Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009601.1 Hibiscus syriacus cultivar Beakdansim tig00116981_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: 125616
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:603 original size:20 final size:19
Alignment explanation
Indices: 580--625 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
570 CGATATAACA
580 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
600 GGTAATAAATGATAAAACC
1 GGTAAAAAATGATAAAACC
619 GGTAAAA
1 GGTAAAA
626 TGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 17 0.71
20 7 0.29
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:4724 original size:19 final size:19
Alignment explanation
Indices: 4680--4723 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
4670 AATGTCGAGT
4680 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
4699 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
4718 T-ATTTT
1 TAATTTT
4724 TTTATGTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.32, C:0.02, G:0.09, T:0.57
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:5138 original size:192 final size:196
Alignment explanation
Indices: 4815--5992 Score: 1956
Period size: 192 Copynumber: 6.1 Consensus size: 196
4805 GTCGATACTA
4815 ATAGTTTGTGTCG--A-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCATCAATAAAGTGTCGA
1 ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCATCAATAAAGTGTCGA
4877 TCCATATATAAAAGTGTCGATCCCAAAAATCATCGAACCCAAAAGAATAATGTAATATGTAATTT
65 TCCATATATAAAAGTGTCGAT-CC-AAAATCATCGAACCCAAAAGAATAATGTAATATGTAATTT
4942 TTCAATCTAACCGGTACAA-T-TACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACAC
128 TTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACAC
5005 TAAT
193 TAAT
5009 ATAGTTTGTGTCGATA-TTTTTTCCCAGAATGAATTAAAAACAAGGTGCATCAA-AAA-TGTCGA
1 ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCATCAATAAAGTGTCGA
5071 TCCATATATAAAAGTGTCGATCCAAAATCATCGAACCCAAAAGAATAATGTAATATGTAATTTTT
65 TCCATATATAAAAGTGTCGATCCAAAATCATCGAACCCAAAAGAATAATGTAATATGTAATTTTT
5136 CAATCTAACCGGTACAATTATACCGG-TTTATGAGAGAATAAGTCTAAATAATGTGTCGACACT-
130 CAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTA
5199 A-
195 AT
* *
5200 ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAAACAAGGTGCACCCATAAAGTGTCGA
1 ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATT-AAAACAAGGTGCATCAATAAAGTGTCGA
*
5265 TCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAA-TATAATGTAATATGTAATT
65 TCCATATAT--AAAAGTGTCGAT-CCAAAATCATCGAACCCAAAAGAATAATGTAATATGTAATT
*
5329 TTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACA
127 TTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACA
5394 CTAAT
192 CTAAT
**
5399 ATAG-TTGTGTCGATATTTTTTTTACAGAATGAATTAAAACAAGGTGCATCAATAAAGTGTCGAT
1 ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCATCAATAAAGTGTCGAT
*
5463 CCATATATAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGAATAATGTAATATGTAATTTTTC
66 CCATATATAAAAGTGTCGATCCAAAATCATCGAACCCAAAAGAATAATGTAATATGTAATTTTTC
5528 AATCTAACCGGTACAATTATA-CGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACAC---
131 AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAA
5589 T
196 T
* *
5590 ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCACCCAT-AAGTGTCGAT
1 ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCATCAATAAAGTGTCGAT
* *
5654 CCATATATAAAAAAGTGTCGATCCCAAATCATCGAACCCAAAAGTATAATGT-ATATGTAATTTT
66 CCATATAT--AAAAGTGTCGATCCAAAATCATCGAACCCAAAAGAATAATGTAATATGTAATTTT
*
5718 TTAATCTAACC-GTACAATTATACCGGTTTTATGAGA-AATAAGTCTAAATAATGTGTCG--ACT
129 TCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACT
5779 AAT
194 AAT
*
5782 ATAGTTTGTGTCGATATTTTTTT-ACAGAATGAATTAAAACAAGGTGCATCAATAAAGTGTCGAT
1 ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCATCAATAAAGTGTCGAT
*
5846 CCATATA-AAAAGTGTCGATCCCAAATCATCGAACCCAAAAGAATAATGTAATATGTAATTTTTT
66 CCATATATAAAAGTGTCGATCCAAAATCATCGAACCCAAAAGAATAATGTAATATGTAA-TTTTT
5910 CAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTA
130 CAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTA
5975 AT
195 AT
5977 ATAGTTTGTGTCGATA
1 ATAGTTTGTGTCGATA
5993 CTAATTTAAA
Statistics
Matches: 934, Mismatches: 22, Indels: 55
0.92 0.02 0.05
Matches are distributed among these distances:
189 43 0.05
190 8 0.01
191 113 0.12
192 241 0.26
193 106 0.11
194 121 0.13
195 79 0.08
196 96 0.10
197 93 0.10
198 30 0.03
199 4 0.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (196 bp):
ATAGTTTGTGTCGATATTTTTTTCCCAGAATGAATTAAAACAAGGTGCATCAATAAAGTGTCGAT
CCATATATAAAAGTGTCGATCCAAAATCATCGAACCCAAAAGAATAATGTAATATGTAATTTTTC
AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAATGTGTCGACACTAA
T
Found at i:7227 original size:6 final size:6
Alignment explanation
Indices: 7202--7299 Score: 56
Period size: 6 Copynumber: 16.3 Consensus size: 6
7192 AATCGTCGCA
* * * *
7202 GAAGAT GAAGCT GACA-AT GAAGAT GACA-AT GATGAT GATGAT GACGAT
1 GAAGAT GAAGAT GA-AGAT GAAGAT GA-AGAT GAAGAT GAAGAT GAAGAT
* ** * * * * *
7250 GAAGCT GGCGAT GAAGAT GATGAC GATGAT GATGAT GATGAT GAAGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT
7298 GA
1 GA
7300 TGATCCAAAC
Statistics
Matches: 73, Mismatches: 15, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
5 1 0.01
6 70 0.96
7 2 0.03
ACGTcount: A:0.39, C:0.07, G:0.33, T:0.21
Consensus pattern (6 bp):
GAAGAT
Found at i:7238 original size:3 final size:3
Alignment explanation
Indices: 7230--7303 Score: 76
Period size: 3 Copynumber: 24.7 Consensus size: 3
7220 GAAGATGACA
* * * ** * *
7230 ATG ATG ATG ATG ATG ACG ATG AAG CTG GCG ATG AAG ATG ATG ACG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
*
7278 ATG ATG ATG ATG ATG AAG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
7304 CCAAACAAGT
Statistics
Matches: 56, Mismatches: 15, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.35, C:0.05, G:0.34, T:0.26
Consensus pattern (3 bp):
ATG
Found at i:7252 original size:42 final size:42
Alignment explanation
Indices: 7205--7295 Score: 128
Period size: 42 Copynumber: 2.2 Consensus size: 42
7195 CGTCGCAGAA
*
7205 GATGAAGCTGACAATGAAGATGACAATGATGATGATGATGAC
1 GATGAAGCTGACAATGAAGATGACAACGATGATGATGATGAC
* * ** *
7247 GATGAAGCTGGCGATGAAGATGATGACGATGATGATGATGAT
1 GATGAAGCTGACAATGAAGATGACAACGATGATGATGATGAC
7289 GATGAAG
1 GATGAAG
7296 ATGATGATCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.37, C:0.08, G:0.33, T:0.22
Consensus pattern (42 bp):
GATGAAGCTGACAATGAAGATGACAACGATGATGATGATGAC
Found at i:9036 original size:184 final size:184
Alignment explanation
Indices: 8726--9426 Score: 1278
Period size: 184 Copynumber: 3.9 Consensus size: 184
8716 GTATGGACAC
*
8726 TTTACAAAAGTGTCGACATTTTACACATCGGAACCCAT-A--ATAATGTAATAGATAATTTTGTA
1 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
*
8788 ATAT-ACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
66 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
8852 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
131 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
8906 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
1 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
8971 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
66 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
9036 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
131 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
9090 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATG---TAGATAATTTTGTA
1 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
9152 ATA-AACCGGTATAAATATACCGG-TTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
66 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
*
9215 TAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGA
131 TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
9269 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAA-TTTGTA
1 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
* *
9333 ATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTA
66 ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
*
9398 TAATATTGTGTCGGTACTTTATGTCCATA
131 TAATATTGTGTCGGTACTTTATATCCATA
9427 CCATTTAAAA
Statistics
Matches: 507, Mismatches: 5, Indels: 15
0.96 0.01 0.03
Matches are distributed among these distances:
179 141 0.28
180 57 0.11
181 27 0.05
182 27 0.05
183 94 0.19
184 161 0.32
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (184 bp):
TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTA
ATATAACCGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTT
TAATATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
Found at i:9263 original size:363 final size:362
Alignment explanation
Indices: 8726--9426 Score: 1289
Period size: 363 Copynumber: 1.9 Consensus size: 362
8716 GTATGGACAC
* *
8726 TTTACAAAAGTGTCGACATTTTACACATCGGAACCCATAATAATGTAATAGATAATTTTGTAATA
1 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAAT-ATATAATAGATAATTTTGTAATA
*
8791 TACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
65 AACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAAT
8856 ATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCG
130 ATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCG
8921 ACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAACCGGTATAA
195 ACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAA-TTTGTAATATAACCGGTATAA
* *
8986 ATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATTGTGTCGGT
259 ATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGT
9051 ACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
324 ACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
9090 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAAT-TATAATGTAGATAATTTTGTAAT
1 TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATATATAA--TAGATAATTTTGTAAT
9154 AAACCGGTATAAATATACCGGT-TTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAA
64 AAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAA
*
9218 TATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTC
129 TATTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTC
9283 GACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTGTAATATAACCGGTATAA
194 GACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTGTAATATAACCGGTATAA
9348 ATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGT
259 ATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGT
*
9413 ACTTTATGTCCATA
324 ACTTTATATCCATA
9427 CCATTTAAAA
Statistics
Matches: 328, Mismatches: 7, Indels: 6
0.96 0.02 0.02
Matches are distributed among these distances:
362 101 0.31
363 150 0.46
364 77 0.23
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (362 bp):
TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATATATAATAGATAATTTTGTAATAA
ACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATA
TTGTGTCGGTACTTTATATCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTGTCGA
CATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTGTAATATAACCGGTATAAAT
ATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATTGTGTCGGTAC
TTTATATCCATATTGGAAGAAAAATGTGTCGATACGA
Found at i:22230 original size:3 final size:3
Alignment explanation
Indices: 22222--22263 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
22212 CTATCTTCAT
22222 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
22264 AATGTCCCTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:26444 original size:19 final size:20
Alignment explanation
Indices: 26427--26471 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
26417 TTTTGTCTCA
*
26427 TTTCGTTGTTTCCCTCTCCAT
1 TTTC-TTGTTCCCCTCTCCAT
*
26448 TTTCTTGTTCCCCTC-CGAT
1 TTTCTTGTTCCCCTCTCCAT
26467 TTTCT
1 TTTCT
26472 CAAGTGGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 8 0.36
20 10 0.45
21 4 0.18
ACGTcount: A:0.04, C:0.33, G:0.09, T:0.53
Consensus pattern (20 bp):
TTTCTTGTTCCCCTCTCCAT
Found at i:29137 original size:13 final size:15
Alignment explanation
Indices: 29100--29140 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
29090 CACATATATA
29100 TATATATATATATGG
1 TATATATATATATGG
29115 TATATATATATATGG
1 TATATATATATATGG
* *
29130 TTTGTATATAT
1 TATATATATAT
29141 TGGGTGCAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (15 bp):
TATATATATATATGG
Found at i:29140 original size:2 final size:2
Alignment explanation
Indices: 29093--29127 Score: 52
Period size: 2 Copynumber: 17.0 Consensus size: 2
29083 ACACACACAC
*
29093 AT AT AT AT AT AT AT AT AT AT GGT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT AT AT
29128 GGTTTGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 29 0.97
3 1 0.03
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33159 original size:45 final size:47
Alignment explanation
Indices: 33103--33191 Score: 155
Period size: 45 Copynumber: 1.9 Consensus size: 47
33093 AATAAATGCT
33103 TGCGAACTAGATATCATGCGGTTAGG-TTTATTTTT-TGAATAAGCA
1 TGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAAGCA
*
33148 TGCGAATTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAA
1 TGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAA
33192 CAAAGCATAG
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
45 25 0.61
46 9 0.22
47 7 0.17
ACGTcount: A:0.29, C:0.09, G:0.22, T:0.39
Consensus pattern (47 bp):
TGCGAACTAGATATCATGCGGTTAGGATTTATTTTTGTGAATAAGCA
Found at i:42844 original size:8 final size:8
Alignment explanation
Indices: 42826--42967 Score: 82
Period size: 8 Copynumber: 17.6 Consensus size: 8
42816 AGAAATGAAA
42826 AAAAGAATG
1 AAAA-AATG
42835 AAAAAATG
1 AAAAAATG
42843 AAAAAATG
1 AAAAAATG
42851 AAAAAATG
1 AAAAAATG
42859 -AAAAATG
1 AAAAAATG
42866 -AAAAATGAG
1 AAAAAAT--G
42875 AAAAAAATG
1 -AAAAAATG
***
42884 GTGAAA-G
1 AAAAAATG
*
42891 AAAAAAAG
1 AAAAAATG
*
42899 AAAAAAAAG
1 -AAAAAATG
42908 AAGAAAAATG
1 -A-AAAAATG
42918 --AAAA-G
1 AAAAAATG
* *
42923 AGAAAATA
1 AAAAAATG
42931 AAAAAATG
1 AAAAAATG
*
42939 AAAAAATA
1 AAAAAATG
*
42947 AAAAAGAAG
1 AAAAA-ATG
42956 AAAAAA-G
1 AAAAAATG
42963 AAAAA
1 AAAAA
42968 GAAATAAAAG
Statistics
Matches: 109, Mismatches: 13, Indels: 24
0.75 0.09 0.16
Matches are distributed among these distances:
5 1 0.01
6 4 0.04
7 27 0.25
8 43 0.39
9 22 0.20
10 6 0.06
11 6 0.06
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.08
Consensus pattern (8 bp):
AAAAAATG
Found at i:42854 original size:7 final size:7
Alignment explanation
Indices: 42818--42878 Score: 63
Period size: 8 Copynumber: 8.4 Consensus size: 7
42808 CTTGAAGAAG
42818 AAATGAA
1 AAATGAA
42825 AAA--AA
1 AAATGAA
*
42830 GAATGAAA
1 AAATG-AA
42838 AAATGAAA
1 AAATG-AA
42846 AAATGAAA
1 AAATG-AA
42854 AAATGAA
1 AAATGAA
42861 AAATGAA
1 AAATGAA
42868 AAATGAGA
1 AAATGA-A
42876 AAA
1 AAA
42879 AAATGGTGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
5 4 0.08
7 18 0.38
8 26 0.54
ACGTcount: A:0.74, C:0.00, G:0.15, T:0.11
Consensus pattern (7 bp):
AAATGAA
Found at i:42904 original size:7 final size:7
Alignment explanation
Indices: 42887--42971 Score: 59
Period size: 7 Copynumber: 12.0 Consensus size: 7
42877 AAAAATGGTG
42887 AAAGAAA
1 AAAGAAA
42894 AAA-AGAA
1 AAAGA-AA
42901 AAA-AAA
1 AAAGAAA
*
42907 GAAGAAA
1 AAAGAAA
*
42914 AATGAAA
1 AAAGAAA
*
42921 AGAGAAA
1 AAAGAAA
42928 ATAA-AAA
1 A-AAGAAA
*
42935 AATGAAA
1 AAAGAAA
*
42942 AAATAAA
1 AAAGAAA
42949 AAAGAAGA
1 AAAGAA-A
*
42957 AAAAAGAA
1 AAAGA-AA
42965 AAAGAAA
1 AAAGAAA
42972 TAAAAGGAGG
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
6 6 0.10
7 42 0.70
8 11 0.18
9 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (7 bp):
AAAGAAA
Found at i:42976 original size:16 final size:14
Alignment explanation
Indices: 42893--42976 Score: 69
Period size: 14 Copynumber: 5.6 Consensus size: 14
42883 GGTGAAAGAA
42893 AAAAAGAAAAAAAAG
1 AAAAA-AAAAAAAAG
*
42908 AAGAAAAATGAAAAGAG
1 AA-AAAAA--AAAAAAG
* *
42925 AAAATAAAAAAATG
1 AAAAAAAAAAAAAG
*
42939 AAAAAATAAAAAAG
1 AAAAAAAAAAAAAG
42953 AAGAAAAAAGAAAAAG
1 AA-AAAAAA-AAAAAG
*
42969 AAATAAAA
1 AAAAAAAA
42977 GGAGGGTTCA
Statistics
Matches: 55, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
14 18 0.33
15 14 0.25
16 15 0.27
17 8 0.15
ACGTcount: A:0.81, C:0.00, G:0.13, T:0.06
Consensus pattern (14 bp):
AAAAAAAAAAAAAG
Found at i:44829 original size:55 final size:55
Alignment explanation
Indices: 44281--44791 Score: 798
Period size: 55 Copynumber: 9.3 Consensus size: 55
44271 TTTATGAAGA
* * *
44281 TCGAG-TCTTATACTCTCTGAAGGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
44336 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
*
44391 TCGAGTTCTATACTCTCTGAATGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
*
44446 TCGAGTTCTATACTCTCTGAAGGAATATAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
*
44501 TCGATTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
**
44556 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACTAGTTT-TATGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGT-TGAAGATTGT
*
44611 TCGAGTTCTATACTCTCTAAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
*
44666 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCATTT-TTAGGAAGATTGT
1 TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTT--GAAGATTGT
* * * * *
44722 TCGAG-TCTTATACTCCCTGAACGAATAGGGAGCAGACACGTTTGTTGAAGATTGT
1 TCGAGTTC-TATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
44777 TCGAG-TCTTATACTC
1 TCGAGTTC-TATACTC
44792 CTTAAAAGAA
Statistics
Matches: 427, Mismatches: 22, Indels: 14
0.92 0.05 0.03
Matches are distributed among these distances:
54 3 0.01
55 376 0.88
56 46 0.11
57 2 0.00
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (55 bp):
TCGAGTTCTATACTCTCTGAAGGAATAGAGAGCGGACCCGTTTGTTGAAGATTGT
Found at i:58689 original size:20 final size:20
Alignment explanation
Indices: 58664--58701 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
58654 CTAACGTGCA
58664 TCGTTTAATGAAACGGTGTT
1 TCGTTTAATGAAACGGTGTT
*
58684 TCGTTTAATGAAATGGTG
1 TCGTTTAATGAAACGGTG
58702 CATATGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.39
Consensus pattern (20 bp):
TCGTTTAATGAAACGGTGTT
Found at i:65208 original size:202 final size:203
Alignment explanation
Indices: 64853--65224 Score: 430
Period size: 202 Copynumber: 1.8 Consensus size: 203
64843 CAATCCAAGT
* * * * *
64853 GAAATTATGTATTTTTTAAATTTTATTTGATTATCATGTCAACTCAACAAATTATTAATGGTCTA
1 GAAATTATGTATTTTCT-AATTTTATTTAATTACCATGCCAACTCAACAAATCATTAATGGTCTA
* * * * * *
64918 ACGACAATTAATTCGTGGTGTCTATCTTAATTAAATAAAAACGAAAATAGTCATATATATTATAT
65 ACGACAATTAATCCGTGATGCCCATCTTAATTAAATAAAAACGAAAATAGACACATATATTATAT
* * * *
64983 TTTTTGAAATTAGTGAGGAAAAGT-GGACAAAACACAAATACAAGATCAATCATGTAGTTAACCT
130 TTTTTGAAATCAATAAAGAAAAGTAGG-CAAAACACAAATACAAGATCAATCATGTAGTTAACCT
65047 AATCCACGCG
194 AATCCACGCG
* *
65057 GAAATTATGTATTTTCT-ATTTTATTTAATTACCGTGCCAACTCAACAAATCGTTAATGGTCTAA
1 GAAATTATGTATTTTCTAATTTTATTTAATTACCATGCCAACTCAACAAATCATTAATGGTCTAA
* * * * *
65121 TGCCAGTTAA-CCAGTGATGACCACATCTTAATTAAATAAAAATGAAAGT-GAC-CATATATTAT
66 CGACAATTAATCC-GTGATG-CC-CATCTTAATTAAATAAAAACGAAAATAGACACATATATTAT
* ** *
65183 GTTTTTTTTAATCAATAAAGAAAAGTAGGCAAAATACAAATA
128 ATTTTTTGAAATCAATAAAGAAAAGTAGGCAAAACACAAATA
65225 TAAGTGATCA
Statistics
Matches: 138, Mismatches: 26, Indels: 10
0.79 0.15 0.06
Matches are distributed among these distances:
201 1 0.01
202 93 0.67
203 5 0.04
204 39 0.28
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (203 bp):
GAAATTATGTATTTTCTAATTTTATTTAATTACCATGCCAACTCAACAAATCATTAATGGTCTAA
CGACAATTAATCCGTGATGCCCATCTTAATTAAATAAAAACGAAAATAGACACATATATTATATT
TTTTGAAATCAATAAAGAAAAGTAGGCAAAACACAAATACAAGATCAATCATGTAGTTAACCTAA
TCCACGCG
Found at i:67858 original size:35 final size:35
Alignment explanation
Indices: 67812--67887 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
67802 AAAACAGTCC
* * *
67812 TCAATTTCATTCTATACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
67847 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
67882 TCAATT
1 TCAATT
67888 AAATTCAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:68430 original size:130 final size:130
Alignment explanation
Indices: 68284--68531 Score: 415
Period size: 130 Copynumber: 1.9 Consensus size: 130
68274 TATTTATATA
* ** *
68284 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTA
* *
68349 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
68414 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTA
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTA
* * *
68479 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
68532 GAAGAAAATT
Statistics
Matches: 109, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
130 109 1.00
ACGTcount: A:0.37, C:0.15, G:0.12, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTA
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:68562 original size:130 final size:129
Alignment explanation
Indices: 68298--68562 Score: 300
Period size: 130 Copynumber: 2.0 Consensus size: 129
68288 ATTTGGTCCT
* ** * *
68298 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTATTAACACATGATCA
* *** * * **** *
68363 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
68428 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTATTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTATTAACACATGATCA
* * * *
68493 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
68557 -A
128 CA
68558 AAATT
1 AAATT
68563 TGGGTCTTGG
Statistics
Matches: 112, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
130 99 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTATTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:68890 original size:28 final size:27
Alignment explanation
Indices: 68859--68921 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
68849 AGTTGATACA
*
68859 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
68887 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
68915 ATATTTT
1 ATATTTT
68922 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:69022 original size:16 final size:18
Alignment explanation
Indices: 69001--69034 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
68991 ATTTCTTATT
69001 AAAAATA-AAAT-ATTCA
1 AAAAATATAAATGATTCA
69017 AAAAATATAAATGATTCA
1 AAAAATATAAATGATTCA
69035 TACATTAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.65, C:0.06, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAATATAAATGATTCA
Found at i:77876 original size:14 final size:12
Alignment explanation
Indices: 77844--77868 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
77834 AAATTTTAAG
77844 ATTTAATTCTTC
1 ATTTAATTCTTC
77856 ATTTAATTCTTC
1 ATTTAATTCTTC
77868 A
1 A
77869 AATTTAATCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.16, G:0.00, T:0.56
Consensus pattern (12 bp):
ATTTAATTCTTC
Found at i:83230 original size:20 final size:20
Alignment explanation
Indices: 83207--83255 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
83197 GCGAATATGT
*
83207 AAATCGCATTGCGATTTTCC
1 AAATCGCATTGCAATTTTCC
**
83227 AAATTCGTGTTGCAATTTTCC
1 AAA-TCGCATTGCAATTTTCC
*
83248 AATTCGCA
1 AAATCGCA
83256 ACTGAATTTC
Statistics
Matches: 22, Mismatches: 6, Indels: 2
0.73 0.20 0.07
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (20 bp):
AAATCGCATTGCAATTTTCC
Found at i:83244 original size:21 final size:20
Alignment explanation
Indices: 83215--83253 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
83205 GTAAATCGCA
*
83215 TTGCGATTTTCCAAATTCGTG
1 TTGCAATTTTCC-AATTCGTG
83236 TTGCAATTTTCCAATTCG
1 TTGCAATTTTCCAATTCG
83254 CAACTGAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGCAATTTTCCAATTCGTG
Found at i:83270 original size:19 final size:20
Alignment explanation
Indices: 83243--83296 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
83233 GTGTTGCAAT
* *
83243 TTTCCAATTCGCAAC-TGAA
1 TTTCAAATTCGCAACACGAA
83262 TTTCAAATTCGCAACACGAA
1 TTTCAAATTCGCAACACGAA
*
83282 TTT-AATTTCGCAACA
1 TTTCAAATTCGCAACA
83297 GGTTTTAGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 25 0.81
20 6 0.19
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.31
Consensus pattern (20 bp):
TTTCAAATTCGCAACACGAA
Found at i:84268 original size:24 final size:24
Alignment explanation
Indices: 84241--84292 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
84231 ATTCAAAATC
84241 TGATCTTGGTCAATACCCGGACTT
1 TGATCTTGGTCAATACCCGGACTT
* *
84265 TGATCTTGGTCAATACTCGGATTT
1 TGATCTTGGTCAATACCCGGACTT
84289 TGAT
1 TGAT
84293 GATGTGATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.38
Consensus pattern (24 bp):
TGATCTTGGTCAATACCCGGACTT
Found at i:86570 original size:6 final size:6
Alignment explanation
Indices: 86548--86582 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
86538 AAGCAAAAGG
* *
86548 AAATCA AAATCT TAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
86583 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.17, G:0.00, T:0.23
Consensus pattern (6 bp):
AAATCA
Found at i:86899 original size:20 final size:20
Alignment explanation
Indices: 86876--86973 Score: 84
Period size: 20 Copynumber: 5.2 Consensus size: 20
86866 ATTCGTAACA
86876 CGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
* **
86896 CGAATTTGACTATCGC--AA
1 CGAATTTGACTTTCGCGTTG
* *
86914 CG--CTT-A-TTTCACGTTG
1 CGAATTTGACTTTCGCGTTG
86930 CGAATTT-ACCTTTCGCGTTG
1 CGAATTTGA-CTTTCGCGTTG
*
86950 TGAATTTGACTTTCGCGTTG
1 CGAATTTGACTTTCGCGTTG
86970 CGAA
1 CGAA
86974 AGTTTACCTT
Statistics
Matches: 59, Mismatches: 12, Indels: 14
0.69 0.14 0.16
Matches are distributed among these distances:
14 4 0.07
15 1 0.02
16 4 0.07
18 5 0.08
20 44 0.75
21 1 0.02
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.38
Consensus pattern (20 bp):
CGAATTTGACTTTCGCGTTG
Found at i:87082 original size:25 final size:25
Alignment explanation
Indices: 87044--87092 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
87034 AAATCAATTA
87044 AACATTGTTGTGGGTACATTATTTG
1 AACATTGTTGTGGGTACATTATTTG
*
87069 AACATTGTTTTGGGTACATTATTT
1 AACATTGTTGTGGGTACATTATTT
87093 AGAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.47
Consensus pattern (25 bp):
AACATTGTTGTGGGTACATTATTTG
Found at i:87501 original size:24 final size:24
Alignment explanation
Indices: 87450--87502 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
87440 TTTCATATGT
* * *
87450 AATTGGAGTTTGAATTTAAATTTT
1 AATTTGAGTTTGAATTTAAATATA
*
87474 AATTTGAGTTTGAATTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
87498 AATTT
1 AATTT
87503 TGGTTCCACT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:88474 original size:20 final size:20
Alignment explanation
Indices: 88451--88493 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
88441 GATCAACAAT
*
88451 AAAGTCAAATTCGCAACGCG
1 AAAGTCAAATTCACAACGCG
*
88471 AAAGTCAAATTCACAATGCG
1 AAAGTCAAATTCACAACGCG
88491 AAA
1 AAA
88494 TCGCAAACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.47, C:0.21, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAGTCAAATTCACAACGCG
Found at i:88680 original size:66 final size:64
Alignment explanation
Indices: 88609--88752 Score: 225
Period size: 66 Copynumber: 2.2 Consensus size: 64
88599 AATTTAAAAC
88609 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAAATAATTCTTATTTACACATCAAATT
1 AACAAATCAACTTTTACAAATCAATTAAACAAGC-AAAAAATAATTCTTATTTACACAT-AAATT
88674 A
64 A
* * * *
88675 AACAAATCAACTTTTATAAATCAATTAAACAAGCAAAAAATAATTCTTATTTCCTCATTAATTA
1 AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATAAATTA
*
88739 AACAAATCATCTTT
1 AACAAATCAACTTT
88753 CAATGTAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
64 18 0.25
65 22 0.30
66 33 0.45
ACGTcount: A:0.50, C:0.17, G:0.01, T:0.32
Consensus pattern (64 bp):
AACAAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATAAATTA
Found at i:88904 original size:24 final size:24
Alignment explanation
Indices: 88876--88928 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
88866 TTTGCTCAAA
88876 CAACACTT-TCTACACATCTAAAAC
1 CAACA-TTGTCTACACATCTAAAAC
* *
88900 CAACATTGTCTTCATATCTAAAAC
1 CAACATTGTCTACACATCTAAAAC
88924 CAACA
1 CAACA
88929 AACAATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 2 0.08
24 24 0.92
ACGTcount: A:0.42, C:0.30, G:0.02, T:0.26
Consensus pattern (24 bp):
CAACATTGTCTACACATCTAAAAC
Found at i:90193 original size:21 final size:21
Alignment explanation
Indices: 90153--90228 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
90143 ACGGGCGGGA
* *
90153 CCTCTTGAACGATCACAGGGG
1 CCTCTTGAACGATGAGAGGGG
* * *
90174 CCTCTTGAACGGTGGGAGGGA
1 CCTCTTGAACGATGAGAGGGG
* *
90195 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
90216 CCTCTTGAACGAT
1 CCTCTTGAACGAT
90229 AGGAGGTACC
Statistics
Matches: 41, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
20 1 0.02
21 39 0.95
22 1 0.02
ACGTcount: A:0.21, C:0.22, G:0.33, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:90195 original size:42 final size:42
Alignment explanation
Indices: 90149--90241 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
90139 AATGACGGGC
* *
90149 GGGACCTCTT-GAACGATCACAGGGGCCTCTTGAACGGTGGGA
1 GGGACCTCTTCG-ACGATCACAGGGGCCTCTTGAACGATAGGA
* * * *
90191 GGGACTTCTTCGATGATGAGAGGGGCCTCTTGAACGATAGGA
1 GGGACCTCTTCGACGATCACAGGGGCCTCTTGAACGATAGGA
*
90233 GGTACCTCT
1 GGGACCTCT
90242 GGAATGATGA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.34, T:0.23
Consensus pattern (42 bp):
GGGACCTCTTCGACGATCACAGGGGCCTCTTGAACGATAGGA
Found at i:92441 original size:19 final size:19
Alignment explanation
Indices: 92390--92444 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
92380 AGAAGTTTCT
* *
92390 GAAACTTAAATTCGCAACGT
1 GAAAC-TAAAATCGCAACGC
*
92410 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
92430 GAAACTAAAATCGCA
1 GAAACTAAAATCGCA
92445 TTACGATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 10 0.33
20 20 0.67
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.16
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:92515 original size:20 final size:20
Alignment explanation
Indices: 92476--92515 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
92466 TGCAATTTTG
* * *
92476 GTGTTGCGATTTTCATTTTC
1 GTGTTGCGAATTTAAGTTTC
92496 GTGTTGCGAATTTAAGTTTC
1 GTGTTGCGAATTTAAGTTTC
92516 AAAAACTATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.12, G:0.23, T:0.50
Consensus pattern (20 bp):
GTGTTGCGAATTTAAGTTTC
Found at i:92879 original size:22 final size:22
Alignment explanation
Indices: 92849--92906 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
92839 GATGGAGATA
92849 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
92871 GACGAATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
92893 GACGGATGTCGCCG
1 GACGGATTTCGCCG
92907 TAGAGAGTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.19, C:0.21, G:0.43, T:0.17
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:93034 original size:20 final size:20
Alignment explanation
Indices: 93011--93149 Score: 201
Period size: 20 Copynumber: 7.0 Consensus size: 20
93001 ATATTGTGTT
*
93011 TCGCGTTGCGAAATTGACTA
1 TCGCGTTGCGAATTTGACTA
*
93031 TCGCGTTGCGAAATTGACT-
1 TCGCGTTGCGAATTTGACTA
**
93050 TCTATGTTGCGAATTTGACTA
1 TC-GCGTTGCGAATTTGACTA
93071 TCGCGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTA
93091 TCGCGTTGCGAATTTGACT-
1 TCGCGTTGCGAATTTGACTA
*
93110 TCTGAGTTGCGAATTTGACTA
1 TC-GCGTTGCGAATTTGACTA
93131 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
93150 TCTATGTTAC
Statistics
Matches: 108, Mismatches: 7, Indels: 8
0.88 0.06 0.07
Matches are distributed among these distances:
19 4 0.04
20 100 0.93
21 4 0.04
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (20 bp):
TCGCGTTGCGAATTTGACTA
Found at i:93108 original size:60 final size:60
Alignment explanation
Indices: 93011--93149 Score: 244
Period size: 60 Copynumber: 2.3 Consensus size: 60
93001 ATATTGTGTT
*
93011 TCGCGTTGCGAAATTGACTATCGCGTTGCGAAATTGACTTCT-ATGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTATCGCGTTGCGAAATTGACTTCTGA-GTTGCGAATTTGACTA
*
93071 TCGCGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGAGTTGCGAATTTGACTA
1 TCGCGTTGCGAATTTGACTATCGCGTTGCGAAATTGACTTCTGAGTTGCGAATTTGACTA
93131 TCGCGTTGCGAATTTGACT
1 TCGCGTTGCGAATTTGACT
93150 TCTATGTTAC
Statistics
Matches: 76, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
60 75 0.99
61 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (60 bp):
TCGCGTTGCGAATTTGACTATCGCGTTGCGAAATTGACTTCTGAGTTGCGAATTTGACTA
Found at i:93175 original size:40 final size:40
Alignment explanation
Indices: 93055--93181 Score: 145
Period size: 40 Copynumber: 3.2 Consensus size: 40
93045 TGACTTCTAT
* * *
93055 GTTGCGAATTTGACTATC-GCGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACT-TCTGAGTTACGAATTTGACAATCGC
* *
93095 GTTGCGAATTTGACTTCTGAGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTCTGAGTTACGAATTTGACAATCGC
93135 GTTGCGAATTTGACTTCT-ATGTTACG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGACTTCTGA-GTTACGAATTTGAC-AA-TCGC
93175 GTTGCGA
1 GTTGCGA
93182 TTTACAGATT
Statistics
Matches: 80, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
38 2 0.03
39 8 0.10
40 70 0.88
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (40 bp):
GTTGCGAATTTGACTTCTGAGTTACGAATTTGACAATCGC
Found at i:93184 original size:20 final size:20
Alignment explanation
Indices: 93159--93242 Score: 78
Period size: 20 Copynumber: 4.2 Consensus size: 20
93149 TTCTATGTTA
93159 CGATTTACAAATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
*
93179 CGATTTACAGATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
* ** * ***
93199 CGAAATTGGAAAATCGCAAAG
1 CG-ATTTACAAATTCGCGTTG
*
93220 CGATTTACATATTCGCGTTG
1 CGATTTACAAATTCGCGTTG
93240 CGA
1 CGA
93243 AATTGGAAAC
Statistics
Matches: 46, Mismatches: 17, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
20 34 0.74
21 12 0.26
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.30
Consensus pattern (20 bp):
CGATTTACAAATTCGCGTTG
Found at i:96292 original size:23 final size:26
Alignment explanation
Indices: 96241--96295 Score: 73
Period size: 26 Copynumber: 2.2 Consensus size: 26
96231 CCATATCCAT
96241 AAAA-ATATTAACATTAAATAATTATA
1 AAAATATATTAACATTAAAT-ATTATA
96267 AAAATATATTAACA-TAAAT-TTA-A
1 AAAATATATTAACATTAAATATTATA
96290 AAAATA
1 AAAATA
96296 AAATATTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 7 0.25
24 3 0.11
26 9 0.32
27 9 0.32
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.33
Consensus pattern (26 bp):
AAAATATATTAACATTAAATATTATA
Found at i:101878 original size:14 final size:14
Alignment explanation
Indices: 101855--101906 Score: 77
Period size: 14 Copynumber: 3.7 Consensus size: 14
101845 TGGGTTAAAA
*
101855 ATAAATGAACGAAC
1 ATAAACGAACGAAC
101869 ATAAACGAACGAAC
1 ATAAACGAACGAAC
*
101883 ATAACCGAACGAAC
1 ATAAACGAACGAAC
*
101897 ATAAATGAAC
1 ATAAACGAAC
101907 ATATAACTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.56, C:0.19, G:0.13, T:0.12
Consensus pattern (14 bp):
ATAAACGAACGAAC
Found at i:103215 original size:16 final size:17
Alignment explanation
Indices: 103189--103231 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
103179 TCTGATTATT
103189 TTTAT-TTTTATT-TAA
1 TTTATATTTTATTCTAA
103204 TTTATATTTTATTCTAA
1 TTTATATTTTATTCTAA
103221 -TTATTATTTTA
1 TTTA-TATTTTA
103232 GTTGTTTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 5 0.20
16 10 0.40
17 10 0.40
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTATATTTTATTCTAA
Found at i:103385 original size:19 final size:19
Alignment explanation
Indices: 103342--103394 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
103332 AAATAACCAA
* * *
103342 CAAATTCACAACGCGATCT
1 CAAATTCGCAACACGAACT
103361 CAAATTCGCAACACGAACT
1 CAAATTCGCAACACGAACT
*
103380 CCAATTTCGCAACAC
1 -CAAATTCGCAACAC
103395 ATTTTCCAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.38, C:0.34, G:0.09, T:0.19
Consensus pattern (19 bp):
CAAATTCGCAACACGAACT
Found at i:103448 original size:20 final size:21
Alignment explanation
Indices: 103343--103481 Score: 85
Period size: 20 Copynumber: 6.9 Consensus size: 21
103333 AATAACCAAC
* *
103343 AAATTCACAACGCG-ATCTC-
1 AAATTCGCAACGCGAATTTCT
* * *
103362 AAATTCGCAACACGAA-CTCC
1 AAATTCGCAACGCGAATTTCT
* * * *
103382 AATTTCGCAACAC-ATTTTCC
1 AAATTCGCAACGCGAATTTCT
* *
103402 AAATTCGCAACTC-AGTTT-T
1 AAATTCGCAACGCGAATTTCT
*
103421 GAAATTCGCAACTCGAATTTCT
1 -AAATTCGCAACGCGAATTTCT
** *
103443 -TTTTCGCAACGCGATTTTCT
1 AAATTCGCAACGCGAATTTCT
103463 AAATTCGCAACGCGAATTT
1 AAATTCGCAACGCGAATTT
103482 GGAATTCGCA
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
19 16 0.17
20 60 0.62
21 19 0.20
22 1 0.01
ACGTcount: A:0.32, C:0.27, G:0.12, T:0.30
Consensus pattern (21 bp):
AAATTCGCAACGCGAATTTCT
Found at i:103554 original size:26 final size:26
Alignment explanation
Indices: 103525--103574 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
103515 CGCATTTACT
* * * *
103525 TTCGCAACGCGAATTTTATTTTCGAA
1 TTCGAAACACGAATATTAATTTCGAA
103551 TTCGAAACACGAATATTAATTTCG
1 TTCGAAACACGAATATTAATTTCG
103575 CAACACAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (26 bp):
TTCGAAACACGAATATTAATTTCGAA
Found at i:104104 original size:20 final size:20
Alignment explanation
Indices: 104081--104136 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
104071 GAAAATGAAA
104081 TTCGCAACACG-ATTTTAGTT
1 TTCGCAACACGAATTTTA-TT
**
104101 TTCGCATTACGAATTTTATT
1 TTCGCAACACGAATTTTATT
**
104121 TTCGCATTACGAATTT
1 TTCGCAACACGAATTT
104137 CGTGTTGCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
20 27 0.82
21 6 0.18
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.45
Consensus pattern (20 bp):
TTCGCAACACGAATTTTATT
Found at i:104118 original size:21 final size:20
Alignment explanation
Indices: 104092--104136 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
104082 TCGCAACACG
104092 ATTTTAGTTTTCGCATTACGA
1 ATTTTA-TTTTCGCATTACGA
104113 ATTTTATTTTCGCATTACGA
1 ATTTTATTTTCGCATTACGA
104133 ATTT
1 ATTT
104137 CGTGTTGCGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 18 0.75
21 6 0.25
ACGTcount: A:0.24, C:0.13, G:0.11, T:0.51
Consensus pattern (20 bp):
ATTTTATTTTCGCATTACGA
Found at i:104163 original size:20 final size:20
Alignment explanation
Indices: 104134--104190 Score: 87
Period size: 20 Copynumber: 2.9 Consensus size: 20
104124 GCATTACGAA
*
104134 TTTCGTGTTGCGAATTTCAT
1 TTTCGAGTTGCGAATTTCAT
104154 TTTCGAGTTGCGAATTTCAT
1 TTTCGAGTTGCGAATTTCAT
* *
104174 TTTTGAGTTGCAAATTT
1 TTTCGAGTTGCGAATTT
104191 AAGTTTCAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.49
Consensus pattern (20 bp):
TTTCGAGTTGCGAATTTCAT
Found at i:112012 original size:19 final size:18
Alignment explanation
Indices: 111988--112039 Score: 61
Period size: 19 Copynumber: 2.8 Consensus size: 18
111978 ATAATGTTTA
111988 AAAGTATCGATACTTATAT-
1 AAAGTATCGATACTT-T-TC
*
112007 AAAGTATCGAAACTTTTC
1 AAAGTATCGATACTTTTC
112025 AGAAGTATCGATACT
1 A-AAGTATCGATACT
112040 CTTGGGCTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 1 0.03
18 2 0.07
19 26 0.90
ACGTcount: A:0.40, C:0.13, G:0.13, T:0.33
Consensus pattern (18 bp):
AAAGTATCGATACTTTTC
Found at i:114240 original size:23 final size:23
Alignment explanation
Indices: 114203--114257 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 23
114193 CAGCTCATAT
* *
114203 AAATACACCAAAGTGCCACGTAG
1 AAATGCACCAAAGTGCCACCTAG
* * *
114226 AATTGCACCATAGTGCCGCCTAG
1 AAATGCACCAAAGTGCCACCTAG
114249 AAATGCACC
1 AAATGCACC
114258 GGAGTGCATG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.29, G:0.18, T:0.16
Consensus pattern (23 bp):
AAATGCACCAAAGTGCCACCTAG
Found at i:114263 original size:23 final size:23
Alignment explanation
Indices: 114203--114264 Score: 61
Period size: 23 Copynumber: 2.7 Consensus size: 23
114193 CAGCTCATAT
* * *
114203 AAATACACCAAAGTGCCACGTAG
1 AAATGCACCAGAGTGCCACCTAG
* * *
114226 AATTGCACCATAGTGCCGCCTAG
1 AAATGCACCAGAGTGCCACCTAG
*
114249 AAATGCACCGGAGTGC
1 AAATGCACCAGAGTGC
114265 ATGTAAGATT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.34, C:0.27, G:0.23, T:0.16
Consensus pattern (23 bp):
AAATGCACCAGAGTGCCACCTAG
Found at i:115339 original size:20 final size:20
Alignment explanation
Indices: 115314--115351 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
115304 TTCCCCTTGA
*
115314 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
115334 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
115352 TTAATATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:119724 original size:20 final size:20
Alignment explanation
Indices: 119699--119736 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
119689 TTCCCCTTGA
*
119699 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
119719 AGTGCATCGATGCATTCT
1 AGTGCATCGATGCATTCT
119737 TTAATATGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:121388 original size:20 final size:20
Alignment explanation
Indices: 121363--121434 Score: 76
Period size: 19 Copynumber: 3.6 Consensus size: 20
121353 TGAAAATATT
121363 TAATAAAATAAAATAGATAA
1 TAATAAAATAAAATAGATAA
** *
121383 TAAT-AAATAAAAGGGAAAA
1 TAATAAAATAAAATAGATAA
*
121402 TAATAAAATAAAAATA-ATAG
1 TAATAAAAT-AAAATAGATAA
*
121422 TAGTAAAATAAAA
1 TAATAAAATAAAA
121435 AAAGGTTTTA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
19 20 0.48
20 18 0.43
21 4 0.10
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.22
Consensus pattern (20 bp):
TAATAAAATAAAATAGATAA
Found at i:121494 original size:17 final size:18
Alignment explanation
Indices: 121458--121499 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
121448 TTTGTTTTTA
121458 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
*
121476 AAATAAAAGA-AATAATT
1 AAATAAAAGATAAGAATT
121493 AAATAAA
1 AAATAAA
121500 TAATCTAAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:122262 original size:74 final size:70
Alignment explanation
Indices: 122086--122289 Score: 227
Period size: 74 Copynumber: 2.9 Consensus size: 70
122076 TAAATCATCT
* * *
122086 TAAATCCTAATTAAAATACTTAAAAACTATTTAAACTAAAATACCTAAAAAATAATATTTAAAAC
1 TAAAACCTAATTAAAATAC-T-AAAACTATTTAAACTAAAATACCTAAAAAATAAAATATAAAAC
*
122151 AATATTC
64 AATATCC
* *
122158 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATATCTAAACAAAGATAAAATATAAA
1 TAAAACCTAATTAAAATACTAAAA-CTATTTAAACTAAAATACCT-AA-AAA-ATAAAATATAAA
122223 A-AATATCC
62 ACAATATCC
* * *
122231 TAAAACTTAATTTAAAATACTAAAACGTATTTAAAATAAAATA-C--AAAGATAAAATATAA
1 TAAAACCTAA-TTAAAATACTAAAAC-TATTTAAACTAAAATACCTAAAAAATAAAATATAA
122290 TGTTTAAAAT
Statistics
Matches: 118, Mismatches: 8, Indels: 16
0.83 0.06 0.11
Matches are distributed among these distances:
68 11 0.09
69 2 0.02
70 5 0.04
71 20 0.17
72 21 0.18
73 19 0.16
74 40 0.34
ACGTcount: A:0.58, C:0.11, G:0.01, T:0.29
Consensus pattern (70 bp):
TAAAACCTAATTAAAATACTAAAACTATTTAAACTAAAATACCTAAAAAATAAAATATAAAACAA
TATCC
Found at i:122264 original size:19 final size:20
Alignment explanation
Indices: 122230--122268 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
122220 AAAAAATATC
*
122230 CTAAAACTTAATTTAAAATA
1 CTAAAACGTAATTTAAAATA
122250 CTAAAACGT-ATTTAAAATA
1 CTAAAACGTAATTTAAAATA
122269 AAATACAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.54, C:0.10, G:0.03, T:0.33
Consensus pattern (20 bp):
CTAAAACGTAATTTAAAATA
Done.