Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168048.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_3, 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: 33276047
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 139000 characters in sequence are not A, C, G, or T
File 29 of 190
Found at i:4969909 original size:13 final size:12
Alignment explanation
Indices: 4969891--4969920 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 12
4969881 ATTATATATA
4969891 TTTTTCTTTTTT
1 TTTTTCTTTTTT
4969903 CTTTTTCTTTTTT
1 -TTTTTCTTTTTT
4969916 TTTTT
1 TTTTT
4969921 GGTTTAGCTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:4971000 original size:13 final size:13
Alignment explanation
Indices: 4970990--4971022 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
4970980 TAATAATAAT
4970990 TAATAAAAATATA
1 TAATAAAAATATA
4971003 TAAT-AAAATATA
1 TAATAAAAATATA
4971015 TAATAAAA
1 TAATAAAA
4971023 GTTTTTGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (13 bp):
TAATAAAAATATA
Found at i:4971012 original size:12 final size:12
Alignment explanation
Indices: 4970978--4971022 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
4970968 TTTGTTATTT
*
4970978 TATAATAATA-A
1 TATAATAAAATA
4970989 T-TAATAAAAATA
1 TATAAT-AAAATA
4971001 TATAATAAAATA
1 TATAATAAAATA
4971013 TATAATAAAA
1 TATAATAAAA
4971023 GTTTTTGATA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
10 4 0.13
11 4 0.13
12 18 0.60
13 4 0.13
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TATAATAAAATA
Found at i:4973738 original size:16 final size:15
Alignment explanation
Indices: 4973699--4973740 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
4973689 TATTTATCGA
*
4973699 AAATTTTTTTCTTTT
1 AAATTTTTTTCTTTC
4973714 ATAATTTTTTTCTTTC
1 A-AATTTTTTTCTTTC
4973730 AAATCTTTTTT
1 AAAT-TTTTTT
4973741 TCATCAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 4 0.17
16 20 0.83
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (15 bp):
AAATTTTTTTCTTTC
Found at i:4975847 original size:14 final size:14
Alignment explanation
Indices: 4975830--4975866 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
4975820 TGTAAAATTT
*
4975830 TTTATTAAAAATAA
1 TTTAATAAAAATAA
4975844 TTTAATAAAAAT-A
1 TTTAATAAAAATAA
4975857 -TTAATAAAAA
1 TTTAATAAAAA
4975867 GTTTAAAGCA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 10 0.45
13 1 0.05
14 11 0.50
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTTAATAAAAATAA
Found at i:4976530 original size:23 final size:22
Alignment explanation
Indices: 4976488--4976530 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
4976478 TTAATTTGTT
*
4976488 TAATTTAATTAATTAGATATAC
1 TAATTTAATTAAGTAGATATAC
4976510 TAATCTTAATTAACGTA-ATAT
1 TAAT-TTAATTAA-GTAGATAT
4976531 TCGCAAGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 12 0.67
24 2 0.11
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (22 bp):
TAATTTAATTAAGTAGATATAC
Found at i:4979374 original size:21 final size:21
Alignment explanation
Indices: 4979349--4979398 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
4979339 TAACATCCAT
* * *
4979349 AAATACTAATAATAAAATTTA
1 AAATAATAAAAATAAAATTAA
*
4979370 AAATAATAAAAATAATATTAA
1 AAATAATAAAAATAAAATTAA
4979391 AAA-AATAA
1 AAATAATAA
4979399 TTCAAAAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 5 0.20
21 20 0.80
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATAATAAAAATAAAATTAA
Found at i:4980344 original size:16 final size:16
Alignment explanation
Indices: 4980310--4980346 Score: 53
Period size: 14 Copynumber: 2.5 Consensus size: 16
4980300 AAGGTGCCAA
4980310 AAAAG-AAAAAAAGAG
1 AAAAGAAAAAAAAGAG
4980325 --AAGAAAAAAAAGAG
1 AAAAGAAAAAAAAGAG
4980339 AAAAGAAA
1 AAAAGAAA
4980347 CGAAATGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 5
0.79 0.00 0.21
Matches are distributed among these distances:
13 3 0.16
14 10 0.53
16 6 0.32
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAGAAAAAAAAGAG
Found at i:4980369 original size:3 final size:3
Alignment explanation
Indices: 4980361--4980407 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
4980351 ATGAAATGAA
4980361 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
4980408 AAAAAAAATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:4980683 original size:53 final size:51
Alignment explanation
Indices: 4980618--4981014 Score: 243
Period size: 50 Copynumber: 7.9 Consensus size: 51
4980608 AAAATCCTTT
* * *
4980618 ATCTTGAAAAAAACTCATCTAGACATAGGCTCAATAACTTTAAAAAAAATCTC
1 ATCTTG-AAAAAACTCCTCTAGATAGAGGCTCAATAACTTT-AAAAAAATCTC
* * * *
4980671 ATCTTGACAAAAACACCTTTAGATAGAGGCTCAACAACTTT--AAAAATTTC
1 ATCTTGA-AAAAACTCCTCTAGATAGAGGCTCAATAACTTTAAAAAAATCTC
* *
4980721 ATCTTGAAAAATGCTCCTCTA-AGTAGAGGCTCAATGAC-TTAAAAAAATCTC
1 ATCTTGAAAAA-ACTCCTCTAGA-TAGAGGCTCAATAACTTTAAAAAAATCTC
** * * *
4980772 ATCTTGAAAAATGTTCATCTA-AGTAGAGGTTCAACAACTTT--AAAAATCTC
1 ATCTTGAAAAA-ACTCCTCTAGA-TAGAGGCTCAATAACTTTAAAAAAATCTC
* * * * * *
4980822 AT-TTTAAAAAATGCTCCTCTA-AGTAGAGGCTTAACAA-TTT-TAAAAATTTT
1 ATCTTGAAAAAA--CTCCTCTAGA-TAGAGGCTCAATAACTTTAAAAAAATCTC
* ** * * *
4980872 ATTTTGAAAAAAACTTATCTA-AGCAGATGCTCAACAACTTT--AAAAATCTC
1 ATCTTG-AAAAAACTCCTCTAGA-TAGAGGCTCAATAACTTTAAAAAAATCTC
* * * *
4980922 ATCTTGAAAAGAGCTCCTCTATATAGAGGCTCAACAAC-TT-AAAAAATTTC
1 ATCTTGAAAA-AACTCCTCTAGATAGAGGCTCAATAACTTTAAAAAAATCTC
* * * * *
4980972 ATTTTG-AAAAACTCATTTAAATAGAGACTCAATAACTTTAAAA
1 ATCTTGAAAAAACTCCTCTAGATAGAGGCTCAATAACTTTAAAA
4981015 TTTAAAATAT
Statistics
Matches: 279, Mismatches: 48, Indels: 37
0.77 0.13 0.10
Matches are distributed among these distances:
48 21 0.08
49 28 0.10
50 141 0.51
51 47 0.17
52 9 0.03
53 33 0.12
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (51 bp):
ATCTTGAAAAAACTCCTCTAGATAGAGGCTCAATAACTTTAAAAAAATCTC
Found at i:4980748 original size:50 final size:50
Alignment explanation
Indices: 4980694--4981014 Score: 335
Period size: 50 Copynumber: 6.4 Consensus size: 50
4980684 CACCTTTAGA
* *
4980694 TAGAGGCTCAACAACTTTAAAAATTTCATCTTGAAAAATGCTCCTCTAAG
1 TAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAATGCTCATCTAAG
** * *
4980744 TAGAGGCTCAATGACTTAAAAAAATCTCATCTTGAAAAATGTTCATCTAAG
1 TAGAGGCTCAACAACTT-TAAAAATCTCATCTTGAAAAATGCTCATCTAAG
* * * *
4980795 TAGAGGTTCAACAACTTTAAAAATCTCATTTTAAAAAATGCTCCTCTAAG
1 TAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAATGCTCATCTAAG
* * * * * ** *
4980845 TAGAGGCTTAACAATTTTAAAAATTTTATTTTGAAAAAAACTTATCTAAG
1 TAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAATGCTCATCTAAG
* * *
4980895 CAGATGCTCAACAACTTTAAAAATCTCATCTTGAAAAGA-GCTCCTCTATA-
1 TAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAA-ATGCTCATCTA-AG
* * * * *
4980945 TAGAGGCTCAACAACTTAAAAAATTTCATTTTGAAAAA--CTCATTTAAA
1 TAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAATGCTCATCTAAG
* *
4980993 TAGAGACTCAATAACTTTAAAA
1 TAGAGGCTCAACAACTTTAAAA
4981015 TTTAAAATAT
Statistics
Matches: 223, Mismatches: 44, Indels: 10
0.81 0.16 0.04
Matches are distributed among these distances:
47 1 0.00
48 25 0.11
49 1 0.00
50 151 0.68
51 45 0.20
ACGTcount: A:0.42, C:0.17, G:0.11, T:0.31
Consensus pattern (50 bp):
TAGAGGCTCAACAACTTTAAAAATCTCATCTTGAAAAATGCTCATCTAAG
Found at i:4991874 original size:17 final size:18
Alignment explanation
Indices: 4991848--4991881 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
4991838 TGCATATGGA
*
4991848 AATTTTTTTTTG-TTTTC
1 AATTTGTTTTTGATTTTC
4991865 AATTTGTTTTTGATTTT
1 AATTTGTTTTTGATTTT
4991882 TGATTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.15, C:0.03, G:0.09, T:0.74
Consensus pattern (18 bp):
AATTTGTTTTTGATTTTC
Found at i:4993157 original size:21 final size:21
Alignment explanation
Indices: 4993133--4993181 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
4993123 TTTATAAAGT
4993133 TTATTTCAAATTTTAACTAAA
1 TTATTTCAAATTTTAACTAAA
*** *
4993154 TTATAAAAAATTTTAACTATA
1 TTATTTCAAATTTTAACTAAA
4993175 -TATTTCA
1 TTATTTCA
4993182 TTATTTATTT
Statistics
Matches: 21, Mismatches: 7, Indels: 1
0.72 0.24 0.03
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.45, C:0.08, G:0.00, T:0.47
Consensus pattern (21 bp):
TTATTTCAAATTTTAACTAAA
Found at i:4994189 original size:14 final size:13
Alignment explanation
Indices: 4994172--4994245 Score: 57
Period size: 12 Copynumber: 5.6 Consensus size: 13
4994162 AAGGTGCAAG
4994172 AAAAGAAAGAAAG-
1 AAAAGAAA-AAAGA
4994185 AAAA-AAAAAAGA
1 AAAAGAAAAAAGA
* *
4994197 AGAA-AAAAATGA
1 AAAAGAAAAAAGA
4994209 AAAAGAAAAAAATGA
1 AAAAG-AAAAAA-GA
4994224 AAAAGAAACAAA-A
1 AAAAGAAA-AAAGA
4994237 GAAAAGAAA
1 -AAAAGAAA
4994246 CAAAACTGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
11 4 0.08
12 16 0.31
13 5 0.10
14 16 0.31
15 10 0.20
ACGTcount: A:0.81, C:0.01, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAAGAAAAAAGA
Found at i:4994190 original size:15 final size:14
Alignment explanation
Indices: 4994172--4994250 Score: 56
Period size: 15 Copynumber: 5.4 Consensus size: 14
4994162 AAGGTGCAAG
*
4994172 AAAAGAAAGAAAGAA
1 AAAAAAAAG-AAGAA
4994187 AAAAAAAAGAAGAA
1 AAAAAAAAGAAGAA
4994201 AAAAATGAAA-AAGAA
1 AAAAA--AAAGAAGAA
4994216 AAAAATGAAA-AAGAA
1 AAAAA--AAAGAAGAA
*
4994231 ACAAAAGAA-AAGAA
1 A-AAAAAAAGAAGAA
4994245 ACAAAA
1 A-AAAA
4994251 CTGAAACAAA
Statistics
Matches: 59, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
14 23 0.39
15 29 0.49
16 7 0.12
ACGTcount: A:0.81, C:0.03, G:0.14, T:0.03
Consensus pattern (14 bp):
AAAAAAAAGAAGAA
Found at i:4994199 original size:18 final size:18
Alignment explanation
Indices: 4994172--4994220 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 18
4994162 AAGGTGCAAG
4994172 AAAAGAAAGAAAGAAAA-AA
1 AAAAG-AAGAAA-AAAATAA
*
4994191 AAAAGAAGAAAAAAATGA
1 AAAAGAAGAAAAAAATAA
4994209 AAAAGAA-AAAAA
1 AAAAGAAGAAAAA
4994221 TGAAAAAGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
17 9 0.32
18 14 0.50
19 5 0.18
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (18 bp):
AAAAGAAGAAAAAAATAA
Found at i:4994246 original size:14 final size:13
Alignment explanation
Indices: 4994169--4994250 Score: 76
Period size: 14 Copynumber: 5.8 Consensus size: 13
4994159 AAAAAGGTGC
4994169 AAGAAAAGAAAG-A
1 AAGAAAA-AAAGAA
*
4994182 AAGAAAAAAAAAA
1 AAGAAAAAAAGAA
4994195 GAAGAAAAAAATGAAA
1 -AAGAAAAAAA-G-AA
4994211 AAGAAAAAAATGAAA
1 AAGAAAAAAA-G-AA
4994226 AAGAAACAAAAGAA
1 AAGAAA-AAAAGAA
4994240 AAGAAACAAAA
1 AAGAAA-AAAA
4994251 CTGAAACAAA
Statistics
Matches: 62, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
12 3 0.05
13 8 0.13
14 23 0.37
15 22 0.35
16 6 0.10
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (13 bp):
AAGAAAAAAAGAA
Found at i:4994275 original size:14 final size:14
Alignment explanation
Indices: 4994181--4994277 Score: 83
Period size: 14 Copynumber: 6.7 Consensus size: 14
4994171 GAAAAGAAAG
4994181 AAAGAAAAAAA-AA
1 AAAGAAAAAAATAA
4994194 AGAAGAAAAAAATGAA
1 A-AAGAAAAAAAT-AA
4994210 AAAGAAAAAAATGAA
1 AAAGAAAAAAAT-AA
*
4994225 AAAGAAACAAAA-GA
1 AAAGAAA-AAAATAA
*
4994239 AAAGAAACAAAACT-G
1 AAAGAAA-AAAA-TAA
*
4994254 AAACAAAAAAATAA
1 AAAGAAAAAAATAA
*
4994268 AAATAAAAAA
1 AAAGAAAAAA
4994278 TAGGTGTTCA
Statistics
Matches: 72, Mismatches: 5, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
13 2 0.03
14 36 0.50
15 27 0.38
16 7 0.10
ACGTcount: A:0.80, C:0.04, G:0.10, T:0.05
Consensus pattern (14 bp):
AAAGAAAAAAATAA
Found at i:4994275 original size:25 final size:25
Alignment explanation
Indices: 4994209--4994275 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 25
4994199 AAAAAAATGA
** *
4994209 AAAAGAAAAAAATGAAAA-AGAAAC
1 AAAAGAAAAAAAACAAAACTGAAAC
*
4994233 AAAAGAAAAGAAACAAAACTGAAAC
1 AAAAGAAAAAAAACAAAACTGAAAC
*
4994258 AAAA-AAATAAAAATAAAA
1 AAAAGAAA-AAAAACAAAA
4994276 AATAGGTGTT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
24 18 0.51
25 17 0.49
ACGTcount: A:0.79, C:0.06, G:0.09, T:0.06
Consensus pattern (25 bp):
AAAAGAAAAAAAACAAAACTGAAAC
Found at i:4997622 original size:15 final size:15
Alignment explanation
Indices: 4997591--4997632 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
4997581 AGAAATTTGA
* *
4997591 ATTTTAAGGTTTTGG
1 ATTTTAGGGTTTGGG
4997606 ATTTTAGGGTTTGGG
1 ATTTTAGGGTTTGGG
*
4997621 ATTTTAGAGTTT
1 ATTTTAGGGTTT
4997633 TATGGTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.29, T:0.52
Consensus pattern (15 bp):
ATTTTAGGGTTTGGG
Found at i:4997633 original size:23 final size:23
Alignment explanation
Indices: 4997607--4997678 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
4997597 AGGTTTTGGA
***
4997607 TTTTAGGGTTTGGGATTTTAGAG
1 TTTTAGGGTTTCAAATTTTAGAG
*
4997630 TTTTATGGTTTCAAATTTTAGAG
1 TTTTAGGGTTTCAAATTTTAGAG
* *
4997653 TTTTAAGGTCTCAAATTTTAGAG
1 TTTTAGGGTTTCAAATTTTAGAG
4997676 TTT
1 TTT
4997679 AGGATTTTAG
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.50
Consensus pattern (23 bp):
TTTTAGGGTTTCAAATTTTAGAG
Found at i:4997685 original size:15 final size:15
Alignment explanation
Indices: 4997667--4997735 Score: 56
Period size: 13 Copynumber: 4.8 Consensus size: 15
4997657 AAGGTCTCAA
4997667 ATTTTAGAGTTTAGG
1 ATTTTAGAGTTTAGG
*
4997682 ATTTTAGGGTTTA--
1 ATTTTAGAGTTTAGG
*
4997695 ATTTTAGGGTTTAGAG
1 ATTTTAGAGTTTAG-G
* * *
4997711 GTTTGAG-GTTT-TG
1 ATTTTAGAGTTTAGG
4997724 ATTTTAGAGTTT
1 ATTTTAGAGTTT
4997736 CATGTTTAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
13 19 0.43
14 4 0.09
15 16 0.36
16 5 0.11
ACGTcount: A:0.22, C:0.00, G:0.28, T:0.51
Consensus pattern (15 bp):
ATTTTAGAGTTTAGG
Found at i:4997700 original size:13 final size:13
Alignment explanation
Indices: 4997666--4997707 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
4997656 TAAGGTCTCA
*
4997666 AATTTTAGAGTTT
1 AATTTTAGGGTTT
4997679 AGGATTTTAGGGTTT
1 A--ATTTTAGGGTTT
4997694 AATTTTAGGGTTT
1 AATTTTAGGGTTT
4997707 A
1 A
4997708 GAGGTTTGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
13 14 0.54
15 12 0.46
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (13 bp):
AATTTTAGGGTTT
Found at i:4997706 original size:28 final size:29
Alignment explanation
Indices: 4997666--4997735 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
4997656 TAAGGTCTCA
*
4997666 AATTTTAGAGTTTAG-GATTTTAGGGTTT
1 AATTTTAGAGTTTAGAGATTTGAGGGTTT
* * *
4997694 AATTTTAGGGTTTAGAGGTTTGAGGTTTT
1 AATTTTAGAGTTTAGAGATTTGAGGGTTT
*
4997723 GATTTTAGAGTTT
1 AATTTTAGAGTTT
4997736 CATGTTTAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
28 14 0.40
29 21 0.60
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (29 bp):
AATTTTAGAGTTTAGAGATTTGAGGGTTT
Found at i:4997806 original size:13 final size:13
Alignment explanation
Indices: 4997788--4997812 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4997778 TTGACTTTTG
4997788 AATTTAGGGTTTC
1 AATTTAGGGTTTC
4997801 AATTTAGGGTTT
1 AATTTAGGGTTT
4997813 GGATGTTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.04, G:0.24, T:0.48
Consensus pattern (13 bp):
AATTTAGGGTTTC
Found at i:4997866 original size:30 final size:30
Alignment explanation
Indices: 4997827--4997918 Score: 96
Period size: 30 Copynumber: 3.1 Consensus size: 30
4997817 GTTTTAGGGA
* * *
4997827 TTTGATTTTAGGATTTGGAGGGTTTAATGT
1 TTTGTTTTTAGGATTTAGAGGGTTTAAGGT
* * *
4997857 TTTGTTTTTA-AAGTTCAGAGGGTTTAGGGT
1 TTTGTTTTTAGGA-TTTAGAGGGTTTAAGGT
* *
4997887 TTTGTTTTTAGGTTTTAGAGGGTTTAGGGT
1 TTTGTTTTTAGGATTTAGAGGGTTTAAGGT
4997917 TT
1 TT
4997919 AATTTAAGGT
Statistics
Matches: 51, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.17, C:0.01, G:0.30, T:0.51
Consensus pattern (30 bp):
TTTGTTTTTAGGATTTAGAGGGTTTAAGGT
Found at i:4997887 original size:7 final size:7
Alignment explanation
Indices: 4997875--4998046 Score: 61
Period size: 7 Copynumber: 24.0 Consensus size: 7
4997865 TAAAGTTCAG
4997875 AGGGTTT
1 AGGGTTT
4997882 AGGGTTT
1 AGGGTTT
* **
4997889 TGTTTTT
1 AGGGTTT
*
4997896 AGGTTTT
1 AGGGTTT
4997903 AGAGGGTTT
1 --AGGGTTT
4997912 AGGGTTT
1 AGGGTTT
*
4997919 A--ATTT
1 AGGGTTT
*
4997924 AAGGTTT
1 AGGGTTT
*
4997931 AAAGTGTTT
1 --AGGGTTT
4997940 AGGGTTT
1 AGGGTTT
*
4997947 A--ATTT
1 AGGGTTT
4997952 AGGGTTT
1 AGGGTTT
*
4997959 AAAGGTTT
1 -AGGGTTT
*
4997967 GGGGTTT
1 AGGGTTT
*
4997974 A--ATTT
1 AGGGTTT
4997979 AGGGTTT
1 AGGGTTT
4997986 AGAGTGTTT
1 AG-G-GTTT
4997995 AGGGTTT
1 AGGGTTT
*
4998002 AAGAGTTTT
1 -AG-GGTTT
4998011 AGGG-TT
1 AGGGTTT
*
4998017 AGGTTTT
1 AGGGTTT
*
4998024 AAGGTTT
1 AGGGTTT
*
4998031 GAAGGATTT
1 --AGGGTTT
4998040 AGGGTTT
1 AGGGTTT
4998047 CAATTTCGAA
Statistics
Matches: 120, Mismatches: 27, Indels: 36
0.66 0.15 0.20
Matches are distributed among these distances:
5 12 0.10
6 5 0.04
7 65 0.54
8 12 0.10
9 26 0.22
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.46
Consensus pattern (7 bp):
AGGGTTT
Found at i:4997929 original size:12 final size:12
Alignment explanation
Indices: 4997909--4997986 Score: 75
Period size: 12 Copynumber: 5.9 Consensus size: 12
4997899 TTTTAGAGGG
4997909 TTTAGGGTTTAA
1 TTTAGGGTTTAA
*
4997921 TTTAAGGTTTAAA
1 TTTAGGGTTT-AA
4997934 GTGTTTAGGGTTTAA
1 ---TTTAGGGTTTAA
4997949 TTTAGGGTTTAAA
1 TTTAGGGTTT-AA
*
4997962 GGTTTGGGGTTTAA
1 --TTTAGGGTTTAA
4997976 TTTAGGGTTTA
1 TTTAGGGTTTA
4997987 GAGTGTTTAG
Statistics
Matches: 55, Mismatches: 4, Indels: 14
0.75 0.05 0.19
Matches are distributed among these distances:
12 29 0.53
13 4 0.07
14 2 0.04
15 11 0.20
16 9 0.16
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.47
Consensus pattern (12 bp):
TTTAGGGTTTAA
Found at i:4997939 original size:28 final size:28
Alignment explanation
Indices: 4997893--4998003 Score: 161
Period size: 28 Copynumber: 4.0 Consensus size: 28
4997883 GGGTTTTGTT
* * *
4997893 TTTAGGTTTTAGAGGGTTTAGGGTTTAA
1 TTTAGGGTTTAAAGTGTTTAGGGTTTAA
*
4997921 TTTAAGGTTTAAAGTGTTTAGGGTTTAA
1 TTTAGGGTTTAAAGTGTTTAGGGTTTAA
*
4997949 TTTAGGGTTTAAAG-GTTTGGGGTTTAA
1 TTTAGGGTTTAAAGTGTTTAGGGTTTAA
*
4997976 TTTAGGGTTTAGAGTGTTTAGGGTTTAA
1 TTTAGGGTTTAAAGTGTTTAGGGTTTAA
4998004 GAGTTTTAGG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
27 25 0.34
28 49 0.66
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (28 bp):
TTTAGGGTTTAAAGTGTTTAGGGTTTAA
Found at i:4997978 original size:55 final size:56
Alignment explanation
Indices: 4997893--4998003 Score: 170
Period size: 55 Copynumber: 2.0 Consensus size: 56
4997883 GGGTTTTGTT
* *
4997893 TTTAGGTTTTAGAGGGTTTAGGGTTTAATTTAAGGTTTAAAGTGTTTAGGGTTTAA
1 TTTAGGGTTTAGAAGGTTTAGGGTTTAATTTAAGGTTTAAAGTGTTTAGGGTTTAA
* * *
4997949 TTTAGGGTTTA-AAGGTTTGGGGTTTAATTTAGGGTTTAGAGTGTTTAGGGTTTAA
1 TTTAGGGTTTAGAAGGTTTAGGGTTTAATTTAAGGTTTAAAGTGTTTAGGGTTTAA
4998004 GAGTTTTAGG
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
55 40 0.80
56 10 0.20
ACGTcount: A:0.23, C:0.00, G:0.31, T:0.46
Consensus pattern (56 bp):
TTTAGGGTTTAGAAGGTTTAGGGTTTAATTTAAGGTTTAAAGTGTTTAGGGTTTAA
Found at i:4998045 original size:16 final size:15
Alignment explanation
Indices: 4997893--4998046 Score: 75
Period size: 16 Copynumber: 10.7 Consensus size: 15
4997883 GGGTTTTGTT
* *
4997893 TTTAGGTTTTAGAGGG
1 TTTAGGGTTTA-AGGA
4997909 TTTAGGGTTT-A--A
1 TTTAGGGTTTAAGGA
*
4997921 TTTAAGGTTTAAAGTG-
1 TTTAGGGTTT-AAG-GA
4997937 TTTAGGGTTT-A--A
1 TTTAGGGTTTAAGGA
4997949 TTTAGGGTTTAAAGG-
1 TTTAGGGTTT-AAGGA
*
4997964 TTTGGGGTTT-A--A
1 TTTAGGGTTTAAGGA
4997976 TTTAGGGTTTAGAGTG-
1 TTTAGGGTTTA-AG-GA
*
4997992 TTTAGGGTTTAAGAGT
1 TTTAGGGTTTAAG-GA
*
4998008 TTTAGGG-TT-AGGT
1 TTTAGGGTTTAAGGA
*
4998021 TTTAAGGTTTGAAGGA
1 TTTAGGGTTT-AAGGA
4998037 TTTAGGGTTT
1 TTTAGGGTTT
4998047 CAATTTCGAA
Statistics
Matches: 108, Mismatches: 10, Indels: 40
0.68 0.06 0.25
Matches are distributed among these distances:
12 28 0.26
13 9 0.08
14 9 0.08
15 14 0.13
16 48 0.44
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (15 bp):
TTTAGGGTTTAAGGA
Found at i:4999484 original size:12 final size:12
Alignment explanation
Indices: 4999451--4999496 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
4999441 CTGGTAAAGG
*
4999451 GGTGGCTAGTCT
1 GGTGGCTGGTCT
*
4999463 GGTGACTGGTCT
1 GGTGGCTGGTCT
*
4999475 GGTGGTTGGTCT
1 GGTGGCTGGTCT
*
4999487 AGTGGCTGGT
1 GGTGGCTGGT
4999497 TACAAGGGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 28 1.00
ACGTcount: A:0.07, C:0.13, G:0.46, T:0.35
Consensus pattern (12 bp):
GGTGGCTGGTCT
Found at i:4999764 original size:28 final size:28
Alignment explanation
Indices: 4999727--4999799 Score: 94
Period size: 28 Copynumber: 2.6 Consensus size: 28
4999717 TGGTTGGATC
* *
4999727 AAATTAGGCTT-GAAGCCCAATTGAGTCA
1 AAATTGGGCTTAG-AGCCCAATTGAATCA
*
4999755 AAATTGGGCTTAGAGCCCAGTTGAATCA
1 AAATTGGGCTTAGAGCCCAATTGAATCA
*
4999783 AAATTGGGCCTAGAGCC
1 AAATTGGGCTTAGAGCC
4999800 TAGTCGAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 39 0.98
29 1 0.03
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.23
Consensus pattern (28 bp):
AAATTGGGCTTAGAGCCCAATTGAATCA
Found at i:4999815 original size:28 final size:28
Alignment explanation
Indices: 4999752--4999808 Score: 87
Period size: 28 Copynumber: 2.0 Consensus size: 28
4999742 CCCAATTGAG
* *
4999752 TCAAAATTGGGCTTAGAGCCCAGTTGAA
1 TCAAAATTGGGCCTAGAGCCCAGTCGAA
*
4999780 TCAAAATTGGGCCTAGAGCCTAGTCGAA
1 TCAAAATTGGGCCTAGAGCCCAGTCGAA
4999808 T
1 T
4999809 TAGAATTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (28 bp):
TCAAAATTGGGCCTAGAGCCCAGTCGAA
Found at i:5000292 original size:35 final size:35
Alignment explanation
Indices: 5000216--5000292 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
5000206 ACTACTACTT
* * *
5000216 AGAAGTAAAGAGATCGAGATTGAACTGCAAGTCAA
1 AGAAATAAAGAGACCGAGATTAAACTGCAAGTCAA
* * *
5000251 AAAAATAAAGAGACCGAGATTAAATTGCAAGTCAG
1 AGAAATAAAGAGACCGAGATTAAACTGCAAGTCAA
5000286 AGAAATA
1 AGAAATA
5000293 CTAAAGAACG
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.51, C:0.10, G:0.22, T:0.17
Consensus pattern (35 bp):
AGAAATAAAGAGACCGAGATTAAACTGCAAGTCAA
Found at i:5000445 original size:205 final size:206
Alignment explanation
Indices: 5000212--5000858 Score: 664
Period size: 206 Copynumber: 3.1 Consensus size: 206
5000202 TTAAACTACT
* *
5000212 ACTTAGAAGTAAAGAGATCGAGATTGAACTGCAAGTCAA-AAAAATAAAGAGACCGAGATTAAAT
1 ACTTAGAAGTAAAAAGATCGAGATTGAACTGCGAGTCAAGAAAAATAAAGAGACCGAGATTAAAT
* *
5000276 TGCAAGTCAGAGAAATACTAAAGAACGGGATTAAACCACAACTTAGAATTAAAAAGAATC-AGGA
66 TGCAAGTCAGAGAAATAATAAAGAACAGGATTAAACCACAACTTAGAATTAAAAAG-ATCGA-GA
* * * * *
5000340 TTGAACTACGAGTCAAGAAAAATAAAAATACTGGGATTAAACTGCAAGTCAGAAAATGAGAATTG
129 TTGAACCACGAGTCAAAAAAAATAAAAAGACCGGGATTAAACCGCAAGTCAGAAAATGAGAATTG
* *
5000405 GGTTAAAATCG-C
194 GGATAAAATCGTA
** * * *
5000417 ACTTAGAAGTAAAAAGATCGAGATTGAACTATGAGTTAAGAAAAATAAAAAGACCCAGATTAAAT
1 ACTTAGAAGTAAAAAGATCGAGATTGAACTGCGAGTCAAGAAAAATAAAGAGACCGAGATTAAAT
* * * * **
5000482 CGCAAGTCAGAGAAATAATAAGGATCAGGATTAAATCATGACTTAGAATTAAAAAGATCGAGATT
66 TGCAAGTCAGAGAAATAATAAAGAACAGGATTAAACCACAACTTAGAATTAAAAAGATCGAGATT
* * * * *
5000547 GAACCACGAGTCAAAAAAAATAAAGAGACCGGGATTAAACCGTAAGTTAGAGAATGAGGATTGGG
131 GAACCACGAGTCAAAAAAAATAAAAAGACCGGGATTAAACCGCAAGTCAGAAAATGAGAATTGGG
5000612 ATAAAATCGTA
196 ATAAAATCGTA
* * * *
5000623 ACTTAGAATTAAAAAGATC-AGGATTGAACCGCGAGTCAAGAAAAATTAAGAGATCG-GAATTAA
1 ACTTAGAAGTAAAAAGATCGA-GATTGAACTGCGAGTCAAGAAAAATAAAGAGACCGAG-ATTAA
* * * * * * *** * * *
5000686 ACTGTAAGTCAGAGAAATAATGAGGATCAGGATTAAATCGTGACTTAAAATTAAAAAGATTGGGA
64 ATTGCAAGTCAGAGAAATAATAAAGAACAGGATTAAACCACAACTTAGAATTAAAAAGATCGAGA
* * * ** * ** *
5000751 TTGAACCAGTGAGTCCAAAAAAATAAAGAGACTAGGATTAAATCATAAGTTAGAGAAA-GA-ATG
129 TTGAACCA-CGAGTCAAAAAAAATAAAAAGACCGGGATTAAACCGCAAGTCAGA-AAATGAGA--
* *
5000814 ATTGAGATAAAATCGTG
190 ATTGGGATAAAATCGTA
5000831 ACTTAGAAG-AAAAAGATC-ATGATTGAAC
1 ACTTAGAAGTAAAAAGATCGA-GATTGAAC
5000859 AGCAAGTTAG
Statistics
Matches: 377, Mismatches: 56, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
205 106 0.28
206 187 0.50
207 59 0.16
208 25 0.07
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.21
Consensus pattern (206 bp):
ACTTAGAAGTAAAAAGATCGAGATTGAACTGCGAGTCAAGAAAAATAAAGAGACCGAGATTAAAT
TGCAAGTCAGAGAAATAATAAAGAACAGGATTAAACCACAACTTAGAATTAAAAAGATCGAGATT
GAACCACGAGTCAAAAAAAATAAAAAGACCGGGATTAAACCGCAAGTCAGAAAATGAGAATTGGG
ATAAAATCGTA
Found at i:5000548 original size:105 final size:105
Alignment explanation
Indices: 5000176--5000858 Score: 518
Period size: 105 Copynumber: 6.6 Consensus size: 105
5000166 TTAAACTATG
* * * *
5000176 AGTCAGAAAAAAAATAAGGATCGGGATTAAA-CTACT-ACTTAGAAGTAAAGAGATCGAGATTGA
1 AGTCAGAGAAATAATAAGGATCGGGATTAAATC-A-TGACTTAGAATTAAAAAGATCGAGATTGA
** * *
5000239 ACTGCAAGTCAA-AAAAATAAAGAGACCGAGATTAAATTGCA
64 ACCACGAGTCAAGAAAAATAAAGAGACCGAGATTAAATCGCA
* * * * **
5000280 AGTCAGAGAAATACTAAAGAACGGGATTAAACCACAACTTAGAATTAAAAAGAATC-AGGATTGA
1 AGTCAGAGAAATAATAAGGATCGGGATTAAATCATGACTTAGAATTAAAAAG-ATCGA-GATTGA
* * * * *
5000344 ACTACGAGTCAAGAAAAATAAAAATACTGGGATTAAA-CTGCA
64 ACCACGAGTCAAGAAAAATAAAGAGACCGAGATTAAATC-GCA
* * * *
5000386 AGTC--AG-AA-AATGAGAATTGGG-TTAAA--ATCGCACTTAGAAGTAAAAAGATCGAGATTGA
1 AGTCAGAGAAATAATAAGGATCGGGATTAAATCAT-G-ACTTAGAATTAAAAAGATCGAGATTGA
* * * * *
5000444 ACTATGAGTTAAGAAAAATAAAAAGACCCAGATTAAATCGCA
64 ACCACGAGTCAAGAAAAATAAAGAGACCGAGATTAAATCGCA
*
5000486 AGTCAGAGAAATAATAAGGATCAGGATTAAATCATGACTTAGAATTAAAAAGATCGAGATTGAAC
1 AGTCAGAGAAATAATAAGGATCGGGATTAAATCATGACTTAGAATTAAAAAGATCGAGATTGAAC
* * * *
5000551 CACGAGTCAAAAAAAATAAAGAGACCGGGATTAAACCGTA
66 CACGAGTCAAGAAAAATAAAGAGACCGAGATTAAATCGCA
* * * * * *
5000591 AGTTAGAG----AATGAGGATTGGGATAAAATCGTAACTTAGAATTAAAAAGATC-AGGATTGAA
1 AGTCAGAGAAATAATAAGGATCGGGATTAAATCATGACTTAGAATTAAAAAGATCGA-GATTGAA
* * * *
5000651 CCGCGAGTCAAGAAAAATTAAGAGATCG-GAATTAAA-CTGTA
65 CCACGAGTCAAGAAAAATAAAGAGACCGAG-ATTAAATC-GCA
* * * * * *
5000692 AGTCAGAGAAATAATGAGGATCAGGATTAAATCGTGACTTAAAATTAAAAAGATTGGGATTGAAC
1 AGTCAGAGAAATAATAAGGATCGGGATTAAATCATGACTTAGAATTAAAAAGATCGAGATTGAAC
* * **
5000757 CAGTGAGTCCAA-AAAAATAAAGAGA-CTAGGATTAAATCATA
66 CA-CGAGT-CAAGAAAAATAAAGAGACCGA-GATTAAATCGCA
* * * * * * *
5000798 AGTTAGAGAAAGAAT---GATTGAGATAAAATCGTGACTTAGAA-GAAAAAGATC-ATGATTGAA
1 AGTCAGAGAAATAATAAGGATCGGGATTAAATCATGACTTAGAATTAAAAAGATCGA-GATTGAA
5000858 C
65 C
5000859 AGCAAGTTAG
Statistics
Matches: 470, Mismatches: 78, Indels: 64
0.77 0.13 0.10
Matches are distributed among these distances:
99 1 0.00
100 50 0.11
101 106 0.23
102 25 0.05
103 25 0.05
104 53 0.11
105 138 0.29
106 65 0.14
107 7 0.01
ACGTcount: A:0.48, C:0.11, G:0.21, T:0.21
Consensus pattern (105 bp):
AGTCAGAGAAATAATAAGGATCGGGATTAAATCATGACTTAGAATTAAAAAGATCGAGATTGAAC
CACGAGTCAAGAAAAATAAAGAGACCGAGATTAAATCGCA
Found at i:5002252 original size:8 final size:7
Alignment explanation
Indices: 5002231--5002269 Score: 53
Period size: 8 Copynumber: 5.4 Consensus size: 7
5002221 TCTGAATCAC
5002231 TTTCTTT
1 TTTCTTT
5002238 TTT-TTT
1 TTTCTTT
5002244 TTTACTTT
1 TTT-CTTT
5002252 TTTCTTT
1 TTTCTTT
5002259 CTTTCTTT
1 -TTTCTTT
5002267 TTT
1 TTT
5002270 TAAGCAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 6 0.21
7 10 0.34
8 13 0.45
ACGTcount: A:0.03, C:0.13, G:0.00, T:0.85
Consensus pattern (7 bp):
TTTCTTT
Found at i:5006644 original size:15 final size:15
Alignment explanation
Indices: 5006606--5006644 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
5006596 GTATCAATTT
*
5006606 TTTTTCAAAATAAAA
1 TTTTCCAAAATAAAA
*
5006621 -TTTCTAAAATAAAA
1 TTTTCCAAAATAAAA
5006635 TTTTCCAAAA
1 TTTTCCAAAA
5006645 GTATTTTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTTCCAAAATAAAA
Found at i:5006687 original size:71 final size:73
Alignment explanation
Indices: 5006548--5006691 Score: 193
Period size: 71 Copynumber: 2.0 Consensus size: 73
5006538 TTTTTATTTT
* ***
5006548 TTTCTTAAGATAAAATTTTCAAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTTTTCA
1 TTTCTTAAAATAAAATTTTCAAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTCCCTTCA
5006613 AAATAAAA
66 AAATAAAA
* * * * *
5006621 TTTC-TAAAATAAAATTTTCCAAAAGTATTTTTG-GAGAAAGTTGAAAGTATCAATTTCCCTTGA
1 TTTCTTAAAATAAAATTTTCAAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTCCCTTCA
5006684 AAATAAAA
66 AAATAAAA
5006692 AGATTTAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
71 32 0.52
72 26 0.42
73 4 0.06
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (73 bp):
TTTCTTAAAATAAAATTTTCAAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTCCCTTCA
AAATAAAA
Found at i:5006737 original size:121 final size:118
Alignment explanation
Indices: 5006615--5006873 Score: 307
Period size: 121 Copynumber: 2.2 Consensus size: 118
5006605 TTTTTTCAAA
*
5006615 ATAAAA-TTTC-T-AAAATAAAATTTTCCAAAAG-TATTTTT--GGAGAAAGTTGAAAGTATCAA
1 ATAAAATTTTCTTGAAAATAAAATTTTCCAAAAGATATTTTTGAGGA-AAAATTGAAAGTATCAA
*
5006674 TTTCCCTTGAAAATAAAAAGATTTAAAAAATTATATTTTTAGGAAAAAGTTGAAAGT
65 TTTCCCTTGAAAATAAAAAGATTTAAAAAA-TAT-TTTTGAGG-AAAAGTTGAAAGT
* * * *
5006731 ATAAAATTTTCTTGAAAATAAATTTTTCTATAAGATATTTTTGAGGAAAAATTGAAAGTTTCAAT
1 ATAAAATTTTCTTGAAAATAAAATTTTCCAAAAGATATTTTTGAGGAAAAATTGAAAGTATCAAT
** ****
5006796 TTTTCTTGAAAATAAATTTTTTTAAAAAATATTTTTGAGGAAAAGTTGAAAGT
66 TTCCCTTGAAAATAAAAAGATTTAAAAAATATTTTTGAGGAAAAGTTGAAAGT
* *
5006849 ATCAATTTTTCTT-AAAATAAAATTT
1 ATAAAATTTTCTTGAAAATAAAATTT
5006874 CTAAAATAAA
Statistics
Matches: 122, Mismatches: 15, Indels: 11
0.82 0.10 0.07
Matches are distributed among these distances:
116 6 0.05
117 15 0.12
118 25 0.20
119 24 0.20
120 10 0.08
121 39 0.32
122 3 0.02
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (118 bp):
ATAAAATTTTCTTGAAAATAAAATTTTCCAAAAGATATTTTTGAGGAAAAATTGAAAGTATCAAT
TTCCCTTGAAAATAAAAAGATTTAAAAAATATTTTTGAGGAAAAGTTGAAAGT
Found at i:5006800 original size:59 final size:59
Alignment explanation
Indices: 5006626--5006879 Score: 259
Period size: 59 Copynumber: 4.3 Consensus size: 59
5006616 TAAAATTTCT
* * * * **
5006626 AAAATAAAATTTTC-CAAAAGTATTTTT--GGAGAAAGTTGAAAGTATCAATTTCCCTTG
1 AAAATAAATTTTTCTAAAAAATATTTTTGAGGA-AAAATTGAAAGTATCAATTTTTCTTG
*** * * *
5006683 AAAATAAAAAGATT-TAAAAAATTATATTTTTAGGAAAAAGTTGAAAGTATAAAATTTTCTTG
1 AAAAT-AAATTTTTCTAAAAAA-TAT-TTTTGAGGAAAAA-TTGAAAGTATCAATTTTTCTTG
* * *
5006745 AAAATAAATTTTTCTATAAGATATTTTTGAGGAAAAATTGAAAGTTTCAATTTTTCTTG
1 AAAATAAATTTTTCTAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTTCTTG
* *
5006804 AAAATAAATTTTTTTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-
1 AAAATAAATTTTTCTAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTTCTTG
*
5006862 AAAATAAA-ATTTCTAAAA
1 AAAATAAATTTTTCTAAAA
5006880 TAAAAATTAT
Statistics
Matches: 164, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
57 13 0.08
58 18 0.11
59 75 0.46
60 16 0.10
61 11 0.07
62 31 0.19
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (59 bp):
AAAATAAATTTTTCTAAAAAATATTTTTGAGGAAAAATTGAAAGTATCAATTTTTCTTG
Found at i:5006887 original size:15 final size:15
Alignment explanation
Indices: 5006856--5006884 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
5006846 AGTATCAATT
5006856 TTTCTTAAAATAAAA
1 TTTCTTAAAATAAAA
5006871 TTTC-TAAAATAAAA
1 TTTCTTAAAATAAAA
5006885 ATTATCAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (15 bp):
TTTCTTAAAATAAAA
Found at i:5006995 original size:58 final size:56
Alignment explanation
Indices: 5006871--5007000 Score: 208
Period size: 58 Copynumber: 2.3 Consensus size: 56
5006861 TAAAATAAAA
*
5006871 TTTC-TAAAATAAAAATTATCAAAAAATATTTTGAGAAAAATTGAAAGTACCAATT
1 TTTCTTAAAATAAAAATTATCAAAAAATATTTTAAGAAAAATTGAAAGTACCAATT
*
5006926 TTTCTTAAAAATAAAAATTATCAAAAAAATATTTTAAGAAAAAGTTGAAAGTATCAATT
1 TTTCTT-AAAATAAAAATTATC-AAAAAATATTTTAAGAAAAA-TTGAAAGTACCAATT
5006985 TTTCTTAAAATAAAAA
1 TTTCTTAAAATAAAAA
5007001 CTCCTAAATG
Statistics
Matches: 69, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
55 4 0.06
56 1 0.01
57 15 0.22
58 29 0.42
59 20 0.29
ACGTcount: A:0.54, C:0.06, G:0.06, T:0.34
Consensus pattern (56 bp):
TTTCTTAAAATAAAAATTATCAAAAAATATTTTAAGAAAAATTGAAAGTACCAATT
Found at i:5007068 original size:250 final size:250
Alignment explanation
Indices: 5006546--5007045 Score: 614
Period size: 250 Copynumber: 2.0 Consensus size: 250
5006536 TATTTTTATT
* * * *
5006546 TTTTTCTT-AAGATAAA-ATTTTCAAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTT
1 TTTTTCTTGAAAATAAATTTTTTTAAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTC
* * * * *
5006609 TTCAAAATAAAATTTCTAAAATAAAATTTTCCAAAAGTATTTTTGGAGAAAGTTGAAAGTATCAA
66 TTCAAAATAAAATTTCTAAAATAAAATTATCAAAAAATATTTTTGGAGAAAATTGAAAGTACCAA
* *
5006674 TTTCCCTTGAAAATAAAAAGATTTAAAAAATTATATTTTTAGGAAAAAGTTGAAAGTATAAAATT
131 TTTCCCTTAAAAATAAAAAGATTTAAAAAA-TATATTTTTAAGAAAAAGTTGAAAGTATAAAATT
*** ** * * *
5006739 TTCTTGAAAATAAATTTTTCTATAAGATATTTTTGAGGAAAAATTGAAAGTTTCAA
195 TTCTTGAAAATAAATAACTCTATAAGATAGCTTTAAAGAAAAATTGAAAGTATCAA
* *
5006795 TTTTTCTTGAAAATAAATTTTTTTAAAAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTC
1 TTTTTCTTGAAAATAAATTTTTTTAAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTC
5006860 TT-AAAATAAAATTTCTAAAATAAAAATTATCAAAAAATA-TTTT-GAGAAAAATTGAAAGTACC
66 TTCAAAATAAAATTTCTAAAAT-AAAATTATCAAAAAATATTTTTGGAG-AAAATTGAAAGTACC
** *
5006922 AATTTTTCTTAAAAAT-AAAA-ATTATCAAAAAA-ATA-TTTTAAGAAAAAGTTGAAAGTATCAA
129 AATTTCCCTTAAAAATAAAAAGATT-T-AAAAAATATATTTTTAAGAAAAAGTTGAAAGTATAAA
* * *
5006983 TTTTTCTT-AAAATAAA-AACTC-CTAA-AT-GCTTTAAAGAAAAGTTGAAAGTATCAA
192 ATTTTCTTGAAAATAAATAACTCTATAAGATAGCTTTAAAGAAAAATTGAAAGTATCAA
5007037 TTTTTCTTG
1 TTTTTCTTG
5007046 TACAAAAGTA
Statistics
Matches: 218, Mismatches: 27, Indels: 19
0.83 0.10 0.07
Matches are distributed among these distances:
242 30 0.14
243 2 0.01
244 3 0.01
245 2 0.01
246 8 0.04
247 31 0.14
248 6 0.03
249 16 0.07
250 62 0.28
251 58 0.27
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.38
Consensus pattern (250 bp):
TTTTTCTTGAAAATAAATTTTTTTAAAAAATATTTTTGAGAAAAAGTTAAAAGTATCAATTTTTC
TTCAAAATAAAATTTCTAAAATAAAATTATCAAAAAATATTTTTGGAGAAAATTGAAAGTACCAA
TTTCCCTTAAAAATAAAAAGATTTAAAAAATATATTTTTAAGAAAAAGTTGAAAGTATAAAATTT
TCTTGAAAATAAATAACTCTATAAGATAGCTTTAAAGAAAAATTGAAAGTATCAA
Found at i:5013895 original size:20 final size:20
Alignment explanation
Indices: 5013870--5013915 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
5013860 AATGTAAATA
* * *
5013870 AAATAAATAAATAAATAAGT
1 AAATAAACAAACAAAAAAGT
5013890 AAATAAACAAACAAAAAAGT
1 AAATAAACAAACAAAAAAGT
5013910 ATAATA
1 A-AATA
5013916 TATGACATAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (20 bp):
AAATAAACAAACAAAAAAGT
Found at i:5015611 original size:8 final size:8
Alignment explanation
Indices: 5015600--5015715 Score: 72
Period size: 8 Copynumber: 15.5 Consensus size: 8
5015590 AAAATTTAAA
*
5015600 TTTTAAGG
1 TTTTAGGG
*
5015608 TTTT-GGA
1 TTTTAGGG
5015615 TTTTAGGG
1 TTTTAGGG
5015623 TTTTAGGG
1 TTTTAGGG
5015631 -TTT-GGG
1 TTTTAGGG
5015637 ATTTTAGGG
1 -TTTTAGGG
5015646 TTTTAGGG
1 TTTTAGGG
* **
5015654 TTTCA-AA
1 TTTTAGGG
*
5015661 TTTTAGAG
1 TTTTAGGG
*
5015669 -TTTAGGA
1 TTTTAGGG
5015676 TTTTAGGG
1 TTTTAGGG
*
5015684 -TTTA--A
1 TTTTAGGG
5015689 TTTTAGGG
1 TTTTAGGG
5015697 -TTTAGAGG
1 TTTTAG-GG
5015705 TTTT-GGG
1 TTTTAGGG
5015712 TTTT
1 TTTT
5015716 GATTTTAAGG
Statistics
Matches: 84, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
6 7 0.08
7 32 0.38
8 39 0.46
9 6 0.07
ACGTcount: A:0.18, C:0.01, G:0.30, T:0.51
Consensus pattern (8 bp):
TTTTAGGG
Found at i:5015626 original size:23 final size:23
Alignment explanation
Indices: 5015600--5015656 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
5015590 AAAATTTAAA
* *
5015600 TTTTAAGGTTTTGGATTTTAGGG
1 TTTTAGGGTTTGGGATTTTAGGG
5015623 TTTTAGGGTTTGGGATTTTAGGG
1 TTTTAGGGTTTGGGATTTTAGGG
5015646 TTTTAGGGTTT
1 TTTTAGGGTTT
5015657 CAAATTTTAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.14, C:0.00, G:0.33, T:0.53
Consensus pattern (23 bp):
TTTTAGGGTTTGGGATTTTAGGG
Found at i:5015663 original size:23 final size:23
Alignment explanation
Indices: 5015614--5015671 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 23
5015604 AAGGTTTTGG
***
5015614 ATTTTAGGGTTTTAGGGTTTGGG
1 ATTTTAGGGTTTTAGGGTTTCAA
5015637 ATTTTAGGGTTTTAGGGTTTCAA
1 ATTTTAGGGTTTTAGGGTTTCAA
*
5015660 ATTTTAGAGTTT
1 ATTTTAGGGTTT
5015672 AGGATTTTAG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.19, C:0.02, G:0.29, T:0.50
Consensus pattern (23 bp):
ATTTTAGGGTTTTAGGGTTTCAA
Found at i:5015664 original size:15 final size:14
Alignment explanation
Indices: 5015646--5015700 Score: 67
Period size: 15 Copynumber: 3.9 Consensus size: 14
5015636 GATTTTAGGG
5015646 TTTTAGGGTTTCAAA
1 TTTTAGGGTTT-AAA
* *
5015661 TTTTAGAGTTTAGGA
1 TTTTAGGGTTTA-AA
5015676 TTTTAGGGTTT-AA
1 TTTTAGGGTTTAAA
5015689 TTTTAGGGTTTA
1 TTTTAGGGTTTA
5015701 GAGGTTTTGG
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
13 12 0.35
14 1 0.03
15 21 0.62
ACGTcount: A:0.24, C:0.02, G:0.24, T:0.51
Consensus pattern (14 bp):
TTTTAGGGTTTAAA
Found at i:5015721 original size:29 final size:28
Alignment explanation
Indices: 5015598--5015995 Score: 105
Period size: 30 Copynumber: 14.0 Consensus size: 28
5015588 TAAAAATTTA
* *
5015598 AATTTTAAGGTTTTGGATTTTAGGGTTTT
1 AATTTTAGGGTTTAGGATTTTAGGG-TTT
** *
5015627 AGGGTTT-GGGATTTTAGGGTTTTAGGGTTT
1 A-ATTTTAGGG--TTTAGGATTTTAGGGTTT
*
5015657 CAAATTTTAGAGTTTAGGATTTTAGGGTTT
1 --AATTTTAGGGTTTAGGATTTTAGGGTTT
*
5015687 AATTTTAGGGTTTAGAGGTTTT-GGGTTTT
1 AATTTTAGGGTTTAG-GATTTTAGGG-TTT
* * * **
5015716 GATTTTAAGGTTTAGTG-TTTAAGGGCTGG
1 AATTTTAGGGTTTAG-GATTTTAGGG-TTT
** *
5015745 AA-TTTAAAGTTTGGGATTTTA--G---
1 AATTTTAGGGTTTAGGATTTTAGGGTTT
* * *
5015767 -ATTTTTGGGTTT-TGAATTTAGGGTTT
1 AATTTTAGGGTTTAGGATTTTAGGGTTT
*
5015793 CAATTTTAGTGTTTA-GATGTTTTAGGGATTT
1 -AATTTTAGGGTTTAGGA--TTTTAGGG-TTT
* * **
5015824 GATTTTAGGGTTTAGAGAGTTTAATGTTT
1 AATTTTAGGGTTTAG-GATTTTAGGGTTT
* * * * *
5015853 CATTTTTAAGGTTCAGAGAGTTTGGGGTTT
1 -AATTTTAGGGTTTAG-GATTTTAGGGTTT
** * * *
5015883 CGTTTTTAAGGTTCA-GAGGTTTAGGGTTT
1 -AATTTTAGGGTTTAGGA-TTTTAGGGTTT
* *
5015912 AA-TTTAGGGTTTA-GAGGTTTGGGGTTT
1 AATTTTAGGGTTTAGGA-TTTTAGGGTTT
*
5015939 AA-TTTAAGGTTTA-GAGTATTTAGGGTTT
1 AATTTTAGGGTTTAGGA-T-TTTAGGGTTT
*
5015967 ACGAGTTTTAGGGTTT-GG-TTTTAAGGTTT
1 A--A-TTTTAGGGTTTAGGATTTTAGGGTTT
5015996 GAAGGATTTA
Statistics
Matches: 283, Mismatches: 54, Indels: 64
0.71 0.13 0.16
Matches are distributed among these distances:
21 7 0.02
22 7 0.02
23 1 0.00
26 1 0.00
27 38 0.13
28 58 0.20
29 52 0.18
30 85 0.30
31 19 0.07
32 15 0.05
ACGTcount: A:0.21, C:0.02, G:0.29, T:0.48
Consensus pattern (28 bp):
AATTTTAGGGTTTAGGATTTTAGGGTTT
Found at i:5015860 original size:30 final size:29
Alignment explanation
Indices: 5015783--5015966 Score: 119
Period size: 30 Copynumber: 6.3 Consensus size: 29
5015773 GGGTTTTGAA
* * *
5015783 TTTAGGGTTTCAATTTT-AGTGTTTAGATGT
1 TTTAGGGTTTCATTTTTAAG-GTTCAGA-GG
* * *
5015813 TTTAGGGATTTGA-TTTTAGGGTTTAGAGAG
1 TTTAGGG-TTTCATTTTTAAGGTTCAGAG-G
**
5015843 TTTAATGTTTCATTTTTAAGGTTCAGAGAG
1 TTTAGGGTTTCATTTTTAAGGTTCAGAG-G
* *
5015873 TTTGGGGTTTCGTTTTTAAGGTTCAGAGG
1 TTTAGGGTTTCATTTTTAAGGTTCAGAGG
* * *
5015902 TTTAGGGTTT-A-ATTTAGGGTTTAGAGG
1 TTTAGGGTTTCATTTTTAAGGTTCAGAGG
* * * *
5015929 TTTGGGGTTT-A-ATTTAAGGTTTAGAGTA
1 TTTAGGGTTTCATTTTTAAGGTTCAGAG-G
5015957 TTTAGGGTTT
1 TTTAGGGTTT
5015967 ACGAGTTTTA
Statistics
Matches: 128, Mismatches: 21, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
27 37 0.29
28 9 0.07
29 15 0.12
30 62 0.48
31 5 0.04
ACGTcount: A:0.21, C:0.03, G:0.29, T:0.47
Consensus pattern (29 bp):
TTTAGGGTTTCATTTTTAAGGTTCAGAGG
Found at i:5015910 original size:15 final size:15
Alignment explanation
Indices: 5015887--5016011 Score: 79
Period size: 16 Copynumber: 8.7 Consensus size: 15
5015877 GGGTTTCGTT
* *
5015887 TTTAAGGTTCAGAGG
1 TTTAGGGTTTAGAGG
5015902 TTTAGGGTTTA-A--
1 TTTAGGGTTTAGAGG
5015914 TTTAGGGTTTAGAGG
1 TTTAGGGTTTAGAGG
*
5015929 TTTGGGGTTTA-A--
1 TTTAGGGTTTAGAGG
* *
5015941 TTTAAGGTTTAGAGTA
1 TTTAGGGTTTAGAG-G
*
5015957 TTTAGGGTTTACGAGT
1 TTTAGGGTTTA-GAGG
*
5015973 TTTAGGGTTT-G-GT
1 TTTAGGGTTTAGAGG
*
5015986 TTTAAGGTTT-GAAGG
1 TTTAGGGTTTAG-AGG
5016001 ATTTAGGGTTT
1 -TTTAGGGTTT
5016012 CAATTTCGGA
Statistics
Matches: 89, Mismatches: 10, Indels: 21
0.74 0.08 0.17
Matches are distributed among these distances:
12 20 0.22
13 14 0.16
14 3 0.03
15 20 0.22
16 29 0.33
17 3 0.03
ACGTcount: A:0.22, C:0.02, G:0.32, T:0.45
Consensus pattern (15 bp):
TTTAGGGTTTAGAGG
Found at i:5015919 original size:12 final size:12
Alignment explanation
Indices: 5015902--5015951 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
5015892 GGTTCAGAGG
5015902 TTTAGGGTTTAA
1 TTTAGGGTTTAA
5015914 TTTAGGGTTTAGA
1 TTTAGGGTTTA-A
*
5015927 GGTTTGGGGTTTAA
1 --TTTAGGGTTTAA
*
5015941 TTTAAGGTTTA
1 TTTAGGGTTTA
5015952 GAGTATTTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 20 0.62
13 1 0.03
14 1 0.03
15 10 0.31
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (12 bp):
TTTAGGGTTTAA
Found at i:5016005 original size:45 final size:43
Alignment explanation
Indices: 5015913--5016011 Score: 119
Period size: 45 Copynumber: 2.3 Consensus size: 43
5015903 TTAGGGTTTA
* *
5015913 ATTTAGGGTTTAGAGGTTTGGGGTTTAATTTAAGGTTTAGAGT
1 ATTTAGGGTTTAGAGGTTTAGGGTTTAATTTAAGGTTTAGAGG
* **
5015956 ATTTAGGGTTTACGAGTTTTAGGGTTTGGTTTTAAGGTTT-GAAGG
1 ATTTAGGGTTTA-GAGGTTTAGGGTTT-AATTTAAGGTTTAG-AGG
5016001 ATTTAGGGTTT
1 ATTTAGGGTTT
5016012 CAATTTCGGA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 12 0.25
44 13 0.27
45 23 0.48
ACGTcount: A:0.21, C:0.01, G:0.32, T:0.45
Consensus pattern (43 bp):
ATTTAGGGTTTAGAGGTTTAGGGTTTAATTTAAGGTTTAGAGG
Found at i:5017674 original size:28 final size:28
Alignment explanation
Indices: 5017585--5017674 Score: 92
Period size: 28 Copynumber: 3.2 Consensus size: 28
5017575 TTTGGGCCTG
* * *
5017585 GTTGGATC-AAATTAGGCCTGAAGCCCA
1 GTTGAATCAAAATTAGGCTTGGAGCCCA
* * * * *
5017612 ATTGAGTCAAAATCAGGTTTGGAGCCTA
1 GTTGAATCAAAATTAGGCTTGGAGCCCA
5017640 GTTGAATCAAAATTAGGCTTGGAGCCCA
1 GTTGAATCAAAATTAGGCTTGGAGCCCA
*
5017668 GTCGAAT
1 GTTGAAT
5017675 TAGAGTCAGA
Statistics
Matches: 48, Mismatches: 14, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
27 5 0.10
28 43 0.90
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (28 bp):
GTTGAATCAAAATTAGGCTTGGAGCCCA
Found at i:5037980 original size:11 final size:11
Alignment explanation
Indices: 5037964--5037993 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
5037954 TATATTTCAC
5037964 ACAAGGAAGAT
1 ACAAGGAAGAT
5037975 ACAAGGAAGAT
1 ACAAGGAAGAT
5037986 ACAAGGAA
1 ACAAGGAA
5037994 AAGAAATTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.57, C:0.10, G:0.27, T:0.07
Consensus pattern (11 bp):
ACAAGGAAGAT
Found at i:5040622 original size:56 final size:55
Alignment explanation
Indices: 5040503--5040625 Score: 135
Period size: 56 Copynumber: 2.2 Consensus size: 55
5040493 TTAAAGCTCG
** *
5040503 TCAGTATA-AATTTATATGTTTTAATTTTCTCACCTATACCGACGACTAGCACTCA
1 TCAGTATAGAA-TTATATGTTTTAATTTTCTCACCTATAAAGACAACTAGCACTCA
* * *
5040558 TCAATATAGAATTATATGTTTTAACTTTTCTTACCTATAAAGACAATTAACGC-CT-A
1 TCAGTATAGAATTATATGTTTTAA-TTTTCTCACCTATAAAGACAACT-A-GCACTCA
5040614 TCAGTATAGAAT
1 TCAGTATAGAAT
5040626 AGTAATTTTT
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
55 20 0.35
56 32 0.56
57 3 0.05
58 2 0.04
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.38
Consensus pattern (55 bp):
TCAGTATAGAATTATATGTTTTAATTTTCTCACCTATAAAGACAACTAGCACTCA
Found at i:5046767 original size:12 final size:12
Alignment explanation
Indices: 5046750--5046783 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5046740 TCAGCGCTAG
5046750 CAAATTTCATAA
1 CAAATTTCATAA
* *
5046762 CAAATTTTAAAA
1 CAAATTTCATAA
5046774 CAAATTTCAT
1 CAAATTTCAT
5046784 CCACCATCAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.15, G:0.00, T:0.35
Consensus pattern (12 bp):
CAAATTTCATAA
Found at i:5047486 original size:16 final size:16
Alignment explanation
Indices: 5047462--5047492 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5047452 TTTGGATCTC
*
5047462 TTTTTTCATTTTTTTA
1 TTTTCTCATTTTTTTA
5047478 TTTTCTCATTTTTTT
1 TTTTCTCATTTTTTT
5047493 TTCTTTTTTC
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:0.10, C:0.10, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTTCTCATTTTTTTA
Found at i:5047491 original size:18 final size:18
Alignment explanation
Indices: 5047470--5047508 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
5047460 TCTTTTTTCA
5047470 TTTTTTTATTTTCTCATT
1 TTTTTTTATTTTCTCATT
* *
5047488 TTTTTTTCTTTTTTCATT
1 TTTTTTTATTTTCTCATT
5047506 TTT
1 TTT
5047509 CATCCAGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.08, C:0.10, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTTTTATTTTCTCATT
Found at i:5050196 original size:15 final size:15
Alignment explanation
Indices: 5050176--5050222 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
5050166 TTGTAAGTGT
5050176 AATGAATGAGAATGC
1 AATGAATGAGAATGC
*
5050191 AATGAATGAGAATGT
1 AATGAATGAGAATGC
5050206 AATGAATGAGAAATGC
1 AATGAATGAG-AATGC
5050222 A
1 A
5050223 TGTATGCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.49, C:0.04, G:0.26, T:0.21
Consensus pattern (15 bp):
AATGAATGAGAATGC
Found at i:5053696 original size:58 final size:57
Alignment explanation
Indices: 5053393--5053785 Score: 564
Period size: 57 Copynumber: 6.7 Consensus size: 57
5053383 TTTTTTTTAG
5053393 GGAAAATTGATACTTTCAACTTTTTCCC-AAAAATA-TTTTTTGAAAATTTCGATTT-TCAA
1 GGAAAATTGATACTTTCAAC-TTTTCCCTAAAAATATTTTTTTG-AAATTT--ATTTCT-AA
**
5053452 GGAAAATTGATACTTTCAACTTTT-CCTCAAAAACCCTTTTTTTGAAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCT-AAAAA-TATTTTTTTG-AAATTTATTTCTAA
*
5053511 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTTGAAATTTTGATTT-TCAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGAAA-TTT-ATTTCT-AA
*
5053571 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTA-TTCTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTC-TAA
5053628 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGAAATTTATTTCTAA
*
5053686 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTCTAA
5053743 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATATTTTTT
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATAT-TTTTTT
5053786 TGAATTTTTT
Statistics
Matches: 309, Mismatches: 10, Indels: 31
0.88 0.03 0.09
Matches are distributed among these distances:
56 2 0.01
57 97 0.31
58 68 0.22
59 85 0.28
60 43 0.14
61 14 0.05
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (57 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGAAATTTATTTCTAA
Found at i:5053887 original size:22 final size:23
Alignment explanation
Indices: 5053857--5053903 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
5053847 ACATAAACCT
* * *
5053857 AATCTAATAAATAAA-AAATAAA
1 AATCAAATAAACAAATAAACAAA
5053879 AATCAAATAAACAAATAAACAAA
1 AATCAAATAAACAAATAAACAAA
5053902 AA
1 AA
5053904 AAAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.17
Consensus pattern (23 bp):
AATCAAATAAACAAATAAACAAA
Found at i:5054222 original size:20 final size:20
Alignment explanation
Indices: 5054197--5054234 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
5054187 GAACACCGGT
*
5054197 GTCGGATTCTGGAAATTTTC
1 GTCGGAATCTGGAAATTTTC
5054217 GTCGGAATCTGGAAATTT
1 GTCGGAATCTGGAAATTT
5054235 CGCCGGAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.13, G:0.26, T:0.37
Consensus pattern (20 bp):
GTCGGAATCTGGAAATTTTC
Found at i:5054241 original size:19 final size:20
Alignment explanation
Indices: 5054199--5054242 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
5054189 ACACCGGTGT
* *
5054199 CGGATTCTGGAAATTTTCGT
1 CGGAATCTGGAAATTTTCGC
5054219 CGGAATCTGGAAA-TTTCGC
1 CGGAATCTGGAAATTTTCGC
5054238 CGGAA
1 CGGAA
5054243 GTTGGCCGGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (20 bp):
CGGAATCTGGAAATTTTCGC
Found at i:5054321 original size:19 final size:19
Alignment explanation
Indices: 5054275--5054322 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
5054265 TCTGGGATTC
* *
5054275 TTCGCCGGAAACTGGACTG
1 TTCGCCGGAAACTGCAATG
* * *
5054294 GTCGTCGGAAACTTCAATG
1 TTCGCCGGAAACTGCAATG
5054313 TTCGCCGGAA
1 TTCGCCGGAA
5054323 TTGTTGCCGG
Statistics
Matches: 22, Mismatches: 7, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.23, C:0.25, G:0.29, T:0.23
Consensus pattern (19 bp):
TTCGCCGGAAACTGCAATG
Found at i:5054341 original size:31 final size:31
Alignment explanation
Indices: 5054299--5054364 Score: 91
Period size: 31 Copynumber: 2.1 Consensus size: 31
5054289 GACTGGTCGT
*
5054299 CGGAAACTTC-AATGTTCGCCGGAATTGTT-GC
1 CGGAAAATTCAAAT-TTCGCCGGAATT-TTCGC
5054330 CGGAAAATTCAAATTTCGCCGGAATTTTCGC
1 CGGAAAATTCAAATTTCGCCGGAATTTTCGC
5054361 CGGA
1 CGGA
5054365 TTCTGGAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 2 0.06
31 27 0.84
32 3 0.09
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (31 bp):
CGGAAAATTCAAATTTCGCCGGAATTTTCGC
Found at i:5054859 original size:3 final size:3
Alignment explanation
Indices: 5054853--5054890 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
5054843 ATTACAAAAA
*
5054853 AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
5054891 ATATATAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:5054967 original size:3 final size:3
Alignment explanation
Indices: 5054959--5054999 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
5054949 AAAGATATAC
5054959 ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA CATA A-A ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
5055000 CCAAAGAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.11
3 28 0.80
4 3 0.09
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:5059294 original size:49 final size:49
Alignment explanation
Indices: 5059222--5059321 Score: 191
Period size: 49 Copynumber: 2.0 Consensus size: 49
5059212 ATCAAAGTAA
*
5059222 CTAAATCATTATCTGAATTCACAGCTGCAATATTGTCATCATTTGAACT
1 CTAAATCATTATCTGAATTCACAGCTGCAATATTGCCATCATTTGAACT
5059271 CTAAATCATTATCTGAATTCACAGCTGCAATATTGCCATCATTTGAACT
1 CTAAATCATTATCTGAATTCACAGCTGCAATATTGCCATCATTTGAACT
5059320 CT
1 CT
5059322 TACTTTTCTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (49 bp):
CTAAATCATTATCTGAATTCACAGCTGCAATATTGCCATCATTTGAACT
Found at i:5066799 original size:105 final size:105
Alignment explanation
Indices: 5066606--5066807 Score: 228
Period size: 105 Copynumber: 1.9 Consensus size: 105
5066596 TATGTTTTAA
*
5066606 TTTTCTCACCTATACCGACGGCTAGCACTCATCAATATAGAATTATATGTTTTAACTTTTCTTAC
1 TTTTCTCACCTATACCGACGGCTAGCACTCATCAATATAGAATTATATGTTTTAAATTTTCTTAC
* * *
5066671 CTATAAAGACAATTAACGCCTATCAGTATAGACTAGTAAT
66 CTATAAAGACAATTAAAGACTATCAATATAGACTAGTAAT
* * * * * *
5066711 TTTTCTTACCTATATCGA-TGCTTAGCATTCATCAATATA-AACTTATATTTTTTAAATTTTTTT
1 TTTTCTCACCTATACCGACGGC-TAGCACTCATCAATATAGAA-TTATATGTTTTAAATTTTCTT
* ** ***
5066774 ACTTATATCGATGGTTAAAGACTATCAATATAGA
64 ACCTATAAAGACAATTAAAGACTATCAATATAGA
5066808 ATTGTATACT
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
104 4 0.05
105 75 0.95
ACGTcount: A:0.33, C:0.17, G:0.09, T:0.40
Consensus pattern (105 bp):
TTTTCTCACCTATACCGACGGCTAGCACTCATCAATATAGAATTATATGTTTTAAATTTTCTTAC
CTATAAAGACAATTAAAGACTATCAATATAGACTAGTAAT
Found at i:5066801 original size:56 final size:54
Alignment explanation
Indices: 5066741--5066890 Score: 149
Period size: 55 Copynumber: 2.7 Consensus size: 54
5066731 CTTAGCATTC
* **
5066741 ATCAATATAAACTTATATTTTTTAAATTTTTTTACTTATATCGATGGTTAAAGACT
1 ATCAATATAAACTTATATATTTT-AATTTTTTTA-TTATATCGACAGTTAAAGACT
* * ** * *
5066797 ATCAATATAGAA-TTGTATACTTTAATTTCCTTATCTATACCGACAGTTAAAGATT
1 ATCAATATA-AACTTATATATTTTAATTTTTTTAT-TATATCGACAGTTAAAGACT
* * *
5066852 ATTAGTATAAACTTATATGTTTTAATTTTTTTATTATAT
1 ATCAATATAAACTTATATATTTTAATTTTTTTATTATAT
5066891 TTTATTGATA
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
54 7 0.09
55 48 0.65
56 17 0.23
57 2 0.03
ACGTcount: A:0.35, C:0.09, G:0.07, T:0.48
Consensus pattern (54 bp):
ATCAATATAAACTTATATATTTTAATTTTTTTATTATATCGACAGTTAAAGACT
Found at i:5067792 original size:68 final size:68
Alignment explanation
Indices: 5067714--5067840 Score: 193
Period size: 68 Copynumber: 1.9 Consensus size: 68
5067704 ATCGAAGGTA
* *
5067714 AGAAGGTAATCATCCATTCATATACCAA-TAGAAATAATTTTATAAACATCTTATTCATTTATGT
1 AGAAAGTAATCATCCATTCATATACCAATTA-AAATAATTTTATAAACATCCTATTCATTTATGT
5067778 ATAC
65 ATAC
* * *
5067782 AGAAAGTAATCATCTATTTATATATCAATTAAAATAATTTTATAAACATCCTATTCATT
1 AGAAAGTAATCATCCATTCATATACCAATTAAAATAATTTTATAAACATCCTATTCATT
5067841 AGTGTAATGC
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
68 51 0.96
69 2 0.04
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.39
Consensus pattern (68 bp):
AGAAAGTAATCATCCATTCATATACCAATTAAAATAATTTTATAAACATCCTATTCATTTATGTA
TAC
Found at i:5074272 original size:21 final size:20
Alignment explanation
Indices: 5074225--5074275 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 20
5074215 ATTTCAGTTG
*
5074225 AATAAACAAGAAAGAGGTAAA
1 AATAAA-AAGAAAGAGCTAAA
*
5074246 AGATAAAAAGAAAGTAGCTCAA
1 A-ATAAAAAGAAAG-AGCTAAA
5074268 AATAAAAA
1 AATAAAAA
5074276 TAAGAAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
21 15 0.58
22 11 0.42
ACGTcount: A:0.67, C:0.06, G:0.16, T:0.12
Consensus pattern (20 bp):
AATAAAAAGAAAGAGCTAAA
Found at i:5074684 original size:17 final size:17
Alignment explanation
Indices: 5074662--5074694 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
5074652 GAATGGTGGA
5074662 TTATTGAAGGCGTTTTC
1 TTATTGAAGGCGTTTTC
5074679 TTATTGAAGGCGTTTT
1 TTATTGAAGGCGTTTT
5074695 TGACTAGAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.09, G:0.24, T:0.48
Consensus pattern (17 bp):
TTATTGAAGGCGTTTTC
Found at i:5075133 original size:61 final size:62
Alignment explanation
Indices: 5075012--5075149 Score: 151
Period size: 61 Copynumber: 2.2 Consensus size: 62
5075002 GCTAAAAATG
* * *
5075012 CCTTAAATAATCTCTTTAAATTTTTTATTAGTAGATTATTCAAAGCATTTTTTGCCAAAACA
1 CCTTAAATAATCTCTCTAAATTTTTTATGAGTAGATTATTCAAAGCATTTTTTACCAAAACA
*
5075074 CCTTAAATAATC-CTCTACAATTTTTTA-GAG-AGGATTATTC-AAG-GTTTTTCTACCAAAAAC
1 CCTTAAATAATCTCTCTA-AATTTTTTATGAGTA-GATTATTCAAAGCATTTTT-TACC-AAAAC
5075134 A
62 A
* *
5075135 TCTTCAATAATCTCT
1 CCTTAAATAATCTCT
5075150 TCCCATTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
59 5 0.08
60 7 0.11
61 30 0.46
62 23 0.35
ACGTcount: A:0.35, C:0.17, G:0.07, T:0.41
Consensus pattern (62 bp):
CCTTAAATAATCTCTCTAAATTTTTTATGAGTAGATTATTCAAAGCATTTTTTACCAAAACA
Found at i:5079582 original size:121 final size:123
Alignment explanation
Indices: 5079441--5079702 Score: 284
Period size: 121 Copynumber: 2.1 Consensus size: 123
5079431 TTTGGTAAAA
* ** *** *
5079441 AAAAATACCTTAAATAATCCCCTCCCATTTTTTTTTA-GGATTATTCAAGTCATTTTTTTG-AGA
1 AAAAATACCTTGAATAATCCCCT-CCAACTTTTACGAGGGATTATTCAAGT-AATTTTTTGCA-A
* * *
5079504 A-AACGCCTTGAATAATCTCTTAGAAAA-ATTAAATGGGGTTATTCAAGGTATTTATGA-C-
63 ATAAAGCCTTGAATAATCTCTTACAAAATATTAAATAGGGTTATTCAAGGTATTT-TGAGCT
** *
5079562 AAAAATACCTTGAATAATCCCCTTTAACTTTTACGAGGGGATTATTGAAGTAATTTTTTGCCAAA
1 AAAAATACCTTGAATAATCCCCTCCAACTTTTACGA-GGGATTATTCAAGTAATTTTTTG-CAAA
* *
5079627 TAAAGCCTTGAATAATCTCTTACAAAATATTAAATAGGGTTATTGAAGGTATTTTTAGCT
64 TAAAGCCTTGAATAATCTCTTACAAAATATTAAATAGGGTTATTCAAGGTATTTTGAGCT
*
5079687 AAAAACACCTTGAATA
1 AAAAATACCTTGAATA
5079703 GTTAATGGAT
Statistics
Matches: 117, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
120 6 0.05
121 30 0.26
122 14 0.12
123 27 0.23
124 25 0.21
125 15 0.13
ACGTcount: A:0.37, C:0.14, G:0.13, T:0.36
Consensus pattern (123 bp):
AAAAATACCTTGAATAATCCCCTCCAACTTTTACGAGGGATTATTCAAGTAATTTTTTGCAAATA
AAGCCTTGAATAATCTCTTACAAAATATTAAATAGGGTTATTCAAGGTATTTTGAGCT
Found at i:5086134 original size:27 final size:29
Alignment explanation
Indices: 5086090--5086148 Score: 79
Period size: 27 Copynumber: 2.1 Consensus size: 29
5086080 ATAATAAATA
*
5086090 TATATATATTTATGTATT-A-AAAATTTT
1 TATATATATTTATATATTAACAAAATTTT
5086117 TATATAT-TTATATATATTAACAAAATTTT
1 TATATATATT-TATATATTAACAAAATTTT
5086146 TAT
1 TAT
5086149 TAAGGTTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
26 2 0.07
27 14 0.50
28 1 0.04
29 11 0.39
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (29 bp):
TATATATATTTATATATTAACAAAATTTT
Found at i:5086892 original size:29 final size:28
Alignment explanation
Indices: 5086846--5086901 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
5086836 TTTTAAAGTG
*
5086846 ATCATTTAAATATTAATTTTTTTAATTTA
1 ATCATTTAAATATTAA-TTTGTTAATTTA
*
5086875 ATCATTTAAGT-TTGAATTTGTTAATTT
1 ATCATTTAAATATT-AATTTGTTAATTT
5086902 TTTGGTTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 12 0.50
29 12 0.50
ACGTcount: A:0.34, C:0.04, G:0.05, T:0.57
Consensus pattern (28 bp):
ATCATTTAAATATTAATTTGTTAATTTA
Found at i:5090866 original size:41 final size:41
Alignment explanation
Indices: 5090809--5090889 Score: 153
Period size: 41 Copynumber: 2.0 Consensus size: 41
5090799 ATAATTAAAC
5090809 AACTACTACTATATTTGATTATTAAAAGTAATGAAAGTAAT
1 AACTACTACTATATTTGATTATTAAAAGTAATGAAAGTAAT
*
5090850 AACTACTACTATATTTGATTATTAAAAGTAATTAAAGTAA
1 AACTACTACTATATTTGATTATTAAAAGTAATGAAAGTAA
5090890 GGTGGAATCA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
41 39 1.00
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (41 bp):
AACTACTACTATATTTGATTATTAAAAGTAATGAAAGTAAT
Found at i:5092257 original size:15 final size:15
Alignment explanation
Indices: 5092229--5092261 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
5092219 CTGAAAGGAG
5092229 AGCAGCAAAAGAAGC
1 AGCAGCAAAAGAAGC
5092244 AGCAG-AAAAGGAAGC
1 AGCAGCAAAA-GAAGC
5092259 AGC
1 AGC
5092262 TAAAGCCCAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.52, C:0.18, G:0.30, T:0.00
Consensus pattern (15 bp):
AGCAGCAAAAGAAGC
Found at i:5098858 original size:12 final size:12
Alignment explanation
Indices: 5098841--5098866 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5098831 ACTTGAATTA
5098841 ATAATAAAAAAG
1 ATAATAAAAAAG
5098853 ATAATAAAAAAG
1 ATAATAAAAAAG
5098865 AT
1 AT
5098867 CCTTTCATTC
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:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (12 bp):
ATAATAAAAAAG
Found at i:5103961 original size:8 final size:7
Alignment explanation
Indices: 5103948--5104007 Score: 50
Period size: 8 Copynumber: 7.7 Consensus size: 7
5103938 ATGATATAAA
5103948 AAAAAATT
1 AAAAAA-T
5103956 AAAAAAT
1 AAAAAAT
5103963 AAATAAAT
1 AAA-AAAT
5103971 AATAAAAAT
1 -A-AAAAAT
5103980 AAAAACAT
1 AAAAA-AT
5103988 AAAATAA-
1 AAAA-AAT
5103995 AATAAAAT
1 AA-AAAAT
5104003 AAAAA
1 AAAAA
5104008 CCTACGAAAC
Statistics
Matches: 45, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
7 15 0.33
8 22 0.49
9 6 0.13
10 2 0.04
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (7 bp):
AAAAAAT
Found at i:5103972 original size:48 final size:46
Alignment explanation
Indices: 5103916--5104007 Score: 112
Period size: 48 Copynumber: 2.0 Consensus size: 46
5103906 ATACTGAGTC
* * * * *
5103916 AAATAATAATAATAATAATAATATGATATAAAAAAAAATTAAAAAAT
1 AAATAATAATAAAAATAAAAACATAAAATAAAAAAAAA-TAAAAAAT
*
5103963 AAATAAATAATAAAAATAAAAACATAAAATAAAATAAAATAAAAA
1 AAAT-AATAATAAAAATAAAAACATAAAATAAAAAAAAATAAAAA
5104008 CCTACGAAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
47 10 0.26
48 28 0.74
ACGTcount: A:0.75, C:0.01, G:0.01, T:0.23
Consensus pattern (46 bp):
AAATAATAATAAAAATAAAAACATAAAATAAAAAAAAATAAAAAAT
Found at i:5103976 original size:18 final size:18
Alignment explanation
Indices: 5103955--5104005 Score: 54
Period size: 17 Copynumber: 2.8 Consensus size: 18
5103945 AAAAAAAAAT
5103955 TAAAAAATAAATAAATAA
1 TAAAAAATAAATAAATAA
5103973 T-AAAAATAAA-AACATAA
1 TAAAAAATAAATAA-ATAA
5103990 -AATAAAATAAAATAAA
1 TAA-AAAAT-AAATAAA
5104006 AACCTACGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
16 2 0.07
17 14 0.50
18 6 0.21
19 4 0.14
20 2 0.07
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (18 bp):
TAAAAAATAAATAAATAA
Found at i:5103991 original size:14 final size:12
Alignment explanation
Indices: 5103943--5104007 Score: 66
Period size: 11 Copynumber: 5.6 Consensus size: 12
5103933 ATAATATGAT
5103943 ATAAAAAA-AAA
1 ATAAAAAATAAA
*
5103954 TTAAAAAAT-AA
1 ATAAAAAATAAA
*
5103965 ATAAATAATAAAA
1 ATAAAAAAT-AAA
5103978 ATAAAAACATAAA
1 ATAAAAA-ATAAA
5103991 AT--AAAATAAA
1 ATAAAAAATAAA
5104001 ATAAAAA
1 ATAAAAA
5104008 CCTACGAAAC
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
10 7 0.16
11 19 0.43
12 3 0.07
13 13 0.30
14 2 0.05
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (12 bp):
ATAAAAAATAAA
Found at i:5105273 original size:16 final size:16
Alignment explanation
Indices: 5105252--5105282 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
5105242 TAAATTTTTG
5105252 ATCTATTCATGTTCAC
1 ATCTATTCATGTTCAC
5105268 ATCTATTCATGTTCA
1 ATCTATTCATGTTCA
5105283 TCGTGTGGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.23, G:0.06, T:0.45
Consensus pattern (16 bp):
ATCTATTCATGTTCAC
Found at i:5108251 original size:23 final size:23
Alignment explanation
Indices: 5108220--5108268 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
5108210 AAATACCATA
*
5108220 TTAAAATAATATAATTTA-AAATT
1 TTAAAATAA-ATAATATATAAATT
* *
5108243 TTAATATAAATTATATATAAATT
1 TTAAAATAAATAATATATAAATT
5108266 TTA
1 TTA
5108269 CAAAAGTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
TTAAAATAAATAATATATAAATT
Found at i:5116323 original size:58 final size:58
Alignment explanation
Indices: 5116258--5116376 Score: 211
Period size: 58 Copynumber: 2.1 Consensus size: 58
5116248 TTTATCTATA
* * *
5116258 ATTAATTGAATTCATTAATATCATAAATTTATGAATGATTAAATTCATAAATAGTTAG
1 ATTAATTGAATTCATTAATATCACAAATTCATGAATGATTAAACTCATAAATAGTTAG
5116316 ATTAATTGAATTCATTAATATCACAAATTCATGAATGATTAAACTCATAAATAGTTAG
1 ATTAATTGAATTCATTAATATCACAAATTCATGAATGATTAAACTCATAAATAGTTAG
5116374 ATT
1 ATT
5116377 CGTTCATTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
58 58 1.00
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (58 bp):
ATTAATTGAATTCATTAATATCACAAATTCATGAATGATTAAACTCATAAATAGTTAG
Found at i:5120030 original size:26 final size:24
Alignment explanation
Indices: 5119993--5120049 Score: 78
Period size: 26 Copynumber: 2.3 Consensus size: 24
5119983 ATTATTAAAT
5119993 ATAAATATTTTTAATATTTCAATA
1 ATAAATATTTTTAATATTTCAATA
* *
5120017 ATAAATAGTATTTTATTATTTTAATA
1 ATAAATA-T-TTTTAATATTTCAATA
5120043 ATAAATA
1 ATAAATA
5120050 ATAACATATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 7 0.24
25 1 0.03
26 21 0.72
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (24 bp):
ATAAATATTTTTAATATTTCAATA
Found at i:5120070 original size:38 final size:38
Alignment explanation
Indices: 5120016--5120119 Score: 124
Period size: 38 Copynumber: 2.7 Consensus size: 38
5120006 ATATTTCAAT
*
5120016 AATAA-ATAGTATTTTATTATTTTAATAATAAATAATA
1 AATAATATAATATTTTATTATTTTAATAATAAATAATA
* * *
5120053 ACAT-ATATAATATTTTATTATTTTGATAATTAATATTA
1 A-ATAATATAATATTTTATTATTTTAATAATAAATAATA
5120091 AATAATATAATATTATTATT-TTCTTAATA
1 AATAATATAATATT-TTATTATT-TTAATA
5120120 TGAATTTTTA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
37 4 0.07
38 43 0.75
39 10 0.18
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (38 bp):
AATAATATAATATTTTATTATTTTAATAATAAATAATA
Found at i:5120133 original size:38 final size:38
Alignment explanation
Indices: 5120016--5120134 Score: 120
Period size: 38 Copynumber: 3.2 Consensus size: 38
5120006 ATATTTCAAT
* * *
5120016 AATAA-ATAGTATTTTATTATTTTAATAATAAATAATA
1 AATAATATAATATTTTATTATTTTAATAATGAATATTA
* *
5120053 ACAT-ATATAATATTTTATTATTTTGATAATTAATATTA
1 A-ATAATATAATATTTTATTATTTTAATAATGAATATTA
* *
5120091 AATAATATAATATTATTATT-TTCTTAAT-ATGAATTTTT
1 AATAATATAATATT-TTATTATT-TTAATAATGAATATTA
5120129 AATAAT
1 AATAAT
5120135 TTCTTATTAT
Statistics
Matches: 69, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
37 4 0.06
38 56 0.81
39 9 0.13
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (38 bp):
AATAATATAATATTTTATTATTTTAATAATGAATATTA
Found at i:5120305 original size:15 final size:16
Alignment explanation
Indices: 5120269--5120306 Score: 60
Period size: 17 Copynumber: 2.4 Consensus size: 16
5120259 AATATAAAAT
5120269 ATAAATATTTTAATAGA
1 ATAAATATTTTAATA-A
5120286 ATAAATATTTTAAT-A
1 ATAAATATTTTAATAA
5120301 ATAAAT
1 ATAAAT
5120307 GTTACTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 7 0.33
17 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
ATAAATATTTTAATAA
Found at i:5120434 original size:19 final size:20
Alignment explanation
Indices: 5120410--5120449 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
5120400 TTATTTTAAG
*
5120410 TATTTTTATATTA-ATATAA
1 TATTTTAATATTACATATAA
5120429 TATTTTAATATTACATATAA
1 TATTTTAATATTACATATAA
5120449 T
1 T
5120450 TAAAATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTTAATATTACATATAA
Found at i:5120536 original size:26 final size:24
Alignment explanation
Indices: 5120473--5120540 Score: 82
Period size: 26 Copynumber: 2.7 Consensus size: 24
5120463 TTCTTGAATA
5120473 TTAATCATTTTAATAATAAATAATT
1 TTAAT-ATTTTAATAATAAATAATT
* *
5120498 TCAATATACTTAAATAATAAATAATTT
1 TTAATAT--TTTAATAATAAATAA-TT
5120525 TTAATATTTTAATAAT
1 TTAATATTTTAATAAT
5120541 TATATTAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 2 0.06
25 12 0.33
26 14 0.39
27 8 0.22
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TTAATATTTTAATAATAAATAATT
Found at i:5120686 original size:13 final size:14
Alignment explanation
Indices: 5120656--5120685 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5120646 TCAAAAAAAT
*
5120656 AAATATTTTTTAAA
1 AAATATTTTATAAA
5120670 AAATATTTTATAAA
1 AAATATTTTATAAA
5120684 AA
1 AA
5120686 TCAAATTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
AAATATTTTATAAA
Found at i:5130033 original size:19 final size:19
Alignment explanation
Indices: 5130006--5130065 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 19
5129996 AATTGTTGAG
*
5130006 GCCTAAATTTCATATTAAA
1 GCCTGAATTTCATATTAAA
*
5130025 GCCTGAATTTCATGTTAAA
1 GCCTGAATTTCATATTAAA
* * **
5130044 GCCAGAGTTTTGTATTAAA
1 GCCTGAATTTCATATTAAA
5130063 GCC
1 GCC
5130066 CAAAATTTAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (19 bp):
GCCTGAATTTCATATTAAA
Found at i:5131182 original size:13 final size:13
Alignment explanation
Indices: 5131166--5131190 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5131156 CAAAATCTAC
5131166 CCAAAAAAAAAAA
1 CCAAAAAAAAAAA
5131179 CCAAAAAAAAAA
1 CCAAAAAAAAAA
5131191 TCAAAACAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (13 bp):
CCAAAAAAAAAAA
Found at i:5131258 original size:14 final size:14
Alignment explanation
Indices: 5131241--5131267 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
5131231 CCAAAAAGAC
5131241 TAAACAAAAAAAAA
1 TAAACAAAAAAAAA
5131255 TAAACAAAAAAAA
1 TAAACAAAAAAAA
5131268 GAACTCTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (14 bp):
TAAACAAAAAAAAA
Found at i:5131544 original size:20 final size:20
Alignment explanation
Indices: 5131519--5131564 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
5131509 AATGTTAACA
5131519 AAAAAAGTTATTTTTATAGC
1 AAAAAAGTTATTTTTATAGC
5131539 AAAAAAGTTATTTTTATAGC
1 AAAAAAGTTATTTTTATAGC
5131559 AAAAAA
1 AAAAAA
5131565 AAAAAAAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (20 bp):
AAAAAAGTTATTTTTATAGC
Found at i:5131910 original size:22 final size:22
Alignment explanation
Indices: 5131871--5131913 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
5131861 ATGCATATAT
5131871 TTTAAAAAATAGGAAAATTAATC
1 TTTAAAAAATA-GAAAATTAATC
5131894 TTTAAAAAATA-ATAAATTAA
1 TTTAAAAAATAGA-AAATTAA
5131914 GAAAAATGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.05
22 7 0.37
23 11 0.58
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (22 bp):
TTTAAAAAATAGAAAATTAATC
Found at i:5144062 original size:16 final size:16
Alignment explanation
Indices: 5144041--5144075 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
5144031 TAAAATCATT
5144041 TTTTAAACATAAATCA
1 TTTTAAACATAAATCA
5144057 TTTTAAACATAAATCA
1 TTTTAAACATAAATCA
5144073 TTT
1 TTT
5144076 ACATAGCAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTTAAACATAAATCA
Found at i:5147802 original size:26 final size:27
Alignment explanation
Indices: 5147765--5147845 Score: 101
Period size: 26 Copynumber: 3.0 Consensus size: 27
5147755 ACCAAAATAC
* *
5147765 TTACTCTAAAAATTCATTGAATTTTTTA
1 TTACTCT-AAAATTCATTGAATCTTTAA
* *
5147793 TTCCTC-AAAATTCATTGAAACTTTAA
1 TTACTCTAAAATTCATTGAATCTTTAA
5147819 TTACTCTAAAATTCATTGAATCATTTA
1 TTACTCTAAAATTCATTGAATC-TTTA
5147846 CTTATACTGA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
26 22 0.49
27 14 0.31
28 9 0.20
ACGTcount: A:0.37, C:0.15, G:0.04, T:0.44
Consensus pattern (27 bp):
TTACTCTAAAATTCATTGAATCTTTAA
Found at i:5148074 original size:33 final size:32
Alignment explanation
Indices: 5148037--5148122 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 32
5148027 TAATCTAATT
*
5148037 ATCATAATTTAATCTCTTAGAAAATCTCCAAA
1 ATCATAATATAATCTCTTAGAAAATCTCCAAA
** *
5148069 GATCATAACCTAAGT-TTTTAGAAAATCTCCAAA
1 -ATCATAATATAA-TCTCTTAGAAAATCTCCAAA
* *
5148102 ATCATAGTATAAGCTCTTAGA
1 ATCATAATATAATCTCTTAGA
5148123 CACCCCACAT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
32 15 0.35
33 27 0.63
34 1 0.02
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (32 bp):
ATCATAATATAATCTCTTAGAAAATCTCCAAA
Found at i:5148122 original size:32 final size:33
Alignment explanation
Indices: 5148050--5148122 Score: 94
Period size: 33 Copynumber: 2.2 Consensus size: 33
5148040 ATAATTTAAT
*
5148050 CTCTTAGAAAATCTCCAAAGATCATAACCTAAG
1 CTCTTAGAAAATCTCCAAAGATCATAACATAAG
* * **
5148083 TTTTTAGAAAATCTCCAAA-ATCATAGTATAAG
1 CTCTTAGAAAATCTCCAAAGATCATAACATAAG
5148115 CTCTTAGA
1 CTCTTAGA
5148123 CACCCCACAT
Statistics
Matches: 33, Mismatches: 7, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
32 16 0.48
33 17 0.52
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.30
Consensus pattern (33 bp):
CTCTTAGAAAATCTCCAAAGATCATAACATAAG
Found at i:5151667 original size:20 final size:19
Alignment explanation
Indices: 5151621--5151667 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 19
5151611 AGAAAGGAGA
*
5151621 AAAAAAAAACTAAATAAAT
1 AAAAAAAAACTAAAAAAAT
5151640 AAATAAAAAAC-AAAAAGAAT
1 AAA-AAAAAACTAAAAA-AAT
*
5151660 TAAAAAAA
1 AAAAAAAA
5151668 GGGCTAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.81, C:0.04, G:0.02, T:0.13
Consensus pattern (19 bp):
AAAAAAAAACTAAAAAAAT
Found at i:5152755 original size:50 final size:47
Alignment explanation
Indices: 5152635--5152850 Score: 207
Period size: 49 Copynumber: 4.4 Consensus size: 47
5152625 AGATAAGATA
* ** * *
5152635 TTTAAAGTTTCAAAGGCTCTACTTATAAAGAGCCATTTCAAGCAAAAAT
1 TTTAAAGTTTCAAA-GCTATGTTTATAGA-AGCCATTTCAAGCAAAATT
* * *
5152684 TTTAAAGTTTCAAAGCTTATGTCTATAGCAAGTCATTTCAAGCAAGATT
1 TTTAAAGTTTCAAAGC-TATGTTTATAG-AAGCCATTTCAAGCAAAATT
* * *
5152733 TTCTTAAGTTTCAAAGTCTATGTTTATGAGGAGCCATTTCAAGCAAGATTTT
1 TT-TAAAGTTTCAAAG-CTATGTTTAT-AGAAGCCATTTCAAGCAA-A-ATT
* * *
5152785 TTTTAAGTTTCAAAGCCTTTGTTTATGGGAAGCCATTTCAAGCAAAATT
1 TTTAAAGTTTCAAAG-CTATGTTTAT-AGAAGCCATTTCAAGCAAAATT
5152834 TTTAAAGTTTCAAAGCT
1 TTTAAAGTTTCAAAGCT
5152851 TCTATTTATT
Statistics
Matches: 140, Mismatches: 20, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
48 4 0.03
49 54 0.39
50 36 0.26
51 42 0.30
52 4 0.03
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (47 bp):
TTTAAAGTTTCAAAGCTATGTTTATAGAAGCCATTTCAAGCAAAATT
Found at i:5152808 original size:51 final size:49
Alignment explanation
Indices: 5152664--5152871 Score: 219
Period size: 49 Copynumber: 4.2 Consensus size: 49
5152654 TACTTATAAA
* *
5152664 GAGCCATTTCAAGCAAAAATTTTAAAGTTTCAAAGCTTATGTCTAT-AG
1 GAGCCATTTCAAGCAAAATTTTTAAAGTTTCAAAGCTTATGTTTATGAG
* * * *
5152712 CAAGTCATTTCAAGCAAGATTTTCTTAAGTTTCAAAG-TCTATGTTTATGAG
1 -GAGCCATTTCAAGCAAAATTTT-TAAAGTTTCAAAGCT-TATGTTTATGAG
* *
5152763 GAGCCATTTCAAGCAAGATTTTTTTTAAGTTTCAAAGCCTT-TGTTTATG-G
1 GAGCCATTTCAAGCAA-A-ATTTTTAAAGTTTCAAAG-CTTATGTTTATGAG
* *
5152813 GAAGCCATTTCAAGCAAAATTTTTAAAGTTTCAAAGCTTCTATTTATTGA-
1 G-AGCCATTTCAAGCAAAATTTTTAAAGTTTCAAAGCTTATGTTTA-TGAG
5152863 GAGCCATTT
1 GAGCCATTT
5152872 TCAGATGGGA
Statistics
Matches: 135, Mismatches: 13, Indels: 22
0.79 0.08 0.13
Matches are distributed among these distances:
48 3 0.02
49 48 0.36
50 40 0.30
51 38 0.28
52 5 0.04
53 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.15, T:0.38
Consensus pattern (49 bp):
GAGCCATTTCAAGCAAAATTTTTAAAGTTTCAAAGCTTATGTTTATGAG
Found at i:5152835 original size:101 final size:98
Alignment explanation
Indices: 5152635--5152848 Score: 250
Period size: 101 Copynumber: 2.2 Consensus size: 98
5152625 AGATAAGATA
* * ** * *
5152635 TTTAAAGTTTCAAAGGCTCTACTTATAAAGAGCCATTTCAAGCAAAAATTTTAAAGTTTCAAAGC
1 TTTAAAGTTTCAAAGTCTATGTTTATGAGGAGCCATTTCAAGCAAAAATTTTAAAGTTTCAAAGC
* *
5152700 TTATGTCTATAGCAAGTCATTTCAAGCAAGATT
66 TTATGTCTATAGCAAGCCATTTCAAGCAAAATT
* ** *
5152733 TTCTTAAGTTTCAAAGTCTATGTTTATGAGGAGCCATTTCAAGCAAGATTTTTTTTAAGTTTCAA
1 TT-TAAAGTTTCAAAGTCTATGTTTATGAGGAGCCATTTCAAGCAA-A-AATTTTAAAGTTTCAA
* * *
5152798 AGCCTT-TGTTTATGGGAAGCCATTTCAAGCAAAATT
63 AG-CTTATGTCTATAGCAAGCCATTTCAAGCAAAATT
5152834 TTTAAAGTTTCAAAG
1 TTTAAAGTTTCAAAG
5152849 CTTCTATTTA
Statistics
Matches: 96, Mismatches: 16, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
98 2 0.02
99 36 0.38
100 13 0.14
101 42 0.44
102 3 0.03
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (98 bp):
TTTAAAGTTTCAAAGTCTATGTTTATGAGGAGCCATTTCAAGCAAAAATTTTAAAGTTTCAAAGC
TTATGTCTATAGCAAGCCATTTCAAGCAAAATT
Found at i:5153417 original size:17 final size:18
Alignment explanation
Indices: 5153378--5153420 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 18
5153368 GTTAAGGACC
5153378 AAATTAAAATAAATACAA
1 AAATTAAAATAAATACAA
*
5153396 TAATTAAAA-AAATA-ATA
1 AAATTAAAATAAATACA-A
5153413 AAATTAAA
1 AAATTAAA
5153421 CAATTAAGAG
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
16 1 0.05
17 13 0.59
18 8 0.36
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATTAAAATAAATACAA
Found at i:5155303 original size:14 final size:14
Alignment explanation
Indices: 5155240--5155310 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
5155230 TGAAAAAGTG
5155240 TAAAAAAATAATAA
1 TAAAAAAATAATAA
*
5155254 TAATAAAATGACA-AA
1 TAAAAAAAT-A-ATAA
* * *
5155269 T-GAAAAACAAGAA
1 TAAAAAAATAATAA
5155282 T-AAAAAATAATAA
1 TAAAAAAATAATAA
*
5155295 TAAAAAAATAAAAA
1 TAAAAAAATAATAA
5155309 TA
1 TA
5155311 TTTGAAGATG
Statistics
Matches: 45, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
12 1 0.02
13 14 0.31
14 25 0.56
15 4 0.09
16 1 0.02
ACGTcount: A:0.75, C:0.03, G:0.04, T:0.18
Consensus pattern (14 bp):
TAAAAAAATAATAA
Found at i:5158039 original size:15 final size:15
Alignment explanation
Indices: 5158021--5158051 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5158011 AACAACAACG
5158021 GTCTAAACAAGTTGA
1 GTCTAAACAAGTTGA
*
5158036 GTCTAAACAATTTGA
1 GTCTAAACAAGTTGA
5158051 G
1 G
5158052 CATCAATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (15 bp):
GTCTAAACAAGTTGA
Found at i:5160322 original size:17 final size:18
Alignment explanation
Indices: 5160287--5160328 Score: 68
Period size: 19 Copynumber: 2.3 Consensus size: 18
5160277 TAAAAAAATC
5160287 AAAAATCAAATAGCCTAAA
1 AAAAATCAAATAG-CTAAA
5160306 AAAAATCAAATAG-TAAA
1 AAAAATCAAATAGCTAAA
5160323 AAAAAT
1 AAAAAT
5160329 AGATAAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.43
19 13 0.57
ACGTcount: A:0.69, C:0.10, G:0.05, T:0.17
Consensus pattern (18 bp):
AAAAATCAAATAGCTAAA
Found at i:5161099 original size:16 final size:16
Alignment explanation
Indices: 5161078--5161126 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
5161068 TTTTATTATC
5161078 TATTCTTTTTAATAAT
1 TATTCTTTTTAATAAT
* * *
5161094 TTTTCTATTTT-TTACT
1 TATTCT-TTTTAATAAT
5161110 TATTCTTTTTAATAAT
1 TATTCTTTTTAATAAT
5161126 T
1 T
5161127 CTTTTATGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 4
0.71 0.17 0.11
Matches are distributed among these distances:
15 4 0.16
16 17 0.68
17 4 0.16
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (16 bp):
TATTCTTTTTAATAAT
Found at i:5161119 original size:32 final size:32
Alignment explanation
Indices: 5161078--5161139 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
5161068 TTTTATTATC
*
5161078 TATTCTTTTTAATAATT-TTTCTATTTTTTACT
1 TATTCTTTTTAATAATTCTTT-TATGTTTTACT
5161110 TATTCTTTTTAATAATTCTTTTATGTTTTA
1 TATTCTTTTTAATAATTCTTTTATGTTTTA
5161140 AGGAAACACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.23, C:0.08, G:0.02, T:0.68
Consensus pattern (32 bp):
TATTCTTTTTAATAATTCTTTTATGTTTTACT
Found at i:5161231 original size:48 final size:49
Alignment explanation
Indices: 5161105--5161246 Score: 196
Period size: 48 Copynumber: 2.9 Consensus size: 49
5161095 TTTCTATTTT
* * * *
5161105 TTACTTATTCTTTTTAATAATTCTTTTATGTTTTAAGGAAACACTCCCA
1 TTACCTATTCCTTTTAATAATTCTTTTATTTTTTAGGGAAACACTCCCA
* * *
5161154 TTACCTATTTCTTTTAATAATTTTTTTATTTTTTAGGGAAACACTCTC-
1 TTACCTATTCCTTTTAATAATTCTTTTATTTTTTAGGGAAACACTCCCA
* *
5161202 TTACCTATTCCTTTTAATAGTTCTCTTATTTTTTAGGGAAACACT
1 TTACCTATTCCTTTTAATAATTCTTTTATTTTTTAGGGAAACACT
5161247 TTTATTACTT
Statistics
Matches: 82, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
48 41 0.50
49 41 0.50
ACGTcount: A:0.26, C:0.16, G:0.07, T:0.51
Consensus pattern (49 bp):
TTACCTATTCCTTTTAATAATTCTTTTATTTTTTAGGGAAACACTCCCA
Found at i:5161281 original size:38 final size:38
Alignment explanation
Indices: 5161230--5161359 Score: 136
Period size: 38 Copynumber: 3.4 Consensus size: 38
5161220 AGTTCTCTTA
** * *
5161230 TTTTTTAGGGAAACACTTTTATTACTTATTCTCTTTTT
1 TTTTTTAAAGAAACACTTTCACTACTTATTCTCTTTTT
* *
5161268 TTTTTTAAAGAAACACTTTCACTACTTATTCTCCTATT
1 TTTTTTAAAGAAACACTTTCACTACTTATTCTCTTTTT
* ** * *
5161306 TTCTCCAAA-AAACACTTTCACTACTTATACTTTTTTT
1 TTTTTTAAAGAAACACTTTCACTACTTATTCTCTTTTT
**
5161343 TTTTTTTTAGAAACACT
1 TTTTTTAAAGAAACACT
5161360 AATGTTATGG
Statistics
Matches: 73, Mismatches: 18, Indels: 2
0.78 0.19 0.02
Matches are distributed among these distances:
37 28 0.38
38 45 0.62
ACGTcount: A:0.27, C:0.18, G:0.04, T:0.51
Consensus pattern (38 bp):
TTTTTTAAAGAAACACTTTCACTACTTATTCTCTTTTT
Found at i:5161522 original size:2 final size:2
Alignment explanation
Indices: 5161517--5161550 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5161507 AAAGTCACAA
*
5161517 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5161551 TTTTTCTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:5163525 original size:33 final size:33
Alignment explanation
Indices: 5163483--5163547 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
5163473 TGTTCTTTCA
5163483 TTGTTTGGAATTTTCAAACTGGTTGAAAATTAC
1 TTGTTTGGAATTTTCAAACTGGTTGAAAATTAC
5163516 TTGTTTGGAATTTTCAAACTGGTTGAAAATTA
1 TTGTTTGGAATTTTCAAACTGGTTGAAAATTA
5163548 TCTGGAACTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (33 bp):
TTGTTTGGAATTTTCAAACTGGTTGAAAATTAC
Done.