Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003719.1 Hibiscus syriacus cultivar Beakdansim tig00007952_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: 341516
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 1 of 2
Found at i:11967 original size:141 final size:141
Alignment explanation
Indices: 11749--12019 Score: 411
Period size: 141 Copynumber: 1.9 Consensus size: 141
11739 AACATCAACT
11749 GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
1 GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
* ** *
11814 GGAACCGAGTTATCACCCTTCTTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATC
66 GGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
11879 TACCCTTAGAC
131 TACCCTTAGAC
* * **
11890 GACCAGA-CTTCCTCATCACGTAGGAGCCGTGTCAACCTTA-GATAATTAGCCGTCCTCATCACG
1 GACCAGATC-TCCTCATCACGTAGGAG-AGTGTCAACATTAGGATAACCAGCCGTCCTCATCACG
* * *
11953 TAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCGCGTATGAGCCGTGTCA
64 TAGGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCA
12018 TC
129 TC
12020 CCTTGACCAG
Statistics
Matches: 117, Mismatches: 11, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
140 1 0.01
141 105 0.90
142 11 0.09
ACGTcount: A:0.27, C:0.28, G:0.19, T:0.25
Consensus pattern (141 bp):
GACCAGATCTCCTCATCACGTAGGAGAGTGTCAACATTAGGATAACCAGCCGTCCTCATCACGTA
GGAACCGAGTTATCACCCTTCTTAAAGATGACCAGAACTCTTCATCACGTATGAACCATGTCATC
TACCCTTAGAC
Found at i:12301 original size:19 final size:19
Alignment explanation
Indices: 12262--12302 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
12252 ATTTATTTTT
*
12262 TTATTATTAATTATTATTA
1 TTATTATTAATTATTAATA
12281 TTATTATTAATT-TTACATA
1 TTATTATTAATTATTA-ATA
12300 TTA
1 TTA
12303 CACTTTTGCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATTATTAATTATTAATA
Found at i:12879 original size:22 final size:22
Alignment explanation
Indices: 12839--12884 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
12829 GAGAATAGAG
* *
12839 AAAAAAGAGAGATACGAAACAA
1 AAAAAAGAGAGAGAAGAAACAA
*
12861 AAAAAAGAGAGAGAAGAAAGAA
1 AAAAAAGAGAGAGAAGAAACAA
12883 AA
1 AA
12885 GTTTTACCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.72, C:0.04, G:0.22, T:0.02
Consensus pattern (22 bp):
AAAAAAGAGAGAGAAGAAACAA
Found at i:14125 original size:30 final size:29
Alignment explanation
Indices: 14091--14148 Score: 98
Period size: 30 Copynumber: 2.0 Consensus size: 29
14081 GACTCTTGAG
14091 TTTCTATTTTTACTATTTTAATCCCTTTAA
1 TTTCTATTTTTACTATTTTAAT-CCTTTAA
*
14121 TTTCTATTTTTATTATTTTAATCCTTTA
1 TTTCTATTTTTACTATTTTAATCCTTTA
14149 TGTTTAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 6 0.22
30 21 0.78
ACGTcount: A:0.22, C:0.14, G:0.00, T:0.64
Consensus pattern (29 bp):
TTTCTATTTTTACTATTTTAATCCTTTAA
Found at i:14160 original size:30 final size:30
Alignment explanation
Indices: 14096--14169 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
14086 TTGAGTTTCT
**
14096 ATTTTTACTATTTTAATCCCTTTAATTTCT
1 ATTTTTACTATTTTAATCCCTTTAATTTAA
* *
14126 ATTTTTATTATTTTAAT-CCTTTATGTTTAA
1 ATTTTTACTATTTTAATCCCTTTA-ATTTAA
*
14156 ATTTTTGCTATTTT
1 ATTTTTACTATTTT
14170 TGTCCTTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 6 0.16
30 31 0.84
ACGTcount: A:0.23, C:0.11, G:0.03, T:0.64
Consensus pattern (30 bp):
ATTTTTACTATTTTAATCCCTTTAATTTAA
Found at i:19631 original size:17 final size:18
Alignment explanation
Indices: 19598--19631 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
19588 CCGCTACTAG
19598 TGAACCGGTCAGAACCGC
1 TGAACCGGTCAGAACCGC
*
19616 TGAACCGTTC-GAACCG
1 TGAACCGGTCAGAACCG
19632 GACTGGCTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.26, C:0.32, G:0.26, T:0.15
Consensus pattern (18 bp):
TGAACCGGTCAGAACCGC
Found at i:25666 original size:30 final size:32
Alignment explanation
Indices: 25632--25714 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 32
25622 TAACGTTTGA
25632 TTTTTGTTTCATTTTAGTACCGT-C-ATTAAC
1 TTTTTGTTTCATTTTAGTACCGTGCTATTAAC
* ** *
25662 TTTTTATTTCATTTTAGTACATTGCTGTTAAC
1 TTTTTGTTTCATTTTAGTACCGTGCTATTAAC
25694 TTTTTGTTTCATTTTAGTACC
1 TTTTTGTTTCATTTTAGTACC
25715 TAAAATTTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 20 0.44
31 1 0.02
32 24 0.53
ACGTcount: A:0.19, C:0.14, G:0.10, T:0.57
Consensus pattern (32 bp):
TTTTTGTTTCATTTTAGTACCGTGCTATTAAC
Found at i:26153 original size:25 final size:24
Alignment explanation
Indices: 26125--26174 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 24
26115 TATTGAATAT
26125 GTTTTATTATTTATTATTTTTTAAA
1 GTTTTATTATTTATTA-TTTTTAAA
26150 GTTTTATTATTTATTATTTTTAAA
1 GTTTTATTATTTATTATTTTTAAA
26174 G
1 G
26175 GTTCATTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 9 0.36
25 16 0.64
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (24 bp):
GTTTTATTATTTATTATTTTTAAA
Found at i:26186 original size:24 final size:25
Alignment explanation
Indices: 26130--26187 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 25
26120 AATATGTTTT
* *
26130 ATTATTTATTATTTTTTAAAGTTTT
1 ATTATTTATTATTTTTTAAAGGTTC
26155 ATTATTTATTA-TTTTTAAAGGTTC
1 ATTATTTATTATTTTTTAAAGGTTC
*
26179 ATTTTTTAT
1 ATTATTTAT
26188 ATATAATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.66
Consensus pattern (25 bp):
ATTATTTATTATTTTTTAAAGGTTC
Found at i:30537 original size:4 final size:4
Alignment explanation
Indices: 30528--30554 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
30518 ATATGTATTT
30528 ATGG ATGG ATGG ATGG ATGG ATGG ATG
1 ATGG ATGG ATGG ATGG ATGG ATGG ATG
30555 AATTCGAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.48, T:0.26
Consensus pattern (4 bp):
ATGG
Found at i:35861 original size:16 final size:17
Alignment explanation
Indices: 35818--35862 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
35808 GTTTATGAGG
*
35818 GAATTGGAATCTGTGAAG
1 GAATTGGAATCTGT-AAC
*
35836 GAATTAGAATCTGT-AC
1 GAATTGGAATCTGTAAC
35852 GAATTGGAATC
1 GAATTGGAATC
35863 CAATTCCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 11 0.46
18 13 0.54
ACGTcount: A:0.36, C:0.09, G:0.27, T:0.29
Consensus pattern (17 bp):
GAATTGGAATCTGTAAC
Found at i:36476 original size:38 final size:37
Alignment explanation
Indices: 36417--36506 Score: 139
Period size: 38 Copynumber: 2.4 Consensus size: 37
36407 TTTTCACCCT
36417 AAACCCGAACCCGACCTGACCCGAATATCACACTTAAAA
1 AAACCCG-ACCCGACCTGACCCGAATATCACACTT-AAA
36456 AAACCCGACCCGA-CTCGACCCGAATATCACACTTAAA
1 AAACCCGACCCGACCT-GACCCGAATATCACACTTAAA
36493 AAACCCGA-CCGACC
1 AAACCCGACCCGACC
36507 CGAACAAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
36 4 0.08
37 14 0.29
38 24 0.49
39 7 0.14
ACGTcount: A:0.39, C:0.39, G:0.11, T:0.11
Consensus pattern (37 bp):
AAACCCGACCCGACCTGACCCGAATATCACACTTAAA
Found at i:36734 original size:227 final size:222
Alignment explanation
Indices: 36375--36958 Score: 735
Period size: 227 Copynumber: 2.6 Consensus size: 222
36365 TATAAGGTAA
36375 AATTATATATATTTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCT-GACCC
1 AATTATATATA-TTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCTCGACCC
* * * * * **
36439 GAATATCACACTTAAAAAAACCCGACCCGACTCGACCCGAATATCACACTTAAAAAACCCGA-CC
65 GAATATCACACTTAAAAAAACCCAACCCGACCCGA-CC-AAAAT-AAAGTT---TTACCCGACCC
** * *
36503 GACCCGAACAAAATAAAGTT-TCATCCGACCCGACCCGACCCGAAATAATAAAAAATTATTTTTA
124 GACCCGAA-AAAATAAA-TTAAAATCCAACCCGACCAGACCCGAAATAATAAAAAATTATTTTTA
*
36567 TTTAATAAAAACAATGACTTAATCCGACCCTACCCG
187 TTTAATAAAAACAATGACTTAATCCGACCCGACCCG
* *
36603 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACTCGAACCCAACCCGATCCGA
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGA-CC--T-CGA
* *
36668 CCCGAATATCACACTTAAAAAAACCCAACCCGACCCGAACAAAATAAAGTTTTATCCGACCCGAC
62 CCCGAATATCACACTTAAAAAAACCCAACCCGACCCGACCAAAATAAAGTTTTACCCGACCCGAC
* * * * *
36733 CCGAATATATGAATTAGAAATCCAACCCGACCAGGCTCGAAATAATAAAAAATTATTTTTATTTA
127 CCGAAAAAATAAATTA-AAATCCAACCCGACCAGACCCGAAATAATAAAAAATTATTTTTATTTA
* *
36798 ATAAAAACAGTGACTTAATCCGACCCGACCTG
191 ATAAAAACAATGACTTAATCCGACCCGACCCG
* *
36830 AATTATATATATTTTCGGATCGGTCCGATTTTTTTCACCCTAAACCCGAACCCGA-CTCGACCCG
1 AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCTCGACCCG
*
36894 AATATCACACTTAAAAAAACCCGATCCGACCCGAACCGACCAAAATAAAGTTTTACCCGACCCGA
66 AATATCACACTTAAAAAAACCC-A----ACCCGACCCGACCAAAATAAAGTTTTACCCGACCCGA
36959 ATATATGAAT
Statistics
Matches: 313, Mismatches: 30, Indels: 27
0.85 0.08 0.07
Matches are distributed among these distances:
222 29 0.09
223 2 0.01
225 3 0.01
226 10 0.03
227 208 0.66
228 13 0.04
229 4 0.01
230 5 0.02
231 1 0.00
232 38 0.12
ACGTcount: A:0.36, C:0.29, G:0.12, T:0.24
Consensus pattern (222 bp):
AATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCTCGACCCG
AATATCACACTTAAAAAAACCCAACCCGACCCGACCAAAATAAAGTTTTACCCGACCCGACCCGA
AAAAATAAATTAAAATCCAACCCGACCAGACCCGAAATAATAAAAAATTATTTTTATTTAATAAA
AACAATGACTTAATCCGACCCGACCCG
Found at i:41360 original size:96 final size:96
Alignment explanation
Indices: 41189--41368 Score: 261
Period size: 96 Copynumber: 1.9 Consensus size: 96
41179 ACTTACGACA
* * * * *
41189 TCACTTGGTACCGATAGTCGCTACAAGAACATACTCCATTCTTGAAAGGGCGGTAACGAATAGGA
1 TCACTTGCTACCAATAGTCGCCACAAGAACATACTCCATTCTGGAAAGGGCGGTAACGAACAGGA
* *
41254 TATCTGATGACGATAAGTCAACTCAATCTGT
66 TATCTAATGACAATAAGTCAACTCAATCTGT
* * *
41285 TCACTTGCTACCAATAGTCGCCACAAGAACATACTCCGTTCTGGAAATGGTGGTAACGAACAGGA
1 TCACTTGCTACCAATAGTCGCCACAAGAACATACTCCATTCTGGAAAGGGCGGTAACGAACAGGA
*
41350 TCTCTAATGACAATAAGTC
66 TATCTAATGACAATAAGTC
41369 GACACTCCAT
Statistics
Matches: 73, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
96 73 1.00
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.25
Consensus pattern (96 bp):
TCACTTGCTACCAATAGTCGCCACAAGAACATACTCCATTCTGGAAAGGGCGGTAACGAACAGGA
TATCTAATGACAATAAGTCAACTCAATCTGT
Found at i:43993 original size:21 final size:22
Alignment explanation
Indices: 43954--43998 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
43944 TACTTTTTCA
*
43954 ATGATGACAATGCATTATC-TT
1 ATGATGACAATGCAATATCATT
43975 ATGATGAC-ATGTCAATATCATT
1 ATGATGACAATG-CAATATCATT
43997 AT
1 AT
43999 TAATTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 14 0.67
22 4 0.19
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (22 bp):
ATGATGACAATGCAATATCATT
Found at i:52623 original size:6 final size:6
Alignment explanation
Indices: 52612--52648 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
52602 CTATCTCGTC
52612 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG T
52649 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.00, C:0.16, G:0.49, T:0.35
Consensus pattern (6 bp):
TCGTGG
Found at i:52818 original size:21 final size:21
Alignment explanation
Indices: 52766--52819 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
52756 TTTAGAATAA
*
52766 ATCGCAACGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
52787 ATCGTAATGCGAACTTCGACT
1 ATCGCAATGCGAACTTCGACT
*
52808 ATCGCATTGCGA
1 ATCGCAATGCGA
52820 TTTACATATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (21 bp):
ATCGCAATGCGAACTTCGACT
Found at i:52854 original size:21 final size:21
Alignment explanation
Indices: 52828--52944 Score: 141
Period size: 21 Copynumber: 5.6 Consensus size: 21
52818 GATTTACATA
52828 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
52849 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
52869 TATCGCATTGCGAT-TTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
52890 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
52911 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
52932 TTCGCGTTGCGAT
1 TTCGCATTGCGAT
52945 TTATTCCAAA
Statistics
Matches: 83, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.20
21 65 0.78
22 1 0.01
ACGTcount: A:0.22, C:0.22, G:0.24, T:0.32
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:52854 original size:41 final size:42
Alignment explanation
Indices: 52809--52944 Score: 140
Period size: 41 Copynumber: 3.3 Consensus size: 42
52799 ACTTCGACTA
*
52809 TCGCATTGCGAT-TTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTACATATTCGCATTGCGATAGTCCAAGT
* *
52850 TCGCATTGCGATAGT-CGACTA-TCGCATTGCGAT-TTACATA-T
1 TCGCATTGCGATAGTAC-A-TATTCGCATTGCGATAGTCCA-AGT
* *
52891 TCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTACATA-TTCGCATTGCGATAGTCCAAGT
*
52933 TCGCGTTGCGAT
1 TCGCATTGCGAT
52945 TTATTCCAAA
Statistics
Matches: 79, Mismatches: 7, Indels: 17
0.77 0.07 0.17
Matches are distributed among these distances:
39 1 0.01
41 46 0.58
42 30 0.38
43 2 0.03
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (42 bp):
TCGCATTGCGATAGTACATATTCGCATTGCGATAGTCCAAGT
Found at i:52860 original size:62 final size:62
Alignment explanation
Indices: 52802--52947 Score: 258
Period size: 62 Copynumber: 2.4 Consensus size: 62
52792 AATGCGAACT
52802 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
52864 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
* *
52926 TCGAAGT-TCGCGTTGCGATTTA
1 TCG-ACTATCGCATTGCGATTTA
52948 TTCCAAATTC
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
62 79 0.98
63 2 0.02
ACGTcount: A:0.23, C:0.22, G:0.22, T:0.33
Consensus pattern (62 bp):
TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
Found at i:53198 original size:18 final size:18
Alignment explanation
Indices: 53159--53198 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
53149 AATTCAATGA
*
53159 AATTAAATTAATCGAATG
1 AATTAAATTAATCGAATC
**
53177 AATTAAATTAATTTAATC
1 AATTAAATTAATCGAATC
53195 AATT
1 AATT
53199 TTTATTAGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.40
Consensus pattern (18 bp):
AATTAAATTAATCGAATC
Found at i:64583 original size:17 final size:17
Alignment explanation
Indices: 64561--64598 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
64551 GCTCCATGAA
64561 CTGCTCAAGCTACTGAC
1 CTGCTCAAGCTACTGAC
64578 CTGCTCAAGCTACTGAC
1 CTGCTCAAGCTACTGAC
64595 CTGC
1 CTGC
64599 CAATGGAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (17 bp):
CTGCTCAAGCTACTGAC
Found at i:66064 original size:31 final size:31
Alignment explanation
Indices: 66041--66116 Score: 125
Period size: 31 Copynumber: 2.5 Consensus size: 31
66031 ATAGATTCTG
* *
66041 AAGAACCTAGGTAAATAGTCCATATGTCCCA
1 AAGAACATAGGTAAACAGTCCATATGTCCCA
*
66072 AAGAACATAGGTAAACAGTCCATATGTCCCG
1 AAGAACATAGGTAAACAGTCCATATGTCCCA
66103 AAGAACATAGGTAA
1 AAGAACATAGGTAA
66117 CCCTCGACCC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (31 bp):
AAGAACATAGGTAAACAGTCCATATGTCCCA
Found at i:68870 original size:15 final size:15
Alignment explanation
Indices: 68844--68898 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
68834 AAGAGTATTG
68844 GTATTG-TACTCACA
1 GTATTGATACTCACA
68858 GTATTGATACTCACA
1 GTATTGATACTCACA
* * *
68873 GTGTTTATACTCGCA
1 GTATTGATACTCACA
*
68888 GTATCGATACT
1 GTATTGATACT
68899 GCAAAAACAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
14 6 0.18
15 28 0.82
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.36
Consensus pattern (15 bp):
GTATTGATACTCACA
Found at i:78741 original size:13 final size:13
Alignment explanation
Indices: 78723--78747 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
78713 AAATTTAAAC
78723 TTTTAAATAAAAG
1 TTTTAAATAAAAG
78736 TTTTAAATAAAA
1 TTTTAAATAAAA
78748 TAAAGTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (13 bp):
TTTTAAATAAAAG
Found at i:80528 original size:21 final size:20
Alignment explanation
Indices: 80503--80546 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
80493 TACTTAAAAA
* *
80503 TTTTAAAATTATTATTATTAT
1 TTTTAAAATAATAATTATT-T
80524 TTTTAAAATAATAATTATTT
1 TTTTAAAATAATAATTATTT
80544 TTT
1 TTT
80547 ATGTATTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTAAAATAATAATTATTT
Found at i:84611 original size:14 final size:14
Alignment explanation
Indices: 84592--84621 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
84582 TCATGTCTTT
*
84592 GGAGGATCCTTGGA
1 GGAGGATCCTCGGA
84606 GGAGGATCCTCGGA
1 GGAGGATCCTCGGA
84620 GG
1 GG
84622 TCATATTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.20, C:0.17, G:0.47, T:0.17
Consensus pattern (14 bp):
GGAGGATCCTCGGA
Found at i:87002 original size:7 final size:7
Alignment explanation
Indices: 86992--87058 Score: 50
Period size: 7 Copynumber: 9.6 Consensus size: 7
86982 TACTTTTAGA
*
86992 GTTTATG
1 GTTTAAG
86999 GTTTAAG
1 GTTTAAG
*
87006 GTTTAAA
1 GTTTAAG
*
87013 GTTTAGG
1 GTTTAAG
87020 GTTT-AG
1 GTTTAAG
*
87026 AGTTTATG
1 -GTTTAAG
87034 GTTT-AG
1 GTTTAAG
87040 AGTTT-AG
1 -GTTTAAG
87047 GATTTAAG
1 G-TTTAAG
87055 GTTT
1 GTTT
87059 TACGATAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
6 3 0.06
7 41 0.85
8 4 0.08
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (7 bp):
GTTTAAG
Found at i:87030 original size:21 final size:20
Alignment explanation
Indices: 86986--87058 Score: 65
Period size: 21 Copynumber: 3.5 Consensus size: 20
86976 ATATTTTACT
* *
86986 TTTAGAGTTTATGGTTTAAGG
1 TTTAAAGTTTAGGGTTT-AGG
87007 TTTAAAGTTTAGGGTTTAGAG
1 TTTAAAGTTTAGGGTTTAG-G
** *
87028 TTTATGGTTTAGAGTTTAGG
1 TTTAAAGTTTAGGGTTTAGG
*
87048 ATTTAAGGTTT
1 -TTTAAAGTTT
87059 TACGATAATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
20 3 0.07
21 41 0.93
ACGTcount: A:0.25, C:0.00, G:0.27, T:0.48
Consensus pattern (20 bp):
TTTAAAGTTTAGGGTTTAGG
Found at i:89431 original size:20 final size:20
Alignment explanation
Indices: 89406--89444 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
89396 TTCTTCTTTT
* *
89406 TTCTTCTTTATTTTTTCTTC
1 TTCTTCTTCATCTTTTCTTC
89426 TTCTTCTTCATCTTTTCTT
1 TTCTTCTTCATCTTTTCTT
89445 TTTTCATTCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (20 bp):
TTCTTCTTCATCTTTTCTTC
Found at i:89446 original size:27 final size:27
Alignment explanation
Indices: 89394--89454 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
89384 CTACGTCAAC
* *
89394 TCTTCTTCTTTTTTCTTCTTTATTTTT
1 TCTTCTTCTTTCTTCATCTTTATTTTT
*
89421 TCTTCTTC-TTCTTCATCTTTTCTTTTT
1 TCTTCTTCTTTCTTCATC-TTTATTTTT
89448 TCATTCT
1 TC-TTCT
89455 CTCTCAAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 7 0.24
27 18 0.62
28 4 0.14
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (27 bp):
TCTTCTTCTTTCTTCATCTTTATTTTT
Found at i:89981 original size:19 final size:19
Alignment explanation
Indices: 89957--90027 Score: 79
Period size: 19 Copynumber: 3.7 Consensus size: 19
89947 AAAATAACCA
* *
89957 TCGAATTCGTAATTCGATT
1 TCGAATTCGCAACTCGATT
*
89976 TCGAATTTGCAACTCGATT
1 TCGAATTCGCAACTCGATT
* *
89995 TCGAATTCGCAACACGGTT
1 TCGAATTCGCAACTCGATT
*
90014 TCCAAATTCGCAAC
1 T-CGAATTCGCAAC
90028 ACAGAAGTCA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 33 0.75
20 11 0.25
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (19 bp):
TCGAATTCGCAACTCGATT
Found at i:95911 original size:11 final size:11
Alignment explanation
Indices: 95895--95928 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
95885 AAATATCTCC
95895 TAAAAATCAAT
1 TAAAAATCAAT
95906 TAAAAATCAAT
1 TAAAAATCAAT
95917 TAAAAATCAAT
1 TAAAAATCAAT
95928 T
1 T
95929 TTTTATTCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.29
Consensus pattern (11 bp):
TAAAAATCAAT
Found at i:96390 original size:31 final size:30
Alignment explanation
Indices: 96355--96426 Score: 74
Period size: 31 Copynumber: 2.4 Consensus size: 30
96345 CCCAAAATAT
* * *
96355 AACTTTTGAAAATTTATACTTTTAGTTACTA
1 AACTTTTGAAAATTTACACTTTGA-TCACTA
* *
96386 AACTTTT-ATAACTTTACACTTTGATCCCTA
1 AACTTTTGA-AAATTTACACTTTGATCACTA
96416 AACTTTTGAAA
1 AACTTTTGAAA
96427 GTTTCATTTC
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
30 14 0.41
31 20 0.59
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (30 bp):
AACTTTTGAAAATTTACACTTTGATCACTA
Found at i:98176 original size:11 final size:12
Alignment explanation
Indices: 98146--98178 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
98136 ATATAATTTT
*
98146 ATTTTTATATAA
1 ATTTATATATAA
98158 ATTTATATATAA
1 ATTTATATATAA
98170 A-TTATATAT
1 ATTTATATAT
98179 CATGTAAACG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 8 0.40
12 12 0.60
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
ATTTATATATAA
Found at i:99642 original size:38 final size:39
Alignment explanation
Indices: 99600--99676 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 39
99590 ATACCTAAAG
*
99600 TTTATTTTTTATTTCATTTTAGTA-CACCCGTT-AAAATT
1 TTTATTTTTTATTTCATTTTAATATCA-CCGTTGAAAATT
* *
99638 TTTATTTTTTGTTTCCTTTTAATATCACCGTTGAAAATT
1 TTTATTTTTTATTTCATTTTAATATCACCGTTGAAAATT
99677 CAACGTTAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 26 0.76
39 8 0.24
ACGTcount: A:0.25, C:0.13, G:0.06, T:0.56
Consensus pattern (39 bp):
TTTATTTTTTATTTCATTTTAATATCACCGTTGAAAATT
Found at i:110888 original size:21 final size:21
Alignment explanation
Indices: 110864--110903 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
110854 TTCTAACATC
110864 ACACAAACAACAAA-AAGAACA
1 ACAC-AACAACAAAGAAGAACA
*
110885 ACACAACCACAAAGAAGAA
1 ACACAACAACAAAGAAGAA
110904 ACAATCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.68, C:0.25, G:0.07, T:0.00
Consensus pattern (21 bp):
ACACAACAACAAAGAAGAACA
Found at i:110907 original size:17 final size:16
Alignment explanation
Indices: 110866--110913 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
110856 CTAACATCAC
110866 ACAAACAACAAAAAGA
1 ACAAACAACAAAAAGA
*
110882 ACAACACAACCACAAAGA
1 ACAA-ACAA-CAAAAAGA
*
110900 AGAAACAATCAAAA
1 ACAAACAA-CAAAA
110914 TACCCAAATC
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
16 4 0.15
17 12 0.46
18 10 0.38
ACGTcount: A:0.69, C:0.23, G:0.06, T:0.02
Consensus pattern (16 bp):
ACAAACAACAAAAAGA
Found at i:111319 original size:14 final size:14
Alignment explanation
Indices: 111296--111336 Score: 55
Period size: 15 Copynumber: 2.8 Consensus size: 14
111286 AATATAATAT
111296 TAAATATTTAATAAA
1 TAAAT-TTTAATAAA
*
111311 TAAATTTTAAAAAA
1 TAAATTTTAATAAA
111325 TGAAATTTTAAT
1 T-AAATTTTAAT
111337 TTTTACAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 9 0.39
15 14 0.61
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (14 bp):
TAAATTTTAATAAA
Found at i:113884 original size:5 final size:5
Alignment explanation
Indices: 113874--113909 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
113864 AAAAATTCCA
* *
113874 ACCCG ACCCG ACCCA ACCCG ACCCG ACCCA ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG ACCCG A
113910 ACTCAAATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.28, C:0.58, G:0.14, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:113891 original size:15 final size:15
Alignment explanation
Indices: 113871--113909 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
113861 TTAAAAAATT
113871 CCAACCCGACCCGAC
1 CCAACCCGACCCGAC
113886 CCAACCCGACCCGAC
1 CCAACCCGACCCGAC
113901 CCAACCCGA
1 CCAACCCGA
113910 ACTCAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.28, C:0.59, G:0.13, T:0.00
Consensus pattern (15 bp):
CCAACCCGACCCGAC
Found at i:119099 original size:32 final size:32
Alignment explanation
Indices: 119063--119127 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
119053 TTTGTTAGTA
119063 TTTTATT-TAATTATTGT-ATTATTTAATTTTTT
1 TTTTATTAT-ATTATT-TAATTATTTAATTTTTT
* *
119095 TTTTATTATTTTATTTAATTATTTTATTTTTT
1 TTTTATTATATTATTTAATTATTTAATTTTTT
119127 T
1 T
119128 GCAGTTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 1 0.03
32 27 0.93
33 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (32 bp):
TTTTATTATATTATTTAATTATTTAATTTTTT
Found at i:119100 original size:24 final size:26
Alignment explanation
Indices: 119073--119124 Score: 72
Period size: 24 Copynumber: 2.1 Consensus size: 26
119063 TTTTATTTAA
*
119073 TTATTGTATTATTTAATT-TTTT-TT
1 TTATTATATTATTTAATTATTTTATT
*
119097 TTATTATTTTATTTAATTATTTTATT
1 TTATTATATTATTTAATTATTTTATT
119123 TT
1 TT
119125 TTTGCAGTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 16 0.67
25 4 0.17
26 4 0.17
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (26 bp):
TTATTATATTATTTAATTATTTTATT
Found at i:119398 original size:13 final size:13
Alignment explanation
Indices: 119379--119425 Score: 67
Period size: 13 Copynumber: 3.5 Consensus size: 13
119369 TAACTGTAAA
119379 AAAATAAAATAAT
1 AAAATAAAATAAT
*
119392 TAAATAAAATAAT
1 AAAATAAAATAAT
*
119405 AAAAATTAAATAAT
1 -AAAATAAAATAAT
119419 AAAATAA
1 AAAATAA
119426 TTAATACAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 18 0.62
14 11 0.38
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAATAAAATAAT
Found at i:119400 original size:19 final size:18
Alignment explanation
Indices: 119375--119429 Score: 71
Period size: 19 Copynumber: 3.2 Consensus size: 18
119365 TTTATAACTG
119375 TAAA-AAAATAAAATAAT
1 TAAATAAAATAAAATAAT
*
119392 TAAATAAAATAATAAAAAT
1 TAAATAAAATAA-AATAAT
119411 TAAAT--AATAAAATAAT
1 TAAATAAAATAAAATAAT
119427 TAA
1 TAA
119430 TACAAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
16 8 0.24
17 9 0.26
18 7 0.21
19 10 0.29
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (18 bp):
TAAATAAAATAAAATAAT
Found at i:119408 original size:27 final size:26
Alignment explanation
Indices: 119378--119438 Score: 77
Period size: 27 Copynumber: 2.3 Consensus size: 26
119368 ATAACTGTAA
*
119378 AAAAATAAAATAATTAAATAAAATAAT
1 AAAAATAAAATAATAAAAT-AAATAAT
* *
119405 AAAAATTAAATAATAAAATAATTAAT
1 AAAAATAAAATAATAAAATAAATAAT
119431 ACAAAATA
1 A-AAAATA
119439 TGATTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (26 bp):
AAAAATAAAATAATAAAATAAATAAT
Found at i:119415 original size:14 final size:14
Alignment explanation
Indices: 119378--119422 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
119368 ATAACTGTAA
119378 AAAAATAAAATAAT
1 AAAAATAAAATAAT
*
119392 -TAAATAAAATAAT
1 AAAAATAAAATAAT
*
119405 AAAAATTAAATAAT
1 AAAAATAAAATAAT
119419 AAAA
1 AAAA
119423 TAATTAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
13 12 0.44
14 15 0.56
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAAAATAAAATAAT
Found at i:119437 original size:22 final size:22
Alignment explanation
Indices: 119394--119438 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
119384 AAAATAATTA
**
119394 AATAAAATAATAAAAATTAAAT
1 AATAAAATAATAAAAACAAAAT
* *
119416 AATAAAATAATTAATACAAAAT
1 AATAAAATAATAAAAACAAAAT
119438 A
1 A
119439 TGATTAAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
AATAAAATAATAAAAACAAAAT
Found at i:121090 original size:25 final size:25
Alignment explanation
Indices: 121058--121114 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
121048 TTTTCTCAAT
* *
121058 GGCGGAGAAGGTCGGCGGCGGTAGC
1 GGCGGAGAAGGCCGACGGCGGTAGC
121083 GGCGGAGAAGGCCGACGGCGGTAGC
1 GGCGGAGAAGGCCGACGGCGGTAGC
121108 GGCGGAG
1 GGCGGAG
121115 GTTCATCGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.18, C:0.21, G:0.56, T:0.05
Consensus pattern (25 bp):
GGCGGAGAAGGCCGACGGCGGTAGC
Found at i:129888 original size:40 final size:39
Alignment explanation
Indices: 129854--129937 Score: 123
Period size: 40 Copynumber: 2.1 Consensus size: 39
129844 TTATTAATTA
*
129854 TAAATTTTATTCTTAATCTATGATGTTATATTATTTTATC
1 TAAATTTGATTCTTAATCTATGATGTTATATTATTTTA-C
* *
129894 TAAATTTGATTCTTATTGTATGATGTTATATTATTTTATC
1 TAAATTTGATTCTTAATCTATGATGTTATATTATTTTA-C
129934 TAAA
1 TAAA
129938 GGGTTATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.31, C:0.06, G:0.07, T:0.56
Consensus pattern (39 bp):
TAAATTTGATTCTTAATCTATGATGTTATATTATTTTAC
Found at i:129891 original size:45 final size:43
Alignment explanation
Indices: 129842--129932 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 43
129832 ATTCATTGAT
*
129842 TTTTATTAATTATAAATTTTATTCTTAATCTATGATGTTATATTA
1 TTTTATT-A-TATAAATTTGATTCTTAATCTATGATGTTATATTA
* * *
129887 --TT-TTATCTAAATTTGATTCTTATTGTATGATGTTATATTA
1 TTTTATTATATAAATTTGATTCTTAATCTATGATGTTATATTA
129927 TTTTAT
1 TTTTAT
129933 CTAAAGGGTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
40 31 0.79
41 1 0.03
42 4 0.10
43 3 0.08
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (43 bp):
TTTTATTATATAAATTTGATTCTTAATCTATGATGTTATATTA
Found at i:130106 original size:40 final size:43
Alignment explanation
Indices: 130030--130121 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 43
130020 TATATAATAT
* *
130030 ACTCATATATATTTTTAATACTATATGCGTTTAATATGTAGTA
1 ACTCATTTATATTTTTAATACTATATGAGTTTAATATGTAGTA
130073 ACTCATTTATATTTTT-A-A-TATATGAGTTTAATATGTAGTA
1 ACTCATTTATATTTTTAATACTATATGAGTTTAATATGTAGTA
*
130113 A-TAATTTAT
1 ACTCATTTAT
130122 TACCTTAATC
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
39 7 0.15
40 22 0.48
41 1 0.02
42 1 0.02
43 15 0.33
ACGTcount: A:0.36, C:0.07, G:0.09, T:0.49
Consensus pattern (43 bp):
ACTCATTTATATTTTTAATACTATATGAGTTTAATATGTAGTA
Found at i:133044 original size:20 final size:20
Alignment explanation
Indices: 133019--133134 Score: 67
Period size: 21 Copynumber: 5.7 Consensus size: 20
133009 GAGAAATAAA
133019 AATCGCAATGCGATTTCTAG
1 AATCGCAATGCGATTTCTAG
*
133039 AATCGCAAAT-C-AGTTCTTAG
1 AATCGC-AATGCGATTTC-TAG
* ** *
133059 AATCGCAACGCGATTATGAAT
1 AATCGCAATGCGATT-TCTAG
**
133080 AATCGCAATGCGA-TAGTACG
1 AATCGCAATGCGATTTCTA-G
* *
133100 AATTCGCATTGCGATTTTCCAG
1 AA-TCGCAATGCGA-TTTCTAG
*
133122 AATCGCAACGCGA
1 AATCGCAATGCGA
133135 ATATGAAAAT
Statistics
Matches: 71, Mismatches: 16, Indels: 17
0.68 0.15 0.16
Matches are distributed among these distances:
19 8 0.11
20 20 0.28
21 37 0.52
22 4 0.06
23 2 0.03
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (20 bp):
AATCGCAATGCGATTTCTAG
Found at i:133240 original size:20 final size:20
Alignment explanation
Indices: 133196--133301 Score: 98
Period size: 20 Copynumber: 5.5 Consensus size: 20
133186 GATTCTGACT
*
133196 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
133217 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * *
133237 ATCGCACCGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
*
133257 ATCGC-A-----ATGCGTAA
1 ATCGCAACGCGTATCCGTAA
*
133271 ATCACAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
133291 ATCGCAACGCG
1 ATCGCAACGCG
133302 ATTTTTAAAG
Statistics
Matches: 69, Mismatches: 10, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
14 11 0.16
15 1 0.01
20 40 0.58
21 17 0.25
ACGTcount: A:0.35, C:0.27, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:133863 original size:20 final size:20
Alignment explanation
Indices: 133838--133878 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
133828 TTCTAAACTT
* *
133838 AAAATCGCAACATGAAAATG
1 AAAATCACAACACGAAAATG
133858 AAAATCACAACACGAAAATG
1 AAAATCACAACACGAAAATG
133878 A
1 A
133879 CTATCGATTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.59, C:0.17, G:0.12, T:0.12
Consensus pattern (20 bp):
AAAATCACAACACGAAAATG
Found at i:135785 original size:94 final size:93
Alignment explanation
Indices: 135624--136003 Score: 589
Period size: 94 Copynumber: 4.1 Consensus size: 93
135614 TAGATTGCTT
* * * *
135624 AGTAAATTTATTCGGTTGCTGTCAATACTGCTAAATTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
135689 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
* *
135718 AGTAAATTTATTCGGTTCCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
135783 ATTTGTCTTTGTTTTGTCTTTTGGTTAAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTT-GA
* * * *
135812 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTATGTATTCTTTAATACTGTGAATTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
135877 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
135906 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTATT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
135971 ATTTGTCTTTGTTTTGTCTTTTGGTTTA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
135999 AGTAA
1 AGTAA
136004 TGCAATTCAT
Statistics
Matches: 265, Mismatches: 19, Indels: 5
0.92 0.07 0.02
Matches are distributed among these distances:
93 25 0.09
94 240 0.91
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.49
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:136202 original size:19 final size:19
Alignment explanation
Indices: 136121--136192 Score: 99
Period size: 19 Copynumber: 3.8 Consensus size: 19
136111 GTCACGAGAG
*
136121 AATCGCAACGAGAAATAAA
1 AATCGCAACGCGAAATAAA
*
136140 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
* **
136159 AATCGTAACGCGAAACCAA
1 AATCGCAACGCGAAATAAA
136178 AATCGCAACGCGAAA
1 AATCGCAACGCGAAA
136193 CTATAATCGC
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 47 1.00
ACGTcount: A:0.50, C:0.22, G:0.18, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:136363 original size:20 final size:20
Alignment explanation
Indices: 136237--136355 Score: 177
Period size: 20 Copynumber: 6.0 Consensus size: 20
136227 GATTCTCTCG
* **
136237 TTGCGATAGTTAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
136257 TTGCGATAGTCAAATTT-GCA
1 TTGCGATAGTC-ATTTTCGCA
*
136277 TTGTGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
136297 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
136317 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
136337 TTGCGATAGTCATTTTCGC
1 TTGCGATAGTCATTTTCGC
136356 GTTACGATTT
Statistics
Matches: 92, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
19 4 0.04
20 84 0.91
21 4 0.04
ACGTcount: A:0.23, C:0.18, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:136888 original size:18 final size:19
Alignment explanation
Indices: 136849--136890 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
136839 CTCACCTGTC
136849 ATCGTTCAAGAGGTCTCCCCT
1 ATCGTTCAAGAGG--TCCCCT
136870 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGTCCCCT
136888 ATC
1 ATC
136891 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.33, G:0.19, T:0.26
Consensus pattern (19 bp):
ATCGTTCAAGAGGTCCCCT
Found at i:138334 original size:14 final size:14
Alignment explanation
Indices: 138302--138336 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
138292 GATTGTTTAA
138302 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
* *
138316 ATGATTTGTAAATG
1 TTGATTTGTAAAAG
138330 TTGATTT
1 TTGATTT
138337 TTTTAATTGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.20, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:138528 original size:34 final size:33
Alignment explanation
Indices: 138440--138530 Score: 128
Period size: 33 Copynumber: 2.7 Consensus size: 33
138430 AAAACAGACT
* **
138440 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
*
138474 ATCGCAATGCGAAATGAAAATCGCAACGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
138507 ATCGCAATGCGAAAATGAAAATCG
1 ATCGCAATGCG-AAATGAAAATCG
138531 TTGCGATTTA
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
33 31 0.60
34 21 0.40
ACGTcount: A:0.42, C:0.20, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:138556 original size:20 final size:20
Alignment explanation
Indices: 138531--138616 Score: 129
Period size: 20 Copynumber: 4.3 Consensus size: 20
138521 ATGAAAATCG
* *
138531 TTGCGATTTACAG-ATTCACA
1 TTGCGATTTAC-GTAATCGCA
138551 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
138571 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
*
138591 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
138611 TTGCGA
1 TTGCGA
138617 ATCTGTAAAT
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 1 0.02
20 61 0.98
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:138628 original size:40 final size:39
Alignment explanation
Indices: 138549--138624 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
138539 TACAGATTCA
*
138549 CATTGCGATTTACGTAATCGCATTGCGATTTACGTAATCG
1 CATTGCGATTTACGTAATCGCATTGCGATCTA-GTAATCG
*
138589 CATTGCGATTTACGTATTCGCATTGCGAATCT-GTAA
1 CATTGCGATTTACGTAATCGCATTGCG-ATCTAGTAA
138625 ATCGTACGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 4 0.12
40 26 0.79
41 3 0.09
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.36
Consensus pattern (39 bp):
CATTGCGATTTACGTAATCGCATTGCGATCTAGTAATCG
Found at i:138716 original size:20 final size:20
Alignment explanation
Indices: 138688--138738 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
138678 AATTTTCATT
*
138688 TCGCATTGCGATTTACGTAA
1 TCGCGTTGCGATTTACGTAA
*
138708 TCGCGTTGCGATTTACGTAT
1 TCGCGTTGCGATTTACGTAA
*
138728 TTGCGTTGCGA
1 TCGCGTTGCGA
138739 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (20 bp):
TCGCGTTGCGATTTACGTAA
Found at i:138851 original size:19 final size:19
Alignment explanation
Indices: 138827--138863 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
138817 ACTCGTTTCG
*
138827 ATTTTCATTTCGTATTGCA
1 ATTTTCATTTCGCATTGCA
138846 ATTTTCATTTCGCATTGC
1 ATTTTCATTTCGCATTGC
138864 GATTCTCTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (19 bp):
ATTTTCATTTCGCATTGCA
Found at i:138897 original size:20 final size:20
Alignment explanation
Indices: 138872--138931 Score: 95
Period size: 20 Copynumber: 3.0 Consensus size: 20
138862 GCGATTCTCT
138872 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
138892 CGTTGCGATAGTCAATTT-CG
1 CGTTGCGATAGTC-ATTTCCG
*
138912 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
138932 TGATGCGATT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 4 0.11
20 29 0.78
21 4 0.11
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:138938 original size:20 final size:19
Alignment explanation
Indices: 138875--138940 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 19
138865 ATTCTCTCGT
*
138875 TGCGATAGTCATTTCCGCGT
1 TGCGATAGTCATTTCCG-GA
*
138895 TGCGATAGTCAATTT-CGCA
1 TGCGATAGTC-ATTTCCGGA
138914 TTGCGATAGTCATTTCCGTGA
1 -TGCGATAGTCATTTCCG-GA
138935 TGCGAT
1 TGCGAT
138941 TTCCGCGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
19 4 0.10
20 30 0.77
21 5 0.13
ACGTcount: A:0.20, C:0.21, G:0.24, T:0.35
Consensus pattern (19 bp):
TGCGATAGTCATTTCCGGA
Found at i:141407 original size:24 final size:24
Alignment explanation
Indices: 141373--141426 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
141363 CTGAAAATTC
141373 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
141397 ATCAAAGTCCGGGTATTGTCCAAG
1 ATCAAAATCCGAGTATTGACCAAG
141421 ATCAAA
1 ATCAAA
141427 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:142302 original size:20 final size:20
Alignment explanation
Indices: 142282--142374 Score: 107
Period size: 20 Copynumber: 4.7 Consensus size: 20
142272 CGATAGTCAG
*
142282 AATCTCGTTGCGATTTACAG-
1 AATCGCGTTGCGATTTAC-GT
* **
142302 ATTCGTATTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
*
142322 ATTCGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
142342 AATCGCGTTGCGATTTACGT
1 AATCGCGTTGCGATTTACGT
* *
142362 ATTCGCATTGCGA
1 AATCGCGTTGCGA
142375 ATTAGGAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
19 1 0.02
20 62 0.98
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (20 bp):
AATCGCGTTGCGATTTACGT
Found at i:142331 original size:40 final size:40
Alignment explanation
Indices: 142287--142374 Score: 124
Period size: 40 Copynumber: 2.2 Consensus size: 40
142277 GTCAGAATCT
* *
142287 CGTTGCGATTTACAG-ATTCGTATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTAATCGCATTGCGATTTACGTATTCG
*
142327 CGTTGCGATTTACGTAATCGCGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTAATCGCATTGCGATTTACGTATTCG
*
142367 CATTGCGA
1 CGTTGCGA
142375 ATTAGGAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 1 0.02
40 42 0.98
ACGTcount: A:0.19, C:0.19, G:0.24, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTAATCGCATTGCGATTTACGTATTCG
Found at i:142395 original size:21 final size:21
Alignment explanation
Indices: 142371--142416 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
142361 TATTCGCATT
142371 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
142392 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
142413 GCGA
1 GCGA
142417 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:142921 original size:18 final size:18
Alignment explanation
Indices: 142900--142956 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 18
142890 ATATAACAAT
142900 TTATTTTAACATCGTTAA
1 TTATTTTAACATCGTTAA
* * *
142918 TTA-TTCAAC--GGTCAA
1 TTATTTTAACATCGTTAA
142933 CTTATTTTAACATCGTTAA
1 -TTATTTTAACATCGTTAA
142952 TTATT
1 TTATT
142957 CAACGGTCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 8
0.67 0.14 0.19
Matches are distributed among these distances:
15 4 0.14
16 3 0.10
17 10 0.34
18 8 0.28
19 4 0.14
ACGTcount: A:0.32, C:0.14, G:0.07, T:0.47
Consensus pattern (18 bp):
TTATTTTAACATCGTTAA
Found at i:142938 original size:34 final size:34
Alignment explanation
Indices: 142900--142964 Score: 130
Period size: 34 Copynumber: 1.9 Consensus size: 34
142890 ATATAACAAT
142900 TTATTTTAACATCGTTAATTATTCAACGGTCAAC
1 TTATTTTAACATCGTTAATTATTCAACGGTCAAC
142934 TTATTTTAACATCGTTAATTATTCAACGGTC
1 TTATTTTAACATCGTTAATTATTCAACGGTC
142965 GAATGACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.31, C:0.17, G:0.09, T:0.43
Consensus pattern (34 bp):
TTATTTTAACATCGTTAATTATTCAACGGTCAAC
Found at i:144379 original size:2 final size:2
Alignment explanation
Indices: 144372--144399 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
144362 AGTAATACTC
144372 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
144400 TTAATTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:146438 original size:33 final size:32
Alignment explanation
Indices: 146396--146461 Score: 123
Period size: 33 Copynumber: 2.0 Consensus size: 32
146386 TGTGCTCTAC
146396 ATATGGTTGTCAATGGAACTTGCCTTTTGTAG
1 ATATGGTTGTCAATGGAACTTGCCTTTTGTAG
146428 ATATGAGTTGTCAATGGAACTTGCCTTTTGTAG
1 ATATG-GTTGTCAATGGAACTTGCCTTTTGTAG
146461 A
1 A
146462 AAGTGTGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
32 5 0.15
33 28 0.85
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (32 bp):
ATATGGTTGTCAATGGAACTTGCCTTTTGTAG
Found at i:151592 original size:37 final size:37
Alignment explanation
Indices: 151519--151593 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
151509 GTTGAAAAAT
* *
151519 ATTTATATATTTCCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTCCTTTAAAAAATTAAAAATCATAAA
** *
151556 ATTTATATAATTTTGTTTACAAAATTAAAAAT-ATAAA
1 ATTTATAT-ATTTCCTTTAAAAAATTAAAAATCATAAA
151593 A
1 A
151594 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.49, C:0.05, G:0.01, T:0.44
Consensus pattern (37 bp):
ATTTATATATTTCCTTTAAAAAATTAAAAATCATAAA
Found at i:152383 original size:13 final size:14
Alignment explanation
Indices: 152365--152397 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
152355 TATTTTACAA
*
152365 AAAATATTTT-TTT
1 AAAATATTTTCATT
152378 AAAATATTTTCATT
1 AAAATATTTTCATT
152392 AAAATA
1 AAAATA
152398 AATAAATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATATTTTCATT
Found at i:157688 original size:26 final size:26
Alignment explanation
Indices: 157657--157718 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
157647 GTCATCTTAT
* * *
157657 AATTTTATAAGTGCGTCTCGTTTTAA
1 AATTTTATAAGTACATATCGTTTTAA
157683 AATTTTATAAGTACATATCGTTTTAA
1 AATTTTATAAGTACATATCGTTTTAA
157709 AATTTTATAA
1 AATTTTATAA
157719 CTTTACCTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.47
Consensus pattern (26 bp):
AATTTTATAAGTACATATCGTTTTAA
Found at i:169718 original size:19 final size:19
Alignment explanation
Indices: 169694--169731 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
169684 CCTAAACTAT
169694 CAATTTTGATTCATTTTAA
1 CAATTTTGATTCATTTTAA
*
169713 CAATTTTGATTCGTTTTAA
1 CAATTTTGATTCATTTTAA
169732 TACCTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.53
Consensus pattern (19 bp):
CAATTTTGATTCATTTTAA
Found at i:171110 original size:30 final size:30
Alignment explanation
Indices: 171048--171106 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
171038 TGCCCGTTTC
*
171048 TTTTTCTTTTTTTGAAAATCAGGTACCCAA
1 TTTTTATTTTTTTGAAAATCAGGTACCCAA
171078 TTTTTATTTTTTTGAAAA-CAGGTACCCAA
1 TTTTTATTTTTTTGAAAATCAGGTACCCAA
171107 ATTTGTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.29, C:0.15, G:0.10, T:0.46
Consensus pattern (30 bp):
TTTTTATTTTTTTGAAAATCAGGTACCCAA
Found at i:172000 original size:25 final size:26
Alignment explanation
Indices: 171972--172037 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 26
171962 TCATAATATT
171972 TTATATATATTAACTT-TAAAAAATA
1 TTATATATATTAACTTATAAAAAATA
* * * *
171997 TTATTTTATAATAACTTATTAAATATA
1 TTA-TATATATTAACTTATAAAAAATA
*
172024 TTTTAT-TATTAACT
1 TTATATATATTAACT
172038 CAATTTAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
25 10 0.31
26 13 0.41
27 9 0.28
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.52
Consensus pattern (26 bp):
TTATATATATTAACTTATAAAAAATA
Found at i:172011 original size:26 final size:24
Alignment explanation
Indices: 171977--172029 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
171967 ATATTTTATA
*
171977 TATATTAACTTTAAAAAATATTATTT
1 TATAATAAC-TTAAAAAATA-TATTT
**
172003 TATAATAACTTATTAAATATATTT
1 TATAATAACTTAAAAAATATATTT
172027 TAT
1 TAT
172030 TATTAACTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 8 0.33
25 8 0.33
26 8 0.33
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (24 bp):
TATAATAACTTAAAAAATATATTT
Found at i:172032 original size:27 final size:26
Alignment explanation
Indices: 171966--172032 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 26
171956 TTAAATTCAT
*
171966 AATATTTTATATATATTAACTTTAAAA
1 AATATTTTAT-TATAATAACTTTAAAA
*
171993 AATATTATT-TTATAATAACTTATTAAA
1 AATATT-TTATTATAATAACTT-TAAAA
*
172020 TATATTTTATTAT
1 AATATTTTATTAT
172033 TAACTCAATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
26 12 0.35
27 20 0.59
28 2 0.06
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (26 bp):
AATATTTTATTATAATAACTTTAAAA
Found at i:178012 original size:14 final size:14
Alignment explanation
Indices: 177968--178005 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
177958 TCTATAAATT
177968 TAAATCTTAAACCC
1 TAAATCTTAAACCC
177982 TAAATCTTAAACCC
1 TAAATCTTAAACCC
*
177996 TAAATTTTAA
1 TAAATCTTAA
178006 GTCCTAACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (14 bp):
TAAATCTTAAACCC
Found at i:184603 original size:21 final size:21
Alignment explanation
Indices: 184537--184632 Score: 72
Period size: 21 Copynumber: 4.6 Consensus size: 21
184527 CGTTATACTA
* *
184537 AAGGGATAGATCTTTTTTTGG
1 AAGGGATCGATCTTTTTTTCG
* * * *
184558 AAGAGACCGATATTTTCTTCG
1 AAGGGATCGATCTTTTTTTCG
184579 -AGGGATCGATCTTTTTTAT-G
1 AAGGGATCGATCTTTTTT-TCG
** *
184599 AAGGGATTAATCTTTTTCCTCG
1 AAGGGATCGATCTTTTT-TTCG
184621 AA-GGATCGATCT
1 AAGGGATCGATCT
184633 GAAACTCATT
Statistics
Matches: 56, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
20 14 0.25
21 39 0.70
22 3 0.05
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.39
Consensus pattern (21 bp):
AAGGGATCGATCTTTTTTTCG
Found at i:184685 original size:20 final size:20
Alignment explanation
Indices: 184650--184726 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
184640 ATTATTGTCT
* *
184650 AAGGGATTGATTATTTTTCA
1 AAGGGATCGATCATTTTTCA
* *
184670 AGGGGATCGATCATTTGGTCA
1 AAGGGATCGATCATTT-TTCA
*
184691 AAGGGATCGATCATTTTGCTA
1 AAGGGATCGATCATTTTTC-A
*
184712 AA-GTATCGATCATTT
1 AAGGGATCGATCATTT
184727 GAGCTAGACA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
20 26 0.55
21 21 0.45
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (20 bp):
AAGGGATCGATCATTTTTCA
Found at i:184732 original size:21 final size:21
Alignment explanation
Indices: 184672--184732 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
184662 ATTTTTCAAG
184672 GGGATCGATCATTTGG-TCAAA
1 GGGATCGATCATTTGGCT-AAA
*
184693 GGGATCGATCATTTTGCTAAA
1 GGGATCGATCATTTGGCTAAA
*
184714 -GTATCGATCATTTGAGCTA
1 GGGATCGATCATTTG-GCTA
184733 GACAAACTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
20 12 0.34
21 22 0.63
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.25, T:0.33
Consensus pattern (21 bp):
GGGATCGATCATTTGGCTAAA
Found at i:185850 original size:55 final size:54
Alignment explanation
Indices: 185740--185850 Score: 152
Period size: 55 Copynumber: 2.0 Consensus size: 54
185730 ATTTTAAAAG
*
185740 ACTCAAGATATAATTATAAATTAGTTAAAAAATTTAAAATAAAATATTAATATAA
1 ACTCAAGATATAATTATAAATTAGTT-AAAAATTTAAAATAAAATATTAAAATAA
* * *
185795 ACTCAATATATAATTATAAATTAGTT-AAAATTTAAAAATATATTATTTAAAATAA
1 ACTCAAGATATAATTATAAATTAGTTAAAAATTT-AAAATAAAATA-TTAAAATAA
185850 A
1 A
185851 ATATTAATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
53 7 0.14
54 9 0.18
55 34 0.68
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.37
Consensus pattern (54 bp):
ACTCAAGATATAATTATAAATTAGTTAAAAATTTAAAATAAAATATTAAAATAA
Found at i:189635 original size:34 final size:34
Alignment explanation
Indices: 189597--189661 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 34
189587 AACACAAATG
* **
189597 AACGAACATAAACGAACGGATGTAAACGAACGTA
1 AACGAACACAAACGAACAAATGTAAACGAACGTA
* *
189631 AACGAACACAAATGATCAAATGTAAACGAAC
1 AACGAACACAAACGAACAAATGTAAACGAAC
189662 ACAATAAATG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
34 26 1.00
ACGTcount: A:0.52, C:0.18, G:0.17, T:0.12
Consensus pattern (34 bp):
AACGAACACAAACGAACAAATGTAAACGAACGTA
Found at i:189902 original size:14 final size:14
Alignment explanation
Indices: 189880--189923 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
189870 AATATAAATA
*
189880 AACACACATAAACG
1 AACAAACATAAACG
* *
189894 AACGAACATAAATG
1 AACAAACATAAACG
189908 AACAAACATAAACG
1 AACAAACATAAACG
189922 AA
1 AA
189924 TATATTATCG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.61, C:0.20, G:0.09, T:0.09
Consensus pattern (14 bp):
AACAAACATAAACG
Found at i:190013 original size:40 final size:40
Alignment explanation
Indices: 189961--190038 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
189951 ATGAACGAAC
*
189961 GAGCCCTTTGCTCATGTCCATTCATTTAATTAAACGAAAT
1 GAGCCCTCTGCTCATGTCCATTCATTTAATTAAACGAAAT
* *
190001 GAGCCCTCTGCTCATGTTCGTTCATTTAATTAAACGAA
1 GAGCCCTCTGCTCATGTCCATTCATTTAATTAAACGAA
190039 CACAAAAACT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.35
Consensus pattern (40 bp):
GAGCCCTCTGCTCATGTCCATTCATTTAATTAAACGAAAT
Found at i:202765 original size:15 final size:15
Alignment explanation
Indices: 202741--202771 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
202731 GTCTTCAACC
*
202741 TTGAGGATTCATAGA
1 TTGAGAATTCATAGA
202756 TTGAGAATTCATAGA
1 TTGAGAATTCATAGA
202771 T
1 T
202772 AAGATATATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.06, G:0.23, T:0.35
Consensus pattern (15 bp):
TTGAGAATTCATAGA
Found at i:208864 original size:2 final size:2
Alignment explanation
Indices: 208859--208891 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
208849 TCGCTCTCTC
*
208859 TG TG TG TG TG TG TG TG TG TG TG TG TG TT TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
208892 TTAGGCTACA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.45, T:0.55
Consensus pattern (2 bp):
TG
Found at i:211425 original size:25 final size:25
Alignment explanation
Indices: 211391--211440 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
211381 CTTTGTATTG
211391 TATGCGTCAAAGACAGTCTGAAAAT
1 TATGCGTCAAAGACAGTCTGAAAAT
*
211416 TATGCGTCAAAGACGGTCTGAAAAT
1 TATGCGTCAAAGACAGTCTGAAAAT
211441 GCTGAGAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.38, C:0.16, G:0.22, T:0.24
Consensus pattern (25 bp):
TATGCGTCAAAGACAGTCTGAAAAT
Found at i:212309 original size:3 final size:3
Alignment explanation
Indices: 212303--212370 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
212293 TTTTTATCCA
*
212303 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT GAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
212351 TAT CAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TA
212371 AATATATAAT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:213770 original size:19 final size:19
Alignment explanation
Indices: 213732--213769 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
213722 TGTAATTTAG
213732 TCATTTATTTTATATGTTT
1 TCATTTATTTTATATGTTT
213751 TCATTTATTTTAT-TGTTT
1 TCATTTATTTTATATGTTT
213769 T
1 T
213770 TAAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.18, C:0.05, G:0.05, T:0.71
Consensus pattern (19 bp):
TCATTTATTTTATATGTTT
Found at i:213841 original size:24 final size:24
Alignment explanation
Indices: 213796--213846 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
213786 ATAGTATTTT
* *
213796 TATTTTTATTTTATTATGAATAAA
1 TATTTTTATTATATTATAAATAAA
*
213820 TATTTTTA-TATATTCATAAATATA
1 TATTTTTATTATATT-ATAAATAAA
213844 TAT
1 TAT
213847 AATAAATAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 5 0.22
24 18 0.78
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (24 bp):
TATTTTTATTATATTATAAATAAA
Found at i:214462 original size:6 final size:6
Alignment explanation
Indices: 214451--214477 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
214441 GGTCAAACTT
214451 TGGATA TGGATA TGGATA TGGATA TGG
1 TGGATA TGGATA TGGATA TGGATA TGG
214478 TGGTGAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (6 bp):
TGGATA
Found at i:219784 original size:204 final size:200
Alignment explanation
Indices: 219440--219846 Score: 728
Period size: 204 Copynumber: 2.0 Consensus size: 200
219430 CCTAAATCGG
*
219440 ATTTAAATTGACTTCCTAATTGACATCGAATATTACCATAAATCGTAAAATATCTAATTCTAGTG
1 ATTTAAATTGACTTCCTAATTGACATCGAATATTACCATAAATAGTAAAATATCTAATTCTAGTG
219505 ATACGGAGGGGAAAACGCAGAATTGAGGTTGAAAAAAGGCCACCTTGAGCTTAGCTCAACGTGAA
66 ATACGGAGGGGAAAACGCAGAATTGAGGTTGAAAAAAGGCCACCTTGAGCTTAGCTCAACGTGAA
219570 GAGCGTGCGCGTCG-AA-AGCTTTCCAGATTGGGGTTTTATGCGCGATTCTGACACCTGTAGCCA
131 GAGCGTGCGCGTCGAAAGAGCTTTCCAGATTGGGGTTTTATGCGCGATTCTGACACCTGTAGCCA
219633 AAGTT
196 AAGTT
219638 ATTTAAATTGACTTCCTAATTGACAATCGAAATATTACCATAAATAGTAAAAAATATCTAATTCT
1 ATTTAAATTGACTTCCTAATTGAC-ATCG-AATATTACCATAAATAGT--AAAATATCTAATTCT
219703 AGTGATACGGAGGGGAAAACGGCAGAATTTGAGGTTGAAAAAAGGCCACCTTGAGCTTAGCTCAA
62 AGTGATACGGAGGGGAAAAC-GCAGAA-TTGAGGTTGAAAAAAGGCCACCTTGAGCTTAGCTCAA
219768 CGTGAAGAGCGTGCGCGTCGAAAAGAGCTTTCCAGATTGGGGTTTTATGCGCGATTCTGACACCT
125 CGTGAAGAGCGTGCGCGTCG-AAAGAGCTTTCCAGATTGGGGTTTTATGCGCGATTCTGACACCT
219833 GTAGCCAAAGTT
189 GTAGCCAAAGTT
219845 AT
1 AT
219847 GGCCAAAAGA
Statistics
Matches: 199, Mismatches: 1, Indels: 9
0.95 0.00 0.04
Matches are distributed among these distances:
198 24 0.12
199 4 0.02
200 17 0.09
202 35 0.18
203 6 0.03
204 57 0.29
206 2 0.01
207 54 0.27
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (200 bp):
ATTTAAATTGACTTCCTAATTGACATCGAATATTACCATAAATAGTAAAATATCTAATTCTAGTG
ATACGGAGGGGAAAACGCAGAATTGAGGTTGAAAAAAGGCCACCTTGAGCTTAGCTCAACGTGAA
GAGCGTGCGCGTCGAAAGAGCTTTCCAGATTGGGGTTTTATGCGCGATTCTGACACCTGTAGCCA
AAGTT
Found at i:227132 original size:15 final size:15
Alignment explanation
Indices: 227087--227133 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
227077 ATACGTTAGG
227087 ATATATCATGTGACA
1 ATATATCATGTGACA
* * *
227102 AAAT-TGATGATCACA
1 ATATATCATG-TGACA
227117 ATATATCATGTGACA
1 ATATATCATGTGACA
227132 AT
1 AT
227134 GATAACTGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 4
0.71 0.18 0.12
Matches are distributed among these distances:
14 4 0.17
15 16 0.67
16 4 0.17
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.32
Consensus pattern (15 bp):
ATATATCATGTGACA
Found at i:228546 original size:26 final size:26
Alignment explanation
Indices: 228510--228559 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
228500 GGGATGAGGG
228510 ATGGAGTATCCGCACCTGATCCGCGA
1 ATGGAGTATCCGCACCTGATCCGCGA
228536 ATGGAGTATCCGCACCTGATCCGC
1 ATGGAGTATCCGCACCTGATCCGC
228560 CCGTTTACCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.22, C:0.32, G:0.26, T:0.20
Consensus pattern (26 bp):
ATGGAGTATCCGCACCTGATCCGCGA
Found at i:232385 original size:65 final size:65
Alignment explanation
Indices: 232304--232435 Score: 255
Period size: 65 Copynumber: 2.0 Consensus size: 65
232294 GGATTCAAAA
*
232304 TACAATTTTATAACATTTAGGACTAAATCATACTTTTATTATTTTTAAGGGGTTGAAATATAATT
1 TACAATTTTATAACATTTAGGACTAAATCATACTTTTATTATTTTTAAGGGCTTGAAATATAATT
232369 TACAATTTTATAACATTTAGGACTAAATCATACTTTTATTATTTTTAAGGGCTTGAAATATAATT
1 TACAATTTTATAACATTTAGGACTAAATCATACTTTTATTATTTTTAAGGGCTTGAAATATAATT
232434 TA
1 TA
232436 TGGGTAAACT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
65 66 1.00
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (65 bp):
TACAATTTTATAACATTTAGGACTAAATCATACTTTTATTATTTTTAAGGGCTTGAAATATAATT
Found at i:233223 original size:21 final size:22
Alignment explanation
Indices: 233198--233238 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
233188 CGCATCATAC
233198 CAAAAT-AATAATAAC-GTAATT
1 CAAAATGAATAA-AACAGTAATT
233219 CAAAATGAATAAAACAGTAA
1 CAAAATGAATAAAACAGTAA
233239 CAAATCGAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.61, C:0.10, G:0.07, T:0.22
Consensus pattern (22 bp):
CAAAATGAATAAAACAGTAATT
Found at i:233532 original size:17 final size:18
Alignment explanation
Indices: 233510--233552 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
233500 ATTATTTTTT
233510 AATTAAATT-A-AAATAAA
1 AATTAAATTGATAAA-AAA
233527 AATTAAATTGATAAAAAA
1 AATTAAATTGATAAAAAA
233545 AATTAAAT
1 AATTAAAT
233553 AATGAGAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.38
18 12 0.50
19 3 0.12
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.30
Consensus pattern (18 bp):
AATTAAATTGATAAAAAA
Found at i:236859 original size:24 final size:24
Alignment explanation
Indices: 236823--236876 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
236813 ACACATGTCT
* **
236823 GGTGGTTCATCCGGTGGTGCTGAA
1 GGTGGTTCATCCGGGGGTGCCCAA
*
236847 GGTGGTTCTTCCGGGGGTGCCCAA
1 GGTGGTTCATCCGGGGGTGCCCAA
236871 GGTGGT
1 GGTGGT
236877 GGTGACCAGG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.09, C:0.19, G:0.44, T:0.28
Consensus pattern (24 bp):
GGTGGTTCATCCGGGGGTGCCCAA
Found at i:238834 original size:3 final size:3
Alignment explanation
Indices: 238826--238907 Score: 157
Period size: 3 Copynumber: 27.7 Consensus size: 3
238816 TCTCATGCAC
238826 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
238874 ATA ATA ATA AT- ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
238908 GTCAACTTTG
Statistics
Matches: 78, Mismatches: 0, Indels: 2
0.98 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 76 0.97
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:245890 original size:4 final size:4
Alignment explanation
Indices: 245881--245912 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
245871 TTCAACTATG
245881 TATT TATT TATT TATT TATT TATT TATT TATT
1 TATT TATT TATT TATT TATT TATT TATT TATT
245913 CATGTATTGC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TATT
Found at i:245920 original size:12 final size:12
Alignment explanation
Indices: 245877--245920 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
245867 ACTGTTCAAC
245877 TATGTATTTATT
1 TATGTATTTATT
*
245889 TATTTATTTATT
1 TATGTATTTATT
*
245901 TATTTATTTATT
1 TATGTATTTATT
*
245913 CATGTATT
1 TATGTATT
245921 GCATTTTATC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (12 bp):
TATGTATTTATT
Found at i:256752 original size:69 final size:69
Alignment explanation
Indices: 256636--256782 Score: 249
Period size: 69 Copynumber: 2.1 Consensus size: 69
256626 AAAAAAATAA
* *
256636 TACAACGGTAAAAGTAAATGCACTGGTGTAAGTAAATAAAATAAACAAGTGTAACACTTAACACA
1 TACACCGGTAAAAGTAAATGCACCGGTGTAAGTAAATAAAATAAACAAGTGTAACACTTAACACA
256701 TACT
66 TACT
* * *
256705 TACACCGGTATAAGTAAATGCACCGGTGTAAGTGAATAAAATAAACAAGTGTAGCACTTAACACA
1 TACACCGGTAAAAGTAAATGCACCGGTGTAAGTAAATAAAATAAACAAGTGTAACACTTAACACA
256770 TACT
66 TACT
256774 TACACCGGT
1 TACACCGGT
256783 GTAAATGAAT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
69 73 1.00
ACGTcount: A:0.44, C:0.17, G:0.16, T:0.23
Consensus pattern (69 bp):
TACACCGGTAAAAGTAAATGCACCGGTGTAAGTAAATAAAATAAACAAGTGTAACACTTAACACA
TACT
Found at i:256785 original size:51 final size:50
Alignment explanation
Indices: 256725--256889 Score: 267
Period size: 51 Copynumber: 3.3 Consensus size: 50
256715 TAAGTAAATG
256725 CACCGGTGTAAGTGAATAAAATAAACAAGTGTAGCACTTAACACATACTTA
1 CACCGGTGTAAGTGAATAAAATAAA-AAGTGTAGCACTTAACACATACTTA
*
256776 CACCGGTGTAAATGAATAAAATAAAAAAGTGTAGCACTTAACACATACTTA
1 CACCGGTGTAAGTGAATAAAAT-AAAAAGTGTAGCACTTAACACATACTTA
** *
256827 CAAAGGTGTAAGTAAATAAAATAAAAAGTGTAGCACTTAACACATACTTA
1 CACCGGTGTAAGTGAATAAAATAAAAAGTGTAGCACTTAACACATACTTA
*
256877 CACCGATGTAAGT
1 CACCGGTGTAAGT
256890 ATCTACATCT
Statistics
Matches: 105, Mismatches: 8, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
50 38 0.36
51 64 0.61
52 3 0.03
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (50 bp):
CACCGGTGTAAGTGAATAAAATAAAAAGTGTAGCACTTAACACATACTTA
Found at i:260982 original size:60 final size:60
Alignment explanation
Indices: 260920--261126 Score: 178
Period size: 61 Copynumber: 3.5 Consensus size: 60
260910 GTCTATATAC
* *
260920 TTTAAATCATTCTGTATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACT
1 TTTAAAT-ATTTTATATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACT
* * * ** ** ** *
260981 TTTAAAATATTTTATATTAATCTCCAACCTATCA-ATATCGTTCCATTTTGA-CCCT----T
1 TTT-AAATATTTTATATTAATCCCCAAACTATGATAT-TCACTATAAATTGATCCATAAACT
* *
261037 TTGTTAACA-TTT-TATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACT
1 TT-TAAATATTTTATATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACT
* *
261096 TTTAAATATTTTATATTAATCTCCAACCTAT
1 TTTAAATATTTTATATTAATCCCCAAACTAT
261127 CAATATCATT
Statistics
Matches: 107, Mismatches: 28, Indels: 23
0.68 0.18 0.15
Matches are distributed among these distances:
54 25 0.23
55 8 0.07
56 6 0.06
57 1 0.01
58 4 0.04
59 6 0.06
60 21 0.20
61 32 0.30
62 4 0.04
ACGTcount: A:0.35, C:0.19, G:0.04, T:0.42
Consensus pattern (60 bp):
TTTAAATATTTTATATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACT
Found at i:261055 original size:54 final size:54
Alignment explanation
Indices: 260995--261169 Score: 147
Period size: 54 Copynumber: 3.1 Consensus size: 54
260985 AAATATTTTA
*
260995 TATTAATCTCCAACCTATCAATATCGTTCCATTTTGACCCTTTTGTTAACATTT
1 TATTAATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGTTAACATTT
* * * * ** ** * * *
261049 TATTAATCCCCAAACTAT-GATATTCACTATAAATTGATCCATAAACTTT-TAAATATTTT
1 TATTAATCTCCAACCTATCAATA-TCATTCCATTTTGA-CCCT----TTTGTTAACA-TTT
*
261108 ATATTAATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGGTAACATTT
1 -TATTAATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGTTAACATTT
261163 TATTAAT
1 TATTAAT
261170 TCTGCTGGTT
Statistics
Matches: 87, Mismatches: 24, Indels: 20
0.66 0.18 0.15
Matches are distributed among these distances:
53 3 0.03
54 31 0.36
55 9 0.10
56 3 0.03
58 4 0.05
59 9 0.10
60 25 0.29
61 3 0.03
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.43
Consensus pattern (54 bp):
TATTAATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGTTAACATTT
Found at i:261152 original size:114 final size:115
Alignment explanation
Indices: 260934--261169 Score: 447
Period size: 114 Copynumber: 2.1 Consensus size: 115
260924 AATCATTCTG
260934 TATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACTTTTAAAATATTTTATATT
1 TATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACTTTTAAAATATTTTATATT
* *
260999 AATCTCCAACCTATCAATATCGTTCCATTTTGACCCTTTTGTTAACATTT
66 AATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGGTAACATTT
261049 TATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACTTTT-AAATATTTTATATT
1 TATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACTTTTAAAATATTTTATATT
261113 AATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGGTAACATTT
66 AATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGGTAACATTT
261163 TATTAAT
1 TATTAAT
261170 TCTGCTGGTT
Statistics
Matches: 119, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
114 69 0.58
115 50 0.42
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.42
Consensus pattern (115 bp):
TATTAATCCCCAAACTATGATATTCACTATAAATTGATCCATAAACTTTTAAAATATTTTATATT
AATCTCCAACCTATCAATATCATTCCATTTTGACCCTTTTGGTAACATTT
Found at i:262693 original size:2 final size:2
Alignment explanation
Indices: 262686--262718 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
262676 TTGTCTTTAT
262686 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
262719 TTAATAAGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:262811 original size:37 final size:38
Alignment explanation
Indices: 262731--262811 Score: 87
Period size: 37 Copynumber: 2.2 Consensus size: 38
262721 AATAAGTTGG
* * *
262731 AAAATATTTATATGTTTTCTTTAAAAAATTTAAATTCAT
1 AAAA-ATTTATATATTTTCTTTAAAAAATTAAAAATCAT
*
262770 -AAAATTTATATAATTTT-TTTACAAAATTAAAAAT-AT
1 AAAAATTTATAT-ATTTTCTTTAAAAAATTAAAAATCAT
262806 AAAAAT
1 AAAAAT
262812 GTTTAATGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
36 2 0.06
37 27 0.75
38 7 0.19
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (38 bp):
AAAAATTTATATATTTTCTTTAAAAAATTAAAAATCAT
Found at i:263167 original size:14 final size:14
Alignment explanation
Indices: 263148--263175 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
263138 TTCCATTCCC
263148 ATGAGAATCTCACA
1 ATGAGAATCTCACA
263162 ATGAGAATCTCACA
1 ATGAGAATCTCACA
263176 TTCCCCCAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.21
Consensus pattern (14 bp):
ATGAGAATCTCACA
Found at i:263685 original size:26 final size:28
Alignment explanation
Indices: 263625--263686 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
263615 GAGTATTGCT
*
263625 GAGCTCGACTCGACTCGAAAACTCTGAAATT
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
263656 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
263682 GAGCT
1 GAGCT
263687 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.19
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:264362 original size:530 final size:528
Alignment explanation
Indices: 263457--264517 Score: 1989
Period size: 530 Copynumber: 2.0 Consensus size: 528
263447 CTATGATCAA
* *
263457 TCAAACTAGTGCATGTTGCTGTTATCTTGACCAACATTAATGTTGGGGACCAATTATTGATAAGG
1 TCAAACTAATGCATGTTGCTATTATCTTGACCAACATTAATGTTGGGGACCAATTATTGATAAGG
263522 TGTAATGAAATTGACATGTAAAACAAATTGTTTTTTCTTTTCTGTGAGAGAATCATATCGTGGTT
66 TGTAATGAAATTGACATGTAAAACAAATTGTTTTTTCTTTTC-GTGAGAGAATCATATCGTGGTT
* *
263587 AGGGGTGTAAACGAGTCGAGTCGAGCTCGAGTATTGCTGAGCTCGACTCGACTCGAAAACTCTGA
130 AGGGGTGTAAACGAGCCAAGTCGAGCTCGAGTATTGCTGAGCTCGACTCGACTCGAAAACTCTGA
*
263652 AATTGAGCTCGACTCGACTCGAAAACTCGCGAGCTTAAAATTTTCAAGCTCGACTCGAACTCGAA
195 AATTGAGCTCGACTCGACTCGAAAACTCGCGAACTTAAAATTTTCAAGCTCGACTCGAACTCGAA
*
263717 ATCCTGAACTGAAGCTCGTGAGCAGCTCGAAAAGGCTCGAAATGAAGAAAAAAATTCTTAAACTT
260 ATCCTGAACTGAAGCTCGTGAGCAGCTCGAAAAGGCTCGAAATGAAGAAAAAAAATCTTAAACTT
263782 AACTTGATTGAAGCCTCAAACTCAAACTCGAACATGAATCTTAAATATATTAAAATCTTACTGTA
325 AACTTGATTGAAGCCTCAAACTCAAACTCGAACATGAATCTTAAATATATTAAAATCTTACTGTA
263847 TTTTAAAAAAAATCCATACATAAATATTAATATTATTAATAATTTTTTTAAAAAAGTTAAAATCT
390 TTTTAAAAAAAATCCATACATAAATATTAATATTATTAATAATTTTTTTAAAAAA--TAAAATCT
*
263912 TAATATATTATATTTTGAGCTCCTGACGAGCTTTTCGAGTCGAATATCGAGTAGCTCGTTTCGGC
453 TAATATATTATATTTTGAGCTCCTGACAAGCTTTTCGAGTCGAATATCGAGTAGCTCGTTTCGGC
263977 TCGTTAAGAAC
518 TCGTTAAGAAC
263988 TCAAACTAATGCATGTTGCTATTATCTTGACCAACATTAATGTTGGGGACCAATTATTGATAAGG
1 TCAAACTAATGCATGTTGCTATTATCTTGACCAACATTAATGTTGGGGACCAATTATTGATAAGG
264053 TGTAATGAAATTGACATGTAAAACAAATTGTTTTTTCTTTTC-TGAGAGAATCATATCGTGGTTA
66 TGTAATGAAATTGACATGTAAAACAAATTGTTTTTTCTTTTCGTGAGAGAATCATATCGTGGTTA
264117 GGGGTGTAAACGAGCCAAGTCGAGCTCGAGTATTGCTGAGCTCGACTCGACTCGAAAACTCTGAA
131 GGGGTGTAAACGAGCCAAGTCGAGCTCGAGTATTGCTGAGCTCGACTCGACTCGAAAACTCTGAA
*
264182 ATTGAGCTCGACTCGACTCGAAAACTCTCGAACTTAAAATTTTTCAAGCTCGACTCGAACTCGAA
196 ATTGAGCTCGACTCGACTCGAAAACTCGCGAACTTAAAA-TTTTCAAGCTCGACTCGAACTCGAA
264247 ATCCTGAACTGAAGCTCGTGAGCAGCTCGAAAAGGCTCGAAATGAAGAAAAAAAATCTTAAACTT
260 ATCCTGAACTGAAGCTCGTGAGCAGCTCGAAAAGGCTCGAAATGAAGAAAAAAAATCTTAAACTT
264312 AACTTGATTGAAGCCTCAAACTCAAACTCGAACATGAATCTTAAATATATTAAAATCTTACTGTA
325 AACTTGATTGAAGCCTCAAACTCAAACTCGAACATGAATCTTAAATATATTAAAATCTTACTGTA
* *
264377 TTTTTAAAAAAATCCATACATAAATATTAATATTATTAATAATTTTTTTTAAAAATAAAATCTTA
390 TTTTAAAAAAAATCCATACATAAATATTAATATTATTAATAATTTTTTTAAAAAATAAAATCTTA
264442 ATATATTATATTTTGAGCTCCTGACAAGCTTTTCGAGTCGAATATCGAGTAGCTCGTTTCGGCTC
455 ATATATTATATTTTGAGCTCCTGACAAGCTTTTCGAGTCGAATATCGAGTAGCTCGTTTCGGCTC
264507 GTTAAGAAC
520 GTTAAGAAC
264516 TC
1 TC
264518 GAGTCGAGCT
Statistics
Matches: 519, Mismatches: 10, Indels: 5
0.97 0.02 0.01
Matches are distributed among these distances:
528 85 0.16
529 122 0.24
530 207 0.40
531 105 0.20
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (528 bp):
TCAAACTAATGCATGTTGCTATTATCTTGACCAACATTAATGTTGGGGACCAATTATTGATAAGG
TGTAATGAAATTGACATGTAAAACAAATTGTTTTTTCTTTTCGTGAGAGAATCATATCGTGGTTA
GGGGTGTAAACGAGCCAAGTCGAGCTCGAGTATTGCTGAGCTCGACTCGACTCGAAAACTCTGAA
ATTGAGCTCGACTCGACTCGAAAACTCGCGAACTTAAAATTTTCAAGCTCGACTCGAACTCGAAA
TCCTGAACTGAAGCTCGTGAGCAGCTCGAAAAGGCTCGAAATGAAGAAAAAAAATCTTAAACTTA
ACTTGATTGAAGCCTCAAACTCAAACTCGAACATGAATCTTAAATATATTAAAATCTTACTGTAT
TTTAAAAAAAATCCATACATAAATATTAATATTATTAATAATTTTTTTAAAAAATAAAATCTTAA
TATATTATATTTTGAGCTCCTGACAAGCTTTTCGAGTCGAATATCGAGTAGCTCGTTTCGGCTCG
TTAAGAAC
Found at i:265109 original size:60 final size:59
Alignment explanation
Indices: 264957--265096 Score: 190
Period size: 60 Copynumber: 2.4 Consensus size: 59
264947 GTCTCTTCTG
* * * *
264957 ACAATCAAAAGTTACAAAATGATCCCCGATTATAGGGTGTTGCTTTGTTGAGTCCCCTA
1 ACAATCAAAAGTTACAAAATGATCCCCGACTATAGGATGTTGCCTTGTTGAGTCCCCCA
* * *
265016 ACAATCAGAAGTTATAAAATGATCCTCCGACTATAGGATGTTGCCTTGTTGAGTCCCCCG
1 ACAATCAAAAGTTACAAAATGATCC-CCGACTATAGGATGTTGCCTTGTTGAGTCCCCCA
* *
265076 ACTATTAAAAGTTACAAAATG
1 ACAATCAAAAGTTACAAAATG
265097 GTCACCTGAC
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
59 23 0.33
60 46 0.67
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (59 bp):
ACAATCAAAAGTTACAAAATGATCCCCGACTATAGGATGTTGCCTTGTTGAGTCCCCCA
Found at i:275184 original size:20 final size:20
Alignment explanation
Indices: 275161--275209 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
275151 CACGGAATGT
275161 AAGATTACCGGTAGGAATAA
1 AAGATTACCGGTAGGAATAA
*
275181 AAGATTACCGGTGGGAATAA
1 AAGATTACCGGTAGGAATAA
275201 AAGATTACC
1 AAGATTACC
275210 AGGGAATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.43, C:0.12, G:0.24, T:0.20
Consensus pattern (20 bp):
AAGATTACCGGTAGGAATAA
Done.