Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017680.1 Corchorus olitorius cultivar O-4 contig17713, 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: 245264
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:1730 original size:16 final size:17
Alignment explanation
Indices: 1697--1730 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1687 GGTAACTCTC
*
1697 TATAAGATTAGGTAAAA
1 TATAAGATTAGCTAAAA
1714 TATAAGATTA-CTAAAA
1 TATAAGATTAGCTAAAA
1730 T
1 T
1731 TGAATTAGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.53, C:0.03, G:0.12, T:0.32
Consensus pattern (17 bp):
TATAAGATTAGCTAAAA
Found at i:5341 original size:11 final size:13
Alignment explanation
Indices: 5314--5357 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
5304 ATTTTATTAC
5314 TGTTTTATTAAAT
1 TGTTTTATTAAAT
5327 TGTTTTA-TAAA-
1 TGTTTTATTAAAT
5338 TGTTTTAATTAAAT
1 TGTTTT-ATTAAAT
5352 TGTTTT
1 TGTTTT
5358 GGGTGCATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 6 0.21
12 5 0.18
13 11 0.39
14 6 0.21
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (13 bp):
TGTTTTATTAAAT
Found at i:5341 original size:24 final size:25
Alignment explanation
Indices: 5305--5357 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 25
5295 TGAGGAACTA
* *
5305 TTTTATTACTGTTTT-ATTAAATTG
1 TTTTATAAATGTTTTAATTAAATTG
5329 TTTTATAAATGTTTTAATTAAATTG
1 TTTTATAAATGTTTTAATTAAATTG
5354 TTTT
1 TTTT
5358 GGGTGCATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 13 0.50
25 13 0.50
ACGTcount: A:0.28, C:0.02, G:0.08, T:0.62
Consensus pattern (25 bp):
TTTTATAAATGTTTTAATTAAATTG
Found at i:14076 original size:197 final size:199
Alignment explanation
Indices: 13731--14186 Score: 738
Period size: 197 Copynumber: 2.3 Consensus size: 199
13721 CAAACATTTG
* *
13731 TTGTATAATAATCCTATAAGAAAAATTATATAATACACCATCAGTGGAGTTTAGTAGACTGCACG
1 TTGTATAATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGTAGACTGCACG
* *
13796 TGCGGGGTTTAAGGGTTGGCATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTA
66 TGCGGGATTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTA
* * *
13861 ATCATGAAATGTGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCAAAAATTTACACTGACAG
131 ATCATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCAAAAATTTACACTAACAC
13926 TGTA
196 TGTA
13930 TTGTATAAATAATCCTATAA-AAAAATTATACAATAC-CCGTCAGTGGAGTTTAGTAGACTGCAC
1 TTGTAT-AATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGTAGACTGCAC
*
13993 GTGCGGGATTTATGGGTTGACATGTGT-CCCTTAGGGAATATGTATTAATATTAAATATTTAATT
65 GTGCGGGATTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATT
* * * *
14057 AATTATTAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCCAAATTTTACACTAACA
130 AATCATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCAAAAATTTACACTAACA
14122 CTGTA
195 CTGTA
* * * *
14127 TTGTATAATAATCCTATAAGAAAAATTATGCAATACATCGTCAATGGAGTTTAGCAGACT
1 TTGTATAATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGTAGACT
14187 AATTTTAAGT
Statistics
Matches: 238, Mismatches: 16, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
196 13 0.05
197 121 0.51
198 70 0.29
199 21 0.09
200 13 0.05
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (199 bp):
TTGTATAATAATCCTATAAGAAAAATTATACAATACACCGTCAGTGGAGTTTAGTAGACTGCACG
TGCGGGATTTAAGGGTTGACATGTGTCCCCTTAGGGAATATGTATTAATATTAAATATTTAATTA
ATCATGAAATGAGGTATGTGTCAACTTCTTAACCCGCTTATGGAGTCAAAAATTTACACTAACAC
TGTA
Found at i:17993 original size:26 final size:26
Alignment explanation
Indices: 17930--17993 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 26
17920 TTTGGTATGA
* *
17930 AAGGTTACTAAAATTTGTAAGAATGC
1 AAGGTTACTAAAATTTCTAAGAACGC
* * *
17956 AAGATTAATAAAATTTCTAAGAACGT
1 AAGGTTACTAAAATTTCTAAGAACGC
*
17982 GAGGTTACTAAA
1 AAGGTTACTAAA
17994 TTTATGTAGA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.30
Consensus pattern (26 bp):
AAGGTTACTAAAATTTCTAAGAACGC
Found at i:18779 original size:134 final size:133
Alignment explanation
Indices: 18636--19261 Score: 729
Period size: 134 Copynumber: 4.7 Consensus size: 133
18626 CCTTTACGTG
* * * *
18636 ACGACATTTATTTGGTTGCGAATAATTTTTAAAAACGACAAAATATTGTTGTCAAAATGTTTACG
1 ACGACATTTAGTTGGTTGCAAATAATTTTT-AAAACGACAAAATGTTGTTGTCAAAATGTTTACA
18701 CAACAAAATTATTTTGGTTGTAAATACTTTTCGACAACAATATTTTTTGGTTGTGTAAAGTTTTT
65 CAACAAAATTATTTTGGTTGTAAATACTTTTCGACAACAATATTTTTTGGTTGTGTAAAGTTTTT
18766 TATA
130 TATA
* * *
18770 ACGACATTTACTTGGTTGCGAATAATTTTTTAAAACGACAAAATGTTGTTGTTAAAATGTTTACA
1 ACGACATTTAGTTGGTTGCAAATAA-TTTTTAAAACGACAAAATGTTGTTGTCAAAATGTTTACA
* **
18835 CAACAAAACTATTTTGGTTGTAAATACTTTTCGACAACAATATTTCCTGGTTGTGTAAAGTTTTT
65 CAACAAAATTATTTTGGTTGTAAATACTTTTCGACAACAATATTTTTTGGTTGTGTAAAGTTTTT
18900 TATA
130 TATA
* * *
18904 ATGATATTTAGTTGGTTGCAAATAAATTTTTAAAATGACAAAATGTTGTTGTCAAAATGTTTACA
1 ACGACATTTAGTTGGTTGCAAAT-AATTTTTAAAACGACAAAATGTTGTTGTCAAAATGTTTACA
* * * ** * *
18969 CAACAAAATTATTTTGGTTGTAAATACTTTTTGACAACAACATTTTTCGGTTACGTAATA-ATAT
65 CAACAAAATTATTTTGGTTGTAAATACTTTTCGACAACAATATTTTTTGGTTGTGTAA-AGTTTT
*
19033 TTACA
129 TTATA
* * * * *
19038 ACGATATCTAGTTGGTTACAAATAATTTTTTAAAACGGCAAAATGTTGTTGTCAAAATATTTACA
1 ACGACATTTAGTTGGTTGCAAATAA-TTTTTAAAACGACAAAATGTTGTTGTCAAAATGTTTACA
* * * * * * *
19103 CAACAATATCATTTTAGTTGTAAATACTTTTATG-TAACGATATTTTAATT-ATTGTGTAAAGTT
65 CAACAAAATTATTTTGGTTGTAAATACTTTT-CGACAACAATATTTT--TTGGTTGTGTAAAGTT
* *
19166 TTATAAA
127 TTTTATA
** * * ** * * * *
19173 ACGACATCAAATTGGTTACAAATTACCTTTTAAAATGACAAAATATTGTTGCCAAAATGCTTACA
1 ACGACATTTAGTTGGTTGCAAA-TAATTTTTAAAACGACAAAATGTTGTTGTCAAAATGTTTACA
*
19238 CAACAACATTA-TTTGGTTGTAAAT
65 CAACAAAATTATTTTGGTTGTAAAT
19262 GATTTTACCT
Statistics
Matches: 425, Mismatches: 58, Indels: 18
0.85 0.12 0.04
Matches are distributed among these distances:
133 2 0.00
134 339 0.80
135 81 0.19
136 3 0.01
ACGTcount: A:0.36, C:0.11, G:0.13, T:0.40
Consensus pattern (133 bp):
ACGACATTTAGTTGGTTGCAAATAATTTTTAAAACGACAAAATGTTGTTGTCAAAATGTTTACAC
AACAAAATTATTTTGGTTGTAAATACTTTTCGACAACAATATTTTTTGGTTGTGTAAAGTTTTTT
ATA
Found at i:18986 original size:67 final size:65
Alignment explanation
Indices: 18646--19133 Score: 179
Period size: 67 Copynumber: 7.3 Consensus size: 65
18636 ACGACATTTA
* * *
18646 TTTGGTTGCGAATAATTTTTAAAAACGACAAAATATTGTTGTCAAAATGTTTACGCAACAAAATT
1 TTTGGTTGCAAATAATTTTT-AAAA-GACAAAATGTTGTTGTCAAAATGTTTACACAACAAAATT
18711 AT
64 AT
* * ** * * * ** ** * * *
18713 TTTGGTTGTAAATACTTTTCGACA-ACAATATTTTTTGGTTGTGTAAA-GTTTTTTATAACGACA
1 TTTGGTTGCAAATAATTTTTAAAAGACAA-A-ATGTT-GTTGTCAAAATG-TTTACACAACAAAA
18776 TT-T
62 TTAT
* * * *
18779 ACTTGGTTGCGAATAATTTTTTAAAACGACAAAATGTTGTTGTTAAAATGTTTACACAACAAAAC
1 -TTTGGTTGCAAATAA-TTTTTAAAA-GACAAAATGTTGTTGTCAAAATGTTTACACAACAAAAT
18844 TAT
63 TAT
* * ** * * * ** ** * ** *
18847 TTTGGTTGTAAATACTTTTCGACA-ACAATATTTCCTGGTTGTGTAAA-GTTTTTTATAATGATA
1 TTTGGTTGCAAATAATTTTTAAAAGACAAAATGT--T-GTTGTCAAAATG-TTTACACAACAAAA
18910 TT-T
62 TTAT
*
18913 AGTTGGTTGCAAATAAATTTTTAAAATGACAAAATGTTGTTGTCAAAATGTTTACACAACAAAAT
1 -TTTGGTTGCAAAT-AATTTTTAAAA-GACAAAATGTTGTTGTCAAAATGTTTACACAACAAAAT
18978 TAT
63 TAT
* * * * * * * *
18981 TTTGGTTGTAAATACTTTTTGACA-ACAACATTTTTCGGTTACGT-AATAATATTT--ACAACGA
1 TTTGGTTGCAAATAATTTTTAAAAGACAA-AATGTT--GTT--GTCAA-AATGTTTACACAACAA
*
19042 TATCTA-
60 AAT-TAT
* * * * * *
19048 GTTGGTTACAAATAATTTTTTAAAACGGCAAAATGTTGTTGTCAAAATATTTACACAACAATATC
1 TTTGGTTGCAAATAA-TTTTTAAAA-GACAAAATGTTGTTGTCAAAATGTTTACACAACAAAATT
19113 AT
64 AT
* * *
19115 TTTAGTTGTAAATACTTTT
1 TTTGGTTGCAAATAATTTT
19134 ATGTAACGAT
Statistics
Matches: 294, Mismatches: 93, Indels: 69
0.64 0.20 0.15
Matches are distributed among these distances:
64 15 0.05
65 14 0.05
66 31 0.11
67 175 0.60
68 32 0.11
69 13 0.04
70 14 0.05
ACGTcount: A:0.35, C:0.10, G:0.13, T:0.41
Consensus pattern (65 bp):
TTTGGTTGCAAATAATTTTTAAAAGACAAAATGTTGTTGTCAAAATGTTTACACAACAAAATTAT
Found at i:25212 original size:20 final size:20
Alignment explanation
Indices: 25183--25222 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
25173 TTCAATTTGT
25183 GAATAAAATCTCATAAATAA
1 GAATAAAATCTCATAAATAA
*
25203 GAATACAATCTCATAAATAA
1 GAATAAAATCTCATAAATAA
25223 ATTAGCGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.57, C:0.12, G:0.05, T:0.25
Consensus pattern (20 bp):
GAATAAAATCTCATAAATAA
Found at i:30321 original size:130 final size:130
Alignment explanation
Indices: 30096--30602 Score: 680
Period size: 130 Copynumber: 3.9 Consensus size: 130
30086 GCGCAACGAC
* * * *** *
30096 TTATAAAGTTGTTACGAATAGTTTATGATTTCACAGC-AATTTAAGAAATTGTTGTTACGAATAC
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTT--GTTTTTGTTGTTACGAAAAC
* * * *
30160 TGTAAACATT-AGCAATAACTAAAAAAGTGTTGTGTAAAATATCATCAAAATCACTTAGGTAACG
64 TGTAAGCATTGA-CAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACG
30224 TTT
128 TTT
* * **
30227 TTATAAAGTTGTTACGAATAGTTTATCATTTCGCAACGACTTTGTTTTTATTGTTACGAAATTTG
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTG
30292 TAAGCATTGACAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTTT
66 TAAGCATTGACAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTTT
* *
30357 TTATAAAGTTGTTACGAATAGTTTATGATATCGCAACGACTTTGTTTTTGTTGTTACGAAAATTG
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTG
* * * * *
30422 TAAGCATTGGA-AACGACTAAAAAAATGTTGTGTAAAATACCATTAAAATCACTTAGACAACGAT
66 TAAGCATT-GACAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTT
30486 T
130 T
* ** *
30487 TTATAAAATTGTTACGAATAAATTATGATTTCGCAACGACTTTGTTTTTGTTGTTACAAAAACTG
1 TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTG
* * *
30552 TAAGCATTGGCAACAATTAAAAAAGTCGTTG-GTAAAATATCATCAAAATCA
66 TAAGCATTGACAACAACTAAAAAAGT-GTTGTGTAAAATACCATCAAAATCA
30603 TTAAAACAAC
Statistics
Matches: 335, Mismatches: 36, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
129 1 0.00
130 289 0.86
131 41 0.12
132 4 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (130 bp):
TTATAAAGTTGTTACGAATAGTTTATGATTTCGCAACGACTTTGTTTTTGTTGTTACGAAAACTG
TAAGCATTGACAACAACTAAAAAAGTGTTGTGTAAAATACCATCAAAATCACTTAGGCAACGTTT
Found at i:31714 original size:21 final size:21
Alignment explanation
Indices: 31688--31792 Score: 92
Period size: 21 Copynumber: 5.1 Consensus size: 21
31678 TATTTTTATG
31688 TATCAACAATATATATAATAA
1 TATCAACAATATATATAATAA
* *
31709 TATCAACAATACATACAATAA
1 TATCAACAATATATATAATAA
* * ** *
31730 TAT--AGAGT-TAT-TTTTATG
1 TATCAACAATATATATAATA-A
31748 TATCAACAATATATATAATAA
1 TATCAACAATATATATAATAA
* *
31769 TATCAACAATACATACAATAA
1 TATCAACAATATATATAATAA
31790 TAT
1 TAT
31793 TAAGATAGGG
Statistics
Matches: 63, Mismatches: 16, Indels: 10
0.71 0.18 0.11
Matches are distributed among these distances:
17 2 0.03
18 5 0.08
19 3 0.05
20 3 0.05
21 47 0.75
22 3 0.05
ACGTcount: A:0.51, C:0.11, G:0.03, T:0.34
Consensus pattern (21 bp):
TATCAACAATATATATAATAA
Found at i:31721 original size:60 final size:60
Alignment explanation
Indices: 31650--31792 Score: 286
Period size: 60 Copynumber: 2.4 Consensus size: 60
31640 TTATGTATCA
31650 ATCAACAATACATACAATAATATAGAGTTATTTTTATGTATCAACAATATATATAATAAT
1 ATCAACAATACATACAATAATATAGAGTTATTTTTATGTATCAACAATATATATAATAAT
31710 ATCAACAATACATACAATAATATAGAGTTATTTTTATGTATCAACAATATATATAATAAT
1 ATCAACAATACATACAATAATATAGAGTTATTTTTATGTATCAACAATATATATAATAAT
31770 ATCAACAATACATACAATAATAT
1 ATCAACAATACATACAATAATAT
31793 TAAGATAGGG
Statistics
Matches: 83, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
60 83 1.00
ACGTcount: A:0.50, C:0.11, G:0.04, T:0.35
Consensus pattern (60 bp):
ATCAACAATACATACAATAATATAGAGTTATTTTTATGTATCAACAATATATATAATAAT
Found at i:39340 original size:18 final size:18
Alignment explanation
Indices: 39317--39351 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
39307 ATCCACAAAC
39317 AGGAAGAGAGAGAGAGGG
1 AGGAAGAGAGAGAGAGGG
*
39335 AGGAAGGGAGAGAGAGG
1 AGGAAGAGAGAGAGAGG
39352 ATTTATCCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.57, T:0.00
Consensus pattern (18 bp):
AGGAAGAGAGAGAGAGGG
Found at i:40387 original size:12 final size:12
Alignment explanation
Indices: 40370--40396 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
40360 TTTGGTGGTG
40370 TTTATTTTATTT
1 TTTATTTTATTT
40382 TTTATTTTATTT
1 TTTATTTTATTT
40394 TTT
1 TTT
40397 TTCTGCATGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (12 bp):
TTTATTTTATTT
Found at i:41744 original size:2 final size:2
Alignment explanation
Indices: 41739--41763 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41729 AAAAAAAAAA
41739 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 A
41764 ATTTGAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:44747 original size:2 final size:2
Alignment explanation
Indices: 44740--44766 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
44730 TCAAATGGAA
44740 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 A
44767 AAAAAGATAC
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:50390 original size:88 final size:89
Alignment explanation
Indices: 50279--50454 Score: 257
Period size: 88 Copynumber: 2.0 Consensus size: 89
50269 TTAATTAAAT
* * * *
50279 TAGTAAAATGGTAAAAATAAAATAGGTATAAAAATATTAGATTTAA-TAAGAT-AAAAATAGAGT
1 TAGTAAAATGCTAAAAATAAAATAGCTATAAAAATATTAGACTTAATTAA-ATAAAAAATAGAAT
50342 TTTTAATTGAGTAAAACTATAAAAA
65 TTTTAATTGAGTAAAACTATAAAAA
* **
50367 TAGTAAACTGCTAAAAATAAAATAGCTATAAGGATATTAGACTTAATTAAATAAAAAATAGAATT
1 TAGTAAAATGCTAAAAATAAAATAGCTATAAAAATATTAGACTTAATTAAATAAAAAATAGAATT
*
50432 TTTAGTTGAGTAAAACTATAAAA
66 TTTAATTGAGTAAAACTATAAAA
50455 CTTTAAATAA
Statistics
Matches: 78, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
88 42 0.54
89 36 0.46
ACGTcount: A:0.54, C:0.03, G:0.12, T:0.31
Consensus pattern (89 bp):
TAGTAAAATGCTAAAAATAAAATAGCTATAAAAATATTAGACTTAATTAAATAAAAAATAGAATT
TTTAATTGAGTAAAACTATAAAAA
Found at i:51448 original size:34 final size:34
Alignment explanation
Indices: 51405--51472 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
51395 ACGGACTCAA
51405 ACTCACTAGATCTAATGGCTAGTTTAATTTTGTG
1 ACTCACTAGATCTAATGGCTAGTTTAATTTTGTG
51439 ACTCACTAGATCTAATGGCTAGTTTAATTTTGTG
1 ACTCACTAGATCTAATGGCTAGTTTAATTTTGTG
51473 TGAAATTAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.26, C:0.15, G:0.18, T:0.41
Consensus pattern (34 bp):
ACTCACTAGATCTAATGGCTAGTTTAATTTTGTG
Found at i:51962 original size:21 final size:19
Alignment explanation
Indices: 51937--51994 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
51927 GCTGCTCTAA
51937 TAATCTCATCTGTACAGTACC
1 TAATCTCATCTGTACAGT--C
* *
51958 TAATCTAATCTGTACAGTG
1 TAATCTCATCTGTACAGTC
51977 TAATCTCATCTGTACAGT
1 TAATCTCATCTGTACAGT
51995 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.36
Consensus pattern (19 bp):
TAATCTCATCTGTACAGTC
Found at i:54089 original size:49 final size:47
Alignment explanation
Indices: 54012--54152 Score: 160
Period size: 49 Copynumber: 2.9 Consensus size: 47
54002 CAAGCAATCC
* * *
54012 TTTACTTTTCACTGCACTTTTTCACAATTTTTACTACAAAATTGAACT
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTA-TACAAAATTGAACT
* *
54060 TTTAATTTT-ACTTGCATCTTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTCA-TTGCA-CTTTTTCTCAATTTTT-ATACAAAATTGAACT
* *
54109 TTTAATTTTCATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTAATTTTCATTGCACTTTTTCTCAATTTTTAT-ACAAAATTGA
54153 TTGGCACGCT
Statistics
Matches: 80, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
47 11 0.14
48 27 0.34
49 40 0.50
50 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.06, T:0.49
Consensus pattern (47 bp):
TTTAATTTTCATTGCACTTTTTCTCAATTTTTATACAAAATTGAACT
Found at i:54709 original size:18 final size:18
Alignment explanation
Indices: 54686--54773 Score: 140
Period size: 18 Copynumber: 4.9 Consensus size: 18
54676 CAACAACAAA
*
54686 TCGCACCGCACCAAATGG
1 TCGCACCGCACCAAGTGG
*
54704 TCGCACCACACCAAGTGG
1 TCGCACCGCACCAAGTGG
*
54722 TCGCACCGCACCCAGTGG
1 TCGCACCGCACCAAGTGG
*
54740 TCGCACCGCACCCAGTGG
1 TCGCACCGCACCAAGTGG
54758 TCGCACCGCACCAAGT
1 TCGCACCGCACCAAGT
54774 TGCCACACTT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.23, C:0.42, G:0.24, T:0.11
Consensus pattern (18 bp):
TCGCACCGCACCAAGTGG
Found at i:56025 original size:15 final size:15
Alignment explanation
Indices: 56002--56099 Score: 78
Period size: 15 Copynumber: 6.5 Consensus size: 15
55992 GGAAGAAGAT
56002 GATGGCACCAACATC
1 GATGGCACCAACATC
* *
56017 GACGGCACCGAAGAT-
1 GATGGCACC-AACATC
* *
56032 GATGGCA-CAAAAAC
1 GATGGCACCAACATC
56046 TGATGGCACCAACATC
1 -GATGGCACCAACATC
*
56062 GATGGCACCAA-AAC
1 GATGGCACCAACATC
*
56076 TGATGGCACCGAAGAT-
1 -GATGGCACC-AACATC
56092 GATGGCAC
1 GATGGCAC
56100 TGAAAGTGGT
Statistics
Matches: 67, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
13 3 0.04
14 3 0.04
15 49 0.73
16 11 0.16
17 1 0.01
ACGTcount: A:0.36, C:0.27, G:0.26, T:0.12
Consensus pattern (15 bp):
GATGGCACCAACATC
Found at i:56030 original size:30 final size:30
Alignment explanation
Indices: 55996--56099 Score: 140
Period size: 30 Copynumber: 3.5 Consensus size: 30
55986 TGTCATGGAA
* *
55996 GAAGATGATGGCACCAACA-TCGACGGCACC
1 GAAGATGATGGCACCAAAACT-GATGGCACC
*
56026 GAAGATGATGGCACAAAAACTGATGGCACC
1 GAAGATGATGGCACCAAAACTGATGGCACC
*
56056 -AACATCGATGGCACCAAAACTGATGGCACC
1 GAAGAT-GATGGCACCAAAACTGATGGCACC
56086 GAAGATGATGGCAC
1 GAAGATGATGGCAC
56100 TGAAAGTGGT
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
29 4 0.06
30 56 0.86
31 5 0.08
ACGTcount: A:0.37, C:0.25, G:0.26, T:0.12
Consensus pattern (30 bp):
GAAGATGATGGCACCAAAACTGATGGCACC
Found at i:56095 original size:45 final size:44
Alignment explanation
Indices: 55996--56099 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 44
55986 TGTCATGGAA
*
55996 GAAGATGATGGCACCAACATCGACGGCACCGAAGATGATGGCAC
1 GAAGATGATGGCACCAACATCGACGGCACCGAAAATGATGGCAC
* * *
56040 AAAAACTGATGGCACCAACATCGATGGCACC-AAAACTGATGGCACC
1 GAAGA-TGATGGCACCAACATCGACGGCACCGAAAA-TGATGGCA-C
56086 GAAGATGATGGCAC
1 GAAGATGATGGCAC
56100 TGAAAGTGGT
Statistics
Matches: 51, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
44 6 0.12
45 41 0.80
46 4 0.08
ACGTcount: A:0.37, C:0.25, G:0.26, T:0.12
Consensus pattern (44 bp):
GAAGATGATGGCACCAACATCGACGGCACCGAAAATGATGGCAC
Found at i:58765 original size:49 final size:47
Alignment explanation
Indices: 58690--58829 Score: 158
Period size: 49 Copynumber: 2.9 Consensus size: 47
58680 CAAGCAATCC
* * **
58690 TTTACTTTTACTGCACTTTTTCTCAATTTTTACTACAAAATTGAACT
1 TTTAATTTTACTGCAATTTTTCTCAATTTTTAAGACAAAATTGAACT
*
58737 TTTAATTTTACTTGCATATTTTTCTCAATTTTTAAGACAAAATTGATCT
1 TTTAATTTTAC-TGCA-ATTTTTCTCAATTTTTAAGACAAAATTGAACT
* * *
58786 TTTAATTTT-CATCGCACTTTTTATCAATTTTT-TGACAAAATTGA
1 TTTAATTTTAC-T-GCAATTTTTCTCAATTTTTAAGACAAAATTGA
58830 TTGGCACGCT
Statistics
Matches: 81, Mismatches: 9, Indels: 6
0.84 0.09 0.06
Matches are distributed among these distances:
47 21 0.26
48 20 0.25
49 40 0.49
ACGTcount: A:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (47 bp):
TTTAATTTTACTGCAATTTTTCTCAATTTTTAAGACAAAATTGAACT
Found at i:59529 original size:21 final size:21
Alignment explanation
Indices: 59499--59538 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
59489 CTAAAAACAG
*
59499 GACAAGTCCTGCCCAGGACTT
1 GACAACTCCTGCCCAGGACTT
59520 GACAACTCCTGCCCAGGAC
1 GACAACTCCTGCCCAGGAC
59539 CTGGTCTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15
Consensus pattern (21 bp):
GACAACTCCTGCCCAGGACTT
Found at i:59596 original size:50 final size:50
Alignment explanation
Indices: 59521--59624 Score: 181
Period size: 50 Copynumber: 2.1 Consensus size: 50
59511 CCAGGACTTG
*
59521 ACAACTCCTGCCCAGGACCTGGTCTGTTGAAAGACGGAAGAAAAATCAGA
1 ACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAACGGAAGAAAAATCAGA
* *
59571 ACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAATTCAGA
1 ACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAACGGAAGAAAAATCAGA
59621 ACAA
1 ACAA
59625 GTCCAAGACT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.38, C:0.23, G:0.22, T:0.17
Consensus pattern (50 bp):
ACAACTCCTGCCCAGGACCTGGTCTGTTGAAAAACGGAAGAAAAATCAGA
Found at i:59637 original size:45 final size:46
Alignment explanation
Indices: 59530--59637 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 46
59520 GACAACTCCT
* * *
59530 GCCCAGGACCTGGTCTGTTGAAAGACGGAAGAAAAATCAGAACAACTCC
1 GCCCAAGACTTGGTCTGTTGAAAAACGGAAGAAAAATCAGAACAA---C
* *
59579 TGCCCAGGACTTGGTCTGTTGAAAAACGGAAGAAAATTCAGAACAA-
1 -GCCCAAGACTTGGTCTGTTGAAAAACGGAAGAAAAATCAGAACAAC
*
59625 GTCCAAGACTTGG
1 GCCCAAGACTTGG
59638 ACAACTCCTG
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
45 11 0.21
50 42 0.79
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (46 bp):
GCCCAAGACTTGGTCTGTTGAAAAACGGAAGAAAAATCAGAACAAC
Found at i:60258 original size:26 final size:23
Alignment explanation
Indices: 60212--60258 Score: 67
Period size: 26 Copynumber: 1.9 Consensus size: 23
60202 TCCTTCTACT
60212 CATCTATCATCAAGTTTTTCATC
1 CATCTATCATCAAGTTTTTCATC
60235 CATCTCATCCATCAAAGTTTTTCA
1 CATCT-AT-CATC-AAGTTTTTCA
60259 AATTTTCTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 2 0.10
25 4 0.19
26 10 0.48
ACGTcount: A:0.28, C:0.28, G:0.04, T:0.40
Consensus pattern (23 bp):
CATCTATCATCAAGTTTTTCATC
Found at i:69475 original size:50 final size:50
Alignment explanation
Indices: 69401--69528 Score: 186
Period size: 50 Copynumber: 2.6 Consensus size: 50
69391 ATTGAAGCCT
* *
69401 AAAAA-CAGGACAAGTCCTGCCCAGGACCTGGTCTGTTGAAATACGGAAG
1 AAAAATCAGAACAAGTCCTGCCCAGGACCTGGTCTGTTGAAAAACGGAAG
* *
69450 AAAAATCAGAACAACTCCTGCCCAGGACTTGGTCTGTTGAAAAACGGAAG
1 AAAAATCAGAACAAGTCCTGCCCAGGACCTGGTCTGTTGAAAAACGGAAG
* *
69500 AAAATTCAGAACAAGTCCTGTCCAAGGAC
1 AAAAATCAGAACAAGTCCTG-CCCAGGAC
69529 TTGGACAACT
Statistics
Matches: 70, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
49 5 0.07
50 58 0.83
51 7 0.10
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (50 bp):
AAAAATCAGAACAAGTCCTGCCCAGGACCTGGTCTGTTGAAAAACGGAAG
Found at i:69552 original size:22 final size:23
Alignment explanation
Indices: 69510--69553 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
69500 AAAATTCAGA
*
69510 ACAAGTCCTGTCCAAGGACTTGG
1 ACAACTCCTGTCCAAGGACTTGG
*
69533 ACAACTCCTG-CCCAGGACTTG
1 ACAACTCCTGTCCAAGGACTTG
69554 TTGCGGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.25, C:0.32, G:0.23, T:0.20
Consensus pattern (23 bp):
ACAACTCCTGTCCAAGGACTTGG
Found at i:73275 original size:26 final size:25
Alignment explanation
Indices: 73213--73271 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
73203 CTTTTTCTCA
73213 ATTTTTACTGCAAAATTGAACTTTT
1 ATTTTTACTGCAAAATTGAACTTTT
73238 ATTTTTACTGCAAAATTGAACTTTT
1 ATTTTTACTGCAAAATTGAACTTTT
73263 ATTTTTACT
1 ATTTTTACT
73272 TGCATCTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.51
Consensus pattern (25 bp):
ATTTTTACTGCAAAATTGAACTTTT
Found at i:73301 original size:49 final size:47
Alignment explanation
Indices: 73248--73352 Score: 140
Period size: 49 Copynumber: 2.2 Consensus size: 47
73238 ATTTTTACTG
* *
73248 CAAAATTGAACTTTT-ATTTTTACTTGCATCTTTTTCTCAATTTTTAAGA
1 CAAAATTGAACTTTTAATTTTCA-TTGCA-CTTTTTATCAATTTTT-AGA
* *
73297 CAAAATTGATCTTTTAATTTTCATTGCACTTTTTATCAATTTTTGGA
1 CAAAATTGAACTTTTAATTTTCATTGCACTTTTTATCAATTTTTAGA
73344 CAAAATTGA
1 CAAAATTGA
73353 TTGGCACGCT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
47 11 0.22
48 15 0.29
49 19 0.37
50 6 0.12
ACGTcount: A:0.30, C:0.13, G:0.08, T:0.49
Consensus pattern (47 bp):
CAAAATTGAACTTTTAATTTTCATTGCACTTTTTATCAATTTTTAGA
Found at i:75584 original size:21 final size:21
Alignment explanation
Indices: 75558--75599 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
75548 TTTAAACCCT
75558 ATTGGAGAC-AAGTGGTACTAA
1 ATTGGA-ACTAAGTGGTACTAA
*
75579 ATTGGATCTAAGTGGTACTAA
1 ATTGGAACTAAGTGGTACTAA
75600 GGTTTTCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.36, C:0.10, G:0.26, T:0.29
Consensus pattern (21 bp):
ATTGGAACTAAGTGGTACTAA
Found at i:76757 original size:66 final size:66
Alignment explanation
Indices: 76651--76813 Score: 281
Period size: 66 Copynumber: 2.5 Consensus size: 66
76641 AAGAGTAATT
**
76651 CTAAATCTGTTTTAGATGTTGTAAGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
76716 A
66 A
* *
76717 CTAAATCTGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
76782 A
66 A
*
76783 CTAAATCTGTTTTAGGTGTTGTTTGTGATGA
1 CTAAATCTGTTTTAGATGTTGTTTGTGATGA
76814 AACAAATTCT
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 91 1.00
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.43
Consensus pattern (66 bp):
CTAAATCTGTTTTAGATGTTGTTTGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
A
Found at i:76825 original size:33 final size:32
Alignment explanation
Indices: 76651--76864 Score: 171
Period size: 33 Copynumber: 6.5 Consensus size: 32
76641 AAGAGTAATT
* ** *
76651 CTAAATCTGTTTTAGATGTTGTAAGTGATGATA
1 CTAAATCTGTTTT-GGTGTTGTTTGTGATGAAA
* ** * *
76684 CTAAACCTAATTTGAGTATTGTTTGTGATGACA
1 CTAAATCTGTTTTG-GTGTTGTTTGTGATGAAA
* * *
76717 CTAAATCTGTTTTAGATGTTGTTTGCGATGATA
1 CTAAATCTGTTTT-GGTGTTGTTTGTGATGAAA
* ** *
76750 CTAAACCTAATTTGAGTGTTGTTTGTGATGACA
1 CTAAATCTGTTTTG-GTGTTGTTTGTGATGAAA
76783 CTAAATCTGTTTTAGGTGTTGTTTGTGATGAAA
1 CTAAATCTGTTTT-GGTGTTGTTTGTGATGAAA
* **
76816 C-AAATTCTGTTTTGGATGCTAATTGTGATGAAAA
1 CTAAA-TCTGTTTTGG-TGTTGTTTGTGATG-AAA
76850 C-AAATCTGTTTTGGT
1 CTAAATCTGTTTTGGT
76865 TGATCATAAC
Statistics
Matches: 146, Mismatches: 28, Indels: 15
0.77 0.15 0.08
Matches are distributed among these distances:
32 8 0.05
33 129 0.88
34 9 0.06
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.42
Consensus pattern (32 bp):
CTAAATCTGTTTTGGTGTTGTTTGTGATGAAA
Found at i:76842 original size:66 final size:66
Alignment explanation
Indices: 76651--76861 Score: 212
Period size: 66 Copynumber: 3.2 Consensus size: 66
76641 AAGAGTAATT
** * * ** **
76651 CTAAATCTGTTTTAGATGTTGTAAGTGATGATACTAAACCTAATTTGAGTATTGTTTGTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC
76716 A
66 A
* * **
76717 CTAAATCTGTTTTAGATGTTGTTTGCGATGATACTAAACCTAATTTGAGTGTTGTTTGTGATGAC
1 CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC
76782 A
66 A
* * * **
76783 CTAAATCTGTTTTAGGTGTTGTTTGTGATGAAAC-AAATTCTGTTTTG-GATGCTAATTGTGATG
1 CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAA-CCTAATTTGAG-TGCTAATTGTGATG
*
76846 AAAA
64 -ACA
76850 C-AAATCTGTTTT
1 CTAAATCTGTTTT
76862 GGTTGATCAT
Statistics
Matches: 128, Mismatches: 14, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
65 4 0.03
66 121 0.95
67 3 0.02
ACGTcount: A:0.28, C:0.09, G:0.20, T:0.42
Consensus pattern (66 bp):
CTAAATCTGTTTTAGATGTTGTTTGCGATGAAACTAAACCTAATTTGAGTGCTAATTGTGATGAC
A
Found at i:79682 original size:15 final size:15
Alignment explanation
Indices: 79633--79669 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
79623 TGCTAGGGTG
79633 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
79648 AATGGTGCAAACAAC
1 AATGGTGCAAACAAC
79663 AATGGTG
1 AATGGTG
79670 TGAATAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.43, C:0.16, G:0.24, T:0.16
Consensus pattern (15 bp):
AATGGTGCAAACAAC
Found at i:102818 original size:49 final size:48
Alignment explanation
Indices: 102753--102869 Score: 155
Period size: 49 Copynumber: 2.4 Consensus size: 48
102743 TACTTTTGAC
** *
102753 TGCACTTTTTCTCAATTTTTACTACAAAATTGAACTTTT-ATTTTTACT
1 TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCA-T
* *
102801 TGCATCTTTTTCTCAATTTTTAAGACAACATTGATCTTTTAATTTTCAT
1 TGCA-CTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCAT
*
102850 TGCACTTTTTATCAATTTTT
1 TGCACTTTTTCTCAATTTTT
102870 GGATAAAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
48 19 0.31
49 36 0.59
50 6 0.10
ACGTcount: A:0.26, C:0.16, G:0.05, T:0.53
Consensus pattern (48 bp):
TGCACTTTTTCTCAATTTTTAAGACAAAATTGAACTTTTAATTTTCAT
Found at i:103430 original size:15 final size:15
Alignment explanation
Indices: 103410--103438 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
103400 TATACATTTT
103410 TTCACCCTATAATAG
1 TTCACCCTATAATAG
103425 TTCACCCTATAATA
1 TTCACCCTATAATA
103439 TCAAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (15 bp):
TTCACCCTATAATAG
Found at i:106667 original size:51 final size:50
Alignment explanation
Indices: 106566--106667 Score: 127
Period size: 51 Copynumber: 2.0 Consensus size: 50
106556 GTTCTTCATA
* **
106566 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCTTTTAGTGT
1 TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
*
106616 TTTTCCCTTGTTTCA-ATCTTGTCTCCGGACATACAAACACT-GTACACGTGT
1 TTTT-CCTTGTTT-AGATCTTGTCTCCGGACAAACAAACACTCGTACA-GTGT
106667 T
1 T
106668 CTTCATTCAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
50 6 0.13
51 38 0.84
52 1 0.02
ACGTcount: A:0.22, C:0.25, G:0.14, T:0.40
Consensus pattern (50 bp):
TTTTCCTTGTTTAGATCTTGTCTCCGGACAAACAAACACTCGTACAGTGT
Found at i:108792 original size:123 final size:128
Alignment explanation
Indices: 108648--108903 Score: 414
Period size: 123 Copynumber: 2.0 Consensus size: 128
108638 CATTGTTTAA
*
108648 ACTTTTATAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-CTT-TA-T
1 ACTTTTACAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATACT
108710 A-ATTTTTACCATTTTACTATTTTAATT-AAAAAACTTATATATATTAGAATTTTTTAAATAT
66 ATATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
* *
108771 ACTTTTACAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACC
1 ACTTTTACAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATA-C
108836 TATTTTATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT
65 TA---TATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAAT
108901 AT
127 AT
108903 A
1 A
108904 TTTCTTAAAT
Statistics
Matches: 121, Mismatches: 3, Indels: 9
0.91 0.02 0.07
Matches are distributed among these distances:
123 53 0.44
124 3 0.02
125 2 0.02
127 2 0.02
131 26 0.21
132 35 0.29
ACGTcount: A:0.39, C:0.11, G:0.01, T:0.50
Consensus pattern (128 bp):
ACTTTTACAATTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATCCTTATACT
ATATTTTTACCATTTTACTATTTTAATTAAAAAAACTTATATATATTAGAATTTTTTAAATAT
Found at i:108925 original size:14 final size:13
Alignment explanation
Indices: 108889--108927 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
108879 TATATATTAG
108889 AATTTTTTAAATA
1 AATTTTTTAAATA
* *
108902 TATTTCTTAAATGA
1 AATTTTTTAAAT-A
108916 AATTTTTTAAAT
1 AATTTTTTAAAT
108928 TTTACAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.41, C:0.03, G:0.03, T:0.54
Consensus pattern (13 bp):
AATTTTTTAAATA
Found at i:111926 original size:24 final size:24
Alignment explanation
Indices: 111891--111938 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
111881 TTTTATTGCC
111891 TCTTTTTATTTTCTGAT-TTTTTCT
1 TCTTTTTATTTT-TGATCTTTTTCT
*
111915 TCTTTTTTTTTTTGATCTTTTTCT
1 TCTTTTTATTTTTGATCTTTTTCT
111939 ATCTCTTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.18
24 18 0.82
ACGTcount: A:0.06, C:0.12, G:0.04, T:0.77
Consensus pattern (24 bp):
TCTTTTTATTTTTGATCTTTTTCT
Found at i:114821 original size:19 final size:19
Alignment explanation
Indices: 114788--114824 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
114778 GCCTGCAATC
**
114788 GGATCTTGTTTGTTTGATT
1 GGATCTTGTAAGTTTGATT
114807 GGATCTTGTAAGTTTGAT
1 GGATCTTGTAAGTTTGAT
114825 AGATCCTATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.16, C:0.05, G:0.27, T:0.51
Consensus pattern (19 bp):
GGATCTTGTAAGTTTGATT
Found at i:115466 original size:20 final size:20
Alignment explanation
Indices: 115441--115481 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
115431 AAAAAGAGCA
115441 CCAATTTGCAAATCAAATGC
1 CCAATTTGCAAATCAAATGC
*
115461 CCAATTTGTAAATCAAATGC
1 CCAATTTGCAAATCAAATGC
115481 C
1 C
115482 TTGTATTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.10, T:0.27
Consensus pattern (20 bp):
CCAATTTGCAAATCAAATGC
Found at i:127062 original size:27 final size:27
Alignment explanation
Indices: 126994--127049 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
126984 AGCAATCCAT
126994 AAATACCAAAATTCACTAAAGATACAA
1 AAATACCAAAATTCACTAAAGATACAA
127021 AAATACCAAAATTCACTAAAGATACAA
1 AAATACCAAAATTCACTAAAGATACAA
127048 AA
1 AA
127050 TTAAGCATGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.61, C:0.18, G:0.04, T:0.18
Consensus pattern (27 bp):
AAATACCAAAATTCACTAAAGATACAA
Found at i:128992 original size:18 final size:18
Alignment explanation
Indices: 128969--129003 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
128959 CATGGATTTA
*
128969 TGTAAAATTGATCACTTT
1 TGTAAAATTGAACACTTT
*
128987 TGTAAATTTGAACACTT
1 TGTAAAATTGAACACTT
129004 ATACCATCTC
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:0.11, G:0.11, T:0.43
Consensus pattern (18 bp):
TGTAAAATTGAACACTTT
Found at i:129566 original size:18 final size:18
Alignment explanation
Indices: 129543--129592 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
129533 GATGTGGCAA
129543 TGCCATGTGGCATTTTTG
1 TGCCATGTGGCATTTTTG
129561 TGCCATGTGGCATTTTTG
1 TGCCATGTGGCATTTTTG
*
129579 TGCCACGTGGCATT
1 TGCCATGTGGCATT
129593 GCCATGTCAG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.12, C:0.20, G:0.28, T:0.40
Consensus pattern (18 bp):
TGCCATGTGGCATTTTTG
Found at i:133285 original size:32 final size:32
Alignment explanation
Indices: 133238--133298 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
133228 TGTAAAATTT
*
133238 TTGAATCGACTATTATACCCTTATTTTTCTAA
1 TTGAATCGACCATTATACCCTTATTTTTCTAA
* *
133270 TTGAATCGGCCATTATATCCTTATTTTTC
1 TTGAATCGACCATTATACCCTTATTTTTC
133299 AAACATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.08, T:0.48
Consensus pattern (32 bp):
TTGAATCGACCATTATACCCTTATTTTTCTAA
Found at i:141783 original size:161 final size:161
Alignment explanation
Indices: 141510--141844 Score: 636
Period size: 161 Copynumber: 2.1 Consensus size: 161
141500 AGAAAGGATT
* *
141510 AAGAAC-TTTGTCTATAAAGAGGAATATGCTGAAATTCCTATAATTGCTATTGACAATGATCAGG
1 AAGAACATATGTCTATAAAGAGGAATATGCTGAAATTCCTATAATTGCTATTAACAATGATCAGG
141574 GTCAGGCTTCCATTCCTGACATTGCTCAAGAAGCAATTCCAGATCAAGACAATGTCTTTGAAACT
66 GTCAGGCTTCCATTCCTGACATTGCTCAAGAAGCAATTCCAGATCAAGACAATGTCTTTGAAACT
141639 CCTACCCTAGAAAAACAAACTCTACAACCTC
131 CCTACCCTAGAAAAACAAACTCTACAACCTC
141670 AAGAACATATGTCTATAAAGAGGAATATGCTGAAATTCCTATAATTGCTATTAACAATGATCAGG
1 AAGAACATATGTCTATAAAGAGGAATATGCTGAAATTCCTATAATTGCTATTAACAATGATCAGG
141735 GTCAGGCTTCCATTCCTGACATTGCTCAAGAAGCAATTCCAGATCAAGACAATGTCTTTGAAACT
66 GTCAGGCTTCCATTCCTGACATTGCTCAAGAAGCAATTCCAGATCAAGACAATGTCTTTGAAACT
*
141800 CTTACCCTAGAAAAACAAACTCTACAACCTC
131 CCTACCCTAGAAAAACAAACTCTACAACCTC
141831 AAGAACATATGTCT
1 AAGAACATATGTCT
141845 TTAAGGAGTT
Statistics
Matches: 171, Mismatches: 3, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
160 6 0.04
161 165 0.96
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.27
Consensus pattern (161 bp):
AAGAACATATGTCTATAAAGAGGAATATGCTGAAATTCCTATAATTGCTATTAACAATGATCAGG
GTCAGGCTTCCATTCCTGACATTGCTCAAGAAGCAATTCCAGATCAAGACAATGTCTTTGAAACT
CCTACCCTAGAAAAACAAACTCTACAACCTC
Found at i:154567 original size:15 final size:15
Alignment explanation
Indices: 154543--154577 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
154533 GGACAATCCC
154543 GACGGCGAAGTTGAT
1 GACGGCGAAGTTGAT
*
154558 GACGGTGAAGTTGAT
1 GACGGCGAAGTTGAT
154573 GACGG
1 GACGG
154578 AGACGGCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.43, T:0.20
Consensus pattern (15 bp):
GACGGCGAAGTTGAT
Found at i:158356 original size:111 final size:111
Alignment explanation
Indices: 158162--158385 Score: 412
Period size: 111 Copynumber: 2.0 Consensus size: 111
158152 AAAACATGAA
158162 TCATCCACCAATAAGTAATTGATTGAGATGGTAGACGGTCTTTACCCTGACAAGGATGAGAACAT
1 TCATCCACCAATAAGTAATTGATTGAGATGGTAGACGGTCTTTACCCTGACAAGGATGAGAACAT
158227 AAGTTTGATCTTCCACCAACAAGTAATTGGTTGAGATAGTAAGCGG
66 AAGTTTGATCTTCCACCAACAAGTAATTGGTTGAGATAGTAAGCGG
* *
158273 TCATCCACCAATAAGTAATTGGTTGAGATGGTAGACGGTCTTTACCCTGACAAGGGTGAGAACAT
1 TCATCCACCAATAAGTAATTGATTGAGATGGTAGACGGTCTTTACCCTGACAAGGATGAGAACAT
* *
158338 AAGTTTGATCTTCCACCAATAAGTAATTGGTTGAGATAGTAAGTGG
66 AAGTTTGATCTTCCACCAACAAGTAATTGGTTGAGATAGTAAGCGG
158384 TC
1 TC
158386 TCTACCCTAA
Statistics
Matches: 109, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 109 1.00
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (111 bp):
TCATCCACCAATAAGTAATTGATTGAGATGGTAGACGGTCTTTACCCTGACAAGGATGAGAACAT
AAGTTTGATCTTCCACCAACAAGTAATTGGTTGAGATAGTAAGCGG
Found at i:158363 original size:73 final size:73
Alignment explanation
Indices: 158276--158421 Score: 222
Period size: 73 Copynumber: 2.0 Consensus size: 73
158266 TAAGCGGTCA
* * *
158276 TCCACCAATAAGTAATTGGTTGAGATGGT-AGACGGTCTTTACCCTGACAAGGGTGAGAACATAA
1 TCCACCAATAAGTAATTGGTTGAGATAGTAAG-CGGTCTCTACCCTAACAAGGGTGAGAACATAA
158340 GTTTGATCT
65 GTTTGATCT
* * *
158349 TCCACCAATAAGTAATTGGTTGAGATAGTAAGTGGTCTCTACCCTAACAAGGGTGAGAGCGTAAG
1 TCCACCAATAAGTAATTGGTTGAGATAGTAAGCGGTCTCTACCCTAACAAGGGTGAGAACATAAG
158414 TTTGATCT
66 TTTGATCT
158422 CCTGTAAACA
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
73 64 0.97
74 2 0.03
ACGTcount: A:0.30, C:0.16, G:0.25, T:0.29
Consensus pattern (73 bp):
TCCACCAATAAGTAATTGGTTGAGATAGTAAGCGGTCTCTACCCTAACAAGGGTGAGAACATAAG
TTTGATCT
Found at i:162189 original size:31 final size:31
Alignment explanation
Indices: 162148--162240 Score: 134
Period size: 31 Copynumber: 3.0 Consensus size: 31
162138 TTTTGTAAAA
* *
162148 CTTTTGAATCGACTATTATATCCATATTTTT
1 CTTTTAAATCGACTATTATATCCTTATTTTT
*
162179 CTTTTAAATCGATTATTATATCCTTA-TTTT
1 CTTTTAAATCGACTATTATATCCTTATTTTT
* *
162209 CTTTTAAATCGACCATTATACCCTTATTTTT
1 CTTTTAAATCGACTATTATATCCTTATTTTT
162240 C
1 C
162241 GAATATATTT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
30 27 0.49
31 28 0.51
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.52
Consensus pattern (31 bp):
CTTTTAAATCGACTATTATATCCTTATTTTT
Found at i:162211 original size:30 final size:30
Alignment explanation
Indices: 162148--162238 Score: 128
Period size: 30 Copynumber: 3.0 Consensus size: 30
162138 TTTTGTAAAA
* *
162148 CTTTTGAATCGACTATTATATCCATATTTTT
1 CTTTTAAATCGACTATTATATCCTTA-TTTT
*
162179 CTTTTAAATCGATTATTATATCCTTATTTT
1 CTTTTAAATCGACTATTATATCCTTATTTT
* *
162209 CTTTTAAATCGACCATTATACCCTTATTTT
1 CTTTTAAATCGACTATTATATCCTTATTTT
162239 TCGAATATAT
Statistics
Matches: 54, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
30 31 0.57
31 23 0.43
ACGTcount: A:0.26, C:0.18, G:0.04, T:0.52
Consensus pattern (30 bp):
CTTTTAAATCGACTATTATATCCTTATTTT
Found at i:162407 original size:85 final size:85
Alignment explanation
Indices: 162308--162482 Score: 264
Period size: 85 Copynumber: 2.1 Consensus size: 85
162298 TCTATTTTTG
*
162308 TTTAATTAAATCTAATCTCTTTATAACTATTTTG-TTTTTACC-ATTTTACTATTTTAATTAAAA
1 TTTAATTAAATCTAATCTATTTATAACTA-TTTGATTTTTACCAATTTTACTATTTTAATT-AAA
* *
162371 AAACTTAGATATGTTATAATTT
64 AAACTTAGATATATTAGAATTT
* *
162393 TTTAATTAAATCTAATTTATTTATAACTATTTGATTTTTACCAATTTTACTATTTTAATTACAAA
1 TTTAATTAAATCTAATCTATTTATAACTATTTGATTTTTACCAATTTTACTATTTTAATTAAAAA
*
162458 ACTTAGGTATATTAGAATTT
66 ACTTAGATATATTAGAATTT
162478 TTTAA
1 TTTAA
162483 ATATATTTCT
Statistics
Matches: 82, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
84 4 0.05
85 61 0.74
86 17 0.21
ACGTcount: A:0.36, C:0.09, G:0.04, T:0.51
Consensus pattern (85 bp):
TTTAATTAAATCTAATCTATTTATAACTATTTGATTTTTACCAATTTTACTATTTTAATTAAAAA
ACTTAGATATATTAGAATTT
Found at i:174560 original size:12 final size:12
Alignment explanation
Indices: 174543--174568 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
174533 TTTGTGTGTT
174543 AACATTAACAGC
1 AACATTAACAGC
174555 AACATTAACAGC
1 AACATTAACAGC
174567 AA
1 AA
174569 GTTACTGTGT
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:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (12 bp):
AACATTAACAGC
Found at i:191900 original size:18 final size:18
Alignment explanation
Indices: 191877--191911 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
191867 GTCAATTCCT
191877 TCTCCTCCTCATATGGGG
1 TCTCCTCCTCATATGGGG
191895 TCTCCTCCTCATATGGG
1 TCTCCTCCTCATATGGG
191912 TCCTTCCCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.34, G:0.20, T:0.34
Consensus pattern (18 bp):
TCTCCTCCTCATATGGGG
Found at i:192728 original size:21 final size:21
Alignment explanation
Indices: 192662--192730 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
192652 TGATTTAGAG
*
192662 AATGATATCCCTAATGGAAGT
1 AATGATATGCCTAATGGAAGT
* * *
192683 AATCATATGCGTAATGGAAAT
1 AATGATATGCCTAATGGAAGT
192704 AATGATATGCCTAATGGAAGT
1 AATGATATGCCTAATGGAAGT
192725 AATGAT
1 AATGAT
192731 CCACCAGTTA
Statistics
Matches: 41, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 41 1.00
ACGTcount: A:0.41, C:0.10, G:0.20, T:0.29
Consensus pattern (21 bp):
AATGATATGCCTAATGGAAGT
Found at i:197119 original size:10 final size:10
Alignment explanation
Indices: 197104--197134 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
197094 AAAGTTCATC
197104 AAAAAAAAAG
1 AAAAAAAAAG
197114 -AAAAAAAAG
1 AAAAAAAAAG
197123 AAAAAAAAAG
1 AAAAAAAAAG
197133 AA
1 AA
197135 GATAAAAGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:197136 original size:22 final size:21
Alignment explanation
Indices: 197104--197150 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
197094 AAAGTTCATC
197104 AAAAAAAAAGAAAAAAAAGAA
1 AAAAAAAAAGAAAAAAAAGAA
* * *
197125 AAAAAAAGAAGATAAAAGAGTA
1 AAAAAAA-AAGAAAAAAAAGAA
197147 AAAA
1 AAAA
197151 TTTAACCGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.04
Consensus pattern (21 bp):
AAAAAAAAAGAAAAAAAAGAA
Found at i:197143 original size:10 final size:9
Alignment explanation
Indices: 197105--197130 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
197095 AAGTTCATCA
197105 AAAAAAAAG
1 AAAAAAAAG
197114 AAAAAAAAG
1 AAAAAAAAG
197123 AAAAAAAA
1 AAAAAAAA
197131 AGAAGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:212018 original size:22 final size:22
Alignment explanation
Indices: 211974--212020 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
211964 TCAGCTTCAC
*
211974 TAGCCTAAGGTTAATTGTCAGT
1 TAGCCTAAGGTTAATTATCAGT
*
211996 TAGCCTATGGTTAATCTAT-AGT
1 TAGCCTAAGGTTAAT-TATCAGT
212018 TAG
1 TAG
212021 ATGTTAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.28, C:0.13, G:0.21, T:0.38
Consensus pattern (22 bp):
TAGCCTAAGGTTAATTATCAGT
Found at i:213794 original size:2 final size:2
Alignment explanation
Indices: 213789--213816 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
213779 TTTTTTTTTC
213789 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
213817 TTGGATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:228150 original size:29 final size:28
Alignment explanation
Indices: 228094--228155 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 28
228084 ACTTGTAGCG
* * *
228094 TTTGGACGTTTTGTCTCTGAATTTCAAT
1 TTTGGACATTTTATCCCTGAATTTCAAT
228122 TTTGGACATTTTATCCCTTGAATTTCAAT
1 TTTGGACATTTTATCCC-TGAATTTCAAT
228151 TTTGG
1 TTTGG
228156 GACGTTTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 14 0.47
29 16 0.53
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.50
Consensus pattern (28 bp):
TTTGGACATTTTATCCCTGAATTTCAAT
Found at i:231864 original size:28 final size:29
Alignment explanation
Indices: 231810--231864 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
231800 ATCTGAAAAG
* * *
231810 GATAATTTGATTCTTGAAATTTGATTTGA
1 GATAATTTGATCCTTGAAATATAATTTGA
*
231839 GATAATTTGA-CCTTGAACTATAATTT
1 GATAATTTGATCCTTGAAATATAATTT
231865 TTTAGACAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 12 0.55
29 10 0.45
ACGTcount: A:0.33, C:0.07, G:0.15, T:0.45
Consensus pattern (29 bp):
GATAATTTGATCCTTGAAATATAATTTGA
Done.