Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008808.1 Hibiscus syriacus cultivar Beakdansim tig00111962_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: 111006
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:11387 original size:15 final size:16
Alignment explanation
Indices: 11361--11392 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
11351 CCCATTTATC
11361 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
11377 ATTTT-AAACACACTT
1 ATTTTAAAACACACTT
11392 A
1 A
11393 AAACACTTCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:13644 original size:21 final size:21
Alignment explanation
Indices: 13597--13646 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
13587 GATTCCCCTG
* *
13597 TGGGGGGAATCGGTTCCTTCA
1 TGGGGGGAATCAGTTCCCTCA
**
13618 AAGGGGGAATCAGTTCCCTCA
1 TGGGGGGAATCAGTTCCCTCA
13639 TGGGGGGA
1 TGGGGGGA
13647 TCGATTCCCT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.20, C:0.18, G:0.40, T:0.22
Consensus pattern (21 bp):
TGGGGGGAATCAGTTCCCTCA
Found at i:13654 original size:20 final size:21
Alignment explanation
Indices: 13578--13657 Score: 58
Period size: 20 Copynumber: 3.9 Consensus size: 21
13568 ACAAACCCCA
* **
13578 GGGGGTATCGATTCCC-CTGT
1 GGGGGGATCGATTCCCTCAAT
* * *
13598 GGGGGGAATCGGTTCCTTCAAA
1 GGGGGG-ATCGATTCCCTCAAT
*
13620 GGGGGAATC-AGTTCCCTC-AT
1 GGGGGGATCGA-TTCCCTCAAT
13640 GGGGGGATCGATTCCCTC
1 GGGGGGATCGATTCCCTC
13658 TGCACCAAAA
Statistics
Matches: 45, Mismatches: 11, Indels: 8
0.70 0.17 0.12
Matches are distributed among these distances:
20 21 0.47
21 18 0.40
22 6 0.13
ACGTcount: A:0.16, C:0.24, G:0.35, T:0.25
Consensus pattern (21 bp):
GGGGGGATCGATTCCCTCAAT
Found at i:21499 original size:20 final size:21
Alignment explanation
Indices: 21447--21507 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
21437 TTCCCCTGTG
21447 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
*
21470 GGGGGAATCGGTTCCCTC-AT
1 GGGGGAATCGGTTCCCTCAAA
* *
21490 GGGGGTATCGATTCCCTC
1 GGGGGAATCGGTTCCCTC
21508 TGCACCAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 17 0.49
21 2 0.06
22 3 0.09
23 13 0.37
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:25311 original size:22 final size:21
Alignment explanation
Indices: 25269--25308 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25259 GAGTTTATTT
*
25269 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
25290 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
25309 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:28027 original size:74 final size:75
Alignment explanation
Indices: 27721--28033 Score: 342
Period size: 75 Copynumber: 4.2 Consensus size: 75
27711 CTTAATCGGT
* * * * ** * * *
27721 TAAAATAAAATAGATGTTATATATTATGTTAAATTACCTACCAATTTTTTTGAAGTTTACTAATA
1 TAAAATAAAATAGGTGTTATCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATA
*
27786 ATGTAAACGG
66 ATGTAAACGA
* * **
27796 TAAAATAAAATAGGTGATACCTATTACGTTAAAATACCTATAGGTTTGTTTAAAGGTTACTAATA
1 TAAAATAAAATAGGTGTTATCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATA
* *
27861 ATGTAAATGG
66 ATGTAAACGA
* * * * * * * * *
27871 TAAAATAAAATAAGCGCTATCTATTACATTAAACTAGCTATCTGTTTGTTTAAAGGTTAATAATA
1 TAAAATAAAATAGGTGTTATCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATA
*
27936 ATGTAAA-TA
66 ATGTAAACGA
* * *
27945 GTAAAATAAAATAGGTGTTATCTATTACGTTAAAATATCTACCGGTTT-TTTAAAGGCTATTAAT
1 -TAAAATAAAATAGGTGTTATCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAAT
28009 AATGTAAACGA
65 AATGTAAACGA
28020 TAAAATAAAATAGG
1 TAAAATAAAATAGG
28034 CGCTGCCTAT
Statistics
Matches: 199, Mismatches: 37, Indels: 5
0.83 0.15 0.02
Matches are distributed among these distances:
74 36 0.18
75 163 0.82
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.36
Consensus pattern (75 bp):
TAAAATAAAATAGGTGTTATCTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATA
ATGTAAACGA
Found at i:28332 original size:155 final size:156
Alignment explanation
Indices: 28127--28406 Score: 420
Period size: 155 Copynumber: 1.8 Consensus size: 156
28117 AAATGTTAAT
* **** **
28127 AATAATGTAAACGGTAAAAATATATACAACTTAACCATTTGAAATATTTTTTTTTTAAATTTGAA
1 AATAATATAAACGGTAAAAATATATACAACTTAACCATTTGAAATATTTTTTAAAAAAATGCGAA
* *
28192 ATTAT-GAATACTTACTCTAAAAGTATGGATACTCTAAAGGTTAATAATAATGTATCCATACTTA
66 AGTATAG-ATACTTACTCTAAAAGTAAGGATACTCTAAAGGTTAATAATAATGTATCCATACTTA
28256 CTCTACAAGTATGGATATTGTTTCGTC
130 CTCTACAAGTATGGATATTGTTTCGTC
*
28283 AATAATATAAACGGT-AAAATATATACAACTTAACCGTTTGAAATATTTTTTAAAAAAATGCGAA
1 AATAATATAAACGGTAAAAATATATACAACTTAACCATTTGAAATATTTTTTAAAAAAATGCGAA
* * *
28347 AGTATAGATACTTCCTCTAAAAGTAAGTATACTCTAAATGTTAATAATAATGTATCCATA
66 AGTATAGATACTTACTCTAAAAGTAAGGATACTCTAAAGGTTAATAATAATGTATCCATA
28407 ATAATAATGT
Statistics
Matches: 110, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
155 95 0.86
156 15 0.14
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.36
Consensus pattern (156 bp):
AATAATATAAACGGTAAAAATATATACAACTTAACCATTTGAAATATTTTTTAAAAAAATGCGAA
AGTATAGATACTTACTCTAAAAGTAAGGATACTCTAAAGGTTAATAATAATGTATCCATACTTAC
TCTACAAGTATGGATATTGTTTCGTC
Found at i:28410 original size:17 final size:17
Alignment explanation
Indices: 28388--28423 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
28378 CTCTAAATGT
28388 TAATAATAATGTATCCA
1 TAATAATAATGTATCCA
28405 TAATAATAATGTATCCA
1 TAATAATAATGTATCCA
28422 TA
1 TA
28424 CTTACTCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (17 bp):
TAATAATAATGTATCCA
Found at i:28821 original size:108 final size:108
Alignment explanation
Indices: 28595--28893 Score: 339
Period size: 108 Copynumber: 2.8 Consensus size: 108
28585 TTTATTCAAA
* * * * * * * *
28595 ATAACATTATTGGGTGCAACCTAGTATGTTAATATTCATTTATAACAAAATAAGAAATTAAAATA
1 ATAACATT-TTAGATGCTACCTAATATGTTGATATT-ATTAATAACAAAATAAGTAATTAACATA
* * *
28660 TTTTGTTATTGTGAGA-TTTTAATGCCCTATCAGCTTAAATTTTG
64 TTTTGTTATTGTCAGATTTTTAAGGCCATATCAGCTTAAATTTTG
* *
28704 GTAACATTTTAGATGCTACCTAATATGTTGATAATATTAATAACAAAATAAGTAATTAACATATT
1 ATAACATTTTAGATGCTACCTAATATGTTGATATTATTAATAACAAAATAAGTAATTAACATATT
* * *
28769 TTCTTATGGTCAGATTTTTAAGGCCATGTCAGCTTAAATTTTG
66 TTGTTATTGTCAGATTTTTAAGGCCATATCAGCTTAAATTTTG
** * ** * * * *
28812 ATAGTATTTTAGGTGCTATTTAATATGTTGATATTATTGATAACAAATTAATTAATTAACCTATT
1 ATAACATTTTAGATGCTACCTAATATGTTGATATTATTAATAACAAAATAAGTAATTAACATATT
*
28877 TTGTTATTGTCGGATTT
66 TTGTTATTGTCAGATTT
28894 CTAAAGTCCC
Statistics
Matches: 159, Mismatches: 30, Indels: 3
0.83 0.16 0.02
Matches are distributed among these distances:
107 38 0.24
108 114 0.72
109 7 0.04
ACGTcount: A:0.35, C:0.09, G:0.13, T:0.42
Consensus pattern (108 bp):
ATAACATTTTAGATGCTACCTAATATGTTGATATTATTAATAACAAAATAAGTAATTAACATATT
TTGTTATTGTCAGATTTTTAAGGCCATATCAGCTTAAATTTTG
Found at i:29172 original size:217 final size:218
Alignment explanation
Indices: 28846--29289 Score: 567
Period size: 218 Copynumber: 2.0 Consensus size: 218
28836 ATGTTGATAT
* * * * * *
28846 TATTGATAACAAATTAATTAATTAACCTATTTTGTTATTGTCGGATTTCTAAAGTCCCATCAGCT
1 TATTGATAACAAATCAAGTAATTAACCAATTTTGTTATAGTAGGATTTCTAAAGCCCCATCAGCT
* * * * *
28911 TTAAAAATGCGCTACATATTAGATTAAATAAGCGTTACTTGTTATGTTA-TTATGGTTGATAATG
66 TTAAAAATGAGCTACATATTACATTAAATAAGCGCTAATTGTTATGTTATTTATAGTTGATAATG
* ** * *
28975 TTTCTAGTAATTAACATATTTTGTTATCGTC-AGATTTCTATTG-TTTCAACAGTTTAAACTTTG
131 TTTCTAGTAATTAACATATTTCGTTATCGTCGA-ATTTCTAAGGCTCT-AACAGCTTAAACTTTG
*
29038 GTAACATTTTACGTGCTACCTAATA
194 ATAACATTTTACGTGCTACCTAATA
*
29063 TATTGATAACAAATCAAGTAATTAACCAATTTTGTTATAGTATGATTTCT-AAGACCCCATCAGC
1 TATTGATAACAAATCAAGTAATTAACCAATTTTGTTATAGTAGGATTTCTAAAG-CCCCATCAG-
* * *
29127 CTTT-AAAATGAGCTACTTATTACTTTAAATTAA-CGCTAATTGTTATGTTATTTATAGTTGATT
64 CTTTAAAAATGAGCTACATATTACATTAAA-TAAGCGCTAATTGTTATGTTATTTATAGTTGATA
* *
29190 ATGTTTCTAGTAATTAACCTATTTCGTTATCGTCGAATTTCTAAGGCTCTATCAGCTTAAACTTT
128 ATGTTTCTAGTAATTAACATATTTCGTTATCGTCGAATTTCTAAGGCTCTAACAGCTTAAACTTT
* *
29255 GATAATATTTTAGGTGCTACCTAATA
193 GATAACATTTTACGTGCTACCTAATA
*
29281 TGTTGATAA
1 TATTGATAA
29290 TATAAATAAC
Statistics
Matches: 195, Mismatches: 26, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
216 3 0.02
217 88 0.45
218 101 0.52
219 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.13, T:0.42
Consensus pattern (218 bp):
TATTGATAACAAATCAAGTAATTAACCAATTTTGTTATAGTAGGATTTCTAAAGCCCCATCAGCT
TTAAAAATGAGCTACATATTACATTAAATAAGCGCTAATTGTTATGTTATTTATAGTTGATAATG
TTTCTAGTAATTAACATATTTCGTTATCGTCGAATTTCTAAGGCTCTAACAGCTTAAACTTTGAT
AACATTTTACGTGCTACCTAATA
Found at i:30042 original size:10 final size:10
Alignment explanation
Indices: 30027--30067 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
30017 TTCATCACAC
30027 CAAATTCTCT
1 CAAATTCTCT
*
30037 CAAATTTTCT
1 CAAATTCTCT
*
30047 CAATTTCTCT
1 CAAATTCTCT
*
30057 CAAATACTCT
1 CAAATTCTCT
30067 C
1 C
30068 TCTATTTAAG
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:30146 original size:17 final size:18
Alignment explanation
Indices: 30109--30149 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
30099 ATATTATGTA
*
30109 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
30127 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
30144 TTTACT
1 TTTACT
30150 AATATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:33943 original size:13 final size:15
Alignment explanation
Indices: 33909--33938 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
33899 CGTGGCGTAT
*
33909 AGCGCGGATCAGGGG
1 AGCGCGAATCAGGGG
33924 AGCGCGAATCAGGGG
1 AGCGCGAATCAGGGG
33939 CGCGATATAC
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:0.23, C:0.20, G:0.50, T:0.07
Consensus pattern (15 bp):
AGCGCGAATCAGGGG
Found at i:34566 original size:2 final size:2
Alignment explanation
Indices: 34559--34587 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
34549 TTAAGCATAT
34559 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
34588 TATCCCCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:35216 original size:126 final size:126
Alignment explanation
Indices: 34991--35229 Score: 442
Period size: 126 Copynumber: 1.9 Consensus size: 126
34981 GTGTGTAGAA
*
34991 ACTGTAGATAGAAATATGTGTAATTGGCCACTTAAGATGAATATTTGTAATTTGATATTTGGTTT
1 ACTGTAGATAGAAATATGTGTAATTGGCCACTTAAGATGAATATTTGTAATTTGATATTTGATTT
*
35056 GGTATATGGTCTGATGTTCTTTAGACTTAAGGTGATAATTGTTTCATGTGCAAAAACTGTG
66 GGTATATGGTCTGATGTTCTTTAGACTTAAGGTGATAACTGTTTCATGTGCAAAAACTGTG
*
35117 ACTGTAGTTAGAAATATGTGTAATTGGCCACTTAAGATGAATATTTGTAATTTGATATTTGATTT
1 ACTGTAGATAGAAATATGTGTAATTGGCCACTTAAGATGAATATTTGTAATTTGATATTTGATTT
*
35182 GGTATATGGTTTGATGTTCTTTAGACTTAAGGTGATAACTGTTTCATG
66 GGTATATGGTCTGATGTTCTTTAGACTTAAGGTGATAACTGTTTCATG
35230 GTTTTCAGTA
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
126 109 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.42
Consensus pattern (126 bp):
ACTGTAGATAGAAATATGTGTAATTGGCCACTTAAGATGAATATTTGTAATTTGATATTTGATTT
GGTATATGGTCTGATGTTCTTTAGACTTAAGGTGATAACTGTTTCATGTGCAAAAACTGTG
Found at i:38891 original size:16 final size:16
Alignment explanation
Indices: 38870--38900 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
38860 GTTGTTGTTT
*
38870 TTTTTTTCTTTCTCTG
1 TTTTTTCCTTTCTCTG
38886 TTTTTTCCTTTCTCT
1 TTTTTTCCTTTCTCT
38901 CCGGTTCTGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTTCCTTTCTCTG
Found at i:38925 original size:26 final size:28
Alignment explanation
Indices: 38896--38948 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 28
38886 TTTTTTCCTT
38896 TCTCTCCGG-TTCTGTC-TCTGTTTTTG
1 TCTCTCCGGTTTCTGTCTTCTGTTTTTG
* *
38922 TCTCTCTGGTTTCTGTCTTCTTTTTTT
1 TCTCTCCGGTTTCTGTCTTCTGTTTTT
38949 TTCTTTTCTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 7 0.30
28 8 0.35
ACGTcount: A:0.00, C:0.25, G:0.15, T:0.60
Consensus pattern (28 bp):
TCTCTCCGGTTTCTGTCTTCTGTTTTTG
Found at i:39365 original size:3 final size:3
Alignment explanation
Indices: 39357--39449 Score: 159
Period size: 3 Copynumber: 31.0 Consensus size: 3
39347 ATTTAATATT
39357 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
39405 TAA TAA TAA TAA TAA TGA TAA TGA CAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39450 AAAAAATATT
Statistics
Matches: 84, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 84 1.00
ACGTcount: A:0.65, C:0.01, G:0.02, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:39860 original size:40 final size:39
Alignment explanation
Indices: 39779--39919 Score: 214
Period size: 40 Copynumber: 3.6 Consensus size: 39
39769 AAGTTGAACA
* *
39779 AGTTCTTCTTATTATGAACTTCT--TCTTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTCCTTTTTCTTCAGATG
39816 AGTTCTTCTCATTATGAACTTCTCCTTTCTTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTCCTTT-TTCTTCAGATG
* *
39856 AGTTCTTCTCATTATGAACTTTTTCTTTATTCTTCAGATG
1 AGTTCTTCTCATTATGAACTTCTCCTTT-TTCTTCAGATG
39896 AGTTCTTCTCATTATGAACTTCTC
1 AGTTCTTCTCATTATGAACTTCTC
39920 TGGAAAAAAT
Statistics
Matches: 94, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
37 22 0.23
39 2 0.02
40 70 0.74
ACGTcount: A:0.19, C:0.21, G:0.10, T:0.50
Consensus pattern (39 bp):
AGTTCTTCTCATTATGAACTTCTCCTTTTTCTTCAGATG
Found at i:40190 original size:116 final size:114
Alignment explanation
Indices: 39858--40497 Score: 862
Period size: 116 Copynumber: 5.6 Consensus size: 114
39848 TTCAGATGAG
* **
39858 TTCTTCTCATTATGAACTTTTTCTTTATTCTTCAGATGAGTTCTTCTCATTATGAACT-T-CTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTCT
* ** * * * * *
39921 GGAAAAAATAATCCATCAATTGATGACTTCAGGTAAAAGGTTGAACAAA
66 GGCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
*
39970 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTCT
* * * * * *
40034 GGAAAGGCTGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GGCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
40083 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTAC
* *
40148 -CTGGCAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAA
63 TCTGGCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
* * *
40199 TTCTTCTTATTATGAATTTCTTCTTCCTTCTTCAGATGATAAGTTCTTCTCATTATGAAC-CTCC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATG---AGTTCTTCTCATTATGAACTCTAC
** * * *
40263 TCTGGCAACAATAATCCATCAAGTGATGAATTCAAACAAAAAGGTTGAACAAA
63 TCTGGCAATGATGATCCATCAAATGATGAATTCAAGC-AAAAGGTTGAACAAA
40316 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAACTCTAC
* *
40381 -CTGGCAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAA
63 TCTGGCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
*
40432 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACT-TTCTCT
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTCT
40496 GG
66 GG
40498 AAAAAATAAT
Statistics
Matches: 474, Mismatches: 39, Indels: 29
0.87 0.07 0.05
Matches are distributed among these distances:
112 58 0.12
113 109 0.23
115 3 0.01
116 200 0.42
117 100 0.21
118 3 0.01
120 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (114 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTCTACTCT
GGCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGGTTGAACAAA
Found at i:40361 original size:233 final size:229
Alignment explanation
Indices: 39858--40519 Score: 992
Period size: 233 Copynumber: 2.9 Consensus size: 229
39848 TTCAGATGAG
* **
39858 TTCTTCTCATTATGAACTTTTTCTTTATTCTTCAGAT---GAGTTCTTCTCATTATGAACT-T-C
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
* *** * * * * * *
39918 TCTGGAAAAAATAATCCATCAATTGATGACTTCAGGTAAAAGGTTGAACAAATTCTTCTCATTAT
66 -CTGGCAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTAT
*** *
39983 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAGGCTGATCC
130 GAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAATAATCC
* * ***
40048 ATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
195 ATCAAGTGATGAATTCAACAAAAAGGTTGAACAAA
40083 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
*
40148 CTGGCAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTTATTATG
66 CTGGCAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
* * * * *
40213 AATTTCTTCTTCCTTCTTCAGATGATAAGTTCTTCTCATTATGAACCTCCTCTGGCAACAATAAT
131 AACTTCTTCTTCCTTCTTCAGATG---AGTTCTTCTCATTATGAACTTTCTCTGGAAAAAATAAT
40278 CCATCAAGTGATGAATTCAAACAAAAAGGTTGAACAAA
193 CCATCAAGTGATGAATTC-AACAAAAAGGTTGAACAAA
40316 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
40381 CTGGCAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
66 CTGGCAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
40446 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAATAATCCA
131 AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAATAATCCA
40511 TCAAGTGAT
196 TCAAGTGAT
40520 AGATTTGAAT
Statistics
Matches: 395, Mismatches: 33, Indels: 13
0.90 0.07 0.03
Matches are distributed among these distances:
225 34 0.09
228 21 0.05
229 78 0.20
230 47 0.12
232 47 0.12
233 168 0.43
ACGTcount: A:0.29, C:0.20, G:0.13, T:0.38
Consensus pattern (229 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC
CTGGCAATGTTGATCCATCAAATGATGAATTTAAGCAAAAGGTTGAACAAATTCTTCTCATTATG
AACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAAATAATCCA
TCAAGTGATGAATTCAACAAAAAGGTTGAACAAA
Found at i:41359 original size:84 final size:84
Alignment explanation
Indices: 41226--41576 Score: 621
Period size: 84 Copynumber: 4.2 Consensus size: 84
41216 TTATCTTTTG
* * **
41226 ATTCGAATGATTGTTTCTGTACTTCCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
1 ATTC-AATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTAT
41291 TGAGCACATTCATCTTCTAA
65 TGAGCACATTCATCTTCTAA
*
41311 TTTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 ATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
41376 GAGCACATTCATCTTCTAA
66 GAGCACATTCATCTTCTAA
*
41395 ATTCAATGATTAGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 ATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
41460 GAGCACATTCATCTTCTAA
66 GAGCACATTCATCTTCTAA
* *
41479 ATTCAATGATGGGTTCTGTCCAACCAGATCATATAACTCAAAGAACACTTCCAGAAGATGCTATT
1 ATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
41544 GAGCACATTCATCTTCTAA
66 GAGCACATTCATCTTCTAA
41563 ATTCAATGATTGGT
1 ATTCAATGATTGGT
41577 CTAAGATATC
Statistics
Matches: 255, Mismatches: 11, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
84 252 0.99
85 3 0.01
ACGTcount: A:0.34, C:0.22, G:0.14, T:0.30
Consensus pattern (84 bp):
ATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
GAGCACATTCATCTTCTAA
Found at i:42613 original size:10 final size:10
Alignment explanation
Indices: 42598--42651 Score: 71
Period size: 10 Copynumber: 5.8 Consensus size: 10
42588 CTTGACCCCC
42598 TTTTTCTTTT
1 TTTTTCTTTT
42608 TTTTTCTTTT
1 TTTTTCTTTT
42618 TTTTTC----
1 TTTTTCTTTT
*
42624 TTTCTCTTTT
1 TTTTTCTTTT
42634 TTTTTCTTTT
1 TTTTTCTTTT
42644 TTTTTCTT
1 TTTTTCTT
42652 CAAGCATAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
6 5 0.13
10 33 0.87
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTCTTTT
Found at i:42618 original size:16 final size:16
Alignment explanation
Indices: 42597--42648 Score: 72
Period size: 16 Copynumber: 3.3 Consensus size: 16
42587 CCTTGACCCC
42597 CTTTTTCTTTT-TTTTT
1 CTTTTT-TTTTCTTTTT
*
42613 CTTTTTTTTTCTTTCT
1 CTTTTTTTTTCTTTTT
42629 CTTTTTTTTTCTTTTT
1 CTTTTTTTTTCTTTTT
42645 -TTTT
1 CTTTT
42649 CTTCAAGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
15 8 0.24
16 25 0.76
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (16 bp):
CTTTTTTTTTCTTTTT
Found at i:42626 original size:26 final size:26
Alignment explanation
Indices: 42597--42651 Score: 101
Period size: 26 Copynumber: 2.1 Consensus size: 26
42587 CCTTGACCCC
*
42597 CTTTTTCTTTTTTTTTCTTTTTTTTT
1 CTTTCTCTTTTTTTTTCTTTTTTTTT
42623 CTTTCTCTTTTTTTTTCTTTTTTTTT
1 CTTTCTCTTTTTTTTTCTTTTTTTTT
42649 CTT
1 CTT
42652 CAAGCATAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (26 bp):
CTTTCTCTTTTTTTTTCTTTTTTTTT
Found at i:54965 original size:28 final size:29
Alignment explanation
Indices: 54929--55004 Score: 90
Period size: 26 Copynumber: 2.8 Consensus size: 29
54919 GTTGTTTTTT
54929 TTTCT-TCTCTGTTTTTTTTTCTCTCCGG
1 TTTCTGTCTCTGTTTTTTTTTCTCTCCGG
* *
54957 -TTCTGTCTCTG--TTTTTGTCTCTCTGG
1 TTTCTGTCTCTGTTTTTTTTTCTCTCCGG
*
54983 TTTCTGTCT-TCTTTTTTTTTCT
1 TTTCTGTCTCTGTTTTTTTTTCT
55005 TTTCTTTCGC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
26 14 0.35
27 12 0.30
28 14 0.35
ACGTcount: A:0.00, C:0.22, G:0.12, T:0.66
Consensus pattern (29 bp):
TTTCTGTCTCTGTTTTTTTTTCTCTCCGG
Found at i:55419 original size:3 final size:3
Alignment explanation
Indices: 55411--55492 Score: 139
Period size: 3 Copynumber: 27.7 Consensus size: 3
55401 TTAATATATT
*
55411 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
55459 TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
55493 TTTAGTATCT
Statistics
Matches: 74, Mismatches: 4, Indels: 2
0.93 0.05 0.03
Matches are distributed among these distances:
2 2 0.03
3 72 0.97
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:62529 original size:19 final size:19
Alignment explanation
Indices: 62505--62542 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
62495 ATATATATCC
62505 TCGTTATGTCCTATTTAAG
1 TCGTTATGTCCTATTTAAG
62524 TCGTTATGTCCTATTTAAG
1 TCGTTATGTCCTATTTAAG
62543 CCCATATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGTTATGTCCTATTTAAG
Found at i:62673 original size:30 final size:30
Alignment explanation
Indices: 62637--62739 Score: 179
Period size: 30 Copynumber: 3.4 Consensus size: 30
62627 TCCGAAGGAC
62637 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
62667 CTATCCAGAGGTCATAAATATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
62697 CTATCCAGAGGTCATTAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
62727 CTATCCATAGGTC
1 CTATCCAGAGGTC
62740 CCGAAGAACC
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 69 1.00
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.26
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:62756 original size:30 final size:30
Alignment explanation
Indices: 62637--62766 Score: 98
Period size: 30 Copynumber: 4.3 Consensus size: 30
62627 TCCGAAGGAC
* ** * *
62637 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCATAGGTCACGAAGAACCTAGGTAA
* ** * * *
62667 CTATCCAGAGGTCATAAATATCCTCGGTAA
1 CTATCCATAGGTCACGAAGAACCTAGGTAA
* ** * *
62697 CTATCCAGAGGTCATTAAGATCCTCGGTAA
1 CTATCCATAGGTCACGAAGAACCTAGGTAA
*
62727 CTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCATAGGTCACGAAGAACCTAGGT-AA
62758 CTATCCATA
1 CTATCCATA
62767 TGTTCCTTAG
Statistics
Matches: 90, Mismatches: 9, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
30 79 0.88
31 11 0.12
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.25
Consensus pattern (30 bp):
CTATCCATAGGTCACGAAGAACCTAGGTAA
Found at i:62756 original size:60 final size:61
Alignment explanation
Indices: 62637--62764 Score: 177
Period size: 60 Copynumber: 2.1 Consensus size: 61
62627 TCCGAAGGAC
* * * *
62637 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCATAAATATCCTCGGT-AA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
* * * *
62697 CTATCCAGAGGTCATTAAGATCCTCGGTAACTATCCATAGGTCCCGAAGAACCTAGGTAAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
62758 CTATCCA
1 CTATCCA
62765 TATGTTCCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
60 50 0.85
61 9 0.15
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (61 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAACTATCCAGAGGTCACAAAGAACCTAGGTAAA
Found at i:62779 original size:31 final size:31
Alignment explanation
Indices: 62725--62817 Score: 98
Period size: 31 Copynumber: 3.0 Consensus size: 31
62715 GATCCTCGGT
* *
62725 AACTATCCATAGGTCCCGAAGAACCTAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* **
62756 AACTATCCATATGTTCCTTAGAACATAGGTA
1 AACTATCCATATGTCCCGAAGAACATAGGTA
* * *
62787 TACTGTCCATATGTCTCGAA-AGACATAGGTA
1 AACTATCCATATGTCCCGAAGA-ACATAGGTA
62818 GTTCTTTGAC
Statistics
Matches: 50, Mismatches: 11, Indels: 2
0.79 0.17 0.03
Matches are distributed among these distances:
30 1 0.02
31 49 0.98
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.27
Consensus pattern (31 bp):
AACTATCCATATGTCCCGAAGAACATAGGTA
Found at i:63001 original size:4 final size:4
Alignment explanation
Indices: 62992--63020 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
62982 ATATAACCAT
62992 TACA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA T
63021 GTCATCATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:63374 original size:2 final size:2
Alignment explanation
Indices: 63362--63408 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
63352 TACACAACTC
63362 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
63403 AT AT AT
1 AT AT AT
63409 TGTAACATGT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:68856 original size:22 final size:21
Alignment explanation
Indices: 68817--68857 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
68807 GATTTTTTTG
*
68817 CATATGATGTTATTATGAACA
1 CATATGATGTTATCATGAACA
*
68838 CATATGATTTTTATCATGAA
1 CATATGA-TGTTATCATGAA
68858 TGTTATTTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.37, C:0.10, G:0.12, T:0.41
Consensus pattern (21 bp):
CATATGATGTTATCATGAACA
Found at i:69095 original size:60 final size:60
Alignment explanation
Indices: 69003--69188 Score: 266
Period size: 60 Copynumber: 3.1 Consensus size: 60
68993 CAGCAGGCTG
* * * * * * * *
69003 CATATTCGGGA-ATACACTAAATGATACCTAGTATATATGGTGGGCACAACCTTATGTGT
1 CATATTCGAGAGATATACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
* *
69062 CATATTCGAGAGATGTACTTAAGGATACCTAGTACAGATGGTGAACACGACCTTATGTGT
1 CATATTCGAGAGATATACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
*
69122 CATATTCGGGAGATATACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
1 CATATTCGAGAGATATACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
69182 CATATTC
1 CATATTC
69189 AAGATTGCAC
Statistics
Matches: 113, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
59 10 0.09
60 103 0.91
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (60 bp):
CATATTCGAGAGATATACTTAAGGATACCTAGTACAGATGGTGGACACGACCTTATGTGT
Found at i:69282 original size:20 final size:20
Alignment explanation
Indices: 69254--69296 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
69244 TATATTGGGC
* * *
69254 TATTGTCTATTGTTTATGGT
1 TATTATCTATAGTATATGGT
69274 TATTATCTATAGTATATGGT
1 TATTATCTATAGTATATGGT
69294 TAT
1 TAT
69297 GGAATAATGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.23, C:0.05, G:0.16, T:0.56
Consensus pattern (20 bp):
TATTATCTATAGTATATGGT
Found at i:69361 original size:44 final size:44
Alignment explanation
Indices: 69293--69404 Score: 163
Period size: 44 Copynumber: 2.5 Consensus size: 44
69283 TAGTATATGG
* * *
69293 TTATGGAATAATGGAAAGTGTATTGGTAAAATAAGCTTACAAGC
1 TTATGGAAAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGC
*
69337 TTATGGAAAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAAAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGC
*
69381 TTATGGGATAAATGGTAAG-ATATT
1 TTAT-GGAAAAATGGTAAGTATATT
69405 TTATCTTATT
Statistics
Matches: 62, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
44 49 0.79
45 13 0.21
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (44 bp):
TTATGGAAAAATGGTAAGTATATTGGTAAAATAAGCTTACAAGC
Found at i:74592 original size:13 final size:13
Alignment explanation
Indices: 74574--74599 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
74564 CATGTGGATC
74574 ATTTCACGGTTTA
1 ATTTCACGGTTTA
74587 ATTTCACGGTTTA
1 ATTTCACGGTTTA
74600 CAAAAAAGAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.46
Consensus pattern (13 bp):
ATTTCACGGTTTA
Found at i:76572 original size:29 final size:29
Alignment explanation
Indices: 76540--76633 Score: 104
Period size: 29 Copynumber: 3.2 Consensus size: 29
76530 TAATTTCGTT
*
76540 AAAATTTTGCTCGACTCGTGCTCATTAAG
1 AAAATTTTGCTCGACTCGTGCTCGTTAAG
76569 AAAATTTGTTGCTCGACTCGTTGCTCGTT---
1 AAAA-TT-TTGCTCGACTCG-TGCTCGTTAAG
* * *
76598 AAAATTTTACTCGACTCGTTCCCGTTAAG
1 AAAATTTTGCTCGACTCGTGCTCGTTAAG
76627 AAAATTT
1 AAAATTT
76634 GTTGCTCAAC
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
26 6 0.11
27 11 0.20
28 2 0.04
29 15 0.27
30 2 0.04
31 12 0.22
32 7 0.13
ACGTcount: A:0.27, C:0.20, G:0.16, T:0.37
Consensus pattern (29 bp):
AAAATTTTGCTCGACTCGTGCTCGTTAAG
Found at i:76584 original size:31 final size:31
Alignment explanation
Indices: 76546--76640 Score: 110
Period size: 31 Copynumber: 3.2 Consensus size: 31
76536 CGTTAAAATT
*
76546 TTGCTCGACTCGTGCTCATTAAGAAAATTTG
1 TTGCTCGACTCGTGCTCGTTAAGAAAATTTG
76577 TTGCTCGACTCGTTGCTCGTT---AAAA-TT-
1 TTGCTCGACTCG-TGCTCGTTAAGAAAATTTG
* * *
76604 TTACTCGACTCGTTCCCGTTAAGAAAATTTG
1 TTGCTCGACTCGTGCTCGTTAAGAAAATTTG
76635 TTGCTC
1 TTGCTC
76641 AACCCGTCAC
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
26 6 0.11
27 11 0.21
28 2 0.04
29 8 0.15
30 2 0.04
31 17 0.32
32 7 0.13
ACGTcount: A:0.22, C:0.22, G:0.18, T:0.38
Consensus pattern (31 bp):
TTGCTCGACTCGTGCTCGTTAAGAAAATTTG
Found at i:76600 original size:58 final size:58
Alignment explanation
Indices: 76535--76658 Score: 176
Period size: 58 Copynumber: 2.1 Consensus size: 58
76525 CTCGTTAATT
* * * * **
76535 TCGTTAAAATTTTGCTCGACTCGTGCTCATTAAGAAAATTTGTTGCTCGACTCGTTGC
1 TCGTTAAAATTTTACTCGACTCGTGCCCATTAAGAAAATTTGTTGCTCAACCCGTCAC
* *
76593 TCGTTAAAATTTTACTCGACTCGTTCCCGTTAAGAAAATTTGTTGCTCAACCCGTCAC
1 TCGTTAAAATTTTACTCGACTCGTGCCCATTAAGAAAATTTGTTGCTCAACCCGTCAC
76651 TCGTTAAA
1 TCGTTAAA
76659 CTCATTAAGT
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (58 bp):
TCGTTAAAATTTTACTCGACTCGTGCCCATTAAGAAAATTTGTTGCTCAACCCGTCAC
Found at i:76839 original size:5 final size:5
Alignment explanation
Indices: 76829--76866 Score: 58
Period size: 5 Copynumber: 7.6 Consensus size: 5
76819 GGCTAAACAC
* *
76829 TAAAA TAAAA TTAAA TACAA TAAAA TAAAA TAAAA TAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TAA
76867 TAATTAGGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (5 bp):
TAAAA
Found at i:76852 original size:15 final size:15
Alignment explanation
Indices: 76829--76872 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
76819 GGCTAAACAC
76829 TAAAATAAAATTAAA
1 TAAAATAAAATTAAA
* *
76844 TACAATAAAATAAAA
1 TAAAATAAAATTAAA
76859 TAAAATAATAATTA
1 TAAAATAA-AATTA
76873 GGGTTTGATA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.27
Consensus pattern (15 bp):
TAAAATAAAATTAAA
Found at i:76958 original size:28 final size:28
Alignment explanation
Indices: 76899--76960 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
76889 TGTTGCAAAA
*
76899 TAATAATTATTAATTATTAATTAATAATT
1 TAAT-ATTATTAATTATTAATTAATAACT
* *
76928 TAATATTTTTAATTATTTATTAGA-AACT
1 TAATATTATTAATTATTAATTA-ATAACT
76956 TAATA
1 TAATA
76961 GATTAGTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 24 0.83
29 5 0.17
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (28 bp):
TAATATTATTAATTATTAATTAATAACT
Found at i:85919 original size:20 final size:20
Alignment explanation
Indices: 85894--85934 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
85884 CCAAACTAAA
85894 CAATACTCAAATTTGACTAT
1 CAATACTCAAATTTGACTAT
85914 CAATACTCAAATTTGACTAT
1 CAATACTCAAATTTGACTAT
85934 C
1 C
85935 TCATTTACAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.39, C:0.22, G:0.05, T:0.34
Consensus pattern (20 bp):
CAATACTCAAATTTGACTAT
Found at i:101295 original size:75 final size:75
Alignment explanation
Indices: 101111--101316 Score: 256
Period size: 74 Copynumber: 2.8 Consensus size: 75
101101 CAAAGCCAAA
* * * * **
101111 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATT-CCCCCTAAACAGT
101176 TTGGCTCCGAG
65 TTGGCTCCGAG
* * *
101187 ATTTCCAGAATGCTCGGAGGGAACTGATT-CCCCCATAGGAGGAACCGATTCCCCCTAAACATTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
* *
101251 TTGTTCCGAG
66 TGGCTCCGAG
* *
101261 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCCCA-AGG-GGTACCGATTCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCT
101317 TGTTCAACGG
Statistics
Matches: 113, Mismatches: 15, Indels: 6
0.84 0.11 0.04
Matches are distributed among these distances:
74 59 0.52
75 24 0.21
76 30 0.27
ACGTcount: A:0.24, C:0.30, G:0.23, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:109867 original size:54 final size:54
Alignment explanation
Indices: 109780--109903 Score: 176
Period size: 54 Copynumber: 2.3 Consensus size: 54
109770 CCCCATAGGA
* ** *
109780 GGAACCGATTCCCCCCTGAATGGTTTGGCTCCGAGATTTCCAGAATGCTCGGAG
1 GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAG
* * * *
109834 GGAACCGATTCCCCCCTAAACATTTTTGTTCCGAGAATTCCAGTATGCTCGGAG
1 GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAG
109888 GGAACCGATTCCCCCC
1 GGAACCGATTCCCCCC
109904 CAAGGGGTAC
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 62 1.00
ACGTcount: A:0.22, C:0.31, G:0.23, T:0.24
Consensus pattern (54 bp):
GGAACCGATTCCCCCCTAAACAGTTTGGCTCCGAGAATTCCAGAATGCTCGGAG
Done.