Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001219.1 Hibiscus syriacus cultivar Beakdansim tig00002408_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: 89154
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:1879 original size:12 final size:12
Alignment explanation
Indices: 1862--1898 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
1852 TTTATCTCAA
1862 TTTCAATAATTT
1 TTTCAATAATTT
1874 TTTCAATAATTT
1 TTTCAATAATTT
*
1886 TTTAACATAATTT
1 TTTCA-ATAATTT
1899 CAAGCTTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 16 0.70
13 7 0.30
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.57
Consensus pattern (12 bp):
TTTCAATAATTT
Found at i:8978 original size:20 final size:20
Alignment explanation
Indices: 8949--9041 Score: 132
Period size: 20 Copynumber: 4.7 Consensus size: 20
8939 GCAGCCTTCG
*
8949 TGCATAGATGCACAACATGA
1 TGCATCGATGCACAACATGA
*
8969 TGCATCGATGCACATCATGA
1 TGCATCGATGCACAACATGA
* *
8989 TGCATCGATGTACAGCATGA
1 TGCATCGATGCACAACATGA
*
9009 TACATCGATGCACAACATGA
1 TGCATCGATGCACAACATGA
*
9029 TGCGTCGATGCAC
1 TGCATCGATGCAC
9042 TAAGTGCATT
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 64 1.00
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.23
Consensus pattern (20 bp):
TGCATCGATGCACAACATGA
Found at i:9112 original size:21 final size:21
Alignment explanation
Indices: 9061--9137 Score: 120
Period size: 21 Copynumber: 3.7 Consensus size: 21
9051 TCGAAATGGA
*
9061 GTGCATGGATGCACTGCA-TG
1 GTGCATGGATGCACTGCAGGG
*
9081 GTGCATCGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
*
9102 GTGTATGGATGCACTGCAGGG
1 GTGCATGGATGCACTGCAGGG
9123 GTGCATGGATGCACT
1 GTGCATGGATGCACT
9138 TTGACACCCT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 17 0.33
21 34 0.67
ACGTcount: A:0.19, C:0.19, G:0.38, T:0.23
Consensus pattern (21 bp):
GTGCATGGATGCACTGCAGGG
Found at i:9383 original size:21 final size:21
Alignment explanation
Indices: 9359--9398 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
9349 ATGTTTAATG
*
9359 AAAAAGATGTCAATTGTTAAC
1 AAAAAGATATCAATTGTTAAC
*
9380 AAAATGATATCAATTGTTA
1 AAAAAGATATCAATTGTTA
9399 CCAATTGTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.07, G:0.12, T:0.33
Consensus pattern (21 bp):
AAAAAGATATCAATTGTTAAC
Found at i:9864 original size:13 final size:13
Alignment explanation
Indices: 9846--9880 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
9836 ATAAACATTT
*
9846 AAATTTAGGTCAA
1 AAATTTAAGTCAA
9859 AAATTTAAAGTCAA
1 AAATTT-AAGTCAA
9873 AAATTTAA
1 AAATTTAA
9881 AATTTGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (13 bp):
AAATTTAAGTCAA
Found at i:9873 original size:14 final size:14
Alignment explanation
Indices: 9854--9881 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
9844 TTAAATTTAG
9854 GTCAAAAATTTAAA
1 GTCAAAAATTTAAA
9868 GTCAAAAATTTAAA
1 GTCAAAAATTTAAA
9882 ATTTGTAAAA
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:0.57, C:0.07, G:0.07, T:0.29
Consensus pattern (14 bp):
GTCAAAAATTTAAA
Found at i:10571 original size:19 final size:20
Alignment explanation
Indices: 10528--10575 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
10518 TCTAAATCCT
*
10528 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
10548 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
10567 TTTTCAAAA
1 TTTTCAAAA
10576 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:11755 original size:21 final size:21
Alignment explanation
Indices: 11721--11781 Score: 88
Period size: 21 Copynumber: 2.9 Consensus size: 21
11711 TGTTGTATAT
11721 AGCCG-TTGGGGATGTTTTGA
1 AGCCGTTTGGGGATGTTTTGA
* *
11741 AGCCGTTTAGGGATGTTTTGG
1 AGCCGTTTGGGGATGTTTTGA
11762 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATG-TTTT
11782 TCTACTCAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 5 0.14
21 27 0.75
22 4 0.11
ACGTcount: A:0.15, C:0.10, G:0.38, T:0.38
Consensus pattern (21 bp):
AGCCGTTTGGGGATGTTTTGA
Found at i:11916 original size:12 final size:12
Alignment explanation
Indices: 11899--11937 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
11889 CTTCATGCAT
11899 GGATGCACATCA
1 GGATGCACATCA
11911 GGATG--CATC-
1 GGATGCACATCA
11920 -GATGCACATCA
1 GGATGCACATCA
11931 GGATGCA
1 GGATGCA
11938 TCAATGCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 4 0.17
10 8 0.35
12 11 0.48
ACGTcount: A:0.31, C:0.23, G:0.28, T:0.18
Consensus pattern (12 bp):
GGATGCACATCA
Found at i:11918 original size:20 final size:20
Alignment explanation
Indices: 11893--11946 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
11883 TGCAGCCTTC
*
11893 ATGCATGGATGCACATCAGG
1 ATGCATCGATGCACATCAGG
11913 ATGCATCGATGCACATCAGG
1 ATGCATCGATGCACATCAGG
*
11933 ATGCATCAATGCAC
1 ATGCATCGATGCAC
11947 TAAGTGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.20
Consensus pattern (20 bp):
ATGCATCGATGCACATCAGG
Found at i:11990 original size:21 final size:21
Alignment explanation
Indices: 11966--12022 Score: 89
Period size: 21 Copynumber: 2.7 Consensus size: 21
11956 TCGAAATGGA
*
11966 GTGCATGGATGCACTGC-AGAG
1 GTGCATGGATACACTGCAAG-G
11987 GTGCATGGATACACTGCAAGG
1 GTGCATGGATACACTGCAAGG
12008 GTGCATGGATACACT
1 GTGCATGGATACACT
12023 TTGACACCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
21 32 0.94
22 2 0.06
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.21
Consensus pattern (21 bp):
GTGCATGGATACACTGCAAGG
Found at i:12394 original size:18 final size:18
Alignment explanation
Indices: 12344--12433 Score: 90
Period size: 18 Copynumber: 4.8 Consensus size: 18
12334 GGGTTTACGC
*
12344 GGTCCTTCGGGACACAGT
1 GGTCCTTCGGGACATAGT
12362 GGTCCTTCGGGACATAGT
1 GGTCCTTCGGGACATAGT
*
12380 GGTCATTCGGGACATATACAGT
1 GGTCCTTCGGGAC--AT--AGT
* *
12402 GGTCCTTCGAGATATAGT
1 GGTCCTTCGGGACATAGT
* *
12420 AGTCCTGCGGGACA
1 GGTCCTTCGGGACA
12434 AATTCTACGC
Statistics
Matches: 59, Mismatches: 9, Indels: 8
0.78 0.12 0.11
Matches are distributed among these distances:
18 42 0.71
20 4 0.07
22 13 0.22
ACGTcount: A:0.21, C:0.22, G:0.31, T:0.26
Consensus pattern (18 bp):
GGTCCTTCGGGACATAGT
Found at i:12405 original size:40 final size:40
Alignment explanation
Indices: 12357--12433 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
12347 CCTTCGGGAC
* * *
12357 ACAGTGGTCCTTCGGGACATAGTGGTCATTCGGGACATAT
1 ACAGTGGTCCTTCGAGACATAGTAGTCATGCGGGACATAT
* *
12397 ACAGTGGTCCTTCGAGATATAGTAGTCCTGCGGGACA
1 ACAGTGGTCCTTCGAGACATAGTAGTCATGCGGGACA
12434 AATTCTACGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (40 bp):
ACAGTGGTCCTTCGAGACATAGTAGTCATGCGGGACATAT
Found at i:13663 original size:17 final size:18
Alignment explanation
Indices: 13632--13673 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
13622 GAACAAAAGC
13632 ATATTAGCATATTTATTA
1 ATATTAGCATATTTATTA
*
13650 ATTTTAGC-TATTTATTA
1 ATATTAGCATATTTATTA
13667 ATATTAG
1 ATATTAG
13674 TCTCCAATGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.36, C:0.05, G:0.07, T:0.52
Consensus pattern (18 bp):
ATATTAGCATATTTATTA
Found at i:16783 original size:16 final size:16
Alignment explanation
Indices: 16762--16800 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
16752 TTTCATTATC
16762 AAATATTA-CATTATTT
1 AAATATTATCATT-TTT
*
16778 AAATATTATTATTTTT
1 AAATATTATCATTTTT
16794 AAATATT
1 AAATATT
16801 TAAAGATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 18 0.86
17 3 0.14
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATTATCATTTTT
Found at i:24017 original size:2 final size:2
Alignment explanation
Indices: 24010--24046 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
24000 ATATTTTACA
24010 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24047 AAAACTTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27078 original size:16 final size:16
Alignment explanation
Indices: 27059--27092 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
27049 CAATATACGA
27059 ATAAAAATATATTTAT
1 ATAAAAATATATTTAT
**
27075 ATAAATGTATATTTAT
1 ATAAAAATATATTTAT
27091 AT
1 AT
27093 TAGATGTATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
ATAAAAATATATTTAT
Found at i:27101 original size:17 final size:16
Alignment explanation
Indices: 27066--27102 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
27056 CGAATAAAAA
27066 TATATTTATATAAATG
1 TATATTTATATAAATG
*
27082 TATATTTATATTAGATG
1 TATATTTATA-TAAATG
27099 TATA
1 TATA
27103 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (16 bp):
TATATTTATATAAATG
Found at i:27164 original size:16 final size:18
Alignment explanation
Indices: 27132--27165 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
27122 TATTAATGTA
27132 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
27150 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
27166 AATAAGAAAT
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:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:27704 original size:21 final size:23
Alignment explanation
Indices: 27659--27705 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
27649 GTGTCACCAA
27659 TAACATATATCATGATCATGTGT
1 TAACATATATCATGATCATGTGT
* *
27682 TAACATATGTCA-GATCCTG-GT
1 TAACATATATCATGATCATGTGT
27703 TAA
1 TAA
27706 ATGATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 5 0.23
22 6 0.27
23 11 0.50
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (23 bp):
TAACATATATCATGATCATGTGT
Found at i:27836 original size:130 final size:130
Alignment explanation
Indices: 27632--27879 Score: 397
Period size: 130 Copynumber: 1.9 Consensus size: 130
27622 AATTTTCTTC
* * * *
27632 TAATTAGGTGGTGACATGTGTCACCAATAACATATATCATGATCATGTGTTAACATATGTCAGAT
1 TAATTAGGTGGTGACATGCGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
** * *
27697 CCTGGTTAAATGATTAATTTATTTAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * *
27762 TAATTAGGTGGTGACATGCGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGTGGTGACATGCGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
27827 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGAT
27880 TATATAAATA
Statistics
Matches: 107, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
130 107 1.00
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.37
Consensus pattern (130 bp):
TAATTAGGTGGTGACATGCGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTCTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:28326 original size:35 final size:35
Alignment explanation
Indices: 28276--28351 Score: 116
Period size: 35 Copynumber: 2.2 Consensus size: 35
28266 AATTGAATTT
* *
28276 AATTGAATTATTTTGGAATTTAGGGTTGAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
* *
28311 AATTGAATTACTTTGGAAATTGGGGTTTAGAATGA
1 AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
28346 AATTGA
1 AATTGA
28352 GGACTGTTTT
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:0.36, C:0.01, G:0.25, T:0.38
Consensus pattern (35 bp):
AATTGAATTACTTTGGAAATTAGGGTTGAGAATGA
Found at i:31402 original size:46 final size:48
Alignment explanation
Indices: 31346--31448 Score: 120
Period size: 49 Copynumber: 2.2 Consensus size: 48
31336 TGGAGAAAAC
* * *
31346 GAAAGGGATTG-GGTG-TGCTGTTGAATTTATGTGGCTTATAAATCTG
1 GAAAGGGATTGTGCTGCTGCTGCTGAATTTATGTGGCTTATAAATCAG
* * * *
31392 GACAGGGATTGTTTCTGCTGCTGCTGATTTTATGTGGCTTGTAAATCAG
1 GAAAGGGATTG-TGCTGCTGCTGCTGAATTTATGTGGCTTATAAATCAG
31441 GAAAGGGA
1 GAAAGGGA
31449 ACCCAATGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
46 10 0.22
48 2 0.04
49 34 0.74
ACGTcount: A:0.23, C:0.10, G:0.32, T:0.35
Consensus pattern (48 bp):
GAAAGGGATTGTGCTGCTGCTGCTGAATTTATGTGGCTTATAAATCAG
Found at i:35185 original size:13 final size:13
Alignment explanation
Indices: 35167--35193 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35157 TTATATTGAG
35167 TTAAGCAAGTTTA
1 TTAAGCAAGTTTA
35180 TTAAGCAAGTTTA
1 TTAAGCAAGTTTA
35193 T
1 T
35194 ATACACGGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (13 bp):
TTAAGCAAGTTTA
Found at i:50188 original size:2 final size:2
Alignment explanation
Indices: 50181--50205 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
50171 TCCCCCACCT
50181 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
50206 GTTTTGGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:50565 original size:49 final size:48
Alignment explanation
Indices: 50488--50582 Score: 172
Period size: 49 Copynumber: 2.0 Consensus size: 48
50478 TCTCTTAATT
50488 TTACATTGATAAGGATTTACTGTATTTTTATAAATATAATTTTAAAATA
1 TTACATTGATAAGGATTTACTGTATTTTTATAAATAT-ATTTTAAAATA
*
50537 TTACCTTGATAAGGATTTACTGTATTTTTATAAATATATTTTAAAA
1 TTACATTGATAAGGATTTACTGTATTTTTATAAATATATTTTAAAA
50583 GAATTGACTT
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 9 0.20
49 36 0.80
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (48 bp):
TTACATTGATAAGGATTTACTGTATTTTTATAAATATATTTTAAAATA
Found at i:50695 original size:23 final size:23
Alignment explanation
Indices: 50669--50721 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
50659 ATACTTATTT
*
50669 TTATTAATAAAATATAAAA-ATAA
1 TTATAAATAAAATA-AAAATATAA
*
50692 TTATAAATTAAATAAAAATATAA
1 TTATAAATAAAATAAAAATATAA
50715 TT-TAAAT
1 TTATAAAT
50722 CAATTTAAGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 9 0.33
23 18 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TTATAAATAAAATAAAAATATAA
Found at i:53738 original size:29 final size:28
Alignment explanation
Indices: 53706--53800 Score: 75
Period size: 29 Copynumber: 3.2 Consensus size: 28
53696 TTTAGATTGG
53706 TCCTTAAACTTTTAAATATTTTAATTTCA
1 TCCTTAAACTTTTAAATATTTTAATTT-A
* * * *
53735 TCCTCAAACTATGATAATTATTTTAAATTA
1 TCCTTAAACT-T-TTAAATATTTTAATTTA
* *
53765 GTCCTTAAACCTTTT-AACATTCTAATTTTA
1 -TCCTTAAA-CTTTTAAATATTTTAA-TTTA
53795 TCCTTA
1 TCCTTA
53801 TACTATGACC
Statistics
Matches: 51, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
29 22 0.43
30 6 0.12
31 21 0.41
32 2 0.04
ACGTcount: A:0.34, C:0.17, G:0.02, T:0.47
Consensus pattern (28 bp):
TCCTTAAACTTTTAAATATTTTAATTTA
Found at i:53748 original size:60 final size:60
Alignment explanation
Indices: 53678--53809 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 60
53668 TCATATGTTT
* * * * * *
53678 TCAAATTATGACAGTTATTTTAGATTGGTCCTTAAA-CTTTTAAATATTTTAATTTCATCC
1 TCAAACTATGACAATTATTTTAAATTAGTCCTTAAACCTTTT-AACATTCTAATTTCATCC
* *
53738 TCAAACTATGATAATTATTTTAAATTAGTCCTTAAACCTTTTAACATTCTAATTTTATCC
1 TCAAACTATGACAATTATTTTAAATTAGTCCTTAAACCTTTTAACATTCTAATTTCATCC
* *
53798 TTATACTATGAC
1 TCAAACTATGAC
53810 CCTCATTCTA
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
60 55 0.92
61 5 0.08
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (60 bp):
TCAAACTATGACAATTATTTTAAATTAGTCCTTAAACCTTTTAACATTCTAATTTCATCC
Found at i:53822 original size:60 final size:60
Alignment explanation
Indices: 53678--53856 Score: 141
Period size: 60 Copynumber: 3.0 Consensus size: 60
53668 TCATATGTTT
* * * * * * * *
53678 TCAAATTATGACAGTTATTTTAGATTGGTCCTTAAACTTTTAAATATTTTAATTTCATCC
1 TCAAACTATGACAATCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCC
* * * *
53738 TCAAACTATGATAATTATTTTAAATTAGTCCTTAAACCTTTT-AACATTCTAATTTTATCC
1 TCAAACTATGACAATCATTCTAAATTAGTCCTTAAA-CTTTTAAACATTCTAATTTCATCC
* * ** * *
53798 TTATACTATGACCCTCATTCTAAATT-GATCC-CAAACTTTTAAATC-TTCCAATTTCATCC
1 TCAAACTATGACAATCATTCTAAATTAG-TCCTTAAACTTTTAAA-CATTCTAATTTCATCC
53857 CCGAATTCAT
Statistics
Matches: 97, Mismatches: 18, Indels: 9
0.78 0.15 0.07
Matches are distributed among these distances:
58 5 0.05
59 18 0.19
60 69 0.71
61 5 0.05
ACGTcount: A:0.32, C:0.19, G:0.05, T:0.44
Consensus pattern (60 bp):
TCAAACTATGACAATCATTCTAAATTAGTCCTTAAACTTTTAAACATTCTAATTTCATCC
Found at i:54029 original size:30 final size:29
Alignment explanation
Indices: 53994--54051 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
53984 TGGGATGAAA
**
53994 TTGAAATGTTGAAAAAGTTTGGGGACAAAG
1 TTGAAAT-TTGAAAAAGTTTAAGGACAAAG
*
54024 TTGAAATTTTAAAAAGTTTAAGGACAAA
1 TTGAAATTTGAAAAAGTTTAAGGACAAA
54052 TTTAGAATGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 18 0.72
30 7 0.28
ACGTcount: A:0.45, C:0.03, G:0.22, T:0.29
Consensus pattern (29 bp):
TTGAAATTTGAAAAAGTTTAAGGACAAAG
Found at i:55021 original size:31 final size:31
Alignment explanation
Indices: 54983--55064 Score: 155
Period size: 31 Copynumber: 2.6 Consensus size: 31
54973 CAAAATTTTT
*
54983 TTTGTTCATGTTCGTTCATTAATGAATATAG
1 TTTGTTCATGTTCGTTCATTAAGGAATATAG
55014 TTTGTTCATGTTCGTTCATTAAGGAATATAG
1 TTTGTTCATGTTCGTTCATTAAGGAATATAG
55045 TTTGTTCATGTTCGTTCATT
1 TTTGTTCATGTTCGTTCATT
55065 TAAATGATAA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 50 1.00
ACGTcount: A:0.22, C:0.11, G:0.17, T:0.50
Consensus pattern (31 bp):
TTTGTTCATGTTCGTTCATTAAGGAATATAG
Found at i:55121 original size:10 final size:10
Alignment explanation
Indices: 55108--55168 Score: 50
Period size: 10 Copynumber: 5.5 Consensus size: 10
55098 AACACAAACG
55108 AACGAACATA
1 AACGAACATA
55118 AACGAACATAATA
1 AACGAAC---ATA
*
55131 AATGAACATA
1 AACGAACATA
*
55141 AACAAACACGATA
1 AAC-GA-AC-ATA
55154 AACGAACATA
1 AACGAACATA
55164 AACGA
1 AACGA
55169 CACAAACACA
Statistics
Matches: 41, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
10 20 0.49
11 3 0.07
12 3 0.07
13 15 0.37
ACGTcount: A:0.61, C:0.18, G:0.10, T:0.11
Consensus pattern (10 bp):
AACGAACATA
Found at i:55141 original size:23 final size:23
Alignment explanation
Indices: 55108--55173 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
55098 AACACAAACG
*
55108 AACGAACATAAACGAACATAATA
1 AACGAACATAAACGAACACAATA
* * *
55131 AATGAACATAAACAAACACGATA
1 AACGAACATAAACGAACACAATA
55154 AACGAACATAAACG-ACACAA
1 AACGAACATAAACGAACACAA
55174 ACACAAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 5 0.14
23 31 0.86
ACGTcount: A:0.61, C:0.20, G:0.09, T:0.11
Consensus pattern (23 bp):
AACGAACATAAACGAACACAATA
Found at i:55451 original size:18 final size:18
Alignment explanation
Indices: 55428--55463 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55418 CCCTCTGTCG
55428 AACATAAATGAATGAACA
1 AACATAAATGAATGAACA
55446 AACATAAATGAATGAACA
1 AACATAAATGAATGAACA
55464 TAAACGAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.17
Consensus pattern (18 bp):
AACATAAATGAATGAACA
Found at i:60718 original size:2 final size:2
Alignment explanation
Indices: 60711--60735 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60701 CATAGTTGTC
60711 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
60736 GCCACGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:69341 original size:13 final size:13
Alignment explanation
Indices: 69323--69349 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
69313 TAATAAAAAT
69323 AAATAAAAATATA
1 AAATAAAAATATA
69336 AAATAAAAATATA
1 AAATAAAAATATA
69349 A
1 A
69350 GGTGATCAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (13 bp):
AAATAAAAATATA
Found at i:77869 original size:21 final size:21
Alignment explanation
Indices: 77844--77885 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
77834 ATCAAGTACA
*
77844 ATAATATATTAGGTAGCGTTT
1 ATAATATAATAGGTAGCGTTT
*
77865 ATAATGTAATAGGTAGCGTTT
1 ATAATATAATAGGTAGCGTTT
77886 TATTTGACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.05, G:0.21, T:0.40
Consensus pattern (21 bp):
ATAATATAATAGGTAGCGTTT
Found at i:78641 original size:179 final size:182
Alignment explanation
Indices: 78310--78745 Score: 621
Period size: 179 Copynumber: 2.5 Consensus size: 182
78300 TCTTTTACTA
* *
78310 CGGTTTTGTCA-TTCGAGACCGAG-TTTATCATA--TTTACATTTTATATTGTTATGGATCGATA
1 CGGTTTTGTCATTTCGAGACCG-GTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATA
* * *
78371 CATTTTTATAAAGTATCGA-CACTTTATTGACACTATAACTCTTTTCTTTTAAATTTCAAAAGTG
65 CATTTTTATAAAGTATCGACCACTTTATAGACACTATAACTCTTCTCTTTTAAATTCCAAAAGTG
* *
78435 TCGATACTTATAATAAAGTACCGACACTTTCAACATATCCGGTAGCTCTTTAC
130 TCGATACTTATAATAAAGTACCGACACTATCAACATATCCGGTAGCGCTTTAC
78488 CGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATAC
1 CGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATAC
*
78553 A-TTTTATAAAGTATCGACCAC-TTATAG-CGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTG
66 ATTTTTATAAAGTATCGACCACTTTATAGACACTATAAC-TCTTCTCTTTTAAATTCCAAAAGTG
*
78615 TCGATA-TTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
130 TCGATACTTATAATAAAGTACCGACACTATCAACATATCCGGTAGCGCTTTAC
* ** * * *
78667 CTGTTTTGTCATTTATAGA-CGGTTTTGT--TATTTTTACATGTTATA-TGTTATCGATCTATAT
1 CGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATAC
78728 ATTTTTATAAAGTA-CGAC
66 ATTTTTATAAAGTATCGAC
78746 ACAAACCGAC
Statistics
Matches: 236, Mismatches: 15, Indels: 17
0.88 0.06 0.06
Matches are distributed among these distances:
175 18 0.08
176 29 0.12
178 21 0.09
179 85 0.36
180 50 0.21
181 33 0.14
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.42
Consensus pattern (182 bp):
CGGTTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACATGTTATATTGTTATGGATCGATAC
ATTTTTATAAAGTATCGACCACTTTATAGACACTATAACTCTTCTCTTTTAAATTCCAAAAGTGT
CGATACTTATAATAAAGTACCGACACTATCAACATATCCGGTAGCGCTTTAC
Found at i:84940 original size:6 final size:6
Alignment explanation
Indices: 84929--84954 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
84919 GGTAAACCAT
84929 TTTAAA TTTAAA TTTAAA TTTAAA TT
1 TTTAAA TTTAAA TTTAAA TTTAAA TT
84955 AGTAGGCTAA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Done.