Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold198
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1589021
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.28
Warning! 220217 characters in sequence are not A, C, G, or T
File 2 of 5
Found at i:4367 original size:20 final size:21
Alignment explanation
Indices: 4329--4367 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
4319 AAAAGAAGAA
*
4329 AAAATATCATGTGTTTATAGG
1 AAAATATCATATGTTTATAGG
4350 AAAATATCATAT-TTTATA
1 AAAATATCATATGTTTATA
4368 CATGTTCATG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (21 bp):
AAAATATCATATGTTTATAGG
Found at i:15234 original size:2 final size:2
Alignment explanation
Indices: 15227--15290 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
15217 ACAAGAAGTG
15227 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
15269 CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT
15291 TACTTCAGTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:18124 original size:3 final size:3
Alignment explanation
Indices: 18116--18144 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
18106 TGATTTAAAT
18116 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
18145 GTCCTTACAT
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:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:28436 original size:21 final size:22
Alignment explanation
Indices: 28388--28438 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
28378 TTTATCAGCT
*
28388 GTTAACTATAGTTTACGGATAC
1 GTTAACTATAGTTAACGGATAC
* *
28410 -TAAACTATAGTTAAC-GATTC
1 GTTAACTATAGTTAACGGATAC
28430 GTTAACTAT
1 GTTAACTAT
28439 GGTTTACATC
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.37
Consensus pattern (22 bp):
GTTAACTATAGTTAACGGATAC
Found at i:29328 original size:20 final size:20
Alignment explanation
Indices: 29305--29358 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 20
29295 TACAGATGTG
*
29305 AAATATAGATTAACG-TCGGT
1 AAATATAG-TTAACGATCCGT
*
29325 AAATATAGTTTACGATCCGT
1 AAATATAGTTAACGATCCGT
29345 AAACTATAGTTAAC
1 AAA-TATAGTTAAC
29359 AGTTGATGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 5 0.17
20 15 0.52
21 9 0.31
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (20 bp):
AAATATAGTTAACGATCCGT
Found at i:30137 original size:11 final size:11
Alignment explanation
Indices: 30121--30148 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
30111 GTCCTAATTT
30121 CTTTAAGCCAC
1 CTTTAAGCCAC
30132 CTTTAAGCCAC
1 CTTTAAGCCAC
30143 CTTTAA
1 CTTTAA
30149 TATGGAGGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.29, C:0.32, G:0.07, T:0.32
Consensus pattern (11 bp):
CTTTAAGCCAC
Found at i:35494 original size:2 final size:2
Alignment explanation
Indices: 35470--35603 Score: 113
Period size: 2 Copynumber: 67.0 Consensus size: 2
35460 TTACTAGTAG
* *
35470 CT CT AT CT CT CT TT CT CAT -T CT CT CT CT CAT C- CT CT CT CAT
1 CT CT CT CT CT CT CT CT C-T CT CT CT CT CT C-T CT CT CT CT C-T
*
35511 -T CT CT CT CAT -T TT CT CT CT CT CT CAT -T CT CT CT CAT -T CT
1 CT CT CT CT C-T CT CT CT CT CT CT CT C-T CT CT CT CT C-T CT CT
35550 CT CT CT CT CAT -T CT CT CAT -T CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT C-T CT CT CT C-T CT CT CT CT CT CT CT CT CT CT CT CT
35592 CT CT CT CT CT CT
1 CT CT CT CT CT CT
35604 GACATAGCTC
Statistics
Matches: 111, Mismatches: 5, Indels: 32
0.75 0.03 0.22
Matches are distributed among these distances:
1 8 0.07
2 94 0.85
3 9 0.08
ACGTcount: A:0.07, C:0.43, G:0.00, T:0.51
Consensus pattern (2 bp):
CT
Found at i:47694 original size:2 final size:2
Alignment explanation
Indices: 47636--47685 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
47626 CACACACACA
47636 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
47678 CT CT CT CT
1 CT CT CT CT
47686 TTTTCTCTCG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:50793 original size:2 final size:2
Alignment explanation
Indices: 50786--50844 Score: 109
Period size: 2 Copynumber: 29.5 Consensus size: 2
50776 TTATTATCAT
50786 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
*
50828 GA GA GA TA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
50845 GTTTTCTATA
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.49, T:0.02
Consensus pattern (2 bp):
GA
Found at i:54797 original size:21 final size:21
Alignment explanation
Indices: 54758--54798 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
54748 CATATTAATG
* * *
54758 AAACATGTGATTTATTTATTA
1 AAACATGAGAGTTAATTATTA
54779 AAACATGAGAGTTAATTATT
1 AAACATGAGAGTTAATTATT
54799 TAACATGCAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.05, G:0.12, T:0.41
Consensus pattern (21 bp):
AAACATGAGAGTTAATTATTA
Found at i:54887 original size:21 final size:21
Alignment explanation
Indices: 54860--54917 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
54850 AAACATTTAT
54860 GTCAACATGCAAGTTAATTAA
1 GTCAACATGCAAGTTAATTAA
* * * *
54881 GTTAACATGCAAGATATTTAT
1 GTCAACATGCAAGTTAATTAA
*
54902 GTCAACATGAAAGTTA
1 GTCAACATGCAAGTTA
54918 TCTCGCATGT
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (21 bp):
GTCAACATGCAAGTTAATTAA
Found at i:54986 original size:21 final size:20
Alignment explanation
Indices: 54960--55007 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
54950 AATGAATGTA
54960 AACATATTTATTTCGCAAGT-T
1 AACATATTT-TTTCGC-AGTGT
* *
54981 AACATAATTTTTGGCAGTGT
1 AACATATTTTTTCGCAGTGT
55001 AACATAT
1 AACATAT
55008 ATGACGCATA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 3 0.13
20 12 0.52
21 8 0.35
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (20 bp):
AACATATTTTTTCGCAGTGT
Found at i:62271 original size:9 final size:9
Alignment explanation
Indices: 62228--62276 Score: 55
Period size: 9 Copynumber: 5.4 Consensus size: 9
62218 GGCTTTCGTC
62228 ATAATAAAAT
1 ATAA-AAAAT
*
62238 ATAAAATAT
1 ATAAAAAAT
62247 -TAAAAAAT
1 ATAAAAAAT
*
62255 ATATAAAAT
1 ATAAAAAAT
*
62264 ATAAAAAAA
1 ATAAAAAAT
62273 ATAA
1 ATAA
62277 TCATAATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
8 7 0.21
9 22 0.67
10 4 0.12
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (9 bp):
ATAAAAAAT
Found at i:62272 original size:19 final size:19
Alignment explanation
Indices: 62236--62272 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
62226 TCATAATAAA
*
62236 ATATAAAATATTAAAAAAT
1 ATATAAAATATAAAAAAAT
62255 ATATAAAATATAAAAAAA
1 ATATAAAATATAAAAAAA
62273 ATAATCATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
ATATAAAATATAAAAAAAT
Found at i:62292 original size:14 final size:14
Alignment explanation
Indices: 62270--62299 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
62260 AAATATAAAA
*
62270 AAAATAATCATAAT
1 AAAAGAATCATAAT
62284 AAAAGAATCATAAT
1 AAAAGAATCATAAT
62298 AA
1 AA
62300 TACGTACCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (14 bp):
AAAAGAATCATAAT
Found at i:62850 original size:2 final size:2
Alignment explanation
Indices: 62843--62876 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
62833 TACTTCCTTG
* *
62843 TA TA TA TA TA CA TG TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
62877 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:62881 original size:2 final size:2
Alignment explanation
Indices: 62876--62927 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
62866 ATATATATAT
62876 AG AG AG AG AG AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
62917 AG AG AG AG AG A
1 AG AG AG AG AG A
62928 TGGGGGTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:69635 original size:2 final size:2
Alignment explanation
Indices: 69628--69691 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
69618 TTGTGACTTT
69628 AG AG AG AG AG AG AG AG AG AG AG AG A- AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
69669 AG AG AG AG AG AG A- AG -G AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
69692 TGCATGTACT
Statistics
Matches: 59, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 3 0.05
2 56 0.95
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:70129 original size:2 final size:2
Alignment explanation
Indices: 70122--70224 Score: 158
Period size: 2 Copynumber: 51.5 Consensus size: 2
70112 TTGTGACTTT
70122 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
70164 AG AG AG AG AG AG AG AG AG TAG -G AG AG AG AG AG TAG -G AG AG AG
1 AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG -AG AG AG AG AG
70206 AG AG AG TAG -G AG AG AG AG A
1 AG AG AG -AG AG AG AG AG AG A
70225 TATGCATGTA
Statistics
Matches: 95, Mismatches: 0, Indels: 12
0.89 0.00 0.11
Matches are distributed among these distances:
1 3 0.03
2 86 0.91
3 6 0.06
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Found at i:80457 original size:12 final size:12
Alignment explanation
Indices: 80437--80468 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
80427 AACTGAAGTA
80437 GGACAGACAGAC
1 GGACAGACAGAC
*
80449 GGACGGACAGAC
1 GGACAGACAGAC
80461 GGACAGAC
1 GGACAGAC
80469 GGACACAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.38, C:0.25, G:0.38, T:0.00
Consensus pattern (12 bp):
GGACAGACAGAC
Found at i:80463 original size:8 final size:8
Alignment explanation
Indices: 80437--80473 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
80427 AACTGAAGTA
80437 GGACAGAC
1 GGACAGAC
* *
80445 AGACGGAC
1 GGACAGAC
80453 GGACAGAC
1 GGACAGAC
80461 GGACAGAC
1 GGACAGAC
80469 GGACA
1 GGACA
80474 CAGAGGAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.38, C:0.24, G:0.38, T:0.00
Consensus pattern (8 bp):
GGACAGAC
Found at i:81267 original size:15 final size:15
Alignment explanation
Indices: 81242--81277 Score: 63
Period size: 15 Copynumber: 2.3 Consensus size: 15
81232 AAGTGGGACA
81242 GACAGGCGGACGGATG
1 GACA-GCGGACGGATG
81258 GACAGCGGACGGATG
1 GACAGCGGACGGATG
81273 GACAG
1 GACAG
81278 ACGCACTGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.28, C:0.19, G:0.47, T:0.06
Consensus pattern (15 bp):
GACAGCGGACGGATG
Found at i:84022 original size:20 final size:20
Alignment explanation
Indices: 83952--84025 Score: 69
Period size: 20 Copynumber: 3.6 Consensus size: 20
83942 TCAGTCTAAG
* *
83952 TTGTATAATATCCAT-TAATA
1 TTGTATAATTTCCATAT-GTA
*
83972 TTGTATAATTTTCCATTTGTA
1 TTGTATAA-TTTCCATATGTA
* *
83993 TGGTACAATTTCCATATGTA
1 TTGTATAATTTCCATATGTA
*
84013 TTGAATAATTTCC
1 TTGTATAATTTCC
84026 TTTTTGTACT
Statistics
Matches: 44, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
20 29 0.66
21 14 0.32
22 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.09, T:0.47
Consensus pattern (20 bp):
TTGTATAATTTCCATATGTA
Found at i:100555 original size:15 final size:15
Alignment explanation
Indices: 100537--100576 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
100527 CCCTGAGATG
*
100537 TTTCCCACCTCGATA
1 TTTCGCACCTCGATA
*
100552 TTTCGCACCTCGATG
1 TTTCGCACCTCGATA
100567 TTTCGCACCT
1 TTTCGCACCT
100577 GCATCGGAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.15, C:0.38, G:0.12, T:0.35
Consensus pattern (15 bp):
TTTCGCACCTCGATA
Found at i:101572 original size:11 final size:10
Alignment explanation
Indices: 101556--101639 Score: 50
Period size: 11 Copynumber: 8.3 Consensus size: 10
101546 GTCAAACTTC
101556 TTTGTTTATGT
1 TTTGTTT-TGT
101567 TTTGTTTTGTT
1 TTTGTTTTG-T
101578 TGTTGTTTTG-
1 T-TTGTTTTGT
*
101588 TTTGTTTTACT
1 TTTGTTTT-GT
* **
101599 TTTGTCTTAA
1 TTTGTTTTGT
*
101609 ATTGATTTTGT
1 TTTG-TTTTGT
101620 TTTG--TTGT
1 TTTGTTTTGT
101628 TTTGTTTT-T
1 TTTGTTTTGT
101637 TTT
1 TTT
101640 AGGGAGGTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 16
0.70 0.11 0.20
Matches are distributed among these distances:
8 8 0.14
9 11 0.19
10 8 0.14
11 22 0.39
12 8 0.14
ACGTcount: A:0.07, C:0.02, G:0.17, T:0.74
Consensus pattern (10 bp):
TTTGTTTTGT
Found at i:101574 original size:5 final size:5
Alignment explanation
Indices: 101556--101639 Score: 50
Period size: 5 Copynumber: 16.6 Consensus size: 5
101546 GTCAAACTTC
*
101556 TTTGT TTATGT TTTGT TTTGTT TGTTGT TTTG- TTTGT TTTACT TTTGT
1 TTTGT TT-TGT TTTGT TTTG-T T-TTGT TTTGT TTTGT TTT-GT TTTGT
* ** *
101604 CTTAA ATTGAT TTTGT TTTG- -TTGT TTTGT TTT-T TTT
1 TTTGT TTTG-T TTTGT TTTGT TTTGT TTTGT TTTGT TTT
101640 AGGGAGGTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 17
0.70 0.10 0.19
Matches are distributed among these distances:
3 3 0.05
4 8 0.13
5 32 0.52
6 16 0.26
7 3 0.05
ACGTcount: A:0.07, C:0.02, G:0.17, T:0.74
Consensus pattern (5 bp):
TTTGT
Found at i:101577 original size:16 final size:16
Alignment explanation
Indices: 101556--101594 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
101546 GTCAAACTTC
101556 TTTGTTT-ATGTTTTG
1 TTTGTTTGATGTTTTG
*
101571 TTTTGTTTGTTGTTTTG
1 -TTTGTTTGATGTTTTG
101588 TTTGTTT
1 TTTGTTT
101595 TACTTTTGTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 14 0.67
17 7 0.33
ACGTcount: A:0.03, C:0.00, G:0.21, T:0.77
Consensus pattern (16 bp):
TTTGTTTGATGTTTTG
Found at i:101585 original size:12 final size:12
Alignment explanation
Indices: 101568--101593 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
101558 TGTTTATGTT
101568 TTGTTTTGTTTG
1 TTGTTTTGTTTG
101580 TTGTTTTGTTTG
1 TTGTTTTGTTTG
101592 TT
1 TT
101594 TTACTTTTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (12 bp):
TTGTTTTGTTTG
Found at i:105808 original size:18 final size:18
Alignment explanation
Indices: 105766--105819 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
105756 TGTTGCTTTA
105766 TGCTTTTTATGCTTCTTG
1 TGCTTTTTATGCTTCTTG
* *
105784 TGTTTTTTATGTTTCTT-
1 TGCTTTTTATGCTTCTTG
105801 TGCCTTTTTA-GACTTCTTG
1 TG-CTTTTTATG-CTTCTTG
105820 CTTCTATGGG
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 3 0.10
18 26 0.90
ACGTcount: A:0.07, C:0.15, G:0.15, T:0.63
Consensus pattern (18 bp):
TGCTTTTTATGCTTCTTG
Found at i:107881 original size:23 final size:24
Alignment explanation
Indices: 107855--107905 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
107845 TCTTTACTAG
**
107855 TTTTAATGTGTTC-ACTGCTTTTC
1 TTTTAATGACTTCTACTGCTTTTC
* *
107878 TTTTTATGACTTCTGCTGCTTTTC
1 TTTTAATGACTTCTACTGCTTTTC
107902 TTTT
1 TTTT
107906 TCTTTGGTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.10, C:0.18, G:0.12, T:0.61
Consensus pattern (24 bp):
TTTTAATGACTTCTACTGCTTTTC
Found at i:108859 original size:22 final size:22
Alignment explanation
Indices: 108834--108884 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 22
108824 ATATGGGCCC
*
108834 ACTCAGGGTTTACTTTGAGTTT
1 ACTCAGGGTTTAATTTGAGTTT
*
108856 ACTCTA-GGTTTAATTTGGGTTT
1 ACTC-AGGGTTTAATTTGAGTTT
108878 ACTCAGG
1 ACTCAGG
108885 AATCGTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
21 1 0.04
22 23 0.92
23 1 0.04
ACGTcount: A:0.20, C:0.14, G:0.24, T:0.43
Consensus pattern (22 bp):
ACTCAGGGTTTAATTTGAGTTT
Found at i:109880 original size:44 final size:44
Alignment explanation
Indices: 109799--109886 Score: 133
Period size: 44 Copynumber: 2.0 Consensus size: 44
109789 TACGTTCATT
*
109799 CAGTGGATGAACGTAGTTTGAGCACAAAGGTTTTTATGATTATC
1 CAGTGGATGAACGTAGTTTGAGCACAAAGGTTATTATGATTATC
**
109843 CAGTGGATGAACGTAGTTTGAGCACTTCA-GTTATTATGATTATC
1 CAGTGGATGAACGTAGTTTGAGCAC-AAAGGTTATTATGATTATC
109887 GACTTATCCA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 39 0.98
45 1 0.03
ACGTcount: A:0.28, C:0.12, G:0.24, T:0.35
Consensus pattern (44 bp):
CAGTGGATGAACGTAGTTTGAGCACAAAGGTTATTATGATTATC
Found at i:113400 original size:144 final size:144
Alignment explanation
Indices: 113140--113427 Score: 576
Period size: 144 Copynumber: 2.0 Consensus size: 144
113130 TTTCATAATA
113140 AACTTGAATTTACAGATGTTGAAATTATTGAAGAAGACAAAGATAATGTTGGCAATGAGAGTATG
1 AACTTGAATTTACAGATGTTGAAATTATTGAAGAAGACAAAGATAATGTTGGCAATGAGAGTATG
113205 TTTAAACCATTCAGTGGCTCGGAGGAAGCAAAGCGACTAGAGTAAGATTAGACTTAAAATTGATT
66 TTTAAACCATTCAGTGGCTCGGAGGAAGCAAAGCGACTAGAGTAAGATTAGACTTAAAATTGATT
113270 TTATAAATCATACT
131 TTATAAATCATACT
113284 AACTTGAATTTACAGATGTTGAAATTATTGAAGAAGACAAAGATAATGTTGGCAATGAGAGTATG
1 AACTTGAATTTACAGATGTTGAAATTATTGAAGAAGACAAAGATAATGTTGGCAATGAGAGTATG
113349 TTTAAACCATTCAGTGGCTCGGAGGAAGCAAAGCGACTAGAGTAAGATTAGACTTAAAATTGATT
66 TTTAAACCATTCAGTGGCTCGGAGGAAGCAAAGCGACTAGAGTAAGATTAGACTTAAAATTGATT
113414 TTATAAATCATACT
131 TTATAAATCATACT
113428 GTAGAAGCAC
Statistics
Matches: 144, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 144 1.00
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (144 bp):
AACTTGAATTTACAGATGTTGAAATTATTGAAGAAGACAAAGATAATGTTGGCAATGAGAGTATG
TTTAAACCATTCAGTGGCTCGGAGGAAGCAAAGCGACTAGAGTAAGATTAGACTTAAAATTGATT
TTATAAATCATACT
Found at i:113478 original size:10 final size:10
Alignment explanation
Indices: 113463--113553 Score: 146
Period size: 10 Copynumber: 8.8 Consensus size: 10
113453 TGCGTCTTTT
113463 AACCCCAAGG
1 AACCCCAAGG
113473 AACCCCAAGG
1 AACCCCAAGG
113483 AACCCCAAGG
1 AACCCCAAGG
113493 AAACCCCAAGG
1 -AACCCCAAGG
113504 AACCCCAAGG
1 AACCCCAAGG
113514 AAACCCCAAGG
1 -AACCCCAAGG
*
113525 AACCTCAAGG
1 AACCCCAAGG
113535 ATACCCCAAGG
1 A-ACCCCAAGG
113546 AACCCCAA
1 AACCCCAA
113554 TGACAAAAAT
Statistics
Matches: 76, Mismatches: 2, Indels: 6
0.90 0.02 0.07
Matches are distributed among these distances:
10 47 0.62
11 29 0.38
ACGTcount: A:0.42, C:0.38, G:0.18, T:0.02
Consensus pattern (10 bp):
AACCCCAAGG
Found at i:113499 original size:21 final size:21
Alignment explanation
Indices: 113463--113553 Score: 157
Period size: 21 Copynumber: 4.4 Consensus size: 21
113453 TGCGTCTTTT
113463 AACCCCAAGG-AACCCCAAGG
1 AACCCCAAGGAAACCCCAAGG
113483 AACCCCAAGGAAACCCCAAGG
1 AACCCCAAGGAAACCCCAAGG
113504 AACCCCAAGGAAACCCCAAGG
1 AACCCCAAGGAAACCCCAAGG
* *
113525 AACCTCAAGGATACCCCAAGG
1 AACCCCAAGGAAACCCCAAGG
113546 AACCCCAA
1 AACCCCAA
113554 TGACAAAAAT
Statistics
Matches: 67, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
20 10 0.15
21 57 0.85
ACGTcount: A:0.42, C:0.38, G:0.18, T:0.02
Consensus pattern (21 bp):
AACCCCAAGGAAACCCCAAGG
Found at i:113501 original size:31 final size:30
Alignment explanation
Indices: 113463--113553 Score: 146
Period size: 31 Copynumber: 2.9 Consensus size: 30
113453 TGCGTCTTTT
113463 AACCCCAAGGAACCCCAAGGAACCCCAAGG
1 AACCCCAAGGAACCCCAAGGAACCCCAAGG
113493 AAACCCCAAGGAACCCCAAGGAAACCCCAAGG
1 -AACCCCAAGGAACCCCAAGG-AACCCCAAGG
*
113525 AACCTCAAGGATACCCCAAGGAACCCCAA
1 AACCCCAAGGA-ACCCCAAGGAACCCCAA
113554 TGACAAAAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
31 38 0.67
32 19 0.33
ACGTcount: A:0.42, C:0.38, G:0.18, T:0.02
Consensus pattern (30 bp):
AACCCCAAGGAACCCCAAGGAACCCCAAGG
Found at i:113802 original size:195 final size:196
Alignment explanation
Indices: 113537--113913 Score: 492
Period size: 195 Copynumber: 1.9 Consensus size: 196
113527 CCTCAAGGAT
* * * *
113537 ACCCCAAGGAACCCCAATGACAAAAATTAATAAATTTTAATACCCAAGGGGTCTTATTGGACTTC
1 ACCCCAAGGAACCCCAATGACAAAAATTAATAAATTTTAATACCCAACGGGTCTCATTGGAATCC
* *
113602 AAGGGTCACCTCTTAGTACCCCAAGGGTACCCCAAGGAACCCCAAGGAAAC-C-TGTAAGAACCC
66 AAGGGTCACCTCGTAGTACCCCAAGGATACCCCAAGGAACCCCAAGGAAACTCAT-T-AGAACCC
* * * * *
113665 CATGGAACCCAAATGATA-AAGTTATTAACCAGTGATACCCCAGGGGTCTCATTCGAATCAAAGG
129 CAAGGAACCCAAATAATAGAAATTAGTAACCAGTGATACCCCAGGAGTCTCATTCGAATCAAAGG
113729 CTC
194 CTC
* * * * * * *
113732 ACCCCAAGGTACTCCAGTGATAGAAATTAATAACTATTT-ATACCCAACGGGTCTCATTTGAATC
1 ACCCCAAGGAACCCCAATGACAAAAATTAATAAAT-TTTAATACCCAACGGGTCTCATTGGAATC
* *
113796 CAAGGGTCACCTCGTAGTACCCCAAGGATACCCCAAGGAACCCCAAGTATACTCATTAGAACCCC
65 CAAGGGTCACCTCGTAGTACCCCAAGGATACCCCAAGGAACCCCAAGGAAACTCATTAGAACCCC
* * *
113861 AAGTAACCCCAATAATAGAAATTAGTAACTAGTGATACCCCAGGAGTCTCATT
130 AAGGAACCCAAATAATAGAAATTAGTAACCAGTGATACCCCAGGAGTCTCATT
113914 ATACCCCTAT
Statistics
Matches: 155, Mismatches: 23, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
195 118 0.76
196 36 0.23
197 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.21
Consensus pattern (196 bp):
ACCCCAAGGAACCCCAATGACAAAAATTAATAAATTTTAATACCCAACGGGTCTCATTGGAATCC
AAGGGTCACCTCGTAGTACCCCAAGGATACCCCAAGGAACCCCAAGGAAACTCATTAGAACCCCA
AGGAACCCAAATAATAGAAATTAGTAACCAGTGATACCCCAGGAGTCTCATTCGAATCAAAGGCT
C
Found at i:113840 original size:10 final size:11
Alignment explanation
Indices: 113813--113847 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
113803 CACCTCGTAG
113813 TACCCCAAGGA
1 TACCCCAAGGA
113824 TACCCCAAGGA
1 TACCCCAAGGA
*
113835 -ACCCCAAGTA
1 TACCCCAAGGA
113845 TAC
1 TAC
113848 TCATTAGAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.37, C:0.37, G:0.14, T:0.11
Consensus pattern (11 bp):
TACCCCAAGGA
Found at i:127427 original size:4 final size:4
Alignment explanation
Indices: 127420--127447 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
127410 TTGTTTGATT
127420 GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA
127448 CAGTGCTGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:127543 original size:5 final size:5
Alignment explanation
Indices: 127535--127561 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
127525 AAGTTAAGTT
127535 CTATC CTATC CTATC CTATC CTATC CT
1 CTATC CTATC CTATC CTATC CTATC CT
127562 GCATCCTGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.41, G:0.00, T:0.41
Consensus pattern (5 bp):
CTATC
Found at i:139351 original size:161 final size:162
Alignment explanation
Indices: 139025--139365 Score: 510
Period size: 162 Copynumber: 2.1 Consensus size: 162
139015 ATAATTGAGG
* *
139025 CTGTCCTAGAGATGTGCAATAAGGTTTTAAAAATTTAATTTTTCATCCAGGGAGTCAAATAGATG
1 CTGTCCTACAGATGTGCAATAAGGTTTTAAAAATTTAATATTTCATCCAGGGAGTCAAATAGATG
* *
139090 CAGAAAATTGACGTTGATCACTAAAAAAAACATAGATCCTAGAACTCCTCTTATGATTGAATGGA
66 CAGAAAATTGACGTTGATCACTAAAAAAAACACAGATCCTAGAACTCCTCTTATGATTAAATGGA
* *
139155 TAGACGCATCATATCTTTGGATATGATAGGGA
131 TAGACACATCATATCTTTGGATACGATAGGGA
* *
139187 CTGTCCTATAGATGTGCAGTAAGGTTTTAAAAATTTAA-ATTTCATCCAGGGAGTCAAATAG-TA
1 CTGTCCTACAGATGTGCAATAAGGTTTTAAAAATTTAATATTTCATCCAGGGAGTCAAATAGAT-
* *
139250 GCAGAAAATTGATGTTTATCACTAAAAAAAACCACAGATCCTAGAACTCCTCTTATGATTAAATG
65 GCAGAAAATTGACGTTGATCACTAAAAAAAA-CACAGATCCTAGAACTCCTCTTATGATTAAATG
*
139315 GATAGACACATCCTAT-TTTGGGATACGATA-GGA
129 GATAGACACATCATATCTTT-GGATACGATAGGGA
**
139348 CTGTTATACAGATGTGCA
1 CTGTCCTACAGATGTGCA
139366 TTACGGGTCT
Statistics
Matches: 163, Mismatches: 13, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
160 1 0.01
161 72 0.44
162 90 0.55
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (162 bp):
CTGTCCTACAGATGTGCAATAAGGTTTTAAAAATTTAATATTTCATCCAGGGAGTCAAATAGATG
CAGAAAATTGACGTTGATCACTAAAAAAAACACAGATCCTAGAACTCCTCTTATGATTAAATGGA
TAGACACATCATATCTTTGGATACGATAGGGA
Found at i:147550 original size:21 final size:21
Alignment explanation
Indices: 147490--147553 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
147480 CAATTATTTC
147490 TAGCATTCCATAACTGGTACA
1 TAGCATTCCATAACTGGTACA
* * *
147511 T-GACCTTTCATTACTGGTACA
1 TAG-CATTCCATAACTGGTACA
* *
147532 TAGCGTTCCATAACGGGTACA
1 TAGCATTCCATAACTGGTACA
147553 T
1 T
147554 GGCCTTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
20 1 0.03
21 32 0.94
22 1 0.03
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.31
Consensus pattern (21 bp):
TAGCATTCCATAACTGGTACA
Found at i:147569 original size:42 final size:42
Alignment explanation
Indices: 147490--147573 Score: 105
Period size: 42 Copynumber: 2.0 Consensus size: 42
147480 CAATTATTTC
* ** **
147490 TAGCATTCCATAACTGGTACATGACCTTTCATTACTGGTACA
1 TAGCATTCCATAACGGGTACATGACCTTAAAAAACTGGTACA
* *
147532 TAGCGTTCCATAACGGGTACATGGCCTTAAAAAACTGGTACA
1 TAGCATTCCATAACGGGTACATGACCTTAAAAAACTGGTACA
147574 CGGCCTTTCA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.31, C:0.23, G:0.18, T:0.29
Consensus pattern (42 bp):
TAGCATTCCATAACGGGTACATGACCTTAAAAAACTGGTACA
Found at i:147586 original size:21 final size:21
Alignment explanation
Indices: 147501--147601 Score: 78
Period size: 21 Copynumber: 4.9 Consensus size: 21
147491 AGCATTCCAT
* *
147501 AACTGGTACATGACCTTTCAT
1 AACTGGTACATGGCCTTTCAA
* * * * *
147522 TACTGGTACATAGCGTTCCAT
1 AACTGGTACATGGCCTTTCAA
* **
147543 AACGGGTACATGGCCTTAAAA
1 AACTGGTACATGGCCTTTCAA
*
147564 AACTGGTACACGGCCTTTCAA
1 AACTGGTACATGGCCTTTCAA
* *
147585 AATTGATACA-GGCCTTT
1 AACTGGTACATGGCCTTT
147602 AATTACTGAA
Statistics
Matches: 62, Mismatches: 18, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
20 7 0.11
21 55 0.89
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (21 bp):
AACTGGTACATGGCCTTTCAA
Found at i:147652 original size:21 final size:21
Alignment explanation
Indices: 147626--147665 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
147616 GTTTGTTTTT
147626 TTTTATTACAGGTACATGGTC
1 TTTTATTACAGGTACATGGTC
* *
147647 TTTTATTACTGGTATATGG
1 TTTTATTACAGGTACATGG
147666 CGTTTCATAA
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:0.23, C:0.10, G:0.20, T:0.47
Consensus pattern (21 bp):
TTTTATTACAGGTACATGGTC
Found at i:147705 original size:21 final size:21
Alignment explanation
Indices: 147679--147720 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
147669 TTCATAACAT
*
147679 GTACTTAACCTTTTATTACTG
1 GTACTTAACCTTTTATCACTG
*
147700 GTACTTGACCTTTTATCACTG
1 GTACTTAACCTTTTATCACTG
147721 ATATACGGCC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.45
Consensus pattern (21 bp):
GTACTTAACCTTTTATCACTG
Found at i:156085 original size:17 final size:17
Alignment explanation
Indices: 156063--156097 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
156053 TTTCTGGCAG
156063 TTGGTAACTATATAAAC
1 TTGGTAACTATATAAAC
156080 TTGGTAACTATATAAAC
1 TTGGTAACTATATAAAC
156097 T
1 T
156098 ATATAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (17 bp):
TTGGTAACTATATAAAC
Found at i:156597 original size:18 final size:17
Alignment explanation
Indices: 156557--156599 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
156547 TTTATCCTAA
**
156557 TATGACATTTTTCCGAT
1 TATGACATTTACCCGAT
*
156574 TTTGACATTTACCTCGAT
1 TATGACATTTACC-CGAT
156592 TATGACAT
1 TATGACAT
156600 GTCAAATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.44
Consensus pattern (17 bp):
TATGACATTTACCCGAT
Found at i:161573 original size:13 final size:13
Alignment explanation
Indices: 161541--161566 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
161531 TGTTTTATAC
161541 CATCACAGAAATA
1 CATCACAGAAATA
161554 CATCACAGAAATA
1 CATCACAGAAATA
161567 TTACACATGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (13 bp):
CATCACAGAAATA
Found at i:166918 original size:166 final size:166
Alignment explanation
Indices: 166221--167845 Score: 1943
Period size: 166 Copynumber: 9.8 Consensus size: 166
166211 TATTTGAGGC
* * * *
166221 AAATTTGTTTGAAAATTTTGCCT-AAAATAAACAAAGTACTCATTAAACAGGACGTTGACGTTCG
1 AAATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTTAACAGGAAGTTGACGTCCG
* * * * * *
166285 ATT-AGTACAAAAATAAATCCCCCGATATGGCATG-CATTAACAAACACTGTGTAAACATTTCAA
66 ATTGA-TACAAAAATATATCCCACAATATGGCATGCCA-AAACAAATACTGTGTAAAAATTTCAA
*
166348 GCATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGA
129 GCATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGA
* * *
166386 AAATTTGTTTGAAAATTTTGGCTAAAAAATAAACAAAGT-CATTATTTAACAGGAAGTTGACATC
1 AAATTTGTTTGAAAATTTTGTCT-AAAAATAAACAAAGTAC-TCATTTAACAGGAAGTTGACGTC
* * * * * *
166450 TGATTGATACAAAAATAAATCTCACAATATGGCTTGCCAAAACAAATAGTGTGTTAAAATTTCAA
64 CGATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAA
*
166515 GCATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGG
129 GCATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGA
* * * **
166553 ATATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTAAAAAGGGCGTTGACGTCCG
1 AAATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTTAACAGGAAGTTGACGTCCG
* * * ** * * * *
166618 ATTGGTACAAAAATACATCCCACGATATGGCATGCCCTACCAAACACTGTTTAAAAATTTTTAAG
66 ATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATACTGTGTAAAAA-TTTCAAG
* *
166683 CATCTGCGATAAGTAGCTGCTGAGAAATCTTTGACGA
130 CATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGA
* ** * * * *
166720 AAATTTGTTTGAAAATGTTGGATAAGAATAAACAAAGT-CATTATTTAACTGGAAGTTGACATCC
1 AAATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTAC-TCATTTAACAGGAAGTTGACGTCC
* * *
166784 GATTGATACAAAAATATATCTCACAATATGGCTTGCCAAAA-ACAATAGTGTGTTAAAAA-TTCA
65 GATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACA-AATACTGTG-TAAAAATTTCA
* *
166847 AGCATCTGCGATAGATAGTTGCTGAGAAATCTTTGACGG
128 AGCATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGA
* * *
166886 ATATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTTATTAAACAGGAAGTTGACGTCCG
1 AAATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTTAACAGGAAGTTGACGTCCG
* * * * * ** * *
166951 ATTAAGACAACAATACATCCCACGATATGGCATGCCTTAACAAACACTGTGT-AAAATGTCAAGC
66 ATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGC
* * *
167015 ATCTGCGATAAATAGCTGCTGAGAAATCGTTGACGG
131 ATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGA
* * *
167051 AAATTTGTTTGAAAATTTTGGCTAAAAATAAACAAAGT-CATTATTTAACAGGAAGTTGACATCC
1 AAATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTAC-TCATTTAACAGGAAGTTGACGTCC
* * * *
167115 GATTGATACAAAAATATATCTCACAATATGGCTTGCCAAAACAAATAGTGTGTAAAAATTTTAAG
65 GATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAG
* *
167180 CATCTGCGATAAATAGTTGCTGAGAATTCTTTGACGG
130 CATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGA
* * *
167217 ATATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTAAACAAGAAGTTGACGTCCG
1 AAATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTTAACAGGAAGTTGACGTCCG
* * * * * * * *
167282 ATTGTTACACAAATACATCCCACGATATAGCATGCCTATACAAATATTGTGTAAAAATTTCAAGC
66 ATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGC
* * * * * *
167347 ATCTGCGATTAACATTTGCTAAGAATTCTTTGACAA
131 ATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGA
* * *
167383 AAATTTGTTTGAAAATTTT-TGCTAAAAATAAACAAAGTCCTTATTTAACAGGAAGTTGACGTCT
1 AAATTTGTTTGAAAATTTTGT-CTAAAAATAAACAAAGTACTCATTTAACAGGAAGTTGACGTCC
* * * * *
167447 GATTGGTTCAAAAATATATCCCACAATATGGCTTGCCAAAATAAATAGTGTGTAAAAATTTCAAG
65 GATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAG
** * *
167512 CATCTGCGATAAATAGTTGCAAAGAATTCTTTGACAA
130 CATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGA
*
167549 AAATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCA-TTAGACAGGAAGTTGACGTCT
1 AAATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTTA-ACAGGAAGTTGACGTCC
* * * * **
167613 GATTGTTACAAAAATATATCCCACAATATGACATGCCTATACAAATACCATGTAAAAATTTCAAG
65 GATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAG
* *
167678 CATCTGCAATAAATAGTTGCTGAGAAATCTTTGACAA
130 CATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGA
*
167715 AAATTTGTTTG-AAATTTTGGT-TAAAAATAAGCAAAGT-CGTCATTTAACAGGAAGTTGACGTC
1 AAATTTGTTTGAAAATTTT-GTCTAAAAATAAACAAAGTAC-TCATTTAACAGGAAGTTGACGTC
* * * ** *
167777 CGATTGGTACAAATATATATTCCC-CGATATGGCATGCCTTAACAAACAC--TGTAAAAATTTCA
64 CGATTGATACAAAAATATA-TCCCACAATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCA
167839 AGCATCT
128 AGCATCT
167846 ATGGACGGAA
Statistics
Matches: 1254, Mismatches: 183, Indels: 48
0.84 0.12 0.03
Matches are distributed among these distances:
163 20 0.02
164 6 0.00
165 243 0.19
166 703 0.56
167 273 0.22
168 9 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (166 bp):
AAATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTTAACAGGAAGTTGACGTCCG
ATTGATACAAAAATATATCCCACAATATGGCATGCCAAAACAAATACTGTGTAAAAATTTCAAGC
ATCTGCGATAAATAGTTGCTGAGAAATCTTTGACGA
Found at i:167521 original size:332 final size:332
Alignment explanation
Indices: 166223--167845 Score: 2325
Period size: 332 Copynumber: 4.9 Consensus size: 332
166213 TTTGAGGCAA
* * *
166223 ATTTGTTTGAAAATTTTGCCT-AAAATAAACAAAGTACTCATTAAACAGGACGTTGACGTTCGAT
1 ATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTAAACAGGAAGTTGACGTCCGAT
* * * *
166287 TAG-TACAAAAATAAATCCCCCGATATGGCATGCAT-TAACAAACACTGTGTAAACATTTCAAGC
66 T-GTTACAAAAATACATCCCACGATATGGCATGCCTAT-ACAAACACTGTGTAAAAATTTCAAGC
166350 ATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAAA
129 ATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCT-AAAAA
* *
166415 TAAACAAAGTCATTATTTAACAGGAAGTTGACATCTGATTGATACAAAAATAAATCTCACAATAT
193 TAAACAAAGTCATTATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCTCACAATAT
*
166480 GGCTTGCCAAAACAAATAGTGTGTTAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATC
258 GGCTTGCCAAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATC
166545 TTTGACGGAT
323 TTTGACGGAT
* **
166555 ATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTAAAAAGGGCGTTGACGTCCGAT
1 ATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTAAACAGGAAGTTGACGTCCGAT
* * * *
166620 TGGTACAAAAATACATCCCACGATATGGCATGCCCTA-CCAAACACTGTTTAAAAATTTTTAAGC
66 TGTTACAAAAATACATCCCACGATATGGCATG-CCTATACAAACACTGTGTAAAAA-TTTCAAGC
* * * *
166684 ATCTGCGATAAGTAGCTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATGTTGGATAAGAAT
129 ATCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAAT
*
166749 AAACAAAGTCATTATTTAACTGGAAGTTGACATCCGATTGATACAAAAATATATCTCACAATATG
194 AAACAAAGTCATTATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCTCACAATATG
*
166814 GCTTGCCAAAA-ACAATAGTGTGTTAAAAA-TTCAAGCATCTGCGATAGATAGTTGCTGAGAAAT
259 GCTTGCCAAAACA-AATAGTGTG-TAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAAT
166877 CTTTGACGGAT
322 CTTTGACGGAT
*
166888 ATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTTATTAAACAGGAAGTTGACGTCCGAT
1 ATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTAAACAGGAAGTTGACGTCCGAT
*** * *
166953 TAAGACAACAATACATCCCACGATATGGCATGCCT-TAACAAACACTGTGT-AAAATGTCAAGCA
66 TGTTACAAAAATACATCCCACGATATGGCATGCCTAT-ACAAACACTGTGTAAAAATTTCAAGCA
* *
167016 TCTGCGATAAATAGCTGCTGAGAAATCGTTGACGGAAATTTGTTTGAAAATTTTGGCTAAAAATA
130 TCTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAATA
167081 AACAAAGTCATTATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCTCACAATATGG
195 AACAAAGTCATTATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCTCACAATATGG
* *
167146 CTTGCCAAAACAAATAGTGTGTAAAAATTTTAAGCATCTGCGATAAATAGTTGCTGAGAATTCTT
260 CTTGCCAAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTT
167211 TGACGGAT
325 TGACGGAT
*
167219 ATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTAAACAAGAAGTTGACGTCCGAT
1 ATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTAAACAGGAAGTTGACGTCCGAT
* * * *
167284 TGTTACACAAATACATCCCACGATATAGCATGCCTATACAAATATTGTGTAAAAATTTCAAGCAT
66 TGTTACAAAAATACATCCCACGATATGGCATGCCTATACAAACACTGTGTAAAAATTTCAAGCAT
* * ** * * * *
167349 CTGCGATTAACATTTGCTAAGAATTCTTTGACAAAAATTTGTTTGAAAATTTTTGCTAAAAATAA
131 CTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAATAA
* * * * * *
167414 ACAAAGTCCTTATTTAACAGGAAGTTGACGTCTGATTGGTTCAAAAATATATCCCACAATATGGC
196 ACAAAGTCATTATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCTCACAATATGGC
* ** *
167479 TTGCCAAAATAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCAAAGAATTCTTT
261 TTGCCAAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTT
** *
167544 GACAAAA
326 GACGGAT
* *
167551 ATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTAGACAGGAAGTTGACGTCTGAT
1 ATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTAAACAGGAAGTTGACGTCCGAT
* * * * **
167616 TGTTACAAAAATATATCCCACAATATGACATGCCTATACAAATACCATGTAAAAATTTCAAGCAT
66 TGTTACAAAAATACATCCCACGATATGGCATGCCTATACAAACACTGTGTAAAAATTTCAAGCAT
* * * *
167681 CTGCAATAAATAGTTGCTGAGAAATCTTTGACAAAAATTTGTTTG-AAATTTTGGTTAAAAATAA
131 CTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAATAA
* * * * * * * *
167745 GCAAAGTCGTCATTTAACAGGAAGTTGACGTCCGATTGGTACAAATATATAT-TCCCCGATATGG
196 ACAAAGTCATTATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCT-CACAATATGG
* ** * *
167809 CATGCCTTAACAAACA--CTGTAAAAATTTCAAGCATCT
260 CTTGCCAAAACAAATAGTGTGTAAAAATTTCAAGCATCT
167846 ATGGACGGAA
Statistics
Matches: 1167, Mismatches: 110, Indels: 31
0.89 0.08 0.02
Matches are distributed among these distances:
329 20 0.02
330 6 0.01
331 376 0.32
332 381 0.33
333 314 0.27
334 70 0.06
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (332 bp):
ATTTGTTTGAAAATTTTGTCTAAAAATAAACAAAGTACTCATTAAACAGGAAGTTGACGTCCGAT
TGTTACAAAAATACATCCCACGATATGGCATGCCTATACAAACACTGTGTAAAAATTTCAAGCAT
CTGCGATAAATAGCTGCTGAGAAATCTTTGACGAAAATTTGTTTGAAAATTTTGGCTAAAAATAA
ACAAAGTCATTATTTAACAGGAAGTTGACATCCGATTGATACAAAAATATATCTCACAATATGGC
TTGCCAAAACAAATAGTGTGTAAAAATTTCAAGCATCTGCGATAAATAGTTGCTGAGAAATCTTT
GACGGAT
Found at i:169135 original size:22 final size:22
Alignment explanation
Indices: 169107--169149 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
169097 AAAAATATTT
*
169107 TTGAATTTGATATAACGAATTC
1 TTGAATTTGATAAAACGAATTC
*
169129 TTGAATTTGTTAAAACGAATT
1 TTGAATTTGATAAAACGAATT
169150 TAAATCGTGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.37, C:0.07, G:0.14, T:0.42
Consensus pattern (22 bp):
TTGAATTTGATAAAACGAATTC
Found at i:169166 original size:19 final size:20
Alignment explanation
Indices: 169117--169235 Score: 89
Period size: 19 Copynumber: 5.7 Consensus size: 20
169107 TTGAATTTGA
* *
169117 TATAACGAATTCTTGAATTTGT
1 TATAACGAA-T-TTAAATTCGT
*
169139 TAAAACGAATTTAAA-TCGT
1 TATAACGAATTTAAATTCGT
* * *
169158 GATAACGAATTGTTGAATCCGT
1 TATAACGAA-T-TTAAATTCGT
*
169180 TATAACGAA-TTAAATTTGT
1 TATAACGAATTTAAATTCGT
*
169199 TATAACAAATTTTAGGAATTCGT
1 TATAACGAA-TTTA--AATTCGT
169222 TATAACGAATTTAA
1 TATAACGAATTTAA
169236 TCTGTTAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
19 25 0.33
20 6 0.08
21 8 0.11
22 23 0.30
23 14 0.18
ACGTcount: A:0.39, C:0.09, G:0.13, T:0.38
Consensus pattern (20 bp):
TATAACGAATTTAAATTCGT
Found at i:169174 original size:41 final size:41
Alignment explanation
Indices: 169118--169235 Score: 132
Period size: 41 Copynumber: 2.8 Consensus size: 41
169108 TGAATTTGAT
* *
169118 ATAACGAATTCTTGAATTTGTTAAAACGAATTTAAA-TCGTG
1 ATAACGAATT-TTGAATTCGTTATAACGAATTTAAATTCGTG
* * *
169159 ATAACGAATTGTTGAATCCGTTATAACGAA-TTAAATTTGTT
1 ATAACGAATT-TTGAATTCGTTATAACGAATTTAAATTCGTG
*
169200 ATAACAAATTTTAGGAATTCGTTATAACGAATTTAA
1 ATAACGAATTTT--GAATTCGTTATAACGAATTTAA
169236 TCTGTTAAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
40 7 0.11
41 38 0.58
42 16 0.25
43 4 0.06
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (41 bp):
ATAACGAATTTTGAATTCGTTATAACGAATTTAAATTCGTG
Found at i:169260 original size:42 final size:41
Alignment explanation
Indices: 169130--169266 Score: 132
Period size: 42 Copynumber: 3.3 Consensus size: 41
169120 AACGAATTCT
* * * * *
169130 TGAATTTGTTAAAACGAATTTAAATC-GTGATAACGAATTGT
1 TGAATTCGTTATAACGAATTT-AATCTGTTATAACAAATTGA
* * * *
169171 TGAATCCGTTATAACGAATTAAATTTGTTATAACAAATTTTA
1 TGAATTCGTTATAACGAATTTAATCTGTTATAACAAA-TTGA
* * *
169213 GGAATTCGTTATAACGAATTTAATCTGTTAAAACAAATTCGC
1 TGAATTCGTTATAACGAATTTAATCTGTTATAACAAATT-GA
169255 TGAATTCGTTAT
1 TGAATTCGTTAT
169267 TTCAAATTTT
Statistics
Matches: 76, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
40 3 0.04
41 28 0.37
42 45 0.59
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (41 bp):
TGAATTCGTTATAACGAATTTAATCTGTTATAACAAATTGA
Found at i:169361 original size:40 final size:41
Alignment explanation
Indices: 169288--169369 Score: 148
Period size: 40 Copynumber: 2.0 Consensus size: 41
169278 AAATCTGTTT
169288 TAACAAATTAAATTTGAAATAACGAATTCTTGAATTCGTTA
1 TAACAAATTAAATTTGAAATAACGAATTCTTGAATTCGTTA
*
169329 TAACAAATTAAATTT-AAATAACGAATTGTTGAATTCGTTA
1 TAACAAATTAAATTTGAAATAACGAATTCTTGAATTCGTTA
169369 T
1 T
169370 TTCGAAGTTT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
40 25 0.62
41 15 0.38
ACGTcount: A:0.44, C:0.09, G:0.10, T:0.38
Consensus pattern (41 bp):
TAACAAATTAAATTTGAAATAACGAATTCTTGAATTCGTTA
Found at i:171705 original size:21 final size:20
Alignment explanation
Indices: 171676--171741 Score: 69
Period size: 21 Copynumber: 3.1 Consensus size: 20
171666 AAAAGCCTGA
*
171676 GTCAATGTACGTATCATCAGG
1 GTCAGTGTACGTATCA-CAGG
*
171697 GTCAGTGTATGTATCACTAGG
1 GTCAGTGTACGTATCAC-AGG
* *
171718 GTCAGAGTTCGTATCACCAGG
1 GTCAGTGTACGTATCA-CAGG
171739 GTC
1 GTC
171742 TGTATACCCA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 1 0.03
21 36 0.95
22 1 0.03
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (20 bp):
GTCAGTGTACGTATCACAGG
Found at i:171836 original size:84 final size:84
Alignment explanation
Indices: 171547--171828 Score: 284
Period size: 84 Copynumber: 3.4 Consensus size: 84
171537 ATGAATCACT
* *
171547 AGGGTCAGTGTTCGTATCACCAGGGTCTGTATACCCATAACCTGGGTCAGTATTACGATTATCAG
1 AGGGTCAGTGTTCGTATCACCAGGGTCTGTATACCCATAACCTGGGTCAATATTACAATTATCAG
171612 GATGTCTATATCTATTACC
66 GATGTCTATATCTATTACC
* * * ** * * * * * * * * * *
171631 AGGGTCTGCGTGCCCATCATCTGGGTATGCATA-CAAAAAGCCTGAGTCAAT-GTACGTATCATC
1 AGGGTCAGTGTTCGTATCACCAGGGTCTGTATACCCATAA-CCTGGGTCAATATTAC-AATTATC
* * * *
171694 AGG--GTCAGTGTATGTATCACT
64 AGGATGTC--TATATCTATTACC
*
171715 AGGGTCAGAGTTCGTATCACCAGGGTCTGTATACCCATAACCTGGGTCAATATTACAATTATCAG
1 AGGGTCAGTGTTCGTATCACCAGGGTCTGTATACCCATAACCTGGGTCAATATTACAATTATCAG
171780 GATGTCTATATCTATTACC
66 GATGTCTATATCTATTACC
* *
171799 AAGGTCAGTGTACGTATCACCAGGGTCTGT
1 AGGGTCAGTGTTCGTATCACCAGGGTCTGT
171829 GTGCCCATCA
Statistics
Matches: 148, Mismatches: 42, Indels: 16
0.72 0.20 0.08
Matches are distributed among these distances:
82 3 0.02
83 7 0.05
84 128 0.86
85 7 0.05
86 3 0.02
ACGTcount: A:0.26, C:0.21, G:0.23, T:0.30
Consensus pattern (84 bp):
AGGGTCAGTGTTCGTATCACCAGGGTCTGTATACCCATAACCTGGGTCAATATTACAATTATCAG
GATGTCTATATCTATTACC
Found at i:171898 original size:168 final size:166
Alignment explanation
Indices: 171534--171898 Score: 376
Period size: 168 Copynumber: 2.2 Consensus size: 166
171524 AATAGCATAT
* * * *
171534 TGTATGAATCACTAGGGTCAGTGTTCGTATCACCAGGGTCTGTATACCCATAACCTGGGTCAGTA
1 TGTATGTATCACCAAGGTCAGTGTTCGTATCACCAGGGTCTGTATACCCATAACCTGGGTCAATA
* * * * * *
171599 TTACGATTATCAGGATGTCTATATCTATTACCAGGGTCTGCGTGCCCATCATCTGGGTATGCATA
66 TTACAATTATCAGGATGTCTATATCTATTACCAAGGTCAGCGTACCCATCACCAGGGTATGCATA
** * **
171664 CAAAAAGCCTGAGTCAATGTACGTATCATCAGGGTCA
131 CAAAAA-CCAAAGTCAATGAACCCATCATCAGGGTCA
* * *
171701 GTGTATGTATCACTAGGGTCAGAGTTCGTATCACCAGGGTCTGTATACCCATAACCTGGGTCAAT
1 -TGTATGTATCACCAAGGTCAGTGTTCGTATCACCAGGGTCTGTATACCCATAACCTGGGTCAAT
* ** * **
171766 ATTACAATTATCAGGATGTCTATATCTATTACCAAGGTCAGTGTACGTATCACCAGGGTCTGTGT
65 ATTACAATTATCAGGATGTCTATATCTATTACCAAGGTCAGCGTACCCATCACCAGGGTATGCAT
* ** * **
171831 GC-CCATCACAAAGTCTTTAGAACCCATCATCAGGGTC-
130 ACAAAAAC-CAAAGTCAAT-GAACCCATCATCAGGGTCA
171868 T-TAATGCATATCACCAAGGTCAGTGTTCGTA
1 TGT-ATG--TATCACCAAGGTCAGTGTTCGTA
171899 CATGTATCAC
Statistics
Matches: 163, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
165 1 0.01
166 5 0.03
167 7 0.04
168 150 0.92
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.30
Consensus pattern (166 bp):
TGTATGTATCACCAAGGTCAGTGTTCGTATCACCAGGGTCTGTATACCCATAACCTGGGTCAATA
TTACAATTATCAGGATGTCTATATCTATTACCAAGGTCAGCGTACCCATCACCAGGGTATGCATA
CAAAAACCAAAGTCAATGAACCCATCATCAGGGTCA
Found at i:172356 original size:21 final size:21
Alignment explanation
Indices: 172332--172435 Score: 70
Period size: 21 Copynumber: 5.0 Consensus size: 21
172322 TCTGGTTATG
172332 CGTATACAGACCCTGGTGATA
1 CGTATACAGACCCTGGTGATA
* * *
172353 CGTACACCGACTCTGGT-AGTA
1 CGTATACAGACCCTGGTGA-TA
* * *
172374 CGTACT-CTGACCTTGGTAATA
1 CGTA-TACAGACCCTGGTGATA
* * *
172395 TGTACT-CTGACCCTGGTGATT
1 CGTA-TACAGACCCTGGTGATA
*
172416 GGTATACAGACCCTGGTGAT
1 CGTATACAGACCCTGGTGAT
172436 GGACACACAG
Statistics
Matches: 66, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
20 2 0.03
21 63 0.95
22 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.24, T:0.29
Consensus pattern (21 bp):
CGTATACAGACCCTGGTGATA
Found at i:172369 original size:42 final size:43
Alignment explanation
Indices: 172322--172435 Score: 101
Period size: 42 Copynumber: 2.7 Consensus size: 43
172312 GTATACTGAA
172322 TCTGGTTA-TGCGTATACAGACCCTGGTGATACGTACACCGAC
1 TCTGGTTAGTGCGTATACAGACCCTGGTGATACGTACACCGAC
* * * * * * *
172364 TCTGG-TAGTACGTACT-CTGACCTTGGTAATATGTACTCTGAC
1 TCTGGTTAGTGCGTA-TACAGACCCTGGTGATACGTACACCGAC
* * *
172406 CCTGGTGATTG-GTATACAGACCCTGGTGAT
1 TCTGGTTAGTGCGTATACAGACCCTGGTGAT
172436 GGACACACAG
Statistics
Matches: 54, Mismatches: 14, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
41 3 0.06
42 48 0.89
43 3 0.06
ACGTcount: A:0.22, C:0.23, G:0.25, T:0.31
Consensus pattern (43 bp):
TCTGGTTAGTGCGTATACAGACCCTGGTGATACGTACACCGAC
Found at i:172445 original size:21 final size:21
Alignment explanation
Indices: 172403--172455 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
172393 TATGTACTCT
* *
172403 GACCCTGGTGATTGGTATACA
1 GACCCTGGTGATTGGCACACA
172424 GACCCTGGTGA-TGGACACACA
1 GACCCTGGTGATTGG-CACACA
*
172445 GACCTTGGTGA
1 GACCCTGGTGA
172456 GGTGTTATGG
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
20 3 0.11
21 25 0.89
ACGTcount: A:0.25, C:0.23, G:0.30, T:0.23
Consensus pattern (21 bp):
GACCCTGGTGATTGGCACACA
Found at i:173233 original size:177 final size:179
Alignment explanation
Indices: 172930--173368 Score: 702
Period size: 177 Copynumber: 2.5 Consensus size: 179
172920 TCTAAATCTT
*
172930 CTGGTCCTAACTTCACCAAACTTGTATGGATGATGCGTCTTATGATACTGATGCACCTGACAAGC
1 CTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAAGC
*
172995 TTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTTAGAGCTGG-T
66 TTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTAAGAGCTGGTT
*** *
173059 -TAAAGTTTTTGTTGCAGGTGCCCTCTGATGATTATATCTTAGTTACTA
131 ATAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTAGTTACTA
173107 CTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAAGC
1 CTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAAGC
*
173172 TTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAGGAGGTTAAGGTTTTAAGAGCTGGTT
66 TTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTAAGAGCTGGTT
*
173237 AAATAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTAGTTATTA
131 --ATAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTAGTTACTA
* * * ** * *
173288 CTTGTCCTTACTTCACCAGACTTCCATGGATGGTGTGTCTTATGATACTGATGCACCTGACAGGC
1 CTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAAGC
*
173353 TTGAATGCTGAGTCTG
66 TTGAATGCTGAATCTG
173369 GTTTCGGTGC
Statistics
Matches: 242, Mismatches: 16, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
177 125 0.52
178 1 0.00
181 116 0.48
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.33
Consensus pattern (179 bp):
CTGGTCCTAACTTCACCAAACTTGTATGGATGGTGCGTCTTATGATACTGATGCACCTGACAAGC
TTGAATGCTGAATCTGAGCAATAGGTTTCGGATGCTGGAAGAGGTTAAGGTTTTAAGAGCTGGTT
ATAAAGTTTTTGAAACAGGTGCCCTCTGATGATGATATCTTAGTTACTA
Found at i:180243 original size:2 final size:2
Alignment explanation
Indices: 180236--180261 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
180226 TAAACGATGC
180236 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
180262 CACGAGAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:180298 original size:22 final size:22
Alignment explanation
Indices: 180263--180357 Score: 68
Period size: 22 Copynumber: 4.4 Consensus size: 22
180253 TATATATATC
* *
180263 ACGAGAAAAATAACTCGTAATA
1 ACGAGATAATTAACTCGTAATA
* *
180285 ACGAGATAATTAACTCGAAATT
1 ACGAGATAATTAACTCGTAATA
* *** *
180307 ACGAGAT-CTTTTGTCATAA-A
1 ACGAGATAATTAACTCGTAATA
* *
180327 ACCGAGATAATTAGCTCCTAATA
1 A-CGAGATAATTAACTCGTAATA
180350 ACGAGATA
1 ACGAGATA
180358 TTTTCTTGTT
Statistics
Matches: 54, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
20 1 0.02
21 12 0.22
22 39 0.72
23 2 0.04
ACGTcount: A:0.44, C:0.16, G:0.15, T:0.25
Consensus pattern (22 bp):
ACGAGATAATTAACTCGTAATA
Found at i:194046 original size:1 final size:1
Alignment explanation
Indices: 194042--194066 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
194032 TGGACGTGAA
194042 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
194067 GCATCTACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:222185 original size:19 final size:19
Alignment explanation
Indices: 222161--222199 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
222151 ATGTTGTTTC
222161 TGTTCACACCAATCATCAT
1 TGTTCACACCAATCATCAT
222180 TGTTCACACCAATCATCAT
1 TGTTCACACCAATCATCAT
222199 T
1 T
222200 ACAAAATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (19 bp):
TGTTCACACCAATCATCAT
Found at i:245938 original size:17 final size:18
Alignment explanation
Indices: 245918--245952 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
245908 GCATGAACAA
245918 AATCAAT-TTTGTTTTGT
1 AATCAATCTTTGTTTTGT
*
245935 AATCATTCTTTGTTTTGT
1 AATCAATCTTTGTTTTGT
245953 TTTGGAAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.20, C:0.09, G:0.11, T:0.60
Consensus pattern (18 bp):
AATCAATCTTTGTTTTGT
Found at i:248391 original size:2 final size:2
Alignment explanation
Indices: 248384--248420 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
248374 CAGTATGTAA
*
248384 AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
248421 AGCTTAATTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:250635 original size:2 final size:2
Alignment explanation
Indices: 250628--250662 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
250618 TTTTTATTAA
250628 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
250663 AGCAGACACT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:263695 original size:2 final size:2
Alignment explanation
Indices: 263688--263771 Score: 100
Period size: 2 Copynumber: 42.5 Consensus size: 2
263678 TATTACAGGC
* *
263688 AG AG AG AG AG AG AG AG ATG -G AG AG AG AG AG AG AA AT AG AG AG
1 AG AG AG AG AG AG AG AG A-G AG AG AG AG AG AG AG AG AG AG AG AG
* * *
263730 AG AG AG AG AG AG AA AG AG AG AG -G AA AG AG TG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
263771 A
1 A
263772 TACTGTCCCT
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
1 2 0.03
2 67 0.96
3 1 0.01
ACGTcount: A:0.51, C:0.00, G:0.45, T:0.04
Consensus pattern (2 bp):
AG
Found at i:277124 original size:21 final size:21
Alignment explanation
Indices: 277078--277133 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
277068 CAAGTTATTC
277078 ATGTTAACATGCAAGAAATTG
1 ATGTTAACATGCAAGAAATTG
*
277099 ATGTTAACATGCGAGAAAATTG
1 ATGTTAACATGCAAG-AAATTG
* *
277121 -TGTTGACGTGCAA
1 ATGTTAACATGCAA
277134 CTTATTTATG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
21 24 0.80
22 6 0.20
ACGTcount: A:0.38, C:0.11, G:0.23, T:0.29
Consensus pattern (21 bp):
ATGTTAACATGCAAGAAATTG
Found at i:277184 original size:21 final size:22
Alignment explanation
Indices: 277160--277203 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
277150 TGTGAGTTAG
277160 TTATGTAAACATGC-AAATAAT
1 TTATGTAAACATGCGAAATAAT
* *
277181 TTATGTCAACATGCGAGATAAT
1 TTATGTAAACATGCGAAATAAT
277203 T
1 T
277204 GAAGATTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.34
Consensus pattern (22 bp):
TTATGTAAACATGCGAAATAAT
Found at i:277583 original size:28 final size:28
Alignment explanation
Indices: 277543--277599 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
277533 TGGAAAGTTA
*
277543 GTTTAGAAAAATGGGTGTCATTACACTC
1 GTTTAGAAAAATGGCTGTCATTACACTC
* *
277571 GTTTAGAATAATGGCTGTCATTGCACTC
1 GTTTAGAAAAATGGCTGTCATTACACTC
277599 G
1 G
277600 CATACCTACT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.28, C:0.16, G:0.23, T:0.33
Consensus pattern (28 bp):
GTTTAGAAAAATGGCTGTCATTACACTC
Found at i:282969 original size:21 final size:22
Alignment explanation
Indices: 282914--282974 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 22
282904 CTTGCATGAC
*
282914 ATATGTTGACATAAATATCTTG
1 ATATGTTGACATAAATAACTTG
* * *
282936 CATGTGTTAACATAATTAACTTG
1 -ATATGTTGACATAAATAACTTG
282959 -TATGTTGACATAAATA
1 ATATGTTGACATAAATA
282975 TGTCGAATGT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
21 13 0.42
23 18 0.58
ACGTcount: A:0.38, C:0.10, G:0.13, T:0.39
Consensus pattern (22 bp):
ATATGTTGACATAAATAACTTG
Found at i:283055 original size:43 final size:42
Alignment explanation
Indices: 283000--283098 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 42
282990 TTAATGAGTC
* * *
283000 GCATGTCGACATAATTAATTCACATG-TCAACATTAGATATA-TT
1 GCATGTCAACATAATTAACTCACATGTTC-ACA-TAAATA-AGTT
* *
283043 GCATGTTAACATAATTAACTCGCATGTTCACATAAATAAGTT
1 GCATGTCAACATAATTAACTCACATGTTCACATAAATAAGTT
283085 GCATGTCAACATAA
1 GCATGTCAACATAA
283099 ATAAGTCGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
41 1 0.02
42 20 0.42
43 25 0.52
44 2 0.04
ACGTcount: A:0.38, C:0.17, G:0.12, T:0.32
Consensus pattern (42 bp):
GCATGTCAACATAATTAACTCACATGTTCACATAAATAAGTT
Found at i:283069 original size:21 final size:21
Alignment explanation
Indices: 282940--283112 Score: 96
Period size: 21 Copynumber: 8.2 Consensus size: 21
282930 ATCTTGCATG
* * * *
282940 TGTTAACATAATTAACTTGTA
1 TGTTAACATAAATAAGTCGCA
* * *
282961 TGTTGACATAAATATGTCGAA
1 TGTTAACATAAATAAGTCGCA
** * *
282982 TGTCGACATTAATGAGTCGCA
1 TGTTAACATAAATAAGTCGCA
** * * *
283003 TGTCGACATAATTAATTCACA
1 TGTTAACATAAATAAGTCGCA
* * *
283024 TGTCAACATTAGATATA-TTGCA
1 TGTTAACA-TAAATA-AGTCGCA
* *
283046 TGTTAACATAATTAACTCGCA
1 TGTTAACATAAATAAGTCGCA
* *
283067 TGTTCACATAAATAAGTTGCA
1 TGTTAACATAAATAAGTCGCA
* *
283088 TGTCAACATAAATAAGTCGTA
1 TGTTAACATAAATAAGTCGCA
283109 TGTT
1 TGTT
283113 GTTATAATTA
Statistics
Matches: 115, Mismatches: 34, Indels: 6
0.74 0.22 0.04
Matches are distributed among these distances:
20 1 0.01
21 99 0.86
22 14 0.12
23 1 0.01
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Consensus pattern (21 bp):
TGTTAACATAAATAAGTCGCA
Found at i:283098 original size:42 final size:44
Alignment explanation
Indices: 283000--283112 Score: 117
Period size: 42 Copynumber: 2.6 Consensus size: 44
282990 TTAATGAGTC
* * * *
283000 GCATGTCGACATAATTAATTCACATG-TCAACATTAGATATATT
1 GCATGTCAACATAATTAACTCGCATGTTCAACATTAAATATATT
*
283043 GCATGTTAACATAATTAACTCGCATGTTC-ACA-TAAATA-AGTT
1 GCATGTCAACATAATTAACTCGCATGTTCAACATTAAATATA-TT
* * *
283085 GCATGTCAACATAAATAAGTCGTATGTT
1 GCATGTCAACATAATTAACTCGCATGTT
283113 GTTATAATTA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
41 1 0.02
42 31 0.53
43 25 0.42
44 2 0.03
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (44 bp):
GCATGTCAACATAATTAACTCGCATGTTCAACATTAAATATATT
Found at i:283237 original size:21 final size:21
Alignment explanation
Indices: 283211--283300 Score: 92
Period size: 21 Copynumber: 4.2 Consensus size: 21
283201 GGATTGCTAA
283211 CTTGCATGTCAACATAATTAT
1 CTTGCATGTCAACATAATTAT
** *
283232 CTTGCATGTCAATGTTATTAT
1 CTTGCATGTCAACATAATTAT
* *
283253 CTTGCATGTTAACATAATTTT
1 CTTGCATGTCAACATAATTAT
* *
283274 CTTGAATGTTGAA-ATAATTTAT
1 CTTGCATG-TCAACATAA-TTAT
283296 CTTGC
1 CTTGC
283301 GTGTAGGGGG
Statistics
Matches: 55, Mismatches: 12, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
21 45 0.82
22 10 0.18
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.44
Consensus pattern (21 bp):
CTTGCATGTCAACATAATTAT
Found at i:287989 original size:142 final size:141
Alignment explanation
Indices: 287733--288016 Score: 559
Period size: 142 Copynumber: 2.0 Consensus size: 141
287723 AAAAGTGACA
287733 ATTTTCCTAGTGATTAGACCACCTACCATAATAAACTTGCTGAATCATATATCTTTTTAAAAAAA
1 ATTTTCCTAGTGATTAGACCACCTACCATAATAAACTTGCTGAATCATATATCTTTTTAAAAAAA
287798 ATGTCCTTTTTGAGAATATGAAAGAGCTCGAGATTAAACATATTTTTATCATGAATCCAAAACTA
66 ATGTCCTTTTTGAGAATATGAAAGAGCTCGAGATTAAACATATTTTTATCATGAATCCAAAACTA
287863 TTATGGGGGGG
131 TTATGGGGGGG
287874 NATTTTCCTAGTGATTAGACCACCTACCATAATAAACTTGCTGAATCATATATCTTTTTAAAAAA
1 -ATTTTCCTAGTGATTAGACCACCTACCATAATAAACTTGCTGAATCATATATCTTTTTAAAAAA
287939 AATGTCCTTTTTGAGAATATGAAAGAGCTCGAGATTAAACATATTTTTATCATGAATCCAAAACT
65 AATGTCCTTTTTGAGAATATGAAAGAGCTCGAGATTAAACATATTTTTATCATGAATCCAAAACT
288004 ATTATGGGGGGG
130 ATTATGGGGGGG
288016 A
1 A
288017 GAACCTCTCG
Statistics
Matches: 142, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
141 1 0.01
142 141 0.99
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (141 bp):
ATTTTCCTAGTGATTAGACCACCTACCATAATAAACTTGCTGAATCATATATCTTTTTAAAAAAA
ATGTCCTTTTTGAGAATATGAAAGAGCTCGAGATTAAACATATTTTTATCATGAATCCAAAACTA
TTATGGGGGGG
Found at i:298510 original size:2 final size:2
Alignment explanation
Indices: 298503--298578 Score: 102
Period size: 2 Copynumber: 38.5 Consensus size: 2
298493 ATTAAATTAC
*
298503 AG AG AG AG AG AG AG AG AG TA- AG AG AG AG AG TG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG -AG AG AG AG AG AG AG AG AG AG AG AG
* *
298545 AG -G AG AG AG AG AG AA AG AG AG AA AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
298579 CCTCACTACT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
1 2 0.03
2 62 0.95
3 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.46, T:0.03
Consensus pattern (2 bp):
AG
Found at i:311013 original size:34 final size:34
Alignment explanation
Indices: 310947--311013 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
310937 AAGACAAATT
*
310947 ATTCCTCAAAATTGCTGTTTATTTCTTTGAAAGG
1 ATTCCTCAAAATTGCTGTTTATTTCTTAGAAAGG
*
310981 ATTCCTCAACATTGCTGTTTATTT-TTAAGAAAG
1 ATTCCTCAAAATTGCTGTTTATTTCTT-AGAAAG
311014 TACAAGCAGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 2 0.07
34 28 0.93
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (34 bp):
ATTCCTCAAAATTGCTGTTTATTTCTTAGAAAGG
Found at i:322796 original size:9 final size:9
Alignment explanation
Indices: 322784--322830 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
322774 TTTTGCGCCA
322784 TTTGTTTTT
1 TTTGTTTTT
*
322793 TTTG-TTTG
1 TTTGTTTTT
322801 TTTGTTTTGT
1 TTTGTTTT-T
322811 TTTGTTTTTT
1 TTTG-TTTTT
322821 TTTGTTTTT
1 TTTGTTTTT
322830 T
1 T
322831 GGCACTGTCA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
8 7 0.21
9 13 0.39
10 9 0.27
11 4 0.12
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (9 bp):
TTTGTTTTT
Found at i:322811 original size:5 final size:5
Alignment explanation
Indices: 322784--322828 Score: 60
Period size: 5 Copynumber: 9.6 Consensus size: 5
322774 TTTTGCGCCA
*
322784 TTTGT TTT-T TTTG- TTTG- TTTGT TTTGT TTTGT TTTTT TTTGT TTT
1 TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTTGT TTT
322829 TTGGCACTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
4 12 0.33
5 24 0.67
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (5 bp):
TTTGT
Found at i:323899 original size:2 final size:2
Alignment explanation
Indices: 323892--323923 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
323882 TCGAGAAATC
323892 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
323924 CTCTTTCTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:326691 original size:2 final size:2
Alignment explanation
Indices: 326684--326720 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
326674 ATTCAAAACA
326684 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
326721 TTTCAAGACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:329916 original size:22 final size:22
Alignment explanation
Indices: 329881--329998 Score: 148
Period size: 22 Copynumber: 5.3 Consensus size: 22
329871 AACCCTGGGC
*
329881 TTACTTTTGCGTCCACTCAGGGT
1 TTAC-TTTGAGTCCACTCAGGGT
* *
329904 TTACTTTGAGTCCAATTAGGGT
1 TTACTTTGAGTCCACTCAGGGT
* *
329926 TTACTTTGAGTCCATTCATGGT
1 TTACTTTGAGTCCACTCAGGGT
*
329948 TTACTTTGAG-CCTACTAAGGGT
1 TTACTTTGAGTCC-ACTCAGGGT
*
329970 TTACTTTGAGTCCACTCATGGT
1 TTACTTTGAGTCCACTCAGGGT
329992 TTACTTT
1 TTACTTT
329999 AGGTTTACTC
Statistics
Matches: 82, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
21 2 0.02
22 74 0.90
23 6 0.07
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (22 bp):
TTACTTTGAGTCCACTCAGGGT
Found at i:330015 original size:44 final size:44
Alignment explanation
Indices: 329881--329998 Score: 166
Period size: 44 Copynumber: 2.7 Consensus size: 44
329871 AACCCTGGGC
* * * *
329881 TTACTTTTGCGTCCACTCAGGGTTTACTTTGAGTCC-AATTAGGGT
1 TTAC-TTTGAGTCCACTCATGGTTTACTTTGAG-CCTACTAAGGGT
*
329926 TTACTTTGAGTCCATTCATGGTTTACTTTGAGCCTACTAAGGGT
1 TTACTTTGAGTCCACTCATGGTTTACTTTGAGCCTACTAAGGGT
329970 TTACTTTGAGTCCACTCATGGTTTACTTT
1 TTACTTTGAGTCCACTCATGGTTTACTTT
329999 AGGTTTACTC
Statistics
Matches: 66, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
43 2 0.03
44 60 0.91
45 4 0.06
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (44 bp):
TTACTTTGAGTCCACTCATGGTTTACTTTGAGCCTACTAAGGGT
Found at i:330195 original size:20 final size:21
Alignment explanation
Indices: 330157--330196 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
330147 CTTATGATCG
*
330157 GGGTTTACTTTCTGTGTCCACT
1 GGGTTTAC-TTCTGGGTCCACT
330179 GGGTTTAC-TCTGGGTCCA
1 GGGTTTACTTCTGGGTCCA
330197 TTCTAGTAAA
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:0.10, C:0.23, G:0.28, T:0.40
Consensus pattern (21 bp):
GGGTTTACTTCTGGGTCCACT
Found at i:332789 original size:23 final size:24
Alignment explanation
Indices: 332733--332789 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
332723 CAGATTGCTT
332733 TCATGAATCTCAATCTTTCAAAAA
1 TCATGAATCTCAATCTTTCAAAAA
* *
332757 TCATAAATCTCAATCTTT-AGAAA
1 TCATGAATCTCAATCTTTCAAAAA
*
332780 TCATGGATCT
1 TCATGAATCT
332790 TTCATCTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 12 0.41
24 17 0.59
ACGTcount: A:0.39, C:0.19, G:0.07, T:0.35
Consensus pattern (24 bp):
TCATGAATCTCAATCTTTCAAAAA
Found at i:333337 original size:25 final size:25
Alignment explanation
Indices: 333286--335281 Score: 2519
Period size: 25 Copynumber: 80.0 Consensus size: 25
333276 CCTCGTTTAT
333286 TTAGACACTTACTGT-CC-GTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
333309 TTAGACATTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* **
333334 TTAGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* **
333359 TTAGATACTTACTACCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
333384 TTAGACACTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
333409 TTAGACACTTATTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* * **
333434 TTAGACACTTATTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* **
333459 TTAGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
333484 TTAGACATTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
333509 TTAGACACTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
333534 TTAGACACTTATTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
333559 TTAGACACTTACTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* * * *
333584 TTAGACATTTACAGTTCCTGTTTTA
1 TTAGACACTTACTGTCCCTGTTTGA
* * **
333609 TTAGACACTTATTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* **
333634 TTAGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
333659 TTAGACATTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
333684 TTAGACACTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
333709 TTAGACACTTATTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
333734 TTAGACACTTACTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* * * *
333759 TTAGACATTTACAGTTCCTGTTTTA
1 TTAGACACTTACTGTCCCTGTTTGA
* * **
333784 TTAGACACTTATTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* **
333809 TTAGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
333834 TTAGACATTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
333859 TTAGACACTTATTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
333884 TTAGACATTTACTGTCCTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* * **
333909 TAAGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* **
333934 TTAGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
333959 TTAGACATTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
333984 TTAGACATTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* **
334009 TTAGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* **
334034 TTAGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
334059 TTAGACACTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
334084 TTAGACACTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334109 TTAGACACTTACTGCCCCTGTATGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
334134 TTAGACACTTACTGTCCCTGTTTAA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334159 TTAGACACTTACTGCCCCTGTTTAA
1 TTAGACACTTACTGTCCCTGTTTGA
**
334184 TTAGACACTTACTCCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
334209 TTAGACATTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
** * **
334234 TGGGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
334259 TTAGACACTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334284 TTAGACACTTATTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334309 TTAGACACTTACTGCCCCTGTTTGT
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334334 TTAGAC-CTTTACTGTTCCTGTTTTA
1 TTAGACAC-TTACTGTCCCTGTTTGA
* * **
334359 TTAGACACTTATTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* **
334384 TTAGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
334409 TTAGACATTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334434 TTAGACACTTATTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334459 TTAGACATTTACTGTCCTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* **
334484 TTAGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* **
334509 TTAGACACTTACTATCTTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* * *
334534 CTAGACATTTACTGTCCTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334559 TTAGACATTTACTGTTCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334584 TTAGACACTTATTGTTCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334609 TTAGACACTTTCTG-CCCCGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334633 TTAGACATTTACTGTCCTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* * *
334658 TGAGACACTTTCTG-CCCAGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* * * *
334682 TCAGACACTTATTGTTCCTGTTTAA
1 TTAGACACTTACTGTCCCTGTTTGA
*
334707 TTAGACACTTACTGTCCTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334732 TTAGACACTTTCTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334757 TTAGACACTTATTTTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334782 TTAGACACTTTCTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334807 TTAGACATTTACTGTCCTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334832 TTAGACACTAACTGTCCCTGTTTAA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334857 TTAGACATTTACTGTTCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
334882 TTAGACACTTACTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
334907 TTAGACACTTACTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334932 TTAGACACTTTCTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* * * * *
334957 TTGGTCACTTAATTTCCCCGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
334982 TTAGACACTTATTTTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
335007 TTAGACACCTT-CTGTCCCTGTTTGA
1 TTAGACA-CTTACTGTCCCTGTTTGA
335032 TTAGACACTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
335057 TTAGACATTTACTGTCCTTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
335082 TTAGACACTTACTGTTCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
335107 TTAGACATTTACTGTTCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
335132 TTAGACACTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
*
335157 TTAGACACTTACTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
335182 TTAGACATTTACTGTTCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
335207 TTAGACACTTTCTGCCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
* *
335232 TTAGACACTTATTTTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
335257 TTAGACACTTACTGTCCCTGTTTGA
1 TTAGACACTTACTGTCCCTGTTTGA
335282 CCAGTATGTC
Statistics
Matches: 1729, Mismatches: 236, Indels: 14
0.87 0.12 0.01
Matches are distributed among these distances:
23 14 0.01
24 45 0.03
25 1666 0.96
26 4 0.00
ACGTcount: A:0.21, C:0.21, G:0.15, T:0.43
Consensus pattern (25 bp):
TTAGACACTTACTGTCCCTGTTTGA
Found at i:339603 original size:24 final size:25
Alignment explanation
Indices: 339570--339620 Score: 86
Period size: 24 Copynumber: 2.1 Consensus size: 25
339560 ATCCACACAG
339570 AACTGTTGGCCTTATTTATGTACTA
1 AACTGTTGGCCTTATTTATGTACTA
*
339595 AACT-TTGGCCTTATTTATTTACTA
1 AACTGTTGGCCTTATTTATGTACTA
339619 AA
1 AA
339621 TATTCACCCT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 21 0.84
25 4 0.16
ACGTcount: A:0.27, C:0.16, G:0.12, T:0.45
Consensus pattern (25 bp):
AACTGTTGGCCTTATTTATGTACTA
Found at i:347606 original size:17 final size:18
Alignment explanation
Indices: 347584--347623 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
347574 GGTAGGTAGG
347584 AAAAAA-ATTTTATTTTT
1 AAAAAATATTTTATTTTT
347601 AAAAAATATTTTATTTTT
1 AAAAAATATTTTATTTTT
347619 AAAAA
1 AAAAA
347624 CTTGGAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAAAATATTTTATTTTT
Found at i:350504 original size:13 final size:13
Alignment explanation
Indices: 350486--350517 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
350476 TGGGACATCG
350486 CGGGACATATGTC
1 CGGGACATATGTC
350499 CGGGACATATGTC
1 CGGGACATATGTC
*
350512 CCGGAC
1 CGGGAC
350518 TACTTTTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (13 bp):
CGGGACATATGTC
Found at i:352846 original size:13 final size:13
Alignment explanation
Indices: 352828--352852 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
352818 ATAATAAAGA
352828 TTTTAACATAATG
1 TTTTAACATAATG
352841 TTTTAACATAAT
1 TTTTAACATAAT
352853 ATTTCCTCTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.48
Consensus pattern (13 bp):
TTTTAACATAATG
Found at i:356978 original size:22 final size:22
Alignment explanation
Indices: 356950--356991 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
356940 CCTTGCCTCC
356950 GGCTCGGTGAATATCGTACTCG
1 GGCTCGGTGAATATCGTACTCG
*
356972 GGCTCGGTGAATATTGTACT
1 GGCTCGGTGAATATCGTACT
356992 TCTCGGATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (22 bp):
GGCTCGGTGAATATCGTACTCG
Found at i:360225 original size:21 final size:21
Alignment explanation
Indices: 360199--360268 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
360189 GTGCGAGAAA
360199 CGTTTCGAGTAAACCGTTTAG
1 CGTTTCGAGTAAACCGTTTAG
* * * **
360220 CGTTTCGTGTGAATCGTGAAG
1 CGTTTCGAGTAAACCGTTTAG
**
360241 CACTTC-ATGTAAACCGTTTAG
1 CGTTTCGA-GTAAACCGTTTAG
360262 CGTTTCG
1 CGTTTCG
360269 GGCAAAGCGT
Statistics
Matches: 33, Mismatches: 14, Indels: 3
0.66 0.28 0.06
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.34
Consensus pattern (21 bp):
CGTTTCGAGTAAACCGTTTAG
Found at i:363031 original size:15 final size:16
Alignment explanation
Indices: 363011--363049 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
363001 ACTCTCAAAG
363011 GCTCGAACTTC-GATC
1 GCTCGAACTTCTGATC
*
363026 GCTCGAAGTTCTTGATC
1 GCTCGAACTTC-TGATC
363043 GCTCGAA
1 GCTCGAA
363050 GTGAGTCTAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 10 0.48
17 11 0.52
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (16 bp):
GCTCGAACTTCTGATC
Found at i:363117 original size:16 final size:16
Alignment explanation
Indices: 363096--363145 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
363086 AAGCAAATTT
*
363096 ACTCTTGATTTCTCGA
1 ACTCTTGATCTCTCGA
363112 ACTCTTGATCTCTCGAA
1 ACTCTTGATCTCTCG-A
*
363129 ACCCTTGATCTCTCGA
1 ACTCTTGATCTCTCGA
363145 A
1 A
363146 GTCAGGGATC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 16 0.52
17 15 0.48
ACGTcount: A:0.22, C:0.30, G:0.12, T:0.36
Consensus pattern (16 bp):
ACTCTTGATCTCTCGA
Found at i:363137 original size:17 final size:17
Alignment explanation
Indices: 363099--363145 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
363089 CAAATTTACT
* *
363099 CTTGATTTCTCG-AACT
1 CTTGATCTCTCGAAACC
363115 CTTGATCTCTCGAAACC
1 CTTGATCTCTCGAAACC
363132 CTTGATCTCTCGAA
1 CTTGATCTCTCGAA
363146 GTCAGGGATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
16 11 0.39
17 17 0.61
ACGTcount: A:0.21, C:0.30, G:0.13, T:0.36
Consensus pattern (17 bp):
CTTGATCTCTCGAAACC
Found at i:368695 original size:438 final size:437
Alignment explanation
Indices: 367881--369391 Score: 2688
Period size: 438 Copynumber: 3.5 Consensus size: 437
367871 NNNNNNNNNN
* *
367881 TTGTGATGCGTTATAGAAGCAATTATGTTTATTCTTAGGTTATTTACCTATACATGGCAATCATT
1 TTGTGATGCGTTATAGAAGCAATTATGTTCATTCTAAGGTTATTTACCTATACATGGCAATCATT
* *
367946 TACTTCTATGTTACGTAATTAGGGATTTTAAGGGGCCAGAAGTCCAAAACTTTGATGC-TCAATA
66 TACTCCTATGTTACGTAATTAGGAATTTTAAGGGGCCAGAAGTCCAAAACTTTGATGCAT-AATA
368010 TCTCAAAATGAAGAAACATTTGGATAAGCAATATTTAACAAAAGATGCTCAAAATATAGAGCTTA
130 TCTCAAAATGAAGAAACATTTGGATAAGCAATATTTAACAAAAGATGCTCAAAATATAGAGCTTA
*
368075 ACAACCTGAAACCATAATTTCCTTGTTATGCAGTCCCTAAAAGGAGTTACAGGGTCGGCCCCTAA
195 ACAACCTGAAACCATAATTTCCTTGTTATGCGGTCCCTAAAAGGAGTTACAGGGTCGGCCCCTAA
368140 AACGACCCTCTCAAGATATCTCGAGAACGGTACATAATTTGTAAACACTTTTTGAACAAAATGTG
260 AACGACCCTCTCAAGATATCTCGAGAACGGTACATAATTTGTAAACACTTTTTGAACAAAATGTG
368205 TTTGAATTGACAAAAGCTTTCATTTGAAATCAAGAAAAAGGGGCTGGCCCTTCAAATTAGGGGCT
325 TTTGAATTGACAAAAGCTTTCATTTGAAATCAAGAAAAAGGGGCTGGCCCTTCAAATTAGGGGCT
368270 GAGGGAGCTCTGAAGTCTTTTAATGATAACCTTTTACCGTGAAATATT
390 GAGGGAGCTCTGAAGTCTTTTAATGATAACCTTTTACCGTGAAATATT
368318 TTGTGATGCGTTATAGAAGCAATTATGTTCATTCTAAGGTTATTTACCTATACATGGCAATCATT
1 TTGTGATGCGTTATAGAAGCAATTATGTTCATTCTAAGGTTATTTACCTATACATGGCAATCATT
* *
368383 TACTCCTATGTTACGTAATAAGTAATTTTTAAGGGGCCAGAAGTCCAAAACTTT-ATTGCATAAT
66 TACTCCTATGTTACGTAATTAGGAA-TTTTAAGGGGCCAGAAGTCCAAAACTTTGA-TGCATAAT
368447 ATCTCAAAATGAAGAAACATTTGGATAAGCAATATTTAACAAAAGATGCTCAAAATATAGAGCTT
129 ATCTCAAAATGAAGAAACATTTGGATAAGCAATATTTAACAAAAGATGCTCAAAATATAGAGCTT
368512 AACAACCTGAAACCATAATTTCCTTGTTATGCGGTCCCTAAAAGGAGTTACAGGGTCGGCCCCTA
194 AACAACCTGAAACCATAATTTCCTTGTTATGCGGTCCCTAAAAGGAGTTACAGGGTCGGCCCCTA
368577 AAACGACCCTCTCAAGATATCTCGAGAACGGTACATAATTTGTAAACACTTTTTGAACAAAATGT
259 AAACGACCCTCTCAAGATATCTCGAGAACGGTACATAATTTGTAAACACTTTTTGAACAAAATGT
368642 GTTTGAATTGACAAAAGCTTTCATTTGAAATCAAGAAAAAGGGGCTGGCCCTTCAAATTAGGGGC
324 GTTTGAATTGACAAAAGCTTTCATTTGAAATCAAGAAAAAGGGGCTGGCCCTTCAAATTAGGGGC
368707 TGAGGGAGCTCTGAAGTCTTTTAATGATAACCTTTTACCGTGAAATATT
389 TGAGGGAGCTCTGAAGTCTTTTAATGATAACCTTTTACCGTGAAATATT
368756 TTGTGATGCGTTATAGAAGCAATTATGTTCATTCTAAGGTTATTTACCTATACATGGCAATCATT
1 TTGTGATGCGTTATAGAAGCAATTATGTTCATTCTAAGGTTATTTACCTATACATGGCAATCATT
* *
368821 TACTCCTATGTTACGTAATTAGTAATTTTTAAGGGGCCAGAAGTCCAAAACTTTAATGCATAATA
66 TACTCCTATGTTACGTAATTAGGAA-TTTTAAGGGGCCAGAAGTCCAAAACTTTGATGCATAATA
368886 TCTCAAAATGAAGAAACATTTGGATAAGCAATATTTAACAAAAGATGCTCAAAATATAGAGCTTA
130 TCTCAAAATGAAGAAACATTTGGATAAGCAATATTTAACAAAAGATGCTCAAAATATAGAGCTTA
368951 ACAACCTGAAACCATAATTTCCTTGTTATGCGGTCCCTAAAAGGAGTTACAGGGTCGGCCCCTAA
195 ACAACCTGAAACCATAATTTCCTTGTTATGCGGTCCCTAAAAGGAGTTACAGGGTCGGCCCCTAA
*
369016 AACGACCCTCTCAAGATATCTCTAGAACGGTACATAATTTGTAAACACTTTTTGAACAAAATGTG
260 AACGACCCTCTCAAGATATCTCGAGAACGGTACATAATTTGTAAACACTTTTTGAACAAAATGTG
* *
369081 TTAGAATTGACAAAAGCTTTCATTTAAAATCAAGAAAAAGGGGCTGGCCCTTCAAATTAGGGGCT
325 TTTGAATTGACAAAAGCTTTCATTTGAAATCAAGAAAAAGGGGCTGGCCCTTCAAATTAGGGGCT
*
369146 GAGGGAGCTCTGAAGTCTTTTAATGATAACCTTTTGCCGTGAAATATT
390 GAGGGAGCTCTGAAGTCTTTTAATGATAACCTTTTACCGTGAAATATT
* * *
369194 TTGTGATGCGTTATAGAAGCAATTATGTTCATTCTAATGTTATGTACCTGTACATGGCAATCATT
1 TTGTGATGCGTTATAGAAGCAATTATGTTCATTCTAAGGTTATTTACCTATACATGGCAATCATT
* * * * * * * * **
369259 TACACTTATGTTACGTAATTAGGGATTTTAAGGGACAAGAGGTCTAAAGCTTTGATGTTTAATAT
66 TACTCCTATGTTACGTAATTAGGAATTTTAAGGGGCCAGAAGTCCAAAACTTTGATGCATAATAT
* *
369324 CTCAAAATAGAGGAAA-ACTTTGGA-AAGCAATATTTAACAAAAGATGCTCAAAATATTGAGCTT
131 CTCAAAAT-GAAGAAACA-TTTGGATAAGCAATATTTAACAAAAGATGCTCAAAATATAGAGCTT
369387 AACAA
194 AACAA
369392 TGTACAACCA
Statistics
Matches: 1039, Mismatches: 29, Indels: 12
0.96 0.03 0.01
Matches are distributed among these distances:
437 169 0.16
438 868 0.84
439 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (437 bp):
TTGTGATGCGTTATAGAAGCAATTATGTTCATTCTAAGGTTATTTACCTATACATGGCAATCATT
TACTCCTATGTTACGTAATTAGGAATTTTAAGGGGCCAGAAGTCCAAAACTTTGATGCATAATAT
CTCAAAATGAAGAAACATTTGGATAAGCAATATTTAACAAAAGATGCTCAAAATATAGAGCTTAA
CAACCTGAAACCATAATTTCCTTGTTATGCGGTCCCTAAAAGGAGTTACAGGGTCGGCCCCTAAA
ACGACCCTCTCAAGATATCTCGAGAACGGTACATAATTTGTAAACACTTTTTGAACAAAATGTGT
TTGAATTGACAAAAGCTTTCATTTGAAATCAAGAAAAAGGGGCTGGCCCTTCAAATTAGGGGCTG
AGGGAGCTCTGAAGTCTTTTAATGATAACCTTTTACCGTGAAATATT
Found at i:370978 original size:437 final size:436
Alignment explanation
Indices: 370167--371448 Score: 1844
Period size: 437 Copynumber: 2.9 Consensus size: 436
370157 ACCTTTCTGC
* *
370167 TGATATCAAA-AAACAGGGGCTGGCCCCTCAA-ATTAGGGACCTAGAAGGCTCTAAAGTC-TTTT
1 TGATA-CAAAGAAAAAGGGGCTGGCCCCT-AATATTAGGGACCTAGAGGGCTCTAAAGTCTTTTT
* ** *
370229 ACCCATAACTCTTTACCGAGGGATATTTTGTAATAAATTATAGAAGCAAATATGTTAATCTTACA
64 A-CTATAGTTCTTTACCGAGGGATATTTTGTAATAAATTATAGAAGCAAATATGTTTATCTTACA
*
370294 GATATGAAGCCAAGCAGTATAACGATTTTCTCATATGTTACGTAATTAGGGATTTTTAGGGGTCA
128 GTTATGAAGCCAAGCAGTATAACGATTTTCTCATATGTTACGTAATTA-GGATTTTTAGGGGTCA
* *
370359 GAAGTCCAAAATTTTGACCACCTATATCTCAAAACGGAAAAATATTTTGAAATGCAGTATAACAG
192 GAAGTCCAAAAATTTGACCACCTATATCTCAAAACGGAAAAATATTTTGAAATGCAGTATAAAAG
* * *
370424 AAAATATGCTCAAAATGATGTCCTTAACACCATGCAACCTAAAAAATTTGGTTCAGCGGCCCCAA
257 AAAAGATGCTCAAAATGATGTCCTTAACAACATGCAACCTTAAAAATTTGGTTCAGCGGCCCCAA
* ** *
370489 TAAGGAGATAAGGGACCGGCCCCTAAAACATTCTTTCTCTGATATTTCAAGAATGGTAAGGAATT
322 TAAGGAGATAAGGGACCGGCCCCTAAAATATTCTTTCTGAGATATCTCAAGAATGGTAAGGAATT
*
370554 TCTAAACACTTGTTGAACAAAATGTCTTTATAATTAAATGACCTTTCATT
387 TCTAAACACTTGTTGAACAAAATGTCTTTATAATCAAATGACCTTTCATT
*
370604 TGATACAAAGAAAAATGGGCTGGCCCCTAATATTAGGGACCTAGAGGGCTCTAAAGTCTTTTTAC
1 TGATACAAAGAAAAAGGGGCTGGCCCCTAATATTAGGGACCTAGAGGGCTCTAAAGTCTTTTTAC
* *
370669 TATAGTTCCTTACTGAGGGATATTTTGTAATAAATTATAGAAGCAAATATGTTTATCTTACAGTT
66 TATAGTTCTTTACCGAGGGATATTTTGTAATAAATTATAGAAGCAAATATGTTTATCTTACAGTT
* *
370734 ATAAAGCCAAGCAGTATAACGGTTTTCTCATATGTTACGTAATTAGGAATTTTTAGGGGTCAGAA
131 ATGAAGCCAAGCAGTATAACGATTTTCTCATATGTTACGTAATTAGG-ATTTTTAGGGGTCAGAA
* *
370799 GTCCAAAACTTTGACCACCTATATCTCAAAACGGAAAAATATTTTGAAATGCAGTATAAAAAAAA
195 GTCCAAAAATTTGACCACCTATATCTCAAAACGGAAAAATATTTTGAAATGCAGTATAAAAGAAA
*
370864 AGATGCTCAAAATGATGTCCTTAACAACATGCAGCCTTAAAAATTTGGTTCAGCGGCCCCAATAA
260 AGATGCTCAAAATGATGTCCTTAACAACATGCAACCTTAAAAATTTGGTTCAGCGGCCCCAATAA
* *
370929 GAAGATAAGGGACCGGCCCCTAAAATGTTCTTTCTGAGATATCTCAAGAATGGTAACGG-ATTTC
325 GGAGATAAGGGACCGGCCCCTAAAATATTCTTTCTGAGATATCTCAAGAATGGTAA-GGAATTTC
*
370993 TGAACACTTGTTGAACAAAATGTCTTTATAATCAAATGACCTTTCATT
389 TAAACACTTGTTGAACAAAATGTCTTTATAATCAAATGACCTTTCATT
* * * **
371041 TGATACCATGAAAAAGGGGCTGGTCCCTAATATTAGGGACCTAGAGGGCTCTAAAGTCTTTTCCC
1 TGATACAAAGAAAAAGGGGCTGGCCCCTAATATTAGGGACCTAGAGGGCTCTAAAGTCTTTTTAC
* * * * * *
371106 TATAGTTCTTTACCGAGGGGTATTTCGTAATAGATTATAGATGCAAATATATTTATCTAACAGTT
66 TATAGTTCTTTACCGAGGGATATTTTGTAATAAATTATAGAAGCAAATATGTTTATCTTACAGTT
* * * * * * *
371171 GTGTAGCCTAA-CATTATAATGATTTTTCTCATGTGTTACGTAATTAAGGATTTTAAGGGGTCAA
131 ATGAAGCC-AAGCAGTATAACGA-TTTTCTCATATGTTACGTAATT-AGGATTTTTAGGGGTCAG
* ** * *
371235 AAGTCCAAAAATGTGAAAACCTATATCTCAAAAAGAAAAAATATTTTGAAATGCAGTATAAAAGA
193 AAGTCCAAAAATTTGACCACCTATATCTCAAAACGGAAAAATATTTTGAAATGCAGTATAAAAGA
* * * *
371300 AAAGATGCTCAAAATAATGTACC-TAATC-ACATGCAACCTTACAATTTTTGTTCAGCGGCCCCA
258 AAAGATGCTCAAAATGATGT-CCTTAA-CAACATGCAACCTTAAAAATTTGGTTCAGCGGCCCCA
* * * * * * *
371363 ATAAGGACATAA-GGTCCGGCCCCTAAAATATTCTTTCTGAGATATCTGAAGAACGGTGA-CAAA
321 ATAAGGAGATAAGGGACCGGCCCCTAAAATATTCTTTCTGAGATATCTCAAGAATGGTAAGGAAT
371426 TTCTAAACACTTGTTGAACAAAA
386 TTCTAAACACTTGTTGAACAAAA
371449 CTCTTACACC
Statistics
Matches: 762, Mismatches: 72, Indels: 23
0.89 0.08 0.03
Matches are distributed among these distances:
436 31 0.04
437 561 0.74
438 164 0.22
439 6 0.01
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (436 bp):
TGATACAAAGAAAAAGGGGCTGGCCCCTAATATTAGGGACCTAGAGGGCTCTAAAGTCTTTTTAC
TATAGTTCTTTACCGAGGGATATTTTGTAATAAATTATAGAAGCAAATATGTTTATCTTACAGTT
ATGAAGCCAAGCAGTATAACGATTTTCTCATATGTTACGTAATTAGGATTTTTAGGGGTCAGAAG
TCCAAAAATTTGACCACCTATATCTCAAAACGGAAAAATATTTTGAAATGCAGTATAAAAGAAAA
GATGCTCAAAATGATGTCCTTAACAACATGCAACCTTAAAAATTTGGTTCAGCGGCCCCAATAAG
GAGATAAGGGACCGGCCCCTAAAATATTCTTTCTGAGATATCTCAAGAATGGTAAGGAATTTCTA
AACACTTGTTGAACAAAATGTCTTTATAATCAAATGACCTTTCATT
Found at i:375191 original size:26 final size:26
Alignment explanation
Indices: 375162--375243 Score: 128
Period size: 26 Copynumber: 3.2 Consensus size: 26
375152 AAAATTAACA
* * * *
375162 TTGATTATTGAAATAAAATCGTAGAG
1 TTGATCATTGAGATTAAATCGTACAG
375188 TTGATCATTGAGATTAAATCGTACAG
1 TTGATCATTGAGATTAAATCGTACAG
375214 TTGATCATTGAGATTAAATCGTACAG
1 TTGATCATTGAGATTAAATCGTACAG
375240 TTGA
1 TTGA
375244 GCATCCAATG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 52 1.00
ACGTcount: A:0.37, C:0.09, G:0.20, T:0.35
Consensus pattern (26 bp):
TTGATCATTGAGATTAAATCGTACAG
Found at i:388600 original size:13 final size:13
Alignment explanation
Indices: 388582--388609 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
388572 GTACTTCCGA
388582 GTGGAGAAAAGAT
1 GTGGAGAAAAGAT
388595 GTGGAGAAAAGAT
1 GTGGAGAAAAGAT
388608 GT
1 GT
388610 AAACATTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.39, T:0.18
Consensus pattern (13 bp):
GTGGAGAAAAGAT
Found at i:389666 original size:2 final size:2
Alignment explanation
Indices: 389659--389691 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
389649 ATGTTTTAAT
389659 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
389692 GGGGTTAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:396938 original size:10 final size:10
Alignment explanation
Indices: 396923--396959 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
396913 AGTTAATCTT
396923 TCTCTCTTTC
1 TCTCTCTTTC
396933 TCTCTCTTTC
1 TCTCTCTTTC
*
396943 TCTCTCATTC
1 TCTCTCTTTC
396953 TCTCTCT
1 TCTCTCT
396960 CGCTCTCTGC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.03, C:0.41, G:0.00, T:0.57
Consensus pattern (10 bp):
TCTCTCTTTC
Found at i:405533 original size:21 final size:21
Alignment explanation
Indices: 405506--405564 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
405496 ATCATCTTTG
*
405506 ACTTGTCAGATTTTAAAGTGGA
1 ACTTGTCAGATTTTAAAGT-CA
* *
405528 AC-TGTCATATTTTTAAGTCA
1 ACTTGTCAGATTTTAAAGTCA
405548 ACTTGTCAGATCTTTAA
1 ACTTGTCAGAT-TTTAA
405565 GTTACACTGT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
20 3 0.10
21 21 0.70
22 6 0.20
ACGTcount: A:0.31, C:0.14, G:0.15, T:0.41
Consensus pattern (21 bp):
ACTTGTCAGATTTTAAAGTCA
Found at i:405575 original size:21 final size:20
Alignment explanation
Indices: 405509--405576 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
405499 ATCTTTGACT
*
405509 TGTCAGAT-TTTAAAGTGGAAC
1 TGTCAGATCTTT-AAGT-CAAC
* *
405530 TGTCATATTTTTAAGTCAAC
1 TGTCAGATCTTTAAGTCAAC
*
405550 TTGTCAGATCTTTAAGTTACAC
1 -TGTCAGATCTTTAAGTCA-AC
405572 TGTCA
1 TGTCA
405577 ACTTGTCAGA
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.08
21 31 0.79
22 5 0.13
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (20 bp):
TGTCAGATCTTTAAGTCAAC
Found at i:405604 original size:29 final size:29
Alignment explanation
Indices: 405544--405605 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 29
405534 ATATTTTTAA
*
405544 GTCAACTTGTCAGATCTTTAAGTTACACT
1 GTCAACTTGTCAGATCTTTAAGTGACACT
*
405573 GTCAACTTGTCAGATCTTTATGTCGACA-T
1 GTCAACTTGTCAGATCTTTAAGT-GACACT
405602 GTCA
1 GTCA
405606 GAAACGTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 27 0.90
30 3 0.10
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (29 bp):
GTCAACTTGTCAGATCTTTAAGTGACACT
Found at i:409163 original size:6 final size:6
Alignment explanation
Indices: 409148--409209 Score: 56
Period size: 7 Copynumber: 9.8 Consensus size: 6
409138 TCGGAGATTT
*
409148 TTTTTG -TTTTG TTTTTTT TCTTTTGG TTTTT- TTTTTG TGTTTTG TTTTTG
1 TTTTTG TTTTTG -TTTTTG T-TTTT-G TTTTTG TTTTTG T-TTTTG TTTTTG
409198 TTTTTTG TTTTT
1 -TTTTTG TTTTT
409210 TTTGTTCCCT
Statistics
Matches: 47, Mismatches: 2, Indels: 14
0.75 0.03 0.22
Matches are distributed among these distances:
5 10 0.21
6 12 0.26
7 24 0.51
8 1 0.02
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.84
Consensus pattern (6 bp):
TTTTTG
Found at i:409164 original size:13 final size:13
Alignment explanation
Indices: 409146--409212 Score: 61
Period size: 13 Copynumber: 5.3 Consensus size: 13
409136 ATTCGGAGAT
409146 TTTTTTTGTTTTG
1 TTTTTTTGTTTTG
*
409159 TTTTTTTTCTTTTG
1 -TTTTTTTGTTTTG
*
409173 GTTTTTT-TTTTG
1 TTTTTTTGTTTTG
*
409185 -TGTTTTGTTTT-
1 TTTTTTTGTTTTG
409196 TGTTTTTTGTTTT-
1 T-TTTTTTGTTTTG
409209 TTTT
1 TTTT
409213 GTTCCCTGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
11 5 0.11
12 12 0.26
13 17 0.37
14 12 0.26
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.85
Consensus pattern (13 bp):
TTTTTTTGTTTTG
Found at i:409183 original size:31 final size:31
Alignment explanation
Indices: 409145--409212 Score: 102
Period size: 33 Copynumber: 2.2 Consensus size: 31
409135 AATTCGGAGA
*
409145 TTTTTTT-TGTTTTGTTTTTTTTCTTTTGGTTT
1 TTTTTTTGTGTTTTGTTTTTGTT-TTTT-GTTT
409177 TTTTTTTGTGTTTTGTTTTTGTTTTTTGTTT
1 TTTTTTTGTGTTTTGTTTTTGTTTTTTGTTT
409208 TTTTT
1 TTTTT
409213 GTTCCCTGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 9 0.26
32 11 0.32
33 14 0.41
ACGTcount: A:0.00, C:0.01, G:0.13, T:0.85
Consensus pattern (31 bp):
TTTTTTTGTGTTTTGTTTTTGTTTTTTGTTT
Found at i:409209 original size:19 final size:19
Alignment explanation
Indices: 409149--409209 Score: 72
Period size: 19 Copynumber: 3.2 Consensus size: 19
409139 CGGAGATTTT
*
409149 TTTTGTTTTGTTTTTTTTC
1 TTTTGTTTTGTTTTTTGTC
*
409168 TTTTGGTTTT-TTTTTTGTG
1 TTTT-GTTTTGTTTTTTGTC
409187 TTTTGTTTTTGTTTTTTGT-
1 TTTTG-TTTTGTTTTTTGTC
409206 TTTT
1 TTTT
409210 TTTGTTCCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
18 1 0.03
19 23 0.62
20 13 0.35
ACGTcount: A:0.00, C:0.02, G:0.15, T:0.84
Consensus pattern (19 bp):
TTTTGTTTTGTTTTTTGTC
Found at i:412311 original size:2 final size:2
Alignment explanation
Indices: 412304--412360 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
412294 ATTCTAGGCA
412304 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
412346 TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC T
412361 GATTAGGAAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:420316 original size:2 final size:2
Alignment explanation
Indices: 420311--420343 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
420301 AGTCGAAACC
420311 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
420344 AAAACAGTGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:420893 original size:21 final size:22
Alignment explanation
Indices: 420868--420916 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 22
420858 CTGATATTAT
*
420868 AAATTCGTTTTTT-GATATCAG
1 AAATTCGTTTTTTCCATATCAG
* **
420889 GAATTTTTTTTTTCCATATCAG
1 AAATTCGTTTTTTCCATATCAG
420911 AAATTC
1 AAATTC
420917 AAACTGATTT
Statistics
Matches: 21, Mismatches: 6, Indels: 1
0.75 0.21 0.04
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (22 bp):
AAATTCGTTTTTTCCATATCAG
Found at i:421448 original size:27 final size:29
Alignment explanation
Indices: 421406--421459 Score: 78
Period size: 27 Copynumber: 1.9 Consensus size: 29
421396 GTTTTTTCTG
421406 ATATCAAAAATCGATTATTT-GATATCATA
1 ATATCAAAAATCGATT-TTTGGATATCATA
421435 ATAT-AAAAAT-GATTTTTGGATATCA
1 ATATCAAAAATCGATTTTTGGATATCA
421460 AAAAATGATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 3 0.12
27 11 0.46
28 6 0.25
29 4 0.17
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.39
Consensus pattern (29 bp):
ATATCAAAAATCGATTTTTGGATATCATA
Found at i:422438 original size:2 final size:2
Alignment explanation
Indices: 422431--422471 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
422421 GTACAAAGTT
422431 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
422472 TAACCCTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:422553 original size:2 final size:2
Alignment explanation
Indices: 422548--422617 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
422538 GGGGGGGGGT
422548 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
422590 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
422618 TTNAGCCATT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:422988 original size:11 final size:11
Alignment explanation
Indices: 422974--423033 Score: 66
Period size: 11 Copynumber: 5.5 Consensus size: 11
422964 GCAAGTGAAC
*
422974 GCACTGTGAGT
1 GCACGGTGAGT
*
422985 GCACGGTGAGC
1 GCACGGTGAGT
*
422996 GCACGGTGAAT
1 GCACGGTGAGT
*
423007 GCACGGTGAGC
1 GCACGGTGAGT
* *
423018 GCATGGTGAAT
1 GCACGGTGAGT
423029 GCACG
1 GCACG
423034 AAAAAATGGG
Statistics
Matches: 39, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
11 39 1.00
ACGTcount: A:0.22, C:0.22, G:0.40, T:0.17
Consensus pattern (11 bp):
GCACGGTGAGT
Done.