Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000389.1 Hibiscus syriacus cultivar Beakdansim tig00000715_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: 2672246
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 15
Found at i:432 original size:43 final size:43
Alignment explanation
Indices: 378--495 Score: 166
Period size: 43 Copynumber: 2.7 Consensus size: 43
368 ATAGATTTAC
* *
378 ATATTTTAACATTATACGTAAAATGATAC-CATTTTCTTTACAT
1 ATATTTTAACATCATACGTAAAATGATACTAATTTT-TTTACAT
* *
421 ATATTTTAACATCATATGTAAAAGGATACTAATTTTTTTACAT
1 ATATTTTAACATCATACGTAAAATGATACTAATTTTTTTACAT
* *
464 ATATTTTAATACCATACGTAAAATGATACTAA
1 ATATTTTAACATCATACGTAAAATGATACTAA
496 AATTTAAAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
43 61 0.92
44 5 0.08
ACGTcount: A:0.41, C:0.12, G:0.06, T:0.42
Consensus pattern (43 bp):
ATATTTTAACATCATACGTAAAATGATACTAATTTTTTTACAT
Found at i:7101 original size:2 final size:2
Alignment explanation
Indices: 7094--7125 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
7084 GAGAACAAGG
7094 TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
7126 TGGATTCATT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10969 original size:2 final size:2
Alignment explanation
Indices: 10962--11011 Score: 68
Period size: 2 Copynumber: 26.0 Consensus size: 2
10952 ATTACTTATC
*
10962 AT AT AT AT AT AT A- AT AT AT AT AT AT AT AT A- AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
11002 AT AA AT AT AT
1 AT AT AT AT AT
11012 CTCAATCAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.05
2 40 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:10984 original size:17 final size:17
Alignment explanation
Indices: 10962--11011 Score: 79
Period size: 17 Copynumber: 3.1 Consensus size: 17
10952 ATTACTTATC
10962 ATATATATATATAATAT
1 ATATATATATATAATAT
10979 ATATATATATATAATAT
1 ATATATATATATAATAT
10996 -T-TATATATA-AATAT
1 ATATATATATATAATAT
11010 AT
1 AT
11012 CTCAATCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.16
15 9 0.28
16 1 0.03
17 17 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
ATATATATATATAATAT
Found at i:10986 original size:19 final size:18
Alignment explanation
Indices: 10962--11010 Score: 64
Period size: 19 Copynumber: 2.7 Consensus size: 18
10952 ATTACTTATC
10962 ATATATATATAT-AATAT
1 ATATATATATATAAATAT
*
10979 ATATATATATATAATATTT
1 ATATATATATATAA-ATAT
*
10998 ATATATAAATATA
1 ATATATATATATA
11011 TCTCAATCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 12 0.43
18 1 0.04
19 15 0.54
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
ATATATATATATAAATAT
Found at i:11526 original size:23 final size:23
Alignment explanation
Indices: 11477--11543 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
11467 TTTTAATAAT
* *
11477 TCTGACTTTTTGACAT-TTATTTT
1 TCTGACTTTATGACATGTT-TTTC
*
11500 TCTGCCTTTATGACATGTTTTTC
1 TCTGACTTTATGACATGTTTTTC
* *
11523 TCTGTCTCTATGACATGTTTT
1 TCTGACTTTATGACATGTTTT
11544 CGGTTGTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
23 36 0.95
24 2 0.05
ACGTcount: A:0.15, C:0.18, G:0.12, T:0.55
Consensus pattern (23 bp):
TCTGACTTTATGACATGTTTTTC
Found at i:12160 original size:30 final size:30
Alignment explanation
Indices: 12124--12185 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
12114 ACTCGGATGC
12124 ATGTATTTTCGGATTATAAATATCCAATTT
1 ATGTATTTTCGGATTATAAATATCCAATTT
12154 ATGTATTTTCGGATTATAAATATCCAATTT
1 ATGTATTTTCGGATTATAAATATCCAATTT
12184 AT
1 AT
12186 ATTTATTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.47
Consensus pattern (30 bp):
ATGTATTTTCGGATTATAAATATCCAATTT
Found at i:17314 original size:39 final size:39
Alignment explanation
Indices: 17242--17348 Score: 151
Period size: 39 Copynumber: 2.7 Consensus size: 39
17232 CAGGGCCAAG
* * * *
17242 TGGATGATACCAAAACACCAAAAGCAGATCAAGGTGAAC
1 TGGATGATACCGAAACACCAAAAGCTGAACAAGGTGAAA
*
17281 TGGATGATACCGAAACACCAAGAGCTGAACAAGGTGAAA
1 TGGATGATACCGAAACACCAAAAGCTGAACAAGGTGAAA
* *
17320 TGGATGATAACGAACCACCAAAAGCTGAA
1 TGGATGATACCGAAACACCAAAAGCTGAA
17349 AAAAGTGGCA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 60 1.00
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (39 bp):
TGGATGATACCGAAACACCAAAAGCTGAACAAGGTGAAA
Found at i:17549 original size:33 final size:33
Alignment explanation
Indices: 17512--17612 Score: 166
Period size: 33 Copynumber: 3.1 Consensus size: 33
17502 GCATCATACC
17512 GATATTTCTAGTGCAGTTTCGGAACAACAGAAT
1 GATATTTCTAGTGCAGTTTCGGAACAACAGAAT
*
17545 GATATTTCTAGTTCAGTTTCGGAACAACAGAAT
1 GATATTTCTAGTGCAGTTTCGGAACAACAGAAT
* * *
17578 GATATTTTTAGTGCAGTTTCCGAACAACAAAAT
1 GATATTTCTAGTGCAGTTTCGGAACAACAGAAT
17611 GA
1 GA
17613 ACATGAGCCT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 63 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.32
Consensus pattern (33 bp):
GATATTTCTAGTGCAGTTTCGGAACAACAGAAT
Found at i:17991 original size:24 final size:24
Alignment explanation
Indices: 17959--18010 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
17949 AGACGCAGAG
17959 ACAGAGGTAGAGGAAGAGGCAAAA
1 ACAGAGGTAGAGGAAGAGGCAAAA
*
17983 ACAGAGGTAGAGGAAGAGGCAGAA
1 ACAGAGGTAGAGGAAGAGGCAAAA
18007 ACAG
1 ACAG
18011 TGGCAAAGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.10, G:0.38, T:0.04
Consensus pattern (24 bp):
ACAGAGGTAGAGGAAGAGGCAAAA
Found at i:18024 original size:24 final size:24
Alignment explanation
Indices: 17953--18029 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
17943 AGAATTAGAC
* * *
17953 GCAGAGACAGAGGTAGAGGAAGAG
1 GCAGAAACAGAGGCAAAGGAAGAG
* * *
17977 GCAAAAACAGAGGTAGAGGAAGAG
1 GCAGAAACAGAGGCAAAGGAAGAG
* *
18001 GCAGAAACAGTGGCAAAGGCAGAG
1 GCAGAAACAGAGGCAAAGGAAGAG
*
18025 CCAGA
1 GCAGA
18030 GGCAGAAATA
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.44, C:0.13, G:0.39, T:0.04
Consensus pattern (24 bp):
GCAGAAACAGAGGCAAAGGAAGAG
Found at i:18139 original size:12 final size:12
Alignment explanation
Indices: 18124--18168 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
18114 GGCAGAAGGG
*
18124 GAGGAAAAGGTA
1 GAGGTAAAGGTA
* *
18136 GAGGCAAAGGAA
1 GAGGTAAAGGTA
*
18148 GAGGTAAACGTA
1 GAGGTAAAGGTA
18160 GAGGTAAAG
1 GAGGTAAAG
18169 ACAAAGACAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.47, C:0.04, G:0.40, T:0.09
Consensus pattern (12 bp):
GAGGTAAAGGTA
Found at i:18151 original size:24 final size:23
Alignment explanation
Indices: 18111--18168 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
18101 AGGTAAAGTC
* *
18111 AGAGGCAGAAGGGGAGGAAAAGGT
1 AGAGGCA-AAGGAGAGGAAAACGT
*
18135 AGAGGCAAAGGAAGAGGTAAACGT
1 AGAGGCAAAGG-AGAGGAAAACGT
*
18159 AGAGGTAAAG
1 AGAGGCAAAG
18169 ACAAAGACAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 4 0.14
24 25 0.86
ACGTcount: A:0.45, C:0.05, G:0.43, T:0.07
Consensus pattern (23 bp):
AGAGGCAAAGGAGAGGAAAACGT
Found at i:22730 original size:18 final size:18
Alignment explanation
Indices: 22709--22743 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
22699 TTGATGCTGC
22709 TGAGCAAGATGATGTTGT
1 TGAGCAAGATGATGTTGT
22727 TGAGCAAGATGATGTTG
1 TGAGCAAGATGATGTTG
22744 CTAGCTCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.34, T:0.31
Consensus pattern (18 bp):
TGAGCAAGATGATGTTGT
Found at i:26571 original size:21 final size:20
Alignment explanation
Indices: 26485--26642 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
26475 AAATGACCAA
**
26485 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
26504 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
26524 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
26544 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
26565 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
26586 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
26606 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
26627 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
26643 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:26671 original size:20 final size:20
Alignment explanation
Indices: 26609--26878 Score: 269
Period size: 20 Copynumber: 13.5 Consensus size: 20
26599 CGATTTTCCA
* ** *
26609 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
26629 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
26649 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
26669 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
26689 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
26709 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
26729 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
26749 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
26769 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
26789 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
26809 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
26829 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
26849 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
26869 AAATCACAAC
1 AAATCGCAAC
26879 ACTGAAATTT
Statistics
Matches: 210, Mismatches: 32, Indels: 16
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 206 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:27595 original size:24 final size:24
Alignment explanation
Indices: 27556--27602 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
27546 AAATTTGGTC
27556 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
27580 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
27603 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:30118 original size:33 final size:33
Alignment explanation
Indices: 30067--30299 Score: 271
Period size: 33 Copynumber: 6.9 Consensus size: 33
30057 CGGAAATTAC
*
30067 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
30100 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACGA-GAAAATCGCAATGC-GAAATGAA
*
30134 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
30167 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAAATCGCAATGCGAAATGAA
*
30200 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
1 AATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAA
30233 AATCGCAATGCGAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG-A-GAAAATCGCAATGCGAAATGAA
*
30270 AATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAACGAGAAAATCGCAATGCGAAAT
30300 TATAAACGCA
Statistics
Matches: 179, Mismatches: 8, Indels: 26
0.84 0.04 0.12
Matches are distributed among these distances:
32 15 0.08
33 102 0.57
34 33 0.18
35 5 0.03
36 3 0.02
37 11 0.06
38 10 0.06
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAAAATCGCAATGCGAAATGAA
Found at i:30153 original size:14 final size:14
Alignment explanation
Indices: 30134--30188 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
30124 CGGAAATGAA
30134 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
30148 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
30167 AATCGCAACGAGAG
1 AATCGCAACGAGAG
30181 AATCGCAA
1 AATCGCAA
30189 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:30165 original size:67 final size:67
Alignment explanation
Indices: 30067--30299 Score: 305
Period size: 67 Copynumber: 3.4 Consensus size: 67
30057 CGGAAATTAC
*
30067 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAAT
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAATGC-GAAAT
30131 GAA
65 GAA
*
30134 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGA-GAGAATCGCAATGCGAAATG
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAATGCGAAATG
30198 AA
66 AA
* * * * *
30200 AATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAATGAAAATCGCAATGC
1 AATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAA--CG-ATGAAAATCGCAATGC
30262 GAAATGAA
60 GAAATGAA
30270 AATCGCAACGAGAGAATCGCAATGCGAAAT
1 AATCGCAACGAGAGAATCGCAATGCGAAAT
30300 TATAAACGCA
Statistics
Matches: 142, Mismatches: 13, Indels: 17
0.83 0.08 0.10
Matches are distributed among these distances:
64 7 0.05
65 7 0.05
66 27 0.19
67 54 0.38
68 3 0.02
69 1 0.01
70 32 0.23
71 6 0.04
72 5 0.04
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.13
Consensus pattern (67 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGATGAAAATCGCAATGCGAAATG
AA
Found at i:30172 original size:19 final size:19
Alignment explanation
Indices: 30081--30277 Score: 202
Period size: 19 Copynumber: 11.4 Consensus size: 19
30071 GCAACGAGAG
30081 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
30100 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
30114 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
30134 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
30148 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
30167 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
30181 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
30200 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
30219 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
30233 AATCGCAATGCG-AATGAA
1 AATCGCAATGCGAAATGAA
30251 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
30270 AATCGCAA
1 AATCGCAA
30278 CGAGAGAATC
Statistics
Matches: 149, Mismatches: 8, Indels: 42
0.75 0.04 0.21
Matches are distributed among these distances:
14 42 0.28
15 3 0.02
16 7 0.05
17 7 0.05
18 17 0.11
19 60 0.40
20 13 0.09
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:30355 original size:19 final size:19
Alignment explanation
Indices: 30324--30420 Score: 125
Period size: 19 Copynumber: 5.4 Consensus size: 19
30314 GATTCTCTCG
30324 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
30344 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
30362 TTACGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
30376 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30395 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
30414 TTGCGAT
1 TTGCGAT
30421 AGTCATTTTT
Statistics
Matches: 68, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
14 5 0.07
16 7 0.10
17 7 0.10
18 9 0.13
19 34 0.50
20 6 0.09
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.45
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:30363 original size:52 final size:52
Alignment explanation
Indices: 30306--30420 Score: 205
Period size: 52 Copynumber: 2.2 Consensus size: 52
30296 AAATTATAAA
30306 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGA-TTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATTT
*
30358 CGCATTACGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
1 CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
30410 CGCATTGCGAT
1 CGCATTGCGAT
30421 AGTCATTTTT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 10 0.17
52 50 0.83
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.43
Consensus pattern (52 bp):
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
Found at i:30428 original size:38 final size:37
Alignment explanation
Indices: 30324--30420 Score: 123
Period size: 33 Copynumber: 2.7 Consensus size: 37
30314 GATTCTCTCG
30324 TTGCGATTTTCATTTCCGCATTGCGATTTCATTTCGCA
1 TTGCGATTTTCATTT-CGCATTGCGATTTCATTTCGCA
* *
30362 TTACGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGCA
30395 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
30421 AGTCATTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 13
0.74 0.06 0.20
Matches are distributed among these distances:
32 6 0.12
33 17 0.35
34 2 0.04
35 5 0.10
36 7 0.14
37 1 0.02
38 11 0.22
ACGTcount: A:0.15, C:0.23, G:0.16, T:0.45
Consensus pattern (37 bp):
TTGCGATTTTCATTTCGCATTGCGATTTCATTTCGCA
Found at i:30545 original size:14 final size:14
Alignment explanation
Indices: 30526--30562 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
30516 CATCAATTAC
30526 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
30540 ACAAATCATCTTTT
1 ACAAATCAACTTTT
30554 ACAAATCAA
1 ACAAATCAA
30563 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:32555 original size:14 final size:14
Alignment explanation
Indices: 32536--32592 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
32526 GCGAAATGAA
*
32536 AATCGCAACGACAG
1 AATCGCAACGAAAG
32550 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
32567 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
32583 AATCGCAACG
1 AATCGCAACG
32593 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:32563 original size:33 final size:33
Alignment explanation
Indices: 32517--32609 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
32507 GCGAAACCAA
*
32517 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
32550 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
32583 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
32610 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:32574 original size:19 final size:19
Alignment explanation
Indices: 32480--32614 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
32470 TAGTTTACTT
* *
32480 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
32500 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
32519 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
32538 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
32552 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
32571 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
32585 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
32604 TCGCAATGCGA
1 TCGCAACGCGA
32615 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:32632 original size:19 final size:19
Alignment explanation
Indices: 32610--32737 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
32600 AAAATCGCAA
32610 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
32629 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
32643 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
32662 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
32676 TGCGA-TTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
32694 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
32713 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
32733 TGCGA
1 TGCGA
32738 AAGTAAACTA
Statistics
Matches: 88, Mismatches: 9, Indels: 23
0.73 0.08 0.19
Matches are distributed among these distances:
13 2 0.02
14 19 0.22
15 1 0.01
16 3 0.03
17 1 0.01
18 10 0.11
19 39 0.44
20 13 0.15
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.45
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:32652 original size:33 final size:33
Alignment explanation
Indices: 32610--32700 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 33
32600 AAAATCGCAA
32610 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
32643 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
32676 TGCGA-TTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
32701 TTGGTTTCGC
Statistics
Matches: 55, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 18 0.33
33 35 0.64
34 2 0.04
ACGTcount: A:0.08, C:0.19, G:0.29, T:0.45
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:32901 original size:93 final size:93
Alignment explanation
Indices: 32785--33253 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
32775 ATGGATTGCA
32785 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
32849 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
32877 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
32942 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
32970 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
33035 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
33063 TTACTTTCAACCGAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
33128 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
33156 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
33221 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
33249 TTACT
1 TTACT
33254 AAGCAATCTA
Statistics
Matches: 373, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 4 0.01
93 369 0.99
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:34963 original size:14 final size:14
Alignment explanation
Indices: 34944--35033 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
34934 GTTGAATGAA
34944 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
34958 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
34977 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
34991 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
35010 AATCGCAACGAGAG
1 AATCGCAACGAGAG
35024 AATCGCAACG
1 AATCGCAACG
35034 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:34975 original size:33 final size:33
Alignment explanation
Indices: 34938--35049 Score: 208
Period size: 33 Copynumber: 3.4 Consensus size: 33
34928 CTTTTGGTTG
34938 AATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGAGAGAATCGCAACGCGA
*
34971 AATGACAATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGAGAGAATCGCAACGCGA
35004 AATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 AATGAAAATCGCAACGAGAGAATCGCAACGCGA
35037 AATG-AAATCGCAA
1 AATGAAAATCGCAA
35050 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 9 0.12
33 68 0.88
ACGTcount: A:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
AATGAAAATCGCAACGAGAGAATCGCAACGCGA
Found at i:34982 original size:19 final size:19
Alignment explanation
Indices: 34955--35054 Score: 96
Period size: 19 Copynumber: 5.8 Consensus size: 19
34945 ATCGCAACGA
34955 GAGAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
*
34974 GACAATCGCAA--CG--A-
1 GAGAATCGCAACGCGAAAT
34988 GAGAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
*
35007 GAAAATCGCAA--CG--A-
1 GAGAATCGCAACGCGAAAT
35021 GAGAATCGCAACGCGAAAT
1 GAGAATCGCAACGCGAAAT
*
35040 GA-AATCGCAATGCGA
1 GAGAATCGCAACGCGA
35055 TTTTGGTTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
14 20 0.30
15 2 0.03
16 4 0.06
17 4 0.06
18 14 0.21
19 22 0.33
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (19 bp):
GAGAATCGCAACGCGAAAT
Found at i:35085 original size:14 final size:14
Alignment explanation
Indices: 35066--35122 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
35056 TTTGGTTTCG
35066 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
35080 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
35099 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
35113 CGTTGCGATT
1 CGTTGCGATT
35123 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:35098 original size:33 final size:33
Alignment explanation
Indices: 35050--35130 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
35040 GAAATCGCAA
**
35050 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
35083 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
35116 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
35131 TCTCGTGCGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:35133 original size:21 final size:21
Alignment explanation
Indices: 35107--35181 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
35097 CGCGTTGCGA
35107 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
35128 TTCTCTCG-TGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
35147 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
35168 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
35182 CTCTTCTGCA
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 8 0.18
20 16 0.36
21 21 0.47
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.45
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:35161 original size:40 final size:41
Alignment explanation
Indices: 35106--35182 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 41
35096 TCGCGTTGCG
*
35106 ATTCTCTCGTTGCGATTTTCATTTCTCTCG-TGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
35146 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
35183 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 29 0.83
41 6 0.17
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.44
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:35303 original size:33 final size:33
Alignment explanation
Indices: 35261--35331 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
35251 AATACTAACT
*
35261 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
35294 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
35327 TGAAA
1 TGAAA
35332 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:35566 original size:22 final size:22
Alignment explanation
Indices: 35514--35568 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
35504 TGGTTGTGAG
**
35514 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
35536 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
35558 GGATTTCTTCG
1 GGATTTCTTCG
35569 TCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:35740 original size:20 final size:20
Alignment explanation
Indices: 35715--35908 Score: 194
Period size: 20 Copynumber: 9.7 Consensus size: 20
35705 CTTTAAATAT
35715 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
***
35735 CGCGTTGCGATTTTATTTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
35757 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
**
35776 CGCGTTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
* **
35796 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
35816 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
35836 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
35856 CACGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
35876 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
35896 CGCGTTGCGATTT
1 CGCGTTGCGATTT
35909 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 129 0.88
21 14 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:35902 original size:60 final size:60
Alignment explanation
Indices: 35715--35908 Score: 226
Period size: 60 Copynumber: 3.2 Consensus size: 60
35705 CTTTAAATAT
* **
35715 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATTTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATCTATTCGCGTTGCGATTTACGGATA
** * * * *
35776 CGCGTTGCGATTTACCCATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATCTATTCGCGTTGCGATTTACGGATA
* * * * * ** *
35836 CACGTTGCGATTTACGGATACACGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATCTATTCGCGTTGCGATTTACGGATA
35896 CGCGTTGCGATTT
1 CGCGTTGCGATTT
35909 TGGAAAATCG
Statistics
Matches: 109, Mismatches: 24, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
60 82 0.75
61 27 0.25
ACGTcount: A:0.19, C:0.21, G:0.24, T:0.37
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATCTATTCGCGTTGCGATTTACGGATA
Found at i:35925 original size:21 final size:21
Alignment explanation
Indices: 35895--35977 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
35885 ATTTTCATAT
*
35895 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
35916 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
35937 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
35958 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
35978 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:35968 original size:42 final size:43
Alignment explanation
Indices: 35875--35973 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
35865 ATTTATGTGT
* *
35875 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
35916 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
35958 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
35974 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:37772 original size:110 final size:109
Alignment explanation
Indices: 37570--37778 Score: 319
Period size: 110 Copynumber: 1.9 Consensus size: 109
37560 TTCAAACAGA
* *
37570 GGCAACAAAGATCAAGTATTGAAGATCCCATATCCAGGCAACAAAGAAGTAAATCCCTTAGGTGC
1 GGCAACAAAGATCAAGCATTGAAGATCCCATAGCCAGGCAACAAAGAAGTAAATCCCTTAGGTGC
* *
37635 GGAAGCAGAAAAGTAATGAGGCAGACCCATAAGATACCAAATGG
66 AGAAGCAGAAAAGTAATGAGGCAGACCCAGAAGATACCAAATGG
* * * * *
37679 GGCACACAATGATCAAGCGTTGAAGATCCCATAGCCGGGCAGCAAAGAAGTAAATCCTTTAGGTG
1 GGCA-ACAAAGATCAAGCATTGAAGATCCCATAGCCAGGCAACAAAGAAGTAAATCCCTTAGGTG
*
37744 TAGAAGCAGAAAAGTAATGAGGCAGACCCAGAAGA
65 CAGAAGCAGAAAAGTAATGAGGCAGACCCAGAAGA
37779 CACCTCAACA
Statistics
Matches: 89, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
109 4 0.04
110 85 0.96
ACGTcount: A:0.41, C:0.19, G:0.25, T:0.15
Consensus pattern (109 bp):
GGCAACAAAGATCAAGCATTGAAGATCCCATAGCCAGGCAACAAAGAAGTAAATCCCTTAGGTGC
AGAAGCAGAAAAGTAATGAGGCAGACCCAGAAGATACCAAATGG
Found at i:41852 original size:23 final size:23
Alignment explanation
Indices: 41824--41871 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
41814 TTTGTTAAAG
41824 TAAGACTTCTTTAGAAGAAAAAT
1 TAAGACTTCTTTAGAAGAAAAAT
41847 TAAGACTTCTTTAGAAGAAAAAT
1 TAAGACTTCTTTAGAAGAAAAAT
41870 TA
1 TA
41872 TCAAATGCCG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.48, C:0.08, G:0.12, T:0.31
Consensus pattern (23 bp):
TAAGACTTCTTTAGAAGAAAAAT
Found at i:45741 original size:156 final size:156
Alignment explanation
Indices: 45466--45773 Score: 526
Period size: 156 Copynumber: 2.0 Consensus size: 156
45456 AGAAAGCTGA
* * *
45466 TCCCTCTCAAGCATAACTGATTGAAGGTCTGCCTCAAGACTAGATACTCTCTTTACTGATTCTTC
1 TCCCTCTCAAGAATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTCTTTACTGACTCTTC
* *
45531 TAAATCAGTAGCTAGTGACCCACAATAATTTTCAAGATTATCAATCTTCTTCTGCAAAGAATTTC
66 CAAATCAGCAGCTAGTGACCCACAATAATTTTCAAGATTATCAATCTTCTTCTGCAAAGAATTTC
45596 TTTCATGATTAGCATCTGAAAGAGCG
131 TTTCATGATTAGCATCTGAAAGAGCG
* *
45622 TCCCTCTCCAGAATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTCTTTTCTGACTCTTC
1 TCCCTCTCAAGAATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTCTTTACTGACTCTTC
* *
45687 CAAATCAGCAGCTAGTGACCCACAATAATTTTCCAGATTATCAATCTTCTTCTGCAAAGAATTTT
66 CAAATCAGCAGCTAGTGACCCACAATAATTTTCAAGATTATCAATCTTCTTCTGCAAAGAATTTC
*
45752 TTTCATGATTAGCTTCTGAAAG
131 TTTCATGATTAGCATCTGAAAG
45774 TGCCCCTCCT
Statistics
Matches: 142, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
156 142 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (156 bp):
TCCCTCTCAAGAATAACTGATTGAAGGTCAGCCTCAAGACTAGATACTCTCTTTACTGACTCTTC
CAAATCAGCAGCTAGTGACCCACAATAATTTTCAAGATTATCAATCTTCTTCTGCAAAGAATTTC
TTTCATGATTAGCATCTGAAAGAGCG
Found at i:49355 original size:24 final size:24
Alignment explanation
Indices: 49326--49381 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
49316 ACAAAGGAAG
*
49326 TTCACCATCAACTTCAGACGTTCT
1 TTCACCACCAACTTCAGACGTTCT
49350 TTCACCACCAACTTCAGACGTTCT
1 TTCACCACCAACTTCAGACGTTCT
49374 TTCACCAC
1 TTCACCAC
49382 TTCTATCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.25, C:0.38, G:0.07, T:0.30
Consensus pattern (24 bp):
TTCACCACCAACTTCAGACGTTCT
Found at i:54778 original size:32 final size:32
Alignment explanation
Indices: 54732--54821 Score: 103
Period size: 32 Copynumber: 2.8 Consensus size: 32
54722 GTATTAAATG
* *
54732 ATTTCTTTCTTTTTGTTTGTGTACATTAA-CT
1 ATTTATTTCCTTTTGTTTGTGTACATTAACCT
* *
54763 AATTTATTTCCTTTTGTTTATGTACACTAACCT
1 -ATTTATTTCCTTTTGTTTGTGTACATTAACCT
* *
54796 ATTTATTTTCTTTTGATTGTGT-CATT
1 ATTTATTTCCTTTTGTTTGTGTACATT
54822 TTTCATCATT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
31 3 0.06
32 44 0.90
33 2 0.04
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.59
Consensus pattern (32 bp):
ATTTATTTCCTTTTGTTTGTGTACATTAACCT
Found at i:57094 original size:21 final size:20
Alignment explanation
Indices: 57056--57095 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
57046 GATCAATATT
*
57056 TTTGCATATGCATTTGCATA
1 TTTGCATATGCATCTGCATA
*
57076 TTTGCATTTTGCATCTGCAT
1 TTTGCA-TATGCATCTGCAT
57096 TTCATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.20, C:0.17, G:0.15, T:0.47
Consensus pattern (20 bp):
TTTGCATATGCATCTGCATA
Found at i:61242 original size:64 final size:65
Alignment explanation
Indices: 61169--61331 Score: 163
Period size: 64 Copynumber: 2.5 Consensus size: 65
61159 ATTGTTTGAA
* *** *
61169 GGTGTATCGATGCACAAGTAGTGCATCGATGCACT-CTTTTAATCTAA-AAACATCGAATGCAAT
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAAT-AAACAAACATCGAATGCAAT
61232 T
65 T
* * * *
61233 GGTGCATCGATGCATAAGGCA-TGCATCGATGCA-TCCCAGTAATAAACAAACATCGAATGTATT
1 GGTGCATCGATGCACAA-GTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAAT
61296 T
65 T
** * *
61297 TATGCACCGATGCACAGGTAGTGCATCGATGCACT
1 GGTGCATCGATGCACAAGTAGTGCATCGATGCACT
61332 GATAGGGAAT
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
63 5 0.06
64 71 0.90
65 3 0.04
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (65 bp):
GGTGCATCGATGCACAAGTAGTGCATCGATGCACTCCCAGTAATAAACAAACATCGAATGCAATT
Found at i:62340 original size:101 final size:102
Alignment explanation
Indices: 62117--62332 Score: 389
Period size: 101 Copynumber: 2.1 Consensus size: 102
62107 GTCGAGGGTC
62117 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACA-GTGTGAAGTCTGGTGAGACACATAC
* *
62182 TTGATCCTTGGCATATGTATATGATTCTTAAGGAATGA
65 TTGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
62220 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACA-TGTGAAGTCTGGTGAGACACATACT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGTGTGAAGTCTGGTGAGACACATACT
*
62284 TGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
62321 TATGTGGTCCTT
1 TATGTGGTCCTT
62333 ATGGACATTA
Statistics
Matches: 110, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
101 71 0.65
103 39 0.35
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.37
Consensus pattern (102 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACAGTGTGAAGTCTGGTGAGACACATACT
TGATCCCTAGCATATGTATATGATTCTTAAGGAATGA
Found at i:62384 original size:23 final size:23
Alignment explanation
Indices: 62348--62414 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
62338 CATTATTATA
* *
62348 TGGCACTACAGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
62371 TGGCACTCCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
* *
62394 TGGCACTTCGGTGTAATTATA
1 TGGCACTACGGTGCAATTATA
62415 TGAGCTGTGG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:65296 original size:46 final size:46
Alignment explanation
Indices: 65239--65384 Score: 137
Period size: 46 Copynumber: 3.3 Consensus size: 46
65229 ATGTGTCAAC
*
65239 TTAGATAACCAGCCGTCCCCATCATAGTGGAACTGTGTTATCACCT
1 TTAGATGACCAGCCGTCCCCATCATAGTGGAACTGTGTTATCACCT
* * * *
65285 TTAGATGACCAGATC-TCCTCATTAT-GTAGGAGA-TGTG---TCAGC-
1 TTAGATGACCAG-CCGTCCCCATCATAGT-GGA-ACTGTGTTATCACCT
* *
65327 TTAGAT-AGCCAGCCGTCCCCATCAGAGTGGAACCGTGTTATCACCT
1 TTAGATGA-CCAGCCGTCCCCATCATAGTGGAACTGTGTTATCACCT
65373 TTAGATGACCAG
1 TTAGATGACCAG
65385 ATTTCCTCAT
Statistics
Matches: 77, Mismatches: 11, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
41 3 0.04
42 23 0.30
43 6 0.08
45 6 0.08
46 36 0.47
47 3 0.04
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.27
Consensus pattern (46 bp):
TTAGATGACCAGCCGTCCCCATCATAGTGGAACTGTGTTATCACCT
Found at i:65356 original size:88 final size:88
Alignment explanation
Indices: 65202--65459 Score: 406
Period size: 88 Copynumber: 3.0 Consensus size: 88
65192 CAAAATCACC
*
65202 TGACCAGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACCAGCCGTCCCCATCATAGT
1 TGACCAGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACCAGCCGTCCCCATCAGAGT
*
65267 GGAACTGTGTTATCACCTTTAGA
66 GGAACCGTGTTATCACCTTTAGA
* *
65290 TGACCAGATCTCCTCATTATGTAGGAGATGTGTCAGCTTAGATAGCCAGCCGTCCCCATCAGAGT
1 TGACCAGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACCAGCCGTCCCCATCAGAGT
65355 GGAACCGTGTTATCACCTTTAGA
66 GGAACCGTGTTATCACCTTTAGA
* *
65378 TGACCAGATTTCCTCATTATGT------TGTGTCAAATTAGATAACCAGCCGTCCCCAT-AGAGT
1 TGACCAGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACCAGCCGTCCCCATCAGAGT
65436 GGAACCGTGTTATCACC-TTAGA
66 GGAACCGTGTTATCACCTTTAGA
65458 TG
1 TG
65460 GCCATAACTC
Statistics
Matches: 162, Mismatches: 8, Indels: 8
0.91 0.04 0.04
Matches are distributed among these distances:
80 7 0.04
81 22 0.14
82 28 0.17
88 105 0.65
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (88 bp):
TGACCAGATCTCCTCATTATGTAGGAGATGTGTCAACTTAGATAACCAGCCGTCCCCATCAGAGT
GGAACCGTGTTATCACCTTTAGA
Found at i:65742 original size:123 final size:124
Alignment explanation
Indices: 65410--65904 Score: 384
Period size: 128 Copynumber: 3.9 Consensus size: 124
65400 TGTGTCAAAT
** *
65410 TAGATAACCAGCCGTCCCCAT-AGAGTGGAACCGTGTTATCACCTTAGATGGCCATAACTCTTCA
1 TAGATAACCAATCGTCCCCATCAGAG-GGAACCGTGTTATCACCTTAGATGGCC-TGACTCTTCA
* * * *
65474 TCACGTATAAGTCGTGACATCACCTGACTAGACCTCCTCATCACGTAGGAGCCGTGTCACCCC
64 TCACGTAGAA-TCGTGTCATCACCTGACTAGATCTCCTCATCACGTAGGAGACG-GTCACCCC
* * * * *
65537 TAGATAACCAGTCGTCCCCGTCAGAGTGGAACTGTGTTATCACATTAGATGGCCAGAGCTCTTCA
1 TAGATAACCAATCGTCCCCATCAGAG-GGAACCGTGTTATCACCTTAGATGGCCTGA-CTCTTCA
** *
65602 TCACGTATGAGCCGTGTCATCACCTGA-TCAGATTTCCTCATCACGTAGGA-AC-GTCACCCC
64 TCACGTA-GAATCGTGTCATCACCTGACT-AGATCTCCTCATCACGTAGGAGACGGTCACCCC
* * ** * *
65662 -AGATAACTAATTGTCCTTATC-GTA-GGAACCGTGTTATTACCCTTAGATGGCCTGACATCCTC
1 TAGATAACCAATCGTCCCCATCAG-AGGGAACCGTGTTATCA-CCTTAGATGGCCTGAC-TCTTC
* * **
65724 ATCACGTAGGAATCGTGTCATCACCCGACCTA-ATCTCCTCATCACGTAAGAG-CTGCGTCAATC
63 ATCACGTA-GAATCGTGTCATCACCTGA-CTAGATCTCCTCATCACGTAGGAGAC-G-GTCACCC
65787 C
124 C
* * ** * ** *
65788 TTGATAACCAGAAC-TCTTCATCACGTA-TGAGTCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TAGATAACCA-ATCGTCCCCATCA-G-AGGGAACCGTGTTATCACC-TTAGATGGCCTG-ACTCT
* * *
65851 TCATCACGTATAATTCGTGTCATCACCTGACCT-GATCTCCTCATTATGTAGGAG
61 TCATCACGTAGAA-TCGTGTCATCACCTGA-CTAGATCTCCTCATCACGTAGGAG
65905 TCGTGATAAT
Statistics
Matches: 298, Mismatches: 49, Indels: 40
0.77 0.13 0.10
Matches are distributed among these distances:
122 14 0.05
123 60 0.20
124 17 0.06
125 9 0.03
126 6 0.02
127 35 0.12
128 82 0.28
129 73 0.24
130 2 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.27
Consensus pattern (124 bp):
TAGATAACCAATCGTCCCCATCAGAGGGAACCGTGTTATCACCTTAGATGGCCTGACTCTTCATC
ACGTAGAATCGTGTCATCACCTGACTAGATCTCCTCATCACGTAGGAGACGGTCACCCC
Found at i:65857 original size:129 final size:127
Alignment explanation
Indices: 65690--66013 Score: 355
Period size: 129 Copynumber: 2.5 Consensus size: 127
65680 ATCGTAGGAA
* * * *
65690 CCGTGTTATTACCCTTAGATGGCCTG-ACATCCTCATCACGTAGGAATCGTGTCATCACCCGACC
1 CCGTGTTATCACCTTTAGATGGCCAGAAC-TCTTCATCACGTA-GAATCGTGTCATCACCCGACC
* *
65754 TAATCTCCTCATCACGTAAGAGCTGCGT-CAATCCTTGATAACCAGAACTCTTCATCACGTATGA
64 TAATCTCCTCATCACGTAAGAG-T-CGTACAATACTTGATAACCAAAACTCTTCATCACGTATGA
65818 G
127 G
* * *
65819 TCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTATAATTCGTGTCATCACCTGACCT
1 CCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTAGAA-TCGTGTCATCACCCGACCT
* * * * * *
65884 GATCTCCTCATTATGTAGGAGTCGTGATAATATTTGATAACCAAAACTCTTCATCACGTATGAG
65 AATCTCCTCATCACGTAAGAGTCGT-ACAATACTTGATAACCAAAACTCTTCATCACGTATGAG
** *
65948 CCGTGTTATCACCCTTCCTAAAGATGGCCAAGAACTCTTCATCACGTATGAGCCGTGTTATCACC
1 CCGTGTTATCA-CCTT--T--AGATGGCC-AGAACTCTTCATCACGTA-GAATCGTGTCATCACC
66013 C
59 C
66014 TTCCTAAAGA
Statistics
Matches: 163, Mismatches: 21, Indels: 16
0.81 0.10 0.08
Matches are distributed among these distances:
127 3 0.02
128 3 0.02
129 112 0.69
130 6 0.04
132 1 0.01
134 8 0.05
135 29 0.18
136 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.30
Consensus pattern (127 bp):
CCGTGTTATCACCTTTAGATGGCCAGAACTCTTCATCACGTAGAATCGTGTCATCACCCGACCTA
ATCTCCTCATCACGTAAGAGTCGTACAATACTTGATAACCAAAACTCTTCATCACGTATGAG
Found at i:66006 original size:52 final size:52
Alignment explanation
Indices: 65924--66048 Score: 243
Period size: 52 Copynumber: 2.4 Consensus size: 52
65914 TATTTGATAA
65924 CCAA-AACTCTTCATCACGTATGAGCCGTGTTATCACCCTTCCTAAAGATGG
1 CCAAGAACTCTTCATCACGTATGAGCCGTGTTATCACCCTTCCTAAAGATGG
65975 CCAAGAACTCTTCATCACGTATGAGCCGTGTTATCACCCTTCCTAAAGATGG
1 CCAAGAACTCTTCATCACGTATGAGCCGTGTTATCACCCTTCCTAAAGATGG
66027 CCAAGAACTCTTCATCACGTAT
1 CCAAGAACTCTTCATCACGTAT
66049 AAACAGTGTC
Statistics
Matches: 73, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
51 4 0.05
52 69 0.95
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.27
Consensus pattern (52 bp):
CCAAGAACTCTTCATCACGTATGAGCCGTGTTATCACCCTTCCTAAAGATGG
Found at i:69114 original size:29 final size:29
Alignment explanation
Indices: 69081--69138 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
69071 TTTGACCCTC
*
69081 AAATTTTCTAAAA-TTTCATTTTAGTCACT
1 AAATTTTC-AAAACTTACATTTTAGTCACT
69110 AAATTTTCAAAACTTACATTTTAGTCACT
1 AAATTTTCAAAACTTACATTTTAGTCACT
69139 GGTCAAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.36, C:0.16, G:0.03, T:0.45
Consensus pattern (29 bp):
AAATTTTCAAAACTTACATTTTAGTCACT
Found at i:74588 original size:18 final size:17
Alignment explanation
Indices: 74555--74588 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
74545 GAATAATTAA
74555 ATAAAATATCAAAATAT
1 ATAAAATATCAAAATAT
*
74572 ATAAAATCATTAAAATA
1 ATAAAAT-ATCAAAATA
74589 AAACAGACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (17 bp):
ATAAAATATCAAAATAT
Found at i:77026 original size:29 final size:29
Alignment explanation
Indices: 76994--77050 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
76984 TTTGAACCTC
*
76994 AAATTTTCCAAAA-TTTCATTTTAGTCACT
1 AAATTTT-CAAAACTTACATTTTAGTCACT
77023 AAATTTTCAAAACTTACATTTTAGTCAC
1 AAATTTTCAAAACTTACATTTTAGTCAC
77051 AGTCAAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
28 5 0.19
29 21 0.81
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.42
Consensus pattern (29 bp):
AAATTTTCAAAACTTACATTTTAGTCACT
Found at i:78038 original size:2 final size:2
Alignment explanation
Indices: 78023--78063 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
78013 AACCTTTGGG
78023 TA TA -A TA T- 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
78063 T
1 T
78064 TTAGCTAAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.05
2 35 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:81284 original size:24 final size:26
Alignment explanation
Indices: 81242--81303 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 26
81232 CTCAGTGATA
*
81242 TTATAA-TAATATATGATATTAT-AT
1 TTATAATTAATATATGATATAATAAT
*
81266 TTTTAATTTAATA-AT-ATATAATAAT
1 TTATAA-TTAATATATGATATAATAAT
81291 TTATAATTAATAT
1 TTATAATTAATAT
81304 TATTTTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
24 17 0.55
25 9 0.29
26 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (26 bp):
TTATAATTAATATATGATATAATAAT
Found at i:81300 original size:29 final size:29
Alignment explanation
Indices: 81245--81301 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
81235 AGTGATATTA
* **
81245 TAATAATATATGATATTATATTTTTAATT
1 TAATAATATATAATATTATATAATTAATT
81274 TAATAATATATAATAATT-TATAATTAAT
1 TAATAATATATAAT-ATTATATAATTAAT
81302 ATTATTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (29 bp):
TAATAATATATAATATTATATAATTAATT
Found at i:84262 original size:2 final size:2
Alignment explanation
Indices: 84255--84293 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
84245 CTTCTTGTCT
84255 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
84294 GCAACTTAGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:88542 original size:15 final size:15
Alignment explanation
Indices: 88524--88604 Score: 76
Period size: 15 Copynumber: 5.5 Consensus size: 15
88514 TTTTGGAAAA
88524 TGAATTACTGGAATT
1 TGAATTACTGGAATT
*
88539 TGAATTA-TTGAATT
1 TGAATTACTGGAATT
** **
88553 TGAATTACTAAAAAA
1 TGAATTACTGGAATT
*
88568 TGAATTATTGGAATT
1 TGAATTACTGGAATT
**
88583 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
88597 TGAATTAC
1 TGAATTAC
88605 ATTTCTGGAA
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
14 24 0.47
15 27 0.53
ACGTcount: A:0.41, C:0.05, G:0.16, T:0.38
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:88557 original size:29 final size:30
Alignment explanation
Indices: 88524--88603 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
88514 TTTTGGAAAA
**
88524 TGAATTACTGGAATTTGAATTATT-GAATT
1 TGAATTACTGGAAAATGAATTATTGGAATT
**
88553 TGAATTACTAAAAAATGAATTATTGGAATT
1 TGAATTACTGGAAAATGAATTATTGGAATT
88583 TGAATT-CTGGAAAATGAATTA
1 TGAATTACTGGAAAATGAATTA
88604 CATTTCTGGA
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
29 33 0.75
30 11 0.25
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTATTGGAATT
Found at i:88601 original size:44 final size:44
Alignment explanation
Indices: 88520--88604 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
88510 TAGTTTTTGG
* **
88520 AAAATGAATTACTGGAATTTGAATTATTGAATTTGAATTACTAA
1 AAAATGAATTACTGGAATTTGAATTATGGAAAATGAATTACTAA
* *
88564 AAAATGAATTATTGGAATTTGAATTCTGGAAAATGAATTAC
1 AAAATGAATTACTGGAATTTGAATTATGGAAAATGAATTAC
88605 ATTTCTGGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.36
Consensus pattern (44 bp):
AAAATGAATTACTGGAATTTGAATTATGGAAAATGAATTACTAA
Found at i:88610 original size:20 final size:20
Alignment explanation
Indices: 88587--88636 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
88577 GGAATTTGAA
88587 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
88607 TTCTGGAAAATGAATTATAT
1 TTCTGGAAAATGAATTACAT
88627 TTCTGGAAAA
1 TTCTGGAAAA
88637 CATCTGGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.16, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:88940 original size:23 final size:23
Alignment explanation
Indices: 88911--88973 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
88901 AGTGTTATAT
* *
88911 TATATTTTAAAAATATTAATTAG
1 TATATTTTAAATATATTAACTAG
* *
88934 TATATTTTAAATATCTTTACTAG
1 TATATTTTAAATATATTAACTAG
88957 TATATTTTTAAATATAT
1 TATA-TTTTAAATATAT
88974 AAATAATATT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 23 0.68
24 11 0.32
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.52
Consensus pattern (23 bp):
TATATTTTAAATATATTAACTAG
Found at i:88996 original size:28 final size:28
Alignment explanation
Indices: 88964--89022 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
88954 TAGTATATTT
* *
88964 TTAAATATATAAATAATATTATTCAT-TA
1 TTAAATATATAAAAAAAATTATT-ATATA
88992 TTAAATATATAAAAAAAATTATTATATA
1 TTAAATATATAAAAAAAATTATTATATA
89020 TTA
1 TTA
89023 TTAAAATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 26 0.93
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
TTAAATATATAAAAAAAATTATTATATA
Found at i:89031 original size:28 final size:28
Alignment explanation
Indices: 88957--89063 Score: 85
Period size: 30 Copynumber: 3.6 Consensus size: 28
88947 TCTTTACTAG
* * *
88957 TATATTTTTAAATATATAAATAATATTA
1 TATATTATTAAATATAAAAAAAATATTA
88985 T-TCATTATTAAATATATAAAAAAAATTATTA
1 TAT-ATTATT-AA-ATATAAAAAAAA-TATTA
89016 TATATTATTAAA-ATAAAAAATATAATATCT-
1 TATATTATTAAATAT-AAAAA-A-AATAT-TA
89046 TATATTATTATAATATAA
1 TATATTATTA-AATATAA
89064 TTGATTATAT
Statistics
Matches: 65, Mismatches: 3, Indels: 19
0.75 0.03 0.22
Matches are distributed among these distances:
27 1 0.02
28 8 0.12
29 8 0.12
30 26 0.40
31 19 0.29
32 3 0.05
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
TATATTATTAAATATAAAAAAAATATTA
Found at i:89125 original size:21 final size:23
Alignment explanation
Indices: 89085--89134 Score: 70
Period size: 21 Copynumber: 2.3 Consensus size: 23
89075 ATTAAACTAA
89085 AAATA-TAATATAATATTATTAT
1 AAATATTAATATAATATTATTAT
*
89107 AAATATTAATA-AATA-TATTTT
1 AAATATTAATATAATATTATTAT
89128 AAATATT
1 AAATATT
89135 TTAATAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
21 12 0.46
22 9 0.35
23 5 0.19
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (23 bp):
AAATATTAATATAATATTATTAT
Found at i:89130 original size:50 final size:52
Alignment explanation
Indices: 89015--89130 Score: 141
Period size: 50 Copynumber: 2.2 Consensus size: 52
89005 AAAAATTATT
* *
89015 ATATATTATTAAAATAAAAAATATAATATCTTATATTATTATAATATAATTGA
1 ATATATTATTAAAATAAAAAATATAATA-CTAATATTATTATAATATAATTAA
* *
89068 TTATATTATTAAACT-AAAAATATAATA-TAATATTATTATAAATATTAA-TAA
1 ATATATTATTAAAATAAAAAATATAATACTAATATTATTAT-AATA-TAATTAA
89119 ATATATT-TTAAA
1 ATATATTATTAAA
89131 TATTTTAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
50 16 0.29
51 12 0.21
52 15 0.27
53 13 0.23
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.44
Consensus pattern (52 bp):
ATATATTATTAAAATAAAAAATATAATACTAATATTATTATAATATAATTAA
Found at i:89375 original size:42 final size:41
Alignment explanation
Indices: 89323--89441 Score: 166
Period size: 42 Copynumber: 2.8 Consensus size: 41
89313 ATGAATTACG
*
89323 TTCCGGAAAACGAATTACGTAAAGCAAACACGAGAAAACATT
1 TTCCGAAAAACGAATTACGTAAA-CAAACACGAGAAAACATT
*
89365 TTCCGAAAAACGAATTACGTGAAACAAACACAAGAAAACATT
1 TTCCGAAAAACGAATTACGT-AAACAAACACGAGAAAACATT
* * *
89407 TTCCAAAAAACGAATTACATAAAATAAACACGAGA
1 TTCCGAAAAACGAATTACGT-AAACAAACACGAGA
89442 TTTCGAGAAA
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 66 0.96
43 3 0.04
ACGTcount: A:0.52, C:0.18, G:0.13, T:0.17
Consensus pattern (41 bp):
TTCCGAAAAACGAATTACGTAAACAAACACGAGAAAACATT
Found at i:93774 original size:17 final size:16
Alignment explanation
Indices: 93743--93776 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
93733 CACGTGAGGA
93743 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
93759 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
93776 T
1 T
93777 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:100164 original size:19 final size:21
Alignment explanation
Indices: 100127--100169 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
100117 TAACTTTTTC
100127 TTTTATCTTTCATTATTAA-T
1 TTTTATCTTTCATTATTAACT
*
100147 TTTTCTCTTTCATT-TTAACT
1 TTTTATCTTTCATTATTAACT
100167 TTT
1 TTT
100170 ACCTTTTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (21 bp):
TTTTATCTTTCATTATTAACT
Found at i:100175 original size:19 final size:20
Alignment explanation
Indices: 100126--100175 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
100116 TTAACTTTTT
*
100126 CTTTTATCTTTCATTATTAA
1 CTTTTACCTTTCATTATTAA
*
100146 -TTTTTCTCTTTCATT-TTAA
1 CTTTTAC-CTTTCATTATTAA
100165 CTTTTACCTTT
1 CTTTTACCTTT
100176 TTTCTTTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.18, C:0.18, G:0.00, T:0.64
Consensus pattern (20 bp):
CTTTTACCTTTCATTATTAA
Found at i:104030 original size:17 final size:16
Alignment explanation
Indices: 103999--104032 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
103989 CACGTGAGGA
103999 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
104015 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
104032 T
1 T
104033 ACTGTTTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:107972 original size:21 final size:21
Alignment explanation
Indices: 107943--108004 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
107933 TATCTGCAAA
*
107943 AAATTAATTAAATAAAATATT
1 AAATAAATTAAATAAAATATT
107964 AAATAAATTAAATACAAAATATT
1 AAATAAATTAAAT--AAAATATT
107987 -AA-AAA-TATAATAAAATAT
1 AAATAAATTA-AATAAAATAT
108005 ATCTTAGACA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
19 7 0.19
20 2 0.05
21 18 0.49
22 2 0.05
23 8 0.22
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
AAATAAATTAAATAAAATATT
Found at i:119383 original size:14 final size:15
Alignment explanation
Indices: 119349--119386 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
119339 AGAGTCAATG
* *
119349 AGTTGACTCTATTCG
1 AGTTGACTCGATTCA
119364 AGTTGACTCGA-TCA
1 AGTTGACTCGATTCA
119378 AGTTGACTC
1 AGTTGACTC
119387 AGTTCGACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (15 bp):
AGTTGACTCGATTCA
Found at i:128848 original size:18 final size:18
Alignment explanation
Indices: 128804--128849 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
128794 TATGAGAGCT
128804 AGCAACATCATCTTGCTC
1 AGCAACATCATCTTGCTC
*
128822 AACAACATCATCTTGCTC
1 AGCAACATCATCTTGCTC
*
128840 AGCAGCATCA
1 AGCAACATCA
128850 ACAACTTGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.33, C:0.33, G:0.11, T:0.24
Consensus pattern (18 bp):
AGCAACATCATCTTGCTC
Found at i:133420 original size:12 final size:12
Alignment explanation
Indices: 133402--133446 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
133392 CTGTCTTTGT
133402 CTTTACCTCTAC
1 CTTTACCTCTAC
* *
133414 GTTTACCTCTTC
1 CTTTACCTCTAC
*
133426 CTTTGCCTCTAC
1 CTTTACCTCTAC
*
133438 CTTTTCCTC
1 CTTTACCTC
133447 CCCTTCTGCC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.09, C:0.40, G:0.04, T:0.47
Consensus pattern (12 bp):
CTTTACCTCTAC
Found at i:133456 original size:24 final size:24
Alignment explanation
Indices: 133402--133469 Score: 68
Period size: 24 Copynumber: 2.8 Consensus size: 24
133392 CTGTCTTTGT
* * *
133402 CTTTACCTCTACGTTTACCTCTTC
1 CTTTGCCTCTACCTTTACCTCTCC
*
133426 CTTTGCCTCTACCTTTTCCTC-CC
1 CTTTGCCTCTACCTTTACCTCTCC
133449 CTTCTGCCTCTGA-CTTTACCT
1 CTT-TGCCTCT-ACCTTTACCT
133470 TTACATTTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
23 4 0.11
24 32 0.86
25 1 0.03
ACGTcount: A:0.09, C:0.41, G:0.06, T:0.44
Consensus pattern (24 bp):
CTTTGCCTCTACCTTTACCTCTCC
Found at i:133544 original size:30 final size:30
Alignment explanation
Indices: 133510--133573 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
133500 CTGCCTTTGG
*
133510 CTCTGCCCCTGCCTTTACCTCTATTTCTGC
1 CTCTGCCCCTGCCTTTACCACTATTTCTGC
* * * *
133540 CTCTGGCTCTGCCTTTGCCACTGTTTCTGC
1 CTCTGCCCCTGCCTTTACCACTATTTCTGC
133570 CTCT
1 CTCT
133574 TCCTCTACCT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.05, C:0.41, G:0.14, T:0.41
Consensus pattern (30 bp):
CTCTGCCCCTGCCTTTACCACTATTTCTGC
Found at i:133573 original size:24 final size:24
Alignment explanation
Indices: 133541--133617 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
133531 TATTTCTGCC
* * *
133541 TCTGGCTCTGCCTTTGCCACTGTT
1 TCTGCCTCTGCCTCTACCACTGTT
* *
133565 TCTGCCTCTTCCTCTACCTCTGTT
1 TCTGCCTCTGCCTCTACCACTGTT
* * * *
133589 TTTGCCTCTTCCTCTACCTCTGTC
1 TCTGCCTCTGCCTCTACCACTGTT
133613 TCTGC
1 TCTGC
133618 GTCTAATTCT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 45 1.00
ACGTcount: A:0.04, C:0.39, G:0.13, T:0.44
Consensus pattern (24 bp):
TCTGCCTCTGCCTCTACCACTGTT
Found at i:134001 original size:33 final size:33
Alignment explanation
Indices: 133958--134092 Score: 180
Period size: 33 Copynumber: 4.1 Consensus size: 33
133948 AGGCTCATGT
* * *
133958 TCATTTTGTTGTTCGGAAACTGCACTAAAAATA
1 TCATTCTGTTGTTCCGAAACTGCACTAGAAATA
*
133991 TCATTCTGTTGTTCCGAAACTGAACTAGAAATA
1 TCATTCTGTTGTTCCGAAACTGCACTAGAAATA
134024 TCATTCTGTTGTTCCGAAACTGCACTAGAAATA
1 TCATTCTGTTGTTCCGAAACTGCACTAGAAATA
** * * * *
134057 TCGGTATGATGTTCCGAAACTGGACTGGAAATA
1 TCATTCTGTTGTTCCGAAACTGCACTAGAAATA
134090 TCA
1 TCA
134093 GTTTTATTTT
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Consensus pattern (33 bp):
TCATTCTGTTGTTCCGAAACTGCACTAGAAATA
Found at i:134287 original size:39 final size:39
Alignment explanation
Indices: 134224--134333 Score: 157
Period size: 39 Copynumber: 2.8 Consensus size: 39
134214 TGCCACTTTT
* *
134224 TTCAGCTTTTGGTGGTTCGTTATCATCCACTTCACCTTG
1 TTCAGCTTTTGGTGTTTCGGTATCATCCACTTCACCTTG
* *
134263 TTCAGCTCTTGGTGTTTCGGTATCATCCAGTTCACCTTG
1 TTCAGCTTTTGGTGTTTCGGTATCATCCACTTCACCTTG
* * *
134302 ATCTGCTTTTGGTGTTTTGGTATCATCCACTT
1 TTCAGCTTTTGGTGTTTCGGTATCATCCACTT
134334 GGCCCTGATC
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 62 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.45
Consensus pattern (39 bp):
TTCAGCTTTTGGTGTTTCGGTATCATCCACTTCACCTTG
Found at i:140062 original size:23 final size:22
Alignment explanation
Indices: 140019--140086 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 22
140009 AAAACAACCG
*
140019 AAAACATGTCATAGAGACAGAGA
1 AAAACATGTCATAAAGACAGA-A
*
140042 AAAACATG-CTATAAAGGCAGAA
1 AAAACATGTC-ATAAAGACAGAA
* * *
140064 AAATAAATGTCAAAAAGTCAGAA
1 AAA-ACATGTCATAAAGACAGAA
140087 TTATTAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 5 0.14
23 31 0.84
24 1 0.03
ACGTcount: A:0.56, C:0.12, G:0.18, T:0.15
Consensus pattern (22 bp):
AAAACATGTCATAAAGACAGAA
Found at i:142617 original size:37 final size:37
Alignment explanation
Indices: 142573--142647 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
142563 CTACGAGAAG
142573 TAGAAAATGATCTTCTTTCTTCTAATGCCATGGTAAC
1 TAGAAAATGATCTTCTTTCTTCTAATGCCATGGTAAC
142610 TAGAAAATGATCTTCTTTCTTCTAATGCCATGGTAAC
1 TAGAAAATGATCTTCTTTCTTCTAATGCCATGGTAAC
142647 T
1 T
142648 TCGTTGCATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.39
Consensus pattern (37 bp):
TAGAAAATGATCTTCTTTCTTCTAATGCCATGGTAAC
Found at i:151332 original size:44 final size:45
Alignment explanation
Indices: 151261--151387 Score: 186
Period size: 44 Copynumber: 2.9 Consensus size: 45
151251 ATTTTAAATT
* *
151261 TTAGTATCATTTTACGTATGGTATTAAAATATATGTAAAA-AAAA
1 TTAGTATCATTTTACGTATGATGTTAAAATATATGTAAAAGAAAA
* *
151305 TTAGTATCCTTTTACATATGATGTTAAAATATATGTAAAAGAAAA
1 TTAGTATCATTTTACGTATGATGTTAAAATATATGTAAAAGAAAA
* *
151350 -TGGTATCATTTTACGTATAATGTTAAAATATATGTAAA
1 TTAGTATCATTTTACGTATGATGTTAAAATATATGTAAA
151388 TCTATCTCGG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
44 70 0.95
45 4 0.05
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (45 bp):
TTAGTATCATTTTACGTATGATGTTAAAATATATGTAAAAGAAAA
Found at i:154307 original size:25 final size:27
Alignment explanation
Indices: 154270--154323 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
154260 TTCAAAATCT
* **
154270 AAAATGATTATTATATTAA-AAATTCA
1 AAAATGATAATTATAAAAATAAATTCA
154296 AAAAT-ATAATTATAAAAATAAATTCA
1 AAAATGATAATTATAAAAATAAATTCA
154322 AA
1 AA
154324 TCGATCCCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 10 0.42
26 14 0.58
ACGTcount: A:0.61, C:0.04, G:0.02, T:0.33
Consensus pattern (27 bp):
AAAATGATAATTATAAAAATAAATTCA
Found at i:165621 original size:19 final size:19
Alignment explanation
Indices: 165593--165630 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
165583 GAATTTGACA
*
165593 TTTTCGCAACACGATTTTT
1 TTTTCACAACACGATTTTT
*
165612 TTTTCACAACTCGATTTTT
1 TTTTCACAACACGATTTTT
165631 AAATTCGCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.21, C:0.21, G:0.08, T:0.50
Consensus pattern (19 bp):
TTTTCACAACACGATTTTT
Found at i:165664 original size:40 final size:38
Alignment explanation
Indices: 165595--165721 Score: 139
Period size: 40 Copynumber: 3.2 Consensus size: 38
165585 ATTTGACATT
** *
165595 TTCGCAACACGATTTTTTTTTCACAACTCGATTTTTAAA
1 TTCGCAACACGATTTCATTTTCGCAACTCGATTTTT-AA
165634 TTCGCAACACGAGTTTCATTTTCGCAACTCGATTTTCTAA
1 TTCGCAACACGA-TTTCATTTTCGCAACTCGATTTT-TAA
* * *
165674 TTCGTAGCACAC-ATTTCGTTTTCGCAACTCGATTTTCGAA
1 TTCGCA--ACACGATTTCATTTTCGCAACTCGATTTT-TAA
165714 TTCGCAAC
1 TTCGCAAC
165722 TCGAATTTAA
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
38 2 0.03
39 12 0.16
40 57 0.74
41 2 0.03
42 4 0.05
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.39
Consensus pattern (38 bp):
TTCGCAACACGATTTCATTTTCGCAACTCGATTTTTAA
Found at i:165670 original size:20 final size:20
Alignment explanation
Indices: 165575--165725 Score: 87
Period size: 20 Copynumber: 7.5 Consensus size: 20
165565 AAGTCGAATA
*
165575 CGCAACTCGAATTTGACATTTT
1 CGCAACTCG-ATTT-TCATTTT
* *
165597 CGCAACACGATTTT-TTTTT
1 CGCAACTCGATTTTCATTTT
* * **
165616 CACAACTCGATTTTTAAATT
1 CGCAACTCGATTTTCATTTT
* *
165636 CGCAACACGAGTTTCATTTT
1 CGCAACTCGATTTTCATTTT
*
165656 CGCAACTCGATTTTC-TAATT
1 CGCAACTCGATTTTCAT-TTT
* * *
165676 CGTAGCACAC-A-TTTCGTTTT
1 CGCA--ACTCGATTTTCATTTT
*
165696 CGCAACTCGATTTTCGA-ATT
1 CGCAACTCGATTTTC-ATTTT
165716 CGCAACTCGA
1 CGCAACTCGA
165726 ATTTAAATTT
Statistics
Matches: 97, Mismatches: 24, Indels: 18
0.70 0.17 0.13
Matches are distributed among these distances:
18 3 0.03
19 18 0.19
20 59 0.61
21 6 0.06
22 11 0.11
ACGTcount: A:0.26, C:0.25, G:0.13, T:0.37
Consensus pattern (20 bp):
CGCAACTCGATTTTCATTTT
Found at i:166220 original size:20 final size:20
Alignment explanation
Indices: 166173--166247 Score: 98
Period size: 20 Copynumber: 3.8 Consensus size: 20
166163 AATTAAAAAA
*
166173 TCGAGTTGCGAATT-CGACT
1 TCGAGTTGCGAATTCCGAAT
*
166192 TCTGTGTTGCGAATTCCGAAT
1 TC-GAGTTGCGAATTCCGAAT
**
166213 TCGAGTTGTAAATTCCGAAT
1 TCGAGTTGCGAATTCCGAAT
166233 TCGAGTTGCGAATTC
1 TCGAGTTGCGAATTC
166248 AAAAACTGTG
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
19 2 0.04
20 39 0.83
21 6 0.13
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.35
Consensus pattern (20 bp):
TCGAGTTGCGAATTCCGAAT
Found at i:166245 original size:60 final size:60
Alignment explanation
Indices: 166173--166307 Score: 152
Period size: 60 Copynumber: 2.3 Consensus size: 60
166163 AATTAAAAAA
* ***
166173 TCGAGTTGCGAATTCGACTTCTGTGTTGCG-AATTCCGAATTCGA-GTTGTAAATTCCG-AAT
1 TCGAGTTGCGAATTCAAAAACTGTGTTGCGAAATT-CGAATTC-ATGTTGTAAATT-CGAAAT
* **
166233 TCGAGTTGCGAATTCAAAAACTGTGTTGCGAAATTGGCTTTCATGTTGTAAATTCGAAAT
1 TCGAGTTGCGAATTCAAAAACTGTGTTGCGAAATTCGAATTCATGTTGTAAATTCGAAAT
166293 T-GAGTTGCGAATTCA
1 TCGAGTTGCGAATTCA
166308 TTAGTTATTT
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
59 17 0.26
60 44 0.68
61 4 0.06
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.35
Consensus pattern (60 bp):
TCGAGTTGCGAATTCAAAAACTGTGTTGCGAAATTCGAATTCATGTTGTAAATTCGAAAT
Found at i:167856 original size:22 final size:22
Alignment explanation
Indices: 167799--167856 Score: 98
Period size: 22 Copynumber: 2.6 Consensus size: 22
167789 ATACAATTGA
* *
167799 AAGTTGCATGGTTCACATGCAT
1 AAGTTACATGGTTTACATGCAT
167821 AAGTTACATGGTTTACATGCAT
1 AAGTTACATGGTTTACATGCAT
167843 AAGTTACATGGTTT
1 AAGTTACATGGTTT
167857 CTTCATTCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.29, C:0.14, G:0.21, T:0.36
Consensus pattern (22 bp):
AAGTTACATGGTTTACATGCAT
Found at i:172786 original size:3 final size:3
Alignment explanation
Indices: 172778--172812 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
172768 TAGATGACAA
172778 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
172813 GGAATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:173783 original size:6 final size:6
Alignment explanation
Indices: 173768--173807 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
173758 ATATCCAATT
*
173768 TCATAA TCATAG TCATAG TCATAG TCATAG TCATAG TCAT
1 TCATAG TCATAG TCATAG TCATAG TCATAG TCATAG TCAT
173808 TATAGCCATC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (6 bp):
TCATAG
Found at i:177995 original size:86 final size:86
Alignment explanation
Indices: 177899--178072 Score: 348
Period size: 86 Copynumber: 2.0 Consensus size: 86
177889 TTCCAAAGAC
177899 AAAATGAAAAAAAAAGAAGCTATCCACTAAGGTTATAATGATATGATAACCCCAGGACCACTCTA
1 AAAATGAAAAAAAAAGAAGCTATCCACTAAGGTTATAATGATATGATAACCCCAGGACCACTCTA
177964 CTAAATAATTGAAGGTGTAAA
66 CTAAATAATTGAAGGTGTAAA
177985 AAAATGAAAAAAAAAGAAGCTATCCACTAAGGTTATAATGATATGATAACCCCAGGACCACTCTA
1 AAAATGAAAAAAAAAGAAGCTATCCACTAAGGTTATAATGATATGATAACCCCAGGACCACTCTA
178050 CTAAATAATTGAAGGTGTAAA
66 CTAAATAATTGAAGGTGTAAA
178071 AA
1 AA
178073 GGGTGAGGGT
Statistics
Matches: 88, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
86 88 1.00
ACGTcount: A:0.48, C:0.15, G:0.15, T:0.22
Consensus pattern (86 bp):
AAAATGAAAAAAAAAGAAGCTATCCACTAAGGTTATAATGATATGATAACCCCAGGACCACTCTA
CTAAATAATTGAAGGTGTAAA
Found at i:178363 original size:2 final size:2
Alignment explanation
Indices: 178337--178379 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
178327 TAAAAACACA
* * *
178337 AT AT -T AT AT AC AT AC AT AT AA 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
178378 AT
1 AT
178380 TACCAGTAAC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:189204 original size:22 final size:21
Alignment explanation
Indices: 189152--189211 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
189142 GATTTCTGGG
189152 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
189173 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGGTACCCATT
*
189193 CAATGGGGAATCGATACCC
1 CAA-GGGGAATCGGTACCC
189212 CTCAAGCGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 20 0.56
21 3 0.08
22 13 0.36
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.18
Consensus pattern (21 bp):
CAAGGGGAATCGGTACCCATT
Found at i:190766 original size:103 final size:103
Alignment explanation
Indices: 190587--190795 Score: 364
Period size: 103 Copynumber: 2.0 Consensus size: 103
190577 CTACGCGGTC
*
190587 CTTCGGGACATATATGTATCCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTAATCCTT
1 CTTCGGGACATATATGTATCCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTAATCCCT
*
190652 GGCATATGTATATGATTCGTAAGGAATGATATGTGGTT
66 AGCATATGTATATGATTCGTAAGGAATGATATGTGGTT
* *
190690 CTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATCCCT
1 CTTCGGGACATATATGTATCCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTAATCCCT
* *
190755 AGTATATGTATATGATTCTTAAGGAATGATATGTGGTT
66 AGCATATGTATATGATTCGTAAGGAATGATATGTGGTT
190793 CTT
1 CTT
190796 ATGGACATTA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.36
Consensus pattern (103 bp):
CTTCGGGACATATATGTATCCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTAATCCCT
AGCATATGTATATGATTCGTAAGGAATGATATGTGGTT
Found at i:190867 original size:22 final size:23
Alignment explanation
Indices: 190812--190878 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
190802 ATTATTATAT
190812 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
*
190835 GGCACTCCGGTGCAATTCTACG-
1 GGCACTACGGTGCAATTCTACGC
* * *
190857 TGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
190879 AGCTGTGGTG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 19 0.47
23 21 0.52
ACGTcount: A:0.21, C:0.28, G:0.25, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:194601 original size:22 final size:21
Alignment explanation
Indices: 194549--194605 Score: 89
Period size: 20 Copynumber: 2.7 Consensus size: 21
194539 GATTTCTGGG
194549 CAAGGGGAATCGATACCCATT
1 CAAGGGGAATCGATACCCATT
*
194570 CAA-GGGAATCGGTACCCATT
1 CAAGGGGAATCGATACCCATT
194590 CAATGGGGAATCGATA
1 CAA-GGGGAATCGATA
194606 TCCCTCAAGC
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
20 19 0.59
21 3 0.09
22 10 0.31
ACGTcount: A:0.33, C:0.21, G:0.26, T:0.19
Consensus pattern (21 bp):
CAAGGGGAATCGATACCCATT
Found at i:196168 original size:101 final size:102
Alignment explanation
Indices: 195980--196190 Score: 352
Period size: 101 Copynumber: 2.1 Consensus size: 102
195970 GGGTCTACGC
195980 GGTCCTTCGGGACATATATGTATCCTTTGGAACATGTGTGAAGTCTGGGGAGACACATACTTGAT
1 GGTCCTTCGGGA-ATATATGTATCCTTTGGAACATGTGTGAAGTCTGGGGAGACACATACTTGAT
* *
196045 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
65 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
* *
196083 GGTCCTTCGGG-ATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1 GGTCCTTCGGGAATATATGTATCCTTTGGAACATGTGTGAAGTCTGGGGAGACACATACTTGATC
* *
196147 CCTAGTATATGTATATGATTCTTAAGGAATTATATGT
66 CCTAGCATATGTATATGATTCTTAAGGAATGATATGT
196184 GGTCCTT
1 GGTCCTT
196191 ATGGACATTA
Statistics
Matches: 102, Mismatches: 6, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
101 91 0.89
103 11 0.11
ACGTcount: A:0.26, C:0.14, G:0.24, T:0.36
Consensus pattern (102 bp):
GGTCCTTCGGGAATATATGTATCCTTTGGAACATGTGTGAAGTCTGGGGAGACACATACTTGATC
CCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:196244 original size:23 final size:23
Alignment explanation
Indices: 196214--196274 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
196204 TATGGCATTA
*
196214 CGGTGCAATTCTACGCGGTACTC
1 CGGTGCAATTCTACGCGGCACTC
* *
196237 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTC
*
196260 CGGTGCAATTATACG
1 CGGTGCAATTCTACG
196275 AGTTGTGGTG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTC
Found at i:200637 original size:35 final size:35
Alignment explanation
Indices: 200591--200665 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
200581 TGTTGGGATA
200591 TTAAATTCATATAAATATCAATTTAAAAATACTTT
1 TTAAATTCATATAAATATCAATTTAAAAATACTTT
200626 TTAAATTCATATAAATATCAATTTAAAAATACTTT
1 TTAAATTCATATAAATATCAATTTAAAAATACTTT
200661 TTAAA
1 TTAAA
200666 ATTTAATATT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (35 bp):
TTAAATTCATATAAATATCAATTTAAAAATACTTT
Found at i:203442 original size:19 final size:20
Alignment explanation
Indices: 203418--203459 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
203408 TGATAATCAA
203418 ATTGAT-ATAATTTTAAAAT
1 ATTGATGATAATTTTAAAAT
**
203437 ATTGATGATTTTTTTAAAAT
1 ATTGATGATAATTTTAAAAT
203457 ATT
1 ATT
203460 CTAATTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
ATTGATGATAATTTTAAAAT
Found at i:209438 original size:541 final size:541
Alignment explanation
Indices: 208390--209482 Score: 1972
Period size: 541 Copynumber: 2.0 Consensus size: 541
208380 TAAGTGATAC
*
208390 AAATAACTGAATTGGACGATTACCAACCCCTAACATTGGTCTCTTCCTAAAGAATACATTAATTA
1 AAATAACCGAATTGGACGATTACCAACCCCTAACATTGGTCTCTTCCTAAAGAATACATTAATTA
208455 TTTTTTAGCAAAATTACCCCTTAACATTTATATGAATGATTATGTTGCATCTTATTCTTCTTTTT
66 TTTTTTAGCAAAATTACCCCTTAACATTTATATGAATGATTATGTTGCATCTTATTCTTCTTTTT
208520 GAAGTATTTTACCCCTTAATATTTTAAATTTTTGTCAAAACATACCTTATTGGATGAAAACGTTA
131 GAAGTATTTTACCCCTTAATATTTTAAATTTTTGTCAAAACATACCTTATTGGATGAAAACGTTA
* *
208585 GTTGACTAATGATCAATTCATATTGTTGACATGACTTTTTTACATGTGTCCAATTGCTAGCATAA
196 GTTGACTAATGATCAATTCATATTATTGACATGACTTTTTTACATGTGTCCAATTCCTAGCATAA
*
208650 CACATAGCATATCATTATTTTGGATGATATAGCACGTGTCATATCATCTCTTTTGGTAACGTGTT
261 CACATAGCATATCATTATTTTGGATGATATAGCACGTGTCATATCATCTCTTTTGGTAACGTGTC
* *
208715 ATGTGTCACCACTTTTCATGACGTGACATCGTCACTTTCAATAACACATCACATGTCATGTCATC
326 ATGTGCCACCACTTTTCATGACGTGACATCGTCACTTTCAATAACACATCACATGACATGTCATC
* *
208780 ACTTTCGATGGTGTGTTACATGACATGTCATCAAACGAACAAATGTAAAAATGACAAGTTAGTCA
391 ACTTTCGATGATGTGTTACATGACATGTCATCAAACGAACAAATGTAAAAATGAAAAGTTAGTCA
*
208845 ACTAACACTTTCTATCCAACACGATATGTTTTGACTAAAAATTGAAACGTTAGAAAAAACACTCC
456 ACTAACACTTTCTATCCAACACAATATGTTTTGACTAAAAATTGAAACGTTAGAAAAAACACTCC
208910 AAAAG-AAAAAACAAAGGACA
521 AAAAGAAAAAAACAAAGGACA
*
208930 AAATAACCGAATTGGACGATTACCGACCCCCTAACATTGGTCTCTTCCTAAAGAATACATTAATT
1 AAATAACCGAATTGGACGATTACC-AACCCCTAACATTGGTCTCTTCCTAAAGAATACATTAATT
208995 ATTTTTTAGCAAAATTACCCCTTAACATTTATATGAATGATTATGTTGCATCTTATTCTTCTTTT
65 ATTTTTTAGCAAAATTACCCCTTAACATTTATATGAATGATTATGTTGCATCTTATTCTTCTTTT
* *
209060 TGAAGTATTTTACCCCTTAATATTTTAATTTTTTGTCAAAACATACCTTATTGGGTGAAAACGTT
130 TGAAGTATTTTACCCCTTAATATTTTAAATTTTTGTCAAAACATACCTTATTGGATGAAAACGTT
209125 AGTTGACTAATGATCAATTCATATTATTGACATGACTTTTTTACATGTGTCCAATTCCTAGCATA
195 AGTTGACTAATGATCAATTCATATTATTGACATGACTTTTTTACATGTGTCCAATTCCTAGCATA
*
209190 ACACATAGCATATCATTATTTTGGATGATGTAGCACGTGTCATATCATCTCTTTTGGTAACGTGT
260 ACACATAGCATATCATTATTTTGGATGATATAGCACGTGTCATATCATCTCTTTTGGTAACGTGT
* *
209255 CATGTGCCACCACTTTTCATGACGTGACATTGTCACTTTCAGTAACACATCACATGACATGTCAT
325 CATGTGCCACCACTTTTCATGACGTGACATCGTCACTTTCAATAACACATCACATGACATGTCAT
***
209320 CACTTTCGATGATGTGTTACATGTTGTGTCATCAAACGAACAAATGTAAAAATGAAAAGTTAGTC
390 CACTTTCGATGATGTGTTACATGACATGTCATCAAACGAACAAATGTAAAAATGAAAAGTTAGTC
*
209385 AACTAACACTTTCTATCCAACACAATATGTTTTGACTAAAAATTGAAACGTTAGAAAAAATACTC
455 AACTAACACTTTCTATCCAACACAATATGTTTTGACTAAAAATTGAAACGTTAGAAAAAACACTC
*
209450 CAAAAGAAAAAAAAACAAGGGACA
520 CAAAAG--AAAAAAACAAAGGACA
209474 AAATAACCG
1 AAATAACCG
209483 TTTGTACAAA
Statistics
Matches: 529, Mismatches: 20, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
540 23 0.04
541 483 0.91
544 23 0.04
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.34
Consensus pattern (541 bp):
AAATAACCGAATTGGACGATTACCAACCCCTAACATTGGTCTCTTCCTAAAGAATACATTAATTA
TTTTTTAGCAAAATTACCCCTTAACATTTATATGAATGATTATGTTGCATCTTATTCTTCTTTTT
GAAGTATTTTACCCCTTAATATTTTAAATTTTTGTCAAAACATACCTTATTGGATGAAAACGTTA
GTTGACTAATGATCAATTCATATTATTGACATGACTTTTTTACATGTGTCCAATTCCTAGCATAA
CACATAGCATATCATTATTTTGGATGATATAGCACGTGTCATATCATCTCTTTTGGTAACGTGTC
ATGTGCCACCACTTTTCATGACGTGACATCGTCACTTTCAATAACACATCACATGACATGTCATC
ACTTTCGATGATGTGTTACATGACATGTCATCAAACGAACAAATGTAAAAATGAAAAGTTAGTCA
ACTAACACTTTCTATCCAACACAATATGTTTTGACTAAAAATTGAAACGTTAGAAAAAACACTCC
AAAAGAAAAAAACAAAGGACA
Found at i:210050 original size:20 final size:21
Alignment explanation
Indices: 210025--210077 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
210015 TTCGCAATGC
*
210025 ATCGCAATGCGAA-TAAGTAA
1 ATCGCAATGCGAATTAAGAAA
* **
210045 ATCGCAATGCAAATTTGGAAA
1 ATCGCAATGCGAATTAAGAAA
210066 ATCGCAATGCGA
1 ATCGCAATGCGA
210078 TACTGACTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
ATCGCAATGCGAATTAAGAAA
Found at i:210090 original size:41 final size:41
Alignment explanation
Indices: 210063--210180 Score: 200
Period size: 41 Copynumber: 2.9 Consensus size: 41
210053 GCAAATTTGG
*
210063 AAAATCGCAATGCGATACTGACTATCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGAGATAATAC
*
210104 AAAATCGCAACGCGATACTGACTTTCGCAACGAGATAATAC
1 AAAATCGCAACGCGATACTGACTATCGCAACGAGATAATAC
* *
210145 AAAATCGCAACGCGATACTGACTTTCGCAATGAGAT
1 AAAATCGCAACGCGATACTGACTATCGCAACGAGAT
210181 TCTGACTATC
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (41 bp):
AAAATCGCAACGCGATACTGACTATCGCAACGAGATAATAC
Found at i:210091 original size:20 final size:20
Alignment explanation
Indices: 210066--210201 Score: 114
Period size: 20 Copynumber: 6.7 Consensus size: 20
210056 AATTTGGAAA
* *
210066 ATCGCAATGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* *
210086 ATCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
210107 ATCGCAACGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* * *
210127 TTCGCAACGAGATAAT-ACAAA
1 ATCGCAACGAGATACTGAC--T
*
210148 ATCGCAACGCGATACTGACT
1 ATCGCAACGAGATACTGACT
* * *
210168 TTCGCAATGAGATTCTGACT
1 ATCGCAACGAGATACTGACT
210188 ATCGCAACGAGATA
1 ATCGCAACGAGATA
210202 ATACAGAATC
Statistics
Matches: 88, Mismatches: 22, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
19 4 0.05
20 53 0.60
21 27 0.31
22 4 0.05
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
ATCGCAACGAGATACTGACT
Found at i:210112 original size:21 final size:21
Alignment explanation
Indices: 210086--210161 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
210076 GATACTGACT
210086 ATCGCAACGAGATAATACAAA
1 ATCGCAACGAGATAATACAAA
* * *
210107 ATCGCAACGCGATACTGAC--T
1 ATCGCAACGAGATAAT-ACAAA
*
210127 TTCGCAACGAGATAATACAAA
1 ATCGCAACGAGATAATACAAA
*
210148 ATCGCAACGCGATA
1 ATCGCAACGAGATA
210162 CTGACTTTCG
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
19 2 0.05
20 13 0.30
21 26 0.60
22 2 0.05
ACGTcount: A:0.42, C:0.24, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGAGATAATACAAA
Found at i:210958 original size:24 final size:24
Alignment explanation
Indices: 210931--210984 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
210921 GTATTCAAAA
*
210931 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
210955 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
210979 TTTGAT
1 TTTGAT
210985 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:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:211176 original size:12 final size:12
Alignment explanation
Indices: 211159--211183 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
211149 ATATAATCCT
211159 GAAGAAGAAAAA
1 GAAGAAGAAAAA
211171 GAAGAAGAAAAA
1 GAAGAAGAAAAA
211183 G
1 G
211184 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:213526 original size:19 final size:19
Alignment explanation
Indices: 213511--213621 Score: 98
Period size: 19 Copynumber: 6.4 Consensus size: 19
213501 GGAAATGACT
213511 ATCGCAATGAGAAATGAAA
1 ATCGCAATGAGAAATGAAA
213530 ATCGCAATGAG--A-G--A
1 ATCGCAATGAGAAATGAAA
*
213544 ATCGCAATGCGAAATGAAA
1 ATCGCAATGAGAAATGAAA
* *
213563 ATTGCAATGCGAAATGAAA
1 ATCGCAATGAGAAATGAAA
* *
213582 ATCGCAACGAG--A-G--G
1 ATCGCAATGAGAAATGAAA
*
213596 ATCGCAATGCGAAATGAAA
1 ATCGCAATGAGAAATGAAA
213615 ATCGCAA
1 ATCGCAA
213622 CGAGGGAATC
Statistics
Matches: 73, Mismatches: 9, Indels: 20
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.27
16 4 0.05
17 4 0.05
19 45 0.62
ACGTcount: A:0.46, C:0.15, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGAGAAATGAAA
Found at i:213570 original size:52 final size:52
Alignment explanation
Indices: 213491--213621 Score: 190
Period size: 52 Copynumber: 2.5 Consensus size: 52
213481 CTTAATGTCT
* ** *
213491 ATCGCAACGCGGAAATGACTATCGCAATGAGAAATGAAAATCGCAATGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAATGAGAAATGAAAATCGCAACGAGAGA
* * *
213544 ATCGCAATGCGAAATGAAAATTGCAATGCGAAATGAAAATCGCAACGAGAGG
1 ATCGCAATGCGAAATGAAAATCGCAATGAGAAATGAAAATCGCAACGAGAGA
213596 ATCGCAATGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
213622 CGAGGGAATC
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
52 61 0.87
53 9 0.13
ACGTcount: A:0.44, C:0.17, G:0.24, T:0.15
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGAGAAATGAAAATCGCAACGAGAGA
Found at i:213603 original size:33 final size:33
Alignment explanation
Indices: 213566--213656 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
213556 AATGAAAATT
213566 GCAATGCGAAATGAAAATCGCAACGAGAGG-ATC
1 GCAATGCGAAATGAAAATCGCAACGAG-GGAATC
213599 GCAATGCGAAATGAAAATCGCAACGAGGGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGGGAATC
* *
213632 GCAAAGCGAAATGAAAATAGCAACG
1 GCAATGCGAAATGAAAATCGCAACG
213657 CGAATTTAGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.45, C:0.18, G:0.26, T:0.11
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCGCAACGAGGGAATC
Done.