Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr11
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: 102024878
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 3234766 characters in sequence are not A, C, G, or T
File 7 of 310
Found at i:1650775 original size:44 final size:43
Alignment explanation
Indices: 1650725--1650871 Score: 129
Period size: 44 Copynumber: 3.4 Consensus size: 43
1650715 TGATTTGCTT
1650725 CCCTACTGCTTAAGGTGATAAGATCTATAAACTTCAGCTTGTTA
1 CCCTACTGCTTAAGGTGATAAGATCTAT-AACTTCAGCTTGTTA
* * * * ** * * *
1650769 CCCTACTGCTTAGGGGGTTAAAGCTCGT-TGCCTT-TGATCTGTTT
1 CCCTACTGCTTAAGGTGAT-AAGATC-TATAACTTCAGCT-TGTTA
* * *
1650813 CCCTACTGCTTAGGGTGATAAGATCTATATCTTCAGCCTGTTA
1 CCCTACTGCTTAAGGTGATAAGATCTATAACTTCAGCTTGTTA
1650856 CCCTACTGCTT-AGGTG
1 CCCTACTGCTTAAGGTG
1650872 GTTAAGGTCT
Statistics
Matches: 79, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
42 5 0.06
43 26 0.33
44 41 0.52
45 6 0.08
46 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.35
Consensus pattern (43 bp):
CCCTACTGCTTAAGGTGATAAGATCTATAACTTCAGCTTGTTA
Found at i:1651455 original size:55 final size:55
Alignment explanation
Indices: 1651385--1651559 Score: 332
Period size: 55 Copynumber: 3.2 Consensus size: 55
1651375 ACAAAATTTG
1651385 AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
1 AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
* *
1651440 AAGGGAATAGATTAATCACAGTAAACAAACATTGCTGGAATATAAAATGAATAAA
1 AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
1651495 AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
1 AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
1651550 AAGGGAATAG
1 AAGGGAATAG
1651560 GTGCCCCAGA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 116 1.00
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (55 bp):
AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
Found at i:1653029 original size:45 final size:45
Alignment explanation
Indices: 1652980--1653083 Score: 113
Period size: 45 Copynumber: 2.3 Consensus size: 45
1652970 CCTCCTGTTG
* * * *
1652980 CTTCAATCTGCTCCA-TTGTAGCTTCAGAGAAATAAGATTTGCT-A
1 CTTCAATCTGCTCCACTTGCAACTTCAAAGAAATAAGACTTG-TGA
* *
1653024 TCTTCAGTCTGCTCCACTTGCAACTTCAAAGAGATAAGACTTGTGA
1 -CTTCAATCTGCTCCACTTGCAACTTCAAAGAAATAAGACTTGTGA
*
1653070 CTTCAATCTACTCC
1 CTTCAATCTGCTCC
1653084 GTTGAAACTT
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
45 27 0.55
46 22 0.45
ACGTcount: A:0.28, C:0.25, G:0.14, T:0.33
Consensus pattern (45 bp):
CTTCAATCTGCTCCACTTGCAACTTCAAAGAAATAAGACTTGTGA
Found at i:1653299 original size:43 final size:41
Alignment explanation
Indices: 1653162--1653314 Score: 110
Period size: 43 Copynumber: 3.6 Consensus size: 41
1653152 ATTTTCAGCC
* * **
1653162 TGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCATTGCT
1 TGTTACCCTACTGCTTAGGGGTTTAAGGTTTGAAAT--TTGCT
* * * * ** *
1653205 CTGTTTCCCTACTGCTGAGGGGTTT-AGATCTGTAAATTCAACC
1 -TGTTACCCTACTGCTTAGGGGTTTAAGGTTTG-AAATT-TGCT
*
1653248 TATTACCCTACTGCTTAGGGGTTTAAGGTTTGAAAATTTGGCT
1 TGTTACCCTACTGCTTAGGGGTTTAAGGTTTG-AAATTT-GCT
*
1653291 TGTTACCCTATTGCTTAGAGGGTT
1 TGTTACCCTACTGCTTAG-GGGTT
1653315 GAAGCCCATC
Statistics
Matches: 82, Mismatches: 22, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
42 22 0.27
43 32 0.39
44 28 0.34
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (41 bp):
TGTTACCCTACTGCTTAGGGGTTTAAGGTTTGAAATTTGCT
Found at i:1653314 original size:86 final size:85
Alignment explanation
Indices: 1653155--1653314 Score: 189
Period size: 86 Copynumber: 1.9 Consensus size: 85
1653145 ACATTTGATT
* * ** *
1653155 TTCAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTTGTCATCATTGCTCTGTTTCCCTACTGC
1 TTCAACCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGAAAT-ATTGCTCTGTTACCCTACTGC
1653220 TGAGGGGTTTAGATCTGTAAA
65 TGAGGGGTTTAGATCTGTAAA
* * *
1653241 TTCAACCTATTACCCTACTGCTTAGGGGTTTAAGGTTTGAAA-ATTTGGCT-TGTTACCCTATTG
1 TTCAACCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGAAATA-TT-GCTCTGTTACCCTACTG
*
1653304 CTTAGAGGGTT
64 CTGAG-GGGTT
1653315 GAAGCCCATC
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
84 1 0.02
85 17 0.27
86 44 0.71
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (85 bp):
TTCAACCTATTACCCTACTGCTTAGGGGGTTAAGGCTTGAAATATTGCTCTGTTACCCTACTGCT
GAGGGGTTTAGATCTGTAAA
Found at i:1653745 original size:44 final size:43
Alignment explanation
Indices: 1653695--1653841 Score: 129
Period size: 44 Copynumber: 3.4 Consensus size: 43
1653685 TGATTTGCTT
1653695 CCCTACTGCTTAAGGTGATAAGATCTATAAACTTCAGCTTGTTA
1 CCCTACTGCTTAAGGTGATAAGATCTAT-AACTTCAGCTTGTTA
* * * * ** * * *
1653739 CCCTACTGCTTAGGGGGTTAAAGCTCGT-TGCCTT-TGATCTGTTT
1 CCCTACTGCTTAAGGTGAT-AAGATC-TATAACTTCAGCT-TGTTA
* * *
1653783 CCCTACTGCTTAGGGTGATAAGATCTATATCTTCAGCCTGTTA
1 CCCTACTGCTTAAGGTGATAAGATCTATAACTTCAGCTTGTTA
1653826 CCCTACTGCTT-AGGTG
1 CCCTACTGCTTAAGGTG
1653842 GTTAAGGTCT
Statistics
Matches: 79, Mismatches: 19, Indels: 12
0.72 0.17 0.11
Matches are distributed among these distances:
42 5 0.06
43 26 0.33
44 41 0.52
45 6 0.08
46 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.35
Consensus pattern (43 bp):
CCCTACTGCTTAAGGTGATAAGATCTATAACTTCAGCTTGTTA
Found at i:1654425 original size:55 final size:55
Alignment explanation
Indices: 1654355--1654529 Score: 332
Period size: 55 Copynumber: 3.2 Consensus size: 55
1654345 ACAAAATTTG
1654355 AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
1 AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
* *
1654410 AAGGGAATAGATTAATCACAGTAAACAAACATTGCTGGAATATAAAATGAATAAA
1 AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
1654465 AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
1 AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
1654520 AAGGGAATAG
1 AAGGGAATAG
1654530 GTGCCCCAGA
Statistics
Matches: 116, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
55 116 1.00
ACGTcount: A:0.51, C:0.11, G:0.18, T:0.20
Consensus pattern (55 bp):
AAGGGAATAGATTAATCACAGTCAACAAACATTGCTGGAATACAAAATGAATAAA
Found at i:1668541 original size:70 final size:70
Alignment explanation
Indices: 1668428--1668592 Score: 258
Period size: 70 Copynumber: 2.4 Consensus size: 70
1668418 TCCTCATTGA
* * * *
1668428 AATACCATACCTACATTTTACAACTCGGTATGGGAAATACCATACCTACATTTCTTAACTCAGTA
1 AATACCATACCTACATTTCACAACTCAGTATAGGAAATACCATACCTACATTTCTCAACTCAGTA
1668493 TGGAT
66 TGGAT
* **
1668498 AATACCATACCTACGTTTCACAACTCAGTATAGTTAATACCATACCTACATTTCTCAACTCAGTA
1 AATACCATACCTACATTTCACAACTCAGTATAGGAAATACCATACCTACATTTCTCAACTCAGTA
1668563 TGGAT
66 TGGAT
*
1668568 GATACCATACCTACATTTCACAACT
1 AATACCATACCTACATTTCACAACT
1668593 TTGTCATGGA
Statistics
Matches: 86, Mismatches: 9, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
70 86 1.00
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (70 bp):
AATACCATACCTACATTTCACAACTCAGTATAGGAAATACCATACCTACATTTCTCAACTCAGTA
TGGAT
Found at i:1668610 original size:35 final size:35
Alignment explanation
Indices: 1668428--1668592 Score: 233
Period size: 35 Copynumber: 4.7 Consensus size: 35
1668418 TCCTCATTGA
* *
1668428 AATACCATACCTACATTTTACAACTCGGTATGGGA-
1 AATACCATACCTACATTTCACAACTCAGTAT-GGAT
**
1668463 AATACCATACCTACATTTCTTAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
* * *
1668498 AATACCATACCTACGTTTCACAACTCAGTATAGTT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
1668533 AATACCATACCTACATTTCTCAACTCAGTATGGAT
1 AATACCATACCTACATTTCACAACTCAGTATGGAT
*
1668568 GATACCATACCTACATTTCACAACT
1 AATACCATACCTACATTTCACAACT
1668593 TTGTCATGGA
Statistics
Matches: 114, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
34 3 0.03
35 111 0.97
ACGTcount: A:0.35, C:0.25, G:0.09, T:0.31
Consensus pattern (35 bp):
AATACCATACCTACATTTCACAACTCAGTATGGAT
Found at i:1669626 original size:45 final size:46
Alignment explanation
Indices: 1669562--1669685 Score: 214
Period size: 45 Copynumber: 2.7 Consensus size: 46
1669552 GTCGAAATAG
*
1669562 GGTATCTTTCACCCATGGTCTTACACATTTCATATCATGTTGCC-T
1 GGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCAT
* *
1669607 GGTATCTTTCATCCATGGTCTTACACATTTCGTATCATGTTGCCAT
1 GGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCAT
1669653 GGTATCTTTCAACCATGGTCTTACACATTTCAT
1 GGTATCTTTCAACCATGGTCTTACACATTTCAT
1669686 TTCAGAAAGC
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
45 42 0.57
46 32 0.43
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (46 bp):
GGTATCTTTCAACCATGGTCTTACACATTTCATATCATGTTGCCAT
Found at i:1688890 original size:8 final size:8
Alignment explanation
Indices: 1688877--1688901 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1688867 GGTGTTCGGC
1688877 GCAAGTGG
1 GCAAGTGG
1688885 GCAAGTGG
1 GCAAGTGG
1688893 GCAAGTGG
1 GCAAGTGG
1688901 G
1 G
1688902 GGGTAGGTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.12, G:0.52, T:0.12
Consensus pattern (8 bp):
GCAAGTGG
Found at i:1697629 original size:91 final size:91
Alignment explanation
Indices: 1697474--1697652 Score: 313
Period size: 91 Copynumber: 2.0 Consensus size: 91
1697464 TGAGCAGCAC
* *
1697474 TTGAAGATGAACCATGCTTGAAGCTTACTACCATGAAAATGGGAAACTCTTTGTCATTGAAAAAG
1 TTGAAGATGAACCATGCTTGAAGATTACTACCATGAAAATGGGAAACTCATTGTCATTGAAAAAG
* *
1697539 AAGAAAATGTACATTTTGGGATTCAA
66 AAGAAAATATACATTTTGAGATTCAA
1697565 TTGAAGATGAACCATGCTTGAAGATTACTACCATGAAAATGGGAAACTCATTGTCATTGAAAAAG
1 TTGAAGATGAACCATGCTTGAAGATTACTACCATGAAAATGGGAAACTCATTGTCATTGAAAAAG
*
1697630 AATAAAATATACATTTTGAGATT
66 AAGAAAATATACATTTTGAGATT
1697653 TTATTCGTTT
Statistics
Matches: 83, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
91 83 1.00
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.29
Consensus pattern (91 bp):
TTGAAGATGAACCATGCTTGAAGATTACTACCATGAAAATGGGAAACTCATTGTCATTGAAAAAG
AAGAAAATATACATTTTGAGATTCAA
Found at i:1698202 original size:31 final size:31
Alignment explanation
Indices: 1698167--1698227 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
1698157 TTCCTGCTTT
*
1698167 AAATCCAACCAAAAACAGCAAATATAGCATG
1 AAATCCAACAAAAAACAGCAAATATAGCATG
*
1698198 AAATCCAACAAAAAACAGCAAATGTAGCAT
1 AAATCCAACAAAAAACAGCAAATATAGCAT
1698228 AAAAAATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.56, C:0.21, G:0.10, T:0.13
Consensus pattern (31 bp):
AAATCCAACAAAAAACAGCAAATATAGCATG
Found at i:1698492 original size:21 final size:21
Alignment explanation
Indices: 1698468--1698528 Score: 79
Period size: 21 Copynumber: 2.9 Consensus size: 21
1698458 TTATGCTCTG
1698468 CTCTG-CTACCCTCGCTGCTAC
1 CTCTGCCT-CCCTCGCTGCTAC
*
1698489 CTCTGCCTCCCTCGCTGCTAT
1 CTCTGCCTCCCTCGCTGCTAC
* *
1698510 CGCTGCCTCCTTCGCTGCT
1 CTCTGCCTCCCTCGCTGCT
1698529 GCATCTGCTC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 34 0.94
22 2 0.06
ACGTcount: A:0.05, C:0.48, G:0.16, T:0.31
Consensus pattern (21 bp):
CTCTGCCTCCCTCGCTGCTAC
Found at i:1698536 original size:21 final size:20
Alignment explanation
Indices: 1698476--1698536 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 20
1698466 TGCTCTGCTA
*
1698476 CCCTCGCTGCTACCTCTGCCT
1 CCCTCGCTGCT-CATCTGCCT
1698497 CCCTCGCTGCT-ATCGCTGCCT
1 CCCTCGCTGCTCAT--CTGCCT
*
1698518 CCTTCGCTGCTGCATCTGC
1 CCCTCGCTGCT-CATCTGC
1698537 TCTAAGTTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
19 1 0.03
21 31 0.91
23 2 0.06
ACGTcount: A:0.05, C:0.48, G:0.18, T:0.30
Consensus pattern (20 bp):
CCCTCGCTGCTCATCTGCCT
Found at i:1703592 original size:4 final size:4
Alignment explanation
Indices: 1703583--1703607 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1703573 TTGTCTTAAG
1703583 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1703608 GTTTTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1707381 original size:70 final size:71
Alignment explanation
Indices: 1707246--1707381 Score: 204
Period size: 70 Copynumber: 1.9 Consensus size: 71
1707236 GGAAAATAAT
* *
1707246 TTGGGGAAGACGCAGTTAGGGAAAATGAGAGAAAAGAAATTGGGTAAATGGGGGAATGAAATCGG
1 TTGGGGAAGACGCAGTTAGGGAAAATCAGAG-AAAGAAATTAGGTAAATGGGGGAATGAAATCGG
1707311 GTTTAAG
65 GTTTAAG
**
1707318 TTGGGGAAGACGCAGTTAGGGAAAATCATTG-AAGAAATTAGG-AAATTGGGGGAATGAAATCGG
1 TTGGGGAAGACGCAGTTAGGGAAAATCAGAGAAAGAAATTAGGTAAA-TGGGGGAATGAAATCGG
1707381 G
65 G
1707382 GTAATCAGAT
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
69 3 0.05
70 28 0.47
72 28 0.47
ACGTcount: A:0.38, C:0.05, G:0.37, T:0.20
Consensus pattern (71 bp):
TTGGGGAAGACGCAGTTAGGGAAAATCAGAGAAAGAAATTAGGTAAATGGGGGAATGAAATCGGG
TTTAAG
Found at i:1707681 original size:115 final size:114
Alignment explanation
Indices: 1707545--1707826 Score: 361
Period size: 115 Copynumber: 2.5 Consensus size: 114
1707535 GTTTTAAACA
* * * *
1707545 TTTTGCACAATCGTAAAACATTTTTGCGGTGTTTTATGAGAAAATGCCACTAAAGGATATCCTTT
1 TTTTGCACACTCTTAAAACATTTTTGCGGCGTTTTATGAGAAAATGCCACTAAAAGAT-TCCTTT
* *
1707610 TGCGGCGTTTTAGT-AAAAACGCCACTAATAGGCAGACAAAAACGACAGCC
65 TGCGGCG-TTTACTAAAAAACGCCACTAATAGGCAGAAAAAAACGACAGCC
* * * *
1707660 TTTTGCACACTCTTAAAACATTTTTCGTGGCGTTTAATGAGAAAATGCCACTAAAAGCTTCTTTT
1 TTTTGCACACTCTTAAAACATTTTT-GCGGCGTTTTATGAGAAAATGCCACTAAAAGATTCCTTT
** *
1707725 TGCGGCGTTTACTAAAAAACGCCACTAATAGTTAGAAAAAAACGACAGCG
65 TGCGGCGTTTACTAAAAAACGCCACTAATAGGCAGAAAAAAACGACAGCC
* * * * *
1707775 TTTTCCACACGCTTAAAACATATTTGCGGCGTTTTCTTA-AAAATGCCACTAA
1 TTTTGCACACTCTTAAAACATTTTTGCGGCGTTTTATGAGAAAATGCCACTAA
1707827 TAGTCAGAAA
Statistics
Matches: 145, Mismatches: 20, Indels: 6
0.85 0.12 0.04
Matches are distributed among these distances:
113 13 0.09
114 15 0.10
115 89 0.61
116 28 0.19
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.30
Consensus pattern (114 bp):
TTTTGCACACTCTTAAAACATTTTTGCGGCGTTTTATGAGAAAATGCCACTAAAAGATTCCTTTT
GCGGCGTTTACTAAAAAACGCCACTAATAGGCAGAAAAAAACGACAGCC
Found at i:1708272 original size:22 final size:22
Alignment explanation
Indices: 1708227--1708274 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1708217 ATGAATTTTT
* * **
1708227 TTTAAGATTTTAGGGTTTTTGG
1 TTTAAGAGTTTAGAGTTTAGGG
1708249 TTTAAGAGTTTAGAGTTTAGGG
1 TTTAAGAGTTTAGAGTTTAGGG
1708271 TTTA
1 TTTA
1708275 TAGTTTAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (22 bp):
TTTAAGAGTTTAGAGTTTAGGG
Found at i:1708279 original size:14 final size:14
Alignment explanation
Indices: 1708235--1708287 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
1708225 TTTTTAAGAT
* *
1708235 TTTAGGGTTTTTGG
1 TTTAGGGTTTATAG
* *
1708249 TTTAAGAGTTTAGAG
1 TTT-AGGGTTTATAG
1708264 TTTAGGGTTTATAG
1 TTTAGGGTTTATAG
*
1708278 TTTAAGGTTT
1 TTTAGGGTTT
1708288 GGAATTTAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (14 bp):
TTTAGGGTTTATAG
Found at i:1708280 original size:29 final size:28
Alignment explanation
Indices: 1708235--1708330 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 28
1708225 TTTTTAAGAT
* *
1708235 TTTAGGGTTTTTGGTTTAAGAGTTTAGAG
1 TTTAGGGTTTATAGTTTAAG-GTTTAGAG
* *
1708264 TTTAGGGTTTATAGTTTAAGGTTTGGAA
1 TTTAGGGTTTATAGTTTAAGGTTTAGAG
* **
1708292 TTTAAGGTCCATAGTTTATAGGTTTAGAGG
1 TTTAGGGTTTATAGTTTA-AGGTTTAGA-G
*
1708322 TTAAGGGTT
1 TTTAGGGTT
1708331 AGGAGTTAGG
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
28 21 0.40
29 26 0.49
30 6 0.11
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.45
Consensus pattern (28 bp):
TTTAGGGTTTATAGTTTAAGGTTTAGAG
Found at i:1708339 original size:21 final size:21
Alignment explanation
Indices: 1708315--1708364 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
1708305 GTTTATAGGT
1708315 TTAGAGGTTAA-GGGTTAGGAG
1 TTAG-GGTTAATGGGTTAGGAG
*
1708336 TTAGGGTTAATGGGTTAGGAT
1 TTAGGGTTAATGGGTTAGGAG
1708357 TTATGGGT
1 TTA-GGGT
1708365 CTAGTTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.23
21 16 0.62
22 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (21 bp):
TTAGGGTTAATGGGTTAGGAG
Found at i:1708932 original size:15 final size:15
Alignment explanation
Indices: 1708882--1708947 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
1708872 AATCATAAAA
1708882 CATAAA-CCATCAA-C
1 CATAAACCCAT-AATC
* *
1708896 CATAAACCC-CAACC
1 CATAAACCCATAATC
*
1708910 CTTAAACCCATAATC
1 CATAAACCCATAATC
* *
1708925 CCTAAACCCATCATC
1 CATAAACCCATAATC
1708940 CATAAACC
1 CATAAACC
1708948 TTAAAATAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
13 2 0.05
14 15 0.36
15 25 0.60
ACGTcount: A:0.42, C:0.41, G:0.00, T:0.17
Consensus pattern (15 bp):
CATAAACCCATAATC
Found at i:1710933 original size:21 final size:21
Alignment explanation
Indices: 1710909--1710958 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1710899 GGGTGCTTCC
*
1710909 GGAGGTTGTGGTGGTGGGGGT
1 GGAGGTTGTGGGGGTGGGGGT
1710930 GGAGGTTGTGGGGGTGGGGGT
1 GGAGGTTGTGGGGGTGGGGGT
1710951 GGAGGTTG
1 GGAGGTTG
1710959 ATGATGATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.06, C:0.00, G:0.68, T:0.26
Consensus pattern (21 bp):
GGAGGTTGTGGGGGTGGGGGT
Found at i:1712403 original size:4 final size:4
Alignment explanation
Indices: 1712394--1712418 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1712384 TTGTCTTAAG
1712394 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1712419 GTTTTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1716876 original size:8 final size:8
Alignment explanation
Indices: 1716865--1716938 Score: 78
Period size: 8 Copynumber: 8.9 Consensus size: 8
1716855 ATATTAAATA
1716865 TTAAATTT
1 TTAAATTT
*
1716873 TTAAGTTT
1 TTAAATTT
*
1716881 TTAAGTTT
1 TTAAATTT
1716889 TT-AATTT
1 TTAAATTT
1716896 TTAAATTT
1 TTAAATTT
*
1716904 TTAATTTTT
1 TTAA-ATTT
1716913 TTAAAGATTT
1 TT-AA-ATTT
1716923 TTATAATTT
1 TTA-AATTT
1716932 TTAAATT
1 TTAAATT
1716939 AACATATAAA
Statistics
Matches: 57, Mismatches: 5, Indels: 8
0.81 0.07 0.11
Matches are distributed among these distances:
7 6 0.11
8 30 0.53
9 13 0.23
10 8 0.14
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (8 bp):
TTAAATTT
Found at i:1716884 original size:23 final size:23
Alignment explanation
Indices: 1716858--1716907 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
1716848 AACTAAAATA
*
1716858 TTAAATATTAAATTTTTAAGTTT
1 TTAAATATTAAATTTTTAAATTT
* * *
1716881 TTAAGTTTTTAATTTTTAAATTT
1 TTAAATATTAAATTTTTAAATTT
1716904 TTAA
1 TTAA
1716908 TTTTTTTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (23 bp):
TTAAATATTAAATTTTTAAATTT
Found at i:1716908 original size:15 final size:15
Alignment explanation
Indices: 1716865--1716912 Score: 78
Period size: 15 Copynumber: 3.1 Consensus size: 15
1716855 ATATTAAATA
1716865 TTAAATTTTTAAGTTT
1 TTAAATTTTTAA-TTT
*
1716881 TTAAGTTTTTAATTT
1 TTAAATTTTTAATTT
1716896 TTAAATTTTTAATTT
1 TTAAATTTTTAATTT
1716911 TT
1 TT
1716913 TTAAAGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 19 0.63
16 11 0.37
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (15 bp):
TTAAATTTTTAATTT
Found at i:1716912 original size:23 final size:23
Alignment explanation
Indices: 1716868--1716913 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1716858 TTAAATATTA
*
1716868 AATTTTTAAGTTTTTAAGTTTTT
1 AATTTTTAAATTTTTAAGTTTTT
*
1716891 AATTTTTAAATTTTTAATTTTTT
1 AATTTTTAAATTTTTAAGTTTTT
1716914 TAAAGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.67
Consensus pattern (23 bp):
AATTTTTAAATTTTTAAGTTTTT
Found at i:1717126 original size:22 final size:22
Alignment explanation
Indices: 1717081--1717128 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
1717071 AAATTTTTTT
* * **
1717081 TTTAAGATTTTAGGGTTTTTGG
1 TTTAAGAGTTTAGAGTTTAGGG
1717103 TTTAAGAGTTTAGAGTTTAGGG
1 TTTAAGAGTTTAGAGTTTAGGG
1717125 TTTA
1 TTTA
1717129 TAGTTTAAGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.27, T:0.50
Consensus pattern (22 bp):
TTTAAGAGTTTAGAGTTTAGGG
Found at i:1717133 original size:14 final size:14
Alignment explanation
Indices: 1717089--1717141 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
1717079 TTTTTAAGAT
* *
1717089 TTTAGGGTTTTTGG
1 TTTAGGGTTTATAG
* *
1717103 TTTAAGAGTTTAGAG
1 TTT-AGGGTTTATAG
1717118 TTTAGGGTTTATAG
1 TTTAGGGTTTATAG
*
1717132 TTTAAGGTTT
1 TTTAGGGTTT
1717142 GGAATTTAAG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
14 21 0.68
15 10 0.32
ACGTcount: A:0.21, C:0.00, G:0.28, T:0.51
Consensus pattern (14 bp):
TTTAGGGTTTATAG
Found at i:1717134 original size:29 final size:28
Alignment explanation
Indices: 1717089--1717184 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 28
1717079 TTTTTAAGAT
* *
1717089 TTTAGGGTTTTTGGTTTAAGAGTTTAGAG
1 TTTAGGGTTTATAGTTTAAG-GTTTAGAG
* *
1717118 TTTAGGGTTTATAGTTTAAGGTTTGGAA
1 TTTAGGGTTTATAGTTTAAGGTTTAGAG
* **
1717146 TTTAAGGTCCATAGTTTATAGGTTTAGAGG
1 TTTAGGGTTTATAGTTTA-AGGTTTAGA-G
*
1717176 TTAAGGGTT
1 TTTAGGGTT
1717185 AGGAGTTAGG
Statistics
Matches: 53, Mismatches: 12, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
28 21 0.40
29 26 0.49
30 6 0.11
ACGTcount: A:0.24, C:0.02, G:0.29, T:0.45
Consensus pattern (28 bp):
TTTAGGGTTTATAGTTTAAGGTTTAGAG
Found at i:1717193 original size:21 final size:21
Alignment explanation
Indices: 1717169--1717218 Score: 66
Period size: 21 Copynumber: 2.3 Consensus size: 21
1717159 GTTTATAGGT
1717169 TTAGAGGTTAA-GGGTTAGGAG
1 TTAG-GGTTAATGGGTTAGGAG
*
1717190 TTAGGGTTAATGGGTTAGGAT
1 TTAGGGTTAATGGGTTAGGAG
1717211 TTATGGGT
1 TTA-GGGT
1717219 CTAGTTGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 6 0.23
21 16 0.62
22 4 0.15
ACGTcount: A:0.24, C:0.00, G:0.40, T:0.36
Consensus pattern (21 bp):
TTAGGGTTAATGGGTTAGGAG
Found at i:1717786 original size:15 final size:15
Alignment explanation
Indices: 1717736--1717801 Score: 57
Period size: 15 Copynumber: 4.5 Consensus size: 15
1717726 AATCATAAAA
1717736 CATAAA-CCATCAA-C
1 CATAAACCCAT-AATC
* *
1717750 CATAAACCC-CAACC
1 CATAAACCCATAATC
*
1717764 CTTAAACCCATAATC
1 CATAAACCCATAATC
* *
1717779 CCTAAACCCATCATC
1 CATAAACCCATAATC
1717794 CATAAACC
1 CATAAACC
1717802 TTAAAATAGT
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
13 2 0.05
14 15 0.36
15 25 0.60
ACGTcount: A:0.42, C:0.41, G:0.00, T:0.17
Consensus pattern (15 bp):
CATAAACCCATAATC
Found at i:1719787 original size:21 final size:21
Alignment explanation
Indices: 1719763--1719812 Score: 91
Period size: 21 Copynumber: 2.4 Consensus size: 21
1719753 GGGTGCTTCC
*
1719763 GGAGGTTGTGGTGGTGGGGGT
1 GGAGGTTGTGGGGGTGGGGGT
1719784 GGAGGTTGTGGGGGTGGGGGT
1 GGAGGTTGTGGGGGTGGGGGT
1719805 GGAGGTTG
1 GGAGGTTG
1719813 ATGATGATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.06, C:0.00, G:0.68, T:0.26
Consensus pattern (21 bp):
GGAGGTTGTGGGGGTGGGGGT
Found at i:1721257 original size:4 final size:4
Alignment explanation
Indices: 1721248--1721272 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1721238 TTGTCTTAAG
1721248 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1721273 GTTTTTTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1722403 original size:87 final size:86
Alignment explanation
Indices: 1722253--1722439 Score: 295
Period size: 87 Copynumber: 2.2 Consensus size: 86
1722243 TTTATTGGGA
* *
1722253 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGTGTTTGTGGGAAAAGCGCCGCTAAAGGTCAAG
1 AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGGGGGAAAAGCGCCGCTAAAGGTCAAG
1722318 GCTTTTAGCGGCGTTTGTGGT
66 GCTTTTAGCGGCGTTTGTGGT
*
1722339 AAAAGCGCCGCTAAAGGTCAAGGCTTTTTAGCGGCGTTTGGGGGAAAAGCGCCGCTAAAGGTCAA
1 AAAAACGCCGCTAAAGGTCAAGGC-TTTTAGCGGCGTTTGGGGGAAAAGCGCCGCTAAAGGTCAA
**
1722404 GGCTTTTAGCGGCGCTTT-TTTT
65 GGCTTTTAGCGGCG-TTTGTGGT
*
1722426 ACAAACGCCGCTAA
1 AAAAACGCCGCTAA
1722440 TTTTGGCAGA
Statistics
Matches: 92, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
86 23 0.25
87 66 0.72
88 3 0.03
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (86 bp):
AAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTGGGGGAAAAGCGCCGCTAAAGGTCAAG
GCTTTTAGCGGCGTTTGTGGT
Found at i:1722439 original size:43 final size:43
Alignment explanation
Indices: 1722248--1722417 Score: 286
Period size: 43 Copynumber: 3.9 Consensus size: 43
1722238 TGGCATTTAT
* *
1722248 TGGGAAAAAACGCCGCTAAAGGTCAAGGCTTTTAGCGGTGTTTG
1 TGGG-AAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTG
1722292 TGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTG
1 TGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTG
*
1722335 TGGTAAAAGCGCCGCTAAAGGTCAAGGCTTTTTAGCGGCGTTTG
1 TGGGAAAAGCGCCGCTAAAGGTCAAGGC-TTTTAGCGGCGTTTG
*
1722379 GGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCG
1 TGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCG
1722418 CTTTTTTTAC
Statistics
Matches: 120, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
43 75 0.62
44 45 0.38
ACGTcount: A:0.25, C:0.18, G:0.34, T:0.23
Consensus pattern (43 bp):
TGGGAAAAGCGCCGCTAAAGGTCAAGGCTTTTAGCGGCGTTTG
Found at i:1722527 original size:31 final size:31
Alignment explanation
Indices: 1722492--1722574 Score: 85
Period size: 31 Copynumber: 2.6 Consensus size: 31
1722482 CTTCCTGCAT
* *
1722492 TAAAATCCAACCAAATACAACAAATATAATA
1 TAAAATCCAACCAAAAACAACAAATATAACA
* * * *
1722523 TAAAATGCAGCCAAAAACAGCAAATTTAACA
1 TAAAATCCAACCAAAAACAACAAATATAACA
*
1722554 TAAAAAATACAACCAAAAACA
1 T--AAAATCCAACCAAAAACA
1722575 TTAATTCTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
31 26 0.62
33 16 0.38
ACGTcount: A:0.61, C:0.19, G:0.04, T:0.16
Consensus pattern (31 bp):
TAAAATCCAACCAAAAACAACAAATATAACA
Found at i:1727059 original size:29 final size:30
Alignment explanation
Indices: 1727000--1727057 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1726990 TCTGAGCCTT
*
1727000 GGGGAAAAAATGTAATTATGTAAAAGTTTA
1 GGGGAAAAAATGTAATTATGAAAAAGTTTA
* * *
1727030 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGAAAAAATGTAATTATGAAAAAGTT
1727058 AGAGTCGAGG
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:0.43, C:0.02, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGAAAAAATGTAATTATGAAAAAGTTTA
Found at i:1727287 original size:13 final size:13
Alignment explanation
Indices: 1727269--1727300 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
1727259 TTTCCAGCAA
1727269 TTATGAATTTATT
1 TTATGAATTTATT
1727282 TTATGAATTTATT
1 TTATGAATTTATT
*
1727295 TGATGA
1 TTATGA
1727301 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:1727508 original size:50 final size:50
Alignment explanation
Indices: 1727395--1728386 Score: 1761
Period size: 50 Copynumber: 19.7 Consensus size: 50
1727385 ATTTGGGTAA
* * * * *
1727395 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCA-TGGGAACC--GAGA-C--G
1727451 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1727501 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1727551 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1727601 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1727651 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1727701 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1727751 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1727801 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1727851 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1727901 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1727951 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1728001 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1728051 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1728101 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1728151 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1728201 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
* * * *
1728251 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
* * *
1728301 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGA-GACG
* ** *
1728351 AAAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 -AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGC
1728387 TTTGGCATGT
Statistics
Matches: 915, Mismatches: 19, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
49 1 0.00
50 840 0.92
51 30 0.03
52 1 0.00
53 3 0.00
55 6 0.01
56 34 0.04
ACGTcount: A:0.26, C:0.24, G:0.33, T:0.17
Consensus pattern (50 bp):
AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGAACCGAGACG
Found at i:1729593 original size:58 final size:58
Alignment explanation
Indices: 1729479--1729594 Score: 196
Period size: 58 Copynumber: 2.0 Consensus size: 58
1729469 AATTTTATGG
* **
1729479 TGAGTAGATATATGAGTCTAGTTTCAGGGAAAATTTACGGAATTAAATTTTGAGTTCT
1 TGAGTAGATATATGAGTCTAGTTTCAGGGAAAATTTACAGAATTAAATTTCAAGTTCT
*
1729537 TGAGTATATATATGAGTCTAGTTTCAGGGAAAATTTACAGAATTAAATTTCAAGTTCT
1 TGAGTAGATATATGAGTCTAGTTTCAGGGAAAATTTACAGAATTAAATTTCAAGTTCT
1729595 GTAGCTCAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 54 1.00
ACGTcount: A:0.34, C:0.08, G:0.20, T:0.38
Consensus pattern (58 bp):
TGAGTAGATATATGAGTCTAGTTTCAGGGAAAATTTACAGAATTAAATTTCAAGTTCT
Found at i:1732066 original size:9 final size:9
Alignment explanation
Indices: 1732052--1732239 Score: 91
Period size: 9 Copynumber: 20.4 Consensus size: 9
1732042 TATCTAAGTA
1732052 TTATGTAAG
1 TTATGTAAG
1732061 TTATGT-A-
1 TTATGTAAG
*
1732068 -TATCTAAG
1 TTATGTAAG
1732076 TATTATGTAAG
1 --TTATGTAAG
1732087 TTATGTAAG
1 TTATGTAAG
*
1732096 TTATGATATG
1 TTATG-TAAG
* * *
1732106 ATATAT-AT
1 TTATGTAAG
*
1732114 TTATGTAAA
1 TTATGTAAG
* *
1732123 TTATAT-AT
1 TTATGTAAG
*
1732131 TTATCTAAG
1 TTATGTAAG
*
1732140 TTATATAAG
1 TTATGTAAG
1732149 TTATGTAAG
1 TTATGTAAG
*
1732158 TTATGTAAA
1 TTATGTAAG
*
1732167 TTATGATATAAAA
1 TTATG---T-AAG
*
1732180 TATATTTAAG
1 T-TATGTAAG
1732190 TATTATGTAAG
1 --TTATGTAAG
1732201 TTATGTAAG
1 TTATGTAAG
* *
1732210 TTATAT-AT
1 TTATGTAAG
*
1732218 TTATCTAAG
1 TTATGTAAG
*
1732227 TTATATAAG
1 TTATGTAAG
1732236 TTAT
1 TTAT
1732240 NNNNNNNNNN
Statistics
Matches: 138, Mismatches: 25, Indels: 32
0.71 0.13 0.16
Matches are distributed among these distances:
6 4 0.03
7 1 0.01
8 17 0.12
9 84 0.61
10 8 0.06
11 15 0.11
12 2 0.01
13 4 0.03
14 3 0.02
ACGTcount: A:0.38, C:0.02, G:0.13, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:1732069 original size:26 final size:26
Alignment explanation
Indices: 1732040--1732093 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1732030 TGATATGATA
1732040 TATATCTAAGTATTATGTAAGTTATG
1 TATATCTAAGTATTATGTAAGTTATG
1732066 TATATCTAAGTATTATGTAAGTTATG
1 TATATCTAAGTATTATGTAAGTTATG
1732092 TA
1 TA
1732094 AGTTATGATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.35, C:0.04, G:0.15, T:0.46
Consensus pattern (26 bp):
TATATCTAAGTATTATGTAAGTTATG
Found at i:1732140 original size:44 final size:45
Alignment explanation
Indices: 1732087--1732235 Score: 125
Period size: 43 Copynumber: 3.4 Consensus size: 45
1732077 ATTATGTAAG
* * *
1732087 TTATGTAAGTTATGATATGATATAT-ATTTATGTAAATTAT-ATAT
1 TTATCTAAGTTAT-ATAAGATATATAAGTTATGTAAATTATGATAT
* *
1732131 TTATCTAAGTTATATAAGTTATGTAAGTTATGTAAATTATGATA-
1 TTATCTAAGTTATATAAGATATATAAGTTATGTAAATTATGATAT
* * * *
1732175 -TA---AAATATATTTAAGTATTATGTAAGTTATGTAAGTTAT-ATAT
1 TTATCTAAGT-TATATAAG-A-TATATAAGTTATGTAAATTATGATAT
1732218 TTATCTAAGTTATATAAG
1 TTATCTAAGTTATATAAG
1732236 TTATNNNNNN
Statistics
Matches: 84, Mismatches: 11, Indels: 18
0.74 0.10 0.16
Matches are distributed among these distances:
40 3 0.04
41 7 0.08
42 3 0.04
43 30 0.36
44 28 0.33
45 3 0.04
46 7 0.08
47 3 0.04
ACGTcount: A:0.40, C:0.01, G:0.12, T:0.47
Consensus pattern (45 bp):
TTATCTAAGTTATATAAGATATATAAGTTATGTAAATTATGATAT
Found at i:1732143 original size:26 final size:25
Alignment explanation
Indices: 1732050--1732171 Score: 84
Period size: 26 Copynumber: 4.6 Consensus size: 25
1732040 TATATCTAAG
*
1732050 TATTATGTAAGTTATGTATATCTA-A
1 TATTATGTAAGTTATGTAAAT-TATA
*
1732075 GTATTATGTAAGTTATGTAAGTTATGA
1 -TATTATGTAAGTTATGTAAATTAT-A
* * *
1732102 TATGATATATATTTATGTAAATTATA
1 TATTATGTA-AGTTATGTAAATTATA
* * * *
1732128 TATTTATCTAAGTTATATAAGTTATG
1 TA-TTATGTAAGTTATGTAAATTATA
*
1732154 TAAGTTATGTAAATTATG
1 T-A-TTATGTAAGTTATG
1732172 ATATAAAATA
Statistics
Matches: 75, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
25 2 0.03
26 42 0.56
27 31 0.41
ACGTcount: A:0.37, C:0.02, G:0.14, T:0.48
Consensus pattern (25 bp):
TATTATGTAAGTTATGTAAATTATA
Found at i:1732161 original size:71 final size:69
Alignment explanation
Indices: 1732016--1732239 Score: 222
Period size: 69 Copynumber: 3.2 Consensus size: 69
1732006 TTCGTAAGCT
* * * * * *
1732016 AGTTATGTAAGATATGATATGATATATATCTAAGTATTATGTAAGTTATGTATA-TCTA-AGTA-
1 AGTTATGTAAGTTATGATATAAAATATATTTAAGTATTATATAAGTTATCTA-AGT-TATA-TAG
1732078 TTATGTA
63 TTATGTA
* * * *
1732085 AGTTATGTAAGTTATGATATGATATATATTTATGTAAATTATAT-ATTTATCTAAGTTATATAAG
1 AGTTATGTAAGTTATGATATAAAATATATTTAAGT--ATTATATAAGTTATCTAAGTTATAT-AG
1732149 TTATGTA
63 TTATGTA
* * * *
1732156 AGTTATGTAAATTATGATATAAAATATATTTAAGTATTATGTAAGTTATGTAAGTTATATATTTA
1 AGTTATGTAAGTTATGATATAAAATATATTTAAGTATTATATAAGTTATCTAAGTTATATAGTTA
*
1732221 TCTA
66 TGTA
*
1732225 AGTTATATAAGTTAT
1 AGTTATGTAAGTTAT
1732240 NNNNNNNNNN
Statistics
Matches: 131, Mismatches: 17, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
69 62 0.47
70 25 0.19
71 44 0.34
ACGTcount: A:0.39, C:0.02, G:0.13, T:0.46
Consensus pattern (69 bp):
AGTTATGTAAGTTATGATATAAAATATATTTAAGTATTATATAAGTTATCTAAGTTATATAGTTA
TGTA
Found at i:1733522 original size:183 final size:183
Alignment explanation
Indices: 1733209--1733760 Score: 1014
Period size: 183 Copynumber: 3.0 Consensus size: 183
1733199 CCTAGAACAG
1733209 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
*
1733274 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGTAGGAGG
66 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
1733339 AGCAGGAATCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
131 AGCAGGAATCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
*
1733392 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTCAAGCAAATATAAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
*
1733457 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTTAGTTGAACCAATAGTTGCAGGAGG
66 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
*
1733522 AGTAGGAATCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
131 AGCAGGAATCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
*
1733575 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATGAAAACTTTATCTAT
1 ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
*
1733640 ATCAGTACCAAATATTAATTCGAATATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
66 ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
* * * *
1733705 AGCAGGAAGCAGTAACTGAAACATATACAACATTAATTCACTAATATAGACAC
131 AGCAGGAATCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
1733758 ATG
1 ATG
1733761 GAACTATATC
Statistics
Matches: 356, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
183 356 1.00
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (183 bp):
ATGTAAGATTATAAGAGTAGCACCAAATATATTTCAGTTTAAGCAAATATAAAAACTTTATCTAT
ATCAGTACCAAATATTAATTCGAAGATTAAATGGCAGCTTCAGTTGAACCAATAGTTGCAGGAGG
AGCAGGAATCAGTAACTGAAATACATACAACATTAATTCACTAATACAGACAC
Found at i:1736702 original size:15 final size:15
Alignment explanation
Indices: 1736682--1736730 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
1736672 GGTAAAAATT
1736682 TTGGGGGAGAAGAAG
1 TTGGGGGAGAAGAAG
*
1736697 TT-GGGG-G-A-AAT
1 TTGGGGGAGAAGAAG
1736708 TTGGGGGAGAAGAAG
1 TTGGGGGAGAAGAAG
1736723 TTGGGGGA
1 TTGGGGGA
1736731 AATCGGGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
11 4 0.14
12 5 0.18
13 2 0.07
14 5 0.18
15 12 0.43
ACGTcount: A:0.29, C:0.00, G:0.53, T:0.18
Consensus pattern (15 bp):
TTGGGGGAGAAGAAG
Found at i:1736712 original size:26 final size:26
Alignment explanation
Indices: 1736681--1736733 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
1736671 GGGTAAAAAT
1736681 TTTGGGGGAGAAGAAGTTGGGGGAAA
1 TTTGGGGGAGAAGAAGTTGGGGGAAA
1736707 TTTGGGGGAGAAGAAGTTGGGGGAAA
1 TTTGGGGGAGAAGAAGTTGGGGGAAA
1736733 T
1 T
1736734 CGGGGAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.30, C:0.00, G:0.49, T:0.21
Consensus pattern (26 bp):
TTTGGGGGAGAAGAAGTTGGGGGAAA
Found at i:1737043 original size:28 final size:28
Alignment explanation
Indices: 1737011--1737068 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
1737001 AATCAAAACT
*
1737011 CTAT-ACCTTAAACCATTAAACTATATCC
1 CTATAACCTTAAACC-CTAAACTATATCC
* *
1737039 CTATAACCTTAATCCCTAAAGTATATCC
1 CTATAACCTTAAACCCTAAACTATATCC
1737067 CT
1 CT
1737069 TAAACCCTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 17 0.65
29 9 0.35
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (28 bp):
CTATAACCTTAAACCCTAAACTATATCC
Found at i:1737069 original size:21 final size:21
Alignment explanation
Indices: 1737045--1737088 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1737035 ATCCCTATAA
* *
1737045 CCTTAATCCCTAAAGTATATC
1 CCTTAAACCCTAAACTATATC
1737066 CCTTAAACCCTAAACTATATC
1 CCTTAAACCCTAAACTATATC
1737087 CC
1 CC
1737089 CTAACCATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.34, C:0.34, G:0.02, T:0.30
Consensus pattern (21 bp):
CCTTAAACCCTAAACTATATC
Found at i:1737351 original size:21 final size:22
Alignment explanation
Indices: 1737316--1737363 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
1737306 AGTATTAACC
1737316 CCAT-AACCCCTAACCCTTAAA
1 CCATAAACCCCTAACCCTTAAA
*
1737337 TCATAAACCCC-AACCCTTAAA
1 CCATAAACCCCTAACCCTTAAA
1737358 CCATAA
1 CCATAA
1737364 TACATAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.42, C:0.40, G:0.00, T:0.19
Consensus pattern (22 bp):
CCATAAACCCCTAACCCTTAAA
Found at i:1737494 original size:41 final size:41
Alignment explanation
Indices: 1737437--1737574 Score: 215
Period size: 41 Copynumber: 3.4 Consensus size: 41
1737427 AACCCTAAAC
*
1737437 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCAA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCTA
*
1737478 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTTA
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCTA
* * *
1737519 TTTTTAGCGGCGTTTTACCAAAAGCGCTGCTATTGCT-CTG
1 TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCTA
*
1737559 TTTTTAGCGGTGTTTT
1 TTTTTAGCGGCGTTTT
1737575 TGGTAAAACA
Statistics
Matches: 90, Mismatches: 7, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
40 16 0.18
41 74 0.82
ACGTcount: A:0.20, C:0.22, G:0.21, T:0.37
Consensus pattern (41 bp):
TTTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCCTA
Found at i:1737644 original size:12 final size:12
Alignment explanation
Indices: 1737629--1737654 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1737619 CTTTTTTGAG
1737629 AAAACGCCGCTA
1 AAAACGCCGCTA
1737641 AAAACGCCGCTA
1 AAAACGCCGCTA
1737653 AA
1 AA
1737655 GACCTGTTTT
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:0.46, C:0.31, G:0.15, T:0.08
Consensus pattern (12 bp):
AAAACGCCGCTA
Found at i:1740844 original size:201 final size:201
Alignment explanation
Indices: 1740499--1740897 Score: 755
Period size: 201 Copynumber: 2.0 Consensus size: 201
1740489 ACCAAGAATG
1740499 TAAAGTCTATGTGCTTTGACTTTGATGTGCTCCTATATTTATTGGAATAAAAGGCTGTAATTTGT
1 TAAAGTCTATGTGCTTTGACTTTGATGTGCTCCTATATTTATTGGAATAAAAGGCTGTAATTTGT
1740564 TTCCACAATTTACACCTTAGTGACAAAATCTTGAATCCATATTCCATCAAAATCGAAGTTTGTAT
66 TTCCACAATTTACACCTTAGTGACAAAATCTTGAATCCATATTCCATCAAAATCGAAGTTTGTAT
* *
1740629 ATCTAATATCTTTAATTTATCAGACCTCCAATATGTGAGCATGTAATATTTTATTCTCTGAAGAT
131 ATCTAATATCTTTAACTTATCAAACCTCCAATATGTGAGCATGTAATATTTTATTCTCTGAAGAT
1740694 ACAATT
196 ACAATT
1740700 TAAAGTCTATGTGCTTTGACTTTGATGTGCTCCTATATTTATTGGAATAAAAGGCTGTAATTTGT
1 TAAAGTCTATGTGCTTTGACTTTGATGTGCTCCTATATTTATTGGAATAAAAGGCTGTAATTTGT
1740765 TTCCACAATTTACACCTTAGTGACAAAATCTTGAATCCATATTCCATCAAAATCGAAGTTTGTAT
66 TTCCACAATTTACACCTTAGTGACAAAATCTTGAATCCATATTCCATCAAAATCGAAGTTTGTAT
*
1740830 A-CTTGATATCTTTAACTTATCAAACCTCCAATATGTGAGCATGTAATATTTTATTCTCTGAAGA
131 ATC-TAATATCTTTAACTTATCAAACCTCCAATATGTGAGCATGTAATATTTTATTCTCTGAAGA
1740894 TACA
195 TACA
1740898 TCATAACTCT
Statistics
Matches: 194, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
200 1 0.01
201 193 0.99
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (201 bp):
TAAAGTCTATGTGCTTTGACTTTGATGTGCTCCTATATTTATTGGAATAAAAGGCTGTAATTTGT
TTCCACAATTTACACCTTAGTGACAAAATCTTGAATCCATATTCCATCAAAATCGAAGTTTGTAT
ATCTAATATCTTTAACTTATCAAACCTCCAATATGTGAGCATGTAATATTTTATTCTCTGAAGAT
ACAATT
Found at i:1746241 original size:44 final size:44
Alignment explanation
Indices: 1746175--1746263 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
1746165 TACTTATATG
1746175 TTTATATCAAAGCTATCAACTTAAGTCATAGTCACTAAATTATT
1 TTTATATCAAAGCTATCAACTTAAGTCATAGTCACTAAATTATT
* *
1746219 TTTATATCAAAGCTGTCCACTTAAGTCATAGTCACTAAATTATT
1 TTTATATCAAAGCTATCAACTTAAGTCATAGTCACTAAATTATT
1746263 T
1 T
1746264 ATATCGTGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.36, C:0.17, G:0.08, T:0.39
Consensus pattern (44 bp):
TTTATATCAAAGCTATCAACTTAAGTCATAGTCACTAAATTATT
Found at i:1747286 original size:11 final size:11
Alignment explanation
Indices: 1747270--1747311 Score: 57
Period size: 11 Copynumber: 3.6 Consensus size: 11
1747260 TAGCTATTTA
1747270 TAATAAAATAT
1 TAATAAAATAT
1747281 TAATAAAATAT
1 TAATAAAATAT
*
1747292 CTCATTAAAATAT
1 -T-AATAAAATAT
1747305 TAATAAA
1 TAATAAA
1747312 GTAATATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 16 0.59
12 2 0.07
13 9 0.33
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATAAAATAT
Found at i:1757340 original size:19 final size:19
Alignment explanation
Indices: 1757318--1757356 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
1757308 TGAAGTTAGT
1757318 ATCAGAGAGTCGGTTGATA
1 ATCAGAGAGTCGGTTGATA
*
1757337 ATCAGAGGGTCGGTTGATA
1 ATCAGAGAGTCGGTTGATA
1757356 A
1 A
1757357 CGATAAATGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.33, T:0.26
Consensus pattern (19 bp):
ATCAGAGAGTCGGTTGATA
Found at i:1763093 original size:44 final size:44
Alignment explanation
Indices: 1763036--1763283 Score: 166
Period size: 44 Copynumber: 5.6 Consensus size: 44
1763026 CTTAGCAAAC
* * * * *
1763036 CTTATCTCTCTGAAGTTATAGTAGAGCGGGTTAAAGTAGCAAGT
1 CTTATCTCCCTGAAGTTGTAGTGGAGCGGCTGAAAGTAGCAAGT
* * *
1763080 CTTATCTCCCTGAAGATGTAGTGGAGTAGACTGAAAGTAGC-AGAT
1 CTTATCTCCCTGAAGTTGTAGTGGAG-CGGCTGAAAGTAGCAAG-T
** *** * *
1763125 CTTATCTCCCTGAAGTTACAGTGGAAAAGATCG-AAGCCA-CAA-T
1 CTTATCTCCCTGAAGTTGTAGTGGAGCGGCT-GAAAG-TAGCAAGT
* * * * *
1763168 CCTTATCTCTCTGAAGTTGCAGTAGAGCGGGTTAAAGTAGCAAGT
1 -CTTATCTCCCTGAAGTTGTAGTGGAGCGGCTGAAAGTAGCAAGT
* * *
1763213 ATTATCTCCCT-AAGTTGTAGTGGAGCAGACTGAAAATAGC-AGAT
1 CTTATCTCCCTGAAGTTGTAGTGGAGC-GGCTGAAAGTAGCAAG-T
* *
1763257 CTTGTCTCCCTGAAGTTGCAGTGGAGC
1 CTTATCTCCCTGAAGTTGTAGTGGAGC
1763284 AATCGAAGCC
Statistics
Matches: 156, Mismatches: 36, Indels: 23
0.73 0.17 0.11
Matches are distributed among these distances:
43 17 0.11
44 88 0.56
45 51 0.33
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGTAGTGGAGCGGCTGAAAGTAGCAAGT
Found at i:1763128 original size:45 final size:43
Alignment explanation
Indices: 1763068--1763282 Score: 177
Period size: 44 Copynumber: 4.9 Consensus size: 43
1763058 AGAGCGGGTT
* *
1763068 AAAGTAGCAAGTCTTATCTCCCTGAAGATGTAGTGGAGTAGACTG
1 AAAGTAGCAA-TCTTATCTCCCTGAAGTTGCAGTGGAG-AGACTG
* *
1763113 AAAGTAGCAGATCTTATCTCCCTGAAGTTACAGTGGAAAAGA-TCG
1 AAAGTAGCA-ATCTTATCTCCCTGAAGTTGCAGTGG-AGAGACT-G
* * * * ** *
1763158 -AAGCCA-CAATCCTTATCTCTCTGAAGTTGCAGTAGAGCGGGTT
1 AAAG-TAGCAAT-CTTATCTCCCTGAAGTTGCAGTGGAGAGACTG
* *
1763201 AAAGTAGCAAGTATTATCTCCCT-AAGTTGTAGTGGAGCAGACTG
1 AAAGTAGCAA-TCTTATCTCCCTGAAGTTGCAGTGGAG-AGACTG
* *
1763245 AAAATAGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAG
1 AAAGTAGCA-ATCTTATCTCCCTGAAGTTGCAGTGGAG
1763283 CAATCGAAGC
Statistics
Matches: 133, Mismatches: 25, Indels: 24
0.73 0.14 0.13
Matches are distributed among these distances:
43 17 0.13
44 63 0.47
45 51 0.38
46 2 0.02
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.27
Consensus pattern (43 bp):
AAAGTAGCAATCTTATCTCCCTGAAGTTGCAGTGGAGAGACTG
Found at i:1763310 original size:133 final size:132
Alignment explanation
Indices: 1763035--1763426 Score: 500
Period size: 133 Copynumber: 2.9 Consensus size: 132
1763025 TCTTAGCAAA
* * *
1763035 CCTTATCTCTCTGAAGTTATAGTAGAGCGGGTTAAAGTAGCAAGTCTTATCTCCCTGAAGATGTA
1 CCTTATCTCTCTGAAGTTACAGTAGAGCGGGTTAAAGTAGCAAGTCTTATCTCCCTAAAGTTGTA
* * *
1763100 GTGGAGTAGACTGAAAGTAGCAGATCTTATCTCCCTGAAGTTACAGTGGAAAAGATCGAAGCCAC
66 GTGGAGCAGACTGAAAATAGCAGATCTT-TCTCCCTGAAGTTACAGTGGAGAAGATCGAAGCCAC
1763165 AAT
130 AAT
* *
1763168 CCTTATCTCTCTGAAGTTGCAGTAGAGCGGGTTAAAGTAGCAAGTATTATCTCCCT-AAGTTGTA
1 CCTTATCTCTCTGAAGTTACAGTAGAGCGGGTTAAAGTAGCAAGTCTTATCTCCCTAAAGTTGTA
* *
1763232 GTGGAGCAGACTGAAAATAGCAGATCTTGTCTCCCTGAAGTTGCAGTGGAGCA-ATCGAAGCCAC
66 GTGGAGCAGACTGAAAATAGCAGATCTT-TCTCCCTGAAGTTACAGTGGAGAAGATCGAAGCCAC
1763296 AAT
130 AAT
* * * * * * * *
1763299 CCTTATCTCTCTGAAGTTACAATAAAGCAGGATAAAATTACCCAAGTCTAATATCCCTAAAGTTG
1 CCTTATCTCTCTGAAGTTACAGTAGAGC-GGGTTAAAGTA-GCAAGTCTTATCTCCCTAAAGTTG
* * * * * * *
1763364 CAGTGGAGCAAACTGAAATTAGCAGATCTATTCTCCCTAAAGTTCCAGCGGAGTAGATCGAAG
64 TAGTGGAGCAGACTGAAAATAGCAGATCT-TTCTCCCTGAAGTTACAGTGGAGAAGATCGAAG
1763427 TTAAAAATCT
Statistics
Matches: 227, Mismatches: 27, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
131 39 0.17
132 62 0.27
133 66 0.29
134 52 0.23
135 8 0.04
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.27
Consensus pattern (132 bp):
CCTTATCTCTCTGAAGTTACAGTAGAGCGGGTTAAAGTAGCAAGTCTTATCTCCCTAAAGTTGTA
GTGGAGCAGACTGAAAATAGCAGATCTTTCTCCCTGAAGTTACAGTGGAGAAGATCGAAGCCACA
AT
Found at i:1776418 original size:40 final size:40
Alignment explanation
Indices: 1776340--1776420 Score: 119
Period size: 40 Copynumber: 2.0 Consensus size: 40
1776330 TTAGTAGTTA
** *
1776340 AAACTATACTTATGTAATTCAGAAGACCATAAGATATGAT
1 AAACTATACTTACATAATTCAGAAGACCACAAGATATGAT
1776380 AAACTATACTTACATAATTCAGAAGACCACAATG-TATGAT
1 AAACTATACTTACATAATTCAGAAGACCACAA-GATATGAT
1776420 A
1 A
1776421 TGATGTGATA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 36 0.97
41 1 0.03
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (40 bp):
AAACTATACTTACATAATTCAGAAGACCACAAGATATGAT
Found at i:1777115 original size:10 final size:10
Alignment explanation
Indices: 1777100--1777159 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
1777090 AAATTTTAGG
1777100 ATTTAT-TTT
1 ATTTATCTTT
1777109 CATTTATCTTT
1 -ATTTATCTTT
1777120 ATTTATCTTT
1 ATTTATCTTT
*
1777130 AATTATCTTT
1 ATTTATCTTT
1777140 ATTTAT-TTGT
1 ATTTATCTT-T
1777150 ATTTATCTTT
1 ATTTATCTTT
1777160 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:1777466 original size:54 final size:54
Alignment explanation
Indices: 1777402--1777507 Score: 185
Period size: 54 Copynumber: 2.0 Consensus size: 54
1777392 AAGGTTCATA
1777402 AGGCTTAGAACCCGCACTTAGCCTTCTCAACAAGGTATTCATCACTTCTCCGTG
1 AGGCTTAGAACCCGCACTTAGCCTTCTCAACAAGGTATTCATCACTTCTCCGTG
* * *
1777456 AGGCTTAGAACTCGCGCTTAGCTTTCTCAACAAGGTATTCATCACTTCTCCG
1 AGGCTTAGAACCCGCACTTAGCCTTCTCAACAAGGTATTCATCACTTCTCCG
1777508 CATTACAGGG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (54 bp):
AGGCTTAGAACCCGCACTTAGCCTTCTCAACAAGGTATTCATCACTTCTCCGTG
Found at i:1778139 original size:12 final size:12
Alignment explanation
Indices: 1778122--1778154 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
1778112 CTACTTCCCC
1778122 TTTACTATTATT
1 TTTACTATTATT
1778134 TTTACTATTATT
1 TTTACTATTATT
1778146 TTTACTATT
1 TTTACTATT
1778155 TTACAGGGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTACTATTATT
Found at i:1783577 original size:5 final size:5
Alignment explanation
Indices: 1783569--1783637 Score: 92
Period size: 5 Copynumber: 14.4 Consensus size: 5
1783559 ATTTTTTATT
1783569 TTTTA TTTTTA TTTTA TTTTA TTTTA -TTTA TTTTA TTTTA TTTTA -TTTA
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
*
1783618 TTTTA TCTTA --TTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TT
1783638 ATCTATTATT
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
3 3 0.05
4 8 0.14
5 42 0.72
6 5 0.09
ACGTcount: A:0.20, C:0.01, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1783577 original size:14 final size:14
Alignment explanation
Indices: 1783558--1783649 Score: 57
Period size: 14 Copynumber: 6.4 Consensus size: 14
1783548 GGAGGCAACC
1783558 TATTTTTTATTTTT
1 TATTTTTTATTTTT
1783572 TA-TTTTTATTTTAT
1 TATTTTTTATTTT-T
1783586 T-TTATTTTATTTATT
1 TATT-TTTTATTT-TT
*
1783601 T-TATTTTATTTTAT
1 TATTTTTTATTTT-T
* *
1783615 T-TATTTTATCTTAT
1 TATTTTTTAT-TTTT
* *
1783629 TATTTTATTATCTAT
1 TATTTT-TTATTTTT
1783644 TATTTT
1 TATTTT
1783650 CATATATTAA
Statistics
Matches: 66, Mismatches: 4, Indels: 15
0.78 0.05 0.18
Matches are distributed among these distances:
13 11 0.17
14 25 0.38
15 25 0.38
16 5 0.08
ACGTcount: A:0.21, C:0.02, G:0.00, T:0.77
Consensus pattern (14 bp):
TATTTTTTATTTTT
Found at i:1783598 original size:19 final size:19
Alignment explanation
Indices: 1783562--1783629 Score: 104
Period size: 19 Copynumber: 3.6 Consensus size: 19
1783552 GCAACCTATT
1783562 TTTTATTTT-TTATT-TTTA
1 TTTTATTTTATT-TTATTTA
1783580 TTTTATTTTATTTTATTTA
1 TTTTATTTTATTTTATTTA
1783599 TTTTATTTTATTTTATTTA
1 TTTTATTTTATTTTATTTA
*
1783618 TTTTATCTTATT
1 TTTTATTTTATT
1783630 ATTTTATTAT
Statistics
Matches: 47, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
18 11 0.23
19 36 0.77
ACGTcount: A:0.19, C:0.01, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTATTTTATTTTATTTA
Found at i:1785208 original size:10 final size:10
Alignment explanation
Indices: 1785193--1785252 Score: 79
Period size: 10 Copynumber: 6.0 Consensus size: 10
1785183 AAATTTTAGG
1785193 ATTTAT-TTT
1 ATTTATCTTT
1785202 CATTTATCTTT
1 -ATTTATCTTT
1785213 ATTTATCTTT
1 ATTTATCTTT
*
1785223 AATTATCTTT
1 ATTTATCTTT
1785233 ATTTAT-TTGT
1 ATTTATCTT-T
1785243 ATTTATCTTT
1 ATTTATCTTT
1785253 TAGAATTTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
9 2 0.04
10 38 0.84
11 5 0.11
ACGTcount: A:0.22, C:0.08, G:0.02, T:0.68
Consensus pattern (10 bp):
ATTTATCTTT
Found at i:1785465 original size:55 final size:55
Alignment explanation
Indices: 1785399--1785513 Score: 214
Period size: 55 Copynumber: 2.1 Consensus size: 55
1785389 CTTCAATAAA
1785399 AATCT-CATTTACATTATATTTATTTCTTTCCCAAAAATCATGAGACACTAAACC
1 AATCTACATTTACATTATATTTATTTCTTTCCCAAAAATCATGAGACACTAAACC
*
1785453 AATCTACATTTACATTATATTTATTTCTTTCCCAAAAATCATGAGCCACTAAACC
1 AATCTACATTTACATTATATTTATTTCTTTCCCAAAAATCATGAGACACTAAACC
1785508 AATCTA
1 AATCTA
1785514 GCCGAAGGTT
Statistics
Matches: 59, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
54 5 0.08
55 54 0.92
ACGTcount: A:0.37, C:0.23, G:0.03, T:0.37
Consensus pattern (55 bp):
AATCTACATTTACATTATATTTATTTCTTTCCCAAAAATCATGAGACACTAAACC
Found at i:1786233 original size:12 final size:12
Alignment explanation
Indices: 1786216--1786249 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
1786206 CCTACTTCCC
1786216 TTTTACTATTAT
1 TTTTACTATTAT
1786228 TTTTACTATTAT
1 TTTTACTATTAT
1786240 TTTTACTATT
1 TTTTACTATT
1786250 TTAAATGGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTACTATTAT
Found at i:1787764 original size:26 final size:26
Alignment explanation
Indices: 1787693--1787771 Score: 106
Period size: 26 Copynumber: 3.0 Consensus size: 26
1787683 CTAATTTAGC
* * *
1787693 ATTACTTTTGAGAAGTGCTGTGGAAAA
1 ATTA-TTTTGAGAAGTACTTTTGAAAA
*
1787720 GTTATTTTGAGAAGTACTTTTGAAAA
1 ATTATTTTGAGAAGTACTTTTGAAAA
1787746 ATTATTTTGAGAAGTACTTTT-AAAA
1 ATTATTTTGAGAAGTACTTTTGAAAA
1787771 A
1 A
1787772 GTTTAGTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 5 0.11
26 39 0.83
27 3 0.06
ACGTcount: A:0.37, C:0.05, G:0.19, T:0.39
Consensus pattern (26 bp):
ATTATTTTGAGAAGTACTTTTGAAAA
Found at i:1787766 original size:13 final size:13
Alignment explanation
Indices: 1787695--1787766 Score: 58
Period size: 13 Copynumber: 5.5 Consensus size: 13
1787685 AATTTAGCAT
1787695 TACTTTTGAGAAG
1 TACTTTTGAGAAG
* * * *
1787708 TGCTGTGGAAAAG
1 TACTTTTGAGAAG
1787721 TTA-TTTTGAGAAG
1 -TACTTTTGAGAAG
* *
1787734 TACTTTTGAAAAAT
1 TACTTTTG-AGAAG
1787748 TA-TTTTGAGAAG
1 TACTTTTGAGAAG
1787760 TACTTTT
1 TACTTTT
1787767 AAAAAGTTTA
Statistics
Matches: 43, Mismatches: 12, Indels: 8
0.68 0.19 0.13
Matches are distributed among these distances:
12 7 0.16
13 30 0.70
14 6 0.14
ACGTcount: A:0.32, C:0.06, G:0.21, T:0.42
Consensus pattern (13 bp):
TACTTTTGAGAAG
Found at i:1789119 original size:30 final size:30
Alignment explanation
Indices: 1789083--1789206 Score: 202
Period size: 30 Copynumber: 4.3 Consensus size: 30
1789073 CTAGCCTTTG
*
1789083 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCTACTCCACTAGCCACACTTGCT
1789113 CCACCACCTACTCCACTAGCCACACTTGCT
1 CCACCACCTACTCCACTAGCCACACTTGCT
1789143 ----CACCTACTCCACTAGCCACACTTGCT
1 CCACCACCTACTCCACTAGCCACACTTGCT
*
1789169 CCACCACCTACTCCATTAGCCACACTTGCT
1 CCACCACCTACTCCACTAGCCACACTTGCT
1789199 CCACCACC
1 CCACCACC
1789207 ACTTGTACCT
Statistics
Matches: 88, Mismatches: 2, Indels: 8
0.90 0.02 0.08
Matches are distributed among these distances:
26 26 0.30
30 62 0.70
ACGTcount: A:0.24, C:0.50, G:0.06, T:0.19
Consensus pattern (30 bp):
CCACCACCTACTCCACTAGCCACACTTGCT
Found at i:1789153 original size:56 final size:56
Alignment explanation
Indices: 1789087--1789204 Score: 209
Period size: 56 Copynumber: 2.1 Consensus size: 56
1789077 CCTTTGCCAC
1789087 CACCAACTCCACTAGCCACACTTGCTCCACCACCTACTCCACTAGCCACACTTGCT
1 CACCAACTCCACTAGCCACACTTGCTCCACCACCTACTCCACTAGCCACACTTGCT
* *
1789143 CACCTACTCCACTAGCCACACTTGCTCCACCACCTACTCCATTAGCCACACTTGCT
1 CACCAACTCCACTAGCCACACTTGCTCCACCACCTACTCCACTAGCCACACTTGCT
1789199 CCACCA
1 -CACCA
1789205 CCACTTGTAC
Statistics
Matches: 58, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
56 54 0.93
57 4 0.07
ACGTcount: A:0.25, C:0.48, G:0.07, T:0.20
Consensus pattern (56 bp):
CACCAACTCCACTAGCCACACTTGCTCCACCACCTACTCCACTAGCCACACTTGCT
Found at i:1789809 original size:25 final size:25
Alignment explanation
Indices: 1789686--1789894 Score: 98
Period size: 25 Copynumber: 8.6 Consensus size: 25
1789676 TTTTTTTTGT
* *
1789686 TATTAT-TATAT-TTTTTAATATTA
1 TATTATGTATATATCTTTAATACTA
* *
1789709 TATTATATATAT-TCTTT--TAATA
1 TATTATGTATATATCTTTAATACTA
* * *
1789731 TATTAGGTATAT-TC-TAAATTCTA
1 TATTATGTATATATCTTTAATACTA
* *
1789754 TATTACGTATATATATATT-ATACTA
1 TATTATGTATATATCT-TTAATACTA
*
1789779 TTTTATGTATATATCTTTAATACTA
1 TATTATGTATATATCTTTAATACTA
* * * **
1789804 TATTATTTATATTTTTTTTTCTACATGTTA
1 TATTATGTATA---TATCTT-TA-ATACTA
*
1789834 TCTTATGTATATAT-TTTAAT--TA
1 TATTATGTATATATCTTTAATACTA
* * * *
1789856 TATTATGTATGTATTTTTTACACTA
1 TATTATGTATATATCTTTAATACTA
*
1789881 TATTATGTACATAT
1 TATTATGTATATAT
1789895 TTTTTTTATA
Statistics
Matches: 142, Mismatches: 29, Indels: 28
0.71 0.15 0.14
Matches are distributed among these distances:
21 1 0.01
22 30 0.21
23 24 0.17
24 14 0.10
25 49 0.35
26 3 0.02
27 2 0.01
28 4 0.03
29 2 0.01
30 13 0.09
ACGTcount: A:0.33, C:0.06, G:0.04, T:0.57
Consensus pattern (25 bp):
TATTATGTATATATCTTTAATACTA
Found at i:1789815 original size:50 final size:49
Alignment explanation
Indices: 1789703--1789815 Score: 111
Period size: 50 Copynumber: 2.3 Consensus size: 49
1789693 ATATTTTTTA
* * *
1789703 ATATTATATTATATATATTCTTTTAATATATTAGGTATATTCTAAATTCT
1 ATATTAT-TTATATATATTATTATAATATATTAGGTATATTCTAAATACT
** * * * *
1789753 ATATTACGTATATATA-TATTATACTATTTTATGTATATATCTTTAATACT
1 ATATTATTTATATATATTATTATAATATATTAGGTATAT-TC-TAAATACT
1789803 ATATTATTTATAT
1 ATATTATTTATAT
1789816 TTTTTTTTCT
Statistics
Matches: 50, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
48 17 0.34
49 10 0.20
50 23 0.46
ACGTcount: A:0.36, C:0.06, G:0.04, T:0.54
Consensus pattern (49 bp):
ATATTATTTATATATATTATTATAATATATTAGGTATATTCTAAATACT
Found at i:1789989 original size:25 final size:24
Alignment explanation
Indices: 1789961--1790016 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 24
1789951 GTTATATTTT
*
1789961 CACTATTTTAT-GTATATACTTCAAA
1 CACTATTATATAGTATAT--TTCAAA
*
1789986 CACTA-TATATAGTATATTTCTAA
1 CACTATTATATAGTATATTTCAAA
1790009 CACTATTA
1 CACTATTA
1790017 CTATTTATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
23 10 0.37
24 6 0.22
25 11 0.41
ACGTcount: A:0.38, C:0.16, G:0.04, T:0.43
Consensus pattern (24 bp):
CACTATTATATAGTATATTTCAAA
Found at i:1792988 original size:43 final size:42
Alignment explanation
Indices: 1792917--1793294 Score: 183
Period size: 43 Copynumber: 8.8 Consensus size: 42
1792907 TTATGTGAAA
* * * * *
1792917 AAAACGCCACTAAAAGT-CATCACTTTTAGCGGCGTTTGAACGG
1 AAAACGCCGCTAAAAGTACA-GACCTTTAGCGGCGTTT-ATCGC
* * *
1792960 AAAACGCCGCTAAAAGTAGATACCTTTAGCGGCACTTTAT--C
1 AAAACGCCGCTAAAAGTACAGACCTTTAGCGGC-GTTTATCGC
* * * * * **
1793001 ATAAACGCCGCTAATAGTATAGAACTTTAGCGGCGCTTAGCAA
1 A-AAACGCCGCTAAAAGTACAGACCTTTAGCGGCGTTTATCGC
* * *
1793044 ACAAACACCGCTAAAAGTACATACCTTTAGCGGCGTTT-TACCC
1 A-AAACGCCGCTAAAAGTACAGACCTTTAGCGGCGTTTAT-CGC
* * ** * * * * *
1793087 ACAAACGCCACTAAAGGTGTAGACCTTTCGCGGTGTTTCTGGG
1 A-AAACGCCGCTAAAAGTACAGACCTTTAGCGGCGTTTATCGC
* * * *
1793130 AAAAGCGCAGCTAAAAGTGCAGACCTTTAGCGGCGTTTGTTTGC
1 AAAA-CGCCGCTAAAAGTACAGACCTTTAGCGGCGTTT-ATCGC
* * *
1793174 AAAGCGCCGCTAAAAGTACAGACCTTTAGCGGAGCTTT-TGCCC
1 AAAACGCCGCTAAAAGTACAGACCTTTAGCGGCG-TTTAT-CGC
* * ** * *
1793217 AAAAAAGACGCTAAATTTACAGACCTATAGCGGCGCTTTCTC-C
1 -AAAACGCCGCTAAAAGTACAGACCTTTAGCGGCG-TTTATCGC
* * * * *
1793260 ACAAATGCTGCCAAAAGTAGAGTCCTTTAGCGGCG
1 A-AAACGCCGCTAAAAGTACAGACCTTTAGCGGCG
1793295 CTTTCCCCAC
Statistics
Matches: 254, Mismatches: 67, Indels: 28
0.73 0.19 0.08
Matches are distributed among these distances:
41 4 0.02
42 33 0.13
43 171 0.67
44 45 0.18
45 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (42 bp):
AAAACGCCGCTAAAAGTACAGACCTTTAGCGGCGTTTATCGC
Found at i:1793669 original size:21 final size:21
Alignment explanation
Indices: 1793645--1793702 Score: 80
Period size: 21 Copynumber: 2.8 Consensus size: 21
1793635 CTCTGCTCCG
* *
1793645 CCTCTCTCGTTGCTGCCGCTA
1 CCTCCCTCGCTGCTGCCGCTA
*
1793666 CCTCCCTCGCTGCTGCCGCTG
1 CCTCCCTCGCTGCTGCCGCTA
*
1793687 CCTCCCTCTCTGCTGC
1 CCTCCCTCGCTGCTGC
1793703 ATCGGCTAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.02, C:0.50, G:0.19, T:0.29
Consensus pattern (21 bp):
CCTCCCTCGCTGCTGCCGCTA
Found at i:1799287 original size:9 final size:9
Alignment explanation
Indices: 1799273--1799409 Score: 112
Period size: 9 Copynumber: 14.6 Consensus size: 9
1799263 ATGTATTAGT
1799273 TAAGTTATG
1 TAAGTTATG
1799282 TAAGTTATG
1 TAAGTTATG
*
1799291 TGAGTTATG
1 TAAGTTATG
*
1799300 TAAGTTGTTATA
1 TAA---GTTATG
*
1799312 TACGTTATG
1 TAAGTTATG
* *
1799321 TGAGTTATA
1 TAAGTTATG
*
1799330 TAAATTATG
1 TAAGTTATG
1799339 TAAGTTATG
1 TAAGTTATG
1799348 TAAGTTATG
1 TAAGTTATG
*
1799357 TAGGTTGTTATG
1 TA---AGTTATG
*
1799369 TAAATTATG
1 TAAGTTATG
*
1799378 TAAGTTACG
1 TAAGTTATG
*
1799387 TGAGTTATG
1 TAAGTTATG
* *
1799396 TAACTTATT
1 TAAGTTATG
1799405 TAAGT
1 TAAGT
1799410 AATGATCAAT
Statistics
Matches: 99, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
9 84 0.85
12 15 0.15
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.45
Consensus pattern (9 bp):
TAAGTTATG
Found at i:1799367 original size:48 final size:48
Alignment explanation
Indices: 1799273--1799404 Score: 149
Period size: 48 Copynumber: 2.8 Consensus size: 48
1799263 ATGTATTAGT
* *
1799273 TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTGTTATATACGTTATG
1 TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATTAGATACGTTATG
* * * * * *
1799321 TGAGTTATATAAATTATGTAAGTTATGTAAGTTATGTAGGT-TGTTATG
1 TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTAT-TAGATACGTTATG
* * *
1799369 TAAATTATGTAAGTTACGTGAGTTATGTAACTTATT
1 TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATT
1799405 TAAGTAATGA
Statistics
Matches: 68, Mismatches: 15, Indels: 3
0.79 0.17 0.03
Matches are distributed among these distances:
47 1 0.01
48 64 0.94
49 3 0.04
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.45
Consensus pattern (48 bp):
TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTATTAGATACGTTATG
Found at i:1799395 original size:57 final size:57
Alignment explanation
Indices: 1799273--1799409 Score: 166
Period size: 57 Copynumber: 2.4 Consensus size: 57
1799263 ATGTATTAGT
* ** * *
1799273 TAAGTTATGTAAGTTATGTGAGTTATGTAAGTTGTTATATACGTTATGTGAGTTATA
1 TAAGTTATGTAAGTTATGTAAGTTATGTAAGTTGTTATATAAATTATGTAAGTTACA
* * * *
1799330 TAAATTATGTAAGTTATGTAAGTTATGTAGGTTGTTATGTAAATTATGTAAGTTACG
1 TAAGTTATGTAAGTTATGTAAGTTATGTAAGTTGTTATATAAATTATGTAAGTTACA
* * *
1799387 TGAGTTATGTAACTTATTTAAGT
1 TAAGTTATGTAAGTTATGTAAGT
1799410 AATGATCAAT
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
57 67 1.00
ACGTcount: A:0.31, C:0.02, G:0.21, T:0.45
Consensus pattern (57 bp):
TAAGTTATGTAAGTTATGTAAGTTATGTAAGTTGTTATATAAATTATGTAAGTTACA
Found at i:1802781 original size:7 final size:7
Alignment explanation
Indices: 1802769--1802818 Score: 55
Period size: 7 Copynumber: 7.0 Consensus size: 7
1802759 ACAAAATCAG
1802769 ACCCTAA
1 ACCCTAA
1802776 ACCCTAA
1 ACCCTAA
* *
1802783 ATCTTAA
1 ACCCTAA
1802790 ACCCTAA
1 ACCCTAA
*
1802797 ACTCTAA
1 ACCCTAA
*
1802804 ACCATAA
1 ACCCTAA
1802811 ACTCCTAA
1 AC-CCTAA
1802819 CATTATAAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
7 30 0.88
8 4 0.12
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (7 bp):
ACCCTAA
Found at i:1802792 original size:14 final size:14
Alignment explanation
Indices: 1802772--1802814 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
1802762 AAATCAGACC
1802772 CTAAACCCTAAA-T
1 CTAAACCCTAAACT
1802785 CTTAAACCCTAAACT
1 C-TAAACCCTAAACT
*
1802800 CTAAACCATAAACT
1 CTAAACCCTAAACT
1802814 C
1 C
1802815 CTAACATTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 1 0.04
14 24 0.89
15 2 0.07
ACGTcount: A:0.44, C:0.33, G:0.00, T:0.23
Consensus pattern (14 bp):
CTAAACCCTAAACT
Found at i:1802794 original size:21 final size:21
Alignment explanation
Indices: 1802769--1802818 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1802759 ACAAAATCAG
* *
1802769 ACCCTAAACCCTAAATCTTAA
1 ACCCTAAACCCTAAACCATAA
*
1802790 ACCCTAAACTCTAAACCATAA
1 ACCCTAAACCCTAAACCATAA
1802811 ACTCCTAA
1 AC-CCTAA
1802819 CATTATAAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.44, C:0.34, G:0.00, T:0.22
Consensus pattern (21 bp):
ACCCTAAACCCTAAACCATAA
Found at i:1803321 original size:21 final size:19
Alignment explanation
Indices: 1803285--1803323 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 19
1803275 CATGCATAAA
*
1803285 CCCTTAACTTATCCCCTAT
1 CCCTTAACTTAACCCCTAT
1803304 CCCTTAAACCTTAACCCCTA
1 CCCTT-AA-CTTAACCCCTA
1803324 ACCACTAACC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 2 0.12
21 10 0.59
ACGTcount: A:0.26, C:0.44, G:0.00, T:0.31
Consensus pattern (19 bp):
CCCTTAACTTAACCCCTAT
Found at i:1804300 original size:35 final size:35
Alignment explanation
Indices: 1804235--1804316 Score: 94
Period size: 35 Copynumber: 2.3 Consensus size: 35
1804225 CAAAATAACA
** *
1804235 AAACCCTAAACCATAAAATTAACATTTTAAATCTT
1 AAACCCTAAACCATAAAATTAACACCTTAAATATT
**
1804270 AAACCCTAAACCATAGACCTTAA-ACCTTAAATATT
1 AAACCCTAAACCATA-AAATTAACACCTTAAATATT
*
1804305 AAACCGTAAACC
1 AAACCCTAAACC
1804317 CAAAAAATAA
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
35 35 0.88
36 5 0.12
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (35 bp):
AAACCCTAAACCATAAAATTAACACCTTAAATATT
Found at i:1804480 original size:57 final size:57
Alignment explanation
Indices: 1804392--1804500 Score: 191
Period size: 57 Copynumber: 1.9 Consensus size: 57
1804382 GCGTTTCTCC
* *
1804392 AAAAACGCCGCTAATGCTTAGACTTTTGGCGGCGTTTTTCCAAAAACGCCGCGAATA
1 AAAAACGCCGCTAATGCTCAGACTTTCGGCGGCGTTTTTCCAAAAACGCCGCGAATA
*
1804449 AAAAACGCCGCTAATGCTCAGACTTTCGGCGGCGTTTTTCCAAAAGCGCCGC
1 AAAAACGCCGCTAATGCTCAGACTTTCGGCGGCGTTTTTCCAAAAACGCCGC
1804501 TAATGCTCAG
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.23
Consensus pattern (57 bp):
AAAAACGCCGCTAATGCTCAGACTTTCGGCGGCGTTTTTCCAAAAACGCCGCGAATA
Found at i:1804511 original size:41 final size:41
Alignment explanation
Indices: 1804449--1804830 Score: 534
Period size: 41 Copynumber: 9.3 Consensus size: 41
1804439 GCCGCGAATA
*
1804449 AAAAACGCCGCTAATGCTCAGACTTTCGGCGGCGTTTTTCC
1 AAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTTCC
* *
1804490 AAAAGCGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTCCC
1 AAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTTCC
* *
1804531 AAAAACGCTGCTAATGCTCAGTA-TTTTGGCGGCGTTTTTCG
1 AAAAACGCCGCTAATGCTCAG-ACTTTTGGCGGCGTTTTTCC
* * *
1804572 AAAAACGCCGCTAATTCTCAAACTTTTAGCGGCGTTTTTCC
1 AAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTTCC
* * *
1804613 AACAACGCCGCTAATGCTCAGACTTTTAGCGGCGCTTTTCC
1 AAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTTCC
*
1804654 AACAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTTCC
1 AAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTTCC
* * **
1804695 AAAAATGCCGCTAATGCTCAGACTTTTGGCGGCATTTTTGG
1 AAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTTCC
* * * *
1804736 AAAAATGCCGCGAATTCTCAGACTTTTGGCGGCGTTTCTT-G
1 AAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTT-TTCC
*
1804777 AAAAACGCCGCTAATTCTCAGACTTTTGGCGGCGTTTTTCC
1 AAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTTCC
*
1804818 GAAAACGCCGCTA
1 AAAAACGCCGCTA
1804831 TTTCACGACT
Statistics
Matches: 307, Mismatches: 30, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
40 3 0.01
41 301 0.98
42 3 0.01
ACGTcount: A:0.23, C:0.26, G:0.22, T:0.29
Consensus pattern (41 bp):
AAAAACGCCGCTAATGCTCAGACTTTTGGCGGCGTTTTTCC
Found at i:1809611 original size:29 final size:29
Alignment explanation
Indices: 1809549--1809615 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
1809539 TAATTTGTAT
* *
1809549 AGATGGATTATGAAAAAATAGTTTTGAGG
1 AGATGGGTTATGAAAAAATAGTTTTGACG
* * *
1809578 GGATGGGTTCTGAAGAAATAGTTTTGACG
1 AGATGGGTTATGAAAAAATAGTTTTGACG
1809607 AGATGGGTT
1 AGATGGGTT
1809616 GAGTTTTGTA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.31
Consensus pattern (29 bp):
AGATGGGTTATGAAAAAATAGTTTTGACG
Found at i:1810019 original size:188 final size:187
Alignment explanation
Indices: 1809611--1810031 Score: 533
Period size: 188 Copynumber: 2.2 Consensus size: 187
1809601 TTGACGAGAT
* * * * * * * * * *
1809611 GGGTTGAGTTTTGTAGA-GAAAAACGCTCCAAGTAGAATGTATTATCAGCAAAAGTACTGAAAAC
1 GGGTTGAGGTTTCTAGACGAAAAACGCTCCAAGCAGGATGCACTGTTAGTAAAAATACTGAAAAC
** * * *
1809675 ACTTCCAATTGGACGCCCTTTTCAGTACTAATGCTTCTGTGAAAATAAATTTGACGAGATGGTTC
66 ACTTCCAATTAAACGCCCTTTTCAATACTAATGCTTCTGTGAAAAAAAATTTCACGAGATGGTTC
*
1809740 TAAAAAAATATCACGGGATTCCCAGGATGAGGTTTGTGAAAAATACCCCGAATAGTAG
131 TAAAAAAATAT-ACGGGATTCCCAGGATGAAGTTTGTGAAAAATACCCCGAATAGTAG
* * *
1809798 GGGTTGAGGTTTTTAGAGGAAAAACGTTCCAAGCAGGATGCACTGTTAGTAAAAATACTGAAAAC
1 GGGTTGAGGTTTCTAGACGAAAAACGCTCCAAGCAGGATGCACTGTTAGTAAAAATACTGAAAAC
* * ** * *
1809863 GCTTCCAATTAAATGCCCTTTTCAATACTGTTTCTTCTGTGAAAAAAAATTTCATGAGATGGTTC
66 ACTTCCAATTAAACGCCCTTTTCAATACTAATGCTTCTGTGAAAAAAAATTTCACGAGATGGTTC
* * *
1809928 T-AAAAAATATATCGGGATTCCCGGGATGAAGTTTGTGAAAAATACCCTGGATAGT-G
131 TAAAAAAATATA-CGGGATTCCCAGGATGAAGTTTGTGAAAAATACCCCGAATAGTAG
1809984 GGGTTTGAGGTTTCTAGACGACAAAACGCTCCAAGCAGGATGCACTGT
1 GGG-TTGAGGTTTCTAGACGA-AAAACGCTCCAAGCAGGATGCACTGT
1810032 AAACAAAAGT
Statistics
Matches: 201, Mismatches: 29, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
186 5 0.02
187 78 0.39
188 118 0.59
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (187 bp):
GGGTTGAGGTTTCTAGACGAAAAACGCTCCAAGCAGGATGCACTGTTAGTAAAAATACTGAAAAC
ACTTCCAATTAAACGCCCTTTTCAATACTAATGCTTCTGTGAAAAAAAATTTCACGAGATGGTTC
TAAAAAAATATACGGGATTCCCAGGATGAAGTTTGTGAAAAATACCCCGAATAGTAG
Found at i:1810409 original size:3 final size:3
Alignment explanation
Indices: 1810401--1810443 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
1810391 AGTTATTTAC
1810401 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1810444 ATTTTATCAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1810871 original size:22 final size:22
Alignment explanation
Indices: 1810846--1810909 Score: 110
Period size: 22 Copynumber: 2.9 Consensus size: 22
1810836 ACTAATGATG
* *
1810846 AAATTATGATTTTAATTGATAA
1 AAATTTTGATTTAAATTGATAA
1810868 AAATTTTGATTTAAATTGATAA
1 AAATTTTGATTTAAATTGATAA
1810890 AAATTTTGATTTAAATTGAT
1 AAATTTTGATTTAAATTGAT
1810910 TAAATGATTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (22 bp):
AAATTTTGATTTAAATTGATAA
Found at i:1812602 original size:42 final size:42
Alignment explanation
Indices: 1812512--1812603 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
1812502 TGGGCGTGTG
*
1812512 CCCA-GGCCGTGTGGCAAAGTCAGAATTGCCCACAGGTTAGT
1 CCCACGGCCGTGTGGCAAAGTCAGAATTGCCCACAGGTTAGC
* *
1812553 CCTACGGCCGTGTGAG-AAAGTCAG-ATCTGCCCACAGGTTGGC
1 CCCACGGCCGTGTG-GCAAAGTCAGAAT-TGCCCACAGGTTAGC
1812595 CCCACGGCC
1 CCCACGGCC
1812604 ATGGGAGCCC
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
41 5 0.11
42 38 0.86
43 1 0.02
ACGTcount: A:0.22, C:0.32, G:0.29, T:0.17
Consensus pattern (42 bp):
CCCACGGCCGTGTGGCAAAGTCAGAATTGCCCACAGGTTAGC
Found at i:1818641 original size:21 final size:22
Alignment explanation
Indices: 1818611--1818653 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
1818601 GCTCCAGGAT
1818611 AAAAAATATCGATA-CTTTTAC
1 AAAAAATATCGATACCTTTTAC
*
1818632 AAAAAGTATCGATACCTTTTAC
1 AAAAAATATCGATACCTTTTAC
1818654 CAGGTATCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (22 bp):
AAAAAATATCGATACCTTTTAC
Found at i:1818756 original size:21 final size:21
Alignment explanation
Indices: 1818727--1818778 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
1818717 ATTAAATGCT
1818727 AAAAGTATCGGTACCTATAAA
1 AAAAGTATCGGTACCTATAAA
* * *
1818748 AAAATTATCGGTACCTGTAGA
1 AAAAGTATCGGTACCTATAAA
1818769 AAAAGTATCG
1 AAAAGTATCG
1818779 ATAACTTTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.44, C:0.13, G:0.17, T:0.25
Consensus pattern (21 bp):
AAAAGTATCGGTACCTATAAA
Found at i:1819504 original size:17 final size:17
Alignment explanation
Indices: 1819482--1819517 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
1819472 AATTATGTTT
1819482 ATTTTAATATT-TTTTAA
1 ATTTTAAT-TTATTTTAA
1819499 ATTTTAATTTATTTTAA
1 ATTTTAATTTATTTTAA
1819516 AT
1 AT
1819518 ATAATCTAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 2 0.11
17 16 0.89
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTAATTTATTTTAA
Found at i:1819646 original size:22 final size:21
Alignment explanation
Indices: 1819603--1819646 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
1819593 CAACCGATAG
*
1819603 ATTTTTTTAATTTAGTATTTT
1 ATTTTTTTAAATTAGTATTTT
1819624 ATTTTTATTAAATTA-TATGTTT
1 ATTTTT-TTAAATTAGTAT-TTT
1819646 A
1 A
1819647 ATGTTATTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.30, C:0.00, G:0.05, T:0.66
Consensus pattern (21 bp):
ATTTTTTTAAATTAGTATTTT
Found at i:1819906 original size:61 final size:61
Alignment explanation
Indices: 1819831--1819954 Score: 248
Period size: 61 Copynumber: 2.0 Consensus size: 61
1819821 TAGTTATTTA
1819831 TTTTAATTATATAAATATAATTAAGTAATTGTGGGTTTAGGTTTAGGGTTTTTATGTTAAG
1 TTTTAATTATATAAATATAATTAAGTAATTGTGGGTTTAGGTTTAGGGTTTTTATGTTAAG
1819892 TTTTAATTATATAAATATAATTAAGTAATTGTGGGTTTAGGTTTAGGGTTTTTATGTTAAG
1 TTTTAATTATATAAATATAATTAAGTAATTGTGGGTTTAGGTTTAGGGTTTTTATGTTAAG
1819953 TT
1 TT
1819955 AATATTTGTG
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 63 1.00
ACGTcount: A:0.31, C:0.00, G:0.19, T:0.50
Consensus pattern (61 bp):
TTTTAATTATATAAATATAATTAAGTAATTGTGGGTTTAGGTTTAGGGTTTTTATGTTAAG
Found at i:1822818 original size:41 final size:42
Alignment explanation
Indices: 1822765--1822843 Score: 110
Period size: 41 Copynumber: 1.9 Consensus size: 42
1822755 TATTTCATAA
1822765 TTATTACATATTACTA-TA-TATTCATTATTTTTTATACTCTTT
1 TTATTACATATTACTACTACTATT-ATT-TTTTTTATACTCTTT
*
1822807 TTATTA-ATATTATTACTACTATTATTTTTTTTATACT
1 TTATTACATATTACTACTACTATTATTTTTTTTATACT
1822844 ATGATTATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
41 19 0.56
42 11 0.32
43 4 0.12
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (42 bp):
TTATTACATATTACTACTACTATTATTTTTTTTATACTCTTT
Found at i:1822875 original size:3 final size:3
Alignment explanation
Indices: 1822867--1822996 Score: 260
Period size: 3 Copynumber: 43.3 Consensus size: 3
1822857 CTTTTTCTGG
1822867 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1822915 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1822963 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1822997 ATTTTTTCAT
Statistics
Matches: 127, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 127 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:1828611 original size:55 final size:54
Alignment explanation
Indices: 1828534--1828637 Score: 181
Period size: 55 Copynumber: 1.9 Consensus size: 54
1828524 AGGTTGGGTT
* *
1828534 GGGGGGGGGGATGGGCAGGTATGTAGATGGGGAAGCCTGGCTGCTTCATTGGGG
1 GGGGGGGGGGATGGGCAGGTATGTAGATGGGGAACCCTGGCCGCTTCATTGGGG
1828588 GGGGGGGGGAGATGGGCAGGTATGTAGATGGGGAACCCTGGCCGCTTCAT
1 GGGGGGGGG-GATGGGCAGGTATGTAGATGGGGAACCCTGGCCGCTTCAT
1828638 CATGTGGGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
54 9 0.19
55 38 0.81
ACGTcount: A:0.16, C:0.13, G:0.51, T:0.19
Consensus pattern (54 bp):
GGGGGGGGGGATGGGCAGGTATGTAGATGGGGAACCCTGGCCGCTTCATTGGGG
Found at i:1833555 original size:56 final size:56
Alignment explanation
Indices: 1833489--1833602 Score: 149
Period size: 56 Copynumber: 2.0 Consensus size: 56
1833479 CTAGACTATG
* **
1833489 ATCCATGTTCAATGATACTATATCG-AGATTTCAAACATAAAGTGGTGGGAAAATAA
1 ATCCATGTTCAATGATACTATAT-GTAGATTGCAAACATAAAGTGGCAGGAAAATAA
* * * *
1833545 ATCCATGTTCAATTATACTTTATGTAGATTGCATACCTAAAGTGGCAGGAAAATAA
1 ATCCATGTTCAATGATACTATATGTAGATTGCAAACATAAAGTGGCAGGAAAATAA
1833601 AT
1 AT
1833603 AGAGGAAATA
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
55 1 0.02
56 49 0.98
ACGTcount: A:0.39, C:0.13, G:0.17, T:0.31
Consensus pattern (56 bp):
ATCCATGTTCAATGATACTATATGTAGATTGCAAACATAAAGTGGCAGGAAAATAA
Found at i:1847795 original size:28 final size:26
Alignment explanation
Indices: 1847745--1847847 Score: 76
Period size: 26 Copynumber: 4.0 Consensus size: 26
1847735 TCCCCCCCCC
*
1847745 CCAAAAAAAAAAAAAAA---A-AAAA
1 CCAAAAAAAAAAAAAAATTGATCAAA
1847767 CCAAAAAACACAAAAAAAATTGATCAAA
1 CCAAAAAA-A-AAAAAAAATTGATCAAA
**
1847795 -CAAGAAAAAAAAAAAAAAAGA--AAA
1 CCAA-AAAAAAAAAAAAATTGATCAAA
*
1847819 CCAAAAAGAGAAAGAAAAATTGATCAAA
1 CCAAAAA-A-AAAAAAAAATTGATCAAA
1847847 C
1 C
1847848 AAGAAATTTG
Statistics
Matches: 63, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
22 8 0.13
23 1 0.02
24 14 0.22
25 4 0.06
26 20 0.32
27 5 0.08
28 11 0.17
ACGTcount: A:0.76, C:0.12, G:0.07, T:0.06
Consensus pattern (26 bp):
CCAAAAAAAAAAAAAAATTGATCAAA
Found at i:1847862 original size:52 final size:52
Alignment explanation
Indices: 1847747--1847853 Score: 171
Period size: 52 Copynumber: 2.1 Consensus size: 52
1847737 CCCCCCCCCC
1847747 AAAAAAAAAAAAAAAAAAAACCAAAAAACACAAAAAAAATTGATCAAACAAG
1 AAAAAAAAAAAAAAAAAAAACCAAAAAACACAAAAAAAATTGATCAAACAAG
* * *
1847799 AAAAAAAAAAAAAAAGAAAACCAAAAAGAGA-AAGAAAAATTGATCAAACAAG
1 AAAAAAAAAAAAAAAAAAAACCAAAAA-ACACAAAAAAAATTGATCAAACAAG
1847851 AAA
1 AAA
1847854 TTTGAAAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
52 49 0.96
53 2 0.04
ACGTcount: A:0.78, C:0.09, G:0.07, T:0.06
Consensus pattern (52 bp):
AAAAAAAAAAAAAAAAAAAACCAAAAAACACAAAAAAAATTGATCAAACAAG
Found at i:1850379 original size:14 final size:15
Alignment explanation
Indices: 1850360--1850388 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1850350 TTATTTCATC
1850360 GAAAAT-AAAAATTT
1 GAAAATGAAAAATTT
1850374 GAAAATGAAAAATTT
1 GAAAATGAAAAATTT
1850389 TAACATTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.62, C:0.00, G:0.10, T:0.28
Consensus pattern (15 bp):
GAAAATGAAAAATTT
Found at i:1862866 original size:29 final size:30
Alignment explanation
Indices: 1862833--1862990 Score: 108
Period size: 30 Copynumber: 5.3 Consensus size: 30
1862823 TAACGAATAG
1862833 GAAAAGGGATAGCTTCGACTATC-AATTAT
1 GAAAAGGGATAGCTTCGACTATCAAATTAT
* * * **
1862862 GAAAAGGGAT-GGTGACGACCAT-AAACAAT
1 GAAAAGGGATAGCT-TCGACTATCAAATTAT
* * * * *
1862891 GAAAAGGGAT-GGTGACAACCATCAAACTAT
1 GAAAAGGGATAGCT-TCGACTATCAAATTAT
** * * *
1862921 GAAAATCGATAGCTTCGGCTATCGATTTAT
1 GAAAAGGGATAGCTTCGACTATCAAATTAT
* * *
1862951 GAAAAGGGATAGTTTTGGCTATCAAATTAT
1 GAAAAGGGATAGCTTCGACTATCAAATTAT
1862981 GAAAAGGGAT
1 GAAAAGGGAT
1862991 GGTGACAGCC
Statistics
Matches: 102, Mismatches: 23, Indels: 7
0.77 0.17 0.05
Matches are distributed among these distances:
28 2 0.02
29 41 0.40
30 57 0.56
31 2 0.02
ACGTcount: A:0.39, C:0.13, G:0.24, T:0.24
Consensus pattern (30 bp):
GAAAAGGGATAGCTTCGACTATCAAATTAT
Found at i:1862925 original size:30 final size:30
Alignment explanation
Indices: 1862859--1863079 Score: 144
Period size: 30 Copynumber: 7.4 Consensus size: 30
1862849 GACTATCAAT
1862859 TATGAAAAGGGATGGTGACGACCAT-AAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
* *
1862888 AATGAAAAGGGATGGTGACAACCATCAAAC
1 TATGAAAAGGGATGGTGACGACCATCAAAC
** * * * * * **
1862918 TATGAAAATCGATAGCT-TCGGCTATCGATT
1 TATGAAAAGGGAT-GGTGACGACCATCAAAC
* *** * * *
1862948 TATGAAAAGGGATAGTTTTGGCTATCAAAT
1 TATGAAAAGGGATGGTGACGACCATCAAAC
*
1862978 TATGAAAAGGGATGGTGAC-AGCCATCGAAC
1 TATGAAAAGGGATGGTGACGA-CCATCAAAC
* * * *
1863008 AATG-AAAGGAGATGGTAATGACCATCGAAC
1 TATGAAAAGG-GATGGTGACGACCATCAAAC
* * * *
1863038 AATGAAAAGGGATGGTGATGACCATAAAAT
1 TATGAAAAGGGATGGTGACGACCATCAAAC
1863068 TATGAAAAGGGA
1 TATGAAAAGGGA
1863080 AAGCTTTGGC
Statistics
Matches: 149, Mismatches: 36, Indels: 13
0.75 0.18 0.07
Matches are distributed among these distances:
29 29 0.19
30 112 0.75
31 8 0.05
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.21
Consensus pattern (30 bp):
TATGAAAAGGGATGGTGACGACCATCAAAC
Found at i:1863141 original size:30 final size:31
Alignment explanation
Indices: 1863065--1863141 Score: 86
Period size: 30 Copynumber: 2.5 Consensus size: 31
1863055 ATGACCATAA
* *
1863065 AATTATGAAAAGGGA-AAGCTTTGGCTATTG
1 AATTATGAAAAGGGATAAGCTTCGGCTATCG
* * *
1863095 AACTATGAAAATGGATAA-CTTCGGTTATCG
1 AATTATGAAAAGGGATAAGCTTCGGCTATCG
*
1863125 AATTACGAAAAGGGATA
1 AATTATGAAAAGGGATA
1863142 GGTTAACCAT
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
30 36 0.95
31 2 0.05
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.27
Consensus pattern (31 bp):
AATTATGAAAAGGGATAAGCTTCGGCTATCG
Found at i:1864922 original size:43 final size:43
Alignment explanation
Indices: 1864874--1865039 Score: 149
Period size: 43 Copynumber: 3.9 Consensus size: 43
1864864 GTTATCGAGA
* *
1864874 TGTGATTACAAGTAAGACCATGTCTGGGACATTGGCATTGTAT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
** * * *
1864917 TGTGATTATGTGTAAGACCCTGTCTGGGACATTGGCAGCGTTAA
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCG-TAT
* * * * *
1864961 T-CGATTTCGTGTAAGACCCTGTCTGGGACAGTGGCATCG-AT
1 TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
* * * *
1865002 ATGTAATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 -TGTGATTACATGTAAGACCATGTCTGGGACATTGGCAT
1865040 TTTATGAGCT
Statistics
Matches: 99, Mismatches: 21, Indels: 7
0.78 0.17 0.06
Matches are distributed among these distances:
41 1 0.01
42 7 0.07
43 88 0.89
44 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.31
Consensus pattern (43 bp):
TGTGATTACATGTAAGACCATGTCTGGGACATTGGCATCGTAT
Found at i:1866778 original size:21 final size:20
Alignment explanation
Indices: 1866754--1866792 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1866744 GAGTATTTTG
1866754 ATGTTTAATGATAGATTATGA
1 ATGTTTAATGATAG-TTATGA
*
1866775 ATGTTTGATGATAGTTAT
1 ATGTTTAATGATAGTTAT
1866793 ACAAGTTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (20 bp):
ATGTTTAATGATAGTTATGA
Found at i:1873522 original size:36 final size:36
Alignment explanation
Indices: 1873476--1873551 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
1873466 GCTTACTTTG
*
1873476 TGTGTGTTTTCATTGTTTTATAGATATCGAAGCTAT
1 TGTGTGTTTTCATTGTTTTATAGATATCGAAGCTAC
1873512 TGTGTGTTTTCATTGTTTTATAGATATCGAAGCTAC
1 TGTGTGTTTTCATTGTTTTATAGATATCGAAGCTAC
1873548 TGTG
1 TGTG
1873552 AGCTCAGGGA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.21, C:0.09, G:0.21, T:0.49
Consensus pattern (36 bp):
TGTGTGTTTTCATTGTTTTATAGATATCGAAGCTAC
Found at i:1888569 original size:155 final size:155
Alignment explanation
Indices: 1888287--1888595 Score: 591
Period size: 155 Copynumber: 2.0 Consensus size: 155
1888277 TGATAATTGT
1888287 TAAATTCATTAAGTTAAGTTTTGATAGTTCCAAAATTTGATGCAGCAGACATATTATCATATGTG
1 TAAATTCATTAAGTTAAGTTTTGATAGTTCCAAAATTTGATGCAGCAGACATATTATCATATGTG
* *
1888352 TAATGCATATCATCTTATTATTTCCACATATTAGTCACTAAAATTCCAGTTAATGGATTAACAAT
66 TAATGCATATCATCTTATTATTTCCACATAGTAGTCACTAAAATCCCAGTTAATGGATTAACAAT
1888417 TGTCATTTGCGTCAACACTAAAATG
131 TGTCATTTGCGTCAACACTAAAATG
*
1888442 TAAATTCATTAAGTTAAGTTTTGATATTTCCAAAATTTGATGCAGCAGACATATTATCATATGTG
1 TAAATTCATTAAGTTAAGTTTTGATAGTTCCAAAATTTGATGCAGCAGACATATTATCATATGTG
1888507 TAATGCATATCATCTTATTATTTCCACATAGTAGTCACTAAAATCCCAGTTAATGGATTAACAAT
66 TAATGCATATCATCTTATTATTTCCACATAGTAGTCACTAAAATCCCAGTTAATGGATTAACAAT
1888572 TGTCATTTGCGTCAACACTAAAAT
131 TGTCATTTGCGTCAACACTAAAAT
1888596 TTCATAATTC
Statistics
Matches: 151, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
155 151 1.00
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (155 bp):
TAAATTCATTAAGTTAAGTTTTGATAGTTCCAAAATTTGATGCAGCAGACATATTATCATATGTG
TAATGCATATCATCTTATTATTTCCACATAGTAGTCACTAAAATCCCAGTTAATGGATTAACAAT
TGTCATTTGCGTCAACACTAAAATG
Found at i:1891140 original size:14 final size:13
Alignment explanation
Indices: 1891109--1891133 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1891099 AATTTTTTGA
1891109 CTTTTTTCTTTCC
1 CTTTTTTCTTTCC
1891122 CTTTTTTCTTTC
1 CTTTTTTCTTTC
1891134 ACGTTTTCCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
CTTTTTTCTTTCC
Found at i:1900134 original size:18 final size:19
Alignment explanation
Indices: 1900110--1900151 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
1900100 TATAATATTT
*
1900110 AATTTAAT-TTTTATTTAA
1 AATTTAATATTTAATTTAA
*
1900128 TATTTAATATTTAATTTAA
1 AATTTAATATTTAATTTAA
1900147 AATTT
1 AATTT
1900152 TTATATAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
AATTTAATATTTAATTTAA
Found at i:1900753 original size:6 final size:6
Alignment explanation
Indices: 1900742--1900770 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
1900732 AAGTTCATGA
1900742 TTTTGC TTTTGC TTTTGC TTTTGC TTTTG
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTG
1900771 ATTCCTCCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.17, T:0.69
Consensus pattern (6 bp):
TTTTGC
Found at i:1906265 original size:6 final size:6
Alignment explanation
Indices: 1906237--1906293 Score: 60
Period size: 6 Copynumber: 9.3 Consensus size: 6
1906227 AAAAATTCTG
** * *
1906237 ATAATT ATGGTT ATAATAA ATAATT ATAATT ATAATT ATAATT ACAATT
1 ATAATT ATAATT ATAAT-T ATAATT ATAATT ATAATT ATAATT ATAATT
*
1906286 ACAATT AT
1 ATAATT AT
1906294 TAGTTAAAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
6 37 0.88
7 5 0.12
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.44
Consensus pattern (6 bp):
ATAATT
Done.