Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000100.1 Hibiscus syriacus cultivar Beakdansim tig00000183_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: 100971
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:8932 original size:21 final size:21
Alignment explanation
Indices: 8906--8955 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
8896 CATAGTGTAC
8906 CGATGCACTAACCCTATGCAT
1 CGATGCACTAACCCTATGCAT
8927 CGATGCACTAACCCTATGCAT
1 CGATGCACTAACCCTATGCAT
8948 CGATGCAC
1 CGATGCAC
8956 CATACGCTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.34, G:0.16, T:0.22
Consensus pattern (21 bp):
CGATGCACTAACCCTATGCAT
Found at i:10825 original size:16 final size:16
Alignment explanation
Indices: 10806--10856 Score: 61
Period size: 15 Copynumber: 3.2 Consensus size: 16
10796 AAAATAAAAA
10806 AATTTAAAGTTAGAGT
1 AATTTAAAGTTAGAGT
* *
10822 AA-TTAAACTAAGAGT
1 AATTTAAAGTTAGAGT
10837 AATTTGAAAGTTA-AGT
1 AATTT-AAAGTTAGAGT
10853 AATT
1 AATT
10857 AAATTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
15 13 0.45
16 11 0.38
17 5 0.17
ACGTcount: A:0.47, C:0.02, G:0.16, T:0.35
Consensus pattern (16 bp):
AATTTAAAGTTAGAGT
Found at i:12208 original size:74 final size:74
Alignment explanation
Indices: 12099--12257 Score: 302
Period size: 74 Copynumber: 2.2 Consensus size: 74
12089 TACTAATTAA
*
12099 TTTG-TTGGTTGTCTTAATTGAGAAATTTTAAATTTAAATTGAAATTTAAAACGTTCGATTCAAA
1 TTTGATTGGTTGTCTTAATTGAGAAAATTTAAATTTAAATTGAAATTTAAAACGTTCGATTCAAA
12163 TTACTTACC
66 TTACTTACC
12172 TTTGATTGGTTGTCTTAATTGAGAAAATTTAAATTTAAATTGAAATTTAAAACGTTCGATTCAAA
1 TTTGATTGGTTGTCTTAATTGAGAAAATTTAAATTTAAATTGAAATTTAAAACGTTCGATTCAAA
12237 TTACTTACC
66 TTACTTACC
12246 TTTGATTGGTTG
1 TTTGATTGGTTG
12258 AAAAATATCC
Statistics
Matches: 84, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
73 4 0.05
74 80 0.95
ACGTcount: A:0.33, C:0.09, G:0.14, T:0.44
Consensus pattern (74 bp):
TTTGATTGGTTGTCTTAATTGAGAAAATTTAAATTTAAATTGAAATTTAAAACGTTCGATTCAAA
TTACTTACC
Found at i:12328 original size:3 final size:3
Alignment explanation
Indices: 12311--12355 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
12301 AAAAAGAAAA
*
12311 AAT ATT AAT -AT AAT AAT AAT AAT AAT AAT AA- AAT AA- AAT AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
12354 AA
1 AA
12356 CAAAGAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
2 6 0.17
3 27 0.75
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:12339 original size:20 final size:19
Alignment explanation
Indices: 12302--12355 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 19
12292 ATAAATATGA
* *
12302 AAAAGAAAA-AATATTAAT
1 AAAATAAAATAATAATAAT
*
12320 ATAATAATAATAATAATAAT
1 AAAATAA-AATAATAATAAT
12340 AAAATAAAATAGATAA
1 AAAATAAAATA-ATAA
12356 CAAAGAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
18 5 0.17
19 6 0.21
20 18 0.62
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (19 bp):
AAAATAAAATAATAATAAT
Found at i:12387 original size:22 final size:23
Alignment explanation
Indices: 12320--12391 Score: 57
Period size: 22 Copynumber: 3.3 Consensus size: 23
12310 AAATATTAAT
* *
12320 ATAATAATA-ATAATAATAATAAA
1 ATAAAAATAGATAACAA-AATAAA
12343 AT-AAAATAGATAACAAAGA-AAA
1 ATAAAAATAGATAACAAA-ATAAA
12365 ATAAAAATTAG-TAA-AAAATAAA
1 ATAAAAA-TAGATAACAAAATAAA
12387 A-AAAA
1 ATAAAA
12392 TAAAAAAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
21 5 0.12
22 18 0.43
23 16 0.38
24 3 0.07
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.21
Consensus pattern (23 bp):
ATAAAAATAGATAACAAAATAAA
Found at i:12387 original size:23 final size:22
Alignment explanation
Indices: 12340--12388 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 22
12330 TAATAATAAT
*
12340 AAAATAAAATAGATAACAAAGA
1 AAAATAAAATAGATAAAAAAGA
*
12362 AAAATAAAAATTAG-TAAAAAATA
1 AAAAT-AAAA-TAGATAAAAAAGA
12385 AAAA
1 AAAA
12389 AAATAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 5 0.22
23 15 0.65
24 3 0.13
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (22 bp):
AAAATAAAATAGATAAAAAAGA
Found at i:19382 original size:3 final size:3
Alignment explanation
Indices: 19374--19414 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
19364 AAATATTAAA
19374 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
19415 ATAAATATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20378 original size:15 final size:15
Alignment explanation
Indices: 20358--20386 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20348 ATTAGGGTTT
20358 TTGCTCTCTCGATTA
1 TTGCTCTCTCGATTA
20373 TTGCTCTCTCGATT
1 TTGCTCTCTCGATT
20387 GTATGGAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.28, G:0.14, T:0.48
Consensus pattern (15 bp):
TTGCTCTCTCGATTA
Found at i:24340 original size:173 final size:173
Alignment explanation
Indices: 24051--24367 Score: 571
Period size: 173 Copynumber: 1.8 Consensus size: 173
24041 GGCGCTTGGT
24051 TTCAAATAGAGATGCCGATCTATGGCAGCCCAAGTCATCTTCCAACAGTCTAAGGCCTTTGGAGA
1 TTCAAATAGAGATGCCGATCTATGGCAGCCCAAGTCATCTTCCAACAGTCTAAGGCCTTTGGAGA
* * *
24116 GTCCGAGTACAGAGTTGTTATCTTTCAGAACAGTGGAAGAGGGGTTTTTGTCAAAGTCTCCTGTA
66 GTCCGAGTACAGAGTTGTTATCTTTCAAAACAGTGAAAGAGGGGTTTTTGTCAAAGTCTCCTATA
*
24181 ATGGATATTTCTGTTCATTCTAGTGAAAATATATTTCTGTTCA
131 ATAGATATTTCTGTTCATTCTAGTGAAAATATATTTCTGTTCA
* *
24224 TTCAAATAGAGATGTCTATCTATGGCAGCCCAAGTCATCTTCCAACAGTCTAAGGCCTTTGGAGA
1 TTCAAATAGAGATGCCGATCTATGGCAGCCCAAGTCATCTTCCAACAGTCTAAGGCCTTTGGAGA
*
24289 GTCCGAGTACAGAGTTGTTATCTTTCAAAACAGTGAAAGAGGGTTTTTTGTCAAAGTCTCCTATA
66 GTCCGAGTACAGAGTTGTTATCTTTCAAAACAGTGAAAGAGGGGTTTTTGTCAAAGTCTCCTATA
24354 ATAGATATTTCTGT
131 ATAGATATTTCTGT
24368 AGGGATATTT
Statistics
Matches: 137, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
173 137 1.00
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (173 bp):
TTCAAATAGAGATGCCGATCTATGGCAGCCCAAGTCATCTTCCAACAGTCTAAGGCCTTTGGAGA
GTCCGAGTACAGAGTTGTTATCTTTCAAAACAGTGAAAGAGGGGTTTTTGTCAAAGTCTCCTATA
ATAGATATTTCTGTTCATTCTAGTGAAAATATATTTCTGTTCA
Found at i:30817 original size:22 final size:23
Alignment explanation
Indices: 30792--30837 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
30782 TATACCTCGT
*
30792 TTTAAATTCT-AAATTTTAAAAA
1 TTTAAATTATAAAATTTTAAAAA
30814 TTTAAATTATAAAATTTTAAAAA
1 TTTAAATTATAAAATTTTAAAAA
30837 T
1 T
30838 AATATTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (23 bp):
TTTAAATTATAAAATTTTAAAAA
Found at i:30821 original size:15 final size:15
Alignment explanation
Indices: 30795--30834 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
30785 ACCTCGTTTT
*
30795 AAATTCTAAATTTTAA
1 AAATT-TAAATTATAA
30811 AAATTTAAATTATAA
1 AAATTTAAATTATAA
*
30826 AATTTTAAA
1 AAATTTAAA
30835 AATAATATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATTTAAATTATAA
Found at i:34631 original size:18 final size:19
Alignment explanation
Indices: 34603--34676 Score: 100
Period size: 18 Copynumber: 4.1 Consensus size: 19
34593 TCGAGGGATT
34603 ATAAGTGGTCCTTCGGGAC
1 ATAAGTGGTCCTTCGGGAC
* *
34622 ATAA-TGGTCCTCCGAGAC
1 ATAAGTGGTCCTTCGGGAC
34640 AT-AGTGGTCCTTCGGGAC
1 ATAAGTGGTCCTTCGGGAC
*
34658 A-AAGTGGTCATTCGGGAC
1 ATAAGTGGTCCTTCGGGAC
34676 A
1 A
34677 AATTTTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
17 1 0.02
18 43 0.90
19 4 0.08
ACGTcount: A:0.24, C:0.22, G:0.30, T:0.24
Consensus pattern (19 bp):
ATAAGTGGTCCTTCGGGAC
Found at i:38766 original size:18 final size:18
Alignment explanation
Indices: 38743--38813 Score: 88
Period size: 18 Copynumber: 3.9 Consensus size: 18
38733 AGGGATTATA
*
38743 AGTGGTCCTTTGGGACAT
1 AGTGGTCCTTCGGGACAT
* *
38761 AGTGGTCCTCCGGGGCAT
1 AGTGGTCCTTCGGGACAT
* * *
38779 AGTGGTCTTTCGGGATAA
1 AGTGGTCCTTCGGGACAT
38797 AGTGGTCCTTCGGGACA
1 AGTGGTCCTTCGGGACA
38814 AATTTTCAGT
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.17, C:0.20, G:0.35, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:39710 original size:21 final size:21
Alignment explanation
Indices: 39672--39722 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
39662 ACATAGTATT
39672 AAATAA-AAATAATAATAGAA
1 AAATAAGAAATAATAATAGAA
39692 AAATAAGAAAT-ATATATAGAA
1 AAATAAGAAATAATA-ATAGAA
*
39713 ATATATAGAA
1 AAATA-AGAA
39723 CAAAATATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 9 0.33
21 14 0.52
22 4 0.15
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.24
Consensus pattern (21 bp):
AAATAAGAAATAATAATAGAA
Found at i:40688 original size:35 final size:36
Alignment explanation
Indices: 40613--40708 Score: 122
Period size: 35 Copynumber: 2.6 Consensus size: 36
40603 GTGCTTGTGG
* * *
40613 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCATAGCAAAATTAT
*
40650 ATCCTATTTTAGGAG-TTGAATCATAGCAGAATTAT
1 ATCCTATTTTAGGAGTTTGAATCATAGCAAAATTAT
*
40685 ATCCTATTTTTGAGAGTTTGAATC
1 ATCCTATTTTAG-GAGTTTGAATC
40709 CTAGTAGGAC
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
35 27 0.52
36 11 0.21
37 14 0.27
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.39
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCATAGCAAAATTAT
Found at i:41814 original size:98 final size:98
Alignment explanation
Indices: 41664--42143 Score: 462
Period size: 105 Copynumber: 4.8 Consensus size: 98
41654 TGTTGACAAC
* * *
41664 CAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTATCTCGAGTCCAATATCCTTCGCTGTGAAG
1 CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
* *
41729 TTGAGATTGGCTCCGAAATTGCTTGTCGACAGT
66 TTGAAATTGGCTCCGAAATTGATTGTCGACAGT
* * * * *
41762 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTCCTGTCTTGGGTCCAATATCCTTCGTTGTGAAG
1 CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
* * *
41827 TTGAAATTAGC-CCTGAAACTGGGAAATTATTGTTGACA-T
66 TTGAAATTGGCTCC-GAAA-T------TGATTGTCGACAGT
* ** * * *
41866 ACAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGTTGTGAA
1 -CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAA
* * *
41931 GTTGAGATTGGCTCCAAAATTGTTTGTCGACAGT
65 GTTGAAATTGGCTCCGAAATTGATTGTCGACAGT
* * * * *
41965 CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGCCTTGGGTCCAATATCCTTCACTGTGAAG
1 CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
* * **
42030 TTGAAATTGGC-CCTGAAACTGGGAAATTATTGTTGACAAC
66 TTGAAATTGGCTCC-GAAA-T------TGATTGTCGACAGT
* * * *
42070 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCTCTGTGAAG
1 CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
*
42135 TCGAAATTG
66 TTGAAATTG
42144 ACTCTAGCTA
Statistics
Matches: 308, Mismatches: 55, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
97 4 0.01
98 146 0.47
99 3 0.01
104 2 0.01
105 151 0.49
106 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (98 bp):
CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCCTTCGCTGTGAAG
TTGAAATTGGCTCCGAAATTGATTGTCGACAGT
Found at i:41898 original size:105 final size:105
Alignment explanation
Indices: 41173--42143 Score: 748
Period size: 109 Copynumber: 9.3 Consensus size: 105
41163 AATATTGTTC
* * * ** * * * *
41173 CGAGTCTAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACCGAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATT-ATTGTTGACA
*
41238 GT-CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
65 -TACAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * *
41279 CGAGTCTAATATCCTTCGCTGTGAAGTTGAAATTGACTCTG-AAC---GAAA-TCTTGTTGACA-
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAT
* * * *
41338 ATCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 A-CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * **
41379 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGT-TTGTTGAC
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAA-CTGGGAAAT-TATTGTTGAC
* * * *
41443 A-ACCAGCCGTCCCTTCGTTGTGAAGTTTAACTTGTGTTGTCT
64 ATA-CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * * ** * *
41485 CGAGTGGCACGATATCCTCCGTCGTGGAGTTGAAA-TCGCGGATGAAACT-GAAAAGTTGTTCGT
1 CGAGT--C-CAATATCCTTCGTTGTGAAGTTGAAATTGGC-CCTGAAACTGGGAAA-TTATT-GT
* * * *
41548 TGACA-ACCAACCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
60 TGACATA-CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * * * * * *
41594 CGGGTAGCACGATATCCTCCGTCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTATTTGTTG
1 CGAGT--C-CAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTA-TTGTTG
* * *
41659 ACA-ACCAGCCGTCCCTTCGCTGTGAAGTTGAACTTGTGTTATCT
62 ACATA-CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * ** *
41703 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGATTGGCTCC-GAAA-T------TGCTTGTCGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC-CCTGAAACTGGGAAATTATTGTTGACA
* *
41760 GT-CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTCCTGTCT
65 -TACAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * *
41801 TGGGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCCCTGAAACTGGGAAATTATTGTTGACAT
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAT
* ** *
41866 ACAGCCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCT
66 ACAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * * * *
41906 CGAGTTCAATATCCTTCGTTGTGAAGTTGAGATTGGCTCC--AAAAT-TG----T-TTGTCGACA
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGC-CCTGAAACTGGGAAATTATTGTTGACA
* *
41963 GT-CAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGCCT
65 -TACAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
* * **
42004 TGGGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTATTGTTGACA-
1 CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAT
* * *
42068 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
66 A-CAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
*
42109 CGAGTCCAATATCCTTC-TCTGTGAAGTCGAAATTG
1 CGAGTCCAATATCCTTCGT-TGTGAAGTTGAAATTG
42144 ACTCTAGCTA
Statistics
Matches: 714, Mismatches: 107, Indels: 89
0.78 0.12 0.10
Matches are distributed among these distances:
97 4 0.01
98 150 0.21
99 8 0.01
100 82 0.11
101 3 0.00
102 4 0.01
103 1 0.00
104 6 0.01
105 153 0.21
106 119 0.17
107 8 0.01
108 8 0.01
109 160 0.22
110 8 0.01
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (105 bp):
CGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAT
ACAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGTCT
Found at i:41960 original size:203 final size:204
Alignment explanation
Indices: 41180--42148 Score: 1036
Period size: 203 Copynumber: 4.7 Consensus size: 204
41170 TTCCGAGTCT
* * * * * * **
41180 AATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACCGAGAAATTGTTTGTTGACAGTCAGCC
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATT-ATTGTTGACAACCAGCC
* * * * * *
41245 GCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCCTTCGCTGTGAAGTTGAA
65 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAA
* * * * * * * *
41310 ATTGACTCTGAACGAAAT-CTTGTTGACAATCAGTCGTCCCTTCGTTGTGAAGTTGAACTTGTGT
130 ATTGGCTCTCAA--AATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGC
*
41374 TGTCTCGAGTCC
193 TGTCTCGGGTCC
* * **
41386 AATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAAAAATGT-TTGTTGACAACCAGC
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-CTGGGAAAT-TATTGTTGACAACCAGC
* * * * *
41450 CGTCCCTTCGTTGTGAAGTTTAACTTGTGTTGTCTCGAGTGGCACGATATCCTCCGTCGTGGAGT
64 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGT--C-CAATATCCTTCGTTGTGAAGT
* * * * * * * *
41515 TGAAATCGCGGATGAAACTGAAAAGTTG-TTCGTTGACAACCAACCGTCCCTTCGTTGTGAAGTT
126 TGAAAT--TGGCT----CTCAAAA-TTGCTT-GTCGACAATCAGCCGCCCCTTCGCTGTGAAGTT
*
41579 GAACTTGTGTTGTCTCGGGTAGCAC
183 GAACTTGTGCTGTCTCGGGT--C-C
* * * * * *
41604 GATATCCTCCG-TCGTGGAGTTGAAATCGGCTCTGGAATTGGGAAATTATTTGTTGACAACCAGC
1 AATATCCTTCGCT-GTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTA-TTGTTGACAACCAGC
* * *
41668 CGTCCCTTCGCTGTGAAGTTGAACTTGTGTTATCTCGAGTCCAATATCCTTCGCTGTGAAGTTGA
64 CGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGA
* * * * *
41733 GATTGGCTC-CGAAATTGCTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTCCT
129 AATTGGCTCTCAAAATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCT
*
41797 GTCTTGGGTCC
194 GTCTCGGGTCC
* * *
41808 AATATCCTTCGTTGTGAAGTTGAAATTAGCCCTGAAACTGGGAAATTATTGTTGACATA-CAGCC
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTGTTGACA-ACCAGCC
* * *
41872 GTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAGTTCAATATCCTTCGTTGTGAAGTTGAG
65 GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAA
* * *
41937 ATTGGCTC-CAAAATTGTTTGTCGACAGTCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTG
130 ATTGGCTCTCAAAATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTG
* *
42001 CCTTGGGTCC
195 TCTCGGGTCC
* *
42011 AATATCCTTCACTGTGAAGTTGAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAACCAGCCG
1 AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTGTTGACAACCAGCCG
*
42076 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTC-TCTGTGAAGTCGAA
66 TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGT-TGTGAAGTTGAA
*
42140 ATTGACTCT
130 ATTGGCTCT
42149 AGCTAAAACC
Statistics
Matches: 653, Mismatches: 84, Indels: 54
0.83 0.11 0.07
Matches are distributed among these distances:
202 2 0.00
203 269 0.41
204 40 0.06
205 2 0.00
206 81 0.12
207 52 0.08
208 7 0.01
209 22 0.03
211 2 0.00
213 5 0.01
214 3 0.00
215 75 0.11
216 2 0.00
217 9 0.01
218 82 0.13
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (204 bp):
AATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTATTGTTGACAACCAGCCG
TCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAA
TTGGCTCTCAAAATTGCTTGTCGACAATCAGCCGCCCCTTCGCTGTGAAGTTGAACTTGTGCTGT
CTCGGGTCC
Found at i:42722 original size:104 final size:102
Alignment explanation
Indices: 42538--42773 Score: 246
Period size: 104 Copynumber: 2.3 Consensus size: 102
42528 ATTTTGTTTT
* * * * *
42538 AAGA-AAAACTGTCTCAAGAGAGATAAAACTTAGTTCCAAAAGAAATTGTCTCACGGGGAGATGA
1 AAGAGAAAACTGTCTCAAG-GAGACAAAATTTAGTTCCAAAAGAAATTGTCTCACAGAGAGACGA
42602 AATTAGTTCCAAGGAAAACATATTCAAAGATGATGCTTC
65 AATTAGTTCCAAGG-AAACATATTCAAAGATGATGCTTC
* * *
42641 AAGAGAAAACTGTCTCAATGGAGACAAAATTTTGTTTCAAGAGAAATTGTCTCA-AGAGAGACGA
1 AAGAGAAAACTGTCTCAA-GGAGACAAAATTTAGTTCCAAAAGAAATTGTCTCACAGAGAGACGA
* ** * * * * *
42705 AATTCA-TTTCAAGGGAAATGTTTTCAATGTTTATGTTTC
65 AATT-AGTTCCAA-GGAAACATATTCAAAGATGATGCTTC
42744 AAGAG-AAACTGTCTCAAGGGAGACAAAATT
1 AAGAGAAAACTGTCTCAA-GGAGACAAAATT
42774 CATTTCAAGG
Statistics
Matches: 112, Mismatches: 17, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
102 24 0.21
103 42 0.38
104 45 0.40
105 1 0.01
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.26
Consensus pattern (102 bp):
AAGAGAAAACTGTCTCAAGGAGACAAAATTTAGTTCCAAAAGAAATTGTCTCACAGAGAGACGAA
ATTAGTTCCAAGGAAACATATTCAAAGATGATGCTTC
Found at i:42777 original size:65 final size:65
Alignment explanation
Indices: 42673--42853 Score: 308
Period size: 65 Copynumber: 2.8 Consensus size: 65
42663 GACAAAATTT
* * *
42673 TGTTTCAAGAGAAATTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
42738 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
**
42803 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAA
1 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAA-TTCATTTCAAGGGAAA
42854 CTATCTCAAG
Statistics
Matches: 110, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
65 96 0.87
66 14 0.13
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:42844 original size:102 final size:102
Alignment explanation
Indices: 42738--43093 Score: 604
Period size: 102 Copynumber: 3.5 Consensus size: 102
42728 TCAATGTTTA
* * *
42738 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
42803 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
42840 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
42905 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* *
42942 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
43007 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
* * * **
43044 TGTTTCCAGGGAAACTGTCTCAAGAGAGACAAAGTTTGTTTCAAGGGAAA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAA
43094 CTGTCTCAAG
Statistics
Matches: 241, Mismatches: 13, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
102 241 1.00
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:42854 original size:37 final size:36
Alignment explanation
Indices: 42803--43111 Score: 238
Period size: 37 Copynumber: 8.9 Consensus size: 36
42793 TCAATGTTTA
* *
42803 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
*
42840 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * *
42876 CATTTCAAGGGAAA-TGTTTTC-A-A-TG-----TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* *
42904 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA-TT
* *
42942 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
** * * **
42978 CATTTCAAGGGAAA-TGTTTTC-A-A-TG--TTAA--
1 TGTTTCAAGGGAAACTG-TCTCAAGAGAGACAAAATT
* * *
43007 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAAATT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAG-ACAAAATT
* *
43044 TGTTTCCAGGGAAACTGTCTCAAGAGAGACAAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
43080 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
43112 TGGTGAGCAC
Statistics
Matches: 209, Mismatches: 41, Indels: 45
0.71 0.14 0.15
Matches are distributed among these distances:
28 2 0.01
29 28 0.13
30 6 0.03
31 2 0.01
32 2 0.01
33 2 0.01
34 2 0.01
35 6 0.03
36 70 0.33
37 87 0.42
38 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
Found at i:42923 original size:167 final size:169
Alignment explanation
Indices: 42638--42955 Score: 559
Period size: 167 Copynumber: 1.9 Consensus size: 169
42628 AAGATGATGC
* * *
42638 TTCAAGAGAAAACTGTCTCAATGGAGACAAAATTTTGTTTCAAGAGAAATTGTCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
*
42703 GAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
42768 AAAA-TTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
131 AAAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
*
42806 TTCAAGAG-AAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTCAAGAGAGAC
1 TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
42870 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
66 AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
**
42935 AAAATTTTGTTTCAAGGGAAA
131 AAAATTTCATTTCAAGGGAAA
42956 CTATCTCAAG
Statistics
Matches: 142, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
167 120 0.85
168 22 0.15
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (169 bp):
TTCAAGAGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGAGAAACTATCTCAAGAGAGAC
AAAATTCATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGAC
AAAATTTCATTTCAAGGGAAATGTTTTCAATGTTTATGT
Found at i:43999 original size:22 final size:22
Alignment explanation
Indices: 43974--44024 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
43964 TTGTGTTTGG
43974 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
43996 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
44018 TCAAAGG
1 TCAAAGG
44025 ATTGATGGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.25, C:0.12, G:0.27, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:44656 original size:13 final size:13
Alignment explanation
Indices: 44640--44690 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
44630 CCCTTTTTTA
*
44640 TTTTTGTTCTTTCT
1 TTTTTGTTC-TTGT
44654 TTTTTGTTCTTGT
1 TTTTTGTTCTTGT
*
44667 TTTTTTTTCTTGT
1 TTTTTGTTCTTGT
*
44680 TTTTTCTTCTT
1 TTTTTGTTCTT
44691 TTGCTTCTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 25 0.74
14 9 0.26
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (13 bp):
TTTTTGTTCTTGT
Found at i:44670 original size:27 final size:26
Alignment explanation
Indices: 44640--44715 Score: 70
Period size: 23 Copynumber: 3.0 Consensus size: 26
44630 CCCTTTTTTA
*
44640 TTTTTGTTCTTTCTTTTTTGTTCTTG
1 TTTTTTTTCTTTCTTTTTTGTTCTTG
*
44666 --TTTTTT-TTTCTTGTTTT-TTCTTC
1 TTTTTTTTCTTTCTT-TTTTGTTCTTG
**
44689 TTTTGCTTCTTTTCTTTTTTGTTCTTG
1 TTTTTTTTC-TTTCTTTTTTGTTCTTG
44716 ATTGGATCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 11
0.71 0.09 0.20
Matches are distributed among these distances:
23 11 0.28
24 9 0.23
25 4 0.10
26 4 0.10
27 11 0.28
ACGTcount: A:0.00, C:0.13, G:0.09, T:0.78
Consensus pattern (26 bp):
TTTTTTTTCTTTCTTTTTTGTTCTTG
Found at i:44686 original size:23 final size:23
Alignment explanation
Indices: 44649--44714 Score: 71
Period size: 27 Copynumber: 2.7 Consensus size: 23
44639 ATTTTTGTTC
*
44649 TTTCTTTTTTGTTCTTGTTTTTT
1 TTTCTTTTTTGTTCTTCTTTTTT
44672 TTTCTTGTTTT-TTCTTCTTTTGCTTCT
1 TTTCTT-TTTTGTTCTTC-TTT--TT-T
44699 TTTCTTTTTTGTTCTT
1 TTTCTTTTTTGTTCTT
44715 GATTGGATCT
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
23 11 0.31
24 7 0.19
26 6 0.17
27 12 0.33
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.79
Consensus pattern (23 bp):
TTTCTTTTTTGTTCTTCTTTTTT
Found at i:44701 original size:19 final size:18
Alignment explanation
Indices: 44649--44714 Score: 63
Period size: 16 Copynumber: 3.9 Consensus size: 18
44639 ATTTTTGTTC
*
44649 TTTCTTTTTTG-TTCTTG
1 TTTCTTTTTTGCTTCTTT
*
44666 TTT-TTTTTT-CTTGTTT
1 TTTCTTTTTTGCTTCTTT
44682 TTTCTTCTTTTGCTTC--T
1 TTTCTT-TTTTGCTTCTTT
44699 TTTCTTTTTTG-TTCTT
1 TTTCTTTTTTGCTTCTT
44715 GATTGGATCT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
15 3 0.08
16 18 0.45
17 12 0.30
18 4 0.10
19 3 0.08
ACGTcount: A:0.00, C:0.14, G:0.08, T:0.79
Consensus pattern (18 bp):
TTTCTTTTTTGCTTCTTT
Found at i:44703 original size:17 final size:15
Alignment explanation
Indices: 44640--44714 Score: 73
Period size: 15 Copynumber: 4.7 Consensus size: 15
44630 CCCTTTTTTA
44640 TTTTTGTTC-TTTCT
1 TTTTTGTTCTTTTCT
*
44654 TTTTTGTTCTTGTTTTTT
1 TTTTTGTTC---TTTTCT
44672 TTTCTTGTT-TTTTCT
1 TTT-TTGTTCTTTTCT
44687 TCTTTTGCTTCTTTTCT
1 T-TTTTG-TTCTTTTCT
44704 TTTTTGTTCTT
1 TTTTTGTTCTT
44715 GATTGGATCT
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
14 9 0.18
15 14 0.27
16 9 0.18
17 7 0.14
18 7 0.14
19 5 0.10
ACGTcount: A:0.00, C:0.13, G:0.08, T:0.79
Consensus pattern (15 bp):
TTTTTGTTCTTTTCT
Found at i:47763 original size:21 final size:21
Alignment explanation
Indices: 47734--47783 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
47724 ACATAGTAGT
47734 AATAA-AAATAATA-ATAGAAA
1 AATAAGAAAT-ATATATAGAAA
47754 AATAAGAAATATATATAGAAA
1 AATAAGAAATATATATAGAAA
*
47775 TATATAGAA
1 AATA-AGAA
47784 CAAAATATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 8 0.31
21 14 0.54
22 4 0.15
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (21 bp):
AATAAGAAATATATATAGAAA
Found at i:47954 original size:2 final size:2
Alignment explanation
Indices: 47947--47993 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
47937 GTATACTTAA
47947 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
47989 AT AT A
1 AT AT A
47994 CTAATATTAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:48735 original size:35 final size:36
Alignment explanation
Indices: 48665--48760 Score: 131
Period size: 35 Copynumber: 2.6 Consensus size: 36
48655 GTGCTTGTGG
* *
48665 ATCCTATCTTTAGGAGTTTAAAACATAGCAAAATTCT
1 ATCCTAT-TTTAGGAGTTTGAATCATAGCAAAATTCT
*
48702 ATCCTATTTTAGGAG-TTGAATCATAGCAGAATTCT
1 ATCCTATTTTAGGAGTTTGAATCATAGCAAAATTCT
*
48737 ATCCTATTTTTGAGAGTTTGAATC
1 ATCCTATTTTAG-GAGTTTGAATC
48761 CTAGTAGGAC
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
35 28 0.53
36 11 0.21
37 14 0.26
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.39
Consensus pattern (36 bp):
ATCCTATTTTAGGAGTTTGAATCATAGCAAAATTCT
Found at i:55202 original size:32 final size:33
Alignment explanation
Indices: 55161--55238 Score: 108
Period size: 32 Copynumber: 2.4 Consensus size: 33
55151 ACCGTGAGCT
55161 AATAAAATTCAAAGT-CATC-TTTCCGGGATAGA
1 AATAAAATTCAAAGTACATCATTT-CGGGATAGA
* *
55193 AATAAAATTCAAA-TATATCATTTGGGGATAGA
1 AATAAAATTCAAAGTACATCATTTCGGGATAGA
55225 AATAAAATTCAAAG
1 AATAAAATTCAAAG
55239 CTTTGATTGT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
31 1 0.02
32 37 0.90
33 3 0.07
ACGTcount: A:0.47, C:0.10, G:0.14, T:0.28
Consensus pattern (33 bp):
AATAAAATTCAAAGTACATCATTTCGGGATAGA
Found at i:55941 original size:20 final size:22
Alignment explanation
Indices: 55890--55942 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
55880 AAAAACGTGC
55890 CACAAAGACAGAGATAAATGTA
1 CACAAAGACAGAGATAAATGTA
* *
55912 CCATAAAGACAGAGA-ACATGT-
1 -CACAAAGACAGAGATAAATGTA
55933 CACAAAGACA
1 CACAAAGACA
55943 TAATTATTCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.33
22 5 0.19
23 13 0.48
ACGTcount: A:0.53, C:0.19, G:0.17, T:0.11
Consensus pattern (22 bp):
CACAAAGACAGAGATAAATGTA
Found at i:57114 original size:30 final size:28
Alignment explanation
Indices: 57050--57114 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
57040 TAAAGACCCA
**
57050 ATTTTTTTCATACTTATTATTAGGGTTT
1 ATTTTTTTCATACTTATTATTAGGGCAT
*
57078 AATTTTTTT-AGTATTTATTATTAAGGGCAT
1 -ATTTTTTTCA-TACTTATTATT-AGGGCAT
57108 ATTTTTT
1 ATTTTTT
57115 AAAATTTATT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 1 0.03
29 25 0.81
30 5 0.16
ACGTcount: A:0.25, C:0.05, G:0.11, T:0.60
Consensus pattern (28 bp):
ATTTTTTTCATACTTATTATTAGGGCAT
Found at i:57138 original size:17 final size:16
Alignment explanation
Indices: 57109--57142 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
57099 TAAGGGCATA
57109 TTTTTTAAAATTTATT
1 TTTTTTAAAATTTATT
*
57125 TTTTTCTAATATTTATT
1 TTTTT-TAAAATTTATT
57142 T
1 T
57143 GTTGTTATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTTTAAAATTTATT
Found at i:58489 original size:25 final size:26
Alignment explanation
Indices: 58456--58506 Score: 61
Period size: 25 Copynumber: 2.0 Consensus size: 26
58446 TACATAATTG
*
58456 AAAGAAAAT-TTATTAAAATTTAAAAT
1 AAAGAAAATATAATT-AAATTTAAAAT
*
58482 AAAG-AAATATAATTAAATTTCAAAT
1 AAAGAAAATATAATTAAATTTAAAAT
58507 GTTTTGAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (26 bp):
AAAGAAAATATAATTAAATTTAAAAT
Found at i:58644 original size:39 final size:39
Alignment explanation
Indices: 58539--58644 Score: 124
Period size: 39 Copynumber: 2.7 Consensus size: 39
58529 TTTAAAAAAT
* ** *
58539 AATTTAGAACATTAATGTGAACTAATTTAAGAAATTAAG
1 AATTTAGAACGTTAGGGTGAAATAATTTAAGAAATTAAG
* *
58578 AATTTAGAACGTTATGGTGTAAA-AATTTAAGAAATTAGG
1 AATTTAGAACGTTAGGGTG-AAATAATTTAAGAAATTAAG
* *
58617 ATTTTAGAATGTTAGGGTGAAATAATTT
1 AATTTAGAACGTTAGGGTGAAATAATTT
58645 GAGGATTATG
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
38 3 0.05
39 52 0.91
40 2 0.04
ACGTcount: A:0.43, C:0.03, G:0.18, T:0.36
Consensus pattern (39 bp):
AATTTAGAACGTTAGGGTGAAATAATTTAAGAAATTAAG
Found at i:60067 original size:208 final size:207
Alignment explanation
Indices: 59681--60285 Score: 935
Period size: 208 Copynumber: 2.9 Consensus size: 207
59671 ATTTTATGAA
* * * * **
59681 AAATACAAATTT-AAGAATTAAATCGAACAAATATTAAACTACAAATTAAAATAAAAATAAATTA
1 AAATA-AAATTTGGAGAATTAAATTGAACAAATATGAAATTACAAA-TAAAATTTAAATAAATTA
*
59745 AACAACACACATTGATGAGGGATCAAGTCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACA
64 AAC-A-ACACA---A--AGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATAC-
*
59810 AAAAAATACTAAATTATACCCATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATA
121 AAAAAATACTAAATTATACCTATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATA
*
59875 AGTATGGGTCAATTTCATATAC
186 AGTATGGGTCAATTTCAGATAC
*
59897 AAATAAAATTTGGAGGATTAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAA
1 AAATAAAATTTGGAGAATTAAATTGAACAAATATGAAATTACAAAT-AAAATTTAAATAAATTAA
* *
59962 ACAACACAAAGGGATCAAATCGAAATAATTTTAAATTGTGAGATTGAAATTAATACAAAAAGTAC
65 ACAACACAAAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAATAC
60027 TAAATTATACCTATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGT
130 TAAATTATACCTATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGT
*
60092 CAATTTTAGATAC
195 CAATTTCAGATAC
*
60105 AAATAAAATTTGGAGAACTAAATTGAACAAATATGAAATTACAAATAAAATATTAAATAAATTAA
1 AAATAAAATTTGGAGAATTAAATTGAACAAATATGAAATTACAAATAAAAT-TTAAATAAATTAA
*
60170 ACAACACAAAGGGATCAAATCGAAATAATTTTAAATTATGAGGTTGAAATTAATACAAAAAATAC
65 ACAACACAAAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAATAC
*
60235 TAAATTATA-CTCATTTAAAAAGTTATGGGCCAATTAAAAAATATAAATAAG
130 TAAATTATACCT-ATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAG
60286 CCTCTCTTTT
Statistics
Matches: 366, Mismatches: 19, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
207 7 0.02
208 249 0.68
209 45 0.12
211 1 0.00
214 5 0.01
215 8 0.02
216 51 0.14
ACGTcount: A:0.52, C:0.08, G:0.11, T:0.28
Consensus pattern (207 bp):
AAATAAAATTTGGAGAATTAAATTGAACAAATATGAAATTACAAATAAAATTTAAATAAATTAAA
CAACACAAAGGGATCAAATCGAAATAATTTTAAATTGTGAGGTTGAAATTAATACAAAAAATACT
AAATTATACCTATTTAAAAAGTTATGGGCCAATTAAAAAATAGAAATAAGTAATAAGTATGGGTC
AATTTCAGATAC
Found at i:60470 original size:13 final size:13
Alignment explanation
Indices: 60452--60494 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
60442 TAATTTACTT
60452 TATATAGTTTATA
1 TATATAGTTTATA
*
60465 TATATAGGTTATA
1 TATATAGTTTATA
60478 TATATAGTTTATA
1 TATATAGTTTATA
60491 TATA
1 TATA
60495 CTATACATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:60499 original size:20 final size:21
Alignment explanation
Indices: 60475--60525 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
60465 TATATAGGTT
*
60475 ATATATATAGTTTATATATAC
1 ATATATATAGTTTATACATAC
* *
60496 -TATACATGGTTTATACATAC
1 ATATATATAGTTTATACATAC
60516 ATATTATATA
1 ATA-TATATA
60526 AAATTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (21 bp):
ATATATATAGTTTATACATAC
Found at i:60915 original size:21 final size:21
Alignment explanation
Indices: 60867--60918 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
60857 TCTATTTATA
*
60867 TTAGGGCTTATGATTTAAGAT
1 TTAGGGTTTATGATTTAAGAT
60888 TTAGGGTTTATGATTTAA-AGT
1 TTAGGGTTTATGATTTAAGA-T
60909 TTAGGGTTTA
1 TTAGGGTTTA
60919 GGTTTAGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 28 0.97
ACGTcount: A:0.27, C:0.02, G:0.25, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTATGATTTAAGAT
Found at i:60924 original size:6 final size:6
Alignment explanation
Indices: 60907--60942 Score: 54
Period size: 6 Copynumber: 5.7 Consensus size: 6
60897 ATGATTTAAA
60907 GTTTAGG GTTTAG GTTTAG GTTTAG GTTTAAG GTTT
1 GTTTA-G GTTTAG GTTTAG GTTTAG GTTT-AG GTTT
60943 CTATAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 17 0.61
7 11 0.39
ACGTcount: A:0.17, C:0.00, G:0.33, T:0.50
Consensus pattern (6 bp):
GTTTAG
Found at i:61067 original size:20 final size:20
Alignment explanation
Indices: 61020--61073 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
61010 TTTATTTTAT
*
61020 ATAGTTTATATATA-TAAAT
1 ATAGTTTATATATACTAAAC
*
61039 ATAGTTTATATATACTATAC
1 ATAGTTTATATATACTAAAC
* *
61059 ATGGTTTATACATAC
1 ATAGTTTATATATAC
61074 ATATTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.41, C:0.07, G:0.07, T:0.44
Consensus pattern (20 bp):
ATAGTTTATATATACTAAAC
Found at i:61277 original size:11 final size:11
Alignment explanation
Indices: 61261--61286 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
61251 GGTTAATTTA
61261 CATTAATAGCC
1 CATTAATAGCC
61272 CATTAATAGCC
1 CATTAATAGCC
61283 CATT
1 CATT
61287 TATTTTGTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.35, C:0.27, G:0.08, T:0.31
Consensus pattern (11 bp):
CATTAATAGCC
Found at i:61447 original size:14 final size:14
Alignment explanation
Indices: 61436--61476 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
61426 AAGGTTTATT
61436 GTTTAGGGTTTAGA
1 GTTTAGGGTTTAGA
*
61450 GTTTAGAGTTTAGA
1 GTTTAGGGTTTAGA
61464 GTTTAGGGTTTAG
1 GTTTAGGGTTTAG
61477 GATTTCTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (14 bp):
GTTTAGGGTTTAGA
Found at i:61477 original size:7 final size:7
Alignment explanation
Indices: 61436--61476 Score: 64
Period size: 7 Copynumber: 5.9 Consensus size: 7
61426 AAGGTTTATT
*
61436 GTTTAGG
1 GTTTAGA
61443 GTTTAGA
1 GTTTAGA
61450 GTTTAGA
1 GTTTAGA
61457 GTTTAGA
1 GTTTAGA
*
61464 GTTTAGG
1 GTTTAGA
61471 GTTTAG
1 GTTTAG
61477 GATTTCTATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (7 bp):
GTTTAGA
Found at i:61526 original size:13 final size:13
Alignment explanation
Indices: 61508--61550 Score: 77
Period size: 13 Copynumber: 3.3 Consensus size: 13
61498 TAATTTACTT
61508 TATATAGTTTATA
1 TATATAGTTTATA
*
61521 TATATAGGTTATA
1 TATATAGTTTATA
61534 TATATAGTTTATA
1 TATATAGTTTATA
61547 TATA
1 TATA
61551 CTATACATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
13 28 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:61555 original size:20 final size:21
Alignment explanation
Indices: 61531--61581 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
61521 TATATAGGTT
*
61531 ATATATATAGTTTATATATAC
1 ATATATATAGTTTATACATAC
* *
61552 -TATACATGGTTTATACATAC
1 ATATATATAGTTTATACATAC
61572 ATATTATATA
1 ATA-TATATA
61582 AAATTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (21 bp):
ATATATATAGTTTATACATAC
Found at i:61577 original size:498 final size:486
Alignment explanation
Indices: 60992--62902 Score: 1925
Period size: 498 Copynumber: 3.8 Consensus size: 486
60982 ATAGTGTTTG
*
60992 TATAAACTATATAAGTAATTTATTTTATATAG-TT-TATATATATA-A-ATATAGTTTATATATA
1 TATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATATATATATAGTTTATATATA
*
61053 CTATACATGGTTTATACATACATATTATATAAAATAATTTAATAAAATTAATAAAATTATTTAAA
66 CTATACATGGTTTATACATACATATTATATAAAATAATTTAATAAAATTAATAAAATAATTTAAA
61118 TGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATA
131 TGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATA
61183 TGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATG
196 TGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATG
*
61248 TTAGGTTAATTTACATTAATAGCCCATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATA
261 TTAGGTTAA-TTAC-----TA-CCCATTAATAACCCATTTATTTTGTTGTTATGAATAAGTAATA
* * * *
61313 ATAGAACCCAAAAATAAGTCTATTTGCATTAGTGTTAGTCCATTCACATTAGTTTACATAGGCCC
319 ATAAAACCAAAAAATAAGTCCATTTGCATTAGTGTTAGTCCATTTACATTAGTTTACATAGGCCC
* *
61378 ATTATTTTATTACAAATATATATGCATTAGTGTTGGTCCATTTATATTAAGGTTTATTGTTTAGG
384 ATTATTTTA-TACAAATATATATGCATTAGTGTTAGTCCATTTATATTAAGGTTTATTGTTTAAG
*
61443 GTTTAGAGTTTAGAGTTTAGAGTTTAGGGTTTAGGATTTC
448 GTTTA-AGTTTAGAGTTTAGAGTTTAGGGTTTAAGATTTC
61483 TATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATAGGTTATATATATAGTTTATAT
1 TATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATA---TATATATATAGTTTATAT
* * *
61548 ATACTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAATTTAAAAAAATAATTT
63 ATACTATACATGGTTTATACATACATATTATATAAAATAATTTAATAAAATTAATAAAATAATTT
61613 AAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATT
128 AAATGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATT
*
61678 ATATGGTTCATAAATAGTAGTACATGTCATATTAATTTTATTTGCATAATTAGTATTTTAGTTGC
193 ATATGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGC
* *
61743 ATGTTAGGTT-A--ACT-CACATTAATAGCCCATTTATTTTGTTGTTATGAATAAGTAATAATAA
258 ATGTTAGGTTAATTACTACCCATTAATAACCCATTTATTTTGTTGTTATGAATAAGTAATAATAA
*
61804 AACCAAAAAATAAGTCCATTTGCATTAGTGTTAATCCATTTACATTAGTTTACATAGGTCCAATA
323 AACCAAAAAATAAGTCCATTTGCATTAGTGTTAGTCCATTTACATTAGTTTACATAGG-CC----
* * *
61869 CATAAGCCCACTCTTTTACTACAAATATATATGCATTAGTGCTAGTCCATTTATATTAGGGTTTG
383 CAT--------TATTTTA-TACAAATATATATGCATTAGTGTTAGTCCATTTATATTAAGG-TT-
* *
61934 TGATTTAGTTTTTATGGTTTAAAGTTTAGGGTTTAG-GTTTAGGGTTTAAGATTTC
437 T-A-TT-G--TTTAAGGTTT-AAGTTTAGAGTTTAGAGTTTAGGGTTTAAGATTTC
** *
61989 TATAAACTATATATTTTA-TTACTTTATATAGTTTATGCATGCTATTTCTATAAACTATATAAGT
1 TATAAACTATATAAGTAATTTACTTTATATAGTTTAT--A---TA----TAT--A-TATAT-A-T
* * * * * *
62053 AATTTACTTTATATAGTTTATATATATATAGGTTATATATATA-GT-TTATATATACTATACATG
52 -A--TAGTTTATATA---TA-CTATACAT-GGTT-TATACATACATATTATATA-A-AATA-AT-
* * *
62116 GTATACATACATATTATATAAAATAATTTAATAAAATTATTTAAATGTAAATTATATAAAAACTT
104 -T-TA-ATA-AAATTA-ATAAAATAA-TT--T--AA--ATGTAAA------TTATAT-AAAACAT
62181 GATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTA
150 GATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATATGGTTCATAAATAGTAGTA
62246 CATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAA
215 CATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATT-AC-----
* * * *
62311 TAGCCCATTAATAACCCATTTATTTTGTTGTTGTGAATAAGTAATAATAAAACCCACAAATAACT
274 TA-CCCATTAATAACCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAACCAAAAAATAAGT
* * ** *** *
62376 CCATTTGCATTAGTGCTAGTCCATTTATATTAGGGTTTAGGGTTTAGAGTTTA-GAGTTTCTATA
338 CCATTTGCATTAGTGTTAGTCCATTTACATTA--GTTTA---CATAG-GCCCATTA-TTT-TATA
* ** * ** * * * **
62440 -AACTATATATTTTATTA-TTTTA-TATAGTTTATGCA-T-A-GTGT-TTCTATAAACTATATAA
395 CAAATATATA-TGCATTAGTGTTAGTCCA-TTTAT--ATTAAGGTTTATTGTTTAAGGT-T-TAA
* * * * *
62498 GTAATT-TACTTT--A-TTTA--CTTTATATAGTTTA
454 GT--TTAGAGTTTAGAGTTTAGGGTTTA-AGA-TTTC
* * * * *
62529 TATATA-TATATAGGT--TATA-TATATATA-TATATATATATATATATATATAGTTTATATATA
1 TATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATATATATATAGTTTATATATA
* *
62589 CTATACATGGTTTATACATACATATTATATAAAATTATTTAATAAATTTAA-AAAATAATTTAAA
66 CTATACATGGTTTATACATACATATTATATAAAATAATTTAATAAAATTAATAAAATAATTTAAA
*
62653 TGTAAATTATATAAAATATGATTAATTAGGTG-TAAATAATTAGTATGTCACATTGCATATTATA
131 TGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATA
*
62717 TGGTTCATAAATAGTAGTACATGTCATATTAATCTCATTTGCATAATTAGTATTTTAGTTGCATG
196 TGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATG
62782 TTAGGTTAATT-C-A--CATTAATAACCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAAC
261 TTAGGTTAATTACTACCCATTAATAACCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAAC
* * * * *
62843 AAAAAAAATAAGTTCATTTACATTAGTGTTAGTCAATTTACATTAGTTTACTTAGGCCCA
326 -CAAAAAATAAGTCCATTTGCATTAGTGTTAGTCCATTTACATTAGTTTACATAGGCCCA
62903 ATATATAAGC
Statistics
Matches: 1207, Mismatches: 106, Indels: 231
0.78 0.07 0.15
Matches are distributed among these distances:
474 2 0.00
475 4 0.00
478 5 0.00
479 47 0.04
480 35 0.03
482 1 0.00
487 99 0.08
488 3 0.00
489 1 0.00
490 107 0.09
491 49 0.04
492 11 0.01
493 8 0.01
494 2 0.00
496 2 0.00
497 2 0.00
498 219 0.18
500 47 0.04
501 2 0.00
502 2 0.00
503 1 0.00
504 4 0.00
505 26 0.02
506 34 0.03
507 27 0.02
508 4 0.00
509 2 0.00
510 3 0.00
512 2 0.00
513 9 0.01
514 14 0.01
515 14 0.01
516 4 0.00
517 1 0.00
519 20 0.02
521 1 0.00
522 3 0.00
523 14 0.01
524 11 0.01
525 10 0.01
526 2 0.00
527 3 0.00
528 1 0.00
529 2 0.00
530 3 0.00
531 6 0.00
532 8 0.01
533 2 0.00
534 1 0.00
535 1 0.00
536 4 0.00
537 9 0.01
538 6 0.00
539 15 0.01
540 16 0.01
541 5 0.00
542 4 0.00
543 4 0.00
545 6 0.00
546 124 0.10
547 2 0.00
548 3 0.00
549 16 0.01
550 13 0.01
551 3 0.00
555 1 0.00
557 85 0.07
558 1 0.00
559 5 0.00
562 3 0.00
563 1 0.00
ACGTcount: A:0.37, C:0.08, G:0.11, T:0.43
Consensus pattern (486 bp):
TATAAACTATATAAGTAATTTACTTTATATAGTTTATATATATATATATATATAGTTTATATATA
CTATACATGGTTTATACATACATATTATATAAAATAATTTAATAAAATTAATAAAATAATTTAAA
TGTAAATTATATAAAACATGATTAATTAGGTGTTAAATAATTAGTATGTCACATTGCATATTATA
TGGTTCATAAATAGTAGTACATGTCATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATG
TTAGGTTAATTACTACCCATTAATAACCCATTTATTTTGTTGTTATGAATAAGTAATAATAAAAC
CAAAAAATAAGTCCATTTGCATTAGTGTTAGTCCATTTACATTAGTTTACATAGGCCCATTATTT
TATACAAATATATATGCATTAGTGTTAGTCCATTTATATTAAGGTTTATTGTTTAAGGTTTAAGT
TTAGAGTTTAGAGTTTAGGGTTTAAGATTTC
Found at i:61961 original size:14 final size:14
Alignment explanation
Indices: 61944--61982 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
61934 TGATTTAGTT
*
61944 TTTATGGTTTAAAG
1 TTTAGGGTTTAAAG
*
61958 TTTAGGGTTT-AGG
1 TTTAGGGTTTAAAG
61971 TTTAGGGTTTAA
1 TTTAGGGTTTAA
61983 GATTTCTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (14 bp):
TTTAGGGTTTAAAG
Found at i:62080 original size:13 final size:13
Alignment explanation
Indices: 62062--62106 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
62052 TAATTTACTT
62062 TATATAGTTTATATA
1 TATATAG-TT-TATA
*
62077 TATATAGGTTATA
1 TATATAGTTTATA
62090 TATATAGTTTATA
1 TATATAGTTTATA
62103 TATA
1 TATA
62107 CTATACATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 20 0.71
14 1 0.04
15 7 0.25
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:62082 original size:15 final size:15
Alignment explanation
Indices: 62062--62111 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
62052 TAATTTACTT
62062 TATATAGTTTATATA
1 TATATAGTTTATATA
*
62077 TATATAG-GT-TATA
1 TATATAGTTTATATA
62090 TATATAGTTTATATA
1 TATATAGTTTATATA
62105 TACTATA
1 TA-TATA
62112 CATGGTATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 11 0.37
14 2 0.07
15 13 0.43
16 4 0.13
ACGTcount: A:0.40, C:0.02, G:0.08, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATATA
Found at i:62532 original size:2 final size:2
Alignment explanation
Indices: 62527--62593 Score: 82
Period size: 2 Copynumber: 33.0 Consensus size: 2
62517 TTATATAGTT
**
62527 TA TA TA TA TA TA TA GG T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
62568 TA TA TA TA TA GTT TA TA TA TA CTA TA
1 TA TA TA TA TA -TA TA TA TA TA -TA TA
62594 CATGGTTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
1 1 0.02
2 53 0.93
3 3 0.05
ACGTcount: A:0.45, C:0.01, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:62958 original size:76 final size:76
Alignment explanation
Indices: 62863--63040 Score: 277
Period size: 76 Copynumber: 2.3 Consensus size: 76
62853 AGTTCATTTA
** * * * *
62863 CATTAGTGTTAGTCAATTTACATTAGTTTACTTAGGCCCAATATATAAGCCTACTATTTTATTAC
1 CATTAGTACTAGTCAATTTACATTAGTCTACATAGGCCCAATACATAAGCCCACTATTTTATTAC
62928 AAATATATATG
66 AAATATATATG
*
62939 CATTAGTACTAGTGC-ATTTACATTAGTCTACATAGGCCCAATACATAAGCCCACTCTTTTATTA
1 CATTAGTACTAGT-CAATTTACATTAGTCTACATAGGCCCAATACATAAGCCCACTATTTTATTA
63003 CAAATATATATG
65 CAAATATATATG
63015 CATTAGTACTAGTCAATTTACATTAG
1 CATTAGTACTAGTCAATTTACATTAG
63041 GATTTATGGT
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
75 1 0.01
76 91 0.98
77 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (76 bp):
CATTAGTACTAGTCAATTTACATTAGTCTACATAGGCCCAATACATAAGCCCACTATTTTATTAC
AAATATATATG
Found at i:63184 original size:11 final size:11
Alignment explanation
Indices: 63168--63208 Score: 64
Period size: 11 Copynumber: 3.5 Consensus size: 11
63158 TAATTTACTT
63168 TATATAGTTTA
1 TATATAGTTTA
63179 TATATAGGTTATA
1 TATATA-GTT-TA
63192 TATATAGTTTA
1 TATATAGTTTA
63203 TATATA
1 TATATA
63209 CTATACATGG
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 14 0.50
12 6 0.21
13 8 0.29
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:63193 original size:13 final size:13
Alignment explanation
Indices: 63168--63208 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
63158 TAATTTACTT
63168 TATATA-GTT-TA
1 TATATAGGTTATA
63179 TATATAGGTTATA
1 TATATAGGTTATA
*
63192 TATATAGTTTATA
1 TATATAGGTTATA
63205 TATA
1 TATA
63209 CTATACATGG
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 6 0.22
12 3 0.11
13 18 0.67
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (13 bp):
TATATAGGTTATA
Found at i:63213 original size:20 final size:21
Alignment explanation
Indices: 63189--63239 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
63179 TATATAGGTT
*
63189 ATATATATAGTTTATATATAC
1 ATATATATAGTTTATACATAC
* *
63210 -TATACATGGTTTATACATAC
1 ATATATATAGTTTATACATAC
63230 ATATTATATA
1 ATA-TATATA
63240 AAATTATTTA
Statistics
Matches: 23, Mismatches: 5, Indels: 3
0.74 0.16 0.10
Matches are distributed among these distances:
20 17 0.74
21 2 0.09
22 4 0.17
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (21 bp):
ATATATATAGTTTATACATAC
Found at i:63627 original size:14 final size:14
Alignment explanation
Indices: 63610--63654 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
63600 GCGTTTACGG
63610 TTTAAAGTTTAGGA
1 TTTAAAGTTTAGGA
*
63624 TTTATAA-TTTATGA
1 TTTA-AAGTTTAGGA
*
63638 TTTATAGTTTAGGA
1 TTTAAAGTTTAGGA
63652 TTT
1 TTT
63655 CTATAAACTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 1 0.04
14 23 0.88
15 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (14 bp):
TTTAAAGTTTAGGA
Found at i:64488 original size:32 final size:32
Alignment explanation
Indices: 64439--64512 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
64429 CGGGTGCAGG
*
64439 TCGGGTTCAGTTTCACAATTTTCAGGTCCAAC
1 TCGGGTTCAGTTCCACAATTTTCAGGTCCAAC
*
64471 TCGGGTTTAGTTCCACAATTTTCAGGTCCAAC
1 TCGGGTTCAGTTCCACAATTTTCAGGTCCAAC
*
64503 TCAGGTTCAG
1 TCGGGTTCAG
64513 GTCAACACCA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (32 bp):
TCGGGTTCAGTTCCACAATTTTCAGGTCCAAC
Found at i:67807 original size:31 final size:32
Alignment explanation
Indices: 67769--67833 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
67759 ATGGTTCATG
* *
67769 ACATTATCGGTCCGTTCGATTTTAGTCC-TTA
1 ACATTATCGGTCCGTTCAATTTTAATCCATTA
67800 ACATTATCGGTCCGTTCAATTTTAATCCATTA
1 ACATTATCGGTCCGTTCAATTTTAATCCATTA
67832 AC
1 AC
67834 CGTTAACTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 26 0.84
32 5 0.16
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (32 bp):
ACATTATCGGTCCGTTCAATTTTAATCCATTA
Found at i:68478 original size:28 final size:28
Alignment explanation
Indices: 68445--68500 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
68435 TTTAATTTTG
* * *
68445 TAAAAAATTTATATAAATTATATAAATT
1 TAAAAAATTTAAAGAAAATATATAAATT
*
68473 TAAAAATTTTAAAGAAAATATATAAATT
1 TAAAAAATTTAAAGAAAATATATAAATT
68501 AAGTATAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (28 bp):
TAAAAAATTTAAAGAAAATATATAAATT
Found at i:68777 original size:22 final size:22
Alignment explanation
Indices: 68752--68793 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
68742 AATACCGAAA
*
68752 AAGTTTTCTCTGGGCGCACGAT
1 AAGTTTTCTCTAGGCGCACGAT
68774 AAGTTTTCTCTAGGCGCACG
1 AAGTTTTCTCTAGGCGCACG
68794 TTAGCAGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.24, G:0.26, T:0.31
Consensus pattern (22 bp):
AAGTTTTCTCTAGGCGCACGAT
Found at i:74501 original size:21 final size:21
Alignment explanation
Indices: 74476--74519 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
74466 GATAATATTA
* *
74476 AAAAATATTGATATTTTAGGT
1 AAAAATAATAATATTTTAGGT
74497 AAAAATAATAATATTTTAGGT
1 AAAAATAATAATATTTTAGGT
74518 AA
1 AA
74520 TTTTTTTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (21 bp):
AAAAATAATAATATTTTAGGT
Found at i:82718 original size:30 final size:30
Alignment explanation
Indices: 82672--82789 Score: 123
Period size: 30 Copynumber: 3.9 Consensus size: 30
82662 GAATGGCCAA
* * * *
82672 TCCATAGGTCCCGAAGAACCTAGGTAGCTG
1 TCCATATGTTCCGAAGAACATAGGTAACTG
* *
82702 TCCATATGTTCTGAAGAACATAAGTATA-TG
1 TCCATATGTTCCGAAGAACATAGGTA-ACTG
* *
82732 TCCATATGTTCCGAAGAATATATGTAACTG
1 TCCATATGTTCCGAAGAACATAGGTAACTG
*
82762 TCCATA-GATTCCGAAGAACCTAGGTAAC
1 TCCATATG-TTCCGAAGAACATAGGTAAC
82790 CCTCGACACT
Statistics
Matches: 73, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
29 2 0.03
30 71 0.97
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.27
Consensus pattern (30 bp):
TCCATATGTTCCGAAGAACATAGGTAACTG
Found at i:83442 original size:63 final size:63
Alignment explanation
Indices: 83337--83469 Score: 162
Period size: 63 Copynumber: 2.1 Consensus size: 63
83327 CTTAACTGGT
* *
83337 GTATCGATACACTACCTATATATCGATACACAAATTACATTCGA-AGTTTTTCATTTCAAGGGG
1 GTATCGATACACTACCTATATATCGATACACAAATTACATTCGAGAGTTTTTC-GTTCAAGAGG
* * ** *
83400 GTATCGATACACTGCCTATGTATCGATACACTTATTGA-ATTCGATGATTTTTTCGTTCAAGAGG
1 GTATCGATACACTACCTATATATCGATACACAAATT-ACATTCGA-GAGTTTTTCGTTCAAGAGG
83464 GTATCG
1 GTATCG
83470 GTACCTGTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
63 38 0.63
64 15 0.25
65 7 0.12
ACGTcount: A:0.29, C:0.18, G:0.17, T:0.35
Consensus pattern (63 bp):
GTATCGATACACTACCTATATATCGATACACAAATTACATTCGAGAGTTTTTCGTTCAAGAGG
Found at i:87442 original size:18 final size:18
Alignment explanation
Indices: 87419--87475 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 18
87409 TATATTTTCC
87419 AACAATTTGTATCTTTTT
1 AACAATTTGTATCTTTTT
87437 AACAA-TTGATATCATTTTGTT
1 AACAATTTG-TATC--TTT-TT
*
87458 AACAATTGGTATCTTTTT
1 AACAATTTGTATCTTTTT
87476 CATTAAACAT
Statistics
Matches: 33, Mismatches: 1, Indels: 10
0.75 0.02 0.23
Matches are distributed among these distances:
17 3 0.09
18 11 0.33
19 3 0.09
20 3 0.09
21 11 0.33
22 2 0.06
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (18 bp):
AACAATTTGTATCTTTTT
Found at i:87461 original size:21 final size:21
Alignment explanation
Indices: 87435--87475 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
87425 TTGTATCTTT
87435 TTAACAATTGATATCATTTTG
1 TTAACAATTGATATCATTTTG
* *
87456 TTAACAATTGGTATCTTTTT
1 TTAACAATTGATATCATTTT
87476 CATTAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.51
Consensus pattern (21 bp):
TTAACAATTGATATCATTTTG
Found at i:94570 original size:31 final size:32
Alignment explanation
Indices: 94530--94590 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
94520 GGACTACCTA
* * *
94530 AGAACATATCTTAGGGCTGCAGGGCCTACCCG
1 AGAACATATCTCAGGGCCGCAGAGCCTACCCG
94562 AGAA-ATATCTCAGGGCCGCAGAGCCTACC
1 AGAACATATCTCAGGGCCGCAGAGCCTACC
94591 TAAGTGTCAC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 22 0.85
32 4 0.15
ACGTcount: A:0.28, C:0.30, G:0.26, T:0.16
Consensus pattern (32 bp):
AGAACATATCTCAGGGCCGCAGAGCCTACCCG
Found at i:96182 original size:21 final size:21
Alignment explanation
Indices: 96156--96240 Score: 134
Period size: 21 Copynumber: 4.0 Consensus size: 21
96146 CCATTAGACA
96156 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
* *
96177 GGGGGGAATCTGTTCCCCCTG
1 GGGGGGAATCGGTACCCCCTG
96198 GGGGGGAATCGGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
* *
96219 GGGGGAAATCTGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTG
96240 G
1 G
96241 ACAATATGAT
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 58 1.00
ACGTcount: A:0.14, C:0.28, G:0.40, T:0.18
Consensus pattern (21 bp):
GGGGGGAATCGGTACCCCCTG
Found at i:96214 original size:42 final size:42
Alignment explanation
Indices: 96156--96240 Score: 152
Period size: 42 Copynumber: 2.0 Consensus size: 42
96146 CCATTAGACA
* *
96156 GGGGGGAATCGGTACCCCCTGGGGGGGAATCTGTTCCCCCTG
1 GGGGGGAATCGGTACCCCCTGGGGGGAAATCTGTACCCCCTG
96198 GGGGGGAATCGGTACCCCCTGGGGGGAAATCTGTACCCCCTG
1 GGGGGGAATCGGTACCCCCTGGGGGGAAATCTGTACCCCCTG
96240 G
1 G
96241 ACAATATGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.14, C:0.28, G:0.40, T:0.18
Consensus pattern (42 bp):
GGGGGGAATCGGTACCCCCTGGGGGGAAATCTGTACCCCCTG
Found at i:96611 original size:24 final size:24
Alignment explanation
Indices: 96582--96644 Score: 117
Period size: 24 Copynumber: 2.6 Consensus size: 24
96572 CCCCCTTACT
96582 TTAACACTTCTCCCCTTTAACACC
1 TTAACACTTCTCCCCTTTAACACC
96606 TTAACACTTCTCCCCTTTAACACC
1 TTAACACTTCTCCCCTTTAACACC
*
96630 TTAATACTTCTCCCC
1 TTAACACTTCTCCCC
96645 CTTTTTGTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.24, C:0.41, G:0.00, T:0.35
Consensus pattern (24 bp):
TTAACACTTCTCCCCTTTAACACC
Found at i:97268 original size:15 final size:15
Alignment explanation
Indices: 97248--97277 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
97238 TCATGCATAC
97248 TTAAAATCAAATGAG
1 TTAAAATCAAATGAG
97263 TTAAAATCAAATGAG
1 TTAAAATCAAATGAG
97278 CAACCAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.07, G:0.13, T:0.27
Consensus pattern (15 bp):
TTAAAATCAAATGAG
Found at i:98226 original size:3 final size:3
Alignment explanation
Indices: 98218--98261 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
98208 TACGTCCTCA
* *
98218 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTG TTT TTC TTC -TC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
98262 CCTTTCTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (3 bp):
TTC
Found at i:99711 original size:20 final size:21
Alignment explanation
Indices: 99680--99724 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
99670 TCGGTACTTA
99680 CTGGGGGAGAATCGGTACCCC
1 CTGGGGGAGAATCGGTACCCC
*
99701 CTGGGGG-GAATCTGTACCCC
1 CTGGGGGAGAATCGGTACCCC
99721 CTGG
1 CTGG
99725 ACAATCTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.16, C:0.29, G:0.38, T:0.18
Consensus pattern (21 bp):
CTGGGGGAGAATCGGTACCCC
Done.