Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
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: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 60 of 199
Found at i:17825647 original size:23 final size:22
Alignment explanation
Indices: 17825596--17825655 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
17825586 GGGTTCAGAT
*
17825596 TCAAAAAAAAATCAAAATCAAAA
1 TCAAAAAAAAA-AAAAATCAAAA
* *
17825619 TAAAAAACAAAAAAAAATCAAAG
1 TCAAAAA-AAAAAAAAATCAAAA
*
17825642 TCAAAAGAAAAAAA
1 TCAAAAAAAAAAAA
17825656 GAGAAATAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
22 7 0.23
23 20 0.65
24 4 0.13
ACGTcount: A:0.77, C:0.10, G:0.03, T:0.10
Consensus pattern (22 bp):
TCAAAAAAAAAAAAAATCAAAA
Found at i:17826594 original size:6 final size:7
Alignment explanation
Indices: 17826575--17826608 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
17826565 AAAAAAAGGG
17826575 TGAAAAA
1 TGAAAAA
17826582 TGAAAAA
1 TGAAAAA
17826589 TGAAAAA
1 TGAAAAA
17826596 TG-AAAA
1 TGAAAAA
17826602 TGAAAAA
1 TGAAAAA
17826609 GTAGAAACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
TGAAAAA
Found at i:17826594 original size:13 final size:14
Alignment explanation
Indices: 17826575--17826608 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
17826565 AAAAAAAGGG
17826575 TGAAAAATGAAAAA
1 TGAAAAATGAAAAA
17826589 TGAAAAATG-AAAA
1 TGAAAAATGAAAAA
17826602 TGAAAAA
1 TGAAAAA
17826609 GTAGAAACGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (14 bp):
TGAAAAATGAAAAA
Found at i:17828827 original size:19 final size:19
Alignment explanation
Indices: 17828803--17828843 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
17828793 TTATTAATAA
*
17828803 ATTTATTGTTACTATTATT
1 ATTTATTATTACTATTATT
**
17828822 ATTTATTATTGGTATTATT
1 ATTTATTATTACTATTATT
17828841 ATT
1 ATT
17828844 ACACTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.63
Consensus pattern (19 bp):
ATTTATTATTACTATTATT
Found at i:17831054 original size:16 final size:17
Alignment explanation
Indices: 17831033--17831065 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
17831023 TTTCAAAGAT
*
17831033 TAATTTTGT-AATTAAA
1 TAATTTAGTAAATTAAA
17831049 TAATTTAGTAAATTAAA
1 TAATTTAGTAAATTAAA
17831066 ACAAAAGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (17 bp):
TAATTTAGTAAATTAAA
Found at i:17833555 original size:2 final size:2
Alignment explanation
Indices: 17833548--17833595 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
17833538 TACATTTTCT
17833548 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17833590 TA TA TA
1 TA TA TA
17833596 AATACCACTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17836141 original size:21 final size:23
Alignment explanation
Indices: 17836106--17836148 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
17836096 CCAAAACACT
*
17836106 ATAAATGATAGGAAAAC-TAAAG
1 ATAAATGACAGGAAAACATAAAG
17836128 ATAAAT-ACAGGAAAACATAAA
1 ATAAATGACAGGAAAACATAAA
17836149 AAACAGTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.63, C:0.07, G:0.14, T:0.16
Consensus pattern (23 bp):
ATAAATGACAGGAAAACATAAAG
Found at i:17838263 original size:2 final size:2
Alignment explanation
Indices: 17838258--17838284 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
17838248 CAACGGTCAA
17838258 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
17838285 AATACCCCCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17838467 original size:10 final size:10
Alignment explanation
Indices: 17838452--17838485 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
17838442 TAATTATAAT
17838452 TTTTTTTATA
1 TTTTTTTATA
*
17838462 TTTTTTTAAA
1 TTTTTTTATA
17838472 TTTTTTTATA
1 TTTTTTTATA
17838482 TTTT
1 TTTT
17838486 CATCAATGGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTATA
Found at i:17838598 original size:15 final size:16
Alignment explanation
Indices: 17838578--17838608 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
17838568 TTTGTAATTA
17838578 TTATTTAAG-ATTTTT
1 TTATTTAAGTATTTTT
17838593 TTATTTAAGTATTTTT
1 TTATTTAAGTATTTTT
17838609 AGATAATTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (16 bp):
TTATTTAAGTATTTTT
Found at i:17839579 original size:7 final size:7
Alignment explanation
Indices: 17839567--17839591 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17839557 AGTCGATTGA
17839567 TATTTAG
1 TATTTAG
17839574 TATTTAG
1 TATTTAG
17839581 TATTTAG
1 TATTTAG
17839588 TATT
1 TATT
17839592 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:17840269 original size:18 final size:18
Alignment explanation
Indices: 17840243--17840277 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
17840233 AGGTATATTT
* *
17840243 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
17840261 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
17840278 TCATTTTCCG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:17840820 original size:23 final size:24
Alignment explanation
Indices: 17840772--17840827 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 24
17840762 ATAAAATAAA
* * * *
17840772 AACCCTAATTTAATTGAAATCTCT
1 AACCCTAACTTAATTAAAAACCCT
17840796 AA-CCTAACTTAATTAAAAACCCT
1 AACCCTAACTTAATTAAAAACCCT
17840819 AACCCTAAC
1 AACCCTAAC
17840828 CCTAACCTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
23 19 0.70
24 8 0.30
ACGTcount: A:0.43, C:0.27, G:0.02, T:0.29
Consensus pattern (24 bp):
AACCCTAACTTAATTAAAAACCCT
Found at i:17840821 original size:18 final size:18
Alignment explanation
Indices: 17840798--17840856 Score: 50
Period size: 18 Copynumber: 3.3 Consensus size: 18
17840788 AAATCTCTAA
17840798 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
* ****
17840816 CCTAACCCTAA-CCCTAA-
1 CCTAA-CTTAATTAAAAAC
17840833 CCTAACTTAATTAAAAAC
1 CCTAACTTAATTAAAAAC
17840851 CCTAAC
1 CCTAAC
17840857 CCTAACCTAA
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
16 4 0.14
17 7 0.25
18 13 0.46
19 4 0.14
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (18 bp):
CCTAACTTAATTAAAAAC
Found at i:17840840 original size:35 final size:33
Alignment explanation
Indices: 17840794--17841059 Score: 284
Period size: 29 Copynumber: 8.5 Consensus size: 33
17840784 ATTGAAATCT
17840794 CTAACCTAACTTAATTAAAAACCCTAACCCTAACC
1 CTAACCTAACTTAATTAAAAA--CTAACCCTAACC
17840829 CTAACCTAACTTAATT--AAA--AACCCTAACC
1 CTAACCTAACTTAATTAAAAACTAACCCTAACC
17840858 CTAACCTAACTTAATTAAAAACTCTAACCCTAACC
1 CTAACCTAACTTAATTAAAAA--CTAACCCTAACC
* *
17840893 CTAACCTAAATTAACTAAAAA-T---CCTAACC
1 CTAACCTAACTTAATTAAAAACTAACCCTAACC
* *
17840922 CTAACCTAAATTAACTAAAAACCCTAACCCTAACC
1 CTAACCTAACTTAATTAAAAA--CTAACCCTAACC
17840957 CTAACCTAACTTAATT--AAA--AACCCTAACC
1 CTAACCTAACTTAATTAAAAACTAACCCTAACC
17840986 CTAACCTAACTTAATTAAAAACT----CTAACC
1 CTAACCTAACTTAATTAAAAACTAACCCTAACC
**
17841015 CTAACCTAAC----TTAAACCCTAACCCTAACC
1 CTAACCTAACTTAATTAAAAACTAACCCTAACC
17841044 CTAACCTAACTTAATT
1 CTAACCTAACTTAATT
17841060 TGATAAATTT
Statistics
Matches: 201, Mismatches: 6, Indels: 50
0.78 0.02 0.19
Matches are distributed among these distances:
25 7 0.03
29 112 0.56
31 6 0.03
32 2 0.01
33 8 0.04
35 66 0.33
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (33 bp):
CTAACCTAACTTAATTAAAAACTAACCCTAACC
Found at i:17840862 original size:64 final size:64
Alignment explanation
Indices: 17840794--17841024 Score: 392
Period size: 64 Copynumber: 3.6 Consensus size: 64
17840784 ATTGAAATCT
17840794 CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACC
1 CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACC
* * * *
17840858 CTAACCTAACTTAATTAAAAACTCTAACCCTAACCCTAACCTAAATTAACTAAAAATCCTAACC
1 CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACC
* *
17840922 CTAACCTAAATTAACTAAAAACCCTAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACC
1 CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACC
*
17840986 CTAACCTAACTTAATTAAAAACTCTAACCCTAA-CCTAAC
1 CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAAC
17841025 TTAAACCCTA
Statistics
Matches: 154, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
63 6 0.04
64 148 0.96
ACGTcount: A:0.45, C:0.32, G:0.00, T:0.24
Consensus pattern (64 bp):
CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACC
Found at i:17840943 original size:93 final size:89
Alignment explanation
Indices: 17840822--17841059 Score: 300
Period size: 93 Copynumber: 2.6 Consensus size: 89
17840812 AAACCCTAAC
*
17840822 CCTAACCCTAACCTAACTTAATTAAAAACCCTAACCCTAACCTAACTTAATTAA-AAACTCTAAC
1 CCTAACCCTAACCTAACTTAACTAAAAACCCTAACCCTAACCTAACTTAATTAATAAA----AAC
17840886 CCTAACCCTAACCTAAATTAACTAAAAA
62 CCTAACCCTAACCTAAATTAACTAAAAA
* *
17840914 TCCTAACCCTAACCTAAATTAACTAAAAACCCTAACCCTAACCCTAACCTAACTTAATTAAAAAC
1 -CCTAACCCTAACCTAACTTAACTAAAAACCCTAACCCTAA-CCTAACTTAA-TTAA-TAAAAAC
* *
17840979 CCTAACCCTAACCTAACTTAATTAAAAA
62 CCTAACCCTAACCTAAATTAACTAAAAA
***
17841007 CTCTAACCCTAACCTAACTTAAAC-CCTAACCCTAACCCTAACCTAACTTAATT
1 C-CTAACCCTAACCTAACTT-AACTAAAAACCCTAACCCTAACCTAACTTAATT
17841060 TGATAAATTT
Statistics
Matches: 129, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
91 2 0.02
92 10 0.08
93 98 0.76
94 12 0.09
95 4 0.03
97 3 0.02
ACGTcount: A:0.43, C:0.32, G:0.00, T:0.24
Consensus pattern (89 bp):
CCTAACCCTAACCTAACTTAACTAAAAACCCTAACCCTAACCTAACTTAATTAATAAAAACCCTA
ACCCTAACCTAAATTAACTAAAAA
Found at i:17840979 original size:23 final size:24
Alignment explanation
Indices: 17840953--17841042 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 24
17840943 CCCTAACCCT
17840953 AACCCTAA-CCTAACTTAATTAAA
1 AACCCTAACCCTAACTTAATTAAA
17840976 AACCCTAACCCTAACCTAACTTAATTAAA
1 AACCCTAA--C---CCTAACTTAATTAAA
* *
17841005 AACTCTAACCCTAACCTAACTT--A
1 AACCCTAACCCTAACTTAA-TTAAA
17841028 AACCCTAACCCTAAC
1 AACCCTAACCCTAAC
17841043 CCTAACCTAA
Statistics
Matches: 57, Mismatches: 3, Indels: 14
0.77 0.04 0.19
Matches are distributed among these distances:
23 23 0.40
24 9 0.16
25 2 0.04
27 1 0.02
29 22 0.39
ACGTcount: A:0.43, C:0.33, G:0.00, T:0.23
Consensus pattern (24 bp):
AACCCTAACCCTAACTTAATTAAA
Found at i:17841020 original size:6 final size:6
Alignment explanation
Indices: 17841009--17841053 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
17840999 ATTAAAAACT
*
17841009 CTAACC CTAA-C CTAA-C TTAAACC CTAACC CTAACC CTAA-C CTAAC
1 CTAACC CTAACC CTAACC CT-AACC CTAACC CTAACC CTAACC CTAAC
17841054 TTAATTTGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
5 12 0.35
6 20 0.59
7 2 0.06
ACGTcount: A:0.38, C:0.42, G:0.00, T:0.20
Consensus pattern (6 bp):
CTAACC
Found at i:17841044 original size:64 final size:64
Alignment explanation
Indices: 17840794--17841059 Score: 375
Period size: 64 Copynumber: 4.2 Consensus size: 64
17840784 ATTGAAATCT
*
17840794 CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACC
1 CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAACCTAACTTAATCAAAAACCCTAACC
* * *
17840858 CTAACCTAACTTAATTAAAAACTCTAACCCTAACCCTAACCTAAATTAA-CTAAAAATCCTAACC
1 CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAACCTAACTTAATC-AAAAACCCTAACC
* * *
17840922 CTAACCTAAATTAACTAAAAACCCTAACCCTAACCCTAACCTAACTTAATTAAAAACCCTAACC
1 CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAACCTAACTTAATCAAAAACCCTAACC
* ***
17840986 CTAACCTAACTTAATTAAAAA--CT----CTAACCCTAACCTAACTTAAACCCTAACCCTAACC
1 CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAACCTAACTTAATCAAAAACCCTAACC
17841044 CTAACCTAACTTAATT
1 CTAACCTAACTTAATT
17841060 TGATAAATTT
Statistics
Matches: 183, Mismatches: 17, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
58 46 0.25
62 2 0.01
64 135 0.74
ACGTcount: A:0.44, C:0.32, G:0.00, T:0.24
Consensus pattern (64 bp):
CTAACCTAACTTAATTAAAAACCCTAACCCTAACCCTAACCTAACTTAATCAAAAACCCTAACC
Found at i:17841123 original size:56 final size:56
Alignment explanation
Indices: 17841057--17841275 Score: 327
Period size: 56 Copynumber: 3.9 Consensus size: 56
17841047 ACCTAACTTA
*
17841057 ATTTGATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTT
1 ATTTCATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTT
* **
17841113 ATTTCATAAATTTTACTAACCATTAATACAATTTTTGG-CTTAATAATTTTA-CAT
1 ATTTCATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTT
* *
17841167 ATTTTGAT-AATTTTACTAACCATTAACACAATTTCTGGACTTAATAATTTTAGTTT
1 A-TTTCATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTT
**
17841223 ATTTCATAAATTTTACTAACCATTAACACAATTTTTTTAGCTTAATAATTTTA
1 ATTTCATAAATTTTACTAACCATTAACACAATTTTTGGA-CTTAATAATTTTA
17841276 CATAATTTTA
Statistics
Matches: 145, Mismatches: 13, Indels: 9
0.87 0.08 0.05
Matches are distributed among these distances:
54 30 0.21
55 36 0.25
56 66 0.46
57 13 0.09
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (56 bp):
ATTTCATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTT
Found at i:17841183 original size:110 final size:113
Alignment explanation
Indices: 17841058--17841284 Score: 397
Period size: 110 Copynumber: 2.0 Consensus size: 113
17841048 CCTAACTTAA
*
17841058 TTTGATAAATTTTACTAACCATTAACACAATTTTTGGACTTAATAATTTTAGTTTATTTCATAAA
1 TTTGATAAATTTTACTAACCATTAACACAATTTCTGGACTTAATAATTTTAGTTTATTTCATAAA
* *
17841123 TTTTACTAACCATTAATACAA-TTTTTGGCTTAATAATTTTACAT-AT
66 TTTTACTAACCATTAACACAATTTTTTAGCTTAATAATTTTACATAAT
17841169 TTTGAT-AATTTTACTAACCATTAACACAATTTCTGGACTTAATAATTTTAGTTTATTTCATAAA
1 TTTGATAAATTTTACTAACCATTAACACAATTTCTGGACTTAATAATTTTAGTTTATTTCATAAA
17841233 TTTTACTAACCATTAACACAATTTTTTTAGCTTAATAATTTTACATAAT
66 TTTTACTAACCATTAACACAA-TTTTTTAGCTTAATAATTTTACATAAT
17841282 TTT
1 TTT
17841285 ACATAATGTT
Statistics
Matches: 110, Mismatches: 3, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
110 77 0.70
111 6 0.05
112 22 0.20
113 5 0.05
ACGTcount: A:0.36, C:0.12, G:0.05, T:0.47
Consensus pattern (113 bp):
TTTGATAAATTTTACTAACCATTAACACAATTTCTGGACTTAATAATTTTAGTTTATTTCATAAA
TTTTACTAACCATTAACACAATTTTTTAGCTTAATAATTTTACATAAT
Found at i:17841282 original size:10 final size:10
Alignment explanation
Indices: 17841267--17841291 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
17841257 TTTTAGCTTA
17841267 ATAATTTTAC
1 ATAATTTTAC
17841277 ATAATTTTAC
1 ATAATTTTAC
17841287 ATAAT
1 ATAAT
17841292 GTTAGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.44, C:0.08, G:0.00, T:0.48
Consensus pattern (10 bp):
ATAATTTTAC
Found at i:17844637 original size:126 final size:126
Alignment explanation
Indices: 17844404--17844758 Score: 597
Period size: 126 Copynumber: 2.8 Consensus size: 126
17844394 CCCAAACTTG
* *
17844404 CTACTGTAGCAAAATCGCGTCCATGAGGGCGCAATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
17844469 TAGAAGTGATTTTATACTATTTGCTCAGAAACGTCAACAAAAAAATTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACAAAAAAATTATTTCTTACATGAC
* *
17844530 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATTCTCG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
* *
17844595 TAGAAACGATTTTATACTATTTGCTCAGAAACATCAGA-AAAAAATTTATTTCTTACATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCA-ACAAAAAAATTATTTCTTACATGAC
17844656 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
1 CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
*
17844721 TAGAAGCGATTTTATACTATTTGAC-CAGAAACGTCAAC
66 TAGAAGCGATTTTATACTATTTG-CTCAGAAACATCAAC
17844759 TCGAAATAAT
Statistics
Matches: 214, Mismatches: 12, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
125 1 0.00
126 211 0.99
127 2 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (126 bp):
CTACTGTAGCAAAATCGCGTCCACGAGGGCGCGATTTCACAATTTCTTCTCAAATAGCATCCTGG
TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACAAAAAAATTATTTCTTACATGAC
Found at i:17846933 original size:28 final size:26
Alignment explanation
Indices: 17846867--17846933 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
17846857 TGAGGTTTAA
*
17846867 GGTTTAGTGTTTTTGAAAAAAATTAG
1 GGTTTAGGGTTTTTGAAAAAAATTAG
* * * *
17846893 GGTTTAAGATTTTTTAAAAATAATTTTG
1 GGTTTAGGGTTTTTGAAAAA-AA-TTAG
17846921 GGTTTAGGGTTTT
1 GGTTTAGGGTTTT
17846934 AGGATTTTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
26 16 0.50
27 2 0.06
28 14 0.44
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (26 bp):
GGTTTAGGGTTTTTGAAAAAAATTAG
Found at i:17850568 original size:59 final size:59
Alignment explanation
Indices: 17850505--17850633 Score: 168
Period size: 59 Copynumber: 2.2 Consensus size: 59
17850495 TGTATTGTCT
* ** *
17850505 TATTCAAAAAAACTTTTATTTTATTAAATGGCACAATATAAAAATAATTTGTACAAAAA
1 TATTCAAAAAAACTTCTATTTTATTAAATGAAACAATATAAAAACAATTTGTACAAAAA
* * * * *
17850564 TATTCAAAACAACTTCTGTTTTATTAAATGAAACAATATAAAAGCAGTTTGTACAAATA
1 TATTCAAAAAAACTTCTATTTTATTAAATGAAACAATATAAAAACAATTTGTACAAAAA
*
17850623 TATTTAAAAAA
1 TATTCAAAAAA
17850634 CAATGCATGT
Statistics
Matches: 59, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (59 bp):
TATTCAAAAAAACTTCTATTTTATTAAATGAAACAATATAAAAACAATTTGTACAAAAA
Found at i:17853174 original size:29 final size:29
Alignment explanation
Indices: 17853116--17853176 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
17853106 TTGGGTTTTT
** * **
17853116 TGGCCCATTTTGGTAAATAATTTTTTAAA
1 TGGCCCATTTCCGTAAATAATGTTGGAAA
17853145 TGGCCCATTTCCGTAAATAATGTTGGAAA
1 TGGCCCATTTCCGTAAATAATGTTGGAAA
17853174 TGG
1 TGG
17853177 GCATTTTGTA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.38
Consensus pattern (29 bp):
TGGCCCATTTCCGTAAATAATGTTGGAAA
Found at i:17855443 original size:27 final size:27
Alignment explanation
Indices: 17855411--17855463 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
17855401 GAAAGAGATG
* *
17855411 AAGATTTTGACGAAGATGCTAAAGAAA
1 AAGATTTCGACGAAGATGCCAAAGAAA
17855438 AAGATTTCGACGAAGATGCCAAAGAA
1 AAGATTTCGACGAAGATGCCAAAGAA
17855464 TATCCACGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.47, C:0.11, G:0.23, T:0.19
Consensus pattern (27 bp):
AAGATTTCGACGAAGATGCCAAAGAAA
Found at i:17856689 original size:41 final size:41
Alignment explanation
Indices: 17856631--17856731 Score: 141
Period size: 41 Copynumber: 2.5 Consensus size: 41
17856621 ACCAACATGG
*
17856631 GTATGTAATCGCCACTATTAAAGATTTTTTAAAATTCCTT-
1 GTATGTAATCGCCACTATTAAAGATTCTTTAAAATTCCTTA
* * **
17856671 GCTATGTAATCGTCACTATTAAAGATTCTTTGAAATTTTTTA
1 G-TATGTAATCGCCACTATTAAAGATTCTTTAAAATTCCTTA
17856713 GTATGTAATCGCCACTATT
1 GTATGTAATCGCCACTATT
17856732 CACTTCTTTC
Statistics
Matches: 53, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
40 1 0.02
41 51 0.96
42 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.43
Consensus pattern (41 bp):
GTATGTAATCGCCACTATTAAAGATTCTTTAAAATTCCTTA
Found at i:17859592 original size:28 final size:29
Alignment explanation
Indices: 17859535--17859595 Score: 81
Period size: 28 Copynumber: 2.1 Consensus size: 29
17859525 GAATTTAATA
*
17859535 GAGAATTGAGAGAATTTTGAGAGTGATTT
1 GAGAATTGAGAGAATTTTGAGAGTAATTT
*
17859564 GAGAA-TGTGAGAATTTTGAGAG-AATTTT
1 GAGAATTGAGAGAATTTTGAGAGTAA-TTT
17859592 GAGA
1 GAGA
17859596 GTGATTTGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
27 1 0.03
28 23 0.79
29 5 0.17
ACGTcount: A:0.36, C:0.00, G:0.31, T:0.33
Consensus pattern (29 bp):
GAGAATTGAGAGAATTTTGAGAGTAATTT
Found at i:17871848 original size:16 final size:16
Alignment explanation
Indices: 17871795--17871841 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
17871785 TTTGGTTCGT
* * *
17871795 TGTAATAGAATAAAGT
1 TGTAATGGAATAGAGC
17871811 TGTAATGGAATAGAGC
1 TGTAATGGAATAGAGC
17871827 TGTAATGGAATAGAG
1 TGTAATGGAATAGAG
17871842 GCGTAATAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 28 1.00
ACGTcount: A:0.43, C:0.02, G:0.28, T:0.28
Consensus pattern (16 bp):
TGTAATGGAATAGAGC
Found at i:17871881 original size:45 final size:43
Alignment explanation
Indices: 17871830--17871922 Score: 118
Period size: 44 Copynumber: 2.1 Consensus size: 43
17871820 ATAGAGCTGT
*
17871830 AATGGAATAGAGGC-GTAATAGTAATTCAATTG-TTTGGTTGAATGG
1 AATGGAATAGA-ACTGTAATAGT-ATTC--TTGATTTGGTTGAATGG
17871875 AATGGAATAGAACTGTAATAGTATTCTTGTATTTGGTTGAATGG
1 AATGGAATAGAACTGTAATAGTATTCTTG-ATTTGGTTGAATGG
17871919 AATG
1 AATG
17871923 ATGTTGTAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
42 3 0.07
44 22 0.50
45 19 0.43
ACGTcount: A:0.33, C:0.04, G:0.27, T:0.35
Consensus pattern (43 bp):
AATGGAATAGAACTGTAATAGTATTCTTGATTTGGTTGAATGG
Found at i:17872274 original size:118 final size:118
Alignment explanation
Indices: 17872060--17872296 Score: 431
Period size: 118 Copynumber: 2.0 Consensus size: 118
17872050 TTAATCATAT
* *
17872060 TTTAACATAATTATTATTACATATAATTTAATAAAAATATATAATTTATAAAATTCTTAATATTA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTATAAAATTCTTAATATTA
17872125 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAA-ATAA
*
17872179 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTA-ATAATTCTTAATATTA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTATAAAATTCTTAATATTA
17872243 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
66 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
17872296 T
1 T
17872297 ATATAATCTA
Statistics
Matches: 115, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
117 5 0.04
118 64 0.56
119 46 0.40
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (118 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTATAAAATTCTTAATATTA
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAAATAA
Found at i:17872277 original size:59 final size:58
Alignment explanation
Indices: 17872095--17872282 Score: 195
Period size: 59 Copynumber: 3.2 Consensus size: 58
17872085 ATTTAATAAA
17872095 AATATATAATTTATAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAA-TT-TAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
* * * * * ** * *
17872155 AATATATAATACTATAAAA-T-ATAAT-TTAAAATAATTATTAT-TAAATATAATTTAATAAA
1 AATATATAAT--T-TAAAATTCTTAATATT-AAAT-ATTCTTATATGAATTTACTAAAATCAT
17872214 AATATATAATTTAATAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
1 AATATATAATTTAA-AATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
17872273 AATATATAAT
1 AATATATAAT
17872283 ACTATAAAAA
Statistics
Matches: 101, Mismatches: 18, Indels: 19
0.73 0.13 0.14
Matches are distributed among these distances:
56 3 0.03
57 3 0.03
58 10 0.10
59 59 0.58
60 19 0.19
61 7 0.07
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.44
Consensus pattern (58 bp):
AATATATAATTTAAAATTCTTAATATTAAATATTCTTATATGAATTTACTAAAATCAT
Found at i:17873761 original size:49 final size:49
Alignment explanation
Indices: 17873689--17873792 Score: 163
Period size: 49 Copynumber: 2.1 Consensus size: 49
17873679 GAAAAAAAAC
* * * *
17873689 AAATTAAAATTAAGTTTAATATCACGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCACGAATCAAAAGCTCAACACATTATA
*
17873738 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACATTATA
1 AAATTAAAATTAAGTTCAATATCACGAATCAAAAGCTCAACACATTATA
17873787 AAATTA
1 AAATTA
17873793 TAACACATGA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.51, C:0.12, G:0.08, T:0.30
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCACGAATCAAAAGCTCAACACATTATA
Found at i:17876149 original size:15 final size:15
Alignment explanation
Indices: 17876138--17876171 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
17876128 AATAAATTGG
17876138 AATATTAAAAATAAA
1 AATATTAAAAATAAA
17876153 AATATTAAAAATAAA
1 AATATTAAAAATAAA
17876168 AATA
1 AATA
17876172 ATTTAATTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATATTAAAAATAAA
Found at i:17878567 original size:50 final size:50
Alignment explanation
Indices: 17878428--17878665 Score: 209
Period size: 50 Copynumber: 4.8 Consensus size: 50
17878418 TGAGATTATG
* *
17878428 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATA
17878478 AGAGGT---ATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATA
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATA
** * * * * * *
17878525 AGAGGTCCCCCGTAAGACCATGTATGGGACATGGCATGGGCACCTATATG
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATA
** * * * * * *
17878575 AGAACTCTCATGTAAGACCATATCTGGGATATGGCATTGGCAGTACAAGA-A
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCA--CCAAGATA
* * * * *
17878626 ATA--TCCCATGTAAGACTATGTCTGGGACATAGCTTTGGCA
1 AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCA
17878666 TGTTATATTC
Statistics
Matches: 153, Mismatches: 30, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
47 45 0.29
49 31 0.20
50 72 0.47
51 2 0.01
52 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGGCACCAAGATA
Found at i:17880267 original size:77 final size:77
Alignment explanation
Indices: 17880124--17880269 Score: 193
Period size: 77 Copynumber: 1.9 Consensus size: 77
17880114 GGGATTAACA
* * * * **
17880124 AGGAGTGAATTTGCAATTGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAAGGCAGTGACA
1 AGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAAGACAGCAACA
17880189 CTCGGGTTAATG
66 CTCGGGTTAATG
* * * * *
17880201 AGGACTGAATTCGTAATGGTGATTCTATCTTATTTGGCTTAGCTTCCTTTGGTAAGACAGCAACA
1 AGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAAGACAGCAACA
17880266 CTCG
66 CTCG
17880270 AAACTTGCAT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
77 58 1.00
ACGTcount: A:0.26, C:0.16, G:0.23, T:0.34
Consensus pattern (77 bp):
AGGACTGAATTCGCAATGGTGATTCTAACTTAATTGGCTTAGCTTCCATTGATAAGACAGCAACA
CTCGGGTTAATG
Found at i:17881118 original size:5 final size:5
Alignment explanation
Indices: 17881108--17881138 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
17881098 TCGATTTTAC
17881108 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA A
17881139 ATAGGGAAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:17881210 original size:20 final size:19
Alignment explanation
Indices: 17881181--17881228 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
17881171 GATAAAATGG
*
17881181 AAAA-AAGAAAAGAAACGT
1 AAAAGAAGAAAAGAAAAGT
17881199 AAATAGAAGAAAAGAAAAGT
1 AAA-AGAAGAAAAGAAAAGT
*
17881219 ACAAGAAGAA
1 AAAAGAAGAA
17881229 GAAGCAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 3 0.12
19 8 0.31
20 15 0.58
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.06
Consensus pattern (19 bp):
AAAAGAAGAAAAGAAAAGT
Found at i:17893378 original size:30 final size:30
Alignment explanation
Indices: 17893342--17893437 Score: 90
Period size: 30 Copynumber: 3.2 Consensus size: 30
17893332 ATTATCTTAC
17893342 ATTTGTATATGGATATTCATTTCCGAATTG
1 ATTTGTATATGGATATTCATTTCCGAATTG
*
17893372 ATTTGTATATAGATA--CATATTGCCGAATTCG
1 ATTTGTATATGGATATTCAT-TT-CCGAATT-G
* ** *
17893403 GTCCGTATATGGATATAT-ATTGCCGAATTG
1 ATTTGTATATGGATAT-TCATTTCCGAATTG
17893433 ATTTG
1 ATTTG
17893438 AGCATTGGAT
Statistics
Matches: 51, Mismatches: 9, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
28 3 0.06
29 2 0.04
30 24 0.47
31 19 0.37
32 1 0.02
33 2 0.04
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (30 bp):
ATTTGTATATGGATATTCATTTCCGAATTG
Found at i:17893423 original size:31 final size:30
Alignment explanation
Indices: 17893346--17893434 Score: 99
Period size: 31 Copynumber: 2.9 Consensus size: 30
17893336 TCTTACATTT
* **
17893346 GTATATGGATAT-TCATTTCCGAATTGATTT
1 GTATATGGATATAT-ATTGCCGAATTGATCC
* * *
17893376 GTATATAGATACATATTGCCGAATTCGGTCC
1 GTATATGGATATATATTGCCGAATT-GATCC
17893407 GTATATGGATATATATTGCCGAATTGAT
1 GTATATGGATATATATTGCCGAATTGAT
17893435 TTGAGCATTG
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
30 22 0.46
31 26 0.54
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.39
Consensus pattern (30 bp):
GTATATGGATATATATTGCCGAATTGATCC
Found at i:17897686 original size:2 final size:2
Alignment explanation
Indices: 17897681--17897708 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
17897671 TTTTTTGTTA
17897681 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17897709 TTAAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17900527 original size:31 final size:31
Alignment explanation
Indices: 17900492--17900563 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 31
17900482 TAATAAAGGT
*
17900492 AAAAT-TATACTTTGACCCTCTT-AAAATTATA
1 AAAATATATA-TTTAACCCT-TTAAAAATTATA
* *
17900523 AAAATCT-TATTTAATCCTTTAAAAATTATA
1 AAAATATATATTTAACCCTTTAAAAATTATA
17900553 AAAATATATAT
1 AAAATATATAT
17900564 ATAGACTATT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
29 2 0.06
30 22 0.63
31 10 0.29
32 1 0.03
ACGTcount: A:0.47, C:0.11, G:0.01, T:0.40
Consensus pattern (31 bp):
AAAATATATATTTAACCCTTTAAAAATTATA
Found at i:17907228 original size:7 final size:7
Alignment explanation
Indices: 17907216--17907266 Score: 93
Period size: 7 Copynumber: 7.3 Consensus size: 7
17907206 ACATCTCATC
17907216 TCACATA
1 TCACATA
17907223 TCACATA
1 TCACATA
17907230 TCACATA
1 TCACATA
17907237 TCACATA
1 TCACATA
*
17907244 TTACATA
1 TCACATA
17907251 TCACATA
1 TCACATA
17907258 TCACATA
1 TCACATA
17907265 TC
1 TC
17907267 GATGGTATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 42 1.00
ACGTcount: A:0.41, C:0.27, G:0.00, T:0.31
Consensus pattern (7 bp):
TCACATA
Found at i:17909174 original size:26 final size:25
Alignment explanation
Indices: 17909106--17909183 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 25
17909096 ATCACTTTAA
*
17909106 TATTAAATTAATATAATATTTATCT
1 TATTAAATTAATATAATATTAATCT
* *
17909131 TATTAGATTAAATTTAATATTAAATCT
1 TATTAAATT-AATATAATATT-AATCT
* *
17909158 TATTAAAATAATATAATATTTATCT
1 TATTAAATTAATATAATATTAATCT
17909183 T
1 T
17909184 GTAGATAAAC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
25 13 0.30
26 20 0.45
27 11 0.25
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.50
Consensus pattern (25 bp):
TATTAAATTAATATAATATTAATCT
Found at i:17909214 original size:52 final size:54
Alignment explanation
Indices: 17909103--17909221 Score: 142
Period size: 52 Copynumber: 2.3 Consensus size: 54
17909093 TTAATCACTT
* * *
17909103 TAATATTAAATTAATATAATATTTATCTTATTAGATTAAATTTAATATTAAATC
1 TAATATTAAAATAATATAATATTTATCTTAGTAGATTAAAATTAATATTAAATC
17909157 T--TATTAAAATAATATAATATTTATCTT-GTAGA-TAAACATTAA-ATTAAAT-
1 TAATATTAAAATAATATAATATTTATCTTAGTAGATTAAA-ATTAATATTAAATC
*
17909206 TAAATATTAAGATAAT
1 T-AATATTAAAATAAT
17909222 CAATTTAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
49 1 0.02
50 11 0.19
51 8 0.14
52 36 0.63
54 1 0.02
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (54 bp):
TAATATTAAAATAATATAATATTTATCTTAGTAGATTAAAATTAATATTAAATC
Found at i:17911585 original size:23 final size:24
Alignment explanation
Indices: 17911541--17911585 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
17911531 AAAATCCTAC
*
17911541 CCATCCAGCCTCTACACACCATCT
1 CCATCCAACCTCTACACACCATCT
*
17911565 CCATCCAACC-CTACACCCCAT
1 CCATCCAACCTCTACACACCAT
17911586 GTGAGGATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.27, C:0.53, G:0.02, T:0.18
Consensus pattern (24 bp):
CCATCCAACCTCTACACACCATCT
Found at i:17912011 original size:18 final size:18
Alignment explanation
Indices: 17911971--17912005 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
17911961 ACATGATGTT
*
17911971 CGCCCGTGTAGGTCCACA
1 CGCCCGTGTAGGCCCACA
17911989 CGCCCGTGT-GGCCCACA
1 CGCCCGTGTAGGCCCACA
17912006 TGGCCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.14, C:0.43, G:0.29, T:0.14
Consensus pattern (18 bp):
CGCCCGTGTAGGCCCACA
Found at i:17928558 original size:42 final size:42
Alignment explanation
Indices: 17928508--17928759 Score: 326
Period size: 42 Copynumber: 6.0 Consensus size: 42
17928498 GAAGCACAAA
* *
17928508 CATTTAAGCTCACATGGGGAGCTTTGCTGATACACAGCTTGT
1 CATTTAAGCTCACATGGGGAGCTTCGCTGATACACAACTTGT
* ** * *
17928550 CACTTAAGCTTGCATGGGGAGCTTCACTAATACACAACTTGT
1 CATTTAAGCTCACATGGGGAGCTTCGCTGATACACAACTTGT
*
17928592 CATTTAAGCTCACGA-GGGGAGCTTCGCTGATGCACAACTTGT
1 CATTTAAGCTCAC-ATGGGGAGCTTCGCTGATACACAACTTGT
* *
17928634 CATTTAAGCTCACGTGAGGAGCTTCGCTGATACACAACTTGT
1 CATTTAAGCTCACATGGGGAGCTTCGCTGATACACAACTTGT
* * *
17928676 CATTTAAGCTCACGTGAGGAGCTTCGCTGATACAGAACTTGT
1 CATTTAAGCTCACATGGGGAGCTTCGCTGATACACAACTTGT
* * * * *
17928718 CACTTAAGCTCACGTAGAGAGCTTCGCTAATACACAACTTGT
1 CATTTAAGCTCACATGGGGAGCTTCGCTGATACACAACTTGT
17928760 AAAATCGTTT
Statistics
Matches: 185, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
42 184 0.99
43 1 0.01
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (42 bp):
CATTTAAGCTCACATGGGGAGCTTCGCTGATACACAACTTGT
Found at i:17935140 original size:15 final size:15
Alignment explanation
Indices: 17935120--17935155 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
17935110 CGTTAGTAGG
*
17935120 AAGGATGTACCTCGA
1 AAGGATGTACCTAGA
17935135 AAGGATGTACCTAGA
1 AAGGATGTACCTAGA
17935150 AAGGAT
1 AAGGAT
17935156 CTAAGACAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.39, C:0.14, G:0.28, T:0.19
Consensus pattern (15 bp):
AAGGATGTACCTAGA
Found at i:17940665 original size:30 final size:30
Alignment explanation
Indices: 17940604--17940666 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
17940594 CAAGCAAGGG
* *
17940604 AGAAATCCAAGGGATCTCTATGCTATTTTT
1 AGAAATCCAAGGGATCTCCATGCTATATTT
*
17940634 AGAAATCCAAGGGATCTCCGTGCT-TAATTT
1 AGAAATCCAAGGGATCTCCATGCTAT-ATTT
17940664 AGA
1 AGA
17940667 TCCTAATCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (30 bp):
AGAAATCCAAGGGATCTCCATGCTATATTT
Found at i:17941074 original size:15 final size:16
Alignment explanation
Indices: 17941042--17941075 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
17941032 TTTTCAACTC
17941042 ATTTGCATTTAGGTTA
1 ATTTGCATTTAGGTTA
17941058 ATTTGCATTTA-GTTA
1 ATTTGCATTTAGGTTA
17941073 ATT
1 ATT
17941076 AATTTAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.26, C:0.06, G:0.15, T:0.53
Consensus pattern (16 bp):
ATTTGCATTTAGGTTA
Found at i:17941344 original size:21 final size:23
Alignment explanation
Indices: 17941313--17941360 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
17941303 TGCAATTTGG
17941313 TTTTATTATTTTTATGT-A-TTTA
1 TTTTATTATTTTT-TGTGACTTTA
17941335 TTTT-TTATTTTTTGTGACTTTA
1 TTTTATTATTTTTTGTGACTTTA
17941357 TTTT
1 TTTT
17941361 CAAGTGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
20 3 0.12
21 9 0.38
22 12 0.50
ACGTcount: A:0.17, C:0.02, G:0.06, T:0.75
Consensus pattern (23 bp):
TTTTATTATTTTTTGTGACTTTA
Found at i:17942707 original size:22 final size:22
Alignment explanation
Indices: 17942669--17942720 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
17942659 ATAATGAAAA
17942669 AAAATAAACAAAAACTAGAACCCT
1 AAAA-AAACAAAAACTA-AACCCT
* *
17942693 AAAAAAAC-AAAACTAAATCTT
1 AAAAAAACAAAAACTAAACCCT
17942714 AAAAAAA
1 AAAAAAA
17942721 AACTAGGTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 7 0.27
23 4 0.15
24 4 0.15
ACGTcount: A:0.69, C:0.15, G:0.02, T:0.13
Consensus pattern (22 bp):
AAAAAAACAAAAACTAAACCCT
Found at i:17950992 original size:51 final size:50
Alignment explanation
Indices: 17950862--17951046 Score: 167
Period size: 51 Copynumber: 3.7 Consensus size: 50
17950852 AAAGTGATGG
* * * * * * * *
17950862 TCACGTGTGCAGTACTATGTGCAGGCTACTACGTGTACCAGA-AATATAGG
1 TCACATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGTAT-GA
* *
17950912 TCGCATGTGTAGTACTATGTGCAGGCTACTATGCGTACCGGATAGCT-TCGA
1 TCACATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATAG-TAT-GA
* * * * * *
17950963 TCACGTGTGTAGTGCTATGTGTAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGT-ATGA
*
17951014 TTACATGTGTAGTACTATGTGTAGGCTACTATG
1 TCACATGTGTAGTACTATGTGTAGGCTACTATG
17951047 TGAACCCGTA
Statistics
Matches: 110, Mismatches: 21, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
50 37 0.34
51 71 0.65
52 2 0.02
ACGTcount: A:0.23, C:0.17, G:0.28, T:0.31
Consensus pattern (50 bp):
TCACATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGATAGTATGA
Found at i:17951140 original size:42 final size:41
Alignment explanation
Indices: 17951051--17951265 Score: 211
Period size: 42 Copynumber: 5.1 Consensus size: 41
17951041 ACTATGTGAA
*
17951051 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGATTC
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
* * * * *
17951092 TACCGTATCCTTGATTGTGAAAGG-GGTTACTATGTGCTGATTC
1 -CCCGTATCATTGATTAT--AAGGTGGTTGCTAAGTGCTGATTC
17951135 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTTC
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGA-TTC
** * * * *
17951177 ATCGTGTCCTTGACTGTGA-AAGG-GGTTGCTATGTTCTGATTC
1 CCCGTATCATTGA-T-T-ATAAGGTGGTTGCTAAGTGCTGATTC
**
17951219 CTTGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
17951260 CACCGT
1 C-CCGT
17951266 GTAACGGTTA
Statistics
Matches: 138, Mismatches: 25, Indels: 20
0.75 0.14 0.11
Matches are distributed among these distances:
39 1 0.01
40 9 0.07
41 33 0.24
42 54 0.39
43 31 0.22
44 9 0.07
45 1 0.01
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.38
Consensus pattern (41 bp):
CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTC
Found at i:17951195 original size:84 final size:84
Alignment explanation
Indices: 17951051--17951267 Score: 337
Period size: 84 Copynumber: 2.6 Consensus size: 84
17951041 ACTATGTGAA
* * *
17951051 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGTTGA-TTCTACCGTATCCTTGATTGTGAAAG
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTTC-ACCGTGTCCTTGACTGTGAAAG
17951115 GGGTTACTATGTGCTGATTC
65 GGGTTACTATGTGCTGATTC
*
17951135 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTTCATCGTGTCCTTGACTGTGAAAGG
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTTCACCGTGTCCTTGACTGTGAAAGG
* *
17951200 GGTTGCTATGTTCTGATTC
66 GGTTACTATGTGCTGATTC
** *
17951219 CTTGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTCCACCGTGT
1 CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTTCACCGTGT
17951268 AACGGTTAAT
Statistics
Matches: 122, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
84 119 0.98
85 3 0.02
ACGTcount: A:0.20, C:0.16, G:0.25, T:0.38
Consensus pattern (84 bp):
CCCGTATCATTGATTATAAGGTGGTTGCTAAGTGCTGATTTCACCGTGTCCTTGACTGTGAAAGG
GGTTACTATGTGCTGATTC
Found at i:17967397 original size:22 final size:21
Alignment explanation
Indices: 17967372--17967424 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 21
17967362 ATAGTCCTAG
*
17967372 TGACATTCTTACCTAATATAT-A
1 TGACATGCTT-CC-AATATATCA
17967394 TGACATGCTTCCAATATATGCA
1 TGACATGCTTCCAATATAT-CA
17967416 TGACATGCT
1 TGACATGCT
17967425 ATGAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
20 7 0.25
21 2 0.07
22 19 0.68
ACGTcount: A:0.32, C:0.21, G:0.11, T:0.36
Consensus pattern (21 bp):
TGACATGCTTCCAATATATCA
Found at i:17968475 original size:25 final size:26
Alignment explanation
Indices: 17968446--17968496 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
17968436 ATTTTTTAAA
17968446 TAAAAAAATATCTTTAGAG-ATTTTC
1 TAAAAAAATATCTTTAGAGAATTTTC
* * *
17968471 TAAAATAATTTCTTTATAGAATTTTC
1 TAAAAAAATATCTTTAGAGAATTTTC
17968497 CCTCTACAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 16 0.73
26 6 0.27
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.45
Consensus pattern (26 bp):
TAAAAAAATATCTTTAGAGAATTTTC
Found at i:17968697 original size:20 final size:19
Alignment explanation
Indices: 17968650--17968699 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
17968640 CAATATAAAC
17968650 ATTAAATT--TAATTTAAT
1 ATTAAATTAATAATTTAAT
17968667 ATTAAGA-TAATAACTTTAAT
1 ATTAA-ATTAATAA-TTTAAT
17968687 ATTAAATTAATAA
1 ATTAAATTAATAA
17968700 AATACTATTA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.21
18 1 0.04
19 4 0.14
20 17 0.61
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (19 bp):
ATTAAATTAATAATTTAAT
Found at i:17968710 original size:25 final size:25
Alignment explanation
Indices: 17968656--17968703 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
17968646 AAACATTAAA
*
17968656 TTTAATTTAATATTAAGATAATAAC
1 TTTAATTTAATATTAAGAAAATAAC
*
17968681 TTTAATATTAA-ATTAATAAAATA
1 TTTAAT-TTAATATTAAGAAAATA
17968704 CTATTAAGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 16 0.80
26 4 0.20
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATAAC
Found at i:17971319 original size:19 final size:19
Alignment explanation
Indices: 17971281--17971320 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
17971271 AAAATGTCAT
*
17971281 ATTAATTTTAATTGATTTG
1 ATTAATTTTAATTGACTTG
* *
17971300 ATTAATTTTATTTTACTTG
1 ATTAATTTTAATTGACTTG
17971319 AT
1 AT
17971321 CAAAATTAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.60
Consensus pattern (19 bp):
ATTAATTTTAATTGACTTG
Found at i:17972759 original size:25 final size:25
Alignment explanation
Indices: 17972721--17972771 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
17972711 CCCTAATTCC
*
17972721 TAAAAACCCCTAACCCTAACAAAAT
1 TAAAAAACCCTAACCCTAACAAAAT
* *
17972746 TAAAAAACCTTAACCCTATCAAAAT
1 TAAAAAACCCTAACCCTAACAAAAT
17972771 T
1 T
17972772 TTTTAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (25 bp):
TAAAAAACCCTAACCCTAACAAAAT
Found at i:17972971 original size:32 final size:33
Alignment explanation
Indices: 17972935--17973000 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
17972925 GTTATACAAT
*
17972935 TTAACTTAAAAT-TTCATTAA-AAAAATGATAGA
1 TTAACTTAAAATATTCA-TAATAAAAATGAAAGA
**
17972967 TTAACTTATTATATTCATAATAAAAATGAAAGA
1 TTAACTTAAAATATTCATAATAAAAATGAAAGA
17973000 T
1 T
17973001 GAAATGATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
32 13 0.45
33 16 0.55
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.36
Consensus pattern (33 bp):
TTAACTTAAAATATTCATAATAAAAATGAAAGA
Found at i:17973011 original size:33 final size:33
Alignment explanation
Indices: 17972947--17973012 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
17972937 AACTTAAAAT
* * * *
17972947 TTCATTAAAAAAATGATAGATTAACTTATTATA
1 TTCATTAAAAAAATGAAAGATGAAATGATTATA
17972980 TTCA-TAATAAAAATGAAAGATGAAATGATTATA
1 TTCATTAA-AAAAATGAAAGATGAAATGATTATA
17973013 AATGTAATAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 3 0.11
33 25 0.89
ACGTcount: A:0.52, C:0.05, G:0.09, T:0.35
Consensus pattern (33 bp):
TTCATTAAAAAAATGAAAGATGAAATGATTATA
Found at i:17986036 original size:29 final size:29
Alignment explanation
Indices: 17985997--17986076 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 29
17985987 TATTGTTCAT
*
17985997 AATTTTATATAATTTGTAATAACTTTTTT-C
1 AATTTCATATAATTT-TAATAA-TTTTTTGC
17986027 AATTTC-TATAATATTTAATAATTTTTTGC
1 AATTTCATATAAT-TTTAATAATTTTTTGC
*
17986056 AATTTCATATTATTTTTAATA
1 AATTTCATA-TAATTTTAATA
17986077 GATAATAATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
28 6 0.14
29 19 0.43
30 16 0.36
31 3 0.07
ACGTcount: A:0.35, C:0.06, G:0.03, T:0.56
Consensus pattern (29 bp):
AATTTCATATAATTTTAATAATTTTTTGC
Found at i:17998946 original size:29 final size:31
Alignment explanation
Indices: 17998899--17998965 Score: 75
Period size: 30 Copynumber: 2.2 Consensus size: 31
17998889 TTGCACAAGA
* * * * *
17998899 GTAAATACTCAAAATTTGAGGGGCTAA-AGT
1 GTAAATACTAAAAAGTTGAAGGACCAATAGT
17998929 GTAAATAC-AAAAAGTTGAAGGACCAATAGT
1 GTAAATACTAAAAAGTTGAAGGACCAATAGT
17998959 GTAAATA
1 GTAAATA
17998966 TTTTAAGGGT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 13 0.42
30 18 0.58
ACGTcount: A:0.46, C:0.09, G:0.21, T:0.24
Consensus pattern (31 bp):
GTAAATACTAAAAAGTTGAAGGACCAATAGT
Found at i:18002293 original size:30 final size:30
Alignment explanation
Indices: 18002252--18002316 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
18002242 ATTTTCGAGC
*
18002252 TTGGGGACAAAAGTGTAATTATGCAAAAGT
1 TTGGGGACAAAAGTGTAATTATGCAAAAAT
* * * *
18002282 TTGGGGGCAAAATTGTAATTTTTCAAAAAT
1 TTGGGGACAAAAGTGTAATTATGCAAAAAT
18002312 TTGGG
1 TTGGG
18002317 TGGTGGGTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.35, C:0.06, G:0.26, T:0.32
Consensus pattern (30 bp):
TTGGGGACAAAAGTGTAATTATGCAAAAAT
Found at i:18002826 original size:105 final size:105
Alignment explanation
Indices: 18002645--18002973 Score: 520
Period size: 105 Copynumber: 3.2 Consensus size: 105
18002635 TGTATATAAA
** * *
18002645 AGGGGTTGCTGTGTGCTGATTCCCCGA-TTCATTGGTGGTGCTAGGTGCG-TGATCCACCATACC
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGAT-ATCCACCGTACC
18002708 TTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
65 TTTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
18002749 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTACCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTACCT
* *
18002814 TTGAAATGTGAAAGGGGGTTGCTACGTGCTGATTCCCCCA
66 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
* * **
18002854 AGGGGTTGCTAAGTGCTGAATCCCTGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTACCT
*
18002919 TTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCCG
66 TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
*
18002958 ATGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
18002974 NNNNNNNNNN
Statistics
Matches: 209, Mismatches: 14, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
104 68 0.33
105 140 0.67
106 1 0.00
ACGTcount: A:0.19, C:0.20, G:0.30, T:0.31
Consensus pattern (105 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTTCATTGGTGGTGCTAAGTGCGATATCCACCGTACCT
TTGAAATGTGAAAGGGGGTTGCTATGTGCTGATTCCCCCG
Found at i:18010858 original size:166 final size:166
Alignment explanation
Indices: 18010584--18010918 Score: 652
Period size: 166 Copynumber: 2.0 Consensus size: 166
18010574 ATTGGAAGAA
18010584 AAAAAATAGTAAGCCACCTTTAAAAAACTGCCAATCGTTCTCTTTTTTTATTCCTCCTCTTTTCT
1 AAAAAATAGTAAGCCACCTTTAAAAAACTGCCAATCGTTCTCTTTTTTTATTCCTCCTCTTTTCT
*
18010649 CCTTTTTCAATGAAGGGAGAGGCCTCTATTTATAGTTGAGCCTCCGCAAATCCAACGGTACAGAT
66 CCTTTTTCAATGAAGGGAGAGGCCTCTATTTATAGTTGAGCCTCCCCAAATCCAACGGTACAGAT
*
18010714 CAATTACATCAACGGCTGAGATTAAAGGGTATCTAC
131 CAATTACATCAACGGCTGAGATTAAAAGGTATCTAC
18010750 AAAAAATAGTAAGCCACCTTTAAAAAACTGCCAATCGTTCTCTTTTTTTATTCCTCCTCTTTTCT
1 AAAAAATAGTAAGCCACCTTTAAAAAACTGCCAATCGTTCTCTTTTTTTATTCCTCCTCTTTTCT
18010815 CCTTTTTCAATGAAGGGAGAGGCCTCTATTTATAGTTGAGCCTCCCCAAATCCAACGGTACAGAT
66 CCTTTTTCAATGAAGGGAGAGGCCTCTATTTATAGTTGAGCCTCCCCAAATCCAACGGTACAGAT
18010880 CAATTACATCAACGGCTGAGATTAAAAGGTATCTAC
131 CAATTACATCAACGGCTGAGATTAAAAGGTATCTAC
18010916 AAA
1 AAA
18010919 TTAAATCTCT
Statistics
Matches: 167, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
166 167 1.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (166 bp):
AAAAAATAGTAAGCCACCTTTAAAAAACTGCCAATCGTTCTCTTTTTTTATTCCTCCTCTTTTCT
CCTTTTTCAATGAAGGGAGAGGCCTCTATTTATAGTTGAGCCTCCCCAAATCCAACGGTACAGAT
CAATTACATCAACGGCTGAGATTAAAAGGTATCTAC
Found at i:18010956 original size:23 final size:22
Alignment explanation
Indices: 18010913--18010970 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
18010903 AAAAGGTATC
* *
18010913 TACAAATTAAATC-TCTAAGAT
1 TACAAATCATATCTTCTAAGAT
18010934 TACAAAATCATATCTTCTAAGAT
1 TAC-AAATCATATCTTCTAAGAT
*
18010957 TACATATCATATCT
1 TACAAATCATATCT
18010971 AAGATTGCAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.56
23 11 0.34
ACGTcount: A:0.43, C:0.17, G:0.03, T:0.36
Consensus pattern (22 bp):
TACAAATCATATCTTCTAAGAT
Found at i:18010973 original size:19 final size:19
Alignment explanation
Indices: 18010926--18011044 Score: 130
Period size: 21 Copynumber: 5.8 Consensus size: 19
18010916 AAATTAAATC
*
18010926 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
18010946 TCTTCTAAGATTACATATCATA
1 ---TCTAAGATTACATATCATA
*
18010968 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
18010989 TCTAAGATTGCATATATCATA
1 TCTAAGATT--ACATATCATA
*
18011010 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
18011029 TCTAAGATTACATATC
1 TCTAAGATTACATATC
18011045 CTCGAAGATT
Statistics
Matches: 89, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
19 32 0.36
21 39 0.44
22 7 0.08
23 11 0.12
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:18010986 original size:21 final size:21
Alignment explanation
Indices: 18010960--18011043 Score: 145
Period size: 21 Copynumber: 4.1 Consensus size: 21
18010950 CTAAGATTAC
18010960 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
18010981 ATATCATATCTAAGATTGCAT
1 ATATCATATCTAAGATTGCAT
18011002 ATATCATATCTAAGATTGC--
1 ATATCATATCTAAGATTGCAT
*
18011021 ATATCATATCTAAGATTACAT
1 ATATCATATCTAAGATTGCAT
18011042 AT
1 AT
18011044 CCTCGAAGAT
Statistics
Matches: 60, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
19 18 0.30
21 42 0.70
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.38
Consensus pattern (21 bp):
ATATCATATCTAAGATTGCAT
Found at i:18011006 original size:42 final size:40
Alignment explanation
Indices: 18010942--18011043 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 40
18010932 ATTACAAAAT
18010942 CATATC-T-TCTAAGATTAC--ATATCATATCTAAGATTG
1 CATATCATATCTAAGATTACATATATCATATCTAAGATTG
*
18010978 CATATATCATATCTAAGATTGCATATATCATATCTAAGATTG
1 C--ATATCATATCTAAGATTACATATATCATATCTAAGATTG
18011020 CATATCATATCTAAGATTACATAT
1 CATATCATATCTAAGATTACATAT
18011044 CCTCGAAGAT
Statistics
Matches: 58, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
36 1 0.02
38 5 0.09
39 1 0.02
40 32 0.55
42 19 0.33
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (40 bp):
CATATCATATCTAAGATTACATATATCATATCTAAGATTG
Found at i:18011749 original size:44 final size:44
Alignment explanation
Indices: 18011680--18012185 Score: 388
Period size: 44 Copynumber: 11.5 Consensus size: 44
18011670 GTCGGTGTAA
* * * * *
18011680 GAAGGCAAGACCTGTTATTTTCGATCTACTTCACGCCAATAAAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATAT
* * * * **
18011724 GAAGACAAGATCTACTTTCTTCGATCTACTTCACAACCATTATGG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATAT
* * * *
18011769 GAAGATAAGATCTGC-ATCTTCGATCCACTTC-CTACCAATATAG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATAT
* * * *
18011812 GAAGACAGGACCTGCTATTTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATAT
* **
18011856 GAAGACAAGATCTGCTTTCTTCGATCTACTT--CGCCACCAGTAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATA-TAT
* * * * *
18011899 GGAAAGATAAGATCTGC-ATCTTCGATCCACTTCGCTACCAATATAG
1 -G-AAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATAT
* *
18011945 GAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATAT
* * * * * *
18011989 GAAGACAAGATTTGC-ATCTTTGATCCACTTC-CTACCAATACAG
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATAT
* * *
18012032 GAAGACAGGACCTGCTATCTTCGATCTACTTCACGCCAATAAAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATAT
* * * *
18012076 GAAGACAAGATTTGCTTTCTTCGATCTAC-TC-TGCCACTAATAT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAAT-ATAT
* * * * *
18012119 GGGAAGACAACATCTGC-ATCTTAGATCCACTTC-CTACCAATATAG
1 --GAAGACAAGATCTGCTATCTTCGATCTACTTCAC-GCCAATATAT
*
18012164 GAAGAC-AGAACCTGCTATCTTC
1 GAAGACAAG-ATCTGCTATCTTC
18012186 ACTGATCTGC
Statistics
Matches: 362, Mismatches: 80, Indels: 40
0.75 0.17 0.08
Matches are distributed among these distances:
42 13 0.04
43 73 0.20
44 197 0.54
45 68 0.19
46 7 0.02
47 4 0.01
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (44 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATATAT
Found at i:18011925 original size:132 final size:133
Alignment explanation
Indices: 18011688--18011999 Score: 536
Period size: 132 Copynumber: 2.4 Consensus size: 133
18011678 AAGAAGGCAA
* *
18011688 GACCTGTTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTACTTTCTTCGATCTAC
1 GACCTGCTATTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTAC
* *
18011753 TTCACAACCATTATGGGAAGATAAGATCTGCATCTTCGATCCACTTC-CTACCAATATAGGAAGA
66 TTCACAACCAGTATGGAAAGATAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGA
18011817 CAG
131 CAG
*
18011820 GACCTGCTATTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTAC
1 GACCTGCTATTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTAC
* *
18011885 TTCGCCACCAGTATGGAAAGATAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGA
66 TTCACAACCAGTATGGAAAGATAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGA
18011950 CAG
131 CAG
* *
18011953 GATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
1 GACCTGCTATTTTCGATCTACTTCACGCCAATACATGAAGACAAGAT
18012000 TTGCATCTTT
Statistics
Matches: 170, Mismatches: 9, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
132 105 0.62
133 65 0.38
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.29
Consensus pattern (133 bp):
GACCTGCTATTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTACTTTCTTCGATCTAC
TTCACAACCAGTATGGAAAGATAAGATCTGCATCTTCGATCCACTTCGCTACCAATATAGGAAGA
CAG
Found at i:18012036 original size:220 final size:220
Alignment explanation
Indices: 18011715--18012185 Score: 685
Period size: 220 Copynumber: 2.1 Consensus size: 220
18011705 CTACTTCACG
* * * * * * ** *
18011715 CCAATAAATGAAGACAAGATCTACTTTCTTCGATCTACTTCACAACCATTATGGGAAGATAAGAT
1 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACAACCAATACAGGAAGACAAGAT
* *
18011780 CTGCATCTTCGATCCACTTCCTACCAATATAGGAAGACAGGACCTGCTATTTTCGATCTACTTCA
66 CTGCATCTTCGATCCACTTCCTACCAATACAGGAAGACAGGACCTGCTATCTTCGATCTACTTCA
* * *
18011845 CGCCAATACATGAAGACAAGATCTGCTTTCTTCGATCTACT-TCGCCACCAGTATGGAAAGATAA
131 CGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTACTCT-GCCACCAATATGGAAAGACAA
* *
18011909 GATCTGCATCTTCGATCCACTTCGCTA
195 CATCTGCATCTTAGATCCACTTC-CTA
* *
18011936 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCAC-GCCAATACATGAAGACAAGAT
1 CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACAACCAATACAGGAAGACAAGAT
* *
18012000 TTGCATCTTTGATCCACTTCCTACCAATACAGGAAGACAGGACCTGCTATCTTCGATCTACTTCA
66 CTGCATCTTCGATCCACTTCCTACCAATACAGGAAGACAGGACCTGCTATCTTCGATCTACTTCA
* * *
18012065 CGCCAATAAATGAAGACAAGATTTGCTTTCTTCGATCTACTCTGCCACTAATATGGGAAGACAAC
131 CGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTACTCTGCCACCAATATGGAAAGACAAC
18012130 ATCTGCATCTTAGATCCACTTCCTA
196 ATCTGCATCTTAGATCCACTTCCTA
* *
18012155 CCAATATAGGAAGACAGAACCTGCTATCTTC
1 CCAATATAGGAAGACAGGATCTGCTATCTTC
18012186 ACTGATCTGC
Statistics
Matches: 224, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
219 32 0.14
220 153 0.68
221 39 0.17
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (220 bp):
CCAATATAGGAAGACAGGATCTGCTATCTTCGATCTACTTCACAACCAATACAGGAAGACAAGAT
CTGCATCTTCGATCCACTTCCTACCAATACAGGAAGACAGGACCTGCTATCTTCGATCTACTTCA
CGCCAATAAATGAAGACAAGATCTGCTTTCTTCGATCTACTCTGCCACCAATATGGAAAGACAAC
ATCTGCATCTTAGATCCACTTCCTA
Found at i:18012137 original size:132 final size:132
Alignment explanation
Indices: 18011680--18012185 Score: 454
Period size: 132 Copynumber: 3.8 Consensus size: 132
18011670 GTCGGTGTAA
* * * * * * * *
18011680 GAAGGCAAGACCTGTTATTTTCGATCTACTTCACGCCAATAAATGAAGACAAGATCTACTTTCTT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAACATCTGC-ATCTT
* * * * ** * *
18011745 CGATCTACTTCACAACCATTATGGGAAGATA-AGATCTGC-ATCTTCGATCCACTTC-CTACCAA
65 AGATCCACTTC-CTACCAATACAGGAAGACAGA-ACCTGCTATCTTCGATCCACTTCACTACCAA
*
18011807 TATAG
128 TAAAG
* * * * *
18011812 GAAGACAGGACCTGCTATTTTCGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAACATCTGC-ATCTT
* * * * * * * *
18011877 CGATCTACTTCGCCACCAGTA-TGGAAAGATA-AGATCTGC-ATCTTCGATCCACTTCGCTACCA
65 AGATCCACTTC-CTACCAATACAGG-AAGACAGA-ACCTGCTATCTTCGATCCACTTCACTACCA
*
18011939 ATATAG
127 ATAAAG
* * * *
18011945 GAAGACAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAAGATTTGCATCTTT
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAACATCTGCATCTTA
* * *
18012010 GATCCACTTCCTACCAATACAGGAAGACAGGACCTGCTATCTTCGATCTACTTCAC-GCCAATAA
66 GATCCACTTCCTACCAATACAGGAAGACAGAACCTGCTATCTTCGATCCACTTCACTACCAATAA
*
18012074 AT
131 AG
* * * * *
18012076 GAAGACAAGATTTGCTTTCTTCGATCTAC-TC-TGCCACTAATATGGGAAGACAACATCTGCATC
1 GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAAT-ACAT--GAAGACAACATCTGCATC
*
18012139 TTAGATCCACTTCCTACCAATATAGGAAGACAGAACCTGCTATCTTC
63 TTAGATCCACTTCCTACCAATACAGGAAGACAGAACCTGCTATCTTC
18012186 ACTGATCTGC
Statistics
Matches: 329, Mismatches: 37, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
129 5 0.02
130 5 0.02
131 52 0.16
132 199 0.60
133 68 0.21
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (132 bp):
GAAGACAAGATCTGCTATCTTCGATCTACTTCACGCCAATACATGAAGACAACATCTGCATCTTA
GATCCACTTCCTACCAATACAGGAAGACAGAACCTGCTATCTTCGATCCACTTCACTACCAATAA
AG
Found at i:18035119 original size:22 final size:21
Alignment explanation
Indices: 18035092--18035145 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
18035082 ATTTATTTAA
*
18035092 TTATTTTTTGGTTATTAGGAAT
1 TTATTTTTTGGTAATTAGG-AT
*
18035114 TTATTTCTTTAGTAATTAGGAT
1 TTATTT-TTTGGTAATTAGGAT
*
18035136 TTAATTTTTG
1 TTATTTTTTG
18035146 CAAATTAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 3 0.11
22 13 0.48
23 11 0.41
ACGTcount: A:0.24, C:0.02, G:0.15, T:0.59
Consensus pattern (21 bp):
TTATTTTTTGGTAATTAGGAT
Found at i:18037316 original size:19 final size:19
Alignment explanation
Indices: 18037294--18037331 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
18037284 TCAATCATCC
18037294 CTCATCTCATCA-TCTCTCA
1 CTCAT-TCATCATTCTCTCA
18037313 CTCATTCATCATTCTCTCA
1 CTCATTCATCATTCTCTCA
18037332 ACTCTTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.33
19 12 0.67
ACGTcount: A:0.21, C:0.39, G:0.00, T:0.39
Consensus pattern (19 bp):
CTCATTCATCATTCTCTCA
Found at i:18043521 original size:55 final size:56
Alignment explanation
Indices: 18043451--18043562 Score: 149
Period size: 55 Copynumber: 2.0 Consensus size: 56
18043441 TCCTTTATCC
*
18043451 ATTAATTTTATTTTCCCTTTCTCTGGATTTG-TT-CCTTCATCTGAATCAATGTTGG
1 ATTAATTTTATTTTCCCTTTCTCTAGATTTGTTTCCCTT-ATCTGAATCAATGTTGG
* * *
18043506 ATTAATTTTCA-TTTCCCTTTCTCTAGTTTTGTTTCCCTTATCTTAATCAATTTTGG
1 ATTAATTTT-ATTTTCCCTTTCTCTAGATTTGTTTCCCTTATCTGAATCAATGTTGG
18043562 A
1 A
18043563 AAATGACGAT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
55 27 0.54
56 19 0.38
57 4 0.08
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.53
Consensus pattern (56 bp):
ATTAATTTTATTTTCCCTTTCTCTAGATTTGTTTCCCTTATCTGAATCAATGTTGG
Found at i:18052928 original size:21 final size:20
Alignment explanation
Indices: 18052904--18052952 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
18052894 TTCGGGATCA
18052904 TTTGGAAAGTAAA-TAGAAAAT
1 TTTGGAAA-TAAATTA-AAAAT
18052925 TTT-GAAATAAATTTAAAAAT
1 TTTGGAAATAAA-TTAAAAAT
18052945 TTTGGAAA
1 TTTGGAAA
18052953 CATGGGTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (20 bp):
TTTGGAAATAAATTAAAAAT
Found at i:18078484 original size:22 final size:23
Alignment explanation
Indices: 18078457--18078501 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
18078447 TTATTTATTT
* *
18078457 AATTATTT-TTTGGTTATTAGGA
1 AATTATTTCTTTAGTAATTAGGA
18078479 AATTATTTCTTTAGTAATTAGGA
1 AATTATTTCTTTAGTAATTAGGA
18078502 TTTAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.31, C:0.02, G:0.16, T:0.51
Consensus pattern (23 bp):
AATTATTTCTTTAGTAATTAGGA
Found at i:18080190 original size:14 final size:14
Alignment explanation
Indices: 18080171--18080198 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18080161 TAAAGTTATA
18080171 TTTAATAATTCATT
1 TTTAATAATTCATT
18080185 TTTAATAATTCATT
1 TTTAATAATTCATT
18080199 AACAAATTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATTCATT
Found at i:18080674 original size:19 final size:19
Alignment explanation
Indices: 18080652--18080689 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
18080642 TCAATCATCC
18080652 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
18080671 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
18080690 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:18089249 original size:55 final size:56
Alignment explanation
Indices: 18089179--18089290 Score: 149
Period size: 55 Copynumber: 2.0 Consensus size: 56
18089169 TCCTTTATCC
*
18089179 ATTAATTTTATTTTCCCTTTCTCTGGATTTG-TT-CCTTCATCTGAATCAATGTTGG
1 ATTAATTTTATTTTCCCTTTCTCTAGATTTGTTTCCCTT-ATCTGAATCAATGTTGG
* * *
18089234 ATTAATTTTCA-TTTCCCTTTCTCTAGTTTTGTTTCCCTTATCTTAATCAATTTTGG
1 ATTAATTTT-ATTTTCCCTTTCTCTAGATTTGTTTCCCTTATCTGAATCAATGTTGG
18089290 A
1 A
18089291 AAATGACGGT
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
55 27 0.54
56 19 0.38
57 4 0.08
ACGTcount: A:0.19, C:0.19, G:0.10, T:0.53
Consensus pattern (56 bp):
ATTAATTTTATTTTCCCTTTCTCTAGATTTGTTTCCCTTATCTGAATCAATGTTGG
Found at i:18097857 original size:21 final size:20
Alignment explanation
Indices: 18097833--18097881 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 20
18097823 TTGGGGATCA
18097833 TTTGGAAAGTAAA-TAGAAAAT
1 TTTGGAAA-TAAATTA-AAAAT
18097854 TTT-GAAATAAATTTAAAAAT
1 TTTGGAAATAAA-TTAAAAAT
18097874 TTTGGAAA
1 TTTGGAAA
18097882 CATGGGTCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.35
Consensus pattern (20 bp):
TTTGGAAATAAATTAAAAAT
Found at i:18111590 original size:19 final size:19
Alignment explanation
Indices: 18111568--18111605 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
18111558 TCAATCATCC
18111568 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
18111587 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
18111606 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:18115549 original size:19 final size:19
Alignment explanation
Indices: 18115527--18115564 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
18115517 TCAATCATCC
18115527 CTCATCCCATCA-TCTCTCA
1 CTCAT-CCATCATTCTCTCA
*
18115546 CTCATTCATCATTCTCTCA
1 CTCATCCATCATTCTCTCA
18115565 ACTCTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.21, C:0.42, G:0.00, T:0.37
Consensus pattern (19 bp):
CTCATCCATCATTCTCTCA
Found at i:18122495 original size:2 final size:2
Alignment explanation
Indices: 18122490--18122520 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18122480 AAAACTAGTG
18122490 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18122521 GGTAAAAACG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:18123949 original size:56 final size:56
Alignment explanation
Indices: 18123864--18123976 Score: 176
Period size: 56 Copynumber: 2.0 Consensus size: 56
18123854 TCCTTTATCC
*
18123864 ATTAATTTTATTTTCCCTTTCTCTGGTTTTG-TT-CCTTCATCTTAATCAATGTTGG
1 ATTAATTTTATTTTCCCTTTCTCTAGTTTTGTTTCCCTT-ATCTTAATCAATGTTGG
*
18123919 ATTAATTTTCATTTTCCCTTTCTCTAGTTTTGTTTCCCTTATCTTAATCAATTTTGG
1 ATTAATTTT-ATTTTCCCTTTCTCTAGTTTTGTTTCCCTTATCTTAATCAATGTTGG
18123976 A
1 A
18123977 AAATGACGAT
Statistics
Matches: 53, Mismatches: 2, Indels: 4
0.90 0.03 0.07
Matches are distributed among these distances:
55 9 0.17
56 21 0.40
57 19 0.36
58 4 0.08
ACGTcount: A:0.18, C:0.19, G:0.09, T:0.55
Consensus pattern (56 bp):
ATTAATTTTATTTTCCCTTTCTCTAGTTTTGTTTCCCTTATCTTAATCAATGTTGG
Found at i:18130005 original size:25 final size:25
Alignment explanation
Indices: 18129977--18130027 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
18129967 CCTTTTCCTC
18129977 TTCATTATTATTTTTCTTTTTTCTT
1 TTCATTATTATTTTTCTTTTTTCTT
18130002 TTCATTATTATTTTTCTTTTTTCTT
1 TTCATTATTATTTTTCTTTTTTCTT
18130027 T
1 T
18130028 GGATTTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (25 bp):
TTCATTATTATTTTTCTTTTTTCTT
Found at i:18130016 original size:13 final size:13
Alignment explanation
Indices: 18129977--18130017 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
18129967 CCTTTTCCTC
18129977 TTCATTATTATTT
1 TTCATTATTATTT
*
18129990 TTC-TT-TTTTCTT
1 TTCATTATTAT-TT
18130002 TTCATTATTATTT
1 TTCATTATTATTT
18130015 TTC
1 TTC
18130018 TTTTTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 6
0.74 0.06 0.19
Matches are distributed among these distances:
11 3 0.13
12 7 0.30
13 10 0.43
14 3 0.13
ACGTcount: A:0.15, C:0.12, G:0.00, T:0.73
Consensus pattern (13 bp):
TTCATTATTATTT
Found at i:18143578 original size:129 final size:129
Alignment explanation
Indices: 18143345--18143766 Score: 691
Period size: 129 Copynumber: 3.3 Consensus size: 129
18143335 CGAAGAATTA
* * *
18143345 CAGATCTTATCTCCATGAGATTACAGCGGAGTAGATTGAAGCCAGTAATCCTATTTGCCTAAGAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCCAGTAATCCTATTTCCCTGAGAT
* *
18143410 TACAGTGGAACGGATTAAAATAAAGGATCTTATCCCTCTGAAGTTACAGTAGAGTAGATCACAT
66 TACAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
* * *
18143474 CAGATCTTATCTCCTTGAGATTACAGCGGAGCAAATTGAAGCCAGTAATCCTATTTCCCTGAGAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCCAGTAATCCTATTTCCCTGAGAT
* *
18143539 TACAGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGTTCGCAT
66 TACAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
* ** *
18143603 CAAATCTTATCTCCCTGAGATTACAGTAGAGTAGATTGAAGCCAGTAATCCTATTTCCTTGAGAT
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCCAGTAATCCTATTTCCCTGAGAT
18143668 TACAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
66 TACAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
* * *
18143732 CAGGTCTTATCTCCCTGAGATTACAGTGGAATAGA
1 CAGATCTTATCTCCCTGAGATTACAGCGGAGTAGA
18143767 CCGAAGAATT
Statistics
Matches: 271, Mismatches: 22, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
129 271 1.00
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (129 bp):
CAGATCTTATCTCCCTGAGATTACAGCGGAGTAGATTGAAGCCAGTAATCCTATTTCCCTGAGAT
TACAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTGAAGTTACAGTAGAGTAGATCGCAT
Found at i:18143586 original size:44 final size:44
Alignment explanation
Indices: 18143406--18143761 Score: 141
Period size: 44 Copynumber: 8.3 Consensus size: 44
18143396 TATTTGCCTA
* * *
18143406 AGATTACAGTGGAACGGATTAAAATAAAGGATCTTATCCCTCTG
1 AGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTG
* * * * *
18143450 A-AGTTACAGTAGAGTAGA-TCACAT-CA-GATCTTATCTC-CTTG
1 AGA-TTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTC-TG
* * * *** * * * *
18143491 AGATTACAGCGGAGCAAATT-GAAGCCAGTAATCCTATTTCCCTG
1 AGATTACAGTGGAGCAGATTAAAATAAAG-GATCTTATCTCTCTG
*
18143535 AGATTACAGTGGAACAGATTAAAATAAAGGATCTTATCTCTCTG
1 AGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTG
* * *** * *
18143579 A-AGTTACAGTAGAGTAG-TTCGCATCAA--ATCTTATCTCCCTG
1 AGA-TTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTG
* * * *** * * *
18143620 AGATTACAGTAGAGTAGATT-GAAGCCAGTAATCCTATTTC-CTTG
1 AGATTACAGTGGAGCAGATTAAAATAAAG-GATCTTATCTCTC-TG
* *
18143664 AGATTACAGTGGAACGGATTAAAATAAAGGATCTTATCTCTCTG
1 AGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTG
* * *** * *
18143708 A-AGTTACAGTAGAGTAGA-TCGCAT-CAGG-TCTTATCTCCCTG
1 AGA-TTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTG
18143749 AGATTACAGTGGA
1 AGATTACAGTGGA
18143762 ATAGACCGAA
Statistics
Matches: 229, Mismatches: 63, Indels: 43
0.68 0.19 0.13
Matches are distributed among these distances:
40 1 0.00
41 79 0.34
42 12 0.05
43 17 0.07
44 110 0.48
45 10 0.04
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (44 bp):
AGATTACAGTGGAGCAGATTAAAATAAAGGATCTTATCTCTCTG
Found at i:18149747 original size:21 final size:21
Alignment explanation
Indices: 18149723--18149772 Score: 61
Period size: 20 Copynumber: 2.4 Consensus size: 21
18149713 TTGGGGATCA
18149723 TTTGGAAACTAAA-TAGAAAAT
1 TTTGGAAACTAAATTA-AAAAT
18149744 TTT-GAAA-TAAATTTAAAAAT
1 TTTGGAAACTAAA-TTAAAAAT
18149764 TTTGGAAAC
1 TTTGGAAAC
18149773 ATGGGTCACA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
19 4 0.16
20 12 0.48
21 9 0.36
ACGTcount: A:0.50, C:0.04, G:0.12, T:0.34
Consensus pattern (21 bp):
TTTGGAAACTAAATTAAAAAT
Found at i:18162572 original size:317 final size:317
Alignment explanation
Indices: 18161997--18162624 Score: 1238
Period size: 317 Copynumber: 2.0 Consensus size: 317
18161987 TCATTGCAAT
*
18161997 CAAGTGACAACTGCACTGAAGAGATATGGAGTTAGTCATAGAATGGCTACTACTTATCATCTGCA
1 CAAGTGACAACCGCACTGAAGAGATATGGAGTTAGTCATAGAATGGCTACTACTTATCATCTGCA
18162062 AACCAATGGACAAGCCAAAGTATCAAATCGACAAATTAAGAACATTCTTGAGAAGGTTGTAAACC
66 AACCAATGGACAAGCCAAAGTATCAAATCGACAAATTAAGAACATTCTTGAGAAGGTTGTAAACC
18162127 CTTCGAGGAAAGATTGGTCTTTCCAATTAGATGATGCTTTATGGGCATTGTGGATAGCATACAAA
131 CTTCGAGGAAAGATTGGTCTTTCCAATTAGATGATGCTTTATGGGCATTGTGGATAGCATACAAA
18162192 ACTCCATTAGGGATGTCATTATATTAAATGGTTTTTGGGAAAGCATGTCACTTGCCAATTGAACT
196 ACTCCATTAGGGATGTCATTATATTAAATGGTTTTTGGGAAAGCATGTCACTTGCCAATTGAACT
18162257 GGAACACAAAGCAATGTGGGCAATTAAGTAAGTGAACATGGACTATGAAGTGACAAC
261 GGAACACAAAGCAATGTGGGCAATTAAGTAAGTGAACATGGACTATGAAGTGACAAC
18162314 CAAGTGACAACCGCACTGAAGAGATATGGAGTTAGTCATAGAATGGCTACTACTTATCATCTGCA
1 CAAGTGACAACCGCACTGAAGAGATATGGAGTTAGTCATAGAATGGCTACTACTTATCATCTGCA
18162379 AACCAATGGACAAGCCAAAGTATCAAATCGACAAATTAAGAACATTCTTGAGAAGGTTGTAAACC
66 AACCAATGGACAAGCCAAAGTATCAAATCGACAAATTAAGAACATTCTTGAGAAGGTTGTAAACC
18162444 CTTCGAGGAAAGATTGGTCTTTCCAATTAGATGATGCTTTATGGGCATTGTGGATAGCATACAAA
131 CTTCGAGGAAAGATTGGTCTTTCCAATTAGATGATGCTTTATGGGCATTGTGGATAGCATACAAA
18162509 ACTCCATTAGGGATGTCATTATATTAAATGGTTTTTGGGAAAGCATGTCACTTGCCAATTGAACT
196 ACTCCATTAGGGATGTCATTATATTAAATGGTTTTTGGGAAAGCATGTCACTTGCCAATTGAACT
*
18162574 GGAACACAAAGTAATGTGGGCAATTAAGTAAGTGAACATGGACTATGAAGT
261 GGAACACAAAGCAATGTGGGCAATTAAGTAAGTGAACATGGACTATGAAGT
18162625 AGATGGAAAG
Statistics
Matches: 309, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
317 309 1.00
ACGTcount: A:0.36, C:0.16, G:0.22, T:0.27
Consensus pattern (317 bp):
CAAGTGACAACCGCACTGAAGAGATATGGAGTTAGTCATAGAATGGCTACTACTTATCATCTGCA
AACCAATGGACAAGCCAAAGTATCAAATCGACAAATTAAGAACATTCTTGAGAAGGTTGTAAACC
CTTCGAGGAAAGATTGGTCTTTCCAATTAGATGATGCTTTATGGGCATTGTGGATAGCATACAAA
ACTCCATTAGGGATGTCATTATATTAAATGGTTTTTGGGAAAGCATGTCACTTGCCAATTGAACT
GGAACACAAAGCAATGTGGGCAATTAAGTAAGTGAACATGGACTATGAAGTGACAAC
Found at i:18165255 original size:16 final size:17
Alignment explanation
Indices: 18165234--18165268 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
18165224 ATAAGTACAC
*
18165234 ATTGTCATTGC-TTTTT
1 ATTGTCATTACATTTTT
18165250 ATTGTCATTACATTTTT
1 ATTGTCATTACATTTTT
18165267 AT
1 AT
18165269 GTTAGTGCGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 10 0.59
17 7 0.41
ACGTcount: A:0.20, C:0.11, G:0.09, T:0.60
Consensus pattern (17 bp):
ATTGTCATTACATTTTT
Found at i:18178019 original size:137 final size:138
Alignment explanation
Indices: 18177771--18178039 Score: 305
Period size: 137 Copynumber: 2.0 Consensus size: 138
18177761 AAAATGGGCC
* * * * * * *
18177771 TGCTCACACAAGTTGTTGGTCGGAATGTAAGCTACACTATGCTGCTCACACAAGTTGTCGATTAT
1 TGCTCACACAAGCTGTTAGTCGGAACGTAAGCTACACGATGCTGCTCACACAAGCTGTCAAGTAT
* * * *
18177836 CTGCAACTAATGTCAGGCTTCAGTCATCGGTAGGACATTCAAGACCAACA-CTCAAAACATGGTA
66 CTGCAACTAATGTCAGACTTCAGCCACCAGTAGGACATTCAAGACCAACACCT-AAAACATGGTA
18177900 ACCTGGGTT
130 ACCTGGGTT
* *
18177909 TGCTCACACATGCTGTTAGTCGGAACGT-AGCTACACGGTGCTGCTCACACAAGCTGTCAAGTAT
1 TGCTCACACAAGCTGTTAGTCGGAACGTAAGCTACACGATGCTGCTCACACAAGCTGTCAAGTAT
* ** * *
18177973 CTGCAAC-ACAT-TCTAGAAC-TCAGCCACCAGTATGACATTCGGGACCAGCACCTAAGACATGG
66 CTGCAACTA-ATGTC-AG-ACTTCAGCCACCAGTAGGACATTCAAGACCAACACCTAAAACATGG
18178035 TAACC
128 TAACC
18178040 CTAATGACAT
Statistics
Matches: 109, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
136 3 0.03
137 79 0.72
138 27 0.25
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (138 bp):
TGCTCACACAAGCTGTTAGTCGGAACGTAAGCTACACGATGCTGCTCACACAAGCTGTCAAGTAT
CTGCAACTAATGTCAGACTTCAGCCACCAGTAGGACATTCAAGACCAACACCTAAAACATGGTAA
CCTGGGTT
Found at i:18200096 original size:14 final size:14
Alignment explanation
Indices: 18200077--18200106 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18200067 AGTGGGAGAG
*
18200077 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
18200091 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
18200105 GA
1 GA
18200107 ATGAGGGATG
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:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:18217333 original size:33 final size:35
Alignment explanation
Indices: 18217282--18217418 Score: 93
Period size: 33 Copynumber: 3.8 Consensus size: 35
18217272 TTCACATTTA
**
18217282 AAATACGGTGGAATCAGCACTTAGCAACCACCAAT
1 AAATACGGTGGAATCAGCACACAGCAACCACCAAT
*
18217317 AAAT-CGG-GGAATCAGCACACAGCAACCCCCTTCACATTT
1 AAATACGGTGGAATCAGCACACAGCAA-CCAC--CA-A--T
* * ** *
18217356 CAGATGCGGTGGAATCAGCACTTAGCAACCACTAAT
1 -AAATACGGTGGAATCAGCACACAGCAACCACCAAT
* *
18217392 GAAT-CGG-GGGATCAGCACACAGCAACC
1 AAATACGGTGGAATCAGCACACAGCAACC
18217419 CCTTTATATG
Statistics
Matches: 80, Mismatches: 13, Indels: 20
0.71 0.12 0.18
Matches are distributed among these distances:
33 33 0.41
34 9 0.11
35 6 0.08
36 3 0.04
37 1 0.01
38 1 0.01
39 2 0.03
40 3 0.04
41 6 0.08
42 16 0.20
ACGTcount: A:0.35, C:0.28, G:0.20, T:0.16
Consensus pattern (35 bp):
AAATACGGTGGAATCAGCACACAGCAACCACCAAT
Found at i:18217376 original size:75 final size:76
Alignment explanation
Indices: 18217252--18217420 Score: 259
Period size: 75 Copynumber: 2.2 Consensus size: 76
18217242 NNNNNNNNNN
**
18217252 TCAGCACTTAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAAT
1 TCAGCACACAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAAT
18217317 AAATCGGGGAA
66 AAATCGGGGAA
* * * *
18217328 TCAGCACACAGCAACCCCC-TTCACATTTCAGATGCGGTGGAATCAGCACTTAGCAACCACTAAT
1 TCAGCACACAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAAT
* *
18217392 GAATCGGGGGA
66 AAATCGGGGAA
18217403 TCAGCACACAGCAACCCC
1 TCAGCACACAGCAACCCC
18217421 TTTATATGCA
Statistics
Matches: 85, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
75 68 0.80
76 17 0.20
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.18
Consensus pattern (76 bp):
TCAGCACACAGCAACCCCCTTTCACATTTAAAATACGGTGGAATCAGCACTTAGCAACCACCAAT
AAATCGGGGAA
Found at i:18221428 original size:14 final size:14
Alignment explanation
Indices: 18221409--18221438 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
18221399 AGTGAGAGAG
*
18221409 GAGAGAAGAGTTGT
1 GAGAGAAGAGATGT
18221423 GAGAGAAGAGATGT
1 GAGAGAAGAGATGT
18221437 GA
1 GA
18221439 ATGAGGGATG
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:0.40, C:0.00, G:0.43, T:0.17
Consensus pattern (14 bp):
GAGAGAAGAGATGT
Found at i:18222084 original size:18 final size:19
Alignment explanation
Indices: 18222056--18222093 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
18222046 AATTTTTAAT
18222056 AAAATTTAATTATTTTATG
1 AAAATTTAATTATTTTATG
18222075 AAAA-TTAATTATTTTATG
1 AAAATTTAATTATTTTATG
18222093 A
1 A
18222094 CAAAAATTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (19 bp):
AAAATTTAATTATTTTATG
Found at i:18223832 original size:41 final size:40
Alignment explanation
Indices: 18223786--18223905 Score: 114
Period size: 41 Copynumber: 2.9 Consensus size: 40
18223776 CAACGGTTAT
* * **
18223786 CTGATTCACTACACTAGCATGCAGCCTGCTAGGCTCAAGTC
1 CTGATTCA-TACACTAGCACGAAGCCTGCTAGGCTCAACAC
* *
18223827 CTGATTTCATACACTGGCACGAAGCTTGCTAGGCTCAACAC
1 CTGA-TTCATACACTAGCACGAAGCCTGCTAGGCTCAACAC
* * * * *
18223868 CTGATTTCATAAACCAACACAAAGCCTGCTAGGTTCAA
1 CTGA-TTCATACACTAGCACGAAGCCTGCTAGGCTCAA
18223906 AACCCGATAC
Statistics
Matches: 65, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 61 0.94
42 4 0.06
ACGTcount: A:0.29, C:0.29, G:0.17, T:0.24
Consensus pattern (40 bp):
CTGATTCATACACTAGCACGAAGCCTGCTAGGCTCAACAC
Found at i:18234735 original size:16 final size:17
Alignment explanation
Indices: 18234698--18234738 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
18234688 TTATATTTTC
18234698 AGAAATTTAAAATAATT
1 AGAAATTTAAAATAATT
18234715 A-AAATTTAAAA-AA-T
1 AGAAATTTAAAATAATT
18234729 AGGAAATTTA
1 A-GAAATTTA
18234739 GTTTTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.09
15 2 0.09
16 17 0.77
17 1 0.05
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (17 bp):
AGAAATTTAAAATAATT
Found at i:18234932 original size:7 final size:7
Alignment explanation
Indices: 18234920--18234945 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
18234910 AATTTCACTA
18234920 TTTTTAT
1 TTTTTAT
18234927 TTTTTAT
1 TTTTTAT
18234934 TTTTTAT
1 TTTTTAT
18234941 TTTTT
1 TTTTT
18234946 TTCATTTCAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTAT
Found at i:18244810 original size:22 final size:22
Alignment explanation
Indices: 18244785--18244830 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
18244775 TAAAATTTAA
18244785 ATTTAAGTTTATAT-TAACTATT
1 ATTT-AGTTTATATCTAACTATT
* *
18244807 ATTTATTTTATATCTAATTATT
1 ATTTAGTTTATATCTAACTATT
18244829 AT
1 AT
18244831 AATTCATATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.59
Consensus pattern (22 bp):
ATTTAGTTTATATCTAACTATT
Found at i:18251808 original size:17 final size:17
Alignment explanation
Indices: 18251785--18251830 Score: 60
Period size: 15 Copynumber: 2.8 Consensus size: 17
18251775 ATCACAATTT
18251785 TTTTTTTAATTTCACGAA
1 TTTTTTTAATTTCAC-AA
*
18251803 TTTTTTTAA-TTCAC-T
1 TTTTTTTAATTTCACAA
18251818 TTTTTTTAATTTC
1 TTTTTTTAATTTC
18251831 GTATGTATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 9 0.35
16 3 0.12
17 5 0.19
18 9 0.35
ACGTcount: A:0.22, C:0.11, G:0.02, T:0.65
Consensus pattern (17 bp):
TTTTTTTAATTTCACAA
Found at i:18253447 original size:30 final size:30
Alignment explanation
Indices: 18253389--18253447 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
18253379 CATAAGTGAT
* *
18253389 TTGAGCTGAAATTGAGCTAGTTCGAGCTCA
1 TTGAGCTGAAATGGAGCTAATTCGAGCTCA
18253419 TTGAGCTGAAATGGAGCTTAATTC-AGCTC
1 TTGAGCTGAAATGGAGC-TAATTCGAGCTC
18253448 GCAACAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (30 bp):
TTGAGCTGAAATGGAGCTAATTCGAGCTCA
Found at i:18253962 original size:18 final size:18
Alignment explanation
Indices: 18253939--18253977 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
18253929 TAATCAAATT
18253939 ATCTCATATTAAAAAAAA
1 ATCTCATATTAAAAAAAA
* **
18253957 ATCTCATGTTTGAAAAAA
1 ATCTCATATTAAAAAAAA
18253975 ATC
1 ATC
18253978 ATTATATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (18 bp):
ATCTCATATTAAAAAAAA
Found at i:18262090 original size:34 final size:34
Alignment explanation
Indices: 18261998--18262096 Score: 137
Period size: 33 Copynumber: 2.9 Consensus size: 34
18261988 AACACATTAC
*
18261998 CAGAAACATATGTCAAATCAGAATGTCATATTTT
1 CAGAAACATATATCAAATCAGAATGTCATATTTT
* *
18262032 -TGAAACATATACCAAATCAGAATGTCATATTTT
1 CAGAAACATATATCAAATCAGAATGTCATATTTT
* * *
18262065 CAGAAACTTATATCATATCAAAATGTCATATT
1 CAGAAACATATATCAAATCAGAATGTCATATT
18262097 ATATCCCAAC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 30 0.54
34 26 0.46
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.33
Consensus pattern (34 bp):
CAGAAACATATATCAAATCAGAATGTCATATTTT
Found at i:18262693 original size:37 final size:37
Alignment explanation
Indices: 18262644--18262716 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
18262634 CTACGTGGCC
** *
18262644 CACACAGGCTACCTGTCCTGCCCGTATGATTTCACAA
1 CACACAGGCTACCTAACATGCCCGTATGATTTCACAA
*
18262681 CACATAGGCTACCTAACATGCCCGTATGATTTCACA
1 CACACAGGCTACCTAACATGCCCGTATGATTTCACA
18262717 CGCCCGTGTG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.27, C:0.33, G:0.15, T:0.25
Consensus pattern (37 bp):
CACACAGGCTACCTAACATGCCCGTATGATTTCACAA
Found at i:18262775 original size:49 final size:49
Alignment explanation
Indices: 18262718--18262826 Score: 139
Period size: 49 Copynumber: 2.2 Consensus size: 49
18262708 GATTTCACAC
* *
18262718 GCCCGTGTGTCC-CACACGACCTACTTGATTTTCTCGTGTAATCGCAGAT
1 GCCCGTGTG-CCTCACACGACCTACCTGATTTGCTCGTGTAATCGCAGAT
* * * *
18262767 GCCCGTGTGCCTCACAGGACCTGCCTGATTTGCTCGTGTAATTGCATAT
1 GCCCGTGTGCCTCACACGACCTACCTGATTTGCTCGTGTAATCGCAGAT
*
18262816 GCTCGTGTGCC
1 GCCCGTGTGCC
18262827 CTAAACAAGC
Statistics
Matches: 52, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
48 2 0.04
49 50 0.96
ACGTcount: A:0.16, C:0.30, G:0.24, T:0.30
Consensus pattern (49 bp):
GCCCGTGTGCCTCACACGACCTACCTGATTTGCTCGTGTAATCGCAGAT
Found at i:18286156 original size:24 final size:25
Alignment explanation
Indices: 18286123--18286181 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
18286113 ATCTAATTAA
18286123 AAAAAT-AAAAAGA-AAACAAA-AAC
1 AAAAATAAAAAAGACAAA-AAAGAAC
*
18286146 AAAAATAAAAAAGACAAAAAAGAAG
1 AAAAATAAAAAAGACAAAAAAGAAC
*
18286171 AAAAAGAAAAA
1 AAAAATAAAAA
18286182 TCAAAATCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 6 0.19
24 10 0.32
25 15 0.48
ACGTcount: A:0.83, C:0.05, G:0.08, T:0.03
Consensus pattern (25 bp):
AAAAATAAAAAAGACAAAAAAGAAC
Found at i:18287142 original size:6 final size:7
Alignment explanation
Indices: 18287129--18287162 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
18287119 AAAAAAAAGG
18287129 ATGAAAA
1 ATGAAAA
18287136 ATGAAAA
1 ATGAAAA
18287143 ATG-AAA
1 ATGAAAA
18287149 ATGAAAA
1 ATGAAAA
18287156 ATGAAAA
1 ATGAAAA
18287163 GTGATGACGG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.23
7 20 0.77
ACGTcount: A:0.71, C:0.00, G:0.15, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:18287149 original size:13 final size:13
Alignment explanation
Indices: 18287133--18287162 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
18287123 AAAAGGATGA
18287133 AAAATGAAAAATG
1 AAAATGAAAAATG
18287146 AAAATGAAAAATG
1 AAAATGAAAAATG
18287159 AAAA
1 AAAA
18287163 GTGATGACGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (13 bp):
AAAATGAAAAATG
Found at i:18288553 original size:88 final size:88
Alignment explanation
Indices: 18288403--18288836 Score: 604
Period size: 88 Copynumber: 4.9 Consensus size: 88
18288393 CAGTGAAGAT
*
18288403 CCTTGCCTCCCTTGGTTGTAGTGGAGCTGG-TGAAAGATAGCAGATCTTGCCTTCCTGCATCGAC
1 CCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTG-AAGATAGCAGATCTTGCCTTCCTGCATCGAC
*
18288467 AGCGAAACAGATCGAAGACACAAA
65 AGCGAAGCAGATCGAAGACACAAA
* * * * * * *
18288491 CCTTGCCTCCCTCGGTTGCAATTGAACTGGTTGAAGATAGCAAATCTTGCCTTTCTGTATCGACA
1 CCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACA
*
18288556 GCGAAGTAGATCGAA-ACACAAA
66 GCGAAGCAGATCGAAGACACAAA
*
18288578 CCTTGCCTCCAC-CGATTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGAC
1 CCTTGCCTCC-CTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGAC
* * ** *
18288642 AACAAAATAGATCAAAGACACAAA
65 AGCGAAGCAGATCGAAGACACAAA
* *
18288666 CCTTGCCTCCCTCAGTTGTAGTGGAGCTGGTTGAAGATATCAGATCTTGCCTTCCTGCATCGACA
1 CCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACA
*
18288731 GTGAAGCAGATCGAAGACACAAA
66 GCGAAGCAGATCGAAGACACAAA
* * * * *
18288754 CCTTGCCTCCCTCGGTTGTAATGGAGCTGGTTGAGGATATCAGATTTTGCCTTCCTGTATCGACA
1 CCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACA
*
18288819 GTGAAGCAGATCGAAGAC
66 GCGAAGCAGATCGAAGAC
18288837 GGCGAGTCTT
Statistics
Matches: 306, Mismatches: 36, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
87 74 0.24
88 230 0.75
89 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.25
Consensus pattern (88 bp):
CCTTGCCTCCCTCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACA
GCGAAGCAGATCGAAGACACAAA
Found at i:18288698 original size:175 final size:176
Alignment explanation
Indices: 18288403--18288818 Score: 586
Period size: 175 Copynumber: 2.4 Consensus size: 176
18288393 CAGTGAAGAT
* *
18288403 CCTTGCCTCCCTTGGTTGTAGTGGAGCTGG-TGAAAGATAGCAGATCTTGCCTTCCTGCATCGAC
1 CCTTGCCTCCCTCGATTGTAGTGGAGCTGGTTG-AAGATAGCAGATCTTGCCTTCCTGCATCGAC
* * * * *
18288467 AGCGAAACAGATCGAAGACACAAACCTTGCCTCCCTCGGTTGCAATTGAACTGGTTGAAGATAGC
65 AACAAAACAGATCAAAGACACAAACCTTGCCTCCCTCAGTTGCAATGGAACTGGTTGAAGATAGC
* * *
18288532 AAATCTTGCCTTTCTGTATCGACAGCGAAGTAGATCGAA-ACACAAA
130 AAATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACAAA
18288578 CCTTGCCTCCAC-CGATTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGAC
1 CCTTGCCTCC-CTCGATTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGAC
* * * * *
18288642 AACAAAATAGATCAAAGACACAAACCTTGCCTCCCTCAGTTGTAGTGGAGCTGGTTGAAGATATC
65 AACAAAACAGATCAAAGACACAAACCTTGCCTCCCTCAGTTGCAATGGAACTGGTTGAAGATAGC
* *
18288707 AGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAGACACAAA
130 AAATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACAAA
* * * * * *
18288754 CCTTGCCTCCCTCGGTTGTAATGGAGCTGGTTGAGGATATCAGATTTTGCCTTCCTGTATCGACA
1 CCTTGCCTCCCTCGATTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACA
18288819 GTGAAGCAGA
Statistics
Matches: 214, Mismatches: 23, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
175 147 0.69
176 67 0.31
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.26
Consensus pattern (176 bp):
CCTTGCCTCCCTCGATTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATCGACA
ACAAAACAGATCAAAGACACAAACCTTGCCTCCCTCAGTTGCAATGGAACTGGTTGAAGATAGCA
AATCTTGCCTTCCTGCATCGACAGCGAAGCAGATCGAAGACACAAA
Done.