Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004185.1 Hibiscus syriacus cultivar Beakdansim tig00009156_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: 89805
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:488 original size:18 final size:18
Alignment explanation
Indices: 465--500 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
455 ACATATCACA
* *
465 TATGTCCCGATGGACCAC
1 TATGTCCCAAAGGACCAC
483 TATGTCCCAAAGGACCAC
1 TATGTCCCAAAGGACCAC
501 ATAGAACCCT
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:0.33, G:0.19, T:0.19
Consensus pattern (18 bp):
TATGTCCCAAAGGACCAC
Found at i:10515 original size:4 final size:4
Alignment explanation
Indices: 10506--10539 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
10496 ACAACCTGTA
10506 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
10540 GTAATTTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:11295 original size:7 final size:7
Alignment explanation
Indices: 11285--11331 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
11275 ATTGACTGAT
11285 CGTTGAC
1 CGTTGAC
11292 CGTTGAC
1 CGTTGAC
11299 CGTTGA-
1 CGTTGAC
*
11305 CTTTGAC
1 CGTTGAC
11312 CGTTGA-
1 CGTTGAC
*
11318 CTTTGAC
1 CGTTGAC
11325 TCGTTGA
1 -CGTTGA
11332 ATTTGACCAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
6 10 0.30
7 18 0.55
8 5 0.15
ACGTcount: A:0.15, C:0.23, G:0.26, T:0.36
Consensus pattern (7 bp):
CGTTGAC
Found at i:11312 original size:13 final size:13
Alignment explanation
Indices: 11294--11339 Score: 74
Period size: 13 Copynumber: 3.5 Consensus size: 13
11284 TCGTTGACCG
11294 TTGACCGTTGACT
1 TTGACCGTTGACT
11307 TTGACCGTTGACT
1 TTGACCGTTGACT
*
11320 TTGACTCGTTGAAT
1 TTGAC-CGTTGACT
11334 TTGACC
1 TTGACC
11340 AAAAAATCAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
13 19 0.61
14 12 0.39
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (13 bp):
TTGACCGTTGACT
Found at i:15254 original size:66 final size:66
Alignment explanation
Indices: 15126--15405 Score: 206
Period size: 66 Copynumber: 4.2 Consensus size: 66
15116 ATTTGAAATT
* * * * * * **
15126 GTTTCCCTTAAAACACAAATCTTTGAGTCTTTTTCTCTTAAAACAAAATTTTGTCTCCCTTGAGA
1 GTTTCTCTTGAAACAAAAATCTTTAAGTCTGTTTCCCTCGAAAC-AAATTTTGTCTCCCTTGAGA
15191 CA
65 CA
* *** * * * *
15193 ATTTCTCTTGAAACACCCATCTTTAAGATC-GTTTTCCTTGAAACGAATTTTGTCTCTCTTGAGA
1 GTTTCTCTTGAAACAAAAATCTTTAAG-TCTGTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGA
*
15257 CG
65 CA
* * * * *
15259 GTTTCTCTTGAAAAAAAAATCTTTGAGTCTGTTTCCCTCGGAACAAATTTTGTCTCCCTTAAGGC
1 GTTTCTCTTGAAACAAAAATCTTTAAGTCTGTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGAC
15324 A
66 A
* * * * * * * *
15325 GTTTCTCTTGAAACATATAA-CATTGAGAT-TGTTTCCTTTGAAACATATTTTTTTCTCGCTTGA
1 GTTTCTCTTGAAACA-AAAATCTTTAAG-TCTGTTTCCCTCGAAACA-AATTTTGTCTCCCTTGA
**
15388 GATG
63 GACA
15392 GTTTCTCTTGAAAC
1 GTTTCTCTTGAAAC
15406 CATTATTCCT
Statistics
Matches: 168, Mismatches: 40, Indels: 10
0.77 0.18 0.05
Matches are distributed among these distances:
65 2 0.01
66 101 0.60
67 63 0.38
68 2 0.01
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.40
Consensus pattern (66 bp):
GTTTCTCTTGAAACAAAAATCTTTAAGTCTGTTTCCCTCGAAACAAATTTTGTCTCCCTTGAGAC
A
Found at i:15366 original size:132 final size:134
Alignment explanation
Indices: 15142--15404 Score: 318
Period size: 133 Copynumber: 2.0 Consensus size: 134
15132 CTTAAAACAC
* * * *
15142 AAATCTTTGAGTCTTTTTCTCTTAAAACAAAATTTTGTCTCCCTTGAGACAATTTCTCTTGAAAC
1 AAATCTTTGAGTCTGTTTCCCTCAAAACAAAATTTTGTCTCCCTTAAGACAATTTCTCTTGAAAC
* * * *
15207 ACCCATCTTTAAGATCGTTTTCCTTGAAACGA-A-TTTTGTCTCTCTTGAGACGGTTTCTCTTGA
66 ACACAACATTAAGATCGTTTTCCTTGAAAC-ATATTTTTGTCTCGCTTGAGACGGTTTCTCTTGA
15270 AAAAA
130 AAAAA
** * *
15275 AAATCTTTGAGTCTGTTTCCCTCGGAAC-AAATTTTGTCTCCCTTAAGGCAGTTTCTCTTGAAAC
1 AAATCTTTGAGTCTGTTTCCCTCAAAACAAAATTTTGTCTCCCTTAAGACAATTTCTCTTGAAAC
* * * * * *
15339 ATATAACATTGAGATTG-TTTCCTTTGAAACATATTTTTTTCTCGCTTGAGATGGTTTCTCTTGA
66 ACACAACATTAAGATCGTTTTCC-TTGAAACATATTTTTGTCTCGCTTGAGACGGTTTCTCTTGA
15403 AA
130 AA
15405 CCATTATTCC
Statistics
Matches: 109, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
131 6 0.06
132 51 0.47
133 52 0.48
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (134 bp):
AAATCTTTGAGTCTGTTTCCCTCAAAACAAAATTTTGTCTCCCTTAAGACAATTTCTCTTGAAAC
ACACAACATTAAGATCGTTTTCCTTGAAACATATTTTTGTCTCGCTTGAGACGGTTTCTCTTGAA
AAAA
Found at i:16800 original size:16 final size:17
Alignment explanation
Indices: 16779--16810 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16769 TTTCAATCGA
16779 CTAAAAT-GGATAGACG
1 CTAAAATAGGATAGACG
16795 CTAAAATAGGATAGAC
1 CTAAAATAGGATAGAC
16811 CACGACTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.47, C:0.12, G:0.22, T:0.19
Consensus pattern (17 bp):
CTAAAATAGGATAGACG
Found at i:27949 original size:3 final size:3
Alignment explanation
Indices: 27943--27977 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
27933 AATTATGTTG
27943 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
27978 ACATTTATTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 29 0.94
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:28211 original size:17 final size:19
Alignment explanation
Indices: 28174--28215 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
28164 CAACAACGCC
28174 CACCATGCCCTGATCCAGT
1 CACCATGCCCTGATCCAGT
*
28193 CACCATTCCCTG-T-CAGT
1 CACCATGCCCTGATCCAGT
28210 CACCAT
1 CACCAT
28216 ACCCCATGCC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.45
18 1 0.05
19 11 0.50
ACGTcount: A:0.21, C:0.43, G:0.12, T:0.24
Consensus pattern (19 bp):
CACCATGCCCTGATCCAGT
Found at i:29530 original size:12 final size:11
Alignment explanation
Indices: 29513--29554 Score: 52
Period size: 10 Copynumber: 3.9 Consensus size: 11
29503 TTTTCACCTC
29513 TTTTCATTTTCA
1 TTTTCATTTT-A
29525 TTTTCATTTTA
1 TTTTCATTTTA
*
29536 TTTT-AGTTTA
1 TTTTCATTTTA
29546 TTTT-ATTTT
1 TTTTCATTTT
29555 TGTGAAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
10 13 0.46
11 5 0.18
12 10 0.36
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (11 bp):
TTTTCATTTTA
Found at i:29821 original size:150 final size:150
Alignment explanation
Indices: 29579--29945 Score: 535
Period size: 150 Copynumber: 2.4 Consensus size: 150
29569 ACTAATGTCT
* * * * *
29579 TTTTGTGA-GGAGAATCTATGGGAAAGTCTCCTAACTACAAAGGAAGTGCATTCCCGATGATTGT
1 TTTTGTGAGGGA-AATCCAT-GAAAAGTCTCCTAATTACAAAGGAAGTGCATTTCTGATGATTGT
29643 TCACACAAAAAGAGCATTCTTTATCCGAGCATTTATATAAGTTAATATAATATTATAATTTTAAA
64 TCACACAAAAAGAGCATTCTTTATCCGAGCATTTATATAAGTTAATATAATATTATAATTTTAAA
*
29708 CTAGAAAATTAAAGACA-CACTG
129 CTAGAAAATTAAAGA-AGCACTA
*
29730 TTTTGTGAGGGAAATCCATGAAAAGTCTCCTAATTACAAAGGAAGTGCATTTCTGAGGATTGTTC
1 TTTTGTGAGGGAAATCCATGAAAAGTCTCCTAATTACAAAGGAAGTGCATTTCTGATGATTGTTC
* * *
29795 ACACAAAAA-AGGCTTTCTTTATCCGAGCATTTCTATAATTTAATATAATATTATAATTTTAAAC
66 ACACAAAAAGA-GCATTCTTTATCCGAGCATTTATATAAGTTAATATAATATTATAATTTTAAAC
29859 TAGAAAATTAAAGAAGCACTA
130 TAGAAAATTAAAGAAGCACTA
* * *
29880 TTTTGTGAGGGAAATTCATGAAAAAGTCTCATAATTACAAAGAAAGTGCATTT-TCGATGATTGT
1 TTTTGTGAGGGAAATCCATG-AAAAGTCTCCTAATTACAAAGGAAGTGCATTTCT-GATGATTGT
29944 TC
64 TC
29946 GTACAAAATG
Statistics
Matches: 197, Mismatches: 14, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
149 2 0.01
150 138 0.70
151 54 0.27
152 3 0.02
ACGTcount: A:0.38, C:0.13, G:0.16, T:0.33
Consensus pattern (150 bp):
TTTTGTGAGGGAAATCCATGAAAAGTCTCCTAATTACAAAGGAAGTGCATTTCTGATGATTGTTC
ACACAAAAAGAGCATTCTTTATCCGAGCATTTATATAAGTTAATATAATATTATAATTTTAAACT
AGAAAATTAAAGAAGCACTA
Found at i:33442 original size:65 final size:64
Alignment explanation
Indices: 33324--33533 Score: 216
Period size: 65 Copynumber: 3.2 Consensus size: 64
33314 TTTTTCAGAG
* * *
33324 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGA-ATTAAACT-AAACATCGAATGC
1 TGATGCATCGATGCACCAA-CCATGCATCGATGCACTCAGGATATT---TTGAAACATCGAATGC
33386 ATT
62 ATT
* * *
33389 TCATGCATCGATGCA-TATACCATGCA-CTGATGCACTGAGGAT-TTTATGAAAACATCGAATGC
1 TGATGCATCGATGCACCA-ACCATGCATC-GATGCACTCAGGATATTT-TG-AAACATCGAATGC
33451 ATT
62 ATT
* * * *
33454 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
33518 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
33534 TCTTAGTGCA
Statistics
Matches: 122, Mismatches: 13, Indels: 21
0.78 0.08 0.13
Matches are distributed among these distances:
63 2 0.02
64 46 0.38
65 69 0.57
66 5 0.04
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCATCGATGCACTCAGGATATTTTGAAACATCGAATGCATT
Found at i:33533 original size:17 final size:19
Alignment explanation
Indices: 33505--33553 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
33495 TATTTTGAAA
33505 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
33523 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
33542 CACCGATGCACT
1 CATCGATGCACT
33554 GAGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:33549 original size:64 final size:64
Alignment explanation
Indices: 33373--33553 Score: 183
Period size: 65 Copynumber: 2.8 Consensus size: 64
33363 GAATTAAACT
* * * * *
33373 AAACATCGAATGCATTTCATGCATCGATGCA-TATACCATGCACTGATGCACTGAGGATTTTATG
1 AAACATCGAATGCATTTGATGCATCGATGCACTCTA--GTGCACCGATGCACTCAGGATTTTATG
33437 A
64 A
* * *
33438 AAACATCGAATGCATTTGATGCATCGATGCAC-C-AGCCATGCATCGATGCACTCTGGCTATTT-
1 AAACATCGAATGCATTTGATGCATCGATGCACTCTAG---TGCACCGATGCACTCAGGAT-TTTA
33500 TG-
62 TGA
*
33502 AAACATCGAATGCACTTGATGCATCGATGCACTCTTAGTGCACCGATGCACT
1 AAACATCGAATGCATTTGATGCATCGATGCACTC-TAGTGCACCGATGCACT
33554 GAGAGTCCAA
Statistics
Matches: 98, Mismatches: 10, Indels: 17
0.78 0.08 0.14
Matches are distributed among these distances:
64 45 0.46
65 48 0.49
66 3 0.03
67 2 0.02
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (64 bp):
AAACATCGAATGCATTTGATGCATCGATGCACTCTAGTGCACCGATGCACTCAGGATTTTATGA
Found at i:39313 original size:42 final size:44
Alignment explanation
Indices: 39266--39360 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
39256 TTGTGCTTCA
* *
39266 TGCATCGATACACC-T-AACAGTGCATCGATGCA-TCCTTGAATG
1 TGCATCGATACACCATGAA-AGTGCACCGATGCACGCCTTGAATG
* *
39308 TGCATCAATACACCATGAAGGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
39352 TGCATCGAT
1 TGCATCGAT
39361 GCACAAGGCC
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
42 13 0.29
43 13 0.29
44 19 0.42
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.24
Consensus pattern (44 bp):
TGCATCGATACACCATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:39354 original size:23 final size:23
Alignment explanation
Indices: 39285--39365 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 23
39275 ACACCTAACA
*
39285 GTGCATCGATGCA-TCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
* * *
39307 GTGCATCAAT--ACACCATGAAG
1 GTGCATCGATGCACACCTTGAAT
* *
39328 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCACACCTTGAAT
39351 GTGCATCGATGCACA
1 GTGCATCGATGCACA
39366 AGGCCATGCA
Statistics
Matches: 45, Mismatches: 11, Indels: 5
0.74 0.18 0.08
Matches are distributed among these distances:
20 1 0.02
21 14 0.31
22 9 0.20
23 21 0.47
ACGTcount: A:0.27, C:0.26, G:0.23, T:0.23
Consensus pattern (23 bp):
GTGCATCGATGCACACCTTGAAT
Found at i:41957 original size:65 final size:63
Alignment explanation
Indices: 41888--42047 Score: 196
Period size: 65 Copynumber: 2.5 Consensus size: 63
41878 AATTAAATTG
* *
41888 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCACCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCACCGATGCACTCAGGATATTT-TG-
41952 A
63 A
* * * * *
41953 AACATCAAATGCATTTGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCACCGATGCACTCAGGATATTTTGA
* *
42017 AACATCGAATGCACTTGATGCATTGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
42048 TCTGGCTATT
Statistics
Matches: 83, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 1 0.01
64 28 0.34
65 49 0.59
66 5 0.06
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCACCGATGCACTCAGGATATTTTGA
Found at i:42045 original size:45 final size:45
Alignment explanation
Indices: 41989--42083 Score: 181
Period size: 45 Copynumber: 2.1 Consensus size: 45
41979 TGCACCAGCC
41989 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
*
42034 ATGCATTGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
1 ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
42079 ATGCA
1 ATGCA
42084 CTCTTAGTGC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.32
Consensus pattern (45 bp):
ATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATGCACTTG
Found at i:45549 original size:17 final size:18
Alignment explanation
Indices: 45518--45551 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
45508 GACCCGACCC
45518 AAAATAATATATTTATTA
1 AAAATAATATATTTATTA
*
45536 AAAATATTAT-TTTATT
1 AAAATAATATATTTATT
45552 CAATAAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
AAAATAATATATTTATTA
Found at i:52979 original size:20 final size:20
Alignment explanation
Indices: 52954--52992 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
52944 TGTGGCGGCG
*
52954 GACGGCTGACGGCGGCAGCA
1 GACGGCGGACGGCGGCAGCA
*
52974 GACGGCGGGCGGCGGCAGC
1 GACGGCGGACGGCGGCAGC
52993 GGCCAGCGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.15, C:0.31, G:0.51, T:0.03
Consensus pattern (20 bp):
GACGGCGGACGGCGGCAGCA
Found at i:53001 original size:20 final size:20
Alignment explanation
Indices: 52963--53003 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
52953 GGACGGCTGA
*
52963 CGGCGGCAGCAGACGGCGGG
1 CGGCGGCAGCAGACAGCGGG
* *
52983 CGGCGGCAGCGGCCAGCGGG
1 CGGCGGCAGCAGACAGCGGG
53003 C
1 C
53004 AACAGACGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.12, C:0.34, G:0.54, T:0.00
Consensus pattern (20 bp):
CGGCGGCAGCAGACAGCGGG
Found at i:59115 original size:89 final size:89
Alignment explanation
Indices: 58954--59130 Score: 309
Period size: 89 Copynumber: 2.0 Consensus size: 89
58944 ATCAAATATA
* *
58954 CTAAATTTAAAAATTAAATAATATAATAACATTAGGATTAAATTTGAAACATCATTGGTCTTGTA
1 CTAAATTTAAAAATTAAATAATATAATAACATTAGGATTAAATTTGAAACAACATTGGTCTTATA
*
59019 ATTAATGAATTCATAAAACCTGAG
66 ATCAATGAATTCATAAAACCTGAG
*
59043 CTAAATTTAAAAATTCAATAATATAATAACATTAGGATTAAATTTGAAACAACATTGGTCTTATA
1 CTAAATTTAAAAATTAAATAATATAATAACATTAGGATTAAATTTGAAACAACATTGGTCTTATA
*
59108 ATCAATGAATTCATAAAATCTGA
66 ATCAATGAATTCATAAAACCTGA
59131 ACCCCTAATG
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 83 1.00
ACGTcount: A:0.47, C:0.10, G:0.09, T:0.34
Consensus pattern (89 bp):
CTAAATTTAAAAATTAAATAATATAATAACATTAGGATTAAATTTGAAACAACATTGGTCTTATA
ATCAATGAATTCATAAAACCTGAG
Found at i:61503 original size:27 final size:28
Alignment explanation
Indices: 61470--61532 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
61460 TTTTATTTTA
61470 TTTATTTTAGTCCCT-AAGATTCTATTT
1 TTTATTTTAGTCCCTGAAGATTCTATTT
* * *
61497 TTTATTTTAGTCCTTGAGGTTTCTATTT
1 TTTATTTTAGTCCCTGAAGATTCTATTT
*
61525 TTAATTTT
1 TTTATTTT
61533 TAGCCCTTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 14 0.45
28 17 0.55
ACGTcount: A:0.19, C:0.11, G:0.10, T:0.60
Consensus pattern (28 bp):
TTTATTTTAGTCCCTGAAGATTCTATTT
Found at i:61538 original size:86 final size:87
Alignment explanation
Indices: 61448--61613 Score: 212
Period size: 86 Copynumber: 1.9 Consensus size: 87
61438 TTGTTGTTTG
* * *
61448 AGCCCTTTAAAATTTTATTTTATT-TATTTTAGTCCCTAAGATTCTA-TTTTT-TATTTTAGTCC
1 AGCCCTTT-AAATTTT-TGTAATTATATTTTAGTCCCTAAGATTCTATTTTTTCTATTCTAGTCC
*
61510 TTGAGGTTTCTATTTTTAATTTTT
64 TTGAAGTTTCTATTTTTAATTTTT
* * *
61534 AGCCCTTTAACTTTTTGTAATTACTATTTTAGTCCCTAAGTTTCTATTTTTTCTATTCTAGTTCT
1 AGCCCTTTAAATTTTTGTAATTA-TATTTTAGTCCCTAAGATTCTATTTTTTCTATTCTAGTCCT
*
61599 TTAAGTTTCTATTTT
65 TGAAGTTTCTATTTT
61614 GGCCATATTA
Statistics
Matches: 68, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
84 5 0.07
85 6 0.09
86 29 0.43
87 5 0.07
88 23 0.34
ACGTcount: A:0.21, C:0.14, G:0.08, T:0.57
Consensus pattern (87 bp):
AGCCCTTTAAATTTTTGTAATTATATTTTAGTCCCTAAGATTCTATTTTTTCTATTCTAGTCCTT
GAAGTTTCTATTTTTAATTTTT
Found at i:61631 original size:30 final size:29
Alignment explanation
Indices: 61561--61642 Score: 76
Period size: 30 Copynumber: 2.8 Consensus size: 29
61551 TAATTACTAT
* ** *
61561 TTTAGTCC-CTAAGTTTCTATTTTTTCTA
1 TTTAGTCCTTTAAGTTTCTATTTTGGCCA
*
61589 TTCTAGTTCTTTAAGTTTCTATTTTGGCCA
1 TT-TAGTCCTTTAAGTTTCTATTTTGGCCA
* *
61619 TATTAGTCCTTTAAATTCCTATTT
1 T-TTAGTCCTTTAAGTTTCTATTT
61643 GTACTATTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 2 0.05
29 5 0.12
30 35 0.81
31 1 0.02
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.55
Consensus pattern (29 bp):
TTTAGTCCTTTAAGTTTCTATTTTGGCCA
Found at i:63543 original size:32 final size:32
Alignment explanation
Indices: 63494--63554 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
63484 CTTACTTGTT
63494 CTAACTAATTTCTTTTCTTTTGTTTGTGTACA
1 CTAACTAATTTCTTTTCTTTTGTTTGTGTACA
*
63526 CTAACTTATTT-TGTTTCTTTTGTTTGTGT
1 CTAACTAATTTCT-TTTCTTTTGTTTGTGT
63555 CATTTTTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 1 0.04
32 26 0.96
ACGTcount: A:0.15, C:0.13, G:0.11, T:0.61
Consensus pattern (32 bp):
CTAACTAATTTCTTTTCTTTTGTTTGTGTACA
Found at i:66190 original size:12 final size:12
Alignment explanation
Indices: 66173--66197 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
66163 CGTATACCCA
66173 ATATATATGTAT
1 ATATATATGTAT
66185 ATATATATGTAT
1 ATATATATGTAT
66197 A
1 A
66198 CAATAAAGCT
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (12 bp):
ATATATATGTAT
Found at i:66791 original size:4 final size:4
Alignment explanation
Indices: 66782--68069 Score: 2445
Period size: 4 Copynumber: 323.8 Consensus size: 4
66772 CTCTCGCAAC
66782 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
66830 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
66878 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
66926 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CCATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA -CATA
66975 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67023 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67071 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67119 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67167 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67215 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67263 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67311 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67359 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
67407 CATA CATA CATA CATA TATA CATA CATA CATA CATA CATA C--A CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67453 CATA CATA CATA CATA CATA CATA CATA C--A CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67499 CATA CATA CATA CATA C--A CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67545 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67593 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67641 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67689 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
67737 CATA CATA CATA CATA CATA CATA TATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67785 CATA CATA CATA C--A CATA CATA CATA CA-A CCATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA -CATA CATA CATA CATA
67831 CATA CATA CA-A CCATA CATA CATA CATA CATA CATA CATA CATA CA-A
1 CATA CATA CATA -CATA CATA CATA CATA CATA CATA CATA CATA CATA
67878 CCATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 -CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67927 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
67975 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
68023 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CAT
68070 GTTTTAGGAC
Statistics
Matches: 1265, Mismatches: 4, Indels: 30
0.97 0.00 0.02
Matches are distributed among these distances:
2 8 0.01
3 3 0.00
4 1247 0.99
5 7 0.01
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:71002 original size:31 final size:31
Alignment explanation
Indices: 70967--71027 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
70957 AAAACATAAT
* **
70967 ATTTGATCATTTTTGTTTTTATTTCATTAAA
1 ATTTGATCATGTTCATTTTTATTTCATTAAA
*
70998 ATTTGATCATGTTCATTTTTATTTTATTAA
1 ATTTGATCATGTTCATTTTTATTTCATTAA
71028 GGTGCGGTCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.61
Consensus pattern (31 bp):
ATTTGATCATGTTCATTTTTATTTCATTAAA
Found at i:71720 original size:19 final size:19
Alignment explanation
Indices: 71696--71732 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
71686 ATGACCAACA
*
71696 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
71715 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
71733 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:71847 original size:20 final size:20
Alignment explanation
Indices: 71822--71870 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
71812 TTAGATAATT
71822 GCAATGCGAATATGTAAATC
1 GCAATGCGAATATGTAAATC
71842 GCAATGCGAATATGTAAATC
1 GCAATGCGAATATGTAAATC
*
71862 GCAACGCGA
1 GCAATGCGA
71871 TAACACGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (20 bp):
GCAATGCGAATATGTAAATC
Found at i:71884 original size:41 final size:41
Alignment explanation
Indices: 71839--71949 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
71829 GAATATGTAA
*
71839 ATCGCAATGCGAATATGTA-AATCGCAACGCGATAACACGTG
1 ATCGCAACGCGAATATG-ACAATCGCAACGCGATAACACGTG
* * * *
71880 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACGTG
1 ATCGCAACGCGAATATGACAATCGCAACGCGATAACACGTG
* * *
71921 ATCGCAACGCGATTCTGACTATCGCAACG
1 ATCGCAACGCGAATATGACAATCGCAACG
71950 AGATTCTGAC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
40 1 0.02
41 63 0.98
ACGTcount: A:0.32, C:0.26, G:0.22, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAATATGACAATCGCAACGCGATAACACGTG
Found at i:71885 original size:21 final size:21
Alignment explanation
Indices: 71859--71933 Score: 93
Period size: 21 Copynumber: 3.6 Consensus size: 21
71849 GAATATGTAA
71859 ATCGCAACGCGATAACACGTG
1 ATCGCAACGCGATAACACGTG
*
71880 ATCGCAACGCGAT-TCTGAC-T-
1 ATCGCAACGCGATAAC--ACGTG
*
71900 ATCGCAACGCGATAATACGTG
1 ATCGCAACGCGATAACACGTG
71921 ATCGCAACGCGAT
1 ATCGCAACGCGAT
71934 TCTGACTATC
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
19 2 0.04
20 15 0.33
21 27 0.59
22 2 0.04
ACGTcount: A:0.31, C:0.28, G:0.23, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGATAACACGTG
Found at i:71905 original size:20 final size:20
Alignment explanation
Indices: 71880--72006 Score: 175
Period size: 20 Copynumber: 6.3 Consensus size: 20
71870 ATAACACGTG
71880 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
71900 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
71920 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
*
71941 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
71961 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* *
71981 ATCACAACGTGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
72001 AACGCA
1 ATCGCA
72007 TCACTGAATT
Statistics
Matches: 94, Mismatches: 10, Indels: 6
0.85 0.09 0.05
Matches are distributed among these distances:
19 2 0.02
20 75 0.80
21 15 0.16
22 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:71906 original size:61 final size:58
Alignment explanation
Indices: 71839--71972 Score: 153
Period size: 61 Copynumber: 2.2 Consensus size: 58
71829 GAATATGTAA
* * *
71839 ATCGCAATGCGAATATGTAAATCGCAACGCGATAAC-ACGTGATCGCAACGCGATTCTGACT
1 ATCGCAACGCGAATACGT-AATCGCAACGCGAT-ACGAC-T-ATCGCAACGAGATTCTGACT
* *
71900 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCG--AATACGTAATCGCAACGCGATAC-GACTATCGCAACGAGATTCTGACT
71961 ATCGCAACGCGA
1 ATCGCAACGCGA
71973 TTCTGACTAT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
59 1 0.02
61 41 0.64
62 14 0.22
63 8 0.12
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (58 bp):
ATCGCAACGCGAATACGTAATCGCAACGCGATACGACTATCGCAACGAGATTCTGACT
Found at i:72881 original size:24 final size:24
Alignment explanation
Indices: 72823--72869 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
72813 AGTCGATATT
*
72823 CGAAATTTGATCTTGGTCAATACC
1 CGAACTTTGATCTTGGTCAATACC
72847 CGAACTTTGATCTTGGTCAATAC
1 CGAACTTTGATCTTGGTCAATAC
72870 TCGGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAACTTTGATCTTGGTCAATACC
Found at i:75166 original size:18 final size:18
Alignment explanation
Indices: 75143--75182 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
75133 AGCAAAAGGC
*
75143 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
*
75161 AATCAAAATCCCAATCAC
1 AATCAAAATCCCAATCAA
75179 AATC
1 AATC
75183 GGCTTCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.28, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:75380 original size:20 final size:20
Alignment explanation
Indices: 75355--75609 Score: 179
Period size: 20 Copynumber: 13.7 Consensus size: 20
75345 CACATTCATT
75355 TGACTATCGCAACGCGAATA
1 TGACTATCGCAACGCGAATA
* *
75375 TGACTATCGCAACGTGAATT
1 TGACTATCGCAACGCGAATA
* *
75395 TGAATATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* * *
75412 T-A--ATCGCAATGCAAAAA
1 TGACTATCGCAACGCGAATA
*
75429 TGACTATCGCAACG-G--GA
1 TGACTATCGCAACGCGAATA
* *
75446 T-A--ATCGCAATGCGAAAA
1 TGACTATCGCAACGCGAATA
* *
75463 TGACTATCGCAACGCTAAAA
1 TGACTATCGCAACGCGAATA
*
75483 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
75503 TAACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* *
75523 TGACTATCACAA--CG-AGA
1 TGACTATCGCAACGCGAATA
75540 T-A--ATCGCAACGCGAA-A
1 TGACTATCGCAACGCGAATA
*
75556 TGACTATCGCAACGCGAATT
1 TGACTATCGCAACGCGAATA
* * * *
75576 TGATTATCGCAATGGGAATT
1 TGACTATCGCAACGCGAATA
75596 TGACTATCGCAACG
1 TGACTATCGCAACG
75610 AGAAAATCGC
Statistics
Matches: 186, Mismatches: 30, Indels: 38
0.73 0.12 0.15
Matches are distributed among these distances:
14 22 0.12
15 1 0.01
16 7 0.04
17 11 0.06
18 4 0.02
19 14 0.08
20 127 0.68
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (20 bp):
TGACTATCGCAACGCGAATA
Found at i:75407 original size:40 final size:40
Alignment explanation
Indices: 75352--75609 Score: 169
Period size: 34 Copynumber: 6.9 Consensus size: 40
75342 TTACACATTC
* *
75352 ATTTGACTATCGCAACGCGAATATGACTATCGCAACGTGA
1 ATTTGAATATCGCAACGCGAATATGACTATCGCAACGCGA
* * *
75392 ATTTGAATATCGCAACG-G--GAT-A--ATCGCAATGCAA
1 ATTTGAATATCGCAACGCGAATATGACTATCGCAACGCGA
** * * *
75426 AAATGACTATCGCAACG-G--GAT-A--ATCGCAATGCGA
1 ATTTGAATATCGCAACGCGAATATGACTATCGCAACGCGA
** * * *
75460 AAATGACTATCGCAACGCTAAAATGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGAATATGACTATCGCAACGCGA
* * *
75500 ATTT-AACTATCGCAACGCGAATTTGACTATCACAACGAG-
1 ATTTGAA-TATCGCAACGCGAATATGACTATCGCAACGCGA
75539 A--T--A-ATCGCAACGCGAA-ATGACTATCGCAACGCGA
1 ATTTGAATATCGCAACGCGAATATGACTATCGCAACGCGA
* * * *
75573 ATTTGATTATCGCAATGGGAATTTGACTATCGCAACG
1 ATTTGAATATCGCAACGCGAATATGACTATCGCAACG
75610 AGAAAATCGC
Statistics
Matches: 177, Mismatches: 27, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
33 14 0.08
34 70 0.40
36 3 0.02
37 5 0.03
38 1 0.01
39 14 0.08
40 70 0.40
ACGTcount: A:0.36, C:0.22, G:0.20, T:0.22
Consensus pattern (40 bp):
ATTTGAATATCGCAACGCGAATATGACTATCGCAACGCGA
Found at i:75574 original size:73 final size:73
Alignment explanation
Indices: 75468--75648 Score: 245
Period size: 73 Copynumber: 2.5 Consensus size: 73
75458 GAAAATGACT
*
75468 ATCGCAACGCTAAAATGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCAC
1 ATCGCAACGC-GAAATGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCAC
*
75533 AACGAGATA
65 AACGAGAAA
* * * * *
75542 ATCGCAACGCGAAATGACTATCGCAACGCGAATTTGATTATCGCAATGGGAATTTGACTATCGCA
1 ATCGCAACGCGAAATGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCACA
75607 ACGAGAAA
66 ACGAGAAA
* * * *
75615 ATCGCAAAGTGTATTAGACTATCGCAACGCGAAT
1 ATCGCAACGCGAAAT-GACTATCGCAACGCGAAT
75649 ATGATGCAGA
Statistics
Matches: 95, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
73 67 0.71
74 28 0.29
ACGTcount: A:0.36, C:0.22, G:0.19, T:0.22
Consensus pattern (73 bp):
ATCGCAACGCGAAATGACTATCGCAACGCGAATTTAACTATCGCAACGCGAATTTGACTATCACA
ACGAGAAA
Found at i:75837 original size:34 final size:30
Alignment explanation
Indices: 75759--75824 Score: 114
Period size: 30 Copynumber: 2.2 Consensus size: 30
75749 TTAAACAAGC
* *
75759 ACAAATAATAATTATTTACACATTAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
75789 ACAAATAAGAATTATTTACACATCAATTAA
1 ACAAATAAGAATTATTTACACATCAATTAA
75819 ACAAAT
1 ACAAAT
75825 CAACTCTTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.55, C:0.12, G:0.02, T:0.32
Consensus pattern (30 bp):
ACAAATAAGAATTATTTACACATCAATTAA
Found at i:77246 original size:21 final size:21
Alignment explanation
Indices: 77197--77303 Score: 97
Period size: 21 Copynumber: 5.1 Consensus size: 21
77187 TCTAGAATGT
* *
77197 TGGGAGGGACCTCTTCAACGA
1 TGGGAGGGGCCTCTTGAACGA
** * *
77218 TGACAGGGCCCTCTTGAACGG
1 TGGGAGGGGCCTCTTGAACGA
* **
77239 TGGGAGGGGACTCTTGAGGGA
1 TGGGAGGGGCCTCTTGAACGA
**
77260 TGATAGGGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
* *
77281 TAGGAGAGGCCTCTTGAACGA
1 TGGGAGGGGCCTCTTGAACGA
77302 TG
1 TG
77304 ACATGTGAGT
Statistics
Matches: 64, Mismatches: 22, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 64 1.00
ACGTcount: A:0.22, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
TGGGAGGGGCCTCTTGAACGA
Found at i:77262 original size:42 final size:42
Alignment explanation
Indices: 77199--77306 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 42
77189 TAGAATGTTG
* * *
77199 GGAG-GGACCTCTTCAACGATGACAGGGCCCTCTTGAACGGTG
1 GGAGAGGA-CTCTTGAACGATGACAGGGCCCTCTTGAACGATA
* ** * *
77241 GGAGGGGACTCTTGAGGGATGATAGGGGCCTCTTGAACGATA
1 GGAGAGGACTCTTGAACGATGACAGGGCCCTCTTGAACGATA
*
77283 GGAGAGGCCTCTTGAACGATGACA
1 GGAGAGGACTCTTGAACGATGACA
77307 TGTGAGTCGG
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
42 50 0.94
43 3 0.06
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.19
Consensus pattern (42 bp):
GGAGAGGACTCTTGAACGATGACAGGGCCCTCTTGAACGATA
Found at i:77815 original size:20 final size:20
Alignment explanation
Indices: 77792--77842 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
77782 TCTGAAACTT
77792 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
* *
77812 AAAATCGTAACACGGAAATG
1 AAAATCGCAACACGAAAATG
**
77832 ATTATCGCAAC
1 AAAATCGCAAC
77843 GAGATAATCG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.49, C:0.20, G:0.16, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:77863 original size:33 final size:33
Alignment explanation
Indices: 77826--77889 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
77816 TCGTAACACG
*
77826 GAAATGATTATCGCAACGAGATAATCGCAACGC
1 GAAATGACTATCGCAACGAGATAATCGCAACGC
*
77859 GAAATGGCTATCGCAACGAGATAATCGCAAC
1 GAAATGACTATCGCAACGAGATAATCGCAAC
77890 ACAAATTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.39, C:0.22, G:0.22, T:0.17
Consensus pattern (33 bp):
GAAATGACTATCGCAACGAGATAATCGCAACGC
Found at i:78263 original size:22 final size:22
Alignment explanation
Indices: 78235--78314 Score: 133
Period size: 22 Copynumber: 3.6 Consensus size: 22
78225 GATGGAAATA
78235 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
78257 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
* * *
78279 GACGGATTTCACCGAAAATGGG
1 GACGGATTTCGCCGGAGATGGG
78301 GACGGATTTCGCCG
1 GACGGATTTCGCCG
78315 TAGAGAGTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.21, C:0.20, G:0.40, T:0.19
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:78539 original size:21 final size:20
Alignment explanation
Indices: 78477--78582 Score: 124
Period size: 20 Copynumber: 5.2 Consensus size: 20
78467 TTATCACAAC
*
78477 GCGATAGTCAGAATCTCGTT
1 GCGATAGTCAGAATCGCGTT
*
78497 GCGATAGTCAGAATCCCGTT
1 GCGATAGTCAGAATCGCGTT
**
78517 GCGATCACGT-ATTATCGCGTT
1 GCGAT-A-GTCAGAATCGCGTT
*
78538 GCGATAGTCCGAATCGCGTT
1 GCGATAGTCAGAATCGCGTT
* *
78558 GTGATAGTCAGAATCGTGTT
1 GCGATAGTCAGAATCGCGTT
78578 GCGAT
1 GCGAT
78583 CACGTGTTAT
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.03
20 54 0.75
21 14 0.19
22 2 0.03
ACGTcount: A:0.23, C:0.21, G:0.27, T:0.29
Consensus pattern (20 bp):
GCGATAGTCAGAATCGCGTT
Found at i:78552 original size:61 final size:61
Alignment explanation
Indices: 78477--78603 Score: 200
Period size: 61 Copynumber: 2.1 Consensus size: 61
78467 TTATCACAAC
*
78477 GCGATAGTCAGAATCTCGTTGCGATAGTCAGAATCCCGTTGCGATCACGTATTATCGCGTT
1 GCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCCCGTTGCGATCACGTATTATCGCGTT
* * ** *
78538 GCGATAGTCCGAATCGCGTTGTGATAGTCAGAATCGTGTTGCGATCACGTGTTATCGCGTT
1 GCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCCCGTTGCGATCACGTATTATCGCGTT
78599 GCGAT
1 GCGAT
78604 TTACATATTC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.30
Consensus pattern (61 bp):
GCGATAGTCAGAATCGCGTTGCGATAGTCAGAATCCCGTTGCGATCACGTATTATCGCGTT
Found at i:78620 original size:20 final size:20
Alignment explanation
Indices: 78592--78644 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
78582 TCACGTGTTA
*
78592 TCGCGTTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
78612 TCGCATTGCGATTTACATAT
1 TCGCATTGCGATTTACATAT
*
78632 TCACATTGCGATT
1 TCGCATTGCGATT
78645 ATCTAAATCG
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:0.23, C:0.21, G:0.17, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACATAT
Found at i:78752 original size:18 final size:18
Alignment explanation
Indices: 78729--78763 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
78719 TGAGATAATG
*
78729 GAGATCGCGTTGCGATTA
1 GAGATCGCATTGCGATTA
78747 GAGATCGCATTGCGATT
1 GAGATCGCATTGCGATT
78764 TTGTTGGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (18 bp):
GAGATCGCATTGCGATTA
Found at i:79085 original size:19 final size:20
Alignment explanation
Indices: 79061--79105 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
79051 GTTTGGCAAT
79061 GAACCG-CTGAAAACCGGTA
1 GAACCGACTGAAAACCGGTA
*
79080 GAACCGACTGAAAATCGGTA
1 GAACCGACTGAAAACCGGTA
*
79100 AAACCG
1 GAACCG
79106 GGATGAACCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.11
Consensus pattern (20 bp):
GAACCGACTGAAAACCGGTA
Found at i:79144 original size:30 final size:30
Alignment explanation
Indices: 79070--79133 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
79060 TGAACCGCTG
* * *
79070 AAAACCGGTA-GAACCGACTGAAAATCGGT
1 AAAACCGGGATGAACCGACTGAAAACCGGC
*
79099 AAAACCGGGATGAACCGGCTGAAAACCGGC
1 AAAACCGGGATGAACCGACTGAAAACCGGC
79129 AAAAC
1 AAAAC
79134 TGGTTTGAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 9 0.30
30 21 0.70
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.09
Consensus pattern (30 bp):
AAAACCGGGATGAACCGACTGAAAACCGGC
Found at i:88101 original size:10 final size:10
Alignment explanation
Indices: 88081--88118 Score: 60
Period size: 10 Copynumber: 3.9 Consensus size: 10
88071 GAAGGGTAGG
88081 GAGAG-AGGA
1 GAGAGAAGGA
88090 GAGAGAAGGA
1 GAGAGAAGGA
88100 GAGAGAAGGA
1 GAGAGAAGGA
*
88110 GAAAGAAGG
1 GAGAGAAGG
88119 GTGAAACTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
9 5 0.19
10 22 0.81
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (10 bp):
GAGAGAAGGA
Done.