Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, 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: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 90 of 133
Found at i:17792014 original size:21 final size:20
Alignment explanation
Indices: 17791987--17792038 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 20
17791977 CATGTTAGTG
17791987 ACATTTGCATTACATGCATT
1 ACATTTGCATTACATGCATT
*
17792007 ACGTTTTGCATTACATGCATT
1 AC-ATTTGCATTACATGCATT
17792028 ACATTTGCATT
1 ACATTTGCATT
17792039 GTAGTTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.34
21 19 0.66
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.42
Consensus pattern (20 bp):
ACATTTGCATTACATGCATT
Found at i:17792504 original size:14 final size:14
Alignment explanation
Indices: 17792485--17792511 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17792475 TTGAGTTTTA
17792485 AATGAGAATCTTTG
1 AATGAGAATCTTTG
17792499 AATGAGAATCTTT
1 AATGAGAATCTTT
17792512 ATCTTTGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (14 bp):
AATGAGAATCTTTG
Found at i:17793048 original size:16 final size:16
Alignment explanation
Indices: 17793026--17793074 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
17793016 GTGAACCTAA
17793026 AAAATCTTATGAATCT
1 AAAATCTTATGAATCT
* ***
17793042 GAAATCTTGCAAATCT
1 AAAATCTTATGAATCT
17793058 AAAAGTCTTATGAATCT
1 AAAA-TCTTATGAATCT
17793075 TTGAATTACA
Statistics
Matches: 24, Mismatches: 8, Indels: 1
0.73 0.24 0.03
Matches are distributed among these distances:
16 15 0.62
17 9 0.38
ACGTcount: A:0.41, C:0.14, G:0.10, T:0.35
Consensus pattern (16 bp):
AAAATCTTATGAATCT
Found at i:17794292 original size:19 final size:18
Alignment explanation
Indices: 17794270--17794313 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
17794260 TTTGTTTTGG
*
17794270 TTTTTTTTATGGTTTTTAT
1 TTTTTTTTAT-GTTATTAT
17794289 TTTTTTTTATGTTATTAT
1 TTTTTTTTATGTTATTAT
17794307 TTCTTTT
1 TT-TTTT
17794314 ATTCACTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.39
19 14 0.61
ACGTcount: A:0.11, C:0.02, G:0.07, T:0.80
Consensus pattern (18 bp):
TTTTTTTTATGTTATTAT
Found at i:17795340 original size:22 final size:22
Alignment explanation
Indices: 17795283--17795340 Score: 62
Period size: 22 Copynumber: 2.6 Consensus size: 22
17795273 AATCAAAATT
*
17795283 TAAGCCCAGATTAGCTGGCACA
1 TAAGCCCAGATTAGCTAGCACA
** * **
17795305 TAAGCTTAGTTTAGCTAGCATG
1 TAAGCCCAGATTAGCTAGCACA
17795327 TAAGCCCAGATTAG
1 TAAGCCCAGATTAG
17795341 TTGAAAAAGT
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (22 bp):
TAAGCCCAGATTAGCTAGCACA
Found at i:17795572 original size:33 final size:33
Alignment explanation
Indices: 17795506--17796258 Score: 281
Period size: 33 Copynumber: 23.4 Consensus size: 33
17795496 TTATCCAGGT
* * *
17795506 TTTAAGCCTGGTTTAGTTGACAC-CTAATGAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTC-AATGAAAA
* *
17795539 TTTAAGCCTAGTGTAGCTGGCACTCAATCAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * * * **
17795572 TATAAGCCCAATTTAGTTAGCA-TCAATGAAGT
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* *
17795604 TTTAAGCCTAGTTTATCTAGCACT-AATGAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * ***
17795636 TTTAAGCCTAGCTTAGTTGCCACTTTGTGAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
** ***
17795669 TTTAAGCCTAGCATAGCTGGCAC-C--T-AGGT
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* ** * *
17795698 TTTAAGCCCACCTTAGCTGGCAC-CTATG---T
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * * *
17795727 TTTAAGCCCACTTTAGCTGGTACCCAATGAAGA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * *
17795760 TTTAAGCCTAGCTTAGCTAGCATTCAATG-AAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * **
17795792 TTTAAGCCTAGATTA-TTAGACACTCAATGAAGT
1 TTTAAGCCTAGTTTAGCT-GGCACTCAATGAAAA
* **
17795825 TTTAAGCCTAG-TTAGTTGGCAC-CTAATGAAGT
1 TTTAAGCCTAGTTTAGCTGGCACTC-AATGAAAA
* * * *
17795857 TTTAAACCCAATTTAGCTGGCACT-AATCAACAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAAT-GA-AAA
* ** * *
17795891 GTTTTAAGCCCAACTTAGCTGACACCCAATG-AAA
1 --TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* *
17795925 TTTAAGCCCAGTTTAACT-G-ATCTCTAATGAAAA
1 TTTAAGCCTAGTTTAGCTGGCA-CTC-AATGAAAA
* * * *
17795958 TTTAAGCCTAATGTAGTTGGCAC-CAAT-AAAGT
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAA-A
** **
17795990 TTTAAGCCCGGTTTATTTGGCA-TCAATGAAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATG-AAAA
* ** * * * *
17796023 TTTAAGCCAAACTTAGTTGGCACCCAGTAAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* ***
17796056 TTTAAGCCTAATTTAGCT-GCAC-C--T-AGGT
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * * *
17796084 TTTAAGCCAAGCTTAACTGGCACCCAATGAAGA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * *
17796117 TTTAA-CCTAGCTTAGTTGGCACTTAATG-AAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * * * **
17796148 TTTAAACCAAGATTATTCTGGCACTTAATGAAGT
1 TTTAAGCCTAGTTTA-GCTGGCACTCAATGAAAA
* * * *
17796182 TTTAAGCCCAATTTAGTTGGCACCCAATG-AAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * *
17796214 TTTAAGCCTAGTTTTGTTGACA-TCCAATTAAAA
1 TTTAAGCCTAGTTTAGCTGGCACT-CAATGAAAA
17796247 TTTAAGCCTAGT
1 TTTAAGCCTAGT
17796259 ATAGTTGGTA
Statistics
Matches: 544, Mismatches: 135, Indels: 82
0.71 0.18 0.11
Matches are distributed among these distances:
28 15 0.03
29 49 0.09
30 7 0.01
31 16 0.03
32 195 0.36
33 213 0.39
34 25 0.05
35 1 0.00
36 20 0.04
37 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.31
Consensus pattern (33 bp):
TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
Found at i:17795714 original size:29 final size:29
Alignment explanation
Indices: 17795682--17795746 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
17795672 AAGCCTAGCA
17795682 TAGCTGGCACCTAGGTTTTAAGCCCACCT
1 TAGCTGGCACCTAGGTTTTAAGCCCACCT
* *
17795711 TAGCTGGCACCTATGTTTTAAGCCCACTT
1 TAGCTGGCACCTAGGTTTTAAGCCCACCT
17795740 TAGCTGG
1 TAGCTGG
17795747 TACCCAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.31
Consensus pattern (29 bp):
TAGCTGGCACCTAGGTTTTAAGCCCACCT
Found at i:17795795 original size:32 final size:33
Alignment explanation
Indices: 17795751--17795839 Score: 112
Period size: 32 Copynumber: 2.7 Consensus size: 33
17795741 AGCTGGTACC
*
17795751 CAATGAAGATTTAAGCCTAGCTTAGCTAG-CATT
1 CAATGAAGATTTAAGCCTAG-TTAGCTAGACACT
*
17795784 CAATGAA-ATTTAAGCCTAGATTA-TTAGACACT
1 CAATGAAGATTTAAGCCTAG-TTAGCTAGACACT
*
17795816 CAATGAAGTTTTAAGCCTAGTTAG
1 CAATGAAGATTTAAGCCTAGTTAG
17795840 TTGGCACCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 3 0.06
32 28 0.57
33 18 0.37
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (33 bp):
CAATGAAGATTTAAGCCTAGTTAGCTAGACACT
Found at i:17795994 original size:65 final size:65
Alignment explanation
Indices: 17795836--17796046 Score: 173
Period size: 65 Copynumber: 3.2 Consensus size: 65
17795826 TTAAGCCTAG
* * * * *
17795836 TTAGTTGGCACCTAATGAAGTTTTAAACCCAATTTAGCTGGCA-CTAATCAACAAAGTTTTAAGC
1 TTAGTTGGCACC-AATAAAGTTTTAAGCCCAGTTTAACTGGCATC-AATGAA-AAA--TTTAAGC
*
17795900 CCAAC
61 CAAAC
* * *
17795905 TTAGCTGACACCCAATGAAA--TTTAAGCCCAGTTTAACTGATC-TCTAATG-AAAATTTAAGCC
1 TTAGTTGGCA-CCAAT-AAAGTTTTAAGCCCAGTTTAACTG-GCATC-AATGAAAAATTTAAGCC
*
17795966 TAA-
62 AAAC
* **
17795969 TGTAGTTGGCACCAATAAAGTTTTAAGCCCGGTTTATTTGGCATCAATGAAAAATTTAAGCCAAA
1 T-TAGTTGGCACCAATAAAGTTTTAAGCCCAGTTTAACTGGCATCAATGAAAAATTTAAGCCAAA
17796034 C
65 C
17796035 TTAGTTGGCACC
1 TTAGTTGGCACC
17796047 CAGTAAAAAT
Statistics
Matches: 116, Mismatches: 16, Indels: 24
0.74 0.10 0.15
Matches are distributed among these distances:
63 3 0.03
64 11 0.09
65 60 0.52
66 1 0.01
67 3 0.03
68 17 0.15
69 17 0.15
70 4 0.03
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (65 bp):
TTAGTTGGCACCAATAAAGTTTTAAGCCCAGTTTAACTGGCATCAATGAAAAATTTAAGCCAAAC
Found at i:17798948 original size:143 final size:142
Alignment explanation
Indices: 17798579--17798971 Score: 360
Period size: 143 Copynumber: 2.7 Consensus size: 142
17798569 GAAAAAATTG
* * *
17798579 ACCTCAAGAAAGTTAAATTATGAAAATAACCTTAAAGAGCATTTTAGTAATTTCACACCT-TGCA
1 ACCTCAA-AAAGGTAAATTATGAAAATAACCCTAAAGGGCATTTTAGTAATTTCACACCTCTG--
** * * * *
17798643 AAATACGATA-TAGGTTTTTAATGCATCAAAAATCATAAAATAATTTCAAAACATAATCTAGAGT
63 AGGTACGA-ACAAGGTTTTTAATGTATCAAAAATCATAAAATAATATCAAAACATAATCTAGAGC
* **
17798707 GTTTCGTGAAAAACCA
127 ATTTCGCAAAAAACCA
** * ** ** * * * *
17798723 ACCTC-TGAAGGTCAAATGACAAAAATATTCCTACAGGGCATTTTAGTAATTTTAAAGCTTCTGA
1 ACCTCAAAAAGGT-AAATTATGAAAATAACCCTAAAGGGCATTTTAGTAATTTCACA-CCTCTGA
** * * * * ** *
17798787 GGTGTGATCAAGGCTTTTAATATATCAAAAATCATAAAATGATATCAAATTATGATCTAGAGCAT
64 GGTACGAACAAGGTTTTTAATGTATCAAAAATCATAAAATAATATCAAAACATAATCTAGAGCAT
17798852 TTCGCAAAAAACCA
129 TTCGCAAAAAACCA
* *
17798866 ACCTCAAAAAGGTAAATTATGAAAATACCCCTAAAGGGCATTGTAGTAATTTCACACCTCCTGAG
1 ACCTCAAAAAGGTAAATTATGAAAATAACCCTAAAGGGCATTTTAGTAATTTCACACCT-CTGAG
* * * *
17798931 GTACGAACAAAGTTTTTAATGTACCAATAATCATCAAATAA
65 GTACGAACAAGGTTTTTAATGTATCAAAAATCATAAAATAA
17798972 CGTTTAAATA
Statistics
Matches: 189, Mismatches: 54, Indels: 13
0.74 0.21 0.05
Matches are distributed among these distances:
142 6 0.03
143 169 0.89
144 12 0.06
145 2 0.01
ACGTcount: A:0.42, C:0.16, G:0.13, T:0.29
Consensus pattern (142 bp):
ACCTCAAAAAGGTAAATTATGAAAATAACCCTAAAGGGCATTTTAGTAATTTCACACCTCTGAGG
TACGAACAAGGTTTTTAATGTATCAAAAATCATAAAATAATATCAAAACATAATCTAGAGCATTT
CGCAAAAAACCA
Found at i:17799210 original size:10 final size:10
Alignment explanation
Indices: 17799197--17799243 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
17799187 TTTGATCGAG
17799197 TTTGACCAAA
1 TTTGACCAAA
*
17799207 TTTGACAAAA
1 TTTGACCAAA
**
17799217 TTTGATTAAA
1 TTTGACCAAA
*
17799227 TTTGACCAAG
1 TTTGACCAAA
17799237 TTTGACC
1 TTTGACC
17799244 CGAAGGCATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
10 31 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (10 bp):
TTTGACCAAA
Found at i:17800057 original size:21 final size:21
Alignment explanation
Indices: 17800009--17800048 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17799999 TGATTCAATT
*
17800009 TTATATTCTAATTTATTTTAG
1 TTATATTATAATTTATTTTAG
17800030 TTATATTATAATTT-TTTTA
1 TTATATTATAATTTATTTTA
17800049 TTGATTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TTATATTATAATTTATTTTAG
Found at i:17801138 original size:2 final size:2
Alignment explanation
Indices: 17801131--17801166 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
17801121 TATTTGTTTG
*
17801131 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17801167 ATTTTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
GA
Found at i:17802616 original size:17 final size:18
Alignment explanation
Indices: 17802588--17802623 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
17802578 ATTCTTTTCC
*
17802588 TTTCATTTTTTTTTATTT
1 TTTCATTTTTTTTAATTT
17802606 TTTCA-TTTTTTTAATTT
1 TTTCATTTTTTTTAATTT
17802623 T
1 T
17802624 GAATTAAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.14, C:0.06, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTCATTTTTTTTAATTT
Found at i:17802823 original size:21 final size:22
Alignment explanation
Indices: 17802775--17802823 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 22
17802765 TAACGATAAT
*
17802775 AGTTTGAAGTATTAAAATTGAA
1 AGTTTTAAGTATTAAAATTGAA
*
17802797 A-ATTTAAGTATTAAAA-TGAA
1 AGTTTTAAGTATTAAAATTGAA
17802817 AGTTTTA
1 AGTTTTA
17802824 TTTCTTTAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 5 0.22
21 17 0.74
22 1 0.04
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (22 bp):
AGTTTTAAGTATTAAAATTGAA
Found at i:17805191 original size:13 final size:13
Alignment explanation
Indices: 17805175--17805215 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
17805165 CATGTTATAT
17805175 AATTATATTATTA
1 AATTATATTATTA
*
17805188 AATTAAATTATT-
1 AATTATATTATTA
17805200 AATT-TATTA-TA
1 AATTATATTATTA
17805211 AATTA
1 AATTA
17805216 ATAAATTAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
10 1 0.04
11 8 0.33
12 4 0.17
13 11 0.46
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (13 bp):
AATTATATTATTA
Found at i:17805278 original size:28 final size:28
Alignment explanation
Indices: 17805212--17805279 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
17805202 TTTATTATAA
*
17805212 ATTAATAAATTAATCTATTAAAATAAAT
1 ATTAATAAATTAATCTATCAAAATAAAT
* *
17805240 ATTTATCAATTAAT-TATCACAAAT-AAT
1 ATTAATAAATTAATCTATCA-AAATAAAT
17805267 ATATAATAAATTA
1 AT-TAATAAATTA
17805280 TTAATTTTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
27 9 0.27
28 24 0.73
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (28 bp):
ATTAATAAATTAATCTATCAAAATAAAT
Found at i:17807567 original size:16 final size:16
Alignment explanation
Indices: 17807546--17807578 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
17807536 ATAAAGTCTT
17807546 AATAATCCTTTTTAGA
1 AATAATCCTTTTTAGA
17807562 AATAATCCTTTTTAGA
1 AATAATCCTTTTTAGA
17807578 A
1 A
17807579 TCTTATATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.39, C:0.12, G:0.06, T:0.42
Consensus pattern (16 bp):
AATAATCCTTTTTAGA
Found at i:17820039 original size:8 final size:8
Alignment explanation
Indices: 17820020--17820062 Score: 52
Period size: 8 Copynumber: 5.5 Consensus size: 8
17820010 GTGGATGAAG
17820020 AAAAAATT
1 AAAAAATT
17820028 -AAAAATT
1 AAAAAATT
17820035 AAAAAATT
1 AAAAAATT
*
17820043 AAAAAAAT
1 AAAAAATT
* *
17820051 GAAAAATG
1 AAAAAATT
17820059 AAAA
1 AAAA
17820063 TGAAAAAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
7 7 0.24
8 22 0.76
ACGTcount: A:0.77, C:0.00, G:0.05, T:0.19
Consensus pattern (8 bp):
AAAAAATT
Found at i:17820070 original size:24 final size:22
Alignment explanation
Indices: 17820043--17820115 Score: 65
Period size: 24 Copynumber: 3.1 Consensus size: 22
17820033 TTAAAAAATT
17820043 AAAAAAATGAAAAATGAAAATGAA
1 AAAAAAATGAAAAATGAAAA--AA
*
17820067 AAAAAAGTGAAAAAGGTGAAAAAA
1 AAAAAAATGAAAAA--TGAAAAAA
** **
17820091 TGAAAAATGAAAAATGTGAAAA
1 AAAAAAATGAAAAATGAAAAAA
17820113 AAA
1 AAA
17820116 TGAAGAAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
22 7 0.18
24 26 0.67
26 6 0.15
ACGTcount: A:0.71, C:0.00, G:0.16, T:0.12
Consensus pattern (22 bp):
AAAAAAATGAAAAATGAAAAAA
Found at i:17820071 original size:9 final size:9
Alignment explanation
Indices: 17820035--17820139 Score: 57
Period size: 9 Copynumber: 12.2 Consensus size: 9
17820025 ATTAAAAATT
*
17820035 AAAAAATTA
1 AAAAAATGA
17820044 AAAAAATG-
1 AAAAAATGA
17820052 -AAAAATG-
1 AAAAAATGA
17820059 --AAAATGAA
1 AAAAAATG-A
17820067 AAAAAAGTGA
1 AAAAAA-TGA
**
17820077 AAAAGGTG-
1 AAAAAATGA
17820085 AAAAAATG-
1 AAAAAATGA
17820093 -AAAAATGA
1 AAAAAATGA
**
17820101 AAAATGTGA
1 AAAAAATGA
17820110 AAAAAATGA
1 AAAAAATGA
*
17820119 AGAAAAAGGA
1 A-AAAAATGA
17820129 AAGAAAA-GA
1 AA-AAAATGA
17820138 AA
1 AA
17820140 GACTCAAATT
Statistics
Matches: 77, Mismatches: 10, Indels: 18
0.73 0.10 0.17
Matches are distributed among these distances:
6 6 0.08
7 14 0.18
8 6 0.08
9 28 0.36
10 21 0.27
11 2 0.03
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.11
Consensus pattern (9 bp):
AAAAAATGA
Found at i:17820072 original size:17 final size:17
Alignment explanation
Indices: 17820052--17820104 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
17820042 TAAAAAAATG
17820052 AAAAATGAAAATGAAAA
1 AAAAATGAAAATGAAAA
* * ***
17820069 AAAAGTGAAAAAGGTGA
1 AAAAATGAAAATGAAAA
17820086 AAAAATGAAAAATGAAAA
1 AAAAATG-AAAATGAAAA
17820104 A
1 A
17820105 TGTGAAAAAA
Statistics
Matches: 25, Mismatches: 10, Indels: 1
0.69 0.28 0.03
Matches are distributed among these distances:
17 18 0.72
18 7 0.28
ACGTcount: A:0.72, C:0.00, G:0.17, T:0.11
Consensus pattern (17 bp):
AAAAATGAAAATGAAAA
Found at i:17820080 original size:33 final size:32
Alignment explanation
Indices: 17820021--17820119 Score: 103
Period size: 33 Copynumber: 3.1 Consensus size: 32
17820011 TGGATGAAGA
* * *
17820021 AAAAATTAAAAATTAAAAAA-TTAAAAAAATG
1 AAAAATGAAAAATGAAAAAAGTGAAAAAAATG
**
17820052 AAAAATG-AAAATGAAAAAAAAGTGAAAAAGGTG
1 AAAAATGAAAAATG--AAAAAAGTGAAAAAAATG
*
17820085 AAAAAATGAAAAATGAAAAATGTGAAAAAAATG
1 -AAAAATGAAAAATGAAAAAAGTGAAAAAAATG
17820118 AA
1 AA
17820120 GAAAAAGGAA
Statistics
Matches: 55, Mismatches: 8, Indels: 9
0.76 0.11 0.12
Matches are distributed among these distances:
30 5 0.09
31 6 0.11
32 8 0.15
33 23 0.42
34 7 0.13
35 6 0.11
ACGTcount: A:0.71, C:0.00, G:0.13, T:0.16
Consensus pattern (32 bp):
AAAAATGAAAAATGAAAAAAGTGAAAAAAATG
Found at i:17820080 original size:48 final size:47
Alignment explanation
Indices: 17820014--17820106 Score: 109
Period size: 48 Copynumber: 1.9 Consensus size: 47
17820004 TCAATAGTGG
* *
17820014 ATGAAGAAAAAATTAAAAA-TTAAAAAATTAAAAAAATGAAAAATGAAA
1 ATGAAGAAAAAATGAAAAAGTGAAAAAA-T-AAAAAATGAAAAATGAAA
*
17820062 ATGAA-AAAAAAGTGAAAAAGGTGAAAAAATGAAAAATGAAAAATG
1 ATGAAGAAAAAA-TGAAAAA-GTGAAAAAATAAAAAATGAAAAATG
17820107 TGAAAAAAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
47 6 0.15
48 25 0.64
49 1 0.03
50 7 0.18
ACGTcount: A:0.70, C:0.00, G:0.14, T:0.16
Consensus pattern (47 bp):
ATGAAGAAAAAATGAAAAAGTGAAAAAATAAAAAATGAAAAATGAAA
Found at i:17820096 original size:25 final size:25
Alignment explanation
Indices: 17820069--17820119 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
17820059 AAAATGAAAA
*
17820069 AAAAGTGAAAAAGGTG-AAAAAATG
1 AAAAATGAAAAAGGTGAAAAAAATG
*
17820093 AAAAATGAAAAATGTGAAAAAAATG
1 AAAAATGAAAAAGGTGAAAAAAATG
17820118 AA
1 AA
17820120 GAAAAAGGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.67, C:0.00, G:0.20, T:0.14
Consensus pattern (25 bp):
AAAAATGAAAAAGGTGAAAAAAATG
Found at i:17820103 original size:6 final size:7
Alignment explanation
Indices: 17820045--17820106 Score: 60
Period size: 7 Copynumber: 9.0 Consensus size: 7
17820035 AAAAAATTAA
17820045 AAAAATG
1 AAAAATG
17820052 AAAAATG
1 AAAAATG
17820059 -AAAATG
1 AAAAATG
17820065 -AAAA--
1 AAAAATG
*
17820069 AAAAGTG
1 AAAAATG
17820076 AAAAAGGTG
1 AAAAA--TG
17820085 AAAAAATG
1 -AAAAATG
17820093 AAAAATG
1 AAAAATG
17820100 AAAAATG
1 AAAAATG
17820107 TGAAAAAAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
5 3 0.06
6 10 0.21
7 25 0.53
8 2 0.04
9 2 0.04
10 5 0.11
ACGTcount: A:0.69, C:0.00, G:0.18, T:0.13
Consensus pattern (7 bp):
AAAAATG
Found at i:17821360 original size:14 final size:14
Alignment explanation
Indices: 17821341--17821367 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17821331 TTGAGTTTTA
17821341 AATGAGAATCTTTG
1 AATGAGAATCTTTG
17821355 AATGAGAATCTTT
1 AATGAGAATCTTT
17821368 ATCTTTGACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.07, G:0.19, T:0.37
Consensus pattern (14 bp):
AATGAGAATCTTTG
Found at i:17821772 original size:17 final size:17
Alignment explanation
Indices: 17821729--17821782 Score: 56
Period size: 17 Copynumber: 3.1 Consensus size: 17
17821719 GCTTACAAAC
*
17821729 CTTAAACTCTTGTGAAT
1 CTTAAAATCTTGTGAAT
17821746 -TTGAAAAATCTTGTGAAT
1 CTT--AAAATCTTGTGAAT
* *
17821764 CTTAAAATCATATGAAT
1 CTTAAAATCTTGTGAAT
17821781 CT
1 CT
17821783 AAGTTCTTGC
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
16 2 0.06
17 14 0.45
18 13 0.42
19 2 0.06
ACGTcount: A:0.37, C:0.13, G:0.11, T:0.39
Consensus pattern (17 bp):
CTTAAAATCTTGTGAAT
Found at i:17822224 original size:3 final size:3
Alignment explanation
Indices: 17822216--17822248 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
17822206 CTTTTCAATT
17822216 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17822249 GTTTTTTCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:17824205 original size:22 final size:22
Alignment explanation
Indices: 17824148--17824205 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
17824138 AATCAAAATT
* *
17824148 TAAGCCCAAATTAGCTGGCACA
1 TAAGCCCAGATTAGCTAGCACA
** * **
17824170 TAAGCTTAGTTTAGCTAGCATG
1 TAAGCCCAGATTAGCTAGCACA
17824192 TAAGCCCAGATTAG
1 TAAGCCCAGATTAG
17824206 TTGAAAAAGT
Statistics
Matches: 26, Mismatches: 10, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (22 bp):
TAAGCCCAGATTAGCTAGCACA
Found at i:17824437 original size:33 final size:33
Alignment explanation
Indices: 17824371--17825160 Score: 285
Period size: 33 Copynumber: 24.5 Consensus size: 33
17824361 TTATCCAGGT
* * *
17824371 TTTAAGCCTGGTTTAGTTGACAC-CTAATGAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTC-AATGAAAA
* *
17824404 TTTAAGCCTAGTGTAGCTGGCACTCAATCAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * * * **
17824437 TATAAGCCCAATTTAGTTAGCA-TCAATGAAGT
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* *
17824469 TTTAAGCCTAGTTTATCTAGCACT-AATGAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * ***
17824501 TTTAAGCCTAGCTTAGTTGCCACTTTGTGAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
** ***
17824534 TTTAAGCCTAGCATAGCTGGCAC-C--T-AGGT
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* ** * *
17824563 TTTAAGCCCACCTTAGCTGGCAC-CTATG---T
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * * *
17824592 TTTAAGCCCACTTTAGCTGGTACCCAATGAAGA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * *
17824625 TTTAAGCCTAGCTTAGCTAGCATTCAATG-AAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * **
17824657 TTTAAGCCTAGATTA-TTAGACACTCAATGAAGT
1 TTTAAGCCTAGTTTAGCT-GGCACTCAATGAAAA
* **
17824690 TTTAAGCCTAG-TTAGTTGGCAC-CTAATGAAGT
1 TTTAAGCCTAGTTTAGCTGGCACTC-AATGAAAA
* * * *
17824722 TTTAAACCCAATTTAGCTGGCACT-AATCAACAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAAT-GA-AAA
* ** * *
17824756 GTTTTAAGCCCAACTTAGCTGACACCCAATG-AAA
1 --TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* *
17824790 TTTAAGCCCAGTTTAACT-G-ATCTCTAATGAAAA
1 TTTAAGCCTAGTTTAGCTGGCA-CTC-AATGAAAA
* * * *
17824823 TTTAAGCCTAATGTAGTTGGCAC-CAAT-AAAGT
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAA-A
** **
17824855 TTTAAGCCCGGTTTATTTGGCA-TCAATGAAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATG-AAAA
* ** * * * *
17824888 TTTAAGCCAAACTTAGTTGGCACCCAGTAAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * ***
17824921 TTTAAGCCTAATTTAGCTGACAC-C--T-AGGT
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * * * *
17824950 TTTAAGCCAAGCTTAACTAGCACCCAATGAAGA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* *
17824983 TTT-AGACCTAGCTTAG-TCGGCACTTAATG-AAA
1 TTTAAG-CCTAGTTTAGCT-GGCACTCAATGAAAA
* * * * * **
17825015 TTTAAACCAAGATTATCTGGCACTTAATGAAGT
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * *
17825048 TTTAAGCCTAATTTAGTTGGCACCCAATG-AAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
* * * * *
17825080 TTTAAACCTAGTTTTGTTGACA-TCCAATTAAAA
1 TTTAAGCCTAGTTTAGCTGGCACT-CAATGAAAA
* * * *
17825113 TTTAAGCCTAGTATAGTTGGTAC-CAATAAAAA
1 TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
*
17825145 TTTAAGCTTAGTTTAG
1 TTTAAGCCTAGTTTAG
17825161 TTAGCATAAT
Statistics
Matches: 568, Mismatches: 146, Indels: 87
0.71 0.18 0.11
Matches are distributed among these distances:
29 62 0.11
30 8 0.01
31 8 0.01
32 215 0.38
33 238 0.42
34 13 0.02
35 1 0.00
36 20 0.04
37 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.16, T:0.31
Consensus pattern (33 bp):
TTTAAGCCTAGTTTAGCTGGCACTCAATGAAAA
Found at i:17824579 original size:29 final size:29
Alignment explanation
Indices: 17824547--17824611 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
17824537 AAGCCTAGCA
17824547 TAGCTGGCACCTAGGTTTTAAGCCCACCT
1 TAGCTGGCACCTAGGTTTTAAGCCCACCT
* *
17824576 TAGCTGGCACCTATGTTTTAAGCCCACTT
1 TAGCTGGCACCTAGGTTTTAAGCCCACCT
17824605 TAGCTGG
1 TAGCTGG
17824612 TACCCAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.20, C:0.28, G:0.22, T:0.31
Consensus pattern (29 bp):
TAGCTGGCACCTAGGTTTTAAGCCCACCT
Found at i:17824660 original size:32 final size:33
Alignment explanation
Indices: 17824616--17824704 Score: 112
Period size: 32 Copynumber: 2.7 Consensus size: 33
17824606 AGCTGGTACC
*
17824616 CAATGAAGATTTAAGCCTAGCTTAGCTAG-CATT
1 CAATGAAGATTTAAGCCTAG-TTAGCTAGACACT
*
17824649 CAATGAA-ATTTAAGCCTAGATTA-TTAGACACT
1 CAATGAAGATTTAAGCCTAG-TTAGCTAGACACT
*
17824681 CAATGAAGTTTTAAGCCTAGTTAG
1 CAATGAAGATTTAAGCCTAGTTAG
17824705 TTGGCACCTA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
31 3 0.06
32 28 0.57
33 18 0.37
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (33 bp):
CAATGAAGATTTAAGCCTAGTTAGCTAGACACT
Found at i:17824859 original size:65 final size:65
Alignment explanation
Indices: 17824701--17824911 Score: 173
Period size: 65 Copynumber: 3.2 Consensus size: 65
17824691 TTAAGCCTAG
* * * * *
17824701 TTAGTTGGCACCTAATGAAGTTTTAAACCCAATTTAGCTGGCA-CTAATCAACAAAGTTTTAAGC
1 TTAGTTGGCACC-AATAAAGTTTTAAGCCCAGTTTAACTGGCATC-AATGAA-AAA--TTTAAGC
*
17824765 CCAAC
61 CAAAC
* * *
17824770 TTAGCTGACACCCAATGAAA--TTTAAGCCCAGTTTAACTGATC-TCTAATG-AAAATTTAAGCC
1 TTAGTTGGCA-CCAAT-AAAGTTTTAAGCCCAGTTTAACTG-GCATC-AATGAAAAATTTAAGCC
*
17824831 TAA-
62 AAAC
* **
17824834 TGTAGTTGGCACCAATAAAGTTTTAAGCCCGGTTTATTTGGCATCAATGAAAAATTTAAGCCAAA
1 T-TAGTTGGCACCAATAAAGTTTTAAGCCCAGTTTAACTGGCATCAATGAAAAATTTAAGCCAAA
17824899 C
65 C
17824900 TTAGTTGGCACC
1 TTAGTTGGCACC
17824912 CAGTAAAAAT
Statistics
Matches: 116, Mismatches: 16, Indels: 24
0.74 0.10 0.15
Matches are distributed among these distances:
63 3 0.03
64 11 0.09
65 60 0.52
66 1 0.01
67 3 0.03
68 17 0.15
69 17 0.15
70 4 0.03
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.30
Consensus pattern (65 bp):
TTAGTTGGCACCAATAAAGTTTTAAGCCCAGTTTAACTGGCATCAATGAAAAATTTAAGCCAAAC
Found at i:17825467 original size:25 final size:25
Alignment explanation
Indices: 17825435--17825508 Score: 87
Period size: 25 Copynumber: 3.0 Consensus size: 25
17825425 ATTAAACAAA
17825435 AAATAAATAATAAAAATATAAAAAT
1 AAATAAATAATAAAAATATAAAAAT
* * *
17825460 CATTAAATAA-AAAATATATAATAAT
1 AAATAAATAATAAAA-ATATAAAAAT
* *
17825485 AAATAAGTAATATAAATATAAAAA
1 AAATAAATAATAAAAATATAAAAA
17825509 AATAAAAACA
Statistics
Matches: 39, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
24 4 0.10
25 32 0.82
26 3 0.08
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (25 bp):
AAATAAATAATAAAAATATAAAAAT
Found at i:17825495 original size:14 final size:14
Alignment explanation
Indices: 17825440--17825514 Score: 52
Period size: 14 Copynumber: 5.6 Consensus size: 14
17825430 ACAAAAAATA
*
17825440 AATAATAAAAATAT
1 AATAATAAATATAT
* *
17825454 AAAAAT-CAT-TA-
1 AATAATAAATATAT
*
17825465 AATAAAAAATATAT
1 AATAATAAATATAT
17825479 AATAATAAATA-AGT
1 AATAATAAATATA-T
*
17825493 AAT-ATAAATATAA
1 AATAATAAATATAT
*
17825506 AAAAATAAA
1 AATAATAAA
17825515 AACAAATTAA
Statistics
Matches: 46, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
11 4 0.09
12 4 0.09
13 13 0.28
14 25 0.54
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (14 bp):
AATAATAAATATAT
Found at i:17825506 original size:36 final size:36
Alignment explanation
Indices: 17825432--17825514 Score: 89
Period size: 36 Copynumber: 2.3 Consensus size: 36
17825422 ACCATTAAAC
*
17825432 AAAAAATAAATAATAAAAATATAAAAATCATTAAAT
1 AAAAAATAAATAATAAAAATATAAAAATCATAAAAT
* **
17825468 AAAAAATATATAATAATAAATA-AGTAAT-ATAAATAT
1 AAAAAATAAATAATAA-AAATATAAAAATCATAAA-AT
17825504 AAAAAAATAAA
1 -AAAAAATAAA
17825515 AACAAATTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
35 4 0.10
36 21 0.54
37 14 0.36
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (36 bp):
AAAAAATAAATAATAAAAATATAAAAATCATAAAAT
Found at i:17825536 original size:17 final size:18
Alignment explanation
Indices: 17825516--17825564 Score: 66
Period size: 17 Copynumber: 2.8 Consensus size: 18
17825506 AAAAATAAAA
*
17825516 ACAAATTAAAATGT-TAT
1 ACAAATTAAAATATATAT
*
17825533 ACAAATTCAAATATATAT
1 ACAAATTAAAATATATAT
17825551 ACAAA-TAAAATATA
1 ACAAATTAAAATATA
17825565 AAAAATATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
17 20 0.71
18 8 0.29
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (18 bp):
ACAAATTAAAATATATAT
Found at i:17825585 original size:10 final size:9
Alignment explanation
Indices: 17825557--17825592 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
17825547 ATATACAAAT
17825557 AAAATATAA
1 AAAATATAA
17825566 AAAATATAA
1 AAAATATAA
17825575 AAAATATTAA
1 AAAATA-TAA
*
17825585 AAGATATA
1 AAAATATA
17825593 TATCAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (9 bp):
AAAATATAA
Found at i:17825591 original size:19 final size:18
Alignment explanation
Indices: 17825557--17825592 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
17825547 ATATACAAAT
17825557 AAAATATAAAAAATATAA
1 AAAATATAAAAAATATAA
*
17825575 AAAATATTAAAAGATATA
1 AAAATA-TAAAAAATATA
17825593 TATCAAAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (18 bp):
AAAATATAAAAAATATAA
Found at i:17827345 original size:18 final size:15
Alignment explanation
Indices: 17827308--17827342 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
17827298 AAAATTATTA
17827308 AATAAAAAATTAAAT
1 AATAAAAAATTAAAT
17827323 AATAAAAAATTAAAT
1 AATAAAAAATTAAAT
17827338 AATAA
1 AATAA
17827343 TAATAATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AATAAAAAATTAAAT
Found at i:17827632 original size:18 final size:18
Alignment explanation
Indices: 17827609--17827646 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
17827599 CCCTAAGGTG
* *
17827609 AAACCTTAAATTCATTCC
1 AAACCTTAAAATCATCCC
17827627 AAACCTTAAAATCATCCC
1 AAACCTTAAAATCATCCC
17827645 AA
1 AA
17827647 GATTCAAGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (18 bp):
AAACCTTAAAATCATCCC
Found at i:17830141 original size:21 final size:21
Alignment explanation
Indices: 17830102--17830142 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
17830092 AATTTTTTAA
* *
17830102 ATTAAAGTTATTTGCTAAAAG
1 ATTAAAATTATTTACTAAAAG
*
17830123 ATTAAAATTATTTATTAAAA
1 ATTAAAATTATTTACTAAAA
17830143 ACTAAAGCCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.49, C:0.02, G:0.07, T:0.41
Consensus pattern (21 bp):
ATTAAAATTATTTACTAAAAG
Found at i:17832976 original size:13 final size:14
Alignment explanation
Indices: 17832958--17832987 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
17832948 TAGAATTATA
17832958 TTATTT-CAAATTT
1 TTATTTACAAATTT
17832971 TTATTTACAAATTT
1 TTATTTACAAATTT
17832985 TTA
1 TTA
17832988 CATATATTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (14 bp):
TTATTTACAAATTT
Found at i:17834551 original size:25 final size:23
Alignment explanation
Indices: 17834510--17834581 Score: 69
Period size: 26 Copynumber: 3.0 Consensus size: 23
17834500 CATGAATACC
17834510 TTACTA-TTTTTCACTTTTTTCTCT
1 TTACTATTTTTTC-CTTTTTTCT-T
17834534 TTCACTATTTTTTCCTTTCTTTACTT
1 TT-ACTATTTTTTCCTTT-TTT-CTT
*
17834560 TTA-T-TTTTTTCTTTTTTTCTT
1 TTACTATTTTTTCCTTTTTTCTT
17834581 T
1 T
17834582 GTTGAAAAGC
Statistics
Matches: 43, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
21 4 0.09
22 3 0.07
23 10 0.23
24 3 0.07
25 9 0.21
26 12 0.28
27 2 0.05
ACGTcount: A:0.10, C:0.18, G:0.00, T:0.72
Consensus pattern (23 bp):
TTACTATTTTTTCCTTTTTTCTT
Found at i:17834564 original size:22 final size:21
Alignment explanation
Indices: 17834539--17834581 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
17834529 TCTCTTTCAC
17834539 TATTTTTTCCTTTCTTTACTTT
1 TATTTTTTCCTTT-TTTACTTT
* *
17834561 TATTTTTTTCTTTTTTTCTTT
1 TATTTTTTCCTTTTTTACTTT
17834582 GTTGAAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (21 bp):
TATTTTTTCCTTTTTTACTTT
Found at i:17835254 original size:13 final size:13
Alignment explanation
Indices: 17835224--17835256 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
17835214 AAATAAGCTC
17835224 AAAAAGAAATTTTG
1 AAAAA-AAATTTTG
17835238 -AAAAAAATTTTG
1 AAAAAAAATTTTG
17835250 AAAAAAA
1 AAAAAAA
17835257 TTGGCATAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 8 0.44
13 10 0.56
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.24
Consensus pattern (13 bp):
AAAAAAAATTTTG
Found at i:17835255 original size:11 final size:12
Alignment explanation
Indices: 17835225--17835258 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
17835215 AATAAGCTCA
17835225 AAAAGAAATTTTG
1 AAAA-AAATTTTG
17835238 AAAAAAATTTTG
1 AAAAAAATTTTG
17835250 AAAAAAATT
1 AAAAAAATT
17835259 GGCATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 17 0.81
13 4 0.19
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (12 bp):
AAAAAAATTTTG
Found at i:17837754 original size:16 final size:17
Alignment explanation
Indices: 17837730--17837770 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
17837720 TGAAAAGATT
* *
17837730 TTTCCTTTATTT-TTTG
1 TTTCTTTTATTTCTTTA
17837746 TTTCTTTTATTTCTTTA
1 TTTCTTTTATTTCTTTA
17837763 TTT-TTTTA
1 TTTCTTTTA
17837771 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTCTTTTATTTCTTTA
Found at i:17837843 original size:11 final size:10
Alignment explanation
Indices: 17837821--17837938 Score: 57
Period size: 10 Copynumber: 11.2 Consensus size: 10
17837811 CAAATTGCTT
17837821 AATAAAAATA
1 AATAAAAATA
17837831 AATAAATAATAA
1 AATAAA-AAT-A
17837843 AAGTTAGCAAAATA
1 AA--TA--AAAATA
*
17837857 AATAAAAAATTG
1 AAT-AAAAA-TA
17837869 AATATAAAATA
1 AATA-AAAATA
17837880 ATATAAAAATA
1 A-ATAAAAATA
** *
17837891 TTTCAAAAT-
1 AATAAAAATA
17837900 -AT-AAAATA
1 AATAAAAATA
17837908 AATAAAAATA
1 AATAAAAATA
*
17837918 AA-ATCAAA-A
1 AATA-AAAATA
17837927 AATAAAAATA
1 AATAAAAATA
17837937 AA
1 AA
17837939 AATAAAATGA
Statistics
Matches: 84, Mismatches: 8, Indels: 32
0.68 0.06 0.26
Matches are distributed among these distances:
7 5 0.06
8 1 0.01
9 9 0.11
10 27 0.32
11 16 0.19
12 15 0.18
13 1 0.01
14 5 0.06
15 3 0.04
16 2 0.02
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (10 bp):
AATAAAAATA
Found at i:17837924 original size:28 final size:28
Alignment explanation
Indices: 17837869--17837951 Score: 93
Period size: 25 Copynumber: 3.1 Consensus size: 28
17837859 TAAAAAATTG
**
17837869 AATATAAAATAATATAAAAAT-ATTTCAA
1 AATATAAAATAA-ATAAAAATAAAATCAA
17837897 AATATAAAATAAATAAAAATAAAATCAA
1 AATATAAAATAAATAAAAATAAAATCAA
* *
17837925 AA-A-ATAA-AAATAAAAATAAAATGAA
1 AATATAAAATAAATAAAAATAAAATCAA
17837950 AA
1 AA
17837952 AAAGGAAACC
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
25 19 0.38
26 3 0.06
27 9 0.18
28 19 0.38
ACGTcount: A:0.73, C:0.02, G:0.01, T:0.23
Consensus pattern (28 bp):
AATATAAAATAAATAAAAATAAAATCAA
Found at i:17837929 original size:13 final size:12
Alignment explanation
Indices: 17837824--17837953 Score: 72
Period size: 12 Copynumber: 10.4 Consensus size: 12
17837814 ATTGCTTAAT
17837824 AAAAAT-AAATA
1 AAAAATAAAATA
*
17837835 AATAATAAAAGTTA
1 AAAAATAAAA--TA
*
17837849 GCAAAAT-AAATA
1 -AAAAATAAAATA
**
17837861 AAAAATTGAATA
1 AAAAATAAAATA
* *
17837873 TAAAATAATATA
1 AAAAATAAAATA
17837885 AAAATATTTCAAAATA
1 AAAA-A--T-AAAATA
*
17837901 TAAAAT-AAAT-
1 AAAAATAAAATA
17837911 AAAAATAAAATCA
1 AAAAATAAAAT-A
17837924 AAAAATAAAA-A
1 AAAAATAAAATA
17837935 TAAAAATAAAATGA
1 -AAAAATAAAAT-A
17837949 AAAAA
1 AAAAA
17837954 AGGAAACCTG
Statistics
Matches: 91, Mismatches: 13, Indels: 28
0.69 0.10 0.21
Matches are distributed among these distances:
10 5 0.05
11 19 0.21
12 30 0.33
13 17 0.19
14 6 0.07
15 6 0.07
16 8 0.09
ACGTcount: A:0.72, C:0.02, G:0.03, T:0.22
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:17837951 original size:6 final size:6
Alignment explanation
Indices: 17837895--17837945 Score: 54
Period size: 6 Copynumber: 8.5 Consensus size: 6
17837885 AAAATATTTC
17837895 AAAATA TAAAAT- -AAATA AAAAT- AAAATCAA AAAATA AAAATA AAAATA
1 AAAATA -AAAATA AAAATA AAAATA AAAAT--A AAAATA AAAATA AAAATA
17837943 AAA
1 AAA
17837946 TGAAAAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
4 4 0.10
5 5 0.13
6 20 0.51
7 5 0.13
8 5 0.13
ACGTcount: A:0.80, C:0.02, G:0.00, T:0.18
Consensus pattern (6 bp):
AAAATA
Found at i:17838106 original size:29 final size:27
Alignment explanation
Indices: 17838056--17838109 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
17838046 TGGTTTGCTA
17838056 TAAAAGCCAAGTTCCTCATTTTCTCTT
1 TAAAAGCCAAGTTCCTCATTTTCTCTT
* *
17838083 TAAAAGCCTCAGTCTCCTCTTTTTCTC
1 TAAAAGCC-AAGT-TCCTCATTTTCTC
17838110 GCCTCAAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 8 0.35
28 3 0.13
29 12 0.52
ACGTcount: A:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (27 bp):
TAAAAGCCAAGTTCCTCATTTTCTCTT
Found at i:17838175 original size:21 final size:20
Alignment explanation
Indices: 17838138--17838179 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 20
17838128 TCTCTCTAAA
17838138 AAAACTAAGAATGTTCAATCG
1 AAAACTAAGAATGTTC-ATCG
*
17838159 AAAACTGAA-AATTTTCATCG
1 AAAACT-AAGAATGTTCATCG
17838179 A
1 A
17838180 TTTCTAGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 5 0.26
21 12 0.63
22 2 0.11
ACGTcount: A:0.48, C:0.14, G:0.12, T:0.26
Consensus pattern (20 bp):
AAAACTAAGAATGTTCATCG
Found at i:17838756 original size:13 final size:14
Alignment explanation
Indices: 17838740--17838929 Score: 106
Period size: 13 Copynumber: 13.4 Consensus size: 14
17838730 AAAAGAAAGA
*
17838740 AAAATGATAA-AAT
1 AAAATAATAATAAT
17838753 AAAATAATAATAAT
1 AAAATAATAATAAT
*
17838767 -AATTATATAATAAT
1 AAAATA-ATAATAAT
*
17838781 ATAATATATATATAAT
1 AAAATA-ATA-ATAAT
*
17838797 ATAATATAATAATGCTAT
1 A-AA-ATAATAAT--AAT
* *
17838815 AATATAATAGTAAT
1 AAAATAATAATAAT
17838829 AATAATAATAATAAT
1 AA-AATAATAATAAT
* **
17838844 AAGATGCT-ATAAT
1 AAAATAATAATAAT
*
17838857 ATAATAAT-ATAAT
1 AAAATAATAATAAT
*
17838870 AATAACAATAAT-AT
1 AA-AATAATAATAAT
*
17838884 AATATAAT-ATAAT
1 AAAATAATAATAAT
* *
17838897 ATAAT-ATGATAAT
1 AAAATAATAATAAT
*
17838910 ATAATAATAATAAT
1 AAAATAATAATAAT
*
17838924 ATAATA
1 AAAATA
17838930 TACCATACTA
Statistics
Matches: 138, Mismatches: 25, Indels: 27
0.73 0.13 0.14
Matches are distributed among these distances:
12 4 0.03
13 47 0.34
14 40 0.29
15 21 0.15
16 15 0.11
17 5 0.04
18 6 0.04
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (14 bp):
AAAATAATAATAAT
Found at i:17838761 original size:8 final size:8
Alignment explanation
Indices: 17838750--17838929 Score: 67
Period size: 8 Copynumber: 21.1 Consensus size: 8
17838740 AAAATGATAA
17838750 AATAAAAT
1 AATAAAAT
17838758 AATAATAAT
1 AATAA-AAT
* *
17838767 AATTATAT
1 AATAAAAT
*
17838775 AATAATAT
1 AATAAAAT
*
17838783 AAT-ATAT
1 AATAAAAT
*
17838790 ATATAATAT
1 A-ATAAAAT
*
17838799 AATATAAT
1 AATAAAAT
***
17838807 AATGCTAT
1 AATAAAAT
*
17838815 AATATAAT
1 AATAAAAT
*
17838823 AGTAATAAT
1 AATAA-AAT
17838832 AATAATAAT
1 AATAA-AAT
17838841 AATAAGATGCTAT
1 AATAA-A----AT
*
17838854 AATATAAT
1 AATAAAAT
*
17838862 AATATAAT
1 AATAAAAT
17838870 AATAACAAT
1 AATAA-AAT
17838879 AATATAATAT
1 AATA-AA-AT
*
17838889 AATATAAT
1 AATAAAAT
*
17838897 -ATAATAT
1 AATAAAAT
* *
17838904 GATAATAT
1 AATAAAAT
17838912 AATAATAAT
1 AATAA-AAT
*
17838921 AATATAAT
1 AATAAAAT
17838929 A
1 A
17838930 TACCATACTA
Statistics
Matches: 136, Mismatches: 23, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
7 10 0.07
8 68 0.50
9 44 0.32
10 7 0.05
12 1 0.01
13 6 0.04
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.36
Consensus pattern (8 bp):
AATAAAAT
Found at i:17838763 original size:3 final size:3
Alignment explanation
Indices: 17838746--17838929 Score: 136
Period size: 3 Copynumber: 67.0 Consensus size: 3
17838736 AAGAAAAATG
*
17838746 ATA A-A ATA A-A ATA ATA ATA ATA ATT AT- ATA ATA AT- ATA ATA TATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA
* * *
17838791 TATA AT- ATA AT- ATA ATA ATG CT- ATA AT- ATA ATA GTA ATA ATA
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
17838833 ATA ATA ATA ATA A-G ATG CT- ATA AT- ATA ATA AT- ATA ATA ATA ACA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
*
17838877 ATA AT- ATA AT- ATA AT- ATA AT- ATA AT- ATG ATA AT- ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17838919 ATA AT- ATA ATA
1 ATA ATA ATA ATA
17838930 TACCATACTA
Statistics
Matches: 149, Mismatches: 12, Indels: 40
0.74 0.06 0.20
Matches are distributed among these distances:
2 35 0.23
3 107 0.72
4 7 0.05
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.36
Consensus pattern (3 bp):
ATA
Found at i:17838786 original size:5 final size:5
Alignment explanation
Indices: 17838746--17838931 Score: 130
Period size: 5 Copynumber: 35.6 Consensus size: 5
17838736 AAGAAAAATG
* * *
17838746 ATAAA ATAAA ATAAT AATAAT A-ATT AT-AT AATAAT ATAAT ATATAT
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT -ATAAT ATAAT ATA-AT
**
17838792 ATAAT ATAAT ATAAT AATGCT ATAAT ATAAT AGTAAT AATAAT AATAAT
1 ATAAT ATAAT ATAAT -ATAAT ATAAT ATAAT A-TAAT -ATAAT -ATAAT
* ** *
17838841 AATAAG ATGCT ATAAT AT-A- ATAAT ATAAT AATAACA ATAAT ATAAT
1 -ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT -ATAA-T ATAAT ATAAT
*
17838887 ATAAT ATAAT ATAAT ATGAT A-ATAT AATAAT AATAAT ATAAT ATA
1 ATAAT ATAAT ATAAT ATAAT ATA-AT -ATAAT -ATAAT ATAAT ATA
17838932 CCATACTATA
Statistics
Matches: 149, Mismatches: 17, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
3 2 0.01
4 6 0.04
5 88 0.59
6 51 0.34
7 2 0.01
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.36
Consensus pattern (5 bp):
ATAAT
Found at i:17838946 original size:92 final size:95
Alignment explanation
Indices: 17838756--17838929 Score: 252
Period size: 95 Copynumber: 1.9 Consensus size: 95
17838746 ATAAAATAAA
*
17838756 ATAATAATAATAAT-TATATAATAATATAATATATATATAATATAATATAATAATGCTATAATAT
1 ATAAT-ATAATAATATATATAATAAAATAATATATATATAATATAATATAATAATGC-ATAATAT
* *
17838820 AATAGTAATAATAATAATAATAATAAGATGCT
64 AATAATAATAATAATAATAATAATAAGATACT
17838852 ATAATATAATAATATA-ATAATAACAATAATATA-ATATAATATAATATAAT-ATG-ATAATATA
1 ATAATATAATAATATATATAATAA-AATAATATATATATAATATAATATAATAATGCATAATATA
17838913 ATAATAATAAT-ATAATA
65 ATAATAATAATAATAATA
17838930 TACCATACTA
Statistics
Matches: 74, Mismatches: 2, Indels: 9
0.87 0.02 0.11
Matches are distributed among these distances:
91 6 0.08
92 18 0.24
94 3 0.04
95 32 0.43
96 15 0.20
ACGTcount: A:0.59, C:0.02, G:0.03, T:0.37
Consensus pattern (95 bp):
ATAATATAATAATATATATAATAAAATAATATATATATAATATAATATAATAATGCATAATATAA
TAATAATAATAATAATAATAATAAGATACT
Found at i:17838971 original size:23 final size:23
Alignment explanation
Indices: 17838944--17839004 Score: 59
Period size: 23 Copynumber: 2.7 Consensus size: 23
17838934 ATACTATACT
17838944 ATACTAGTAATAATAACAAAATA
1 ATACTAGTAATAATAACAAAATA
* ** * *
17838967 ATACTAATGCTAATAGCGAAATA
1 ATACTAGTAATAATAACAAAATA
* *
17838990 ATAATAGTAAAAATA
1 ATACTAGTAATAATA
17839005 GACTCCAATT
Statistics
Matches: 28, Mismatches: 10, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.57, C:0.08, G:0.08, T:0.26
Consensus pattern (23 bp):
ATACTAGTAATAATAACAAAATA
Found at i:17839220 original size:55 final size:55
Alignment explanation
Indices: 17839158--17839294 Score: 148
Period size: 55 Copynumber: 2.5 Consensus size: 55
17839148 TGGGACTAAG
* * * * *
17839158 CCACAAGTCTAAAAAATGATTTGGACTGATCCGAGATTGAACAACCGAGATTAAA
1 CCACAAGTTTAAAAAATGATTTGGACTAAGCCAAGATCGAACAACCGAGATTAAA
* ** * * *
17839213 CTACAAGTTTGGAAAATGATCTGGACTAAGCCAAGATCGAGCGACCGAGATTAAA
1 CCACAAGTTTAAAAAATGATTTGGACTAAGCCAAGATCGAACAACCGAGATTAAA
* *
17839268 CCAAAAGTTTAAAAAGTTGATTTGGAC
1 CCACAAGTTTAAAAA-ATGATTTGGAC
17839295 CAAGTCGAGG
Statistics
Matches: 64, Mismatches: 17, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
55 55 0.86
56 9 0.14
ACGTcount: A:0.40, C:0.17, G:0.20, T:0.23
Consensus pattern (55 bp):
CCACAAGTTTAAAAAATGATTTGGACTAAGCCAAGATCGAACAACCGAGATTAAA
Found at i:17845215 original size:21 final size:21
Alignment explanation
Indices: 17845191--17845246 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
17845181 ATTGAGTAAA
17845191 AATAAATAAATAATAAAAGTC
1 AATAAATAAATAATAAAAGTC
* *
17845212 AATAAAATAAAT-ATAAAATTG
1 AAT-AAATAAATAATAAAAGTC
*
17845233 AATATA-AAATAATA
1 AATAAATAAATAATA
17845247 TAAAATTTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
19 4 0.13
20 5 0.17
21 13 0.43
22 8 0.27
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (21 bp):
AATAAATAAATAATAAAAGTC
Found at i:17845238 original size:12 final size:11
Alignment explanation
Indices: 17845213--17845253 Score: 57
Period size: 10 Copynumber: 3.7 Consensus size: 11
17845203 ATAAAAGTCA
*
17845213 ATAAAATAAAT
1 ATAAAATTAAT
17845224 ATAAAATTGAAT
1 ATAAAATT-AAT
17845236 ATAAAA-TAAT
1 ATAAAATTAAT
17845246 ATAAAATT
1 ATAAAATT
17845254 TGCAAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
10 9 0.33
11 9 0.33
12 9 0.33
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (11 bp):
ATAAAATTAAT
Found at i:17845248 original size:10 final size:10
Alignment explanation
Indices: 17845189--17845252 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
17845179 TTATTGAGTA
17845189 AAAATAA-AT
1 AAAATAATAT
17845198 -AAATAATA-
1 AAAATAATAT
* *
17845206 AAAGTCA-AT
1 AAAATAATAT
17845215 AAAATAAATAT
1 AAAAT-AATAT
17845226 AAAATTGAATAT
1 AAAA-T-AATAT
17845238 AAAATAATAT
1 AAAATAATAT
17845248 AAAAT
1 AAAAT
17845253 TTGCAAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 11
0.73 0.08 0.18
Matches are distributed among these distances:
8 7 0.16
9 9 0.20
10 11 0.25
11 7 0.16
12 10 0.23
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.27
Consensus pattern (10 bp):
AAAATAATAT
Found at i:17845278 original size:26 final size:23
Alignment explanation
Indices: 17845213--17845278 Score: 80
Period size: 26 Copynumber: 2.7 Consensus size: 23
17845203 ATAAAAGTCA
*
17845213 ATAAAATAAATATAAAATTGAAT
1 ATAAAATAAATATAAATTTGAAT
17845236 ATAAAAT-AATATAAAATTTGCAAAAT
1 ATAAAATAAATAT-AAATTTG---AAT
17845262 ATAAAATAAATATAAAT
1 ATAAAATAAATATAAAT
17845279 AAAAATAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
22 5 0.14
23 13 0.35
26 14 0.38
27 5 0.14
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (23 bp):
ATAAAATAAATATAAATTTGAAT
Found at i:17846119 original size:8 final size:8
Alignment explanation
Indices: 17846108--17846198 Score: 51
Period size: 8 Copynumber: 11.1 Consensus size: 8
17846098 AAAGGAAAGA
*
17846108 AAAATGAT
1 AAAATAAT
17846116 AAAATAAT
1 AAAATAAT
17846124 --AATAAT
1 AAAATAAT
17846130 AATAATAAT
1 AA-AATAAT
**
17846139 ACTATAAT
1 AAAATAAT
*
17846147 ATAATAAT
1 AAAATAAT
*
17846155 AAGATACTAT
1 AAAATA--AT
*
17846165 AACATAAT
1 AAAATAAT
* *
17846173 ATAGTAAT
1 AAAATAAT
17846181 AACAATAAT
1 AA-AATAAT
*
17846190 AATATAAT
1 AAAATAAT
17846198 A
1 A
17846199 TATACAATAT
Statistics
Matches: 63, Mismatches: 14, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
6 6 0.10
8 36 0.57
9 14 0.22
10 7 0.11
ACGTcount: A:0.62, C:0.04, G:0.03, T:0.31
Consensus pattern (8 bp):
AAAATAAT
Found at i:17846126 original size:3 final size:3
Alignment explanation
Indices: 17846114--17846264 Score: 77
Period size: 3 Copynumber: 56.0 Consensus size: 3
17846104 AAGAAAAATG
* *
17846114 ATA A-A ATA ATA ATA ATA ATA ATA ATA CT- ATA AT- ATA ATA ATA A-G
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
17846158 ATA CT- ATA A-C ATA AT- ATA GTA ATA ACA ATA ATA AT- ATA AT- ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
17846201 TACA AT- ATG AT- ATA AT- ATA AT- ATG ATA A-A AT- ATA AT- ATG
1 -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17846240 ATA AT- ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
17846265 TACCACACTA
Statistics
Matches: 113, Mismatches: 16, Indels: 38
0.68 0.10 0.23
Matches are distributed among these distances:
2 32 0.28
3 79 0.70
4 2 0.02
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:17846151 original size:5 final size:5
Alignment explanation
Indices: 17846114--17846266 Score: 89
Period size: 5 Copynumber: 29.6 Consensus size: 5
17846104 AAGAAAAATG
* * * *
17846114 ATAAA ATAAT AATAAT AATAAT AATACT ATAAT ATAAT AATAAG ATACT
1 ATAAT ATAAT -ATAAT -ATAAT -ATAAT ATAAT ATAAT -ATAAT ATAAT
* * * * *
17846163 ATAAC ATAAT AT-A- GTAAT AACAAT AATAAT ATAAT AT-AT ACAAT ATGAT
1 ATAAT ATAAT ATAAT ATAAT -ATAAT -ATAAT ATAAT ATAAT ATAAT ATAAT
* * *
17846212 ATAAT ATAAT ATGAT AAAAT ATAAT ATGAT A-ATAT AATAAT AATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT ATA-AT -ATAAT -ATAAT
17846259 ATAAT ATA
1 ATAAT ATA
17846267 CCACACTATT
Statistics
Matches: 116, Mismatches: 23, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
3 1 0.01
4 5 0.04
5 72 0.62
6 37 0.32
7 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (5 bp):
ATAAT
Found at i:17846163 original size:21 final size:22
Alignment explanation
Indices: 17846119--17846264 Score: 97
Period size: 22 Copynumber: 6.5 Consensus size: 22
17846109 AAATGATAAA
17846119 ATAATAATAATAATAATAATACT
1 ATAAT-ATAATAATAATAATACT
*
17846142 ATAATATAATAATAA-GATACT
1 ATAATATAATAATAATAATACT
* * *
17846163 ATAACATAATATAGTAATAACAAT
1 ATAATATAATA-A-TAATAATACT
17846187 AATAATATAATATATACA-ATATGA-T
1 -ATAATATAATA-ATA-ATA-AT-ACT
* *
17846212 ATAATATAAT-ATGATAA-AAT
1 ATAATATAATAATAATAATACT
* *
17846232 ATAATATGATAAT-ATAATAAT
1 ATAATATAATAATAATAATACT
17846253 AATAATATAATA
1 -ATAATATAATA
17846265 TACCACACTA
Statistics
Matches: 101, Mismatches: 10, Indels: 25
0.74 0.07 0.18
Matches are distributed among these distances:
19 1 0.01
20 14 0.14
21 22 0.22
22 24 0.24
23 8 0.08
24 16 0.16
25 15 0.15
26 1 0.01
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (22 bp):
ATAATATAATAATAATAATACT
Found at i:17846220 original size:54 final size:49
Alignment explanation
Indices: 17846114--17846212 Score: 117
Period size: 51 Copynumber: 2.0 Consensus size: 49
17846104 AAGAAAAATG
* * * *
17846114 ATAAAATAATAATAATAATAATAATACTATAATATAATAATAAGATACT
1 ATAAAATAATAATAATAACAATAATAATATAATATAACAATAAGATAAT
* *
17846163 ATAACATAATATAGTAATAACAATAATAATATAATATATACAATATGATA
1 ATAAAATAATA-A-TAATAACAATAATAATATAATATA-ACAATAAGATA
17846213 TAATATAATA
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
49 10 0.24
50 1 0.02
51 22 0.52
52 9 0.21
ACGTcount: A:0.60, C:0.05, G:0.03, T:0.32
Consensus pattern (49 bp):
ATAAAATAATAATAATAACAATAATAATATAATATAACAATAAGATAAT
Found at i:17847725 original size:19 final size:19
Alignment explanation
Indices: 17847698--17847741 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
17847688 AACAAAACCC
*
17847698 AAACTAACTAAGCA-ATAAT
1 AAACCAACTAA-CATATAAT
17847717 AAACCAACTAACATATAAT
1 AAACCAACTAACATATAAT
17847736 AAACCA
1 AAACCA
17847742 TAAACTGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 2 0.09
19 21 0.91
ACGTcount: A:0.59, C:0.20, G:0.02, T:0.18
Consensus pattern (19 bp):
AAACCAACTAACATATAAT
Found at i:17847952 original size:29 final size:31
Alignment explanation
Indices: 17847895--17847955 Score: 83
Period size: 29 Copynumber: 2.0 Consensus size: 31
17847885 AACATTACTT
*
17847895 ATCTTTAAAATCATGCAATAAACTTAAATTA
1 ATCTTTAAAATCATGCAATAAACTCAAATTA
17847926 ATCTTT-AAA-CATGCAATTAAAC-CAAATTA
1 ATCTTTAAAATCATGCAA-TAAACTCAAATTA
17847955 A
1 A
17847956 ATCAAAATAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 14 0.50
30 8 0.29
31 6 0.21
ACGTcount: A:0.49, C:0.15, G:0.03, T:0.33
Consensus pattern (31 bp):
ATCTTTAAAATCATGCAATAAACTCAAATTA
Found at i:17848328 original size:13 final size:13
Alignment explanation
Indices: 17848306--17848338 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
17848296 TGAACCAGAA
17848306 CAAAAAATT-AAC
1 CAAAAAATTAAAC
17848318 CAAAAAGATTAAAC
1 CAAAAA-ATTAAAC
17848332 CAAAAAA
1 CAAAAAA
17848339 AAAAAAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 6 0.32
13 4 0.21
14 9 0.47
ACGTcount: A:0.70, C:0.15, G:0.03, T:0.12
Consensus pattern (13 bp):
CAAAAAATTAAAC
Found at i:17849499 original size:10 final size:10
Alignment explanation
Indices: 17849480--17849513 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
17849470 TATACATAAA
17849480 AATCATCAAG
1 AATCATCAAG
* *
17849490 ATTGATCAAG
1 AATCATCAAG
17849500 AATCATCAAG
1 AATCATCAAG
17849510 AATC
1 AATC
17849514 TCTCAAATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.47, C:0.18, G:0.12, T:0.24
Consensus pattern (10 bp):
AATCATCAAG
Found at i:17851799 original size:22 final size:22
Alignment explanation
Indices: 17851772--17851820 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
17851762 GTTTAAGGTA
*
17851772 GGTTTGATTCAATTTTTGGGTT
1 GGTTTGATTCAATTTTGGGGTT
* *
17851794 GGTTTGGTTCGATTTTGGGGTT
1 GGTTTGATTCAATTTTGGGGTT
17851816 GGTTT
1 GGTTT
17851821 TCGATTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.08, C:0.04, G:0.35, T:0.53
Consensus pattern (22 bp):
GGTTTGATTCAATTTTGGGGTT
Found at i:17851851 original size:11 final size:12
Alignment explanation
Indices: 17851831--17851864 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
17851821 TCGATTTAAA
17851831 GTTTAGGGTTT-
1 GTTTAGGGTTTG
*
17851842 GTTTAAGGTTTG
1 GTTTAGGGTTTG
17851854 GTTTAGGGTTT
1 GTTTAGGGTTT
17851865 AGAATTGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.12, C:0.00, G:0.35, T:0.53
Consensus pattern (12 bp):
GTTTAGGGTTTG
Found at i:17851931 original size:7 final size:7
Alignment explanation
Indices: 17851908--17852166 Score: 118
Period size: 7 Copynumber: 38.7 Consensus size: 7
17851898 CTTTAGTATA
17851908 GGTTTAG
1 GGTTTAG
* *
17851915 AGTTT-T
1 GGTTTAG
17851921 GGTTTAG
1 GGTTTAG
* *
17851928 GGTTCAA
1 GGTTTAG
17851935 GGTTTAG
1 GGTTTAG
*
17851942 GATTTAG
1 GGTTTAG
17851949 GGTTTTAG
1 GG-TTTAG
*
17851957 GGTTTAA
1 GGTTTAG
*
17851964 GG-TAAG
1 GGTTTAG
* *
17851970 AGTTT-T
1 GGTTTAG
17851976 GGTTTAG
1 GGTTTAG
17851983 GGTTT-G
1 GGTTTAG
17851989 GGATTTAG
1 GG-TTTAG
*
17851997 GATTTA-
1 GGTTTAG
*
17852003 AGTTTAG
1 GGTTTAG
* * *
17852010 GATTCAA
1 GGTTTAG
*
17852017 GGTTT-C
1 GGTTTAG
17852023 GGTTTAG
1 GGTTTAG
* *
17852030 TGTTTGG
1 GGTTTAG
17852037 GGTTTA-
1 GGTTTAG
17852043 GGTTT--
1 GGTTTAG
*
17852048 GATTTAAG
1 GGTTT-AG
*
17852056 GTTTTA-
1 GGTTTAG
* *
17852062 GATTT-T
1 GGTTTAG
17852068 GGTTTAG
1 GGTTTAG
*
17852075 AGTTTAG
1 GGTTTAG
17852082 GGTTTAG
1 GGTTTAG
17852089 GGTATT--
1 GGT-TTAG
*
17852095 GGCTTAG
1 GGTTTAG
*
17852102 GGTTT-T
1 GGTTTAG
*
17852108 GGTTTAA
1 GGTTTAG
17852115 GGTTTAG
1 GGTTTAG
17852122 GGTTTAG
1 GGTTTAG
*
17852129 AGTTT-G
1 GGTTTAG
*
17852135 GTTTTAG
1 GGTTTAG
*
17852142 TGTTTA-
1 GGTTTAG
17852148 GGTTTAG
1 GGTTTAG
17852155 GGTTTAG
1 GGTTTAG
17852162 GGTTT
1 GGTTT
17852167 GCATGTAAAA
Statistics
Matches: 182, Mismatches: 51, Indels: 38
0.67 0.19 0.14
Matches are distributed among these distances:
5 6 0.03
6 52 0.29
7 109 0.60
8 15 0.08
ACGTcount: A:0.18, C:0.02, G:0.34, T:0.47
Consensus pattern (7 bp):
GGTTTAG
Found at i:17852110 original size:40 final size:40
Alignment explanation
Indices: 17852064--17852166 Score: 129
Period size: 40 Copynumber: 2.6 Consensus size: 40
17852054 AGGTTTTAGA
*
17852064 TTTTGGTTTAGAGTTTAGGGTTTAGGGTATTGG-CTTAGGG
1 TTTTGGTTTAGAGTTTAGGGTTTAGAGT-TTGGTCTTAGGG
* *
17852104 TTTTGGTTTA-AGGTTTAGGGTTTAGAGTTTGGTTTTAGTG
1 TTTTGGTTTAGA-GTTTAGGGTTTAGAGTTTGGTCTTAGGG
* *
17852144 TTTAGGTTTAGGGTTTAGGGTTT
1 TTTTGGTTTAGAGTTTAGGGTTT
17852167 GCATGTAAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
39 5 0.09
40 50 0.91
ACGTcount: A:0.15, C:0.01, G:0.35, T:0.50
Consensus pattern (40 bp):
TTTTGGTTTAGAGTTTAGGGTTTAGAGTTTGGTCTTAGGG
Found at i:17852121 original size:20 final size:19
Alignment explanation
Indices: 17851916--17852166 Score: 85
Period size: 20 Copynumber: 12.9 Consensus size: 19
17851906 TAGGTTTAGA
* **
17851916 GTTTTGGTTTAGGGTTCAAG
1 GTTTAGGTTTAGGGTT-TTG
17851936 GTTTAGGATTTAGGGTTTTAGG
1 GTTTAGG-TTTAGGGTTTT--G
* *
17851958 GTTTAAGG-TAAGAGTTTTG
1 GTTT-AGGTTTAGGGTTTTG
*
17851977 GTTTAGGGTTT-GGGATTTAG
1 GTTTA-GGTTTAGGG-TTTTG
* * **
17851997 GATTTAAGTTTAGGATTCAAG
1 G-TTTAGGTTTAGGGTT-TTG
* *
17852018 GTTTCGGTTTAGTG-TTTG
1 GTTTAGGTTTAGGGTTTTG
17852036 G----GGTTTA-GG-TTTG
1 GTTTAGGTTTAGGGTTTTG
* *
17852049 ATTTAAGGTTTTA-GATTTTG
1 GTTT-AGG-TTTAGGGTTTTG
*
17852069 GTTTAGAGTTTAGGGTTTAGG
1 GTTTAG-GTTTAGGGTTT-TG
*
17852090 GTATT-GGCTTAGGGTTTTG
1 GT-TTAGGTTTAGGGTTTTG
*
17852109 GTTTAAGGTTTAGGGTTTAG
1 GTTT-AGGTTTAGGGTTTTG
* *
17852129 AGTTT-GGTTTTAGTGTTTAG
1 -GTTTAGG-TTTAGGGTTTTG
17852149 GTTTAGGGTTTAGGGTTT
1 GTTTA-GGTTTAGGGTTT
17852167 GCATGTAAAA
Statistics
Matches: 175, Mismatches: 29, Indels: 54
0.68 0.11 0.21
Matches are distributed among these distances:
13 5 0.03
14 6 0.03
18 7 0.04
19 30 0.17
20 81 0.46
21 36 0.21
22 7 0.04
23 3 0.02
ACGTcount: A:0.18, C:0.02, G:0.34, T:0.47
Consensus pattern (19 bp):
GTTTAGGTTTAGGGTTTTG
Found at i:17852160 original size:13 final size:13
Alignment explanation
Indices: 17851906--17852162 Score: 141
Period size: 13 Copynumber: 19.3 Consensus size: 13
17851896 GGCTTTAGTA
*
17851906 TAGGTTTAGAGTT
1 TAGGTTTAGGGTT
*
17851919 TTGGTTTAGGGTT
1 TAGGTTTAGGGTT
* *
17851932 CAAGGTTTAGGATT
1 -TAGGTTTAGGGTT
17851946 TAGGGTTTTAGGGTT
1 TA-GG-TTTAGGGTT
* *
17851961 TAAGG-TAAGAGTT
1 T-AGGTTTAGGGTT
*
17851974 TTGGTTTAGGGTT
1 TAGGTTTAGGGTT
* *
17851987 TGGGATTTAGGATT
1 TAGG-TTTAGGGTT
* *
17852001 TAAGTTTAGGATT
1 TAGGTTTAGGGTT
* *
17852014 CAAGGTTT-CGGTT
1 -TAGGTTTAGGGTT
*
17852027 TAGTGTTTGGGGTT
1 TAG-GTTTAGGGTT
*
17852041 TAGGTTT--GATT
1 TAGGTTTAGGGTT
*
17852052 TAAGGTTTTA-GATT
1 T-AGG-TTTAGGGTT
* *
17852066 TTGGTTTAGAGTT
1 TAGGTTTAGGGTT
17852079 TAGGGTTTAGGGTAT
1 TA-GGTTTAGGGT-T
*
17852094 T-GGCTTAGGGTT
1 TAGGTTTAGGGTT
* *
17852106 TTGGTTTAAGGTT
1 TAGGTTTAGGGTT
*
17852119 TAGGGTTTAGAGTT
1 TA-GGTTTAGGGTT
*
17852133 T-GGTTTTAGTGTT
1 TAGG-TTTAGGGTT
17852146 TAGGTTTAGGGTT
1 TAGGTTTAGGGTT
17852159 TAGG
1 TAGG
17852163 GTTTGCATGT
Statistics
Matches: 189, Mismatches: 36, Indels: 38
0.72 0.14 0.14
Matches are distributed among these distances:
11 4 0.02
12 15 0.08
13 96 0.51
14 60 0.32
15 13 0.07
16 1 0.01
ACGTcount: A:0.18, C:0.02, G:0.34, T:0.46
Consensus pattern (13 bp):
TAGGTTTAGGGTT
Found at i:17854914 original size:44 final size:44
Alignment explanation
Indices: 17854866--17854970 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 44
17854856 TCCCCTAAGT
* * *
17854866 AGAGGTTTAACAACTTTTT-AAAATTTAAAAAAGCTCCTCTAAAC
1 AGAGGCTTAACAACTTTTTAAAAATTTAAAAAA-CCCCTATAAAC
* * * *
17854910 AGAGGCTCAATAACTTTTTAAAAATTTAAAAAACCCCTATGAAT
1 AGAGGCTTAACAACTTTTTAAAAATTTAAAAAACCCCTATAAAC
17854954 AGAGGCTTAACAACTTT
1 AGAGGCTTAACAACTTT
17854971 AAAATGCTCC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
44 38 0.75
45 13 0.25
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.30
Consensus pattern (44 bp):
AGAGGCTTAACAACTTTTTAAAAATTTAAAAAACCCCTATAAAC
Found at i:17855153 original size:59 final size:59
Alignment explanation
Indices: 17855081--17855193 Score: 149
Period size: 59 Copynumber: 1.9 Consensus size: 59
17855071 AGGCTCAACA
* *
17855081 ACTTTAAAAATTTCATCTT-GAAAAATCTCCTCTAAGTAAAGG-TTCAACAACTTTCATTG
1 ACTTTAAAAATTTC-TCTTCAAAAAAGCTCCTCTAAGTAAAGGCTT-AACAACTTTCATTG
* * *
17855140 ACTTTAAAAATTTCTTTTCAAAAAAGCTCCTTTAAGTAGAGGCTTAACAACTTT
1 ACTTTAAAAATTTCTCTTCAAAAAAGCTCCTCTAAGTAAAGGCTTAACAACTTT
17855194 AAAAAATTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
58 3 0.06
59 42 0.89
60 2 0.04
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (59 bp):
ACTTTAAAAATTTCTCTTCAAAAAAGCTCCTCTAAGTAAAGGCTTAACAACTTTCATTG
Found at i:17855214 original size:49 final size:49
Alignment explanation
Indices: 17855160--17855444 Score: 258
Period size: 49 Copynumber: 5.8 Consensus size: 49
17855150 TTTCTTTTCA
* *
17855160 AAAAAGCTCCTTTAAGTAGAGGCTTAACAACTTTAAAAAATTTATCATG
1 AAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTTATCTTG
* * * * * *
17855209 CAAAAGGCTCATCTAAGTAAAGGCTCAATAACTTTAAAAATTTTATCTTG
1 -AAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTTATCTTG
* * * *
17855259 -AAAAGTTTCCTCTAAGCAAAGG-TTCAACAACTTT-AAAAATTTCAT-TTT
1 AAAAAG-CTCCTCTAAGTAGAGGCTT-AACAACTTTAAAAAATTT-ATCTTG
* * *
17855307 AAAAAACTCCTCTAAGTAGAGGCTTAA-AACTTTAAAAAATTCATGTTG
1 AAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTTATCTTG
* * * * **
17855355 AAAAAGGCTCATCTAAGCAGAGACTCAACAACTTT-AAAAATTTCATCTAA
1 AAAAA-GCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTT-ATCTTG
* * *
17855405 AAAAAGTTCCTCTAAATAGAGGCTTAACAACTTAAAAAAA
1 AAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAA
17855445 AATTCATCTT
Statistics
Matches: 186, Mismatches: 38, Indels: 22
0.76 0.15 0.09
Matches are distributed among these distances:
47 8 0.04
48 43 0.23
49 75 0.40
50 60 0.32
ACGTcount: A:0.44, C:0.16, G:0.11, T:0.29
Consensus pattern (49 bp):
AAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTTATCTTG
Found at i:17855360 original size:97 final size:98
Alignment explanation
Indices: 17855185--17855454 Score: 285
Period size: 97 Copynumber: 2.7 Consensus size: 98
17855175 GTAGAGGCTT
** * * * * *
17855185 AACAACTTTAAAAAATTT-ATCATGCAAAAGGCTCATCTAAGTAAAGGCTCAATAACTTTAAAAA
1 AACAACTTT-AAAAATTTCATC-TAAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAA
* * ** * **
17855249 TTTTATCTTGAAAAGTTTCCTCTAAGCAAAGGTTC
64 ATTCATCTTGAAAAGGCTCATCTAAGCAAAGACTC
* *
17855284 AACAACTTTAAAAATTTCATTTTAAAAAA-CTCCTCTAAGTAGAGGCTTAA-AACTTTAAAAAAT
1 AACAACTTTAAAAATTTCATCTAAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAAT
* *
17855347 TCATGTTGAAAAAGGCTCATCTAAGCAGAGACTC
66 TCATCTTG-AAAAGGCTCATCTAAGCAAAGACTC
* * *
17855381 AACAACTTTAAAAATTTCATCTAAAAAAAGTTCCTCTAAATAGAGGCTTAACAACTTAAAAAAAA
1 AACAACTTTAAAAATTTCATCTAAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTT--TAAAAA
17855446 ATTCATCTT
64 ATTCATCTT
17855455 TTCTTGAAAC
Statistics
Matches: 143, Mismatches: 22, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
96 18 0.13
97 64 0.45
98 32 0.22
99 16 0.11
101 13 0.09
ACGTcount: A:0.44, C:0.16, G:0.10, T:0.30
Consensus pattern (98 bp):
AACAACTTTAAAAATTTCATCTAAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAAT
TCATCTTGAAAAGGCTCATCTAAGCAAAGACTC
Found at i:17855371 original size:146 final size:148
Alignment explanation
Indices: 17855140--17855419 Score: 406
Period size: 146 Copynumber: 1.9 Consensus size: 148
17855130 ACTTTCATTG
* *
17855140 ACTTTAAAAATTTCTTTTCAAAAAAGCTCCTTTAAGTAGAGGCTTAACAACTTTAAAAAATTTAT
1 ACTTTAAAAATTTCTTTTCAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCAT
* * * * * **
17855205 CATGCAAAAGGCTCATCTAAGTAAAGGCTCAATAACTTTAAAAATTTTATCT-TGAAAAGTTTCC
66 CATGAAAAAGGCTCATCTAAGCAAAGACTCAACAACTTTAAAAATTTCATCTAAAAAAAG-TTCC
17855269 TCTAAGCAAAGGTTCAACA
130 TCTAAGCAAAGGTTCAACA
17855288 ACTTTAAAAATTTCATTTT-AAAAAA-CTCCTCTAAGTAGAGGCTTAA-AACTTTAAAAAATTCA
1 ACTTTAAAAATTTC-TTTTCAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCA
** *
17855350 TGTTGAAAAAGGCTCATCTAAGCAGAGACTCAACAACTTTAAAAATTTCATCTAAAAAAAGTTCC
65 TCATGAAAAAGGCTCATCTAAGCAAAGACTCAACAACTTTAAAAATTTCATCTAAAAAAAGTTCC
17855415 TCTAA
130 TCTAA
17855420 ATAGAGGCTT
Statistics
Matches: 118, Mismatches: 12, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
146 69 0.58
147 25 0.21
148 20 0.17
149 4 0.03
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.31
Consensus pattern (148 bp):
ACTTTAAAAATTTCTTTTCAAAAAAGCTCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCAT
CATGAAAAAGGCTCATCTAAGCAAAGACTCAACAACTTTAAAAATTTCATCTAAAAAAAGTTCCT
CTAAGCAAAGGTTCAACA
Found at i:17867107 original size:18 final size:18
Alignment explanation
Indices: 17867084--17867119 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
17867074 ATTTTAACTA
17867084 TATATTT-TATTATTTATT
1 TATATTTAT-TTATTTATT
17867102 TATATTTATTTATTTATT
1 TATATTTATTTATTTATT
17867120 ATTATTATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 16 0.94
19 1 0.06
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
TATATTTATTTATTTATT
Found at i:17867124 original size:14 final size:14
Alignment explanation
Indices: 17867090--17867125 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
17867080 ACTATATATT
17867090 TTATTATTTATTTA
1 TTATTATTTATTTA
17867104 -TATTTATTTATTTA
1 TTA-TTATTTATTTA
17867118 TTATTATT
1 TTATTATT
17867126 ATAAAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.10
14 16 0.80
15 2 0.10
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
TTATTATTTATTTA
Found at i:17868055 original size:44 final size:44
Alignment explanation
Indices: 17867959--17868063 Score: 131
Period size: 44 Copynumber: 2.4 Consensus size: 44
17867949 CTCCCTAAGG
* * * * *
17867959 AAAGGCTTAACAACTTTTTGAAATTTTAAAAAGCTCTTTTAAAC
1 AAAGGCTTAACAACTTTTTAAAAATTTAAAAAGCCCCTCTAAAC
*
17868003 AGAA-GCTTAACAACTTTTTAAAAATTTAAAAAGCCCCTCTGAAC
1 A-AAGGCTTAACAACTTTTTAAAAATTTAAAAAGCCCCTCTAAAC
*
17868047 AAAGGCTTAATAACTTT
1 AAAGGCTTAACAACTTT
17868064 AAAAAGCTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
43 2 0.04
44 48 0.92
45 2 0.04
ACGTcount: A:0.42, C:0.16, G:0.10, T:0.32
Consensus pattern (44 bp):
AAAGGCTTAACAACTTTTTAAAAATTTAAAAAGCCCCTCTAAAC
Found at i:17868216 original size:49 final size:49
Alignment explanation
Indices: 17868148--17868489 Score: 287
Period size: 49 Copynumber: 6.8 Consensus size: 49
17868138 CTTGATAATG
* *
17868148 AAAGCTCCTCTATA-CAAAGGCTCAACAACTTTAAAAATTTCATCTTGGA
1 AAAGCTCCTCTA-AGTAAAGGCTCAACAACTTTAAAAATTTCATCTTGAA
* **
17868197 AAAGCTCCTCTAAGTAAAGGTTCAATAACTTTCATTGACTTTAAAAATTTCATCTCAAA
1 AAAGCTCCTCTAAGTAAAGGCTC---AA----CA---ACTTTAAAAATTTCATCTTGAA
* * *
17868256 AAAGCTCCTCTAAGTAGAGGTTTAACAACTTTAAAAACTTT-ATCTTGCAA
1 AAAGCTCCTCTAAGTAAAGGCTCAACAACTTTAAAAA-TTTCATCTTG-AA
* ** * * *
17868306 AAGGCTCCTCTAAGTAAAGGCTCAATGACTTTAAACATTTTATCTTG-C
1 AAAGCTCCTCTAAGTAAAGGCTCAACAACTTTAAAAATTTCATCTTGAA
* * * *
17868354 AAAGTTTCCTCTAAGCAGAGGTTCAACAACTTTAAAAATTTCATCTT-AA
1 AAAG-CTCCTCTAAGTAAAGGCTCAACAACTTTAAAAATTTCATCTTGAA
** * * *
17868403 AAAAATCCTCTAAGTAGAGGCTTAACAACTTTAAAAAATTCATCTTGAA
1 AAAGCTCCTCTAAGTAAAGGCTCAACAACTTTAAAAATTTCATCTTGAA
* * *
17868452 AAAGGCTCCTCTAAATAAAGGCTTAACAACTTAAAAAA
1 AAA-GCTCCTCTAAGTAAAGGCTCAACAACTTTAAAAA
17868490 AAAATTCATC
Statistics
Matches: 237, Mismatches: 38, Indels: 35
0.76 0.12 0.11
Matches are distributed among these distances:
48 41 0.17
49 78 0.33
50 70 0.30
52 4 0.02
56 4 0.02
59 40 0.17
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.30
Consensus pattern (49 bp):
AAAGCTCCTCTAAGTAAAGGCTCAACAACTTTAAAAATTTCATCTTGAA
Found at i:17868267 original size:59 final size:59
Alignment explanation
Indices: 17868175--17868287 Score: 172
Period size: 59 Copynumber: 1.9 Consensus size: 59
17868165 AGGCTCAACA
*** *
17868175 ACTTTAAAAATTTCATCTTGGAAAAGCTCCTCTAAGTAAAGGTTCAATAACTTTCATTG
1 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAAAGGTTCAACAACTTTCATTG
* *
17868234 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAGAGGTTTAACAACTTT
1 ACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAAAGGTTCAACAACTTT
17868288 AAAAACTTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 48 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.35
Consensus pattern (59 bp):
ACTTTAAAAATTTCATCTCAAAAAAGCTCCTCTAAGTAAAGGTTCAACAACTTTCATTG
Found at i:17868490 original size:50 final size:50
Alignment explanation
Indices: 17868234--17868489 Score: 272
Period size: 50 Copynumber: 5.2 Consensus size: 50
17868224 ACTTTCATTG
* * *
17868234 ACTTTAAAAATTTCATC-TCAAAAAAGCTCCTCTAAGTAGAGGTTTAACA
1 ACTTTAAAAATTTCATCTTGAAAAAGGCTCCTCTAAGTAGAGGCTTAACA
* * * **
17868283 ACTTTAAAAACTTT-ATCTTGCAAAAGGCTCCTCTAAGTAAAGGCTCAATG
1 ACTTTAAAAA-TTTCATCTTGAAAAAGGCTCCTCTAAGTAGAGGCTTAACA
* * * ** *
17868333 ACTTTAAACATTTTATCTTG-CAAAGTTTCCTCTAAGCAGAGG-TTCAACA
1 ACTTTAAAAATTTCATCTTGAAAAAGGCTCCTCTAAGTAGAGGCTT-AACA
**
17868382 ACTTTAAAAATTTCATCTT-AAAAA-AATCCTCTAAGTAGAGGCTTAACA
1 ACTTTAAAAATTTCATCTTGAAAAAGGCTCCTCTAAGTAGAGGCTTAACA
* * *
17868430 ACTTTAAAAAATTCATCTTGAAAAAGGCTCCTCTAAATAAAGGCTTAACA
1 ACTTTAAAAATTTCATCTTGAAAAAGGCTCCTCTAAGTAGAGGCTTAACA
*
17868480 ACTTAAAAAA
1 ACTTTAAAAA
17868490 AAAATTCATC
Statistics
Matches: 170, Mismatches: 29, Indels: 15
0.79 0.14 0.07
Matches are distributed among these distances:
48 37 0.22
49 62 0.36
50 71 0.42
ACGTcount: A:0.41, C:0.18, G:0.11, T:0.30
Consensus pattern (50 bp):
ACTTTAAAAATTTCATCTTGAAAAAGGCTCCTCTAAGTAGAGGCTTAACA
Found at i:17879357 original size:146 final size:144
Alignment explanation
Indices: 17878986--17879357 Score: 358
Period size: 145 Copynumber: 2.6 Consensus size: 144
17878976 TAAAATTTTC
* * * * *
17878986 ATAGTGCCCCGAAAAGGGTAAAATTACCAAAATACCCTTATAGGGGTATTTTCATAAATTGATCT
1 ATAGTACCCCAAAAAGGATGAAATTACCAAAATACCCTTATAGGGGTATTTTCATAATTTGA-CT
*
17879051 TTTCGAGGTTGAATTTTTGTGAAACTTCTCAAATCTTAATTTTATAATATTTCATAAATTTTTGT
65 TTTCGAGCTTGAATTTTTGTGAAACTTCTCAAATCTTAATTTTATAATATTTCATAAATTTTTGT
* * *
17879116 GCATTTAAAATCATG
130 GCATTCAAAACCAAG
* ***
17879131 ATGGTACCCCGGGAAGGATGAAATTACCAAAATACCCTTATTA-GGGTATTTTCATAATTTGACT
1 ATAGTACCCCAAAAAGGATGAAATTACCAAAATACCCTTA-TAGGGGTATTTTCATAATTTGAC-
* * ** * * * * *
17879195 TTTTTGAACTCAAATTTTTGTGAACCTTTTTCAAATTTTAATTTTATAATATTTCATGATTTTTT
64 TTTTCGAGCTTGAATTTTTGTGAAAC-TTCTCAAATCTTAATTTTATAATATTTCATAAATTTTT
*
17879260 GTG-AGTTCAAAGCCACAG
128 GTGCA-TTCAAAACCA-AG
* * * * ** *
17879278 -TAGTA-CCTAAAAAGTG-TGATATTACCAAAATACCTTTATAGGGGTCTTTTTGTAATTTGGCT
1 ATAGTACCCCAAAAAG-GATGAAATTACCAAAATACCCTTATAGGGGTATTTTCATAATTTGACT
17879340 TTATCGAGCTTGGAATTT
65 TT-TCGAGCTT-GAATTT
17879358 CACAAAAATT
Statistics
Matches: 182, Mismatches: 36, Indels: 17
0.77 0.15 0.07
Matches are distributed among these distances:
144 6 0.03
145 119 0.65
146 56 0.31
147 1 0.01
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.40
Consensus pattern (144 bp):
ATAGTACCCCAAAAAGGATGAAATTACCAAAATACCCTTATAGGGGTATTTTCATAATTTGACTT
TTCGAGCTTGAATTTTTGTGAAACTTCTCAAATCTTAATTTTATAATATTTCATAAATTTTTGTG
CATTCAAAACCAAG
Found at i:17882956 original size:17 final size:17
Alignment explanation
Indices: 17882934--17882968 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
17882924 TTTGTGCTTA
*
17882934 TGATTTATTTATGATAT
1 TGATTTATTTATAATAT
17882951 TGATTTATTTATAATAT
1 TGATTTATTTATAATAT
17882968 T
1 T
17882969 TTGATTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.09, T:0.60
Consensus pattern (17 bp):
TGATTTATTTATAATAT
Found at i:17888340 original size:144 final size:140
Alignment explanation
Indices: 17887969--17888383 Score: 352
Period size: 143 Copynumber: 2.9 Consensus size: 140
17887959 CAAGAAAGTT
* * * *
17887969 AAATTATGAAAATAACCCTAAAGAGCATTTTAGTAATTTCACACCTTTTGAGATACGACATAGGT
1 AAATTATGAAAAT-ACCCTAAAG-GCATTTTAGTAATTTCACACCTTCTGAGGTAC-AAATAAGT
* * * * *
17888034 TTTTAATGCATCAAAAATCATAAAATAATTTCAAAATATAATCTAGAGTGTTTCATGAAAAACCA
63 TTTTAATGTATCAAAAATCATAAAATAATATCAAAATATAATCTAAAGTATTTCACGAAAAACCA
*
17888099 ACCTCTAAAGGTC
128 ACCTCTAAAGGTA
* ** * * * * * ***
17888112 AAATGACAAAAATATTCCTACAAGGCATTTTAGTAATTTTAAAGCTTCCGAGGT-GTGATCAAGA
1 AAATTATGAAAATA-CCCTA-AAGGCATTTTAGTAATTTCACACCTTCTGAGGTACAAAT-AAG-
* * * * * * *
17888176 CTTTTAATATATCAAAAATCATAAAATGATATCAAATTATGATCTAAAGTATTTCGCGAAAAATC
62 TTTTTAATGTATCAAAAATCATAAAATAATATCAAAATATAATCTAAAGTATTTCACGAAAAACC
17888241 AACCT-TAAAAAGGTA
127 AACCTCT--AAAGGTA
*
17888256 AAATTATGAAAATACCCTTAAAGTGCATTGTAGTAATTTCACACCTTCTGAGGTACAAATAAAGT
1 AAATTATGAAAATACCC-TAAAG-GCATTTTAGTAATTTCACACCTTCTGAGGTACAAAT-AAGT
* * * ** *
17888321 TTTTAATGTACCAATAATCATCAAATAACGT-TTTAAATATAATCTGAAAGT-TTTCACTAAAAA
63 TTTTAATGTATCAAAAATCATAAAATAA--TATCAAAATATAATCT-AAAGTATTTCACGAAAAA
17888384 TTAACTTTAA
Statistics
Matches: 208, Mismatches: 52, Indels: 22
0.74 0.18 0.08
Matches are distributed among these distances:
141 2 0.01
142 4 0.02
143 101 0.49
144 70 0.34
145 25 0.12
146 6 0.03
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (140 bp):
AAATTATGAAAATACCCTAAAGGCATTTTAGTAATTTCACACCTTCTGAGGTACAAATAAGTTTT
TAATGTATCAAAAATCATAAAATAATATCAAAATATAATCTAAAGTATTTCACGAAAAACCAACC
TCTAAAGGTA
Found at i:17889442 original size:21 final size:21
Alignment explanation
Indices: 17889418--17889458 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17889408 TGATTCAATT
*
17889418 TTATATTCTAATTTATTTTAG
1 TTATATTATAATTTATTTTAG
*
17889439 TTATATTATAATTTTTTTTA
1 TTATATTATAATTTATTTTA
17889459 TTGATTATTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (21 bp):
TTATATTATAATTTATTTTAG
Found at i:17890448 original size:23 final size:22
Alignment explanation
Indices: 17890429--17890476 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 22
17890419 ACTTTTTTAG
17890429 TTTAGGATTTATTATATTTTCTA
1 TTTA-GATTTATTATATTTTCTA
*
17890452 TTTAGCTTTATTATATTTTCTA
1 TTTAGATTTATTATATTTTCTA
17890474 TTT
1 TTT
17890477 GACTTTAAGG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.23, C:0.06, G:0.06, T:0.65
Consensus pattern (22 bp):
TTTAGATTTATTATATTTTCTA
Found at i:17890688 original size:27 final size:26
Alignment explanation
Indices: 17890636--17890694 Score: 73
Period size: 27 Copynumber: 2.2 Consensus size: 26
17890626 AACTATGCGT
* *
17890636 CCAACCTTAAAACCTAAACTAGAAAA
1 CCAACCTGAAAACCTAAACTAAAAAA
**
17890662 CTCAACCTGAAAACCTAGCCTAAAAAA
1 C-CAACCTGAAAACCTAAACTAAAAAA
17890689 CCAACC
1 CCAACC
17890695 ACAAACCCAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.49, C:0.32, G:0.05, T:0.14
Consensus pattern (26 bp):
CCAACCTGAAAACCTAAACTAAAAAA
Found at i:17893310 original size:2 final size:2
Alignment explanation
Indices: 17893298--17893337 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
17893288 TACTTGTTTG
* *
17893298 GA GA GA AA GA GA GA GA GA GA GT GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
17893338 ATTTTAAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.47, T:0.03
Consensus pattern (2 bp):
GA
Found at i:17894485 original size:18 final size:17
Alignment explanation
Indices: 17894460--17894501 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
17894450 ATAATTTTTT
17894460 AAAA-AAATAAAAAATGA
1 AAAATAAATAAAAAAT-A
17894477 AAAATAAATAAAAAATA
1 AAAATAAATAAAAAATA
*
17894494 AAAGTAAA
1 AAAATAAA
17894502 AGATTGGGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 12 0.52
18 11 0.48
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAATAAATAAAAAATA
Found at i:17896466 original size:23 final size:22
Alignment explanation
Indices: 17896439--17896481 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
17896429 AAAATTAATC
17896439 AAAAG-AATAATAAAACAAAAATT
1 AAAAGAAATAA-AAAA-AAAAATT
17896462 AAAAGAAATAAAAAAAAAAA
1 AAAAGAAATAAAAAAAAAAA
17896482 GAAAATGGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 5 0.26
23 9 0.47
24 5 0.26
ACGTcount: A:0.81, C:0.02, G:0.05, T:0.12
Consensus pattern (22 bp):
AAAAGAAATAAAAAAAAAAATT
Found at i:17896486 original size:21 final size:21
Alignment explanation
Indices: 17896447--17896486 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
17896437 TCAAAAGAAT
* **
17896447 AATAAAACAAAAATTAAAAGA
1 AATAAAAAAAAAAAGAAAAGA
17896468 AATAAAAAAAAAAAGAAAA
1 AATAAAAAAAAAAAGAAAA
17896487 TGGGTAATCC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.82, C:0.03, G:0.05, T:0.10
Consensus pattern (21 bp):
AATAAAAAAAAAAAGAAAAGA
Found at i:17897411 original size:23 final size:22
Alignment explanation
Indices: 17897385--17897428 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
17897375 ATATTATATT
* *
17897385 ATTAATTTATTATAAATTAATAA
1 ATTAATCTATTA-AAATAAATAA
17897408 ATTAATCTATTAAAATAAATA
1 ATTAATCTATTAAAATAAATA
17897429 TTTATCAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAATCTATTAAAATAAATAA
Found at i:17899751 original size:16 final size:16
Alignment explanation
Indices: 17899730--17899762 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
17899720 ATAAAGTTTT
*
17899730 AATAATCTTTTTTAGA
1 AATAATCCTTTTTAGA
17899746 AATAATCCTTTTTAGA
1 AATAATCCTTTTTAGA
17899762 A
1 A
17899763 TCTTATATAT
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:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (16 bp):
AATAATCCTTTTTAGA
Found at i:17910117 original size:20 final size:21
Alignment explanation
Indices: 17910092--17910137 Score: 67
Period size: 20 Copynumber: 2.2 Consensus size: 21
17910082 AGAATGACTC
*
17910092 AATTTTGATCTAGTTCGA-CA
1 AATTTTGATCGAGTTCGACCA
*
17910112 AATTTTGATCGAGTTTGACCA
1 AATTTTGATCGAGTTCGACCA
17910133 AATTT
1 AATTT
17910138 AACAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.41
Consensus pattern (21 bp):
AATTTTGATCGAGTTCGACCA
Found at i:17912253 original size:8 final size:8
Alignment explanation
Indices: 17912240--17912337 Score: 92
Period size: 8 Copynumber: 11.6 Consensus size: 8
17912230 AATGGATGAA
17912240 GAAAAAAT
1 GAAAAAAT
17912248 G-AAAAAT
1 GAAAAAAT
17912255 GAAAAAAT
1 GAAAAAAT
17912263 GAAAAAAAAAT
1 G---AAAAAAT
*
17912274 GAAAAAGT
1 GAAAAAAT
17912282 GAAAAAAGT
1 GAAAAAA-T
17912291 GAAAAAAT
1 GAAAAAAT
17912299 G-AAAAAT
1 GAAAAAAT
*
17912306 GAAAAATGT
1 GAAAAA-AT
17912315 GAAAAAAAT
1 G-AAAAAAT
*
17912324 GAAGAAAAG
1 GAA-AAAAT
17912333 GAAAA
1 GAAAA
17912338 GAAAGAAAGA
Statistics
Matches: 76, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
7 14 0.18
8 30 0.39
9 19 0.25
10 5 0.07
11 8 0.11
ACGTcount: A:0.71, C:0.00, G:0.17, T:0.11
Consensus pattern (8 bp):
GAAAAAAT
Found at i:17912261 original size:9 final size:9
Alignment explanation
Indices: 17912241--17912337 Score: 73
Period size: 9 Copynumber: 11.3 Consensus size: 9
17912231 ATGGATGAAG
17912241 AAAAAATG-
1 AAAAAATGA
17912249 -AAAAATG-
1 AAAAAATGA
17912256 AAAAAATGAAA
1 AAAAAATG--A
17912267 AAAAAATG-
1 AAAAAATGA
*
17912275 AAAAAGTGA
1 AAAAAATGA
*
17912284 AAAAAGTG-
1 AAAAAATGA
17912292 AAAAAATG-
1 AAAAAATGA
17912300 -AAAAATGA
1 AAAAAATGA
**
17912308 AAAATGTGA
1 AAAAAATGA
17912317 AAAAAATGA
1 AAAAAATGA
* *
17912326 AGAAAAGGA
1 AAAAAATGA
17912335 AAA
1 AAA
17912338 GAAAGAAAGA
Statistics
Matches: 73, Mismatches: 9, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
7 14 0.19
8 21 0.29
9 30 0.41
11 8 0.11
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.11
Consensus pattern (9 bp):
AAAAAATGA
Found at i:17912310 original size:6 final size:7
Alignment explanation
Indices: 17912242--17912313 Score: 78
Period size: 7 Copynumber: 10.0 Consensus size: 7
17912232 TGGATGAAGA
17912242 AAAAATG
1 AAAAATG
17912249 AAAAATG
1 AAAAATG
17912256 AAAAAATG
1 -AAAAATG
17912264 -AAAA--
1 AAAAATG
17912268 AAAAATG
1 AAAAATG
17912275 AAAAAGTG
1 AAAAA-TG
17912283 AAAAAAGTG
1 -AAAAA-TG
17912292 AAAAAATG
1 -AAAAATG
17912300 AAAAATG
1 AAAAATG
17912307 AAAAATG
1 AAAAATG
17912314 TGAAAAAAAT
Statistics
Matches: 59, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
5 4 0.07
6 4 0.07
7 26 0.44
8 11 0.19
9 14 0.24
ACGTcount: A:0.72, C:0.00, G:0.15, T:0.12
Consensus pattern (7 bp):
AAAAATG
Found at i:17913576 original size:15 final size:15
Alignment explanation
Indices: 17913553--17913585 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
17913543 TGTCTTTGAG
17913553 TTTTAAATGAGAATC
1 TTTTAAATGAGAATC
*
17913568 TTTTGAATGAGAATC
1 TTTTAAATGAGAATC
17913583 TTT
1 TTT
17913586 ATCTTTGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.33, C:0.06, G:0.15, T:0.45
Consensus pattern (15 bp):
TTTTAAATGAGAATC
Found at i:17913919 original size:17 final size:17
Alignment explanation
Indices: 17913897--17913965 Score: 61
Period size: 17 Copynumber: 4.1 Consensus size: 17
17913887 AAACTTTGAT
17913897 AACCTTAAATCCTTGCG
1 AACCTTAAATCCTTGCG
* *
17913914 AACCTTAAATTCTCGCG
1 AACCTTAAATCCTTGCG
* ** *
17913931 AATC-TAAAAGCTTGCA
1 AACCTTAAATCCTTGCG
17913947 AACCTTAAA-CTCTTGCG
1 AACCTTAAATC-CTTGCG
17913964 AA
1 AA
17913966 TTTGAAAAAT
Statistics
Matches: 40, Mismatches: 10, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
16 11 0.28
17 29 0.73
ACGTcount: A:0.35, C:0.26, G:0.12, T:0.28
Consensus pattern (17 bp):
AACCTTAAATCCTTGCG
Found at i:17914033 original size:32 final size:34
Alignment explanation
Indices: 17913997--17914071 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 34
17913987 TAAAATCATA
*
17913997 TGAATCTGAGT-TCTTGCAAAT-ATAAAATT-TTG
1 TGAATCTGAGTGTC-TACAAATCATAAAATTCTTG
** *
17914029 TGAATCTTTGTGTCTACAAATCTTAAAATTCTTG
1 TGAATCTGAGTGTCTACAAATCATAAAATTCTTG
17914063 TGAATCTGA
1 TGAATCTGA
17914072 ATTTTGTGAA
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
32 15 0.44
33 9 0.26
34 10 0.29
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (34 bp):
TGAATCTGAGTGTCTACAAATCATAAAATTCTTG
Found at i:17914080 original size:15 final size:16
Alignment explanation
Indices: 17914055--17914084 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
17914045 CAAATCTTAA
17914055 AATTCTTGTGAATCTG
1 AATTCTTGTGAATCTG
17914071 AATT-TTGTGAATCT
1 AATTCTTGTGAATCT
17914085 TTGTGTGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.10, G:0.17, T:0.47
Consensus pattern (16 bp):
AATTCTTGTGAATCTG
Found at i:17918237 original size:16 final size:16
Alignment explanation
Indices: 17918216--17918247 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
17918206 ATAAAGTCTT
17918216 AATAATCCTTTTTAGA
1 AATAATCCTTTTTAGA
17918232 AATAATCCTTTTTAGA
1 AATAATCCTTTTTAGA
17918248 TCTTATATCT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (16 bp):
AATAATCCTTTTTAGA
Found at i:17918595 original size:77 final size:77
Alignment explanation
Indices: 17918468--17918623 Score: 285
Period size: 77 Copynumber: 2.0 Consensus size: 77
17918458 GATGGAAGAG
* * *
17918468 CATAAATCTTGTCAGCATAAATCTGACACTTATGTCATCTTCTGACATAATCAATATAGTCACTT
1 CATAAATCTTGTCAGCATAAATCTAACACTTATGACATCTTCTAACATAATCAATATAGTCACTT
17918533 TTCATTGTCAAC
66 TTCATTGTCAAC
17918545 CATAAATCTTGTCAGCATAAATCTAACACTTATGACATCTTCTAACATAATCAATATAGTCACTT
1 CATAAATCTTGTCAGCATAAATCTAACACTTATGACATCTTCTAACATAATCAATATAGTCACTT
17918610 TTCATTGTCAAC
66 TTCATTGTCAAC
17918622 CA
1 CA
17918624 ATAATAGCCA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.35, C:0.22, G:0.08, T:0.35
Consensus pattern (77 bp):
CATAAATCTTGTCAGCATAAATCTAACACTTATGACATCTTCTAACATAATCAATATAGTCACTT
TTCATTGTCAAC
Found at i:17930793 original size:6 final size:7
Alignment explanation
Indices: 17930776--17930845 Score: 67
Period size: 7 Copynumber: 10.0 Consensus size: 7
17930766 TGGATGAAGA
17930776 AAAAATG
1 AAAAATG
17930783 AAAAATG
1 AAAAATG
17930790 AAAAAATG
1 -AAAAATG
17930798 AAAAA--
1 AAAAATG
17930803 AAAAA--
1 AAAAATG
*
17930808 AAAAGTG
1 AAAAATG
17930815 AAAAAAGTG
1 -AAAAA-TG
17930824 AAAAAATG
1 -AAAAATG
17930832 AAAAATG
1 AAAAATG
17930839 AAAAATG
1 AAAAATG
17930846 TGAAAAAAAT
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
5 9 0.16
7 26 0.46
8 13 0.23
9 8 0.14
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.11
Consensus pattern (7 bp):
AAAAATG
Found at i:17930795 original size:9 final size:9
Alignment explanation
Indices: 17930775--17930877 Score: 80
Period size: 9 Copynumber: 12.2 Consensus size: 9
17930765 ATGGATGAAG
17930775 AAAAAATG-
1 AAAAAATGA
17930783 -AAAAATG-
1 AAAAAATGA
17930790 AAAAAATGA
1 AAAAAATGA
17930799 AAAAAA--A
1 AAAAAATGA
17930806 AAAAAAGTGA
1 AAAAAA-TGA
*
17930816 AAAAAGTG-
1 AAAAAATGA
17930824 AAAAAATG-
1 AAAAAATGA
17930832 -AAAAATGA
1 AAAAAATGA
**
17930840 AAAATGTGA
1 AAAAAATGA
17930849 AAAAAATGA
1 AAAAAATGA
* *
17930858 AGAAAAGGA
1 AAAAAATGA
17930867 AAGAAAA-GA
1 AA-AAAATGA
17930876 AA
1 AA
17930878 GACTCAAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 15
0.76 0.09 0.15
Matches are distributed among these distances:
7 21 0.27
8 14 0.18
9 33 0.42
10 10 0.13
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.10
Consensus pattern (9 bp):
AAAAAATGA
Found at i:17930855 original size:25 final size:24
Alignment explanation
Indices: 17930775--17930858 Score: 107
Period size: 25 Copynumber: 3.4 Consensus size: 24
17930765 ATGGATGAAG
*
17930775 AAAAAATGAAAAATGAAAAAATGA
1 AAAAAATGAAAAATGAAAAAGTGA
**
17930799 AAAAAAAAAAAAAGTGAAAAAAGTG-
1 AAAAAATGAAAAA-TG-AAAAAGTGA
17930824 AAAAAATGAAAAATGAAAAATGTGA
1 AAAAAATGAAAAATGAAAAA-GTGA
17930849 AAAAAATGAA
1 AAAAAATGAA
17930859 GAAAAGGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
23 5 0.10
24 16 0.31
25 23 0.45
26 7 0.14
ACGTcount: A:0.74, C:0.00, G:0.14, T:0.12
Consensus pattern (24 bp):
AAAAAATGAAAAATGAAAAAGTGA
Found at i:17932272 original size:21 final size:22
Alignment explanation
Indices: 17932246--17932301 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 22
17932236 TTTCGAATAA
* **
17932246 AAATCTTTAACTTTT-TGGTGT
1 AAATCTTTAAATTTTAAAGTGT
*
17932267 AAATCTCTAGAATTTTAAAGTGT
1 AAATCTTTA-AATTTTAAAGTGT
17932290 AAATCTTTAAAT
1 AAATCTTTAAAT
17932302 GTTGGATGTG
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
21 8 0.29
22 8 0.29
23 12 0.43
ACGTcount: A:0.36, C:0.09, G:0.11, T:0.45
Consensus pattern (22 bp):
AAATCTTTAAATTTTAAAGTGT
Found at i:17932502 original size:17 final size:17
Alignment explanation
Indices: 17932412--17932502 Score: 60
Period size: 17 Copynumber: 5.3 Consensus size: 17
17932402 TGATAACCTT
* *
17932412 AAATCCTTGTGAACCTTA
1 AAAT-CTTGCGAATCTTA
* *
17932430 AATTCTCGCGAATC-TA
1 AAATCTTGCGAATCTTA
* * *
17932446 AAAGCTTGCAAACCTTA
1 AAATCTTGCGAATCTTA
*
17932463 AACTCTTGCGAAT-TTGAA
1 AAATCTTGCGAATCTT--A
*
17932481 AAATCTTGTGAATCTTA
1 AAATCTTGCGAATCTTA
17932498 AAATC
1 AAATC
17932503 ATATGAATCT
Statistics
Matches: 54, Mismatches: 15, Indels: 9
0.69 0.19 0.12
Matches are distributed among these distances:
16 13 0.24
17 24 0.44
18 15 0.28
19 2 0.04
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (17 bp):
AAATCTTGCGAATCTTA
Found at i:17933902 original size:17 final size:15
Alignment explanation
Indices: 17933867--17933911 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
17933857 TTTTATGGTT
*
17933867 TTTATTTATTTTTCT
1 TTTATTTATTTTTCC
17933882 TTTATGTTATTATTTCC
1 TTTAT-TTATT-TTTCC
*
17933899 TTTATTCATTTTT
1 TTTATTTATTTTT
17933912 TGTGGAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
15 8 0.31
16 9 0.35
17 9 0.35
ACGTcount: A:0.16, C:0.09, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTATTTATTTTTCC
Done.