Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 87 of 125
Found at i:17080980 original size:22 final size:22
Alignment explanation
Indices: 17080928--17081005 Score: 69
Period size: 22 Copynumber: 3.7 Consensus size: 22
17080918 GGGTTTTCAA
*
17080928 TTAA-ATTT-AGGGTTTAGGGT
1 TTAAGATTTAAGGTTTTAGGGT
17080948 TT--GATTTAAGGTTTTAGGGT
1 TTAAGATTTAAGGTTTTAGGGT
*
17080968 TTAAGGTTTAAGGTTTATA--GT
1 TTAAGATTTAAGGTTT-TAGGGT
*
17080989 TTAGAGTTTTAAGGTTT
1 TTA-AGATTTAAGGTTT
17081006 AATGATTATG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
19 4 0.08
20 15 0.31
21 5 0.10
22 23 0.47
23 2 0.04
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (22 bp):
TTAAGATTTAAGGTTTTAGGGT
Found at i:17081006 original size:7 final size:7
Alignment explanation
Indices: 17080952--17081007 Score: 60
Period size: 7 Copynumber: 7.7 Consensus size: 7
17080942 TAGGGTTTGA
17080952 TTTAAGG
1 TTTAAGG
*
17080959 TTTTAGGG
1 -TTTAAGG
17080967 TTTAAGG
1 TTTAAGG
17080974 TTTAAGG
1 TTTAAGG
17080981 TTTATA-G
1 TTTA-AGG
*
17080988 TTTAGAGT
1 TTTA-AGG
17080996 TTTAAGG
1 TTTAAGG
17081003 TTTAA
1 TTTAA
17081008 TGATTATGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
7 30 0.73
8 11 0.27
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (7 bp):
TTTAAGG
Found at i:17081278 original size:16 final size:16
Alignment explanation
Indices: 17081257--17081289 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17081247 CTTTGAAAGC
17081257 AAATTGAAAACCTTTT
1 AAATTGAAAACCTTTT
*
17081273 AAATTGAAACCCTTTT
1 AAATTGAAAACCTTTT
17081289 A
1 A
17081290 TTTTCAAAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.42, C:0.15, G:0.06, T:0.36
Consensus pattern (16 bp):
AAATTGAAAACCTTTT
Found at i:17085171 original size:19 final size:19
Alignment explanation
Indices: 17085149--17085216 Score: 75
Period size: 19 Copynumber: 3.6 Consensus size: 19
17085139 AGGGATTATT
17085149 TTAGGGTTTGGTTTAAGGG
1 TTAGGGTTTGGTTTAAGGG
***
17085168 TTAGTAATTGG-TTAAGGG
1 TTAGGGTTTGGTTTAAGGG
*
17085186 TTGAGGGTTTGGTTTAAGGT
1 TT-AGGGTTTGGTTTAAGGG
*
17085206 TTATGGTTTGG
1 TTAGGGTTTGG
17085217 CAAAATTTTC
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
18 9 0.23
19 22 0.56
20 8 0.21
ACGTcount: A:0.18, C:0.00, G:0.38, T:0.44
Consensus pattern (19 bp):
TTAGGGTTTGGTTTAAGGG
Found at i:17085524 original size:26 final size:26
Alignment explanation
Indices: 17085495--17085583 Score: 99
Period size: 26 Copynumber: 3.4 Consensus size: 26
17085485 TAAATACAAT
**
17085495 CATGGTGGTTTAAAGTTTAAGGTTTG
1 CATGGTGGTTTAGGGTTTAAGGTTTG
* * *
17085521 CATGGTAGTTTGGGGTTTACA-ATTTG
1 CATGGTGGTTTAGGGTTTA-AGGTTTG
* *
17085547 TATGGTGGTTTAGGGTTTAGGGTTTG
1 CATGGTGGTTTAGGGTTTAAGGTTTG
17085573 CATGGTGGTTT
1 CATGGTGGTTT
17085584 GAGGTTTCAT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
26 49 0.98
27 1 0.02
ACGTcount: A:0.17, C:0.04, G:0.35, T:0.44
Consensus pattern (26 bp):
CATGGTGGTTTAGGGTTTAAGGTTTG
Found at i:17086854 original size:21 final size:21
Alignment explanation
Indices: 17086828--17086893 Score: 75
Period size: 21 Copynumber: 3.2 Consensus size: 21
17086818 ATTCTATGGG
*
17086828 TTGACTCTAGTTTGA-CATAGT
1 TTGACT-TATTTTGACCATAGT
*
17086849 TTGACTAATTTTGACCA-AGT
1 TTGACTTATTTTGACCATAGT
17086869 TTGACTTTATTTTGACCAT-GT
1 TTGAC-TTATTTTGACCATAGT
17086890 TTGA
1 TTGA
17086894 TCATGTGGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
20 14 0.36
21 25 0.64
ACGTcount: A:0.24, C:0.14, G:0.17, T:0.45
Consensus pattern (21 bp):
TTGACTTATTTTGACCATAGT
Found at i:17087951 original size:51 final size:51
Alignment explanation
Indices: 17087893--17088037 Score: 211
Period size: 51 Copynumber: 2.8 Consensus size: 51
17087883 CGAAAACAAA
* *
17087893 ATAAATAAAGCTAAACAATTAACTTAATTCAAGAGATAAACAATCATGAAG
1 ATAAATAAAACTAAACAGTTAACTTAATTCAAGAGATAAACAATCATGAAG
** * *
17087944 ATAAATAAAACTAAATGGTT-ACATTAATTCAAGAAATAAGCAATCATGAAG
1 ATAAATAAAACTAAACAGTTAAC-TTAATTCAAGAGATAAACAATCATGAAG
*
17087995 ATAAATAAAACTAAACAGTTAAATTAATTCAAGAGATAAACAA
1 ATAAATAAAACTAAACAGTTAACTTAATTCAAGAGATAAACAA
17088038 ATATGATAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
50 2 0.02
51 78 0.96
52 1 0.01
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.24
Consensus pattern (51 bp):
ATAAATAAAACTAAACAGTTAACTTAATTCAAGAGATAAACAATCATGAAG
Found at i:17088114 original size:5 final size:5
Alignment explanation
Indices: 17088089--17088134 Score: 65
Period size: 5 Copynumber: 8.6 Consensus size: 5
17088079 ATTAAGATAG
17088089 ATAACA ATAAA AGTGAAA ATAAA ATAAA ATAAA ATAAA ATAAA ATA
1 ATAA-A ATAAA A-T-AAA ATAAA ATAAA ATAAA ATAAA ATAAA ATA
17088135 TATACAAAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
5 28 0.74
6 6 0.16
7 4 0.11
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (5 bp):
ATAAA
Found at i:17088461 original size:42 final size:42
Alignment explanation
Indices: 17088415--17088520 Score: 144
Period size: 42 Copynumber: 2.6 Consensus size: 42
17088405 CTTAAAAAAA
* *
17088415 AAAAAAAAAAAAGGGCTCCTTCAACATGAAGGCATACAACTT
1 AAAAAAAAAAAAGGACTCCTTCAACATGAAGGCACACAACTT
* * *
17088457 AAAAAAAAATAAGGACTTCTTCAACATGAAGGCACATAACTT
1 AAAAAAAAAAAAGGACTCCTTCAACATGAAGGCACACAACTT
*
17088499 --AAAAAAATAAGGACTCCTTCAA
1 AAAAAAAAAAAAGGACTCCTTCAA
17088521 AACAAAGGTG
Statistics
Matches: 58, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
40 21 0.36
42 37 0.64
ACGTcount: A:0.51, C:0.18, G:0.12, T:0.19
Consensus pattern (42 bp):
AAAAAAAAAAAAGGACTCCTTCAACATGAAGGCACACAACTT
Found at i:17088503 original size:40 final size:40
Alignment explanation
Indices: 17088417--17088589 Score: 148
Period size: 40 Copynumber: 4.2 Consensus size: 40
17088407 TAAAAAAAAA
* * ** *
17088417 AAAAAAAAAAGGGCTCCTTCAACATGAAGGCATACAACTT
1 AAAAAAATAAGGACTCCTTCAACACAAAGGCACACAACTT
* ** *
17088457 AAAAAAAAATAAGGACTTCTTCAACATGAAGGCACATAACTT
1 --AAAAAAATAAGGACTCCTTCAACACAAAGGCACACAACTT
* ** *
17088499 AAAAAAATAAGGACTCCTTCAAAACAAAGGTGCATAACTT
1 AAAAAAATAAGGACTCCTTCAACACAAAGGCACACAACTT
* * ** * *
17088539 TAAAAAATAAGGGCTTATTCAACACAAAGACATACAACTTT
1 AAAAAAATAAGGACTCCTTCAACACAAAGGCACACAAC-TT
17088580 AAAAAAATAA
1 AAAAAAATAA
17088590 AGCCCTTTTG
Statistics
Matches: 108, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
40 62 0.57
41 11 0.10
42 35 0.32
ACGTcount: A:0.51, C:0.17, G:0.12, T:0.20
Consensus pattern (40 bp):
AAAAAAATAAGGACTCCTTCAACACAAAGGCACACAACTT
Found at i:17091917 original size:22 final size:22
Alignment explanation
Indices: 17091892--17091947 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
17091882 TTAGGTAGTA
*
17091892 AATGGGAAAATTGGTTGTACAT
1 AATGGGAAAATTGGTTATACAT
*
17091914 AATGGGAAAATTGGTTATAGAT
1 AATGGGAAAATTGGTTATACAT
17091936 AATGGGAAAATT
1 AATGGGAAAATT
17091948 TTTTGAATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.41, C:0.02, G:0.27, T:0.30
Consensus pattern (22 bp):
AATGGGAAAATTGGTTATACAT
Found at i:17095717 original size:21 final size:21
Alignment explanation
Indices: 17095691--17095774 Score: 168
Period size: 21 Copynumber: 4.0 Consensus size: 21
17095681 GCTCGAGTGT
17095691 AGAGCTTATGCTATGCATATG
1 AGAGCTTATGCTATGCATATG
17095712 AGAGCTTATGCTATGCATATG
1 AGAGCTTATGCTATGCATATG
17095733 AGAGCTTATGCTATGCATATG
1 AGAGCTTATGCTATGCATATG
17095754 AGAGCTTATGCTATGCATATG
1 AGAGCTTATGCTATGCATATG
17095775 CAAATGAATG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 63 1.00
ACGTcount: A:0.29, C:0.14, G:0.24, T:0.33
Consensus pattern (21 bp):
AGAGCTTATGCTATGCATATG
Found at i:17097636 original size:35 final size:35
Alignment explanation
Indices: 17097594--17097670 Score: 109
Period size: 35 Copynumber: 2.2 Consensus size: 35
17097584 ATCAAAAACA
* * * *
17097594 AAATAAATAAACCTAAATAGTTAACTTAATTTAAG
1 AAATAAATAAAACTAAAGAGTTAAATTAATTCAAG
*
17097629 AGATAAATAAAACTAAAGAGTTAAATTAATTCAAG
1 AAATAAATAAAACTAAAGAGTTAAATTAATTCAAG
17097664 AAATAAA
1 AAATAAA
17097671 CAATCATGAA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.58, C:0.06, G:0.08, T:0.27
Consensus pattern (35 bp):
AAATAAATAAAACTAAAGAGTTAAATTAATTCAAG
Found at i:17097825 original size:17 final size:18
Alignment explanation
Indices: 17097795--17097841 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
17097785 AAGTGAAAAT
17097795 AAATAAAATAATAAAAC-A
1 AAATAAAAT-ATAAAACTA
*
17097813 AAATAAAGTAT-AAACTA
1 AAATAAAATATAAAACTA
17097830 AAATAAAATATA
1 AAATAAAATATA
17097842 TACAAAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 4 0.16
17 13 0.52
18 8 0.32
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (18 bp):
AAATAAAATATAAAACTA
Found at i:17099476 original size:12 final size:12
Alignment explanation
Indices: 17099461--17099504 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
17099451 TTTCAATAGA
17099461 TTAAAAAATTTT
1 TTAAAAAATTTT
17099473 TT-AAAAA-TTT
1 TTAAAAAATTTT
*
17099483 TTAAAAAAATTT
1 TTAAAAAATTTT
*
17099495 ATAAAAAATT
1 TTAAAAAATT
17099505 GATAGTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 5 0.18
11 10 0.36
12 13 0.46
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (12 bp):
TTAAAAAATTTT
Found at i:17099502 original size:11 final size:11
Alignment explanation
Indices: 17099461--17099504 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
17099451 TTTCAATAGA
17099461 TTAAAAAATTT
1 TTAAAAAATTT
*
17099472 TTTAAAAATTT
1 TTAAAAAATTT
17099483 TTAAAAAAATTT
1 TT-AAAAAATTT
*
17099495 ATAAAAAATT
1 TTAAAAAATT
17099505 GATAGTTCTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 20 0.69
12 9 0.31
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
TTAAAAAATTT
Found at i:17109991 original size:28 final size:28
Alignment explanation
Indices: 17109959--17110025 Score: 116
Period size: 28 Copynumber: 2.4 Consensus size: 28
17109949 GCCTTGCCTC
*
17109959 TTGTTTGGGCTTTGAAATTTTTATTTAT
1 TTGTTTGGGCCTTGAAATTTTTATTTAT
*
17109987 TTGTTTGGGCCTTGAAATTTTTATTTGT
1 TTGTTTGGGCCTTGAAATTTTTATTTAT
17110015 TTGTTTGGGCC
1 TTGTTTGGGCC
17110026 AAGCCTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.13, C:0.07, G:0.22, T:0.57
Consensus pattern (28 bp):
TTGTTTGGGCCTTGAAATTTTTATTTAT
Found at i:17110082 original size:34 final size:34
Alignment explanation
Indices: 17110053--17110130 Score: 126
Period size: 34 Copynumber: 2.4 Consensus size: 34
17110043 TATTTCTACA
17110053 TATTTTT-TA-TTTAT-TTTCATATTTTATTTCT
1 TATTTTTATATTTTATATTTCATATTTTATTTCT
*
17110084 TATTTTTATATTTTATATTTTATATTTTATTTCT
1 TATTTTTATATTTTATATTTCATATTTTATTTCT
17110118 TATTTTTATATTT
1 TATTTTTATATTT
17110131 AATGGCCAAC
Statistics
Matches: 43, Mismatches: 1, Indels: 3
0.91 0.02 0.06
Matches are distributed among these distances:
31 7 0.16
32 2 0.05
33 5 0.12
34 29 0.67
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (34 bp):
TATTTTTATATTTTATATTTCATATTTTATTTCT
Found at i:17110088 original size:20 final size:19
Alignment explanation
Indices: 17110039--17110126 Score: 81
Period size: 20 Copynumber: 4.4 Consensus size: 19
17110029 CCTTTTTAAT
17110039 TTTTTATTTCTACATATTTT-
1 TTTTTATTT-T-CATATTTTA
17110059 TTATTTATTTTCATATTTTA
1 TT-TTTATTTTCATATTTTA
*
17110079 TTTCTTATTTTTATATTTTA
1 TTT-TTATTTTCATATTTTA
*
17110099 TATTTTATATTTTAT-TTCTTA
1 T-TTTTAT-TTTCATATT-TTA
17110120 TTTTTAT
1 TTTTTAT
17110127 ATTTAATGGC
Statistics
Matches: 61, Mismatches: 1, Indels: 12
0.82 0.01 0.16
Matches are distributed among these distances:
19 9 0.15
20 33 0.54
21 19 0.31
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTATTTTCATATTTTA
Found at i:17110127 original size:20 final size:20
Alignment explanation
Indices: 17110063--17110130 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
17110053 TATTTTTTAT
*
17110063 TTATTTTCATATTTTATTTC
1 TTATTTTTATATTTTATTTC
17110083 TTATTTTTATATTTTA----
1 TTATTTTTATATTTTATTTC
17110099 -TA-TTTTATATTTTATTTC
1 TTATTTTTATATTTTATTTC
17110117 TTATTTTTATATTT
1 TTATTTTTATATTT
17110131 AATGGCCAAC
Statistics
Matches: 41, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
14 12 0.29
15 2 0.05
19 2 0.05
20 25 0.61
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTTTATATTTTATTTC
Found at i:17112555 original size:9 final size:9
Alignment explanation
Indices: 17112532--17112564 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
17112522 ATAAAGATGT
17112532 GAAAAGCAAA
1 GAAAAG-AAA
17112542 G-AAAGAAA
1 GAAAAGAAA
17112550 GAAAAGAAA
1 GAAAAGAAA
17112559 GAAAAG
1 GAAAAG
17112565 TGAGCAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.18
9 17 0.77
10 1 0.05
ACGTcount: A:0.73, C:0.03, G:0.24, T:0.00
Consensus pattern (9 bp):
GAAAAGAAA
Found at i:17115093 original size:17 final size:19
Alignment explanation
Indices: 17115071--17115106 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
17115061 GGCAGTTGGA
17115071 AGTTAGTT-TTT-GGTTAT
1 AGTTAGTTATTTCGGTTAT
17115088 AGTTAGTTATTTCGGTTAT
1 AGTTAGTTATTTCGGTTAT
17115107 GTTTACTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.47
18 3 0.18
19 6 0.35
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (19 bp):
AGTTAGTTATTTCGGTTAT
Found at i:17116627 original size:16 final size:16
Alignment explanation
Indices: 17116606--17116639 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
17116596 TATTTTGTGC
17116606 AACTGGGAGATGTTGG
1 AACTGGGAGATGTTGG
17116622 AACTGGGAGATGTTGG
1 AACTGGGAGATGTTGG
17116638 AA
1 AA
17116640 AAGGTCACCG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.29, C:0.06, G:0.41, T:0.24
Consensus pattern (16 bp):
AACTGGGAGATGTTGG
Found at i:17120185 original size:11 final size:11
Alignment explanation
Indices: 17120169--17120196 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
17120159 AATATGGGCT
17120169 CGAATGGTCAA
1 CGAATGGTCAA
17120180 CGAATGGTCAA
1 CGAATGGTCAA
17120191 CGAATG
1 CGAATG
17120197 ATAGAGGGAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.18
Consensus pattern (11 bp):
CGAATGGTCAA
Found at i:17129923 original size:16 final size:17
Alignment explanation
Indices: 17129902--17129933 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
17129892 CCAATACTTT
17129902 AACTAAAGAAA-TAAAG
1 AACTAAAGAAACTAAAG
17129918 AACTAAAGAAACTAAA
1 AACTAAAGAAACTAAA
17129934 AGGAAAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.12
Consensus pattern (17 bp):
AACTAAAGAAACTAAAG
Found at i:17140053 original size:21 final size:21
Alignment explanation
Indices: 17140029--17140068 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
17140019 AAAGTAAGTT
*
17140029 GTCTTGTTT-TTTTATTATGTC
1 GTCTT-TTTCTTTCATTATGTC
17140050 GTCTTTTTCTTTCATTATG
1 GTCTTTTTCTTTCATTATG
17140069 GTAAACCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.65
Consensus pattern (21 bp):
GTCTTTTTCTTTCATTATGTC
Found at i:17141787 original size:20 final size:18
Alignment explanation
Indices: 17141764--17141801 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 18
17141754 GTCAGTTCCT
17141764 TTTAAAAAAGGAGAAAAAAA
1 TTTAAAAAA--AGAAAAAAA
17141784 TTTAAAAAAAGAAAAAAA
1 TTTAAAAAAAGAAAAAAA
17141802 ACTTCAGAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 9 0.50
20 9 0.50
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (18 bp):
TTTAAAAAAAGAAAAAAA
Found at i:17141802 original size:20 final size:20
Alignment explanation
Indices: 17141764--17141802 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
17141754 GTCAGTTCCT
* *
17141764 TTTAAAAAAGGAGAAAAAAA
1 TTTAAAAAAAGAAAAAAAAA
17141784 TTTAAAAAAAGAAAAAAAA
1 TTTAAAAAAAGAAAAAAAA
17141803 CTTCAGAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.10, T:0.15
Consensus pattern (20 bp):
TTTAAAAAAAGAAAAAAAAA
Found at i:17144377 original size:4 final size:4
Alignment explanation
Indices: 17144368--17144404 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
17144358 CCAACAAAAT
17144368 AACA AACA AACA AACA AACA AACA AACA AACA AACA A
1 AACA AACA AACA AACA AACA AACA AACA AACA AACA A
17144405 TTTTGTTTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.76, C:0.24, G:0.00, T:0.00
Consensus pattern (4 bp):
AACA
Found at i:17149361 original size:14 final size:14
Alignment explanation
Indices: 17149339--17149368 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17149329 TAATGGCTAT
*
17149339 AATACAAAAATAAA
1 AATAAAAAAATAAA
17149353 AATAAAAAAATAAA
1 AATAAAAAAATAAA
17149367 AA
1 AA
17149369 AGAAGCCTTT
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:0.83, C:0.03, G:0.00, T:0.13
Consensus pattern (14 bp):
AATAAAAAAATAAA
Found at i:17151556 original size:21 final size:21
Alignment explanation
Indices: 17151512--17151632 Score: 115
Period size: 21 Copynumber: 6.0 Consensus size: 21
17151502 TATGTTAATT
* * * *
17151512 AATATTAATATCATAAAATGA
1 AATATTAATTTAATAATATTA
*
17151533 AATATTAATTTAATTATATTA
1 AATATTAATTTAATAATATTA
*
17151554 AATATTAA-TTAATAATATTC
1 AATATTAATTTAATAATATTA
* *
17151574 TATATTAATTTAATAATATTC
1 AATATTAATTTAATAATATTA
* *
17151595 AACATTAATTAAATAATATT-
1 AATATTAATTTAATAATATTA
*
17151615 -ATA-TATTTTAATAATATT
1 AATATTAATTTAATAATATT
17151633 TTATACTAAA
Statistics
Matches: 85, Mismatches: 14, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
18 13 0.15
19 2 0.02
20 17 0.20
21 53 0.62
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (21 bp):
AATATTAATTTAATAATATTA
Found at i:17151579 original size:41 final size:42
Alignment explanation
Indices: 17151534--17151632 Score: 134
Period size: 41 Copynumber: 2.5 Consensus size: 42
17151524 ATAAAATGAA
* * *
17151534 ATATTAATTTAATTATATTAAATATTAATT-AATAATATTCT
1 ATATTAATTTAATAATATTAAACATTAATTAAATAATATTAT
*
17151575 ATATTAATTTAATAATATTCAACATTAATTAAATAATATTAT
1 ATATTAATTTAATAATATTAAACATTAATTAAATAATATTAT
17151617 ATA-T--TTTAATAATATT
1 ATATTAATTTAATAATATT
17151633 TTATACTAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
39 12 0.23
41 28 0.53
42 13 0.25
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.49
Consensus pattern (42 bp):
ATATTAATTTAATAATATTAAACATTAATTAAATAATATTAT
Found at i:17151633 original size:11 final size:11
Alignment explanation
Indices: 17151617--17151783 Score: 65
Period size: 11 Copynumber: 15.5 Consensus size: 11
17151607 ATAATATTAT
17151617 ATATTTTAATA
1 ATATTTTAATA
17151628 ATATTTTATACTAA
1 ATATTTTA-A-T-A
17151642 ATATTGATTTAATA
1 ATA-T--TTTAATA
17151656 ATA-TTT--TA
1 ATATTTTAATA
17151664 ATA-TTTAATA
1 ATATTTTAATA
*
17151674 TTATTTTAAT-
1 ATATTTTAATA
17151684 A-ATTTTAATA
1 ATATTTTAATA
* *
17151694 TTAGGTATTAGATA
1 ATA--TTTTA-ATA
*
17151708 TTAATTTTAATA
1 AT-ATTTTAATA
17151720 ATA-TTT--TA
1 ATATTTTAATA
*
17151728 ATA-TTAAATA
1 ATATTTTAATA
* *
17151738 TTAATTTAATA
1 ATATTTTAATA
17151749 ATATTTTAAT-
1 ATATTTTAATA
* *
17151759 AT-TTTTTATT
1 ATATTTTAATA
17151769 A-ATTTT-ATA
1 ATATTTTAATA
17151778 ATATTT
1 ATATTT
17151784 AAAATTTATA
Statistics
Matches: 122, Mismatches: 13, Indels: 43
0.69 0.07 0.24
Matches are distributed among these distances:
8 15 0.12
9 17 0.14
10 25 0.20
11 30 0.25
12 5 0.04
13 9 0.07
14 13 0.11
15 3 0.02
16 1 0.01
17 4 0.03
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (11 bp):
ATATTTTAATA
Found at i:17151674 original size:29 final size:29
Alignment explanation
Indices: 17151621--17151791 Score: 168
Period size: 29 Copynumber: 5.8 Consensus size: 29
17151611 TATTATATAT
* * *
17151621 TTTAATAATATTTT-ATACTAAATATTGA
1 TTTAATAATATTTTAATATTTAATATTAA
*
17151649 TTTAATAATATTTTAATATTTAATATTAT
1 TTTAATAATATTTTAATATTTAATATTAA
*
17151678 TTTAATAAT-TTTAATATTAGGTATTAGATATTAA
1 TTTAATAATATTT--TAATA--T-TTA-ATATTAA
*
17151712 TTTTAATAATATTTTAATATTAAATATTAA
1 -TTTAATAATATTTTAATATTTAATATTAA
**
17151742 TTTAATAATATTTTAATATTTTTTATTAA
1 TTTAATAATATTTTAATATTTAATATTAA
* *
17151771 TTTTATAATA-TTTAAAATTTA
1 TTTAATAATATTTTAATATTTA
17151792 TAATATGATA
Statistics
Matches: 120, Mismatches: 14, Indels: 18
0.79 0.09 0.12
Matches are distributed among these distances:
28 26 0.22
29 54 0.45
30 11 0.09
31 2 0.02
32 2 0.02
33 3 0.03
34 10 0.08
35 9 0.08
36 3 0.03
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (29 bp):
TTTAATAATATTTTAATATTTAATATTAA
Found at i:17151747 original size:35 final size:34
Alignment explanation
Indices: 17151654--17151761 Score: 102
Period size: 35 Copynumber: 3.2 Consensus size: 34
17151644 ATTGATTTAA
*
17151654 TAATATTTTAATATTTAATATT-ATTTTAATAATTT
1 TAATA-TTAAATA-TTAATATTAATTTTAATAATTT
**
17151689 TAATATTAGGTATTAGATATTAATTTTAATAATATTT
1 TAATATTAAATATTA-ATATTAATTTTAAT-A-ATTT
17151726 TAATATTAAATATTAAT-TTAA---TAAT-ATTT
1 TAATATTAAATATTAATATTAATTTTAATAATTT
17151755 TAATATT
1 TAATATT
17151762 TTTTATTAAT
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
29 11 0.17
32 4 0.06
33 3 0.05
34 9 0.14
35 17 0.27
36 3 0.05
37 17 0.27
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (34 bp):
TAATATTAAATATTAATATTAATTTTAATAATTT
Found at i:17159267 original size:18 final size:19
Alignment explanation
Indices: 17159233--17159275 Score: 54
Period size: 18 Copynumber: 2.3 Consensus size: 19
17159223 ATATCATGCA
17159233 TATTTTAATTATGTTAT-T
1 TATTTTAATTATGTTATCT
*
17159251 TATTTTAA-TGTGCTTATCT
1 TATTTTAATTATG-TTATCT
17159270 TATTTT
1 TATTTT
17159276 TAATAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 3 0.14
18 12 0.55
19 7 0.32
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (19 bp):
TATTTTAATTATGTTATCT
Found at i:17159853 original size:13 final size:14
Alignment explanation
Indices: 17159785--17159845 Score: 52
Period size: 15 Copynumber: 4.3 Consensus size: 14
17159775 AACAATAGCA
*
17159785 AAAAAAAGAAAAAAG
1 AAAAAAA-AAAAATG
* *
17159800 AAAAAAACCAACATG
1 AAAAAAA-AAAAATG
* *
17159815 AAGAATAAAAAATG
1 AAAAAAAAAAAATG
17159829 AAAAAAAAAAAA-G
1 AAAAAAAAAAAATG
17159842 AAAA
1 AAAA
17159846 CACAAAAACA
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
13 5 0.14
14 15 0.42
15 16 0.44
ACGTcount: A:0.80, C:0.05, G:0.10, T:0.05
Consensus pattern (14 bp):
AAAAAAAAAAAATG
Found at i:17160222 original size:17 final size:18
Alignment explanation
Indices: 17160196--17160230 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17160186 AAGATGAAAT
*
17160196 GATATGTTAGAATTAATG
1 GATATGTTAGAACTAATG
17160214 GATAT-TTAGAACTAATG
1 GATATGTTAGAACTAATG
17160231 AAGGGTGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.40, C:0.03, G:0.20, T:0.37
Consensus pattern (18 bp):
GATATGTTAGAACTAATG
Found at i:17161202 original size:40 final size:40
Alignment explanation
Indices: 17161147--17161542 Score: 166
Period size: 41 Copynumber: 9.6 Consensus size: 40
17161137 AAAGACTTTG
*
17161147 GATTCATAGCAGAGTAAACAATTCATAGTTGGAAATTCTA
1 GATTCACAGCAGAGTAAACAATTCATAGTTGGAAATTCTA
* * *
17161187 AATTCACAGTAGAGTAAACAATTCATAGTTGTGAGAACTCTA
1 GATTCACAGCAGAGTAAACAATTCATAGTTG-GA-AATTCTA
* * * * *
17161229 GATTCACAGCAAAGTAAACGATTCACAATTGGAATATTCTG
1 GATTCACAGCAGAGTAAACAATTCATAGTTGGAA-ATTCTA
* * ** * *
17161270 GATTCACAGCAAAATAAGTAATTTATAGTTCAGAAGACTT-TA
1 GATTCACAGCAGAGTAAACAATTCATAGTT-GGAA-A-TTCTA
* ** * ** ***
17161312 GATTCATAATAAAGTAAATGATTCATAGTTAGGAGGCTCTA
1 GATTCACAGCAGAGTAAACAATTCATAGTT-GGAAATTCTA
* * * * *
17161353 GATTCACAACAGAGTAAATAATTCA-CGATTTGAAGACTCTA
1 GATTCACAGCAGAGTAAACAATTCATAG-TTGGAA-ATTCTA
* * ** * * * * *
17161394 GATTCATAGTAGAGTAAATGATTAACAGGTGAAAAACTCTA
1 GATTCACAGCAGAGTAAACAATTCATAGTTG-GAAATTCTA
* * * ** *
17161435 GATTTATAACAGAGTAAATGATTCATAGTTGTAAGATTCTA
1 GATTCACAGCAGAGTAAACAATTCATAGTTGGAA-ATTCTA
* * * * * * * *
17161476 TATACACAACAAAGTAAACGATTCACATTTTGAAAGATTCTA
1 GATTCACAGCAGAGTAAACAATTCATA-GTTGGAA-ATTCTA
* * *
17161518 GATTCACAACAAAGTAAACGATTCA
1 GATTCACAGCAGAGTAAACAATTCA
17161543 CATCAGAATA
Statistics
Matches: 274, Mismatches: 70, Indels: 22
0.75 0.19 0.06
Matches are distributed among these distances:
40 35 0.13
41 138 0.50
42 99 0.36
43 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.16, T:0.29
Consensus pattern (40 bp):
GATTCACAGCAGAGTAAACAATTCATAGTTGGAAATTCTA
Found at i:17161309 original size:165 final size:166
Alignment explanation
Indices: 17160951--17161399 Score: 384
Period size: 165 Copynumber: 2.7 Consensus size: 166
17160941 TCCATAACAT
* * * *
17160951 AGTAAATGATTCAC-AGTTTAAAGGACTCTAGATTAATAACAGAGTAAACAATTCACTATTGGAG
1 AGTAAATAATTCACTA-TTCAAA-GACTTTAGATTCATAACAGAGTAAACAATTCACTATTGGAG
* * * ** * * *
17161015 GATTCTATATTCATAGTAGAGTAAATGATTCACAGTTTAGAAGATTCTAGATTCACAATATAGTA
64 AATTCTAAATTCACAGTAGAGTAAACAATTCACAGTTTAGAAGACTCTAGATTCACAACAAAGTA
* * *
17161080 AATGATTCACAATTAGGAGAACTCTATATTCACATAAA
129 AACGATTCACAATTAGGAGAACTCTAGATTCACACAAA
* * * *
17161118 AGTAAATGATTCACTATTTAAAGACTTTGGATTCATAGCAGAGTAAACAATTCA-TAGTTGGA-A
1 AGTAAATAATTCACTATTCAAAGACTTTAGATTCATAACAGAGTAAACAATTCACTA-TTGGAGA
* *
17161181 ATTCTAAATTCACAGTAGAGTAAACAATTCATAGTTGT-G-AGAACTCTAGATTCACAGCAAAGT
65 ATTCTAAATTCACAGTAGAGTAAACAATTCACAGTT-TAGAAG-ACTCTAGATTCACAACAAAGT
* *
17161244 AAACGATTCACAATT-GGA-ATATTCTGGATTCACAGCAAA
128 AAACGATTCACAATTAGGAGA-ACTCTAGATTCACA-CAAA
* * * * **
17161283 A-TAAGTAATTTA-TAGTTCAGAAGACTTTAGATTCATAATAAAGTAAATGATTCA-TAGTTAGG
1 AGTAAATAATTCACTA-TTCA-AAGACTTTAGATTCATAACAGAGTAAACAATTCACTA-TT-GG
** * ** *
17161345 AG-GCTCTAGATTCACAACAGAGTAAATAATTCAC-GATTT-GAAGACTCTAGATTCA
62 AGAATTCTAAATTCACAGTAGAGTAAACAATTCACAG-TTTAGAAGACTCTAGATTCA
17161400 TAGTAGAGTA
Statistics
Matches: 234, Mismatches: 36, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
163 3 0.01
164 27 0.12
165 117 0.50
166 66 0.28
167 20 0.09
168 1 0.00
ACGTcount: A:0.41, C:0.13, G:0.16, T:0.31
Consensus pattern (166 bp):
AGTAAATAATTCACTATTCAAAGACTTTAGATTCATAACAGAGTAAACAATTCACTATTGGAGAA
TTCTAAATTCACAGTAGAGTAAACAATTCACAGTTTAGAAGACTCTAGATTCACAACAAAGTAAA
CGATTCACAATTAGGAGAACTCTAGATTCACACAAA
Found at i:17161314 original size:83 final size:82
Alignment explanation
Indices: 17161076--17161336 Score: 197
Period size: 83 Copynumber: 3.2 Consensus size: 82
17161066 TTCACAATAT
* * * * ** *
17161076 AGTAAATGATTCACAATTAGGAGAACTCTATATTCACA-TAAAAGTAAATGATTCACTA-TTTA-
1 AGTAAACGATTCACAATT-GGA-AATTCTAAATTCACAGCAAAA-TAAACAATTCA-TAGTTCAG
* *
17161138 AAGACTTTGGATTCATAGCAG
62 AAGACTTTAGATTCATAGCAA
* * * * * * **
17161159 AGTAAACAATTCATAGTTGGAAATTCTAAATTCACAGTAGAGTAAACAATTCATAGTTGTG-AGA
1 AGTAAACGATTCACAATTGGAAATTCTAAATTCACAGCAAAATAAACAATTCATAGTTCAGAAG-
* *
17161223 ACTCTAGATTCACAGCAA
65 ACTTTAGATTCATAGCAA
** ** *
17161241 AGTAAACGATTCACAATTGGAATATTCTGGATTCACAGCAAAATAAGTAATTTATAGTTCAGAAG
1 AGTAAACGATTCACAATTGGAA-ATTCTAAATTCACAGCAAAATAAACAATTCATAGTTCAGAAG
**
17161306 ACTTTAGATTCATAATAA
65 ACTTTAGATTCATAGCAA
*
17161324 AGTAAATGATTCA
1 AGTAAACGATTCA
17161337 TAGTTAGGAG
Statistics
Matches: 138, Mismatches: 34, Indels: 12
0.75 0.18 0.07
Matches are distributed among these distances:
80 2 0.01
81 26 0.19
82 39 0.28
83 69 0.50
84 2 0.01
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (82 bp):
AGTAAACGATTCACAATTGGAAATTCTAAATTCACAGCAAAATAAACAATTCATAGTTCAGAAGA
CTTTAGATTCATAGCAA
Found at i:17161492 original size:41 final size:42
Alignment explanation
Indices: 17161442--17161545 Score: 138
Period size: 42 Copynumber: 2.5 Consensus size: 42
17161432 CTAGATTTAT
* * * * *
17161442 AACAGAGTAAATGATTCATA-GTTGTAAGATTCTATATACAC
1 AACAAAGTAAACGATTCACATGTTGAAAGATTCTAGATACAC
* *
17161483 AACAAAGTAAACGATTCACATTTTGAAAGATTCTAGATTCAC
1 AACAAAGTAAACGATTCACATGTTGAAAGATTCTAGATACAC
17161525 AACAAAGTAAACGATTCACAT
1 AACAAAGTAAACGATTCACAT
17161546 CAGAATAAAT
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 17 0.31
42 38 0.69
ACGTcount: A:0.44, C:0.15, G:0.12, T:0.28
Consensus pattern (42 bp):
AACAAAGTAAACGATTCACATGTTGAAAGATTCTAGATACAC
Found at i:17161596 original size:41 final size:41
Alignment explanation
Indices: 17161551--17161651 Score: 116
Period size: 41 Copynumber: 2.4 Consensus size: 41
17161541 CACATCAGAA
*
17161551 TAAATGATTCATAGTCT-GAAGA-CACTAGATTCATAGCAAAG
1 TAAATGATTCACAGT-TGGAAGATCA-TAGATTCATAGCAAAG
* * *
17161592 TAAATGATTCACAGTTGGAAGATTATGGATTCATAGCAGAG
1 TAAATGATTCACAGTTGGAAGATCATAGATTCATAGCAAAG
*
17161633 TAAAATGATTCACACTTGG
1 T-AAATGATTCACAGTTGG
17161652 GAAAATTTTG
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
40 1 0.02
41 34 0.65
42 17 0.33
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (41 bp):
TAAATGATTCACAGTTGGAAGATCATAGATTCATAGCAAAG
Found at i:17161750 original size:42 final size:42
Alignment explanation
Indices: 17161694--17162721 Score: 350
Period size: 42 Copynumber: 24.6 Consensus size: 42
17161684 TCACAATTGG
* * * *
17161694 AAGATTCTAGATTCACAGTAGAGTAAATGATTCGTAGTTCAA
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* **
17161736 AAGACTCTGGATTCACAATAGAGTAAATAATTCATAGTT-TG
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * * ** * **
17161777 GAGAATTTTGGATTCACAATAGAGTAAGCAATTCAGAGTT-TG
1 AAG-ACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * * * **
17161819 AAGACTTTAGATTCACAGTAAAGTAAACAATTCACAACT-AA
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * * * **
17161860 AAAACTCTAGATTCATAACAAAGTAAATGATTCATAGTT-TG
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * * * *
17161901 AAGACTTTATATTCATAGTAGAGTAAATAATTCACAGTTTGAA
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAG-TTCAA
* * * **
17161944 AA-ACTCTAGATTCACAACAAAGTAAATGATTCATAGTT-TG
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* ** *** * ***
17161984 AAGACT-TTGAATTCACGTTAGAGTAAGCGATTCATAATTTGG
1 AAGACTCTAG-ATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * * ** **
17162026 AAGACTCTGGATTCATAACAAAGTAAACGATTCATAGTTTGGA
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAG-TTCAA
* * * * * * **
17162069 AA-ACTTTGGATTCACAAAAAAATAAACAATTCATAGTTTGA
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * * * * *
17162110 AAGACTTTACATTCACAACAGAGTAAACGATTTACA-ATTTGAA
1 AAGACTCTAGATTCACAATAGAGTAAA-TAATT-CATAGTTCAA
* * * * *
17162153 GA-ACTCTAGATTCATAATAGAGTTAACAATTCAGAGTT-AA
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * * * **
17162193 GAAGACTTTGGATTCACAGTAAAGTAAATAATTTATAGTT-GG
1 -AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * * * *
17162235 AAGACTCTAGATTCATAGTAAAGTAAATTATTCATAGTTTAT
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * *
17162277 AAGACTCT-GCATTCATAGTAGAGTAAACAATTCATAGTTTAA
1 AAGACTCTAG-ATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * **
17162319 AAGATTCTAGATTCACAACAGAGTAAATGATTCAT-GTTTGA
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* ** * * * **
17162360 AATACTCTAGATTCACAGCAGAGTAAATGATTCACAATTTGA
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * * * ***
17162402 AAGACTCTGGATTCATAATA-ATATAAACAATTTATAGTTTGG
1 AAGACTCTAGATTCACAATAGA-GTAAATAATTCATAGTTCAA
* * * * * ** * ***
17162444 AAGACTTTGGATTTACAACAGAATAAACCATTCACAGTTTGG
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * ** *
17162486 AAGACTCTTGATTCACAATAAAGTAAACGATTCATAGTT-AG
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * ** ** * *
17162527 GAGAACTCCATATTCACAACGGAGTAAGCAATTCACT--TTTAG
1 AAG-ACTCTAGATTCACAATAGAGTAAATAATTCA-TAGTTCAA
* * * * * ***
17162569 AAGACTTTGGATTCACAATAGAGTAAACAATTTACAGTTTGG
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
* * * **
17162611 AAGACTTTGGATTCACAATAG-GATAAACAATTCACTA-TTTGA
1 AAGACTCTAGATTCACAATAGAG-TAAATAATTCA-TAGTTCAA
* * * * *
17162653 AAGACTCTAGTTTCATAATAGAGTAAGTGATTCATAGTTTGAA
1 AAGACTCTAGATTCACAATAGAGTAAATAATTCATAG-TTCAA
17162696 AAGACTCTAGATTCACAATAGAGTAA
1 AAGACTCTAGATTCACAATAGAGTAA
17162722 GCGATTCATA
Statistics
Matches: 759, Mismatches: 197, Indels: 59
0.75 0.19 0.06
Matches are distributed among these distances:
40 8 0.01
41 231 0.30
42 469 0.62
43 49 0.06
44 2 0.00
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (42 bp):
AAGACTCTAGATTCACAATAGAGTAAATAATTCATAGTTCAA
Found at i:17161976 original size:124 final size:123
Alignment explanation
Indices: 17161734--17161969 Score: 285
Period size: 124 Copynumber: 1.9 Consensus size: 123
17161724 TTCGTAGTTC
* * * * *
17161734 AAAAGACTCTGGATTCACAATAGAGTAAATAATTCATAGTTTGGAGAATTTTGGATTCACAATAG
1 AAAAAACTCTAGATTCACAACAAAGTAAATAATTCATAGTTTGAAGAATTTT-GATTCACAATAG
* * * * **
17161799 AGTAAGCAATTCAGAGTTTGAAGACTTTAGATTCACAGTAAAGTAAACAATTCACAACT
65 AGTAAACAATTCACAGTTTGAAAACTCTAGATTCACAACAAAGTAAACAATTCACAACT
* * * * *
17161858 AAAAAACTCTAGATTCATAACAAAGTAAATGATTCATAGTTTGAAGACTTTAT-ATTCATAGTAG
1 AAAAAACTCTAGATTCACAACAAAGTAAATAATTCATAGTTTGAAGAATTT-TGATTCACAATAG
*
17161922 AGTAAATAATTCACAGTTTGAAAAACTCTAGATTCACAACAAAGTAAA
65 AGTAAACAATTCACAGTTTG-AAAACTCTAGATTCACAACAAAGTAAA
17161970 TGATTCATAG
Statistics
Matches: 93, Mismatches: 17, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
123 26 0.28
124 66 0.71
125 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.14, T:0.29
Consensus pattern (123 bp):
AAAAAACTCTAGATTCACAACAAAGTAAATAATTCATAGTTTGAAGAATTTTGATTCACAATAGA
GTAAACAATTCACAGTTTGAAAACTCTAGATTCACAACAAAGTAAACAATTCACAACT
Found at i:17162081 original size:125 final size:125
Alignment explanation
Indices: 17161736--17162740 Score: 658
Period size: 125 Copynumber: 8.0 Consensus size: 125
17161726 CGTAGTTCAA
* * ** * * * * *
17161736 AAGACTCTGGATTCACAATAGAGTAAATAATTCATAGTTTGG-AGAATTTTGGATTCACAATAGA
1 AAGACTTTAGATTCACAATAGAGTAAACGATTCATAATTTGGAAG-ACTCTAGATTCATAATAGA
* * * * ** * ** **
17161800 GTAAGCAATTCAGAGTTT-GAAGACTTTAGATTCACAGTAAAGTAAACAATTCACAACTAA
65 GTAAACAATTCATAGTTTGGAAAACTTTGGATTCACAACAAAGTAAACAATTCATAGTTTG
* * * * * * * * * *
17161860 AAAACTCTAGATTCATAACAAAGTAAATGATTCATAGTTT-GAAGACTTTATATTCATAGTAGAG
1 AAGACTTTAGATTCACAATAGAGTAAACGATTCATAATTTGGAAGACTCTAGATTCATAATAGAG
* * * * * **
17161924 TAAATAATTCACAGTTTGAAAAACTCTAGATTCACAACAAAGTAAATGATTCATAGTTTG
66 TAAACAATTCATAGTTTGGAAAACTTTGGATTCACAACAAAGTAAACAATTCATAGTTTG
** * * * *
17161984 AAGACTTT-GAATTCACGTTAGAGTAAGCGATTCATAATTTGGAAGACTCTGGATTCATAACAAA
1 AAGACTTTAG-ATTCACAATAGAGTAAACGATTCATAATTTGGAAGACTCTAGATTCATAATAGA
* * *
17162048 GTAAACGATTCATAGTTTGGAAAACTTTGGATTCACAAAAAAATAAACAATTCATAGTTTG
65 GTAAACAATTCATAGTTTGGAAAACTTTGGATTCACAACAAAGTAAACAATTCATAGTTTG
* * * *
17162109 AAAGACTTTACATTCACAACAGAGTAAACGATTTACAATTT-GAAGAACTCTAGATTCATAATAG
1 -AAGACTTTAGATTCACAATAGAGTAAACGATTCATAATTTGGAAG-ACTCTAGATTCATAATAG
* * ** * ** * * *
17162173 AGTTAACAATTCAGAGTTAAGAAGACTTTGGATTCACAGTAAAGTAAATAATTTATAGTTGG
64 AGTAAACAATTCATAGTTTGGAAAACTTTGGATTCACAACAAAGTAAACAATTCATAGTTTG
* * * * ** * ** *
17162235 AAGACTCTAGATTCATAGTAAAGTAAATTATTCATAGTTTATAAGACTCT-GCATTCATAGTAGA
1 AAGACTTTAGATTCACAATAGAGTAAACGATTCATAATTTGGAAGACTCTAG-ATTCATAATAGA
* * * **
17162299 GTAAACAATTCATAGTTT--AAAAGATTCTAGATTCACAACAGAGTAAATGATTCAT-GTTTG
65 GTAAACAATTCATAGTTTGGAAAA-CTT-TGGATTCACAACAAAGTAAACAATTCATAGTTTG
* * ** * * * *
17162359 AAATACTCTAGATTCACAGCAGAGTAAATGATTCACAATTTGAAAGACTCTGGATTCATAATA-A
1 -AAGACTTTAGATTCACAATAGAGTAAACGATTCATAATTTGGAAGACTCTAGATTCATAATAGA
* * * * * *
17162423 TATAAACAATTTATAGTTTGGAAGACTTTGGATTTACAACAGAA-TAAACCATTCACAGTTTGG
65 -GTAAACAATTCATAGTTTGGAAAACTTTGGATTCACAACA-AAGTAAACAATTCATAGTTT-G
* * * * * * **
17162486 AAGACTCTT-GATTCACAATAAAGTAAACGATTCATAGTTAGG-AGAACTCCATATTCACAACGG
1 AAGACT-TTAGATTCACAATAGAGTAAACGATTCATAATTTGGAAG-ACTCTAGATTCATAATAG
* * * * * * *
17162549 AGTAAGCAATTCACT--TTTAGAAGACTTTGGATTCACAATAGAGTAAACAATTTACAGTTTGG
64 AGTAAACAATTCA-TAGTTTGGAAAACTTTGGATTCACAACAAAGTAAACAATTCATAGTTT-G
* * * *
17162611 AAGACTTTGGATTCACAATAG-GATAAACAATTCACT-ATTTGAAAGACTCTAGTTTCATAATAG
1 AAGACTTTAGATTCACAATAGAG-TAAACGATTCA-TAATTTGGAAGACTCTAGATTCATAATAG
*** * * * * * * *
17162674 AGTAAGTGATTCATAGTTTGAAAAGACTCTAGATTCACAATAGAGTAAGCGATTCATAGTTTAG
64 AGTAAACAATTCATAGTTTGGAAA-ACTTTGGATTCACAACAAAGTAAACAATTCATAGTTT-G
17162738 AAG
1 AAG
17162741 GCCCTGGATT
Statistics
Matches: 683, Mismatches: 167, Indels: 59
0.75 0.18 0.06
Matches are distributed among these distances:
123 34 0.05
124 107 0.16
125 334 0.49
126 166 0.24
127 42 0.06
ACGTcount: A:0.40, C:0.13, G:0.16, T:0.31
Consensus pattern (125 bp):
AAGACTTTAGATTCACAATAGAGTAAACGATTCATAATTTGGAAGACTCTAGATTCATAATAGAG
TAAACAATTCATAGTTTGGAAAACTTTGGATTCACAACAAAGTAAACAATTCATAGTTTG
Found at i:17162776 original size:26 final size:26
Alignment explanation
Indices: 17162727--17162776 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
17162717 AGTAAGCGAT
* *
17162727 TCATAGTTTAGAAGGCCCTGGATTGC
1 TCATAGTTTAGAAGACCCTAGATTGC
*
17162753 TCATAGTTTAGAAGACTCTAGATT
1 TCATAGTTTAGAAGACCCTAGATT
17162777 CACAATAAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.34
Consensus pattern (26 bp):
TCATAGTTTAGAAGACCCTAGATTGC
Found at i:17163046 original size:17 final size:16
Alignment explanation
Indices: 17163010--17163085 Score: 71
Period size: 17 Copynumber: 4.5 Consensus size: 16
17163000 ACATAAACCC
*
17163010 AAGAATCACAAATTCTA
1 AAGATTCACAAATTC-A
17163027 AAGATTCACAAATTTCA
1 AAGATTCACAAA-TTCA
** *
17163044 AAGATTCGTAAGAGTCA
1 AAGATTCACAA-ATTCA
*
17163061 TAGATTCACAAATTTCA
1 AAGATTCACAAA-TTCA
17163078 AAGATTCA
1 AAGATTCA
17163086 TAAAAGGAGT
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
16 1 0.02
17 42 0.89
18 4 0.09
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.28
Consensus pattern (16 bp):
AAGATTCACAAATTCA
Found at i:17163112 original size:37 final size:36
Alignment explanation
Indices: 17163025--17163126 Score: 136
Period size: 37 Copynumber: 2.9 Consensus size: 36
17163015 TCACAAATTC
*
17163025 TAAAGATTCACAAATTTCAAAGATTCGT--AAGAGT
1 TAAAGATTCACAAATTTCAAAGATTCATAAAAGAGT
* *
17163059 CATAGATTCACAAATTTCAAAGATTCATAAAAGGAGT
1 TAAAGATTCACAAATTTCAAAGATTCATAAAA-GAGT
* *
17163096 TAAAGATTCACAAATTTTAGAGATTCATAAA
1 TAAAGATTCACAAATTTCAAAGATTCATAAA
17163127 CATAAATGAT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
34 25 0.43
36 2 0.03
37 31 0.53
ACGTcount: A:0.46, C:0.12, G:0.13, T:0.29
Consensus pattern (36 bp):
TAAAGATTCACAAATTTCAAAGATTCATAAAAGAGT
Found at i:17164728 original size:23 final size:21
Alignment explanation
Indices: 17164688--17164731 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
17164678 TTTCATTTTC
*
17164688 TCATTTTTTTTTGTTTTTCTT
1 TCATTTTTTTTTATTTTTCTT
17164709 TCATTTTTTTTTCATATTTTCTT
1 TCATTTTTTTTT-AT-TTTTCTT
17164732 CTTCTTTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 12 0.60
22 1 0.05
23 7 0.35
ACGTcount: A:0.09, C:0.11, G:0.02, T:0.77
Consensus pattern (21 bp):
TCATTTTTTTTTATTTTTCTT
Found at i:17165802 original size:22 final size:20
Alignment explanation
Indices: 17165783--17165820 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
17165773 TTTTTTATTG
*
17165783 AAAGGATTTTTTGTTTTTAT
1 AAAGAATTTTTTGTTTTTAT
*
17165803 AAATAATTTTTTGTTTTT
1 AAAGAATTTTTTGTTTTT
17165821 TCATTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.11, T:0.63
Consensus pattern (20 bp):
AAAGAATTTTTTGTTTTTAT
Found at i:17165965 original size:23 final size:23
Alignment explanation
Indices: 17165938--17165991 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 23
17165928 ATAAAACCAA
17165938 AAAAATAG-TGAAAA-CTAAAAAAT
1 AAAAATAGCT-AAAATC-AAAAAAT
*
17165961 TAAAATGAGCTAAAATCAAAAAAT
1 AAAAAT-AGCTAAAATCAAAAAAT
17165985 AAAAATA
1 AAAAATA
17165992 AAATGGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
23 6 0.23
24 18 0.69
25 2 0.08
ACGTcount: A:0.69, C:0.06, G:0.07, T:0.19
Consensus pattern (23 bp):
AAAAATAGCTAAAATCAAAAAAT
Found at i:17166945 original size:13 final size:13
Alignment explanation
Indices: 17166927--17166968 Score: 59
Period size: 13 Copynumber: 3.3 Consensus size: 13
17166917 AATAATTTAC
*
17166927 AATATTATACCAT
1 AATATTATACTAT
*
17166940 AATATTATATTAT
1 AATATTATACTAT
17166953 AATA-TATACTAT
1 AATATTATACTAT
17166965 AATA
1 AATA
17166969 ATAACAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 11 0.42
13 15 0.58
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (13 bp):
AATATTATACTAT
Found at i:17167381 original size:120 final size:120
Alignment explanation
Indices: 17167150--17167779 Score: 616
Period size: 120 Copynumber: 5.3 Consensus size: 120
17167140 TGAGTTAGGA
* * * * *
17167150 AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACAAAACTAAGAGTCAGAAATGAAGCGAC
1 AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACGAAACCACGAGTCAAAAATGAAGTGAC
* * * * * *
17167215 CAAGATCACGTCAAAGTCGAAAATAAATAACCAAGATGAAACCATGAATCATAAG
66 CAAGATCAAGTCAAGGTCAAAAATAAATGATCGAGATGAAACCATGAATCATAAG
* * * * * * * * *
17167270 AAATGATTTGTATTGAGTCAAGATCAGGTGATTGGGACGAAACCATGAGTCAAAAATAAAATGAC
1 AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACGAAACCACGAGTCAAAAATGAAGTGAC
* * * ** *
17167335 CAAGATCGAGTCAAGGTCGAAAATACATGATCGAGACAAAATCATGAATCATAAG
66 CAAGATCAAGTCAAGGTCAAAAATAAATGATCGAGATGAAACCATGAATCATAAG
* * * * *
17167390 AAATGATTTGGATTAAGCTAAGATCAAGTGGTCGAGATGAAACCACGAGTCAAAAATGAAGTGAC
1 AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACGAAACCACGAGTCAAAAATGAAGTGAC
* * **
17167455 CAAGATTAAGTCAAGGTAAAAAATAAATGAAAGAGATGAAACCATGAATCATAAG
66 CAAGATCAAGTCAAGGTCAAAAATAAATGATCGAGATGAAACCATGAATCATAAG
* * * * * * * * ** * *
17167510 AAATGGTATGGACTAAGCCAAGATTAGGTGACCAAGATAAAACCACGGGTCAAAAATAAAGTGAC
1 AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACGAAACCACGAGTCAAAAATGAAGTGAC
* * * * * *
17167575 CAAAACCGAGTCGAGGTCAAAAATAAATGA-CTAGGATGAAACCATAAATCATAAG
66 CAAGATCAAGTCAAGGTCAAAAATAAATGATCGA-GATGAAACCATGAATCATAAG
* * * * * * * * * *
17167630 AAATAATCTGGACTGAGCCAAGATTAAATGACCGGGACGAAACCATGGGCCAAAGATGAAGTGAC
1 AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACGAAACCACGAGTCAAAAATGAAGTGAC
* *
17167695 CAAGATCAAGTCAAGATCAAAAATAAATGATCGA-ATGAAACCATGAATCATAAA
66 CAAGATCAAGTCAAGGTCAAAAATAAATGATCGAGATGAAACCATGAATCATAAG
* * * *
17167749 AAATGACCTGGACTAAGCCAAGATCAGGTGA
1 AAATGATCTGGATTGAGCCAAGATCAAGTGA
17167780 ATGAGTAATG
Statistics
Matches: 414, Mismatches: 94, Indels: 5
0.81 0.18 0.01
Matches are distributed among these distances:
119 44 0.11
120 368 0.89
121 2 0.00
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (120 bp):
AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACGAAACCACGAGTCAAAAATGAAGTGAC
CAAGATCAAGTCAAGGTCAAAAATAAATGATCGAGATGAAACCATGAATCATAAG
Found at i:17167577 original size:240 final size:240
Alignment explanation
Indices: 17167150--17167779 Score: 692
Period size: 240 Copynumber: 2.6 Consensus size: 240
17167140 TGAGTTAGGA
* * * *
17167150 AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACAAAACTAAGAGTCAGAAATGAAGCGAC
1 AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACGAAACCAAGAGTCAAAAATGAAGTGAC
* * * *
17167215 CAAGATCACGTCAAAGTCGAAAATAAAT-AACCA-AGATGAAACCATGAATCATAAGAAATGATT
66 CAAGATCAAGTCAAGGTCAAAAATAAATGAA--AGAGATGAAACCATGAATCATAAGAAATGATA
* * * * **** * * * *
17167278 TGTATTGAGTCAAGATCAGGTGATTGGGACGAAACCATGAGTCAAAAATAAAATGACCAAGATCG
129 TGGACTAAGCCAAGATCAGGTGACCAAGACAAAACCACGAGTCAAAAATAAAATGACCAAAACCG
* * * *
17167343 AGTCAAGGTCGAAAATACATGATCGA-GACAAAATCATGAATCATAAG
194 AGTCAAGGTCAAAAATAAATGA-CGAGGACAAAACCATAAATCATAAG
* * * * * *
17167390 AAATGATTTGGATTAAGCTAAGATCAAGTGGTCGAGATGAAACCACGAGTCAAAAATGAAGTGAC
1 AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACGAAACCAAGAGTCAAAAATGAAGTGAC
* * *
17167455 CAAGATTAAGTCAAGGTAAAAAATAAATGAAAGAGATGAAACCATGAATCATAAGAAATGGTATG
66 CAAGATCAAGTCAAGGTCAAAAATAAATGAAAGAGATGAAACCATGAATCATAAGAAATGATATG
* * * *
17167520 GACTAAGCCAAGATTAGGTGACCAAGATAAAACCACGGGTCAAAAATAAAGTGACCAAAACCGAG
131 GACTAAGCCAAGATCAGGTGACCAAGACAAAACCACGAGTCAAAAATAAAATGACCAAAACCGAG
* * **
17167585 TCGAGGTCAAAAATAAATGACTAGGATGAAACCATAAATCATAAG
196 TCAAGGTCAAAAATAAATGACGAGGACAAAACCATAAATCATAAG
* * * * * * * * * *
17167630 AAATAATCTGGACTGAGCCAAGATTAAATGACCGGGACGAAACCATGGGCCAAAGATGAAGTGAC
1 AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACGAAACCAAGAGTCAAAAATGAAGTGAC
* ** * **
17167695 CAAGATCAAGTCAAGATCAAAAATAAATGATCGA-ATGAAACCATGAATCATAAAAAATGACCTG
66 CAAGATCAAGTCAAGGTCAAAAATAAATGAAAGAGATGAAACCATGAATCATAAGAAATGATATG
17167759 GACTAAGCCAAGATCAGGTGA
131 GACTAAGCCAAGATCAGGTGA
17167780 ATGAGTAATG
Statistics
Matches: 321, Mismatches: 66, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
239 49 0.15
240 270 0.84
241 2 0.01
ACGTcount: A:0.46, C:0.15, G:0.21, T:0.18
Consensus pattern (240 bp):
AAATGATCTGGATTGAGCCAAGATCAAGTGATCGAGACGAAACCAAGAGTCAAAAATGAAGTGAC
CAAGATCAAGTCAAGGTCAAAAATAAATGAAAGAGATGAAACCATGAATCATAAGAAATGATATG
GACTAAGCCAAGATCAGGTGACCAAGACAAAACCACGAGTCAAAAATAAAATGACCAAAACCGAG
TCAAGGTCAAAAATAAATGACGAGGACAAAACCATAAATCATAAG
Found at i:17169322 original size:29 final size:25
Alignment explanation
Indices: 17169257--17169312 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
17169247 AAAAAATAAT
* *
17169257 ATAT-CAT-AAATGACATAATTAAA
1 ATATGCATAAAATAACATAACTAAA
17169280 ATATGCATAAAATAACATAACTAAA
1 ATATGCATAAAATAACATAACTAAA
17169305 ATATGCAT
1 ATATGCAT
17169313 GAAACAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 4 0.14
24 3 0.10
25 22 0.76
ACGTcount: A:0.55, C:0.11, G:0.05, T:0.29
Consensus pattern (25 bp):
ATATGCATAAAATAACATAACTAAA
Found at i:17169365 original size:18 final size:17
Alignment explanation
Indices: 17169335--17169374 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
17169325 ACATACACCT
*
17169335 TTTTTTTGCTTTTTTAA
1 TTTTTTTCCTTTTTTAA
*
17169352 TTTTTTTCCATTTTTTAG
1 TTTTTTTCC-TTTTTTAA
17169370 TTTTT
1 TTTTT
17169375 CTTTTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.10, C:0.07, G:0.05, T:0.78
Consensus pattern (17 bp):
TTTTTTTCCTTTTTTAA
Found at i:17170315 original size:18 final size:17
Alignment explanation
Indices: 17170294--17170327 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
17170284 AATGATAAGG
17170294 TATGAATGCATGACAATT
1 TATGAATGCATG-CAATT
17170312 TATGAATGCATGCAAT
1 TATGAATGCATGCAAT
17170328 AATGTAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (17 bp):
TATGAATGCATGCAATT
Found at i:17170420 original size:19 final size:19
Alignment explanation
Indices: 17170365--17170421 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
17170355 TTGGTTTAAG
**
17170365 GGTTGGTTTAGGGTTTGAAA
1 GGTT-GTTTAGGGTTTGGGA
* *
17170385 GGTGGTTGAGGGTTTGGGA
1 GGTTGTTTAGGGTTTGGGA
*
17170404 GGTTGTTTAGGATTTGGG
1 GGTTGTTTAGGGTTTGGG
17170422 TCTAGATTCT
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
19 27 0.90
20 3 0.10
ACGTcount: A:0.14, C:0.00, G:0.47, T:0.39
Consensus pattern (19 bp):
GGTTGTTTAGGGTTTGGGA
Found at i:17170479 original size:27 final size:28
Alignment explanation
Indices: 17170431--17170486 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 28
17170421 GTCTAGATTC
17170431 TAGGGTTTAGGGTGTAAGATTT-AGGTT
1 TAGGGTTTAGGGTGTAAGATTTGAGGTT
* *
17170458 TAGGGTTTAGAGTTTTAA-ATTTGAGGTT
1 TAGGGTTTAG-GGTGTAAGATTTGAGGTT
17170486 T
1 T
17170487 CATAGGAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 14 0.56
28 11 0.44
ACGTcount: A:0.23, C:0.00, G:0.32, T:0.45
Consensus pattern (28 bp):
TAGGGTTTAGGGTGTAAGATTTGAGGTT
Found at i:17171459 original size:16 final size:17
Alignment explanation
Indices: 17171424--17171456 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
17171414 GGAATATGCA
17171424 AAAAAACAAAAGATGGG
1 AAAAAACAAAAGATGGG
*
17171441 AAAAAATAAAAGATGG
1 AAAAAACAAAAGATGG
17171457 AAATTAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.21, T:0.09
Consensus pattern (17 bp):
AAAAAACAAAAGATGGG
Found at i:17176215 original size:20 final size:20
Alignment explanation
Indices: 17176190--17176232 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
17176180 TTCCCTCAAG
17176190 TTTTCCATTCTTGATGGCAT
1 TTTTCCATTCTTGATGGCAT
17176210 TTTTCCATTCTTGATGGCAT
1 TTTTCCATTCTTGATGGCAT
17176230 TTT
1 TTT
17176233 ACTATCTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.14, C:0.19, G:0.14, T:0.53
Consensus pattern (20 bp):
TTTTCCATTCTTGATGGCAT
Found at i:17176240 original size:19 final size:20
Alignment explanation
Indices: 17176190--17176243 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
17176180 TTCCCTCAAG
17176190 TTTT-CCATTCTTGATGGCA
1 TTTTACCATTCTTGATGGCA
*
17176209 TTTTTCCATTCTTGATGGCA
1 TTTTACCATTCTTGATGGCA
*
17176229 TTTTACTA-TCTTGAT
1 TTTTACCATTCTTGAT
17176244 TGGTACTGCC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 11 0.34
20 21 0.66
ACGTcount: A:0.17, C:0.19, G:0.13, T:0.52
Consensus pattern (20 bp):
TTTTACCATTCTTGATGGCA
Found at i:17181102 original size:13 final size:13
Alignment explanation
Indices: 17181084--17181140 Score: 50
Period size: 13 Copynumber: 4.6 Consensus size: 13
17181074 AAAAACTAAC
17181084 ATAAATAATCAAA
1 ATAAATAATCAAA
17181097 ATAAATAATCCAAA
1 ATAAATAAT-CAAA
*
17181111 A-AAACAA--AAA
1 ATAAATAATCAAA
* *
17181121 A-AAATATTTAAA
1 ATAAATAATCAAA
17181133 ATAAATAA
1 ATAAATAA
17181141 ATAGAAATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
10 8 0.22
12 4 0.11
13 19 0.53
14 5 0.14
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.21
Consensus pattern (13 bp):
ATAAATAATCAAA
Found at i:17182677 original size:18 final size:17
Alignment explanation
Indices: 17182654--17182688 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
17182644 AACTAAAATT
*
17182654 AATATATTTTTATTAAAA
1 AATATATATTTA-TAAAA
17182672 AATATATATTTATAAAA
1 AATATATATTTATAAAA
17182689 GAATTACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATATATTTATAAAA
Found at i:17183628 original size:71 final size:71
Alignment explanation
Indices: 17183497--17183632 Score: 186
Period size: 71 Copynumber: 1.9 Consensus size: 71
17183487 AAAAACTTAT
* ** *
17183497 GGATGTTAAAACTTTATTTTCAAAAATTTAAAATTTTAACAAAAATTGTGTTTGTGAGATAAAAA
1 GGATGTTAAAACTTTATTTTCAAAAATTTAAAATGTTAACAAAAACCGTGTTTGTAAGATAAAAA
17183562 TGTAGC
66 TGTAGC
* *
17183568 GGATGTTAAAA-TTATATTTTTAAAATTTTAAAATGTTAACAAAAACCGTAGTTT-TAAGATAAA
1 GGATGTTAAAACTT-TATTTTCAAAAATTTAAAATGTTAACAAAAACCGT-GTTTGTAAGATAAA
17183631 AA
64 AA
17183633 ACATAATGGA
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
70 2 0.04
71 51 0.89
72 4 0.07
ACGTcount: A:0.45, C:0.05, G:0.12, T:0.38
Consensus pattern (71 bp):
GGATGTTAAAACTTTATTTTCAAAAATTTAAAATGTTAACAAAAACCGTGTTTGTAAGATAAAAA
TGTAGC
Found at i:17183774 original size:70 final size:70
Alignment explanation
Indices: 17183682--17183991 Score: 234
Period size: 70 Copynumber: 4.4 Consensus size: 70
17183672 AAAAATAGTA
* * * * *
17183682 GATATTGAACTATAATTTTGAAAATTTGAAAATTTAACAAAAACCATAGTTTTAAGATAAAAATG
1 GATATTGAATTATATTTTTGAAAATTTGAAAATTTAACAAAAACCACAGTTTTAAAATAAAAACG
*
17183747 TAGTG
66 TAATG
* * * *
17183752 GATATTGAATTATATTTTTGAAAATTTGAAACTTTAACAAAAACCACATTTTTAAAATAAATACA
1 GATATTGAATTATATTTTTGAAAATTTGAAAATTTAACAAAAACCACAGTTTTAAAATAAAAACG
* *
17183817 CAATT
66 TAATG
* * * * * * * *
17183822 GATGTTGAGATTTTA-TTTTCAAAATTATGAAATTTTAATAAAGATCA-TGTTTTTAAAAATAAA
1 GATATTGA-ATTATATTTTTGAAAATT-TGAAAATTTAACAAAAACCACAG-TTTT-AAAATAAA
17183885 AACGTAATG
62 AACGTAATG
* * * * * * *
17183894 GATATTAAAACTATATTTTTG-AAATTCT-AGAATATTAATAAAAACTACAATTTTAAGATAAAA
1 GATATT-GAATTATATTTTTGAAAATT-TGAAAAT-TTAACAAAAACCACAGTTTTAAAATAAAA
* *
17183957 ATGTTATG
63 ACGTAATG
* *
17183965 GATATATAAATTTTATTTTT-AAAATTT
1 GATAT-TGAATTATATTTTTGAAAATTT
17183992 TAACAAAAAT
Statistics
Matches: 187, Mismatches: 43, Indels: 20
0.75 0.17 0.08
Matches are distributed among these distances:
70 76 0.41
71 63 0.34
72 43 0.23
73 5 0.03
ACGTcount: A:0.46, C:0.06, G:0.09, T:0.39
Consensus pattern (70 bp):
GATATTGAATTATATTTTTGAAAATTTGAAAATTTAACAAAAACCACAGTTTTAAAATAAAAACG
TAATG
Found at i:17186058 original size:14 final size:15
Alignment explanation
Indices: 17186035--17186068 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
17186025 CATTTTATAA
*
17186035 TATTTTTAATAAA-T
1 TATTTGTAATAAATT
17186049 TATTTGTAATAAATT
1 TATTTGTAATAAATT
17186064 TATTT
1 TATTT
17186069 TTTGGGTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
TATTTGTAATAAATT
Found at i:17187715 original size:7 final size:7
Alignment explanation
Indices: 17187665--17187716 Score: 52
Period size: 7 Copynumber: 7.1 Consensus size: 7
17187655 TTTTAATAAC
17187665 AATAAAA
1 AATAAAA
*
17187672 AATTAAAT
1 AA-TAAAA
17187680 AATAAATA
1 AATAAA-A
17187688 AATAAATA
1 AATAAA-A
*
17187696 CAT-AAA
1 AATAAAA
17187702 AATAAAA
1 AATAAAA
17187709 AATAAAA
1 AATAAAA
17187716 A
1 A
17187717 CAAAATTGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
6 3 0.08
7 19 0.50
8 16 0.42
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (7 bp):
AATAAAA
Found at i:17192265 original size:21 final size:22
Alignment explanation
Indices: 17192239--17192281 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
17192229 AATTAAATTT
17192239 ATTAAACTTAA-GAACATGCAA
1 ATTAAACTTAACGAACATGCAA
*
17192260 ATTAAACTTAACTAACATGCAA
1 ATTAAACTTAACGAACATGCAA
17192282 TAACATAAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.51, C:0.16, G:0.07, T:0.26
Consensus pattern (22 bp):
ATTAAACTTAACGAACATGCAA
Found at i:17192617 original size:21 final size:20
Alignment explanation
Indices: 17192576--17192623 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
17192566 GTTTGAAAAC
* *
17192576 TTAAATTAAACTTGTATAAA
1 TTAAATTAAACTTGAAGAAA
17192596 TTTAAATT-AACTTGAAAGAAA
1 -TTAAATTAAACTTG-AAGAAA
17192617 TTAAATT
1 TTAAATT
17192624 TAATAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (20 bp):
TTAAATTAAACTTGAAGAAA
Found at i:17192656 original size:23 final size:23
Alignment explanation
Indices: 17192628--17192671 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
17192618 TAAATTTAAT
17192628 AGAAAACTTAAGAA-AACAATGCA
1 AGAAAACTTAA-AATAACAATGCA
17192651 AGAAAACTTAAAATAACAATG
1 AGAAAACTTAAAATAACAATG
17192672 GTTTATCACC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 2 0.10
23 18 0.90
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.16
Consensus pattern (23 bp):
AGAAAACTTAAAATAACAATGCA
Found at i:17203599 original size:26 final size:26
Alignment explanation
Indices: 17203550--17203616 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
17203540 CCTAGACCAC
17203550 AAACTTGAAATCCAAAATTCCAAACCCT
1 AAACTT-AAA-CCAAAATTCCAAACCCT
* *
17203578 AAACTTAAACCTAAATTTCAAACCCT
1 AAACTTAAACCAAAATTCCAAACCCT
17203604 AAACTTTAAACCA
1 AAAC-TTAAACCA
17203617 CCTTCCAAAC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
26 19 0.54
27 10 0.29
28 6 0.17
ACGTcount: A:0.48, C:0.27, G:0.01, T:0.24
Consensus pattern (26 bp):
AAACTTAAACCAAAATTCCAAACCCT
Found at i:17203606 original size:14 final size:13
Alignment explanation
Indices: 17203571--17203615 Score: 56
Period size: 14 Copynumber: 3.4 Consensus size: 13
17203561 CCAAAATTCC
*
17203571 AAACCCTAAACTT
1 AAACCCTAAATTT
17203584 AAA-CCTAAATTT
1 AAACCCTAAATTT
17203596 CAAACCCTAAACTTT
1 -AAACCCTAAA-TTT
17203611 AAACC
1 AAACC
17203616 ACCTTCCAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
12 8 0.29
13 6 0.21
14 11 0.39
15 3 0.11
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (13 bp):
AAACCCTAAATTT
Found at i:17204659 original size:12 final size:12
Alignment explanation
Indices: 17204642--17204676 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
17204632 ATCAAAACTC
*
17204642 AAAAAAATTTTG
1 AAAAAAATGTTG
*
17204654 AAAAAAAAGTTG
1 AAAAAAATGTTG
17204666 AAAAAAATGTT
1 AAAAAAATGTT
17204677 TTGATTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (12 bp):
AAAAAAATGTTG
Found at i:17205080 original size:30 final size:30
Alignment explanation
Indices: 17205046--17205110 Score: 121
Period size: 30 Copynumber: 2.2 Consensus size: 30
17205036 ATCAGAGATT
17205046 AATCTATGCCATTTTTAAAATAAATAGAGA
1 AATCTATGCCATTTTTAAAATAAATAGAGA
*
17205076 AATCTATGGCATTTTTAAAATAAATAGAGA
1 AATCTATGCCATTTTTAAAATAAATAGAGA
17205106 AATCT
1 AATCT
17205111 TTATCAGAGA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (30 bp):
AATCTATGCCATTTTTAAAATAAATAGAGA
Found at i:17206074 original size:80 final size:80
Alignment explanation
Indices: 17205934--17206097 Score: 235
Period size: 80 Copynumber: 2.0 Consensus size: 80
17205924 TTTTTTAGAT
* * * *
17205934 ATCTTGATATTTTAGTGGTATTTTAAAAGAATTTTTTCACTTATAGTTTTTTTAAGAATCTCTAC
1 ATCTTGATACTTTAGTGGTATTTTAAAAGAATTTTCTCACCTATAGTTTTCTTAAGAATCTCTAC
*
17205999 TCATACTTCCTTAAA
66 TCAGACTTCCTTAAA
17206014 ATCTTGATACTTTAGTGGTATTTTAAAAGAATTTTC-CTACCTA-AGGTTTTCTT-AGAAATCTC
1 ATCTTGATACTTTAGTGGTATTTTAAAAGAATTTTCTC-ACCTATA-GTTTTCTTAAG-AATCTC
17206076 TACTCAGACTTCCTTAAA
63 TACTCAGACTTCCTTAAA
17206094 ATCT
1 ATCT
17206098 CATCCTTGGA
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
79 4 0.05
80 72 0.95
ACGTcount: A:0.30, C:0.15, G:0.10, T:0.45
Consensus pattern (80 bp):
ATCTTGATACTTTAGTGGTATTTTAAAAGAATTTTCTCACCTATAGTTTTCTTAAGAATCTCTAC
TCAGACTTCCTTAAA
Found at i:17217699 original size:30 final size:30
Alignment explanation
Indices: 17217665--17217764 Score: 98
Period size: 30 Copynumber: 3.4 Consensus size: 30
17217655 TATTATATTA
*
17217665 AAATAAACTCTTAATTTTTATTTTATATCC
1 AAATAAACTCTTAATTTTTAATTTATATCC
* * * *
17217695 AAATAAGCTTTTAAATTTTAATTTGTAT-C
1 AAATAAACTCTTAATTTTTAATTTATATCC
* * *
17217724 AAAAAAGACT-TTAATCTTTAATTTATATCT
1 AAATAA-ACTCTTAATTTTTAATTTATATCC
17217754 AAATAAA-TCTT
1 AAATAAACTCTT
17217765 TATAAATTAT
Statistics
Matches: 55, Mismatches: 12, Indels: 7
0.74 0.16 0.09
Matches are distributed among these distances:
28 1 0.02
29 24 0.44
30 30 0.55
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (30 bp):
AAATAAACTCTTAATTTTTAATTTATATCC
Found at i:17217713 original size:59 final size:60
Alignment explanation
Indices: 17217650--17217791 Score: 148
Period size: 59 Copynumber: 2.4 Consensus size: 60
17217640 AATGCCATAT
* *
17217650 ATTTTTATTATATTAAAATAAACTCTTAATTTTTATTTTATATCCAAAT-AAGCTTT-TAA
1 ATTTTTATTATATTAAAATAAACT-TTAATCTTTAATTTATATCCAAATAAAGCTTTATAA
* * * * *
17217709 ATTTTAATTTGTATCAAAA-AAGACTTTAATCTTTAATTTATATCTAAATAAATCTTTATAA
1 ATTTTTA-TTATATTAAAATAA-ACTTTAATCTTTAATTTATATCCAAATAAAGCTTTATAA
*
17217770 ATTATTTTTTAT-TTAAAATAAA
1 ATT-TTTATTATATTAAAATAAA
17217792 GATTTATTTG
Statistics
Matches: 66, Mismatches: 11, Indels: 11
0.75 0.12 0.12
Matches are distributed among these distances:
59 29 0.44
60 24 0.36
61 11 0.17
62 2 0.03
ACGTcount: A:0.42, C:0.07, G:0.02, T:0.49
Consensus pattern (60 bp):
ATTTTTATTATATTAAAATAAACTTTAATCTTTAATTTATATCCAAATAAAGCTTTATAA
Found at i:17217856 original size:29 final size:30
Alignment explanation
Indices: 17217784--17217860 Score: 86
Period size: 29 Copynumber: 2.6 Consensus size: 30
17217774 TTTTTTATTT
* *
17217784 AAAATAAAGATTTATTTGGATAAAAATAAA
1 AAAATAAAGATTTATTTAGATAAAAACAAA
*
17217814 AAAATAAA-AGTTTATTTAGAT-ATAACAAA
1 AAAATAAAGA-TTTATTTAGATAAAAACAAA
* *
17217843 GATATAAAGATTTATTTA
1 AAAATAAAGATTTATTTA
17217861 AACAACATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 21 0.52
30 19 0.47
ACGTcount: A:0.56, C:0.01, G:0.09, T:0.34
Consensus pattern (30 bp):
AAAATAAAGATTTATTTAGATAAAAACAAA
Found at i:17220559 original size:41 final size:41
Alignment explanation
Indices: 17220481--17220560 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 41
17220471 TTCGCAAACC
* * *
17220481 AAATGAATATCACAAACAACCTTTAAATTCAAGTAAAATGT
1 AAATAAATATCACAAACAACCTCTAAATTCAAATAAAATGT
* *
17220522 AAATAAATATCACAAATAATCTCTAAATT-ATAATAAAAT
1 AAATAAATATCACAAACAACCTCTAAATTCA-AATAAAAT
17220561 ATTCAGTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
40 1 0.03
41 32 0.97
ACGTcount: A:0.55, C:0.12, G:0.04, T:0.29
Consensus pattern (41 bp):
AAATAAATATCACAAACAACCTCTAAATTCAAATAAAATGT
Found at i:17220615 original size:29 final size:30
Alignment explanation
Indices: 17220545--17220615 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 30
17220535 AAATAATCTC
*
17220545 TAAATTATAATAAAATATTCAGTAAAATATT
1 TAAATTATAA-AAAATATTCAATAAAATATT
* *
17220576 TAAAATT-TAAAAAAT-TTTAATATAATATT
1 T-AAATTATAAAAAATATTCAATAAAATATT
17220605 TAAATTATAAA
1 TAAATTATAAA
17220616 TTTATTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
28 5 0.14
29 16 0.46
30 5 0.14
31 4 0.11
32 5 0.14
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.41
Consensus pattern (30 bp):
TAAATTATAAAAAATATTCAATAAAATATT
Found at i:17220737 original size:28 final size:30
Alignment explanation
Indices: 17220699--17220763 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
17220689 ATATTATATT
* *
17220699 AATTAATAAATTTAT-AATT-TAAATATAA
1 AATTAAAAAATTTATAAATTCAAAATATAA
* *
17220727 AATTAAAAAATTTTTAAATTCAAAATATCA
1 AATTAAAAAATTTATAAATTCAAAATATAA
17220757 AATTAAA
1 AATTAAA
17220764 TATTTTATTA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 13 0.42
29 4 0.13
30 14 0.45
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.38
Consensus pattern (30 bp):
AATTAAAAAATTTATAAATTCAAAATATAA
Found at i:17227457 original size:22 final size:23
Alignment explanation
Indices: 17227425--17227474 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
17227415 AAATATACAA
*
17227425 AATATATTATAATGATAATAAAT
1 AATATATTATAATGATAAGAAAT
17227448 AATAT-TTATAATGATAAGAAAT
1 AATATATTATAATGATAAGAAAT
*
17227470 TATAT
1 AATAT
17227475 GATCATCTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 20 0.80
23 5 0.20
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (23 bp):
AATATATTATAATGATAAGAAAT
Found at i:17227754 original size:19 final size:19
Alignment explanation
Indices: 17227730--17227794 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
17227720 TATCTACTAT
* *
17227730 TTATTCATATATGTTAATG
1 TTATTCATATATATCAATG
* *
17227749 TTATTCATGTATATCATTG
1 TTATTCATATATATCAATG
* *
17227768 TTATTCTTATATATCAATA
1 TTATTCATATATATCAATG
17227787 TTATTCAT
1 TTATTCAT
17227795 GTGTATTTGT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 37 1.00
ACGTcount: A:0.31, C:0.09, G:0.06, T:0.54
Consensus pattern (19 bp):
TTATTCATATATATCAATG
Found at i:17228275 original size:14 final size:14
Alignment explanation
Indices: 17228256--17228288 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
17228246 ATTTAACATT
*
17228256 TATAAAATTTCTTA
1 TATAAAATTTATTA
17228270 TATAAAATTTATTA
1 TATAAAATTTATTA
17228284 -ATAAA
1 TATAAA
17228289 TAATAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (14 bp):
TATAAAATTTATTA
Found at i:17228300 original size:20 final size:20
Alignment explanation
Indices: 17228271--17228322 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
17228261 AATTTCTTAT
17228271 ATAAAATTTATTAATAAATA
1 ATAAAATTTATTAATAAATA
*
17228291 ATAAATTTTATTAATAAATA
1 ATAAAATTTATTAATAAATA
*
17228311 GTAAAATTTATT
1 ATAAAATTTATT
17228323 TAAATTATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
ATAAAATTTATTAATAAATA
Found at i:17231907 original size:14 final size:14
Alignment explanation
Indices: 17231888--17231925 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
17231878 CGATGAAAAC
*
17231888 AAAAAACACACATT
1 AAAAAACACACATA
17231902 AAAAAACACA-ATA
1 AAAAAACACACATA
*
17231915 AAAAAAGACAC
1 AAAAAACACAC
17231926 CAAAAGCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.71, C:0.18, G:0.03, T:0.08
Consensus pattern (14 bp):
AAAAAACACACATA
Found at i:17236466 original size:15 final size:15
Alignment explanation
Indices: 17236446--17236476 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
17236436 TATATTAAAG
17236446 CACTAAAATTCAATT
1 CACTAAAATTCAATT
17236461 CACTAAAATTCAATT
1 CACTAAAATTCAATT
17236476 C
1 C
17236477 GATTCATTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.32
Consensus pattern (15 bp):
CACTAAAATTCAATT
Found at i:17242077 original size:13 final size:13
Alignment explanation
Indices: 17242034--17242229 Score: 84
Period size: 13 Copynumber: 15.3 Consensus size: 13
17242024 TTAAGGTTGC
17242034 ATTTAAGGTTTTGA
1 ATTTAAGGTTTT-A
* **
17242048 TTTTAAGGTTCCA
1 ATTTAAGGTTTTA
*
17242061 ATTTAAGGTTTTG
1 ATTTAAGGTTTTA
*
17242074 ATTTAGGGTTTTA
1 ATTTAAGGTTTTA
* *
17242087 ATTTAGGGTTTCA
1 ATTTAAGGTTTTA
* * * *
17242100 AGTTAAAGCTTCA
1 ATTTAAGGTTTTA
*
17242113 ATTTAGGGTTTTA
1 ATTTAAGGTTTTA
*
17242126 ATCTT-AGTGTTTTG
1 AT-TTAAG-GTTTTA
* *
17242140 ATTTAGGGTTTTG
1 ATTTAAGGTTTTA
*
17242153 TTTTAA-G---T-
1 ATTTAAGGTTTTA
*
17242161 -TTTAAGGTTTCA
1 ATTTAAGGTTTTA
* *
17242173 ATTTAAGGGTTTC
1 ATTTAAGGTTTTA
*
17242186 ATTT-AGGATTTTG
1 ATTTAAGG-TTTTA
*
17242199 ATTTAAGGTTTGA
1 ATTTAAGGTTTTA
* *
17242212 ATTTTAGGGTTTGA
1 A-TTTAAGGTTTTA
17242226 ATTT
1 ATTT
17242230 TAAGAATTTA
Statistics
Matches: 137, Mismatches: 33, Indels: 25
0.70 0.17 0.13
Matches are distributed among these distances:
7 5 0.04
8 1 0.01
9 1 0.01
12 4 0.03
13 92 0.67
14 34 0.25
ACGTcount: A:0.24, C:0.04, G:0.21, T:0.51
Consensus pattern (13 bp):
ATTTAAGGTTTTA
Found at i:17242091 original size:26 final size:27
Alignment explanation
Indices: 17242022--17242077 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
17242012 AAGATTTCAG
*
17242022 TTTTAAGGTTGC-ATTTAAGGTTTTGA
1 TTTTAAGGTTCCAATTTAAGGTTTTGA
17242048 TTTTAAGGTTCCAATTTAAGGTTTTGA
1 TTTTAAGGTTCCAATTTAAGGTTTTGA
17242075 TTT
1 TTT
17242078 AGGGTTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 11 0.39
27 17 0.61
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.52
Consensus pattern (27 bp):
TTTTAAGGTTCCAATTTAAGGTTTTGA
Found at i:17242096 original size:26 final size:26
Alignment explanation
Indices: 17242034--17242223 Score: 115
Period size: 26 Copynumber: 7.4 Consensus size: 26
17242024 TTAAGGTTGC
* **
17242034 ATTTAAGGTTTTGATTTTAAGGTTCCA
1 ATTTAGGGTTTTGA-TTTAAGGTTTTA
* *
17242061 ATTTAAGGTTTTGATTTAGGGTTTTA
1 ATTTAGGGTTTTGATTTAAGGTTTTA
** * * * *
17242087 ATTTAGGGTTTCAAGTTAAAGCTTCA
1 ATTTAGGGTTTTGATTTAAGGTTTTA
* *
17242113 ATTTAGGGTTTTAATCTT-AGTGTTTTG
1 ATTTAGGGTTTTGAT-TTAAG-GTTTTA
*
17242140 ATTTAGGGTTTTGTTTTAA-GTTTT-
1 ATTTAGGGTTTTGATTTAAGGTTTTA
** * *
17242164 A---A-GGTTTCAATTTAAGGGTTTC
1 ATTTAGGGTTTTGATTTAAGGTTTTA
* *
17242186 ATTTAGGATTTTGATTTAAGGTTTGA
1 ATTTAGGGTTTTGATTTAAGGTTTTA
17242212 ATTTTAGGGTTT
1 A-TTTAGGGTTT
17242224 GAATTTTAAG
Statistics
Matches: 123, Mismatches: 30, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
20 10 0.08
21 5 0.04
22 1 0.01
24 1 0.01
25 6 0.05
26 58 0.47
27 42 0.34
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.51
Consensus pattern (26 bp):
ATTTAGGGTTTTGATTTAAGGTTTTA
Found at i:17242137 original size:14 final size:13
Alignment explanation
Indices: 17242060--17242151 Score: 85
Period size: 13 Copynumber: 7.0 Consensus size: 13
17242050 TTAAGGTTCC
*
17242060 AATTTAAGGTTTT
1 AATTTAGGGTTTT
*
17242073 GATTTAGGGTTTT
1 AATTTAGGGTTTT
*
17242086 AATTTAGGGTTTC
1 AATTTAGGGTTTT
* ** * *
17242099 AAGTTAAAGCTTC
1 AATTTAGGGTTTT
17242112 AATTTAGGGTTTT
1 AATTTAGGGTTTT
*
17242125 AATCTTAGTGTTTT
1 AAT-TTAGGGTTTT
*
17242139 GATTTAGGGTTTT
1 AATTTAGGGTTTT
17242152 GTTTTAAGTT
Statistics
Matches: 62, Mismatches: 16, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
13 51 0.82
14 11 0.18
ACGTcount: A:0.24, C:0.04, G:0.22, T:0.50
Consensus pattern (13 bp):
AATTTAGGGTTTT
Found at i:17242230 original size:14 final size:14
Alignment explanation
Indices: 17242200--17242233 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
17242190 AGGATTTTGA
17242200 TTTAAGGTTTGAAT
1 TTTAAGGTTTGAAT
*
17242214 TTTAGGGTTTGAAT
1 TTTAAGGTTTGAAT
17242228 TTTAAG
1 TTTAAG
17242234 AATTTACAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (14 bp):
TTTAAGGTTTGAAT
Found at i:17243794 original size:3 final size:3
Alignment explanation
Indices: 17243780--17243809 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
17243770 AGTTATTTAT
17243780 TTA TTAA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT
17243810 GAATTTGTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:17244290 original size:32 final size:33
Alignment explanation
Indices: 17244254--17244470 Score: 164
Period size: 32 Copynumber: 6.7 Consensus size: 33
17244244 AGTTAAATTA
*
17244254 GGCTTAAATTTTCATT-AGTACTAGGTAATCTG
1 GGCTTAAATTTTCATTGAGTACTAGATAATCTG
*
17244286 GGCTTAAATTTTCATT-AGGTGCTAGATAATCTG
1 GGCTTAAATTTTCATTGA-GTACTAGATAATCTG
* * *
17244319 AGCTTAAAATTTCATTGGGTA-TAGATAATCTG
1 GGCTTAAATTTTCATTGAGTACTAGATAATCTG
* * * *
17244351 GACTTAAATTTTCATTGGGTACAAGATAATCTA
1 GGCTTAAATTTTCATTGAGTACTAGATAATCTG
* * * * *
17244384 GGTTTAAA-TTTCTTTG-GATGCCA-ACTAAGCTG
1 GGCTTAAATTTTCATTGAG-TACTAGA-TAATCTG
* * *
17244416 GGCTTAAA-TTTCATTGAGTACCA-ACTAAACTA
1 GGCTTAAATTTTCATTGAGTACTAGA-TAATCTG
17244448 GGCTTAAATCTTTTCA-TGAGTAC
1 GGCTTAAA--TTTTCATTGAGTAC
17244471 GAGCTAAACT
Statistics
Matches: 153, Mismatches: 23, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
31 2 0.01
32 94 0.61
33 45 0.29
34 7 0.05
35 5 0.03
ACGTcount: A:0.31, C:0.14, G:0.18, T:0.37
Consensus pattern (33 bp):
GGCTTAAATTTTCATTGAGTACTAGATAATCTG
Found at i:17244324 original size:33 final size:32
Alignment explanation
Indices: 17244254--17244394 Score: 169
Period size: 32 Copynumber: 4.3 Consensus size: 32
17244244 AGTTAAATTA
*
17244254 GGCTTAAATTTTCATTA-GTACTAGGTAATCT
1 GGCTTAAATTTTCATTAGGTACTAGATAATCT
*
17244285 GGGCTTAAATTTTCATTAGGTGCTAGATAATCT
1 -GGCTTAAATTTTCATTAGGTACTAGATAATCT
* *
17244318 GAGCTTAAAATTTCATTGGGTA-TAGATAATCT
1 G-GCTTAAATTTTCATTAGGTACTAGATAATCT
* *
17244350 GGACTTAAATTTTCATTGGGTACAAGATAATCT
1 GG-CTTAAATTTTCATTAGGTACTAGATAATCT
*
17244383 AGGTTTAAATTT
1 -GGCTTAAATTT
17244395 CTTTGGATGC
Statistics
Matches: 96, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
31 1 0.01
32 47 0.49
33 46 0.48
34 2 0.02
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (32 bp):
GGCTTAAATTTTCATTAGGTACTAGATAATCT
Found at i:17244332 original size:65 final size:64
Alignment explanation
Indices: 17244255--17244395 Score: 176
Period size: 65 Copynumber: 2.2 Consensus size: 64
17244245 GTTAAATTAG
* * * * *
17244255 GCTTAAATTTTCATT-AGTACTAGGTAATCTGGGCTTAAATTTTCATTAGGTGCTAGATAATCTG
1 GCTTAAAATTTCATTGAGTA-TAGATAATCTGGACTTAAATTTTCATTAGGTACAAGATAATCT-
17244319 A
64 A
* *
17244320 GCTTAAAATTTCATTGGGTATAGATAATCTGGACTTAAATTTTCATTGGGTACAAGATAATCTA
1 GCTTAAAATTTCATTGAGTATAGATAATCTGGACTTAAATTTTCATTAGGTACAAGATAATCTA
* *
17244384 GGTTTAAATTTC
1 GCTTAAAATTTC
17244396 TTTGGATGCC
Statistics
Matches: 66, Mismatches: 9, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
64 11 0.17
65 52 0.79
66 3 0.05
ACGTcount: A:0.31, C:0.11, G:0.18, T:0.40
Consensus pattern (64 bp):
GCTTAAAATTTCATTGAGTATAGATAATCTGGACTTAAATTTTCATTAGGTACAAGATAATCTA
Found at i:17244422 original size:65 final size:65
Alignment explanation
Indices: 17244255--17244436 Score: 165
Period size: 65 Copynumber: 2.8 Consensus size: 65
17244245 GTTAAATTAG
* * * * * * *
17244255 GCTTAAATTTTCATTAG-TACTAGGTAATCTGGGCTTAAATTTTCATTAGGTGCTAGATAATCTG
1 GCTTAAAATTTCATTGGATAC-AGATAAGCTGGGCTTAAATTTTCATTGGGTACAAGATAATCTG
17244319 A
65 A
* * * *
17244320 GCTTAAAATTTCATTGGGTATAGATAATCTGGACTTAAATTTTCATTGGGTACAAGATAATCT-A
1 GCTTAAAATTTCATTGGATACAGATAAGCTGGGCTTAAATTTTCATTGGGTACAAGATAATCTGA
* * * * *
17244384 GGTTTAAATTTCTTTGGATGCCA-ACTAAGCTGGGCTTAAA-TTTCATTGAGTAC
1 GCTTAAAATTTCATTGGAT-ACAGA-TAAGCTGGGCTTAAATTTTCATTGGGTAC
17244437 CAACTAAACT
Statistics
Matches: 97, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
64 29 0.30
65 66 0.68
66 2 0.02
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.38
Consensus pattern (65 bp):
GCTTAAAATTTCATTGGATACAGATAAGCTGGGCTTAAATTTTCATTGGGTACAAGATAATCTGA
Found at i:17244478 original size:34 final size:35
Alignment explanation
Indices: 17244424--17244495 Score: 101
Period size: 34 Copynumber: 2.1 Consensus size: 35
17244414 TGGGCTTAAA
* *
17244424 TTTCATTGAGTACCAACTAAACTAGGCTTAAATCT
1 TTTCATTGAGTACCAACTAAACTAAGCATAAATCT
* *
17244459 TTTCA-TGAGTACGAGCTAAACTAAGCATAAATCT
1 TTTCATTGAGTACCAACTAAACTAAGCATAAATCT
17244493 TTT
1 TTT
17244496 TATGTGTGCC
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
34 28 0.85
35 5 0.15
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (35 bp):
TTTCATTGAGTACCAACTAAACTAAGCATAAATCT
Found at i:17244572 original size:67 final size:66
Alignment explanation
Indices: 17244501--17244631 Score: 165
Period size: 66 Copynumber: 2.0 Consensus size: 66
17244491 CTTTTTATGT
* * * * * *
17244501 GTGCCAAATAAATTGGGCTTAAAAT-TTTATTAGGTTTTAGCTAAATTGGGCTTAAATATTTCAT
1 GTGCCAAACAAACTGGGCTT-AAATCTTTATT-GGTGTTAGCTAAACTGCGCTTAAATATTGCAT
17244565 TAA
64 TAA
* *
17244568 GTGCCAACCAAACTGGGCTTAAATCTTTATTGGTGTTAGTTAAACTGCGCTTAAATATTGCATT
1 GTGCCAAACAAACTGGGCTTAAATCTTTATTGGTGTTAGCTAAACTGCGCTTAAATATTGCATT
17244632 GGGTGTCAGT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
66 32 0.58
67 23 0.42
ACGTcount: A:0.31, C:0.13, G:0.18, T:0.38
Consensus pattern (66 bp):
GTGCCAAACAAACTGGGCTTAAATCTTTATTGGTGTTAGCTAAACTGCGCTTAAATATTGCATTA
A
Found at i:17244643 original size:34 final size:32
Alignment explanation
Indices: 17244577--17244689 Score: 127
Period size: 32 Copynumber: 3.5 Consensus size: 32
17244567 AGTGCCAACC
* * * *
17244577 AAACTGGGCTTAAATCTTTATTGGTGTTAGTT
1 AAACTGCGCTTAAATATTCATTGGTGTCAGTT
17244609 AAACTGCGCTTAAATATTGCATTGGGTGTCAGTT
1 AAACTGCGCTTAAATATT-CATT-GGTGTCAGTT
** **
17244643 AAACTGCATTTAAATATTCATTGGTACCAGTT
1 AAACTGCGCTTAAATATTCATTGGTGTCAGTT
*
17244675 AAACTGAGCTTAAAT
1 AAACTGCGCTTAAAT
17244690 CTTGTGTTGA
Statistics
Matches: 68, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
32 36 0.53
33 7 0.10
34 25 0.37
ACGTcount: A:0.31, C:0.13, G:0.19, T:0.37
Consensus pattern (32 bp):
AAACTGCGCTTAAATATTCATTGGTGTCAGTT
Found at i:17244647 original size:66 final size:65
Alignment explanation
Indices: 17244501--17244689 Score: 153
Period size: 66 Copynumber: 2.8 Consensus size: 65
17244491 CTTTTTATGT
* * * * * * *
17244501 GTGCCAAATAAATTGGGCTTAAAATTTTATTAGGTTTTAGCTAAATTGGGCTTAAATATTTCATT
1 GTGCCAACTAAACTGGGCTT-AAATTTTATT-GGTATTAGTTAAACTGAGCTTAAATATTGCATT
17244566 AA
64 AA
* * * *
17244568 GTGCCAACCAAACTGGGCTTAAATCTTTATTGGTGTTAGTTAAACTGCGCTTAAATATTGCATTG
1 GTGCCAACTAAACTGGGCTTAAAT-TTTATTGGTATTAGTTAAACTGAGCTTAAATATTGCATTA
*
17244633 G
65 A
* ** *** * **
17244634 GTGTCAGTTAAACTGCATTTAAATATTCATTGGTACCAGTTAAACTGAGCTTAAAT
1 GTGCCAACTAAACTGGGCTTAAAT-TTTATTGGTATTAGTTAAACTGAGCTTAAAT
17244690 CTTGTGTTGA
Statistics
Matches: 98, Mismatches: 23, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
66 75 0.77
67 23 0.23
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (65 bp):
GTGCCAACTAAACTGGGCTTAAATTTTATTGGTATTAGTTAAACTGAGCTTAAATATTGCATTAA
Found at i:17244955 original size:22 final size:22
Alignment explanation
Indices: 17244923--17244976 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
17244913 TAAATATTAG
17244923 GTGTCAACTAATCTAGGCTTAT
1 GTGTCAACTAATCTAGGCTTAT
* * *
17244945 GTGTCAGCTAATCTGGGCTTGT
1 GTGTCAACTAATCTAGGCTTAT
*
17244967 GTGCCAACTA
1 GTGTCAACTA
17244977 GACTGGATGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.33
Consensus pattern (22 bp):
GTGTCAACTAATCTAGGCTTAT
Found at i:17246449 original size:17 final size:16
Alignment explanation
Indices: 17246401--17246475 Score: 53
Period size: 16 Copynumber: 4.5 Consensus size: 16
17246391 TTCACTTGAC
17246401 TTTTCTTTTGGTTTTT-
1 TTTT-TTTTGGTTTTTG
* * *
17246417 TTGATTTTAGGCTTTTG
1 TT-TTTTTTGGTTTTTG
* *
17246434 TTTTGTTTTGTTTTTTTT
1 TTTT-TTTTG-GTTTTTG
*
17246452 TTTTTTTTGGTTTTGG
1 TTTTTTTTGGTTTTTG
17246468 TTTTTTTT
1 TTTTTTTT
17246476 CCAAAAGTTT
Statistics
Matches: 44, Mismatches: 11, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
16 24 0.55
17 12 0.27
18 8 0.18
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.79
Consensus pattern (16 bp):
TTTTTTTTGGTTTTTG
Found at i:17246455 original size:23 final size:23
Alignment explanation
Indices: 17246429--17246475 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
17246419 GATTTTAGGC
* *
17246429 TTTTGTTTT-GTTTTGTTTTTTT
1 TTTTTTTTTGGTTTTGGTTTTTT
17246451 TTTTTTTTTGGTTTTGGTTTTTT
1 TTTTTTTTTGGTTTTGGTTTTTT
17246474 TT
1 TT
17246476 CCAAAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (23 bp):
TTTTTTTTTGGTTTTGGTTTTTT
Found at i:17246558 original size:5 final size:5
Alignment explanation
Indices: 17246548--17246580 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
17246538 TTATAACCAT
*
17246548 TTTTC TTTTC TTTTT TTTTC TTTT- TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
17246581 TATTTTGTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (5 bp):
TTTTC
Found at i:17246566 original size:10 final size:10
Alignment explanation
Indices: 17246547--17246603 Score: 62
Period size: 10 Copynumber: 5.6 Consensus size: 10
17246537 GTTATAACCA
17246547 TTTTTCTTTTC
1 TTTTT-TTTTC
17246558 TTTTTTTTTC
1 TTTTTTTTTC
17246568 -TTTTTTTTC
1 TTTTTTTTTC
*
17246577 TTTTTATTTTG
1 TTTTT-TTTTC
* *
17246588 TTTGTTTTTG
1 TTTTTTTTTC
17246598 TTTTTT
1 TTTTTT
17246604 ACGTGCCCTC
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
9 9 0.22
10 19 0.46
11 13 0.32
ACGTcount: A:0.02, C:0.07, G:0.05, T:0.86
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:17246567 original size:15 final size:14
Alignment explanation
Indices: 17246547--17246603 Score: 60
Period size: 15 Copynumber: 3.9 Consensus size: 14
17246537 GTTATAACCA
17246547 TTTTTCTTTTCTTTT
1 TTTTTCTTTT-TTTT
17246562 TTTTTCTTTTTTTT
1 TTTTTCTTTTTTTT
* *
17246576 CTTTTTATTTTGTTTG
1 -TTTTTCTTTT-TTTT
*
17246592 TTTTTGTTTTTT
1 TTTTTCTTTTTT
17246604 ACGTGCCCTC
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
14 6 0.16
15 28 0.76
16 3 0.08
ACGTcount: A:0.02, C:0.07, G:0.05, T:0.86
Consensus pattern (14 bp):
TTTTTCTTTTTTTT
Found at i:17246571 original size:9 final size:9
Alignment explanation
Indices: 17246548--17246581 Score: 50
Period size: 9 Copynumber: 3.6 Consensus size: 9
17246538 TTATAACCAT
17246548 TTTTCTTTTC
1 TTTT-TTTTC
17246558 TTTTTTTTTC
1 -TTTTTTTTC
17246568 TTTTTTTTC
1 TTTTTTTTC
17246577 TTTTT
1 TTTTT
17246582 ATTTTGTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 5 0.22
11 4 0.17
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:17246586 original size:24 final size:24
Alignment explanation
Indices: 17246547--17246596 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
17246537 GTTATAACCA
*
17246547 TTTTTCTTTTCTTTTTTTTTCTTT
1 TTTTTCTTTTCTTTTTGTTTCTTT
*
17246571 TTTTTCTTTT-TATTTTGTTTGTTT
1 TTTTTCTTTTCT-TTTTGTTTCTTT
17246595 TT
1 TT
17246597 GTTTTTTACG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 1 0.04
24 22 0.96
ACGTcount: A:0.02, C:0.08, G:0.04, T:0.86
Consensus pattern (24 bp):
TTTTTCTTTTCTTTTTGTTTCTTT
Found at i:17246732 original size:25 final size:25
Alignment explanation
Indices: 17246703--17246752 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
17246693 AAGTTATTGT
*
17246703 AAGAAAAAGGTCATGTGAAATAAAC
1 AAGAAAAAGGTCATATGAAATAAAC
* *
17246728 AAGAAAAGGGTCATATGGAATAAAC
1 AAGAAAAAGGTCATATGAAATAAAC
17246753 CCATTTAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.54, C:0.08, G:0.22, T:0.16
Consensus pattern (25 bp):
AAGAAAAAGGTCATATGAAATAAAC
Found at i:17247302 original size:9 final size:9
Alignment explanation
Indices: 17247284--17247335 Score: 52
Period size: 9 Copynumber: 5.8 Consensus size: 9
17247274 GAATTAAAAC
17247284 TTTCTTTTT
1 TTTCTTTTT
*
17247293 TCT-TTTTT
1 TTTCTTTTT
17247301 TTTCTCTTTT
1 TTTCT-TTTT
* *
17247311 TTCCATTTT
1 TTTCTTTTT
*
17247320 TTTCATTTT
1 TTTCTTTTT
17247329 TTTCTTT
1 TTTCTTT
17247336 CATTTTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
8 7 0.20
9 21 0.60
10 7 0.20
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTCTTTTT
Found at i:17247303 original size:10 final size:10
Alignment explanation
Indices: 17247283--17247349 Score: 55
Period size: 10 Copynumber: 6.4 Consensus size: 10
17247273 AGAATTAAAA
17247283 CTTTCTTTTTT
1 CTTT-TTTTTT
17247294 CTTTTTTTTT
1 CTTTTTTTTT
* *
17247304 CTCTTTTTTC
1 CTTTTTTTTT
17247314 CATTTTTTTCATT
1 C-TTTTTTT--TT
*
17247327 -TTTTTCTTT
1 CTTTTTTTTT
*
17247336 CATTTTTTTT
1 CTTTTTTTTT
17247346 CTTT
1 CTTT
17247350 AAGGCATTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 9
0.72 0.13 0.15
Matches are distributed among these distances:
9 2 0.05
10 25 0.57
11 16 0.36
13 1 0.02
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.79
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:17247310 original size:19 final size:19
Alignment explanation
Indices: 17247286--17247349 Score: 67
Period size: 19 Copynumber: 3.3 Consensus size: 19
17247276 ATTAAAACTT
17247286 TCTTTTTTCTTTTTTTTTC
1 TCTTTTTTCTTTTTTTTTC
**
17247305 TCTTTTTTCCATTTTTTTC
1 TCTTTTTTCTTTTTTTTTC
*
17247324 AT-TTTTTTCTTTCATTTTTTT
1 -TCTTTTTTCTTT--TTTTTTC
17247345 TCTTT
1 TCTTT
17247350 AAGGCATTTC
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
19 25 0.69
20 2 0.06
21 9 0.25
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.80
Consensus pattern (19 bp):
TCTTTTTTCTTTTTTTTTC
Found at i:17247338 original size:13 final size:14
Alignment explanation
Indices: 17247316--17247349 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
17247306 CTTTTTTCCA
17247316 TTTT-TTTCA-TTT
1 TTTTCTTTCATTTT
17247328 TTTTCTTTCATTTT
1 TTTTCTTTCATTTT
17247342 TTTTCTTT
1 TTTTCTTT
17247350 AAGGCATTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 4 0.20
13 5 0.25
14 11 0.55
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (14 bp):
TTTTCTTTCATTTT
Found at i:17252522 original size:27 final size:26
Alignment explanation
Indices: 17252488--17252591 Score: 93
Period size: 27 Copynumber: 4.0 Consensus size: 26
17252478 TTTAAGTTGC
*
17252488 ATTTAGGGTTTTAATTTTGGGATTTTA
1 ATTTAGGGTTTTAATTTAGGG-TTTTA
*
17252515 ATTTAGGGTTTTGATTTAGGGTTTTA
1 ATTTAGGGTTTTAATTTAGGGTTTTA
** * ** * *
17252541 ATTTA-GGTTTCGAGTTAAAGCTTCA
1 ATTTAGGGTTTTAATTTAGGGTTTTA
*
17252566 ATTTAGGCTTTTAATCTTAGGGTTTT
1 ATTTAGGGTTTTAAT-TTAGGGTTTT
17252592 GGTTTACATT
Statistics
Matches: 59, Mismatches: 16, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
25 19 0.32
26 15 0.25
27 25 0.42
ACGTcount: A:0.22, C:0.05, G:0.22, T:0.51
Consensus pattern (26 bp):
ATTTAGGGTTTTAATTTAGGGTTTTA
Found at i:17252531 original size:13 final size:13
Alignment explanation
Indices: 17252488--17252547 Score: 93
Period size: 13 Copynumber: 4.5 Consensus size: 13
17252478 TTTAAGTTGC
17252488 ATTTAGGGTTTTA
1 ATTTAGGGTTTTA
*
17252501 ATTTTGGGATTTTA
1 ATTTAGGG-TTTTA
*
17252515 ATTTAGGGTTTTG
1 ATTTAGGGTTTTA
17252528 ATTTAGGGTTTTA
1 ATTTAGGGTTTTA
17252541 ATTTAGG
1 ATTTAGG
17252548 TTTCGAGTTA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
13 30 0.71
14 12 0.29
ACGTcount: A:0.22, C:0.00, G:0.25, T:0.53
Consensus pattern (13 bp):
ATTTAGGGTTTTA
Found at i:17252921 original size:10 final size:10
Alignment explanation
Indices: 17252899--17252936 Score: 60
Period size: 10 Copynumber: 3.8 Consensus size: 10
17252889 TTGAAATTTA
17252899 TTATTATTGT
1 TTATTATTGT
17252909 TTATTTATT-T
1 TTA-TTATTGT
17252919 TTATTATTGT
1 TTATTATTGT
17252929 TTATTATT
1 TTATTATT
17252937 TAATAATTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 5 0.19
10 16 0.62
11 5 0.19
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (10 bp):
TTATTATTGT
Found at i:17252924 original size:20 final size:20
Alignment explanation
Indices: 17252894--17252938 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 20
17252884 ATCCATTGAA
17252894 ATTTATTATTATTGTTTATTT
1 ATTTATTATTATTGTTTA-TT
17252915 ATTT-TTATTATTGTTTATT
1 ATTTATTATTATTGTTTATT
17252934 ATTTA
1 ATTTA
17252939 ATAATTCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 6 0.26
20 13 0.57
21 4 0.17
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (20 bp):
ATTTATTATTATTGTTTATT
Done.