Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012580.1 Kokia drynarioides strain JFW-HI SEQ_127589, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 232682
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 83 characters in sequence are not A, C, G, or T
Found at i:9600 original size:237 final size:237
Alignment explanation
Indices: 9185--9645 Score: 904
Period size: 237 Copynumber: 1.9 Consensus size: 237
9175 GGATTTACTC
9185 CCTCAATCATCAGCTATGGATGTCTTATTAATCTTTACTCTAAGGCAAGGATTTTTAATTTTTAT
1 CCTCAATCATCAGCTATGGATGTCTTATTAATCTTTACTCTAAGGCAAGGATTTTTAATTTTTAT
*
9250 TTAATAATTTTTTTCCTACTGTATGCACTCCCCCAAACCCCCCTTGTATGGTGTATTCCTCTTCT
66 TTAATAAATTTTTTCCTACTGTATGCACTCCCCCAAACCCCCCTTGTATGGTGTATTCCTCTTCT
9315 GTGTGCGCGTGTGTGTGTTTTGGGGAGTGTTGAAGTTCAGTGAATCCCTTTGTTGAATTGAAGCA
131 GTGTGCGCGTGTGTGTGTTTTGGGGAGTGTTGAAGTTCAGTGAATCCCTTTGTTGAATTGAAGCA
9380 TTTTATCCTACTTTGACTGTCCTTTCCCTAGGATTTTTAATT
196 TTTTATCCTACTTTGACTGTCCTTTCCCTAGGATTTTTAATT
9422 CCTCAATCATCAGCTATGGATGTCTTATTAATCTTTACTCTAAGGCAAGGATTTTTAATTTTTAT
1 CCTCAATCATCAGCTATGGATGTCTTATTAATCTTTACTCTAAGGCAAGGATTTTTAATTTTTAT
9487 TTAATAAATTTTTTCCTACTGTATGCACTCCCCCAAACCCCCCTTGTATGGTGTATTCCTCTTCT
66 TTAATAAATTTTTTCCTACTGTATGCACTCCCCCAAACCCCCCTTGTATGGTGTATTCCTCTTCT
*
9552 GTGTGCGGGTGTGTGTGTTTTGGGGAGTGTTGAAGTTCAGTGAATCCCTTTGTTGAATTGAAGCA
131 GTGTGCGCGTGTGTGTGTTTTGGGGAGTGTTGAAGTTCAGTGAATCCCTTTGTTGAATTGAAGCA
9617 TTTTATCCTACTTTGACTGTCCTTTCCCT
196 TTTTATCCTACTTTGACTGTCCTTTCCCT
9646 CGAAAGTAGT
Statistics
Matches: 222, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
237 222 1.00
ACGTcount: A:0.20, C:0.20, G:0.18, T:0.42
Consensus pattern (237 bp):
CCTCAATCATCAGCTATGGATGTCTTATTAATCTTTACTCTAAGGCAAGGATTTTTAATTTTTAT
TTAATAAATTTTTTCCTACTGTATGCACTCCCCCAAACCCCCCTTGTATGGTGTATTCCTCTTCT
GTGTGCGCGTGTGTGTGTTTTGGGGAGTGTTGAAGTTCAGTGAATCCCTTTGTTGAATTGAAGCA
TTTTATCCTACTTTGACTGTCCTTTCCCTAGGATTTTTAATT
Found at i:15401 original size:23 final size:23
Alignment explanation
Indices: 15375--15430 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
15365 GCTTGAGTCG
*
15375 TTCAATAACTTCG-ATTAGATATA
1 TTCAATAACCTCGAATTAG-TATA
*
15398 TTCAATACCCTCGAATTAGTATA
1 TTCAATAACCTCGAATTAGTATA
15421 TTACAA-AACC
1 TT-CAATAACC
15431 CAAAACAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 20 0.71
24 8 0.29
ACGTcount: A:0.39, C:0.20, G:0.07, T:0.34
Consensus pattern (23 bp):
TTCAATAACCTCGAATTAGTATA
Found at i:16727 original size:18 final size:18
Alignment explanation
Indices: 16693--16727 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
16683 TCGATTAATT
* *
16693 TCAGAGATTTTAGTGATA
1 TCAGAGATTTCAATGATA
16711 TCAGAGATTTCAATGAT
1 TCAGAGATTTCAATGAT
16728 GTCAAAAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.34, C:0.09, G:0.20, T:0.37
Consensus pattern (18 bp):
TCAGAGATTTCAATGATA
Found at i:22080 original size:15 final size:15
Alignment explanation
Indices: 22060--22096 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
22050 AAGACATGTC
22060 AAAAAAAAAAAAAAT
1 AAAAAAAAAAAAAAT
*
22075 AAAAAAAAAAATAAT
1 AAAAAAAAAAAAAAT
*
22090 AATAAAA
1 AAAAAAA
22097 TTAAATCTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAAAAAAAAAAT
Found at i:22096 original size:12 final size:12
Alignment explanation
Indices: 22063--22088 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
22053 ACATGTCAAA
22063 AAAAAAAAAAAT
1 AAAAAAAAAAAT
22075 AAAAAAAAAAAT
1 AAAAAAAAAAAT
22087 AA
1 AA
22089 TAATAAAATT
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAAAAAAT
Found at i:23335 original size:9 final size:9
Alignment explanation
Indices: 23321--23356 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
23311 CTCTTGCTTA
23321 ATTTCAGAG
1 ATTTCAGAG
*
23330 ATTTCAGTG
1 ATTTCAGAG
*
23339 ATATCAGAG
1 ATTTCAGAG
23348 ATTTCAGAG
1 ATTTCAGAG
23357 GCTATTGATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.33, C:0.11, G:0.22, T:0.33
Consensus pattern (9 bp):
ATTTCAGAG
Found at i:24643 original size:6 final size:6
Alignment explanation
Indices: 24632--24662 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
24622 CCAGTTTTAT
24632 GATGGG GATGGG GATGGG GATGGG GATGGG G
1 GATGGG GATGGG GATGGG GATGGG GATGGG G
24663 GACAGCCAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.68, T:0.16
Consensus pattern (6 bp):
GATGGG
Found at i:26772 original size:3 final size:3
Alignment explanation
Indices: 26766--26798 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
26756 TGGGTAGGTC
26766 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
26799 GGGGTTGATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:28712 original size:44 final size:44
Alignment explanation
Indices: 28660--28748 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
28650 TAGTTTGGAG
28660 AACAACATTAAACTTAAACTTAAAACCCAATACAAAAATAACTT
1 AACAACATTAAACTTAAACTTAAAACCCAATACAAAAATAACTT
*
28704 AACAACATTAAACTTAAACTTAAAACCCAATACAGAAATAACTT
1 AACAACATTAAACTTAAACTTAAAACCCAATACAAAAATAACTT
28748 A
1 A
28749 CTTAGGGAGA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.56, C:0.20, G:0.01, T:0.22
Consensus pattern (44 bp):
AACAACATTAAACTTAAACTTAAAACCCAATACAAAAATAACTT
Found at i:29720 original size:3 final size:3
Alignment explanation
Indices: 29712--29740 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
29702 GAGTATGTAG
29712 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
29741 TTATTATTAT
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:29745 original size:3 final size:3
Alignment explanation
Indices: 29739--29771 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
29729 ATAATAATAA
29739 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
29772 CTTGTACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:30595 original size:21 final size:21
Alignment explanation
Indices: 30569--30610 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
30559 ATAATGTTAC
30569 TTAAAG-TCATTTTTAAAACAA
1 TTAAAGCT-ATTTTTAAAACAA
30590 TTAAAGCTATTTTTAAAACAA
1 TTAAAGCTATTTTTAAAACAA
30611 AAATTGGTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.38
Consensus pattern (21 bp):
TTAAAGCTATTTTTAAAACAA
Found at i:32989 original size:39 final size:39
Alignment explanation
Indices: 32925--33004 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
32915 CCAATTATAA
**
32925 TAGGGGTAATCTTGGCATTTAGATATTTTAATTTTTAAT
1 TAGGGGTAATCTTGAAATTTAGATATTTTAATTTTTAAT
*
32964 TAGGGGTAATCTTGAAATTTGGATATTTTAATTTTTAAT
1 TAGGGGTAATCTTGAAATTTAGATATTTTAATTTTTAAT
33003 TA
1 TA
33005 TTTATTTTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.49
Consensus pattern (39 bp):
TAGGGGTAATCTTGAAATTTAGATATTTTAATTTTTAAT
Found at i:33720 original size:29 final size:29
Alignment explanation
Indices: 33688--33754 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
33678 TTAAATTAGT
* *
33688 AATGATAAAATTATATTTTGATCT-TTTAA
1 AATGATAAAATTATAATTTAAT-TATTTAA
*
33717 AATGATAAAATTTTAATTTAATTATTTAA
1 AATGATAAAATTATAATTTAATTATTTAA
*
33746 AATTATAAA
1 AATGATAAA
33755 GATATAGGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 1 0.03
29 32 0.97
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.46
Consensus pattern (29 bp):
AATGATAAAATTATAATTTAATTATTTAA
Found at i:33883 original size:123 final size:124
Alignment explanation
Indices: 33687--33935 Score: 367
Period size: 123 Copynumber: 2.0 Consensus size: 124
33677 TTTAAATTAG
* * *
33687 TAATGATAAAATTATATTTTGATCTTTTAAAATGATAAAATTTTAATTTAATTATTTAAAATTAT
1 TAATGATAAAATTACACTTTGATCTTTCAAAATGAT-AAATTTTAATTTAATTATTTAAAATTAT
* *
33752 AAAGATATAGGCTATTATGGTGAAATTATATTTTTACGATAGTAAAAATATACAATTTAA
65 AAAGATATAAGCTATCATGGTGAAATTATATTTTTACGATAGTAAAAATATACAATTTAA
* * *
33812 TAATGATAAAATTGCACTTT-ATCCTTTCAAAATGAT-AATTTTAATTTAATTCTTTGAAATTAT
1 TAATGATAAAATTACACTTTGAT-CTTTCAAAATGATAAATTTTAATTTAATTATTTAAAATTAT
* * *
33875 AAATATATAAGCTATCATGGTGAAATTATATTTTTACTATCGTAAAAATATACAATTTAA
65 AAAGATATAAGCTATCATGGTGAAATTATATTTTTACGATAGTAAAAATATACAATTTAA
33935 T
1 T
33936 TCCATCTCAA
Statistics
Matches: 112, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
123 81 0.72
124 2 0.02
125 29 0.26
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.43
Consensus pattern (124 bp):
TAATGATAAAATTACACTTTGATCTTTCAAAATGATAAATTTTAATTTAATTATTTAAAATTATA
AAGATATAAGCTATCATGGTGAAATTATATTTTTACGATAGTAAAAATATACAATTTAA
Found at i:39905 original size:32 final size:32
Alignment explanation
Indices: 39869--39932 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
39859 ATATCATTTT
39869 AAATTCAATTACACTATTTCACAAAAAAAAAA
1 AAATTCAATTACACTATTTCACAAAAAAAAAA
* *
39901 AAATTCAGTTACACTATTTCACCAAAAAAAAA
1 AAATTCAATTACACTATTTCACAAAAAAAAAA
39933 TTCAGTTACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.56, C:0.17, G:0.02, T:0.25
Consensus pattern (32 bp):
AAATTCAATTACACTATTTCACAAAAAAAAAA
Found at i:39937 original size:29 final size:30
Alignment explanation
Indices: 39869--39946 Score: 113
Period size: 29 Copynumber: 2.6 Consensus size: 30
39859 ATATCATTTT
*
39869 AAATTCAATTACACTATTTCACAAAAAAAAAA
1 AAATTCAGTTACACTATTTCAC--AAAAAAAA
*
39901 AAATTCAGTTACACTATTTCAC-CAAAAAA
1 AAATTCAGTTACACTATTTCACAAAAAAAA
39930 AAATTCAGTTACACTAT
1 AAATTCAGTTACACTAT
39947 AATCATATTT
Statistics
Matches: 44, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 23 0.52
32 21 0.48
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (30 bp):
AAATTCAGTTACACTATTTCACAAAAAAAA
Found at i:40701 original size:22 final size:24
Alignment explanation
Indices: 40657--40701 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 24
40647 TAATTGTTAT
*
40657 TATATGGATTATACTAGTGTAATC
1 TATATGGATTATACTAGTATAATC
*
40681 TATATGGA-TA-ACTATTATAAT
1 TATATGGATTATACTAGTATAAT
40702 TAGTGAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 2 0.11
24 8 0.42
ACGTcount: A:0.38, C:0.07, G:0.13, T:0.42
Consensus pattern (24 bp):
TATATGGATTATACTAGTATAATC
Found at i:41750 original size:31 final size:30
Alignment explanation
Indices: 41697--41758 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
41687 AATTTTTTTT
*
41697 AAATTATAGTTTAATTATTGAATTATTCAAA
1 AAATTATAGTTTAATTACTGAATTATT-AAA
*
41728 AAATTTTA-TTTAAGTTACTGAATTATTAAA
1 AAATTATAGTTTAA-TTACTGAATTATTAAA
41758 A
1 A
41759 TCGTTATTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 9 0.32
31 19 0.68
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.45
Consensus pattern (30 bp):
AAATTATAGTTTAATTACTGAATTATTAAA
Found at i:47937 original size:16 final size:17
Alignment explanation
Indices: 47911--47955 Score: 56
Period size: 16 Copynumber: 2.6 Consensus size: 17
47901 ATTTATTAAA
47911 TTAATTTAAATTATTTTC
1 TTAA-TTAAATTATTTTC
*
47929 -TAATTAAATGATTTTC
1 TTAATTAAATTATTTTC
*
47945 TTAATTCAATT
1 TTAATTAAATT
47956 CTAATCTCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 12 0.52
17 11 0.48
ACGTcount: A:0.36, C:0.07, G:0.02, T:0.56
Consensus pattern (17 bp):
TTAATTAAATTATTTTC
Found at i:48881 original size:23 final size:24
Alignment explanation
Indices: 48830--48883 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 24
48820 TTTGGAGAAC
*
48830 AACATTAAAATTAAAAATAAAACT
1 AACATTAAAATTAAAAATAAAACA
* * *
48854 TACATTAACATT-AAAATAAACCA
1 AACATTAAAATTAAAAATAAAACA
48877 AACATTA
1 AACATTA
48884 CATATATAGT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 15 0.60
24 10 0.40
ACGTcount: A:0.61, C:0.13, G:0.00, T:0.26
Consensus pattern (24 bp):
AACATTAAAATTAAAAATAAAACA
Found at i:50903 original size:18 final size:19
Alignment explanation
Indices: 50870--50905 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
50860 TTTGAAAATT
*
50870 AAAATATTTAAAATTTAAG
1 AAAATAATTAAAATTTAAG
50889 AAAATAATT-AAATTTAA
1 AAAATAATTAAAATTTAA
50906 ACGTATCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (19 bp):
AAAATAATTAAAATTTAAG
Found at i:51874 original size:8 final size:8
Alignment explanation
Indices: 51861--51885 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
51851 TATCTAAAAA
51861 TATAGTTT
1 TATAGTTT
51869 TATAGTTT
1 TATAGTTT
51877 TATAGTTT
1 TATAGTTT
51885 T
1 T
51886 TTAAATACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.12, T:0.64
Consensus pattern (8 bp):
TATAGTTT
Found at i:51898 original size:28 final size:27
Alignment explanation
Indices: 51866--51942 Score: 75
Period size: 28 Copynumber: 2.8 Consensus size: 27
51856 AAAAATATAG
*
51866 TTTTATAGTTTTATAGTTTTTTAAATAC
1 TTTTATAATTTTATA-TTTTTTAAATAC
* *
51894 TTTTAATAATGTTTA-ATTTTTAAAATAT
1 TTTT-ATAAT-TTTATATTTTTTAAATAC
* *
51922 TTTTATACTTTTTTATTTTTT
1 TTTTATAATTTTATATTTTTT
51943 TAATTTTAAA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
26 3 0.08
27 10 0.25
28 18 0.45
29 5 0.12
30 4 0.10
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.65
Consensus pattern (27 bp):
TTTTATAATTTTATATTTTTTAAATAC
Found at i:53163 original size:81 final size:81
Alignment explanation
Indices: 53052--53235 Score: 341
Period size: 81 Copynumber: 2.2 Consensus size: 81
53042 TAAACAAATT
53052 TTTTTTATGAATAAGTATATTATTTTTATATATATAGTATGGACAAGTAAATAAGTCATGTTTAT
1 TTTTTTAT-AATAAGTATATTATTTTTATATATATAGTATGGACAAGTAAATAAGTCATGTTTAT
53117 ATATTTTTTTGTCTCAA
65 ATATTTTTTTGTCTCAA
53134 TTTTTTATAATAAGTATATTATTTTTATATATATAGTATGGACAAGTAAATAAGTCATGTTTATA
1 TTTTTTATAATAAGTATATTATTTTTATATATATAGTATGGACAAGTAAATAAGTCATGTTTATA
53199 TATTTTTTTGTCTCAA
66 TATTTTTTTGTCTCAA
*
53215 TTTTTTATAGATAAATATATT
1 TTTTTTATA-ATAAGTATATT
53236 GTAACACTTT
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
81 82 0.82
82 18 0.18
ACGTcount: A:0.35, C:0.04, G:0.10, T:0.51
Consensus pattern (81 bp):
TTTTTTATAATAAGTATATTATTTTTATATATATAGTATGGACAAGTAAATAAGTCATGTTTATA
TATTTTTTTGTCTCAA
Found at i:79140 original size:21 final size:21
Alignment explanation
Indices: 79116--79156 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
79106 TGTCACAAAT
*
79116 TAATTACACA-ATCAATATTTA
1 TAATTAAACACAT-AATATTTA
79137 TAATTAAACACATAATATTT
1 TAATTAAACACATAATATTT
79157 CACATATACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (21 bp):
TAATTAAACACATAATATTTA
Found at i:80553 original size:41 final size:41
Alignment explanation
Indices: 80508--80589 Score: 164
Period size: 41 Copynumber: 2.0 Consensus size: 41
80498 AACTTCCACA
80508 AAATTACTCTTTTGCCCCTCCTCAATCAATCTAATTCCCAT
1 AAATTACTCTTTTGCCCCTCCTCAATCAATCTAATTCCCAT
80549 AAATTACTCTTTTGCCCCTCCTCAATCAATCTAATTCCCAT
1 AAATTACTCTTTTGCCCCTCCTCAATCAATCTAATTCCCAT
80590 GATGACTCAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.27, C:0.34, G:0.02, T:0.37
Consensus pattern (41 bp):
AAATTACTCTTTTGCCCCTCCTCAATCAATCTAATTCCCAT
Found at i:86983 original size:19 final size:19
Alignment explanation
Indices: 86961--86997 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
86951 TATTATTTAT
86961 TATATA-TAAT-TTTTAAA
1 TATATATTAATATTTTAAA
*
86978 TATATATTTATATTTTAAA
1 TATATATTAATATTTTAAA
86997 T
1 T
86998 TTATTATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATATATTAATATTTTAAA
Found at i:95349 original size:24 final size:24
Alignment explanation
Indices: 95308--95361 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
95298 TTGATGAAAG
* *
95308 ATGAACTGTTAAATACATGCAGAA
1 ATGAACTGTTAAACACATACAGAA
* *
95332 ATGAACTGTTCAGCACATACAGAA
1 ATGAACTGTTAAACACATACAGAA
95356 A-GAACT
1 ATGAACT
95362 TACTTTTCCC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
23 5 0.19
24 21 0.81
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.22
Consensus pattern (24 bp):
ATGAACTGTTAAACACATACAGAA
Found at i:100206 original size:3 final size:3
Alignment explanation
Indices: 100198--100243 Score: 69
Period size: 3 Copynumber: 16.0 Consensus size: 3
100188 TTCTCCGTAA
*
100198 CTC CTC CT- CTC CT- CTG CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
1 CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC CTC
100244 AGCATCCACG
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
2 4 0.10
3 36 0.90
ACGTcount: A:0.00, C:0.63, G:0.02, T:0.35
Consensus pattern (3 bp):
CTC
Found at i:114450 original size:6 final size:6
Alignment explanation
Indices: 114435--114469 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
114425 TTGAAGGATA
*
114435 TGTTGT TGTTGC TGTTGC TGTTGC TGTTGC TGTTG
1 TGTTGC TGTTGC TGTTGC TGTTGC TGTTGC TGTTG
114470 TATGGGAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.00, C:0.11, G:0.34, T:0.54
Consensus pattern (6 bp):
TGTTGC
Found at i:114520 original size:6 final size:6
Alignment explanation
Indices: 114509--114543 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
114499 TAGTAAAGGT
114509 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
114544 TAATCTTTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTTTC
Found at i:115208 original size:29 final size:28
Alignment explanation
Indices: 115147--115208 Score: 70
Period size: 29 Copynumber: 2.2 Consensus size: 28
115137 GTTCTTCGTG
* *
115147 AATTTGAAATTTAAATTTTATATTTTCA
1 AATTTGAAATATAAATTTTATATTTTAA
* * *
115175 TATTTAGAAATATATATTTTTTATTTTAA
1 AATTT-GAAATATAAATTTTATATTTTAA
115204 AATTT
1 AATTT
115209 TAAAATTCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
28 4 0.15
29 23 0.85
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (28 bp):
AATTTGAAATATAAATTTTATATTTTAA
Found at i:115753 original size:15 final size:16
Alignment explanation
Indices: 115733--115763 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
115723 GATTTTATAT
115733 AAAAAATAA-AAAATA
1 AAAAAATAAGAAAATA
115748 AAAAAATAAGAAAATA
1 AAAAAATAAGAAAATA
115764 CCCTCAGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAAATAAGAAAATA
Found at i:119196 original size:16 final size:16
Alignment explanation
Indices: 119172--119202 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
119162 GTAAGTATAG
119172 ATATCAATTATAAAAA
1 ATATCAATTATAAAAA
*
119188 ATATTAATTATAAAA
1 ATATCAATTATAAAA
119203 TATTCAGAGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.35
Consensus pattern (16 bp):
ATATCAATTATAAAAA
Found at i:119679 original size:25 final size:25
Alignment explanation
Indices: 119625--119679 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
119615 GTTATATCAA
* *
119625 ATTTTAATAGAAAGAATTAATAAAT
1 ATTTTAATAAAAAGAATTAATAAAC
* **
119650 TTTTTAATAAAAAGAATTAATTTAC
1 ATTTTAATAAAAAGAATTAATAAAC
119675 ATTTT
1 ATTTT
119680 GAGTTAACAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (25 bp):
ATTTTAATAAAAAGAATTAATAAAC
Found at i:121552 original size:3 final size:3
Alignment explanation
Indices: 121546--121575 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
121536 TAATATCCAA
121546 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
121576 TACAGCTACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:122558 original size:21 final size:21
Alignment explanation
Indices: 122519--122569 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
122509 TTTTACTTTT
122519 ATATGTTTTTAAAATTATTATG
1 ATAT-TTTTTAAAATTATTATG
* *
122541 ATATTTTTTGAAAA-TATTTTT
1 ATATTTTTT-AAAATTATTATG
122562 ATATTTTT
1 ATATTTTT
122570 GTTTGAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 18 0.69
22 8 0.31
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (21 bp):
ATATTTTTTAAAATTATTATG
Found at i:123475 original size:17 final size:17
Alignment explanation
Indices: 123455--123530 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
123445 AATACTACTC
123455 TAATATAAATATTAAAA
1 TAATATAAATATTAAAA
* * * *
123472 TAATGTTAAGATGACAATA
1 TAATATAAATATTA-AA-A
123491 TAA-A-AAATATATAAAA
1 TAATATAAATAT-TAAAA
*
123507 TTAT-TAAATATTAAAA
1 TAATATAAATATTAAAA
123523 TAATATAA
1 TAATATAA
123531 TATAAATATT
Statistics
Matches: 43, Mismatches: 10, Indels: 12
0.66 0.15 0.18
Matches are distributed among these distances:
16 11 0.26
17 25 0.58
18 3 0.07
19 4 0.09
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (17 bp):
TAATATAAATATTAAAA
Found at i:130673 original size:38 final size:39
Alignment explanation
Indices: 130631--130714 Score: 100
Period size: 38 Copynumber: 2.2 Consensus size: 39
130621 TGATGTTTAT
*
130631 TAAATATTATGCTAAATAGTAT-TTATAAATTAAAATAA
1 TAAATATTATGCTAAATAGCATATTATAAATTAAAATAA
** **
130669 TAAAT-TTATTTTAAATAGCATATTATGGATTAAAATAA
1 TAAATATTATGCTAAATAGCATATTATAAATTAAAATAA
130707 TAATATAT
1 TAA-ATAT
130715 AAATCTCATA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
37 13 0.34
38 22 0.58
39 2 0.05
40 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.06, T:0.42
Consensus pattern (39 bp):
TAAATATTATGCTAAATAGCATATTATAAATTAAAATAA
Found at i:134662 original size:31 final size:31
Alignment explanation
Indices: 134627--134698 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
134617 TCAATATGTC
* *
134627 ATTTGATACCTGCA-TTTGACTTTAATGTTTA
1 ATTTGATACCTG-AGTTTAACTTTAATGTTAA
*
134658 ATTTGATACTTGAGTTTAACTTTAATGTTAA
1 ATTTGATACCTGAGTTTAACTTTAATGTTAA
*
134689 ATTTGGTACC
1 ATTTGATACC
134699 GCCACAAGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.28, C:0.11, G:0.14, T:0.47
Consensus pattern (31 bp):
ATTTGATACCTGAGTTTAACTTTAATGTTAA
Found at i:135240 original size:12 final size:11
Alignment explanation
Indices: 135215--135248 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
135205 TGAATTTAGA
*
135215 TTTTTTTCTGT
1 TTTTTTTTTGT
135226 TTTTGTTTTTGT
1 TTTT-TTTTTGT
135238 TTTTTTTTTGT
1 TTTTTTTTTGT
135249 AACCCTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.00, C:0.03, G:0.12, T:0.85
Consensus pattern (11 bp):
TTTTTTTTTGT
Found at i:144392 original size:59 final size:59
Alignment explanation
Indices: 144329--144830 Score: 686
Period size: 59 Copynumber: 8.5 Consensus size: 59
144319 ACATTTGGGA
* * * * **
144329 GTAAAATAGTAATTTTTGGATGTTTCGGGGTCAAAAATGGGATTTTTGGGAGTTCAAGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
* * * *
144388 GTAAAATGGTAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
* * * * *
144447 GT-ACATGGTAATTTTTTGAAGGTTCGGGGTCAAGAATGGGATTTTTGGAAATTCGGGA
1 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
*
144505 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTC-AAAATGGGATTTTTAGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
* * * *
144563 GTAGAATGGTAATTTTTGAAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAGTTCGGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
* *
144622 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
* * * *
144681 GTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAGTGGGATTTTTTGAAGTTTGGGG
1 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
* * * * * *
144740 GTAGAATGGCAATTTTTGGAAGGTT-GAGGGTTAAAAATAGGATTTTTGGAAGTTTGAGG
1 GTAAAATGGTAATTTTTGGAAGGTTCG-GGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
144799 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTC
1 GTAAAATGGTAATTTTTGGAAGGTTCGGGGTC
144831 CTCCGGGGTA
Statistics
Matches: 394, Mismatches: 45, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
58 101 0.26
59 292 0.74
60 1 0.00
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.34
Consensus pattern (59 bp):
GTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAGTTCGGGG
Found at i:144726 original size:29 final size:29
Alignment explanation
Indices: 144340--144830 Score: 364
Period size: 30 Copynumber: 16.7 Consensus size: 29
144330 TAAAATAGTA
* *
144340 ATTTTTGGATGTTTCGGGGTCAAAAATGGG
1 ATTTTTGGAAGGTTCGGGGTC-AAAATGGG
* * *
144370 ATTTTTGGGA-GTTCAAGGGT-AAAATGGTA
1 ATTTTTGGAAGGTTC-GGGGTCAAAATGG-G
* * *
144399 ATTTTTGGAAGTTTTGAGGTCAAAAATGGG
1 ATTTTTGGAAGGTTCGGGGTC-AAAATGGG
* * * *
144429 ATTTTTGGAAGTTTGGGGGT--ACATGGTA
1 ATTTTTGGAAGGTTCGGGGTCAAAATGG-G
*
144457 ATTTTTTGAAGGTTCGGGGTCAAGAATGGG
1 ATTTTTGGAAGGTTCGGGGTCAA-AATGGG
* *
144487 ATTTTTGGAA-ATTCGGGAGT-AAAATGGTA
1 ATTTTTGGAAGGTTCGGG-GTCAAAATGG-G
144516 ATTTTTGGAAGGTTCGGGGTCAAAATGGG
1 ATTTTTGGAAGGTTCGGGGTCAAAATGGG
* * *
144545 ATTTTTAGAA-GTTCGGGGGT-AGAATGGTA
1 ATTTTTGGAAGGTTC-GGGGTCAAAATGG-G
* * *
144574 ATTTTTGAAAGGTTCGAGGTCAAAAATGAG
1 ATTTTTGGAAGGTTCGGGGTC-AAAATGGG
*
144604 ATTTTTGGAA-GTTCGGGGGT-AAAATGGTA
1 ATTTTTGGAAGGTTC-GGGGTCAAAATGG-G
*
144633 ATTTTTGGAAGGTTCGAGGTCAAAAATGGG
1 ATTTTTGGAAGGTTCGGGGTC-AAAATGGG
* * *
144663 ATTTTTGGAAGTTTGGGGGT-AAAATGGTA
1 ATTTTTGGAAGGTTCGGGGTCAAAATGG-G
*
144692 ATTTTTGGAAGGTTCGAGGTCAAAAGTGGG
1 ATTTTTGGAAGGTTCGGGGTCAAAA-TGGG
* * * * *
144722 ATTTTTTGAAGTTTGGGGGT-AGAATGGCA
1 ATTTTTGGAAGGTTCGGGGTCAAAATGG-G
* *
144751 ATTTTTGGAAGGTT-GAGGGTTAAAAATAGG
1 ATTTTTGGAAGGTTCG-GGG-TCAAAATGGG
* *
144781 ATTTTTGGAA-GTTTGAGGGT-AAAATGGTA
1 ATTTTTGGAAGGTTCG-GGGTCAAAATGG-G
144810 ATTTTTGGAAGGTTCGGGGTC
1 ATTTTTGGAAGGTTCGGGGTC
144831 CTCCGGGGTA
Statistics
Matches: 365, Mismatches: 62, Indels: 68
0.74 0.13 0.14
Matches are distributed among these distances:
27 5 0.01
28 62 0.17
29 132 0.36
30 135 0.37
31 31 0.08
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.35
Consensus pattern (29 bp):
ATTTTTGGAAGGTTCGGGGTCAAAATGGG
Found at i:144733 original size:118 final size:118
Alignment explanation
Indices: 144263--144830 Score: 727
Period size: 118 Copynumber: 4.8 Consensus size: 118
144253 ATTTAAAACA
* * * * *
144263 TTCGAGGGTAAAAATGGTAA-TTTT-GAGAGTTTCGAGGTCAAAAA-CGGAGTCTTCGGACA-TT
1 TTCGGGGGT-AAAATGGTAATTTTTGGA-AGGTTCGAGGTCAAAAATGGGA-TTTTTGGA-AGTT
* * * * *
144324 TGGGAGTAAAATAGTAATTTTTGGATGTTTCGGGGTCAAAAATGGGATTTTTGGGAG
62 TGGGGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
** * *
144381 TTCAAGGGTAAAATGGTAATTTTTGGAAGTTTTGAGGTCAAAAATGGGATTTTTGGAAGTTTGGG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGG
* * * *
144446 GGT-ACATGGTAATTTTTTGAAGGTTCGGGGTCAAGAATGGGATTTTTGGAAA
66 GGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * *
144498 TTCGGGAGTAAAATGGTAATTTTTGGAAGGTTCGGGGTC-AAAATGGGATTTTTAGAAGTTCGGG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGG
* * * *
144562 GGTAGAATGGTAATTTTTGAAAGGTTCGAGGTCAAAAATGAGATTTTTGGAAG
66 GGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
144615 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGG
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGG
* * *
144680 GGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAGTGGGATTTTTTGAAG
66 GGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
* * * * * *
144733 TTTGGGGGTAGAATGGCAATTTTTGGAAGGTT-GAGGGTTAAAAATAGGATTTTTGGAAGTTTGA
1 TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGA-GGTCAAAAATGGGATTTTTGGAAGTTTGG
144797 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTC
65 GGGTAAAATGGTAATTTTTGGAAGGTTCGGGGTC
144831 CTCCGGGGTA
Statistics
Matches: 397, Mismatches: 46, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
116 26 0.07
117 165 0.42
118 201 0.51
119 5 0.01
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.34
Consensus pattern (118 bp):
TTCGGGGGTAAAATGGTAATTTTTGGAAGGTTCGAGGTCAAAAATGGGATTTTTGGAAGTTTGGG
GGTAAAATGGTAATTTTTGGAAGGTTCGGGGTCAAAAATGGGATTTTTGGAAG
Found at i:144787 original size:30 final size:30
Alignment explanation
Indices: 144330--144829 Score: 293
Period size: 29 Copynumber: 17.0 Consensus size: 30
144320 CATTTGGGAG
* * *
144330 TAAAATAGTAATTTTTGGATGTTTCG-GGGT
1 TAAAAT-GGAATTTTTGGAAGGTTCGAGGGT
* * * *
144360 CAAAAATGGGATTTTTGGGA-GTTCAAGGG-
1 -TAAAATGGAATTTTTGGAAGGTTCGAGGGT
* *
144389 TAAAATGGTAATTTTTGGAAGTTTTGA-GGT
1 TAAAATGG-AATTTTTGGAAGGTTCGAGGGT
* * * *
144419 CAAAAATGGGATTTTTGGAA-GTTTG-GGGG
1 -TAAAATGGAATTTTTGGAAGGTTCGAGGGT
* *
144448 T-ACATGGTAATTTTTTGAAGGTTCG-GGGT
1 TAAAATGG-AATTTTTGGAAGGTTCGAGGGT
* * *
144477 CAAGAATGGGATTTTTGGAA-ATTCG-GGAG-
1 TAA-AATGGAATTTTTGGAAGGTTCGAGG-GT
144506 TAAAATGGTAATTTTTGGAAGGTTCG-GGGT
1 TAAAATGG-AATTTTTGGAAGGTTCGAGGGT
* * * *
144536 CAAAATGGGATTTTTAGAA-GTTCG-GGGG
1 TAAAATGGAATTTTTGGAAGGTTCGAGGGT
* *
144564 TAGAATGGTAATTTTTGAAAGGTTCGA-GGT
1 TAAAATGG-AATTTTTGGAAGGTTCGAGGGT
* *
144594 CAAAAAT-GAGATTTTTGGAA-GTTCG-GGGG
1 -TAAAATGGA-ATTTTTGGAAGGTTCGAGGGT
144623 TAAAATGGTAATTTTTGGAAGGTTCGA-GGT
1 TAAAATGG-AATTTTTGGAAGGTTCGAGGGT
* * * *
144653 CAAAAATGGGATTTTTGGAA-GTTTG-GGGG
1 -TAAAATGGAATTTTTGGAAGGTTCGAGGGT
144682 TAAAATGGTAATTTTTGGAAGGTTCGA-GGT
1 TAAAATGG-AATTTTTGGAAGGTTCGAGGGT
* * * * *
144712 CAAAAGTGGGATTTTTTGAA-GTTTG-GGGG
1 TAAAA-TGGAATTTTTGGAAGGTTCGAGGGT
*
144741 TAGAATGGCAATTTTTGGAAGGTT-GAGGGT
1 TAAAATGG-AATTTTTGGAAGGTTCGAGGGT
*
144771 TAAAAATAGG-ATTTTTGGAA-GTTTGAGGG-
1 T-AAAAT-GGAATTTTTGGAAGGTTCGAGGGT
144800 TAAAATGGTAATTTTTGGAAGGTTCG-GGGT
1 TAAAATGG-AATTTTTGGAAGGTTCGAGGGT
144830 CCTCCGGGGT
Statistics
Matches: 361, Mismatches: 67, Indels: 83
0.71 0.13 0.16
Matches are distributed among these distances:
27 7 0.02
28 55 0.15
29 134 0.37
30 129 0.36
31 34 0.09
32 2 0.01
ACGTcount: A:0.28, C:0.04, G:0.33, T:0.35
Consensus pattern (30 bp):
TAAAATGGAATTTTTGGAAGGTTCGAGGGT
Found at i:146627 original size:6 final size:6
Alignment explanation
Indices: 146618--146674 Score: 75
Period size: 6 Copynumber: 9.8 Consensus size: 6
146608 TATTTTGTAA
146618 TTAAAT TTAAAT TTAAAT TTAAGA- TT-AAT TTAAAT TTAAAT TTAAA-
1 TTAAAT TTAAAT TTAAAT TTAA-AT TTAAAT TTAAAT TTAAAT TTAAAT
*
146664 TCAAAT TTAAA
1 TTAAAT TTAAA
146675 ATAAATTAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
4 1 0.02
5 7 0.16
6 36 0.80
7 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.46
Consensus pattern (6 bp):
TTAAAT
Found at i:146636 original size:17 final size:16
Alignment explanation
Indices: 146618--146684 Score: 71
Period size: 17 Copynumber: 3.9 Consensus size: 16
146608 TATTTTGTAA
146618 TTAAATTTAAATTTAAAT
1 TTAAA-TTAAA-TTAAAT
*
146636 TTAAGATTAATTTAAAT
1 TTAA-ATTAAATTAAAT
*
146653 TTAAATTTAAATCAAAT
1 TTAAA-TTAAATTAAAT
*
146670 TTAAAATAAATTAAA
1 TTAAATTAAATTAAA
146685 AAAAAGGGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
16 9 0.21
17 24 0.57
18 8 0.19
19 1 0.02
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.43
Consensus pattern (16 bp):
TTAAATTAAATTAAAT
Found at i:146670 original size:23 final size:23
Alignment explanation
Indices: 146619--146674 Score: 87
Period size: 23 Copynumber: 2.4 Consensus size: 23
146609 ATTTTGTAAT
146619 TAAATTTAAATTTAAATTTAAGA
1 TAAATTTAAATTTAAATTTAAGA
*
146642 TTAATTTAAATTTAAATTTAA-A
1 TAAATTTAAATTTAAATTTAAGA
146664 TCAAATTTAAA
1 T-AAATTTAAA
146675 ATAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 2 0.07
23 28 0.93
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (23 bp):
TAAATTTAAATTTAAATTTAAGA
Found at i:148003 original size:17 final size:17
Alignment explanation
Indices: 147983--148027 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
147973 GCTTTTGTTC
*
147983 TAAATTTAAATTCACTT
1 TAAATTTAAATTCACTG
*
148000 TAAATTTAAATTTACTG
1 TAAATTTAAATTCACTG
*
148017 TAAATTAAAAT
1 TAAATTTAAAT
148028 CAATTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (17 bp):
TAAATTTAAATTCACTG
Found at i:149982 original size:19 final size:20
Alignment explanation
Indices: 149950--149987 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
149940 AAATTGTCCG
149950 AAAATTACATTTTTGACCCA
1 AAAATTACATTTTTGACCCA
*
149970 AAAATTCCATTTTT-ACCC
1 AAAATTACATTTTTGACCC
149988 CCGAACCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.37, C:0.24, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATTACATTTTTGACCCA
Found at i:150124 original size:58 final size:58
Alignment explanation
Indices: 149968--150163 Score: 166
Period size: 58 Copynumber: 3.4 Consensus size: 58
149958 ATTTTTGACC
** * *
149968 CAAAAATT-CCATTTTTACCCCCGAACCTCCAAAATTTCCATTTTTGACC-CTAAAACTTT
1 CAAAAATTACCA-TTTTACCCCCGAATGT-CAAAAATTCCATTTTTGACCTC-AAAACTCT
* * * * * *
150027 CAAAAATTGCCATTTTTCCCCCGGATGTCCAAAACTCCATTTTCGACCTCAAAACTCT
1 CAAAAATTACCATTTTACCCCCGAATGTCAAAAATTCCATTTTTGACCTCAAAACTCT
* * * * *
150085 C-AAAATTACCCTTTTACCCTCGAATGTCTAAAAATTCCATTTTTAACCTC-AAGCTTT
1 CAAAAATTACCATTTTACCCCCGAATGTC-AAAAATTCCATTTTTGACCTCAAAACTCT
* *
150142 CCCAAAATTACCATTTTGCCCC
1 -CAAAAATTACCATTTTACCCC
150164 TGAGAATCCA
Statistics
Matches: 109, Mismatches: 23, Indels: 10
0.77 0.16 0.07
Matches are distributed among these distances:
57 27 0.25
58 42 0.39
59 37 0.34
60 3 0.03
ACGTcount: A:0.31, C:0.31, G:0.06, T:0.33
Consensus pattern (58 bp):
CAAAAATTACCATTTTACCCCCGAATGTCAAAAATTCCATTTTTGACCTCAAAACTCT
Found at i:150128 original size:29 final size:28
Alignment explanation
Indices: 149968--150134 Score: 81
Period size: 29 Copynumber: 5.8 Consensus size: 28
149958 ATTTTTGACC
* *
149968 CAAAAATTCCATTTTTACCCCCGAACCT
1 CAAAAATTCCATTTTTACCCTCGAATCT
* ** *
149996 CCAAAATTTCCATTTTTGACCCTAAAACTTT
1 -CAAAAATTCCATTTTT-ACCCTCGAA-TCT
* * *
150027 CAAAAATTGCCATTTTT-CCCCCGGATGT
1 CAAAAATT-CCATTTTTACCCTCGAATCT
* * * *
150055 CCAAAACTCCATTTTCGA-CCTCAAAACTCT
1 CAAAAATTCCATTTT-TACCCTC-GAA-TCT
* *
150085 C-AAAATTACC-CTTTTACCCTCGAATGT
1 CAAAAATT-CCATTTTTACCCTCGAATCT
*
150112 CTAAAAATTCCATTTTTAACCTC
1 C-AAAAATTCCATTTTTACCCTC
150135 AAGCTTTCCC
Statistics
Matches: 100, Mismatches: 26, Indels: 24
0.67 0.17 0.16
Matches are distributed among these distances:
27 10 0.10
28 16 0.16
29 47 0.47
30 18 0.18
31 9 0.09
ACGTcount: A:0.31, C:0.31, G:0.05, T:0.33
Consensus pattern (28 bp):
CAAAAATTCCATTTTTACCCTCGAATCT
Found at i:150177 original size:28 final size:28
Alignment explanation
Indices: 150143--150205 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
150133 TCAAGCTTTC
*
150143 CCAAAATTACCATTTTGCCCCTGAGAAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
* *
150171 CCAAAATTGCCATTTTGCCCCCGAGTAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
150199 CCGAAAA
1 CC-AAAA
150206 GTCTTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 27 0.87
29 4 0.13
ACGTcount: A:0.32, C:0.30, G:0.13, T:0.25
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGAGAAT
Found at i:157737 original size:20 final size:20
Alignment explanation
Indices: 157699--157737 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
157689 ATTAATATAT
* **
157699 ATATATACTTACATGCATAC
1 ATATATACATACACACATAC
157719 ATATATACATACACACATA
1 ATATATACATACACACATA
157738 TATGTATATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.31
Consensus pattern (20 bp):
ATATATACATACACACATAC
Found at i:164376 original size:14 final size:14
Alignment explanation
Indices: 164357--164385 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
164347 TGAAAAGCTT
164357 GATAATATTCGCGA
1 GATAATATTCGCGA
164371 GATAATATTCGCGA
1 GATAATATTCGCGA
164385 G
1 G
164386 TTGTTGGAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (14 bp):
GATAATATTCGCGA
Found at i:167991 original size:308 final size:309
Alignment explanation
Indices: 167432--168180 Score: 1428
Period size: 308 Copynumber: 2.4 Consensus size: 309
167422 TTAATTTGTA
167432 ATACTTGGATTTATTTTTACATTTATGAACATGACACATATCTAATTTGAATTTTATTATTTTAT
1 ATACTTGGATTTATTTTTACATTTATGAACATGACACATATCTAATTTGAATTTTATTATTTTAT
167497 GAAATGTTAGTTAAAATTAAAAAGTGATAAAAAAATTTTGGGTTTCGATTATTAAATAAAGTATG
66 GAAATGTTAGTTAAAATTAAAAAGTGATAAAAAAATTTTGGGTTTCGATTATTAAATAAAGTATG
167562 GTTTAATCTATGTTTAAACCCCCTTTTTTAATGTTTAGATTTCTATACATGTAGGATATTCCATA
131 GTTTAATCTATGTTTAAACCCCCTTTTTTAATGTTTAGATTTCTATACATGTAGGATATTCCATA
167627 ATTCACATGATATTATGTAGTTTGTCGTTTATGTTAATTGAAATCGTGACATCATCTCCCACTTG
196 ATTCACATGATATTATGTAGTTTGTCGTTTATGTTAATTGAAATCGTGACATCATCTCCCACTTG
167692 CCATACAACACTCACCCTCACTTATGTATTAATAACATAGAAACATGTC
261 CCATACAACACTCACCCTCACTTATGTATTAATAACATAGAAACATGTC
*
167741 ATACTTGGATTTATTTTTACATTTATGAACATGACACATATCTGATTTGAATTTTATTATTTTAT
1 ATACTTGGATTTATTTTTACATTTATGAACATGACACATATCTAATTTGAATTTTATTATTTTAT
167806 GAAATGTTAGTTAAAATTAAAAAGTGAT-AAAAAATTTTGGGTTTCGATTATTAAATAAAGTATG
66 GAAATGTTAGTTAAAATTAAAAAGTGATAAAAAAATTTTGGGTTTCGATTATTAAATAAAGTATG
167870 GTTTAATCTATGTTTAAACCCCCTTTTTTAATGTTTAGATTTCTATACATGTAGGATATTCCATA
131 GTTTAATCTATGTTTAAACCCCCTTTTTTAATGTTTAGATTTCTATACATGTAGGATATTCCATA
167935 ATTCACATGATATTATGTAGTTTGTCGTTTATGTTAATTGAAATCGTGACATCATCTCCCACTTG
196 ATTCACATGATATTATGTAGTTTGTCGTTTATGTTAATTGAAATCGTGACATCATCTCCCACTTG
*
168000 CCATACAACACTCACCCTCACTTATGTATTATTAACATAGAAACATGTC
261 CCATACAACACTCACCCTCACTTATGTATTAATAACATAGAAACATGTC
168049 ATACTTGGATTTATTTTTACATTTATGAACATGACACATATCTAATTTGAATTTTATTATTTTAT
1 ATACTTGGATTTATTTTTACATTTATGAACATGACACATATCTAATTTGAATTTTATTATTTTAT
* * *
168114 GAAATGTTAGTCAATATTAAAAAGTGATAAAAAAAAATTTTGGGTTTCGGTTATTAAATAAAGTA
66 GAAATGTTAGTTAAAATTAAAAAGTGAT--AAAAAAATTTTGGGTTTCGATTATTAAATAAAGTA
168179 TG
129 TG
168181 AGTAAAATAT
Statistics
Matches: 431, Mismatches: 6, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
308 304 0.71
309 92 0.21
311 35 0.08
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (309 bp):
ATACTTGGATTTATTTTTACATTTATGAACATGACACATATCTAATTTGAATTTTATTATTTTAT
GAAATGTTAGTTAAAATTAAAAAGTGATAAAAAAATTTTGGGTTTCGATTATTAAATAAAGTATG
GTTTAATCTATGTTTAAACCCCCTTTTTTAATGTTTAGATTTCTATACATGTAGGATATTCCATA
ATTCACATGATATTATGTAGTTTGTCGTTTATGTTAATTGAAATCGTGACATCATCTCCCACTTG
CCATACAACACTCACCCTCACTTATGTATTAATAACATAGAAACATGTC
Found at i:172787 original size:15 final size:16
Alignment explanation
Indices: 172763--172802 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
172753 AAACCTTTAA
*
172763 CCATTAAAGTCTAAAC
1 CCATTAAAGTCCAAAC
172779 CCATT-AAGTCCAAAC
1 CCATTAAAGTCCAAAC
172794 CCATCTAAA
1 CCAT-TAAA
172803 AGCCAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 13 0.62
16 6 0.29
17 2 0.10
ACGTcount: A:0.42, C:0.30, G:0.05, T:0.23
Consensus pattern (16 bp):
CCATTAAAGTCCAAAC
Found at i:173165 original size:22 final size:23
Alignment explanation
Indices: 173113--173165 Score: 54
Period size: 23 Copynumber: 2.3 Consensus size: 23
173103 TAATAGAAAC
*
173113 TAAATTTTGAAAATTAAAAGAAT
1 TAAATTTTGAAAATAAAAAGAAT
** * *
173136 TATTTTTTTACAATAAAAAG-AT
1 TAAATTTTGAAAATAAAAAGAAT
173158 TAAATTTT
1 TAAATTTT
173166 AAATGTATAA
Statistics
Matches: 23, Mismatches: 7, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.49, C:0.02, G:0.06, T:0.43
Consensus pattern (23 bp):
TAAATTTTGAAAATAAAAAGAAT
Found at i:176418 original size:3 final size:3
Alignment explanation
Indices: 176410--176435 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
176400 TTGAAATCTG
176410 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
176436 AACTACGTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:177478 original size:38 final size:38
Alignment explanation
Indices: 177434--177514 Score: 135
Period size: 38 Copynumber: 2.1 Consensus size: 38
177424 GAACGGATCG
*
177434 ATTCAAAATCCGTCCCATCCCACCCCACCCCACTCCAC
1 ATTCAAAATCCGTCCCATCCCACCCCAACCCACTCCAC
* *
177472 ATTCAAAATCCGTCCCGTCCCATCCCAACCCACTCCAC
1 ATTCAAAATCCGTCCCATCCCACCCCAACCCACTCCAC
177510 ATTCA
1 ATTCA
177515 CTTTTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.27, C:0.51, G:0.04, T:0.19
Consensus pattern (38 bp):
ATTCAAAATCCGTCCCATCCCACCCCAACCCACTCCAC
Found at i:192791 original size:2 final size:2
Alignment explanation
Indices: 192784--192810 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
192774 TGTTCTTTTA
192784 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
192811 CAATTAAAGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:205040 original size:23 final size:23
Alignment explanation
Indices: 204996--205040 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
204986 TTTTACAAGT
*
204996 GATTGCATGAAAAATTGGGGTTA
1 GATTGCATGAAAAATTGAGGTTA
*
205019 GATTG-ATGAATAATTAGAGGTT
1 GATTGCATGAAAAATT-GAGGTT
205041 GGTGGTCTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.36, C:0.02, G:0.29, T:0.33
Consensus pattern (23 bp):
GATTGCATGAAAAATTGAGGTTA
Found at i:205657 original size:23 final size:23
Alignment explanation
Indices: 205627--205728 Score: 107
Period size: 23 Copynumber: 4.3 Consensus size: 23
205617 TGCTGGGTAA
*
205627 CAGAGGGCACACAAAATGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
* *
205650 GAGAGGGCACACGAAGTGCTAAT
1 CAGAGGGCACACAAAGTGCTAAT
* *
205673 AACAGAGGGCACACACAGTGCTAAA
1 --CAGAGGGCACACAAAGTGCTAAT
* *
205698 CAGAGGGCACGA-AACGTGCTAAA
1 CAGAGGGCAC-ACAAAGTGCTAAT
205721 CAGAGGGC
1 CAGAGGGC
205729 GCCCTAGTGT
Statistics
Matches: 67, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
23 47 0.70
24 1 0.01
25 19 0.28
ACGTcount: A:0.39, C:0.22, G:0.29, T:0.10
Consensus pattern (23 bp):
CAGAGGGCACACAAAGTGCTAAT
Found at i:205684 original size:25 final size:24
Alignment explanation
Indices: 205599--205728 Score: 103
Period size: 23 Copynumber: 5.5 Consensus size: 24
205589 CCGAAGTACT
* * **
205599 TAACAGAGGACACATAAGTGCTGGG
1 TAACAGAGGGCACACAAGTGCT-AA
*
205624 TAACAGAGGGCACACAAAATGCTAA
1 TAACAGAGGGCACAC-AAGTGCTAA
*
205649 T--GAGAGGGCACACGAAGTGCTAA
1 TAACAGAGGGCACAC-AAGTGCTAA
205672 TAACAGAGGGCACACACAGTGCT-A
1 TAACAGAGGGCACACA-AGTGCTAA
205696 -AACAGAGGGCACGA-AACGTGCT-A
1 TAACAGAGGGCAC-ACAA-GTGCTAA
205719 -AACAGAGGGC
1 TAACAGAGGGC
205729 GCCCTAGTGT
Statistics
Matches: 90, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
22 1 0.01
23 49 0.54
24 3 0.03
25 31 0.34
26 6 0.07
ACGTcount: A:0.39, C:0.20, G:0.29, T:0.12
Consensus pattern (24 bp):
TAACAGAGGGCACACAAGTGCTAA
Found at i:205717 original size:48 final size:46
Alignment explanation
Indices: 205600--205728 Score: 127
Period size: 48 Copynumber: 2.7 Consensus size: 46
205590 CGAAGTACTT
* * *
205600 AACAGAGGACACATAAGTGCTGGGTAACAGAGGGCACACAAAATGCTA
1 AACAGAGGGCACACAAGTGCT--ATAACAGAGGGCACACAAAATGCTA
** * *
205648 ATGAGAGGGCACACGAAGTGCTAATAACAGAGGGCACACACAGTGCTA
1 AACAGAGGGCACAC-AAGTGCT-ATAACAGAGGGCACACAAAATGCTA
205696 AACAGAGGGCACGA-AACGTGCTA-AACAGAGGGC
1 AACAGAGGGCAC-ACAA-GTGCTATAACAGAGGGC
205729 GCCCTAGTGT
Statistics
Matches: 68, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
46 10 0.15
47 3 0.04
48 47 0.69
49 8 0.12
ACGTcount: A:0.40, C:0.20, G:0.29, T:0.11
Consensus pattern (46 bp):
AACAGAGGGCACACAAGTGCTATAACAGAGGGCACACAAAATGCTA
Found at i:209119 original size:31 final size:30
Alignment explanation
Indices: 209081--209179 Score: 144
Period size: 30 Copynumber: 3.3 Consensus size: 30
209071 ACCTAATTTT
* *
209081 TTTTTTTTTTAATTTAATTTGATATTTAAG
1 TTTTTTTTTTAATTCAATTTGATACTTAAG
*
209111 CTTTTTTTTTAATTCAATTTGATACTTAAG
1 TTTTTTTTTTAATTCAATTTGATACTTAAG
* *
209141 TTTTTTTTTTTAATTCAATTTGGTACCTAAG
1 -TTTTTTTTTTAATTCAATTTGATACTTAAG
209172 TTTTTTTT
1 TTTTTTTT
209180 CCTAATTTGG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
30 35 0.56
31 27 0.44
ACGTcount: A:0.23, C:0.06, G:0.07, T:0.64
Consensus pattern (30 bp):
TTTTTTTTTTAATTCAATTTGATACTTAAG
Found at i:209175 original size:26 final size:26
Alignment explanation
Indices: 209146--209234 Score: 92
Period size: 26 Copynumber: 3.3 Consensus size: 26
209136 TTAAGTTTTT
*
209146 TTTTTTAATTCAATTTGGTACCTAAG
1 TTTTTTAATTCAATTTGGTACCTAAA
*
209172 TTTTTT--TTCCTAATTTGGTATCTAAA
1 TTTTTTAATT-C-AATTTGGTACCTAAA
209198 TTTTTTTAAAATTCAATTTGGTACCTAAA
1 -TTTTTT--AATTCAATTTGGTACCTAAA
*
209227 TTTATTAA
1 TTTTTTAA
209235 ATATTATAAA
Statistics
Matches: 52, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
24 2 0.04
25 1 0.02
26 21 0.40
27 6 0.12
28 5 0.10
29 14 0.27
30 1 0.02
31 2 0.04
ACGTcount: A:0.29, C:0.10, G:0.08, T:0.53
Consensus pattern (26 bp):
TTTTTTAATTCAATTTGGTACCTAAA
Found at i:209186 original size:31 final size:31
Alignment explanation
Indices: 209080--209179 Score: 148
Period size: 31 Copynumber: 3.3 Consensus size: 31
209070 TACCTAATTT
* *
209080 TTTTTTTTTTTAATTTAATTTGATATTTAAG
1 TTTTTTTTTTTAATTCAATTTGATACTTAAG
*
209111 -CTTTTTTTTTAATTCAATTTGATACTTAAG
1 TTTTTTTTTTTAATTCAATTTGATACTTAAG
* *
209141 TTTTTTTTTTTAATTCAATTTGGTACCTAAG
1 TTTTTTTTTTTAATTCAATTTGATACTTAAG
209172 TTTTTTTT
1 TTTTTTTT
209180 CCTAATTTGG
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
30 27 0.44
31 35 0.56
ACGTcount: A:0.23, C:0.06, G:0.07, T:0.64
Consensus pattern (31 bp):
TTTTTTTTTTTAATTCAATTTGATACTTAAG
Found at i:209463 original size:31 final size:30
Alignment explanation
Indices: 209426--209560 Score: 102
Period size: 31 Copynumber: 4.6 Consensus size: 30
209416 GGTCCCCAAA
*
209426 AAGTTTAAGTACCAACTTA-AAAAGAAGTATC
1 AAGTTTAAGTACCAAATTAGAAAA-AA-TATC
* * *
209457 AAGTTTAGGTATCAAATTAGGAAAAAATGTC
1 AAGTTTAAGTACCAAATTA-GAAAAAATATC
* * *
209488 AAGTTTGAGTACCAAATTGGACAAAA-A--
1 AAGTTTAAGTACCAAATTAGAAAAAATATC
* *
209515 AA--TTAAGAACCAAATTAAGAAAAAATGTC
1 AAGTTTAAGTACCAAATT-AGAAAAAATATC
*
209544 AAATTTAAGTACCAAAT
1 AAGTTTAAGTACCAAAT
209561 ATTATATTAA
Statistics
Matches: 80, Mismatches: 16, Indels: 16
0.71 0.14 0.14
Matches are distributed among these distances:
25 12 0.15
26 6 0.08
27 2 0.03
29 2 0.03
30 6 0.08
31 46 0.57
32 2 0.03
33 4 0.05
ACGTcount: A:0.50, C:0.10, G:0.14, T:0.25
Consensus pattern (30 bp):
AAGTTTAAGTACCAAATTAGAAAAAATATC
Found at i:213634 original size:142 final size:141
Alignment explanation
Indices: 213314--214176 Score: 994
Period size: 142 Copynumber: 6.0 Consensus size: 141
213304 CAAAAGTCTC
* * *
213314 GAAGAACGTAAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGTCTCATG
1 GAAGAACG-GAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCGGACTCATG
* * * * * *
213379 AATTCAAATTTCAACGAAAATTGGAAGAACTTTG-ATGAAAAATGGGGTAAAGAACTCAAATACA
65 AATTCAAATTTCAACGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACTCAATTACA
213443 CACAGATCAAAA
130 CACAGATCAAAA
* *
213455 GAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAATCGGACTCATG
1 GAAGAACGGAA-TTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCGGACTCATG
* *
213520 AATTCAAATTTCCACGCAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACTCAATTACA
65 AATTCAAATTTCAACGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACTCAATTACA
213585 CACAGATCAAAA
130 CACAGATCAAAA
* * * *
213597 GAAGAACGCAATGTCGAATTCAAATCTAAAATTACAAAAGCGTTCGCATTGGAATCGGACTCATG
1 GAAGAACGGAAT-TTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCGGACTCATG
* * * * * * *
213662 AATTAAAATTTCAACGTAAATTTGAAGAATTTTG-ATGAAAACTGAGGTAAAGCACTCGATTACA
65 AATTCAAATTTCAACGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACTCAATTACA
213726 CACAGATC--AA
130 CACAGATCAAAA
* **
213736 -AAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCAAACTCATG
1 GAAGAACGGAA-TTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCGGACTCATG
* * *
213800 AATTC-AATTTCGACTTAATTCTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACTCAATTTAC
65 AATTCAAATTTCAACGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACTCAA-TTAC
213864 ACACAGATCAAAA
129 ACACAGATCAAAA
* * * *
213877 CAAGAGCGTGACTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCAGA-TACAT
1 GAAGAACG-GAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCGGACT-CAT
* *
213941 GAATTCAAATTTCGACGTGATTTTGAAGAACTTGGAATGAAAATGGAATGAAAAATGAGCTAAAG
64 GAATTCAAATTTCAACGTAATTTTGAAGAACTTGGAATG-AAA---AATG----A-G-G-TAAAG
214006 AACTCAAATT--ACACAGATCAAAA
118 AACTC-AATTACACACAGATCAAAA
* * * * * * * *
214029 CAATAACGTGACTTTGAATTCAAATCCAAAACTACAAATGCATTCGCATTGGAATCGAACTCATG
1 GAAGAACG-GAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCGGACTCATG
* * * *
214094 TATTCAAATTTCCACGTGATTTTGAAGAACTAT--AATGAAAGAA-GTGGTAAAGAACTCAATTA
65 AATTCAAATTTCAACGTAATTTTGAAGAACT-TGGAATGAAA-AATGAGGTAAAGAACTCAATTA
214156 CACACAGATCAGAAA
128 CACACAGATCA-AAA
*
214171 GGAGAA
1 GAAGAA
214177 AACAAACAGT
Statistics
Matches: 631, Mismatches: 62, Indels: 57
0.84 0.08 0.08
Matches are distributed among these distances:
137 22 0.03
138 82 0.13
139 20 0.03
140 12 0.02
141 137 0.22
142 194 0.31
143 30 0.05
144 3 0.00
147 5 0.01
148 3 0.00
150 3 0.00
151 5 0.01
152 98 0.16
153 3 0.00
154 12 0.02
155 2 0.00
ACGTcount: A:0.44, C:0.15, G:0.16, T:0.25
Consensus pattern (141 bp):
GAAGAACGGAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCGGACTCATGA
ATTCAAATTTCAACGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACTCAATTACAC
ACAGATCAAAA
Found at i:213906 original size:280 final size:281
Alignment explanation
Indices: 213315--214166 Score: 1074
Period size: 280 Copynumber: 3.0 Consensus size: 281
213305 AAAAGTCTCG
* *
213315 AAGAACGTAAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGTCTCATGA
1 AAGAACG-CAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATGA
* * * * *
213380 ATTCAAATTTCAACGAAAATTGGAAGAACTTTGATGAAAAATGGGGTAAAGAACTCAAATACACA
65 ATTCAAATTTCAACGTAAATTTGAAGAATTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
* *
213445 CAGATCAAAAGAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCACATTGAAAT
130 CAGATC-AAACAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAAT
* *
213510 CGGACTCATGAATTCAAATTTCCACGCAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAA
194 CGAACTCATGAATTCAAATTTCCACGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAA
*
213575 CTCAATTACACACAGATCAAAAG
259 CTCAATTACACACAGATCAAAAC
* *
213598 AAGAACGCAATGTCGAATTCAAATCTAAAATTACAAAAGCGTTCGCATTGGAATCGGACTCATGA
1 AAGAACGCAAT-TTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATGA
* * * *
213663 ATTAAAATTTCAACGTAAATTTGAAGAATTTTGATGAAAACTGAGGTAAAGCACTCGATTACACA
65 ATTCAAATTTCAACGTAAATTTGAAGAATTTTGATGAAAAATGAGGTAAAGAACTCAATTACACA
213728 CAGATC-AA-AAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATC
130 CAGATCAAACAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATC
* * * *
213791 AAACTCATGAATTC-AATTTCGACTTAATTCTGAAGAACTTGGAATGAAAAATGAGGTAAAGAAC
195 GAACTCATGAATTCAAATTTCCACGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAAC
213855 TCAATTTACACACAGATCAAAAC
260 TCAA-TTACACACAGATCAAAAC
* * * * *
213878 AAGAGCGTGACTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCAGA-TACATG
1 AAGAACG-CAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACT-CATG
* * * *
213942 AATTCAAATTTCGACGTGATTTTGAAGAACTTGGAATGAAAATGGAATGAAAAATGAGCTAAAGA
64 AATTCAAATTTCAACGTAAATTTGAAGAA-TT----T-----T-G-ATGAAAAATGAGGTAAAGA
* * * * * *
214007 ACTCAAATT--ACACAGATCAAAACAATAACGTGACTTTGAATTCAAATCCAAAACTACAAATGC
117 ACTC-AATTACACACAGATC-AAACAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGC
* * *
214070 ATTCGCATTGGAATCGAACTCATGTATTCAAATTTCCACGTGATTTTGAAGAACTAT--AATGAA
180 ATTCGCATTGAAATCGAACTCATGAATTCAAATTTCCACGTAATTTTGAAGAACT-TGGAATGAA
*
214133 AGAA-GTGGTAAAGAACTCAATTACACACAGATCA
244 A-AATGAGGTAAAGAACTCAATTACACACAGATCA
214167 GAAAGGAGAA
Statistics
Matches: 496, Mismatches: 50, Indels: 36
0.85 0.09 0.06
Matches are distributed among these distances:
279 51 0.10
280 160 0.32
281 6 0.01
282 3 0.01
283 119 0.24
285 1 0.00
290 1 0.00
291 10 0.02
292 20 0.04
293 19 0.04
294 82 0.17
295 23 0.05
296 1 0.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (281 bp):
AAGAACGCAATTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGGAATCGGACTCATGAA
TTCAAATTTCAACGTAAATTTGAAGAATTTTGATGAAAAATGAGGTAAAGAACTCAATTACACAC
AGATCAAACAAGAACGTAATTTTGAATTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCG
AACTCATGAATTCAAATTTCCACGTAATTTTGAAGAACTTGGAATGAAAAATGAGGTAAAGAACT
CAATTACACACAGATCAAAAC
Found at i:214111 original size:152 final size:153
Alignment explanation
Indices: 213830--214124 Score: 452
Period size: 152 Copynumber: 1.9 Consensus size: 153
213820 CTGAAGAACT
* * *
213830 TGGAATGAAAAATGAGGTAAAGAACTCAATTTACACACAGATCAAAACAAGAGCGTGACTTTGAA
1 TGGAATGAAAAATGAGCTAAAGAACTCAAATTA-ACACAGATCAAAACAAGAACGTGACTTTGAA
* * *
213895 TTCAAATCTAAAATTACAAAAGCATTCGCATTGAAATCAGATACATGAATTCAAATTTCGACGTG
65 TTCAAATCCAAAACTACAAAAGCATTCGCATTGAAATCAGATACATGAATTCAAATTTCCACGTG
213960 ATTTTGAAGAACTTGGAATGAAAA
130 ATTTTGAAGAACTTGGAATGAAAA
*
213984 TGGAATGAAAAATGAGCTAAAGAACTCAAATT-ACACAGATCAAAACAATAACGTGACTTTGAAT
1 TGGAATGAAAAATGAGCTAAAGAACTCAAATTAACACAGATCAAAACAAGAACGTGACTTTGAAT
* * *
214048 TCAAATCCAAAACTACAAATGCATTCGCATTGGAATC-GA-ACTCATGTATTCAAATTTCCACGT
66 TCAAATCCAAAACTACAAAAGCATTCGCATTGAAATCAGATA--CATGAATTCAAATTTCCACGT
214111 GATTTTGAAGAACT
129 GATTTTGAAGAACT
214125 ATAATGAAAG
Statistics
Matches: 129, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
150 1 0.01
151 2 0.02
152 96 0.74
154 30 0.23
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.26
Consensus pattern (153 bp):
TGGAATGAAAAATGAGCTAAAGAACTCAAATTAACACAGATCAAAACAAGAACGTGACTTTGAAT
TCAAATCCAAAACTACAAAAGCATTCGCATTGAAATCAGATACATGAATTCAAATTTCCACGTGA
TTTTGAAGAACTTGGAATGAAAA
Found at i:215235 original size:31 final size:31
Alignment explanation
Indices: 215197--215255 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
215187 TTTATGGTTC
215197 AATTTGGTA-CTCAAACTTGACACATTTTCCT
1 AATTTGGTACCT-AAACTTGACACATTTTCCT
*
215228 AATTTGGTACCTAAACTTGACACTTTTT
1 AATTTGGTACCTAAACTTGACACATTTT
215256 GTTTAAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 24 0.92
32 2 0.08
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (31 bp):
AATTTGGTACCTAAACTTGACACATTTTCCT
Found at i:215276 original size:33 final size:31
Alignment explanation
Indices: 215200--215278 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 31
215190 ATGGTTCAAT
* *
215200 TTGGTACTCAAACTTGACACATTTTCCTAAT
1 TTGGTACTTAAACTTGACACATTTTCCTAAG
* * **
215231 TTGGTACCTAAACTTGACACTTTTTGTTTAAAG
1 TTGGTACTTAAACTTGACACATTTT-CCT-AAG
215264 TTGGTACTTAAACTT
1 TTGGTACTTAAACTT
215279 TTTAGGGTCC
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 22 0.56
32 1 0.03
33 16 0.41
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.42
Consensus pattern (31 bp):
TTGGTACTTAAACTTGACACATTTTCCTAAG
Found at i:215624 original size:61 final size:59
Alignment explanation
Indices: 215506--215665 Score: 187
Period size: 61 Copynumber: 2.6 Consensus size: 59
215496 AATCTAAAAC
* * * * * *
215506 AAAGCTTAGGTGCCAAATTAGGGAAAAAAAAATGCCAAGCTCATGTACCAAATTGGGTCCAAA
1 AAAGTTTAGGTACCAAATTA--G-AAAAAAAATGTCAAGTTAAAGTACCAAATTGGGT-CAAA
* *
215569 AAATTTATAGGTACCAAATTAGAAAAAAAATGTCAAGTTAAAGTATCAAATTGGGTCAAA
1 AAAGTT-TAGGTACCAAATTAGAAAAAAAATGTCAAGTTAAAGTACCAAATTGGGTCAAA
*
215629 AAAGTTTAGGTACCAAATTAG-GAAAAAATGTCAAGTT
1 AAAGTTTAGGTACCAAATTAGAAAAAAAATGTCAAGTT
215666 CAGATACAAA
Statistics
Matches: 86, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
58 15 0.17
59 15 0.17
60 9 0.10
61 29 0.34
62 1 0.01
63 4 0.05
64 13 0.15
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (59 bp):
AAAGTTTAGGTACCAAATTAGAAAAAAAATGTCAAGTTAAAGTACCAAATTGGGTCAAA
Found at i:222436 original size:16 final size:16
Alignment explanation
Indices: 222417--222456 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
222407 ATGAAAAACT
222417 TAAAAAATTAATATTA
1 TAAAAAATTAATATTA
* *
222433 T-AAAAATAAATATTG
1 TAAAAAATTAATATTA
222448 TAAAAAATT
1 TAAAAAATT
222457 TTGTTTTGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
15 13 0.65
16 7 0.35
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TAAAAAATTAATATTA
Found at i:223143 original size:22 final size:24
Alignment explanation
Indices: 223118--223166 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 24
223108 AGCTTCCATT
**
223118 TATTGAATTTATTATA-ATAT-TA
1 TATTGAATAAATTATATATATATA
*
223140 TATTTAATAAATTATATATATATA
1 TATTGAATAAATTATATATATATA
223164 TAT
1 TAT
223167 ATATAACCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.59
23 4 0.18
24 5 0.23
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TATTGAATAAATTATATATATATA
Found at i:223980 original size:39 final size:40
Alignment explanation
Indices: 223891--223983 Score: 109
Period size: 40 Copynumber: 2.3 Consensus size: 40
223881 CATTTTGTTG
* * *
223891 TTATCACATATTAGTAAATAAAATACTAATAAATTATTTTTA
1 TTATCA-AT-TTAATAAATAAAATACTAATAAAATATATTTA
*
223933 TTATCAATTTAATAATATAATATA-TAATAAAATATATTT-
1 TTATCAATTTAATAA-ATAAAATACTAATAAAATATATTTA
223972 TTATCAATTTAA
1 TTATCAATTTAA
223984 AATTTATTTC
Statistics
Matches: 46, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
39 12 0.26
40 19 0.41
41 9 0.20
42 6 0.13
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.45
Consensus pattern (40 bp):
TTATCAATTTAATAAATAAAATACTAATAAAATATATTTA
Found at i:225568 original size:22 final size:22
Alignment explanation
Indices: 225527--225569 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
225517 GCTCCTCATT
*
225527 TTTAGGTAGATCCTTCTAGTGA
1 TTTAGGTAGATCATTCTAGTGA
* *
225549 TTTAGGTATATCATTTTAGTG
1 TTTAGGTAGATCATTCTAGTG
225570 CTTGTACAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.23, C:0.09, G:0.21, T:0.47
Consensus pattern (22 bp):
TTTAGGTAGATCATTCTAGTGA
Done.