Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008241.1 Hibiscus syriacus cultivar Beakdansim tig00110889_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: 1355325
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 8
Found at i:420436 original size:118 final size:118
Alignment explanation
Indices: 420314--420563 Score: 430
Period size: 118 Copynumber: 2.1 Consensus size: 118
420304 ATTCCTTAAT
* * *
420314 GCATCCTTTCATTCATTTTAGTTATGGCATCCTTTCATGCCTTAATGAATTCTTTCATGCATTTT
1 GCATCCTTTCATGCATTTTAGTTATGGCATACTTTCATGCCTTAATGAATCCTTTCATGCATTTT
*
420379 AGTTACGGCATCCTTTCATGCCTTAAT-CTATCCTTTCATGCATTTTAGTTATG
66 AGTTACGGAATCCTTTCATGCCTTAATGC-ATCCTTTCATGCATTTTAGTTATG
*
420432 GCATCCTTTCATGCATTTTAGTTATGGCATACTTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 GCATCCTTTCATGCATTTTAGTTATGGCATACTTTCATGCCTTAATGAATCCTTTCATGCATTTT
*
420497 AGTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
66 AGTTACGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
420550 GCATCCTTTCATGC
1 GCATCCTTTCATGC
420564 CTTAATGCAT
Statistics
Matches: 125, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
118 124 0.99
119 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.44
Consensus pattern (118 bp):
GCATCCTTTCATGCATTTTAGTTATGGCATACTTTCATGCCTTAATGAATCCTTTCATGCATTTT
AGTTACGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATG
Found at i:420452 original size:164 final size:164
Alignment explanation
Indices: 420268--420608 Score: 560
Period size: 164 Copynumber: 2.1 Consensus size: 164
420258 ATGCCTTAAT
* * * *
420268 GCATCATTTCATGTATTTTAGTTATGGCAT-CTTTGCATTCCTTAATGCATCCTTTCATTCATTT
1 GCATCCTTTCATGCATTTTAGTTATGGCATACTTT-CATGCCTTAATGCATCCTTTCATGCATTT
* *
420332 TAGTTATGGCATCCTTTCATGCCTTAATGAATTCTTTCATGCATTTTAGTTACGGCATCCTTTCA
65 TAGTTATGGAATCCTTTCATGCCTTAATGAATCCTTTCATGCATTTTAGTTACGGCATCCTTTCA
*
420397 TGCCTTAAT-CTATCCTTTCATGCATTTTAGTTATG
130 TGCCTTAATGC-ATCCTTTCATACATTTTAGTTATG
420432 GCATCCTTTCATGCATTTTAGTTATGGCATACTTTCATGCCTTAATGCATCCTTTCATGCATTTT
1 GCATCCTTTCATGCATTTTAGTTATGGCATACTTTCATGCCTTAATGCATCCTTTCATGCATTTT
* *
420497 AGTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCAT
66 AGTTATGGAATCCTTTCATGCCTTAATGAATCCTTTCATGCATTTTAGTTACGGCATCCTTTCAT
*
420562 GCCTTAATGCATCCTTTGATACATTTTAGTTATG
131 GCCTTAATGCATCCTTTCATACATTTTAGTTATG
420596 GCATCCTTTCATG
1 GCATCCTTTCATG
420609 TCTTAATGCA
Statistics
Matches: 165, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
164 160 0.97
165 5 0.03
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (164 bp):
GCATCCTTTCATGCATTTTAGTTATGGCATACTTTCATGCCTTAATGCATCCTTTCATGCATTTT
AGTTATGGAATCCTTTCATGCCTTAATGAATCCTTTCATGCATTTTAGTTACGGCATCCTTTCAT
GCCTTAATGCATCCTTTCATACATTTTAGTTATG
Found at i:420482 original size:46 final size:46
Alignment explanation
Indices: 420432--420701 Score: 470
Period size: 46 Copynumber: 5.9 Consensus size: 46
420422 TTTAGTTATG
*
420432 GCATCCTTTCATGCATTTTAGTTATGGCATACTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
*
420478 GCATCCTTTCATGCATTTTAGTTATGGAATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
420524 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
* * *
420570 GCATCCTTTGATACATTTTAGTTATGGCATCCTTTCATGTCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
*
420616 GCATCCTTTCATGTATTTTAGTTATGGCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
420662 -CTATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGC
1 GC-ATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGC
420702 ATTTTAGTTA
Statistics
Matches: 212, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
45 1 0.00
46 211 1.00
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.44
Consensus pattern (46 bp):
GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCCTTAAT
Found at i:420482 original size:138 final size:134
Alignment explanation
Indices: 420199--420491 Score: 337
Period size: 138 Copynumber: 2.1 Consensus size: 134
420189 CATTTTAATC
* * *
420199 ATGGCACCCTTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCATTTCATGCCT
1 ATGGCATCCTTTCATGCCTTAATGAATCATTTCATGCATTTTAGTTACGGCATCATTTCATGCCT
* * *
420264 TAATGCATCATTTCATGTATTTTAGTTATGGCATCTTTGCATTCCTTAATGCATCCTTTCATTCA
66 TAATGCATCATTTCATGCATTTTAGTTATGGCATCTTTGCATT-CTTAATGCATACTTTCATGCA
*
420329 TTTTAGTT
130 -CTTA--T
*
420337 ATGGCATCCTTTCATGCCTTAATGAATTC-TTTCATGCATTTTAGTTACGGCATCCTTTCATGCC
1 ATGGCATCCTTTCATGCCTTAATGAA-TCATTTCATGCATTTTAGTTACGGCATCATTTCATGCC
*
420401 TTAAT-CTATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCATT-TTAGTTATGGCATAC
65 TTAATGC-ATCATTTCATGCATTTTAGTTATGGCAT-C-TT--TGCATTCTTA---AT-GCATAC
420464 TTTCATGC-CTTA-
121 TTTCATGCACTTAT
420476 AT-GCATCCTTTCATGC
1 ATGGCATCCTTTCATGC
420492 ATTTTAGTTA
Statistics
Matches: 136, Mismatches: 9, Indels: 20
0.82 0.05 0.12
Matches are distributed among these distances:
137 1 0.01
138 102 0.75
139 5 0.04
140 5 0.04
142 9 0.07
143 2 0.01
144 12 0.09
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.44
Consensus pattern (134 bp):
ATGGCATCCTTTCATGCCTTAATGAATCATTTCATGCATTTTAGTTACGGCATCATTTCATGCCT
TAATGCATCATTTCATGCATTTTAGTTATGGCATCTTTGCATTCTTAATGCATACTTTCATGCAC
TTAT
Found at i:420523 original size:210 final size:210
Alignment explanation
Indices: 420222--420655 Score: 703
Period size: 210 Copynumber: 2.1 Consensus size: 210
420212 ATGCCTTAAT
* *
420222 GCATCATTTCATGCATTTTAGTTATGGCATCATTTCATGCCTTAATGCATCATTTCATGTATTTT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCATTTCATGCCTTAATGCATCATTTCATGCATTTT
* * *
420287 AGTTATGGCATCTTTGCATTCCTTAATGCATCCTTTCATTCATTTTAGTTATGGCATCCTTTCAT
66 AGTTATGGAATCTTTGCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCAT
* *
420352 GCCTTAATGAATTCTTTCATGCATTTTAGTTACGGCATCCTTTCATGCCTTAAT-CTATCCTTTC
131 GCCTTAATGAATCCTTTCATACATTTTAGTTACGGCATCCTTTCATGCCTTAATGC-ATCCTTTC
420416 ATGCATTTTAGTTATG
195 ATGCATTTTAGTTATG
*
420432 GCATCCTTTCATGCATTTTAGTTATGGCAT-ACTTTCATGCCTTAATGCATCCTTTCATGCATTT
1 GCATCCTTTCATGCATTTTAGTTATGGCATCA-TTTCATGCCTTAATGCATCATTTCATGCATTT
420496 TAGTTATGGAATCCTTT-CATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTC
65 TAGTTATGGAAT-CTTTGCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTC
* * * *
420560 ATGCCTTAATGCATCCTTTGATACATTTTAGTTATGGCATCCTTTCATGTCTTAATGCATCCTTT
129 ATGCCTTAATGAATCCTTTCATACATTTTAGTTACGGCATCCTTTCATGCCTTAATGCATCCTTT
*
420625 CATGTATTTTAGTTATG
194 CATGCATTTTAGTTATG
420642 GCATCCTTTCATGC
1 GCATCCTTTCATGC
420656 CTTAATCTAT
Statistics
Matches: 208, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
209 1 0.00
210 202 0.97
211 5 0.02
ACGTcount: A:0.21, C:0.21, G:0.13, T:0.45
Consensus pattern (210 bp):
GCATCCTTTCATGCATTTTAGTTATGGCATCATTTCATGCCTTAATGCATCATTTCATGCATTTT
AGTTATGGAATCTTTGCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCAT
GCCTTAATGAATCCTTTCATACATTTTAGTTACGGCATCCTTTCATGCCTTAATGCATCCTTTCA
TGCATTTTAGTTATG
Found at i:420528 original size:138 final size:140
Alignment explanation
Indices: 420386--420715 Score: 428
Period size: 138 Copynumber: 2.4 Consensus size: 140
420376 TTTAGTTACG
* *
420386 GCATCCTTTCATGC-CTTA-AT-CTATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCAT
1 GCATCCTTTCATGCATTTATATGC-ATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATACAT
420448 TTTAGTTATGGCATACTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGAATCCTTT
65 TTTAGTTATGGCATACTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGAATCCTTT
420513 CATGCCTTAAT
130 CATGCCTTAAT
* *
420524 GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGC--CTTA---AT-GCATCCTTTGATA
1 GCATCCTTTCATGCA-TTTA--TAT-GCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATA
* * * *
420583 CATTTTAGTTATGGCATCCTTTCATGTCTTAATGCATCCTTTCATGTATTTTAGTTATGGCATCC
62 CATTTTAGTTATGGCATACTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGAATCC
420648 TTTCATGCCTTAAT
127 TTTCATGCCTTAAT
420662 -CTATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATGCATTTTAGTTATGGC
1 GC-ATCCTTTCATGCA-TTTA--TAT-GCATCCTTTCATGCATTTTAGTTATGGC
420716 TATAAGATCA
Statistics
Matches: 169, Mismatches: 9, Indels: 22
0.85 0.05 0.11
Matches are distributed among these distances:
137 1 0.01
138 138 0.82
139 2 0.01
140 6 0.04
142 3 0.02
143 4 0.02
144 14 0.08
145 1 0.01
ACGTcount: A:0.20, C:0.22, G:0.13, T:0.45
Consensus pattern (140 bp):
GCATCCTTTCATGCATTTATATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTTCATACATT
TTAGTTATGGCATACTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGAATCCTTTC
ATGCCTTAAT
Found at i:420638 original size:256 final size:256
Alignment explanation
Indices: 420177--420715 Score: 900
Period size: 256 Copynumber: 2.1 Consensus size: 256
420167 TGCATTAATA
* * * *
420177 CATCCATTCATGCATTTTAATCATGGCACCCTTTCATGCCTTAATGCATCATTTCATGCATTTTA
1 CATCCTTTCATGCATTTTAGTTATGGCACACTTTCATGCCTTAATGCATCATTTCATGCATTTTA
* * *
420242 GTTATGGCATCATTTCATGCCTTAATGCATCATTTCATGTATTTTAGTTATGGCATCTTTGCATT
66 GTTATGGAATCATTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCTTTGCATG
* *
420307 CCTTAATGCATCCTTTCATTCATTTTAGTTATGGCATCCTTTCATGCCTTAATGAATTCTTTCAT
131 CCTTAATGCATCCTTTCATACATTTTAGTTATGGCATCCTTTCATGCCTTAATGAATCCTTTCAT
420372 GCATTTTAGTTACGGCATCCTTTCATGCCTTAATCTATCCTTTCATGCATTTTAGTTATGG
196 GCATTTTAGTTACGGCATCCTTTCATGCCTTAATCTATCCTTTCATGCATTTTAGTTATGG
* *
420433 CATCCTTTCATGCATTTTAGTTATGGCATACTTTCATGCCTTAATGCATCCTTTCATGCATTTTA
1 CATCCTTTCATGCATTTTAGTTATGGCACACTTTCATGCCTTAATGCATCATTTCATGCATTTTA
* *
420498 GTTATGGAATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAGTTATGGCATCCTTT-CAT
66 GTTATGGAATCATTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCAT-CTTTGCAT
* * *
420562 GCCTTAATGCATCCTTTGATACATTTTAGTTATGGCATCCTTTCATGTCTTAATGCATCCTTTCA
130 GCCTTAATGCATCCTTTCATACATTTTAGTTATGGCATCCTTTCATGCCTTAATGAATCCTTTCA
* *
420627 TGTATTTTAGTTATGGCATCCTTTCATGCCTTAATCTATCCTTTCATGCATTTTAGTTATGG
195 TGCATTTTAGTTACGGCATCCTTTCATGCCTTAATCTATCCTTTCATGCATTTTAGTTATGG
420689 CATCCTTTCATGCATTTTAGTTATGGC
1 CATCCTTTCATGCATTTTAGTTATGGC
420716 TATAAGATCA
Statistics
Matches: 264, Mismatches: 18, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
256 260 0.98
257 4 0.02
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.45
Consensus pattern (256 bp):
CATCCTTTCATGCATTTTAGTTATGGCACACTTTCATGCCTTAATGCATCATTTCATGCATTTTA
GTTATGGAATCATTTCATGCCTTAATGCATCATTTCATGCATTTTAGTTATGGCATCTTTGCATG
CCTTAATGCATCCTTTCATACATTTTAGTTATGGCATCCTTTCATGCCTTAATGAATCCTTTCAT
GCATTTTAGTTACGGCATCCTTTCATGCCTTAATCTATCCTTTCATGCATTTTAGTTATGG
Found at i:422499 original size:31 final size:31
Alignment explanation
Indices: 422464--422523 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
422454 AAGAGTTTGA
*
422464 GAGTTCCAAGTGAGAAGGACATATTGAATGG
1 GAGTTCCAAGTGAAAAGGACATATTGAATGG
* *
422495 GAGTTCCTAGTGAAAATGACATATTGAAT
1 GAGTTCCAAGTGAAAAGGACATATTGAAT
422524 TCATCGAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.27
Consensus pattern (31 bp):
GAGTTCCAAGTGAAAAGGACATATTGAATGG
Found at i:423144 original size:36 final size:36
Alignment explanation
Indices: 423096--423208 Score: 169
Period size: 36 Copynumber: 3.2 Consensus size: 36
423086 CAATTGAATG
* *
423096 TTGGAAAAATGCTCAAATTAGGTTATCCCACTGGTA
1 TTGGAAATATGCTCAAATTAGGTTATCCCACTAGTA
*
423132 TTGGAAATATGCT--AGTTAGGTTATCCCA-TAGTA
1 TTGGAAATATGCTCAAATTAGGTTATCCCACTAGTA
*
423165 TTGGAAATATGCTCAAATTAGGTTATTCCACTAGTA
1 TTGGAAATATGCTCAAATTAGGTTATCCCACTAGTA
423201 TTGGAAAT
1 TTGGAAAT
423209 GATCATTTTA
Statistics
Matches: 69, Mismatches: 5, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
33 17 0.25
34 14 0.20
35 13 0.19
36 25 0.36
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (36 bp):
TTGGAAATATGCTCAAATTAGGTTATCCCACTAGTA
Found at i:423755 original size:30 final size:30
Alignment explanation
Indices: 423719--423781 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
423709 TGAACATGAT
423719 TCAGATAAGGGCTTCA-AGTTGGATAAACTA
1 TCAGATAAGGGCTTCAGA-TTGGATAAACTA
423749 TCAGATAAGGGCTTCAGATTGGATAAACTA
1 TCAGATAAGGGCTTCAGATTGGATAAACTA
423779 TCA
1 TCA
423782 CCAAGTCGTA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (30 bp):
TCAGATAAGGGCTTCAGATTGGATAAACTA
Found at i:428285 original size:30 final size:29
Alignment explanation
Indices: 428222--428289 Score: 77
Period size: 29 Copynumber: 2.3 Consensus size: 29
428212 AGTATGCTCA
* *
428222 TAATAATAAATATTGAAAAAATGGACTTC
1 TAATAATAAATACTGAAAAAATAGACTTC
428251 TAATAA-AAAGTACTGAAAAAATTAGAC-TC
1 TAATAATAAA-TACTGAAAAAA-TAGACTTC
428280 GTAATAATAA
1 -TAATAATAA
428290 CAAATAAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
28 3 0.09
29 18 0.55
30 10 0.30
31 2 0.06
ACGTcount: A:0.54, C:0.07, G:0.10, T:0.28
Consensus pattern (29 bp):
TAATAATAAATACTGAAAAAATAGACTTC
Found at i:428460 original size:44 final size:43
Alignment explanation
Indices: 428409--428499 Score: 105
Period size: 44 Copynumber: 2.1 Consensus size: 43
428399 AATAAATGTT
428409 AAAAAAT-ATTAGTAAAGAATTAAACACTAAT-ACAAATATTAGGA
1 AAAAAATAATTA-T-AAGAA-TAAACACTAATAACAAATATTAGGA
* * *
428453 AAAAAATAAATTATAAGAATAGACCCTAATAATAAATATTAGGA
1 AAAAAAT-AATTATAAGAATAAACACTAATAACAAATATTAGGA
428497 AAA
1 AAA
428500 TATGAACCTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
43 9 0.22
44 27 0.66
45 1 0.02
46 4 0.10
ACGTcount: A:0.60, C:0.07, G:0.09, T:0.24
Consensus pattern (43 bp):
AAAAAATAATTATAAGAATAAACACTAATAACAAATATTAGGA
Found at i:429485 original size:17 final size:17
Alignment explanation
Indices: 429444--429492 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
429434 CCCTATTTGA
**
429444 TTAAATATTTAATAAAT
1 TTAAATATTTTTTAAAT
**
429461 TTTTATATTTTTTAAAT
1 TTAAATATTTTTTAAAT
429478 TTAAATATTTATTTA
1 TTAAATATTT-TTTA
429493 TATGAATCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAAATATTTTTTAAAT
Found at i:430613 original size:4 final size:4
Alignment explanation
Indices: 430604--430703 Score: 105
Period size: 4 Copynumber: 24.2 Consensus size: 4
430594 TATGAAGCAC
* * *
430604 AGAA AGAA AGAA AGAA AGAGA GAGAG AGAG AGAG AGAA AGAA AGAA AGAA
1 AGAA AGAA AGAA AGAA AGA-A -AGAA AGAA AGAA AGAA AGAA AGAA AGAA
*
430654 AGAA AGAAA AGAGA AGAA AGAA AGGAA AGAA A-CA AG-A AGAA AGAA AGAA
1 AGAA AG-AA AGA-A AGAA AGAA A-GAA AGAA AGAA AGAA AGAA AGAA AGAA
430703 A
1 A
430704 AGTTCCAAAC
Statistics
Matches: 86, Mismatches: 3, Indels: 14
0.83 0.03 0.14
Matches are distributed among these distances:
3 5 0.06
4 65 0.76
5 13 0.15
6 3 0.03
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:430644 original size:30 final size:30
Alignment explanation
Indices: 430604--430685 Score: 110
Period size: 34 Copynumber: 2.6 Consensus size: 30
430594 TATGAAGCAC
*
430604 AGAAAGAAAGAAAGAAAGAGAGAGAGAGAGAGA
1 AGAAAGAAAGAAAGAAAGA-A-AGA-AAAGAGA
430637 GAGAAAGAAAGAAAGAAAGAAAGAAAAGAGA
1 -AGAAAGAAAGAAAGAAAGAAAGAAAAGAGA
430668 AGAAAGAAAGGAAAGAAA
1 AGAAAGAAA-GAAAGAAA
430686 CAAGAAGAAA
Statistics
Matches: 46, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
30 9 0.20
31 14 0.30
32 3 0.07
33 1 0.02
34 19 0.41
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (30 bp):
AGAAAGAAAGAAAGAAAGAAAGAAAAGAGA
Found at i:430681 original size:27 final size:27
Alignment explanation
Indices: 430607--430703 Score: 101
Period size: 27 Copynumber: 3.6 Consensus size: 27
430597 GAAGCACAGA
* * *
430607 AAGA-AAGAAAGAAAGAGAGAGAGAGAG
1 AAGAGAAGAAAGAAAGAAAGAAACA-AG
*
430634 AGAGAGAAAGAAAGAAAGAAAGAAAGAA-
1 A-AGAG-AAGAAAGAAAGAAAGAAACAAG
430662 AAGAGAAGAAAGAAAGGAAAGAAACAAG
1 AAGAGAAGAAAGAAA-GAAAGAAACAAG
430690 AAGA-AAGAAAGAAA
1 AAGAGAAGAAAGAAA
430704 AGTTCCAAAC
Statistics
Matches: 62, Mismatches: 3, Indels: 10
0.83 0.04 0.13
Matches are distributed among these distances:
26 10 0.16
27 25 0.40
28 8 0.13
29 1 0.02
30 18 0.29
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.00
Consensus pattern (27 bp):
AAGAGAAGAAAGAAAGAAAGAAACAAG
Found at i:430691 original size:30 final size:29
Alignment explanation
Indices: 430604--430703 Score: 98
Period size: 34 Copynumber: 3.3 Consensus size: 29
430594 TATGAAGCAC
*
430604 AGAAAGAAAGAAAGAAAGAGAGAGAGAGAGAGA
1 AGAAAGAAAGAAAGAAA-A-A-AGA-AAAGAGA
430637 GAGAAAGAAAGAAAGAAAGAAAGAAAAGAGA
1 -AGAAAGAAAGAAAGAAA-AAAGAAAAGAGA
*
430668 AGAAAGAAAGGAAAGAAACAAG--AAGA-A
1 AGAAAGAAA-GAAAGAAAAAAGAAAAGAGA
430695 AGAAAGAAA
1 AGAAAGAAA
430704 AGTTCCAAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
27 10 0.16
28 4 0.06
30 12 0.19
31 14 0.22
32 3 0.05
33 1 0.02
34 19 0.30
ACGTcount: A:0.69, C:0.01, G:0.30, T:0.00
Consensus pattern (29 bp):
AGAAAGAAAGAAAGAAAAAAGAAAAGAGA
Found at i:430798 original size:21 final size:21
Alignment explanation
Indices: 430773--430815 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
430763 AAACAAAAAT
430773 TTAGTTTGTTAGTTTAAATTA
1 TTAGTTTGTTAGTTTAAATTA
*
430794 TTAGTTTGTTAGTTTAAGTTA
1 TTAGTTTGTTAGTTTAAATTA
430815 T
1 T
430816 ATATTATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.16, T:0.58
Consensus pattern (21 bp):
TTAGTTTGTTAGTTTAAATTA
Found at i:431328 original size:17 final size:17
Alignment explanation
Indices: 431306--431365 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
431296 ATTTATTTCC
431306 GTTTAAAAAAATATTTT
1 GTTTAAAAAAATATTTT
*
431323 GTTTAAAAATATTTATTGTT
1 GTTTAAAAA-A-ATATT-TT
*
431343 GTTTACAAAAATATTTT
1 GTTTAAAAAAATATTTT
431360 GTTTAA
1 GTTTAA
431366 TTTATATTAG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
17 16 0.44
18 5 0.14
19 5 0.14
20 10 0.28
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (17 bp):
GTTTAAAAAAATATTTT
Found at i:431346 original size:20 final size:20
Alignment explanation
Indices: 431296--431358 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 20
431286 TATTTTTTTA
*
431296 ATTTATTTCCGTTTAAAAAA-
1 ATTTATTT-TGTTTAAAAAAT
431316 A--TATTTTGTTT-AAAAAT
1 ATTTATTTTGTTTAAAAAAT
431333 ATTTATTGTTGTTTACAAAAAT
1 ATTTATT-TTGTTTA-AAAAAT
431355 ATTT
1 ATTT
431359 TGTTTAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
16 5 0.14
17 5 0.14
18 5 0.14
19 4 0.11
20 7 0.19
22 10 0.28
ACGTcount: A:0.38, C:0.05, G:0.06, T:0.51
Consensus pattern (20 bp):
ATTTATTTTGTTTAAAAAAT
Found at i:431921 original size:20 final size:20
Alignment explanation
Indices: 431857--431942 Score: 91
Period size: 20 Copynumber: 4.2 Consensus size: 20
431847 TTCCAAATTT
431857 GCAACGCGAATATGTAAATC
1 GCAACGCGAATATGTAAATC
** * * **
431877 GCATTGCGATTTTCCAAATTC
1 GCAACGCGAATATGTAAA-TC
431898 GCAACGCGAATATGTAAATC
1 GCAACGCGAATATGTAAATC
* *
431918 GCAACGCGAATTTGTAATTC
1 GCAACGCGAATATGTAAATC
431938 GCAAC
1 GCAAC
431943 ACAGAAGTCA
Statistics
Matches: 51, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 37 0.73
21 14 0.27
ACGTcount: A:0.34, C:0.22, G:0.19, T:0.26
Consensus pattern (20 bp):
GCAACGCGAATATGTAAATC
Found at i:433794 original size:24 final size:24
Alignment explanation
Indices: 433760--433813 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
433750 CTGAAACATC
433760 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
433784 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
433808 ATCAAA
1 ATCAAA
433814 TTTTGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:434862 original size:40 final size:40
Alignment explanation
Indices: 434771--434846 Score: 118
Period size: 40 Copynumber: 1.9 Consensus size: 40
434761 TTGTGAAATT
* *
434771 AAAATTCGTGTTGCAAATTCGAAAATCGATTTGCGAAAAC
1 AAAATTCGTGTTGCAAATTAGAAAATCGAGTTGCGAAAAC
*
434811 AAAATTCGTGTTGTAAATTAG-AAATCGAGTTGCGAA
1 AAAATTCGTGTTGCAAATTAGAAAATCGAGTTGCGAA
434847 TTTGAAATTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
39 14 0.42
40 19 0.58
ACGTcount: A:0.39, C:0.12, G:0.20, T:0.29
Consensus pattern (40 bp):
AAAATTCGTGTTGCAAATTAGAAAATCGAGTTGCGAAAAC
Found at i:434890 original size:20 final size:21
Alignment explanation
Indices: 434865--434915 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
434855 TCAGTGTTAC
*
434865 GAATTTGGAAATCGCGTTG-A
1 GAATTTGGAAATCGCGCTGCA
434885 GAATTTGGAAATCGCGCTGCA
1 GAATTTGGAAATCGCGCTGCA
434906 -AATTTGGAAA
1 GAATTTGGAAA
434916 ATCACAATGT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (21 bp):
GAATTTGGAAATCGCGCTGCA
Found at i:434930 original size:21 final size:21
Alignment explanation
Indices: 434906--434945 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
434896 TCGCGCTGCA
434906 AATTTGGAAAATCACAATGTG
1 AATTTGGAAAATCACAATGTG
*
434927 AATTTGGAAAATCGCAATG
1 AATTTGGAAAATCACAATG
434946 CGATTTACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.42, C:0.10, G:0.20, T:0.28
Consensus pattern (21 bp):
AATTTGGAAAATCACAATGTG
Found at i:441730 original size:23 final size:23
Alignment explanation
Indices: 441682--441753 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
441672 GGAATCGATA
441682 CCCCCTTGAAGGGGAACCGATT-
1 CCCCCTTGAAGGGGAACCGATTC
441704 CCCCCTTGAAGGGGAACCGATTC
1 CCCCCTTGAAGGGGAACCGATTC
* *
441727 CCCCTTTGAAGGGGAACCAATTC
1 CCCCCTTGAAGGGGAACCGATTC
441750 CCCC
1 CCCC
441754 ATGTAGGGGA
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
22 22 0.47
23 25 0.53
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (23 bp):
CCCCCTTGAAGGGGAACCGATTC
Found at i:441743 original size:45 final size:44
Alignment explanation
Indices: 441671--441776 Score: 140
Period size: 45 Copynumber: 2.4 Consensus size: 44
441661 TTAGTACAGA
* * *
441671 GGGAATCGATACCCCCTTGAAGGGGAACCGATTCCCCCTTGAAG
1 GGGAACCGATACCCCCTTGAAGGGGAACCAATTCCCCCATGAAG
* *
441715 GGGAACCGATTCCCCCTTTGAAGGGGAACCAATTCCCCCATGTAG
1 GGGAACCGATACCCCC-TTGAAGGGGAACCAATTCCCCCATGAAG
* *
441760 GGGAATCAATACCCCCT
1 GGGAACCGATACCCCCT
441777 GGAGGTTCTA
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
44 15 0.28
45 38 0.72
ACGTcount: A:0.25, C:0.31, G:0.25, T:0.19
Consensus pattern (44 bp):
GGGAACCGATACCCCCTTGAAGGGGAACCAATTCCCCCATGAAG
Found at i:441775 original size:22 final size:22
Alignment explanation
Indices: 441671--441764 Score: 134
Period size: 22 Copynumber: 4.2 Consensus size: 22
441661 TTAGTACAGA
* *
441671 GGGAATCGATACCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
441693 GGGAACCGATTCCCCCTTGAAG
1 GGGAACCGATTCCCCCTTGAAG
441715 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TTGAAG
* * *
441738 GGGAACCAATTCCCCCATGTAG
1 GGGAACCGATTCCCCCTTGAAG
441760 GGGAA
1 GGGAA
441765 TCAATACCCC
Statistics
Matches: 66, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
22 45 0.68
23 21 0.32
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.18
Consensus pattern (22 bp):
GGGAACCGATTCCCCCTTGAAG
Found at i:443371 original size:18 final size:19
Alignment explanation
Indices: 443344--443379 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
443334 GAACCAGAGC
443344 AGCATGAGGAACAAGCACG
1 AGCATGAGGAACAAGCACG
443363 AGCAT-AGGAACAAGCAC
1 AGCATGAGGAACAAGCAC
443380 AACCAGAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.44, C:0.22, G:0.28, T:0.06
Consensus pattern (19 bp):
AGCATGAGGAACAAGCACG
Found at i:443389 original size:18 final size:18
Alignment explanation
Indices: 443349--443389 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
443339 AGAGCAGCAT
* *
443349 GAGGAACAAGCACGAGCA
1 GAGGAACAAGCACAACCA
*
443367 TAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
443385 GAGGA
1 GAGGA
443390 TCAAATGCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.22, G:0.29, T:0.02
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:443923 original size:2 final size:2
Alignment explanation
Indices: 443916--443972 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
443906 GCAGCTTAAG
443916 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
443958 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
443973 ATCAATTAGC
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:447257 original size:12 final size:12
Alignment explanation
Indices: 447240--447265 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
447230 GACCATTTTA
447240 TCCTTCTATTCC
1 TCCTTCTATTCC
447252 TCCTTCTATTCC
1 TCCTTCTATTCC
447264 TC
1 TC
447266 GTATCTTCTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.42, G:0.00, T:0.50
Consensus pattern (12 bp):
TCCTTCTATTCC
Found at i:452444 original size:18 final size:18
Alignment explanation
Indices: 452418--452489 Score: 99
Period size: 18 Copynumber: 4.0 Consensus size: 18
452408 ACTGAATATT
* *
452418 TGTCTCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
*
452436 TGTCCCGAATGACCACTA
1 TGTCCCGAAGGACCACTA
**
452454 TGTCTTGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
452472 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
452490 ATAATCCCTC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 48 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:452468 original size:36 final size:36
Alignment explanation
Indices: 452418--452489 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
452408 ACTGAATATT
* *
452418 TGTCTCGAATGACCACTATGTCCCGAATGACCACTA
1 TGTCTCGAAGGACCACTATGTCCCGAAGGACCACTA
*
452454 TGTCTTGAAGGACCACTATGTCCCGAAGGACCACTA
1 TGTCTCGAAGGACCACTATGTCCCGAAGGACCACTA
452490 ATAATCCCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.24
Consensus pattern (36 bp):
TGTCTCGAAGGACCACTATGTCCCGAAGGACCACTA
Found at i:454166 original size:21 final size:22
Alignment explanation
Indices: 454128--454172 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
454118 TGATTACTAA
*
454128 TAATGATTTATTATTAAT-ATT
1 TAATGATTTATTACTAATGATT
454149 TAATGATTTGA-TACTAATGATT
1 TAATGATTT-ATTACTAATGATT
454171 TA
1 TA
454173 GTAATGATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 15 0.71
22 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.09, T:0.51
Consensus pattern (22 bp):
TAATGATTTATTACTAATGATT
Found at i:454168 original size:14 final size:14
Alignment explanation
Indices: 454149--454229 Score: 64
Period size: 14 Copynumber: 6.1 Consensus size: 14
454139 TATTAATATT
*
454149 TAATGATTTGATAC
1 TAATGATTTGATAA
*
454163 TAATGA-TT--TAG
1 TAATGATTTGATAA
*
454174 TAATGATTAG-TAA
1 TAATGATTTGATAA
*
454187 TAATGAAATT-ATAA
1 TAATG-ATTTGATAA
*
454201 TAATGATTTGATAC
1 TAATGATTTGATAA
*
454215 TAATGATTTAATAA
1 TAATGATTTGATAA
454229 T
1 T
454230 GATTACTAAT
Statistics
Matches: 53, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 8 0.15
12 1 0.02
13 12 0.23
14 32 0.60
ACGTcount: A:0.43, C:0.02, G:0.12, T:0.42
Consensus pattern (14 bp):
TAATGATTTGATAA
Found at i:454209 original size:52 final size:49
Alignment explanation
Indices: 454149--454257 Score: 164
Period size: 52 Copynumber: 2.2 Consensus size: 49
454139 TATTAATATT
* *
454149 TAATGATTTGATACTAATGATTTAGTAATGATTAGTAATAATGAAATTATAA
1 TAATGATTTGATACTAATGATTTAATAATGATTACTAATAAT--AATT-TAA
454201 TAATGATTTGATACTAATGATTTAATAATGATTACTAATAATAATTTAA
1 TAATGATTTGATACTAATGATTTAATAATGATTACTAATAATAATTTAA
*
454250 TTATGATT
1 TAATGATT
454258 AAATATTTAA
Statistics
Matches: 54, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
49 10 0.19
50 4 0.07
52 40 0.74
ACGTcount: A:0.43, C:0.03, G:0.11, T:0.43
Consensus pattern (49 bp):
TAATGATTTGATACTAATGATTTAATAATGATTACTAATAATAATTTAA
Found at i:454231 original size:11 final size:11
Alignment explanation
Indices: 454149--454262 Score: 75
Period size: 11 Copynumber: 9.2 Consensus size: 11
454139 TATTAATATT
454149 TAATGATTTGATA
1 TAATGATTT-A-A
*
454162 CTAATGATTTAG
1 -TAATGATTTAA
454174 TAATGATTAGTAA
1 TAATGATT--TAA
454187 TAATGAAATTATAA
1 TAATG--ATT-TAA
454201 TAATGATTTGATA
1 TAATGATTT-A-A
454214 CTAATGATTTAA
1 -TAATGATTTAA
454226 TAATGATTACTAA
1 TAATGATT--TAA
*
454239 TAATAATTTAA
1 TAATGATTTAA
* *
454250 TTATGATTAAA
1 TAATGATTTAA
454261 TA
1 TA
454263 TTTAAATAGA
Statistics
Matches: 83, Mismatches: 8, Indels: 21
0.74 0.07 0.19
Matches are distributed among these distances:
11 29 0.35
12 5 0.06
13 20 0.24
14 26 0.31
15 3 0.04
ACGTcount: A:0.45, C:0.03, G:0.11, T:0.42
Consensus pattern (11 bp):
TAATGATTTAA
Found at i:454277 original size:127 final size:126
Alignment explanation
Indices: 454039--454264 Score: 291
Period size: 127 Copynumber: 1.8 Consensus size: 126
454029 AAATTCATGT
*
454039 TGATTTAGTAATGATTAATAAAAATAAAATTATAATAATGATTTGATAATAATATTTTAGTAATG
1 TGATTTAGTAATGATTAATAAAAATAAAATTATAATAATGATTTGATAATAATATTTTAATAATG
* ** * * *
454104 ATATGATTTTCTAATGATTACTAATAATGATTTATTATTAATATTTAATGATTTGATACTAA
66 ATATGATCTAATAATAATTA-TAATAATGATTAAATATTAATATTTAATGATTTGATACTAA
* * * *
454166 TGATTTAGTAATGATTAGTAATAATGAAATTATAATAATGATTTGATACTAATGA-TTTAATAAT
1 TGATTTAGTAATGATTAATAAAAATAAAATTATAATAATGATTTGATAATAAT-ATTTTAATAAT
*
454230 GAT-T-A-CTAATAATAATT-TAATTATGATTAAATATT
65 GATATGATCTAATAATAATTATAATAATGATTAAATATT
454265 TAAATAGAAT
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
122 15 0.17
124 8 0.09
125 1 0.01
126 1 0.01
127 60 0.70
128 1 0.01
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (126 bp):
TGATTTAGTAATGATTAATAAAAATAAAATTATAATAATGATTTGATAATAATATTTTAATAATG
ATATGATCTAATAATAATTATAATAATGATTAAATATTAATATTTAATGATTTGATACTAA
Found at i:454309 original size:16 final size:16
Alignment explanation
Indices: 454290--454327 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
454280 CAATTTAAAT
*
454290 TTTATAAATAGTTGAA
1 TTTATAAATAGTCGAA
*
454306 TTTATAACTAGTCGAA
1 TTTATAAATAGTCGAA
454322 TTTATA
1 TTTATA
454328 TTTATAAATA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (16 bp):
TTTATAAATAGTCGAA
Found at i:454333 original size:22 final size:23
Alignment explanation
Indices: 454305--454349 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
454295 AAATAGTTGA
*
454305 ATTTATAACTA-GTCGAATTTAT
1 ATTTATAAATATGTCGAATTTAT
*
454327 ATTTATAAATATTTCGAATTTAT
1 ATTTATAAATATGTCGAATTTAT
454350 TCTTTTTGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.49
Consensus pattern (23 bp):
ATTTATAAATATGTCGAATTTAT
Found at i:454409 original size:14 final size:15
Alignment explanation
Indices: 454378--454414 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
454368 AAAGACATGC
*
454378 ATATTTAATATTATA
1 ATATTTAATATAATA
454393 ATATTTAAT-TAATA
1 ATATTTAATATAATA
454407 ATATTTAA
1 ATATTTAA
454415 CATATGCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTTAATATAATA
Found at i:456904 original size:30 final size:34
Alignment explanation
Indices: 456868--456946 Score: 94
Period size: 36 Copynumber: 2.4 Consensus size: 34
456858 GCCCTTAAAC
*
456868 AACTAATAAATTA-TTCT-TT-T-ATATAACTTA
1 AACTAATAAACTACTTCTATTATAATATAACTTA
*
456898 AACTAATAAACTACTTTTTAATTATAATATAACTTA
1 AACTAATAAACTAC-TTCT-ATTATAATATAACTTA
456934 AACTAATAAACTA
1 AACTAATAAACTA
456947 ATTTACTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 12 0.29
32 3 0.07
34 2 0.05
35 1 0.02
36 23 0.56
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (34 bp):
AACTAATAAACTACTTCTATTATAATATAACTTA
Found at i:457027 original size:37 final size:36
Alignment explanation
Indices: 456986--457100 Score: 133
Period size: 38 Copynumber: 3.1 Consensus size: 36
456976 CAACAAACAA
456986 ATATAACTTAGAAACACAAACTAATTAAATATTTTTTAT
1 ATATAAC-TA-AAA-ACAAACTAATTAAATATTTTTTAT
* *
457025 ATATAACTAACAAACTAACTAATTAATTATTTTTTAAT
1 ATATAACTAA-AAACAAACTAATTAAATATTTTTT-AT
* *
457063 ATATAACTATCAAACAAACTAATTAAATA-ATTTTAT
1 ATATAACTA-AAAACAAACTAATTAAATATTTTTTAT
457099 AT
1 AT
457101 TTATCTATGA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
36 4 0.06
37 25 0.37
38 31 0.46
39 7 0.10
ACGTcount: A:0.50, C:0.10, G:0.01, T:0.39
Consensus pattern (36 bp):
ATATAACTAAAAACAAACTAATTAAATATTTTTTAT
Found at i:457068 original size:38 final size:37
Alignment explanation
Indices: 457001--457100 Score: 148
Period size: 38 Copynumber: 2.7 Consensus size: 37
456991 ACTTAGAAAC
457001 ACAAACTAATTAAATATTTTTTATATATAACTAACAA
1 ACAAACTAATTAAATATTTTTTATATATAACTAACAA
* * *
457038 ACTAACTAATTAATTATTTTTTAATATATAACTATCAA
1 ACAAACTAATTAAATATTTTTT-ATATATAACTAACAA
*
457076 ACAAACTAATTAAATA-ATTTTATAT
1 ACAAACTAATTAAATATTTTTTATAT
457101 TTATCTATGA
Statistics
Matches: 56, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
36 4 0.07
37 24 0.43
38 28 0.50
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (37 bp):
ACAAACTAATTAAATATTTTTTATATATAACTAACAA
Found at i:457163 original size:21 final size:21
Alignment explanation
Indices: 457110--457160 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
457100 TTTATCTATG
*
457110 ATATAACTTAAACTACCAATA
1 ATATAACTTAAACTACAAATA
457131 ATATAACTTAAACTAACAAACTA
1 ATATAACTTAAACT-ACAAA-TA
457154 AT-TAACT
1 ATATAACT
457161 AAATTTTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 14 0.52
22 9 0.33
23 4 0.15
ACGTcount: A:0.53, C:0.18, G:0.00, T:0.29
Consensus pattern (21 bp):
ATATAACTTAAACTACAAATA
Found at i:457222 original size:17 final size:18
Alignment explanation
Indices: 457193--457226 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
457183 AACAAACTAA
457193 TAATTTAAAATAATAAAC
1 TAATTTAAAATAATAAAC
457211 TAATTT-AAATAATAAA
1 TAATTTAAAATAATAAA
457227 AAATTATCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (18 bp):
TAATTTAAAATAATAAAC
Found at i:458644 original size:12 final size:12
Alignment explanation
Indices: 458627--458652 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
458617 TGATTTCTTT
458627 TTTATTATTTTA
1 TTTATTATTTTA
458639 TTTATTATTTTA
1 TTTATTATTTTA
458651 TT
1 TT
458653 AAACCAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (12 bp):
TTTATTATTTTA
Found at i:459900 original size:100 final size:100
Alignment explanation
Indices: 459727--459925 Score: 371
Period size: 100 Copynumber: 2.0 Consensus size: 100
459717 GATGTTGCAG
*
459727 CACAGATAATATGATCCCCTTGTTCAAATACGAGAACGTCGAAACGCGTTTGAACCGACGGAGCT
1 CACAGATAATATGATCCCCTCGTTCAAATACGAGAACGTCGAAACGCGTTTGAACCGACGGAGCT
* *
459792 CTGAAGGCAGCAAAGTAGGAGCTTCTCTAGGTCAT
66 CTGAAGGCAGCAAAGAAGGAGCTTCTCTAAGTCAT
459827 CACAGATAATATGATCCCCTCGTTCAAATACGAGAACGTCGAAACGCGTTTGAACCGACGGAGCT
1 CACAGATAATATGATCCCCTCGTTCAAATACGAGAACGTCGAAACGCGTTTGAACCGACGGAGCT
459892 CTGAAGGCAGCAAAGAAGGAGCTTCTCTAAGTCA
66 CTGAAGGCAGCAAAGAAGGAGCTTCTCTAAGTCA
459926 AACGAACAAG
Statistics
Matches: 96, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.32, C:0.24, G:0.24, T:0.21
Consensus pattern (100 bp):
CACAGATAATATGATCCCCTCGTTCAAATACGAGAACGTCGAAACGCGTTTGAACCGACGGAGCT
CTGAAGGCAGCAAAGAAGGAGCTTCTCTAAGTCAT
Found at i:460664 original size:26 final size:26
Alignment explanation
Indices: 460613--460693 Score: 65
Period size: 26 Copynumber: 3.0 Consensus size: 26
460603 ACCCGAACCG
* **
460613 AACCGAATCAAAAAATGAAGCC-TTTA
1 AACCGAACCAAAAACCGAA-CCGTTTA
460639 AACCGAACCAAAAACCGAACCGTTTA
1 AACCGAACCAAAAACCGAACCGTTTA
* *
460665 AAGCCAAACCGAACCGAACCGAACCGTTT
1 AA-CCGAACC-AA--AAACCGAACCGTTT
460694 TACTCGGTTC
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
25 2 0.04
26 22 0.49
27 6 0.13
28 2 0.04
30 13 0.29
ACGTcount: A:0.44, C:0.28, G:0.14, T:0.14
Consensus pattern (26 bp):
AACCGAACCAAAAACCGAACCGTTTA
Found at i:461371 original size:18 final size:18
Alignment explanation
Indices: 461348--461382 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
461338 GTCATAACCC
461348 GACCCGACCCGTTGACCT
1 GACCCGACCCGTTGACCT
461366 GACCCGACCCGTTGACC
1 GACCCGACCCGTTGACC
461383 GATGAACGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.46, G:0.23, T:0.14
Consensus pattern (18 bp):
GACCCGACCCGTTGACCT
Found at i:463896 original size:12 final size:12
Alignment explanation
Indices: 463881--463938 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
463871 GATACATGAC
463881 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
463893 CTGATTTCTGAT
1 CTGAATTCTGTT
*
463905 CTGGATTCTGTT
1 CTGAATTCTGTT
463917 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
463929 TTGATTTCTG
1 CTGAATTCTG
463939 ATATCTCCGT
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 38 1.00
ACGTcount: A:0.14, C:0.16, G:0.19, T:0.52
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:466603 original size:38 final size:37
Alignment explanation
Indices: 466535--466658 Score: 159
Period size: 33 Copynumber: 3.4 Consensus size: 37
466525 ATTTTGTTTG
*
466535 GGTCGGTTCGGG-TTTTTTAAGTGTGATATTCGGGTC
1 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
*
466571 GAGTCGGGTCGGGTTTTTTTAAGTGTGGTATTC--G--
1 G-GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
*
466605 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTTGGGTC
1 GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
466642 GGGTCGGGTTCGGGTTT
1 -GGTCGGG-TCGGGTTT
466659 AGGGTGAAAA
Statistics
Matches: 76, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
33 29 0.38
34 1 0.01
35 1 0.01
36 2 0.03
37 10 0.13
38 25 0.33
39 8 0.11
ACGTcount: A:0.10, C:0.10, G:0.40, T:0.41
Consensus pattern (37 bp):
GGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
Found at i:467546 original size:22 final size:22
Alignment explanation
Indices: 467520--467572 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
467510 TCTGACTATT
467520 TAATTATTGTATATTTTTAATA
1 TAATTATTGTATATTTTTAATA
*
467542 TAATTATGGTATATTTTTAATA
1 TAATTATTGTATATTTTTAATA
467564 TAATTATTG
1 TAATTATTG
467573 ATGTTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (22 bp):
TAATTATTGTATATTTTTAATA
Found at i:469858 original size:16 final size:16
Alignment explanation
Indices: 469839--469873 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
469829 ATTAAATAAA
469839 TATATATTTAATCAAC
1 TATATATTTAATCAAC
*
469855 TATATTTTTAATCAAC
1 TATATATTTAATCAAC
469871 TAT
1 TAT
469874 TTCTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.00, T:0.49
Consensus pattern (16 bp):
TATATATTTAATCAAC
Found at i:469933 original size:71 final size:71
Alignment explanation
Indices: 469800--469933 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 71
469790 TATTTTAGAT
* * *
469800 TATTTCTTAAAATAATATTTGTATACCTTATTAAATAAATATATATTTAATCAACTATATTTTTA
1 TATTTCTTAAAATAATATTTATATACCTTATTAAATAAATATACATTTAATCAACTAAATTTTTA
469865 ATCAAC
66 ATCAAC
*
469871 TATTTCTTAAAATAATATTTATATACCTTA-TAAATAAATATACCTTTAA-CGAACTTAAATTTT
1 TATTTCTTAAAATAATATTTATATACCTTATTAAATAAATATACATTTAATC-AAC-TAAATTTT
469934 GCTTGGTTTT
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
69 1 0.02
70 20 0.35
71 36 0.63
ACGTcount: A:0.43, C:0.10, G:0.01, T:0.46
Consensus pattern (71 bp):
TATTTCTTAAAATAATATTTATATACCTTATTAAATAAATATACATTTAATCAACTAAATTTTTA
ATCAAC
Found at i:479376 original size:28 final size:28
Alignment explanation
Indices: 479336--479389 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
479326 TTTACATCTA
479336 GTAGTTCACTTGATCACTATATTCTGGT
1 GTAGTTCACTTGATCACTATATTCTGGT
*
479364 GTAGTTCACTTGATCATTATATTCTG
1 GTAGTTCACTTGATCACTATATTCTG
479390 TCCAATTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
GTAGTTCACTTGATCACTATATTCTGGT
Found at i:489345 original size:64 final size:62
Alignment explanation
Indices: 489277--489436 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 62
489267 ATTCAAGGTT
* *
489277 TATCGATGCATATGAGGTGTATCGATGCACTCCT-TTAAAATAAAAACATCGAATGTCA-TTAGT
1 TATCGATGCATA-GA-GTGCATCGATGCAC-CCTCTTAAAATAAAAACATCGAATGACATTTA-T
489340 G
62 G
* * *
489341 TATCGATGCACAAGTAGTGCATCGATGCACCCTCTTAAAATACAAACATCGAATGAGATTTATG
1 TATCGATGCA-TAG-AGTGCATCGATGCACCCTCTTAAAATAAAAACATCGAATGACATTTATG
*
489405 TACCGATGCATAGATTGTGCATCGATGCACCC
1 TATCGATGCATAGA--GTGCATCGATGCACCC
489437 GTTAAGGTAT
Statistics
Matches: 83, Mismatches: 7, Indels: 12
0.81 0.07 0.12
Matches are distributed among these distances:
62 1 0.01
63 5 0.06
64 72 0.87
65 5 0.06
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (62 bp):
TATCGATGCATAGAGTGCATCGATGCACCCTCTTAAAATAAAAACATCGAATGACATTTATG
Found at i:490024 original size:18 final size:18
Alignment explanation
Indices: 490001--490069 Score: 75
Period size: 18 Copynumber: 3.7 Consensus size: 18
489991 AGGGATTATC
*
490001 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGAACAT
* * *
490019 AGTGGTTCTTCAGAATAAT
1 AGTGGTCCTTCGGAA-CAT
*
490038 CAGTGGTCCTTTGGAACAT
1 -AGTGGTCCTTCGGAACAT
490057 AGTGGTCCTTCGG
1 AGTGGTCCTTCGG
490070 GACAAATATT
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 24 0.60
19 4 0.10
20 12 0.30
ACGTcount: A:0.20, C:0.19, G:0.29, T:0.32
Consensus pattern (18 bp):
AGTGGTCCTTCGGAACAT
Found at i:490324 original size:2 final size:2
Alignment explanation
Indices: 490317--490449 Score: 234
Period size: 2 Copynumber: 67.5 Consensus size: 2
490307 AATGCATTGT
*
490317 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
490359 TA TA TA TA TA TA GA -A TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
490400 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
490441 TA TA TA TA T
1 TA TA TA TA T
490450 GCCTCACTAA
Statistics
Matches: 126, Mismatches: 3, Indels: 4
0.95 0.02 0.03
Matches are distributed among these distances:
1 2 0.02
2 124 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:495434 original size:2 final size:2
Alignment explanation
Indices: 495427--495465 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
495417 CATGAGTTAG
* *
495427 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AC AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
495466 GGAGTTTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:496202 original size:31 final size:31
Alignment explanation
Indices: 496114--496265 Score: 87
Period size: 31 Copynumber: 5.0 Consensus size: 31
496104 AGTCGAGGGT
* * *
496114 TTTACCTA-TTTCTTTCGAGACATATGGATAG
1 TTTACCTAGGTTCTTT-GGGACCTATGGATAG
* * * ** * *
496145 TATACCTATGTTATAAGGAACATATGGATAG
1 TTTACCTAGGTTCTTTGGGACCTATGGATAG
*
496176 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACCTATGGATAG
* * * ** *
496207 -TTGCCGAGGTACTTTATGACCTCTGGATAG
1 TTTACCTAGGTTCTTTGGGACCTATGGATAG
* * *
496237 -TTACC-AGGGTCTTTGTGACCTCTGGATAG
1 TTTACCTAGGTTCTTTGGGACCTATGGATAG
496266 GTCCTTCGGG
Statistics
Matches: 94, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
29 21 0.22
30 27 0.29
31 43 0.46
32 3 0.03
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACCTATGGATAG
Found at i:496255 original size:29 final size:29
Alignment explanation
Indices: 496169--496265 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 29
496159 AAGGAACATA
* * *
496169 TGGATAGTTTACCTAGGTTCTTTGGGACCTA
1 TGGATAG-TTACC-AGGGTCTTTGTGACCTC
* * *
496200 TGGACAGTTGCC-GAGGTACTTTATGACCTC
1 TGGATAGTTACCAG-GGT-CTTTGTGACCTC
496230 TGGATAGTTACCAGGGTCTTTGTGACCTC
1 TGGATAGTTACCAGGGTCTTTGTGACCTC
496259 TGGATAG
1 TGGATAG
496266 GTCCTTCGGG
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
28 1 0.02
29 20 0.37
30 26 0.48
31 7 0.13
ACGTcount: A:0.20, C:0.19, G:0.28, T:0.34
Consensus pattern (29 bp):
TGGATAGTTACCAGGGTCTTTGTGACCTC
Found at i:498407 original size:23 final size:22
Alignment explanation
Indices: 498363--498410 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 22
498353 AAAAGTGTGT
*
498363 AAGGTTATGTGAATATTCTTTA
1 AAGGTTATGTGAATATTATTTA
498385 AAGGTTATGTTGAATCA-TATTTA
1 AAGGTTATG-TGAAT-ATTATTTA
498408 AAG
1 AAG
498411 AAGATTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 9 0.39
23 13 0.57
24 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.19, T:0.42
Consensus pattern (22 bp):
AAGGTTATGTGAATATTATTTA
Found at i:498552 original size:2 final size:2
Alignment explanation
Indices: 498541--498576 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
498531 CATGATATGA
498541 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
498577 AAGGAAAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:499558 original size:64 final size:63
Alignment explanation
Indices: 499487--499626 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 63
499477 TTGTTTAAGG
* *
499487 TGCATCGATGCACATGCAGTACATCGATGCAT-TAATTTAAAAAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCACAAGCAGTACATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAGGATTTA
* * * * * *
499551 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAGGATTTA
1 TGCATCGATGCACAAGCAGTACATCGATGCAT-CCAATTAAAAAAAAACATCGAATAGGATTTA
499615 TGCATCGATGCA
1 TGCATCGATGCA
499627 TGGTGTAGTG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
64 59 0.89
65 6 0.09
66 1 0.02
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCACAAGCAGTACATCGATGCATCCAATTAAAAAAAAACATCGAATAGGATTTA
Found at i:500815 original size:31 final size:31
Alignment explanation
Indices: 500721--500828 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
500711 AGTCGAGGGT
* *
500721 TTTACCTATG-TCTTTCGAGACATATGGACAG
1 TTTACCTAGGTTCTTT-GGGACATATGGACAG
* * * ** *
500752 TATACCTATGTTATAAGGAACATATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
*
500783 TTTACCTAGGTTCTTTGGGACCTATGGACAG
1 TTTACCTAGGTTCTTTGGGACATATGGACAG
* *
500814 -TTGCCGAGGTTCTTT
1 TTTACCTAGGTTCTTT
500829 ATGACCTCTA
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
30 13 0.21
31 46 0.75
32 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (31 bp):
TTTACCTAGGTTCTTTGGGACATATGGACAG
Found at i:500835 original size:30 final size:31
Alignment explanation
Indices: 500774--500835 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
500764 ATAAGGAACA
* *
500774 TATGGACAGTTTACCTAGGTTCTTTGGGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
* *
500805 TATGGACAG-TTGCCGAGGTTCTTTATGACC
1 TATGGACAGTTTACCGAGGTTCTTTAGGACC
500835 T
1 T
500836 CTAGATAGTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.35
Consensus pattern (31 bp):
TATGGACAGTTTACCGAGGTTCTTTAGGACC
Found at i:506008 original size:18 final size:20
Alignment explanation
Indices: 505960--506010 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 20
505950 ACCATGCATG
505960 TAGTATCGATACTCCCTAGTC
1 TAGTATCGATACTCCCTA-TC
* *
505981 AAGTAACGATACTCCCT-T-
1 TAGTATCGATACTCCCTATC
505999 TAGTATCGATAC
1 TAGTATCGATAC
506011 CAAAAATAGC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 10 0.38
19 1 0.04
21 15 0.58
ACGTcount: A:0.29, C:0.25, G:0.14, T:0.31
Consensus pattern (20 bp):
TAGTATCGATACTCCCTATC
Found at i:506721 original size:22 final size:23
Alignment explanation
Indices: 506687--506745 Score: 70
Period size: 22 Copynumber: 2.7 Consensus size: 23
506677 ACTTGCTATG
506687 AAAGAGGGGGAAAGA-AGAGAGAA
1 AAAGAGGGGGAAAGATAGAGA-AA
506710 AAAGA-GGGGAAA-ATAGAGAAA
1 AAAGAGGGGGAAAGATAGAGAAA
* *
506731 AAAGATGAGGAAAGA
1 AAAGAGGGGGAAAGA
506746 GGATAAGAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 8 0.25
22 18 0.56
23 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.37, T:0.03
Consensus pattern (23 bp):
AAAGAGGGGGAAAGATAGAGAAA
Found at i:512027 original size:45 final size:45
Alignment explanation
Indices: 511978--512089 Score: 107
Period size: 51 Copynumber: 2.4 Consensus size: 45
511968 CCCGAAGAAT
*
511978 AGATCCATGAAGAACCCGATTTAGGTGAGACCCAAACCCAGGTAG
1 AGATCCATGAAGAACCCGATTTAGGTGAGACCCAAACCCAGGAAG
* * *
512023 AGATCTGTGATGGTGAAGAACACGATTTAGGTGAGACTCAAACCCAGGAAG
1 AGATC---CA---TGAAGAACCCGATTTAGGTGAGACCCAAACCCAGGAAG
* * *
512074 AAATCCGTGACGAACC
1 AGATCCATGAAGAACC
512090 TATTTTCGGC
Statistics
Matches: 52, Mismatches: 9, Indels: 12
0.71 0.12 0.16
Matches are distributed among these distances:
45 12 0.23
48 1 0.02
51 39 0.75
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (45 bp):
AGATCCATGAAGAACCCGATTTAGGTGAGACCCAAACCCAGGAAG
Found at i:513472 original size:158 final size:159
Alignment explanation
Indices: 513183--513497 Score: 607
Period size: 158 Copynumber: 2.0 Consensus size: 159
513173 GATGTCGTCA
513183 GGGCACTAATACCAAATTGAGGTAAAATGTTAGAGAAAAATAAATCAATATTGATACCCTATTTA
1 GGGCACTAATACCAAATTGAGGTAAAATGTTAGAGAAAAATAAATCAATATTGATACCCTATTTA
513248 GGGTGTCAATACTTCTACTTTGTATAATATCAATACTCCTTGAGTATTGGTACCAAAATTAACTA
66 GGGTGTCAATACTTCTACTTTGTATAATATCAATACTCCTTGAGTATTGGTACCAAAATTAACTA
513313 TTGGAATTTACAATTTGATGCTGGTATAT
131 TTGGAATTTACAATTTGATGCTGGTATAT
513342 GGGCACTAATACCAAATTGAGGT-AAATGTTAGAG-AAAATAAATCAATATTGATACCCTTATTT
1 GGGCACTAATACCAAATTGAGGTAAAATGTTAGAGAAAAATAAATCAATATTGATACCC-TATTT
513405 AGGGTGTCAATACTTCTACTTTGTATAATATCAATACTCCTTGAGTATTGGTACCAAAATTAACT
65 AGGGTGTCAATACTTCTACTTTGTATAATATCAATACTCCTTGAGTATTGGTACCAAAATTAACT
513470 ATTGGAATTTACAATTTGATGCTGGTAT
130 ATTGGAATTTACAATTTGATGCTGGTAT
513498 TGATACTCGA
Statistics
Matches: 155, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
157 23 0.15
158 109 0.70
159 23 0.15
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (159 bp):
GGGCACTAATACCAAATTGAGGTAAAATGTTAGAGAAAAATAAATCAATATTGATACCCTATTTA
GGGTGTCAATACTTCTACTTTGTATAATATCAATACTCCTTGAGTATTGGTACCAAAATTAACTA
TTGGAATTTACAATTTGATGCTGGTATAT
Found at i:515253 original size:29 final size:30
Alignment explanation
Indices: 515212--515275 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
515202 TTAAAATATT
*
515212 TTTTTATCAAAATAAAT-TTATAAAGTTATA
1 TTTTTATCAAAATAAATATT-TAAAGTAATA
* *
515242 TTTTTCTC-AAATAGATATTTAAAGTAATA
1 TTTTTATCAAAATAAATATTTAAAGTAATA
515271 TTTTT
1 TTTTT
515276 GCAAATAGGT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 21 0.70
30 9 0.30
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (30 bp):
TTTTTATCAAAATAAATATTTAAAGTAATA
Found at i:526881 original size:20 final size:20
Alignment explanation
Indices: 526856--526904 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
526846 TGGCCACCAA
526856 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
526876 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
*
526896 CCCTCCACT
1 GCCTCCACT
526905 CACAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.45, G:0.12, T:0.33
Consensus pattern (20 bp):
GCCTCCACTAGTCCTTGTCT
Found at i:527197 original size:25 final size:25
Alignment explanation
Indices: 527137--527189 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
527127 TCTGTTTTGA
*
527137 ATTTTTAATAG-TTTTTATTTATTT
1 ATTTTCAATAGTTTTTTATTTATTT
527161 ATTTTCAATAGTTTTTTA-TTA-TT
1 ATTTTCAATAGTTTTTTATTTATTT
527184 ATTTTC
1 ATTTTC
527190 GAAATAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
24 13 0.48
25 6 0.22
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (25 bp):
ATTTTCAATAGTTTTTTATTTATTT
Found at i:528886 original size:16 final size:16
Alignment explanation
Indices: 528865--528904 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
528855 TTTTTTGTAT
*
528865 TTTTTTTCTTTCG-TTA
1 TTTTTTTATTT-GTTTA
528881 TTTTTTTATTTGTTTA
1 TTTTTTTATTTGTTTA
528897 TTTTTTTA
1 TTTTTTTA
528905 CTAACTTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 1 0.05
16 21 0.95
ACGTcount: A:0.10, C:0.05, G:0.05, T:0.80
Consensus pattern (16 bp):
TTTTTTTATTTGTTTA
Found at i:533476 original size:6 final size:6
Alignment explanation
Indices: 533465--533505 Score: 59
Period size: 6 Copynumber: 7.0 Consensus size: 6
533455 ATCCTAAGTC
533465 GAAAAA GAAAAA GAAAAA -AAAAA GAACAAA -AAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAA-AAA GAAAAA GAAAAA
533506 TGTTTAGGGT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 8 0.25
6 21 0.66
7 3 0.09
ACGTcount: A:0.85, C:0.02, G:0.12, T:0.00
Consensus pattern (6 bp):
GAAAAA
Found at i:534511 original size:80 final size:80
Alignment explanation
Indices: 534412--534686 Score: 194
Period size: 80 Copynumber: 3.3 Consensus size: 80
534402 ACAACATTGG
*
534412 ATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
1 ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
534477 TTTCATTCAGAGCCA
66 TTTCATTCAGAGCCA
* * ** *
534492 ATTTCAACTTCAC-GACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCAC-GACGAA
1 ATTTCAACTTCACAG-CGAAGGATA-T---C-C---A-ATTCA-AAGCTCAACTCCACAG-CGAA
* * *
534555 --GGATAT--C-GTGCTCA--CA-AACAACA
54 GGGGCT-TCCCAGT-TTCATTCAGAGC--CA
*
534578 TTGGATTTCAACTTTACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTC
1 ----ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTC
534643 CCAGTTTCATTCAGAGCCA
62 CCAGTTTCATTCAGAGCCA
534662 ATTTCAACTTCAC-GACGAAGGATAT
1 ATTTCAACTTCACAG-CGAAGGATAT
534687 TGGACTCAAA
Statistics
Matches: 145, Mismatches: 19, Indels: 62
0.64 0.08 0.27
Matches are distributed among these distances:
79 2 0.01
80 57 0.39
81 7 0.05
82 4 0.03
83 4 0.03
84 7 0.05
85 6 0.04
86 7 0.05
87 4 0.03
88 4 0.03
89 7 0.05
90 35 0.24
91 1 0.01
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (80 bp):
ATTTCAACTTCACAGCGAAGGATATCCAATTCAAAGCTCAACTCCACAGCGAAGGGGCTTCCCAG
TTTCATTCAGAGCCA
Found at i:534919 original size:170 final size:170
Alignment explanation
Indices: 534315--534904 Score: 1126
Period size: 170 Copynumber: 3.5 Consensus size: 170
534305 GGTTCTAGCT
* *
534315 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
534380 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
66 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
534445 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
131 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
534485 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
534550 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
66 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
534615 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
131 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
*
534655 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCAAAACATCCACGATTTCAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
534720 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
66 ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
*
534785 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAATTTCATTC
131 AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
* *
534825 AGAGCCAATTTCAACTTCATGACGAAGGATATTGGACTCGAAACATCCACGATTTTAACTTCACG
1 AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
534890 ACGAAGGATATCGTG
66 ACGAAGGATATCGTG
534905 TCCACCAGCA
Statistics
Matches: 413, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
170 413 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (170 bp):
AGAGCCAATTTCAACTTCACGACGAAGGATATTGGACTCGAAACATCCACGATTTCAACTTCACG
ACGAAGGATATCGTGCTCACAAACAACATTGGATTTCAACTTTACAGCGAAGGATATCCAATTCA
AAGCTCAACTCCACAGCGAAGGGGCTTCCCAGTTTCATTC
Found at i:535551 original size:20 final size:20
Alignment explanation
Indices: 535526--535574 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
535516 TGGCCACCAA
535526 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
535546 GCCTCCACTAGTCCTTGTCT
1 GCCTCCACTAGTCCTTGTCT
*
535566 CCCTCCACT
1 GCCTCCACT
535575 CACAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.10, C:0.45, G:0.12, T:0.33
Consensus pattern (20 bp):
GCCTCCACTAGTCCTTGTCT
Found at i:535870 original size:25 final size:25
Alignment explanation
Indices: 535810--535862 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
535800 TCTGTTTTGA
*
535810 ATTTTTAATAG-TTTTTATTTATTT
1 ATTTTCAATAGTTTTTTATTTATTT
535834 ATTTTCAATAGTTTTTTA-TTA-TT
1 ATTTTCAATAGTTTTTTATTTATTT
535857 ATTTTC
1 ATTTTC
535863 GAAATAGTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 8 0.30
24 13 0.48
25 6 0.22
ACGTcount: A:0.25, C:0.04, G:0.04, T:0.68
Consensus pattern (25 bp):
ATTTTCAATAGTTTTTTATTTATTT
Found at i:537785 original size:85 final size:85
Alignment explanation
Indices: 537642--537813 Score: 301
Period size: 85 Copynumber: 2.0 Consensus size: 85
537632 AGTTAAAAAA
*
537642 ATAAGTGCATTTGGTCCTTTATATTATCAATCTGTTTGGTTTTAATCTATTAGTCATTGACTTTC
1 ATAAGTGCATTTGGTCCTTTATATTATCAATCTGTTTGGTTTTAATCTATCAGTCATTGACTTTC
537707 GTTAACACCTTAATAAGAGT
66 GTTAACACCTTAATAAGAGT
*
537727 ATAAGTGCATTTGGTCCTTTATATTATCAAT-TCGTTTGGTTTTAATCTATCAGTCATTGATTTT
1 ATAAGTGCATTTGGTCCTTTATATTATCAATCT-GTTTGGTTTTAATCTATCAGTCATTGACTTT
*
537791 CGTTAACACCTTAATAGGAGT
65 CGTTAACACCTTAATAAGAGT
537812 AT
1 AT
537814 TATGTAGAAA
Statistics
Matches: 83, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
84 1 0.01
85 82 0.99
ACGTcount: A:0.27, C:0.14, G:0.15, T:0.45
Consensus pattern (85 bp):
ATAAGTGCATTTGGTCCTTTATATTATCAATCTGTTTGGTTTTAATCTATCAGTCATTGACTTTC
GTTAACACCTTAATAAGAGT
Found at i:542928 original size:15 final size:15
Alignment explanation
Indices: 542908--542942 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
542898 TGCTCACCAT
542908 TCGAACAAACTTCAC
1 TCGAACAAACTTCAC
*
542923 TCGAACAAGCTTCAC
1 TCGAACAAACTTCAC
542938 TCGAA
1 TCGAA
542943 GAGCCTTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.37, C:0.31, G:0.11, T:0.20
Consensus pattern (15 bp):
TCGAACAAACTTCAC
Found at i:543733 original size:117 final size:117
Alignment explanation
Indices: 543611--543862 Score: 378
Period size: 117 Copynumber: 2.2 Consensus size: 117
543601 CTTGGCTTTC
* * * * *
543611 GCACCGAGCTTTACTTTGGTGGTGCAATCTCGCACCTTGTGTTGTCCACCGCATTGGAAACACTT
1 GCACCGAGCTTTGCTTTGGTGGTACAATCTCGCACCTTGTGTTCTCCACCACATCGGAAACACTT
543676 CAACGGCTCTCGCTTCTTTACCCTCGGCTTAGTTGCTTCGCCACACGCATTG
66 CAACGGCTCTCGCTTCTTTACCCTCGGCTTAGTTGCTTCGCCACACGCATTG
* ** ** *
543728 TCACCGAGCCCTGCTTTATTGGTACAATCTCGCACCTTGTGTTCTCCATCACATCGGAAACACTT
1 GCACCGAGCTTTGCTTTGGTGGTACAATCTCGCACCTTGTGTTCTCCACCACATCGGAAACACTT
* * *
543793 CAATGGCTCTCGCTTCTTTATCCTCGGCTTAGTTGCTTCGCCACTCGCATTG
66 CAACGGCTCTCGCTTCTTTACCCTCGGCTTAGTTGCTTCGCCACACGCATTG
543845 GCACCGAGCTTTGCTTTG
1 GCACCGAGCTTTGCTTTG
543863 TTTGGGCAAC
Statistics
Matches: 117, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
117 117 1.00
ACGTcount: A:0.16, C:0.32, G:0.20, T:0.32
Consensus pattern (117 bp):
GCACCGAGCTTTGCTTTGGTGGTACAATCTCGCACCTTGTGTTCTCCACCACATCGGAAACACTT
CAACGGCTCTCGCTTCTTTACCCTCGGCTTAGTTGCTTCGCCACACGCATTG
Found at i:543909 original size:117 final size:116
Alignment explanation
Indices: 543630--543939 Score: 347
Period size: 117 Copynumber: 2.6 Consensus size: 116
543620 TTTACTTTGG
* * * * * *
543630 TGGTGCAATCTCGCACCTTGTGTTGTCCACCGCATTGGAAACACTTCAACGGCTCTCGCTTCTTT
1 TGGTACAATCTCGCACCTTGTG-TCTCCATCACATAGGAAACACTTCAATGGCTCTCGCTTCTTT
*
543695 ACCCTCGGCTTAGTTGCTTCGCCACACGCATTGTCACCGAGCCCTGCTTTAT
65 ACCCTCGGCTTAGTTGCTTCGCCACACGCATTGGCACCGAGCCCTGCTTTAT
*
543747 TGGTACAATCTCGCACCTTGTGTTCTCCATCACATCGGAAACACTTCAATGGCTCTCGCTTCTTT
1 TGGTACAATCTCGCACCTTGTG-TCTCCATCACATAGGAAACACTTCAATGGCTCTCGCTTCTTT
* * ** *
543812 ATCCTCGGCTTAGTTGCTTCGCCACTCGCATTGGCACCGAGCTTTGCTTTGTT
65 ACCCTCGGCTTAGTTGCTTCGCCACACGCATTGGCACCGAGCCCTGCTTT-AT
* * * * * * * * *
543865 TGG-GCAACTCTTGGC-CCTATGTG-CTCCTTGACATATGAAGCACTTCAGTGGATCTCGCTTGT
1 TGGTACAA-TC-TCGCACCT-TGTGTCTCCATCACATAGGAAACACTTCAATGGCTCTCGCTTCT
543927 TTACCCTCGGCTT
63 TTACCCTCGGCTT
543940 TCCTGCACCA
Statistics
Matches: 166, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
117 150 0.90
118 9 0.05
119 7 0.04
ACGTcount: A:0.16, C:0.31, G:0.20, T:0.33
Consensus pattern (116 bp):
TGGTACAATCTCGCACCTTGTGTCTCCATCACATAGGAAACACTTCAATGGCTCTCGCTTCTTTA
CCCTCGGCTTAGTTGCTTCGCCACACGCATTGGCACCGAGCCCTGCTTTAT
Found at i:547970 original size:17 final size:16
Alignment explanation
Indices: 547950--547993 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
547940 CGGATGTTCT
*
547950 GGGTACCCGAATTTTAC
1 GGGTACCCGAATTGT-C
*
547967 GGGTACCCGTA-TGTC
1 GGGTACCCGAATTGTC
547982 GGGTACCCGAAT
1 GGGTACCCGAAT
547994 ACTCGGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 11 0.48
16 2 0.09
17 10 0.43
ACGTcount: A:0.20, C:0.25, G:0.30, T:0.25
Consensus pattern (16 bp):
GGGTACCCGAATTGTC
Found at i:554868 original size:17 final size:17
Alignment explanation
Indices: 554848--554891 Score: 70
Period size: 18 Copynumber: 2.5 Consensus size: 17
554838 TTGTTCCTCT
554848 TAATTTATTGTTAATTA
1 TAATTTATTGTTAATTA
554865 TAATTTTATTGTTAATTA
1 TAA-TTTATTGTTAATTA
*
554883 TACTTTATT
1 TAATTTATT
554892 CTTCTTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.36
18 16 0.64
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (17 bp):
TAATTTATTGTTAATTA
Found at i:557442 original size:37 final size:34
Alignment explanation
Indices: 557397--557467 Score: 106
Period size: 37 Copynumber: 2.0 Consensus size: 34
557387 AACATCTACC
557397 AAACTTTACCAAACTTTGAAAAAACATTTTTCAAAG
1 AAACTTTACCAAACTTTG-AAAAACA-TTTTCAAAG
*
557433 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAAC-TTTACCAAACTTTGAAAAACATTTTCAAAG
557468 TTGGTTGTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
35 9 0.27
36 10 0.30
37 14 0.42
ACGTcount: A:0.46, C:0.18, G:0.06, T:0.30
Consensus pattern (34 bp):
AAACTTTACCAAACTTTGAAAAACATTTTCAAAG
Found at i:561838 original size:15 final size:15
Alignment explanation
Indices: 561818--561849 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
561808 CCAAACTTTG
*
561818 AAAAAACATTTTTCA
1 AAAAAACATTTATCA
561833 AAAAAACATTTATCA
1 AAAAAACATTTATCA
561848 AA
1 AA
561850 CTTTGAAAAC
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:0.59, C:0.12, G:0.00, T:0.28
Consensus pattern (15 bp):
AAAAAACATTTATCA
Found at i:561864 original size:36 final size:36
Alignment explanation
Indices: 561790--561869 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 36
561780 ACTCATTCTT
*
561790 ATTTTC-AACAAACATCTACCAAACTTTGAAAAAAC
1 ATTTTCAAAAAAACATCTACCAAACTTTGAAAAAAC
* * *
561825 ATTTTTCAAAAAAACATTTATCAAACTTTG-AAAACC
1 A-TTTTCAAAAAAACATCTACCAAACTTTGAAAAAAC
561861 ATTTTCAAA
1 ATTTTCAAA
561870 GTTGGTTGCC
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
35 9 0.23
36 11 0.28
37 19 0.49
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (36 bp):
ATTTTCAAAAAAACATCTACCAAACTTTGAAAAAAC
Found at i:563412 original size:2 final size:2
Alignment explanation
Indices: 563354--563397 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
563344 AATTTATCAA
563354 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
563396 AT
1 AT
563398 TTAAGTATCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:566025 original size:2 final size:2
Alignment explanation
Indices: 566018--566044 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
566008 GGCGTCAATT
566018 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
566045 TTCCCATACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:580989 original size:2 final size:2
Alignment explanation
Indices: 580977--581008 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
580967 CCCAATGGAA
580977 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
581009 ATAAAAAGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:581405 original size:15 final size:15
Alignment explanation
Indices: 581385--581466 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
581375 TTCCAGAAAA
581385 TGAATTACTGGAATT
1 TGAATTACTGGAATT
581400 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
581415 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
581430 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
581445 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
581459 TGAATTAC
1 TGAATTAC
581467 ATTTCTGTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:581419 original size:30 final size:30
Alignment explanation
Indices: 581385--581466 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
581375 TTCCAGAAAA
**
581385 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
581415 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
581445 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
581467 ATTTCTGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:581444 original size:45 final size:44
Alignment explanation
Indices: 581380--581466 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
581370 TGGTTTTCCA
**
581380 GAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTG
581425 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
581467 ATTTCTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:581472 original size:20 final size:20
Alignment explanation
Indices: 581449--581518 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
581439 GGAATTTGAA
581449 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
581469 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
581489 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
581509 TTCTGGAAAA
1 TTCTGGAAAA
581519 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:581742 original size:29 final size:27
Alignment explanation
Indices: 581686--581751 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
581676 TTTACTAAAA
* *
581686 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAAAATTAT
581714 TCATTATTAAATATATAAAAAAAATTTAT
1 T-ATTATTAAATATATAAAAAAAA-TTAT
581743 TATATATTA
1 TAT-TATTA
581752 TTAAAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAAAATTAT
Found at i:581783 original size:32 final size:33
Alignment explanation
Indices: 581702--581784 Score: 84
Period size: 32 Copynumber: 2.6 Consensus size: 33
581692 TGAAATATAT
*
581702 AAATAATATTAT-TCATTATTAAATATATAAAAA
1 AAAT-ATATTATATTATTATTAAATATATAAAAA
*
581735 AAATTTATTATA-TATTATTAAA-ATA-AAAATA
1 AAATATATTATATTATTATTAAATATATAAAA-A
* *
581766 TAATATCTTATATTATTAT
1 AAATATATTATATTATTAT
581785 AATATAATTG
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
30 4 0.10
31 13 0.31
32 21 0.50
33 4 0.10
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (33 bp):
AAATATATTATATTATTATTAAATATATAAAAA
Found at i:581822 original size:52 final size:52
Alignment explanation
Indices: 581744--581862 Score: 149
Period size: 52 Copynumber: 2.3 Consensus size: 52
581734 AAAATTTATT
**
581744 ATATATTATTAAA-A-TAAAAATATAATATCTTATATTATTAT-AATA-TAATTG
1 ATATATT-TTAAATATTAAAAATATAATA--TTATATTATTATAAATATTAATAA
581795 AT-TATTTTATAATATTAAAAATATAATATTATATTATTATAAATATTAATAA
1 ATATATTTTA-AATATTAAAAATATAATATTATATTATTATAAATATTAATAA
581847 ATATATTTTAAATATT
1 ATATATTTTAAATATT
581863 TTAATAATTA
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
49 3 0.05
50 18 0.30
51 7 0.12
52 25 0.42
53 7 0.12
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (52 bp):
ATATATTTTAAATATTAAAAATATAATATTATATTATTATAAATATTAATAA
Found at i:581823 original size:34 final size:32
Alignment explanation
Indices: 581782--581851 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 32
581772 CTTATATTAT
*
581782 TATAATATAATTGATTATTTTATAATATTAA-AAA
1 TATAATATAA-T-ATTATTATA-AATATTAATAAA
*
581816 TATAATATTATATTATTATAAATATTAATAAA
1 TATAATATAATATTATTATAAATATTAATAAA
581848 TATA
1 TATA
581852 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
31 8 0.24
32 15 0.45
33 1 0.03
34 9 0.27
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.47
Consensus pattern (32 bp):
TATAATATAATATTATTATAAATATTAATAAA
Found at i:581832 original size:22 final size:24
Alignment explanation
Indices: 581801--581877 Score: 79
Period size: 23 Copynumber: 3.3 Consensus size: 24
581791 ATTGATTATT
*
581801 TTATAATATTAAAAATA-TAAT-A
1 TTATATTATTAAAAATATTAATAA
*
581823 TTATATTATTATAAATATTAATAA
1 TTATATTATTAAAAATATTAATAA
* * *
581847 ATATATT-TTAAATATTTTAATAA
1 TTATATTATTAAAAATATTAATAA
581870 TTAATATT
1 TT-ATATT
581878 TTGATGAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
22 15 0.33
23 18 0.40
24 12 0.27
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTATATTATTAAAAATATTAATAA
Found at i:582110 original size:42 final size:42
Alignment explanation
Indices: 582051--582170 Score: 204
Period size: 42 Copynumber: 2.9 Consensus size: 42
582041 ATGAATTACA
* *
582051 TTCCGGAAAATGAATTACGTGAAACAAACACGGGAAAACGTT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
582093 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
* *
582135 TTCCGAAAAACGAATTACGTGAAACAAACACTGGAA
1 TTCCGGAAAACGAATTACGTGAAACAAACACGGGAA
582171 TTCGGGGAAA
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 74 1.00
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.17
Consensus pattern (42 bp):
TTCCGGAAAACGAATTACGTGAAACAAACACGGGAAAACATT
Found at i:583745 original size:13 final size:13
Alignment explanation
Indices: 583708--583750 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
583698 ACGTATGATT
583708 TATATAAATAAAA
1 TATATAAATAAAA
* ** *
583721 TATTTATTTAAAT
1 TATATAAATAAAA
583734 TATATAAATAAAA
1 TATATAAATAAAA
583747 TATA
1 TATA
583751 CATTAACTTA
Statistics
Matches: 22, Mismatches: 8, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TATATAAATAAAA
Found at i:587461 original size:24 final size:24
Alignment explanation
Indices: 587404--587479 Score: 63
Period size: 22 Copynumber: 3.2 Consensus size: 24
587394 ATTAATATAT
*
587404 ATATATATATATTTAATATT-TTAAGA
1 ATATAT-TAT-TTTTATATTATTAA-A
*
587430 AT-TTTTATTTTTATATTATTAAA
1 ATATATTATTTTTATATTATTAAA
587453 ATATATTA--TTTA-ATTATTAAAA
1 ATATATTATTTTTATATTATT-AAA
587475 ATATA
1 ATATA
587480 ATAATTATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 6 0.14
22 12 0.27
23 11 0.25
24 11 0.25
25 2 0.05
26 2 0.05
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (24 bp):
ATATATTATTTTTATATTATTAAA
Found at i:587468 original size:21 final size:21
Alignment explanation
Indices: 587435--587496 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
587425 TAAGAATTTT
587435 TATT-TTTATATTATTAAAATA
1 TATTATTTA-ATTATTAAAATA
587456 TATTATTTAATTATTAAAAATA
1 TATTATTTAATTATT-AAAATA
* *
587478 TAATAATT-ATTA-TAAAATA
1 TATTATTTAATTATTAAAATA
587497 GGTGGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 6 0.16
20 1 0.03
21 14 0.38
22 16 0.43
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TATTATTTAATTATTAAAATA
Found at i:587484 original size:18 final size:20
Alignment explanation
Indices: 587444--587496 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
587434 TTATTTTTAT
*
587444 ATTATTAAAATATATTATTTA
1 ATTATTAAAA-ATATTATATA
587465 ATTATTAAAAATA-TA-ATA
1 ATTATTAAAAATATTATATA
587483 ATTATTATAAAATA
1 ATTATTA-AAAATA
587497 GGTGGAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
18 9 0.30
19 8 0.27
20 3 0.10
21 10 0.33
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATTATTAAAAATATTATATA
Found at i:593918 original size:16 final size:17
Alignment explanation
Indices: 593897--593928 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
593887 CCTTCTTGTT
593897 TATTTT-TTTTTAAATA
1 TATTTTATTTTTAAATA
593913 TATTTTATTTTTAAAT
1 TATTTTATTTTTAAAT
593929 TCTTTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TATTTTATTTTTAAATA
Found at i:601813 original size:3 final size:3
Alignment explanation
Indices: 601805--601836 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
601795 AGGAAGATCT
601805 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
601837 GATCTAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:602650 original size:16 final size:17
Alignment explanation
Indices: 602612--602651 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
602602 AATGTAAAAC
602612 TATTATTTTTATTATAT
1 TATTATTTTTATTATAT
602629 TA-TATTTTTA-TAT-T
1 TATTATTTTTATTATAT
602643 TAATTATTT
1 T-ATTATTT
602652 GACAAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.10
15 4 0.19
16 13 0.62
17 2 0.10
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TATTATTTTTATTATAT
Found at i:604440 original size:13 final size:12
Alignment explanation
Indices: 604420--604483 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 12
604410 AGAGAAAGGG
604420 AAAAATAAAAAA
1 AAAAATAAAAAA
604432 AACAAATAAATCAAA
1 AA-AAATAAA--AAA
604447 GGAAAAATAAAATAA
1 --AAAAATAAAA-AA
*
604462 TAAAATAAAAATA
1 AAAAATAAAAA-A
604475 AAAAATAAA
1 AAAAATAAA
604484 CTAAACTAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 13
0.74 0.03 0.22
Matches are distributed among these distances:
12 3 0.07
13 25 0.58
14 1 0.02
15 5 0.12
16 7 0.16
17 2 0.05
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (12 bp):
AAAAATAAAAAA
Found at i:604591 original size:2 final size:2
Alignment explanation
Indices: 604584--604625 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
604574 AGTAGTAATA
604584 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
604626 GGAAAAAATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:604852 original size:3 final size:3
Alignment explanation
Indices: 604840--604871 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
604830 GAGAAAAAAC
604840 AAT AAT -AT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
604872 TGCATGAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:606546 original size:165 final size:164
Alignment explanation
Indices: 606192--606755 Score: 853
Period size: 164 Copynumber: 3.4 Consensus size: 164
606182 TTTGCCTCTG
* *
606192 AGCTGAATGTAATCGAACTCG-GAGGTCTTCAGTTGGCAGATAGCCCTTCTCGACTTAAGCTATA
1 AGCTGAGTGTAATCGAACTCGAG-GGTC-T---TTGGCAGATAGCCCTTCTCGACTTAAGCTATG
* *
606256 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTCTTTGGTGACAAATAACCC
61 CTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCC
* * *
606321 TTCTAGCCTTGAGTTATGATGTAAATGATGTGTCATCTA
126 TTCTAGCCTTGAGTTATGATGTAAATGATGTGCCCTCGA
*
606360 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
1 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* *
606425 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTTGGTGATAGATAACCCTTCT
66 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGATAACCCTTCT
*
606490 AGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGA
130 AGCCTTGAGTTATGATGTAAATGATGTGCCCTCGA
* * *
606525 AGCTGAGTGTAATCGAACTCGATGGTCTTTGGCAGATAGCCCTTCTTGACTTAAGTTATGCTGCA
1 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* * * *
606590 AATGATGTGCCTTTGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTGGTGACAGATAATCCTTCTA
66 AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTA
* * *
606655 GCCTTGAGTTATGCTGTAAATGATGTGCTCTTGA
131 GCCTTGAGTTATGATGTAAATGATGTGCCCTCGA
* *
606689 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAG-CCTTCTCGACTTAAGCAATGTTGCA
1 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
606753 AAT
66 AAT
606756 ATTTTCTTTA
Statistics
Matches: 365, Mismatches: 29, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
163 24 0.07
164 165 0.45
165 150 0.41
167 1 0.00
168 24 0.07
169 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (164 bp):
AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
AATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAACCCTTCTA
GCCTTGAGTTATGATGTAAATGATGTGCCCTCGA
Found at i:611001 original size:15 final size:14
Alignment explanation
Indices: 610981--611038 Score: 50
Period size: 14 Copynumber: 4.2 Consensus size: 14
610971 ATATATATAC
610981 AAAATAAATCAAAGA
1 AAAATAAATCAAA-A
610996 AAAAT-AAT-AAAA
1 AAAATAAATCAAAA
* *
611008 TAAAA-AAAACTAAA
1 -AAAATAAATCAAAA
*
611022 ATAATAAATCAAAA
1 AAAATAAATCAAAA
611036 AAA
1 AAA
611039 TAATAAACTA
Statistics
Matches: 33, Mismatches: 6, Indels: 9
0.69 0.12 0.19
Matches are distributed among these distances:
12 1 0.03
13 12 0.36
14 15 0.45
15 5 0.15
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.16
Consensus pattern (14 bp):
AAAATAAATCAAAA
Found at i:611009 original size:8 final size:8
Alignment explanation
Indices: 610996--611051 Score: 55
Period size: 8 Copynumber: 7.1 Consensus size: 8
610986 AAATCAAAGA
610996 AAAATAAT
1 AAAATAAT
611004 AAAATAA-
1 AAAATAAT
611011 AAAA-AACT
1 AAAATAA-T
611019 AAAATAAT
1 AAAATAAT
*
611027 -AAATCAAA
1 AAAAT-AAT
611035 AAAATAAT
1 AAAATAAT
*
611043 AAACTAAT
1 AAAATAAT
611051 A
1 A
611052 TATATATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
6 2 0.05
7 8 0.20
8 24 0.60
9 6 0.15
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (8 bp):
AAAATAAT
Found at i:611011 original size:23 final size:23
Alignment explanation
Indices: 610981--611038 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
610971 ATATATATAC
** *
610981 AAAATAAATCAAAGAAAAATAAT
1 AAAATAAAAAAAACAAAAATAAT
*
611004 AAAATAAAAAAAACTAAAATAAT
1 AAAATAAAAAAAACAAAAATAAT
*
611027 -AAATCAAAAAAA
1 AAAATAAAAAAAA
611039 TAATAAACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.78, C:0.05, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAATAAAAAAAACAAAAATAAT
Found at i:613808 original size:12 final size:12
Alignment explanation
Indices: 613791--613830 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
613781 TACTCAAGTG
613791 AAAATTAAATAA
1 AAAATTAAATAA
*
613803 AAAATT--AT-G
1 AAAATTAAATAA
613812 AAAATTAAATAA
1 AAAATTAAATAA
613824 AAAATTA
1 AAAATTA
613831 TAAACTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
9 6 0.26
10 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (12 bp):
AAAATTAAATAA
Found at i:613815 original size:21 final size:21
Alignment explanation
Indices: 613789--613847 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 21
613779 GTTACTCAAG
613789 TGAAAATTAAATAAAAAATTA
1 TGAAAATTAAATAAAAAATTA
613810 TGAAAATTAAATAAAAAATTA
1 TGAAAATTAAATAAAAAATTA
*
613831 T--AAACTAAATAATAAAA
1 TGAAAATTAAATAA-AAAA
613848 ATAATTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
19 10 0.28
20 4 0.11
21 22 0.61
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.27
Consensus pattern (21 bp):
TGAAAATTAAATAAAAAATTA
Found at i:614011 original size:44 final size:44
Alignment explanation
Indices: 613899--614016 Score: 188
Period size: 44 Copynumber: 2.8 Consensus size: 44
613889 ACAATTAAAT
613899 AATAAAAACATTAAGAAACAAAAT--A-AAAAAGTCAATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCAATAATTA
* *
613940 AATAAAAACATTAAGAAACAAAATAAATAAAAATTCCATAATTA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCAATAATTA
*
613984 AATAAAAATATTAAGAAACAAAATAAATAAAAA
1 AATAAAAACATTAAGAAACAAAATAAATAAAAA
614017 CAAGTCTATT
Statistics
Matches: 71, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
41 24 0.34
43 1 0.01
44 46 0.65
ACGTcount: A:0.69, C:0.07, G:0.03, T:0.20
Consensus pattern (44 bp):
AATAAAAACATTAAGAAACAAAATAAATAAAAAGTCAATAATTA
Done.