Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000798.1 Hibiscus syriacus cultivar Beakdansim tig00001549_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: 118331
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:4937 original size:19 final size:20
Alignment explanation
Indices: 4901--4940 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
4891 CAAAATATCA
*
4901 TTCATGATAAATATCATATG
1 TTCATGATAAACATCATATG
4921 TTCATGAT-AACATCATATG
1 TTCATGATAAACATCATATG
4940 T
1 T
4941 AACGATCAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.38, C:0.12, G:0.10, T:0.40
Consensus pattern (20 bp):
TTCATGATAAACATCATATG
Found at i:14417 original size:10 final size:10
Alignment explanation
Indices: 14404--14437 Score: 68
Period size: 10 Copynumber: 3.4 Consensus size: 10
14394 TTGATTTTGT
14404 TTCTTTTTAA
1 TTCTTTTTAA
14414 TTCTTTTTAA
1 TTCTTTTTAA
14424 TTCTTTTTAA
1 TTCTTTTTAA
14434 TTCT
1 TTCT
14438 GACATTTACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (10 bp):
TTCTTTTTAA
Found at i:14635 original size:20 final size:20
Alignment explanation
Indices: 14592--14636 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
14582 TTAACTTTTT
* *
14592 CTTTTCTCTTTCATCCTTAG
1 CTTTTCTATTTCATCCTTAA
**
14612 CTTTTCTATTTCATTTTTAA
1 CTTTTCTATTTCATCCTTAA
14632 CTTTT
1 CTTTT
14637 ACTTTTCTCT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.13, C:0.22, G:0.02, T:0.62
Consensus pattern (20 bp):
CTTTTCTATTTCATCCTTAA
Found at i:17881 original size:23 final size:23
Alignment explanation
Indices: 17851--17899 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
17841 TGGTGGTTGG
*
17851 TTTAATGG-ATGTTTAAACTTTAT
1 TTTAATGGTATATTT-AACTTTAT
*
17874 TTTAATGGTATATTTAAGTTTAT
1 TTTAATGGTATATTTAACTTTAT
17897 TTT
1 TTT
17900 GGTTCTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (23 bp):
TTTAATGGTATATTTAACTTTAT
Found at i:19365 original size:37 final size:36
Alignment explanation
Indices: 19245--19434 Score: 105
Period size: 38 Copynumber: 5.1 Consensus size: 36
19235 CCATTAAAAC
* *
19245 AAAAGTTTTATCTCACTAGAGATAGCTTTTT-CTCAA
1 AAAAATTTTATCTCACTAGAGACAG-TTTTTCCTCAA
* * * * * *
19281 AAAATATTTTTTGTCTCACTCGAGACAATTTATCTTGAA
1 AAAA-A--TTTTATCTCACTAGAGACAGTTTTTCCTCAA
*
19320 ACAAAATTTTATCTCACTAGAGAGAGTTTTTCCTCAA
1 A-AAAATTTTATCTCACTAGAGACAGTTTTTCCTCAA
* * ** * * * *
19357 AAACAATTTTTTTCACACCCGAGACAATTTCTCTTGAA
1 AAA-AA-TTTTATCTCACTAGAGACAGTTTTTCCTCAA
* * *
19395 ACAAAATTTTTATCTCACTCGAGATA-TCTTTCCTCAA
1 A-AAAA-TTTTATCTCACTAGAGACAGTTTTTCCTCAA
19432 AAA
1 AAA
19435 CAAGTTTCGT
Statistics
Matches: 114, Mismatches: 32, Indels: 16
0.70 0.20 0.10
Matches are distributed among these distances:
36 8 0.07
37 35 0.31
38 45 0.39
39 23 0.20
40 3 0.03
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (36 bp):
AAAAATTTTATCTCACTAGAGACAGTTTTTCCTCAA
Found at i:19392 original size:75 final size:76
Alignment explanation
Indices: 19241--19641 Score: 305
Period size: 75 Copynumber: 5.4 Consensus size: 76
19231 TATTCCATTA
*
19241 AAACAAAAGTTTTATCTCACTAGAGATAGCTTTTT-CTCAAAAA-ATATTTTTTGTCTCACTCGA
1 AAACAAAAGTTTTATCTCACTAGAGATAG-TTTTTCCTCAAAAACA-ATTTTTT-TCACACTCGA
*
19304 GACAATTTATCTTG
63 GACAATTTCTCTTG
* *
19318 AAACAAAA-TTTTATCTCACTAGAGAGAGTTTTTCCTCAAAAACAATTTTTTTCACACCCGAGAC
1 AAACAAAAGTTTTATCTCACTAGAGATAGTTTTTCCTCAAAAACAATTTTTTTCACACTCGAGAC
19382 AATTTCTCTTG
66 AATTTCTCTTG
* * * * ** *
19393 AAACAAAATTTTTATCTCACTCGAGATA-TCTTTCCTCAAAAACAAGTTTCGTCACACTTGAGAC
1 AAACAAAAGTTTTATCTCACTAGAGATAGTTTTTCCTCAAAAACAATTTTTTTCACACTCGAGAC
* *
19457 AATCTC-CCTG
66 AATTTCTCTTG
** * * ** *** * *
19467 AAACAAAA-TTACATCTCACTTGAGATA-TTTCTCCT--TGAA-AATTTCCATCTCACTGGATG-
1 AAACAAAAGTTTTATCTCACTAGAGATAGTTTTTCCTCAAAAACAATTTTTTTCACACTCGA-GA
19526 CAATTTCTCTTG
65 CAATTTCTCTTG
* * * * ** * *
19538 AAACAAAA-TTTCATCTCCCTTGAGATA-TTTTACCT--TGAA-AATTTTCTGTCTCACTCGAGA
1 AAACAAAAGTTTTATCTCACTAGAGATAGTTTTTCCTCAAAAACAATTTT-TTTCACACTCGAGA
*
19598 CATTTTCTCTTG
65 CAATTTCTCTTG
* * * *
19610 AAACAAAAATTTCATCTCCCTTGAGATA-TTTT
1 AAACAAAAGTTTTATCTCACTAGAGATAGTTTT
19642 CCCTTGGAAA
Statistics
Matches: 279, Mismatches: 37, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
70 19 0.07
71 47 0.17
72 28 0.10
73 45 0.16
74 11 0.04
75 69 0.25
76 51 0.18
77 9 0.03
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.36
Consensus pattern (76 bp):
AAACAAAAGTTTTATCTCACTAGAGATAGTTTTTCCTCAAAAACAATTTTTTTCACACTCGAGAC
AATTTCTCTTG
Found at i:19633 original size:144 final size:140
Alignment explanation
Indices: 19286--19829 Score: 452
Period size: 144 Copynumber: 3.8 Consensus size: 140
19276 CTCAAAAAAT
* * * ** * * *
19286 ATTTTTTGTCTCACTCGAGACAATTTATCTTGAAACAAAATTTTATCTCACTAGAGAGAGTTTTT
1 ATTTTCTGTCTCACTTGAGACAATTTCTCTTGAAACAAAATTACATCTCCCTTGAGATA--TTTT
** ** * * * * *
19351 CCTCAAAAACAATTTTTTTCACACCCGAGACAATTTCTCTTGAAACAAAATTTTTATCTCACTCG
64 CCT--TGAA-AA-TTTCATCTCACTCGAGACAATTTCTCTTGAAACAAAA-TTTCATCTCCCTTG
**
19416 AGATATCTTTCCTCAAAAACA
124 AGATAT-TTTCCT--TGAA-A
* * * * *
19437 AGTTTC-GTCACACTTGAGACAATCTC-CCTGAAACAAAATTACATCTCACTTGAGATATTTCTC
1 ATTTTCTGTCTCACTTGAGACAATTTCTCTTGAAACAAAATTACATCTCCCTTGAGATATTT-TC
*
19500 CTTGAAAATTTCCATCTCACTGGATG-CAATTTCTCTTGAAACAAAATTTCATCTCCCTTGAGAT
65 CTTGAAAATTT-CATCTCACTCGA-GACAATTTCTCTTGAAACAAAATTTCATCTCCCTTGAGAT
19564 ATTTTACCTTGAAA
128 ATTTT-CCTTGAAA
* * *
19578 ATTTTCTGTCTCACTCGAGACATTTTCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTTTC
1 ATTTTCTGTCTCACTTGAGACAATTTCTCTTGAAAC-AAAATTACATCTCCCTTGAGATATTTT-
* * *
19643 CCTTGGAAATATTTTC-TCTCACCCGAGACAATTTCTC-TCAAACAAAATTTCATTTCCCTTGAG
64 CCTT-GAAA-A-TTTCATCTCACTCGAGACAATTTCTCTTGAAACAAAATTTCATCTCCCTTGAG
19706 ATATTTTCCCTTG-AA
126 ATATTTT-CCTTGAAA
* * * * *
19721 ATTTTTTGTCTCACTTGAGACAGTTTCTCTCGAAAGAAAATTGCATCTCCTCCTTTGAGATATTT
1 ATTTTCTGTCTCACTTGAGACAATTTCTCTTGAAACAAAATTACATCT-C-CC-TTGAGATATTT
* * ** *
19786 TCCTTGAAAAGTTTTATCTCACTCGAAACGGTTTCTCTCGAAAC
63 TCCTTGAAAA-TTTCATCTCACTCGAGACAATTTCTCTTGAAAC
19830 GGTTTCTCTC
Statistics
Matches: 326, Mismatches: 50, Indels: 41
0.78 0.12 0.10
Matches are distributed among these distances:
141 6 0.02
142 33 0.10
143 66 0.20
144 98 0.30
145 62 0.19
146 5 0.02
147 6 0.02
148 4 0.01
149 26 0.08
150 16 0.05
151 4 0.01
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (140 bp):
ATTTTCTGTCTCACTTGAGACAATTTCTCTTGAAACAAAATTACATCTCCCTTGAGATATTTTCC
TTGAAAATTTCATCTCACTCGAGACAATTTCTCTTGAAACAAAATTTCATCTCCCTTGAGATATT
TTCCTTGAAA
Found at i:19638 original size:73 final size:71
Alignment explanation
Indices: 19286--19829 Score: 451
Period size: 73 Copynumber: 7.5 Consensus size: 71
19276 CTCAAAAAAT
* * * * * *
19286 ATTTTTTGTCTCACTCGAGACAATTTATCTTGAAACAAAATTTTATCTCACTAGAGAGAGTTTTT
1 ATTTTCTGTCTCACTCGAGACAATTTCTCTTGAAACAAAATTTCATCTCCCTTGAGATA--TTTT
**
19351 CCTCAAAAACA
64 CCT--TGAA-A
* * * * * *
19362 ATTTT-TTTCACACCCGAGACAATTTCTCTTGAAACAAAATTTTTATCTCACTCGAGATATCTTT
1 ATTTTCTGTCTCACTCGAGACAATTTCTCTTGAAACAAAA-TTTCATCTCCCTTGAGATAT-TTT
**
19426 CCTCAAAAACA
64 CCT--TGAA-A
* * * * * * *
19437 AGTTTC-GTCACACTTGAGACAATCTC-CCTGAAACAAAATTACATCTCACTTGAGATATTTCTC
1 ATTTTCTGTCTCACTCGAGACAATTTCTCTTGAAACAAAATTTCATCTCCCTTGAGATATTT-TC
19500 CTTGAAA
65 CTTGAAA
** *
19507 A-TTTCCATCTCACTGGATG-CAATTTCTCTTGAAACAAAATTTCATCTCCCTTGAGATATTTTA
1 ATTTTCTGTCTCACTCGA-GACAATTTCTCTTGAAACAAAATTTCATCTCCCTTGAGATATTTT-
19570 CCTTGAAA
64 CCTTGAAA
*
19578 ATTTTCTGTCTCACTCGAGACATTTTCTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTTTC
1 ATTTTCTGTCTCACTCGAGACAATTTCTCTTGAAAC-AAAATTTCATCTCCCTTGAGATATTTT-
19643 CCTTGGAAA
64 CCTT-GAAA
* * *
19652 TATTTTC--TCTCACCCGAGACAATTTCTC-TCAAACAAAATTTCATTTCCCTTGAGATATTTTC
1 -ATTTTCTGTCTCACTCGAGACAATTTCTCTTGAAACAAAATTTCATCTCCCTTGAGATATTTT-
19714 CCTTG-AA
64 CCTTGAAA
* * * * * *
19721 ATTTTTTGTCTCACTTGAGACAGTTTCTCTCGAAAGAAAATTGCATCTCCTCCTTTGAGATATTT
1 ATTTTCTGTCTCACTCGAGACAATTTCTCTTGAAACAAAATTTCATCT-C-CC-TTGAGATATTT
19786 TCCTTGAAA
63 TCCTTGAAA
* * * ** *
19795 AGTTT-TATCTCACTCGAAACGGTTTCTCTCGAAAC
1 ATTTTCTGTCTCACTCGAGACAATTTCTCTTGAAAC
19830 GGTTTCTCTC
Statistics
Matches: 400, Mismatches: 48, Indels: 43
0.81 0.10 0.09
Matches are distributed among these distances:
68 5 0.01
69 6 0.01
70 36 0.09
71 88 0.22
72 36 0.09
73 103 0.26
74 34 0.09
75 70 0.17
76 22 0.05
ACGTcount: A:0.30, C:0.23, G:0.10, T:0.37
Consensus pattern (71 bp):
ATTTTCTGTCTCACTCGAGACAATTTCTCTTGAAACAAAATTTCATCTCCCTTGAGATATTTTCC
TTGAAA
Found at i:19646 original size:15 final size:16
Alignment explanation
Indices: 19626--19658 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
19616 AAATTTCATC
*
19626 TCCCTT-GAGATATTT
1 TCCCTTGGAAATATTT
19641 TCCCTTGGAAATATTT
1 TCCCTTGGAAATATTT
19657 TC
1 TC
19659 TCTCACCCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (16 bp):
TCCCTTGGAAATATTT
Found at i:19852 original size:13 final size:15
Alignment explanation
Indices: 19807--19859 Score: 106
Period size: 15 Copynumber: 3.5 Consensus size: 15
19797 TTTTATCTCA
19807 CTCGAAACGGTTTCT
1 CTCGAAACGGTTTCT
19822 CTCGAAACGGTTTCT
1 CTCGAAACGGTTTCT
19837 CTCGAAACGGTTTCT
1 CTCGAAACGGTTTCT
19852 CTCGAAAC
1 CTCGAAAC
19860 AAATTTTATC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 38 1.00
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (15 bp):
CTCGAAACGGTTTCT
Found at i:28983 original size:18 final size:19
Alignment explanation
Indices: 28942--28983 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
28932 GTAAGATTAA
*
28942 AGATAATTAAAGACAATGT
1 AGATAATTAAAGACAAAGT
28961 A-ATAATTAAAGACAAAG-
1 AGATAATTAAAGACAAAGT
28978 AGATAA
1 AGATAA
28984 ATATGTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.60, C:0.05, G:0.14, T:0.21
Consensus pattern (19 bp):
AGATAATTAAAGACAAAGT
Found at i:31078 original size:17 final size:17
Alignment explanation
Indices: 31056--31094 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
31046 CTCTCAATAC
31056 TTTTTTG-CTCACATCTT
1 TTTTTTGACTCAC-TCTT
*
31073 TTTTTTGAGTCACTCTT
1 TTTTTTGACTCACTCTT
31090 TTTTT
1 TTTTT
31095 CTCACAAGTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.10, C:0.18, G:0.08, T:0.64
Consensus pattern (17 bp):
TTTTTTGACTCACTCTT
Found at i:31405 original size:21 final size:21
Alignment explanation
Indices: 31379--31446 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
31369 GAAGAAGTGG
31379 AAGTAGATGAATTACCTTGGT
1 AAGTAGATGAATTACCTTGGT
*
31400 AAGTAGATGAAATACCTTGGT
1 AAGTAGATGAATTACCTTGGT
* * *
31421 AAATAGGTG-ATGTACTTTGGT
1 AAGTAGATGAAT-TACCTTGGT
31442 AAGTA
1 AAGTA
31447 TCTCTAGAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
20 1 0.03
21 39 0.98
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.32
Consensus pattern (21 bp):
AAGTAGATGAATTACCTTGGT
Found at i:54576 original size:18 final size:18
Alignment explanation
Indices: 54553--54594 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
54543 GAGAGTTCTA
*
54553 TTTATTTTTGATGTTG-TT
1 TTTATTATT-ATGTTGATT
*
54571 TTTATTATTATTTTGATT
1 TTTATTATTATGTTGATT
54589 TTTATT
1 TTTATT
54595 CATGTTAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.74
Consensus pattern (18 bp):
TTTATTATTATGTTGATT
Found at i:57703 original size:18 final size:18
Alignment explanation
Indices: 57682--57762 Score: 100
Period size: 18 Copynumber: 4.7 Consensus size: 18
57672 ATTTAGGGTC
57682 TTTTTATTATTTTAAGAT
1 TTTTTATTATTTTAAGAT
*
57700 TTTTTATTATTTTAGGAT
1 TTTTTATTATTTTAAGAT
57718 TTTTTATTA-TTTAA-A-
1 TTTTTATTATTTTAAGAT
*
57733 TTTTTATTATTTGT--GAA
1 TTTTTATTATTT-TAAGAT
57750 TTTTTATTATTTT
1 TTTTTATTATTTT
57763 TATTAATGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
15 9 0.16
16 5 0.09
17 17 0.30
18 26 0.46
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTTTATTATTTTAAGAT
Found at i:58846 original size:28 final size:26
Alignment explanation
Indices: 58814--58881 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 26
58804 TTAATTAATT
*
58814 AATAAATCAATAATCAATTATTATATAA
1 AATAAATCAATAATCAA-TA-AATATAA
*
58842 AATAAA-CTAATAATTAATAAATATAA
1 AATAAATC-AATAATCAATAAATATAA
58868 AATTAAATCAATAA
1 AA-TAAATCAATAA
58882 ATTTATCATA
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
26 8 0.23
27 12 0.34
28 15 0.43
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (26 bp):
AATAAATCAATAATCAATAAATATAA
Found at i:60794 original size:24 final size:24
Alignment explanation
Indices: 60745--60794 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
60735 GGCAAACTTG
*
60745 AACTTATAAAATTTTAGGAGTGTA
1 AACTTATAAAATTTTAGGAGGGTA
*
60769 AACTTATGAAATTTTA-GAGGGATA
1 AACTTATAAAATTTTAGGAGGG-TA
60793 AA
1 AA
60795 ATAAATTTTC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.44, C:0.04, G:0.18, T:0.34
Consensus pattern (24 bp):
AACTTATAAAATTTTAGGAGGGTA
Found at i:62969 original size:12 final size:12
Alignment explanation
Indices: 62952--62978 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
62942 GAGCAAAGAT
62952 GAAATAGAGGAA
1 GAAATAGAGGAA
62964 GAAATAGAGGAA
1 GAAATAGAGGAA
62976 GAA
1 GAA
62979 CAATGAGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.33, T:0.07
Consensus pattern (12 bp):
GAAATAGAGGAA
Found at i:63216 original size:60 final size:63
Alignment explanation
Indices: 63117--63247 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 63
63107 TTGGGTTTTT
* * *
63117 GAAACCACTTAAGAGTGGTTTTAAAACCCTTGAGGCAATGTCAAAACTCCACATATG-GTTTA
1 GAAACCCCTTAAGAGTGGTTTTAAAACCCTTAAGACAATGTCAAAACTCCACATATGAGTTTA
* * * *
63179 GAAACCCCTT-AG-GTGGTTTTGAAACCAC-TAAGACAATGTCAAAACTTCACTTATGATTTTA
1 GAAACCCCTTAAGAGTGGTTTTAAAACC-CTTAAGACAATGTCAAAACTCCACATATGAGTTTA
63240 -AAACCCCT
1 GAAACCCCT
63248 GGTTTTGAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
60 44 0.73
61 7 0.12
62 9 0.15
ACGTcount: A:0.35, C:0.21, G:0.15, T:0.28
Consensus pattern (63 bp):
GAAACCCCTTAAGAGTGGTTTTAAAACCCTTAAGACAATGTCAAAACTCCACATATGAGTTTA
Found at i:63577 original size:39 final size:39
Alignment explanation
Indices: 63527--63605 Score: 122
Period size: 39 Copynumber: 2.0 Consensus size: 39
63517 CAAATAAACC
*
63527 AACCATGGAAGGAAAGCACAAGGGAAGTGAAGATCACCA
1 AACCATAGAAGGAAAGCACAAGGGAAGTGAAGATCACCA
* * *
63566 AACCATAGAAGGTAAGCACAAGGGACGTGAATATCACCA
1 AACCATAGAAGGAAAGCACAAGGGAAGTGAAGATCACCA
63605 A
1 A
63606 CTTATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.46, C:0.19, G:0.25, T:0.10
Consensus pattern (39 bp):
AACCATAGAAGGAAAGCACAAGGGAAGTGAAGATCACCA
Found at i:68177 original size:53 final size:53
Alignment explanation
Indices: 68048--68239 Score: 226
Period size: 53 Copynumber: 3.6 Consensus size: 53
68038 GCACCCACGA
* * * *
68048 TATTCATAATGAGTTTGTGAAATTGCCATTTCAGCACTATGTGTGCATCCATGG
1 TATTCATAATGAGTTTGTG-AATTACCATTTCGGCTCTATGTGTGCATTCATGG
* ** * * * *
68102 TATTCATAATCAGTTTACGAATTACCAATTCGGCTTTATGTGTGTATTCATAG
1 TATTCATAATGAGTTTGTGAATTACCATTTCGGCTCTATGTGTGCATTCATGG
* *
68155 TATTTATAATGAGTTTGTGAATTATCATTTCGG-TACTATGTGTGCA-TCTATGG
1 TATTCATAATGAGTTTGTGAATTACCATTTCGGCT-CTATGTGTGCATTC-ATGG
68208 TATTCATAATGAGTTTGTGAATTACCATTTCG
1 TATTCATAATGAGTTTGTGAATTACCATTTCG
68240 TTACCTTAGT
Statistics
Matches: 114, Mismatches: 22, Indels: 5
0.81 0.16 0.04
Matches are distributed among these distances:
52 3 0.03
53 95 0.83
54 16 0.14
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.42
Consensus pattern (53 bp):
TATTCATAATGAGTTTGTGAATTACCATTTCGGCTCTATGTGTGCATTCATGG
Found at i:68198 original size:106 final size:107
Alignment explanation
Indices: 68048--68239 Score: 287
Period size: 106 Copynumber: 1.8 Consensus size: 107
68038 GCACCCACGA
*
68048 TATTCATAATGAGTTTGTGAAATTGCCATTTCAGCACTATGTGTGCATCCATGGTATTCATAATC
1 TATTCATAATGAGTTTGTGAAATTACCATTTCAGCACTATGTGTGCATCCATGGTATTCATAATC
68113 AGTTTACGAATTACCAATTCGGCTTTATGTGTGTATTCATAG
66 AGTTTACGAATTACCAATTCGGCTTTATGTGTGTATTCATAG
* * * * * *
68155 TATTTATAATGAGTTTGTG-AATTATCATTTCGGTACTATGTGTGCATCTATGGTATTCATAATG
1 TATTCATAATGAGTTTGTGAAATTACCATTTCAGCACTATGTGTGCATCCATGGTATTCATAATC
** *
68219 AGTTTGTGAATTACCATTTCG
66 AGTTTACGAATTACCAATTCG
68240 TTACCTTAGT
Statistics
Matches: 75, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
106 57 0.76
107 18 0.24
ACGTcount: A:0.27, C:0.14, G:0.18, T:0.42
Consensus pattern (107 bp):
TATTCATAATGAGTTTGTGAAATTACCATTTCAGCACTATGTGTGCATCCATGGTATTCATAATC
AGTTTACGAATTACCAATTCGGCTTTATGTGTGTATTCATAG
Found at i:75139 original size:19 final size:19
Alignment explanation
Indices: 75115--75153 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
75105 TAGCTTGCTT
75115 TTGACATTGCAATAATCAG
1 TTGACATTGCAATAATCAG
75134 TTGACATTGCAATAATCAG
1 TTGACATTGCAATAATCAG
75153 T
1 T
75154 ATAAAGTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (19 bp):
TTGACATTGCAATAATCAG
Found at i:76569 original size:6 final size:6
Alignment explanation
Indices: 76558--76592 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
76548 CCCTGAATCG
* *
76558 ATCTCT ATCTCT ATCTCT ATCTCG ATCTCT GTCTC
1 ATCTCT ATCTCT ATCTCT ATCTCT ATCTCT ATCTC
76593 GGTCCTCATC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.14, C:0.34, G:0.06, T:0.46
Consensus pattern (6 bp):
ATCTCT
Found at i:76575 original size:12 final size:12
Alignment explanation
Indices: 76555--76593 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
76545 ATCCCCTGAA
76555 TCGATCTCTATC
1 TCGATCTCTATC
*
76567 TCTATCTCTATC
1 TCGATCTCTATC
*
76579 TCGATCTCTGTC
1 TCGATCTCTATC
76591 TCG
1 TCG
76594 GTCCTCATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.13, C:0.33, G:0.10, T:0.44
Consensus pattern (12 bp):
TCGATCTCTATC
Found at i:81418 original size:6 final size:6
Alignment explanation
Indices: 81403--81457 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
81393 TTGAGTTCAT
* * *
81403 AAAAGA AAAA-A GAAAAGA AAATGGA AAAAGA AAAAGA AAAATA GAAAGA
1 AAAAGA AAAAGA -AAAAGA AAA-AGA AAAAGA AAAAGA AAAAGA AAAAGA
81452 AAAAGA
1 AAAAGA
81458 GATAAAGAGA
Statistics
Matches: 40, Mismatches: 6, Indels: 6
0.77 0.12 0.12
Matches are distributed among these distances:
5 1 0.03
6 33 0.82
7 6 0.15
ACGTcount: A:0.78, C:0.00, G:0.18, T:0.04
Consensus pattern (6 bp):
AAAAGA
Found at i:82682 original size:17 final size:18
Alignment explanation
Indices: 82647--82684 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
82637 CTTTGTCACG
82647 AGATAAAGACTCAAACAA
1 AGATAAAGACTCAAACAA
82665 AGATAAAGACTC-AACAA
1 AGATAAAGACTCAAACAA
82682 AGA
1 AGA
82685 GAATGAAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.61, C:0.16, G:0.13, T:0.11
Consensus pattern (18 bp):
AGATAAAGACTCAAACAA
Found at i:83215 original size:116 final size:115
Alignment explanation
Indices: 83001--83434 Score: 324
Period size: 116 Copynumber: 3.7 Consensus size: 115
82991 AGAAAATAGT
** * * * * *
83001 TCAACATTTCCGGTGGAGGGGTTTATAATGAGAAGAATTCGTCTGATGAGGGAGAAGAA-TTTCA
1 TCAACATTTCTAGTGGAAGGGTTCATAATGAGAAGAACTCATCTGATGAAGGAGAAGAAGTTT-A
* * * * * *
83065 TAATGAGAAGAACTTTTTCAACCTTGGTTTGTCCATTACAGAAAGAGGTGGA
65 TAATGAGAAAAACTTGTTCAA-CTTTGCTCGTCCATAACAGAAAGAGGTGGA
* * * *
83117 TCAATATTTCTAGTGGAAGGGTTCATAATGAGAAGAACTCATCTGATAAAGGAAAATAAGTTTAT
1 TCAACATTTCTAGTGGAAGGGTTCATAATGAGAAGAACTCATCTGATGAAGGAGAAGAAGTTTAT
* * * *
83182 AATGAGAAAAACTTGTTCAACGTTTGCTCGTCCATAAAAAAAAGATGCGGA
66 AATGAGAAAAACTTGTTCAAC-TTTGCTCGTCCATAACAGAAAGAGGTGGA
* * ** * * * * *
83233 TTAACATTTCAAACGGAAGAGTACATAATGATAAGAGCTTC-TCTGATG-AGAGATAAGAAGTTT
1 TCAACATTTCTAGTGGAAGGGTTCATAATGAGAAGAAC-TCATCTGATGAAG-GAGAAGAAGTTT
* * * * **
83296 CTAATGATAAGAACTTGTTCAAACTTAT-CTCATCCACCACAG-AAGAAGGTGGA
64 ATAATGAGAAAAACTTGTTC-AACTT-TGCTCGTCCATAACAGAAAG-AGGTGGA
* * * * * * *
83349 TCACCATCTCT-GATGGAA-GGTTCATAATGAGAAAAAACTTATCCGATGAGGGAGAAGAAGTTC
1 TCAACATTTCTAG-TGGAAGGGTTCATAATGAG-AAGAACTCATCTGATGAAGGAGAAGAAGTTT
* *
83412 CTTATGAGAAAAACTTGTTCAAC
64 ATAATGAGAAAAACTTGTTCAAC
83435 ATTTATTCTT
Statistics
Matches: 245, Mismatches: 62, Indels: 23
0.74 0.19 0.07
Matches are distributed among these distances:
115 20 0.08
116 215 0.88
117 10 0.04
ACGTcount: A:0.37, C:0.14, G:0.22, T:0.27
Consensus pattern (115 bp):
TCAACATTTCTAGTGGAAGGGTTCATAATGAGAAGAACTCATCTGATGAAGGAGAAGAAGTTTAT
AATGAGAAAAACTTGTTCAACTTTGCTCGTCCATAACAGAAAGAGGTGGA
Found at i:83538 original size:44 final size:44
Alignment explanation
Indices: 83443--83553 Score: 132
Period size: 44 Copynumber: 2.5 Consensus size: 44
83433 ACATTTATTC
* * * ** **
83443 TTCCATCATATAAGAAGTTGGATTAACATCAACATTTTGTTTGA
1 TTCCATCATATAAGGAGTTGGATCAACATCAAAATTTCATTCAA
* *
83487 TTTCATCACATAAGGAGTTGGATCAACATCAAAATTTCATTCAA
1 TTCCATCATATAAGGAGTTGGATCAACATCAAAATTTCATTCAA
*
83531 TTCCATCATATAAGGTGTTGGAT
1 TTCCATCATATAAGGAGTTGGAT
83554 TCTCACTTGG
Statistics
Matches: 55, Mismatches: 12, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
44 55 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.36
Consensus pattern (44 bp):
TTCCATCATATAAGGAGTTGGATCAACATCAAAATTTCATTCAA
Found at i:85696 original size:17 final size:18
Alignment explanation
Indices: 85664--85697 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
85654 TTGTATCTTG
85664 AATTTATTTCTTCTTTTC
1 AATTTATTTCTTCTTTTC
85682 AATTTATTT-TTCTTTT
1 AATTTATTTCTTCTTTT
85698 AATATATGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.71
Consensus pattern (18 bp):
AATTTATTTCTTCTTTTC
Found at i:85805 original size:17 final size:18
Alignment explanation
Indices: 85783--85822 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
85773 AACTTTATTT
*
85783 CCTTTGATT-TTTAATTA
1 CCTTTGATTATTCAATTA
*
85800 CCTTTGATTATTCATTTA
1 CCTTTGATTATTCAATTA
85818 CCTTT
1 CCTTT
85823 ATATGTATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.20, C:0.17, G:0.05, T:0.57
Consensus pattern (18 bp):
CCTTTGATTATTCAATTA
Found at i:85888 original size:31 final size:31
Alignment explanation
Indices: 85845--85914 Score: 122
Period size: 31 Copynumber: 2.3 Consensus size: 31
85835 TTGCTGATTA
* *
85845 TTTAGCTTTCTTCATCTTTTCTTTTATGCCC
1 TTTAACTTTCTTCATCTTTTCTTTTACGCCC
85876 TTTAACTTTCTTCATCTTTTCTTTTACGCCC
1 TTTAACTTTCTTCATCTTTTCTTTTACGCCC
85907 TTTAACTT
1 TTTAACTT
85915 CCTACCGTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.13, C:0.26, G:0.04, T:0.57
Consensus pattern (31 bp):
TTTAACTTTCTTCATCTTTTCTTTTACGCCC
Found at i:89051 original size:58 final size:58
Alignment explanation
Indices: 88988--89552 Score: 753
Period size: 58 Copynumber: 9.8 Consensus size: 58
88978 ATGGCACTAA
* * *
88988 GTGTGCAAAAAGCGAAGAAATTCATACTAAGTGTATGAATTTCCGAATTAGGCACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
89046 GTGTGCAAAAAGCTAAGAAATTCATATTAAGTGTGTGAAATTT-CGTATTGGGAACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATG-AATTTCCGTATTGGGCACTTT
* * * *
89104 GTGTGTAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTTCGAATTAGGCACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
89162 GTGTGCAAAAAGCTAAGAAATTCATATTAAGTGTGTGAATTTTCGTATTGGGAACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * * *
89220 GTGTGCAAAATA-TTAAGAAATTCATATTAAGTGTGTGTGAATTTCCGTATTAGGCACTTT
1 GTGTGCAAAA-AGCTAAGAAATTCATACTAA--GTGTATGAATTTCCGTATTGGGCACTTT
* * * *
89280 GTATGCAAAAAGCTAAAAAATTCATACTAAGAGTATGAATTTCCATATTGGGCACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* ** *
89338 GTGTGCAAAAAGTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGGCAATTT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
89396 GTGTACAAAAAGTTAAGAAATTCATACTAAGTGTATGAATATCCGTATTGGGCACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* *
89454 GTGTGCAAAAAGCTAAGAAATTCATATTAAGTGTATGAATTTCCGTA-TGGGCACTAT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
89511 GTGTG-TAGAA-CTAAGAAATTCATACTAAATGTATGAATTTCC
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCC
89553 ATATGGGAAA
Statistics
Matches: 449, Mismatches: 52, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
55 30 0.07
56 3 0.01
57 19 0.04
58 341 0.76
59 7 0.02
60 49 0.11
ACGTcount: A:0.35, C:0.11, G:0.20, T:0.34
Consensus pattern (58 bp):
GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:89399 original size:234 final size:232
Alignment explanation
Indices: 88988--89561 Score: 793
Period size: 234 Copynumber: 2.5 Consensus size: 232
88978 ATGGCACTAA
* * *
88988 GTGTGCAAAAAGCGAAGAAATTCATACTAAGTGTATGAATTTCCGAATTAGGCACTTTGTGTGCA
1 GTGTGCAAAAAGCTAAGAAATTCATATTAAGTGTATGAATTTCCGTATTAGGCACTTTGTGTGCA
* * * * *
89053 AAAAGCTAAGAAATTCATATTAAGTGTGTGAAATTT-CGTATTGGGAACTTTGTGTGTAAAAAGC
66 AAAAGCTAAGAAATTCATACTAAGAGTATG-AATTTCCATATTGGGAACTTTGTGTGCAAAAAGC
* *
89117 TAAGAAATTCATACTAAGTGTATGAATTTTCGAATTAGGCACTTTGTGTGCAAAAAGCTAAGAAA
130 TAAGAAATTCATACTAAGTGTATGAATTTTCGAATTAGGCAATTTGTGTACAAAAAGCTAAGAAA
* * * *
89182 TTCATATTAAGTGTGTGAATTTTCGTATTGGGAACTTT
195 TTCATACTAAGTGTATGAATATCCGTATTGGGAACTTT
* * *
89220 GTGTGCAAAATA-TTAAGAAATTCATATTAAGTGTGTGTGAATTTCCGTATTAGGCACTTTGTAT
1 GTGTGCAAAA-AGCTAAGAAATTCATATTAA--GTGTATGAATTTCCGTATTAGGCACTTTGTGT
* *
89284 GCAAAAAGCTAAAAAATTCATACTAAGAGTATGAATTTCCATATTGGGCACTTTGTGTGCAAAAA
63 GCAAAAAGCTAAGAAATTCATACTAAGAGTATGAATTTCCATATTGGGAACTTTGTGTGCAAAAA
* * * * *
89349 GTTAAGAAATTCATACTAAGTGTATGAATTTTTGTATTGGGCAATTTGTGTACAAAAAGTTAAGA
128 GCTAAGAAATTCATACTAAGTGTATGAATTTTCGAATTAGGCAATTTGTGTACAAAAAGCTAAGA
*
89414 AATTCATACTAAGTGTATGAATATCCGTATTGGGCACTTT
193 AATTCATACTAAGTGTATGAATATCCGTATTGGGAACTTT
* * *
89454 GTGTGCAAAAAGCTAAGAAATTCATATTAAGTGTATGAATTTCCGTA-TGGGCACTATGTGTG-T
1 GTGTGCAAAAAGCTAAGAAATTCATATTAAGTGTATGAATTTCCGTATTAGGCACTTTGTGTGCA
*
89517 AGAA-CTAAGAAATTCATACTAA-ATGTATGAATTTCCATA-TGGGAA
66 AAAAGCTAAGAAATTCATACTAAGA-GTATGAATTTCCATATTGGGAA
89562 ATATATGTAC
Statistics
Matches: 302, Mismatches: 34, Indels: 16
0.86 0.10 0.05
Matches are distributed among these distances:
228 6 0.02
229 32 0.11
230 3 0.01
231 12 0.04
232 41 0.14
233 7 0.02
234 201 0.67
ACGTcount: A:0.36, C:0.11, G:0.20, T:0.34
Consensus pattern (232 bp):
GTGTGCAAAAAGCTAAGAAATTCATATTAAGTGTATGAATTTCCGTATTAGGCACTTTGTGTGCA
AAAAGCTAAGAAATTCATACTAAGAGTATGAATTTCCATATTGGGAACTTTGTGTGCAAAAAGCT
AAGAAATTCATACTAAGTGTATGAATTTTCGAATTAGGCAATTTGTGTACAAAAAGCTAAGAAAT
TCATACTAAGTGTATGAATATCCGTATTGGGAACTTT
Found at i:89895 original size:68 final size:67
Alignment explanation
Indices: 89786--89997 Score: 223
Period size: 68 Copynumber: 3.1 Consensus size: 67
89776 TCTAATTGTT
* * * * *
89786 CATTTGACATAA-ATGTGTCAATCATGCCAGTTAGATGAAAGGCTAGGTTCTTTTGTGGCATAAC
1 CATTTGACA-AACATGTGTCAATCATG-CAGTTAGATGAAAGGATAAGTGCCTTTGAGGCATAAC
89850 TGTG
64 TGTG
* * *
89854 CATTTGATAGAA-TTGTGTCAATCATGTCAGTTAGATGAAAGGATAAGTGCCTTTGAGGCCTAAC
1 CATTTGACA-AACATGTGTCAATCATG-CAGTTAGATGAAAGGATAAGTGCCTTTGAGGCATAAC
89918 TGTG
64 TGTG
* * ** * *
89922 GATTTGACAAACATGTGTCAATCATGCAAGTTAGACGAAAGTCTAAGTGCCTTTGAGGCCTAATT
1 CATTTGACAAACATGTGTCAATCATGC-AGTTAGATGAAAGGATAAGTGCCTTTGAGGCATAACT
89987 GTG
65 GTG
*
89990 TA-TTGACA
1 CATTTGACA
89998 GAAAGGTGGT
Statistics
Matches: 124, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
67 9 0.07
68 115 0.93
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.32
Consensus pattern (67 bp):
CATTTGACAAACATGTGTCAATCATGCAGTTAGATGAAAGGATAAGTGCCTTTGAGGCATAACTG
TG
Found at i:94624 original size:58 final size:58
Alignment explanation
Indices: 94559--94817 Score: 412
Period size: 58 Copynumber: 4.5 Consensus size: 58
94549 ATTGCACTAA
*
94559 GTGTGCAAAAAGCTAAGAAATTCATAATAAGTGTATGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
*
94617 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTGTGAATTTCCGTATTGGGCACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
94675 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTGTGAATTTCCCTATTGGGTACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
* * *
94733 GTGTGCAAAAAGGTAAGACATTCATACTAAGTGTATGAAATTT-CATATTGGGCACTTT
1 GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATG-AATTTCCGTATTGGGCACTTT
* *
94791 GTGTGTAAAAAGTTAAGAAATTCATAC
1 GTGTGCAAAAAGCTAAGAAATTCATAC
94818 CCAAAAGATA
Statistics
Matches: 188, Mismatches: 12, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
58 183 0.97
59 5 0.03
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (58 bp):
GTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTT
Found at i:94829 original size:22 final size:22
Alignment explanation
Indices: 94798--94839 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
94788 TTTGTGTGTA
*
94798 AAAAGTTAAGAAATTCATACCC
1 AAAAGATAAGAAATTCATACCC
94820 AAAAGATAAGAAATTCATAC
1 AAAAGATAAGAAATTCATAC
94840 TAAGTGTGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.14, G:0.10, T:0.21
Consensus pattern (22 bp):
AAAAGATAAGAAATTCATACCC
Found at i:94830 original size:80 final size:82
Alignment explanation
Indices: 94740--94899 Score: 243
Period size: 82 Copynumber: 2.0 Consensus size: 82
94730 TTTGTGTGCA
* *
94740 AAAAGGTAAGACATTCATACTAAGTGTATG-AAATTT-CATATTGGGCACTTTGTGTGTAAAAAG
1 AAAAGATAAGAAATTCATACTAAGTGTATGTAAATTTCCATATTGGGCACTTTGTGTGTAAAAAG
*
94803 TTAAGAAATTCATACCC
66 CTAAGAAATTCATACCC
* * * *
94820 AAAAGATAAGAAATTCATACTAAGTGTGTGTGAATTTCCGTATTGGGCACTTTGTGTGTCAAAAG
1 AAAAGATAAGAAATTCATACTAAGTGTATGTAAATTTCCATATTGGGCACTTTGTGTGTAAAAAG
94885 CTAAGAAATTCATAC
66 CTAAGAAATTCATAC
94900 TAAGTGTATG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
80 27 0.38
81 5 0.07
82 39 0.55
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (82 bp):
AAAAGATAAGAAATTCATACTAAGTGTATGTAAATTTCCATATTGGGCACTTTGTGTGTAAAAAG
CTAAGAAATTCATACCC
Found at i:94932 original size:140 final size:138
Alignment explanation
Indices: 94682--94957 Score: 428
Period size: 140 Copynumber: 2.0 Consensus size: 138
94672 TTTGTGTGCA
* * *
94682 AAAAGCTAAGAAATTCATACTAAGTGTGTGAATTTCCCTATTGGGTACTTTGTGTGCAAAAAGGT
1 AAAAGATAAGAAATTCATACTAAGTGTGTGAATTTCCCTATTGGGCACTTTGTGTGCAAAAAGCT
* * **
94747 AAGACATTCATACTAAGTGTATGAAATTTCATATTGGGCACTTTGTGTGTAAAAAGTTAAGAAAT
66 AAGAAATTCATACTAAGTGTATGAAATTTCATATTGGGCACTTTGTGTGCAAAAAACTAAGAAAT
94812 TCATACCC
131 TCATACCC
*
94820 AAAAGATAAGAAATTCATACTAAGTGTGTGTGAATTTCCGTATTGGGCACTTTGTGTGTC-AAAA
1 AAAAGATAAGAAATTCATACTAA--GTGTGTGAATTTCCCTATTGGGCACTTTGTGTG-CAAAAA
* *
94884 GCTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCAAAAAACTAAGA
63 GCTAAGAAATTCATACTAAGTGTATGAAATTTCATATTGGGCACTTTGTGTGCAAAAAACTAAGA
94949 AATTCATAC
128 AATTCATAC
94958 TAAGTGTATG
Statistics
Matches: 125, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
138 22 0.18
140 102 0.82
141 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.33
Consensus pattern (138 bp):
AAAAGATAAGAAATTCATACTAAGTGTGTGAATTTCCCTATTGGGCACTTTGTGTGCAAAAAGCT
AAGAAATTCATACTAAGTGTATGAAATTTCATATTGGGCACTTTGTGTGCAAAAAACTAAGAAAT
TCATACCC
Found at i:94935 original size:58 final size:57
Alignment explanation
Indices: 94819--95033 Score: 299
Period size: 58 Copynumber: 3.7 Consensus size: 57
94809 AATTCATACC
* *
94819 CAAAAGATAAGAAATTCATACTAAGTGTGTGTGAATTTCCGTATTGGGCACTTTGTGTG
1 CAAAAGCTAAGAAATTCATACTAA--GTGTATGAATTTCCGTATTGGGCACTTTGTGTG
*
94878 TCAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTG
1 -CAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTG
* *
94936 CAAAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTA-TGGGCACTATGTGTG
1 C-AAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTG
* * * *
94993 CAGAA-CTAAGAAATTGATACTAAATGTATGAATTTTCGTAT
1 CAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTAT
95034 GGGAAATATA
Statistics
Matches: 143, Mismatches: 10, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
55 32 0.22
56 3 0.02
57 16 0.11
58 69 0.48
60 23 0.16
ACGTcount: A:0.34, C:0.12, G:0.20, T:0.33
Consensus pattern (57 bp):
CAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATTGGGCACTTTGTGTG
Found at i:94966 original size:198 final size:195
Alignment explanation
Indices: 94624--94992 Score: 589
Period size: 198 Copynumber: 1.9 Consensus size: 195
94614 TTTGTGTGCA
*
94624 AAAAGCTAAGAAATTCATACTAAGTGTGTGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGCT
1 AAAAGATAAGAAATTCATACTAAGTGTGTGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGCT
* * ** *
94689 AAGAAATTCATACTAAGTGTGTGAATTTCCCTATTGGGTACTTTGTGTGCAAAAAGGTAAGACAT
66 AAGAAATTCATACTAAGTGTATGAATTTCCCTATTGGGCACTTTGTGTGCAAAAAACTAAGAAAT
*
94754 TCATACTAAGTGTATGAAATTT-CATATTGGGCACTTTGTGTGTAAAAAGTTAAGAAATTCATAC
131 TCATACTAAGTGTATG-AATTTCCATA-TGGGCACTATGTGTGTAAAAAGTTAAGAAATTCATAC
94818 CC
194 CC
94820 AAAAGATAAGAAATTCATACTAAGTGTGTGTGAATTTCCGTATTGGGCACTTTGTGTGTC-AAAA
1 AAAAGATAAGAAATTCATACTAA--GTGTGTGAATTTCCGTATTGGGCACTTTGTGTG-CAAAAA
* *
94884 GCTAAGAAATTCATACTAAGTGTATGAATTTTCGTATTGGGCACTTTGTGTGCAAAAAACTAAGA
63 GCTAAGAAATTCATACTAAGTGTATGAATTTCCCTATTGGGCACTTTGTGTGCAAAAAACTAAGA
*
94949 AATTCATACTAAGTGTATGAATTTCCGTATGGGCACTATGTGTG
128 AATTCATACTAAGTGTATGAATTTCCATATGGGCACTATGTGTG
94993 CAGAACTAAG
Statistics
Matches: 159, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
196 22 0.14
197 19 0.12
198 117 0.74
199 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.33
Consensus pattern (195 bp):
AAAAGATAAGAAATTCATACTAAGTGTGTGAATTTCCGTATTGGGCACTTTGTGTGCAAAAAGCT
AAGAAATTCATACTAAGTGTATGAATTTCCCTATTGGGCACTTTGTGTGCAAAAAACTAAGAAAT
TCATACTAAGTGTATGAATTTCCATATGGGCACTATGTGTGTAAAAAGTTAAGAAATTCATACCC
Found at i:95363 original size:68 final size:68
Alignment explanation
Indices: 95251--95510 Score: 371
Period size: 68 Copynumber: 3.9 Consensus size: 68
95241 CAATATTAAT
*
95251 GGCCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCTAGTTAGATGAAAGGTTAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAAGTGCCTT
95316 TGA
66 TGA
* *
95319 GGCCTAACTGTGCATTTGACATAAATGTGTCAATCATGCCAGTTAGATGAAAGGATAAGTGCCTT
1 GGCCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAAGTGCCTT
95384 TGA
66 TGA
* * * * **
95387 GGCCTAACTGTGCATTTGACAGACATGTATCAATCATGCCAATTAGATG-AAGGCTAAGTTTCTT
1 GGCCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAAGTGCCTT
95451 TGA
66 TGA
* * * * * *
95454 GGCCAAACTGTGCA-TTGACAGAAAGGTGTCAATTAGGCTAGTTAGATGAACGGTTAA
1 GGCCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAA
95511 AGACCGTTGA
Statistics
Matches: 171, Mismatches: 20, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
66 27 0.16
67 34 0.20
68 110 0.64
ACGTcount: A:0.31, C:0.16, G:0.24, T:0.29
Consensus pattern (68 bp):
GGCCTAACTGTGCATTTGACAGAAATGTGTCAATCATGCCAGTTAGATGAAAGGTTAAGTGCCTT
TGA
Found at i:95708 original size:49 final size:49
Alignment explanation
Indices: 95654--95769 Score: 196
Period size: 49 Copynumber: 2.4 Consensus size: 49
95644 TGCATAAGTA
* *
95654 GTATGAAAGGATGTCATATAGATATAAAATGTATAATAATGCATGATTG
1 GTATGAATGGATGTCATATAGATATAAAATGTACAATAATGCATGATTG
* *
95703 GTATGAATGGATGTCATATAGATATAAAATTTACAATAATGCATGATTT
1 GTATGAATGGATGTCATATAGATATAAAATGTACAATAATGCATGATTG
95752 GTATGAATGGATGTCATA
1 GTATGAATGGATGTCATA
95770 AAGGCAAAAC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 63 1.00
ACGTcount: A:0.41, C:0.05, G:0.20, T:0.34
Consensus pattern (49 bp):
GTATGAATGGATGTCATATAGATATAAAATGTACAATAATGCATGATTG
Found at i:96800 original size:15 final size:15
Alignment explanation
Indices: 96776--96805 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
96766 CATCATCGTG
96776 TAAATATTGATATTT
1 TAAATATTGATATTT
*
96791 TAAATTTTGATATTT
1 TAAATATTGATATTT
96806 GTATCAACCT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.57
Consensus pattern (15 bp):
TAAATATTGATATTT
Found at i:101959 original size:19 final size:19
Alignment explanation
Indices: 101935--102008 Score: 103
Period size: 19 Copynumber: 3.7 Consensus size: 19
101925 TCAGAACTCC
101935 AGGGGGTATCGATTCCCCT
1 AGGGGGTATCGATTCCCCT
101954 AGGGGGTATCGATTCCCCT
1 AGGGGGTATCGATTCCCCT
* *
101973 AGGGGGAATCGGTTCCCCTT
1 AGGGGGTATCGATTCCCC-T
101993 CAAGGGGGTATCGATT
1 --AGGGGGTATCGATT
102009 ACCTCTGCCC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
19 35 0.73
20 1 0.02
22 12 0.25
ACGTcount: A:0.18, C:0.23, G:0.34, T:0.26
Consensus pattern (19 bp):
AGGGGGTATCGATTCCCCT
Found at i:105230 original size:16 final size:17
Alignment explanation
Indices: 105198--105230 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
105188 AATTTCTAAT
105198 TTTTGGTACCCAAATTC
1 TTTTGGTACCCAAATTC
*
105215 TTTTGG-ACCCATATTC
1 TTTTGGTACCCAAATTC
105231 ATTAGTTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.42
Consensus pattern (17 bp):
TTTTGGTACCCAAATTC
Found at i:110730 original size:22 final size:22
Alignment explanation
Indices: 110703--110747 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
110693 TTGATCATTG
*
110703 TATATATGATTTTTATCATGAA
1 TATATATGATGTTTATCATGAA
*
110725 TATATATGATGTTTATTATGAA
1 TATATATGATGTTTATCATGAA
110747 T
1 T
110748 GTTACTTCAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.36, C:0.02, G:0.11, T:0.51
Consensus pattern (22 bp):
TATATATGATGTTTATCATGAA
Found at i:111006 original size:61 final size:61
Alignment explanation
Indices: 110896--111099 Score: 221
Period size: 61 Copynumber: 3.3 Consensus size: 61
110886 GCATGTTTAT
* * ** *
110896 ATTAGCACTAGTGTGTAAGAACACTAGGTGTAGGTGGTGAGCACAACCTTATGTGTAATATTCGG
1 ATTAGCACTAGAGTGT-A-AAC-CTA-GTGTAGGTGGTGGGCATGACCTTATGTTTAATATTCGG
* **
110961 ATTAGCACTAGAGTGTAAACCTAGTGTAGGTGGTGGGCATGACCTTATGTTTCATATTTAG
1 ATTAGCACTAGAGTGTAAACCTAGTGTAGGTGGTGGGCATGACCTTATGTTTAATATTCGG
* * * * * * *
111022 ATCAACACTACAGTGTAAACCTAATGTAGGTTGTGGGCCTGACCTTATGTTTAATA-TCGA
1 ATTAGCACTAGAGTGTAAACCTAGTGTAGGTGGTGGGCATGACCTTATGTTTAATATTCGG
*
111082 ATTAGCACTAGAGCGTAA
1 ATTAGCACTAGAGTGTAA
111100 GCTTTGTGCA
Statistics
Matches: 117, Mismatches: 22, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
60 15 0.13
61 80 0.68
62 3 0.03
63 3 0.03
64 1 0.01
65 15 0.13
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (61 bp):
ATTAGCACTAGAGTGTAAACCTAGTGTAGGTGGTGGGCATGACCTTATGTTTAATATTCGG
Found at i:112582 original size:28 final size:28
Alignment explanation
Indices: 112550--112629 Score: 160
Period size: 28 Copynumber: 2.9 Consensus size: 28
112540 GCTAAGCTAC
112550 TTAAAAAGGACTAAACCTAAAATTCTAA
1 TTAAAAAGGACTAAACCTAAAATTCTAA
112578 TTAAAAAGGACTAAACCTAAAATTCTAA
1 TTAAAAAGGACTAAACCTAAAATTCTAA
112606 TTAAAAAGGACTAAACCTAAAATT
1 TTAAAAAGGACTAAACCTAAAATT
112630 AAATATTCAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 52 1.00
ACGTcount: A:0.54, C:0.14, G:0.07, T:0.25
Consensus pattern (28 bp):
TTAAAAAGGACTAAACCTAAAATTCTAA
Found at i:113244 original size:4 final size:4
Alignment explanation
Indices: 113221--113280 Score: 52
Period size: 4 Copynumber: 15.0 Consensus size: 4
113211 TATACCCAAA
* ** *
113221 AAAT AAA- AAA- AAAT AGAAT AAAT ATAAT TAAT ATCT ATAT AAAT AAAT
1 AAAT AAAT AAAT AAAT A-AAT AAAT A-AAT AAAT AAAT AAAT AAAT AAAT
113269 AAAT AAAT AAAT
1 AAAT AAAT AAAT
113281 GCAATAAAAC
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
3 6 0.13
4 34 0.72
5 7 0.15
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (4 bp):
AAAT
Done.