Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005546.1 Hibiscus syriacus cultivar Beakdansim tig00012840_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: 1755203
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 8
Found at i:13598 original size:19 final size:19
Alignment explanation
Indices: 13574--13623 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
13564 CCCTAGTTGT
13574 GGTATCGATACCAAGCTTA
1 GGTATCGATACCAAGCTTA
13593 GGTATCGATACCAAGCTTA
1 GGTATCGATACCAAGCTTA
13612 GGTATCGATACC
1 GGTATCGATACC
13624 CATTTTTCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (19 bp):
GGTATCGATACCAAGCTTA
Found at i:17286 original size:22 final size:22
Alignment explanation
Indices: 17258--17387 Score: 233
Period size: 22 Copynumber: 5.9 Consensus size: 22
17248 ATGTGAAATC
17258 TATGTCCCGAAGGGCCTATGCA
1 TATGTCCCGAAGGGCCTATGCA
17280 TATGTCCCGAAGGGCCTATGCA
1 TATGTCCCGAAGGGCCTATGCA
17302 TATGTCCCGAAGGGCCTATGCA
1 TATGTCCCGAAGGGCCTATGCA
*
17324 TATGTCTCGAAGGGCCTATGCA
1 TATGTCCCGAAGGGCCTATGCA
*
17346 TATATCCCGAAGGGCCTATGCA
1 TATGTCCCGAAGGGCCTATGCA
*
17368 TATGTCCCGAAGGACCTATG
1 TATGTCCCGAAGGGCCTATG
17388 TAACCCTCGA
Statistics
Matches: 103, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 103 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (22 bp):
TATGTCCCGAAGGGCCTATGCA
Found at i:17631 original size:19 final size:19
Alignment explanation
Indices: 17591--17634 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
17581 TATTCACATG
* *
17591 AATCATATAGCATGTATCA
1 AATCATATAACATATATCA
17610 AATCATATAAACATATAT-A
1 AATCATAT-AACATATATCA
17629 AATCAT
1 AATCAT
17635 GCATGTGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.50, C:0.14, G:0.05, T:0.32
Consensus pattern (19 bp):
AATCATATAACATATATCA
Found at i:24184 original size:63 final size:62
Alignment explanation
Indices: 24110--24269 Score: 167
Period size: 64 Copynumber: 2.5 Consensus size: 62
24100 ATTGTTCAGT
* * *
24110 GTGTATCGATGCACAGGAAGTGCATCGATGCACCTATTAAAATGGAAACATCGAATGCAATTG
1 GTGTATCGATGCACAGG-AGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTG
* * * * ** *
24173 GTGTATCGATGCATAAGGAGTGCATCAATGCATCCCCTTAAAATGAAAACATTGAAGGTGATTT
1 GTGTATCGATGCA-CAGGAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGGCAATTG
* * *
24237 GTGCATCGATGCACGGGTACTGCATCGATGCAC
1 GTGTATCGATGCACAGG-AGTGCATCGATGCAC
24270 ATGCTAAAGA
Statistics
Matches: 79, Mismatches: 15, Indels: 6
0.79 0.15 0.06
Matches are distributed among these distances:
63 29 0.37
64 50 0.63
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (62 bp):
GTGTATCGATGCACAGGAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGGCAATTG
Found at i:24303 original size:20 final size:20
Alignment explanation
Indices: 24238--24334 Score: 97
Period size: 20 Copynumber: 4.7 Consensus size: 20
24228 AGGTGATTTG
* * *
24238 TGCATCGATGCACGGGT-AC
1 TGCATCGATGCACTGTTGAA
*
24257 TGCATCGATGCACATGCTAAAGAA
1 TGCATCGATGCAC-TG-T--TGAA
24281 TGCATCGATGCACTGTTGAA
1 TGCATCGATGCACTGTTGAA
*
24301 TGCATCAATGCACTGTTGAA
1 TGCATCGATGCACTGTTGAA
*
24321 TGCATCAATGCACT
1 TGCATCGATGCACT
24335 TCAAGAGAAA
Statistics
Matches: 67, Mismatches: 6, Indels: 9
0.82 0.07 0.11
Matches are distributed among these distances:
19 13 0.19
20 37 0.55
22 1 0.01
23 2 0.03
24 14 0.21
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.26
Consensus pattern (20 bp):
TGCATCGATGCACTGTTGAA
Found at i:25420 original size:31 final size:30
Alignment explanation
Indices: 25382--25460 Score: 86
Period size: 31 Copynumber: 2.6 Consensus size: 30
25372 GTCTTTCGAG
*
25382 ACATATGGACAGTATACCTATGTTCTAAGGA
1 ACATATGGACAGT-TACCTAGGTTCTAAGGA
* ** *
25413 ACATATGGATAGTTTACCTAGGTTCTTCGGG
1 ACATATGGACAG-TTACCTAGGTTCTAAGGA
*
25444 ACCTATGGACAGTTACC
1 ACATATGGACAGTTACC
25461 GAGGATCTTT
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
30 5 0.12
31 34 0.85
32 1 0.03
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (30 bp):
ACATATGGACAGTTACCTAGGTTCTAAGGA
Found at i:25513 original size:30 final size:30
Alignment explanation
Indices: 25443--25515 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
25433 GGTTCTTCGG
* *
25443 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
25473 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
25503 GACCTCTGGATAG
1 GACCTCTGGATAG
25516 GTCCTTCGGA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:30352 original size:9 final size:9
Alignment explanation
Indices: 30340--30371 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
30330 GCTTTTTGGC
30340 TTTTTGTTTT
1 TTTTTG-TTT
30350 TTTTTGTTT
1 TTTTTGTTT
30359 TTTTTGTTT
1 TTTTTGTTT
30368 TTTT
1 TTTT
30372 AAAAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (9 bp):
TTTTTGTTT
Found at i:30355 original size:10 final size:10
Alignment explanation
Indices: 30340--30371 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
30330 GCTTTTTGGC
30340 TTTTTGTTTT
1 TTTTTGTTTT
30350 TTTTTG-TTT
1 TTTTTGTTTT
30359 TTTTTGTTTT
1 TTTTTGTTTT
30369 TTT
1 TTT
30372 AAAAAAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.43
10 12 0.57
ACGTcount: A:0.00, C:0.00, G:0.09, T:0.91
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:31705 original size:21 final size:21
Alignment explanation
Indices: 31676--31724 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
31666 AAGAAGCTAT
*
31676 TGAAGCTTCATTTAATGGAAA
1 TGAATCTTCATTTAATGGAAA
31697 TGAATCTTCATTTAATGGAAA
1 TGAATCTTCATTTAATGGAAA
31718 TGAATCT
1 TGAATCT
31725 AAGTATTTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.37
Consensus pattern (21 bp):
TGAATCTTCATTTAATGGAAA
Found at i:33908 original size:21 final size:21
Alignment explanation
Indices: 33882--33940 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
33872 GTACTCCTCT
*
33882 TGGAGTATTTGTACTACTTAG
1 TGGAGTACTTGTACTACTTAG
*
33903 TGGAGTACTTGTACTACTTGG
1 TGGAGTACTTGTACTACTTAG
* * *
33924 AGGAGTACCTATACTAC
1 TGGAGTACTTGTACTAC
33941 ATGGTGGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.15, G:0.24, T:0.36
Consensus pattern (21 bp):
TGGAGTACTTGTACTACTTAG
Found at i:33956 original size:21 final size:21
Alignment explanation
Indices: 33914--33957 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
33904 GGAGTACTTG
* *
33914 TACTACTTGGAGGAGTACCTA
1 TACTACATGGAGGAATACCTA
* *
33935 TACTACATGGTGGAATATCTA
1 TACTACATGGAGGAATACCTA
33956 TA
1 TA
33958 ATACCTAGTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (21 bp):
TACTACATGGAGGAATACCTA
Found at i:36724 original size:25 final size:26
Alignment explanation
Indices: 36677--36725 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
36667 TTGACTTAAA
* *
36677 AAAATTTCGAGTCGATTCGAGTTTAT
1 AAAATTTCGAGTCGAGTCAAGTTTAT
36703 AAAATTT-GAGTCGAGTCAAGTTT
1 AAAATTTCGAGTCGAGTCAAGTTT
36726 TTGAGTTTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 14 0.67
26 7 0.33
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (26 bp):
AAAATTTCGAGTCGAGTCAAGTTTAT
Found at i:36879 original size:15 final size:15
Alignment explanation
Indices: 36861--36890 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
36851 ATATACATAT
36861 ATCATATAGAGTCAA
1 ATCATATAGAGTCAA
*
36876 ATCATATAGTGTCAA
1 ATCATATAGAGTCAA
36891 GGGATTCGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (15 bp):
ATCATATAGAGTCAA
Found at i:42275 original size:3 final size:3
Alignment explanation
Indices: 42267--42295 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
42257 ATTCACACCC
42267 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
42296 ATTTTAATAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:43734 original size:19 final size:19
Alignment explanation
Indices: 43707--43754 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
43697 TTGAACAAGT
43707 GTATCAGTACCTCCCAGGG
1 GTATCAGTACCTCCCAGGG
*
43726 GTATTAGTACCTCCCAGGG
1 GTATCAGTACCTCCCAGGG
43745 GTATCAGTAC
1 GTATCAGTAC
43755 ACCTATGACA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (19 bp):
GTATCAGTACCTCCCAGGG
Found at i:45444 original size:16 final size:17
Alignment explanation
Indices: 45423--45456 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
45413 ACTATTCATA
*
45423 TGAATAGT-GAATTTTG
1 TGAATAGTAAAATTTTG
45439 TGAATAGTAAAATTTTG
1 TGAATAGTAAAATTTTG
45456 T
1 T
45457 CGGCAATATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (17 bp):
TGAATAGTAAAATTTTG
Found at i:49377 original size:21 final size:22
Alignment explanation
Indices: 49324--49377 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 22
49314 CCTCGAGGGG
* *
49324 TATCGATACATATTCAAGAAATG
1 TATCGATACACATTCAAG-AATA
49347 TATCGATACACATTCAAG-ATA
1 TATCGATACACATTCAAGAATA
*
49368 TATTGATACA
1 TATCGATACA
49378 TAGTAAGAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 11 0.39
23 17 0.61
ACGTcount: A:0.43, C:0.15, G:0.11, T:0.31
Consensus pattern (22 bp):
TATCGATACACATTCAAGAATA
Found at i:55665 original size:17 final size:17
Alignment explanation
Indices: 55643--55676 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
55633 TATAAATTAT
55643 AAAGAAAGAAACAAAAG
1 AAAGAAAGAAACAAAAG
*
55660 AAAGAAAGAAAGAAAAG
1 AAAGAAAGAAACAAAAG
55677 GGGGAGGGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAACAAAAG
Found at i:55707 original size:3 final size:3
Alignment explanation
Indices: 55699--55746 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
55689 GGAGAGCGGC
55699 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
55747 AGGTTAGCAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:56497 original size:20 final size:20
Alignment explanation
Indices: 56461--56498 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
56451 ATCCTATTCC
**
56461 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
56481 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
56499 GTAAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:62053 original size:10 final size:10
Alignment explanation
Indices: 62038--62076 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
62028 TTTATGTGCC
62038 TTGTAATTAG
1 TTGTAATTAG
*
62048 TTGTAAATATAC
1 TTGT-AAT-TAG
62060 TTGTAATTAG
1 TTGTAATTAG
62070 TTGTAAT
1 TTGTAAT
62077 CCTCCAACTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 13 0.52
11 6 0.24
12 6 0.24
ACGTcount: A:0.33, C:0.03, G:0.15, T:0.49
Consensus pattern (10 bp):
TTGTAATTAG
Found at i:66637 original size:74 final size:74
Alignment explanation
Indices: 66553--66701 Score: 280
Period size: 74 Copynumber: 2.0 Consensus size: 74
66543 AAATAATTAT
66553 AATATCCTTGTAATTAGTTGTAATCCCCCAACTATAAGCTAGTTTCCTATTTCTGTGCCTTGTAA
1 AATATCCTTGTAATTAGTTGTAATCCCCCAACTATAAGCTAGTTTCCTATTTCTGTGCCTTGTAA
66618 TTAGTTGTA
66 TTAGTTGTA
* *
66627 AATATCCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTCTGTGCCTTGTAA
1 AATATCCTTGTAATTAGTTGTAATCCCCCAACTATAAGCTAGTTTCCTATTTCTGTGCCTTGTAA
66692 TTAGTTGTA
66 TTAGTTGTA
66701 A
1 A
66702 TCCCCCAACT
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.25, C:0.19, G:0.14, T:0.42
Consensus pattern (74 bp):
AATATCCTTGTAATTAGTTGTAATCCCCCAACTATAAGCTAGTTTCCTATTTCTGTGCCTTGTAA
TTAGTTGTA
Found at i:66689 original size:52 final size:52
Alignment explanation
Indices: 66632--66735 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
66622 TTGTAAATAT
*
66632 CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTCTGTG
1 CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTATGTG
66684 CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTATGTG
1 CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTATGTG
66736 TGCCCAATCT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.40
Consensus pattern (52 bp):
CCTTGTAATTAGTTGTAATCCCCCAACTCTAGGCTAGTTTCCTATTTATGTG
Found at i:73297 original size:13 final size:13
Alignment explanation
Indices: 73261--73300 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
73251 GAGTAAATAG
*
73261 TTAATTAAATTAT
1 TTAATTATATTAT
*
73274 TTACTTTATATTAT
1 TTA-ATTATATTAT
73288 TTAATTATATTAT
1 TTAATTATATTAT
73301 ACATTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (13 bp):
TTAATTATATTAT
Found at i:75491 original size:19 final size:19
Alignment explanation
Indices: 75467--75512 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
75457 CAAAATTATT
* *
75467 TTTCAAATTTTCATTTTTG-
1 TTTCAAAATTT-AATTTTGC
75486 TTTCAAAATTTAATTTTGC
1 TTTCAAAATTTAATTTTGC
75505 TTTCAAAA
1 TTTCAAAA
75513 GAAAATCATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.30, C:0.11, G:0.04, T:0.54
Consensus pattern (19 bp):
TTTCAAAATTTAATTTTGC
Found at i:75773 original size:20 final size:20
Alignment explanation
Indices: 75737--75774 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
75727 CTCATACCTC
*
75737 ATTCTTTTTATTGTTCTTTT
1 ATTCTTTTTATTATTCTTTT
*
75757 ATTCTTTTTCTTATTCTT
1 ATTCTTTTTATTATTCTT
75775 GCTTCCTTTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.13, G:0.03, T:0.74
Consensus pattern (20 bp):
ATTCTTTTTATTATTCTTTT
Found at i:77690 original size:13 final size:12
Alignment explanation
Indices: 77666--77695 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
77656 GAGATTAGCC
77666 ATCAATTTCATA
1 ATCAATTTCATA
77678 ATCAATATTCATA
1 ATCAAT-TTCATA
77691 ATCAA
1 ATCAA
77696 ATGTGAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.35
13 11 0.65
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (12 bp):
ATCAATTTCATA
Found at i:79755 original size:21 final size:23
Alignment explanation
Indices: 79702--79755 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
79692 TGGCCTTGTC
79702 TATCGATGCACATTCAAGGCGTG
1 TATCGATGCACATTCAAGGCGTG
* * * *
79725 CATCGGTGCACCTTC-ATG-GTG
1 TATCGATGCACATTCAAGGCGTG
79746 TATCGATGCA
1 TATCGATGCA
79756 TATTAAAAGG
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 11 0.44
22 2 0.08
23 12 0.48
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TATCGATGCACATTCAAGGCGTG
Found at i:85577 original size:19 final size:19
Alignment explanation
Indices: 85553--85591 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
85543 TGGACCCTTC
85553 GTGCATCAGTGCACTAAGA
1 GTGCATCAGTGCACTAAGA
*
85572 GTGCATCGGTGCACTAAGA
1 GTGCATCAGTGCACTAAGA
85591 G
1 G
85592 GGCAACGATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.21, G:0.31, T:0.21
Consensus pattern (19 bp):
GTGCATCAGTGCACTAAGA
Found at i:85603 original size:19 final size:19
Alignment explanation
Indices: 85562--85603 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
85552 CGTGCATCAG
* * *
85562 TGCACTAAGAGTGCATCGG
1 TGCACTAAGAGGGCAACGA
85581 TGCACTAAGAGGGCAACGA
1 TGCACTAAGAGGGCAACGA
85600 TGCA
1 TGCA
85604 TGAAATGCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.21, G:0.31, T:0.17
Consensus pattern (19 bp):
TGCACTAAGAGGGCAACGA
Found at i:85674 original size:64 final size:63
Alignment explanation
Indices: 85597--85800 Score: 218
Period size: 65 Copynumber: 3.2 Consensus size: 63
85587 AAGAGGGCAA
*
85597 CGATGCATGAAATGCATTCGATGTTTCAAAATAGCTAGAGTGCATCGATGCATGGATGGTGCAT
1 CGATGCATCAAATGCATTCGATGTTTCAAAATA-CTAGAGTGCATCGATGCATGGATGGTGCAT
* * * *
85661 CGATGGATCAAATGCATTCGATGTTTTCATAAA-ACTCTGAGTGCATCAATGCATAGTAT-GTGC
1 CGATGCATCAAATGCATTCGATG-TTTCA-AAATACT-AGAGTGCATCGATGCAT-GGATGGTGC
85724 AT
62 AT
* * * *
85726 CGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATGCATGGATTGGTGC
1 CGATGCATCAAATGCATTCGATGTTTCAA--AATACTA-GAGTGCATCGATGCATGGA-TGGTGC
85789 AT
62 AT
85791 CGATGCATCA
1 CGATGCATCA
85801 CTTTGAAAAA
Statistics
Matches: 116, Mismatches: 14, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
62 1 0.01
63 6 0.05
64 38 0.33
65 65 0.56
66 6 0.05
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (63 bp):
CGATGCATCAAATGCATTCGATGTTTCAAAATACTAGAGTGCATCGATGCATGGATGGTGCAT
Found at i:87073 original size:54 final size:54
Alignment explanation
Indices: 87013--87117 Score: 165
Period size: 54 Copynumber: 1.9 Consensus size: 54
87003 AACAATATTG
* *
87013 TTCATGTATTATCGATACTGTAAGAATAATATCGATACTACTTACCCAAAACTA
1 TTCATGTAGTATCGATACTGTAAGAACAATATCGATACTACTTACCCAAAACTA
* * *
87067 TTCATGTAGTATCGATAGTGTAAGAACAATATTGGTACTACTTACCCAAAA
1 TTCATGTAGTATCGATACTGTAAGAACAATATCGATACTACTTACCCAAAA
87118 AACTGTTTTG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 46 1.00
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (54 bp):
TTCATGTAGTATCGATACTGTAAGAACAATATCGATACTACTTACCCAAAACTA
Found at i:91622 original size:18 final size:20
Alignment explanation
Indices: 91599--91646 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
91589 AAACTCGAAC
91599 AACTCGAC-CAAACTT-TTA
1 AACTCGACTCAAACTTCTTA
**
91617 AACTCGACTTGAACTTCTTA
1 AACTCGACTCAAACTTCTTA
91637 AACTCGACTC
1 AACTCGACTC
91647 GACTCAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 8 0.32
19 5 0.20
20 12 0.48
ACGTcount: A:0.33, C:0.29, G:0.08, T:0.29
Consensus pattern (20 bp):
AACTCGACTCAAACTTCTTA
Found at i:94746 original size:26 final size:26
Alignment explanation
Indices: 94691--94746 Score: 76
Period size: 26 Copynumber: 2.2 Consensus size: 26
94681 TGTTGGGGAT
* * *
94691 AAACTTTTAAAATTTTAGGAGGAGAC
1 AAACTTATAAAATTTAAGGAGGAGAA
*
94717 AAACTTATAAAATTTAAGGAGGATAA
1 AAACTTATAAAATTTAAGGAGGAGAA
94743 AAAC
1 AAAC
94747 AGATTTTCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.27
Consensus pattern (26 bp):
AAACTTATAAAATTTAAGGAGGAGAA
Found at i:101865 original size:67 final size:67
Alignment explanation
Indices: 101755--101881 Score: 236
Period size: 67 Copynumber: 1.9 Consensus size: 67
101745 TTTATTTAAC
* *
101755 AGTAAATGCATCCATTGCTAACTAATGCCTCACCATATGTGGTGCCTGTGTTATAAGACCACGCC
1 AGTAAATGCATCCACTGCTAACTAATGCCTCACCATATATGGTGCCTGTGTTATAAGACCACGCC
101820 TA
66 TA
101822 AGTAAATGCATCCACTGCTAACTAATGCCTCACCATATATGGTGCCTGTGTTATAAGACC
1 AGTAAATGCATCCACTGCTAACTAATGCCTCACCATATATGGTGCCTGTGTTATAAGACC
101882 GCAATATTTT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.28
Consensus pattern (67 bp):
AGTAAATGCATCCACTGCTAACTAATGCCTCACCATATATGGTGCCTGTGTTATAAGACCACGCC
TA
Found at i:107196 original size:123 final size:123
Alignment explanation
Indices: 106958--107214 Score: 307
Period size: 123 Copynumber: 2.1 Consensus size: 123
106948 AATCTTTTGG
106958 TATTCGGGTTAGATCTTTTTAAAAAAAAATTCGGGATTCGATCGGAATTTTTTTAAAAAATTACG
1 TATTCGGGTTAGATCTTTTTAAAAAAAAATTCGGGATTCGATCGGAATTTTTTTAAAAAATTACG
107023 GATTCGGGTTGGGTTTTTTTAAGTTTGATATTCTGGTCAGGTTAGGTTTTTTAAGTGTGA
66 GATTCGGGTTGGGTTTTTTTAAGTTTGATATTC-GG-CAGGTTAGGTTTTTTAAGTGTGA
* * *
107083 TATTCGGGTTA-AGT-TTTTTTAAAAAAAA-TCGGGA-TCGGGTCGG-ATTTTTTTAAAAAATTT
1 TATTCGGGTTAGA-TCTTTTTAAAAAAAAATTCGGGATTC-GATCGGAATTTTTTTAAAAAATTA
* *
107143 CAGG-TTTGGGTTGGGTCGGGTTTTTTAAAGTTTGATATTC-G-A-GTTGAGTTTTTTTAAGTGT
64 C-GGATTCGGGTTGGGT----TTTTTT-AAGTTTGATATTCGGCAGGTT-AGGTTTTTTAAGTGT
107204 GA
122 GA
107206 TATTCGGGT
1 TATTCGGGT
107215 CGGGTTTAGG
Statistics
Matches: 118, Mismatches: 5, Indels: 20
0.83 0.03 0.14
Matches are distributed among these distances:
122 33 0.28
123 39 0.33
124 14 0.12
125 13 0.11
126 6 0.05
127 13 0.11
ACGTcount: A:0.25, C:0.07, G:0.25, T:0.44
Consensus pattern (123 bp):
TATTCGGGTTAGATCTTTTTAAAAAAAAATTCGGGATTCGATCGGAATTTTTTTAAAAAATTACG
GATTCGGGTTGGGTTTTTTTAAGTTTGATATTCGGCAGGTTAGGTTTTTTAAGTGTGA
Found at i:107221 original size:28 final size:28
Alignment explanation
Indices: 107155--107221 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
107145 GGTTTGGGTT
*
107155 GGGTCGGGTTTTTTAAAGTTTGATATTC
1 GGGTCGGGTTTTTTAAAGTGTGATATTC
* * * *
107183 GAGTTGAGTTTTTTTAAGTGTGATATTC
1 GGGTCGGGTTTTTTAAAGTGTGATATTC
107211 GGGTCGGGTTT
1 GGGTCGGGTTT
107222 AGGGTGAAAA
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.16, C:0.06, G:0.31, T:0.46
Consensus pattern (28 bp):
GGGTCGGGTTTTTTAAAGTGTGATATTC
Found at i:107766 original size:16 final size:17
Alignment explanation
Indices: 107742--107790 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
107732 AGGTTTCAGA
*
107742 TTCAAATTCCAATTC-T
1 TTCAGATTCCAATTCAT
*
107758 TTCAGATTCAAATTCAT
1 TTCAGATTCCAATTCAT
*
107775 TCACAGATTCCAATTC
1 T-TCAGATTCCAATTC
107791 CCTCAGAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
16 13 0.48
17 2 0.07
18 12 0.44
ACGTcount: A:0.33, C:0.24, G:0.04, T:0.39
Consensus pattern (17 bp):
TTCAGATTCCAATTCAT
Found at i:110880 original size:161 final size:162
Alignment explanation
Indices: 110603--110977 Score: 619
Period size: 161 Copynumber: 2.3 Consensus size: 162
110593 TTACCAAATG
* * * *
110603 GGCACTATGTG-GCAACTTAAGAAATTCATAATGAGTTTATTAATTTTCATATTGGCACTGTGTG
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTGTG
* *
110667 TGCAACTTAAGAATTTCATAATAAGTTTATAAATTTCCGTATTGGCACTGTGTGTGCAACTTAAG
66 TGCAACTTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTGGCACTGTGTGTACAACTTAAG
*
110732 AAATTCATAATAAGTTTATGAATTTCCGTATT
131 AAATTCATAATAAGTTTATAAATTTCCGTATT
*
110764 GGCACTGTGTGTGCAACTTAAGAAAATCATAATGA-TTTATGAATTTCCGTATTGGCACTGTGTG
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTGTG
* * *
110828 TGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATTGGCACTGTGTGTATAACTTAAG
66 TGCAACTTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTGGCACTGTGTGTACAACTTAAG
110893 AAATTCATAATAAGTTTATAAATTTCCGTATT
131 AAATTCATAATAAGTTTATAAATTTCCGTATT
* *
110925 GGCATTGTGTGTACAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT
110978 CGGTATTAAG
Statistics
Matches: 198, Mismatches: 14, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
161 159 0.80
162 39 0.20
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (162 bp):
GGCACTGTGTGTGCAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTATTGGCACTGTGTG
TGCAACTTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTGGCACTGTGTGTACAACTTAAG
AAATTCATAATAAGTTTATAAATTTCCGTATT
Found at i:110995 original size:54 final size:54
Alignment explanation
Indices: 110603--110977 Score: 592
Period size: 54 Copynumber: 7.0 Consensus size: 54
110593 TTACCAAATG
* * * * *
110603 GGCACTATGTG-GCAACTTAAGAAATTCATAATGAGTTTATTAATTTTCATATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
110656 GGCACTGTGTGTGCAACTTAAGAATTTCATAATAAGTTTATAAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
110710 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* *
110764 GGCACTGTGTGTGCAACTTAAGAAAATCATAATGA-TTTATGAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
*
110817 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
** *
110871 GGCACTGTGTGTATAACTTAAGAAATTCATAATAAGTTTATAAATTTCCGTATT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
* * *
110925 GGCATTGTGTGTACAACTTAAGAAATTCATAATGAGTTTATGAATTTCCGTAT
1 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
110978 CGGTATTAAG
Statistics
Matches: 299, Mismatches: 21, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
53 61 0.20
54 238 0.80
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (54 bp):
GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTCCGTATT
Found at i:111013 original size:215 final size:214
Alignment explanation
Indices: 110603--111022 Score: 617
Period size: 215 Copynumber: 2.0 Consensus size: 214
110593 TTACCAAATG
* *
110603 GGCACTATGTGGCAACTTAAGAAATTCATAATGAGTTTATTAATTTTCATATTGGCACTGTGTGT
1 GGCACTATGTGGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCATATTGGCACTGTGTGT
* * *
110668 GCAACTTAAGAATTTCATAATAAGTTTATAAATTTCCGTATTGGCACTGTGTGTGCAACTTAAGA
66 ACAACTTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTGGCACTGTGTGTACAACTTAAGA
* ** * **
110733 AATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTGTGTGCAACTTAAGAAAATCATAATG
131 AATTCATAATAAGTTTATGAATTTCCGTATCGGCACTAAGTGTACAACCCAAGAAAATCATAATG
*
110798 ATTTATGAATTTCCGTATT
196 AATTATGAATTTCCGTATT
* *
110817 GGCACTGTGTGTGCAACTTAAGAAATTCATAATAAGTTTATGAA-TTTCTGTATTGGCACTGTGT
1 GGCACTATGTG-GCAACTTAAGAAATTCATAATAAGTTTATGAATTTTC-ATATTGGCACTGTGT
* *
110881 GTATAACTTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTGGCATTGTGTGTACAACTTAA
64 GTACAACTTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTGGCACTGTGTGTACAACTTAA
* * * * * *
110946 GAAATTCATAATGAGTTTATGAATTTCCGTATCGGTATTAAGTGTACAACCCATGAAATTTATAA
129 GAAATTCATAATAAGTTTATGAATTTCCGTATCGGCACTAAGTGTACAACCCAAGAAAATCATAA
111011 TGAATTATGAAT
194 TGAATTATGAAT
111023 ATTGTATCGA
Statistics
Matches: 182, Mismatches: 22, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
214 14 0.08
215 168 0.92
ACGTcount: A:0.33, C:0.12, G:0.17, T:0.38
Consensus pattern (214 bp):
GGCACTATGTGGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCATATTGGCACTGTGTGT
ACAACTTAAGAAATTCATAATAAGTTTATAAATTTCCGTATTGGCACTGTGTGTACAACTTAAGA
AATTCATAATAAGTTTATGAATTTCCGTATCGGCACTAAGTGTACAACCCAAGAAAATCATAATG
AATTATGAATTTCCGTATT
Found at i:113556 original size:23 final size:23
Alignment explanation
Indices: 113529--113576 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
113519 AATATATGTA
113529 ACTATTCATCATGAAT-GAATATG
1 ACTATTCATCATGAATAG-ATATG
*
113552 ACTATTCATGATGAATAGATATG
1 ACTATTCATCATGAATAGATATG
113575 AC
1 AC
113577 CATGTAGATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (23 bp):
ACTATTCATCATGAATAGATATG
Found at i:115826 original size:29 final size:29
Alignment explanation
Indices: 115784--115894 Score: 186
Period size: 29 Copynumber: 3.8 Consensus size: 29
115774 ATCGTTGACC
* *
115784 GGTGTTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
115813 GGTGCTATTCTGGTAAATAATTTGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
115842 GGTGCTATTCTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCGGTTTT
*
115871 GGTGCTATTCTGGTAATTAATTCG
1 GGTGCTATTCTGGTAAATAATTCG
115895 AAATGGGTAC
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 77 1.00
ACGTcount: A:0.22, C:0.09, G:0.23, T:0.46
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCGGTTTT
Found at i:115907 original size:29 final size:29
Alignment explanation
Indices: 115789--115918 Score: 84
Period size: 29 Copynumber: 4.5 Consensus size: 29
115779 TGACCGGTGT
** * *
115789 TATTCTGGTAAATAATTC-AGTTTTGGTGC
1 TATTCTGGTAAATAATTCGA-AATGGGTAC
* *** * *
115818 TATTCTGGTAAATAATTTGGTTTTGGTGC
1 TATTCTGGTAAATAATTCGAAATGGGTAC
*** * *
115847 TATTCTGGTAAATAATTCGGTTTTGGTGC
1 TATTCTGGTAAATAATTCGAAATGGGTAC
*
115876 TATTCTGGTAATTAATTCGAAATGGGTAC
1 TATTCTGGTAAATAATTCGAAATGGGTAC
115905 TATGT-TGGTAAATA
1 TAT-TCTGGTAAATA
115919 TTTTAAAAAG
Statistics
Matches: 89, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
29 88 0.99
30 1 0.01
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.44
Consensus pattern (29 bp):
TATTCTGGTAAATAATTCGAAATGGGTAC
Found at i:115914 original size:58 final size:58
Alignment explanation
Indices: 115789--115918 Score: 172
Period size: 58 Copynumber: 2.2 Consensus size: 58
115779 TGACCGGTGT
* *** * *
115789 TATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTGGTAAATAATTTGGTTTTGGTGC
1 TATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGAAATGGGTAC
* *
115847 TATTCTGGTAAATAATTCGGTTTTGGTGCTATTCTGGTAATTAATTCGAAATGGGTAC
1 TATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGAAATGGGTAC
115905 TATGT-TGGTAAATA
1 TAT-TCTGGTAAATA
115919 TTTTAAAAAG
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
58 62 0.98
59 1 0.02
ACGTcount: A:0.25, C:0.08, G:0.22, T:0.44
Consensus pattern (58 bp):
TATTCTGGTAAATAATTCAGTTTTGGTGCTATTCTGGTAAATAATTCGAAATGGGTAC
Found at i:123648 original size:3 final size:3
Alignment explanation
Indices: 123640--123675 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
123630 CTTGATTTAT
123640 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
123676 GGATAGGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:124202 original size:116 final size:115
Alignment explanation
Indices: 123985--124314 Score: 355
Period size: 116 Copynumber: 2.9 Consensus size: 115
123975 TATGAACTTC
* * *
123985 CTTCCACCTAT-TTAAAAAGAGTAGACGAGCTCTCTTATATAAGCTCTC-TATTCT-CATAAA-G
1 CTTCCTCCTATATGAAAAA-AGTAGACGAGCTCTCCTATATAAGCTC-CATATTCTCCATAAAGG
* * * * *
124046 TCCATGTTGAGGTCAAACAATCTTTCCTATATGAAGTTCTTCTCCCTTGATTG
64 T-CATGTTGAGGTCGAACAAGCTCTCCTATATAAACTTCTTCTCCCTTGATTG
124099 CTTCCTCCTATATGAAAAAAGTAGACGAGCTCTCCTATATAAGCTCCATATTCTCCCATAAAGGT
1 CTTCCTCCTATATGAAAAAAGTAGACGAGCTCTCCTATATAAGCTCCATATTCT-CCATAAAGGT
* *
124164 CATGTTGAGGTCGAACAAGCTCTCCTATATTAACTTCTTCTCCTTTGATTG
65 CATGTTGAGGTCGAACAAGCTCTCCTATATAAACTTCTTCTCCCTTGATTG
* ** * * * * * * *
124215 CCTCCTTATATATGGAAATAGTAGATGTGCTCTCCTATATAAACCCCATATTCATCCAAAAAGGT
1 CTTCCTCCTATATGAAAAAAGTAGACGAGCTCTCCTATATAAGCTCCATATTC-TCCATAAAGGT
* * * *
124280 CATGGTT-TGGTCGAACGAGTTCTCTTATATAAACT
65 CAT-GTTGAGGTCGAACAAGCTCTCCTATATAAACT
124315 CATTATTCAC
Statistics
Matches: 185, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
113 1 0.01
114 42 0.23
115 6 0.03
116 130 0.70
117 6 0.03
ACGTcount: A:0.29, C:0.23, G:0.14, T:0.34
Consensus pattern (115 bp):
CTTCCTCCTATATGAAAAAAGTAGACGAGCTCTCCTATATAAGCTCCATATTCTCCATAAAGGTC
ATGTTGAGGTCGAACAAGCTCTCCTATATAAACTTCTTCTCCCTTGATTG
Found at i:124616 original size:44 final size:44
Alignment explanation
Indices: 124549--124694 Score: 125
Period size: 44 Copynumber: 3.3 Consensus size: 44
124539 GTGAAATATA
* * *
124549 ATGTTGATCCACCT-ACTTCTGTGATGGAATCAAACTAAATATCG
1 ATGTTGATCTACCTCA-TTATGTGATAGAATCAAACTAAATATCG
* * **
124593 ATGTTGATCTACCTCATTATGTGATAGAATCAAGCAAAATAAGG
1 ATGTTGATCTACCTCATTATGTGATAGAATCAAACTAAATATCG
* * * * * *
124637 TTATGTTTATTCAACTTC-TTTTGTGATTGAATCAAATTAAATATCG
1 --ATGTTGA-TCTACCTCATTATGTGATAGAATCAAACTAAATATCG
124683 ATGTTGATCTAC
1 ATGTTGATCTAC
124695 ATCTTTCTAT
Statistics
Matches: 79, Mismatches: 19, Indels: 9
0.74 0.18 0.08
Matches are distributed among these distances:
43 4 0.05
44 41 0.52
45 1 0.01
46 27 0.34
47 6 0.08
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (44 bp):
ATGTTGATCTACCTCATTATGTGATAGAATCAAACTAAATATCG
Found at i:124623 original size:87 final size:89
Alignment explanation
Indices: 124512--124694 Score: 208
Period size: 90 Copynumber: 2.1 Consensus size: 89
124502 AGTGACGCTA
* * * * ** *
124512 ATCTAACTCATTTTGTCATGGAATCGAGTGAAAT-A-TAATGTTGATCCACCTACTTCTGTGATG
1 ATCTACCTCATTATGTCATAGAATCAAGCAAAATAAGTAATGTTGATCCAACTACTTCTGTGATG
124575 GAATCAAACTAAATATCGATGTTG
66 GAATCAAACTAAATATCGATGTTG
* * * * * *
124599 ATCTACCTCATTATGTGATAGAATCAAGCAAAATAAGGTTATGTTTATTCAACTTCTTTTGTGAT
1 ATCTACCTCATTATGTCATAGAATCAAGCAAAATAA-GTAATGTTGATCCAACTACTTCTGTGAT
* *
124664 TGAATCAAATTAAATATCGATGTTG
65 GGAATCAAACTAAATATCGATGTTG
124689 ATCTAC
1 ATCTAC
124695 ATCTTTCTAT
Statistics
Matches: 78, Mismatches: 15, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
87 27 0.35
88 1 0.01
90 50 0.64
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (89 bp):
ATCTACCTCATTATGTCATAGAATCAAGCAAAATAAGTAATGTTGATCCAACTACTTCTGTGATG
GAATCAAACTAAATATCGATGTTG
Found at i:126288 original size:24 final size:24
Alignment explanation
Indices: 126261--126306 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
126251 ATAAATGGAG
126261 ATATCAGAAATCAAAACAGAATTC
1 ATATCAGAAATCAAAACAGAATTC
* * *
126285 ATATCATATATCAGAACAGAAT
1 ATATCAGAAATCAAAACAGAAT
126307 CCAGAACAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (24 bp):
ATATCAGAAATCAAAACAGAATTC
Found at i:126313 original size:12 final size:12
Alignment explanation
Indices: 126296--126329 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
126286 TATCATATAT
126296 CAGAACAGAATC
1 CAGAACAGAATC
*
126308 CAGAACAGAATT
1 CAGAACAGAATC
*
126320 CAGATCAGAA
1 CAGAACAGAA
126330 ATTAGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.12
Consensus pattern (12 bp):
CAGAACAGAATC
Found at i:132345 original size:22 final size:22
Alignment explanation
Indices: 132298--132368 Score: 65
Period size: 22 Copynumber: 3.2 Consensus size: 22
132288 AACAAAAGGC
*
132298 AAAAAGAAAAAAGAAAAGAAAC
1 AAAAAGAAAAAAGAAAAGAAAA
* *
132320 AAAAAGGAAAAA-ATAAGAACAA
1 AAAAAGAAAAAAGAAAAGAA-AA
* *
132342 AAAAAGAAGAACA-AAAATAAAA
1 AAAAAGAA-AAAAGAAAAGAAAA
132364 AAAAA
1 AAAAA
132369 TGGGACAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
21 6 0.15
22 26 0.65
23 8 0.20
ACGTcount: A:0.82, C:0.04, G:0.11, T:0.03
Consensus pattern (22 bp):
AAAAAGAAAAAAGAAAAGAAAA
Found at i:132346 original size:14 final size:14
Alignment explanation
Indices: 132327--132358 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
132317 AACAAAAAGG
*
132327 AAAAAATAAGAACA
1 AAAAAAGAAGAACA
132341 AAAAAAGAAGAACA
1 AAAAAAGAAGAACA
132355 AAAA
1 AAAA
132359 TAAAAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.81, C:0.06, G:0.09, T:0.03
Consensus pattern (14 bp):
AAAAAAGAAGAACA
Found at i:132346 original size:23 final size:22
Alignment explanation
Indices: 132297--132357 Score: 59
Period size: 24 Copynumber: 2.6 Consensus size: 22
132287 GAACAAAAGG
*
132297 CAAAAAGAAAAAAGAAAAGAAA
1 CAAAAAGAAAAAAGAAAACAAA
*
132319 CAAAAAGGAAAAAATAAGAACAAA
1 CAAAAA-GAAAAAAGAA-AACAAA
*
132343 AAAAGAAGAACAAAA
1 CAAA-AAGAA-AAAA
132358 ATAAAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
22 6 0.19
23 9 0.28
24 11 0.34
25 6 0.19
ACGTcount: A:0.79, C:0.07, G:0.13, T:0.02
Consensus pattern (22 bp):
CAAAAAGAAAAAAGAAAACAAA
Found at i:133924 original size:34 final size:36
Alignment explanation
Indices: 133837--133935 Score: 148
Period size: 36 Copynumber: 2.8 Consensus size: 36
133827 ATGCTTACCA
133837 TTGTCTCTCTTGAGACAGTTTCCCTTGAACAAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAACAAAACT
* *
133873 TTGTCTCTCTTGAGACAGTTTCCCTTTAA-AAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAACAAAACT
* *
133908 TTTTCTC-CTTGAGACAGTTTCTCTTGAA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAA
133936 ACATAAACAT
Statistics
Matches: 58, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
34 19 0.33
35 11 0.19
36 28 0.48
ACGTcount: A:0.23, C:0.22, G:0.13, T:0.41
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAACAAAACT
Found at i:134001 original size:36 final size:35
Alignment explanation
Indices: 133954--134038 Score: 100
Period size: 36 Copynumber: 2.4 Consensus size: 35
133944 ATTGAAAACA
** * *
133954 TTTCCCTTGAAATGAGTTT-GTCTCTCTTGAGATAGG
1 TTTCCCTTGAAACAAATTTCGTCTC-CTTGAGACA-G
133990 TTTCCCTTGAAACAAATTTCGTCTCCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCCTTGAGACAG
*
134025 TTTCTCTTGAAACA
1 TTTCCCTTGAAACA
134039 TAACATTGGA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
35 14 0.33
36 24 0.56
37 5 0.12
ACGTcount: A:0.24, C:0.21, G:0.16, T:0.39
Consensus pattern (35 bp):
TTTCCCTTGAAACAAATTTCGTCTCCTTGAGACAG
Found at i:134027 original size:100 final size:97
Alignment explanation
Indices: 133872--134051 Score: 288
Period size: 100 Copynumber: 1.8 Consensus size: 97
133862 TGAACAAAAC
* **
133872 TTTGTCTCTCTTGAGACAGTTTCCCTTTAAAAAATTTTTTCTCCTTGAGACAGTTTCTCTTGAAA
1 TTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAATTTCGTCTCCTTGAGACAGTTTCTCTTGAAA
133937 CATAAACATTGAAAACATTTCCCTTGAAATGAG
66 CAT-AACATTGAAAACATTTCCCTTGAAATGAG
*
133970 TTTGTCTCTCTTGAGATAGGTTTCCCTTGAAACAAATTTCGTCTCCTTGAGACAGTTTCTCTTGA
1 TTTGTCTCTCTTGAGACA-GTTTCCCTTGAAA-AAATTTCGTCTCCTTGAGACAGTTTCTCTTGA
*
134035 AACATAACATTGGAAAC
64 AACATAACATTGAAAAC
134052 CTTGAGACGT
Statistics
Matches: 75, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
98 17 0.23
99 23 0.31
100 35 0.47
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (97 bp):
TTTGTCTCTCTTGAGACAGTTTCCCTTGAAAAAATTTCGTCTCCTTGAGACAGTTTCTCTTGAAA
CATAACATTGAAAACATTTCCCTTGAAATGAG
Found at i:134068 original size:36 final size:37
Alignment explanation
Indices: 134014--134087 Score: 132
Period size: 36 Copynumber: 2.0 Consensus size: 37
134004 AATTTCGTCT
*
134014 CCTTGAGACAGTTTCTCTTGAAACATAACATTGGAAA
1 CCTTGAGACAGTTTCTCTTGAAACATAACATTGAAAA
134051 CCTTGAGAC-GTTTCTCTTGAAACATAACATTGAAAA
1 CCTTGAGACAGTTTCTCTTGAAACATAACATTGAAAA
134087 C
1 C
134088 ATTTCCCTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
36 27 0.75
37 9 0.25
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (37 bp):
CCTTGAGACAGTTTCTCTTGAAACATAACATTGAAAA
Found at i:134087 original size:135 final size:137
Alignment explanation
Indices: 133837--134183 Score: 466
Period size: 135 Copynumber: 2.6 Consensus size: 137
133827 ATGCTTACCA
* * *
133837 TTGTCTCTCTTGAGACAGTTTCCCTTG-AACAAAACTTT-GTCTCTCTTGAGACAGTTTCCCTTT
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA-TTTCGTCTC-CTTGAGACAGTTTCTCTTG
* *****
133900 AAA-A-AA-TTTTTTCTCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTT
64 AAACATAACATTGAAAACCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTT
*
133962 GAAATGAGT
129 GAAATGAAT
133971 TTGTCTCTCTTGAGATAGGTTTCCCTTGAAAC-AAATTTCGTCTCCTTGAGACAGTTTCTCTTGA
1 TTGTCTCTCTTGAGATA-GTTTCCCTTGAAACAAAATTTCGTCTCCTTGAGACAGTTTCTCTTGA
*
134035 AACATAACATTGGAAACCTTGAGAC-GTTTCTCTTGAAACAT-AACATTGAAAACATTTCCCTTG
65 AACATAACATTGAAAACCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTG
134098 AAATGAAT
130 AAATGAAT
*
134106 TTGTCTCTCTT--GATAGTTTCCCTCGAAACAAAATTTC-TC-CCTTGAGACAGTTTCTCTTGAA
1 TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTCGTCTCCTTGAGACAGTTTCTCTTGAA
134167 ACATAAACATTGAAAAC
66 ACAT-AACATTGAAAAC
134184 ATTTCCCTTG
Statistics
Matches: 193, Mismatches: 12, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
131 26 0.13
132 26 0.13
133 11 0.06
134 39 0.20
135 59 0.31
136 21 0.11
137 11 0.06
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (137 bp):
TTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTCGTCTCCTTGAGACAGTTTCTCTTGAA
ACATAACATTGAAAACCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGA
AATGAAT
Found at i:134288 original size:63 final size:65
Alignment explanation
Indices: 134141--134297 Score: 273
Period size: 63 Copynumber: 2.4 Consensus size: 65
134131 AAACAAAATT
*
134141 TCTCCCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCG
1 TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCG
* *
134206 TCTCTCTTGAGATAATTTCTCTTGAAACATAAACATTG-AAA-ATTTCCCTTGAAATGAATTTCG
1 TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCG
134269 TCTCTCTTGAGACAGTTTCTCTTGAAACA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACA
134298 AAATTTTGTC
Statistics
Matches: 87, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
63 49 0.56
64 3 0.03
65 35 0.40
ACGTcount: A:0.31, C:0.20, G:0.12, T:0.36
Consensus pattern (65 bp):
TCTCTCTTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAATTTCG
Found at i:135200 original size:104 final size:106
Alignment explanation
Indices: 135057--135508 Score: 614
Period size: 105 Copynumber: 4.3 Consensus size: 106
135047 GCCATCCGCG
* *
135057 ATTTC-ACTCCACAACGGAGGATATCGTGGCAC-TCGAGAC-ACACAAGTTC-ACTTCACAACGA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTTCGAGACAACACAAGTTCAACTTCACAACGA
* * *
135118 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 AGGGACCGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
135163 ATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCGAGACAACACAAGTTCAACTTCACAACGAAGG
*
135227 GACCGCTGCTTGTCAAAAACAACTTCCCAATTTCAGAGCCA
66 GACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* ** *
135268 ATTTCAACTTCACAACGAAGGATATTGGAC-TCCAGACAATGCAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCGAGACAACACAAGTTCAACTTCACAACGAAGG
*
135332 GACCGCTGCTTGTCAACAAC-ACTTCCCAATCTCAGAGCCA
66 GACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
135372 ATTTCAACTTCACGACGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCGAGACAACACAAGTTCAACTTCACAACGAAGG
* * * ** *
135436 GACGGCTGGTTGTCAACAACAATTTCCCGGTTCCAGAGCCA
66 GACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
135477 ATTTCAACTTCACGACGGAGGATATTGGACTT
1 ATTTCAACTTCACAACGAAGGATATTGGACTT
135509 GGAACAATGC
Statistics
Matches: 315, Mismatches: 24, Indels: 14
0.89 0.07 0.04
Matches are distributed among these distances:
104 104 0.33
105 160 0.51
106 34 0.11
107 17 0.05
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.22
Consensus pattern (106 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTTCGAGACAACACAAGTTCAACTTCACAACGAAGG
GACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:135392 original size:209 final size:209
Alignment explanation
Indices: 135057--135507 Score: 633
Period size: 209 Copynumber: 2.1 Consensus size: 209
135047 GCCATCCGCG
* *
135057 ATTTC-ACTCCACAACGGAGGATATCGTGGCACTCGAGACACACAAGTTCACTTCACAACGAAGG
1 ATTTCAACTTCACAACGGAGGATAT--TGG-ACTCCAGACACACAAGTTCACTTCACAACGAAGG
* * * *
135121 GACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
63 GACCGCTGCTTGTCAACAAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* *
135186 ATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAAAACAAC
128 ATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAAAACAAC
*
135250 TTCCCAATTTCAGAGCCA
192 TTCCCAATTCCAGAGCCA
* *
135268 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACA-ATGCAAGTTCAACTTCACGACGAAGG
1 ATTTCAACTTCACAACGGAGGATATTGGACTCCAGACACA--CAAGTTC-ACTTCACAACGAAGG
*
135332 GACCGCTGCTTGTCAAC-AAC-ACTTCCCAATCTCAGAGCCAATTTCAACTTCACGACGAAGGAT
63 GACCGCTGCTTGTCAACAAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGAT
* * * *
135395 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAACAATT
128 ATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAAAACAACT
**
135460 TCCCGGTTCCAGAGCCA
193 TCCCAATTCCAGAGCCA
*
135477 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGGAGGATATTGGACT
135508 TGGAACAATG
Statistics
Matches: 215, Mismatches: 20, Indels: 12
0.87 0.08 0.05
Matches are distributed among these distances:
208 3 0.01
209 148 0.69
210 13 0.06
211 34 0.16
212 17 0.08
ACGTcount: A:0.33, C:0.27, G:0.19, T:0.22
Consensus pattern (209 bp):
ATTTCAACTTCACAACGGAGGATATTGGACTCCAGACACACAAGTTCACTTCACAACGAAGGGAC
CGCTGCTTGTCAACAAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATT
GGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACCGCTGCTTGTCAAAAACAACTTCC
CAATTCCAGAGCCA
Found at i:136093 original size:32 final size:34
Alignment explanation
Indices: 136056--136186 Score: 144
Period size: 32 Copynumber: 3.8 Consensus size: 34
136046 TTTCGTCCTA
136056 CTAGGATTCAAACTCCTAAAAATAGGATA-ATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATACATTT
136089 -TAGGATTCAAACTCCTAAAAATA-GATAACATTT
1 CTAGGATTCAAACTCCTAAAAATAGGAT-ACATTT
*
136122 GCTAGGATTC-AACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATACA-TT-T
* * * *
136158 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
136187 CCACAAGCAC
Statistics
Matches: 84, Mismatches: 6, Indels: 12
0.82 0.06 0.12
Matches are distributed among these distances:
31 3 0.04
32 24 0.29
33 4 0.05
34 16 0.19
35 13 0.15
36 8 0.10
37 16 0.19
ACGTcount: A:0.42, C:0.15, G:0.14, T:0.30
Consensus pattern (34 bp):
CTAGGATTCAAACTCCTAAAAATAGGATACATTT
Found at i:136647 original size:42 final size:43
Alignment explanation
Indices: 136588--136687 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
136578 TTATATGTAT
* * * *
136588 ATATATATTAAAT-TATTTTCATTTGAT-TTTTAC-TATATTTTA
1 ATAT-TATTATATATATTTTC-TTTAATATTTTACTTATAGTCTA
*
136630 TTATTATTATATATA-TTTCTTTAATATTTTACTTATAGTCTA
1 ATATTATTATATATATTTTCTTTAATATTTTACTTATAGTCTA
*
136672 ATATTACTATATATAT
1 ATATTATTATATATAT
136688 ATTAAATTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
40 5 0.11
41 17 0.36
42 25 0.53
ACGTcount: A:0.34, C:0.06, G:0.02, T:0.58
Consensus pattern (43 bp):
ATATTATTATATATATTTTCTTTAATATTTTACTTATAGTCTA
Found at i:138075 original size:16 final size:17
Alignment explanation
Indices: 138046--138087 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
138036 GGTCAACACC
* *
138046 GGTCAACAGTCAACG-G
1 GGTCAACGGCCAACGCG
*
138062 GGTCAACGGCCAACGCT
1 GGTCAACGGCCAACGCG
138079 GGTCAACGG
1 GGTCAACGG
138088 GTCGGGTCAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.26, C:0.29, G:0.33, T:0.12
Consensus pattern (17 bp):
GGTCAACGGCCAACGCG
Found at i:148331 original size:18 final size:18
Alignment explanation
Indices: 148308--148344 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
148298 TCGGTACTGA
*
148308 TGCAATTAGTATCGATAC
1 TGCAATGAGTATCGATAC
*
148326 TGCAATGGGTATCGATAC
1 TGCAATGAGTATCGATAC
148344 T
1 T
148345 AGGAGGAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (18 bp):
TGCAATGAGTATCGATAC
Found at i:150655 original size:23 final size:23
Alignment explanation
Indices: 150629--150715 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 23
150619 GGGGATCTTG
150629 TTAATTTTATTAATTATTATTAT
1 TTAATTTTATTAATTATTATTAT
*
150652 TTAATTATTATTTCTATTTCTATTATTATT
1 TTAATT-TTA--T-TA-AT-TATTATTA-T
150682 TTAA-TTT-TTAATTTATTATATAT
1 TTAATTTTATTAA-TTATTAT-TAT
*
150705 TTATTTTTATT
1 TTAATTTTATT
150716 TCTACAGGCC
Statistics
Matches: 50, Mismatches: 3, Indels: 20
0.68 0.04 0.27
Matches are distributed among these distances:
23 16 0.32
24 11 0.22
25 3 0.06
26 1 0.02
27 2 0.04
28 3 0.06
29 9 0.18
30 5 0.10
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (23 bp):
TTAATTTTATTAATTATTATTAT
Found at i:150688 original size:18 final size:16
Alignment explanation
Indices: 150632--150716 Score: 64
Period size: 17 Copynumber: 4.9 Consensus size: 16
150622 GATCTTGTTA
150632 ATTTTATTAATTATTATT
1 ATTTTATT-ATTATT-TT
*
150650 ATTTAATTATTATTTCT
1 ATTTTATTATTATTT-T
150667 ATTTCTATTATTATTTT
1 ATTT-TATTATTATTTT
* *
150684 AATTTT-TAATTTATTAT
1 -ATTTTATTA-TTATTTT
*
150701 ATATTTATTTTTATTT
1 AT-TTTATTATTATTT
150717 CTACAGGCCC
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
16 5 0.09
17 27 0.50
18 22 0.41
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.68
Consensus pattern (16 bp):
ATTTTATTATTATTTT
Found at i:150698 original size:29 final size:29
Alignment explanation
Indices: 150643--150698 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
150633 TTTTATTAAT
*
150643 TATTATTATTTAATTATTATTTCTATTTC
1 TATTATTATTTAATTATTAATTCTATTTC
*
150672 TATTATTATTTTAATTTTTAATT-TATT
1 TATTATTA-TTTAATTATTAATTCTATT
150699 ATATATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 12 0.50
30 12 0.50
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.68
Consensus pattern (29 bp):
TATTATTATTTAATTATTAATTCTATTTC
Found at i:150757 original size:25 final size:25
Alignment explanation
Indices: 150723--150780 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
150713 ATTTCTACAG
150723 GCCCAAATTACAACAAATACTCCCA
1 GCCCAAATTACAACAAATACTCCCA
150748 GCCCAAATTACAACAAATACTCCCA
1 GCCCAAATTACAACAAATACTCCCA
150773 GCCCAAAT
1 GCCCAAAT
150781 CGGGCCCCAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.43, C:0.36, G:0.05, T:0.16
Consensus pattern (25 bp):
GCCCAAATTACAACAAATACTCCCA
Found at i:151872 original size:108 final size:108
Alignment explanation
Indices: 151723--151923 Score: 280
Period size: 108 Copynumber: 1.9 Consensus size: 108
151713 GATGCGATAG
*
151723 CCAAAGTTGCTATTTACCCATTTCCATGCATGTTATATATTTTT-GAGATATTTATTGTTTAGTC
1 CCAAAGTAGCTATTTACCCATTTCCATGCATGTTATATATTTTTGGA-ATATTTATTGTTTAGTC
*
151787 CCCCAAAGTTTA-GCGTGTTTTTGCATTTTGGTCACCTATAGGGA
65 CCCCAAA-TTCAGGCGTGTTTTTGCATTTTGGTCACCTATAGGGA
* * * * * *
151831 CCAAAGTAGTTATTTACCCGTTTTCATGCATTTTATGTATTTTTGGAATATTTGTTGTTTAGTCC
1 CCAAAGTAGCTATTTACCCATTTCCATGCATGTTATATATTTTTGGAATATTTATTGTTTAGTCC
**
151896 CCCTTATTCAGGCGTGTTTTTGCATTTT
66 CCCAAATTCAGGCGTGTTTTTGCATTTT
151924 AATCATGTGT
Statistics
Matches: 81, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
107 3 0.04
108 76 0.94
109 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.16, T:0.46
Consensus pattern (108 bp):
CCAAAGTAGCTATTTACCCATTTCCATGCATGTTATATATTTTTGGAATATTTATTGTTTAGTCC
CCCAAATTCAGGCGTGTTTTTGCATTTTGGTCACCTATAGGGA
Found at i:153003 original size:131 final size:131
Alignment explanation
Indices: 152762--153152 Score: 570
Period size: 131 Copynumber: 3.0 Consensus size: 131
152752 ATAAACAACA
* *
152762 CTCGAATTAATATCGAATTTTGGGACGAAATAGTAATATCTCTTCATTTCAATTGAAGTAATAAA
1 CTCGAATTAATATTGAATTTTGGGACGAAATAGTAATATCTCTTCATTTCGATTGAAGTAATAAA
* *
152827 TGACTTCTTTAAGGCATGAGAGGTCATTTATTCTCAATTGGAAATAATTAGATATTATCATTTTC
66 TGACTTCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATTATTTTC
152892 T
131 T
* * * *
152893 CTCTAATTAATATTGAATTTCGGGACGAAATAATAATATATCTTCATTTCGATTGAAGTAATAAA
1 CTCGAATTAATATTGAATTTTGGGACGAAATAGTAATATCTCTTCATTTCGATTGAAGTAATAAA
* * *** *
152958 TGACTACTTTAAGGCATGAGAAGTCATTTATTCTCGATAAAAAATAATTAGATATTATTGTTTTC
66 TGACTTCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATTATTTTC
153023 T
131 T
* * **
153024 CTCGAATTAATATTGAATTTTAGGACGAAATAGTACTATCTCATT-ATTTCGATTGGTGTAATAA
1 CTCGAATTAATATTGAATTTTGGGACGAAATAGTAATATCTC-TTCATTTCGATTGAAGTAATAA
* *
153088 AT-AGTTTCTTTAAGGCATGAGAGGTCATTTATTCTGGATTGGAAATAATTAGATATTATTATTT
65 ATGA-CTTCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATTATTT
153152 T
129 T
153153 TTTCTCTTAA
Statistics
Matches: 228, Mismatches: 30, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
130 1 0.00
131 225 0.99
132 2 0.01
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (131 bp):
CTCGAATTAATATTGAATTTTGGGACGAAATAGTAATATCTCTTCATTTCGATTGAAGTAATAAA
TGACTTCTTTAAGGCATGAGAGGTCATTTATTCTCGATTGGAAATAATTAGATATTATTATTTTC
T
Found at i:164958 original size:134 final size:135
Alignment explanation
Indices: 164658--164969 Score: 346
Period size: 138 Copynumber: 2.3 Consensus size: 135
164648 GAAAATCAAA
* * * *
164658 CTCGATTCAATCTTCCCTGAAGAACAGTGGAATGAATCAATATTTCTGGATCTGATTTTCCTTGA
1 CTCGATTCAATCTTCCCTGAAGAAAAGTGGAATGAATCAATATTTCTAGATCTGATTTACCCTGA
* * ** * *
164723 AGAAGTATTGGAGAAGATCCCATTTCTTTTTCCAAATTTGATCTTCCCTGAAGAACTAGTGGAAC
66 AAAAATAGCGGAGAAGATCCC---TCTTTTTCCAAATTTGATATTCCCTGAAGAACTAATGGAAC
164788 AAGTCTTC
128 AAGTCTTC
* * *
164796 CTCGATTCAATTTTCCCTGAAGATAAGTGGAATGAATCAATGTTTCTAGATCTG-TTCTACCCTG
1 CTCGATTCAATCTTCCCTGAAGAAAAGTGGAATGAATCAATATTTCTAGATCTGATT-TACCCTG
* * * * *
164860 AAAAAAATAGCGGAGCAGATCCC-CTTTTTCTAGATTTGATATTCTCTG-AGTAGC-AATGGAAC
65 -AAAAAATAGCGGAGAAGATCCCTCTTTTTCCAAATTTGATATTCCCTGAAG-AACTAATGGAAC
164922 AAGT-TTAC
128 AAGTCTT-C
* *
164930 CTCGATTTAATCTTCCTTGAAGAAAAGTGGAATGAATCAA
1 CTCGATTCAATCTTCCCTGAAGAAAAGTGGAATGAATCAA
164970 CACTTCCAAA
Statistics
Matches: 148, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
133 2 0.01
134 50 0.34
135 23 0.16
137 2 0.01
138 54 0.36
139 17 0.11
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.33
Consensus pattern (135 bp):
CTCGATTCAATCTTCCCTGAAGAAAAGTGGAATGAATCAATATTTCTAGATCTGATTTACCCTGA
AAAAATAGCGGAGAAGATCCCTCTTTTTCCAAATTTGATATTCCCTGAAGAACTAATGGAACAAG
TCTTC
Found at i:165241 original size:11 final size:11
Alignment explanation
Indices: 165215--165263 Score: 57
Period size: 11 Copynumber: 4.6 Consensus size: 11
165205 TTAATTATTA
*
165215 TTATTTAATAT
1 TTATTTTATAT
165226 TT-TTTTAT-T
1 TTATTTTATAT
165235 TTATTTTATAT
1 TTATTTTATAT
* *
165246 TTATATTATCT
1 TTATTTTATAT
165257 TTATTTT
1 TTATTTT
165264 TTTATTTTTG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 3 0.09
10 11 0.34
11 18 0.56
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (11 bp):
TTATTTTATAT
Found at i:165374 original size:22 final size:23
Alignment explanation
Indices: 165333--165385 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
165323 AAAGCTAACT
165333 GGCCCAAACAGAAATCCAAACCAA
1 GGCCCAAACAG-AATCCAAACCAA
*
165357 GGCCCAAACAG-ATCCAAACCCA
1 GGCCCAAACAGAATCCAAACCAA
*
165379 TGCCCAA
1 GGCCCAA
165386 CTACCAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 16 0.59
24 11 0.41
ACGTcount: A:0.43, C:0.38, G:0.13, T:0.06
Consensus pattern (23 bp):
GGCCCAAACAGAATCCAAACCAA
Found at i:166401 original size:109 final size:110
Alignment explanation
Indices: 166259--166462 Score: 295
Period size: 109 Copynumber: 1.9 Consensus size: 110
166249 TGCGAGGTCT
* * *
166259 AAAGTTGTTATTTACCCGTTTTCATGCATGTTATATATTT-TTTAGTATATTTTTTGTTTAGTCC
1 AAAGTTCTTATTTACCCATTTTCATGCATGTTATATATTTGTTTAGAATATTTTTTGTTTAGTCC
*
166323 CCCATGGTTTA-GCGTGTTTTTGAATTTTGGGCACATGTAGGTACC
66 CCC-TGATTTAGGCGTGTTTTTGAATTTTGGGCACATGTAGGTACC
* * **
166368 AAAGTTCTTATTTACCCATTTTCATGCATGTTATGTATTTGTTTGGAATATTTTTTGTTTAGTTT
1 AAAGTTCTTATTTACCCATTTTCATGCATGTTATATATTTGTTTAGAATATTTTTTGTTTAGTCC
* *
166433 CCCTTATTTAGGCGTGTTTTTGTATTTTGG
66 CCCTGATTTAGGCGTGTTTTTGAATTTTGG
166463 TCATGTGTAA
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
109 42 0.51
110 41 0.49
ACGTcount: A:0.19, C:0.12, G:0.18, T:0.51
Consensus pattern (110 bp):
AAAGTTCTTATTTACCCATTTTCATGCATGTTATATATTTGTTTAGAATATTTTTTGTTTAGTCC
CCCTGATTTAGGCGTGTTTTTGAATTTTGGGCACATGTAGGTACC
Found at i:167764 original size:131 final size:131
Alignment explanation
Indices: 167521--167869 Score: 472
Period size: 131 Copynumber: 2.7 Consensus size: 131
167511 ATAAATAACA
** *
167521 CTCGAATTAATATCAAATTTTGGGAAGAAATAGTAATATCTCTTCATTTCAATTGAAGAAATAAA
1 CTCGAATTAATATTGAATTTTGGGAAGAAATAGTAATATCTCTTCATTTCAATTGAAGTAATAAA
* * *
167586 TGATTGCTTTAAGGCATGTGAGCTCATTTATTCTCAATCAGATATAATTAGATA-TCATCATTTT
66 TGATTGCCTTAAGGCATGAGAGCTCATTTATTCTCAATCAGAAATAATTAGATACT-ATCATTTT
167650 CT
130 CT
* *
167652 CTCGAATTAATATTGAATTTTGGGAAGAAATAGTAATATCTCTTCATTTCTACTGAAGTAATAAA
1 CTCGAATTAATATTGAATTTTGGGAAGAAATAGTAATATCTCTTCATTTCAATTGAAGTAATAAA
* * * * *
167717 TGATTGCCTTAAGGCGTGAGAGTTCATTTATTCTCGAT-TGAAAATAATTAGATACTATCGTTTT
66 TGATTGCCTTAAGGCATGAGAGCTCATTTATTCTCAATCAG-AAATAATTAGATACTATCATTTT
167781 CT
130 CT
* * *
167783 CTCGAATTAATATTGAATTTTAGGATA-AAATAATAATATCTCTTCATTTCAATTGGAGTAATAA
1 CTCGAATTAATATTGAATTTTGGGA-AGAAATAGTAATATCTCTTCATTTCAATTGAAGTAATAA
**
167847 AT-AGTTGTTTTAAGGCATGAGAG
65 ATGA-TTGCCTTAAGGCATGAGAG
167870 ATGTAACATC
Statistics
Matches: 193, Mismatches: 21, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
130 2 0.01
131 189 0.98
132 2 0.01
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.38
Consensus pattern (131 bp):
CTCGAATTAATATTGAATTTTGGGAAGAAATAGTAATATCTCTTCATTTCAATTGAAGTAATAAA
TGATTGCCTTAAGGCATGAGAGCTCATTTATTCTCAATCAGAAATAATTAGATACTATCATTTTC
T
Found at i:169426 original size:20 final size:21
Alignment explanation
Indices: 169387--169426 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
169377 GATATAAGCC
169387 ATGTGATATGTGACATATGATT
1 ATGTGATA-GTGACATATGATT
*
169409 ATGTGATA-TGAGATATGA
1 ATGTGATAGTGACATATGA
169427 GACTCCATGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
22 8 0.47
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.38
Consensus pattern (21 bp):
ATGTGATAGTGACATATGATT
Found at i:169625 original size:21 final size:21
Alignment explanation
Indices: 169592--169631 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
169582 TTCTACGTGG
*
169592 TCCTTCGGGACATATATGTAA
1 TCCTTCGGAACATATATGTAA
*
169613 TCCTTTGGAACATATATGT
1 TCCTTCGGAACATATATGT
169632 GGTACTTCGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (21 bp):
TCCTTCGGAACATATATGTAA
Found at i:172991 original size:7 final size:7
Alignment explanation
Indices: 172979--173039 Score: 59
Period size: 7 Copynumber: 8.4 Consensus size: 7
172969 GATATAAGCC
172979 ATGTGAT
1 ATGTGAT
172986 ATGTGAT
1 ATGTGAT
*
172993 ATGTGAC
1 ATGTGAT
*
173000 ATGCGATT
1 ATGTGA-T
173008 ATGTGAT
1 ATGTGAT
*
173015 ATGAGAT
1 ATGTGAT
*
173022 ATATGAT
1 ATGTGAT
*
173029 AATGAGAT
1 -ATGTGAT
173037 ATG
1 ATG
173040 AGACTCCATG
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
7 33 0.77
8 10 0.23
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (7 bp):
ATGTGAT
Found at i:173035 original size:15 final size:14
Alignment explanation
Indices: 172982--173038 Score: 51
Period size: 15 Copynumber: 3.9 Consensus size: 14
172972 ATAAGCCATG
* *
172982 TGATATGTGATATG
1 TGATATGAGATATA
* * *
172996 TGACATGCGATTATG
1 TGATATGAGA-TATA
173011 TGATATGAGATATA
1 TGATATGAGATATA
173025 TGATAATGAGATAT
1 TGAT-ATGAGATAT
173039 GAGACTCCAT
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
14 15 0.42
15 21 0.58
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (14 bp):
TGATATGAGATATA
Found at i:173039 original size:29 final size:29
Alignment explanation
Indices: 172979--173036 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
172969 GATATAAGCC
* * * *
172979 ATGTGATATGTGATATGTGACATGCGATT
1 ATGTGATATGAGATATATGAAATGAGATT
173008 ATGTGATATGAGATATATGATAATGAGAT
1 ATGTGATATGAGATATATGA-AATGAGAT
173037 ATGAGACTCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (29 bp):
ATGTGATATGAGATATATGAAATGAGATT
Found at i:173222 original size:21 final size:21
Alignment explanation
Indices: 173197--173248 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 21
173187 AGTCGAGGGT
**
173197 TATATGTGGTCATTTGGGGCA
1 TATATGTGGTCATTTGGAACA
** *
173218 TATATGTAATCCTTTGGAACA
1 TATATGTGGTCATTTGGAACA
173239 TATATGTGGT
1 TATATGTGGT
173249 ACTTCGGTAC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.40
Consensus pattern (21 bp):
TATATGTGGTCATTTGGAACA
Found at i:174016 original size:16 final size:17
Alignment explanation
Indices: 173989--174022 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
173979 TTCTTCATTC
173989 TTTTGTAAAAGTAAATG
1 TTTTGTAAAAGTAAATG
*
174006 TTTTG-AAAAGTCAATG
1 TTTTGTAAAAGTAAATG
174022 T
1 T
174023 GACACCTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.38, C:0.03, G:0.18, T:0.41
Consensus pattern (17 bp):
TTTTGTAAAAGTAAATG
Found at i:180332 original size:2 final size:2
Alignment explanation
Indices: 180327--180354 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
180317 TTTTATAAAT
180327 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
180355 AACTCGAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:182092 original size:31 final size:30
Alignment explanation
Indices: 182067--182150 Score: 109
Period size: 30 Copynumber: 2.8 Consensus size: 30
182057 GGGCCTGAAA
*
182067 GCCTACCCAAGAAAGTTCTCAGGGCC-ACGGG
1 GCCTACCCAAGAAAGATCTCAGGGCCGA--GG
182098 GCCTA-CCAAGAAAGATCTCAGGGCCGCAGG
1 GCCTACCCAAGAAAGATCTCAGGGCCG-AGG
*
182128 GCCTACCCAAGAATGATCTCAGG
1 GCCTACCCAAGAAAGATCTCAGG
182151 ACCACAGGGC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
30 26 0.54
31 21 0.44
32 1 0.02
ACGTcount: A:0.29, C:0.31, G:0.27, T:0.13
Consensus pattern (30 bp):
GCCTACCCAAGAAAGATCTCAGGGCCGAGG
Found at i:182159 original size:31 final size:31
Alignment explanation
Indices: 182067--182165 Score: 137
Period size: 31 Copynumber: 3.2 Consensus size: 31
182057 GGGCCTGAAA
* *
182067 GCCTACCCAAGAAAGTTCTCAGGGCCACGGG
1 GCCTACCCAAGAAAGATCTCAGGGCCACAGG
*
182098 GCCTA-CCAAGAAAGATCTCAGGGCCGCAGG
1 GCCTACCCAAGAAAGATCTCAGGGCCACAGG
* *
182128 GCCTACCCAAGAATGATCTCAGGACCACAGG
1 GCCTACCCAAGAAAGATCTCAGGGCCACAGG
*
182159 GCGTACC
1 GCCTACC
182166 TACCCAAGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 27 0.45
31 33 0.55
ACGTcount: A:0.28, C:0.32, G:0.27, T:0.12
Consensus pattern (31 bp):
GCCTACCCAAGAAAGATCTCAGGGCCACAGG
Found at i:187050 original size:31 final size:31
Alignment explanation
Indices: 187015--187190 Score: 109
Period size: 31 Copynumber: 5.7 Consensus size: 31
187005 GAACAACTTG
* *
187015 GGGCCTGAGAGCCTACCCAAGAAAGT-TCTTA
1 GGGCCTAAGAGCCTACCCAAGAAA-TATCTCA
*
187046 GGGCC-ACAGGGCCTACCCAAGAAATATCTCA
1 GGGCCTA-AGAGCCTACCCAAGAAATATCTCA
*
187077 GGGCCGTAAGA-CCTACCCAAG-AATGATTTCA
1 GGGCC-TAAGAGCCTACCCAAGAAAT-ATCTCA
* * *
187108 GGGCC-ACGAGTCTACCCAAGAAAAATC-CTA
1 GGGCCTAAGAGCCTACCCAAGAAATATCTC-A
* * * *
187138 -GGACTGCAGGGCCTACCCAAG-AATGATCTCG
1 GGGCCT-AAGAGCCTACCCAAGAAAT-ATCTCA
*
187169 GGGTC-ACAGAGCCTACCCAAGA
1 GGGCCTA-AGAGCCTACCCAAGA
187191 GTCACATTAG
Statistics
Matches: 111, Mismatches: 19, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
29 7 0.06
30 18 0.16
31 79 0.71
32 6 0.05
33 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.15
Consensus pattern (31 bp):
GGGCCTAAGAGCCTACCCAAGAAATATCTCA
Found at i:187934 original size:14 final size:14
Alignment explanation
Indices: 187915--187950 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
187905 CGAATTATCA
187915 AACAACTCGAGTTG
1 AACAACTCGAGTTG
187929 AACAACTCGAGTTG
1 AACAACTCGAGTTG
187943 AACAACTC
1 AACAACTC
187951 ATAGAACAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (14 bp):
AACAACTCGAGTTG
Found at i:187959 original size:12 final size:14
Alignment explanation
Indices: 187915--187959 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
187905 CGAATTATCA
*
187915 AACAACTCGAGTTG
1 AACAACTCGAGTAG
*
187929 AACAACTCGAGTTG
1 AACAACTCGAGTAG
187943 AACAACTC-A-TAG
1 AACAACTCGAGTAG
187955 AACAA
1 AACAA
187960 ATGCTTGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 7 0.23
13 1 0.03
14 22 0.73
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (14 bp):
AACAACTCGAGTAG
Found at i:188445 original size:19 final size:19
Alignment explanation
Indices: 188421--188460 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
188411 TCATCGATCG
188421 AAACTTGAGGATACGAACA
1 AAACTTGAGGATACGAACA
188440 AAACTTGAGGATACGAACA
1 AAACTTGAGGATACGAACA
188459 AA
1 AA
188461 CATTCAAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.50, C:0.15, G:0.20, T:0.15
Consensus pattern (19 bp):
AAACTTGAGGATACGAACA
Found at i:189339 original size:160 final size:160
Alignment explanation
Indices: 189075--189399 Score: 632
Period size: 160 Copynumber: 2.0 Consensus size: 160
189065 TAATTATCAT
*
189075 TTAGAGATCACAGGTTTAATTGCTTTCTCGGATATTCTCTGAACTTGAAATGATTCCTTATCAAA
1 TTAGAGATCACAGGTTTAATTGCTATCTCGGATATTCTCTGAACTTGAAATGATTCCTTATCAAA
189140 CTTCTAGTATCTTTTACATACCCTCTTGAGGTTAAAAATCGGTTATAAGATTTTCTAAGCAAAAC
66 CTTCTAGTATCTTTTACATACCCTCTTGAGGTTAAAAATCGGTTATAAGATTTTCTAAGCAAAAC
189205 TAGTATTTTCTATGCACTTCAGTAGTTTCA
131 TAGTATTTTCTATGCACTTCAGTAGTTTCA
*
189235 TTAGAGATCATAGGTTTAATTGCTATCTCGGATATTCTCTGAACTTGAAATGATTCCTTATCAAA
1 TTAGAGATCACAGGTTTAATTGCTATCTCGGATATTCTCTGAACTTGAAATGATTCCTTATCAAA
189300 CTTCTAGTATCTTTTACATACCCTCTTGAGGTTAAAAATCGGTTATAAGATTTTCTAAGCAAAAC
66 CTTCTAGTATCTTTTACATACCCTCTTGAGGTTAAAAATCGGTTATAAGATTTTCTAAGCAAAAC
189365 TAGTATTTTCTATGCACTTCAGTAGTTTCA
131 TAGTATTTTCTATGCACTTCAGTAGTTTCA
189395 TTAGA
1 TTAGA
189400 TCAATATGTC
Statistics
Matches: 163, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
160 163 1.00
ACGTcount: A:0.30, C:0.17, G:0.14, T:0.39
Consensus pattern (160 bp):
TTAGAGATCACAGGTTTAATTGCTATCTCGGATATTCTCTGAACTTGAAATGATTCCTTATCAAA
CTTCTAGTATCTTTTACATACCCTCTTGAGGTTAAAAATCGGTTATAAGATTTTCTAAGCAAAAC
TAGTATTTTCTATGCACTTCAGTAGTTTCA
Found at i:190995 original size:30 final size:32
Alignment explanation
Indices: 190959--191025 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
190949 CAAAGGTGGC
*
190959 TCTCTTTTC-CCT-TTTTTTTTGTTTGGTTGT
1 TCTCTTTTCTCCTATTTTTTTTGTTTCGTTGT
** *
190989 TCTCTTTTCTTTTATTTTTTTTGTTTCTTTGT
1 TCTCTTTTCTCCTATTTTTTTTGTTTCGTTGT
191021 TCTCT
1 TCTCT
191026 CTCGTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
30 9 0.29
31 1 0.03
32 21 0.68
ACGTcount: A:0.01, C:0.16, G:0.09, T:0.73
Consensus pattern (32 bp):
TCTCTTTTCTCCTATTTTTTTTGTTTCGTTGT
Found at i:192032 original size:134 final size:134
Alignment explanation
Indices: 191808--192249 Score: 542
Period size: 134 Copynumber: 3.3 Consensus size: 134
191798 TCGAGAAATG
* * * * * *
191808 TTGACTCATTCCACTTTTCTTCAGGGAAGATTGAATCCAGGTAGATTTGTTCCACTGTCATTTAG
1 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTTAG
* * * * *
191873 AGAATATCAAATCTTCAAAGAGAGGGATTTGTTTTGCTTCTTCTTCAGGGAAAATCAGATCTGGG
66 GGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGG
191938 GACT
131 GACT
* * * * *
191942 TTGATTCATTTCACTATTCTTGAGGGAAGATTTAATCGAGGCAGACTTGTTCCACTGTTACTTAG
1 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTTAG
** * *
192007 GGAATATCAAATCTTGAAAGAGAGGGACCTGTTTCGCTTCTTCTTGAGGGAAAATTAGATTTGGG
66 GGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGG
192072 GACT
131 GACT
* * * * * * *
192076 TTGATTCATTCTATTGTTCTTCAGGGAATACTGAATCAAGGTAGACTTGTTCCACTATTACTCAG
1 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTTAG
* ** * * * * * *
192141 GGAATATCAAATCTTGAAAAAGAGAAATATGATCCACTTCTTCTTGAGAGAAAATCAGGTCTAGG
66 GGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGG
*
192206 GACG
131 GACT
*
192210 ATGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG
1 TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAG
192250 TTCGATTTGC
Statistics
Matches: 258, Mismatches: 50, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
134 258 1.00
ACGTcount: A:0.29, C:0.16, G:0.21, T:0.33
Consensus pattern (134 bp):
TTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGTAGACTTGTTCCACTGTTACTTAG
GGAATATCAAATCTTGAAAGAGAGGGATATGTTTCGCTTCTTCTTGAGGGAAAATCAGATCTGGG
GACT
Found at i:193519 original size:9 final size:9
Alignment explanation
Indices: 193505--193583 Score: 66
Period size: 8 Copynumber: 9.4 Consensus size: 9
193495 TATTTTTCCT
193505 TTTTCTTTC
1 TTTTCTTTC
193514 TTTTCTTTC
1 TTTTCTTTC
*
193523 TTTT-TCTC
1 TTTTCTTTC
193531 TTTTC--TC
1 TTTTCTTTC
*
193538 TTTT-TTCC
1 TTTTCTTTC
193546 TTTTCTTT-
1 TTTTCTTTC
193554 TCTTT-TTTC
1 T-TTTCTTTC
193563 ATTTTCTTTC
1 -TTTTCTTTC
193573 -TTTCTTT-
1 TTTTCTTTC
193580 TTTT
1 TTTT
193584 ATTTTTTTTA
Statistics
Matches: 58, Mismatches: 3, Indels: 19
0.73 0.04 0.24
Matches are distributed among these distances:
7 6 0.10
8 26 0.45
9 21 0.36
10 5 0.09
ACGTcount: A:0.01, C:0.20, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:193524 original size:13 final size:13
Alignment explanation
Indices: 193506--193580 Score: 77
Period size: 13 Copynumber: 5.9 Consensus size: 13
193496 ATTTTTCCTT
193506 TTTCTTTCTTTTC
1 TTTCTTTCTTTTC
*
193519 TTTCTTT-TTCTC
1 TTTCTTTCTTTTC
*
193531 TTT-TCTCTTTT-
1 TTTCTTTCTTTTC
*
193542 TTCCTTTTCTTTTC
1 TTTC-TTTCTTTTC
193556 TTT-TTTCATTTTC
1 TTTCTTTC-TTTTC
193569 TTTCTTTCTTTT
1 TTTCTTTCTTTT
193581 TTTATTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
11 4 0.08
12 14 0.28
13 26 0.52
14 6 0.12
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTCTTTCTTTTC
Found at i:193526 original size:26 final size:25
Alignment explanation
Indices: 193497--193581 Score: 91
Period size: 27 Copynumber: 3.2 Consensus size: 25
193487 GTTTATTCTA
193497 TTTTTCCTTTTTCTTTCTTTTCTTTC
1 TTTTTCCTTTTTCTTT-TTTTCTTTC
*
193523 TTTTTCTCTTTTCTCTTTTTTCCTTT-
1 TTTTTC-CTTTT-TCTTTTTTTCTTTC
*
193549 TCTTTTCTTTTTTCATTTTCTTTCTTTC
1 T-TTTTCCTTTTTC-TTTT-TTTCTTTC
193577 TTTTT
1 TTTTT
193582 TTATTTTTTT
Statistics
Matches: 50, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
25 2 0.04
26 15 0.30
27 27 0.54
28 6 0.12
ACGTcount: A:0.01, C:0.21, G:0.00, T:0.78
Consensus pattern (25 bp):
TTTTTCCTTTTTCTTTTTTTCTTTC
Found at i:193532 original size:17 final size:17
Alignment explanation
Indices: 193512--193575 Score: 80
Period size: 17 Copynumber: 3.8 Consensus size: 17
193502 CCTTTTTCTT
193512 TCTTTTCTTTCTTTTTC
1 TCTTTTCTTTCTTTTTC
*
193529 TCTTTTCTCT-TTTTTC
1 TCTTTTCTTTCTTTTTC
193545 -CTTTTCTTTTCTTTTT-
1 TCTTTTC-TTTCTTTTTC
193561 TCATTTTCTTTCTTT
1 TC-TTTTCTTTCTTT
193576 CTTTTTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
15 6 0.15
16 8 0.20
17 22 0.54
18 5 0.12
ACGTcount: A:0.02, C:0.22, G:0.00, T:0.77
Consensus pattern (17 bp):
TCTTTTCTTTCTTTTTC
Found at i:193548 original size:42 final size:40
Alignment explanation
Indices: 193492--193604 Score: 110
Period size: 40 Copynumber: 2.9 Consensus size: 40
193482 CTTTTGTTTA
* *
193492 TTCTATTTTTCCTTTT-TCTTTCTTTTCTTTCTTTTTCTCT-T
1 TTCTTTTTTTCCTTTTCT-TTTC-TTT-TTTCATTTTCTCTCT
*
193533 TTCTCTTTTTTCCTTTTCTTTTCTTTTTTCATTTTCTTTCT
1 TTCT-TTTTTTCCTTTTCTTTTCTTTTTTCATTTTCTCTCT
* *
193574 TTCTTTTTTT-ATTTT-TTTT-ATTTTTCATTTT
1 TTCTTTTTTTCCTTTTCTTTTCTTTTTTCATTTT
193605 TCATTCTTCA
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
37 11 0.17
38 4 0.06
39 4 0.06
40 17 0.27
41 12 0.19
42 15 0.23
43 1 0.02
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (40 bp):
TTCTTTTTTTCCTTTTCTTTTCTTTTTTCATTTTCTCTCT
Found at i:193561 original size:7 final size:7
Alignment explanation
Indices: 193492--193606 Score: 69
Period size: 7 Copynumber: 16.4 Consensus size: 7
193482 CTTTTGTTTA
193492 TTCTATTT
1 TTCT-TTT
*
193500 TTCCTTT
1 TTCTTTT
*
193507 TTCTTTC
1 TTCTTTT
*
193514 TT-TTCT
1 TTCTTTT
193520 TTCTTTT
1 TTCTTTT
193527 TCTCTTTT
1 T-TCTTTT
*
193535 CTCTTTT
1 TTCTTTT
*
193542 TTC-CTT
1 TTCTTTT
193548 TTC--TT
1 TTCTTTT
193553 TTCTTTT
1 TTCTTTT
*
193560 TTC-ATT
1 TTCTTTT
193566 TTCTTTCT
1 TTCTTT-T
193574 TTCTTTTT
1 TTC-TTTT
*
193582 TTATTTT
1 TTCTTTT
*
193589 TTTTATTT
1 TTCT-TTT
*
193597 TTCATTT
1 TTCTTTT
193604 TTC
1 TTC
193607 ATTCTTCAGG
Statistics
Matches: 84, Mismatches: 15, Indels: 17
0.72 0.13 0.15
Matches are distributed among these distances:
5 5 0.06
6 14 0.17
7 41 0.49
8 21 0.25
9 3 0.04
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.77
Consensus pattern (7 bp):
TTCTTTT
Found at i:193573 original size:37 final size:39
Alignment explanation
Indices: 193510--193604 Score: 94
Period size: 37 Copynumber: 2.5 Consensus size: 39
193500 TTCCTTTTTC
* *
193510 TTTCTTTTCTTTCTTT--TTCTCTTTTC-TCTTTTTTCCT
1 TTTCTTTTCTTT-TTTCATTTTCTTTTCTTCTTTTTTCAT
*
193547 TTTCTTTTCTTTTTTCATTTTC-TTTCTTTCTTTTTTTAT
1 TTTCTTTTCTTTTTTCATTTTCTTTTC-TTCTTTTTTCAT
*
193586 TTT-TTTT-ATTTTTCATTTT
1 TTTCTTTTCTTTTTTCATTTT
193605 TCATTCTTCA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
36 3 0.06
37 27 0.54
38 8 0.16
39 12 0.24
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (39 bp):
TTTCTTTTCTTTTTTCATTTTCTTTTCTTCTTTTTTCAT
Found at i:204852 original size:2 final size:2
Alignment explanation
Indices: 204841--204905 Score: 109
Period size: 2 Copynumber: 34.0 Consensus size: 2
204831 CTATTTTATT
204841 TA TA -A TA TA TA TA TA TA -A TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
204880 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
204906 AACTCGAAAT
Statistics
Matches: 60, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 3 0.05
2 57 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:207268 original size:38 final size:38
Alignment explanation
Indices: 207217--207318 Score: 186
Period size: 38 Copynumber: 2.7 Consensus size: 38
207207 GTTTGGTTTG
*
207217 TTTATGTTGATGAACAAGCTCGTTTTTTGAGTCATTCA
1 TTTATGTTGATGAACAAGCTCGTTTATTGAGTCATTCA
*
207255 TTTATGTTGATGAACAAGCTCGTTTATTGAGTTATTCA
1 TTTATGTTGATGAACAAGCTCGTTTATTGAGTCATTCA
207293 TTTATGTTGATGAACAAGCTCGTTTA
1 TTTATGTTGATGAACAAGCTCGTTTA
207319 CTCGGTTTTC
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 62 1.00
ACGTcount: A:0.25, C:0.12, G:0.19, T:0.44
Consensus pattern (38 bp):
TTTATGTTGATGAACAAGCTCGTTTATTGAGTCATTCA
Found at i:209352 original size:34 final size:34
Alignment explanation
Indices: 209299--209363 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
209289 CCATAGTTGA
* *
209299 AATGCATATGGGTGCATTATCGGCATAAAAGAAT
1 AATGCATATAGGTGAATTATCGGCATAAAAGAAT
* *
209333 AATGCATATAGGTGAATTATTGGCATGAAAG
1 AATGCATATAGGTGAATTATCGGCATAAAAG
209364 GATGCCATAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.38, C:0.09, G:0.25, T:0.28
Consensus pattern (34 bp):
AATGCATATAGGTGAATTATCGGCATAAAAGAAT
Found at i:209379 original size:79 final size:79
Alignment explanation
Indices: 209253--209607 Score: 515
Period size: 79 Copynumber: 4.6 Consensus size: 79
209243 AATTAACCTT
*
209253 AAGAATAATGCATATGGGTGCA-TAGTT-G-A--AAA-GATGCCATAGTTGAAATGCATATGGGT
1 AAGAATAATGCATATGGGTGCATTA-TTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGT
209312 GCATTATCGGCATAA
65 GCATTATCGGCATAA
* * * *
209327 AAGAATAATGCATATAGGTGAATTATTGGCATGAAAGGATGCCATAGCTGAAATTCATATGGCTG
1 AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTG
209392 CATTATCGGCATAA
66 CATTATCGGCATAA
* *
209406 AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTGAAATGCATATGTGTG
1 AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTG
*
209471 CATTATTGGCATAA
66 CATTATCGGCATAA
* * * *
209485 AATAATATTGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGAATATGGGTG
1 AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTG
*
209550 CATTATAGGCATAA
66 CATTATCGGCATAA
* * *
209564 AAGAATAATGCATATGGGTGCATTATCGACATTAAAGGATGCCA
1 AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA
209608 AAAAATAATT
Statistics
Matches: 250, Mismatches: 25, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
74 22 0.09
75 3 0.01
76 1 0.00
78 3 0.01
79 221 0.88
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (79 bp):
AAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATGGGTG
CATTATCGGCATAA
Found at i:209403 original size:45 final size:43
Alignment explanation
Indices: 209333--209711 Score: 236
Period size: 45 Copynumber: 9.2 Consensus size: 43
209323 ATAAAAGAAT
* *
209333 AATGCATATAGGTGAATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-A-CTGA
* * *
209378 AATTCATATGGCTGCATTATCGGCAT-AAA--A-G--AA-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAACTGA
*
209412 AATGCATATGGGTGCATTATTGGCATGAAAGGATTCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-A-CTGA
*
209457 AATGCATATGTGTGCATTATTGGCAT-AAA--AT---AA-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAACTGA
* *
209491 ATTGCATATGAGTGCATTATTGGCATGAAAGGATGCCATAGCTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-A-CTGA
* *
209536 AATGAATATGGGTGCATTATAGGCAT-AAA--A-G--AA-T--
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAACTGA
* * * ***
209570 AATGCATATGGGTGCATTATCGACATTAAAGGATGCCAAAAAA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAACTGA
* * * *
209613 TAATTCATATGGGTCCATTATTGGCATGAATGGATGCTATAGCTGA
1 -AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-A-CTGA
* * * * *
209659 AATGCATATGGGTGCATTATCGGTATAAAAGTATGCTATACTTGA
1 AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCA-AC-TGA
209704 AATGCATA
1 AATGCATA
209712 ATGGTGTATT
Statistics
Matches: 262, Mismatches: 37, Indels: 70
0.71 0.10 0.19
Matches are distributed among these distances:
34 70 0.27
35 9 0.03
36 3 0.01
37 4 0.02
38 4 0.02
39 3 0.01
40 4 0.02
41 4 0.02
42 4 0.02
43 2 0.01
44 41 0.16
45 113 0.43
46 1 0.00
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.30
Consensus pattern (43 bp):
AATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAACTGA
Found at i:209648 original size:44 final size:45
Alignment explanation
Indices: 209562--209649 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 45
209552 TTATAGGCAT
* *
209562 AAAAGAATAATGCATATGGGTGCATTATCGACATTAAAGGATGCC
1 AAAAGAATAATGCATATGGGTCCATTATCGACATGAAAGGATGCC
* * * *
209607 AAAA-AATAATTCATATGGGTCCATTATTGGCATGAATGGATGC
1 AAAAGAATAATGCATATGGGTCCATTATCGACATGAAAGGATGC
209650 TATAGCTGAA
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
44 33 0.89
45 4 0.11
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (45 bp):
AAAAGAATAATGCATATGGGTCCATTATCGACATGAAAGGATGCC
Found at i:212512 original size:134 final size:135
Alignment explanation
Indices: 212211--212514 Score: 346
Period size: 134 Copynumber: 2.3 Consensus size: 135
212201 AGGGTAGATC
* * * * *
212211 AGATC-GAGAAACGTTGACTCATTCTACTATTCTTCAGGGAATAATGAATCGAGGTAGACTTGTT
1 AGATCTGAGGAACGTTGATTCATTCCACTATTCTTCAGGGAAGAATGAATCGAGGCAGACTTGTT
* * * *
212275 CCACTGTCATTCTGGGAATATCAAATCTTGAAAGGGAGGGAACTGTTCCACTTCTTCTTAAGGGA
66 CCACTGTCACTCTGGGAATATAAAATCTTGAAAGAGAGGGAACTGTTCCACTTATTCTTAAGGGA
*
212340 AAATC
131 AAATA
* * * * * * *
212345 AGATCTGAGG-ATGTCGATTCATTCCACTGTTCTTTAGGGAAGATTGAATCGAGGCATATTTGTT
1 AGATCTGAGGAACGTTGATTCATTCCACTATTCTTCAGGGAAGAATGAATCGAGGCAGACTTGTT
* * * * * * *
212409 CTATTGTTACTCAT-GGAATATAAAATCTTGAAAGAGATGGATCTTTTCCACTTATTCTTGAGGG
66 CCACTGTCACTC-TGGGAATATAAAATCTTGAAAGAGAGGGAACTGTTCCACTTATTCTTAAGGG
212473 AAAATA
130 AAAATA
*
212479 AGATCTG-GGAACGTTGATTCATTCCACCATTCTTCA
1 AGATCTGAGGAACGTTGATTCATTCCACTATTCTTCA
212515 AATAAGATTG
Statistics
Matches: 138, Mismatches: 29, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
133 2 0.01
134 132 0.96
135 4 0.03
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (135 bp):
AGATCTGAGGAACGTTGATTCATTCCACTATTCTTCAGGGAAGAATGAATCGAGGCAGACTTGTT
CCACTGTCACTCTGGGAATATAAAATCTTGAAAGAGAGGGAACTGTTCCACTTATTCTTAAGGGA
AAATA
Found at i:213092 original size:20 final size:20
Alignment explanation
Indices: 213064--213118 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
213054 AAAACACCCT
213064 GCCCGAAGGTCTTATGGATC
1 GCCCGAAGGTCTTATGGATC
* *
213084 GCCCAAAGGTCTTATGGATG
1 GCCCGAAGGTCTTATGGATC
*
213104 GCCCGAAGGACTTAT
1 GCCCGAAGGTCTTAT
213119 CATCTTGCTC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.24, G:0.29, T:0.24
Consensus pattern (20 bp):
GCCCGAAGGTCTTATGGATC
Found at i:213957 original size:232 final size:233
Alignment explanation
Indices: 213089--214141 Score: 1283
Period size: 233 Copynumber: 4.5 Consensus size: 233
213079 GGATCGCCCA
* * * *
213089 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTATAGATAACCCGAAAG
1 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGG
* * * * *
213154 ATTT-ACTCATTATGCTCGAAAGACTTACTGATCGTCTGAAGGACTTACCAATTTTGGAAATAGT
66 ATTTAAGT-ATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
* * * * * * *
213218 TTATTAGGAAAAAAATTTGGAAATTGTTTTCTTGCTTTTCAAAAAATTCAATTTTCATATTTAAA
130 TTACTAGG----TAA----GAAA--CTTTTCTTACTTTTCAAAAAATTTAAATTTCAAATTTAAA
*** * *
213283 TGAGATTTTTTTCTCATTTTTTGAGAAACATGTGAAAACATCCTACCCG
185 TGAGAAACTTTTCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCG
* * * * * * *
213332 ACGGTCTTGTGGATGGCCCGAAGGATTTATCATTTTTCTCAAAAGACTTAC-GAATGACCCAAAG
1 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAG-ATGACCCGAAG
* * * *
213396 GATTTAAGTATCATACTCGAAAGACTTACTGATGGCCCGGAGGACATACCAATTTCGGAAATAGT
65 GATTTAAGTATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
* * *
213461 TTACTATGTAAGAAATTTTTCTTACTTTT-TAAAAATTTCAAATTTCAAATTTAAATGAGAAACT
130 TTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAAATTT-AAATTTCAAATTTAAATGAGAAACT
* * *
213525 TTTCTTATTTTTCGAGAGATATGTGAAAATATCCTACCCG
194 TTTCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCG
* * * * *
213565 AAGGCCTTATGGATGGCTCGAAAGACTTATCATCTTGCTCGAAAGACTTACATATGGCCCGAAGG
1 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGG
* * *
213630 ATTTTAGTATCATGCTCGAAAGACTTACTGATGGCCTGAAGAACTTACCAATTTTGGAAATAGTT
66 ATTTAAGTATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTT
*
213695 TACTAGGTAAGAAACTTTTCTTACTTTTCAAAAAATTTAAATTTCAGATTTAAATGAGAAACTTT
131 TACTAGGTAAGAAACTTTTCTTACTTTTCAAAAAATTTAAATTTCAAATTTAAATGAGAAACTTT
* * * *
213760 TCTCATTTTTGGAGAGACATGTGAAAATATCCTGCCTG
196 TCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCG
* * *
213798 AAGGTCTTATAGATGGCCCGAAGGACTTATCATCTTGCAT-GAAAGGCTTACAGATGACCTGAAG
1 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC-TCGAAAGACTTACAGATGACCCGAAG
* * * ** * *
213862 TATTTAAGCAT-ATGCTCGAAAGACATACTGATAACCCGAATGACTTACTAATTTTGGAAATAGT
65 GATTTAAGTATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGT
*
213926 TTACTAGGTAAGAAACTTTTCTTAGTTTTCAAAAAATTTAAATTTCAAATTTAAATGAGAAA-TT
130 TTACTAGGTAAGAAACTTTTCTTACTTTTCAAAAAATTTAAATTTCAAATTTAAATGAGAAACTT
* *
213990 TTCTCATTTTACAAGAGACATGTGAAAACATCCTGA-CCG
195 TTCTCATTTTTCGAGAGACATGTGAAAACATCCT-ACCCG
* * *
214029 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACATATGATCCAAAGG
1 AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGG
* ** *
214094 ATTTAAATATCATGCTCGAACTACTTACTGATTGCCCGAAGGACTTAC
66 ATTTAAGTATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
214142 TAAATAAGAA
Statistics
Matches: 695, Mismatches: 106, Indels: 29
0.84 0.13 0.03
Matches are distributed among these distances:
230 1 0.00
231 98 0.14
232 144 0.21
233 324 0.47
234 9 0.01
235 4 0.01
239 2 0.00
242 1 0.00
243 110 0.16
244 2 0.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (233 bp):
AAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATGACCCGAAGG
ATTTAAGTATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACCAATTTTGGAAATAGTT
TACTAGGTAAGAAACTTTTCTTACTTTTCAAAAAATTTAAATTTCAAATTTAAATGAGAAACTTT
TCTCATTTTTCGAGAGACATGTGAAAACATCCTACCCG
Found at i:223751 original size:3 final size:3
Alignment explanation
Indices: 223743--223777 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
223733 AAAGAAATGA
223743 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
223778 GAAGAAGAAG
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:229739 original size:81 final size:81
Alignment explanation
Indices: 229627--230524 Score: 1293
Period size: 81 Copynumber: 11.1 Consensus size: 81
229617 ATTCCTTTAG
* * ** * * * * **
229627 TCTTTTACCCAAAGGCATTTAGTCGTTCATCTAACTTGCATGATTGACACCTTTATGGAAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
229692 ACAACTAGGCTATTAA
66 ACAACTAGGCTATTAA
* * * *
229708 TCATTTACTCAAAGGTATTTAACCTTTCATCTAACTGGTATAACTGACACCTTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
* * * *
229773 ATAGCTAGGCCATGAA
66 ACAACTAGGCTATTAA
* * *
229789 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACATTTCTACTAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
229854 ACAGCTAGGCTATTAA
66 ACAACTAGGCTATTAA
* * *
229870 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGTATAATTGACACATTTCTGCCAAATAC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
229935 ACAGCTAGGCTATTAA
66 ACAACTAGGCTATTAA
229951 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
230016 ACAACTAGGCTATTAA
66 ACAACTAGGCTATTAA
* * *
230032 TCTTTTACTCAAAGGCATTTAACCTTTCATCAAACTGGCATAATTAACACCTTTCTGCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
230097 A-AAGCTAGGATATTAA
66 ACAA-CTAGGCTATTAA
* * *
230113 TATTTTACTCAAAGGTATTTAACCATTCATCTAACTGGCATAATTGACACCTTTCTTCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
230178 ACAACTAGGCCATTAA
66 ACAACTAGGCTATTAA
* * * *
230194 TCTTTTACTTAAAGGTATTTAACTTTTCATCTAACTGGCATAATTGACACATTTCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
230259 ACAACTAGGCCATTAA
66 ACAACTAGGCTATTAA
* *
230275 TCTTTTACTCAAAGGTATTTAACGTTTCATCTAACTGGCATAATTGACACC-TTCTTCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
**
230339 ACAGTTAGGCTATTAA
66 ACAACTAGGCTATTAA
*
230355 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACC-TTCTTCCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
230419 ACAGA-TAGGCTATTAA
66 ACA-ACTAGGCTATTAA
** * *
230435 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACATATTCCTGTCAAATGC
1 TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
*
230500 ACAACTATGAC-ATTAA
66 ACAACTA-GGCTATTAA
230516 TCTTTTACT
1 TCTTTTACT
230525 TTGGAATAGT
Statistics
Matches: 741, Mismatches: 70, Indels: 12
0.90 0.09 0.01
Matches are distributed among these distances:
80 153 0.21
81 584 0.79
82 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.11, T:0.35
Consensus pattern (81 bp):
TCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATAATTGACACCTTTCTGCCAAATGC
ACAACTAGGCTATTAA
Found at i:230907 original size:54 final size:55
Alignment explanation
Indices: 230819--230946 Score: 170
Period size: 54 Copynumber: 2.3 Consensus size: 55
230809 TTTATTAAAA
* * * *
230819 TGCACACGTAGTGCCTATACGGTAGTTCACCAACTCATGATGAATTTCGTGG-GT
1 TGCACACGTAGTGCATGTACGGTAGTTCACCAACTAATGATGAATTTCATGGAGT
* *
230873 TGCACACGTAGTGCATGTACGGTTA-TTCATCAACTAATGATGAATTTCATGGATT
1 TGCACACGTAGTGCATGTACGG-TAGTTCACCAACTAATGATGAATTTCATGGAGT
*
230928 TGCACACATAGTGCATGTA
1 TGCACACGTAGTGCATGTA
230947 GTACACATAG
Statistics
Matches: 65, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
54 44 0.68
55 21 0.32
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (55 bp):
TGCACACGTAGTGCATGTACGGTAGTTCACCAACTAATGATGAATTTCATGGAGT
Found at i:231299 original size:20 final size:22
Alignment explanation
Indices: 231274--231330 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
231264 TGGATCAATA
231274 GTATCGATACTCCTAT-C-ATG
1 GTATCGATACTCCTATACTATG
*
231294 GTATCGATACTACTATACTATG
1 GTATCGATACTCCTATACTATG
*
231316 GTATTGATAC-CCTAT
1 GTATCGATACTCCTAT
231331 TACGGTACCA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 15 0.47
21 5 0.16
22 12 0.38
ACGTcount: A:0.28, C:0.21, G:0.14, T:0.37
Consensus pattern (22 bp):
GTATCGATACTCCTATACTATG
Found at i:231394 original size:20 final size:20
Alignment explanation
Indices: 231369--231421 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
231359 GTTAACAATG
*
231369 GTATCGATACCATCCTCATA
1 GTATCGATACCACCCTCATA
* *
231389 GTATCGATACTC-CCCTCTTG
1 GTATCGATAC-CACCCTCATA
231409 GTATCGATACCAC
1 GTATCGATACCAC
231422 TTGAATCGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.25, C:0.32, G:0.13, T:0.30
Consensus pattern (20 bp):
GTATCGATACCACCCTCATA
Found at i:233040 original size:30 final size:30
Alignment explanation
Indices: 233006--233062 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
232996 ATAATGATGA
* * *
233006 ACAATACCGTGAACAGTGTATCGATGCGCT
1 ACAATAACATGAACAGTGCATCGATGCGCT
233036 ACAATAACATGAACAGTGCATCGATGC
1 ACAATAACATGAACAGTGCATCGATGC
233063 ATCAAAACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.21
Consensus pattern (30 bp):
ACAATAACATGAACAGTGCATCGATGCGCT
Found at i:233477 original size:59 final size:59
Alignment explanation
Indices: 233355--233483 Score: 150
Period size: 59 Copynumber: 2.2 Consensus size: 59
233345 CGTAATGCAA
* * * * ** * *
233355 TCCCGAGTATGACATATAAGGTCGTGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTACGTATCATTAAGTACAG
* ** *
233414 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTACGTATCATTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTACGTATCATTAAGTACAG
233473 TCCCGAATATG
1 TCCCGAATATG
233484 CAGCTTGCTG
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.29
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCGTGCCCACCATATACACTACGTATCATTAAGTACAG
Found at i:241801 original size:49 final size:49
Alignment explanation
Indices: 241742--241985 Score: 328
Period size: 49 Copynumber: 5.0 Consensus size: 49
241732 AAATGAATGG
* * * *
241742 ATGAAGGTTAAATGCATAACGGTGCATTTCTGCATAAAAGGTGCCATTG
1 ATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACTA
* * *
241791 ATGAAAGTTAAATGCATAACGATGTATTTCAGCATAAAAGGTGCCAATA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACTA
* * * *
241840 ATGAAAGTTAAATGCATAATGTTGCATTTC-GATATAAAAGGTGTCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCAG-CATAAAAGGTGCCACTA
* *
241889 ATGAAAGTTAAATGCATAATGGTGCATTTCGGCATAAAAGGTGCCACTA
1 ATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACTA
* * *
241938 ATGAATGTTAAATACATAACGGTGCATTTCACCATAAAAGGTGCCACT
1 ATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACT
241986 CATGGTATTT
Statistics
Matches: 173, Mismatches: 20, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
48 1 0.01
49 171 0.99
50 1 0.01
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (49 bp):
ATGAAAGTTAAATGCATAACGGTGCATTTCAGCATAAAAGGTGCCACTA
Found at i:246328 original size:55 final size:55
Alignment explanation
Indices: 246268--246374 Score: 153
Period size: 55 Copynumber: 1.9 Consensus size: 55
246258 GCATGTACGG
* *
246268 TGATTCATCAAATTATGATGAATTCCT-TGAATATGCACACGAAGTGCCTGTATAA
1 TGATTCATCAAATCATGATGAATT-CTGTGAATATGCACACGAAGTGACTGTATAA
* * *
246323 TGATTCATCAACTCATGATGAATTCTGTGATTGTGCACACGAAGTGACTGTA
1 TGATTCATCAAATCATGATGAATTCTGTGAATATGCACACGAAGTGACTGTA
246375 GTACACATAG
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
54 2 0.04
55 44 0.96
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (55 bp):
TGATTCATCAAATCATGATGAATTCTGTGAATATGCACACGAAGTGACTGTATAA
Done.