Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007833.1 Hibiscus syriacus cultivar Beakdansim tig00110177_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: 816380
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:451431 original size:21 final size:21
Alignment explanation
Indices: 451405--451444 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
451395 GACTATCGCA
451405 TTGCGATTTCCCAAATTCGTG
1 TTGCGATTTCCCAAATTCGTG
* *
451426 TTGCGATTTTCCTAATTCG
1 TTGCGATTTCCCAAATTCG
451445 CAACGCGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.17, T:0.42
Consensus pattern (21 bp):
TTGCGATTTCCCAAATTCGTG
Found at i:451488 original size:20 final size:20
Alignment explanation
Indices: 451442--451488 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
451432 TTTTCCTAAT
*
451442 TCGCAACGCGAATACATAAA
1 TCGCAATGCGAATACATAAA
*
451462 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACATAAA
451482 TCGCAAT
1 TCGCAAT
451489 TCAAATCTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.40, C:0.23, G:0.17, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATACATAAA
Found at i:451500 original size:20 final size:20
Alignment explanation
Indices: 451442--451504 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
451432 TTTTCCTAAT
* * *
451442 TCGCAACGCGAATACATAAA
1 TCGCAATGCAAATACGTAAA
*
451462 TCGCAATGCGAATACGTAAA
1 TCGCAATGCAAATACGTAAA
*
451482 TCGCAATTCAAAT-CTGTAAA
1 TCGCAATGCAAATAC-GTAAA
451502 TCG
1 TCG
451505 AAACGAGATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.40, C:0.22, G:0.16, T:0.22
Consensus pattern (20 bp):
TCGCAATGCAAATACGTAAA
Found at i:452523 original size:15 final size:14
Alignment explanation
Indices: 452505--452540 Score: 54
Period size: 14 Copynumber: 2.5 Consensus size: 14
452495 GAAAAAGAAG
452505 AAGAAGAAATCCCCA
1 AAGAA-AAATCCCCA
*
452520 AAGAAAAGTCCCCA
1 AAGAAAAATCCCCA
452534 AAGAAAA
1 AAGAAAA
452541 TACCACGGGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
14 15 0.75
15 5 0.25
ACGTcount: A:0.58, C:0.22, G:0.14, T:0.06
Consensus pattern (14 bp):
AAGAAAAATCCCCA
Found at i:454612 original size:20 final size:20
Alignment explanation
Indices: 454575--454663 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
454565 CAACGCGGAA
*
454575 ATCGCAACGC-AAATATGACT
1 ATCGCAACGCGGAA-ATGACT
* *
454595 ATCACAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
* * *
454615 ATCGCAATGCAGAATTGACT
1 ATCGCAACGCGGAAATGACT
454635 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
454655 ATCGCAACG
1 ATCGCAACG
454664 AGAGAATCGC
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 55 0.96
21 2 0.04
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:454634 original size:40 final size:40
Alignment explanation
Indices: 454575--454663 Score: 135
Period size: 40 Copynumber: 2.2 Consensus size: 40
454565 CAACGCGGAA
454575 ATCGCAACGCAAATATGACTATCACAACACGGAAATGACT
1 ATCGCAACGCAAATATGACTATCACAACACGGAAATGACT
* * *
454615 ATCGCAATGCAGAAT-TGACTATCGCAACGCGGAAATGACT
1 ATCGCAACGCA-AATATGACTATCACAACACGGAAATGACT
454655 ATCGCAACG
1 ATCGCAACG
454664 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
40 41 0.93
41 3 0.07
ACGTcount: A:0.38, C:0.25, G:0.19, T:0.18
Consensus pattern (40 bp):
ATCGCAACGCAAATATGACTATCACAACACGGAAATGACT
Found at i:454776 original size:33 final size:33
Alignment explanation
Indices: 454719--454803 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
454709 CGCGTTTTCG
454719 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
454753 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
454786 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
454804 CGCGTTGTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.71
34 14 0.29
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:454935 original size:14 final size:14
Alignment explanation
Indices: 454916--454952 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
454906 CATCAATTAA
454916 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
454930 ACAAATCATCTTTT
1 ACAAATCAACATTT
454944 ACAAATCAA
1 ACAAATCAA
454953 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:456414 original size:42 final size:42
Alignment explanation
Indices: 456307--456418 Score: 104
Period size: 42 Copynumber: 2.7 Consensus size: 42
456297 TCTAGAATGT
* *
456307 TGGGAG-GGACCTCTTCAACGATGACAGTGGCCTCTTGAACTG
1 TGGGAGAGG-CCTCTTGAACGATGACAGGGGCCTCTTGAACTG
* * ** *
456349 TGGGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAAC-G
1 TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACTG
*
456390 ATAGGG-GAGGCCTCTTGAATGATGACAGG
1 -T-GGGAGAGGCCTCTTGAACGATGACAGG
456419 TGATTCGGGC
Statistics
Matches: 56, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.02
42 50 0.89
43 5 0.09
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (42 bp):
TGGGAGAGGCCTCTTGAACGATGACAGGGGCCTCTTGAACTG
Found at i:456921 original size:20 final size:20
Alignment explanation
Indices: 456898--456966 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
456888 GAAACTTAAA
*
456898 ATCGCAACGTGAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
456918 ATCGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
456938 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
456958 ATCGCAACG
1 ATCGCAACG
456967 AGAGAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:457021 original size:19 final size:19
Alignment explanation
Indices: 456999--457150 Score: 138
Period size: 19 Copynumber: 8.2 Consensus size: 19
456989 AAATCGCAAC
**
456999 GCGATTTTGGTTTCGCGTT
1 GCGATTTTCATTTCGCGTT
457018 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
457037 GCGATTTTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
*
457056 GCGATTTTCATTTCTCGTT
1 GCGATTTTCATTTCGCGTT
*
457075 GCGA--TTC---TCTCGTT
1 GCGATTTTCATTTCGCGTT
*
457089 GTGA--TTCATTTCGCGTT
1 GCGATTTTCATTTCGCGTT
** *
457106 GCGATAGTCATTTTTCACGTT
1 GCGATTTTCA--TTTCGCGTT
* *
457127 GCGATTTTAAGTTTCGTGTT
1 GCGATTTTCA-TTTCGCGTT
457147 GCGA
1 GCGA
457151 AAGTAAACTA
Statistics
Matches: 112, Mismatches: 14, Indels: 13
0.81 0.10 0.09
Matches are distributed among these distances:
14 13 0.12
17 12 0.11
19 61 0.54
20 11 0.10
21 15 0.13
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (19 bp):
GCGATTTTCATTTCGCGTT
Found at i:457344 original size:94 final size:93
Alignment explanation
Indices: 457198--457576 Score: 659
Period size: 94 Copynumber: 4.0 Consensus size: 93
457188 ATGGATTGCA
* *
457198 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
457263 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
457291 TTACTTTCAACTAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
457356 TTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
457385 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
457450 TTAGCAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
* *
457479 TTACTTCAACCAAAATACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
457544 TTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
457573 TTAC
1 TTAC
457577 AAAGCAATCT
Statistics
Matches: 276, Mismatches: 8, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 22 0.08
94 254 0.92
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.21
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:459288 original size:20 final size:20
Alignment explanation
Indices: 459265--459320 Score: 78
Period size: 20 Copynumber: 2.8 Consensus size: 20
459255 TGAAATGAAA
*
459265 ATCGCAACAAGAGAATGACT
1 ATCGCAACGAGAGAATGACT
*
459285 ATCGCAACGCG-GAAATGACT
1 ATCGCAACGAGAG-AATGACT
459305 ATCGCAACGAGAGAAT
1 ATCGCAACGAGAGAAT
459321 CGCAACGCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.41, C:0.21, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGAGAGAATGACT
Found at i:459301 original size:40 final size:33
Alignment explanation
Indices: 459256--459344 Score: 97
Period size: 40 Copynumber: 2.5 Consensus size: 33
459246 TCTTTTGGTT
459256 GAAATGAAAATCGCAACAAGAGAATGACTATCGCAACGC
1 GAAATGAAAATCGCAAC--GAG-A-GA--ATCGCAACGC
**
459295 GGAAATGACTATCGCAACGAGAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGAGAGAATCGCAACGC
459329 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
459345 TGCGATTTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
33 14 0.31
34 10 0.22
36 2 0.04
37 1 0.02
38 3 0.07
40 15 0.33
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.12
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:459441 original size:20 final size:20
Alignment explanation
Indices: 459376--459466 Score: 114
Period size: 20 Copynumber: 4.5 Consensus size: 20
459366 CGATTATCTC
*
459376 GTTGCGATTTTCA-TTTCGC
1 GTTGCGATTTTCATTTTCGT
459395 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCGT
**
459415 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCGT
*
459436 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCGT
459456 GTTGCGATTTT
1 GTTGCGATTTT
459467 AAGTTTAGAA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
19 13 0.21
20 32 0.52
21 17 0.27
ACGTcount: A:0.12, C:0.18, G:0.20, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCGT
Found at i:460028 original size:20 final size:20
Alignment explanation
Indices: 460003--460214 Score: 166
Period size: 20 Copynumber: 10.5 Consensus size: 20
459993 TTTAAAAATC
460003 GCGTTGCGATTTACGGATAT
1 GCGTTGCGATTTACGGATAT
460023 GCGTTGCGATTTTAC-G-TAT
1 GCGTTGCGA-TTTACGGATAT
*
460042 GTCGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTACGGATAT
* * *
460063 GCATTACGATTTACGTAT-T
1 GCGTTGCGATTTACGGATAT
* * *
460082 CTCGTTGCGATTTACAGATAC
1 -GCGTTGCGATTTACGGATAT
* * *
460103 ACATTGCGATTTACGTAT-T
1 GCGTTGCGATTTACGGATAT
* *
460122 CTCGTTGCGATTTACGGATAC
1 -GCGTTGCGATTTACGGATAT
*
460143 GCGTTGCGATTTTACGTAT-T
1 GCGTTGCGA-TTTACGGATAT
* *
460163 GTTGTTGCGATTTACGGATAC
1 G-CGTTGCGATTTACGGATAT
*
460184 GCATTGCGATTTTACGGATACT
1 GCGTTGCGA-TTTACGGATA-T
460206 -CGTTGCGAT
1 GCGTTGCGAT
460215 AGTCAGAATC
Statistics
Matches: 149, Mismatches: 30, Indels: 26
0.73 0.15 0.13
Matches are distributed among these distances:
19 9 0.06
20 99 0.66
21 41 0.28
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (20 bp):
GCGTTGCGATTTACGGATAT
Found at i:460059 original size:40 final size:41
Alignment explanation
Indices: 460004--460214 Score: 302
Period size: 40 Copynumber: 5.2 Consensus size: 41
459994 TTAAAAATCG
* * *
460004 CGTTGCGATTTACGGATATGCGTTGCGATTTTACGTA-TGT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCT
*
460044 CGTTGCGATTTACGGATACGCATTACGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCT
* *
460084 CGTTGCGATTTACAGATACACATTGCGA-TTTACGTATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCT
* *
460124 CGTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCT
* * *
460165 TGTTGCGATTTACGGATACGCATTGCGATTTTACGGATACT
1 CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCT
460206 CGTTGCGAT
1 CGTTGCGAT
460215 AGTCAGAATC
Statistics
Matches: 152, Mismatches: 17, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
39 8 0.05
40 89 0.59
41 55 0.36
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (41 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTTACGTATTCT
Found at i:460262 original size:22 final size:20
Alignment explanation
Indices: 460223--460275 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
460213 ATAGTCAGAA
* * *
460223 TCGCGTTGTGATTTATATGT
1 TCGCGTTGCGATTTTTATAT
460243 TCGCGTTGCGATTTTTATAT
1 TCGCGTTGCGATTTTTATAT
460263 TCGCGTTGCGATT
1 TCGCGTTGCGATT
460276 CTGGAAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.13, C:0.15, G:0.25, T:0.47
Consensus pattern (20 bp):
TCGCGTTGCGATTTTTATAT
Found at i:460293 original size:21 final size:21
Alignment explanation
Indices: 460263--460378 Score: 78
Period size: 21 Copynumber: 5.6 Consensus size: 21
460253 ATTTTTATAT
*
460263 TCGCGTTGCGATTCTGGAAAA
1 TCGCATTGCGATTCTGGAAAA
* * **
460284 TCGCAATGCGAATT-TGTACTA
1 TCGCATTGCG-ATTCTGGAAAA
** *
460305 TCGCATTGCGATTCTTCATAA
1 TCGCATTGCGATTCTGGAAAA
* *
460326 TCGCATTGCGATTCTGGGAAC
1 TCGCATTGCGATTCTGGAAAA
*
460347 T-G-ATTTGCGATTCTGG-AGA
1 TCGCA-TTGCGATTCTGGAAAA
*
460366 TCGCGTTGCGATT
1 TCGCATTGCGATT
460379 TTTATTTCGC
Statistics
Matches: 72, Mismatches: 18, Indels: 11
0.71 0.18 0.11
Matches are distributed among these distances:
19 3 0.04
20 25 0.35
21 41 0.57
22 3 0.04
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTCTGGAAAA
Found at i:460870 original size:23 final size:23
Alignment explanation
Indices: 460825--460872 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
460815 ATCAAGTACA
* **
460825 ATAATATATTAGGTAGCGGTTAT
1 ATAATATAATAGGTAGCACTTAT
*
460848 ATAATGTAATAGGTAGCACTTAT
1 ATAATATAATAGGTAGCACTTAT
460871 AT
1 AT
460873 TGATCTATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCACTTAT
Found at i:461530 original size:20 final size:20
Alignment explanation
Indices: 461483--461530 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
461473 ATCCGGTAGC
*
461483 TCTTTATCGGTTTTGTCATT
1 TCTTTACCGGTTTTGTCATT
**
461503 TCGATACCGGTTTTGTCATAT
1 TCTTTACCGGTTTTGTCAT-T
461524 T-TTTACC
1 TCTTTACC
461531 TGTTATATTG
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 20 0.91
21 2 0.09
ACGTcount: A:0.15, C:0.19, G:0.15, T:0.52
Consensus pattern (20 bp):
TCTTTACCGGTTTTGTCATT
Found at i:461616 original size:182 final size:182
Alignment explanation
Indices: 461309--461754 Score: 664
Period size: 182 Copynumber: 2.5 Consensus size: 182
461299 TTTTACTACA
* * *
461309 GGTTTTGTCGTTTTGAGACCAATTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACA
1 GGTTTTGTCATTTAGAGACCAGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACA
* * * *
461374 TTTTTATAAAGTATCGACATTTTATTGGCGCTATAACTTTTTTTCTTTTAAATTCCAAAAGTATC
66 TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTATC
**
461439 GATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGCTCTTTA-T
131 GATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGAGCTTTACT
* * * *
461490 CGGTTTTGTCATTTCGATACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATAC
1 -GGTTTTGTCATTTAGAGACCAGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATAC
*
461555 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
65 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTAT
* *
461620 TGATACTTATAATAAAGTATCGACACTTTCAATATATCCGGTAGAGCTTTACT
130 CGATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGAGCTTTACT
* * * * * *
461673 TGTTTTGTTATTTATAGACCAG--TTGTCATTTTTTTACCTGTTATATTTTTATAGATCGATACA
1 GGTTTTGTCATTTAGAGACCAGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACA
461736 TTTTTATAAAGTATCGACA
66 TTTTTATAAAGTATCGACA
461755 ATTTCAATAT
Statistics
Matches: 239, Mismatches: 24, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
180 57 0.24
182 181 0.76
183 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.45
Consensus pattern (182 bp):
GGTTTTGTCATTTAGAGACCAGTTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATACA
TTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTATC
GATACTTATAATAAAGTATCGACACTTTCAACATATCCGGTAGAGCTTTACT
Found at i:461872 original size:112 final size:112
Alignment explanation
Indices: 461631--462202 Score: 898
Period size: 112 Copynumber: 5.1 Consensus size: 112
461621 GATACTTATA
* * * *
461631 ATAAAGTATCGACACTTTCAATATATCCGGTAGAGCTTTACTTGTTTTGTTATTTATAGACCAG-
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
461695 -TTGTCATTTTTTTACCTGTTATATTTTTATAGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* ** *
461741 ATAAAGTATCGACAATTTCAATATATTTGGTAGCGCTTTACCTGTTTTGTCAATTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
461806 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
461853 ATAAAGTATCGGCACTTTCAATATATCCGGTAGCGCTTTATCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
461918 TTTGTCATTTTTTTAGCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
461965 ATAAAGTATTGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
462030 TTTTTCATTTTGTTACCTATTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
462077 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAAACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* *
462142 TTTGTCA-TTTTTTACCTGTTATATTGTTATGGATCAATATATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
462188 ATAAAATATCGACAC
1 ATAAAGTATCGACAC
462203 AAACCGACAA
Statistics
Matches: 424, Mismatches: 36, Indels: 3
0.92 0.08 0.01
Matches are distributed among these distances:
110 56 0.13
111 49 0.12
112 319 0.75
ACGTcount: A:0.26, C:0.14, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:462805 original size:31 final size:31
Alignment explanation
Indices: 462770--462854 Score: 116
Period size: 31 Copynumber: 2.7 Consensus size: 31
462760 ATAATTTTTT
**
462770 AATATTTAGTCTATTTGTAATATAGTCCCTC
1 AATATTTAGTCCGTTTGTAATATAGTCCCTC
* *
462801 AATATTTAGTCCGTTTATAATATAGTCCTTC
1 AATATTTAGTCCGTTTGTAATATAGTCCCTC
* *
462832 AACATTTAATCCGTTTGTAATAT
1 AATATTTAGTCCGTTTGTAATAT
462855 GATCCCCGTC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.45
Consensus pattern (31 bp):
AATATTTAGTCCGTTTGTAATATAGTCCCTC
Found at i:463493 original size:30 final size:31
Alignment explanation
Indices: 463457--463516 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
463447 TTATACGGCG
*
463457 TAGAATAGTCGTG-TCAACCCCAAATTGGCA
1 TAGAATAATCGTGCTCAACCCCAAATTGGCA
* *
463487 TAGAATAATCGTGCTCAACCTCGAATTGGC
1 TAGAATAATCGTGCTCAACCCCAAATTGGC
463517 GAATTATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (31 bp):
TAGAATAATCGTGCTCAACCCCAAATTGGCA
Found at i:468935 original size:55 final size:55
Alignment explanation
Indices: 468882--469470 Score: 749
Period size: 55 Copynumber: 10.7 Consensus size: 55
468872 ACGAGTCTGT
* * * * *
468882 TCCCTATTCTTTCAGGGAGTATA-AGACTCGAACAATCTTTAACAAATGTGTCTGC
1 TCCCTATTCCTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCCGC
* * * *
468937 TCCCTATTCATTCAGGGAGTGTA-AGACTCAAACAATCTTCAATAAACGGGTCCGC
1 TCCCTATTCCTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCCGC
*
468992 TCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGC
1 TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGC
* *
469047 TCTCTATTCCTTCAGTGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGC
1 TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGC
* * *
469102 TCTCTATTCCTTCAGAG-GTATAGAACTCGAACAATCTTCAACAAACGGGTCTGC
1 TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGC
* * * * * *
469156 TCCCTATTCGTTCAGGGAGTATAGAACTCAAAAAATCTTCATA-AAATGGGTACAC
1 TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCA-ACAAACGGGTCCGC
* * * *
469211 TCTCTATTCCTTCAGAGAGTATAGAAATCAAACAATCTTCAACAAACGGGTCCGC
1 TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGC
** * * *
469266 TCTTTATTCATTCAGAGAGTATAGAATTCGAACAATCTTCAACAAACGGGTCCGC
1 TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGC
* * * * *
469321 TCCCTATTCGTTCAGGGAGTATAGAACTCGAAAAATCTTC-ATAAACAGGTTCGC
1 TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGC
* *
469375 TCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGC
1 TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGC
* *
469430 TCCCTATTCGTTCAGGGAGTATAGAACTCGAAAAATCTTCA
1 TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCA
469471 TAAAACGAGT
Statistics
Matches: 470, Mismatches: 57, Indels: 14
0.87 0.11 0.03
Matches are distributed among these distances:
54 99 0.21
55 368 0.78
56 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (55 bp):
TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGC
Found at i:469288 original size:219 final size:220
Alignment explanation
Indices: 468882--469477 Score: 812
Period size: 219 Copynumber: 2.7 Consensus size: 220
468872 ACGAGTCTGT
* * * *
468882 TCCCTATTCTTTCAGGGAGTATA-AGACTCGAACAATCTTTAACAAATGTGTCTGCTCCCTATTC
1 TCCCTATTCCTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTC
* *
468946 ATTCAGGGAGTGTA-AGACTCAAACAATCTTCAATAAACGGGTCCGCTCCCTATTCGTTCAGGGA
65 ATTCAGGGAGTATAGA-ACTCAAACAATCTTCAACAAACGGGTCCGCTCCCTATTCGTTCAGGGA
* * *
469010 GTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGTGAGTATAGAACT
129 GTATAGAACTCAAACAATCTTCATAAAACGGGTCCGCTCTCTATTCATTCAGAGAGTATAGAACT
469075 CGAACAATCTTCAACAAACGGGTCCGC
194 CGAACAATCTTCAACAAACGGGTCCGC
* * *
469102 TCTCTATTCCTTCAGAG-GTATAGAACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTCG
1 TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTCA
* * * * * * *
469166 TTCAGGGAGTATAGAACTCAAAAAATCTTCATA-AAATGGGTACACTCTCTATTCCTTCAGAGAG
66 TTCAGGGAGTATAGAACTCAAACAATCTTCA-ACAAACGGGTCCGCTCCCTATTCGTTCAGGGAG
* * *
469230 TATAGAAATCAAACAATCTTCA-ACAAACGGGTCCGCTCTTTATTCATTCAGAGAGTATAGAATT
130 TATAGAACTCAAACAATCTTCATA-AAACGGGTCCGCTCTCTATTCATTCAGAGAGTATAGAACT
469294 CGAACAATCTTCAACAAACGGGTCCGC
194 CGAACAATCTTCAACAAACGGGTCCGC
* * * * *
469321 TCCCTATTCGTTCAGGGAGTATAGAACTCGAAAAATCTTC-ATAAACAGGT-TCGCTCTCTATTC
1 TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCT-GCTCCCTATTC
* * *
469384 CTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATTCGTTCAGGGAG
65 ATTCAGGGAGTATAGAACTCAAACAATCTTCAACAAACGGGTCCGCTCCCTATTCGTTCAGGGAG
469449 TATAGAACTCGAAA-AATCTTCATAAAACG
130 TATAGAACTC-AAACAATCTTCATAAAACG
469478 AGTTTGCTTC
Statistics
Matches: 328, Mismatches: 39, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
218 3 0.01
219 283 0.86
220 42 0.13
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (220 bp):
TCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGGTCTGCTCCCTATTCA
TTCAGGGAGTATAGAACTCAAACAATCTTCAACAAACGGGTCCGCTCCCTATTCGTTCAGGGAGT
ATAGAACTCAAACAATCTTCATAAAACGGGTCCGCTCTCTATTCATTCAGAGAGTATAGAACTCG
AACAATCTTCAACAAACGGGTCCGC
Found at i:469349 original size:274 final size:274
Alignment explanation
Indices: 468876--469475 Score: 870
Period size: 274 Copynumber: 2.2 Consensus size: 274
468866 CAAATGACGA
* * * * * *
468876 GTCTGTTCCCTATTCTTTCAGGGAGTATA-AGACTCGAACAATCTTTA-ACAAATGTGTCTGCTC
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAGA-ACTCGAAAAATCTTCATA-AAATGGGTCTACTC
* * * * *
468939 CCTATTCATTCAGGGAGTGTAAGACTCAAACAATCTTCAATAAACGGGTCCGCTCCCTATTCGTT
64 CCTATTCATTCAGAGAGTATAAGAATCAAACAATCTTCAACAAACGGGTCCGCTCCCTATTCATT
* * *
469004 CAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCTCTATTCCTTCAGTGAGTAT
129 CAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATTCCTTCAGGGAGTAT
* *
469069 AGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTATTCCTTCAGAG-GTATAGAACTCGAA
194 AGAACTCGAAAAATCTTC-ACAAACAGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA
469133 CAATCTTCAACAAACGG
258 CAATCTTCAACAAACGG
* *
469150 GTCTGCTCCCTATTCGTTCAGGGAGTATAGAACTCAAAAAATCTTCATAAAATGGGTAC-ACTCT
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAAAAATCTTCATAAAATGGGT-CTACTCC
* **
469214 CTATTCCTTCAGAGAGTAT-AGAAATCAAACAATCTTCAACAAACGGGTCCGCTCTTTATTCATT
65 CTATTCATTCAGAGAGTATAAG-AATCAAACAATCTTCAACAAACGGGTCCGCTCCCTATTCATT
* *
469278 CAGAGAGTATAGAATTCGAACAATCTTCA-ACAAACGGGTCCGCTCCCTATTCGTTCAGGGAGTA
129 CAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCCCTATTCCTTCAGGGAGTA
* *
469342 TAGAACTCGAAAAATCTTCATAAACAGGTTCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA
193 TAGAACTCGAAAAATCTTCACAAACAGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA
469407 CAATCTTCAACAAACGG
258 CAATCTTCAACAAACGG
*
469424 GTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAAAAATCTTCATAAAA
1 GTCTGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAAAAATCTTCATAAAA
469476 CGAGTTTGCT
Statistics
Matches: 293, Mismatches: 27, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
273 31 0.11
274 259 0.88
275 3 0.01
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.28
Consensus pattern (274 bp):
GTCTGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAAAAATCTTCATAAAATGGGTCTACTCCC
TATTCATTCAGAGAGTATAAGAATCAAACAATCTTCAACAAACGGGTCCGCTCCCTATTCATTCA
GAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCGCTCCCTATTCCTTCAGGGAGTATAG
AACTCGAAAAATCTTCACAAACAGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAA
TCTTCAACAAACGG
Found at i:470858 original size:7 final size:7
Alignment explanation
Indices: 470848--470988 Score: 110
Period size: 7 Copynumber: 19.7 Consensus size: 7
470838 TTTATTTTAT
470848 TTTTTCA
1 TTTTTCA
470855 TTTTTCA
1 TTTTTCA
*
470862 TTTTTCTC
1 TTTTTC-A
470870 TTTCTTC-
1 TTT-TTCA
*
470877 TTTCTTCT
1 TTT-TTCA
*
470885 TTTTTTA
1 TTTTTCA
470892 TTTTTTCA
1 -TTTTTCA
*
470900 TTTTTTA
1 TTTTTCA
*
470907 TTTTCACCA
1 TTTT--TCA
470916 TTTTTCA
1 TTTTTCA
470923 TTTTTCA
1 TTTTTCA
**
470930 TTTTTTT
1 TTTTTCA
470937 TTTTTCA
1 TTTTTCA
470944 TTTTTCA
1 TTTTTCA
470951 -TTTT--
1 TTTTTCA
*
470955 TTTCTCA
1 TTTTTCA
*
470962 TTTTTTA
1 TTTTTCA
470969 TTTTTCA
1 TTTTTCA
470976 TTTTTTCA
1 -TTTTTCA
470984 TTTTT
1 TTTTT
470989 TTATTTCTTC
Statistics
Matches: 108, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
5 3 0.03
6 4 0.04
7 74 0.69
8 19 0.18
9 8 0.07
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (7 bp):
TTTTTCA
Found at i:470891 original size:45 final size:46
Alignment explanation
Indices: 470842--470994 Score: 172
Period size: 45 Copynumber: 3.3 Consensus size: 46
470832 CCCCCTTTTA
* *
470842 TTTTATTTTTTCATTTTTCATTTTTC-TC-TTTCTTC-TTTCTTCTTT
1 TTTTATTTTTTCATTTTTCATTTTTCACCATTT-TTCATTT-TTCATT
*
470887 TTTTATTTTTTCATTTTTTA-TTTTCACCATTTTTCATTTTTCATT
1 TTTTATTTTTTCATTTTTCATTTTTCACCATTTTTCATTTTTCATT
** *
470932 TTTT-TTTTTTCATTTTTCATTTTTTTCTCATTTTTTATTTTTCATT
1 TTTTATTTTTTCATTTTTCATTTTTCAC-CATTTTTCATTTTTCATT
*
470978 TTTTCATTTTTTTATTT
1 TTTT-ATTTTTTCATTT
470995 CTTCTTCAAG
Statistics
Matches: 93, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
44 19 0.20
45 37 0.40
46 27 0.29
48 10 0.11
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (46 bp):
TTTTATTTTTTCATTTTTCATTTTTCACCATTTTTCATTTTTCATT
Found at i:470957 original size:61 final size:62
Alignment explanation
Indices: 470842--471000 Score: 172
Period size: 61 Copynumber: 2.6 Consensus size: 62
470832 CCCCCTTTTA
*
470842 TTTTATTTTT-TCATTTTTCATTTTTCTCTTTCTTCTTTCTTCTTTTTTTATTTTT-TCATT
1 TTTTATTTTTCACATTTTTCATTTTTCTCTTTCTTCTTTCTTCTTTTTTTATTTTTCTCATT
*
470902 TTTTA-TTTTCACCATTTTTCATTTTTCAT-TTT-TT-TTTTTTCATTTTTCATT-TTTTTCTCA
1 TTTTATTTTTCA-CATTTTTCATTTTTC-TCTTTCTTCTTTCTTC-TTTTT--TTATTTTTCTCA
470962 TT
61 TT
* * *
470964 TTTTATTTTTCA-TTTTTTCATTTTTTTATTTCTTCTT
1 TTTTATTTTTCACATTTTTCATTTTTCTCTTTCTTCTT
471001 CAAGCAAAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 19
0.79 0.04 0.18
Matches are distributed among these distances:
59 10 0.12
60 13 0.15
61 38 0.45
62 15 0.18
63 8 0.10
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (62 bp):
TTTTATTTTTCACATTTTTCATTTTTCTCTTTCTTCTTTCTTCTTTTTTTATTTTTCTCATT
Found at i:480714 original size:45 final size:46
Alignment explanation
Indices: 480642--480729 Score: 124
Period size: 45 Copynumber: 1.9 Consensus size: 46
480632 AAATAGAAAT
*
480642 CCTAACCGCATGATATCTAATTCGCATGC-TTGTTCGAAAAATAAA
1 CCTAACCGCATGATATCTAATTCGCATGCATTATTCGAAAAATAAA
** *
480687 CCTAACCGCATGATATCTGGTTTGCATGCATTTATTCGAAAAA
1 CCTAACCGCATGATATCTAATTCGCATGCA-TTATTCGAAAAA
480730 CGAAAATAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
45 26 0.70
47 11 0.30
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.31
Consensus pattern (46 bp):
CCTAACCGCATGATATCTAATTCGCATGCATTATTCGAAAAATAAA
Found at i:481706 original size:41 final size:41
Alignment explanation
Indices: 481660--481741 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
481650 TTGAGGTATG
481660 GTTACCAAAAAATGCGTTCGGGAGTCAGTTACGTGTGGGGA
1 GTTACCAAAAAATGCGTTCGGGAGTCAGTTACGTGTGGGGA
*
481701 GTTACCAAAAAATGCGTTCGGGAGTCGGTTACGTGTGGGGA
1 GTTACCAAAAAATGCGTTCGGGAGTCAGTTACGTGTGGGGA
481742 ATGATTAGCA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.26, C:0.15, G:0.35, T:0.24
Consensus pattern (41 bp):
GTTACCAAAAAATGCGTTCGGGAGTCAGTTACGTGTGGGGA
Found at i:485418 original size:50 final size:50
Alignment explanation
Indices: 485359--485457 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
485349 AGCAGGAAAG
* * * *
485359 CGCGTCCCCTGCACCGCGTTATATGCTAATTTGGCGCCACGTGGGTATAA
1 CGCGTCCCCTGCACCGCGATATACGCTAATCTGGCGCCACGTGAGTATAA
* * *
485409 CGCGTCCCCTGCCCCGCGATATACGGTGATCTGGCGCCACGTGAGTATA
1 CGCGTCCCCTGCACCGCGATATACGCTAATCTGGCGCCACGTGAGTATA
485458 GTAGCGCGGA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 42 1.00
ACGTcount: A:0.17, C:0.32, G:0.27, T:0.23
Consensus pattern (50 bp):
CGCGTCCCCTGCACCGCGATATACGCTAATCTGGCGCCACGTGAGTATAA
Found at i:488658 original size:35 final size:36
Alignment explanation
Indices: 488614--488700 Score: 103
Period size: 35 Copynumber: 2.5 Consensus size: 36
488604 ATTTGATATT
488614 TAAATATAA-CAAACTTACAATAA-GA-ATTAAATGG
1 TAAATATAACCAAA-TTACAATAACGATATTAAATGG
488648 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ATAACCAAATTACAATAAC-GATATTAAATGG
*
488686 T-AATA-AACAAAATTA
1 TAAATATAACCAAATTA
488701 ACTAAAATAT
Statistics
Matches: 47, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
34 5 0.11
35 22 0.47
36 5 0.11
37 5 0.11
38 10 0.21
ACGTcount: A:0.55, C:0.09, G:0.08, T:0.28
Consensus pattern (36 bp):
TAAATATAACCAAATTACAATAACGATATTAAATGG
Found at i:488932 original size:21 final size:21
Alignment explanation
Indices: 488908--488957 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
488898 TTCTGACTCC
* *
488908 TCGTTGTCATCATCATCGTCA
1 TCGTCGTCATCACCATCGTCA
*
488929 TCGTCGTCGTCACCATCGTCA
1 TCGTCGTCATCACCATCGTCA
488950 TCGTCGTC
1 TCGTCGTC
488958 GTCCGGAGCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.14, C:0.34, G:0.18, T:0.34
Consensus pattern (21 bp):
TCGTCGTCATCACCATCGTCA
Found at i:488958 original size:21 final size:21
Alignment explanation
Indices: 488921--488960 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
488911 TTGTCATCAT
488921 CATCGTCATCGTCGTCGTCAC
1 CATCGTCATCGTCGTCGTCAC
488942 CATCGTCATCGTCGTCGTC
1 CATCGTCATCGTCGTCGTC
488961 CGGAGCAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.12, C:0.38, G:0.20, T:0.30
Consensus pattern (21 bp):
CATCGTCATCGTCGTCGTCAC
Found at i:489316 original size:18 final size:18
Alignment explanation
Indices: 489293--489350 Score: 80
Period size: 18 Copynumber: 3.2 Consensus size: 18
489283 AAAAGCGATG
*
489293 GCGGCATCATATATAGCT
1 GCGGCATCATATATGGCT
*
489311 GCGGCATCATATATGGTT
1 GCGGCATCATATATGGCT
* *
489329 GCAGTATCATATATGGCT
1 GCGGCATCATATATGGCT
489347 GCGG
1 GCGG
489351 TGGCTGTTGG
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (18 bp):
GCGGCATCATATATGGCT
Found at i:490982 original size:111 final size:111
Alignment explanation
Indices: 490844--491065 Score: 372
Period size: 111 Copynumber: 2.0 Consensus size: 111
490834 ATTACAAAAA
* * *
490844 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAGTTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
* * * *
490909 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACATTAAAATGTTAACGTATCAGCAAAGTATAGAGATAT
*
490955 TTAATTTTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
491020 AATTAAAACATTAAAATGTTAACGTATCAGCAAAGTATAGAGATAT
66 AATTAAAACATTAAAATGTTAACGTATCAGCAAAGTATAGAGATAT
491066 ATGATTTCCA
Statistics
Matches: 103, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 103 1.00
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATCAACTAAATATTACTAATAATTTAAATTA
AATTAAAACATTAAAATGTTAACGTATCAGCAAAGTATAGAGATAT
Found at i:491203 original size:12 final size:10
Alignment explanation
Indices: 491189--491229 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
491179 ACCTTAAAAA
*
491189 GAGAGTATTT
1 GAGAGAATTT
491199 GAGAGAAATTT
1 GAGAG-AATTT
491210 -AGAGAATTT
1 GAGAGAATTT
491219 GAGAGAATTT
1 GAGAGAATTT
491229 G
1 G
491230 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:491405 original size:50 final size:50
Alignment explanation
Indices: 491351--491448 Score: 135
Period size: 50 Copynumber: 2.0 Consensus size: 50
491341 AGATATCCAG
* * *
491351 GTATAACGC-AGATCAGGGGGCGCGCTATACCCACGTGGCGCCAGATCACC
1 GTATAACGCGAGA-CAGAGGGCGCGCTATACCCACGTGGCACCAAATCACC
* *
491401 GTATATCGCGGGACAGAGGGCGCGCTATACCCACGTGGCACCAAATCA
1 GTATAACGCGAGACAGAGGGCGCGCTATACCCACGTGGCACCAAATCA
491449 ACATATAGCG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 40 0.95
51 2 0.05
ACGTcount: A:0.26, C:0.31, G:0.30, T:0.14
Consensus pattern (50 bp):
GTATAACGCGAGACAGAGGGCGCGCTATACCCACGTGGCACCAAATCACC
Found at i:493391 original size:243 final size:244
Alignment explanation
Indices: 492898--493434 Score: 779
Period size: 243 Copynumber: 2.2 Consensus size: 244
492888 TTTAACTGAC
* * * * *
492898 AATGACATCCTTGAAATGCTTAGGAATTTTCTTAGTGACTATTATGTTTATGTTCACATTTATTA
1 AATGATATCCTTGAAATGCTTAGGGATTTACCTAGTGACCATTATGTTTATGTTCACATTTATTA
* * *
492963 GGAGACTAATGTTAGAATAGACTAAAATATTAGTGGATTACTTTAATAATTGTGATGCTGATTAA
66 GGAAACTAATGTTAGAATACACTAAAATACTAGTGGATTACTTTAATAATTGTGATGCTGATTAA
* *
493028 ATGTCCTTCTTTGCAGTTACTGATATGATAAGTAAGTTGGGAATTAATTATACAATTAAGGTATA
131 ATGTCCTTCTTTACAGTTACTGATATGATAAGTAAGTTAGGAATTAATTATACAATTAAGGTATA
** * *
493093 TTGGTAAGTGTCAAACAATCCACTAGAGGTAAAACCACTTATAACCAAA
196 TAAGCAAGTGTCAAACAATCCACTAGAGGTAAAACCACTCATAACCAAA
*
493142 AATGATATCCTTGAAATGCTTAGGGATTTACCTAGTAACCATTATGTTTATGTTCACATTTATTA
1 AATGATATCCTTGAAATGCTTAGGGATTTACCTAGTGACCATTATGTTTATGTTCACATTTATTA
* * * * **
493207 GGAAACTAATGTTGGAATACACTGACATACTAGTGGATTACTTTGATAATTGTGATG-TTTTTAA
66 GGAAACTAATGTTAGAATACACTAAAATACTAGTGGATTACTTTAATAATTGTGATGCTGATTAA
* * * **
493271 ATGTCCTTCTTTATAGTTACTGATATGATAAGTAAGTTAGGAGTTAGTTATACTCTTAAGGTATA
131 ATGTCCTTCTTTACAGTTACTGATATGATAAGTAAGTTAGGAATTAATTATACAATTAAGGTATA
* * *** *
493336 TAAGCAAGTGTCAAACAATCCACTAGAGGTAAAATCACTCCTAATTGAT
196 TAAGCAAGTGTCAAACAATCCACTAGAGGTAAAACCACTCATAACCAAA
493385 AATGATATCCTTGAAATGCTTAGGGATTTACCTAGTGACCATTATGTTTA
1 AATGATATCCTTGAAATGCTTAGGGATTTACCTAGTGACCATTATGTTTA
493435 CATTTATTTG
Statistics
Matches: 260, Mismatches: 33, Indels: 1
0.88 0.11 0.00
Matches are distributed among these distances:
243 151 0.58
244 109 0.42
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (244 bp):
AATGATATCCTTGAAATGCTTAGGGATTTACCTAGTGACCATTATGTTTATGTTCACATTTATTA
GGAAACTAATGTTAGAATACACTAAAATACTAGTGGATTACTTTAATAATTGTGATGCTGATTAA
ATGTCCTTCTTTACAGTTACTGATATGATAAGTAAGTTAGGAATTAATTATACAATTAAGGTATA
TAAGCAAGTGTCAAACAATCCACTAGAGGTAAAACCACTCATAACCAAA
Found at i:497583 original size:19 final size:19
Alignment explanation
Indices: 497559--497600 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
497549 ACAATATAAT
497559 ATTTAAAAATATTCCTTTC
1 ATTTAAAAATATTCCTTTC
497578 ATTTAAAAATATTCCTTTC
1 ATTTAAAAATATTCCTTTC
497597 ATTT
1 ATTT
497601 TTATAAAAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (19 bp):
ATTTAAAAATATTCCTTTC
Found at i:497943 original size:16 final size:15
Alignment explanation
Indices: 497919--497954 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
497909 ATTATATAAA
*
497919 ATATAATGAATTATTT
1 ATATTATGAATTA-TT
497935 ATATTATGAATTATT
1 ATATTATGAATTATT
497950 ATATT
1 ATATT
497955 TTGTATTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (15 bp):
ATATTATGAATTATT
Found at i:504116 original size:2 final size:2
Alignment explanation
Indices: 504109--504138 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
504099 GTTTAGCCAT
504109 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
504139 GGTGTAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:508434 original size:24 final size:24
Alignment explanation
Indices: 508406--508453 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
508396 ATTACAGTTC
508406 CCCTAAGGCTTATCATCCTTCCCT
1 CCCTAAGGCTTATCATCCTTCCCT
*
508430 CCCTATGGCTTATCATCCTTCCCT
1 CCCTAAGGCTTATCATCCTTCCCT
508454 TGTTTCTGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.15, C:0.42, G:0.08, T:0.35
Consensus pattern (24 bp):
CCCTAAGGCTTATCATCCTTCCCT
Found at i:514846 original size:31 final size:31
Alignment explanation
Indices: 514802--514903 Score: 136
Period size: 32 Copynumber: 3.3 Consensus size: 31
514792 TCTTTAGAAC
*
514802 ATAGGT-ATACTGTCCATATGTCTCAAAGAT
1 ATAGGTAATTCTGTCCATATGTCTCAAAGAT
*
514832 ATAGGTAATTCTGTCCATATGTCCTGAAAG-T
1 ATAGGTAATTCTGTCCATATGT-CTCAAAGAT
*
514863 CATAGGTAATTCTGTCCATATGTCTCAAAAGAC
1 -ATAGGTAATTCTGTCCATATGTCTC-AAAGAT
514896 ATAGGTAA
1 ATAGGTAA
514904 CCCTCGACTC
Statistics
Matches: 63, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
30 6 0.10
31 17 0.27
32 40 0.63
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (31 bp):
ATAGGTAATTCTGTCCATATGTCTCAAAGAT
Found at i:519068 original size:32 final size:31
Alignment explanation
Indices: 519014--519117 Score: 140
Period size: 31 Copynumber: 3.3 Consensus size: 31
519004 GCTCTTTAGA
519014 ACATAGGTATATTA-TCCATATGTCTCAAAAG
1 ACATAGGTA-ATTATTCCATATGTCTCAAAAG
* *
519045 ACATAGGTAATTATGTCCATATGTCCCGAAAG
1 ACATAGGTAATTAT-TCCATATGTCTCAAAAG
*
519077 ACATAGGTAATTCTAT-CATATGTCTCAAAAG
1 ACATAGGTAATTAT-TCCATATGTCTCAAAAG
519108 ACATAGGTAA
1 ACATAGGTAA
519118 CCCTCGACTC
Statistics
Matches: 65, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
30 4 0.06
31 32 0.49
32 29 0.45
ACGTcount: A:0.38, C:0.16, G:0.15, T:0.30
Consensus pattern (31 bp):
ACATAGGTAATTATTCCATATGTCTCAAAAG
Found at i:520045 original size:20 final size:20
Alignment explanation
Indices: 520017--520054 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
520007 TTCCCATTGA
520017 AGTGCATCGATACATTCTAT
1 AGTGCATCGATACATTCTAT
* *
520037 AGTGTATCGATGCATTCT
1 AGTGCATCGATACATTCT
520055 TTAACATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAT
Found at i:526489 original size:113 final size:112
Alignment explanation
Indices: 526315--526531 Score: 371
Period size: 113 Copynumber: 1.9 Consensus size: 112
526305 GTACAAAAAA
* *
526315 TATCGATACTTTTAATATATCTAGTAGCTTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCA
1 TATCGATACTTGTAACATATCTAGTAGCTTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCA
*
526380 TATTTTTACTTGTTATATTGTTATGTATCGATACATTTTTTCTAAAG
66 TATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTTCTAAAG
* *
526427 TATCGATACTTGTAACATATCTGGTAGCTCTTTACTGGTTTTGTCATAATGAAACTGGTTTTGTC
1 TATCGATACTTGTAACATATCTAGTAGCT-TTTACCGGTTTTGTCATAATGAAACTGGTTTTGTC
*
526492 GTATTTTTACCTGTTATATTGTTATGTATCGATACATTTT
65 ATATTTTTACCTGTTATATTGTTATGTATCGATACATTTT
526532 GATACTTGTA
Statistics
Matches: 98, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
112 26 0.27
113 72 0.73
ACGTcount: A:0.24, C:0.12, G:0.15, T:0.48
Consensus pattern (112 bp):
TATCGATACTTGTAACATATCTAGTAGCTTTTACCGGTTTTGTCATAATGAAACTGGTTTTGTCA
TATTTTTACCTGTTATATTGTTATGTATCGATACATTTTTTCTAAAG
Found at i:526609 original size:100 final size:101
Alignment explanation
Indices: 526431--526742 Score: 378
Period size: 111 Copynumber: 3.0 Consensus size: 101
526421 CTAAAGTATC
* * * * * *
526431 GATACTTGTAACATATCTGGTAGCTCTTTACTGGTTTTGTCATAATGAAACTGGTTTTGTCGTAT
1 GATACTTGTAACATATCCGATAGTTCTTTACCGGTTTTGTCATAATGAAACTGATTTT-TCATAT
*
526496 TTTTACCTGTTATATTGTTATGTATCGATACATTTT-
65 TTTTACTTGTTATATTGTTATGTATCGATACATTTTA
*
526532 GATACTTGTAACATATCCGATAGTTCTTTACCGGTTTT-TCATAATGAAACTGTTTTTATCATAT
1 GATACTTGTAACATATCCGATAGTTCTTTACCGGTTTTGTCATAATGAAACTGATTTT-TCATAT
*
526596 TTTTACTTGTTATATTATTATGTATCGATACATTTTTATAAA
65 TTTTACTTGTTATATTGTTATGTATCGATACA--TTT-T--A
* *
526638 GTATTAATACTTTTAACATATTCGATA-TCTCTTTACCGGTTTTGTCATAATGAAACTGATTTTT
1 G-----ATACTTGTAACATATCCGATAGT-TCTTTACCGGTTTTGTCATAATGAAACTGATTTTT
*
526702 CATATTTTTACTTGTTATATTGTTATGTAACGATACATTTT
60 CATATTTTTACTTGTTATATTGTTATGTATCGATACATTTT
526743 TATAAAGTAT
Statistics
Matches: 184, Mismatches: 14, Indels: 19
0.85 0.06 0.09
Matches are distributed among these distances:
100 53 0.29
101 34 0.18
102 3 0.02
103 1 0.01
106 1 0.01
108 1 0.01
109 3 0.02
110 1 0.01
111 69 0.38
112 18 0.10
ACGTcount: A:0.27, C:0.12, G:0.12, T:0.48
Consensus pattern (101 bp):
GATACTTGTAACATATCCGATAGTTCTTTACCGGTTTTGTCATAATGAAACTGATTTTTCATATT
TTTACTTGTTATATTGTTATGTATCGATACATTTTA
Found at i:526974 original size:75 final size:74
Alignment explanation
Indices: 526851--527102 Score: 276
Period size: 75 Copynumber: 3.4 Consensus size: 74
526841 ATGGTAGGTA
* ** * * * * *
526851 TTTTAATGTAATAGGTAGATCCAATTTTATTTTACCGTTTACATTATTAGTAATCTTTAAATAAA
1 TTTTAATATAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAATCTTCAAAAAAA
526916 CCAGTATGTG
66 CCAGTA-GTG
* * *
526926 TTTTAATATAATATGTAGCGCCTATTTTTTTTTACCGTTTACGTTATTAGCAACCTTCAAAAAAA
1 TTTTAATATAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAATCTTCAAAAAAA
*
526991 CCAATAGATAG
66 CCAGTAG-T-G
* * *
527002 -TTTAATGTAATAGGTAACGCCTA-TTTTTTTTACCATTTACATTATTAGCAATCTTCAAAAAAA
1 TTTTAATATAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAATCTTCAAAAAAA
*
527065 CC-GATAGGTT
66 CCAG-TA-GTG
* *
527075 TTTTAATATAATAAGTAGCGTCTATTTT
1 TTTTAATATAATAGGTAGCGCCTATTTT
527103 ATATTTCTGG
Statistics
Matches: 147, Mismatches: 24, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
74 62 0.42
75 84 0.57
76 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.11, T:0.42
Consensus pattern (74 bp):
TTTTAATATAATAGGTAGCGCCTATTTTTTTTTACCGTTTACATTATTAGCAATCTTCAAAAAAA
CCAGTAGTG
Found at i:528145 original size:21 final size:20
Alignment explanation
Indices: 528105--528146 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
528095 CTAACTTACA
*
528105 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
528125 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
528146 A
1 A
528147 ATTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:532492 original size:21 final size:20
Alignment explanation
Indices: 532452--532493 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
532442 CCAACTTACA
*
532452 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
532472 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
532493 A
1 A
532494 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:534922 original size:21 final size:20
Alignment explanation
Indices: 534882--534923 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
534872 CCAACTTACA
*
534882 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
534902 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
534923 A
1 A
534924 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Found at i:544883 original size:14 final size:15
Alignment explanation
Indices: 544861--544894 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
544851 TACATAAATT
*
544861 TATATTAAAAAATAA
1 TATAATAAAAAATAA
544876 -ATAATAAAAAATAA
1 TATAATAAAAAATAA
544890 TATAA
1 TATAA
544895 ACTTGAGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
TATAATAAAAAATAA
Found at i:555941 original size:19 final size:20
Alignment explanation
Indices: 555917--555967 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
555907 TTTCAGCCTT
*
555917 GATGCATGGATGCAT-GCAG
1 GATGCATCGATGCATGGCAG
*
555936 GATGCATCGATGCATGGCAT
1 GATGCATCGATGCATGGCAG
555956 GATGCATCGATG
1 GATGCATCGATG
555968 TACTAAGTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.25, C:0.18, G:0.33, T:0.24
Consensus pattern (20 bp):
GATGCATCGATGCATGGCAG
Found at i:556052 original size:19 final size:21
Alignment explanation
Indices: 556034--556087 Score: 85
Period size: 19 Copynumber: 2.7 Consensus size: 21
556024 TTAGTGCAGG
556034 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCAGGGA
*
556055 TGCAGGGATGCACT--AGGGA
1 TGCATGGATGCACTGCAGGGA
556074 TGCATGGATGCACT
1 TGCATGGATGCACT
556088 TTGACACCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 18 0.58
21 13 0.42
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.20
Consensus pattern (21 bp):
TGCATGGATGCACTGCAGGGA
Found at i:559540 original size:21 final size:20
Alignment explanation
Indices: 559472--559590 Score: 141
Period size: 21 Copynumber: 5.7 Consensus size: 20
559462 GATGTTTGAG
* *
559472 TGCATGGATGCATTGCATGA
1 TGCATGGATGCACTGCAGGA
* *
559492 TGCATCGATGCATTAGTGCAGG-
1 TGCATGGATGC---ACTGCAGGA
559514 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
559535 TGCATGGATGCACTGCAGGGA
1 TGCATGGATGCACTGCA-GGA
559556 TGCATGGATGCACTGCAAGGA
1 TGCATGGATGCACTGC-AGGA
559577 TGCATGGATGCACT
1 TGCATGGATGCACT
559591 TTGACACCCT
Statistics
Matches: 88, Mismatches: 5, Indels: 11
0.85 0.05 0.11
Matches are distributed among these distances:
19 5 0.06
20 12 0.14
21 54 0.61
22 11 0.12
23 6 0.07
ACGTcount: A:0.24, C:0.18, G:0.34, T:0.24
Consensus pattern (20 bp):
TGCATGGATGCACTGCAGGA
Found at i:559572 original size:13 final size:13
Alignment explanation
Indices: 559514--559580 Score: 55
Period size: 13 Copynumber: 5.9 Consensus size: 13
559504 TTAGTGCAGG
559514 TGCATGGATGCAC
1 TGCATGGATGCAC
559527 TGCA-GG--G-A-
1 TGCATGGATGCAC
559535 TGCATGGATGCAC
1 TGCATGGATGCAC
559548 TGCA-GG--G-A-
1 TGCATGGATGCAC
559556 TGCATGGATGCAC
1 TGCATGGATGCAC
*
559569 TGCAAGGATGCA
1 TGCATGGATGCA
559581 TGGATGCACT
Statistics
Matches: 43, Mismatches: 1, Indels: 20
0.67 0.02 0.31
Matches are distributed among these distances:
8 8 0.19
9 6 0.14
10 2 0.05
11 2 0.05
12 6 0.14
13 19 0.44
ACGTcount: A:0.25, C:0.19, G:0.36, T:0.19
Consensus pattern (13 bp):
TGCATGGATGCAC
Found at i:560200 original size:29 final size:29
Alignment explanation
Indices: 560168--560230 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 29
560158 GAAACATTTT
560168 AAAACTTTGAATAAATTCAATT-AAGTCCAA
1 AAAACTTTG--TAAATTCAATTCAAGTCCAA
*
560198 AAATATTTTGTAAATTCAATTCAAGTCCAA
1 AAA-ACTTTGTAAATTCAATTCAAGTCCAA
560228 AAA
1 AAA
560231 CATTTTGCCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 11 0.37
30 14 0.47
31 5 0.17
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (29 bp):
AAAACTTTGTAAATTCAATTCAAGTCCAA
Found at i:560226 original size:30 final size:29
Alignment explanation
Indices: 560179--560237 Score: 100
Period size: 30 Copynumber: 2.0 Consensus size: 29
560169 AAACTTTGAA
*
560179 TAAATTCAATTAAGTCCAAAAATATTTTG
1 TAAATTCAATTAAGTCCAAAAACATTTTG
560208 TAAATTCAATTCAAGTCCAAAAACATTTTG
1 TAAATTCAATT-AAGTCCAAAAACATTTTG
560238 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.44, C:0.14, G:0.07, T:0.36
Consensus pattern (29 bp):
TAAATTCAATTAAGTCCAAAAACATTTTG
Found at i:560909 original size:3 final size:3
Alignment explanation
Indices: 560901--560968 Score: 70
Period size: 3 Copynumber: 23.0 Consensus size: 3
560891 CATTTTTCAT
560901 TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA TT- TTA TTA TTA TTAA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A
* * *
560946 TTA ATA -AA TTA TTA TTA CTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
560969 CAGACCTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
2 5 0.09
3 44 0.80
4 6 0.11
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:560927 original size:21 final size:20
Alignment explanation
Indices: 560901--560968 Score: 82
Period size: 21 Copynumber: 3.3 Consensus size: 20
560891 CATTTTTCAT
560901 TTATTATTATTTTATTTATTA
1 TTATTATTATTTTA-TTATTA
560922 TTATTATTATTTTATTATTA
1 TTATTATTATTTTATTATTA
* **
560942 TTAATTAATAAATTATTATTA
1 TT-ATTATTATTTTATTATTA
*
560963 CTATTA
1 TTATTA
560969 CAGACCTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
20 12 0.29
21 30 0.71
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (20 bp):
TTATTATTATTTTATTATTA
Found at i:566518 original size:15 final size:15
Alignment explanation
Indices: 566498--566529 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
566488 GATCAATACC
566498 TTTTGCATACATTCA
1 TTTTGCATACATTCA
*
566513 TTTTGCATATATTCA
1 TTTTGCATACATTCA
566528 TT
1 TT
566530 ATTCATTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.16, G:0.06, T:0.53
Consensus pattern (15 bp):
TTTTGCATACATTCA
Found at i:579400 original size:21 final size:21
Alignment explanation
Indices: 579376--579442 Score: 75
Period size: 21 Copynumber: 3.1 Consensus size: 21
579366 ATGCATCCCT
579376 TGAATGTGCATCGATACACTA
1 TGAATGTGCATCGATACACTA
*
579397 TGAA-GTTGCATCGATGCATGCCT-
1 TGAATG-TGCATCGATACA---CTA
579420 TGAATGTGCATCGATACACTA
1 TGAATGTGCATCGATACACTA
579441 TG
1 TG
579443 CAGTGTACCA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
20 3 0.08
21 17 0.45
23 15 0.39
24 3 0.08
ACGTcount: A:0.28, C:0.19, G:0.22, T:0.30
Consensus pattern (21 bp):
TGAATGTGCATCGATACACTA
Found at i:579412 original size:44 final size:44
Alignment explanation
Indices: 579337--579442 Score: 160
Period size: 44 Copynumber: 2.4 Consensus size: 44
579327 TTTATGCGCA
* *
579337 GTGCATTGATACACTATGATAGTGTACCGATGCATCCCTTGAAT
1 GTGCATCGATACACTATGATAGTGCACCGATGCATCCCTTGAAT
* *
579381 GTGCATCGATACACTATGA-AGTTGCATCGATGCATGCCTTGAAT
1 GTGCATCGATACACTATGATAG-TGCACCGATGCATCCCTTGAAT
579425 GTGCATCGATACACTATG
1 GTGCATCGATACACTATG
579443 CAGTGTACCA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
43 2 0.04
44 55 0.96
ACGTcount: A:0.27, C:0.21, G:0.22, T:0.30
Consensus pattern (44 bp):
GTGCATCGATACACTATGATAGTGCACCGATGCATCCCTTGAAT
Found at i:579429 original size:23 final size:22
Alignment explanation
Indices: 579364--579434 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
579354 GATAGTGTAC
579364 CGATGCATCCCTTGAATGTGCAT
1 CGATGCAT-CCTTGAATGTGCAT
*
579387 CGATACA--CTATGAA-GTTGCAT
1 CGATGCATCCT-TGAATG-TGCAT
579408 CGATGCATGCCTTGAATGTGCAT
1 CGATGCAT-CCTTGAATGTGCAT
579431 CGAT
1 CGAT
579435 ACACTATGCA
Statistics
Matches: 40, Mismatches: 2, Indels: 12
0.74 0.04 0.22
Matches are distributed among these distances:
20 3 0.08
21 15 0.38
23 19 0.47
24 3 0.08
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (22 bp):
CGATGCATCCTTGAATGTGCAT
Found at i:581392 original size:26 final size:26
Alignment explanation
Indices: 581341--581394 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
581331 TGTTTAAACA
* **
581341 TTTTGGATGTTTATGGATTATTATGT
1 TTTTGGATGTATATGGATTAGGATGT
581367 TTTTGGATG-ATATGGATGTAGGATGT
1 TTTTGGATGTATATGGAT-TAGGATGT
581393 TT
1 TT
581395 AAACTTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.20, C:0.00, G:0.28, T:0.52
Consensus pattern (26 bp):
TTTTGGATGTATATGGATTAGGATGT
Found at i:583410 original size:6 final size:6
Alignment explanation
Indices: 583401--583461 Score: 69
Period size: 6 Copynumber: 10.8 Consensus size: 6
583391 AGAAAAAATG
*
583401 AAAAGA AAAAG- GAAA-A AAAAGA AAAAGA AAAAGA AAAAG- -AAAG-
1 AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
583444 AAAAGA AAATAGA AAAAG
1 AAAAGA AAA-AGA AAAAG
583462 GGGGTCAAGA
Statistics
Matches: 48, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
4 4 0.08
5 10 0.21
6 28 0.58
7 6 0.12
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (6 bp):
AAAAGA
Found at i:583426 original size:22 final size:20
Alignment explanation
Indices: 583387--583460 Score: 94
Period size: 22 Copynumber: 3.4 Consensus size: 20
583377 ATTATGCTTG
583387 AAGAAGAAAAAATGAAAAGAAA
1 AAGAA-AAAAAA-GAAAAGAAA
583409 AAGGAAAAAAAAGAAAAAGAAA
1 AA-GAAAAAAAAG-AAAAGAAA
583431 AAGAAAAAGAAAGAAAAGAAA
1 AAGAAAAA-AAAGAAAAGAAA
583452 ATAGAAAAA
1 A-AGAAAAA
583461 GGGGGTCAAG
Statistics
Matches: 48, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
21 16 0.33
22 29 0.60
23 3 0.06
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.03
Consensus pattern (20 bp):
AAGAAAAAAAAGAAAAGAAA
Found at i:583457 original size:28 final size:28
Alignment explanation
Indices: 583401--583461 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
583391 AGAAAAAATG
583401 AAAAGAAAAAGGAAAAAAAAGAAAAAGA
1 AAAAGAAAAAGGAAAAAAAAGAAAAAGA
*
583429 AAAAGAAAAA-GAAAGAAAAGAAAATAGA
1 AAAAGAAAAAGGAAAAAAAAGAAAA-AGA
583457 AAAAG
1 AAAAG
583462 GGGGTCAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 13 0.42
28 18 0.58
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (28 bp):
AAAAGAAAAAGGAAAAAAAAGAAAAAGA
Found at i:584163 original size:17 final size:17
Alignment explanation
Indices: 584127--584160 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
584117 CCAAGTAAAG
*
584127 AGCAAAGATTAAATTCC
1 AGCAAAGATAAAATTCC
584144 AGCAAAGATAAAGATTC
1 AGCAAAGATAAA-ATTC
584161 AGCGAAGAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.50, C:0.15, G:0.15, T:0.21
Consensus pattern (17 bp):
AGCAAAGATAAAATTCC
Found at i:584553 original size:123 final size:123
Alignment explanation
Indices: 584331--585041 Score: 676
Period size: 123 Copynumber: 5.7 Consensus size: 123
584321 CACTCGATAG
* *
584331 ACCAACATTGCCAGATAGAGTTCATAACGAGAAGAACTTATCTG-AGAAGGAAGAAGAAGTTCAT
1 ACCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCAT
584395 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
* * *
584454 ACCAACATTGCCAAATAGAGTTCATAATGAGAATAACTCATCTG-AGAATGAAGAAGAAGTTCAT
1 ACCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAAGAAGAAGTTCAT
* * * * *
584518 AATGAGAAGAACTTGTTCAATCTTTTTCTCAACTCTATCACGGAAGGAGATAAATCAGC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
* * * **
584577 ACCAACATTTCCAGAGAGAATTCATAATGAGAAGAACTCATCTGAAGATAAAGAAGAAGTTCATA
1 ACCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
** * * *
584642 ATCTGAAGAACTTATTCAACCTTTTGCTCGACTCTATCACAGAAGAAGATAGATCAAC
66 ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
* * * *
584700 ATCAACATTTCCAGATAGAGTTTAAAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
1 ACCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
* *
584765 ATGAGAAGAACTTGTTCAA-C-TTTGC-CTTAAT-TAATCACATATGAAGTTGA-ATCAACGATA
66 ATGAGAAGAACTTGTTCAACCTTTTGCTC-GACTCT-ATCAC--A-GAAG--GAGAT--A-G--A
*
584825 CCTCTTTTGAGG
119 --TC-----AGC
* ** * *
584837 ATCAGTATTTCCAGA-AGGAGTTCATAATGAGAAGAACTCATCTGAAAAGGAAGAAGAAGTTCAT
1 ACCAACATTGCCAGATA-GAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCAT
* * * * ***
584901 AATGAGAAGAACTTGTTCAACATTTTGCTAGA-TTTCATCACAGAAGGAGATGGATTTTC
65 AATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCT-ATCACAGAAGGAGATAGATCAGC
* * * * * * **
584960 ATTC-ATAGTG---GA-AAAGTTCATAATGAGAAGAATTAATCCCAAAGAGGAAGAAGAAGTTCA
1 A-CCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCAT-CTGAAGAGGAAGAAGAAGTTCA
585020 TAATGAGAAGAACTTGTTCAAC
64 TAATGAGAAGAACTTGTTCAAC
585042 ATTTCCATCA
Statistics
Matches: 496, Mismatches: 64, Indels: 59
0.80 0.10 0.10
Matches are distributed among these distances:
119 21 0.04
120 46 0.09
121 12 0.02
122 1 0.00
123 296 0.60
124 8 0.02
125 2 0.00
126 1 0.00
127 1 0.00
128 2 0.00
130 2 0.00
132 3 0.01
134 2 0.00
135 2 0.00
136 5 0.01
137 79 0.16
138 1 0.00
139 12 0.02
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.26
Consensus pattern (123 bp):
ACCAACATTGCCAGATAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTTTGCTCGACTCTATCACAGAAGGAGATAGATCAGC
Found at i:585195 original size:14 final size:14
Alignment explanation
Indices: 585176--585216 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
585166 CATTTTTTCA
585176 TTTATTATTATTAT
1 TTTATTATTATTAT
*
585190 TTTATTAGTATTAT
1 TTTATTATTATTAT
585204 TATTA-TATTATTA
1 T-TTATTATTATTA
585217 ATAATAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
14 21 0.88
15 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTATTATTATTAT
Found at i:585201 original size:20 final size:20
Alignment explanation
Indices: 585178--585216 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
585168 TTTTTTCATT
*
585178 TATTATTATTATTTTATTAG
1 TATTATTATTATATTATTAG
585198 TATTATTATTATATTATTA
1 TATTATTATTATATTATTA
585217 ATAATAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (20 bp):
TATTATTATTATATTATTAG
Found at i:585203 original size:17 final size:17
Alignment explanation
Indices: 585181--585213 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
585171 TTTCATTTAT
*
585181 TATTATTATTTTATTAG
1 TATTATTATTATATTAG
585198 TATTATTATTATATTA
1 TATTATTATTATATTA
585214 TTAATAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (17 bp):
TATTATTATTATATTAG
Found at i:585236 original size:3 final size:3
Alignment explanation
Indices: 585177--585216 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
585167 ATTTTTTCAT
*
585177 TTA TTA TTA TTA TT- TTA TTA GTA TTA TTA TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
585217 ATAATAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 4 0.12
3 29 0.88
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:586906 original size:105 final size:105
Alignment explanation
Indices: 586791--587001 Score: 422
Period size: 105 Copynumber: 2.0 Consensus size: 105
586781 TATTTTTTTC
586791 TGATATTTTAAAATAAATAAATATCCTATTTATAAAAACCTAAAAAATATATATATTTACTTTAG
1 TGATATTTTAAAATAAATAAATATCCTATTTATAAAAACCTAAAAAATATATATATTTACTTTAG
586856 TTTTATAAAATTTATTTTAATATATATTTTCTTAGAATTA
66 TTTTATAAAATTTATTTTAATATATATTTTCTTAGAATTA
586896 TGATATTTTAAAATAAATAAATATCCTATTTATAAAAACCTAAAAAATATATATATTTACTTTAG
1 TGATATTTTAAAATAAATAAATATCCTATTTATAAAAACCTAAAAAATATATATATTTACTTTAG
586961 TTTTATAAAATTTATTTTAATATATATTTTCTTAGAATTA
66 TTTTATAAAATTTATTTTAATATATATTTTCTTAGAATTA
587001 T
1 T
587002 CCTAGTAAAT
Statistics
Matches: 106, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
105 106 1.00
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.47
Consensus pattern (105 bp):
TGATATTTTAAAATAAATAAATATCCTATTTATAAAAACCTAAAAAATATATATATTTACTTTAG
TTTTATAAAATTTATTTTAATATATATTTTCTTAGAATTA
Found at i:587397 original size:2 final size:2
Alignment explanation
Indices: 587390--587430 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
587380 AATTGAGTGT
*
587390 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
587431 TAAACCGTAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:591297 original size:14 final size:14
Alignment explanation
Indices: 591278--591304 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
591268 AAAATCCATT
591278 TTAAATTTATTATA
1 TTAAATTTATTATA
591292 TTAAATTTATTAT
1 TTAAATTTATTAT
591305 GATTTAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAATTTATTATA
Found at i:591669 original size:18 final size:19
Alignment explanation
Indices: 591646--591687 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
591636 ATCTCTTAAA
**
591646 ATTTTAAAATTAA-TATGT
1 ATTTTAAAAACAATTATGT
591664 ATTTTAAAAACAATTATGT
1 ATTTTAAAAACAATTATGT
591683 ATTTT
1 ATTTT
591688 TTTATTGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (19 bp):
ATTTTAAAAACAATTATGT
Found at i:595771 original size:22 final size:22
Alignment explanation
Indices: 595746--595787 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
595736 TATTTTACTA
595746 ATATTTCTAATAATATAATATT
1 ATATTTCTAATAATATAATATT
* *
595768 ATATTTTTAATATTATAATA
1 ATATTTCTAATAATATAATA
595788 AAATTATCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
ATATTTCTAATAATATAATATT
Found at i:595887 original size:18 final size:19
Alignment explanation
Indices: 595866--595911 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
595856 TATATAATAA
595866 ATTATTAATAAAATTT-AT
1 ATTATTAATAAAATTTCAT
* *
595884 ATTATTTAT-TAATTTCAT
1 ATTATTAATAAAATTTCAT
*
595902 ATAATTAATA
1 ATTATTAATA
595912 CTATTAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
17 5 0.23
18 17 0.77
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
ATTATTAATAAAATTTCAT
Found at i:596166 original size:89 final size:89
Alignment explanation
Indices: 595995--596166 Score: 190
Period size: 91 Copynumber: 1.9 Consensus size: 89
595985 TAATGATATT
* * * * * *
595995 TAAAATATACTAATTAATATTTTTAAAATATAATATAACACTATTACTTTAATAAATAATTAATA
1 TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
*
596060 TAATTTATAATATTTTTATTTCAA
66 TAATTTATAATAATTTTATTTCAA
* *
596084 TAAAATATACCAATATTAATATTTTTATTAATAAAATTATAAAAATAATATTTTAAT-AATAAAT
1 TAAAATATA-CAA-ATTAATATTTTTA-AAATAAAA-TATAAAAATAATACTTTAATAAATAAAT
*
596148 AA-ATTATTT-TAA-AATTTTA
62 AATATAATTTATAATAATTTTA
596167 AAATTAATAA
Statistics
Matches: 69, Mismatches: 10, Indels: 8
0.79 0.11 0.09
Matches are distributed among these distances:
89 15 0.22
90 5 0.07
91 19 0.28
92 14 0.20
93 16 0.23
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (89 bp):
TAAAATATACAAATTAATATTTTTAAAATAAAATATAAAAATAATACTTTAATAAATAAATAATA
TAATTTATAATAATTTTATTTCAA
Found at i:596187 original size:22 final size:22
Alignment explanation
Indices: 596144--596203 Score: 57
Period size: 22 Copynumber: 2.7 Consensus size: 22
596134 TTTTAATAAT
* * *
596144 AAATAAATTATTTTAAAATTTTA
1 AAATAAATAATATT-AAGTTTTA
*
596167 AAATTAATAATATTAAGTTTTA
1 AAATAAATAATATTAAGTTTTA
**
596189 TGATAAATAATATTA
1 AAATAAATAATATTA
596204 TTTATTGTAT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 19 0.63
23 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (22 bp):
AAATAAATAATATTAAGTTTTA
Found at i:596499 original size:18 final size:18
Alignment explanation
Indices: 596473--596517 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
596463 TCACGAAATG
*
596473 TAAGATTACCGGTGGTAA
1 TAAGATTACCGGTGGGAA
*
596491 TAGGATTACCGGTGGGAA
1 TAAGATTACCGGTGGGAA
596509 TAAGATTAC
1 TAAGATTAC
596518 TGGGAATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.33, C:0.11, G:0.29, T:0.27
Consensus pattern (18 bp):
TAAGATTACCGGTGGGAA
Found at i:601428 original size:46 final size:46
Alignment explanation
Indices: 601362--601449 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
601352 CGTGTTTTGA
* *
601362 TGATGATGTTTAAGTAGCTGAAGCCGAATGAGAATTGGAGAAATGT
1 TGATGATGTTCAAGAAGCTGAAGCCGAATGAGAATTGGAGAAATGT
*
601408 TGATGATGTTCAGGAAGCTGAAGCCGAATGAGAATTGGAGAA
1 TGATGATGTTCAAGAAGCTGAAGCCGAATGAGAATTGGAGAA
601450 CTATTGAAGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.35, C:0.08, G:0.32, T:0.25
Consensus pattern (46 bp):
TGATGATGTTCAAGAAGCTGAAGCCGAATGAGAATTGGAGAAATGT
Found at i:601514 original size:4 final size:4
Alignment explanation
Indices: 601505--601999 Score: 120
Period size: 4 Copynumber: 122.2 Consensus size: 4
601495 TGAATCCTCA
601505 GAGG GAGG GAGG GAGG GAGG GAGG G-GG AGAGG GAGG GAGG GAGG GAGG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG -GAGG GAGG GAGG GAGG GAGG
* * *
601553 GAGG GAAGG G-GA GAGG GA-- GAGG GAGG GA-G AAGG AGAGTG AGAGA
1 GAGG G-AGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG -GAG-G -GAGG
* * * * *
601597 GAGG GAGAG AAAG G-GG GAGA GAGG G-GG AGAGA GAGA GAGCG GA-- GAGG
1 GAGG GAG-G GAGG GAGG GAGG GAGG GAGG -GAGG GAGG GAG-G GAGG GAGG
* * * * * * * *
601644 GAGAG AGATG G-GG GAGA GAGA GA-G AAGG G-GA GAGA GAGT GTGG GAGTG
1 GAG-G -GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG-G
* * * * * *
601692 AGAGA GAGG GAGAG AGAGG G-GG G-GG GAGA GAGA GAGG TG-GA AAGA
1 -GAGG GAGG GAG-G -GAGG GAGG GAGG GAGG GAGG GAGG -GAGG GAGG
* * * * *
601737 GAGA GAGG GAGA GAGTG AGAGA AAGG GA-- GAGG GAGG GAGG GAAGG AGAGA
1 GAGG GAGG GAGG GAG-G -GAGG GAGG GAGG GAGG GAGG GAGG G-AGG -GAGG
* * * * *
601787 GAGA GAGG GAGG GAGAG GGGG AGAGG GAGG GAGA GAGA GATAG G-GG GAGG
1 GAGG GAGG GAGG GAG-G GAGG -GAGG GAGG GAGG GAGG GA-GG GAGG GAGG
* * * * *
601837 GAGG GAGG GAGG GAGA GAGA GAGG GAGG GAGG GAGG GAGAAA GAGA GAGA
1 GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAGG GAG--G GAGG GAGG
* * * ** * *
601887 GATG GAGG GAGA GATGG G-GA GAAA GAGA GAGG GA-- GAGG GAGAG AGAGA
1 GAGG GAGG GAGG GA-GG GAGG GAGG GAGG GAGG GAGG GAGG GAG-G -GAGG
* * *
601935 GAGG GAGA GAGG GGGG GAGG GAGG GAGAG AGAGG GA-G G-GG GAGG GTGG
1 GAGG GAGG GAGG GAGG GAGG GAGG GAG-G -GAGG GAGG GAGG GAGG GAGG
*
601983 GAGAG G-GA GAGG GAGG G
1 GAG-G GAGG GAGG GAGG G
602000 GGAGAGTTAC
Statistics
Matches: 370, Mismatches: 69, Indels: 104
0.68 0.13 0.19
Matches are distributed among these distances:
2 8 0.02
3 30 0.08
4 268 0.72
5 38 0.10
6 26 0.07
ACGTcount: A:0.34, C:0.00, G:0.63, T:0.02
Consensus pattern (4 bp):
GAGG
Found at i:601544 original size:28 final size:28
Alignment explanation
Indices: 601504--601999 Score: 200
Period size: 28 Copynumber: 17.4 Consensus size: 28
601494 CTGAATCCTC
601504 AGAGGGAGGGAGGGAGGGAGGGAGGGGG
1 AGAGGGAGGGAGGGAGGGAGGGAGGGGG
*
601532 AGAGGGAGGGAGGGAGGGAGGGA-GGGA
1 AGAGGGAGGGAGGGAGGGAGGGAGGGGG
* **
601559 AG-GGGAGAGG-GAGAGGGAGGGAGAAGG
1 AGAGGGAG-GGAGGGAGGGAGGGAGGGGG
* **
601586 AGAGTGAGAGAGAGGGA--GAGAAAGGGGG
1 AGAG-G-GAGGGAGGGAGGGAGGGAGGGGG
* *
601614 AGAGAGG-GGGAGAGAGAGAGAGCGGAGAGGG
1 AGAG-GGAGGGAG-G-GAGGGAG-GGAGGGGG
* * * *
601645 AGAGAGATGGG-GGAGAGAGAGAGAAGGGG
1 AGAGGGA-GGGAGG-GAGGGAGGGAGGGGG
* * * *
601674 AGAGAGAGTGTGGGAGTGAGAGAGAGGGAGAG
1 AGAGGGAGGGAGGGAG-G-GAGGGAGGG-G-G
* *
601706 AGAGGG-GGG-GGGAGAGAGAGAGGTGGAAAG
1 AGAGGGAGGGAGGGAGGGAGGGAGG-GG---G
* * * * **
601736 AGAGAGAGGGAGAGAGTGAGAGAAAGGG
1 AGAGGGAGGGAGGGAGGGAGGGAGGGGG
*
601764 AGAGGGAGGGAGGGAAGGAGAGAGAGAGAGGG
1 AGAGGGAGGGAGGG-AGG-GAG-G-GAGGGGG
* *
601796 AG-GGAGAGGG-GGAGAGGGAGGGAGAGAG
1 AGAGG-GAGGGAGG-GAGGGAGGGAGGGGG
* *
601824 AGATAGG-GGGAGGGAGGGAGGGAGGGAG
1 AGA-GGGAGGGAGGGAGGGAGGGAGGGGG
* **
601852 AGAGAGAGGGAGGGAGGGAGGGA--GAA
1 AGAGGGAGGGAGGGAGGGAGGGAGGGGG
* * * * *
601878 AGAGAGAGAGATGGAGGGAGAGATGGGG
1 AGAGGGAGGGAGGGAGGGAGGGAGGGGG
** * *
601906 AGAAAGAGAGAGGGA--GAGGGAGAGAGAG
1 AGAGGGAGGGAGGGAGGGAGGGAG-G-GGG
* *
601934 AGAGGGAGAGAGGGGGGGAGGGAGGGAGAG
1 AGAGGGAGGGAGGGAGGGAGGGAGGG-G-G
* *
601964 AGAGGGA-GG-GGGAGGGTGGGAGAGGG
1 AGAGGGAGGGAGGGAGGGAGGGAGGGGG
601990 AGAGGGAGGG
1 AGAGGGAGGG
602000 GGAGAGTTAC
Statistics
Matches: 366, Mismatches: 60, Indels: 85
0.72 0.12 0.17
Matches are distributed among these distances:
26 55 0.15
27 17 0.05
28 150 0.41
29 25 0.07
30 61 0.17
31 25 0.07
32 33 0.09
ACGTcount: A:0.34, C:0.00, G:0.63, T:0.02
Consensus pattern (28 bp):
AGAGGGAGGGAGGGAGGGAGGGAGGGGG
Found at i:601546 original size:32 final size:32
Alignment explanation
Indices: 601505--601999 Score: 196
Period size: 32 Copynumber: 15.2 Consensus size: 32
601495 TGAATCCTCA
601505 GAGGGAGGGAGGGAGGGAGGGAGGGGGAGAGG
1 GAGGGAGGGAGGGAGGGAGGGAGGGGGAGAGG
*
601537 GAGGGAGGGAGGGAGGGAGGGAAGGGGAGAGG
1 GAGGGAGGGAGGGAGGGAGGGAGGGGGAGAGG
* * * *
601569 GA--GAGGGAGGGA--GAAGGAGAGTGAGAGA
1 GAGGGAGGGAGGGAGGGAGGGAGGGGGAGAGG
* * * *
601597 GAGGGAGAGAAAGG-GGGAGAGAGGGGGAGAGA
1 GAGGGAG-GGAGGGAGGGAGGGAGGGGGAGAGG
* *
601629 GAGAGAGCGGA--GAGGGAGAGAGATGGGGGAGAGA
1 GAGGGAG-GGAGGGAGGGAG-G-GA-GGGGGAGAGG
* * * *
601663 GAGAGAAGGGGAGAGAGAGTGTGGGAGTGAGAGAGAGG
1 GAG-GGA-GGGAG-G-GAGGGAGGGAG-G-GGGAGAGG
* *
601701 GAGAGAGAGGG-GGG-GGGAGAGAGAGAGGTGGAAAGA
1 GAG-G-GAGGGAGGGAGGGAG-G-GAG-GG-GGAGAGG
* * * * **
601737 GAGAGAGGGAGAGAGTGAGAGAAAGGGAGAGG
1 GAGGGAGGGAGGGAGGGAGGGAGGGGGAGAGG
* * * *
601769 GAGGGAGGGAAGGAGAGAGAGA-GAGG-GAGG
1 GAGGGAGGGAGGGAGGGAGGGAGGGGGAGAGG
* * *
601799 GA--GAGGG-GGAGAGGGAGGGAGAGAGAGATAG
1 GAGGGAGGGAGG-GAGGGAGGGAGGGGGAGA-GG
* *
601830 G-GGGAGGGAGGGAGGGAGGGAGAGAGAGAGG
1 GAGGGAGGGAGGGAGGGAGGGAGGGGGAGAGG
** * * *
601861 GAGGGAGGGAGGGAGAAAGAGAGAGAGATGGAGG
1 GAGGGAGGGAGGGAGGGAGGGAGGGGGA--GAGG
* * * * *
601895 GAGAGATGGGGAGAAAGAGAGAGGGAGAGGGAGAGA
1 GAGGGA--GGGAG--GGAGGGAGGGAGGGGGAGAGG
* * * *
601931 GAGAGAGGGAGAGAGGGGGGGAGGGAGGGAGAGA
1 GAGGGAGGGAGGGAGGGAGGGA-GG-GGGAGAGG
* *
601965 GAGGGA-GG-GGGAGGGTGGGAGAGGGAGAGG
1 GAGGGAGGGAGGGAGGGAGGGAGGGGGAGAGG
601995 GAGGG
1 GAGGG
602000 GGAGAGTTAC
Statistics
Matches: 356, Mismatches: 68, Indels: 80
0.71 0.13 0.16
Matches are distributed among these distances:
27 1 0.00
28 26 0.07
29 1 0.00
30 34 0.10
31 16 0.04
32 141 0.40
33 8 0.02
34 50 0.14
35 9 0.03
36 32 0.09
37 4 0.01
38 28 0.08
39 6 0.02
ACGTcount: A:0.34, C:0.00, G:0.63, T:0.02
Consensus pattern (32 bp):
GAGGGAGGGAGGGAGGGAGGGAGGGGGAGAGG
Found at i:604186 original size:29 final size:29
Alignment explanation
Indices: 604117--604272 Score: 209
Period size: 29 Copynumber: 5.6 Consensus size: 29
604107 GTTGCCATGG
*
604117 CCGGCGACATGGTAGGTCACCATGGAGT-
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
*
604145 -C-TCGACATGGTAGGTCGCCATGGAGTC
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
604172 CCGGCGACATGGTAGGTCG-C---GAGTC
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
*
604197 CGGCGACGACATGGTAGGTCGCCATGGAGTC
1 C--CGGCGACATGGTAGGTCGCCATGGAGTC
604228 CCGGCGACATGGTAGGTCGCCATGGAGTC
1 CCGGCGACATGGTAGGTCGCCATGGAGTC
*
604257 CCAGCGACATGGTAGG
1 CCGGCGACATGGTAGG
604273 GGAGATTCCT
Statistics
Matches: 113, Mismatches: 6, Indels: 17
0.83 0.04 0.12
Matches are distributed among these distances:
25 6 0.05
26 23 0.20
27 18 0.16
28 3 0.03
29 57 0.50
31 6 0.05
ACGTcount: A:0.19, C:0.26, G:0.37, T:0.17
Consensus pattern (29 bp):
CCGGCGACATGGTAGGTCGCCATGGAGTC
Found at i:604783 original size:21 final size:21
Alignment explanation
Indices: 604758--604801 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
604748 AATCTAGTTA
604758 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
604779 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
604800 AT
1 AT
604802 ATATTATATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:605220 original size:14 final size:14
Alignment explanation
Indices: 605201--605227 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
605191 AGTAATTTAT
605201 TATTTTTTGTTGTC
1 TATTTTTTGTTGTC
605215 TATTTTTTGTTGT
1 TATTTTTTGTTGT
605228 TGTGTATGTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.04, G:0.15, T:0.74
Consensus pattern (14 bp):
TATTTTTTGTTGTC
Found at i:605227 original size:17 final size:17
Alignment explanation
Indices: 605198--605230 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
605188 GTGAGTAATT
605198 TATTATTTTTTGTTGTC
1 TATTATTTTTTGTTGTC
605215 TATT-TTTTGTTGTTGT
1 TATTATTTT-TTGTTGT
605231 GTATGTGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.03, G:0.15, T:0.73
Consensus pattern (17 bp):
TATTATTTTTTGTTGTC
Found at i:608584 original size:60 final size:60
Alignment explanation
Indices: 608508--609245 Score: 947
Period size: 60 Copynumber: 12.7 Consensus size: 60
608498 GTATTTATAA
*
608508 GATTTAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
608568 GATTTAGTAATAATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
608628 GA-TTAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * *
608687 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGA-TT--TG-----ATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATAGTAAT
*
608736 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
608796 GATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* *
608856 GAATTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
608916 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * * *
608976 GA-TTAGTAAT-AAT-GAAATTAT--TATTAATTTTTAATGA-TT--TG-----ATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATT-ATTATTAAT-ATTTAATGATTTGATAGTAAT
* * *
609025 GATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
*
609085 GATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * *
609145 GATTTAGTAATGACTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAAT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
* * * *
609205 GATTTAGTAATGATTTGATAGTAATG-ATTTATTATAAATAT
1 GATTTAGTAATGATTAG-TAATAATGAAATTATTATTAATAT
609246 GTCGAATTTG
Statistics
Matches: 595, Mismatches: 52, Indels: 62
0.84 0.07 0.09
Matches are distributed among these distances:
49 20 0.03
50 15 0.03
51 4 0.01
52 13 0.02
53 19 0.03
54 10 0.02
55 10 0.02
56 19 0.03
57 13 0.02
58 4 0.01
59 71 0.12
60 391 0.66
61 6 0.01
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (60 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATAGTAAT
Found at i:608724 original size:35 final size:34
Alignment explanation
Indices: 608683--608965 Score: 107
Period size: 35 Copynumber: 9.2 Consensus size: 34
608673 GATTTGATAG
608683 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAA-TTT
* * * *
608718 TAATGATT--TGAT-A-GTAATGA-T-TT-A--G
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
608743 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAA-TTT
* * *
608778 TAATGATT--TGAT-A-GTAATGA-T-TTAA---
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
608803 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
* * * *
608838 TAATGATT--TGAT-A-GTAATGA--ATT-A--G
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
608863 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
* * * *
608898 TAATGATT--TGAT-A-GTAATGA-T-TT-A--G
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
608923 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
608958 TAATGATT
1 TAATGATT
608966 TGATAGTAAT
Statistics
Matches: 173, Mismatches: 35, Indels: 80
0.60 0.12 0.28
Matches are distributed among these distances:
25 32 0.18
27 12 0.07
28 7 0.04
29 28 0.16
30 6 0.03
31 29 0.17
32 7 0.04
33 12 0.07
35 40 0.23
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (34 bp):
TAATGATTAGTAATAATGAAATTATTATTAATTT
Found at i:608999 original size:229 final size:229
Alignment explanation
Indices: 608512--609215 Score: 1089
Period size: 229 Copynumber: 3.1 Consensus size: 229
608502 TTATAAGATT
* * *
608512 TAGTAATGATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATAGTAATGATTTAGTA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAATA
* * * *
608577 ATAATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATG-ATTAGTAATGAT
66 ATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGTAATGAATTAGTAATGAT
* * * * *
608641 TAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TTAGTAAT-AAT-GAA
131 TAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTA
* * * * *
608703 ATTATTATTAATTTTTAATGATTTGATAGTAATGA-TT--
196 ATAATGA--AATTATTATTAATTT--T--TAATGATTTGA
608740 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAATA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAATA
*
608805 ATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGAATTAGTAATGAT
66 ATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGTAATGAATTAGTAATGAT
608870 TAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTA
131 TAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTA
* *
608935 ATAATGAAATTGTTATTAATATTTAATGATTTGA
196 ATAATGAAATTATTATTAATTTTTAATGATTTGA
608969 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAATA
1 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAATA
*
609034 ATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGTAATGATTTAGTAATGAT
66 ATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGTAATGAATTAGTAATGAT
*
609099 TAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGACTAGTA
131 TAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTA
*
609164 ATAATTAAATTATTATTAATTTTTAATGATTTGA
196 ATAATGAAATTATTATTAATTTTTAATGATTTGA
609198 TAGTAATGATTTAGTAAT
1 TAGTAATGA-TTAGTAAT
609216 GATTTGATAG
Statistics
Matches: 445, Mismatches: 23, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
226 6 0.01
227 2 0.00
228 112 0.25
229 289 0.65
230 27 0.06
231 2 0.00
232 7 0.02
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.45
Consensus pattern (229 bp):
TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAATA
ATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGTAATGAATTAGTAATGAT
TAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAGTAATGATTAGTA
ATAATGAAATTATTATTAATTTTTAATGATTTGA
Found at i:609013 original size:35 final size:34
Alignment explanation
Indices: 608972--609134 Score: 92
Period size: 35 Copynumber: 5.2 Consensus size: 34
608962 GATTTGATAG
608972 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAA-TTT
* * *
609007 TAATGATT--TGAT-A-GTAATGA-T-TTAA---
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
609032 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
* * * *
609067 TAATGATT--TGA-AA-GTAATGA-T-TT-A--G
1 TAATGATTAGTAATAATGAAATTATTATTAATTT
*
609092 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAAT-TT
609127 TAATGATT
1 TAATGATT
609135 TGATAGTAAT
Statistics
Matches: 91, Mismatches: 17, Indels: 40
0.61 0.11 0.27
Matches are distributed among these distances:
25 16 0.18
27 5 0.05
28 4 0.04
29 14 0.15
30 4 0.04
31 15 0.16
32 4 0.04
33 5 0.05
35 24 0.26
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (34 bp):
TAATGATTAGTAATAATGAAATTATTATTAATTT
Found at i:609206 original size:14 final size:14
Alignment explanation
Indices: 609187--609234 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
609177 TATTAATTTT
609187 TAATGATTTGATAG
1 TAATGATTTGATAG
609201 TAATGA-TT--TAG
1 TAATGATTTGATAG
609212 TAATGATTTGATAG
1 TAATGATTTGATAG
609226 TAATGATTT
1 TAATGATTT
609235 ATTATAAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 2 0.06
14 18 0.58
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:609215 original size:25 final size:25
Alignment explanation
Indices: 609187--609235 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
609177 TATTAATTTT
609187 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
609212 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
609236 TTATAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:609981 original size:35 final size:35
Alignment explanation
Indices: 609940--610042 Score: 109
Period size: 35 Copynumber: 3.2 Consensus size: 35
609930 AATGATTTAA
609940 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTGTTATTAATATT
* * *
609975 TAATGATT--TGA-AA-GTAA-TG--ATT--TA-G
1 TAATGATTAGTAATAATGAAATTGTTATTAATATT
610000 TAATGATTAGTAATAATGAAATTGTTATTAATATT
1 TAATGATTAGTAATAATGAAATTGTTATTAATATT
610035 TAATGATT
1 TAATGATT
610043 TGATAGTAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 20
0.67 0.08 0.26
Matches are distributed among these distances:
25 8 0.15
26 2 0.04
27 2 0.04
28 5 0.10
29 3 0.06
30 4 0.08
31 3 0.06
32 5 0.10
33 2 0.04
34 2 0.04
35 16 0.31
ACGTcount: A:0.42, C:0.00, G:0.14, T:0.45
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTGTTATTAATATT
Found at i:610023 original size:60 final size:60
Alignment explanation
Indices: 609930--610127 Score: 351
Period size: 60 Copynumber: 3.3 Consensus size: 60
609920 CATATACAAA
* *
609930 AATGATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGT
1 AATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGT
609990 AATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGT
1 AATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGT
* * *
610050 AATGATTTAGTAATGATTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGT
1 AATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGT
610110 AATGATTTAGTAATGATT
1 AATGATTTAGTAATGATT
610128 TGATAGTAAT
Statistics
Matches: 133, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 133 1.00
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (60 bp):
AATGATTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGT
Found at i:610062 original size:11 final size:11
Alignment explanation
Indices: 610046--610143 Score: 52
Period size: 11 Copynumber: 9.2 Consensus size: 11
610036 AATGATTTGA
610046 TAGTAATGATT
1 TAGTAATGATT
610057 TAGTAATGA-T
1 TAGTAATGATT
*
610067 TAGTAAT-AAT
1 TAGTAATGATT
*
610077 TA--AATTA-T
1 TAGTAATGATT
*
610085 TATTAAT--TT
1 TAGTAATGATT
610094 T--TAATGATTT
1 TAGTAATGA-TT
610104 GATAGTAATGATT
1 --TAGTAATGATT
610117 TAGTAATGATTT
1 TAGTAATGA-TT
610129 GATAGTAATGATT
1 --TAGTAATGATT
610142 TA
1 TA
610144 TTATAATTAT
Statistics
Matches: 72, Mismatches: 0, Indels: 30
0.71 0.00 0.29
Matches are distributed among these distances:
7 4 0.06
8 6 0.08
9 4 0.06
10 16 0.22
11 20 0.28
12 3 0.04
13 4 0.06
14 15 0.21
ACGTcount: A:0.39, C:0.00, G:0.14, T:0.47
Consensus pattern (11 bp):
TAGTAATGATT
Found at i:610114 original size:14 final size:14
Alignment explanation
Indices: 610095--610142 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
610085 TATTAATTTT
610095 TAATGATTTGATAG
1 TAATGATTTGATAG
610109 TAATGA-TT--TAG
1 TAATGATTTGATAG
610120 TAATGATTTGATAG
1 TAATGATTTGATAG
610134 TAATGATTT
1 TAATGATTT
610143 ATTATAATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 2 0.06
14 18 0.58
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (14 bp):
TAATGATTTGATAG
Found at i:610123 original size:25 final size:25
Alignment explanation
Indices: 610095--610143 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
610085 TATTAATTTT
610095 TAATGATTTGATAGTAATGATTTAG
1 TAATGATTTGATAGTAATGATTTAG
610120 TAATGATTTGATAGTAATGATTTA
1 TAATGATTTGATAGTAATGATTTA
610144 TTATAATTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.18, T:0.45
Consensus pattern (25 bp):
TAATGATTTGATAGTAATGATTTAG
Found at i:610776 original size:908 final size:908
Alignment explanation
Indices: 609022--610818 Score: 3495
Period size: 908 Copynumber: 2.0 Consensus size: 908
609012 ATTTGATAGT
609022 AATGATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGTAATGA
1 AATGATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGTAATGA
609087 TTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAG
66 TTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAG
609152 TAATGACTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATG
131 TAATGACTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATG
609217 ATTTGATAGTAATGATTTATTATAAATATGTCGAATTTGTTAAGGTTTGAAAAAACTAGTCTAAT
196 ATTTGATAGTAATGATTTATTATAAATATGTCGAATTTGTTAAGGTTTGAAAAAACTAGTCTAAT
609282 TTCAATATTAAATTTGTAACAAATAACAAACTAGTTTACAATTGTTGCCGATGTCGGGGTGTTGT
261 TTCAATATTAAATTTGTAACAAATAACAAACTAGTTTACAATTGTTGCCGATGTCGGGGTGTTGT
*
609347 TGAATGATAATGTTGGGGCAGACGTCTGATGCGTTGTGGCCATTGCGGTTGCTTAGGAGTATAGT
326 TGAATGATAATGTTGGGGCAGACGTCTGATGCGTTGTGGCCATTGCGGTTGCTCAGGAGTATAGT
609412 ACCCATCCTCCTCATTCGTTGGGGGCATTTGAACTGACATGTGTTCAAAGTCATACGTCGACGAA
391 ACCCATCCTCCTCATTCGTTGGGGGCATTTGAACTGACATGTGTTCAAAGTCATACGTCGACGAA
609477 AACATGGGAGAGTAGATGGATGCATCAGGCTGCACAAACTCTGGTATGTATGCATCGCCGAACGG
456 AACATGGGAGAGTAGATGGATGCATCAGGCTGCACAAACTCTGGTATGTATGCATCGCCGAACGG
609542 TTGTGGTGCGCTATTATCCACATCGGTCATTTCCGCTTCAGGTTGTTGAGATGAACTCCCACTCC
521 TTGTGGTGCGCTATTATCCACATCGGTCATTTCCGCTTCAGGTTGTTGAGATGAACTCCCACTCC
* *
609607 CACTTGGTAGAGAGTATTCAGCTTTACCAAATCTTTTCTTAAACCTCAAAAATTGTCGTCTCTCT
586 CACTTGGTAAAGAGTATTCAGCTTTACCAAATCTTTTCTTAAACCTCAAAAATTGTCGCCTCTCT
609672 ACAATTGTTGTCAAGAATGGCTTTCCATTATCCAAAAAATAAGCAAGGTAAGCCGAAGTCTCAAA
651 ACAATTGTTGTCAAGAATGGCTTTCCATTATCCAAAAAATAAGCAAGGTAAGCCGAAGTCTCAAA
*
609737 ATTAAAGTCGTCGTCTTGAATGTCGTCAAGAGTTGGCATGAATGATGCCCTATTGTTCCAAGCAT
716 ATTAAAGTCGTCGTCTTGAATGTCGTCAAGAGTTGGCATGAATGAAGCCCTATTGTTCCAAGCAT
609802 TAATGTAGGTTGCATGCTTCTCAACCCAATTAACATTTTCTTTACGACGACCATCAAATCTGTGC
781 TAATGTAGGTTGCATGCTTCTCAACCCAATTAACATTTTCTTTACGACGACCATCAAATCTGTGC
609867 AGCTGGTCATGCGTCTCAACCCAATTCACCTGACGACGACCATCAAATCAGTACATATACAAA
846 AGCTGGTCATGCGTCTCAACCCAATTCACCTGACGACGACCATCAAATCAGTACATATACAAA
609930 AATGATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGTAATGA
1 AATGATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGTAATGA
609995 TTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAG
66 TTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAG
*
610060 TAATGATTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATG
131 TAATGACTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATG
*
610125 ATTTGATAGTAATGATTTATTATAATTATGTCGAATTTGTTAAGGTTTGAAAAAACTAGTCTAAT
196 ATTTGATAGTAATGATTTATTATAAATATGTCGAATTTGTTAAGGTTTGAAAAAACTAGTCTAAT
* *
610190 TTCAATATTAAATTTGTAACAACTAATAAACTAGTTTACAATTGTTGCCGATGTCGGGGTGTTGT
261 TTCAATATTAAATTTGTAACAAATAACAAACTAGTTTACAATTGTTGCCGATGTCGGGGTGTTGT
* *
610255 TGAATGATAATGTTGGGGCGGACGTCTGATGCGTTGTGGCCGTTGCGGTTGCTCAGGAGTATAGT
326 TGAATGATAATGTTGGGGCAGACGTCTGATGCGTTGTGGCCATTGCGGTTGCTCAGGAGTATAGT
610320 ACCCATCCTCCTCATTCGTTGGGGGCATTTGAACTGACATGTGTTCAAAGTCATACGTCGACGAA
391 ACCCATCCTCCTCATTCGTTGGGGGCATTTGAACTGACATGTGTTCAAAGTCATACGTCGACGAA
610385 AACATGGGAGAGTAGATGGATGCATCAGGCTGCACAAACTCTGGTATGTATGCATCGCCGAACGG
456 AACATGGGAGAGTAGATGGATGCATCAGGCTGCACAAACTCTGGTATGTATGCATCGCCGAACGG
610450 TTGTGGTGCGCTATTATCCACATCGGTCATTTCCGCTTCAGGTTGTTGAGATGAACTCCCACTCC
521 TTGTGGTGCGCTATTATCCACATCGGTCATTTCCGCTTCAGGTTGTTGAGATGAACTCCCACTCC
610515 CACTTGGTAAAGAGTATTCAGCTTTACCAAATCTTTTCTTAAACCTCAAAAATTGTCGCCTCTCT
586 CACTTGGTAAAGAGTATTCAGCTTTACCAAATCTTTTCTTAAACCTCAAAAATTGTCGCCTCTCT
610580 ACAATTGTTGTCAAGAATGGCTTTCCATTATCCAAAAAATAAGCAAGGTAAGCCGAAGTCTCAAA
651 ACAATTGTTGTCAAGAATGGCTTTCCATTATCCAAAAAATAAGCAAGGTAAGCCGAAGTCTCAAA
610645 ATTAAAGTCGTCGTCTTGAATGTCGTCAAGAGTTGGCATGAATGAAGCCCTATTGTTCCAAGCAT
716 ATTAAAGTCGTCGTCTTGAATGTCGTCAAGAGTTGGCATGAATGAAGCCCTATTGTTCCAAGCAT
610710 TAATGTAGGTTGCATGCTTCTCAACCCAATTAACATTTTCTTTACGACGACCATCAAATCTGTGC
781 TAATGTAGGTTGCATGCTTCTCAACCCAATTAACATTTTCTTTACGACGACCATCAAATCTGTGC
*
610775 AGTTGGTCATGCGTCTCAACCCAATTCACCTGACGACGACCATC
846 AGCTGGTCATGCGTCTCAACCCAATTCACCTGACGACGACCATC
610819 TAAGATTTGG
Statistics
Matches: 878, Mismatches: 11, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
908 878 1.00
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Consensus pattern (908 bp):
AATGATTTAATAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGAAAGTAATGA
TTTAGTAATGATTAGTAATAATGAAATTGTTATTAATATTTAATGATTTGATAGTAATGATTTAG
TAATGACTAGTAATAATTAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTTAGTAATG
ATTTGATAGTAATGATTTATTATAAATATGTCGAATTTGTTAAGGTTTGAAAAAACTAGTCTAAT
TTCAATATTAAATTTGTAACAAATAACAAACTAGTTTACAATTGTTGCCGATGTCGGGGTGTTGT
TGAATGATAATGTTGGGGCAGACGTCTGATGCGTTGTGGCCATTGCGGTTGCTCAGGAGTATAGT
ACCCATCCTCCTCATTCGTTGGGGGCATTTGAACTGACATGTGTTCAAAGTCATACGTCGACGAA
AACATGGGAGAGTAGATGGATGCATCAGGCTGCACAAACTCTGGTATGTATGCATCGCCGAACGG
TTGTGGTGCGCTATTATCCACATCGGTCATTTCCGCTTCAGGTTGTTGAGATGAACTCCCACTCC
CACTTGGTAAAGAGTATTCAGCTTTACCAAATCTTTTCTTAAACCTCAAAAATTGTCGCCTCTCT
ACAATTGTTGTCAAGAATGGCTTTCCATTATCCAAAAAATAAGCAAGGTAAGCCGAAGTCTCAAA
ATTAAAGTCGTCGTCTTGAATGTCGTCAAGAGTTGGCATGAATGAAGCCCTATTGTTCCAAGCAT
TAATGTAGGTTGCATGCTTCTCAACCCAATTAACATTTTCTTTACGACGACCATCAAATCTGTGC
AGCTGGTCATGCGTCTCAACCCAATTCACCTGACGACGACCATCAAATCAGTACATATACAAA
Found at i:612311 original size:16 final size:16
Alignment explanation
Indices: 612281--612325 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
612271 CAAAAAAATT
612281 TAATATAAT-AACTTA
1 TAATATAATAAACTTA
612296 TAATATAATAAACTTA
1 TAATATAATAAACTTA
612312 TAA-AGTAATAAACT
1 TAATA-TAATAAACT
612326 AAACTTTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 10 0.36
16 18 0.64
ACGTcount: A:0.56, C:0.07, G:0.02, T:0.36
Consensus pattern (16 bp):
TAATATAATAAACTTA
Found at i:612401 original size:30 final size:30
Alignment explanation
Indices: 612367--612472 Score: 142
Period size: 30 Copynumber: 3.5 Consensus size: 30
612357 TTTCTTTAAA
612367 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
612397 CAACTAATAAACTATTCTTTAATATAACTT
1 CAACTAATAAACTATTCTTTAATATAACTT
* * *
612427 AAACTAATAAAATATTTTTTAATTATAA-TT
1 CAACTAATAAACTATTCTTTAA-TATAACTT
*
612457 CACTACTAAAAAACTA
1 CA--ACTAATAAACTA
612473 ATTAACCAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
30 52 0.78
31 5 0.07
32 10 0.15
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (30 bp):
CAACTAATAAACTATTCTTTAATATAACTT
Found at i:612419 original size:15 final size:16
Alignment explanation
Indices: 612371--612425 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
612361 TTTAAACAAC
612371 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
**
612386 TAATATAAC--TTCAAC
1 TAATATAACTATTC-TT
612401 TAATA-AACTATTCTT
1 TAATATAACTATTCTT
612416 TAATATAACT
1 TAATATAACT
612426 TAAACTAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 6 0.19
15 15 0.48
16 10 0.32
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.42
Consensus pattern (16 bp):
TAATATAACTATTCTT
Found at i:612623 original size:17 final size:17
Alignment explanation
Indices: 612601--612636 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
612591 GTAAATTTTT
612601 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
612618 ACCCTAACCCTAAACTA
1 ACCCTAACCCTAAACTA
612635 AC
1 AC
612637 AAACTAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.17
Consensus pattern (17 bp):
ACCCTAACCCTAAACTA
Found at i:613037 original size:29 final size:29
Alignment explanation
Indices: 613000--613111 Score: 161
Period size: 29 Copynumber: 3.9 Consensus size: 29
612990 AGCAGGGGAT
*
613000 GTCGTCGGGCGTGCATGGAGACCTAGGAG
1 GTCGCCGGGCGTGCATGGAGACCTAGGAG
* *
613029 GTCGCCGGGCATGCATGGCGACCTAGGAG
1 GTCGCCGGGCGTGCATGGAGACCTAGGAG
*
613058 GTCGTCGGGCGTGCATGGAGACCTAGGAG
1 GTCGCCGGGCGTGCATGGAGACCTAGGAG
* * *
613087 GTCGCCGGGAGTGTATGGCGACCTA
1 GTCGCCGGGCGTGCATGGAGACCTA
613112 TGGTTGGGTT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 73 1.00
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (29 bp):
GTCGCCGGGCGTGCATGGAGACCTAGGAG
Found at i:613064 original size:58 final size:58
Alignment explanation
Indices: 613000--613111 Score: 199
Period size: 58 Copynumber: 1.9 Consensus size: 58
612990 AGCAGGGGAT
613000 GTCGTCGGGCGTGCATGGAGACCTAGGAGGTCGCCGGGCA-TGCATGGCGACCTAGGAG
1 GTCGTCGGGCGTGCATGGAGACCTAGGAGGTCGCCGGG-AGTGCATGGCGACCTAGGAG
*
613058 GTCGTCGGGCGTGCATGGAGACCTAGGAGGTCGCCGGGAGTGTATGGCGACCTA
1 GTCGTCGGGCGTGCATGGAGACCTAGGAGGTCGCCGGGAGTGCATGGCGACCTA
613112 TGGTTGGGTT
Statistics
Matches: 52, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
57 1 0.02
58 51 0.98
ACGTcount: A:0.17, C:0.23, G:0.43, T:0.17
Consensus pattern (58 bp):
GTCGTCGGGCGTGCATGGAGACCTAGGAGGTCGCCGGGAGTGCATGGCGACCTAGGAG
Found at i:617817 original size:14 final size:14
Alignment explanation
Indices: 617798--617824 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
617788 AAAATCCCTT
617798 TTAAATTTATTATA
1 TTAAATTTATTATA
617812 TTAAATTTATTAT
1 TTAAATTTATTAT
617825 GATTTAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAATTTATTATA
Found at i:618269 original size:29 final size:29
Alignment explanation
Indices: 618205--618269 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
618195 AAAATATATT
* * * *
618205 TTCGTCTCTTAAAATTTTATATGTTTAAG
1 TTCGTCCCTTAAAATTTTATAAGTTCAAA
*
618234 TTTGTCCCTTAAAATTTTATAAGTTCAAA
1 TTCGTCCCTTAAAATTTTATAAGTTCAAA
618263 TTCGTCC
1 TTCGTCC
618270 ACTAACATAA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.28, C:0.15, G:0.09, T:0.48
Consensus pattern (29 bp):
TTCGTCCCTTAAAATTTTATAAGTTCAAA
Found at i:619871 original size:46 final size:46
Alignment explanation
Indices: 619820--619911 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
619810 AGCAAATTTG
619820 TTGACCTTTGAAATTTCAGATTTGGGATGCTGGGTTTGTATATAAA
1 TTGACCTTTGAAATTTCAGATTTGGGATGCTGGGTTTGTATATAAA
619866 TTGACCTTTGAAATTTCAGATTTGGGATGCTGGGTTTGTATATAAA
1 TTGACCTTTGAAATTTCAGATTTGGGATGCTGGGTTTGTATATAAA
619912 AAGACTGATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.26, C:0.09, G:0.24, T:0.41
Consensus pattern (46 bp):
TTGACCTTTGAAATTTCAGATTTGGGATGCTGGGTTTGTATATAAA
Found at i:621198 original size:5 final size:5
Alignment explanation
Indices: 621188--621236 Score: 55
Period size: 5 Copynumber: 9.8 Consensus size: 5
621178 AAACACTATG
* * *
621188 AAAAT AAAAT AAAAAC AAAAT AGAAT AGAAT -AAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
621237 ATATAATGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
4 3 0.08
5 31 0.82
6 4 0.11
ACGTcount: A:0.78, C:0.02, G:0.04, T:0.16
Consensus pattern (5 bp):
AAAAT
Found at i:623537 original size:3 final size:3
Alignment explanation
Indices: 623525--623568 Score: 52
Period size: 3 Copynumber: 14.3 Consensus size: 3
623515 CATAATAATA
* * *
623525 ATT ATA ATT ATT ATT AAT ATA ATAT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT A
623569 AAAATATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 32 0.94
4 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
ATT
Found at i:623542 original size:19 final size:19
Alignment explanation
Indices: 623517--623559 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 19
623507 TTTTTTTTCA
623517 TAATAATAATTATAATTATTAT
1 TAAT-ATAA-TAT-ATTATTAT
623539 TAATATAATATATTATTAT
1 TAATATAATATATTATTAT
623558 TA
1 TA
623560 TTATTATTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 10 0.48
20 3 0.14
21 4 0.19
22 4 0.19
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TAATATAATATATTATTAT
Found at i:623556 original size:22 final size:22
Alignment explanation
Indices: 623517--623562 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
623507 TTTTTTTTCA
623517 TAATAATAATTATAATTATTAT
1 TAATAATAATTATAATTATTAT
*
623539 TAAT-ATAATATATTATTATTAT
1 TAATAATAAT-TATAATTATTAT
623561 TA
1 TA
623563 TTATTAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (22 bp):
TAATAATAATTATAATTATTAT
Done.