Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002090.1 Hibiscus syriacus cultivar Beakdansim tig00004263_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: 82935
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6629 original size:4 final size:4
Alignment explanation
Indices: 6620--6646 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
6610 CGTTAAATTA
6620 TAAT TAAT TAAT TAAT TAAT TAAT TAA
1 TAAT TAAT TAAT TAAT TAAT TAAT TAA
6647 AAATAGCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
TAAT
Found at i:12518 original size:6 final size:6
Alignment explanation
Indices: 12497--12532 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
12487 TGACTGTATG
*
12497 ATATATC ATCTAC ATATAC ATATAC ATATAC ATATA
1 ATATA-C ATATAC ATATAC ATATAC ATATAC ATATA
12533 AAATAGAGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 23 0.85
7 4 0.15
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.36
Consensus pattern (6 bp):
ATATAC
Found at i:16317 original size:45 final size:45
Alignment explanation
Indices: 16253--16344 Score: 175
Period size: 45 Copynumber: 2.0 Consensus size: 45
16243 AGTGATTTCA
*
16253 CAAAGGTGAACAAACTTTAAAATCAGGTCAGGGATTAACTAATAT
1 CAAAGGTGAACAAACTTTAAAATCAGGTCAGGGATTAACTAAAAT
16298 CAAAGGTGAACAAACTTTAAAATCAGGTCAGGGATTAACTAAAAT
1 CAAAGGTGAACAAACTTTAAAATCAGGTCAGGGATTAACTAAAAT
16343 CA
1 CA
16345 GGATGGATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (45 bp):
CAAAGGTGAACAAACTTTAAAATCAGGTCAGGGATTAACTAAAAT
Found at i:19435 original size:26 final size:26
Alignment explanation
Indices: 19396--19477 Score: 137
Period size: 26 Copynumber: 3.2 Consensus size: 26
19386 GGTTGTAAAC
*
19396 GAGCCGAGTTGAGCTCAAGTATTGCT
1 GAGCCGAGTCGAGCTCAAGTATTGCT
19422 GAGCCGAGTCGAGCTCAAGTATTGCT
1 GAGCCGAGTCGAGCTCAAGTATTGCT
* *
19448 GAGCCGAGTCGAGCTCAAATTTTGCT
1 GAGCCGAGTCGAGCTCAAGTATTGCT
19474 GAGC
1 GAGC
19478 TCGACTCCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 53 1.00
ACGTcount: A:0.23, C:0.22, G:0.30, T:0.24
Consensus pattern (26 bp):
GAGCCGAGTCGAGCTCAAGTATTGCT
Found at i:23516 original size:20 final size:20
Alignment explanation
Indices: 23493--23544 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
23483 CGCCATCAAT
23493 TTGGTATCAATACTCTTTGA
1 TTGGTATCAATACTCTTTGA
23513 TTGGTATCAATACTCTTTGA
1 TTGGTATCAATACTCTTTGA
23533 TTGGTATCAATA
1 TTGGTATCAATA
23545 TCATTAAGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.44
Consensus pattern (20 bp):
TTGGTATCAATACTCTTTGA
Found at i:23639 original size:19 final size:19
Alignment explanation
Indices: 23575--23645 Score: 72
Period size: 21 Copynumber: 3.5 Consensus size: 19
23565 TCAAGTATAT
23575 ATACTCTCTATTTGAGTATCC
1 ATACTCTCTA-TTGAGTAT-C
*
23596 AAACTCTTCGTA-TGAGTATTC
1 ATACTC-TC-TATTGAGTA-TC
*
23617 ATACTTTCTATTGAGTATC
1 ATACTCTCTATTGAGTATC
23636 ATACTCTCTA
1 ATACTCTCTA
23646 ATGTTGGAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
19 13 0.31
20 8 0.19
21 16 0.38
22 3 0.07
23 2 0.05
ACGTcount: A:0.27, C:0.21, G:0.10, T:0.42
Consensus pattern (19 bp):
ATACTCTCTATTGAGTATC
Found at i:28093 original size:2 final size:2
Alignment explanation
Indices: 28086--28117 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
28076 ACAACTCTGG
28086 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
28118 AAAATATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:28225 original size:2 final size:2
Alignment explanation
Indices: 28218--28287 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
28208 GAAAATTGTA
28218 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
28260 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
28288 GAAGGAATTG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31261 original size:38 final size:38
Alignment explanation
Indices: 31187--31267 Score: 153
Period size: 38 Copynumber: 2.1 Consensus size: 38
31177 TATAAGCTCA
*
31187 TTTATCAACTCTTTCGTTTATGTTCATGAACAAACTTG
1 TTTATCAACTCATTCGTTTATGTTCATGAACAAACTTG
31225 TTTATCAACTCATTCGTTTATGTTCATGAACAAACTTG
1 TTTATCAACTCATTCGTTTATGTTCATGAACAAACTTG
31263 TTTAT
1 TTTAT
31268 AAGCTCGTTT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.27, C:0.17, G:0.10, T:0.46
Consensus pattern (38 bp):
TTTATCAACTCATTCGTTTATGTTCATGAACAAACTTG
Found at i:35194 original size:41 final size:39
Alignment explanation
Indices: 35146--35239 Score: 98
Period size: 40 Copynumber: 2.4 Consensus size: 39
35136 TCAGTTTCCA
** *
35146 AAATCGCAACGCGATTCTTGAAAATCGCAATGCGATATACG
1 AAATCGCAACGCGATT-TCCAAAATCGCAACGCGA-ATACG
* * ** *
35187 GATTCGCATTGCGATTTCCAAAATCGCAACGCGAATATG
1 AAATCGCAACGCGATTTCCAAAATCGCAACGCGAATACG
35226 AAATCGCAACGCGA
1 AAATCGCAACGCGA
35240 ACACATAAAT
Statistics
Matches: 41, Mismatches: 12, Indels: 2
0.75 0.22 0.04
Matches are distributed among these distances:
39 14 0.34
40 15 0.37
41 12 0.29
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (39 bp):
AAATCGCAACGCGATTTCCAAAATCGCAACGCGAATACG
Found at i:35213 original size:20 final size:20
Alignment explanation
Indices: 35105--35220 Score: 65
Period size: 20 Copynumber: 5.8 Consensus size: 20
35095 ACGCGAAATA
* **
35105 AAAATCGCAACGCGATCCCC
1 AAAATCGCAATGCGATTTCC
*
35125 AGAATCGCAAAT-C-AGTTTCC
1 AAAATCGC-AATGCGA-TTTCC
* **
35145 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAATGCGATT-TCC
* *
35166 AAAATCGCAATGCGATATAC
1 AAAATCGCAATGCGATTTCC
** * *
35186 GGATTCGCATTGCGATTTCC
1 AAAATCGCAATGCGATTTCC
*
35206 AAAATCGCAACGCGA
1 AAAATCGCAATGCGA
35221 ATATGAAATC
Statistics
Matches: 68, Mismatches: 23, Indels: 10
0.67 0.23 0.10
Matches are distributed among these distances:
19 3 0.04
20 46 0.68
21 19 0.28
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (20 bp):
AAAATCGCAATGCGATTTCC
Found at i:35251 original size:20 final size:19
Alignment explanation
Indices: 35207--35256 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
35197 GCGATTTCCA
*
35207 AAATCGCAACGCGAATATG
1 AAATCGCAACGCGAACATG
35226 AAATCGCAACGCGAACACAT-
1 AAATCGCAACGCG-A-ACATG
35246 AAATCGCAACG
1 AAATCGCAACG
35257 TGTATCCGTA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 13 0.46
20 12 0.43
21 3 0.11
ACGTcount: A:0.44, C:0.26, G:0.18, T:0.12
Consensus pattern (19 bp):
AAATCGCAACGCGAACATG
Found at i:35271 original size:20 final size:20
Alignment explanation
Indices: 35207--35455 Score: 229
Period size: 20 Copynumber: 12.5 Consensus size: 20
35197 GCGATTTCCA
* **
35207 AAATCGCAACGCGAATATG-
1 AAATCGCAACGTGAATCCGT
* *
35226 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
35246 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
35266 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
35286 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
35306 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
35326 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
35346 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
35366 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
35386 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
35406 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
35426 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
35446 AAATCACAAC
1 AAATCGCAAC
35456 ACTGAAATTT
Statistics
Matches: 195, Mismatches: 26, Indels: 17
0.82 0.11 0.07
Matches are distributed among these distances:
19 15 0.08
20 179 0.92
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:36173 original size:24 final size:24
Alignment explanation
Indices: 36134--36180 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
36124 AAATTTGGTC
36134 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
36158 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
36181 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:38749 original size:19 final size:19
Alignment explanation
Indices: 38709--38806 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
38699 GATTCTCTCG
38709 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
38729 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
38748 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
38762 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
38781 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
38800 TTGCGAT
1 TTGCGAT
38807 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:38803 original size:52 final size:53
Alignment explanation
Indices: 38690--38806 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
38680 GAAATGAAAA
38690 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
38743 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
38795 TCGCATTGCGAT
1 TCGCATTGCGAT
38807 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:38932 original size:14 final size:14
Alignment explanation
Indices: 38913--38949 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
38903 CATCAATTAC
38913 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
38927 ACAAATCATCTTTT
1 ACAAATCAACTTTT
38941 ACAAATCAA
1 ACAAATCAA
38950 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:40458 original size:21 final size:21
Alignment explanation
Indices: 40419--40459 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
40409 ACTCTCGAGG
* *
40419 AATGATAGGGGGGGCCTCTTC
1 AATGATAGGAGGGGACTCTTC
*
40440 AATGATAGGAGTGGACTCTT
1 AATGATAGGAGGGGACTCTT
40460 GAGGGATGAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.15, G:0.34, T:0.27
Consensus pattern (21 bp):
AATGATAGGAGGGGACTCTTC
Found at i:40943 original size:14 final size:14
Alignment explanation
Indices: 40924--40980 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
40914 GCGAAATGAA
*
40924 AATCGCAACGACAG
1 AATCGCAACGAAAG
40938 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
40955 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
40971 AATCGCAACG
1 AATCGCAACG
40981 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:40951 original size:33 final size:33
Alignment explanation
Indices: 40905--40997 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
40895 GCGAAACCAA
*
40905 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
40938 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
40971 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
40998 TGCGATTTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:40962 original size:19 final size:19
Alignment explanation
Indices: 40868--41002 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
40858 TAGTTTACTT
* *
40868 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
40888 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
40907 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
40926 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
40940 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
40959 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
40973 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
40992 TCGCAATGCGA
1 TCGCAACGCGA
41003 TTTGGTTTCG
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:41043 original size:33 final size:33
Alignment explanation
Indices: 40998--41088 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
40988 AAAATCGCAA
40998 TGCGA-TTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
41030 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
41063 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
41089 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 5 0.09
33 48 0.87
34 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:41051 original size:19 final size:19
Alignment explanation
Indices: 40998--41125 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
40988 AAAATCGCAA
40998 TGCGA-TTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
41016 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
41030 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
41049 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
41063 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
41082 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
41101 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
41121 TGCGA
1 TGCGA
41126 AAGTAAACTA
Statistics
Matches: 89, Mismatches: 9, Indels: 22
0.74 0.08 0.18
Matches are distributed among these distances:
14 22 0.25
15 1 0.01
16 2 0.02
17 2 0.02
18 7 0.08
19 42 0.47
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:41421 original size:92 final size:93
Alignment explanation
Indices: 41169--41546 Score: 717
Period size: 92 Copynumber: 4.1 Consensus size: 93
41159 TTGAATGGAT
41169 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
41234 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
41262 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATAC-C
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
41326 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
41354 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
41418 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
41446 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
41511 AGTTT-GCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
41538 AAATTTACT
1 AAATTTACT
41547 AAGCAATCTA
Statistics
Matches: 280, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
91 38 0.14
92 134 0.48
93 108 0.39
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:42264 original size:20 final size:20
Alignment explanation
Indices: 42241--42292 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
42231 AACGCGATCC
42241 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
42261 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
42281 CCAAAATCGCAA
1 CCAGAATCGCAA
42293 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:42433 original size:20 final size:20
Alignment explanation
Indices: 42348--42716 Score: 424
Period size: 20 Copynumber: 18.4 Consensus size: 20
42338 GATTTTCCAT
* ** *
42348 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
42368 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
42388 AATCGCAACGCGTATCCGTAA
1 AATCGCAACGCGTATCCGT-A
**
42409 AATCGCAACGTATATCCGTA
1 AATCGCAACGCGTATCCGTA
* **
42429 AATCGCAACACGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
42449 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
42469 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
42489 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
42509 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
42529 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
42549 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
42569 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
42589 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
42609 AATCGCAACGC-TATCCGTA
1 AATCGCAACGCGTATCCGTA
*
42628 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
42648 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
42668 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
42688 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
42708 AATCACAAC
1 AATCGCAAC
42717 ACTGAAATTT
Statistics
Matches: 301, Mismatches: 38, Indels: 20
0.84 0.11 0.06
Matches are distributed among these distances:
19 20 0.07
20 261 0.87
21 20 0.07
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:43433 original size:24 final size:24
Alignment explanation
Indices: 43394--43440 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
43384 AAATTTGGTC
43394 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
43418 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
43441 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:45921 original size:19 final size:19
Alignment explanation
Indices: 45899--46163 Score: 273
Period size: 19 Copynumber: 15.4 Consensus size: 19
45889 CGGAAAATAC
*
45899 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
45918 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
45932 AAT-GCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
45951 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
45965 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
45984 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
46003 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
46022 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
*
46036 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
46055 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
46074 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
46088 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
46107 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
46121 AATCGCAATGCG-AATG-A
1 AATCGCAATGCGAAATGAA
46138 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
46156 AATCGCAA
1 AATCGCAA
46164 CGAGATAATC
Statistics
Matches: 211, Mismatches: 8, Indels: 55
0.77 0.03 0.20
Matches are distributed among these distances:
13 3 0.01
14 42 0.20
15 4 0.02
16 17 0.08
17 29 0.14
18 15 0.07
19 97 0.46
20 4 0.02
ACGTcount: A:0.47, C:0.18, G:0.21, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:45952 original size:33 final size:34
Alignment explanation
Indices: 45899--46185 Score: 221
Period size: 33 Copynumber: 8.5 Consensus size: 34
45889 CGGAAAATAC
* *
45899 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
* *
45932 AAT-GCAATGCGGAAATGAAAATCGCAACGA-GAG
1 AATCGCAATGC-GAAATGAAAATCGCAACAATGAA
45965 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
* * *
46003 AATCGCAATGCGAAATGAAAATCGCAACGA-CAG
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
*
46036 AATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
46074 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C--AATGAA
46107 AATCGCAA--CGAAA-G--AATCGCAATGCGAATG-A
1 AATCGCAATGCGAAATGAAAATCGCAA--C-AATGAA
* *
46138 AATCGCAATGCGAAATG-AAATCGCAACGA-GAT
1 AATCGCAATGCGAAATGAAAATCGCAACAATGAA
46170 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
46186 TATAAACGCA
Statistics
Matches: 220, Mismatches: 16, Indels: 37
0.81 0.06 0.14
Matches are distributed among these distances:
31 10 0.05
32 27 0.12
33 117 0.53
34 10 0.05
35 10 0.05
36 6 0.03
37 2 0.01
38 38 0.17
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (34 bp):
AATCGCAATGCGAAATGAAAATCGCAACAATGAA
Found at i:45983 original size:52 final size:52
Alignment explanation
Indices: 45927--46185 Score: 272
Period size: 52 Copynumber: 5.0 Consensus size: 52
45917 AAATCCCAAC
45927 ATGAAAAT-GCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
* * * *
45979 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAA
* * *
46029 ACGACAGAATCGCAATGCGAAATTAAAATCGCAATGCGAAATGAAAATCGCAA--CGAA
1 ATGA-A-AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
*
46086 A-G--AATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG-A
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
46134 ATG-AAATCGCAATGCGAAATG-AAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
46184 AT
1 AT
46186 TATAAACGCA
Statistics
Matches: 176, Mismatches: 15, Indels: 34
0.78 0.07 0.15
Matches are distributed among these distances:
47 9 0.05
48 3 0.02
49 28 0.16
50 29 0.16
51 7 0.04
52 79 0.45
53 7 0.04
54 1 0.01
56 1 0.01
57 6 0.03
58 5 0.03
59 1 0.01
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:46300 original size:19 final size:19
Alignment explanation
Indices: 46192--46292 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
46182 AAATTATAAA
46192 CGCATTGCGA-TTTCATTT
1 CGCATTGCGATTTTCATTT
46210 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
46230 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
46246 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
46263 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
46282 CGCATTGCGAT
1 CGCATTGCGAT
46293 AGTCATTTTG
Statistics
Matches: 74, Mismatches: 2, Indels: 12
0.84 0.02 0.14
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 46 0.62
20 8 0.11
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:46427 original size:14 final size:15
Alignment explanation
Indices: 46397--46434 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
46387 CATCAATTAC
46397 ACAAATCAACTTTTT
1 ACAAATCAACTTTTT
*
46412 ACAAATCATC-TTTT
1 ACAAATCAACTTTTT
46426 ACAAATCAA
1 ACAAATCAA
46435 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (15 bp):
ACAAATCAACTTTTT
Found at i:47859 original size:21 final size:21
Alignment explanation
Indices: 47829--47891 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
47819 GTGAATCGGG
47829 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
* * **
47850 CTCTTCAATGATGACAGTGG-C
1 CTCTTGAATGGTGGGAG-GGAC
*
47871 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGGAC
47892 TCTCGAGGAA
Statistics
Matches: 31, Mismatches: 9, Indels: 4
0.70 0.20 0.09
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
22 2 0.06
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.24
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGAC
Found at i:48423 original size:14 final size:14
Alignment explanation
Indices: 48404--48460 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
48394 GCGAAATGAA
*
48404 AATCGCAACGACAG
1 AATCGCAACGAAAG
48418 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
48435 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
48451 AATCGCAACG
1 AATCGCAACG
48461 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:48431 original size:33 final size:33
Alignment explanation
Indices: 48385--48476 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
48375 GCGAAACCAA
*
48385 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
48418 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
48451 AATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
48477 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 9 0.16
33 47 0.84
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:48442 original size:19 final size:19
Alignment explanation
Indices: 48348--48481 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
48338 TAGTTTACTT
* *
48348 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
48368 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
48387 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
48406 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
48420 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
48439 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
48453 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
48471 TCGCAATGCGA
1 TCGCAACGCGA
48482 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
18 12 0.12
19 35 0.36
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:48499 original size:19 final size:19
Alignment explanation
Indices: 48477--48605 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
48467 GAAATCGCAA
48477 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
48496 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
48510 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
48529 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
48543 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
48562 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
48581 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
48601 TGCGA
1 TGCGA
48606 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:48519 original size:33 final size:33
Alignment explanation
Indices: 48477--48568 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
48467 GAAATCGCAA
48477 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
48510 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
48543 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
48569 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:48795 original size:93 final size:93
Alignment explanation
Indices: 48637--49102 Score: 891
Period size: 93 Copynumber: 5.0 Consensus size: 93
48627 GCAAATTGAA
*
48637 ACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTATTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
48701 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
48729 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
48794 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
48822 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
48887 GCAGAATTGGCATCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
48915 ACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
48979 GCAGAATTGGCAGCAACCGAACAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
49007 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
49072 GCAGAATTGGCAGCAACCGAATAAATTT
66 GCAGAATTGGCAGCAACCGAACAAATTT
49100 ACT
1 ACT
49103 AAGCAATCTA
Statistics
Matches: 368, Mismatches: 4, Indels: 3
0.98 0.01 0.01
Matches are distributed among these distances:
92 113 0.31
93 255 0.69
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (93 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTT
Found at i:48975 original size:185 final size:186
Alignment explanation
Indices: 48637--49102 Score: 891
Period size: 185 Copynumber: 2.5 Consensus size: 186
48627 GCAAATTGAA
*
48637 ACTTTCAACCAAAAGACAAAAC-AAGACAAATACTATTTCACAGTATTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
48701 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
48766 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
48822 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
48887 GCAGAATTGGCATCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TAT
66 GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
48951 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
131 TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
49007 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
1 ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
*
49072 GCAGAATTGGCAGCAACCGAATAAATTTACT
66 GCAGAATTGGCAGCAACCGAACAAATTTACT
49103 AAGCAATCTA
Statistics
Matches: 276, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
185 175 0.63
186 101 0.37
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.22
Consensus pattern (186 bp):
ACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTA
GCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAT
TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTT
Found at i:50826 original size:14 final size:14
Alignment explanation
Indices: 50807--50897 Score: 74
Period size: 14 Copynumber: 5.7 Consensus size: 14
50797 TTGAAATGAA
50807 AATCGCAACGAGAG
1 AATCGCAACGAGAG
50821 AATCGCAACGAGAG
1 AATCGCAACGAGAG
50835 AATGACTGTCGCAACGAGAG
1 -A--A---TCGCAACGAGAG
*
50855 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
50874 AATCGCAACGAGAG
1 AATCGCAACGAGAG
50888 AATCGCAACG
1 AATCGCAACG
50898 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 22
0.73 0.02 0.25
Matches are distributed among these distances:
14 32 0.50
15 2 0.03
16 2 0.03
17 4 0.06
18 1 0.02
19 11 0.17
20 12 0.19
ACGTcount: A:0.42, C:0.22, G:0.26, T:0.10
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:50879 original size:19 final size:19
Alignment explanation
Indices: 50855--50919 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
50845 GCAACGAGAG
50855 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
50874 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
50888 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
50907 AATCGCAATGCGA
1 AATCGCAACGCGA
50920 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:50880 original size:33 final size:33
Alignment explanation
Indices: 50799--50914 Score: 187
Period size: 33 Copynumber: 3.5 Consensus size: 33
50789 TCTTTTGGTT
*
50799 GAAATGAAAATCGCAACGAGAGAATCGCAACGA
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
***
50832 GAGAATGACTGTCGCAACGAGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGAGAGAATCGCAACGC
50866 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
50899 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
50915 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
33 46 0.61
34 29 0.39
ACGTcount: A:0.45, C:0.20, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:50995 original size:41 final size:41
Alignment explanation
Indices: 50938--51015 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
50928 TCGCGTTGCG
*
50938 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
50979 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
51016 TCTTCTGTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:51000 original size:20 final size:21
Alignment explanation
Indices: 50939--51014 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
50929 CGCGTTGCGA
50939 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
50960 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
50980 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
51001 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
51015 CTCTTCTGTA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:51136 original size:33 final size:33
Alignment explanation
Indices: 51094--51164 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
51084 AATACTAACT
*
51094 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
51127 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
51160 TGAAA
1 TGAAA
51165 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:51397 original size:22 final size:22
Alignment explanation
Indices: 51345--51399 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
51335 TGGTTGTGAG
**
51345 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
51367 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
51389 GGATTTCTTCG
1 GGATTTCTTCG
51400 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:51570 original size:20 final size:20
Alignment explanation
Indices: 51545--51737 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
51535 CTTTAAATAT
51545 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
51565 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
51587 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
51606 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
51626 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
51646 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
51666 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
51686 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
51706 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
51726 CGCGTTGCGATT
1 CGCGTTGCGATT
51738 ATGGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:51732 original size:60 final size:60
Alignment explanation
Indices: 51545--51737 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
51535 CTTTAAATAT
**
51545 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
51606 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
51666 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
51726 CGCGTTGCGATT
1 CGCGTTGCGATT
51738 ATGGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:51818 original size:20 final size:20
Alignment explanation
Indices: 51793--51844 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
51783 AAGAATCGCG
*
51793 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
51813 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
51833 TTGCGATTCTGG
1 TTGCGATTCTGG
51845 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:53123 original size:14 final size:14
Alignment explanation
Indices: 53104--53193 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
53094 TTGAAATGAA
53104 AATCGCAACGAGAG
1 AATCGCAACGAGAG
53118 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
53135 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
53151 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
53170 AATCGCAACGAGAG
1 AATCGCAACGAGAG
53184 AATCGCAACG
1 AATCGCAACG
53194 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:53141 original size:33 final size:33
Alignment explanation
Indices: 53096--53210 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
53086 GTCTTTGGTT
53096 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
53129 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
53162 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
53195 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
53211 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:53142 original size:19 final size:18
Alignment explanation
Indices: 53103--53215 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
53093 GTTGAAATGA
53103 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
53118 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
53135 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
53151 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
53168 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
53184 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
53201 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
53216 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:53246 original size:14 final size:14
Alignment explanation
Indices: 53227--53283 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
53217 TTTGGTTTCG
53227 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
53241 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
53260 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
53274 CGTTGCGATT
1 CGTTGCGATT
53284 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:53259 original size:33 final size:33
Alignment explanation
Indices: 53211--53291 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
53201 AAAATCGCAA
**
53211 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
53244 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
53277 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
53292 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:53294 original size:21 final size:21
Alignment explanation
Indices: 53268--53343 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
53258 CGCGTTGCGA
53268 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
53289 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
53309 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
53330 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
53344 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:53324 original size:41 final size:41
Alignment explanation
Indices: 53267--53344 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
53257 TCGCGTTGCG
*
53267 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
53308 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
53345 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:53470 original size:33 final size:33
Alignment explanation
Indices: 53423--53493 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
53413 AATACTAACT
* *
53423 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
53456 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
53489 TGAAA
1 TGAAA
53494 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:53727 original size:22 final size:22
Alignment explanation
Indices: 53675--53729 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
53665 TGGTTGTGAG
**
53675 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
53697 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
53719 GGATTTCTTCG
1 GGATTTCTTCG
53730 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:53900 original size:20 final size:20
Alignment explanation
Indices: 53875--54068 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
53865 CTTTAAATAT
53875 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
53895 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
53917 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
53936 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
53956 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
53976 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
53996 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
54016 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
54036 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
54056 CGCGTTGCGATTT
1 CGCGTTGCGATTT
54069 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:54062 original size:60 final size:60
Alignment explanation
Indices: 53875--54068 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
53865 CTTTAAATAT
**
53875 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
53936 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
53996 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
54056 CGCGTTGCGATTT
1 CGCGTTGCGATTT
54069 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:54085 original size:21 final size:21
Alignment explanation
Indices: 54055--54137 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
54045 ATTTTCATAT
*
54055 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
54076 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
54097 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
54118 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
54138 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:54128 original size:42 final size:43
Alignment explanation
Indices: 54035--54133 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
54025 ATTTATGTGT
* *
54035 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
54076 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
54118 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
54134 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:56658 original size:2 final size:2
Alignment explanation
Indices: 56651--56686 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
56641 ATTTAGATTG
56651 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
56687 TAAGGCTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:56761 original size:30 final size:32
Alignment explanation
Indices: 56713--56773 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
56703 ATTTATCCTC
* *
56713 TATTATTTTTCGGAATGTTTTGTCC-CTAAAT
1 TATTATTTTTCAGAATGTTTTATCCTCTAAAT
56744 TATTATTTTT-AGAATGTTTTATCCTCTAAA
1 TATTATTTTTCAGAATGTTTTATCCTCTAAA
56774 CTATAAATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 12 0.44
31 15 0.56
ACGTcount: A:0.26, C:0.11, G:0.10, T:0.52
Consensus pattern (32 bp):
TATTATTTTTCAGAATGTTTTATCCTCTAAAT
Found at i:65178 original size:21 final size:22
Alignment explanation
Indices: 65154--65198 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
65144 ATTAAAATAA
*
65154 TTTGTAAA-TTAATTTAATAGT
1 TTTGAAAAGTTAATTTAATAGT
* *
65175 TTTGAAAAGTTATTTTAGTAGT
1 TTTGAAAAGTTAATTTAATAGT
65197 TT
1 TT
65199 CAAAGTAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.13, T:0.53
Consensus pattern (22 bp):
TTTGAAAAGTTAATTTAATAGT
Found at i:76358 original size:29 final size:30
Alignment explanation
Indices: 76289--76348 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
76279 AATTTAAGGC
76289 AAAATGGTTTTTGGACTTGAATTGAATTTAT
1 AAAAT-GTTTTTGGACTTGAATTGAATTTAT
76320 AAAATGTTTTTGGACTT-AATTGAATTTAT
1 AAAATGTTTTTGGACTTGAATTGAATTTAT
76349 TCAAAGTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 12 0.41
30 12 0.41
31 5 0.17
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTAT
Found at i:76453 original size:21 final size:20
Alignment explanation
Indices: 76427--76524 Score: 117
Period size: 21 Copynumber: 4.7 Consensus size: 20
76417 AGGGTGTCAA
*
76427 AGTGCATCCCTGCATCCCTGC
1 AGTGCATCCATGCAT-CCTGC
76448 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCAT-CCTGC
76469 AGTGCATCCATGCA-CCTGCAC
1 AGTGCATCCATGCATCCTG--C
* *
76490 TAGTGCATCGATGCATCATGC
1 -AGTGCATCCATGCATCCTGC
76511 AGTGCATCCATGCA
1 AGTGCATCCATGCA
76525 CTCAAACACC
Statistics
Matches: 69, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.06
20 13 0.19
21 36 0.52
22 13 0.19
23 3 0.04
ACGTcount: A:0.21, C:0.35, G:0.20, T:0.23
Consensus pattern (20 bp):
AGTGCATCCATGCATCCTGC
Found at i:76524 original size:13 final size:13
Alignment explanation
Indices: 76437--76524 Score: 55
Period size: 13 Copynumber: 6.9 Consensus size: 13
76427 AGTGCATCCC
*
76437 TGCATCCCTGCAG
1 TGCATCCATGCAG
76450 TGCATCCATGCA-
1 TGCATCCATGCAG
76462 T-C--CC-TGCAG
1 TGCATCCATGCAG
*
76471 TGCATCCATGCACC
1 TGCATCCATGCA-G
*
76485 TGCA-CTAGTGCATCG
1 TGCATCCA-TGCA--G
76500 ATGCAT-CATGCAG
1 -TGCATCCATGCAG
76513 TGCATCCATGCA
1 TGCATCCATGCA
76525 CTCAAACACC
Statistics
Matches: 59, Mismatches: 5, Indels: 22
0.69 0.06 0.26
Matches are distributed among these distances:
8 4 0.07
9 3 0.05
10 1 0.02
11 1 0.02
12 8 0.14
13 24 0.41
14 8 0.14
15 5 0.08
16 5 0.08
ACGTcount: A:0.22, C:0.34, G:0.20, T:0.24
Consensus pattern (13 bp):
TGCATCCATGCAG
Found at i:76594 original size:41 final size:41
Alignment explanation
Indices: 76547--76625 Score: 115
Period size: 41 Copynumber: 1.9 Consensus size: 41
76537 ATGCAATTAG
** *
76547 TGCATCGATGCATCCTTG-TGTGCATCTATGCATCAAGGCCA
1 TGCATCGATGCATCC-TGCCATGCATCCATGCATCAAGGCCA
76588 TGCATCGATGCATCCTGCCATGCATCCATGCATCAAGG
1 TGCATCGATGCATCCTGCCATGCATCCATGCATCAAGG
76626 TTGCAACGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.06
41 32 0.94
ACGTcount: A:0.23, C:0.29, G:0.22, T:0.27
Consensus pattern (41 bp):
TGCATCGATGCATCCTGCCATGCATCCATGCATCAAGGCCA
Found at i:76609 original size:20 final size:20
Alignment explanation
Indices: 76547--76621 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
76537 ATGCAATTAG
**
76547 TGCATCGATGCATCCTTG-TG
1 TGCATCGATGCATCC-TGCCA
* **
76567 TGCATCTATGCATCAAGGCCA
1 TGCATCGATGCATC-CTGCCA
76588 TGCATCGATGCATCCTGCCA
1 TGCATCGATGCATCCTGCCA
*
76608 TGCATCCATGCATC
1 TGCATCGATGCATC
76622 AAGGTTGCAA
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
20 31 0.70
21 13 0.30
ACGTcount: A:0.21, C:0.31, G:0.20, T:0.28
Consensus pattern (20 bp):
TGCATCGATGCATCCTGCCA
Done.