Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004301.1 Hibiscus syriacus cultivar Beakdansim tig00009434_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: 112842
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2238 original size:31 final size:32
Alignment explanation
Indices: 2152--2242 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 32
2142 AGAGTCGAGG
*
2152 TATACCTATGTTCTACGGAACATATGGACAGA
1 TATACCTATGTTCTAAGGAACATATGGACAGA
*
2184 -ATTACCTATGTCTTTCAA-G-ACATATGGACA-A
1 TA-TACCTATGT-TCT-AAGGAACATATGGACAGA
2215 TATACCTATGTTCTAAGGAACATATGGA
1 TATACCTATGTTCTAAGGAACATATGGA
2243 TTGTTTACCT
Statistics
Matches: 50, Mismatches: 3, Indels: 13
0.76 0.05 0.20
Matches are distributed among these distances:
29 2 0.04
30 3 0.06
31 20 0.40
32 21 0.42
33 3 0.06
34 1 0.02
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (32 bp):
TATACCTATGTTCTAAGGAACATATGGACAGA
Found at i:2252 original size:31 final size:31
Alignment explanation
Indices: 2154--2259 Score: 99
Period size: 31 Copynumber: 3.4 Consensus size: 31
2144 AGTCGAGGTA
* *
2154 TACCTATGTTCTACGGAACATATGGACAGAAT
1 TACCTATGTTCTAAGGAACATATGGACAG-TT
* * *
2186 TACCTATGTCTTTCAA-G-ACATATGGACAATA
1 TACCTATGT-TCT-AAGGAACATATGGACAGTT
**
2217 TACCTATGTTCTAAGGAACATATGGATTGTT
1 TACCTATGTTCTAAGGAACATATGGACAGTT
*
2248 TACCTAGGTTCT
1 TACCTATGTTCT
2260 TCGGCCCTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
29 2 0.03
30 3 0.05
31 30 0.51
32 20 0.34
33 3 0.05
34 1 0.02
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (31 bp):
TACCTATGTTCTAAGGAACATATGGACAGTT
Found at i:12516 original size:2 final size:2
Alignment explanation
Indices: 12511--12539 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12501 AAAATCCCTA
12511 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 A
12540 GGGTTGGCTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12852 original size:27 final size:27
Alignment explanation
Indices: 12822--12876 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
12812 GGTTATTAGG
* *
12822 TTTGTTTAATAAAATAAATAGAGATTA
1 TTTGTTCAAAAAAATAAATAGAGATTA
12849 TTTGTTCAAAAAAATAAATAGAGATTA
1 TTTGTTCAAAAAAATAAATAGAGATTA
12876 T
1 T
12877 GTCTTAGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (27 bp):
TTTGTTCAAAAAAATAAATAGAGATTA
Found at i:16637 original size:21 final size:21
Alignment explanation
Indices: 16603--16643 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16593 ATATGTGTTA
* * *
16603 TATGTGGTCTTTCGGGACATC
1 TATGTAGTCCTTCGAGACATC
16624 TATGTAGTCCTTCGAGACAT
1 TATGTAGTCCTTCGAGACAT
16644 TTCTACATTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.37
Consensus pattern (21 bp):
TATGTAGTCCTTCGAGACATC
Found at i:20927 original size:23 final size:21
Alignment explanation
Indices: 20871--20928 Score: 53
Period size: 23 Copynumber: 2.7 Consensus size: 21
20861 TGTTATATGT
* * *
20871 GGTCCTTTGGGACATCTATGT
1 GGTCCTTTGGGATATCTACGC
**
20892 GGTCCTTCAGGATATTTCTACGC
1 GGTCCTTTGGGATA--TCTACGC
20915 GGTCCTTTGGGATA
1 GGTCCTTTGGGATA
20929 AATTTTATGT
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
21 11 0.39
23 17 0.61
ACGTcount: A:0.16, C:0.21, G:0.28, T:0.36
Consensus pattern (21 bp):
GGTCCTTTGGGATATCTACGC
Found at i:21956 original size:12 final size:12
Alignment explanation
Indices: 21939--21972 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
21929 TAACTATTAA
21939 TATATAAAATTT
1 TATATAAAATTT
21951 TATAT-AAATTT
1 TATATAAAATTT
21962 TATGATAAAAT
1 TAT-ATAAAAT
21973 AACACGCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
11 9 0.45
12 7 0.35
13 4 0.20
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (12 bp):
TATATAAAATTT
Found at i:24226 original size:24 final size:23
Alignment explanation
Indices: 24176--24230 Score: 101
Period size: 23 Copynumber: 2.4 Consensus size: 23
24166 TTCAAAATAA
*
24176 AAAAACCCTGTTTACCAGAACCG
1 AAAAACTCTGTTTACCAGAACCG
24199 AAAAACTCTGTTTACCAGAACCG
1 AAAAACTCTGTTTACCAGAACCG
24222 AAAAACTCT
1 AAAAACTCT
24231 ATTTCTACAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.42, C:0.27, G:0.11, T:0.20
Consensus pattern (23 bp):
AAAAACTCTGTTTACCAGAACCG
Found at i:31755 original size:14 final size:14
Alignment explanation
Indices: 31736--31772 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
31726 AACGAACGTA
31736 AACGAATACAAACG
1 AACGAATACAAACG
*
31750 AACGAATATAAACG
1 AACGAATACAAACG
31764 AACGTAATA
1 AACG-AATA
31773 AATGAACATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.57, C:0.16, G:0.14, T:0.14
Consensus pattern (14 bp):
AACGAATACAAACG
Found at i:33050 original size:20 final size:20
Alignment explanation
Indices: 33025--33064 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
33015 AATTCTTTAT
*
33025 CGGTTTTGTCATTTTGAGAC
1 CGGTTTTGTCATTTTAAGAC
33045 CGGTTTTGTCATTTTAAGAC
1 CGGTTTTGTCATTTTAAGAC
33065 TGATTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.15, G:0.23, T:0.45
Consensus pattern (20 bp):
CGGTTTTGTCATTTTAAGAC
Found at i:33071 original size:20 final size:20
Alignment explanation
Indices: 33028--33076 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
33018 TCTTTATCGG
* *
33028 TTTTGTCATTTTGAGACCGG
1 TTTTGTCATTTTAAGACCGA
*
33048 TTTTGTCATTTTAAGACTGA
1 TTTTGTCATTTTAAGACCGA
*
33068 TTTTATCAT
1 TTTTGTCAT
33077 ATTTTTAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.20, C:0.12, G:0.16, T:0.51
Consensus pattern (20 bp):
TTTTGTCATTTTAAGACCGA
Found at i:33198 original size:202 final size:194
Alignment explanation
Indices: 32922--33604 Score: 758
Period size: 183 Copynumber: 3.6 Consensus size: 194
32912 TTAAAGAGTG
* * * *
32922 TCGATACTTAATAGGCGCTATAACTTCTTCTCTTTTACATTCCAAAAGTGTCGATACTTATATTA
1 TCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTA
* *
32987 AAGTATCGACACTTTCAACATATACGATAATTCTTTATCGGTTTTGTCATTTTGAGACCGGTTTT
66 AATTATCGACACTTTCAACATATACGAT-ATTCTTTACCGGTTTTGTCATTTTGAGACCGGTTTT
* * *
33052 GTCATTTTAAGACTGATTTTATCATATTTTTAGTTGTTATATTGTTATGGATCGATATATTTTTA
130 GTCA-TTT---A-TG-TTTTATCATATTTTTA-CTGTTATATTGTTATGGATCGATACATTTTTT
33117 TAAAATA
188 TAAAATA
* * * *
33124 TCGATACTTTTTAGGCGCTATAACTTCTTCTTTTTTAAATTCAAAAAGTTTCGATACTTATATTA
1 TCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTA
* * * *
33189 AATTATCGACACTTTCAACATATCCGATA-GCGTTTTACCGGATTTGTCATTTTGGGACCGGTTT
66 AATTATCGACACTTTCAACATATACGATATTC--TTTACCGGTTTTGTCATTTTGAGACCGGTTT
* *
33253 TGTCA--TAT-TTTTA-C---------CTGTTATATTGTTATGAATCGATACATTTTTTTTAAAG
129 TGTCATTTATGTTTTATCATATTTTTACTGTTATATTGTTATGGATCGATACA-TTTTTTTAAAA
33305 TA
193 TA
* * *
33307 TCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAAATTTTGATACTTATATT
1 TCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTC-AAAAAGTGTCGATACTTATATT
* *
33372 AAATTATCGACACTTTCAACATATTA-GATATTTTTTACCGGTTTTGTCATTTTTGAGACCTGTT
65 AAATTATCGACACTTTCAACATA-TACGATATTCTTTACCGGTTTTGTCA-TTTTGAGACCGGTT
33436 TTGTCA--TAT-TTTTA-C---------CTGTTATATTGTTATGGATCGATACATTTTTTTAAAA
128 TTGTCATTTATGTTTTATCATATTTTTACTGTTATATTGTTATGGATCGATACATTTTTTTAAAA
33488 TA
193 TA
* * * *
33490 TCGACACTTTATAGGCGTTATAACTTATTATCTTTTAAATTCTAAAAGTGTCGATACTTATATTA
1 TCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTA
*
33555 AATTATCGACACTTTCAACATATCCGATA-TCGTTTTACCGGTTTTGTCAT
66 AATTATCGACACTTTCAACATATACGATATTC--TTTACCGGTTTTGTCAT
33605 ATTTTTACCT
Statistics
Matches: 432, Mismatches: 39, Indels: 40
0.85 0.08 0.08
Matches are distributed among these distances:
181 2 0.00
182 69 0.16
183 132 0.31
184 99 0.23
185 1 0.00
192 1 0.00
193 5 0.01
195 1 0.00
196 1 0.00
199 1 0.00
200 1 0.00
201 1 0.00
202 118 0.27
ACGTcount: A:0.28, C:0.15, G:0.12, T:0.45
Consensus pattern (194 bp):
TCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAAGTGTCGATACTTATATTA
AATTATCGACACTTTCAACATATACGATATTCTTTACCGGTTTTGTCATTTTGAGACCGGTTTTG
TCATTTATGTTTTATCATATTTTTACTGTTATATTGTTATGGATCGATACATTTTTTTAAAATA
Found at i:33446 original size:184 final size:182
Alignment explanation
Indices: 33043--33604 Score: 842
Period size: 183 Copynumber: 3.1 Consensus size: 182
33033 TCATTTTGAG
* * **
33043 ACCGGTTTTGTCATTTTAAGA-CTGATTTTATCATATTTTTAGTTGTTATATTGTTATGGATCGA
1 ACCGGTTTTGTCATTTTGAGACCTG-TTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * * * *
33107 TATATTTTTATAAAATATCGATACTTTTTAGGCGCTATAACTTCTTCTTTTTTAAATTC-AAAAA
65 TACATTTTTTTAAAATATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAA
*
33171 GTTTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGATAGCGTTTT
130 GTTTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGATA-TGTTTT
* * * *
33225 ACCGGATTTGTCATTTTGGGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGAATCGAT
1 ACCGGTTTTGTCATTTTGAGACCTGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGAT
*
33290 ACATTTTTTTTAAAGTATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAA
66 ACA-TTTTTTTAAAATATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAA
* * ** *
33355 ATTTTGATACTTATATTAAATTATCGACACTTTCAACATATTAGATATTTTTT
130 GTTTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGATATGTTTT
33408 ACCGGTTTTGTCATTTTTGAGACCTGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
1 ACCGGTTTTGTCA-TTTTGAGACCTGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGA
* * *
33473 TACATTTTTTTAAAATATCGACACTTTATAGGCGTTATAACTTATTATCTTTTAAATTCT-AAAA
65 TACATTTTTTTAAAATATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAA
*
33537 GTGTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGATATCGTTTT
130 GTTTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGATAT-GTTTT
33591 ACCGGTTTTGTCAT
1 ACCGGTTTTGTCAT
33605 ATTTTTACCT
Statistics
Matches: 341, Mismatches: 34, Indels: 10
0.89 0.09 0.03
Matches are distributed among these distances:
182 104 0.30
183 137 0.40
184 100 0.29
ACGTcount: A:0.28, C:0.14, G:0.12, T:0.46
Consensus pattern (182 bp):
ACCGGTTTTGTCATTTTGAGACCTGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGAT
ACATTTTTTTAAAATATCGACACTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCTAAAAAG
TTTCGATACTTATATTAAATTATCGACACTTTCAACATATCCGATATGTTTT
Found at i:33454 original size:20 final size:19
Alignment explanation
Indices: 33401--33455 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 19
33391 CATATTAGAT
*
33401 ATTTTTTACCGGTTTTGTC
1 ATTTTTTACCTGTTTTGTC
*
33420 ATTTTTGAGACCTGTTTTGTC
1 ATTTTT--TACCTGTTTTGTC
33441 ATATTTTTACCTGTT
1 AT-TTTTTACCTGTT
33456 ATATTGTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 6 0.20
20 7 0.23
21 13 0.43
22 4 0.13
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (19 bp):
ATTTTTTACCTGTTTTGTC
Found at i:38756 original size:12 final size:12
Alignment explanation
Indices: 38739--38789 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
38729 TTTCCTTTGT
38739 TATTATTATTTA
1 TATTATTATTTA
38751 TATTA-TATTT-
1 TATTATTATTTA
38761 TATTATATATTTCA
1 TATTAT-TATTT-A
* *
38775 TGTCATTATTTA
1 TATTATTATTTA
38787 TAT
1 TAT
38790 ATAGGTATGT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
10 5 0.16
11 5 0.16
12 13 0.41
13 5 0.16
14 4 0.12
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (12 bp):
TATTATTATTTA
Found at i:38759 original size:17 final size:16
Alignment explanation
Indices: 38738--38789 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 16
38728 TTTTCCTTTG
38738 TTATTATTATTTATAT
1 TTATTATTATTTATAT
38754 TATATT-TTATTATATAT
1 T-TATTATTATT-TATAT
38771 TTCATGTCATTATTTATAT
1 TT-AT-T-ATTATTTATAT
38790 ATAGGTATGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
16 7 0.23
17 12 0.40
18 1 0.03
19 5 0.17
20 5 0.17
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (16 bp):
TTATTATTATTTATAT
Found at i:49743 original size:13 final size:13
Alignment explanation
Indices: 49727--49769 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
49717 GGAAAAAAAG
49727 AACAAAAAAACAA
1 AACAAAAAAACAA
*
49740 AACAAAAGAACAAA
1 AACAAAAAAAC-AA
*
49754 AAAATAAAAAACAA
1 AACA-AAAAAACAA
49768 AA
1 AA
49770 AGAGAAAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 10 0.40
14 9 0.36
15 6 0.24
ACGTcount: A:0.84, C:0.12, G:0.02, T:0.02
Consensus pattern (13 bp):
AACAAAAAAACAA
Found at i:49746 original size:21 final size:21
Alignment explanation
Indices: 49722--49762 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
49712 AGTTGGGAAA
49722 AAAAGAACAAAAAAACAAAAC
1 AAAAGAACAAAAAAACAAAAC
*
49743 AAAAGAACAAAAAAATAAAA
1 AAAAGAACAAAAAAACAAAA
49763 AACAAAAAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.83, C:0.10, G:0.05, T:0.02
Consensus pattern (21 bp):
AAAAGAACAAAAAAACAAAAC
Found at i:50817 original size:105 final size:105
Alignment explanation
Indices: 50571--51319 Score: 1277
Period size: 105 Copynumber: 7.1 Consensus size: 105
50561 CAGGTTTTAC
* *
50571 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAAACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
50636 GACGAAGGGACCGCTGGTTGTCAAACAAACATCTCTCAATT
66 GACGAAGGGACCGCTGGTTGTC-AACAAACATTTCTCAATT
50677 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
50742 GACGAAGGGACCGCTGGTTGTCAACAAACATCTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
*
50782 TCAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
50847 GACGAAGGGACCGCTGGTTGTCAAACAAACATCTCTCAATT
66 GACGAAGGGACCGCTGGTTGTC-AACAAACATTTCTCAATT
*
50888 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAT
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
50953 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
* *
50993 TCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
*
51058 GACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAA-T
66 GACGAAGGGACCGCTGGTTGTCAACAAACATTTCT-CAATT
*
51098 TCAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
51163 GACGAAGGGACCGCTGGTTGTCAACAAACATTTTCTCCAA-T
66 GACGAAGGGACCGCTGGTTGTCAACAAACA-TTTCT-CAATT
* * * *
51204 TCAGAGCCAATTTCAACTTCACAATGAAGCATATTGGACTTCAAACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
* *
51269 GACGAAGGGACCGCTGGTTGTCAAACACATATTTCTCAATT
66 GACGAAGGGACCGCTGGTTGTC-AACAAACATTTCTCAATT
51310 TCAGAGCCAA
1 TCAGAGCCAA
51320 CGAAGGATAT
Statistics
Matches: 617, Mismatches: 21, Indels: 10
0.95 0.03 0.02
Matches are distributed among these distances:
105 312 0.51
106 299 0.48
107 6 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATT
Found at i:50935 original size:211 final size:211
Alignment explanation
Indices: 50571--51319 Score: 1297
Period size: 211 Copynumber: 3.5 Consensus size: 211
50561 CAGGTTTTAC
*
50571 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAAACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCAC
50636 GACGAAGGGACCGCTGGTTGTCAAACAAACATCTCTCAATTTCAGAGCCAATTTCAACTTCACAA
66 GACGAAGGGACCGCTGGTTGTCAAACAAACATCTCTCAATTTCAGAGCCAATTTCAACTTCACAA
50701 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
*
50766 CAAACATCTCTCAATT
196 CAAACATTTCTCAATT
* *
50782 TCAGAGCCAATCTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCAC
50847 GACGAAGGGACCGCTGGTTGTCAAACAAACATCTCTCAATTTCAGAGCCAATTTCAACTTCACAA
66 GACGAAGGGACCGCTGGTTGTCAAACAAACATCTCTCAATTTCAGAGCCAATTTCAACTTCACAA
*
50912 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAA
131 CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
50977 CAAACATTTCTCAATT
196 CAAACATTTCTCAATT
* * *
50993 TCGGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCAC
* * *
51058 GACGAAGGGACCGCTGGTTGTC-ACCAAACATTTCTCCAA-TTCAGAGCCAATCTCAACTTCACA
66 GACGAAGGGACCGCTGGTTGTCAAACAAACATCTCT-CAATTTCAGAGCCAATTTCAACTTCACA
51121 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
130 ACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCA
51186 ACAAACATTTTCTCCAA-T
195 ACAAACA-TTTCT-CAATT
* * *
51204 TCAGAGCCAATTTCAACTTCACAATGAAGCATATTGGACTTCAAACAACGCAAGTTCAACTTCAC
1 TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCAC
* * *
51269 GACGAAGGGACCGCTGGTTGTCAAACACATATTTCTCAATTTCAGAGCCAA
66 GACGAAGGGACCGCTGGTTGTCAAACAAACATCTCTCAATTTCAGAGCCAA
51320 CGAAGGATAT
Statistics
Matches: 512, Mismatches: 21, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
210 105 0.21
211 383 0.75
212 24 0.05
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.22
Consensus pattern (211 bp):
TCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAAACAACGCAAGTTCAACTTCAC
GACGAAGGGACCGCTGGTTGTCAAACAAACATCTCTCAATTTCAGAGCCAATTTCAACTTCACAA
CGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAA
CAAACATTTCTCAATT
Found at i:53032 original size:27 final size:28
Alignment explanation
Indices: 52972--53040 Score: 71
Period size: 23 Copynumber: 2.7 Consensus size: 28
52962 TATATATATA
*
52972 TATGTATATA-TTTTA-TTATTATTACT
1 TATGTATATATTTTTATTTATTAATACT
52998 TA---AT-TATTTTTATTTATTAAT-CT
1 TATGTATATATTTTTATTTATTAATACT
53021 TATGTATATATTTTTCATTT
1 TATGTATATATTTTT-ATTT
53041 TCATTGATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
22 2 0.06
23 11 0.31
24 7 0.20
26 4 0.11
27 7 0.20
28 4 0.11
ACGTcount: A:0.29, C:0.04, G:0.03, T:0.64
Consensus pattern (28 bp):
TATGTATATATTTTTATTTATTAATACT
Found at i:54976 original size:13 final size:14
Alignment explanation
Indices: 54948--54986 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
54938 ATAAACTAAA
*
54948 ATAATTTTTATTTT
1 ATAAATTTTATTTT
54962 ATAAATTTT-TTTT
1 ATAAATTTTATTTT
*
54975 ATCAATTTTATT
1 ATAAATTTTATT
54987 ATTTTATATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 12 0.55
14 10 0.45
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (14 bp):
ATAAATTTTATTTT
Found at i:58664 original size:22 final size:22
Alignment explanation
Indices: 58639--58689 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
58629 TTGACTTTTT
* *
58639 CGATCAAATTTAACGGTCAGAC
1 CGATCAAAGTCAACGGTCAGAC
*
58661 CGATCAAGGTCAACGGTCAGAC
1 CGATCAAAGTCAACGGTCAGAC
*
58683 CGGTCAA
1 CGATCAA
58690 TGGTTCGGGT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.25, G:0.24, T:0.18
Consensus pattern (22 bp):
CGATCAAAGTCAACGGTCAGAC
Found at i:58724 original size:18 final size:18
Alignment explanation
Indices: 58684--58725 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
58674 CGGTCAGACC
*
58684 GGTCAATGGTTCGGGTCA
1 GGTCAACGGTTCGGGTCA
* *
58702 TGTCAACGGTTCGGGTCG
1 GGTCAACGGTTCGGGTCA
58720 GGTCAA
1 GGTCAA
58726 ACCTGGTTCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.38, T:0.26
Consensus pattern (18 bp):
GGTCAACGGTTCGGGTCA
Found at i:65827 original size:18 final size:18
Alignment explanation
Indices: 65787--65828 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
65777 CAAAGTCAAC
65787 GGTCAACGGTTCAGGTCA
1 GGTCAACGGTTCAGGTCA
* * *
65805 TGTCAACGGTTCGGGTCG
1 GGTCAACGGTTCAGGTCA
65823 GGTCAA
1 GGTCAA
65829 ACCCTATTCG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (18 bp):
GGTCAACGGTTCAGGTCA
Found at i:66017 original size:23 final size:22
Alignment explanation
Indices: 65984--66030 Score: 76
Period size: 23 Copynumber: 2.1 Consensus size: 22
65974 CCAAAATTAG
65984 TCCAATATCACCAATAAACCAA
1 TCCAATATCACCAATAAACCAA
*
66006 TCCAATTATCACCAATCAACCAA
1 TCCAA-TATCACCAATAAACCAA
66029 TC
1 TC
66031 GTTAACTTAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 5 0.22
23 18 0.78
ACGTcount: A:0.45, C:0.34, G:0.00, T:0.21
Consensus pattern (22 bp):
TCCAATATCACCAATAAACCAA
Found at i:68678 original size:16 final size:16
Alignment explanation
Indices: 68590--68694 Score: 88
Period size: 16 Copynumber: 6.6 Consensus size: 16
68580 AATTTAGCGA
68590 AACCGAAATTAAC-CAG
1 AACCGAAATTAACAC-G
* * *
68606 AAGCGAAATTAACCCA
1 AACCGAAATTAACACG
* ** *
68622 AACCAAAAGCAACCCG
1 AACCGAAATTAACACG
* **
68638 AATCGAAAGCAACACG
1 AACCGAAATTAACACG
68654 AACCGAAATTAACACG
1 AACCGAAATTAACACG
*
68670 AACCGAAATTAACTCG
1 AACCGAAATTAACACG
68686 AACC-AAATT
1 AACCGAAATT
68695 TTAACCTGAT
Statistics
Matches: 74, Mismatches: 14, Indels: 3
0.81 0.15 0.03
Matches are distributed among these distances:
15 5 0.07
16 68 0.92
17 1 0.01
ACGTcount: A:0.50, C:0.27, G:0.12, T:0.11
Consensus pattern (16 bp):
AACCGAAATTAACACG
Found at i:68688 original size:32 final size:31
Alignment explanation
Indices: 68590--68737 Score: 91
Period size: 32 Copynumber: 4.6 Consensus size: 31
68580 AATTTAGCGA
* * *
68590 AACCGAAATTAACCAGAAGCGAAATTAACCCA
1 AACCGAAATTAACC-GAACCGAAATTAACACG
* ** * **
68622 AACCAAAAGCAACCCGAATCGAAAGCAACACG
1 AACCGAAATTAA-CCGAACCGAAATTAACACG
*
68654 AACCGAAATTAACACGAACCGAAATTAACTCG
1 AACCGAAATTAAC-CGAACCGAAATTAACACG
* * *
68686 AACC-AAATTTTAACCTGATCCGAAAATAACCCG
1 AACCGAAA--TTAACC-GAACCGAAATTAACACG
* * *
68719 AATCGAATTTAACCCAACC
1 AACCGAAATTAACCGAACC
68738 CAAAAACAAC
Statistics
Matches: 88, Mismatches: 22, Indels: 13
0.72 0.18 0.11
Matches are distributed among these distances:
31 7 0.08
32 55 0.62
33 24 0.27
34 2 0.02
ACGTcount: A:0.47, C:0.28, G:0.11, T:0.14
Consensus pattern (31 bp):
AACCGAAATTAACCGAACCGAAATTAACACG
Found at i:68807 original size:17 final size:16
Alignment explanation
Indices: 68783--68821 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
68773 TTATTAAACG
* *
68783 ATAAAAATTATTTTCA
1 ATAAAAATTAATTTAA
68799 ATAATAAATTAATTTAA
1 ATAA-AAATTAATTTAA
68816 ATAAAA
1 ATAAAA
68822 TTGATAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (16 bp):
ATAAAAATTAATTTAA
Found at i:69502 original size:32 final size:32
Alignment explanation
Indices: 69456--69533 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
69446 AACCAATCCA
* *
69456 ATATTGACCCGACCC-GAAATCTAACAGATATG
1 ATATTAACCCGACCCAAAAATC-AACAGATATG
* * * *
69488 GTATTAACCTGACCCAAAAATCAACTGATCTG
1 ATATTAACCCGACCCAAAAATCAACAGATATG
69520 ATATTAACCCGACC
1 ATATTAACCCGACC
69534 TGATAATTAC
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
32 32 0.86
33 5 0.14
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (32 bp):
ATATTAACCCGACCCAAAAATCAACAGATATG
Found at i:70778 original size:23 final size:23
Alignment explanation
Indices: 70746--70839 Score: 143
Period size: 23 Copynumber: 4.1 Consensus size: 23
70736 GTCTTAGGAA
* *
70746 AAAGTCAACGTTGATCAACGGTC
1 AAAGTTAACGTTGGTCAACGGTC
70769 AAAGTTAACGTTGGTCAACGGTC
1 AAAGTTAACGTTGGTCAACGGTC
*
70792 AAAGTTAACGTTGGTCAATGGTC
1 AAAGTTAACGTTGGTCAACGGTC
* *
70815 AAAGTTAACGTCGGTCAACAGTC
1 AAAGTTAACGTTGGTCAACGGTC
70838 AA
1 AA
70840 TGGATGAGCT
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.24
Consensus pattern (23 bp):
AAAGTTAACGTTGGTCAACGGTC
Found at i:71758 original size:11 final size:11
Alignment explanation
Indices: 71742--71774 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
71732 AAGTGGGGGT
71742 TTTATTTTTAA
1 TTTATTTTTAA
71753 TTTATTTTTAA
1 TTTATTTTTAA
71764 TATTATTTTTA
1 T-TTATTTTTA
71775 TTATTAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.57
12 9 0.43
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTATTTTTAA
Found at i:71769 original size:12 final size:12
Alignment explanation
Indices: 71743--71780 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
71733 AGTGGGGGTT
71743 TTATTTTTAAT-
1 TTATTTTTAATA
71754 TTATTTTTAATA
1 TTATTTTTAATA
*
71766 TTATTTTTATTA
1 TTATTTTTAATA
71778 TTA
1 TTA
71781 AAAAACTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
11 11 0.44
12 14 0.56
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTTTTAATA
Found at i:72128 original size:15 final size:13
Alignment explanation
Indices: 72108--72181 Score: 58
Period size: 15 Copynumber: 5.0 Consensus size: 13
72098 TATTTTAAAT
72108 ATTTTAAATAATTAA
1 ATTTTAAA-AA-TAA
*
72123 ATTTTATAAAATAC
1 ATTTTA-AAAATAA
72137 ATATTTAAAAATATA
1 AT-TTTAAAAATA-A
72152 ATTTTATCAAAAATAA
1 A-TTT-T-AAAAATAA
72168 ATTTTAAATAATAA
1 ATTTTAAA-AATAA
72182 TTAGTCAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
13 3 0.06
14 16 0.32
15 18 0.36
16 6 0.12
17 7 0.14
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (13 bp):
ATTTTAAAAATAA
Found at i:72141 original size:31 final size:32
Alignment explanation
Indices: 72105--72179 Score: 90
Period size: 30 Copynumber: 2.5 Consensus size: 32
72095 GATTATTTTA
72105 AATATTTTAAATAATTA-AATTTTAT-AAAAT
1 AATATTTTAAATAATTATAATTTTATAAAAAT
72135 ACATA-TTTAAA-AA-TATAATTTTATCAAAAAT
1 A-ATATTTTAAATAATTATAATTTTAT-AAAAAT
72166 AA-ATTTTAAATAAT
1 AATATTTTAAATAAT
72180 AATTAGTCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
28 2 0.05
29 11 0.29
30 14 0.37
31 11 0.29
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.43
Consensus pattern (32 bp):
AATATTTTAAATAATTATAATTTTATAAAAAT
Found at i:72154 original size:29 final size:30
Alignment explanation
Indices: 72108--72180 Score: 89
Period size: 29 Copynumber: 2.4 Consensus size: 30
72098 TATTTTAAAT
*
72108 ATTTTAAATAAT-TAAATTTTAT-AAAATAC
1 ATTTTAAATAATAT-AATTTTATAAAAATAA
72137 ATATTTAAA-AATATAATTTTATCAAAAATAA
1 AT-TTTAAATAATATAATTTTAT-AAAAATAA
72168 ATTTTAAATAATA
1 ATTTTAAATAATA
72181 ATTAGTCAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
29 13 0.34
30 13 0.34
31 12 0.32
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
ATTTTAAATAATATAATTTTATAAAAATAA
Found at i:72607 original size:23 final size:22
Alignment explanation
Indices: 72575--72617 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
72565 TTCACGAGCT
*
72575 TTCTTAGTTTTTTACTTTCTTGA
1 TTCTTAGTTTATT-CTTTCTTGA
*
72598 TTCTTGGTTTATTCTTTCTT
1 TTCTTAGTTTATTCTTTCTT
72618 TTGTATATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.09, C:0.14, G:0.09, T:0.67
Consensus pattern (22 bp):
TTCTTAGTTTATTCTTTCTTGA
Found at i:74327 original size:12 final size:12
Alignment explanation
Indices: 74310--74335 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
74300 CACTTGGTGA
74310 AATTTGTTATAC
1 AATTTGTTATAC
74322 AATTTGTTATAC
1 AATTTGTTATAC
74334 AA
1 AA
74336 ATGAGAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (12 bp):
AATTTGTTATAC
Found at i:74578 original size:20 final size:20
Alignment explanation
Indices: 74534--74578 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
74524 GACTTTTTGG
74534 GTCAAAGTCAATGGTCAACA
1 GTCAAAGTCAATGGTCAACA
*
74554 ATCAAAGTCAATGTGTCAA-A
1 GTCAAAGTCAATG-GTCAACA
74574 GTCAA
1 GTCAA
74579 CGGGTTGACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (20 bp):
GTCAAAGTCAATGGTCAACA
Found at i:79543 original size:23 final size:23
Alignment explanation
Indices: 79516--79567 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
79506 CTGAGTGGCA
*
79516 TATGAAATTTGTCCCT-AAGGACC
1 TATGAAATATG-CCCTAAAGGACC
*
79539 TATG-AATATGCCTTAAAGGACC
1 TATGAAATATGCCCTAAAGGACC
79561 TATGAAA
1 TATGAAA
79568 CCCTCGAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 3 0.12
22 16 0.64
23 6 0.24
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (23 bp):
TATGAAATATGCCCTAAAGGACC
Found at i:92213 original size:35 final size:33
Alignment explanation
Indices: 92133--92215 Score: 89
Period size: 35 Copynumber: 2.5 Consensus size: 33
92123 ATATAATTTT
*
92133 AAATACAACAAACTTACAATAAGTATTAAATGAC
1 AAATA-AACAAAATTACAATAAGTATTAAATGAC
*
92167 AAATAAA-AAAATTACAATAACTGGTATTAAATG-G
1 AAATAAACAAAATTACAATAA---GTATTAAATGAC
*
92201 TAATAAACAAAATTA
1 AAATAAACAAAATTA
92216 ACAAAAAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
32 12 0.29
33 2 0.05
34 11 0.26
35 17 0.40
ACGTcount: A:0.58, C:0.10, G:0.07, T:0.25
Consensus pattern (33 bp):
AAATAAACAAAATTACAATAAGTATTAAATGAC
Found at i:92231 original size:21 final size:20
Alignment explanation
Indices: 92206--92255 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
92196 AATGGTAATA
92206 AACAAAATTAACAAAAAAATT
1 AACAAAATT-ACAAAAAAATT
* * *
92227 AACAAAAAGTCCAACAAAATT
1 AAC-AAAATTACAAAAAAATT
92248 AACAAAAT
1 AACAAAAT
92256 AAATTAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 4 0.17
21 15 0.62
22 5 0.21
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (20 bp):
AACAAAATTACAAAAAAATT
Found at i:92233 original size:11 final size:12
Alignment explanation
Indices: 92209--92234 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
92199 GGTAATAAAC
92209 AAAATTAACAAA
1 AAAATTAACAAA
92221 AAAATTAACAAA
1 AAAATTAACAAA
92233 AA
1 AA
92235 GTCCAACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (12 bp):
AAAATTAACAAA
Found at i:94549 original size:29 final size:31
Alignment explanation
Indices: 94507--94579 Score: 84
Period size: 29 Copynumber: 2.5 Consensus size: 31
94497 GCAGAAAAAT
* *
94507 TAATTAAGTAAAATATTAA-AATA-ATTAAA
1 TAATTAAATAAAATATTAACAAAATATTAAA
*
94536 TAATTAAATAAAATACTAACAAAATATTAAA
1 TAATTAAATAAAATATTAACAAAATATTAAA
94567 T-A-T-AATAAAATAT
1 TAATTAAATAAAATAT
94580 ACCTTAAAGA
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
28 9 0.24
29 18 0.47
30 4 0.11
31 7 0.18
ACGTcount: A:0.63, C:0.03, G:0.01, T:0.33
Consensus pattern (31 bp):
TAATTAAATAAAATATTAACAAAATATTAAA
Found at i:94578 original size:17 final size:18
Alignment explanation
Indices: 94546--94579 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
94536 TAATTAAATA
94546 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
*
94564 AAATA-TAATAAAATAT
1 AAATACTAACAAAATAT
94580 ACCTTAAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:95000 original size:29 final size:29
Alignment explanation
Indices: 94968--95068 Score: 139
Period size: 29 Copynumber: 3.5 Consensus size: 29
94958 TTAGATCGAG
* *
94968 AAATAAAGATAGAAGGGTGACTGACAGGA
1 AAATAAAGATGGAAGGGTGCCTGACAGGA
*
94997 AAATAAAGATGGAAGGGTGCCTGACAGGG
1 AAATAAAGATGGAAGGGTGCCTGACAGGA
* * *
95026 AAATAAAGATGGAAGGGTGCCTAAAAGGT
1 AAATAAAGATGGAAGGGTGCCTGACAGGA
*
95055 AAATAAAGAGGGAA
1 AAATAAAGATGGAA
95069 ATGGTGATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 65 1.00
ACGTcount: A:0.47, C:0.07, G:0.33, T:0.14
Consensus pattern (29 bp):
AAATAAAGATGGAAGGGTGCCTGACAGGA
Found at i:101392 original size:20 final size:20
Alignment explanation
Indices: 101367--101419 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
101357 CATATGTTTG
101367 ATATTTTTTTATTTTTAATA
1 ATATTTTTTTATTTTTAATA
* * *
101387 ATA-TTTATTAGTTTTGATA
1 ATATTTTTTTATTTTTAATA
101406 A-ATTTATTTTATTT
1 ATATTT-TTTTATTT
101420 AATTTATCTC
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
18 1 0.04
19 16 0.62
20 9 0.35
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (20 bp):
ATATTTTTTTATTTTTAATA
Found at i:102437 original size:21 final size:21
Alignment explanation
Indices: 102413--102481 Score: 95
Period size: 20 Copynumber: 3.3 Consensus size: 21
102403 TATAATAATA
102413 TAATAATTTCCTTTAATTTAC
1 TAATAATTTCCTTTAATTTAC
* *
102434 TAATAA-TTACGTTAATTTAC
1 TAATAATTTCCTTTAATTTAC
*
102454 TAATAAATTACCTTTAATTTAC
1 TAAT-AATTTCCTTTAATTTAC
102476 TAATAA
1 TAATAA
102482 ATTAATACAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 16 0.39
21 10 0.24
22 15 0.37
ACGTcount: A:0.41, C:0.12, G:0.01, T:0.46
Consensus pattern (21 bp):
TAATAATTTCCTTTAATTTAC
Found at i:102485 original size:22 final size:21
Alignment explanation
Indices: 102413--102481 Score: 104
Period size: 21 Copynumber: 3.3 Consensus size: 21
102403 TATAATAATA
*
102413 TAATAATTTCCTTTAATTTAC
1 TAATAATTACCTTTAATTTAC
*
102434 TAATAATTA-CGTTAATTTAC
1 TAATAATTACCTTTAATTTAC
102454 TAATAAATTACCTTTAATTTAC
1 TAAT-AATTACCTTTAATTTAC
102476 TAATAA
1 TAATAA
102482 ATTAATACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 14 0.33
21 15 0.35
22 14 0.33
ACGTcount: A:0.41, C:0.12, G:0.01, T:0.46
Consensus pattern (21 bp):
TAATAATTACCTTTAATTTAC
Found at i:104431 original size:36 final size:36
Alignment explanation
Indices: 104382--104491 Score: 166
Period size: 36 Copynumber: 3.1 Consensus size: 36
104372 TGAATATTAG
* * * *
104382 AAAATGCTTAAATTAGGTGTTTCTACTAGCGTTGGA
1 AAAATGCTCAAATTAGGTTTTTCCACTAGCATTGGA
104418 AAAATGCTCAAATTAGGTTTTTCCACTAGCATTGGA
1 AAAATGCTCAAATTAGGTTTTTCCACTAGCATTGGA
* *
104454 AATATGCTCAAATTAGGTTTTTCCACTAGTATTGGA
1 AAAATGCTCAAATTAGGTTTTTCCACTAGCATTGGA
104490 AA
1 AA
104492 TGATGATTTG
Statistics
Matches: 68, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 68 1.00
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.35
Consensus pattern (36 bp):
AAAATGCTCAAATTAGGTTTTTCCACTAGCATTGGA
Found at i:109173 original size:31 final size:31
Alignment explanation
Indices: 109135--109197 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
109125 CCCAAGAGTT
109135 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
1 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
109166 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
1 TGGGAGTTCCTAGTGAGAAGGACATATTGAA
109197 T
1 T
109198 TCACCGAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.10, G:0.32, T:0.27
Consensus pattern (31 bp):
TGGGAGTTCCTAGTGAGAAGGACATATTGAA
Found at i:109813 original size:37 final size:36
Alignment explanation
Indices: 109746--109860 Score: 173
Period size: 37 Copynumber: 3.2 Consensus size: 36
109736 TCACTTGAAT
*
109746 ATTGGAAAAAATGCTCAAATTAGGTATTTCCACTAGC
1 ATTGG-AAAAATGCTCAAATTAGGTTTTTCCACTAGC
109783 ATTGGAAAAATGCTCAAATTAGGTTTTTTCCACTAGC
1 ATTGGAAAAATGCTCAAATTAGG-TTTTTCCACTAGC
109820 ATTGG--AAATGCTCAAATTAGGTTTTTCCACTAG-
1 ATTGGAAAAATGCTCAAATTAGGTTTTTCCACTAGC
*
109853 TTTGGAAA
1 ATTGGAAA
109861 TGATGATTTT
Statistics
Matches: 73, Mismatches: 2, Indels: 8
0.88 0.02 0.10
Matches are distributed among these distances:
33 4 0.05
34 12 0.16
35 17 0.23
36 18 0.25
37 22 0.30
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (36 bp):
ATTGGAAAAATGCTCAAATTAGGTTTTTCCACTAGC
Found at i:110371 original size:21 final size:21
Alignment explanation
Indices: 110345--110387 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
110335 AGGGTTGTAA
* * *
110345 CAGAAGAATTTGTGGGAGGAT
1 CAGAAGAAATTGGGGGAAGAT
110366 CAGAAGAAATTGGGGGAAGAT
1 CAGAAGAAATTGGGGGAAGAT
110387 C
1 C
110388 GAATAGATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.37, T:0.19
Consensus pattern (21 bp):
CAGAAGAAATTGGGGGAAGAT
Done.