Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005438.1 Hibiscus syriacus cultivar Beakdansim tig00012465_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: 72380
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:833 original size:29 final size:30
Alignment explanation
Indices: 772--857 Score: 113
Period size: 29 Copynumber: 2.9 Consensus size: 30
762 GTTTGACCTA
* * *
772 TAAATTTTAAATAAAATACTAATTT-ATCTC
1 TAAATTTTAAATAAAATA-TTATTTAACCCC
802 TAAATTTT-AATAAAATATTATTTAACCCC
1 TAAATTTTAAATAAAATATTATTTAACCCC
831 TAAATTTTAAATAAAATATTAATTTAA
1 TAAATTTTAAATAAAATATT-ATTTAA
858 ACACTGAATT
Statistics
Matches: 50, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
28 5 0.10
29 20 0.40
30 19 0.38
31 6 0.12
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (30 bp):
TAAATTTTAAATAAAATATTATTTAACCCC
Found at i:1607 original size:176 final size:180
Alignment explanation
Indices: 1299--1948 Score: 790
Period size: 178 Copynumber: 3.7 Consensus size: 180
1289 TATGTCGACA
* * * * * *
1299 CTTTATAAAAATATATTGATCCACATCAATATAACAGG-AAAAA-ATGACAAAACCGATCACGAA
1 CTTTATAAATATGTATCGAT-CACAACGATATAATAGGTAAAAATATGACAAAACCGATCACGAA
* * * * * * *
1362 AAGACAAAACCGATAAAGCGCTATCGG-ATAATTGCAAGTGTCGCTACTTTAATATAAGTATCTA
65 AAGACAAAACCGGTAAAGAGATACCGGAAT-ATTGAAAGTGTCGATACTTTAATATAAGTATCGA
1426 CACATAGTGAATTTAAAGGAGAAGCA-TTTTAGCGCCTATAAAGTGTCGATT
129 CACATAGTGAATTTAAAGGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATT
* * *
1477 CTTTATAAATATGTATCGATCTACAACGATATAATAGCTAAAAATATGAC-AAA-CGGTCAGGAA
1 CTTTATAAATATGTATCGATC-ACAACGATATAATAGGTAAAAATATGACAAAACCGATCACGAA
*
1540 AAGACAAAACCGGT-AAGAGATACCGG-ATATTGAAAGTGTTGATACTTTAATATAAGTATCGAC
65 AAGACAAAACCGGTAAAGAGATACCGGAATATTGAAAGTGTCGATACTTTAATATAAGTATCGAC
*
1603 ACATAGTGAATTT-AAGGAGAAGTAGTTTTAGCGCCTATAAAGTGTCGATT
130 ACATAGTGAATTTAAAGGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATT
* *
1653 CTTTATAAATA--TATCGATCCACAACGATATAACT-GGTAAAAATATGACAAAACCGGTCAGGA
1 CTTTATAAATATGTATCGAT-CACAACGATATAA-TAGGTAAAAATATGACAAAACCGATCACGA
* *
1715 AAAGACAAAACC-GTAAAGAGATACTGGATATATTGAAAGTGTCAATACTTTAATATAAGTATCG
64 AAAGACAAAACCGGTAAAGAGATACCGGA-ATATTGAAAGTGTCGATACTTTAATATAAGTATCG
* * * *
1779 -CACATTGTAAATTTAAAGGAGAAGCAGTTTTAGAGCATATAAAGTGTCGATT
128 ACACATAGTGAATTTAAAGGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATT
* * * * * * *
1831 CTTTAAAAAAATGTATCGATCATAACGATATAAAAGGTAAAAATATGA-TAAACCGATCTCTAAA
1 CTTTATAAATATGTATCGATCACAACGATATAATAGGTAAAAATATGACAAAACCGATCACGAAA
** * * *
1895 TTACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
66 AGACAAAACCGGTAAAGAGATACCGGA-ATATTGAAAGTGTCGATACTTTAATA
1949 AGTACGCGTA
Statistics
Matches: 413, Mismatches: 43, Indels: 31
0.85 0.09 0.06
Matches are distributed among these distances:
174 32 0.08
175 17 0.04
176 112 0.27
177 24 0.06
178 144 0.35
179 72 0.17
180 12 0.03
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (180 bp):
CTTTATAAATATGTATCGATCACAACGATATAATAGGTAAAAATATGACAAAACCGATCACGAAA
AGACAAAACCGGTAAAGAGATACCGGAATATTGAAAGTGTCGATACTTTAATATAAGTATCGACA
CATAGTGAATTTAAAGGAGAAGCAGTTTTAGCGCCTATAAAGTGTCGATT
Found at i:3895 original size:22 final size:20
Alignment explanation
Indices: 3870--3917 Score: 51
Period size: 22 Copynumber: 2.3 Consensus size: 20
3860 TTGTTTCTTA
3870 TATAAAATGATAATATAGTTAT
1 TATAAAATGATAA-AT-GTTAT
* * *
3892 TATATAATTATAAATTTTAT
1 TATAAAATGATAAATGTTAT
3912 TATAAA
1 TATAAA
3918 TACAGGTTGC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 9 0.41
21 2 0.09
22 11 0.50
ACGTcount: A:0.50, C:0.00, G:0.04, T:0.46
Consensus pattern (20 bp):
TATAAAATGATAAATGTTAT
Found at i:4308 original size:21 final size:21
Alignment explanation
Indices: 4284--4327 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4274 AAGATAATCA
*
4284 AGAGTCGAAGAAAAACTTGAG
1 AGAGTCAAAGAAAAACTTGAG
* *
4305 AGAGTCAAAGAGACACTTGAG
1 AGAGTCAAAGAAAAACTTGAG
4326 AG
1 AG
4328 GCATAAGAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.11, G:0.30, T:0.14
Consensus pattern (21 bp):
AGAGTCAAAGAAAAACTTGAG
Found at i:4435 original size:32 final size:30
Alignment explanation
Indices: 4365--4456 Score: 114
Period size: 32 Copynumber: 3.0 Consensus size: 30
4355 AAATGGAGTG
*
4365 GTGAAAGAAGTTGTGGTGTTGAGGGGTG-AA
1 GTGAAAGAAGTTG-AGTGTTGAGGGGTGAAA
* *
4395 GTGAAAGAAGTTGAGTATTGAGAGGTGAAGTA
1 GTGAAAGAAGTTGAGTGTTGAGGGGTGAA--A
4427 GTGAAAGAAGTTGAGGTGTTGAGGGGTGAA
1 GTGAAAGAAGTTGA-GTGTTGAGGGGTGAA
4457 CTTAAGATGG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
29 11 0.21
30 14 0.26
32 15 0.28
33 13 0.25
ACGTcount: A:0.32, C:0.00, G:0.43, T:0.25
Consensus pattern (30 bp):
GTGAAAGAAGTTGAGTGTTGAGGGGTGAAA
Found at i:6197 original size:18 final size:19
Alignment explanation
Indices: 6151--6206 Score: 96
Period size: 19 Copynumber: 3.0 Consensus size: 19
6141 AATGTAGAGT
*
6151 TAATTTTGTATAAGATTTA
1 TAATTTTGTATACGATTTA
6170 TAATTTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
6189 TAA-TTTGTATACGATTTA
1 TAATTTTGTATACGATTTA
6207 AGATTTATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
18 15 0.42
19 21 0.58
ACGTcount: A:0.34, C:0.04, G:0.11, T:0.52
Consensus pattern (19 bp):
TAATTTTGTATACGATTTA
Found at i:6934 original size:200 final size:198
Alignment explanation
Indices: 6551--7870 Score: 1591
Period size: 200 Copynumber: 6.6 Consensus size: 198
6541 GTAAGCATAT
* * * * *
6551 GTGTCGATACGTTTATAAAACGTATCGATCCCAAAAACATCGAAACCCATAATTATAATATAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* *
6616 GGTAATTTTGT-AATATAACAGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACAGAATG
66 GGTAATTTT-TCAATATAACTGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACA-AATG
*** * * *
6680 TATCGACACTTTTTCGTTATGTGTCGATACTTTTTGTTCAGAATGAATGCCCAAAATGATGAACG
129 TATCGACACTTTTGAATT-TGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGATGAACG
*
6745 CATAAC
193 CATAAA
* ** * *
6751 GTGTTGATACATTTATTGAAAGTGTCAATCCCAGAAACACCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * *
6816 GGTAATTTTTCAATATAACTGGTATAATTAAACCAGTTTTATGAGAGAATATGTCTACATAATGT
66 GGTAATTTTTCAATATAACTGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACA-AATGT
* * * *
6881 ATCGACACTTCTAGAATTTGTATCGATACTGTTTT-TCCAGAAGGAATGCCCAAAAGGGTGCACG
130 ATCGACACTT-TTGAATTTGTGTCGATACT-TTTTGTCCAGAAGGAATGCCCAAAAGGATGAACG
*
6945 CAAAAA
193 CATAAA
*
6951 GTGTCGATACATTTATAAACAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAA-AAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAAT
* * * *
7016 AGGTAATTTTTCAATGTAA-TCGGTATACATATACTGGTTTTATGAGAGAATAGGTGTACAATAT
65 AGGTAATTTTTCAATATAACT-GGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAA-AT
* * * * *
7080 GTATCGACACTTTTATAATTTGTGTCGATACTTTTGGTCCAGAAAGAATGCCCAAAAAGGGTGCA
128 GTATCGACACTTTT-GAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCC-AAAAGGATGAA
7145 C-CACT-AA
191 CGCA-TAAA
* * * *
7152 GTGTCGATACATTAATAAGAAGTGTCGATCCCAGAAATATCGAAAACCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* ** *
7217 GGTAATTTTTCAATGTAACTGGTATACTTATACCGGTTTTATGAGAGAATAGGTGTACAATATGT
66 GGTAATTTTTCAATATAACTGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAA-ATGT
* * * *
7282 ATCAACACTTGTGTAATTTGTGTCGATACTTTTGGTCCAGAAGGAATGCCCAAAAAGGGT-ACAC
130 ATCGACACTTTTG-AATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCC-AAAAGGATGA-AC
7346 -CACT-AA
192 GCA-TAAA
* * *
7352 GTGTCGATACATTTATACAAAGTGTCGATCCTAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
*
7417 GGTAATTTTGT-AATATAACTGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATG
66 GGTAATTTT-TCAATATAACTGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACA-AATG
* * * ** *
7481 TATCGACACTTTTTTATTTTGTGTCGATACGTTTTGTCCAGATTGAATGCCCAAAATGATGAACG
129 TATCGACAC-TTTTGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGATGAACG
7546 CATAAA
193 CATAAA
* * * * *
7552 GTGTCGATATATTTATAAAAATTGTCGATACCAGAAACATCAAAACCCATAAATATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * * *
7617 GGTAAATTTACAATATAACCGGTATAACTATACCGGTTTTATGAGAGAATAGGTCTACAACATGT
66 GGTAATTTTTCAATATAACTGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAA-ATGT
* * * * * * * *
7682 ATCGAAACTTGTGGATTTGGTATCGATACTTTTTGTCCAGAAGGAATG-CCAAAGGGTTGCATGC
130 ATCGACACTTTTGAATTT-GTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGATGAACGC
7746 ATAAA
194 ATAAA
* * *
7751 GTGTCGATAC-TCTTTTAAAAAGTGTCGATCCCAGGAACATCGAAACCGATAATTATAATGTAAT
1 GTGTCGATACAT-TTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAAT
* * * * *
7815 AGGTAAATTTTAAATGTAACTTGTATAAATATACCGGTTTTATGAGAAAATAGGTC
65 AGGTAATTTTTCAATATAACTGGTATAAATATACCGGTTTTATGAGAGAATAGGTC
7871 ATCATAAAGT
Statistics
Matches: 972, Mismatches: 125, Indels: 47
0.85 0.11 0.04
Matches are distributed among these distances:
198 1 0.00
199 136 0.14
200 653 0.67
201 170 0.17
202 12 0.01
ACGTcount: A:0.36, C:0.15, G:0.17, T:0.32
Consensus pattern (198 bp):
GTGTCGATACATTTATAAAAAGTGTCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTTCAATATAACTGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACAAATGTA
TCGACACTTTTGAATTTGTGTCGATACTTTTTGTCCAGAAGGAATGCCCAAAAGGATGAACGCAT
AAA
Found at i:10417 original size:11 final size:11
Alignment explanation
Indices: 10401--10441 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
10391 TGTTGTGGGT
10401 ACATTATTTGA
1 ACATTATTTGA
10412 ACATTATTATGTA
1 ACATTATT-TG-A
10425 TACATTATTTGA
1 -ACATTATTTGA
10437 ACATT
1 ACATT
10442 GTTATGTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 13 0.48
12 3 0.11
13 3 0.11
14 8 0.30
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (11 bp):
ACATTATTTGA
Found at i:10434 original size:25 final size:25
Alignment explanation
Indices: 10400--10451 Score: 95
Period size: 25 Copynumber: 2.1 Consensus size: 25
10390 TTGTTGTGGG
10400 TACATTATTTGAACATTATTATGTA
1 TACATTATTTGAACATTATTATGTA
*
10425 TACATTATTTGAACATTGTTATGTA
1 TACATTATTTGAACATTATTATGTA
10450 TA
1 TA
10452 AATTTCTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (25 bp):
TACATTATTTGAACATTATTATGTA
Found at i:11093 original size:201 final size:199
Alignment explanation
Indices: 10749--11839 Score: 1203
Period size: 200 Copynumber: 5.5 Consensus size: 199
10739 TAAAGTTTCC
* ** * *
10749 CATAAAGTGTCGATACAGTTTT-AAAAGTATCGATATCAGAAACATCGAAATCC-ATAAATATAA
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAA-CCGATAATTATAA
* * * **
10812 TGTAAAAGGTAAATTTACAATGTAACCGGTATAACTA-AACCGATTTTATAAGAGAATAGGTCTA
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATAACAG-TTTTATGTGAGAATAGGTCTA
* * * * * * *
10876 CAAAATTTATCGACACTTCTGGAATTTGTATCGATACTGTTTGTCCAGAAGGAATGCCAATAAGG
129 CATAATATATCGACACTT-TAGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAA-AAGG
* *
10941 GGTGCACT
192 GGTGAACG
* * * *
10949 CATAAAGTGTCGAAACATTTTTAAAACGTATCGATCCAAAAAACATCGAAACCTATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* ** * * *
11014 GTAATAGGTAATTTTTTAATATAATCGGTATAAATATAACAGTTTTATGTGAGAATAGGTCTATA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATAACAGTTTTATGTGAGAATAGGTCTACA
* ** * ** * *
11079 TAATATGTCGACACTTTTTAATGTTATGTCGATACTTTTTGTATAGAATGAATTCCCAAAA-GGG
131 TAATATATCGACACTTTAGAAT-TTGTGTCGATACTTTTTGTCCAAAATGAA-TGCCAAAAGGGG
11143 TGAACG
194 TGAACG
* *
11149 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAC
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * * *
11214 GTAATAGGTAAATTTACAATGTAACCGGTATAAATA-AACCAATTTTATGTTAAAATATGT-GAG
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATAA-CAGTTTTATGTGAGAATAGGTCTA-
* **
11277 CATAATGTATAAACACGTTTTAG-ATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGG
129 CATAATATATCGACAC--TTTAGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGG
* *
11341 GTTGTACG
192 GGTGAACG
* * * *
11349 CATAAAGTGTTGATACATGTTTTAAAACGTATCGATCCCAAAAACATCAAAACCAATAATTATAA
1 CATAAAGTGTCGATACAT-TTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
* * * * * * * * * *
11414 TATAATAGATAATTTTATAATATAACTGGTATATATATACCGGTTTTATGTGAGAATAGGTCTAT
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATAACAGTTTTATGTGAGAATAGGTCTAC
* ** * ** * *
11479 ATAATATGTCGACACTTTTTAATGTGTGTCGATACTTTTTGAACATAATGAATACCCAAAA-GGG
130 ATAATATATCGACACTTTAGAATTTGTGTCGATACTTTTTGTCCAAAATGAAT-GCCAAAAGGGG
11543 TGAACG
194 TGAACG
*
11549 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * * **
11614 GTAATAGGTAAATTTACAATGTAACCAGTATAAATAT-ACCGATTTTATGTTAAAATAGGTGAAC
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATAACAG-TTTTATGTGAGAATAGGTCTAC
*
11678 ATAATGTATCGACACGTTTTAG-ATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGG
130 ATAATATATCGACAC--TTTAGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGG
* *
11742 TTGCACG
193 GTGAACG
* * * *
11749 TATAAAGTGTCAATACATGTTTTAAAAAGTATCAATCCAAAAAACATCGAAACCGATAATTATAA
1 CATAAAGTGTCGATACAT-TTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
11814 TGTAATAGGTAAATTTACAATGTAAC
65 TGTAATAGGTAAATTTACAATGTAAC
11840 TGTTTTATAA
Statistics
Matches: 738, Mismatches: 133, Indels: 39
0.81 0.15 0.04
Matches are distributed among these distances:
198 2 0.00
199 121 0.16
200 303 0.41
201 298 0.40
202 14 0.02
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (199 bp):
CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATATAACAGTTTTATGTGAGAATAGGTCTACA
TAATATATCGACACTTTAGAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGGTG
AACG
Found at i:11220 original size:200 final size:198
Alignment explanation
Indices: 10749--11839 Score: 1249
Period size: 201 Copynumber: 5.5 Consensus size: 198
10739 TAAAGTTTCC
* ** * *
10749 CATAAAGTGTCGATACAGTTTT-AAAAGTATCGATATCAGAAACATCGAAATCC-ATAAATATAA
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAA-CCGATAATTATAA
* * * **
10812 TGTAAAAGGTAAATTTACAATGTAACCGGTATAACTA-AACCGATTTTATAAGAGAATAGGTCTA
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATAACAG-TTTTATGTGAGAATAGGTCTA
* * ** * * * *
10876 CAAAATTTATCGACACTTCTGGAATTTGTATCGATACTGTTTGTCCAGAAGGAATGCCAATAAGG
129 CATAATATATCGACACTT-TTTAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAA-AA-G
* *
10941 GGTGCACT
191 GGTGAACG
* * * *
10949 CATAAAGTGTCGAAACATTTTTAAAACGTATCGATCCAAAAAACATCGAAACCTATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* ** * * *
11014 GTAATAGGTAATTTTTTAATATAATCGGTATAAATATAACAGTTTTATGTGAGAATAGGTCTATA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATAACAGTTTTATGTGAGAATAGGTCTACA
* * ** * *
11079 TAATATGTCGACACTTTTTAATGTTATGTCGATACTTTTTGTATAGAATGAATTCCCAAAAGGGT
131 TAATATATCGACACTTTTTAAT-TTGTGTCGATACTTTTTGTCCAAAATGAA-TGCCAAAAGGGT
11144 GAACG
194 GAACG
* *
11149 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAC
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * * *
11214 GTAATAGGTAAATTTACAATGTAACCGGTATAAATA-AACCAATTTTATGTTAAAATATGT-GAG
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATAA-CAGTTTTATGTGAGAATAGGTCTA-
* ** *
11277 CATAATGTATAAACACGTTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGG
129 CATAATATATCGACACTTTTTA-ATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGG
*
11342 TTGTACG
193 -TGAACG
* * * *
11349 CATAAAGTGTTGATACATGTTTTAAAACGTATCGATCCCAAAAACATCAAAACCAATAATTATAA
1 CATAAAGTGTCGATACAT-TTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
* * * * * * * * * *
11414 TATAATAGATAATTTTATAATATAACTGGTATATATATACCGGTTTTATGTGAGAATAGGTCTAT
65 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATATAACAGTTTTATGTGAGAATAGGTCTAC
* * ** * *
11479 ATAATATGTCGACACTTTTTAATGTGTGTCGATACTTTTTGAACATAATGAATACCCAAAAGGGT
130 ATAATATATCGACACTTTTTAATTTGTGTCGATACTTTTTGTCCAAAATGAAT-GCCAAAAGGGT
11544 GAACG
194 GAACG
*
11549 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* * * * **
11614 GTAATAGGTAAATTTACAATGTAACCAGTATAAATAT-ACCGATTTTATGTTAAAATAGGTGAAC
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATATAACAG-TTTTATGTGAGAATAGGTCTAC
* *
11678 ATAATGTATCGACACGTTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGT
130 ATAATATATCGACACTTTTTA-ATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGG-
*
11743 TGCACG
193 TGAACG
* * * *
11749 TATAAAGTGTCAATACATGTTTTAAAAAGTATCAATCCAAAAAACATCGAAACCGATAATTATAA
1 CATAAAGTGTCGATACAT-TTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
11814 TGTAATAGGTAAATTTACAATGTAAC
65 TGTAATAGGTAAATTTACAATGTAAC
11840 TGTTTTATAA
Statistics
Matches: 747, Mismatches: 127, Indels: 33
0.82 0.14 0.04
Matches are distributed among these distances:
198 2 0.00
199 129 0.17
200 302 0.40
201 303 0.41
202 11 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (198 bp):
CATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATATAACAGTTTTATGTGAGAATAGGTCTACA
TAATATATCGACACTTTTTAATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTGA
ACG
Found at i:11647 original size:400 final size:400
Alignment explanation
Indices: 10749--11841 Score: 1588
Period size: 400 Copynumber: 2.7 Consensus size: 400
10739 TAAAGTTTCC
** * *
10749 CATAAAGTGTCGATACAGTTT-T-AAAAGTATCGATATCAGAAACATCGAAATCC-ATAAATATA
1 CATAAAGTGTCGATACA-TTTATAAAAAGTATCGATCCCAAAAACATCGAAA-CCGATAATTATA
* * *** * *
10811 ATGTAAAAGGTAAATTTACAATGTAACCGGTATAACTAAACCGATTTTATAAGAGAATAGGTCTA
64 ATGTAATAGGTAAATTTACAATGTAACCGGTATAAATAAACCGATTTTATGTTAAAATAGGT-GA
* * * * * * * *
10876 CAAAATTTATCGACAC-TTCTGGAATTTGTATCGATACTGTTTGTCCAGAAGGAATGCCAATAAG
128 CATAATGTATCGACACGTTTTAG-ATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAA-AAG
* * * *
10940 GGGTGCACTCATAAAGTGTCGAAACAT-TTTTAAAACGTATCGATCCAAAAAACATCGAAACCTA
191 GGTTGCACGCATAAAGTGTCGATACATGTTTTAAAACGTATCGATCCAAAAAACATCGAAACCAA
*
11004 TAATTATAATGTAATAGGTAATTTTTTAATATAA-TCGGTATAAATATAACAGTTTTATGTGAGA
256 TAATTATAATGTAATAGGTAATTTTATAATATAACT-GGTATAAATATAACAGTTTTATGTGAGA
* * *
11068 ATAGGTCTATATAATATGTCGACACTTTTTAATGTTATGTCGATACTTTTTGTATAGAATGAATT
320 ATAGGTCTATATAATATGTCGACACTTTTTAATGTTATGTCGATACTTTTTGAACAGAATGAATA
11133 CCCAAAAGGGTGAACG
385 CCCAAAAGGGTGAACG
*
11149 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAC
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* *
11214 GTAATAGGTAAATTTACAATGTAACCGGTATAAATAAACCAATTTTATGTTAAAATATGTGAGCA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATAAACCGATTTTATGTTAAAATAGGTGA-CA
**
11279 TAATGTATAAACACGTTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTT
130 TAATGTATCGACACGTTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTT
* * * *
11344 GTACGCATAAAGTGTTGATACATGTTTTAAAACGTATCGATCCCAAAAACATCAAAACCAATAAT
195 GCACGCATAAAGTGTCGATACATGTTTTAAAACGTATCGATCCAAAAAACATCGAAACCAATAAT
* * * * *
11409 TATAATATAATAGATAATTTTATAATATAACTGGTATATATATACCGGTTTTATGTGAGAATAGG
260 TATAATGTAATAGGTAATTTTATAATATAACTGGTATAAATATAACAGTTTTATGTGAGAATAGG
* *
11474 TCTATATAATATGTCGACACTTTTTAATG-TGTGTCGATACTTTTTGAACATAATGAATACCCAA
325 TCTATATAATATGTCGACACTTTTTAATGTTATGTCGATACTTTTTGAACAGAATGAATACCCAA
11538 AAGGGTGAACG
390 AAGGGTGAACG
11549 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
1 CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
* *
11614 GTAATAGGTAAATTTACAATGTAACCAGTATAAATATACCGATTTTATGTTAAAATAGGTGAACA
66 GTAATAGGTAAATTTACAATGTAACCGGTATAAATAAACCGATTTTATGTTAAAATAGGTG-ACA
11679 TAATGTATCGACACGTTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTT
130 TAATGTATCGACACGTTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTT
* * * * *
11744 GCACGTATAAAGTGTCAATACATGTTTTAAAAAGTATCAATCCAAAAAACATCGAAACCGATAAT
195 GCACGCATAAAGTGTCGATACATGTTTTAAAACGTATCGATCCAAAAAACATCGAAACCAATAAT
* * *
11809 TATAATGTAATAGGTAAATTTACAATGTAACTG
260 TATAATGTAATAGGTAATTTTATAATATAACTG
11842 TTTTATAAGA
Statistics
Matches: 621, Mismatches: 64, Indels: 16
0.89 0.09 0.02
Matches are distributed among these distances:
399 3 0.00
400 357 0.57
401 256 0.41
402 5 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (400 bp):
CATAAAGTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTATAAATAAACCGATTTTATGTTAAAATAGGTGACAT
AATGTATCGACACGTTTTAGATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGGTTG
CACGCATAAAGTGTCGATACATGTTTTAAAACGTATCGATCCAAAAAACATCGAAACCAATAATT
ATAATGTAATAGGTAATTTTATAATATAACTGGTATAAATATAACAGTTTTATGTGAGAATAGGT
CTATATAATATGTCGACACTTTTTAATGTTATGTCGATACTTTTTGAACAGAATGAATACCCAAA
AGGGTGAACG
Found at i:16441 original size:201 final size:196
Alignment explanation
Indices: 15987--16902 Score: 992
Period size: 201 Copynumber: 4.6 Consensus size: 196
15977 TAAATGTGTA
* * *
15987 TCGATACATTTTCTAAAAGTATCGACCCAAAAAACATCGAAACCAATAATTATAATGCAATAGGT
1 TCGATACATTTT-TAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGT
* * *
16052 AAATTAACAATGTAACTGGTATAAATATACCGGTTAATTA-G-AAAATAGGTCAACATAATGTAT
65 AAATTTACAATGTAACCGGTATAAATATACCGATT--TTATGAAAAATAGGTC-ACATAATGTAT
* * * * * *
16115 CGACACTTGTGTAATTTGTGTCGATACTTATTGTCCAGAATAAATGCCCAAACGAGGTGCACGCA
127 CGACACTTAT-TAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGGA-TTGCACGCA
16180 TAAAGTG
190 TAAAGTG
* * * *
16187 TTGATACAATTATTAAAAGTATTGATCCCAATAAA-ATCGAAACCGATAATTATAATGTAATAGG
1 TCGATAC-ATTTTTAAAAGTATCGAT-CCAAAAAACATCGAAACCGATAATTATAATGTAATAGG
* *
16251 TAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGTTAAAATAGGTGAGCATAATGTAT
64 TAAATTTACAATGTAACCGGTATAAATATACCGATTTTATG-AAAAATAGGTCA-CATAATGTAT
* * *
16316 TGACACGTT-TTATATTTGTGTCGATACTTTTTGTCCAAAATGAATGCCAAAAGGATTGTACGCA
127 CGACAC-TTATTA-ATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGGATTGCACGCA
16380 TAAAGTG
190 TAAAGTG
* * ** * *
16387 TTGATACATGTTTTAAAAAGTATCGATCCAAAAAATATCGAAACAAAAAATTATAATGTAATATG
1 TCGATACAT-TTTT-AAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGG
* *
16452 TAAATTTACAATGTAACCGGTATAAATATACTGATTTTATGAGAAAATAGGTCATCATAAAGTAT
64 TAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGA-AAAATAGGTCA-CATAATGTAT
* * * * * *
16517 CGAAACTTATTAAATTTGTGTTGATACATTTTGTCCATAATGAATGCCAAACGGGTT-CACGCAT
127 CGACACTTATT-AATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGGATTGCACGCAT
16581 AAAGTG
191 AAAGTG
* * * * *
16587 TCGATACATTTATTAAAACTATCGATCCCAAAAATATCGAAACCGATAATTACAATGTGATAGGT
1 TCGATACATTT-TTAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGT
* * * * * * *
16652 AAATTTACAATGTATCAGATAAAAATATATCGGTTTTATGAAAAAATAGGTCTAAATAATGTATC
65 AAATTTACAATGTAACCGGTATAAATATACCGATTTTATG-AAAAATAGGTC-ACATAATGTATC
* * * *
16717 GACACTCT-TTAAGTTTATGTCGATACTTGTT-TCCAGAATGAATGTCCAACGAGG--TGCATGC
128 GACACT-TATTAA-TTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAA-AAGGATTGCACGC
16778 ATAAAGTG
189 ATAAAGTG
* *
16786 TCGATACA--TTTAAAGTTGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAAG
1 TCGATACATTTTTAAA--AGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGG
* * *
16849 TAAATTTACAATGTTACCGGTATAAATATATCGA-TTTACTTATAAAATAGGTCA
64 TAAATTTACAATGTAACCGGTATAAATATACCGATTTTA-TGA-AAAATAGGTCA
16903 ATATAAGCGT
Statistics
Matches: 610, Mismatches: 80, Indels: 55
0.82 0.11 0.07
Matches are distributed among these distances:
196 5 0.01
197 7 0.01
198 97 0.16
199 145 0.24
200 140 0.23
201 213 0.35
202 3 0.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (196 bp):
TCGATACATTTTTAAAAGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAGGTA
AATTTACAATGTAACCGGTATAAATATACCGATTTTATGAAAAATAGGTCACATAATGTATCGAC
ACTTATTAATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAAAGGATTGCACGCATAAAGT
G
Found at i:16674 original size:20 final size:20
Alignment explanation
Indices: 16636--16674 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
16626 AAACCGATAA
*
16636 TTACAATGTGATAGGTAAAT
1 TTACAATGTGATAGATAAAT
16656 TTACAATGT-ATCAGATAAA
1 TTACAATGTGAT-AGATAAA
16675 AATATATCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (20 bp):
TTACAATGTGATAGATAAAT
Found at i:16740 original size:400 final size:399
Alignment explanation
Indices: 15987--16878 Score: 1135
Period size: 400 Copynumber: 2.2 Consensus size: 399
15977 TAAATGTGTA
* * *
15987 TCGATACATTTTCT-AAAAGTATCGACCCAAAAAACATCGAAACCAATAATTATAATGCAATAGG
1 TCGATACATTTT-TAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATAAG
* * * *
16051 TAAATTAACAATGTAACTGGTATAAATATACCGGTTAATTAGAAAATAGGTCAACATAATGTATC
65 TAAATTTACAATGTAACCGGTATAAATATACCGGTTAATGAGAAAATAGGTCAACATAAAGTATC
* *
16116 GACACTTGTGTAATTTGTGTCGATACTTATTGTCCAGAATAAATGCCCAAACGAGGTGCACGCAT
130 GAAACTTATGTAATTTGTGTCGATACTTATTGTCCAGAATAAATGCCCAAACGAGGTGCACGCAT
* * * *
16181 AAAGTGTTGATACAATTATTAAAAGTATTGATCCCAATAAAATCGAAACCGATAATTATAATGTA
195 AAAGTGTCGATACAATTATTAAAACTATCGATCCCAATAAAATCGAAACCGATAATTACAATGTA
* * * ** *
16246 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCGATTTTATGTTAAAATAGGTGAGCATAA
260 ATAGGTAAATTTACAATGTAACAGATAAAAATATACCGATTTTATGAAAAAATAGGTGAGAATAA
* * *
16311 TGTATTGACACGTTTTATATTTGTGTCGATACTTTTTGTCCAAAATGAATG-CCAA-AAGGATTG
325 TGTATCGACACGTTTTATATTTATGTCGATACTTGTT-TCCAAAATGAATGTCCAACAAGG--TG
*
16374 TACGCATAAAGTG
387 CACGCATAAAGTG
* * * * *
16387 TTGATACATGTTTTAAAAAGTATCGATCCAAAAAATATCGAAACAAAAAATTATAATGTAATATG
1 TCGATACAT-TTTTAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATAAG
* * * *
16452 TAAATTTACAATGTAACCGGTATAAATATACTGATTTTATGAGAAAATAGGTCATCATAAAGTAT
65 TAAATTTACAATGTAACCGGTATAAATATACCG-GTTAATGAGAAAATAGGTCAACATAAAGTAT
* * * *
16517 CGAAACTTAT-TAAATTTGTGTTGATACATT-TTGTCCATAATGAATG-CCAAACG-GGTTCACG
129 CGAAACTTATGT-AATTTGTGTCGATAC-TTATTGTCCAGAATAAATGCCCAAACGAGGTGCACG
*
16578 CATAAAGTGTCGATACATTTATTAAAACTATCGATCCCAA-AAATATCGAAACCGATAATTACAA
192 CATAAAGTGTCGATACAATTATTAAAACTATCGATCCCAATAAA-ATCGAAACCGATAATTACAA
* * * * *
16642 TGTGATAGGTAAATTTACAATGTATCAGATAAAAATATATCGGTTTTATGAAAAAATAGGTCTA-
256 TGTAATAGGTAAATTTACAATGTAACAGATAAAAATATACCGATTTTATGAAAAAATAGGT-GAG
* *
16706 AATAATGTATCGACAC-TCTTTA-AGTTTATGTCGATACTTGTTTCCAGAATGAATGTCCAACGA
320 AATAATGTATCGACACGT-TTTATA-TTTATGTCGATACTTGTTTCCAAAATGAATGTCCAACAA
*
16769 GGTGCATGCATAAAGTG
383 GGTGCACGCATAAAGTG
** *
16786 TCGATACA--TTTAAAGTTGTATCGATCCAAAAAACATCGAAACCGATAATTATAATGTAATAAG
1 TCGATACATTTTTAAA-AAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATAAG
*
16849 TAAATTTACAATGTTACCGGTATAAATATA
65 TAAATTTACAATGTAACCGGTATAAATATA
16879 TCGATTTACT
Statistics
Matches: 427, Mismatches: 53, Indels: 27
0.84 0.10 0.05
Matches are distributed among these distances:
396 6 0.01
397 70 0.16
399 37 0.09
400 161 0.38
401 89 0.21
402 62 0.15
403 2 0.00
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (399 bp):
TCGATACATTTTTAAAAAGTATCGATCCAAAAAACATCGAAACCAATAATTATAATGTAATAAGT
AAATTTACAATGTAACCGGTATAAATATACCGGTTAATGAGAAAATAGGTCAACATAAAGTATCG
AAACTTATGTAATTTGTGTCGATACTTATTGTCCAGAATAAATGCCCAAACGAGGTGCACGCATA
AAGTGTCGATACAATTATTAAAACTATCGATCCCAATAAAATCGAAACCGATAATTACAATGTAA
TAGGTAAATTTACAATGTAACAGATAAAAATATACCGATTTTATGAAAAAATAGGTGAGAATAAT
GTATCGACACGTTTTATATTTATGTCGATACTTGTTTCCAAAATGAATGTCCAACAAGGTGCACG
CATAAAGTG
Found at i:17003 original size:64 final size:64
Alignment explanation
Indices: 16924--17077 Score: 229
Period size: 64 Copynumber: 2.4 Consensus size: 64
16914 ACTTATTACA
* *
16924 TATATAAGCGATACCTAATATATTATTATACTTAATAATATTT-TCGGTTAAATGTCTATTTTAT
1 TATATAAGCGCTACCTAATATATTATTATACTTAATAATATTTCT-GATTAAATGTCTATTTTAT
* * *
16988 TATATAAGCGCTACCTAATATGTTATTGTACTTGATAATATTTCTGATTAAATGTCTATTTTAT
1 TATATAAGCGCTACCTAATATATTATTATACTTAATAATATTTCTGATTAAATGTCTATTTTAT
* *
17052 TATATAAGCGCTACCTATTACATTAT
1 TATATAAGCGCTACCTAATATATTAT
17078 ATAAACGTTA
Statistics
Matches: 81, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
64 80 0.99
65 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (64 bp):
TATATAAGCGCTACCTAATATATTATTATACTTAATAATATTTCTGATTAAATGTCTATTTTAT
Found at i:17069 original size:23 final size:23
Alignment explanation
Indices: 17043--17100 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
17033 GATTAAATGT
* *
17043 CTATTTTATTATATAAGCGCTAC
1 CTATTATATTATATAAACGCTAC
* *
17066 CTATTACATTATATAAACGTTAC
1 CTATTATATTATATAAACGCTAC
*
17089 CTAATATATTAT
1 CTATTATATTAT
17101 TGTACTTGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (23 bp):
CTATTATATTATATAAACGCTAC
Found at i:19775 original size:12 final size:11
Alignment explanation
Indices: 19756--19799 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
19746 AGTTGATATA
19756 ATTTTATTTAT
1 ATTTTATTTAT
19767 ATTTATATTTAT
1 ATTT-TATTTAT
*
19779 ATTTTTTTTATT
1 ATTTTATTTA-T
19791 ATTATTATT
1 ATT-TTATT
19800 ATTTTGTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 9 0.32
12 15 0.54
13 4 0.14
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATTTTATTTAT
Found at i:24804 original size:22 final size:22
Alignment explanation
Indices: 24778--24832 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
24768 TATACCTTGT
24778 TTTGCCTGTTTTACTTATATGG
1 TTTGCCTGTTTTACTTATATGG
24800 TTTGCCTGTTTTACTTATATGG
1 TTTGCCTGTTTTACTTATATGG
* *
24822 TTGGGCTGTTT
1 TTTGCCTGTTT
24833 CTTTCTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.11, C:0.13, G:0.22, T:0.55
Consensus pattern (22 bp):
TTTGCCTGTTTTACTTATATGG
Found at i:25457 original size:12 final size:12
Alignment explanation
Indices: 25442--25487 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
25432 CGGTTTTTTT
*
25442 ACCGGATAAAAA
1 ACCGGTTAAAAA
25454 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
25469 ACCGGTTAAAAA
1 ACCGGTTAAAAA
25481 ACCGGTT
1 ACCGGTT
25488 TTTATCCGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:25469 original size:15 final size:13
Alignment explanation
Indices: 25448--25488 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
25438 TTTTACCGGA
25448 TAAAAAACCGGTT
1 TAAAAAACCGGTT
25461 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
25475 TAAAAAACCGGTT
1 TAAAAAACCGGTT
25488 T
1 T
25489 TTATCCGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Found at i:27800 original size:21 final size:21
Alignment explanation
Indices: 27776--27815 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
27766 TTTATTTTAT
27776 AACTTTATTTCAATTATCGTA
1 AACTTTATTTCAATTATCGTA
*
27797 AACTTTGTTTCAATTATCG
1 AACTTTATTTCAATTATCG
27816 AACTTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.47
Consensus pattern (21 bp):
AACTTTATTTCAATTATCGTA
Found at i:27863 original size:33 final size:33
Alignment explanation
Indices: 27810--27908 Score: 164
Period size: 33 Copynumber: 3.0 Consensus size: 33
27800 TTTGTTTCAA
27810 TTATCGAACTT-GAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
27842 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* * *
27875 TTATCAAACTTGGAAGTATTTAAGTATTTCAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
27908 T
1 T
27909 ATGTTGAGTT
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
32 11 0.17
33 52 0.83
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.45
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:27937 original size:13 final size:13
Alignment explanation
Indices: 27894--27948 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
27884 TTGGAAGTAT
27894 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
27907 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
27921 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
27934 TTAAGTATTTGAA
1 TTAAGTATTTCAA
27947 TT
1 TT
27949 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:28330 original size:15 final size:15
Alignment explanation
Indices: 28278--28330 Score: 61
Period size: 15 Copynumber: 3.4 Consensus size: 15
28268 ATCTGGAATA
28278 TTAAAATCGGTTTTT
1 TTAAAATCGGTTTTT
* *
28293 TTATAACCGGTTTTT
1 TTAAAATCGGTTTTT
*
28308 TAAAAAAATCGGTTTTT
1 T--TAAAATCGGTTTTT
28325 TTAAAA
1 TTAAAA
28331 CCGAAACCGG
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
15 18 0.60
17 12 0.40
ACGTcount: A:0.34, C:0.08, G:0.11, T:0.47
Consensus pattern (15 bp):
TTAAAATCGGTTTTT
Found at i:28450 original size:15 final size:17
Alignment explanation
Indices: 28424--28455 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
28414 TTCTATGGGA
28424 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
28440 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
28456 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:30201 original size:20 final size:21
Alignment explanation
Indices: 30176--30268 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
30166 TTTTCCCAAT
*
30176 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
30196 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
30217 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
30237 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
30258 TCGCAATGCGA
1 TCGCAATGCGA
30269 TACTTACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:30221 original size:41 final size:41
Alignment explanation
Indices: 30176--30268 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
30166 TTTTCCCAAT
30176 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
30217 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
30258 TCGCAATGCGA
1 TCGCAATGCGA
30269 TACTTACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:30281 original size:41 final size:41
Alignment explanation
Indices: 30195--30329 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
30185 GAATAAGTAA
** *
30195 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATAAGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTTACT
30236 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
* * ** * * *
30277 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTGACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTTACT
*
30318 TTCGCAACGCGA
1 ATCGCAACGCGA
30330 TTCTGACTTT
Statistics
Matches: 80, Mismatches: 12, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
40 5 0.06
41 73 0.91
42 2 0.03
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTTACT
Found at i:30347 original size:20 final size:20
Alignment explanation
Indices: 30299--30351 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
30289 TAATACAAAA
* *
30299 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
30319 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
30339 TCGCAACGCGATT
1 TCGCAACGCGATT
30352 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:30928 original size:19 final size:19
Alignment explanation
Indices: 30904--30948 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
30894 GCAAAGAGAT
*
30904 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
30923 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
30942 AATCGCA
1 AATCGCA
30949 TTGCGATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:30966 original size:19 final size:19
Alignment explanation
Indices: 30944--31075 Score: 130
Period size: 19 Copynumber: 7.1 Consensus size: 19
30934 GAAACCAAAA
* *
30944 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTGTCATT
*
30963 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTGTCATT
30982 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTGTCATT
* *
30998 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTGTCATT
*
31015 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTGTCATT
*
31034 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTGTCATT
* *
31054 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTGTCATT
31074 TC
1 TC
31076 AACCAAAAGA
Statistics
Matches: 97, Mismatches: 9, Indels: 14
0.81 0.08 0.12
Matches are distributed among these distances:
14 10 0.10
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 50 0.52
20 32 0.33
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.22, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTGTCATT
Found at i:33134 original size:42 final size:42
Alignment explanation
Indices: 33074--33196 Score: 122
Period size: 42 Copynumber: 2.9 Consensus size: 42
33064 GCCCGACTCG
* * *
33074 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * *
33116 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
33158 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
33197 CCCGATTCAC
Statistics
Matches: 66, Mismatches: 14, Indels: 2
0.80 0.17 0.02
Matches are distributed among these distances:
42 62 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.23
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:33154 original size:21 final size:21
Alignment explanation
Indices: 33130--33196 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
33120 TCATTCCTCG
33130 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
33151 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
33172 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
33193 AGAG
1 AGAG
33197 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:34575 original size:14 final size:14
Alignment explanation
Indices: 34556--34591 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
34546 ATTGTTTAAT
34556 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
34570 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
34584 TGATTTGT
1 TGATTTGT
34592 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:34792 original size:19 final size:19
Alignment explanation
Indices: 34770--34920 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
34760 CGAAATTAAA
34770 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
34789 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
34804 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
34822 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
34836 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
34855 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
34870 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
34888 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
34907 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
34921 GGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 28 0.29
16 6 0.06
17 6 0.06
19 45 0.47
20 10 0.11
ACGTcount: A:0.15, C:0.23, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:34816 original size:33 final size:32
Alignment explanation
Indices: 34774--34900 Score: 193
Period size: 33 Copynumber: 3.9 Consensus size: 32
34764 ATTAAATTCG
34774 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
**
34807 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
34840 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
34873 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
34901 AGTAATTTCC
Statistics
Matches: 86, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
31 3 0.03
33 80 0.93
35 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:34863 original size:66 final size:66
Alignment explanation
Indices: 34767--34899 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
34757 ACGCGAAATT
*
34767 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
34832 G
66 G
*
34833 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
34898 G
66 G
34899 A
1 A
34900 TAGTAATTTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:37207 original size:12 final size:12
Alignment explanation
Indices: 37190--37214 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
37180 TCTTCGGGGA
37190 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37202 CTTTTTCTTCTT
1 CTTTTTCTTCTT
37214 C
1 C
37215 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:37423 original size:24 final size:24
Alignment explanation
Indices: 37389--37442 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
37379 CTGAAACATC
* *
37389 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
37413 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
37437 ATCAAA
1 ATCAAA
37443 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:38536 original size:20 final size:20
Alignment explanation
Indices: 38511--38568 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
38501 ATTCATTTGA
*
38511 CTATCGCAACGCGAAAATTG
1 CTATCGCAACGCGAAAATGG
38531 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
38551 TTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
38569 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.38, C:0.22, G:0.21, T:0.19
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:38611 original size:14 final size:16
Alignment explanation
Indices: 38591--38664 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
38581 TGAAAATCGC
38591 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
38606 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
38623 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
38642 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
38658 -TTGCGAT
1 ATTGCGAT
38665 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:38628 original size:19 final size:19
Alignment explanation
Indices: 38587--38654 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
38577 GAAATGAAAA
38587 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
38603 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
38620 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
38639 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
38655 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:38630 original size:52 final size:52
Alignment explanation
Indices: 38568--38682 Score: 131
Period size: 52 Copynumber: 2.2 Consensus size: 52
38558 AACGAGAAAA
* ***
38568 TCGCAATGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATTTTCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
** ** **
38620 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCTCGTTGCGATAGCCATT
1 TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
*
38672 TCGCGTTGCGA
1 TCGCATTGCGA
38683 TAGTCTGTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (52 bp):
TCGCATTGCGAAATGAAAATCGCATTGCGATTTTCTCGTTGCGATAGCCATT
Found at i:40709 original size:20 final size:19
Alignment explanation
Indices: 40674--40729 Score: 85
Period size: 20 Copynumber: 2.9 Consensus size: 19
40664 AAAACTTAAA
40674 ATCGCAATGCGAAATGACT
1 ATCGCAATGCGAAATGACT
* *
40693 ATCGCAACGCGGAAATGGCT
1 ATCGCAATGC-GAAATGACT
40713 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
40730 AAATCACAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
19 15 0.47
20 17 0.53
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (19 bp):
ATCGCAATGCGAAATGACT
Found at i:40739 original size:19 final size:19
Alignment explanation
Indices: 40671--40740 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
40661 CACAAAACTT
40671 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
** *
40690 ACTATCGCAACGCGGAAATG
1 AAAATCGCAATGC-GAAATG
***
40710 GCTATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
40729 AAAATCACAATG
1 AAAATCGCAATG
40741 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.41, C:0.20, G:0.21, T:0.17
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:40779 original size:32 final size:33
Alignment explanation
Indices: 40713--40791 Score: 115
Period size: 32 Copynumber: 2.4 Consensus size: 33
40703 GGAAATGGCT
* * *
40713 ATCGCAATGCGAAATGAAAATCACAATGACAAA
1 ATCGCAACGCGAAATGAAAATCACAACGAAAAA
*
40746 ATCGCAACGCGAAATG-AAATCGCAACGAAAAA
1 ATCGCAACGCGAAATGAAAATCACAACGAAAAA
40778 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
40792 CACAAATCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
32 27 0.64
33 15 0.36
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCACAACGAAAAA
Found at i:40781 original size:14 final size:14
Alignment explanation
Indices: 40729--40786 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
40719 ATGCGAAATG
* * *
40729 AAAATCACAATGAC
1 AAAATCGCAACGAA
40743 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAA
40759 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
40775 AAAATCGCAACG
1 AAAATCGCAACG
40787 CGAAACACAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.52, C:0.22, G:0.16, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:40798 original size:19 final size:17
Alignment explanation
Indices: 40743--40802 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 17
40733 TCACAATGAC
40743 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
*
40760 TGAAATCGCAA--CG-AA
1 -AAAATCGCAACGCGAAA
40775 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
40792 CACAAATCGCA
1 -A-AAATCGCA
40803 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
14 9 0.26
15 2 0.06
16 4 0.11
17 2 0.06
18 10 0.29
19 8 0.23
ACGTcount: A:0.50, C:0.25, G:0.17, T:0.08
Consensus pattern (17 bp):
AAAATCGCAACGCGAAA
Found at i:40840 original size:14 final size:14
Alignment explanation
Indices: 40821--40877 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
40811 TTCATTTCGT
40821 GTTGCGATTTTTTC
1 GTTGCGATTTTTTC
40835 GTTGCGATTTCATTTC
1 GTTGCGATTT--TTTC
*
40851 GCATTGCGATTTTGTC
1 G--TTGCGATTTTTTC
40867 GTTGCGATTTT
1 GTTGCGATTTT
40878 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 20 0.53
16 9 0.24
18 9 0.24
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.51
Consensus pattern (14 bp):
GTTGCGATTTTTTC
Found at i:40884 original size:33 final size:33
Alignment explanation
Indices: 40803--40893 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
40793 ACAAATCGCA
** *
40803 TTGCGATTTTCATTTCGTGTTGCGATTTTTTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
40836 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
40868 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
40894 AGCCATTTCC
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 29 0.54
33 25 0.46
ACGTcount: A:0.12, C:0.18, G:0.21, T:0.49
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:40912 original size:20 final size:19
Alignment explanation
Indices: 40878--40932 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
40868 TTGCGATTTT
*
40878 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
40897 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
40917 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
40933 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:41434 original size:18 final size:18
Alignment explanation
Indices: 41408--41452 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
41398 GTCGATCAGA
*
41408 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
41426 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
41444 TGATGGCTC
1 TGATGGCTC
41453 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:43097 original size:22 final size:22
Alignment explanation
Indices: 43072--43115 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
43062 GATTTAGATA
43072 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
43094 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
43116 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:43368 original size:41 final size:41
Alignment explanation
Indices: 43323--43400 Score: 111
Period size: 41 Copynumber: 1.9 Consensus size: 41
43313 TGAAAGTCAG
* * *
43323 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
* *
43364 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
43401 CCCAATTCGC
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
41 32 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.40
Consensus pattern (41 bp):
TATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTTTAT
Found at i:43389 original size:20 final size:20
Alignment explanation
Indices: 43283--43397 Score: 79
Period size: 20 Copynumber: 5.7 Consensus size: 20
43273 CGCTTTGAAA
*
43283 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
43304 ATCGCGTTGTGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
43324 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
43344 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
43365 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
43385 ATCGCATTGCGAT
1 ATCGCATTGCGAT
43398 TTTCCCAATT
Statistics
Matches: 74, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
19 2 0.03
20 49 0.66
21 23 0.31
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.37
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:43416 original size:41 final size:41
Alignment explanation
Indices: 43323--43418 Score: 104
Period size: 41 Copynumber: 2.3 Consensus size: 41
43313 TGAAAGTCAG
* * * ** *
43323 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
* *
43364 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAA
43406 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
43419 TTACTTATTC
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 43 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAA
Found at i:71024 original size:2 final size:2
Alignment explanation
Indices: 71017--71053 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
71007 AAACATAGCC
71017 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
71054 GCTAAGCTGC
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
Done.