Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004486.1 Hibiscus syriacus cultivar Beakdansim tig00009885_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: 72074
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1486 original size:19 final size:19
Alignment explanation
Indices: 1435--1488 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
1425 TGTAGTTTCT
*
1435 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
1455 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
1475 GAAACTAAAATCGC
1 GAAACTAAAATCGC
1489 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:2101 original size:20 final size:20
Alignment explanation
Indices: 2076--2122 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
2066 TGACTTCTGT
2076 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
2096 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACAAATTCGC
*
2116 CTTGCGA
1 GTTGCGA
2123 ATTTGGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:21781 original size:12 final size:12
Alignment explanation
Indices: 21764--21788 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
21754 TTGCTTAATA
21764 TTCAACAATTGT
1 TTCAACAATTGT
21776 TTCAACAATTGT
1 TTCAACAATTGT
21788 T
1 T
21789 GGTGCCACTT
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:0.32, C:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TTCAACAATTGT
Found at i:23920 original size:19 final size:19
Alignment explanation
Indices: 23881--23921 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
23871 AGGATTTTTT
*
23881 AATTAATTAATTTGAAGTA
1 AATTAATTAATTTCAAGTA
23900 AATTAATTAAATTTCAA-TA
1 AATTAATT-AATTTCAAGTA
23919 AAT
1 AAT
23922 AGATCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (19 bp):
AATTAATTAATTTCAAGTA
Found at i:28413 original size:64 final size:65
Alignment explanation
Indices: 28327--28489 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 65
28317 CGGTGCACCA
*
28327 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCCTG-GTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCCAGAGTGCATCGATGCATGG
** * ** **
28391 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCAGAGTGCATCGATGCATGG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCCAGAGTGCATCGATGCATGG
* * *
28456 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
28490 CAATTAATTC
Statistics
Matches: 84, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
64 40 0.48
65 44 0.52
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (65 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCCAGAGTGCATCGATGCATGG
Found at i:28461 original size:19 final size:19
Alignment explanation
Indices: 28437--28487 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
28427 GAAAATATTC
28437 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
28456 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
28475 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
28488 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:28529 original size:65 final size:63
Alignment explanation
Indices: 28331--28538 Score: 201
Period size: 65 Copynumber: 3.2 Consensus size: 63
28321 GCACCAAGTG
* * * *
28331 TGCATCGATGCATGAAATGCATTCGATGTTTAAAAAATAGCCTGGTGCATCGATGCATGG-CTTG
1 TGCATCGATGCATGAAATGCATTCGATG-TTCAAAAAT-TCATGATGCATCGATGCATGGAC-TG
28395 -
63 A
* *
28395 TGCATCGATGCATCAAATGCATTCGATGTTTTGAAAATATTCA-GAGTGCATCGATGCATGGA--
1 TGCATCGATGCATGAAATGCATTCGATG--TTCAAAA-ATTCATGA-TGCATCGATGCATGGACT
28457 GA
62 GA
* * *
28459 GTGCATCGGTGCATGGAATGCATTCGATGTTCAATTAATTCATCGATGCATCGATGCATGGACTG
1 -TGCATCGATGCATGAAATGCATTCGATGTTCAA-AAATTCAT-GATGCATCGATGCATGGACTG
28524 A
63 A
*
28525 TGCATCGGTGCATG
1 TGCATCGATGCATG
28539 CCTTTGAATA
Statistics
Matches: 123, Mismatches: 10, Indels: 21
0.80 0.06 0.14
Matches are distributed among these distances:
63 10 0.08
64 45 0.37
65 64 0.52
66 4 0.03
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.30
Consensus pattern (63 bp):
TGCATCGATGCATGAAATGCATTCGATGTTCAAAAATTCATGATGCATCGATGCATGGACTGA
Found at i:33373 original size:22 final size:21
Alignment explanation
Indices: 33347--33393 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 21
33337 AAGGTCAAAA
*
33347 ATCAAATTGTTTGAAAATTG-AT
1 ATCAAATGGTTT-AAAA-TGAAT
33369 ATC-AATGGTTTAAAATGAAT
1 ATCAAATGGTTTAAAATGAAT
33389 ATCAA
1 ATCAA
33394 TTACGTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
19 2 0.09
20 9 0.41
21 8 0.36
22 3 0.14
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (21 bp):
ATCAAATGGTTTAAAATGAAT
Found at i:35586 original size:64 final size:66
Alignment explanation
Indices: 35481--35643 Score: 206
Period size: 65 Copynumber: 2.5 Consensus size: 66
35471 CGGTGCACCA
*** *
35481 AGTGTGCATCGATGCATGAAATGCATTCGATG-TTTGAAAAATA-GCCTGGTGGATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATGCAAAGTGCATCGATGCATG
35544 G
66 G
** * *
35545 CTTGTGCATCGATGCATCAAATGCATTCGATGTTTTG-AAAATATTCAAAGTGCATCGATGCATG
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATGCAAAGTGCATCGATGCATG
35609 G
66 G
* * *
35610 AGAGTGCATCGGTGCATGGAATGCATTCGATGTT
1 AGTGTGCATCGATGCATGAAATGCATTCGATGTT
35644 CAATTAATTC
Statistics
Matches: 83, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 35 0.42
65 48 0.58
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (66 bp):
AGTGTGCATCGATGCATGAAATGCATTCGATGTTTTGAAAAATATGCAAAGTGCATCGATGCATG
G
Found at i:35617 original size:19 final size:18
Alignment explanation
Indices: 35592--35641 Score: 66
Period size: 19 Copynumber: 2.7 Consensus size: 18
35582 AAAATATTCA
35592 AAGTGCATCGATGCATGG
1 AAGTGCATCGATGCATGG
*
35610 AGAGTGCATCGGTGCATGG
1 A-AGTGCATCGATGCATGG
35629 AA-TGCATTCGATG
1 AAGTGCA-TCGATG
35642 TTCAATTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
17 4 0.14
18 7 0.25
19 17 0.61
ACGTcount: A:0.26, C:0.16, G:0.34, T:0.24
Consensus pattern (18 bp):
AAGTGCATCGATGCATGG
Found at i:36325 original size:29 final size:30
Alignment explanation
Indices: 36257--36328 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
36247 CATTATGCAT
* * * *
36257 AATAAAATGCATCATTTGTAACATATTACT
1 AATAAAATGCATCATTTATAAAACATTACC
*
36287 AACAAAATGCATCA-TTATAAAACATTACC
1 AATAAAATGCATCATTTATAAAACATTACC
*
36316 AATAACATGCATC
1 AATAAAATGCATC
36329 TGAATTTAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 1
0.81 0.16 0.02
Matches are distributed among these distances:
29 22 0.63
30 13 0.37
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (30 bp):
AATAAAATGCATCATTTATAAAACATTACC
Found at i:44275 original size:27 final size:27
Alignment explanation
Indices: 44245--44309 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
44235 AAAACAGTGT
*
44245 TGAATGATTCAGTACAGAAGTACATTA
1 TGAATGATTCAGTACAAAAGTACATTA
44272 TGAATGATTCAGTACAAAAGTACATTA
1 TGAATGATTCAGTACAAAAGTACATTA
44299 TGAATGATTCA
1 TGAATGATTCA
44310 AAGCTATTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.31
Consensus pattern (27 bp):
TGAATGATTCAGTACAAAAGTACATTA
Found at i:45280 original size:3 final size:3
Alignment explanation
Indices: 45272--45320 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
45262 CTGTTTTCCG
45272 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
45320 A
1 A
45321 ACCTAATATG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:46903 original size:43 final size:43
Alignment explanation
Indices: 46807--47097 Score: 257
Period size: 43 Copynumber: 6.7 Consensus size: 43
46797 AAAATTGACT
** * * * *
46807 AAATTAGGGGTTTAAATTATAAAAGTAAAAAGT-ATGGTT-GAA
1 AAATTAGGGGCCTCAATTATAAATGTAAAAAGTGA-GATTAAAA
* *
46849 AAATTAGGGGCCTCAATTTTAAATGTAAAAAGTGATATTAAAA
1 AAATTAGGGGCCTCAATTATAAATGTAAAAAGTGAGATTAAAA
* *
46892 AAATTAGGGGCCTCAATTATAAAGGTAAAATGTGAGATTGAAAAA
1 AAATTAGGGGCCTCAATTATAAATGTAAAAAGTGAGATT--AAAA
* * * *
46937 AAAATAGGAG-TTCAATTATAAACGTAAAAAGTGAGATTGAAAA
1 AAATTAGGGGCCTCAATTATAAATGTAAAAAGTGAGATT-AAAA
** * * *
46980 AAATTAGGATCATCAATTATAAATATAAAAAAGTGAGATTGAAA
1 AAATTAGGGGCCTCAATTATAAATGT-AAAAAGTGAGATTAAAA
** ** * * *
47024 AAATTAATGATCTCAATTATAAA-GATAAAATGTGTGATTACAA
1 AAATTAGGGGCCTCAATTATAAATG-TAAAAAGTGAGATTAAAA
*
47067 AAATTAGGGGCCTCAATTATAAATATAAAAA
1 AAATTAGGGGCCTCAATTATAAATGTAAAAA
47098 AATTAAAATT
Statistics
Matches: 200, Mismatches: 41, Indels: 15
0.78 0.16 0.06
Matches are distributed among these distances:
42 30 0.15
43 87 0.44
44 58 0.29
45 25 0.12
ACGTcount: A:0.50, C:0.05, G:0.17, T:0.28
Consensus pattern (43 bp):
AAATTAGGGGCCTCAATTATAAATGTAAAAAGTGAGATTAAAA
Found at i:47094 original size:87 final size:88
Alignment explanation
Indices: 46860--47098 Score: 283
Period size: 87 Copynumber: 2.7 Consensus size: 88
46850 AATTAGGGGC
* * ** *
46860 CTCAATTTTAAATGTAAAAAGTGAT-ATTAAAAAAATTAGGGGCCTCAATTATAAAGGT-AAAAT
1 CTCAATTATAAACGTAAAAAGTG-TGATTAAAAAAATTAGGGGCCTCAATTATAAATATAAAAAA
46923 GTGAGATTGAAAAAAAAATAGGAGT
65 GTGAGATTGAAAAAAAAATA-GAGT
* ** *
46948 -TCAATTATAAACGTAAAAAGTGAGATTGAAAAAAATTAGGATCATCAATTATAAATATAAAAAA
1 CTCAATTATAAACGTAAAAAGTGTGATT-AAAAAAATTAGGGGCCTCAATTATAAATATAAAAAA
*
47012 GTGAGATTGAAAAAATTAAT-GA-T
65 GTGAGATTGAAAAAA-AAATAGAGT
* *
47035 CTCAATTATAAA-GATAAAATGTGTGATTACAAAAATTAGGGGCCTCAATTATAAATATAAAAAA
1 CTCAATTATAAACG-TAAAAAGTGTGATTAAAAAAATTAGGGGCCTCAATTATAAATATAAAAAA
47099 ATTAAAATTT
Statistics
Matches: 129, Mismatches: 16, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
87 57 0.44
88 50 0.39
89 19 0.15
90 3 0.02
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (88 bp):
CTCAATTATAAACGTAAAAAGTGTGATTAAAAAAATTAGGGGCCTCAATTATAAATATAAAAAAG
TGAGATTGAAAAAAAAATAGAGT
Found at i:47581 original size:21 final size:20
Alignment explanation
Indices: 47557--47616 Score: 51
Period size: 21 Copynumber: 3.2 Consensus size: 20
47547 AACTTTGAAA
47557 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
*
47578 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
47592 AAATAGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
47613 AAAT
1 AAAT
47617 ATTTCTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.43
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:47595 original size:35 final size:36
Alignment explanation
Indices: 47549--47657 Score: 166
Period size: 35 Copynumber: 3.0 Consensus size: 36
47539 TGGCAACCAA
47549 CTTTGAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
* *
47586 CTTTG-AAAATAGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
47621 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
47658 GTTGAAATAT
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
35 33 0.51
36 6 0.09
37 26 0.40
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:51426 original size:36 final size:36
Alignment explanation
Indices: 51311--51419 Score: 166
Period size: 35 Copynumber: 3.0 Consensus size: 36
51301 TGGCAACCAA
* *
51311 CTTTGAAAAAATGATTTTCAAAGTTTGATAAATGTTT
1 CTTTG-AAAAATGGTTTTCAAAGTTTGGTAAATGTTT
51348 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
51383 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
51420 GTTGAAATAT
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
35 33 0.49
36 7 0.10
37 27 0.40
ACGTcount: A:0.31, C:0.06, G:0.18, T:0.45
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:59191 original size:45 final size:45
Alignment explanation
Indices: 59137--59242 Score: 124
Period size: 45 Copynumber: 2.4 Consensus size: 45
59127 ACCAGGAATG
* * *
59137 TTAATGGATAATTAATAACCACCAACCAATAACCTACTCGA-GTTA
1 TTAAAGGATAATTAATAACCACCAACCAACAACCTA-TCGACATTA
* * * *
59182 TTAAAGGATAATTATTAATCACCAACCACCAACCTATTGACATTA
1 TTAAAGGATAATTAATAACCACCAACCAACAACCTATCGACATTA
*
59227 TTAACGGATAATTAAT
1 TTAAAGGATAATTAAT
59243 GCTTAAATCT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 3 0.06
45 48 0.94
ACGTcount: A:0.42, C:0.20, G:0.08, T:0.29
Consensus pattern (45 bp):
TTAAAGGATAATTAATAACCACCAACCAACAACCTATCGACATTA
Found at i:60822 original size:20 final size:20
Alignment explanation
Indices: 60782--60837 Score: 76
Period size: 20 Copynumber: 2.7 Consensus size: 20
60772 TTTTAATATA
* *
60782 TGAAATTTTACAATTTATTTT
1 TGAAATTATA-AATATATTTT
60803 TGAAATTATAAATATATTTT
1 TGAAATTATAAATATATTTT
60823 TGAAATTATTAAATA
1 TGAAATTA-TAAATA
60838 ATAATTAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.50
Consensus pattern (20 bp):
TGAAATTATAAATATATTTT
Found at i:61035 original size:19 final size:20
Alignment explanation
Indices: 60993--61035 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
60983 TTGAAGAATT
*
60993 TTTAAAAATACTTTTATGAT
1 TTTAAAAATACTTTTATGAG
61013 TTTAAAAATGA-TTTT-TGAG
1 TTTAAAAAT-ACTTTTATGAG
61032 TTTA
1 TTTA
61036 TATATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 7 0.33
20 13 0.62
21 1 0.05
ACGTcount: A:0.37, C:0.02, G:0.09, T:0.51
Consensus pattern (20 bp):
TTTAAAAATACTTTTATGAG
Found at i:66423 original size:182 final size:182
Alignment explanation
Indices: 66088--66579 Score: 745
Period size: 182 Copynumber: 2.7 Consensus size: 182
66078 TATCGGTTTA
***
66088 TGTCGATACTTTATAAAAATGTATCGATCCATATTAATATAACAGGTAAAAATATGAC-AAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCG
* * * * *
66152 ATCTCGAAAAGACAAAATCGGTAAAGCGCTATCGGATATATTGAAAGTGTCGATACTTTAATATA
66 GTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
* * * *
66217 AGTATCGACACTTTGTGTATTTAAAAGAGAAGTATTTTTAGCGCCTATAAAAG
131 AGTATCAACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTAT-AAAG
*
66270 TGTCGATACTTTATAAAAATGTATCGGTCCATAACGATATAACAGGTAAAAATATGACAAAACCG
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCG
* * * *
66335 GTCTCTAAATGACAAAACCGGTATAGAGTTACCGGATATATTGAAAGTGTCGATATTTTAATATA
66 GTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
66400 AGTATCAACACTTTGT-AATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
131 AGTATCAACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
* * * *
66451 TATCGATACTTTATAAAAATATATTGATCCATAACGATATAACATGTAAAAAATATGACAAAACC
1 TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGT-AAAAATATGACAAAACC
* *
66516 GGTATCGAAATGACAAAACCGGTAAAGAGCTACCGAATATATTGAAAGTGTCGATACTTTAATA
65 GGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATA
66580 AGTACACATA
Statistics
Matches: 280, Mismatches: 28, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
181 46 0.16
182 157 0.56
183 77 0.28
ACGTcount: A:0.41, C:0.14, G:0.16, T:0.29
Consensus pattern (182 bp):
TGTCGATACTTTATAAAAATGTATCGATCCATAACGATATAACAGGTAAAAATATGACAAAACCG
GTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATATTGAAAGTGTCGATACTTTAATATA
AGTATCAACACTTTGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAAAG
Found at i:69043 original size:33 final size:33
Alignment explanation
Indices: 69006--69072 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
68996 AAATAGATGG
*
69006 AGTGGTGAAAGAAGTTGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGAGGTGA
69039 AGTGGTGAAAGAAGTTGAGGTGTTGAGAGGTGA
1 AGTGGTGAAAGAAGTTGAGGTGTTGAGAGGTGA
69072 A
1 A
69073 CTTAAGATGG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.00, G:0.46, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTTGAGGTGTTGAGAGGTGA
Found at i:70847 original size:19 final size:19
Alignment explanation
Indices: 70823--70871 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
70813 AATGTAGGGT
*
70823 TAATTTTGTATAATATTTA
1 TAATTTTGTATAAGATTTA
* *
70842 TAATTTTTTATACGATTTA
1 TAATTTTGTATAAGATTTA
70861 TAATTTTGTAT
1 TAATTTTGTAT
70872 GTGAATGTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:71588 original size:200 final size:198
Alignment explanation
Indices: 71222--71983 Score: 954
Period size: 200 Copynumber: 3.8 Consensus size: 198
71212 GTAAGCAGAT
71222 GTGTCGATACATTTAT-AAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
71286 TGTAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGTGAGAATAGGTCTACATAATAT
66 GGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATAT
* * * *
71351 ATCGACACTTTTGAAATTGGTGTCGATACTTTTTGTCCATAATGAATGCACAAAATGGTGAACGC
131 ATCGACAC-TTTGGAATTTGTGTCGATAC-TTTTGTCCACAATGAATGCACAAAATGGTGCACGC
71416 ATAAA
194 ATAAA
* * *
71421 GTGTCGATACATTTACAAAAAGTATTGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * * *
71486 GGTAAATTTACAATGTAATCGATATAACTATACCGGTTTTATGAGAGAATATGTCTACATAATAT
66 GGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATAT
* * * *
71551 ATCGATACTTCTGGAATTTGTGTCGATACTGTTTGTCCACAAGGAATGCCCAAAAAGGTGCAC-C
131 ATCGACACTT-TGGAATTTGTGTCGATACT-TTTGTCCACAATGAATGCACAAAATGGTGCACGC
71615 AATAAA
194 -ATAAA
* * * *
71621 GTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAGACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * ** * * * *
71686 AGTAATTTTGTAAGGTAACCGGTATAAATATATCGGTTTTATGTGAGAATAGGTCAACATAATGT
66 GGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATAT
** * *
71751 ATCGACACTTTTTAATTTTGTGTCGATACATTTTGTCCAGAATGAATGCCCAAAAAAATGGTGCA
131 ATCGACACTTTGGAA-TTTGTGTCGATAC-TTTTGTCCACAATGAATG--C-ACAAAATGGTGCA
71816 CGCATAAA
191 CGCATAAA
* * * **
71824 GTGTCGATACATTTTTAAAAAATGTCGATCCCAAAAACATCGAAACATATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
* * * * *
71889 GGTAAATTT-CAATATAATCGGTATAAATATACCGATTTTATGAGAGAATAGCTCTACAAAATGT
66 GGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATAT
*
71953 ATCGACACTTGTTGAATTTGTGTCGATACTT
131 ATCGACACTT-TGGAATTTGTGTCGATACTT
71984 GTTGAATTTG
Statistics
Matches: 486, Mismatches: 66, Indels: 20
0.85 0.12 0.03
Matches are distributed among these distances:
199 22 0.05
200 304 0.63
201 3 0.01
202 69 0.14
203 87 0.18
204 1 0.00
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (198 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
GGTAAATTTGCAATATAACCGGTATAAATATACCGGTTTTATGAGAGAATAGGTCTACATAATAT
ATCGACACTTTGGAATTTGTGTCGATACTTTTGTCCACAATGAATGCACAAAATGGTGCACGCAT
AAA
Found at i:71983 original size:21 final size:21
Alignment explanation
Indices: 71954--72004 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
71944 ACAAAATGTA
*
71954 TCGACACTTGTTGAATTTGTG
1 TCGATACTTGTTGAATTTGTG
71975 TCGATACTTGTTGAATTTGTG
1 TCGATACTTGTTGAATTTGTG
*
71996 TCAATACTT
1 TCGATACTT
72005 TTTGTCCCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.20, T:0.45
Consensus pattern (21 bp):
TCGATACTTGTTGAATTTGTG
Done.