Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007805.1 Hibiscus syriacus cultivar Beakdansim tig00110123_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2708727
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 11
Found at i:1721844 original size:95 final size:98
Alignment explanation
Indices: 1721630--1721894 Score: 344
Period size: 95 Copynumber: 2.7 Consensus size: 98
1721620 AGCTAGCTGA
* * * * *
1721630 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTCTAGATGGACAGCTCAA--TATTATTGTATAAA
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCT-TTATTGTATAAA
1721693 TATAATTATCACCTTTATCAGTCTAGCTAAATATT
65 TATAA-TATCACCTTTATCAGTCTAGCTAAATATT
*
1721728 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTAT-AGT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAAAT
* * * *
1721792 AT-A-ATCATCTTTATCAGGT-TAGCTGACTCTT
66 ATAATATCACCTTTATCA-GTCTAGCTAAATATT
* * *
1721823 ATCCATAAAGTCGGGGTGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTTTATAT
1 ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAAAT
1721888 ATAATAT
66 ATAATAT
1721895 TATAATCTGG
Statistics
Matches: 147, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
95 80 0.54
96 5 0.03
97 2 0.01
98 50 0.34
99 9 0.06
100 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Consensus pattern (98 bp):
ATCCATAAAGTCGGGGCGTTTAACCAATTGCTTTAGAGGGACAACTCAAGCTTTATTGTATAAAT
ATAATATCACCTTTATCAGTCTAGCTAAATATT
Found at i:1731530 original size:90 final size:88
Alignment explanation
Indices: 1731357--1731522 Score: 280
Period size: 90 Copynumber: 1.9 Consensus size: 88
1731347 ACACACCCTT
1731357 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
1731422 ATTAATTGGAATTTAATAATCCTC
66 ATTAATT-GAATTAAATAATCCTC
* *
1731446 TTATATCCAAGTTACCCTAATCATATTGGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
1731511 AATTAATT-AATT
65 AATTAATTGAATT
1731523 GAAAATAAAT
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
88 4 0.05
89 29 0.39
90 41 0.55
ACGTcount: A:0.36, C:0.11, G:0.07, T:0.45
Consensus pattern (88 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAATTAAATAATCCTC
Found at i:1734339 original size:3 final size:3
Alignment explanation
Indices: 1734331--1734360 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
1734321 AGACAAAACC
1734331 AAT AAT AAT AAT AAT AAT AAT AAT AA- AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1734361 TAAAAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1735234 original size:20 final size:20
Alignment explanation
Indices: 1735209--1735246 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1735199 TTGCAAAATA
1735209 TGCTTCGAAAACTTTGTGTT
1 TGCTTCGAAAACTTTGTGTT
* *
1735229 TGCTTCGGAATCTTTGTG
1 TGCTTCGAAAACTTTGTG
1735247 CGTATTTTCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.16, G:0.24, T:0.45
Consensus pattern (20 bp):
TGCTTCGAAAACTTTGTGTT
Found at i:1736045 original size:183 final size:184
Alignment explanation
Indices: 1735736--1736201 Score: 810
Period size: 183 Copynumber: 2.5 Consensus size: 184
1735726 AGTGTCTACA
1735736 GTTCCAATGGACCTCTTTGATAGTAGACTCGGAATTCGTGCATTCGTATAATGTTCATGTACTTT
1 GTTCCAATGGACCTCTTTGATAGTAGACTCGGAATTCGTGCATTCGTATAATGTTCATGTACTTT
1735801 TTCGTATCATAATCTCGTTAAAGGTGTCTTATATACTAGCATTATTTAACATGATCTTGTTAAGA
66 TTCGTATCATAATCTCGTTAAAGGTGTCTTATATACTAGCATTATTTAACATGATCTTGTTAAGA
1735866 TTAGGTTTTTCTGGGTTCATCTACCCCTATA-TCAAATGTCAAACGCTTAGCAGT
131 TTAGG-TTTTCTGGGTTCATCTACCCCTATACTCAAATGTCAAACGCTTAGCAGT
1735920 GTTCCAATGGACCTCTTTGATAGT-GACTCGGAATTCGTGCATTCGTATAATGTTCATGTACTTT
1 GTTCCAATGGACCTCTTTGATAGTAGACTCGGAATTCGTGCATTCGTATAATGTTCATGTACTTT
1735984 TTCGTATCATAATCTCGTTAAAGGTGTCTTATATACTAGCATTATTTAACATGATCTTGTTAAGA
66 TTCGTATCATAATCTCGTTAAAGGTGTCTTATATACTAGCATTATTTAACATGATCTTGTTAAGA
*
1736049 TTAGGTTTTCTGGGTTCATCTACCCCTATACTCAAATGTCAAATGCTTAGCAGT
131 TTAGGTTTTCTGGGTTCATCTACCCCTATACTCAAATGTCAAACGCTTAGCAGT
* * ** * *
1736103 GTTCCAATGGACCTCTTAGATAGTAGACTTGGGAATTCGTGCATTCGTATTGTGGTCATGTATTT
1 GTTCCAATGGACCTCTTTGATAGTAGAC-TCGGAATTCGTGCATTCGTATAATGTTCATGTACTT
* * *
1736168 TTTCATATCATAATCTTGTTAAAAGTGTCTTATA
65 TTTCGTATCATAATCTCGTTAAAGGTGTCTTATA
1736202 AGTGTGTGTT
Statistics
Matches: 269, Mismatches: 10, Indels: 5
0.95 0.04 0.02
Matches are distributed among these distances:
182 25 0.09
183 155 0.58
184 27 0.10
185 62 0.23
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (184 bp):
GTTCCAATGGACCTCTTTGATAGTAGACTCGGAATTCGTGCATTCGTATAATGTTCATGTACTTT
TTCGTATCATAATCTCGTTAAAGGTGTCTTATATACTAGCATTATTTAACATGATCTTGTTAAGA
TTAGGTTTTCTGGGTTCATCTACCCCTATACTCAAATGTCAAACGCTTAGCAGT
Found at i:1737760 original size:119 final size:119
Alignment explanation
Indices: 1737540--1737762 Score: 277
Period size: 119 Copynumber: 1.9 Consensus size: 119
1737530 TAGGGAATAT
* * * * * *
1737540 ATATGTAATTATATTATTTTAGTTAATTGTCACGTCAATATTAAAAATCAAATGTGTAATTATAC
1 ATATGTAATTATACTATTTTAGTTAATTGTCACGTCAATAGTAAAAACCAAATATATAATTACAC
* *
1737605 TACTCTTATTAATTATCACGTCACCTCTTTCATTAAATAAAGATTGAAGATTAA
66 TACTCTTATTAATTATCACGTCACCTATTCCATTAAATAAAGATTGAAGATTAA
* * * **
1737659 ATATGTAATTATACTATTTTAGTTAGTTGTTATGTCAATAGTAAGGACCAAATATATAATTACAC
1 ATATGTAATTATACTATTTTAGTTAATTGTCACGTCAATAGTAAAAACCAAATATATAATTACAC
* * * *
1737724 TA-TTTTAATTAATTTTCACGTCATCTATTCCGTTAAATA
66 TACTCTT-ATTAATTATCACGTCACCTATTCCATTAAATA
1737763 TTAACAGTTA
Statistics
Matches: 86, Mismatches: 17, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
118 3 0.03
119 83 0.97
ACGTcount: A:0.37, C:0.12, G:0.09, T:0.42
Consensus pattern (119 bp):
ATATGTAATTATACTATTTTAGTTAATTGTCACGTCAATAGTAAAAACCAAATATATAATTACAC
TACTCTTATTAATTATCACGTCACCTATTCCATTAAATAAAGATTGAAGATTAA
Found at i:1742484 original size:3 final size:3
Alignment explanation
Indices: 1742476--1742533 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
1742466 TGTATGATTT
1742476 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
1742524 ATA ATA ATA A
1 ATA ATA ATA A
1742534 ACCTATATGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1747582 original size:55 final size:55
Alignment explanation
Indices: 1747516--1747983 Score: 652
Period size: 55 Copynumber: 8.5 Consensus size: 55
1747506 TTCCATGGTT
* * ** * * * * *
1747516 TTGCACACATAGTGTCGATACGGTAATTCACAAATTTATTATGAATTACATTG-GG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTC-GTGAGG
* *
1747571 TTGCACACATAGTGCAAATACGGAAATTCATAAACTCATTATGAATTTCGTG-GG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGG
* *
1747625 ATTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCGTGAGG
1 -TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGG
* *
1747681 TTGCACACATAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTTGTGAGG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGG
*
1747736 TTGCACACATAATGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGG
* * *
1747791 TTGTACACCTAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAAG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGG
*
1747846 TTGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCGTGAGG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGG
* * * * *
1747901 TTGCACAAATAGTGTCAACACGAAAATTCATAAACTTATTATGAATATCGTGAGG
1 TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGG
* * *
1747956 TTACAAACATAGTGCCAATACGGAAATT
1 TTGCACACATAGTGCCAATACGAAAATT
1747984 GCAACATATA
Statistics
Matches: 377, Mismatches: 34, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
54 4 0.01
55 371 0.98
56 2 0.01
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.30
Consensus pattern (55 bp):
TTGCACACATAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCGTGAGG
Found at i:1758951 original size:35 final size:36
Alignment explanation
Indices: 1758877--1758966 Score: 114
Period size: 36 Copynumber: 2.5 Consensus size: 36
1758867 GATATAATAA
* *
1758877 AATAAAATAAATAATTATAATTTAAAAAGAAAAATT
1 AATAAAATAAATAATAATAATATAAAAAGAAAAATT
*
1758913 AATAAAATAAATAATAATAA-ATAAAAAGGGAAAA-T
1 AATAAAATAAATAATAATAATATAAAAA-GAAAAATT
1758948 AATAAAAT-AATAAATAATA
1 AATAAAATAAAT-AATAATA
1758967 GTAGTAAATA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
34 3 0.06
35 22 0.45
36 24 0.49
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (36 bp):
AATAAAATAAATAATAATAATATAAAAAGAAAAATT
Found at i:1759031 original size:18 final size:18
Alignment explanation
Indices: 1759010--1759047 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
1759000 GTTGTTTTTA
1759010 AAATAAAAGATAAA-AATT
1 AAATAAAAGA-AAATAATT
1759028 AAATAAAAGAAAATAATT
1 AAATAAAAGAAAATAATT
1759046 AA
1 AA
1759048 TCTAAGAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 3 0.16
18 16 0.84
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAATAATT
Found at i:1759743 original size:24 final size:24
Alignment explanation
Indices: 1759716--1759830 Score: 72
Period size: 25 Copynumber: 4.6 Consensus size: 24
1759706 AAATCCTAAT
1759716 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
** ** *
1759740 TAAAATACCTAAAACAAAGATAAAA
1 TAAAATA-CTAAAACCTATTTAAAC
* * * *
1759765 TATAAA-AATAATATCCTAAAACTT-AAT
1 TA-AAATACTAA-AACCT---ATTTAAAC
1759792 TAAAATACTAAAACCTATTTAAAC
1 TAAAATACTAAAACCTATTTAAAC
1759816 TAAAATACCTAAAAC
1 TAAAATA-CTAAAAC
1759831 AAAGATAAAA
Statistics
Matches: 66, Mismatches: 16, Indels: 17
0.67 0.16 0.17
Matches are distributed among these distances:
23 3 0.05
24 19 0.29
25 24 0.36
26 10 0.15
27 8 0.12
28 2 0.03
ACGTcount: A:0.58, C:0.15, G:0.01, T:0.26
Consensus pattern (24 bp):
TAAAATACTAAAACCTATTTAAAC
Found at i:1759764 original size:44 final size:44
Alignment explanation
Indices: 1759716--1759842 Score: 136
Period size: 44 Copynumber: 3.2 Consensus size: 44
1759706 AAATCCTAAT
1759716 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
1 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
* *
1759760 TAAAATA-TAAAA---A--T-AA-T---AT-CCTAAAACTTAA-T
1 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAAC-AAAGA
1759792 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
1 TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
1759836 TAAAATA
1 TAAAATA
1759843 TAATGTTTAA
Statistics
Matches: 65, Mismatches: 4, Indels: 28
0.67 0.04 0.29
Matches are distributed among these distances:
32 15 0.23
33 9 0.14
36 2 0.03
37 2 0.03
38 2 0.03
39 2 0.03
40 2 0.03
43 9 0.14
44 22 0.34
ACGTcount: A:0.60, C:0.13, G:0.02, T:0.25
Consensus pattern (44 bp):
TAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGA
Found at i:1759796 original size:76 final size:76
Alignment explanation
Indices: 1759635--1759845 Score: 301
Period size: 76 Copynumber: 2.9 Consensus size: 76
1759625 TAAAACATCT
* * * *
1759635 TAAATCTTAGTTAAAACACTTAAAA-CTATTTAAACTAAAATACCT---A-AAA-ATAATAT-TT
1 TAAATCTTAATTAAAATAC-TAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATA
*
1759693 AAAATAATATTC
65 AAAATAATATCC
*
1759705 TAAATCCTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1759770 AAATAATATCC
66 AAATAATATCC
*
1759781 TAAAACTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1759846 TGTTTAAAAT
Statistics
Matches: 126, Mismatches: 8, Indels: 8
0.89 0.06 0.06
Matches are distributed among these distances:
69 5 0.04
70 36 0.29
73 1 0.01
74 3 0.02
75 6 0.05
76 75 0.60
ACGTcount: A:0.57, C:0.13, G:0.01, T:0.29
Consensus pattern (76 bp):
TAAATCTTAATTAAAATACTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
AAATAATATCC
Found at i:1768379 original size:85 final size:85
Alignment explanation
Indices: 1768231--1768396 Score: 194
Period size: 85 Copynumber: 2.0 Consensus size: 85
1768221 ATACAATAAC
* * * *
1768231 GACACAAGAATGTGTGTCATCTTTTTTAATGACGTGTGCTTCAATGACATGCAATGTAAGTCATA
1 GACACAAAAATGTGTGTCATCTTATTTAATGACGAGTGCTTCAATGACACGCAATGTAAGTCATA
* **
1768296 CATGCGTGTCATAAATTTAT
66 AATGCGCATCATAAATTTAT
* * *
1768316 GACACAAAAATGTGTGTCATCTTCATTT-ATGACAGAG-GCTTTAATGACGCGCAATG-AGTGTC
1 GACACAAAAATGTGTGTCATCTT-ATTTAATGAC-GAGTGCTTCAATGACACGCAATGTA-AGTC
1768378 ATAAATGCGCATCATAAAT
63 ATAAATGCGCATCATAAAT
1768397 GTGCGTCATA
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
84 1 0.01
85 62 0.91
86 5 0.07
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Consensus pattern (85 bp):
GACACAAAAATGTGTGTCATCTTATTTAATGACGAGTGCTTCAATGACACGCAATGTAAGTCATA
AATGCGCATCATAAATTTAT
Found at i:1768392 original size:13 final size:13
Alignment explanation
Indices: 1768375--1768432 Score: 80
Period size: 13 Copynumber: 4.5 Consensus size: 13
1768365 CGCAATGAGT
1768375 GTCATAAATGCGC
1 GTCATAAATGCGC
* *
1768388 ATCATAAATGTGC
1 GTCATAAATGCGC
*
1768401 GTCATAAATGCGT
1 GTCATAAATGCGC
1768414 GTCATAAATGCGC
1 GTCATAAATGCGC
*
1768427 TTCATA
1 GTCATA
1768433 GATTTATGAC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (13 bp):
GTCATAAATGCGC
Found at i:1768397 original size:26 final size:26
Alignment explanation
Indices: 1768368--1768432 Score: 76
Period size: 26 Copynumber: 2.5 Consensus size: 26
1768358 AATGACGCGC
*
1768368 AATGAGTGTCATAAATGCGCATCATA
1 AATGAGCGTCATAAATGCGCATCATA
* **
1768394 AATGTGCGTCATAAATGCGTGTCATA
1 AATGAGCGTCATAAATGCGCATCATA
* *
1768420 AATGCGCTTCATA
1 AATGAGCGTCATA
1768433 GATTTATGAC
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (26 bp):
AATGAGCGTCATAAATGCGCATCATA
Found at i:1768935 original size:17 final size:16
Alignment explanation
Indices: 1768913--1768946 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1768903 TAAAAACAAT
1768913 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1768930 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1768946 A
1 A
1768947 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1772787 original size:26 final size:27
Alignment explanation
Indices: 1772745--1772816 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 27
1772735 ATGAATGAAA
** * *
1772745 GAAAGAGAAAAGGTAAAAGTTAAA-AT
1 GAAAGAGAAAAATTAAAAATGAAAGAT
1772771 GAAAGAGAAAAATTAAAAATGAAAGAT
1 GAAAGAGAAAAATTAAAAATGAAAGAT
1772798 -AAA-AGAAAAAGTTAAAAAT
1 GAAAGAGAAAAA-TTAAAAAT
1772817 TTGGGAGGGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
25 7 0.17
26 31 0.77
27 2 0.05
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (27 bp):
GAAAGAGAAAAATTAAAAATGAAAGAT
Found at i:1779164 original size:17 final size:16
Alignment explanation
Indices: 1779142--1779175 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1779132 TAAAAACAAT
1779142 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
1779159 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
1779175 A
1 A
1779176 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:1787056 original size:20 final size:19
Alignment explanation
Indices: 1787031--1787073 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
1787021 AGAAAACACT
*
1787031 TTGAGAGTGAATTGTGAATG
1 TTGAGAGTGAATTGAGAA-G
*
1787051 TTGAGAGTGAGTTGAGAAG
1 TTGAGAGTGAATTGAGAAG
1787070 TTGA
1 TTGA
1787074 ATATAACTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (19 bp):
TTGAGAGTGAATTGAGAAG
Found at i:1787535 original size:6 final size:6
Alignment explanation
Indices: 1787524--1787548 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
1787514 GACACGTATT
1787524 ACCACG ACCACG ACCACG ACCACG A
1 ACCACG ACCACG ACCACG ACCACG A
1787549 ACACAAACAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.48, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1787832 original size:185 final size:176
Alignment explanation
Indices: 1787538--1787900 Score: 629
Period size: 185 Copynumber: 2.0 Consensus size: 176
1787528 CGACCACGAC
1787538 CACGACCACGAACACAAACACAAACATGACGAGCCGAGCCGAGCCGACGAGACGGACGGCGCGGT
1 CACGACCACGAACACAAACACAAACATGACGAGCCGAGCCGAGCCGACGAGACGGACGGCGCGGT
1787603 GCGCGAGAGTCTCCTTGTTCTCTATCACTCAACAAGGAAGTGGGAAATCCAAACCTTAAATA-CC
66 GCGCGAGAGTCTCCTTGTTCTCTATCACTCAACAAGGAAGTGGGAAATCCAAACCTTAAATACCC
1787667 ATTCCCAATAGTGTTTCCAATACTATGTGGGATTGAGCATTACCAA
131 ATTCCCAATAGTGTTTCCAATACTATGTGGGATTGAGCATTACCAA
1787713 CACGACCACGAACACAAACACAAACATGACCACGAGCCGAGCCGAGCCGAGACGAGACGGACGGC
1 CACGACCACGAACACAAACACAAACATG---ACGAGCCGAGCCGAGCC--GACGAGACGGAC-G-
1787778 AGCGGCGGTGCGCGAGAGTCTCCCTTGTTCTCTATCACTCAACAAGGAAGTGGGAAATCCAAACC
59 -GC-GCGGTGCGCGAGAGTCT-CCTTGTTCTCTATCACTCAACAAGGAAGTGGGAAATCCAAACC
1787843 TTAAATACCCATTCCCAATAGTGTTTCCAATACTATGTGGGATTGAGCATTACCAA
121 TTAAATACCCATTCCCAATAGTGTTTCCAATACTATGTGGGATTGAGCATTACCAA
1787899 CA
1 CA
1787901 TTCTCCCACT
Statistics
Matches: 177, Mismatches: 0, Indels: 11
0.94 0.00 0.06
Matches are distributed among these distances:
175 28 0.16
178 17 0.10
180 12 0.07
181 1 0.01
183 2 0.01
184 17 0.10
185 50 0.28
186 50 0.28
ACGTcount: A:0.32, C:0.28, G:0.22, T:0.18
Consensus pattern (176 bp):
CACGACCACGAACACAAACACAAACATGACGAGCCGAGCCGAGCCGACGAGACGGACGGCGCGGT
GCGCGAGAGTCTCCTTGTTCTCTATCACTCAACAAGGAAGTGGGAAATCCAAACCTTAAATACCC
ATTCCCAATAGTGTTTCCAATACTATGTGGGATTGAGCATTACCAA
Found at i:1798845 original size:179 final size:176
Alignment explanation
Indices: 1798424--1799215 Score: 671
Period size: 179 Copynumber: 4.4 Consensus size: 176
1798414 TTGGGCGCAA
* * * * * ** * * *
1798424 CTTTTTTCTTAGTGACCCATGAAATTAATGTGCGCAACCACATTTTTTATATATGTTCATAAAAT
1 CTTTTTTATTATTGAACCATGAAATTATTG-GGGCAACCGTATTTCTTATATATATTCATAACAT
* ** * * * * *
1798489 TTTTAGTTTTAAACTTATTTTCCAATATTCGGAAAATCCAAGGTCTTATCCGCTTAAACTTTGAT
65 TTTCAGTTTTAAACTTATTTTCTTATACTGGGATAATCCAA-G----A--C-TTTAAACTCTGAT
* ** *
1798554 AATATTTTCGGCGTAACCTACTTTATTATTAAAAATATTAACATTCCATATTACA-
122 AACATTTTCGGCACAACCT-GTTTATTATTAAAAATATTAACATTCCATATTACAC
* * ***
1798609 ATTTTTTCATTATTGAACTATGAAATTATTAGACACAACCGTATTTCTTATATATATTCA-AAGC
1 CTTTTTT-ATTATTGAACCATGAAATTATT-GGGGCAACCGTATTTCTTATATATATTCATAA-C
* * *
1798673 ATTTTCAGTTTTAAATTTATTTTCTTATATTGGGATAATCCAAGACTTTAAACTCTGACAACATT
63 ATTTTCAGTTTTAAACTTATTTTCTTATACTGGGATAATCCAAGACTTTAAACTCTGATAACATT
** * * *
1798738 TTCGGTGCAATCTGTTTTATTATTAAAAGTATTAACATTCTATATTACCAC
128 TTCGGCACAACCTG-TTTATTATTAAAAATATTAACATTCCATATTA-CAC
* * *
1798789 CTATTTTATTATTGAACCATGAAATTATTAGGGGCAACCGTATTTCTTATATATATTTATTACAT
1 CTTTTTTATTATTGAACCATGAAATTATT-GGGGCAACCGTATTTCTTATATATATTCATAACAT
* * * * * * *
1798854 TTTAAGTTTTAAACTTATTTTCTTATACTGTGATAATCCAAGGC---AAAATATAATAAAATTTT
65 TTTCAGTTTTAAACTTATTTTCTTATACTGGGATAATCCAAGACTTTAAACTCTGATAACATTTT
* * * *
1798916 CGGCACAAGCTACTTTATTATTAAAAATATTAGCATTCCATATTACAGT
130 CGGCACAACCT-GTTTATTATTAAAAATATTAACATTCCATATTACA-C
* *
1798965 CTTTTTTAGTATTGAACCATGAAATTATT-GGGCAACTGTATTTCTTATATATATGTTCATAACA
1 CTTTTTTATTATTGAACCATGAAATTATTGGGGCAACCGTATTTCTTATATATA--TTCATAACA
* *
1799029 TTTTTCA-TATTTAAACTTATTTTTTTATACTAGGATAATCCAAGACTCCATTATCTTAAACTCT
64 -TTTTCAGT-TTTAAACTTATTTTCTTATACTGGGATAATCCAAGA---C----T-TTAAACTCT
* * * *
1799093 GATAACATTTTCGACACAACCTGTTTATTATTAAAAAGTATTAAAATTCTAGATTACAAC
119 GATAACATTTTCGGCACAACCTGTTTATTATTAAAAA-TATTAACATTCCATATTAC-AC
* * * * * *
1799153 CTTTTCTATTATTAAATCATGATATTATTGGGAGCAATCGTATTTCTTATATATGTTCATAAC
1 CTTTTTTATTATTGAACCATGAAATTATTGGG-GCAACCGTATTTCTTATATATATTCATAAC
1799216 GTACTCTGAT
Statistics
Matches: 494, Mismatches: 85, Indels: 53
0.78 0.13 0.08
Matches are distributed among these distances:
174 23 0.05
175 2 0.00
176 85 0.17
177 37 0.07
178 55 0.11
179 92 0.19
180 7 0.01
181 1 0.00
185 9 0.02
186 76 0.15
187 15 0.03
188 70 0.14
189 3 0.01
190 19 0.04
ACGTcount: A:0.34, C:0.15, G:0.09, T:0.42
Consensus pattern (176 bp):
CTTTTTTATTATTGAACCATGAAATTATTGGGGCAACCGTATTTCTTATATATATTCATAACATT
TTCAGTTTTAAACTTATTTTCTTATACTGGGATAATCCAAGACTTTAAACTCTGATAACATTTTC
GGCACAACCTGTTTATTATTAAAAATATTAACATTCCATATTACAC
Found at i:1799197 original size:364 final size:354
Alignment explanation
Indices: 1798552--1799206 Score: 856
Period size: 364 Copynumber: 1.8 Consensus size: 354
1798542 TTAAACTTTG
* **
1798552 ATAATATTTTCGGCGTAACCTACTTTATTATTAAAAATATTAACATTCCATATTACAATTTTTTC
1 ATAAAATTTTCGGCACAACCTACTTTATTATTAAAAATATTAACATTCCATATTACAATTTTTTC
* *
1798617 ATTATTGAACTATGAAATTATTAGACACAACCGTATTTCTTATATATATTCAAAGCATTTTCAGT
66 AGTATTGAACCATGAAATTATTAGACACAACCGTATTTCTTATATATATTCAAAGCATTTTCAGT
* * * ***
1798682 TTTAAATTTATTTTCTTATATTGGGATAATCCAAGACTTTAAACTCTGACAACATTTTCGGTGCA
131 TTTAAACTTATTTTCTTATACTAGGATAATCCAAGACTTTAAACTCTGACAACATTTTCGACACA
* * * * *
1798747 ATCTGTTTTATTATTAAAAGTATTAACATTCTATATTACCACCTATTTTATTATTGAACCATGAA
196 ACCTGTTTTATTATTAAAAGTATTAAAATTCTAGATTACAACCTATTTTATTATTAAACCATGAA
1798812 ATTATTAGGGGCAACCGTATTTCTTATATATATTTATTACATTTTAAGTTTTAAACTTATTTTCT
261 ATTATTAGGGGCAACCGTATTTCTTATATATATTTATTACATTTTAAGTTTTAAACTTATTTTCT
1798877 TATACTGTGATAATCCAAGGCAAAATATA
326 TATACTGTGATAATCCAAGGCAAAATATA
* * *
1798906 ATAAAATTTTCGGCACAAGCTACTTTATTATTAAAAATATTAGCATTCCATATTACAGTCTTTTT
1 ATAAAATTTTCGGCACAACCTACTTTATTATTAAAAATATTAACATTCCATATTACAAT-TTTTT
* ** *
1798971 TAGTATTGAACCATGAAATTATT-G-GGCAACTGTATTTCTTATATATATGTTCATAA-CATTTT
65 CAGTATTGAACCATGAAATTATTAGACACAACCGTATTTCTTATATATA--TTCA-AAGCA-TTT
* *
1799033 TCA-TATTTAAACTTATTTTTTTATACTAGGATAATCCAAGACTCCATTATCTTAAACTCTGATA
126 TCAGT-TTTAAACTTATTTTCTTATACTAGGATAATCCAAGA---C----T-TTAAACTCTGACA
1799097 ACATTTTCGACACAACCTG-TTTATTATTAAAAAGTATTAAAATTCTAGATTACAACCT-TTTCT
182 ACATTTTCGACACAACCTGTTTTATTATT-AAAAGTATTAAAATTCTAGATTACAACCTATTT-T
* * *
1799160 ATTATTAAATCATGATATTATT-GGGAGCAATCGTATTTCTTATATAT
245 ATTATTAAACCATGAAATTATTAGGG-GCAACCGTATTTCTTATATAT
1799207 GTTCATAACG
Statistics
Matches: 256, Mismatches: 28, Indels: 24
0.83 0.09 0.08
Matches are distributed among these distances:
353 20 0.08
354 54 0.21
355 32 0.12
356 40 0.16
359 1 0.00
363 16 0.06
364 93 0.36
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.43
Consensus pattern (354 bp):
ATAAAATTTTCGGCACAACCTACTTTATTATTAAAAATATTAACATTCCATATTACAATTTTTTC
AGTATTGAACCATGAAATTATTAGACACAACCGTATTTCTTATATATATTCAAAGCATTTTCAGT
TTTAAACTTATTTTCTTATACTAGGATAATCCAAGACTTTAAACTCTGACAACATTTTCGACACA
ACCTGTTTTATTATTAAAAGTATTAAAATTCTAGATTACAACCTATTTTATTATTAAACCATGAA
ATTATTAGGGGCAACCGTATTTCTTATATATATTTATTACATTTTAAGTTTTAAACTTATTTTCT
TATACTGTGATAATCCAAGGCAAAATATA
Found at i:1799544 original size:37 final size:37
Alignment explanation
Indices: 1799471--1799544 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 37
1799461 GTTGAAAAAT
*
1799471 ATTTATATATTTTCTTTAAAAAAATTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
* *
1799508 ATTTATATAATTTT-TTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAAATCATAAA
1799545 TATGTTTAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 23 0.72
38 9 0.28
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.46
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAAATCATAAA
Found at i:1805277 original size:20 final size:21
Alignment explanation
Indices: 1805254--1805297 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1805244 GAAATTTATT
1805254 ATATTTATC-AAAAATAAAAA
1 ATATTTATCTAAAAATAAAAA
* *
1805274 ATATTTATCTAAAAGTGAAAA
1 ATATTTATCTAAAAATAAAAA
1805295 ATA
1 ATA
1805298 AAATACAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (21 bp):
ATATTTATCTAAAAATAAAAA
Found at i:1805812 original size:14 final size:14
Alignment explanation
Indices: 1805793--1805831 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1805783 TAATGGGGAG
1805793 TAATCCCTGCAAAA
1 TAATCCCTGCAAAA
*
1805807 TAATCCCTGCGAAA
1 TAATCCCTGCAAAA
* *
1805821 GAATCTCTGCA
1 TAATCCCTGCA
1805832 TATAGACAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.28, G:0.13, T:0.23
Consensus pattern (14 bp):
TAATCCCTGCAAAA
Found at i:1808047 original size:32 final size:31
Alignment explanation
Indices: 1807985--1808071 Score: 93
Period size: 32 Copynumber: 2.7 Consensus size: 31
1807975 TATATGGTCT
* * **
1807985 GTCAATATCGAATCGGTTGATTTTTAGGTCGG
1 GTCAATACCGGATCGGTTGA-TTTCGGGTCGG
*
1808017 GTTAATACCGGATCGGTTAGATTTCGGGTCGG
1 GTCAATACCGGATCGGTT-GATTTCGGGTCGG
* *
1808049 GTCAATATCTGATCGGTTGATTT
1 GTCAATACCGGATCGGTTGATTT
1808072 TTGGTTTAGG
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
31 5 0.11
32 39 0.85
33 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.29, T:0.37
Consensus pattern (31 bp):
GTCAATACCGGATCGGTTGATTTCGGGTCGG
Found at i:1809375 original size:2 final size:2
Alignment explanation
Indices: 1809368--1809394 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1809358 TGTATCTATG
1809368 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 T
1809395 GAAAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1809856 original size:21 final size:20
Alignment explanation
Indices: 1809826--1809871 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1809816 ACTAATTTTA
* *
1809826 AAATAATTTAAGATTAAAAT
1 AAATAATTTAAAAATAAAAT
*
1809846 AAATAATTTTAAAAATAAATT
1 AAATAA-TTTAAAAATAAAAT
1809867 AAATA
1 AAATA
1809872 TTAAGATGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (20 bp):
AAATAATTTAAAAATAAAAT
Found at i:1816862 original size:17 final size:16
Alignment explanation
Indices: 1816820--1816865 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 16
1816810 TTTTAATTGG
1816820 AAAATATTAATATATAT
1 AAAA-ATTAATATATAT
1816837 AAAAA-TAATATAT-T
1 AAAAATTAATATATAT
1816851 AAATAAATTAATATA
1 -AA-AAATTAATATA
1816866 AGATTTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.04
15 10 0.38
16 4 0.15
17 11 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
AAAAATTAATATATAT
Found at i:1816975 original size:29 final size:29
Alignment explanation
Indices: 1816941--1817000 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
1816931 TTAAACATTT
*
1816941 TTTAAATAATATAA-ATAAAGTATTAAATA
1 TTTAAA-AATATAATATAAACTATTAAATA
* *
1816970 TTTAAAAATTTAATTTAAACTATTAAATA
1 TTTAAAAATATAATATAAACTATTAAATA
1816999 TT
1 TT
1817001 GATATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 6 0.22
29 21 0.78
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.43
Consensus pattern (29 bp):
TTTAAAAATATAATATAAACTATTAAATA
Found at i:1817034 original size:15 final size:16
Alignment explanation
Indices: 1817016--1817050 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
1817006 AAAAATAATT
1817016 AAATAAAA-ATTTTGA
1 AAATAAAATATTTTGA
*
1817031 AAATAAAATATTTTTA
1 AAATAAAATATTTTGA
1817047 AAAT
1 AAAT
1817051 CCAGTTCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (16 bp):
AAATAAAATATTTTGA
Found at i:1817887 original size:3 final size:3
Alignment explanation
Indices: 1817879--1817922 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
1817869 CAGACCTTAT
1817879 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1817923 TTGTAATCAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1819345 original size:446 final size:447
Alignment explanation
Indices: 1818510--1819345 Score: 1243
Period size: 446 Copynumber: 1.9 Consensus size: 447
1818500 ATTACATAAA
* *
1818510 GACATTTACGGTTTGAAACTGGCACAATTAGCGTGATATTTATGGTTAAAAATTAATTAAATGAG
1 GACATTTACGGTTTGAAACTAGCACAATTAGCGTGATATTTATGGTTAAAAATTAATTAAATAAG
* * ** * * * * *
1818575 CATGGGAAAGGGAACAGAAATCCTCTGCCCCTATGTGTATCCCTCCAAAATTTTTCTTATATGTG
66 CATGGGAAAGAGAACAAAAATAATCTACCCCTATATATATCACTCCAAAATTTTTCTTATACGTG
* * *
1818640 TCGATTATATTTTTTTCCTACTTTCCTACGTTTTACTTAATCTTCTACCTTTAAACTCATTCGGT
131 TCAATTATATTTTTTTACTACTTTCCTAC-TTTTACTTAATCTTCTAACTTTAAACTCATTCGGT
* * * * *
1818705 AAAATCCTGAACCTCCACACACTGAAATGTAGGGTCATCTTCGTTATTTGAGATTCAAACTAATT
195 AAAATCCTGAACATCAACACACTGAAAAGTAGGGCCATCATCGTTATTTGAGATTCAAACTAATT
* * *
1818770 TATCTCCATGTTTGTTAATAGTTTATTTTTATGCAAAATGAAATATTTGGCAATGGAAGATGCAA
260 TATCTCCATGTTCGTTAATAGTTTATTTTCATGCAAAATGAAACATTTGGCAATGGAAGATGCAA
* *
1818835 GTTGATACGAACTCTTTTAACATGATTTTTGGCCTGCAAATAACAAACGTCTAAATCAGTATAAT
325 GTTGATACAAACTCTTTTAACATGATTTTTGGCCTGCAAATAACAAACATCTAAATCAGTATAAT
1818900 TTGCATAGTTTTATTTCCATGTTCCAATCAATTAAGAACTAATCAAACACCCGGAAAT
390 TTGCATAGTTTTATTTCCATGTTCCAATCAATTAAGAACTAATCAAACACCCGGAAAT
* * *
1818958 GACATTTACGGTTTGAAACTAGCACACTTTGTGTGATATTTATGGTTAAAAGA-TAATTAAAATA
1 GACATTTACGGTTTGAAACTAGCACAATTAGCGTGATATTTATGGTTAAAA-ATTAATT-AAATA
* * *
1819022 AGCAT-GGACAAGAGAACAAAAATAATTTACCCCTGTATATATCACTCCAATATTTTTCTTATAC
64 AGCATGGGA-AAGAGAACAAAAATAATCTACCCCTATATATATCACTCCAAAATTTTTCTTATAC
* * *
1819086 GTGTCAATTTTA-TTTTTTACTACTTTCCTA-TTTTACTTCATCTTCTAACTTTAAACTCATTTG
128 GTGTCAATTATATTTTTTTACTACTTTCCTACTTTTACTTAATCTTCTAACTTTAAACTCATTCG
1819149 GTAAAATCCTGAACATCAACACACTGAAAAGTAGGGCCATCATCGTTATTTGAGATTCAAACTAA
193 GTAAAATCCTGAACATCAACACACTGAAAAGTAGGGCCATCATCGTTATTTGAGATTCAAACTAA
1819214 TTTATCTCCATGTTCGTTAATAGTTTATTTTCATGCAAAATGAAACATTTGGCAAT-GAGAGATG
258 TTTATCTCCATGTTCGTTAATAGTTTATTTTCATGCAAAATGAAACATTTGGCAATGGA-AGATG
* * * *
1819278 CAAGTTGATACAAACTCTTTTAACTTGATTTTTGGCTTGCTAATAGA-AAACATCTAAATCGGTA
322 CAAGTTGATACAAACTCTTTTAACATGATTTTTGGCCTGCAAATA-ACAAACATCTAAATCAGTA
1819342 TAAT
386 TAAT
1819346 CTGTGTCGAC
Statistics
Matches: 346, Mismatches: 37, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
445 2 0.01
446 208 0.60
447 1 0.00
448 72 0.21
449 63 0.18
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (447 bp):
GACATTTACGGTTTGAAACTAGCACAATTAGCGTGATATTTATGGTTAAAAATTAATTAAATAAG
CATGGGAAAGAGAACAAAAATAATCTACCCCTATATATATCACTCCAAAATTTTTCTTATACGTG
TCAATTATATTTTTTTACTACTTTCCTACTTTTACTTAATCTTCTAACTTTAAACTCATTCGGTA
AAATCCTGAACATCAACACACTGAAAAGTAGGGCCATCATCGTTATTTGAGATTCAAACTAATTT
ATCTCCATGTTCGTTAATAGTTTATTTTCATGCAAAATGAAACATTTGGCAATGGAAGATGCAAG
TTGATACAAACTCTTTTAACATGATTTTTGGCCTGCAAATAACAAACATCTAAATCAGTATAATT
TGCATAGTTTTATTTCCATGTTCCAATCAATTAAGAACTAATCAAACACCCGGAAAT
Found at i:1820171 original size:30 final size:31
Alignment explanation
Indices: 1820135--1820204 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
1820125 TCGAATTATC
1820135 CCTAAATT-AAAGGACTAGCGTGAAATCTAA
1 CCTAAATTAAAAGGACTAGCGTGAAATCTAA
1820165 CCTAAATTAAAAGGACTAGCGTGAAATCTAA
1 CCTAAATTAAAAGGACTAGCGTGAAATCTAA
1820196 CCTTAAATT
1 CC-TAAATT
1820205 CATTTTAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
30 8 0.21
31 24 0.63
32 6 0.16
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (31 bp):
CCTAAATTAAAAGGACTAGCGTGAAATCTAA
Found at i:1825658 original size:35 final size:36
Alignment explanation
Indices: 1825614--1825687 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 36
1825604 AAAATTGATG
*
1825614 TTATCTATAATAAGTCATGTCACTTGGTGAATAGAC
1 TTATCTATAATAAGTCATGTCACTTAGTGAATAGAC
*
1825650 TTAT-TATAATAAGTCATGTCACTTAGTGAATGGAC
1 TTATCTATAATAAGTCATGTCACTTAGTGAATAGAC
1825685 TTA
1 TTA
1825688 ATTTTTAGTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
35 32 0.89
36 4 0.11
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (36 bp):
TTATCTATAATAAGTCATGTCACTTAGTGAATAGAC
Found at i:1826734 original size:95 final size:95
Alignment explanation
Indices: 1826569--1826745 Score: 273
Period size: 95 Copynumber: 1.9 Consensus size: 95
1826559 CATTACTCAA
* *
1826569 AGTATCGATACTACTAATCTAAGTAGTATCGATATCATATATGGTATCGGTACCATTCTAGAATT
1 AGTATCGATACTACTAATCTAAGTAGTATCGATATCATATATGGTATCAGTACCATTATAGAATT
*
1826634 CTGTTTTGAAAGTATCGTTACTGCCTCAGC
66 ATGTTTTGAAAGTATCGTTACTGCCTCAGC
* * ** *
1826664 AGTATCGGTACTACTACTCTGTGTAGTATCGATATCATATATGGTATCAGTACCATTATAGCATT
1 AGTATCGATACTACTAATCTAAGTAGTATCGATATCATATATGGTATCAGTACCATTATAGAATT
*
1826729 ATGTTTTGATAGTATCG
66 ATGTTTTGAAAGTATCG
1826746 GTACAATTTT
Statistics
Matches: 73, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
95 73 1.00
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (95 bp):
AGTATCGATACTACTAATCTAAGTAGTATCGATATCATATATGGTATCAGTACCATTATAGAATT
ATGTTTTGAAAGTATCGTTACTGCCTCAGC
Found at i:1826781 original size:33 final size:33
Alignment explanation
Indices: 1826713--1826781 Score: 93
Period size: 33 Copynumber: 2.1 Consensus size: 33
1826703 TATGGTATCA
* * *
1826713 GTACCATTATAGCATTATGTTTTGATAGTATCG
1 GTACAATTATAGCATTATGTTTTGACAGTACCG
* *
1826746 GTACAATTTTAGCATTATGTTTTTACAGTACCG
1 GTACAATTATAGCATTATGTTTTGACAGTACCG
1826779 GTA
1 GTA
1826782 TTGCATCAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.13, G:0.17, T:0.42
Consensus pattern (33 bp):
GTACAATTATAGCATTATGTTTTGACAGTACCG
Found at i:1827504 original size:22 final size:21
Alignment explanation
Indices: 1827478--1827532 Score: 85
Period size: 20 Copynumber: 2.6 Consensus size: 21
1827468 TGATGAATAG
1827478 TATCGATACTAAGCAAGAACAA
1 TATCGATACTAAG-AAGAACAA
*
1827500 TATCGATACT-AGATGAACAA
1 TATCGATACTAAGAAGAACAA
1827520 TATCGATACTAAG
1 TATCGATACTAAG
1827533 TGCACAAATG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
20 17 0.55
21 4 0.13
22 10 0.32
ACGTcount: A:0.45, C:0.16, G:0.15, T:0.24
Consensus pattern (21 bp):
TATCGATACTAAGAAGAACAA
Found at i:1832289 original size:2 final size:2
Alignment explanation
Indices: 1832282--1832320 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
1832272 TGTAGTGACA
1832282 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1832321 ATACTTATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1832342 original size:21 final size:21
Alignment explanation
Indices: 1832288--1832349 Score: 58
Period size: 22 Copynumber: 2.9 Consensus size: 21
1832278 GACAATATAT
1832288 ATATATATAT-ATA-TATATATA
1 ATATATATATAATACT-TAT-TA
1832309 TATATATATATAATACTTATTA
1 -ATATATATATAATACTTATTA
*
1832331 ATATCATA-ATAATATTTAT
1 ATAT-ATATATAATACTTAT
1832350 AGAGATATGT
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 14 0.39
22 15 0.42
23 6 0.17
24 1 0.03
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (21 bp):
ATATATATATAATACTTATTA
Found at i:1833082 original size:26 final size:26
Alignment explanation
Indices: 1833053--1833141 Score: 151
Period size: 26 Copynumber: 3.4 Consensus size: 26
1833043 TGACGTGACA
1833053 GTTTCTAGAAGGTCCAGTCAACGGCG
1 GTTTCTAGAAGGTCCAGTCAACGGCG
** *
1833079 GTTTCTAGAAGGTCCAGTCAGTGACG
1 GTTTCTAGAAGGTCCAGTCAACGGCG
1833105 GTTTCTAGAAGGTCCAGTCAACGGCG
1 GTTTCTAGAAGGTCCAGTCAACGGCG
1833131 GTTTCTAGAAG
1 GTTTCTAGAAG
1833142 ACCCCCTCAG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.24, C:0.20, G:0.30, T:0.26
Consensus pattern (26 bp):
GTTTCTAGAAGGTCCAGTCAACGGCG
Found at i:1833413 original size:25 final size:26
Alignment explanation
Indices: 1833366--1833414 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
1833356 AGCTTTCTCT
*
1833366 TTTTACTTTTCAAGTTTTATTTTTTC
1 TTTTACTTTTCAAGATTTATTTTTTC
* *
1833392 TTTTA-TTTTTAAGATTTGTTTTT
1 TTTTACTTTTCAAGATTTATTTTT
1833415 AATATGCTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.16, C:0.06, G:0.06, T:0.71
Consensus pattern (26 bp):
TTTTACTTTTCAAGATTTATTTTTTC
Found at i:1836943 original size:16 final size:14
Alignment explanation
Indices: 1836930--1836961 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1836920 TCTGTTACAT
1836930 TTTTTTACTTTTAC
1 TTTTTTACTTTTAC
1836944 TTTTTTACTTTTA-
1 TTTTTTACTTTTAC
1836957 TTTTT
1 TTTTT
1836962 ATTTCAATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTTTACTTTTAC
Found at i:1839711 original size:25 final size:26
Alignment explanation
Indices: 1839675--1839723 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
1839665 CTTTCTCTTT
*
1839675 TTTTACTTTTCAAGTTTTATTTTTTC
1 TTTTACTTTTCAAGCTTTATTTTTTC
*
1839701 TTTTA-TTTTCAAGCTTTGTTTTT
1 TTTTACTTTTCAAGCTTTATTTTT
1839724 AATATGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.14, C:0.10, G:0.06, T:0.69
Consensus pattern (26 bp):
TTTTACTTTTCAAGCTTTATTTTTTC
Found at i:1841628 original size:17 final size:18
Alignment explanation
Indices: 1841597--1841639 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
1841587 CATTAAAACG
*
1841597 TTTATTTTTTCATTTTAA
1 TTTATTTTTTCATTTGAA
1841615 TTTATTTTTT-ATTTGAA
1 TTTATTTTTTCATTTGAA
1841632 TTT-TTTTT
1 TTTATTTTT
1841640 AATATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 9 0.38
18 10 0.42
ACGTcount: A:0.19, C:0.02, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTATTTTTTCATTTGAA
Found at i:1842053 original size:23 final size:23
Alignment explanation
Indices: 1842005--1842057 Score: 72
Period size: 23 Copynumber: 2.3 Consensus size: 23
1841995 AACTAAAACA
*
1842005 TAATATTGTATTTTAAATTAAAT
1 TAATATTGAATTTTAAATTAAAT
*
1842028 TAATATATGAATTTTAAATT-ATT
1 TAATAT-TGAATTTTAAATTAAAT
1842051 TAATATT
1 TAATATT
1842058 ATTCCAATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 1 0.04
23 14 0.52
24 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (23 bp):
TAATATTGAATTTTAAATTAAAT
Found at i:1843744 original size:17 final size:19
Alignment explanation
Indices: 1843718--1843752 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
1843708 TTTATGAACG
1843718 TTTTTGTAGT-AAATATAA
1 TTTTTGTAGTGAAATATAA
1843736 TTTTT-TAGTGAAATATA
1 TTTTTGTAGTGAAATATA
1843753 TAATACATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (19 bp):
TTTTTGTAGTGAAATATAA
Found at i:1845863 original size:164 final size:167
Alignment explanation
Indices: 1845592--1845923 Score: 634
Period size: 164 Copynumber: 2.0 Consensus size: 167
1845582 AGCTCAGTGT
1845592 ACTCCTTGCGGTGTATAGAAACATTCAGATAAATACTTCAGTAAAAATTAATTTATAAAATATTT
1 ACTCCTTGCGGTGTATAGAAACATTCAGATAAATACTTCAGTAAAAATTAATTTATAAAATATTT
1845657 TTTTAAAACATGAACACTACCCACATCCGAACACTAGAATGTGTAGATTCCCCTGAAC-TATACC
66 TTTTAAAACATGAACACTACCCACATCCGAACACTAGAATGTGTAGATTCCCCTGAACATATACC
1845721 CACATGTCCCAAT-AATATC-TATACTTATAGTATAA
131 CACATGTCCCAATAAATATCTTATACTTATAGTATAA
1845756 ACTCCTTGCGGTGTATAGAAACATTCAGATAAATACTTCAGTAAAAATTAATTTATAAAATATTT
1 ACTCCTTGCGGTGTATAGAAACATTCAGATAAATACTTCAGTAAAAATTAATTTATAAAATATTT
1845821 TTTTAAAACATGAACACTACCCACATCCGAACACTAGAATGTGTAGATTCCCCTGAACTATATAC
66 TTTTAAAACATGAACACTACCCACATCCGAACACTAGAATGTGTAGATTCCCCTGAAC-ATATAC
1845886 CCACATGTCCCAATAAATATCTTATACTTATAGTATAA
130 CCACATGTCCCAATAAATATCTTATACTTATAGTATAA
1845924 GGGCATGCGG
Statistics
Matches: 164, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
164 123 0.75
166 19 0.12
167 6 0.04
168 16 0.10
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (167 bp):
ACTCCTTGCGGTGTATAGAAACATTCAGATAAATACTTCAGTAAAAATTAATTTATAAAATATTT
TTTTAAAACATGAACACTACCCACATCCGAACACTAGAATGTGTAGATTCCCCTGAACATATACC
CACATGTCCCAATAAATATCTTATACTTATAGTATAA
Found at i:1846933 original size:15 final size:15
Alignment explanation
Indices: 1846913--1846950 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
1846903 TGTCAGGTCA
1846913 GTCGAATCGGAACCC
1 GTCGAATCGGAACCC
1846928 GTCGAATCGGAACCC
1 GTCGAATCGGAACCC
*
1846943 ATCGAATC
1 GTCGAATC
1846951 TGATTCAATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.29, C:0.32, G:0.24, T:0.16
Consensus pattern (15 bp):
GTCGAATCGGAACCC
Found at i:1846961 original size:15 final size:15
Alignment explanation
Indices: 1846943--1846973 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1846933 ATCGGAACCC
*
1846943 ATCGAATCTGATTCA
1 ATCGAATCCGATTCA
1846958 ATCGAATCCGATTCA
1 ATCGAATCCGATTCA
1846973 A
1 A
1846974 ATTGCCATCT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.29
Consensus pattern (15 bp):
ATCGAATCCGATTCA
Found at i:1848295 original size:19 final size:19
Alignment explanation
Indices: 1848271--1848308 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1848261 TTAGGATTTT
1848271 TGGGGATTTATAAACCTAA
1 TGGGGATTTATAAACCTAA
1848290 TGGGGATTTATAAACCTAA
1 TGGGGATTTATAAACCTAA
1848309 CATATTAGGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.32
Consensus pattern (19 bp):
TGGGGATTTATAAACCTAA
Found at i:1850593 original size:102 final size:103
Alignment explanation
Indices: 1850417--1850622 Score: 405
Period size: 102 Copynumber: 2.0 Consensus size: 103
1850407 TTTCCTCTTC
1850417 TGATATCCCACACTCAATTCCTTTTTCCTTTCCTTCTTCTCTTTTTAAGTTTAAAATAACTAACT
1 TGATATCCCACACTCAATTCCTTTTTCCTTTCCTTCTTCTCTTTTTAAGTTTAAAATAACTAACT
1850482 CAAGACTTAGACAAG-TTTTATGCTTTTGTAACGTTGG
66 CAAGACTTAGACAAGATTTTATGCTTTTGTAACGTTGG
1850519 TGATATCCCACACTCAATTCCTTTTTCCTTTCCTTCTTCTCTTTTTAAGTTTAAAATAACTAACT
1 TGATATCCCACACTCAATTCCTTTTTCCTTTCCTTCTTCTCTTTTTAAGTTTAAAATAACTAACT
1850584 CAAGACTTAGACAAGATTTTATGCTTTTGTAACGTTGG
66 CAAGACTTAGACAAGATTTTATGCTTTTGTAACGTTGG
1850622 T
1 T
1850623 TGAAACAAAG
Statistics
Matches: 103, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 80 0.78
103 23 0.22
ACGTcount: A:0.26, C:0.21, G:0.10, T:0.43
Consensus pattern (103 bp):
TGATATCCCACACTCAATTCCTTTTTCCTTTCCTTCTTCTCTTTTTAAGTTTAAAATAACTAACT
CAAGACTTAGACAAGATTTTATGCTTTTGTAACGTTGG
Found at i:1851957 original size:144 final size:144
Alignment explanation
Indices: 1851749--1852037 Score: 578
Period size: 144 Copynumber: 2.0 Consensus size: 144
1851739 GCCAAGATGA
1851749 GTGGTTGCAAGCCTTAGCTGAATGATGATGTCCTTTGGTTGCTTAGGAGGCTAAATGAAGTCACA
1 GTGGTTGCAAGCCTTAGCTGAATGATGATGTCCTTTGGTTGCTTAGGAGGCTAAATGAAGTCACA
1851814 TGGGTTGTACATGTTGTGATAAGGCACATGAGTTCTCCTTGGTGTCACATGATCTCCATGCCTTG
66 TGGGTTGTACATGTTGTGATAAGGCACATGAGTTCTCCTTGGTGTCACATGATCTCCATGCCTTG
1851879 GTAAGATGAGCATG
131 GTAAGATGAGCATG
1851893 GTGGTTGCAAGCCTTAGCTGAATGATGATGTCCTTTGGTTGCTTAGGAGGCTAAATGAAGTCACA
1 GTGGTTGCAAGCCTTAGCTGAATGATGATGTCCTTTGGTTGCTTAGGAGGCTAAATGAAGTCACA
1851958 TGGGTTGTACATGTTGTGATAAGGCACATGAGTTCTCCTTGGTGTCACATGATCTCCATGCCTTG
66 TGGGTTGTACATGTTGTGATAAGGCACATGAGTTCTCCTTGGTGTCACATGATCTCCATGCCTTG
1852023 GTAAGATGAGCATG
131 GTAAGATGAGCATG
1852037 G
1 G
1852038 GTTCGGTCAT
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
144 145 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.32
Consensus pattern (144 bp):
GTGGTTGCAAGCCTTAGCTGAATGATGATGTCCTTTGGTTGCTTAGGAGGCTAAATGAAGTCACA
TGGGTTGTACATGTTGTGATAAGGCACATGAGTTCTCCTTGGTGTCACATGATCTCCATGCCTTG
GTAAGATGAGCATG
Found at i:1853716 original size:13 final size:13
Alignment explanation
Indices: 1853690--1853730 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
1853680 GTCACAATCT
*
1853690 AATAATTTTAAAA
1 AATAATTTTTAAA
*
1853703 AATTATTTTTAAA
1 AATAATTTTTAAA
*
1853716 AATAATTATTAAA
1 AATAATTTTTAAA
1853729 AA
1 AA
1853731 CATTATTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATAATTTTTAAA
Found at i:1853724 original size:16 final size:14
Alignment explanation
Indices: 1853695--1853737 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
1853685 AATCTAATAA
1853695 TTTTAAAAAATTAT
1 TTTTAAAAAATTAT
*
1853709 TTTT-AAAAATAAT
1 TTTTAAAAAATTAT
*
1853722 TATTAAAAACATTAT
1 TTTTAAAAA-ATTAT
1853737 T
1 T
1853738 ATATTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 11 0.46
14 8 0.33
15 5 0.21
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (14 bp):
TTTTAAAAAATTAT
Found at i:1855156 original size:21 final size:21
Alignment explanation
Indices: 1855131--1855170 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1855121 ACCCTAAAAC
* *
1855131 TAAACCCTAAACTCTAAATTA
1 TAAACCATAAACCCTAAATTA
*
1855152 TAAACTATAAACCCTAAAT
1 TAAACCATAAACCCTAAAT
1855171 CTTAAATCTC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.28
Consensus pattern (21 bp):
TAAACCATAAACCCTAAATTA
Found at i:1855184 original size:28 final size:28
Alignment explanation
Indices: 1855131--1855198 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
1855121 ACCCTAAAAC
* *
1855131 TAAACCCTAAACTCTAAATTATAAACTA
1 TAAACCCTAAACTCTAAATTACAAACCA
1855159 TAAACCCTAAA-TCTTAAATCT-CAAACCA
1 TAAACCCTAAACTC-TAAAT-TACAAACCA
*
1855187 TAAACCATAAAC
1 TAAACCCTAAAC
1855199 CCTATGCCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
27 2 0.06
28 31 0.91
29 1 0.03
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (28 bp):
TAAACCCTAAACTCTAAATTACAAACCA
Found at i:1855325 original size:21 final size:20
Alignment explanation
Indices: 1855297--1855335 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1855287 GATTACACTC
*
1855297 TAAACCTAAACCCTAAACTA
1 TAAACCTAAACACTAAACTA
1855317 TAAATCCTAAACACTAAAC
1 TAAA-CCTAAACACTAAAC
1855336 CTCAAACTCT
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:0.51, C:0.28, G:0.00, T:0.21
Consensus pattern (20 bp):
TAAACCTAAACACTAAACTA
Found at i:1855361 original size:14 final size:13
Alignment explanation
Indices: 1855296--1855355 Score: 59
Period size: 14 Copynumber: 4.4 Consensus size: 13
1855286 AGATTACACT
1855296 CTAAAC-CTAAACC
1 CTAAACTCTAAA-C
*
1855309 CTAAACTATAAATC
1 CTAAACTCTAAA-C
*
1855323 CTAAACACTAAAC
1 CTAAACTCTAAAC
1855336 CTCAAACTCTAAAC
1 CT-AAACTCTAAAC
1855350 TCTAAA
1 -CTAAA
1855356 TCCTAAGTCT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
13 9 0.23
14 28 0.72
15 2 0.05
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (13 bp):
CTAAACTCTAAAC
Found at i:1855400 original size:172 final size:172
Alignment explanation
Indices: 1855072--1855413 Score: 397
Period size: 172 Copynumber: 2.0 Consensus size: 172
1855062 CATTGTATAT
* * *
1855072 TACTAAAAGAAAAATAAAAGTCTATTTAATTAATCACATGTTAGATTACACCCTAAAACTAAACC
1 TACTAAAAGAAAAATAAAAGCCCATTTAATTAAGCACATGTTAGATTACACCCTAAAACTAAACC
* *
1855137 CTAAACTCTAAATTATAAACTATAAACCCTAAATCTTAAATCTCAAACCATAAACCATAAACCCT
66 CTAAACTATAAATCATAAACTATAAACCCTAAATCTTAAATCTCAAACCATAAACCATAAACCCT
** * * * *
1855202 ATGCCCTAAACATTAAACCCTTAATCTGTTTATGTGATAGGA
131 AAACCCTAAACACTAAACCATTAATCTGATTATATGATAGGA
* *
1855244 TACTAAAAGAAAAATAAAAGCCCATTTAATTAAGCACATGTTAGATTACACTCTAAACCTAAACC
1 TACTAAAAGAAAAATAAAAGCCCATTTAATTAAGCACATGTTAGATTACACCCTAAAACTAAACC
* ** *
1855309 CTAAACTATAAATCCTAAAC-ACTAAA-CCTCAAA-CTCTAAA-CTCTAAATCC-TAAGTCTTAA
66 CTAAACTATAAATCATAAACTA-TAAACCCT-AAATCT-TAAATCTC-AAA-CCATAAACCATAA
** *** *
1855369 GGCCTAAATTTTAAACCCTAAACCATTAATCTGATTATATGATAG
126 ACCCTAAACCCTAAACACTAAACCATTAATCTGATTATATGATAG
1855414 AGGTTAAGTT
Statistics
Matches: 142, Mismatches: 23, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
171 9 0.06
172 131 0.92
173 2 0.01
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.28
Consensus pattern (172 bp):
TACTAAAAGAAAAATAAAAGCCCATTTAATTAAGCACATGTTAGATTACACCCTAAAACTAAACC
CTAAACTATAAATCATAAACTATAAACCCTAAATCTTAAATCTCAAACCATAAACCATAAACCCT
AAACCCTAAACACTAAACCATTAATCTGATTATATGATAGGA
Found at i:1856757 original size:12 final size:12
Alignment explanation
Indices: 1856740--1856782 Score: 79
Period size: 12 Copynumber: 3.7 Consensus size: 12
1856730 TTCCCTCTTA
1856740 AAATCGAGCTTG
1 AAATCGAGCTTG
1856752 AAATCGAGCTTG
1 AAATCGAGCTTG
1856764 AAATCGAGCTTG
1 AAATCGAGCTTG
1856776 -AATCGAG
1 AAATCGAG
1856783 TCCAAAATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
11 7 0.23
12 24 0.77
ACGTcount: A:0.35, C:0.16, G:0.26, T:0.23
Consensus pattern (12 bp):
AAATCGAGCTTG
Found at i:1856790 original size:23 final size:23
Alignment explanation
Indices: 1856739--1856808 Score: 88
Period size: 23 Copynumber: 3.0 Consensus size: 23
1856729 ATTCCCTCTT
*
1856739 AAAATCGAGCTTGAAATCGAGCTT
1 AAAATCGAGCTTG-AATCGAGCTC
*
1856763 GAAATCGAGCTTGAATCGAG-TCC
1 AAAATCGAGCTTGAATCGAGCT-C
*
1856786 AAAATTGAGCTTGAATCGAGCTC
1 AAAATCGAGCTTGAATCGAGCTC
1856809 GAGTCTTGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
22 1 0.03
23 26 0.65
24 13 0.32
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (23 bp):
AAAATCGAGCTTGAATCGAGCTC
Found at i:1856917 original size:31 final size:31
Alignment explanation
Indices: 1856858--1856918 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
1856848 GTTCAAGCCT
* * *
1856858 TTTCGAGTTCGAGTCGAGTTTTAATATTTTA
1 TTTCAAGTTCGAGTCGAGCTTGAATATTTTA
* *
1856889 TTTCAAGTTCGAGTTGAGCTTGATTATTTT
1 TTTCAAGTTCGAGTCGAGCTTGAATATTTT
1856919 TAGCTCACGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.21, C:0.10, G:0.20, T:0.49
Consensus pattern (31 bp):
TTTCAAGTTCGAGTCGAGCTTGAATATTTTA
Found at i:1857393 original size:29 final size:29
Alignment explanation
Indices: 1857361--1857475 Score: 81
Period size: 29 Copynumber: 3.9 Consensus size: 29
1857351 TATTTTATAA
*
1857361 AAAAACATATATCATTTATTATAATTTCT
1 AAAAACATATATCCTTTATTATAATTTCT
* * * * *
1857390 AAAAACTTTTATCCTTTACTGTAATTTTCA
1 AAAAACATATATCCTTTATTATAA-TTTCT
* * * *
1857420 AAAAAAAGATTATCCCTTATTAT-ATTTTT
1 AAAAACATA-TATCCTTTATTATAATTTCT
**
1857449 AAAAAGTTTATAT-CTTTATTATAATTT
1 AAAAA-CATATATCCTTTATTATAATTT
1857476 TAATATTTTT
Statistics
Matches: 63, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
28 8 0.13
29 34 0.54
30 11 0.17
31 10 0.16
ACGTcount: A:0.40, C:0.10, G:0.03, T:0.47
Consensus pattern (29 bp):
AAAAACATATATCCTTTATTATAATTTCT
Found at i:1857459 original size:27 final size:28
Alignment explanation
Indices: 1857422--1857478 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
1857412 AATTTTCAAA
*
1857422 AAAAAGATTAT-CCCTTATTATATTTTT
1 AAAAAGATTATACCCTTATTATAATTTT
* * *
1857449 AAAAAGTTTATATCTTTATTATAATTTT
1 AAAAAGATTATACCCTTATTATAATTTT
1857477 AA
1 AA
1857479 TATTTTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 10 0.40
28 15 0.60
ACGTcount: A:0.40, C:0.07, G:0.04, T:0.49
Consensus pattern (28 bp):
AAAAAGATTATACCCTTATTATAATTTT
Found at i:1858404 original size:5 final size:5
Alignment explanation
Indices: 1858376--1858485 Score: 66
Period size: 5 Copynumber: 21.8 Consensus size: 5
1858366 AATCAATAAA
* * *
1858376 AAAAT AAAAT -TAAT AAAAC AAAAT AAAAT AAGAT GAAAAT AAAAAT AAAA-
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT -AAAAT AAAAT
* * * * **
1858426 AGAAT TAAAT AAAA- AAATAG AAAAT AAATAG AAAAT AAAATT TTAA-
1 AAAAT AAAAT AAAAT AAA-AT AAAAT AAA-AT AAAAT AAAA-T AAAAT
1858472 AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAA
1858486 AATATATATA
Statistics
Matches: 79, Mismatches: 18, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
4 11 0.14
5 49 0.62
6 19 0.24
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:1858415 original size:35 final size:35
Alignment explanation
Indices: 1858376--1858453 Score: 88
Period size: 35 Copynumber: 2.2 Consensus size: 35
1858366 AATCAATAAA
* *
1858376 AAAATAAAATTAATAA-AACAAAATAAAATAAGAT-G
1 AAAATAAAAATAAAAAGAACAAAATAAAA-AA-ATAG
**
1858411 AAAATAAAAATAAAAAGAATTAAATAAAAAAATAG
1 AAAATAAAAATAAAAAGAACAAAATAAAAAAATAG
1858446 AAAATAAA
1 AAAATAAA
1858454 TAGAAAATAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
34 2 0.05
35 25 0.68
36 10 0.27
ACGTcount: A:0.76, C:0.01, G:0.05, T:0.18
Consensus pattern (35 bp):
AAAATAAAAATAAAAAGAACAAAATAAAAAAATAG
Found at i:1858450 original size:46 final size:44
Alignment explanation
Indices: 1858370--1858487 Score: 125
Period size: 46 Copynumber: 2.6 Consensus size: 44
1858360 AATAATAATC
* *
1858370 AATAAAAA-AATAAAATT-AATAAAACAAAATAAAATAAGAT-GAA
1 AATAAAAATAAAAAAATTAAATAAAA-AAAAGAAAATAA-ATAGAA
1858413 AATAAAAATAAAAAGAATTAAATAAAAAAATAGAAAATAAATAGAA
1 AATAAAAATAAAAA-AATTAAATAAAAAAA-AGAAAATAAATAGAA
* * *
1858459 AATAAAATTTTAAAAAATAAAATAAAAAA
1 AATAAAA-ATAAAAAAATTAAATAAAAAA
1858488 TATATATATG
Statistics
Matches: 64, Mismatches: 5, Indels: 9
0.82 0.06 0.12
Matches are distributed among these distances:
43 8 0.12
44 4 0.06
45 9 0.14
46 38 0.59
47 5 0.08
ACGTcount: A:0.75, C:0.01, G:0.04, T:0.19
Consensus pattern (44 bp):
AATAAAAATAAAAAAATTAAATAAAAAAAAGAAAATAAATAGAA
Found at i:1858683 original size:16 final size:18
Alignment explanation
Indices: 1858653--1858690 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
1858643 TATGTTAGAT
1858653 AAAAAATAAATAAT-AAG
1 AAAAAATAAATAATAAAG
*
1858670 AAAAAATAGA-AATAAAG
1 AAAAAATAAATAATAAAG
1858687 AAAA
1 AAAA
1858691 GGGAGGAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 3 0.16
17 16 0.84
ACGTcount: A:0.79, C:0.00, G:0.08, T:0.13
Consensus pattern (18 bp):
AAAAAATAAATAATAAAG
Found at i:1858709 original size:7 final size:7
Alignment explanation
Indices: 1858697--1858721 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1858687 AAAAGGGAGG
1858697 AAAAAAT
1 AAAAAAT
1858704 AAAAAAT
1 AAAAAAT
1858711 AAAAAAT
1 AAAAAAT
1858718 AAAA
1 AAAA
1858722 TAAATACAAT
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:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:1858773 original size:3 final size:3
Alignment explanation
Indices: 1858765--1858814 Score: 59
Period size: 3 Copynumber: 16.7 Consensus size: 3
1858755 ATTAGGGGCA
*
1858765 AAT AAT AAT AAT AAT AAT AAAT AA- AAT -AT ATAT AAT AAT AAT TAT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT A-AT AAT AAT AAT AAT
1858810 AAT AA
1 AAT AA
1858815 AAGGGATAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
2 4 0.10
3 31 0.76
4 6 0.15
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1861672 original size:14 final size:14
Alignment explanation
Indices: 1861644--1861701 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
1861634 CTTGGACTTA
1861644 CCTTATTTTCTTTTT
1 CCTT-TTTTCTTTTT
1861659 -CTTTTTTCCTTTTT
1 CCTTTTTT-CTTTTT
1861673 CCTTTTTT-TTCTTT
1 CCTTTTTTCTT-TTT
*
1861687 -CTTTTCTTTTTTTT
1 CCTTTT-TTCTTTTT
1861701 C
1 C
1861702 AATTTAGGGC
Statistics
Matches: 37, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.30
14 17 0.46
15 9 0.24
ACGTcount: A:0.02, C:0.21, G:0.00, T:0.78
Consensus pattern (14 bp):
CCTTTTTTCTTTTT
Found at i:1861690 original size:20 final size:19
Alignment explanation
Indices: 1861649--1861701 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 19
1861639 ACTTACCTTA
1861649 TTTTCTTTTTCTTT-TTTCC
1 TTTTCTTTTT-TTTCTTTCC
1861668 TTTTTCCTTTTTTTTCTTT-C
1 -TTTT-CTTTTTTTTCTTTCC
1861688 TTTTCTTTTTTTTC
1 TTTTCTTTTTTTTC
1861702 AATTTAGGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
18 10 0.32
19 4 0.13
20 8 0.26
21 9 0.29
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (19 bp):
TTTTCTTTTTTTTCTTTCC
Found at i:1861774 original size:59 final size:57
Alignment explanation
Indices: 1861680--1861793 Score: 133
Period size: 59 Copynumber: 2.0 Consensus size: 57
1861670 TTTCCTTTTT
* * *
1861680 TTTCTTTCTTTTCTTTTTTTTCAATTTAGGGCGCCCTTTC-GGATTTTCACCCTAAAC
1 TTTCTTTCTTTTCTTTTTTTTCAACTTAGGACGCCCTCTCAGG-TTTTCACCCTAAAC
* *
1861737 TTTCTTT-TTTTCTTTTTCATTTTCGACTTAGGACGCCCTCTCAGGTTTTCATCCTAA
1 TTTCTTTCTTTTC-TTTT--TTTTCAACTTAGGACGCCCTCTCAGGTTTTCACCCTAA
1861794 GCAAAGTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
56 5 0.10
57 11 0.23
59 30 0.62
60 2 0.04
ACGTcount: A:0.14, C:0.25, G:0.11, T:0.51
Consensus pattern (57 bp):
TTTCTTTCTTTTCTTTTTTTTCAACTTAGGACGCCCTCTCAGGTTTTCACCCTAAAC
Found at i:1862802 original size:15 final size:15
Alignment explanation
Indices: 1862782--1862813 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1862772 TCTTATTTTC
1862782 TTTTTCTTTTTTCCT
1 TTTTTCTTTTTTCCT
*
1862797 TTTTTCTTTTTTTCT
1 TTTTTCTTTTTTCCT
1862812 TT
1 TT
1862814 CTTTTTTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (15 bp):
TTTTTCTTTTTTCCT
Found at i:1862821 original size:15 final size:14
Alignment explanation
Indices: 1862777--1862821 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
1862767 ACTCATCTTA
*
1862777 TTTTCTTTTTCTTT
1 TTTTCTTTTTTTTT
*
1862791 TTTCCTTTTTTCTTT
1 TTTTCTTTTTT-TTT
*
1862806 TTTTCTTTCTTTTT
1 TTTTCTTTTTTTTT
1862820 TT
1 TT
1862822 AATTTAGGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
14 14 0.54
15 12 0.46
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTCTTTTTTTTT
Found at i:1862862 original size:58 final size:59
Alignment explanation
Indices: 1862800--1862913 Score: 160
Period size: 59 Copynumber: 1.9 Consensus size: 59
1862790 TTTTCCTTTT
* * *
1862800 TTCTTTTTTTCTTTCTT-TTTTT-AATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACG
1 TTCTTTTTTTCTTT-TTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
* *
1862858 TTCTTTTTTTCTTTTTCTTTTTCGACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTCTTTTTTTCTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
1862914 GCAAAGTATT
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
57 2 0.04
58 19 0.39
59 28 0.57
ACGTcount: A:0.11, C:0.24, G:0.13, T:0.52
Consensus pattern (59 bp):
TTCTTTTTTTCTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
Found at i:1863907 original size:8 final size:8
Alignment explanation
Indices: 1863896--1863935 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
1863886 TCTTATTTTC
1863896 TTTTTC-T
1 TTTTTCTT
1863903 TTTTTCTT
1 TTTTTCTT
1863911 TTTTTCTT
1 TTTTTCTT
1863919 TTTTTCTT
1 TTTTTCTT
1863927 TTTTT-TT
1 TTTTTCTT
1863934 TT
1 TT
1863936 AATTTAGGGC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 10 0.31
8 22 0.69
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1863915 original size:21 final size:21
Alignment explanation
Indices: 1863886--1863935 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
1863876 CTTGGACTCA
*
1863886 TCTTATTTTCTTTTTCTT-TTT
1 TCTTTTTTTCTTTTT-TTCTTT
1863907 TCTTTTTTTCTTTTTTTCTTT
1 TCTTTTTTTCTTTTTTTCTTT
1863928 T-TTTTTTT
1 TCTTTTTTT
1863936 AATTTAGGGC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 9 0.33
21 18 0.67
ACGTcount: A:0.02, C:0.12, G:0.00, T:0.86
Consensus pattern (21 bp):
TCTTTTTTTCTTTTTTTCTTT
Found at i:1863976 original size:58 final size:59
Alignment explanation
Indices: 1863914--1864027 Score: 167
Period size: 59 Copynumber: 1.9 Consensus size: 59
1863904 TTTTCTTTTT
* * * *
1863914 TTCTTTTTTTCTTTTT-TTTTTTAATTTAGGGCGCCCTTTCGGGTTTTCACCCTAAACG
1 TTCTTTTTTTCTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
* *
1863972 TTCTTTTTTTCTTTTTCTTTTTCGACTTAGGACGCCCTCTCGGGTTTTCATCCTAA
1 TTCTTTTTTTCTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAA
1864028 GCAAAGTATT
Statistics
Matches: 49, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
58 16 0.33
59 33 0.67
ACGTcount: A:0.11, C:0.23, G:0.13, T:0.53
Consensus pattern (59 bp):
TTCTTTTTTTCTTTTTCTTTTTCAACTTAGGACGCCCTCTCGGGTTTTCACCCTAAACG
Found at i:1873580 original size:24 final size:23
Alignment explanation
Indices: 1873553--1873597 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
1873543 AAAAATAGCT
*
1873553 AAATAATAATCAATACAAAATAAA
1 AAATAATAAT-AAAACAAAATAAA
1873577 AAATAATAATAAAACAAAATA
1 AAATAATAATAAAACAAAATA
1873598 GAATAAGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.73, C:0.07, G:0.00, T:0.20
Consensus pattern (23 bp):
AAATAATAATAAAACAAAATAAA
Found at i:1873628 original size:17 final size:16
Alignment explanation
Indices: 1873570--1873631 Score: 54
Period size: 17 Copynumber: 3.8 Consensus size: 16
1873560 AATCAATACA
*
1873570 AAATAAAAAATAATAAT
1 AAATAAAAAA-AAGAAT
* *
1873587 AAA-ACAAAATAGAAT
1 AAATAAAAAAAAGAAT
*
1873602 AAGATGAAAAAAAGAATT
1 AA-ATAAAAAAAAGAA-T
1873620 AAATAAAAAAAA
1 AAATAAAAAAAA
1873632 CGAAAATGAA
Statistics
Matches: 35, Mismatches: 7, Indels: 6
0.73 0.15 0.12
Matches are distributed among these distances:
15 6 0.17
16 6 0.17
17 20 0.57
18 3 0.09
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (16 bp):
AAATAAAAAAAAGAAT
Found at i:1873882 original size:16 final size:16
Alignment explanation
Indices: 1873852--1873889 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
1873842 TGTGTTAGAT
*
1873852 AAAAAATAAATAATAA
1 AAAAAACAAATAATAA
1873868 GAAAAAACAAA-AATAA
1 -AAAAAACAAATAATAA
1873884 AAAAAA
1 AAAAAA
1873890 GGGAGGAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 6 0.30
16 5 0.25
17 9 0.45
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.11
Consensus pattern (16 bp):
AAAAAACAAATAATAA
Found at i:1873963 original size:3 final size:3
Alignment explanation
Indices: 1873955--1874048 Score: 152
Period size: 3 Copynumber: 30.7 Consensus size: 3
1873945 ATTAGGGAGA
1873955 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
1874003 AAT AAT AAT AAAT AAA AAT AAA AAT ATAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT -AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AA
1874049 AAGGGCTAGA
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
3 79 0.93
4 6 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1881928 original size:22 final size:21
Alignment explanation
Indices: 1881896--1881940 Score: 72
Period size: 22 Copynumber: 2.1 Consensus size: 21
1881886 AAAATATACA
*
1881896 ATATATATAGTTTTTGAAGAT
1 ATATATATAGTTTTTGAAAAT
1881917 ATATAATATAGTTTTTGAAAAT
1 ATAT-ATATAGTTTTTGAAAAT
1881939 AT
1 AT
1881941 TGTTGAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 4 0.18
22 18 0.82
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (21 bp):
ATATATATAGTTTTTGAAAAT
Found at i:1881960 original size:39 final size:37
Alignment explanation
Indices: 1881917--1882038 Score: 115
Period size: 39 Copynumber: 3.2 Consensus size: 37
1881907 TTTTGAAGAT
*
1881917 ATATAATATAGTTTTTGAAAATATTGTTGAAAACATAT-
1 ATAT-ATATAGTTTTTAAAAATATT-TTGAAAACATATA
**
1881955 A-ATATATAGTTTTTTAAAAACCGGTTTTGAAAACATATA
1 ATATATATAG-TTTTTAAAAA--TATTTTGAAAACATATA
*
1881994 ATATATAGTAG-TTTTAAAAATGGTTTTTGAAAACATATA
1 ATATATA-TAGTTTTTAAAAAT--ATTTTGAAAACATATA
1882033 ATATAT
1 ATATAT
1882039 TGTAAAACGA
Statistics
Matches: 71, Mismatches: 5, Indels: 15
0.78 0.05 0.16
Matches are distributed among these distances:
36 6 0.08
37 11 0.15
38 13 0.18
39 33 0.46
40 5 0.07
41 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.11, T:0.41
Consensus pattern (37 bp):
ATATATATAGTTTTTAAAAATATTTTGAAAACATATA
Found at i:1881991 original size:38 final size:39
Alignment explanation
Indices: 1881943--1882038 Score: 151
Period size: 39 Copynumber: 2.5 Consensus size: 39
1881933 GAAAATATTG
*
1881943 TTGAAAACATATAATATATAGT-TTTTTAAAAACCGG-TT
1 TTGAAAACATATAATATATAGTAGTTTTAAAAA-CGGTTT
*
1881981 TTGAAAACATATAATATATAGTAGTTTTAAAAATGGTTT
1 TTGAAAACATATAATATATAGTAGTTTTAAAAACGGTTT
1882020 TTGAAAACATATAATATAT
1 TTGAAAACATATAATATAT
1882039 TGTAAAACGA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
38 24 0.44
39 30 0.56
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (39 bp):
TTGAAAACATATAATATATAGTAGTTTTAAAAACGGTTT
Found at i:1883090 original size:20 final size:21
Alignment explanation
Indices: 1883067--1883111 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
1883057 AATCCTTTTA
* *
1883067 ATTTAAATTTTCTTTTATTT-
1 ATTTAAATTTTATTTCATTTC
*
1883087 ATTTAATTTTTATTTCATTTC
1 ATTTAAATTTTATTTCATTTC
1883108 ATTT
1 ATTT
1883112 TTTGTATTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (21 bp):
ATTTAAATTTTATTTCATTTC
Found at i:1883106 original size:16 final size:15
Alignment explanation
Indices: 1883079--1883126 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
1883069 TTAAATTTTC
1883079 TTTTATTTATTTAAT
1 TTTTATTTATTTAAT
*
1883094 TTTTATTTCATTTCAT
1 TTTTATTT-ATTTAAT
* *
1883110 TTTT-TGTATTTTAT
1 TTTTATTTATTTAAT
1883124 TTT
1 TTT
1883127 AATCTTAATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 9 0.31
15 10 0.34
16 10 0.34
ACGTcount: A:0.19, C:0.04, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTTATTTATTTAAT
Found at i:1884156 original size:15 final size:15
Alignment explanation
Indices: 1884136--1884175 Score: 73
Period size: 15 Copynumber: 2.7 Consensus size: 15
1884126 TTTTATTTTC
1884136 ATTATTGTTTTGATT
1 ATTATTGTTTTGATT
1884151 ATTATTGTTTTGATT
1 ATTATTGTTTTGATT
1884166 ATTATT-TTTT
1 ATTATTGTTTT
1884176 ACTAACTTGC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 4 0.16
15 21 0.84
ACGTcount: A:0.20, C:0.00, G:0.10, T:0.70
Consensus pattern (15 bp):
ATTATTGTTTTGATT
Found at i:1886860 original size:24 final size:24
Alignment explanation
Indices: 1886833--1886895 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
1886823 TCAAGGGGAC
*
1886833 TCATCTGCTATAAAAGCACAAGTT
1 TCATCTGCTACAAAAGCACAAGTT
* * *
1886857 TCATCTACCACAAAGGCACAAGTT
1 TCATCTGCTACAAAAGCACAAGTT
*
1886881 TCGTCTGCTACAAAA
1 TCATCTGCTACAAAA
1886896 ACCATAAGCT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (24 bp):
TCATCTGCTACAAAAGCACAAGTT
Found at i:1906288 original size:23 final size:23
Alignment explanation
Indices: 1906251--1906317 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
1906241 CAATTGCACA
* *
1906251 TGTCCCAAAGAACCACATAGTA-T
1 TGTCCCGAAGGACCACATAG-AGT
*
1906274 TGTCCCGAAGGACCACGTAGAGT
1 TGTCCCGAAGGACCACATAGAGT
* * *
1906297 TGTCTCGAAAGACCACGTAGA
1 TGTCCCGAAGGACCACATAGA
1906318 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
22 1 0.03
23 37 0.97
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.19
Consensus pattern (23 bp):
TGTCCCGAAGGACCACATAGAGT
Found at i:1908513 original size:21 final size:22
Alignment explanation
Indices: 1908487--1908534 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
1908477 AAAAATATAC
1908487 AATATATA-TATAGTTTTTGAA
1 AATATATAGTATAGTTTTTGAA
*
1908508 GATATATAGTATAGTTTTTGAA
1 AATATATAGTATAGTTTTTGAA
1908530 AATAT
1 AATAT
1908535 TGTTGAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (22 bp):
AATATATAGTATAGTTTTTGAA
Found at i:1908562 original size:36 final size:36
Alignment explanation
Indices: 1908509--1908736 Score: 202
Period size: 36 Copynumber: 6.3 Consensus size: 36
1908499 GTTTTTGAAG
* *
1908509 ATAT-ATAGTATAGTTTTTGAAAATATTGTTGAAAAC
1 ATATAATA-TATAGTTTTTAAAAATATTTTTGAAAAC
* ***
1908545 ATATAATATATAATTTTT---AACGGTTTTGAAAAC
1 ATATAATATATAGTTTTTAAAAATATTTTTGAAAAC
*
1908578 ATATAATATATAG-TTTTAAAAACAGTTTTTGAAAAC
1 ATATAATATATAGTTTTTAAAAATA-TTTTTGAAAAC
* * *
1908614 ATAAAATATATAGTTTTTAAAAAACTTTTTTTTAAAAC
1 ATATAATATATAGTTTTT-AAAAA-TATTTTTGAAAAC
* *
1908652 GTAT-ATAATATAGTTTGTAAAACATA-TTTTGAAAAC
1 ATATAAT-ATATAGTTTTTAAAA-ATATTTTTGAAAAC
**
1908688 ATATAA-ATATAGTTTTTAAAACGATTTTTGAAAAC
1 ATATAATATATAGTTTTTAAAAATATTTTTGAAAAC
1908723 ATATATAATATATA
1 --ATATAATATATA
1908737 TAATTTTTAG
Statistics
Matches: 156, Mismatches: 21, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
32 4 0.03
33 23 0.15
34 1 0.01
35 27 0.17
36 47 0.30
37 21 0.13
38 33 0.21
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (36 bp):
ATATAATATATAGTTTTTAAAAATATTTTTGAAAAC
Found at i:1908752 original size:24 final size:24
Alignment explanation
Indices: 1908725--1908781 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
1908715 TTGAAAACAT
1908725 ATATAATATATATAATTTTT-AGAA
1 ATATAATATATATAATTTTTGA-AA
*
1908749 ATAT-AT-TATATAGTTTTTGAAA
1 ATATAATATATATAATTTTTGAAA
1908771 ATATAATATAT
1 ATATAATATAT
1908782 GTTATATAGT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
22 17 0.59
23 5 0.17
24 7 0.24
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (24 bp):
ATATAATATATATAATTTTTGAAA
Found at i:1908781 original size:29 final size:26
Alignment explanation
Indices: 1908749--1908808 Score: 84
Period size: 29 Copynumber: 2.2 Consensus size: 26
1908739 ATTTTTAGAA
1908749 ATATATTATATAGTTTTTGAAAATATAAT
1 ATATATTATATAGTTTTT--AAATA-AAT
*
1908778 ATATGTTATATAGTTTTTAAATAAAT
1 ATATATTATATAGTTTTTAAATAAAT
1908804 ATATA
1 ATATA
1908809 GTACGTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
26 7 0.24
27 5 0.17
29 17 0.59
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (26 bp):
ATATATTATATAGTTTTTAAATAAAT
Found at i:1908833 original size:16 final size:16
Alignment explanation
Indices: 1908814--1908885 Score: 80
Period size: 16 Copynumber: 4.6 Consensus size: 16
1908804 ATATAGTACG
1908814 TATTATATTTATATTA
1 TATTATATTTATATTA
1908830 TATTATATATTAT-TTA
1 TATTATAT-TTATATTA
*
1908846 TAGTATTATTTATTATT-
1 TATTA-TATTTA-TATTA
1908863 TATTAT-TTT-TATTA
1 TATTATATTTATATTA
1908877 TATTATATT
1 TATTATATT
1908886 ATTAATAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
13 4 0.08
14 6 0.12
15 5 0.10
16 19 0.40
17 12 0.25
18 2 0.04
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.65
Consensus pattern (16 bp):
TATTATATTTATATTA
Found at i:1908854 original size:19 final size:18
Alignment explanation
Indices: 1908814--1908900 Score: 74
Period size: 19 Copynumber: 4.8 Consensus size: 18
1908804 ATATAGTACG
*
1908814 TATTATAT-TTATAT-TA
1 TATTATATATTATTTATA
1908830 TATTATATATTATTTATA
1 TATTATATATTATTTATA
*
1908848 GTATTATTTATTATTTAT-
1 -TATTATATATTATTTATA
*
1908866 TATT-TTTATTATATTATA
1 TATTATATATTAT-TTATA
1908884 TTATTAATAATATTATT
1 -TATT-AT-ATATTATT
1908901 AGGTTTATTC
Statistics
Matches: 59, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
16 16 0.27
17 13 0.22
18 2 0.03
19 20 0.34
21 2 0.03
22 6 0.10
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (18 bp):
TATTATATATTATTTATA
Found at i:1908855 original size:3 final size:3
Alignment explanation
Indices: 1908825--1908901 Score: 54
Period size: 3 Copynumber: 25.7 Consensus size: 3
1908815 ATTATATTTA
* *
1908825 TAT TA- TAT TAT ATAT TAT T-T ATAG TAT TATT TAT TATT TAT TAT TTT
1 TAT TAT TAT TAT -TAT TAT TAT -TAT TAT TA-T TAT TA-T TAT TAT TAT
* *
1908872 TAT TA- TAT TA- TAT TAT TAA TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1908902 GGTTTATTCT
Statistics
Matches: 60, Mismatches: 6, Indels: 16
0.73 0.07 0.20
Matches are distributed among these distances:
2 7 0.12
3 44 0.73
4 9 0.15
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:1908888 original size:26 final size:26
Alignment explanation
Indices: 1908816--1908888 Score: 94
Period size: 26 Copynumber: 2.8 Consensus size: 26
1908806 ATAGTACGTA
*
1908816 TTATATTTATATTATATTATATATTAT
1 TTATA-TTATATTATATTATTTATTAT
*
1908843 TTATAGTATTATT-TATTATTTATTAT
1 TTATATTA-TATTATATTATTTATTAT
*
1908869 TTTTATTATATTATATTATT
1 TTATATTATATTATATTATT
1908889 AATAATATTA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
25 4 0.10
26 27 0.68
27 9 0.22
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (26 bp):
TTATATTATATTATATTATTTATTAT
Found at i:1912621 original size:13 final size:13
Alignment explanation
Indices: 1912603--1912644 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
1912593 CTGAGATCAT
1912603 GAAGATGTACCAG
1 GAAGATGTACCAG
1912616 GAAGATG----AG
1 GAAGATGTACCAG
1912625 GAAGATGTACCAG
1 GAAGATGTACCAG
1912638 GAAGATG
1 GAAGATG
1912645 AGGAAGATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
9 9 0.36
13 16 0.64
ACGTcount: A:0.40, C:0.10, G:0.36, T:0.14
Consensus pattern (13 bp):
GAAGATGTACCAG
Found at i:1912628 original size:22 final size:22
Alignment explanation
Indices: 1912603--1912654 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
1912593 CTGAGATCAT
1912603 GAAGATGTACCAGGAAGATGAG
1 GAAGATGTACCAGGAAGATGAG
1912625 GAAGATGTACCAGGAAGATGAG
1 GAAGATGTACCAGGAAGATGAG
1912647 GAAGATGT
1 GAAGATGT
1912655 TTAGACTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.40, C:0.08, G:0.37, T:0.15
Consensus pattern (22 bp):
GAAGATGTACCAGGAAGATGAG
Found at i:1916460 original size:20 final size:20
Alignment explanation
Indices: 1916437--1916480 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
1916427 ACAACTCAGT
*
1916437 TTTCAAATTCGCAACGCGAA
1 TTTCAAATTCACAACGCGAA
***
1916457 TTTCGTTTTCACAACGCGAA
1 TTTCAAATTCACAACGCGAA
1916477 TTTC
1 TTTC
1916481 GCAACTCGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.27, C:0.25, G:0.14, T:0.34
Consensus pattern (20 bp):
TTTCAAATTCACAACGCGAA
Found at i:1916501 original size:22 final size:22
Alignment explanation
Indices: 1916472--1916530 Score: 93
Period size: 22 Copynumber: 2.7 Consensus size: 22
1916462 TTTTCACAAC
1916472 GCGAATTTCGCAACTCGAATTCA
1 GCGAATTTCGCAACTCGAATT-A
1916495 -CGAATTTCGCAACTCGAATTA
1 GCGAATTTCGCAACTCGAATTA
*
1916516 GCCAATTTCGCAACT
1 GCGAATTTCGCAACT
1916531 AAATTACCGA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
21 1 0.03
22 33 0.97
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (22 bp):
GCGAATTTCGCAACTCGAATTA
Found at i:1916883 original size:20 final size:20
Alignment explanation
Indices: 1916835--1916884 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1916825 GCGAAATTCA
*
1916835 AGTTGTGAATTTGAAAATCG
1 AGTTGCGAATTTGAAAATCG
* *
1916855 CGTTACGAATTTGAAAA-CTG
1 AGTTGCGAATTTGAAAATC-G
1916875 AGTTGCGAAT
1 AGTTGCGAAT
1916885 AGTTGTATTT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.34, C:0.10, G:0.24, T:0.32
Consensus pattern (20 bp):
AGTTGCGAATTTGAAAATCG
Found at i:1916910 original size:92 final size:93
Alignment explanation
Indices: 1916601--1916983 Score: 498
Period size: 93 Copynumber: 4.0 Consensus size: 93
1916591 TTGAAAACTG
*
1916601 AGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAATTCGCGTTGCGAATTTGGAGA
1 AGTTGTGTTTACCTATATCGGTAATTAGCGTT--G----CGAAATTCGAGTTGCGAATTTGGAGA
1916666 ATCGCGTTGCAAATTTGAAAACTGAGTTGCGAAT
60 ATCGCGTTGCAAATTTGAAAACTGAGTTGCGAAT
* * *
1916700 AGTTGTGTTTACCTATATCGGTAATCAGCGTTGCAAAATTCGAGTTGCGATTTTGGAGAATCGCG
1 AGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAATTCGAGTTGCGAATTTGGAGAATCGCG
1916765 TTGCAAATTTGAAAACTGAGTTGCGAAT
66 TTGCAAATTTGAAAACTGAGTTGCGAAT
* * *
1916793 AGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAATTCAAGTTGTGAATTT-GAAAATCGCG
1 AGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAATTCGAGTTGCGAATTTGGAGAATCGCG
* *
1916857 TTACGAATTTGAAAACTGAGTTGCGAAT
66 TTGCAAATTTGAAAACTGAGTTGCGAAT
* * * * * *
1916885 AGTTGTATTTACCTATATCGGTAATTAGTGTTGCGATTTTGGAGAATCGCGTTGCGATTTTGGAT
1 AGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGA------A-ATTCGAGTTGCGAATTTGGAG
*
1916950 AATCGCGTTGCAAATTTGAAAACTGTGTTGCGAA
59 AATCGCGTTGCAAATTTGAAAACTGAGTTGCGAA
1916984 ACTGGAGTTC
Statistics
Matches: 253, Mismatches: 23, Indels: 15
0.87 0.08 0.05
Matches are distributed among these distances:
92 69 0.27
93 106 0.42
97 1 0.00
98 1 0.00
99 43 0.17
100 33 0.13
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (93 bp):
AGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAATTCGAGTTGCGAATTTGGAGAATCGCG
TTGCAAATTTGAAAACTGAGTTGCGAAT
Found at i:1916940 original size:21 final size:21
Alignment explanation
Indices: 1916914--1916960 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
1916904 GGTAATTAGT
1916914 GTTGCGATTTTGGAGAATCGC
1 GTTGCGATTTTGGAGAATCGC
*
1916935 GTTGCGATTTTGGATAATCGC
1 GTTGCGATTTTGGAGAATCGC
1916956 GTTGC
1 GTTGC
1916961 AAATTTGAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.17, C:0.15, G:0.32, T:0.36
Consensus pattern (21 bp):
GTTGCGATTTTGGAGAATCGC
Found at i:1916956 original size:192 final size:188
Alignment explanation
Indices: 1916601--1916983 Score: 522
Period size: 192 Copynumber: 2.0 Consensus size: 188
1916591 TTGAAAACTG
** *
1916601 AGTTGTGTTTACCTATATCGGTAATTAGCGTTGCGAAAACGAAATTCGCGTTGCGAATTTGGAGA
1 AGTTGTGTTTACCTATATCGGTAATTAGCGTT-CG---ACGAAATTCAAGTTGCGAATTTGGAAA
* *
1916666 ATCGCGTTGCAAATTTGAAAACTGAGTTGCGAATAGTTGTGTTTACCTATATCGGTAATCAGCGT
62 ATCGCGTTACAAATTTGAAAACTGAGTTGCGAATAGTTGTATTTACCTATATCGGTAATCAGCGT
1916731 TGCAAAATTCGAGTTGCGATTTTGGAGAATCGCGTTGCAAATTTGAAAACTGAGTTGCGAAT
127 TGCAAAATTCGAGTTGCGATTTTGGAGAATCGCGTTGCAAATTTGAAAACTGAGTTGCGAAT
*
1916793 AGTTGTGTTTACCTATATCGGTAATTAGCGTT-G-CGAAATTCAAGTTGTGAATTT-GAAAATCG
1 AGTTGTGTTTACCTATATCGGTAATTAGCGTTCGACGAAATTCAAGTTGCGAATTTGGAAAATCG
* * *
1916855 CGTTACGAATTTGAAAACTGAGTTGCGAATAGTTGTATTTACCTATATCGGTAATTAGTGTTGCG
66 CGTTACAAATTTGAAAACTGAGTTGCGAATAGTTGTATTTACCTATATCGGTAATCAGCGTTGC-
* * *
1916920 ATTTTGGAGAA-TCGCGTTGCGATTTTGGATAATCGCGTTGCAAATTTGAAAACTGTGTTGCGAA
130 A------A-AATTCGAGTTGCGATTTTGGAGAATCGCGTTGCAAATTTGAAAACTGAGTTGCGAA
1916984 ACTGGAGTTC
Statistics
Matches: 171, Mismatches: 12, Indels: 16
0.86 0.06 0.08
Matches are distributed among these distances:
185 66 0.39
186 19 0.11
190 1 0.01
192 83 0.49
193 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.25, T:0.34
Consensus pattern (188 bp):
AGTTGTGTTTACCTATATCGGTAATTAGCGTTCGACGAAATTCAAGTTGCGAATTTGGAAAATCG
CGTTACAAATTTGAAAACTGAGTTGCGAATAGTTGTATTTACCTATATCGGTAATCAGCGTTGCA
AAATTCGAGTTGCGATTTTGGAGAATCGCGTTGCAAATTTGAAAACTGAGTTGCGAAT
Found at i:1916967 original size:21 final size:21
Alignment explanation
Indices: 1916922--1916967 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
1916912 GTGTTGCGAT
* *
1916922 TTTGGAGAATCGCGTTGCGAT
1 TTTGGAGAATCGCGTTGCAAA
*
1916943 TTTGGATAATCGCGTTGCAAA
1 TTTGGAGAATCGCGTTGCAAA
1916964 TTTG
1 TTTG
1916968 AAAACTGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.13, G:0.28, T:0.37
Consensus pattern (21 bp):
TTTGGAGAATCGCGTTGCAAA
Found at i:1921051 original size:8 final size:8
Alignment explanation
Indices: 1921040--1921068 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1921030 TTCTGCCTCC
1921040 CCTTCCCT
1 CCTTCCCT
1921048 CCTT-CCT
1 CCTTCCCT
1921055 CCTTCCCT
1 CCTTCCCT
1921063 CCTTCC
1 CCTTCC
1921069 AATCATTGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (8 bp):
CCTTCCCT
Found at i:1921060 original size:15 final size:15
Alignment explanation
Indices: 1921040--1921068 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1921030 TTCTGCCTCC
1921040 CCTTCCCTCCTTCCT
1 CCTTCCCTCCTTCCT
1921055 CCTTCCCTCCTTCC
1 CCTTCCCTCCTTCC
1921069 AATCATTGTC
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:0.00, C:0.62, G:0.00, T:0.38
Consensus pattern (15 bp):
CCTTCCCTCCTTCCT
Found at i:1923140 original size:33 final size:33
Alignment explanation
Indices: 1923066--1923130 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
1923056 TTTTCTCACG
1923066 CCTCTTCACCAGAAGGTGCCATTTCAAGTCATT
1 CCTCTTCACCAGAAGGTGCCATTTCAAGTCATT
*
1923099 CCTCTTCACCA-AAGGATGCCATTTTAAGTCAT
1 CCTCTTCACCAGAAGG-TGCCATTTCAAGTCAT
1923131 GTTTGTTCAC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
32 4 0.13
33 26 0.87
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (33 bp):
CCTCTTCACCAGAAGGTGCCATTTCAAGTCATT
Found at i:1924139 original size:21 final size:21
Alignment explanation
Indices: 1924113--1924152 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1924103 CATTTTGTGC
1924113 AAAG-AAGAAAAAGAAAAGAAG
1 AAAGAAAGAAAAA-AAAAGAAG
*
1924134 AAAGAAAGGAAAAAAAAGA
1 AAAGAAAGAAAAAAAAAGA
1924153 TTTCATCTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.78, C:0.00, G:0.23, T:0.00
Consensus pattern (21 bp):
AAAGAAAGAAAAAAAAAGAAG
Found at i:1929376 original size:21 final size:21
Alignment explanation
Indices: 1929350--1929389 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1929340 CAGAACCCCA
*
1929350 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
1929371 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
1929390 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:1929424 original size:20 final size:21
Alignment explanation
Indices: 1929370--1929432 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
1929360 GATTCCCCTG
1929370 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
1929394 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
1929414 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
1929433 TGTACCAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:1943265 original size:8 final size:9
Alignment explanation
Indices: 1943240--1943264 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
1943230 TTGTTTCACA
1943240 GAAAAAAAT
1 GAAAAAAAT
1943249 GAAAAAAAT
1 GAAAAAAAT
1943258 GAAAAAA
1 GAAAAAA
1943265 TAGTGAAGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.80, C:0.00, G:0.12, T:0.08
Consensus pattern (9 bp):
GAAAAAAAT
Found at i:1944176 original size:20 final size:21
Alignment explanation
Indices: 1944151--1944189 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1944141 TTATTTGAAT
1944151 ATTTTTA-TTAATCTTTAGCC
1 ATTTTTACTTAATCTTTAGCC
*
1944171 ATTTTTACTTAATTTTTAG
1 ATTTTTACTTAATCTTTAG
1944190 GGTATTAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.26, C:0.10, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTTTACTTAATCTTTAGCC
Found at i:1947141 original size:33 final size:33
Alignment explanation
Indices: 1947094--1947184 Score: 112
Period size: 33 Copynumber: 2.8 Consensus size: 33
1947084 ATACCTTTTT
* * *
1947094 AAGTCGTGCGTCTTCTCCAAAAGTTGTCATTTC
1 AAGTCATGCCTCTTCACCAAAAGTTGTCATTTC
*
1947127 AAGTCATGCCTCTTCACC-AAAGAATGTCATTTC
1 AAGTCATGCCTCTTCACCAAAAG-TTGTCATTTC
* *
1947160 AAGTCATGCTTATTCACCAAAAGTT
1 AAGTCATGCCTCTTCACCAAAAGTT
1947185 CTTCATTGAA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
32 4 0.08
33 41 0.84
34 4 0.08
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (33 bp):
AAGTCATGCCTCTTCACCAAAAGTTGTCATTTC
Done.