Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr13 ID=Chr13-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 58321163
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 747533 characters in sequence are not A, C, G, or T
File 187 of 199
Found at i:54570094 original size:26 final size:28
Alignment explanation
Indices: 54570058--54570115 Score: 75
Period size: 26 Copynumber: 2.1 Consensus size: 28
54570048 CTCAAATAAA
*
54570058 AAATAATAATATT-TTATAATTAAAT-T
1 AAATAAGAATATTATTATAATTAAATAT
* *
54570084 AAATAAGAATATTATTGTTATTAAATAT
1 AAATAAGAATATTATTATAATTAAATAT
54570112 AAAT
1 AAAT
54570116 TCCAAGGCAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
26 12 0.44
27 10 0.37
28 5 0.19
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (28 bp):
AAATAAGAATATTATTATAATTAAATAT
Found at i:54572815 original size:132 final size:132
Alignment explanation
Indices: 54572564--54572958 Score: 639
Period size: 132 Copynumber: 3.0 Consensus size: 132
54572554 CACGAGCATA
54572564 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCATGCCAGGATTAAT
1 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCATGCCAGGATTAAT
* * * * * * *
54572629 TTCATCAACTTGTGGGGTTTCTACGGTTGATAAAGTAGCCGCAAGGGAAACTTCCTCCGACCTAG
66 TTCAACAACTTGAGGGTTTTCTACTGTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTAG
54572694 CC
131 CC
* * *
54572696 TCTCCTTGATTGGAGGGATGAAGCTGAGAACGTTCTTCAAAATTTTCTCCCACGCCAGGATTAAT
1 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCATGCCAGGATTAAT
*
54572761 TTCAACAACTTGAGGGTTTTCTACTGTTGATAAAGTAGCCACGAGGGTACCTTCCTCCGACCTAG
66 TTCAACAACTTGAGGGTTTTCTACTGTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTAG
54572826 CC
131 CC
*
54572828 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTACTCCCATGCCAGGATTAAT
1 TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCATGCCAGGATTAAT
* * *
54572893 TTCAACAACTTCAGGGTTTTCTA-TGGTTGATAAAGTAGCCACGAAGGTAACTGCCTCCGACCTA
66 TTCAACAACTTGAGGGTTTTCTACT-GTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTA
54572957 GC
130 GC
54572959 TTGTTCTTCT
Statistics
Matches: 243, Mismatches: 19, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
131 1 0.00
132 242 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (132 bp):
TCTCCTTGATTAGAGGGATGAAGCTGAGAACATTCTTCAAAATTTTCTCCCATGCCAGGATTAAT
TTCAACAACTTGAGGGTTTTCTACTGTTGATAAAGTAGCCACGAGGGTAACTTCCTCCGACCTAG
CC
Found at i:54584247 original size:48 final size:49
Alignment explanation
Indices: 54584168--54584281 Score: 124
Period size: 49 Copynumber: 2.3 Consensus size: 49
54584158 GTGGTATGAA
*
54584168 ACTTGAACTCGTGACTGCATAATAATAATCAACT-GGAGCCCGAGTTAT
1 ACTTGAACTCGTGACTGCATAACAATAATCAACTGGGAGCCCGAGTTAT
* * * * **
54584216 ACTTGAACTTGTGACTGCATAGCCACT-ATCAATTGGGAGCCTTAGTTAT
1 ACTTGAACTCGTGACTGCATA-ACAATAATCAACTGGGAGCCCGAGTTAT
* *
54584265 ATTTCAACTCGTGACTG
1 ACTTGAACTCGTGACTG
54584282 TATCCACCAT
Statistics
Matches: 54, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
48 26 0.48
49 28 0.52
ACGTcount: A:0.29, C:0.21, G:0.19, T:0.31
Consensus pattern (49 bp):
ACTTGAACTCGTGACTGCATAACAATAATCAACTGGGAGCCCGAGTTAT
Found at i:54585474 original size:30 final size:28
Alignment explanation
Indices: 54585423--54585518 Score: 72
Period size: 30 Copynumber: 3.3 Consensus size: 28
54585413 AATTTATAAA
* *
54585423 ATTTTAAA--TTAATAATAATAAAGTTAT
1 ATTTTAAACTTTAAAAATGATAAA-TTAT
54585450 ATTTTAAACTTCTAAAAATGATAAAAATT-T
1 ATTTTAAACTT-TAAAAATGAT--AAATTAT
* *
54585480 AATTTAAGCCTTTAAAAATGATAAATATAT
1 ATTTTAA-ACTTTAAAAATGATAAAT-TAT
54585510 ATTATTAAA
1 ATT-TTAAA
54585519 ATGATAATTA
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
27 8 0.15
28 4 0.07
29 2 0.04
30 28 0.52
31 9 0.17
32 3 0.06
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (28 bp):
ATTTTAAACTTTAAAAATGATAAATTAT
Found at i:54586539 original size:33 final size:33
Alignment explanation
Indices: 54586497--54586601 Score: 112
Period size: 33 Copynumber: 3.3 Consensus size: 33
54586487 TTACTTTACA
54586497 TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
1 TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
* ** ****
54586530 TTCATGTTTA-T-AATTTATTT--ACT-TTACA
1 TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
54586558 TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
1 TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
54586591 TTCATGTTTAT
1 TTCATGTTTAT
54586602 AATTTAAGAA
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
28 11 0.21
29 4 0.08
30 6 0.11
31 6 0.11
32 4 0.08
33 22 0.42
ACGTcount: A:0.23, C:0.08, G:0.17, T:0.52
Consensus pattern (33 bp):
TTCATGTTTATTGTAGGTATTTAAACTGTGGGT
Found at i:54586581 original size:61 final size:61
Alignment explanation
Indices: 54586486--54586607 Score: 244
Period size: 61 Copynumber: 2.0 Consensus size: 61
54586476 CTTTTTTTTT
54586486 TTTACTTTACATTCATGTTTATTGTAGGTATTTAAACTGTGGGTTTCATGTTTATAATTTA
1 TTTACTTTACATTCATGTTTATTGTAGGTATTTAAACTGTGGGTTTCATGTTTATAATTTA
54586547 TTTACTTTACATTCATGTTTATTGTAGGTATTTAAACTGTGGGTTTCATGTTTATAATTTA
1 TTTACTTTACATTCATGTTTATTGTAGGTATTTAAACTGTGGGTTTCATGTTTATAATTTA
54586608 AGAAAATGGA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 61 1.00
ACGTcount: A:0.25, C:0.08, G:0.15, T:0.52
Consensus pattern (61 bp):
TTTACTTTACATTCATGTTTATTGTAGGTATTTAAACTGTGGGTTTCATGTTTATAATTTA
Found at i:54604539 original size:25 final size:26
Alignment explanation
Indices: 54604487--54604552 Score: 98
Period size: 25 Copynumber: 2.5 Consensus size: 26
54604477 AAATAAAAAA
*
54604487 TTACCAAAATGTTATACATTTTTTTAT
1 TTACCAAAAT-ATATACATTTTTTTAT
*
54604514 TTACCAAAATATATA-TTTTTTTTAT
1 TTACCAAAATATATACATTTTTTTAT
54604539 TTACCAAAATATAT
1 TTACCAAAATATAT
54604553 CAAAAAAACC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 23 0.62
26 4 0.11
27 10 0.27
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (26 bp):
TTACCAAAATATATACATTTTTTTAT
Found at i:54604650 original size:27 final size:27
Alignment explanation
Indices: 54604609--54604687 Score: 99
Period size: 27 Copynumber: 2.9 Consensus size: 27
54604599 TTCCCTGGGT
* *
54604609 CAAGGGAACAC-TGTTGGTGGCACTAAA
1 CAAGGGAAC-CTTGTTGGCGGCACCAAA
54604636 CAAGGGAACCTTGTTGGCGGCACCAAA
1 CAAGGGAACCTTGTTGGCGGCACCAAA
*
54604663 CAA-GGATTCCTTGTTGGCGGCACCA
1 CAAGGGA-ACCTTGTTGGCGGCACCA
54604688 CCTTAAATAT
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
26 4 0.09
27 43 0.91
ACGTcount: A:0.28, C:0.24, G:0.29, T:0.19
Consensus pattern (27 bp):
CAAGGGAACCTTGTTGGCGGCACCAAA
Found at i:54604757 original size:18 final size:17
Alignment explanation
Indices: 54604734--54604886 Score: 78
Period size: 18 Copynumber: 8.4 Consensus size: 17
54604724 AAAGGAGAGG
54604734 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
54604752 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
54604769 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
54604785 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
** *
54604803 GGAAAGAAAAGGAAAGGGGA
1 GG-AAG-AAA-GAAAAAGAA
*
54604823 GGAAAGAAAGAAAAATAA
1 GG-AAGAAAGAAAAAGAA
*
54604841 GGAAAGAAAAGGAAAGGAGAA
1 GG-AAG-AAA-GAAA-AAGAA
* *
54604862 GAGAAAAAAAAAAAAGAA
1 G-GAAGAAAGAAAAAGAA
*
54604880 AGAAGAA
1 GGAAGAA
54604887 GAAGAGGGAA
Statistics
Matches: 106, Mismatches: 18, Indels: 23
0.72 0.12 0.16
Matches are distributed among these distances:
15 9 0.08
16 4 0.04
17 9 0.08
18 32 0.30
19 26 0.25
20 19 0.18
21 6 0.06
22 1 0.01
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:54604767 original size:10 final size:10
Alignment explanation
Indices: 54604736--54604889 Score: 57
Period size: 10 Copynumber: 15.1 Consensus size: 10
54604726 AGGAGAGGGG
*
54604736 AAGAAGAAGA
1 AAGAAAAAGA
54604746 AAGAAAGGAAGA
1 AAGAAA--AAGA
54604758 AAGAAAAAGA
1 AAGAAAAAGA
* *
54604768 AGGAAAAGGA
1 AAGAAAAAGA
54604778 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
54604792 AAGAAAAAGA
1 AAGAAAAAGA
* *
54604802 AGGAAAGA-A
1 AAGAAAAAGA
* * *
54604811 AAGGAAAGGG
1 AAGAAAAAGA
* *
54604821 GAG-GAAAGA
1 AAGAAAAAGA
*
54604830 AAGAAAAATA
1 AAGAAAAAGA
* *
54604840 AGGAAAGA-A
1 AAGAAAAAGA
* *
54604849 AAGGAAAGGA
1 AAGAAAAAGA
54604859 GAAGAGAAAA-A
1 -AAGA-AAAAGA
54604870 AA-AAAAAGA
1 AAGAAAAAGA
*
54604879 AAGAAGAAGA
1 AAGAAAAAGA
54604889 A
1 A
54604890 GAGGGAAGGA
Statistics
Matches: 103, Mismatches: 28, Indels: 26
0.66 0.18 0.17
Matches are distributed among these distances:
8 4 0.04
9 19 0.18
10 51 0.50
11 6 0.06
12 15 0.15
13 2 0.02
14 6 0.06
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:54604767 original size:22 final size:23
Alignment explanation
Indices: 54604736--54604837 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
54604726 AGGAGAGGGG
*
54604736 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
54604758 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
54604780 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* ***
54604806 AAGAAAAGGAAAGGGGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
54604830 AAGAAAAA
1 AAGAAAAA
54604838 TAAGGAAAGA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
22 12 0.20
23 10 0.17
24 32 0.53
25 5 0.08
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:54604812 original size:38 final size:38
Alignment explanation
Indices: 54604754--54604915 Score: 174
Period size: 38 Copynumber: 4.3 Consensus size: 38
54604744 GAAAGAAAGG
54604754 AAGAAAGAAAAAGAA-G---GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
54604788 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
*
54604826 AAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGAAGAGA
1 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAG-AG-GA
* * * *
54604866 AA-AAAAAAAAAGAAAGAAGAAGAAGAGGGAAGGA-AGGA
1 AAGAAAGAAAAAG-AAGGA-AAGAAAAGGAAAGGAGAGGA
* *
54604904 AGGAAGGAAAAA
1 AAGAAAGAAAAA
54604916 AAAGAAAATA
Statistics
Matches: 108, Mismatches: 11, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
34 15 0.14
35 1 0.01
38 52 0.48
39 19 0.18
40 8 0.07
41 13 0.12
ACGTcount: A:0.66, C:0.00, G:0.33, T:0.01
Consensus pattern (38 bp):
AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGAGAGGA
Found at i:54605636 original size:19 final size:19
Alignment explanation
Indices: 54605603--54605654 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
54605593 AAAATATATA
**
54605603 TAATATTTTGGTATTTTT-
1 TAATATTTTATTATTTTTG
54605621 TAAATATTTTATTATTTTTG
1 T-AATATTTTATTATTTTTG
*
54605641 TAATGTTTTATTAT
1 TAATATTTTATTAT
54605655 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
18 1 0.03
19 27 0.93
20 1 0.03
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (19 bp):
TAATATTTTATTATTTTTG
Found at i:54605680 original size:14 final size:14
Alignment explanation
Indices: 54605661--54605688 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54605651 TTATGGGTTT
54605661 TATAAAAAAAATAA
1 TATAAAAAAAATAA
54605675 TATAAAAAAAATAA
1 TATAAAAAAAATAA
54605689 AAAATTACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (14 bp):
TATAAAAAAAATAA
Found at i:54605747 original size:28 final size:28
Alignment explanation
Indices: 54605695--54605764 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
54605685 ATAAAAAATT
54605695 ACCAAAATAT-TATAACTTTTTTTATTG
1 ACCAAAATATATATAACTTTTTTTATTG
*
54605722 ACCAAAATATATATAA-TTTTTATTATTT
1 ACCAAAATATATATAACTTTTT-TTATTG
54605750 ACCAAAATATA-ATAA
1 ACCAAAATATATATAA
54605765 AAAAAGTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
27 19 0.47
28 21 0.52
ACGTcount: A:0.46, C:0.10, G:0.01, T:0.43
Consensus pattern (28 bp):
ACCAAAATATATATAACTTTTTTTATTG
Found at i:54605880 original size:31 final size:31
Alignment explanation
Indices: 54605842--54605900 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
54605832 TAAATACACT
54605842 AAAAAAAAGTTGTAATATTTTGGTAAATAAA
1 AAAAAAAAGTTGTAATATTTTGGTAAATAAA
54605873 AAAAAAAAGTTGTAATATTTTGGTAAAT
1 AAAAAAAAGTTGTAATATTTTGGTAAAT
54605901 TTTTTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.53, C:0.00, G:0.14, T:0.34
Consensus pattern (31 bp):
AAAAAAAAGTTGTAATATTTTGGTAAATAAA
Found at i:54607979 original size:27 final size:27
Alignment explanation
Indices: 54607941--54608100 Score: 245
Period size: 27 Copynumber: 5.9 Consensus size: 27
54607931 ATAACACGAG
**
54607941 TGGTGCCGCCAAC-AGAGAACCCTTGTT
1 TGGTGCCGCCAACAAG-GTTCCCTTGTT
*
54607968 TGGTGCCGCCAACAAGGAAT-CCTTGTT
1 TGGTGCCGCCAACAAGG-TTCCCTTGTT
54607995 TGGTGCCGCCAACAAGGTTCCCTTGTT
1 TGGTGCCGCCAACAAGGTTCCCTTGTT
54608022 TGGTGCCGCCAACAAGGTTCCCTTGTT
1 TGGTGCCGCCAACAAGGTTCCCTTGTT
54608049 TGGTGCCGCCAACAAGGTTCCCTTGTT
1 TGGTGCCGCCAACAAGGTTCCCTTGTT
54608076 TGGTGCCGCCAAC-AGTGTTCCCTTG
1 TGGTGCCGCCAACAAG-GTTCCCTTG
54608101 ACCCAGGGAA
Statistics
Matches: 127, Mismatches: 2, Indels: 8
0.93 0.01 0.06
Matches are distributed among these distances:
26 3 0.02
27 121 0.95
28 3 0.02
ACGTcount: A:0.17, C:0.29, G:0.26, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAACAAGGTTCCCTTGTT
Found at i:54608183 original size:27 final size:29
Alignment explanation
Indices: 54608150--54608218 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 29
54608140 GTTTTTTTTG
54608150 ATATATTTTGGTAAAT-AAAAAAAT-TAT
1 ATATATTTTGGTAAATAAAAAAAATGTAT
54608177 ATATATTTTGGTAAATAAAAAAAATGTAT
1 ATATATTTTGGTAAATAAAAAAAATGTAT
*
54608206 A-ACATTTTGGTAA
1 ATATATTTTGGTAA
54608219 TTTTTTATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 16 0.41
28 19 0.49
29 4 0.10
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAATGTAT
Found at i:54615227 original size:28 final size:28
Alignment explanation
Indices: 54615189--54615286 Score: 117
Period size: 28 Copynumber: 3.5 Consensus size: 28
54615179 ACAAAGTGCA
* * *
54615189 AATAACAATAACCACCGAAGTGCAAAAT
1 AATAACGATAAGCACCAAAGTGCAAAAT
*
54615217 AATAACGATAAGCACCAAAGTGCAAATTTT
1 AATAACGATAAGCACCAAAGTGCAAA--AT
* *
54615247 TACAACGATAAGCACCAAAGTGCAAAAT
1 AATAACGATAAGCACCAAAGTGCAAAAT
54615275 AAT-ACGATAAGC
1 AATAACGATAAGC
54615287 GCACTAATTT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
27 9 0.15
28 25 0.42
30 25 0.42
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.17
Consensus pattern (28 bp):
AATAACGATAAGCACCAAAGTGCAAAAT
Found at i:54621861 original size:16 final size:17
Alignment explanation
Indices: 54621819--54621865 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
54621809 TTTTTAAGTT
* *
54621819 TATAATATATTATATTA
1 TATAATTTATAATATTA
54621836 TATTATATTTATAAT-TTA
1 TA-TA-ATTTATAATATTA
54621854 TATAATTTATAA
1 TATAATTTATAA
54621866 CATATTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 8 0.31
17 4 0.15
18 7 0.27
19 7 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
TATAATTTATAATATTA
Found at i:54623026 original size:17 final size:19
Alignment explanation
Indices: 54623004--54623042 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
54622994 ATTGACTTGC
54623004 AAACAA-CA-CAAAAAAAG
1 AAACAAGCAGCAAAAAAAG
*
54623021 AAACAAGCAGCAAAAAACG
1 AAACAAGCAGCAAAAAAAG
54623040 AAA
1 AAA
54623043 TATCAGCAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 2 0.11
19 11 0.58
ACGTcount: A:0.72, C:0.18, G:0.10, T:0.00
Consensus pattern (19 bp):
AAACAAGCAGCAAAAAAAG
Found at i:54624162 original size:3 final size:3
Alignment explanation
Indices: 54624154--54624261 Score: 207
Period size: 3 Copynumber: 36.0 Consensus size: 3
54624144 CAAAACTTAG
54624154 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
54624202 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
54624250 ATG ATT ATT ATT
1 ATT ATT ATT ATT
54624262 GTATTAGTTC
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 103 1.00
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:54624567 original size:4 final size:4
Alignment explanation
Indices: 54624558--54624607 Score: 100
Period size: 4 Copynumber: 12.5 Consensus size: 4
54624548 TAAATTTCGT
54624558 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
54624606 AT
1 AT
54624608 CTCCCTGACA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 46 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:54625416 original size:11 final size:10
Alignment explanation
Indices: 54625395--54625430 Score: 54
Period size: 11 Copynumber: 3.4 Consensus size: 10
54625385 GTGTTGAATC
54625395 TTTTTTCATT
1 TTTTTTCATT
54625405 TTTTTTCTATT
1 TTTTTTC-ATT
54625416 TTATTTTCATT
1 TT-TTTTCATT
54625427 TTTT
1 TTTT
54625431 CTTTTACATA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.38
11 10 0.42
12 5 0.21
ACGTcount: A:0.11, C:0.08, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTCATT
Found at i:54642678 original size:5 final size:6
Alignment explanation
Indices: 54642663--54642688 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
54642653 CTGAAAAGCT
54642663 TTTTTA TTTTTA TTTTTA TTTTTA TT
1 TTTTTA TTTTTA TTTTTA TTTTTA TT
54642689 GAGGCTATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTTTA
Found at i:54647560 original size:29 final size:29
Alignment explanation
Indices: 54647512--54647596 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
54647502 GGTTCATTTC
* *
54647512 AAGTCATTTACGTATATAATAAAAAAAGT-
1 AAGTCATTTTCATA-ATAATAAAAAAAGTA
* * ***
54647541 AGGTCATTTTCATAATTAATCAAAATTTTA
1 AAGTCATTTTCATAA-TAATAAAAAAAGTA
*
54647571 AAGTCATTTTTATAATAATAAAAAAA
1 AAGTCATTTTCATAATAATAAAAAAA
54647597 CCCAATTTTC
Statistics
Matches: 42, Mismatches: 12, Indels: 4
0.72 0.21 0.07
Matches are distributed among these distances:
28 1 0.02
29 28 0.67
30 13 0.31
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.36
Consensus pattern (29 bp):
AAGTCATTTTCATAATAATAAAAAAAGTA
Found at i:54649634 original size:3 final size:3
Alignment explanation
Indices: 54649626--54649691 Score: 87
Period size: 3 Copynumber: 22.0 Consensus size: 3
54649616 ATTCCCACTC
* *
54649626 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATG ATA ATA CTA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * *
54649674 CTA ATA CTA ATA TTA ATA
1 ATA ATA ATA ATA ATA ATA
54649692 CTTACCTCAC
Statistics
Matches: 53, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.59, C:0.05, G:0.02, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:54650751 original size:12 final size:13
Alignment explanation
Indices: 54650702--54650753 Score: 63
Period size: 12 Copynumber: 4.1 Consensus size: 13
54650692 ATTTATTTGA
54650702 AATATAATAATAT
1 AATATAATAATAT
54650715 AATATAATTAATAT
1 AATATAA-TAATAT
* *
54650729 AAT-TTACAATAT
1 AATATAATAATAT
54650741 AATA-AATAATAT
1 AATATAATAATAT
54650753 A
1 A
54650754 TACTTAAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
12 15 0.45
13 9 0.27
14 9 0.27
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
AATATAATAATAT
Found at i:54658133 original size:7 final size:7
Alignment explanation
Indices: 54658121--54658160 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
54658111 AAAATATTTT
54658121 AAAATTA
1 AAAATTA
54658128 AAAATTA
1 AAAATTA
54658135 AAAATTA
1 AAAATTA
*
54658142 AAAAATA
1 AAAATTA
*
54658149 AAAATAA
1 AAAATTA
54658156 AAAAT
1 AAAAT
54658161 ATATATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.23
Consensus pattern (7 bp):
AAAATTA
Found at i:54658159 original size:13 final size:13
Alignment explanation
Indices: 54658120--54658161 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
54658110 AAAAATATTT
* *
54658120 TAAAATTAAAAAT
1 TAAAAATAAAAAA
54658133 TAAAAATTAAAAAA
1 TAAAAA-TAAAAAA
54658147 TAAAAATAAAAAA
1 TAAAAATAAAAAA
54658160 TA
1 TA
54658162 TATATTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 14 0.54
14 12 0.46
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAAAATAAAAAA
Found at i:54658439 original size:10 final size:9
Alignment explanation
Indices: 54658422--54658554 Score: 65
Period size: 9 Copynumber: 13.9 Consensus size: 9
54658412 TATGATAAAA
*
54658422 ATAAAATTT
1 ATAAAAATT
54658431 ATAAAAATT
1 ATAAAAATT
54658440 ATAAAAATT
1 ATAAAAATT
*
54658449 ATTAAATATT
1 A-TAAAAATT
54658459 AATAAAAA-T
1 -ATAAAAATT
*
54658468 AGAAAAAATT
1 A-TAAAAATT
54658478 AT-AAAATT
1 ATAAAAATT
* *
54658486 TTATAAAGTCGT
1 ATA-AAAAT--T
54658498 A-AGAAAATT
1 ATA-AAAATT
**
54658507 ATAAAAAAA
1 ATAAAAATT
54658516 AGTAAAGAATT
1 A-TAAA-AATT
*
54658527 ATAAAATCTGT
1 ATAAAA-AT-T
*
54658538 AAAAAAATT
1 ATAAAAATT
54658547 ATAAAAAT
1 ATAAAAAT
54658555 CATATTACTA
Statistics
Matches: 93, Mismatches: 18, Indels: 26
0.68 0.13 0.19
Matches are distributed among these distances:
8 8 0.09
9 40 0.43
10 29 0.31
11 15 0.16
12 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.31
Consensus pattern (9 bp):
ATAAAAATT
Found at i:54658464 original size:29 final size:29
Alignment explanation
Indices: 54658423--54658492 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
54658413 ATGATAAAAA
*
54658423 TAAA-ATTTATAAAAATTA-TAAAAATTAT
1 TAAATATTTATAAAAA-TAGAAAAAATTAT
*
54658451 TAAATATTAATAAAAATAGAAAAAATTAT
1 TAAATATTTATAAAAATAGAAAAAATTAT
*
54658480 AAAAT-TTTATAAA
1 TAAATATTTATAAA
54658493 GTCGTAAGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 13 0.36
29 23 0.64
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (29 bp):
TAAATATTTATAAAAATAGAAAAAATTAT
Found at i:54659880 original size:12 final size:12
Alignment explanation
Indices: 54659856--54659894 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
54659846 ACCCCTTTTT
54659856 TCTTTTTTCCTTC
1 TCTTTTTT-CTTC
54659869 TCTTTTTTCTTC
1 TCTTTTTTCTTC
*
54659881 TTTTTTTTC-TC
1 TCTTTTTTCTTC
54659892 TCT
1 TCT
54659895 GCTGGGCCAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 4 0.17
12 12 0.50
13 8 0.33
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TCTTTTTTCTTC
Found at i:54660200 original size:18 final size:18
Alignment explanation
Indices: 54660161--54660216 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 18
54660151 AAAAAATTCT
**
54660161 TTTCTTCTTT-TTTCCCC
1 TTTCTTCTTTCTTTCTTC
54660178 TTTTCTTCTTTCTTTCTTC
1 -TTTCTTCTTTCTTTCTTC
*
54660197 TTTCTTTCTCTCTTT-TTC
1 TTTC-TTCTTTCTTTCTTC
54660215 TT
1 TT
54660217 CTCCTTCGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
18 19 0.58
19 14 0.42
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (18 bp):
TTTCTTCTTTCTTTCTTC
Found at i:54660219 original size:11 final size:11
Alignment explanation
Indices: 54660179--54660211 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
54660169 TTTTTCCCCT
54660179 TTTCTTCTTTC
1 TTTCTTCTTTC
54660190 TTTCTTCTTTC
1 TTTCTTCTTTC
54660201 TTTCTCTCTTT
1 TTTCT-TCTTT
54660212 TTCTTCTCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTCTTCTTTC
Found at i:54660373 original size:31 final size:30
Alignment explanation
Indices: 54660319--54660377 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
54660309 TTTGAAAAAA
* *
54660319 AAAGCTCTCTTTTTTTTATTTTTTCTTTTTC
1 AAAGCTCTCTTTTTTCTACTTTTT-TTTTTC
54660350 AAAGCTCTCTTTTTCTCT-CTTTTTTTTT
1 AAAGCTCTCTTTTT-TCTACTTTTTTTTT
54660378 GAAATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 4 0.16
31 19 0.76
32 2 0.08
ACGTcount: A:0.12, C:0.19, G:0.03, T:0.66
Consensus pattern (30 bp):
AAAGCTCTCTTTTTTCTACTTTTTTTTTTC
Found at i:54660622 original size:30 final size:30
Alignment explanation
Indices: 54660586--54660739 Score: 168
Period size: 30 Copynumber: 5.2 Consensus size: 30
54660576 GGCTGAAACA
* * * *
54660586 TAATTTTGATAAATTTTAGGGGTCAAAATG
1 TAATTTTCAAAAAGTTTAGGGGTAAAAATG
* * *
54660616 TAATTTTGAGAAAGTTTAGGGGTCAAAATG
1 TAATTTTCAAAAAGTTTAGGGGTAAAAATG
*
54660646 TAA-TTTCAAAAAGTTTAGGGGTAAAAATA
1 TAATTTTCAAAAAGTTTAGGGGTAAAAATG
* * * * *
54660675 TGATTTTAAAAAATTTTAGGGATTAAAATG
1 TAATTTTCAAAAAGTTTAGGGGTAAAAATG
*
54660705 TAA-TTTCAAAAAGTTTAGGGGTAAAAATA
1 TAATTTTCAAAAAGTTTAGGGGTAAAAATG
54660734 TAATTT
1 TAATTT
54660740 AAAAAAATTG
Statistics
Matches: 104, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
29 48 0.46
30 56 0.54
ACGTcount: A:0.42, C:0.03, G:0.19, T:0.36
Consensus pattern (30 bp):
TAATTTTCAAAAAGTTTAGGGGTAAAAATG
Found at i:54660672 original size:29 final size:29
Alignment explanation
Indices: 54660600--54660745 Score: 166
Period size: 29 Copynumber: 5.0 Consensus size: 29
54660590 TTTGATAAAT
* * *
54660600 TTTAGGGGTCAAAATGTAATTTTGAGAAAG
1 TTTAGGGGTAAAAATGTAA-TTTAAAAAAG
* *
54660630 TTTAGGGGTCAAAATGTAATTTCAAAAAG
1 TTTAGGGGTAAAAATGTAATTTAAAAAAG
* * *
54660659 TTTAGGGGTAAAAATATGATTTTAAAAAAT
1 TTTAGGGGTAAAAATGT-AATTTAAAAAAG
* * *
54660689 TTTAGGGATTAAAATGTAATTTCAAAAAG
1 TTTAGGGGTAAAAATGTAATTTAAAAAAG
*
54660718 TTTAGGGGTAAAAATATAATTTAAAAAA
1 TTTAGGGGTAAAAATGTAATTTAAAAAA
54660746 ATTGAGCCGG
Statistics
Matches: 98, Mismatches: 17, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
29 56 0.57
30 42 0.43
ACGTcount: A:0.45, C:0.03, G:0.19, T:0.34
Consensus pattern (29 bp):
TTTAGGGGTAAAAATGTAATTTAAAAAAG
Found at i:54660747 original size:59 final size:59
Alignment explanation
Indices: 54660600--54660748 Score: 217
Period size: 59 Copynumber: 2.5 Consensus size: 59
54660590 TTTGATAAAT
* * * * * *
54660600 TTTAGGGGTCAAAATGTAATTTTGAGAAAGTTTAGGGGTCAAAATGTAATTTCAAAAAG
1 TTTAGGGGTAAAAATATAATTTTAAAAAATTTTAGGGATCAAAATGTAATTTCAAAAAG
* *
54660659 TTTAGGGGTAAAAATATGATTTTAAAAAATTTTAGGGATTAAAATGTAATTTCAAAAAG
1 TTTAGGGGTAAAAATATAATTTTAAAAAATTTTAGGGATCAAAATGTAATTTCAAAAAG
*
54660718 TTTAGGGGTAAAAATATAATTTAAAAAAATT
1 TTTAGGGGTAAAAATATAATTTTAAAAAATT
54660749 GAGCCGGACA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
59 80 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (59 bp):
TTTAGGGGTAAAAATATAATTTTAAAAAATTTTAGGGATCAAAATGTAATTTCAAAAAG
Found at i:54660956 original size:79 final size:79
Alignment explanation
Indices: 54660862--54661177 Score: 271
Period size: 79 Copynumber: 4.1 Consensus size: 79
54660852 AAAATTTTTC
* *
54660862 TTTTTATTTAAAAAACAGAAATTGAAAATACCTCGCCGTGTGGCCCGAGGCTCAACTCACCTCTA
1 TTTTTTTTTAAAAAACAGAAATTGAAAATACCTCGCCGTGTGGCCCGAGGCTCAACTCACCTCTC
*
54660927 GCATTAAGAGTTGA
66 GCATTATGAGTTGA
* * * * * * *
54660941 TTTTTTTTTGAAAAACAGAAATATAAAAGAAATACCTCGGCATGT-GTCCAAGGCTCAACTCACT
1 TTTTTTTTTAAAAAACAGAAAT-T--GA-AAATACCTCGCCGTGTGGCCCGAGGCTCAACTCACC
*
54661005 TCTCGCAATATGAGTTGA
62 TCTCGCATTATGAGTTGA
*** * * *
54661023 ---TTTAAAAAAAAACAGAAATTGAAAATACCT--CAGAGTGACCCGAGGCTCAACTCACCTCTC
1 TTTTTTTTTAAAAAACAGAAATTGAAAATACCTCGCCGTGTGGCCCGAGGCTCAACTCACCTCTC
54661083 GCATTATGAGTTGA
66 GCATTATGAGTTGA
* * * * *
54661097 -----TTTTAAAAAATAGAAATTTAAAATAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACC
1 TTTTTTTTTAAAAAACAGAAA-TT--GA-AAATACCTCGCCGTGTGGCCCGAGGCTCAACTCACC
54661157 TCTCGCA--ATGAGTTGA
62 TCTCGCATTATGAGTTGA
54661173 TTTTT
1 TTTTT
54661178 GCAAAAATAG
Statistics
Matches: 187, Mismatches: 34, Indels: 30
0.75 0.14 0.12
Matches are distributed among these distances:
72 12 0.06
73 4 0.02
74 32 0.17
75 9 0.05
76 18 0.10
78 30 0.16
79 35 0.19
80 1 0.01
82 32 0.17
83 14 0.07
ACGTcount: A:0.35, C:0.20, G:0.16, T:0.28
Consensus pattern (79 bp):
TTTTTTTTTAAAAAACAGAAATTGAAAATACCTCGCCGTGTGGCCCGAGGCTCAACTCACCTCTC
GCATTATGAGTTGA
Found at i:54661079 original size:156 final size:151
Alignment explanation
Indices: 54660871--54661175 Score: 407
Period size: 151 Copynumber: 2.0 Consensus size: 151
54660861 CTTTTTATTT
* * *
54660871 AAAAAACAGAAATTGAAAATACCTCGCCGTGTGGCCCGAGGCTCAACTCACCTCTAGCATTAAGA
1 AAAAAACAGAAATTGAAAATACCTC-CAGAGTGACCCGAGGCTCAACTCACCTCTAGCATTAAGA
* *
54660936 GTTGATTTTTTTTTGAAAAACAGAAATATAAAAGAAATACCTCGGCATGTGTCC-AAGGCTCAAC
65 GTTGA-----TTTTAAAAAACAGAAATATAAAAGAAATACCTCGGCATGTGACCTAAGGCTCAAC
*
54661000 TCACTTCTCGCAATATGAGTTGATTTAAA
125 TCACCTCTCGC-A-ATGAGTTGATTTAAA
* *
54661029 AAAAAACAGAAATTGAAAATACCT-CAGAGTGACCCGAGGCTCAACTCACCTCTCGCATTATGAG
1 AAAAAACAGAAATTGAAAATACCTCCAGAGTGACCCGAGGCTCAACTCACCTCTAGCATTAAGAG
* * * * *
54661093 TTGATTTTAAAAAATAGAAATTTAAAATAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCT
66 TTGATTTTAAAAAACAGAAATATAAAAGAAATACCTCGGCATGTGACCTAAGGCTCAACTCACCT
54661158 CTCGCAATGAGTTGATTT
131 CTCGCAATGAGTTGATTT
54661176 TTGCAAAAAT
Statistics
Matches: 133, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
150 12 0.09
151 39 0.29
152 19 0.14
156 39 0.29
158 24 0.18
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (151 bp):
AAAAAACAGAAATTGAAAATACCTCCAGAGTGACCCGAGGCTCAACTCACCTCTAGCATTAAGAG
TTGATTTTAAAAAACAGAAATATAAAAGAAATACCTCGGCATGTGACCTAAGGCTCAACTCACCT
CTCGCAATGAGTTGATTTAAA
Found at i:54661083 original size:74 final size:74
Alignment explanation
Indices: 54660868--54661176 Score: 245
Period size: 74 Copynumber: 4.0 Consensus size: 74
54660858 TTTCTTTTTA
* * * * *
54660868 TTTAAAAAACAGAAATT-GA-AAATACCTCGCCGTGTGGCCCGAGGCTCAACTCACCTCTAGCAT
1 TTTAAAAAACAGAAATTAAAGAAATACCT--CCGAGTGACCCGAGGCTCAACTCACCTCTCGCAA
*
54660931 TAAGAGTTGATTTTTT
64 TATGAGTTGA-----T
* * * * *
54660947 TTTGAAAAACAGAAATATAAAAGAAATACCTCGGCATGTG-TCCAAGGCTCAACTCACTTCTCGC
1 TTTAAAAAACAGAAAT-T-AAAGAAATACCTCCG-A-GTGACCCGAGGCTCAACTCACCTCTCGC
54661011 AATATGAGTTGAT
62 AATATGAGTTGAT
* * * *
54661024 TTAAAAAAAAACAGAAATT-GA-AAATACCTCAGAGTGACCCGAGGCTCAACTCACCTCTCGCAT
1 TT--TAAAAAACAGAAATTAAAGAAATACCTCCGAGTGACCCGAGGCTCAACTCACCTCTCGCAA
54661087 TATGAGTTGAT
64 TATGAGTTGAT
* * * *
54661098 TTTAAAAAATAGAAATTTAAAATAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGC
1 TTTAAAAAACAGAAA-TT-AAAGAAATACCTC--CGAGTGACCCGAGGCTCAACTCACCTCTCGC
54661163 -A-ATGAGTTGAT
62 AATATGAGTTGAT
54661174 TTT
1 TTT
54661177 TGCAAAAATA
Statistics
Matches: 190, Mismatches: 25, Indels: 33
0.77 0.10 0.13
Matches are distributed among these distances:
72 11 0.06
73 5 0.03
74 36 0.19
75 11 0.06
76 23 0.12
77 3 0.02
78 29 0.15
79 27 0.14
80 1 0.01
81 2 0.01
82 31 0.16
83 11 0.06
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (74 bp):
TTTAAAAAACAGAAATTAAAGAAATACCTCCGAGTGACCCGAGGCTCAACTCACCTCTCGCAATA
TGAGTTGAT
Found at i:54661184 original size:78 final size:78
Alignment explanation
Indices: 54660871--54661198 Score: 288
Period size: 78 Copynumber: 4.3 Consensus size: 78
54660861 CTTTTTATTT
* * * *
54660871 AAAAAACAGAAA-TT--GAAAATACCTCGCCGTGTGGCCCGAGGCTCAACTCACCTCTAGCATTA
1 AAAAAACAGAAATTTAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA-TA
*
54660933 AGAGTTGATTTTTTTTTG
65 TGAGTTGA----TTTTTG
* * * * *
54660951 -AAAAACAGAAATATAAAAGAAATACCTCGGCATGTG-TCCAAGGCTCAACTCACTTCTCGCAAT
1 AAAAAACAGAAATTTAAAA-AAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGC-AT
***
54661014 ATGAGTTGATTTAAA
64 ATGAGTTGATTTTTG
* * *
54661029 AAAAAACAGAAA-TT--GAAAATACCTC--AGAGTGACCCGAGGCTCAACTCACCTCTCGCATTA
1 AAAAAACAGAAATTTAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCA-TA
54661089 TGAGTTGA-TTTT-
65 TGAGTTGATTTTTG
* *
54661101 AAAAAATAGAAATTTAAAATAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCA-A
1 AAAAAACAGAAATTTAAAA-AAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATA
54661165 TGAGTTGATTTTTG
65 TGAGTTGATTTTTG
* * *
54661179 CAAAAATAG-AATTTGAAAAA
1 AAAAAACAGAAATTTAAAAAA
54661199 TAATTCCTGA
Statistics
Matches: 203, Mismatches: 29, Indels: 36
0.76 0.11 0.13
Matches are distributed among these distances:
72 11 0.05
73 8 0.04
74 31 0.15
75 10 0.05
76 21 0.10
77 12 0.06
78 41 0.20
79 22 0.11
80 1 0.00
82 30 0.15
83 16 0.08
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (78 bp):
AAAAAACAGAAATTTAAAAAAATACCTCGGCGTGTGACCCGAGGCTCAACTCACCTCTCGCATAT
GAGTTGATTTTTG
Found at i:54662083 original size:11 final size:11
Alignment explanation
Indices: 54662057--54662112 Score: 50
Period size: 11 Copynumber: 5.3 Consensus size: 11
54662047 TTCATCTTGA
54662057 TTTTTCTTT-T
1 TTTTTCTTTGT
54662067 TCTTTTCTTTG-
1 T-TTTTCTTTGT
54662078 TTTTT-TTTGT
1 TTTTTCTTTGT
54662088 TTTTGT-TTTGT
1 TTTT-TCTTTGT
54662099 TTTTGTCTTT-T
1 TTTT-TCTTTGT
54662110 TTT
1 TTT
54662113 GTTTTTTTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
9 4 0.10
10 9 0.22
11 25 0.61
12 3 0.07
ACGTcount: A:0.00, C:0.07, G:0.09, T:0.84
Consensus pattern (11 bp):
TTTTTCTTTGT
Found at i:54662120 original size:11 final size:11
Alignment explanation
Indices: 54662057--54662120 Score: 51
Period size: 12 Copynumber: 5.6 Consensus size: 11
54662047 TTCATCTTGA
*
54662057 TTTTTCTTTTTC
1 TTTTT-TTTTTG
54662069 TTTTCTTTGTTT-
1 TTTT-TTT-TTTG
54662081 TTTTTGTTTTTG
1 TTTTT-TTTTTG
*
54662093 TTTTGTTTTTG
1 TTTTTTTTTTG
*
54662104 -TCTTTTTTTG
1 TTTTTTTTTTG
54662114 TTTTTTT
1 TTTTTTT
54662121 GTCTATTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
10 8 0.19
11 15 0.35
12 16 0.37
13 4 0.09
ACGTcount: A:0.00, C:0.06, G:0.09, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:54662121 original size:18 final size:19
Alignment explanation
Indices: 54662063--54662124 Score: 69
Period size: 18 Copynumber: 3.4 Consensus size: 19
54662053 TTGATTTTTC
54662063 TTTT-TCTTTTCTTTGTTTT
1 TTTTGTCTTTTCTTTG-TTT
* *
54662082 TTTTGT-TTTTGTTT-TGT
1 TTTTGTCTTTTCTTTGTTT
54662099 TTTTGTCTTTT-TTTGTTT
1 TTTTGTCTTTTCTTTGTTT
54662117 TTTTGTCT
1 TTTTGTCT
54662125 ATTTTTTTAG
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
17 11 0.30
18 14 0.38
19 11 0.30
20 1 0.03
ACGTcount: A:0.00, C:0.06, G:0.11, T:0.82
Consensus pattern (19 bp):
TTTTGTCTTTTCTTTGTTT
Found at i:54662129 original size:20 final size:19
Alignment explanation
Indices: 54662063--54662132 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 19
54662053 TTGATTTTTC
*
54662063 TTTT-TCTTTTCTTTGTTTT
1 TTTTGTCTTTTTTTTG-TTT
54662082 TTTTGT-TTTTGTTTTG--T
1 TTTTGTCTTTT-TTTTGTTT
54662099 TTTTGTC-TTTTTTTGTTT
1 TTTTGTCTTTTTTTTGTTT
54662117 TTTTGTCTATTTTTTT
1 TTTTGTCT-TTTTTTT
54662133 AGACATAATA
Statistics
Matches: 43, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
16 5 0.12
17 10 0.23
18 8 0.19
19 8 0.19
20 12 0.28
ACGTcount: A:0.01, C:0.06, G:0.10, T:0.83
Consensus pattern (19 bp):
TTTTGTCTTTTTTTTGTTT
Found at i:54669653 original size:18 final size:18
Alignment explanation
Indices: 54669632--54670100 Score: 277
Period size: 18 Copynumber: 26.3 Consensus size: 18
54669622 CAATTATTTT
*
54669632 TTTTTGAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
* *
54669650 TTTTTTAAAACACGAGAA
1 TTTTTGAAAACACGAAAA
* * *
54669668 TTTTAG-AGACACAAAAA
1 TTTTTGAAAACACGAAAA
* *
54669685 TTATTAAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * **
54669703 TTTTTGAAGACGCGACGA
1 TTTTTGAAAACACGAAAA
*
54669721 -TTTTG-AGACACGAGAAA
1 TTTTTGAAAACACGA-AAA
* *
54669738 TTTTTTGAAAACGCG--AT
1 -TTTTTGAAAACACGAAAA
***
54669755 TTTTTG-AAATGTGAAAA
1 TTTTTGAAAACACGAAAA
* *
54669772 TTTGTG-AAACACGAGAA
1 TTTTTGAAAACACGAAAA
*
54669789 TTGTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
*
54669807 TTTTTGAAAACACGCAAA
1 TTTTTGAAAACACGAAAA
* *
54669825 TTTTTG-AAACACGGAAG
1 TTTTTGAAAACACGAAAA
*
54669842 TTTTTAGAAAACATGAAAAA
1 TTTTT-GAAAACACG-AAAA
* * *
54669862 ATTTTG--ATCATCGAAAT
1 TTTTTGAAAACA-CGAAAA
*
54669879 TTTTTGAAAACACGAAAT
1 TTTTTGAAAACACGAAAA
* *
54669897 TTTTTG-AAACACCAGAA
1 TTTTTGAAAACACGAAAA
* **
54669914 TTTTTGAAAACATGAGGA
1 TTTTTGAAAACACGAAAA
54669932 TTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
54669949 TTTTTGAAAACATGGGAAT
1 TTTTTGAAAACA-CGAAAA
* *
54669968 TTTTTTAAAACATGAAAA
1 TTTTTGAAAACACGAAAA
*
54669986 TTTTTGAAAACATCG-GAA
1 TTTTTGAAAACA-CGAAAA
* *
54670004 TTTTTGAAGACACGAAGA
1 TTTTTGAAAACACGAAAA
* **
54670022 TTTTTGAAACACAGGAATTTT
1 TTTTTGAAA-ACACGAA--AA
54670043 TTTTTGAAAACACGAAAA
1 TTTTTGAAAACACGAAAA
* * *
54670061 -ATTTGAAAA-ATTG-AAT
1 TTTTTGAAAACA-CGAAAA
*
54670077 TTTTTGAAAACACGGGAAA
1 TTTTTGAAAACAC-GAAAA
54670096 TTTTT
1 TTTTT
54670101 TTGAAAACAT
Statistics
Matches: 340, Mismatches: 84, Indels: 53
0.71 0.18 0.11
Matches are distributed among these distances:
15 5 0.01
16 16 0.05
17 107 0.31
18 143 0.42
19 43 0.13
20 17 0.05
21 9 0.03
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (18 bp):
TTTTTGAAAACACGAAAA
Found at i:54669811 original size:52 final size:53
Alignment explanation
Indices: 54669635--54670031 Score: 162
Period size: 53 Copynumber: 7.5 Consensus size: 53
54669625 TTATTTTTTT
* * * * * * *
54669635 TTGAAAACATGAAAATTTTTTAAAACACGAGAATTTTAGAGACAC-A-AAAATTA
1 TTGAAAACACGAAAA-TTTTTGAAACGCGAAAATTTT-GAAACACGAGAAATTTG
* ** * *
54669688 TTAAAAACACGAAAATTTTTGAAGACGCGACGATTTTGAGACACGAGAAATTTT
1 TTGAAAACACGAAAATTTTTGAA-ACGCGAAAATTTTGAAACACGAGAAATTTG
* * * *
54669742 TTGAAAACGCG--ATTTTTTGAAATGTGAAAATTTGTGAAACACGAG-AA-TTG
1 TTGAAAACACGAAAATTTTTGAAACGCGAAAATTT-TGAAACACGAGAAATTTG
* * *
54669792 TTGAAAACACGAAAATTTTTGAAAACACGCAAATTTTTGAAACACG-GAAGTTT-
1 TTGAAAACACGAAAATTTTTG-AAACGCG-AAAATTTTGAAACACGAGAAATTTG
* * * * * *
54669845 TTAGAAAACATGAAAAAATTTTG-ATCATCGAAATTTTTTGAAA-AC-ACGAAATTTT
1 TT-GAAAACACG-AAAATTTTTGAAAC-GCGAAA-ATTTTGAAACACGA-GAAATTTG
* * ** * *
54669900 TTG-AAACACCAGAATTTTTGAAAACATGAGGATTTTTGAAACACGA-AAATTT-
1 TTGAAAACACGAAAATTTTTG-AAACGCGA-AAATTTTGAAACACGAGAAATTTG
* ** * **
54669952 TTGAAAACATGGGAATTTTTTTAAAACATGAAAATTTTTGAAAACATCG-G-AATTT-
1 TTGAAAACA--CGAAAATTTTTGAAACGCGAAAA-TTTTG-AAACA-CGAGAAATTTG
* *
54670007 TTGAAGACACGAAGATTTTTGAAAC
1 TTGAAAACACGAAAATTTTTGAAAC
54670032 ACAGGAATTT
Statistics
Matches: 265, Mismatches: 50, Indels: 58
0.71 0.13 0.16
Matches are distributed among these distances:
50 12 0.05
51 10 0.04
52 52 0.20
53 87 0.33
54 66 0.25
55 36 0.14
56 2 0.01
ACGTcount: A:0.43, C:0.10, G:0.16, T:0.31
Consensus pattern (53 bp):
TTGAAAACACGAAAATTTTTGAAACGCGAAAATTTTGAAACACGAGAAATTTG
Found at i:54669832 original size:36 final size:35
Alignment explanation
Indices: 54669632--54670118 Score: 273
Period size: 35 Copynumber: 13.6 Consensus size: 35
54669622 CAATTATTTT
* * *
54669632 TTTTTGAAAACATGAAAATTTTTTAAAACACGAGAA
1 TTTTTGAAAACACG-AAATTTTTGAAAACACGAAAA
* * * * *
54669668 TTTTAG-AGACACAAAAATTATTAAAAACACGAAAA
1 TTTTTGAAAACAC-GAAATTTTTGAAAACACGAAAA
* * * *
54669703 TTTTTGAAGACGCGACGA-TTTTG-AGACACGAGAAA
1 TTTTTGAAAACACGA-AATTTTTGAAAACACGA-AAA
* * ***
54669738 TTTTTTGAAAACGCG-ATTTTTTG-AAATGTGAAAA
1 -TTTTTGAAAACACGAAATTTTTGAAAACACGAAAA
* *
54669772 TTTGTG-AAACACGAGAATTGTTGAAAACACGAAAA
1 TTTTTGAAAACACGA-AATTTTTGAAAACACGAAAA
* *
54669807 TTTTTGAAAACACGCAAATTTTTG-AAACACGGAAG
1 TTTTTGAAAACACG-AAATTTTTGAAAACACGAAAA
* * * *
54669842 TTTTTAGAAAACATGAAAAAATTTTG--ATCATCGAAAT
1 TTTTT-GAAAACACG--AAATTTTTGAAAACA-CGAAAA
* *
54669879 TTTTTGAAAACACGAAATTTTTTG-AAACACCAGAA
1 TTTTTGAAAACACGAAA-TTTTTGAAAACACGAAAA
* *
54669914 TTTTTGAAAACATGAGGATTTTTG-AAACACGAAAA
1 TTTTTGAAAACACGA-AATTTTTGAAAACACGAAAA
* * * *
54669949 TTTTTGAAAACATGGGAATTTTTTTAAAACATGAAAA
1 TTTTTGAAAACA--CGAAATTTTTGAAAACACGAAAA
* * *
54669986 TTTTTGAAAACATCGGAATTTTTGAAGACACGAAGA
1 TTTTTGAAAACA-CGAAATTTTTGAAAACACGAAAA
* *
54670022 TTTTTGAAACACAGGAATTTTTTTTTGAAAACACGAAAA
1 TTTTTGAAA-ACACGAA---ATTTTTGAAAACACGAAAA
* * * *
54670061 -ATTTGAAAA-ATTGAATTTTTTGAAAACACGGGAAATT
1 TTTTTGAAAACA-CGAAATTTTTGAAAACAC--GAAA-A
*
54670098 TTTTTGAAAACA-TAAATTTTT
1 TTTTTGAAAACACGAAATTTTT
54670119 TTTGAATTTT
Statistics
Matches: 349, Mismatches: 72, Indels: 59
0.73 0.15 0.12
Matches are distributed among these distances:
32 6 0.02
33 5 0.01
34 33 0.09
35 119 0.34
36 98 0.28
37 56 0.16
38 15 0.04
39 17 0.05
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.33
Consensus pattern (35 bp):
TTTTTGAAAACACGAAATTTTTGAAAACACGAAAA
Found at i:54670045 original size:55 final size:57
Alignment explanation
Indices: 54669986--54670110 Score: 132
Period size: 56 Copynumber: 2.2 Consensus size: 57
54669976 AACATGAAAA
* ** * *
54669986 TTTTTGAAAACATCGGAATTTTTGAAGACA-CGAAGATTTTTG-AAACACAGGAATTTT
1 TTTTTGAAAACATCGAAAAATTTGAA-AAATCGAA-ATTTTTGAAAACACAGGAAATTT
* * *
54670043 TTTTTGAAAACA-CGAAAAATTTGAAAAATTGAATTTTTTGAAAACACGGGAAA-TT
1 TTTTTGAAAACATCGAAAAATTTGAAAAATCGAAATTTTTGAAAACACAGGAAATTT
54670098 TTTTTGAAAACAT
1 TTTTTGAAAACAT
54670111 AAATTTTTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
55 22 0.39
56 23 0.40
57 12 0.21
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (57 bp):
TTTTTGAAAACATCGAAAAATTTGAAAAATCGAAATTTTTGAAAACACAGGAAATTT
Found at i:54670130 original size:10 final size:10
Alignment explanation
Indices: 54670115--54670141 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
54670105 AAACATAAAT
54670115 TTTTTTTGAA
1 TTTTTTTGAA
54670125 TTTTTTTGAA
1 TTTTTTTGAA
54670135 TTTTTTT
1 TTTTTTT
54670142 CGTTTTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.15, C:0.00, G:0.07, T:0.78
Consensus pattern (10 bp):
TTTTTTTGAA
Found at i:54670271 original size:5 final size:5
Alignment explanation
Indices: 54670247--54670303 Score: 87
Period size: 5 Copynumber: 11.2 Consensus size: 5
54670237 TGCCTTATTT
* *
54670247 ATTAA AATAA TTTAAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATT-AA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA ATTAA
54670298 ATTAA A
1 ATTAA A
54670304 AATATAAATA
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
5 43 0.91
6 4 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATTAA
Found at i:54670372 original size:29 final size:28
Alignment explanation
Indices: 54670326--54670408 Score: 121
Period size: 29 Copynumber: 2.9 Consensus size: 28
54670316 AAAATATAGA
54670326 AATTTTAAAAAGTTTAGGGGTAAAATGT
1 AATTTTAAAAAGTTTAGGGGTAAAATGT
* *
54670354 AATTTTAAAAAATTTTAGGGATCAAAATGT
1 AATTTT-AAAAAGTTTAGGGGT-AAAATGT
*
54670384 AATTTCAAAAAGTTTAGGGGTAAAA
1 AATTTTAAAAAGTTTAGGGGTAAAA
54670409 ATATTATTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
28 10 0.21
29 26 0.54
30 12 0.25
ACGTcount: A:0.46, C:0.02, G:0.18, T:0.34
Consensus pattern (28 bp):
AATTTTAAAAAGTTTAGGGGTAAAATGT
Found at i:54670409 original size:29 final size:28
Alignment explanation
Indices: 54670326--54670423 Score: 115
Period size: 29 Copynumber: 3.4 Consensus size: 28
54670316 AAAATATAGA
*
54670326 AATTTTAAAAAGTTTAGGGGTAAAATGT
1 AATTTAAAAAAGTTTAGGGGTAAAATGT
* *
54670354 AATTTTAAAAAATTTTAGGGATCAAAATGT
1 AA-TTTAAAAAAGTTTAGGGGT-AAAATGT
* *
54670384 AATTTCAAAAAGTTTAGGGGTAAAAATAT
1 AATTTAAAAAAGTTTAGGGGT-AAAATGT
*
54670413 TATTTAAAAAA
1 AATTTAAAAAA
54670424 ATCGAGCCGG
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
28 2 0.03
29 47 0.81
30 9 0.16
ACGTcount: A:0.48, C:0.02, G:0.15, T:0.35
Consensus pattern (28 bp):
AATTTAAAAAAGTTTAGGGGTAAAATGT
Found at i:54675624 original size:4 final size:4
Alignment explanation
Indices: 54675615--54675676 Score: 124
Period size: 4 Copynumber: 15.5 Consensus size: 4
54675605 GAGAGATGTT
54675615 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
54675663 TACA TACA TACA TA
1 TACA TACA TACA TA
54675677 TTATAATTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 58 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:54676444 original size:3 final size:3
Alignment explanation
Indices: 54676436--54676460 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54676426 AGAAAAATGC
54676436 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
54676461 CAATATAGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:54679785 original size:20 final size:18
Alignment explanation
Indices: 54679750--54679786 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
54679740 ATGTAAATTG
54679750 TATATATGTATAAAATGA
1 TATATATGTATAAAATGA
54679768 TATATATCGTATATAAATG
1 TATATAT-GTATA-AAATG
54679787 TTAACACTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
19 5 0.29
20 5 0.29
ACGTcount: A:0.46, C:0.03, G:0.11, T:0.41
Consensus pattern (18 bp):
TATATATGTATAAAATGA
Found at i:54680733 original size:12 final size:13
Alignment explanation
Indices: 54680716--54680744 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
54680706 AAGAATACAA
54680716 CTTTCT-TTTTTT
1 CTTTCTGTTTTTT
54680728 CTTTCTGTTTTTT
1 CTTTCTGTTTTTT
54680741 CTTT
1 CTTT
54680745 TTTCTGCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 6 0.38
13 10 0.62
ACGTcount: A:0.00, C:0.17, G:0.03, T:0.79
Consensus pattern (13 bp):
CTTTCTGTTTTTT
Found at i:54681325 original size:8 final size:8
Alignment explanation
Indices: 54681312--54681338 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
54681302 TATTATTTTC
54681312 ATAAAAAT
1 ATAAAAAT
54681320 ATAAAAAT
1 ATAAAAAT
54681328 ATAAAAAT
1 ATAAAAAT
54681336 ATA
1 ATA
54681339 TTATATATAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (8 bp):
ATAAAAAT
Found at i:54682560 original size:20 final size:20
Alignment explanation
Indices: 54682535--54682588 Score: 90
Period size: 20 Copynumber: 2.7 Consensus size: 20
54682525 AAAATTAAAT
*
54682535 AAAGAAAAGGATGAAATTGG
1 AAAGAAAAAGATGAAATTGG
54682555 AAAGAAAAAGATGAAATTGG
1 AAAGAAAAAGATGAAATTGG
*
54682575 AAAGAAAAAAATGA
1 AAAGAAAAAGATGA
54682589 TAGGATGATA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.63, C:0.00, G:0.24, T:0.13
Consensus pattern (20 bp):
AAAGAAAAAGATGAAATTGG
Found at i:54683783 original size:23 final size:24
Alignment explanation
Indices: 54683757--54683806 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
54683747 CCGTTACTTG
*
54683757 TTAAGCTC-AATGAGCTTCATGTT
1 TTAAACTCTAATGAGCTTCATGTT
* * *
54683780 TTAAACTCTTATGAGTTTCCTGTT
1 TTAAACTCTAATGAGCTTCATGTT
54683804 TTA
1 TTA
54683807 GCCCGGATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
23 7 0.32
24 15 0.68
ACGTcount: A:0.24, C:0.16, G:0.14, T:0.46
Consensus pattern (24 bp):
TTAAACTCTAATGAGCTTCATGTT
Found at i:54692182 original size:55 final size:55
Alignment explanation
Indices: 54692098--54692206 Score: 173
Period size: 55 Copynumber: 2.0 Consensus size: 55
54692088 AGATACACCG
* *
54692098 TTCATGGGTTGAGTTATTTGTTCATGCTTGAAGGTCTGTTTGAAATTTGAAAGGA
1 TTCATGGGTTGAGTTATTTGTTCAAGCTTGAAGGTCTGTCTGAAATTTGAAAGGA
* * *
54692153 TTCATGGGTTGAGTTATTTTTTTAAGCTTGAAGGTTTGTCTGAAATTTGAAAGG
1 TTCATGGGTTGAGTTATTTGTTCAAGCTTGAAGGTCTGTCTGAAATTTGAAAGG
54692207 GTGTGGACAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.24, C:0.06, G:0.27, T:0.43
Consensus pattern (55 bp):
TTCATGGGTTGAGTTATTTGTTCAAGCTTGAAGGTCTGTCTGAAATTTGAAAGGA
Found at i:54697322 original size:3 final size:3
Alignment explanation
Indices: 54697314--54697346 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
54697304 TATTATATAA
*
54697314 ATG ATG ATG ATG ATG ATG ATG ATG GTG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
54697347 TTCACCGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:54698458 original size:31 final size:31
Alignment explanation
Indices: 54698415--54698475 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
54698405 TTGCAAGATC
*
54698415 AACGGCTCTGATATCCTT-GTGATGGACATCT
1 AACGGCTCTGATAT-CTTCATGATGGACATCT
*
54698446 AACGGCTTTGATATCTTCATGATGGACATC
1 AACGGCTCTGATATCTTCATGATGGACATC
54698476 ACACGGGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (31 bp):
AACGGCTCTGATATCTTCATGATGGACATCT
Found at i:54701432 original size:3 final size:3
Alignment explanation
Indices: 54701420--54701483 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
54701410 AGATCTACAA
54701420 ATT A-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
54701467 ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT AT
54701484 CAAACTCATT
Statistics
Matches: 60, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 58 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:54708114 original size:2 final size:2
Alignment explanation
Indices: 54708107--54708136 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
54708097 ATGTTTATGA
54708107 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
54708137 TCTTTGAATT
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):
AT
Found at i:54708647 original size:31 final size:30
Alignment explanation
Indices: 54708612--54708669 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
54708602 TTATTGTTTG
54708612 GGTAAATTAT-ATTTGTAGTCATCCAATTTTT
1 GGTAAATT-TCATTT-TAGTCATCCAATTTTT
* *
54708643 GGTAAGTTTCATTTTGGTCATCCAATT
1 GGTAAATTTCATTTTAGTCATCCAATT
54708670 ATAAAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.54
31 11 0.46
ACGTcount: A:0.26, C:0.12, G:0.16, T:0.47
Consensus pattern (30 bp):
GGTAAATTTCATTTTAGTCATCCAATTTTT
Found at i:54711703 original size:2 final size:2
Alignment explanation
Indices: 54711696--54711735 Score: 64
Period size: 2 Copynumber: 20.0 Consensus size: 2
54711686 TATTTGACAA
54711696 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CAT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT AT AT AT
54711736 TGGTACAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 1 0.03
2 33 0.92
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54714266 original size:30 final size:31
Alignment explanation
Indices: 54714232--54714290 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
54714222 AGAAGAACTT
54714232 AATAGCCCAGTGATTTAAAT-AAAACTTTTG
1 AATAGCCCAGTGATTTAAATAAAAACTTTTG
**
54714262 AATAGTTCAGTGATTTAAATAAAAACTTT
1 AATAGCCCAGTGATTTAAATAAAAACTTT
54714291 CAAATGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.42, C:0.10, G:0.12, T:0.36
Consensus pattern (31 bp):
AATAGCCCAGTGATTTAAATAAAAACTTTTG
Found at i:54718863 original size:17 final size:17
Alignment explanation
Indices: 54718837--54718870 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54718827 CAAAGTTTGA
* *
54718837 ATTATTATTTGTATTCC
1 ATTATAATTTATATTCC
54718854 ATTATAATTTATATTCC
1 ATTATAATTTATATTCC
54718871 CGATTTTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.12, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTATAATTTATATTCC
Found at i:54723800 original size:16 final size:16
Alignment explanation
Indices: 54723781--54723822 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
54723771 GTTTGAGTTG
54723781 TTTCAAGTTCAGATCA
1 TTTCAAGTTCAGATCA
* *
54723797 TTTCAAATTCAGGTCA
1 TTTCAAGTTCAGATCA
*
54723813 TTCCAAGTTC
1 TTTCAAGTTC
54723823 GGGTATGGGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (16 bp):
TTTCAAGTTCAGATCA
Found at i:54725874 original size:18 final size:20
Alignment explanation
Indices: 54725837--54725877 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
54725827 AAATACTAAC
54725837 AAAAGCTAAAAATTTAATTTA
1 AAAAGCTAAAAA-TTAATTTA
54725858 AAAAG-TAAAAA-TAATTTA
1 AAAAGCTAAAAATTAATTTA
54725876 AA
1 AA
54725878 TTTCAACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
20 6 0.30
21 5 0.25
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (20 bp):
AAAAGCTAAAAATTAATTTA
Found at i:54728554 original size:40 final size:40
Alignment explanation
Indices: 54728510--54728644 Score: 123
Period size: 37 Copynumber: 3.4 Consensus size: 40
54728500 ACCAGTTTGG
* *
54728510 CACCCGGTGCCTCATCGGATAATTCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGATAATACGAAGTAATAAATTGA
* * * * * *
54728550 CACCCAATGTCTCATCGGTTAA-ACCAA--AGTAAATTGG
1 CACCCAGTGCCTCATCGGATAATACGAAGTAATAAATTGA
* * *
54728587 CACCCAGTGCATCATCGAATTAATCCGAAGTAATAAATTGA
1 CACCCAGTGCCTCATCGGA-TAATACGAAGTAATAAATTGA
* *
54728628 CACCTAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
54728645 ACTCGAAGTC
Statistics
Matches: 71, Mismatches: 20, Indels: 7
0.72 0.20 0.07
Matches are distributed among these distances:
37 22 0.31
38 3 0.04
39 6 0.08
40 18 0.25
41 22 0.31
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (40 bp):
CACCCAGTGCCTCATCGGATAATACGAAGTAATAAATTGA
Found at i:54728643 original size:41 final size:41
Alignment explanation
Indices: 54728510--54728645 Score: 131
Period size: 41 Copynumber: 3.4 Consensus size: 41
54728500 ACCAGTTTGG
* * * *
54728510 CACCCGGTGCCTCATCGGA-TAATTCGAAGTAATAAATTGA
1 CACCCAGTGTCTCATCGAATTAATCCGAAGTAATAAATTGA
* * * * *
54728550 CACCCAATGTCTCATCG-GTTAAACC-AA--AGTAAATTGG
1 CACCCAGTGTCTCATCGAATTAATCCGAAGTAATAAATTGA
54728587 CACCCAGTG-CATCATCGAATTAATCCGAAGTAATAAATTGA
1 CACCCAGTGTC-TCATCGAATTAATCCGAAGTAATAAATTGA
*
54728628 CACCTAGTGTCTCATCGA
1 CACCCAGTGTCTCATCGA
54728646 CTCGAAGTCG
Statistics
Matches: 75, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
36 1 0.01
37 22 0.29
38 6 0.08
39 4 0.05
40 18 0.24
41 23 0.31
42 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.17, T:0.25
Consensus pattern (41 bp):
CACCCAGTGTCTCATCGAATTAATCCGAAGTAATAAATTGA
Found at i:54728803 original size:21 final size:21
Alignment explanation
Indices: 54728764--54728830 Score: 59
Period size: 21 Copynumber: 3.2 Consensus size: 21
54728754 CAATATTCAT
54728764 TTCAAT-TCAAATAATCAATATA
1 TTCAATAT-AAAT-ATCAATATA
*
54728786 TTCAATATATATATCAAT-TCA
1 TTCAATATAAATATCAATAT-A
* *
54728807 ATCAATATAAAT-TCAATAAA
1 TTCAATATAAATATCAATATA
54728827 TTCA
1 TTCA
54728831 TCACATACTA
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
20 10 0.27
21 17 0.46
22 9 0.24
23 1 0.03
ACGTcount: A:0.49, C:0.13, G:0.00, T:0.37
Consensus pattern (21 bp):
TTCAATATAAATATCAATATA
Found at i:54728846 original size:24 final size:24
Alignment explanation
Indices: 54728801--54728847 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
54728791 TATATATATC
54728801 AATTCAATCAATATAAATTCAATA
1 AATTCAATCAATATAAATTCAATA
54728825 AATTC-ATCACATACTAAA-TCAAT
1 AATTCAATCA-ATA-TAAATTCAAT
54728848 CCATTTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 4 0.19
24 13 0.62
25 4 0.19
ACGTcount: A:0.51, C:0.17, G:0.00, T:0.32
Consensus pattern (24 bp):
AATTCAATCAATATAAATTCAATA
Found at i:54729193 original size:18 final size:19
Alignment explanation
Indices: 54729167--54729202 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
54729157 TAAACTAAAT
*
54729167 TTAACTCCCT-AATTTCAC
1 TTAAATCCCTAAATTTCAC
54729185 TTAAATCCCTAAATTTCA
1 TTAAATCCCTAAATTTCA
54729203 ATTTTTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAATCCCTAAATTTCAC
Found at i:54730479 original size:11 final size:11
Alignment explanation
Indices: 54730463--54730524 Score: 54
Period size: 11 Copynumber: 5.6 Consensus size: 11
54730453 AAAAATATGT
54730463 TATTTTGCTAC
1 TATTTTGCTAC
54730474 TATTTT-CTCAC
1 TATTTTGCT-AC
*
54730485 TATTTTGCGAC
1 TATTTTGCTAC
* ** *
54730496 AATTTCACTAT
1 TATTTTGCTAC
*
54730507 TATGTTGCTAC
1 TATTTTGCTAC
54730518 TATTTTG
1 TATTTTG
54730525 TTGTTATTGT
Statistics
Matches: 37, Mismatches: 12, Indels: 4
0.70 0.23 0.08
Matches are distributed among these distances:
10 2 0.05
11 34 0.92
12 1 0.03
ACGTcount: A:0.21, C:0.18, G:0.10, T:0.52
Consensus pattern (11 bp):
TATTTTGCTAC
Found at i:54730489 original size:22 final size:23
Alignment explanation
Indices: 54730463--54730523 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
54730453 AAAAATATGT
*
54730463 TATTTTGCTACTATTTTCTC-AC
1 TATTTTGCTACTATTTTCACTAC
* * *
54730485 TATTTTGCGAC-AATTTCACTAT
1 TATTTTGCTACTATTTTCACTAC
*
54730507 TATGTTGCTACTATTTT
1 TATTTTGCTACTATTTT
54730524 GTTGTTATTG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 6 0.20
22 20 0.67
23 4 0.13
ACGTcount: A:0.21, C:0.18, G:0.08, T:0.52
Consensus pattern (23 bp):
TATTTTGCTACTATTTTCACTAC
Found at i:54730770 original size:7 final size:7
Alignment explanation
Indices: 54730760--54730790 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
54730750 GCATTTGAGA
54730760 TTTTCTT
1 TTTTCTT
54730767 TTTTCTT
1 TTTTCTT
54730774 TTTTCTT
1 TTTTCTT
54730781 TTTTCTT
1 TTTTCTT
54730788 TTT
1 TTT
54730791 GTATTGTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTCTT
Found at i:54731750 original size:25 final size:24
Alignment explanation
Indices: 54731700--54731751 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
54731690 TTGGAGCAAT
* * *
54731700 TTAATTTTTTTCTTTTATGTTTTC
1 TTAATTTCTTTCTTTTATATTCTC
*
54731724 TTAACTTTCTTTCTTTTCTATTCTC
1 TTAA-TTTCTTTCTTTTATATTCTC
54731749 TTA
1 TTA
54731752 TGCTTCTCCC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 4 0.17
25 19 0.83
ACGTcount: A:0.13, C:0.15, G:0.02, T:0.69
Consensus pattern (24 bp):
TTAATTTCTTTCTTTTATATTCTC
Found at i:54734671 original size:16 final size:15
Alignment explanation
Indices: 54734643--54734684 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
54734633 AGGAAAAAAT
54734643 TAAAAAACA-ATATGA
1 TAAAAAACATATAT-A
54734658 TAAAAAACATATATA
1 TAAAAAACATATATA
54734673 TAAAAAAACATA
1 T-AAAAAACATA
54734685 AAATACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 11 0.44
16 14 0.56
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.21
Consensus pattern (15 bp):
TAAAAAACATATATA
Found at i:54735550 original size:17 final size:17
Alignment explanation
Indices: 54735525--54735558 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
54735515 ATCCATTGCT
* *
54735525 TTTTGTTTTTGTTTTTA
1 TTTTCTTTTTCTTTTTA
54735542 TTTTCTTTTTCTTTTTA
1 TTTTCTTTTTCTTTTTA
54735559 ATCTAACTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.06, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTCTTTTTCTTTTTA
Found at i:54739515 original size:9 final size:9
Alignment explanation
Indices: 54739503--54739530 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
54739493 TTTTTTTAGA
54739503 ATTTTGATT
1 ATTTTGATT
54739512 ATTTTGATT
1 ATTTTGATT
54739521 ATTTTGATT
1 ATTTTGATT
54739530 A
1 A
54739531 CTCTTTCGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.25, C:0.00, G:0.11, T:0.64
Consensus pattern (9 bp):
ATTTTGATT
Found at i:54742625 original size:27 final size:28
Alignment explanation
Indices: 54742590--54742646 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
54742580 ATTTACATTG
54742590 TTATGATTTTATCCATA-ATTTCATGATT
1 TTATGATTTT-TCCATATATTTCATGATT
* *
54742618 TTAT-ATTTTTTCATATTTTTCATGATT
1 TTATGATTTTTCCATATATTTCATGATT
54742645 TT
1 TT
54742647 TGTGTTGTCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 5 0.19
27 17 0.65
28 4 0.15
ACGTcount: A:0.25, C:0.09, G:0.05, T:0.61
Consensus pattern (28 bp):
TTATGATTTTTCCATATATTTCATGATT
Found at i:54748995 original size:23 final size:22
Alignment explanation
Indices: 54748961--54749035 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 22
54748951 GTAAACTTGT
54748961 TTGTGATCTAAAAGTATGTTAAC
1 TTGTGATCTAAAA-TATGTTAAC
* *
54748984 TTGTGATGT-AAATTTG-T---
1 TTGTGATCTAAAATATGTTAAC
54749001 TTGTGATCTAAAAATATGTTAAC
1 TTGTGATCT-AAAATATGTTAAC
*
54749024 TTGTGATGTAAA
1 TTGTGATCTAAA
54749036 TTTGTTTGTG
Statistics
Matches: 41, Mismatches: 5, Indels: 13
0.69 0.08 0.22
Matches are distributed among these distances:
17 8 0.20
19 6 0.15
20 2 0.05
21 3 0.07
22 6 0.15
23 16 0.39
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (22 bp):
TTGTGATCTAAAATATGTTAAC
Found at i:54749002 original size:40 final size:40
Alignment explanation
Indices: 54748947--54749065 Score: 211
Period size: 40 Copynumber: 3.0 Consensus size: 40
54748937 ATGCCTAGTT
* *
54748947 TGATGTAAACTTGTTTGTGATCTAAAAGTATGTTAACTTG
1 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
54748987 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
1 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
*
54749027 TGATGTAAATTTGTTTGTGATTTAAAAATATGTTAACTT
1 TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTT
54749066 CCTACTTAGA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 76 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (40 bp):
TGATGTAAATTTGTTTGTGATCTAAAAATATGTTAACTTG
Found at i:54749006 original size:17 final size:17
Alignment explanation
Indices: 54748984--54749052 Score: 57
Period size: 17 Copynumber: 3.7 Consensus size: 17
54748974 GTATGTTAAC
54748984 TTGTGATGTAAATTTGT
1 TTGTGATGTAAATTTGT
* *
54749001 TTGTGATCTAAAAATATGTT
1 TTGTGATGT--AAATTTG-T
54749021 AACTTGTGATGTAAATTTGT
1 ---TTGTGATGTAAATTTGT
*
54749041 TTGTGATTTAAA
1 TTGTGATGTAAA
54749053 AATATGTTAA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
17 19 0.46
19 6 0.15
20 2 0.05
21 6 0.15
23 8 0.20
ACGTcount: A:0.30, C:0.03, G:0.19, T:0.48
Consensus pattern (17 bp):
TTGTGATGTAAATTTGT
Found at i:54751117 original size:33 final size:33
Alignment explanation
Indices: 54751078--54751164 Score: 165
Period size: 33 Copynumber: 2.6 Consensus size: 33
54751068 TTTAAAGGAG
54751078 ATAGTCTCCGCTCAGACAGTGGTAAGCAAAGTA
1 ATAGTCTCCGCTCAGACAGTGGTAAGCAAAGTA
*
54751111 ATAGTCTCCGCTCAGACAGCGGTAAGCAAAGTA
1 ATAGTCTCCGCTCAGACAGTGGTAAGCAAAGTA
54751144 ATAGTCTCCGCTCAGACAGTG
1 ATAGTCTCCGCTCAGACAGTG
54751165 CGAAACGTAT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.31, C:0.24, G:0.24, T:0.21
Consensus pattern (33 bp):
ATAGTCTCCGCTCAGACAGTGGTAAGCAAAGTA
Found at i:54758776 original size:63 final size:63
Alignment explanation
Indices: 54758673--54758829 Score: 296
Period size: 63 Copynumber: 2.5 Consensus size: 63
54758663 GAGGATTAAG
*
54758673 ATAAGCAGATAAGGAGGAATCTGCTTTTACAAACATAAAGGACATGACTCATACATAAAGGAC
1 ATAAGCAGATAAGGAGGAATCTGCTTTTACAAACACAAAGGACATGACTCATACATAAAGGAC
*
54758736 ATAAGCAGATAAGGAGGAATCTGCTTTTACAGACACAAAGGACATGACTCATACATAAAGGAC
1 ATAAGCAGATAAGGAGGAATCTGCTTTTACAAACACAAAGGACATGACTCATACATAAAGGAC
54758799 ATAAGCAGATAAGGAGGAATCTGCTTTTACA
1 ATAAGCAGATAAGGAGGAATCTGCTTTTACA
54758830 TTAACCTATC
Statistics
Matches: 92, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 92 1.00
ACGTcount: A:0.43, C:0.16, G:0.20, T:0.21
Consensus pattern (63 bp):
ATAAGCAGATAAGGAGGAATCTGCTTTTACAAACACAAAGGACATGACTCATACATAAAGGAC
Found at i:54763611 original size:16 final size:16
Alignment explanation
Indices: 54763590--54763624 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
54763580 GATTGGCTAG
*
54763590 CATACAAATATGCATA
1 CATACAAATATACATA
*
54763606 CATACATATATACATA
1 CATACAAATATACATA
54763622 CAT
1 CAT
54763625 CATACATGGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.49, C:0.20, G:0.03, T:0.29
Consensus pattern (16 bp):
CATACAAATATACATA
Found at i:54766719 original size:31 final size:29
Alignment explanation
Indices: 54766668--54766740 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
54766658 AAGTTATGAA
54766668 TTTAATCTCTATATTTTAATTTGA-TCAAT
1 TTTAATCTCTATATTTTAATTT-ATTCAAT
*
54766697 TTTAATCTCTGCATTTTTTAATTTATTCAAT
1 TTTAATCTCT--ATATTTTAATTTATTCAAT
* *
54766728 TTTAGTCCCTATA
1 TTTAATCTCTATA
54766741 CAGATTTCTT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
29 12 0.32
30 1 0.03
31 24 0.65
ACGTcount: A:0.27, C:0.14, G:0.04, T:0.55
Consensus pattern (29 bp):
TTTAATCTCTATATTTTAATTTATTCAAT
Found at i:54767534 original size:12 final size:12
Alignment explanation
Indices: 54767517--54767541 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
54767507 GCTAAAAAAG
54767517 ATGAATAATTAA
1 ATGAATAATTAA
54767529 ATGAATAATTAA
1 ATGAATAATTAA
54767541 A
1 A
54767542 ATATTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (12 bp):
ATGAATAATTAA
Found at i:54769639 original size:13 final size:13
Alignment explanation
Indices: 54769623--54769659 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
54769613 TTTAAACCAA
54769623 ACTTTTCAAAAAC
1 ACTTTTCAAAAAC
*
54769636 ACTTCTCAAAAAC
1 ACTTTTCAAAAAC
54769649 ACTTTTCAAAA
1 ACTTTTCAAAA
54769660 TCAATAAAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:54776860 original size:7 final size:7
Alignment explanation
Indices: 54776848--54776872 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
54776838 CGTCTGGTGC
54776848 TGCAAAA
1 TGCAAAA
54776855 TGCAAAA
1 TGCAAAA
54776862 TGCAAAA
1 TGCAAAA
54776869 TGCA
1 TGCA
54776873 GTCTGTATTC
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:0.52, C:0.16, G:0.16, T:0.16
Consensus pattern (7 bp):
TGCAAAA
Found at i:54781760 original size:43 final size:43
Alignment explanation
Indices: 54781699--54781864 Score: 203
Period size: 43 Copynumber: 3.9 Consensus size: 43
54781689 TTTCCTATAA
* *
54781699 GTGTTTTCGTGTGAGACCACGTTTGGGACGTTGGCATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
* *
54781742 GTGTTTTCGTGTAAGACCACGTTTAGGACGTTGGCATCGACTT
1 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
* *
54781785 GTGTTTTCGTATAAGACC-CTGTCTGGGATAG-TGGCATCGA-TCT
1 GTGTTTTCGTGTAAGACCAC-GTCTGGGA-CGTTGGCATCGACT-T
* * *
54781828 GTGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
1 GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCAT
54781865 TGTACGAGCC
Statistics
Matches: 107, Mismatches: 11, Indels: 10
0.84 0.09 0.08
Matches are distributed among these distances:
42 3 0.03
43 102 0.95
44 2 0.02
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (43 bp):
GTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCATCGACTT
Found at i:54786358 original size:18 final size:20
Alignment explanation
Indices: 54786314--54786379 Score: 50
Period size: 19 Copynumber: 3.4 Consensus size: 20
54786304 ATAAATTATA
* *
54786314 ATATTTTATTAATTTTTATC
1 ATATTTTATGAATTTTAATC
*
54786334 ATTTTTTA-GAATTTTAAT-
1 ATATTTTATGAATTTTAATC
*
54786352 ATATTTTTATAAAATTTTAA--
1 ATA-TTTTAT-GAATTTTAATC
54786372 ATATTTTA
1 ATATTTTA
54786380 AACATGTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
18 2 0.05
19 18 0.47
20 10 0.26
21 8 0.21
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (20 bp):
ATATTTTATGAATTTTAATC
Found at i:54786367 original size:21 final size:19
Alignment explanation
Indices: 54786334--54786378 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
54786324 AATTTTTATC
*
54786334 ATTTTTTAGAATTTTAATAT
1 ATTTTTTAAAATTTTAA-AT
54786354 ATTTTTATAAAATTTTAAAT
1 ATTTTT-TAAAATTTTAAAT
54786374 ATTTT
1 ATTTT
54786379 AAACATGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (19 bp):
ATTTTTTAAAATTTTAAAT
Found at i:54786379 original size:19 final size:19
Alignment explanation
Indices: 54786313--54786379 Score: 57
Period size: 21 Copynumber: 3.5 Consensus size: 19
54786303 TATAAATTAT
*
54786313 AATATTTTAT-TAATTTT-
1 AATATTTTATAAAATTTTA
* * *
54786330 TATCATTTTTTAGAATTTTA
1 AAT-ATTTTATAAAATTTTA
54786350 ATATATTTTTATAAAATTTTA
1 A-ATA-TTTTATAAAATTTTA
54786371 AATATTTTA
1 AATATTTTA
54786380 AACATGTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
17 2 0.05
18 6 0.15
19 11 0.28
20 4 0.10
21 16 0.41
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (19 bp):
AATATTTTATAAAATTTTA
Found at i:54786417 original size:26 final size:28
Alignment explanation
Indices: 54786388--54786442 Score: 87
Period size: 26 Copynumber: 2.0 Consensus size: 28
54786378 TAAACATGTT
*
54786388 TTTATTAATTTTATGAA-TTT-TTATAA
1 TTTATTAAATTTATGAAGTTTATTATAA
54786414 TTTATTAAATTTATGAAGTTTATTATAA
1 TTTATTAAATTTATGAAGTTTATTATAA
54786442 T
1 T
54786443 ATTTACAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 16 0.62
27 3 0.12
28 7 0.27
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.58
Consensus pattern (28 bp):
TTTATTAAATTTATGAAGTTTATTATAA
Found at i:54787418 original size:8 final size:8
Alignment explanation
Indices: 54787384--54787428 Score: 65
Period size: 8 Copynumber: 5.6 Consensus size: 8
54787374 ATGAAGATAT
54787384 TTATAAAA
1 TTATAAAA
*
54787392 TT-TAAAG
1 TTATAAAA
54787399 TTATATAAA
1 TTATA-AAA
54787408 TTATAAAA
1 TTATAAAA
54787416 TTATAAAA
1 TTATAAAA
54787424 TTATA
1 TTATA
54787429 TATTAATGTT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
7 6 0.18
8 20 0.61
9 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (8 bp):
TTATAAAA
Found at i:54787428 original size:25 final size:24
Alignment explanation
Indices: 54787384--54787430 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
54787374 ATGAAGATAT
*
54787384 TTATAAAATTTAAAGTTATATAAA
1 TTATAAAATTTAAAATTATATAAA
54787408 TTATAAAATTATAAAATTATATA
1 TTATAAAATT-TAAAATTATATA
54787431 TTAATGTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TTATAAAATTTAAAATTATATAAA
Found at i:54788227 original size:24 final size:24
Alignment explanation
Indices: 54788200--54788246 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
54788190 ATTGAAATGG
54788200 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
54788224 ATTGAATTTATATTGATTGAATT
1 ATTGAATTTATATTGATTGAATT
54788247 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:54788535 original size:40 final size:40
Alignment explanation
Indices: 54788405--54788543 Score: 128
Period size: 40 Copynumber: 3.5 Consensus size: 40
54788395 GACTTCGAGT
*
54788405 CGATG-AGACACTGGGTGTCAAATTATTACTTCGGATTAATT
1 CGATGAAG-CACTGGGTGTCAAATTATTACTTCGGATT-ATC
* * * * *
54788446 CGGTGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAAGCACTGGGTGTCAAATTATTACTTCGGATTATC
* *
54788483 CGATG-AGACACTGGATGTCAAATTATTACTTCGAATTATC
1 CGATGAAG-CACTGGGTGTCAAATTATTACTTCGGATTATC
*
54788523 CAATGAAGCACTGGGTG-CAAA
1 CGATGAAGCACTGGGTGTCAAA
54788544 ACTGGTGTGT
Statistics
Matches: 77, Mismatches: 15, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
36 1 0.01
37 13 0.17
38 14 0.18
39 6 0.08
40 27 0.35
41 15 0.19
42 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.29
Consensus pattern (40 bp):
CGATGAAGCACTGGGTGTCAAATTATTACTTCGGATTATC
Found at i:54791089 original size:14 final size:16
Alignment explanation
Indices: 54791058--54791089 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
54791048 TCTACCCCTT
54791058 CAATTTTTCTTCTTTC
1 CAATTTTTCTTCTTTC
54791074 CAATTTTT-TT-TTTC
1 CAATTTTTCTTCTTTC
54791088 CA
1 CA
54791090 CCTTACCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.38
15 2 0.12
16 8 0.50
ACGTcount: A:0.16, C:0.22, G:0.00, T:0.62
Consensus pattern (16 bp):
CAATTTTTCTTCTTTC
Found at i:54802265 original size:26 final size:26
Alignment explanation
Indices: 54802229--54802280 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
54802219 CCGGTCTGCC
* *
54802229 TATTTTTAAAATAAACATTAAAAAAT
1 TATTTTTAAAATAAAAATAAAAAAAT
54802255 TATTTTTAAAATAAAAATAAAAAAAT
1 TATTTTTAAAATAAAAATAAAAAAAT
54802281 AAAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (26 bp):
TATTTTTAAAATAAAAATAAAAAAAT
Found at i:54805285 original size:29 final size:32
Alignment explanation
Indices: 54805244--54805308 Score: 82
Period size: 30 Copynumber: 2.1 Consensus size: 32
54805234 TAAAAAAATG
54805244 AGGGACTTAAATAA-AATTTTCAAAAGTTTTA
1 AGGGACTTAAATAATAATTTTCAAAAGTTTTA
* * *
54805275 AGGG-CTT-AATAATAGTTTTCTAAATTTTTA
1 AGGGACTTAAATAATAATTTTCAAAAGTTTTA
54805305 AGGG
1 AGGG
54805309 TATGCAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 5 0.17
30 21 0.70
31 4 0.13
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (32 bp):
AGGGACTTAAATAATAATTTTCAAAAGTTTTA
Found at i:54808653 original size:31 final size:31
Alignment explanation
Indices: 54808618--54808680 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
54808608 TTAATAAACC
* *
54808618 AGTGACTTAAATGATAACTTTTGAATAGTTT
1 AGTGACTTAAATGAAAACTTTTGAATAATTT
54808649 AGTGACTTAAATGAAAACTTTTGAATAATTT
1 AGTGACTTAAATGAAAACTTTTGAATAATTT
54808680 A
1 A
54808681 ATGATCAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.40
Consensus pattern (31 bp):
AGTGACTTAAATGAAAACTTTTGAATAATTT
Found at i:54810824 original size:16 final size:16
Alignment explanation
Indices: 54810779--54810824 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
54810769 GCGGTTTTTT
54810779 ACTTAAATAATATA-A
1 ACTTAAATAATATATA
* * *
54810794 A-ATAAACAATTTATA
1 ACTTAAATAATATATA
54810809 ACTTAAATAATATATA
1 ACTTAAATAATATATA
54810825 CCCAATATCA
Statistics
Matches: 23, Mismatches: 6, Indels: 3
0.72 0.19 0.09
Matches are distributed among these distances:
14 9 0.39
15 3 0.13
16 11 0.48
ACGTcount: A:0.59, C:0.07, G:0.00, T:0.35
Consensus pattern (16 bp):
ACTTAAATAATATATA
Found at i:54811358 original size:22 final size:22
Alignment explanation
Indices: 54811332--54811416 Score: 62
Period size: 22 Copynumber: 3.8 Consensus size: 22
54811322 ATATCTAACC
54811332 AATAACAATAAAACAATAGCAA
1 AATAACAATAAAACAATAGCAA
* * **
54811354 TATAATAATAAAATGATAGCAA
1 AATAACAATAAAACAATAGCAA
** * **
54811376 AACGACAGTAAAACAATAAAAAA
1 AATAACAATAAAACAAT-AGCAA
* *
54811399 AATGACAACAAAACAATA
1 AATAACAATAAAACAATA
54811417 TATGAGAAAA
Statistics
Matches: 46, Mismatches: 16, Indels: 2
0.72 0.25 0.03
Matches are distributed among these distances:
22 29 0.63
23 17 0.37
ACGTcount: A:0.66, C:0.12, G:0.07, T:0.15
Consensus pattern (22 bp):
AATAACAATAAAACAATAGCAA
Found at i:54812905 original size:28 final size:29
Alignment explanation
Indices: 54812851--54812909 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 29
54812841 TATTCTTATA
* *
54812851 TTAATTTTATAATTATTTATGACATATATT
1 TTAATTTTATAAATATGTAT-ACATATATT
*
54812881 TTAATTTTATAAATATGTAT-TATATATT
1 TTAATTTTATAAATATGTATACATATATT
54812909 T
1 T
54812910 CATTATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
28 8 0.31
30 18 0.69
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (29 bp):
TTAATTTTATAAATATGTATACATATATT
Found at i:54813406 original size:7 final size:7
Alignment explanation
Indices: 54813394--54813429 Score: 56
Period size: 7 Copynumber: 5.3 Consensus size: 7
54813384 ACAATTTTAC
54813394 TAAATAT
1 TAAATAT
54813401 TAAATAT
1 TAAATAT
54813408 TAAATAT
1 TAAATAT
54813415 TAAATA-
1 TAAATAT
*
54813421 AAAATAT
1 TAAATAT
54813428 TA
1 TA
54813430 TATTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
6 5 0.19
7 21 0.81
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (7 bp):
TAAATAT
Found at i:54813441 original size:18 final size:20
Alignment explanation
Indices: 54813402--54813441 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
54813392 ACTAAATATT
54813402 AAATATTAAATATTAAATAA
1 AAATATTAAATATTAAATAA
*
54813422 AAATATTATAT-TTAAA-AA
1 AAATATTAAATATTAAATAA
54813440 AA
1 AA
54813442 CAACTATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 5 0.26
20 10 0.53
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (20 bp):
AAATATTAAATATTAAATAA
Found at i:54827575 original size:22 final size:23
Alignment explanation
Indices: 54827543--54827590 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
54827533 CCCGATGTAA
54827543 TAAATATATTTATTTT-TTAATTT
1 TAAATATATTT-TTTTATTAATTT
*
54827566 TAAAT-TATTTTTTTATTATTTT
1 TAAATATATTTTTTTATTAATTT
54827588 TAA
1 TAA
54827591 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 14 0.61
23 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TAAATATATTTTTTTATTAATTT
Found at i:54827591 original size:28 final size:28
Alignment explanation
Indices: 54827556--54827644 Score: 94
Period size: 28 Copynumber: 3.2 Consensus size: 28
54827546 ATATATTTAT
* ** *
54827556 TTTTTAATTTTAAATTATTTTTTTATTA
1 TTTTTAATTTTAAAATATTTTTAAAATA
54827584 TTTTTAATTTTAAAATATTTTTAAAATA
1 TTTTTAATTTTAAAATATTTTTAAAATA
* *
54827612 TTTTTAAATTTT---TTAATTTTAAAATA
1 TTTTT-AATTTTAAAATATTTTTAAAATA
54827638 TTTTTAA
1 TTTTTAA
54827645 AATACTTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
25 2 0.04
26 17 0.31
28 29 0.54
29 6 0.11
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (28 bp):
TTTTTAATTTTAAAATATTTTTAAAATA
Found at i:54827605 original size:11 final size:11
Alignment explanation
Indices: 54827591--54827654 Score: 70
Period size: 11 Copynumber: 6.4 Consensus size: 11
54827581 TTATTTTTAA
54827591 TTTTAAAATAT
1 TTTTAAAATAT
54827602 TTTTAAAATAT
1 TTTTAAAATAT
54827613 TTTT-AAAT-T
1 TTTTAAAATAT
54827622 TTTT---A-A-
1 TTTTAAAATAT
54827628 TTTTAAAATAT
1 TTTTAAAATAT
54827639 TTTTAAAATACT
1 TTTTAAAATA-T
54827651 TTTT
1 TTTT
54827655 TAATTTTTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
6 4 0.09
7 1 0.02
9 6 0.13
10 5 0.11
11 25 0.54
12 5 0.11
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:54827625 original size:37 final size:38
Alignment explanation
Indices: 54827584--54827662 Score: 142
Period size: 37 Copynumber: 2.1 Consensus size: 38
54827574 TTTTTTATTA
54827584 TTTTTAATTTTAAAATATTTTTAAAATA-TTTTTAAAT
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAAT
*
54827621 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTAAT
1 TTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAAT
54827659 TTTT
1 TTTT
54827663 AAAATAAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
37 28 0.70
38 12 0.30
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (38 bp):
TTTTTAATTTTAAAATATTTTTAAAATACTTTTTAAAT
Found at i:54827663 original size:37 final size:36
Alignment explanation
Indices: 54827563--54827664 Score: 141
Period size: 37 Copynumber: 2.7 Consensus size: 36
54827553 TATTTTTTAA
*
54827563 TTTTAAATTATTTTTTTATTATTTTTAATTTTAAAATAT
1 TTTTAAAATA-TTTTTTA--ATTTTTAATTTTAAAATAT
*
54827602 TTTTAAAATATTTTTAAATTTTTTAATTTTAAAATAT
1 TTTTAAAATATTTTTTAA-TTTTTAATTTTAAAATAT
54827639 TTTTAAAATACTTTTTTAATTTTTAA
1 TTTTAAAATA-TTTTTTAATTTTTAA
54827665 AATAAATTTT
Statistics
Matches: 58, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
36 1 0.02
37 35 0.60
38 13 0.22
39 9 0.16
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (36 bp):
TTTTAAAATATTTTTTAATTTTTAATTTTAAAATAT
Found at i:54827674 original size:20 final size:20
Alignment explanation
Indices: 54827637--54827675 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
54827627 ATTTTAAAAT
**
54827637 ATTTTTAAAATACTTTTTTA
1 ATTTTTAAAATAAATTTTTA
54827657 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
54827676 GGTATTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (20 bp):
ATTTTTAAAATAAATTTTTA
Done.