Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002824.1 Hibiscus syriacus cultivar Beakdansim tig00005807_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: 94471
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:1217 original size:19 final size:20
Alignment explanation
Indices: 1193--1233 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
1183 TAAAGATCAA
*
1193 ACTTTCACTT-GGTATCGAT
1 ACTTTCACTTAAGTATCGAT
1212 ACTTTCACTTAAGTATCGAT
1 ACTTTCACTTAAGTATCGAT
1232 AC
1 AC
1234 CCTACATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.27, C:0.22, G:0.12, T:0.39
Consensus pattern (20 bp):
ACTTTCACTTAAGTATCGAT
Found at i:3729 original size:4 final size:4
Alignment explanation
Indices: 3720--3746 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3710 CAATGCATGT
3720 ATAA ATAA ATAA ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA
3747 CATAGTTGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAA
Found at i:7946 original size:14 final size:15
Alignment explanation
Indices: 7927--7956 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
7917 ATAGATGGAG
7927 AGAAAT-AAAATAAA
1 AGAAATAAAAATAAA
7941 AGAAATAAAAATAAA
1 AGAAATAAAAATAAA
7956 A
1 A
7957 AGATTTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (15 bp):
AGAAATAAAAATAAA
Found at i:8664 original size:18 final size:18
Alignment explanation
Indices: 8638--8672 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
8628 AAAATCCTAA
*
8638 AAGATAATTCCTAAAAAC
1 AAGAGAATTCCTAAAAAC
8656 AAGAGAATTCCTAAAAA
1 AAGAGAATTCCTAAAAA
8673 TAATTCTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.57, C:0.14, G:0.09, T:0.20
Consensus pattern (18 bp):
AAGAGAATTCCTAAAAAC
Found at i:9312 original size:22 final size:23
Alignment explanation
Indices: 9278--9358 Score: 60
Period size: 23 Copynumber: 3.5 Consensus size: 23
9268 ATTTATTTAT
*
9278 TAATATTTATAATA-ATATAATA
1 TAATATTTATAATATATATAAAA
9300 TAATACTTT-TAATATTATATAAAA
1 TAATA-TTTATAATA-TATATAAAA
* * *
9324 TAATCAATTATATTATA-ATAATA
1 TAAT-ATTTATAATATATATAAAA
*
9347 TAAGATATTATA
1 TAATAT-TTATA
9359 TTTTTATTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
22 11 0.23
23 16 0.34
24 15 0.32
25 5 0.11
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (23 bp):
TAATATTTATAATATATATAAAA
Found at i:9447 original size:13 final size:12
Alignment explanation
Indices: 9414--9477 Score: 55
Period size: 12 Copynumber: 5.4 Consensus size: 12
9404 AATATTATTT
9414 ATATATTTAGATA
1 ATATATTTA-ATA
9427 ATAT-TTTAATAA
1 ATATATTTAAT-A
9439 ATATATTTAA-A
1 ATATATTTAATA
*
9450 ATATA-CTAATTA
1 ATATATTTAA-TA
*
9462 ATATTTTTAA-A
1 ATATATTTAATA
9473 ATATA
1 ATATA
9478 ATATAACACT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 3 0.07
11 13 0.31
12 14 0.33
13 12 0.29
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (12 bp):
ATATATTTAATA
Found at i:9452 original size:23 final size:23
Alignment explanation
Indices: 9414--9477 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
9404 AATATTATTT
**
9414 ATATATTTAGATAATATTTTAATAA
1 ATATATTTA-A-AATATACTAATAA
*
9439 ATATATTTAAAATATACTAATTA
1 ATATATTTAAAATATACTAATAA
*
9462 ATATTTTTAAAATATA
1 ATATATTTAAAATATA
9478 ATATAACACT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 25 0.71
24 1 0.03
25 9 0.26
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATATTTAAAATATACTAATAA
Found at i:9773 original size:14 final size:15
Alignment explanation
Indices: 9754--9795 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
9744 TACAGAAATG
9754 TAATTCATTTTCC-A
1 TAATTCATTTTCCAA
**
9768 TAATTCAAATTCCAA
1 TAATTCATTTTCCAA
9783 TAATTCATTTTCC
1 TAATTCATTTTCC
9796 GAAAAACCAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.33, C:0.21, G:0.00, T:0.45
Consensus pattern (15 bp):
TAATTCATTTTCCAA
Found at i:10493 original size:25 final size:25
Alignment explanation
Indices: 10465--10521 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
10455 TCTTTTCACT
10465 GGAACAATCCACGAACAATCAATTA
1 GGAACAATCCACGAACAATCAATTA
10490 GGAACAATCCACGAACAATCAATTA
1 GGAACAATCCACGAACAATCAATTA
10515 GGAACAA
1 GGAACAA
10522 AGGGCCATTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.49, C:0.23, G:0.14, T:0.14
Consensus pattern (25 bp):
GGAACAATCCACGAACAATCAATTA
Found at i:10496 original size:14 final size:14
Alignment explanation
Indices: 10477--10521 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
10467 AACAATCCAC
10477 GAACAATCAATTAG
1 GAACAATCAATTAG
* *
10491 GAACAATC---CAC
1 GAACAATCAATTAG
10502 GAACAATCAATTAG
1 GAACAATCAATTAG
10516 GAACAA
1 GAACAA
10522 AGGGCCATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
11 9 0.38
14 15 0.62
ACGTcount: A:0.51, C:0.20, G:0.13, T:0.16
Consensus pattern (14 bp):
GAACAATCAATTAG
Found at i:12898 original size:31 final size:31
Alignment explanation
Indices: 12860--12924 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
12850 ACAATTGAGA
* * *
12860 GACTAAAATCGAATAAATCGATAATGTTATG
1 GACTAAAATCGAACAAATCGATAATATTAGG
* *
12891 GACTAAAATTGAACAGATCGATAATATTAGG
1 GACTAAAATCGAACAAATCGATAATATTAGG
12922 GAC
1 GAC
12925 CATTCTCCCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (31 bp):
GACTAAAATCGAACAAATCGATAATATTAGG
Found at i:14605 original size:15 final size:15
Alignment explanation
Indices: 14585--14619 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
14575 TTTTTCTTTC
14585 ATTTTATTTGTTATT
1 ATTTTATTTGTTATT
14600 ATTTTATTTGTTATT
1 ATTTTATTTGTTATT
*
14615 GTTTT
1 ATTTT
14620 TTTATTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (15 bp):
ATTTTATTTGTTATT
Found at i:16030 original size:17 final size:16
Alignment explanation
Indices: 15992--16030 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
15982 CTTACTAACC
15992 TTTTTCCTTTAATTTT
1 TTTTTCCTTTAATTTT
*
16008 TATTTTCTTTTAATTTGT
1 T-TTTTCCTTTAATTT-T
16026 TTTTT
1 TTTTT
16031 TAATCATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 17 0.85
18 2 0.10
ACGTcount: A:0.13, C:0.08, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTTCCTTTAATTTT
Found at i:17633 original size:95 final size:96
Alignment explanation
Indices: 17514--17774 Score: 366
Period size: 95 Copynumber: 2.7 Consensus size: 96
17504 ATTATAATTA
*
17514 TATATATATCTACAATAAAGCTTGATTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
1 TATA-ATA-CTACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
*
17579 TGGATAAGATTTAGCTAGCCTGATAAAGGTGAT
64 TGGATAAGATTCAGCTAGCCTGATAAAGGTGAT
* * * *
17612 TATAATA-TACAATAAAGCTTGAGTTATCCCTCTAGAGCAATTGGTTAAACGTCCCTGCTTAATG
1 TATAATACTACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
* *
17676 GATAATATTCAGCTAGTCTGATAAAGGTGAT
66 GATAAGATTCAGCTAGCCTGATAAAGGTGAT
* * *
17707 TATAATATCTACAACGATA--TTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGACTTTA
1 TATAATA-CTACAA-TAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTA
17770 TGGAT
64 TGGAT
17775 TCAGCTAGCC
Statistics
Matches: 145, Mismatches: 15, Indels: 8
0.86 0.09 0.05
Matches are distributed among these distances:
95 87 0.60
96 44 0.30
97 8 0.06
98 6 0.04
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Consensus pattern (96 bp):
TATAATACTACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
GATAAGATTCAGCTAGCCTGATAAAGGTGAT
Found at i:19181 original size:84 final size:84
Alignment explanation
Indices: 18901--20289 Score: 1467
Period size: 84 Copynumber: 16.5 Consensus size: 84
18891 GAAACTATTG
*
18901 GCAGCATAACTCAAGGCTAGAAGGATTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
18966 GCTCAAAGGCACAAT-ATTT
66 GCTCAAAGGCAC-ATCATTT
* * * * * *
18985 GCAGCATAGCTCAAGGCGAGAAGGGCTATCTGCCAATAAAAGACCTTCGAGTTTCGACTACGCTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAG-TTCGATTACACTC
* *
19050 AGCTCCAAGGCATATCATTT
65 AGCTCAAAGGCACATCATTT
* * * * *
19070 GCAACATAACTCAAGGGTAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGACTACACTAA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* *
19135 ACTCCAAGGCACATCATTT
66 GCTCAAAGGCACATCATTT
* * * * * * * ** *
19154 ACAACATAGCTCAAGGCAAGAATGGTTATTTGCCAACAAAAGACCTTCGAGTTTGGCTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
19219 GCTCAAAGGCATATCATTT
66 GCTCAAAGGCACATCATTT
* * * * * * * *
19238 GTAGCATAAATCAAGGCTAGAAGGGTTATCTTCCAACCAAAGACCTTCGAGTTCAACTACTCTTA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
19303 GCTCCCAA-GCACATCATTT
66 GCT-CAAAGGCACATCATTT
** * * * * * * * *
19322 GCAATATAGCTCAAGGCAATAAGGGATATTTGGCAACAAAAGACCTTCGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
19387 GCTCCAAGGCACATCATTT
66 GCTCAAAGGCACATCATTT
** ** *
19406 GCAGTGTAACTCAAGGCTAGAAGGGTTATAAGCCAATAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* *
19471 GCTTAAAGGCACAACATTT
66 GCTCAAAGGCACATCATTT
* * * * * * *
19490 ACAGCATAACTCAAGGCGATAAGGGCTATATGCCAACAAAATACCTTCGAGTTCGATTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* *
19555 ACTCCAAGGCACATCATTT
66 GCTCAAAGGCACATCATTT
* * * * * * * * * * *
19574 GCAACATAGCTCAAGGCAATAAGGGCTATTTGTCAACAAAATACCTTTGAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* *
19639 GCTCAAAAGCATATCATTT
66 GCTCAAAGGCACATCATTT
* * * * * * *
19658 GTAGCATAACTTAAGGCTAGAAGGGTTATCTGCCAACCAAATACCTTCAAGTTCGACTACGCTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
**
19723 GCTCAAAGATACATCATTT
66 GCTCAAAGGCACATCATTT
* * * * * * * * * *
19742 ACAACATGACTCAAAGCAAGAAGGGCTATTTGCCAACGAAAGACCTTTGAGTTCCGATTACGCTC
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTT-CGATTACACTC
* *
19807 GGCTCCAAGGCACATCATTT
65 AGCTCAAAGGCACATCATTT
* ** *
19827 GCAGTATAACTCAAGGCTAGAAGGGTTATCTGTTAACAAAAGTCCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
*
19892 GTTCAAAGGCACAAT-ATTT
66 GCTCAAAGGCAC-ATCATTT
* * * *
19911 ACAGCATAGCTCAAGGCGAGAAGGGTTATCTGCCAATAAAAGACCTTCGAGTTCGATTACACTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
19976 GCTCAAAGGCACATCATTT
66 GCTCAAAGGCACATCATTT
* * * *
19995 ACAGCATAACTCAAGGCTAGAAGGGTTATCTGACAAC-AAAGACCTTCGAGTTTGATTACATTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
20059 GCTCAAAGGCACATCATTT
66 GCTCAAAGGCACATCATTT
* * *
20078 GCAGCATAGCTCAAGG-TGAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCAATTACATTC
1 GCAGCATAACTCAAGGCT-AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTC
*
20142 AGCTCAAAGGCATATCCAATTT
65 AGCTCAAAGGCACAT-C-ATTT
* * * * * * * *
20164 ACAACATAACTCAAGGCGAGAAGGGTTATCTGTC-ATAAAATACCTTCGAGTTCGATTTCATTCA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
* * * *
20228 ACTCAGAGGCAAATAAAATTT
66 GCTCAAAGGCACAT--CATTT
* * ** *
20249 ACAGCATAACTCAAAGAAAGAAGGGCTATCTGCCAACAAAA
1 GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAA
20290 ATTATCGAGT
Statistics
Matches: 1093, Mismatches: 198, Indels: 26
0.83 0.15 0.02
Matches are distributed among these distances:
82 1 0.00
83 82 0.08
84 760 0.70
85 213 0.19
86 37 0.03
ACGTcount: A:0.34, C:0.23, G:0.19, T:0.24
Consensus pattern (84 bp):
GCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGATTACACTCA
GCTCAAAGGCACATCATTT
Found at i:20857 original size:16 final size:16
Alignment explanation
Indices: 20828--20865 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
20818 ATACTATAGT
*
20828 TATA-ATTATATAATG
1 TATATATTATATAATA
*
20843 TATATATTATCTAATA
1 TATATATTATATAATA
20859 TATATAT
1 TATATAT
20866 ATTATCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (16 bp):
TATATATTATATAATA
Found at i:22118 original size:15 final size:15
Alignment explanation
Indices: 22094--22128 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
22084 TTTTTCTTTC
22094 ATTTTATTTGTTATT
1 ATTTTATTTGTTATT
*
22109 ATTTTCTTTGTTATT
1 ATTTTATTTGTTATT
*
22124 GTTTT
1 ATTTT
22129 TTTTATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.03, G:0.09, T:0.74
Consensus pattern (15 bp):
ATTTTATTTGTTATT
Found at i:22429 original size:14 final size:15
Alignment explanation
Indices: 22405--22435 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
22395 TTGTTTTGTC
22405 TTATTATTTTTTACA
1 TTATTATTTTTTACA
22420 TTATTA-TTTTTACA
1 TTATTATTTTTTACA
22434 TT
1 TT
22436 TACACACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.06, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTATTTTTTACA
Found at i:22918 original size:4 final size:4
Alignment explanation
Indices: 22909--22933 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
22899 GACTCAAACT
22909 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
22934 CAAAAACTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:22977 original size:11 final size:11
Alignment explanation
Indices: 22961--23034 Score: 76
Period size: 11 Copynumber: 6.7 Consensus size: 11
22951 CTCGAAACTA
*
22961 AAGCTCGATTC
1 AAGCTCGATAC
22972 AAGCTCGATAC
1 AAGCTCGATAC
* * *
22983 AAACTCAATAA
1 AAGCTCGATAC
* *
22994 AAACTCGTTAC
1 AAGCTCGATAC
23005 AAGCTCGATAC
1 AAGCTCGATAC
* *
23016 AAGCTCAATTC
1 AAGCTCGATAC
23027 AAGCTCGA
1 AAGCTCGA
23035 CGGATTAATA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
11 51 1.00
ACGTcount: A:0.39, C:0.26, G:0.14, T:0.22
Consensus pattern (11 bp):
AAGCTCGATAC
Found at i:25391 original size:21 final size:20
Alignment explanation
Indices: 25363--25427 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 20
25353 AAAACCCTAG
*
25363 ACCCTAAATACTAAACCATAA
1 ACCCTAAA-ACTAAATCATAA
* *
25384 ACCTTAAACCTTAAATCATAA
1 ACCCTAAAAC-TAAATCATAA
25405 ACCCTAAACACTAAATCATAA
1 ACCCTAAA-ACTAAATCATAA
25426 AC
1 AC
25428 ACTATCACAT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 35 0.95
22 1 0.03
ACGTcount: A:0.51, C:0.28, G:0.00, T:0.22
Consensus pattern (20 bp):
ACCCTAAAACTAAATCATAA
Found at i:25528 original size:14 final size:14
Alignment explanation
Indices: 25509--25538 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
25499 TATAATTATC
*
25509 AATAATGTATTTTT
1 AATAATGTAATTTT
25523 AATAATGTAATTTT
1 AATAATGTAATTTT
25537 AA
1 AA
25539 AAAATCTAAA
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:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (14 bp):
AATAATGTAATTTT
Found at i:28300 original size:28 final size:28
Alignment explanation
Indices: 28260--28315 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
28250 ATATACTAAG
28260 GTAAAATTATTCATAAGCCCAAAAGAAT
1 GTAAAATTATTCATAAGCCCAAAAGAAT
28288 GTAAAATTATTCATAAGCCCAAAAGAAT
1 GTAAAATTATTCATAAGCCCAAAAGAAT
28316 AAACCTAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (28 bp):
GTAAAATTATTCATAAGCCCAAAAGAAT
Found at i:34684 original size:145 final size:146
Alignment explanation
Indices: 34413--34702 Score: 564
Period size: 145 Copynumber: 2.0 Consensus size: 146
34403 AATGGCTCTG
34413 AGGCTGATTTTTTTAGGATATGCTTAAGCTTGTGTTATATTTATGAGTTCTTACCTGTTGAACAA
1 AGGCTGATTTTTTTAGGATATGCTTAAGCTTGTGTTATATTTATGAGTTCTTACCTGTTGAACAA
34478 AAAGATGAGCGTGATTCATCTCCCGAGTAAACTTATCTACAAAAATTCTTCCAAAGTCTGGCATT
66 AAAGATGAGCGTGATTCATCTCCCGAGTAAACTTATCTACAAAAATTCTTCCAAAGTCTGGCATT
*
34543 TAGACCTTTCTGTTTT
131 CAGACCTTTCTGTTTT
34559 AGGCTGA-TTTTTTAGGATATGCTTAAGCTTGTGTTATATTTATGAGTTCTTACCTGTTGAACAA
1 AGGCTGATTTTTTTAGGATATGCTTAAGCTTGTGTTATATTTATGAGTTCTTACCTGTTGAACAA
34623 AAAGATGAGCGTGATTCATCTCCCGAGTAAACTTATCTACAAAAATTCTTCCAAAGTCTGGCATT
66 AAAGATGAGCGTGATTCATCTCCCGAGTAAACTTATCTACAAAAATTCTTCCAAAGTCTGGCATT
34688 CAGACCTTTCTGTTT
131 CAGACCTTTCTGTTT
34703 AGCACAATGG
Statistics
Matches: 143, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
145 136 0.95
146 7 0.05
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (146 bp):
AGGCTGATTTTTTTAGGATATGCTTAAGCTTGTGTTATATTTATGAGTTCTTACCTGTTGAACAA
AAAGATGAGCGTGATTCATCTCCCGAGTAAACTTATCTACAAAAATTCTTCCAAAGTCTGGCATT
CAGACCTTTCTGTTTT
Found at i:43149 original size:39 final size:39
Alignment explanation
Indices: 43094--43169 Score: 116
Period size: 39 Copynumber: 1.9 Consensus size: 39
43084 CGAGGGACTC
* * *
43094 GATGTATTTAATATCTATTTGTTTGTAGAATATTACATA
1 GATGTATGTAAAATCTAATTGTTTGTAGAATATTACATA
*
43133 GATGTATGTAAAATCTAATTGTTTGTAGTATATTACA
1 GATGTATGTAAAATCTAATTGTTTGTAGAATATTACA
43170 AGAACAAAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 33 1.00
ACGTcount: A:0.34, C:0.05, G:0.14, T:0.46
Consensus pattern (39 bp):
GATGTATGTAAAATCTAATTGTTTGTAGAATATTACATA
Found at i:53093 original size:13 final size:13
Alignment explanation
Indices: 53075--53101 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
53065 GCACATACTC
53075 TTCCCTTTGATGG
1 TTCCCTTTGATGG
53088 TTCCCTTTGATGG
1 TTCCCTTTGATGG
53101 T
1 T
53102 AGCACGGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.22, G:0.22, T:0.48
Consensus pattern (13 bp):
TTCCCTTTGATGG
Found at i:55110 original size:2 final size:2
Alignment explanation
Indices: 55105--55146 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
55095 AAAAATGAAA
55105 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
55147 CAAAGTATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:55395 original size:16 final size:15
Alignment explanation
Indices: 55331--55392 Score: 56
Period size: 16 Copynumber: 4.0 Consensus size: 15
55321 AAAGTTTTTT
55331 TAAAAAA-AA-ATAA
1 TAAAAAATAATATAA
*
55344 TAATATAATAATAATGAA
1 TAA-AAAATAAT-AT-AA
*
55362 TAAAAAATGAAAATAA
1 TAAAAAAT-AATATAA
55378 TAAAAAATAATATAA
1 TAAAAAATAATATAA
55393 ATATATAAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
13 3 0.08
14 3 0.08
15 8 0.21
16 10 0.26
17 8 0.21
18 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (15 bp):
TAAAAAATAATATAA
Found at i:55676 original size:18 final size:17
Alignment explanation
Indices: 55655--55697 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
55645 ATATATACAT
55655 ATAATAATAATAACATGA
1 ATAATAATAATAA-ATGA
*
55673 ATAATAAAAATAAATGA
1 ATAATAATAATAAATGA
55690 ATAA-AATA
1 ATAATAATA
55698 TCCATATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.26
Consensus pattern (17 bp):
ATAATAATAATAAATGA
Found at i:55698 original size:60 final size:59
Alignment explanation
Indices: 55575--55698 Score: 144
Period size: 62 Copynumber: 2.0 Consensus size: 59
55565 TATTAAAGAA
* * * *
55575 ATATATATATATATATATATAATAATAAAATATAGTAAAAAATTAAATGAAAATAATTTAAT
1 ATATATATATATATACATATAATAATAAAACATAATAAAAAAATAAATG-AAATAA--TAAT
55637 ATATATATATATATACATATAATAATAATAACATGAATAATAAAAATAAATG-AATAA-AAT
1 ATATATATATATATACATATAATAATAA-AACAT-AATAA-AAAAATAAATGAAATAATAAT
55697 AT
1 AT
55699 CCATATAATA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
60 5 0.09
62 27 0.49
63 9 0.16
64 4 0.07
65 10 0.18
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (59 bp):
ATATATATATATATACATATAATAATAAAACATAATAAAAAAATAAATGAAATAATAAT
Found at i:56147 original size:36 final size:36
Alignment explanation
Indices: 56054--56156 Score: 116
Period size: 37 Copynumber: 2.8 Consensus size: 36
56044 GTGTTTGTAG
* *
56054 ATCCTATCTTTAGGAATTTAAATCTTAGTAGAACTCT
1 ATCCTAT-TTTAGGAATTTGAATCTTAGTAAAACTCT
* * * * *
56091 ATCATATTTTTAGGAGTTTGAATCCTAGTAAAATTTT
1 ATCCTA-TTTTAGGAATTTGAATCTTAGTAAAACTCT
*
56128 ATCCTATTTTAAGAATTTGAATCTTAGTA
1 ATCCTATTTTAGGAATTTGAATCTTAGTA
56157 GGACGAAAAT
Statistics
Matches: 54, Mismatches: 11, Indels: 3
0.79 0.16 0.04
Matches are distributed among these distances:
36 20 0.37
37 33 0.61
38 1 0.02
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (36 bp):
ATCCTATTTTAGGAATTTGAATCTTAGTAAAACTCT
Found at i:57995 original size:13 final size:13
Alignment explanation
Indices: 57971--58005 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
57961 TATTTATTAT
57971 ATATTT-ATAAAA
1 ATATTTAATAAAA
57983 ATATTTAAT-AAA
1 ATATTTAATAAAA
57995 ATATTTAATAA
1 ATATTTAATAA
58006 TATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTTAATAAAA
Found at i:58073 original size:19 final size:18
Alignment explanation
Indices: 58045--58093 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
58035 AATATATTTA
*
58045 AAAACAATAAAATAAATG
1 AAAACAATAAAATAAACG
58063 AAAACATATAAAATAAACG
1 AAAACA-ATAAAATAAACG
58082 AAAA-AATAAAAT
1 AAAACAATAAAAT
58094 TAAAAATCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (18 bp):
AAAACAATAAAATAAACG
Found at i:64736 original size:13 final size:13
Alignment explanation
Indices: 64712--64746 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
64702 ACTATTTATT
64712 ATATTT-ATAAAA
1 ATATTTAATAAAA
64724 ATATTTAAT-AAA
1 ATATTTAATAAAA
64736 ATATTTAATAA
1 ATATTTAATAA
64747 TATAATAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 18 0.86
13 3 0.14
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
ATATTTAATAAAA
Found at i:64814 original size:19 final size:18
Alignment explanation
Indices: 64786--64834 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
64776 AATATATTTA
*
64786 AAAACAATAAAATAAATG
1 AAAACAATAAAATAAACG
64804 AAAACATATAAAATAAACG
1 AAAACA-ATAAAATAAACG
64823 AAAA-AATAAAAT
1 AAAACAATAAAAT
64835 TAAAAATCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
17 7 0.24
18 7 0.24
19 15 0.52
ACGTcount: A:0.73, C:0.06, G:0.04, T:0.16
Consensus pattern (18 bp):
AAAACAATAAAATAAACG
Found at i:65626 original size:18 final size:18
Alignment explanation
Indices: 65603--65668 Score: 64
Period size: 17 Copynumber: 3.6 Consensus size: 18
65593 TGGTATAGTT
*
65603 TGTTTTTTTTTCTTTCTC
1 TGTTTTTTTTTCTGTCTC
65621 TG-TTTTTTTTCTGTCTC
1 TGTTTTTTTTTCTGTCTC
**
65638 TGTCTCTAGTTTT-TGTCTC
1 TGT-T-TTTTTTTCTGTCTC
65657 TGCTTTTTTTTT
1 TG-TTTTTTTTT
65669 TTTTTCAGGT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
17 16 0.41
18 7 0.18
19 10 0.26
20 6 0.15
ACGTcount: A:0.02, C:0.17, G:0.11, T:0.71
Consensus pattern (18 bp):
TGTTTTTTTTTCTGTCTC
Found at i:65669 original size:19 final size:18
Alignment explanation
Indices: 65603--65670 Score: 59
Period size: 19 Copynumber: 3.7 Consensus size: 18
65593 TGGTATAGTT
65603 TGTTTTTTTTTCTT-TCTC
1 TGTTTTTTTTT-TTGTCTC
*
65621 TG-TTTTTTTTCTGTCTC
1 TGTTTTTTTTTTTGTCTC
* **
65638 TGTCTCTAGTTTTTGTCTC
1 TGT-TTTTTTTTTTGTCTC
65657 TGCTTTTTTTTTTT
1 TG-TTTTTTTTTTT
65671 TTTCAGGTTC
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
16 1 0.03
17 14 0.37
18 2 0.05
19 20 0.53
20 1 0.03
ACGTcount: A:0.01, C:0.16, G:0.10, T:0.72
Consensus pattern (18 bp):
TGTTTTTTTTTTTGTCTC
Found at i:66134 original size:3 final size:3
Alignment explanation
Indices: 66126--66204 Score: 133
Period size: 3 Copynumber: 26.7 Consensus size: 3
66116 TTAATATATT
*
66126 TAA TAA TAA T-A TAA TGA 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 TAA
*
66173 TAA TAA TAA TAA TAA TAC TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
66205 TGGATAAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
2 2 0.03
3 69 0.97
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:68812 original size:25 final size:24
Alignment explanation
Indices: 68783--68856 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 24
68773 TCTGTAAAAA
* *
68783 AATTTAATTAAATACAATATTAAAT
1 AATTTAAATAATTA-AATATTAAAT
*
68808 AATTTAAATACTTAAATACTTAAAT
1 AATTTAAATAATTAAATA-TTAAAT
*
68833 AAATTAAAT-ATTAAATATTAAAT
1 AATTTAAATAATTAAATATTAAAT
68856 A
1 A
68857 TAATAAAATA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
23 7 0.16
24 11 0.26
25 25 0.58
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (24 bp):
AATTTAAATAATTAAATATTAAAT
Found at i:68847 original size:7 final size:7
Alignment explanation
Indices: 68798--68857 Score: 66
Period size: 7 Copynumber: 7.7 Consensus size: 7
68788 AATTAAATAC
68798 AATATTA
1 AATATTA
68805 AATAATTTA
1 AAT-A-TTA
68814 AATACTTA
1 AATA-TTA
68822 AATACTTA
1 AATA-TTA
68830 AATAAATTA
1 AAT--ATTA
68839 AATATTA
1 AATATTA
68846 AATATTA
1 AATATTA
68853 AATAT
1 AATAT
68858 AATAAAATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
7 19 0.40
8 16 0.33
9 12 0.25
10 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (7 bp):
AATATTA
Found at i:68863 original size:16 final size:14
Alignment explanation
Indices: 68798--68857 Score: 66
Period size: 16 Copynumber: 3.9 Consensus size: 14
68788 AATTAAATAC
68798 AATATTAAATAATTTA
1 AATATTAAAT-A-TTA
68814 AATACTTAAATACTTA
1 AATA-TTAAATA-TTA
68830 AATAAATTAAATATTA
1 AAT--ATTAAATATTA
68846 AATATTAAATAT
1 AATATTAAATAT
68858 AATAAAATAT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
14 9 0.22
16 17 0.43
17 13 0.32
18 1 0.03
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (14 bp):
AATATTAAATATTA
Found at i:70211 original size:37 final size:35
Alignment explanation
Indices: 70160--70422 Score: 170
Period size: 37 Copynumber: 7.2 Consensus size: 35
70150 ATATATATAT
*
70160 ATATATTATTATATAATTTGTAAACA-ATTTTTAAAA
1 ATATA-TATAATATAATTT-TAAACACATTTTTAAAA
*
70196 ATACGTATATAATATATAATTTTTAAA-ATCATTTTGAAAA
1 ATA--TATAT-A-ATATAA-TTTTAAACA-CATTTTTAAAA
*
70236 TTATATA-ATATATAATTTTAAA-ATCATTTTTAAAAA
1 ATATATATA-ATATAATTTTAAACA-CATTTTT-AAAA
* * * *
70272 ATTACATATTATATATTTTTATAA-TCATTTTTGAAAA
1 A-TATATATAATATAATTTTA-AACACATTTTT-AAAA
*
70309 AT-TATATAATATATAGTTTTAAAAACATTTTTAAAA
1 ATATATATAATATA-A-TTTTAAACACATTTTTAAAA
*
70345 A-ATTATATAATATATAGTTTTAAAAACATTTTTAAAA
1 ATA-TATATAATATA-A-TTTTAAACACATTTTTAAAA
70382 A-ACTTATATAATAT--TTTTAAAC-CATTTTTAAAA
1 ATA--TATATAATATAATTTTAAACACATTTTTAAAA
70415 ACTATATA
1 A-TATATA
70423 ATGTATAGTT
Statistics
Matches: 193, Mismatches: 15, Indels: 41
0.78 0.06 0.16
Matches are distributed among these distances:
33 16 0.08
34 7 0.04
35 25 0.13
36 23 0.12
37 78 0.40
38 20 0.10
39 10 0.05
40 14 0.07
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.46
Consensus pattern (35 bp):
ATATATATAATATAATTTTAAACACATTTTTAAAA
Found at i:70249 original size:75 final size:72
Alignment explanation
Indices: 70169--70460 Score: 293
Period size: 74 Copynumber: 4.1 Consensus size: 72
70159 TATATATTAT
*
70169 TATATAATTTGT-AAACAATTTTTAAAAATACGTATATAATATATAATTTTTAAAATCA-TTTTG
1 TATATAATTT-TAAAAC-ATTTTTAAAAA-A-TTATATAATATAT-ATTTTTAAAATCATTTTTG
70232 AAAATTATATAA
61 AAAATTATATAA
* * *
70244 TATATAATTTTAAAATCATTTTTAAAAAATTACATATTATATATTTTTATAATCATTTTTGAAAA
1 TATATAATTTTAAAA-CATTTTTAAAAAATTATATAATATATATTTTTAAAATCATTTTTG-AAA
70309 ATTATATAA
64 ATTATATAA
* * * *
70318 TATATAGTTTTAAAAACATTTTTAAAAAATTATATAATATATAGTTTTAAAAACATTTTTAAAAA
1 TATATAATTTT-AAAACATTTTTAAAAAATTATATAATATATATTTTTAAAATCATTTTT-GAAA
70383 ACTTATAT-A
64 A-TTATATAA
* * * * *
70392 -ATAT--TTTTAAACCATTTTT-AAAAACTATATAATGTATAGTTTTGAAAT--TTTTT-AAAA-
1 TATATAATTTTAAAACATTTTTAAAAAATTATATAATATATATTTTTAAAATCATTTTTGAAAAT
70449 -ATATAA
66 TATATAA
70455 TATATA
1 TATATA
70461 GTTTAAATTT
Statistics
Matches: 191, Mismatches: 16, Indels: 30
0.81 0.07 0.13
Matches are distributed among these distances:
62 4 0.02
63 1 0.01
64 4 0.02
65 4 0.02
67 5 0.03
69 25 0.13
70 10 0.05
71 4 0.02
72 12 0.06
73 19 0.10
74 68 0.36
75 34 0.18
76 1 0.01
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (72 bp):
TATATAATTTTAAAACATTTTTAAAAAATTATATAATATATATTTTTAAAATCATTTTTGAAAAT
TATATAA
Found at i:70492 original size:33 final size:30
Alignment explanation
Indices: 70405--70498 Score: 100
Period size: 33 Copynumber: 3.0 Consensus size: 30
70395 TTTTTAAACC
* *
70405 ATTTTTAAAAACTATATAATGTATAGTTTTGAA
1 ATTTTTTAAAA-TATATAATATATAG-TTT-AA
70438 ATTTTTTAAAA-ATATAATATATAGTTTAA
1 ATTTTTTAAAATATATAATATATAGTTTAA
*
70467 ATTTTTTTGAAATATATATATTATATAGTTTA
1 A-TTTTTT-AAA-ATATATAATATATAGTTTA
70499 TATCATATTA
Statistics
Matches: 54, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
29 3 0.06
30 9 0.17
31 15 0.28
32 1 0.02
33 26 0.48
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (30 bp):
ATTTTTTAAAATATATAATATATAGTTTAA
Found at i:71723 original size:2 final size:2
Alignment explanation
Indices: 71716--71771 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
71706 TTTTAATTTC
*
71716 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT -T TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
71756 AT AT AC AT AT AC AT AT
1 AT AT AT AT AT AT AT AT
71772 TTATTATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
1 2 0.04
2 45 0.96
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:71888 original size:20 final size:20
Alignment explanation
Indices: 71840--71890 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
71830 TACATATATT
71840 TTTTGTTTATTTAATAGTTA
1 TTTTGTTTATTTAATAGTTA
*
71860 TTATT-TTTATTTAAT-TTTA
1 TT-TTGTTTATTTAATAGTTA
71879 TTTTGGTTTATT
1 TTTT-GTTTATT
71891 CTTTTATTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 2 0.07
19 5 0.19
20 18 0.67
21 2 0.07
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.71
Consensus pattern (20 bp):
TTTTGTTTATTTAATAGTTA
Found at i:77328 original size:84 final size:84
Alignment explanation
Indices: 77172--77734 Score: 578
Period size: 84 Copynumber: 6.8 Consensus size: 84
77162 TTTAAAACAA
* * * * * * * *
77172 ATCATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTATCTGCCAA--AAAGACCTTCAAGTTTGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
77235 ACGCTCAGCTCCAAGGCAT
66 ACGCTCAGCTCCAAGGCAC
*
77254 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* *
77319 ACGCTCAGCTCCAAGACTC
66 ACGCTCAGCTCCAAGGCAC
* * * * *
77338 ATTATTTGCAACATAACTTATGTCGAGAAGGGCTATCTG----CCAAAGACCCTT-GAGTTCGAT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGA-CCTTCGAGTTCGAC
* * *
77398 TACACTCAGCT-TAGAGGGTAC
65 TACGCTCAGCTCCA-A-GGCAC
* * * * * * *
77419 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
77484 ACGCTCAGCTCCAAGGCAC
66 ACGCTCAGCTCCAAGGCAC
* * *
77503 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG----CCAAAGACCCTCGAGTTCGATT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
* *
77564 ACACTCAGCTTCAAGGGCAC
66 ACGCTCAGCTCCAA-GGCAC
** * * * * *
77584 ATCATTTATAGCATAACTCAAGGCTATAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
*
77648 ACGCTCAGCTCCAAGGTAC
66 ACGCTCAGCTCCAAGGCAC
* * * * *
77667 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAACCGAAGACC-TCTGAGTTCGAT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTC-GAGTTCGAC
77731 TACG
65 TACG
77735 TTTAGCTCAG
Statistics
Matches: 393, Mismatches: 71, Indels: 32
0.79 0.14 0.06
Matches are distributed among these distances:
79 1 0.00
80 56 0.14
81 74 0.19
82 36 0.09
83 37 0.09
84 163 0.41
85 25 0.06
86 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (84 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCCAAGGCAC
Found at i:77452 original size:165 final size:164
Alignment explanation
Indices: 77172--77706 Score: 725
Period size: 165 Copynumber: 3.2 Consensus size: 164
77162 TTTAAAACAA
* * * * * * * *
77172 ATCATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTATCTGCCAAAAAGACCTTCAAGTTTGACTAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCC--AAAGACCCTCGAGTTCGATTAC
* * * * * * * **
77237 GCTCAGCTCCAA-GGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAA
64 ACTCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAA
77301 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACTC
129 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAG-CTC
* * * * *
77338 ATTATTTGCAACATAACTTATGTCGAGAAGGGCTATCTGCCAAAGACCCTTGAGTTCGATTACAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACAC
* *
77403 TCAGCTT-AGAGGGTACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAA
66 TCAGCTTCA-AGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAA
* *
77467 GACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCAC
130 GACCTTCGAGTTCGACTACGCTCAGCTCCAA-GCTC
*
77503 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACCCTCGAGTTCGATTACAC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACAC
* *
77568 TCAGCTTCAAGGGCACATCATTTATAGCATAACTCAAGGCTATAAGGGTTATCTGTC-ACCAAAG
66 TCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAG
*
77632 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGGTAC
131 ACCTTCGAGTTCGACTACGCTCAGCTCCAAGCT-C
77667 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
1 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGC
77707 TAACCGAAGA
Statistics
Matches: 324, Mismatches: 40, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
163 2 0.01
164 100 0.31
165 187 0.58
166 35 0.11
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (164 bp):
ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCTCGAGTTCGATTACAC
TCAGCTTCAAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACCAAAG
ACCTTCGAGTTCGACTACGCTCAGCTCCAAGCTC
Found at i:77657 original size:249 final size:244
Alignment explanation
Indices: 77172--77734 Score: 648
Period size: 249 Copynumber: 2.3 Consensus size: 244
77162 TTTAAAACAA
* * ** *
77172 ATCATTTGCAGCTTAGCTCAAGGCCAGAAGGGCTATCTGCCA-AAAAGACCTTCAAGTTTGACTA
1 ATCATTTGCAGCATAGCTCAAGGCCAGAAGGGCTATCTGCAACAAAAGACCTTTGAGTTCGACTA
*
77236 CGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTACCAACCAA
66 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT---AACCAA
* * * * * * * *
77301 AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGACTCATTATTTGCAACATAACTTATGTCGAGA
128 AGACCCTCGAGTTCGACTACACTCAGCTCCAAGACACATCATTTACAACATAACTCAAGGCGAGA
* *
77366 AGGGCTATCTGCCAAAGACCCTTGAGTTCGATTACACTCAGCT-TAGAGGGTAC
193 AGGGCTATCTGCCAAAGACCCTTGAGTTCGACTACACTCAGCTCCA-A-GGTAC
* * * *
77419 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTCAACAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAGCTCAAGGCCAGAAGGGCTATCTG-CAACAAAAGACCTTTGAGTTCGACT
* *
77484 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT-GCCAAAG
65 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTAACCAAAG
* * * * * * *
77548 ACCCTCGAGTTCGATTACACTCAGCTTCAAGGGCACATCATTTATAGCATAACTCAAGGCTATAA
130 ACCCTCGAGTTCGACTACACTCAGCTCCAA-GACACATCATTTACAACATAACTCAAGGCGAGAA
* *
77613 GGGTTATCTGTCACCAAAGA-CCTTCGAGTTCGACTACGCTCAGCTCCAAGGTAC
194 GGGCTATCTG---CCAAAGACCCTT-GAGTTCGACTACACTCAGCTCCAAGGTAC
* * * ** * *
77667 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCTAACCGAAGACCTCTGAGTTCGATT
1 ATCATTTGCAGCATAGCTCAAGGCCAGAAGGGCTATCTGC-AACAAAAGACCTTTGAGTTCGACT
77732 ACG
65 ACG
77735 TTTAGCTCAG
Statistics
Matches: 266, Mismatches: 41, Indels: 17
0.82 0.13 0.05
Matches are distributed among these distances:
245 32 0.12
246 32 0.12
247 35 0.13
248 67 0.25
249 99 0.37
250 1 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (244 bp):
ATCATTTGCAGCATAGCTCAAGGCCAGAAGGGCTATCTGCAACAAAAGACCTTTGAGTTCGACTA
CGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTAACCAAAGA
CCCTCGAGTTCGACTACACTCAGCTCCAAGACACATCATTTACAACATAACTCAAGGCGAGAAGG
GCTATCTGCCAAAGACCCTTGAGTTCGACTACACTCAGCTCCAAGGTAC
Found at i:84780 original size:13 final size:13
Alignment explanation
Indices: 84762--84800 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
84752 CGTTGTACCT
84762 TCAAAAATTAAAA
1 TCAAAAATTAAAA
84775 TCAAAAATTAAAA
1 TCAAAAATTAAAA
84788 TCAAAAATTAAAA
1 TCAAAAATTAAAA
84801 ATGGACAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.23
Consensus pattern (13 bp):
TCAAAAATTAAAA
Found at i:92999 original size:18 final size:18
Alignment explanation
Indices: 92976--93013 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
92966 AATTCGAGGG
*
92976 AATTAATTTTGAATCAGA
1 AATTAATCTTGAATCAGA
92994 AATTAATCTTGAATCAGA
1 AATTAATCTTGAATCAGA
93012 AA
1 AA
93014 ATATAGAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.08, G:0.11, T:0.34
Consensus pattern (18 bp):
AATTAATCTTGAATCAGA
Done.