Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007153.1 Hibiscus syriacus cultivar Beakdansim tig00018715_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: 101695
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:17273 original size:30 final size:31
Alignment explanation
Indices: 17198--17276 Score: 108
Period size: 30 Copynumber: 2.6 Consensus size: 31
17188 AAATGATGTT
* *
17198 ATTTTAGGCACTAAACTCTAGAAATATATCA
1 ATTTTAGGCACTAAACTTTAAAAATATATCA
*
17229 ATTTT-GTCACTAAACTTTAAAAATAT-TCA
1 ATTTTAGGCACTAAACTTTAAAAATATATCA
*
17258 ATTTTAGGCATTAAACTTT
1 ATTTTAGGCACTAAACTTT
17277 TTCGACCATC
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 8 0.19
30 29 0.69
31 5 0.12
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (31 bp):
ATTTTAGGCACTAAACTTTAAAAATATATCA
Found at i:29581 original size:162 final size:157
Alignment explanation
Indices: 29319--29635 Score: 562
Period size: 162 Copynumber: 2.0 Consensus size: 157
29309 TATTCGGGTC
* *
29319 GGGTCGGGTTCGGGTTTAGGGTGAAAAATACCCGACCCGAAAATATATATAATTTTACTTTATAT
1 GGGTCGGGTTCGGGTTTAGGGTGAAAAAGACCCGACCCGAAAATATATATAATTTTACCTTATAT
*
29384 ATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCACTGTTTTTA
66 ATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTTTA
29449 TTGAATAAAAATAATTTTTTTTATTTT
131 TTGAATAAAAATAATTTTTTTTATTTT
29476 GGGTCGGGTTCGGGTTTAGGGTGAAAAAACCGGACCCGACCCGGAAAATATATATAATTTTACCT
1 GGGTCGGGTTCGGGTTTAGGGTG-AAAAA---GACCCGACCC-GAAAATATATATAATTTTACCT
29541 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGT
61 TATATATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGT
29606 TTTTATTGAATAAAAATAATTTTTTTTATT
126 TTTTATTGAATAAAAATAATTTTTTTTATT
29636 ATTTCGTGTC
Statistics
Matches: 152, Mismatches: 3, Indels: 5
0.95 0.02 0.03
Matches are distributed among these distances:
157 23 0.15
158 5 0.03
161 9 0.06
162 115 0.76
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (157 bp):
GGGTCGGGTTCGGGTTTAGGGTGAAAAAGACCCGACCCGAAAATATATATAATTTTACCTTATAT
ATTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGTCAATGTTTTTA
TTGAATAAAAATAATTTTTTTTATTTT
Found at i:30081 original size:18 final size:17
Alignment explanation
Indices: 30035--30082 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 17
30025 ATATGGAATT
* *
30035 AGATTTCAATTCCTGAC
1 AGATTACAATTCCTCAC
*
30052 ATATTACAATTCCTTCAC
1 AGATTACAATTCC-TCAC
*
30070 AGATTCCAATTCC
1 AGATTACAATTCC
30083 CTCATAAACA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.35
Consensus pattern (17 bp):
AGATTACAATTCCTCAC
Found at i:33097 original size:38 final size:38
Alignment explanation
Indices: 33046--33132 Score: 156
Period size: 38 Copynumber: 2.3 Consensus size: 38
33036 TATTAACTGT
* *
33046 CACATCTTATTTTCATTATCGTTTTTAATTCCACATGA
1 CACATCATATTTTCATTATAGTTTTTAATTCCACATGA
33084 CACATCATATTTTCATTATAGTTTTTAATTCCACATGA
1 CACATCATATTTTCATTATAGTTTTTAATTCCACATGA
33122 CACATCATATT
1 CACATCATATT
33133 ATCACTCTAC
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
38 47 1.00
ACGTcount: A:0.30, C:0.21, G:0.05, T:0.45
Consensus pattern (38 bp):
CACATCATATTTTCATTATAGTTTTTAATTCCACATGA
Found at i:40932 original size:182 final size:183
Alignment explanation
Indices: 40623--41075 Score: 745
Period size: 182 Copynumber: 2.5 Consensus size: 183
40613 TTTTTTACTA
* * *
40623 CTGATTTTGTCATTTCGAGATCGATTTTGTCATATTTTTACCTGTTATATTATTATGGATCGATA
1 CTGATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
* *
40688 TATTTTTATAAAGTATCGACACTTTATTGATTCTATAACTTCTTTTCTATTAAATTCCAAAAGTG
66 TATTTTTATAAAGTATCGACACTTTATTGACTCTATAACTTCTTCTCTATTAAATTCCAAAAGTG
*
40753 TCGATACTTATAATAAAGTATCGACACTTTCAACATATCTGGTAGCT-CTTTAC
131 TCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAG-TGCTTTAC
40806 C-GATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
1 CTGATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
*
40870 TATTTTTATAAAGTATCGACACTTTATT-AGCTCTATAACTTCTTCTCTTTTAAATTCCAAAAGT
66 TATTTTTATAAAGTATCGACACTTTATTGA-CTCTATAACTTCTTCTCTATTAAATTCCAAAAGT
*
40934 GTCGATATTTATAATAAAGTATCGACACTATCAACATATCTGGTAGTGCTTTAC
130 GTCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGTGCTTTAC
** *
40988 CTG-TTTTGTCATTTATAGACCGGTTTTGT-ATTTTTTTACCTGTTATATTGTTATGGATCGATA
1 CTGATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
*
41051 CATTTTTATAAAGTATCGACACTTT
66 TATTTTTATAAAGTATCGACACTTT
41076 CAATATATCC
Statistics
Matches: 255, Mismatches: 12, Indels: 8
0.93 0.04 0.03
Matches are distributed among these distances:
181 59 0.23
182 194 0.76
183 2 0.01
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (183 bp):
CTGATTTTGTCATTTCGAGACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATA
TATTTTTATAAAGTATCGACACTTTATTGACTCTATAACTTCTTCTCTATTAAATTCCAAAAGTG
TCGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGTGCTTTAC
Found at i:41201 original size:113 final size:112
Alignment explanation
Indices: 40947--41406 Score: 725
Period size: 113 Copynumber: 4.1 Consensus size: 112
40937 GATATTTATA
* * * *
40947 ATAAAGTATCGACACTATCAACATATCTGGTAGTGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
41012 TTTGT-ATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* *
41058 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATATACAC-A
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGAC-CGG
41122 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATATTTT
65 TTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACAT-TTTT
*
41171 ATAAAGTATCGACATTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
41236 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
** * *
41283 ATAAAGTATCGACACTTTCAATATATCCAATAGTGTTTTACCTGTTTTGTCATTTATAGACC-G-
1 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
41346 TTTGTCATTTTTTTACCTATTATATTGTTATGGAT-TA-ATATGTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACAT-TTTT
41392 ATAAAGTATCGACAC
1 ATAAAGTATCGACAC
41407 AAACCAACAA
Statistics
Matches: 327, Mismatches: 17, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
108 3 0.01
109 20 0.06
110 34 0.10
111 63 0.19
112 100 0.31
113 107 0.33
ACGTcount: A:0.26, C:0.15, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:41337 original size:225 final size:220
Alignment explanation
Indices: 40938--41406 Score: 740
Period size: 225 Copynumber: 2.1 Consensus size: 220
40928 AAAAGTGTCG
* *
40938 ATATTTATAATAAAGTATCGACACTATCAACATATCTGGTAGTGCTTTACCTGTTTTGTCATTTA
1 ATATTT-T-ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTA
41003 TAGACCGGTTTTGTATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
64 TAGACCGGTTTTGTATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATC
** * *
41068 GACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATATACACATTTTGTCATTT
129 GACACTTTCAATATATCCAATAGCGCTTTACCTGTTTTGTCATTTATAGAC-C-GTTTGTCATTT
*
41133 TTTTACCTGTTATATTGTTATGGATCGATAC
192 TTTTACCTATTATATTGTTATGGAT-GA-AC
* * *
41164 ATATTTTATAAAGTATCGACATTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATA
1 ATATTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATA
41229 GACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
66 GACCGGTTTTGT-ATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCG
* *
41294 ACACTTTCAATATATCCAATAGTGTTTTACCTGTTTTGTCATTTATAGACCGTTTGTCATTTTTT
130 ACACTTTCAATATATCCAATAGCGCTTTACCTGTTTTGTCATTTATAGACCGTTTGTCATTTTTT
* *
41359 TACCTATTATATTGTTATGGATTAAT
195 TACCTATTATATTGTTATGGATGAAC
*
41385 ATGTTTTATAAAGTATCGACAC
1 ATATTTTATAAAGTATCGACAC
41407 AAACCAACAA
Statistics
Matches: 226, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
221 21 0.09
222 1 0.00
223 34 0.15
224 66 0.29
225 98 0.43
226 6 0.03
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.46
Consensus pattern (220 bp):
ATATTTTATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATA
GACCGGTTTTGTATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGA
CACTTTCAATATATCCAATAGCGCTTTACCTGTTTTGTCATTTATAGACCGTTTGTCATTTTTTT
ACCTATTATATTGTTATGGATGAAC
Found at i:41623 original size:3 final size:3
Alignment explanation
Indices: 41615--41640 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41605 GAATTGAGTT
41615 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
41641 CATGATTTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:42692 original size:229 final size:228
Alignment explanation
Indices: 42285--42771 Score: 848
Period size: 229 Copynumber: 2.1 Consensus size: 228
42275 GTAAATTATC
* *
42285 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAATATATTTATTATTATCTTTAGT
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
*
42350 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
66 TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
* *
42415 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTAGAAAATATGAAACACTATTAAAAAAATTG
131 TGTATAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAAATTG
*
42480 AAACATAAATTAAATAACTTTCAAAAAAGTATA
196 AAACATAAATTAAATAACTTTAAAAAAAGTATA
* *
42513 TATCATTTTTATAAAAGTGTTCATACTTATTTCACTGTTGAAAACATATTTATTATTATATTTGG
1 TATCATTTTTATAAAAGTGTCCATACTTATTTCACTG-TGAAAACATATTTATTATTATATTTAG
*
42578 TTAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
65 TTAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATT
* * *
42643 TTGTATAAATTAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAATAAATT
130 TTGTATAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAAATT
*
42708 GAAACATAAATTACATAACTTTAAAAAAAGTATA
195 GAAACATAAATTAAATAACTTTAAAAAAAGTATA
42742 TATCATTTTTATAAAAGTGTCCATACTTAT
1 TATCATTTTTATAAAAGTGTCCATACTTAT
42772 AAAAGTAGGT
Statistics
Matches: 244, Mismatches: 14, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
228 36 0.15
229 208 0.85
ACGTcount: A:0.45, C:0.07, G:0.07, T:0.40
Consensus pattern (228 bp):
TATCATTTTTATAAAAGTGTCCATACTTATTTCACTGTGAAAACATATTTATTATTATATTTAGT
TAATATTGTTAAATTTAAAATCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATATTT
TGTATAAATGAAATTATTAAATTAATATTGTAGGTAGAAAACATGAAACACTATTAAAAAAATTG
AAACATAAATTAAATAACTTTAAAAAAAGTATA
Found at i:43073 original size:20 final size:19
Alignment explanation
Indices: 43050--43096 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 19
43040 CGATATACCA
43050 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
43070 GGTAACAAAATGATAAAACC
1 GGTAA-AAAATGATAAAACC
43090 GGTAAAA
1 GGTAAAA
43097 CGTTACCGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.55, C:0.11, G:0.17, T:0.17
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:43264 original size:180 final size:182
Alignment explanation
Indices: 42838--43309 Score: 698
Period size: 180 Copynumber: 2.6 Consensus size: 182
42828 GATCCAAATT
* * *
42838 AAAAATGTGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTAT-AGAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCA-AAATGAT
* * * * * *
42902 AAAACCGGTCAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
65 AAAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTT
* *
42967 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
130 CGTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTTA
* *
43020 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTAACAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* *
43085 AAACCGGTAAAACGTTACCGGATATATTAAAAGTGTCGATACTTT-ATATAAGGATCGACACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
** *
43149 GTGAATTTAAAAGAGAAGCAGTTATAGCGCCTATAATGTGTCGATAC-TTTA
131 GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTTA
* * *
43200 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCCGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * *
43265 AAACCGGTAAAATGATACCAGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTT
43310 CGTAAGTACG
Statistics
Matches: 263, Mismatches: 26, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
180 105 0.40
181 60 0.23
182 97 0.37
183 1 0.00
ACGTcount: A:0.43, C:0.15, G:0.17, T:0.26
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGATACCGGATATATTAAAAGTGTCGATACTTTAATATAAGGATCGACACTTC
GTGAATTTAAAAGAGAAGCAGTTATAAAGCCTATAAAGTGTCGATACTTTTA
Found at i:45538 original size:21 final size:21
Alignment explanation
Indices: 45511--45575 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
45501 AAGATAATCA
*
45511 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAG
* * *
45532 CGAGTCGTAGAGAAACTCGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
45553 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
45574 AG
1 AG
45576 GCATAAGGGG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.31, T:0.17
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:45651 original size:33 final size:33
Alignment explanation
Indices: 45609--45674 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
45599 AAATAGATGG
* *
45609 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
* *
45642 AGTGGTGAAAGAAGTTGGGGTGTTAAGAGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
45675 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.47, T:0.23
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGAGGTGA
Found at i:48654 original size:182 final size:182
Alignment explanation
Indices: 48380--48871 Score: 869
Period size: 183 Copynumber: 2.7 Consensus size: 182
48370 GCAATGCTAT
*
48380 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATCTT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
*
48445 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTGT-TAAAAGTGTCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATT-TAAAAAAGTGTCGACA
*
48509 TTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
48562 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
* *
48627 GTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACGATTTAAAAAAGTATCGACA
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATAC-ATTTAAAAAAGTGTCGACA
*
48692 TTTACACATCGGAACCCAGATTTATAATGTAATAGATAATTTTGTAATATAAC
130 TTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
* * *
48745 CGGTATAAATATACCAGTTTTATGAGCGAATAGGTCTACAACCTATATCGACACTTTATAATATT
1 CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
48810 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACCATTTAAAAAAGTGTCG
66 GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATA-CATTTAAAAAAGTGTCG
48872 GTAATTTTAA
Statistics
Matches: 296, Mismatches: 11, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
182 109 0.37
183 186 0.63
184 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (182 bp):
CGGTATAAATATACCGGTTTTATGCGCGAATAGGTCTACAACCTATATCGACACTTTTTAATATT
GTGTCGGTACTTTATGTCCAGATTGGAAGAAAAATGTGTCGATACATTTAAAAAAGTGTCGACAT
TTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTGTAATATAAC
Found at i:51368 original size:25 final size:25
Alignment explanation
Indices: 51340--51404 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
51330 TTATCATTAA
51340 ATTTAGGTATGTACAATAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
****
51365 ATTTAGGTATGTTTGTTAACTACAT
1 ATTTAGGTATGTACAATAACTACAT
*
51390 ATTTAGGTATATACA
1 ATTTAGGTATGTACA
51405 TCTTTTGAGT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.35, C:0.09, G:0.14, T:0.42
Consensus pattern (25 bp):
ATTTAGGTATGTACAATAACTACAT
Found at i:51728 original size:21 final size:22
Alignment explanation
Indices: 51682--51728 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
51672 AAATTACATA
51682 ACTTTTAAAAAAAGTATCGATC
1 ACTTTTAAAAAAAGTATCGATC
* * *
51704 -CTTTTTATAAAAGTATGGA-C
1 ACTTTTAAAAAAAGTATCGATC
51724 ACTTT
1 ACTTT
51729 CAATATAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (22 bp):
ACTTTTAAAAAAAGTATCGATC
Found at i:51777 original size:23 final size:23
Alignment explanation
Indices: 51746--51818 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
51736 ATAGGTAAAC
*
51746 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
51769 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
51792 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
51815 ATAT
1 ATAT
51819 TGTAAAGTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:52267 original size:18 final size:18
Alignment explanation
Indices: 52246--52282 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
52236 GTAATTGGAG
52246 TTTGAATTTAAATTTCAA
1 TTTGAATTTAAATTTCAA
* *
52264 TTTGAGTTTGAATTTCAA
1 TTTGAATTTAAATTTCAA
52282 T
1 T
52283 ATATATTTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.51
Consensus pattern (18 bp):
TTTGAATTTAAATTTCAA
Found at i:52290 original size:24 final size:24
Alignment explanation
Indices: 52238--52284 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
52228 TTTCATATGT
* *
52238 AATTGGAGTTTGAATTTAAATTTC
1 AATTTGAGTTTGAATTTAAATATC
*
52262 AATTTGAGTTTGAATTTCAATAT
1 AATTTGAGTTTGAATTTAAATAT
52285 ATATTTCGGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (24 bp):
AATTTGAGTTTGAATTTAAATATC
Found at i:52584 original size:39 final size:39
Alignment explanation
Indices: 52541--52616 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
52531 TCCGATGCTC
*
52541 ATCAAAATCCAAAGCTCATATGGTGCCAAGCAAAAGGAA
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
* *
52580 ATCAAAATTCAAATCTCATATGATGCCAAGCAAAAGG
1 ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGG
52617 TTATCTTTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.46, C:0.20, G:0.16, T:0.18
Consensus pattern (39 bp):
ATCAAAATCCAAAGCTCATATGATGCCAAGCAAAAGGAA
Found at i:52753 original size:30 final size:29
Alignment explanation
Indices: 52694--52760 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
52684 GTTACGATAT
* *
52694 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
52724 ATATTTTATAAAATATCAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
52754 ATTTTTT
1 ATATTTT
52761 GTACAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:52937 original size:23 final size:23
Alignment explanation
Indices: 52906--52978 Score: 101
Period size: 23 Copynumber: 3.2 Consensus size: 23
52896 ATAGGTAAAA
*
52906 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
* *
52929 ATATAATGTAATAGGTATCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
52952 ATATAATGTAATAGGTAGTGGTT
1 ATATAATGTAATAGGTAGCGCTT
52975 ATAT
1 ATAT
52979 TGTAAAGTGT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.34, C:0.04, G:0.22, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:53183 original size:30 final size:29
Alignment explanation
Indices: 53124--53190 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
53114 GTTACGATAT
* *
53124 ATATTATTATTAAATTAAAAATTCTAAATA
1 ATATT-TTATAAAATTAAAAAATCTAAATA
53154 ATATTTTATAAAATATCAAAAAATC-AAATA
1 ATATTTTATAAAAT-T-AAAAAATCTAAATA
*
53184 ATTTTTT
1 ATATTTT
53191 GTGCAAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 8 0.25
30 17 0.53
31 7 0.22
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.43
Consensus pattern (29 bp):
ATATTTTATAAAATTAAAAAATCTAAATA
Found at i:60117 original size:19 final size:19
Alignment explanation
Indices: 60093--60130 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
60083 AGAATGTCCA
60093 GGGGGTATCGATTCCCTCT
1 GGGGGTATCGATTCCCTCT
60112 GGGGGTATCGATTCCCTCT
1 GGGGGTATCGATTCCCTCT
60131 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.26, G:0.32, T:0.32
Consensus pattern (19 bp):
GGGGGTATCGATTCCCTCT
Found at i:66255 original size:2 final size:2
Alignment explanation
Indices: 66248--66308 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
66238 CATGAGTTAG
66248 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
66290 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
66309 GAATTGTATA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:67044 original size:30 final size:30
Alignment explanation
Indices: 67000--67093 Score: 136
Period size: 30 Copynumber: 3.1 Consensus size: 30
66990 TCAGGACTTA
*
67000 TGGACAGTTTACCGAGGATATTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
67031 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
67061 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
67090 TGGA
1 TGGA
67094 TAGGTCCTTC
Statistics
Matches: 59, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
29 18 0.31
30 34 0.58
31 7 0.12
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:69876 original size:20 final size:19
Alignment explanation
Indices: 69840--69877 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
69830 AGAATGTCCA
69840 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
69859 GGGGGTATCGATTCCCCCT
1 GGGGGTATCGATTCCCCCT
69878 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.11, C:0.32, G:0.32, T:0.26
Consensus pattern (19 bp):
GGGGGTATCGATTCCCCCT
Found at i:75065 original size:273 final size:273
Alignment explanation
Indices: 74578--75395 Score: 1492
Period size: 273 Copynumber: 3.0 Consensus size: 273
74568 TCTACTACAT
*
74578 GAACAAAGATGACCCTTAAGCCTAAAAATTTATACATAAAAATATGAAATCAATATAGAATAAAT
1 GAACAAAGATGACCCTTAAGCCTGAAAATTTATACATAAAAATATGAAATCAATATAGAATAAAT
74643 CACACGTAAGATATTAAATTTAACATGACTTAATCTTATACGTTTACATGGATGAAAGAAACAAT
66 CACACGTAAGATATTAAATTTAACATGACTTAATCTTATACGTTTACATGGATGAAAGAAACAAT
*
74708 AACTAAAAAAATATACACTACATCATGACTCATACAAAATCTATCTCTATGACATAGTAACACGC
131 AACTAAAAAAATATACACTACATCATGACTCATACAAAATCTATCTCTATGACATAGTAACACAC
* * *
74773 GGGGAAAAACACAAGATTTTATGTTAGAGATGACAAATTTGAACTTATAAAATTTTAGAGAACGA
196 GGGGAAAAACACAAGATTTTATGTTAGAGATGACAAATTTGAACTTTTAAAATTCTAGAGAGCGA
*
74838 ACTTGGATTTCAG
261 ACTTGGATTTCAA
74851 GAACAAAGATGACCCTTAAGCCTGAAAATTTATACATAAAAATATGAAATCAATATAGAATAAAT
1 GAACAAAGATGACCCTTAAGCCTGAAAATTTATACATAAAAATATGAAATCAATATAGAATAAAT
74916 CACACGTAAGATATTAAATTTAACATGACTTAATCTTATACGTTTACATGGATGAAAGAAACAAT
66 CACACGTAAGATATTAAATTTAACATGACTTAATCTTATACGTTTACATGGATGAAAGAAACAAT
*
74981 AACTAAAGAAATATACACTACATCATGACTCATACAAAATCTATCTCTATGACATAGTAACACAC
131 AACTAAAAAAATATACACTACATCATGACTCATACAAAATCTATCTCTATGACATAGTAACACAC
75046 GGGGAAAAACACAAGATTTTATGTTAGAGATGACAAATTTGAACTTTTAAAATTCTAGAGAGCGA
196 GGGGAAAAACACAAGATTTTATGTTAGAGATGACAAATTTGAACTTTTAAAATTCTAGAGAGCGA
75111 ACTTGGATTTCAA
261 ACTTGGATTTCAA
* *
75124 GAACAAAGATAACCCTTAAGCCTGAAAATTTATACATAAAAATATGAAATCGATATAGAATAAAT
1 GAACAAAGATGACCCTTAAGCCTGAAAATTTATACATAAAAATATGAAATCAATATAGAATAAAT
*
75189 CACGCGTAAGATATTAAATTTAACATGACTTAATCTTATACGTTTACATGGATGAAAGAAACAAT
66 CACACGTAAGATATTAAATTTAACATGACTTAATCTTATACGTTTACATGGATGAAAGAAACAAT
* *
75254 AACTAAAAAAATATACACTACATCATGGCTCATACAAAATCTATCTCTATGAGATAGTAACACAC
131 AACTAAAAAAATATACACTACATCATGACTCATACAAAATCTATCTCTATGACATAGTAACACAC
* * * *
75319 GGGGATAAACATAAGATTTTATGTTAGAGAGGATAAATTTGAACTTTTAAAATTCTAGAGAGCGA
196 GGGGAAAAACACAAGATTTTATGTTAGAGATGACAAATTTGAACTTTTAAAATTCTAGAGAGCGA
75384 ACTTGGATTTCA
261 ACTTGGATTTCA
75396 TGGGGTAAAA
Statistics
Matches: 528, Mismatches: 17, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
273 528 1.00
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (273 bp):
GAACAAAGATGACCCTTAAGCCTGAAAATTTATACATAAAAATATGAAATCAATATAGAATAAAT
CACACGTAAGATATTAAATTTAACATGACTTAATCTTATACGTTTACATGGATGAAAGAAACAAT
AACTAAAAAAATATACACTACATCATGACTCATACAAAATCTATCTCTATGACATAGTAACACAC
GGGGAAAAACACAAGATTTTATGTTAGAGATGACAAATTTGAACTTTTAAAATTCTAGAGAGCGA
ACTTGGATTTCAA
Found at i:76352 original size:2 final size:2
Alignment explanation
Indices: 76345--76388 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
76335 TACATAAAAT
76345 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
76387 TA
1 TA
76389 AAAGATTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:80097 original size:108 final size:108
Alignment explanation
Indices: 79769--80060 Score: 475
Period size: 108 Copynumber: 2.7 Consensus size: 108
79759 TGATCACGAC
* * * * *
79769 GATAATGATGATAATGGCTTCTCTT-ATTCTCTAGAGGAAGG-TGGTCGTCA-CATACATGCTGG
1 GATAATGATGATAACGGCTTCT-TTAATTCTCCAGAGG-AGGATGGTC-ACAGTAGACATGCTGG
79831 GGGATCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGGGCAG
63 GGGATCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGGGCAG
79877 GATAATGATGATAACGGCTTCTTTAATTCTCCAGAGGAGGATGGTCACAGTAGACATGCTGGGGG
1 GATAATGATGATAACGGCTTCTTTAATTCTCCAGAGGAGGATGGTCACAGTAGACATGCTGGGGG
79942 ATCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGGGCAG
66 ATCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGGGCAG
79985 GATAATGATGATAACGGCTTCTTTAATTCTCCAGAGGAGGATGGTCACAGTAGACATGCT-GGGG
1 GATAATGATGATAACGGCTTCTTTAATTCTCCAGAGGAGGATGGTCACAGTAGACATGCTGGGGG
80049 ATTCTTCATCTG
66 A-TCTTCATCTG
80061 GCTCAGACGC
Statistics
Matches: 175, Mismatches: 5, Indels: 8
0.93 0.03 0.04
Matches are distributed among these distances:
107 12 0.07
108 163 0.93
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.30
Consensus pattern (108 bp):
GATAATGATGATAACGGCTTCTTTAATTCTCCAGAGGAGGATGGTCACAGTAGACATGCTGGGGG
ATCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGGGCAG
Found at i:83279 original size:31 final size:31
Alignment explanation
Indices: 83241--83317 Score: 145
Period size: 31 Copynumber: 2.5 Consensus size: 31
83231 AAACTACGAA
83241 TTTAGTACCTAAACTATCAATCTTGATTTAT
1 TTTAGTACCTAAACTATCAATCTTGATTTAT
*
83272 TTTAGTACCTAAACTATCAATCTTGATTTGT
1 TTTAGTACCTAAACTATCAATCTTGATTTAT
83303 TTTAGTACCTAAACT
1 TTTAGTACCTAAACT
83318 TTTAATTTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (31 bp):
TTTAGTACCTAAACTATCAATCTTGATTTAT
Found at i:89374 original size:24 final size:24
Alignment explanation
Indices: 89347--89393 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
89337 TCAAATGATT
89347 AAGAATATTTAGTAAATATACTTA
1 AAGAATATTTAGTAAATATACTTA
89371 AAGAATATTTAGTAAATATACTT
1 AAGAATATTTAGTAAATATACTT
89394 CTTACATGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (24 bp):
AAGAATATTTAGTAAATATACTTA
Found at i:97022 original size:16 final size:15
Alignment explanation
Indices: 97001--97035 Score: 52
Period size: 16 Copynumber: 2.3 Consensus size: 15
96991 AATATTTTAT
*
97001 ATAAATTAATTAGTTA
1 ATAAATTAAATA-TTA
97017 ATAAATTAAATATTA
1 ATAAATTAAATATTA
97032 ATAA
1 ATAA
97036 TTATATTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (15 bp):
ATAAATTAAATATTA
Found at i:98401 original size:29 final size:30
Alignment explanation
Indices: 98355--98415 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 30
98345 TATTTTGAGT
* *
98355 AACGAAATGAAACGATAGGCACCAAACTGA
1 AACGAAATAAAACAATAGGCACCAAACTGA
*
98385 AACGAAA-AAAACAATAGGCACTAAACTGA
1 AACGAAATAAAACAATAGGCACCAAACTGA
98414 AA
1 AA
98416 AAAAGACATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.56, C:0.18, G:0.16, T:0.10
Consensus pattern (30 bp):
AACGAAATAAAACAATAGGCACCAAACTGA
Done.