Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006974.1 Hibiscus syriacus cultivar Beakdansim tig00017960_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: 366595
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:187167 original size:32 final size:32
Alignment explanation
Indices: 187131--187191 Score: 122
Period size: 32 Copynumber: 1.9 Consensus size: 32
187121 TAGGGGTATT
187131 AGCGTTCATTGTAAAATAGTTGAAAGTCTATG
1 AGCGTTCATTGTAAAATAGTTGAAAGTCTATG
187163 AGCGTTCATTGTAAAATAGTTGAAAGTCT
1 AGCGTTCATTGTAAAATAGTTGAAAGTCT
187192 TTGTACAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.34, C:0.10, G:0.21, T:0.34
Consensus pattern (32 bp):
AGCGTTCATTGTAAAATAGTTGAAAGTCTATG
Found at i:191979 original size:30 final size:30
Alignment explanation
Indices: 191945--192046 Score: 78
Period size: 30 Copynumber: 3.2 Consensus size: 30
191935 AAATTTAGTT
191945 TATGATCATCATATAATAATTAATTTCCTA
1 TATGATCATCATATAATAATTAATTTCCTA
* * * * * * * *
191975 TATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATC--A-TCATATAATAA-T-TAATTTCCTA
*
192010 TATGATCATCATATAATACTTAATTTCCTA
1 TATGATCATCATATAATAATTAATTTCCTA
192040 TATGATC
1 TATGATC
192047 TAAGTAAAAG
Statistics
Matches: 50, Mismatches: 17, Indels: 10
0.65 0.22 0.13
Matches are distributed among these distances:
30 20 0.40
31 1 0.02
32 7 0.14
33 8 0.16
34 1 0.02
35 13 0.26
ACGTcount: A:0.41, C:0.13, G:0.08, T:0.38
Consensus pattern (30 bp):
TATGATCATCATATAATAATTAATTTCCTA
Found at i:192138 original size:64 final size:65
Alignment explanation
Indices: 191945--192202 Score: 450
Period size: 64 Copynumber: 4.0 Consensus size: 65
191935 AAATTTAGTT
191945 TATGATCATCATATAATAATTAATTTCCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATAATTAATTTCCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
*
192010 TATGATCATCATATAATACTTAATTTCCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATAATTAATTTCCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
* * *
192075 TATGATCATCATATAATACTTAATTT-CTATATGA-CTTAAGTAAAAGAAAAAGTCTTGGGTACA
1 TATGATCATCATATAATAATTAATTTCCTATATGATC-TAAGTAAAAGAAAAAGTCTTAGTTACA
192138 A
65 A
192139 TATGATCATCATATAATAATTAATTT-CTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
1 TATGATCATCATATAATAATTAATTTCCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
192203 GTCTAGACTC
Statistics
Matches: 185, Mismatches: 6, Indels: 5
0.94 0.03 0.03
Matches are distributed among these distances:
63 1 0.01
64 93 0.50
65 91 0.49
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (65 bp):
TATGATCATCATATAATAATTAATTTCCTATATGATCTAAGTAAAAGAAAAAGTCTTAGTTACAA
Found at i:196537 original size:179 final size:180
Alignment explanation
Indices: 196280--196639 Score: 713
Period size: 179 Copynumber: 2.0 Consensus size: 180
196270 GATTAATCTC
196280 ATCACGCAAAGGCAACAACTTCCTTAGCCCCCTCATAGACCCCTTCAGATCCAAACATCGAAAAT
1 ATCACGCAAAGGCAACAACTTCCTTAGCCCCCTCATAGACCCCTTCAGATCCAAACATCGAAAAT
196345 CTCTCCCCTTAATAACATAAACATGAACCCAAACAACCCATAAGGAGCCTTCATTGCCAGGATAT
66 CTCTCCCCTTAATAACATAAACATGAACCCAAACAACCCATAAGGAGCCTTCATTGCCAGGATAT
196410 GCTTCATCAACTTGAAGTGACAAGCTTTGTTCCACCAACCT-AATCCTTT
131 GCTTCATCAACTTGAAGTGACAAGCTTTGTTCCACCAACCTAAATCCTTT
196459 ATCACGCAAAGGCAACAACTTCCTTAGCCCCCTCATAGACCCCTTCAGATCCAAACATCGAAAAT
1 ATCACGCAAAGGCAACAACTTCCTTAGCCCCCTCATAGACCCCTTCAGATCCAAACATCGAAAAT
196524 CTCTCCCCTTAATAACATAAACATGAACCCAAACAACCCATAAGGAGCCTTCATTGCCAGGATAT
66 CTCTCCCCTTAATAACATAAACATGAACCCAAACAACCCATAAGGAGCCTTCATTGCCAGGATAT
196589 GCTTCATCAACTTGAAGTGACAAGCTTTGTTCCACCAACCTAAATCCTTT
131 GCTTCATCAACTTGAAGTGACAAGCTTTGTTCCACCAACCTAAATCCTTT
196639 A
1 A
196640 AGTCAAGGAC
Statistics
Matches: 180, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
179 171 0.95
180 9 0.05
ACGTcount: A:0.34, C:0.32, G:0.11, T:0.23
Consensus pattern (180 bp):
ATCACGCAAAGGCAACAACTTCCTTAGCCCCCTCATAGACCCCTTCAGATCCAAACATCGAAAAT
CTCTCCCCTTAATAACATAAACATGAACCCAAACAACCCATAAGGAGCCTTCATTGCCAGGATAT
GCTTCATCAACTTGAAGTGACAAGCTTTGTTCCACCAACCTAAATCCTTT
Found at i:198604 original size:22 final size:22
Alignment explanation
Indices: 198577--198618 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
198567 AATTTAAAAG
198577 TTAAATAGTTAA-ATTAAAATTT
1 TTAAAT-GTTAATATTAAAATTT
*
198599 TTAAATTTTAATATTAAAAT
1 TTAAATGTTAATATTAAAAT
198619 AGAAATGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
TTAAATGTTAATATTAAAATTT
Found at i:204905 original size:115 final size:115
Alignment explanation
Indices: 204675--204886 Score: 289
Period size: 115 Copynumber: 1.8 Consensus size: 115
204665 CAACAAGATA
* * * *
204675 ACAAACAAATGTTATCTTCATCAGACGAGACGATGTCAAATCCGATCTTGAAAAAAAACAACTTA
1 ACAAACAAATGTTATATTCATCAGACGAGACGACGTCAAATCCAATCTTGAAAAAAAACAACTGA
**
204740 AAAGAACAATCAAACGACTGGTAAAAGAAACCGAAAACGTGCCCACAAAT
66 AAAGAACAATCAAACGACTAATAAAAGAAACCGAAAACGTGCCCACAAAT
* * * *
204790 ACAAATAAATGTTATATTGATCAGCCGAGACGACGTCAAATCCAATCTTGAAAAAAAATATAACT
1 ACAAACAAATGTTATATTCATCAGACGAGACGACGTCAAATCCAATCTTG-AAAAAAA-ACAACT
* * *
204855 GAAAAGCACAATCAAATGACTAATAAAGGAAA
64 GAAAAGAACAATCAAACGACTAATAAAAGAAA
204887 TTGAAAATGT
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
115 44 0.54
116 7 0.09
117 31 0.38
ACGTcount: A:0.49, C:0.18, G:0.14, T:0.19
Consensus pattern (115 bp):
ACAAACAAATGTTATATTCATCAGACGAGACGACGTCAAATCCAATCTTGAAAAAAAACAACTGA
AAAGAACAATCAAACGACTAATAAAAGAAACCGAAAACGTGCCCACAAAT
Found at i:206770 original size:22 final size:21
Alignment explanation
Indices: 206731--206775 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
206721 TATCTATTTA
*
206731 ATTTTTTGATATATTTCTAAT
1 ATTTTTTGATATAGTTCTAAT
* *
206752 ATTTTATTTATATAGTTCTTAT
1 ATTTT-TTGATATAGTTCTAAT
206774 AT
1 AT
206776 AATCTTAAGT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (21 bp):
ATTTTTTGATATAGTTCTAAT
Found at i:213224 original size:31 final size:31
Alignment explanation
Indices: 213186--213265 Score: 124
Period size: 31 Copynumber: 2.6 Consensus size: 31
213176 AGGGTCGAGG
213186 GTTTACCTACGTTCTTCGAGACATATGGACT
1 GTTTACCTACGTTCTTCGAGACATATGGACT
* *
213217 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTACGTTCTTCGAGACATATGGACT
* *
213248 GATTACCTAGGTTCTTCG
1 GTTTACCTACGTTCTTCG
213266 GAATCTATGG
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.20, C:0.21, G:0.21, T:0.38
Consensus pattern (31 bp):
GTTTACCTACGTTCTTCGAGACATATGGACT
Found at i:213266 original size:31 final size:31
Alignment explanation
Indices: 213188--213279 Score: 123
Period size: 31 Copynumber: 3.0 Consensus size: 31
213178 GGTCGAGGGT
* *
213188 TTACCTACGTTCTTCGAGACATATGGACTGT
1 TTACCTACGTTCTTCGGGACATATGGACTGA
*
213219 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTACGTTCTTCGGGACATATGGACTGA
* *
213250 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTACGTTCTTCGGGA-CATATGGACTG
213280 GTCATTCGGG
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
31 54 0.98
32 1 0.02
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (31 bp):
TTACCTACGTTCTTCGGGACATATGGACTGA
Found at i:218810 original size:19 final size:21
Alignment explanation
Indices: 218776--218816 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 21
218766 TCTTAAAGTA
*
218776 AATTTGTTTGTTATTTTTTTC
1 AATTTGTTTGTTATTTTATTC
218797 AATTT-TTT-TTATTTTATTC
1 AATTTGTTTGTTATTTTATTC
218816 A
1 A
218817 TTATTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 11 0.58
20 3 0.16
21 5 0.26
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.71
Consensus pattern (21 bp):
AATTTGTTTGTTATTTTATTC
Found at i:225336 original size:18 final size:18
Alignment explanation
Indices: 225310--225360 Score: 84
Period size: 18 Copynumber: 2.8 Consensus size: 18
225300 TGAATATTTT
225310 TCCCGAAGGACCACTATG
1 TCCCGAAGGACCACTATG
* *
225328 TCCCAAAGGACCACCATG
1 TCCCGAAGGACCACTATG
225346 TCCCGAAGGACCACT
1 TCCCGAAGGACCACT
225361 GTTAATCCCT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.37, G:0.20, T:0.14
Consensus pattern (18 bp):
TCCCGAAGGACCACTATG
Found at i:225817 original size:17 final size:18
Alignment explanation
Indices: 225792--225841 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 18
225782 ACTTAATAGT
*
225792 ATTTTATTTATATAC-TA
1 ATTTAATTTATATACTTA
*
225809 ATTTAATTTATTTACTTA
1 ATTTAATTTATATACTTA
*
225827 ATTCTATTTTATATA
1 ATT-TAATTTATATA
225842 TTTCTTATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
17 13 0.48
18 5 0.19
19 9 0.33
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTAATTTATATACTTA
Found at i:226318 original size:20 final size:20
Alignment explanation
Indices: 226290--226328 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
226280 TATCTTTTAG
226290 ATTCATATAATT-TCATATAT
1 ATTCATAT-ATTATCATATAT
*
226310 ATTCTTATATTATCATATA
1 ATTCATATATTATCATATA
226329 ACTTATGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (20 bp):
ATTCATATATTATCATATAT
Found at i:231109 original size:24 final size:24
Alignment explanation
Indices: 231077--231133 Score: 114
Period size: 24 Copynumber: 2.4 Consensus size: 24
231067 AATCATGAAT
231077 TGAGTGGTTACATTTGAGAAAATA
1 TGAGTGGTTACATTTGAGAAAATA
231101 TGAGTGGTTACATTTGAGAAAATA
1 TGAGTGGTTACATTTGAGAAAATA
231125 TGAGTGGTT
1 TGAGTGGTT
231134 TATTAGAAGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (24 bp):
TGAGTGGTTACATTTGAGAAAATA
Found at i:232748 original size:18 final size:18
Alignment explanation
Indices: 232721--232773 Score: 81
Period size: 18 Copynumber: 3.0 Consensus size: 18
232711 TGACCGGTCA
*
232721 CGACCAGACCCGTTGACC
1 CGACCCGACCCGTTGACC
*
232739 TGACCCGACCCGTTGACC
1 CGACCCGACCCGTTGACC
232757 CGACCCGA-CCGTTGACC
1 CGACCCGACCCGTTGACC
232774 GGTGCTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
17 9 0.28
18 23 0.72
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (18 bp):
CGACCCGACCCGTTGACC
Found at i:232755 original size:13 final size:13
Alignment explanation
Indices: 232739--232763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
232729 CCCGTTGACC
232739 TGACCCGACCCGT
1 TGACCCGACCCGT
232752 TGACCCGACCCG
1 TGACCCGACCCG
232764 ACCGTTGACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.48, G:0.24, T:0.12
Consensus pattern (13 bp):
TGACCCGACCCGT
Found at i:232855 original size:29 final size:29
Alignment explanation
Indices: 232774--232855 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 29
232764 ACCGTTGACC
* * * *
232774 GGTGCTATTTTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGATAAATAATTCGGTTTA
*
232803 GGTGCCATTCTGATAAATAATTCGGTTTA
1 GGTGCTATTCTGATAAATAATTCGGTTTA
*
232832 GGTGCTATTCTGATAATTAATTCG
1 GGTGCTATTCTGATAAATAATTCG
232856 AAAGGGGTGC
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 46 1.00
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.43
Consensus pattern (29 bp):
GGTGCTATTCTGATAAATAATTCGGTTTA
Found at i:232888 original size:29 final size:28
Alignment explanation
Indices: 232832--232898 Score: 71
Period size: 29 Copynumber: 2.4 Consensus size: 28
232822 ATTCGGTTTA
* *
232832 GGTGCTATTCTGATAATTAATTCGAAAGG
1 GGTGCTATTTTGATAATTAATTC-AAAAG
* * *
232861 GGTGCTATTTTGGTAATTATTTTAAAAG
1 GGTGCTATTTTGATAATTAATTCAAAAG
*
232889 GGTGATATTT
1 GGTGCTATTT
232899 GTGTAAAATG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 13 0.41
29 19 0.59
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (28 bp):
GGTGCTATTTTGATAATTAATTCAAAAG
Found at i:239461 original size:13 final size:13
Alignment explanation
Indices: 239440--239476 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
239430 GACCGGTCAC
*
239440 GACCCGACCCGTT
1 GACCAGACCCGTT
239453 GACCAGACCCGTT
1 GACCAGACCCGTT
*
239466 GACCTGACCCG
1 GACCAGACCCG
239477 ACCGTTGACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.19, C:0.43, G:0.24, T:0.14
Consensus pattern (13 bp):
GACCAGACCCGTT
Found at i:239483 original size:17 final size:17
Alignment explanation
Indices: 239461--239516 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
239451 TTGACCAGAC
239461 CCGTTGACCTGACCCGA
1 CCGTTGACCTGACCCGA
239478 CCGTTGACCTGA-CC-A
1 CCGTTGACCTGACCCGA
*
239493 --GTTGACCCGACCCGA
1 CCGTTGACCTGACCCGA
239508 CCGTTGACC
1 CCGTTGACC
239517 GTTGACCGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
13 9 0.26
14 2 0.06
15 2 0.06
16 2 0.06
17 19 0.56
ACGTcount: A:0.18, C:0.41, G:0.23, T:0.18
Consensus pattern (17 bp):
CCGTTGACCTGACCCGA
Found at i:239484 original size:30 final size:30
Alignment explanation
Indices: 239439--239516 Score: 120
Period size: 30 Copynumber: 2.6 Consensus size: 30
239429 TGACCGGTCA
*
239439 CGACCCGACCCGTTGACCAGACCCGTTGACC
1 CGACCCGA-CCGTTGACCAGACCAGTTGACC
* *
239470 TGACCCGACCGTTGACCTGACCAGTTGACC
1 CGACCCGACCGTTGACCAGACCAGTTGACC
239500 CGACCCGACCGTTGACC
1 CGACCCGACCGTTGACC
239517 GTTGACCGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 36 0.84
31 7 0.16
ACGTcount: A:0.19, C:0.42, G:0.23, T:0.15
Consensus pattern (30 bp):
CGACCCGACCGTTGACCAGACCAGTTGACC
Found at i:239498 original size:13 final size:13
Alignment explanation
Indices: 239470--239504 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
239460 CCCGTTGACC
239470 TGACCCGACC-GT
1 TGACCCGACCAGT
*
239482 TGACCTGACCAGT
1 TGACCCGACCAGT
239495 TGACCCGACC
1 TGACCCGACC
239505 CGACCGTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.20, C:0.40, G:0.23, T:0.17
Consensus pattern (13 bp):
TGACCCGACCAGT
Found at i:239566 original size:29 final size:29
Alignment explanation
Indices: 239524--239603 Score: 133
Period size: 29 Copynumber: 2.8 Consensus size: 29
239514 ACCGTTGACC
*
239524 GGTGCTATTTTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
*
239553 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
*
239582 GGTGCTATTCTGGTAATTAATT
1 GGTGCTATTCTGGTAAATAATT
239604 TAAAATGGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.46
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAGTTTT
Found at i:239628 original size:30 final size:30
Alignment explanation
Indices: 239582--239650 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
239572 ATTCGGTTTT
*
239582 GGTGCTA-TTCTGGTAATTAATTTAAAATG
1 GGTGCTATTTCTGGTAATTAATTTAAAAAG
* *
239611 GGTGCTATTTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTCTGGTAATTAATTTAAAAAG
*
239641 GGTGATATTT
1 GGTGCTATTT
239651 GTGTAAAATG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
29 7 0.20
30 28 0.80
ACGTcount: A:0.29, C:0.04, G:0.22, T:0.45
Consensus pattern (30 bp):
GGTGCTATTTCTGGTAATTAATTTAAAAAG
Found at i:245409 original size:77 final size:79
Alignment explanation
Indices: 245281--245434 Score: 276
Period size: 77 Copynumber: 2.0 Consensus size: 79
245271 AATGTTAAAG
* *
245281 ATGAACTTAAAAGATTTTCTGTAAATGGATATGGTTTGGTGTACAAATGGTGACTGACC-TGGTT
1 ATGAACTTAAAAGATTTACTGTAAATGGATATGGTTTGGTGTACAAATGGTGACTGACCACGGTT
245345 GGATGTTTGTAGTT
66 GGATGTTTGTAGTT
245359 ATGAACTT-AAAGATTTACTGTAAATGGATATGGTTTGGTGTACAAATGGTGACTGACCACGGTT
1 ATGAACTTAAAAGATTTACTGTAAATGGATATGGTTTGGTGTACAAATGGTGACTGACCACGGTT
245423 GGATGTTTGTAG
66 GGATGTTTGTAG
245435 CTTCAAAGCT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
77 49 0.67
78 24 0.33
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.36
Consensus pattern (79 bp):
ATGAACTTAAAAGATTTACTGTAAATGGATATGGTTTGGTGTACAAATGGTGACTGACCACGGTT
GGATGTTTGTAGTT
Found at i:253105 original size:6 final size:6
Alignment explanation
Indices: 253094--253118 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
253084 ACCCGAAAAG
253094 AAAACC AAAACC AAAACC AAAACC A
1 AAAACC AAAACC AAAACC AAAACC A
253119 CAATCACACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAACC
Found at i:260068 original size:16 final size:16
Alignment explanation
Indices: 260047--260080 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
260037 TCGACATATT
260047 TCTTCCTTATCGTTTA
1 TCTTCCTTATCGTTTA
260063 TCTTCCTTATCGTTTA
1 TCTTCCTTATCGTTTA
260079 TC
1 TC
260081 CCCCTCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.12, C:0.26, G:0.06, T:0.56
Consensus pattern (16 bp):
TCTTCCTTATCGTTTA
Found at i:266321 original size:24 final size:24
Alignment explanation
Indices: 266293--266403 Score: 141
Period size: 24 Copynumber: 4.6 Consensus size: 24
266283 GAATGTTTTA
* *
266293 TCTGATTTCCGATTTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
266317 TCTGATTTCTGATCTGAATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
*
266341 TCTGATTTCTGATATGGATTCTGT
1 TCTGATTTCTGATATGAATTCTGT
* * * *
266365 TCTGATATATGATGTGAATTCTAT
1 TCTGATTTCTGATATGAATTCTGT
*
266389 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
266404 CTCCATTTAC
Statistics
Matches: 74, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 74 1.00
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGATATGAATTCTGT
Found at i:266332 original size:12 final size:12
Alignment explanation
Indices: 266292--266401 Score: 71
Period size: 12 Copynumber: 9.2 Consensus size: 12
266282 TGAATGTTTT
*
266292 ATCTGATTTCCG
1 ATCTGATTTCTG
* *
266304 ATTTGAATTCTG
1 ATCTGATTTCTG
*
266316 TTCTGATTTCTG
1 ATCTGATTTCTG
*
266328 ATCTGAATTCTG
1 ATCTGATTTCTG
*
266340 TTCTGATTTCTG
1 ATCTGATTTCTG
*
266352 ATATGGA-TTCTG
1 ATCT-GATTTCTG
* * *
266364 TTCTGATATATG
1 ATCTGATTTCTG
* *
266376 ATGTGAATTCT-
1 ATCTGATTTCTG
*
266387 ATTTTGATTTCTG
1 A-TCTGATTTCTG
266400 AT
1 AT
266402 ATCTCCATTT
Statistics
Matches: 71, Mismatches: 23, Indels: 8
0.70 0.23 0.08
Matches are distributed among these distances:
11 3 0.04
12 65 0.92
13 3 0.04
ACGTcount: A:0.20, C:0.13, G:0.17, T:0.50
Consensus pattern (12 bp):
ATCTGATTTCTG
Found at i:268569 original size:22 final size:22
Alignment explanation
Indices: 268524--268582 Score: 84
Period size: 22 Copynumber: 2.6 Consensus size: 22
268514 TTTGGTCAGA
268524 GTTGACTGTTGACCGTCCAGACT
1 GTTGACT-TTGACCGTCCAGACT
*
268547 GTTGACTTTGACCAGTCTA-ACT
1 GTTGACTTTGACC-GTCCAGACT
268569 GTTGACTTTGACCG
1 GTTGACTTTGACCG
268583 AAAAAGTCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
21 1 0.03
22 22 0.65
23 11 0.32
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.34
Consensus pattern (22 bp):
GTTGACTTTGACCGTCCAGACT
Found at i:271068 original size:59 final size:59
Alignment explanation
Indices: 270988--271100 Score: 163
Period size: 59 Copynumber: 1.9 Consensus size: 59
270978 GAATACACTA
* * * * *
270988 AAGGATACATAGTGTATATGGTGGGCACAACCTTATGTGTCATATTCGGGATTGTACTT
1 AAGGATACATAGTATAGATGGTGGACACAACCTTATGTGTCATACTCGAGATTGTACTT
* *
271047 AAGGATACCTAGTATAGATGGTGGACACGACCTTATGTGTCATACTCGAGATTG
1 AAGGATACATAGTATAGATGGTGGACACAACCTTATGTGTCATACTCGAGATTG
271101 CACTACGGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
59 47 1.00
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.31
Consensus pattern (59 bp):
AAGGATACATAGTATAGATGGTGGACACAACCTTATGTGTCATACTCGAGATTGTACTT
Found at i:271184 original size:20 final size:21
Alignment explanation
Indices: 271159--271204 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
271149 TATATTGGGA
**
271159 TATTGTCTATTGTTTATGG-T
1 TATTGTCTATCATTTATGGTT
271179 TATTGTCTATCATTTATGGTT
1 TATTGTCTATCATTTATGGTT
271200 TATTG
1 TATTG
271205 GTTAATAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 17 0.74
21 6 0.26
ACGTcount: A:0.17, C:0.07, G:0.17, T:0.59
Consensus pattern (21 bp):
TATTGTCTATCATTTATGGTT
Found at i:271372 original size:92 final size:91
Alignment explanation
Indices: 271226--271398 Score: 256
Period size: 92 Copynumber: 1.9 Consensus size: 91
271216 ATAAACTGGT
* * *
271226 AAAATAAGCTTACGAGCTTATGGAATAAATGATAAGTGTATTGATAAAATAAGCTTACGAGCTTA
1 AAAATAAGATTACGAGCTTATGGAATAAATGATAAGTATATTGATAAAAGAAGCTTACGAGCTTA
271291 TGGAATAAATGGTAAGTATATGGGTA
66 TGGAATAAATGGTAAGTATATGGGTA
* * * * *
271317 AAAATAGGATTACGAGCTTATGTGATTAAATGGTAAGTATTTTGGTAAAAGAAGCTTACGAGCTT
1 AAAATAAGATTACGAGCTTATG-GAATAAATGATAAGTATATTGATAAAAGAAGCTTACGAGCTT
*
271382 ATGGGATAAATGGTAAG
65 ATGGAATAAATGGTAAG
271399 AAATTTTATA
Statistics
Matches: 72, Mismatches: 9, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
91 20 0.28
92 52 0.72
ACGTcount: A:0.40, C:0.06, G:0.24, T:0.30
Consensus pattern (91 bp):
AAAATAAGATTACGAGCTTATGGAATAAATGATAAGTATATTGATAAAAGAAGCTTACGAGCTTA
TGGAATAAATGGTAAGTATATGGGTA
Found at i:271405 original size:46 final size:45
Alignment explanation
Indices: 271222--271398 Score: 246
Period size: 45 Copynumber: 3.9 Consensus size: 45
271212 AATGATAAAC
* *
271222 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGATAAGTGTAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
*
271267 TGATAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* * * * *
271312 GGGTAAAAATAGGATTACGAGCTTATGTGATTAAATGGTAAGTATTT
1 TGGT-AAAATAAGCTTACGAGCTTATG-GAATAAATGGTAAGTATAT
* *
271359 TGGTAAAAGAAGCTTACGAGCTTATGGGATAAATGGTAAG
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAG
271399 AAATTTTATA
Statistics
Matches: 115, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
45 56 0.49
46 39 0.34
47 20 0.17
ACGTcount: A:0.39, C:0.06, G:0.24, T:0.31
Consensus pattern (45 bp):
TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
Found at i:271911 original size:22 final size:22
Alignment explanation
Indices: 271883--271930 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
271873 CTGTTCATTG
271883 TTCACGGTACGGTTCATTACTC
1 TTCACGGTACGGTTCATTACTC
* *
271905 TTCACGGTACTGTTCATTACTG
1 TTCACGGTACGGTTCATTACTC
271927 TTCA
1 TTCA
271931 TAAATACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.19, C:0.25, G:0.17, T:0.40
Consensus pattern (22 bp):
TTCACGGTACGGTTCATTACTC
Found at i:274267 original size:6 final size:6
Alignment explanation
Indices: 274256--274345 Score: 80
Period size: 6 Copynumber: 15.3 Consensus size: 6
274246 ATAAAAAAAG
* * *
274256 AAGAAA AAGAAA AA-ACA GA-AAA AAGAAAA GAAAAAA AAGAAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAG-AAA -AAGAAA AAGAAA AAGAAA
* * *
274304 AAGAAA ATGAAG AAG-AA AA-AAA TAGAAA AAGAAA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA
274346 AAATGAATGA
Statistics
Matches: 67, Mismatches: 12, Indels: 10
0.75 0.13 0.11
Matches are distributed among these distances:
5 12 0.18
6 47 0.70
7 6 0.09
8 2 0.03
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.02
Consensus pattern (6 bp):
AAGAAA
Found at i:274268 original size:15 final size:14
Alignment explanation
Indices: 274234--274348 Score: 87
Period size: 14 Copynumber: 8.2 Consensus size: 14
274224 ATTATATATG
** *
274234 AAAAAAAGAATCAT
1 AAAAAAAGAAGAAA
274248 AAAAAAAGAAGAAA
1 AAAAAAAGAAGAAA
274262 AAGAAAAA-ACAGAAA
1 AA-AAAAAGA-AGAAA
274277 AAAGAAAAGAA-AAA
1 AAA-AAAAGAAGAAA
*
274291 AAAGAAA-AAGAAA
1 AAAAAAAGAAGAAA
* *
274304 AAGAAAATGAAGAAG
1 AA-AAAAAGAAGAAA
*
274319 AAAAAAA-TAGAAA
1 AAAAAAAGAAGAAA
274332 AAGAAAAAGAA-AAA
1 AA-AAAAAGAAGAAA
274346 AAA
1 AAA
274349 TGAATGAGAT
Statistics
Matches: 81, Mismatches: 11, Indels: 19
0.73 0.10 0.17
Matches are distributed among these distances:
12 2 0.02
13 15 0.19
14 38 0.47
15 25 0.31
16 1 0.01
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAGAAA
Found at i:274269 original size:30 final size:30
Alignment explanation
Indices: 274251--274333 Score: 96
Period size: 30 Copynumber: 2.6 Consensus size: 30
274241 GAATCATAAA
*
274251 AAAAGAAGAAAAAGAAAAAACAGAAAAAAG
1 AAAAGAAAAAAAAGAAAAAACAGAAAAAAG
*
274281 AAAAGAAAAAAAAGAAAAAGA-AAAAGAAAATG
1 AAAAGAAAAAAAAGAAAAA-ACAGAA-AAAA-G
274313 AAGAAGAAAAAAATAGAAAAA
1 AA-AAGAAAAAAA-AGAAAAA
274334 GAAAAAGAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
30 21 0.46
31 5 0.11
32 3 0.07
33 10 0.22
34 7 0.15
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.02
Consensus pattern (30 bp):
AAAAGAAAAAAAAGAAAAAACAGAAAAAAG
Found at i:274331 original size:34 final size:32
Alignment explanation
Indices: 274256--274345 Score: 76
Period size: 33 Copynumber: 2.7 Consensus size: 32
274246 ATAAAAAAAG
*
274256 AAGAAAAAGAAA-AAACAGAAAAA-AGAAAAGAA
1 AAGAAAAA-AAAGAAAAAGAAAAAGA-AAAAGAA
* * *
274288 AAAAAAGAAAAAGAAAAAGAAAATGAAGAAGAA
1 AAGAAA-AAAAAGAAAAAGAAAAAGAAAAAGAA
*
274321 AAAAATAGAAAAAGAAAAAGAAAAA
1 AAGAA-A-AAAAAGAAAAAGAAAAA
274346 AAATGAATGA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
32 8 0.16
33 22 0.45
34 19 0.39
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.02
Consensus pattern (32 bp):
AAGAAAAAAAAGAAAAAGAAAAAGAAAAAGAA
Found at i:274347 original size:22 final size:20
Alignment explanation
Indices: 274256--274345 Score: 94
Period size: 21 Copynumber: 4.4 Consensus size: 20
274246 ATAAAAAAAG
274256 AAGAAAAAGAAAAAACAGAAA
1 AAGAAAAAGAAAAAA-AGAAA
274277 AA-AGAAAAGAAAAAAAAGAAA
1 AAGA-AAAAG-AAAAAAAGAAA
* *
274298 AAGAAAAAGAAAATGAAGAAG
1 AAGAAAAAGAAAA-AAAGAAA
* *
274319 AA-AAAAATAGAAAAAGAAA
1 AAGAAAAAGAAAAAAAGAAA
274338 AAGAAAAA
1 AAGAAAAA
274346 AAATGAATGA
Statistics
Matches: 58, Mismatches: 6, Indels: 11
0.77 0.08 0.15
Matches are distributed among these distances:
19 7 0.12
20 18 0.31
21 26 0.45
22 7 0.12
ACGTcount: A:0.81, C:0.01, G:0.16, T:0.02
Consensus pattern (20 bp):
AAGAAAAAGAAAAAAAGAAA
Found at i:274355 original size:42 final size:38
Alignment explanation
Indices: 274248--274355 Score: 123
Period size: 36 Copynumber: 2.8 Consensus size: 38
274238 AAAGAATCAT
* *
274248 AAAAAAAGAAGAAAAAGAAAAAACAGAA--AAAAGAAA
1 AAAAAAAAAAGAAAAAGAAAAAAAAGAATGAAAAGAAA
* *
274284 AGAAAAAAAAGAAAAAGAAAAAGAA-AATGAAGAAGAAA
1 AAAAAAAAAAGAAAAAGAAAAAAAAGAATGAA-AAGAAA
274322 AAAATAGAAAAAGAAAAAGAAAAAAAATGAATGA
1 AAAA-A-AAAAAGAAAAAGAAAAAAAA-GAATGA
274356 GATATGATTA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
35 2 0.03
36 21 0.36
37 2 0.03
38 9 0.15
39 1 0.02
40 19 0.32
42 5 0.08
ACGTcount: A:0.80, C:0.01, G:0.16, T:0.04
Consensus pattern (38 bp):
AAAAAAAAAAGAAAAAGAAAAAAAAGAATGAAAAGAAA
Found at i:278979 original size:17 final size:16
Alignment explanation
Indices: 278948--278981 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
278938 CACGTGAAGA
278948 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
278964 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
278981 T
1 T
278982 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:283485 original size:22 final size:22
Alignment explanation
Indices: 283442--283496 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
283432 GTGCATCGGT
* *
283442 TCACTGTTCACGGCACTGTTCA
1 TCACTGTTCATGGCACTATTCA
* * *
283464 TTATTGTTCATGGTACTATTCA
1 TCACTGTTCATGGCACTATTCA
283486 TCACTGTTCAT
1 TCACTGTTCAT
283497 AAATACATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.42
Consensus pattern (22 bp):
TCACTGTTCATGGCACTATTCA
Found at i:285810 original size:12 final size:11
Alignment explanation
Indices: 285793--285894 Score: 57
Period size: 11 Copynumber: 8.9 Consensus size: 11
285783 ATATAAGAAA
285793 AAAAAGAAACAT
1 AAAAAGAAA-AT
*
285805 AAAAAGAAAGAAG
1 AAAAAG-AA-AAT
285818 AAAAAGAAAAT
1 AAAAAGAAAAT
*
285829 AAAAA-ACAA-
1 AAAAAGAAAAT
*
285838 AAAAAGAAAAGAA
1 AAAAAG-AAA-AT
*
285851 AAAAATGAAGAAG
1 AAAAA-GAA-AAT
* *
285864 AAAAA-AACAG
1 AAAAAGAAAAT
*
285874 AAAAAGAAAAG
1 AAAAAGAAAAT
285885 AAAAAGAAAA
1 AAAAAGAAAA
285895 AAATGAATGA
Statistics
Matches: 74, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
9 5 0.07
10 10 0.14
11 25 0.34
12 9 0.12
13 22 0.30
14 3 0.04
ACGTcount: A:0.80, C:0.03, G:0.14, T:0.03
Consensus pattern (11 bp):
AAAAAGAAAAT
Found at i:285815 original size:25 final size:24
Alignment explanation
Indices: 285787--285897 Score: 95
Period size: 25 Copynumber: 4.5 Consensus size: 24
285777 AATATTATAT
285787 AAGAAAAAAAAGAAACATAAAAAGA
1 AAGAAAAAAAAGAAA-ATAAAAAGA
*
285812 AAGAAGAAAAAGAAAATAAAAA-A
1 AAGAAAAAAAAGAAAATAAAAAGA
*
285835 CAAAAAAAGAAAAGAAAA-AAATGAAG-
1 -AAGAAAA-AAAAGAAAATAAA--AAGA
285861 AAGAAAAAAACAGAAAA-AGAAAAGA
1 AAGAAAAAAA-AGAAAATA-AAAAGA
*
285886 AAAAGAAAAAAA
1 AAGA-AAAAAAA
285898 TGAATGAGAA
Statistics
Matches: 72, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
23 1 0.01
24 21 0.29
25 40 0.56
26 10 0.14
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (24 bp):
AAGAAAAAAAAGAAAATAAAAAGA
Found at i:285826 original size:6 final size:6
Alignment explanation
Indices: 285793--285895 Score: 79
Period size: 6 Copynumber: 16.8 Consensus size: 6
285783 ATATAAGAAA
* * * *
285793 AAAAAG AAACAT AAAAAG AAAGAAG AAAAAG AAAATA- AAAAAC AAAAAA
1 AAAAAG AAAAAG AAAAAG AAA-AAG AAAAAG AAAA-AG AAAAAG AAAAAG
*
285842 AGAAAAG AAAAA- AATGAAG AAGAAA- AAAACAG AAAAAG -AAAAG AAAAAG
1 A-AAAAG AAAAAG AA-AAAG AA-AAAG AAAA-AG AAAAAG AAAAAG AAAAAG
285891 AAAAA
1 AAAAA
285896 AATGAATGAG
Statistics
Matches: 79, Mismatches: 9, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
5 10 0.13
6 49 0.62
7 20 0.25
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (6 bp):
AAAAAG
Found at i:285832 original size:5 final size:5
Alignment explanation
Indices: 285787--285894 Score: 66
Period size: 5 Copynumber: 21.4 Consensus size: 5
285777 AATATTATAT
* * *
285787 AAGAA AA-AA AAGAA ACATAA AA-AGA AAGAA GA-AA AAGAA AATAA AA-AA
1 AAGAA AAGAA AAGAA A-AGAA AAGA-A AAGAA AAGAA AAGAA AAGAA AAGAA
* *
285835 CAAAAA AAGAA AAGAA AA-AA ATGAA GAAGAA AA-AA ACAGAAA AAGAA
1 -AAGAA AAGAA AAGAA AAGAA AAGAA -AAGAA AAGAA A-AG-AA AAGAA
285882 AAGAAA AAGAA AA
1 AAG-AA AAGAA AA
285895 AAATGAATGA
Statistics
Matches: 83, Mismatches: 7, Indels: 26
0.72 0.06 0.22
Matches are distributed among these distances:
4 16 0.19
5 46 0.55
6 18 0.22
7 3 0.04
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (5 bp):
AAGAA
Found at i:285878 original size:36 final size:33
Alignment explanation
Indices: 285787--285897 Score: 129
Period size: 34 Copynumber: 3.3 Consensus size: 33
285777 AATATTATAT
*
285787 AAGAAAAAAAAGAAACATAAAAAG-AAAGAAGAAA
1 AAGAAAAAAAA-AAACAAAAAAAGAAAAGAA-AAA
*
285821 AAGAAAATAAAAAACAAAAAAAGAAAAGAAAAA
1 AAGAAAAAAAAAAACAAAAAAAGAAAAGAAAAA
*
285854 AATGAAGAAGAAAAAAACAGAAAAAGAAAAG--AAA
1 AA-GAA-AA-AAAAAAACAAAAAAAGAAAAGAAAAA
285888 AAGAAAAAAA
1 AAGAAAAAAA
285898 TGAATGAGAA
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
31 3 0.04
32 2 0.03
33 19 0.28
34 24 0.35
35 2 0.03
36 19 0.28
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (33 bp):
AAGAAAAAAAAAAACAAAAAAAGAAAAGAAAAA
Found at i:285896 original size:13 final size:13
Alignment explanation
Indices: 285805--285896 Score: 68
Period size: 13 Copynumber: 6.9 Consensus size: 13
285795 AAAGAAACAT
*
285805 AAAAAGAAAGAAG
1 AAAAAGAAAAAAG
285818 AAAAAGAAAATAA-
1 AAAAAGAAAA-AAG
285831 AAAACA-AAAAAAG
1 AAAA-AGAAAAAAG
285844 -AAAAGAAAAAAATG
1 AAAAAG-AAAAAA-G
*
285858 AAGAAGAAAAAA-
1 AAAAAGAAAAAAG
285870 ACAGAAA-AAGAAAAG
1 A-A-AAAGAA-AAAAG
285885 AAAAAGAAAAAA
1 AAAAAGAAAAAA
285897 ATGAATGAGA
Statistics
Matches: 64, Mismatches: 3, Indels: 24
0.70 0.03 0.26
Matches are distributed among these distances:
11 1 0.02
12 6 0.09
13 33 0.52
14 19 0.30
15 5 0.08
ACGTcount: A:0.82, C:0.02, G:0.14, T:0.02
Consensus pattern (13 bp):
AAAAAGAAAAAAG
Found at i:285920 original size:42 final size:41
Alignment explanation
Indices: 285821--285901 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
285811 AAAGAAGAAA
* *
285821 AAGAAAATAA-AAAACAAAAAAAGAAAAGAAAAAAATGAAG
1 AAGAAAAAAACAAAAAAAAAAAAGAAAAGAAAAAAATGAAG
* *
285861 AAGAAAAAAACAGAAAAAGAAAAGAAAAAGAAAAAAATGAA
1 AAGAAAAAAACAAAAAAAAAAAAG-AAAAGAAAAAAATGAA
285902 TGAGAAATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 9 0.26
41 10 0.29
42 16 0.46
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (41 bp):
AAGAAAAAAACAAAAAAAAAAAAGAAAAGAAAAAAATGAAG
Found at i:289845 original size:19 final size:19
Alignment explanation
Indices: 289821--289891 Score: 61
Period size: 19 Copynumber: 3.5 Consensus size: 19
289811 CAGACATAGA
289821 AAAAAAGAGAGCACAAAGT
1 AAAAAAGAGAGCACAAAGT
* * *
289840 AAAAAAGAGGGGACCAGACATAGA
1 AAAAAAGA---GAGC--ACAAAGT
*
289864 AAAAAAGAGAGCACAGAGT
1 AAAAAAGAGAGCACAAAGT
289883 AAAAAAGAG
1 AAAAAAGAG
289892 GGAACCAGAC
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
19 22 0.54
21 3 0.07
22 3 0.07
24 13 0.32
ACGTcount: A:0.61, C:0.10, G:0.25, T:0.04
Consensus pattern (19 bp):
AAAAAAGAGAGCACAAAGT
Found at i:289936 original size:42 final size:43
Alignment explanation
Indices: 289803--289936 Score: 209
Period size: 43 Copynumber: 3.2 Consensus size: 43
289793 TACGAAAAGG
*
289803 AGAGGG-ACCAGACATAGAAAAAAAGAGAGCACAAAGTAAAAA
1 AGAGGGAACCAGACATAGAAAAAAAGAGAGCACAGAGTAAAAA
*
289845 AGAGGGGACCAGACATAGAAAAAAAGAGAGCACAGAGTAAAAA
1 AGAGGGAACCAGACATAGAAAAAAAGAGAGCACAGAGTAAAAA
* *
289888 AGAGGGAACCAGACATAG-AAAAAGGAGAGCACAGAGTTAAAA
1 AGAGGGAACCAGACATAGAAAAAAAGAGAGCACAGAGTAAAAA
*
289930 CGAGGGA
1 AGAGGGA
289937 GAATAGACAT
Statistics
Matches: 86, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
42 34 0.40
43 52 0.60
ACGTcount: A:0.54, C:0.12, G:0.28, T:0.05
Consensus pattern (43 bp):
AGAGGGAACCAGACATAGAAAAAAAGAGAGCACAGAGTAAAAA
Found at i:299331 original size:42 final size:42
Alignment explanation
Indices: 299228--299448 Score: 142
Period size: 42 Copynumber: 5.0 Consensus size: 42
299218 ACTTAGTAAG
* ** *
299228 TCCTTCGGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAA
1 TCCTTAGGGCCATCGGTAAGTCTTTCGAGCATGATGATTAAA
*
299270 TCTTTAGGGCCATCGGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTAGGGCCATCGGTAAGTCTTTCGAGCATGATGATTAAA
* * ** * * **
299312 TCCTTCGGG-TATTTTGTAAGCCTTCACCGAAG-A-GTAGTGAAGCAAA
1 TCCTTAGGGCCA-TCGGTAAGTCTT--TCG-AGCATG-A-TG-ATTAAA
* * *
299358 TCCATCAGTAAGTGCCATCAGTAAGTCTTTCGATCATGATGATTAAA
1 TCC-T---T-AGGGCCATCGGTAAGTCTTTCGAGCATGATGATTAAA
* * *
299405 TCATTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAA
1 TCCTTAGGGCCATCGGTAAGTCTTTCGAGCATGATGATTAAA
299447 TC
1 TC
299449 ATTCGGGTCA
Statistics
Matches: 136, Mismatches: 28, Indels: 30
0.70 0.14 0.15
Matches are distributed among these distances:
41 1 0.01
42 89 0.65
43 2 0.01
44 4 0.03
45 4 0.03
46 8 0.06
47 7 0.05
48 3 0.02
49 4 0.03
50 2 0.01
51 11 0.08
52 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (42 bp):
TCCTTAGGGCCATCGGTAAGTCTTTCGAGCATGATGATTAAA
Found at i:299377 original size:13 final size:13
Alignment explanation
Indices: 299359--299383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
299349 TGAAGCAAAT
299359 CCATCAGTAAGTG
1 CCATCAGTAAGTG
299372 CCATCAGTAAGT
1 CCATCAGTAAGT
299384 CTTTCGATCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:299449 original size:42 final size:42
Alignment explanation
Indices: 299371--299500 Score: 163
Period size: 42 Copynumber: 3.1 Consensus size: 42
299361 ATCAGTAAGT
*
299371 GCCATCAGTAAGTCTTTCGATCATGATGATTAAATCATTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGG
299413 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGG
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGG
* ** * * * * * *
299455 GTCATTTGTAAGGCTTTCAAGAAAGATGA-TAAGTCATTCGT
1 GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGG
299496 GCCAT
1 GCCAT
299501 TTTAAGCCTT
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 14 0.18
42 63 0.82
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (42 bp):
GCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCATTCGG
Found at i:300097 original size:106 final size:106
Alignment explanation
Indices: 299886--300128 Score: 317
Period size: 106 Copynumber: 2.3 Consensus size: 106
299876 ATACCAAAAT
* * * **
299886 ATTGTTTGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCGTAGGCAGAAGATTGTTCGAGTT
1 ATTGTTCGAGTTCTAATCCCTGAAGCAAGAGGGAGCGAACCCGTAAACAGAAGATTGTTCGAGTT
* *
299951 CTACTCCCTGAAGTAAGAGGGAGAGAACCCGTAGGCAGAAG
66 CTACTCCCTGAAGCAAGAGGGAGAGAACCCATAGGCAGAAG
* *
299992 ATTGTTCGAGTTCTATTCCCTGAAGCAAGAGGGAGCGAACTCGTAAACAGAAGATTGTTCGAGTT
1 ATTGTTCGAGTTCTAATCCCTGAAGCAAGAGGGAGCGAACCCGTAAACAGAAGATTGTTCGAGTT
* * ****
300057 CTACTCCCTGAAGCAATAGGGAGTGAACCCATTTTTAGAAG
66 CTACTCCCTGAAGCAAGAGGGAGAGAACCCATAGGCAGAAG
*
300098 ATTATTCGAGTTCCTTAATCCCTGAA-CAAGA
1 ATTGTTCGAGTT-C-TAATCCCTGAAGCAAGA
300129 AGAAGCAGAC
Statistics
Matches: 119, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
106 103 0.87
107 6 0.05
108 10 0.08
ACGTcount: A:0.30, C:0.20, G:0.25, T:0.25
Consensus pattern (106 bp):
ATTGTTCGAGTTCTAATCCCTGAAGCAAGAGGGAGCGAACCCGTAAACAGAAGATTGTTCGAGTT
CTACTCCCTGAAGCAAGAGGGAGAGAACCCATAGGCAGAAG
Found at i:300110 original size:53 final size:53
Alignment explanation
Indices: 299886--300086 Score: 312
Period size: 53 Copynumber: 3.8 Consensus size: 53
299876 ATACCAAAAT
* *
299886 ATTGTTTGAGTTCTACTCCCTGAAGCAATAGGGAGCGAACCCGTAGGCAGAAG
1 ATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAG
* *
299939 ATTGTTCGAGTTCTACTCCCTGAAGTAAGAGGGAGAGAACCCGTAGGCAGAAG
1 ATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAG
* * **
299992 ATTGTTCGAGTTCTATTCCCTGAAGCAAGAGGGAGCGAACTCGTAAACAGAAG
1 ATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAG
* *
300045 ATTGTTCGAGTTCTACTCCCTGAAGCAATAGGGAGTGAACCC
1 ATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCC
300087 ATTTTTAGAA
Statistics
Matches: 134, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
53 134 1.00
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.23
Consensus pattern (53 bp):
ATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGGCAGAAG
Found at i:300605 original size:42 final size:42
Alignment explanation
Indices: 300527--300656 Score: 206
Period size: 42 Copynumber: 3.1 Consensus size: 42
300517 CGAAAAGGAG
*
300527 GGGGACCAGACATAGAAAAAAAGAGAGCACAAAGTAAAAAAGA
1 GGGGACCAGACATAG-AAAAAAGAGAGCACAGAGTAAAAAAGA
300570 GGGGACCAGACATAGAAAAAAGAGAGCACAGAGTAAAAAAGA
1 GGGGACCAGACATAGAAAAAAGAGAGCACAGAGTAAAAAAGA
* * * *
300612 GGGAACCAGACATAGAGAAAGGAGAGCACAGAGTAAAAACGA
1 GGGGACCAGACATAGAAAAAAGAGAGCACAGAGTAAAAAAGA
300654 GGG
1 GGG
300657 AGAATAGACA
Statistics
Matches: 82, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
42 67 0.82
43 15 0.18
ACGTcount: A:0.53, C:0.12, G:0.30, T:0.05
Consensus pattern (42 bp):
GGGGACCAGACATAGAAAAAAGAGAGCACAGAGTAAAAAAGA
Found at i:300643 original size:22 final size:21
Alignment explanation
Indices: 300533--300643 Score: 70
Period size: 19 Copynumber: 5.2 Consensus size: 21
300523 GGAGGGGGAC
300533 CAGACATAGAAAAAAAGAGAGCA
1 CAGACATAG--AAAAAGAGAGCA
* *
300556 CA-A-AGTA-AAAAAGAGGGGA
1 CAGACA-TAGAAAAAGAGAGCA
300575 CCAGACATAGAAAAAAGAGAGCA
1 -CAGACATAG-AAAAAGAGAGCA
* * *
300598 CAGA-GTA-AAAAAGAGGGAA
1 CAGACATAGAAAAAGAGAGCA
*
300617 CCAGACATAGAGAAAGGAGAGCA
1 -CAGACATAGA-AAAAGAGAGCA
300640 CAGA
1 CAGA
300644 GTAAAAACGA
Statistics
Matches: 67, Mismatches: 11, Indels: 21
0.68 0.11 0.21
Matches are distributed among these distances:
19 20 0.30
20 6 0.09
21 8 0.12
22 13 0.19
23 20 0.30
ACGTcount: A:0.56, C:0.13, G:0.27, T:0.05
Consensus pattern (21 bp):
CAGACATAGAAAAAGAGAGCA
Found at i:302894 original size:59 final size:59
Alignment explanation
Indices: 302795--302923 Score: 168
Period size: 59 Copynumber: 2.2 Consensus size: 59
302785 CAGCAGGCTG
** * *
302795 CATATTCGGGAATACACTAAAGGATACCTAGTGTATATGGTGGGCACAACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
* ** * *
302854 CATATTCGGGACTGTACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
*
302913 CATACTCGGGA
1 CATATTCGGGA
302924 TTGCACTACG
Statistics
Matches: 60, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.29, C:0.19, G:0.25, T:0.28
Consensus pattern (59 bp):
CATATTCGGGAATACACTAAAGGATACCTAGTACAGATGGTGGACACAACCTTATGTGT
Found at i:303100 original size:45 final size:45
Alignment explanation
Indices: 303048--303264 Score: 328
Period size: 45 Copynumber: 4.8 Consensus size: 45
303038 AATGATAAAC
* *
303048 TGGTAAAATAAGCTTACGATCTTATGGAATAAATGGTAAGTGTAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* * *
303093 TGGTAAAATAAGTTTACGAGCTTAGGGAATAAATGGTAAGTGTAT
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
*
303138 TGGTAATATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATA-
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
* *
303182 TGAGTAAAATAAGCTTACGAGCTTATGTGATTAAATGGTAAGTATTT
1 TG-GTAAAATAAGCTTACGAGCTTATG-GAATAAATGGTAAGTATAT
*
303229 TGGTAAAATAAGCTTACGAGCTTATGGGATAAATGG
1 TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGG
303265 CAAGAAATTT
Statistics
Matches: 157, Mismatches: 12, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
44 2 0.01
45 113 0.72
46 40 0.25
47 2 0.01
ACGTcount: A:0.37, C:0.06, G:0.24, T:0.32
Consensus pattern (45 bp):
TGGTAAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATAT
Found at i:307338 original size:24 final size:24
Alignment explanation
Indices: 307298--307354 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
307288 ATGTTAGTTT
307298 TATCAC-TTTTTTGATTATCAATC
1 TATCACTTTTTTTGATTATCAATC
* *
307321 TATCACTTTTTTTTATTATCATTC
1 TATCACTTTTTTTGATTATCAATC
*
307345 TGTCACTTTT
1 TATCACTTTT
307355 AATTCAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
23 6 0.20
24 24 0.80
ACGTcount: A:0.21, C:0.18, G:0.04, T:0.58
Consensus pattern (24 bp):
TATCACTTTTTTTGATTATCAATC
Found at i:308589 original size:2 final size:2
Alignment explanation
Indices: 308582--308636 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
308572 GAATTTTGAG
308582 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
308624 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
308637 GGGATGAATA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:310209 original size:26 final size:23
Alignment explanation
Indices: 310152--310209 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 23
310142 TTTAAATTAG
310152 TATTTATTTATTTATTATTCATA
1 TATTTATTTATTTATTATTCATA
*
310175 TATTATTATTTATATTTTTATTCACTAA
1 TA-T-TTATTTAT-TTATTATTCA-T-A
310203 TATTTAT
1 TATTTAT
310210 ATGAAATGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 1 0.03
25 8 0.28
26 13 0.45
27 2 0.07
28 3 0.10
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (23 bp):
TATTTATTTATTTATTATTCATA
Found at i:310570 original size:6 final size:7
Alignment explanation
Indices: 310545--310574 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
310535 AATTAAATAT
*
310545 ATTTTGA
1 ATTTTTA
310552 ATTTTTA
1 ATTTTTA
310559 ATTTTTA
1 ATTTTTA
310566 ATTTTTA
1 ATTTTTA
310573 AT
1 AT
310575 AATAGAGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (7 bp):
ATTTTTA
Found at i:312635 original size:14 final size:14
Alignment explanation
Indices: 312597--312650 Score: 63
Period size: 14 Copynumber: 3.8 Consensus size: 14
312587 ATTTTAAATA
*
312597 ATTTACATTTACAT
1 ATTTACATTTGCAT
*
312611 TTTTACATTTGCAT
1 ATTTACATTTGCAT
312625 ATTTACATTTGGCAT
1 ATTTACATTT-GCAT
* *
312640 CTTTGCATTTG
1 ATTTACATTTG
312651 TATTGCACAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
14 22 0.65
15 12 0.35
ACGTcount: A:0.24, C:0.15, G:0.09, T:0.52
Consensus pattern (14 bp):
ATTTACATTTGCAT
Found at i:315910 original size:15 final size:14
Alignment explanation
Indices: 315890--315919 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
315880 ACCATCCAGC
315890 AAAGAAAGAAAAAAA
1 AAAGAAA-AAAAAAA
315905 AAAGAAAAAAAAAA
1 AAAGAAAAAAAAAA
315919 A
1 A
315920 GAAAATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAGAAAAAAAAAA
Found at i:315915 original size:12 final size:12
Alignment explanation
Indices: 315894--315924 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
315884 TCCAGCAAAG
315894 AAAG-AAAAAAA
1 AAAGAAAAAAAA
315905 AAAGAAAAAAAA
1 AAAGAAAAAAAA
315917 AAAGAAAA
1 AAAGAAAA
315925 TTGAATCAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 4 0.21
12 15 0.79
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (12 bp):
AAAGAAAAAAAA
Found at i:319897 original size:32 final size:33
Alignment explanation
Indices: 319860--319924 Score: 123
Period size: 32 Copynumber: 2.0 Consensus size: 33
319850 GAATACTCGA
319860 CTCACTTACATTACTGTTATTC-CGTTGTTATT
1 CTCACTTACATTACTGTTATTCACGTTGTTATT
319892 CTCACTTACATTACTGTTATTCACGTTGTTATT
1 CTCACTTACATTACTGTTATTCACGTTGTTATT
319925 GGGGTCATCA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 22 0.69
33 10 0.31
ACGTcount: A:0.20, C:0.22, G:0.09, T:0.49
Consensus pattern (33 bp):
CTCACTTACATTACTGTTATTCACGTTGTTATT
Found at i:320542 original size:50 final size:50
Alignment explanation
Indices: 320462--320562 Score: 152
Period size: 50 Copynumber: 2.0 Consensus size: 50
320452 CAATGATTGA
*
320462 ACATCTGAGCAGAATACACAGAAAAGGATGAATGTGTTGTCAAATGTTTT
1 ACATCTGAGCAGAATACACAGAAAAGGATGAATGTATTGTCAAATGTTTT
*
320512 ACATCTGAGTAGAA-ACCACATGAAAA-GATGAATGTATTGTCAAATGTTTT
1 ACATCTGAGCAGAATA-CACA-GAAAAGGATGAATGTATTGTCAAATGTTTT
320562 A
1 A
320563 TGAACCATGA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
49 1 0.02
50 41 0.87
51 5 0.11
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.29
Consensus pattern (50 bp):
ACATCTGAGCAGAATACACAGAAAAGGATGAATGTATTGTCAAATGTTTT
Found at i:320901 original size:22 final size:22
Alignment explanation
Indices: 320872--320926 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
320862 ATCTACACTC
**
320872 TTCAAAGATGGTAGATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
* *
320894 TTTAAAGATGACATATTCTCTT
1 TTCAAAGATGACAGATTCTCTT
320916 TTCAAAGATGA
1 TTCAAAGATGA
320927 AAACTTTATG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCTCTT
Found at i:321712 original size:113 final size:113
Alignment explanation
Indices: 321330--322323 Score: 1432
Period size: 113 Copynumber: 8.9 Consensus size: 113
321320 GATTCAAATC
* *
321330 CATCATAT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGA
1 CATCAT-TCGATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* * ** *
321394 AAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*
321443 CATCA-TCTGA-GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTC-GATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
** *
321506 AAGAAGAA-TTCATAATGAGAAGAA-TTGTTCAACCTTTTGCTCAAATC
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*
321553 CATCA-TCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTC-GATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
321617 AAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*
321666 CATCATTCGATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAA-GA
1 CATCATTCGATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
*
321730 AGAAGAAATTCATAATG-GAAGAA-TTGTTCAACCTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* * ****
321776 CATCATTCGATGGATCAACATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
321841 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTTGAATT
* ****
321889 CATCATTCGAT-GATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTCGATGGA-TCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
* ** *
321953 AAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATC
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
*
322002 CATCA-TCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
1 CATCATTC-GATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGG
*
322066 AAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATT
65 AAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* *
322115 CATCATTCGATGGATCAGCATTTCC-G-AAGAGTTCATAATGAGAAGAACACATCTGAAGAAGGA
1 CATCATTCGATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
* *
322178 AGAAGAAGTTCATAATGAGAAGAACTTGTTTAACATTTTGC-TGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
* ****
322225 CATCATTCGATGGATCAGCATTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAG-AGG-
1 CATCATTCGATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
322288 AG-AG-AGTTCATAATGAGAAGAACTTGTTCAACCTTT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
322324 GCATGACTCT
Statistics
Matches: 817, Mismatches: 47, Indels: 39
0.90 0.05 0.04
Matches are distributed among these distances:
108 30 0.04
109 2 0.00
110 143 0.18
111 179 0.22
112 137 0.17
113 315 0.39
114 11 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (113 bp):
CATCATTCGATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATT
Found at i:321734 original size:223 final size:225
Alignment explanation
Indices: 321323--322323 Score: 1467
Period size: 223 Copynumber: 4.5 Consensus size: 225
321313 TAGCAAAGAT
321323 TCAAATCCATCATATGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCAT-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
* * * ** *
321388 AGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCA-TCTG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTC-G
* *
321452 A-GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA-T
129 ATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGT
321515 TCATAATGAGAAGAA-TTGTTCAACCTTTTGC
194 TCATAATGAGAAGAACTTGTTCAACCTTTTGC
321546 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCAT-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
321611 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGA
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGA
*
321676 TGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAA-GAAGAAGAAATT
130 TGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTT
321740 CATAATG-GAAGAA-TTGTTCAACCTTTTGC
195 CATAATGAGAAGAACTTGTTCAACCTTTTGC
** * * * * ****
321769 TTGAATTCATCATTCGATGGATCAACATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
321834 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGCTTGAATTCATCATTCG
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-GCTTGAATTCATCATTCG
* **** *
321898 AT-GATTCAGTATTTCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
129 ATGGA-TCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAG
*
321962 TTCATAATGAGAAGAATTTGTTCAACCTTTTGC
193 TTCATAATGAGAAGAACTTGTTCAACCTTTTGC
321995 TCAAATCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCAT-TGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
*
322060 AGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGA
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGA
*
322125 TGGATCAGCATTTCC-G-AAGAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTT
130 TGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTT
* *
322188 CATAATGAGAAGAACTTGTTTAACATTTTGC
195 CATAATGAGAAGAACTTGTTCAACCTTTTGC
* * * * ****
322219 T-GAATTCATCATTCGATGGATCAGCATTGCCAGTTCGAGTTCATAATGAGAAGAACTCATCTGA
1 TCAAATCCATCATT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
322283 AG-AGG-AG-AG-AGTTCATAATGAGAAGAACTTGTTCAACCTTT
65 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTT
322324 GCATGACTCT
Statistics
Matches: 710, Mismatches: 55, Indels: 30
0.89 0.07 0.04
Matches are distributed among these distances:
219 31 0.04
220 2 0.00
221 2 0.00
222 12 0.02
223 359 0.51
224 151 0.21
225 7 0.01
226 138 0.19
227 8 0.01
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (225 bp):
TCAAATCCATCATTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAA
GAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGAT
GGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTTTGC
Found at i:321951 original size:336 final size:335
Alignment explanation
Indices: 321323--322323 Score: 1485
Period size: 336 Copynumber: 3.0 Consensus size: 335
321313 TAGCAAAGAT
321323 TCAAATCCATCATAT-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCAT-TCGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* ** *
321387 AAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCA-TCT
65 AAGAAG-AAGAAGAAATTCATAATG-GAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTC-
* *
321451 GA-GGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAA-
127 GATGGATCAGCATTTCCAG-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAG
** *
321514 TTCATAATGAGAAGAA-TTGTTCAACCTTTTGCTCAAATCCATCA-TCTGATGGATCAGCT-TTT
191 TTCATAATGAGAAGAACTTGTTCAA-CTTTTGCTTGAATTCATCATTC-GATGGATCAG-TATTT
**** *
321576 CCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATAAGAAGA
253 CCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGA
321641 ACTTGTTCAACCTTTTGC
318 ACTTGTTCAACCTTTTGC
** * * *
321659 TTGAATTCATCATTCGATGGATCAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGA
1 TCAAATCCATCATTCGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
321724 AGAAGAAGAAGAAATTCATAATGGAAGAA-TTGTTCAACCTTTTGCTTGAATTCATCATTCGATG
66 AGAAGAAGAAGAAATTCATAATGGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATG
* * **
321788 GATCAACATTACCAGTTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
131 GATCAGCATTTCCAG-AAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCA
321853 TAATGAGAAGAACTTGTTCAACTTTTCGCTTGAATTCATCATTCGAT-GATTCAGTATTTCCAGT
195 TAATGAGAAGAACTTGTTCAACTTTT-GCTTGAATTCATCATTCGATGGA-TCAGTATTTCCAGT
*
321917 TCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTG
258 TCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTG
321982 TTCAACCTTTTGC
323 TTCAACCTTTTGC
321995 TCAAATCCATCA-TCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
1 TCAAATCCATCATTC-GATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTG
* *
322059 AAGAAGGAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCG
65 AAGAA-GAAGAAGAAATTCATAAT-GGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCG
*
322124 ATGGATCAGCATTTCC-GAAGAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTT
128 ATGGATCAGCATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTT
* * *
322188 CATAATGAGAAGAACTTGTTTAACATTTTGC-TGAATTCATCATTCGATGGATCAGCATTGCCAG
193 CATAATGAGAAGAACTTGTTCAAC-TTTTGCTTGAATTCATCATTCGATGGATCAGTATTTCCAG
322252 TTCGAGTTCATAATGAGAAGAACTCATCTGAAG-AGG-AG-AG-AGTTCATAATGAGAAGAACTT
257 TTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
322313 GTTCAACCTTT
322 GTTCAACCTTT
322324 GCATGACTCT
Statistics
Matches: 610, Mismatches: 40, Indels: 34
0.89 0.06 0.05
Matches are distributed among these distances:
332 31 0.05
333 29 0.05
334 64 0.10
335 48 0.08
336 291 0.48
337 90 0.15
338 11 0.02
339 46 0.08
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (335 bp):
TCAAATCCATCATTCGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGAAGAAGAAATTCATAATGGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATG
GATCAGCATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCAT
AATGAGAAGAACTTGTTCAACTTTTGCTTGAATTCATCATTCGATGGATCAGTATTTCCAGTTCG
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTGC
Found at i:322225 original size:449 final size:445
Alignment explanation
Indices: 321361--322325 Score: 1615
Period size: 449 Copynumber: 2.2 Consensus size: 445
321351 TTCCAGAAAA
* * *
321361 AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
321426 AACCTTTTGCTCAAATCCATCATCTGAGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAA
66 AA-CTTTTGCTCAAATCCATCATCTGAGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAA
321491 CTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAATTGTTCAACCTTTTGCTCAAATCCAT
130 CTCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAATTGTTCAACCTTTTGCTCAAATCCAT
321556 CATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
195 CATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGA
321621 AGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAGCA
260 AGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAGCA
321686 TTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGAAGAAGAAATTCATAATGGAAG
325 TTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGAAGAAGAAATTCATAATGGAAG
*
321751 AATTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAACATTACCAGTTCG
390 AATTGTTCAACATTTTGCTTGAATTCATCATTCGATGGATCAACATTACCAGTTCG
321807 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
** * * ****
321872 AACTTTTCGCTTGAATTCATCAT-TCGATGATTCAG-TATTTCCAGTTCGAGTTCATAATGAGAA
66 AACTTTT-GCTCAAATCCATCATCT-GAGGA-TCAGCT-TTTCCAGAAAAAGTTCATAATGAGAA
321935 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAA
127 GAACTCATCTGAAGAAGGAAGAAGAA-TTCATAATGAGAAGAA-TTGTTCAACCTTTTGCTCAAA
322000 TCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
190 TCCATCATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAG
322065 GAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGAT
255 GAAGAAGAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGAT
* *
322130 CAGCATTTCC-G-AAGAGTTCATAATGAGAAGAACACATCTGAAGAAGGAAGAAGAAGTTCATAA
320 CAGCATTTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAA-GAAGAAGAAATTCATAA
* * *
322193 TGAGAAGAACTTGTTTAACATTTTGC-TGAATTCATCATTCGATGGATCAGCATTGCCAGTTCG
384 TG-GAAGAA-TTGTTCAACATTTTGCTTGAATTCATCATTCGATGGATCAACATTACCAGTTCG
322256 AGTTCATAATGAGAAGAACTCATCTGAAG-AGG-AG-AG-AGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
*
322317 AACCTTTGC
66 AACTTTTGC
322326 ATGACTCTAT
Statistics
Matches: 492, Mismatches: 18, Indels: 20
0.93 0.03 0.04
Matches are distributed among these distances:
444 2 0.00
445 37 0.08
446 83 0.17
447 87 0.18
448 38 0.08
449 231 0.47
450 14 0.03
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.28
Consensus pattern (445 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACTTTTGCTCAAATCCATCATCTGAGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAAC
TCATCTGAAGAAGGAAGAAGAATTCATAATGAGAAGAATTGTTCAACCTTTTGCTCAAATCCATC
ATCTGATGGATCAGCTTTTCCAGAAAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
GAAGTTCATAATAAGAAGAACTTGTTCAACCTTTTGCTTGAATTCATCATTCGATGGATCAGCAT
TTCCAGAAAAAGTTCATAATGAGAAGAACACATCTGAAGAAGAAGAAGAAATTCATAATGGAAGA
ATTGTTCAACATTTTGCTTGAATTCATCATTCGATGGATCAACATTACCAGTTCG
Found at i:323591 original size:15 final size:15
Alignment explanation
Indices: 323548--323591 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
323538 TTGGTCATTT
*
323548 TTTATATTTTTATCA
1 TTTATATTTTTATTA
323563 TTTAT-TTATTTATTA
1 TTTATATT-TTTATTA
323578 TTTATATTTTTATT
1 TTTATATTTTTATT
323592 CACTAATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 2 0.08
15 22 0.85
16 2 0.08
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTATATTTTTATTA
Found at i:324373 original size:14 final size:14
Alignment explanation
Indices: 324333--324365 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
324323 GTATGAAAAA
324333 TAACGAATTAAATT
1 TAACGAATTAAATT
324347 TAACGAATTAAATT
1 TAACGAATTAAATT
324361 TAACG
1 TAACG
324366 TCTTAAATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.48, C:0.09, G:0.09, T:0.33
Consensus pattern (14 bp):
TAACGAATTAAATT
Found at i:324559 original size:18 final size:19
Alignment explanation
Indices: 324524--324560 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
324514 CACGGAATGT
324524 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
324544 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
324561 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:328418 original size:13 final size:12
Alignment explanation
Indices: 328377--328419 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
328367 GCAGCTTGGT
328377 GAGCCACTGAGC
1 GAGCCACTGAGC
328389 TGAGCCACTGAGCC
1 -GAGCCACTGAG-C
*
328403 GAGCCATTGAGTC
1 GAGCCACTGAG-C
328416 GAGC
1 GAGC
328420 TGAGCCACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
13 26 0.96
14 1 0.04
ACGTcount: A:0.23, C:0.30, G:0.33, T:0.14
Consensus pattern (12 bp):
GAGCCACTGAGC
Found at i:328432 original size:13 final size:13
Alignment explanation
Indices: 328376--328413 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
328366 GGCAGCTTGG
328376 TGAGCCACTGAGC
1 TGAGCCACTGAGC
328389 TGAGCCACTGAGC
1 TGAGCCACTGAGC
* *
328402 CGAGCCATTGAG
1 TGAGCCACTGAG
328414 TCGAGCTGAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.24, C:0.29, G:0.32, T:0.16
Consensus pattern (13 bp):
TGAGCCACTGAGC
Found at i:329939 original size:24 final size:24
Alignment explanation
Indices: 329912--329960 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
329902 TTTTGCTTTA
*
329912 AATTATGTTGAGATTTCTGCTCTG
1 AATTATGTTGAGATTTCTACTCTG
* **
329936 AATTTTGTTTTGATTTCTACTCTG
1 AATTATGTTGAGATTTCTACTCTG
329960 A
1 A
329961 TTTCTACTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.51
Consensus pattern (24 bp):
AATTATGTTGAGATTTCTACTCTG
Found at i:329963 original size:12 final size:12
Alignment explanation
Indices: 329946--329977 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
329936 AATTTTGTTT
329946 TGATTTCTACTC
1 TGATTTCTACTC
*
329958 TGATTTCTACTT
1 TGATTTCTACTC
329970 TGATTTCT
1 TGATTTCT
329978 GATATCTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.19, G:0.09, T:0.56
Consensus pattern (12 bp):
TGATTTCTACTC
Found at i:333070 original size:3 final size:3
Alignment explanation
Indices: 333062--333112 Score: 50
Period size: 3 Copynumber: 17.0 Consensus size: 3
333052 GGGTTCTCAT
* ** *
333062 TTA TTA TTA AT- TTA TTA TTAA CAA TTA TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
333107 TTA TTA
1 TTA TTA
333113 ATATATTTTA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
2 1 0.03
3 36 0.95
4 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:333105 original size:12 final size:12
Alignment explanation
Indices: 333062--333116 Score: 59
Period size: 12 Copynumber: 5.1 Consensus size: 12
333052 GGGTTCTCAT
333062 TTATTATTAAT-
1 TTATTATTAATA
*
333073 TTATTATTAACA
1 TTATTATTAATA
333085 --ATTA-T--TA
1 TTATTATTAATA
333092 TTATTATTAATA
1 TTATTATTAATA
333104 TTATTATTAATA
1 TTATTATTAATA
333116 T
1 T
333117 ATTTTACATT
Statistics
Matches: 36, Mismatches: 2, Indels: 11
0.73 0.04 0.22
Matches are distributed among these distances:
7 1 0.03
9 5 0.14
10 5 0.14
11 10 0.28
12 15 0.42
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (12 bp):
TTATTATTAATA
Found at i:335823 original size:30 final size:30
Alignment explanation
Indices: 335789--335848 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
335779 AAAGCTTTTC
335789 CTGCAAATATGCATGAAGTAAAGAGCTGTA
1 CTGCAAATATGCATGAAGTAAAGAGCTGTA
335819 CTGCAAATATGCATGAAGTAAAGAGCTGTA
1 CTGCAAATATGCATGAAGTAAAGAGCTGTA
335849 GGAAAATTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (30 bp):
CTGCAAATATGCATGAAGTAAAGAGCTGTA
Found at i:337053 original size:85 final size:86
Alignment explanation
Indices: 336958--337122 Score: 253
Period size: 85 Copynumber: 1.9 Consensus size: 86
336948 ACAATCACGA
* *
336958 CACACGAATGTGTGTCATCTTTATTTATGACGGGGGCTTCAATGACACGCAATGTAA-GTCATT-
1 CACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACGCAATG-AACGTCATTA
*
337021 TATGCGTGTCATAAATTTATGC
65 AATGCGTGTCATAAATTTATGC
**
337043 CACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACTTAATGAACGTCATTAA
1 CACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACGCAATGAACGTCATTAA
*
337108 ATGTGTGTCATAAAT
66 ATGCGTGTCATAAAT
337123 GCGCGTCATA
Statistics
Matches: 72, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
84 2 0.03
85 56 0.78
86 14 0.19
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.33
Consensus pattern (86 bp):
CACACAAATGTGTGTCATCTTAATTTATGACGGGGGCTTCAATGACACGCAATGAACGTCATTAA
ATGCGTGTCATAAATTTATGC
Found at i:339084 original size:191 final size:192
Alignment explanation
Indices: 338681--339098 Score: 457
Period size: 191 Copynumber: 2.2 Consensus size: 192
338671 CTATTAGCAG
* * * *
338681 TATGAATGACGTTTATACATAACGTCACTTTATAATTGATACTCAATGACAACTAGTTACGTCAT
1 TATGAATGA-GATTATGCATAACGTCACTTTATAATTGATACTCAATGACAACTAGTTACATCAC
* * * *
338746 TAAATTATATAAAATTTTGTTATTAATAATTCACATCGTTACAAATAATACATTCAAATCAATCT
65 TAAATTATATAAAATTTTGTTATTAATAATTCACATCGTCACAAATAATACAATAAAATCAACCT
* *
338811 ATATGTGACGAAAGAGATATTGTCACATTTTCAGTGACGTAATATAACATTACCTAATAGTAT
130 ATATGTGACGAAAGAGATATTGTCAAATTTTCAGTGACATAATATAACATTACCTAATAGTAT
* * * * * *
338874 TATGAATGACACCTATGCATAATGTCATTTTATAACTT-ATATTGC-ATGACAATTAGTTACATC
1 TATGAATGAGA-TTATGCATAACGTCACTTTATAA-TTGATACT-CAATGACAACTAGTTACATC
* * * * * * * *
338937 ACTAAATTATATAATA-TTT-TTATTAATAATTTATATTGTCACGAATACTACAATAAAATTAGC
63 ACTAAATTATATAAAATTTTGTTATTAATAATTCACATCGTCACAAATAATACAATAAAATCAAC
* * * * ** **
339000 CTATTTGTTACGAAAGATATATTGTCAAATTTTTAGTGACATAATATAATGTTATGTAATAGTAT
128 CTATATGTGACGAAAGAGATATTGTCAAATTTTCAGTGACATAATATAACATTACCTAATAGTAT
* *
339065 TTTGAATGATGATTATGCATAACGTCACCTTATA
1 TATGAATGA-GATTATGCATAACGTCACTTTATA
339099 CAATTTTCTC
Statistics
Matches: 183, Mismatches: 38, Indels: 10
0.79 0.16 0.04
Matches are distributed among these distances:
191 114 0.62
192 4 0.02
193 62 0.34
194 3 0.02
ACGTcount: A:0.39, C:0.12, G:0.11, T:0.39
Consensus pattern (192 bp):
TATGAATGAGATTATGCATAACGTCACTTTATAATTGATACTCAATGACAACTAGTTACATCACT
AAATTATATAAAATTTTGTTATTAATAATTCACATCGTCACAAATAATACAATAAAATCAACCTA
TATGTGACGAAAGAGATATTGTCAAATTTTCAGTGACATAATATAACATTACCTAATAGTAT
Found at i:342317 original size:16 final size:16
Alignment explanation
Indices: 342296--342330 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
342286 TAGCAAGTCT
*
342296 TAACTAATGAAATAAA
1 TAACTAAGGAAATAAA
342312 TAACTAAGGAAATAAA
1 TAACTAAGGAAATAAA
342328 TAA
1 TAA
342331 TTTACCATGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.63, C:0.06, G:0.09, T:0.23
Consensus pattern (16 bp):
TAACTAAGGAAATAAA
Found at i:351354 original size:38 final size:34
Alignment explanation
Indices: 351278--351378 Score: 94
Period size: 36 Copynumber: 2.8 Consensus size: 34
351268 TCTTAAAAAT
* * *
351278 AAATTTTGTCTAGCTTGACACAATTTCTATTGAA
1 AAATTTTGTCTCGCTTGAGACAATTTCTATCGAA
* *
351312 AAATTTTTTGTCTCGCTTGAGACAATTTTTCTCGAAA
1 AAA--TTTTGTCTCGCTTGAGACAATTTCTATCG-AA
* *
351349 CAAATTTAGTCTCGCTTGAGAAAAATTTCT
1 -AAATTTTGTCTCGCTTGAG-ACAATTTCT
351379 CTTGAGATGC
Statistics
Matches: 54, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
34 3 0.06
36 39 0.72
37 9 0.17
38 3 0.06
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.41
Consensus pattern (34 bp):
AAATTTTGTCTCGCTTGAGACAATTTCTATCGAA
Found at i:351612 original size:103 final size:103
Alignment explanation
Indices: 351489--351760 Score: 318
Period size: 103 Copynumber: 2.6 Consensus size: 103
351479 TTAAGACACG
*
351489 AACATTTGAGATTATTTTTCTTAAAAACAAATTTTGTCTCACTTGAGACATTTTGCCC-TAGAAA
1 AACATTTGAGATT-TTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACATTTT-CCCTTA-AAA
*
351553 CACAAATTCT-GAAATTGTTTCACTTGAAA-AACAATTAAT-
63 CACAAATTCTGGAAATGGTTTCACTTGAAACAA-AATTAATA
** * *
351592 AACATTTGAGATTGTTTTTCTTAAAAACAAATTTCATCCCGGTTGAGACAATTTTCCCTTAAAAC
1 AACATTTGAGATT-TTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGAC-ATTTTCCCTTAAAAC
* *
351657 ACAAATTTTGGAAATGGTTTCACTTGAAACAAAATTGATA
64 ACAAATTCTGGAAATGGTTTCACTTGAAACAAAATTAATA
* * ** * * * *
351697 AACCTTTGAGATTATTTTCTTTGAAACAAATTTTGTCTTGCTTGAGACAGTTTCTCTTGAAACA
1 AACATTTGAGATTTTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTAAAACA
351761 AAGTTTTGTC
Statistics
Matches: 143, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
103 71 0.50
104 58 0.41
105 14 0.10
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (103 bp):
AACATTTGAGATTTTTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTAAAACAC
AAATTCTGGAAATGGTTTCACTTGAAACAAAATTAATA
Found at i:351742 original size:36 final size:37
Alignment explanation
Indices: 351712--351797 Score: 142
Period size: 37 Copynumber: 2.4 Consensus size: 37
351702 TTGAGATTAT
351712 TTTCT-TTGAAACAAA-TTTTGTCT-TGCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCT-CTTGAGACAG
351747 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
351784 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
351798 TAAACAATTG
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
35 5 0.10
36 10 0.21
37 32 0.67
38 1 0.02
ACGTcount: A:0.26, C:0.17, G:0.15, T:0.42
Consensus pattern (37 bp):
TTTCTCTTGAAACAAAGTTTTGTCTCTCTTGAGACAG
Found at i:351742 original size:104 final size:103
Alignment explanation
Indices: 351489--351745 Score: 315
Period size: 104 Copynumber: 2.5 Consensus size: 103
351479 TTAAGACACG
*
351489 AACATTTGAGATTATTTTTCTTAAAAACAAATTTTGTCTCACTTGAGAC-ATTTTGCCCTAGAAA
1 AACATTTGAGATTA-TTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAATTTTGCCCTAGAAA
*
351553 CACAAATTCTGAAATTGTTTCACTTGAAAAACAATTAAT
65 CACAAATTCTGAAATGGTTTCACTTGAAAAACAATTAAT
* ** * *
351592 AACATTTGAGATTGTTTTTCTTAAAAACAAATTTCATCCCGGTTGAGACAATTTT-CCCTTA-AA
1 AACATTTGAGATT-ATTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAATTTTGCCC-TAGAA
* *
351655 ACACAAATTTTGGAAATGGTTTCACTTGAAACAA-AATTGAT
64 ACACAAATTCT-GAAATGGTTTCACTTGAAA-AACAATTAAT
* ** *
351696 AAACCTTTGAGATTATTTTCTTTGAAACAAATTTTGTCTTGCTTGAGACA
1 -AACATTTGAGATTATTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACA
351746 GTTTCTCTTG
Statistics
Matches: 130, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
103 57 0.44
104 59 0.45
105 14 0.11
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (103 bp):
AACATTTGAGATTATTTTCTTAAAAACAAATTTTGTCTCGCTTGAGACAATTTTGCCCTAGAAAC
ACAAATTCTGAAATGGTTTCACTTGAAAAACAATTAAT
Found at i:352132 original size:140 final size:138
Alignment explanation
Indices: 351877--352150 Score: 377
Period size: 140 Copynumber: 2.0 Consensus size: 138
351867 CCTTAAGACA
* *
351877 GCTAGACATCCTCATCACGTAGGAACAATGTTGTCCACCAACCAGATCTCCTCATCACGTAGGAG
1 GCTAGACATCCTCATCACGTAGGAAAAATGTTATCCACCAACCAGATCTCCTCATCACGTAGGAG
* * *
351942 CAACATCACCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCGTGTTGTTTCCCAAATTATC
66 CAACATCACCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCATGTTGTCT-CCAAATT-TA
352007 CCTAAAGAAG
129 CCTAAAGAAG
* * * * *
352017 GCTAGACGTCCTCATCACGTAGGAAAAATGTTATCCACCGACCATATCTCTTCATCACGTATGAG
1 GCTAGACATCCTCATCACGTAGGAAAAATGTTATCCACCAACCAGATCTCCTCATCACGTAGGAG
* * * * * * *
352082 CAACGTCACCTTTAGATAATCATATTTCCTCATCATGTAGGAACCATGTTGTCTCCAAATTTACC
66 CAACATCACCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCATGTTGTCTCCAAATTTACC
352147 TAAA
131 TAAA
352151 AATGACCAGA
Statistics
Matches: 117, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
138 7 0.06
139 7 0.06
140 103 0.88
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (138 bp):
GCTAGACATCCTCATCACGTAGGAAAAATGTTATCCACCAACCAGATCTCCTCATCACGTAGGAG
CAACATCACCCTCAGATAACCAGACTTCCTCATCACGTAGGAACCATGTTGTCTCCAAATTTACC
TAAAGAAG
Found at i:352924 original size:18 final size:18
Alignment explanation
Indices: 352901--352941 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
352891 TCAACAGTGG
352901 GAAAATAGATAAAAATTA
1 GAAAATAGATAAAAATTA
352919 GAAAATAGATAAAAATTA
1 GAAAATAGATAAAAATTA
352937 GAAAA
1 GAAAA
352942 AACCCCAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.68, C:0.00, G:0.12, T:0.20
Consensus pattern (18 bp):
GAAAATAGATAAAAATTA
Found at i:355512 original size:5 final size:5
Alignment explanation
Indices: 355492--355582 Score: 61
Period size: 5 Copynumber: 19.4 Consensus size: 5
355482 CCTTCCCTTC
* * * *
355492 ATTTT GTTTT GTTTT ATTTT A-TTT ATTTT A--TT ATTTC GTTTT -TTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT
* * *
355538 A--TT ATTTT A-TTT ATTTT AATTT GTTTT CTTTTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT -ATTTT ATTTT ATTTT AT
355583 GTCTAGCCAT
Statistics
Matches: 68, Mismatches: 10, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
3 6 0.09
4 12 0.18
5 46 0.68
6 4 0.06
ACGTcount: A:0.16, C:0.02, G:0.04, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:355518 original size:9 final size:9
Alignment explanation
Indices: 355504--355582 Score: 67
Period size: 9 Copynumber: 9.1 Consensus size: 9
355494 TTTGTTTTGT
355504 TTTATTTTA
1 TTTATTTTA
355513 TTTATTTTA
1 TTTATTTTA
**
355522 -TTATTTCG
1 TTTATTTTA
*
355530 TTTTTTTTA
1 TTTATTTTA
355539 -TTATTTTA
1 TTTATTTTA
355547 TTTATTTTAA
1 TTTATTTT-A
* *
355557 TTTGTTTTC
1 TTTATTTTA
*
355566 TTT-TTAT-
1 TTTATTTTA
355573 TTTATTTTA
1 TTTATTTTA
355582 T
1 T
355583 GTCTAGCCAT
Statistics
Matches: 55, Mismatches: 10, Indels: 10
0.73 0.13 0.13
Matches are distributed among these distances:
7 3 0.05
8 19 0.35
9 25 0.45
10 8 0.15
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:355527 original size:17 final size:17
Alignment explanation
Indices: 355505--355555 Score: 75
Period size: 17 Copynumber: 3.0 Consensus size: 17
355495 TTGTTTTGTT
355505 TTATTTTATTTATTTTA
1 TTATTTTATTTATTTTA
** *
355522 TTATTTCGTTTTTTTTA
1 TTATTTTATTTATTTTA
355539 TTATTTTATTTATTTTA
1 TTATTTTATTTATTTTA
355556 ATTTGTTTTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.20, C:0.02, G:0.02, T:0.76
Consensus pattern (17 bp):
TTATTTTATTTATTTTA
Found at i:355538 original size:22 final size:22
Alignment explanation
Indices: 355508--355549 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
355498 TTTTGTTTTA
355508 TTTTATTTATT-TTATTATTTCG
1 TTTTATTTATTATT-TTATTTCG
*
355530 TTTTTTTTATTATTTTATTT
1 TTTTATTTATTATTTTATTT
355550 ATTTTAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (22 bp):
TTTTATTTATTATTTTATTTCG
Found at i:366089 original size:8 final size:7
Alignment explanation
Indices: 366047--366081 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
366037 TGAAAAAATT
366047 GAAAAAGA
1 GAAAAA-A
366055 GAAAAAA
1 GAAAAAA
366062 GAACAAAA
1 GAA-AAAA
366070 GAAAAAA
1 GAAAAAA
366077 GAAAA
1 GAAAA
366082 GAACAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 13 0.50
8 13 0.50
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (7 bp):
GAAAAAA
Done.