Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008255.1 Hibiscus syriacus cultivar Beakdansim tig00110908_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: 300600
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 2 of 3
Found at i:143546 original size:20 final size:22
Alignment explanation
Indices: 143501--143558 Score: 75
Period size: 20 Copynumber: 2.6 Consensus size: 22
143491 GCATGGGTAG
143501 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TGTT-AAGAA
143525 TGCATCGATGCACTG-T-AGAA
1 TGCATCGATGCACTGTTAAGAA
*
143545 TGTATCGATGCACT
1 TGCATCGATGCACT
143559 TCAAGAGGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 17 0.52
22 1 0.03
23 2 0.06
24 13 0.39
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCACTGTTAAGAA
Found at i:144278 original size:25 final size:27
Alignment explanation
Indices: 144237--144288 Score: 65
Period size: 25 Copynumber: 2.0 Consensus size: 27
144227 ACTATCAACT
*
144237 TATATGAACATGTGAT-A-TGAAAATG
1 TATATGAACATGAGATAAGTGAAAATG
144262 TATAGTGAA-ATGAGATAAGTGAAAATG
1 TATA-TGAACATGAGATAAGTGAAAATG
144289 CCCATGTTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 10 0.43
26 5 0.22
27 8 0.35
ACGTcount: A:0.46, C:0.02, G:0.23, T:0.29
Consensus pattern (27 bp):
TATATGAACATGAGATAAGTGAAAATG
Found at i:151394 original size:23 final size:23
Alignment explanation
Indices: 151342--151394 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
151332 CGATTCCCTA
*
151342 AAGGAGGGAATCAGTTCCCATTC
1 AAGGGGGGAATCAGTTCCCATTC
* * * *
151365 AAAGGGGGAATCGGTTCCCCTTT
1 AAGGGGGGAATCAGTTCCCATTC
151388 AAGGGGG
1 AAGGGGG
151395 TATTGATTCC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.34, T:0.21
Consensus pattern (23 bp):
AAGGGGGGAATCAGTTCCCATTC
Found at i:155487 original size:117 final size:117
Alignment explanation
Indices: 155272--155487 Score: 276
Period size: 117 Copynumber: 1.8 Consensus size: 117
155262 AAATTGAATT
*
155272 TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAAGATTTCATTT
1 TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCATTT
* *
155337 TGATTTTCAAAATCCATTTTCGTTTCTAGAAGAAGTTTGTTTAATTTGAAAA
66 TGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTGAAAA
* * * * *
155389 TTTCTTTTTCAA-ATTTTTCAGATTTTATTTTTGAAAGCTCTAACTCATT-TCTCAACATTTCAT
1 TTTCTTTTTCAATA-CTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCT-TCAACATTTCAT
* * **
155452 TTTGATTTTCCAAGTCTGTTTTAGCTTTC-AAAAGAA
64 TTTGATTTTCAAAATCCATTTTAG-TTTCTAAAAGAA
155488 TATCATTTTT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
116 2 0.02
117 78 0.93
118 4 0.05
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.49
Consensus pattern (117 bp):
TTTCTTTTTCAATACTTTCAAATTTCATTTTTGAAAGCTCTAAATCCTTCTTCAACATTTCATTT
TGATTTTCAAAATCCATTTTAGTTTCTAAAAGAAGTTTGTTTAATTTGAAAA
Found at i:161222 original size:18 final size:19
Alignment explanation
Indices: 161194--161248 Score: 60
Period size: 18 Copynumber: 2.9 Consensus size: 19
161184 AATCACTGTT
161194 ATCTGTATTTTTTATTTTTC
1 ATCT-TATTTTTTATTTTTC
* **
161214 AT-TTATTTTTTATCTAAC
1 ATCTTATTTTTTATTTTTC
161232 ATCTT-TTTTTTATTTTT
1 ATCTTATTTTTTATTTTT
161249 TAATTAATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
18 23 0.82
19 3 0.11
20 2 0.07
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.71
Consensus pattern (19 bp):
ATCTTATTTTTTATTTTTC
Found at i:162194 original size:38 final size:39
Alignment explanation
Indices: 162141--162218 Score: 131
Period size: 38 Copynumber: 2.0 Consensus size: 39
162131 AACTCGTTAT
*
162141 GCCGGCGTGATGAGTTCCATGAAATAT-TTTTTTAATGG
1 GCCGGCGTGACGAGTTCCATGAAATATATTTTTTAATGG
*
162179 GCCGGCGTGACGAGTTCCATGAGATATATTTTTTAATGG
1 GCCGGCGTGACGAGTTCCATGAAATATATTTTTTAATGG
162218 G
1 G
162219 TTGTGTCACG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
38 25 0.68
39 12 0.32
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (39 bp):
GCCGGCGTGACGAGTTCCATGAAATATATTTTTTAATGG
Found at i:168468 original size:3 final size:3
Alignment explanation
Indices: 168460--168569 Score: 220
Period size: 3 Copynumber: 36.7 Consensus size: 3
168450 TAATCCCATT
168460 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
168508 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
168556 GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GA
168570 GGGTTAACGG
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 107 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:169277 original size:4 final size:4
Alignment explanation
Indices: 169270--169298 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
169260 ACTTAATTAA
169270 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
169299 CAGTTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:170519 original size:20 final size:20
Alignment explanation
Indices: 170494--170545 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
170484 ACGCGATATC
*
170494 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGGTAAAAAG
*
170514 AAAATCGCAACGGTCAAAAG
1 AAAATCGCAACGGTAAAAAG
170534 AAAATCGCAACG
1 AAAATCGCAACG
170546 CGAGCTTCCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.52, C:0.19, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACGGTAAAAAG
Found at i:170605 original size:20 final size:20
Alignment explanation
Indices: 170580--170668 Score: 178
Period size: 20 Copynumber: 4.5 Consensus size: 20
170570 TTTAGAAGAA
170580 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
170600 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
170620 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
170640 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGATAG
170660 AATCGCAAT
1 AATCGCAAT
170669 AAAATCGCAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.25
Consensus pattern (20 bp):
AATCGCAATGCGATTGATAG
Found at i:170776 original size:6 final size:6
Alignment explanation
Indices: 170765--170839 Score: 129
Period size: 6 Copynumber: 13.0 Consensus size: 6
170755 GAAGACACGT
170765 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC ACGACC
170813 ACGACC ACGACC -CGACC -CGACC -CGACC
1 ACGACC ACGACC ACGACC ACGACC ACGACC
170840 CGAGACGAGA
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.22
6 54 0.78
ACGTcount: A:0.31, C:0.52, G:0.17, T:0.00
Consensus pattern (6 bp):
ACGACC
Found at i:171534 original size:5 final size:5
Alignment explanation
Indices: 171526--171577 Score: 68
Period size: 5 Copynumber: 9.6 Consensus size: 5
171516 CCGTCTCGTC
171526 TCGGG TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TCGTGG TCGTGG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG-GG
171575 TCG
1 TCG
171578 TGGTAATACG
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 23 0.50
6 23 0.50
ACGTcount: A:0.00, C:0.19, G:0.54, T:0.27
Consensus pattern (5 bp):
TCGGG
Found at i:171560 original size:6 final size:6
Alignment explanation
Indices: 171529--171581 Score: 78
Period size: 6 Copynumber: 9.5 Consensus size: 6
171519 TCTCGTCTCG
171529 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
171573 GGTCGT GGT
1 GGTCGT GGT
171582 AATACGTGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 20 0.43
6 27 0.57
ACGTcount: A:0.00, C:0.17, G:0.55, T:0.28
Consensus pattern (6 bp):
GGTCGT
Found at i:172867 original size:81 final size:81
Alignment explanation
Indices: 172780--172928 Score: 192
Period size: 81 Copynumber: 1.8 Consensus size: 81
172770 TAGATCCTCA
** * * * * **
172780 TTACTTACACAT-TTAATTAATTTGATCCTGATTTTAATTTAATTTAATAAATTTAATATTCAAA
1 TTACTTACA-ATCTTAACCAATTTGATCCTAATTTCAATTTAAATTAATAAATCTAATACCCAAA
172844 TCAGGTGGTGACACTCG
65 TCAGGTGGTGACACTCG
* *
172861 TTACTTACATTCTTAACCAATTTGATCTTAATTTCAATTTAAATTAATAAATCTAATACCCAAAT
1 TTACTTACAATCTTAACCAATTTGATCCTAATTTCAATTTAAATTAATAAATCTAATACCCAAAT
172926 CAG
66 CAG
172929 ACAATGACAT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
80 1 0.02
81 56 0.98
ACGTcount: A:0.37, C:0.15, G:0.07, T:0.42
Consensus pattern (81 bp):
TTACTTACAATCTTAACCAATTTGATCCTAATTTCAATTTAAATTAATAAATCTAATACCCAAAT
CAGGTGGTGACACTCG
Found at i:173342 original size:41 final size:42
Alignment explanation
Indices: 173247--173363 Score: 116
Period size: 40 Copynumber: 2.8 Consensus size: 42
173237 TGCGATCGAT
* * *
173247 AATTCGCAACGCGATCTCCG-GTATCGCAAAT-C-AGTTTCCA
1 AATTCGCAACGCGATTTCCGACTATCGC-AATGCGATTTTCCA
* *
173287 AATTCGCAACGCGA-TTCTGACTATCGCATTGCGATTTTCCA
1 AATTCGCAACGCGATTTCCGACTATCGCAATGCGATTTTCCA
***
173328 AATTCGCGTTGCGATTTTCCGACTATCGCAATGCGA
1 AATTCGCAACGCGA-TTTCCGACTATCGCAATGCGA
173364 ATATGTAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
39 5 0.08
40 21 0.34
41 18 0.29
43 18 0.29
ACGTcount: A:0.25, C:0.27, G:0.19, T:0.29
Consensus pattern (42 bp):
AATTCGCAACGCGATTTCCGACTATCGCAATGCGATTTTCCA
Found at i:173362 original size:22 final size:22
Alignment explanation
Indices: 173305--173363 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
173295 ACGCGATTCT
173305 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
173327 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
173348 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
173364 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:173394 original size:20 final size:20
Alignment explanation
Indices: 173352--173418 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
173342 TTTTCCGACT
173352 ATCGCAATGCGAATATGTA-A
1 ATCGCAATGCGAATATG-ACA
*
173372 ATCGCAATGCGAGTATGACA
1 ATCGCAATGCGAATATGACA
* * * * *
173392 ATCGAAACGCGATTCTGACT
1 ATCGCAATGCGAATATGACA
173412 ATCGCAA
1 ATCGCAA
173419 CGAGATTTAT
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.03
20 38 0.97
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAATATGACA
Found at i:173640 original size:22 final size:22
Alignment explanation
Indices: 173615--173657 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
173605 GGCGACATCC
173615 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
*
173637 GTCCCCATCTCCGGCGAAATC
1 GTCCCCATCTCCGACGAAATC
173658 CGTCTATCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.42, G:0.16, T:0.19
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:174069 original size:19 final size:20
Alignment explanation
Indices: 174047--174138 Score: 98
Period size: 20 Copynumber: 4.7 Consensus size: 20
174037 AATCGCAATA
*
174047 CGATTTT-AGTTTCGCATTG
1 CGATTTTCAGTTTCGCGTTG
174066 CGATTTTCA-TTTCGCGTTG
1 CGATTTTCAGTTTCGCGTTG
** **
174085 CGATAGTCAAATTCGCGTTG
1 CGATTTTCAGTTTCGCGTTG
* *
174105 CGATTTTCATTTTCGTGTTG
1 CGATTTTCAGTTTCGCGTTG
*
174125 CGATTTTAAGTTTC
1 CGATTTTCAGTTTC
174139 AGAAACTATT
Statistics
Matches: 60, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
19 23 0.38
20 37 0.62
ACGTcount: A:0.16, C:0.17, G:0.21, T:0.46
Consensus pattern (20 bp):
CGATTTTCAGTTTCGCGTTG
Found at i:176068 original size:20 final size:20
Alignment explanation
Indices: 176039--176104 Score: 105
Period size: 20 Copynumber: 3.3 Consensus size: 20
176029 TAGTTTACTT
*
176039 TCGCATCGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
176059 TCGCAACGCGAAAATGACTA
1 TCGCAACGCGAAAATGACTA
**
176079 TCGCAACGCGAATTTGACTA
1 TCGCAACGCGAAAATGACTA
176099 TCGCAA
1 TCGCAA
176105 TGAAAGAATC
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.20
Consensus pattern (20 bp):
TCGCAACGCGAAAATGACTA
Found at i:176193 original size:20 final size:20
Alignment explanation
Indices: 176170--176224 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
176160 TTAAATTTGA
*
176170 GTTGCGATAGTCATTTTCGC
1 GTTGCGATAGTCATTTTCAC
*
176190 GTTGCGATAGTCATTTTCAT
1 GTTGCGATAGTCATTTTCAC
176210 GTTGCGATAGTCATT
1 GTTGCGATAGTCATT
176225 CGTGTTGCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCAC
Found at i:176767 original size:18 final size:20
Alignment explanation
Indices: 176727--176768 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
176717 CTCACTTGTC
176727 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-CTCCCCT
176748 ATCGTTCAAGAGG-T-CCCT
1 ATCGTTCAAGAGGCTCCCCT
176766 ATC
1 ATC
176769 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 7 0.33
19 1 0.05
21 13 0.62
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.26
Consensus pattern (20 bp):
ATCGTTCAAGAGGCTCCCCT
Found at i:178251 original size:14 final size:14
Alignment explanation
Indices: 178214--178275 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
178204 TTGCTTGTTT
*
178214 AATTGATTTATAAA
1 AATTGATTTGTAAA
178228 AATTGATTTGTAAA
1 AATTGATTTGTAAA
* *
178242 AGTTGATTTGTTTAA
1 AATTGATTTG-TAAA
* *
178257 TATTGATGTGTAAA
1 AATTGATTTGTAAA
178271 TAATT
1 -AATT
178276 TTTATTTGTG
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 13 0.34
ACGTcount: A:0.39, C:0.00, G:0.15, T:0.47
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:178399 original size:20 final size:20
Alignment explanation
Indices: 178374--178426 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
178364 AGGTACACTT
* *
178374 TCGCAACGCTAAACTCAAAA
1 TCGCAACGCGAAACACAAAA
* *
178394 TCGCAATGCGAAAGACAAAA
1 TCGCAACGCGAAACACAAAA
*
178414 TCACAACGCGAAA
1 TCGCAACGCGAAA
178427 GTCAATTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.47, C:0.26, G:0.15, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAACACAAAA
Found at i:178495 original size:20 final size:20
Alignment explanation
Indices: 178470--178753 Score: 272
Period size: 20 Copynumber: 14.8 Consensus size: 20
178460 GCGATTTACT
* *
178470 CGTTGCGATAGTCAAATACC
1 CGTTGCGATAGTCAAATTCG
**
178490 CGTTGCGATAACCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
178510 CGTTACGATACTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
178530 CATTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
178550 CGTTGCGAT--T----TTCT
1 CGTTGCGATAGTCAAATTCG
*
178564 CGTTGCGATAGTCAAA-TAG
1 CGTTGCGATAGTCAAATTCG
*
178583 CCGTTGCGATAGTCAAATTTG
1 -CGTTGCGATAGTCAAATTCG
*
178604 CGTTGCGATAGACAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
178624 CGTTGCGAT--T----TTTG
1 CGTTGCGATAGTCAAATTCG
* *
178638 CGTTGCAATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
178658 TGTTGCGATAGTCATATTCG
1 CGTTGCGATAGTCAAATTCG
* *
178678 TGTTGCGATAGTCAAATTTG
1 CGTTGCGATAGTCAAATTCG
*
178698 CGTTGCGATAATCAAATTCG
1 CGTTGCGATAGTCAAATTCG
178718 CGTTGCGAT-GTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
*
178737 CGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAAT
178754 GAATGTGTAA
Statistics
Matches: 217, Mismatches: 32, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
14 23 0.11
16 2 0.01
18 1 0.00
19 19 0.09
20 170 0.78
21 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:178566 original size:94 final size:94
Alignment explanation
Indices: 178442--178624 Score: 267
Period size: 94 Copynumber: 1.9 Consensus size: 94
178432 TTCGCGTTAC
* *
178442 GATAGTCTAATACGCTTTGCGATTTACTCGTTGCGATAGTCAAATACCCGTTGCGATAACCAAAT
1 GATAGTCAAATACGCGTTGCGATTTACTCGTTGCGATAGTCAAATACCCGTTGCGATAACCAAAT
*
178507 TCGCGTTACGATACTCAAATTCGCATTGT
66 TCGCGTTACGATACACAAATTCGCATTGT
* * * **
178536 GATAGTCAAATTCGCGTTGCGATTTTCTCGTTGCGATAGTCAAATAGCCGTTGCGATAGTCAAAT
1 GATAGTCAAATACGCGTTGCGATTTACTCGTTGCGATAGTCAAATACCCGTTGCGATAACCAAAT
* * *
178601 TTGCGTTGCGATAGACAAATTCGC
66 TCGCGTTACGATACACAAATTCGC
178625 GTTGCGATTT
Statistics
Matches: 78, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
94 78 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.32
Consensus pattern (94 bp):
GATAGTCAAATACGCGTTGCGATTTACTCGTTGCGATAGTCAAATACCCGTTGCGATAACCAAAT
TCGCGTTACGATACACAAATTCGCATTGT
Found at i:178568 original size:74 final size:74
Alignment explanation
Indices: 178490--178753 Score: 282
Period size: 74 Copynumber: 3.5 Consensus size: 74
178480 GTCAAATACC
** * * * *
178490 CGTTGCGATAACCAAATTCGCGTTACGATACTCAAATTCGCATTGTGATAGTCAAATTCGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
178555 CGATTTTCT-
66 CGATTTT-TG
* * *
178564 CGTTGCGATAGTCAAA-TAGCCGTTGCGATAGTCAAATTTGCGTTGCGATAGACAAATTCGCGTT
1 CGTTGCGATAGTCAAATTCG-CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTT
178628 GCGATTTTTG
65 GCGATTTTTG
* * * * * *
178638 CGTTGCAATAGTCATATTCGTGTTGCGATAGTCATATTCGTGTTGCGATAGTCAAATTTGCGTTG
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
*
178703 CGATAATCAAATTCG
66 CGAT--T----TTTG
*
178718 CGTTGCGAT-GTCAAATTCGCGTTGCGATATTCAAAT
1 CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAAT
178754 GAATGTGTAA
Statistics
Matches: 157, Mismatches: 24, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
73 3 0.02
74 117 0.75
75 2 0.01
76 1 0.01
79 23 0.15
80 11 0.07
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (74 bp):
CGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTGCGATAGTCAAATTCGCGTTG
CGATTTTTG
Found at i:178979 original size:140 final size:140
Alignment explanation
Indices: 178727--178993 Score: 507
Period size: 140 Copynumber: 1.9 Consensus size: 140
178717 GCGTTGCGAT
* * *
178727 GTCAAATTCGCGTTGCGATATTCAAATGAATGTGTAATAAGTGATAACAACTGAACATATCATAT
1 GTCAAATTCGCGTTGCGATATTCAAAAGAATGTGTAATAAGTGATAACAACTGAACAGATCATAG
178792 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAAT
66 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAAT
178857 ACACATAATA
131 ACACATAATA
178867 GTCAAATTCGCGTTGCGATATTCAAAAGAATGTGTAATAAGTGATAACAACTGAACAGATCATAG
1 GTCAAATTCGCGTTGCGATATTCAAAAGAATGTGTAATAAGTGATAACAACTGAACAGATCATAG
178932 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
66 CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAA
178994 TACAACGTTT
Statistics
Matches: 124, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.28
Consensus pattern (140 bp):
GTCAAATTCGCGTTGCGATATTCAAAAGAATGTGTAATAAGTGATAACAACTGAACAGATCATAG
CAATGTTCAAACTCAAGTTACTAATACATGCCTAACTGAAAATGTTAAAAGTTTACACATAAAAT
ACACATAATA
Found at i:179076 original size:18 final size:18
Alignment explanation
Indices: 179053--179087 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
179043 AAGCCGGTTG
*
179053 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
179071 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
179088 GCCTTTTTCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:180261 original size:20 final size:21
Alignment explanation
Indices: 180221--180263 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
180211 TGAATCAGAG
*
180221 GTTTCAGATTTTCCAAACCCC
1 GTTTCAGATTTGCCAAACCCC
180242 GTTTCAGATTTGCC-AACCCC
1 GTTTCAGATTTGCCAAACCCC
180262 GT
1 GT
180264 AAGCTATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.33, G:0.14, T:0.33
Consensus pattern (21 bp):
GTTTCAGATTTGCCAAACCCC
Found at i:181164 original size:14 final size:14
Alignment explanation
Indices: 181145--181181 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
181135 TCCCGTGGTA
181145 TTTTCTTCGGGGAC
1 TTTTCTTCGGGGAC
*
181159 TTTTCTTCGGGGAT
1 TTTTCTTCGGGGAC
181173 TTCTTCTTC
1 TT-TTCTTC
181182 TTATTTTTCT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.05, C:0.22, G:0.22, T:0.51
Consensus pattern (14 bp):
TTTTCTTCGGGGAC
Found at i:182330 original size:20 final size:20
Alignment explanation
Indices: 182244--182330 Score: 102
Period size: 20 Copynumber: 4.3 Consensus size: 20
182234 AAATTCAGTG
* *
182244 TTGCGACAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
* * *
182264 TTGCGACAGTTAGAATCGCG
1 TTGCGATAGTCAGAATCGCA
* *
182284 TTGCGATAGTTAGAATCACA
1 TTGCGATAGTCAGAATCGCA
*
182304 TTGCGATAGTCATAATCGCA
1 TTGCGATAGTCAGAATCGCA
182324 TTGCGAT
1 TTGCGAT
182331 TTACATATTC
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 60 1.00
ACGTcount: A:0.28, C:0.20, G:0.25, T:0.28
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCA
Found at i:182330 original size:40 final size:40
Alignment explanation
Indices: 182244--182374 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 40
182234 AAATTCAGTG
* * * * * * *
182244 TTGCGACAGTCAGAATCGCGTTGCGACAGTTAGAATCGCG
1 TTGCGATAGTTAGAATCGCATTGCGATAGTCATAATCGCA
*
182284 TTGCGATAGTTAGAATCACATTGCGATAGTCATAATCGCA
1 TTGCGATAGTTAGAATCGCATTGCGATAGTCATAATCGCA
* * *
182324 TTGCGAT--TTACATATTCGCATTGCGAT-TTACATATTCGCA
1 TTGCGATAGTTAGA-A-TCGCATTGCGATAGT-CATAATCGCA
182364 TTGCGATAGTT
1 TTGCGATAGTT
182375 GAAAAATTAC
Statistics
Matches: 74, Mismatches: 12, Indels: 8
0.79 0.13 0.09
Matches are distributed among these distances:
38 4 0.05
39 2 0.03
40 66 0.89
42 2 0.03
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.32
Consensus pattern (40 bp):
TTGCGATAGTTAGAATCGCATTGCGATAGTCATAATCGCA
Found at i:182337 original size:20 final size:20
Alignment explanation
Indices: 182314--182370 Score: 105
Period size: 20 Copynumber: 2.9 Consensus size: 20
182304 TTGCGATAGT
*
182314 CATAATCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
182334 CATATTCGCATTGCGATTTA
1 CATATTCGCATTGCGATTTA
182354 CATATTCGCATTGCGAT
1 CATATTCGCATTGCGAT
182371 AGTTGAAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (20 bp):
CATATTCGCATTGCGATTTA
Found at i:190421 original size:19 final size:22
Alignment explanation
Indices: 190368--190423 Score: 64
Period size: 22 Copynumber: 2.7 Consensus size: 22
190358 GGTACTCTTA
*
190368 CTATAGTACCGATACTACCCAC
1 CTATGGTACCGATACTACCCAC
* *
190390 CTATGGTATCGATGCT-CCC-C
1 CTATGGTACCGATACTACCCAC
190410 CTA-GGTACCGATAC
1 CTATGGTACCGATAC
190424 AATTTTTACA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
19 9 0.31
20 4 0.14
21 3 0.10
22 13 0.45
ACGTcount: A:0.25, C:0.34, G:0.16, T:0.25
Consensus pattern (22 bp):
CTATGGTACCGATACTACCCAC
Found at i:195199 original size:16 final size:19
Alignment explanation
Indices: 195151--195201 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
195141 AAAATGCTAA
195151 AGTGTACCGATACACTCTG
1 AGTGTACCGATACACTCTG
195170 TAGTGTATCC-ATACA-T-TG
1 -AGTGTA-CCGATACACTCTG
195188 -GTGTACCGATACAC
1 AGTGTACCGATACAC
195202 CCTACAGTGT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.07
16 10 0.36
18 2 0.07
19 1 0.04
20 11 0.39
21 2 0.07
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (19 bp):
AGTGTACCGATACACTCTG
Found at i:195319 original size:20 final size:18
Alignment explanation
Indices: 195270--195320 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 18
195260 ATACACACGA
195270 TAGTGTATCCATACATTG
1 TAGTGTATCCATACATTG
195288 --GTGTA-CCGATACATTTTG
1 TAGTGTATCC-ATACA--TTG
195306 TAGTGTATCCATACA
1 TAGTGTATCCATACA
195321 CCCTGGCTGC
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
15 2 0.07
16 10 0.37
18 3 0.11
20 10 0.37
21 2 0.07
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (18 bp):
TAGTGTATCCATACATTG
Found at i:195383 original size:22 final size:22
Alignment explanation
Indices: 195355--195397 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
195345 TTTGAATTTA
* *
195355 ATGAAGGTGTATCGATACCCCT
1 ATGAAGGGGTACCGATACCCCT
195377 ATGAAGGGGTACCGATACCCC
1 ATGAAGGGGTACCGATACCCC
195398 ATGTTATGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.21
Consensus pattern (22 bp):
ATGAAGGGGTACCGATACCCCT
Found at i:196856 original size:17 final size:18
Alignment explanation
Indices: 196821--196856 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
196811 TGAGGTGGAT
196821 GAAGATGATGATGAACAA
1 GAAGATGATGATGAACAA
*
196839 GAAGATGA-GATGATCAA
1 GAAGATGATGATGAACAA
196856 G
1 G
196857 CTTTTAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.47, C:0.06, G:0.31, T:0.17
Consensus pattern (18 bp):
GAAGATGATGATGAACAA
Found at i:198132 original size:22 final size:22
Alignment explanation
Indices: 198104--198148 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
198094 TCATTGAATT
*
198104 TCATGTATTACTAACATGTTTG
1 TCATGTACTACTAACATGTTTG
198126 TCATGTACTACTAACATGTTTG
1 TCATGTACTACTAACATGTTTG
198148 T
1 T
198149 TATTCTTTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (22 bp):
TCATGTACTACTAACATGTTTG
Found at i:198694 original size:16 final size:17
Alignment explanation
Indices: 198646--198696 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 17
198636 AAAATGCTGA
198646 AGTGTACCGATACACTCTG
1 AGTGTACCGATACA--CTG
198665 CAGTGTATCC-ATACACTG
1 -AGTGTA-CCGATACACTG
198683 -GTGTACCGATACAC
1 AGTGTACCGATACAC
198697 CCTGCAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.07
16 11 0.38
18 3 0.10
20 11 0.38
21 2 0.07
ACGTcount: A:0.27, C:0.27, G:0.20, T:0.25
Consensus pattern (17 bp):
AGTGTACCGATACACTG
Found at i:198714 original size:20 final size:20
Alignment explanation
Indices: 198646--198707 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
198636 AAAATGCTGA
*
198646 AGTGTACCGATACACTCTGC
1 AGTGTACCGATACACCCTGC
198666 AGTGTATCC-ATACA--CTG-
1 AGTGTA-CCGATACACCCTGC
198683 -GTGTACCGATACACCCTGC
1 AGTGTACCGATACACCCTGC
198702 AGTGTA
1 AGTGTA
198708 TCCATACCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 12
0.75 0.00 0.25
Matches are distributed among these distances:
15 2 0.06
16 10 0.28
18 6 0.17
20 16 0.44
21 2 0.06
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (20 bp):
AGTGTACCGATACACCCTGC
Found at i:198771 original size:20 final size:19
Alignment explanation
Indices: 198746--198807 Score: 60
Period size: 20 Copynumber: 3.3 Consensus size: 19
198736 AAATGTAATT
198746 AGTGTACCGATACACCCTGC
1 AGTGTACCGATACA-CCTGC
198766 AGTGTATCC-ATACA-CTG-
1 AGTGTA-CCGATACACCTGC
*
198783 -GTATACCGATACACTCTGC
1 AGTGTACCGATACAC-CTGC
198802 AGTGTA
1 AGTGTA
198808 TCTATACACT
Statistics
Matches: 34, Mismatches: 2, Indels: 12
0.71 0.04 0.25
Matches are distributed among these distances:
15 2 0.06
16 9 0.26
18 6 0.18
20 15 0.44
21 2 0.06
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.26
Consensus pattern (19 bp):
AGTGTACCGATACACCTGC
Found at i:198886 original size:21 final size:21
Alignment explanation
Indices: 198860--198900 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
198850 TTTGAATTTA
*
198860 ATGAAGGTGTA-TCGATACCCT
1 ATGAAGGGGTACT-GATACCCT
198881 ATGAAGGGGTACTGATACCC
1 ATGAAGGGGTACTGATACCC
198901 CATGTTATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.29, C:0.20, G:0.27, T:0.24
Consensus pattern (21 bp):
ATGAAGGGGTACTGATACCCT
Found at i:200796 original size:19 final size:19
Alignment explanation
Indices: 200757--200797 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
200747 ATTAAAGATG
*
200757 AATTGATTTTGAAAGTAAA
1 AATTGATTTTGAAAATAAA
*
200776 AATTGATTTTGAAAATCAA
1 AATTGATTTTGAAAATAAA
200795 AAT
1 AAT
200798 GAAAATTTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.49, C:0.02, G:0.12, T:0.37
Consensus pattern (19 bp):
AATTGATTTTGAAAATAAA
Found at i:202184 original size:16 final size:16
Alignment explanation
Indices: 202143--202193 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 16
202133 AAAATGCTAA
202143 AGTGTACCGATACACTCT
1 AGTGTACCGATACA--CT
202161 GCAGTGTATCC-ATACACT
1 --AGTGTA-CCGATACACT
202179 AGTGTACCGATACAC
1 AGTGTACCGATACAC
202194 CCTACAGTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.07
16 12 0.41
18 2 0.07
20 11 0.38
21 2 0.07
ACGTcount: A:0.29, C:0.27, G:0.18, T:0.25
Consensus pattern (16 bp):
AGTGTACCGATACACT
Found at i:202190 original size:36 final size:36
Alignment explanation
Indices: 202143--202313 Score: 139
Period size: 36 Copynumber: 5.0 Consensus size: 36
202133 AAAATGCTAA
202143 AGTGTACCGATACACTCTGCAGTGTATCCATACACT
1 AGTGTACCGATACACTCTGCAGTGTATCCATACACT
* * *
202179 AGTGTACCGATACACCCTACAGTGTATCCATACCCCT
1 AGTGTACCGATACACTCTGCAGTGTATCCATA-CACT
* * * *
202216 A-TG-ACTGCTCAAACATC-G-A----AT-C-TA-ATT
1 AGTGTACCGAT-ACAC-TCTGCAGTGTATCCATACACT
*
202243 AGTGTACCGATACACCCTGCAGTGTATCCATACACT
1 AGTGTACCGATACACTCTGCAGTGTATCCATACACT
* * *
202279 GGTGTACTGATACACTCTGTAGTGTATCCATACAC
1 AGTGTACCGATACACTCTGCAGTGTATCCATACAC
202314 CCTGGGTGCA
Statistics
Matches: 102, Mismatches: 19, Indels: 28
0.68 0.13 0.19
Matches are distributed among these distances:
27 3 0.03
28 6 0.06
29 7 0.07
30 1 0.01
31 2 0.02
33 2 0.02
34 1 0.01
35 7 0.07
36 68 0.67
37 5 0.05
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (36 bp):
AGTGTACCGATACACTCTGCAGTGTATCCATACACT
Found at i:202211 original size:20 final size:20
Alignment explanation
Indices: 202143--202216 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
202133 AAAATGCTAA
* *
202143 AGTGTACCGATACACTCTGC
1 AGTGTACCGATACACCCTAC
202163 AGTGTATCC-ATACA--CT--
1 AGTGTA-CCGATACACCCTAC
202179 AGTGTACCGATACACCCTAC
1 AGTGTACCGATACACCCTAC
202199 AGTGTATCC-ATAC-CCCTA
1 AGTGTA-CCGATACACCCTA
202217 TGACTGCTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 15
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.04
16 11 0.23
18 4 0.09
19 5 0.11
20 21 0.45
21 4 0.09
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (20 bp):
AGTGTACCGATACACCCTAC
Found at i:202268 original size:20 final size:19
Alignment explanation
Indices: 202243--202317 Score: 61
Period size: 20 Copynumber: 4.0 Consensus size: 19
202233 GAATCTAATT
202243 AGTGTA-CCGATACACCCTG
1 AGTGTATCC-ATACACCCTG
202262 CAGTGTATCCATACA--CTG
1 -AGTGTATCCATACACCCTG
* *
202280 -GTGTA-CTGATACACTCTG
1 AGTGTATC-CATACACCCTG
202298 TAGTGTATCCATACACCCTG
1 -AGTGTATCCATACACCCTG
202318 GGTGCAATGG
Statistics
Matches: 45, Mismatches: 3, Indels: 14
0.73 0.05 0.23
Matches are distributed among these distances:
15 1 0.02
16 10 0.22
18 6 0.13
20 25 0.56
21 3 0.07
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (19 bp):
AGTGTATCCATACACCCTG
Found at i:203294 original size:24 final size:24
Alignment explanation
Indices: 203265--203321 Score: 78
Period size: 24 Copynumber: 2.4 Consensus size: 24
203255 GCAAGAGTGT
*
203265 ACTAATACAAGAGTGCGCAAAGGC
1 ACTAATACAAGAGTACGCAAAGGC
* * *
203289 ATTAATACAGGTGTACGCAAAGGC
1 ACTAATACAAGAGTACGCAAAGGC
203313 ACTAATACA
1 ACTAATACA
203322 TGATTAATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.18
Consensus pattern (24 bp):
ACTAATACAAGAGTACGCAAAGGC
Found at i:211955 original size:15 final size:15
Alignment explanation
Indices: 211937--211971 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
211927 CGAGGGTATT
*
211937 GTAGTCCTTCGGGAC
1 GTAGTCCTTCAGGAC
211952 GTAGTCCTTCAGGAC
1 GTAGTCCTTCAGGAC
211967 GTAGT
1 GTAGT
211972 GGTCCTACGG
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:0.17, C:0.23, G:0.31, T:0.29
Consensus pattern (15 bp):
GTAGTCCTTCAGGAC
Found at i:218350 original size:28 final size:29
Alignment explanation
Indices: 218309--218371 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
218299 TTGTTCCAAC
* * *
218309 AAAACCAGTGACAATGTACAA-ATCTTTTT
1 AAAA-CAGTAACAATGTAAAACATATTTTT
*
218338 AAAACAGTAACAATTTAAAACATATTTTT
1 AAAACAGTAACAATGTAAAACATATTTTT
218367 AAAAC
1 AAAAC
218372 CATAGTAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 13 0.45
29 16 0.55
ACGTcount: A:0.49, C:0.14, G:0.06, T:0.30
Consensus pattern (29 bp):
AAAACAGTAACAATGTAAAACATATTTTT
Found at i:218764 original size:31 final size:32
Alignment explanation
Indices: 218719--218779 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
218709 TACTCAAGGG
*
218719 AGTTCCTTGGGGCCTAAAAGCCTATCCAAGAA
1 AGTTCCTTGGGGCCTAAAAGCCTACCCAAGAA
* * *
218751 AGTTTCTT-GGGCCTCAGAGCCTACCCAAG
1 AGTTCCTTGGGGCCTAAAAGCCTACCCAAG
218780 GGTCACCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 18 0.72
32 7 0.28
ACGTcount: A:0.26, C:0.28, G:0.23, T:0.23
Consensus pattern (32 bp):
AGTTCCTTGGGGCCTAAAAGCCTACCCAAGAA
Found at i:219007 original size:96 final size:96
Alignment explanation
Indices: 218889--219063 Score: 235
Period size: 96 Copynumber: 1.8 Consensus size: 96
218879 GTAGATCTCA
* *
218889 TGATCCATAAATCAGGAGCGATTATATTTTCCAGTGTAAACAAGAAATCAGATAACACAT-TCTA
1 TGATCCATAAATCAGGAACGATTATATTTTCCAGTGAAAACAAGAAATCAGATAACACATATC-A
218953 GGTAACCATAGTTCATAAACCAGTAGATTCCT
65 GGTAACCATAGTTCATAAACCAGTAGATTCCT
* *** * * * *
218985 TGATCCATAAATCAGGAACGATTGTATTTTTTGGTGAAAACAGGTAATCAGATGACACATATCAT
1 TGATCCATAAATCAGGAACGATTATATTTTCCAGTGAAAACAAGAAATCAGATAACACATATCAG
*
219050 GTAGCCATAGTTCA
66 GTAACCATAGTTCA
219064 GTTACAAGCA
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
96 65 0.97
97 2 0.03
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (96 bp):
TGATCCATAAATCAGGAACGATTATATTTTCCAGTGAAAACAAGAAATCAGATAACACATATCAG
GTAACCATAGTTCATAAACCAGTAGATTCCT
Found at i:222329 original size:14 final size:15
Alignment explanation
Indices: 222310--222343 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
222300 TGTATTAGGC
222310 TATGAAAAG-TGAAA
1 TATGAAAAGATGAAA
222324 TATGAAAAGTATGAAA
1 TATGAAAAG-ATGAAA
222340 TATG
1 TATG
222344 TCAAATTGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
16 9 0.50
ACGTcount: A:0.53, C:0.00, G:0.21, T:0.26
Consensus pattern (15 bp):
TATGAAAAGATGAAA
Found at i:236612 original size:70 final size:68
Alignment explanation
Indices: 236536--236754 Score: 210
Period size: 70 Copynumber: 3.1 Consensus size: 68
236526 AGAAACACTT
* * *
236536 TCAAGTGAAATAAAATTTGTTTTAAGGAAAACAATCTCAAGTGATAAAATATGTTTTGAGGAAAA
1 TCAAGTG-AATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGATAAAATAT-TTTTAAGAAAAA
236601 CAATC
64 CAATC
* * * * * * *
236606 TAAAGTGAGGT-AAACTCGTTTTAAGAAAAACAATATCAAGTGACATAAACTTTATTTTAAGAAA
1 TCAAGTGA-ATAAAATTTGTTTTAAGAAAAACAATCTCAAGTG--ATAAAATAT-TTTTAAGAAA
236670 AAC-ATCC
62 AACAAT-C
* * *
236677 GCAAGTG-ATAAAATATGATTTAAGAAAAACAATCTCAAGTGAGATAAAATATTCTTTAAGAAAA
1 TCAAGTGAATAAAATTTGTTTTAAGAAAAACAATCTCAAGT--GATAAAATATT-TTTAAGAAAA
236741 ACAATC
63 ACAATC
236747 TCAAGTGA
1 TCAAGTGA
236755 GATATAATCT
Statistics
Matches: 117, Mismatches: 22, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
69 30 0.26
70 60 0.51
71 26 0.22
72 1 0.01
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (68 bp):
TCAAGTGAATAAAATTTGTTTTAAGAAAAACAATCTCAAGTGATAAAATATTTTTAAGAAAAACA
ATC
Found at i:236654 original size:105 final size:105
Alignment explanation
Indices: 236518--236754 Score: 287
Period size: 105 Copynumber: 2.2 Consensus size: 105
236508 GAAATATTTT
* * * * * * *
236518 GTTTCAAGAGAAACACTTTCAAGTGAAATAAAATTTGTTTTAAGGAAAACAAT-CTCAAGTGATA
1 GTTTTAAGAAAAACAATATCAAGTGAAATAAAATTTATTTTAAGAAAAAC-ATCCGCAAGTGATA
* * * * * *
236582 AAATATGTTTTGAGGAAAACAATCTAAAGTGAGGTAAACTC
65 AAATATGATTTAAGAAAAACAATCTAAAGTGAGATAAAATA
* *
236623 GTTTTAAGAAAAACAATATCAAGTGACATAAACTTTATTTTAAGAAAAACATCCGCAAGTGATAA
1 GTTTTAAGAAAAACAATATCAAGTGAAATAAAATTTATTTTAAGAAAAACATCCGCAAGTGATAA
*
236688 AATATGATTTAAGAAAAACAATCTCAAGTGAGATAAAATA
66 AATATGATTTAAGAAAAACAATCTAAAGTGAGATAAAATA
* *
236728 TTCTTTAAGAAAAACAATCTCAAGTGA
1 GT-TTTAAGAAAAACAATATCAAGTGA
236755 GATATAATCT
Statistics
Matches: 112, Mismatches: 18, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
104 2 0.02
105 87 0.78
106 23 0.21
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (105 bp):
GTTTTAAGAAAAACAATATCAAGTGAAATAAAATTTATTTTAAGAAAAACATCCGCAAGTGATAA
AATATGATTTAAGAAAAACAATCTAAAGTGAGATAAAATA
Found at i:236755 original size:36 final size:35
Alignment explanation
Indices: 236536--236758 Score: 213
Period size: 36 Copynumber: 6.3 Consensus size: 35
236526 AGAAACACTT
* * *
236536 TCAAGTGAAATAAAATTTGTTTTAAGGAAAACAATC
1 TCAAGTGAGATAAAATAT-TTTTAAGAAAAACAATC
* *
236572 TCAAGT--GATAAAATATGTTTTGAGGAAAACAATC
1 TCAAGTGAGATAAAATAT-TTTTAAGAAAAACAATC
* * * ** *
236606 TAAAGTGAGGTAAACTCGTTTTAAGAAAAACAATA
1 TCAAGTGAGATAAAATATTTTTAAGAAAAACAATC
* * *
236641 TCAAGTGACATAAACTTTATTTTAAGAAAAAC-ATCC
1 TCAAGTGAGATAAAATAT-TTTTAAGAAAAACAAT-C
* *
236677 GCAAGT--GATAAAATATGATTTAAGAAAAACAATC
1 TCAAGTGAGATAAAATAT-TTTTAAGAAAAACAATC
236711 TCAAGTGAGATAAAATATTCTTTAAGAAAAACAATC
1 TCAAGTGAGATAAAATATT-TTTAAGAAAAACAATC
236747 TCAAGTGAGATA
1 TCAAGTGAGATA
236759 TAATCTTGAG
Statistics
Matches: 154, Mismatches: 25, Indels: 16
0.79 0.13 0.08
Matches are distributed among these distances:
34 55 0.36
35 31 0.20
36 68 0.44
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (35 bp):
TCAAGTGAGATAAAATATTTTTAAGAAAAACAATC
Found at i:239470 original size:2 final size:2
Alignment explanation
Indices: 239458--239511 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
239448 AAAACCGTAA
239458 AT AT A- 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
239499 AT AT AT AT AT AT A
1 AT AT AT AT AT AT A
239512 ATTTTTAATT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:244151 original size:37 final size:37
Alignment explanation
Indices: 244067--244151 Score: 102
Period size: 36 Copynumber: 2.3 Consensus size: 37
244057 ATTAAACCTT
*
244067 TTTTATAATTTTAATTTTGTAAAAAAATTATATAAATA
1 TTTTACAA-TTTAATTTTGTAAAAAAATTATATAAATA
* * *
244105 TTAT-GAATTTAATTTTTTAAAGAAAA-TATATAAATA
1 TTTTACAATTTAATTTTGTAAA-AAAATTATATAAATA
244141 TTTTACAATTT
1 TTTTACAATTT
244152 GTAATATTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
36 26 0.65
37 11 0.28
38 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (37 bp):
TTTTACAATTTAATTTTGTAAAAAAATTATATAAATA
Found at i:244544 original size:43 final size:43
Alignment explanation
Indices: 244483--244924 Score: 246
Period size: 43 Copynumber: 10.5 Consensus size: 43
244473 GAAAATGATT
* * * *
244483 AAATTAGGGGCTTAAATTATAAAAGTAAAAAGTAAGATTGAAA
1 AAATTAGAGGCCTCAATTATAAAGGTAAAAAGTAAGATTGAAA
* * *
244526 AAATTAGAGGACTCAATTATAAAGGTAAAAGGTTAGATT-AAA
1 AAATTAGAGGCCTCAATTATAAAGGTAAAAAGTAAGATTGAAA
* * * *
244568 AATATCA-AGGGCCTTAACTATAAAGGTAAAAAGTGAGATTGAAA
1 AA-ATTAGA-GGCCTCAATTATAAAGGTAAAAAGTAAGATTGAAA
* * * * *
244612 GAATTAG-GAGCCTAAATAATAAAAGTAAAAAGTAGGATTG-AA
1 AAATTAGAG-GCCTCAATTATAAAGGTAAAAAGTAAGATTGAAA
* *
244654 AAATTAGGGGTCTCAATTATAAAGGT-AAAAG---G--TG---
1 AAATTAGAGGCCTCAATTATAAAGGTAAAAAGTAAGATTGAAA
* * * * *
244688 AGATT-GA-GTCTCAACTATAAAGGTAAAAAATGAGATTTG-AA
1 AAATTAGAGGCCTCAATTATAAAGGTAAAAAGTAAGA-TTGAAA
* * *
244729 AAATTA-AGGGCCTTAATTATAAAGGTAAAAAGTAGGATCGAAAA
1 AAATTAGA-GGCCTCAATTATAAAGGTAAAAAGTAAGATTG-AAA
* * *
244773 AAATTAG-GAGCCTCAATTATAAAGGTAGAAAGTGAGATTTAAA
1 AAATTAGAG-GCCTCAATTATAAAGGTAAAAAGTAAGATTGAAA
** * * * *
244816 AAATTAGAAACCTCGATTAGAAAGGTTAAAAA-TGAGAATGAAAA
1 AAATTAGAGGCCTCAATTATAAAGG-TAAAAAGTAAGATTG-AAA
* * * * *
244860 AAATTA-AGATCCTCAATTACAAATGTAAAATA-TGATATTG-AA
1 AAATTAGAG-GCCTCAATTATAAAGGTAAAA-AGTAAGATTGAAA
*
244902 AAATTAGTA-ACCTCAATTATAAA
1 AAATTAG-AGGCCTCAATTATAAA
244925 ACAAAAATAA
Statistics
Matches: 310, Mismatches: 60, Indels: 59
0.72 0.14 0.14
Matches are distributed among these distances:
32 16 0.05
33 5 0.02
34 4 0.01
36 3 0.01
38 1 0.00
39 2 0.01
41 10 0.03
42 50 0.16
43 148 0.48
44 71 0.23
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.25
Consensus pattern (43 bp):
AAATTAGAGGCCTCAATTATAAAGGTAAAAAGTAAGATTGAAA
Found at i:244699 original size:32 final size:32
Alignment explanation
Indices: 244663--244724 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
244653 AAAATTAGGG
* **
244663 GTCTCAATTATAAAGGTAAAAGGTGAGATTGA
1 GTCTCAACTATAAAGGTAAAAAATGAGATTGA
244695 GTCTCAACTATAAAGGTAAAAAATGAGATT
1 GTCTCAACTATAAAGGTAAAAAATGAGATT
244725 TGAAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (32 bp):
GTCTCAACTATAAAGGTAAAAAATGAGATTGA
Found at i:244714 original size:117 final size:118
Alignment explanation
Indices: 244583--244811 Score: 331
Period size: 117 Copynumber: 1.9 Consensus size: 118
244573 CAAGGGCCTT
*
244583 AACTATAAAGGTAAAAAGTGAGA-TTGAAAGAATT-AGGAGCCTAAATAATAAAAGTAAAAAGTA
1 AACTATAAAGGTAAAAAATGAGATTTGAAA-AATTAAGG-GCCTAAATAATAAAAGTAAAAAGTA
* * *
244646 GGATTG-AAAAATTAGGGGTCTCAATTATAAAGGTA-AAAGGTGAGATTGAGTCTC
64 GGATCGAAAAAATTAGGAGCCTCAATTATAAAGGTAGAAA-GTGAGATTGAGTCTC
* * *
244700 AACTATAAAGGTAAAAAATGAGATTTGAAAAATTAAGGGCCTTAATTATAAAGGTAAAAAGTAGG
1 AACTATAAAGGTAAAAAATGAGATTTGAAAAATTAAGGGCCTAAATAATAAAAGTAAAAAGTAGG
244765 ATCGAAAAAAATTAGGAGCCTCAATTATAAAGGTAGAAAGTGAGATT
66 ATCG-AAAAAATTAGGAGCCTCAATTATAAAGGTAGAAAGTGAGATT
244812 TAAAAAATTA
Statistics
Matches: 100, Mismatches: 7, Indels: 8
0.87 0.06 0.07
Matches are distributed among these distances:
117 53 0.53
118 9 0.09
119 35 0.35
120 3 0.03
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.24
Consensus pattern (118 bp):
AACTATAAAGGTAAAAAATGAGATTTGAAAAATTAAGGGCCTAAATAATAAAAGTAAAAAGTAGG
ATCGAAAAAATTAGGAGCCTCAATTATAAAGGTAGAAAGTGAGATTGAGTCTC
Found at i:244859 original size:87 final size:85
Alignment explanation
Indices: 244697--244920 Score: 222
Period size: 87 Copynumber: 2.6 Consensus size: 85
244687 GAGATTGAGT
* ** * *
244697 CTCAACTATAAAGGTAAAAAATGAGATTTGAAAAATTA-AGGGCCTTAATTATAAAGGTAAAAAG
1 CTCAATTATAAAGGT--AAAATGAGATTTGAAAAATTAGA-AACCTCAATTAGAAAGGTAAAAAG
* *
244761 TAGGATCGAAAAAAATTAGGAGC
63 TAGAATCGAAAAAAATTAAGAGC
* *
244784 CTCAATTATAAAGGTAGAAAGTGAGATTTAAAAAATTAGAAACCTCGATTAGAAAGGTTAAAAA-
1 CTCAATTATAAAGGTA-AAA-TGAGATTTGAAAAATTAGAAACCTCAATTAGAAAGG-TAAAAAG
*
244848 TGAGAAT-GAAAAAAATTAAGATC
63 T-AGAATCGAAAAAAATTAAGAGC
* * *
244871 CTCAATTACAAATGTAAAAT-ATGATATTGAAAAATTAGTAACCTCAATTA
1 CTCAATTATAAAGGTAAAATGA-GAT-TTGAAAAATTAGAAACCTCAATTA
244921 TAAAACAAAA
Statistics
Matches: 115, Mismatches: 15, Indels: 15
0.79 0.10 0.10
Matches are distributed among these distances:
84 1 0.01
85 5 0.04
86 27 0.23
87 71 0.62
88 11 0.10
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.25
Consensus pattern (85 bp):
CTCAATTATAAAGGTAAAATGAGATTTGAAAAATTAGAAACCTCAATTAGAAAGGTAAAAAGTAG
AATCGAAAAAAATTAAGAGC
Found at i:244902 original size:44 final size:43
Alignment explanation
Indices: 244697--244920 Score: 149
Period size: 44 Copynumber: 5.2 Consensus size: 43
244687 GAGATTGAGT
* * **
244697 CTCAACTATAAAGGTAAAAAATGAGATTTG--AAAAATTAAGGGC
1 CTCAATTACAAAGGT-AAAAATGAGA-TTGAAAAAAATTAAGAAC
* * * * *
244740 CTTAATTATAAAGGTAAAAA-GTAGGATCGAAAAAAATTAGGAGC
1 CTCAATTACAAAGGTAAAAATG-A-GATTGAAAAAAATTAAGAAC
* * *
244784 CTCAATTATAAAGGTAGAAAGTGAGATT-TAAAAAATT-AGAAAC
1 CTCAATTACAAAGGTA-AAAATGAGATTGAAAAAAATTAAG-AAC
* * * *
244827 CTCGATTAGAAAGGTTAAAAATGAGAATGAAAAAAATTAAGATC
1 CTCAATTACAAAGG-TAAAAATGAGATTGAAAAAAATTAAGAAC
* *
244871 CTCAATTACAAATGTAAAATATGATATTG--AAAAATT-AGTAAC
1 CTCAATTACAAAGGTAAAA-ATGAGATTGAAAAAAATTAAG-AAC
244913 CTCAATTA
1 CTCAATTA
244921 TAAAACAAAA
Statistics
Matches: 146, Mismatches: 23, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
41 3 0.02
42 26 0.18
43 51 0.35
44 59 0.40
45 6 0.04
46 1 0.01
ACGTcount: A:0.50, C:0.08, G:0.16, T:0.25
Consensus pattern (43 bp):
CTCAATTACAAAGGTAAAAATGAGATTGAAAAAAATTAAGAAC
Found at i:245956 original size:17 final size:18
Alignment explanation
Indices: 245934--245967 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
245924 TCAGCCGGTC
245934 CGGTTC-GAACGGTTCAA
1 CGGTTCAGAACGGTTCAA
*
245951 CGGTTCAGACCGGTTCA
1 CGGTTCAGAACGGTTCA
245968 CTAATAGCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.26, G:0.29, T:0.24
Consensus pattern (18 bp):
CGGTTCAGAACGGTTCAA
Found at i:246396 original size:31 final size:30
Alignment explanation
Indices: 246359--246442 Score: 80
Period size: 30 Copynumber: 2.7 Consensus size: 30
246349 TTAATCCCTA
246359 AACTTTAGACAAAATATTAATTTCACCCATAG
1 AACTTTAGA-AAAATATTAATTTCA-CCATAG
* * * * * *
246391 -CCTTTAGATAAATACTAATTTGACCTTTG
1 AACTTTAGAAAAATATTAATTTCACCATAG
246420 AACTTTAGATAAAATATTAATTT
1 AACTTTAGA-AAAATATTAATTT
246443 TACTCCCAAA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
29 4 0.10
30 19 0.46
31 18 0.44
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.38
Consensus pattern (30 bp):
AACTTTAGAAAAATATTAATTTCACCATAG
Found at i:247295 original size:31 final size:31
Alignment explanation
Indices: 247251--247312 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
247241 TTTAAGTTGG
*
247251 ATTTAAGTATTAAATTGATATTTTATCTAAA
1 ATTTAAGTATTAAATTAATATTTTATCTAAA
* *
247282 ATTTAAG-AGTTAAATTAATGTTTTATTTAAA
1 ATTTAAGTA-TTAAATTAATATTTTATCTAAA
247313 GTATATGGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (31 bp):
ATTTAAGTATTAAATTAATATTTTATCTAAA
Found at i:247846 original size:2 final size:2
Alignment explanation
Indices: 247839--247878 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
247829 TATTTTATTT
* *
247839 TA TA TA TA TA TA TA TA TA TA TA AA TA TA T- TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
247879 TTTTTGAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:247945 original size:35 final size:35
Alignment explanation
Indices: 247906--248209 Score: 228
Period size: 35 Copynumber: 8.5 Consensus size: 35
247896 TTGAAAATGT
247906 ATATATTATATAGTTTTTGAAAACATTTTGAAAAC
1 ATATATTATATAGTTTTTGAAAACATTTTGAAAAC
* ** *
247941 ATATATAATATATAG-TTTT-AAAAAAAATTGAAAATTT
1 ATATAT--TATATAGTTTTTGAAAACATTTTGAAAA--C
* * *
247978 ATATAATATATGGTTTTTAAAAACATTTTGAAAAC
1 ATATATTATATAGTTTTTGAAAACATTTTGAAAAC
* * **
248013 TATATAATATATGGTTTTT-AATGCATTTTGAAAAC
1 -ATATATTATATAGTTTTTGAAAACATTTTGAAAAC
* * *
248048 TATATAATATATAGTTTTTGAAAGCATTTTGAAAAT
1 -ATATATTATATAGTTTTTGAAAACATTTTGAAAAC
* * *
248084 ATATATAATATATGTTTTTGAAAACATTTTAAAAAT
1 ATATATTATATA-GTTTTTGAAAACATTTTGAAAAC
* *
248120 ATATAATAATATATAG-TTTTAAAAACAATTTTTAAAAC
1 ATAT-AT--TATATAGTTTTTGAAAAC-ATTTTGAAAAC
* *
248158 ATATATTATAT--TATTTTGAAAATACTTTTTAAAAAGC
1 ATATATTATATAGT-TTTTG-AAA-ACATTTTGAAAA-C
248195 ATATA--ATATAGTTTT
1 ATATATTATATAGTTTT
248210 AAATTTATTA
Statistics
Matches: 223, Mismatches: 26, Indels: 39
0.77 0.09 0.14
Matches are distributed among these distances:
35 79 0.35
36 79 0.35
37 46 0.21
38 14 0.06
39 5 0.02
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.43
Consensus pattern (35 bp):
ATATATTATATAGTTTTTGAAAACATTTTGAAAAC
Found at i:247946 original size:37 final size:37
Alignment explanation
Indices: 247894--248179 Score: 304
Period size: 37 Copynumber: 7.9 Consensus size: 37
247884 GAAAAATGGT
** *
247894 TTTTGAAAATGTATATATTATATAGTTTTTGAAAACA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
*
247931 TTTTGAAAACATATATAATATATAG-TTTT-AAAAAA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
** ** * *
247966 AATTGAAAATTTATATAATATATGGTTTTTAAAAACA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
* **
248003 TTTTGAAAAC-TATATAATATATGGTTTTT-AATGCA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
*
248038 TTTTGAAAAC-TATATAATATATAGTTTTTGAAAGCA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
*
248074 TTTTGAAAATATATATAATATAT-GTTTTTGAAAACA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
* * *
248110 TTTTAAAAATATATAATAATATATAG-TTTTAAAAACAA
1 TTTTGAAAACATAT-ATAATATATAGTTTTTGAAAAC-A
* *
248148 TTTTTAAAACATATATTATAT-TA--TTTTGAAAA
1 TTTTGAAAACATATATAATATATAGTTTTTGAAAA
248180 TACTTTTTAA
Statistics
Matches: 217, Mismatches: 25, Indels: 16
0.84 0.10 0.06
Matches are distributed among these distances:
35 65 0.30
36 68 0.31
37 70 0.32
38 14 0.06
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.43
Consensus pattern (37 bp):
TTTTGAAAACATATATAATATATAGTTTTTGAAAACA
Found at i:247975 original size:72 final size:72
Alignment explanation
Indices: 247894--248168 Score: 324
Period size: 72 Copynumber: 3.8 Consensus size: 72
247884 GAAAAATGGT
* * *
247894 TTTTGAAAATGTATATATTATATAGTTTTTGAAAACATTTTGAAAACATATATAATATATAG-TT
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAACATATATAATATAT-GTTT
*
247958 TTAAAAAA
65 TTAAAACA
** * *
247966 AATTGAAAATTTATATAATATATGGTTTTTAAAAACATTTTGAAAAC-TATATAATATATGGTTT
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAACATATATAATATAT-GTTT
**
248030 TTAATGCA
65 TTAAAACA
* * * *
248038 TTTTGAAAA-CTATATAATATATAGTTTTTGAAAGCATTTTGAAAATATATATAATATATGTTTT
1 TTTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAACATATATAATATATGTTTT
248102 TGAAAACA
66 T-AAAACA
* * *
248110 TTTTAAAAATATATAATAATATATAG-TTTTAAAAACAATTTTTAAAACATATATTATAT
1 TTTTGAAAATATAT-ATAATATATAGTTTTTAAAAAC-ATTTTGAAAACATATATAATAT
248169 TATTTTGAAA
Statistics
Matches: 171, Mismatches: 26, Indels: 10
0.83 0.13 0.05
Matches are distributed among these distances:
71 51 0.30
72 79 0.46
73 11 0.06
74 30 0.18
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (72 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAAACATTTTGAAAACATATATAATATATGTTTT
TAAAACA
Found at i:248201 original size:72 final size:71
Alignment explanation
Indices: 247874--248204 Score: 255
Period size: 72 Copynumber: 4.6 Consensus size: 71
247864 ATATTAAATA
*** * * *
247874 TATATTTTTTGAAAAATGGTTTTTGAAAATGTATATATTATATAGTTTTTGAAAACATTTTGAAA
1 TATATTTTTTG-AAAATACATTTT-AAAAAGTATATAATATATAGTTTTTAAAAACATTTTGAAA
247939 ACATATAT
64 ACATATAT
* * * * ** *
247947 AATATATAGTTTT-AAAA-AAAATTGAAAATTTATATAATATATGGTTTTTAAAAACATTTTGAA
1 --TATAT-TTTTTGAAAATACATTTTAAAAAGTATATAATATATAGTTTTTAAAAACATTTTGAA
*
248010 AACTATATAA
63 AAC-ATATAT
* * * * *
248020 TATATGGTTTTT---AATGCATTTTGAAAACTATATAATATATAGTTTTTGAAAGCATTTTGAAA
1 TATAT--TTTTTGAAAATACATTTTAAAAAGTATATAATATATAGTTTTTAAAAACATTTTGAAA
*
248082 ATATATAT
64 ACATATAT
*
248090 AATATATGTTTTTG-AAA-ACATTTTAAAAATATATAATAATATATAG-TTTTAAAAACAATTTT
1 --TATAT-TTTTTGAAAATACATTTTAAAAA-GTAT-ATAATATATAGTTTTTAAAAAC-ATTTT
*
248152 TAAAACATATAT
60 GAAAACATATAT
* *
248164 TATATTATTTTGAAAATACTTTTTAAAAAGCATATAATATA
1 TATATT-TTTTGAAAATACATTTTAAAAAGTATATAATATA
248205 GTTTTAAATT
Statistics
Matches: 207, Mismatches: 35, Indels: 31
0.76 0.13 0.11
Matches are distributed among these distances:
70 7 0.03
71 50 0.24
72 75 0.36
73 25 0.12
74 41 0.20
75 5 0.02
76 4 0.02
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.44
Consensus pattern (71 bp):
TATATTTTTTGAAAATACATTTTAAAAAGTATATAATATATAGTTTTTAAAAACATTTTGAAAAC
ATATAT
Found at i:248234 original size:17 final size:18
Alignment explanation
Indices: 248212--248259 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
248202 ATAGTTTTAA
248212 ATTTATTATTATTAT-TT
1 ATTTATTATTATTATATT
248229 ATTTATTATTATT-TATT
1 ATTTATTATTATTATATT
248246 ATTT-TTATTTATTA
1 ATTTATTA-TTATTA
248260 CATATTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
16 4 0.14
17 24 0.86
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
ATTTATTATTATTATATT
Found at i:248265 original size:20 final size:22
Alignment explanation
Indices: 248216--248277 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 22
248206 TTTTAAATTT
*
248216 ATTATTATTATTTATTTATTATT
1 ATTATTATT-TTTATTTATTATC
248239 ATTTATTATTTTTATTTATTA-C
1 A-TTATTATTTTTATTTATTATC
248261 A-TATT-TTTTTACTTTAT
1 ATTATTATTTTTA-TTTAT
248278 CCTCGTTTTA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
19 6 0.17
20 9 0.25
22 1 0.03
23 12 0.33
24 8 0.22
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.69
Consensus pattern (22 bp):
ATTATTATTTTTATTTATTATC
Found at i:248699 original size:21 final size:21
Alignment explanation
Indices: 248658--248701 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
248648 ACTGAACTAT
*
248658 CCGAGATAACCGGGAATAACC
1 CCGAGATAACCGGGAACAACC
* *
248679 CCGAGATAATCGGGAGCAACC
1 CCGAGATAACCGGGAACAACC
248700 CC
1 CC
248702 AAAACAATCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.32, G:0.25, T:0.09
Consensus pattern (21 bp):
CCGAGATAACCGGGAACAACC
Found at i:249648 original size:18 final size:19
Alignment explanation
Indices: 249625--249667 Score: 70
Period size: 18 Copynumber: 2.3 Consensus size: 19
249615 TTTTTGTTAT
*
249625 TTTTTTATTTTCTTATTA-
1 TTTTTTATTTTATTATTAC
249643 TTTTTTATTTTATTATTAC
1 TTTTTTATTTTATTATTAC
249662 TTTTTT
1 TTTTTT
249668 CTCTTTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 17 0.74
19 6 0.26
ACGTcount: A:0.16, C:0.05, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTTATTTTATTATTAC
Found at i:249658 original size:26 final size:25
Alignment explanation
Indices: 249608--249659 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
249598 TTCTGATTTA
*
249608 TTTCATATTTTTGTTATTTTTTTAT
1 TTTCATATTTTTGTTATTTTATTAT
* *
249633 TTTCTTATTATTTTTTATTTTATTAT
1 TTTCATATT-TTTGTTATTTTATTAT
249659 T
1 T
249660 ACTTTTTTCT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (25 bp):
TTTCATATTTTTGTTATTTTATTAT
Found at i:255372 original size:86 final size:85
Alignment explanation
Indices: 255125--255445 Score: 405
Period size: 85 Copynumber: 3.8 Consensus size: 85
255115 TCCCAGCCTA
* * * *
255125 TTACAGTATAACTCAAGGTGAGAAGGGTTATTTGTC-ACCAAAACCTTCGAGTTCGATTACATTC
1 TTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
*
255189 AGCTC-AAGGACATATTAAAT
66 AGCTCAAAGG-CATATCAAAT
* * * * *
255209 TTATAGTATAACTCAAGGCAAAAAGGGTTATCTGTCAACCAAAACCTTCGAGTTCGATTACATTC
1 TTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
* *
255274 AGCTCAAGGGCATACCAAAT
66 AGCTCAAAGGCATATCAAAT
* * *
255294 TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAGCAAAAAACCTTCGAGTTTGATTACATT
1 TTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAAACCTTCGAGTTCGATTACATT
255359 CAGCTCAAAGGCATATCAAAT
65 CAGCTCAAAGGCATATCAAAT
* * * * * *
255380 TTACTGCATAGCTCAAGGAGAGAAGGGCTATCTGTCAACAAAAA-CTGTCGAGTTTGATTCCATT
1 TTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCT-TCGAGTTCGATTACATT
255444 CA
65 CA
255446 ACTCGATGAC
Statistics
Matches: 210, Mismatches: 23, Indels: 7
0.88 0.10 0.03
Matches are distributed among these distances:
84 33 0.16
85 97 0.46
86 80 0.38
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (85 bp):
TTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCAACAAAAACCTTCGAGTTCGATTACATTC
AGCTCAAAGGCATATCAAAT
Found at i:255433 original size:171 final size:169
Alignment explanation
Indices: 255125--255445 Score: 434
Period size: 171 Copynumber: 1.9 Consensus size: 169
255115 TCCCAGCCTA
* * * *
255125 TTACAGTATAACTCAAGGTGAGAAGGGTTATTTGTCACCAAAACCTTCGAGTTCGATTACATTCA
1 TTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACAAAAACCTTCGAGTTCGATTACATTCA
* * * *
255190 GCTCAAGGACATATTAAATTTATAGTATAACTCAAGGCAAAAAGGGTTATCTGTCAACCAAAACC
66 GCTCAAGGACATATCAAATTTATAGCATAACTCAAGGCAAAAAGGGCTATCTGTCAACCAAAAAC
255255 TTCGAGTTCGATTACATTCAGCTCAAGGGCATACCAAAT
131 TTCGAGTTCGATTACATTCAGCTCAAGGGCATACCAAAT
* *
255294 TTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAGCAAAAAACCTTCGAGTTTGATTACATT
1 TTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCA-C-AAAAACCTTCGAGTTCGATTACATT
* *
255359 CAGCTCAAAGG-CATATCAAATTTACT-GCATAGCTCAAGG-AGAGAAGGGCTATCTGTCAA-CA
64 CAGCTC-AAGGACATATCAAATTTA-TAGCATAACTCAAGGCA-AAAAGGGCTATCTGTCAACCA
* *
255420 AAAACTGTCGAGTTTGATTCCATTCA
126 AAAACT-TCGAGTTCGATTACATTCA
255446 ACTCGATGAC
Statistics
Matches: 132, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
169 33 0.25
170 9 0.07
171 85 0.64
172 5 0.04
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.27
Consensus pattern (169 bp):
TTACAGCATAACTCAAGGCGAGAAGGGTTATCTGTCACAAAAACCTTCGAGTTCGATTACATTCA
GCTCAAGGACATATCAAATTTATAGCATAACTCAAGGCAAAAAGGGCTATCTGTCAACCAAAAAC
TTCGAGTTCGATTACATTCAGCTCAAGGGCATACCAAAT
Found at i:256040 original size:2 final size:2
Alignment explanation
Indices: 256033--256057 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
256023 TAGTCCGGAT
256033 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
256058 TACTATAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:256176 original size:62 final size:62
Alignment explanation
Indices: 256140--256350 Score: 175
Period size: 62 Copynumber: 3.5 Consensus size: 62
256130 TCGATTTTCG
*
256140 AAATATATAATATATAGTATTGAAAACATATATATAATATATAGTTTTTGAAAACATTTCAA
1 AAATATATAATATATAGTATTGAAAACATATATATAATATATAGTTTTTAAAAACATTTCAA
* * * * * * * *
256202 AAATATATATTATATAGTTTTTAAAACAT-TTTGAAAATATATAG-TTTTGAAAACGTTTTGAA
1 AAATATATAATATATAGTATTGAAAACATATAT-ATAATATATAGTTTTTAAAAAC-ATTTCAA
* * * * * * * *
256264 AACATATATAATATATGGTTTTTAAAA-AAAAATAT-AT-TATGGTTTTTAAAAATATTT-GA
1 AA-ATATATAATATATAGTATTGAAAACATATATATAATATATAGTTTTTAAAAACATTTCAA
* *
256323 AAATATAT-ATATATAATTTTGAAAACAT
1 AAATATATAATATATAGTATTGAAAACAT
256351 TTTGAAAACT
Statistics
Matches: 121, Mismatches: 22, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
57 14 0.12
58 7 0.06
59 3 0.02
60 7 0.06
61 22 0.18
62 45 0.37
63 23 0.19
ACGTcount: A:0.48, C:0.03, G:0.08, T:0.41
Consensus pattern (62 bp):
AAATATATAATATATAGTATTGAAAACATATATATAATATATAGTTTTTAAAAACATTTCAA
Found at i:256178 original size:27 final size:28
Alignment explanation
Indices: 256142--256196 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 28
256132 GATTTTCGAA
256142 ATATATAATATATAG-TATTGAAAACAT
1 ATATATAATATATAGTTATTGAAAACAT
*
256169 ATATATAATATATAGTTTTTGAAAACAT
1 ATATATAATATATAGTTATTGAAAACAT
256197 TTCAAAAATA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.49, C:0.04, G:0.07, T:0.40
Consensus pattern (28 bp):
ATATATAATATATAGTTATTGAAAACAT
Found at i:256206 original size:28 final size:27
Alignment explanation
Indices: 256142--256210 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 27
256132 GATTTTCGAA
*
256142 ATATATAATATATAGTATTGAAAACAT
1 ATATAAAATATATAGTATTGAAAACAT
* *
256169 ATATATAATATATAGTTTTTGAAAACAT
1 ATATAAAATATATAG-TATTGAAAACAT
*
256197 TTCA-AAAATATATA
1 AT-ATAAAATATATA
256211 TTATATAGTT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
27 15 0.41
28 21 0.57
29 1 0.03
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (27 bp):
ATATAAAATATATAGTATTGAAAACAT
Found at i:256239 original size:34 final size:33
Alignment explanation
Indices: 256169--256406 Score: 166
Period size: 35 Copynumber: 7.4 Consensus size: 33
256159 TTGAAAACAT
**
256169 ATATATAATATATAGTTTTTGAAAACATTTCAAAA
1 ATATAT-ATATATAGTTTTT-AAAACATTTTGAAA
256204 ATATATATTATATAGTTTTTAAAACATTTTG---
1 ATATATA-TATATAGTTTTTAAAACATTTTGAAA
* *
256235 A-A-A-ATATATAGTTTTGAAAACGTTTTGAAAA
1 ATATATATATATAGTTTTTAAAACATTTTG-AAA
*
256266 CATATATAATATATGGTTTTT-AAA-A-----AAA
1 -ATATAT-ATATATAGTTTTTAAAACATTTTGAAA
*
256294 A-ATATAT-TATGGTTTTTAAAA-ATATTTGAAA
1 ATATATATATATAGTTTTTAAAACAT-TTTGAAA
* *
256325 ATATATATATATAATTTTGAAAACATTTTGAAA
1 ATATATATATATAGTTTTTAAAACATTTTGAAA
* * * *
256358 ACTATATAATATATAGTTTTGAAAACTTTTTTATAT
1 A-TATAT-ATATATAGTTTTTAAAACATTTTGA-AA
256394 ATATATATATATA
1 ATATATATATATA
256407 TATATATATA
Statistics
Matches: 166, Mismatches: 14, Indels: 47
0.73 0.06 0.21
Matches are distributed among these distances:
24 10 0.06
25 6 0.04
26 4 0.02
27 22 0.13
28 4 0.02
29 1 0.01
30 1 0.01
31 5 0.03
32 7 0.04
33 20 0.12
34 25 0.15
35 48 0.29
36 13 0.08
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (33 bp):
ATATATATATATAGTTTTTAAAACATTTTGAAA
Found at i:256243 original size:27 final size:27
Alignment explanation
Indices: 256212--256271 Score: 93
Period size: 27 Copynumber: 2.2 Consensus size: 27
256202 AAATATATAT
*
256212 TATATAGTTTTTAAAACATTTTGAAAA
1 TATATAGTTTTGAAAACATTTTGAAAA
*
256239 TATATAGTTTTGAAAACGTTTTGAAAA
1 TATATAGTTTTGAAAACATTTTGAAAA
*
256266 CATATA
1 TATATA
256272 TAATATATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.43, C:0.05, G:0.10, T:0.42
Consensus pattern (27 bp):
TATATAGTTTTGAAAACATTTTGAAAA
Found at i:256394 original size:2 final size:2
Alignment explanation
Indices: 256389--256421 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
256379 AAAACTTTTT
256389 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
256422 CAATTTTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:258121 original size:85 final size:83
Alignment explanation
Indices: 257978--258307 Score: 338
Period size: 85 Copynumber: 3.9 Consensus size: 83
257968 TACCATGTGA
* * * ** *
257978 TTGATATGTCATCGAGCTGAATGGAATCAAACTC-AACAATTTTTATTGACAGATAGCCCTTCTC
1 TTGATATGTC-TTGAGCTGAATGTAATCGAACTCGAA-GGTTTTT-TTGACAGATAACCCTTCTC
*
258042 GCCTTGAGCTATGTTGTAAAT
63 GCCTTGAGCTATGCTGTAAAT
* * * * *
258063 TTGATATGTTTATGAGCTGAATGTAATTGAACTCGAAGGTTTTTTCTGACCGATAGCCCTTCTTG
1 TTGATATGTCT-TGAGCTGAATGTAATCGAACTCGAAGGTTTTTT-TGACAGATAACCCTTCTCG
258128 CCTTGAGCTATGCTGTAAAT
64 CCTTGAGCTATGCTGTAAAT
* * * ** *
258148 TTGGTATGCCCTTCAGCTGAATGTAATCGAACTCGAAGGATTTGGTTGACATATAACCCTTCTCG
1 TTGATATG-TCTTGAGCTGAATGTAATCGAACTCGAAGG-TTTTTTTGACAGATAACCCTTCTCG
* *
258213 CCTTGAGTTATACTGTAAAT
64 CCTTGAGCTATGCTGTAAAT
* * * ** * *
258233 TTGATATGTCCTTGAGCTGAATATAATCAAACTTGAAGGTTTTGGTGACAGATAACCCTTATTGC
1 TTGATATGT-CTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTTGACAGATAACCCTTCTCGC
258298 CTTGAGCTAT
65 CTTGAGCTAT
258308 ACTATAATAG
Statistics
Matches: 204, Mismatches: 35, Indels: 13
0.81 0.14 0.05
Matches are distributed among these distances:
84 32 0.16
85 165 0.81
86 7 0.03
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.36
Consensus pattern (83 bp):
TTGATATGTCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTTTGACAGATAACCCTTCTCGCC
TTGAGCTATGCTGTAAAT
Found at i:259945 original size:99 final size:99
Alignment explanation
Indices: 259775--259968 Score: 316
Period size: 99 Copynumber: 2.0 Consensus size: 99
259765 CAATATTATA
* * * *
259775 ATCACCTTTATCAGGCTAGATGAATCTTATCCATAAATCCGGGGCATTTAACCAATTGCTTTAGT
1 ATCACCATTATCAGGATAGATGAATCTTATCCATAAAGCCGGGGCATTTAACCAATTGCTTTAGA
*
259840 GGGACAACTCAAGCTTTATTATATAGATATTACG
66 GAGACAACTCAAGCTTTATTATATAGATATTACG
* *
259874 ATCACCATTATCAGGATAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCTTTAGA
1 ATCACCATTATCAGGATAGATGAATCTTATCCATAAAGCCGGGGCATTTAACCAATTGCTTTAGA
*
259939 GAGACAACTCAAGCTTTATTATATATATAT
66 GAGACAACTCAAGCTTTATTATATAGATAT
259969 ATAATATTAT
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 87 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (99 bp):
ATCACCATTATCAGGATAGATGAATCTTATCCATAAAGCCGGGGCATTTAACCAATTGCTTTAGA
GAGACAACTCAAGCTTTATTATATAGATATTACG
Found at i:261404 original size:8 final size:8
Alignment explanation
Indices: 261393--261433 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
261383 AAAACAGAAA
261393 AAAATAAT
1 AAAATAAT
*
261401 AAAATAAG
1 AAAATAAT
261409 AAAATAAT
1 AAAATAAT
261417 AAGAA-AAT
1 AA-AATAAT
261425 AAAA-AAT
1 AAAATAAT
261432 AA
1 AA
261434 TAAGAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
7 7 0.23
8 21 0.70
9 2 0.07
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (8 bp):
AAAATAAT
Found at i:261410 original size:19 final size:19
Alignment explanation
Indices: 261388--261439 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
261378 AAGGAAAAAC
* *
261388 AGAAAAAAATAATAAAATA
1 AGAAAATAATAAGAAAATA
261407 AGAAAATAATAAGAAAATA
1 AGAAAATAATAAGAAAATA
261426 A-AAAATAATAAGAA
1 AGAAAATAATAAGAA
261440 TATTAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
18 13 0.42
19 18 0.58
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (19 bp):
AGAAAATAATAAGAAAATA
Found at i:261414 original size:16 final size:15
Alignment explanation
Indices: 261391--261441 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 15
261381 GAAAAACAGA
261391 AAAAAATAATAAAAT
1 AAAAAATAATAAAAT
261406 AAGAAAATAATAAGAAAAT
1 AA-AAAATAAT---AAAAT
261425 AAAAAATAATAAGAAT
1 AAAAAATAATAA-AAT
261441 A
1 A
261442 TTAAATAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
15 4 0.13
16 12 0.39
18 8 0.26
19 7 0.23
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.18
Consensus pattern (15 bp):
AAAAAATAATAAAAT
Found at i:262789 original size:35 final size:34
Alignment explanation
Indices: 262730--263035 Score: 222
Period size: 35 Copynumber: 8.4 Consensus size: 34
262720 AAAAAAAAAG
* *
262730 AACTATATATTATATATGCTTTTTAAAAATTATTTTCAA
1 AACTATATA--ATATATG--TTTTCAAAA-TGTTTTCAA
* *
262769 AACCATATAATATATGTTTT-AAAACTTGTTTTTAA
1 AACTATATAATATATGTTTTCAAAA--TGTTTTCAA
* *
262804 AACTATATACTATATGTATTT-TAAATGTTTTCAAA
1 AACTATATAATATATGT-TTTCAAAATGTTTTC-AA
* *
262839 AACTATATATTATATATATTTTCAAAATGCTTTCAAA
1 AACTATATA--ATATATGTTTTCAAAATGTTTTC-AA
* * *
262876 AACTCTATATTCTATAGTTTTCAAAATGTTTT-AA
1 AACTATATAATATAT-GTTTTCAAAATGTTTTCAA
* * *
262910 AAATCATATATTATATAGTTTTCAAAATGTGTTTTAAA
1 AACT-ATATAATATAT-GTTTTCAAAA--TGTTTTCAA
* * * *
262948 AACTATATATTATATAAGTTTTCAGAATTTTTTTAA
1 AACTATATA--ATATATGTTTTCAAAATGTTTTCAA
*
262984 AACTGTATATTATATATGTTTTCAAAATGTTTTCAAA
1 AAC--TATATAATATATGTTTTCAAAATGTTTTC-AA
263021 AACTATATAATATAT
1 AACTATATAATATAT
263036 AAATTTTCAA
Statistics
Matches: 220, Mismatches: 31, Indels: 36
0.77 0.11 0.13
Matches are distributed among these distances:
34 15 0.07
35 73 0.33
36 52 0.24
37 49 0.22
38 19 0.09
39 12 0.05
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (34 bp):
AACTATATAATATATGTTTTCAAAATGTTTTCAA
Found at i:262848 original size:37 final size:36
Alignment explanation
Indices: 262730--263047 Score: 262
Period size: 37 Copynumber: 8.7 Consensus size: 36
262720 AAAAAAAAAG
* *
262730 AACTATATATTATATATGCTTTTTAAAAATTATTTTC-AA
1 AACTATATA-TATATATG--TTTTCAAAA-TGTTTTCAAA
* *
262769 AACCATATA-ATATATGTTTT-AAAACTTGTTTT-TAA
1 AACTATATATATATATGTTTTCAAAA--TGTTTTCAAA
* *
262804 AACTATATA-CTATATGTATTT-TAAATGTTTTCAAA
1 AACTATATATATATATGT-TTTCAAAATGTTTTCAAA
* *
262839 AACTATATATTATATATATTTTCAAAATGCTTTCAAA
1 AACTATATA-TATATATGTTTTCAAAATGTTTTCAAA
* *
262876 AACTCTATAT-TCTATAGTTTTCAAAATGTTTT-AAA
1 AACTATATATATATAT-GTTTTCAAAATGTTTTCAAA
*
262911 AA-TCATATAT-TATATAGTTTTCAAAATGTGTTTTAAA
1 AACT-ATATATATATAT-GTTTTCAAAATGT-TTTCAAA
* * **
262948 AACTATATATTATATAAGTTTTCAGAAT-TTTTTTAA
1 AACTATATA-TATATATGTTTTCAAAATGTTTTCAAA
*
262984 AACTGTATATTATATATGTTTTCAAAATGTTTTCAAA
1 AACTATATA-TATATATGTTTTCAAAATGTTTTCAAA
**
263021 AACTATATAATATATAAATTTTCAAAA
1 AACTATAT-ATATATATGTTTTCAAAA
263048 ATCATTTTCT
Statistics
Matches: 236, Mismatches: 27, Indels: 34
0.79 0.09 0.11
Matches are distributed among these distances:
34 11 0.05
35 70 0.30
36 58 0.25
37 72 0.31
38 13 0.06
39 12 0.05
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (36 bp):
AACTATATATATATATGTTTTCAAAATGTTTTCAAA
Found at i:262854 original size:72 final size:70
Alignment explanation
Indices: 262762--263035 Score: 251
Period size: 73 Copynumber: 3.8 Consensus size: 70
262752 TTAAAAATTA
* *
262762 TTTTC-AAAACCATATA--ATATATGTTTT-AAAACTTGTTTTTAAAACTATATACTATATGTAT
1 TTTTCAAAAACTATATATTATATATGTTTTCAAAA--TGTTTTAAAAACTATATACTATATGT-T
*
262823 TTTAAATG
63 TTAAAATG
* * *
262831 TTTTCAAAAACTATATATTATATATATTTTCAAAATGCTTTCAAAAACTCTATATTCTATA-GTT
1 TTTTCAAAAACTATATATTATATATGTTTTCAAAATG-TTTTAAAAA--CTATATACTATATGTT
262895 TTCAAAATG
63 TT-AAAATG
*
262904 TTTT-AAAAA-TCATATATTATATA-GTTTTCAAAATGTGTTTTAAAAACTATATATTATATAAG
1 TTTTCAAAAACT-ATATATTATATATGTTTTCAAAA--TGTTTTAAAAACTATATACTATAT--G
*
262966 TTTTCAGAAT-
61 TTTT-AAAATG
** * *
262976 TTTTTTAAAACTGTATATTATATATGTTTTCAAAATGTTTTCAAAAACTATATAATATAT
1 TTTTCAAAAACTATATATTATATATGTTTTCAAAATGTTTT-AAAAACTATATACTATAT
263036 AAATTTTCAA
Statistics
Matches: 173, Mismatches: 14, Indels: 32
0.79 0.06 0.15
Matches are distributed among these distances:
69 5 0.03
70 20 0.12
71 12 0.07
72 55 0.32
73 59 0.34
74 22 0.13
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.46
Consensus pattern (70 bp):
TTTTCAAAAACTATATATTATATATGTTTTCAAAATGTTTTAAAAACTATATACTATATGTTTTA
AAATG
Found at i:263069 original size:2 final size:2
Alignment explanation
Indices: 263064--263111 Score: 78
Period size: 2 Copynumber: 23.5 Consensus size: 2
263054 TTCTAAAAAA
*
263064 AT AT AT AT ACT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
263107 AT AT A
1 AT AT A
263112 AAATAAAATA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:263373 original size:19 final size:20
Alignment explanation
Indices: 263351--263392 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
263341 AAATTTTAGG
263351 TTAAAG-GATGAATTTAAAT
1 TTAAAGAGATGAATTTAAAT
263370 TTAAAGAGATGAATTTAAAT
1 TTAAAGAGATGAATTTAAAT
263390 TTA
1 TTA
263393 TAAAATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (20 bp):
TTAAAGAGATGAATTTAAAT
Found at i:263427 original size:30 final size:29
Alignment explanation
Indices: 263366--263427 Score: 70
Period size: 30 Copynumber: 2.1 Consensus size: 29
263356 GGATGAATTT
**
263366 AAATTTAAAGAGATGAATTTAAATTTATA
1 AAATTTAAAGAGATGAACATAAATTTATA
* * *
263395 AAATTTGAATGAGATGAACATATATTTTTA
1 AAATTT-AAAGAGATGAACATAAATTTATA
263425 AAA
1 AAA
263428 AAGTATAGAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (29 bp):
AAATTTAAAGAGATGAACATAAATTTATA
Found at i:267901 original size:33 final size:33
Alignment explanation
Indices: 267859--267952 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
267849 TCTTCTTCAT
267859 CCAATAATGCATGCACGGGACGCAATAGGTCCA
1 CCAATAATGCATGCACGGGACGCAATAGGTCCA
*
267892 CCAATAATGCATGCACAGGACGCAATAGGTCCA
1 CCAATAATGCATGCACGGGACGCAATAGGTCCA
*
267925 CCAATAATGCATGCACGAGACGCCAATA
1 CCAATAATGCATGCACGGGACG-CAATA
267953 ATTCAATGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 52 0.91
34 5 0.09
ACGTcount: A:0.36, C:0.28, G:0.21, T:0.15
Consensus pattern (33 bp):
CCAATAATGCATGCACGGGACGCAATAGGTCCA
Found at i:270905 original size:14 final size:14
Alignment explanation
Indices: 270888--270954 Score: 91
Period size: 14 Copynumber: 4.8 Consensus size: 14
270878 ATTATTATTA
270888 TTAAATCATTAAAG
1 TTAAATCATTAAAG
270902 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
270916 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
*
270930 TTAAATTATTAAAG
1 TTAAATCATTAAAG
270944 TTAAATCATTA
1 TTAAATCATTA
270955 TTAGTATCAT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
13 1 0.02
14 44 0.96
15 1 0.02
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:270956 original size:28 final size:29
Alignment explanation
Indices: 270888--270959 Score: 103
Period size: 28 Copynumber: 2.6 Consensus size: 29
270878 ATTATTATTA
*
270888 TTAAATCATTA-AAGTTAAATCATTAAAG
1 TTAAATCATTATTAGTTAAATCATTAAAG
* *
270916 TTAAATAATTATTA-TTAAATTATTAAAG
1 TTAAATCATTATTAGTTAAATCATTAAAG
270944 TTAAATCATTATTAGT
1 TTAAATCATTATTAGT
270960 ATCATTATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 36 0.95
29 2 0.05
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.43
Consensus pattern (29 bp):
TTAAATCATTATTAGTTAAATCATTAAAG
Found at i:271578 original size:23 final size:23
Alignment explanation
Indices: 271547--271661 Score: 176
Period size: 23 Copynumber: 5.0 Consensus size: 23
271537 CACCACAGCT
* * *
271547 CGTATAATTGTACCGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
271570 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
271593 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
*
271616 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
* *
271639 CGTAGAATTGCATCGTAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
271662 TATAATAATG
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 85 1.00
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:277948 original size:2 final size:2
Alignment explanation
Indices: 277941--277977 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
277931 GATAATCTAC
277941 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
277978 GGTTTATACA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:278449 original size:23 final size:23
Alignment explanation
Indices: 278412--278475 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
278402 CAGCTCGTAT
* * *
278412 AATTGCAACGAAGTGCCACGTAG
1 AATTGCACCGTAGTGCCACATAG
**
278435 AATTGCACCAG-AGTGCTGCATAG
1 AATTGCACC-GTAGTGCCACATAG
278458 AATTGCACCGTAGTGCCA
1 AATTGCACCGTAGTGCCA
278476 TATAATAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.94
24 1 0.03
ACGTcount: A:0.31, C:0.23, G:0.25, T:0.20
Consensus pattern (23 bp):
AATTGCACCGTAGTGCCACATAG
Found at i:279924 original size:8 final size:8
Alignment explanation
Indices: 279911--279959 Score: 50
Period size: 8 Copynumber: 6.5 Consensus size: 8
279901 AGTAATCATT
279911 ATTAAATC
1 ATTAAATC
279919 ATTAAAT-
1 ATTAAATC
*
279926 ATCAAATC
1 ATTAAATC
*
279934 ATT-AGT-
1 ATTAAATC
*
279940 ATCAAATC
1 ATTAAATC
279948 ATTAAATC
1 ATTAAATC
279956 ATTA
1 ATTA
279960 TTATTAAATC
Statistics
Matches: 32, Mismatches: 6, Indels: 6
0.73 0.14 0.14
Matches are distributed among these distances:
6 2 0.06
7 10 0.31
8 20 0.62
ACGTcount: A:0.49, C:0.12, G:0.02, T:0.37
Consensus pattern (8 bp):
ATTAAATC
Found at i:279934 original size:15 final size:15
Alignment explanation
Indices: 279914--279954 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
279904 AATCATTATT
279914 AAATCATTAAATATC
1 AAATCATTAAATATC
*
279929 AAATCATT-AGTATC
1 AAATCATTAAATATC
279943 AAATCATTAAAT
1 AAATCATTAAAT
279955 CATTATTATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 13 0.57
15 10 0.43
ACGTcount: A:0.51, C:0.12, G:0.02, T:0.34
Consensus pattern (15 bp):
AAATCATTAAATATC
Found at i:279965 original size:14 final size:14
Alignment explanation
Indices: 279948--280016 Score: 61
Period size: 14 Copynumber: 4.9 Consensus size: 14
279938 GTATCAAATC
279948 ATTAAATCATTATT
1 ATTAAATCATTATT
*
279962 ATTAAATCAATAGTT
1 ATTAAATCATTA-TT
* * *
279977 A--AAATTTAATAATG
1 ATTAAA--TCATTATT
279991 ATTAAATCATTATT
1 ATTAAATCATTATT
280005 ATTAAATCATTA
1 ATTAAATCATTA
280017 AATTTTACTA
Statistics
Matches: 42, Mismatches: 8, Indels: 10
0.70 0.13 0.17
Matches are distributed among these distances:
13 3 0.07
14 30 0.71
15 6 0.14
16 3 0.07
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.43
Consensus pattern (14 bp):
ATTAAATCATTATT
Found at i:280016 original size:22 final size:22
Alignment explanation
Indices: 279919--280019 Score: 82
Period size: 22 Copynumber: 4.7 Consensus size: 22
279909 TTATTAAATC
* *
279919 ATTAAAT-ATCAAATCATTAGT
1 ATTAAATCATTAAATCATTATT
*
279940 ATCAAATCATTAAATCATTATT
1 ATTAAATCATTAAATCATTATT
* * * **
279962 ATTAAATCAAT-AGTTAAAATT
1 ATTAAATCATTAAATCATTATT
* *
279983 -TAATAATGATTAAATCATTATT
1 ATTA-AATCATTAAATCATTATT
280005 ATTAAATCATTAAAT
1 ATTAAATCATTAAAT
280020 TTTACTATTA
Statistics
Matches: 58, Mismatches: 18, Indels: 7
0.70 0.22 0.08
Matches are distributed among these distances:
20 2 0.03
21 17 0.29
22 37 0.64
23 2 0.03
ACGTcount: A:0.49, C:0.08, G:0.03, T:0.41
Consensus pattern (22 bp):
ATTAAATCATTAAATCATTATT
Found at i:282703 original size:19 final size:19
Alignment explanation
Indices: 282682--282717 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
282672 AATATATTTA
282682 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
282700 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
282718 GACTAAATTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Found at i:283286 original size:13 final size:13
Alignment explanation
Indices: 283268--283296 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
283258 CCACCGTACT
283268 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
283281 CCGCCGCCGGCCA
1 CCGCCGCCGGCCA
283294 CCG
1 CCG
283297 TAACGGTGGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.07, C:0.62, G:0.31, T:0.00
Consensus pattern (13 bp):
CCGCCGCCGGCCA
Found at i:283996 original size:3 final size:3
Alignment explanation
Indices: 283982--284135 Score: 222
Period size: 3 Copynumber: 51.7 Consensus size: 3
283972 TTATTTATTA
*
283982 AAT AAT AA- AAT AAT AAT AAT -AT AAT ATT AAT AAT AAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
* *
284026 ACT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * *
284074 AAT AAT AAT AAT ATT AAT AAT ATT AAT AAT GAT AAT AAT AAT ATT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
284122 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
284136 AATGGATAAA
Statistics
Matches: 134, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
2 4 0.03
3 127 0.95
4 3 0.02
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:284715 original size:113 final size:113
Alignment explanation
Indices: 284429--285766 Score: 2309
Period size: 113 Copynumber: 11.9 Consensus size: 113
284419 TGATATCAAC
*
284429 AAAGGTTGAACAAGCTCTTCTCATTATGAA-TTCTTCTTCCTTCTTCAGATGAG---TTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* ** * * * * * **
284490 CATGAACTTTCTTTGGCCATGTTGATCCATCAAATGATGAATTTAAACA
66 -ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
*
284539 AAAAG-TGAACAAGTTCTTCTCATTATGAACTTCTT-TTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
284602 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
*
284650 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
284715 ATGAACTTTCTCTGG-AAA-A-GATCCACCAAATGATGGTTTCAGGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
284760 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
284825 ATGAACCTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
284873 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
284937 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
*
284985 AAAGGTTGAACAAATTCTTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAGGTTGAACAAGTTC-TTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
*
285050 TATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGTTTCAGGCA
65 TATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
285099 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
285164 ATGAACCTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
285212 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
285277 ATGAACCTTCTCTGGTAATGATGATCCACCAAATGATGGATTCAGGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
285325 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
285390 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
*
285438 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
285503 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGTTTCAGGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
285551 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
285616 ATGAACCTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
285664 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
285729 ATGAACCTTCTCTGGTAATGATGATCCATCAAATGATG
66 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATG
285767 AATTTGAATC
Statistics
Matches: 1174, Mismatches: 43, Indels: 19
0.95 0.03 0.02
Matches are distributed among these distances:
109 40 0.03
110 111 0.09
111 45 0.04
112 130 0.11
113 759 0.65
114 89 0.08
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.36
Consensus pattern (113 bp):
AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGCA
Found at i:286450 original size:52 final size:51
Alignment explanation
Indices: 286387--286969 Score: 621
Period size: 52 Copynumber: 11.1 Consensus size: 51
286377 TCCAAATTAA
*
286387 ATGCT-TGATTCTGTCCAATCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATG-TTCT-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
286439 ATGCTATATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCT-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* *
286491 ATGCTATATTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCT-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
** * *** * *
286543 ATGCTATGAATTTCTT-CTTCC--TTCTTCTAAC-CAGATCAGATA-AC-TCAAAGAAC
1 ATGCTATG---TTCTTCCAACCAGATCAGATAACTCA-A--AGA-ACACTTC-CAGAAG
** * *** *
286596 ACTTCCAGAAGATGCTATGTTCTGTCCA-ACCAGATCAGACAACTCAAAGAACACTTCCAGAAG
1 A--T---G-CTATG-T-TCTTCCAACCAGATCAGAT-----AACTCAAAGAACACTTCCAGAAG
*
286659 ATGCTATGTTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
286710 ATGCTATGTTCTT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
286760 ATGCTATGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCT-TCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
286812 ATGCTATGTTCTT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
*
286862 ATGCTATATTCTT-CAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
1 ATGCTATGTTCTTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
* * *
286912 ATGCTATGTTCTTCTAAACAGATCAGATAACTCAAAGAACACTTCCAAAAG
1 ATGCTATGTTCTTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
286963 ATGCTAT
1 ATGCTAT
286970 TGAGCACATA
Statistics
Matches: 461, Mismatches: 40, Indels: 61
0.82 0.07 0.11
Matches are distributed among these distances:
50 147 0.32
51 86 0.19
52 156 0.34
53 13 0.03
54 2 0.00
55 13 0.03
56 7 0.02
57 4 0.01
58 5 0.01
59 6 0.01
60 2 0.00
61 1 0.00
62 1 0.00
63 10 0.02
64 2 0.00
65 4 0.01
66 2 0.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (51 bp):
ATGCTATGTTCTTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
Found at i:286749 original size:50 final size:51
Alignment explanation
Indices: 286564--286969 Score: 728
Period size: 50 Copynumber: 8.0 Consensus size: 51
286554 TTCTTCTTCC
286564 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
* *
286615 TTCTGTCCAACCAGATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
286667 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
286718 TTCTTC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
286768 TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
286820 TTCTTC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATA
1 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
286870 TTCTTC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
1 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
* *
286920 TTCTTCTAAACAGATCAGATAACTCAAAGAACACTTCCAAAAGATGCTAT
1 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
286970 TGAGCACATA
Statistics
Matches: 343, Mismatches: 8, Indels: 8
0.96 0.02 0.02
Matches are distributed among these distances:
50 146 0.43
51 100 0.29
52 97 0.28
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (51 bp):
TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
Found at i:286824 original size:102 final size:101
Alignment explanation
Indices: 286564--286969 Score: 733
Period size: 102 Copynumber: 4.0 Consensus size: 101
286554 TTCTTCTTCC
286564 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTGTCCAACCAG
1 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCT-T-CAACCAG
*
286629 ATCAGACAACTCAAAGAACACTTCCAGAAGATGCTATG
64 ATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
286667 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCAACCAGAT
1 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCAACCAGAT
286732 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
66 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
286768 TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCAACCAGA
1 TTCT-TCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCAACCAGA
*
286833 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATA
65 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
*
286870 TTCTTC-AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCTAAACAGA
1 TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTC-AACCAGA
*
286934 TCAGATAACTCAAAGAACACTTCCAAAAGATGCTAT
65 TCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
286970 TGAGCACATA
Statistics
Matches: 297, Mismatches: 4, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
100 50 0.17
101 91 0.31
102 101 0.34
103 55 0.19
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (101 bp):
TTCTTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGTTCTTCAACCAGAT
CAGATAACTCAAAGAACACTTCCAGAAGATGCTATG
Found at i:287908 original size:6 final size:6
Alignment explanation
Indices: 287899--287971 Score: 86
Period size: 5 Copynumber: 13.0 Consensus size: 6
287889 CACCTTGACC
*
287899 TTCTTT TTC-TT TTCTTT TT-TTT TTC-TT TT-TTT TTCTTT TTCATT
1 TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT TTCTTT
287943 TTCTATT TT-TTT TTCTTT TT-TTT TTCTTT
1 TTCT-TT TTCTTT TTCTTT TTCTTT TTCTTT
287972 CTTCAAGCAT
Statistics
Matches: 58, Mismatches: 2, Indels: 14
0.78 0.03 0.19
Matches are distributed among these distances:
5 27 0.47
6 27 0.47
7 4 0.07
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (6 bp):
TTCTTT
Found at i:287915 original size:11 final size:11
Alignment explanation
Indices: 287899--287971 Score: 103
Period size: 11 Copynumber: 6.5 Consensus size: 11
287889 CACCTTGACC
*
287899 TTCTTTTTCTT
1 TTCTTTTTTTT
287910 TTCTTTTTTTT
1 TTCTTTTTTTT
287921 TTC-TTTTTTT
1 TTCTTTTTTTT
*
287931 TTCTTTTTCATT
1 TTCTTTTT-TTT
287943 TTCTATTTTTTT
1 TTCT-TTTTTTT
287955 TTCTTTTTTTT
1 TTCTTTTTTTT
287966 TTCTTT
1 TTCTTT
287972 CTTCAAGCAT
Statistics
Matches: 56, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
10 10 0.18
11 30 0.54
12 12 0.21
13 4 0.07
ACGTcount: A:0.03, C:0.12, G:0.00, T:0.85
Consensus pattern (11 bp):
TTCTTTTTTTT
Found at i:287917 original size:1 final size:1
Alignment explanation
Indices: 287902--287967 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
287892 CTTGACCTTC
* * * * ** * * *
287902 TTTTTCTTTTCTTTTTTTTTTCTTTTTTTTTCTTTTTCATTTTCTATTTTTTTTTCTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
287967 T
1 T
287968 CTTTCTTCAA
Statistics
Matches: 48, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 48 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (1 bp):
T
Found at i:299195 original size:18 final size:18
Alignment explanation
Indices: 299172--299215 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
299162 TTCTATTAAA
*
299172 AAAATATTTAAAAACA-AT
1 AAAATAATT-AAAACATAT
299190 AAAATAAATTAAAACATAT
1 AAAAT-AATTAAAACATAT
299209 AAAATAA
1 AAAATAA
299216 ATGACTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 13 0.57
19 10 0.43
ACGTcount: A:0.70, C:0.05, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAATAATTAAAACATAT
Found at i:299201 original size:19 final size:19
Alignment explanation
Indices: 299182--299217 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
299172 AAAATATTTA
299182 AAAACA-ATAAAATAAATT
1 AAAACATATAAAATAAATT
299200 AAAACATATAAAATAAAT
1 AAAACATATAAAATAAAT
299218 GACTAATTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAACATATAAAATAAATT
Done.