Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008620.1 Hibiscus syriacus cultivar Beakdansim tig00111582_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: 13158977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 20 of 64
Found at i:3822286 original size:17 final size:17
Alignment explanation
Indices: 3822261--3822323 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
3822251 ATGAAAACAT
*
3822261 TTAAAGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
3822278 TTAATGAACTAATTTAAA
1 TTAATGAACTAGTTT-AA
*
3822296 TGAATGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
3822313 TTAGTGAACTA
1 TTAATGAACTA
3822324 TCTTTATTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 24 0.62
18 15 0.38
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (17 bp):
TTAATGAACTAGTTTAA
Found at i:3822303 original size:18 final size:18
Alignment explanation
Indices: 3822266--3822312 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
3822256 AACATTTAAA
*
3822266 GAACTAGTTT-AATTAAT
1 GAACTAGTTTAAATGAAT
*
3822283 GAACTAATTTAAATGAAT
1 GAACTAGTTTAAATGAAT
3822301 GAACTAGTTTAA
1 GAACTAGTTTAA
3822313 TTAGTGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.36
Consensus pattern (18 bp):
GAACTAGTTTAAATGAAT
Found at i:3822329 original size:18 final size:17
Alignment explanation
Indices: 3822261--3822338 Score: 68
Period size: 17 Copynumber: 4.5 Consensus size: 17
3822251 ATGAAAACAT
* *
3822261 TTAAAGAACTAGTTTAA
1 TTAATGAACTATTTTAA
*
3822278 TTAATGAACTAATTTAAA
1 TTAATGAACT-ATTTTAA
* *
3822296 TGAATGAACTAGTTTAA
1 TTAATGAACTATTTTAA
*
3822313 TTAGTGAACTATCTTT-A
1 TTAATGAACTAT-TTTAA
3822330 TTGAATGAA
1 TT-AATGAA
3822339 AGAGGATACT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
17 26 0.54
18 22 0.46
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.38
Consensus pattern (17 bp):
TTAATGAACTATTTTAA
Found at i:3822476 original size:20 final size:20
Alignment explanation
Indices: 3822438--3822476 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3822428 CAACTTAATG
* *
3822438 TCATGAAAATTTATTAACAC
1 TCATGAAAATTCATGAACAC
*
3822458 TCATGGAAATTCATGAACA
1 TCATGAAAATTCATGAACA
3822477 AGTAAAAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.44, C:0.15, G:0.10, T:0.31
Consensus pattern (20 bp):
TCATGAAAATTCATGAACAC
Found at i:3823329 original size:21 final size:21
Alignment explanation
Indices: 3823305--3823348 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3823295 TTTTTCTTTT
3823305 CACTTCCAAGT-TTTTCAACTA
1 CACTTCCAA-TCTTTTCAACTA
* *
3823326 CACTTTCAATCTTTTTAACTA
1 CACTTCCAATCTTTTCAACTA
3823347 CA
1 CA
3823349 ATTTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.30, C:0.27, G:0.02, T:0.41
Consensus pattern (21 bp):
CACTTCCAATCTTTTCAACTA
Found at i:3825021 original size:21 final size:22
Alignment explanation
Indices: 3824979--3825022 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3824969 GGATGAATAT
**
3824979 TCTAGATCATTTTGGGGATGAA
1 TCTAGATCATTTTGAAGATGAA
*
3825001 TCTAGAT-ATTTTGAAGCTGAA
1 TCTAGATCATTTTGAAGATGAA
3825022 T
1 T
3825023 ATGGCCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.39
Consensus pattern (22 bp):
TCTAGATCATTTTGAAGATGAA
Found at i:3825794 original size:18 final size:17
Alignment explanation
Indices: 3825752--3825814 Score: 90
Period size: 17 Copynumber: 3.6 Consensus size: 17
3825742 ATGAAAACAT
*
3825752 TTAAAGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
3825769 TTAATGAACCAGTTTAA
1 TTAATGAACTAGTTTAA
3825786 TTGAATGAACTAGTTTAA
1 TT-AATGAACTAGTTTAA
*
3825804 TTAGTGAACTA
1 TTAATGAACTA
3825815 TCTTTATTGA
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
17 25 0.61
18 16 0.39
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (17 bp):
TTAATGAACTAGTTTAA
Found at i:3825803 original size:35 final size:35
Alignment explanation
Indices: 3825757--3825829 Score: 103
Period size: 35 Copynumber: 2.1 Consensus size: 35
3825747 AACATTTAAA
3825757 GAACTAGTTTAATTAATGAACCAGT-TTAATTGAAT
1 GAACTAGTTTAATTAATGAACCA-TCTTAATTGAAT
* * *
3825792 GAACTAGTTTAATTAGTGAACTATCTTTATTGAAT
1 GAACTAGTTTAATTAATGAACCATCTTAATTGAAT
3825827 GAA
1 GAA
3825830 AGAGGATACT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (35 bp):
GAACTAGTTTAATTAATGAACCATCTTAATTGAAT
Found at i:3825820 original size:18 final size:18
Alignment explanation
Indices: 3825757--3825829 Score: 71
Period size: 17 Copynumber: 4.2 Consensus size: 18
3825747 AACATTTAAA
*
3825757 GAACTAGTTTAATT-AAT
1 GAACTACTTTAATTGAAT
* *
3825774 GAACCAGTTTAATTGAAT
1 GAACTACTTTAATTGAAT
* *
3825792 GAACTAGTTTAATT-AGT
1 GAACTACTTTAATTGAAT
3825809 GAACTATCTTT-ATTGAAT
1 GAACTA-CTTTAATTGAAT
3825827 GAA
1 GAA
3825830 AGAGGATACT
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
17 24 0.50
18 24 0.50
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (18 bp):
GAACTACTTTAATTGAAT
Found at i:3825967 original size:20 final size:20
Alignment explanation
Indices: 3825929--3825967 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3825919 CAATTTAATG
* *
3825929 TCATGCAAATTTATTAACAC
1 TCATGCAAATTCATGAACAC
*
3825949 TCATGGAAATTCATGAACA
1 TCATGCAAATTCATGAACA
3825968 AGTAAAAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
TCATGCAAATTCATGAACAC
Found at i:3828524 original size:17 final size:17
Alignment explanation
Indices: 3828499--3828560 Score: 79
Period size: 17 Copynumber: 3.6 Consensus size: 17
3828489 ATGAAAACAT
*
3828499 TTAAAGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
3828516 TTAATGAACCAGTTTAAA
1 TTAATGAACTAGTTT-AA
*
3828534 TGAATGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
3828551 TTAGTGAACT
1 TTAATGAACT
3828561 TTCTTTATTG
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 23 0.61
18 15 0.39
ACGTcount: A:0.42, C:0.08, G:0.15, T:0.35
Consensus pattern (17 bp):
TTAATGAACTAGTTTAA
Found at i:3828541 original size:18 final size:18
Alignment explanation
Indices: 3828504--3828550 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
3828494 AACATTTAAA
*
3828504 GAACTAGTTT-AATTAAT
1 GAACTAGTTTAAATGAAT
*
3828521 GAACCAGTTTAAATGAAT
1 GAACTAGTTTAAATGAAT
3828539 GAACTAGTTTAA
1 GAACTAGTTTAA
3828551 TTAGTGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (18 bp):
GAACTAGTTTAAATGAAT
Found at i:3834020 original size:21 final size:21
Alignment explanation
Indices: 3833996--3834039 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3833986 TTTTTCTTTT
3833996 CACTTCCAAGT-TTTTCAACTA
1 CACTTCCAA-TCTTTTCAACTA
* *
3834017 CACTTTCAATCTTTTTAACTA
1 CACTTCCAATCTTTTCAACTA
3834038 CA
1 CA
3834040 ATTTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.30, C:0.27, G:0.02, T:0.41
Consensus pattern (21 bp):
CACTTCCAATCTTTTCAACTA
Found at i:3835706 original size:21 final size:22
Alignment explanation
Indices: 3835664--3835707 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3835654 GGATGAATAT
**
3835664 TCTAGATCATTTTGGGGATGAA
1 TCTAGATCATTTTGAAGATGAA
*
3835686 TCTAGAT-ATTTTGAAGCTGAA
1 TCTAGATCATTTTGAAGATGAA
3835707 T
1 T
3835708 ATGGCCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.39
Consensus pattern (22 bp):
TCTAGATCATTTTGAAGATGAA
Found at i:3836471 original size:17 final size:17
Alignment explanation
Indices: 3836446--3836508 Score: 81
Period size: 17 Copynumber: 3.6 Consensus size: 17
3836436 ATGAAAACAT
*
3836446 TTAAAGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
3836463 TTAATGAACCAGTTTAAA
1 TTAATGAACTAGTTT-AA
*
3836481 TGAATGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
3836498 TTAGTGAACTA
1 TTAATGAACTA
3836509 TCTTTATTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
17 24 0.62
18 15 0.38
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.35
Consensus pattern (17 bp):
TTAATGAACTAGTTTAA
Found at i:3836488 original size:18 final size:18
Alignment explanation
Indices: 3836451--3836497 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
3836441 AACATTTAAA
*
3836451 GAACTAGTTT-AATTAAT
1 GAACTAGTTTAAATGAAT
*
3836468 GAACCAGTTTAAATGAAT
1 GAACTAGTTTAAATGAAT
3836486 GAACTAGTTTAA
1 GAACTAGTTTAA
3836498 TTAGTGAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 9 0.35
18 17 0.65
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (18 bp):
GAACTAGTTTAAATGAAT
Found at i:3843909 original size:21 final size:22
Alignment explanation
Indices: 3843867--3843910 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3843857 GGATGAATAT
**
3843867 TCTAGATCATTTTGGGGATGAA
1 TCTAGATCATTTTGAAGATGAA
*
3843889 TCTAGAT-ATTTTGAAGCTGAA
1 TCTAGATCATTTTGAAGATGAA
3843910 T
1 T
3843911 ATGGCCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.39
Consensus pattern (22 bp):
TCTAGATCATTTTGAAGATGAA
Found at i:3844672 original size:17 final size:17
Alignment explanation
Indices: 3844647--3844724 Score: 84
Period size: 18 Copynumber: 4.5 Consensus size: 17
3844637 ATGAAAACAT
*
3844647 TTAAAGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
3844664 TTAATGAACCAGTTTAAA
1 TTAATGAACTAGTTT-AA
*
3844682 TGAATGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
* * *
3844699 TTAGTGAACTATCTTTAT
1 TTAATGAACTA-GTTTAA
3844717 TTAATGAA
1 TTAATGAA
3844725 AGAGGATACT
Statistics
Matches: 50, Mismatches: 9, Indels: 3
0.81 0.15 0.05
Matches are distributed among these distances:
17 24 0.48
18 26 0.52
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (17 bp):
TTAATGAACTAGTTTAA
Found at i:3844723 original size:35 final size:35
Alignment explanation
Indices: 3844645--3844724 Score: 90
Period size: 35 Copynumber: 2.3 Consensus size: 35
3844635 TTATGAAAAC
*
3844645 ATTTAAAGAACTAGTTTAATTAATGAACCAGTTTA
1 ATTTAATGAACTAGTTTAATTAATGAACCAGTTTA
* * * * *
3844680 AATGAATGAACTAGTTTAATTAGTGAACTA-TCTTT
1 ATTTAATGAACTAGTTTAATTAATGAACCAGT-TTA
3844715 ATTTAATGAA
1 ATTTAATGAA
3844725 AGAGGATACT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
34 1 0.03
35 35 0.97
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.39
Consensus pattern (35 bp):
ATTTAATGAACTAGTTTAATTAATGAACCAGTTTA
Found at i:3845764 original size:21 final size:21
Alignment explanation
Indices: 3845740--3845783 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
3845730 TTTTTCTTTT
3845740 CACTTCCAAGT-TTTTCAACTA
1 CACTTCCAA-TCTTTTCAACTA
* *
3845761 CACTTTCAATCTTTTTAACTA
1 CACTTCCAATCTTTTCAACTA
3845782 CA
1 CA
3845784 ATTTCTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 19 0.95
ACGTcount: A:0.30, C:0.27, G:0.02, T:0.41
Consensus pattern (21 bp):
CACTTCCAATCTTTTCAACTA
Found at i:3847275 original size:21 final size:22
Alignment explanation
Indices: 3847233--3847276 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3847223 GGATGAATAT
**
3847233 TCTAGATCATTTTGGGGATGAA
1 TCTAGATCATTTTGAAGATGAA
*
3847255 TCTAGAT-ATTTTGAAGCTGAA
1 TCTAGATCATTTTGAAGATGAA
3847276 T
1 T
3847277 ATGGTCTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.30, C:0.09, G:0.23, T:0.39
Consensus pattern (22 bp):
TCTAGATCATTTTGAAGATGAA
Found at i:3848038 original size:17 final size:17
Alignment explanation
Indices: 3848013--3848075 Score: 72
Period size: 17 Copynumber: 3.6 Consensus size: 17
3848003 ATGAAAACAT
* *
3848013 TTAAAGAACTAATTTAA
1 TTAATGAACTAGTTTAA
*
3848030 TTAATGAACCAGTTTAAA
1 TTAATGAACTAGTTT-AA
*
3848048 TGAATGAACTAGTTTAA
1 TTAATGAACTAGTTTAA
*
3848065 TTAGTGAACTA
1 TTAATGAACTA
3848076 TCTTTATTGA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
17 23 0.61
18 15 0.39
ACGTcount: A:0.44, C:0.08, G:0.13, T:0.35
Consensus pattern (17 bp):
TTAATGAACTAGTTTAA
Found at i:3848228 original size:20 final size:20
Alignment explanation
Indices: 3848190--3848228 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3848180 CAACTTAATG
* *
3848190 TCATGCAAATTTATTAACAC
1 TCATGCAAATTCATGAACAC
*
3848210 TCATGGAAATTCATGAACA
1 TCATGCAAATTCATGAACA
3848229 AGTAAAAGAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (20 bp):
TCATGCAAATTCATGAACAC
Found at i:3850509 original size:16 final size:16
Alignment explanation
Indices: 3850488--3850520 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3850478 ATCTCTTTGG
3850488 ATCGACAAAGGGAAGC
1 ATCGACAAAGGGAAGC
3850504 ATCGACAAAGGGAAGC
1 ATCGACAAAGGGAAGC
3850520 A
1 A
3850521 AATAAGTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.30, T:0.06
Consensus pattern (16 bp):
ATCGACAAAGGGAAGC
Found at i:3855445 original size:55 final size:55
Alignment explanation
Indices: 3855304--3855539 Score: 298
Period size: 55 Copynumber: 4.3 Consensus size: 55
3855294 TTTATTAAGA
* * *
3855304 TGCACACGTAGTGCCTATAC-GATAGTTCATCAACTCATGATGAATTCCGTGG-GT
1 TGCACACATAGTGCCTATACGGTTA-TTCATCAACTCATGATGAATTCCGTGGATT
* * * * *
3855358 TGCACACATTGTGCATGTACGGTTATTCATCAACTAATGATGAATTCCATGGATT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* *
3855413 TGTACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGGTT
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
* * * * *
3855468 TGCACACATAGTGCCTGTACGATTATTCATCAAATCATGATGAATTTCGTTGA-T
1 TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
*
3855522 TGCACACATAGTACCTAT
1 TGCACACATAGTGCCTAT
3855540 TTGGTAATCG
Statistics
Matches: 156, Mismatches: 24, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
54 58 0.37
55 98 0.63
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (55 bp):
TGCACACATAGTGCCTATACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
Found at i:3855456 original size:109 final size:109
Alignment explanation
Indices: 3855304--3855539 Score: 332
Period size: 109 Copynumber: 2.2 Consensus size: 109
3855294 TTTATTAAGA
* *
3855304 TGCACACGTAGTGCCTATACGATAGTTCATCAACTCATGATGAATTCCGTGGG-TTGCACACATT
1 TGCACACATAGTGCCTATACGATAGTTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATA
* *
3855368 GTGCATGTACGGTTATTCATCAACTAATGATGAATTCCATGGATT
66 GTGCATGTACGATTATTCATCAAATAATGATGAATTCCATGGA-T
* *
3855413 TGTACACATAGTGCCTATACGGTTA-TTCATCAACTCATGATGAATTCCGTGGGTTTGCACACAT
1 TGCACACATAGTGCCTATAC-GATAGTTCATCAACTCATGATGAATTCCGTGGGTTTGCACACAT
* * * * *
3855477 AGTGCCTGTACGATTATTCATCAAATCATGATGAATTTCGTTGAT
65 AGTGCATGTACGATTATTCATCAAATAATGATGAATTCCATGGAT
*
3855522 TGCACACATAGTACCTAT
1 TGCACACATAGTGCCTAT
3855540 TTGGTAATCG
Statistics
Matches: 112, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
109 63 0.56
110 49 0.44
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.33
Consensus pattern (109 bp):
TGCACACATAGTGCCTATACGATAGTTCATCAACTCATGATGAATTCCGTGGGTTTGCACACATA
GTGCATGTACGATTATTCATCAAATAATGATGAATTCCATGGAT
Found at i:3855906 original size:22 final size:21
Alignment explanation
Indices: 3855875--3855918 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
3855865 TTGATACCCC
3855875 TACCAAGGTA-TCGATACTACTA
1 TACCAAGGTACT-GATACT-CTA
*
3855897 TACCATGGTACTGATACTCTA
1 TACCAAGGTACTGATACTCTA
3855918 T
1 T
3855919 TGCGGTACCA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 4 0.20
22 15 0.75
23 1 0.05
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (21 bp):
TACCAAGGTACTGATACTCTA
Found at i:3863285 original size:9 final size:9
Alignment explanation
Indices: 3863273--3863317 Score: 63
Period size: 9 Copynumber: 5.0 Consensus size: 9
3863263 AAGAGATATG
3863273 AATGATAAT
1 AATGATAAT
*
3863282 AATGCTAAT
1 AATGATAAT
*
3863291 AATGATAAG
1 AATGATAAT
*
3863300 AATAATAAT
1 AATGATAAT
3863309 AATGATAAT
1 AATGATAAT
3863318 GAAATGATAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.56, C:0.02, G:0.11, T:0.31
Consensus pattern (9 bp):
AATGATAAT
Found at i:3867277 original size:26 final size:26
Alignment explanation
Indices: 3867243--3867384 Score: 155
Period size: 26 Copynumber: 5.9 Consensus size: 26
3867233 ATTTATACAT
3867243 TTAATTTATGGCATCCTTTCATGCATC
1 TTAA-TTATGGCATCCTTTCATGCATC
*
3867270 TTAATTATGCCATCCTTTCATGC--C
1 TTAATTATGGCATCCTTTCATGCATC
* *
3867294 TT-A--AT-GCATCATTTCATGCATT
1 TTAATTATGGCATCCTTTCATGCATC
*
3867316 TTAATTATGACATCCTTTCATG-A-C
1 TTAATTATGGCATCCTTTCATGCATC
3867340 TTAA-TA---CATCCTTTCATGCATC
1 TTAATTATGGCATCCTTTCATGCATC
3867362 TTAATTATGGCATCCTTTCATGC
1 TTAATTATGGCATCCTTTCATGC
3867385 CTATTATATT
Statistics
Matches: 96, Mismatches: 7, Indels: 25
0.75 0.05 0.20
Matches are distributed among these distances:
20 24 0.25
21 3 0.03
22 7 0.07
23 6 0.06
24 7 0.07
25 3 0.03
26 42 0.44
27 4 0.04
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.43
Consensus pattern (26 bp):
TTAATTATGGCATCCTTTCATGCATC
Found at i:3867303 original size:46 final size:46
Alignment explanation
Indices: 3867253--3867386 Score: 214
Period size: 46 Copynumber: 2.9 Consensus size: 46
3867243 TTAATTTATG
*
3867253 GCATCCTTTCATGCATCTTAATTATGCCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCATCTTAATTATGACATCCTTTCATGCCTTAAT
* * *
3867299 GCATCATTTCATGCATTTTAATTATGACATCCTTTCATGACTTAAT
1 GCATCCTTTCATGCATCTTAATTATGACATCCTTTCATGCCTTAAT
* *
3867345 ACATCCTTTCATGCATCTTAATTATGGCATCCTTTCATGCCT
1 GCATCCTTTCATGCATCTTAATTATGACATCCTTTCATGCCT
3867387 ATTATATTAT
Statistics
Matches: 79, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 79 1.00
ACGTcount: A:0.24, C:0.25, G:0.09, T:0.42
Consensus pattern (46 bp):
GCATCCTTTCATGCATCTTAATTATGACATCCTTTCATGCCTTAAT
Found at i:3867459 original size:2 final size:2
Alignment explanation
Indices: 3867452--3867486 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
3867442 TTTTGAACAT
3867452 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3867487 CATCCCTTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3867684 original size:81 final size:81
Alignment explanation
Indices: 3867598--3867943 Score: 521
Period size: 81 Copynumber: 4.3 Consensus size: 81
3867588 TGACACTATC
* * ** * *
3867598 CTGTCAAATGCACAGATAATCCATTATTCTTTTATTCAACGGTATTTAACTGTTCATCTAACTGG
1 CTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGG
* *
3867663 CATAATTGACACCTTT
66 TATAAATGACACCTTT
* *
3867679 CTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTTATCTAATTGG
1 CTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGG
3867744 TATAAATGACACCTTT
66 TATAAATGACACCTTT
* * * *
3867760 CTGGCAATTGTACAGTTAGGCCATTATTCTTTTACTCAATGGTATTTAACTGTTCATCTAACTGG
1 CTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGG
3867825 TATAAATGACACCTTT
66 TATAAATGACACCTTT
* *
3867841 CTGCCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCATTCATCTAACTGG
1 CTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGG
*
3867906 TATAAATGACATCTTT
66 TATAAATGACACCTTT
* *
3867922 CTGCCATTTGCACAGTTAGGCC
1 CTGTCAATTGCACAGTTAGGCC
3867944 TCAAAGGCAC
Statistics
Matches: 242, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
81 242 1.00
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (81 bp):
CTGTCAATTGCACAGTTAGGCCATTATTCTTTTACTCAACGGTATTTAACCGTTCATCTAACTGG
TATAAATGACACCTTT
Found at i:3867972 original size:68 final size:68
Alignment explanation
Indices: 3867893--3868352 Score: 677
Period size: 68 Copynumber: 6.8 Consensus size: 68
3867883 TATTTAACCA
* * *
3867893 TTCATCTAACTGGTATAAATGACATCTTTCTGCCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
3867958 CCT
66 CCT
* * * * * *
3867961 TTCATCTAACTGGTATAAATGACACCTTTCTATAATTTTCATAGTTAGGCCTCAAAGGCATTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
3868026 CCT
66 CCT
* * * *
3868029 ATCATCTAACTGGCATAAAGGACACCTTTCTTTCATTTGCACAGTTAGGCCTTAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
3868094 CCT
66 CCT
* * *
3868097 TTCAGCTAACTGACATAAATGACACCTTTCTGTCAATTGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
3868162 CCT
66 CCT
* * * *
3868165 TTTATCTAACTGGAATAAATGACATCTTTCTGTCATTTACACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
3868230 CCT
66 CCT
* *
3868233 TTCATCTAACTGTCATAAATGACACCTTTCTGTCATTTGCATAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
3868298 CCT
66 CCT
* * * * *
3868301 TTAACCTAACTAGCATAAATGACACATTTCTGTCATGTGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCT
3868353 ATAATCTTTT
Statistics
Matches: 349, Mismatches: 43, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
68 349 1.00
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.32
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:3869046 original size:19 final size:19
Alignment explanation
Indices: 3869021--3869066 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
3869011 ATTATGGTAC
3869021 CGATACCCCATTCCATTAT
1 CGATACCCCATTCCATTAT
* *
3869040 TGATACCCCCTTCCATTAT
1 CGATACCCCATTCCATTAT
3869059 CGATACCC
1 CGATACCC
3869067 ATTTTAGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.24, C:0.39, G:0.07, T:0.30
Consensus pattern (19 bp):
CGATACCCCATTCCATTAT
Found at i:3869212 original size:14 final size:14
Alignment explanation
Indices: 3869193--3869245 Score: 72
Period size: 14 Copynumber: 3.8 Consensus size: 14
3869183 TAGCCTATAG
*
3869193 TATCGGTGTTGTTC
1 TATCGGTATTGTTC
3869207 TATCGGTACTT-TTC
1 TATCGGTA-TTGTTC
3869221 TATCGGTATTGTTC
1 TATCGGTATTGTTC
*
3869235 TATCAGTATTG
1 TATCGGTATTG
3869246 ATACCCTTGC
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 2 0.06
14 31 0.89
15 2 0.06
ACGTcount: A:0.15, C:0.15, G:0.21, T:0.49
Consensus pattern (14 bp):
TATCGGTATTGTTC
Found at i:3872658 original size:20 final size:20
Alignment explanation
Indices: 3872633--3872711 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
3872623 AATTTATAGT
*
3872633 ATCCTTTTATGCCTTAATGC
1 ATCCTTTCATGCCTTAATGC
* *
3872653 ATCCTTTCATGCATTTTAATATGGA
1 ATCCTTTCATGC--CTT-A-AT-GC
*
3872678 ATCCTTTCATGTCTTAATGC
1 ATCCTTTCATGCCTTAATGC
3872698 ATCCTTTCATGCCT
1 ATCCTTTCATGCCT
3872712 ATTATGTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 25 0.53
21 2 0.04
22 3 0.06
23 3 0.06
24 2 0.04
25 12 0.26
ACGTcount: A:0.22, C:0.24, G:0.10, T:0.44
Consensus pattern (20 bp):
ATCCTTTCATGCCTTAATGC
Found at i:3873247 original size:81 final size:81
Alignment explanation
Indices: 3872949--3873250 Score: 376
Period size: 81 Copynumber: 3.7 Consensus size: 81
3872939 TTCAACAGTG
* * *
3872949 TTTAACTGTTCATCTAACTGGCATAATTAACACCTTTCTGT-CAATTGCACAGTTAGGCCATTAT
1 TTTAACCGTTCATCTAACTGGCATAAATGACACCTTTCT-TCCAATTGCACAGTTAGGCCATTAT
3873013 TCTTTTACTCAAC-AGTA
65 TCTTTTACTCAACGA-TA
* * * * * *
3873030 TTTAACCATTCATCTAACTGGTATAAATGACACATTT-TTGCCAATTGTATAGTTAGACCATTAT
1 TTTAACCGTTCATCTAACTGGCATAAATGACACCTTTCTT-CCAATTGCACAGTTAGGCCATTAT
* *
3873094 TCTTTTACTCAATGGTA
65 TCTTTTACTCAACGATA
* * *
3873111 TTTAACCGTTCATCTAACTGGTATAAATGACACCTTTCTGCCAATTACACAGTTAGGCCATTATT
1 TTTAACCGTTCATCTAACTGGCATAAATGACACCTTTCTTCCAATTGCACAGTTAGGCCATTATT
*
3873176 CTTTTACTCAGCGATA
66 CTTTTACTCAACGATA
** * * *
3873192 TTTAATTGTTCATCTAATTGGCATAAATGACATCTTTCTTCCATTTGCACAGTTAGGCC
1 TTTAACCGTTCATCTAACTGGCATAAATGACACCTTTCTTCCAATTGCACAGTTAGGCC
3873251 TCAAAGGCAC
Statistics
Matches: 188, Mismatches: 29, Indels: 8
0.84 0.13 0.04
Matches are distributed among these distances:
79 1 0.01
80 1 0.01
81 185 0.98
82 1 0.01
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (81 bp):
TTTAACCGTTCATCTAACTGGCATAAATGACACCTTTCTTCCAATTGCACAGTTAGGCCATTATT
CTTTTACTCAACGATA
Found at i:3873309 original size:68 final size:68
Alignment explanation
Indices: 3873200--3873591 Score: 570
Period size: 68 Copynumber: 5.8 Consensus size: 68
3873190 TATTTAATTG
* *
3873200 TTCATCTAATTGGCATAAATGACATCTTTCT-TCCATTTGCACAGTTAGGCCTCAAAGGCACTTA
1 TTCATCTAACTGGCATAAATGACACCTTTCTGT-CATTTGCACAGTTAGGCCTCAAAGGCACTTA
*
3873264 GCAT
65 GCCT
* * * *
3873268 TTCATCTAACTGTCATAAATGACACATTTATGTCATTTGCACAATTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
3873333 CCT
66 CCT
* * * * * *
3873336 TTCATCTAACTGGCATAAATGACACCTTTTTATCATTTACAGAATTAGGCCTCAAAGGAACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
*
3873401 CTT
66 CCT
*
3873404 TTCATCTAACTGGAATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
3873469 CCT
66 CCT
* * * * * *
3873472 TTCATCTAACTGGCATAAATGATATCTTTCTGTTATTTACTCAGTTAGGGCTCAAAGGCACTTAG
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
3873537 CCT
66 CCT
*
3873540 TTAATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCT
1 TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCT
3873592 ATAATCTTTT
Statistics
Matches: 286, Mismatches: 37, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
68 285 1.00
69 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.34
Consensus pattern (68 bp):
TTCATCTAACTGGCATAAATGACACCTTTCTGTCATTTGCACAGTTAGGCCTCAAAGGCACTTAG
CCT
Found at i:3874396 original size:95 final size:95
Alignment explanation
Indices: 3874232--3874456 Score: 281
Period size: 95 Copynumber: 2.4 Consensus size: 95
3874222 TCTGGCTTTA
* * * * * * *
3874232 TAGTATCGATACCCCTACTATGGTATCGACACTACTATACTATGGTACTGATACCCCGTTATGGC
1 TAGTATCGATACCCTTACCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTACGGA
**
3874297 ATCGATACCTATTTTTTATTCAATGTTG-CC
66 ATCGATACCTATTTTACATTCAATG-TGACC
* * * *
3874327 TAGTATTGATACCCTTACCATGGTATCGATACTACTATATTATGGTACCGATACCCCCTTCCGTA
1 TAGTATCGATACCCTTACCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTACGGA
* *
3874392 ATCGATACCTATTTTACGTTCGATGTGACC
66 ATCGATACCTATTTTACATTCAATGTGACC
* *
3874422 TGGTATCGATACCCTTACCATGGTATCAATACTAC
1 TAGTATCGATACCCTTACCATGGTATCGATACTAC
3874457 CTCGTTGGTA
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
94 2 0.02
95 109 0.98
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.35
Consensus pattern (95 bp):
TAGTATCGATACCCTTACCATGGTATCGATACTACTATACTATGGTACCGATACCCCCTTACGGA
ATCGATACCTATTTTACATTCAATGTGACC
Found at i:3876055 original size:13 final size:13
Alignment explanation
Indices: 3876041--3876082 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
3876031 ATGTAAGTTG
*
3876041 CATTTATGTGTTG
1 CATTTATGTGTTC
*
3876054 CATGT-TGTGTTC
1 CATTTATGTGTTC
*
3876066 CATTTATATGTTC
1 CATTTATGTGTTC
3876079 CATT
1 CATT
3876083 AATTTGTTTC
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
12 10 0.42
13 14 0.58
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (13 bp):
CATTTATGTGTTC
Found at i:3878920 original size:101 final size:101
Alignment explanation
Indices: 3878745--3878946 Score: 404
Period size: 101 Copynumber: 2.0 Consensus size: 101
3878735 CTTGGACTAG
3878745 TGGATAATTTGGAAGAGTTATTACTTCTTCCTTTGATGTGAGTCTTGTGATGTATGTATCAACCT
1 TGGATAATTTGGAAGAGTTATTACTTCTTCCTTTGATGTGAGTCTTGTGATGTATGTATCAACCT
3878810 CCTTTTTTTCAAAACGATTCGACCTCGAATCTGAAA
66 CCTTTTTTTCAAAACGATTCGACCTCGAATCTGAAA
3878846 TGGATAATTTGGAAGAGTTATTACTTCTTCCTTTGATGTGAGTCTTGTGATGTATGTATCAACCT
1 TGGATAATTTGGAAGAGTTATTACTTCTTCCTTTGATGTGAGTCTTGTGATGTATGTATCAACCT
3878911 CCTTTTTTTCAAAACGATTCGACCTCGAATCTGAAA
66 CCTTTTTTTCAAAACGATTCGACCTCGAATCTGAAA
3878947 CATTAAAGGG
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.26, C:0.17, G:0.18, T:0.40
Consensus pattern (101 bp):
TGGATAATTTGGAAGAGTTATTACTTCTTCCTTTGATGTGAGTCTTGTGATGTATGTATCAACCT
CCTTTTTTTCAAAACGATTCGACCTCGAATCTGAAA
Found at i:3889670 original size:21 final size:21
Alignment explanation
Indices: 3889646--3889696 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
3889636 ATAGTATCGG
3889646 TACTACTGTTCACGGTATCAA
1 TACTACTGTTCACGGTATCAA
* * **
3889667 TACTACTGTTTATGGTATCGG
1 TACTACTGTTCACGGTATCAA
3889688 TACTACTGT
1 TACTACTGT
3889697 AGCAATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (21 bp):
TACTACTGTTCACGGTATCAA
Found at i:3889793 original size:21 final size:21
Alignment explanation
Indices: 3889744--3889794 Score: 68
Period size: 21 Copynumber: 2.4 Consensus size: 21
3889734 TTAGAATCTG
3889744 TACTGTTCATGTTATCGATAC
1 TACTGTTCATGTTATCGATAC
*
3889765 TACAGTTCAT-TGTATCGATAC
1 TACTGTTCATGT-TATCGATAC
*
3889786 TATTGTTCA
1 TACTGTTCA
3889795 CATAGTATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
20 1 0.04
21 25 0.96
ACGTcount: A:0.25, C:0.18, G:0.14, T:0.43
Consensus pattern (21 bp):
TACTGTTCATGTTATCGATAC
Found at i:3889834 original size:19 final size:20
Alignment explanation
Indices: 3889776--3889835 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 20
3889766 ACAGTTCATT
*
3889776 GTATCGATACTATTGTTCACATA
1 GTATCGATACTA---TTCATATA
* *
3889799 GTATCGGTACTACTCATATA
1 GTATCGATACTATTCATATA
3889819 GTA-CGATACTATTCATA
1 GTATCGATACTATTCATA
3889836 AAAAAATTTG
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
19 12 0.38
20 9 0.28
23 11 0.34
ACGTcount: A:0.32, C:0.18, G:0.13, T:0.37
Consensus pattern (20 bp):
GTATCGATACTATTCATATA
Found at i:3891585 original size:19 final size:20
Alignment explanation
Indices: 3891548--3891593 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
3891538 TATCGGTGTA
3891548 ATTCATACAGTATCAGTACT
1 ATTCATACAGTATCAGTACT
*
3891568 ATTCATATAGTA-CAGTACT
1 ATTCATACAGTATCAGTACT
3891587 ATTCATA
1 ATTCATA
3891594 AAAATATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (20 bp):
ATTCATACAGTATCAGTACT
Found at i:3894360 original size:21 final size:21
Alignment explanation
Indices: 3894313--3894360 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3894303 GCATCGTTAC
*
3894313 TATTCATGGTATCAATACTAT
1 TATTCATGGTATCAATACTAA
* *
3894334 TGTTCATGGTATCGATACTAA
1 TATTCATGGTATCAATACTAA
3894355 TATTCA
1 TATTCA
3894361 CACAGTACCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.15, G:0.12, T:0.42
Consensus pattern (21 bp):
TATTCATGGTATCAATACTAA
Found at i:3894408 original size:20 final size:20
Alignment explanation
Indices: 3894355--3894421 Score: 82
Period size: 20 Copynumber: 3.4 Consensus size: 20
3894345 TCGATACTAA
* * *
3894355 TATTCACACAGTACCTATAC
1 TATTCATACAGTATCTGTAC
*
3894375 TATTCATATAGTATCTGTAC
1 TATTCATACAGTATCTGTAC
*
3894395 TATTCATACAGTAT-GGTAC
1 TATTCATACAGTATCTGTAC
3894414 TATTCATA
1 TATTCATA
3894422 AAAAAAATTG
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 12 0.29
20 29 0.71
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (20 bp):
TATTCATACAGTATCTGTAC
Found at i:3901943 original size:28 final size:28
Alignment explanation
Indices: 3901901--3901966 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
3901891 ATTCTAATGT
3901901 ACAGAGGTGCCAGATTTTAGACTGAAGC
1 ACAGAGGTGCCAGATTTTAGACTGAAGC
*
3901929 ATAGAGGTGCCAGATTTTAGACTGAAGC
1 ACAGAGGTGCCAGATTTTAGACTGAAGC
3901957 ACAGAGGTGC
1 ACAGAGGTGC
3901967 TCAGTCATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.32, C:0.17, G:0.30, T:0.21
Consensus pattern (28 bp):
ACAGAGGTGCCAGATTTTAGACTGAAGC
Found at i:3902022 original size:55 final size:55
Alignment explanation
Indices: 3901951--3902134 Score: 208
Period size: 55 Copynumber: 3.3 Consensus size: 55
3901941 GATTTTAGAC
* * ** *
3901951 TGAAGCACAGAGGTGCTCAGTCATTTTTAACTGGACAGAGGTGTCAGTTCTCGAT
1 TGAAGCACAAAGGTGCTCAGTCAATTTTAACTACACAGAGGTGTCAGCTCTCGAT
* * * * * * **
3902006 TGAAGCACAAAGGTGCTCAATCAGTCTTAGCTACACAGAAGTATCAGCTC-CTGGC
1 TGAAGCACAAAGGTGCTCAGTCAATTTTAACTACACAGAGGTGTCAGCTCTC-GAT
* * *
3902061 TAAAGCACATAGGTGCTCAGCCAATTTTAACTACACAGAGGTGTCAGCTCTCGAT
1 TGAAGCACAAAGGTGCTCAGTCAATTTTAACTACACAGAGGTGTCAGCTCTCGAT
3902116 TGAAGCACAAAGGTGCTCA
1 TGAAGCACAAAGGTGCTCA
3902135 ATCGTTAATT
Statistics
Matches: 102, Mismatches: 25, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
54 1 0.01
55 100 0.98
56 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.23, T:0.24
Consensus pattern (55 bp):
TGAAGCACAAAGGTGCTCAGTCAATTTTAACTACACAGAGGTGTCAGCTCTCGAT
Found at i:3905785 original size:96 final size:96
Alignment explanation
Indices: 3905617--3905813 Score: 387
Period size: 96 Copynumber: 2.1 Consensus size: 96
3905607 TCCACGAATG
3905617 TTTG-TTCCTCGAGTTGGGAACTTGCGACAGAAGCTGTTGAAGGAATGTCATGATACCCAATGGG
1 TTTGTTTCCTCGAGTTGGGAACTTGCGACAGAAGCTGTTGAAGGAATGTCATGATACCCAATGGG
3905681 TTGGGCATCCCGGTTCGAGGCGTACTGTTGC
66 TTGGGCATCCCGGTTCGAGGCGTACTGTTGC
3905712 TTTGTTTCCTCGAGTTGGGAACTTGCGACAGAAGCTGTTGAAGGAATGTCATGATACCCAATGGG
1 TTTGTTTCCTCGAGTTGGGAACTTGCGACAGAAGCTGTTGAAGGAATGTCATGATACCCAATGGG
3905777 TTGGGCATCCCGGTTCGAGGCGTACTGTTGC
66 TTGGGCATCCCGGTTCGAGGCGTACTGTTGC
3905808 TTTGTT
1 TTTGTT
3905814 GGGACAAGGG
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
95 4 0.04
96 97 0.96
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.30
Consensus pattern (96 bp):
TTTGTTTCCTCGAGTTGGGAACTTGCGACAGAAGCTGTTGAAGGAATGTCATGATACCCAATGGG
TTGGGCATCCCGGTTCGAGGCGTACTGTTGC
Found at i:3908879 original size:75 final size:75
Alignment explanation
Indices: 3908786--3908968 Score: 213
Period size: 75 Copynumber: 2.4 Consensus size: 75
3908776 ATAAATAAAG
* * ** *
3908786 TCAAATATCAAGACTCAAACCACAATATTAAATTTAGAACAATAAAATTTATAAACAAATCACAA
1 TCAAATCTCAAGACTCAAACCACAATATTAAATCTAGAACAATAAAATCCATAAACAAACCACAA
3908851 TATTAAAATA
66 TATTAAAATA
* * * * * *
3908861 TCAAATCTCAATATTCAAACCACAATATTAACTCTAGAATAATAAAATCCATAATCAAACCATAA
1 TCAAATCTCAAGACTCAAACCACAATATTAAATCTAGAACAATAAAATCCATAAACAAACCACAA
* *
3908926 TATTAAAGTG
66 TATTAAAATA
* * * *
3908936 TCAAATCTTAAGACTGAAATCATAATATTAAAT
1 TCAAATCTCAAGACTCAAACCACAATATTAAAT
3908969 ATAAAAAAAC
Statistics
Matches: 88, Mismatches: 20, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
75 88 1.00
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.28
Consensus pattern (75 bp):
TCAAATCTCAAGACTCAAACCACAATATTAAATCTAGAACAATAAAATCCATAAACAAACCACAA
TATTAAAATA
Found at i:3913033 original size:17 final size:18
Alignment explanation
Indices: 3913009--3913053 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
3912999 TAACCAGTCT
3913009 GACCCGACCCGTTGA-CC
1 GACCCGACCCGTTGACCC
* *
3913026 GTCCCGACTCGTTGACCC
1 GACCCGACCCGTTGACCC
3913044 GACCCGACCC
1 GACCCGACCC
3913054 AGTGACATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.16, C:0.49, G:0.22, T:0.13
Consensus pattern (18 bp):
GACCCGACCCGTTGACCC
Found at i:3913125 original size:29 final size:29
Alignment explanation
Indices: 3913056--3913240 Score: 153
Period size: 29 Copynumber: 6.3 Consensus size: 29
3913046 CCCGACCCAG
*
3913056 TGACATTTTGGGAATTATTTTGAAAAAAGG
1 TGACATTTTGGGAATTATTTTG-AAAAAGA
* *
3913086 TGCCATTTTTGGGAATTATTTTGAAAAAGG
1 TGACA-TTTTGGGAATTATTTTGAAAAAGA
*
3913116 TGACATTTTGGGAATT-TTTAT-AAAACA-T
1 TGACATTTTGGGAATTATTT-TGAAAA-AGA
* * * * *
3913144 TGACATTCTGGTAATTGTTTTTAAAATGA
1 TGACATTTTGGGAATTATTTTGAAAAAGA
* *
3913173 TAACATTTTGGGAATTA-TTTGTAAAACGA
1 TGACATTTTGGGAATTATTTTG-AAAAAGA
* * *
3913202 TGATATTTTGGTAATTATTTTTAATAAAGA
1 TGACATTTTGGGAATTATTTTGAA-AAAGA
*
3913232 TGATATTTT
1 TGACATTTT
3913241 TGTAATTTTC
Statistics
Matches: 128, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
28 25 0.20
29 55 0.43
30 31 0.24
31 17 0.13
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (29 bp):
TGACATTTTGGGAATTATTTTGAAAAAGA
Found at i:3913217 original size:58 final size:58
Alignment explanation
Indices: 3913058--3913232 Score: 176
Period size: 58 Copynumber: 3.0 Consensus size: 58
3913048 CGACCCAGTG
* * * * * * *
3913058 ACATTTTGGGAATTATTTTGAAAAAAGGTGCCAT-TTTTGGGAATTATTTTGAAAAAGGTG
1 ACATTTTGGGAATTA-TTTGTAAAACGATG--ATATTTTGGTAATTATTTTTAAAAAGATA
* * * * *
3913118 ACATTTTGGGAATT-TTTATAAAAC-ATTGACATTCTGGTAATTGTTTTTAAAATGATA
1 ACATTTTGGGAATTATTTGTAAAACGA-TGATATTTTGGTAATTATTTTTAAAAAGATA
3913175 ACATTTTGGGAATTATTTGTAAAACGATGATATTTTGGTAATTATTTTTAATAAAGAT
1 ACATTTTGGGAATTATTTGTAAAACGATGATATTTTGGTAATTATTTTTAA-AAAGAT
3913233 GATATTTTTG
Statistics
Matches: 93, Mismatches: 17, Indels: 11
0.77 0.14 0.09
Matches are distributed among these distances:
56 1 0.01
57 33 0.35
58 39 0.42
59 6 0.06
60 14 0.15
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.42
Consensus pattern (58 bp):
ACATTTTGGGAATTATTTGTAAAACGATGATATTTTGGTAATTATTTTTAAAAAGATA
Found at i:3918283 original size:30 final size:30
Alignment explanation
Indices: 3918249--3918306 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 30
3918239 TGACGATGGC
3918249 ACTTT-GTTAGC-AGAATTACAAGTTAAGTCA
1 ACTTTGGTTAGCGA-AATTA-AAGTTAAGTCA
3918279 ACTTTGGTTAGCGAAATTAAAGTTAAGT
1 ACTTTGGTTAGCGAAATTAAAGTTAAGT
3918307 AGCCCCTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
30 14 0.54
31 11 0.42
32 1 0.04
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.34
Consensus pattern (30 bp):
ACTTTGGTTAGCGAAATTAAAGTTAAGTCA
Found at i:3920243 original size:20 final size:20
Alignment explanation
Indices: 3920218--3920285 Score: 127
Period size: 20 Copynumber: 3.4 Consensus size: 20
3920208 TCGTGTTCCT
3920218 GGTGTCGTTCCGAGTCCGAC
1 GGTGTCGTTCCGAGTCCGAC
*
3920238 GGTGTCGTTCCGAGTTCGAC
1 GGTGTCGTTCCGAGTCCGAC
3920258 GGTGTCGTTCCGAGTCCGAC
1 GGTGTCGTTCCGAGTCCGAC
3920278 GGTGTCGT
1 GGTGTCGT
3920286 CCTTGTCTCC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 46 1.00
ACGTcount: A:0.09, C:0.26, G:0.37, T:0.28
Consensus pattern (20 bp):
GGTGTCGTTCCGAGTCCGAC
Found at i:3920558 original size:17 final size:17
Alignment explanation
Indices: 3920532--3920593 Score: 97
Period size: 17 Copynumber: 3.6 Consensus size: 17
3920522 TGACCGGTCT
*
3920532 GACCCTACCCGTTGACC
1 GACCCGACCCGTTGACC
*
3920549 GACCTGACCCGTTGACC
1 GACCCGACCCGTTGACC
3920566 GACCCGACCCGTTGACCC
1 GACCCGACCCGTTGA-CC
3920584 GACCCGACCC
1 GACCCGACCC
3920594 AGTGATATTT
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
17 29 0.71
18 12 0.29
ACGTcount: A:0.18, C:0.48, G:0.21, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGTTGACC
Found at i:3920683 original size:29 final size:29
Alignment explanation
Indices: 3920595--3920815 Score: 308
Period size: 29 Copynumber: 7.7 Consensus size: 29
3920585 ACCCGACCCA
* *
3920595 GTGATATTTTGGGAATTATTTTGAAAAAA
1 GTGACATTTTGGGAATTATTTTGAAAAAT
*
3920624 ATGACA-TTTGGGAATTA-TTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAT
3920651 GTGACATTTTGGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAT
3920680 GTGACATTTTGGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAT
3920709 GTGACATTTTGGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAT
** *
3920738 GTGACATTTTTAGAATT-TTTTTAAAACA-
1 GTGACATTTTGGGAATTATTTTGAAAA-AT
* *
3920766 GTGACATTTTGGTAATTATTTT-TAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAAT
*
3920794 GATAACATTTTGGGAATTATTT
1 G-TGACATTTTGGGAATTATTT
3920816 GTATTGGTAA
Statistics
Matches: 173, Mismatches: 13, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
27 15 0.09
28 48 0.28
29 110 0.64
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (29 bp):
GTGACATTTTGGGAATTATTTTGAAAAAT
Found at i:3920783 original size:86 final size:87
Alignment explanation
Indices: 3920593--3920815 Score: 312
Period size: 86 Copynumber: 2.6 Consensus size: 87
3920583 CGACCCGACC
* **
3920593 CAGTGATATTTTGGGAATTATTTTGAAAAAAATGACA-TTTGGGAATTA-TTTGAAAAATGTGAC
1 CAGTGACATTTTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATTATTTTGAAAAATGTGAC
*
3920656 ATTTTGGGAATTATTTTGAAAA
66 ATTTTGAGAATTATTTTGAAAA
3920678 -ATGTGACATTTTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATTATTTTGAAAAATGTGA
1 CA-GTGACATTTTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATTATTTTGAAAAATGTGA
* *
3920742 CATTTTTAGAATT-TTTTTAAAA
65 CATTTTGAGAATTATTTTGAAAA
* * *
3920764 CAGTGACATTTTGGTAATTATTTT-TAAAATGATAACATTTTGGGAATTATTT
1 CAGTGACATTTTGGGAATTATTTTGAAAAATG-TGACATTTTGGGAATTATTT
3920816 GTATTGGTAA
Statistics
Matches: 124, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
84 1 0.01
85 38 0.31
86 59 0.48
87 26 0.21
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (87 bp):
CAGTGACATTTTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATTATTTTGAAAAATGTGAC
ATTTTGAGAATTATTTTGAAAA
Found at i:3920811 original size:57 final size:57
Alignment explanation
Indices: 3920595--3920816 Score: 297
Period size: 57 Copynumber: 3.9 Consensus size: 57
3920585 ACCCGACCCA
* ** *
3920595 GTGATATTTTGGGAATTATTTTGAAAAAAATGACA-TTTGGGAATTATTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATTTTTTGAAAAAT
3920651 GTGACATTTTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATTATTTTGAAAAAT
1 GTGACATTTTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATT-TTTTGAAAAAT
** *
3920709 GTGACATTTTGGGAATTATTTTGAAAAATGTGACATTTTTAGAATTTTTTTAAAACA-
1 GTGACATTTTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATTTTTTGAAAA-AT
* * * *
3920766 GTGACATTTTGGTAATTATTTT-TAAAATGATAACATTTTGGGAATTATTTG
1 GTGACATTTTGGGAATTATTTTGAAAAATG-TGACATTTTGGGAATTTTTTG
3920817 TATTGGTAAT
Statistics
Matches: 148, Mismatches: 14, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
56 38 0.26
57 55 0.37
58 55 0.37
ACGTcount: A:0.35, C:0.04, G:0.18, T:0.43
Consensus pattern (57 bp):
GTGACATTTTGGGAATTATTTTGAAAAATGTGACATTTTGGGAATTTTTTGAAAAAT
Found at i:3924709 original size:23 final size:23
Alignment explanation
Indices: 3924666--3924716 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
3924656 AGAAAAATTA
*
3924666 TATGAAATTTATGTAATTTAAAT
1 TATGAAATTTATCTAATTTAAAT
* *
3924689 TATGAATATTTGTCTAATTAATAAT
1 TATGAA-ATTTATCTAATTTA-AAT
3924714 TAT
1 TAT
3924717 TGTCATTTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 6 0.26
24 11 0.48
25 6 0.26
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (23 bp):
TATGAAATTTATCTAATTTAAAT
Found at i:3925431 original size:41 final size:41
Alignment explanation
Indices: 3925386--3925530 Score: 132
Period size: 41 Copynumber: 3.4 Consensus size: 41
3925376 GATTCTGACT
*
3925386 ATCGCATTGCGATTTCCCAAATTCGCGTTGCGA-TTACGTAA
1 ATCGCATTGCGATTTCCCAAATTCGCATTGCGATTTACGT-A
* * *
3925427 ATCGCAATGCGAATTTGCGATTTACGTATTCGCATTGCGATTTACGTA
1 ATCGCATTGCG-ATTTCCCA---A---ATTCGCATTGCGATTTACGTA
* *
3925475 ATCGCATTGCGATTTTCCTAATTCGCACTT-CGATTTACGTA
1 ATCGCATTGCGATTTCCCAAATTCGCA-TTGCGATTTACGTA
*
3925516 ATCGTATTGCGATTT
1 ATCGCATTGCGATTT
3925531 AGTAAATCGC
Statistics
Matches: 86, Mismatches: 9, Indels: 18
0.76 0.08 0.16
Matches are distributed among these distances:
41 42 0.49
42 8 0.09
44 1 0.01
45 1 0.01
47 5 0.06
48 23 0.27
49 6 0.07
ACGTcount: A:0.23, C:0.21, G:0.19, T:0.37
Consensus pattern (41 bp):
ATCGCATTGCGATTTCCCAAATTCGCATTGCGATTTACGTA
Found at i:3925466 original size:20 final size:20
Alignment explanation
Indices: 3925441--3925541 Score: 125
Period size: 20 Copynumber: 5.0 Consensus size: 20
3925431 CAATGCGAAT
*
3925441 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCA
3925461 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCA
* *
3925481 TTGCGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAA-TCGCA
*
3925502 CTT-CGATTTACGTAATCGTA
1 -TTGCGATTTACGTAATCGCA
3925522 TTGCGATTTA-GTAAATCGCA
1 TTGCGATTTACGT-AATCGCA
3925542 ACGAGATTCT
Statistics
Matches: 70, Mismatches: 7, Indels: 8
0.82 0.08 0.09
Matches are distributed among these distances:
19 4 0.06
20 49 0.70
21 15 0.21
22 2 0.03
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.39
Consensus pattern (20 bp):
TTGCGATTTACGTAATCGCA
Found at i:3928779 original size:19 final size:20
Alignment explanation
Indices: 3928737--3928791 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
3928727 CAATCATCTT
*
3928737 AATGTCTATCGCAACGCGGA
1 AATGACTATCGCAACGCGGA
*
3928757 AATGACTATCGCAATGC-GA
1 AATGACTATCGCAACGCGGA
**
3928776 AATGAAAATCGCAACG
1 AATGACTATCGCAACG
3928792 ATTCTCTCGT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.18
Consensus pattern (20 bp):
AATGACTATCGCAACGCGGA
Found at i:3928823 original size:19 final size:19
Alignment explanation
Indices: 3928799--3928835 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
3928789 ACGATTCTCT
*
3928799 CGTTGCGATTTTCGTTTCG
1 CGTTGCGATTTTCATTTCG
3928818 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
3928836 AACCAAAAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.08, C:0.22, G:0.22, T:0.49
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:3929038 original size:94 final size:93
Alignment explanation
Indices: 3928926--3929301 Score: 580
Period size: 94 Copynumber: 4.1 Consensus size: 93
3928916 ATGGATTGCA
* * *
3928926 TTACTTCATCCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAGTT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
3928991 TAGCAGAATTGGCAGCAAACGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
3929019 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
3929084 TTAGCAGAATTGGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
3929113 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAATGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
3929178 TTAACAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
3929207 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTT----AATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *** *
3929268 TTAGCAGTATTTATAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
3929297 TTACT
1 TTACT
3929302 AAGCAATCTA
Statistics
Matches: 267, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
90 38 0.14
93 23 0.09
94 206 0.77
ACGTcount: A:0.48, C:0.19, G:0.11, T:0.22
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:3930981 original size:20 final size:20
Alignment explanation
Indices: 3930956--3931038 Score: 98
Period size: 20 Copynumber: 4.2 Consensus size: 20
3930946 TTTTGGTTGA
3930956 AATGAAAATCGCAACGAGAG
1 AATGAAAATCGCAACGAGAG
*
3930976 AATGAAAATCGCAATGAG-G
1 AATGAAAATCGCAACGAGAG
** *
3930995 AAATGACTATCGCAACGCGA-
1 -AATGAAAATCGCAACGAGAG
3931015 AATGAAAAATCGCAACGAGAG
1 AATG-AAAATCGCAACGAGAG
3931036 AAT
1 AAT
3931039 CGCAACGCGA
Statistics
Matches: 51, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
19 5 0.10
20 43 0.84
21 3 0.06
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGAGAG
Found at i:3930998 original size:40 final size:37
Alignment explanation
Indices: 3930954--3931064 Score: 122
Period size: 40 Copynumber: 3.0 Consensus size: 37
3930944 TCTTTTGGTT
*
3930954 GAAATGAAAATCGCAACGAGAGAATGAAAATCGCAATGA
1 GAAATG-AAATCGCAACGCGA-AATGAAAATCGCAATGA
* *
3930993 GGAAATGACTATCGCAACGCGAAATGAAAAATCGCAACGA
1 -GAAATGA-AATCGCAACGCGAAATG-AAAATCGCAATGA
3931033 G--A-G-AATCGCAACGCGAAATGAAAATCGCAATG
1 GAAATGAAATCGCAACGCGAAATGAAAATCGCAATG
3931065 CGATTTTGGT
Statistics
Matches: 64, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
33 11 0.17
34 16 0.25
36 1 0.02
37 1 0.02
39 6 0.09
40 29 0.45
ACGTcount: A:0.47, C:0.17, G:0.23, T:0.13
Consensus pattern (37 bp):
GAAATGAAATCGCAACGCGAAATGAAAATCGCAATGA
Found at i:3931096 original size:19 final size:19
Alignment explanation
Indices: 3931063--3931180 Score: 94
Period size: 19 Copynumber: 6.7 Consensus size: 19
3931053 AAAATCGCAA
**
3931063 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
3931082 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
3931101 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
3931115 TGTGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
3931134 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
**
3931148 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
3931168 TGCGATTTTCATT
1 TGCGATTTTCATT
3931181 CTCGAAACTA
Statistics
Matches: 77, Mismatches: 11, Indels: 21
0.71 0.10 0.19
Matches are distributed among these distances:
14 19 0.25
16 5 0.06
17 6 0.08
19 32 0.42
20 15 0.19
ACGTcount: A:0.10, C:0.21, G:0.23, T:0.46
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:3931122 original size:33 final size:33
Alignment explanation
Indices: 3931079--3931174 Score: 156
Period size: 33 Copynumber: 2.9 Consensus size: 33
3931069 TTTGGTTTCG
3931079 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
*
3931112 CGTTGTGATTTTCATTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
**
3931145 CGTTGCGATAGTCATTTCCGCGTTGCGATT
1 CGTTGCGATTTTCATTT-CGCGTTGCGATT
3931175 TTCATTCTCG
Statistics
Matches: 58, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 46 0.79
34 12 0.21
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:3931761 original size:21 final size:21
Alignment explanation
Indices: 3931737--3931782 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3931727 TATTCGCATT
3931737 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
3931758 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
3931779 GCGA
1 GCGA
3931783 TAGTCAGAAT
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:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:3934225 original size:2 final size:2
Alignment explanation
Indices: 3934220--3934249 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3934210 AAAACTGATT
3934220 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3934250 ATCTTAAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3935788 original size:178 final size:179
Alignment explanation
Indices: 3935488--3935845 Score: 693
Period size: 178 Copynumber: 2.0 Consensus size: 179
3935478 ATACAGAAAT
3935488 AAATTTTCTCAAATTACTTTCAGCTGCAATTTCCATAATCTTAGAAATCAATGGCTAAAACAAGC
1 AAATTTTCTCAAATTACTTTCAGCTGCAATTTCCATAATCTTAGAAATCAATGGCTAAAACAAGC
3935553 TAACACCATCAGAGTTTTTTCTTTTGATAAAAAAGAAAGTGATTTTTTTTACTAGTAATTGATTC
66 TAACACCATCAGAGTTTTTTCTTTTGATAAAAAAGAAAGTGATTTTTTTTACTAGTAATTGATTC
3935618 GAAACATAGAAGCTTTGAGAAACTCAG-AATCCATTCAAACATCACTCA
131 GAAACATAGAAGCTTTGAGAAACTCAGAAATCCATTCAAACATCACTCA
3935666 AAATTTTCTCAAATTACTTTCAGCTGCAATTTCCATAATCTTAGAAATCAATGGCTAAAACAAGC
1 AAATTTTCTCAAATTACTTTCAGCTGCAATTTCCATAATCTTAGAAATCAATGGCTAAAACAAGC
3935731 TAACACCATCAGAGTTTTTTCTTTTGATAAAAAAGAAAGTGA-TTTTTTTACCTAGTAATTGATT
66 TAACACCATCAGAGTTTTTTCTTTTGATAAAAAAGAAAGTGATTTTTTTTA-CTAGTAATTGATT
3935795 CGAAACATAGAAGCTTTGAGAAACTCAGAAATCCATTCAAACATCACTCA
130 CGAAACATAGAAGCTTTGAGAAACTCAGAAATCCATTCAAACATCACTCA
3935845 A
1 A
3935846 CGAACCACTC
Statistics
Matches: 178, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
177 8 0.04
178 148 0.83
179 22 0.12
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.33
Consensus pattern (179 bp):
AAATTTTCTCAAATTACTTTCAGCTGCAATTTCCATAATCTTAGAAATCAATGGCTAAAACAAGC
TAACACCATCAGAGTTTTTTCTTTTGATAAAAAAGAAAGTGATTTTTTTTACTAGTAATTGATTC
GAAACATAGAAGCTTTGAGAAACTCAGAAATCCATTCAAACATCACTCA
Found at i:3937215 original size:32 final size:31
Alignment explanation
Indices: 3937179--3937247 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
3937169 ATTACCTTTG
* *
3937179 TTATTTGCTT-TATTATTTTATAAAGTTTTCTT
1 TTATTT-CTTATATTACTTT-TAAAGTTTTCCT
* *
3937211 TTATTTCTTATTTTACTTTTCAAGTTTTCCT
1 TTATTTCTTATATTACTTTTAAAGTTTTCCT
3937242 TTATTT
1 TTATTT
3937248 TACCTTTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
31 19 0.59
32 13 0.41
ACGTcount: A:0.19, C:0.10, G:0.04, T:0.67
Consensus pattern (31 bp):
TTATTTCTTATATTACTTTTAAAGTTTTCCT
Found at i:3937278 original size:32 final size:32
Alignment explanation
Indices: 3937242--3937306 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
3937232 AAGTTTTCCT
*
3937242 TTATTTTACCTTTTTTTAAATGCTAAGTATGA
1 TTATTTCACCTTTTTTTAAATGCTAAGTATGA
*
3937274 TTATTTCACTTTTTTTTAAATGCTAAGTATGA
1 TTATTTCACCTTTTTTTAAATGCTAAGTATGA
3937306 T
1 T
3937307 CTCTATCATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (32 bp):
TTATTTCACCTTTTTTTAAATGCTAAGTATGA
Found at i:3938603 original size:15 final size:16
Alignment explanation
Indices: 3938570--3938606 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
3938560 TGAGATTATT
3938570 TTAA-ATTATATTTTA
1 TTAAGATTATATTTTA
3938585 -TAAGATTAT-TTTTA
1 TTAAGATTATATTTTA
3938599 TTAAGATT
1 TTAAGATT
3938607 TAAGAAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
14 8 0.40
15 12 0.60
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.57
Consensus pattern (16 bp):
TTAAGATTATATTTTA
Found at i:3941631 original size:89 final size:89
Alignment explanation
Indices: 3941480--3941661 Score: 364
Period size: 89 Copynumber: 2.0 Consensus size: 89
3941470 ATTAAACCTA
3941480 AATATGTAAGTTTTAATCCAAATCATTTTTAATAAATTATTAAATTGAATAGTCAAAATGGAAAC
1 AATATGTAAGTTTTAATCCAAATCATTTTTAATAAATTATTAAATTGAATAGTCAAAATGGAAAC
3941545 TCGAGCATAAGCGAGGACCAAACT
66 TCGAGCATAAGCGAGGACCAAACT
3941569 AATATGTAAGTTTTAATCCAAATCATTTTTAATAAATTATTAAATTGAATAGTCAAAATGGAAAC
1 AATATGTAAGTTTTAATCCAAATCATTTTTAATAAATTATTAAATTGAATAGTCAAAATGGAAAC
3941634 TCGAGCATAAGCGAGGACCAAACT
66 TCGAGCATAAGCGAGGACCAAACT
3941658 AATA
1 AATA
3941662 ATTTCCCTAA
Statistics
Matches: 93, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
89 93 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (89 bp):
AATATGTAAGTTTTAATCCAAATCATTTTTAATAAATTATTAAATTGAATAGTCAAAATGGAAAC
TCGAGCATAAGCGAGGACCAAACT
Found at i:3942181 original size:15 final size:16
Alignment explanation
Indices: 3942153--3942199 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 16
3942143 AGAGAAGAAA
3942153 TTAAAATAACAAAAAT
1 TTAAAATAACAAAAAT
*
3942169 TTAAAGTAA-AAAAAT
1 TTAAAATAACAAAAAT
* *
3942184 GT-AAATAACATAAAT
1 TTAAAATAACAAAAAT
3942199 T
1 T
3942200 AATCAATCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 5 0.20
15 12 0.48
16 8 0.32
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (16 bp):
TTAAAATAACAAAAAT
Found at i:3942917 original size:103 final size:102
Alignment explanation
Indices: 3942806--3942994 Score: 245
Period size: 103 Copynumber: 1.8 Consensus size: 102
3942796 AACTCAAGTA
* * * * *
3942806 AGATAAAAATTTGTTTCAATTGAAA-CAATTTCAAAATTTGTGCTTCAAGGGAATCTGTCTCAAG
1 AGATAAAAATTTGTTTCAAGTGAAATC-ATTTCAAAACTTGTGCTTCAAAGGAAACTGACTCAAG
*
3942870 AGAGATGAAATTTTGTTTCAAGAGATCAATCTCATGTG
65 AGAAATGAAATTTTGTTTCAAGAGATCAATCTCATGTG
** * * *
3942908 AGATAAAAAATTTGTTTTGAGTGAAATCATTTTAAAACTTGTGTTTCAAAGGAAACTGACTTAAG
1 AGAT-AAAAATTTGTTTCAAGTGAAATCATTTCAAAACTTGTGCTTCAAAGGAAACTGACTCAAG
*
3942973 CGAAATGAAATTTTGTTTCAAG
65 AGAAATGAAATTTTGTTTCAAG
3942995 GGAAACAATT
Statistics
Matches: 73, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
102 4 0.05
103 68 0.93
104 1 0.01
ACGTcount: A:0.38, C:0.10, G:0.17, T:0.35
Consensus pattern (102 bp):
AGATAAAAATTTGTTTCAAGTGAAATCATTTCAAAACTTGTGCTTCAAAGGAAACTGACTCAAGA
GAAATGAAATTTTGTTTCAAGAGATCAATCTCATGTG
Found at i:3950419 original size:42 final size:41
Alignment explanation
Indices: 3950306--3950421 Score: 101
Period size: 42 Copynumber: 2.8 Consensus size: 41
3950296 TCCCGAAGCT
* * * *
3950306 CTTATGGATTGCCCAAAGGACTTATCATCTTA-CTCGAAAGA
1 CTTATAGATGGCCCGAAGGACTTATCATC-AAGCTCGAAAGA
* * * *
3950347 CTTATAGATGACCCGAAGGATTTAAGCATCAAGCTTGAAAGA
1 CTTATAGATGGCCCGAAGGACTT-ATCATCAAGCTCGAAAGA
*
3950389 CTTACT-TATGGCCCGAAGGACTTACTCATCAAG
1 CTTA-TAGATGGCCCGAAGGACTTA-TCATCAAG
3950422 AAACTTTGAA
Statistics
Matches: 59, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
41 20 0.34
42 38 0.64
43 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.19, T:0.27
Consensus pattern (41 bp):
CTTATAGATGGCCCGAAGGACTTATCATCAAGCTCGAAAGA
Found at i:3950563 original size:57 final size:58
Alignment explanation
Indices: 3950470--3950757 Score: 234
Period size: 60 Copynumber: 5.1 Consensus size: 58
3950460 GTTTATAGTT
* * ** * * * *
3950470 ATCATTAAGAAACCCCTAAAAAGT-AAACTTAACTTC-TTAAAAAAATCATTGGAAATA
1 ATCATCAAGAAACCCCTGAAAA-TCAGGCTTAGCTTCTTTAAAAAATTCATTAGAAATC
* *
3950527 ATCATCAAGAAACCCCTGAAAATCAGGCTTCGCTTCTTTTTTAAAAATTCATTAGAAATC
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGCTTC--TTTAAAAAATTCATTAGAAATC
* ** ***
3950587 ATCATCAAGAAACCCCTGAAAATCAGGATTAAATTCTTTTTTAAATTCATTAGAAATC
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAAATTCATTAGAAATC
* * * *
3950645 ATCATCAAGAAA-CCCTGAAAATCAAGCTTAG-TT-TCTAAAAAACTCATTTGAAA--
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAAATTCATTAGAAATC
* * * * * * *
3950698 A-CATTAA-AAAACCCTAAAAATTAGGCTTAGCTTCTTTTTAAAAATTCATTTGAAAAC
1 ATCATCAAGAAACCCCTGAAAATCAGGCTTAGCTTC-TTTAAAAAATTCATTAGAAATC
3950755 ATC
1 ATC
3950758 CTATCAATAA
Statistics
Matches: 188, Mismatches: 32, Indels: 21
0.78 0.13 0.09
Matches are distributed among these distances:
51 3 0.02
52 21 0.11
53 3 0.02
55 31 0.16
56 3 0.02
57 45 0.24
58 33 0.18
60 49 0.26
ACGTcount: A:0.43, C:0.18, G:0.08, T:0.30
Consensus pattern (58 bp):
ATCATCAAGAAACCCCTGAAAATCAGGCTTAGCTTCTTTAAAAAATTCATTAGAAATC
Found at i:3950596 original size:60 final size:60
Alignment explanation
Indices: 3950509--3950674 Score: 239
Period size: 60 Copynumber: 2.8 Consensus size: 60
3950499 TAACTTCTTA
* * * ***
3950509 AAAAAATCATTGGAAATAATCATCAAGAAACCCCTGAAAATCAGGCTTCGCTTCTTTTTT
1 AAAAATTCATTAGAAATCATCATCAAGAAACCCCTGAAAATCAGGCTTAAATTCTTTTTT
*
3950569 AAAAATTCATTAGAAATCATCATCAAGAAACCCCTGAAAATCAGGATTAAATTCTTTTTT
1 AAAAATTCATTAGAAATCATCATCAAGAAACCCCTGAAAATCAGGCTTAAATTCTTTTTT
*
3950629 --AAATTCATTAGAAATCATCATCAAGAAA-CCCTGAAAATCAAGCTTA
1 AAAAATTCATTAGAAATCATCATCAAGAAACCCCTGAAAATCAGGCTTA
3950675 GTTTCTAAAA
Statistics
Matches: 97, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
57 16 0.16
58 28 0.29
60 53 0.55
ACGTcount: A:0.43, C:0.19, G:0.10, T:0.29
Consensus pattern (60 bp):
AAAAATTCATTAGAAATCATCATCAAGAAACCCCTGAAAATCAGGCTTAAATTCTTTTTT
Found at i:3950718 original size:52 final size:54
Alignment explanation
Indices: 3950654--3950756 Score: 129
Period size: 55 Copynumber: 1.9 Consensus size: 54
3950644 CATCATCAAG
*
3950654 AAACCCTGAAAATCAAGCTTAG-T-TTCTAAAAAACTCATTTGAAAACATTAAA
1 AAACCCTAAAAATCAAGCTTAGCTCTTCTAAAAAACTCATTTGAAAACATTAAA
* * * * *
3950706 AAACCCTAAAAATTAGGCTTAGCTTCTTTTTAAAAATTCATTTGAAAACAT
1 AAACCCTAAAAATCAAGCTTAGC-TCTTCTAAAAAACTCATTTGAAAACAT
3950757 CCTATCAATA
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
52 19 0.45
54 1 0.02
55 22 0.52
ACGTcount: A:0.45, C:0.17, G:0.08, T:0.31
Consensus pattern (54 bp):
AAACCCTAAAAATCAAGCTTAGCTCTTCTAAAAAACTCATTTGAAAACATTAAA
Found at i:3954444 original size:116 final size:117
Alignment explanation
Indices: 3954230--3954463 Score: 461
Period size: 116 Copynumber: 2.0 Consensus size: 117
3954220 TCAGGTACCC
3954230 TAAACTCATGGGGAATAACCAAGGTGGGGACTAAGCTTACCTCTCTTGCGTCTAAGTTTTCACGG
1 TAAACTCATGGGGAATAACCAAGGTGGGGACTAAGCTTACCTCTCTTGCGTCTAAGTTTTCACGG
3954295 GATGCCTAACCAACCTTTATTGCCTCAATTGACTATTATAACTGCTTAATTT
66 GATGCCTAACCAACCTTTATTGCCTCAATTGACTATTATAACTGCTTAATTT
3954347 TAAACTCAT-GGGAATAACCAAGGTGGGGACTAAGCTTACCTCTCTTGCGTCTAAGTTTTCACGG
1 TAAACTCATGGGGAATAACCAAGGTGGGGACTAAGCTTACCTCTCTTGCGTCTAAGTTTTCACGG
3954411 GATGCCTAACCAACCTTTATTGCCTCAATTGACTATTATAACTGCTTAATTT
66 GATGCCTAACCAACCTTTATTGCCTCAATTGACTATTATAACTGCTTAATTT
3954463 T
1 T
3954464 TCCTTTAAAA
Statistics
Matches: 117, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
116 108 0.92
117 9 0.08
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (117 bp):
TAAACTCATGGGGAATAACCAAGGTGGGGACTAAGCTTACCTCTCTTGCGTCTAAGTTTTCACGG
GATGCCTAACCAACCTTTATTGCCTCAATTGACTATTATAACTGCTTAATTT
Found at i:3960377 original size:19 final size:18
Alignment explanation
Indices: 3960353--3960401 Score: 73
Period size: 17 Copynumber: 2.7 Consensus size: 18
3960343 TTCCCTTATT
3960353 CACTCTCTCTGCTTCCTCA
1 CACTCTCTC-GCTTCCTCA
*
3960372 CACTCTCTC-ATTCCTCA
1 CACTCTCTCGCTTCCTCA
3960389 CACTCTCTCGCTT
1 CACTCTCTCGCTT
3960402 TTCTCTACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 16 0.59
18 2 0.07
19 9 0.33
ACGTcount: A:0.12, C:0.47, G:0.04, T:0.37
Consensus pattern (18 bp):
CACTCTCTCGCTTCCTCA
Found at i:3961119 original size:19 final size:19
Alignment explanation
Indices: 3961097--3961137 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
3961087 ATGGTGACAT
* *
3961097 GAGTAGCTTGTGGTGGCAG
1 GAGTAGCTGGTAGTGGCAG
*
3961116 GAGTAGCTGGTAGTGGTAG
1 GAGTAGCTGGTAGTGGCAG
3961135 GAG
1 GAG
3961138 CTTGCTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.20, C:0.07, G:0.49, T:0.24
Consensus pattern (19 bp):
GAGTAGCTGGTAGTGGCAG
Found at i:3962237 original size:21 final size:22
Alignment explanation
Indices: 3962200--3962242 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
3962190 GGTGATCTCC
*
3962200 TAACCGGGTTGGGTTGG-GTTG
1 TAACCGGGTCGGGTTGGAGTTG
3962221 TAACC-GGTCGGGTTTGGAGTTG
1 TAACCGGGTCGGG-TTGGAGTTG
3962243 AGTCCTTTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.12, C:0.12, G:0.44, T:0.33
Consensus pattern (22 bp):
TAACCGGGTCGGGTTGGAGTTG
Found at i:3962360 original size:3 final size:3
Alignment explanation
Indices: 3962352--3962402 Score: 61
Period size: 3 Copynumber: 17.7 Consensus size: 3
3962342 CTTGCAAGAA
* * *
3962352 AAT AAT AAT AAT AA- AAT AAT AAT AAC AAT AAT ATT ATT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3962398 AAT AA
1 AAT AA
3962403 ATATGGGTCC
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 4 0.10
3 38 0.90
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3964140 original size:51 final size:51
Alignment explanation
Indices: 3964067--3964223 Score: 215
Period size: 51 Copynumber: 3.1 Consensus size: 51
3964057 AAGAAAGAGC
* * * * *
3964067 CAAGTTGAGGAACGATACTACTGAATAGTTAATTCCTCTCCACGAGAAAGT
1 CAAGTTGAGAAACGATACTACTGAAAAGTTGACTCCTCTCCGCGAGAAAGT
* *
3964118 CAAGTTGAGAAATGATAATACTGAAAAGTTGACTCCTCTCCGCGAGAAAGT
1 CAAGTTGAGAAACGATACTACTGAAAAGTTGACTCCTCTCCGCGAGAAAGT
* * * *
3964169 CAAGTTGAGAAAGGATACTATTGAAAAGTTGACTCATCTTCGCGAGAAAGT
1 CAAGTTGAGAAACGATACTACTGAAAAGTTGACTCCTCTCCGCGAGAAAGT
3964220 CAAG
1 CAAG
3964224 AAGGACCACA
Statistics
Matches: 94, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 94 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (51 bp):
CAAGTTGAGAAACGATACTACTGAAAAGTTGACTCCTCTCCGCGAGAAAGT
Found at i:3964256 original size:45 final size:45
Alignment explanation
Indices: 3964192--3964669 Score: 448
Period size: 45 Copynumber: 10.6 Consensus size: 45
3964182 GATACTATTG
*
3964192 AAAAG-TTGACTCATCTTCGCGAGAAAGTCAAGAAGGACCACACT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGGACAACACT
** * *
3964236 AAACTATTTACTTC-TCTTCGCGAGAAAGTCAAGAAGGACAACACC
1 AAAAGATTGAC-TCATCTTCGCGAGAAAGTCAAGAAGGACAACACT
* ** * * * * *
3964281 AAAATATTGACTCATCTTCATGACAAAATCAAGGAA-AACAATACC
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAA-GAAGGACAACACT
* * *
3964326 GAAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGAAAACACT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGGACAACACT
** * *
3964371 AAAAGATTGACTCATCTTCATGAGAAAGTCAAGAAAGACAACATT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGGACAACACT
* * * * * *
3964416 GAAAGATTGATTCCTCTTTGCGAGAAAGTCAAGAAGGAAAACAAT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGGACAACACT
* * * *
3964461 AAAAGATTTACTCTTTTTCACGAGAAAGTCAAGGAA-GACAACACT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAA-GAAGGACAACACT
* * * *
3964506 GAAAGATTGACTCCTCTTTGCGAGAAAGTCAAGAAGGACAACATT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGGACAACACT
* * *
3964551 AAAAGATTGACTCATCTTCACGAGAAAGTCAATGAA-GAAAACATT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAA-GAAGGACAACACT
* * * * * *
3964596 GAAAGATTGACTCTTCTTCACGAGAAAGTCAATAATGACAATACT
1 AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGGACAACACT
* *
3964641 GAGAA-ATTGACTTC-TCTTCACGAGAAAGT
1 -AAAAGATTGAC-TCATCTTCGCGAGAAAGT
3964670 AAAAAATAAC
Statistics
Matches: 354, Mismatches: 69, Indels: 21
0.80 0.16 0.05
Matches are distributed among these distances:
44 13 0.04
45 326 0.92
46 15 0.04
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (45 bp):
AAAAGATTGACTCATCTTCGCGAGAAAGTCAAGAAGGACAACACT
Found at i:3964343 original size:90 final size:90
Alignment explanation
Indices: 3964192--3964669 Score: 547
Period size: 90 Copynumber: 5.3 Consensus size: 90
3964182 GATACTATTG
* * * * * *
3964192 AAAAG-TTGACTCATCTTCGCGAGAAAGTCAA-GAAGGACCACACT-AAACTATTTACTTCTCTT
1 AAAAGATTGACTCATCTTCACGAGAAAGTCAAGGAA-AACAACACTGAAA-GATTGACTCCTCTT
*
3964254 CGCGAGAAAGTCAAGAAGGACAACACC
64 CGCGAGAAAGTCAAGAAGGACAACACT
* * * * * *
3964281 AAAATATTGACTCATCTTCATGACAAAATCAAGGAAAACAATACCGAAAGATTGACTCCTCTTCG
1 AAAAGATTGACTCATCTTCACGAGAAAGTCAAGGAAAACAACACTGAAAGATTGACTCCTCTTCG
*
3964346 CGAGAAAGTCAAGAAGGAAAACACT
66 CGAGAAAGTCAAGAAGGACAACACT
* * * *
3964371 AAAAGATTGACTCATCTTCATGAGAAAGTCAA-GAAAGACAACATTGAAAGATTGATTCCTCTTT
1 AAAAGATTGACTCATCTTCACGAGAAAGTCAAGGAAA-ACAACACTGAAAGATTGACTCCTCTTC
* *
3964435 GCGAGAAAGTCAAGAAGGAAAACAAT
65 GCGAGAAAGTCAAGAAGGACAACACT
* * * * *
3964461 AAAAGATTTACTCTTTTTCACGAGAAAGTCAAGGAAGACAACACTGAAAGATTGACTCCTCTTTG
1 AAAAGATTGACTCATCTTCACGAGAAAGTCAAGGAAAACAACACTGAAAGATTGACTCCTCTTCG
*
3964526 CGAGAAAGTCAAGAAGGACAACATT
66 CGAGAAAGTCAAGAAGGACAACACT
* * *
3964551 AAAAGATTGACTCATCTTCACGAGAAAGTCAATGAAGAA-AACATTGAAAGATTGACTCTTCTTC
1 AAAAGATTGACTCATCTTCACGAGAAAGTCAAGGAA-AACAACACTGAAAGATTGACTCCTCTTC
* * * *
3964615 ACGAGAAAGTCAATAATGACAATACT
65 GCGAGAAAGTCAAGAAGGACAACACT
*
3964641 GAGAA-ATTGACTTC-TCTTCACGAGAAAGT
1 -AAAAGATTGAC-TCATCTTCACGAGAAAGT
3964670 AAAAAATAAC
Statistics
Matches: 335, Mismatches: 46, Indels: 15
0.85 0.12 0.04
Matches are distributed among these distances:
89 8 0.02
90 312 0.93
91 15 0.04
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (90 bp):
AAAAGATTGACTCATCTTCACGAGAAAGTCAAGGAAAACAACACTGAAAGATTGACTCCTCTTCG
CGAGAAAGTCAAGAAGGACAACACT
Found at i:3964448 original size:135 final size:132
Alignment explanation
Indices: 3964193--3964669 Score: 496
Period size: 135 Copynumber: 3.5 Consensus size: 132
3964183 ATACTATTGA
* * * ** *
3964193 AAAG-TTGACTCATCTTCGCGAGAAAGTCAAGAAGGACCACACTAAACTATTTACTTCTCTTCGC
1 AAAGATTGACTCTTCTTCACGAGAAAGTCAAGAAGGACAACACTAAAAGATTGAC-TCTCTTCGC
** * * * *
3964257 GAGAAAGTCAAGAAGGACAACACCAAAATATTGACTCATCTTCATGACAAAATCAAGGAAAACAA
65 GAGAAAGTCAAGAAGGACAACATTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGGAAAACAA
3964322 TACCG
130 TA--G
* * * **
3964327 AAAGATTGACTCCTCTTCGCGAGAAAGTCAAGAAGGAAAACACTAAAAGATTGACTCATCTTCAT
1 AAAGATTGACTCTTCTTCACGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTC-TCTTCGC
* * * * **
3964392 GAGAAAGTCAAGAAAGACAACATTGAAAGATTGATTCCTCTTTGCGAGAAAGTCAAGAAGGAAAA
65 GAGAAAGTCAAGAAGGACAACATTAAAAGATTGACTCATCTTCACGAGAAAGTC---AAGGAAAA
3964457 CAATA-
127 CAATAG
* * * *
3964462 AAAGATTTACTCTTTTTCACGAGAAAGTCAAGGAA-GACAACACTGAAAGATTGACTCCTCTTTG
1 AAAGATTGACTCTTCTTCACGAGAAAGTCAA-GAAGGACAACACTAAAAGATTGACT-CTCTTCG
3964526 CGAGAAAGTCAAGAAGGACAACATTAAAAGATTGACTCATCTTCACGAGAAAGTCAATGAAGAAA
64 CGAGAAAGTCAAGAAGGACAACATTAAAAGATTGACTCATCTTCACGAGAAAGTCAA-G--GAAA
*
3964591 AC-ATTG
126 ACAATAG
* * * * *
3964597 AAAGATTGACTCTTCTTCACGAGAAAGTCAATAATGACAATACTGAGAA-ATTGACTTCTCTTCA
1 AAAGATTGACTCTTCTTCACGAGAAAGTCAAGAAGGACAACACT-AAAAGATTGAC-TCTCTTCG
3964661 CGAGAAAGT
64 CGAGAAAGT
3964670 AAAAAATAAC
Statistics
Matches: 285, Mismatches: 44, Indels: 27
0.80 0.12 0.08
Matches are distributed among these distances:
132 2 0.01
133 1 0.00
134 10 0.04
135 252 0.88
136 7 0.02
138 13 0.05
ACGTcount: A:0.42, C:0.18, G:0.18, T:0.22
Consensus pattern (132 bp):
AAAGATTGACTCTTCTTCACGAGAAAGTCAAGAAGGACAACACTAAAAGATTGACTCTCTTCGCG
AGAAAGTCAAGAAGGACAACATTAAAAGATTGACTCATCTTCACGAGAAAGTCAAGGAAAACAAT
AG
Found at i:3964697 original size:38 final size:38
Alignment explanation
Indices: 3964646--3964848 Score: 255
Period size: 38 Copynumber: 5.3 Consensus size: 38
3964636 ATACTGAGAA
* * *
3964646 ATTGACTTCTCTTCACGAGAAAGTAAAAAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
3964684 ATTGACTTCTCTTCACAAGGAAGTCAAGAATAATAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * *
3964722 ATCGACTTATCTTCACGAGGAAGTCAAGGATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
3964760 ATTGAATTCCCTTCACGAAGG-AGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACG-AGGAAGTCAAGAATAACAAAG
* * *
3964798 ATTAACTTATCTTCACGAGGGAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
3964836 AATGAATTCTCTT
1 ATTGACTTCTCTT
3964849 TACAATGAAT
Statistics
Matches: 140, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
37 3 0.02
38 134 0.96
39 3 0.02
ACGTcount: A:0.42, C:0.17, G:0.17, T:0.25
Consensus pattern (38 bp):
ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
Found at i:3964775 original size:76 final size:76
Alignment explanation
Indices: 3964649--3964870 Score: 284
Period size: 76 Copynumber: 2.9 Consensus size: 76
3964639 CTGAGAAATT
* * * * *
3964649 GACTTCTCTTCACGAGAAAGTAAAAAATAACAAAGATTGACTTCTCTTCACAAGGAAGTCAAGAA
1 GACTTATCTTCACGAGGAAGTCAAGAATAACAAAGATTGAATTCTCTTCACAAGGAAGTCAAGAA
*
3964714 TAATAAAGATC
66 TAACAAAGATC
* *
3964725 GACTTATCTTCACGAGGAAGTCAAGGATAACAAAGATTGAATTCCCTTCACGAAGG-AGTCAAGA
1 GACTTATCTTCACGAGGAAGTCAAGAATAACAAAGATTGAATTCTCTTCAC-AAGGAAGTCAAGA
*
3964789 ATAACAAAGATT
65 ATAACAAAGATC
* * * * * * *
3964801 AACTTATCTTCACGAGGGAGTCAAGAATAACAAAGAATGAATTCTCTTTACAATGAATTCAAGTA
1 GACTTATCTTCACGAGGAAGTCAAGAATAACAAAGATTGAATTCTCTTCACAAGGAAGTCAAGAA
3964866 TAACA
66 TAACA
3964871 TTGAAAGATT
Statistics
Matches: 126, Mismatches: 18, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
75 3 0.02
76 119 0.94
77 4 0.03
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (76 bp):
GACTTATCTTCACGAGGAAGTCAAGAATAACAAAGATTGAATTCTCTTCACAAGGAAGTCAAGAA
TAACAAAGATC
Found at i:3964863 original size:38 final size:38
Alignment explanation
Indices: 3964652--3964870 Score: 201
Period size: 38 Copynumber: 5.8 Consensus size: 38
3964642 AGAAATTGAC
* * * * * *
3964652 TTCTCTTCACGAGAAAGTAAAAAATAACAAAGATTGAC
1 TTCTCTTCACAAGGAAGTCAAGAATAACAAAGAATGAA
* *
3964690 TTCTCTTCACAAGGAAGTCAAGAATAATAAAG-ATCGAC
1 TTCTCTTCACAAGGAAGTCAAGAATAACAAAGAAT-GAA
* * * *
3964728 TTATCTTCACGAGGAAGTCAAGGATAACAAAGATTGAA
1 TTCTCTTCACAAGGAAGTCAAGAATAACAAAGAATGAA
* *
3964766 TTCCCTTCACGAAGG-AGTCAAGAATAACAAAG-ATTAA
1 TTCTCTTCAC-AAGGAAGTCAAGAATAACAAAGAATGAA
* * *
3964803 CTTATCTTCACGAGGGAGTCAAGAATAACAAAGAATGAA
1 -TTCTCTTCACAAGGAAGTCAAGAATAACAAAGAATGAA
* * * *
3964842 TTCTCTTTACAATGAATTCAAGTATAACA
1 TTCTCTTCACAAGGAAGTCAAGAATAACA
3964871 TTGAAAGATT
Statistics
Matches: 146, Mismatches: 29, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
37 7 0.05
38 131 0.90
39 8 0.05
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.25
Consensus pattern (38 bp):
TTCTCTTCACAAGGAAGTCAAGAATAACAAAGAATGAA
Found at i:3966763 original size:22 final size:22
Alignment explanation
Indices: 3966730--3966784 Score: 83
Period size: 22 Copynumber: 2.4 Consensus size: 22
3966720 TTATTTTGTT
3966730 TCTTCTTCTTTTTCTATCTTTTC
1 TCTT-TTCTTTTTCTATCTTTTC
3966753 TCTTTTCTTTTTCTATCTTTTC
1 TCTTTTCTTTTTCTATCTTTTC
*
3966775 TTTGTTTCTT
1 TCT-TTTCTT
3966785 CTTTTTTCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 20 0.67
23 10 0.33
ACGTcount: A:0.04, C:0.22, G:0.02, T:0.73
Consensus pattern (22 bp):
TCTTTTCTTTTTCTATCTTTTC
Found at i:3975417 original size:3 final size:3
Alignment explanation
Indices: 3975411--3975462 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
3975401 CTTTTTTTGC
*
3975411 AAT AAT AAA 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
3975459 AAT A
1 AAT A
3975463 TATACGTATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3976557 original size:21 final size:21
Alignment explanation
Indices: 3976538--3976580 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3976528 AATTTTTAAT
3976538 ATATATATATATAATATTAATTA
1 ATAT-TAT-TATAATATTAATTA
*
3976561 ATATTATTATAATAATAATT
1 ATATTATTATAATATTAATT
3976581 TAATTAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 3 0.16
23 4 0.21
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
ATATTATTATAATATTAATTA
Found at i:3978248 original size:2 final size:2
Alignment explanation
Indices: 3978241--3978271 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3978231 GTAGTGATAG
3978241 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3978272 TAATAGCGGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3978524 original size:26 final size:26
Alignment explanation
Indices: 3978472--3978524 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
3978462 TATGATGATA
**
3978472 ATAATAATAATAATGGGATAATAAAT
1 ATAATAATAATAATAAGATAATAAAT
*
3978498 ATAATACTAATAATAAG-TAATACAAT
1 ATAATAATAATAATAAGATAATA-AAT
3978524 A
1 A
3978525 AGAATAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.30
Consensus pattern (26 bp):
ATAATAATAATAATAAGATAATAAAT
Found at i:3978879 original size:9 final size:9
Alignment explanation
Indices: 3978867--3978891 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3978857 ATATATATAA
3978867 TTTTTAAAT
1 TTTTTAAAT
3978876 TTTTTAAAT
1 TTTTTAAAT
3978885 TTTTTAA
1 TTTTTAA
3978892 TAATTTATAA
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTTTAAAT
Found at i:3978903 original size:18 final size:18
Alignment explanation
Indices: 3978862--3978905 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
3978852 TATATATATA
**
3978862 TATAATTTTTAAATTTTT
1 TATAATTTTTAAATAATT
*
3978880 TA-AATTTTTTAATAATT
1 TATAATTTTTAAATAATT
3978897 TATAATTTT
1 TATAATTTT
3978906 ATAACTTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 14 0.64
18 8 0.36
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TATAATTTTTAAATAATT
Found at i:3978982 original size:20 final size:19
Alignment explanation
Indices: 3978959--3979002 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
3978949 ATTTTTTGTA
3978959 TTTTTAATATATATAATTAT
1 TTTTTAATA-ATATAATTAT
* *
3978979 TTTTTAGTAATTTAATTAT
1 TTTTTAATAATATAATTAT
3978998 TTTTT
1 TTTTT
3979003 TATAGAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (19 bp):
TTTTTAATAATATAATTAT
Found at i:3979051 original size:29 final size:28
Alignment explanation
Indices: 3978979--3979061 Score: 80
Period size: 29 Copynumber: 2.8 Consensus size: 28
3978969 ATATAATTAT
3978979 TTTTTAGTAATTTAATTATTTTTTTATAGAA
1 TTTTTA-T-ATTTAATT-TTTTTTTATAGAA
*
3979010 TTTTTATATTTAATTTTTTTTAATATTGAA
1 TTTTTATATTTAATTTTTTTT--TATAGAA
3979040 TATTTTA-A-TTAATTTTTATTTT
1 T-TTTTATATTTAATTTTT-TTTT
3979062 TTTTAAAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 11
0.80 0.02 0.19
Matches are distributed among these distances:
28 7 0.15
29 17 0.36
30 12 0.26
31 11 0.23
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (28 bp):
TTTTTATATTTAATTTTTTTTTATAGAA
Found at i:3979056 original size:73 final size:68
Alignment explanation
Indices: 3978921--3979057 Score: 159
Period size: 73 Copynumber: 1.9 Consensus size: 68
3978911 TTATGATATT
* * *
3978921 TTTAATTTTTTTTTTAAATTTTTATAGTATTTTTTGTATTTTTAATATATATAATTATTTTTTAG
1 TTTAATTTTTTTTTTAAATTTTTATAGTATTTTTTGTATATTGAATATATATAATTAATTTTTAG
3978986 TAA
66 TAA
* * *
3978989 TTTAATTATTTTTTTATAGAATTTTTATATTTAATTTTTTTTAATATTGAATAT-TTTAATTAAT
1 TTTAATT-TTTTTTT-TA-AATTTTTATA-GT-ATTTTTTGT-ATATTGAATATATATAATTAAT
3979053 TTTTA
60 TTTTA
3979058 TTTTTTTTAA
Statistics
Matches: 57, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
68 7 0.12
69 7 0.12
70 2 0.04
71 10 0.18
72 1 0.02
73 21 0.37
74 9 0.16
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.66
Consensus pattern (68 bp):
TTTAATTTTTTTTTTAAATTTTTATAGTATTTTTTGTATATTGAATATATATAATTAATTTTTAG
TAA
Found at i:3983003 original size:13 final size:13
Alignment explanation
Indices: 3982977--3983009 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
3982967 AACAGTTAAA
3982977 TTTTAAATTACAC
1 TTTTAAATTACAC
3982990 TTTTGAAATT-CAC
1 TTTT-AAATTACAC
3983003 TTTTAAA
1 TTTTAAA
3983010 AGTTTTTTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 11 0.58
14 5 0.26
ACGTcount: A:0.36, C:0.12, G:0.03, T:0.48
Consensus pattern (13 bp):
TTTTAAATTACAC
Found at i:3983044 original size:22 final size:22
Alignment explanation
Indices: 3983016--3983058 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3983006 TAAAAGTTTT
**
3983016 TTTCTACGTTACATTTAAAAAG
1 TTTCTACAATACATTTAAAAAG
*
3983038 TTTCTACAATACTTTTAAAAA
1 TTTCTACAATACATTTAAAAA
3983059 TCACTTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.14, G:0.05, T:0.42
Consensus pattern (22 bp):
TTTCTACAATACATTTAAAAAG
Found at i:3983559 original size:21 final size:21
Alignment explanation
Indices: 3983533--3983576 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3983523 GTTTCCAGAT
3983533 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
* *
3983554 TCGCAATGCGAACTTGGACTA
1 TCGCAACGCGAACTTCGACTA
3983575 TC
1 TC
3983577 ACAATGCTCG
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:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:3983581 original size:21 final size:21
Alignment explanation
Indices: 3983540--3983583 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
3983530 GATTCGCAAC
*
3983540 GCGAACTTCGACTATCGCAAT
1 GCGAACTTCGACTATCACAAT
*
3983561 GCGAACTTGGACTATCACAAT
1 GCGAACTTCGACTATCACAAT
3983582 GC
1 GC
3983584 TCGCATTGCG
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:0.30, C:0.27, G:0.20, T:0.23
Consensus pattern (21 bp):
GCGAACTTCGACTATCACAAT
Found at i:3983743 original size:6 final size:6
Alignment explanation
Indices: 3983732--3983762 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
3983722 GTGTCGAAGA
3983732 CACGAC CACGAC CACGAC CACGAC CACGAC C
1 CACGAC CACGAC CACGAC CACGAC CACGAC C
3983763 CGAGACGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
CACGAC
Found at i:3984425 original size:42 final size:42
Alignment explanation
Indices: 3984360--3984499 Score: 244
Period size: 42 Copynumber: 3.3 Consensus size: 42
3984350 CGTTGCGATT
*
3984360 TTGGACTATCGCAATGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
* *
3984402 TTGGACTATTGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
*
3984444 TTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
3984486 TTGGACTATCGCAA
1 TTGGACTATCGCAA
3984500 TGCGAATATG
Statistics
Matches: 91, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 91 1.00
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (42 bp):
TTGGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
Found at i:3984496 original size:21 final size:20
Alignment explanation
Indices: 3984360--3984505 Score: 118
Period size: 21 Copynumber: 7.0 Consensus size: 20
3984350 CGTTGCGATT
*
3984360 TTGGACTATCGCAA-TGAAC
1 TTGGACTATCGCAAGCGAAC
*
3984379 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
* *
3984402 TTGGACTATTGCAA-CGAAT
1 TTGGACTATCGCAAGCGAAC
*
3984421 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
*
3984444 TTCGACTATCGCAA-CGAAC
1 TTGGACTATCGCAAGCGAAC
*
3984463 TTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAA-GCGAAC
3984486 TTGGACTATCGCAATGCGAA
1 TTGGACTATCGCAA-GCGAA
3984506 TATGTAAATC
Statistics
Matches: 101, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
19 26 0.26
21 45 0.45
23 30 0.30
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (20 bp):
TTGGACTATCGCAAGCGAAC
Found at i:3989584 original size:22 final size:22
Alignment explanation
Indices: 3989556--3989603 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
3989546 TACTTCTTGT
*
3989556 TCAAAGTCAACACTAGTCAATG
1 TCAAAGTCAACACTAGTCAAAG
* *
3989578 TCAAAGTCAACTCTGGTCAAAG
1 TCAAAGTCAACACTAGTCAAAG
3989600 TCAA
1 TCAA
3989604 TGGTCAATGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (22 bp):
TCAAAGTCAACACTAGTCAAAG
Found at i:3990139 original size:20 final size:21
Alignment explanation
Indices: 3990114--3990183 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 21
3990104 TATTATTTCA
3990114 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* * *
3990134 AATTAATTGAAATTAAATATTCG
1 AATTAATT-AAAATATATATT-T
3990157 AGATT-ATTAAAATATATATTT
1 A-ATTAATTAAAATATATATTT
3990178 AATTAA
1 AATTAA
3990184 CTCTAGATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
20 11 0.28
21 2 0.05
22 19 0.49
23 4 0.10
24 3 0.08
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:3996902 original size:90 final size:89
Alignment explanation
Indices: 3996744--3996920 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 89
3996734 CCTAACACAC
3996744 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
* * *
3996809 TTTATTTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
*
3996833 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
3996898 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
3996921 TTCGGGATTA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 34 0.41
90 49 0.59
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:4009814 original size:29 final size:29
Alignment explanation
Indices: 4009780--4009838 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
4009770 CCTAAATTAA
4009780 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4009809 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
4009838 T
1 T
4009839 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:4014497 original size:30 final size:30
Alignment explanation
Indices: 4014463--4014522 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
4014453 CCTAAATTAA
4014463 TTTGATGTCATTGCTTACATCAATTTAGTT
1 TTTGATGTCATTGCTTACATCAATTTAGTT
4014493 TTTGATGTCATTGCTTACATCAATTTAGTT
1 TTTGATGTCATTGCTTACATCAATTTAGTT
4014523 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (30 bp):
TTTGATGTCATTGCTTACATCAATTTAGTT
Found at i:4025904 original size:21 final size:22
Alignment explanation
Indices: 4025880--4025921 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
4025870 GATACCCCCA
4025880 TGAA-GGAACCGATTCCCCCTT
1 TGAAGGGAACCGATTCCCCCTT
4025901 TGAAGGGGAACCGATTCCCCC
1 TGAA-GGGAACCGATTCCCCC
4025922 CATAGGGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
23 15 0.79
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (22 bp):
TGAAGGGAACCGATTCCCCCTT
Found at i:4025930 original size:21 final size:22
Alignment explanation
Indices: 4025884--4025943 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
4025874 CCCCCATGAA
**
4025884 GGAACCGATTCCCCCTTTGAAGG
1 GGAACCGATTCCCCCCAT-AAGG
4025907 GGAACCGATTCCCCCCAT-AGG
1 GGAACCGATTCCCCCCATAAGG
* *
4025928 GGAATCGATACCCCCC
1 GGAACCGATTCCCCCC
4025944 TGGGGTTCTG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 17 0.52
23 16 0.48
ACGTcount: A:0.23, C:0.37, G:0.23, T:0.17
Consensus pattern (22 bp):
GGAACCGATTCCCCCCATAAGG
Found at i:4026330 original size:20 final size:20
Alignment explanation
Indices: 4026305--4026365 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
4026295 TTTTGGTGCA
*
4026305 GAGGGAATCGATACCCCCAT
1 GAGGGAACCGATACCCCCAT
* *
4026325 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATACCCCC-AT
*
4026346 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATACCCCC
4026366 CACAGGGGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 16 0.46
21 2 0.06
22 1 0.03
23 16 0.46
ACGTcount: A:0.25, C:0.33, G:0.26, T:0.16
Consensus pattern (20 bp):
GAGGGAACCGATACCCCCAT
Done.