATGAAAGGATGCCATAATTAAAATG
*
215294 CATGAACGGATG-C
59 CATGAAAGGATGAC
* * * *
215307 AT---T--AAGGCATGAAAGGATGTCATAACTAAAATGCATGAAGGGATGCCATAATTAAAATGC
1 ATAACTAAAATGCATGAAAGGAT-ACAT---TAAGA--CATGAAAGGATGCCATAATTAAAATGC
*
215367 ATGAAAGGGTG-C
60 ATGAAAGGATGAC
* * * *
215379 AT---T--AAGGCATGAAAGGATGCCATAATTAAAATGCAT-AAACGGATG-C---ATT--AAGG
1 ATAACTAAAATGCATGAAAGGAT---A-CATTAAGA--CATGAAA-GGATGCCATAATTAAAATG
*
215432 CATGAAAGGATGTC
59 CATGAAAGGATGAC
* * * * * *
215446 ATAAGTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATACCATAACTAAAATGCATGAAA
1 ATAACTAAAATGCATGAAAGGATACATTAAGACATGAAAGGATGCCATAATTAAAATGCATGAAA
*
215511 GGATGCC
66 GGATGAC
* * * * * *
215518 ATAACTAAAATGCATGAAAAGATGCATTAGGGCATGAAAGGATGCCATGATTAAAATGCATGAAC
1 ATAACTAAAATGCATGAAAGGATACATTAAGACATGAAAGGATGCCATAATTAAAATGCATGAAA
215583 GGATG
66 GGATG
215588 TATTAATGCA
Statistics
Matches: 551, Mismatches: 75, Indels: 148
0.71 0.10 0.19
Matches are distributed among these distances:
64 3 0.01
65 1 0.00
66 133 0.24
67 21 0.04
68 22 0.04
69 5 0.01
70 13 0.02
71 13 0.02
72 307 0.56
73 5 0.01
74 1 0.00
75 5 0.01
76 3 0.01
77 5 0.01
78 14 0.03
ACGTcount: A:0.44, C:0.12, G:0.23, T:0.22
Consensus pattern (72 bp):
ATAACTAAAATGCATGAAAGGATACATTAAGACATGAAAGGATGCCATAATTAAAATGCATGAAA
GGATGAC
Found at i:214923 original size:46 final size:46
Alignment explanation
Indices: 214873--215516 Score: 270
Period size: 46 Copynumber: 13.9 Consensus size: 46
214863 TAATTAAAAT
* *
214873 GCATGAAAGGATGACATAATTAAAATGCATGAAATGATACATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
* *
214919 GCATGAAAGGATGCCATAATTAAAATGCATGAACGGATGCATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
* * * * *
214965 GCAAGAAAAGATGTCATAACTAAAATACATGAAAGGATGCATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
* *
215011 GCATGAAAGGATG-C---ATT--AAGGCATGAAAGGATGTCATAATTAAAAT
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATG-C---ATT--AAG
* * *
215057 GCATGAAAGGATG-C---ATT--AAGGAATGAAAGGATGTCAAAATTAAAAT
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATG-C---ATT--AAG
* * *
215103 GCATGAAAGGATG-C---ATT--AAGGCATGAAATGATGCCATAATTAAAAT
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATG-C---ATT--AAG
* *
215149 GCATGAACA-GATG-C---ATT--AAGGCATGAAAGGATGCCATAACTAAAAT
1 GCATGAA-AGGATGACATAATTAAAATGCATGAAAGGATG-CAT---T--AAG
* *
215195 TCATGAAAGGATG-C---ATT--AAGGCATGAAAGGATGTCATAATTAAAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATG-C---ATT--AAG
* * * *
215241 GCATGAAATGATGCCATAATT-AAATGGCATGAACGGATGCCATAATTAAAAT
1 GCATGAAAGGATGACATAATTAAAAT-GCATGAAAGGATG-C---ATT--AAG
* * *
215293 GCATGAACGGATG-C---ATT--AAGGCATGAAAGGATGTCATAACTAAAAT
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATG-CAT---T--AAG
* * *
215339 GCATGAAGGGATGCCATAATTAAAATGCATGAAAGGGTGCATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
*
215385 GCATGAAAGGATGCCATAATTAAAATGCAT-AAACGGATGCATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAA-GGATGCATTAAG
* * *
215431 GCATGAAAGGATGTCATAAGTAAAATGCATGAACGGATGCATTAAG
1 GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
*
215477 GCATGAAAGGAT-ACCATAACTAAAATGCATGAAAGGATGC
1 GCATGAAAGGATGA-CATAATTAAAATGCATGAAAGGATGC
215517 CATAACTAAA
Statistics
Matches: 517, Mismatches: 49, Indels: 64
0.82 0.08 0.10
Matches are distributed among these distances:
40 14 0.03
41 1 0.00
42 2 0.00
43 4 0.01
44 3 0.01
45 5 0.01
46 415 0.80
47 7 0.01
48 4 0.01
49 2 0.00
50 6 0.01
51 6 0.01
52 48 0.09
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (46 bp):
GCATGAAAGGATGACATAATTAAAATGCATGAAAGGATGCATTAAG
Found at i:215107 original size:92 final size:92
Alignment explanation
Indices: 215011--215352 Score: 497
Period size: 92 Copynumber: 3.7 Consensus size: 92
215001 ATGCATTAAG
215011 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTAAAATGCATGAAAGGATGCATTAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTAAAATGCATGAAAGGATGCATTAA
* * *
215076 GGAATGAAAGGATGTCAAAATTAAAAT
66 GGCATGAAAGGATGCCATAATTAAAAT
* *
215103 GCATGAAAGGATGCATTAAGGCATGAAATGATGCCATAATTAAAATGCATGAACA-GATGCATTA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTAAAATGCATGAA-AGGATGCATTA
*
215167 AGGCATGAAAGGATGCCATAACTAAAAT
65 AGGCATGAAAGGATGCCATAATTAAAAT
* * *
215195 TCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTAAAAGGCATGAAATGATGCCATAA
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTAAAATGCATGAAAGGATG-C---A
*
215260 TTAAATGGCATGAACGGATGCCATAATTAAAAT
62 TT-AA-GGCATGAAAGGATGCCATAATTAAAAT
* * *
215293 GCATGAACGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAGGGATGC
1 GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTAAAATGCATGAAAGGATGC
215353 CATAATTAAA
Statistics
Matches: 224, Mismatches: 18, Indels: 11
0.89 0.07 0.04
Matches are distributed among these distances:
91 1 0.00
92 137 0.61
93 2 0.01
96 3 0.01
97 3 0.01
98 78 0.35
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (92 bp):
GCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAATTAAAATGCATGAAAGGATGCATTAA
GGCATGAAAGGATGCCATAATTAAAAT
Found at i:215115 original size:158 final size:160
Alignment explanation
Indices: 214816--215182 Score: 515
Period size: 158 Copynumber: 2.3 Consensus size: 160
214806 AACAGAATTA
* * * * *
214816 ATAACTAAAATGCATGAACGGGTGCATTAAGACATGAAAGTATGCCATAATTAAAATGCATGAAA
1 ATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATG-C--AATT-AAAGGCATGAAA
* * *
214881 GGATGACATAATTAAAATGCATGAAATGATACATTAAGGCATGAAAGGATGCCATAATTAAAATG
62 GGATGACATAATTAAAATGCATGAAAGGATACATTAAGGAATGAAAGGATGCCAAAATTAAAATG
* *
214946 CATGAACGGATGCATTAAGGCAAGAAAAGATGTC
127 CATGAAAGGATGCATTAAGGCAAGAAAAGATGCC
*
214980 ATAACTAAAATACATGAAAGGATGCATTAAGGCATGAAAGGATGC-ATT-AAGGCATGAAAGGAT
1 ATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCAATTAAAGGCATGAAAGGAT
* * *
215043 GTCATAATTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGTCAAAATTAAAATGCATG
66 GACATAATTAAAATGCATGAAAGGATACATTAAGGAATGAAAGGATGCCAAAATTAAAATGCATG
* *
215108 AAAGGATGCATTAAGGCATGAAATGATGCC
131 AAAGGATGCATTAAGGCAAGAAAAGATGCC
*
215138 ATAATTAAAATGCATGAACA-GATGCATTAAGGCATGAAAGGATGC
1 ATAACTAAAATGCATGAA-AGGATGCATTAAGGCATGAAAGGATGC
215183 CATAACTAAA
Statistics
Matches: 184, Mismatches: 18, Indels: 8
0.88 0.09 0.04
Matches are distributed among these distances:
158 140 0.76
159 1 0.01
160 3 0.02
163 1 0.01
164 39 0.21
ACGTcount: A:0.45, C:0.11, G:0.22, T:0.22
Consensus pattern (160 bp):
ATAACTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCAATTAAAGGCATGAAAGGAT
GACATAATTAAAATGCATGAAAGGATACATTAAGGAATGAAAGGATGCCAAAATTAAAATGCATG
AAAGGATGCATTAAGGCAAGAAAAGATGCC
Found at i:215541 original size:26 final size:25
Alignment explanation
Indices: 214848--215587 Score: 435
Period size: 26 Copynumber: 31.5 Consensus size: 25
214838 TGCATTAAGA
*
214848 CATGAAAGTATGCCATAATTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
*
214874 CATGAAAGGATGACATAATTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
* * *
214900 CATGAAATGAT-ACAT--T--AAGG
1 CATGAAAGGATGCCATAATAAAATG
214920 CATGAAAGGATGCCATAATTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
* *
214946 CATGAACGGATG-CAT--T--AAGG
1 CATGAAAGGATGCCATAATAAAATG
* * * *
214966 CAAGAAAAGATGTCATAACTAAAATA
1 CATGAAAGGATGCCATAA-TAAAATG
*
214992 CATGAAAGGATG-CAT--T--AAGG
1 CATGAAAGGATGCCATAATAAAATG
*
215012 CATGAAAGGATG-CAT--T--AAGG
1 CATGAAAGGATGCCATAATAAAATG
*
215032 CATGAAAGGATGTCATAATTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
*
215058 CATGAAAGGATG-CAT--T--AAGG
1 CATGAAAGGATGCCATAATAAAATG
* * *
215078 AATGAAAGGATGTCAAAATTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
*
215104 CATGAAAGGATG-CAT--T--AAGG
1 CATGAAAGGATGCCATAATAAAATG
*
215124 CATGAAATGATGCCATAATTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
*
215150 CATGAACA-GATG-CAT--T--AAGG
1 CATGAA-AGGATGCCATAATAAAATG
*
215170 CATGAAAGGATGCCATAACTAAAATT
1 CATGAAAGGATGCCATAA-TAAAATG
*
215196 CATGAAAGGATG-CAT--T--AAGG
1 CATGAAAGGATGCCATAATAAAATG
* *
215216 CATGAAAGGATGTCATAATTAAAAGG
1 CATGAAAGGATGCCATAA-TAAAATG
* *
215242 CATGAAATGATGCCATAATTAAATGG
1 CATGAAAGGATGCCATAATAAAAT-G
*
215268 CATGAACGGATGCCATAATTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
* *
215294 CATGAACGGATG-CAT--T--AAGG
1 CATGAAAGGATGCCATAATAAAATG
*
215314 CATGAAAGGATGTCATAACTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
*
215340 CATGAAGGGATGCCATAATTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
* *
215366 CATGAAAGGGTG-CAT--T--AAGG
1 CATGAAAGGATGCCATAATAAAATG
215386 CATGAAAGGATGCCATAATTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
*
215412 CAT-AAACGGATG-CAT--T--AAGG
1 CATGAAA-GGATGCCATAATAAAATG
*
215432 CATGAAAGGATGTCATAAGTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
* *
215458 CATGAACGGATG-CAT--T--AAGG
1 CATGAAAGGATGCCATAATAAAATG
*
215478 CATGAAAGGATACCATAACTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
215504 CATGAAAGGATGCCATAACTAAAATG
1 CATGAAAGGATGCCATAA-TAAAATG
* **
215530 CATGAAAAGATG-CAT--T--AGGG
1 CATGAAAGGATGCCATAATAAAATG
*
215550 CATGAAAGGATGCCATGATTAAAATG
1 CATGAAAGGATGCCAT-AATAAAATG
*
215576 CATGAACGGATG
1 CATGAAAGGATG
215588 TATTAATGCA
Statistics
Matches: 570, Mismatches: 66, Indels: 156
0.72 0.08 0.20
Matches are distributed among these distances:
19 1 0.00
20 179 0.31
21 38 0.07
22 12 0.02
24 12 0.02
25 43 0.08
26 279 0.49
27 6 0.01
ACGTcount: A:0.44, C:0.11, G:0.23, T:0.22
Consensus pattern (25 bp):
CATGAAAGGATGCCATAATAAAATG
Found at i:215553 original size:46 final size:46
Alignment explanation
Indices: 215503--215629 Score: 148
Period size: 46 Copynumber: 2.8 Consensus size: 46
215493 TAACTAAAAT
*
215503 GCATGAAAGGATGCCATAACTAAAATGCATGAAAAGATGCATTAGG
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAAGATGCATTAAG
* * ** * *
215549 GCATGAAAGGATGCCATGATTAAAATGCATGAACGGATGTATTAAT
1 GCATGAAAGGATGCCATAACTAAAATGCATGAAAAGATGCATTAAG
* **
215595 GCATGAAAAGA-GACCATAACTAAAATTAATGAAAA
1 GCATGAAAGGATG-CCATAACTAAAATGCATGAAAA
215630 ATTACTAAAG
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
45 1 0.02
46 65 0.98
ACGTcount: A:0.46, C:0.12, G:0.21, T:0.21
Consensus pattern (46 bp):
GCATGAAAGGATGCCATAACTAAAATGCATGAAAAGATGCATTAAG
Found at i:215628 original size:118 final size:118
Alignment explanation
Indices: 214816--215620 Score: 593
Period size: 118 Copynumber: 6.9 Consensus size: 118
214806 AACAGAATTA
* * * * * * * *
214816 ATAACTAAAATGCATGAACGGGTGCATTAAGACATGAAAGTATGCCATAATTAAAATGCATGAAA
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAC
* * *
214881 GGATGACATAATTAAAATGCATGAAATGATA-CAT---T--AAGGCATGAAAGGATGCC
66 GGATG---T-ATT--AATGCATGAAAAGAGACCATAACTAAAATGCATGAAAGGATGCC
* * * * *
214934 ATAATTAAAATGCATGAACGGATGCATTAAGGCAAGAAAAGATGTCATAACTAAAATACATGAAA
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAC
* * * * *
214999 GGATGCATTAAGGCATG-AAAG-GATGCAT---T--AAGGCATGAAAGGATGTC
66 GGATGTATTAATGCATGAAAAGAGA-CCATAACTAAAATGCATGAAAGGATGCC
* * * *
215046 ATAATTAAAATGCATGAAAGGATGCATTAAGGAATGAAAGGATGTCAAAATTAAAATGCATGAAA
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAC
* * * *
215111 GGATGCATTAAGGCATGAAATGATG-CCATAATTAAAATGCATGAACA-GATG-C
66 GGATGTATTAATGCATGAAAAGA-GACCATAACTAAAATGCATGAA-AGGATGCC
* ** *
215163 ---ATT--AAGGCATGAAAGGATGCCATAACTAAAATTCATGAAAGGATG-CAT---T--AAGGC
1 ATAATTAAAATGCATGAAAGGATG-CAT---T--AAGGCATGAAAGGATGTCATAACTAAAATGC
* * * * *
215217 ATGAAAGGATGTCATAATTAAAAGGCATGAAATGATG-CCATAA-TTAAATGGCATGAACGGATG
60 ATGAACGGATG---T-ATT--AATGCATGAAAAGA-GACCATAACTAAAAT-GCATGAAAGGATG
215280 CC
117 CC
* *
215282 ATAATTAAAATGCATGAACGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAG
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAC
* ** *
215347 GGATGCCATAATTAAAATGCATG-AAAGGGTGCAT---T--AAGGCATGAAAGGATGCC
66 GGATG---T-ATT--AATGCATGAAAAGAGACCATAACTAAAATGCATGAAAGGATGCC
*
215400 ATAATTAAAATGCAT-AAACGGATGCATTAAGGCATGAAAGGATGTCATAAGTAAAATGCATGAA
1 ATAATTAAAATGCATGAAA-GGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAA
* * * *
215464 CGGATGCATTAAGGCATGAAAGGATACCATAACTAAAATGCATGAAAGGATGCC
65 CGGATGTATTAATGCATGAAAAGAGACCATAACTAAAATGCATGAAAGGATGCC
* * * * * *
215518 ATAACTAAAATGCATGAAAAGATGCATTAGGGCATGAAAGGATGCCATGATTAAAATGCATGAAC
1 ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAC
215583 GGATGTATTAATGCATGAAAAGAGACCATAACTAAAAT
66 GGATGTATTAATGCATGAAAAGAGACCATAACTAAAAT
215621 TAATGAAAAA
Statistics
Matches: 574, Mismatches: 67, Indels: 92
0.78 0.09 0.13
Matches are distributed among these distances:
110 1 0.00
111 3 0.01
112 140 0.24
113 15 0.03
114 10 0.02
115 1 0.00
116 6 0.01
117 10 0.02
118 318 0.55
119 10 0.02
120 1 0.00
121 1 0.00
122 5 0.01
123 9 0.02
124 44 0.08
ACGTcount: A:0.44, C:0.12, G:0.22, T:0.22
Consensus pattern (118 bp):
ATAATTAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGTCATAACTAAAATGCATGAAC
GGATGTATTAATGCATGAAAAGAGACCATAACTAAAATGCATGAAAGGATGCC
Found at i:225488 original size:21 final size:21
Alignment explanation
Indices: 225462--225513 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
225452 GGGAGTGTGT
225462 GTGCATCGATGCATAGTCAAG
1 GTGCATCGATGCATAGTCAAG
* *
225483 GTGCATCGATGCTTAGTTAAG
1 GTGCATCGATGCATAGTCAAG
225504 GTGCATCGAT
1 GTGCATCGAT
225514 ACATCAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.25, C:0.17, G:0.29, T:0.29
Consensus pattern (21 bp):
GTGCATCGATGCATAGTCAAG
Found at i:232238 original size:22 final size:21
Alignment explanation
Indices: 232196--232235 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
232186 AAGACTATTT
232196 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
232217 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
232236 ATAGAGTCTT
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:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:243473 original size:35 final size:35
Alignment explanation
Indices: 243427--243502 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
243417 AAAACAGTCC
* *
243427 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
243462 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
243497 TCAATT
1 TCAATT
243503 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:244041 original size:130 final size:130
Alignment explanation
Indices: 243895--244142 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
243885 TATTTATATA
* **
243895 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
243960 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
244025 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
244090 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
244143 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:244173 original size:130 final size:129
Alignment explanation
Indices: 243909--244173 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
243899 ATTTGGTCCT
* ** *
243909 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
243974 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
244039 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
244104 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
244168 -A
128 CA
244169 AAATT
1 AAATT
244174 GGGTCTTGGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:244426 original size:23 final size:25
Alignment explanation
Indices: 244380--244426 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
244370 AAATGATGGG
**
244380 AAAATATTATATTTTTTTACAATAA
1 AAAATATTATATTTTGATACAATAA
244405 AAAATATTATA-TTTGATA-AATA
1 AAAATATTATATTTTGATACAATA
244427 GTTTGATAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 5 0.25
25 11 0.55
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (25 bp):
AAAATATTATATTTTGATACAATAA
Found at i:244505 original size:30 final size:28
Alignment explanation
Indices: 244469--244560 Score: 96
Period size: 28 Copynumber: 3.2 Consensus size: 28
244459 AGTTGATACA
244469 ATATTTTAAAAGAATAAATTTAAGATTTAT
1 ATATTTT-AAA-AATAAATTTAAGATTTAT
* *
244499 ATATTTTTAAACTAAATTTAAGATTTAT
1 ATATTTTAAAAATAAATTTAAGATTTAT
* * * * *
244527 ATATTTTTAAACTAATTTTAATAATTAT
1 ATATTTTAAAAATAAATTTAAGATTTAT
244555 AT-TTTT
1 ATATTTT
244561 CATATTTATA
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
27 4 0.07
28 44 0.77
29 2 0.04
30 7 0.12
ACGTcount: A:0.43, C:0.02, G:0.03, T:0.51
Consensus pattern (28 bp):
ATATTTTAAAAATAAATTTAAGATTTAT
Found at i:244543 original size:27 final size:28
Alignment explanation
Indices: 244483--244560 Score: 122
Period size: 28 Copynumber: 2.8 Consensus size: 28
244473 TTTAAAAGAA
244483 TAAATTTAAGATTTATATATTTTTAAAC
1 TAAATTTAAGATTTATATATTTTTAAAC
244511 TAAATTTAAGATTTATATATTTTTAAAC
1 TAAATTTAAGATTTATATATTTTTAAAC
* * *
244539 TAATTTTAATAATTATAT-TTTT
1 TAAATTTAAGATTTATATATTTT
244561 CATATTTATA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 4 0.09
28 43 0.91
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (28 bp):
TAAATTTAAGATTTATATATTTTTAAAC
Found at i:252350 original size:50 final size:49
Alignment explanation
Indices: 252278--252373 Score: 147
Period size: 50 Copynumber: 1.9 Consensus size: 49
252268 TTAAAAAATA
* *
252278 TTTTAAATTAATGAATTTAATTCATTAAAATCATAGATGATGTGATCAT
1 TTTTAAATTAATGAATCTAATTCATTAAAATCATAGATGATATGATCAT
* *
252327 TTTTAAAATTAATGGATCTAATTCATTAGAATCATAGATGATATGAT
1 TTTT-AAATTAATGAATCTAATTCATTAAAATCATAGATGATATGAT
252374 GAGTCGAGTT
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
49 4 0.10
50 38 0.90
ACGTcount: A:0.41, C:0.06, G:0.11, T:0.42
Consensus pattern (49 bp):
TTTTAAATTAATGAATCTAATTCATTAAAATCATAGATGATATGATCAT
Found at i:254205 original size:23 final size:24
Alignment explanation
Indices: 254179--254232 Score: 58
Period size: 23 Copynumber: 2.3 Consensus size: 24
254169 TATGAACTAG
*
254179 TATAATTAATACTATTT-ATTTTT
1 TATAATTAATACTATTTAATATTT
* *
254202 TATAA-AAATATTATTTAATATTT
1 TATAATTAATACTATTTAATATTT
*
254225 TAAAATTA
1 TATAATTA
254233 TTTTTATTTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
22 9 0.38
23 14 0.58
24 1 0.04
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (24 bp):
TATAATTAATACTATTTAATATTT
Found at i:254216 original size:22 final size:21
Alignment explanation
Indices: 254186--254241 Score: 60
Period size: 22 Copynumber: 2.7 Consensus size: 21
254176 TAGTATAATT
*
254186 AATACTATTTATTTTTTATAAA
1 AATATTATTTATTTTTT-TAAA
* *
254208 AATATTATTTAATATTTTAAA
1 AATATTATTTATTTTTTTAAA
*
254229 ATTATT-TTTATTT
1 AATATTATTTATTT
254242 AAAAAACTAT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
20 5 0.18
21 9 0.32
22 14 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (21 bp):
AATATTATTTATTTTTTTAAA
Found at i:254247 original size:18 final size:18
Alignment explanation
Indices: 254194--254258 Score: 53
Period size: 18 Copynumber: 3.6 Consensus size: 18
254184 TTAATACTAT
*
254194 TTATTTTT-TATAAAAATA
1 TTATTTTTATTTAAAAA-A
* *
254212 TTATTTAATATTT-TAAAA
1 TTATTT-TTATTTAAAAAA
254230 TTATTTTTATTTAAAAAA
1 TTATTTTTATTTAAAAAA
* *
254248 CTATTATTATT
1 TTATTTTTATT
254259 CAATAATAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
17 5 0.14
18 26 0.70
19 4 0.11
20 2 0.05
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.57
Consensus pattern (18 bp):
TTATTTTTATTTAAAAAA
Found at i:256334 original size:64 final size:63
Alignment explanation
Indices: 256207--256366 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
256197 TTGTTTAAGG
* * * * *
256207 TGCATCGATGCACATGCAGTGCATCGATGCATGAATTTAAATAGAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCAATTTAAATACAAACATCGAATAGGATTTA
*
256270 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCAT--CAATTTAAATACAAACATCGAATAGGATTTA
*
256334 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
256367 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 30 0.35
64 40 0.47
65 16 0.19
ACGTcount: A:0.33, C:0.18, G:0.22, T:0.27
Consensus pattern (63 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCAATTTAAATACAAACATCGAATAGGATTTA
Found at i:257805 original size:21 final size:21
Alignment explanation
Indices: 257779--257862 Score: 132
Period size: 21 Copynumber: 4.0 Consensus size: 21
257769 GTCGAGGGTT
*
257779 TCATAGGTCATTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
257800 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
257821 TCATAGGTCCTTCGGGACAAAT
1 TCATAGGTCCTTCGGGAC-AAC
*
257843 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
257863 ATTTCATATG
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
21 40 0.68
22 19 0.32
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:261282 original size:65 final size:65
Alignment explanation
Indices: 261122--261282 Score: 195
Period size: 64 Copynumber: 2.5 Consensus size: 65
261112 TTGTTTAAGG
* * * **
261122 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
261185 A
65 A
* *
261186 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCTAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
261250 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
261283 ACCTTCATTA
Statistics
Matches: 85, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
63 1 0.01
64 61 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:262725 original size:21 final size:21
Alignment explanation
Indices: 262699--262761 Score: 81
Period size: 21 Copynumber: 3.0 Consensus size: 21
262689 GTCGAGGGTT
262699 TCATAGGTCCTTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
* *
262720 TCATAGGTCATTCGGGACAAAT
1 TCATAGGTCCTTCGGGAC-AAC
* *
262742 TCACAGGTCCTTCGAGACAA
1 TCATAGGTCCTTCGGGACAA
262762 ATTTCATATG
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
21 19 0.53
22 17 0.47
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:262755 original size:22 final size:22
Alignment explanation
Indices: 262698--262769 Score: 92
Period size: 22 Copynumber: 3.3 Consensus size: 22
262688 AGTCGAGGGT
262698 TTCATAGGTCCTTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
* *
262719 CTCATAGGTCATTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
* *
262741 TTCACAGGTCCTTCGAGACAAA
1 TTCATAGGTCCTTCGGGACAAA
262763 TTTCATA
1 -TTCATA
262770 TGCCACTGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 17 0.40
22 20 0.48
23 5 0.12
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:264903 original size:3 final size:3
Alignment explanation
Indices: 264895--265016 Score: 214
Period size: 3 Copynumber: 41.7 Consensus size: 3
264885 TTGTAATATG
264895 TAA TAA TAA TAA TAA TAA 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
264943 TAA TAA TAA T-A TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
264989 TAA TAA TAA TAA TAA TAA T-T TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
265017 GTTTTGTAGA
Statistics
Matches: 114, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
2 5 0.04
3 109 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:265246 original size:43 final size:40
Alignment explanation
Indices: 265178--265287 Score: 123
Period size: 40 Copynumber: 2.7 Consensus size: 40
265168 GACGACATGG
* * *
265178 CTCATACGTGATGAAGAGGTCTGGTC-GTCTAAGGGTGACACGA
1 CTCATATGTGATGAAGAGATCTGGTCAG--T--GGATGACACGA
* *
265221 CTCCTATGTGATGAGGAGATCTGGTCAGTGGATGACACGA
1 CTCATATGTGATGAAGAGATCTGGTCAGTGGATGACACGA
*
265261 CTCATATGTGATGAAGAGTTCTGGTCA
1 CTCATATGTGATGAAGAGATCTGGTCA
265288 TCTTTAGGAG
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
40 34 0.59
42 1 0.02
43 22 0.38
44 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.26
Consensus pattern (40 bp):
CTCATATGTGATGAAGAGATCTGGTCAGTGGATGACACGA
Found at i:265716 original size:31 final size:31
Alignment explanation
Indices: 265634--265708 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
265624 GACAAAATTC
*
265634 GTTTCAAG-GAAA-TGACTCAAAGATGGTTTT
1 GTTTCAAGAGAAACAGACTCAAAGAT-GTTTT
265664 GTTTCAAGAGAAACAGACTCAAAGAT-TTTGT
1 GTTTCAAGAGAAACAGACTCAAAGATGTTT-T
265695 GTTTCCAA-AGAAAC
1 GTTT-CAAGAGAAAC
265709 TGCCTCAAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
30 11 0.28
31 15 0.38
32 14 0.35
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.29
Consensus pattern (31 bp):
GTTTCAAGAGAAACAGACTCAAAGATGTTTT
Found at i:265810 original size:66 final size:66
Alignment explanation
Indices: 265664--265822 Score: 182
Period size: 66 Copynumber: 2.4 Consensus size: 66
265654 AGATGGTTTT
*
265664 GTTTCAAGAGAAACAGACTCAAAGAT-TTTGTGTTTCCAAAGAAACTGCCTCAAGGGAGACAAAA
1 GTTTCAAGAGAAAC-GACTCAAAGATGTTTGTGTTTCCAAAGAAAATGCCTCAA-GGAGACAAAA
*
265728 TTT
64 TTC
* * * *
265731 GTTTTAATAGAAACGATCTCAAAGATGATTT-TGTTT-TAAGAGAAAATGTCTCAA-GAGACAAA
1 GTTTCAAGAGAAACGA-CTCAAAGATG-TTTGTGTTTCCAA-AGAAAATGCCTCAAGGAGACAAA
265793 ATTC
63 ATTC
*
265797 GTTTCAAGGGAAACGACTCAAAGATG
1 GTTTCAAGAGAAACGACTCAAAGATG
265823 GTAAATTTTG
Statistics
Matches: 79, Mismatches: 9, Indels: 10
0.81 0.09 0.10
Matches are distributed among these distances:
65 10 0.13
66 26 0.33
67 23 0.29
68 17 0.22
69 3 0.04
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (66 bp):
GTTTCAAGAGAAACGACTCAAAGATGTTTGTGTTTCCAAAGAAAATGCCTCAAGGAGACAAAATT
C
Found at i:271360 original size:15 final size:14
Alignment explanation
Indices: 271332--271371 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
271322 ATAAACAAAA
271332 AAATATTATGATAAT
1 AAATATTAT-ATAAT
*
271347 ATATATATATATAAT
1 AAATAT-TATATAAT
271362 AAATATTATA
1 AAATATTATA
271372 ACGAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
14 4 0.18
15 15 0.68
16 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (14 bp):
AAATATTATATAAT
Found at i:272143 original size:35 final size:37
Alignment explanation
Indices: 272068--272170 Score: 122
Period size: 35 Copynumber: 2.8 Consensus size: 37
272058 GTGCTTGTGG
* * * * *
272068 ATCCTATCTTTAG-GAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGAGAGTTTGAATCCTAGTAGAATTCT
272105 ATCCTATTTTAG-GAG-TTGAATCCTAGTAGAATTCT
1 ATCCTATTTTAGAGAGTTTGAATCCTAGTAGAATTCT
*
272140 ATCCTATTTTTGAGAGTTTGAATCCTAGTAG
1 ATCCTATTTTAGAGAGTTTGAATCCTAGTAG
272171 GACGAAAAAT
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
35 26 0.45
36 11 0.19
37 21 0.36
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.39
Consensus pattern (37 bp):
ATCCTATTTTAGAGAGTTTGAATCCTAGTAGAATTCT
Found at i:272935 original size:106 final size:105
Alignment explanation
Indices: 272628--273345 Score: 651
Period size: 109 Copynumber: 6.9 Consensus size: 105
272618 AATATTGTTC
* * * * * *
272628 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTAGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATTGGAAAATGTTTGTTGACA
** * * * *
272693 GTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * *
272734 CGAGTCTAATATCCTTCGCTGTGAAGATGAAATTGACTCTG-AA--CG-AAAT-CTTGTTGATAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATGTTTGTTGACAA
* *
272794 TCAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* *
272834 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TTGGAAAATGTTTGTTGACA
*
272899 ACCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
65 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * ** * *
272940 CGAGTGGCACGATATCCTCCG-TCGTGGAGTTGAAA-TCGCAGATGAAACT-GAAAAGTTGTTCG
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGC-TCTGAAATTGGAAAA--TGTTTG
273002 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
59 TTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * *
273049 CGGGTAGCACGATATCCTCCG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTGTTTGTT
1 CGAGT--C-CAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAATT-GGAAAATGTTTGTT
* *
273113 GAAAACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTGTCT
61 GACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
** * * * *
273158 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGTTTGGCTCCGAAA-T------TGCTTGTCGACAG
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATGTTTGTTGACAA
* * * * *
273216 TCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * * * * * * *
273256 TGGGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACCCTGAAACTGGGAAAT-TATTATTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATGT-TTGTTGACA
273320 ACCAGCCGTCCCTTCGTTGTGAAGTT
65 ACCAGCCGTCCCTTCGTTGTGAAGTT
273346 AAGATTGGCT
Statistics
Matches: 505, Mismatches: 82, Indels: 51
0.79 0.13 0.08
Matches are distributed among these distances:
98 81 0.16
99 1 0.00
100 80 0.16
101 5 0.01
102 1 0.00
104 1 0.00
105 36 0.07
106 114 0.23
107 6 0.01
108 6 0.01
109 168 0.33
110 2 0.00
111 4 0.01
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGAAAATGTTTGTTGACAA
CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:273441 original size:160 final size:160
Alignment explanation
Indices: 273170--273505 Score: 582
Period size: 160 Copynumber: 2.1 Consensus size: 160
273160 AGTCCAATAT
* * *
273170 CCTTCGCTGTGAAGTTGAGTTTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGT
1 CCTTCGTTGTGAAGTTAAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGT
273235 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACCCTGAAA
66 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACCCTGAAA
273300 CTGGGAAATTATTATTGACAACCAGCCGTC
131 CTGGGAAATTATTATTGACAACCAGCCGTC
* *
273330 CCTTCGTTGTGAAGTTAAGATTGGCTCCGAAATTGTTTGTCGAGAGTCAGCCGCCCCTTCGCTGT
1 CCTTCGTTGTGAAGTTAAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGT
* * * *
273395 GAAGTTGAGCTTGTGCTGTCTTGGTTCTAATATCCTTCGTTGTGAAGTTAAAATTGGCCCTGAAA
66 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACCCTGAAA
*
273460 CTGGGAAATTATTGTTGACAACCAGCCGTC
131 CTGGGAAATTATTATTGACAACCAGCCGTC
273490 CCTTCGTTGTGAAGTT
1 CCTTCGTTGTGAAGTT
273506 GAACTTGTGT
Statistics
Matches: 166, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
160 166 1.00
ACGTcount: A:0.21, C:0.22, G:0.25, T:0.32
Consensus pattern (160 bp):
CCTTCGTTGTGAAGTTAAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGT
GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGCTGTGAAGTTAAAATTGACCCTGAAA
CTGGGAAATTATTATTGACAACCAGCCGTC
Found at i:274113 original size:65 final size:65
Alignment explanation
Indices: 274009--274174 Score: 305
Period size: 65 Copynumber: 2.6 Consensus size: 65
273999 GACAAAATTT
274009 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
274074 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
274139 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
274175 TTGTTTCGAG
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 97 1.00
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:274180 original size:102 final size:102
Alignment explanation
Indices: 274074--274522 Score: 736
Period size: 102 Copynumber: 4.3 Consensus size: 102
274064 TCAATGTTTA
* *
274074 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
274139 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
274176 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
274241 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
274278 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTC
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATG-------T-TTT-
* **
274343 CAATGTTTATGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTT
57 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
274389 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
274454 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
274491 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAA
274523 TGGTGAGCAC
Statistics
Matches: 325, Mismatches: 13, Indels: 18
0.91 0.04 0.05
Matches are distributed among these distances:
102 223 0.69
103 3 0.01
104 1 0.00
109 1 0.00
110 3 0.01
111 94 0.29
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:274264 original size:167 final size:169
Alignment explanation
Indices: 273974--274291 Score: 532
Period size: 167 Copynumber: 1.9 Consensus size: 169
273964 AAGATGATGC
* *
273974 TTCAAGAGAAAACTGTTTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
274039 GAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
274104 GAAA-TTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
131 AAAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
* *
274142 TTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTTTGTTTCGAGGGAAACTATCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
* *
274206 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
**
274271 AAAATTTTGTTTCAAGGGAAA
131 AAAATTTCATTTCAAGGGAAA
274292 CTATCTCAAG
Statistics
Matches: 139, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
167 117 0.84
168 22 0.16
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (169 bp):
TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
Found at i:274340 original size:9 final size:9
Alignment explanation
Indices: 274326--274350 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
274316 TTTCAAGGGA
274326 AATGTTTCC
1 AATGTTTCC
274335 AATGTTTCC
1 AATGTTTCC
274344 AATGTTT
1 AATGTTT
274351 ATGTTTCAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (9 bp):
AATGTTTCC
Found at i:274432 original size:213 final size:204
Alignment explanation
Indices: 274074--274522 Score: 736
Period size: 213 Copynumber: 2.2 Consensus size: 204
274064 TCAATGTTTA
* *
274074 TGTTTCAAGAGAAACTATCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
274139 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCGAGGGAAACTATCTCAAGAGAG
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
*
274204 ACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAG
131 ACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAG
*
274269 ACAAAATTT
196 AAAAAATTT
274278 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTC
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATG-------T-TTT-
* **
274343 CAATGTTTATGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTTTGTTTCAAGGGAAACTATC
57 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATC
274408 TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTC
122 TCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTC
274473 TCAAGGGAGAAAAAATTT
187 TCAAGGGAGAAAAAATTT
*
274491 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAA
274523 TGGTGAGCAC
Statistics
Matches: 227, Mismatches: 9, Indels: 9
0.93 0.04 0.04
Matches are distributed among these distances:
204 50 0.22
211 1 0.00
212 3 0.01
213 173 0.76
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (204 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAG
ACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAG
AAAAAATTT
Found at i:275407 original size:22 final size:22
Alignment explanation
Indices: 275382--275432 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
275372 TTGTGTTTGG
275382 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
275404 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
275426 TCAAAGG
1 TCAAAGG
275433 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:276066 original size:20 final size:21
Alignment explanation
Indices: 276043--276102 Score: 61
Period size: 20 Copynumber: 2.9 Consensus size: 21
276033 TTTGTCCCCT
*
276043 TTTTTTATTTTTGTTCTTT-C
1 TTTTTTATTCTTGTTCTTTCC
* *
276063 TTTTTTGTTCTTGTTTTTTCC
1 TTTTTTATTCTTGTTCTTTCC
*
276084 TTTTTTGCTTCTT-TTCTTT
1 TTTTTT-ATTCTTGTTCTTT
276103 TTTCTTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 16 0.48
21 12 0.36
22 5 0.15
ACGTcount: A:0.02, C:0.13, G:0.07, T:0.78
Consensus pattern (21 bp):
TTTTTTATTCTTGTTCTTTCC
Found at i:277276 original size:22 final size:20
Alignment explanation
Indices: 277251--277291 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
277241 TTTCATGTTT
277251 ATGAAAATGCTTAAAAATGTAG
1 ATGAAAATGC--AAAAATGTAG
*
277273 ATGAAGATGCAAAAATGTA
1 ATGAAAATGCAAAAATGTA
277292 AGAATGCATG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.51, C:0.05, G:0.20, T:0.24
Consensus pattern (20 bp):
ATGAAAATGCAAAAATGTAG
Found at i:279476 original size:16 final size:16
Alignment explanation
Indices: 279455--279492 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
279445 AAAAATAATT
279455 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
279471 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
279487 T-ATAAA
1 TAATAAA
279493 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:279670 original size:11 final size:12
Alignment explanation
Indices: 279654--279707 Score: 51
Period size: 11 Copynumber: 4.5 Consensus size: 12
279644 TTATATACGT
279654 TAATAATAAA-A
1 TAATAATAAATA
279665 TAATAATAAATA
1 TAATAATAAATA
279677 TAATAGTTATAAATA
1 TAATA---ATAAATA
*
279692 T-AT-ATATATA
1 TAATAATAAATA
279702 TAATAA
1 TAATAA
279708 CTTTAAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
10 7 0.19
11 12 0.33
12 7 0.19
14 2 0.06
15 8 0.22
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (12 bp):
TAATAATAAATA
Found at i:279738 original size:11 final size:11
Alignment explanation
Indices: 279654--279739 Score: 50
Period size: 11 Copynumber: 7.3 Consensus size: 11
279644 TTATATACGT
*
279654 TAATAATAAAA
1 TAATATTAAAA
*
279665 TAATAATAAATA
1 TAATATTAAA-A
279677 TAATAGTTATAAA
1 TAATA-TTA-AAA
279690 TATATATATATATAA
1 TA-ATAT-TA-A-AA
279705 TAACT-TTAAAA
1 TAA-TATTAAAA
*
279716 -AAAATTAAAA
1 TAATATTAAAA
*
279726 TAATATTAGAA
1 TAATATTAAAA
279737 TAA
1 TAA
279740 AAATAATTAA
Statistics
Matches: 62, Mismatches: 4, Indels: 18
0.74 0.05 0.21
Matches are distributed among these distances:
10 8 0.13
11 23 0.37
12 7 0.11
13 8 0.13
14 11 0.18
15 5 0.08
ACGTcount: A:0.62, C:0.01, G:0.02, T:0.35
Consensus pattern (11 bp):
TAATATTAAAA
Found at i:280226 original size:35 final size:36
Alignment explanation
Indices: 280156--280255 Score: 130
Period size: 35 Copynumber: 2.8 Consensus size: 36
280146 GTGCTTGTGG
* * *
280156 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCCTAGCAAAATTCT
*
280193 ATCCTATTTTAGGAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
*
280228 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAG-GAGTTTGAATCCTAG
280256 TAGGACGAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 27 0.48
36 11 0.20
37 18 0.32
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCCTAGCAAAATTCT
Found at i:281265 original size:29 final size:29
Alignment explanation
Indices: 281233--281319 Score: 95
Period size: 30 Copynumber: 2.9 Consensus size: 29
281223 TTAAAAGACT
*
281233 TAAATAACAAAAACATAAACGTAAAGGG-C
1 TAAATAACAAAAACAGAAAC-TAAAGGGTC
* * *
281262 TAAAACAACAAAAATAGAAACTTAAGGGTC
1 T-AAATAACAAAAACAGAAACTAAAGGGTC
*
281292 TAAATAGCAAAAACAGAAACTTAAAGGG
1 TAAATAACAAAAACAGAAAC-TAAAGGG
281320 GTAAGATAGA
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
29 23 0.49
30 24 0.51
ACGTcount: A:0.57, C:0.13, G:0.15, T:0.15
Consensus pattern (29 bp):
TAAATAACAAAAACAGAAACTAAAGGGTC
Found at i:282724 original size:11 final size:11
Alignment explanation
Indices: 282676--282724 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
282666 TAAAAAATTG
282676 TAAT-ATATAA
1 TAATAATATAA
*
282686 TATTAATAATAA
1 TAATAAT-ATAA
282698 TAATAATATAA
1 TAATAATATAA
* *
282709 GAATAATTTAA
1 TAATAATATAA
282720 TAATA
1 TAATA
282725 TTTTTTGTAG
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
10 3 0.09
11 19 0.59
12 10 0.31
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
TAATAATATAA
Found at i:283166 original size:73 final size:72
Alignment explanation
Indices: 283080--283225 Score: 222
Period size: 73 Copynumber: 2.0 Consensus size: 72
283070 AAAAGCTTAC
* * *
283080 TTTTATTATAGTTTAAGTTTATATATTTTAAATATCATAGTATTAAATATAGTATTAAAT-TAAA
1 TTTTATTATAGTTTAAGTGTATATATTTCAAATATCATAGTATTAAATATAAT-TTAAATGT-AA
283144 TATTTTTAA
64 TATTTTTAA
* *
283153 TTTTATTATAGTTTAAGTGTATATATTTCAAATATTATAGTATTAAATATAATTTAAATGTTATA
1 TTTTATTATAGTTTAAGTGTATATATTTCAAATATCATAGTATTAAATATAATTTAAATGTAATA
283218 TTTTTAA
66 TTTTTAA
283225 T
1 T
283226 CTAATGTAAT
Statistics
Matches: 67, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
72 17 0.25
73 50 0.75
ACGTcount: A:0.40, C:0.01, G:0.06, T:0.53
Consensus pattern (72 bp):
TTTTATTATAGTTTAAGTGTATATATTTCAAATATCATAGTATTAAATATAATTTAAATGTAATA
TTTTTAA
Found at i:283371 original size:26 final size:24
Alignment explanation
Indices: 283315--283371 Score: 60
Period size: 26 Copynumber: 2.3 Consensus size: 24
283305 TGTAATTTTG
* *
283315 AAAATCACTTTTTAAGTACTTTTC
1 AAAAGCACTTTTTAAGTACTCTTC
* *
283339 TACAGCACTTTTTAACCGTACTCTTC
1 AAAAGCACTTTTTAA--GTACTCTTC
283365 AAAAGCA
1 AAAAGCA
283372 ATGCCAAATC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
24 12 0.48
26 13 0.52
ACGTcount: A:0.33, C:0.23, G:0.07, T:0.37
Consensus pattern (24 bp):
AAAAGCACTTTTTAAGTACTCTTC
Found at i:286799 original size:36 final size:36
Alignment explanation
Indices: 286752--286824 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
286742 AGTTATGGAA
*
286752 TTAAGTGATAAAAGAATCAGCCATGGATATATAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
*
286788 TTAAGTGATAAAAGAATCAACCATGGATATGTAGAT
1 TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
286824 T
1 T
286825 ATAATTTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (36 bp):
TTAAGTGATAAAAGAATCAACCATGGATATATAGAT
Found at i:288632 original size:24 final size:24
Alignment explanation
Indices: 288605--288720 Score: 144
Period size: 24 Copynumber: 4.8 Consensus size: 24
288595 TTCGATTTGA
288605 ATTCTGATATGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
*
288629 ATTCTGATATGATA-TCTGACATGA
1 ATTCTGATATGATACT-TGACATGG
* *
288653 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
* * *
288677 ATTTTGATCTGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
* *
288701 ATTTTGATATTATACTTGAC
1 ATTCTGATATGATACTTGAC
288721 CTGATTTATG
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
23 1 0.01
24 81 0.98
25 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:294528 original size:30 final size:30
Alignment explanation
Indices: 294487--294543 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
294477 ATCAGATTAG
*
294487 CACTATAGTGTGCAAGGATACTTAGTGCAT
1 CACTATAGTGTGCAAGGACACTTAGTGCAT
* * *
294517 CACTATGGTGTGTAAGGACATTTAGTG
1 CACTATAGTGTGCAAGGACACTTAGTG
294544 AATATGGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (30 bp):
CACTATAGTGTGCAAGGACACTTAGTGCAT
Found at i:294660 original size:21 final size:22
Alignment explanation
Indices: 294622--294663 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
294612 ATTGTGGTGT
*
294622 GTAAGGACATTCAATGCATATG
1 GTAAGCACATTCAATGCATATG
*
294644 GTAAGCAC-TTCAGTGCATAT
1 GTAAGCACATTCAATGCATAT
294664 TTGACTCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (22 bp):
GTAAGCACATTCAATGCATATG
Found at i:296463 original size:312 final size:312
Alignment explanation
Indices: 295886--296508 Score: 1009
Period size: 312 Copynumber: 2.0 Consensus size: 312
295876 AACGAGAGTG
* *
295886 AGTCATATTTGTAGACAGTAATTGTCTGGTAAGGATCCAACGTGTTGATTTATAATAGACTTGAT
1 AGTCATATTTGTAGACAGTAATTGTCTGGTAAGAATCCAACGTATTGATTTATAATAGACTTGAT
* * *
295951 AGAATTACCTTTCGAATGTAATTTTTGGAATGAATTGATTACCCCTACCATGTTGCAATGAATTA
66 AGAATTACCTTTCGAAGGTAATATTTGGAATGAATTGATTACCCCTACCATGTTACAATGAATTA
* *
296016 CTGCTTAAAGCGATTGAATTTTTAGAACTGAAAAAGTTTCGAGATATTTGTGGAAGGGAAAAATA
131 CTGCTTAAAGAGATTGAATTTTTAGAACTGAAAAAGTTTCGAGATATTTGTGGAAGGGAAAAAGA
* * *
296081 GTAAATTTTTTTTCTAATGCGATTTTAAAATCAGCTGCTATAAAGTTATTGCTACTAGGTTGTCA
196 GTAAATTTGTTTTCTAATGCGATTCTAAAATCAACTGCTATAAAGTTATTGCTACTAGGTTGTCA
*
296146 AACCTTCTTAGTAAAGGAGGTGGATACTCAAACTTTCTTAGTTAAGTTGGAA
261 AACCTTCTTAGTAAAGGAGGTGGATACTCAAACTTTCTTAGATAAGTTGGAA
* * *
296198 AGTCGTATTTGTAGACAGTAATTGTCTGGTAAGAATTCAACGTATTGA-TTATAATATACTTGAT
1 AGTCATATTTGTAGACAGTAATTGTCTGGTAAGAATCCAACGTATTGATTTATAATAGACTTGAT
*
296262 AGAATTACCTTTC-ATAGGTAATATTTGGAATGAATTGATTACCTCCTACCATGTTACACTGAAT
66 AGAATTACCTTTCGA-AGGTAATATTTGGAATGAATTGATTACC-CCTACCATGTTACAATGAAT
296326 TACTGCTTAAAGAGATTGAATTTTTAGAACTCG-AAAAGTTTCGAGATATTTGTGGAAGGGAAAA
129 TACTGCTTAAAGAGATTGAATTTTTAGAACT-GAAAAAGTTTCGAGATATTTGTGGAAGGGAAAA
* ** *
296390 AGAGTAAATTTGTTTTCTAATGTGATTCTAGCATTAACTGCTATAAAGTTATTGCTACTAGGTTG
193 AGAGTAAATTTGTTTTCTAATGCGATTCTAAAATCAACTGCTATAAAGTTATTGCTACTAGGTTG
* *
296455 TTAAACCTTCTTAGTAAAGTAGGTGGATACTCAAACTTTCTTAGATAAGTTGGA
258 TCAAACCTTCTTAGTAAAGGAGGTGGATACTCAAACTTTCTTAGATAAGTTGGA
296509 CTATTCGAGG
Statistics
Matches: 287, Mismatches: 21, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
310 1 0.00
311 54 0.19
312 231 0.80
313 1 0.00
ACGTcount: A:0.33, C:0.12, G:0.19, T:0.36
Consensus pattern (312 bp):
AGTCATATTTGTAGACAGTAATTGTCTGGTAAGAATCCAACGTATTGATTTATAATAGACTTGAT
AGAATTACCTTTCGAAGGTAATATTTGGAATGAATTGATTACCCCTACCATGTTACAATGAATTA
CTGCTTAAAGAGATTGAATTTTTAGAACTGAAAAAGTTTCGAGATATTTGTGGAAGGGAAAAAGA
GTAAATTTGTTTTCTAATGCGATTCTAAAATCAACTGCTATAAAGTTATTGCTACTAGGTTGTCA
AACCTTCTTAGTAAAGGAGGTGGATACTCAAACTTTCTTAGATAAGTTGGAA
Found at i:301063 original size:30 final size:30
Alignment explanation
Indices: 301029--301181 Score: 110
Period size: 30 Copynumber: 5.0 Consensus size: 30
301019 ATCGGATTAG
*
301029 CACTATAGTGTGTAAGAAAACTTAGTGCAA
1 CACTATAGTGTGTAAGAACACTTAGTGCAA
* ** *
301059 CACTATGGTGTGTAAGGGCACTTAGCGCATATGA
1 CACTATAGTGTGTAAGAACACTTAGTGC--A--A
* *
301093 TACTATAGTGTGTAA-AGACACTTAGTACAA
1 CACTATAGTGTGTAAGA-ACACTTAGTGCAA
* * * * * *
301123 CACTGTAGTGTGTAAGGACGCTCATTGTAA
1 CACTATAGTGTGTAAGAACACTTAGTGCAA
* * *
301153 CACTGTGGTGTGTAAGAACACTCAGTGCA
1 CACTATAGTGTGTAAGAACACTTAGTGCA
301182 TATGGTAAGA
Statistics
Matches: 93, Mismatches: 24, Indels: 12
0.72 0.19 0.09
Matches are distributed among these distances:
30 69 0.74
32 2 0.02
34 22 0.24
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.27
Consensus pattern (30 bp):
CACTATAGTGTGTAAGAACACTTAGTGCAA
Found at i:304207 original size:19 final size:19
Alignment explanation
Indices: 304183--304247 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
304173 TATGCATTGG
304183 GCTATGAATTTAAAAATAA
1 GCTATGAATTTAAAAATAA
* * *
304202 GCTATGAATCTAAGATTAA
1 GCTATGAATTTAAAAATAA
* * *
304221 GTTATGAGTTTGAAAATAA
1 GCTATGAATTTAAAAATAA
*
304240 GTTATGAA
1 GCTATGAA
304248 CATGGAAATA
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.45, C:0.05, G:0.17, T:0.34
Consensus pattern (19 bp):
GCTATGAATTTAAAAATAA
Found at i:304333 original size:19 final size:19
Alignment explanation
Indices: 304309--304345 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
304299 GGTTATGTAA
304309 ATGAAATGTGAAA-ATGAAT
1 ATGAAA-GTGAAAGATGAAT
304328 ATGAAAGTGAAAGATGAA
1 ATGAAAGTGAAAGATGAA
304346 AATAAGATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (19 bp):
ATGAAAGTGAAAGATGAAT
Found at i:304790 original size:157 final size:156
Alignment explanation
Indices: 304578--304902 Score: 449
Period size: 158 Copynumber: 2.1 Consensus size: 156
304568 TAAGTCTATG
* *
304578 TTTTTACCAAATTTGGGTCACATGCTCCTAAACCATATTAGAATACATGTGTACTTTCAATTCCT
1 TTTTTACCAAATTTGGCTCACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCT
*
304643 ATTTTTGATAACAAATTTTTTA-TT-TCAATTTAGTCCTTCAATTTTTCATAATCTCCATATTTC
66 ATTTTTGAT-A-AAATTTTTTATTTCTCAATTTAGTCCTTCAATTTTTCATAATCTCCATATTCC
* *
304706 TTCAATTTGTCATTTATTTTAAGTCCCC
129 TTAAATTTGTCATTTATTTTAAGTCACC
*
304734 TTTTTAACCAAATTTGAGCT-ACATGCTCCTAAAGCATAGTAGAATACATGTGTACTTTCAATTC
1 TTTTT-ACCAAATTTG-GCTCACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTC
* ** * * *
304798 CTCTTTTTGATAATTTTTTTTATTTTCTCAATTTAGTCCTTTAATTTTTCATAATCTTCTTATTC
64 CTATTTTTGATAAAATTTTTTA-TTTCTCAATTTAGTCCTTCAATTTTTCATAATCTCCATATTC
* *
304863 CTTAAATTTGTGATTTATTTTAAGTCACTT
128 CTTAAATTTGTCATTTATTTTAAGTCAC-C
304893 TTTTTACCAA
1 TTTTTACCAA
304903 TTTAAACCAC
Statistics
Matches: 149, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
155 8 0.05
156 6 0.04
157 64 0.43
158 66 0.44
159 5 0.03
ACGTcount: A:0.27, C:0.18, G:0.07, T:0.48
Consensus pattern (156 bp):
TTTTTACCAAATTTGGCTCACATGCTCCTAAACCATAGTAGAATACATGTGTACTTTCAATTCCT
ATTTTTGATAAAATTTTTTATTTCTCAATTTAGTCCTTCAATTTTTCATAATCTCCATATTCCTT
AAATTTGTCATTTATTTTAAGTCACC
Found at i:304905 original size:157 final size:157
Alignment explanation
Indices: 304565--304902 Score: 459
Period size: 157 Copynumber: 2.1 Consensus size: 157
304555 AATTTTTGAG
* * *
304565 TTTTAAGTCTA-TGTTTTTACCAAATTTGGGTCACATGCTCCTAAACCATATTAGAATACATGTG
1 TTTTAAGTC-ACTTTTTTTACCAAATTTGGCTCACATGCTCCTAAACCATAGTAGAATACATGTG
304629 TACTTTCAATTCCTATTTTTGATAACAAATTTTTTATTTCAATTTAGTCCTTCAATTTTTCATAA
65 TACTTTCAATTCCTATTTTTGATAACAAATTTTTTATTTCAATTTAGTCCTTCAATTTTTCATAA
* *
304694 TCTCCATATTTCTTCAATTTGTCATTTA
130 TCTCCATATTCCTTAAATTTGTCATTTA
* * * *
304722 TTTTAAGTCCCCTTTTTAACCAAATTTGAGCT-ACATGCTCCTAAAGCATAGTAGAATACATGTG
1 TTTTAAGTCACTTTTTTTACCAAATTTG-GCTCACATGCTCCTAAACCATAGTAGAATACATGTG
* ** *
304786 TACTTTCAATTCCTCTTTTTGAT-A-ATTTTTTTTATTTTCTCAATTTAGTCCTTTAATTTTTCA
65 TACTTTCAATTCCTATTTTTGATAACAAATTTTTTA--TT-TCAATTTAGTCCTTCAATTTTTCA
* * *
304849 TAATCTTCTTATTCCTTAAATTTGTGATTTA
127 TAATCTCCATATTCCTTAAATTTGTCATTTA
304880 TTTTAAGTCACTTTTTTTACCAA
1 TTTTAAGTCACTTTTTTTACCAA
304903 TTTAAACCAC
Statistics
Matches: 157, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
155 8 0.05
156 1 0.01
157 77 0.49
158 71 0.45
ACGTcount: A:0.27, C:0.17, G:0.08, T:0.48
Consensus pattern (157 bp):
TTTTAAGTCACTTTTTTTACCAAATTTGGCTCACATGCTCCTAAACCATAGTAGAATACATGTGT
ACTTTCAATTCCTATTTTTGATAACAAATTTTTTATTTCAATTTAGTCCTTCAATTTTTCATAAT
CTCCATATTCCTTAAATTTGTCATTTA
Found at i:304949 original size:158 final size:157
Alignment explanation
Indices: 304596--304962 Score: 445
Period size: 157 Copynumber: 2.3 Consensus size: 157
304586 AAATTTGGGT
*
304596 CACATGCTCCTAAACCATATTAGAATACATGTGTACTTTCAATTCCTATTTTTGATAACAAATTT
1 CACATGCTCCTAAACCATAATAGAATACATGTGTACTTTCAATTCCTATTTTTGATAACAAATTT
* *
304661 TTTATTTCAATTTAGTCCTTCAATTTTTCATAATCTCCATATTTCTTCAATTTGTCATTTATTTT
66 TTTATTTCAATTTAGTCCTTCAATTTTTCATAATCTCCATATTCCTTAAATTTGTCATTTATTTT
* * *
304726 AAGTCCCCTTTTTAACCAAATTTGAGC
131 AAGTCACCTTTTTAACCAAATTTAAAC
* * * * **
304753 TACATGCTCCTAAAGCATAGTAGAATACATGTGTACTTTCAATTCCTCTTTTTGAT-A-ATTTTT
1 CACATGCTCCTAAACCATAATAGAATACATGTGTACTTTCAATTCCTATTTTTGATAACAAATTT
* * * *
304816 TTTATTTTCTCAATTTAGTCCTTTAATTTTTCATAATCTTCTTATTCCTTAAATTTGTGATTTAT
66 TTTA--TT-TCAATTTAGTCCTTCAATTTTTCATAATCTCCATATTCCTTAAATTTGTCATTTAT
* *
304881 TTTAAGTCACTTTTTTTACC-AATTTAAAC
128 TTTAAGTCACCTTTTTAACCAAATTTAAAC
* * * * * **
304910 CACATGCTCGTATACCACAATAAAATACATATGTAACTTT-AATTGTTATTTTT
1 CACATGCTCCTAAACCATAATAGAATACATGTGT-ACTTTCAATTCCTATTTTT
304963 TAACTGAATA
Statistics
Matches: 178, Mismatches: 28, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
155 8 0.04
156 1 0.01
157 97 0.54
158 72 0.40
ACGTcount: A:0.29, C:0.18, G:0.07, T:0.47
Consensus pattern (157 bp):
CACATGCTCCTAAACCATAATAGAATACATGTGTACTTTCAATTCCTATTTTTGATAACAAATTT
TTTATTTCAATTTAGTCCTTCAATTTTTCATAATCTCCATATTCCTTAAATTTGTCATTTATTTT
AAGTCACCTTTTTAACCAAATTTAAAC
Found at i:305206 original size:2 final size:2
Alignment explanation
Indices: 305199--305224 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
305189 TGAAAGAATA
305199 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
305225 TATGGTTAGA
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:308512 original size:25 final size:25
Alignment explanation
Indices: 308478--308529 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
308468 TCGAAAATGA
308478 GTTCTCCAACGTCAATCTTCCTCCC
1 GTTCTCCAACGTCAATCTTCCTCCC
*
308503 GTTCTCCAACGTCAATCTTTCTCCC
1 GTTCTCCAACGTCAATCTTCCTCCC
308528 GT
1 GT
308530 ATATGATTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.15, C:0.40, G:0.10, T:0.35
Consensus pattern (25 bp):
GTTCTCCAACGTCAATCTTCCTCCC
Found at i:317341 original size:20 final size:20
Alignment explanation
Indices: 317316--317354 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
317306 TTAGGGTTTG
317316 AGTATCGATACTGGATGAAC
1 AGTATCGATACTGGATGAAC
*
317336 AGTATCGATACTGGTTGAA
1 AGTATCGATACTGGATGAA
317355 TTGGGGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.13, G:0.26, T:0.28
Consensus pattern (20 bp):
AGTATCGATACTGGATGAAC
Found at i:317413 original size:23 final size:24
Alignment explanation
Indices: 317386--317442 Score: 98
Period size: 23 Copynumber: 2.4 Consensus size: 24
317376 CAAAAGGGAG
*
317386 TATCGATACTGCCAAGGG-GGCAT
1 TATCGATACTGCCAAGGGTGACAT
317409 TATCGATACTGCCAAGGGTGACAT
1 TATCGATACTGCCAAGGGTGACAT
317433 TATCGATACT
1 TATCGATACT
317443 AAGGCCCCAT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
23 18 0.56
24 14 0.44
ACGTcount: A:0.28, C:0.21, G:0.25, T:0.26
Consensus pattern (24 bp):
TATCGATACTGCCAAGGGTGACAT
Found at i:318699 original size:31 final size:31
Alignment explanation
Indices: 318634--318699 Score: 78
Period size: 31 Copynumber: 2.1 Consensus size: 31
318624 ACTAGTCCAT
* * *
318634 TTTGTATTCAGATAATGCACAATATATTATG
1 TTTGTACTCAGATAATGCACAATATATCAGG
* * *
318665 TTTGTACTCAGATAATGCATAGTATATCCGG
1 TTTGTACTCAGATAATGCACAATATATCAGG
318696 TTTG
1 TTTG
318700 CATTTAGTTA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (31 bp):
TTTGTACTCAGATAATGCACAATATATCAGG
Found at i:322794 original size:2 final size:2
Alignment explanation
Indices: 322783--322814 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
322773 TTAAAACGTA
322783 AT AT -T AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
322815 TCATTCATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 26 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:326360 original size:5 final size:5
Alignment explanation
Indices: 326347--326381 Score: 52
Period size: 5 Copynumber: 6.8 Consensus size: 5
326337 AAAATGTTAA
*
326347 AAAAG AAAAT AAAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAA
326382 AAGTGGGAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:326360 original size:11 final size:11
Alignment explanation
Indices: 326346--326382 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
326336 AAAAATGTTA
*
326346 AAAAAGAAAAT
1 AAAAATAAAAT
326357 AAAAATAAAAT
1 AAAAATAAAAT
326368 -AAAATAAAAT
1 AAAAATAAAAT
326378 AAAAA
1 AAAAA
326383 AGTGGGAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.14
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:326501 original size:18 final size:18
Alignment explanation
Indices: 326480--326522 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
326470 TTGTTTTTTA
*
326480 AAATAAAAGATAATAATT
1 AAATAAAAGAAAATAATT
326498 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
326516 AAATAAA
1 AAATAAA
326523 TAATCTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.23
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:330151 original size:8 final size:8
Alignment explanation
Indices: 330140--330199 Score: 59
Period size: 8 Copynumber: 6.9 Consensus size: 8
330130 ATGATTTTTA
330140 TTTTTATT
1 TTTTTATT
330148 TTTTTATT
1 TTTTTATT
330156 ATTTTACTATT
1 -TTTT--TATT
330167 TTTTCT-TT
1 TTTT-TATT
330175 ATGTTTTATT
1 -T-TTTTATT
330185 TTTTTATT
1 TTTTTATT
330193 TTTTTAT
1 TTTTTAT
330200 CTAACATTAT
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
8 24 0.52
9 9 0.20
10 9 0.20
11 4 0.09
ACGTcount: A:0.15, C:0.03, G:0.02, T:0.80
Consensus pattern (8 bp):
TTTTTATT
Found at i:330169 original size:26 final size:26
Alignment explanation
Indices: 330092--330196 Score: 65
Period size: 26 Copynumber: 3.9 Consensus size: 26
330082 AATTTAGCCC
330092 TTTTTATTATTATTACTATATATTTTTATGTAT
1 TTTTTATTATT-TTAC--TAT-TTTTTA--T-T
*
330125 TTTTTATGATTTT--TA-TTTTTATT
1 TTTTTATTATTTTACTATTTTTTATT
*
330148 TTTTTATTATTTTACTATTTTTTCTT
1 TTTTTATTATTTTACTATTTTTTATT
* **
330174 TATGTT-TTATTTTTTTATTTTTT
1 T-TTTTATTATTTTACTATTTTTT
330197 TATCTAACAT
Statistics
Matches: 62, Mismatches: 6, Indels: 15
0.75 0.07 0.18
Matches are distributed among these distances:
23 13 0.21
24 1 0.02
25 2 0.03
26 29 0.47
27 3 0.05
28 2 0.03
32 2 0.03
33 10 0.16
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.75
Consensus pattern (26 bp):
TTTTTATTATTTTACTATTTTTTATT
Found at i:330212 original size:2 final size:2
Alignment explanation
Indices: 330207--330243 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
330197 TATCTAACAT
330207 TA TA 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 TA TA T
330244 TATTATTTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:330335 original size:13 final size:12
Alignment explanation
Indices: 330314--330348 Score: 61
Period size: 13 Copynumber: 2.8 Consensus size: 12
330304 TCTTTTTTCC
330314 TTTTTTTATTTA
1 TTTTTTTATTTA
330326 TTTATTTTATTTA
1 TTT-TTTTATTTA
330339 TTTTTTTATT
1 TTTTTTTATT
330349 GAACACTATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
TTTTTTTATTTA
Found at i:330340 original size:17 final size:16
Alignment explanation
Indices: 330314--330348 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
330304 TCTTTTTTCC
330314 TTTTTTTATTTATTTA
1 TTTTTTTATTTATTTA
*
330330 TTTTATTTATTTTTTTA
1 TTTT-TTTATTTATTTA
330347 TT
1 TT
330349 GAACACTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 4 0.24
17 13 0.76
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTTATTTATTTA
Found at i:330399 original size:19 final size:18
Alignment explanation
Indices: 330370--330412 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
330360 TATATATATA
*
330370 TATTTTTT-TTTTT-TAT
1 TATTTTTTCTTTTTGTTT
330386 TATTCTTTTCTTTTTGTTT
1 TATT-TTTTCTTTTTGTTT
330405 TATTTTTT
1 TATTTTTT
330413 TAATTTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
18 9 0.39
19 6 0.26
ACGTcount: A:0.09, C:0.05, G:0.02, T:0.84
Consensus pattern (18 bp):
TATTTTTTCTTTTTGTTT
Found at i:330413 original size:19 final size:17
Alignment explanation
Indices: 330372--330413 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
330362 TATATATATA
330372 TTTTTTTTTTTTATTAT
1 TTTTTTTTTTTTATTAT
330389 TCTTTTCTTTTTGTT-TTAT
1 T-TTTT-TTTTT-TTATTAT
330408 TTTTTT
1 TTTTTT
330414 AATTTTTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 2 0.09
18 8 0.36
19 10 0.45
20 2 0.09
ACGTcount: A:0.07, C:0.05, G:0.02, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTTTTATTAT
Found at i:330471 original size:5 final size:5
Alignment explanation
Indices: 330449--330491 Score: 52
Period size: 5 Copynumber: 8.6 Consensus size: 5
330439 TTTTCCCTTT
* *
330449 TTTTA TTTTTA TCTTA TTCTA TTTTA TTTTA TTTTA -TTTA TTT
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTT
330492 ACCTTTTCTC
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
4 4 0.12
5 23 0.72
6 5 0.16
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:330557 original size:3 final size:3
Alignment explanation
Indices: 330549--330592 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
330539 GGTTAGTCTT
330549 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
330593 TAGCTTTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:335505 original size:7 final size:7
Alignment explanation
Indices: 335495--335545 Score: 59
Period size: 7 Copynumber: 7.4 Consensus size: 7
335485 ATATATATTA
335495 TTTTTAT
1 TTTTTAT
335502 TTTTTAT
1 TTTTTAT
335509 TTTTT-T
1 TTTTTAT
*
335515 TTTCTAT
1 TTTTTAT
*
335522 TCTTTAT
1 TTTTTAT
* *
335529 GTTTTCT
1 TTTTTAT
335536 TTTTTAT
1 TTTTTAT
335543 TTT
1 TTT
335546 GTTTCTTTTT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
6 5 0.14
7 30 0.86
ACGTcount: A:0.10, C:0.06, G:0.02, T:0.82
Consensus pattern (7 bp):
TTTTTAT
Found at i:335515 original size:16 final size:16
Alignment explanation
Indices: 335490--335556 Score: 55
Period size: 16 Copynumber: 4.1 Consensus size: 16
335480 TTCATATATA
* *
335490 TATTATTTTTATTTTT
1 TATTTTTTTTCTTTTT
*
335506 TATTTTTTTT-TTCTAT
1 TATTTTTTTTCTT-TTT
*
335522 TCTTTATGTTTTCTTTTT
1 TATTT-T-TTTTCTTTTT
*
335540 TATTTTGTTTCTTTTT
1 TATTTTTTTTCTTTTT
335556 T
1 T
335557 TTAAATCTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
15 2 0.05
16 25 0.61
17 2 0.05
18 10 0.24
19 2 0.05
ACGTcount: A:0.10, C:0.06, G:0.03, T:0.81
Consensus pattern (16 bp):
TATTTTTTTTCTTTTT
Found at i:335533 original size:27 final size:28
Alignment explanation
Indices: 335493--335553 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
335483 ATATATATAT
*
335493 TATT-TTTATTTTTTATTTTTT-TTTTC
1 TATTCTTTATGTTTTATTTTTTATTTTC
* *
335519 TATTCTTTATGTTTTCTTTTTTATTTTG
1 TATTCTTTATGTTTTATTTTTTATTTTC
335547 T-TTCTTT
1 TATTCTTT
335554 TTTTTAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 4 0.13
27 21 0.70
28 5 0.17
ACGTcount: A:0.10, C:0.07, G:0.03, T:0.80
Consensus pattern (28 bp):
TATTCTTTATGTTTTATTTTTTATTTTC
Found at i:335637 original size:19 final size:19
Alignment explanation
Indices: 335594--335637 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
335584 ATTATTTTTA
335594 TTTTTATCTTATTCTATTT
1 TTTTTATCTTATTCTATTT
*
335613 TGTTTTAT-TTATTTTATCTT
1 T-TTTTATCTTATTCTAT-TT
335633 TTTTT
1 TTTTT
335638 CTCTCTCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.14, C:0.07, G:0.02, T:0.77
Consensus pattern (19 bp):
TTTTTATCTTATTCTATTT
Found at i:335716 original size:3 final size:3
Alignment explanation
Indices: 335708--335748 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
335698 AGTCTTTTAC
335708 TAT TAT TAT TAT TAT TAT TAT TAT TAT TATT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT T
335749 TAGCTTTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:336761 original size:21 final size:21
Alignment explanation
Indices: 336729--336798 Score: 55
Period size: 21 Copynumber: 3.7 Consensus size: 21
336719 AACATCTATC
336729 AAAC-TTTATCAAACTTTGAA
1 AAACATTTATCAAACTTTGAA
*
336749 AAACATTTTTCAAA----G--
1 AAACATTTATCAAACTTTGAA
* *
336764 AAACATTTACCAAACTTTAAA
1 AAACATTTATCAAACTTTGAA
*
336785 AAACATTTTTCAAA
1 AAACATTTATCAAA
336799 GTTGGTTGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 13
0.66 0.11 0.23
Matches are distributed among these distances:
15 12 0.32
17 1 0.03
20 4 0.11
21 20 0.54
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.33
Consensus pattern (21 bp):
AAACATTTATCAAACTTTGAA
Found at i:336787 original size:36 final size:35
Alignment explanation
Indices: 336729--336799 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 35
336719 AACATCTATC
* *
336729 AAACTTTATCAAACTTTGAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTAAAAAACATTTTTCAAAG
336764 AAACATTTACCAAACTTTAAAAAACATTTTTCAAAG
1 AAAC-TTTACCAAACTTTAAAAAACATTTTTCAAAG
336800 TTGGTTGCCA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
35 4 0.12
36 29 0.88
ACGTcount: A:0.48, C:0.15, G:0.04, T:0.32
Consensus pattern (35 bp):
AAACTTTACCAAACTTTAAAAAACATTTTTCAAAG
Found at i:339375 original size:3 final size:3
Alignment explanation
Indices: 339367--339494 Score: 226
Period size: 3 Copynumber: 43.7 Consensus size: 3
339357 CTGTATTAGC
339367 AAT AAT AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
339414 AAT AAT AAT AAT AAT AAT -AT TAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
339460 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
339495 CAACAGACTT
Statistics
Matches: 121, Mismatches: 1, Indels: 6
0.95 0.01 0.05
Matches are distributed among these distances:
2 6 0.05
3 115 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:349883 original size:2 final size:2
Alignment explanation
Indices: 349872--349900 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
349862 TTTTAAGAAA
349872 AT AT AT -T 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
349901 TTATTTTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:351687 original size:3 final size:3
Alignment explanation
Indices: 351681--351754 Score: 55
Period size: 3 Copynumber: 24.7 Consensus size: 3
351671 TTTATTATAT
* * *
351681 TAA TAA TAA TAA TAA TAAA TAA -AA TAA -AA TAT TTA TAA TAA TAT
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
351725 TTA TAA TAAA TAA -AA CTAA TAA TAA AAA TA
1 TAA TAA T-AA TAA TAA -TAA TAA TAA TAA TA
351755 TAAATAAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
2 6 0.11
3 41 0.75
4 8 0.15
ACGTcount: A:0.65, C:0.01, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Done.