Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008059.1 Hibiscus syriacus cultivar Beakdansim tig00110554_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: 130087
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:10423 original size:27 final size:25
Alignment explanation
Indices: 10396--10445 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
10386 TGCTAGAATA
10396 AAATAATATTTTTATATATTTTAAAT
1 AAAT-ATATTTTTATATATTTTAAAT
* * *
10422 AAGTCTATTTTTATCTATTTTAAA
1 AAATATATTTTTATATATTTTAAA
10446 ATATTGTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.54
Consensus pattern (25 bp):
AAATATATTTTTATATATTTTAAAT
Found at i:10769 original size:14 final size:14
Alignment explanation
Indices: 10750--10776 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
10740 TTTTTATCTT
10750 TTAAAATTATTTTC
1 TTAAAATTATTTTC
10764 TTAAAATTATTTT
1 TTAAAATTATTTT
10777 AAAAGGTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTAAAATTATTTTC
Found at i:13707 original size:16 final size:16
Alignment explanation
Indices: 13686--13716 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13676 GAACTTGAAG
13686 CTGAGAAAAGACGAAC
1 CTGAGAAAAGACGAAC
13702 CTGAGAAAAGACGAA
1 CTGAGAAAAGACGAA
13717 GCTGTGAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.16, G:0.26, T:0.06
Consensus pattern (16 bp):
CTGAGAAAAGACGAAC
Found at i:22781 original size:89 final size:88
Alignment explanation
Indices: 22644--22920 Score: 371
Period size: 89 Copynumber: 3.1 Consensus size: 88
22634 TACTAAAACT
* * * *
22644 AATCTCGAGTTTGATCTCCCCGAAAGAGTAGTGGAGCAAATTCTTCTTATTTCAGATTTGGTCTT
1 AATCTCGAGTCTGATCTCCCCGAAAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCTT
* *
22709 CCTAAAG-A-AGCAATGAATCAAATC
66 CCGAAAGAATAGC-A--AAGCAAATC
*
22733 AATCTTGAGTCTGATCTCCCC-AGAAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCT
1 AATCTCGAGTCTGATCTCCCCGA-AAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCT
22797 TCCCGAAAGAATAGCAAAGCAAATC
65 T-CCGAAAGAATAGCAAAGCAAATC
* * * *
22822 AATCTCAAGTCTGAACTCCCCGAAAGATTAGAGGAGCAGATTCATCTTATTTTAGATTTGGTCTT
1 AATCTCGAGTCTGATCTCCCCGAAAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCTT
*
22887 CCCGAAAGAGTAGCAAAGCAAATC
66 -CCGAAAGAATAGCAAAGCAAATC
22911 AATCTCGAGT
1 AATCTCGAGT
22921 AGGAGTAGAT
Statistics
Matches: 169, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
88 1 0.01
89 156 0.92
90 7 0.04
91 2 0.01
92 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (88 bp):
AATCTCGAGTCTGATCTCCCCGAAAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCTT
CCGAAAGAATAGCAAAGCAAATC
Found at i:22962 original size:68 final size:68
Alignment explanation
Indices: 22853--22988 Score: 236
Period size: 68 Copynumber: 2.0 Consensus size: 68
22843 GAAAGATTAG
22853 AGGAGCAGATTCATCTTATTTTAGATTTGGTCTTCCCGAAAGAGTAGCAAAGCAAATCAATCTCG
1 AGGAGCAGATTCATCTTATTTTAGATTTGGTCTTCCCGAAAGAGTAGCAAAGCAAATCAATCTCG
22918 AGT
66 AGT
* * **
22921 AGGAGTAGATTCTTCTTATTTTAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCG
1 AGGAGCAGATTCATCTTATTTTAGATTTGGTCTTCCCGAAAGAGTAGCAAAGCAAATCAATCTCG
22986 AGT
66 AGT
22989 TTGATCTCCC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
68 64 1.00
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Consensus pattern (68 bp):
AGGAGCAGATTCATCTTATTTTAGATTTGGTCTTCCCGAAAGAGTAGCAAAGCAAATCAATCTCG
AGT
Found at i:23026 original size:89 final size:89
Alignment explanation
Indices: 22921--23445 Score: 578
Period size: 89 Copynumber: 5.9 Consensus size: 89
22911 AATCTCGAGT
*
22921 AGGAGTAGATTCTTCTTATTTTAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCG
1 AGGAGTAGATTCTTCTTATTTCAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCG
*
22986 AGTTTGATCTCCCTGGAAGAGTAG
66 AGTCTGATCTCCCTGGAAGAGTAG
* * **
23010 AGGAGTAGATTCTTCTTATTTCAGATTTGGTCTTCTCGAAAGAGTGGCAAAGCAAATCAATCTCG
1 AGGAGTAGATTCTTCTTATTTCAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCG
*
23075 AGTCTGATCTCCCTAGAAGAGTAG
66 AGTCTGATCTCCCTGGAAGAGTAG
* * *
23099 ATGAGTTGATTCTTCTTATTTCAGATTTGGTCTTCCCGAAAGAGTAGCGAAG-AAGATCAATCTC
1 AGGAGTAGATTCTTCTTATTTCAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAA-ATCAATCTC
*
23163 GAGTTTGATCTCCCCT-GAAGAGTA-
65 GAGTCTGATCT-CCCTGGAAGAGTAG
* * * * * *
23187 ATAGAGCAAATTCTTCTTATTTCAGATTTGGTCTTCCTGAAAGAGTAGTGAAGCAAGTCAATCTT
1 A-GGAGTAGATTCTTCTTATTTCAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTC
* * *
23252 AAGTCTGATATCCCCGGAAGAGTAG
65 GAGTCTGATCTCCCTGGAAGAGTAG
* * * * * * * * *
23277 TA-GAGCATATTTTTCTTATTTCATATTTGGTCTTCCTGAAAAAGGAGAGAATCAAATCAATCTC
1 -AGGAGTAGATTCTTCTTATTTCAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTC
* *
23341 GAGTCTGATGT-TCTCGGAAGAGTAG
65 GAGTCTGATCTCCCT-GGAAGAGTAG
* ** * * * *
23366 TGGAAAAGATTATTCTTATTTCAGATTTGGTCTTCCTG-AAGAAGCA-TCGAAGCAAATCATTCT
1 AGGAGTAGATTCTTCTTATTTCAGATTTGGTCTTCCCGAAAG-AGTAGT-GAAGCAAATCAATCT
*
23429 CGAGTCTTATCTACCCT
64 CGAGTCTGATCT-CCCT
23446 TAAAGATGAG
Statistics
Matches: 371, Mismatches: 52, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
88 9 0.02
89 353 0.95
90 6 0.02
91 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (89 bp):
AGGAGTAGATTCTTCTTATTTCAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCG
AGTCTGATCTCCCTGGAAGAGTAG
Found at i:23050 original size:157 final size:157
Alignment explanation
Indices: 22764--23077 Score: 475
Period size: 157 Copynumber: 2.0 Consensus size: 157
22754 AGAAGAGTAG
22764 AGGAGCAGATTCATCTTATTTCAGATTTGGTCTTCCCGAAAGAATAGCAAAGCAAATCAATCTCA
1 AGGAGCAGATTCATCTTATTTCAGATTTGGTCTTCCCGAAAGAATAGCAAAGCAAATCAATCTCA
* *
22829 AGTCTGAACTCCCCGAAAGATTAGAGGAGCAGATTCATCTTATTTTAGATTTGGTCTTCCCGAAA
66 AGTCTGAACTCCCCGAAAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCTTCCCGAAA
22894 GAGTAGCAAAGCAAATCAATCTCGAGT
131 GAGTAGCAAAGCAAATCAATCTCGAGT
* * * * ** *
22921 AGGAGTAGATTCTTCTTATTTTAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCG
1 AGGAGCAGATTCATCTTATTTCAGATTTGGTCTTCCCGAAAGAATAGCAAAGCAAATCAATCTCA
* * * * * * *
22986 AGTTTGATCTCCCTGGAAGAGTAGAGGAGTAGATTCTTCTTATTTCAGATTTGGTCTTCTCGAAA
66 AGTCTGAACTCCCCGAAAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCTTCCCGAAA
*
23051 GAGTGGCAAAGCAAATCAATCTCGAGT
131 GAGTAGCAAAGCAAATCAATCTCGAGT
23078 CTGATCTCCC
Statistics
Matches: 140, Mismatches: 17, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
157 140 1.00
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.30
Consensus pattern (157 bp):
AGGAGCAGATTCATCTTATTTCAGATTTGGTCTTCCCGAAAGAATAGCAAAGCAAATCAATCTCA
AGTCTGAACTCCCCGAAAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCTTCCCGAAA
GAGTAGCAAAGCAAATCAATCTCGAGT
Found at i:23118 original size:246 final size:246
Alignment explanation
Indices: 22683--23166 Score: 704
Period size: 246 Copynumber: 2.0 Consensus size: 246
22673 AGTGGAGCAA
* * *
22683 ATTCTTCTTATTTCAGATTTGGTCTTCCTAAAGAAGCAATGAATCAAATCAATCTTGAGTCTGAT
1 ATTCTTCTTATTTCAGATTTGGTCTTCCGAAAGAAGCAATGAAGCAAATCAATCTCGAGTCTGAT
22748 CTCCCCAGAAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCTTCCCGAAAGAATAGCA
66 CTCCCCAGAAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCTTCCCGAAAGAATAGCA
* * *
22813 AAGCAAATCAATCTCAAGTCTGAACTCCCCGAAAGATTAGAGGAGCAGATTCATCTTATTTTAGA
131 AAGCAAATCAATCTCAAGTCTGAACTCCCAGAAAGAGTAGAGGAGCAGATTCATCTTATTTCAGA
22878 TTTGGTCTTCCCGAAAGAGTAGCAAAGCAA-ATCAATCTCGAGTAGGAGTAG
196 TTTGGTCTTCCCGAAAGAGTAGCAAAG-AAGATCAATCTCGAGTAGGAGTAG
* * * *
22929 ATTCTTCTTATTTTAGATTTGGTCTTCCCGAAAG-AGTAGTGAAGCAAATCAATCTCGAGTTTGA
1 ATTCTTCTTATTTCAGATTTGGTCTT-CCGAAAGAAGCAATGAAGCAAATCAATCTCGAGTCTGA
** * * * * *
22993 TCTCCCTGGAAGAGTAGAGGAGTAGATTCTTCTTATTTCAGATTTGGTCTTCTCGAAAGAGTGGC
65 TCTCCCCAGAAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCTTCCCGAAAGAATAGC
* * * ** *
23058 AAAGCAAATCAATCTCGAGTCTGATCTCCCTAG-AAGAGTAGATGAGTTGATTCTTCTTATTTCA
130 AAAGCAAATCAATCTCAAGTCTGAACTCCC-AGAAAGAGTAGAGGAGCAGATTCATCTTATTTCA
*
23122 GATTTGGTCTTCCCGAAAGAGTAGCGAAGAAGATCAATCTCGAGT
194 GATTTGGTCTTCCCGAAAGAGTAGCAAAGAAGATCAATCTCGAGT
23167 TTGATCTCCC
Statistics
Matches: 211, Mismatches: 24, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
245 2 0.01
246 202 0.96
247 7 0.03
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (246 bp):
ATTCTTCTTATTTCAGATTTGGTCTTCCGAAAGAAGCAATGAAGCAAATCAATCTCGAGTCTGAT
CTCCCCAGAAGAGTAGAGGAGCAGATTCATCTTATTTCAGATTTGGTCTTCCCGAAAGAATAGCA
AAGCAAATCAATCTCAAGTCTGAACTCCCAGAAAGAGTAGAGGAGCAGATTCATCTTATTTCAGA
TTTGGTCTTCCCGAAAGAGTAGCAAAGAAGATCAATCTCGAGTAGGAGTAG
Found at i:23252 original size:47 final size:47
Alignment explanation
Indices: 23112--23252 Score: 104
Period size: 47 Copynumber: 3.1 Consensus size: 47
23102 AGTTGATTCT
* *
23112 TCTTATTTCAGATTTGGTCTTCCCGAAAGAGTAGCGAAG-AAGATCAA
1 TCTTATTTCAGATTTGGTCTTCCTGAAAGAGTAGTGAAGCAAG-TCAA
* * * * *
23159 TC-----TC-GAGTTTGATCTCCCCTG-AAGAGTAAT-AGAGCAAATTC-T
1 TCTTATTTCAGA-TTTGGTCT-TCCTGAAAGAGTAGTGA-AGC-AAGTCAA
23201 TCTTATTTCAGATTTGGTCTTCCTGAAAGAGTAGTGAAGCAAGTCAA
1 TCTTATTTCAGATTTGGTCTTCCTGAAAGAGTAGTGAAGCAAGTCAA
23248 TCTTA
1 TCTTA
23253 AGTCTGATAT
Statistics
Matches: 68, Mismatches: 12, Indels: 28
0.63 0.11 0.26
Matches are distributed among these distances:
41 3 0.04
42 20 0.29
43 5 0.07
44 2 0.03
46 8 0.12
47 27 0.40
48 3 0.04
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (47 bp):
TCTTATTTCAGATTTGGTCTTCCTGAAAGAGTAGTGAAGCAAGTCAA
Found at i:23432 original size:267 final size:267
Alignment explanation
Indices: 22929--23433 Score: 657
Period size: 267 Copynumber: 1.9 Consensus size: 267
22919 GTAGGAGTAG
* * *
22929 ATTCTTCTTATTTTAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCGAGTTTGAT
1 ATTCTTCTTATTTCAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCAAGTCTGAT
* * * *
22994 CTCCCTGGAAGAGTAGAGGAGTAGATTCTTCTTATTTCAGATTTGGTCTTCTCGAAAGAGTGGCA
66 ATCCCCGGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATTTGGTCTTCTCGAAAAAGTGGCA
*** *
23059 AAGCAAATCAATCTCGAGTCTGATCTCCCTAGAAGAGTAGATGAGTTGATTCTTCTTATTTCAGA
131 AAGCAAATCAATCTCGAGTCTGATCTCCCTAGAAGAGTAGATGAAAAGATTATTCTTATTTCAGA
*
23124 TTTGGTCTTCCCGAAAGAGTAGCGAAGAAGATCAATCTCGAGTTTGATCTCCCCTGAAGAGTAAT
196 TTTGGTCTTCCCGAAAGAGCAGCGAAGAAGATCAATCTCGAGTTTGATCTCCCCTGAAGAGTAAT
23189 AGAGCAA
261 AGAGCAA
* * *
23196 ATTCTTCTTATTTCAGATTTGGTCTTCCTGAAAGAGTAGTGAAGCAAGTCAATCTTAAGTCTGAT
1 ATTCTTCTTATTTCAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCAAGTCTGAT
* * *
23261 ATCCCCGGAAGAGTAGTA-GAGCATATTTTTCTTATTTCATATTTGGTCTTC-CTGAAAAAG-GA
66 ATCCCCGGAAGAGTAG-AGGAGCAGATTCTTCTTATTTCAGATTTGGTCTTCTC-GAAAAAGTG-
* * * *
23323 G-AGAATCAAATCAATCTCGAGTCTGATGT-TCTCGGAAGAGTAG-TGGAAAAGATTATTCTTAT
128 GCA-AAGCAAATCAATCTCGAGTCTGATCTCCCT-AGAAGAGTAGAT-GAAAAGATTATTCTTAT
* * *
23385 TTCAGATTTGGTCTTCCTG-AAGAAGCATCGAAGCAA-ATCATTCTCGAGT
190 TTCAGATTTGGTCTTCCCGAAAG-AGCAGCGAAG-AAGATCAATCTCGAGT
23434 CTTATCTACC
Statistics
Matches: 205, Mismatches: 25, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
266 9 0.04
267 193 0.94
268 3 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.33
Consensus pattern (267 bp):
ATTCTTCTTATTTCAGATTTGGTCTTCCCGAAAGAGTAGTGAAGCAAATCAATCTCAAGTCTGAT
ATCCCCGGAAGAGTAGAGGAGCAGATTCTTCTTATTTCAGATTTGGTCTTCTCGAAAAAGTGGCA
AAGCAAATCAATCTCGAGTCTGATCTCCCTAGAAGAGTAGATGAAAAGATTATTCTTATTTCAGA
TTTGGTCTTCCCGAAAGAGCAGCGAAGAAGATCAATCTCGAGTTTGATCTCCCCTGAAGAGTAAT
AGAGCAA
Found at i:23632 original size:86 final size:81
Alignment explanation
Indices: 23487--23671 Score: 280
Period size: 86 Copynumber: 2.2 Consensus size: 81
23477 AGATTTCTCG
* *
23487 AGTCTTATCTCCTTGAAAGAATAGTGGAGCAGACTCATTTTCGAAAATTGATCTGACTACCTGAA
1 AGTCTTATCTCCTTGAAAGAATAGTGGAGCAGACTCATTTTCCAAAATTGATATGACTACC---A
23552 GAAAAAAAAAGGAACAAATCA
63 G--AAAAAAAGGAACAAATCA
* *
23573 AGTCTTATCTCCCTGAAAGAATAGTGGAGCAGACTCATTTTCCAAAATTGATATGACTACCCGAA
1 AGTCTTATCTCCTTGAAAGAATAGTGGAGCAGACTCATTTTCCAAAATTGATATGACTACCAGAA
*
23638 AAAGAGGAACAAATCA
66 AAAAAGGAACAAATCA
23654 AGTCTTATCTCCTTGAAA
1 AGTCTTATCTCCTTGAAA
23672 AAAGAATGCA
Statistics
Matches: 93, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
81 34 0.37
83 1 0.01
86 58 0.62
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.25
Consensus pattern (81 bp):
AGTCTTATCTCCTTGAAAGAATAGTGGAGCAGACTCATTTTCCAAAATTGATATGACTACCAGAA
AAAAAGGAACAAATCA
Found at i:23856 original size:81 final size:82
Alignment explanation
Indices: 23718--23899 Score: 253
Period size: 81 Copynumber: 2.2 Consensus size: 82
23708 ATTCTTGTCT
* *
23718 CCCTGAAAGAAGAGTGGAGCATACTCGTTTTCCAAAATTGATCTAACTACCCGAAAAAAG-GAAA
1 CCCTGAAAGAAGAGTGGAGCATACTAGTCTTCCAAAATTGATCTAACTACCCG-AAAAAGTGAAA
**
23782 AAG-TCAAGTTTGATCTC
65 AAGATCAAGGCTGATCTC
* * *
23799 CCCTAAAAGAAGAGTGGAGCATAAC-AGTCTTCCAAAATTGATCTGACTACCCGAAAAAGTGGAA
1 CCCTGAAAGAAGAGTGGAGCAT-ACTAGTCTTCCAAAATTGATCTAACTACCCGAAAAAGTGAAA
*
23863 CAGATCAAGGCTGATCTC
65 AAGATCAAGGCTGATCTC
23881 CCCTGAAAGAAGAGTGGAG
1 CCCTGAAAGAAGAGTGGAG
23900 AGGTTTTCCC
Statistics
Matches: 89, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
80 6 0.07
81 51 0.57
82 32 0.36
ACGTcount: A:0.38, C:0.20, G:0.21, T:0.20
Consensus pattern (82 bp):
CCCTGAAAGAAGAGTGGAGCATACTAGTCTTCCAAAATTGATCTAACTACCCGAAAAAGTGAAAA
AGATCAAGGCTGATCTC
Found at i:24034 original size:3 final size:3
Alignment explanation
Indices: 24026--24076 Score: 84
Period size: 3 Copynumber: 17.0 Consensus size: 3
24016 TGTCCCTATG
* *
24026 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ACT ATT ACT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
24074 ATT
1 ATT
24077 TACATTTTAC
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:38892 original size:20 final size:20
Alignment explanation
Indices: 38867--38918 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
38857 ATGTGAAATT
*
38867 TGTCCCGAAGGACCTCTGTA
1 TGTCCCGAAGGAACTCTGTA
38887 TGTCCCGAAGGAACTCTGTA
1 TGTCCCGAAGGAACTCTGTA
*
38907 TGTCCCAAAGGA
1 TGTCCCGAAGGA
38919 TCTATGAACC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.27, G:0.25, T:0.23
Consensus pattern (20 bp):
TGTCCCGAAGGAACTCTGTA
Found at i:39930 original size:11 final size:11
Alignment explanation
Indices: 39902--39933 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
39892 TTTAAGCTAC
*
39902 CTTAAGATTTA
1 CTTAAGCTTTA
39913 CTTAAGCTTTA
1 CTTAAGCTTTA
39924 CTTAAGCTTT
1 CTTAAGCTTT
39934 CTCACTGTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.09, T:0.47
Consensus pattern (11 bp):
CTTAAGCTTTA
Found at i:43399 original size:19 final size:19
Alignment explanation
Indices: 43343--43401 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
43333 ATATCTTATC
*
43343 ACAATAACATAT-ATTCAT
1 ACAATAACATATAACTCAT
* *
43361 ACAAT--CATGTCACACACAT
1 ACAATAACATAT-A-ACTCAT
43380 ACAATAACATATAACTCAT
1 ACAATAACATATAACTCAT
43399 ACA
1 ACA
43402 CACATGCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 9
0.69 0.11 0.20
Matches are distributed among these distances:
16 4 0.13
18 5 0.16
19 17 0.55
20 1 0.03
21 4 0.13
ACGTcount: A:0.49, C:0.24, G:0.02, T:0.25
Consensus pattern (19 bp):
ACAATAACATATAACTCAT
Found at i:45139 original size:3 final size:3
Alignment explanation
Indices: 45127--45162 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
45117 TTAAATGAAA
45127 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
45163 TTAAAAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 30 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:48856 original size:58 final size:58
Alignment explanation
Indices: 48763--48984 Score: 390
Period size: 58 Copynumber: 3.8 Consensus size: 58
48753 TGGCACTAAG
*
48763 TGTGCAAAAATGTTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTA
1 TGTGCAAAAA-GATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTA
*
48822 TGTGCAAAAAGATAAGAAATTTATACTAAGTGTATGAATTTCCGTATTGGGCACTTTA
1 TGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTA
48880 TGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTA
1 TGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTA
* * *
48938 TGTGAAAAAAGATAAGAAACTCATACTAAGTGTATGAATTTACGTAT
1 TGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
48985 GGGAAATATG
Statistics
Matches: 157, Mismatches: 6, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
58 147 0.94
59 10 0.06
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.33
Consensus pattern (58 bp):
TGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTA
Found at i:49510 original size:45 final size:45
Alignment explanation
Indices: 49447--49793 Score: 274
Period size: 45 Copynumber: 8.4 Consensus size: 45
49437 TTAAAAAAAT
*
49447 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGA
* *
49492 AATACATATGGGTGCATTATCGGCAT-AAA--A-G----A-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGA
* **
49526 AATGCATATGGGTGCATTATTGGCATGAAAGGTTGCCTTAGCCGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGA
* *
49571 AATGAATATGGGTGCATTATCGGCAT-AAA--A-G----A-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGA
* *
49605 AATGCATATGGGTGCATTATTGGCATAAAAGGATGCCTTAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGA
* * * *
49650 AATGCATATAGGTGTATTATCGGTAT-AAA--A-G----A-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGA
* * *
49684 AATTCATATGGGTGCATTATTGGCATGAAAGGATGTCTTAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGA
** *
49729 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGA
*
49774 AATGCACATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
49794 CAATATAAAA
Statistics
Matches: 236, Mismatches: 33, Indels: 66
0.70 0.10 0.20
Matches are distributed among these distances:
34 69 0.29
35 9 0.04
36 2 0.01
37 5 0.02
38 3 0.01
41 3 0.01
42 5 0.02
43 2 0.01
44 9 0.04
45 129 0.55
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (45 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGA
Found at i:49539 original size:34 final size:34
Alignment explanation
Indices: 49496--49714 Score: 132
Period size: 34 Copynumber: 5.8 Consensus size: 34
49486 AGCTGAAATA
49496 CATATGGGTGCATTATCGGCATAAAAGAATAATG
1 CATATGGGTGCATTATCGGCATAAAAGAATAATG
* ***
49530 CATATGGGTGCATTATTGGCATGAAAGGTTGCCTTAGCCGAAATG
1 CATATGGGTGCATTATCGGCAT-AAA---------AG-AATAATG
*
49575 AATATGGGTGCATTATCGGCATAAAAGAATAATG
1 CATATGGGTGCATTATCGGCATAAAAGAATAATG
*
49609 CATATGGGTGCATTATTGGCATAAAAGGATGCCTTAGTTGAAATG
1 CATATGGGTGCATTATCGGCATAAAA-GA------A--T--AATG
* * * *
49654 CATATAGGTGTATTATCGGTATAAAAGAATAATT
1 CATATGGGTGCATTATCGGCATAAAAGAATAATG
* *
49688 CATATGGGTGCATTATTGGCATGAAAG
1 CATATGGGTGCATTATCGGCATAAAAG
49715 GATGTCTTAG
Statistics
Matches: 142, Mismatches: 21, Indels: 44
0.69 0.10 0.21
Matches are distributed among these distances:
34 74 0.52
35 7 0.05
36 1 0.01
38 1 0.01
41 1 0.01
43 1 0.01
44 7 0.05
45 50 0.35
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (34 bp):
CATATGGGTGCATTATCGGCATAAAAGAATAATG
Found at i:49573 original size:79 final size:79
Alignment explanation
Indices: 49438--49759 Score: 502
Period size: 79 Copynumber: 4.1 Consensus size: 79
49428 AACAAATAAT
*
49438 TAAAAAAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATACATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATACATATGG
49503 GTGCATTATCGGCA
66 GTGCATTATCGGCA
* *
49517 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGTTGCCTTAGCCGAAATGA-ATATG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAAT-ACATATG
49581 GGTGCATTATCGGCA
65 GGTGCATTATCGGCA
* * * *
49596 TAAAAGAATAATGCATATGGGTGCATTATTGGCATAAAAGGATGCCTTAGTTGAAATGCATATAG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATACATATGG
* *
49661 GTGTATTATCGGTA
66 GTGCATTATCGGCA
* * *
49675 TAAAAGAATAATTCATATGGGTGCATTATTGGCATGAAAGGATGTCTTAGCTGAAATGCATATGG
1 TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATACATATGG
*
49740 GTGCATTATTGGCA
66 GTGCATTATCGGCA
*
49754 TGAAAG
1 TAAAAG
49760 GATGCCAAAG
Statistics
Matches: 221, Mismatches: 20, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
79 220 1.00
80 1 0.00
ACGTcount: A:0.34, C:0.11, G:0.25, T:0.30
Consensus pattern (79 bp):
TAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATACATATGG
GTGCATTATCGGCA
Found at i:50138 original size:58 final size:58
Alignment explanation
Indices: 50048--50157 Score: 220
Period size: 58 Copynumber: 1.9 Consensus size: 58
50038 TAGATGAGCT
50048 GTTAAACATTGTTGAGTAAAAGATGAATGGTTAAACACTGTTGAGTAAAAGAGGAATG
1 GTTAAACATTGTTGAGTAAAAGATGAATGGTTAAACACTGTTGAGTAAAAGAGGAATG
50106 GTTAAACATTGTTGAGTAAAAGATGAATGGTTAAACACTGTTGAGTAAAAGA
1 GTTAAACATTGTTGAGTAAAAGATGAATGGTTAAACACTGTTGAGTAAAAGA
50158 ATAATGGACT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 52 1.00
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (58 bp):
GTTAAACATTGTTGAGTAAAAGATGAATGGTTAAACACTGTTGAGTAAAAGAGGAATG
Found at i:50164 original size:29 final size:29
Alignment explanation
Indices: 50048--50157 Score: 193
Period size: 29 Copynumber: 3.8 Consensus size: 29
50038 TAGATGAGCT
*
50048 GTTAAACATTGTTGAGTAAAAGATGAATG
1 GTTAAACACTGTTGAGTAAAAGATGAATG
*
50077 GTTAAACACTGTTGAGTAAAAGAGGAATG
1 GTTAAACACTGTTGAGTAAAAGATGAATG
*
50106 GTTAAACATTGTTGAGTAAAAGATGAATG
1 GTTAAACACTGTTGAGTAAAAGATGAATG
50135 GTTAAACACTGTTGAGTAAAAGA
1 GTTAAACACTGTTGAGTAAAAGA
50158 ATAATGGACT
Statistics
Matches: 76, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 76 1.00
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (29 bp):
GTTAAACACTGTTGAGTAAAAGATGAATG
Found at i:53372 original size:479 final size:479
Alignment explanation
Indices: 52475--53422 Score: 1896
Period size: 479 Copynumber: 2.0 Consensus size: 479
52465 TTAAAGGAAA
52475 GATATGTCTTTTTGTAGAACGAAAAAGGGTCAAGAGAGTTTTGAAATACTATAAAGGATTGTAAT
1 GATATGTCTTTTTGTAGAACGAAAAAGGGTCAAGAGAGTTTTGAAATACTATAAAGGATTGTAAT
52540 AGAGACACCAGTGTTTATACAACTTGAGTTGGACAAAGAATTGGTGGTTTTTACTAATATATATC
66 AGAGACACCAGTGTTTATACAACTTGAGTTGGACAAAGAATTGGTGGTTTTTACTAATATATATC
52605 CCAACGATTAAGAATTTAGAAAGATATTCTTTTTAAGACATTAAATACGTTGACTATGCATTTAG
131 CCAACGATTAAGAATTTAGAAAGATATTCTTTTTAAGACATTAAATACGTTGACTATGCATTTAG
52670 GTGAAATCAAGAGGTATCAAGATTTAACGAATTGGGTTGGTGACCTGGTTTGAATAGAACCATCA
196 GTGAAATCAAGAGGTATCAAGATTTAACGAATTGGGTTGGTGACCTGGTTTGAATAGAACCATCA
52735 CAAAAATAGAAATTCGATTAGAATTGAATCATGAAAAAGAACCAATACAGATTTGAACTAGAGAA
261 CAAAAATAGAAATTCGATTAGAATTGAATCATGAAAAAGAACCAATACAGATTTGAACTAGAGAA
52800 ATCCAAAAACAGTGTAATAAAATGATTCCCCTAGTTGTAGTATTGTGGTAAACGCAAAAAGCCTT
326 ATCCAAAAACAGTGTAATAAAATGATTCCCCTAGTTGTAGTATTGTGGTAAACGCAAAAAGCCTT
52865 TAAATTCGAGGATGAATTTTCTTAAGGGGGAAGTGTAATACCCCAAATATCAGGTAAGGGACTAT
391 TAAATTCGAGGATGAATTTTCTTAAGGGGGAAGTGTAATACCCCAAATATCAGGTAAGGGACTAT
52930 ATTAAAAAATATTTTCTTAAGGGG
456 ATTAAAAAATATTTTCTTAAGGGG
52954 GATATGTCTTTTTGTAGAACGAAAAAGGGTCAAGAGAGTTTTGAAATACTATAAAGGATTGTAAT
1 GATATGTCTTTTTGTAGAACGAAAAAGGGTCAAGAGAGTTTTGAAATACTATAAAGGATTGTAAT
53019 AGAGACACCAGTGTTTATACAACTTGAGTTGGACAAAGAATTGGTGGTTTTTACTAATATATATC
66 AGAGACACCAGTGTTTATACAACTTGAGTTGGACAAAGAATTGGTGGTTTTTACTAATATATATC
53084 CCAACGATTAAGAATTTAGAAAGATATTCTTTTTAAGACATTAAATACGTTGACTATGCATTTAG
131 CCAACGATTAAGAATTTAGAAAGATATTCTTTTTAAGACATTAAATACGTTGACTATGCATTTAG
53149 GTGAAATCAAGAGGTATCAAGATTTAACGAATTGGGTTGGTGACCTGGTTTGAATAGAACCATCA
196 GTGAAATCAAGAGGTATCAAGATTTAACGAATTGGGTTGGTGACCTGGTTTGAATAGAACCATCA
53214 CAAAAATAGAAATTCGATTAGAATTGAATCATGAAAAAGAACCAATACAGATTTGAACTAGAGAA
261 CAAAAATAGAAATTCGATTAGAATTGAATCATGAAAAAGAACCAATACAGATTTGAACTAGAGAA
53279 ATCCAAAAACAGTGTAATAAAATGATTCCCCTAGTTGTAGTATTGTGGTAAACGCAAAAAGCCTT
326 ATCCAAAAACAGTGTAATAAAATGATTCCCCTAGTTGTAGTATTGTGGTAAACGCAAAAAGCCTT
53344 TAAATTCGAGGATGAATTTTCTTAAGGGGGAAGTGTAATACCCCAAATATCAGGTAAGGGACTAT
391 TAAATTCGAGGATGAATTTTCTTAAGGGGGAAGTGTAATACCCCAAATATCAGGTAAGGGACTAT
53409 ATTAAAAAATATTT
456 ATTAAAAAATATTT
53423 GAAATTTGAA
Statistics
Matches: 469, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
479 469 1.00
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (479 bp):
GATATGTCTTTTTGTAGAACGAAAAAGGGTCAAGAGAGTTTTGAAATACTATAAAGGATTGTAAT
AGAGACACCAGTGTTTATACAACTTGAGTTGGACAAAGAATTGGTGGTTTTTACTAATATATATC
CCAACGATTAAGAATTTAGAAAGATATTCTTTTTAAGACATTAAATACGTTGACTATGCATTTAG
GTGAAATCAAGAGGTATCAAGATTTAACGAATTGGGTTGGTGACCTGGTTTGAATAGAACCATCA
CAAAAATAGAAATTCGATTAGAATTGAATCATGAAAAAGAACCAATACAGATTTGAACTAGAGAA
ATCCAAAAACAGTGTAATAAAATGATTCCCCTAGTTGTAGTATTGTGGTAAACGCAAAAAGCCTT
TAAATTCGAGGATGAATTTTCTTAAGGGGGAAGTGTAATACCCCAAATATCAGGTAAGGGACTAT
ATTAAAAAATATTTTCTTAAGGGG
Found at i:54738 original size:58 final size:58
Alignment explanation
Indices: 54663--54878 Score: 342
Period size: 58 Copynumber: 3.7 Consensus size: 58
54653 TGGCAATAAG
* * *
54663 TGTGCAAAAATGTTAAGAAATTCATACTAAGAGTATGAATTTCCGTATTGGGAACTTTA
1 TGTGCAAAAA-GATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTA
* * *
54722 TGTGAAAAAAGATAAGAAATTTATACTAAGTGTATGAATTTTCGTATTGGGCACTTTA
1 TGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTA
*
54780 TGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCATATTGGGCACTTTA
1 TGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTA
* *
54838 TGTGCAAAAAGATAATAAACTCATACTAAGTGTATGAATTT
1 TGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTT
54879 TCGCATGGGA
Statistics
Matches: 145, Mismatches: 12, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
58 136 0.94
59 9 0.06
ACGTcount: A:0.39, C:0.10, G:0.18, T:0.34
Consensus pattern (58 bp):
TGTGCAAAAAGATAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTA
Found at i:55192 original size:45 final size:42
Alignment explanation
Indices: 55142--55364 Score: 199
Period size: 45 Copynumber: 5.5 Consensus size: 42
55132 ATAAAAGAAT
55142 AATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGATGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCC--AGATGA
* *
55187 AATGCATATGGGTGCATTGTCGGCAT-AAA-A-G--A-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCCAGATGA
* *
55221 AACGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCC--AGATGA
*
55266 AATGCATATGGGTGCATTATCGGCAT-AAA-A-G--A-AT--
1 AATGCATATGGGTGCATTATTGGCATGAAAGATGCCAGATGA
*
55300 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAA-GATGCC--AGATGA
55345 AATGCATATGGGTGCATTAT
1 AATGCATATGGGTGCATTAT
55365 CAACATAAAA
Statistics
Matches: 145, Mismatches: 11, Indels: 44
0.73 0.05 0.22
Matches are distributed among these distances:
34 48 0.33
35 6 0.04
36 3 0.02
37 4 0.03
38 2 0.01
41 2 0.01
42 4 0.03
43 2 0.01
44 6 0.04
45 68 0.47
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.28
Consensus pattern (42 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGATGCCAGATGA
Found at i:55218 original size:79 final size:79
Alignment explanation
Indices: 55132--55375 Score: 407
Period size: 79 Copynumber: 3.1 Consensus size: 79
55122 GAACAAATGA
*
55132 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAATGATGCCTTAGATGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGAAATGCATATG
*
55197 GGTGCATTGTCGGC
66 GGTGCATTATCGGC
* *
55211 ATAAAAGAATAACGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGAAATGCATATG
55276 GGTGCATTATCGGC
66 GGTGCATTATCGGC
** *
55290 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGAAATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGAAATGCATATG
**
55355 GGTGCATTATCAAC
66 GGTGCATTATCGGC
55369 ATAAAAG
1 ATAAAAG
55376 TATACTATAA
Statistics
Matches: 155, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
79 155 1.00
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGATGAAATGCATATG
GGTGCATTATCGGC
Found at i:55233 original size:34 final size:34
Alignment explanation
Indices: 55187--55330 Score: 135
Period size: 34 Copynumber: 3.9 Consensus size: 34
55177 CCTTAGATGA
*
55187 AATGCATATGGGTGCATTGTCGGCATAAAAGAAT
1 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* * *
55221 AACGCATATGGGTGCATTATTGGCATGAAAGGATGCCTTAGCT
1 AATGCATATGGGTGCATTATCGGCAT-AAA--A-G----A-AT
55264 GAAATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 --AATGCATATGGGTGCATTATCGGCATAAAAGAAT
* *
55300 AATGCATATGGGTGCATTATTGGCATGAAAG
1 AATGCATATGGGTGCATTATCGGCATAAAAG
55331 GATGCCAAAG
Statistics
Matches: 90, Mismatches: 9, Indels: 22
0.74 0.07 0.18
Matches are distributed among these distances:
34 52 0.58
35 3 0.03
36 1 0.01
37 2 0.02
38 1 0.01
41 1 0.01
42 2 0.02
43 1 0.01
44 3 0.03
45 24 0.27
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.27
Consensus pattern (34 bp):
AATGCATATGGGTGCATTATCGGCATAAAAGAAT
Found at i:55732 original size:29 final size:29
Alignment explanation
Indices: 55616--55726 Score: 168
Period size: 29 Copynumber: 3.8 Consensus size: 29
55606 TTAGATGAGC
*
55616 GGTTAAACACTGTTGAGGAAAAGATGAAT
1 GGTTAAACACTGTTGAGTAAAAGATGAAT
*
55645 GGTTAAACACTGTTGAGTAAAAGAGGAAT
1 GGTTAAACACTGTTGAGTAAAAGATGAAT
*
55674 GGTTAAACACTATTGAGTAAAAGATGAAT
1 GGTTAAACACTGTTGAGTAAAAGATGAAT
** *
55703 GGTTAAACTGTGTTAAGTAAAAGA
1 GGTTAAACACTGTTGAGTAAAAGA
55727 ATAATGAACT
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 74 1.00
ACGTcount: A:0.42, C:0.06, G:0.25, T:0.26
Consensus pattern (29 bp):
GGTTAAACACTGTTGAGTAAAAGATGAAT
Found at i:58594 original size:10 final size:10
Alignment explanation
Indices: 58579--58607 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
58569 TTTGTAATCA
58579 CCCCCACCCG
1 CCCCCACCCG
58589 CCCCCACCCG
1 CCCCCACCCG
58599 CCCCCACCC
1 CCCCCACCC
58608 CACAAAGTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.83, G:0.07, T:0.00
Consensus pattern (10 bp):
CCCCCACCCG
Found at i:59840 original size:30 final size:30
Alignment explanation
Indices: 59806--59902 Score: 76
Period size: 30 Copynumber: 3.2 Consensus size: 30
59796 AAATTAGATC
59806 AATAATGCAAACAAAATAATTAATTAGCAA
1 AATAATGCAAACAAAATAATTAATTAGCAA
* * * *
59836 AATAAGGC-ACCTTCAAATCGCAA--AATTAG-ATC
1 AATAATGCAAAC--AAAAT---AATTAATTAGCA-A
59868 AATAATGCAAACAAAATAATTAATTAGCAA
1 AATAATGCAAACAAAATAATTAATTAGCAA
59898 AATAA
1 AATAA
59903 GGCACCTTCA
Statistics
Matches: 49, Mismatches: 8, Indels: 20
0.64 0.10 0.26
Matches are distributed among these distances:
28 2 0.04
29 2 0.04
30 18 0.37
31 10 0.20
32 13 0.27
33 2 0.04
34 2 0.04
ACGTcount: A:0.56, C:0.13, G:0.08, T:0.23
Consensus pattern (30 bp):
AATAATGCAAACAAAATAATTAATTAGCAA
Found at i:59889 original size:62 final size:62
Alignment explanation
Indices: 59792--59915 Score: 248
Period size: 62 Copynumber: 2.0 Consensus size: 62
59782 ATTCTTTTAC
59792 CGCAAAATTAGATCAATAATGCAAACAAAATAATTAATTAGCAAAATAAGGCACCTTCAAAT
1 CGCAAAATTAGATCAATAATGCAAACAAAATAATTAATTAGCAAAATAAGGCACCTTCAAAT
59854 CGCAAAATTAGATCAATAATGCAAACAAAATAATTAATTAGCAAAATAAGGCACCTTCAAAT
1 CGCAAAATTAGATCAATAATGCAAACAAAATAATTAATTAGCAAAATAAGGCACCTTCAAAT
59916 TTATCTTGGA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.52, C:0.16, G:0.10, T:0.23
Consensus pattern (62 bp):
CGCAAAATTAGATCAATAATGCAAACAAAATAATTAATTAGCAAAATAAGGCACCTTCAAAT
Found at i:64577 original size:60 final size:60
Alignment explanation
Indices: 64477--64632 Score: 149
Period size: 60 Copynumber: 2.6 Consensus size: 60
64467 CATAACTCTC
* * * * * *
64477 ATTCTAAATTGGT-CTCGAAACTTTT-AAATATTTCATTTTCATTCCTAAAATAT-GACTATA
1 ATTCTAAATTGATCCTC-AAACTTTTGAACT-TTTCAATTTCATCCCCAAAATATAGAAT-TA
* * *
64537 ATTTTAAATT-AGTCCTTAAACTTTTGAACTTTTCAATTTCATCCCCAAAATATAGAATTT
1 ATTCTAAATTGA-TCCTCAAACTTTTGAACTTTTCAATTTCATCCCCAAAATATAGAATTA
*
64597 ATTCTAAATTGATCCTCAAACCTTTTGAACATTTCA
1 ATTCTAAATTGATCCTCAAA-CTTTTGAACTTTTCA
64633 TTTTTTTATC
Statistics
Matches: 78, Mismatches: 12, Indels: 11
0.77 0.12 0.11
Matches are distributed among these distances:
60 55 0.71
61 23 0.29
ACGTcount: A:0.35, C:0.17, G:0.06, T:0.42
Consensus pattern (60 bp):
ATTCTAAATTGATCCTCAAACTTTTGAACTTTTCAATTTCATCCCCAAAATATAGAATTA
Found at i:66539 original size:186 final size:186
Alignment explanation
Indices: 66212--66603 Score: 705
Period size: 186 Copynumber: 2.1 Consensus size: 186
66202 TTTTCTAATT
* * *
66212 TATATAA-AAATTAAATATTTTATAATTCAAAAAAACAGGTTATAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAGGTTACAATTAATTTAAATAATATATA
66276 ATTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
66341 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
131 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
* * *
66397 TATATAATATATTTAATATTTTTTAATTCAAAAAAATAGTTTACAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAGGTTACAATTAATTTAAATAATATATA
*
66462 ATTATAAAATAAAAATTTTATATAAAATTTTTAATTATTTAATATTGATTTAGGTTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
*
66527 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGTTGAGCCCATATGTTA
131 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
66583 TATATAATATATTTAATATTT
1 TATATAATATATTTAATATTT
66604 AAAATTTTAT
Statistics
Matches: 198, Mismatches: 8, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
185 7 0.04
186 191 0.96
ACGTcount: A:0.42, C:0.03, G:0.09, T:0.45
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAACAGGTTACAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAAATTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTTA
TTGGATCTTAAATTATTAATTGGGTTTTAAATGGTTTGGGCTGAGCCCATATGTTA
Found at i:67303 original size:15 final size:15
Alignment explanation
Indices: 67283--67316 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
67273 AGCTCCATAA
*
67283 TTATACTGCATTTAT
1 TTATACTGCATTAAT
67298 TTATACTGCATTAAT
1 TTATACTGCATTAAT
67313 TTAT
1 TTAT
67317 TGTAGATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.53
Consensus pattern (15 bp):
TTATACTGCATTAAT
Found at i:67564 original size:16 final size:16
Alignment explanation
Indices: 67517--67570 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
67507 TGGTTAATTT
*
67517 TTATTTTTATTAT-ATA
1 TTATTTATATTATGA-A
* *
67533 TATATATATATAATGAA
1 T-TATTTATATTATGAA
67550 TTATTTATATTATGAA
1 TTATTTATATTATGAA
67566 TTATT
1 TTATT
67571 AGATTTTATA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
16 19 0.61
17 11 0.35
18 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (16 bp):
TTATTTATATTATGAA
Found at i:68145 original size:27 final size:27
Alignment explanation
Indices: 68115--68174 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
68105 AGCTAGACCC
* *
68115 GACCCGAAAATTATACACCC-TCTACCT
1 GACCCAAAAAATATACACCCTTC-ACCT
68142 GACCCAAAAAATATACACCCTTCACCT
1 GACCCAAAAAATATACACCCTTCACCT
68169 GACCCA
1 GACCCA
68175 CCATTTTGAG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 28 0.93
28 2 0.07
ACGTcount: A:0.37, C:0.38, G:0.07, T:0.18
Consensus pattern (27 bp):
GACCCAAAAAATATACACCCTTCACCT
Found at i:68991 original size:3 final size:3
Alignment explanation
Indices: 68978--69010 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
68968 AAGTCGCATG
68978 ATT ATTT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT AT
69011 AAATTAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:70738 original size:60 final size:60
Alignment explanation
Indices: 70671--70783 Score: 149
Period size: 60 Copynumber: 1.9 Consensus size: 60
70661 ATTATAATTC
* *
70671 TCATTTTAATTTGA-TCCTTAAATTTTTAAATATTTTAATTTCAT-CTTCAAACTATTATTT
1 TCATTTTAAATT-ATTCCTTAAACTTTTAAATATTTTAATTTCATCCTT-AAACTATTATTT
** *
70731 TCATTTTAAATTATTCCTTAAACTTTTGGATATTTTAGTTTCATCCTTAAACT
1 TCATTTTAAATTATTCCTTAAACTTTTAAATATTTTAATTTCATCCTTAAACT
70784 TTGACACTCT
Statistics
Matches: 46, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
59 1 0.02
60 42 0.91
61 3 0.07
ACGTcount: A:0.30, C:0.13, G:0.04, T:0.53
Consensus pattern (60 bp):
TCATTTTAAATTATTCCTTAAACTTTTAAATATTTTAATTTCATCCTTAAACTATTATTT
Found at i:71087 original size:52 final size:53
Alignment explanation
Indices: 70981--71087 Score: 119
Period size: 52 Copynumber: 2.0 Consensus size: 53
70971 AATTGAAATG
* * * * *
70981 TTCAAAATGTTTGGGGATCAATTTAGAATGAAAGCCATAGTTTGGGGATGAAA
1 TTCAAAATGTTTGAGGATCAATTTAAAATGAAAGCCATAGTTTAGAGATAAAA
* * *
71034 TTCAAAA-GTTTGAGGA-CTAATTTAAAATGAGAGTCATAGTTTAGATATAAAA
1 TTCAAAATGTTTGAGGATC-AATTTAAAATGAAAGCCATAGTTTAGAGATAAAA
71086 TT
1 TT
71088 AAATCATTTA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
51 1 0.02
52 37 0.82
53 7 0.16
ACGTcount: A:0.39, C:0.07, G:0.21, T:0.33
Consensus pattern (53 bp):
TTCAAAATGTTTGAGGATCAATTTAAAATGAAAGCCATAGTTTAGAGATAAAA
Found at i:79594 original size:16 final size:15
Alignment explanation
Indices: 79573--79608 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
79563 TTATAAACGT
79573 TAATAATAACGAATAA
1 TAATAATAAC-AATAA
*
79589 TAATAATAACAATTA
1 TAATAATAACAATAA
79604 TAATA
1 TAATA
79609 TAAATAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (15 bp):
TAATAATAACAATAA
Found at i:81135 original size:29 final size:30
Alignment explanation
Indices: 81040--81115 Score: 93
Period size: 30 Copynumber: 2.5 Consensus size: 30
81030 CTATATATTA
* *
81040 TATATAAATTTCCAAAAAT-ACTTTAAAAAAC
1 TATAT-AATTTTCAAAAATGTCTTT-AAAAAC
81071 TATATAATTTTCAAAAATGTCTTTAAAAAC
1 TATATAATTTTCAAAAATGTCTTTAAAAAC
*
81101 CATATAATTTT-AAAA
1 TATATAATTTTCAAAA
81116 TCTGTTTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
29 4 0.10
30 28 0.68
31 9 0.22
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (30 bp):
TATATAATTTTCAAAAATGTCTTTAAAAAC
Found at i:81173 original size:39 final size:36
Alignment explanation
Indices: 81102--81365 Score: 218
Period size: 38 Copynumber: 7.1 Consensus size: 36
81092 TTTAAAAACC
* *
81102 ATATA-ATTTT-AAAATCTGTTTTAAATATTATATATT
1 ATATATATTTTCAAAA--TGTTTTAAAAACTATATATT
* *
81138 ATATATGTTTTCAAAATGTTTTTCAAAATATTATATATTTT
1 ATATATATTTTCAAAATG-TTTT-AAAA-ACTATATA--TT
* *
81179 ATATTTATTTTCAAAACGTTTTAAAAACTATATAATAT
1 ATATATATTTTCAAAATGTTTTAAAAACTATAT-AT-T
* *
81217 ATATATATTTTCAAAAATGTCTTGAAAACTATATATT
1 ATATATATTTTC-AAAATGTTTTAAAAACTATATATT
*
81254 ATATTTATTTTCAAAAATGTTTTAAAAAACTATATAATAT
1 ATATATATTTTC-AAAATGTTTT-AAAAACTATAT-AT-T
* * *
81294 ATAAATTTTTTCAAAATGTTTTAAAAACTATATATC
1 ATATATATTTTCAAAATGTTTTAAAAACTATATATT
* * *
81330 AT-T-TATTTTC--AAT-TTTTTAAAATTATATAAT
1 ATATATATTTTCAAAATGTTTTAAAAACTATATATT
81361 ATATA
1 ATATA
81366 AATAAAAAAC
Statistics
Matches: 190, Mismatches: 23, Indels: 33
0.77 0.09 0.13
Matches are distributed among these distances:
31 16 0.08
32 4 0.02
34 6 0.03
36 9 0.05
37 33 0.17
38 48 0.25
39 43 0.23
40 14 0.07
41 17 0.09
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.48
Consensus pattern (36 bp):
ATATATATTTTCAAAATGTTTTAAAAACTATATATT
Found at i:81211 original size:77 final size:76
Alignment explanation
Indices: 81119--81341 Score: 253
Period size: 77 Copynumber: 2.9 Consensus size: 76
81109 TTTAAAATCT
* * * *
81119 GTTTTAAATATTATAT-AT-TATATATGTTTTCAAAATGTTTTTCAAAATATTATATATTTTATA
1 GTTTTAAAAACTATATAATATATATATATTTTCAAAATGTTTTT-AAAA-ACTATATA--TTATA
81182 TTTATTTTC-AAAAC
62 TTTATTTTCAAAAAC
* *
81196 GTTTTAAAAACTATATAATATATATATATTTTCAAAAATG-TCTTGAAAACTATATATTATATTT
1 GTTTTAAAAACTATATAATATATATATATTTTC-AAAATGTTTTTAAAAACTATATATTATATTT
*
81260 ATTTTCAAAAAT
65 ATTTTCAAAAAC
* * *
81272 GTTTTAAAAAACTATATAATATATAAATTTTTTCAAAATG-TTTTAAAAACTATATA-T-CATTT
1 GTTTT-AAAAACTATATAATATATATATATTTTCAAAATGTTTTTAAAAACTATATATTATATTT
81334 ATTTTCAA
65 ATTTTCAA
81342 TTTTTTAAAA
Statistics
Matches: 129, Mismatches: 12, Indels: 13
0.84 0.08 0.08
Matches are distributed among these distances:
74 12 0.09
75 15 0.12
76 29 0.22
77 47 0.36
78 5 0.04
79 15 0.12
80 6 0.05
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (76 bp):
GTTTTAAAAACTATATAATATATATATATTTTCAAAATGTTTTTAAAAACTATATATTATATTTA
TTTTCAAAAAC
Found at i:81261 original size:75 final size:73
Alignment explanation
Indices: 81171--81369 Score: 244
Period size: 76 Copynumber: 2.7 Consensus size: 73
81161 CAAAATATTA
* *
81171 TATATTTTATATTTATTTTCAAAACGTTTTAAAAACTATATAATATATATATATTTTCAAAAATG
1 TATATATTATATTTATTTTCAAAA-GTTTTAAAAACTATATAATATATAAATATTTTC-AAAATG
*
81236 TCTTGAAAAC
64 TCTTAAAAAC
*
81246 TATATATTATATTTATTTTCAAAAATGTTTTAAAAAACTATATAATATATAAATTTTTTCAAAAT
1 TATATATTATATTTATTTTC-AAAA-GTTTT-AAAAACTATATAATATATAAATATTTTCAAAAT
*
81311 GTTTTAAAAAC
63 GTCTTAAAAAC
* * * *
81322 TATATA-T-CATTTATTTTC--AATTTTTTAAAATTATATAATATATAAATA
1 TATATATTATATTTATTTTCAAAAGTTTTAAAAACTATATAATATATAAATA
81370 AAAAACAAAT
Statistics
Matches: 111, Mismatches: 11, Indels: 10
0.84 0.08 0.08
Matches are distributed among these distances:
69 20 0.18
70 4 0.04
71 2 0.02
74 10 0.09
75 20 0.18
76 29 0.26
77 26 0.23
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (73 bp):
TATATATTATATTTATTTTCAAAAGTTTTAAAAACTATATAATATATAAATATTTTCAAAATGTC
TTAAAAAC
Found at i:82047 original size:165 final size:163
Alignment explanation
Indices: 81733--82744 Score: 1065
Period size: 165 Copynumber: 6.2 Consensus size: 163
81723 CAGATAGCTT
* * * *
81733 TTCTCGACTTAAGCTATGCTGCAAATAATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGT
1 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGT
* * *
81797 CTTTGGTTGGCGGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAG
66 C-TT--TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAG
81862 CGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCC
128 CGTAGTCGAACTCGAAGGTC-TT--TTGGCAGATAACCC
* * * * * **
81901 TTCTCGACTTAAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGTAATTGAACTCGGGGGT
1 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGT
* * * * * *
81966 C-TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCGAATGATGTACCGTT-GAGCTGAGCG
66 CTTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCC-TTGGAGCTGAGCG
* * * *
82029 CAGTCAAACTCAAAGGTCTTTTGTTGGCAGACAACCC
130 TAGTCGAACTCGAAGGTC--TT-TTGGCAGATAACCC
* * * * *
82066 TTCTAGACTTAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGGAGTCGAACTCGAAGGT
1 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGT
* * * * *
82130 CTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGA
66 CTTTTGG---CAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATG-CCTTGGAGCTGA
* * * *
82195 GTGTAATCGAATTCGAAGGTC-TTTGGCAGATAGCCC
127 GCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAACCC
*
82231 TTCTCGACTTAAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT
1 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGT
* * *
82295 CTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGTGCCATCGAAGCTGA
66 C-TT--TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCC-TTGGAGCTGA
* * ** *
82360 GTGTAATCGAACTCGGGGGTC-TTTGGCAGATAGCCC
127 GCGTAGTCGAACTCGAAGGTCTTTTGGCAGATAACCC
* * *
82396 TTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGAGCGTAGTCGAACTCAAAGGT
1 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGT
* *
82460 CTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAG
66 C--TT-TTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAG
* *
82525 CGTAGTCGAACTCGAAGGTCTTTTGGTC--A-CAGCC
128 CGTAGTCGAACTCGAAGGTCTTTTGG-CAGATAACCC
* * * *
82559 -T-T-G-----AGTTATGCTGCAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAAGGT
1 TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGT
* * * * *
82616 C-TTTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGT
66 CTTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGT
* * *
82680 AGTCGAACTCAAAGGTCTTTGGTTAGTAGATAACCC
131 AGTCGAACTCGAAGGTC-TT--TTGGCAGATAACCC
82716 TTCTCGACTTAAGTTATGCTGCAAATGAT
1 TTCTCGACTTAAGTTATGCTGCAAATGAT
82745 ATCTTAAAAA
Statistics
Matches: 712, Mismatches: 100, Indels: 67
0.81 0.11 0.08
Matches are distributed among these distances:
152 71 0.10
153 3 0.00
155 27 0.04
156 24 0.03
157 3 0.00
158 1 0.00
159 1 0.00
160 2 0.00
161 1 0.00
162 1 0.00
163 2 0.00
164 53 0.07
165 391 0.55
166 16 0.02
167 1 0.00
168 67 0.09
169 48 0.07
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (163 bp):
TTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTTGAAGCTGAGCGTAGTCGAACTCGAAGGT
CTTTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGT
AGTCGAACTCGAAGGTCTTTTGGCAGATAACCC
Found at i:82167 original size:249 final size:246
Alignment explanation
Indices: 81697--82744 Score: 1180
Period size: 249 Copynumber: 4.2 Consensus size: 246
81687 AGATGAATGA
* ** *
81697 AATCGAACTCGAAAAGTCTTTGTTGACAGATAGCTTTTCTCGACTTAAGCTATGCTGCAAATAAT
1 AATCGAACTCG-AAGGTCTTTG--G-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
*
81762 GTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCGGACAACCCTTCTAGACTT
62 GTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTT
81827 AAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGC
127 AAGTTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-T--C
*
81892 AGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGTGCCCTCGAAGCTGAGTGT
189 AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGT
* ** * *
81950 AATTGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCGAATGATGTAC
1 AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
* * *
82015 CGTT-GAGCTGAGCGCAGTCAAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAG
66 C-TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAG
*
82079 TTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCTTTTGGTCACAGA
130 TTGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGT--CAGA
* * * * *
82144 TAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATATGCCCTCGAAGCTGAGTGT
192 TAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGT
* *
82199 AATCGAATTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGC
1 AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
* *
82264 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGT
66 CTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGT
* * * * * * ** *
82329 TATGCTGCAAATGATGTGCCATCGAAGCTGAGTGTAATCGAACTCGGGGGTCTTTGG-CAGATAG
131 TGTGCTGCAAATGATATGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCAGATAA
* * * *
82393 CCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCGTTG-AGCTGAGCGT
195 CCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGT
* * * * * * *
82444 AGTCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGAT
1 AATCGAACTCGAAGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
* * *
82509 ATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TT--TTGGTC--AC-AGCC-T-T-G---
62 GTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGG-CAGACAACCCTTCTAGACT
* * * * * * *
82562 --AGTTATGCTGCAAATGATGTGCCCTCGAAGTTGAGTGTAATCGAACTCGAAGGTCTTTGG-CA
126 TAAGTTGTGCTGCAAATGATATG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCA
* * * * * *
82624 GATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGT
190 GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGT
* * * * *
82680 AGTCGAACTCAAAGGTCTTTGGTTAGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
1 AATCGAACTCGAAGGTCTTT-G---GCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGAT
82745 ATCTTAAAAA
Statistics
Matches: 708, Mismatches: 72, Indels: 47
0.86 0.09 0.06
Matches are distributed among these distances:
232 2 0.00
233 2 0.00
235 4 0.01
236 158 0.22
237 2 0.00
241 1 0.00
242 1 0.00
243 1 0.00
244 3 0.00
245 24 0.03
246 43 0.06
247 1 0.00
248 5 0.01
249 412 0.58
250 32 0.05
252 7 0.01
253 10 0.01
ACGTcount: A:0.25, C:0.20, G:0.26, T:0.29
Consensus pattern (246 bp):
AATCGAACTCGAAGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGC
CTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGCAGACAACCCTTCTAGACTTAAGT
TGTGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTCAGATAAC
CCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGT
Found at i:82548 original size:84 final size:84
Alignment explanation
Indices: 81699--82744 Score: 1033
Period size: 84 Copynumber: 12.8 Consensus size: 84
81689 ATGAATGAAA
* * * ** * *
81699 TCGAACTCGAAAAGTC-TTTGTTGACAGATAGCTTTTCTCGACTTAAGCTATGCTGCAAATAATG
1 TCGAACTCG-AAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
81763 TGCCTTGGAGCTGAGCGTAG
65 TGCCTTGGAGCTGAGCGTAG
* * * * * * *
81783 TCGAACTCAAAGGTCTTTGGTTGGCGGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
81848 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* *
81867 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * *
81932 GCCCTCGAAGCTGAGTGTAA
66 G-CCTTGGAGCTGAGCGTAG
* ** * * *
81952 TTGAACTCGGGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCGAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* *
82013 ACCGTT-GAGCTGAGCGCAG
66 GCC-TTGGAGCTGAGCGTAG
* * * * * *
82032 TCAAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
82097 GCCTTGGAGCTGAGCGGAG
66 GCCTTGGAGCTGAGCGTAG
* ** * * * * *
82116 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * *
82181 GCCCTCGAAGCTGAGTGTAA
66 G-CCTTGGAGCTGAGCGTAG
* *
82201 TCGAATTCGAAGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
82262 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* *
82281 TCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTAGACTTAAGTTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* * * *
82346 GCCATCGAAGCTGAGTGTAA
66 GCC-TTGGAGCTGAGCGTAG
** * *
82366 TCGAACTCGGGGGTC---T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
82427 GCCGTT-GAGCTGAGCGTAG
66 GCC-TTGGAGCTGAGCGTAG
* * * * *
82446 TCGAACTCAAAGGTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
82511 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * ** *
82530 TCGAACTCGAAGGTCTTTTG--GTC--A-CAGCC-T-T-GAGTT-A-TGCTGC--AAATGATG-T
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAA--ATGAT
* * * * * *
82582 G-CCCTCGAAGTTGAGTGTAA
64 GTGCCTTGGAGCTGAGCGTAG
* * *
82602 TCGAACTCGAAGGTC---T-TTGGCAGATAGCTCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
82663 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
* * * *
82682 TCGAACTCAAAGGTCTTTGGTTAGTAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
1 TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
82745 ATCTTAAAAA
Statistics
Matches: 775, Mismatches: 148, Indels: 78
0.77 0.15 0.08
Matches are distributed among these distances:
69 1 0.00
70 2 0.00
72 31 0.04
73 2 0.00
74 8 0.01
75 2 0.00
76 8 0.01
77 2 0.00
78 7 0.01
79 5 0.01
80 101 0.13
81 125 0.16
82 3 0.00
83 11 0.01
84 389 0.50
85 78 0.10
ACGTcount: A:0.24, C:0.20, G:0.26, T:0.30
Consensus pattern (84 bp):
TCGAACTCGAAGGTCTTTTGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:86186 original size:18 final size:19
Alignment explanation
Indices: 86146--86190 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
86136 AGTTAATGTG
86146 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
86165 AATGCAAAGAAAATAA-AA
1 AATGCAAAGAAAATAACAA
86183 AATGCAAA
1 AATGCAAA
86191 ATGTCTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
18 10 0.38
19 16 0.62
ACGTcount: A:0.69, C:0.09, G:0.11, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:86916 original size:21 final size:21
Alignment explanation
Indices: 86890--86937 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
86880 CACATGATAT
86890 CTACCCCGCATGCTTTAATTC
1 CTACCCCGCATGCTTTAATTC
86911 CTACCCCGCATGCTTTAATTC
1 CTACCCCGCATGCTTTAATTC
86932 CTACCC
1 CTACCC
86938 GGACATGATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.19, C:0.42, G:0.08, T:0.31
Consensus pattern (21 bp):
CTACCCCGCATGCTTTAATTC
Found at i:88009 original size:16 final size:15
Alignment explanation
Indices: 87988--88023 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
87978 TTATAAACGT
87988 TAATAATAACGAATAA
1 TAATAATAAC-AATAA
*
88004 TAATAATAACAATTA
1 TAATAATAACAATAA
88019 TAATA
1 TAATA
88024 TAAATAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.31
Consensus pattern (15 bp):
TAATAATAACAATAA
Found at i:89401 original size:19 final size:19
Alignment explanation
Indices: 89372--89430 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
89362 AAAAAAAAGT
*
89372 AAAAT-AAAATAAGTAATA
1 AAAATAAAAATAAATAATA
*
89390 AAAATAAAAATAATTAATA
1 AAAATAAAAATAAATAATA
* *
89409 ATAATAATAATAAAT-ATA
1 AAAATAAAAATAAATAATA
89427 AAAA
1 AAAA
89431 ACTATATAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
18 11 0.31
19 24 0.69
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.25
Consensus pattern (19 bp):
AAAATAAAAATAAATAATA
Found at i:89412 original size:3 final size:3
Alignment explanation
Indices: 89374--89421 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
89364 AAAAAAGTAA
* *
89374 AAT AA- AAT AAGT AAT AAA AAT AAA AAT AATT AAT AAT AAT AAT AAT
1 AAT AAT AAT AA-T AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT
89420 AA
1 AA
89422 ATATAAAAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:89575 original size:29 final size:30
Alignment explanation
Indices: 89481--89576 Score: 108
Period size: 30 Copynumber: 3.2 Consensus size: 30
89471 CTACATATTA
* *
89481 TATATAAATTTCCAAAAAT-ACTTTAAAAAAC
1 TATAT-AATTTTCAAAAATGTCTTT-AAAAAC
89512 TATATAATTTTCAAAAATGTCTTTAAAAAC
1 TATATAATTTTCAAAAATGTCTTTAAAAAC
* *
89542 CATATAATTTT-AAAAACTGT-TTTAAAAAT
1 TATATAATTTTCAAAAA-TGTCTTTAAAAAC
89571 TATATA
1 TATATA
89577 TTATATATGT
Statistics
Matches: 58, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
29 18 0.31
30 31 0.53
31 9 0.16
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (30 bp):
TATATAATTTTCAAAAATGTCTTTAAAAAC
Found at i:89614 original size:39 final size:36
Alignment explanation
Indices: 89543--89782 Score: 216
Period size: 38 Copynumber: 6.4 Consensus size: 36
89533 TTTAAAAACC
* *
89543 ATATA-ATTTTAAAAACTGTTTTAAAAATTATATATT
1 ATATATATTTTCAAAA-TGTTTTAAAAACTATATATT
* *
89579 ATATATGTTTTCAAAATGTTTTTCAAAAAATTATATATTTT
1 ATATATATTTTCAAAATG-TTTT--AAAAACTATATA--TT
* **
89620 ATATTTATTTTCAAAACATTTTAAAAACTATATAATAT
1 ATATATATTTTCAAAATGTTTTAAAAACTATAT-AT-T
* *
89658 ATATATATTTTCAAAAATGTCTTGAAAACTATATATT
1 ATATATATTTTC-AAAATGTTTTAAAAACTATATATT
* *
89695 ATATTTATTTTCAAAAACGTTTTAAAAAACTATATAATAT
1 ATATATATTTTC-AAAATGTTTT-AAAAACTATAT-AT-T
* * *
89735 ATAAATGTTTTCAAAATGTTTTAAAAACTATATATC
1 ATATATATTTTCAAAATGTTTTAAAAACTATATATT
89771 AT-T-TATTTTCAA
1 ATATATATTTTCAA
89783 TTTTTTTTAA
Statistics
Matches: 169, Mismatches: 23, Indels: 26
0.78 0.11 0.12
Matches are distributed among these distances:
34 8 0.05
36 9 0.05
37 36 0.21
38 45 0.27
39 41 0.24
40 14 0.08
41 16 0.09
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (36 bp):
ATATATATTTTCAAAATGTTTTAAAAACTATATATT
Found at i:89652 original size:77 final size:76
Alignment explanation
Indices: 89548--89782 Score: 270
Period size: 77 Copynumber: 3.1 Consensus size: 76
89538 AAACCATATA
* * *
89548 ATTTT-AAAAACTGTTTTAAAAATTATAT-AT-TATATATGTTTTCAAAATGTTTTTCAAAAAAT
1 ATTTTCAAAAAC-ATTTTAAAAACTATATAATATATATATGTTTTCAAAATGTTTTT--AAAAAC
89610 TATATATTTTATATTT
63 TATATA--TTATATTT
* * *
89626 ATTTTC-AAAACATTTTAAAAACTATATAATATATATATATTTTCAAAAATG-TCTTGAAAACTA
1 ATTTTCAAAAACATTTTAAAAACTATATAATATATATATGTTTTC-AAAATGTTTTTAAAAACTA
89689 TATATTATATTT
65 TATATTATATTT
* *
89701 ATTTTCAAAAACGTTTTAAAAAACTATATAATATATAAATGTTTTCAAAATG-TTTTAAAAACTA
1 ATTTTCAAAAACATTTT-AAAAACTATATAATATATATATGTTTTCAAAATGTTTTTAAAAACTA
*
89765 TATA-T-CATTT
65 TATATTATATTT
89775 ATTTTCAA
1 ATTTTCAA
89783 TTTTTTTTAA
Statistics
Matches: 139, Mismatches: 12, Indels: 16
0.83 0.07 0.10
Matches are distributed among these distances:
74 12 0.09
75 15 0.11
76 29 0.21
77 50 0.36
78 12 0.09
79 15 0.11
80 6 0.04
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (76 bp):
ATTTTCAAAAACATTTTAAAAACTATATAATATATATATGTTTTCAAAATGTTTTTAAAAACTAT
ATATTATATTT
Found at i:89702 original size:75 final size:75
Alignment explanation
Indices: 89612--89782 Score: 240
Period size: 76 Copynumber: 2.3 Consensus size: 75
89602 CAAAAAATTA
* *
89612 TATATTTTATATTTATTTTCAAAACATTTT-AAAAACTATATAATATATATATATTTTCAAAAAT
1 TATATATTATATTTATTTTCAAAACATTTTAAAAAACTATATAATATATAAATATTTTC-AAAAT
*
89676 GTCTTGAAAAC
65 GTCTTAAAAAC
* *
89687 TATATATTATATTTATTTTCAAAAACGTTTTAAAAAACTATATAATATATAAATGTTTTCAAAAT
1 TATATATTATATTTATTTTC-AAAACATTTTAAAAAACTATATAATATATAAATATTTTCAAAAT
*
89752 GTTTTAAAAAC
65 GTCTTAAAAAC
*
89763 TATATA-T-CATTTATTTTCAA
1 TATATATTATATTTATTTTCAA
89783 TTTTTTTTAA
Statistics
Matches: 87, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
73 2 0.02
74 10 0.11
75 20 0.23
76 29 0.33
77 26 0.30
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (75 bp):
TATATATTATATTTATTTTCAAAACATTTTAAAAAACTATATAATATATAAATATTTTCAAAATG
TCTTAAAAAC
Found at i:91695 original size:21 final size:20
Alignment explanation
Indices: 91654--91699 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
91644 AAAAATATTT
*
91654 TTTATTTTTACAAATAA-AAA
1 TTTATTTTTA-AAAAAATAAA
91674 TATTATTTTTAAAAAAATAAA
1 T-TTATTTTTAAAAAAATAAA
91695 TTTAT
1 TTTAT
91700 AGAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
20 10 0.43
21 13 0.57
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (20 bp):
TTTATTTTTAAAAAAATAAA
Found at i:92083 original size:28 final size:28
Alignment explanation
Indices: 92043--92099 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
92033 TTTTTTTAAT
* *
92043 ATTTTGGGGTTTTGTTATAATTGAGAAA
1 ATTTTAGGGTTTTGTTAGAATTGAGAAA
* *
92071 ATTTTAGGGTTTTTTTAGATTTGAGAAA
1 ATTTTAGGGTTTTGTTAGAATTGAGAAA
92099 A
1 A
92100 GTTTGAGATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.30, C:0.00, G:0.23, T:0.47
Consensus pattern (28 bp):
ATTTTAGGGTTTTGTTAGAATTGAGAAA
Found at i:96407 original size:17 final size:17
Alignment explanation
Indices: 96385--96425 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
96375 TTGAGTAAAA
96385 AATGAGTTATTTAAGTT
1 AATGAGTTATTTAAGTT
96402 AATGAGTTATTTAAGTT
1 AATGAGTTATTTAAGTT
*
96419 GATGAGT
1 AATGAGT
96426 CTTATTTTGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.34, C:0.00, G:0.22, T:0.44
Consensus pattern (17 bp):
AATGAGTTATTTAAGTT
Found at i:99786 original size:67 final size:67
Alignment explanation
Indices: 99664--99792 Score: 170
Period size: 67 Copynumber: 1.9 Consensus size: 67
99654 TACAAAGACT
* * *
99664 GCAGGTTCATTCGCTACTAGTAATTCATTGTATAGGTTCAACATTGACTCGTAATTCCTTATCTC
1 GCAGGTTCAGTCGCTACTAGTAATTCATTGAATAGGTTCAACACTGACTCGTAATTCCTTATCTC
99729 TG
66 TG
* * * * *
99731 GCAGGTTCAGTCGCTGCTGGTAATTCCTTGAATAGGTTCAGCACTGA-TTGATAATTCCTTAT
1 GCAGGTTCAGTCGCTACTAGTAATTCATTGAATAGGTTCAACACTGACTCG-TAATTCCTTAT
99793 GGACCTAAGG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
66 2 0.04
67 51 0.96
ACGTcount: A:0.23, C:0.20, G:0.19, T:0.37
Consensus pattern (67 bp):
GCAGGTTCAGTCGCTACTAGTAATTCATTGAATAGGTTCAACACTGACTCGTAATTCCTTATCTC
TG
Found at i:104023 original size:18 final size:17
Alignment explanation
Indices: 103984--104026 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
103974 ATTATATGGA
103984 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
104000 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
104018 TATTATTAT
1 TATTATTAT
104027 ATGTATATAT
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:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:107131 original size:15 final size:15
Alignment explanation
Indices: 107111--107148 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
107101 GAACATTTCA
107111 TGCATTCTTG-CATTT
1 TGCATT-TTGCCATTT
*
107126 TGCATTTTGCCTTTT
1 TGCATTTTGCCATTT
107141 TGCATTTT
1 TGCATTTT
107149 CATCTACAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 3 0.14
15 18 0.86
ACGTcount: A:0.11, C:0.18, G:0.13, T:0.58
Consensus pattern (15 bp):
TGCATTTTGCCATTT
Found at i:108343 original size:18 final size:17
Alignment explanation
Indices: 108329--108389 Score: 60
Period size: 18 Copynumber: 3.8 Consensus size: 17
108319 AATAAAAAGG
108329 GCAAAAAGAAAAAAAAA
1 GCAAAAAGAAAAAAAAA
108346 GC---AA-AAAAAAAAA
1 GCAAAAAGAAAAAAAAA
108359 GCAAAAA-AAGAACAAAAA
1 GCAAAAAGAA-AA-AAAAA
*
108377 GAAAAAAGAAAAA
1 GCAAAAAGAAAAA
108390 GGGACAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
13 11 0.30
14 2 0.05
16 4 0.11
17 5 0.14
18 13 0.35
19 2 0.05
ACGTcount: A:0.82, C:0.07, G:0.11, T:0.00
Consensus pattern (17 bp):
GCAAAAAGAAAAAAAAA
Found at i:108355 original size:13 final size:13
Alignment explanation
Indices: 108337--108389 Score: 67
Period size: 13 Copynumber: 4.2 Consensus size: 13
108327 GGGCAAAAAG
108337 AAAAAAAAAGCAA
1 AAAAAAAAAGCAA
108350 AAAAAAAAAGC-A
1 AAAAAAAAAGCAA
*
108362 AAAAAAGAA-CAA
1 AAAAAAAAAGCAA
108374 AAAGAAAAAAG-AA
1 AAA-AAAAAAGCAA
108387 AAA
1 AAA
108390 GGGACAAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 1 0.03
12 13 0.37
13 21 0.60
ACGTcount: A:0.85, C:0.06, G:0.09, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGCAA
Found at i:108359 original size:32 final size:33
Alignment explanation
Indices: 108322--108400 Score: 96
Period size: 30 Copynumber: 2.5 Consensus size: 33
108312 TAATCAGAAT
108322 AAAAAGGGCAAAAAGAA-AA-AAAAAGCAAAAAA-
1 AAAAAGGGCAAAAA-AAGAACAAAAAG-AAAAAAG
108354 AAAAA--GCAAAAAAAGAACAAAAAGAAAAAAG
1 AAAAAGGGCAAAAAAAGAACAAAAAGAAAAAAG
108385 AAAAAGGGACAAAAAA
1 AAAAAGGG-CAAAAAA
108401 CACATGCAAA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
29 2 0.05
30 15 0.37
31 11 0.27
32 5 0.12
33 1 0.02
34 7 0.17
ACGTcount: A:0.78, C:0.06, G:0.15, T:0.00
Consensus pattern (33 bp):
AAAAAGGGCAAAAAAAGAACAAAAAGAAAAAAG
Found at i:108364 original size:24 final size:24
Alignment explanation
Indices: 108331--108389 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
108321 TAAAAAGGGC
108331 AAAAAGAAAAAAA-AAGCAAAAA-A
1 AAAAAGAAAAAAAGAA-CAAAAAGA
108354 AAAAAGCAAAAAAAGAACAAAAAGA
1 AAAAAG-AAAAAAAGAACAAAAAGA
108379 AAAAAGAAAAA
1 AAAAAGAAAAA
108390 GGGACAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
23 6 0.18
24 18 0.55
25 9 0.27
ACGTcount: A:0.85, C:0.05, G:0.10, T:0.00
Consensus pattern (24 bp):
AAAAAGAAAAAAAGAACAAAAAGA
Found at i:109015 original size:22 final size:22
Alignment explanation
Indices: 108987--109030 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
108977 AGCTACCCCA
108987 TCAAACC-TTTGAGCATCAAATG
1 TCAAACCATTT-AGCATCAAATG
109009 TCAAACCATTTAGCATCAAATG
1 TCAAACCATTTAGCATCAAATG
109031 AACAAAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 18 0.86
23 3 0.14
ACGTcount: A:0.39, C:0.23, G:0.11, T:0.27
Consensus pattern (22 bp):
TCAAACCATTTAGCATCAAATG
Found at i:110028 original size:36 final size:36
Alignment explanation
Indices: 109981--110240 Score: 263
Period size: 36 Copynumber: 7.4 Consensus size: 36
109971 ATTGAAAACA
* *
109981 TTTCCCTTGAAATAAATTTCGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
110017 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* * *
110054 TTTCTCTTGAAATAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
110090 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
* *
110119 TTT-CTTTGAAACAAATTTCGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * * *
110154 TTT-CTTTGGAACTAAGTTTTGTCTCTCTTGAGACA-
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
110189 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
110225 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
110241 ATCTTTGAAT
Statistics
Matches: 185, Mismatches: 26, Indels: 26
0.78 0.11 0.11
Matches are distributed among these distances:
28 13 0.07
29 8 0.04
30 2 0.01
34 1 0.01
35 38 0.21
36 91 0.49
37 32 0.17
ACGTcount: A:0.27, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:110299 original size:65 final size:65
Alignment explanation
Indices: 110198--110372 Score: 224
Period size: 65 Copynumber: 2.6 Consensus size: 65
110188 ATTTCTCTTG
* ** * **
110198 AAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAATCTTTGAATTTATTTCCCCTA
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
* *
110263 AAACAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG-AA-ACAAAATCTTCAAATTTATTTCCCC
110328 TA
64 TA
* * *
110330 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACAA
1 AAACA-AATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAA
110373 CATATATCTT
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
65 31 0.33
66 6 0.06
67 31 0.33
68 27 0.28
ACGTcount: A:0.33, C:0.22, G:0.09, T:0.36
Consensus pattern (65 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAAATCTTCAAATTTATTTCCCCTA
Found at i:111136 original size:105 final size:105
Alignment explanation
Indices: 110975--111424 Score: 694
Period size: 105 Copynumber: 4.3 Consensus size: 105
110965 GCCATCCGCG
* * * *
110975 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACGCAAGTTCAACTTCACGACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
111040 GGGACCGCTGCTTGTCAACAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
111083 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
111148 ACCGCTGCTTGTCAACAACAACTTCCCAATCGCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
*
111188 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
111253 ACCGTTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
111293 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
111358 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGATTCA
66 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
** *
111393 ATTTCAACTTCACGGCGGAGGATATTGGACTC
1 ATTTCAACTTCACAACGAAGGATATTGGACTC
111425 TGAACAATGC
Statistics
Matches: 322, Mismatches: 20, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
100 36 0.11
101 2 0.01
102 1 0.00
103 2 0.01
104 2 0.01
105 254 0.79
106 3 0.01
108 22 0.07
ACGTcount: A:0.32, C:0.27, G:0.19, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
Found at i:112609 original size:18 final size:17
Alignment explanation
Indices: 112570--112612 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
112560 ATTATATGGA
112570 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
112586 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
112604 TATTATTAT
1 TATTATTAT
112613 ATTATATATA
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:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:113867 original size:24 final size:26
Alignment explanation
Indices: 113813--113870 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
113803 CCGGTGGAAC
*
113813 AAAGTAGGGTGCGCTCGGGGTTTCAG
1 AAAGTAGGGTGCGCTCGAGGTTTCAG
113839 AAAGTAGGGTGCGCTC-AGG-TTCAG
1 AAAGTAGGGTGCGCTCGAGGTTTCAG
*
113863 CAAGTAGG
1 AAAGTAGG
113871 CCCATCGAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 12 0.40
25 2 0.07
26 16 0.53
ACGTcount: A:0.24, C:0.16, G:0.40, T:0.21
Consensus pattern (26 bp):
AAAGTAGGGTGCGCTCGAGGTTTCAG
Found at i:114647 original size:267 final size:267
Alignment explanation
Indices: 114172--114701 Score: 970
Period size: 267 Copynumber: 2.0 Consensus size: 267
114162 TCGGGTCATT
* *
114172 GATAAGATGAACTCGAGTCGAGCGAGCGTTGAACGTATGTCTAGCCAAGCCAGTAAGTGTCTCTT
1 GATAAGATGAACTCGAGTCGAGCGAGCGATGAACGTATGTCTAGCCAAGCCAGTAAGTGTCTCAT
*
114237 AGGCCATATTGGCATTGAATTCCTACGGAATCTCAAGTAAAACAGTCAAATACACAAGATTCGTG
66 AGGCCATATTGGCATTGAATTCCTACGGAATCTCAAGTAAAACAATCAAATACACAAGATTCGTG
114302 ATATCTGTCACCAACCCCATAGTAAGATTAAATTCCAAAATAGACATTGAAAAATAATTTTCGCA
131 ATATCTGTCACCAACCCCATAGTAAGATTAAATTCCAAAATAGACATTGAAAAATAATTTTCGCA
* * *
114367 AAGTCGGAATGTAACGACATCGGGCAAATTAACATTAAGAAGATGATTTGGCGAAAAATTAAAAG
196 AAGTCGGAATGTAACGACATCGGACAAATTAACATTAAGAAGACGATTTGGCAAAAAATTAAAAG
114432 TGGTGTG
261 TGGTGTG
114439 GATAAGATGAACTCGAGTCGAGCGAGCGATGAACGTATGTCTAGCCAAGCCAGTAAGTGTCTCAT
1 GATAAGATGAACTCGAGTCGAGCGAGCGATGAACGTATGTCTAGCCAAGCCAGTAAGTGTCTCAT
*
114504 AGGCCATATTGGCATTGAATTCCTACGGAATCTCAAGTAAAACAATCAAATACACATGATTCGTG
66 AGGCCATATTGGCATTGAATTCCTACGGAATCTCAAGTAAAACAATCAAATACACAAGATTCGTG
**
114569 ATATCTGTCACCAACCCCATAGTAAGATTAAATTCTGAAATAGACATTGAAAAATAATTTTCGCA
131 ATATCTGTCACCAACCCCATAGTAAGATTAAATTCCAAAATAGACATTGAAAAATAATTTTCGCA
*
114634 AAGTCGGAATGTAACGACATCGGACGAATTAACATTAAGAAGACGATTTGGCAAAAAATTAAAAG
196 AAGTCGGAATGTAACGACATCGGACAAATTAACATTAAGAAGACGATTTGGCAAAAAATTAAAAG
114699 TGG
261 TGG
114702 CGTAAAATTT
Statistics
Matches: 253, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
267 253 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (267 bp):
GATAAGATGAACTCGAGTCGAGCGAGCGATGAACGTATGTCTAGCCAAGCCAGTAAGTGTCTCAT
AGGCCATATTGGCATTGAATTCCTACGGAATCTCAAGTAAAACAATCAAATACACAAGATTCGTG
ATATCTGTCACCAACCCCATAGTAAGATTAAATTCCAAAATAGACATTGAAAAATAATTTTCGCA
AAGTCGGAATGTAACGACATCGGACAAATTAACATTAAGAAGACGATTTGGCAAAAAATTAAAAG
TGGTGTG
Found at i:127722 original size:30 final size:32
Alignment explanation
Indices: 127675--127736 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 32
127665 TAAGTTTGCA
*
127675 CATCATTCAATATCTTAC-CTAACACACTCCTT
1 CATCATTCAATATCTTACAC-AACAAACTCCTT
127707 CATC-TTCAAT-TCTTACACAACAAACTCCTT
1 CATCATTCAATATCTTACACAACAAACTCCTT
127737 TCAGCTAACC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 17 0.61
31 7 0.25
32 4 0.14
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (32 bp):
CATCATTCAATATCTTACACAACAAACTCCTT
Done.