Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004123.1 Hibiscus syriacus cultivar Beakdansim tig00009023_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: 1596068
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 9
Found at i:790986 original size:33 final size:33
Alignment explanation
Indices: 790877--790990 Score: 95
Period size: 33 Copynumber: 3.2 Consensus size: 33
790867 TGAAACTTAA
* *
790877 AATCGCAACACGAAAATGAAAATCGCAACACGAAAATG
1 AATCGCAACGCG-AAATGAAAATCGC-A-ACG-ACA-G
* **
790915 ACTATCGCAACGCGAATTTGACTATCGCAACG-CAAG
1 A--ATCGCAACGCGAA-ATGAAAATCGCAACGAC-AG
790951 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGACAG
790984 AATCGCA
1 AATCGCA
790991 TTGCGATAGT
Statistics
Matches: 63, Mismatches: 8, Indels: 15
0.73 0.09 0.17
Matches are distributed among these distances:
33 21 0.33
34 14 0.22
36 2 0.03
37 1 0.02
38 4 0.06
39 3 0.05
40 18 0.29
ACGTcount: A:0.44, C:0.25, G:0.18, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGACAG
Found at i:791375 original size:22 final size:22
Alignment explanation
Indices: 791313--791378 Score: 105
Period size: 22 Copynumber: 3.0 Consensus size: 22
791303 TGACCGTGAA
* *
791313 TGATTTCGCCGGAGATGGAGAC
1 TGATTTCGTCGGAGATGGGGAC
*
791335 TGATATCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
791357 TGATTTCGTCGGAGATGGGGAC
1 TGATTTCGTCGGAGATGGGGAC
791379 GGATGTCGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.21, C:0.15, G:0.39, T:0.24
Consensus pattern (22 bp):
TGATTTCGTCGGAGATGGGGAC
Found at i:791600 original size:20 final size:20
Alignment explanation
Indices: 791577--791649 Score: 128
Period size: 20 Copynumber: 3.6 Consensus size: 20
791567 CAATAGTCAG
*
791577 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
791597 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
791617 ATTCGTATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
791637 ATTCGCATTGCGA
1 ATTCGCATTGCGA
791650 ATTAGGAAAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.19, C:0.19, G:0.22, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:791670 original size:21 final size:20
Alignment explanation
Indices: 791646--791690 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
791636 TATTCGCATT
791646 GCGAATTAGGAAAATCGCAAC
1 GCGAATT-GGAAAATCGCAAC
* *
791667 GCGAATTTGAAAATCGCAAT
1 GCGAATTGGAAAATCGCAAC
791687 GCGA
1 GCGA
791691 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.18
Consensus pattern (20 bp):
GCGAATTGGAAAATCGCAAC
Found at i:800240 original size:123 final size:123
Alignment explanation
Indices: 800055--800368 Score: 440
Period size: 123 Copynumber: 2.5 Consensus size: 123
800045 AAATTAAGGT
800055 AAGGTTGAACAAATTCTTCTCATTATGAAC--TTCTTCCTCTTCAGATGAGTTCTTCTCATTATG
1 AAGGTTGAACAAATTCTTCTCATTATGAACTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATG
* * * *
800118 AAC-TCTTTCTGGAAATGTTGATGTTGATCTATCTCTTTCTGTGATAGCGTCGA-GC-AA
66 AACTTC-ATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTC-ATGCAAA
*
800175 AAGGTTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTCTTCAGATGAGCTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAAC-TTTTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
*
800240 GAACTTCATCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAAAA
65 GAACTTCATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGC--AAA
** * * *
800301 AAAATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTTAGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAATTCTTCTCATTATGAACTT-TTCTTCCTCTTCAGATGAGTTCTTCTCATTAT
800366 GAA
65 GAA
800369 TTTCTTCTTC
Statistics
Matches: 173, Mismatches: 12, Indels: 12
0.88 0.06 0.06
Matches are distributed among these distances:
120 30 0.17
122 1 0.01
123 77 0.45
124 2 0.01
125 2 0.01
126 61 0.35
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.40
Consensus pattern (123 bp):
AAGGTTGAACAAATTCTTCTCATTATGAACTTTTCTTCCTCTTCAGATGAGTTCTTCTCATTATG
AACTTCATCTGGAAATGTTGATGCTGATCTATCTCCTTCTGTGATAGAGTCATGCAAA
Found at i:800337 original size:20 final size:19
Alignment explanation
Indices: 800314--800378 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
800304 ATTGAACAAG
800314 TTCTTCTCATTATGAACTTC
1 TTCTTCTCATTATGAA-TTC
* **
800334 TTCTTCTTCTTTA-G-ATGAG
1 TTCTTC-TCATTATGAAT-TC
800353 TTCTTCTCATTATGAATTTC
1 TTCTTCTCATTATGAA-TTC
800373 TTCTTC
1 TTCTTC
800379 CTTCTTCAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 10
0.68 0.12 0.20
Matches are distributed among these distances:
18 6 0.18
19 8 0.24
20 14 0.41
21 6 0.18
ACGTcount: A:0.17, C:0.22, G:0.08, T:0.54
Consensus pattern (19 bp):
TTCTTCTCATTATGAATTC
Found at i:800355 original size:39 final size:40
Alignment explanation
Indices: 800312--800410 Score: 173
Period size: 40 Copynumber: 2.5 Consensus size: 40
800302 AAATTGAACA
*
800312 AGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTTAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
*
800351 AGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
800391 AGTTCTTCTCATTATGAACT
1 AGTTCTTCTCATTATGAACT
800411 CTACCTAGCA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 26 0.46
40 30 0.54
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.49
Consensus pattern (40 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG
Found at i:800558 original size:113 final size:113
Alignment explanation
Indices: 800351--800635 Score: 462
Period size: 113 Copynumber: 2.5 Consensus size: 113
800341 TCTTTAGATG
*
800351 AGTTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
* * * * **
800416 TAGCAATGTTGATCAATCAAGTGATGAATTCGAGCAAAAGGTTGAACA
66 TAGCAATGCTAATCAATCAAGGGACGAATTAAAGCAAAAGGTTGAACA
800464 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
* * * *
800529 TGGCAATGCTAATCCATCGAGGGACGAATTAAAGTAAAAGGTTGAACA
66 TAGCAATGCTAATCAATCAAGGGACGAATTAAAGCAAAAGGTTGAACA
*
800577 AATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
1 AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC
800636 ACTTCTGGAA
Statistics
Matches: 160, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
113 160 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (113 bp):
AGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACC
TAGCAATGCTAATCAATCAAGGGACGAATTAAAGCAAAAGGTTGAACA
Found at i:801477 original size:22 final size:22
Alignment explanation
Indices: 801422--801479 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
801412 AATAAAGCTT
* *
801422 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
801444 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
801466 TCATCTTTGAAGAG
1 TCATCTTTGAAGAG
801480 TGTAGATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.34
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:817938 original size:30 final size:31
Alignment explanation
Indices: 817904--817964 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
817894 TTTGTCAAAA
* * * *
817904 TTTA-GGGCCAAATTGATATTTTATCTAAAG
1 TTTAGGGGACAAAGTGATACTTCATCTAAAG
817934 TTTAGGGGACAAAGTGATACTTCATCTAAAG
1 TTTAGGGGACAAAGTGATACTTCATCTAAAG
817965 CTTAAGGGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (31 bp):
TTTAGGGGACAAAGTGATACTTCATCTAAAG
Found at i:826253 original size:17 final size:18
Alignment explanation
Indices: 826231--826269 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
826221 CATAGAGGTT
826231 TTATATTTAATTTT-ATA
1 TTATATTTAATTTTAATA
*
826248 TTATATTTGATTTTAATA
1 TTATATTTAATTTTAATA
826266 TTAT
1 TTAT
826270 TTTTTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (18 bp):
TTATATTTAATTTTAATA
Found at i:826305 original size:14 final size:13
Alignment explanation
Indices: 826286--826369 Score: 54
Period size: 14 Copynumber: 6.5 Consensus size: 13
826276 AAATAAATTA
826286 AATATTAATTTTTT
1 AATATTAA-TTTTT
*
826300 AATATT-ATATTAT
1 AATATTAAT-TTTT
826313 AGATATTAA-TTTT
1 A-ATATTAATTTTT
826326 AATATT-ATATTTT
1 AATATTAAT-TTTT
* *
826339 AA-A-TAA-ATTA
1 AATATTAATTTTT
826349 AATATTAATTTTTT
1 AATATTAA-TTTTT
826363 AATATTA
1 AATATTA
826370 TTATAGATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 20
0.68 0.08 0.25
Matches are distributed among these distances:
10 4 0.07
11 3 0.06
12 11 0.20
13 15 0.28
14 20 0.37
15 1 0.02
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (13 bp):
AATATTAATTTTT
Found at i:826311 original size:26 final size:27
Alignment explanation
Indices: 826261--826336 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 27
826251 TATTTGATTT
* *
826261 TAATATTATTTTTTTAA-A-TAAATTA
1 TAATATTAATTTTTTAATATTATATTA
826286 -AATATTAATTTTTTAATATTATATTA
1 TAATATTAATTTTTTAATATTATATTA
826312 TAGATATTAA--TTTTAATATTATATT
1 TA-ATATTAATTTTTTAATATTATATT
826337 TTAAATAAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
24 15 0.33
25 1 0.02
26 21 0.47
27 1 0.02
28 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (27 bp):
TAATATTAATTTTTTAATATTATATTA
Found at i:826350 original size:63 final size:63
Alignment explanation
Indices: 826236--826396 Score: 226
Period size: 63 Copynumber: 2.6 Consensus size: 63
826226 AGGTTTTATA
* * *
826236 TTTAATTTTATATTAT--AT-TTGATTTTAATATTATTTTTTTAAATAAATTAAATATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTA-TATTTTAAATAAATTAAATATTAATTT
826297 TTTAATATTATATTATAGATATTAATTTTAATATTATATTTTAAATAAATTAAATATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTAATATTATATTTTAAATAAATTAAATATTAATTT
*
826360 TTTAATA-T-TATTATAGATATTTAATTTT-ATATCATAT
1 TTTAATATTATATTATAGATA-TTAATTTTAATATTATAT
826397 AAATTATTTT
Statistics
Matches: 92, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
61 34 0.37
62 9 0.10
63 35 0.38
64 14 0.15
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.57
Consensus pattern (63 bp):
TTTAATATTATATTATAGATATTAATTTTAATATTATATTTTAAATAAATTAAATATTAATTT
Found at i:826443 original size:20 final size:19
Alignment explanation
Indices: 826383--826444 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
826373 TAGATATTTA
*
826383 ATTTTATATCA-TATAAATT
1 ATTTTATAT-ATTATTAATT
*
826402 ATTTTATATATTATTAA-A
1 ATTTTATATATTATTAATT
826420 ATTTTATAT-TTATTTTAATT
1 ATTTTATATATTA--TTAATT
826440 ATTTT
1 ATTTT
826445 GATTTAAGTT
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
17 3 0.08
18 10 0.28
19 18 0.50
20 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
ATTTTATATATTATTAATT
Found at i:829389 original size:44 final size:44
Alignment explanation
Indices: 829283--829374 Score: 121
Period size: 44 Copynumber: 2.0 Consensus size: 44
829273 GTGTAATATT
* *
829283 TTACCATTTAATACCATAAGCTCGCAAGCTTACTTTACCAATATAC
1 TTACCA-TTCATA-CATAAGCTCGCAAGCTTACTTTACCAATACAC
* * *
829329 TTACCATTCATCCATAAGCTCGTAAGCTTATTTTACCAATACAC
1 TTACCATTCATACATAAGCTCGCAAGCTTACTTTACCAATACAC
829373 TT
1 TT
829375 TTCATTATTA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 31 0.76
45 4 0.10
46 6 0.15
ACGTcount: A:0.33, C:0.26, G:0.07, T:0.35
Consensus pattern (44 bp):
TTACCATTCATACATAAGCTCGCAAGCTTACTTTACCAATACAC
Found at i:829568 original size:25 final size:25
Alignment explanation
Indices: 829540--829666 Score: 94
Period size: 23 Copynumber: 5.2 Consensus size: 25
829530 CCCGATTATG
829540 ACACATAAGGTCGTGCCCACCATAT
1 ACACATAAGGTCGTGCCCACCATAT
*
829565 ACAC-T-AGGT-AT-CCTC-CCGAATAT
1 ACACATAAGGTCGTGCC-CACC--ATAT
829588 GACACATAAGGTCGTGCCCACCATAT
1 -ACACATAAGGTCGTGCCCACCATAT
*
829614 ACAC-T-AGGT-AT-CCTC-CCGAATAT
1 ACACATAAGGTCGTGCC-CACC--ATAT
829637 GACACATAAGGTCGTGCCCACCATAT
1 -ACACATAAGGTCGTGCCCACCATAT
829663 ACAC
1 ACAC
829667 TAGGTATCCT
Statistics
Matches: 80, Mismatches: 4, Indels: 36
0.67 0.03 0.30
Matches are distributed among these distances:
21 8 0.10
22 4 0.05
23 16 0.20
24 10 0.12
25 14 0.17
26 16 0.20
27 4 0.05
28 8 0.10
ACGTcount: A:0.31, C:0.31, G:0.16, T:0.21
Consensus pattern (25 bp):
ACACATAAGGTCGTGCCCACCATAT
Found at i:829599 original size:26 final size:26
Alignment explanation
Indices: 829570--829648 Score: 80
Period size: 24 Copynumber: 3.2 Consensus size: 26
829560 CATATACACT
829570 AGGTATCCTCCCGAATATGACACATA
1 AGGTATCCTCCCGAATATGACACATA
*
829596 AGG--TCGTGCCC-ACCATAT-ACAC-T-
1 AGGTATCCT-CCCGA--ATATGACACATA
829619 AGGTATCCTCCCGAATATGACACATA
1 AGGTATCCTCCCGAATATGACACATA
829645 AGGT
1 AGGT
829649 CGTGCCCACC
Statistics
Matches: 42, Mismatches: 2, Indels: 18
0.68 0.03 0.29
Matches are distributed among these distances:
23 7 0.17
24 12 0.29
25 12 0.29
26 11 0.26
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.23
Consensus pattern (26 bp):
AGGTATCCTCCCGAATATGACACATA
Found at i:829601 original size:49 final size:49
Alignment explanation
Indices: 829529--829676 Score: 287
Period size: 49 Copynumber: 3.0 Consensus size: 49
829519 TTAAGTACAG
*
829529 TCCCGATTATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCC
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCC
829578 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCC
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCC
829627 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCC
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCC
829676 T
1 T
829677 TTAGTGTATT
Statistics
Matches: 98, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 98 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (49 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTAGGTATCC
Found at i:833218 original size:6 final size:6
Alignment explanation
Indices: 833207--833247 Score: 82
Period size: 6 Copynumber: 6.8 Consensus size: 6
833197 TTCGGAGTTC
833207 GGGATA GGGATA GGGATA GGGATA GGGATA GGGATA GGGAT
1 GGGATA GGGATA GGGATA GGGATA GGGATA GGGATA GGGAT
833248 GATAAACGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.51, T:0.17
Consensus pattern (6 bp):
GGGATA
Found at i:834291 original size:65 final size:65
Alignment explanation
Indices: 834171--834325 Score: 161
Period size: 65 Copynumber: 2.4 Consensus size: 65
834161 TACACTAGGG
* ** *
834171 GTGCATCGGTACACT-AATTACATTCGATGTTTTGAAAGAGCCAGGAGGGCATCGATGCATGG-T
1 GTGCATCGGTACA-TAAAATACATTCGATGTTTCAAAAGAGCCAAGAGGGCATCGATGCATGGAT
834234 CT
65 -T
* ** * *
834236 GTGCATCGGTACATAAAATACATTCGATGTTTCAAAATATTCAAGAGTGCGTCGATGCATGGATT
1 GTGCATCGGTACATAAAATACATTCGATGTTTCAAAAGAGCCAAGAGGGCATCGATGCATGGATT
* * * *
834301 GCGTATCGGTACACAAAATGCATTC
1 GTGCATCGGTACATAAAATACATTC
834326 AAAATAGGTG
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
64 1 0.01
65 73 0.97
66 1 0.01
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.28
Consensus pattern (65 bp):
GTGCATCGGTACATAAAATACATTCGATGTTTCAAAAGAGCCAAGAGGGCATCGATGCATGGATT
Found at i:837211 original size:23 final size:22
Alignment explanation
Indices: 837179--837294 Score: 92
Period size: 23 Copynumber: 5.2 Consensus size: 22
837169 CATCATAGTA
837179 CATCGATGCACATTCAAGGAATG
1 CATCGATGCACATTCAAGG-ATG
* * *
837202 CATCGGTGCACCTTCATGG-TG
1 CATCGATGCACATTCAAGGATG
* *
837223 TATCGATGCACATTCAAGGAATT
1 CATCGATGCACATTCAAGG-ATG
* * * *
837246 CATCGGTGCACCTCCATGG-TG
1 CATCGATGCACATTCAAGGATG
* *
837267 TATTGATGCACATTCAAGGGATG
1 CATCGATGCACATTCAA-GGATG
837290 CATCG
1 CATCG
837295 GTACACTGTC
Statistics
Matches: 67, Mismatches: 22, Indels: 8
0.69 0.23 0.08
Matches are distributed among these distances:
21 29 0.43
22 2 0.03
23 36 0.54
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGATG
Found at i:837230 original size:44 final size:44
Alignment explanation
Indices: 837180--837321 Score: 198
Period size: 44 Copynumber: 3.2 Consensus size: 44
837170 ATCATAGTAC
837180 ATCGATGCACATTCAAGGAATGCATCGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGAATGCATCGGTGCACCTTCATGGTGT
* *
837224 ATCGATGCACATTCAAGGAATTCATCGGTGCACCTCCATGGTGT
1 ATCGATGCACATTCAAGGAATGCATCGGTGCACCTTCATGGTGT
* * * *
837268 ATTGATGCACATTCAAGGGATGCATCGGTACA-CTGTC-TAGTGT
1 ATCGATGCACATTCAAGGAATGCATCGGTGCACCT-TCATGGTGT
*
837311 ATCAATGCACA
1 ATCGATGCACA
837322 AAGCATAAAA
Statistics
Matches: 87, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
43 16 0.18
44 71 0.82
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (44 bp):
ATCGATGCACATTCAAGGAATGCATCGGTGCACCTTCATGGTGT
Found at i:841069 original size:21 final size:21
Alignment explanation
Indices: 841035--841076 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
841025 GAGATTATTT
*
841035 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTAAAATA
**
841056 TCATTTTTGTATTTTAAAATA
1 TCATTTTTCAATTTTAAAATA
841077 ATTTCTTATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAATA
Found at i:850656 original size:11 final size:12
Alignment explanation
Indices: 850611--850656 Score: 56
Period size: 12 Copynumber: 3.7 Consensus size: 12
850601 ATAATCAATA
*
850611 AAAGAAAAAAAT
1 AAAGAAAAAAAC
850623 ACAAGAATAAAAAC
1 A-AAGAA-AAAAAC
850637 AAAGAAAAAAAC
1 AAAGAAAAAAAC
*
850649 AAATAAAA
1 AAAGAAAA
850657 GAAAATAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 14 0.47
13 10 0.33
14 6 0.20
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.07
Consensus pattern (12 bp):
AAAGAAAAAAAC
Found at i:850666 original size:13 final size:13
Alignment explanation
Indices: 850607--850667 Score: 50
Period size: 13 Copynumber: 4.4 Consensus size: 13
850597 AAGAATAATC
850607 AATAAAAGAAAAA
1 AATAAAAGAAAAA
*
850620 AATACAAGAATAAA
1 AATAAAAGAA-AAA
* *
850634 AACAAAGAAAAAAACA
1 AA-TAA-AAGAAAA-A
*
850650 AATAAAAGAAAAT
1 AATAAAAGAAAAA
850663 AATAA
1 AATAA
850668 TAATGAATAA
Statistics
Matches: 37, Mismatches: 7, Indels: 8
0.71 0.13 0.15
Matches are distributed among these distances:
13 14 0.38
14 11 0.30
15 5 0.14
16 7 0.19
ACGTcount: A:0.79, C:0.05, G:0.07, T:0.10
Consensus pattern (13 bp):
AATAAAAGAAAAA
Found at i:850777 original size:3 final size:3
Alignment explanation
Indices: 850758--850829 Score: 67
Period size: 3 Copynumber: 23.7 Consensus size: 3
850748 TAGGAAGACA
* * *
850758 AAT AAT AAAT AAA AAT AAT -AT ATAT ATAT AAG AA- AAT AAT AAT AGT
1 AAT AAT -AAT AAT AAT AAT AAT A-AT A-AT AAT AAT AAT AAT AAT AAT
*
850804 AAT AAT AAT AGT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
850830 ATAAAGTAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
2 4 0.07
3 44 0.76
4 10 0.17
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:852616 original size:34 final size:34
Alignment explanation
Indices: 852573--852726 Score: 91
Period size: 34 Copynumber: 4.3 Consensus size: 34
852563 CTCATTCGCT
852573 GTGAAGTTGAGCTTTGAATTGGATATCCTTCGTC
1 GTGAAGTTGAGCTTTGAATTGGATATCCTTCGTC
* * *
852607 GTGAAGTTGAAATCCAATCTAGAGTTGGCACAATATCCTTCG-C
1 GTGAAGTTG--A-GC--T-TTGAATTGG----ATATCCTTCGTC
** ** *
852650 TGTGAAGTTGAAATTGTGAA-TGG--CCCCTTCGTT
1 -GTGAAGTTGAGCTT-TGAATTGGATATCCTTCGTC
*
852683 GTGAAGTTGAGCCTTGAATTGGATATCCTTCGTC
1 GTGAAGTTGAGCTTTGAATTGGATATCCTTCGTC
852717 GTGAAGTTGA
1 GTGAAGTTGA
852727 AATCCAAATA
Statistics
Matches: 88, Mismatches: 16, Indels: 32
0.65 0.12 0.24
Matches are distributed among these distances:
31 4 0.05
32 20 0.23
34 26 0.30
36 1 0.01
37 1 0.01
38 4 0.05
39 4 0.05
40 7 0.08
42 1 0.01
43 1 0.01
44 19 0.22
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (34 bp):
GTGAAGTTGAGCTTTGAATTGGATATCCTTCGTC
Found at i:852844 original size:119 final size:117
Alignment explanation
Indices: 852567--852968 Score: 511
Period size: 119 Copynumber: 3.5 Consensus size: 117
852557 AGAATGCTCA
* * ** *
852567 TTCGCTGTGAAGTTGAGCTTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTAG-A-
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGATTGAAT
* * *
852630 ---G-TT-GGCACAATATCCTTCG-CTGTGAAGTTGAAATTGTGAATGGCCCC
66 TCTGCTTGGGCACGATATCCTTCGTC-GTGAAGTTGAAATTGTGGATGGCCCT
852677 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA-ATATGAA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGAT-TGAA
852741 TAT-TGCTGGTGGGCACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATGGCCCT
65 T-TCTGCT--TGGGCACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATGGCCCT
* * * *
852796 TTCATTGTGAAGTTGAGCCTTGAATTGGATATCATTCGTCGTGAAGTTGAAATCCAAGGGTTGCA
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAA-GATTGAA
* * * *
852861 TTCCTGCTTGTGCATGATATCTTTCGTCGTGAAGTTGAAATCGTGGATGGCCCCT
65 TT-CTGCTTGGGCACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATGG-CCCT
852916 TT-GTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
1 TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATC
852969 TAAGTGTTGT
Statistics
Matches: 259, Mismatches: 17, Indels: 23
0.87 0.06 0.08
Matches are distributed among these distances:
109 1 0.00
110 56 0.22
111 1 0.00
115 1 0.00
116 1 0.00
118 1 0.00
119 182 0.70
120 11 0.04
121 5 0.02
ACGTcount: A:0.23, C:0.17, G:0.26, T:0.34
Consensus pattern (117 bp):
TTCGTTGTGAAGTTGAGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCCAAGATTGAAT
TCTGCTTGGGCACGATATCCTTCGTCGTGAAGTTGAAATTGTGGATGGCCCT
Found at i:853069 original size:65 final size:64
Alignment explanation
Indices: 852930--853105 Score: 234
Period size: 65 Copynumber: 2.8 Consensus size: 64
852920 TGTGAAGTTG
* * * *
852930 AGCCTTGAATTGGATATCCTTCGTCGTGAAGTTGAAATCTAA---GTGT-TGTTTCACCAAATT
1 AGCCTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAGTATGTCTCACCAAATT
* *
852990 AGCTTTGAGTTGGATATCCTTCGTCATGAAGTTGAAATCCAATCTTGAGTATGTCTCACCAAATT
1 AGCCTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATC-TGAGTATGTCTCACCAAATT
* *
853055 GGCCTTGAGTTGGATATCCTTCGTTGTGAAGTTGAAATCCAATCTCGAGTA
1 AGCCTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCT-GAGTA
853106 CATGGTGTCG
Statistics
Matches: 100, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
60 38 0.38
64 4 0.04
65 58 0.58
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.35
Consensus pattern (64 bp):
AGCCTTGAGTTGGATATCCTTCGTCGTGAAGTTGAAATCCAATCTGAGTATGTCTCACCAAATT
Found at i:854020 original size:9 final size:8
Alignment explanation
Indices: 853970--854021 Score: 50
Period size: 8 Copynumber: 6.2 Consensus size: 8
853960 ACCCTAAATG
*
853970 TTTTTCTC
1 TTTTTTTC
*
853978 TTTTTTTG
1 TTTTTTTC
*
853986 TTTTTTTT
1 TTTTTTTC
853994 TGTTTTTTC
1 T-TTTTTTC
*
854003 TCTTTTTC
1 TTTTTTTC
854011 TTTTTCTTC
1 TTTTT-TTC
854020 TT
1 TT
854022 CGATTTAGGA
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
8 24 0.67
9 12 0.33
ACGTcount: A:0.00, C:0.13, G:0.04, T:0.83
Consensus pattern (8 bp):
TTTTTTTC
Found at i:855175 original size:18 final size:19
Alignment explanation
Indices: 855130--855181 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
855120 ATGTTAGCAT
855130 GAAAAATATAAC-ATAACAA
1 GAAAAATA-AACAATAACAA
*
855149 AAAAGAATAAACAATAA-AA
1 GAAA-AATAAACAATAACAA
855168 GAAAAATAATACAA
1 GAAAAATAA-ACAA
855182 GAATAAAACA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
18 5 0.18
19 15 0.54
20 8 0.29
ACGTcount: A:0.73, C:0.08, G:0.06, T:0.13
Consensus pattern (19 bp):
GAAAAATAAACAATAACAA
Found at i:855186 original size:11 final size:11
Alignment explanation
Indices: 855161--855210 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
855151 AAGAATAAAC
* *
855161 AATAAAAGAAA
1 AATAAAACAAG
*
855172 AATAATACAAG
1 AATAAAACAAG
855183 AATAAAACAAAG
1 AATAAAAC-AAG
855195 AA-AAAACAA-
1 AATAAAACAAG
855204 AATAAAA
1 AATAAAA
855211 GAAAATTAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
9 2 0.06
10 6 0.18
11 20 0.61
12 5 0.15
ACGTcount: A:0.78, C:0.06, G:0.06, T:0.10
Consensus pattern (11 bp):
AATAAAACAAG
Found at i:855186 original size:22 final size:21
Alignment explanation
Indices: 855148--855221 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 21
855138 TAACATAACA
*
855148 AAAAAGAATA-AACAATAAAAG
1 AAAAATAATACAA-AATAAAAG
*
855169 AAAAATAATACAAGAATAAAAC
1 AAAAATAATACAA-AATAAAAG
*
855191 AAAGAA-AAAACAAAATAAAAG
1 AAA-AATAATACAAAATAAAAG
*
855212 AAAATTAATA
1 AAAAATAATA
855222 ATAAAAAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
20 1 0.02
21 22 0.51
22 18 0.42
23 2 0.05
ACGTcount: A:0.76, C:0.05, G:0.07, T:0.12
Consensus pattern (21 bp):
AAAAATAATACAAAATAAAAG
Found at i:855207 original size:29 final size:29
Alignment explanation
Indices: 855149--855213 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 29
855139 AACATAACAA
855149 AAAAGAATAAACAATAAAAGAAAAATAAT
1 AAAAGAATAAACAATAAAAGAAAAATAAT
*
855178 ACAAGAATAAAACAA-AGAAA-AAACAA-AAT
1 AAAAGAAT-AAACAATA-AAAGAAA-AATAAT
855207 AAAAGAA
1 AAAAGAA
855214 AATTAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
29 20 0.65
30 11 0.35
ACGTcount: A:0.77, C:0.06, G:0.08, T:0.09
Consensus pattern (29 bp):
AAAAGAATAAACAATAAAAGAAAAATAAT
Found at i:855323 original size:3 final size:3
Alignment explanation
Indices: 855310--855385 Score: 50
Period size: 3 Copynumber: 24.7 Consensus size: 3
855300 AGGAAGACAA
* *
855310 AAT AAT AAAT AAT AGAT AAA AAT AAAT AAT -AT ATAT ATAT AAG AA-
1 AAT AAT -AAT AAT A-AT AAT AAT -AAT AAT AAT A-AT A-AT AAT AAT
* *
855355 AAT AAT AAT AGT AA- AAT AAT AGT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
855386 GTAAATAAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 14
0.74 0.09 0.17
Matches are distributed among these distances:
2 6 0.10
3 37 0.63
4 16 0.27
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:855361 original size:24 final size:21
Alignment explanation
Indices: 855308--855364 Score: 62
Period size: 24 Copynumber: 2.6 Consensus size: 21
855298 CTAGGAAGAC
855308 AAAATAATAA-ATAATAGATA
1 AAAATAATAATATAATAGATA
*
855328 AAAATAAATAATATATATATATAA
1 AAAAT-AATAATATA-ATAGAT-A
855352 GAAAATAATAATA
1 -AAAATAATAATA
855365 GTAAAATAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
20 5 0.16
21 5 0.16
22 3 0.10
23 5 0.16
24 8 0.26
25 5 0.16
ACGTcount: A:0.68, C:0.00, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAATAATAATATAATAGATA
Found at i:855372 original size:11 final size:12
Alignment explanation
Indices: 855355--855385 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
855345 TATATAAGAA
855355 AATAATAATAGT
1 AATAATAATAGT
855367 AA-AATAATAGT
1 AATAATAATAGT
855378 AATAATAA
1 AATAATAA
855386 GTAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (12 bp):
AATAATAATAGT
Found at i:855486 original size:16 final size:16
Alignment explanation
Indices: 855449--855496 Score: 55
Period size: 14 Copynumber: 3.0 Consensus size: 16
855439 TAATAAGTAA
*
855449 AAATAAAATATAACAAAC
1 AAATAAAATA-AA-AAAG
855467 AAATAAAATAAAAAAG
1 AAATAAAATAAAAAAG
855483 AAAT--AATAAAAAAG
1 AAATAAAATAAAAAAG
855497 TAAAAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.34
16 7 0.24
17 2 0.07
18 10 0.34
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (16 bp):
AAATAAAATAAAAAAG
Found at i:855492 original size:14 final size:14
Alignment explanation
Indices: 855471--855507 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
855461 ACAAACAAAT
855471 AAAATAAAAAAG-A
1 AAAATAAAAAAGTA
855484 AATAATAAAAAAGTA
1 AA-AATAAAAAAGTA
855499 AAAATAAAA
1 AAAATAAAA
855508 GGACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 17 0.77
15 3 0.14
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (14 bp):
AAAATAAAAAAGTA
Found at i:855704 original size:1 final size:1
Alignment explanation
Indices: 855698--855731 Score: 59
Period size: 1 Copynumber: 34.0 Consensus size: 1
855688 GTCCAAATTC
*
855698 AAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
855732 TGAGTCTCAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.97, C:0.00, G:0.00, T:0.03
Consensus pattern (1 bp):
A
Found at i:860183 original size:14 final size:15
Alignment explanation
Indices: 860160--860192 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
860150 TATAAAAAGT
860160 ATATAGTTTATAA-A
1 ATATAGTTTATAATA
*
860174 ATATATTTTATAATA
1 ATATAGTTTATAATA
860189 ATAT
1 ATAT
860193 GTACGTACGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATATAGTTTATAATA
Found at i:860202 original size:4 final size:4
Alignment explanation
Indices: 860193--860274 Score: 74
Period size: 4 Copynumber: 20.5 Consensus size: 4
860183 ATAATAATAT
* * * * * * *
860193 GTAC GTAC GTAC GTAC GTAT GAAT GTAC GTAT GTAT GTAT GTAC GTAT
1 GTAC GTAC GTAC GTAC GTAC GTAC GTAC GTAC GTAC GTAC GTAC GTAC
* * *
860241 GTAT GTAT GTAC GTAC GTAC GTAC GTAT GTAC GT
1 GTAC GTAC GTAC GTAC GTAC GTAC GTAC GTAC GT
860275 GTGTGTGTGT
Statistics
Matches: 68, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 68 1.00
ACGTcount: A:0.26, C:0.13, G:0.26, T:0.35
Consensus pattern (4 bp):
GTAC
Found at i:860222 original size:16 final size:16
Alignment explanation
Indices: 860201--860701 Score: 185
Period size: 16 Copynumber: 32.4 Consensus size: 16
860191 ATGTACGTAC
*
860201 GTACGTACGTATGAAT
1 GTACGTACGTATGTAT
*
860217 GTACGTATGTATGTAT
1 GTACGTACGTATGTAT
*
860233 GTACGTATGTATGTAT
1 GTACGTACGTATGTAT
* *
860249 GTACGTACGTACGTAC
1 GTACGTACGTATGTAT
* * *
860265 GTATGTACGTGTGTGT
1 GTACGTACGTATGTAT
* *
860281 GT--GT--GTGTGTGT
1 GTACGTACGTATGTAT
** *
860293 GTACGTACGTACATAC
1 GTACGTACGTATGTAT
** ** *
860309 GTATATATATATATAT
1 GTACGTACGTATGTAT
* ** ** *
860325 ATATATATATATATAT
1 GTACGTACGTATGTAT
860341 GTACGTACGTATGTAT
1 GTACGTACGTATGTAT
860357 GTA--TA--TATGTAT
1 GTACGTACGTATGTAT
** *
860369 GTATATATGTATGTAT
1 GTACGTACGTATGTAT
* * ** *
860385 ATATGTATATATATAT
1 GTACGTACGTATGTAT
* *
860401 GTATGTATGTATGTAT
1 GTACGTACGTATGTAT
** *
860417 GTATATATGTATGTAT
1 GTACGTACGTATGTAT
* *
860433 GTATGTATGTATGTAT
1 GTACGTACGTATGTAT
* *
860449 GTATGTATGTATGTAT
1 GTACGTACGTATGTAT
* *
860465 GTATGTATGTATGTAT
1 GTACGTACGTATGTAT
* *
860481 GTATGTATGTATGTAT
1 GTACGTACGTATGTAT
* *
860497 GTATGTATGTATGTAT
1 GTACGTACGTATGTAT
*
860513 GTA--TATGTATGTAT
1 GTACGTACGTATGTAT
* * *
860527 ATATGTATGTATGTAT
1 GTACGTACGTATGTAT
*
860543 GTA--TATGTATGTAT
1 GTACGTACGTATGTAT
*
860557 GTATGTA--TATGTAT
1 GTACGTACGTATGTAT
* ** *
860571 ATATATATGTA--TAT
1 GTACGTACGTATGTAT
*
860585 GTA--TATGTATGTAT
1 GTACGTACGTATGTAT
* ** *
860599 GTATGTATATATATAT
1 GTACGTACGTATGTAT
* *
860615 GTACATACGTACGTAT
1 GTACGTACGTATGTAT
** ** *
860631 GTATATATATATCTAT
1 GTACGTACGTATGTAT
* * *
860647 GTATGTACGTACGTAC
1 GTACGTACGTATGTAT
** *
860663 GTACGTATATATTTAT
1 GTACGTACGTATGTAT
860679 GTATC-TACGTATGTAT
1 GTA-CGTACGTATGTAT
860695 GTACGTA
1 GTACGTA
860702 TGTACATGCA
Statistics
Matches: 395, Mismatches: 70, Indels: 40
0.78 0.14 0.08
Matches are distributed among these distances:
12 26 0.07
14 58 0.15
15 1 0.00
16 309 0.78
17 1 0.00
ACGTcount: A:0.29, C:0.05, G:0.20, T:0.45
Consensus pattern (16 bp):
GTACGTACGTATGTAT
Found at i:860337 original size:4 final size:4
Alignment explanation
Indices: 860338--860846 Score: 476
Period size: 4 Copynumber: 128.8 Consensus size: 4
860328 TATATATATA
* * * * *
860338 TATG TACG TACG TATG TATG TATA TATG TATG TATA TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
860386 TATG TATA TATA TATG TATG TATG TATG TATG TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
860434 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
860482 TATG TATG TATG TATG TATG TATG TATG TATG TA-- TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
860528 TATG TATG TATG TATG TA-- TATG TATG TATG TATG TA-- TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * **
860572 TATA TATG TATA TGTA TATG TATG TATG TATG TATA TATA TATG TACA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * * * *
860620 TACG TACG TATG TATA TATA TATC TATG TATG TACG TACG TACG TACG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * * * *
860668 TATA TATT TATG TATC TACG TATG TATG TACG TATG TACATG CATA TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T--ATG TATG TATG
* * * * * * * * * * *
860718 TGTG TGTG TGTG TGTG TGTG TATC TATA TACG TACG TATA TATA TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
860766 TATG TATG TACG TACG TATG TA-- TATA TATG TATG CATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
860812 TATA TATG CATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TAT
860847 CTAAACTATA
Statistics
Matches: 433, Mismatches: 62, Indels: 20
0.84 0.12 0.04
Matches are distributed among these distances:
2 8 0.02
4 422 0.97
6 3 0.01
ACGTcount: A:0.29, C:0.04, G:0.20, T:0.47
Consensus pattern (4 bp):
TATG
Found at i:860920 original size:2 final size:2
Alignment explanation
Indices: 860907--860996 Score: 89
Period size: 2 Copynumber: 45.5 Consensus size: 2
860897 ATTTATATTA
* *
860907 AT AT AGT AT AT AT AT AT GT AT GT AT A- ACT A- AT AT AGT A- AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A-T AT AT
* *
860947 CT AT AG A- 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
860988 AT AT AT AT A
1 AT AT AT AT A
860997 AAGAACACTA
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
1 4 0.05
2 65 0.88
3 5 0.07
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:861099 original size:21 final size:21
Alignment explanation
Indices: 861058--861122 Score: 98
Period size: 21 Copynumber: 3.2 Consensus size: 21
861048 ACTCTAAACG
*
861058 CTAA-ACATAAA-CCTTAATC
1 CTAATACATAAACCCTAAATC
861077 CTAATACATAAACCCTAAATC
1 CTAATACATAAACCCTAAATC
*
861098 CTAATACATAAACCCTAAACC
1 CTAATACATAAACCCTAAATC
861119 CTAA
1 CTAA
861123 AATTTATAAA
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
19 4 0.10
20 7 0.17
21 31 0.74
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (21 bp):
CTAATACATAAACCCTAAATC
Found at i:861321 original size:20 final size:20
Alignment explanation
Indices: 861298--861431 Score: 79
Period size: 16 Copynumber: 7.6 Consensus size: 20
861288 TATAATACAT
* *
861298 GTATGTATAAACTATGTATA
1 GTATATATAAACTATATATA
861318 GTATATATAAAC----TATA
1 GTATATATAAACTATATATA
*
861334 -TATATATAACCTATATATA
1 GTATATATAAACTATATATA
861353 -TATATAT--A-TATATATA
1 GTATATATAAACTATATATA
861369 -TATATAT--A-TATATATA
1 GTATATATAAACTATATATA
* *
861385 -TATATATAAACCATATAAA
1 GTATATATAAACTATATATA
*
861404 GTA-A-AT-TACT-TATATA
1 GTATATATAAACTATATATA
*
861420 GTTTATATAAAC
1 GTATATATAAAC
861432 ACTATGCATA
Statistics
Matches: 93, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
15 10 0.11
16 42 0.45
17 3 0.03
18 5 0.05
19 20 0.22
20 13 0.14
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (20 bp):
GTATATATAAACTATATATA
Found at i:861326 original size:2 final size:2
Alignment explanation
Indices: 861314--861392 Score: 106
Period size: 2 Copynumber: 39.0 Consensus size: 2
861304 ATAAACTATG
* **
861314 TA TA GTA TA TA TA AA CTA TA TA TA TA TA -A CC 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
861357 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
861393 AACCATATAA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
1 1 0.01
2 65 0.94
3 3 0.04
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:861613 original size:2 final size:2
Alignment explanation
Indices: 861602--861679 Score: 104
Period size: 2 Copynumber: 39.0 Consensus size: 2
861592 ATAAACTATG
861602 TA TA -A 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
* ** *
861643 TA TA TA TA TA TA TA AA CC TA TA GTA TA TG TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
861680 CATCTATTTA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.01
2 64 0.96
3 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:861892 original size:21 final size:21
Alignment explanation
Indices: 861751--861892 Score: 67
Period size: 21 Copynumber: 6.6 Consensus size: 21
861741 TTAGTGTACT
* * *
861751 ATATAGTTTATACTTTATAAT
1 ATATAGTATATAATTTATAAC
*
861772 ATTTAGTATATAATTTATAAC
1 ATATAGTATATAATTTATAAC
* *
861793 CTATAGTTTATATTAATGT-TAA-
1 ATATAG--TATA-TAATTTATAAC
* ** *
861815 TTATCTTAACCATAATTTATATTA-
1 ATATAGT-A-TATAATTTATA--AC
*
861839 ATATAGTATATAGTTTATAA-
1 ATATAGTATATAATTTATAAC
*
861859 ACTATACTATATAATTTATAAC
1 A-TATAGTATATAATTTATAAC
*
861881 ATATAGTTTATA
1 ATATAGTATATA
861893 TTAATATTAA
Statistics
Matches: 90, Mismatches: 21, Indels: 20
0.69 0.16 0.15
Matches are distributed among these distances:
20 3 0.03
21 53 0.59
22 16 0.18
23 8 0.09
24 10 0.11
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (21 bp):
ATATAGTATATAATTTATAAC
Found at i:862063 original size:21 final size:21
Alignment explanation
Indices: 862020--862067 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
862010 TATTTTATAA
* * *
862020 AAACCCTAAACCTTAAAATAT
1 AAACCTTAAACCCTAAAACAT
*
862041 AAACCTTAAACCCTAATACAT
1 AAACCTTAAACCCTAAAACAT
862062 -AACCTT
1 AAACCTT
862068 GTGGTCGTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.25
Consensus pattern (21 bp):
AAACCTTAAACCCTAAAACAT
Found at i:862295 original size:15 final size:15
Alignment explanation
Indices: 862263--862304 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
862253 AAACTATATT
*
862263 ATATTAATATAAGTTA
1 ATATTAAT-TATGTTA
862279 ATATTAATTATGTTA
1 ATATTAATTATGTTA
862294 ATATTAATTAT
1 ATATTAATTAT
862305 AAATAGTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 17 0.68
16 8 0.32
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (15 bp):
ATATTAATTATGTTA
Found at i:863071 original size:13 final size:13
Alignment explanation
Indices: 863055--863102 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
863045 CCTTAACTAA
863055 AACCCTAAACTTG
1 AACCCTAAACTTG
*
863068 AACCTTAATA-TTG
1 AACCCTAA-ACTTG
*
863081 AACCCTAAACTAG
1 AACCCTAAACTTG
863094 AA-CCTAAAC
1 AACCCTAAAC
863103 CTAAACCCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 8 0.27
13 21 0.70
14 1 0.03
ACGTcount: A:0.44, C:0.27, G:0.06, T:0.23
Consensus pattern (13 bp):
AACCCTAAACTTG
Found at i:863105 original size:6 final size:6
Alignment explanation
Indices: 863094--863180 Score: 102
Period size: 6 Copynumber: 14.3 Consensus size: 6
863084 CCTAAACTAG
* * * *
863094 AACCTA AACCTA AACCCA AACCCA AACCCA AACCCA AACCCG AACCCG
1 AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA AACCCA
* * *
863142 AACCCA AACCCAA AACCCG AACACA AACTCA AACCCA AA
1 AACCCA AACCC-A AACCCA AACCCA AACCCA AACCCA AA
863181 TCTGAACCTG
Statistics
Matches: 72, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
6 66 0.92
7 6 0.08
ACGTcount: A:0.49, C:0.44, G:0.03, T:0.03
Consensus pattern (6 bp):
AACCCA
Found at i:863206 original size:19 final size:18
Alignment explanation
Indices: 863173--863209 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
863163 CACAAACTCA
*
863173 AACCCAAATCTGAACCTG
1 AACCCAAACCTGAACCTG
863191 AACCCAAAACCTGAACCTG
1 AACCC-AAACCTGAACCTG
863210 GATTCAAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.41, C:0.35, G:0.11, T:0.14
Consensus pattern (18 bp):
AACCCAAACCTGAACCTG
Found at i:865256 original size:21 final size:21
Alignment explanation
Indices: 865232--865274 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
865222 TCTAGTTAAA
* *
865232 TTTTAACTTATTTATTTCTTG
1 TTTTAACTTAATAATTTCTTG
* *
865253 TTTTCATTTAATAATTTCTTG
1 TTTTAACTTAATAATTTCTTG
865274 T
1 T
865275 CTTTTGTTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTTAACTTAATAATTTCTTG
Found at i:866711 original size:13 final size:13
Alignment explanation
Indices: 866679--866705 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
866669 TAATTTACAT
866679 TTAAATAATTTTA
1 TTAAATAATTTTA
866692 TTAAATAATTTTA
1 TTAAATAATTTTA
866705 T
1 T
866706 ATAATAGGTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:866892 original size:16 final size:16
Alignment explanation
Indices: 866844--866886 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
866834 TTTCGCCAAT
866844 GATAATATAT-AAGTCA
1 GATAA-ATATCAAGTCA
*
866860 GGTAAATATCAAGTCA
1 GATAAATATCAAGTCA
866876 GATAAATATCA
1 GATAAATATCA
866887 TATCAGGTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.49, C:0.09, G:0.14, T:0.28
Consensus pattern (16 bp):
GATAAATATCAAGTCA
Found at i:871269 original size:23 final size:23
Alignment explanation
Indices: 871208--871269 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
871198 CTAATATGAA
* * *
871208 AATAATAAAATAATAACGAAAGT
1 AATAATAAAATAATATCAAAAGC
*
871231 AATAATTTAAAT-ATATCAAAAGC
1 AATAA-TAAAATAATATCAAAAGC
871254 AATAATAAAATAATAT
1 AATAATAAAATAATAT
871270 TGCAAATAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
22 5 0.16
23 22 0.69
24 5 0.16
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (23 bp):
AATAATAAAATAATATCAAAAGC
Found at i:872561 original size:3 final size:3
Alignment explanation
Indices: 872553--872618 Score: 87
Period size: 3 Copynumber: 21.3 Consensus size: 3
872543 TTATTTATTT
* **
872553 TAA TAA TAA TAA TATA TAA TAT TAA TAA TAA TAA TAA TTT TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
872599 TTAA TAA TAA TAA TAA TAA T
1 -TAA TAA TAA TAA TAA TAA T
872619 TTTTAAAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
3 49 0.89
4 6 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:872565 original size:22 final size:22
Alignment explanation
Indices: 872540--872612 Score: 67
Period size: 22 Copynumber: 3.2 Consensus size: 22
872530 TTTGGGCTTG
872540 TAATTATTTATTTTAATAATAA
1 TAATTATTTATTTTAATAATAA
* *
872562 TAATATATAATATTAATAATAATAA
1 TAAT-TAT-TTATT-TTAATAATAA
* *
872587 TAATT-TTAATAATTAATAATAA
1 TAATTATTTAT-TTTAATAATAA
872609 TAAT
1 TAAT
872613 AATAATTTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
22 19 0.46
23 4 0.10
24 5 0.12
25 13 0.32
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATTATTTATTTTAATAATAA
Found at i:872587 original size:25 final size:26
Alignment explanation
Indices: 872553--872616 Score: 105
Period size: 25 Copynumber: 2.5 Consensus size: 26
872543 TTATTTATTT
872553 TAATAATAATAATATATAAT-ATTAA
1 TAATAATAATAATATATAATAATTAA
*
872578 TAATAATAATAAT-TTTAATAATTAA
1 TAATAATAATAATATATAATAATTAA
872603 TAATAATAATAATA
1 TAATAATAATAATA
872617 ATTTTTAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
24 5 0.14
25 31 0.86
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
TAATAATAATAATATATAATAATTAA
Found at i:872618 original size:22 final size:21
Alignment explanation
Indices: 872552--872618 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 21
872542 ATTATTTATT
872552 TTAATAATAATAATATATAATA
1 TTAATAATAATAATA-ATAATA
872574 TTAATAATAATAATAATTTTAATAA
1 TTAATAATAATAATAA---TAAT-A
872599 TTAATAATAATAATAATAAT
1 TTAATAATAATAATAATAAT
872619 TTTTAAAAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
21 1 0.02
22 19 0.46
24 4 0.10
25 17 0.41
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
TTAATAATAATAATAATAATA
Found at i:872624 original size:22 final size:22
Alignment explanation
Indices: 872552--872630 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
872542 ATTATTTATT
872552 TTAATAATAATAATATATAA-TA
1 TTAATAATAATAATA-ATAATTA
*
872574 TTAATAATAATAATAATTTTAATAA
1 TTAATAATAATAATAA---TAATTA
*
872599 TTAATAATAATAATAATAATTT
1 TTAATAATAATAATAATAATTA
*
872621 TTAAAAATAA
1 TTAATAATAA
872631 AATGAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
21 1 0.02
22 28 0.57
24 3 0.06
25 17 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (22 bp):
TTAATAATAATAATAATAATTA
Found at i:872629 original size:19 final size:19
Alignment explanation
Indices: 872553--872630 Score: 61
Period size: 19 Copynumber: 4.2 Consensus size: 19
872543 TTATTTATTT
*
872553 TAATAATAA-TAATATATAA
1 TAATAATAATTAATA-AAAA
* *
872572 TATTAATAA-TAATAATAA
1 TAATAATAATTAATAAAAA
** *
872590 TTTTAATAATTAATAATAA
1 TAATAATAATTAATAAAAA
**
872609 TAATAATAATTTTTAAAAA
1 TAATAATAATTAATAAAAA
872628 TAA
1 TAA
872631 AATGAAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
18 12 0.24
19 39 0.76
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
TAATAATAATTAATAAAAA
Found at i:872629 original size:25 final size:25
Alignment explanation
Indices: 872553--872630 Score: 93
Period size: 28 Copynumber: 3.0 Consensus size: 25
872543 TTATTTATTT
* * *
872553 TAATAATAATAATATATAATATTAA
1 TAATAATAATAATTTTTAATAATAA
872578 TAATAATAATAATTTTAATAATTAATAA
1 TAATAATAATAATTTT--TAA-TAATAA
*
872606 TAATAATAATAATTTTTAAAAATAA
1 TAATAATAATAATTTTTAATAATAA
872631 AATGAAAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
25 19 0.41
26 3 0.07
27 3 0.07
28 21 0.46
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (25 bp):
TAATAATAATAATTTTTAATAATAA
Found at i:872641 original size:22 final size:22
Alignment explanation
Indices: 872599--872641 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
872589 ATTTTAATAA
* *
872599 TTAATAATAATAATAATAATTT
1 TTAAAAATAATAATAAAAATTT
872621 TTAAAAATAA-AATGAAAAATT
1 TTAAAAATAATAAT-AAAAATT
872642 AGTGTTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (22 bp):
TTAAAAATAATAATAAAAATTT
Found at i:872843 original size:45 final size:45
Alignment explanation
Indices: 872793--873501 Score: 1116
Period size: 45 Copynumber: 15.8 Consensus size: 45
872783 GCCTGGAGGT
* * * * *
872793 CTTTGAAAACATCATGCACTGTAGGTCTTACAGATTACTCTAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
872838 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
872883 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATAACCCGAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* * *
872928 TTTTGAAAACATCATGCACTGAAGGTCTTACAGATGACCCAAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
872973 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
873018 CTTTGAAAACATCATGTAGTGAAGGGCTTACAGATGACCCGAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
873063 CTTTGAAAACATCATGCACTGAAGGGC-TACAGATGACCCGAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
873107 CTTTGAAAACATCATGCACTGAAGGGC-TACAGATGACCCGAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* *
873151 CTTTGAAAGCATCATGCACTGAAGGTCTTACAGATGACCCGAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
873196 CTTTGAAAACATCATGCACTAAAGGGCTTACAGATGACCCGAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* * *
873241 TTTTGAAAACATCATGCACTGAAAGGTTTACAGATGACCCGAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* * *
873286 TTTTGAAAACATCATACACTGAAGGGCTTACAGATGACCCAAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* **
873331 CTTTGAAAACATCATGAACTGAAGGTTTTACAGATGACCCGAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
*
873376 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCAAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
**
873421 CTTTGAAAACATCATGCACTGAAGGTTTTACAGATGACCCGAAGG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
* * **
873466 CTTTAAAAACATCATGCACTGTAGGTTTTACAGATG
1 CTTTGAAAACATCATGCACTGAAGGGCTTACAGATG
873502 TGGGAAATAG
Statistics
Matches: 618, Mismatches: 45, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
44 86 0.14
45 532 0.86
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.23
Consensus pattern (45 bp):
CTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGG
Found at i:873355 original size:25 final size:25
Alignment explanation
Indices: 873327--873400 Score: 68
Period size: 25 Copynumber: 3.2 Consensus size: 25
873317 AGATGACCCA
873327 AAGGCTTTGAAAACATCATGAACTG
1 AAGGCTTTGAAAACATCATGAACTG
* * * *
873352 AAGG-TTT---TACA-GATGACCCG
1 AAGGCTTTGAAAACATCATGAACTG
*
873372 AAGGCTTTGAAAACATCATGCACTG
1 AAGGCTTTGAAAACATCATGAACTG
873397 AAGG
1 AAGG
873401 GCTTACAGAT
Statistics
Matches: 35, Mismatches: 9, Indels: 10
0.65 0.17 0.19
Matches are distributed among these distances:
20 10 0.29
21 6 0.17
24 6 0.17
25 13 0.37
ACGTcount: A:0.36, C:0.18, G:0.23, T:0.23
Consensus pattern (25 bp):
AAGGCTTTGAAAACATCATGAACTG
Found at i:874114 original size:22 final size:22
Alignment explanation
Indices: 874084--874136 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 22
874074 AATAAAGTTT
874084 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
* *
874106 TCATATTTG--GAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
874126 TCTTCTTTGAA
1 TCATCTTTGAA
874137 GAATGTAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 17 0.68
22 8 0.32
ACGTcount: A:0.34, C:0.13, G:0.15, T:0.38
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:874568 original size:54 final size:54
Alignment explanation
Indices: 874504--874607 Score: 181
Period size: 54 Copynumber: 1.9 Consensus size: 54
874494 TAACTAGTTT
*
874504 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCCCAAATGTTC
1 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAAATGTTC
* *
874558 GTAAAACATTTGACAACACATTCATCCTTTTCTGTGGTTTCTGCACAAAT
1 GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAAAT
874608 TTCTGGTCAG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCCTTTCCTGTGGCTTCTGCACAAATGTTC
Found at i:875839 original size:41 final size:40
Alignment explanation
Indices: 875752--875839 Score: 90
Period size: 41 Copynumber: 2.1 Consensus size: 40
875742 GTTATGAGCC
*
875752 TTCAAAATGCCCCACATGGATCATTTCTGTTTGAATTAGGCA
1 TTCAAAATGCCCCACAT-G-TCATTTCTGTTTGAAATAGGCA
* *
875794 TTCAAAATGCCCCAACAT-TCTATTTCTAG-TTGAAATGGGCT
1 TTCAAAATGCCCC-ACATGTC-ATTTCT-GTTTGAAATAGGCA
875835 TTCAA
1 TTCAA
875840 GATATCCCAC
Statistics
Matches: 40, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
40 2 0.05
41 20 0.50
42 14 0.35
43 4 0.10
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.34
Consensus pattern (40 bp):
TTCAAAATGCCCCACATGTCATTTCTGTTTGAAATAGGCA
Found at i:879734 original size:19 final size:18
Alignment explanation
Indices: 879701--879736 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
879691 TTATTGATCA
*
879701 CATTTTCAATTAATTCTG
1 CATTTTCAATAAATTCTG
879719 CATTTATCAATAAATTCT
1 CATTT-TCAATAAATTCT
879737 CGAATTCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.33, C:0.17, G:0.03, T:0.47
Consensus pattern (18 bp):
CATTTTCAATAAATTCTG
Found at i:880760 original size:12 final size:12
Alignment explanation
Indices: 880745--880796 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
880735 AACAAACATA
880745 AAATGAAAATGT
1 AAATGAAAATGT
*
880757 AAATGAAAATAT
1 AAATGAAAATGT
*
880769 AAATTCAAAGATGT
1 AAA-TGAAA-ATGT
*
880783 GAAATGCAAATGT
1 -AAATGAAAATGT
880796 A
1 A
880797 TGTATGAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 15 0.47
13 8 0.25
14 6 0.19
15 3 0.09
ACGTcount: A:0.56, C:0.04, G:0.15, T:0.25
Consensus pattern (12 bp):
AAATGAAAATGT
Found at i:884111 original size:11 final size:11
Alignment explanation
Indices: 884095--884158 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 11
884085 GACTAAGATG
884095 AAAATAATAAT
1 AAAATAATAAT
*
884106 AAAATAATAACG
1 AAAATAATAA-T
*
884118 AAAGTAATAATT
1 AAAATAATAA-T
*
884130 TAAAT-AT-AT
1 AAAATAATAAT
884139 CAAAAGTAATAAT
1 -AAAA-TAATAAT
884152 AAAATAA
1 AAAATAA
884159 AATTGCAAAT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
9 1 0.02
10 4 0.10
11 16 0.39
12 18 0.44
13 2 0.05
ACGTcount: A:0.66, C:0.03, G:0.05, T:0.27
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:884125 original size:23 final size:23
Alignment explanation
Indices: 884094--884158 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
884084 TGACTAAGAT
*
884094 GAAAATAATAATAAAATAATAAC
1 GAAAGTAATAATAAAATAATAAC
* *
884117 GAAAGTAATAATTTAAAT-ATATC
1 GAAAGTAATAA-TAAAATAATAAC
*
884140 AAAAGTAATAATAAAATAA
1 GAAAGTAATAATAAAATAA
884159 AATTGCAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 5 0.14
23 25 0.71
24 5 0.14
ACGTcount: A:0.65, C:0.03, G:0.06, T:0.26
Consensus pattern (23 bp):
GAAAGTAATAATAAAATAATAAC
Found at i:885449 original size:3 final size:3
Alignment explanation
Indices: 885441--885515 Score: 125
Period size: 3 Copynumber: 25.3 Consensus size: 3
885431 TTATTTATTT
885441 TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
**
885488 TAA TTT TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA T
885516 TTTTAAAAAT
Statistics
Matches: 67, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 2 0.03
3 65 0.97
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:887960 original size:16 final size:16
Alignment explanation
Indices: 887939--887969 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
887929 AGTCCCAATA
887939 AGTGAAGAGGAAAAAC
1 AGTGAAGAGGAAAAAC
*
887955 AGTGAAGATGAAAAA
1 AGTGAAGAGGAAAAA
887970 TAACTCTTGA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.03, G:0.29, T:0.10
Consensus pattern (16 bp):
AGTGAAGAGGAAAAAC
Found at i:892157 original size:30 final size:30
Alignment explanation
Indices: 892101--892192 Score: 80
Period size: 30 Copynumber: 3.0 Consensus size: 30
892091 CCCAAAGGAC
* * *
892101 CTATCCATAAGT-TTCGAAGAAAATAGGTAA
1 CTATCCATATGTCTCCGAAG-ACATAGGTAA
* *
892131 CTGTCTATATGTC-CCGAAGGACATAGGTAAA
1 CTATCCATATGTCTCCGAA-GACATAGGT-AA
* *
892162 CTATCCATATGTCTCGGAAGACATGGGTAA
1 CTATCCATATGTCTCCGAAGACATAGGTAA
892192 C
1 C
892193 CCTCAACTCT
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
30 23 0.47
31 22 0.45
32 4 0.08
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (30 bp):
CTATCCATATGTCTCCGAAGACATAGGTAA
Found at i:892185 original size:31 final size:30
Alignment explanation
Indices: 892101--892191 Score: 85
Period size: 31 Copynumber: 3.0 Consensus size: 30
892091 CCCAAAGGAC
* * *
892101 CTATCCATAAGTTTCGAAGAAAATAGGT-AA
1 CTATCCATATGTCTCGAAG-ACATAGGTAAA
* * *
892131 CTGTCTATATGTCCCGAAGGACATAGGTAAA
1 CTATCCATATGTCTCGAA-GACATAGGTAAA
*
892162 CTATCCATATGTCTCGGAAGACATGGGTAA
1 CTATCCATATGTCTC-GAAGACATAGGTAA
892192 CCCTCAACTC
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
30 20 0.42
31 25 0.52
32 3 0.06
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (30 bp):
CTATCCATATGTCTCGAAGACATAGGTAAA
Found at i:895466 original size:61 final size:63
Alignment explanation
Indices: 895372--895498 Score: 181
Period size: 61 Copynumber: 2.0 Consensus size: 63
895362 AAAACATCTT
* *
895372 AAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAA-ATAATATAATATTTA
1 AAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACA-AATATAAAATATA
*
895435 AAATCCTAA-T-AAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATA
1 AAATCCTAATTAAAACACTTAAAA-CTATTTAAACTAAAATACCTAAAACAAATATAAAATATA
895496 AAA
1 AAA
895499 ATAATATCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
60 5 0.08
61 43 0.73
62 2 0.03
63 9 0.15
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.28
Consensus pattern (63 bp):
AAATCCTAATTAAAACACTTAAAACTATTTAAACTAAAATACCTAAAACAAATATAAAATATA
Found at i:895511 original size:32 final size:32
Alignment explanation
Indices: 895470--895532 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
895460 TTTAAACTAA
895470 AATACCTAAAAC-AAATATAAAATA-TAAAAAT
1 AATACCTAAAACTAAAT-TAAAATACTAAAAAT
*
895501 AATATCCTAAAACTTAATTAAAATACTAAAAA
1 AATA-CCTAAAACTAAATTAAAATACTAAAAA
895533 CCTATTTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
31 4 0.14
32 15 0.54
33 9 0.32
ACGTcount: A:0.63, C:0.11, G:0.00, T:0.25
Consensus pattern (32 bp):
AATACCTAAAACTAAATTAAAATACTAAAAAT
Found at i:895575 original size:77 final size:75
Alignment explanation
Indices: 895445--895587 Score: 191
Period size: 77 Copynumber: 1.9 Consensus size: 75
895435 AAATCCTAAT
*
895445 AAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAATATAAAATATAAAAATAATATCCTA
1 AAATACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAAAATAT-AAAATAATATCCTA
895510 AAACTTAATTA
65 AAACTTAATTA
** * *
895521 AAATACTAAAAACCTATTTAAACTAAAATA-C-AAAGATAAAATATAATGTTTAAAATATTATCC
1 AAATACT-AAAACCTATTTAAACTAAAATACCTAAA-A-AAAATATAAAATATAAAATAATATCC
895584 TAAA
63 TAAA
895588 CTTGAGTTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
75 3 0.05
76 24 0.41
77 32 0.54
ACGTcount: A:0.58, C:0.12, G:0.01, T:0.29
Consensus pattern (75 bp):
AAATACTAAAACCTATTTAAACTAAAATACCTAAAAAAAATATAAAATATAAAATAATATCCTAA
AACTTAATTA
Found at i:900392 original size:13 final size:13
Alignment explanation
Indices: 900361--900386 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
900351 TAATAACATT
900361 GAGAATTAAAGTC
1 GAGAATTAAAGTC
900374 GAGAATTAAAGTC
1 GAGAATTAAAGTC
900387 ATGAATAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (13 bp):
GAGAATTAAAGTC
Found at i:904904 original size:30 final size:30
Alignment explanation
Indices: 904870--904943 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 30
904860 CATAATTTTT
*
904870 ATCATTGAAAATTTTGAAA-ATTATAAAATA
1 ATCATT-AAAATTTTCAAAGATTATAAAATA
*
904900 ATCATTAAACTTTTCAAATGATTATAAAATA
1 ATCATTAAAATTTTCAAA-GATTATAAAATA
*
904931 AACATT-AAATTTT
1 ATCATTAAAATTTT
904944 ATTAAATTTA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 10 0.26
30 12 0.32
31 16 0.42
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (30 bp):
ATCATTAAAATTTTCAAAGATTATAAAATA
Found at i:904948 original size:41 final size:38
Alignment explanation
Indices: 904903--904995 Score: 98
Period size: 39 Copynumber: 2.3 Consensus size: 38
904893 TAAAATAATC
904903 ATTAAACTTT-TCAAATGATTATAAAATAAACATTAAATTTT
1 ATTAAA-TTTATCAAATGATTA-AAAAT-AACATTAAA-TTT
* * * *
904944 ATTAAATTTATCGAATTATTAAAAATATCTTTAAATTT
1 ATTAAATTTATCAAATGATTAAAAATAACATTAAATTT
904982 ATTAAAATTTATCA
1 ATT-AAATTTATCA
904996 TTATTCTATA
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
38 6 0.13
39 16 0.36
40 8 0.18
41 15 0.33
ACGTcount: A:0.47, C:0.06, G:0.02, T:0.44
Consensus pattern (38 bp):
ATTAAATTTATCAAATGATTAAAAATAACATTAAATTT
Found at i:908176 original size:15 final size:15
Alignment explanation
Indices: 908156--908189 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
908146 AAGCAAGATC
908156 AAAGCAATAGACACA
1 AAAGCAATAGACACA
*
908171 AAAGCAATAGACATA
1 AAAGCAATAGACACA
908186 AAAG
1 AAAG
908190 AAAAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.09
Consensus pattern (15 bp):
AAAGCAATAGACACA
Found at i:908458 original size:13 final size:11
Alignment explanation
Indices: 908425--908456 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
908415 TTTTCCTCCC
908425 TCTCTTTCTCA
1 TCTCTTTCTCA
908436 TCTCTTTCTCA
1 TCTCTTTCTCA
908447 TCTCTTTCTC
1 TCTCTTTCTC
908457 TCTGTTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.06, C:0.38, G:0.00, T:0.56
Consensus pattern (11 bp):
TCTCTTTCTCA
Found at i:908873 original size:23 final size:23
Alignment explanation
Indices: 908843--908890 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
908833 TAAAAAAAAC
908843 TTATTTTTGTCCGATTGAGGTAG
1 TTATTTTTGTCCGATTGAGGTAG
908866 TTATTTTTGTCCGATTGAGGTAG
1 TTATTTTTGTCCGATTGAGGTAG
908889 TT
1 TT
908891 CTATATTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.17, C:0.08, G:0.25, T:0.50
Consensus pattern (23 bp):
TTATTTTTGTCCGATTGAGGTAG
Found at i:909577 original size:131 final size:132
Alignment explanation
Indices: 909391--909634 Score: 325
Period size: 131 Copynumber: 1.9 Consensus size: 132
909381 AAGTTGGATG
* * * *
909391 AAAATAGCTCCTCGCTATTAAGTTAAGCTATGTTGTGGATGACTCATTCGTCGTGAAGTTGAGTC
1 AAAATAGCTCCTAGCTATTAAGTTAAGCTATATTGTGGATGACTCATTCGTCGTGAAATTAAGTC
* * *
909456 GATCTCAGATGAC-TCGAGCTTGAT-TTACTTCGTCGTGAAGTTGAAATCCGATCAAAATCTAGG
66 GATCTCAGATGACAT-AAGCATGATATCA-TTCGTCGTGAAGTTGAAATCCGATCAAAATCTAGG
909519 ATAA
129 ATAA
* *
909523 AAAATAGCTCCTAGTTATTGAGTTAAGCTA-ATTGTGG-TCGACTCATTCGTCGTGAAATTAAGT
1 AAAATAGCTCCTAGCTATTAAGTTAAGCTATATTGTGGAT-GACTCATTCGTCGTGAAATTAAGT
** *
909586 CGATCTTGGATGACATAAGCATGATATCATTTGTCGTGAAGTTGAAATC
65 CGATCTCAGATGACATAAGCATGATATCATTCGTCGTGAAGTTGAAATC
909635 TAGCTCGAAA
Statistics
Matches: 97, Mismatches: 12, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
130 1 0.01
131 66 0.68
132 30 0.31
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.33
Consensus pattern (132 bp):
AAAATAGCTCCTAGCTATTAAGTTAAGCTATATTGTGGATGACTCATTCGTCGTGAAATTAAGTC
GATCTCAGATGACATAAGCATGATATCATTCGTCGTGAAGTTGAAATCCGATCAAAATCTAGGAT
AA
Found at i:916918 original size:88 final size:88
Alignment explanation
Indices: 916800--916976 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
916790 GCATGTTTCT
916800 TTTTAGTCCAGTATATGTGTTTAGGGTTTATTTCAATGTTAATCGTTTATGATGGTGATTTGTTT
1 TTTTAGTCCAGTATATGTGTTTAGGGTTTATTTCAATGTTAATCGTTTATGATGGTGATTTGTTT
916865 CATTTTAGCTATATTGTTTATTA
66 CATTTTAGCTATATTGTTTATTA
916888 TTTTAGTCCAGTATATGTGTTTAGGGTTTATTTCAATGTTAATCGTTTATGATGGTGATTTGTTT
1 TTTTAGTCCAGTATATGTGTTTAGGGTTTATTTCAATGTTAATCGTTTATGATGGTGATTTGTTT
916953 CATTTTAGCTATATTGTTTATTA
66 CATTTTAGCTATATTGTTTATTA
916976 T
1 T
916977 AGTATAATAT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.21, C:0.07, G:0.18, T:0.54
Consensus pattern (88 bp):
TTTTAGTCCAGTATATGTGTTTAGGGTTTATTTCAATGTTAATCGTTTATGATGGTGATTTGTTT
CATTTTAGCTATATTGTTTATTA
Found at i:917818 original size:21 final size:21
Alignment explanation
Indices: 917788--917954 Score: 157
Period size: 21 Copynumber: 8.0 Consensus size: 21
917778 GATTTACATA
*
917788 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
917809 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
917830 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
* *
917853 TT--CGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
917874 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
917893 TTCTCGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
* *
917914 TTCGCGTTGCGATTTATTCCAAA
1 TTCGCGTTGCGA--TAGTCCAAG
917937 TT--CGTTGCGATAGTCCAA
1 TTCGCGTTGCGATAGTCCAA
917955 AATCGCAACG
Statistics
Matches: 129, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
19 16 0.12
21 96 0.74
23 17 0.13
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:917880 original size:63 final size:62
Alignment explanation
Indices: 917813--917954 Score: 214
Period size: 63 Copynumber: 2.3 Consensus size: 62
917803 TCCAAGTTCG
* *
917813 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATT-CGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGA--TAGTCCAAATTCCGTTGCGATTTATTCCAAATT
* *
917876 CGTTGCGATAGTCCAAGTTCTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAATTC-CGTTGCGATTTATTCCAAATT
917939 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
917955 AATCGCAACG
Statistics
Matches: 73, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
61 9 0.12
63 64 0.88
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (62 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAATTCCGTTGCGATTTATTCCAAATT
Found at i:917915 original size:84 final size:84
Alignment explanation
Indices: 917794--917947 Score: 290
Period size: 84 Copynumber: 1.8 Consensus size: 84
917784 CATATTCGCA
*
917794 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
917859 GCGATTTATTCCAAATTCG
66 GCGATTTATTCCAAATTCG
*
917878 TTGCGATAGTCCAAGTTCTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
917943 GCGAT
66 GCGAT
917948 AGTCCAAAAT
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 68 1.00
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (84 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTT
GCGATTTATTCCAAATTCG
Found at i:918824 original size:21 final size:20
Alignment explanation
Indices: 918640--918825 Score: 119
Period size: 21 Copynumber: 8.9 Consensus size: 20
918630 CGTTGCGATT
* *
918640 TTGGACTATCGCAA-CGAAT
1 TTGGAATATCGCAAGCGAAC
918659 TTGGAATAAATCGCAACGCGAAC
1 TTGGAAT--ATCGCAA-GCGAAC
* * *
918682 TTCGACTATCGCAA-CGAAT
1 TTGGAATATCGCAAGCGAAC
918701 TTGGAATAAATCGCAATGCGAAC
1 TTGGAAT--ATCGCAA-GCGAAC
* * *
918724 TTCGACTATCGCAA-CGAAT
1 TTGGAATATCGCAAGCGAAC
*
918743 TTGGAATAAAGCGCAACGCGAAC
1 TTGGAAT--ATCGCAA-GCGAAC
* * *
918766 TTCGACTATCGCAA-CGAAT
1 TTGGAATATCGCAAGCGAAC
* *
918785 TTGGAAAATCACAACGCGAAC
1 TTGGAATATCGCAA-GCGAAC
918806 TTGGAATATCGCAATGCGAA
1 TTGGAATATCGCAA-GCGAA
918826 TATGTAAATC
Statistics
Matches: 126, Mismatches: 27, Indels: 26
0.70 0.15 0.15
Matches are distributed among these distances:
19 38 0.30
21 61 0.48
23 27 0.21
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TTGGAATATCGCAAGCGAAC
Found at i:918826 original size:42 final size:42
Alignment explanation
Indices: 918643--918819 Score: 295
Period size: 42 Copynumber: 4.3 Consensus size: 42
918633 TGCGATTTTG
918643 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
918685 GACTATCGCAACGAATTTGGAATAAATCGCAATGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
918727 GACTATCGCAACGAATTTGGAATAAAGCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
* *
918769 GACTATCGCAACGAATTTGG-A-AAATCACAACGCGAACTTG
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
918809 GAATATCGCAA
1 GACTATCGCAA
918820 TGCGAATATG
Statistics
Matches: 128, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
40 26 0.20
41 1 0.01
42 101 0.79
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:918906 original size:21 final size:21
Alignment explanation
Indices: 918882--918936 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
918872 AATTTGGAAA
918882 ATCGCAAAGCGAACTTCGACT
1 ATCGCAAAGCGAACTTCGACT
*
918903 ATCGCAATA-CGAACTTGGACT
1 ATCGCAA-AGCGAACTTCGACT
* *
918924 ATCGTAATGCGAA
1 ATCGCAAAGCGAA
918937 TATGTAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 28 0.97
22 1 0.03
ACGTcount: A:0.35, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
ATCGCAAAGCGAACTTCGACT
Found at i:918976 original size:132 final size:133
Alignment explanation
Indices: 918738--919127 Score: 401
Period size: 132 Copynumber: 3.0 Consensus size: 133
918728 ACTATCGCAA
* * * ** ** *
918738 CGAATTTGGAATAAAGCGCAACGCGAACTTCGACTATCGC-A-ACGAATTTGGAAAATCACAACG
1 CGAATTTGG-A-AAATCGCAAAGCGAACTTCGACTATCGCAATACGAACTTGGACTATCGTAATG
* * **
918801 CGAACT-TGGAATATCGCAATGCGAATA-T-GTAA-ATCGCAATGCGATAGTCGAAGTTCGCGTT
64 CGAA-TATGTAA-ATCGCAATGCG-ATAGTCG-AAGTTCGCGTTGCGATAGTCGAAGTTCGCGTT
918862 GCGAT-A-G
125 GCGATAACG
918869 TCGAATTTGGAAAATCGCAAAGCGAACTTCGACTATCGCAATACGAACTTGGACTATCGTAATGC
1 -CGAATTTGGAAAATCGCAAAGCGAACTTCGACTATCGCAATACGAACTTGGACTATCGTAATGC
* * ***
918934 GAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAATTTGGAAAAT-CG-
65 GAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCG-CGTTGCGA
918997 TAACG
129 TAACG
* * ** * *
919002 CGAACTTCGACTATCGCAATA-CGAACTTGGACTATCGTAATACGAACTTGGACTATCGTAATGC
1 CGAATTTGGAAAATCGCAA-AGCGAACTTCGACTATCGCAATACGAACTTGGACTATCGTAATGC
919066 GAATA--TAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGA
65 GAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGA
919128 ATCTGGAAAA
Statistics
Matches: 218, Mismatches: 28, Indels: 25
0.80 0.10 0.09
Matches are distributed among these distances:
129 1 0.00
130 78 0.36
131 18 0.08
132 118 0.54
133 3 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (133 bp):
CGAATTTGGAAAATCGCAAAGCGAACTTCGACTATCGCAATACGAACTTGGACTATCGTAATGCG
AATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATA
ACG
Found at i:918995 original size:111 final size:111
Alignment explanation
Indices: 918801--919047 Score: 449
Period size: 111 Copynumber: 2.2 Consensus size: 111
918791 AATCACAACG
* *
918801 CGAACTTGGAATATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGA
1 CGAACTTGGACTATCGTAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGA
918866 TAGTCGAATTTGGAAAATCGCAAAGCGAACTTCGACTATCGCAATA
66 TAGTCGAATTTGGAAAATCGCAAAGCGAACTTCGACTATCGCAATA
918912 CGAACTTGGACTATCGTAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGA
1 CGAACTTGGACTATCGTAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGA
* *
918977 TAGTCGAATTTGGAAAATCGTAACGCGAACTTCGACTATCGCAATA
66 TAGTCGAATTTGGAAAATCGCAAAGCGAACTTCGACTATCGCAATA
*
919023 CGAACTTGGACTATCGTAATACGAA
1 CGAACTTGGACTATCGTAATGCGAA
919048 CTTGGACTAT
Statistics
Matches: 131, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 131 1.00
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.25
Consensus pattern (111 bp):
CGAACTTGGACTATCGTAATGCGAATATGTAAATCGCAATGCGATAGTCGAAGTTCGCGTTGCGA
TAGTCGAATTTGGAAAATCGCAAAGCGAACTTCGACTATCGCAATA
Found at i:919017 original size:21 final size:21
Alignment explanation
Indices: 918993--919068 Score: 107
Period size: 21 Copynumber: 3.6 Consensus size: 21
918983 AATTTGGAAA
** *
918993 ATCGTAACGCGAACTTCGACT
1 ATCGTAATACGAACTTGGACT
*
919014 ATCGCAATACGAACTTGGACT
1 ATCGTAATACGAACTTGGACT
919035 ATCGTAATACGAACTTGGACT
1 ATCGTAATACGAACTTGGACT
*
919056 ATCGTAATGCGAA
1 ATCGTAATACGAA
919069 TATAAATCGC
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (21 bp):
ATCGTAATACGAACTTGGACT
Found at i:919105 original size:21 final size:21
Alignment explanation
Indices: 919081--919127 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
919071 TAAATCGCAA
919081 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
919102 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTCGCGT
919123 TGCGA
1 TGCGA
919128 ATCTGGAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.19, G:0.34, T:0.28
Consensus pattern (21 bp):
TGCGATAGTCGAAGTTCGCGT
Found at i:922145 original size:23 final size:23
Alignment explanation
Indices: 922097--922146 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
922087 AACATCTCTA
*
922097 TTCATGAAAAATAGTTAAGTTTT
1 TTCATGAAAAATAGTTAAGTTAT
922120 TTCATGAAAAATAGTTAA-TTCAT
1 TTCATGAAAAATAGTTAAGTT-AT
922143 TTCA
1 TTCA
922147 CCCAAAAAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 2 0.08
23 23 0.92
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (23 bp):
TTCATGAAAAATAGTTAAGTTAT
Found at i:927386 original size:23 final size:23
Alignment explanation
Indices: 927360--927409 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
927350 TACATCTCTA
*
927360 TTCATGAAAAATAGTTAAGTCTT
1 TTCATGAAAAATAGTTAAGTCAT
*
927383 TTCATGAAAAATAGTTAATTCAT
1 TTCATGAAAAATAGTTAAGTCAT
927406 TTCA
1 TTCA
927410 CCCAAAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (23 bp):
TTCATGAAAAATAGTTAAGTCAT
Found at i:927416 original size:24 final size:23
Alignment explanation
Indices: 927366--927417 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
927356 TCTATTCATG
* **
927366 AAAAATAGTTAAGTCTTTTCATG
1 AAAAATAGTTAAGTCATTTCACC
*
927389 AAAAATAGTTAATTCATTTCACCC
1 AAAAATAGTTAAGTCATTTCA-CC
927413 AAAAA
1 AAAAA
927418 GTCAATTATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
23 19 0.79
24 5 0.21
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (23 bp):
AAAAATAGTTAAGTCATTTCACC
Found at i:927539 original size:31 final size:31
Alignment explanation
Indices: 927499--927563 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
927489 TTAAAGGTCT
*
927499 TAACATTTTAATACAAATTCATCTCCCTATA
1 TAACATTTTAATACAAATTCATCTCCATATA
*
927530 TAACCTTTTAATACAAATTCATCTCCATATA
1 TAACATTTTAATACAAATTCATCTCCATATA
927561 TAA
1 TAA
927564 AGGTTAAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (31 bp):
TAACATTTTAATACAAATTCATCTCCATATA
Found at i:929509 original size:64 final size:65
Alignment explanation
Indices: 929440--929561 Score: 185
Period size: 65 Copynumber: 1.9 Consensus size: 65
929430 CACTAAAGTC
* *
929440 CATCGATGCATAAAATGCATTCGATG-TTTCA-AAATAGCCTGAGTGCATCGATGCATGGTTGGT
1 CATCGATGCATAAAATGAATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGGTTGGT
929503 G
65 G
* *
929504 CATCGATGCATCAAATGAATTTGATGTTTTCATAAAACCCTGAGTGCATCGATGCATG
1 CATCGATGCATAAAATGAATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATG
929562 AAATGCATTC
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 23 0.44
65 26 0.50
66 3 0.06
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (65 bp):
CATCGATGCATAAAATGAATTCGATGTTTTCATAAAACCCTGAGTGCATCGATGCATGGTTGGTG
Found at i:929574 original size:64 final size:62
Alignment explanation
Indices: 929412--929575 Score: 161
Period size: 64 Copynumber: 2.6 Consensus size: 62
929402 TGACCGTTGG
* * * *
929412 ACCCTTAGTGCATCGGTGCACT-AAAGTCCATCGATGCATAAAATGCATTCGATGTTTCAAAAT
1 ACCCTGAGTGCATCGATGCA-TGAAA-TGCATCGATGCATAAAATGAATTCGATGTTTCAAAAT
* *** * *
929475 AGCCTGAGTGCATCGATGCATGGTTGGTGCATCGATGCATCAAATGAATTTGATGTTTTCATAAA
1 ACCCTGAGTGCATCGATGCAT-G-AAATGCATCGATGCATAAAATGAATTCGATG-TTTCA-AAA
929540 -
62 T
929540 ACCCTGAGTGCATCGATGCATGAAATGCATTCGATG
1 ACCCTGAGTGCATCGATGCATGAAATGCA-TCGATG
929576 TTCAATTTAT
Statistics
Matches: 81, Mismatches: 14, Indels: 11
0.76 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 21 0.26
64 31 0.38
65 25 0.31
66 3 0.04
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (62 bp):
ACCCTGAGTGCATCGATGCATGAAATGCATCGATGCATAAAATGAATTCGATGTTTCAAAAT
Found at i:932324 original size:21 final size:22
Alignment explanation
Indices: 932269--932346 Score: 72
Period size: 21 Copynumber: 3.6 Consensus size: 22
932259 CATGGCAGTG
932269 TGCATCGATGCACATTCAAGGTA
1 TGCATCGATGCACATTCAAGG-A
* * *
932292 TGCATCGGTGCACCTTCATGG-
1 TGCATCGATGCACATTCAAGGA
*
932313 TGTATCGATGCACA-TCAAAGG-
1 TGCATCGATGCACATTC-AAGGA
*
932334 TACATCGATGCAC
1 TGCATCGATGCAC
932347 TGTTAAGTGT
Statistics
Matches: 45, Mismatches: 9, Indels: 4
0.78 0.16 0.07
Matches are distributed among these distances:
20 2 0.04
21 25 0.56
23 18 0.40
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (22 bp):
TGCATCGATGCACATTCAAGGA
Found at i:936215 original size:22 final size:21
Alignment explanation
Indices: 936173--936212 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
936163 GAGCTTATTT
*
936173 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
936194 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
936213 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:938158 original size:19 final size:19
Alignment explanation
Indices: 938134--938185 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
938124 TTGGACCCTT
938134 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
*
938153 AGTGCAGCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
*
938172 AGTGCATCGATGCA
1 AGTGCATCGGTGCA
938186 TAAAATGCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.27, C:0.21, G:0.33, T:0.19
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:938256 original size:64 final size:64
Alignment explanation
Indices: 938173--938374 Score: 241
Period size: 65 Copynumber: 3.1 Consensus size: 64
938163 TGCACTAAGA
*
938173 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATAGCCTGAGTGCATCGATGGATGGTTG
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGGATGGTTG
* *
938237 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ACCCTGAGTGCATCGATGCATGGTA
1 GTGCATCGATGCATAAAATGCATTCGATG-TTTCA-AAATACCCTGAGTGCATCGATGGATGGT-
938301 T-
63 TG
* * * * * *
938302 GTTCATCGATGCATGAATTGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGGATGGAT
1 GTGCATCGATGCATAAAATGCATTCGATGTTTCAA--AATACCCTGAGTGCATCGATGGATGG-T
938365 TG
63 TG
938367 GTGCATCG
1 GTGCATCG
938375 GTACATCACT
Statistics
Matches: 119, Mismatches: 11, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 45 0.38
65 65 0.55
66 4 0.03
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATGTTTCAAAATACCCTGAGTGCATCGATGGATGGTTG
Found at i:938672 original size:20 final size:21
Alignment explanation
Indices: 938639--938677 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
938629 ATAACAGGTA
*
938639 AAAATATGATAAAACCGGTCT
1 AAAATATGACAAAACCGGTCT
*
938660 AAAA-ATGACAAAATCGGT
1 AAAATATGACAAAACCGGT
938678 AAAGAGCTAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.51, C:0.13, G:0.15, T:0.21
Consensus pattern (21 bp):
AAAATATGACAAAACCGGTCT
Found at i:940892 original size:22 final size:23
Alignment explanation
Indices: 940840--940896 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 23
940830 GAACGTTTTT
* *
940840 ATTTTTTTATATAAAATAATAGT
1 ATTTTATTATATAAAATAATAGA
* *
940863 ATAGTTATTATATAAAATGATA-A
1 AT-TTTATTATATAAAATAATAGA
940886 ATTTTATTATA
1 ATTTTATTATA
940897 AATGCAGGTT
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 8 0.29
23 4 0.14
24 16 0.57
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (23 bp):
ATTTTATTATATAAAATAATAGA
Found at i:943124 original size:19 final size:19
Alignment explanation
Indices: 943100--943148 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
943090 AATGTAGGGT
*
943100 TAATTTTTTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
943119 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
943138 TAATTTTGTAT
1 TAATTTTGTAT
943149 GTGCATGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.33, C:0.02, G:0.08, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:944245 original size:198 final size:198
Alignment explanation
Indices: 943593--944755 Score: 1467
Period size: 198 Copynumber: 5.8 Consensus size: 198
943583 ATAGGTACGC
* * * * * *
943593 ATAAAGTGCCGATACATTTATAAAAAGCATCGATCCAAAAAATATCGAAA-CCCATAATTATAAT
1 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATC-AAATACGATAATTATAAT
* * * * * *
943657 GTAATGGGT-AATGTTTTCAATGTAACCGGTATAAATATACC-GTTTATTAGAGAATATGTCTAC
65 GTAATAGGTCAA--TTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTAC
* ** * * * * *
943720 ATAATGTATCGACACTTGTGGAACTTGTGCCGATACTTTTTGTCCAGAATGAATGCCCAAAAGTG
128 ATAATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTTTGACCAGAATGAATGCCC-AACGAG
*
943785 GTGCACGC
192 GTGCAC-T
* * * *
943793 ATAAAATGTCGATACATTTATAAAAAAG-ATCGACCCCAAAAACATCGAAA-CCCATAATTATAA
1 ATAAAGTGTCGATACATTTAT-AAAAAGTATCGATCCCAAAAACATC-AAATACGATAATTATAA
** ** * * * *
943856 TGTAATAGGT-AATTTTTTAATGTAACCGGTATTAATATACCAGTTTTATGAGAGAATAGGTCTA
64 TGTAATAGGTCAA-TTTCCAATGTAACCGGTAGAAATATACC-GGTTAATTAGAAAATAGGTCTA
* * * ** * * * * * *
943920 CATAATATATCAACACTTGTGGAACTTGTGTTGATACCTTTTGTCCAGAATGAATTCCCAA-AAT
127 CATAATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTTTGACCAGAATGAATGCCCAACGA-
*
943984 GGGTGCACGC
191 -GGTGCAC-T
* * *
943994 ATAAAGTGTCAATACATTTATAAAAAGTATCGATCCAAAAAACATCGAATACGATAATTATAATG
1 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAATACGATAATTATAATG
* *
944059 TAATAGGTCAATTTCCAATATAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTATACATA
66 TAATAGGTCAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATA
944124 ATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTTTGACCAGAATGAATGCCCAACGAGGTGC
131 ATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTTTGACCAGAATGAATGCCCAACGAGGTGC
944189 ACT
196 ACT
* * *
944192 ATAAAGTGTCGATACATTTATAAGACGTATCGATCCTAAAAACATCAAATACGATAATTATAATG
1 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAATACGATAATTATAATG
** * *
944257 TAATAGGTCAATTTCCAATGTAACCATTAGAAATATACTGGTTAATTAGAAAATAGGTGTACATA
66 TAATAGGTCAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATA
* * * * *
944322 ACGTATCGACACTTTTTAAAGTTTTGTCGATACTTTTTAACTAGAATGAATGCCCAACAAGGTGC
131 ATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTTTGACCAGAATGAATGCCCAACGAGGTGC
944387 ACT
196 ACT
* * * *
944390 ATAAAGTGTCGATACATTTATAAAACGTATCGATCCCAAAAGCATCGAATACAATAATTATAATG
1 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAATACGATAATTATAATG
* * *
944455 TAATAGGTTAATTTCCAATATAACCGGTAGAAATATACCAGTTAATTAGAAAATAGGTCTACATA
66 TAATAGGTCAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATA
* * * *
944520 AAGTATCAACACTTTTTAAAGTTGTGTCGATACTTTTTTACTAGAATGAATGCCCAACGAGGTGC
131 ATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTTTGACCAGAATGAATGCCCAACGAGGTGC
944585 ACT
196 ACT
* *
944588 ATAAAGTGTCGATACATTTATAAAACGTATCGATCCCAAAAACATCAAACACGATAATTATAATG
1 ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAATACGATAATTATAATG
* *
944653 GAATAGGTCAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACCTA
66 TAATAGGTCAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATA
*
944718 AAGTATCGACACTTTTTAAAGTTGTGTCGATACTTTTT
131 ATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTTT
944756 TAAATTACAC
Statistics
Matches: 863, Mismatches: 91, Indels: 20
0.89 0.09 0.02
Matches are distributed among these distances:
198 522 0.60
199 33 0.04
200 140 0.16
201 166 0.19
202 2 0.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (198 bp):
ATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCAAATACGATAATTATAATG
TAATAGGTCAATTTCCAATGTAACCGGTAGAAATATACCGGTTAATTAGAAAATAGGTCTACATA
ATGTATCGACACTTTTTAAAGTTGTGTCGATACTTTTTGACCAGAATGAATGCCCAACGAGGTGC
ACT
Found at i:946405 original size:19 final size:19
Alignment explanation
Indices: 946381--946428 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
946371 ATGTAGGGGA
*
946381 AATTTTGTATTCGATTCAT
1 AATTTTGTATACGATTCAT
*
946400 AATTTTGTATACGATTTAT
1 AATTTTGTATACGATTCAT
946419 AATTTTGTAT
1 AATTTTGTAT
946429 GTGAATGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.54
Consensus pattern (19 bp):
AATTTTGTATACGATTCAT
Found at i:949010 original size:19 final size:20
Alignment explanation
Indices: 948988--949029 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
948978 AAATTAATAA
*
948988 AATAGATAAATT-ATAATGT
1 AATAGATAAATTAACAATGT
*
949007 AATAGGTAAATTAACAATGT
1 AATAGATAAATTAACAATGT
949027 AAT
1 AAT
949030 CGGTATAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.33
Consensus pattern (20 bp):
AATAGATAAATTAACAATGT
Found at i:949027 original size:20 final size:19
Alignment explanation
Indices: 948988--949034 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
948978 AAATTAATAA
* *
948988 AATAGATAAATTATAATGT
1 AATAGGTAAATTACAATGT
949007 AATAGGTAAATTAACAATGT
1 AATAGGTAAATT-ACAATGT
*
949027 AATCGGTA
1 AATAGGTA
949035 TAAATATACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.49, C:0.04, G:0.15, T:0.32
Consensus pattern (19 bp):
AATAGGTAAATTACAATGT
Found at i:949430 original size:197 final size:198
Alignment explanation
Indices: 948996--949441 Score: 549
Period size: 199 Copynumber: 2.3 Consensus size: 198
948986 AAAATAGATA
* * *
948996 AATTATAATGTAATAGGTAAATTAACAATGTAATCGGTATAAATATACCGATTAATTACAAAACA
1 AATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTAATGACAAAACA
* * *
949061 GGTAAACATAACGTATTGGCATTTGTGAAATTTGTGTCGATACTTATTGTCCAGAATGAATGCTC
66 GGTAAACATAACGTATCGACATTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCTC
949126 AAACGAGGTGCACGCATAAAGTGACAATACATTTATTAAAAGCATCGATCCAAAAAACATCGAAA
131 AAACGAGGTGCACGCATAAAGTGACAATACATTTA-TAAAAGCATCGATCCAAAAAACATCGAAA
949191 CAAT
195 CAAT
* * * * * * *
949195 AATTATGATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACTGTTTTATGAGAGAATA
1 AATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTAATGACAAAACA
* * * *
949260 GGTCAACATAATGTATCGACACTTT-TTAAATATGTGTCGATACTT-TTTTCCAGAATGAATGC-
66 GGTAAACATAACGTATCGACA-TTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCT
* ** * * * * ** *
949322 CCAACGAGGTGCACGCATTTAGTGTCGATACATTTA-AAATTGTATCGATCCCTAAAACATTGAA
130 CAAACGAGGTGCACGCATAAAGTGACAATACATTTATAAA-AGCATCGATCCAAAAAACATCGAA
*
949386 ACTGAT
194 AC-AAT
* * *
949392 AATTATAATGTAATAGGTAAATTTGCAATGTTACCGGTATAAATAAACCG
1 AATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCG
949442 GTTTATTGGA
Statistics
Matches: 211, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
195 3 0.01
196 21 0.10
197 78 0.37
198 16 0.08
199 90 0.43
200 3 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.31
Consensus pattern (198 bp):
AATTATAATGTAATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTAATGACAAAACA
GGTAAACATAACGTATCGACATTTGTGAAATATGTGTCGATACTTATTGTCCAGAATGAATGCTC
AAACGAGGTGCACGCATAAAGTGACAATACATTTATAAAAGCATCGATCCAAAAAACATCGAAAC
AAT
Done.