Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003856.1 Hibiscus syriacus cultivar Beakdansim tig00008289_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: 822684
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:477160 original size:112 final size:112
Alignment explanation
Indices: 476960--477163 Score: 392
Period size: 112 Copynumber: 1.8 Consensus size: 112
476950 CGATAGACAT
476960 TAAGATGATTGCGAACGTCATTTCCGTGTTGCGATAGTCAAATGAATGCTAATAAGTGATAACAA
1 TAAGATGATTGCGAACGTCATTTCCGTGTTGCGATAGTCAAATGAATGCTAATAAGTGATAACAA
477025 CTGAACAGATCATAGAAATTTTCAAACGTTGCGATTTTCATTTCGCA
66 CTGAACAGATCATAGAAATTTTCAAACGTTGCGATTTTCATTTCGCA
477072 TAAGATGATTGCGAACGTCATTTCCGTGTTGCGATAGTCAAATGAATGCCTAATAAGTGATAACA
1 TAAGATGATTGCGAACGTCATTTCCGTGTTGCGATAGTCAAATGAATG-CTAATAAGTGATAACA
477137 ACTGAACAGATCATAGAAA-TTTCAAAC
65 ACTGAACAGATCATAGAAATTTTCAAAC
477164 TCAAGTTACT
Statistics
Matches: 91, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
112 56 0.62
113 35 0.38
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (112 bp):
TAAGATGATTGCGAACGTCATTTCCGTGTTGCGATAGTCAAATGAATGCTAATAAGTGATAACAA
CTGAACAGATCATAGAAATTTTCAAACGTTGCGATTTTCATTTCGCA
Found at i:479522 original size:24 final size:24
Alignment explanation
Indices: 479488--479541 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
479478 CTGAAAAATC
479488 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
479512 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
479536 ATCAAA
1 ATCAAA
479542 TTTCGAATAC
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:479555 original size:24 final size:24
Alignment explanation
Indices: 479488--479555 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
479478 CTGAAAAATC
* * *
479488 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
479512 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
479536 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
479556 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:480424 original size:20 final size:21
Alignment explanation
Indices: 480401--480546 Score: 151
Period size: 21 Copynumber: 7.2 Consensus size: 21
480391 AGAATCTCGT
480401 TGCGATTTAC-TAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
480421 TGCGA-TTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
480441 TGCGAATTAGGAAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
*
480462 TGTGATTTACGTAAATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
480483 TGCGA-ATACGT-AATTGCAT
1 TGCGATTTACGTAAATCGCAA
480502 TGCGATTTACGT-AATCGCAA
1 TGCGATTTACGTAAATCGCAA
* * *
480522 CGCGAATTT-GGGAAATCGCAA
1 TGCG-ATTTACGTAAATCGCAA
480543 TGCG
1 TGCG
480547 GTAGTCGGAA
Statistics
Matches: 104, Mismatches: 17, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
19 15 0.14
20 40 0.38
21 49 0.47
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (21 bp):
TGCGATTTACGTAAATCGCAA
Found at i:481462 original size:13 final size:13
Alignment explanation
Indices: 481427--481456 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
481417 TAATTAATAC
481427 TTAGATTTTAGAT
1 TTAGATTTTAGAT
*
481440 TTAGATTTTAGCT
1 TTAGATTTTAGAT
481453 TTAG
1 TTAG
481457 TCTTTAAGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.27, C:0.03, G:0.17, T:0.53
Consensus pattern (13 bp):
TTAGATTTTAGAT
Found at i:483944 original size:20 final size:20
Alignment explanation
Indices: 483919--483956 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
483909 TTCGAAATGG
483919 TGAGTGCATCGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
483939 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
483957 CCTTCACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:486510 original size:20 final size:20
Alignment explanation
Indices: 486485--486537 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
486475 ACCCGATTGA
486485 TGTATCGATGCACGGCAGTG
1 TGTATCGATGCACGGCAGTG
486505 TGTATCGATGCACGGCAGTG
1 TGTATCGATGCACGGCAGTG
*
486525 TGCATCGATGCAC
1 TGTATCGATGCAC
486538 ATTCAAGGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.21, C:0.23, G:0.32, T:0.25
Consensus pattern (20 bp):
TGTATCGATGCACGGCAGTG
Found at i:486586 original size:21 final size:20
Alignment explanation
Indices: 486482--486625 Score: 78
Period size: 20 Copynumber: 6.8 Consensus size: 20
486472 AAAACCCGAT
**
486482 TGATGTATCGATGCACGGCA
1 TGATGTATCGATGCACTTCA
**
486502 GTG-TGTATCGATGCACGGCA
1 -TGATGTATCGATGCACTTCA
*
486522 GTG-TGCATCGATGCACATTCAA
1 -TGATGTATCGATGCAC-TTC-A
* *
486544 GGAGTGTATCGGTGCATCTTCA
1 TGA-TGTATCGATGCA-CTTCA
486566 TGATGTATCGATGCACATTCA
1 TGATGTATCGATGCAC-TTCA
*
486587 TAGGGATGCATCGATGCACCTTCA
1 T---GATGTATCGATGCA-CTTCA
*
486611 T-AGTGTATCAATGCA
1 TGA-TGTATCGATGCA
486626 TTATGCACAA
Statistics
Matches: 101, Mismatches: 11, Indels: 22
0.75 0.08 0.16
Matches are distributed among these distances:
20 34 0.34
21 30 0.30
22 4 0.04
23 13 0.13
24 19 0.19
25 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.28
Consensus pattern (20 bp):
TGATGTATCGATGCACTTCA
Found at i:486599 original size:24 final size:23
Alignment explanation
Indices: 486525--486613 Score: 87
Period size: 24 Copynumber: 3.9 Consensus size: 23
486515 CACGGCAGTG
486525 TGCATCGATGCACATTCA-AGGA
1 TGCATCGATGCACATTCATAGGA
* *
486547 GTGTATCGGTGCATC-TTCAT--GA
1 -TGCATCGATGCA-CATTCATAGGA
*
486569 TGTATCGATGCACATTCATAGGGA
1 TGCATCGATGCACATTCATA-GGA
*
486593 TGCATCGATGCACCTTCATAG
1 TGCATCGATGCACATTCATAG
486614 TGTATCAATG
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
20 1 0.02
21 16 0.29
22 2 0.04
23 15 0.27
24 21 0.38
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (23 bp):
TGCATCGATGCACATTCATAGGA
Found at i:486625 original size:45 final size:44
Alignment explanation
Indices: 486532--486625 Score: 111
Period size: 45 Copynumber: 2.1 Consensus size: 44
486522 GTGTGCATCG
* * * *
486532 ATGCACATTCAAGGAGTGTATCGGTGCATCTTCATGATGTATCG
1 ATGCACATTCAAGGAGTGCATCGATGCACCTTCATGATGTATCA
486576 ATGCACATTCATAGG-GATGCATCGATGCACCTTCAT-AGTGTATCA
1 ATGCACATTCA-AGGAG-TGCATCGATGCACCTTCATGA-TGTATCA
486621 ATGCA
1 ATGCA
486626 TTATGCACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
44 13 0.30
45 30 0.70
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (44 bp):
ATGCACATTCAAGGAGTGCATCGATGCACCTTCATGATGTATCA
Found at i:490453 original size:22 final size:21
Alignment explanation
Indices: 490411--490450 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
490401 AAGACTATTT
490411 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
490432 TCATTTTT-ATATTTTGAAA
1 TCATTTTTCA-ATTTTGAAA
490451 ATAGAGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.33, C:0.07, G:0.05, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:491790 original size:23 final size:22
Alignment explanation
Indices: 491764--491827 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
491754 CAGCTCATAT
491764 AATTGCACCTAAGTGCCACGTAG
1 AATTGCACCT-AGTGCCACGTAG
* * *
491787 AATTGCACCGGAGTTCCGCGTAG
1 AATTGCACC-TAGTGCCACGTAG
491810 AATTGCACCGTAGTGCCA
1 AATTGCACC-TAGTGCCA
491828 TATAATAATG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.27, C:0.27, G:0.25, T:0.22
Consensus pattern (22 bp):
AATTGCACCTAGTGCCACGTAG
Found at i:491969 original size:103 final size:103
Alignment explanation
Indices: 491843--492163 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
491833 TAATGTCCAT
491843 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
491908 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
491946 AAGGATCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
*
492011 GACCTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
492049 AAGGACCACATATCATTCCCTAATAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
492114 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
492152 AAGGACCACATA
1 AAGGACCACATA
492164 GACCCTCTAC
Statistics
Matches: 210, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 210 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:494750 original size:64 final size:64
Alignment explanation
Indices: 494676--494821 Score: 197
Period size: 64 Copynumber: 2.3 Consensus size: 64
494666 AGGGTGCAAA
* * * * **
494676 GATGCATAAAATGCATTTGATG-TTTCA-AACAAGCCTGAGTGCATCGATGCATGGTTTGTGCAT
1 GATGCATAAAATGCATTCGATGTTTTCATAA-AAACCTCAGTGCATCAATGCATGG-AAGTGCAT
494739 C
64 C
494740 GATGCATAAAATGCATTCGATGTTTTCATAAAAACCTCAGTGCATCAATGCATGGAAGTGCATC
1 GATGCATAAAATGCATTCGATGTTTTCATAAAAACCTCAGTGCATCAATGCATGGAAGTGCATC
*
494804 GATACATAAAATGCATTC
1 GATGCATAAAATGCATTC
494822 AAAATGGTGA
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
64 45 0.62
65 26 0.36
66 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (64 bp):
GATGCATAAAATGCATTCGATGTTTTCATAAAAACCTCAGTGCATCAATGCATGGAAGTGCATC
Found at i:494864 original size:20 final size:20
Alignment explanation
Indices: 494829--494866 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
494819 TTCAAAATGG
*
494829 TGAGTGCATTGATGCATCAA
1 TGAGTGCATCGATGCATCAA
*
494849 TGAGTGCATCGGTGCATC
1 TGAGTGCATCGATGCATC
494867 CCTTCACAAA
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:0.18, G:0.29, T:0.29
Consensus pattern (20 bp):
TGAGTGCATCGATGCATCAA
Found at i:498610 original size:53 final size:53
Alignment explanation
Indices: 498511--498618 Score: 130
Period size: 53 Copynumber: 2.0 Consensus size: 53
498501 TCTACTACTC
* * * *
498511 TCTCCCTCTCTCTCTCTCTCTCTCCTTTCTTCCTCTCTATCCTTCTCTCTTTT
1 TCTCCCACTCTCTCTATCTCTCTCCTTTCTTCCTCTCTATCATTCTCTCTCTT
* *
498564 TCTCCCACTCTTTCTATCTCTCT-CTTATTTTCTCTCTCT-TCATTCTCTCTCTT
1 TCTCCCACTCTCTCTATCTCTCTCCTT-TCTTC-CTCTCTATCATTCTCTCTCTT
498617 TC
1 TC
498619 AGTCATTCTC
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
52 3 0.06
53 38 0.81
54 6 0.13
ACGTcount: A:0.05, C:0.42, G:0.00, T:0.54
Consensus pattern (53 bp):
TCTCCCACTCTCTCTATCTCTCTCCTTTCTTCCTCTCTATCATTCTCTCTCTT
Found at i:498653 original size:22 final size:22
Alignment explanation
Indices: 498626--498728 Score: 98
Period size: 24 Copynumber: 4.4 Consensus size: 22
498616 TTCAGTCATT
498626 CTCTCTCTCCCTTCATCTCTCTCC
1 CTCTCTCT-CCTTC-TCTCTCTCC
*
498650 CTCTCTTGCTCTTTCTCTCTCTCC
1 CTCTC-T-CTCCTTCTCTCTCTCC
* *
498674 CCCTCTTGCTCTTTCTCTCTCTCC
1 CTCTC-T-CTCCTTCTCTCTCTCC
* **
498698 CTCTATCTCCTTCTCTCTCTGT
1 CTCTCTCTCCTTCTCTCTCTCC
498720 CTCTCTCTC
1 CTCTCTCTC
498729 TTATTCTCTC
Statistics
Matches: 69, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
22 21 0.30
23 1 0.01
24 40 0.58
25 5 0.07
26 2 0.03
ACGTcount: A:0.02, C:0.49, G:0.03, T:0.47
Consensus pattern (22 bp):
CTCTCTCTCCTTCTCTCTCTCC
Found at i:498739 original size:2 final size:2
Alignment explanation
Indices: 498508--498729 Score: 87
Period size: 2 Copynumber: 116.0 Consensus size: 2
498498 CCCTCTACTA
* *
498508 CT CT CT CC CT CT CT CT CT CT CT CT CT C- CT TT CT -T C- CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * * * * *
498547 CT AT C- CT -T CT CT CT TT TT CT CC CA CT CT TT CT AT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
* * * * *
498587 CT -T AT -T TT CT CT CT CT -T CAT -T CT CT CT CT TT CA GT CAT -T
1 CT CT CT CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT CT C-T CT
* * *
498626 CT CT CT CT CC CT -T CAT CT CT CT CC CT CT CT -T GCT CT TT CT CT
1 CT CT CT CT CT CT CT C-T CT CT CT CT CT CT CT CT -CT CT CT CT CT
* * * * *
498668 CT CT CC CC CT CT -T GCT CT TT CT CT CT CT CC CT CT AT CT C- CT
1 CT CT CT CT CT CT CT -CT CT CT CT CT CT CT CT CT CT CT CT CT CT
*
498709 -T CT CT CT CT GT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
498730 TATTCTCTCT
Statistics
Matches: 162, Mismatches: 38, Indels: 40
0.68 0.16 0.17
Matches are distributed among these distances:
1 15 0.09
2 141 0.87
3 6 0.04
ACGTcount: A:0.04, C:0.44, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:500321 original size:152 final size:152
Alignment explanation
Indices: 500038--500347 Score: 523
Period size: 152 Copynumber: 2.0 Consensus size: 152
500028 TACAAAAACA
*
500038 TTTT-ATAACTATCATATTAGTGCAACTAGAACATCTATAATATGAATGCCACTAAATAAGTCAA
1 TTTTCATAACTATCATATTAGAGCAACTAGAACATCTATAATATGAATGCCACTAAATAAGTCAA
* *
500102 ATTAACATCAAAAGATGTTCTTACTGATACTGGATGTATATATGATTATACAAAAGTGATACCCA
66 AATAACATCAAAAGATGTTCTTACTGATACTGGATGTAGATATGATTATACAAAAGTGATACCCA
500167 CTATGCTCCTCACTCCTCAGCT
131 CTATGCTCCTCACTCCTCAGCT
* *
500189 TTTTCATAACTATCATATTAGAGCAACTAGAATATCTATAATATGCATGCCACTAAATAAGTCAA
1 TTTTCATAACTATCATATTAGAGCAACTAGAACATCTATAATATGAATGCCACTAAATAAGTCAA
* * * *
500254 AATAACATCAAAAGATGTTCTTACTGATATTGGATGTAGATATGATTATTCAAAAGTGATGCTCA
66 AATAACATCAAAAGATGTTCTTACTGATACTGGATGTAGATATGATTATACAAAAGTGATACCCA
*
500319 CTATGCTCTTCACTCCTCAGCT
131 CTATGCTCCTCACTCCTCAGCT
500341 TTTTCAT
1 TTTTCAT
500348 TTCCTTTACC
Statistics
Matches: 148, Mismatches: 10, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
151 4 0.03
152 144 0.97
ACGTcount: A:0.36, C:0.18, G:0.12, T:0.34
Consensus pattern (152 bp):
TTTTCATAACTATCATATTAGAGCAACTAGAACATCTATAATATGAATGCCACTAAATAAGTCAA
AATAACATCAAAAGATGTTCTTACTGATACTGGATGTAGATATGATTATACAAAAGTGATACCCA
CTATGCTCCTCACTCCTCAGCT
Found at i:504859 original size:65 final size:61
Alignment explanation
Indices: 504771--504961 Score: 161
Period size: 62 Copynumber: 3.0 Consensus size: 61
504761 TAAATTATCT
* * * *
504771 AAAAA-TAAATTATTTGATAAATTTAACAATAATATATATATATAATCATAATTTAAATTTT
1 AAAAATTAAATTATTTTAAAAATTTAACAATAATATATATATATAATCATAAATT-AATTTA
* * ** *
504832 ATAACTTAAATAATAATTTTAAAAATTTTATTAATAATTTCATATATATATAACTCA-AAATTAC
1 AAAAATTAAAT--T-ATTTTAAAAA-TTTAACAATAA--T-ATATATATATAA-TCATAAATTAA
504896 TTTA
58 TTTA
* * * *
504900 AAAAATTAAATTATTTTATATATTTAACAACAATTTATATATATAATCATTAAATTAATTTA
1 AAAAATTAAATTATTTTAAAAATTTAACAATAATATATATATATAATCA-TAAATTAATTTA
504962 TTTAAGTAAT
Statistics
Matches: 101, Mismatches: 18, Indels: 21
0.72 0.13 0.15
Matches are distributed among these distances:
60 3 0.03
61 14 0.14
62 16 0.16
64 9 0.09
65 16 0.16
66 10 0.10
68 14 0.14
69 16 0.16
70 3 0.03
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.44
Consensus pattern (61 bp):
AAAAATTAAATTATTTTAAAAATTTAACAATAATATATATATATAATCATAAATTAATTTA
Found at i:511908 original size:23 final size:22
Alignment explanation
Indices: 511868--511916 Score: 53
Period size: 23 Copynumber: 2.2 Consensus size: 22
511858 TCGTTGACCG
**
511868 TTGACTTTGACCCTGGTTTAACT
1 TTGACTTTGACCAAGG-TTAACT
* *
511891 TTGACTTTGAGCAAGGTTGACT
1 TTGACTTTGACCAAGGTTAACT
511913 TTGA
1 TTGA
511917 TGAAATAGTC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.20, C:0.16, G:0.22, T:0.41
Consensus pattern (22 bp):
TTGACTTTGACCAAGGTTAACT
Found at i:513178 original size:11 final size:12
Alignment explanation
Indices: 513152--513177 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
513142 TTGGATCTAT
513152 AAATGTTTTTGA
1 AAATGTTTTTGA
513164 AAATGTTTTTGA
1 AAATGTTTTTGA
513176 AA
1 AA
513178 TTTGTAATGT
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:0.38, C:0.00, G:0.15, T:0.46
Consensus pattern (12 bp):
AAATGTTTTTGA
Found at i:514487 original size:19 final size:19
Alignment explanation
Indices: 514460--514509 Score: 77
Period size: 18 Copynumber: 2.7 Consensus size: 19
514450 CACCCAAGAG
514460 TTCTAGAATCCCAAAACCC
1 TTCTAGAATCCCAAAACCC
*
514479 TTTTAGAAT-CCAAAACCC
1 TTCTAGAATCCCAAAACCC
514497 TTCTAGAA-CCCAA
1 TTCTAGAATCCCAA
514510 CTATGGCCAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
18 20 0.71
19 8 0.29
ACGTcount: A:0.38, C:0.32, G:0.06, T:0.24
Consensus pattern (19 bp):
TTCTAGAATCCCAAAACCC
Found at i:515913 original size:22 final size:22
Alignment explanation
Indices: 515879--515921 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
515869 AGTTGAATGG
515879 TTTTTTAATTAGCTATATAAAT
1 TTTTTTAATTAGCTATATAAAT
515901 TTTTGTTAA-TAGCTATATAAA
1 TTTT-TTAATTAGCTATATAAA
515922 AGTTGATGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (22 bp):
TTTTTTAATTAGCTATATAAAT
Found at i:521303 original size:2 final size:2
Alignment explanation
Indices: 521296--521397 Score: 204
Period size: 2 Copynumber: 51.0 Consensus size: 2
521286 ACCCAATCAA
521296 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
521338 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
521380 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
521398 GTCAAAACAA
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 100 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:526350 original size:2 final size:2
Alignment explanation
Indices: 526343--526367 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
526333 GTAAAAACAA
526343 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 A
526368 GTCCGAGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:527362 original size:20 final size:20
Alignment explanation
Indices: 527307--527383 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
527297 TATGGAATCC
*
527307 AAGAGATCGATCCTTTTTTA
1 AAGAGATCGATCCTTTTTCA
* *
527327 AGGGGATCGATCCTTTTGTCA
1 AAGAGATCGATCCTTTT-TCA
* *
527348 AAGAGATCGAT-CTTTTAGCT
1 AAGAGATCGATCCTTTT-TCA
*
527368 AGGAGATCGATCCTTT
1 AAGAGATCGATCCTTT
527384 GAGACAAAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
20 31 0.67
21 15 0.33
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (20 bp):
AAGAGATCGATCCTTTTTCA
Found at i:530559 original size:43 final size:42
Alignment explanation
Indices: 530512--530595 Score: 96
Period size: 43 Copynumber: 2.0 Consensus size: 42
530502 TATCAAGCTT
* * *
530512 AATTTTTAAATCAAAAAATTCTTTTTCAAAATTTTCATTTTTC
1 AATTTTGAAAGCAAAAAATCCTTTTTCAAAATTTT-ATTTTTC
*** *
530555 AATTTTGAAAGCTCCAAATCCTTTTTCAAAGTTTTATTTTT
1 AATTTTGAAAGCAAAAAATCCTTTTTCAAAATTTTATTTTT
530596 GCTTTCAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
42 6 0.18
43 28 0.82
ACGTcount: A:0.33, C:0.13, G:0.04, T:0.50
Consensus pattern (42 bp):
AATTTTGAAAGCAAAAAATCCTTTTTCAAAATTTTATTTTTC
Found at i:532564 original size:21 final size:21
Alignment explanation
Indices: 532540--532612 Score: 87
Period size: 21 Copynumber: 3.5 Consensus size: 21
532530 ATTTTTATCG
532540 AGGGATCGATCCTTTTGCTGA
1 AGGGATCGATCCTTTTGCTGA
*
532561 AGGGATAGATCCTTTTGCTTG-
1 AGGGATCGATCCTTTTGC-TGA
* *
532582 AGGTATCGATCCTTTTG-TATA
1 AGGGATCGATCCTTTTGCT-GA
532603 AGGGATCGAT
1 AGGGATCGAT
532613 TTAAAAGTTT
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.02
21 41 0.93
22 2 0.05
ACGTcount: A:0.22, C:0.15, G:0.27, T:0.36
Consensus pattern (21 bp):
AGGGATCGATCCTTTTGCTGA
Found at i:534002 original size:18 final size:18
Alignment explanation
Indices: 533959--534002 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
533949 CTTTAACCTT
*
533959 ACAACACTTACCACGACA
1 ACAACATTTACCACGACA
533977 ACAACATTTACCACGACA
1 ACAACATTTACCACGACA
*
533995 ACACCATT
1 ACAACATT
534003 CATACTTCAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.43, C:0.36, G:0.05, T:0.16
Consensus pattern (18 bp):
ACAACATTTACCACGACA
Found at i:541002 original size:21 final size:22
Alignment explanation
Indices: 540955--541010 Score: 71
Period size: 21 Copynumber: 2.6 Consensus size: 22
540945 TCATTTAAGG
*
540955 GAAGGGATCGATCATTTTCATC
1 GAAGGGATCGATCCTTTTCATC
* *
540977 G-AGGGATCGATCCTTTT-GTT
1 GAAGGGATCGATCCTTTTCATC
540997 GAAGGGATCGATCC
1 GAAGGGATCGATCC
541011 AAAAGTTTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.07
21 27 0.90
22 1 0.03
ACGTcount: A:0.23, C:0.18, G:0.29, T:0.30
Consensus pattern (22 bp):
GAAGGGATCGATCCTTTTCATC
Found at i:551421 original size:12 final size:12
Alignment explanation
Indices: 551386--551424 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
551376 ATCAAAACAT
551386 AAAAAAATAATC
1 AAAAAAATAATC
* * *
551398 AAAGATACAATC
1 AAAAAAATAATC
551410 AAAAAAATAATC
1 AAAAAAATAATC
551422 AAA
1 AAA
551425 CATAAAAAAA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.72, C:0.10, G:0.03, T:0.15
Consensus pattern (12 bp):
AAAAAAATAATC
Found at i:551773 original size:31 final size:29
Alignment explanation
Indices: 551724--551786 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
551714 CTAGTTAATT
*
551724 TGTGGCTACTTTTGTTTTTTTTTAATTAAGA
1 TGTGGCTAC-TTT-TATTTTTTTAATTAAGA
* *
551755 TGTGGTTATTTTTATTTTTTTAATTAAGA
1 TGTGGCTACTTTTATTTTTTTAATTAAGA
551784 TGT
1 TGT
551787 AGTCACTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 19 0.66
30 3 0.10
31 7 0.24
ACGTcount: A:0.21, C:0.03, G:0.16, T:0.60
Consensus pattern (29 bp):
TGTGGCTACTTTTATTTTTTTAATTAAGA
Found at i:553574 original size:29 final size:28
Alignment explanation
Indices: 553524--553588 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
553514 ATACTAATTT
* * **
553524 TAATATTTTTATTTATAAGTTTGTAGAAA
1 TAATA-TTTTAATAATAAGTTTCCAGAAA
*
553553 TAATATTTTAATAATAATGTTTCCATAAA
1 TAATATTTTAATAATAA-GTTTCCAGAAA
553582 TAATATT
1 TAATATT
553589 GAATAAATTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.49
Consensus pattern (28 bp):
TAATATTTTAATAATAAGTTTCCAGAAA
Found at i:556617 original size:16 final size:16
Alignment explanation
Indices: 556596--556629 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
556586 TTTTGTGTAA
556596 ATAAT-GTGACATGATC
1 ATAATGGTGA-ATGATC
556612 ATAATGGTGAATGATC
1 ATAATGGTGAATGATC
556628 AT
1 AT
556630 TATGAAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.38, C:0.09, G:0.21, T:0.32
Consensus pattern (16 bp):
ATAATGGTGAATGATC
Found at i:557883 original size:17 final size:18
Alignment explanation
Indices: 557861--557908 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
557851 ATTCTAAATG
557861 TTTACAGTTATCAGAT-A
1 TTTACAGTTATCAGATGA
* *
557878 TTTACA-TATATCATATGT
1 TTTACAGT-TATCAGATGA
557896 TTTACAGTTATCA
1 TTTACAGTTATCA
557909 AATACAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 1 0.04
17 13 0.50
18 11 0.42
19 1 0.04
ACGTcount: A:0.33, C:0.12, G:0.08, T:0.46
Consensus pattern (18 bp):
TTTACAGTTATCAGATGA
Found at i:558929 original size:23 final size:23
Alignment explanation
Indices: 558903--558959 Score: 105
Period size: 23 Copynumber: 2.5 Consensus size: 23
558893 GAATAAGATA
558903 AAAGTTTAAAAGTTGAAACAGTG
1 AAAGTTTAAAAGTTGAAACAGTG
558926 AAAGTTTAAAAGTTGAAACAGTG
1 AAAGTTTAAAAGTTGAAACAGTG
*
558949 AAGGTTTAAAA
1 AAAGTTTAAAA
558960 AGAAACGATA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.49, C:0.04, G:0.21, T:0.26
Consensus pattern (23 bp):
AAAGTTTAAAAGTTGAAACAGTG
Found at i:562707 original size:21 final size:21
Alignment explanation
Indices: 562683--562735 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
562673 TTTAAAATAT
*
562683 AATTAACACCCCTTAGAAAGA
1 AATTGACACCCCTTAGAAAGA
562704 AATTGACACCCCTTAGAAAGA
1 AATTGACACCCCTTAGAAAGA
562725 AATTGACACCC
1 AATTGACACCC
562736 ATGGTTTGCC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.43, C:0.26, G:0.11, T:0.19
Consensus pattern (21 bp):
AATTGACACCCCTTAGAAAGA
Found at i:570432 original size:45 final size:46
Alignment explanation
Indices: 570368--570458 Score: 148
Period size: 45 Copynumber: 2.0 Consensus size: 46
570358 AAAGTGTCGA
570368 AGTTAGATGATCAAAGGCTAT-CACTCTACGTAAATAATCAGAGTC
1 AGTTAGATGATCAAAGGCTATACACTCTACGTAAATAATCAGAGTC
* *
570413 AGTTAGATGATCAAAGGCTATAATACTGTACGTAAATAATCAGAGT
1 AGTTAGATGATCAAAGGCTAT-ACACTCTACGTAAATAATCAGAGT
570459 TTCATCTAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
45 21 0.50
47 21 0.50
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (46 bp):
AGTTAGATGATCAAAGGCTATACACTCTACGTAAATAATCAGAGTC
Found at i:572102 original size:20 final size:20
Alignment explanation
Indices: 572077--572121 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
572067 ACCCACTACT
572077 GAAAGTGCCAGCACCAACAA
1 GAAAGTGCCAGCACCAACAA
*
572097 GAAAGTGCCAGCACCAATAA
1 GAAAGTGCCAGCACCAACAA
572117 GAAAG
1 GAAAG
572122 CACCGAACCA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.47, C:0.24, G:0.22, T:0.07
Consensus pattern (20 bp):
GAAAGTGCCAGCACCAACAA
Found at i:582015 original size:29 final size:29
Alignment explanation
Indices: 581973--582031 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
581963 ATTTTCACCT
581973 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
582002 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
582031 A
1 A
582032 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:586698 original size:29 final size:29
Alignment explanation
Indices: 586656--586714 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
586646 ATTTTCACCT
586656 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
586685 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
586714 A
1 A
586715 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:591466 original size:21 final size:21
Alignment explanation
Indices: 591440--591481 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
591430 ACAAGGAAGG
591440 TAAGGTTAGG-ATTAGGGATTT
1 TAAGGTT-GGTATTAGGGATTT
*
591461 TAAGGTTGGTTTTAGGGATTT
1 TAAGGTTGGTATTAGGGATTT
591482 GAGACTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (21 bp):
TAAGGTTGGTATTAGGGATTT
Found at i:592084 original size:33 final size:35
Alignment explanation
Indices: 592046--592120 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
592036 AGTAATAATA
* * *
592046 AAAGAGATGGAA-TTATCAAGCGCTTT-AGTGATT
1 AAAGAGATGAAACTTATCAAACGATTTCAGTGATT
*
592079 AAAGAGATGAAACTTATCAAACGATTTCAGTGGTT
1 AAAGAGATGAAACTTATCAAACGATTTCAGTGATT
592114 AAAGAGA
1 AAAGAGA
592121 GTGTTGTTCT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
33 11 0.31
34 12 0.33
35 13 0.36
ACGTcount: A:0.41, C:0.09, G:0.23, T:0.27
Consensus pattern (35 bp):
AAAGAGATGAAACTTATCAAACGATTTCAGTGATT
Found at i:593224 original size:16 final size:18
Alignment explanation
Indices: 593203--593241 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
593193 TATGAAAATA
593203 TTTTAAAAT-AT-TTATT
1 TTTTAAAATCATATTATT
593219 TTTTAAAATCATATTATT
1 TTTTAAAATCATATTATT
*
593237 ATTTA
1 TTTTA
593242 TTTGAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 9 0.45
17 2 0.10
18 9 0.45
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTAAAATCATATTATT
Found at i:593398 original size:19 final size:18
Alignment explanation
Indices: 593347--593401 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 18
593337 CTAAATTTAA
593347 ATTATTTAAAATTAAATAGAT
1 ATTATTT-AAA-TAAATA-AT
593368 A--ATTTAAA-AAATAAT
1 ATTATTTAAATAAATAAT
593383 ATTATTTCAAATAAATAAT
1 ATTATTT-AAATAAATAAT
593402 TAATTAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
15 3 0.10
16 5 0.17
17 4 0.13
18 6 0.20
19 11 0.37
21 1 0.03
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTATTTAAATAAATAAT
Found at i:593478 original size:22 final size:24
Alignment explanation
Indices: 593430--593484 Score: 71
Period size: 22 Copynumber: 2.4 Consensus size: 24
593420 TAAATAAATG
593430 TTTTTATAATATTATAAATATACC
1 TTTTTATAATATTATAAATATACC
*
593454 TTTTTATAATTATT-T-CATATA-C
1 TTTTTATAA-TATTATAAATATACC
593476 TTTTTATAA
1 TTTTTATAA
593485 AAATATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 10 0.34
23 5 0.17
24 10 0.34
25 4 0.14
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.56
Consensus pattern (24 bp):
TTTTTATAATATTATAAATATACC
Found at i:598717 original size:23 final size:23
Alignment explanation
Indices: 598685--598766 Score: 110
Period size: 23 Copynumber: 3.6 Consensus size: 23
598675 ATTTTATATT
*
598685 GCACTTCGGTGCAATTCTACGCG
1 GCACTCCGGTGCAATTCTACGCG
598708 GCACTCCGGTGCAATTCTACGCG
1 GCACTCCGGTGCAATTCTACGCG
* * *
598731 GCACTCCGGGGCAATTCCATGCG
1 GCACTCCGGTGCAATTCTACGCG
* *
598754 GTACTTCGGTGCA
1 GCACTCCGGTGCA
598767 TTTATATGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 52 1.00
ACGTcount: A:0.17, C:0.32, G:0.28, T:0.23
Consensus pattern (23 bp):
GCACTCCGGTGCAATTCTACGCG
Found at i:603920 original size:21 final size:22
Alignment explanation
Indices: 603895--603939 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
603885 GAATATGAAG
603895 AGTTATAAGAGAA-TAAATATA
1 AGTTATAAGAGAATTAAATATA
* *
603916 AGTTATATGATAATTAAATATA
1 AGTTATAAGAGAATTAAATATA
603938 AG
1 AG
603940 ACTATGTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 11 0.52
22 10 0.48
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.33
Consensus pattern (22 bp):
AGTTATAAGAGAATTAAATATA
Found at i:604249 original size:19 final size:21
Alignment explanation
Indices: 604226--604274 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 21
604216 TGATATACAC
*
604226 ATATAATATA-GATATATGTT
1 ATATAATATATGACATATGTT
604246 -TATAA-ATATGACATATGTT
1 ATATAATATATGACATATGTT
604265 ATATAATATA
1 ATATAATATA
604275 AATGCATACC
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
18 3 0.12
19 14 0.56
20 5 0.20
21 3 0.12
ACGTcount: A:0.47, C:0.02, G:0.08, T:0.43
Consensus pattern (21 bp):
ATATAATATATGACATATGTT
Found at i:605073 original size:23 final size:23
Alignment explanation
Indices: 605006--605065 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
604996 CATTTTATAT
*
605006 GGCACTTCGGTGCAATTCTATGC
1 GGCACTTCGGTGCAATTCTACGC
* *
605029 GGCACTTCGATGTAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
605052 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
605066 TTTATACGAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:615920 original size:16 final size:16
Alignment explanation
Indices: 615899--615937 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
615889 GGTATTACCC
615899 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
*
615915 GACCTGTTTTTAACCT
1 GACCTGTTTTCAACCT
*
615931 GATCTGT
1 GACCTGT
615938 AAATGATCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.18, C:0.26, G:0.15, T:0.41
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:616176 original size:24 final size:24
Alignment explanation
Indices: 616127--616185 Score: 66
Period size: 24 Copynumber: 2.5 Consensus size: 24
616117 AAATAGACAT
*
616127 ATTATATAAAAGTATTTAATAAAA
1 ATTAGATAAAAGTATTTAATAAAA
* **
616151 ATTA-ATAAAATTATTTAAATGTAA
1 ATTAGATAAAAGTATTT-AATAAAA
616175 ATTAGATAAAA
1 ATTAGATAAAA
616186 CATGATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.37
24 13 0.43
25 6 0.20
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (24 bp):
ATTAGATAAAAGTATTTAATAAAA
Found at i:616229 original size:14 final size:14
Alignment explanation
Indices: 616207--616253 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
616197 ATGCAAAAAA
*
616207 AATTAATATAGTTT
1 AATTTATATAGTTT
616221 AATTTATATA----
1 AATTTATATAGTTT
616231 AA-TTATATAGTTT
1 AATTTATATAGTTT
616244 AATTTATATA
1 AATTTATATA
616254 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:616240 original size:23 final size:24
Alignment explanation
Indices: 616206--616255 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
616196 AATGCAAAAA
616206 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
616230 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
616253 AAA
1 AAA
616256 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:616443 original size:21 final size:21
Alignment explanation
Indices: 616419--616469 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
616409 TCTATTTATA
*
616419 TTATGGTTTAGTGTTTAAT-GT
1 TTATGGTTTAGAGTTT-ATGGT
616440 TTATGGTTTAGAGTTTATGGT
1 TTATGGTTTAGAGTTTATGGT
*
616461 TTAGGGTTT
1 TTATGGTTT
616470 CTATAAACTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 2 0.07
21 25 0.93
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (21 bp):
TTATGGTTTAGAGTTTATGGT
Found at i:616448 original size:14 final size:14
Alignment explanation
Indices: 616438--616469 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
616428 AGTGTTTAAT
616438 GTTTATGGTTTAGA
1 GTTTATGGTTTAGA
*
616452 GTTTATGGTTTAGG
1 GTTTATGGTTTAGA
616466 GTTT
1 GTTT
616470 CTATAAACTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.31, T:0.53
Consensus pattern (14 bp):
GTTTATGGTTTAGA
Found at i:616564 original size:15 final size:15
Alignment explanation
Indices: 616544--616597 Score: 65
Period size: 15 Copynumber: 3.4 Consensus size: 15
616534 TAATTTATTT
616544 TATATAGTTTATATA
1 TATATAGTTTATATA
616559 TATATA-TATTATACATA
1 TATATAGT-TTAT--ATA
616576 TATATAGTTTATATA
1 TATATAGTTTATATA
616591 TACTATA
1 TA-TATA
616598 CATGGTTTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.03
15 15 0.44
16 4 0.12
17 13 0.38
18 1 0.03
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:616605 original size:20 final size:21
Alignment explanation
Indices: 616563--616617 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
616553 TATATATATA
*
616563 TATATTATACATATATATAGTT
1 TATA-TATACATATACATAGTT
*
616585 TATATATAC-TATACATGGTT
1 TATATATACATATACATAGTT
*
616605 TATACATACATAT
1 TATATATACATAT
616618 TATATAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.59
21 8 0.28
22 4 0.14
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.45
Consensus pattern (21 bp):
TATATATACATATACATAGTT
Found at i:616649 original size:22 final size:24
Alignment explanation
Indices: 616610--616673 Score: 78
Period size: 22 Copynumber: 2.7 Consensus size: 24
616600 TGGTTTATAC
*
616610 ATACATATTATATAAAATTATTTA
1 ATACATATTATATAAAATAATTTA
616634 ATACA-ATTA-ATAAAATAATTTAA
1 ATACATATTATATAAAATAATTT-A
* *
616657 ATATAAATTATATAAAA
1 ATACATATTATATAAAA
616674 CATGATTAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
22 11 0.31
23 9 0.26
24 9 0.26
25 6 0.17
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (24 bp):
ATACATATTATATAAAATAATTTA
Found at i:616835 original size:14 final size:14
Alignment explanation
Indices: 616818--616889 Score: 63
Period size: 14 Copynumber: 5.1 Consensus size: 14
616808 CCTATTTATA
*
616818 TTAGGGTTTATGGT
1 TTAGGGTTTAAGGT
* ***
616832 TTAGTGTTTACTAT
1 TTAGGGTTTAAGGT
* *
616846 TTATGGTTTAAAGT
1 TTAGGGTTTAAGGT
*
616860 TTAGGGTTCAAGGT
1 TTAGGGTTTAAGGT
*
616874 TTAGGGTTCAAGGT
1 TTAGGGTTTAAGGT
616888 TT
1 TT
616890 CTATAAACTA
Statistics
Matches: 46, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 46 1.00
ACGTcount: A:0.21, C:0.04, G:0.28, T:0.47
Consensus pattern (14 bp):
TTAGGGTTTAAGGT
Found at i:616960 original size:9 final size:9
Alignment explanation
Indices: 616948--616987 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
616938 TATATAAGTA
*
616948 ATATACTTT
1 ATATAGTTT
616957 ATATAGTTT
1 ATATAGTTT
*
616966 ATATA-TAT
1 ATATAGTTT
616974 ATATAGTTT
1 ATATAGTTT
616983 ATATA
1 ATATA
616988 TACTATAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (9 bp):
ATATAGTTT
Found at i:616978 original size:17 final size:18
Alignment explanation
Indices: 616956--616994 Score: 71
Period size: 17 Copynumber: 2.2 Consensus size: 18
616946 TAATATACTT
616956 TATATAGTTTATATATA-
1 TATATAGTTTATATATAC
616973 TATATAGTTTATATATAC
1 TATATAGTTTATATATAC
616991 TATA
1 TATA
616995 AATGGTTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 17 0.81
18 4 0.19
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
TATATAGTTTATATATAC
Found at i:617046 original size:22 final size:23
Alignment explanation
Indices: 617013--617055 Score: 79
Period size: 22 Copynumber: 1.9 Consensus size: 23
617003 ATACATACAT
617013 ATTATATAAAATTATTTAATAAA
1 ATTATATAAAATTATTTAATAAA
617036 ATTA-ATAAAATTATTTAATA
1 ATTATATAAAATTATTTAATA
617056 TTGGTTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
ATTATATAAAATTATTTAATAAA
Found at i:617878 original size:2 final size:2
Alignment explanation
Indices: 617873--617927 Score: 58
Period size: 2 Copynumber: 27.0 Consensus size: 2
617863 TAATTTACTT
**
617873 TA TA TA GTA TA TA TA TA TA TA TA TA TA TA TA GG T- 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
*
617915 TA GTT TA TA TA TA
1 TA -TA TA TA TA TA
617928 CTAACATGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
1 1 0.02
2 41 0.91
3 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (2 bp):
TA
Found at i:617891 original size:13 final size:13
Alignment explanation
Indices: 617873--617927 Score: 78
Period size: 13 Copynumber: 4.3 Consensus size: 13
617863 TAATTTACTT
617873 TATATAGTATATA
1 TATATAGTATATA
617886 TATATA-TATATA
1 TATATAGTATATA
617898 TATATAGGT-TATA
1 TATATA-GTATATA
*
617911 TATATAGTTTATA
1 TATATAGTATATA
617924 TATA
1 TATA
617928 CTAACATGGT
Statistics
Matches: 39, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
12 14 0.36
13 24 0.62
14 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (13 bp):
TATATAGTATATA
Found at i:617977 original size:20 final size:22
Alignment explanation
Indices: 617954--617995 Score: 70
Period size: 20 Copynumber: 2.0 Consensus size: 22
617944 ATACATATAT
617954 AAAATTATTT-AATA-AAATTA
1 AAAATTATTTAAATATAAATTA
617974 AAAATTATTTAAATATAAATTA
1 AAAATTATTTAAATATAAATTA
617996 TATAAACATG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
21 4 0.20
22 6 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AAAATTATTTAAATATAAATTA
Found at i:619509 original size:20 final size:20
Alignment explanation
Indices: 619484--619532 Score: 98
Period size: 20 Copynumber: 2.5 Consensus size: 20
619474 GGTCATAGGT
619484 GGTCAACGGTTAACAGGTCG
1 GGTCAACGGTTAACAGGTCG
619504 GGTCAACGGTTAACAGGTCG
1 GGTCAACGGTTAACAGGTCG
619524 GGTCAACGG
1 GGTCAACGG
619533 GCTGGGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.20, G:0.37, T:0.18
Consensus pattern (20 bp):
GGTCAACGGTTAACAGGTCG
Found at i:625753 original size:15 final size:15
Alignment explanation
Indices: 625722--625771 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
625712 GCAAATCAGT
* *
625722 AGTATACAGAAATTC
1 AGTATTCAGAAAATC
*
625737 AG-ATATCAGATAATC
1 AGTAT-TCAGAAAATC
625752 AGTATTCAGAAAATC
1 AGTATTCAGAAAATC
625767 AGTAT
1 AGTAT
625772 AAAATATCGT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 2 0.07
15 25 0.86
16 2 0.07
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.28
Consensus pattern (15 bp):
AGTATTCAGAAAATC
Found at i:626559 original size:19 final size:19
Alignment explanation
Indices: 626535--626583 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
626525 GGTTGGGTCG
* *
626535 GGTCAAACCGGGTCGGATC
1 GGTCAAACCGGGTCAGACC
* * *
626554 GGTCAACCCGGTTTAGACC
1 GGTCAAACCGGGTCAGACC
626573 GGTCAAACCGG
1 GGTCAAACCGG
626584 TTTCAAGCAG
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.22, C:0.29, G:0.33, T:0.16
Consensus pattern (19 bp):
GGTCAAACCGGGTCAGACC
Found at i:627574 original size:14 final size:14
Alignment explanation
Indices: 627552--627616 Score: 58
Period size: 14 Copynumber: 4.6 Consensus size: 14
627542 TCCATTTATA
627552 TTAGGGTTTATGGT
1 TTAGGGTTTATGGT
*
627566 TTAGTGTTTATGGT
1 TTAGGGTTTATGGT
** *
627580 TTAAAGTTTATGAT
1 TTAGGGTTTATGGT
*** *
627594 TTATTATTTAGGGT
1 TTAGGGTTTATGGT
627608 TTAGGGTTT
1 TTAGGGTTT
627617 CTATAAACCT
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
14 39 1.00
ACGTcount: A:0.20, C:0.00, G:0.26, T:0.54
Consensus pattern (14 bp):
TTAGGGTTTATGGT
Found at i:627709 original size:13 final size:13
Alignment explanation
Indices: 627691--627720 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
627681 TAATTTACTT
627691 TATATAGTTTATA
1 TATATAGTTTATA
627704 TATATAGTTTATA
1 TATATAGTTTATA
627717 TATA
1 TATA
627721 CTATATATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:627725 original size:20 final size:20
Alignment explanation
Indices: 627702--627746 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
627692 ATATAGTTTA
*
627702 TATATAT-AGTTTATATATAC
1 TATATATGA-TTTATACATAC
627722 TATATATGATTTATACATAC
1 TATATATGATTTATACATAC
627742 -ATATA
1 TATATA
627747 CTATAAGTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 5 0.22
20 17 0.74
21 1 0.04
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (20 bp):
TATATATGATTTATACATAC
Found at i:627797 original size:14 final size:14
Alignment explanation
Indices: 627780--627813 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
627770 GGGGTTAGGG
*
627780 TTTAGGGCTCATGA
1 TTTAGGGCTCATAA
*
627794 TTTAGGGTTCATAA
1 TTTAGGGCTCATAA
627808 TTTAGG
1 TTTAGG
627814 ATTTAAGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.26, T:0.41
Consensus pattern (14 bp):
TTTAGGGCTCATAA
Found at i:628035 original size:12 final size:12
Alignment explanation
Indices: 627980--628070 Score: 85
Period size: 12 Copynumber: 7.6 Consensus size: 12
627970 TATAGTTTAT
*
627980 ATACATGCATAC
1 ATACATACATAC
* * *
627992 ATGCATATATGC
1 ATACATACATAC
*
628004 ATACATGCATAC
1 ATACATACATAC
** *
628016 ATGTATACATAG
1 ATACATACATAC
628028 ATACATACATAC
1 ATACATACATAC
628040 GA-ACATACATAC
1 -ATACATACATAC
*
628052 ATACATACGTAC
1 ATACATACATAC
628064 ATACATA
1 ATACATA
628071 TATATAGAAA
Statistics
Matches: 61, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
11 1 0.02
12 59 0.97
13 1 0.02
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (12 bp):
ATACATACATAC
Found at i:628058 original size:8 final size:8
Alignment explanation
Indices: 627980--628070 Score: 85
Period size: 8 Copynumber: 11.4 Consensus size: 8
627970 TATAGTTTAT
*
627980 ATACATGC
1 ATACATAC
*
627988 ATACATGC
1 ATACATAC
* *
627996 ATATATGC
1 ATACATAC
*
628004 ATACATGC
1 ATACATAC
**
628012 ATACATGT
1 ATACATAC
*
628020 ATACATAG
1 ATACATAC
628028 ATACATAC
1 ATACATAC
628036 ATACGA-AC
1 ATAC-ATAC
628044 ATACATAC
1 ATACATAC
628052 ATACATAC
1 ATACATAC
*
628060 GTACATAC
1 ATACATAC
628068 ATA
1 ATA
628071 TATATAGAAA
Statistics
Matches: 73, Mismatches: 8, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
7 1 0.01
8 71 0.97
9 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (8 bp):
ATACATAC
Found at i:628305 original size:18 final size:20
Alignment explanation
Indices: 628282--628328 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
628272 TTTCCCTCCA
628282 AAATTT-TC-TATTCCCTCT
1 AAATTTCTCATATTCCCTCT
*
628300 AAATTTCTCATTTTCCCTCT
1 AAATTTCTCATATTCCCTCT
628320 AAA-TTCTCA
1 AAATTTCTCA
628329 ATTTCCCTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 6 0.23
19 8 0.31
20 12 0.46
ACGTcount: A:0.26, C:0.28, G:0.00, T:0.47
Consensus pattern (20 bp):
AAATTTCTCATATTCCCTCT
Found at i:628317 original size:20 final size:20
Alignment explanation
Indices: 628265--628336 Score: 87
Period size: 19 Copynumber: 3.7 Consensus size: 20
628255 AAAATCTCAA
*
628265 TTCTCAATTTCCCTCCAAAAT
1 TTCTCAATTTCCCT-CTAAAT
*
628286 TT-TCTA-TTCCCTCTAAAT
1 TTCTCAATTTCCCTCTAAAT
*
628304 TTCTCATTTTCCCTCTAAA-
1 TTCTCAATTTCCCTCTAAAT
628323 TTCTCAATTTCCCT
1 TTCTCAATTTCCCT
628337 ATATTATCAA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
18 7 0.16
19 21 0.48
20 14 0.32
21 2 0.05
ACGTcount: A:0.22, C:0.32, G:0.00, T:0.46
Consensus pattern (20 bp):
TTCTCAATTTCCCTCTAAAT
Found at i:628454 original size:2 final size:2
Alignment explanation
Indices: 628447--628642 Score: 119
Period size: 2 Copynumber: 100.0 Consensus size: 2
628437 ACTTTGAATA
* * *
628447 AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT -T AT AGT TT AT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
* * * * *
628489 AT AT AT AGT TT AG AT AT AT AGT -T CAT AT AA AC AT A- AT TT AT
1 AT AT AT A-T AT AT AT AT AT A-T AT -AT AT AT AT AT AT AT AT AT
* *
628530 AT AT AT A- ACT -T AT A- AT A- AT -T AT AT AGT TT AT A- AT AT AA
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT
* * *
628568 AT AT AGT TT AT AT AT AT AT -T TT AT AT AT AA ACT -T AT AT -T AT
1 AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
628609 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
628643 TTCAATTTTT
Statistics
Matches: 150, Mismatches: 24, Indels: 40
0.70 0.11 0.19
Matches are distributed among these distances:
1 12 0.08
2 132 0.88
3 6 0.04
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:628532 original size:77 final size:82
Alignment explanation
Indices: 628444--628639 Score: 221
Period size: 77 Copynumber: 2.5 Consensus size: 82
628434 CTCACTTTGA
*
628444 ATAATATATATATATATATATATATATATAAAT-TATAGTTTAT-ACAT-ATATAGTTTAGATAT
1 ATAATTTATATATATATATATATATATATAAATATATAGTTTATAACATAATATAGTTTAGATAT
628506 ATA-GTT-CATATAAAC
66 ATATGTTACATATAAAC
* * * *
628521 ATAATTTATATATATA-A-CT-TATA-ATAATTATATAGTTTATAATATAAATATAGTTTATATA
1 ATAATTTATATATATATATATATATATATAAATATATAGTTTATAACAT-AATATAGTTTAGATA
* *
628582 TATATTTTATATATAAAC
65 TATATGTTACATATAAAC
* *
628600 TTATATTATATATATATATATATATATATATATATATATA
1 ATA-ATT-TATATATATATATATATATATATAAATATATA
628640 TATTTCAATT
Statistics
Matches: 96, Mismatches: 11, Indels: 16
0.78 0.09 0.13
Matches are distributed among these distances:
73 5 0.05
74 14 0.15
75 4 0.04
76 1 0.01
77 32 0.33
78 2 0.02
79 10 0.10
80 3 0.03
81 10 0.10
82 1 0.01
83 1 0.01
84 4 0.04
85 9 0.09
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (82 bp):
ATAATTTATATATATATATATATATATATAAATATATAGTTTATAACATAATATAGTTTAGATAT
ATATGTTACATATAAAC
Found at i:631951 original size:3 final size:3
Alignment explanation
Indices: 631943--632031 Score: 126
Period size: 3 Copynumber: 29.7 Consensus size: 3
631933 TATATTAAAT
*
631943 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* **
631990 TAT TAA TAA TAA TAA GGA TAA TAA TAA TTAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TA
632032 TGGATAAAAA
Statistics
Matches: 77, Mismatches: 7, Indels: 4
0.88 0.08 0.05
Matches are distributed among these distances:
2 2 0.03
3 72 0.94
4 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:632450 original size:113 final size:113
Alignment explanation
Indices: 632287--633159 Score: 1331
Period size: 113 Copynumber: 7.7 Consensus size: 113
632277 TCTTGATGAG
632287 TTCTTCTCATTATGAACTTC-TCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
*
632350 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
65 GGAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
632399 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTAC-CT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTT-CTCT
*
632463 GGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
65 GGAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
*
632512 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * * *
632577 GAAAAGATGATTCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* * *
632625 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
632690 GAAATGTTGATCCATCAAATGATGAATTTAGGTAAAAGGTTGAACAAA
66 GAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* * *
632738 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAATTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * *
632803 GAAATGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
*
632851 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
632916 GAAAAGCTGATCCATCAAATGACGGATTCAAGTAAAAGGTTGAACAAA
66 GAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* * *
632964 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAATTCTTCTCATTATGAACCTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * *
633029 GAACTGTTGATCCATCAAATGATGAATTTAAACAAAAAGTTGAACAAG
66 GAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
*
633077 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTATCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
633141 GTAATGAATGATCCATCAA
66 GAAATG-TTGATCCATCAA
633160 GTGGATTTGA
Statistics
Matches: 701, Mismatches: 57, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
112 31 0.04
113 670 0.96
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.38
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
Found at i:633898 original size:50 final size:50
Alignment explanation
Indices: 633844--633945 Score: 170
Period size: 50 Copynumber: 2.0 Consensus size: 50
633834 TCAATGCTTG
*
633844 TTCTG-CTACACCAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTA
1 TTCTGTCTA-ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
*
633894 TTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
633944 TT
1 TT
633946 GATAAATTCA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
50 46 0.94
51 3 0.06
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (50 bp):
TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
Found at i:634030 original size:50 final size:50
Alignment explanation
Indices: 633976--634077 Score: 179
Period size: 50 Copynumber: 2.0 Consensus size: 50
633966 TCAATGCTTG
633976 TTCTG-CTACACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 TTCTGTCTA-ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
*
634026 TTCTGTCTAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
1 TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
634076 TT
1 TT
634078 GGCAAATTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
50 47 0.94
51 3 0.06
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.25
Consensus pattern (50 bp):
TTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA
Found at i:634197 original size:133 final size:133
Alignment explanation
Indices: 633723--634888 Score: 2042
Period size: 133 Copynumber: 8.8 Consensus size: 133
633713 TACACTTCTT
* *
633723 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
* * * *
633788 AAAGAACACTTCCAGAAGATGCTATTGATAAATTCATCTT-TCAAATTCAATGCTT-GTTCTGCT
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCT-AAATTCACTGATTGGTTCTGTT
633851 -ACAC
130 CA-AC
*
633855 CAGATCAGATAACTCAAAGAACATTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
* * * *
633920 AAAGAACACTTCCAGAAGATGCTATTGATAAATTCATCTT-TCAAATTCAATGCTT-GTTCTGCT
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCT-AAATTCACTGATTGGTTCTGTT
633983 -ACAC
130 CA-AC
633987 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
* *
634052 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTA
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
634117 AAC
131 AAC
634120 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
*
634185 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
634250 AAC
131 AAC
*
634253 CAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
*
634318 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
634383 AAC
131 AAC
634386 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
* *
634451 AAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAATTTCACTGATTGGTTCTGTTC
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
634516 AAC
131 AAC
634519 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
*
634584 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTTTAAATTCACTGATTGGTTCTGTTC
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
634649 AAC
131 AAC
*
634652 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTATCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
* *
634717 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTT-T-CATTTACTGATTGGTTCTGTTC
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
634780 AAC
131 AAC
634783 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
634848 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTC
66 AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTC
634889 ATTTAATGTT
Statistics
Matches: 1010, Mismatches: 20, Indels: 8
0.97 0.02 0.01
Matches are distributed among these distances:
131 127 0.13
132 243 0.24
133 639 0.63
134 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (133 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTCTGTCTAATCAGATCAGATAACTC
AAAGAACACTTCCAGAAGATGCTATTGGTAAATTCATCTTCTAAATTCACTGATTGGTTCTGTTC
AAC
Found at i:636017 original size:13 final size:13
Alignment explanation
Indices: 635999--636036 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
635989 CTTGACCCCC
635999 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
636012 TTTTTTCTTTTTT
1 TTTTTTCTTTTTT
636025 TCTTTTT-TTTTT
1 T-TTTTTCTTTTT
636037 CAAGCATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 19 0.79
14 5 0.21
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (13 bp):
TTTTTTCTTTTTT
Found at i:648779 original size:3 final size:3
Alignment explanation
Indices: 648762--648913 Score: 198
Period size: 3 Copynumber: 50.7 Consensus size: 3
648752 TTAATATATT
648762 TAA T-A TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** *
648807 TAA TGA TAA TAA TAT TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * ** *
648855 TAA TAA TGA TAA TAA TAT TAA TAA TAA TAA GGA TAA TAA TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
648903 TAA TAA TAA TA
1 TAA TAA TAA TA
648914 TGGATAAAAA
Statistics
Matches: 127, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
2 2 0.02
3 122 0.96
4 3 0.02
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:649370 original size:60 final size:60
Alignment explanation
Indices: 649249--649375 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 60
649239 TTTCTTCCTT
** * * *
649249 AAACTATGATTTTCATTATAAATTAATCCTCAAACTTTTAAGCATTTTAATTCTATCCCC
1 AAACTATGACCTTCATTATAAATTAATCCCCAAACTTTTAAGCATCTCAATTCTATCCCC
* *
649309 AAACTATGACCTTCATTCTAAATTAGTCCCCAAACTTTTTGAA-CATCTCAATT-TCAT-CCC
1 AAACTATGACCTTCATTATAAATTAATCCCCAAAC-TTTT-AAGCATCTCAATTCT-ATCCCC
649369 AAACTAT
1 AAACTAT
649376 ATGTATGTAC
Statistics
Matches: 57, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
60 41 0.72
61 14 0.25
62 2 0.04
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (60 bp):
AAACTATGACCTTCATTATAAATTAATCCCCAAACTTTTAAGCATCTCAATTCTATCCCC
Found at i:649983 original size:23 final size:23
Alignment explanation
Indices: 649925--649986 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
649915 CTAAAACAAA
**
649925 AATATAATATCATATATAATTAT
1 AATATAATAAAATATATAATTAT
* *
649948 AATATAATTAAATATATTATTAT
1 AATATAATAAAATATATAATTAT
649971 AATACTAA-AAAATATA
1 AATA-TAATAAAATATA
649987 ATGATATGCT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
23 30 0.91
24 3 0.09
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (23 bp):
AATATAATAAAATATATAATTAT
Found at i:653803 original size:22 final size:23
Alignment explanation
Indices: 653770--653812 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
653760 TTAAGGTATA
653770 TTTTATTATATTTAA-TATTTTT
1 TTTTATTATATTTAAGTATTTTT
653792 TTTTAATT-TATTTAAGTATTT
1 TTTT-ATTATATTTAAGTATTT
653813 AAATTTTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (23 bp):
TTTTATTATATTTAAGTATTTTT
Found at i:653822 original size:17 final size:17
Alignment explanation
Indices: 653796--653828 Score: 50
Period size: 16 Copynumber: 1.9 Consensus size: 17
653786 ATTTTTTTTT
653796 AATTTATTTAAGTATTTA
1 AATTTATTTAA-TATTTA
653814 AATTT-TTTAATATTT
1 AATTTATTTAATATTT
653829 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:653830 original size:17 final size:19
Alignment explanation
Indices: 653791--653830 Score: 50
Period size: 17 Copynumber: 2.3 Consensus size: 19
653781 TTAATATTTT
*
653791 TTTTTAATTTATTTAAGTA
1 TTTTAAATTTATTTAAGTA
653810 -TTTAAATTT-TTTAA-TA
1 TTTTAAATTTATTTAAGTA
653826 TTTTA
1 TTTTA
653831 TTTAATTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 4
0.79 0.04 0.17
Matches are distributed among these distances:
16 2 0.11
17 9 0.47
18 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (19 bp):
TTTTAAATTTATTTAAGTA
Found at i:656182 original size:25 final size:24
Alignment explanation
Indices: 656131--656193 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 24
656121 TATTTCATTA
* *
656131 ATTTTGTTGGATTTATTTTAATTT
1 ATTTTGTTGAATTTATTTTAATGT
656155 ATTTTGTTGAACTTT-TTGTTAATGT
1 ATTTTGTTGAA-TTTATT-TTAATGT
656180 ATTTTGGTT-AATTT
1 ATTTT-GTTGAATTT
656194 TGTTTATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 15 0.44
25 16 0.47
26 3 0.09
ACGTcount: A:0.21, C:0.02, G:0.14, T:0.63
Consensus pattern (24 bp):
ATTTTGTTGAATTTATTTTAATGT
Found at i:659826 original size:21 final size:21
Alignment explanation
Indices: 659800--659845 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
659790 AGAGAGTAGT
659800 CGAGAGATGATGCTTTAAAGC
1 CGAGAGATGATGCTTTAAAGC
*
659821 CGAGAGATGATGCTTTAAATC
1 CGAGAGATGATGCTTTAAAGC
659842 CGAG
1 CGAG
659846 TGGTCGGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.24
Consensus pattern (21 bp):
CGAGAGATGATGCTTTAAAGC
Found at i:661988 original size:3 final size:3
Alignment explanation
Indices: 661975--662026 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
661965 TCTACAAAAA
*
661975 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAA TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
662020 TAT TAT T
1 TAT TAT T
662027 TTTTAATTTA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 40 0.89
4 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:663352 original size:5 final size:5
Alignment explanation
Indices: 663339--663369 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
663329 CTCTTTCCAC
*
663339 TTTTA TTTTG TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
663370 CTTTGCGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:665371 original size:22 final size:23
Alignment explanation
Indices: 665343--665385 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
665333 TCTTTATACC
665343 TATAGAT-GCTTA-TTTCATATGT
1 TATAGATAG-TTATTTTCATATGT
665365 TATAGATAGTTATTTTCATAT
1 TATAGATAGTTATTTTCATAT
665386 ATATATATCT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.30, C:0.07, G:0.12, T:0.51
Consensus pattern (23 bp):
TATAGATAGTTATTTTCATATGT
Found at i:665390 original size:22 final size:22
Alignment explanation
Indices: 665343--665390 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
665333 TCTTTATACC
*
665343 TATAGATGCTTATTTCATATGT
1 TATAGATGCTTATTTCATATGA
665365 TATAGATAG-TTATTTTCATAT-A
1 TATAGAT-GCTTA-TTTCATATGA
665387 TATA
1 TATA
665391 TATCTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
22 14 0.61
23 9 0.39
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.50
Consensus pattern (22 bp):
TATAGATGCTTATTTCATATGA
Found at i:666567 original size:161 final size:163
Alignment explanation
Indices: 666300--666612 Score: 612
Period size: 161 Copynumber: 1.9 Consensus size: 163
666290 TCCTAGAGAC
666300 ATGTATCTAGCCGAAACAACTTGTAACCATTCGGCCAAGCCCTCTCATTTCCTATAAATAGAGTG
1 ATGTATCTAGCCGAAACAACTTGTAACCATTCGGCCAAGCCCTCTCATTTCCTATAAATAGAGTG
666365 GTTTGCCTTCATTTGTACCCATCTCATCTATTATATAAAATATACTCTTGTGAGTTATTTCTCTT
66 GTTTGCCTTCATTTGTACCCATCTCATCTATTATATAAAATATACTCTTGTGAGTTATTTCTCTT
666430 CAAAGTTCTTTGTGAACTTTATTAAACAAGTAT
131 CAAAGTTCTTTGTGAACTTTATTAAACAAGTAT
666463 ATGTATCTAGCCGAAACAACTTGTAACCATTCGGCCAAG-CC-CTCATTTCCTATAAATAGAGTG
1 ATGTATCTAGCCGAAACAACTTGTAACCATTCGGCCAAGCCCTCTCATTTCCTATAAATAGAGTG
666526 GTTTGCCTTCATTTGTACCCATCTCATCTATTATATAAAATATACTCTTGTGAGTTATTTCTCTT
66 GTTTGCCTTCATTTGTACCCATCTCATCTATTATATAAAATATACTCTTGTGAGTTATTTCTCTT
666591 CAAAGTTCTTTGTGAACTTTAT
131 CAAAGTTCTTTGTGAACTTTAT
666613 CGATTAAACA
Statistics
Matches: 150, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
161 109 0.73
162 2 0.01
163 39 0.26
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.38
Consensus pattern (163 bp):
ATGTATCTAGCCGAAACAACTTGTAACCATTCGGCCAAGCCCTCTCATTTCCTATAAATAGAGTG
GTTTGCCTTCATTTGTACCCATCTCATCTATTATATAAAATATACTCTTGTGAGTTATTTCTCTT
CAAAGTTCTTTGTGAACTTTATTAAACAAGTAT
Found at i:667170 original size:17 final size:17
Alignment explanation
Indices: 667148--667197 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
667138 TTGGAGTGCA
667148 AAAAGAAAGAAAAAGAC
1 AAAAGAAAGAAAAAGAC
*
667165 AAAAGAAGAGAAAAA-TC
1 AAAAGAA-AGAAAAAGAC
* *
667182 AGAAGAAAAAAAAAGA
1 AAAAGAAAGAAAAAGA
667198 AAAGAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
16 6 0.22
17 14 0.52
18 7 0.26
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (17 bp):
AAAAGAAAGAAAAAGAC
Found at i:675125 original size:70 final size:70
Alignment explanation
Indices: 675011--675192 Score: 280
Period size: 70 Copynumber: 2.6 Consensus size: 70
675001 ATTGTTTCAC
* *
675011 TTGAAACAAAAATCATCTTTGAGTCTGTTTCTTTGGAAATAAAGTTTTGTCTTTCTTGAGACAAT
1 TTGAAACAAAAATCATCTTTGAGTCTGTTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAAT
675076 TTCTT
66 TTCTT
* *
675081 TTGAAACAAAAATCATCTTTGAGTTTGTTTTTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAAT
1 TTGAAACAAAAATCATCTTTGAGTCTGTTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAAT
675146 TTCTT
66 TTCTT
*
675151 TTGAGGA-AAAAATCATCTTTGAGTC-GTTTCTCTT-GAAACAAA
1 TTGA-AACAAAAATCATCTTTGAGTCTGTTTCT-TTGGAAACAAA
675193 AGTGGAAATT
Statistics
Matches: 103, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
69 13 0.13
70 89 0.86
71 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.42
Consensus pattern (70 bp):
TTGAAACAAAAATCATCTTTGAGTCTGTTTCTTTGGAAACAAAGTTTTGTCTCTCTTGAGACAAT
TTCTT
Found at i:675961 original size:3 final size:3
Alignment explanation
Indices: 675948--676018 Score: 97
Period size: 3 Copynumber: 23.3 Consensus size: 3
675938 TCTATAAAAA
675948 TAT TAAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * *
675994 TAT TAT GCT TAT TTT TAT TAA TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
676019 TTTAATTTAC
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
3 56 0.95
4 3 0.05
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:677607 original size:30 final size:29
Alignment explanation
Indices: 677573--677685 Score: 88
Period size: 29 Copynumber: 3.8 Consensus size: 29
677563 GTTATAGCCT
* *
677573 TTTAAGTTTATGTTTTTGCCATTTTATTCC
1 TTTAAATTT-TGTTTTTGCTATTTTATTCC
* *
677603 TTTAAATTTCTG-TTTTGTTGTTTTAGTTCC
1 TTTAAATTT-TGTTTTTGCTATTTTA-TTCC
677633 -TTAAATTGTTGTTTTT-CTATTTTATTCC
1 TTTAAATT-TTGTTTTTGCTATTTTATTCC
* * *
677661 ATTAAGTTTTTTTTTTTTGCTATTT
1 TTTAA--ATTTTGTTTTTGCTATTT
677686 GGGTCCTTTT
Statistics
Matches: 67, Mismatches: 9, Indels: 13
0.75 0.10 0.15
Matches are distributed among these distances:
28 4 0.06
29 29 0.43
30 26 0.39
31 8 0.12
ACGTcount: A:0.16, C:0.10, G:0.10, T:0.65
Consensus pattern (29 bp):
TTTAAATTTTGTTTTTGCTATTTTATTCC
Found at i:677985 original size:5 final size:5
Alignment explanation
Indices: 677972--678002 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
677962 CTCTTTTCAC
*
677972 TTTTA TTTTG TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T
678003 CTTTGCGAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:679116 original size:18 final size:19
Alignment explanation
Indices: 679073--679124 Score: 63
Period size: 18 Copynumber: 2.8 Consensus size: 19
679063 CTCTCTATAT
679073 AAAAT-AATATAACTTTTCA
1 AAAATAAATATAA-TTTTCA
*
679092 TAAATAAATATAATTTT-A
1 AAAATAAATATAATTTTCA
*
679110 AAAATAATTATAATT
1 AAAATAAATATAATT
679125 AAATAAAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 14 0.48
19 8 0.28
20 7 0.24
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAATAAATATAATTTTCA
Found at i:685962 original size:15 final size:15
Alignment explanation
Indices: 685944--685986 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
685934 CTGGGCGAGA
685944 GGATGTGGGGCGGGC
1 GGATGTGGGGCGGGC
*
685959 GGATATGGGGCGCGGGC
1 GGATGT-GGG-GCGGGC
*
685976 GGATGCGGGGC
1 GGATGTGGGGC
685987 AGATAATGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 7 0.30
16 6 0.26
17 10 0.43
ACGTcount: A:0.09, C:0.16, G:0.63, T:0.12
Consensus pattern (15 bp):
GGATGTGGGGCGGGC
Found at i:688822 original size:15 final size:15
Alignment explanation
Indices: 688783--688822 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
688773 GAGGCAAGAC
688783 AACATGCTATTCTCT
1 AACATGCTATTCTCT
* *
688798 -GCATGATATTCTCT
1 AACATGCTATTCTCT
688812 AACATGCTATT
1 AACATGCTATT
688823 TTCTTTTTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.40
Consensus pattern (15 bp):
AACATGCTATTCTCT
Found at i:691667 original size:3 final size:3
Alignment explanation
Indices: 691661--691739 Score: 158
Period size: 3 Copynumber: 26.3 Consensus size: 3
691651 TTACTACTAC
691661 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
691709 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
691740 TGTTTTTGTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 76 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:692869 original size:31 final size:31
Alignment explanation
Indices: 692821--692888 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
692811 CGTCAGTGAC
* *
692821 CATATTGTAAACGGACTAAATGTT-GAGGGAT
1 CATATTGCAAACAGACTAAATGTTAG-GGGAT
692852 CATATTGCAAACAGACTAAATGTTAGGGGAT
1 CATATTGCAAACAGACTAAATGTTAGGGGAT
*
692883 TATATT
1 CATATT
692889 ACAAGTTTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 32 0.97
32 1 0.03
ACGTcount: A:0.37, C:0.10, G:0.22, T:0.31
Consensus pattern (31 bp):
CATATTGCAAACAGACTAAATGTTAGGGGAT
Found at i:694821 original size:25 final size:25
Alignment explanation
Indices: 694793--694840 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
694783 AAAACGGTTT
694793 TTCTCGGGATCAGGTCGGGTTCGAG
1 TTCTCGGGATCAGGTCGGGTTCGAG
*
694818 TTCTCGGGATCGGGTCGGGTTCG
1 TTCTCGGGATCAGGTCGGGTTCG
694841 GGGACGGGGC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.08, C:0.21, G:0.42, T:0.29
Consensus pattern (25 bp):
TTCTCGGGATCAGGTCGGGTTCGAG
Found at i:695066 original size:21 final size:21
Alignment explanation
Indices: 695040--695080 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
695030 TATTTCCAGT
*
695040 ATGCATGTCCGCATGAACAAG
1 ATGCATGCCCGCATGAACAAG
695061 ATGCATGCCCGCATGAACAA
1 ATGCATGCCCGCATGAACAA
695081 AATTATCTGG
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:0.34, C:0.27, G:0.22, T:0.17
Consensus pattern (21 bp):
ATGCATGCCCGCATGAACAAG
Found at i:697179 original size:20 final size:20
Alignment explanation
Indices: 697154--697210 Score: 78
Period size: 20 Copynumber: 2.9 Consensus size: 20
697144 AAATAAAAAA
697154 ATATTGTATGAATAGTATCG
1 ATATTGTATGAATAGTATCG
*
697174 ATATTGTACGAATAGTATCG
1 ATATTGTATGAATAGTATCG
* * *
697194 ATACTGTGTGAACAGTA
1 ATATTGTATGAATAGTA
697211 ATGAACAGTA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.21, T:0.35
Consensus pattern (20 bp):
ATATTGTATGAATAGTATCG
Found at i:698055 original size:15 final size:15
Alignment explanation
Indices: 698035--698064 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
698025 CAGTGCCTAT
*
698035 TACATTGAAGATTCA
1 TACATTCAAGATTCA
698050 TACATTCAAGATTCA
1 TACATTCAAGATTCA
698065 CAACCGGTCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (15 bp):
TACATTCAAGATTCA
Found at i:705035 original size:29 final size:29
Alignment explanation
Indices: 705002--705093 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
704992 AAACTTTGTC
*
705002 TAGTGACTAAAATATAATTTTTGAAAGTT
1 TAGTGACTAAAATATAATTTTTGAAAGTA
* * **
705031 TAGTGGCTAAAGTATAAACTTTGAAAAGTA
1 TAGTGACTAAAATATAATTTTTG-AAAGTA
* *
705061 TAG-GAACTAAAATTGTAATTTTTAAAAGATA
1 TAGTG-ACTAAAA-TATAATTTTTGAAAG-TA
705092 TA
1 TA
705094 TATTTTAGCC
Statistics
Matches: 48, Mismatches: 11, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
29 20 0.42
30 17 0.35
31 11 0.23
ACGTcount: A:0.45, C:0.04, G:0.15, T:0.36
Consensus pattern (29 bp):
TAGTGACTAAAATATAATTTTTGAAAGTA
Found at i:707539 original size:148 final size:148
Alignment explanation
Indices: 707360--707657 Score: 517
Period size: 148 Copynumber: 2.0 Consensus size: 148
707350 ATAATCTGTA
* *
707360 ATAGTAAACTAGAACTATTTTAATTTATTTTACTTGGTTTAGTTTTATCAGTATCTATGTATGAA
1 ATAGTAAACTAGAACTATTTTAATTTATTTTACTTGGCTTAGTTTTATCAGTATCTATGCATGAA
*
707425 AAGAATATATTACGTTATTAGGTTTTTAAAAGTTTTCATGAAAAGACAT-GATTTAATAAAATTA
66 AAGAATATATTACGTTATTAGGTTTTTAAAAGTTTTCACGAAAAGACATAG-TTTAATAAAATTA
707489 CTGATTAACAAAAGAATTT
130 CTGATTAACAAAAGAATTT
* *
707508 ATAGTAAACTAGAACTATTTTAGTTTATTTTACTTGGCTTAGTTTTATCCGTATCTATGCATGAA
1 ATAGTAAACTAGAACTATTTTAATTTATTTTACTTGGCTTAGTTTTATCAGTATCTATGCATGAA
* *
707573 AAGAATATATTACGTTATTATGTTTTTAAAAGTTTTCACGAAGAGACATAGTTTAATAAAATTAC
66 AAGAATATATTACGTTATTAGGTTTTTAAAAGTTTTCACGAAAAGACATAGTTTAATAAAATTAC
707638 TGATTAACAAAAGAATTT
131 TGATTAACAAAAGAATTT
707656 AT
1 AT
707658 TTTCCAGTAA
Statistics
Matches: 142, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
148 141 0.99
149 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.12, T:0.41
Consensus pattern (148 bp):
ATAGTAAACTAGAACTATTTTAATTTATTTTACTTGGCTTAGTTTTATCAGTATCTATGCATGAA
AAGAATATATTACGTTATTAGGTTTTTAAAAGTTTTCACGAAAAGACATAGTTTAATAAAATTAC
TGATTAACAAAAGAATTT
Found at i:711760 original size:31 final size:31
Alignment explanation
Indices: 711722--711877 Score: 217
Period size: 31 Copynumber: 5.0 Consensus size: 31
711712 CCCGAAGGAC
* *
711722 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
711753 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
* *
711784 CAGTCCGTATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
*
711815 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
711846 CAGTCCATATG-TCCAGAAGAACATAGGTAAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAAA
711877 C
1 C
711878 CCTCGACCCT
Statistics
Matches: 111, Mismatches: 12, Indels: 4
0.87 0.09 0.03
Matches are distributed among these distances:
30 2 0.02
31 108 0.97
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.21, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:711819 original size:62 final size:62
Alignment explanation
Indices: 711722--711875 Score: 249
Period size: 62 Copynumber: 2.5 Consensus size: 62
711712 CCCGAAGGAC
* *
711722 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
*
711784 CAGTCCGTATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
711846 CAGTCCATATG-TCCAGAAGAACATAGGTAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAA
711876 ACCCTCGACC
Statistics
Matches: 86, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
61 3 0.03
62 82 0.95
63 1 0.01
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.21
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:712723 original size:21 final size:21
Alignment explanation
Indices: 712693--712737 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
712683 ATTCTGTCGT
* *
712693 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
712714 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
712735 TTG
1 TTG
712738 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:715737 original size:31 final size:31
Alignment explanation
Indices: 715714--715854 Score: 219
Period size: 31 Copynumber: 4.5 Consensus size: 31
715704 CATAGATTCT
* *
715714 GAAGAACCTAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
* * *
715745 GAAGGACATAGGTAAACAGTCCGTATGTTCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
715776 GAAGAACATAGGTAATCAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
*
715807 GAAGAACATAGGTAAACAGTCCATATGTCCA
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
715838 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
715855 CCTCGACCCT
Statistics
Matches: 99, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 99 1.00
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:716057 original size:23 final size:24
Alignment explanation
Indices: 716031--716077 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
716021 ATATACTTGT
*
716031 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
716054 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
716078 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Done.