Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007712.1 Hibiscus syriacus cultivar Beakdansim tig00109936_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: 920388
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:356028 original size:131 final size:130
Alignment explanation
Indices: 355893--356197 Score: 432
Period size: 131 Copynumber: 2.3 Consensus size: 130
355883 TATTGTTTGT
* *
355893 CTTGAAACAAGTTTGTCTCCCTTGAGACAGTTTCACTTGAAACATATAATCTTTGAGATTGTTTC
1 CTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCACTTGAAACA-ATAATCTTTGAG-TCGTTTC
* *
355958 TCTTGAAAC-AATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACCCATCTTTGAGATCATTT
64 CCTTGAAACGAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACCAATCTTTGAGATCATTT
356022 CC
129 CC
* * * *
356024 CTTGAAACGAATTTTGTCTCTCTTGGGACAGTTTCTCTTGAAACAATCATCTTTGAGTCGTTTCC
1 CTTGAAAC-AAGTTTGTCTCTCTTGAGACAGTTTCACTTGAAACAATAATCTTTGAGTCGTTTCC
* * * * * **
356089 CTTGAAACGAGTTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACACCAATCTTTGTGTTTGTTTC
65 CTTGAAACGAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACCAATCTTTGAGATCATTTC
356154 C
130 C
*
356155 CTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC
1 CTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCACTTGAAAC
356198 CATTTCCCTA
Statistics
Matches: 154, Mismatches: 18, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
130 46 0.30
131 76 0.49
132 32 0.21
ACGTcount: A:0.24, C:0.22, G:0.15, T:0.39
Consensus pattern (130 bp):
CTTGAAACAAGTTTGTCTCTCTTGAGACAGTTTCACTTGAAACAATAATCTTTGAGTCGTTTCCC
TTGAAACGAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAACACCAATCTTTGAGATCATTTCC
Found at i:356438 original size:131 final size:132
Alignment explanation
Indices: 356204--356566 Score: 435
Period size: 131 Copynumber: 2.7 Consensus size: 132
356194 AAACCATTTC
* * * * *
356204 CCTAAAGATGGACAGTCGTCCTCATTACGTAAGAACCGTGTTATCCCCTGACGAGACCTCCTCAT
1 CCTAAAGATGGACAGTCGTCCTCATCACGTAGGAACCGTGTCATCCACTGACCAGACCTCCTCAT
* ** * * *
356269 CACGTAGGAGCTGCATCAACCTTAGATAA-TATGTCGTCCTCATCACATAAGAATCGTGTTATCA
66 CACGTAGGAGCCGTGTCACCCTTAGATAACCA-GTCGTCCTCATCACATAAGAACCGTGTTATCA
356333 -TT
130 CTT
* * *
356335 CCTAAAGATGG-CATGTCGTCATCATCACATAGGAACCGTGTCATCCACTGACCAAACCTCCTCA
1 CCTAAAGATGGACA-GTCGTCCTCATCACGTAGGAACCGTGTCATCCACTGACCAGACCTCCTCA
* * * *
356399 TCACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCGCGTAGGAACCGTGTTATCA
65 TCACGTAGGAGCCGTGTCACCCTTAGATAACCAGTCGTCCTCATCACATAAGAACCGTGTTATCA
356464 CCCTT
130 --CTT
* * * * *
356469 CCTAAAGATGGCCAGCCGTCCTCATCGCGTAGGAACCGTGTCATCCACCGACCAGATCTCCTCAT
1 CCTAAAGATGGACAGTCGTCCTCATCACGTAGGAACCGTGTCATCCACTGACCAGACCTCCTCAT
* * *
356534 CATGTAGGAGCCGTGCCACCCTTAGACAACCAG
66 CACGTAGGAGCCGTGTCACCCTTAGATAACCAG
356567 AACTCTTCAT
Statistics
Matches: 197, Mismatches: 29, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
130 2 0.01
131 106 0.54
132 1 0.01
134 86 0.44
135 2 0.01
ACGTcount: A:0.26, C:0.31, G:0.19, T:0.23
Consensus pattern (132 bp):
CCTAAAGATGGACAGTCGTCCTCATCACGTAGGAACCGTGTCATCCACTGACCAGACCTCCTCAT
CACGTAGGAGCCGTGTCACCCTTAGATAACCAGTCGTCCTCATCACATAAGAACCGTGTTATCAC
TT
Found at i:356750 original size:3 final size:3
Alignment explanation
Indices: 356742--356767 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
356732 TGGGTCGAAA
356742 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
356768 AATGTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:376409 original size:24 final size:24
Alignment explanation
Indices: 376382--376481 Score: 76
Period size: 24 Copynumber: 4.2 Consensus size: 24
376372 GATATAAAAA
* *
376382 ATCAAAACATAATTCAGATCAAAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
376406 ATCAGAACAGAATCCAGGTTAGGA-
1 ATCAAAACAGAATTCAGATCA-GAT
* * *
376430 ATCAGAACATATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
376454 GTCAAAACAGAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
376478 ATCA
1 ATCA
376482 GATAAAATAT
Statistics
Matches: 56, Mismatches: 18, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
23 2 0.04
24 53 0.95
25 1 0.02
ACGTcount: A:0.48, C:0.17, G:0.13, T:0.22
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:376481 original size:48 final size:48
Alignment explanation
Indices: 376380--376483 Score: 118
Period size: 48 Copynumber: 2.2 Consensus size: 48
376370 GAGATATAAA
* * ** *
376380 AAATCAAAACATAATTCAGATCAAATATCAGAACAGAATCCAGGTTAG
1 AAATCAGAACATAATTCAGATCAAATATCAAAACAGAATCCAAATCAG
* * * * *
376428 GAATCAGAACATATTTCAGATCAGATGTCAAAACAGAATTCAAATCAG
1 AAATCAGAACATAATTCAGATCAAATATCAAAACAGAATCCAAATCAG
376476 AAATCAGA
1 AAATCAGA
376484 TAAAATATTC
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.49, C:0.16, G:0.13, T:0.21
Consensus pattern (48 bp):
AAATCAGAACATAATTCAGATCAAATATCAAAACAGAATCCAAATCAG
Found at i:383640 original size:20 final size:19
Alignment explanation
Indices: 383593--383647 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
383583 ACTTTGAATC
*
383593 ATAAACTCTAAATCATAAT
1 ATAAACTTTAAATCATAAT
*
383612 ATCTAAACTTTAAATCATACGT
1 A--TAAACTTTAAATCATA-AT
383634 ATAAACTTTAAATC
1 ATAAACTTTAAATC
383648 TTAAATCCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 1 0.03
20 13 0.42
21 15 0.48
22 2 0.06
ACGTcount: A:0.47, C:0.16, G:0.02, T:0.35
Consensus pattern (19 bp):
ATAAACTTTAAATCATAAT
Found at i:384387 original size:17 final size:17
Alignment explanation
Indices: 384360--384393 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
384350 TAATATTTAA
384360 TAAATTAATAATCTTTCT
1 TAAATTAATAAT-TTTCT
384378 TAAA-TAATAATTTTCT
1 TAAATTAATAATTTTCT
384394 ATTCTTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 7 0.44
18 4 0.25
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTAATAATTTTCT
Found at i:391199 original size:15 final size:16
Alignment explanation
Indices: 391171--391208 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
391161 TATAAATTAA
391171 TAAATTTAATTATAATT
1 TAAA-TTAATTATAATT
*
391188 TAAATTAA-TATATTT
1 TAAATTAATTATAATT
391203 TAAATT
1 TAAATT
391209 TTATAAGATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
16 4 0.20
17 4 0.20
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TAAATTAATTATAATT
Found at i:392236 original size:61 final size:59
Alignment explanation
Indices: 392165--392345 Score: 193
Period size: 60 Copynumber: 3.0 Consensus size: 59
392155 TATTTGGATG
*
392165 AATTTGGGGATAAAATTAGAATATTTAAAATCTTGGGGACTAATTTAGAAAAAAGAGTTAT
1 AATTTGGGGATAAAATTAGAATATTTAAAAT-TTGAGGACTAATTTA-AAAAAAGAGTTAT
* * * ** * ** *
392226 AATTTAGGGATGAAAA-TAAAATATTCAAAAGTTAAAAGACTAATTTAAAATGAGAGATAT
1 AATTTGGGGAT-AAAATTAGAATATTTAAAA-TTTGAGGACTAATTTAAAAAAAGAGTTAT
* *
392286 AATTTGGGGATGAAATTAGAATATTTAAAATTTGAAGGACCAATTTAAAATAAAGAGTTA
1 AATTTGGGGATAAAATTAGAATATTTAAAATTTG-AGGACTAATTTAAAA-AAAGAGTTA
392346 ATTGCATCAC
Statistics
Matches: 94, Mismatches: 21, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
59 5 0.05
60 45 0.48
61 39 0.41
62 5 0.05
ACGTcount: A:0.48, C:0.03, G:0.18, T:0.31
Consensus pattern (59 bp):
AATTTGGGGATAAAATTAGAATATTTAAAATTTGAGGACTAATTTAAAAAAAGAGTTAT
Found at i:392507 original size:60 final size:61
Alignment explanation
Indices: 392374--392544 Score: 188
Period size: 60 Copynumber: 2.8 Consensus size: 61
392364 AAACTATAAT
* * * *
392374 CCTCATTT-TAAATTGGTCCTTAAACATTTT-AATATTCTAATTTCATCCTTAATTTACGAC
1 CCTCATTTCTAAATTAGTCCTTAAAC-TTTTGAATATTCTAATTTTATCCCTAAATTACGAC
* *
392434 TCTCATTTC-AAATTAGTCCTTAAACTTTTGAATATTCTAATTTTATCCCTAAATTATGAC
1 CCTCATTTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTTATCCCTAAATTACGAC
* ** * *
392494 CCT-TTTTCTAAATTAGTCCCCCAAAATTTTTGAATATTCCAATTTTATCCC
1 CCTCATTTCTAAATTAGT--CCTTAAACTTTTGAATATTCTAATTTTATCCC
392545 CAAAGCATCC
Statistics
Matches: 94, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
59 8 0.09
60 58 0.62
62 28 0.30
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.44
Consensus pattern (61 bp):
CCTCATTTCTAAATTAGTCCTTAAACTTTTGAATATTCTAATTTTATCCCTAAATTACGAC
Found at i:406038 original size:51 final size:51
Alignment explanation
Indices: 405870--406183 Score: 389
Period size: 51 Copynumber: 6.0 Consensus size: 51
405860 TGATGAGCCT
* * **
405870 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATA-AAACGTGTTT
1 GCTCCCTATTCCTTCAGAG-AGTATAGGACT----CAATCTTCA-ACAAACTTGTCC
* * * * **
405925 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAAATCTTCAATAAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGAC-T---C-AATCTTCAA-CAAACTTGTCC
* *
405982 GCTCCCTATTCTTTCAGGGAGTATAGGACTCAATCTTCAACAAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCC
406033 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCC
*
406084 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCC
406135 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGT
406184 TTGCTTCACT
Statistics
Matches: 238, Mismatches: 16, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
51 155 0.65
52 9 0.04
53 1 0.00
55 30 0.13
56 11 0.05
57 32 0.13
ACGTcount: A:0.29, C:0.26, G:0.15, T:0.30
Consensus pattern (51 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTCAATCTTCAACAAACTTGTCC
Found at i:407520 original size:20 final size:20
Alignment explanation
Indices: 407497--407559 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 20
407487 TGAACCCTCC
407497 TTTTATTTCTTTTTTTTTCA
1 TTTTATTTCTTTTTTTTTCA
* *
407517 --TT-TTTCTCTTTTTAT--
1 TTTTATTTCTTTTTTTTTCA
407532 TTTTATTTC-TTTTTTTTCA
1 TTTTATTTCTTTTTTTTTCA
407551 TTTTTATTT
1 -TTTTATTT
407560 TTTCTCATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 12
0.67 0.08 0.24
Matches are distributed among these distances:
17 19 0.58
18 6 0.18
20 8 0.24
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (20 bp):
TTTTATTTCTTTTTTTTTCA
Found at i:407645 original size:11 final size:10
Alignment explanation
Indices: 407497--407661 Score: 50
Period size: 11 Copynumber: 15.1 Consensus size: 10
407487 TGAACCCTCC
*
407497 TTTTATTTCT
1 TTTTTTTTCT
407507 TTTTTTTTCAT
1 TTTTTTTTC-T
*
407518 TTTTCTCTTTTT
1 TTTT-T-TTTCT
407530 ATTTTTATTTC-
1 -TTTTT-TTTCT
407541 TTTTTTTTCAT
1 TTTTTTTTC-T
407552 TTTTATTTT-T
1 TTTT-TTTTCT
*
407562 TCTCATTTTTCTT
1 T-T-TTTTTTC-T
407575 TTCTTCTTTTCT
1 TT-TT-TTTTCT
*
407587 TCTTTTCTTCT
1 T-TTTTTTTCT
407598 TTTTCTTTT-T
1 TTTT-TTTTCT
** *
407608 CTCATTTTTAT
1 -TTTTTTTTCT
*
407619 TATTTTTT-T
1 TTTTTTTTCT
**
407628 TCATTTTTCGT
1 TTTTTTTTC-T
407639 TTTTTTTTCT
1 TTTTTTTTCT
407649 TTTATTTCTTCT
1 TTT-TTT-TTCT
407661 T
1 T
407662 CAAGCGAAAT
Statistics
Matches: 119, Mismatches: 16, Indels: 38
0.69 0.09 0.22
Matches are distributed among these distances:
9 11 0.09
10 33 0.28
11 37 0.31
12 23 0.19
13 15 0.13
ACGTcount: A:0.07, C:0.14, G:0.01, T:0.78
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:407651 original size:8 final size:8
Alignment explanation
Indices: 407508--407658 Score: 71
Period size: 8 Copynumber: 18.2 Consensus size: 8
407498 TTTATTTCTT
407508 TTTTTTTC
1 TTTTTTTC
*
407516 ATTTTTCTC
1 -TTTTTTTC
407525 TTTTTATT-
1 TTTTT-TTC
*
407533 TTTATTTC
1 TTTTTTTC
407541 TTTTTTT-
1 TTTTTTTC
*
407548 TCATTTTT-
1 T-TTTTTTC
*
407556 ATTTTTTC
1 TTTTTTTC
*
407564 TCATTTTTC
1 T-TTTTTTC
*
407573 TTTTCTTC
1 TTTTTTTC
*
407581 TTTTCTTC
1 TTTTTTTC
*
407589 TTTTCTTC
1 TTTTTTTC
407597 --TTTTTC
1 TTTTTTTC
*
407603 TTTTTCTC
1 TTTTTTTC
*
407611 ATTTTTATTAT
1 -TTTTT-TT-C
407622 TTTTTTTC
1 TTTTTTTC
407630 ATTTTTCGTT-
1 -TTTTT--TTC
407640 TTTTTTTC
1 TTTTTTTC
407648 TTTTATTTC
1 TTTT-TTTC
407657 TT
1 TT
407659 CTTCAAGCGA
Statistics
Matches: 111, Mismatches: 16, Indels: 30
0.71 0.10 0.19
Matches are distributed among these distances:
6 5 0.05
7 10 0.09
8 50 0.45
9 38 0.34
10 6 0.05
11 2 0.02
ACGTcount: A:0.07, C:0.14, G:0.01, T:0.78
Consensus pattern (8 bp):
TTTTTTTC
Found at i:407651 original size:9 final size:9
Alignment explanation
Indices: 407496--407658 Score: 66
Period size: 9 Copynumber: 17.3 Consensus size: 9
407486 TTGAACCCTC
*
407496 CTTTTATTT
1 CTTTTTTTT
407505 CTTTTTTTT
1 CTTTTTTTT
**
407514 -TCATTTTT
1 CTTTTTTTT
*
407522 CTCTTTTTAT
1 CT-TTTTTTT
*
407532 -TTTTATTT
1 CTTTTTTTT
407540 CTTTTTTTT
1 CTTTTTTTT
407549 CATTTTTATTT
1 C-TTTTT-TTT
*
407560 TTTCTCATTTTT
1 CTT-T--TTTTT
407572 CTTTTCTTCTT
1 CTTTT-TT-TT
407583 -TTCTTCTTTT
1 CTT-TT-TTTT
*
407593 CTTCTTTTT
1 CTTTTTTTT
*
407602 C-TTTTTCT
1 CTTTTTTTT
*
407610 CATTTTTATT
1 C-TTTTTTTT
*
407620 ATTTTTTTT
1 CTTTTTTTT
**
407629 CATTTTTCGT
1 C-TTTTTTTT
407639 -TTTTTTTT
1 CTTTTTTTT
*
407647 CTTTTATTT
1 CTTTTTTTT
407656 CTT
1 CTT
407659 CTTCAAGCGA
Statistics
Matches: 114, Mismatches: 24, Indels: 32
0.67 0.14 0.19
Matches are distributed among these distances:
8 23 0.20
9 41 0.36
10 29 0.25
11 14 0.12
12 5 0.04
13 2 0.02
ACGTcount: A:0.07, C:0.14, G:0.01, T:0.78
Consensus pattern (9 bp):
CTTTTTTTT
Found at i:417300 original size:42 final size:41
Alignment explanation
Indices: 417217--417294 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 41
417207 ATTTGTTCAA
*
417217 AAATCCTACCCACATATGTTGACTACCCCATCATGCTTTATC
1 AAATCCTACCCACATATGATGACTACCCCA-CATGCTTTATC
417259 AAATCCTACCCA-ATATGAT-ATCTACCCC-CATGCTTT
1 AAATCCTACCCACATATGATGA-CTACCCCACATGCTTT
417295 GTTATCCACA
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
39 8 0.24
40 1 0.03
41 13 0.38
42 12 0.35
ACGTcount: A:0.29, C:0.33, G:0.06, T:0.31
Consensus pattern (41 bp):
AAATCCTACCCACATATGATGACTACCCCACATGCTTTATC
Found at i:417371 original size:45 final size:46
Alignment explanation
Indices: 417305--417400 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
417295 GTTATCCACA
*
417305 AAAAGAAATCCTAACCTCATGATATCTAATTCGCATGC-TTATTCAG
1 AAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTC-G
* *
417351 AAAATAAA-CCTAACCGCATGATATCTAGTTCGCATGCATTTATTCG
1 AAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCA-TTATTCG
417397 AAAA
1 AAAA
417401 AACGAAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 27 0.60
46 12 0.27
47 6 0.13
ACGTcount: A:0.39, C:0.21, G:0.11, T:0.29
Consensus pattern (46 bp):
AAAAGAAATCCTAACCGCATGATATCTAATTCGCATGCATTATTCG
Found at i:417850 original size:13 final size:13
Alignment explanation
Indices: 417834--417858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
417824 AAGCGAAAGA
417834 AAAAACACTCAAT
1 AAAAACACTCAAT
417847 AAAAACACTCAA
1 AAAAACACTCAA
417859 AATCAATTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.24, G:0.00, T:0.12
Consensus pattern (13 bp):
AAAAACACTCAAT
Found at i:421463 original size:45 final size:45
Alignment explanation
Indices: 421408--421602 Score: 156
Period size: 45 Copynumber: 4.4 Consensus size: 45
421398 GGATTTATTC
* *
421408 CACTCCTCTTCAGGGTAGATCAGATCTGGAAACGTTGATTCACTT
1 CACTGCTCTTCAGGGAAGATCAGATCTGGAAACGTTGATTCACTT
* * *
421453 CACTGCTCTTCAGGGAAGAT-TGAATCGAGGCAAA-TTTG-TT--C--
1 CACTGCTCTTCAGGGAAGATCAG-ATC-TGG-AAACGTTGATTCACTT
* * * * * *
421494 CACTGCTCCTCAGGGAATATCAAATCTGAAAAAG-GGA-TCTACTT
1 CACTGCTCTTCAGGGAAGATCAGATCTGGAAACGTTGATTC-ACTT
* * * *
421538 CGCTGGTCTTCAGGGTAGATCAGATCTGGAAACGTTAATTCACTT
1 CACTGCTCTTCAGGGAAGATCAGATCTGGAAACGTTGATTCACTT
421583 CACTGCTCTTCAGGGAAGAT
1 CACTGCTCTTCAGGGAAGAT
421603 TAAATCGGGT
Statistics
Matches: 111, Mismatches: 26, Indels: 26
0.68 0.16 0.16
Matches are distributed among these distances:
39 5 0.05
40 1 0.01
41 21 0.19
42 1 0.01
43 1 0.01
44 27 0.24
45 45 0.41
46 7 0.06
47 3 0.03
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (45 bp):
CACTGCTCTTCAGGGAAGATCAGATCTGGAAACGTTGATTCACTT
Found at i:421596 original size:130 final size:131
Alignment explanation
Indices: 421317--421740 Score: 523
Period size: 130 Copynumber: 3.2 Consensus size: 131
421307 GGTTTATTAG
* * * * *
421317 CTTCACTGCTCTTCAGGGAGGATTGAATCGAGGTAGATTTGTTCCATTACTCCTCTGGGAAGATC
1 CTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCAGGGAATATC
* **
421382 AAATCTAGAAAAAAAGGGATTTA-TTCCACTCCTCTTCAGGGTAGATCAGATCTGGAAACGTTGA
66 AAATCT-G-AAAAAAGGGATCTACTT-CACTGATCTTCAGGGTAGATCAGATCTGGAAACGTTGA
421446 TTCA
128 TTCA
* *
421450 CTTCACTGCTCTTCAGGGAAGATTGAATCGAGGCAAATTTGTTCCACTGCTCCTCAGGGAATATC
1 CTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCAGGGAATATC
* * *
421515 AAATCTG-AAAAAGGGATCTACTTCGCTGGTCTTCAGGGTAGATCAGATCTGGAAACGTTAATTC
66 AAATCTGAAAAAAGGGATCTACTTCACTGATCTTCAGGGTAGATCAGATCTGGAAACGTTGATTC
421579 A
131 A
* * * ** *
421580 CTTCACTGCTCTTCAGGGAAGATTAAATCG-GGTTTGATTTGCTT-CACTGTTTTTTAGGGAATA
1 CTTCACTGCTCTTCAGGGAAGATTGAATCGAGG-TAGATTTG-TTCCACTGCTCCTCAGGGAATA
* * * * * *
421643 TCAAATCTGAAAAAAAGGATCTACTCCACTGATCTTCCGGGTAGACCAGATCCGGAAACTTTGAT
64 TCAAATCTGAAAAAAGGGATCTACTTCACTGATCTTCAGGGTAGATCAGATCTGGAAACGTTGAT
421708 TCA
129 TCA
* * *
421711 CTCCAATGCTTTTCAGGGAAGATTGAATCG
1 CTTCACTGCTCTTCAGGGAAGATTGAATCG
421741 GATTTGATTT
Statistics
Matches: 254, Mismatches: 33, Indels: 10
0.86 0.11 0.03
Matches are distributed among these distances:
129 2 0.01
130 108 0.43
131 79 0.31
132 1 0.00
133 64 0.25
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.30
Consensus pattern (131 bp):
CTTCACTGCTCTTCAGGGAAGATTGAATCGAGGTAGATTTGTTCCACTGCTCCTCAGGGAATATC
AAATCTGAAAAAAGGGATCTACTTCACTGATCTTCAGGGTAGATCAGATCTGGAAACGTTGATTC
A
Found at i:422493 original size:19 final size:19
Alignment explanation
Indices: 422469--422521 Score: 79
Period size: 19 Copynumber: 2.8 Consensus size: 19
422459 TATGCATTGG
422469 GCTATGAATTTGAAAATAA
1 GCTATGAATTTGAAAATAA
*
422488 GCTATGAATTTGAAACTAA
1 GCTATGAATTTGAAAATAA
* *
422507 GTTATGAATCTGAAA
1 GCTATGAATTTGAAA
422522 GTGAGTTCTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.43, C:0.08, G:0.17, T:0.32
Consensus pattern (19 bp):
GCTATGAATTTGAAAATAA
Found at i:422528 original size:19 final size:19
Alignment explanation
Indices: 422471--422535 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
422461 TGCATTGGGC
* *
422471 TATGAATTTGAAAATAAGC
1 TATGAATCTGAAAATAAGT
* *
422490 TATGAATTTGAAACTAAGT
1 TATGAATCTGAAAATAAGT
* *
422509 TATGAATCTGAAAGTGAGT
1 TATGAATCTGAAAATAAGT
*
422528 TCTGAATC
1 TATGAATC
422536 ATAAATGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.40, C:0.08, G:0.18, T:0.34
Consensus pattern (19 bp):
TATGAATCTGAAAATAAGT
Found at i:423920 original size:14 final size:14
Alignment explanation
Indices: 423901--423927 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
423891 TCTTTAACTA
423901 GTATTTAAGTAAGC
1 GTATTTAAGTAAGC
423915 GTATTTAAGTAAG
1 GTATTTAAGTAAG
423928 GGTAAAACTT
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:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (14 bp):
GTATTTAAGTAAGC
Found at i:425358 original size:21 final size:21
Alignment explanation
Indices: 425325--425377 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
425315 ATTCTGACTA
425325 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * * *
425346 TCGCGTTGTGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
425367 TCGCAATGCGA
1 TCGCATTGCGA
425378 ATACGTAAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.21, C:0.25, G:0.19, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:425392 original size:20 final size:20
Alignment explanation
Indices: 425367--425453 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
425357 TTTTCCTAAT
425367 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
425387 TCGCAACGCGAATTTGAAAAA
1 TCGCAATGCGAATACG-TAAA
425408 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
425428 TCGCAATGCGAAT-CTGTAAA
1 TCGCAATGCGAATAC-GTAAA
425448 TCGCAA
1 TCGCAA
425454 CGAGATTCTG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
19 1 0.02
20 40 0.70
21 16 0.28
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:425413 original size:41 final size:40
Alignment explanation
Indices: 425367--425453 Score: 138
Period size: 41 Copynumber: 2.1 Consensus size: 40
425357 TTTTCCTAAT
*
425367 TCGCAATGCGAATACGTAAATCGCAACGCGAATTTGAAAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTG-AAAA
* *
425408 TCGCAATGCGAATACGTAAATCGCAATGCGAATCTGTAAA
1 TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAA
425448 TCGCAA
1 TCGCAA
425454 CGAGATTCTG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
40 9 0.21
41 34 0.79
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.21
Consensus pattern (40 bp):
TCGCAATGCGAATACGTAAATCGCAACGCGAATCTGAAAA
Found at i:425463 original size:20 final size:20
Alignment explanation
Indices: 425382--425463 Score: 67
Period size: 20 Copynumber: 4.0 Consensus size: 20
425372 ATGCGAATAC
* *
425382 GTAAATCGCAACGCGAATTT
1 GTAAATCGCAACGAGAATCT
* * *
425402 GAAAAATCGCAATGCGAATAC-
1 G-TAAATCGCAACGAGAAT-CT
* *
425423 GTAAATCGCAATGCGAATCT
1 GTAAATCGCAACGAGAATCT
*
425443 GTAAATCGCAACGAGATTCT
1 GTAAATCGCAACGAGAATCT
425463 G
1 G
425464 ACTATCGCAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
19 1 0.02
20 35 0.67
21 16 0.31
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.22
Consensus pattern (20 bp):
GTAAATCGCAACGAGAATCT
Found at i:426367 original size:24 final size:24
Alignment explanation
Indices: 426314--426360 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
426304 GTATTCGAAA
426314 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
*
426338 TTTGATCTTGGTCAATACTCGGA
1 TTTGATCTTGGTCAATACCCGGA
426361 TTATGATGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:428822 original size:20 final size:20
Alignment explanation
Indices: 428797--428885 Score: 144
Period size: 20 Copynumber: 4.5 Consensus size: 20
428787 CAACGCGGAA
428797 ATCGCAACGC-GAATATGACT
1 ATCGCAACGCGGAA-ATGACT
*
428817 ATCGCAACACGGAAATGACT
1 ATCGCAACGCGGAAATGACT
*
428837 ATCGCAACGCGGAATTGACT
1 ATCGCAACGCGGAAATGACT
428857 ATCGCAACGCGGAAATGACT
1 ATCGCAACGCGGAAATGACT
428877 ATCGCAACG
1 ATCGCAACG
428886 AGAGAATCGC
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
20 61 0.95
21 3 0.05
ACGTcount: A:0.35, C:0.26, G:0.22, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGGAAATGACT
Found at i:428945 original size:34 final size:33
Alignment explanation
Indices: 428857--428952 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
428847 GGAATTGACT
* **
428857 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
428891 ATCGCAATGCGAAATGAAAATCGCAATGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
428924 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
428953 CGAAACTAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:428948 original size:20 final size:19
Alignment explanation
Indices: 428890--428957 Score: 74
Period size: 19 Copynumber: 3.8 Consensus size: 19
428880 GCAACGAGAG
428890 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
428909 AATCGCAAT--G-AGTG--
1 AATCGCAATGCGAAATGAA
428923 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
428943 AATCGCAACGCGAAA
1 AATCGCAATGCGAAA
428958 CTAATTTCGC
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 9 0.22
16 4 0.10
17 1 0.03
18 3 0.08
19 12 0.30
20 11 0.28
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:429024 original size:33 final size:34
Alignment explanation
Indices: 428969--429062 Score: 118
Period size: 33 Copynumber: 2.8 Consensus size: 34
428959 TAATTTCGCG
428969 TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
* * *
429003 TTGCGGTTTTCA-TTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
** * *
429036 TTGCGATAGTCATTTCCGCGTTGCGAT
1 TTGCGATTTTCATTTTCGCATTGCGAT
429063 AGTCTGTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 28 0.55
34 23 0.45
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.43
Consensus pattern (34 bp):
TTGCGATTTTCATTTTCGCATTGCGATTCACTCA
Found at i:429183 original size:14 final size:14
Alignment explanation
Indices: 429164--429200 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
429154 CATCAATTAA
429164 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
429178 ACAAATCATCTTTT
1 ACAAATCAACATTT
429192 ACAAATCAA
1 ACAAATCAA
429201 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:430619 original size:42 final size:42
Alignment explanation
Indices: 430555--430665 Score: 125
Period size: 42 Copynumber: 2.6 Consensus size: 42
430545 CTAGAATGTT
* * *
430555 GGGAGGGACCTCTTCAACGATGACAGTGGCCTCTTGAACGGTAG
1 GGGA-GGA-CTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
** *
430599 GAGG-GGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATAG
1 G-GGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
*
430641 GGGAGGCCTCTTGAACGATGACAGG
1 GGGAGGACTCTTGAACGATGACAGG
430666 TGAGTCGGGC
Statistics
Matches: 55, Mismatches: 10, Indels: 6
0.77 0.14 0.08
Matches are distributed among these distances:
41 2 0.04
42 47 0.85
43 3 0.05
44 1 0.02
45 2 0.04
ACGTcount: A:0.23, C:0.19, G:0.38, T:0.20
Consensus pattern (42 bp):
GGGAGGACTCTTGAACGATGACAGGGGCCTCTTGAACGATAG
Found at i:431170 original size:20 final size:20
Alignment explanation
Indices: 431145--431266 Score: 96
Period size: 20 Copynumber: 6.5 Consensus size: 20
431135 GAAACTTAAA
*
431145 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCGAAAATGACT
*
431165 ATCGCAA--CG-AGA-GA--
1 ATCGCAACGCGAAAATGACT
* * **
431179 ATCGCAATGTG-AAATGAAA
1 ATCGCAACGCGAAAATGACT
431198 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* *
431218 ATTGCAATGCGAAAATGACT
1 ATCGCAACGCGAAAATGACT
* **
431238 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
431258 ATCGCAACG
1 ATCGCAACG
431267 AGAGAATCGC
Statistics
Matches: 82, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
14 7 0.09
16 5 0.06
17 4 0.05
18 1 0.01
19 9 0.11
20 56 0.68
ACGTcount: A:0.40, C:0.20, G:0.20, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:431339 original size:20 final size:20
Alignment explanation
Indices: 431314--431434 Score: 137
Period size: 20 Copynumber: 6.3 Consensus size: 20
431304 TCTTTCGTTA
**
431314 CGATAGTCAAATTCGCATTG
1 CGATAGTCATTTTCGCATTG
431334 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
431354 TGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
431374 CGAT--TC--TCTCG--TTG
1 CGATAGTCATTTTCGCATTG
* *
431388 CGATAGTCATTTTTGCGTTG
1 CGATAGTCATTTTCGCATTG
431408 CGATAGTCATTTTCGCATTG
1 CGATAGTCATTTTCGCATTG
*
431428 TGATAGT
1 CGATAGT
431435 AAACTATTCT
Statistics
Matches: 85, Mismatches: 10, Indels: 12
0.79 0.09 0.11
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
18 5 0.06
20 67 0.79
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.40
Consensus pattern (20 bp):
CGATAGTCATTTTCGCATTG
Found at i:431375 original size:74 final size:74
Alignment explanation
Indices: 431290--431434 Score: 236
Period size: 74 Copynumber: 2.0 Consensus size: 74
431280 GCGATTTTCA
*
431290 TTTCGCATTGCGATTCTTTCGTTACGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGT
1 TTTCGCATTGCGATTCTCTCGTTACGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGT
431355 GATAGTCAT
66 GATAGTCAT
* ** * *
431364 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTTTTGCGTTGCGATAGTCATTTTCGCATTGT
1 TTTCGCATTGCGATTCTCTCGTTACGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGT
431429 GATAGT
66 GATAGT
431435 AAACTATTCT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
74 65 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.42
Consensus pattern (74 bp):
TTTCGCATTGCGATTCTCTCGTTACGATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGT
GATAGTCAT
Found at i:431398 original size:34 final size:34
Alignment explanation
Indices: 431290--431411 Score: 127
Period size: 34 Copynumber: 3.4 Consensus size: 34
431280 GCGATTTTCA
* *
431290 TTTCGCATTGCGATTCTTTCGTTACGATAGTCAA
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
* *
431324 ATTCGCATTGCGATAGTCATTTTCGCATTGTGATAGTCAT
1 TTTCGCATTGCGAT--TC--TTTCG--TTGCGATAGTCAT
*
431364 TTTCGCATTGCGATTCTCTCGTTGCGATAGTCAT
1 TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
* *
431398 TTTTGCGTTGCGAT
1 TTTCGCATTGCGAT
431412 AGTCATTTTC
Statistics
Matches: 73, Mismatches: 9, Indels: 12
0.78 0.10 0.13
Matches are distributed among these distances:
34 37 0.51
36 6 0.08
38 7 0.10
40 23 0.32
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (34 bp):
TTTCGCATTGCGATTCTTTCGTTGCGATAGTCAT
Found at i:433369 original size:20 final size:20
Alignment explanation
Indices: 433321--433370 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
433311 GAAACTTTAA
*
433321 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
433341 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
433361 ATCGCAACGC
1 ATCGCAACGC
433371 AAGAATCGCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.36, C:0.28, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:433409 original size:33 final size:34
Alignment explanation
Indices: 433341--433413 Score: 96
Period size: 33 Copynumber: 2.2 Consensus size: 34
433331 GAAAATGACT
* **
433341 ATCGCAACGCGAATTTGACTATCGCAACGCAAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
433375 ATCGCAACGCGAA-ATGAAAATCGCAACG-ACAGA
1 ATCGCAACGCGAATATGAAAATCGCAACGCA-AGA
433408 ATCGCA
1 ATCGCA
433414 TTGCGATAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
32 1 0.03
33 21 0.60
34 13 0.37
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (34 bp):
ATCGCAACGCGAATATGAAAATCGCAACGCAAGA
Found at i:434018 original size:22 final size:21
Alignment explanation
Indices: 433975--434030 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
433965 GGCGCTATGT
*
433975 AAATCGCATTGCG-ATTTAGG
1 AAATCGCAATGCGAATTTAGG
* *
433995 AAAATCGCAACGCGAATTTGGG
1 -AAATCGCAATGCGAATTTAGG
434017 AAATCGCAATGCGA
1 AAATCGCAATGCGA
434031 TAGTCAGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (21 bp):
AAATCGCAATGCGAATTTAGG
Found at i:436083 original size:19 final size:18
Alignment explanation
Indices: 436049--436084 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
436039 TCTAGTTTTG
436049 AAATTTTAATTGATAATA
1 AAATTTTAATTGATAATA
*
436067 AAATTTATAATTTATAAT
1 AAATTT-TAATTGATAAT
436085 TTTATTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (18 bp):
AAATTTTAATTGATAATA
Found at i:438752 original size:25 final size:25
Alignment explanation
Indices: 438718--438770 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
438708 ATGAACTGTG
438718 ATTTTTTTATCCGTTTGATTCATCA
1 ATTTTTTTATCCGTTTGATTCATCA
438743 ATTTTTTTATCCGTTTGATTCATCA
1 ATTTTTTTATCCGTTTGATTCATCA
438768 ATT
1 ATT
438771 ATTTCAGATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.21, C:0.15, G:0.08, T:0.57
Consensus pattern (25 bp):
ATTTTTTTATCCGTTTGATTCATCA
Found at i:447903 original size:13 final size:13
Alignment explanation
Indices: 447836--447897 Score: 88
Period size: 13 Copynumber: 4.8 Consensus size: 13
447826 TGTGTCATAA
*
447836 ATTTATGACGCGC
1 ATTTATGACGCAC
*
447849 ATTTATGACACAC
1 ATTTATGACGCAC
*
447862 ATTTATGACACAC
1 ATTTATGACGCAC
*
447875 ATTTATGACGTAC
1 ATTTATGACGCAC
447888 ATTTATGACG
1 ATTTATGACG
447898 TTCATTGAGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 45 1.00
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.34
Consensus pattern (13 bp):
ATTTATGACGCAC
Found at i:448066 original size:2 final size:2
Alignment explanation
Indices: 448059--448087 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
448049 TTTCGTAAAT
448059 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
448088 GTAGATTGAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:452937 original size:14 final size:14
Alignment explanation
Indices: 452918--452945 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
452908 ATACCTGTGG
452918 AAACCCTTGAATTT
1 AAACCCTTGAATTT
452932 AAACCCTTGAATTT
1 AAACCCTTGAATTT
452946 TGACTCCCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
AAACCCTTGAATTT
Found at i:453018 original size:16 final size:16
Alignment explanation
Indices: 452997--453031 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
452987 GGGAGGTTGC
452997 AAAGAGAAAAAGGGAA
1 AAAGAGAAAAAGGGAA
*
453013 AAAGAGAAAAATGGAA
1 AAAGAGAAAAAGGGAA
453029 AAA
1 AAA
453032 CATGCGGCGT
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:0.71, C:0.00, G:0.26, T:0.03
Consensus pattern (16 bp):
AAAGAGAAAAAGGGAA
Found at i:474661 original size:18 final size:18
Alignment explanation
Indices: 474638--474678 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
474628 ATGTATAAAT
474638 AATCACAGCCA-ATTATTA
1 AATCAC-GCCATATTATTA
*
474656 AATCACGTCATATTATTA
1 AATCACGCCATATTATTA
474674 AATCA
1 AATCA
474679 GGTATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.32
Consensus pattern (18 bp):
AATCACGCCATATTATTA
Found at i:483508 original size:31 final size:31
Alignment explanation
Indices: 483473--483536 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
483463 ACTAAAAGGG
* *
483473 TTAATATT-AATTTTGCTACCTAAATTTGTCT
1 TTAATATTCAA-TTTGATACCTAAATTTGGCT
* *
483504 TTAATGTTCAATTTGATACCTAATTTTGGCT
1 TTAATATTCAATTTGATACCTAAATTTGGCT
483535 TT
1 TT
483537 TTGTTTGAAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
31 26 0.93
32 2 0.07
ACGTcount: A:0.27, C:0.12, G:0.09, T:0.52
Consensus pattern (31 bp):
TTAATATTCAATTTGATACCTAAATTTGGCT
Found at i:486542 original size:21 final size:21
Alignment explanation
Indices: 486518--486558 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
486508 CCATGAACAG
*
486518 TGCTATAGTGTACCGATGCAT
1 TGCTACAGTGTACCGATGCAT
486539 TGCTACAGTGTACCGATGCA
1 TGCTACAGTGTACCGATGCA
486559 CAAAAACATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.29
Consensus pattern (21 bp):
TGCTACAGTGTACCGATGCAT
Found at i:487363 original size:31 final size:31
Alignment explanation
Indices: 487325--487461 Score: 98
Period size: 37 Copynumber: 4.0 Consensus size: 31
487315 CCCGAAGGAC
487325 CAGTCCATA-GATCCCAAAGAATC-TAGGTAAT
1 CAGTCCATATG-TCCCAAAGAA-CATAGGTAAT
*
487356 CAGTCCATATGTCCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCAAAGAACATAGGTAAT
*
487387 CTATAACTGTCCATATGTCCCGAAGAACATAGGTAAT
1 C----A--GTCCATATGTCCCAAAGAACATAGGTAAT
* *
487424 CTGTAAATGTCCATATGTCTCGAAGAACATAGGTAAT
1 C-----A-GTCCATATGTCCCAAAGAACATAGGTAAT
487461 C
1 C
487462 CTCGACTCTT
Statistics
Matches: 92, Mismatches: 5, Indels: 12
0.84 0.05 0.11
Matches are distributed among these distances:
30 1 0.01
31 27 0.29
32 1 0.01
35 1 0.01
37 60 0.65
38 2 0.02
ACGTcount: A:0.36, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
CAGTCCATATGTCCCAAAGAACATAGGTAAT
Found at i:487400 original size:37 final size:37
Alignment explanation
Indices: 487358--487461 Score: 181
Period size: 37 Copynumber: 2.8 Consensus size: 37
487348 TAGGTAATCA
*
487358 GTCCATATGTCCCGAAGAACATAGGTAATCTATAACT
1 GTCCATATGTCCCGAAGAACATAGGTAATCTATAAAT
*
487395 GTCCATATGTCCCGAAGAACATAGGTAATCTGTAAAT
1 GTCCATATGTCCCGAAGAACATAGGTAATCTATAAAT
*
487432 GTCCATATGTCTCGAAGAACATAGGTAATC
1 GTCCATATGTCCCGAAGAACATAGGTAATC
487462 CTCGACTCTT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (37 bp):
GTCCATATGTCCCGAAGAACATAGGTAATCTATAAAT
Found at i:489083 original size:21 final size:21
Alignment explanation
Indices: 489057--489098 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
489047 CCAGAATGGG
*
489057 GGGAATCGATACCCCTTCATA
1 GGGAATCAATACCCCTTCATA
*
489078 GGGAATCAATACGCCTTCATA
1 GGGAATCAATACCCCTTCATA
489099 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (21 bp):
GGGAATCAATACCCCTTCATA
Found at i:489232 original size:15 final size:15
Alignment explanation
Indices: 489212--489268 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
489202 AACCATGCAG
489212 GGGGAATCTGTACCT
1 GGGGAATCTGTACCT
489227 GGGGAATC-GATACCCCT
1 GGGGAATCTG-TA--CCT
*
489244 GGGGGGAATCTGTTCCT
1 --GGGGAATCTGTACCT
489261 GGGGAATC
1 GGGGAATC
489269 GATACCCCCT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 18 0.51
17 6 0.17
19 9 0.26
20 1 0.03
ACGTcount: A:0.19, C:0.21, G:0.37, T:0.23
Consensus pattern (15 bp):
GGGGAATCTGTACCT
Found at i:489246 original size:17 final size:17
Alignment explanation
Indices: 489224--489282 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 17
489214 GGAATCTGTA
489224 CCTGGGGAATCGATACC
1 CCTGGGGAATCGATACC
*
489241 CCTGGGGGGAATCTG-T--T
1 CCT--GGGGAATC-GATACC
489258 CCTGGGGAATCGATACCC
1 CCTGGGGAATCGATA-CC
489276 CCTGGGG
1 CCTGGGG
489283 GGAATCTGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 13
0.69 0.04 0.27
Matches are distributed among these distances:
14 1 0.03
15 9 0.27
17 6 0.18
18 7 0.21
19 9 0.27
20 1 0.03
ACGTcount: A:0.17, C:0.27, G:0.36, T:0.20
Consensus pattern (17 bp):
CCTGGGGAATCGATACC
Found at i:489285 original size:35 final size:34
Alignment explanation
Indices: 489211--489294 Score: 150
Period size: 34 Copynumber: 2.4 Consensus size: 34
489201 AAACCATGCA
*
489211 GGGGGAATCTGTACCTGGGGAATCGATACCCCTG
1 GGGGGAATCTGTTCCTGGGGAATCGATACCCCTG
489245 GGGGGAATCTGTTCCTGGGGAATCGATACCCCCTG
1 GGGGGAATCTGTTCCTGGGGAATCGATA-CCCCTG
489280 GGGGGAATCTGTTCC
1 GGGGGAATCTGTTCC
489295 CCCTGGGGGG
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
34 27 0.56
35 21 0.44
ACGTcount: A:0.18, C:0.24, G:0.36, T:0.23
Consensus pattern (34 bp):
GGGGGAATCTGTTCCTGGGGAATCGATACCCCTG
Found at i:489303 original size:21 final size:21
Alignment explanation
Indices: 489261--489321 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
489251 ATCTGTTCCT
489261 GGGGAATC-GATACCCCCT-GG
1 GGGGAATCTG-TACCCCCTGGG
*
489281 GGGGAATCTGTTCCCCCTGGG
1 GGGGAATCTGTACCCCCTGGG
489302 GGGGAATCTGTACCCCCTGG
1 GGGGAATCTGTACCCCCTGG
489322 ACAATCTGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 15 0.41
21 22 0.59
ACGTcount: A:0.15, C:0.30, G:0.36, T:0.20
Consensus pattern (21 bp):
GGGGAATCTGTACCCCCTGGG
Found at i:491277 original size:3 final size:3
Alignment explanation
Indices: 491269--491320 Score: 77
Period size: 3 Copynumber: 17.3 Consensus size: 3
491259 TACGTCCTCA
* * *
491269 TTC TTC TTC TTA TTC TTC TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
491317 TTC T
1 TTC T
491321 CTTTCCTTTC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.02, C:0.27, G:0.02, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:492375 original size:34 final size:32
Alignment explanation
Indices: 492315--492384 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
492305 CCTTACAAAC
* *
492315 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGAGCTAAACTAGAACCTT
*
492347 TCCCTAGCTTTTACACGAGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGAGCTAAACTAGAACCTT
492381 TCCC
1 TCCC
492385 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGAGCTAAACTAGAACCTT
Found at i:492692 original size:21 final size:21
Alignment explanation
Indices: 492666--492707 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
492656 CCAGAATAGG
*
492666 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
492687 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
492708 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:492841 original size:15 final size:15
Alignment explanation
Indices: 492821--492877 Score: 53
Period size: 15 Copynumber: 3.5 Consensus size: 15
492811 AACCATGTAG
492821 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
492836 GGGGAATC-GATACCCC
1 GGGGAATCTG-TA-CCC
*
492852 TGGGGGAAATCTGTTCCC
1 --GGGG-AATCTGTACCC
492870 GGGGAATC
1 GGGGAATC
492878 GATACCCCTT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
14 1 0.03
15 14 0.40
16 7 0.20
18 7 0.20
19 5 0.14
20 1 0.03
ACGTcount: A:0.21, C:0.25, G:0.35, T:0.19
Consensus pattern (15 bp):
GGGGAATCTGTACCC
Found at i:492894 original size:19 final size:19
Alignment explanation
Indices: 492836--492928 Score: 70
Period size: 20 Copynumber: 5.0 Consensus size: 19
492826 ATCTGTACCC
492836 GGGGAATCGATACCCCTGG
1 GGGGAATCGATACCCCTGG
* *
492855 GGGAAATCTG-T-TCCC---
1 GGGGAATC-GATACCCCTGG
*
492870 GGGGAATCGATACCCCTTG
1 GGGGAATCGATACCCCTGG
* *
492889 GGGGAATCTGTTCCCCCTGG
1 GGGGAATC-GATACCCCTGG
*
492909 GGGGAATCTATACCCTCTGG
1 GGGGAATCGATACCC-CTGG
492929 ATAATCTGAT
Statistics
Matches: 56, Mismatches: 10, Indels: 15
0.69 0.12 0.19
Matches are distributed among these distances:
14 1 0.02
15 8 0.14
16 3 0.05
18 3 0.05
19 20 0.36
20 21 0.38
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (19 bp):
GGGGAATCGATACCCCTGG
Found at i:492900 original size:34 final size:33
Alignment explanation
Indices: 492820--492903 Score: 141
Period size: 34 Copynumber: 2.5 Consensus size: 33
492810 AAACCATGTA
*
492820 GGGGGAATCTGTACCCGGGGAATCGATACCCCT
1 GGGGGAATCTGTTCCCGGGGAATCGATACCCCT
492853 GGGGGAAATCTGTTCCCGGGGAATCGATACCCCTT
1 GGGGG-AATCTGTTCCCGGGGAATCGATACCCC-T
492888 GGGGGAATCTGTTCCC
1 GGGGGAATCTGTTCCC
492904 CCTGGGGGGA
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
33 5 0.10
34 37 0.77
35 6 0.12
ACGTcount: A:0.19, C:0.26, G:0.33, T:0.21
Consensus pattern (33 bp):
GGGGGAATCTGTTCCCGGGGAATCGATACCCCT
Found at i:492928 original size:20 final size:19
Alignment explanation
Indices: 492836--492928 Score: 68
Period size: 19 Copynumber: 5.0 Consensus size: 19
492826 ATCTGTACCC
*
492836 GGGGAATCGATACCCCTGG
1 GGGGAATCTATACCCCTGG
* * *
492855 GGGAAATCTGT-TCCC---
1 GGGGAATCTATACCCCTGG
* *
492870 GGGGAATCGATACCCCTTG
1 GGGGAATCTATACCCCTGG
* *
492889 GGGGAATCTGTTCCCCCTGG
1 GGGGAATCT-ATACCCCTGG
492909 GGGGAATCTATACCCTCTGG
1 GGGGAATCTATACCC-CTGG
492929 ATAATCTGAT
Statistics
Matches: 54, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
15 8 0.15
16 3 0.06
18 3 0.06
19 20 0.37
20 20 0.37
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (19 bp):
GGGGAATCTATACCCCTGG
Found at i:502086 original size:19 final size:19
Alignment explanation
Indices: 502062--502106 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
502052 CAGTGCTTGA
*
502062 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCCG
* *
502081 AACCGGGTTGATCGGTCCG
1 AACCGGTTTGACCGGTCCG
502100 AACCGGT
1 AACCGGT
502107 CCGACCCGAC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.18, C:0.27, G:0.33, T:0.22
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCCG
Found at i:518180 original size:37 final size:37
Alignment explanation
Indices: 518107--518181 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
518097 GTTAGAAAAT
*
518107 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
518144 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
518181 A
1 A
518182 AGATTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 24 0.73
38 9 0.27
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:520366 original size:17 final size:18
Alignment explanation
Indices: 520334--520367 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
520324 AGAATTATAG
*
520334 AAAATGTCCATAAAGTGT
1 AAAATGACCATAAAGTGT
520352 AAAATGACC-TAAAGTG
1 AAAATGACCATAAAGTG
520368 ACTCCAAGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.24
Consensus pattern (18 bp):
AAAATGACCATAAAGTGT
Found at i:523503 original size:16 final size:17
Alignment explanation
Indices: 523468--523511 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
523458 TTATTAGGTG
523468 AAAAATAATATTATTGT
1 AAAAATAATATTATTGT
523485 AAAAAT-ATAATTATT-T
1 AAAAATAAT-ATTATTGT
523501 -AAAATAATATT
1 AAAAATAATATT
523512 TAACTTTAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 8 0.32
16 5 0.20
17 12 0.48
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (17 bp):
AAAAATAATATTATTGT
Found at i:524231 original size:2 final size:2
Alignment explanation
Indices: 524224--524258 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
524214 AATAAAAATG
524224 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
524259 AGGTTAGAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:526786 original size:21 final size:21
Alignment explanation
Indices: 526760--526802 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
526750 TTTTCGGGCT
* *
526760 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
526781 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
526802 A
1 A
526803 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:526876 original size:66 final size:68
Alignment explanation
Indices: 526782--526931 Score: 216
Period size: 67 Copynumber: 2.2 Consensus size: 68
526772 ACCCATTCAA
*
526782 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCAAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCTTCAACGAATATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCA
526846 -GG
66 GGG
* * **
526848 GGGGAACCGATACCTCC-TCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCC
1 GGGGAACCGATACC-CCTTCAACGAATATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCC
526912 AGGG
65 AGGG
*
526916 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
526932 CATGAGAAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
66 24 0.32
67 36 0.48
68 15 0.20
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCTTCAACGAATATGAAATTCCAGAATGCAAGAGGGGAATCGATACCCCCA
GGG
Found at i:527269 original size:29 final size:29
Alignment explanation
Indices: 527235--527306 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
527225 CATATTATGA
* *
527235 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
527264 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
527293 TGCATGACATGAAT
1 TACATGACATGAAT
527307 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:527362 original size:30 final size:30
Alignment explanation
Indices: 527320--527396 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
527310 CAGAAAAGTT
* *
527320 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
527351 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
527381 ATATGACTACGTGATA
1 ATATGACTATGTGATA
527397 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:527629 original size:13 final size:13
Alignment explanation
Indices: 527611--527673 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
527601 TTATATGGCA
527611 CTACGGTGCAATT
1 CTACGGTGCAATT
527624 CTACGG-GC-A--
1 CTACGGTGCAATT
*
527633 CTTCGGTGCAATT
1 CTACGGTGCAATT
527646 CTACGG-GC-A--
1 CTACGGTGCAATT
*
527655 CTTCGGTGCAATT
1 CTACGGTGCAATT
527668 CTACGG
1 CTACGG
527674 GGCACTTCGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:527639 original size:22 final size:22
Alignment explanation
Indices: 527607--527687 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
527597 ATCATTATAT
*
527607 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
527629 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
527651 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
527674 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
527688 TTTATACGAG
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 42 0.74
23 15 0.26
ACGTcount: A:0.19, C:0.27, G:0.30, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:533754 original size:21 final size:21
Alignment explanation
Indices: 533728--533770 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
533718 TTTTCGGGCT
* *
533728 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
533749 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
533770 A
1 A
533771 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:533844 original size:66 final size:67
Alignment explanation
Indices: 533750--533898 Score: 230
Period size: 67 Copynumber: 2.2 Consensus size: 67
533740 ACCCATTCAA
*
533750 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCTTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
533814 GG
66 GG
* * *
533816 GGGGAACCGATACCTCC-TCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCC
1 GGGGAACCGATACC-CCTTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCC
533880 AGG
65 AGG
*
533883 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
533899 CATGAGAAAA
Statistics
Matches: 76, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
66 26 0.34
67 50 0.66
ACGTcount: A:0.28, C:0.27, G:0.26, T:0.19
Consensus pattern (67 bp):
GGGGAACCGATACCCCTTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:533888 original size:20 final size:20
Alignment explanation
Indices: 533863--533900 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
533853 GAATGCTTGA
*
533863 GGGGAATCGATACCCCCAGG
1 GGGGAACCGATACCCCCAGG
*
533883 GGGGAACCGATTCCCCCA
1 GGGGAACCGATACCCCCA
533901 TGAGAAAAAA
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:0.24, C:0.34, G:0.32, T:0.11
Consensus pattern (20 bp):
GGGGAACCGATACCCCCAGG
Found at i:534236 original size:29 final size:29
Alignment explanation
Indices: 534202--534273 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
534192 CATATTATGA
* *
534202 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
534231 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
534260 TGCATGACATGAAT
1 TACATGACATGAAT
534274 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:534329 original size:30 final size:30
Alignment explanation
Indices: 534287--534363 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
534277 CAGAAAAGTT
* *
534287 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
534318 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
534348 ATATGACTACGTGATA
1 ATATGACTATGTGATA
534364 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:534596 original size:13 final size:13
Alignment explanation
Indices: 534578--534640 Score: 52
Period size: 13 Copynumber: 5.5 Consensus size: 13
534568 TTATATGGCA
534578 CTACGGTGCAATT
1 CTACGGTGCAATT
534591 CTACGG-GC-A--
1 CTACGGTGCAATT
*
534600 CTTCGGTGCAATT
1 CTACGGTGCAATT
534613 CTACGG-GC-A--
1 CTACGGTGCAATT
*
534622 CTTCGGTGCAATT
1 CTACGGTGCAATT
534635 CTACGG
1 CTACGG
534641 GGTACTTTGG
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 10 0.26
10 4 0.11
11 4 0.11
12 4 0.11
13 16 0.42
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.27
Consensus pattern (13 bp):
CTACGGTGCAATT
Found at i:534606 original size:22 final size:22
Alignment explanation
Indices: 534574--534641 Score: 127
Period size: 22 Copynumber: 3.1 Consensus size: 22
534564 ATCATTATAT
*
534574 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
534596 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
534618 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
534640 GG
1 GG
534642 GTACTTTGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.19, C:0.26, G:0.29, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:536335 original size:18 final size:21
Alignment explanation
Indices: 536312--536361 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
536302 TCCATTTTTG
*
536312 GTATCGATACTC-A-TG-AGA
1 GTATCGATACTCAAGGGTAGA
536330 GTATCGATAC-CAAGGGTAGA
1 GTATCGATACTCAAGGGTAGA
536350 GTATCGATACTC
1 GTATCGATACTC
536362 CTTAATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 1 0.04
18 11 0.41
19 1 0.04
20 13 0.48
21 1 0.04
ACGTcount: A:0.32, C:0.18, G:0.24, T:0.26
Consensus pattern (21 bp):
GTATCGATACTCAAGGGTAGA
Found at i:536440 original size:20 final size:21
Alignment explanation
Indices: 536388--536443 Score: 62
Period size: 22 Copynumber: 2.7 Consensus size: 21
536378 ATACTTCCTT
*
536388 GAGTATCAATACCATAGACCA
1 GAGTATCAATACCATAGACAA
*
536409 GAAGTATTAATACTCA-AGA-AA
1 G-AGTATCAATAC-CATAGACAA
536430 GAGTATCAATACCA
1 GAGTATCAATACCA
536444 ACCCTTTGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 2 0.07
20 10 0.33
21 3 0.10
22 13 0.43
23 2 0.07
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.21
Consensus pattern (21 bp):
GAGTATCAATACCATAGACAA
Found at i:540361 original size:30 final size:30
Alignment explanation
Indices: 540327--540386 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
540317 ACTGGAGATG
*
540327 TTGATACTGCTAGGCTAGGAATTCAACAAA
1 TTGATACTGCTAGGCTAGAAATTCAACAAA
*
540357 TTGATACTGCTAGGTTAGAAATTCAACAAA
1 TTGATACTGCTAGGCTAGAAATTCAACAAA
540387 GTCATTCACC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.15, G:0.18, T:0.28
Consensus pattern (30 bp):
TTGATACTGCTAGGCTAGAAATTCAACAAA
Found at i:546535 original size:31 final size:31
Alignment explanation
Indices: 546500--546566 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
546490 ATATAATATT
546500 TGGTCA-TTTTCGTTTTTATTTAATTAAGATG
1 TGGTCACTTTT-GTTTTTATTTAATTAAGATG
546531 TGGTCACTTTTGTTTTTATTTAATTAAGATG
1 TGGTCACTTTTGTTTTTATTTAATTAAGATG
546562 TGGTC
1 TGGTC
546567 GCTAAAGATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 31 0.89
32 4 0.11
ACGTcount: A:0.21, C:0.07, G:0.18, T:0.54
Consensus pattern (31 bp):
TGGTCACTTTTGTTTTTATTTAATTAAGATG
Found at i:549419 original size:2 final size:2
Alignment explanation
Indices: 549404--549437 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
549394 ATTAAACACT
* *
549404 TA TA TA TC TT 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
549438 GTGTTCGAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:550173 original size:100 final size:100
Alignment explanation
Indices: 550003--550202 Score: 400
Period size: 100 Copynumber: 2.0 Consensus size: 100
549993 AGCTCATACC
550003 TCTGGTTCATAGCAGGAAGAAGAAGATGAAGAATAGAGCTTACCATTGCGAGCTTTGGATAAGAA
1 TCTGGTTCATAGCAGGAAGAAGAAGATGAAGAATAGAGCTTACCATTGCGAGCTTTGGATAAGAA
550068 TGCTTGGCCCACCCTATTCCCATATGTAATGGGGT
66 TGCTTGGCCCACCCTATTCCCATATGTAATGGGGT
550103 TCTGGTTCATAGCAGGAAGAAGAAGATGAAGAATAGAGCTTACCATTGCGAGCTTTGGATAAGAA
1 TCTGGTTCATAGCAGGAAGAAGAAGATGAAGAATAGAGCTTACCATTGCGAGCTTTGGATAAGAA
550168 TGCTTGGCCCACCCTATTCCCATATGTAATGGGGT
66 TGCTTGGCCCACCCTATTCCCATATGTAATGGGGT
550203 AAGGGGAGGT
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
100 100 1.00
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (100 bp):
TCTGGTTCATAGCAGGAAGAAGAAGATGAAGAATAGAGCTTACCATTGCGAGCTTTGGATAAGAA
TGCTTGGCCCACCCTATTCCCATATGTAATGGGGT
Found at i:550240 original size:49 final size:49
Alignment explanation
Indices: 550187--550287 Score: 193
Period size: 49 Copynumber: 2.1 Consensus size: 49
550177 CACCCTATTC
*
550187 CCATATGTAATGGGGTAAGGGGAGGTAAGATAGTAGGCTGCCCCTAACG
1 CCATATGTAATGGGGTAAGGGGAGGTAAGATAGTAGGCTGCCCCCAACG
550236 CCATATGTAATGGGGTAAGGGGAGGTAAGATAGTAGGCTGCCCCCAACG
1 CCATATGTAATGGGGTAAGGGGAGGTAAGATAGTAGGCTGCCCCCAACG
550285 CCA
1 CCA
550288 GGTTGAGAAC
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.29, C:0.19, G:0.34, T:0.19
Consensus pattern (49 bp):
CCATATGTAATGGGGTAAGGGGAGGTAAGATAGTAGGCTGCCCCCAACG
Found at i:550530 original size:27 final size:27
Alignment explanation
Indices: 550500--550590 Score: 168
Period size: 26 Copynumber: 3.4 Consensus size: 27
550490 ATATGTCAAT
550500 TTAAAAATGTATTTATTATTATTTTAA
1 TTAAAAATGTATTTATTATTATTTTAA
550527 TTAAAAATGTATTTATTATTA-TTTAA
1 TTAAAAATGTATTTATTATTATTTTAA
550553 TTAAAAATGTATTTATTATT-TTTTAA
1 TTAAAAATGTATTTATTATTATTTTAA
550579 TTAAAAATGTAT
1 TTAAAAATGTAT
550591 ATAAATTAAA
Statistics
Matches: 63, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
26 42 0.67
27 21 0.33
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (27 bp):
TTAAAAATGTATTTATTATTATTTTAA
Found at i:554251 original size:21 final size:20
Alignment explanation
Indices: 554227--554276 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
554217 CAATTTAAAA
*
554227 TTTAAGATTTAAAGGTTTATG
1 TTTAAGATTTAAA-ATTTATG
554248 TTT-AGAATTTAAAATTTATG
1 TTTAAG-ATTTAAAATTTATG
*
554268 ATTAAGATT
1 TTTAAGATT
554277 GTTTGGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.38, C:0.00, G:0.14, T:0.48
Consensus pattern (20 bp):
TTTAAGATTTAAAATTTATG
Found at i:560925 original size:23 final size:23
Alignment explanation
Indices: 560895--560945 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
560885 GGTAGATCAG
560895 TAGATCGAGAGTTCGAGAAGCAA
1 TAGATCGAGAGTTCGAGAAGCAA
*
560918 TAGATCGAGAGTTCGAGAAGCAG
1 TAGATCGAGAGTTCGAGAAGCAA
560941 TAGAT
1 TAGAT
560946 AAATCAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.37, C:0.12, G:0.31, T:0.20
Consensus pattern (23 bp):
TAGATCGAGAGTTCGAGAAGCAA
Found at i:562678 original size:53 final size:53
Alignment explanation
Indices: 562598--562709 Score: 215
Period size: 53 Copynumber: 2.1 Consensus size: 53
562588 CGTTTTGGAC
562598 TAAAATGCCTTTAAATTTTTATTGTTTTTTTCAAAAATATCATTATTCTGTCA
1 TAAAATGCCTTTAAATTTTTATTGTTTTTTTCAAAAATATCATTATTCTGTCA
562651 TAAAATGCCTTTAAATTTTTATTGTTTTTTTCAAAAATATCATTATTCTGTCA
1 TAAAATGCCTTTAAATTTTTATTGTTTTTTTCAAAAATATCATTATTCTGTCA
*
562704 TTAAAT
1 TAAAAT
562710 AATAAAAATT
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 58 1.00
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.51
Consensus pattern (53 bp):
TAAAATGCCTTTAAATTTTTATTGTTTTTTTCAAAAATATCATTATTCTGTCA
Found at i:564993 original size:31 final size:31
Alignment explanation
Indices: 564958--565115 Score: 128
Period size: 31 Copynumber: 5.1 Consensus size: 31
564948 AATTTGCACA
*
564958 TTTAGGCACCTTAGTGAGACCAAAAATAAAC
1 TTTAGACACCTTAGTGAGACCAAAAATAAAC
*
564989 TTTAGACACCTTATTGAGACCAAAAATAAAC
1 TTTAGACACCTTAGTGAGACCAAAAATAAAC
* * *
565020 TTTAGACACCCTT--TTACAACAAAAAATAAAC
1 TTTAGACA-CCTTAGTGA-GACCAAAAATAAAC
* **
565051 TTTA-AGCACCTT-GATGTG-TTAAAAATAAAC
1 TTTAGA-CACCTTAG-TGAGACCAAAAATAAAC
* * * * *
565081 TTTAGACTCCCTATTAATACCAAAAATAAAC
1 TTTAGACACCTTAGTGAGACCAAAAATAAAC
565112 TTTA
1 TTTA
565116 AGATAACCAT
Statistics
Matches: 101, Mismatches: 18, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
30 26 0.26
31 70 0.69
32 5 0.05
ACGTcount: A:0.44, C:0.19, G:0.09, T:0.28
Consensus pattern (31 bp):
TTTAGACACCTTAGTGAGACCAAAAATAAAC
Found at i:565408 original size:68 final size:67
Alignment explanation
Indices: 565333--565465 Score: 257
Period size: 68 Copynumber: 2.0 Consensus size: 67
565323 AGCTCCAACA
565333 ATTTTTATAAGTTCCTTTAATTCACTATTTTTGGCTTTGATTTTTTTTATTCTCGACCATCACCA
1 ATTTTTATAAGTTCCTTTAATTCACTATTTTTGGCTTTGA-TTTTTTTATTCTCGACCATCACCA
565398 TCG
65 TCG
565401 ATTTTTATAAGTTCCTTTAATTCACTATTTTTGGCTTTGATTTTTTTATTCTCGACCATCACCAT
1 ATTTTTATAAGTTCCTTTAATTCACTATTTTTGGCTTTGATTTTTTTATTCTCGACCATCACCAT
565466 TTCAAGTGTT
Statistics
Matches: 65, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
67 25 0.38
68 40 0.62
ACGTcount: A:0.21, C:0.19, G:0.08, T:0.52
Consensus pattern (67 bp):
ATTTTTATAAGTTCCTTTAATTCACTATTTTTGGCTTTGATTTTTTTATTCTCGACCATCACCAT
CG
Found at i:565721 original size:66 final size:70
Alignment explanation
Indices: 565646--565831 Score: 227
Period size: 72 Copynumber: 2.7 Consensus size: 70
565636 AGATACAAGC
** *
565646 ATCAATTACAACATT-AG-AATTAC-AA-CAAATATGTTGAATTTCCAAAAGTACATGCAGCTTT
1 ATCAATTACAACATTAAGTAAAAACAAACCAAATATGTTGAATTTCCAAAAGTACATGCAACTTT
565707 CAAAG
66 CAAAG
* *
565712 ATCAATTACAACATTCAAAGTAAAAACAAACCAAATATGTTGAATTTTCAATAGTACATGCAACT
1 ATCAATTACAACATT--AAGTAAAAACAAACCAAATATGTTGAATTTCCAAAAGTACATGCAACT
*
565777 TTGAAAG
64 TTCAAAG
* * *
565784 ATCAGTTACAAAATTTAAAGTAAAAACAAACTAAATATGTTGAATTTC
1 ATCAATTACAACA-TT-AAGTAAAAACAAACCAAATATGTTGAATTTC
565832 GAGTTGATTC
Statistics
Matches: 103, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
66 15 0.15
69 2 0.02
70 4 0.04
71 2 0.02
72 78 0.76
73 2 0.02
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.29
Consensus pattern (70 bp):
ATCAATTACAACATTAAGTAAAAACAAACCAAATATGTTGAATTTCCAAAAGTACATGCAACTTT
CAAAG
Found at i:565757 original size:72 final size:72
Alignment explanation
Indices: 565671--565831 Score: 250
Period size: 72 Copynumber: 2.2 Consensus size: 72
565661 AGAATTACAA
* *
565671 CAAATATGTTGAATTTCCAAAAGTACATGCAGCTTTCAAAGATCAATTACAACATTCAAAGTAAA
1 CAAATATGTTGAATTTCCAAAAGTACATGCAACTTTCAAAGATCAATTACAAAATTCAAAGTAAA
565736 AACAAAC
66 AACAAAC
* * * * *
565743 CAAATATGTTGAATTTTCAATAGTACATGCAACTTTGAAAGATCAGTTACAAAATTTAAAGTAAA
1 CAAATATGTTGAATTTCCAAAAGTACATGCAACTTTCAAAGATCAATTACAAAATTCAAAGTAAA
565808 AACAAAC
66 AACAAAC
*
565815 TAAATATGTTGAATTTC
1 CAAATATGTTGAATTTC
565832 GAGTTGATTC
Statistics
Matches: 80, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
72 80 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (72 bp):
CAAATATGTTGAATTTCCAAAAGTACATGCAACTTTCAAAGATCAATTACAAAATTCAAAGTAAA
AACAAAC
Found at i:568248 original size:12 final size:12
Alignment explanation
Indices: 568231--568255 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
568221 GATGACCCGG
568231 ATTGTATTAAGA
1 ATTGTATTAAGA
568243 ATTGTATTAAGA
1 ATTGTATTAAGA
568255 A
1 A
568256 CGATGTACTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (12 bp):
ATTGTATTAAGA
Found at i:575084 original size:8 final size:8
Alignment explanation
Indices: 575071--575111 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
575061 CTCATTTTCA
575071 GAGAATTT
1 GAGAATTT
575079 GAGAATTT
1 GAGAATTT
*
575087 -AGAGTTT
1 GAGAATTT
*
575094 GGGAATTT
1 GAGAATTT
575102 GAGAATTT
1 GAGAATTT
575110 GA
1 GA
575112 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:575598 original size:125 final size:126
Alignment explanation
Indices: 575179--575908 Score: 1367
Period size: 126 Copynumber: 5.8 Consensus size: 126
575169 CTATAATCGG
575179 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
* *
575244 TCATTGCCCTATTATGTCATTCATGTCCATCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
575305 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
575370 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
575431 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
575496 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
575556 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
*
575621 TCATTGCCCTATTATGTCATTCATGTCCCTC-GGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
575681 TTCACTATTCACATGAAGGCGCGTTCCC-GGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
575745 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
66 TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
*
575806 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGTGCCTTCCATTATTTCGTCAGAGAATATGT
1 TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATA--T
575871 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
64 TATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGA
575909 ATAACTTAAA
Statistics
Matches: 593, Mismatches: 7, Indels: 6
0.98 0.01 0.01
Matches are distributed among these distances:
124 66 0.11
125 239 0.40
126 249 0.42
128 39 0.07
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (126 bp):
TTCACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTCGTCAGAGAATATTA
TCATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTAT
Found at i:576375 original size:31 final size:34
Alignment explanation
Indices: 576295--576389 Score: 103
Period size: 30 Copynumber: 3.0 Consensus size: 34
576285 AAATTTAATG
*
576295 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
* * *
576329 TTAAATTT-GAATAATAT-TTTTTTA-TTT-ATT
1 TTAAATTTCGAATAATATAATTTATATTTTAAAT
*
576359 TTAAATTTCGAAT-A-ATAATTTGTATTTTAAA
1 TTAAATTTCGAATAATATAATTTATATTTTAAA
576390 AACATTTATC
Statistics
Matches: 50, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
29 2 0.04
30 16 0.32
31 10 0.20
32 6 0.12
33 8 0.16
34 8 0.16
ACGTcount: A:0.39, C:0.03, G:0.04, T:0.54
Consensus pattern (34 bp):
TTAAATTTCGAATAATATAATTTATATTTTAAAT
Found at i:576939 original size:21 final size:21
Alignment explanation
Indices: 576909--576981 Score: 105
Period size: 21 Copynumber: 3.5 Consensus size: 21
576899 TATGGTATAA
*
576909 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
576930 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
576951 AACCCTGCGGGCTCA-GAATGT
1 AACCCTGCGGGCT-AGGAATGT
576972 AACCCTGCGG
1 AACCCTGCGG
576982 AGATGGCATA
Statistics
Matches: 48, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
20 3 0.06
21 41 0.85
22 4 0.08
ACGTcount: A:0.22, C:0.27, G:0.33, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:577011 original size:21 final size:21
Alignment explanation
Indices: 576985--577032 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
576975 CCTGCGGAGA
*
576985 TGGCATATAAACTGGTGGGCT
1 TGGCATATAAACTGGAGGGCT
* *
577006 TGGCATATGAAGTGGAGGGCT
1 TGGCATATAAACTGGAGGGCT
*
577027 GGGCAT
1 TGGCAT
577033 GTACCCCTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.23, C:0.12, G:0.40, T:0.25
Consensus pattern (21 bp):
TGGCATATAAACTGGAGGGCT
Found at i:578798 original size:34 final size:31
Alignment explanation
Indices: 578753--578839 Score: 86
Period size: 34 Copynumber: 2.7 Consensus size: 31
578743 TTAATAATTC
*
578753 TAAATAATAATAATTATATAAATATTATTTTAATA
1 TAAAAAATAATAATTATATAAATA-TA---TAATA
* *
578788 -AAAAAATAATATTTACATAAATATATAATA
1 TAAAAAATAATAATTATATAAATATATAATA
* *
578818 TAAAAAATAATAACTATTTAAA
1 TAAAAAATAATAATTATATAAA
578840 AAAATACTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
30 5 0.11
31 17 0.39
33 2 0.05
34 20 0.45
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
TAAAAAATAATAATTATATAAATATATAATA
Found at i:578807 original size:19 final size:18
Alignment explanation
Indices: 578781--578843 Score: 53
Period size: 19 Copynumber: 3.6 Consensus size: 18
578771 TAAATATTAT
578781 TTTAATAAAAAAATAATA
1 TTTAATAAAAAAATAATA
* *
578799 TTTACATAAATATATAATA
1 TTTA-ATAAAAAAATAATA
*
578818 --TAA-AAAATAATAACTA
1 TTTAATAAAAAAATAA-TA
578834 TTTAA-AAAAA
1 TTTAATAAAAA
578844 TACTAACATA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
15 7 0.20
16 3 0.09
17 2 0.06
18 11 0.31
19 12 0.34
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTAATAAAAAAATAATA
Found at i:578855 original size:34 final size:33
Alignment explanation
Indices: 578787--578862 Score: 84
Period size: 34 Copynumber: 2.2 Consensus size: 33
578777 TTATTTTAAT
* *
578787 AAAAAAATAATATTTACATAAATATATAATATA
1 AAAAAAATAATATTTACATAAAAATATAACATA
578820 AAAAATAATAACTATTTA-A-AAAAATACTAACATA
1 AAAAA-AATAA-TATTTACATAAAAATA-TAACATA
578854 AAAATAAAT
1 AAAA-AAAT
578863 TTCTTACCAC
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
33 11 0.30
34 19 0.51
35 7 0.19
ACGTcount: A:0.66, C:0.05, G:0.00, T:0.29
Consensus pattern (33 bp):
AAAAAAATAATATTTACATAAAAATATAACATA
Found at i:580297 original size:19 final size:17
Alignment explanation
Indices: 580257--580292 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
580247 TACATATAAC
580257 AATATATAATCTTAATT
1 AATATATAATCTTAATT
580274 AATATA-AATCTTAA-T
1 AATATATAATCTTAATT
580289 AATA
1 AATA
580293 AATATTAACC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.26
16 8 0.42
17 6 0.32
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
AATATATAATCTTAATT
Found at i:584656 original size:13 final size:13
Alignment explanation
Indices: 584638--584663 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
584628 AGTTATTCAG
584638 ACCCTTTGAGACC
1 ACCCTTTGAGACC
584651 ACCCTTTGAGACC
1 ACCCTTTGAGACC
584664 GTCAGTTGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.38, G:0.15, T:0.23
Consensus pattern (13 bp):
ACCCTTTGAGACC
Found at i:587025 original size:98 final size:98
Alignment explanation
Indices: 586852--587041 Score: 308
Period size: 98 Copynumber: 1.9 Consensus size: 98
586842 ATTTTTATTG
* * * *
586852 GACTCGAAGAATAAATAAATAAATTACTTTTCTAATTTATTTCGAAAGTTAATTTGTTTAAACAA
1 GACTCAAAGAATAAATAAATAAATTACTTTTCGAATTTATTTCAAAAGCTAATTTGTTTAAACAA
*
586917 GCCTAATTAAGATTGATTTTAACTTAGGAACAT
66 GCCTAATTAAGATTGATTTCAACTTAGGAACAT
*
586950 GACTCAAAGAATAAATAAATAAATTACTTTTCGAATTTATTTCAAAAGCTAGTTTGTTTAAACAA
1 GACTCAAAGAATAAATAAATAAATTACTTTTCGAATTTATTTCAAAAGCTAATTTGTTTAAACAA
* *
587015 GTCTATTTAAGATTGATTTCAACTTAG
66 GCCTAATTAAGATTGATTTCAACTTAG
587042 CAACTTGAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
98 84 1.00
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.38
Consensus pattern (98 bp):
GACTCAAAGAATAAATAAATAAATTACTTTTCGAATTTATTTCAAAAGCTAATTTGTTTAAACAA
GCCTAATTAAGATTGATTTCAACTTAGGAACAT
Found at i:589371 original size:3 final size:3
Alignment explanation
Indices: 589358--589397 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
589348 AGACTTTACA
589358 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
589398 CAAATATTAT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:589744 original size:26 final size:26
Alignment explanation
Indices: 589708--589766 Score: 91
Period size: 26 Copynumber: 2.3 Consensus size: 26
589698 AAGTTGAAAG
*
589708 GAATTTTATAAGTAACTTCCTATTCA
1 GAATTTTATAAGAAACTTCCTATTCA
*
589734 GAATTTTATAAGAAACTTCCTGTTCA
1 GAATTTTATAAGAAACTTCCTATTCA
*
589760 AAATTTT
1 GAATTTT
589767 GAGGTGTCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (26 bp):
GAATTTTATAAGAAACTTCCTATTCA
Found at i:590129 original size:4 final size:4
Alignment explanation
Indices: 590120--590183 Score: 50
Period size: 4 Copynumber: 17.0 Consensus size: 4
590110 TTAATGAAAG
* *
590120 TAAA TAAA T-AA TAAA T-AA TAAC T-AA TGAA TAAA -AAA T-AA TAAGA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAA-A
590164 -AAA TAAA TAAA GTAAA TAAA
1 TAAA TAAA TAAA -TAAA TAAA
590184 GTACAAGAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 16
0.72 0.04 0.24
Matches are distributed among these distances:
3 15 0.31
4 29 0.59
5 5 0.10
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (4 bp):
TAAA
Found at i:590134 original size:7 final size:7
Alignment explanation
Indices: 590122--590173 Score: 59
Period size: 7 Copynumber: 7.3 Consensus size: 7
590112 AATGAAAGTA
590122 AATAAAT
1 AATAAAT
590129 AATAAAT
1 AATAAAT
*
590136 AATAACT
1 AATAAAT
*
590143 AATGAAT
1 AATAAAT
*
590150 AAAAAAT
1 AATAAAT
*
590157 AATAAGAA
1 AATAA-AT
590165 AATAAAT
1 AATAAAT
590172 AA
1 AA
590174 AGTAAATAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
7 30 0.83
8 6 0.17
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.23
Consensus pattern (7 bp):
AATAAAT
Found at i:595957 original size:29 final size:30
Alignment explanation
Indices: 595907--595967 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 30
595897 TTTAGAAATC
* *
595907 TATTTTTTATTTTATTATA-TTTATT-TAA
1 TATTTTTTATTTTATAAGATTTTATTCTAA
595935 TATTTTATTATTTTATAAGATTTTATTCTAA
1 TATTTT-TTATTTTATAAGATTTTATTCTAA
595966 TA
1 TA
595968 AGTAAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.21
29 11 0.39
30 6 0.21
31 5 0.18
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (30 bp):
TATTTTTTATTTTATAAGATTTTATTCTAA
Found at i:595961 original size:18 final size:20
Alignment explanation
Indices: 595915--595961 Score: 62
Period size: 18 Copynumber: 2.4 Consensus size: 20
595905 TCTATTTTTT
*
595915 ATTTTATTATATTTATTTAAT
1 ATTTTATTATATTTA-TTAAG
595936 ATTTTATTAT-TTTA-TAAG
1 ATTTTATTATATTTATTAAG
595954 ATTTTATT
1 ATTTTATT
595962 CTAATAAGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 11 0.44
20 4 0.16
21 10 0.40
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTTTATTATATTTATTAAG
Found at i:597867 original size:23 final size:21
Alignment explanation
Indices: 597841--597893 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
597831 ATATCACATG
*
597841 TTCATATAAGCTCATAGCTTCTT
1 TTCATATAA-CTCATAGC-ACTT
* * *
597864 TTCATGTAATTCATATCACTT
1 TTCATATAACTCATAGCACTT
597885 TTCATATAA
1 TTCATATAA
597894 TTCACATGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 11 0.44
22 6 0.24
23 8 0.32
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (21 bp):
TTCATATAACTCATAGCACTT
Found at i:598653 original size:64 final size:64
Alignment explanation
Indices: 598501--598661 Score: 173
Period size: 64 Copynumber: 2.5 Consensus size: 64
598491 TCTTTAACAT
* * * * * *
598501 GTGCATCGATGCACTACCCATGCATCGATATACTAATCACCTTCGATGTTTTCATTTTAAGGGG
1 GTGCATCGATGCACTTCCTATGCATCAATACACTAATCACATTCGATGTTTCCATTTTAAGGGG
* * ** *
598565 GTGTATCGATGCAC-TCCTTATGCATCAATGCACTAATTGCATTCGATGTTTCCATTTTTAA-TG
1 GTGCATCGATGCACTTCC-TATGCATCAATACACTAATCACATTCGATGTTTCCA-TTTTAAGGG
598628 G
64 G
* *
598629 GTGCATCGATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCACTTCCTATGCATCAATACAC
598662 ACTAAACAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
63 2 0.03
64 68 0.86
65 9 0.11
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTTCCTATGCATCAATACACTAATCACATTCGATGTTTCCATTTTAAGGGG
Found at i:601609 original size:18 final size:19
Alignment explanation
Indices: 601582--601619 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
601572 CAAGCAATTG
*
601582 TATCATTATC-TTCATTCT
1 TATCACTATCATTCATTCT
*
601600 TATCACTATCATTGATTCT
1 TATCACTATCATTCATTCT
601619 T
1 T
601620 TTTATCATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.24, C:0.21, G:0.03, T:0.53
Consensus pattern (19 bp):
TATCACTATCATTCATTCT
Found at i:602728 original size:24 final size:20
Alignment explanation
Indices: 602677--602732 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 20
602667 TCCCTTGAAC
*
602677 TGCATCGATGTATTCTACAG
1 TGCATCGATGCATTCTACAG
602697 TGCATCGATGCATTCTTTAACATG
1 TGCATCGATGCATTC--T-ACA-G
602721 TGCATCGATGCA
1 TGCATCGATGCA
602733 CTACCCATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 14 0.45
22 1 0.03
23 3 0.10
24 13 0.42
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (20 bp):
TGCATCGATGCATTCTACAG
Found at i:602811 original size:19 final size:19
Alignment explanation
Indices: 602787--602835 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
602777 TAAGGGGGTG
*
602787 CATCGATGCACTCTTTATA
1 CATCGATGCACTCCTTATA
* *
602806 CATCGATGTACTCCTTATG
1 CATCGATGCACTCCTTATA
602825 CATCGATGCAC
1 CATCGATGCAC
602836 AAATTGCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.24, C:0.29, G:0.14, T:0.33
Consensus pattern (19 bp):
CATCGATGCACTCCTTATA
Done.