Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008369.1 Hibiscus syriacus cultivar Beakdansim tig00111124_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: 99524
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:328 original size:14 final size:14
Alignment explanation
Indices: 309--396 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
299 GCGAAATGAA
309 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
323 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
342 AATCGCAACGAGGG
1 AATCGCAACGAGAG
*
356 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
375 AATCGCAACGAGGG
1 AATCGCAACGAGAG
389 AATCGCAA
1 AATCGCAA
397 TGCGAAATGA
Statistics
Matches: 57, Mismatches: 7, Indels: 20
0.68 0.08 0.24
Matches are distributed among these distances:
14 26 0.46
15 2 0.04
16 4 0.07
17 4 0.07
18 2 0.04
19 19 0.33
ACGTcount: A:0.43, C:0.19, G:0.26, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:333 original size:33 final size:33
Alignment explanation
Indices: 291--417 Score: 245
Period size: 33 Copynumber: 3.8 Consensus size: 33
281 GGAAATTACT
*
291 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
324 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
357 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
390 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
418 CGAATTTAAT
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
33 93 1.00
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
Found at i:439 original size:19 final size:20
Alignment explanation
Indices: 417--459 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
407 AAATCGCAAC
417 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
436 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
456 GCGA
1 GCGA
460 TTCCCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:619 original size:14 final size:14
Alignment explanation
Indices: 600--635 Score: 65
Period size: 13 Copynumber: 2.6 Consensus size: 14
590 CATCAATTAA
600 ACAAATCAACTTTT
1 ACAAATCAACTTTT
614 ACAAATC-ACTTTT
1 ACAAATCAACTTTT
627 ACAAATCAA
1 ACAAATCAA
636 TTAAACAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.62
14 8 0.38
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:643 original size:13 final size:13
Alignment explanation
Indices: 591--647 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
581 TTATGTTAAC
591 ATCAATTAAACAA
1 ATCAATTAAACAA
**
604 ATCAACTTTTACAA
1 ATCAA-TTAAACAA
* **
618 ATCACTTTTACAA
1 ATCAATTAAACAA
631 ATCAATTAAAC-A
1 ATCAATTAAACAA
643 ATCAA
1 ATCAA
648 AATAAGCAAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
12 6 0.16
13 21 0.57
14 10 0.27
ACGTcount: A:0.51, C:0.19, G:0.00, T:0.30
Consensus pattern (13 bp):
ATCAATTAAACAA
Found at i:2048 original size:21 final size:21
Alignment explanation
Indices: 1982--2048 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1972 GTGAATCGGG
*
1982 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
2002 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
2024 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
2045 CTCT
1 CTCT
2049 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:2067 original size:42 final size:41
Alignment explanation
Indices: 1982--2104 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1972 GTGAATCGGG
* * * * *
1982 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
2024 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
2066 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
2105 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:4139 original size:20 final size:19
Alignment explanation
Indices: 4094--4234 Score: 86
Period size: 19 Copynumber: 7.8 Consensus size: 19
4084 TCTTTTGGTT
4094 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* * *
4113 GATAATGAGAATTGCAACGCG
1 GA-AATGAAAATCGCAACG-A
** *
4134 GAAATGACTATCGCAATGA
1 GAAATGAAAATCGCAACGA
*
4153 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
4167 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
4186 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
*
4200 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
4219 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
4235 TGCGATTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 18 0.19
16 4 0.04
17 4 0.04
19 39 0.42
20 26 0.28
21 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:4176 original size:33 final size:33
Alignment explanation
Indices: 4119--4217 Score: 144
Period size: 33 Copynumber: 3.0 Consensus size: 33
4109 ACGAGATAAT
* *
4119 GAGAATTGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
4153 GAGAATCGCAACGCGAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
4186 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
4218 CGAAATGAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 46 0.78
34 13 0.22
ACGTcount: A:0.39, C:0.21, G:0.26, T:0.13
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:4211 original size:19 final size:19
Alignment explanation
Indices: 4189--4239 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
4179 GCGACGAGAG
4189 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
4208 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
4227 AATCGCAATGCGA
1 AATCGCAACGCGA
4240 TTTTGGTTTC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:4269 original size:18 final size:18
Alignment explanation
Indices: 4235--4300 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 18
4225 AAAATCGCAA
*
4235 TGCGATTTTGGTTTCGCGT
1 TGCGATTTT-ATTTCGCGT
4254 TGCGATTTTATTTCGCGT
1 TGCGATTTTATTTCGCGT
* *
4272 TGCGATAGTTATTTCCGCTT
1 TGCGAT-TTTATTT-CGCGT
4292 TGCGATTTT
1 TGCGATTTT
4301 CATTCTCGAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
18 14 0.34
19 17 0.41
20 10 0.24
ACGTcount: A:0.11, C:0.17, G:0.24, T:0.48
Consensus pattern (18 bp):
TGCGATTTTATTTCGCGT
Found at i:4296 original size:20 final size:19
Alignment explanation
Indices: 4246--4297 Score: 70
Period size: 18 Copynumber: 2.7 Consensus size: 19
4236 GCGATTTTGG
*
4246 TTTCGCGTTGCGAT-TTTA
1 TTTCGCGTTGCGATAGTTA
4264 TTTCGCGTTGCGATAGTTA
1 TTTCGCGTTGCGATAGTTA
*
4283 TTTCCGCTTTGCGAT
1 TTT-CGCGTTGCGAT
4298 TTTCATTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 14 0.47
19 6 0.20
20 10 0.33
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (19 bp):
TTTCGCGTTGCGATAGTTA
Found at i:4916 original size:20 final size:20
Alignment explanation
Indices: 4823--4916 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
4813 CGCTAAGTAA
*
4823 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* *
4843 ATCGCGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
4863 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
4884 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
4904 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
4917 TTTCCTAATT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:4935 original size:41 final size:41
Alignment explanation
Indices: 4842--4937 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 41
4832 CGAAAGTCAG
* * * * *
4842 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTAA
* *
4883 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCTAA
1 TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CTAA
4925 T-TCGCGTTGCGAT
1 TATCGCGTTGCGAT
4938 TTACTTATTC
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
41 43 0.93
42 3 0.07
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.39
Consensus pattern (41 bp):
TATCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCTAA
Found at i:4949 original size:20 final size:21
Alignment explanation
Indices: 4905--4956 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
4895 ATAGTCAGTA
*
4905 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTACTAAT
* *
4926 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACTAAT
4946 TCGCATTGCGA
1 TCGCATTGCGA
4957 ATTGGGAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 17 0.63
21 10 0.37
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACTAAT
Found at i:6080 original size:23 final size:21
Alignment explanation
Indices: 6046--6089 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
6036 ATATAAAAAA
6046 TTATTTTTTATTAAATATTTTT
1 TTATTTTTTATTAAAT-TTTTT
*
6068 TTATATTTTTATTTAATTTTTT
1 TTAT-TTTTTATTAAATTTTTT
6090 AAATAATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (21 bp):
TTATTTTTTATTAAATTTTTT
Found at i:8290 original size:16 final size:16
Alignment explanation
Indices: 8269--8348 Score: 115
Period size: 16 Copynumber: 5.0 Consensus size: 16
8259 ATAAACGAAT
8269 ATAAACGAACACAAAC
1 ATAAACGAACACAAAC
*
8285 ATAAACGATCACAAAC
1 ATAAACGAACACAAAC
*
8301 ATAAACGAACACGAAC
1 ATAAACGAACACAAAC
* *
8317 ATAAATGAACACGAAC
1 ATAAACGAACACAAAC
*
8333 ATAAACGAACATAAAC
1 ATAAACGAACACAAAC
8349 GTTGGAGACC
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 57 1.00
ACGTcount: A:0.59, C:0.23, G:0.09, T:0.10
Consensus pattern (16 bp):
ATAAACGAACACAAAC
Found at i:9443 original size:24 final size:24
Alignment explanation
Indices: 9416--9477 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
9406 ATAAATGAAT
9416 GAACATAAATGAACATAACCGAAC
1 GAACATAAATGAACATAACCGAAC
*
9440 GAACATAAACGAACATAACCGAAC
1 GAACATAAATGAACATAACCGAAC
* *
9464 AAACGTAAATGAAC
1 GAACATAAATGAAC
9478 GAACGAGACA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.55, C:0.21, G:0.13, T:0.11
Consensus pattern (24 bp):
GAACATAAATGAACATAACCGAAC
Found at i:9865 original size:18 final size:19
Alignment explanation
Indices: 9826--9872 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
9816 ATTTTTCAAG
**
9826 TAAAA-ATAATAAATTTTA
1 TAAAATATAATAAATAATA
9844 TAAAATATAATAAATAAT-
1 TAAAATATAATAAATAATA
*
9862 TAAAATTTAAT
1 TAAAATATAAT
9873 TGTGTTAACA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATATAATAAATAATA
Found at i:11214 original size:39 final size:40
Alignment explanation
Indices: 11129--11214 Score: 99
Period size: 39 Copynumber: 2.2 Consensus size: 40
11119 TGCACTCCTG
* *
11129 GAATCTTCTCTATTTGCCTGAAGACGTCATGCACTCGTTA
1 GAATCTTCTCTATTTACCTGAAGACGTCATGCAATCGTTA
*
11169 G-GTCTTCT-TCATTTACCTGAAGACG-CGATGCAATCG-TA
1 GAATCTTCTCT-ATTTACCTGAAGACGTC-ATGCAATCGTTA
11207 GAATCTTC
1 GAATCTTC
11215 ATATTTAACT
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
38 5 0.13
39 33 0.85
40 1 0.03
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.34
Consensus pattern (40 bp):
GAATCTTCTCTATTTACCTGAAGACGTCATGCAATCGTTA
Found at i:14938 original size:2 final size:2
Alignment explanation
Indices: 14931--14991 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
14921 TGACAACTTT
14931 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
14973 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
14992 TCTACACTAC
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:15153 original size:6 final size:7
Alignment explanation
Indices: 15122--15161 Score: 55
Period size: 7 Copynumber: 5.7 Consensus size: 7
15112 TTTTAAACCC
15122 TAAATCA
1 TAAATCA
*
15129 TAAAATCT
1 T-AAATCA
15137 TAAATCA
1 TAAATCA
15144 TAAA-CA
1 TAAATCA
15150 TAAATCA
1 TAAATCA
15157 TAAAT
1 TAAAT
15162 TTTAAACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
6 6 0.21
7 17 0.59
8 6 0.21
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (7 bp):
TAAATCA
Found at i:15153 original size:21 final size:21
Alignment explanation
Indices: 15122--15183 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
15112 TTTTAAACCC
*
15122 TAAATCATAAAATCTTAAATCA
1 TAAACCAT-AAATCTTAAATCA
* **
15144 TAAA-CATAAATCATAAATTT
1 TAAACCATAAATCTTAAATCA
*
15164 TAAACCCTAAATCTTAAATC
1 TAAACCATAAATCTTAAATC
15184 TTAAGCCCTA
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
20 14 0.42
21 15 0.45
22 4 0.12
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (21 bp):
TAAACCATAAATCTTAAATCA
Found at i:15155 original size:13 final size:14
Alignment explanation
Indices: 15122--15161 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
15112 TTTTAAACCC
*
15122 TAAATCATAAAATCT
1 TAAATCAT-AAATCA
15137 TAAATCATAAA-CA
1 TAAATCATAAATCA
15150 TAAATCATAAAT
1 TAAATCATAAAT
15162 TTTAAACCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 12 0.52
14 3 0.13
15 8 0.35
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.30
Consensus pattern (14 bp):
TAAATCATAAATCA
Found at i:15181 original size:7 final size:7
Alignment explanation
Indices: 15131--15187 Score: 53
Period size: 7 Copynumber: 8.3 Consensus size: 7
15121 CTAAATCATA
15131 AAATCTT
1 AAATCTT
*
15138 AAATCAT
1 AAATCTT
*
15145 AAA-CAT
1 AAATCTT
*
15151 AAATCAT
1 AAATCTT
*
15158 AAATTTT
1 AAATCTT
* *
15165 AAACCCT
1 AAATCTT
15172 AAATCTT
1 AAATCTT
15179 AAATCTT
1 AAATCTT
15186 AA
1 AA
15188 GCCCTAATTC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
6 6 0.15
7 35 0.85
ACGTcount: A:0.51, C:0.16, G:0.00, T:0.33
Consensus pattern (7 bp):
AAATCTT
Found at i:15181 original size:28 final size:28
Alignment explanation
Indices: 15122--15183 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
15112 TTTTAAACCC
*
15122 TAAATCATAAAATCTTAAATCATAAACA
1 TAAATCATAAAATCTTAAACCATAAACA
* * *
15150 TAAATCAT-AAATTTTAAACCCTAAATCT
1 TAAATCATAAAATCTTAAACCATAAA-CA
15178 TAAATC
1 TAAATC
15184 TTAAGCCCTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (28 bp):
TAAATCATAAAATCTTAAACCATAAACA
Found at i:15187 original size:21 final size:21
Alignment explanation
Indices: 15131--15194 Score: 76
Period size: 21 Copynumber: 3.1 Consensus size: 21
15121 CTAAATCATA
* *
15131 AAATCTTAAATCATAAA-CAT
1 AAATCTTAAATCTTAAACCCT
* *
15151 AAATCATAAATTTTAAACCCT
1 AAATCTTAAATCTTAAACCCT
*
15172 AAATCTTAAATCTTAAGCCCT
1 AAATCTTAAATCTTAAACCCT
15193 AA
1 AA
15195 TTCTAAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
20 14 0.39
21 22 0.61
ACGTcount: A:0.48, C:0.19, G:0.02, T:0.31
Consensus pattern (21 bp):
AAATCTTAAATCTTAAACCCT
Found at i:17327 original size:26 final size:28
Alignment explanation
Indices: 17267--17328 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
17257 GAGTATTGCT
*
17267 GAGCTCGACTCGACTCGAAAACTCTGAAATG
1 GAGCTCGACTCGACTCGAAAACTCTG--A-C
17298 GAGCTCGACTCGACTCGAAAACTC-G-C
1 GAGCTCGACTCGACTCGAAAACTCTGAC
17324 GAGCT
1 GAGCT
17329 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
26 5 0.17
30 1 0.03
31 24 0.80
ACGTcount: A:0.29, C:0.29, G:0.24, T:0.18
Consensus pattern (28 bp):
GAGCTCGACTCGACTCGAAAACTCTGAC
Found at i:19969 original size:35 final size:35
Alignment explanation
Indices: 19918--19987 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
19908 AACAATAATA
*
19918 TATTTGTTTAATGAGATAACATATTAGAATTTTAT
1 TATTTGTTTAAAGAGATAACATATTAGAATTTTAT
19953 TATTTGTTTAAAGAGATAACATATTAGAATTTTAT
1 TATTTGTTTAAAGAGATAACATATTAGAATTTTAT
19988 GTAAAATCAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.03, G:0.11, T:0.47
Consensus pattern (35 bp):
TATTTGTTTAAAGAGATAACATATTAGAATTTTAT
Found at i:21290 original size:17 final size:17
Alignment explanation
Indices: 21268--21300 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
21258 GATCATCAAA
21268 TTCAGCTCTATCTTTTT
1 TTCAGCTCTATCTTTTT
21285 TTCAGCTCTATCTTTT
1 TTCAGCTCTATCTTTT
21301 AACCACGTGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.24, G:0.06, T:0.58
Consensus pattern (17 bp):
TTCAGCTCTATCTTTTT
Found at i:24119 original size:306 final size:306
Alignment explanation
Indices: 23359--24207 Score: 941
Period size: 306 Copynumber: 2.8 Consensus size: 306
23349 TGGATCGTTC
* * * *
23359 GGATCGGATACAAGGTGATTACTGATTTTCGG---GGCAAACGAGCTTTTTTTTCCTTAATCAAA
1 GGATCCGATACAAGGTGATTAATGATTTTTGGTATGGAAAACGAGCTTTTTTTTCCTTAATCAAA
** * * **
23421 GGCAAGTTACCTTAATAATTAAAAATAAATTACATGCTTGAAACCATTTTGTCACTTGTTGTCTT
66 GGCAAACTACCTTAATAATTAAAAAGAAATTACATGCTTGAAACCTTTTTGTCAC-TAATGTCTT
* ** * * * *
23486 AGATCAGCTGGTAGAGCATGTGGCTTTTAACCATATGGTTGTGGGTTTGATTCCCACGGAAGGCG
130 AGCTCAGCTGGTAGAGCATGTGGCTTTTAACCACGTGGTCGTGGGTTTGATTCCCACAGTAGGTG
* * * *
23551 TTGTTGTTC-ATGTGTAGTTGAATGTGTTCATATACTAGGTACGGGTAGTGATATGAATTTCATG
195 TTGTTGTTCGA-GTGTAGTTGAATATGTTCATATACTAGGTACGGATAATGATATGAATTTCATC
* *
23615 TGTCGCATTTTGCATTTGAATGGATAATCAAGGCAATTCACAAGAAAATTAA
259 CGTCGCA--TT--ATTTGAATAGATAATCAAGGCAATTCACAAGAAAATTAA
** *
23667 GGATGGGATACAAGGTGATTAATGATTTTTGGTATGGAAAACGAGCTTTTTTCTCTCCTTTATCA
1 GGATCCGATACAAGGTGATTAATGATTTTTGGTATGGAAAACGAGCTTTTTT-T-TCCTTAATCA
* * **
23732 AAGGCAAACTACCTTAATAATTATAAAGAAATTACATGCTTGAAACCTTTTCGTCACTTGTCGTC
64 AAGGCAAACTACCTTAATAATTAAAAAGAAATTACATGCTTGAAACCTTTTTGTCACTAAT-GTC
* * * *** * *
23797 TTAACTCAGTTGGTAGAGCATGTGGCTTTTAATCACGTGGTCAAAGGTTCGAATTCCCACAGTCG
128 TTAGCTCAGCTGGTAGAGCATGTGGCTTTTAACCACGTGGTCGTGGGTTTG-ATTCCCACAGTAG
* *
23862 GTGTTGTTGTTCGCGTGTAGTTAAATATGTTCATATACTAGGTA-GTGATAATGATCA-GAATTT
192 GTGTTGTTGTTCGAGTGTAGTTGAATATGTTCATATACTAGGTACG-GATAATGAT-ATGAATTT
* * * **
23925 GATCCCGT-GCA-T-TTTGAATAGAT-ATCAAGGCGATTCACCTA-AAAATTTC
255 CAT-CCGTCGCATTATTTGAATAGATAATCAAGGCAATTCA-CAAGAAAATTAA
* * *
23974 GGATCCGTTACAAGGTGATTAATGATTTTTTTGGTATGGGAAACGAG-TTTTTTTTTCTTAATCA
1 GGATCCGATACAAGGTGATTAATGA--TTTTTGGTATGGAAAACGAGCTTTTTTTTCCTTAATCA
* *
24038 AACGCAAACTACCATAATAATTAAAAAGAAATTACATGCTTGAAACCTTTTTGTCACTCAATGTC
64 AAGGCAAACTACCTTAATAATTAAAAAGAAATTACATGCTTGAAACCTTTTTGTCACT-AATGTC
* ** *
24103 TTAGCTCAACTGGTAGAGCGCGTGGCTTTTAACCACGTGGTCGTGGGTTTGATTCGCACA-TATG
128 TTAGCTCAGCTGGTAGAGCATGTGGCTTTTAACCACGTGGTCGTGGGTTTGATTCCCACAGTA-G
* *
24167 GTGTTGTTGTTCGATTGTAGTTGAATATGTTCATACACTAG
192 GTGTTGTTGTTCGAGTGTAGTTGAATATGTTCATATACTAG
24208 TGTCGCAACC
Statistics
Matches: 456, Mismatches: 69, Indels: 35
0.81 0.12 0.06
Matches are distributed among these distances:
304 1 0.00
305 46 0.10
306 106 0.23
307 43 0.09
308 47 0.10
309 19 0.04
311 17 0.04
312 3 0.01
313 104 0.23
314 67 0.15
315 3 0.01
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.35
Consensus pattern (306 bp):
GGATCCGATACAAGGTGATTAATGATTTTTGGTATGGAAAACGAGCTTTTTTTTCCTTAATCAAA
GGCAAACTACCTTAATAATTAAAAAGAAATTACATGCTTGAAACCTTTTTGTCACTAATGTCTTA
GCTCAGCTGGTAGAGCATGTGGCTTTTAACCACGTGGTCGTGGGTTTGATTCCCACAGTAGGTGT
TGTTGTTCGAGTGTAGTTGAATATGTTCATATACTAGGTACGGATAATGATATGAATTTCATCCG
TCGCATTATTTGAATAGATAATCAAGGCAATTCACAAGAAAATTAA
Found at i:24771 original size:16 final size:18
Alignment explanation
Indices: 24739--24773 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
24729 ATATAAAAAC
24739 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
24757 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
24773 A
1 A
24774 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:24903 original size:2 final size:2
Alignment explanation
Indices: 24890--24936 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
24880 AAAATAGGAA
*
24890 AT AT AT AA 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
24932 AT AT A
1 AT AT A
24937 ATAACACTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24967 original size:33 final size:33
Alignment explanation
Indices: 24922--25015 Score: 102
Period size: 33 Copynumber: 2.9 Consensus size: 33
24912 ATATATATAT
* *
24922 ATATATATATATATAATAACACTAATAAAAAAC
1 ATATATACATATATAATAAAACTAATAAAAAAC
* * *
24955 ATATATACATATATAATAAAATTAATAGAAAAT
1 ATATATACATATATAATAAAACTAATAAAAAAC
* *
24988 A-ATATGCATATATAACAAGAA-TAATAAA
1 ATATATACATATATAATAA-AACTAATAAA
25016 GTAGGAAAAA
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
32 21 0.40
33 31 0.60
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (33 bp):
ATATATACATATATAATAAAACTAATAAAAAAC
Found at i:26289 original size:105 final size:105
Alignment explanation
Indices: 25990--27162 Score: 1701
Period size: 105 Copynumber: 11.3 Consensus size: 105
25980 CATTGTTCCA
* * **
25990 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAATTG-TTGTTGACAA
* * * *
26054 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
64 GCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
26096 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
26156 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
26196 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
*
26261 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
26301 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGCTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
26361 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
26401 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
26461 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
26501 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAA-TTGTTGTTGACAAG
*
26565 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
**
26606 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
*
26666 AGCGCTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
26706 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATT-GGAAAGTTGTTGTTGACAAG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAA-TTGTTGTTGACAAG
*
26770 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
26811 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
26876 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
26916 AATCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGG-AAATTG-TTGTTGACAA
*
26981 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * *
27023 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTG-TTGTTGACAAG
* * * *
27088 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
27129 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
27163 CGCGGATGGC
Statistics
Matches: 989, Mismatches: 55, Indels: 43
0.91 0.05 0.04
Matches are distributed among these distances:
99 1 0.00
100 357 0.36
101 10 0.01
102 13 0.01
103 10 0.01
104 11 0.01
105 368 0.37
106 100 0.10
107 97 0.10
109 22 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAATTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:26343 original size:205 final size:207
Alignment explanation
Indices: 25990--27162 Score: 1701
Period size: 205 Copynumber: 5.7 Consensus size: 207
25980 CATTGTTCCA
* * **
25990 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGG-ATTGGGAAATTG-TTGTTGACAAC
* * *
26055 CAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAA
64 CAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
**
26119 GTTGAAATTGAATCTGAA-T-GAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
128 GTTGAAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
26181 ACTTGCGTTGTCTGG
193 ACTTGCGTTGTCTGG
* * *
26196 AGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAGTTGTTGTTGACAAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GGATTGGGAAATTGTTGTTGACAACC
* *
26261 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCCTTCGCTGTGAAGT
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
*
26326 TGAAATTGGCTCTGAA-T-GAAA-TTTTGCTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
130 TGAAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
26388 TTGCGTTGTCTGG
195 TTGCGTTGTCTGG
* * *
26401 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAACCA
26462 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
26527 GAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGA-ATTGGAAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
26592 CTTGCATTGTCTGG
194 CTTGCGTTGTCTGG
** * *
26606 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCT-GAAT--GAAATT-TTGTTGACAAGCA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAACCA
*
26667 GCGCTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
66 GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
26732 GAAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
131 GAAATTGGCTCTGA-ATTGGAAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
26797 CTTGCATTGTCTGG
194 CTTGCGTTGTCTGG
*
26811 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAACC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAATTGTTGTTGACAACC
* *
26876 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAATCCAATATCCTTCGCTGTGAAGT
65 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGT
* * *
26941 TGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTT
130 TGAAATTGGCTCTG-AATT-GG-AAAGT-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTT
27006 GAACTTGCGTTGTCTGG
191 GAACTTGCGTTGTCTGG
* * * *
27023 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG-GATTGGGAAATTG-TTGTTGACAAC
* * * * * *
27088 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTG
64 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT-CCA--ATATCCTTCGTTGTG
*
27153 GAGTTGAAAT
126 AAGTTGAAAT
27163 CGCGGATGGC
Statistics
Matches: 897, Mismatches: 50, Indels: 30
0.92 0.05 0.03
Matches are distributed among these distances:
200 89 0.10
201 6 0.01
202 1 0.00
203 7 0.01
204 3 0.00
205 466 0.52
206 44 0.05
207 5 0.01
209 5 0.01
210 90 0.10
211 3 0.00
212 103 0.11
213 51 0.06
214 3 0.00
216 21 0.02
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (207 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGGATTGGGAAATTGTTGTTGACAACCA
GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTT
GAAATTGGCTCTGAATTGGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACT
TGCGTTGTCTGG
Found at i:26536 original size:305 final size:310
Alignment explanation
Indices: 25990--27162 Score: 1803
Period size: 305 Copynumber: 3.8 Consensus size: 310
25980 CATTGTTCCA
* *
25990 AGTCCAATATCCTCCG-TCGTGAAGTTGAAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGCT-GTGAAGTTGAAATTGGCTCT-GAA-C-TGAAATTGTTTGTTGACAA
* * *
26054 CCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGA
62 CCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGA
**
26118 AGTTGAAATTGAATCTGAA-TGAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
126 AGTTGAAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGA
* *
26181 ACTTGCGTTGTCTGGAGTCCAATATCTTTCGTTGTGAAGTTGAAATTGGCTCTGGGATTGGGAAG
191 ACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAG
26246 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
256 TTGTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
26301 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAA-TGAAA-T-TTTGCTGACAAGCAG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAACTGAAATTGTTTGTTGACAACCAG
*
26363 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
26428 AAATTGGCTCTGAA-TGAAA-TTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
131 AAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
*
26491 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGAAAGTTGTT
196 CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTT
*
26556 GTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
261 GTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* *
26606 AGTCCAATATCCTTCACTGTGAAGTTGAAATTGGCTCTGAA-TGAAA-T-TTTGTTGACAAGCAG
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAACTGAAATTGTTTGTTGACAACCAG
*
26668 CGCTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
26733 AAATTGGCTCTGAGATTGGAAAGTTGTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGA-ATT-GAAAGTT-TTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
26798 TTGCATTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
193 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTT
* *
26863 GTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
258 GTTGTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
* * *
26916 AATCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AACT--G-AAATTGTTTGTTGACAA
26981 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
62 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAA
* * * *
27046 GTTGAAATTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGT
127 GTTGAAATTGGCTCTG-AATTGA-AAG-T-TTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGT
* * * * *
27111 TGAACTTGTGTTGTCTCGAGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
188 TGAACTTGCGTTGTCTGGAGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
27163 CGCGGATGGC
Statistics
Matches: 804, Mismatches: 37, Indels: 32
0.92 0.04 0.04
Matches are distributed among these distances:
304 1 0.00
305 380 0.47
306 2 0.00
307 5 0.01
308 4 0.00
309 2 0.00
310 193 0.24
311 37 0.05
312 2 0.00
314 1 0.00
315 3 0.00
316 3 0.00
317 94 0.12
318 51 0.06
319 4 0.00
321 22 0.03
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (310 bp):
AGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAACTGAAATTGTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAATTGAAAGTTTTGTTGACAAGCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG
CGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTT
GTTGACAAACAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
Found at i:27856 original size:68 final size:65
Alignment explanation
Indices: 27766--28152 Score: 235
Period size: 65 Copynumber: 5.8 Consensus size: 65
27756 AAGATATCTG
* * **
27766 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTATGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGA-
27831 TT
64 TT
* * *
27833 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGAT
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
27898 T
65 T
* ** * * *
27899 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAAC-AAAATTTGTTTTAAGGGAAA-----T--A-A-A
** *
27963 GACAAA-ACT
56 TTCAAAGATT
* * * **** * * * * *
27972 TAGTTCCAAAAGAAACTGTCTCAAGGGAAATGGTATTTGTTTCAA-AGAAACATATTCAAATATT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
* * * * ** * *** *
28036 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATG-TT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
*
28100 TATGTTTCAAGAGAAACTGTCTCAAGGGAGAA-AAAATTTTGTTTCAAGGGAAA
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGA-AACAAAA-TTTGTTTTAAGGGAAA
28153 CTGTCTCAAG
Statistics
Matches: 245, Mismatches: 58, Indels: 35
0.72 0.17 0.10
Matches are distributed among these distances:
63 5 0.02
64 37 0.15
65 78 0.32
66 21 0.09
67 24 0.10
68 32 0.13
70 1 0.00
72 7 0.03
73 35 0.14
74 5 0.02
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (65 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
Found at i:27950 original size:36 final size:36
Alignment explanation
Indices: 27899--28206 Score: 166
Period size: 36 Copynumber: 8.9 Consensus size: 36
27889 TTCAAAGATT
* *
27899 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAAC
27935 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
* * * * **** *
27971 TTAGTTCCAAAAGAAACTGTCTCAAGGGAAATGGTAT
1 TT-GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
* * **
28008 TTGTTTCAA-AGAAACATAT-TC-----A-A-ATATT
1 TTGTTTCAAGAGAAAC-TGTCTCAAGAGAGACAAAAC
*
28036 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAC
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
** * * * ***
28072 TCATTTCAAGGGAAA-TGTTTTC-A-A-TG--TTTA-
1 TTGTTTCAAGAGAAACTG-TCTCAAGAGAGACAAAAC
* * *
28102 -TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-C
* **
28138 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAGT
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
*
28174 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAA
28207 TGATGAGCAC
Statistics
Matches: 208, Mismatches: 42, Indels: 44
0.71 0.14 0.15
Matches are distributed among these distances:
28 12 0.06
29 22 0.11
30 4 0.02
31 1 0.00
32 1 0.00
33 1 0.00
34 3 0.01
35 16 0.08
36 91 0.44
37 57 0.27
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (36 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAAC
Found at i:28087 original size:202 final size:201
Alignment explanation
Indices: 27835--28198 Score: 480
Period size: 202 Copynumber: 1.8 Consensus size: 201
27825 GAAGATTTTG
* * * ** * *
27835 TGTTTCAAGAGTAACTGTCTCAAGGGAGACAAAATTTGTTTTAGGGGAAATAAATTCAAAGATTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTCATTTCAAGGGAAATAAATTCAAAG-TTT
* * *
27900 -TGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGA
65 ATGTTTCAAGAGAAACTGTCTCAAGAGAGA-AAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
27963 GACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAAATGGTATTTGTTTCAAAGAAACATATT
129 GAC-AAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAAATGGTATTTGTTTCAAAGAAACATATT
28028 CAAATATTT
193 CAAATATTT
* *** *
28037 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTCATTTCAAGGGAAATAAATTCAAAGTTTA
* *
28102 TGTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTTGTTTCAAGGGAAACTGTCTCAAGAGAG
66 TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAG
* * * **
28167 ACAAAGTTTGTTTCAAGGGAAACTGTCTCAAG
130 ACAAACTTAGTTCCAAAAGAAACTGTCTCAAG
28199 AGAGACAATG
Statistics
Matches: 137, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
201 7 0.05
202 100 0.73
203 30 0.22
ACGTcount: A:0.38, C:0.13, G:0.21, T:0.29
Consensus pattern (201 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTCATTTCAAGGGAAATAAATTCAAAGTTTA
TGTTTCAAGAGAAACTGTCTCAAGAGAGAAAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGAGA
CAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAAATGGTATTTGTTTCAAAGAAACATATTCAA
ATATTT
Found at i:29093 original size:22 final size:22
Alignment explanation
Indices: 29066--29116 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
29056 TTGTGTTTGG
29066 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
* *
29088 TTAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
29110 TCAAAGG
1 TCAAAGG
29117 ATTGATGGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.25, C:0.10, G:0.27, T:0.37
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:29748 original size:20 final size:21
Alignment explanation
Indices: 29722--29783 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 21
29712 CTTTTTGTTC
*
29722 CCTTTTTTATTTTTGTTCTTT
1 CCTTTTTTATTCTTGTTCTTT
* *
29743 -CTTTTTTGTTCTTGTTTTTT
1 CCTTTTTTATTCTTGTTCTTT
*
29763 CCTTTTTTGCTTCTT-TTCTTT
1 CCTTTTTT-ATTCTTGTTCTTT
29784 TTTCTTTTTG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 12 0.35
22 5 0.15
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (21 bp):
CCTTTTTTATTCTTGTTCTTT
Found at i:29794 original size:22 final size:22
Alignment explanation
Indices: 29740--29792 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
29730 ATTTTTGTTC
29740 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
29761 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
29784 TTTCTTTTT
1 TTTCTTTTT
29793 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:33014 original size:16 final size:18
Alignment explanation
Indices: 32982--33016 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
32972 ATATAAAAAC
32982 ATAAAATATAGGATAAAT
1 ATAAAATATAGGATAAAT
33000 ATAAAA-ATA-GATAAAT
1 ATAAAATATAGGATAAAT
33016 A
1 A
33017 AATGAGTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.47
17 3 0.18
18 6 0.35
ACGTcount: A:0.66, C:0.00, G:0.09, T:0.26
Consensus pattern (18 bp):
ATAAAATATAGGATAAAT
Found at i:33138 original size:2 final size:2
Alignment explanation
Indices: 33131--33175 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
33121 AAAATAGGAA
33131 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
33173 AT A
1 AT A
33176 ATAACACTAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33219 original size:32 final size:33
Alignment explanation
Indices: 33161--33224 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
33151 ATATATATAT
* *
33161 ATATATATATATATAATAACACTAATA-AAAAC
1 ATATATACATATATAATAAAACTAATAGAAAAC
*
33193 ATATATACATATATAATAAAATTAATAGAAAA
1 ATATATACATATATAATAAAACTAATAGAAAA
33225 TATGCATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 24 0.86
33 4 0.14
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (33 bp):
ATATATACATATATAATAAAACTAATAGAAAAC
Found at i:36616 original size:22 final size:22
Alignment explanation
Indices: 36591--36644 Score: 99
Period size: 22 Copynumber: 2.5 Consensus size: 22
36581 TTTGTTATAC
*
36591 TTTTGTTAATTTAACACTTTTA
1 TTTTGTTAACTTAACACTTTTA
36613 TTTTGTTAACTTAACACTTTTA
1 TTTTGTTAACTTAACACTTTTA
36635 TTTTGTTAAC
1 TTTTGTTAAC
36645 ATTATGCACT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.26, C:0.11, G:0.06, T:0.57
Consensus pattern (22 bp):
TTTTGTTAACTTAACACTTTTA
Found at i:38382 original size:20 final size:19
Alignment explanation
Indices: 38359--38402 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
38349 TTTTATGTTC
*
38359 TTTTAAATATATAATTTTAA
1 TTTTAAATA-AAAATTTTAA
38379 TTTTAAATAAAAATTTTAA
1 TTTTAAATAAAAATTTTAA
*
38398 ATTTA
1 TTTTA
38403 CCAAATCGTG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTTTAAATAAAAATTTTAA
Found at i:42209 original size:66 final size:64
Alignment explanation
Indices: 42099--42223 Score: 151
Period size: 66 Copynumber: 1.9 Consensus size: 64
42089 GGATTGTTGA
*
42099 GTTGCTTTCGATATTAATGCTCATAGTGCGCCTAATATGGGTTTTGAAGGGCTAAACATGGAAAC
1 GTTGCTTTCGATATTAATGCTCATAGTACGCCTAATATGGGTTTTGAAGGGC--AACATGGAAAC
42164 T
64 T
* * * * * * * *
42165 GTTGCTTTTGATGTTAATGCTTATGGTACGGCTAATTTGTGTTTTGATGGGCAACATGG
1 GTTGCTTTCGATATTAATGCTCATAGTACGCCTAATATGGGTTTTGAAGGGCAACATGG
42224 GCTAAACAAC
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
64 7 0.14
66 43 0.86
ACGTcount: A:0.23, C:0.13, G:0.26, T:0.38
Consensus pattern (64 bp):
GTTGCTTTCGATATTAATGCTCATAGTACGCCTAATATGGGTTTTGAAGGGCAACATGGAAACT
Found at i:42457 original size:15 final size:15
Alignment explanation
Indices: 42437--42473 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
42427 ATATTTAGCT
*
42437 GGGCGGGCGGATGTG
1 GGGCGGGCGGATGCG
42452 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
42467 GGGCGGG
1 GGGCGGG
42474 TAATGTCTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.05, C:0.16, G:0.70, T:0.08
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:45919 original size:24 final size:26
Alignment explanation
Indices: 45882--45929 Score: 66
Period size: 24 Copynumber: 1.9 Consensus size: 26
45872 ATATAATTAT
45882 TAAATAAAATATTAA-AAA-ATAACA
1 TAAATAAAATATTAATAAAGATAACA
45906 TAAATAATAA-ATTAATAAAGATAA
1 TAAATAA-AATATTAATAAAGATAA
45930 AATCATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 12 0.57
25 5 0.24
26 4 0.19
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (26 bp):
TAAATAAAATATTAATAAAGATAACA
Found at i:47336 original size:30 final size:31
Alignment explanation
Indices: 47291--47351 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 31
47281 AATCATCAAT
*
47291 AAAATATAAAAAAAATACTTGGATTACAAAA
1 AAAATATAAAAAAAATACTTGAATTACAAAA
* *
47322 AAAAT-TATAAAAAATACTTGAATTATAAAA
1 AAAATATAAAAAAAATACTTGAATTACAAAA
47352 GAATCAACTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.64, C:0.05, G:0.05, T:0.26
Consensus pattern (31 bp):
AAAATATAAAAAAAATACTTGAATTACAAAA
Found at i:47547 original size:14 final size:14
Alignment explanation
Indices: 47528--47556 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
47518 AACTCAATAA
47528 AAATATATAAAAAT
1 AAATATATAAAAAT
47542 AAATATATAAAAAT
1 AAATATATAAAAAT
47556 A
1 A
47557 TAGATGTAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAATATATAAAAAT
Found at i:50371 original size:106 final size:105
Alignment explanation
Indices: 49789--50626 Score: 1090
Period size: 105 Copynumber: 8.0 Consensus size: 105
49779 AAATTACCAT
** * * * *
49789 AAGCATTGTTAAGTAAGACGACGAAACAAAGGAACTTAAGCCAATCCAGCTACAACTGCCTCAGA
1 AAGCATTGTCGAGGAAGACGACGAAATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGA
* * *
49854 TATGAATGTGCTGAC--T-GT-A-C-TTAGTTATACAAAG
66 TATGAATGTGCTGACTATAATGATCAATAGTTCTACAAAG
* * *
49888 AAGCATTGTCGAGGAAGACGACGGAATAAAGGAACTTAAGCCAATCCAGCTACACCTGCCTAAGA
1 AAGCATTGTCGAGGAAGACGACGAAATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGA
**
49953 TATGAATGTGCCAACTATAATGATCAATAGTTCTACAAAG
66 TATGAATGTGCTGACTATAATGATCAATAGTTCTACAAAG
* *
49993 AAGCATTGTCGAGGAAGACGACGGAATAAAGGAACTTAATCCAATCCAGCCACAACTGCCTAA-A
1 AAGCATTGTCGAGGAAGACGACGAAATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGA
* *
50057 AATGAATGTTCTGACTAT-ATCGATCAATAGTTCTACAAAG
66 TATGAATGTGCTGACTATAAT-GATCAATAGTTCTACAAAG
* * *
50097 AAGCATTGTCGAGGAAGAC-ACGGAATAAAGGAACTTAAACCAATCCAGCCACACCTGCCTAAGA
1 AAGCATTGTCGAGGAAGACGACGAAATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGA
* *
50161 TATGAATGTTCTGATCTGACTATATCGATCAATAGTCCTACAAAG
66 TATGAATGTGCTGA-CT-A-TA-AT-GATCAATAGTTCTACAAAG
* * * * *
50206 AAGCATCGTCAAGGAAAACGACGGAATAAAGGAACTTAATCCAATCCAGCCACAACTGCCTAAGA
1 AAGCATTGTCGAGGAAGACGACGAAATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGA
* *
50271 TATGAATGTTCTGACTAT-ATCAATCAATAGTTCTACAAAG
66 TATGAATGTGCTGACTATAAT-GATCAATAGTTCTACAAAG
* * *
50311 AAGCATTGTCGAAGAAGAAGACGAAATAAAGGAAACTTAAGCCTATCCAGCCACAACTGCCTAAG
1 AAGCATTGTCGAGGAAGACGACGAAATAAAGG-AACTTAAGCCAATCCAGCCACAACTGCCTAAG
50376 ATATGAATGTGCTGACTATAATGATCAATAGTTCTACAAAG
65 ATATGAATGTGCTGACTATAATGATCAATAGTTCTACAAAG
* *
50417 AAGCATTGTCGAGGAAGACGACGAAATAAAGAAAACTTAAGCCAATCCA-CCTACACCTGCCTAA
1 AAGCATTGTCGAGGAAGACGACGAAATAAAG-GAACTTAAGCCAATCCAGCC-ACAACTGCCTAA
*
50481 GAT-TGAATGTGCTGACTATAATGATCACTAGTTCTACAAAG
64 GATATGAATGTGCTGACTATAATGATCAATAGTTCTACAAAG
* * * * * *
50522 AAGCATTGTCCAGGATGGCGACGAAACAAAGGAAACTTAAGCCTATCCAGCCACAATTGCCTAAG
1 AAGCATTGTCGAGGAAGACGACGAAATAAAGG-AACTTAAGCCAATCCAGCCACAACTGCCTAAG
*
50587 ATATGAATGTGCTGTA-TGTAATGATCAATAGTTCTACAAA
65 ATATGAATGTGCTG-ACTATAATGATCAATAGTTCTACAAA
50627 CAATCTAAAA
Statistics
Matches: 661, Mismatches: 56, Indels: 37
0.88 0.07 0.05
Matches are distributed among these distances:
99 71 0.11
101 1 0.00
102 1 0.00
103 44 0.07
104 68 0.10
105 214 0.32
106 160 0.24
107 5 0.01
108 1 0.00
109 39 0.06
110 57 0.09
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (105 bp):
AAGCATTGTCGAGGAAGACGACGAAATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGA
TATGAATGTGCTGACTATAATGATCAATAGTTCTACAAAG
Found at i:50498 original size:211 final size:210
Alignment explanation
Indices: 49789--50626 Score: 1097
Period size: 211 Copynumber: 4.0 Consensus size: 210
49779 AAATTACCAT
* * * * *
49789 AAGCATTGTTAAGTAAGACGACGAAACAAAGGAACTTAAGCCAATCCAGCTACAACTGCCTCAGA
1 AAGCATTGTCAAGGAAGACGACGAAATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGA
* * * *
49854 TATGAATGTGCTGACTGTA-C--T---TAGTTATACAAAGAAGCATTGTCGAGGAAGACGACGGA
66 TATGAATGTGCTGACTATATCGATCAATAGTTCTACAAAGAAGCATTGTCGAGGAAGAAGACGAA
* * **
49913 ATAAAGGAACTTAAGCCAATCCAGCTACACCTGCCTAAGATATGAATGTGCCAACTATAATGATC
131 ATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGATATGAATGTGCTGACTATAATGATC
49978 AATAGTTCTACAAAG
196 AATAGTTCTACAAAG
* * *
49993 AAGCATTGTCGAGGAAGACGACGGAATAAAGGAACTTAATCCAATCCAGCCACAACTGCCTAA-A
1 AAGCATTGTCAAGGAAGACGACGAAATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGA
* * * *
50057 AATGAATGTTCTGACTATATCGATCAATAGTTCTACAAAGAAGCATTGTCGAGGAAG-ACACGGA
66 TATGAATGTGCTGACTATATCGATCAATAGTTCTACAAAGAAGCATTGTCGAGGAAGAAGACGAA
* * *
50121 ATAAAGGAACTTAAACCAATCCAGCCACACCTGCCTAAGATATGAATGTTCTGATCTGACTATAT
131 ATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGATATGAATGTGCTGA-CT-A-TA-AT
*
50186 CGATCAATAGTCCTACAAAG
192 -GATCAATAGTTCTACAAAG
* * * *
50206 AAGCATCGTCAAGGAAAACGACGGAATAAAGGAACTTAATCCAATCCAGCCACAACTGCCTAAGA
1 AAGCATTGTCAAGGAAGACGACGAAATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGA
* * *
50271 TATGAATGTTCTGACTATATCAATCAATAGTTCTACAAAGAAGCATTGTCGAAGAAGAAGACGAA
66 TATGAATGTGCTGACTATATCGATCAATAGTTCTACAAAGAAGCATTGTCGAGGAAGAAGACGAA
*
50336 ATAAAGGAAACTTAAGCCTATCCAGCCACAACTGCCTAAGATATGAATGTGCTGACTATAATGAT
131 ATAAAGG-AACTTAAGCCAATCCAGCCACAACTGCCTAAGATATGAATGTGCTGACTATAATGAT
50401 CAATAGTTCTACAAAG
195 CAATAGTTCTACAAAG
* * *
50417 AAGCATTGTCGAGGAAGACGACGAAATAAAGAAAACTTAAGCCAATCCA-CCTACACCTGCCTAA
1 AAGCATTGTCAAGGAAGACGACGAAATAAAG-GAACTTAAGCCAATCCAGCC-ACAACTGCCTAA
* * * **
50481 GAT-TGAATGTGCTGACTATAAT-GATCACTAGTTCTACAAAGAAGCATTGTCCAGGATGGCGAC
64 GATATGAATGTGCTGACTAT-ATCGATCAATAGTTCTACAAAGAAGCATTGTCGAGGAAGAAGAC
* * * *
50544 GAAACAAAGGAAACTTAAGCCTATCCAGCCACAATTGCCTAAGATATGAATGTGCTGTA-TGTAA
128 GAAATAAAGG-AACTTAAGCCAATCCAGCCACAACTGCCTAAGATATGAATGTGCTG-ACTATAA
50608 TGATCAATAGTTCTACAAA
191 TGATCAATAGTTCTACAAA
50627 CAATCTAAAA
Statistics
Matches: 565, Mismatches: 51, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
203 17 0.03
204 56 0.10
206 1 0.00
208 54 0.10
209 31 0.05
210 1 0.00
211 176 0.31
212 36 0.06
213 80 0.14
214 56 0.10
215 14 0.02
216 43 0.08
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (210 bp):
AAGCATTGTCAAGGAAGACGACGAAATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGA
TATGAATGTGCTGACTATATCGATCAATAGTTCTACAAAGAAGCATTGTCGAGGAAGAAGACGAA
ATAAAGGAACTTAAGCCAATCCAGCCACAACTGCCTAAGATATGAATGTGCTGACTATAATGATC
AATAGTTCTACAAAG
Found at i:54088 original size:60 final size:60
Alignment explanation
Indices: 54015--54145 Score: 183
Period size: 60 Copynumber: 2.2 Consensus size: 60
54005 ACAACATTAG
* *
54015 GGACTAATTTAGAATGATATTCACA-TTATGTGGATGAAATTAGAATGTTCAAAAATTTAA
1 GGACTAATTTAGAATGAAAGTCACAGTTATG-GGATGAAATTAGAATGTTCAAAAATTTAA
* * * * *
54075 GGACTAATTTAGAATGAAAGTCATAGTTTTGGGATGAAATTGGAATGTTTAAAATTTTAA
1 GGACTAATTTAGAATGAAAGTCACAGTTATGGGATGAAATTAGAATGTTCAAAAATTTAA
54135 GGACTAATTTA
1 GGACTAATTTA
54146 AAATAAGGAT
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
60 59 0.94
61 4 0.06
ACGTcount: A:0.40, C:0.05, G:0.19, T:0.36
Consensus pattern (60 bp):
GGACTAATTTAGAATGAAAGTCACAGTTATGGGATGAAATTAGAATGTTCAAAAATTTAA
Found at i:54159 original size:60 final size:60
Alignment explanation
Indices: 54015--54168 Score: 177
Period size: 60 Copynumber: 2.6 Consensus size: 60
54005 ACAACATTAG
* * * * *
54015 GGACTAATTTAGAATGATATTCACA-TTATGTGGATGAAATTAGAATGTTCAAAAATTTAA
1 GGACTAATTTAAAATGAAAGTCATAGTT-TGGGGATGAAATTAGAATGTTCAAAAATTTAA
* * * * *
54075 GGACTAATTTAGAATGAAAGTCATAGTTTTGGGATGAAATTGGAATGTTTAAAATTTTAA
1 GGACTAATTTAAAATGAAAGTCATAGTTTGGGGATGAAATTAGAATGTTCAAAAATTTAA
*
54135 GGACTAATTTAAAAT-AAGGATCATAGTTTGGGGA
1 GGACTAATTTAAAATGAAAG-TCATAGTTTGGGGA
54169 CATATAATAC
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
59 3 0.04
60 76 0.94
61 2 0.02
ACGTcount: A:0.40, C:0.05, G:0.21, T:0.34
Consensus pattern (60 bp):
GGACTAATTTAAAATGAAAGTCATAGTTTGGGGATGAAATTAGAATGTTCAAAAATTTAA
Found at i:62407 original size:15 final size:15
Alignment explanation
Indices: 62364--62408 Score: 63
Period size: 17 Copynumber: 2.9 Consensus size: 15
62354 CGATAAGGAC
62364 ATATACATTCTATAA
1 ATATACATTCTATAA
*
62379 ATATAGTTATTCTATAA
1 ATATA--CATTCTATAA
62396 ATATACATTCTAT
1 ATATACATTCTAT
62409 TTTACTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 12 0.46
17 14 0.54
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.44
Consensus pattern (15 bp):
ATATACATTCTATAA
Found at i:67107 original size:21 final size:21
Alignment explanation
Indices: 67059--67119 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
67049 TTCCCCTGTG
67059 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGGTT-CCC-TCAAA
67082 GGGGGAATCGGTTCCCTC-AA
1 GGGGGAATCGGTTCCCTCAAA
*
67102 GTGGGG-ATCGATTCCCTC
1 G-GGGGAATCGGTTCCCTC
67120 TGCACCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
20 14 0.39
21 6 0.17
22 3 0.08
23 13 0.36
ACGTcount: A:0.18, C:0.26, G:0.33, T:0.23
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTCAAA
Found at i:80860 original size:30 final size:30
Alignment explanation
Indices: 80826--80937 Score: 116
Period size: 30 Copynumber: 3.6 Consensus size: 30
80816 GCACTGAGCA
* *
80826 TCCTTACACACTACAGTGATGTACTAAGTG
1 TCCTTACACACTATAGTGATGCACTAAGTG
* * * *
80856 TCCTTGCACACTATAGTACCATATGCACTCAGTT
1 TCCTTACACACTATAGT----GATGCACTAAGTG
* *
80890 TCCTTACACACCATAGTGTTGCACTAAGTG
1 TCCTTACACACTATAGTGATGCACTAAGTG
80920 TCCTTACACACTATAGTG
1 TCCTTACACACTATAGTG
80938 CTAATCCGAT
Statistics
Matches: 65, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
30 41 0.63
34 24 0.37
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.31
Consensus pattern (30 bp):
TCCTTACACACTATAGTGATGCACTAAGTG
Found at i:82388 original size:20 final size:19
Alignment explanation
Indices: 82345--82389 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
82335 CAAAATAATC
* *
82345 CAATTTCACATTCTAACAT
1 CAATTTCACACTCAAACAT
82364 CAATTTCAACACTCAAACAT
1 CAATTTC-ACACTCAAACAT
*
82384 TAATTT
1 CAATTT
82390 ACAGCATAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (19 bp):
CAATTTCACACTCAAACAT
Found at i:93072 original size:21 final size:21
Alignment explanation
Indices: 93026--93073 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
93016 GATTTTGACT
93026 ATCGCATTACGATTTCTCAAA
1 ATCGCATTACGATTTCTCAAA
* *
93047 TTCGCGTTACGATTT-TCATAA
1 ATCGCATTACGATTTCTCA-AA
93068 ATCGCA
1 ATCGCA
93074 ATGTGAATCT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (21 bp):
ATCGCATTACGATTTCTCAAA
Found at i:93693 original size:21 final size:21
Alignment explanation
Indices: 93632--93710 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
93622 TTCTAAACTT
93632 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
93652 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
93672 ACTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
93693 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
93711 TCGTAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.18, G:0.19, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:93729 original size:33 final size:33
Alignment explanation
Indices: 93687--93800 Score: 183
Period size: 33 Copynumber: 3.5 Consensus size: 33
93677 CGCAACGAGA
*
93687 GAAATGAAAATCGCAACGAGAGAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
93720 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
93753 GAAATGAAAATCACAACGAGATAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
93786 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
93801 TTGCGATTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:93783 original size:14 final size:14
Alignment explanation
Indices: 93692--93789 Score: 52
Period size: 14 Copynumber: 6.3 Consensus size: 14
93682 CGAGAGAAAT
93692 GAAAATCGCAACGA
1 GAAAATCGCAACGA
* *
93706 GAGAATCGTAACGCGAAA
1 GAAAATCGCAA--CG--A
93724 TGAAAATCGCAACGA
1 -GAAAATCGCAACGA
*
93739 GAGAATCGCAACGCGAAA
1 GAAAATCGCAA--CG--A
*
93757 TGAAAATCACAACGA
1 -GAAAATCGCAACGA
* *
93772 GATAATCGCAACGC
1 GAAAATCGCAACGA
93786 GAAA
1 GAAA
93790 CCAAAATCGC
Statistics
Matches: 63, Mismatches: 11, Indels: 20
0.67 0.12 0.21
Matches are distributed among these distances:
14 33 0.52
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 18 0.29
ACGTcount: A:0.47, C:0.20, G:0.22, T:0.10
Consensus pattern (14 bp):
GAAAATCGCAACGA
Found at i:95639 original size:94 final size:94
Alignment explanation
Indices: 95514--95893 Score: 638
Period size: 94 Copynumber: 4.1 Consensus size: 94
95504 TTGATTGCTT
* *
95514 AGTAAATTTATTCGGTTGCTACCAATACTGCTAAACTGTTTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
95579 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
95608 AGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
95673 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * *
95702 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
95767 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * * *
95796 AGTAAATTTGTTTGGTTGCTGCTAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
95861 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
95889 AGTAA
1 AGTAA
95894 TGCAATCCAT
Statistics
Matches: 276, Mismatches: 9, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
93 26 0.09
94 250 0.91
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTACCAATTCTGCTAAACTGTGTATTCTTTAACACTATGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:95997 original size:19 final size:17
Alignment explanation
Indices: 95981--96063 Score: 73
Period size: 19 Copynumber: 4.8 Consensus size: 17
95971 AAAAATGACT
95981 ATCGCAACGCGAAATGA
1 ATCGCAACGCGAAATGA
*
95998 ATCGCAA--CGAGA-GA
1 ATCGCAACGCGAAATGA
*
96012 ATCGCAACGAGAAATGAAA
1 ATCGCAACGCGAAATG--A
**
96031 ATCGCAACGCGAAACCAAA
1 ATCGCAACGCGAAA--TGA
96050 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
96064 CTATAATCGC
Statistics
Matches: 53, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
14 9 0.17
15 4 0.08
16 3 0.06
17 8 0.15
19 29 0.55
ACGTcount: A:0.46, C:0.24, G:0.22, T:0.08
Consensus pattern (17 bp):
ATCGCAACGCGAAATGA
Found at i:96015 original size:14 final size:14
Alignment explanation
Indices: 95996--96023 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
95986 AACGCGAAAT
95996 GAATCGCAACGAGA
1 GAATCGCAACGAGA
96010 GAATCGCAACGAGA
1 GAATCGCAACGAGA
96024 AATGAAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.29, T:0.07
Consensus pattern (14 bp):
GAATCGCAACGAGA
Found at i:96071 original size:19 final size:19
Alignment explanation
Indices: 96011--96073 Score: 83
Period size: 19 Copynumber: 3.3 Consensus size: 19
96001 GCAACGAGAG
*
96011 AATCGCAACGAGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
*
96030 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACTAA
*
96049 AATCGCAACGCGAAACTAT
1 AATCGCAACGCGAAACTAA
96068 AATCGC
1 AATCGC
96074 GTTGTGATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
19 39 1.00
ACGTcount: A:0.46, C:0.25, G:0.17, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:96160 original size:20 final size:20
Alignment explanation
Indices: 96108--96174 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
96098 GATTCTCTCG
**
96108 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
96128 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
* *
96148 TTGCGATAGTCATTTTCACG
1 TTGCGATAGTCATTTTCGCA
96168 TTGCGAT
1 TTGCGAT
96175 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:96694 original size:18 final size:20
Alignment explanation
Indices: 96656--96697 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
96646 CTCACCTGTC
96656 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-CTCCCCT
96677 ATCGTTCAAGA-G-TCCCCT
1 ATCGTTCAAGAGGCTCCCCT
96695 ATC
1 ATC
96698 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 9 0.43
20 1 0.05
21 11 0.52
ACGTcount: A:0.21, C:0.36, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGTTCAAGAGGCTCCCCT
Found at i:98383 original size:33 final size:33
Alignment explanation
Indices: 98345--98500 Score: 172
Period size: 33 Copynumber: 4.6 Consensus size: 33
98335 TAGTTACGAT
*
98345 TTTCATTTTCGCATTGTGATTCACTCGTTGCGA
1 TTTCATTTTCGCATTGCGATTCACTCGTTGCGA
*
98378 TTTCA-TTTCGCATTGCGATTCTCGCTTCGCGTTGCGA
1 TTTCATTTTCGCATTGCGA-T-TCAC-T--CGTTGCGA
98415 TTTCATTTTCGCATTGCGATTCACTCGTTGCGA
1 TTTCATTTTCGCATTGCGATTCACTCGTTGCGA
* * *
98448 TTT-TTATTTCGCATTGCGATTCTCTCGTTGTGA
1 TTTCAT-TTTCGCATTGCGATTCACTCGTTGCGA
* * *
98481 TGTCATTTCCGCGTTGCGAT
1 TTTCATTTTCGCATTGCGAT
98501 AGTTCAATTC
Statistics
Matches: 105, Mismatches: 10, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
32 13 0.12
33 56 0.53
34 4 0.04
35 2 0.02
36 3 0.03
37 14 0.13
38 13 0.12
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (33 bp):
TTTCATTTTCGCATTGCGATTCACTCGTTGCGA
Found at i:98466 original size:19 final size:18
Alignment explanation
Indices: 98372--98468 Score: 94
Period size: 19 Copynumber: 5.4 Consensus size: 18
98362 GATTCACTCG
98372 TTGCGATTTCATTTCGCA
1 TTGCGATTTCATTTCGCA
** *
98390 TTGCGATTCTCGCTTCGCG
1 TTGCGATT-TCATTTCGCA
98409 TTGCGATTTCATTTTCGCA
1 TTGCGATTTCA-TTTCGCA
*
98428 TTGCGA-TTCA-CTCG--
1 TTGCGATTTCATTTCGCA
*
98442 TTGCGATTTTTATTTCGCA
1 TTGCGA-TTTCATTTCGCA
98461 TTGCGATT
1 TTGCGATT
98469 CTCTCGTTGT
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
14 6 0.10
16 6 0.10
17 3 0.05
18 16 0.25
19 32 0.51
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (18 bp):
TTGCGATTTCATTTCGCA
Found at i:98538 original size:20 final size:20
Alignment explanation
Indices: 98473--98546 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 20
98463 GCGATTCTCT
*
98473 CGTTGTGAT-GTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* *
98492 CGTTGCGATAGTTCAATTCCA
1 CGTTGCGATAG-TCATTTCCG
*
98513 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
98533 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
98547 AATGAATGTA
Statistics
Matches: 45, Mismatches: 8, Indels: 3
0.80 0.14 0.05
Matches are distributed among these distances:
19 8 0.18
20 20 0.44
21 17 0.38
ACGTcount: A:0.19, C:0.22, G:0.23, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Done.