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 58 of 199
Found at i:17202785 original size:30 final size:30
Alignment explanation
Indices: 17202749--17202815 Score: 107
Period size: 30 Copynumber: 2.2 Consensus size: 30
17202739 GTGAGGTTTG
** *
17202749 CCCATTATCACCTTGGGATACACAGAGAAC
1 CCCATTATCACCCCGGGACACACAGAGAAC
17202779 CCCATTATCACCCCGGGACACACAGAGAAC
1 CCCATTATCACCCCGGGACACACAGAGAAC
17202809 CCCATTA
1 CCCATTA
17202816 GATATAATGC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.33, C:0.36, G:0.15, T:0.16
Consensus pattern (30 bp):
CCCATTATCACCCCGGGACACACAGAGAAC
Found at i:17207621 original size:60 final size:62
Alignment explanation
Indices: 17207507--17207625 Score: 170
Period size: 63 Copynumber: 1.9 Consensus size: 62
17207497 TCAATTTGTA
* * *
17207507 TTAGATATTATAATTATTTAAGTTTACTTTTTTACCTAATTAATATTTAAATACTATTTATAC
1 TTAGATATTATAATTATTGAACTTTAC-TTTTTACCAAATTAATATTTAAATACTATTTATAC
* *
17207570 TTAGATATTGTAATTATTGAACTTTA-TTTTTA-CAAATTAATATTTAGATACTATTT
1 TTAGATATTATAATTATTGAACTTTACTTTTTACCAAATTAATATTTAAATACTATTT
17207626 GTATTAGTTT
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
60 22 0.43
61 6 0.12
63 23 0.45
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (62 bp):
TTAGATATTATAATTATTGAACTTTACTTTTTACCAAATTAATATTTAAATACTATTTATAC
Found at i:17209738 original size:22 final size:22
Alignment explanation
Indices: 17209713--17209755 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
17209703 AATTGTTCTA
17209713 ACGTACTAAGCTCTCATGTTTC
1 ACGTACTAAGCTCTCATGTTTC
17209735 ACGTACTAAGCTCTCATGTTT
1 ACGTACTAAGCTCTCATGTTT
17209756 GAACAATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (22 bp):
ACGTACTAAGCTCTCATGTTTC
Found at i:17212432 original size:8 final size:8
Alignment explanation
Indices: 17212416--17212446 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
17212406 ATATAATATA
*
17212416 TTATTAAT
1 TTATAAAT
17212424 TTATAAAT
1 TTATAAAT
17212432 TTATAAAT
1 TTATAAAT
17212440 TTATAAA
1 TTATAAA
17212447 AATCATTGGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (8 bp):
TTATAAAT
Found at i:17215273 original size:2 final size:2
Alignment explanation
Indices: 17215268--17215292 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17215258 ATAATTCATA
17215268 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 A
17215293 CAAGTGTAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17218584 original size:14 final size:13
Alignment explanation
Indices: 17218565--17218610 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 13
17218555 ACTTAAATTT
17218565 TAATAATAATAAAA
1 TAATAA-AATAAAA
17218579 TAATAAAAATAAAA
1 TAAT-AAAATAAAA
*
17218593 TAAATAAAGTAAAA
1 T-AATAAAATAAAA
17218607 TAAT
1 TAAT
17218611 TTAAAATACT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
13 3 0.10
14 21 0.72
15 5 0.17
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
TAATAAAATAAAA
Found at i:17221345 original size:14 final size:13
Alignment explanation
Indices: 17221309--17221348 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
17221299 TTAAATCGTA
17221309 ATTTTAGTAAAAT
1 ATTTTAGTAAAAT
17221322 ATTTTAGTAAAACT
1 ATTTTAGTAAAA-T
* *
17221336 TTTTTTGTAAAAT
1 ATTTTAGTAAAAT
17221349 CGAGGGTGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 13 0.54
14 11 0.46
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (13 bp):
ATTTTAGTAAAAT
Found at i:17231054 original size:104 final size:103
Alignment explanation
Indices: 17230863--17231175 Score: 484
Period size: 104 Copynumber: 3.0 Consensus size: 103
17230853 CACCACTGAA
* * * *
17230863 TCGGGGAAATCAGCACTTAGCAACCCCCTTTTTCATTTCGAAGATACGGTGGATATCGCACTTAG
1 TCGGGGGAATCAGCACATAGCAACCCCC-TTTTCATTTCAAAGATATGGTGGATATCGCACTTAG
17230928 CACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
65 CACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
*
17230967 TCGGGGGAATCAGCACATAGCAGCCCCCTTTTCATTTCAAAGATATGGTGGATATCGCACTTAGC
1 TCGGGGGAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATATGGTGGATATCGCACTTAGC
17231032 ACCACCAATGAAATCGGGGAATCAGCACTTAGCAACCCC
66 ACCACCAATG-AATCGGGGAATCAGCACTTAGCAACCCC
* *
17231071 TCGGGGGAATCAGCACATAGCAACCCCCTTTCACATTTCAAAGATATGGTGGATCA-CGCACATA
1 TCGGGGGAATCAGCACATAGCAACCCCCTTT-TCATTTCAAAGATATGGTGGAT-ATCGCACTTA
* * **
17231135 GCACCACCAATGAATCGAGGAATCAACACACAGCAACCCC
64 GCACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
17231175 T
1 T
17231176 TTTATATACA
Statistics
Matches: 194, Mismatches: 12, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
103 45 0.23
104 108 0.56
105 40 0.21
106 1 0.01
ACGTcount: A:0.31, C:0.29, G:0.20, T:0.20
Consensus pattern (103 bp):
TCGGGGGAATCAGCACATAGCAACCCCCTTTTCATTTCAAAGATATGGTGGATATCGCACTTAGC
ACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCC
Found at i:17231538 original size:30 final size:29
Alignment explanation
Indices: 17231504--17231568 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
17231494 TAATCCACCA
17231504 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
17231534 CCCAAACTTTTGCATAATTACACTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
17231564 CCCAA
1 CCCAA
17231569 GCTCGGAAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.28, G:0.06, T:0.35
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:17231542 original size:31 final size:30
Alignment explanation
Indices: 17231511--17231568 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
17231501 CCACCCAACT
17231511 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
17231541 TTTTGCATAATTACACTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
17231569 GCTCGGAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.07, T:0.38
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:17232509 original size:34 final size:34
Alignment explanation
Indices: 17232466--17232570 Score: 149
Period size: 34 Copynumber: 3.1 Consensus size: 34
17232456 CATGGCATTC
17232466 ATAGAGATAAGTCCGCTGGGACAGTAAACACGAA
1 ATAGAGATAAGTCCGCTGGGACAGTAAACACGAA
** * *
17232500 ATAGAGATAAGT-CTATCGGGATAGTAAACACAAA
1 ATAGAGATAAGTCCGCT-GGGACAGTAAACACGAA
*
17232534 ATAGAGATAAGTCCGCTGGGACAATAAACACGAA
1 ATAGAGATAAGTCCGCTGGGACAGTAAACACGAA
17232568 ATA
1 ATA
17232571 TATATAAATC
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
33 2 0.03
34 56 0.93
35 2 0.03
ACGTcount: A:0.45, C:0.15, G:0.23, T:0.17
Consensus pattern (34 bp):
ATAGAGATAAGTCCGCTGGGACAGTAAACACGAA
Found at i:17232592 original size:68 final size:68
Alignment explanation
Indices: 17232466--17232593 Score: 175
Period size: 68 Copynumber: 1.9 Consensus size: 68
17232456 CATGGCATTC
* * * * ***
17232466 ATAGAGATAAGTCCGCTGGGACAGTAAACACGAAATAGAGATAAGTCTATCGGGATAGTAAACAC
1 ATAGAGATAAGTCCGCTGGGACAATAAACACGAAATAGAGATAAATCCACCAAAATAGTAAACAC
17232531 AAA
66 AAA
* *
17232534 ATAGAGATAAGTCCGCTGGGACAATAAACACGAAATATATATAAATCCACCAAAATAGTA
1 ATAGAGATAAGTCCGCTGGGACAATAAACACGAAATAGAGATAAATCCACCAAAATAGTA
17232594 GATATGGAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
68 51 1.00
ACGTcount: A:0.46, C:0.16, G:0.20, T:0.19
Consensus pattern (68 bp):
ATAGAGATAAGTCCGCTGGGACAATAAACACGAAATAGAGATAAATCCACCAAAATAGTAAACAC
AAA
Found at i:17234702 original size:18 final size:18
Alignment explanation
Indices: 17234665--17234704 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
17234655 AAATCAAGAT
* **
17234665 AATGATTTTGAAATGGCA
1 AATGATATTGAAATAACA
17234683 AATGATATTGAAATAACA
1 AATGATATTGAAATAACA
17234701 AATG
1 AATG
17234705 TTATGGAATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.47, C:0.05, G:0.17, T:0.30
Consensus pattern (18 bp):
AATGATATTGAAATAACA
Found at i:17237112 original size:36 final size:36
Alignment explanation
Indices: 17237072--17237143 Score: 103
Period size: 36 Copynumber: 2.0 Consensus size: 36
17237062 ATGACAATTC
*
17237072 TTTTCT-TTCTATTA-TATTAGTATTTTCTATTCTATT
1 TTTTCTATTCTATTAGTATTAG-A-TTACTATTCTATT
17237108 TTTTCTATTCTATTAGTATTAGATTACTATTCTATT
1 TTTTCTATTCTATTAGTATTAGATTACTATTCTATT
17237144 CTATTATTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
36 18 0.55
37 9 0.27
38 6 0.18
ACGTcount: A:0.22, C:0.11, G:0.04, T:0.62
Consensus pattern (36 bp):
TTTTCTATTCTATTAGTATTAGATTACTATTCTATT
Found at i:17237113 original size:14 final size:14
Alignment explanation
Indices: 17237094--17237121 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17237084 TATATTAGTA
17237094 TTTTCTATTCTATT
1 TTTTCTATTCTATT
17237108 TTTTCTATTCTATT
1 TTTTCTATTCTATT
17237122 AGTATTAGAT
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:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTTCTATTCTATT
Found at i:17237140 original size:27 final size:27
Alignment explanation
Indices: 17237110--17237165 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
17237100 ATTCTATTTT
17237110 TTCTATTCTATTAGTATTAGATTACTA
1 TTCTATTCTATTAGTATTAGATTACTA
* *
17237137 TTCTATTCTATTATTATTAGATTAGTA
1 TTCTATTCTATTAGTATTAGATTACTA
17237164 TT
1 TT
17237166 AGTTAGTGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.55
Consensus pattern (27 bp):
TTCTATTCTATTAGTATTAGATTACTA
Found at i:17239332 original size:33 final size:33
Alignment explanation
Indices: 17239241--17239340 Score: 112
Period size: 34 Copynumber: 3.0 Consensus size: 33
17239231 TATGGCATCC
* *
17239241 ATAGAGATAAGTCTGCTGGGACAGTAAACATAGA
1 ATAGAGATAAGTCCGC-GGGACAGTAAACATGGA
* ** *
17239275 ATAGAGATAAGTCCACCGAAACAGTAAATATGGA
1 ATAGAGATAAGTCC-GCGGGACAGTAAACATGGA
17239309 ATAGAG-TAAGTCCGTCGGGACAGTAAACATGG
1 ATAGAGATAAGTCCG-CGGGACAGTAAACATGG
17239341 GTAACTCCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 5
0.78 0.14 0.07
Matches are distributed among these distances:
33 21 0.39
34 32 0.59
35 1 0.02
ACGTcount: A:0.41, C:0.14, G:0.26, T:0.19
Consensus pattern (33 bp):
ATAGAGATAAGTCCGCGGGACAGTAAACATGGA
Found at i:17240517 original size:26 final size:27
Alignment explanation
Indices: 17240455--17240518 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
17240445 TTTATCGAGG
* * *
17240455 TTATTAGTGTATCGATAAATGAATATT
1 TTATTAATTTATCGATAAATGAATACT
*
17240482 TTATTAATTTATCGATAAATTAAT-CT
1 TTATTAATTTATCGATAAATGAATACT
17240508 TTATTAATTTA
1 TTATTAATTTA
17240519 GAGAATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.38, C:0.05, G:0.08, T:0.50
Consensus pattern (27 bp):
TTATTAATTTATCGATAAATGAATACT
Found at i:17240635 original size:34 final size:37
Alignment explanation
Indices: 17240596--17240665 Score: 110
Period size: 34 Copynumber: 2.0 Consensus size: 37
17240586 AATCAAAGTC
*
17240596 AATTGGTTCATGTAA-C-AAAA-AAAGAGAGTTAATT
1 AATTGGTTCATGTAACCAAAAAGAAAAAGAGTTAATT
17240630 AATTGGTTCATGTAACCAAAAAGAAAAAGAGTTAAT
1 AATTGGTTCATGTAACCAAAAAGAAAAAGAGTTAAT
17240666 GGTTTCAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
34 15 0.47
35 1 0.03
36 4 0.12
37 12 0.38
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (37 bp):
AATTGGTTCATGTAACCAAAAAGAAAAAGAGTTAATT
Found at i:17241764 original size:15 final size:15
Alignment explanation
Indices: 17241744--17241772 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17241734 TAACCAAGAT
17241744 TATTAATTTATCGAA
1 TATTAATTTATCGAA
17241759 TATTAATTTATCGA
1 TATTAATTTATCGA
17241773 GGTTTTACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.07, G:0.07, T:0.48
Consensus pattern (15 bp):
TATTAATTTATCGAA
Found at i:17242804 original size:25 final size:26
Alignment explanation
Indices: 17242763--17242813 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 26
17242753 AGTTGTAGAG
17242763 AGAAAATTCTCTAAAGAGATTATTTT
1 AGAAAATTCTCTAAAGAGATTATTTT
* *
17242789 AGAAAATT-TCTAAAGATATTTTTTT
1 AGAAAATTCTCTAAAGAGATTATTTT
17242814 GATTTACAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 15 0.65
26 8 0.35
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (26 bp):
AGAAAATTCTCTAAAGAGATTATTTT
Found at i:17244188 original size:28 final size:28
Alignment explanation
Indices: 17244152--17244247 Score: 75
Period size: 28 Copynumber: 3.4 Consensus size: 28
17244142 TAAGATAAAC
*
17244152 CTTAGCGGACTTCCCAACATTAGATAGT
1 CTTAACGGACTTCCCAACATTAGATAGT
* ** ***
17244180 CTTAACGGACATCCTCTTCATTTTTTAGT
1 CTTAACGGACTTCC-CAACATTAGATAGT
** *
17244209 CCTTGGCGGACTTCCCAACACTAGATAGT
1 -CTTAACGGACTTCCCAACATTAGATAGT
*
17244238 CCTAACGGAC
1 CTTAACGGAC
17244248 ATCCTTCTTA
Statistics
Matches: 47, Mismatches: 19, Indels: 4
0.67 0.27 0.06
Matches are distributed among these distances:
28 19 0.40
29 17 0.36
30 11 0.23
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.30
Consensus pattern (28 bp):
CTTAACGGACTTCCCAACATTAGATAGT
Found at i:17244201 original size:29 final size:29
Alignment explanation
Indices: 17244169--17244269 Score: 71
Period size: 29 Copynumber: 3.5 Consensus size: 29
17244159 GACTTCCCAA
17244169 CATTAGATAGTCTTAACGGACATCCTCTT
1 CATTAGATAGTCTTAACGGACATCCTCTT
*** ** * **
17244198 CATTTTTTAGTCCTTGGCGGACTTCC-CAA
1 CATTAGATAGT-CTTAACGGACATCCTCTT
* *
17244227 CACTAGATAGTCCTAACGGACATCCTTCTT
1 CATTAGATAGTCTTAACGGACATCC-TCTT
*
17244257 -ATTCGATAGTCTT
1 CATTAGATAGTCTT
17244270 TAGCGTATTT
Statistics
Matches: 48, Mismatches: 21, Indels: 6
0.64 0.28 0.08
Matches are distributed among these distances:
28 10 0.21
29 26 0.54
30 12 0.25
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.36
Consensus pattern (29 bp):
CATTAGATAGTCTTAACGGACATCCTCTT
Found at i:17244226 original size:58 final size:58
Alignment explanation
Indices: 17244151--17244326 Score: 212
Period size: 58 Copynumber: 3.0 Consensus size: 58
17244141 GTAAGATAAA
* * **
17244151 CCTTAGCGGACTTCCCAACATTAGATAGTCTTAACGGACATCCTCTTCATTTTTTAGT
1 CCTTAGCGGACTTCCCAACACTAGATAGTCCTAACGGACATCCTCTTCATTTGATAGT
* *
17244209 CCTTGGCGGACTTCCCAACACTAGATAGTCCTAACGGACATCCTTCTT-ATTCGATAGT
1 CCTTAGCGGACTTCCCAACACTAGATAGTCCTAACGGACATCC-TCTTCATTTGATAGT
* * * * * *
17244267 CTTTAGCGTATTTCCCAACACTAAATAGTCCT-ACTAGACATCCTCTTCATTTGGTAGT
1 CCTTAGCGGACTTCCCAACACTAGATAGTCCTAAC-GGACATCCTCTTCATTTGATAGT
17244325 CC
1 CC
17244327 CTGGCAAACT
Statistics
Matches: 100, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
57 6 0.06
58 90 0.90
59 4 0.04
ACGTcount: A:0.24, C:0.28, G:0.14, T:0.34
Consensus pattern (58 bp):
CCTTAGCGGACTTCCCAACACTAGATAGTCCTAACGGACATCCTCTTCATTTGATAGT
Found at i:17247976 original size:38 final size:38
Alignment explanation
Indices: 17247900--17247981 Score: 101
Period size: 38 Copynumber: 2.2 Consensus size: 38
17247890 GTGAAAGGGA
* * *
17247900 TCAACTGGTCCTTCGGGGCAGCACCATGATAGCAGTAT
1 TCAACTGGTCCTTCGAGGCAACACCATGACAGCAGTAT
* * **
17247938 TCAACTGGTCCTTCGAGGCAACACCGTGACGGTGGTAT
1 TCAACTGGTCCTTCGAGGCAACACCATGACAGCAGTAT
17247976 TCAACT
1 TCAACT
17247982 AGTCTTTCAA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.23, C:0.27, G:0.26, T:0.24
Consensus pattern (38 bp):
TCAACTGGTCCTTCGAGGCAACACCATGACAGCAGTAT
Found at i:17248058 original size:38 final size:37
Alignment explanation
Indices: 17247999--17248079 Score: 108
Period size: 38 Copynumber: 2.2 Consensus size: 37
17247989 CAAGGTGACA
* * *
17247999 GTATTCGACTGTCCTTTAGGGAAACACTATGATAACG
1 GTATTCGACTGTCCTTCAGGGAAACACCATGACAACG
*
17248036 GTATTTGACTGGTCCTTCAGGGAAACACCATGACAACG
1 GTATTCGACT-GTCCTTCAGGGAAACACCATGACAACG
*
17248074 ATATTC
1 GTATTC
17248080 AAATGGTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 9 0.24
38 28 0.76
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (37 bp):
GTATTCGACTGTCCTTCAGGGAAACACCATGACAACG
Found at i:17248087 original size:38 final size:38
Alignment explanation
Indices: 17248009--17248087 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
17247999 GTATTCGACT
* * * * ** *
17248009 GTCCTTTAGGGAAACACTATGATAACGGTATTTGACTG
1 GTCCTTCAGGGAAACACCATGACAACGATATTCAAATG
17248047 GTCCTTCAGGGAAACACCATGACAACGATATTCAAATG
1 GTCCTTCAGGGAAACACCATGACAACGATATTCAAATG
17248085 GTC
1 GTC
17248088 ATTCGGGGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (38 bp):
GTCCTTCAGGGAAACACCATGACAACGATATTCAAATG
Found at i:17249484 original size:41 final size:41
Alignment explanation
Indices: 17249427--17249510 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
17249417 ATAGAAGAAA
17249427 AACTGGTGAGCAGCATTTACTAGCATGCTCTATGGATTTTG
1 AACTGGTGAGCAGCATTTACTAGCATGCTCTATGGATTTTG
17249468 AACTGGTGAGCAGCATTTACTAGCATGCTCTATGGATTTTG
1 AACTGGTGAGCAGCATTTACTAGCATGCTCTATGGATTTTG
17249509 AA
1 AA
17249511 TTTAGGTAGC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.33
Consensus pattern (41 bp):
AACTGGTGAGCAGCATTTACTAGCATGCTCTATGGATTTTG
Found at i:17252622 original size:43 final size:41
Alignment explanation
Indices: 17252573--17252801 Score: 233
Period size: 43 Copynumber: 5.3 Consensus size: 41
17252563 TTTTATAAAT
17252573 AAACGCCGCTAAAAATCATGACCTTTAGCGGCGCTTTTCTCAC
1 AAACGCCGCTAAAAA-CATGACCTTTAGCGGCGCTTTTC-CAC
* * *
17252616 AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTAACCAC
1 AAACGCCGCTAAA-AACATGACCTTTAGCGGCGCTTT-TCCAC
* *
17252659 AAACGCCGCTATAGAACATGAGCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTA-AAAACATGACCTTTAGCGGCGCTTTT-CCAC
* * * *
17252702 AAACGCCGCTAAAGACCAAGACCTTTAGCGACGCTTTAACCAC
1 AAACGCCGCTAAA-AACATGACCTTTAGCGGCGCTTT-TCCAC
* * * ** *
17252745 AAACGCTGCTAAAGAACATGATCTTCAGCTACGCTTTTATCAC
1 AAACGCCGCTAAA-AACATGACCTTTAGCGGCGCTTTT-CCAC
17252788 AAACGCCGCTAAAA
1 AAACGCCGCTAAAA
17252802 GTACAACTCT
Statistics
Matches: 156, Mismatches: 23, Indels: 15
0.80 0.12 0.08
Matches are distributed among these distances:
42 2 0.01
43 151 0.97
44 3 0.02
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (41 bp):
AAACGCCGCTAAAAACATGACCTTTAGCGGCGCTTTTCCAC
Found at i:17252817 original size:86 final size:86
Alignment explanation
Indices: 17252573--17252800 Score: 350
Period size: 86 Copynumber: 2.7 Consensus size: 86
17252563 TTTTATAAAT
17252573 AAACGCCGCTAAA-AATCATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGA
1 AAACGCCGCTAAAGAA-CATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGA
*
17252637 CCTTTAGCGGCGCTTTAACCAC
65 CCTTTAGCGACGCTTTAACCAC
* * *
17252659 AAACGCCGCTATAGAACATGAGCTTTAGCGGCGCTTTTCCCACAAACGCCGCTAAAGACCAAGAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGAC
17252724 CTTTAGCGACGCTTTAACCAC
66 CTTTAGCGACGCTTTAACCAC
* * * ** *
17252745 AAACGCTGCTAAAGAACATGATCTTCAGCTACGCTTTTATCACAAACGCCGCTAAA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAA
17252801 AGTACAACTC
Statistics
Matches: 129, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
86 127 0.98
87 2 0.02
ACGTcount: A:0.32, C:0.30, G:0.17, T:0.21
Consensus pattern (86 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTCTCACAAACGCCGCTAAAGACCAAGAC
CTTTAGCGACGCTTTAACCAC
Found at i:17258609 original size:14 final size:14
Alignment explanation
Indices: 17258580--17258644 Score: 60
Period size: 14 Copynumber: 4.6 Consensus size: 14
17258570 TGAATCTATA
*
17258580 AACCCTAAATCCCT
1 AACCCTTAATCCCT
* *
17258594 AACTCTTAATCTCT
1 AACCCTTAATCCCT
*
17258608 AACCCTTAACCCCT
1 AACCCTTAATCCCT
*
17258622 AACCCCTAA-CCCAT
1 AACCCTTAATCCC-T
*
17258636 AAACCTTAA
1 AACCCTTAA
17258645 ATCACAATCC
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
13 3 0.07
14 38 0.93
ACGTcount: A:0.35, C:0.40, G:0.00, T:0.25
Consensus pattern (14 bp):
AACCCTTAATCCCT
Found at i:17258658 original size:14 final size:14
Alignment explanation
Indices: 17258639--17258668 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
17258629 AACCCATAAA
17258639 CCTTAAATCACAAT
1 CCTTAAATCACAAT
*
17258653 CCTTAAATCAGAAT
1 CCTTAAATCACAAT
17258667 CC
1 CC
17258669 CTGATTAATC
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:0.30, G:0.03, T:0.27
Consensus pattern (14 bp):
CCTTAAATCACAAT
Found at i:17258770 original size:20 final size:21
Alignment explanation
Indices: 17258745--17258783 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17258735 CTAAATTAAC
*
17258745 TATATA-TACACCCTAAACCA
1 TATATATTAAACCCTAAACCA
17258765 TATATATTAAACCCTAAAC
1 TATATATTAAACCCTAAAC
17258784 TATAATGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.28
Consensus pattern (21 bp):
TATATATTAAACCCTAAACCA
Found at i:17259152 original size:42 final size:41
Alignment explanation
Indices: 17259046--17259159 Score: 192
Period size: 41 Copynumber: 2.8 Consensus size: 41
17259036 ATTTTTGCGA
* *
17259046 CGCTTTTTCAAAAACGCCGCTAAAGACCTGAGCATTAGCGG
1 CGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCGG
17259087 CGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCGG
1 CGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCGG
*
17259128 CGCTTTTTTTAAAAACGCCACTAAAGATCTGA
1 CGC-TTTTTTAAAAACGCCGCTAAAGATCTGA
17259160 AAGGTACAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
41 42 0.61
42 27 0.39
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (41 bp):
CGCTTTTTTAAAAACGCCGCTAAAGATCTGAGCATTAGCGG
Found at i:17259276 original size:40 final size:40
Alignment explanation
Indices: 17259219--17259316 Score: 119
Period size: 40 Copynumber: 2.5 Consensus size: 40
17259209 AAAAAATGTC
* *
17259219 GCTAATGCT-AATTTTTAGCGGCGCTTTCCTGGAAA-CGCA
1 GCTAATGCTCGATTTTTAGCGGCG-TTTCATGGAAAGCGCA
* * * *
17259258 GCTAATGCTCGATCTTTAGCGGCGTTTTATGTAAAGCGCC
1 GCTAATGCTCGATTTTTAGCGGCGTTTCATGGAAAGCGCA
17259298 GCTAATGCTCGATTTTTAG
1 GCTAATGCTCGATTTTTAG
17259317 TGGCTTTTTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
39 17 0.34
40 33 0.66
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.34
Consensus pattern (40 bp):
GCTAATGCTCGATTTTTAGCGGCGTTTCATGGAAAGCGCA
Found at i:17262805 original size:12 final size:12
Alignment explanation
Indices: 17262788--17262813 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17262778 ATAAAGCTTT
17262788 AATTAAGTAGTA
1 AATTAAGTAGTA
17262800 AATTAAGTAGTA
1 AATTAAGTAGTA
17262812 AA
1 AA
17262814 ATATGTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.00, G:0.15, T:0.31
Consensus pattern (12 bp):
AATTAAGTAGTA
Found at i:17263999 original size:28 final size:25
Alignment explanation
Indices: 17263927--17263999 Score: 74
Period size: 28 Copynumber: 2.7 Consensus size: 25
17263917 TATGTTATGT
* *
17263927 AATTTATATTATATGAAAATTAAAT
1 AATTTATATTATATTAAAATTAAAA
*
17263952 AATTTATATTATGTTATAAACATTAAAA
1 AATTTATATTAT-AT-TAAA-ATTAAAA
17263980 AATTTAATACTTATATTAAA
1 AATTT-ATA-TTATATTAAA
17264000 GTACTTTATA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
25 12 0.31
26 1 0.03
27 3 0.08
28 15 0.38
29 4 0.10
30 4 0.10
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (25 bp):
AATTTATATTATATTAAAATTAAAA
Found at i:17264423 original size:3 final size:3
Alignment explanation
Indices: 17264415--17264465 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
17264405 TAATGGTTAG
17264415 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
17264463 ATA
1 ATA
17264466 TGGACGATCC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:17269154 original size:36 final size:35
Alignment explanation
Indices: 17269114--17269193 Score: 108
Period size: 36 Copynumber: 2.3 Consensus size: 35
17269104 ACTCTTTGTT
*
17269114 TTGGTGTGTTTCAGTTGGACTAGCTCTTCA-GAGCCA
1 TTGGTGTGTTTCAGATGGACTAGCTCTT-ATGAG-CA
* *
17269150 TTGGTGTGTTTCGGATGGATTAGCTCTTATGAGCA
1 TTGGTGTGTTTCAGATGGACTAGCTCTTATGAGCA
17269185 TTGGTGTGT
1 TTGGTGTGT
17269194 GGCCTGAATG
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 12 0.30
36 28 0.70
ACGTcount: A:0.15, C:0.14, G:0.31, T:0.40
Consensus pattern (35 bp):
TTGGTGTGTTTCAGATGGACTAGCTCTTATGAGCA
Found at i:17273200 original size:30 final size:30
Alignment explanation
Indices: 17273145--17273201 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
17273135 GAGTCGTTAG
*
17273145 TGTCGTATTAATATTTTGGTTAAGAAATTT
1 TGTCGTATTAATATTTTGATTAAGAAATTT
17273175 TGTCGT-TTAGATATTTT-ATTAAAGAAA
1 TGTCGTATTA-ATATTTTGATT-AAGAAA
17273202 AAGTACTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 5 0.21
30 19 0.79
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (30 bp):
TGTCGTATTAATATTTTGATTAAGAAATTT
Found at i:17285887 original size:15 final size:14
Alignment explanation
Indices: 17285852--17285881 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
17285842 ATTTTGTTCC
17285852 AAAATTTCAAAAAT
1 AAAATTTCAAAAAT
17285866 AAAATTTCAAAAAT
1 AAAATTTCAAAAAT
17285880 AA
1 AA
17285882 TTATTTAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.27
Consensus pattern (14 bp):
AAAATTTCAAAAAT
Found at i:17287957 original size:17 final size:17
Alignment explanation
Indices: 17287911--17287948 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
17287901 TTTTTATAAT
17287911 ATTTT-AAAAAAATGAC
1 ATTTTAAAAAAAATGAC
17287927 ATTTTAAAAAAAATGAC
1 ATTTTAAAAAAAATGAC
17287944 ATTTT
1 ATTTT
17287949 TTTAAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (17 bp):
ATTTTAAAAAAAATGAC
Found at i:17294173 original size:20 final size:21
Alignment explanation
Indices: 17294136--17294176 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17294126 TATATAATCA
17294136 TTATTTTCATAATCTATATAT
1 TTATTTTCATAATCTATATAT
17294157 TTATTTT-ATAA-CTTATATAT
1 TTATTTTCATAATC-TATATAT
17294177 GTACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 11 0.58
21 7 0.37
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTCATAATCTATATAT
Found at i:17303618 original size:39 final size:39
Alignment explanation
Indices: 17303564--17303641 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
17303554 AAGACTTGAT
17303564 GTGTGTGGCAAATGCTGAAGAGGATTCTCAAGAAAATCA
1 GTGTGTGGCAAATGCTGAAGAGGATTCTCAAGAAAATCA
17303603 GTGTGTGGCAAATGCTGAAGAGGATTCTCAAGAAAATCA
1 GTGTGTGGCAAATGCTGAAGAGGATTCTCAAGAAAATCA
17303642 TTCTTGGAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.36, C:0.13, G:0.28, T:0.23
Consensus pattern (39 bp):
GTGTGTGGCAAATGCTGAAGAGGATTCTCAAGAAAATCA
Found at i:17306235 original size:108 final size:108
Alignment explanation
Indices: 17306046--17306270 Score: 423
Period size: 108 Copynumber: 2.1 Consensus size: 108
17306036 CTTTAATGAA
* *
17306046 CAAAAAAGCAATGATCACCAAGGGATAAGAAGAAGTTCCCTTTAAAAAGAAAATTCTTCATTTGT
1 CAAAAGAGTAATGATCACCAAGGGATAAGAAGAAGTTCCCTTTAAAAAGAAAATTCTTCATTTGT
17306111 GCATAAGAATTTGGTATGACACCCTGGGAATGGTGAAAAGAAC
66 GCATAAGAATTTGGTATGACACCCTGGGAATGGTGAAAAGAAC
17306154 CAAAAGAGTAATGATCACCAAGGGATAAGAAGAAGTTCCCTTTAAAAAGAAAATTCTTCATTTGT
1 CAAAAGAGTAATGATCACCAAGGGATAAGAAGAAGTTCCCTTTAAAAAGAAAATTCTTCATTTGT
*
17306219 GCATAAGAATTTGGTATGACACCCTGGGAATGGTGAAAAGGAC
66 GCATAAGAATTTGGTATGACACCCTGGGAATGGTGAAAAGAAC
17306262 CAAAAGAGT
1 CAAAAGAGT
17306271 TTTAGAATCT
Statistics
Matches: 114, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
108 114 1.00
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.23
Consensus pattern (108 bp):
CAAAAGAGTAATGATCACCAAGGGATAAGAAGAAGTTCCCTTTAAAAAGAAAATTCTTCATTTGT
GCATAAGAATTTGGTATGACACCCTGGGAATGGTGAAAAGAAC
Found at i:17306871 original size:44 final size:44
Alignment explanation
Indices: 17306774--17306881 Score: 121
Period size: 44 Copynumber: 2.5 Consensus size: 44
17306764 GAAGATGGCA
* *
17306774 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTACAATGGAGCAGATTAAAGCCAAT
* ***
17306818 AAT-TCTATCTCCCTGAAGTTACAATGGAGCGGATT-AAGGTGAT
1 AATCT-TATCTCCCTGAAGTTACAATGGAGCAGATTAAAGCCAAT
*
17306861 AGATCTTATCTCTCTGAAGTT
1 A-ATCTTATCTCCCTGAAGTT
17306882 GCAGTAGGGT
Statistics
Matches: 54, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
43 7 0.13
44 46 0.85
45 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTACAATGGAGCAGATTAAAGCCAAT
Found at i:17307092 original size:44 final size:44
Alignment explanation
Indices: 17306724--17307328 Score: 427
Period size: 45 Copynumber: 13.8 Consensus size: 44
17306714 GGATTGGATT
17306724 AAGCAAGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGA
1 AAGCAAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACT-AAGA
** * * *
17306769 TGGCAAATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCC
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAG-A
* * * * * *
17306815 AA-TAATTC-TATCTCCCTGAAGTTACAATGGAGCGGATTAAG-
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGA
** * * *
17306856 GTG-ATAGATCTTATCTCTCTGAAGTTGCAGTAGG-GTAGA-T--CA
1 AAGCA-AG-TCTTATCTCCCTGAAGTTGCAGT-GGAGCAGACTAAGA
* * * *
17306898 CATCAGGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTCAAGA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGA
* * * *
17306943 AAGCAGGTCTTATCTCCCTGAGGTTGCAATGAAGCAGACCTAAGA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGA
* * * *
17306988 AAACAAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAAACCCAAGA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTAAGA
** * * *
17307033 AAGTGACTTTTATCTCCCTGAAGTTACAGTGGAGCAGACTAAGA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGA
17307077 AAGCAAGTCTTATCTCCCT-AAGGTTGCAGTGGAGCAGACTCAAGA
1 AAGCAAGTCTTATCTCCCTGAA-GTTGCAGTGGAGCAGACT-AAGA
* *
17307122 AAGCAAGTCTTATCTCCCTAAATTTG-AGTGGAGCAGACTTAAGA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC-TAAGA
* * * * *
17307166 AAACAAGTCTTATCCCCCTGAAATTGCAGTGGGGCAGACTGAATA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAGA
* * * * ** *
17307211 AA-CAAATCCTATCTCCCTAAAGTTGTAGTGGAGTGGA-TTAGA
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGA
* * * * * *
17307253 ATG-ATGGATATTATCTCTCTGAAGTTGCAGTAGAGCAGA-T--CA
1 AAGCA-AG-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGA
* * *
17307295 TATCAAATCTTATCTCCCTGAAGTTGCAGTGGAG
1 AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAG
17307329 TAGATTGAGA
Statistics
Matches: 438, Mismatches: 96, Indels: 56
0.74 0.16 0.09
Matches are distributed among these distances:
40 2 0.00
41 50 0.11
42 8 0.02
43 11 0.03
44 173 0.39
45 187 0.43
46 7 0.02
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (44 bp):
AAGCAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAGA
Found at i:17307103 original size:134 final size:134
Alignment explanation
Indices: 17306907--17307156 Score: 378
Period size: 134 Copynumber: 1.9 Consensus size: 134
17306897 ACATCAGGTC
* * * *
17306907 TTATCTCCTTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAGGTCTTATCTCCCTGAGGTTGCAA
1 TTATCTCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCTAAGGTTGCAA
* *
17306972 TGAAGCAGAC-CTAAGAAAACAAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAAACCCAAGAAAG
66 TGAAGCAGACTC-AAGAAAACAAGTCTTATCTCCCTAAAGTTG-AGTGGAGCAAACCCAAGAAAG
17307036 TGACTT
129 TGACTT
*
17307042 TTATCTCCCTGAAGTTACAGTGGAGCAGACT-AAGAAAGCAAGTCTTATCTCCCTAAGGTTGCAG
1 TTATCTCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCTAAGGTTGCAA
* * *
17307106 TGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCTAAATTTGAGTGGAGCA
66 TGAAGCAGACTCAAGAAAACAAGTCTTATCTCCCTAAAGTTGAGTGGAGCA
17307157 GACTTAAGAA
Statistics
Matches: 104, Mismatches: 10, Indels: 4
0.88 0.08 0.03
Matches are distributed among these distances:
133 9 0.09
134 65 0.62
135 30 0.29
ACGTcount: A:0.32, C:0.21, G:0.23, T:0.25
Consensus pattern (134 bp):
TTATCTCCCTGAAGTTACAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCTAAGGTTGCAA
TGAAGCAGACTCAAGAAAACAAGTCTTATCTCCCTAAAGTTGAGTGGAGCAAACCCAAGAAAGTG
ACTT
Found at i:17307121 original size:89 final size:88
Alignment explanation
Indices: 17306727--17307243 Score: 390
Period size: 89 Copynumber: 5.9 Consensus size: 88
17306717 TTGGATTAAG
* ** *
17306727 CAAGTCTTATC-CTCCTGAAGTTGCAGT-GAGGCAGACTGAAGATGGCAAATCTTATCTCCCTGA
1 CAAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGACTCAAGAAAG-AAGTCTTATCTCCCTGA
* * **
17306790 AGTTGCAGTGGAGCAGATTAAAGCCAA
63 AGTTACAGTGGAGCAGACT-AAGAAAA
* * * * * * ** *
17306817 TAATTC-TATCTCCCTGAAGTTACAATGGAGCGGA-TTAAG-GTGATAGATCTTATCTCTCTGAA
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGA-AG-TCTTATCTCCCTGAA
* * * * *
17306879 GTTGCAGTAGG-GTAGA-T--CACAT
64 GTTACAGT-GGAGCAGACTAAGAAAA
* * * *
17306901 CAGGTCTTATCTCCTTGAAGTTGCAGTGGAGCAGACTCAAGAAAGCAGGTCTTATCTCCCTGAGG
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAG-AAGTCTTATCTCCCTGAAG
* * *
17306966 TTGCAATGAAGCAGACCTAAGAAAA
65 TTACAGTGGAGCAGA-CTAAGAAAA
* * * * * *
17306991 CAAGTCTTATCTCTCTGAAGTTGCAGTGGAGCAAACCCAAGAAAGTGACTTTTATCTCCCTGAAG
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAG-AAGTCTTATCTCCCTGAAG
*
17307056 TTACAGTGGAGCAGACTAAGAAAG
65 TTACAGTGGAGCAGACTAAGAAAA
17307080 CAAGTCTTATCTCCCT-AAGGTTGCAGTGGAGCAGACTCAAGAAAGCAAGTCTTATCTCCCT-AA
1 CAAGTCTTATCTCCCTGAA-GTTGCAGTGGAGCAGACTCAAGAAAG-AAGTCTTATCTCCCTGAA
* **
17307143 ATTTGAGTGGAGCAGACTTAAGAAAA
64 GTTACAGTGGAGCAGAC-TAAGAAAA
* * * * * * * * *
17307169 CAAGTCTTATCCCCCTGAAATTGCAGTGGGGCAGACTGAATAAACAAATCCTATCTCCCTAAAGT
1 CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGAAGTCTTATCTCCCTGAAGT
**
17307234 TGTAGTGGAG
66 TACAGTGGAG
17307244 TGGATTAGAA
Statistics
Matches: 339, Mismatches: 70, Indels: 37
0.76 0.16 0.08
Matches are distributed among these distances:
84 5 0.01
85 25 0.07
86 29 0.09
87 5 0.01
88 63 0.19
89 135 0.40
90 77 0.23
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (88 bp):
CAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTCAAGAAAGAAGTCTTATCTCCCTGAAGT
TACAGTGGAGCAGACTAAGAAAA
Found at i:17308900 original size:20 final size:21
Alignment explanation
Indices: 17308863--17308903 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
17308853 TATATAATCA
17308863 TTATTTTCATAATCTATATAT
1 TTATTTTCATAATCTATATAT
17308884 TTATTTT-ATAA-CTTATATAT
1 TTATTTTCATAATC-TATATAT
17308904 GTACATATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 1 0.05
20 11 0.58
21 7 0.37
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (21 bp):
TTATTTTCATAATCTATATAT
Found at i:17309696 original size:33 final size:33
Alignment explanation
Indices: 17309650--17309717 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
17309640 CGTATTGATG
17309650 TCACGTGTCCATTTCTCGAGATGAAGATTTTTT
1 TCACGTGTCCATTTCTCGAGATGAAGATTTTTT
*
17309683 TCACGTGTTCATTTCTCGAGATGAAGATTTTTT
1 TCACGTGTCCATTTCTCGAGATGAAGATTTTTT
17309716 TC
1 TC
17309718 TAAAAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.44
Consensus pattern (33 bp):
TCACGTGTCCATTTCTCGAGATGAAGATTTTTT
Found at i:17312675 original size:12 final size:11
Alignment explanation
Indices: 17312658--17312690 Score: 50
Period size: 10 Copynumber: 3.0 Consensus size: 11
17312648 GAATTAGTTG
17312658 AAATTTAAATCT
1 AAATTTAAAT-T
17312670 AAATTTAAATT
1 AAATTTAAATT
17312681 -AATTTAAATT
1 AAATTTAAATT
17312691 TTAAATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
11 1 0.05
12 10 0.48
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (11 bp):
AAATTTAAATT
Found at i:17312702 original size:16 final size:16
Alignment explanation
Indices: 17312669--17312714 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
17312659 AATTTAAATC
17312669 TAAA-TTTAAATTAATT
1 TAAATTTTAAA-TAATT
17312685 TAAATTTTAAAT-ATT
1 TAAATTTTAAATAATT
*
17312700 TTAATTTTCAAATAA
1 TAAATTTT-AAATAA
17312715 AAAATTTAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
15 10 0.38
16 9 0.35
17 7 0.27
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (16 bp):
TAAATTTTAAATAATT
Found at i:17316909 original size:2 final size:2
Alignment explanation
Indices: 17316898--17316951 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
17316888 AATCTTTTCT
17316898 TA TA TA -A 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
17316939 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
17316952 GCGTGTTTTA
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:17317338 original size:6 final size:6
Alignment explanation
Indices: 17317313--17317351 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
17317303 ATACATATTG
* *
17317313 TACATA TATAT- TATATA TACATA TACATA TACATA TACA
1 TACATA TACATA TACATA TACATA TACATA TACATA TACA
17317352 GTTTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.38
Consensus pattern (6 bp):
TACATA
Found at i:17321002 original size:45 final size:44
Alignment explanation
Indices: 17320908--17321089 Score: 199
Period size: 45 Copynumber: 4.1 Consensus size: 44
17320898 AACAAATACA
* * * * * *
17320908 CGGTGG-ATCAGCACATAGC-ATCACCCTTATAGTTAATGATACT
1 CGGTGGAATCAGCACACAACAACCACCTTTATAATCAATG-TACT
* * * *
17320951 CGGTGGAATTAGCACATAGCAACCACCTTCATAATCAATAGTACT
1 CGGTGGAATCAGCACACAACAACCACCTTTATAATCAAT-GTACT
17320996 CGGTGGAATCAGCACACAACAACCACCTTTATAATCAATGATAC-
1 CGGTGGAATCAGCACACAACAACCACCTTTATAATCAATG-TACT
*
17321040 CTGGTGGAATCAGCACACAACAACCACCTTTATAATCAATGGTACC
1 C-GGTGGAATCAGCACACAACAACCACCTTTATAATCAAT-GTACT
17321086 CGGT
1 CGGT
17321090 ACACGTAGTA
Statistics
Matches: 122, Mismatches: 10, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
43 6 0.05
44 14 0.11
45 99 0.81
46 3 0.02
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (44 bp):
CGGTGGAATCAGCACACAACAACCACCTTTATAATCAATGTACT
Found at i:17321046 original size:90 final size:88
Alignment explanation
Indices: 17320908--17321089 Score: 222
Period size: 90 Copynumber: 2.0 Consensus size: 88
17320898 AACAAATACA
* * * * * * * *
17320908 CGGTGGATCAGCACATAGCATCACCCTTATAGTTAATGATACTCGGTGGAATTAGCACATAGCAA
1 CGGTGGATCAGCACACAACACCACCCTTATAATCAATGATACTCGGTGGAATCAGCACACAACAA
*
17320973 CCACCTTCATAATCAATAGTACT
66 CCACCTTCATAATCAATAGTACC
*
17320996 CGGTGGAATCAGCACACAACAACCACCTTTATAATCAATGATAC-CTGGTGGAATCAGCACACAA
1 CGGTGG-ATCAGCACACAAC-ACCACCCTTATAATCAATGATACTC-GGTGGAATCAGCACACAA
* *
17321060 CAACCACCTTTATAATCAATGGTACC
63 CAACCACCTTCATAATCAATAGTACC
17321086 CGGT
1 CGGT
17321090 ACACGTAGTA
Statistics
Matches: 79, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
88 6 0.08
89 12 0.15
90 61 0.77
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.24
Consensus pattern (88 bp):
CGGTGGATCAGCACACAACACCACCCTTATAATCAATGATACTCGGTGGAATCAGCACACAACAA
CCACCTTCATAATCAATAGTACC
Found at i:17328341 original size:33 final size:33
Alignment explanation
Indices: 17328304--17328374 Score: 117
Period size: 33 Copynumber: 2.2 Consensus size: 33
17328294 GAAGTCCAAG
17328304 GAGCTTGCTCTTGAAGCCTCCAAGAAA-GCCGAT
1 GAGCTTGCTCTTGAAGCCTCCAA-AAAGGCCGAT
*
17328337 GAGCTTGCTCTTGAAGCTTCCAAAAAGGCCGAT
1 GAGCTTGCTCTTGAAGCCTCCAAAAAGGCCGAT
17328370 GAGCT
1 GAGCT
17328375 CAAAGTCGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
32 3 0.08
33 33 0.92
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.23
Consensus pattern (33 bp):
GAGCTTGCTCTTGAAGCCTCCAAAAAGGCCGAT
Found at i:17329816 original size:6 final size:6
Alignment explanation
Indices: 17329805--17329840 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
17329795 ATTATTCAGA
17329805 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
1 TGATGG TGATGG TGATGG TGATGG TGATGG TGATGG
17329841 GAGCTTTGGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.17, C:0.00, G:0.50, T:0.33
Consensus pattern (6 bp):
TGATGG
Found at i:17330656 original size:126 final size:125
Alignment explanation
Indices: 17330454--17330708 Score: 372
Period size: 126 Copynumber: 2.0 Consensus size: 125
17330444 TGCATTACTA
* *
17330454 TTTTATATCATATCATGTGACATGACTTTTTTTAATAAAATATTTTAATTTTATATAATTAATAT
1 TTTTATATCATATCATATGACATAACTTTTTTTAATAAAATATTTTAATTTTATATAATTAATAT
* * * * *
17330519 AAATAATCATTATTAGTAGATATGT-AAATGTATAAAATATTTTAAAATATTCTTTAGT-
66 AAATAACCATTATTAGGAGATAAGTAAAATATATAAAATATTTTAAAATATTCATTAGTG
*
17330577 TTTTATATCATATCATATAGACATAATTTTTTTTTAAAATAAAATA-TTTAATTTTATATAATTA
1 TTTTATATCATATCATAT-GACATAA-CTTTTTTT--AATAAAATATTTTAATTTTATATAATTA
*
17330641 ATATAAATAACCATTATTAGGAGATAAGTAAAATATATAATATATTTTAAAATATTCATTAGTG
62 ATATAAATAACCATTATTAGGAGATAAGTAAAATATATAAAATATTTTAAAATATTCATTAGTG
17330705 TTTT
1 TTTT
17330709 TTGAAGGGCA
Statistics
Matches: 117, Mismatches: 9, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
123 17 0.15
124 6 0.05
125 7 0.06
126 44 0.38
127 39 0.33
128 4 0.03
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (125 bp):
TTTTATATCATATCATATGACATAACTTTTTTTAATAAAATATTTTAATTTTATATAATTAATAT
AAATAACCATTATTAGGAGATAAGTAAAATATATAAAATATTTTAAAATATTCATTAGTG
Found at i:17330771 original size:29 final size:28
Alignment explanation
Indices: 17330739--17330799 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
17330729 AAAAGCTATT
*
17330739 TTTTTTCAAAATTTACCGAAATGGGTCGA
1 TTTTTTCAAAATTTACCGAAAT-GGTCCA
* ** *
17330768 TTTTTTTATTATTTACCGGAATGGTCCA
1 TTTTTTCAAAATTTACCGAAATGGTCCA
17330796 TTTT
1 TTTT
17330800 CCGGGAAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.48
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGTCCA
Found at i:17331227 original size:125 final size:126
Alignment explanation
Indices: 17331005--17331342 Score: 608
Period size: 126 Copynumber: 2.7 Consensus size: 126
17330995 CGTCTCTGGT
* * *
17331005 CAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCTCGCCCTCG
* *
17331070 TGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAA-TTTTTTTCTGATTTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAAGTCATGTAAGAAATAATTTTTTTTCTGATGTTTCTGAG
17331130 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCTCGCCCTCG
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCTCGCCCTCG
17331195 TGGACGCGATTTTGCTACAGTAAGTCATGTAAGAAATAATTTTTTTTCTGATGTTTCTGAG
66 TGGACGCGATTTTGCTACAGTAAGTCATGTAAGAAATAATTTTTTTTCTGATGTTTCTGAG
17331256 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCGT-GCCCTC
1 CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATC-TCGCCCTC
17331320 GTGGACGCGATTTTGCTACAGTA
65 GTGGACGCGATTTTGCTACAGTA
17331343 GCAAGTTTGG
Statistics
Matches: 206, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
125 100 0.49
126 105 0.51
127 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.33
Consensus pattern (126 bp):
CAAATAGTATAAAATCGTTTCTACGAGGATGCTATTTGAGAAGAAATTGTGAAATCTCGCCCTCG
TGGACGCGATTTTGCTACAGTAAGTCATGTAAGAAATAATTTTTTTTCTGATGTTTCTGAG
Found at i:17334574 original size:7 final size:7
Alignment explanation
Indices: 17334564--17334588 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
17334554 TTACATACAT
17334564 AATACTA
1 AATACTA
17334571 AATACTA
1 AATACTA
17334578 AATACTA
1 AATACTA
17334585 AATA
1 AATA
17334589 TCAATCGACT
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:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:17335887 original size:22 final size:22
Alignment explanation
Indices: 17335862--17335912 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
17335852 AAATATGGGT
*
17335862 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGAAAGGAAA
17335884 TTGAGAGAATTTTGAAAGGAAA
1 TTGAGAGAATTTTGAAAGGAAA
17335906 TTGAGAG
1 TTGAGAG
17335913 GATTAGAGAG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.27
Consensus pattern (22 bp):
TTGAGAGAATTTTGAAAGGAAA
Found at i:17335926 original size:21 final size:22
Alignment explanation
Indices: 17335862--17335926 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
17335852 AAATATGGGT
* *
17335862 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTAGAAAGGAAA
*
17335884 TTGAGAGAATTTTGAAAGGAAA
1 TTGAGAGAATTTAGAAAGGAAA
* *
17335906 TTGAGAGGA-TTAGAGAGGAAA
1 TTGAGAGAATTTAGAAAGGAAA
17335927 AATTAGATAG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 10 0.26
22 29 0.74
ACGTcount: A:0.43, C:0.00, G:0.32, T:0.25
Consensus pattern (22 bp):
TTGAGAGAATTTAGAAAGGAAA
Found at i:17336200 original size:28 final size:27
Alignment explanation
Indices: 17336139--17336201 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 27
17336129 GCGCGATTTC
17336139 TTGAAAAATGGACCATTCCGGTAAATA
1 TTGAAAAATGGACCATTCCGGTAAATA
* * * * *
17336166 ATAAAAAATCGGCCCATTTCGGTAAATT
1 TTGAAAAAT-GGACCATTCCGGTAAATA
17336194 TTGAAAAA
1 TTGAAAAA
17336202 AAGGGCTTTT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
27 7 0.25
28 21 0.75
ACGTcount: A:0.43, C:0.14, G:0.16, T:0.27
Consensus pattern (27 bp):
TTGAAAAATGGACCATTCCGGTAAATA
Found at i:17339308 original size:22 final size:23
Alignment explanation
Indices: 17339262--17339310 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
17339252 CGGAAAAATA
*
17339262 ATAATAAAAGTAAAATGCATAAT
1 ATAATAAAAGTAAAATACATAAT
17339285 ATAATAAAA-TAAAATACA-ACAT
1 ATAATAAAAGTAAAATACATA-AT
17339307 ATAA
1 ATAA
17339311 GTCTGACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 1 0.04
22 14 0.58
23 9 0.38
ACGTcount: A:0.65, C:0.06, G:0.04, T:0.24
Consensus pattern (23 bp):
ATAATAAAAGTAAAATACATAAT
Found at i:17339892 original size:3 final size:3
Alignment explanation
Indices: 17339886--17339913 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17339876 AAATGGAAAT
17339886 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
17339914 AACATTCGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:17355079 original size:28 final size:28
Alignment explanation
Indices: 17355048--17355104 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
17355038 CATATTCACT
17355048 TACATCTATTATCAAAAGAGTCATTTAA
1 TACATCTATTATCAAAAGAGTCATTTAA
* *
17355076 TACATCTATTGTCAAAAGCGTCATTTAA
1 TACATCTATTATCAAAAGAGTCATTTAA
17355104 T
1 T
17355105 TAATTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.37
Consensus pattern (28 bp):
TACATCTATTATCAAAAGAGTCATTTAA
Found at i:17358163 original size:18 final size:17
Alignment explanation
Indices: 17358140--17358204 Score: 58
Period size: 18 Copynumber: 3.5 Consensus size: 17
17358130 GTATTCCTTC
17358140 TTTCTTTATTTTTTTTCT
1 TTTCTTT-TTTTTTTTCT
*
17358158 TTTCTTTCTTTTTCTTCCT
1 TTTCTTT-TTTTT-TTTCT
* *
17358177 GTTTCTCTTTTCTTTTTAT
1 -TTTCT-TTTTTTTTTTCT
17358196 TTTCTTTTT
1 TTTCTTTTT
17358205 GATTGCATTC
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 4 0.10
18 17 0.44
19 7 0.18
20 9 0.23
21 2 0.05
ACGTcount: A:0.03, C:0.17, G:0.02, T:0.78
Consensus pattern (17 bp):
TTTCTTTTTTTTTTTCT
Found at i:17358435 original size:63 final size:62
Alignment explanation
Indices: 17358353--17358542 Score: 229
Period size: 63 Copynumber: 3.0 Consensus size: 62
17358343 TGTGTTAGGC
* * * * *
17358353 CGTGTGACTCAGTGCTTGCCACTATAGATCACACGGGCTAGAGACACGGGCGCGTGTCCAGG
1 CGTGTGACTTACTGTTTGCCACTATAGATCACACGGGCCAGAGACACGGGCGTGTGTCCAGG
*
17358415 TCGTGTGACTTACTGTTTGCCACTATTGATCACACGGGCCAGAGACACGGGCGTGTGTCCAGG
1 -CGTGTGACTTACTGTTTGCCACTATAGATCACACGGGCCAGAGACACGGGCGTGTGTCCAGG
* * * * * * *
17358478 CTGTATGA-TTCACTGTTGGCCACTATAAATCATACGAGCCAGAGACACAGGCGTGTGTCTAGG
1 C-GTGTGACTT-ACTGTTTGCCACTATAGATCACACGGGCCAGAGACACGGGCGTGTGTCCAGG
17358541 CG
1 CG
17358543 GTGTAACACT
Statistics
Matches: 111, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
62 4 0.04
63 107 0.96
ACGTcount: A:0.22, C:0.25, G:0.29, T:0.23
Consensus pattern (62 bp):
CGTGTGACTTACTGTTTGCCACTATAGATCACACGGGCCAGAGACACGGGCGTGTGTCCAGG
Found at i:17360322 original size:10 final size:10
Alignment explanation
Indices: 17360293--17360325 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
17360283 GCGAATTAAT
17360293 TTTCTTATGA
1 TTTCTTATGA
*
17360303 TATC-TATGA
1 TTTCTTATGA
17360312 TTTCTTATGA
1 TTTCTTATGA
17360322 TTTC
1 TTTC
17360326 AGAATAAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
9 8 0.40
10 12 0.60
ACGTcount: A:0.21, C:0.12, G:0.09, T:0.58
Consensus pattern (10 bp):
TTTCTTATGA
Found at i:17363742 original size:2 final size:2
Alignment explanation
Indices: 17363731--17363774 Score: 72
Period size: 2 Copynumber: 22.0 Consensus size: 2
17363721 TTTTAAGTAT
17363731 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA GTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
17363773 TA
1 TA
17363775 NNNNNNNNNN
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
1 1 0.03
2 37 0.93
3 2 0.05
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17366894 original size:2 final size:2
Alignment explanation
Indices: 17366887--17366911 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17366877 CCATAGACGG
17366887 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 T
17366912 TCTTTTACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17371257 original size:37 final size:38
Alignment explanation
Indices: 17371216--17371289 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 38
17371206 GTTGTTCAAC
*
17371216 TCGAAAAGAAGAAATA-AA-AAATTTAATAACAAAGAAA
1 TCGAAAAGAAGAAA-AGAAGAAATTTAAGAACAAAGAAA
* *
17371253 TCGAAAGGAAGAAAAGAAGAAATTTGAGAACAAAGAA
1 TCGAAAAGAAGAAAAGAAGAAATTTAAGAACAAAGAA
17371290 CAAATAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 1 0.03
37 15 0.47
38 16 0.50
ACGTcount: A:0.64, C:0.05, G:0.18, T:0.14
Consensus pattern (38 bp):
TCGAAAAGAAGAAAAGAAGAAATTTAAGAACAAAGAAA
Found at i:17373812 original size:22 final size:21
Alignment explanation
Indices: 17373761--17373812 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 21
17373751 ATTTAGTAAT
17373761 AAATAAATTGAAAACAATAAA
1 AAATAAATTGAAAACAATAAA
* *
17373782 AGAAGAAATTTAATAACAA-ATAA
1 A-AATAAATTGAA-AACAATA-AA
17373805 AAATAAAT
1 AAATAAAT
17373813 AAATGATAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.04
22 16 0.64
23 8 0.32
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (21 bp):
AAATAAATTGAAAACAATAAA
Found at i:17373834 original size:11 final size:11
Alignment explanation
Indices: 17373793--17373834 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
17373783 GAAGAAATTT
*
17373793 AATAACAAATA
1 AATAATAAATA
17373804 AA-AATAAATA
1 AATAATAAATA
*
17373814 AATGATAAATA
1 AATAATAAATA
*
17373825 AATAAGAAAT
1 AATAATAAAT
17373835 GGAAAATTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.71, C:0.02, G:0.05, T:0.21
Consensus pattern (11 bp):
AATAATAAATA
Found at i:17380406 original size:30 final size:30
Alignment explanation
Indices: 17380370--17380432 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
17380360 CAGTCATGAA
* *
17380370 AAAAACAAGGTTA-CTAAAACCACAGGGGCT
1 AAAAACAAGGTCATCT-AAACCACAAGGGCT
* *
17380400 AAAAACACGGTCATCTGAACCACAAGGGCT
1 AAAAACAAGGTCATCTAAACCACAAGGGCT
17380430 AAA
1 AAA
17380433 GACATGGCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 26 0.93
31 2 0.07
ACGTcount: A:0.46, C:0.22, G:0.19, T:0.13
Consensus pattern (30 bp):
AAAAACAAGGTCATCTAAACCACAAGGGCT
Found at i:17393455 original size:26 final size:25
Alignment explanation
Indices: 17393413--17393468 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 25
17393403 AAACAAATAC
17393413 TCATA-TTTATATAATTAAAACAT-
1 TCATATTTTATATAATTAAAACATG
*
17393436 TCATATTTTATACTAGATTAAAATATG
1 TCATATTTTATA-TA-ATTAAAACATG
17393463 TCATAT
1 TCATAT
17393469 GTCCCTATAC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
23 5 0.18
24 6 0.21
25 2 0.07
26 9 0.32
27 6 0.21
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.45
Consensus pattern (25 bp):
TCATATTTTATATAATTAAAACATG
Found at i:17393882 original size:8 final size:8
Alignment explanation
Indices: 17393859--17393893 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
17393849 TAATTGTAAT
*
17393859 ATATATTT
1 ATATATTA
17393867 AT-TATTA
1 ATATATTA
17393874 ATATATTA
1 ATATATTA
17393882 ATATATTA
1 ATATATTA
17393890 ATAT
1 ATAT
17393894 TTTTCAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 6 0.24
8 19 0.76
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (8 bp):
ATATATTA
Found at i:17393888 original size:19 final size:18
Alignment explanation
Indices: 17393832--17393893 Score: 53
Period size: 17 Copynumber: 3.7 Consensus size: 18
17393822 ATAAAACATT
*
17393832 TATTTTTAATATATT-TA
1 TATTATTAATATATTATA
* *
17393849 TAATT-GTAATATA-TATT
1 T-ATTATTAATATATTATA
17393866 TATTATTAATATATTA-A
1 TATTATTAATATATTATA
17393883 TA-TATTAATAT
1 TATTATTAATAT
17393894 TTTTCAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
16 13 0.35
17 19 0.51
18 5 0.14
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (18 bp):
TATTATTAATATATTATA
Found at i:17393947 original size:15 final size:16
Alignment explanation
Indices: 17393927--17393957 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17393917 TTATTAAAAC
17393927 TTTAAAA-TTATTATT
1 TTTAAAATTTATTATT
17393942 TTTAAAATTTATTATT
1 TTTAAAATTTATTATT
17393958 ACAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.47
16 8 0.53
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAAAATTTATTATT
Found at i:17399631 original size:110 final size:110
Alignment explanation
Indices: 17399466--17399685 Score: 440
Period size: 110 Copynumber: 2.0 Consensus size: 110
17399456 GTTATTTTTG
17399466 CTTCCTATAAATATAGTCATTGGACGAGGTGTTGAACTAAGTACAAAGAAACAATTAAAATTGAA
1 CTTCCTATAAATATAGTCATTGGACGAGGTGTTGAACTAAGTACAAAGAAACAATTAAAATTGAA
17399531 TACAGTTTTCTTCTAAAAATTTCAAGTTTACCTGCGTTTCTTTCA
66 TACAGTTTTCTTCTAAAAATTTCAAGTTTACCTGCGTTTCTTTCA
17399576 CTTCCTATAAATATAGTCATTGGACGAGGTGTTGAACTAAGTACAAAGAAACAATTAAAATTGAA
1 CTTCCTATAAATATAGTCATTGGACGAGGTGTTGAACTAAGTACAAAGAAACAATTAAAATTGAA
17399641 TACAGTTTTCTTCTAAAAATTTCAAGTTTACCTGCGTTTCTTTCA
66 TACAGTTTTCTTCTAAAAATTTCAAGTTTACCTGCGTTTCTTTCA
17399686 TGTAGTGGTG
Statistics
Matches: 110, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 110 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.35
Consensus pattern (110 bp):
CTTCCTATAAATATAGTCATTGGACGAGGTGTTGAACTAAGTACAAAGAAACAATTAAAATTGAA
TACAGTTTTCTTCTAAAAATTTCAAGTTTACCTGCGTTTCTTTCA
Found at i:17400294 original size:9 final size:9
Alignment explanation
Indices: 17400272--17400308 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
17400262 GGTTTTTGGA
17400272 TTTTAGGG-
1 TTTTAGGGT
17400280 -TTTAGGGT
1 TTTTAGGGT
*
17400288 TTTTAGGAT
1 TTTTAGGGT
17400297 TTTTAGGGT
1 TTTTAGGGT
17400306 TTT
1 TTT
17400309 GGAGAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
7 7 0.28
9 18 0.72
ACGTcount: A:0.14, C:0.00, G:0.30, T:0.57
Consensus pattern (9 bp):
TTTTAGGGT
Found at i:17401339 original size:9 final size:9
Alignment explanation
Indices: 17401317--17401494 Score: 55
Period size: 9 Copynumber: 19.4 Consensus size: 9
17401307 TAAAAGAAAA
17401317 TAAAAATAT
1 TAAAAATAT
17401326 T--AAATAT
1 TAAAAATAT
17401333 TAAAAATAT
1 TAAAAATAT
* *
17401342 TAATATTGAT
1 TAAAAAT-AT
**
17401352 ATAAACTTAT
1 -TAAAAATAT
17401362 T-AAAAT-T
1 TAAAAATAT
*
17401369 AAAAAATAT
1 TAAAAATAT
*
17401378 ATAAAAA-CT
1 -TAAAAATAT
*
17401387 TATAAATAT
1 TAAAAATAT
17401396 TATAAAAT-T
1 TA-AAAATAT
*
17401405 ATAAAAAAAT
1 -TAAAAATAT
* * *
17401415 ATGAAATTAA
1 -TAAAAATAT
*
17401425 TAAAACTTAT
1 TAAAA-ATAT
**
17401435 TTGAAATAT
1 TAAAAATAT
*
17401444 TTAAAAT-T
1 TAAAAATAT
17401452 TAAAAAAATAT
1 T--AAAAATAT
* *
17401463 TAGAATTAT
1 TAAAAATAT
*
17401472 TAAAAAATAA
1 T-AAAAATAT
17401482 TAAAAATAT
1 TAAAAATAT
17401491 TAAA
1 TAAA
17401495 TTGATATAAA
Statistics
Matches: 123, Mismatches: 30, Indels: 32
0.66 0.16 0.17
Matches are distributed among these distances:
7 8 0.07
8 15 0.12
9 54 0.44
10 39 0.32
11 7 0.06
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (9 bp):
TAAAAATAT
Found at i:17401346 original size:28 final size:27
Alignment explanation
Indices: 17401315--17401495 Score: 81
Period size: 28 Copynumber: 6.6 Consensus size: 27
17401305 TATAAAAGAA
17401315 AATAAAAATATTAAATATTAAAAATATT
1 AATAAAAATATTAAATATTAAAAA-ATT
***
17401343 AATATTGATA-TAAACTTATT--AAAATT
1 AATAAAAATATTAAA--TATTAAAAAATT
* *
17401369 -A-AAAAATATATAAAAACTTATAAATATT
1 AATAAAAATAT-TAAATA-TTA-AAAAATT
* * * * **
17401397 -ATAAAATTATAAAAAAATATGAAATT
1 AATAAAAATATTAAATATTAAAAAATT
* * *
17401423 AATAAAACTTATTTGAAATATTTAAAATTT
1 AATAAAA-ATA-TT-AAATATTAAAAAATT
17401453 AA-AAAAATATTAGAATTATTAAAAAA-T
1 AATAAAAATATTA-AA-TATTAAAAAATT
17401480 AATAAAAATATTAAAT
1 AATAAAAATATTAAAT
17401496 TGATATAAAC
Statistics
Matches: 113, Mismatches: 24, Indels: 34
0.66 0.14 0.20
Matches are distributed among these distances:
24 5 0.04
25 3 0.03
26 13 0.12
27 24 0.21
28 41 0.36
29 16 0.14
30 11 0.10
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (27 bp):
AATAAAAATATTAAATATTAAAAAATT
Found at i:17401390 original size:10 final size:9
Alignment explanation
Indices: 17401358--17401411 Score: 58
Period size: 9 Copynumber: 6.0 Consensus size: 9
17401348 TGATATAAAC
*
17401358 TTATTAAAA
1 TTATAAAAA
17401367 TTA-AAAAA
1 TTATAAAAA
17401375 TATATAAAAA
1 T-TATAAAAA
*
17401385 CTTATAAATA
1 -TTATAAAAA
17401395 TTAT-AAAA
1 TTATAAAAA
17401403 TTATAAAAA
1 TTATAAAAA
17401412 AATATGAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
8 12 0.32
9 13 0.34
10 12 0.32
11 1 0.03
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (9 bp):
TTATAAAAA
Found at i:17401408 original size:17 final size:18
Alignment explanation
Indices: 17401316--17401429 Score: 71
Period size: 18 Copynumber: 6.3 Consensus size: 18
17401306 ATAAAAGAAA
17401316 ATAAAAATAT-T-AAA-T
1 ATAAAAATATATAAAATT
*
17401331 ATTAAAAATAT-TAATATT
1 A-TAAAAATATATAAAATT
*
17401349 GATATAAACT-TATTAAAATT
1 -ATA-AAAATATA-TAAAATT
17401369 A-AAAAATATATAAAAACTT
1 ATAAAAATATAT-AAAA-TT
*
17401388 ATAAATAT-TATAAAATT
1 ATAAAAATATATAAAATT
* *
17401405 ATAAAAAAATATGAAATT
1 ATAAAAATATATAAAATT
17401423 AATAAAA
1 -ATAAAA
17401430 CTTATTTGAA
Statistics
Matches: 78, Mismatches: 8, Indels: 22
0.72 0.07 0.20
Matches are distributed among these distances:
15 1 0.01
16 10 0.13
17 15 0.19
18 23 0.29
19 18 0.23
20 11 0.14
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (18 bp):
ATAAAAATATATAAAATT
Found at i:17401462 original size:19 final size:18
Alignment explanation
Indices: 17401438--17401486 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
17401428 AACTTATTTG
17401438 AAATATTTAAAATTTAAAA
1 AAATA-TTAAAATTTAAAA
* *
17401457 AAATATTAGAATTATTAAA
1 AAATATTAAAATT-TAAAA
*
17401476 AAATAATAAAA
1 AAATATTAAAA
17401487 ATATTAAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 7 0.28
19 18 0.72
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (18 bp):
AAATATTAAAATTTAAAA
Found at i:17401489 original size:47 final size:48
Alignment explanation
Indices: 17401390--17401492 Score: 120
Period size: 47 Copynumber: 2.2 Consensus size: 48
17401380 AAAAACTTAT
** * **
17401390 AAATATTATAAAATTATAAAAAAATATGAAATTAATAAAACTTATTTG
1 AAATATTATAAAATTATAAAAAAATATGAAATTAATAAAAAATAATAA
* *
17401438 AAATATT-TAAAATT-TAAAAAAATATTAGAATTATTAAAAAATAATAA
1 AAATATTATAAAATTATAAAAAAATATGA-AATTAATAAAAAATAATAA
17401485 AAATATTA
1 AAATATTA
17401493 AATTGATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
46 12 0.26
47 27 0.59
48 7 0.15
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (48 bp):
AAATATTATAAAATTATAAAAAAATATGAAATTAATAAAAAATAATAA
Found at i:17401491 original size:19 final size:19
Alignment explanation
Indices: 17401454--17401494 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
17401444 TTAAAATTTA
* * *
17401454 AAAAAATATTAGAATTATT
1 AAAAAATAATAAAAATATT
17401473 AAAAAATAATAAAAATATT
1 AAAAAATAATAAAAATATT
17401492 AAA
1 AAA
17401495 TTGATATAAA
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:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAAATAATAAAAATATT
Found at i:17401956 original size:9 final size:9
Alignment explanation
Indices: 17401944--17402180 Score: 87
Period size: 9 Copynumber: 25.8 Consensus size: 9
17401934 TTTATGATTT
17401944 TTTTTATAA
1 TTTTTATAA
17401953 TTTTTATAAA
1 TTTTTAT-AA
*
17401963 TTTATATGAA
1 TTTTTAT-AA
*
17401973 TTTTAAT-A
1 TTTTTATAA
*
17401981 TTTTTATCA
1 TTTTTATAA
*
17401990 TTTTTATGA
1 TTTTTATAA
17401999 TTTTTATGTAA
1 TTTTTA--TAA
* * *
17402010 CTTTAATATG
1 TTTTTATA-A
17402020 TTTTTATAAAAA
1 TTTTTAT---AA
** ** *
17402032 AATAAATAT
1 TTTTTATAA
17402041 TTTTTATTAA
1 TTTTTA-TAA
*
17402051 -TTTTATAT
1 TTTTTATAA
17402059 TTTTTATAA
1 TTTTTATAA
*
17402068 TTTATTAGAA
1 TTT-TTATAA
17402078 TTTTTATAA
1 TTTTTATAA
17402087 TTTTT-TAA
1 TTTTTATAA
*
17402095 GTTTATATAAA
1 -TTTTTAT-AA
*
17402106 TTTTCAT-A
1 TTTTTATAA
17402114 TTTTT-TAA
1 TTTTTATAA
*
17402122 -TATT-TAA
1 TTTTTATAA
*
17402129 TTTTTTTATA
1 TTTTTATA-A
17402139 TTTTT-T-A
1 TTTTTATAA
*
17402146 TTTTTAAAA
1 TTTTTATAA
*
17402155 TTTTGTTTAA
1 TTTT-TATAA
*
17402165 TATTTATAA
1 TTTTTATAA
*
17402174 TTATTAT
1 TTTTTAT
17402181 TTAATCATTT
Statistics
Matches: 167, Mismatches: 40, Indels: 42
0.67 0.16 0.17
Matches are distributed among these distances:
7 13 0.08
8 21 0.13
9 73 0.44
10 48 0.29
11 8 0.05
12 3 0.02
13 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (9 bp):
TTTTTATAA
Found at i:17401993 original size:37 final size:37
Alignment explanation
Indices: 17401944--17402028 Score: 100
Period size: 37 Copynumber: 2.2 Consensus size: 37
17401934 TTTATGATTT
*
17401944 TTTTTATAATTTTTATAAATTTATATG-AATTTTAATA
1 TTTTTATAATTTTTAT-AATTTATATGTAACTTTAATA
* * *
17401981 TTTTTATCATTTTTATGATTTTTATGTAACTTTAATA
1 TTTTTATAATTTTTATAATTTATATGTAACTTTAATA
17402018 TGTTTTTATAA
1 --TTTTTATAA
17402029 AAAAATAAAT
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
36 8 0.20
37 24 0.60
39 8 0.20
ACGTcount: A:0.32, C:0.02, G:0.05, T:0.61
Consensus pattern (37 bp):
TTTTTATAATTTTTATAATTTATATGTAACTTTAATA
Found at i:17402082 original size:28 final size:27
Alignment explanation
Indices: 17402051--17402145 Score: 99
Period size: 28 Copynumber: 3.5 Consensus size: 27
17402041 TTTTTATTAA
17402051 TTTTATATTTTTTATAATTTAT-TAGAAT
1 TTTTATATTTTTTA-AATTTATATA-AAT
*
17402079 TTTTATAATTTTTTAAGTTTATATAAAT
1 TTTTAT-ATTTTTTAAATTTATATAAAT
* *
17402107 TTTCATATTTTTTAATATTTA-AT--TT
1 TTTTATATTTTTTAA-ATTTATATAAAT
17402132 TTTTATATTTTTTA
1 TTTTATATTTTTTA
17402146 TTTTTAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
25 14 0.24
27 11 0.19
28 24 0.41
29 10 0.17
ACGTcount: A:0.31, C:0.01, G:0.02, T:0.66
Consensus pattern (27 bp):
TTTTATATTTTTTAAATTTATATAAAT
Found at i:17409079 original size:20 final size:17
Alignment explanation
Indices: 17409028--17409073 Score: 83
Period size: 17 Copynumber: 2.7 Consensus size: 17
17409018 AATTTTGCGA
*
17409028 AAACGAAAAGGGATAAT
1 AAACAAAAAGGGATAAT
17409045 AAACAAAAAGGGATAAT
1 AAACAAAAAGGGATAAT
17409062 AAACAAAAAGGG
1 AAACAAAAAGGG
17409074 TTGATATATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.63, C:0.07, G:0.22, T:0.09
Consensus pattern (17 bp):
AAACAAAAAGGGATAAT
Found at i:17410864 original size:2 final size:2
Alignment explanation
Indices: 17410851--17410883 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
17410841 CCTTTCTGTC
*
17410851 TG TG TG TA TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
17410884 TTTATTTGTC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.00, G:0.45, T:0.52
Consensus pattern (2 bp):
TG
Found at i:17416502 original size:67 final size:67
Alignment explanation
Indices: 17416394--17416525 Score: 219
Period size: 67 Copynumber: 2.0 Consensus size: 67
17416384 GTTTATATTA
*
17416394 CAGGGGATTTAGCCTAGACTGATAATCCCATTGTAAGAAATGAAGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTAGACTGATAATCCCACTGTAAGAAATGAAGTTCGCGGGAGTGTGCTCTCT
17416459 TG
66 TG
* * * *
17416461 CAGGGGATTTAGCCTGGACTGGTAATCCCGCTGTAAGAAATGAGGTTCGCGGGAGTGTGCTCTCT
1 CAGGGGATTTAGCCTAGACTGATAATCCCACTGTAAGAAATGAAGTTCGCGGGAGTGTGCTCTCT
17416526 GAATTGGAAA
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
67 60 1.00
ACGTcount: A:0.23, C:0.19, G:0.31, T:0.27
Consensus pattern (67 bp):
CAGGGGATTTAGCCTAGACTGATAATCCCACTGTAAGAAATGAAGTTCGCGGGAGTGTGCTCTCT
TG
Found at i:17422656 original size:58 final size:56
Alignment explanation
Indices: 17422564--17422798 Score: 156
Period size: 56 Copynumber: 4.2 Consensus size: 56
17422554 GGCTTTAAGT
* * * * * * * *
17422564 AAAATCTTCAAAAATCATCAGCTGCGAATATGGATAT-ACAAGTTATTTTGTACTTGGG
1 AAAATTTTCTAAAATAATAAGCTGGGAATGTGGATATGACAA-CT-TTTTATACTT-GG
* ** *
17422622 AAAATTTTCTAAAATAATAAGCTGGGAATGTGGATTTGTGAACTTTTTATCCTTGG
1 AAAATTTTCTAAAATAATAAGCTGGGAATGTGGATATGACAACTTTTTATACTTGG
* * ** *
17422678 -AAATTTTCTAAAATAATAAGTTGGGAATGTGAAT-TCGTGAACTATTTTATCCTT--
1 AAAATTTTCTAAAATAATAAGCTGGGAATGTGGATAT-GACAACT-TTTTATACTTGG
* * * * * * *
17422732 AAAATTTTTCTAAAATAATAAGCTGGAAATGTGAATCTGAGAGCTATTTTATATTTAG
1 AAAA-TTTTCTAAAATAATAAGCTGGGAATGTGGATATGACAACT-TTTTATACTTGG
17422790 AAAATTTTC
1 AAAATTTTC
17422799 GAGGATGGTA
Statistics
Matches: 149, Mismatches: 20, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
54 1 0.01
55 42 0.28
56 55 0.37
57 14 0.09
58 35 0.23
59 2 0.01
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (56 bp):
AAAATTTTCTAAAATAATAAGCTGGGAATGTGGATATGACAACTTTTTATACTTGG
Found at i:17422752 original size:56 final size:56
Alignment explanation
Indices: 17422621--17422798 Score: 229
Period size: 56 Copynumber: 3.2 Consensus size: 56
17422611 TTGTACTTGG
* *
17422621 GAAAATTTTCTAAAATAATAAGCTGGGAATGTGGATTTGTGAACT-TTTTATCCTT
1 GAAAATTTTCTAAAATAATAAGCTGGGAATGTGAATTCGTGAACTATTTTATCCTT
* *
17422676 GGAAATTTTCTAAAATAATAAGTTGGGAATGTGAATTCGTGAACTATTTTATCCTT
1 GAAAATTTTCTAAAATAATAAGCTGGGAATGTGAATTCGTGAACTATTTTATCCTT
* **
17422732 -AAAATTTTTCTAAAATAATAAGCTGGAAATGTGAA-TC-TGAGAGCTATTTTATATTT
1 GAAAA-TTTTCTAAAATAATAAGCTGGGAATGTGAATTCGTGA-A-CTATTTTATCCTT
17422788 AGAAAATTTTC
1 -GAAAATTTTC
17422799 GAGGATGGTA
Statistics
Matches: 108, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
54 3 0.03
55 47 0.44
56 49 0.45
57 5 0.05
58 4 0.04
ACGTcount: A:0.36, C:0.08, G:0.16, T:0.39
Consensus pattern (56 bp):
GAAAATTTTCTAAAATAATAAGCTGGGAATGTGAATTCGTGAACTATTTTATCCTT
Found at i:17423018 original size:69 final size:69
Alignment explanation
Indices: 17422935--17423272 Score: 270
Period size: 69 Copynumber: 4.9 Consensus size: 69
17422925 TTTCGCCTGC
* * * ** *
17422935 AAGCTTTAACATGATAGTTGGGAGCTTTGATCTCGCTAACTATGTTGGAGGCTGTAGCACTTCAT
1 AAGCCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCACTTCAC
17423000 TTGT
66 TTGT
* * * * * * ** **
17423004 GAGCCTTAATATGATAGCTGGGAGCTTTGATCTTGCTAATTGA-GTTAGAGGCTGCGGCTGTTTG
1 AAGCCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAACT-ATGTTGGAGGCTGCGGCACTTCA
17423068 CTTG-
65 CTTGT
* * * *
17423072 AGAGCCTTAATATAATAGTTGGGAGCTCTGCTCTCGCTAATTATGTTGAAGGCTGCGGCTA-TTC
1 A-AGCCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGC-ACTTC
*
17423136 ACCTGT
64 ACTTGT
* * * * * * ** * *
17423142 AAGCCTTAATATGACAATTGGGAACTTTTCTCTCGCTAACTTTATTGGAGGCTATGGCTCTTCGC
1 AAGCCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCACTTCAC
17423207 TTGT
66 TTGT
* * * * * * * *
17423211 AAGCCTTAATATAACAGCTGAG-GCTTTGCTCTCACTAACTACGTTGGAGGGTGCGGCTCTTC
1 AAGCCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCACTTC
17423273 GCCTACGAGC
Statistics
Matches: 209, Mismatches: 54, Indels: 13
0.76 0.20 0.05
Matches are distributed among these distances:
68 32 0.15
69 175 0.84
70 2 0.01
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (69 bp):
AAGCCTTAATATGATAGTTGGGAGCTTTGCTCTCGCTAACTATGTTGGAGGCTGCGGCACTTCAC
TTGT
Found at i:17423180 original size:138 final size:138
Alignment explanation
Indices: 17422855--17423297 Score: 349
Period size: 138 Copynumber: 3.2 Consensus size: 138
17422845 GGTCTACGGT
* * * * ** * * *
17422855 TATTCACCTAGT-AGCTTTAATATGGCAGCTGGGAGCTTTCCTCTCACTAAC-TGCGTTGGAGGC
1 TATTCACCT-GTGAGCCTTAATATGACAACTGGGAACTTTGATCTCGCTAACTTG-ATTAGAGGC
* * * * * * * * *
17422918 TAAGACTTTTCGCCTGCAAGCTTTAACATGATAGTTGGGAGCTTTGATCTCGCTAACTATGTTGG
64 TACGGCTCTTCGCTTGTAAGCCTTAATATAATAGTTGGGAGCTTTGCTCTCGCTAACTATGTTGG
**
17422983 AGGCTGTAGC
129 AGGCTGCGGC
** * * * *
17422993 -ACTTCATTTGTGAGCCTTAATATGATAGCTGGGAGCTTTGATCTTGCTAA-TTGAGTTAGAGGC
1 TA-TTCACCTGTGAGCCTTAATATGACAACTGGGAACTTTGATCTCGCTAACTTGA-TTAGAGGC
* * * * *
17423056 TGCGGCTGTTTGCTTG-AGAGCCTTAATATAATAGTTGGGAGCTCTGCTCTCGCTAATTATGTTG
64 TACGGCTCTTCGCTTGTA-AGCCTTAATATAATAGTTGGGAGCTTTGCTCTCGCTAACTATGTTG
*
17423120 AAGGCTGCGGC
128 GAGGCTGCGGC
* * ** * *
17423131 TATTCACCTGTAAGCCTTAATATGACAATTGGGAACTTTTCTCTCGCTAACTTTATTGGAGGCTA
1 TATTCACCTGTGAGCCTTAATATGACAACTGGGAACTTTGATCTCGCTAACTTGATTAGAGGCTA
* * * * * *
17423196 TGGCTCTTCGCTTGTAAGCCTTAATATAACAGCTGAG-GCTTTGCTCTCACTAACTACGTTGGAG
66 CGGCTCTTCGCTTGTAAGCCTTAATATAATAGTTGGGAGCTTTGCTCTCGCTAACTATGTTGGAG
*
17423260 GGTGCGGC
131 GCTGCGGC
* * ** *
17423268 TCTTCGCCTACGAGCCTTAATATAACAACT
1 TATTCACCTGTGAGCCTTAATATGACAACT
17423298 AGGAGTTTTG
Statistics
Matches: 239, Mismatches: 58, Indels: 17
0.76 0.18 0.05
Matches are distributed among these distances:
137 56 0.23
138 178 0.74
139 5 0.02
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (138 bp):
TATTCACCTGTGAGCCTTAATATGACAACTGGGAACTTTGATCTCGCTAACTTGATTAGAGGCTA
CGGCTCTTCGCTTGTAAGCCTTAATATAATAGTTGGGAGCTTTGCTCTCGCTAACTATGTTGGAG
GCTGCGGC
Found at i:17423327 original size:137 final size:138
Alignment explanation
Indices: 17423074--17423329 Score: 291
Period size: 137 Copynumber: 1.9 Consensus size: 138
17423064 TTTGCTTGAG
* * * * * *
17423074 AGCCTTAATATAATAGTTGGGAGCTCTGCTCTCGCTAATTATGTTGAAGGCTGCGGCTATTCACC
1 AGCCTTAATATAACAGCTGAGAGCTCTGCTCTCACTAACTACGTTGAAGGCTGCGGCTATTCACC
** * * * * *
17423139 TGTAAGCCTTAATATGACAATTGGGAACTTTTCTCTCGCTAACTTTATTGGAGGCTATGGCTCTT
66 TACAAGCCTTAATATAACAACTAGGAACTTTTCTCTCACTAACTGTATTGGAGGCTATGGCTCTT
17423204 CGCTTGTA
131 CGCTTGTA
* * * * *
17423212 AGCCTTAATATAACAGCTGAG-GCTTTGCTCTCACTAACTACGTTGGAGGGTGCGGCTCTTCGCC
1 AGCCTTAATATAACAGCTGAGAGCTCTGCTCTCACTAACTACGTTGAAGGCTGCGGCTATTCACC
* * * *
17423276 TACGAGCCTTAATATAACAACTAGG-AGTTTTGCTCTCACTATCTGTGTTGGAGG
66 TACAAGCCTTAATATAACAACTAGGAACTTTT-CTCTCACTAACTGTATTGGAGG
17423330 TTGCAGTTCT
Statistics
Matches: 95, Mismatches: 22, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
136 5 0.05
137 72 0.76
138 18 0.19
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (138 bp):
AGCCTTAATATAACAGCTGAGAGCTCTGCTCTCACTAACTACGTTGAAGGCTGCGGCTATTCACC
TACAAGCCTTAATATAACAACTAGGAACTTTTCTCTCACTAACTGTATTGGAGGCTATGGCTCTT
CGCTTGTA
Found at i:17423341 original size:69 final size:68
Alignment explanation
Indices: 17423212--17423364 Score: 173
Period size: 69 Copynumber: 2.2 Consensus size: 68
17423202 TTCGCTTGTA
* *
17423212 AGCCTTAATATAACAGCTGAGGCTTTGCTCTCACTAACTACGTTGGAGGGTGCGGCTCTTCGCCT
1 AGCCTTAATATAACAACTGAGGCTTTGCTCTCACTAACTACGTTGGAGGGTGCAGCTCTTCGCCT
17423277 ACG
66 ACG
* * ** * * *
17423280 AGCCTTAATATAACAACT-AGGAGTTTTGCTCTCACTATCTGTGTTGGAGGTTGCAGTTCTTCGT
1 AGCCTTAATATAACAACTGA-G-GCTTTGCTCTCACTAACTACGTTGGAGGGTGCAGCTCTTCGC
**
17423344 CTGTG
64 CTACG
*
17423349 AGCCTTAATATGACAA
1 AGCCTTAATATAACAA
17423365 AAAATGCTAT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
67 1 0.01
68 18 0.25
69 52 0.73
ACGTcount: A:0.23, C:0.22, G:0.23, T:0.32
Consensus pattern (68 bp):
AGCCTTAATATAACAACTGAGGCTTTGCTCTCACTAACTACGTTGGAGGGTGCAGCTCTTCGCCT
ACG
Found at i:17431409 original size:16 final size:17
Alignment explanation
Indices: 17431377--17431411 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
17431367 CATTGGAAGA
*
17431377 TTTGGTTTTGTTGGCCT
1 TTTGATTTTGTTGGCCT
17431394 TTTGATTTTG-TGGCCT
1 TTTGATTTTGTTGGCCT
17431410 TT
1 TT
17431412 ATAGAATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.03, C:0.11, G:0.26, T:0.60
Consensus pattern (17 bp):
TTTGATTTTGTTGGCCT
Found at i:17437192 original size:41 final size:41
Alignment explanation
Indices: 17436957--17437180 Score: 358
Period size: 41 Copynumber: 5.5 Consensus size: 41
17436947 ACAGATTCAG
* * ** * * *
17436957 CGGCACATAGACTGCTAGACTTATAGCTTGATTCAGATCAC
1 CGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAATCAC
17436998 CGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAATCAC
1 CGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAATCAC
*
17437039 CGGCACGTAGCCTGCTAGGTTTATAACCCGATTCAAATCAC
1 CGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAATCAC
*
17437080 CGGCACGTAGCCTGCTAGGTTTATAACCCGATTCAAATCAC
1 CGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAATCAC
*
17437121 CGGCACATAGCCTGCTAGGTTTATAACCTGATTCAAATCAC
1 CGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAATCAC
17437162 CGGCACGTAGCCTGCTAGG
1 CGGCACGTAGCCTGCTAGG
17437181 CGCTTAGCCT
Statistics
Matches: 172, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 172 1.00
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.25
Consensus pattern (41 bp):
CGGCACGTAGCCTGCTAGGTTTATAACCTGATTCAAATCAC
Found at i:17437595 original size:2 final size:2
Alignment explanation
Indices: 17437582--17437611 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17437572 GATGTACATT
*
17437582 TA TA TT 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
17437612 ACACTCATAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:17437745 original size:2 final size:2
Alignment explanation
Indices: 17437740--17437825 Score: 113
Period size: 2 Copynumber: 43.5 Consensus size: 2
17437730 ATATGCCTAC
17437740 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
** **
17437782 AT AT AT AT AT -T CGC CC AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17437823 AT A
1 AT A
17437826 CAATTCTTTA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
1 2 0.03
2 75 0.97
ACGTcount: A:0.47, C:0.05, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:17437749 original size:20 final size:20
Alignment explanation
Indices: 17437720--17437811 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
17437710 TATCTATTTA
* *
17437720 ATATACATATATATGCCTAC
1 ATATATATATATATGCATAC
*
17437740 ATATATATATATAT--ATAT
1 ATATATATATATATGCATAC
** *
17437758 ATATATATATATATATATAT
1 ATATATATATATATGCATAC
* ***
17437778 ATATATATATATATTCGCCC
1 ATATATATATATATGCATAC
17437798 ATATATATATATAT
1 ATATATATATATAT
17437812 ATATATATAT
Statistics
Matches: 61, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
18 16 0.26
20 45 0.74
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.45
Consensus pattern (20 bp):
ATATATATATATATGCATAC
Found at i:17437903 original size:2 final size:2
Alignment explanation
Indices: 17437896--17437966 Score: 92
Period size: 2 Copynumber: 36.0 Consensus size: 2
17437886 CAATAACTTT
17437896 TA TA TA TA TA 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 TA TA TA TA TA TA
* * *
17437937 TC TA GCA T- TA TA TA TA TA CA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
17437967 CATGCTTATT
Statistics
Matches: 61, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
1 2 0.03
2 58 0.95
3 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17439134 original size:14 final size:15
Alignment explanation
Indices: 17439117--17439145 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
17439107 ACACGAAAAT
17439117 TTCACACA-ATTAAA
1 TTCACACATATTAAA
17439131 TTCACACATATTAAA
1 TTCACACATATTAAA
17439146 CACACAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (15 bp):
TTCACACATATTAAA
Found at i:17440556 original size:41 final size:39
Alignment explanation
Indices: 17440497--17440590 Score: 161
Period size: 41 Copynumber: 2.4 Consensus size: 39
17440487 AATATATTTA
17440497 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
17440536 TTTTTTATTATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTA--ATTTTTTTAATTTTAAAATATTTTTAAAATAC
*
17440577 TTTTTTAAATTTTT
1 TTTTTTAATTTTTT
17440591 AAAATAAATT
Statistics
Matches: 52, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
39 13 0.25
41 39 0.75
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (39 bp):
TTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:17440559 original size:30 final size:32
Alignment explanation
Indices: 17440523--17440596 Score: 91
Period size: 30 Copynumber: 2.4 Consensus size: 32
17440513 ATTTTAAAAT
* * *
17440523 ATTTTTAAAATACTTTTT-TATTA-TTTTTTTA
1 ATTTTTAAAATA-TTTTTAAAATACTTTTTTAA
17440554 A-TTTTAAAATATTTTTAAAATACTTTTTTAA
1 ATTTTTAAAATATTTTTAAAATACTTTTTTAA
17440585 ATTTTTAAAATA
1 ATTTTTAAAATA
17440597 AATTTTTGGT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 5 0.14
30 13 0.35
31 9 0.24
32 10 0.27
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (32 bp):
ATTTTTAAAATATTTTTAAAATACTTTTTTAA
Found at i:17440586 original size:12 final size:11
Alignment explanation
Indices: 17440514--17440596 Score: 61
Period size: 11 Copynumber: 7.9 Consensus size: 11
17440504 ATTTTTTTAA
17440514 TTTTAAAATAT
1 TTTTAAAATAT
17440525 TTTTAAAATACT
1 TTTTAAAATA-T
* *
17440537 TTTT-TATTAT
1 TTTTAAAATAT
* *
17440547 TTTT---TTAA
1 TTTTAAAATAT
17440555 TTTTAAAATAT
1 TTTTAAAATAT
17440566 TTTTAAAATACT
1 TTTTAAAATA-T
*
17440578 TTTT-TAA-AT
1 TTTTAAAATAT
17440587 TTTTAAAATA
1 TTTTAAAATA
17440597 AATTTTTGGT
Statistics
Matches: 58, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
8 7 0.12
9 5 0.09
10 8 0.14
11 28 0.48
12 10 0.17
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:17440602 original size:21 final size:21
Alignment explanation
Indices: 17440564--17440603 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17440554 ATTTTAAAAT
**
17440564 ATTTTTAAAATACTTTTTTAA
1 ATTTTTAAAATAAATTTTTAA
17440585 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
17440604 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTAA
Found at i:17443014 original size:2 final size:2
Alignment explanation
Indices: 17443007--17443032 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
17442997 ACCGTGCCAA
17443007 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
17443033 GTTGATGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17447430 original size:2 final size:2
Alignment explanation
Indices: 17447423--17447460 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
17447413 ATTGATTTCA
*
17447423 CT CT CT CT CT CT CT CT CT CT CT CT TT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
17447461 TTAGATGTGG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
CT
Found at i:17458489 original size:19 final size:19
Alignment explanation
Indices: 17458465--17458539 Score: 114
Period size: 19 Copynumber: 3.8 Consensus size: 19
17458455 AATTTTTGAG
17458465 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
17458484 GATATGCAATCTTAGTTAT
1 GATATGCAATCTTAGATAT
17458503 GATATGTGCAATCTTAGATAT
1 GATA--TGCAATCTTAGATAT
*
17458524 AATATGCAATCTTAGA
1 GATATGCAATCTTAGA
17458540 ATATATGATT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
19 34 0.67
21 17 0.33
ACGTcount: A:0.36, C:0.11, G:0.16, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:17458514 original size:21 final size:20
Alignment explanation
Indices: 17458465--17458562 Score: 103
Period size: 19 Copynumber: 4.8 Consensus size: 20
17458455 AATTTTTGAG
17458465 GATA-TGCAATCTTAGATAT
1 GATATTGCAATCTTAGATAT
*
17458484 GATA-TGCAATCTTAGTTAT
1 GATATTGCAATCTTAGATAT
17458503 GATATGTGCAATCTTAGATAT
1 GATAT-TGCAATCTTAGATAT
*
17458524 AATA-TGCAATCTTAGAATATAT
1 GATATTGCAATCTTAG---ATAT
* *
17458546 GATTTTGTAATCTTAGA
1 GATATTGCAATCTTAGA
17458563 GATTTAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 11
0.80 0.07 0.13
Matches are distributed among these distances:
19 33 0.49
20 1 0.01
21 17 0.25
22 6 0.09
23 10 0.15
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (20 bp):
GATATTGCAATCTTAGATAT
Found at i:17467146 original size:19 final size:18
Alignment explanation
Indices: 17467100--17467147 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
17467090 AATTAATGTG
* *
17467100 TTAAATAGTTGAAACTAA
1 TTAAATATTTAAAACTAA
* *
17467118 TTAAAGATTTAAAATTAA
1 TTAAATATTTAAAACTAA
17467136 TATAAATATTTA
1 T-TAAATATTTA
17467148 GTAAATAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.52, C:0.02, G:0.06, T:0.40
Consensus pattern (18 bp):
TTAAATATTTAAAACTAA
Found at i:17470639 original size:25 final size:25
Alignment explanation
Indices: 17470524--17470635 Score: 129
Period size: 25 Copynumber: 4.5 Consensus size: 25
17470514 AACACACCAC
*
17470524 AGCTCGTATGAGCTTCCCGATTTAT
1 AGCTCGTATGAGCTTCCCGATTCAT
*
17470549 AGCTCGTATGAGCTTCCCGACTGC--
1 AGCTCGTATGAGCTTCCCGA-TTCAT
* *
17470573 AGCTCATATGAGCTTCCCGATTCAA
1 AGCTCGTATGAGCTTCCCGATTCAT
* * * *
17470598 AGCTCGTAAGAGCATACTGATTCAT
1 AGCTCGTATGAGCTTCCCGATTCAT
17470623 AGCTCGTATGAGC
1 AGCTCGTATGAGC
17470636 ATACATGAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
23 2 0.03
24 19 0.26
25 51 0.70
26 1 0.01
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (25 bp):
AGCTCGTATGAGCTTCCCGATTCAT
Done.