Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002269.1 Hibiscus syriacus cultivar Beakdansim tig00004614_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: 95239
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:515 original size:2 final size:2
Alignment explanation
Indices: 508--533 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
498 TATTCAAAAT
508 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
534 AGAATGCAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4732 original size:24 final size:23
Alignment explanation
Indices: 4699--4748 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
4689 AAAATATATC
*
4699 AAAAAGATAAAAAAAATGTGTCAT
1 AAAAACAT-AAAAAAATGTGTCAT
*
4723 AAAAACATAAGAAAATGTGTCAT
1 AAAAACATAAAAAAATGTGTCAT
4746 AAA
1 AAA
4749 TACAATGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.62, C:0.06, G:0.12, T:0.20
Consensus pattern (23 bp):
AAAAACATAAAAAAATGTGTCAT
Found at i:7593 original size:35 final size:35
Alignment explanation
Indices: 7544--7611 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
7534 TAGTCACATG
* * *
7544 TGCATGGATGCACTGCAGGGTACATTGATACACTA
1 TGCATGGATACACTGCAGAGTACATGGATACACTA
*
7579 TGCATGGATACACTGCAGAGTGCATGGATACAC
1 TGCATGGATACACTGCAGAGTACATGGATACAC
7612 GCAGGGTGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.29, C:0.21, G:0.26, T:0.24
Consensus pattern (35 bp):
TGCATGGATACACTGCAGAGTACATGGATACACTA
Found at i:7624 original size:19 final size:20
Alignment explanation
Indices: 7543--7631 Score: 82
Period size: 20 Copynumber: 4.8 Consensus size: 20
7533 GTAGTCACAT
* *
7543 GTGCATGGATGCACTGCAGG
1 GTGCATGGATACACTGCAGA
* *
7563 GTACATTGATACACT----A
1 GTGCATGGATACACTGCAGA
7579 -TGCATGGATACACTGCAGA
1 GTGCATGGATACACTGCAGA
*
7598 GTGCATGGATACAC-GCAGG
1 GTGCATGGATACACTGCAGA
*
7617 GTGTATGGATACACT
1 GTGCATGGATACACT
7632 TTGACACCCT
Statistics
Matches: 55, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
15 12 0.22
19 18 0.33
20 25 0.45
ACGTcount: A:0.28, C:0.19, G:0.29, T:0.24
Consensus pattern (20 bp):
GTGCATGGATACACTGCAGA
Found at i:7879 original size:22 final size:22
Alignment explanation
Indices: 7854--7895 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
7844 ATGTTTAATG
*
7854 AAAAAGATACCAATTGTTAACA
1 AAAAAGATACCAATTATTAACA
* *
7876 AAAAGGATATCAATTATTAA
1 AAAAAGATACCAATTATTAA
7896 AAATATACCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.55, C:0.10, G:0.10, T:0.26
Consensus pattern (22 bp):
AAAAAGATACCAATTATTAACA
Found at i:16031 original size:9 final size:8
Alignment explanation
Indices: 15959--16036 Score: 51
Period size: 7 Copynumber: 10.0 Consensus size: 8
15949 CTATATTTAC
15959 ATATTATT
1 ATATTATT
15967 ATATT-TT
1 ATATTATT
15974 A-ATTATT
1 ATATTATT
15981 -TATTA-T
1 ATATTATT
*
15987 AT-TTAAT
1 ATATTATT
*
15994 A-ATTAAT
1 ATATTATT
16001 ATTATTAGTT
1 A-TATTA-TT
16011 ATTATTATT
1 A-TATTATT
16020 ATATTCATT
1 ATATT-ATT
*
16029 ATAATATT
1 ATATTATT
16037 TTCATTATTT
Statistics
Matches: 59, Mismatches: 2, Indels: 18
0.75 0.03 0.23
Matches are distributed among these distances:
6 7 0.12
7 18 0.31
8 12 0.20
9 14 0.24
10 8 0.14
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.59
Consensus pattern (8 bp):
ATATTATT
Found at i:16079 original size:150 final size:148
Alignment explanation
Indices: 15911--16262 Score: 554
Period size: 150 Copynumber: 2.4 Consensus size: 148
15901 ATTTTAAATT
* *
15911 ATATTATAATTTTTTTTATAAAATATCTATTTTAATAACTATATTTACATATTATTATATTTTAA
1 ATATTATAATTTTTTTTATAAAATATCTATTTTAATTACTATATTTATATATTATTATATTTTAA
*
15976 TTATTTATTATATTTAATAATTAATATTATTAGTTATTATTATTATATTCATTATAATATTTTCA
66 TTATTTATTATATTTAATAATTAATATTATTATTTATTATTATTATATT-ATTATAATATTTTCA
16041 TTATTTCAAAATTTACAAA
130 TTATTTCAAAATTTACAAA
*
16060 ATATTTTAATTATTTTTTATAAAATATCTATTTTAATTACTATATTTATATATTATTATATTTTA
1 ATATTATAATT-TTTTTTATAAAATATCTATTTTAATTACTATATTTATATATTATTATATTTTA
16125 ATTATTTATTATATTTAAT-ATTAATATTATTATTTA-T-TTATT-TATTATAATATAAT-TTTT
65 ATTATTTATTATATTTAATAATTAATATTATTATTTATTATTATTATATTAT--TATAATATTTT
*
16185 CATTATTTCAAAATTTAAAAA
128 CATTATTTCAAAATTTACAAA
16206 ATGTATTATAATTATTTTTTAT-AAATATCTATTTTAATTACTATATTTATATATTAT
1 A--TATTATAATT-TTTTTTATAAAATATCTATTTTAATTACTATATTTATATATTAT
16263 ATTTAATATT
Statistics
Matches: 192, Mismatches: 6, Indels: 12
0.91 0.03 0.06
Matches are distributed among these distances:
145 2 0.01
146 29 0.15
147 46 0.24
148 19 0.10
149 26 0.14
150 70 0.36
ACGTcount: A:0.39, C:0.04, G:0.01, T:0.57
Consensus pattern (148 bp):
ATATTATAATTTTTTTTATAAAATATCTATTTTAATTACTATATTTATATATTATTATATTTTAA
TTATTTATTATATTTAATAATTAATATTATTATTTATTATTATTATATTATTATAATATTTTCAT
TATTTCAAAATTTACAAA
Found at i:16129 original size:21 final size:22
Alignment explanation
Indices: 16105--16157 Score: 62
Period size: 18 Copynumber: 2.6 Consensus size: 22
16095 ATTACTATAT
16105 TTATATATTATTATATTT--TA
1 TTATATATTATTATATTTAATA
*
16125 AT-TAT-TTATTATATTTAATA
1 TTATATATTATTATATTTAATA
16145 TTA-ATATTATTAT
1 TTATATATTATTAT
16158 TTATTTATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
18 11 0.41
19 3 0.11
20 6 0.22
21 7 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTATATATTATTATATTTAATA
Found at i:16135 original size:18 final size:18
Alignment explanation
Indices: 16112--16173 Score: 67
Period size: 18 Copynumber: 3.4 Consensus size: 18
16102 TATTTATATA
16112 TTATTATATTTTAATTAT
1 TTATTATATTTTAATTAT
16130 TTATTATA-TTTAA-TAT
1 TTATTATATTTTAATTAT
*
16146 TAATATTAT-TATTTATTTAT
1 T--TATTATAT-TTTAATTAT
16166 TTATTATA
1 TTATTATA
16174 ATATAATTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
16 4 0.11
17 5 0.14
18 20 0.54
19 4 0.11
20 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TTATTATATTTTAATTAT
Found at i:16163 original size:57 final size:57
Alignment explanation
Indices: 16059--16177 Score: 136
Period size: 57 Copynumber: 2.1 Consensus size: 57
16049 AAATTTACAA
*
16059 AATATTTTAATTATTTTTTATAAAATATCTATTTTAATTACTATATTTATATATTAT
1 AATATTTTAATTATTTTTTATAAAATATCTATATTAATTACTATATTTATATATTAT
* ** * *
16116 TATATTTTAATTATTTATTATATTTAATAT-TAATATT-ATTA-TTTATTTATTTATTAT
1 AATATTTTAATTATTT-TT-TATAAAATATCT-ATATTAATTACTATATTTATATATTAT
16173 AATAT
1 AATAT
16178 AATTTTTCAT
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
57 33 0.63
58 7 0.13
59 12 0.23
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.61
Consensus pattern (57 bp):
AATATTTTAATTATTTTTTATAAAATATCTATATTAATTACTATATTTATATATTAT
Found at i:16166 original size:36 final size:34
Alignment explanation
Indices: 16091--16173 Score: 96
Period size: 36 Copynumber: 2.4 Consensus size: 34
16081 AAATATCTAT
* * *
16091 TTTAATTACTATATTTATATATTATTATATTTTA
1 TTTATTTATTATATTTATATAATATTATATTTTA
*
16125 ATTATTTATTATATTTAATATTAATATTAT-TATTTA
1 TTTATTTATTATATTT-ATA-TAATATTATAT-TTTA
16161 TTTATTTATTATA
1 TTTATTTATTATA
16174 ATATAATTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
34 13 0.32
35 4 0.10
36 24 0.59
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (34 bp):
TTTATTTATTATATTTATATAATATTATATTTTA
Found at i:16263 original size:13 final size:13
Alignment explanation
Indices: 16247--16304 Score: 64
Period size: 13 Copynumber: 4.3 Consensus size: 13
16237 TTTTAATTAC
16247 TATATTTATATAT
1 TATATTTATATAT
16260 TATATTTA-ATAT
1 TATATTTATATAT
*
16272 TAATATTAATTATTAT
1 T-ATATTTA-TA-TAT
*
16288 TATATTTATTTAT
1 TATATTTATATAT
16301 TATA
1 TATA
16305 ATATAATTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
12 5 0.13
13 21 0.55
14 1 0.03
15 7 0.18
16 4 0.11
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATATTTATATAT
Found at i:16300 original size:16 final size:16
Alignment explanation
Indices: 16255--16308 Score: 56
Period size: 16 Copynumber: 3.3 Consensus size: 16
16245 ACTATATTTA
*
16255 TATATTATATTTAATAT
1 TATATT-TATTTATTAT
*
16272 TA-ATATTAATTATTAT
1 TATAT-TTATTTATTAT
16288 TATATTTATTTATTAT
1 TATATTTATTTATTAT
*
16304 AATAT
1 TATAT
16309 AATTTTTCAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 26 0.84
17 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATATTTATTTATTAT
Found at i:16316 original size:131 final size:125
Alignment explanation
Indices: 16126--16397 Score: 429
Period size: 131 Copynumber: 2.1 Consensus size: 125
16116 TATATTTTAA
*
16126 TTATTTATTATATTTAATATTAATATTATTATTTATTTATTTATTATAATATAATTTTTCATTAT
1 TTATATATTATATTTAATATTAATATTATTATTTATTTATTTATTATAATATAATTTTTCATTAT
*
16191 TTCAAAATTTAAAAAATGTATTATAATTATTTTT-TATAAATATCTATTTTAATTACTATAT
66 TTCAAAATTTAAAAAATATATTATAATT-TTTTTATA-AAATATCTATTTTAATTACTATAT
16252 TTATATATTATATTTAATATTAATATTAATTATTATTATATTTATTTATTATAATATAATTTTTC
1 TTATATATTATATTTAATATT-A-A-T-ATTATTATT-TATTTATTTATTATAATATAATTTTTC
* *
16317 ATTATTTCAAAATTTACAAAATATATTATAATTTTTTTATAAAATTTCTATTTTAATTACTATAT
61 ATTATTTCAAAATTTAAAAAATATATTATAATTTTTTTATAAAATATCTATTTTAATTACTATAT
16382 TTATATATTATTATTT
1 TTATATATTA-TATTT
16398 TTAATTATTT
Statistics
Matches: 135, Mismatches: 4, Indels: 9
0.91 0.03 0.06
Matches are distributed among these distances:
126 20 0.15
127 1 0.01
128 1 0.01
129 1 0.01
130 47 0.35
131 65 0.48
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.57
Consensus pattern (125 bp):
TTATATATTATATTTAATATTAATATTATTATTTATTTATTTATTATAATATAATTTTTCATTAT
TTCAAAATTTAAAAAATATATTATAATTTTTTTATAAAATATCTATTTTAATTACTATAT
Found at i:16446 original size:33 final size:34
Alignment explanation
Indices: 16377--16450 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 34
16367 TTTTAATTAC
* * *
16377 TATATTT-ATATATTATTATTTTTAATTATTTAT
1 TATATTTAATATATTAATATTATGAATTATTTAT
* *
16410 TATATTTAATA-ATTAATATTATGAATTTTTTTT
1 TATATTTAATATATTAATATTATGAATTATTTAT
16443 TATATTTA
1 TATATTTA
16451 TTTATTATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
33 32 0.91
34 3 0.09
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (34 bp):
TATATTTAATATATTAATATTATGAATTATTTAT
Found at i:18204 original size:182 final size:180
Alignment explanation
Indices: 17826--18483 Score: 720
Period size: 182 Copynumber: 3.6 Consensus size: 180
17816 ATACAAATGA
* * * * * * ** *
17826 AAAATGTATTGCTCCATAGCAATATAACATGTAAAAATATGATAAAACCGGTTTC-ATTATGAT-
1 AAAATGTATCGATCCATAACAATATAACAGGT-AAAATATGACAAAACAGGTCACGA-AATGATA
* ** * * * *
17889 AAATCGGTAAACCGCTA-CTGAATATATCGAAAGTATCGATTAGATTTAA-ATAAGTATCGACAC
64 AAACCGGTAAAGAGCTACCAG-ATATATTGAAAGTGTCGA-TACA-TTAATATAAGTATCGACAC
* * *
17952 TTTTAGAATTT-AAAGAGAAGAAGTAACAGCGCCTATAAAGTGTCGATACTTTAT
126 TTTTAGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT
* ** *
18006 AAAAACGTATCGATCCATAACAATATAACAGGTATAAGCATGACAAAACCGGTCACGAAATGATA
1 -AAAATGTATCGATCCATAACAATATAACAGGTA-AAATATGACAAAACAGGTCACGAAATGATA
* *
18071 AAATCGGTAAAGAGCTACCAGATATATTGAAAGTGTCGATACGTTAATATAAGTATCGACACTTT
64 AAACCGGTAAAGAGCTACCAGATATATTGAAAGTGTCGATACATTAATATAAGTATCGACACTTT
* * * *
18136 TTGAATTTAAAAGAGAAGAAGTTATAGCGCTTACAAGGTGTCGATACTTTAT
129 TAGAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT
* * *
18188 ACAAATGTATCGATCCATAGCAATATAACAGGTAAGAATATGACAAAACAGGTCTCGAAATTATA
1 A-AAATGTATCGATCCATAACAATATAACAGGTAA-AATATGACAAAACAGGTCACGAAATGATA
* * * *
18253 AAACCGGTAAAAAGATA-CAGGATATATTGAAAGTGTAGATAAATTAATATAAGTATCGACAC-T
64 AAACCGGTAAAGAGCTACCA-GATATATTGAAAGTGTCGATACATTAATATAAGTATCGACACTT
*
18316 TTCGTAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT
128 TTAG-AATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT
* * *
18370 GAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAACTGGT-ATCGAAATGAC
1 -AAAATGTATCGATCCATAACAATATAACAGGT-AAAATATGACAAAACAGGTCA-CGAAATGAT
* * * * * *
18434 AAAACCGGTAAAGCGCTACCGGTTATGTTGAAAGTGTCGGTACTTTAATA
63 AAAACCGGTAAAGAGCTACCAGATATATTGAAAGTGTCGATACATTAATA
18484 AGTACGCATA
Statistics
Matches: 406, Mismatches: 57, Indels: 27
0.83 0.12 0.06
Matches are distributed among these distances:
180 5 0.01
181 82 0.20
182 313 0.77
183 6 0.01
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.27
Consensus pattern (180 bp):
AAAATGTATCGATCCATAACAATATAACAGGTAAAATATGACAAAACAGGTCACGAAATGATAAA
ACCGGTAAAGAGCTACCAGATATATTGAAAGTGTCGATACATTAATATAAGTATCGACACTTTTA
GAATTTAAAAGAGAAGAAGTTATAGCGCCTAAAAAGTGTCGATACTTTAT
Found at i:24575 original size:22 final size:22
Alignment explanation
Indices: 24524--24579 Score: 60
Period size: 24 Copynumber: 2.5 Consensus size: 22
24514 ATGTTTTTGT
*
24524 TTTTTTTATATAAAATGATGGTA
1 TTTTATTATATAAAATGAT-GTA
*
24547 TAGTTATTATATAAAATGAT-TA
1 T-TTTATTATATAAAATGATGTA
24569 GTTTTATTATA
1 -TTTTATTATA
24580 AATTCATGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 10 0.36
23 2 0.07
24 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.52
Consensus pattern (22 bp):
TTTTATTATATAAAATGATGTA
Found at i:26692 original size:198 final size:196
Alignment explanation
Indices: 26286--26807 Score: 561
Period size: 198 Copynumber: 2.6 Consensus size: 196
26276 GTTAGATTTT
* * * ** *
26286 GTGTCGATACATTTATAACAAGTATCGATCCCAAAATTAAAGAGACCGATAATTATAATGTAATA
1 GTGTCGATACATTT-TAAAAAGTATCGATCCCGAAA-CATCGAAACCGATAATTATAATGTAATA
*
26351 GGTAAATTT-CTAATGTAACCGG-TAGAAATATACCGGGTTCATGAGAGAATAGGTCAACATAAA
64 GGTAAATTTAC-AATGTAACCGGTTA-AAATATACC-GGTTAATGAGAGAATAGGTCAACATAAA
* * * * * * *
26414 GTATCGACACTTTTTTAATTTGTGTCGATACATTTTTCCAAAATGAATGGCAAACGAGGTGTACG
126 GTATCGACACTCTTTAAATATGTGTCGAAACATTTTTCCAAAATGAAAGACAAACGAGGTGCACG
26479 CATAAA
191 CATAAA
* * * *
26485 GTTTCGATACATTTGTAAAAAGTATCGATCCTCGAAACATCGAAATCGATAATTATTATGTAACA
1 GTGTCGATACATTT-TAAAAAGTATCGATCC-CGAAACATCGAAACCGATAATTATAATGTAATA
* * * * *
26550 TGTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATTAGCA-AATAGGTCTACATTATGT
64 GGTAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATGAG-AGAATAGGTCAACATAAAGT
* *
26614 ATCGACACTCTTTAAATATGTGTCGAAACTTTTTTCCAAAAT-AAAGCACAAACGAGTTGCACGC
128 ATCGACACTCTTTAAATATGTGTCGAAACATTTTTCCAAAATGAAAG-ACAAACGAGGTGCACGC
26678 ATAAA
192 ATAAA
* * *
26683 GTGTCGATACA-TTTAAAATTGTATCGATCCCGAAAACATCAAAACCGATATTTATAATGTAATA
1 GTGTCGATACATTTTAAAA-AGTATCGATCCCG-AAACATCGAAACCGATAATTATAATGTAATA
** * * * * * * *
26747 GGCCAATTTATAATGTAACC-GTTTAAATTTACCGGTTTTATGAGAAAATAAGTCAATATAA
64 GGTAAATTTACAATGTAACCGGTTAAAATATACCGG-TTAATGAGAGAATAGGTCAACATAA
26808 GCGCTACCTA
Statistics
Matches: 269, Mismatches: 45, Indels: 20
0.81 0.13 0.06
Matches are distributed among these distances:
196 21 0.08
197 74 0.28
198 89 0.33
199 78 0.29
200 7 0.03
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.31
Consensus pattern (196 bp):
GTGTCGATACATTTTAAAAAGTATCGATCCCGAAACATCGAAACCGATAATTATAATGTAATAGG
TAAATTTACAATGTAACCGGTTAAAATATACCGGTTAATGAGAGAATAGGTCAACATAAAGTATC
GACACTCTTTAAATATGTGTCGAAACATTTTTCCAAAATGAAAGACAAACGAGGTGCACGCATAA
A
Found at i:26906 original size:87 final size:87
Alignment explanation
Indices: 26802--26964 Score: 281
Period size: 87 Copynumber: 1.9 Consensus size: 87
26792 AAATAAGTCA
* * *
26802 ATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATTTGTTATTGTACTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATATTATTGTACTTGATAATATTT
26867 CCGGTTAAATGTCTATTTTATT
66 CCGGTTAAATGTCTATTTTATT
* *
26889 ATATAAGCGCTATCTATTACATTATATAAGCGATACCTAATATATTATTGTGCTTGATAATATTT
1 ATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATATTATTGTACTTGATAATATTT
26954 CCGGTTAAATG
66 CCGGTTAAATG
26965 ATATAACATA
Statistics
Matches: 71, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 71 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (87 bp):
ATATAAGCGCTACCTATTACATTATATAAGCGATACCTAATATATTATTGTACTTGATAATATTT
CCGGTTAAATGTCTATTTTATT
Found at i:26935 original size:23 final size:23
Alignment explanation
Indices: 26885--26936 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
26875 ATGTCTATTT
* * *
26885 TATTATATAAGCGCTATCTATTA
1 TATTATATAAGCGATACCTAATA
*
26908 CATTATATAAGCGATACCTAATA
1 TATTATATAAGCGATACCTAATA
26931 TATTAT
1 TATTAT
26937 TGTGCTTGAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.40
Consensus pattern (23 bp):
TATTATATAAGCGATACCTAATA
Found at i:27529 original size:20 final size:20
Alignment explanation
Indices: 27504--27566 Score: 126
Period size: 20 Copynumber: 3.1 Consensus size: 20
27494 TTATATCATT
27504 ATTGGACAATTAAAATAATA
1 ATTGGACAATTAAAATAATA
27524 ATTGGACAATTAAAATAATA
1 ATTGGACAATTAAAATAATA
27544 ATTGGACAATTAAAATAATA
1 ATTGGACAATTAAAATAATA
27564 ATT
1 ATT
27567 AGATGACTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.54, C:0.05, G:0.10, T:0.32
Consensus pattern (20 bp):
ATTGGACAATTAAAATAATA
Found at i:27777 original size:277 final size:277
Alignment explanation
Indices: 27277--27783 Score: 969
Period size: 277 Copynumber: 1.8 Consensus size: 277
27267 GTATAATTTC
*
27277 TAAAACAATAATTAGATGACTAATCGAAATCAAAATAATAATTGGACAATTAAATGTGTAGTTTA
1 TAAAACAATAATTAGATGACTAATCGAAATCAAAATAATAATTGGACAATTAAATATGTAGTTTA
* *
27342 TCGTAAGCATTAACATGCGTTAATATCATGTTTTTATTATAGCTAAAAGATAATAAATATATAAT
66 TCCTAAGCATTAACATGCGTTAATATCATGTTTTTATTATAGCCAAAAGATAATAAATATATAAT
27407 GTTGATATCATATTTTATGATTGTTAAGATGATAAGATCTTTCCCCAGTTTTCCTCTTATTCTAG
131 GTTGATATCATATTTTATGATTGTTAAGATGATAAGATCTTTCCCCAGTTTTCCTCTTATTCTAG
27472 AAATAAGTTTCATTACTATCTTTTATATCATTATTGGACAATTAAAATAATAATTGGACAATTAA
196 AAATAAGTTTCATTACTATCTTTTATATCATTATTGGACAATTAAAATAATAATTGGACAATTAA
27537 AATAATAATTGGACAAT
261 AATAATAATTGGACAAT
*
27554 TAAAATAATAATTAGATGACTAATCGAAATCAAAATAATAATTGGACAATTAAATATGTAGTTTA
1 TAAAACAATAATTAGATGACTAATCGAAATCAAAATAATAATTGGACAATTAAATATGTAGTTTA
27619 TCCTAAGCATTAACATGCGTTAATATCATGTTTTTATTATAGCCAAAAGATAATAAATATATAAT
66 TCCTAAGCATTAACATGCGTTAATATCATGTTTTTATTATAGCCAAAAGATAATAAATATATAAT
27684 GTTGATATCATATTTTATGATTGTTAAGATGATAAGATCTTTCCCCAGTTTTCCTCTTATTCTAG
131 GTTGATATCATATTTTATGATTGTTAAGATGATAAGATCTTTCCCCAGTTTTCCTCTTATTCTAG
*
27749 AAATAAGTTTCATTGCTATCTTTTATATCATTATT
196 AAATAAGTTTCATTACTATCTTTTATATCATTATT
27784 TGGGTAATTT
Statistics
Matches: 225, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
277 225 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (277 bp):
TAAAACAATAATTAGATGACTAATCGAAATCAAAATAATAATTGGACAATTAAATATGTAGTTTA
TCCTAAGCATTAACATGCGTTAATATCATGTTTTTATTATAGCCAAAAGATAATAAATATATAAT
GTTGATATCATATTTTATGATTGTTAAGATGATAAGATCTTTCCCCAGTTTTCCTCTTATTCTAG
AAATAAGTTTCATTACTATCTTTTATATCATTATTGGACAATTAAAATAATAATTGGACAATTAA
AATAATAATTGGACAAT
Found at i:29188 original size:59 final size:59
Alignment explanation
Indices: 29063--29207 Score: 181
Period size: 59 Copynumber: 2.4 Consensus size: 59
29053 AATTTTAGGG
* *
29063 AAAAG-TACACAAATGGTCCCTCAACTATAGGGTGTTACTTTGTTAGGTTCTCTGACTATT
1 AAAAGTTACA-AAATGGTCCCT-AACTATAAGGTGTTACTTTGTTAGGTTCTCCGACTATT
29123 AAAAGTTACAAAATGGTCTCCTAACTATAAGGTGTTGA-TTTGTT-GAG-TCTCCGACTATT
1 AAAAGTTACAAAATGGTC-CCTAACTATAAGGTGTT-ACTTTGTTAG-GTTCTCCGACTATT
*
29182 AAAAGTTACAAAATAGTCACCTAACT
1 AAAAGTTACAAAATGGTC-CCTAACT
29208 CTTCATTATG
Statistics
Matches: 77, Mismatches: 4, Indels: 9
0.86 0.04 0.10
Matches are distributed among these distances:
59 36 0.47
60 33 0.43
61 8 0.10
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (59 bp):
AAAAGTTACAAAATGGTCCCTAACTATAAGGTGTTACTTTGTTAGGTTCTCCGACTATT
Found at i:30349 original size:40 final size:40
Alignment explanation
Indices: 30264--30345 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
30254 GTTTATGGTT
*
30264 ATTACTATGATCATTGTTTTCTGTTAATGTTTTAAAAAAA
1 ATTAATATGATCATTGTTTTCTGTTAATGTTTTAAAAAAA
30304 ATTAATATGATCATTGTTTTCTGTTAATG-TTTAAAAAAA
1 ATTAATATGATCATTGTTTTCTGTTAATGTTTTAAAAAAA
30343 ATT
1 ATT
30346 TAATGTGACG
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
39 13 0.32
40 28 0.68
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.48
Consensus pattern (40 bp):
ATTAATATGATCATTGTTTTCTGTTAATGTTTTAAAAAAA
Found at i:33259 original size:21 final size:21
Alignment explanation
Indices: 33233--33272 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33223 AAACAATTGG
33233 TAACAATTGATATCATTTTGT
1 TAACAATTGATATCATTTTGT
* *
33254 TAACAATTGGTATCTTTTT
1 TAACAATTGATATCATTTT
33273 CATTAAACAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (21 bp):
TAACAATTGATATCATTTTGT
Found at i:33520 original size:21 final size:21
Alignment explanation
Indices: 33494--33619 Score: 141
Period size: 23 Copynumber: 5.9 Consensus size: 21
33484 AGAGTGTCAA
*
33494 AGTGCATCCATGCACTCCTGC
1 AGTGCATCCATGCACTCCTAC
*
33515 AGTGCATCCATGCACTCCTGC
1 AGTGCATCCATGCACTCCTAC
33536 AGTGCATCCATGCACCTGCC-AC
1 AGTGCATCCATGCA-CT-CCTAC
33558 TAGTGCATCCATGCACCTGCC-AC
1 -AGTGCATCCATGCA-CT-CCTAC
* *
33581 TAGTGCATCCATGCAC-CATTC
1 -AGTGCATCCATGCACTCCTAC
33602 AGTGCATCCATGCACTCC
1 AGTGCATCCATGCACTCC
33620 ATTTCGAATG
Statistics
Matches: 96, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
20 16 0.17
21 37 0.39
22 4 0.04
23 39 0.41
ACGTcount: A:0.21, C:0.38, G:0.17, T:0.23
Consensus pattern (21 bp):
AGTGCATCCATGCACTCCTAC
Found at i:33577 original size:42 final size:44
Alignment explanation
Indices: 33494--33616 Score: 127
Period size: 42 Copynumber: 2.8 Consensus size: 44
33484 AGAGTGTCAA
*
33494 AGTGCATCCATGCA-CTCCTGCAGTGCATCCATGCACTCCTG-C-
1 AGTGCATCCATGCACCTCCTACAGTGCATCCATGCAC-CCTGCCT
33536 AGTGCATCCATGCACCTGCC-ACTAGTGCATCCATGCA-CCTGCCACT
1 AGTGCATCCATGCACCT-CCTAC-AGTGCATCCATGCACCCTG-C-CT
33582 AGTGCATCCATGCACCAT--T-CAGTGCATCCATGCAC
1 AGTGCATCCATGCACC-TCCTACAGTGCATCCATGCAC
33617 TCCATTTCGA
Statistics
Matches: 70, Mismatches: 1, Indels: 18
0.79 0.01 0.20
Matches are distributed among these distances:
42 18 0.26
43 17 0.24
44 17 0.24
45 1 0.01
46 16 0.23
47 1 0.01
ACGTcount: A:0.22, C:0.37, G:0.18, T:0.23
Consensus pattern (44 bp):
AGTGCATCCATGCACCTCCTACAGTGCATCCATGCACCCTGCCT
Found at i:33955 original size:17 final size:17
Alignment explanation
Indices: 33935--33974 Score: 80
Period size: 17 Copynumber: 2.4 Consensus size: 17
33925 TTCATCTTTC
33935 TCTTGTAAATATTTTGT
1 TCTTGTAAATATTTTGT
33952 TCTTGTAAATATTTTGT
1 TCTTGTAAATATTTTGT
33969 TCTTGT
1 TCTTGT
33975 GAGCTCAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.20, C:0.07, G:0.12, T:0.60
Consensus pattern (17 bp):
TCTTGTAAATATTTTGT
Found at i:34438 original size:52 final size:52
Alignment explanation
Indices: 34370--34493 Score: 158
Period size: 52 Copynumber: 2.3 Consensus size: 52
34360 AGGGGTCCCG
* *
34370 AAATCGAATATATCTATAAGTTGTTTCCATTAATAAGCATAAAAATAGGGGC
1 AAATCGAATATATCTATAAGTTGTTGCCATTAAGAAGCATAAAAATAGGGGC
* * * *
34422 AAATCGAGTATATCTATCAGTTGTTGCTATTAAGAAGTATAAAAATAGGGGCCCC
1 AAATCGAATATATCTATAAGTTGTTGCCATTAAGAAGCATAAAAATAGGGG---C
34477 AGAATCGAATATATCTA
1 A-AATCGAATATATCTA
34494 GAAAATAGGG
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
52 45 0.74
55 2 0.03
56 14 0.23
ACGTcount: A:0.40, C:0.13, G:0.17, T:0.30
Consensus pattern (52 bp):
AAATCGAATATATCTATAAGTTGTTGCCATTAAGAAGCATAAAAATAGGGGC
Found at i:37566 original size:5 final size:5
Alignment explanation
Indices: 37558--37614 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
37548 AGATGAAGAC
*
37558 TAAAT TAAAT TAAAT TAAAT TAAATTT TAACAT T-GAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAA--T TAA-AT TAAAT TAAAT TAAAT
37605 TAAAAT TAAA
1 T-AAAT TAAA
37615 AATAGGGGGA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
4 3 0.07
5 30 0.67
6 7 0.16
7 4 0.09
8 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:38502 original size:38 final size:37
Alignment explanation
Indices: 38445--38521 Score: 109
Period size: 38 Copynumber: 2.1 Consensus size: 37
38435 ATTTAATGTT
*
38445 AAGTTTTGAACGAGTTACTAAAATGAAAAAAAAAACTA
1 AAGTTTTGAACGAGATACTAAAATG-AAAAAAAAACTA
* * *
38483 AAGTTTTTAACGTGATACTAAAATGAAATAAAAACTA
1 AAGTTTTGAACGAGATACTAAAATGAAAAAAAAACTA
38520 AA
1 AA
38522 CTTTAGATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
37 13 0.37
38 22 0.63
ACGTcount: A:0.55, C:0.08, G:0.12, T:0.26
Consensus pattern (37 bp):
AAGTTTTGAACGAGATACTAAAATGAAAAAAAAACTA
Found at i:43540 original size:25 final size:25
Alignment explanation
Indices: 43494--43542 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
43484 GTAACAAGCA
*
43494 AAACATATTTCATTAACCTTTTGCT
1 AAACATATTACATTAACCTTTTGCT
*
43519 AAACATA-TACATTAATCGTTTTGC
1 AAACATATTACATTAA-CCTTTTGC
43543 ATATTTGCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.35, C:0.18, G:0.06, T:0.41
Consensus pattern (25 bp):
AAACATATTACATTAACCTTTTGCT
Found at i:47565 original size:16 final size:16
Alignment explanation
Indices: 47544--47588 Score: 81
Period size: 16 Copynumber: 2.8 Consensus size: 16
47534 GTCAAATCAT
47544 TCTGAATCATTCAGCA
1 TCTGAATCATTCAGCA
47560 TCTGAATCATTCAGCA
1 TCTGAATCATTCAGCA
*
47576 TTTGAATCATTCA
1 TCTGAATCATTCA
47589 ACATTTAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (16 bp):
TCTGAATCATTCAGCA
Found at i:47593 original size:16 final size:16
Alignment explanation
Indices: 47541--47606 Score: 78
Period size: 16 Copynumber: 4.1 Consensus size: 16
47531 AGAGTCAAAT
*
47541 CATTCTGAATCATTCAG
1 CATT-TGAATCATTCAA
* *
47558 CATCTGAATCATTCAG
1 CATTTGAATCATTCAA
47574 CATTTGAATCATTCAA
1 CATTTGAATCATTCAA
* *
47590 CATTTAAATTATTCAA
1 CATTTGAATCATTCAA
47606 C
1 C
47607 GCTTAATCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
16 41 0.93
17 3 0.07
ACGTcount: A:0.35, C:0.21, G:0.08, T:0.36
Consensus pattern (16 bp):
CATTTGAATCATTCAA
Found at i:48521 original size:30 final size:30
Alignment explanation
Indices: 48426--48510 Score: 152
Period size: 30 Copynumber: 2.8 Consensus size: 30
48416 TTCATGGATG
*
48426 GTTAATCGTATCGTTTAGTGTAAACAGACA
1 GTTAACCGTATCGTTTAGTGTAAACAGACA
48456 GTTAACCGTATCGTTTAGTGTAAACAGACA
1 GTTAACCGTATCGTTTAGTGTAAACAGACA
*
48486 GTTAACCGTATCGTTTAGTCTAAAC
1 GTTAACCGTATCGTTTAGTGTAAAC
48511 GGTCGGTTAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Consensus pattern (30 bp):
GTTAACCGTATCGTTTAGTGTAAACAGACA
Found at i:48814 original size:51 final size:51
Alignment explanation
Indices: 48676--48914 Score: 254
Period size: 51 Copynumber: 4.8 Consensus size: 51
48666 TTCATACTAC
* * * **
48676 AAAAAAGTGTAGCA-TTAACACATATTTACA-TCGATATAAGTGAATAATGT
1 AAAAAAGTGTAGCACTTAACACATACTTACACTAG-TGTAAGTGAATAAAAT
* * * ** *
48726 AAAAAA-TATATCACTTAACACATACTTATACCGGTGTAAGTAAATAAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACTAGTGTAAGTGAATAAAAT
* * * *
48776 AAAAAAGTGTAGCACTTAACAGATACCTACACTAGTGTAAATGAATTAAAT
1 AAAAAAGTGTAGCACTTAACACATACTTACACTAGTGTAAGTGAATAAAAT
* *
48827 AAAAAAGTGTAGCACTTAACAGATACTTACACTATTGTAAGTGAAT-AAA-
1 AAAAAAGTGTAGCACTTAACACATACTTACACTAGTGTAAGTGAATAAAAT
* * *
48876 AAAAAACTGTAGCACTTAACCCATACTTACACCAGTGTA
1 AAAAAAGTGTAGCACTTAACACATACTTACACTAGTGTA
48915 CGTACTAAGT
Statistics
Matches: 158, Mismatches: 28, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
49 39 0.25
50 41 0.26
51 78 0.49
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (51 bp):
AAAAAAGTGTAGCACTTAACACATACTTACACTAGTGTAAGTGAATAAAAT
Found at i:50256 original size:20 final size:22
Alignment explanation
Indices: 50207--50263 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 22
50197 CCGGTTGAAC
*
50207 AGTATCGATACCATAGTATAGT
1 AGTATCGATACCATAGTATAGG
50229 AGTATCGATACCAT-GT-TAAGG
1 AGTATCGATACCATAGTAT-AGG
50250 A-TATCGATACCATA
1 AGTATCGATACCATA
50264 AAACATCGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 13 0.41
21 5 0.16
22 14 0.44
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.30
Consensus pattern (22 bp):
AGTATCGATACCATAGTATAGG
Found at i:53849 original size:2 final size:2
Alignment explanation
Indices: 53844--53870 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
53834 AAGAGATAAA
53844 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 A
53871 ACGTTTGAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:54555 original size:14 final size:14
Alignment explanation
Indices: 54532--54561 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
54522 GAACTCAACT
*
54532 TTTCCTGATTACCA
1 TTTCCAGATTACCA
54546 TTTCCAGATTACCA
1 TTTCCAGATTACCA
54560 TT
1 TT
54562 CGTCGGTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.23, C:0.27, G:0.07, T:0.43
Consensus pattern (14 bp):
TTTCCAGATTACCA
Found at i:55717 original size:34 final size:34
Alignment explanation
Indices: 55674--55756 Score: 159
Period size: 34 Copynumber: 2.5 Consensus size: 34
55664 TTTCGCAAAA
55674 ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
1 ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
55708 ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
1 ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
55742 ATTAATATTTC-TATT
1 ATTAATATTTCGTATT
55757 ATATGATGTT
Statistics
Matches: 49, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 4 0.08
34 45 0.92
ACGTcount: A:0.25, C:0.13, G:0.10, T:0.52
Consensus pattern (34 bp):
ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
Found at i:59822 original size:15 final size:15
Alignment explanation
Indices: 59804--59832 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
59794 TTCATTTCAA
59804 AATTTTATAAAATAC
1 AATTTTATAAAATAC
59819 AATTTTATAAAATA
1 AATTTTATAAAATA
59833 ACTTAAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.41
Consensus pattern (15 bp):
AATTTTATAAAATAC
Found at i:59993 original size:14 final size:14
Alignment explanation
Indices: 59974--60037 Score: 56
Period size: 14 Copynumber: 4.1 Consensus size: 14
59964 CAAACAGCGT
59974 AATTGGTTTTCTGG
1 AATTGGTTTTCTGG
*
59988 AATTGGTTTTCCAGAAATGT
1 AATTGGTTTT-C-----TGG
60008 AATTGGTTTTCTGG
1 AATTGGTTTTCTGG
*
60022 AATTGGTTTTCCGG
1 AATTGGTTTTCTGG
60036 AA
1 AA
60038 AACCAATTAC
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 27 0.66
15 1 0.02
19 1 0.02
20 12 0.29
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.44
Consensus pattern (14 bp):
AATTGGTTTTCTGG
Found at i:60015 original size:34 final size:34
Alignment explanation
Indices: 59972--60038 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
59962 TCCAAACAGC
59972 GTAATTGGTTTTCTGGAATTGGTTTTCCAGAAAT
1 GTAATTGGTTTTCTGGAATTGGTTTTCCAGAAAT
*
60006 GTAATTGGTTTTCTGGAATTGGTTTTCCGGAAA
1 GTAATTGGTTTTCTGGAATTGGTTTTCCAGAAA
60039 ACCAATTACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.22, C:0.09, G:0.25, T:0.43
Consensus pattern (34 bp):
GTAATTGGTTTTCTGGAATTGGTTTTCCAGAAAT
Found at i:67092 original size:8 final size:8
Alignment explanation
Indices: 67079--67106 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
67069 ATAAAGAAGA
67079 TTCAAGGT
1 TTCAAGGT
67087 TTCAAGGT
1 TTCAAGGT
67095 TTCAAGGT
1 TTCAAGGT
67103 TTCA
1 TTCA
67107 GTTGAACTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.39
Consensus pattern (8 bp):
TTCAAGGT
Found at i:69556 original size:31 final size:31
Alignment explanation
Indices: 69521--69600 Score: 106
Period size: 31 Copynumber: 2.6 Consensus size: 31
69511 TGACTAATCT
*
69521 TTAATTTGACCTATAAATTTTAAACAAAATA
1 TTAATTTGACCCATAAATTTTAAACAAAATA
* * *
69552 TTAATTTGACCCATAAACTTTAAATAAAGTA
1 TTAATTTGACCCATAAATTTTAAACAAAATA
* *
69583 TCAATTTAACCCATAAAT
1 TTAATTTGACCCATAAAT
69601 CAAGTCAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.46, C:0.14, G:0.04, T:0.36
Consensus pattern (31 bp):
TTAATTTGACCCATAAATTTTAAACAAAATA
Found at i:71825 original size:69 final size:71
Alignment explanation
Indices: 71742--71886 Score: 258
Period size: 71 Copynumber: 2.1 Consensus size: 71
71732 TTTGATAAAT
* *
71742 TTAATAATTTATATTT-AAAA-TCTGTGAATTTAATCTTTTTCTTCTTCTTTTAAATTCTATCTT
1 TTAATAACTTATATTTAAAAATTCTGTGAATTTAATCTTTTTCTTCTTCTTTTAAATTATATCTT
71805 CTCGTA
66 CTCGTA
71811 TTAATAACTTATATTTAAAAATTCTGTGAATTTAATCTTTTTCTTCTTCTTTTAAATTATATCTT
1 TTAATAACTTATATTTAAAAATTCTGTGAATTTAATCTTTTTCTTCTTCTTTTAAATTATATCTT
71876 CTCGTA
66 CTCGTA
71882 TTAAT
1 TTAAT
71887 GTTACTACCT
Statistics
Matches: 72, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
69 15 0.21
70 4 0.06
71 53 0.74
ACGTcount: A:0.29, C:0.12, G:0.04, T:0.54
Consensus pattern (71 bp):
TTAATAACTTATATTTAAAAATTCTGTGAATTTAATCTTTTTCTTCTTCTTTTAAATTATATCTT
CTCGTA
Found at i:72472 original size:18 final size:19
Alignment explanation
Indices: 72451--72487 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
72441 GATTTGACAG
72451 CATTGTG-AAAAATGACTA
1 CATTGTGAAAAAATGACTA
72469 CATTGTGAAAAAATGACTA
1 CATTGTGAAAAAATGACTA
72488 ATTAATGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (19 bp):
CATTGTGAAAAAATGACTA
Found at i:72496 original size:19 final size:19
Alignment explanation
Indices: 72458--72497 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
72448 CAGCATTGTG
*
72458 AAAAATGACTACATTGTGA
1 AAAAATGACTACATTATGA
72477 AAAAATGACTA-ATTAATGA
1 AAAAATGACTACATT-ATGA
72496 AA
1 AA
72498 TTGTTGAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 3 0.16
19 16 0.84
ACGTcount: A:0.55, C:0.07, G:0.12, T:0.25
Consensus pattern (19 bp):
AAAAATGACTACATTATGA
Found at i:76598 original size:31 final size:31
Alignment explanation
Indices: 76560--76652 Score: 99
Period size: 31 Copynumber: 3.1 Consensus size: 31
76550 AACTTATTAA
*
76560 ATATATTTTATTTTTATGTT-AATGTAAAAAT
1 ATATATTTTATCTTTATGTTCAAT-TAAAAAT
*
76591 ATATATTTTATCTTTATTTTCAATTAAAAAT
1 ATATATTTTATCTTTATGTTCAATTAAAAAT
*
76622 AT-T-TTAT-TC-TTAT-TTCAACTTAAAAAT
1 ATATATTTTATCTTTATGTTCAA-TTAAAAAT
76649 ATAT
1 ATAT
76653 TTTATTGTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
26 5 0.09
27 14 0.25
28 3 0.05
29 3 0.05
30 1 0.02
31 27 0.48
32 3 0.05
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (31 bp):
ATATATTTTATCTTTATGTTCAATTAAAAAT
Found at i:76646 original size:26 final size:27
Alignment explanation
Indices: 76593--76650 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 27
76583 GTAAAAATAT
76593 ATATTTTATCTTTATTTTCAATTAAAA
1 ATATTTTATCTTTATTTTCAATTAAAA
76620 ATATTTTAT-TCTTA-TTTCAACTTAAAA
1 ATATTTTATCT-TTATTTTCAA-TTAAAA
76647 ATAT
1 ATAT
76651 ATTTTATTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
26 7 0.24
27 22 0.76
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (27 bp):
ATATTTTATCTTTATTTTCAATTAAAA
Found at i:76670 original size:29 final size:28
Alignment explanation
Indices: 76547--76719 Score: 101
Period size: 30 Copynumber: 5.9 Consensus size: 28
76537 TTAATTTTGG
*
76547 CTTAACTTATTAAATATATTTTATTTTTAT
1 CTTAACTTA-AAAATATATTTTA-TTTTAT
*
76577 GTTAA-TGTAAAAATATATATTTTATCTTTAT
1 CTTAACT-T-AAAA-ATATATTTTAT-TTTAT
*
76608 TTTCAA-TT-AAAA-ATATTTTATTCTTAT
1 CTT-AACTTAAAAATATATTTTATT-TTAT
76635 -TTCAACTTAAAAATATATTTTATTGTTAT
1 CTT-AACTTAAAAATATATTTTATT-TTAT
* *
76664 CTTAACTTCTAAAAA-ATGTTTT-TTAAATAT
1 CTTAAC-T-TAAAAATATATTTTATT--TTAT
*
76694 CTTAGCTT-AAAATATATTTTAATTTT
1 CTTAACTTAAAAATATATTTT-ATTTT
76720 TTATTAAAAA
Statistics
Matches: 117, Mismatches: 10, Indels: 34
0.73 0.06 0.21
Matches are distributed among these distances:
26 6 0.05
27 19 0.16
28 13 0.11
29 24 0.21
30 27 0.23
31 25 0.21
32 3 0.03
ACGTcount: A:0.37, C:0.07, G:0.03, T:0.53
Consensus pattern (28 bp):
CTTAACTTAAAAATATATTTTATTTTAT
Found at i:76758 original size:23 final size:23
Alignment explanation
Indices: 76700--76758 Score: 77
Period size: 22 Copynumber: 2.6 Consensus size: 23
76690 ATATCTTAGC
**
76700 TTAAAATATATTTTAATTTTTTA
1 TTAAAATATATTTTAATTTTAAA
76723 TTAAAA-ATATTTT-ATTCTTAAA
1 TTAAAATATATTTTAATT-TTAAA
76745 TTAAAATATATTTT
1 TTAAAATATATTTT
76759 GCACGTAAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 3 0.09
22 16 0.50
23 13 0.41
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (23 bp):
TTAAAATATATTTTAATTTTAAA
Found at i:76835 original size:28 final size:28
Alignment explanation
Indices: 76815--76871 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
76805 ATAAATTTAT
* *
76815 TTTTAATTTAAAATAAGAATAAAATATA
1 TTTTAAGTGAAAATAAGAATAAAATATA
* *
76843 TTTTAAGTGAACATAAGAATAATATATA
1 TTTTAAGTGAAAATAAGAATAAAATATA
76871 T
1 T
76872 ATATATATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.39
Consensus pattern (28 bp):
TTTTAAGTGAAAATAAGAATAAAATATA
Found at i:77051 original size:31 final size:31
Alignment explanation
Indices: 77013--77077 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
77003 TTTTTATATT
*
77013 AAAAAAACAAAATATATTTAATAAGTTAAGA
1 AAAAAAACAAAATATATTTAATAAGATAAGA
*
77044 AAAAAAACAAAATATATTTAATAAGATAATA
1 AAAAAAACAAAATATATTTAATAAGATAAGA
77075 AAA
1 AAA
77078 GATATTTTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (31 bp):
AAAAAAACAAAATATATTTAATAAGATAAGA
Found at i:77111 original size:28 final size:27
Alignment explanation
Indices: 77065--77120 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 27
77055 ATATATTTAA
*
77065 TAAGATAATAAAAGATATTTTTAAATTT
1 TAAGATAATAAAAGATATTATT-AATTT
*
77093 TAAGATATATAAAA-TTATTATTAATTT
1 TAAGATA-ATAAAAGATATTATTAATTT
77120 T
1 T
77121 GAGGGAAGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 6 0.24
28 13 0.52
29 6 0.24
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.46
Consensus pattern (27 bp):
TAAGATAATAAAAGATATTATTAATTT
Found at i:78274 original size:18 final size:18
Alignment explanation
Indices: 78236--78275 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
78226 AATGTACCGG
*
78236 AGGACCACTATGTTCTCA
1 AGGACCACTATGTTCCCA
78254 AGGACCACTATG-TCCCGA
1 AGGACCACTATGTTCCC-A
78272 AGGA
1 AGGA
78276 TCACATATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 3 0.15
18 17 0.85
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.20
Consensus pattern (18 bp):
AGGACCACTATGTTCCCA
Found at i:84029 original size:21 final size:21
Alignment explanation
Indices: 84003--84046 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
83993 AGCAAATTTA
84003 TGCATCGATACACTGCTACAG
1 TGCATCGATACACTGCTACAG
*
84024 TGCATCGATGCACTGCTACAG
1 TGCATCGATACACTGCTACAG
84045 TG
1 TG
84047 ATTTTCGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACTGCTACAG
Found at i:84715 original size:18 final size:18
Alignment explanation
Indices: 84692--84727 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
84682 CCGCGTAGAA
* *
84692 ATGTCCTGAAGGATCACT
1 ATGTCCCGAAGGACCACT
84710 ATGTCCCGAAGGACCACT
1 ATGTCCCGAAGGACCACT
84728 CCTTAAGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:85147 original size:47 final size:45
Alignment explanation
Indices: 85081--85176 Score: 111
Period size: 47 Copynumber: 2.1 Consensus size: 45
85071 TCACATAAAC
** * * * *
85081 ATATATATCATTTGATTCATGTCTTATTCTTATATCATATCATAT
1 ATATATATCATTTGATTCATCACTTAATCTCATATCATATAACAT
*
85126 ATATATATCATCTATGTTTCATCACTTAATCTCATATCATATAACAT
1 ATATATATCAT-T-TGATTCATCACTTAATCTCATATCATATAACAT
85173 ATAT
1 ATAT
85177 CAAATAGCAC
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 11 0.26
46 1 0.02
47 30 0.71
ACGTcount: A:0.34, C:0.16, G:0.03, T:0.47
Consensus pattern (45 bp):
ATATATATCATTTGATTCATCACTTAATCTCATATCATATAACAT
Found at i:90770 original size:27 final size:27
Alignment explanation
Indices: 90660--90761 Score: 145
Period size: 27 Copynumber: 3.8 Consensus size: 27
90650 TTTGGATGAG
*
90660 AAATTATGAAAATA--CTTATGTTAGGTA
1 AAATTATGAAAATACCCTTATG--GGGTA
90687 AAATTATGAAAATACCCTTATGGGGTA
1 AAATTATGAAAATACCCTTATGGGGTA
**
90714 AAATTACAAAAATACCCTTATGGGGTA
1 AAATTATGAAAATACCCTTATGGGGTA
90741 AAATTATGAAAATACCCTTAT
1 AAATTATGAAAATACCCTTAT
90762 ATTGTAAAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
27 62 0.91
29 6 0.09
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (27 bp):
AAATTATGAAAATACCCTTATGGGGTA
Found at i:94782 original size:18 final size:18
Alignment explanation
Indices: 94761--94796 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
94751 CTTAATTGAA
*
94761 AAAAAAAATTATTAAATT
1 AAAAAAAATAATTAAATT
*
94779 AAAAAATATAATTAAATT
1 AAAAAAAATAATTAAATT
94797 TCAAGTGTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAAAAAATAATTAAATT
Found at i:94792 original size:21 final size:21
Alignment explanation
Indices: 94744--94784 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
94734 TTAAAAATTC
94744 AAAATTACTTAATTGAAAAAA
1 AAAATTACTTAATTGAAAAAA
94765 AAAATTA-TTAAATT-AAAAAA
1 AAAATTACTT-AATTGAAAAAA
94785 TATAATTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.29
Consensus pattern (21 bp):
AAAATTACTTAATTGAAAAAA
Found at i:94904 original size:22 final size:21
Alignment explanation
Indices: 94866--94918 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
94856 ATAGTTTAAG
*
94866 AAATTAAAAATATTAAATATT
1 AAATTAAAAATATTAAAAATT
94887 AAATTGAAATAAT-TTAAAAATT
1 AAATT-AAA-AATATTAAAAATT
*
94909 ATAAATAAAA
1 A-AATTAAAA
94919 TTTAAGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
21 6 0.22
22 15 0.56
23 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
AAATTAAAAATATTAAAAATT
Done.