Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003683.1 Hibiscus syriacus cultivar Beakdansim tig00007867_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: 143997
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4197 original size:48 final size:44
Alignment explanation
Indices: 4013--4216 Score: 363
Period size: 44 Copynumber: 4.5 Consensus size: 44
4003 AATCCGAGGT
4013 GCATTACTTACAAATATCAGTTCCATCTCTCTCCCTCCCGAGAA
1 GCATTACTTACAAATATCAGTTCCATCTCTCTCCCTCCCGAGAA
4057 GCATTACTTACAAATATCAGTTCCATCTCTCTCCCTCCCGAGAA
1 GCATTACTTACAAATATCAGTTCCATCTCTCTCCCTCCCGAGAA
4101 GCATTACTTACAAATATCAGTTCCATCTCTCTCCCTCCCGAGAA
1 GCATTACTTACAAATATCAGTTCCATCTCTCTCCCTCCCGAGAA
*
4145 GCATTACTTACAAATATCAGTCCCATCTCTCTCTCTCTCTCCCGAGAA
1 GCATTACTTACAAATATCAGTTCCA--TCTCTCTC-C-CTCCCGAGAA
4193 GCATTACTTACAAATATCAGTTCC
1 GCATTACTTACAAATATCAGTTCC
4217 TCACACACAC
Statistics
Matches: 154, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
44 112 0.73
46 8 0.05
47 1 0.01
48 33 0.21
ACGTcount: A:0.27, C:0.33, G:0.09, T:0.30
Consensus pattern (44 bp):
GCATTACTTACAAATATCAGTTCCATCTCTCTCCCTCCCGAGAA
Found at i:9933 original size:2 final size:2
Alignment explanation
Indices: 9849--9925 Score: 136
Period size: 2 Copynumber: 38.5 Consensus size: 2
9839 TGCAAATTAT
* *
9849 TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9891 TA TA TA 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 TA TA TA T
9926 TTTATATACT
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17727 original size:18 final size:18
Alignment explanation
Indices: 17704--17741 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
17694 AAAAAACCTC
17704 TGGAAACTCCTTAACTGT
1 TGGAAACTCCTTAACTGT
17722 TGGAAACTCCTTAACTGT
1 TGGAAACTCCTTAACTGT
17740 TG
1 TG
17742 AGGTGGCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (18 bp):
TGGAAACTCCTTAACTGT
Found at i:19169 original size:240 final size:240
Alignment explanation
Indices: 18733--19215 Score: 849
Period size: 240 Copynumber: 2.0 Consensus size: 240
18723 TGCAGGAGTA
* * *
18733 TTTCAACAATCACAAAGTGTAGTAAAGGCATAACGACACACACAACTCTGATCCTTCAAAAACTC
1 TTTCAACAATCACAAAGTGTAGTAAAGGAATAACGACACACACAACTCGGATCCTTCAAAAAATC
18798 TCGGTGGTAGTAACCGGAAGATCTCATCGTCATAATACGACATCCAAGAAAACTATAAATATTAA
66 TCGGTGGTAGTAACCGGAAGATCTCATCGTCATAATACGACATCCAAGAAAACTATAAATATTAA
* **
18863 TAATAAAAGTTAGTATAAATAAAGTCAAAAAATATAATTAAATTTTAATAATTAAAAACTTTAAT
131 TAATAAAAGTTAGTATAAATAAAGTCAAAAAATATAATTAAATTTTAATAATAAAAAAAATTAAT
* *
18928 ATTTATCGCATGTTAACCGATGATATCGATTCTCATTTGTATATC
196 ATCTACCGCATGTTAACCGATGATATCGATTCTCATTTGTATATC
* *
18973 TTTCAACAATCGCAAAGTGTAGTAAAGGAATAACGACACCCACAACTCGGATCCTTCAAAAAATC
1 TTTCAACAATCACAAAGTGTAGTAAAGGAATAACGACACACACAACTCGGATCCTTCAAAAAATC
*
19038 TCGGTGGTAGTAACCGGAAGATCTCATCGTCATAATACGTCATCCAAGAAAACTATAAATATTAA
66 TCGGTGGTAGTAACCGGAAGATCTCATCGTCATAATACGACATCCAAGAAAACTATAAATATTAA
* *
19103 TAGTAAAAGTTAGTATAAATAAAGTGAAAAAATATAATTAAATTTTAATAATAAAAAAAATTAAT
131 TAATAAAAGTTAGTATAAATAAAGTCAAAAAATATAATTAAATTTTAATAATAAAAAAAATTAAT
19168 ATCTACCGCATGTTAACCGATGATATCGATTCTCATTTGTATATC
196 ATCTACCGCATGTTAACCGATGATATCGATTCTCATTTGTATATC
19213 TTT
1 TTT
19216 TTTAGTTGTC
Statistics
Matches: 230, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
240 230 1.00
ACGTcount: A:0.42, C:0.16, G:0.12, T:0.30
Consensus pattern (240 bp):
TTTCAACAATCACAAAGTGTAGTAAAGGAATAACGACACACACAACTCGGATCCTTCAAAAAATC
TCGGTGGTAGTAACCGGAAGATCTCATCGTCATAATACGACATCCAAGAAAACTATAAATATTAA
TAATAAAAGTTAGTATAAATAAAGTCAAAAAATATAATTAAATTTTAATAATAAAAAAAATTAAT
ATCTACCGCATGTTAACCGATGATATCGATTCTCATTTGTATATC
Found at i:19320 original size:24 final size:24
Alignment explanation
Indices: 19293--19339 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
19283 AAAACATTCC
19293 AAAAAATAAAT-TTAAAAATTTACT
1 AAAAAAT-AATGTTAAAAATTTACT
19317 AAAAAATAATGTTAAAAATTTAC
1 AAAAAATAATGTTAAAAATTTAC
19340 CTTGCAGCGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (24 bp):
AAAAAATAATGTTAAAAATTTACT
Found at i:21582 original size:44 final size:44
Alignment explanation
Indices: 21532--21708 Score: 223
Period size: 44 Copynumber: 4.0 Consensus size: 44
21522 TCTTACCGAA
*
21532 ATAAATGAAAATGCATAA-AGGTGCATTATTGGAAGAAAGGTACC
1 ATAAATGAAAATGCATAACA-GTGCATTATTGGAAGAAAGGTGCC
* **
21576 ATAAATGAAAATGCATAACGGTGCATTATT-GACAGAAATATGCC
1 ATAAATGAAAATGCATAACAGTGCATTATTGGA-AGAAAGGTGCC
* * *
21620 ATAAATGAAAATGCATAACAGTGCATTATTAGCAGAAAGGTGTC
1 ATAAATGAAAATGCATAACAGTGCATTATTGGAAGAAAGGTGCC
* * * *
21664 ATAAATGAAAATGAATAACAATGCATTACTGGGAGAAAGGTGCC
1 ATAAATGAAAATGCATAACAGTGCATTATTGGAAGAAAGGTGCC
21708 A
1 A
21709 CTCATGGTAT
Statistics
Matches: 115, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
43 2 0.02
44 112 0.97
45 1 0.01
ACGTcount: A:0.45, C:0.11, G:0.21, T:0.23
Consensus pattern (44 bp):
ATAAATGAAAATGCATAACAGTGCATTATTGGAAGAAAGGTGCC
Found at i:26063 original size:3 final size:3
Alignment explanation
Indices: 26055--26145 Score: 89
Period size: 3 Copynumber: 30.0 Consensus size: 3
26045 TCGTCTGATC
* *
26055 TTA TTA TTA TTA TTA TTA TTA TATA TAA TTA -TA TATA TTA -TA CTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA T-TA TTA TTA TTA
* *
26100 CTA TTA TTA TATA TGA -TA TTA TTA TATA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA
26146 AATAATATTA
Statistics
Matches: 76, Mismatches: 5, Indels: 14
0.80 0.05 0.15
Matches are distributed among these distances:
2 5 0.07
3 59 0.78
4 12 0.16
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:27997 original size:15 final size:15
Alignment explanation
Indices: 27977--28015 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
27967 ATTTTCAAAC
27977 AAAGCATGAAACTAG
1 AAAGCATGAAACTAG
*
27992 AAAGCATGGAACTAG
1 AAAGCATGAAACTAG
28007 AAAGCATGA
1 AAAGCATGA
28016 GGATAGGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.51, C:0.13, G:0.23, T:0.13
Consensus pattern (15 bp):
AAAGCATGAAACTAG
Found at i:33446 original size:22 final size:20
Alignment explanation
Indices: 33411--33460 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
33401 ATATATTAAG
* *
33411 ATAATTTTACAATATAATTGTA
1 ATAATATTACAATAGAA-T-TA
*
33433 ATAATATTATAATAGAATTA
1 ATAATATTACAATAGAATTA
33453 ATAATATT
1 ATAATATT
33461 TATATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 10 0.40
21 1 0.04
22 14 0.56
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
ATAATATTACAATAGAATTA
Found at i:47637 original size:23 final size:24
Alignment explanation
Indices: 47570--47630 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
47560 ATTAGGTTAG
47570 GGTTTTAATTTGGGCCCGGGTTTA
1 GGTTTTAATTTGGGCCCGGGTTTA
47594 GGTTTTAATTTGGGCCCGGGTTTA
1 GGTTTTAATTTGGGCCCGGGTTTA
*
47618 GG-TTTGATTTGGG
1 GGTTTTAATTTGGG
47631 TCTGGGTATG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
23 10 0.28
24 26 0.72
ACGTcount: A:0.11, C:0.10, G:0.36, T:0.43
Consensus pattern (24 bp):
GGTTTTAATTTGGGCCCGGGTTTA
Found at i:47701 original size:3 final size:3
Alignment explanation
Indices: 47695--47720 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
47685 TATATTTTTT
47695 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
47721 GTAATGGTTG
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:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:49003 original size:32 final size:32
Alignment explanation
Indices: 48967--49063 Score: 106
Period size: 32 Copynumber: 3.0 Consensus size: 32
48957 TTTGATAATC
*
48967 TTAAAAACCATTTTATAATAGTTCGATAAGTT
1 TTAAAAACCATTTTATAATAGTTCAATAAGTT
* * * * **
48999 TTAAAGACTATTTTATACTAGTTAAATAAACT
1 TTAAAAACCATTTTATAATAGTTCAATAAGTT
*
49031 TTAACAACCATTTT-TCAATAGTTCAATAAGTT
1 TTAAAAACCATTTTAT-AATAGTTCAATAAGTT
49063 T
1 T
49064 AATGAACATT
Statistics
Matches: 50, Mismatches: 14, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
31 1 0.02
32 49 0.98
ACGTcount: A:0.40, C:0.11, G:0.07, T:0.41
Consensus pattern (32 bp):
TTAAAAACCATTTTATAATAGTTCAATAAGTT
Found at i:53079 original size:2 final size:2
Alignment explanation
Indices: 53072--53096 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
53062 AGACTCTTTC
53072 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
53097 ACAAACCCTT
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:53284 original size:60 final size:60
Alignment explanation
Indices: 53227--53357 Score: 147
Period size: 60 Copynumber: 2.2 Consensus size: 60
53217 CACAAATGGT
* *
53227 CTCTCAACTATA-GAGTATTGCTTTGTTGAGTTCTTCAAATATTAAAAGTTATAAAATGATC
1 CTCT-AACTATATGA-TATTGCTTTGTTGAGTCCCTCAAATATTAAAAGTTATAAAATGATC
* * * ** *
53288 CTCTGACTATATGATGTTGCTTTGTTGAGTCCCTCAACTATTAAATTTTACAAAATGATC
1 CTCTAACTATATGATATTGCTTTGTTGAGTCCCTCAAATATTAAAAGTTATAAAATGATC
* *
53348 ATTTAACTAT
1 CTCTAACTAT
53358 TCATATGATC
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
60 52 0.90
61 6 0.10
ACGTcount: A:0.32, C:0.15, G:0.12, T:0.40
Consensus pattern (60 bp):
CTCTAACTATATGATATTGCTTTGTTGAGTCCCTCAAATATTAAAAGTTATAAAATGATC
Found at i:54575 original size:19 final size:21
Alignment explanation
Indices: 54551--54621 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 21
54541 TGCAAAAATG
*
54551 GTATCGATACCGTA-ATAG-A
1 GTATCGATACCATAGATAGTA
*
54570 GTATCGGTACCATAGTATAGTA
1 GTATCGATACCATAG-ATAGTA
* **
54592 GTATCGATACCAT-GGTAGGG
1 GTATCGATACCATAGATAGTA
54612 GTATCGATAC
1 GTATCGATAC
54622 TATGGAGCCA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
19 12 0.28
20 13 0.30
21 5 0.12
22 13 0.30
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (21 bp):
GTATCGATACCATAGATAGTA
Found at i:58863 original size:24 final size:23
Alignment explanation
Indices: 58811--58864 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
58801 TACTTTTAAA
58811 TTATA-TATAAAAATAGATATCT
1 TTATATTATAAAAATAGATATCT
* * *
58833 TTGTATTATAAAAATAAGTTATTT
1 TTATATTATAAAAAT-AGATATCT
58857 TTATATTA
1 TTATATTA
58865 AATTTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
22 4 0.15
23 9 0.35
24 13 0.50
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (23 bp):
TTATATTATAAAAATAGATATCT
Found at i:58866 original size:22 final size:23
Alignment explanation
Indices: 58811--58866 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
58801 TACTTTTAAA
58811 TTATATATAAAAATAGATATCTT
1 TTATATATAAAAATAGATATCTT
*
58834 TGTAT-TATAAAAATAAGTTAT-TT
1 T-TATATATAAAAAT-AGATATCTT
58857 TTATAT-TAAA
1 TTATATATAAA
58867 TTTAAATAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
22 7 0.24
23 14 0.48
24 8 0.28
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.46
Consensus pattern (23 bp):
TTATATATAAAAATAGATATCTT
Found at i:59434 original size:24 final size:24
Alignment explanation
Indices: 59389--59435 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 24
59379 AATTTAAATA
59389 TTTAAGTAAATAAAAATAATTAAAG
1 TTTAAGTAAAT-AAAATAATTAAAG
59414 TTTAAGTCAAAT-AAATAATTAA
1 TTTAAGT-AAATAAAATAATTAA
59436 TATATATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.48
25 7 0.33
26 4 0.19
ACGTcount: A:0.57, C:0.02, G:0.06, T:0.34
Consensus pattern (24 bp):
TTTAAGTAAATAAAATAATTAAAG
Found at i:59609 original size:16 final size:16
Alignment explanation
Indices: 59590--59644 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
59580 TTAAATTCAC
59590 GTTACTTTCGATTCGG
1 GTTACTTTCGATTCGG
*
59606 GTTATTTTCGATTC-G
1 GTTACTTTCGATTCGG
* * * *
59621 ATAACTTTCGGTTCGA
1 GTTACTTTCGATTCGG
59637 GTTACTTT
1 GTTACTTT
59645 TGGTTGGCTA
Statistics
Matches: 30, Mismatches: 8, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
15 11 0.37
16 19 0.63
ACGTcount: A:0.16, C:0.16, G:0.20, T:0.47
Consensus pattern (16 bp):
GTTACTTTCGATTCGG
Found at i:60647 original size:68 final size:68
Alignment explanation
Indices: 60521--60649 Score: 163
Period size: 68 Copynumber: 1.9 Consensus size: 68
60511 GCTCAAAAAA
* * * * *
60521 AATCTTAACCAACAATTAGTTGGTTTAATGAGATAAGATACTATATTTTTTAGACAAGAATATTT
1 AATCTTAACCAACAATCAGTTGGTCTAATGAGATAAGATACTAGATTCTTAAGACAAGAATATTT
60586 AAG
66 AAG
* *
60589 AATCTTAATCAATAATCAGTTGGTCTAATGAGATGAA-ATACTAGATTGCTTAAG-CAAGAAT
1 AATCTTAACCAACAATCAGTTGGTCTAATGAGAT-AAGATACTAGATT-CTTAAGACAAGAAT
60650 CAGGGGTTCA
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
68 46 0.88
69 6 0.12
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (68 bp):
AATCTTAACCAACAATCAGTTGGTCTAATGAGATAAGATACTAGATTCTTAAGACAAGAATATTT
AAG
Found at i:61157 original size:2 final size:2
Alignment explanation
Indices: 61150--61208 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
61140 AGAATTTAAT
61150 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61192 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
61209 CTTAAATCAT
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:64719 original size:102 final size:101
Alignment explanation
Indices: 64505--64732 Score: 239
Period size: 102 Copynumber: 2.2 Consensus size: 101
64495 CATTGCTTCC
* *
64505 AGTTCAAGGGGAAGACATTCATCTGCCAATTTCTTTGACCAGAATATGAAGATATTCTCGACACA
1 AGTTCAAGGGGAAGACATTCAACTGCCAATTTCTTAGACCAGAATATGAAGATA-TCTCGACACA
* ** *
64570 ACAATCTATTCAATACCCATTTGACACGATGCCTATA
65 ACAATCTATTCAAAACCCATACGACACGATACCTATA
** * * *
64607 AGTTTTAGGGGGAGACATTCAACTG-CAAGTTTCTTAGACCATAATATGGAGATA-CATGCGACA
1 AGTTCAAGGGGAAGACATTCAACTGCCAA-TTTCTTAGACCAGAATATGAAGATATC-T-CGACA
* *
64670 CAACACTC-AGTTCAAAACCCATACGACAGGATACCT-TCA
63 CAACAATCTA-TTCAAAACCCATACGACACGATACCTAT-A
* *
64709 TGTTCAAGGGGAATACATTCAACT
1 AGTTCAAGGGGAAGACATTCAACT
64733 ACTAATTTGT
Statistics
Matches: 103, Mismatches: 18, Indels: 10
0.79 0.14 0.08
Matches are distributed among these distances:
100 1 0.01
101 6 0.06
102 96 0.93
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (101 bp):
AGTTCAAGGGGAAGACATTCAACTGCCAATTTCTTAGACCAGAATATGAAGATATCTCGACACAA
CAATCTATTCAAAACCCATACGACACGATACCTATA
Found at i:65423 original size:29 final size:29
Alignment explanation
Indices: 65381--65472 Score: 148
Period size: 29 Copynumber: 3.2 Consensus size: 29
65371 ATTCTACAGT
*
65381 GACCTCGTAGGTCGCCATGGCATCCGGGC
1 GACCTTGTAGGTCGCCATGGCATCCGGGC
65410 GACCTTGTAGGTCGCCATGGCATCCGGGC
1 GACCTTGTAGGTCGCCATGGCATCCGGGC
* **
65439 GACCTTGGAGGTCGCCATGGCATCCAAGC
1 GACCTTGTAGGTCGCCATGGCATCCGGGC
65468 GACCT
1 GACCT
65473 GTGTGGTGTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 59 1.00
ACGTcount: A:0.16, C:0.33, G:0.33, T:0.18
Consensus pattern (29 bp):
GACCTTGTAGGTCGCCATGGCATCCGGGC
Found at i:65564 original size:20 final size:20
Alignment explanation
Indices: 65539--65576 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
65529 TGGGGGAGTT
*
65539 GTGGGAGCTGTGAATGGGAC
1 GTGGGAACTGTGAATGGGAC
*
65559 GTGGGAACTGTGCATGGG
1 GTGGGAACTGTGAATGGG
65577 CATGGGGGAG
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:0.18, C:0.11, G:0.50, T:0.21
Consensus pattern (20 bp):
GTGGGAACTGTGAATGGGAC
Found at i:65595 original size:50 final size:51
Alignment explanation
Indices: 65526--65631 Score: 187
Period size: 50 Copynumber: 2.1 Consensus size: 51
65516 ATTGGAGCAT
65526 GCATGGGGGAGTTGTGGGAGCTGTGAATGGGACGTGGGAACTGTGCAT-GG
1 GCATGGGGGAGTTGTGGGAGCTGTGAATGGGACGTGGGAACTGTGCATGGG
* *
65576 GCATGGGGGAGTTGTGGGAGTTGTGCATGGGACGTGGGAACTGTGCATGGG
1 GCATGGGGGAGTTGTGGGAGCTGTGAATGGGACGTGGGAACTGTGCATGGG
65627 GCATG
1 GCATG
65632 CACGTCGAAC
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
50 46 0.87
51 7 0.13
ACGTcount: A:0.17, C:0.10, G:0.50, T:0.23
Consensus pattern (51 bp):
GCATGGGGGAGTTGTGGGAGCTGTGAATGGGACGTGGGAACTGTGCATGGG
Found at i:65770 original size:43 final size:40
Alignment explanation
Indices: 65694--65776 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 40
65684 CGACCAAGCT
65694 CTGGGAGATTCCTGTGTAACTGCATGCGTTGCAT-CATAG
1 CTGGGAGATTCCTGTGTAACTGCATGCGTTGCATCCATAG
* *
65733 CTGGGAGATTCCTGCATCCGTAGCTGCATGTGTTGCATCCATAG
1 CTGGGAGATTCCTG--T--GTAACTGCATGCGTTGCATCCATAG
65777 TTGCGTTATT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
39 14 0.38
41 1 0.03
43 17 0.46
44 5 0.14
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (40 bp):
CTGGGAGATTCCTGTGTAACTGCATGCGTTGCATCCATAG
Found at i:66171 original size:21 final size:21
Alignment explanation
Indices: 66146--66189 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
66136 AATCTAGTTA
66146 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
66167 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
66188 AT
1 AT
66190 ATTATATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:66199 original size:28 final size:30
Alignment explanation
Indices: 66166--66228 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 30
66156 TAGTATAAAT
*
66166 TATTAGTTTGTTAGTTTAAG-T-TATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
66194 TATTAGTTTATTAGTTTAAGTTATATATTA
1 TATTAGTTTATTAGTTTAAGTTATATATTA
66224 TATTA
1 TATTA
66229 TATAAAAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 19 0.59
29 1 0.03
30 12 0.38
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (30 bp):
TATTAGTTTATTAGTTTAAGTTATATATTA
Found at i:66773 original size:20 final size:21
Alignment explanation
Indices: 66729--66773 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
66719 AAATATTGTG
**
66729 TTTAAAAATATTTAGTGTTGT
1 TTTAAAAATATTTAGTGTTAA
*
66750 TTTAAAAATATTTTGT-TTAA
1 TTTAAAAATATTTAGTGTTAA
66770 TTTA
1 TTTA
66774 CATTGTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTAAAAATATTTAGTGTTAA
Found at i:67061 original size:26 final size:25
Alignment explanation
Indices: 67032--67090 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
67022 AAATCATATT
*
67032 ATTATTAAATCATTAAATATCAAATC
1 ATTATTAAAT-AGTAAATATCAAATC
*
67058 ATTAGATT-AATAGTAATTATCAAATC
1 ATT--ATTAAATAGTAAATATCAAATC
67084 ATTATTA
1 ATTATTA
67091 GGTTTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 3 0.11
26 19 0.68
27 3 0.11
28 3 0.11
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.41
Consensus pattern (25 bp):
ATTATTAAATAGTAAATATCAAATC
Found at i:69447 original size:40 final size:41
Alignment explanation
Indices: 69385--69507 Score: 112
Period size: 40 Copynumber: 3.0 Consensus size: 41
69375 CAAATATAAC
* *
69385 TTAACTATTTAACTA--ACACAAACTAATTAAATAATTTTT
1 TTAACTATATAACTATCAAACAAACTAATTAAATAATTTTT
* * * *
69424 TT-A-TATAACTAACTAT-TAACAAACAAACTAATTAATTATTT
1 TTAACTAT-A-TAACTATCAAACAAACTAATTAAATAATT-TTT
69465 TTAACTATATAACTATCAAACATATACTAATTAAATAATTTTT
1 TTAACTATATAACTATCAAACA-A-ACTAATTAAATAATTTTT
69508 AATTTATGTA
Statistics
Matches: 65, Mismatches: 10, Indels: 14
0.73 0.11 0.16
Matches are distributed among these distances:
37 3 0.05
38 1 0.02
39 8 0.12
40 16 0.25
41 12 0.18
42 6 0.09
43 7 0.11
44 12 0.18
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (41 bp):
TTAACTATATAACTATCAAACAAACTAATTAAATAATTTTT
Found at i:69535 original size:41 final size:39
Alignment explanation
Indices: 69399--69535 Score: 89
Period size: 41 Copynumber: 3.3 Consensus size: 39
69389 CTATTTAACT
* *
69399 AACACAAACTAATTAAATAATTTTTTTA-TATAACTAACTATTA
1 AACATAAACTAATT-AATAA-TTTTTAACTAT-A-TAACTA-TA
* * *
69442 ACAAACAAACTAATTAATTATTTTTAACTATATAACTATCA
1 A-ACATAAACTAATTAATAATTTTTAACTATATAACTAT-A
* * *
69483 AACATATACTAATTAAATAATTTTTAATTTATGTATACTAT-
1 AACATAAACTAATT-AATAATTTTTAA-CTATATA-ACTATA
*
69524 AACTTAAACTAA
1 AACATAAACTAA
69536 CAATCATATA
Statistics
Matches: 77, Mismatches: 11, Indels: 14
0.75 0.11 0.14
Matches are distributed among these distances:
40 11 0.14
41 29 0.38
42 12 0.16
43 13 0.17
44 12 0.16
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (39 bp):
AACATAAACTAATTAATAATTTTTAACTATATAACTATA
Found at i:69969 original size:29 final size:29
Alignment explanation
Indices: 69910--70069 Score: 261
Period size: 29 Copynumber: 5.6 Consensus size: 29
69900 TCGTGAGCTA
*
69910 GGACTACATGGCGACCT--AAGGTCGCCA
1 GGACTACATGGCGACCTACAAGGTCGCCG
69937 GGACTACATGGCGACCTACAAGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
69966 GGACTACATGGCGACCTACAAGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
69995 GGACTACATGGCGACCTACAAGGTCGCCG
1 GGACTACATGGCGACCTACAAGGTCGCCG
*
70024 GGACTACATGGCGACCTACAAGGTCGCCC
1 GGACTACATGGCGACCTACAAGGTCGCCG
* * *
70053 AGACTGCATGGTGACCT
1 GGACTACATGGCGACCT
70070 CTCGATTGGC
Statistics
Matches: 126, Mismatches: 5, Indels: 2
0.95 0.04 0.02
Matches are distributed among these distances:
27 17 0.13
29 109 0.87
ACGTcount: A:0.24, C:0.31, G:0.30, T:0.15
Consensus pattern (29 bp):
GGACTACATGGCGACCTACAAGGTCGCCG
Found at i:70190 original size:21 final size:21
Alignment explanation
Indices: 70164--70210 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
70154 TATATGCCTT
70164 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
70185 GTATGGCTCGTATGTCACCCC
1 GTATGGCTCGTATGTCACCCC
70206 GTATG
1 GTATG
70211 TCGCCTGGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.15, C:0.30, G:0.26, T:0.30
Consensus pattern (21 bp):
GTATGGCTCGTATGTCACCCC
Found at i:70253 original size:29 final size:29
Alignment explanation
Indices: 70211--70270 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
70201 ACCCCGTATG
70211 TCGCCTGGATTGCATGGCGTCCTACAAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
*
70240 TCGCCTGGATTGCATGGCGTCCTACGAGA
1 TCGCCTGGATTGCATGGCGTCCTACAAGA
70269 TC
1 TC
70271 ACTGTAGAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.18, C:0.28, G:0.28, T:0.25
Consensus pattern (29 bp):
TCGCCTGGATTGCATGGCGTCCTACAAGA
Found at i:71893 original size:19 final size:18
Alignment explanation
Indices: 71822--71893 Score: 56
Period size: 19 Copynumber: 3.8 Consensus size: 18
71812 GAAAAACACT
71822 AAAATAACTTAAATTATTA
1 AAAATAA-TTAAATTATTA
**
71841 AAAATTAGATATTCA-TATTA
1 AAAA-TA-AT-TAAATTATTA
*
71861 AAAATAATAAAATTATTA
1 AAAATAATTAAATTATTA
*
71879 TAAAATAATTTAATT
1 -AAAATAATTAAATT
71894 TTTTTAATAT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
17 1 0.02
18 7 0.17
19 18 0.44
20 12 0.29
21 3 0.07
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (18 bp):
AAAATAATTAAATTATTA
Found at i:72481 original size:16 final size:15
Alignment explanation
Indices: 72417--72484 Score: 59
Period size: 15 Copynumber: 4.5 Consensus size: 15
72407 TTTTAATATG
*
72417 AATATTTAATTTTTT
1 AATATTTTATTTTTT
* * *
72432 AATAATTTAATTATT
1 AATATTTTATTTTTT
72447 -AT-TTTTAGTATTTTT
1 AATATTTTA-T-TTTTT
72462 AATATTTTATTTTTT
1 AATATTTTATTTTTT
72477 GAATATTT
1 -AATATTT
72485 GAATAAATTT
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
13 4 0.10
14 2 0.05
15 20 0.49
16 10 0.24
17 5 0.12
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (15 bp):
AATATTTTATTTTTT
Found at i:76026 original size:32 final size:33
Alignment explanation
Indices: 75990--76051 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
75980 ATGAATTTCT
75990 AAAAATTCT-AGAGGCCAAATTA-AATTTTTTGA
1 AAAAATT-TAAGAGGCCAAATTATAATTTTTTGA
* *
76022 AAAAATTTAAGAGTCTAAATTATAATTTTT
1 AAAAATTTAAGAGGCCAAATTATAATTTTT
76052 AAAATTTTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 1 0.04
32 18 0.69
33 7 0.27
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (33 bp):
AAAAATTTAAGAGGCCAAATTATAATTTTTTGA
Found at i:78818 original size:68 final size:68
Alignment explanation
Indices: 78709--78961 Score: 364
Period size: 68 Copynumber: 3.7 Consensus size: 68
78699 AGAATAAAGG
* * * *
78709 CCTAACTGCGCATATGACAGAAAGGTGTCATTTATACCAGTTAGATGAATGGCTAAGTTCCTTTG
1 CCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTACCTTTG
*
78774 AGT
66 AGA
* * *
78777 CCTAATTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAAGCTAAGTGCCTTTG
1 CCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTACCTTTG
78842 AGA
66 AGA
78845 CCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTACCTTTG
1 CCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTACCTTTG
*
78910 AGG
66 AGA
* * * * *
78913 CCTAACTGTGCA-ATTGGCAGAAATGTGTCAATTATGTCAATTAGATGAA
1 CCTAACTGTGCATA-TGACAGAAAGGTGTCATTTATGCCAGTTAGATGAA
78962 CATTAAGTAC
Statistics
Matches: 168, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
67 1 0.01
68 167 0.99
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.30
Consensus pattern (68 bp):
CCTAACTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTACCTTTG
AGA
Found at i:79080 original size:81 final size:81
Alignment explanation
Indices: 78911--79150 Score: 335
Period size: 81 Copynumber: 3.0 Consensus size: 81
78901 GTACCTTTGA
* * * *
78911 GGCCTAACTGTGCAATTGGCAGAAATGTGTCAATTATGTCAATTAGATGAAC-ATTAAGTACCAT
1 GGCCTAATTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACCAT
78975 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* *
78991 GGCCTAATTGTGCAATTGGCAGAAAGGTGCCAATTATGCCAGTTAGATGAACGATTAAGTACCTT
1 GGCCTAATTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACCAT
79056 TGAGTAAAAGAATAAT
66 TGAGTAAAAGAATAAT
* * * *
79072 GGTCTAATTGTTCAATTGGCAGAAAGGTGTCAATTATACCAGTTAGACGAACG-TTAA--ACACA
1 GGCCTAATTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAGTAC-CA
*
79134 GTTGAGTAAGAGAATAA
65 -TTGAGTAAAAGAATAA
79151 AATTATAATG
Statistics
Matches: 144, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
78 2 0.01
79 1 0.01
80 66 0.46
81 75 0.52
ACGTcount: A:0.38, C:0.13, G:0.22, T:0.28
Consensus pattern (81 bp):
GGCCTAATTGTGCAATTGGCAGAAAGGTGTCAATTATGCCAGTTAGATGAACGATTAAGTACCAT
TGAGTAAAAGAATAAT
Found at i:79210 original size:2 final size:2
Alignment explanation
Indices: 79203--79234 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
79193 AAAGGATAAG
79203 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
79235 GTAACGTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82934 original size:21 final size:21
Alignment explanation
Indices: 82910--82958 Score: 98
Period size: 21 Copynumber: 2.3 Consensus size: 21
82900 GGGGTATCTG
82910 TACCCTATAGAACAGTATCGA
1 TACCCTATAGAACAGTATCGA
82931 TACCCTATAGAACAGTATCGA
1 TACCCTATAGAACAGTATCGA
82952 TACCCTA
1 TACCCTA
82959 GGCAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.24
Consensus pattern (21 bp):
TACCCTATAGAACAGTATCGA
Found at i:83149 original size:95 final size:94
Alignment explanation
Indices: 83028--83250 Score: 236
Period size: 95 Copynumber: 2.3 Consensus size: 94
83018 CCAGCAATGT
* * * * *
83028 GTATCGATACCATGGTAAGGGTATCGATACCAGTAAACATCGAATCTAATTGGGGTATCGATACC
1 GTATCGATACCATGATGAGGGTATCGATACCAGGAAACATCGAAGCTAATTGGGGTATCGATACA
* *
83093 T-AGAGGGGGTATCGGTGCCATAACATAGGG-
66 TGA-AGGGGGTATCGATACCAT-A-ATAGGGA
** * **
83123 GTATCGATACCATGATGAGGGTATCGATACCAGGCTACATTGAAGCTAATTTTGGTATCGATACA
1 GTATCGATACCATGATGAGGGTATCGATACCAGGAAACATCGAAGCTAATTGGGGTATCGATACA
* *
83188 TGAAGGGGGTATTGATACCCTAATAGGGTA
66 TGAAGGGGGTATCGATACCATAATAGGG-A
*
83218 GTATCGATACCATTA-GTAGGGGTATCGATACCA
1 GTATCGATACCATGATG-A-GGGTATCGATACCA
83251 AAACGCCAAA
Statistics
Matches: 108, Mismatches: 15, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
93 6 0.06
94 2 0.02
95 85 0.79
96 15 0.14
ACGTcount: A:0.30, C:0.16, G:0.27, T:0.26
Consensus pattern (94 bp):
GTATCGATACCATGATGAGGGTATCGATACCAGGAAACATCGAAGCTAATTGGGGTATCGATACA
TGAAGGGGGTATCGATACCATAATAGGGA
Found at i:83226 original size:22 final size:21
Alignment explanation
Indices: 83193--83250 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 21
83183 ATACATGAAG
*
83193 GGGGTATTGATACC-CTAATA
1 GGGGTATCGATACCACTAATA
* *
83213 GGGTAGTATCGATACCATTAGTA
1 GGG--GTATCGATACCACTAATA
83236 GGGGTATCGATACCA
1 GGGGTATCGATACCA
83251 AAACGCCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 3 0.09
21 12 0.38
22 10 0.31
23 7 0.22
ACGTcount: A:0.29, C:0.16, G:0.28, T:0.28
Consensus pattern (21 bp):
GGGGTATCGATACCACTAATA
Found at i:83657 original size:59 final size:58
Alignment explanation
Indices: 83561--83733 Score: 262
Period size: 58 Copynumber: 3.0 Consensus size: 58
83551 ATTACAAAAT
** *
83561 GGCACTTCGTGTGAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCAGTAT-A
1 GGCACTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCAGTATCA
83618 GGTCACTTCGTGTGCTAACATGATAAGAAATTCATACTAAGTGTATGAATTTCTA-TATCA
1 GG-CACTTCGTGTGCTAA-ATGATAAGAAATTCATACTAAGTGTATGAATTTC-AGTATCA
83678 GGCACCTT-GTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCAGTAT
1 GGCA-CTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCAGTAT
83734 GGAAAATATG
Statistics
Matches: 107, Mismatches: 3, Indels: 11
0.88 0.02 0.09
Matches are distributed among these distances:
57 3 0.03
58 50 0.47
59 47 0.44
60 7 0.07
ACGTcount: A:0.35, C:0.13, G:0.18, T:0.34
Consensus pattern (58 bp):
GGCACTTCGTGTGCTAAATGATAAGAAATTCATACTAAGTGTATGAATTTCAGTATCA
Found at i:84161 original size:68 final size:67
Alignment explanation
Indices: 84082--84276 Score: 322
Period size: 68 Copynumber: 2.9 Consensus size: 67
84072 AAAAGAATAA
84082 AGGCCTAATTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 AGGCCTAATTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCC-
84147 TTG
65 TTG
* *
84150 AGGCCTAATTGTGCATATGACAGAAAGGTGTCATTTATGCTAGTTTGATGAAAGGCTAAGTGCCT
1 AGGCCTAATTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
84215 TG
66 TG
* * *
84217 AGACCTAACTGTGCATATGAC--AAAGGTGTCATTTATGCCAGTTAGATGAAAGCCTAAGTG
1 AGGCCTAATTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTG
84277 ATATAAGTAG
Statistics
Matches: 120, Mismatches: 7, Indels: 3
0.92 0.05 0.02
Matches are distributed among these distances:
65 36 0.30
67 22 0.18
68 62 0.52
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.29
Consensus pattern (67 bp):
AGGCCTAATTGTGCATATGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TG
Found at i:86403 original size:29 final size:29
Alignment explanation
Indices: 86338--86410 Score: 80
Period size: 29 Copynumber: 2.5 Consensus size: 29
86328 GTGACCAAAA
86338 TGTAATTTTTG-AAAGTTTAGTGGCTAATG
1 TGTAA-TTTTGAAAAGTTTAGTGGCTAATG
*
86367 TATAAATTTTGAAAAGTTTAG-GGACTAAAT-
1 TGT-AATTTTGAAAAGTTTAGTGG-CT-AATG
86397 TGTAATTTTGAAAA
1 TGTAATTTTGAAAA
86411 ATTATGCATT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
29 20 0.53
30 15 0.39
31 3 0.08
ACGTcount: A:0.37, C:0.03, G:0.19, T:0.41
Consensus pattern (29 bp):
TGTAATTTTGAAAAGTTTAGTGGCTAATG
Found at i:88888 original size:168 final size:168
Alignment explanation
Indices: 88611--88946 Score: 640
Period size: 168 Copynumber: 2.0 Consensus size: 168
88601 TGTTTTGTCT
88611 TGTTTCTACTAACTTGATTCCTTTGTCTTATCTTGGCTTTGTTGTATTTTTGTATGAACATGACA
1 TGTTTCTACTAACTTGATTCCTTTGTCTTATCTTGGCTTTGTTGTATTTTTGTATGAACATGACA
88676 TATCCTTCAAAGGTATTGATCCCTGGAATAACTGATCTTTAGAAGGTTCTTGAAAAC-ATGCCCA
66 TATCCTTCAAAGGTATTGATCCCTGGAATAACTGATCTTTAGAAGGTTCTTGAAAACAATGCCCA
88740 CAACAATGCCTTTCATTAGGTTAGATAGAATTTTGAAG
131 CAACAATGCCTTTCATTAGGTTAGATAGAATTTTGAAG
88778 TGTTTCTACTAACTTGATTTCCTTTGTCTTATCTTGGCTTTGTTGTATTTTTGTATGAACATGAC
1 TGTTTCTACTAACTTGA-TTCCTTTGTCTTATCTTGGCTTTGTTGTATTTTTGTATGAACATGAC
88843 ATATCCTTCAAAGGTATTGAT-CCTGGAATAACTGATCTTTTAGAAGGTTCTTGAAAACAATGCC
65 ATATCCTTCAAAGGTATTGATCCCTGGAATAACTGATC-TTTAGAAGGTTCTTGAAAACAATGCC
88907 CACAACAATGCCTTTCATTAGGTTAGATAGAATTTTGAAG
129 CACAACAATGCCTTTCATTAGGTTAGATAGAATTTTGAAG
88947 ATTCTCTATA
Statistics
Matches: 166, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
167 33 0.20
168 88 0.53
169 45 0.27
ACGTcount: A:0.27, C:0.16, G:0.17, T:0.40
Consensus pattern (168 bp):
TGTTTCTACTAACTTGATTCCTTTGTCTTATCTTGGCTTTGTTGTATTTTTGTATGAACATGACA
TATCCTTCAAAGGTATTGATCCCTGGAATAACTGATCTTTAGAAGGTTCTTGAAAACAATGCCCA
CAACAATGCCTTTCATTAGGTTAGATAGAATTTTGAAG
Found at i:89347 original size:3 final size:3
Alignment explanation
Indices: 89341--89428 Score: 94
Period size: 3 Copynumber: 30.7 Consensus size: 3
89331 TTTTTATCCA
* * * * *
89341 TAT TAT TAT TAT TAA TAA TAA TAA TAA TAT TAT TAT TAT TAT TA- TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
89388 TAT TAT TAT TAT TA- TAT TAT CAT TA- TAT TAT TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
89429 ATATATTAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
2 8 0.10
3 69 0.90
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:89390 original size:11 final size:11
Alignment explanation
Indices: 89340--89436 Score: 81
Period size: 11 Copynumber: 8.5 Consensus size: 11
89330 TTTTTTATCC
89340 ATATTATTATT
1 ATATTATTATT
* * *
89351 AT-TAATAATA
1 ATATTATTATT
* *
89361 ATAATAATATT
1 ATATTATTATT
89372 ATTATTATTATT
1 A-TATTATTATT
89384 ATATTATTATT
1 ATATTATTATT
89395 ATTATTA-TATT
1 A-TATTATTATT
89406 ATCATTATATTATT
1 AT-A-T-TATTATT
*
89420 ATATTATTAAT
1 ATATTATTATT
89431 ATATTA
1 ATATTA
89437 AATACAATAA
Statistics
Matches: 68, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
10 8 0.12
11 35 0.51
12 16 0.24
13 3 0.04
14 6 0.09
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (11 bp):
ATATTATTATT
Found at i:91394 original size:66 final size:66
Alignment explanation
Indices: 91322--91454 Score: 266
Period size: 66 Copynumber: 2.0 Consensus size: 66
91312 TATTTTCAAA
91322 ATTATTTATTCACATCAATTTCCCCGCCAAATTTAATATTTCGTGCCCGGACGAAAACCGGTTAC
1 ATTATTTATTCACATCAATTTCCCCGCCAAATTTAATATTTCGTGCCCGGACGAAAACCGGTTAC
91387 G
66 G
91388 ATTATTTATTCACATCAATTTCCCCGCCAAATTTAATATTTCGTGCCCGGACGAAAACCGGTTAC
1 ATTATTTATTCACATCAATTTCCCCGCCAAATTTAATATTTCGTGCCCGGACGAAAACCGGTTAC
91453 G
66 G
91454 A
1 A
91455 CAGCTTGGCG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.32
Consensus pattern (66 bp):
ATTATTTATTCACATCAATTTCCCCGCCAAATTTAATATTTCGTGCCCGGACGAAAACCGGTTAC
G
Found at i:94988 original size:14 final size:15
Alignment explanation
Indices: 94959--94990 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
94949 GAATTATTTT
94959 ATTCATTAAGTTAAA
1 ATTCATTAAGTTAAA
94974 ATTCATTAA-TTAAA
1 ATTCATTAAGTTAAA
94988 ATT
1 ATT
94991 TGAAAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (15 bp):
ATTCATTAAGTTAAA
Found at i:102264 original size:9 final size:9
Alignment explanation
Indices: 102250--102314 Score: 58
Period size: 9 Copynumber: 7.1 Consensus size: 9
102240 ATGCTTGAAG
102250 AAAAAAGAA
1 AAAAAAGAA
102259 AAAAAAGAA
1 AAAAAAGAA
*
102268 AGAAAAGGAA
1 A-AAAAAGAA
**
102278 AAAATTGAA
1 AAAAAAGAA
* *
102287 AGAAAACAA
1 AAAAAAGAA
*
102296 AAAAGAGAA
1 AAAAAAGAA
*
102305 GAAAAAGAA
1 AAAAAAGAA
102314 A
1 A
102315 GGGGGTCAAG
Statistics
Matches: 42, Mismatches: 13, Indels: 2
0.74 0.23 0.04
Matches are distributed among these distances:
9 34 0.81
10 8 0.19
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAAAAGAA
Found at i:102278 original size:19 final size:19
Alignment explanation
Indices: 102251--102314 Score: 69
Period size: 18 Copynumber: 3.5 Consensus size: 19
102241 TGCTTGAAGA
102251 AAAAAGAAAAAAAAGAAAG
1 AAAAAGAAAAAAAAGAAAG
* **
102270 AAAAGGAAAAAATTGAAAG
1 AAAAAGAAAAAAAAGAAAG
* *
102289 -AAAACAAAAAAGAG-AAG
1 AAAAAGAAAAAAAAGAAAG
102306 AAAAAGAAA
1 AAAAAGAAA
102315 GGGGGTCAAG
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
17 3 0.08
18 17 0.47
19 16 0.44
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (19 bp):
AAAAAGAAAAAAAAGAAAG
Found at i:102279 original size:18 final size:18
Alignment explanation
Indices: 102252--102314 Score: 58
Period size: 17 Copynumber: 3.5 Consensus size: 18
102242 GCTTGAAGAA
*
102252 AAAAGAAAAAAAAGAAAG
1 AAAAGGAAAAAAAGAAAG
*
102270 AAAAGGAAAAAATTGAAAG
1 AAAAGGAAAAAA-AGAAAG
*
102289 AAAA--CAAAAAAGAGAAG
1 AAAAGGAAAAAAAGA-AAG
*
102306 AAAAAGAAA
1 AAAAGGAAA
102315 GGGGGTCAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
16 2 0.06
17 12 0.33
18 11 0.31
19 11 0.31
ACGTcount: A:0.78, C:0.02, G:0.17, T:0.03
Consensus pattern (18 bp):
AAAAGGAAAAAAAGAAAG
Found at i:103553 original size:84 final size:84
Alignment explanation
Indices: 103451--103764 Score: 495
Period size: 84 Copynumber: 3.7 Consensus size: 84
103441 CATTAACTGA
* *
103451 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTTGGCAG
1 AAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
* *
103516 AACCAATCGTTGAATTTGG
66 AACCAATCATTGAATTTAG
* *
103535 AAGATGAATTTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACG
1 AAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CA
103599 GAACCAATCATTGAATTTAG
65 GAACCAATCATTGAATTTAG
* * * *
103619 AAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAATTATCTGATTTGGTTTGGTAA
1 AAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
103684 AACCAATCATTGAATTTAG
66 AACCAATCATTGAATTTAG
* * *
103703 AAGATAAATGTGCTCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATTTGATCTGGTTTGG
1 AAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
103765 TAAAAATTAC
Statistics
Matches: 213, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
83 4 0.02
84 205 0.96
85 4 0.02
ACGTcount: A:0.27, C:0.13, G:0.22, T:0.38
Consensus pattern (84 bp):
AAGATGAATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAG
AACCAATCATTGAATTTAG
Found at i:104646 original size:113 final size:113
Alignment explanation
Indices: 104381--104920 Score: 834
Period size: 113 Copynumber: 4.8 Consensus size: 113
104371 TTCCAGTTCG
104381 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
104446 AACCTTTTTG-CTTAAATCTATCACTTGATGGATTATCTTTTCCAGAGAA
66 AACC-TTTTGCCTGAATTC-ATCACTTGATGGATTATCTTTTCCAGAGAA
*
104495 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
** *
104560 AACCTTTTGTTTGAATTCATCACTTGATGGATTAACTTTTCCAGAGAA
66 AACCTTTTGCCTGAATTCATCACTTGATGGATTATCTTTTCCAGAGAA
*
104608 GGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* * * * * * *
104673 AACCTTTTACCTGAGTCCATCATTTGATGGATCAGCCTTTCCAGAGAA
66 AACCTTTTGCCTGAATTCATCACTTGATGGATTATCTTTTCCAGAGAA
104721 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
104786 AACCTTTTACCTGAATTCATCAATTGATGGATTATCTTTTCCAGAG-A
66 AACCTTTTGCCTGAATTCATCACTTGATGGATTATCTTTTCCAGAGAA
* * * *
104833 AGTTCATAATAAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
* *
104898 AACTTTTTGCAT-AATTCTATCAC
66 AACCTTTTGCCTGAATTC-ATCAC
104921 AGAAGGAGAT
Statistics
Matches: 393, Mismatches: 31, Indels: 6
0.91 0.07 0.01
Matches are distributed among these distances:
111 5 0.01
112 75 0.19
113 240 0.61
114 73 0.19
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
AACCTTTTGCCTGAATTCATCACTTGATGGATTATCTTTTCCAGAGAA
Found at i:105230 original size:3 final size:3
Alignment explanation
Indices: 105224--105318 Score: 172
Period size: 3 Copynumber: 31.7 Consensus size: 3
105214 TTTTTATCCA
*
105224 TAT TAT TAT TAT TAA 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
*
105272 TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
105319 AATATATTAA
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 88 1.00
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:108977 original size:14 final size:14
Alignment explanation
Indices: 108958--108987 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
108948 TCGCGTAGAT
108958 GATCTTAGTGCGGA
1 GATCTTAGTGCGGA
*
108972 GATCTTAGTGTGGA
1 GATCTTAGTGCGGA
108986 GA
1 GA
108988 CCCAAGTGTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.10, G:0.37, T:0.30
Consensus pattern (14 bp):
GATCTTAGTGCGGA
Found at i:110971 original size:21 final size:21
Alignment explanation
Indices: 110947--111001 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
110937 TCTGGCAGGG
110947 AGTATCGATATTGAAGGAAGT
1 AGTATCGATATTGAAGGAAGT
* * * **
110968 AGTATTGATACTGAGGGTTGT
1 AGTATCGATATTGAAGGAAGT
110989 AGTATCGATATTG
1 AGTATCGATATTG
111002 GATCCTCAGT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.31, C:0.05, G:0.29, T:0.35
Consensus pattern (21 bp):
AGTATCGATATTGAAGGAAGT
Found at i:111062 original size:20 final size:20
Alignment explanation
Indices: 111037--111095 Score: 82
Period size: 20 Copynumber: 3.0 Consensus size: 20
111027 TCTCCAAATC
111037 GAAGGACTGGTCTCTATACT
1 GAAGGACTGGTCTCTATACT
* * *
111057 GTAGGACTGATCTCCATACT
1 GAAGGACTGGTCTCTATACT
*
111077 GAAAGACTGGTCTCTATAC
1 GAAGGACTGGTCTCTATAC
111096 CAAATGACTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (20 bp):
GAAGGACTGGTCTCTATACT
Found at i:118851 original size:25 final size:26
Alignment explanation
Indices: 118813--118861 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
118803 TTCTAAGGTA
*
118813 TATTTTATTATATTTTTAA-TATTTTG
1 TATTTAATTATA-TTTTAAGTATTTTG
118839 TATTTAATT-TATTTTAAGTATTT
1 TATTTAATTATATTTTAAGTATTT
118862 AATTTATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 7 0.33
26 8 0.38
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (26 bp):
TATTTAATTATATTTTAAGTATTTTG
Found at i:118876 original size:25 final size:26
Alignment explanation
Indices: 118839--118891 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 26
118829 TAATATTTTG
118839 TATTTAATTTATTTTAAGTATTTAATT
1 TATTTAA-TTATTTTAAGTATTTAATT
**
118866 TATTTAA-TATTTTACTTATTTAATT
1 TATTTAATTATTTTAAGTATTTAATT
118891 T
1 T
118892 TTTTTCATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 17 0.71
27 7 0.29
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (26 bp):
TATTTAATTATTTTAAGTATTTAATT
Found at i:118884 original size:16 final size:16
Alignment explanation
Indices: 118851--118893 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
118841 TTTAATTTAT
* *
118851 TTTAAGTATTTAATTTA
1 TTTAA-TATTTTACTTA
118868 TTTAATATTTTACTTA
1 TTTAATATTTTACTTA
118884 TTTAAT-TTTT
1 TTTAATATTTT
118894 TTTCATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 4 0.17
16 15 0.62
17 5 0.21
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TTTAATATTTTACTTA
Found at i:124377 original size:24 final size:24
Alignment explanation
Indices: 124346--124395 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
124336 AAGTCGCGTC
124346 ATTATTTGAGTTTAAACAAATAAT
1 ATTATTTGAGTTTAAACAAATAAT
** *
124370 ATTATTTGTTTTTAAATAAATAAT
1 ATTATTTGAGTTTAAACAAATAAT
124394 AT
1 AT
124396 ATGAACAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (24 bp):
ATTATTTGAGTTTAAACAAATAAT
Found at i:126430 original size:15 final size:13
Alignment explanation
Indices: 126392--126437 Score: 56
Period size: 15 Copynumber: 3.3 Consensus size: 13
126382 AAATACCGAG
*
126392 AAAATCAAATTTT
1 AAAATAAAATTTT
126405 AAAAGTAAAATTATT
1 AAAA-TAAAATT-TT
126420 AGAAATAAAATTTT
1 A-AAATAAAATTTT
126434 AAAA
1 AAAA
126438 AATACGATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
13 7 0.24
14 9 0.31
15 10 0.34
16 3 0.10
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (13 bp):
AAAATAAAATTTT
Found at i:126441 original size:15 final size:14
Alignment explanation
Indices: 126392--126438 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
126382 AAATACCGAG
*
126392 AAAATCAAATTTTA
1 AAAATAAAATTTTA
*
126406 AAAGTAAAATTATTA
1 AAAATAAAATT-TTA
*
126421 GAAATAAAATTTTA
1 AAAATAAAATTTTA
126435 AAAA
1 AAAA
126439 ATACGATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 15 0.56
15 12 0.44
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (14 bp):
AAAATAAAATTTTA
Found at i:137331 original size:68 final size:68
Alignment explanation
Indices: 137222--137355 Score: 232
Period size: 68 Copynumber: 2.0 Consensus size: 68
137212 TGATTAACGG
* *
137222 TGATCACGAATGGTTCGAATCGTAAGCCTCCACGAAAACACGTCTCAGCCTCTACTCAGTTCACC
1 TGATCACGAATGGTTCGAATCGTAAGCCTCCACGAAAACACGTCTCAACCTCTACTCAGATCACC
137287 CAA
66 CAA
* *
137290 TGATCACGAATGGTTTGAATCGTAAGCCTCCTCGAAAACACGTCTCAACCTCTACTCAGATCACC
1 TGATCACGAATGGTTCGAATCGTAAGCCTCCACGAAAACACGTCTCAACCTCTACTCAGATCACC
137355 C
66 C
137356 GATTGAGAGA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 62 1.00
ACGTcount: A:0.29, C:0.32, G:0.16, T:0.23
Consensus pattern (68 bp):
TGATCACGAATGGTTCGAATCGTAAGCCTCCACGAAAACACGTCTCAACCTCTACTCAGATCACC
CAA
Found at i:143478 original size:43 final size:42
Alignment explanation
Indices: 143412--143508 Score: 124
Period size: 43 Copynumber: 2.2 Consensus size: 42
143402 AATGTCACAT
**
143412 AATTGAAAAAATTAGGGACCTTAATTATAAAAG-TAAAAAAGTGG
1 AATTG-AAAAATTAAAGACCTTAATTATAAAAGAT-AAAAAGT-G
*
143456 AATTGAAAAATTAAAGATCTTAATTATAAAAGATAAAAAGTG
1 AATTGAAAAATTAAAGACCTTAATTATAAAAGATAAAAAGTG
143498 ATATTGAAAAA
1 A-ATTGAAAAA
143509 AATTAAGGGT
Statistics
Matches: 48, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
42 2 0.04
43 40 0.83
44 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.14, T:0.27
Consensus pattern (42 bp):
AATTGAAAAATTAAAGACCTTAATTATAAAAGATAAAAAGTG
Done.