Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008922.1 Hibiscus syriacus cultivar Beakdansim tig00112226_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: 568381
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:582 original size:14 final size:14
Alignment explanation
Indices: 563--598 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
553 ATTGTTTAAT
563 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
577 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
591 TGATTTGT
1 TGATTTGT
599 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:724 original size:14 final size:14
Alignment explanation
Indices: 705--757 Score: 61
Period size: 14 Copynumber: 3.4 Consensus size: 14
695 CGAAATGGCT
705 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
719 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
738 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
752 ATCGCA
1 ATCGCA
758 TTGCGATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
14 17 0.50
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:731 original size:33 final size:33
Alignment explanation
Indices: 686--763 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
676 AAAACATACT
* ***
686 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
719 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
752 ATCGCATTGCGA
1 ATCGCAATGCGA
764 TTTTCTCGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.41, C:0.22, G:0.23, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:751 original size:19 final size:19
Alignment explanation
Indices: 715--751 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
705 ATCGCAACGA
* *
715 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
734 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
752 ATCGCATTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:788 original size:20 final size:20
Alignment explanation
Indices: 763--820 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
753 TCGCATTGCG
* *
763 ATTTTCTCGTTGTGATAGCC
1 ATTTTCGCGTTGCGATAGCC
783 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
803 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
821 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.16, C:0.21, G:0.24, T:0.40
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:1901 original size:24 final size:24
Alignment explanation
Indices: 1874--1927 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1864 GTATTCGAAA
* *
1874 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
1898 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
1922 TTTGAT
1 TTTGAT
1928 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:2119 original size:12 final size:12
Alignment explanation
Indices: 2102--2126 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2092 ATATAATCCT
2102 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2114 GAAGAAGAAAAA
1 GAAGAAGAAAAA
2126 G
1 G
2127 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:4435 original size:19 final size:19
Alignment explanation
Indices: 4413--4510 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
4403 GGAAATTACT
4413 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4432 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
4446 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
4465 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
4479 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
4498 ATCGCAACGCGAA
1 ATCGCAATGCGAA
4511 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:4455 original size:33 final size:33
Alignment explanation
Indices: 4413--4506 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
4403 GGAAATTACT
4413 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
4446 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
4479 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
4507 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:4528 original size:19 final size:20
Alignment explanation
Indices: 4506--4548 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
4496 AAATCGCAAC
4506 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
4525 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
4545 GCGA
1 GCGA
4549 TTCTCTCGTT
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:4533 original size:14 final size:14
Alignment explanation
Indices: 4534--4567 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
4524 TGCGATTTTC
4534 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
4548 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
4562 ATTTTC
1 ATTTTC
4568 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:4708 original size:14 final size:14
Alignment explanation
Indices: 4689--4725 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
4679 CATCAATTAA
4689 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
4703 ACAAATCACCTTTT
1 ACAAATCAACTTTT
4717 ACAAATCAA
1 ACAAATCAA
4726 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:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:6166 original size:42 final size:42
Alignment explanation
Indices: 6081--6203 Score: 117
Period size: 42 Copynumber: 2.9 Consensus size: 42
6071 GTGAATCGGG
* * * * *
6081 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTCTTCGAGGATGATAGGGGC
6123 CTCTTGAACGGTGGGAGGGGACT-TTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTTCGAGG-ATGATAGGGGC
* * * *
6165 CTCTTCAACGATAGGAGTGGACTCTT-GAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTTCGA-GGATGATAGG
6204 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
41 5 0.07
42 55 0.81
43 8 0.12
ACGTcount: A:0.23, C:0.17, G:0.37, T:0.24
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGGACTCTTCGAGGATGATAGGGGC
Found at i:8250 original size:20 final size:20
Alignment explanation
Indices: 8205--8268 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
8195 TCTTTTGGTT
8205 GAAATGAAAATCGCAAC-AA
1 GAAATGAAAATCGCAACGAA
* **
8224 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACGAA
**
8245 GAAATGACTATCGCAACGAGA
1 GAAATGAAAATCGCAACGA-A
8266 GAA
1 GAA
8269 TCGCAACGCG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.06
20 28 0.80
21 5 0.14
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.12
Consensus pattern (20 bp):
GAAATGAAAATCGCAACGAA
Found at i:8290 original size:33 final size:33
Alignment explanation
Indices: 8230--8326 Score: 131
Period size: 33 Copynumber: 2.9 Consensus size: 33
8220 ACAAGATAAT
* *
8230 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGAATATCGCAACCA
* *
8264 GAGAATCGCAACGCGAAATGAGTATCGCGACCA
1 GAGAATCGCAACGCGAAATGAATATCGCAACCA
* *
8297 GACAATCGCAACGCGAAATGAAAATCGCAA
1 GAGAATCGCAACGCGAAATGAATATCGCAA
8327 TGCGATTTTT
Statistics
Matches: 56, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 42 0.75
34 14 0.25
ACGTcount: A:0.40, C:0.24, G:0.25, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGAATATCGCAACCA
Found at i:8349 original size:19 final size:20
Alignment explanation
Indices: 8327--8374 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
8317 AAAATCGCAA
*
8327 TGCGATTTTTGTTT-CGCGT
1 TGCGATTTTTATTTCCGCGT
**
8346 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTTCCGCGT
8366 TGCGATTTT
1 TGCGATTTT
8375 CATTCTCGAA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.10, C:0.17, G:0.25, T:0.48
Consensus pattern (20 bp):
TGCGATTTTTATTTCCGCGT
Found at i:8914 original size:20 final size:20
Alignment explanation
Indices: 8889--8941 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
8879 GCGCTATGTA
8889 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
8909 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
8929 TATCTCGTTGCGA
1 AATCGCGTTGCGA
8942 TTTTTGTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:8976 original size:20 final size:20
Alignment explanation
Indices: 8951--9004 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
8941 ATTTTTGTAT
8951 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
8971 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
8991 TATCGCATTGCGAT
1 TATCGCATTGCGAT
9005 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:8989 original size:62 final size:62
Alignment explanation
Indices: 8890--9007 Score: 164
Period size: 62 Copynumber: 1.9 Consensus size: 62
8880 CGCTATGTAA
* * * * *
8890 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTTGTATT
* * *
8952 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
9008 CCCAATTTGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
62 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.34
Consensus pattern (62 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTTGTATT
Found at i:9115 original size:21 final size:21
Alignment explanation
Indices: 9075--9115 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
9065 ATTGTATACC
**
9075 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
9096 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
9116 GCGAATTTGC
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:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:15592 original size:9 final size:9
Alignment explanation
Indices: 15570--15603 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
15560 TAATTAATCG
15570 AAAT-TATT
1 AAATATATT
15578 AAATATATT
1 AAATATATT
*
15587 ATATATATT
1 AAATATATT
15596 AAATATAT
1 AAATATAT
15604 ATTTTTTGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
8 4 0.17
9 19 0.83
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
AAATATATT
Found at i:21500 original size:18 final size:20
Alignment explanation
Indices: 21477--21520 Score: 60
Period size: 18 Copynumber: 2.4 Consensus size: 20
21467 GTATAGGAAG
21477 TTTATTATTTTAA-T-ATTT
1 TTTATTATTTTAATTAATTT
21495 TTTA-T-TTTTAATTAATTT
1 TTTATTATTTTAATTAATTT
21513 TTTATTAT
1 TTTATTAT
21521 ATTTTGAGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
16 6 0.27
17 2 0.09
18 12 0.55
19 1 0.05
20 1 0.05
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTATTATTTTAATTAATTT
Found at i:37131 original size:161 final size:162
Alignment explanation
Indices: 36907--37210 Score: 424
Period size: 161 Copynumber: 1.9 Consensus size: 162
36897 AGTTTTATAT
* * *
36907 TTTTCAATTTCAACAAACTATATACGATGTTGAAAGATCTAAAATGACATGAGATTGGTTCTCAA
1 TTTTCAATATCAACAAACTATATACGATGTTAAAAGATCTAAAATGACATGAGATTAGTTCTCAA
* * * *
36972 AAGTTGTTCATTTCAA-TTTT-TAGGCAA-ACAATAA-AA-AAATTAAAAAAGAAATATTTATGA
66 AAGTTGTTCATTGCAATTTTTGTAGCCAATAAAAAAATAACAAATTAAAAAAGAAATATTTATGA
37032 CTGAATTTTCTAATAAAAAAGGAAAGTTCCATAA
131 CTG-A-TTTCTAATAAAAAAGGAAAGTTCCATAA
37066 TTTTCAATATCAACAAACTATATA-G-TGTTAAAAAAAGATCTAAAAATGACATGAGATTAGTTC
1 TTTTCAATATCAACAAACTATATACGATGTT---AAAAGATCT-AAAATGACATGAGATTAGTTC
37129 TCAAAAGTTGTTCATTGCAATTTTTTGGTAGCCAATAAAAAAATAACAAATTAAAAAAGAAATAT
62 TCAAAAGTTGTTCATTGCAA-TTTTT-GTAGCCAATAAAAAAATAACAAATTAAAAAAGAAATAT
37194 TTATGACTGATTTCTAA
125 TTATGACTGATTTCTAA
37211 AAGACTAATC
Statistics
Matches: 127, Mismatches: 7, Indels: 15
0.85 0.05 0.10
Matches are distributed among these distances:
157 4 0.03
158 1 0.01
159 23 0.18
160 8 0.06
161 39 0.31
163 4 0.03
165 6 0.05
166 12 0.09
167 3 0.02
168 27 0.21
ACGTcount: A:0.45, C:0.11, G:0.12, T:0.33
Consensus pattern (162 bp):
TTTTCAATATCAACAAACTATATACGATGTTAAAAGATCTAAAATGACATGAGATTAGTTCTCAA
AAGTTGTTCATTGCAATTTTTGTAGCCAATAAAAAAATAACAAATTAAAAAAGAAATATTTATGA
CTGATTTCTAATAAAAAAGGAAAGTTCCATAA
Found at i:47057 original size:46 final size:46
Alignment explanation
Indices: 47001--47140 Score: 262
Period size: 46 Copynumber: 3.0 Consensus size: 46
46991 AAAGTTTAGG
* *
47001 TACTAAAATGAACTAAAACTGATAGTTTAGGTATTAAACCAAGTTT
1 TACTAAAATGAACCAAAACTGATAGTTTAGGTATTAAACTAAGTTT
47047 TACTAAAATGAACCAAAACTGATAGTTTAGGTATTAAACTAAGTTT
1 TACTAAAATGAACCAAAACTGATAGTTTAGGTATTAAACTAAGTTT
47093 TACTAAAATGAACCAAAACTGATAGTTTAGGTATTAAACTAAGTTT
1 TACTAAAATGAACCAAAACTGATAGTTTAGGTATTAAACTAAGTTT
47139 TA
1 TA
47141 ACGGCGATAT
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 92 1.00
ACGTcount: A:0.44, C:0.11, G:0.13, T:0.33
Consensus pattern (46 bp):
TACTAAAATGAACCAAAACTGATAGTTTAGGTATTAAACTAAGTTT
Found at i:48597 original size:25 final size:22
Alignment explanation
Indices: 48554--48598 Score: 54
Period size: 25 Copynumber: 1.9 Consensus size: 22
48544 CCCGAAATAA
*
48554 TAATAAAAATATTATTTTTACT
1 TAATAAAAATATTAATTTTACT
48576 TAATAAAAAATGATTTAATTTTA
1 TAAT-AAAAAT-A-TTAATTTTA
48599 AAATAATATA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 4 0.21
23 6 0.32
24 1 0.05
25 8 0.42
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TAATAAAAATATTAATTTTACT
Found at i:52580 original size:2 final size:2
Alignment explanation
Indices: 52569--52605 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
52559 TTAAGTTCTA
52569 AT AT -T 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
52606 CACTGGGAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:58408 original size:81 final size:81
Alignment explanation
Indices: 58248--58646 Score: 311
Period size: 79 Copynumber: 5.0 Consensus size: 81
58238 TTTTAGTTTA
* * * * * * * *
58248 ATACGCTTTTGCTATTGCTGTGTTTCGTTG-GCCAATTTGTGTAAATTTTTCTGCGAATTTGCGT
1 ATACCCTTTTGCTCTTGCTGTATTTCCTTGAG-TAATTTGTG-ATATTTTTCTGGGAATTTGCAT
* * *
58312 GAGGGGAAACTAATTTTT
64 GAGGGAAAACAAATTTTG
* * *
58330 ATACCCTTTTGCTCTTGTTGTATTTCCTTGAGTAATTTGTGATTTTTTTTTGGGAATTTGCATGA
1 ATACCCTTTTGCTCTTGCTGTATTTCCTTGAGTAATTTGTGATATTTTTCTGGGAATTTGCATGA
58395 GGGAAAACAAATTTTG
66 GGGAAAACAAATTTTG
* * * * ** * * *
58411 ATACCTTTTTGCTCTTGC--TATAT-ATTGAGTAATTTGTGAAAAATTGCTGAGAATTT-CAAGA
1 ATACCCTTTTGCTCTTGCTGTATTTCCTTGAGTAATTTGTGATATTTTTCTGGGAATTTGCATGA
*
58472 -GGAAAGCAAATTTTG
66 GGGAAAACAAATTTTG
* * ** * * **
58487 ACACCCTTCTGCTCTAACTGTGTTTCGTTGAGTAATTTGTGATAAATTTCTGGGAATTTGCATGA
1 ATACCCTTTTGCTCTTGCTGTATTTCCTTGAGTAATTTGTGATATTTTTCTGGGAATTTGCATG-
58552 AGGG--AACAAA-TTTG
65 AGGGAAAACAAATTTTG
* * * * * *
58566 ATACCC-TTT-CTCTTGCTGTGTTTCCTTTAAGTAATCTGTGAATTTTTTTCTGGGAATTAGCAA
1 ATACCCTTTTGCTCTTGCTGTATTTCC-TTGAGTAATTTGTG-ATATTTTTCTGGGAATTTGCAT
*
58629 GA-GG-AAACTAATTTTG
64 GAGGGAAAACAAATTTTG
58645 AT
1 AT
58647 GCTGTATTTC
Statistics
Matches: 253, Mismatches: 53, Indels: 25
0.76 0.16 0.08
Matches are distributed among these distances:
76 27 0.11
77 19 0.08
78 48 0.19
79 66 0.26
80 8 0.03
81 49 0.19
82 35 0.14
83 1 0.00
ACGTcount: A:0.25, C:0.13, G:0.20, T:0.42
Consensus pattern (81 bp):
ATACCCTTTTGCTCTTGCTGTATTTCCTTGAGTAATTTGTGATATTTTTCTGGGAATTTGCATGA
GGGAAAACAAATTTTG
Found at i:60260 original size:13 final size:13
Alignment explanation
Indices: 60242--60267 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60232 CAATACAATA
60242 ATGTTCAAACATG
1 ATGTTCAAACATG
60255 ATGTTCAAACATG
1 ATGTTCAAACATG
60268 TTTAGGCCAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTTCAAACATG
Found at i:62701 original size:45 final size:44
Alignment explanation
Indices: 62646--62735 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
62636 ATAGCTAAAT
* *
62646 TGGTCTCATATCTGGATAATCTGAAAAA-AAATAAACAGAGTGAGC
1 TGGTCCCATATCTGGATAATCTGAAAAAGAAAGAAACA-A-TGAGC
*
62691 TGGTCCCATATTTGGATAATCTGAAAAAGAAAGAAACAATGAGC
1 TGGTCCCATATCTGGATAATCTGAAAAAGAAAGAAACAATGAGC
62735 T
1 T
62736 ACGAAACTTA
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
44 6 0.15
45 27 0.66
46 8 0.20
ACGTcount: A:0.42, C:0.13, G:0.20, T:0.24
Consensus pattern (44 bp):
TGGTCCCATATCTGGATAATCTGAAAAAGAAAGAAACAATGAGC
Found at i:62783 original size:12 final size:12
Alignment explanation
Indices: 62766--62792 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
62756 TAAATTTAAT
62766 TAAATAAAATAA
1 TAAATAAAATAA
62778 TAAATAAAATAA
1 TAAATAAAATAA
62790 TAA
1 TAA
62793 TTGAACAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (12 bp):
TAAATAAAATAA
Found at i:67572 original size:41 final size:41
Alignment explanation
Indices: 67509--67730 Score: 144
Period size: 42 Copynumber: 5.2 Consensus size: 41
67499 GGTTTGATGT
* * *
67509 AAAAAATTAGGGACTTTGATTATAAAGGTAAAAAGTGATTA
1 AAAAAATTAGGGGCCTTAATTATAAAGGTAAAAAGTGATTA
* * *
67550 AAAAAATTAGGGGCCTAAATTATATAA-GTAAAAATGGGATTGG
1 AAAAAATTAGGGGCCTTAATTATA-AAGGTAAAAA-GTGATT-A
* * *
67593 AAAAAA-TAGGGGCCTTACTTATAAAGGTAAAATATGAGATTG
1 AAAAAATTAGGGGCCTTAATTATAAAGGTAAAA-A-GTGATTA
* * * **
67635 AAAAAATCATGAG-CTTAATTATAAAGGTACATATTGTGATTGAA
1 AAAAAATTAGGGGCCTTAATTATAAAGGTA-A-AAAGTGATT--A
** * * *
67679 AAAAAATTAAAGGTCTCAATTATAAAGATAAAAAGTAGGATTA
1 AAAAAATTAGGGGCCTTAATTATAAAGGTAAAAAGT--GATTA
*
67722 CAAAAATTA
1 AAAAAATTA
67731 AGAACCTCAA
Statistics
Matches: 142, Mismatches: 26, Indels: 24
0.74 0.14 0.12
Matches are distributed among these distances:
41 29 0.20
42 55 0.39
43 29 0.20
44 11 0.08
45 18 0.13
ACGTcount: A:0.49, C:0.05, G:0.18, T:0.27
Consensus pattern (41 bp):
AAAAAATTAGGGGCCTTAATTATAAAGGTAAAAAGTGATTA
Found at i:82438 original size:21 final size:21
Alignment explanation
Indices: 82414--82454 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
82404 ATTCGCAACG
*
82414 CGATTTTTCAAATTCGCGTTT
1 CGATTTTCCAAATTCGCGTTT
*
82435 CGATTTTCCGAATTCGCGTT
1 CGATTTTCCAAATTCGCGTT
82455 GCGAATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (21 bp):
CGATTTTCCAAATTCGCGTTT
Found at i:82503 original size:20 final size:20
Alignment explanation
Indices: 82486--82580 Score: 100
Period size: 20 Copynumber: 4.8 Consensus size: 20
82476 TCAATATGTA
82486 AATCGCAACGCGATTATGAC
1 AATCGCAACGCGATTATGAC
* *
82506 TATCGCAACGCGATTCTGAC
1 AATCGCAACGCGATTATGAC
* * *
82526 CATCGCAACGAGATTCTGAC
1 AATCGCAACGCGATTATGAC
* **
82546 TATCGCAACGCGATGCTGAC
1 AATCGCAACGCGATTATGAC
* *
82566 TATCGCAATGCGATT
1 AATCGCAACGCGATT
82581 TTCAAAGCGC
Statistics
Matches: 66, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 66 1.00
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.23
Consensus pattern (20 bp):
AATCGCAACGCGATTATGAC
Found at i:82531 original size:40 final size:40
Alignment explanation
Indices: 82487--82580 Score: 143
Period size: 40 Copynumber: 2.4 Consensus size: 40
82477 CAATATGTAA
*
82487 ATCGCAACGCGATTATGACTATCGCAACGCGATTCTGACC
1 ATCGCAACGCGATTATGACTATCGCAACGCGATGCTGACC
* * *
82527 ATCGCAACGAGATTCTGACTATCGCAACGCGATGCTGACT
1 ATCGCAACGCGATTATGACTATCGCAACGCGATGCTGACC
*
82567 ATCGCAATGCGATT
1 ATCGCAACGCGATT
82581 TTCAAAGCGC
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (40 bp):
ATCGCAACGCGATTATGACTATCGCAACGCGATGCTGACC
Found at i:83252 original size:20 final size:20
Alignment explanation
Indices: 83229--83269 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
83219 GTTGTAATAG
*
83229 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTACGATTT
*
83249 TCATTTTCGTTTTACGATTT
1 TCATTTTCGTGTTACGATTT
83269 T
1 T
83270 AAGTTTCAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.59
Consensus pattern (20 bp):
TCATTTTCGTGTTACGATTT
Found at i:83276 original size:20 final size:20
Alignment explanation
Indices: 83233--83276 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
83223 TAATAGTCAT
* * *
83233 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTACGATTTTAAG
*
83253 TTTCGTTTTACGATTTTAAG
1 TTTCGTGTTACGATTTTAAG
83273 TTTC
1 TTTC
83277 AGAAATTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.16, T:0.57
Consensus pattern (20 bp):
TTTCGTGTTACGATTTTAAG
Found at i:87064 original size:2 final size:2
Alignment explanation
Indices: 87057--87089 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
87047 ATTATAAAAT
87057 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
87090 TCAATTTTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:93580 original size:26 final size:26
Alignment explanation
Indices: 93544--93598 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
93534 CGTAAAGAGG
93544 AAATAAACAGAGAGGGCCTATCTGGT
1 AAATAAACAGAGAGGGCCTATCTGGT
93570 AAATAAACAGAGAGGGCCTATCTGGT
1 AAATAAACAGAGAGGGCCTATCTGGT
93596 AAA
1 AAA
93599 ATGTCATGAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.25, T:0.18
Consensus pattern (26 bp):
AAATAAACAGAGAGGGCCTATCTGGT
Found at i:94452 original size:2 final size:2
Alignment explanation
Indices: 94445--94498 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
94435 TCAACAAATA
94445 AT AT AT AT AT -T AT AT AT AT AT AT AT AT A- 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
94485 AT AT AT -T AT AT AT A
1 AT AT AT AT AT AT AT A
94499 GAGAGAGGAG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94469 original size:19 final size:19
Alignment explanation
Indices: 94445--94498 Score: 94
Period size: 17 Copynumber: 2.9 Consensus size: 19
94435 TCAACAAATA
94445 ATATATATATTATATATAT
1 ATATATATATTATATATAT
94464 ATATATATA--ATATATAT
1 ATATATATATTATATATAT
94481 ATATATATATTATATATA
1 ATATATATATTATATATA
94499 GAGAGAGGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 17 0.52
19 16 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
ATATATATATTATATATAT
Found at i:94503 original size:2 final size:2
Alignment explanation
Indices: 94498--94533 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
94488 TATTATATAT
94498 AG AG AG AG -G AG -G AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
94534 CAAAGCACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:95847 original size:3 final size:3
Alignment explanation
Indices: 95828--95907 Score: 135
Period size: 3 Copynumber: 26.3 Consensus size: 3
95818 GAACATCAGT
95828 ATA ATA A-A TATA CATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA -ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
95874 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
95908 AACTCGAATG
Statistics
Matches: 74, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
2 1 0.01
3 69 0.93
4 4 0.05
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:96515 original size:20 final size:17
Alignment explanation
Indices: 96480--96520 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 17
96470 TTAAATTTAA
96480 TAAATATATATTAAATT
1 TAAATATATATTAAATT
96497 TAAATATGATATTCAAAATT
1 TAAATAT-ATATT--AAATT
96517 TAAA
1 TAAA
96521 AGTTAATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 7 0.33
18 5 0.24
20 9 0.43
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (17 bp):
TAAATATATATTAAATT
Found at i:99462 original size:3 final size:3
Alignment explanation
Indices: 99454--99491 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
99444 TCATTTGTGC
99454 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
99492 AAACTCTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:104651 original size:32 final size:34
Alignment explanation
Indices: 104610--104684 Score: 95
Period size: 32 Copynumber: 2.3 Consensus size: 34
104600 GGTAAGAAAT
* *
104610 TTATTTTTATGTTAGTAT-TTT-T-TAAATAGTTA
1 TTATTTTTATATTAATATATTTATGTAAATA-TTA
104642 TTATTTTTATATTAATATATTTATGTAAATATTA
1 TTATTTTTATATTAATATATTTATGTAAATATTA
104676 TT-TTTTTAT
1 TTATTTTTAT
104685 TAAAATAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
32 16 0.42
33 10 0.26
34 6 0.16
35 6 0.16
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (34 bp):
TTATTTTTATATTAATATATTTATGTAAATATTA
Found at i:104877 original size:17 final size:17
Alignment explanation
Indices: 104855--104908 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
104845 AATGTTAATA
104855 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
104872 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
104889 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
104906 TTT
1 TTT
104909 TTATAATGTA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:106442 original size:21 final size:21
Alignment explanation
Indices: 106412--106459 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
106402 GCAGGGGTAC
* *
106412 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
106433 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
106454 ATGCCA
1 ATGCCA
106460 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:106489 original size:21 final size:21
Alignment explanation
Indices: 106463--106556 Score: 136
Period size: 21 Copynumber: 4.5 Consensus size: 21
106453 TATGCCATCT
106463 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
106484 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCGAGC
*
106505 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCGAGC
* * *
106526 CCGCCA-GGTTACATGCCTACC
1 CCG-CAGGGTTACATTCCGAGC
106547 CCGCAGGGTT
1 CCGCAGGGTT
106557 TTATACCATA
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
20 2 0.03
21 64 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCGAGC
Found at i:107129 original size:34 final size:34
Alignment explanation
Indices: 107079--107176 Score: 142
Period size: 34 Copynumber: 2.9 Consensus size: 34
107069 AAATGTTTTT
*
107079 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
107113 AAAATAAAAATAATATTATTCGAAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
107147 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
107177 CATTAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 57 1.00
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:107793 original size:128 final size:128
Alignment explanation
Indices: 107565--108317 Score: 1257
Period size: 128 Copynumber: 5.9 Consensus size: 128
107555 TTACCTGATT
107565 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* * *** *
107630 TGACAAAATAATGGAAGGCGCGCCCTCGGGAACGCGCCTTCAAGTCCCCT-GAGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* * *
107693 TACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATATTCT
1 TACTGATAT-ATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCT
** *
107757 ATGACAAAATAATGGAAGGCGCGCCCATGGGAACGCGCATTCATGTGAATAGTGAAATAATAGG
65 ATGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
107821 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
107886 TGACAAAATAATGGAAGGCGCG-CCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
107948 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
108013 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
108076 TACTGATATATCTAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* *
108141 TGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGG
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
108204 TACTGATATATATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* *
108269 TG---AAATAATGGAATGCGCGCCCCCGGGAACTCGCCTTCATGTGAATAGT
66 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
108318 ACTCCGATTA
Statistics
Matches: 595, Mismatches: 26, Indels: 11
0.94 0.04 0.02
Matches are distributed among these distances:
125 44 0.07
127 125 0.21
128 425 0.71
129 1 0.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:108019 original size:255 final size:255
Alignment explanation
Indices: 107565--108317 Score: 1273
Period size: 255 Copynumber: 3.0 Consensus size: 255
107555 TTACCTGATT
107565 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* *** *
107630 TGACAAAATAATGGAAGGCGCGCCCTCGGGAACGCGCCTTCAAGTCCCCT-GAGAAATAATAGGT
66 TGACAAAATAATGGAAGGCGCGCCC-CGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGGT
* * *
107694 ACTGATATGA-ATAATGTCCCCGAGGGACATGAGTGACATAATAGGACAATGATAACATATTCTA
129 ACTGATAT-ATATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
** *
107758 TGACAAAATAATGGAAGGCGCGCCCATGGGAACGCGCATTCATGTGAATAGTGAAATAATAGG
193 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
107821 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
107886 TGACAAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
66 TGACAAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
*
107951 TGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
131 TGATATATATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
108016 CAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
196 CAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
* *
108076 TACTGATATATCTAGTGTCCCTGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
* *
108141 TGACAAAATAATGGAAGGCGCACCCCCGGGAACGCGCCTTCATGTGAATAGTAAAATAATAGGTA
66 TGACAAAATAATGGAAGGCGC-GCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTA
108206 CTGATATATATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
130 CTGATATATATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTG
* *
108271 ---AAATAATGGAATGCGCGCCCCCGGGAACTCGCCTTCATGTGAATAGT
195 ACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
108318 ACTCCGATTA
Statistics
Matches: 475, Mismatches: 19, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
253 45 0.09
254 2 0.00
255 233 0.49
256 195 0.41
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (255 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTA
TGACAAAATAATGGAAGGCGCGCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGGTAC
TGATATATATAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTCTGA
CAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:112926 original size:21 final size:19
Alignment explanation
Indices: 112873--112945 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 19
112863 GACCCGATCT
*
112873 AAAATAATATATCTATTAAA
1 AAAAT-ATATATTTATTAAA
*
112893 AAAAT-TATTTTTATTCAATA
1 AAAATATATATTTATT-AA-A
112913 AAAATATATATTTAATTAAA
1 AAAATATATATTT-ATTAAA
112933 AGAAATAATATAT
1 A-AAAT-ATATAT
112946 AGAGATATTA
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
18 8 0.18
19 2 0.05
20 13 0.30
21 12 0.27
22 9 0.20
ACGTcount: A:0.56, C:0.03, G:0.01, T:0.40
Consensus pattern (19 bp):
AAAATATATATTTATTAAA
Found at i:123066 original size:60 final size:60
Alignment explanation
Indices: 122954--123132 Score: 184
Period size: 60 Copynumber: 3.0 Consensus size: 60
122944 ACATATAGTA
* * * * * * * *
122954 CTCCGACTATAGGATACTACTTTGTTAAGTCC-CCAACTATCAAAAGTTACAAAATGCTC
1 CTCCGACTATAGAACATTACTTTATTAAGTCCATCGACTATAAAAAGTTACAAAATGATC
* * *
123013 CTCTGACTATAGAACGTTACTTTGTTGAA-TCTC-TCGACTATAAAAAGTTACAAAATGATC
1 CTCCGACTATAGAACATTACTTTATT-AAGTC-CATCGACTATAAAAAGTTACAAAATGATC
* * * *
123073 CTCCGACTGTAGGACATTACTTTATTAAGTCCATCGACTATTAAAAGTTATAAAATGATC
1 CTCCGACTATAGAACATTACTTTATTAAGTCCATCGACTATAAAAAGTTACAAAATGATC
123133 AACTAACTAT
Statistics
Matches: 100, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
59 26 0.26
60 74 0.74
ACGTcount: A:0.35, C:0.21, G:0.13, T:0.32
Consensus pattern (60 bp):
CTCCGACTATAGAACATTACTTTATTAAGTCCATCGACTATAAAAAGTTACAAAATGATC
Found at i:125157 original size:50 final size:51
Alignment explanation
Indices: 125038--125162 Score: 173
Period size: 51 Copynumber: 2.5 Consensus size: 51
125028 AGCAGTAAAA
**
125038 CGCGCCCCCTGCACCATGCTATACGCTGATGTGGCGCCACGTGGGGTATAG
1 CGCGCCCCCTGCACCGCGCTATACGCTGATGTGGCGCCACGTGGGGTATAG
*
125089 CGCGCCCCCTGCACCGCGCTATACGGTGA-GCTGGCGCCACGT-GGGTATAG
1 CGCGCCCCCTGCACCGCGCTATACGCTGATG-TGGCGCCACGTGGGGTATAG
* * *
125139 CGCGGCCTCTGCAGCGCGCTATAC
1 CGCGCCCCCTGCACCGCGCTATAC
125163 CCCTAACTAC
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
50 30 0.45
51 37 0.55
ACGTcount: A:0.14, C:0.36, G:0.32, T:0.18
Consensus pattern (51 bp):
CGCGCCCCCTGCACCGCGCTATACGCTGATGTGGCGCCACGTGGGGTATAG
Found at i:125248 original size:8 final size:10
Alignment explanation
Indices: 125222--125262 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
125212 TTTATCACAC
125222 CAAATTCTCT
1 CAAATTCTCT
125232 CAAATTCTCT
1 CAAATTCTCT
125242 -AAATCTCTCT
1 CAAAT-TCTCT
*
125252 CAAATACTCT
1 CAAATTCTCT
125262 C
1 C
125263 TTTTTAAGGT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 4 0.14
10 20 0.71
11 4 0.14
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.37
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:125526 original size:110 final size:111
Alignment explanation
Indices: 125387--125607 Score: 354
Period size: 110 Copynumber: 2.0 Consensus size: 111
125377 TAGAAATCAT
*
125387 ATATCTCTACACTTTACTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
* * * * *
125452 TATTTAGTT-ATTTATTTAATGCATGATTATTATATTAATAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATCAGATTAAGAATTAA
* * *
125497 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTATTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
125562 TAATTAGTTGATTCATTTAATGCATGATTATCAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATCAGATTAAGAATTAA
125608 TTTTTGTAAT
Statistics
Matches: 101, Mismatches: 9, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
110 69 0.68
111 32 0.32
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAACATTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATCAGATTAAGAATTAA
Found at i:126814 original size:15 final size:15
Alignment explanation
Indices: 126794--126828 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
126784 TTGCATAGCT
126794 TAGACAGACGCGGCA
1 TAGACAGACGCGGCA
126809 TAGACAGACGCGGCA
1 TAGACAGACGCGGCA
126824 -AGACA
1 TAGACA
126829 AATACAGATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 5 0.25
15 15 0.75
ACGTcount: A:0.37, C:0.26, G:0.31, T:0.06
Consensus pattern (15 bp):
TAGACAGACGCGGCA
Found at i:130599 original size:48 final size:48
Alignment explanation
Indices: 130486--130600 Score: 119
Period size: 48 Copynumber: 2.3 Consensus size: 48
130476 CCCTACGTGG
*
130486 CGTATAGCGCGCTGCAGGGGCCGCGCTATACCCACGTGACGCCAGCTCAT
1 CGTATA-CGCGGTGCAGGGG-CGCGCTATACCCACGTGACGCCAGCTCAT
* * *
130536 CGTATAACGCAGTGCAGGGG-GCGCTATACCCCACGTGGCGTCA-CATC-T
1 CGTAT-ACGCGGTGCAGGGGCGCGCTATA-CCCACGTGACGCCAGC-TCAT
130584 ACGTATACGCGGTGCAG
1 -CGTATACGCGGTGCAG
130601 AGAGCGCGTT
Statistics
Matches: 56, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
48 20 0.36
49 19 0.34
50 16 0.29
51 1 0.02
ACGTcount: A:0.20, C:0.32, G:0.30, T:0.17
Consensus pattern (48 bp):
CGTATACGCGGTGCAGGGGCGCGCTATACCCACGTGACGCCAGCTCAT
Found at i:131231 original size:3 final size:3
Alignment explanation
Indices: 131216--131256 Score: 57
Period size: 3 Copynumber: 13.7 Consensus size: 3
131206 ATCAAAAAGA
*
131216 AAG AAG GAG AAG AAG AAGG AA- AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AA-G AAG AAG AAG AAG AAG AAG AAG AA
131257 AGATGGGGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 2 0.06
3 29 0.85
4 3 0.09
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:131233 original size:12 final size:12
Alignment explanation
Indices: 131216--131256 Score: 64
Period size: 12 Copynumber: 3.4 Consensus size: 12
131206 ATCAAAAAGA
131216 AAGAAGGAGAAG
1 AAGAAGGAGAAG
*
131228 AAGAAGGAAAAG
1 AAGAAGGAGAAG
*
131240 AAGAAGAAGAAG
1 AAGAAGGAGAAG
131252 AAGAA
1 AAGAA
131257 AGATGGGGGC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (12 bp):
AAGAAGGAGAAG
Found at i:135595 original size:16 final size:15
Alignment explanation
Indices: 135557--135596 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
135547 TATTTTATCT
135557 AAAATAAAATATTAA
1 AAAATAAAATATTAA
* *
135572 GAATTAAAATATTTAA
1 AAAATAAAATA-TTAA
135588 AAAATAAAA
1 AAAATAAAA
135597 ATAACTATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAAATAAAATATTAA
Found at i:140028 original size:35 final size:35
Alignment explanation
Indices: 139989--140055 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
139979 TTTGATCTGG
*
139989 GTTTTAGCTTTGAATAAATATAATGTTGTGTTATT
1 GTTTTAGCTTTGAATAAATAGAATGTTGTGTTATT
* *
140024 GTTTTAGCTTTGTATAAATCGAATGTTGTGTT
1 GTTTTAGCTTTGAATAAATAGAATGTTGTGTT
140056 GTTTGAAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.25, C:0.04, G:0.19, T:0.51
Consensus pattern (35 bp):
GTTTTAGCTTTGAATAAATAGAATGTTGTGTTATT
Found at i:149435 original size:2 final size:2
Alignment explanation
Indices: 149430--149458 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
149420 ATTTTTTTAA
149430 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
149459 CGATGATTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:153085 original size:33 final size:32
Alignment explanation
Indices: 153048--153124 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 32
153038 TTTTCACCCT
*
153048 AAACCCGAACCCGACCCA-AATATCACACTTAAA
1 AAACCCG-ACCCGA-CCAGAATATCAAACTTAAA
*
153081 AAACCTGACCCGACCAGAATATCAAACTTAAAA
1 AAACCCGACCCGACCAGAATATCAAACTT-AAA
*
153114 AAAACCGACCC
1 AAACCCGACCC
153125 CGAATTTTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
31 3 0.08
32 17 0.45
33 18 0.47
ACGTcount: A:0.47, C:0.34, G:0.08, T:0.12
Consensus pattern (32 bp):
AAACCCGACCCGACCAGAATATCAAACTTAAA
Found at i:153127 original size:34 final size:31
Alignment explanation
Indices: 153056--153124 Score: 86
Period size: 32 Copynumber: 2.1 Consensus size: 31
153046 CTAAACCCGA
*
153056 ACCCGACCCAAATATCACACTTAAAAAACCTG
1 ACCCGACCCAAATATCAAACTTAAAAAACC-G
153088 ACCCGA-CCAGAATATCAAACTTAAAAAAAACCG
1 ACCCGACCCA-AATATCAAACTT--AAAAAACCG
153121 ACCC
1 ACCC
153125 CGAATTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
31 3 0.09
32 17 0.52
33 5 0.15
34 8 0.24
ACGTcount: A:0.46, C:0.33, G:0.07, T:0.13
Consensus pattern (31 bp):
ACCCGACCCAAATATCAAACTTAAAAAACCG
Found at i:155058 original size:2 final size:2
Alignment explanation
Indices: 155051--155077 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
155041 AACATTATTC
155051 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
155078 GCTTATTCTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:159393 original size:123 final size:123
Alignment explanation
Indices: 159174--159402 Score: 422
Period size: 123 Copynumber: 1.9 Consensus size: 123
159164 TGGTACCTGG
*
159174 TAATCCATTTATACAATTATCCTTGGAGGTCCATAAATCTCAGATAGGAAAAATGTCTTGCATCT
1 TAATCCATTTATACAATTATCCTTGGAGGTCCATAAATCTCAGATAGAAAAAATGTCTTGCATCT
159239 ATATGAGAAATTTCAAGAAAGTGATGCTCAAAGGAAAGAGCAACATCTCCACACATGA
66 ATATGAGAAATTTCAAGAAAGTGATGCTCAAAGGAAAGAGCAACATCTCCACACATGA
*
159297 TAATCCATTTATACAATTATCCTTGGAGGTCCATAAATCTCAGATAGAAAAAATGTCTTGCGTCT
1 TAATCCATTTATACAATTATCCTTGGAGGTCCATAAATCTCAGATAGAAAAAATGTCTTGCATCT
* *
159362 ATATGGGAATTTTCAAGAAAGTGATGCTCAAAGGAAAGAGC
66 ATATGAGAAATTTCAAGAAAGTGATGCTCAAAGGAAAGAGC
159403 CCGTGTTGCC
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
123 102 1.00
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (123 bp):
TAATCCATTTATACAATTATCCTTGGAGGTCCATAAATCTCAGATAGAAAAAATGTCTTGCATCT
ATATGAGAAATTTCAAGAAAGTGATGCTCAAAGGAAAGAGCAACATCTCCACACATGA
Found at i:160807 original size:22 final size:23
Alignment explanation
Indices: 160779--160825 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
160769 ATCATAACTA
*
160779 AACTTTAGTTTTTGTTT-ATTTT
1 AACTTTAGTTTTCGTTTCATTTT
160801 AACTTTAGTTTTCGTTTCATTTT
1 AACTTTAGTTTTCGTTTCATTTT
160824 AA
1 AA
160826 TATACTGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (23 bp):
AACTTTAGTTTTCGTTTCATTTT
Found at i:161977 original size:33 final size:33
Alignment explanation
Indices: 161927--161990 Score: 112
Period size: 33 Copynumber: 1.9 Consensus size: 33
161917 CCAAGCTCTG
161927 GCATCGCGACCAAGCTTTAACCCTATCCCTCAT
1 GCATCGCGACCAAGCTTTAACCCTATCCCTCAT
161960 GCAT-GCGTACCAAGCTTTAACCCTATCCCTC
1 GCATCGCG-ACCAAGCTTTAACCCTATCCCTC
161991 CATGACGACC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 3 0.10
33 27 0.90
ACGTcount: A:0.23, C:0.39, G:0.12, T:0.25
Consensus pattern (33 bp):
GCATCGCGACCAAGCTTTAACCCTATCCCTCAT
Found at i:162123 original size:29 final size:29
Alignment explanation
Indices: 162087--162163 Score: 127
Period size: 29 Copynumber: 2.7 Consensus size: 29
162077 AGCAAAGATC
162087 GGCGTGCATGGCGACCTATAAAGACGCCG
1 GGCGTGCATGGCGACCTATAAAGACGCCG
* * *
162116 GGCTTGCATGGCGACCTATAAGGACGTCG
1 GGCGTGCATGGCGACCTATAAAGACGCCG
162145 GGCGTGCATGGCGACCTAT
1 GGCGTGCATGGCGACCTAT
162164 GGTGGTTCAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.21, C:0.26, G:0.35, T:0.18
Consensus pattern (29 bp):
GGCGTGCATGGCGACCTATAAAGACGCCG
Found at i:164031 original size:25 final size:25
Alignment explanation
Indices: 164002--164053 Score: 72
Period size: 25 Copynumber: 2.1 Consensus size: 25
163992 TTCATCTCAT
164002 TATTC-ATTT-AATTAAATTCGATTAA
1 TATTCAATTTGAATT-AA-TCGATTAA
164027 TATTCAATTTGAATTAATCGATTAA
1 TATTCAATTTGAATTAATCGATTAA
164052 TA
1 TA
164054 AATTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 15 0.60
26 6 0.24
27 4 0.16
ACGTcount: A:0.40, C:0.08, G:0.06, T:0.46
Consensus pattern (25 bp):
TATTCAATTTGAATTAATCGATTAA
Found at i:169916 original size:3 final size:3
Alignment explanation
Indices: 169910--169951 Score: 61
Period size: 3 Copynumber: 14.7 Consensus size: 3
169900 ATTCCGTTGA
*
169910 TAT TAT TAT TAT TAT TAT TAT TAG T-T TAT TAT TA- TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
169952 AACATATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
2 3 0.09
3 32 0.91
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:169949 original size:11 final size:12
Alignment explanation
Indices: 169910--169951 Score: 61
Period size: 11 Copynumber: 3.7 Consensus size: 12
169900 ATTCCGTTGA
*
169910 TATTATTATTAT
1 TATTATTATTAG
169922 TATTATTATTAG
1 TATTATTATTAG
169934 T-TTATTATTA-
1 TATTATTATTAG
169944 TATTATTA
1 TATTATTA
169952 AACATATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
10 1 0.04
11 15 0.54
12 12 0.43
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (12 bp):
TATTATTATTAG
Found at i:172876 original size:16 final size:16
Alignment explanation
Indices: 172855--172921 Score: 93
Period size: 16 Copynumber: 4.3 Consensus size: 16
172845 GTCTCCAACG
172855 TTTATGTTCGTGTTCA
1 TTTATGTTCGTGTTCA
*
172871 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
172887 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
*
172903 TTTATGTCCGT-TT-A
1 TTTATGTTCGTGTTCA
172917 TTTAT
1 TTTAT
172922 TAAATGAACG
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
14 5 0.10
15 2 0.04
16 41 0.85
ACGTcount: A:0.10, C:0.12, G:0.19, T:0.58
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:173004 original size:16 final size:16
Alignment explanation
Indices: 172983--173015 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
172973 CAAAAAAATC
172983 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
172999 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
173015 T
1 T
173016 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:174109 original size:20 final size:21
Alignment explanation
Indices: 174077--174133 Score: 98
Period size: 20 Copynumber: 2.8 Consensus size: 21
174067 ATGTTAAAAA
*
174077 AATAATGTTTTAGGTAGAAAT
1 AATAATATTTTAGGTAGAAAT
174098 AATAAT-TTTTAGGTAGAAAT
1 AATAATATTTTAGGTAGAAAT
174118 AATAATATTTTAGGTA
1 AATAATATTTTAGGTA
174134 ATTTTTTATC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
20 20 0.57
21 15 0.43
ACGTcount: A:0.44, C:0.00, G:0.16, T:0.40
Consensus pattern (21 bp):
AATAATATTTTAGGTAGAAAT
Found at i:187799 original size:15 final size:15
Alignment explanation
Indices: 187779--187809 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
187769 ACCCGTCACT
187779 CCCTCTTAATTATCA
1 CCCTCTTAATTATCA
187794 CCCTCTTAATTATCA
1 CCCTCTTAATTATCA
187809 C
1 C
187810 ATATTCCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (15 bp):
CCCTCTTAATTATCA
Found at i:189085 original size:2 final size:2
Alignment explanation
Indices: 189078--189143 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
189068 AATAAAAATC
189078 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
189120 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
189144 GTTTTAATGG
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:192446 original size:849 final size:839
Alignment explanation
Indices: 190737--192420 Score: 3030
Period size: 849 Copynumber: 2.0 Consensus size: 839
190727 AAACTAATGT
190737 TAAAAATTAAAAAAATCACAGTAAATTAAATAACATAATTTAATATTGTTACCGTATTGGTAAAA
1 TAAAAATTAAAAAAATCACAGTAAATTAAATAACATAATTTAATATTGTTACCGTATTGGTAAAA
190802 TCTCGAGAGTTAATCACCTCTTCCATTTTACAACCGCAAAAAGTAATACCAAATAGTTAGTACAA
66 TCTCGAGAGTTAATCACCTCTTCCATTTTACAACCGCAAAAAGTAATACCAAATAGTTAGTAC-A
190867 AAAATTTTGGTCAAATAAATATAATATAATAAAAATAATTTTACATTTTAAGAACTATAACAAAA
130 AAAATTTTGGTCAAATAAATATAATATAATAAAAATAATTTTACATTTTAAGAACTATAACAAAA
190932 TCTACTTAGTTTGATAGAATGAATTGATAGAAGGAAAAATGTGAAAGTATTTTGGTGTGGTTTGA
195 TCTACTTAGTTTGATAGAATGAATTGATAGAAGGAAAAATGTGAAAGTATTTTGGTGTGGTTTGA
190997 TGTTTGCATTCGAGAGTATTATAAGAGAGGGGGTGGGTGAGTCGTCGAACTCGGGTAACAATGGA
260 TGTTTGCATTCGAGAGTATTATAAGAGAGGGGGTGGGTGAGTCGTCGAACTCGGGTAACAATGGA
191062 GTACCCAATAATGGAAGGCGTGGATGGTGATCCGCTTTCCGTCGCGTGTCAGGTTTACCATGAAG
325 GTACCCAATAATGGAAGGCGTGGATGGTGATCCGCTTTCCGTCGCGTGTCAGGTTTACCATGAAG
191127 ACACGGATGGTGAACGACTTTTTTGCCGCGTGGCGCCAGCTCAGAGGAAAACCTAAGGAAGGCGC
390 ACACGGATGGTGAACGACTTTTTTGCCGCGTGGCGCCAGCTCAGAGGAAAACCTAAGGAAGGCGC
* *
191192 GGATGGTGATCCGCGCTTTACTCTTGTGGTGCCAGCTCGGAAGAAAACCCAAGGAAGGCACGCTT
455 GGATGGTGATCCACGCTTTACTCTTGTGGCGCCAGCTCGGAAGAAAACCCAAGGAAGGCACGCTT
*
191257 GATGATCCGCACCTTCCGTCCATGTCAGCAAATAGGTGTTAGATCGATAAATTTTAGTCAATAGG
520 GATAATCCGCACCTTCCGTCCATGTCAGCAAATAGGTGTTAGATCGATAAATTTTAGTCAATAGG
* *
191322 TGTCTGACAGATAATTATTGATTCTTTGGGTAAAACGCCATATTATGTATCACTAATTAATTATC
585 TGTCTGACAGATAATTATTGATTATTAGGGTAAAACGCCATATTATGTATCACTAATTAATTATC
*
191387 TGAAGATTAAAAATAAATAATTAATCGTGAATATATTAGAATAGATATAAAAGAATATTCAAATT
650 CGAAGATTAAAAATAAATAATTAATCGTGAATATATTAGAATAGATATAAAAGAATATTCAAATT
191452 TAAAAAAAGGATAATTAGTTATCCACTAACTTGTTAGTGACTAGTCGACATATTTATTTTATAAT
715 TAAAAAAAGGATAATTAGTTATCCACTAACTTGTTAGTGACTAGTCGACATATTTATTTTATAAT
* *
191517 AAATCAAAAAGCATACAAAATTTAACATATAAGAATTAAACCGTAATTAAAATATAAACTAATGT
780 AAATCAAAAAGCATACAAAATTTAACATATAAGAATTAAACCGTAAGT-AAATAT--A-T-ATGA
191582 TAAAAATTAAAAAAATCACAGTAAATTAAATAACATAATTTAATATTGTTACCGTATTGGTAAAA
1 TAAAAATTAAAAAAATCACAGTAAATTAAATAACATAATTTAATATTGTTACCGTATTGGTAAAA
191647 TGTCTCGAGAGTTAATCACCTCTTCCATTTTACAACCGCAAAAAGTAATACCAAATAGTTAGTAC
66 --TCTCGAGAGTTAATCACCTCTTCCATTTTACAACCGCAAAAAGTAATACCAAATAGTTAGTAC
191712 -AAAA-TTTGGTCAAATAAATATAATATAATAAAAATAATTTTACATTTTAAGAACTATAACAAA
129 AAAAATTTTGGTCAAATAAATATAATATAATAAAAATAATTTTACATTTTAAGAACTATAACAAA
191775 ATCTACTTAGTTTGATAGAATGAATTGATAGAAGGAAAAATGTGAAAGTAATTTTGGTGTGGTTT
194 ATCTACTTAGTTTGATAGAATGAATTGATAGAAGGAAAAATGTGAAAGT-ATTTTGGTGTGGTTT
191840 GATGTTTGCATTCGAGAGTATTTATAAGAGAGGGGGTGGGTGAGTCGTCGAACTCGGGTAACAAT
258 GATGTTTGCATTCGAGAGTA-TTATAAGAGAGGGGGTGGGTGAGTCGTCGAACTCGGGTAACAAT
191905 GGAGTACCCGAATAATGGAAGGCGTGGATGGTGATCCACGCTTTCCGTCGCGTGTCAGGTTTACC
322 GGAGTACCC-AATAATGGAAGGCGTGGATGGTGAT-C-CGCTTTCCGTCGCGTGTCAGGTTTACC
*
191970 ATGAAGACACGGATGGTGAACGACTTTTTTGCCGCGTGGCGCCGGCTCAGAGGAAAACCTAAGGA
384 ATGAAGACACGGATGGTGAACGACTTTTTTGCCGCGTGGCGCCAGCTCAGAGGAAAACCTAAGGA
*
192035 AGGCGCGGATGGTGATCCACGCTTTACTCTTGTGGCGTCAGCTCGGAAGAAAACCCAAGGAAGGC
449 AGGCGCGGATGGTGATCCACGCTTTACTCTTGTGGCGCCAGCTCGGAAGAAAACCCAAGGAAGGC
*
192100 ACGCTTGATAATCCGCACCTTCCGTCCATGTCAGCAAATAGGTGTTAGATTGATAAATTTTAGTC
514 ACGCTTGATAATCCGCACCTTCCGTCCATGTCAGCAAATAGGTGTTAGATCGATAAATTTTAGTC
* *
192165 AATAGGTGTCTGACATATAATTATTGATTATTAGGGTAAAAATGTCCATATTATGTATCCACTAA
579 AATAGGTGTCTGACAGATAATTATTGATTATTAGGGT-AAAACG-CCATATTATGTAT-CACTAA
192230 TTAATTATCCGAAGATTAAAAATAAAATAATTAATCGATGAATATATTAGAATAGATATAAAAGA
641 TTAATTATCCGAAGATTAAAAAT-AAATAATTAATCG-TGAATATATTAGAATAGATATAAAAGA
192295 ATATTCAAATTTAAAAAAAAGGATAATTAGTTATCCACTAACTTTGTTAGTGACTAGTCGACATA
704 ATATTCAAATTT-AAAAAAAGGATAATTAGTTATCCACTAAC-TTGTTAGTGACTAGTCGACATA
192360 TTTATTTTATAAATAAATCAAAAAGCATTACAAAATTTTAACATATAAGAATTAAACCGTA
767 TTTATTTTAT-AATAAATCAAAAAGCA-TACAAAA-TTTAACATATAAGAATTAAACCGTA
192421 GGGTCATATT
Statistics
Matches: 811, Mismatches: 11, Indels: 20
0.96 0.01 0.02
Matches are distributed among these distances:
844 108 0.13
845 104 0.13
846 53 0.07
847 88 0.11
848 1 0.00
849 250 0.31
850 5 0.01
851 13 0.02
852 28 0.03
853 13 0.02
854 39 0.05
855 29 0.04
856 32 0.04
857 16 0.02
858 7 0.01
859 25 0.03
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (839 bp):
TAAAAATTAAAAAAATCACAGTAAATTAAATAACATAATTTAATATTGTTACCGTATTGGTAAAA
TCTCGAGAGTTAATCACCTCTTCCATTTTACAACCGCAAAAAGTAATACCAAATAGTTAGTACAA
AAATTTTGGTCAAATAAATATAATATAATAAAAATAATTTTACATTTTAAGAACTATAACAAAAT
CTACTTAGTTTGATAGAATGAATTGATAGAAGGAAAAATGTGAAAGTATTTTGGTGTGGTTTGAT
GTTTGCATTCGAGAGTATTATAAGAGAGGGGGTGGGTGAGTCGTCGAACTCGGGTAACAATGGAG
TACCCAATAATGGAAGGCGTGGATGGTGATCCGCTTTCCGTCGCGTGTCAGGTTTACCATGAAGA
CACGGATGGTGAACGACTTTTTTGCCGCGTGGCGCCAGCTCAGAGGAAAACCTAAGGAAGGCGCG
GATGGTGATCCACGCTTTACTCTTGTGGCGCCAGCTCGGAAGAAAACCCAAGGAAGGCACGCTTG
ATAATCCGCACCTTCCGTCCATGTCAGCAAATAGGTGTTAGATCGATAAATTTTAGTCAATAGGT
GTCTGACAGATAATTATTGATTATTAGGGTAAAACGCCATATTATGTATCACTAATTAATTATCC
GAAGATTAAAAATAAATAATTAATCGTGAATATATTAGAATAGATATAAAAGAATATTCAAATTT
AAAAAAAGGATAATTAGTTATCCACTAACTTGTTAGTGACTAGTCGACATATTTATTTTATAATA
AATCAAAAAGCATACAAAATTTAACATATAAGAATTAAACCGTAAGTAAATATATATGA
Found at i:192593 original size:30 final size:29
Alignment explanation
Indices: 192557--192615 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
192547 TTATTTATAT
*
192557 ATAATTATTTTATAACTTTTGATAAATTTA
1 ATAATTATTTTATAA-TTTTGAAAAATTTA
*
192587 ATAATTATTTTATAATTTTTAAAAATTTA
1 ATAATTATTTTATAATTTTGAAAAATTTA
192616 TCTTAGTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 12 0.44
30 15 0.56
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (29 bp):
ATAATTATTTTATAATTTTGAAAAATTTA
Found at i:197325 original size:26 final size:26
Alignment explanation
Indices: 197296--197366 Score: 117
Period size: 26 Copynumber: 2.7 Consensus size: 26
197286 TCACAAGTTT
*
197296 TCGAG-TCGAGTCGAGCTCAGCAATAC
1 TCGAGCTCGACTCG-GCTCAGCAATAC
197322 TCGAGCTCGACTCGGCTCAGCAATAC
1 TCGAGCTCGACTCGGCTCAGCAATAC
197348 TCGAGCTCGACTCGGCTCA
1 TCGAGCTCGACTCGGCTCA
197367 TTTACACCCC
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
26 36 0.84
27 7 0.16
ACGTcount: A:0.23, C:0.32, G:0.25, T:0.20
Consensus pattern (26 bp):
TCGAGCTCGACTCGGCTCAGCAATAC
Found at i:197327 original size:16 final size:16
Alignment explanation
Indices: 197306--197355 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
197296 TCGAGTCGAG
197306 TCGAGCTCAGCAATAC
1 TCGAGCTCAGCAATAC
197322 TCGAGCTC-G----AC
1 TCGAGCTCAGCAATAC
197333 TCG-GCTCAGCAATAC
1 TCGAGCTCAGCAATAC
197348 TCGAGCTC
1 TCGAGCTC
197356 GACTCGGCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
10 4 0.14
11 6 0.21
15 6 0.21
16 12 0.43
ACGTcount: A:0.24, C:0.34, G:0.22, T:0.20
Consensus pattern (16 bp):
TCGAGCTCAGCAATAC
Found at i:198125 original size:28 final size:29
Alignment explanation
Indices: 198065--198126 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 29
198055 GTTGATGAGT
* * *
198065 GTTTATGGGTTAAATGTCTAAGAATTTAG
1 GTTTATGGGTTAAATGTCTAACAATTGAA
* *
198094 GTTTATGGGTT-AATGTTTAACCATTGAA
1 GTTTATGGGTTAAATGTCTAACAATTGAA
198122 GTTTA
1 GTTTA
198127 CTGCTTTTTG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 17 0.61
29 11 0.39
ACGTcount: A:0.29, C:0.05, G:0.23, T:0.44
Consensus pattern (29 bp):
GTTTATGGGTTAAATGTCTAACAATTGAA
Found at i:199123 original size:21 final size:21
Alignment explanation
Indices: 199093--199150 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
199083 GCCGATTTCT
*
199093 TCGATGTGGTTGACTTCTTAG
1 TCGAAGTGGTTGACTTCTTAG
* * *
199114 TTGAAGTGGTTGATTTTTTAG
1 TCGAAGTGGTTGACTTCTTAG
199135 TCGAAGTGGTTGACTT
1 TCGAAGTGGTTGACTT
199151 ATTCGATGTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.17, C:0.09, G:0.29, T:0.45
Consensus pattern (21 bp):
TCGAAGTGGTTGACTTCTTAG
Found at i:199435 original size:29 final size:30
Alignment explanation
Indices: 199398--199458 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 30
199388 ATTTTTGACC
**
199398 AGTGACTAAAATGTAAGTTTTG-AAAGTTT
1 AGTGACTAAAATGTAAACTTTGAAAAGTTT
* *
199427 AGTGGCTAAAGTGTAAACTTTGAAAAGTTT
1 AGTGACTAAAATGTAAACTTTGAAAAGTTT
199457 AG
1 AG
199459 GACCCTGAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
29 18 0.67
30 9 0.33
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (30 bp):
AGTGACTAAAATGTAAACTTTGAAAAGTTT
Found at i:201354 original size:33 final size:32
Alignment explanation
Indices: 201293--201354 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
201283 TTTTGTAAAG
*
201293 GGGAAAGTTCTAGCTTAGCCGTGTAAAAGCTA
1 GGGAAAGTTCTAGCTTAGCCGTGAAAAAGCTA
*
201325 GGGAAAGGTTCTAGTTTAGCCCG-GAAAAAG
1 GGGAAA-GTTCTAGCTTAG-CCGTGAAAAAG
201355 GGAGTTTGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 6 0.23
33 17 0.65
34 3 0.12
ACGTcount: A:0.32, C:0.15, G:0.31, T:0.23
Consensus pattern (32 bp):
GGGAAAGTTCTAGCTTAGCCGTGAAAAAGCTA
Found at i:202881 original size:20 final size:20
Alignment explanation
Indices: 202856--202916 Score: 104
Period size: 20 Copynumber: 3.0 Consensus size: 20
202846 ATTAGATTGT
202856 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
202876 CCAGGGGGAACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
*
202896 CCAGGGGGTACCGATTCCCC
1 CCAGGGGGTACAGATTCCCC
202916 C
1 C
202917 TGTCTAACGG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.20, C:0.38, G:0.30, T:0.13
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:205060 original size:2 final size:2
Alignment explanation
Indices: 205053--205086 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
205043 TTTATTTTAA
205053 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
205087 AGATATGATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:206605 original size:17 final size:18
Alignment explanation
Indices: 206579--206616 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 18
206569 TGTATCGTTC
206579 CTTTCACTATATTG-TTT
1 CTTTCACTATATTGATTT
*
206596 CTTTCTCTATATTGATTT
1 CTTTCACTATATTGATTT
206614 CTT
1 CTT
206617 CATTGTATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.16, C:0.18, G:0.05, T:0.61
Consensus pattern (18 bp):
CTTTCACTATATTGATTT
Found at i:211222 original size:27 final size:27
Alignment explanation
Indices: 211190--211241 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
211180 AAAATAAAAA
*
211190 TAAATTTAA-TTTGTTAATTATTTAAAT
1 TAAA-TTAATTTTGTTAATTAGTTAAAT
*
211217 TAAATTAATTTTTTTAATTAGTTAA
1 TAAATTAATTTTGTTAATTAGTTAA
211242 TAATATTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (27 bp):
TAAATTAATTTTGTTAATTAGTTAAAT
Found at i:219420 original size:60 final size:60
Alignment explanation
Indices: 219351--219471 Score: 134
Period size: 60 Copynumber: 2.0 Consensus size: 60
219341 AGTTAATTAG
* * * * * * *
219351 TCCTTAAACTATAATACGTATTTTAAATTAGTCTTTAAATTTTTTAACATTCCAATTTCA
1 TCCTCAAACTACAATACGTATTCTAAATTAGTCCTTAAACTTTTAAACATTCAAATTTCA
** * * *
219411 TCCTCAAACTACGTTCCTTATTCTAAATTAGTCCTTAAACTTTTAAACCTTCAAATTTCA
1 TCCTCAAACTACAATACGTATTCTAAATTAGTCCTTAAACTTTTAAACATTCAAATTTCA
219471 T
1 T
219472 TCCCAAGTTC
Statistics
Matches: 49, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
60 49 1.00
ACGTcount: A:0.33, C:0.20, G:0.03, T:0.44
Consensus pattern (60 bp):
TCCTCAAACTACAATACGTATTCTAAATTAGTCCTTAAACTTTTAAACATTCAAATTTCA
Found at i:220279 original size:19 final size:20
Alignment explanation
Indices: 220255--220305 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
220245 AATGACCAAT
220255 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
220274 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
220294 AAAATCGCAACG
1 AAAATCGCAACG
220306 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:220299 original size:20 final size:20
Alignment explanation
Indices: 220255--220509 Score: 120
Period size: 20 Copynumber: 12.6 Consensus size: 20
220245 AATGACCAAT
* *
220255 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
220274 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
220294 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
220314 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
220334 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
220355 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
220378 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
** * *
220398 TGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * * *
220418 AGAATCGTAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* * * * *
220438 AGAGTCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* ** *
220458 AGAATCGCATTGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
220478 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
220498 AAAATCGCAACG
1 AAAATCGCAACG
220510 TTAAAAAGAA
Statistics
Matches: 186, Mismatches: 41, Indels: 17
0.76 0.17 0.07
Matches are distributed among these distances:
19 17 0.09
20 141 0.76
21 14 0.08
23 14 0.08
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:220434 original size:40 final size:40
Alignment explanation
Indices: 220359--220507 Score: 172
Period size: 40 Copynumber: 3.6 Consensus size: 40
220349 GCTTCCAAGT
* **
220359 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAA
1 TCGCAATGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
220402 TCGCAATGCGATTTATAGAATCGTAATGCGATTGAGAGAG
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* * *
220442 TCGCAATGCGACTGAGAGAATCGCATTGCGATTGAGAGAA
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* *
220482 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAATGCGATTTAGAGAATCGCAA
220508 CGTTAAAAAG
Statistics
Matches: 89, Mismatches: 17, Indels: 3
0.82 0.16 0.03
Matches are distributed among these distances:
40 73 0.82
42 2 0.02
43 14 0.16
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.23
Consensus pattern (40 bp):
TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:220506 original size:60 final size:60
Alignment explanation
Indices: 220359--220507 Score: 172
Period size: 60 Copynumber: 2.4 Consensus size: 60
220349 GCTTCCAAGT
* ** * *
220359 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATTGAATCGCAATGCGATTTATAGAA
1 TCGCAACGCGATTT---AGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
* * * * * *
220422 TCGTAATGCGATTGAGAGAGTCGCAATGCGACTGAGAGAATCGCATTGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
220482 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAAAATCGCAA
220508 CGTTAAAAAG
Statistics
Matches: 70, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
60 59 0.84
63 11 0.16
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.23
Consensus pattern (60 bp):
TCGCAACGCGATTTAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGATTGAGAGAA
Found at i:220519 original size:20 final size:20
Alignment explanation
Indices: 220496--220539 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
220486 AACGCGATTT
*
220496 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
220516 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
220536 AGAA
1 AGAA
220540 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:221356 original size:6 final size:6
Alignment explanation
Indices: 221335--221383 Score: 84
Period size: 6 Copynumber: 8.5 Consensus size: 6
221325 TCTCGTCTCG
221335 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
221381 GGT
1 GGT
221384 AATACGTGTC
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 10 0.23
6 33 0.77
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:221486 original size:20 final size:20
Alignment explanation
Indices: 221461--221504 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
221451 TTTTTAACTA
*
221461 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
221481 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
221501 TTCT
1 TTCT
221505 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:221514 original size:20 final size:20
Alignment explanation
Indices: 221491--221768 Score: 130
Period size: 20 Copynumber: 13.6 Consensus size: 20
221481 TTCTTTTTAA
221491 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
221511 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
221531 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * * *
221551 CATTGCGAATCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
221571 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
221594 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
221614 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
221634 CATTGCGATTTTCTTTTAAATCG
1 CGTTGCGATTTTC---TAAATCG
** ** *
221657 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
221678 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
*** **
221696 ACCGTTGCGATTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
*
221718 CGTTACGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
221738 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
221757 CGTTGCGATTTT
1 CGTTGCGATTTT
221769 ATTGGTCATT
Statistics
Matches: 203, Mismatches: 44, Indels: 23
0.75 0.16 0.09
Matches are distributed among these distances:
18 2 0.01
19 17 0.08
20 138 0.68
21 14 0.07
22 3 0.01
23 29 0.14
ACGTcount: A:0.18, C:0.23, G:0.19, T:0.39
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:221537 original size:40 final size:40
Alignment explanation
Indices: 221493--221623 Score: 172
Period size: 40 Copynumber: 3.2 Consensus size: 40
221483 CTTTTTAACG
*
221493 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGAATCTCTCAATCGCA
* * * * *
221533 TTGCGATTCTCTCAGTCGCATTGCGAATCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGAATCTCTCAATCGCA
*
221573 TTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA-T-T-TTCTAAATCGCGTTGCGAATCTCTCAATCGCA
221616 TTGCGATT
1 TTGCGATT
221624 CAATCAATCG
Statistics
Matches: 76, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
40 40 0.53
41 2 0.03
42 2 0.03
43 32 0.42
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGAATCTCTCAATCGCA
Found at i:221608 original size:63 final size:63
Alignment explanation
Indices: 221506--221664 Score: 207
Period size: 63 Copynumber: 2.6 Consensus size: 63
221496 CGATTTTCTA
* * * * **
221506 AATCGCGTTGCGATTCTC-TC--AATCGCATTGCGATTCTCTCAGTCGCATTGCGAATCTCTC
1 AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGAATCAATC
* *
221566 AGTCGCATTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGATTCAATC
1 AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGAATCAATC
* *
221629 AATCGCATTGCGATTTTCTTTTAAATCGCGTTGCGA
1 AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGA
221665 ACTTGGAAGC
Statistics
Matches: 85, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
60 16 0.19
61 2 0.02
63 67 0.79
ACGTcount: A:0.20, C:0.27, G:0.18, T:0.35
Consensus pattern (63 bp):
AATCGCATTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCATTGCGAATCAATC
Found at i:225502 original size:92 final size:92
Alignment explanation
Indices: 225345--225705 Score: 438
Period size: 92 Copynumber: 3.9 Consensus size: 92
225335 TTAAGTTACT
* * * * *
225345 TTTCATCTACTTTTTAGAGGTCATTTATTACAACAATAATACGCCGTTTTAACTACTTTTTAGAG
1 TTTCATCTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCGTTTCAACTACTTTTCAGAG
*
225410 GCCATTTATTATAGCAATGATTCACCG
66 GCCATTTATTATAGCAATAATTCACCG
*
225437 TTTCATCTACTTTTCAGAGGTCATTTATTA-AATCAATAATTCACCGTTTCAACTACTTTCCAGA
1 TTTCATCTACTTTTCAGAGGTCATTTATTACAA-CAATAATTCACCGTTTCAACTACTTTTCAGA
** * * *
225501 GGTTA-TTATTACAACAATAATTCATCG
65 GGCCATTTATTATAGCAATAATTCACCG
* * * * * * *
225528 TTTCAACTACTTTTCAGAGGCCATTTATTACAATAATAATTCACTGTTTCAGCTAATTTTCATAG
1 TTTCATCTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCGTTTCAACTACTTTTCAGAG
*
225593 GCCATTTATTGTAGCAATAATTCACCG
66 GCCATTTATTATAGCAATAATTCACCG
* * * ** * *
225620 TTTCAGCTACTTTTCAGAGGTTATTTATTACAACAATAATGCACTATTTTAGCTACTTTTCAGAG
1 TTTCATCTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCGTTTCAACTACTTTTCAGAG
* *
225685 GTCATTTATTGTAGCAATAAT
66 GCCATTTATTATAGCAATAAT
225706 ACTCCGATTG
Statistics
Matches: 230, Mismatches: 36, Indels: 6
0.85 0.13 0.02
Matches are distributed among these distances:
91 76 0.33
92 154 0.67
ACGTcount: A:0.30, C:0.18, G:0.11, T:0.40
Consensus pattern (92 bp):
TTTCATCTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCGTTTCAACTACTTTTCAGAG
GCCATTTATTATAGCAATAATTCACCG
Found at i:225659 original size:183 final size:183
Alignment explanation
Indices: 225345--225686 Score: 470
Period size: 183 Copynumber: 1.9 Consensus size: 183
225335 TTAAGTTACT
* * * * * * *
225345 TTTCATCTACTTTTTAGAGGTCATTTATTACAACAATAATACGCCGTTTTAACTACTTTTTAGAG
1 TTTCAACTACTTTTCAGAGGCCATTTATTACAACAATAATACACCGTTTCAACTAATTTTCAGAG
* *
225410 GCCATTTATTATAGCAATGATTCACCGTTTCATCTACTTTTCAGAGGTCATTTATTAAATCAATA
66 GCCATTTATTATAGCAATAATTCACCGTTTCAGCTACTTTTCAGAGGTCATTTATTAAATCAATA
* *
225475 ATTCACCGTTTCAACTACTTTCCAGAGGTTATTATTACAACAATAATTCATCG
131 ATGCACCATTTCAACTACTTTCCAGAGGTTATTATTACAACAATAATTCATCG
* * * * *
225528 TTTCAACTACTTTTCAGAGGCCATTTATTACAATAATAATTCACTGTTTCAGCTAATTTTCATAG
1 TTTCAACTACTTTTCAGAGGCCATTTATTACAACAATAATACACCGTTTCAACTAATTTTCAGAG
* *
225593 GCCATTTATTGTAGCAATAATTCACCGTTTCAGCTACTTTTCAGAGGTTATTTATTACAA-CAAT
66 GCCATTTATTATAGCAATAATTCACCGTTTCAGCTACTTTTCAGAGGTCATTTATTA-AATCAAT
* * * *
225657 AATGCACTATTTTAGCTACTTTTCAGAGGT
130 AATGCACCATTTCAACTACTTTCCAGAGGT
225687 CATTTATTGT
Statistics
Matches: 136, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
183 134 0.99
184 2 0.01
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.40
Consensus pattern (183 bp):
TTTCAACTACTTTTCAGAGGCCATTTATTACAACAATAATACACCGTTTCAACTAATTTTCAGAG
GCCATTTATTATAGCAATAATTCACCGTTTCAGCTACTTTTCAGAGGTCATTTATTAAATCAATA
ATGCACCATTTCAACTACTTTCCAGAGGTTATTATTACAACAATAATTCATCG
Found at i:225705 original size:46 final size:46
Alignment explanation
Indices: 225345--225694 Score: 398
Period size: 46 Copynumber: 7.6 Consensus size: 46
225335 TTAAGTTACT
* * * *
225345 TTTCATCTACTTTTTAGAGGTCATTTATTACAACAATAATACGCCG
1 TTTCAACTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCG
* * * * * *
225391 TTTTAACTACTTTTTAGAGGCCATTTATTATAGCAATGATTCACCG
1 TTTCAACTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCG
*
225437 TTTCATCTACTTTTCAGAGGTCATTTATTA-AATCAATAATTCACCG
1 TTTCAACTACTTTTCAGAGGTCATTTATTACAA-CAATAATTCACCG
* * *
225483 TTTCAACTACTTTCCAGAGGTTA-TTATTACAACAATAATTCATCG
1 TTTCAACTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCG
* * *
225528 TTTCAACTACTTTTCAGAGGCCATTTATTACAATAATAATTCACTG
1 TTTCAACTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCG
* * * * ** *
225574 TTTCAGCTAATTTTCATAGGCCATTTATTGTAGCAATAATTCACCG
1 TTTCAACTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCG
* * * **
225620 TTTCAGCTACTTTTCAGAGGTTATTTATTACAACAATAATGCACTA
1 TTTCAACTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCG
* *
225666 TTTTAGCTACTTTTCAGAGGTCATTTATT
1 TTTCAACTACTTTTCAGAGGTCATTTATT
225695 GTAGCAATAA
Statistics
Matches: 257, Mismatches: 44, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
45 39 0.15
46 218 0.85
ACGTcount: A:0.30, C:0.19, G:0.11, T:0.41
Consensus pattern (46 bp):
TTTCAACTACTTTTCAGAGGTCATTTATTACAACAATAATTCACCG
Found at i:226508 original size:19 final size:20
Alignment explanation
Indices: 226486--226529 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
226476 CCCTGCACTG
226486 CAAAA-ATTACTATAGATCC
1 CAAAAGATTACTATAGATCC
* *
226505 CAAAATGTTTACTATATATCC
1 CAAAA-GATTACTATAGATCC
226526 CAAA
1 CAAA
226530 TTAAATTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.24
21 16 0.76
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (20 bp):
CAAAAGATTACTATAGATCC
Found at i:228658 original size:18 final size:18
Alignment explanation
Indices: 228635--228669 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
228625 GTCATTTGAA
*
228635 GGTTTCATTGATTTGTCT
1 GGTTTCATTAATTTGTCT
228653 GGTTTCATTAATTTGTC
1 GGTTTCATTAATTTGTC
228670 CGCTTTCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.11, G:0.20, T:0.54
Consensus pattern (18 bp):
GGTTTCATTAATTTGTCT
Found at i:228676 original size:18 final size:18
Alignment explanation
Indices: 228637--228676 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
228627 CATTTGAAGG
* * *
228637 TTTCATTGATTTGTCTGG
1 TTTCATTAATTTGTCCGC
228655 TTTCATTAATTTGTCCGC
1 TTTCATTAATTTGTCCGC
228673 TTTC
1 TTTC
228677 GGTTAGGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.12, C:0.17, G:0.15, T:0.55
Consensus pattern (18 bp):
TTTCATTAATTTGTCCGC
Found at i:240211 original size:24 final size:26
Alignment explanation
Indices: 240166--240217 Score: 81
Period size: 24 Copynumber: 2.1 Consensus size: 26
240156 CGTTCGTGAA
*
240166 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
240192 CGTTC-ATT-TATGTTCATTTATGTT
1 CGTTCGATTATATGTTCATTTATGTT
240216 CG
1 CG
240218 AACAGAGGGC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 17 0.68
25 3 0.12
26 5 0.20
ACGTcount: A:0.15, C:0.13, G:0.17, T:0.54
Consensus pattern (26 bp):
CGTTCGATTATATGTTCATTTATGTT
Found at i:247032 original size:3 final size:3
Alignment explanation
Indices: 247024--247064 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
247014 GGCATTATAT
247024 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
247065 TTTTCCTTAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:247235 original size:51 final size:51
Alignment explanation
Indices: 247180--247304 Score: 205
Period size: 51 Copynumber: 2.5 Consensus size: 51
247170 CACTTGTTCA
* *
247180 TCTTCAACAATCTCCCTTCCATTAGTCAGTTCTGCAATTTCATATGTTTCT
1 TCTTCAACAATCTCCCTTCCATTAATCACTTCTGCAATTTCATATGTTTCT
* *
247231 TCTTCAACAATCTCCCTTCCATTAATCTCTTCTGCTATTTCATATGTTTCT
1 TCTTCAACAATCTCCCTTCCATTAATCACTTCTGCAATTTCATATGTTTCT
*
247282 TCTTCAACAATCTCCCTTTCATT
1 TCTTCAACAATCTCCCTTCCATT
247305 TTCTTCTGCA
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 69 1.00
ACGTcount: A:0.21, C:0.30, G:0.05, T:0.45
Consensus pattern (51 bp):
TCTTCAACAATCTCCCTTCCATTAATCACTTCTGCAATTTCATATGTTTCT
Found at i:248257 original size:20 final size:20
Alignment explanation
Indices: 248232--248281 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
248222 GACCAACAAA
*
248232 TTCGCAACGCAAATTCTAAT
1 TTCGCAACGCAAATTCCAAT
* **
248252 TTCGCAACCCAGTTTCCAAT
1 TTCGCAACGCAAATTCCAAT
248272 TTCGCAACGC
1 TTCGCAACGC
248282 GAATATGTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.28, C:0.32, G:0.12, T:0.28
Consensus pattern (20 bp):
TTCGCAACGCAAATTCCAAT
Found at i:248326 original size:21 final size:21
Alignment explanation
Indices: 248289--248339 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
248279 CGCGAATATG
248289 TAAA-TCGCATTGCGATATTC
1 TAAATTCGCATTGCGATATTC
* *
248309 TAAATTCGCGTTGTGATATTC
1 TAAATTCGCATTGCGATATTC
*
248330 CAAATTCGCA
1 TAAATTCGCA
248340 ACGTGATAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 4 0.15
21 22 0.85
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (21 bp):
TAAATTCGCATTGCGATATTC
Found at i:248355 original size:20 final size:20
Alignment explanation
Indices: 248330--248414 Score: 134
Period size: 20 Copynumber: 4.2 Consensus size: 20
248320 TGTGATATTC
* *
248330 CAAATTCGCAACGTGATAGT
1 CAAATTCGCAACGCGAAAGT
*
248350 CAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
248370 CAAATTCGCAACGCGATAGT
1 CAAATTCGCAACGCGAAAGT
248390 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
248410 CAAAT
1 CAAAT
248415 GTTTTTACGC
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 59 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:248375 original size:40 final size:40
Alignment explanation
Indices: 248330--248414 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
248320 TGTGATATTC
* *
248330 CAAATTCGCAACGTGATAGTCAAATTCTCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT
248370 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT
248410 CAAAT
1 CAAAT
248415 GTTTTTACGC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.20
Consensus pattern (40 bp):
CAAATTCGCAACGCGATAGTCAAATTCGCAACGCGAAAGT
Found at i:248586 original size:22 final size:22
Alignment explanation
Indices: 248542--248592 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
248532 CTACGGCGAC
*
248542 ATCCATCCCCATCTCCAACGAA
1 ATCCGTCCCCATCTCCAACGAA
* * * *
248564 ATTCGTCCCCATTTCCGATGAA
1 ATCCGTCCCCATCTCCAACGAA
248586 ATCCGTC
1 ATCCGTC
248593 TATCTCCATC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.25, C:0.39, G:0.10, T:0.25
Consensus pattern (22 bp):
ATCCGTCCCCATCTCCAACGAA
Found at i:250640 original size:21 final size:21
Alignment explanation
Indices: 250616--250665 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
250606 GTTAGGGGAA
250616 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTCGGTGCT
*
250637 TTACGTCATGAGGTCGGTGCT
1 TTACGTGATGAGGTCGGTGCT
250658 TTACGTGA
1 TTACGTGA
250666 AGATAATGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.16, C:0.16, G:0.34, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTGCT
Found at i:250897 original size:4 final size:4
Alignment explanation
Indices: 250888--250929 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
250878 TTTTTCGGTA
* *
250888 TTAT TTAT TTAT TTAT TTAT TTAT TTAT ATAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
250930 TTAGCGGCCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:251119 original size:15 final size:15
Alignment explanation
Indices: 251099--251130 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
251089 GTCTCCTATC
*
251099 GTTCAAGAGGCCCCT
1 GTTCAAGAGGCCACT
251114 GTTCAAGAGGCCACT
1 GTTCAAGAGGCCACT
251129 GT
1 GT
251131 CATCGTTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.28, G:0.28, T:0.22
Consensus pattern (15 bp):
GTTCAAGAGGCCACT
Found at i:252598 original size:14 final size:14
Alignment explanation
Indices: 252579--252618 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
252569 TTTTGATTAA
252579 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
** *
252593 TTGATTTGTTTAAT
1 TTGATTTGTAAAAG
252607 TTGATTTGTAAA
1 TTGATTTGTAAA
252619 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:253155 original size:18 final size:18
Alignment explanation
Indices: 253132--253167 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
253122 AAGCCGGTTG
*
253132 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
253150 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
253168 CCTTTTGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Done.