Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006233.1 Hibiscus syriacus cultivar Beakdansim tig00014857_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: 84115
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:149 original size:24 final size:24
Alignment explanation
Indices: 98--150 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
88 TTTCATATGT
* * *
98 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATA
* *
122 AATTTGAGTTTGAGTTTCAATATA
1 AATTTGAGTTTGAATTTAAATATA
146 AATTT
1 AATTT
151 CGGCTCCTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATA
Found at i:2050 original size:200 final size:197
Alignment explanation
Indices: 1669--2404 Score: 865
Period size: 200 Copynumber: 3.7 Consensus size: 197
1659 GTGCACACAT
* * * ** *
1669 AAAGTGTCGATCCCAAAAACATTGAAACCCATAATTATAATGTAATAGGTAATTTTGTAATATAA
1 AAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
* * * * * *
1734 CCAGTATAAATATACCGGTTTTATGTGAAAATAGGTCTACATAATGTGTCGACACTTTTGAATTT
66 CCGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACATAATGTATCGACACTTTAGAA-TT
* * * * *
1799 TGTGTCGATACTTTTTGTCCAGAATGATTGCCCAAAATGGTGAATGCATAAAGTGTCGATACATT
130 TGTGTCGATACTTTTTGTCCAAAATGAATG-CCAAAAGGGTGCACGCATAAAGTGTCGATACATT
1864 TATAA
194 T-TAA
* * *
1869 AAAGTATCAATCCTAGAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
1 AAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
* * * ** * *
1934 CCGTTATAACTATACCGATTTTATGAGAGAATAGGTTTACATAATGTATTGACACTTGTGGAATT
66 CCGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACATAATGTATCGACACTT-TAGAATT
* *
1999 TGTGTTGATCCTTTTTGTCCAAAATGAATGCCAAAAGGGTTGCACGCATAAAGTGTCGATACAGT
130 TGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGG-TGCACGCATAAAGTGTCGATACA-T
2064 TTTAA
193 TTTAA
* *
2069 AAAGTATCGATCCCAAAAACATCGAAATCGAT--TTATAATGTAATAGGTAAATTTACAATGTAA
1 AAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
* * * *
2132 CGGGTAT-AATTTACCGGTTTTATGAGAAAATAGGTGAACATAATGTATCGACACATTTTAG-AT
66 CCGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACATAATGTATCGACAC--TTTAGAAT
* * * * * *
2195 TTGTGTCAATAC-ATTTGTCCATAATGAATGCCAAACAGGGTGCAGGAACAAAGTGTCGATACAT
129 TTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAA-AGGGTGCACGCATAAAGTGTCGATACAT
*
2259 TTGAA
193 TTTAA
** * * *
2264 ATTGTATCGATCCCAAAAACATCGAAACCGATAATTATAACGTAATAGGTAAATTTATAATGTAA
1 AAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
* * * *
2329 CAGGTATAAATATATC-AGTTTTATGAGAGAATAGGCCAACATAATGTATCGACACTTTTA-AAT
66 CCGGTATAAATATACCGA-TTTTATGAGAAAATAGGTCAACATAATGTATCGACAC-TTTAGAAT
2392 TTGTGTCGATACT
129 TTGTGTCGATACT
2405 ATTTAAATAA
Statistics
Matches: 461, Mismatches: 63, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
195 34 0.07
196 41 0.09
197 108 0.23
198 78 0.17
199 10 0.02
200 183 0.40
201 7 0.02
ACGTcount: A:0.38, C:0.14, G:0.17, T:0.32
Consensus pattern (197 bp):
AAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAGGTAAATTTACAATGTAA
CCGGTATAAATATACCGATTTTATGAGAAAATAGGTCAACATAATGTATCGACACTTTAGAATTT
GTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTGCACGCATAAAGTGTCGATACATTTT
AA
Found at i:2128 original size:20 final size:21
Alignment explanation
Indices: 2099--2145 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
2089 ATCGAAATCG
* *
2099 ATTTATAATGTAATAGGTA-A
1 ATTTACAATGTAACAGGTATA
*
2119 ATTTACAATGTAACGGGTATA
1 ATTTACAATGTAACAGGTATA
2140 ATTTAC
1 ATTTAC
2146 CGGTTTTATG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.38
Consensus pattern (21 bp):
ATTTACAATGTAACAGGTATA
Found at i:4035 original size:19 final size:19
Alignment explanation
Indices: 4011--4059 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
4001 AATATAGGGT
*
4011 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTCA
** *
4030 TAATTTTACATACGATTCA
1 TAATTTTGTATAAGATTCA
4049 TAATTTTGTAT
1 TAATTTTGTAT
4060 GTGAATGTAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.35, C:0.06, G:0.08, T:0.51
Consensus pattern (19 bp):
TAATTTTGTATAAGATTCA
Found at i:5599 original size:45 final size:44
Alignment explanation
Indices: 5548--5650 Score: 120
Period size: 45 Copynumber: 2.3 Consensus size: 44
5538 GTACATGCAG
*
5548 TGCATCGATGCAT-TAATTTAAAAAGAAAACATCGAAT-AGAATTTA
1 TGCATCGATGCATCCAA-TTAAAAA-AAAACATCGAATAAG-ATTTA
* * *
5593 TGCATCGATGCATCCCCATTAAATACAAACATCGAATAAGATTTA
1 TGCATCGATGCAT-CCAATTAAAAAAAAACATCGAATAAGATTTA
5638 TGCATCGATGCAT
1 TGCATCGATGCAT
5651 GGTGTAGTGC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
45 42 0.82
46 8 0.16
47 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (44 bp):
TGCATCGATGCATCCAATTAAAAAAAAACATCGAATAAGATTTA
Found at i:6316 original size:23 final size:23
Alignment explanation
Indices: 6258--6321 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
6248 CATTATTATA
6258 TGGCAC-TACGGTGCAATTCTACG
1 TGGCACTTA-GGTGCAATTCTACG
* *
6281 TGACA-TTCCGGTGCAATTCTACG
1 TGGCACTT-AGGTGCAATTCTACG
*
6304 TGGCACTTAGGTGTAATT
1 TGGCACTTAGGTGCAATT
6322 ATATGAGCTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
23 31 0.94
24 2 0.06
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (23 bp):
TGGCACTTAGGTGCAATTCTACG
Found at i:15815 original size:199 final size:199
Alignment explanation
Indices: 15426--16124 Score: 844
Period size: 199 Copynumber: 3.5 Consensus size: 199
15416 ACCTAAATAT
*
15426 GTGTCGATACATTT-TCT-AAAGTATCGA-CCCAAAAAACATCGAAACCAATAATTATAATGTAA
1 GTGTCGATACATTTAT-TAAAAGTATCGATCCCAAAAAACATCGAAACCGATAATTATAATGTAA
* * * * * *
15488 TAGGTAAATTAACAATGTAACCGATAT-AATATATCAG-TTAATTACAAAACATGTCAACATAAT
65 TAAGTAAATTTACAATGTAACCGATATAAATATATCAGTTTTATGAGAAAATATGTC-ACATAAT
** * * *
15551 GTATCGACACTTGTGCAATTTGTATCGATACTTAATGTCTAGAATGAATGCTCAAACGAGGTGCA
129 GTATCGACACTTGTTAAATTTGTGTCGATACTT-TTGTCCAGAATGAATGC-CAAACGAGGTGCA
15616 CGCATAAA
192 CGCATAAA
* *
15624 GTGTTGATACATTTATTAAAAGTATCGATCCCAATAAA-ATCGAAACCGATAATTATAATGTAAT
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAAACATCGAAACCGATAATTATAATGTAAT
* * *
15688 AAGTAAATTTACAATGTAACCGGTATAAATATATCAGTTTTATGAGAAAATAGGTCAGCATAAAG
66 AAGTAAATTTACAATGTAACCGATATAAATATATCAGTTTTATGAGAAAATATGTCA-CATAATG
* * *
15753 TATCGACACTTGTTAAATTTGTGTCGATACATTTTGTCCATAATAAATACCAAACG-GGTGCACG
130 TATCGACACTTGTTAAATTTGTGTCGATAC-TTTTGTCCAGAATGAATGCCAAACGAGGTGCACG
15817 CATAAA
194 CATAAA
* * *
15823 GTGTCGATACATTTATTAAAAGTATCGATCGC-AAAAACATCGAAACCGATAATTACAATGTGAT
1 GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAAACATCGAAACCGATAATTATAATGTAAT
* * * * * * * *
15887 AGGTAAATTTACAATGTACCCGATAGAAATATACCGGTTTTATGAGAAAATATATCTAAATGATG
66 AAGTAAATTTACAATGTAACCGATATAAATATATCAGTTTTATGAGAAAATATGTC-ACATAATG
* * * * *
15952 TATCGACATTTTTTAAGTTTGTGTCGATACTTTTTTCCAGAATGAATGCCCAACGAGGTGCACGC
130 TATCGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGC
16017 ATAAA
195 ATAAA
* ** * *
16022 GTATCGATACATTTCA--AATTGTATCGAT-CCAAAAAATATCGAAACCGATAATTGTAATGTAA
1 GTGTCGATACATTT-ATTAAAAGTATCGATCCCAAAAAACATCGAAACCGATAATTATAATGTAA
* * * *
16084 TAAGTAAATTTACAATGTTACTGGTATAAATATATCGGTTT
65 TAAGTAAATTTACAATGTAACCGATATAAATATATCAGTTT
16125 CCTTATAAAA
Statistics
Matches: 430, Mismatches: 59, Indels: 24
0.84 0.12 0.05
Matches are distributed among these distances:
197 1 0.00
198 109 0.25
199 233 0.54
200 27 0.06
201 58 0.13
202 2 0.00
ACGTcount: A:0.39, C:0.14, G:0.15, T:0.31
Consensus pattern (199 bp):
GTGTCGATACATTTATTAAAAGTATCGATCCCAAAAAACATCGAAACCGATAATTATAATGTAAT
AAGTAAATTTACAATGTAACCGATATAAATATATCAGTTTTATGAGAAAATATGTCACATAATGT
ATCGACACTTGTTAAATTTGTGTCGATACTTTTGTCCAGAATGAATGCCAAACGAGGTGCACGCA
TAAA
Found at i:16251 original size:87 final size:86
Alignment explanation
Indices: 16144--16308 Score: 267
Period size: 87 Copynumber: 1.9 Consensus size: 86
16134 ATAGGTTAAT
* *
16144 ATAAGCGCTACCTATCACATTATATAAACTCTACCTAATATGTTATTGTATTTGATAATATTTCC
1 ATAAGCGCTACCTATCACATTATATAAACACTACCTAATATGTTATTATATTTGATAATATTTCC
16209 GGTTAAATGCATATTTTATTAG
66 GGTTAAATG-ATATTTTATTAG
* * * *
16231 ATAAGCGCTACTTATTACATTATATAAGCACTACCTAATATGTTATTATATTTGATAATATTTCT
1 ATAAGCGCTACCTATCACATTATATAAACACTACCTAATATGTTATTATATTTGATAATATTTCC
16296 GGTTAAATGATAT
66 GGTTAAATGATAT
16309 AATATAACCG
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
86 4 0.06
87 68 0.94
ACGTcount: A:0.35, C:0.13, G:0.10, T:0.42
Consensus pattern (86 bp):
ATAAGCGCTACCTATCACATTATATAAACACTACCTAATATGTTATTATATTTGATAATATTTCC
GGTTAAATGATATTTTATTAG
Found at i:20860 original size:38 final size:38
Alignment explanation
Indices: 20783--20860 Score: 86
Period size: 38 Copynumber: 2.1 Consensus size: 38
20773 ATTAAACATG
* * * *
20783 ATATATTTTTATATAAATTATGTTGAAGTAAAATTTTA
1 ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
**
20821 ATATATTTTTCAAATAAATTATG-TAAAATTTAATATTA
1 ATATATTTTT-AAATAAATTATGTTAAAATAAAATATTA
20859 AT
1 AT
20861 TAAAATTAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
38 22 0.67
39 11 0.33
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (38 bp):
ATATATTTTTAAATAAATTATGTTAAAATAAAATATTA
Found at i:20926 original size:21 final size:21
Alignment explanation
Indices: 20902--20969 Score: 52
Period size: 21 Copynumber: 3.2 Consensus size: 21
20892 TAATAAAATA
20902 ATATATTATCGATGATTTTTT
1 ATATATTATCGATGATTTTTT
* * *
20923 ATATA-AAT-AAT-TTTTATTT
1 ATATATTATCGATGATTT-TTT
*
20942 AAATATATTATCGATGAATTTTT
1 --ATATATTATCGATGATTTTTT
20965 ATATA
1 ATATA
20970 AATAATTTTT
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
18 3 0.09
19 5 0.15
20 2 0.06
21 15 0.44
22 2 0.06
23 5 0.15
24 2 0.06
ACGTcount: A:0.38, C:0.03, G:0.06, T:0.53
Consensus pattern (21 bp):
ATATATTATCGATGATTTTTT
Found at i:20938 original size:15 final size:15
Alignment explanation
Indices: 20918--20991 Score: 66
Period size: 15 Copynumber: 5.1 Consensus size: 15
20908 TATCGATGAT
20918 TTTTTATATAAATAA
1 TTTTTATATAAATAA
*
20933 TTTTTATTTAAAT-A
1 TTTTTATATAAATAA
* **
20947 --TAT-TATCGATGAA
1 TTTTTATATAAAT-AA
20960 TTTTTATATAAATAA
1 TTTTTATATAAATAA
*
20975 TTTTTATTTAAATAA
1 TTTTTATATAAATAA
20990 TT
1 TT
20992 AGAATTTCAC
Statistics
Matches: 45, Mismatches: 9, Indels: 10
0.70 0.14 0.16
Matches are distributed among these distances:
11 4 0.09
12 2 0.04
13 1 0.02
14 1 0.02
15 32 0.71
16 5 0.11
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (15 bp):
TTTTTATATAAATAA
Found at i:20947 original size:42 final size:42
Alignment explanation
Indices: 20901--20992 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
20891 ATAATAAAAT
*
20901 AATATATTATCGATGATTTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
20943 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
1 AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
20985 AATA-ATTA
1 AATATATTA
20993 GAATTTCACA
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
41 4 0.08
42 45 0.92
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.52
Consensus pattern (42 bp):
AATATATTATCGATGAATTTTTATATAAATAATTTTTATTTA
Found at i:25279 original size:22 final size:22
Alignment explanation
Indices: 25254--25298 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
25244 TGTTCCTTAC
25254 ATAGAACAAATTTTGTAATTAT
1 ATAGAACAAATTTTGTAATTAT
25276 ATAGAACAAATTTTGTAATTAT
1 ATAGAACAAATTTTGTAATTAT
25298 A
1 A
25299 ACTTCATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (22 bp):
ATAGAACAAATTTTGTAATTAT
Found at i:30230 original size:90 final size:91
Alignment explanation
Indices: 30095--30259 Score: 233
Period size: 90 Copynumber: 1.8 Consensus size: 91
30085 GATACGTTAG
* * * * * * *
30095 ACACCTATTTTTATCAAAACATTCTTAAGGCACCAAAAGTCAATTTGAGATATAGTCTAGGCACT
1 ACACCTATTTTTAACAAAACAATCTTAAGGCACAAAAAGTCAATTTGACATATAATCTAGACACC
30160 TAAAAGTGTAACGGAGAGAACGATAA
66 TAAAAGTGTAACGGAGAGAACGATAA
* * *
30186 ACACCTATTTTTAAGAAAA-AATCTTTAGGCACAAAAAGTCAATTTGACATATAATTTAGACACC
1 ACACCTATTTTTAACAAAACAATCTTAAGGCACAAAAAGTCAATTTGACATATAATCTAGACACC
30250 TAAAAGTGTA
66 TAAAAGTGTA
30260 TTAAGCCGTA
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
90 47 0.73
91 17 0.27
ACGTcount: A:0.42, C:0.16, G:0.14, T:0.28
Consensus pattern (91 bp):
ACACCTATTTTTAACAAAACAATCTTAAGGCACAAAAAGTCAATTTGACATATAATCTAGACACC
TAAAAGTGTAACGGAGAGAACGATAA
Found at i:30493 original size:86 final size:86
Alignment explanation
Indices: 30348--30526 Score: 349
Period size: 86 Copynumber: 2.1 Consensus size: 86
30338 CAAGTGAGAA
30348 TTATCAAGTGGATTAAGTGATAAAAGAGAATGTTATATTCTTTAGAGATTTTAAGTTGGAGAAGC
1 TTATCAAGTGGATTAAGTGATAAAAGAGAATGTTATATTCTTTAGAGATTTTAAGTTGGAGAAGC
30413 TACGATTACAAGATGTATATG
66 TACGATTACAAGATGTATATG
30434 TTATCAAGTGGATTAAGTGATAAAAGAGAATGTTATATTCTTTAGAGATTTTAAGTTGGAGAAGC
1 TTATCAAGTGGATTAAGTGATAAAAGAGAATGTTATATTCTTTAGAGATTTTAAGTTGGAGAAGC
*
30499 TACGATTACAGGATGTATATG
66 TACGATTACAAGATGTATATG
30520 TTATCAA
1 TTATCAA
30527 TTGATCAACT
Statistics
Matches: 92, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
86 92 1.00
ACGTcount: A:0.37, C:0.06, G:0.22, T:0.35
Consensus pattern (86 bp):
TTATCAAGTGGATTAAGTGATAAAAGAGAATGTTATATTCTTTAGAGATTTTAAGTTGGAGAAGC
TACGATTACAAGATGTATATG
Found at i:34356 original size:17 final size:19
Alignment explanation
Indices: 34322--34356 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
34312 TAGACTCATT
34322 AAATTATTAATACCAAATC
1 AAATTATTAATACCAAATC
34341 AAATT-TTAAT-CCAAAT
1 AAATTATTAATACCAAAT
34357 TTAAAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 5 0.31
19 5 0.31
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATTATTAATACCAAATC
Found at i:34407 original size:28 final size:27
Alignment explanation
Indices: 34354--34408 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
34344 TTTTAATCCA
* ***
34354 AATTTAAAAAAATATTATATTCAAATT
1 AATTTAAAAAAAAATTATAAAAAAATT
34381 AATTTAAATAAAAAATTATAAAAAAATT
1 AATTTAAA-AAAAAATTATAAAAAAATT
34409 CTGTTAATTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (27 bp):
AATTTAAAAAAAAATTATAAAAAAATT
Found at i:35775 original size:70 final size:69
Alignment explanation
Indices: 35658--35982 Score: 322
Period size: 70 Copynumber: 4.6 Consensus size: 69
35648 TATTTGTAAG
* *
35658 AAACGTATAATATATAGTTTTTAAAATAGTTTTAAAAAAACGTATAATATATA-TTTTTAAAATG
1 AAACATATAATATATAGTTTTTAAAATAGTTTT--GAAAACGTATAATATATAGTTTTTAAAAT-
35722 ATTTTGA
63 ATTTTGA
* *
35729 AAACATATAGTATATAGTTTTTCAAAATAGTTTGGAAAACGTATAATATATAGTTTTTAAAATAG
1 AAACATATAATATATAGTTTTT-AAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAATA-
*
35794 TTTTAA
64 TTTTGA
* * * * * *
35800 AAACGTATAATATATAG-TTTTAAAATGGTTTTGAAAACATATAGTATATAGTTTTTTAAATA-G
1 AAACATATAATATATAGTTTTTAAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAATATT
35863 TTGAA
66 TTG-A
* ** * **
35868 AAAAATGTATAATATATAG-TTTTAAAACGGTTTTGAAAACATAT-ATAATATAGTTTTCGAAAT
1 AAACA--TATAATATATAGTTTTTAAAATAGTTTTGAAAACGTATAAT-ATATAGTTTTTAAAAT
35931 GATTTTGA
63 -ATTTTGA
* *
35939 AAAC-TAGTAATATATAGTTTTTTAAA-GGATTTTGAAAACGTATA
1 AAACATA-TAATATATAGTTTTTAAAATAG-TTTTGAAAACGTATA
35983 TTTTAAAAAA
Statistics
Matches: 217, Mismatches: 24, Indels: 26
0.81 0.09 0.10
Matches are distributed among these distances:
67 2 0.01
68 6 0.03
69 49 0.23
70 92 0.42
71 55 0.25
72 13 0.06
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.41
Consensus pattern (69 bp):
AAACATATAATATATAGTTTTTAAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAATATT
TTGA
Found at i:35842 original size:105 final size:104
Alignment explanation
Indices: 35658--35982 Score: 408
Period size: 105 Copynumber: 3.1 Consensus size: 104
35648 TATTTGTAAG
*
35658 AAACGTATAATATATAGTTTTTAAAATAGTTTTAAAAAAACGTATAATATATATTTTTAAAATGA
1 AAACGTATAATATATAGTTTTTAAAATAGTTTT--AAAAACGTATAATATATAGTTTTAAAATGA
35723 TTTTGAAAACATATAGTATATAGTTTTTCAAAATAGTTTGGA
64 TTTTGAAAACATATAGTATATAGTTTTT-AAAATAGTTTGGA
*
35765 AAACGTATAATATATAGTTTTTAAAATAGTTTTAAAAACGTATAATATATAGTTTTAAAATGGTT
1 AAACGTATAATATATAGTTTTTAAAATAGTTTTAAAAACGTATAATATATAGTTTTAAAATGATT
* *
35830 TTGAAAACATATAGTATATAGTTTTTTAAATAG-TTGAAAA
66 TTGAAAACATATAGTATATAGTTTTTAAAATAGTTTG--GA
* ** * * *
35870 AAATGTATAATATATAG-TTTTAAAACGGTTTTGAAAACATAT-ATAATATAGTTTTCGAAATGA
1 AAACGTATAATATATAGTTTTTAAAATAGTTTTAAAAACGTATAAT-ATATAGTTTT-AAAATGA
* * * *
35933 TTTTGAAAAC-TAGTAATATATAGTTTTTTAAA-GGATTTTGA
64 TTTTGAAAACATA-TAGTATATAGTTTTTAAAATAG-TTTGGA
35974 AAACGTATA
1 AAACGTATA
35983 TTTTAAAAAA
Statistics
Matches: 195, Mismatches: 16, Indels: 17
0.86 0.07 0.07
Matches are distributed among these distances:
103 5 0.03
104 49 0.25
105 106 0.54
106 2 0.01
107 33 0.17
ACGTcount: A:0.44, C:0.04, G:0.12, T:0.41
Consensus pattern (104 bp):
AAACGTATAATATATAGTTTTTAAAATAGTTTTAAAAACGTATAATATATAGTTTTAAAATGATT
TTGAAAACATATAGTATATAGTTTTTAAAATAGTTTGGA
Found at i:36059 original size:13 final size:12
Alignment explanation
Indices: 36040--36094 Score: 58
Period size: 13 Copynumber: 4.4 Consensus size: 12
36030 TTATTACATA
36040 TTATTATTTATT
1 TTATTATTTATT
36052 TTATTTATTTATT
1 TTA-TTATTTATT
* *
36065 TCGATT-TTTAAT
1 T-TATTATTTATT
36077 TTATTATTTTATT
1 TTATTA-TTTATT
36090 TTATT
1 TTATT
36095 TTCGGTCAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 3 0.09
12 9 0.26
13 22 0.63
14 1 0.03
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (12 bp):
TTATTATTTATT
Found at i:37286 original size:24 final size:23
Alignment explanation
Indices: 37234--37290 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
37224 TGTTTTTCAT
*
37234 TATTTTTTATTTATTTTTAAATA
1 TATTTTTTATTTATCTTTAAATA
*
37257 TATTTTTTATTTATCTTTCAATA
1 TATTTTTTATTTATCTTTAAATA
*
37280 T-TCTTTTATTT
1 TATTTTTTATTT
37291 TTATTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 9 0.29
23 22 0.71
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (23 bp):
TATTTTTTATTTATCTTTAAATA
Found at i:37303 original size:10 final size:10
Alignment explanation
Indices: 37226--37372 Score: 56
Period size: 10 Copynumber: 14.6 Consensus size: 10
37216 CTTTAACATG
*
37226 TTTTTCATTA
1 TTTTTTATTA
37236 TTTTTTATTTA
1 TTTTTTA-TTA
*
37247 TTTTTAAATATA
1 TTTTT-TAT-TA
37259 TTTTTTATTTA
1 TTTTTTA-TTA
* * *
37270 TCTTTCAATA
1 TTTTTTATTA
*
37280 -TTCTT-TTA
1 TTTTTTATTA
37288 -TTTTTATTA
1 TTTTTTATTA
37297 TTTTTTATTA
1 TTTTTTATTA
*
37307 CTCTTTTT-TTC
1 -T-TTTTTATTA
37318 TTTATTT-TTA
1 TTT-TTTATTA
**
37328 -AATTTATT-
1 TTTTTTATTA
*
37336 TTTTTCATTA
1 TTTTTTATTA
*
37346 TCTTTTATTA
1 TTTTTTATTA
* *
37356 TATTATATTA
1 TTTTTTATTA
37366 TATTTTT
1 T-TTTTT
37373 CACTTTTAAC
Statistics
Matches: 100, Mismatches: 24, Indels: 25
0.67 0.16 0.17
Matches are distributed among these distances:
8 9 0.09
9 14 0.14
10 40 0.40
11 23 0.23
12 14 0.14
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTTTATTA
Found at i:37322 original size:52 final size:49
Alignment explanation
Indices: 37259--37355 Score: 115
Period size: 49 Copynumber: 1.9 Consensus size: 49
37249 TTTAAATATA
* *
37259 TTTTTTATTTATCTTTCAATATTCT-TTTATTTTTATTATTTTTTATTACTCT
1 TTTTTTATTTAT-TTTCAA-ATT-TATTT-TTTTCATTATCTTTTATTACTCT
* *
37311 TTTTTTCTTTATTTTTAAATTTATTTTTTTCATTATCTTTTATTA
1 TTTTTTATTTATTTTCAAATTTATTTTTTTCATTATCTTTTATTA
37356 TATTATATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
49 18 0.45
50 6 0.15
51 5 0.12
52 11 0.28
ACGTcount: A:0.20, C:0.08, G:0.00, T:0.72
Consensus pattern (49 bp):
TTTTTTATTTATTTTCAAATTTATTTTTTTCATTATCTTTTATTACTCT
Found at i:37341 original size:24 final size:24
Alignment explanation
Indices: 37236--37340 Score: 81
Period size: 24 Copynumber: 4.2 Consensus size: 24
37226 TTTTTCATTA
*
37236 TTTTTTATTTATTTTTAAATATA-
1 TTTTTTATTTATTTTTAAATTTAT
* *
37259 TTTTTTATTTATCTTTCAATATTCTTT
1 TTTTTTATTTAT-TTTTAA-ATT-TAT
* *
37286 TATTTTTA-TTATTTTT-TATTACTCT
1 T-TTTTTATTTATTTTTAAATT--TAT
*
37311 TTTTTTCTTTATTTTTAAATTTAT
1 TTTTTTATTTATTTTTAAATTTAT
37335 TTTTTT
1 TTTTTT
37341 CATTATCTTT
Statistics
Matches: 65, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
23 12 0.18
24 21 0.32
25 14 0.22
26 7 0.11
27 5 0.08
28 6 0.09
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (24 bp):
TTTTTTATTTATTTTTAAATTTAT
Found at i:37359 original size:24 final size:23
Alignment explanation
Indices: 37288--37359 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 23
37278 TATTCTTTTA
*
37288 TTTTT-ATTATTTTTTATTACTCTT
1 TTTTTCATTA-TTTTTATTA-TATT
*
37312 TTTTTCTTTATTTTTAAATT-TATT
1 TTTTTCATTATTTTT--ATTATATT
37336 TTTTTCATTATCTTTTATTATATT
1 TTTTTCATTAT-TTTTATTATATT
37360 ATATTATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
23 3 0.08
24 27 0.68
25 7 0.17
26 3 0.08
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (23 bp):
TTTTTCATTATTTTTATTATATT
Found at i:40547 original size:23 final size:23
Alignment explanation
Indices: 40502--40547 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
40492 CATCTTTATA
* *
40502 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGATGCAATTATACG
*
40525 TGGCACTTCGATGCATTTATACG
1 TGGCACTTCGATGCAATTATACG
40548 AGATGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (23 bp):
TGGCACTTCGATGCAATTATACG
Found at i:40757 original size:3 final size:3
Alignment explanation
Indices: 40743--40816 Score: 121
Period size: 3 Copynumber: 24.7 Consensus size: 3
40733 TCATTATGCC
* * *
40743 ATT ATC ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT TTT ATT TTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
40791 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
40817 GCCACACTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.31, C:0.01, G:0.00, T:0.68
Consensus pattern (3 bp):
ATT
Found at i:47681 original size:3 final size:3
Alignment explanation
Indices: 47659--47762 Score: 183
Period size: 3 Copynumber: 34.7 Consensus size: 3
47649 TTATTATGGC
*
47659 ATT ATC ATT A-T ATAT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
47704 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
47752 ATT ATT ATT AT
1 ATT ATT ATT AT
47763 GCCTCACTAA
Statistics
Matches: 97, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
2 2 0.02
3 92 0.95
4 3 0.03
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:53679 original size:22 final size:20
Alignment explanation
Indices: 53634--53703 Score: 76
Period size: 18 Copynumber: 3.6 Consensus size: 20
53624 TTCAGTATTC
*
53634 GTCCCGTAGGACCACTATA-
1 GTCCCGAAGGACCACTATAT
53653 -TCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCAC--TATAT
*
53674 GTCCCGTAGGACCAC--TAT
1 GTCCCGAAGGACCACTATAT
53692 GTCCCGAAGGAC
1 GTCCCGAAGGAC
53704 TACTCCTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
18 27 0.61
20 4 0.09
22 13 0.30
ACGTcount: A:0.26, C:0.31, G:0.23, T:0.20
Consensus pattern (20 bp):
GTCCCGAAGGACCACTATAT
Found at i:54801 original size:64 final size:62
Alignment explanation
Indices: 54668--54828 Score: 180
Period size: 64 Copynumber: 2.5 Consensus size: 62
54658 TAATGAAGGT
* * * *
54668 ATGCATCGATGCACTACACCATGCATCGATACATAAATCCTATTCGATGTTTGTATTTAATGGGG
1 ATGCATCGATGCACT-C-CTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAAT-GGA
* *
54733 ATGCATCGATGCACTCCTTATGCATCGATGCATAAATCCTATTCGATGTTTTCTTTTTAAAT-TA
1 ATGCATCGATGCACTCC-TATGCATCGATGCATAAATCCTATTCGATG-TTTCTATTT-AATGGA
* *
54797 ATGCATCGATGCACTACATGTGCATCGATGCA
1 ATGCATCGATGCACT-CCTATGCATCGATGCA
54829 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
63 1 0.01
64 57 0.68
65 23 0.27
66 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (62 bp):
ATGCATCGATGCACTCCTATGCATCGATGCATAAATCCTATTCGATGTTTCTATTTAATGGA
Found at i:54885 original size:21 final size:21
Alignment explanation
Indices: 54859--54914 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
54849 TTATCATCGA
54859 TGCATCGGTGCACAATGAATG
1 TGCATCGGTGCACAATGAATG
54880 TGCATCGGTGCACAATGAATG
1 TGCATCGGTGCACAATGAATG
*
54901 TGCATCGATGCACA
1 TGCATCGGTGCACA
54915 TTGCCCAGAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.27, T:0.23
Consensus pattern (21 bp):
TGCATCGGTGCACAATGAATG
Found at i:61559 original size:35 final size:35
Alignment explanation
Indices: 61415--61702 Score: 300
Period size: 35 Copynumber: 8.3 Consensus size: 35
61405 TATTTTTAAG
* *
61415 AAACATATAATATATAGTTTTTAAAATAGTTTTAAAA
1 AAACGTATAATATATAGTTTTTAAAATAGTTTT--GA
*
61452 AAACGTATAATATATAG-TTTTAAAATGGTTTTGA
1 AAACGTATAATATATAGTTTTTAAAATAGTTTTGA
* * * * *
61486 TAACATATAGTATATATTTTTTCAAAATAGTTTGGA
1 AAACGTATAATATATAGTTTTT-AAAATAGTTTTGA
*
61522 AAATGTATAATATATAGTTTTTAAAATAGTTTTGA
1 AAACGTATAATATATAGTTTTTAAAATAGTTTTGA
* * * *
61557 AAATGTGTAATATATAGTTTTTTAAATAG-TTTAA
1 AAACGTATAATATATAGTTTTTAAAATAGTTTTGA
*
61591 AAACGTATAATATATAG-TTTTAAAATGGTTTTGA
1 AAACGTATAATATATAGTTTTTAAAATAGTTTTGA
* *
61625 AAACATAT-ATAATATA-TTTTTCAAAATGGTTTTGA
1 AAACGTATAAT-ATATAGTTTTT-AAAATAGTTTTGA
* * * **
61660 AAACATGTAATATATGGTTTTTAAAGGA-TTTTGA
1 AAACGTATAATATATAGTTTTTAAAATAGTTTTGA
61694 AAACGTATA
1 AAACGTATA
61703 TTAAAAAAAT
Statistics
Matches: 212, Mismatches: 31, Indels: 19
0.81 0.12 0.07
Matches are distributed among these distances:
33 11 0.05
34 66 0.31
35 70 0.33
36 49 0.23
37 16 0.08
ACGTcount: A:0.43, C:0.03, G:0.12, T:0.42
Consensus pattern (35 bp):
AAACGTATAATATATAGTTTTTAAAATAGTTTTGA
Found at i:63076 original size:10 final size:10
Alignment explanation
Indices: 63033--63077 Score: 54
Period size: 10 Copynumber: 4.4 Consensus size: 10
63023 ATTTAGTTTT
*
63033 TTTTCATTATC
1 TTTT-ATTATA
63044 TTTTATTATA
1 TTTTATTATA
*
63054 TTATATTATA
1 TTTTATTATA
*
63064 TTTTATTTTA
1 TTTTATTATA
63074 TTTT
1 TTTT
63078 TCTCTTTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
10 26 0.87
11 4 0.13
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.71
Consensus pattern (10 bp):
TTTTATTATA
Found at i:67852 original size:24 final size:25
Alignment explanation
Indices: 67825--67871 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
67815 CTTAGATTAG
67825 AAATCTAAGGA-GTACGAAATTACA
1 AAATCTAAGGAGGTACGAAATTACA
* * *
67849 AAATTTCAGGAGGTATGAAATTA
1 AAATCTAAGGAGGTACGAAATTA
67872 GATTGTCGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 9 0.47
25 10 0.53
ACGTcount: A:0.47, C:0.09, G:0.19, T:0.26
Consensus pattern (25 bp):
AAATCTAAGGAGGTACGAAATTACA
Found at i:71173 original size:27 final size:28
Alignment explanation
Indices: 71143--71197 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
71133 AAAAGTTTTC
71143 TATA-ACCATATATAATATACATATATA
1 TATATACCATATATAATATACATATATA
** *
71170 TATATTTTCATATGTAATATACATATAT
1 TATA-TACCATATATAATATACATATAT
71198 CGTGGAAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 4 0.17
29 19 0.83
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (28 bp):
TATATACCATATATAATATACATATATA
Found at i:72356 original size:6 final size:6
Alignment explanation
Indices: 72345--72370 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
72335 TATAATGCAC
72345 GAAGAT GAAGAT GAAGAT GAAGAT GA
1 GAAGAT GAAGAT GAAGAT GAAGAT GA
72371 TGTTGATAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.35, T:0.15
Consensus pattern (6 bp):
GAAGAT
Found at i:73239 original size:44 final size:43
Alignment explanation
Indices: 73172--73506 Score: 168
Period size: 43 Copynumber: 7.7 Consensus size: 43
73162 TCAAAGGTAT
* * * ** *
73172 GATTGAAAAAAAA-TAGAGACCTCAATTATATAGGTATCAAGTTA
1 GATT-AAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAG-GA
* *
73216 GATTAAAAAAAATTAGGGGCCTCAATTTTAAAGGTAATAAACGA
1 GATTAAAAAAAATTAGGGGCCTCAATTATAAAGGTAA-AAAGGA
* *
73260 GATT---GAAAATTAGGGGCCTAAATTATAGAA-GTAAAAAAGGA
1 GATTAAAAAAAATTAGGGGCCTCAATTATA-AAGGT-AAAAAGGA
* *
73301 GA-TAGAAAAAATTAGGGGCTTCAATTATAAAGGTAAAAAGTGA
1 GATTAAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAG-GA
* * * * * *
73344 GATTGAAAAAAATCAGGAG-TTCAATTATAAAGGTACAAAGTA
1 GATTAAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGGA
* * * **** *
73386 GGATT-GAAAAACTTAAGATTATCAATTATAAATGTAAAAAAACGG-
1 -GATTAAAAAAAATTAGGGGCCTCAATTATAAAGGT--AAAAA-GGA
* * * * * *
73431 GTTTGAAAAAAAAATAAGGGCTTCAATTATAAAGATAAAAAGTA
1 GATT-AAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGGA
* * * *
73475 TGATT-ACAAAAATTATGGACATCAATTATAAA
1 -GATTAAAAAAAATTAGGGGCCTCAATTATAAA
73507 AATAAAAAAC
Statistics
Matches: 225, Mismatches: 47, Indels: 39
0.72 0.15 0.13
Matches are distributed among these distances:
40 1 0.00
41 29 0.13
42 22 0.10
43 94 0.42
44 48 0.21
45 9 0.04
46 22 0.10
ACGTcount: A:0.50, C:0.07, G:0.18, T:0.25
Consensus pattern (43 bp):
GATTAAAAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAGGA
Found at i:73303 original size:41 final size:41
Alignment explanation
Indices: 73224--73352 Score: 154
Period size: 41 Copynumber: 3.1 Consensus size: 41
73214 TAGATTAAAA
* * *
73224 AAAATTAGGGGCCTCAATTTTAAAGGTAATAAACGAGATTG
1 AAAATTAGGGGCCTCAATTATAAAGGTAAAAAAGGAGATTG
* *
73265 AAAATTAGGGGCCTAAATTATAGAA-GTAAAAAAGGAGATAG
1 AAAATTAGGGGCCTCAATTATA-AAGGTAAAAAAGGAGATTG
*
73306 AAAAAATTAGGGGCTTCAATTATAAAGGT-AAAAAGTGAGATTG
1 --AAAATTAGGGGCCTCAATTATAAAGGTAAAAAAG-GAGATTG
73349 AAAA
1 AAAA
73353 AAATCAGGAG
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
41 37 0.49
42 10 0.13
43 28 0.37
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.23
Consensus pattern (41 bp):
AAAATTAGGGGCCTCAATTATAAAGGTAAAAAAGGAGATTG
Found at i:73319 original size:43 final size:43
Alignment explanation
Indices: 73222--73515 Score: 174
Period size: 43 Copynumber: 6.8 Consensus size: 43
73212 GTTAGATTAA
* * *
73222 AAAAAATTAGGGGCCTCAATTTTAAAGGTAATAAACGAGATTG
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAAGGAGATTG
* *
73265 --AAAATTAGGGGCCTAAATTATAGAA-GTAAAAAAGGAGATAG
1 AAAAAATTAGGGGCCTCAATTATA-AAGGTAAAAAAGGAGATTG
*
73306 AAAAAATTAGGGGCTTCAATTATAAAGGT-AAAAAGTGAGATTG
1 AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAAG-GAGATTG
* * * * *
73349 AAAAAAATCAGGAG-TTCAATTATAAAGGT-ACAAAGTAGGATTG
1 -AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAAGGA-GATTG
* * **** * *
73392 AAAAACTTAAGATTATCAATTATAAATGTAAAAAAACGG-GTTTG
1 AAAAAATTAGGGGCCTCAATTATAAAGGT-AAAAAA-GGAGATTG
* * * * *
73436 AAAAAAAAATAAGGGCTTCAATTATAAAGAT-AAAAAGTATGATT-
1 --AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAAGGA-GATTG
* * * **
73480 ACAAAAATTATGGACATCAATTATAAAAATAAAAAA
1 A-AAAAATTAGGGGCCTCAATTATAAAGGTAAAAAA
73516 CTAAAATTAA
Statistics
Matches: 198, Mismatches: 36, Indels: 33
0.74 0.13 0.12
Matches are distributed among these distances:
41 33 0.17
42 21 0.11
43 90 0.45
44 25 0.13
45 7 0.04
46 22 0.11
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.24
Consensus pattern (43 bp):
AAAAAATTAGGGGCCTCAATTATAAAGGTAAAAAAGGAGATTG
Found at i:73499 original size:89 final size:89
Alignment explanation
Indices: 73349--73515 Score: 205
Period size: 89 Copynumber: 1.9 Consensus size: 89
73339 AGTGAGATTG
* * * * *
73349 AAAAAAATCAGGAGTTCAATTATAAAGGTACAAAGTAGGATTGAAAAACTTAAGATTATCAATTA
1 AAAAAAATAAGGAGTTCAATTATAAAGATAAAAAGTAGGATTGAAAAAATTAAGATCATCAATTA
**
73414 TAAATGTAAAAAAACGGGTTTGAA
66 TAAAAATAAAAAAACGGGTTTGAA
* *
73438 AAAAAAATAAGG-GCTTCAATTATAAAGATAAAAAGTATGATT-ACAAAAATTATGGA-CATCAA
1 AAAAAAATAAGGAG-TTCAATTATAAAGATAAAAAGTAGGATTGA-AAAAATTA-AGATCATCAA
73500 TTATAAAAATAAAAAA
63 TTATAAAAATAAAAAA
73516 CTAAAATTAA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
88 2 0.03
89 62 0.94
90 2 0.03
ACGTcount: A:0.54, C:0.07, G:0.14, T:0.25
Consensus pattern (89 bp):
AAAAAAATAAGGAGTTCAATTATAAAGATAAAAAGTAGGATTGAAAAAATTAAGATCATCAATTA
TAAAAATAAAAAAACGGGTTTGAA
Found at i:74369 original size:21 final size:21
Alignment explanation
Indices: 74316--74371 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
74306 CACGGCACTA
* *
74316 ACGTGGCAGTCCATGATACTG
1 ACGTGACAGTCTATGATACTG
74337 ACGTGACAGTCTATGATACTG
1 ACGTGACAGTCTATGATACTG
74358 ACGTGACAGTCTAT
1 ACGTGACAGTCTAT
74372 CTGTCATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.27
Consensus pattern (21 bp):
ACGTGACAGTCTATGATACTG
Found at i:76948 original size:31 final size:32
Alignment explanation
Indices: 76890--76965 Score: 91
Period size: 31 Copynumber: 2.4 Consensus size: 32
76880 TTAGCCCGAG
*
76890 CCGAAAGCAACCCGAACAGAATATAACTC-AA
1 CCGAAAGTAACCCGAACAGAATATAACTCTAA
* * * *
76921 CCGAAAGTAACCCGAACTGAGTTTAACTCTAT
1 CCGAAAGTAACCCGAACAGAATATAACTCTAA
*
76953 CCAAAAGTAACCC
1 CCGAAAGTAACCC
76966 AAACCAAATT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
31 25 0.66
32 13 0.34
ACGTcount: A:0.42, C:0.29, G:0.13, T:0.16
Consensus pattern (32 bp):
CCGAAAGTAACCCGAACAGAATATAACTCTAA
Found at i:77341 original size:16 final size:17
Alignment explanation
Indices: 77322--77361 Score: 57
Period size: 16 Copynumber: 2.5 Consensus size: 17
77312 TCCGATAATC
77322 ACTCGACCC-AAAATTG
1 ACTCGACCCGAAAATTG
77338 ACTC-ACCCGAAAATTG
1 ACTCGACCCGAAAATTG
*
77354 ACCCGACC
1 ACTCGACC
77362 TGATTTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 4 0.19
16 14 0.67
17 3 0.14
ACGTcount: A:0.35, C:0.38, G:0.12, T:0.15
Consensus pattern (17 bp):
ACTCGACCCGAAAATTG
Done.