Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006152.1 Hibiscus syriacus cultivar Beakdansim tig00014614_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: 66445
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:241 original size:24 final size:23
Alignment explanation
Indices: 214--261 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
204 TTTTTGGGTG
214 AAATGAATTAACTATTTTTCATGA
1 AAAT-AATTAACTATTTTTCATGA
*
238 AAATACTTAACTATTTTTCATGA
1 AAATAATTAACTATTTTTCATGA
261 A
1 A
262 TAGAGATGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.42, C:0.10, G:0.06, T:0.42
Consensus pattern (23 bp):
AAATAATTAACTATTTTTCATGA
Found at i:5421 original size:23 final size:23
Alignment explanation
Indices: 5395--5444 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
5385 ACTTTTTGGG
*
5395 TGAAATGAATTAACTATTTTTCA
1 TGAAAAGAATTAACTATTTTTCA
* *
5418 TGAAAAGACTTAACTATTTTTTA
1 TGAAAAGAATTAACTATTTTTCA
5441 TGAA
1 TGAA
5445 TAGAGATGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.10, T:0.42
Consensus pattern (23 bp):
TGAAAAGAATTAACTATTTTTCA
Found at i:13312 original size:35 final size:36
Alignment explanation
Indices: 13281--13357 Score: 91
Period size: 36 Copynumber: 2.1 Consensus size: 36
13271 ATAACAATAC
13281 CCTCACAGTGTTGAGGTTCGTAACTAGAACAAGTCT
1 CCTCACAGTGTTGAGGTTCGTAACTAGAACAAGTCT
* * * * *
13317 CTTGACAGTGTTGAGTTTCGTAATTGGAACAAAAGTCT
1 CCTCACAGTGTTGAGGTTCGTAACTAGAAC--AAGTCT
13355 CCT
1 CCT
13358 GATAGTCTAC
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
36 25 0.76
38 8 0.24
ACGTcount: A:0.27, C:0.19, G:0.22, T:0.31
Consensus pattern (36 bp):
CCTCACAGTGTTGAGGTTCGTAACTAGAACAAGTCT
Found at i:15156 original size:12 final size:12
Alignment explanation
Indices: 15139--15164 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15129 GCGGCATTTG
15139 TTCCCAAATTGT
1 TTCCCAAATTGT
15151 TTCCCAAATTGT
1 TTCCCAAATTGT
15163 TT
1 TT
15165 ATTAATAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (12 bp):
TTCCCAAATTGT
Found at i:21289 original size:222 final size:222
Alignment explanation
Indices: 20903--21348 Score: 865
Period size: 222 Copynumber: 2.0 Consensus size: 222
20893 TCGCAAAAGG
20903 TTTAGAAGAGCGATATGGGGAAGGATGATATGTACTGCGAATTTGTTTGGGAAGAAGACAAATAT
1 TTTAGAAGAGCGATATGGGGAAGGATGATATGTACTGCGAATTTGTTTGGGAAGAAGACAAATAT
20968 CACAAGAGAAAGATGCAGGATTTTTATCAATGAAGAGTTTGGGAAACAACTTTGCAAGATAGAAA
66 CACAAGAGAAAGATGCAGGATTTTTATCAATGAAGAGTTTGGGAAACAACTTTGCAAGATAGAAA
*
21033 TAATTAGGATGACCTAACCTAAAATGCCATAAAACAATCTCAGTAGAAACATCATTAGATGATGG
131 AAATTAGGATGACCTAACCTAAAATGCCATAAAACAATCTCAGTAGAAACATCATTAGATGATGG
21098 AAATATCGAAACAATACTAGAGTTTGC
196 AAATATCGAAACAATACTAGAGTTTGC
* *
21125 TTTAGAAGAGCGATATGGGGAAGGATGATATGTACTGTGAATTTGTTTGGGAAGATGACAAATAT
1 TTTAGAAGAGCGATATGGGGAAGGATGATATGTACTGCGAATTTGTTTGGGAAGAAGACAAATAT
21190 CACAAGAGAAAGATGCAGGATTTTTATCAATGAAGAGTTTGGGAAACAACTTTGCAAGATAGAAA
66 CACAAGAGAAAGATGCAGGATTTTTATCAATGAAGAGTTTGGGAAACAACTTTGCAAGATAGAAA
21255 AAATTAGGATGACCTAACCTAAAATGCCATAAAACAATCTCAGTAGAAACATCATTAGATGATGG
131 AAATTAGGATGACCTAACCTAAAATGCCATAAAACAATCTCAGTAGAAACATCATTAGATGATGG
21320 AAATATCGAAACAATACTAGAGTTTGC
196 AAATATCGAAACAATACTAGAGTTTGC
21347 TT
1 TT
21349 GGGTATGAAC
Statistics
Matches: 221, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
222 221 1.00
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.26
Consensus pattern (222 bp):
TTTAGAAGAGCGATATGGGGAAGGATGATATGTACTGCGAATTTGTTTGGGAAGAAGACAAATAT
CACAAGAGAAAGATGCAGGATTTTTATCAATGAAGAGTTTGGGAAACAACTTTGCAAGATAGAAA
AAATTAGGATGACCTAACCTAAAATGCCATAAAACAATCTCAGTAGAAACATCATTAGATGATGG
AAATATCGAAACAATACTAGAGTTTGC
Found at i:29736 original size:18 final size:18
Alignment explanation
Indices: 29713--29747 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
29703 TAACATTTAA
29713 CTTAGCTAGAACTCTTAT
1 CTTAGCTAGAACTCTTAT
*
29731 CTTAGCTAGGACTCTTA
1 CTTAGCTAGAACTCTTA
29748 GTAATTTATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (18 bp):
CTTAGCTAGAACTCTTAT
Found at i:34411 original size:39 final size:39
Alignment explanation
Indices: 34363--34489 Score: 173
Period size: 39 Copynumber: 3.3 Consensus size: 39
34353 CGAAAATCAC
* * *
34363 CACCTGCTCCTGCTCCATTTCCAAAACCACCATCACCTA
1 CACCAGCTCCGGCTCCATTTCCAAAACCTCCATCACCTA
* * *
34402 TACGAGCTCCGGCTCCATTTCCAAAACCTCCATCACTTA
1 CACCAGCTCCGGCTCCATTTCCAAAACCTCCATCACCTA
* * *
34441 CACCAACTCCGGCTCCATTTCCAGAACCTCCATCATCTA
1 CACCAGCTCCGGCTCCATTTCCAAAACCTCCATCACCTA
34480 CACCAGCTCC
1 CACCAGCTCC
34490 ATCTCCATCA
Statistics
Matches: 75, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 75 1.00
ACGTcount: A:0.25, C:0.44, G:0.08, T:0.23
Consensus pattern (39 bp):
CACCAGCTCCGGCTCCATTTCCAAAACCTCCATCACCTA
Found at i:34554 original size:33 final size:32
Alignment explanation
Indices: 34511--34680 Score: 129
Period size: 33 Copynumber: 5.3 Consensus size: 32
34501 CTTTATCAAC
* * *
34511 ACCATTATCTCTACCTCTATTACCTGCGCGAAT
1 ACCATCATCTCTACCTC-ATTACCTGCACCAAT
* * *
34544 ACCATCATCTCCATCTCCATCACCTGCACCAA-
1 ACCATCATCTCTACCT-CATTACCTGCACCAAT
*
34576 AGCCATCATCTCTACCTACATTACCTTCACCAAT
1 A-CCATCATCTCTACCT-CATTACCTGCACCAAT
* *
34610 ACCATCATCTC--CATC--T-CCAT-CACCAAC
1 ACCATCATCTCTACCTCATTACC-TGCACCAAT
* * *
34637 ACCATCACCTCTACCTCCGTTACCTGCACTAAT
1 ACCATCATCTCTACCT-CATTACCTGCACCAAT
34670 ACCATCATCTC
1 ACCATCATCTC
34681 CATCTCCATC
Statistics
Matches: 108, Mismatches: 18, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
27 18 0.17
28 2 0.02
29 2 0.02
30 2 0.02
31 2 0.02
32 3 0.03
33 77 0.71
34 2 0.02
ACGTcount: A:0.27, C:0.42, G:0.04, T:0.27
Consensus pattern (32 bp):
ACCATCATCTCTACCTCATTACCTGCACCAAT
Found at i:34654 original size:27 final size:27
Alignment explanation
Indices: 34602--34654 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
34592 TACATTACCT
* * *
34602 TCACCAATACCATCATCTCCATCTCCA
1 TCACCAACACCATCACCTCCACCTCCA
*
34629 TCACCAACACCATCACCTCTACCTCC
1 TCACCAACACCATCACCTCCACCTCC
34655 GTTACCTGCA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.28, C:0.49, G:0.00, T:0.23
Consensus pattern (27 bp):
TCACCAACACCATCACCTCCACCTCCA
Found at i:34686 original size:6 final size:6
Alignment explanation
Indices: 34675--34708 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
34665 CTAATACCAT
*
34675 CATCTC CATCTC CATCTC CGTCTC CATCTC CATC
1 CATCTC CATCTC CATCTC CATCTC CATCTC CATC
34709 ACCAACACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.15, C:0.50, G:0.03, T:0.32
Consensus pattern (6 bp):
CATCTC
Found at i:34693 original size:66 final size:65
Alignment explanation
Indices: 34486--34690 Score: 233
Period size: 66 Copynumber: 3.2 Consensus size: 65
34476 TCTACACCAG
* * * * * * *
34486 CTCCATCTCCATCACCTTTATCAACACCATTATCTCTACCTCTATTACCTGCGCGAATACCATCA
1 CTCCATCTCCATCACC-TCACCAACACCATCACCTCTACCTCCATTACCTGCACCAATACCATCA
34551 T
65 T
* * *
34552 CTCCATCTCCATCACCTGCACCAA-AGCCATCATCTCTACCTACATTACCTTCACCAATACCATC
1 CTCCATCTCCATCACCT-CACCAACA-CCATCACCTCTACCTCCATTACCTGCACCAATACCATC
34616 AT
64 AT
* *
34618 CTCCATCT-C--CA--TCACCAACACCATCACCTCTACCTCCGTTACCTGCACTAATACCATCAT
1 CTCCATCTCCATCACCTCACCAACACCATCACCTCTACCTCCATTACCTGCACCAATACCATCAT
34678 CTCCATCTCCATC
1 CTCCATCTCCATC
34691 TCCGTCTCCA
Statistics
Matches: 120, Mismatches: 13, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
60 49 0.41
61 3 0.03
63 3 0.03
65 3 0.03
66 62 0.52
ACGTcount: A:0.26, C:0.42, G:0.03, T:0.28
Consensus pattern (65 bp):
CTCCATCTCCATCACCTCACCAACACCATCACCTCTACCTCCATTACCTGCACCAATACCATCAT
Found at i:37296 original size:21 final size:20
Alignment explanation
Indices: 37210--37367 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
37200 AAATGACTAA
**
37210 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
37229 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
37249 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
37269 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
37290 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
37311 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
37331 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
37352 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
37368 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:37358 original size:20 final size:20
Alignment explanation
Indices: 37334--37643 Score: 352
Period size: 20 Copynumber: 15.5 Consensus size: 20
37324 CGATTTTCCA
* ** *
37334 AAATCGCAACGCGAATATGA
1 AAATCGCAACGAGAATCCGT
* *
37354 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGAGAATC-CGT
* *
37374 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* *
37394 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
37414 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
37434 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
* * *
37454 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGAGAATCCGT
*
37474 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
37494 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
37514 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
37534 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
37554 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
37574 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
37594 AAATCGCAACGATAATCCGT
1 AAATCGCAACGAGAATCCGT
*
37614 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGAGAATCCGT
*
37634 AAATCACAAC
1 AAATCGCAAC
37644 ACTGAAATTT
Statistics
Matches: 256, Mismatches: 32, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
20 255 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGAGAATCCGT
Found at i:40856 original size:19 final size:19
Alignment explanation
Indices: 40811--41038 Score: 261
Period size: 19 Copynumber: 12.7 Consensus size: 19
40801 GCAACGAGAG
*
40811 AATCGCAATGCGAAATTGAC
1 AATCGCAATGCGAAA-TGAA
*
40831 TATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
40850 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
40869 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
40883 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
40902 AATCGCAATGCGGAAATTAA
1 AATCGCAATGC-GAAATGAA
40922 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
40941 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
40955 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
40974 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
40993 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
41007 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
41026 AATCGCATTGCGA
1 AATCGCAATGCGA
41039 TTCTCCCGTT
Statistics
Matches: 179, Mismatches: 13, Indels: 33
0.80 0.06 0.15
Matches are distributed among these distances:
14 30 0.17
15 3 0.02
16 6 0.03
17 6 0.03
18 3 0.02
19 99 0.55
20 32 0.18
ACGTcount: A:0.44, C:0.18, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:40876 original size:72 final size:71
Alignment explanation
Indices: 40797--41000 Score: 363
Period size: 72 Copynumber: 2.8 Consensus size: 71
40787 CGGAAATTAC
**
40797 AATCGCAACGAGAGAATCGCAATGCGAAATTGACTATCGCAATGCGAAATGAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGAAA-TGAAAATCGCAATGCGAAATGAAAATCGCAATGCG
40862 AAATGAA
65 AAATGAA
*
40869 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGGAAATTAAAATCGCAATGCG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAATGCG
40934 AAATGAA
65 AAATGAA
40941 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA
41001 CGAGAGAATC
Statistics
Matches: 127, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
71 28 0.22
72 99 0.78
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (71 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA
AATGAA
Found at i:40892 original size:33 final size:33
Alignment explanation
Indices: 40797--40981 Score: 217
Period size: 33 Copynumber: 5.2 Consensus size: 33
40787 CGGAAATTAC
*
40797 AATCGCAACGAGAGAATCGCAATGCGAAATTGAC
1 AATCGCAACGAGAGAATCGCAATGCGAAA-TGAA
* *
40831 TATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
40869 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
40902 AATCGCAATGCGGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C-G--A-GAGAATCGCAATGCGAAATGAA
40941 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
40974 AATCGCAA
1 AATCGCAA
40982 TGCGAAATGA
Statistics
Matches: 131, Mismatches: 9, Indels: 23
0.80 0.06 0.14
Matches are distributed among these distances:
33 57 0.44
34 9 0.07
35 1 0.01
36 6 0.05
37 1 0.01
38 12 0.09
39 45 0.34
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:40896 original size:52 final size:52
Alignment explanation
Indices: 40850--41038 Score: 240
Period size: 52 Copynumber: 3.6 Consensus size: 52
40840 GCGAAATGAA
* * * *
40850 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-
1 AATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGAAACGAGAG
* *
40902 AATCGCAATGCGGAAATTAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAATGCGAAATGAAAATCGAAACGAGAG
*
40955 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGAAACGAGAG
* *
41007 AATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGA
41039 TTCTCCCGTT
Statistics
Matches: 124, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
51 7 0.06
52 88 0.71
53 29 0.23
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGAAACGAGAG
Found at i:41087 original size:19 final size:19
Alignment explanation
Indices: 41047--41144 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
41037 GATTCTCCCG
41047 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
41067 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
41086 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
41100 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41119 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
41138 TTGCGAT
1 TTGCGAT
41145 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:41141 original size:52 final size:53
Alignment explanation
Indices: 41028--41144 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
41018 GAAATTAAAA
41028 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
41081 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
41133 TCGCATTGCGAT
1 TCGCATTGCGAT
41145 AGTCAATTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:41270 original size:14 final size:14
Alignment explanation
Indices: 41251--41287 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
41241 CATCAATTAC
41251 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
41265 ACAAATCATCTTTT
1 ACAAATCAACTTTT
41279 ACAAATCAA
1 ACAAATCAA
41288 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:43288 original size:33 final size:33
Alignment explanation
Indices: 43242--43334 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
43232 GCGAAACCAA
* *
43242 AATCGCAACGCGAAATGAAAATCTCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
43275 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
43308 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
43335 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:43299 original size:19 final size:19
Alignment explanation
Indices: 43205--43339 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
43195 TAGTTTACTT
* *
43205 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
43225 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
43244 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
43263 TCTCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
43277 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
43296 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
43310 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
43329 TCGCAATGCGA
1 TCGCAACGCGA
43340 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.12
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:43313 original size:14 final size:14
Alignment explanation
Indices: 43261--43317 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
43251 GCGAAATGAA
* *
43261 AATCTCAACGACAG
1 AATCGCAACGAAAG
43275 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
43292 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
43308 AATCGCAACG
1 AATCGCAACG
43318 CGAAATGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 17 0.47
16 5 0.14
17 6 0.17
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.19, T:0.12
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:43357 original size:19 final size:19
Alignment explanation
Indices: 43335--43463 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
43325 AAAATCGCAA
43335 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
43354 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
43368 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
43387 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
43401 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
43420 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
43439 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
43459 TGCGA
1 TGCGA
43464 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:43377 original size:33 final size:33
Alignment explanation
Indices: 43335--43426 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
43325 AAAATCGCAA
43335 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
43368 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
43401 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
43427 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:43627 original size:93 final size:93
Alignment explanation
Indices: 43511--43886 Score: 718
Period size: 93 Copynumber: 4.1 Consensus size: 93
43501 ATGGATTGCA
43511 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
43575 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
43603 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
43668 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
43696 TTACTTTCAACCAAAAGACAAAACAAAGAAAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
43761 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
43789 TTATTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
43854 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
43882 TTACT
1 TTACT
43887 AAGCAATCTA
Statistics
Matches: 278, Mismatches: 5, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
92 4 0.01
93 274 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:45606 original size:14 final size:14
Alignment explanation
Indices: 45587--45675 Score: 70
Period size: 14 Copynumber: 5.7 Consensus size: 14
45577 TTGAAATGAA
45587 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
45601 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
45620 AATCGCAACTAGAG
1 AATCGCAACGAGAG
*
45634 AATCGCAACGCGAAATG
1 AATCGCAA--CGAGA-G
45651 AAATCGCAACGAGAG
1 -AATCGCAACGAGAG
45666 AATCGCAACG
1 AATCGCAACG
45676 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
14 28 0.47
15 2 0.03
16 9 0.15
17 2 0.03
18 9 0.15
19 10 0.17
ACGTcount: A:0.44, C:0.22, G:0.24, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:45660 original size:32 final size:33
Alignment explanation
Indices: 45579--45692 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
45569 TCTTTTGGTT
45579 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
45612 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
45645 GAAATG-AAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
45677 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
45693 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
32 31 0.40
33 47 0.60
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:45750 original size:19 final size:19
Alignment explanation
Indices: 45723--45759 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
45713 GCGATTCTCT
*
45723 CGTTGCGATTTTCATTTCG
1 CGTTACGATTTTCATTTCG
45742 CGTTACGATTTTCATTTC
1 CGTTACGATTTTCATTTC
45760 TCTCGTTGCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.22, G:0.16, T:0.49
Consensus pattern (19 bp):
CGTTACGATTTTCATTTCG
Found at i:45777 original size:21 final size:21
Alignment explanation
Indices: 45753--45812 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
45743 GTTACGATTT
45753 TCATTTCTCTCGTTGCGACAG
1 TCATTTCTCTCGTTGCGACAG
***
45774 TCA-TTCTCTCGTTGCGATTT
1 TCATTTCTCTCGTTGCGACAG
*
45794 TCATTTATCTCGTTGCGAC
1 TCATTTCTCTCGTTGCGAC
45813 TCTTCTGCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
20 17 0.52
21 16 0.48
ACGTcount: A:0.13, C:0.27, G:0.17, T:0.43
Consensus pattern (21 bp):
TCATTTCTCTCGTTGCGACAG
Found at i:45805 original size:41 final size:40
Alignment explanation
Indices: 45720--45812 Score: 123
Period size: 41 Copynumber: 2.3 Consensus size: 40
45710 GTTGCGATTC
*** *
45720 TCTCGTTGCGATTTTCATTTCGCGTTACGATTTTCATTTC
1 TCTCGTTGCGACAGTCATTTCGCGTTACGATTTTCATTTA
* *
45760 TCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCATTTA
1 TCTCGTTGCGACAGTCATT-TCGCGTTACGATTTTCATTTA
45801 TCTCGTTGCGAC
1 TCTCGTTGCGAC
45813 TCTTCTGCAA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
40 16 0.35
41 30 0.65
ACGTcount: A:0.13, C:0.25, G:0.17, T:0.45
Consensus pattern (40 bp):
TCTCGTTGCGACAGTCATTTCGCGTTACGATTTTCATTTA
Found at i:45933 original size:33 final size:33
Alignment explanation
Indices: 45891--45961 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
45881 AATACTAACT
*
45891 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
45924 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
45957 TGAAA
1 TGAAA
45962 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:46195 original size:22 final size:22
Alignment explanation
Indices: 46143--46197 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
46133 TGGTTGTGAG
**
46143 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
46165 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
46187 GGATTTCTTCG
1 GGATTTCTTCG
46198 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:46369 original size:20 final size:20
Alignment explanation
Indices: 46344--46497 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
46334 CTTTAAATAT
46344 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
46364 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
46386 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
46405 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
46425 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
46445 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
46465 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
46485 CGCGTTGCGATTT
1 CGCGTTGCGATTT
46498 TGGAAAATCG
Statistics
Matches: 113, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 94 0.83
21 15 0.13
22 2 0.02
ACGTcount: A:0.18, C:0.18, G:0.27, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:46471 original size:40 final size:40
Alignment explanation
Indices: 46343--46497 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
46333 GCTTTAAATA
*
46343 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGT
** * *
46384 TATCGTTGCGATTTACGGATACGCGTTGCGATATACG-GAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTG-T
* *
46424 ACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
* ** *
46464 TCGCGTTGCGATTTTCATATTCGCGTTGCGATTT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTT
46498 TGGAAAATCG
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
40 66 0.69
41 30 0.31
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (40 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
Found at i:46514 original size:21 final size:21
Alignment explanation
Indices: 46484--46566 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
46474 ATTTTCATAT
*
46484 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
46505 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
46526 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
46547 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
46567 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:46557 original size:42 final size:43
Alignment explanation
Indices: 46464--46562 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
46454 ATTTATGTGT
* *
46464 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
46505 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
46547 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
46563 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:47530 original size:123 final size:124
Alignment explanation
Indices: 47303--47536 Score: 307
Period size: 123 Copynumber: 1.9 Consensus size: 124
47293 AGGGTATCAC
** * *
47303 TTTAGCGGCGTTTTTATACAAACACCGCAATAGGTTCATCTATGTGGCATTTTTTCAACAAACGC
1 TTTAGCGGCGTTTCGATACAAACACCGCAATAGGCTCATCTATATGGCATTTTTTCAACAAACGC
* *
47368 CGCAATGTGAGTAGTACTTTAACAGCGTTTTTATAAAAAT-GCCGCTATAAATTAGTAT
66 CGCAATGTGAGTAGCACTTTAACAGCGTTTTAATAAAAATCGCCGCTATAAATTAGTAT
*
47426 TTTAGCGGCGTTTCGATACAAACGCCGCAATAGGCTCATCTATAATGGCA-TTTTTCAACAAACG
1 TTTAGCGGCGTTTCGATACAAACACCGCAATAGGCTCATCTAT-ATGGCATTTTTTCAACAAACG
***
47490 CCGCAACT-T-AGTAGCACTTTAGTGGCGTTTGTAACT-AAAATCGCCGC
65 CCGCAA-TGTGAGTAGCACTTTAACAGCGTTT-TAA-TAAAAATCGCCGC
47537 AATAGGTTAA
Statistics
Matches: 96, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
122 17 0.18
123 67 0.70
124 12 0.12
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (124 bp):
TTTAGCGGCGTTTCGATACAAACACCGCAATAGGCTCATCTATATGGCATTTTTTCAACAAACGC
CGCAATGTGAGTAGCACTTTAACAGCGTTTTAATAAAAATCGCCGCTATAAATTAGTAT
Found at i:49151 original size:2 final size:2
Alignment explanation
Indices: 49144--49207 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
49134 AATAAAATTG
49144 AT AT AT 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
49186 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
49208 TACTAATTCT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51861 original size:27 final size:28
Alignment explanation
Indices: 51809--51867 Score: 68
Period size: 27 Copynumber: 2.1 Consensus size: 28
51799 TCCATGGTTT
*
51809 ATTCATCGAGTTTTCTACATTCTATT-C
1 ATTCATAGAGTTTTCTACATTCTATTCC
* *
51836 ATTCATAGAGTTTTC-CCATCTTTATTCC
1 ATTCATAGAGTTTTCTACAT-TCTATTCC
51864 ATTC
1 ATTC
51868 TTTCTCAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 3 0.11
27 19 0.70
28 5 0.19
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.47
Consensus pattern (28 bp):
ATTCATAGAGTTTTCTACATTCTATTCC
Found at i:52367 original size:16 final size:16
Alignment explanation
Indices: 52319--52361 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
52309 TAATAAATAA
52319 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
52335 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
52351 ACGAACATAAA
1 ACGAACATAAA
52362 AAAACAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.58, C:0.23, G:0.12, T:0.07
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:52459 original size:16 final size:16
Alignment explanation
Indices: 52438--52468 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
52428 ATAAATAAAT
*
52438 GAACATAAATGAACAC
1 GAACATAAACGAACAC
52454 GAACATAAACGAACA
1 GAACATAAACGAACA
52469 TAAACGTTTG
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:0.58, C:0.19, G:0.13, T:0.10
Consensus pattern (16 bp):
GAACATAAACGAACAC
Found at i:53226 original size:10 final size:10
Alignment explanation
Indices: 53211--53260 Score: 55
Period size: 10 Copynumber: 4.6 Consensus size: 10
53201 ATAAATGAAT
53211 GAACATAAAC
1 GAACATAAAC
53221 GAACATAACCGAAC
1 GAACAT-A---AAC
53235 GAACATAAAC
1 GAACATAAAC
*
53245 GAACATAACC
1 GAACATAAAC
53255 GAACAT
1 GAACAT
53261 TCATGAACGT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
10 24 0.69
11 1 0.03
13 1 0.03
14 9 0.26
ACGTcount: A:0.54, C:0.24, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:53235 original size:14 final size:14
Alignment explanation
Indices: 53218--53258 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
53208 AATGAACATA
53218 AACGAACATAACCG
1 AACGAACATAACCG
53232 AACGAACAT-A---
1 AACGAACATAACCG
53242 AACGAACATAACCG
1 AACGAACATAACCG
53256 AAC
1 AAC
53259 ATTCATGAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
10 9 0.39
11 1 0.04
13 1 0.04
14 12 0.52
ACGTcount: A:0.54, C:0.27, G:0.12, T:0.07
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:53269 original size:24 final size:24
Alignment explanation
Indices: 53211--53258 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
53201 ATAAATGAAT
53211 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
53235 GAACATAAACGAACATAACCGAAC
1 GAACATAAACGAACATAACCGAAC
53259 ATTCATGAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.25, G:0.12, T:0.08
Consensus pattern (24 bp):
GAACATAAACGAACATAACCGAAC
Found at i:54180 original size:43 final size:43
Alignment explanation
Indices: 54132--54457 Score: 358
Period size: 43 Copynumber: 7.6 Consensus size: 43
54122 GGTAATTAGT
*
54132 GGCGTTTATATCCAAAAACGCCGCTATAGATCTGACCTTTTGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC
* *
54175 GGCGTTTGTATCCAAAAACGCCGCTATATATCTTACCTTTTGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC
*
54218 GGCGTTT-TTTCCAAAAAC-CCGCTATAGATCTTGACCTTTTGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATC-TGACCTTTTGC
* * * * *
54260 GGCATTTGTATCCAACAACGTCGTTATATATCT-ACCCTTTTGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGA-CCTTTTGC
* * * * *
54303 GGTGTTT-T-TGCCAAAAACACCGCTAGAGAACTTGACATTTTGC
1 GGCGTTTGTAT-CCAAAAACGCCGCTATAGATC-TGACCTTTTGC
* *
54346 GGCGTTTGTATCCAAAAATGCCGCTATAGATCTCAACCTTTTGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATCT-GACCTTTTGC
* *
54390 GGCGTTTGT-TCCAAAAACGCCACTATAGATCTTGACTTTTTGC
1 GGCGTTTGTATCCAAAAACGCCGCTATAGATC-TGACCTTTTGC
* * *
54433 GGCGTTTTTATATCACAAACGCCGC
1 GGCGTTTGTAT-CCAAAAACGCCGC
54458 CAATATTAGT
Statistics
Matches: 233, Mismatches: 37, Indels: 24
0.79 0.13 0.08
Matches are distributed among these distances:
41 12 0.05
42 42 0.18
43 121 0.52
44 47 0.20
45 11 0.05
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (43 bp):
GGCGTTTGTATCCAAAAACGCCGCTATAGATCTGACCTTTTGC
Found at i:54288 original size:85 final size:86
Alignment explanation
Indices: 54132--54457 Score: 415
Period size: 85 Copynumber: 3.8 Consensus size: 86
54122 GGTAATTAGT
*
54132 GGCGTTTATATCCAAAAACGCCGCTATAGATC-TGACCTTTTGCGGCGTTTGTATCCAAAAACGC
1 GGCGTTT-TTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAACGC
54196 CGCTATATATCTTACCTTTTGC
65 CGCTATATATCTTACCTTTTGC
* * *
54218 GGCGTTTTTTCCAAAAAC-CCGCTATAGATCTTGACCTTTTGCGGCATTTGTATCCAACAACGTC
1 GGCGTTTTTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAACGCC
*
54282 GTTATATATC-TACCCTTTTGC
66 GCTATATATCTTA-CCTTTTGC
* * * * * * *
54303 GGTGTTTTTGCCAAAAACACCGCTAGAGAACTTGACATTTTGCGGCGTTTGTATCCAAAAATGCC
1 GGCGTTTTTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAACGCC
* *
54368 GCTATAGATCTCAACCTTTTGC
66 GCTATATATCT-TACCTTTTGC
* * * * * *
54390 GGCGTTTGTTCCAAAAACGCCACTATAGATCTTGACTTTTTGCGGCGTTTTTATATCACAAACGC
1 GGCGTTTTTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTAT-CCAAAAACGC
54455 CGC
65 CGC
54458 CAATATTAGT
Statistics
Matches: 205, Mismatches: 29, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
84 14 0.07
85 73 0.36
86 54 0.26
87 53 0.26
88 11 0.05
ACGTcount: A:0.24, C:0.25, G:0.18, T:0.33
Consensus pattern (86 bp):
GGCGTTTTTTCCAAAAACGCCGCTATAGATCTTGACCTTTTGCGGCGTTTGTATCCAAAAACGCC
GCTATATATCTTACCTTTTGC
Found at i:55684 original size:30 final size:30
Alignment explanation
Indices: 55650--55807 Score: 203
Period size: 30 Copynumber: 5.3 Consensus size: 30
55640 ATTCAATTTA
* **
55650 AAAGGACCAAAATATCAAAAATAGAAACTT
1 AAAGGACTAAAATAGAAAAAATAGAAACTT
* *
55680 AAAGGACTAAAATAGTAAAAACAGAAACTT
1 AAAGGACTAAAATAGAAAAAATAGAAACTT
* *
55710 AAAAGACTAAAATAGAAAAAACCA-AAACTT
1 AAAGGACTAAAATAGAAAAAA-TAGAAACTT
*
55740 AAAGGACTAAAATA-ACAAAAATAGAAACGT
1 AAAGGACTAAAATAGA-AAAAATAGAAACTT
*
55770 AAAGGACTAAAATAGAAAAAATATAAACTT
1 AAAGGACTAAAATAGAAAAAATAGAAACTT
55800 AAAGGACT
1 AAAGGACT
55808 TAACCATTAA
Statistics
Matches: 113, Mismatches: 11, Indels: 8
0.86 0.08 0.06
Matches are distributed among these distances:
29 2 0.02
30 108 0.96
31 3 0.03
ACGTcount: A:0.62, C:0.11, G:0.11, T:0.16
Consensus pattern (30 bp):
AAAGGACTAAAATAGAAAAAATAGAAACTT
Found at i:57277 original size:15 final size:14
Alignment explanation
Indices: 57259--57300 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
57249 AATATTGATT
57259 TAATAAAAAATATAA
1 TAATAAAAAATA-AA
*
57274 TAATAATAAATAAA
1 TAATAAAAAATAAA
*
57288 TAA-ATAAAATAAA
1 TAATAAAAAATAAA
57301 ATTTTTGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAATAAAAAATAAA
Found at i:57280 original size:18 final size:17
Alignment explanation
Indices: 57259--57301 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
57249 AATATTGATT
57259 TAATAAAAAATATAATAA
1 TAATAAAAAATA-AATAA
57277 TAATAAATAAATAAATAA
1 TAATAAA-AAATAAATAA
57295 -AATAAAA
1 TAATAAAA
57302 TTTTTGATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 1 0.04
17 6 0.25
18 12 0.50
19 5 0.21
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
TAATAAAAAATAAATAA
Found at i:59169 original size:12 final size:12
Alignment explanation
Indices: 59152--59179 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
59142 ATTTTTTTTT
59152 AAAAAAAAAGCC
1 AAAAAAAAAGCC
59164 AAAAAAAAAGCC
1 AAAAAAAAAGCC
59176 AAAA
1 AAAA
59180 TTTCAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.14, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGCC
Done.