Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, 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: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 64 of 129
Found at i:12192066 original size:40 final size:39
Alignment explanation
Indices: 12191932--12192375 Score: 298
Period size: 40 Copynumber: 11.7 Consensus size: 39
12191922 TTAAAGGAGC
** *
12191932 CATTTAAAGTTCATTGCTTCTGGTGAGAA-GAGCCTTTTAA
1 CATTTAAAGTTTGTTGCCTCTGGTGA-AAGGAG-CTTTTAA
* * * *
12191972 CATTTAAAGTTTGTTGCCTTTGGTTAAAGTAGCTTTTGA
1 CATTTAAAGTTTGTTGCCTCTGGTGAAAGGAGCTTTTAA
12192011 -ATTTAAAGTTTGTTGCCTCTGGTGAAAGGAGCCTTTTAA
1 CATTTAAAGTTTGTTGCCTCTGGTGAAAGGAG-CTTTTAA
* * *
12192050 CATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTTGA
1 CATTTAAAGTTTGTTGCCTCTGGTGAAAGGAGCTTTTAA
* *
12192089 -ATTTAAAGTTTGTTGCCTCTGGTGAGAGAAGTCTTTTAA
1 CATTTAAAGTTTGTTGCCTCTGGTGAAAGGAG-CTTTTAA
** * *
12192128 CATTTAAAGTTTGAAGCCT-T--T--TA--A-CATTTAA
1 CATTTAAAGTTTGTTGCCTCTGGTGAAAGGAGCTTTTAA
* *** ** * *
12192159 AATTTGTTGCCT-TTG---AT--T-AAATGAGCTTTTCAA
1 CATTTAAAGTTTGTTGCCTCTGGTGAAAGGAGCTTTT-AA
* * * * *
12192192 CATTTAAAGTTTGTTACCTCTGGTTAGAGAAGCCTTTCAA
1 CATTTAAAGTTTGTTGCCTCTGGTGAAAGGAG-CTTTTAA
* * *
12192232 CATTTAAAGTTTGTTGCCTTTGGTTAAAAGAGCTTTTCAA
1 CATTTAAAGTTTGTTGCCTCTGGTGAAAGGAGCTTTT-AA
* * *
12192272 CATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGCCTTTCAA
1 CATTTAAAGTTTGTTGCCTCTGGTGAAAGGAG-CTTTTAA
* * *
12192312 CATTTAAAGTTTGTTACCT-TGGTTAAAGGAGCCTTTTGA
1 CATTTAAAGTTTGTTGCCTCTGGTGAAAGGAG-CTTTTAA
* **
12192351 -ATTTAAAATTCATTGCCTCTGGTGA
1 CATTTAAAGTTTGTTGCCTCTGGTGA
12192376 GAAAAGCCTT
Statistics
Matches: 318, Mismatches: 64, Indels: 45
0.74 0.15 0.11
Matches are distributed among these distances:
28 2 0.01
29 1 0.00
30 1 0.00
31 13 0.04
32 4 0.01
33 9 0.03
34 2 0.01
35 1 0.00
37 2 0.01
38 69 0.22
39 54 0.17
40 152 0.48
41 8 0.03
ACGTcount: A:0.26, C:0.13, G:0.19, T:0.41
Consensus pattern (39 bp):
CATTTAAAGTTTGTTGCCTCTGGTGAAAGGAGCTTTTAA
Found at i:12192157 original size:102 final size:104
Alignment explanation
Indices: 12192040--12192244 Score: 324
Period size: 104 Copynumber: 2.0 Consensus size: 104
12192030 TGGTGAAAGG
* * *
12192040 AGCCTTTTAACATTTAAAGTTTGTTGCCTTTGGTTAAAGGAGCTTTT-GA-ATTTAAAGTTTGTT
1 AGCCTTTTAACATTTAAAATTTGTTGCCTTTGATTAAAGGAGCTTTTCAACATTTAAAGTTTGTT
* * *
12192103 GCCTCTGGTGAGAGAAGTCTTTTAACATTTAAAGTTTGA
66 ACCTCTGGTGAGAGAAGCCTTTCAACATTTAAAGTTTGA
*
12192142 AGCCTTTTAACATTTAAAATTTGTTGCCTTTGATTAAATGAGCTTTTCAACATTTAAAGTTTGTT
1 AGCCTTTTAACATTTAAAATTTGTTGCCTTTGATTAAAGGAGCTTTTCAACATTTAAAGTTTGTT
*
12192207 ACCTCTGGTTAGAGAAGCCTTTCAACATTTAAAGTTTG
66 ACCTCTGGTGAGAGAAGCCTTTCAACATTTAAAGTTTG
12192245 TTGCCTTTGG
Statistics
Matches: 93, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
102 44 0.47
103 1 0.01
104 48 0.52
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.42
Consensus pattern (104 bp):
AGCCTTTTAACATTTAAAATTTGTTGCCTTTGATTAAAGGAGCTTTTCAACATTTAAAGTTTGTT
ACCTCTGGTGAGAGAAGCCTTTCAACATTTAAAGTTTGA
Found at i:12192172 original size:24 final size:24
Alignment explanation
Indices: 12192116--12192164 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
12192106 TCTGGTGAGA
* *
12192116 GAAGTCTTTTAACATTTAAAGTTT
1 GAAGCCTTTTAACATTTAAAATTT
12192140 GAAGCCTTTTAACATTTAAAATTT
1 GAAGCCTTTTAACATTTAAAATTT
12192164 G
1 G
12192165 TTGCCTTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (24 bp):
GAAGCCTTTTAACATTTAAAATTT
Found at i:12192234 original size:80 final size:80
Alignment explanation
Indices: 12192140--12192401 Score: 334
Period size: 80 Copynumber: 3.3 Consensus size: 80
12192130 TTTAAAGTTT
* * *
12192140 GAAGCCTTTTAACATTTAAAATTTGTTGCCTTTGATTAAATGAGCTTTTCAACATTTAAAGTTTG
1 GAAGCCTTTCAACATTTAAAATTTGTTGCCTTTGGTTAAAAGAGCTTTTCAACATTTAAAGTTTG
*
12192205 TTACCTCTGGTTAGA
66 TTGCCTCTGGTTAGA
*
12192220 GAAGCCTTTCAACATTTAAAGTTTGTTGCCTTTGGTTAAAAGAGCTTTTCAACATTTAAAGTTTG
1 GAAGCCTTTCAACATTTAAAATTTGTTGCCTTTGGTTAAAAGAGCTTTTCAACATTTAAAGTTTG
12192285 TTGCCTCTGGTTAGA
66 TTGCCTCTGGTTAGA
* * * * * * *
12192300 GGAGCCTTTCAACATTTAAAGTTTGTTACC-TTGGTTAAAGGAGCCTTTT-GA-ATTTAAAATTC
1 GAAGCCTTTCAACATTTAAAATTTGTTGCCTTTGGTTAAAAGAG-CTTTTCAACATTTAAAGTTT
* *
12192362 ATTGCCTCTGGTGAGA
65 GTTGCCTCTGGTTAGA
* * *
12192378 AAAGCCTTTTAA-ATTTAACATTTG
1 GAAGCCTTTCAACATTTAAAATTTG
12192402 CATAACCTCT
Statistics
Matches: 163, Mismatches: 18, Indels: 5
0.88 0.10 0.03
Matches are distributed among these distances:
77 10 0.06
78 32 0.20
79 13 0.08
80 108 0.66
ACGTcount: A:0.28, C:0.15, G:0.17, T:0.40
Consensus pattern (80 bp):
GAAGCCTTTCAACATTTAAAATTTGTTGCCTTTGGTTAAAAGAGCTTTTCAACATTTAAAGTTTG
TTGCCTCTGGTTAGA
Found at i:12192430 original size:120 final size:119
Alignment explanation
Indices: 12192141--12192435 Score: 316
Period size: 120 Copynumber: 2.5 Consensus size: 119
12192131 TTAAAGTTTG
* *
12192141 AAGCCTTTTAACATTTAAAATTTGTTGCCTTTGATTAAATGAG-CTTTTCAACATTTAAAGTTTG
1 AAGCCTTTTAACATTT-AAATTTGTTGCCTCTGATTAAAAGAGCCTTTTCAACATTTAAAGTTTG
* * ** * *
12192205 TTACCTCTGGTTAGAGAAGCCTTTCAACATTTAAAGTTTGTTGCCTTTGGTTAAA
65 TTACCTCTGGTTAAAGAAGCCTTTCAACATTTAAAATTCATTGCCTCTGGTGAAA
* * *
12192260 AGAG-CTTTTCAACATTTAAAGTTTGTTGCCTCTGGTTAGAGGAGCC-TTTCAACATTTAAAGTT
1 A-AGCCTTTT-AACATTTAAA-TTTGTTGCCTCTGATTAAAAGAGCCTTTTCAACATTTAAAGTT
* **
12192323 TGTTACCT-TGGTTAAAGGAGCCTTTTGA-ATTTAAAATTCATTGCCTCTGGTGAGAA
63 TGTTACCTCTGGTTAAAGAAGCCTTTCAACATTTAAAATTCATTGCCTCTGGTGA-AA
** *
12192379 AAGCCTTTTAA-ATTTAACATTTGCATAACCTCTGTTTAAAAGAGCCTTTTCAA-ATTT
1 AAGCCTTTTAACATTTAA-ATTTG--TTGCCTCTGATTAAAAGAGCCTTTTCAACATTT
12192436 TCTTTAAAAA
Statistics
Matches: 148, Mismatches: 18, Indels: 20
0.80 0.10 0.11
Matches are distributed among these distances:
117 10 0.07
118 25 0.17
119 53 0.36
120 59 0.40
121 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (119 bp):
AAGCCTTTTAACATTTAAATTTGTTGCCTCTGATTAAAAGAGCCTTTTCAACATTTAAAGTTTGT
TACCTCTGGTTAAAGAAGCCTTTCAACATTTAAAATTCATTGCCTCTGGTGAAA
Found at i:12193483 original size:12 final size:11
Alignment explanation
Indices: 12193449--12193483 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
12193439 GTTTCATAGG
*
12193449 TTTTTCCTTTT
1 TTTTTTCTTTT
12193460 TTTTTTCTTTT
1 TTTTTTCTTTT
*
12193471 TTTTTTCTATT
1 TTTTTTCTTTT
12193482 TT
1 TT
12193484 GATTTTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTCTTTT
Found at i:12195516 original size:76 final size:76
Alignment explanation
Indices: 12195390--12195537 Score: 251
Period size: 76 Copynumber: 1.9 Consensus size: 76
12195380 ATGGTCGTTG
**
12195390 CATCCCTTGCAAGTTAGTCCATACTTATTATCCTTTCCCTACCACTTCTTTAAGGGTTATCTTGG
1 CATCCCTTGCAAGTTAGTCCATACTTATTATCCTTTCCCTACCACTTCTTTAAGGGCCATCTTGG
12195455 AAGCTTTGTCA
66 AAGCTTTGTCA
* * *
12195466 CATCCCTTGCAAGTTAGTCCATACTTATTGTCTTTTCCTTACCACTTCTTTAAGGGCCATCTTGG
1 CATCCCTTGCAAGTTAGTCCATACTTATTATCCTTTCCCTACCACTTCTTTAAGGGCCATCTTGG
12195531 AAGCTTT
66 AAGCTTT
12195538 AGATAGACAT
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 67 1.00
ACGTcount: A:0.20, C:0.26, G:0.14, T:0.40
Consensus pattern (76 bp):
CATCCCTTGCAAGTTAGTCCATACTTATTATCCTTTCCCTACCACTTCTTTAAGGGCCATCTTGG
AAGCTTTGTCA
Found at i:12201186 original size:28 final size:28
Alignment explanation
Indices: 12201152--12201208 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
12201142 TGGAATTTAT
*
12201152 AGAAAA-TCACTATTTAAAAAATATTTCG
1 AGAAAATTCACCATTTAAAAAAT-TTTCG
* *
12201180 AGAAAATTGACCATTTACAAAATTTTCG
1 AGAAAATTCACCATTTAAAAAATTTTCG
12201208 A
1 A
12201209 AATCTTGTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 12 0.48
29 13 0.52
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (28 bp):
AGAAAATTCACCATTTAAAAAATTTTCG
Found at i:12202639 original size:19 final size:18
Alignment explanation
Indices: 12202611--12202647 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
12202601 TTATTACTAG
12202611 TAATAATATAAAATAATAA
1 TAATAATATAAAA-AATAA
*
12202630 TAATATTATAAAAAATAA
1 TAATAATATAAAAAATAA
12202648 CATAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
TAATAATATAAAAAATAA
Found at i:12202654 original size:11 final size:11
Alignment explanation
Indices: 12202640--12202676 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12202630 TAATATTATA
12202640 AAAAATAACAT
1 AAAAATAACAT
12202651 AAAAATAACAT
1 AAAAATAACAT
*
12202662 -AGAATAA-AT
1 AAAAATAACAT
12202671 AAAAAT
1 AAAAAT
12202677 CAAAATCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
9 2 0.09
10 10 0.43
11 11 0.48
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.19
Consensus pattern (11 bp):
AAAAATAACAT
Found at i:12202890 original size:18 final size:20
Alignment explanation
Indices: 12202856--12202895 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
12202846 TTTTTTCTTT
12202856 CCCCAGAGCCTCTCTCTCTA
1 CCCCAGAGCCTCTCTCTCTA
12202876 CCCCAGAGCCTCTCTCTCTA
1 CCCCAGAGCCTCTCTCTCTA
12202896 AAAACTCAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.50, G:0.10, T:0.25
Consensus pattern (20 bp):
CCCCAGAGCCTCTCTCTCTA
Found at i:12208535 original size:4 final size:4
Alignment explanation
Indices: 12208526--12208552 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
12208516 TTCAAATCGA
12208526 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
12208553 ACAAGTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:12209633 original size:16 final size:16
Alignment explanation
Indices: 12209612--12209642 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
12209602 TTACACATAA
12209612 GTAGTGTTTGGTATAG
1 GTAGTGTTTGGTATAG
12209628 GTAGTGTTTGGTATA
1 GTAGTGTTTGGTATA
12209643 AGGTGATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.45
Consensus pattern (16 bp):
GTAGTGTTTGGTATAG
Found at i:12210769 original size:16 final size:17
Alignment explanation
Indices: 12210736--12210772 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
12210726 ACATATTCTC
*
12210736 AACATTTTGAACAATAA
1 AACACTTTGAACAATAA
12210753 AACACTTTGAA-AATAA
1 AACACTTTGAACAATAA
12210769 AACA
1 AACA
12210773 GATTGTCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.57, C:0.14, G:0.05, T:0.24
Consensus pattern (17 bp):
AACACTTTGAACAATAA
Found at i:12213140 original size:22 final size:22
Alignment explanation
Indices: 12213114--12213158 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
12213104 CTGTATATTT
*
12213114 ATATTTGTATCTCTAGAATTAA
1 ATATTTGTATCCCTAGAATTAA
12213136 ATATTTGTATCCCTAGAATTAA
1 ATATTTGTATCCCTAGAATTAA
12213158 A
1 A
12213159 GAAGATTTAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (22 bp):
ATATTTGTATCCCTAGAATTAA
Found at i:12217012 original size:22 final size:22
Alignment explanation
Indices: 12216986--12217029 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12216976 TGTATATTTA
**
12216986 TATTTGTATCTTTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
12217008 TATTTGTATCCCTAGAATTAAG
1 TATTTGTATCCCTAGAATTAAG
12217030 GAAGATTTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCCTAGAATTAAG
Found at i:12223304 original size:83 final size:83
Alignment explanation
Indices: 12223207--12223371 Score: 312
Period size: 83 Copynumber: 2.0 Consensus size: 83
12223197 TTAAAACATA
* *
12223207 ATTTAACTTAATGTATTTTATTATTTGGCTAGTCGAAAAAATTAATCGAACCGATCGAATTAATT
1 ATTTAACTTAATGTATTTTATTATTTGACTAATCGAAAAAATTAATCGAACCGATCGAATTAATT
12223272 TTGATCAATCAATTTTTT
66 TTGATCAATCAATTTTTT
12223290 ATTTAACTTAATGTATTTTATTATTTGACTAATCGAAAAAATTAATCGAACCGATCGAATTAATT
1 ATTTAACTTAATGTATTTTATTATTTGACTAATCGAAAAAATTAATCGAACCGATCGAATTAATT
12223355 TTGATCAATCAATTTTT
66 TTGATCAATCAATTTTT
12223372 GAAATTAAAA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 80 1.00
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (83 bp):
ATTTAACTTAATGTATTTTATTATTTGACTAATCGAAAAAATTAATCGAACCGATCGAATTAATT
TTGATCAATCAATTTTTT
Found at i:12223706 original size:29 final size:30
Alignment explanation
Indices: 12223650--12223708 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
12223640 AAACTTAACA
12223650 AAATTGAAAGTATCAATAACAAAATCAATG
1 AAATTGAAAGTATCAATAACAAAATCAATG
*
12223680 AAATTG-AAGTAT-AATGACAAAATTCAATG
1 AAATTGAAAGTATCAATAACAAAA-TCAATG
12223709 TGTCAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.33
29 12 0.44
30 6 0.22
ACGTcount: A:0.54, C:0.08, G:0.12, T:0.25
Consensus pattern (30 bp):
AAATTGAAAGTATCAATAACAAAATCAATG
Found at i:12224997 original size:18 final size:18
Alignment explanation
Indices: 12224974--12225014 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
12224964 GTTCATTTAT
*
12224974 AAAAACACAATTCAATTG
1 AAAAACACAATTCAATTC
* *
12224992 AAAAACATAATTCGATTC
1 AAAAACACAATTCAATTC
12225010 AAAAA
1 AAAAA
12225015 TAACTCTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.59, C:0.15, G:0.05, T:0.22
Consensus pattern (18 bp):
AAAAACACAATTCAATTC
Found at i:12226390 original size:20 final size:20
Alignment explanation
Indices: 12226365--12226414 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
12226355 AAAATAAAAC
12226365 ATTTGAATGCTAAACCAAGA
1 ATTTGAATGCTAAACCAAGA
* * *
12226385 ATTTGAATTCTCAACCAAGC
1 ATTTGAATGCTAAACCAAGA
12226405 ATTTGAATGC
1 ATTTGAATGC
12226415 CCTTTTGTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (20 bp):
ATTTGAATGCTAAACCAAGA
Found at i:12226816 original size:15 final size:15
Alignment explanation
Indices: 12226796--12226826 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
12226786 GCGAACCACG
12226796 TATGTCTTTGTGTTC
1 TATGTCTTTGTGTTC
12226811 TATGTCTTTGTGTTC
1 TATGTCTTTGTGTTC
12226826 T
1 T
12226827 TATCTTCTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.06, C:0.13, G:0.19, T:0.61
Consensus pattern (15 bp):
TATGTCTTTGTGTTC
Found at i:12229391 original size:23 final size:23
Alignment explanation
Indices: 12229361--12229406 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
12229351 CTCATTTGGC
12229361 ATGTTTTGGATAATTTTCTTATT
1 ATGTTTTGGATAATTTTCTTATT
*
12229384 ATGTTTTGGATAATTTTTTTATT
1 ATGTTTTGGATAATTTTCTTATT
12229407 TTAGATTATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.02, G:0.13, T:0.63
Consensus pattern (23 bp):
ATGTTTTGGATAATTTTCTTATT
Found at i:12230082 original size:61 final size:59
Alignment explanation
Indices: 12229975--12230091 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 59
12229965 TATATACATG
* * * *
12229975 ATCCATGCATTAAAGTTTGCATTTTTATTAATGGCATTTTTGTAATTTTTTGTTACATTAT
1 ATCCATGCATCAAAATTTGCATTTTTATCAATGGCATTTATGTAA--TTTTGTTACATTAT
12230036 ATCCATGCATCAAAATTTGCATTTTTATCAATGGCATCTTAT-TAATTTTGTTACAT
1 ATCCATGCATCAAAATTTGCATTTTTATCAATGGCAT-TTATGTAATTTTGTTACAT
12230092 GCATCAAAGT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
59 11 0.22
61 37 0.73
62 3 0.06
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (59 bp):
ATCCATGCATCAAAATTTGCATTTTTATCAATGGCATTTATGTAATTTTGTTACATTAT
Found at i:12230184 original size:7 final size:7
Alignment explanation
Indices: 12230156--12230272 Score: 54
Period size: 7 Copynumber: 17.4 Consensus size: 7
12230146 TTTTTCCATG
12230156 AAACCCT
1 AAACCCT
12230163 AAA-CC-
1 AAACCCT
*
12230168 AAACAC-
1 AAACCCT
12230174 AAACCCT
1 AAACCCT
*
12230181 AAACGCT
1 AAACCCT
*
12230188 AAATCCTT
1 AAA-CCCT
12230196 AAA--CT
1 AAACCCT
*
12230201 AAACCTT
1 AAACCCT
12230208 AAACCCT
1 AAACCCT
*
12230215 AAACCAT
1 AAACCCT
*
12230222 AAA-CTT
1 AAACCCT
*
12230228 AAA-CAT
1 AAACCCT
12230234 AAACACCCT
1 -AA-ACCCT
*
12230243 AAAACCAT
1 -AAACCCT
12230251 AAACCCT
1 AAACCCT
12230258 -AA-CCT
1 AAACCCT
*
12230263 AGACCCT
1 AAACCCT
12230270 AAA
1 AAA
12230273 ACCAAAACCT
Statistics
Matches: 84, Mismatches: 16, Indels: 20
0.70 0.13 0.17
Matches are distributed among these distances:
5 10 0.12
6 18 0.21
7 41 0.49
8 10 0.12
9 5 0.06
ACGTcount: A:0.50, C:0.32, G:0.02, T:0.16
Consensus pattern (7 bp):
AAACCCT
Found at i:12230210 original size:27 final size:27
Alignment explanation
Indices: 12230156--12230313 Score: 82
Period size: 27 Copynumber: 5.8 Consensus size: 27
12230146 TTTTTCCATG
12230156 AAACCCTAAACCA-AACAC--AAACCCT
1 AAACCCTAAACCATAA-ACTTAAACCCT
* * *
12230181 AAACGCTAAATCCTTAAAC-TAAACCTT
1 AAACCCTAAA-CCATAAACTTAAACCCT
*
12230208 AAACCCTAAACCATAAACTTAAA-CAT
1 AAACCCTAAACCATAAACTTAAACCCT
*
12230234 AAACACCCTAAAACCATAAACCCT-AA-CCT
1 -AA-ACCCT-AAACCATAAA-CTTAAACCCT
* *
12230263 AGACCCTAAAACCA-AAACCTT-AACCCA
1 AAACCCT-AAACCATAAA-CTTAAACCCT
**
12230290 AAACTTTAAAACCATAAATCTTAA
1 AAACCCT-AAACCATAAA-CTTAA
12230314 CTTAGACCCT
Statistics
Matches: 107, Mismatches: 15, Indels: 18
0.76 0.11 0.13
Matches are distributed among these distances:
25 9 0.08
26 21 0.20
27 48 0.45
28 12 0.11
29 15 0.14
30 2 0.02
ACGTcount: A:0.50, C:0.31, G:0.01, T:0.18
Consensus pattern (27 bp):
AAACCCTAAACCATAAACTTAAACCCT
Found at i:12239576 original size:24 final size:25
Alignment explanation
Indices: 12239549--12239613 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
12239539 TCATATTGAT
* *
12239549 TATAATTATTATAATAT-TTTTTAC
1 TATAATTATAAAAATATATTTTTAC
12239573 TATAATTATAAAAATATATTTTTTA-
1 TATAATTATAAAAATATA-TTTTTAC
12239598 TCATAATTAATAAAAA
1 T-ATAATT-ATAAAAA
12239614 ATTTTATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
24 15 0.43
25 1 0.03
26 12 0.34
27 7 0.20
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (25 bp):
TATAATTATAAAAATATATTTTTAC
Found at i:12239603 original size:26 final size:27
Alignment explanation
Indices: 12239562--12239613 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
12239552 AATTATTATA
12239562 ATATTTTTTACTATAATT-ATAAAAAT
1 ATATTTTTTACTATAATTAATAAAAAT
12239588 ATATTTTTTA-TCATAATTAATAAAAA
1 ATATTTTTTACT-ATAATTAATAAAAA
12239614 ATTTTATAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 1 0.04
26 16 0.67
27 7 0.29
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (27 bp):
ATATTTTTTACTATAATTAATAAAAAT
Found at i:12239617 original size:24 final size:24
Alignment explanation
Indices: 12239549--12239618 Score: 63
Period size: 26 Copynumber: 2.8 Consensus size: 24
12239539 TCATATTGAT
* * *
12239549 TATAATTATTATAATATTTTTTAC
1 TATAATTAATAAAAAATTTTTTAC
12239573 TATAATT-ATAAAAATATATTTTTTA-
1 TATAATTAAT-AAAA-A-ATTTTTTAC
12239598 TCATAATTAATAAAAAATTTT
1 T-ATAATTAATAAAAAATTTT
12239619 ATAATACTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
23 1 0.03
24 15 0.39
25 2 0.05
26 18 0.47
27 2 0.05
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (24 bp):
TATAATTAATAAAAAATTTTTTAC
Found at i:12243969 original size:32 final size:31
Alignment explanation
Indices: 12243933--12244048 Score: 99
Period size: 32 Copynumber: 3.6 Consensus size: 31
12243923 AATCCCTTTC
12243933 AAAAAATTCTATATCATTTTGAAAAATTAAAT
1 AAAAAATTCTATATCATTTT-AAAAATTAAAT
* * * *
12243965 AAAAATTTTTATATGGATTTAAAAAATTAAAT
1 AAAAAATTCTATAT-CATTTTAAAAATTAAAT
* * *
12243997 AGAAAACTTC-ATATCAGTTTAAAATATTAAGT
1 A-AAAAATTCTATATCATTTTAAAA-ATTAAAT
* * *
12244029 AAATAGTTCCATATCATTTT
1 AAAAAATTCTATATCATTTT
12244049 TTAAAAATAG
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
31 13 0.19
32 44 0.66
33 10 0.15
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (31 bp):
AAAAAATTCTATATCATTTTAAAAATTAAAT
Found at i:12244084 original size:20 final size:19
Alignment explanation
Indices: 12244059--12244098 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
12244049 TTAAAAATAG
12244059 ATTTATTAATCTATCCAAAA
1 ATTTATTAATCTAT-CAAAA
**
12244079 ATTTATTTTTCTATCAAAA
1 ATTTATTAATCTATCAAAA
12244098 A
1 A
12244099 AGTCTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTATTAATCTATCAAAA
Found at i:12244106 original size:21 final size:20
Alignment explanation
Indices: 12244068--12244107 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12244058 GATTTATTAA
* *
12244068 TCTATCCAAAAATTTATTTT
1 TCTATCAAAAAATCTATTTT
12244088 TCTATCAAAAAAGTCTATTT
1 TCTATCAAAAAA-TCTATTT
12244108 AAAACATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (20 bp):
TCTATCAAAAAATCTATTTT
Found at i:12244313 original size:29 final size:31
Alignment explanation
Indices: 12244244--12244354 Score: 127
Period size: 31 Copynumber: 3.6 Consensus size: 31
12244234 TTTATAAATA
* **
12244244 TAAAATGATTTGAAATTTTTACTTAACATTT
1 TAAAATGATATGAAATTTTTACTTAATTTTT
* * *
12244275 TAAAAAGATATGAAGTTTTTA-TTTA-TTTT
1 TAAAATGATATGAAATTTTTACTTAATTTTT
* *
12244304 TAAATTGATATAAAATTTTTACTTAATTTTT
1 TAAAATGATATGAAATTTTTACTTAATTTTT
*
12244335 TAAAATGATAAGAAATTTTT
1 TAAAATGATATGAAATTTTT
12244355 TTTCAAAAGA
Statistics
Matches: 65, Mismatches: 13, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
29 20 0.31
30 6 0.09
31 39 0.60
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.50
Consensus pattern (31 bp):
TAAAATGATATGAAATTTTTACTTAATTTTT
Found at i:12258165 original size:32 final size:31
Alignment explanation
Indices: 12258129--12258244 Score: 99
Period size: 32 Copynumber: 3.6 Consensus size: 31
12258119 AATCCCTTTC
12258129 AAAAAATTCTATATCATTTTGAAAAATTAAAT
1 AAAAAATTCTATATCATTTT-AAAAATTAAAT
* * * *
12258161 AAAAATTTTTATATGGATTTAAAAAATTAAAT
1 AAAAAATTCTATAT-CATTTTAAAAATTAAAT
* * *
12258193 AGAAAACTTC-ATATCAGTTTAAAATATTAAGT
1 A-AAAAATTCTATATCATTTTAAAA-ATTAAAT
* * *
12258225 AAATAGTTCCATATCATTTT
1 AAAAAATTCTATATCATTTT
12258245 TTAAAAATAG
Statistics
Matches: 67, Mismatches: 13, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
31 13 0.19
32 44 0.66
33 10 0.15
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.39
Consensus pattern (31 bp):
AAAAAATTCTATATCATTTTAAAAATTAAAT
Found at i:12258280 original size:20 final size:19
Alignment explanation
Indices: 12258255--12258294 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
12258245 TTAAAAATAG
12258255 ATTTATTAATCTATCCAAAA
1 ATTTATTAATCTAT-CAAAA
**
12258275 ATTTATTTTTCTATCAAAA
1 ATTTATTAATCTATCAAAA
12258294 A
1 A
12258295 AGTCTATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTATTAATCTATCAAAA
Found at i:12258302 original size:21 final size:20
Alignment explanation
Indices: 12258264--12258303 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
12258254 GATTTATTAA
* *
12258264 TCTATCCAAAAATTTATTTT
1 TCTATCAAAAAATCTATTTT
12258284 TCTATCAAAAAAGTCTATTT
1 TCTATCAAAAAA-TCTATTT
12258304 AAAACATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.38, C:0.15, G:0.03, T:0.45
Consensus pattern (20 bp):
TCTATCAAAAAATCTATTTT
Found at i:12258505 original size:30 final size:31
Alignment explanation
Indices: 12258440--12258552 Score: 129
Period size: 31 Copynumber: 3.6 Consensus size: 31
12258430 TTTATAAATA
* **
12258440 TAAAATGATTTGAAATTTTTTACTTAACATTT
1 TAAAATGATATGAAA-TTTTTACTTAATTTTT
* * *
12258472 TAAAAAGATATGAAGTTTTTA-TTTATTTTT
1 TAAAATGATATGAAATTTTTACTTAATTTTT
* *
12258502 TAAATTGATATAAAATTTTTACTTAATTTTT
1 TAAAATGATATGAAATTTTTACTTAATTTTT
*
12258533 TAAAATGATAAGAAATTTTT
1 TAAAATGATATGAAATTTTT
12258553 TTTCAAAAGA
Statistics
Matches: 66, Mismatches: 14, Indels: 3
0.80 0.17 0.04
Matches are distributed among these distances:
30 23 0.35
31 31 0.47
32 12 0.18
ACGTcount: A:0.40, C:0.03, G:0.07, T:0.50
Consensus pattern (31 bp):
TAAAATGATATGAAATTTTTACTTAATTTTT
Found at i:12270166 original size:74 final size:73
Alignment explanation
Indices: 12270031--12270220 Score: 185
Period size: 73 Copynumber: 2.6 Consensus size: 73
12270021 GGTGTGATAG
* * ***
12270031 CATTTTTAAGAT-AAAAATATA-ATGGATAC-TGAAATTATA-TTTTAAAAATTTTAAAATTTTA
1 CATTTTTAAGATAAAAAACATAGA-GGAT-CTTGAAACTATATTTTTTTTAATTTTAAAATTTTA
*
12270092 ACAAAGACCC
64 ACAAAAACCC
*
12270102 CATTTTTAAGATAATAAAACATAGTA-GATCTTGAAACTTTATTTTTTTTAATTTTGAAAA-TTT
1 CATTTTTAAGATAA-AAAACATAG-AGGATCTTGAAACTATATTTTTTTTAATTTT-AAAATTTT
**
12270165 AACAAAAACTG
63 AACAAAAACCC
* * *
12270176 TATTTTTAAGATAAAAAATATAGAGGATGTTGAAACTATATTTTT
1 CATTTTTAAGATAAAAAACATAGAGGATCTTGAAACTATATTTTT
12270221 GAAATATTAG
Statistics
Matches: 98, Mismatches: 13, Indels: 14
0.78 0.10 0.11
Matches are distributed among these distances:
71 12 0.12
72 3 0.03
73 44 0.45
74 34 0.35
75 5 0.05
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.40
Consensus pattern (73 bp):
CATTTTTAAGATAAAAAACATAGAGGATCTTGAAACTATATTTTTTTTAATTTTAAAATTTTAAC
AAAAACCC
Found at i:12270253 original size:71 final size:71
Alignment explanation
Indices: 12270033--12270421 Score: 285
Period size: 71 Copynumber: 5.4 Consensus size: 71
12270023 TGTGATAGCA
** * **
12270033 TTTTTAAGAT-AAAAATATA-ATGGATACTGAAATTATATTTTAAAAATTTTAAAATTTTAACAA
1 TTTTTAAGATAAAAAATATAGA-GGATGTTGAAACTATATTTTTGAAA-TTTAAAATTTTAACAA
****
12270096 AGACCCCA
64 AGACTGTG
* * * * *
12270104 TTTTTAAGATAATAAAACATAGTA-GATCTTGAAACTTTATTTTTTTTAATTTTGAAAA-TTTAA
1 TTTTTAAGATAA-AAAATATAG-AGGATGTTGAAAC--TATATTTTTGAAATTT-AAAATTTTAA
* *
12270167 CAAAAACTGTA
61 CAAAGACTGTG
*
12270178 TTTTTAAGATAAAAAATATAGAGGATGTTGAAACTATATTTTTGAAATATT-AGATTTTAACAAA
1 TTTTTAAGATAAAAAATATAGAGGATGTTGAAACTATATTTTTGAAAT-TTAAAATTTTAACAAA
*
12270242 GATTGCT-
65 GACTG-TG
* * * * * * * *
12270249 TTTTTAATATAAAAAGTATAGTGGATATTGAAACTTTATTTTCGAGATTCTAGAATTTTAACAAA
1 TTTTTAAGATAAAAAATATAGAGGATGTTGAAACTATATTTTTGAAATT-TAAAATTTTAACAAA
*
12270314 GAATGTG
65 GACTGTG
* *
12270321 TTTTTAAGATAAAACCA-A-AGTA-GATGTTAAAACTATATTTTTGAAATTTAAAAATTTTAACA
1 TTTTTAAGATAAAA-AATATAG-AGGATGTTGAAACTATATTTTTGAAATTT-AAAATTTTAACA
*
12270383 AA-AATCGTG
63 AAGACT-GTG
* * *
12270392 TTTTTAAGATAAACAACATAGTGGATGTTG
1 TTTTTAAGATAAAAAATATAGAGGATGTTG
12270422 CTACTCATAA
Statistics
Matches: 253, Mismatches: 44, Indels: 41
0.75 0.13 0.12
Matches are distributed among these distances:
70 8 0.03
71 129 0.51
72 42 0.17
73 33 0.13
74 27 0.11
75 14 0.06
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (71 bp):
TTTTTAAGATAAAAAATATAGAGGATGTTGAAACTATATTTTTGAAATTTAAAATTTTAACAAAG
ACTGTG
Found at i:12270479 original size:102 final size:101
Alignment explanation
Indices: 12270348--12270559 Score: 343
Period size: 102 Copynumber: 2.1 Consensus size: 101
12270338 AAGTAGATGT
* * *
12270348 TAAAACTATATTTTTGAAATTTAAAAATTTTAACAAAAATCGTGTTTTTAAGATAAACAACATAG
1 TAAAA-TATATTTTTGAAATTTAAAAATTTTAACAAAAATCATGTTTTTAAAATAAACAACATAA
* *
12270413 TGGATGTTGCTACTCATAACAAAATTAAAATAAAACG
65 TGGATATTGCTACTCATAACAAAAGTAAAATAAAACG
*
12270450 TAAAATATATTTATTGAAATTTAAAAATTTTAACAAAAATCATGTTTTTAAAATAAACAATATAA
1 TAAAATATATTT-TTGAAATTTAAAAATTTTAACAAAAATCATGTTTTTAAAATAAACAACATAA
*
12270515 TGGATATTGCTAGTCATAACAAAAGTAAAATAAAACG
65 TGGATATTGCTACTCATAACAAAAGTAAAATAAAACG
12270552 TAAAATAT
1 TAAAATAT
12270560 CTTACTGAAT
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 7 0.07
102 95 0.93
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.33
Consensus pattern (101 bp):
TAAAATATATTTTTGAAATTTAAAAATTTTAACAAAAATCATGTTTTTAAAATAAACAACATAAT
GGATATTGCTACTCATAACAAAAGTAAAATAAAACG
Found at i:12271461 original size:90 final size:90
Alignment explanation
Indices: 12271359--12271535 Score: 345
Period size: 90 Copynumber: 2.0 Consensus size: 90
12271349 AAAAGTGAGG
12271359 GAAAAAAAAAGGAAATTTTATACCAAGCAAGGAATAACATAGTTTTCACTTAAAGTTTCTTTGCA
1 GAAAAAAAAAGGAAATTTTATACCAAGCAAGGAATAACATAGTTTTCACTTAAAGTTTCTTTGCA
12271424 AACTCATGGCCTGACCCTACTAGAA
66 AACTCATGGCCTGACCCTACTAGAA
*
12271449 GAAAAAAAAAGGAAATTTTATACCAAGCAAGGAATAACATAGTTTTCTCTTAAAGTTTCTTTGCA
1 GAAAAAAAAAGGAAATTTTATACCAAGCAAGGAATAACATAGTTTTCACTTAAAGTTTCTTTGCA
12271514 AACTCATGGCCTGACCCTACTA
66 AACTCATGGCCTGACCCTACTA
12271536 AATTTGTACG
Statistics
Matches: 86, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
90 86 1.00
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (90 bp):
GAAAAAAAAAGGAAATTTTATACCAAGCAAGGAATAACATAGTTTTCACTTAAAGTTTCTTTGCA
AACTCATGGCCTGACCCTACTAGAA
Found at i:12271700 original size:13 final size:13
Alignment explanation
Indices: 12271682--12271741 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
12271672 TTTTTAGATA
12271682 ATTTATTTTCATT
1 ATTTATTTTCATT
12271695 ATTTA-TTTCAATT
1 ATTTATTTTC-ATT
12271708 ATTTATCTTT-ATTT
1 ATTTAT-TTTCA-TT
* *
12271722 TTTTATTTTTTATT
1 ATTTA-TTTTCATT
12271736 ATTTAT
1 ATTTAT
12271742 ACTTGGTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
12 4 0.10
13 15 0.38
14 15 0.38
15 5 0.13
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTATTTTCATT
Found at i:12271830 original size:22 final size:23
Alignment explanation
Indices: 12271805--12271847 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12271795 ATTTGTTTAT
* *
12271805 TTAATT-TGTAAAAATTAATTTG
1 TTAATTATATAAAAAATAATTTG
12271827 TTAATTATATAAAAAATAATT
1 TTAATTATATAAAAAATAATT
12271848 AGTAACAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (23 bp):
TTAATTATATAAAAAATAATTTG
Found at i:12273336 original size:13 final size:13
Alignment explanation
Indices: 12273318--12273377 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
12273308 TTTTTAGATA
12273318 ATTTATTTTCATT
1 ATTTATTTTCATT
12273331 ATTTA-TTTCAATT
1 ATTTATTTTC-ATT
12273344 ATTTATCTTT-ATTT
1 ATTTAT-TTTCA-TT
* *
12273358 TTTTATTTTTTATT
1 ATTTA-TTTTCATT
12273372 ATTTAT
1 ATTTAT
12273378 ACTTGGTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
12 4 0.10
13 15 0.38
14 15 0.38
15 5 0.13
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTATTTTCATT
Found at i:12273466 original size:22 final size:22
Alignment explanation
Indices: 12273441--12273482 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12273431 ATTTGTTTAT
*
12273441 TTAATT-TGTAAAAATTAATTTG
1 TTAATTATATAAAAA-TAATTTG
12273463 TTAATTATATAAAAATAATT
1 TTAATTATATAAAAATAATT
12273483 AGTAACAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (22 bp):
TTAATTATATAAAAATAATTTG
Found at i:12274976 original size:13 final size:13
Alignment explanation
Indices: 12274958--12275016 Score: 59
Period size: 13 Copynumber: 4.5 Consensus size: 13
12274948 TTTTTAGATA
12274958 ATTTATTTTCATT
1 ATTTATTTTCATT
12274971 ATTTA-TTTCAATT
1 ATTTATTTTC-ATT
12274984 ATTTATCTTT-ATT
1 ATTTAT-TTTCATT
* *
12274997 TTTTATTTTTTATT
1 ATTTA-TTTTCATT
12275011 ATTTAT
1 ATTTAT
12275017 ACTTGGTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
12 4 0.10
13 24 0.62
14 8 0.21
15 3 0.08
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTTATTTTCATT
Found at i:12275105 original size:22 final size:23
Alignment explanation
Indices: 12275080--12275122 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12275070 ATTTGTTTAT
* *
12275080 TTAATT-TGTAAAAATTAATTTG
1 TTAATTATATAAAAAATAATTTG
12275102 TTAATTATATAAAAAATAATT
1 TTAATTATATAAAAAATAATT
12275123 AGTAACAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (23 bp):
TTAATTATATAAAAAATAATTTG
Found at i:12276603 original size:13 final size:13
Alignment explanation
Indices: 12276585--12276644 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
12276575 TTTTTAGATA
12276585 ATTTATTTTCATT
1 ATTTATTTTCATT
12276598 ATTTA-TTTCAATT
1 ATTTATTTTC-ATT
12276611 ATTTATCTTT-ATTT
1 ATTTAT-TTTCA-TT
* *
12276625 TTTTATTTTTTATT
1 ATTTA-TTTTCATT
12276639 ATTTAT
1 ATTTAT
12276645 ACTTGGTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
12 4 0.10
13 15 0.38
14 15 0.38
15 5 0.13
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (13 bp):
ATTTATTTTCATT
Found at i:12276733 original size:22 final size:23
Alignment explanation
Indices: 12276708--12276750 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12276698 ATTTGTTTAT
* *
12276708 TTAATT-TGTAAAAATTAATTTG
1 TTAATTATATAAAAAATAATTTG
12276730 TTAATTATATAAAAAATAATT
1 TTAATTATATAAAAAATAATT
12276751 AGTAACAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.47
Consensus pattern (23 bp):
TTAATTATATAAAAAATAATTTG
Found at i:12277518 original size:58 final size:57
Alignment explanation
Indices: 12277418--12277568 Score: 180
Period size: 57 Copynumber: 2.6 Consensus size: 57
12277408 TTTTACAAGG
* * *
12277418 ACTATGTTTTTTAAATGGAAACATGGTTTTTAATTGACAAAAAAATTATTGTACAAAA
1 ACTATGTTTTTAAAATGAAAACATGGTTTTTAATTG-CAAAAAAATAATTGTACAAAA
*
12277476 ACTATGTTTCTTAAAATGAAAACATGGTTTTTAATTG-AAAAAAATAATTGTACAAAG
1 ACTATGTTT-TTAAAATGAAAACATGGTTTTTAATTGCAAAAAAATAATTGTACAAAA
* * * *
12277533 ACTACT-TGTTTAAAGTACAAAACGTGGTTTTTAATT
1 ACTA-TGTTTTTAAAAT-GAAAACATGGTTTTTAATT
12277569 AAAATTTTGA
Statistics
Matches: 82, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
56 6 0.07
57 41 0.50
58 10 0.12
59 25 0.30
ACGTcount: A:0.42, C:0.08, G:0.13, T:0.38
Consensus pattern (57 bp):
ACTATGTTTTTAAAATGAAAACATGGTTTTTAATTGCAAAAAAATAATTGTACAAAA
Found at i:12277771 original size:113 final size:110
Alignment explanation
Indices: 12277596--12277881 Score: 344
Period size: 113 Copynumber: 2.6 Consensus size: 110
12277586 ATTATTATAG
* ** *
12277596 AAAAATTATTATACAAAGACTATAGATTTTAAA-TGGAAGTGTGCTCTTTAATTGAAAAAAAATT
1 AAAAATTATTATACAAAGACTACATTTTTTAAAGTGGAAATGTG-TCTTTAATTGAAAAAAAATT
* * * *
12277660 GTATAAAGACTGA-GTTTTTTAAAGTTAAAACGTGGTCTTTAATTGAA
65 GTACAAAGACT-ACATTTTTTAAAATGAAAACGTGGTCTTTAATT-AA
* * *
12277707 AAAAATTACTATACAAAGATTACATTTTTTTAAAGTGGAAATGTAGTCTTTAATTGAAAGAAAAT
1 AAAAATTATTATACAAAGACTACA-TTTTTTAAAGTGGAAATGT-GTCTTTAATTGAAAAAAAAT
*
12277772 TGTACAAAGACTACATTTTTTAAAATGAAAATGTGGTCTTTAATTAA
64 TGTACAAAGACTACATTTTTTAAAATGAAAACGTGGTCTTTAATTAA
* * * *
12277819 AAATATTATTATACAAAGACTACGTTTCTTAAAGTGAAAACATG-GTCTTTAATTGAAAAAAAA
1 AAAAATTATTATACAAAGACTACATTTTTTAAAGTG-GAA-ATGTGTCTTTAATTGAAAAAAAA
12277882 AAGAGTTATT
Statistics
Matches: 150, Mismatches: 19, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
111 50 0.33
112 32 0.21
113 67 0.45
114 1 0.01
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.35
Consensus pattern (110 bp):
AAAAATTATTATACAAAGACTACATTTTTTAAAGTGGAAATGTGTCTTTAATTGAAAAAAAATTG
TACAAAGACTACATTTTTTAAAATGAAAACGTGGTCTTTAATTAA
Found at i:12277787 original size:56 final size:55
Alignment explanation
Indices: 12277603--12277880 Score: 271
Period size: 56 Copynumber: 5.0 Consensus size: 55
12277593 TAGAAAAATT
* * * * *
12277603 ATTATACAAAGACTATAG-ATTTTAAA-TGGAAGTGTGCTCTTTAATTGAAAAAAA
1 ATTATACAAAGACTACAGTTTTTTAAAGTGAAAATGTGGTCTTTAATTG-AAAAAA
* * * * *
12277657 ATTGTATAAAGACT-GAGTTTTTTAAAGTTAAAACGTGGTCTTTAATTGAAAAAA
1 ATTATACAAAGACTACAGTTTTTTAAAGTGAAAATGTGGTCTTTAATTGAAAAAA
* * * *
12277711 ATTACTATACAAAGATTACATTTTTTTAAAGTGGAAATGTAGTCTTTAATTGAAAGAAA
1 A-T--TATACAAAGACTACAGTTTTTTAAAGTGAAAATGTGGTCTTTAATTGAAA-AAA
* *
12277770 ATTGTACAAAGACTACA-TTTTTTAAAATGAAAATGTGGTCTTTAATT-AAAAATA
1 ATTATACAAAGACTACAGTTTTTTAAAGTGAAAATGTGGTCTTTAATTGAAAAA-A
* **
12277824 TTATTATACAAAGACTAC-GTTTCTTAAAGTGAAAACATGGTCTTTAATTGAAAAAA
1 --ATTATACAAAGACTACAGTTTTTTAAAGTGAAAATGTGGTCTTTAATTGAAAAAA
12277880 A
1 A
12277881 AAAGAGTTAT
Statistics
Matches: 184, Mismatches: 28, Indels: 24
0.78 0.12 0.10
Matches are distributed among these distances:
53 4 0.02
54 31 0.17
55 44 0.24
56 55 0.30
57 14 0.08
58 32 0.17
59 4 0.02
ACGTcount: A:0.43, C:0.08, G:0.14, T:0.36
Consensus pattern (55 bp):
ATTATACAAAGACTACAGTTTTTTAAAGTGAAAATGTGGTCTTTAATTGAAAAAA
Found at i:12279220 original size:25 final size:25
Alignment explanation
Indices: 12279166--12279221 Score: 76
Period size: 25 Copynumber: 2.2 Consensus size: 25
12279156 TTGAAACTGG
*
12279166 TTTGTTTGTTTCATGTGTTATTAAA
1 TTTGTTTGTTTCATATGTTATTAAA
* * *
12279191 ATTGTTTGTTTCATATGTTCTTGAA
1 TTTGTTTGTTTCATATGTTATTAAA
12279216 TTTGTT
1 TTTGTT
12279222 GGTCATAGAA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.18, C:0.05, G:0.16, T:0.61
Consensus pattern (25 bp):
TTTGTTTGTTTCATATGTTATTAAA
Found at i:12280481 original size:18 final size:18
Alignment explanation
Indices: 12280461--12280494 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12280451 CTATTTTTAT
*
12280461 TTTTATTTTT-TTTCTTC
1 TTTTCTTTTTCTTTCTTC
12280478 TTTTCTTTTTCTTTCTT
1 TTTTCTTTTTCTTTCTT
12280495 TTCTATTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.03, C:0.15, G:0.00, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTCTTTCTTC
Found at i:12280481 original size:23 final size:23
Alignment explanation
Indices: 12280455--12280498 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
12280445 TTATTGCTAT
*
12280455 TTTTATTTTTATTTTTTTTCTTC
1 TTTTATTTTTATTTCTTTTCTTC
* *
12280478 TTTTCTTTTTCTTTCTTTTCT
1 TTTTATTTTTATTTCTTTTCT
12280499 ATTAATATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.05, C:0.14, G:0.00, T:0.82
Consensus pattern (23 bp):
TTTTATTTTTATTTCTTTTCTTC
Found at i:12280486 original size:14 final size:15
Alignment explanation
Indices: 12280469--12280498 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
12280459 ATTTTTATTT
12280469 TTTTTC-TTCTTTTC
1 TTTTTCTTTCTTTTC
12280483 TTTTTCTTTCTTTTC
1 TTTTTCTTTCTTTTC
12280498 T
1 T
12280499 ATTAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (15 bp):
TTTTTCTTTCTTTTC
Found at i:12281475 original size:11 final size:11
Alignment explanation
Indices: 12281459--12281487 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
12281449 CAATTTCAGG
12281459 TTTTTTTTAAA
1 TTTTTTTTAAA
12281470 TTTTTTTTAAA
1 TTTTTTTTAAA
12281481 TTTTTTT
1 TTTTTTT
12281488 CTTTTATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTTTTTTAAA
Found at i:12281575 original size:17 final size:18
Alignment explanation
Indices: 12281550--12281594 Score: 65
Period size: 17 Copynumber: 2.6 Consensus size: 18
12281540 GTTTAATATT
*
12281550 CTTTGATTTTTATCTTCA
1 CTTTTATTTTTATCTTCA
*
12281568 -TTTTATTTTTATTTTCA
1 CTTTTATTTTTATCTTCA
12281585 CTTTTATTTT
1 CTTTTATTTT
12281595 GTTTTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (18 bp):
CTTTTATTTTTATCTTCA
Found at i:12281599 original size:17 final size:17
Alignment explanation
Indices: 12281555--12281612 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 17
12281545 ATATTCTTTG
*
12281555 ATTTTTATCTTCATTTT
1 ATTTTTATTTTCATTTT
12281572 ATTTTTATTTTCACTTTT
1 ATTTTTATTTTCA-TTTT
*
12281590 ATTTTGT-TTTATTATTTT
1 ATTTT-TATTT-TCATTTT
12281608 ATTTT
1 ATTTT
12281613 CTTTAAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
17 12 0.33
18 21 0.58
19 3 0.08
ACGTcount: A:0.17, C:0.07, G:0.02, T:0.74
Consensus pattern (17 bp):
ATTTTTATTTTCATTTT
Found at i:12281810 original size:58 final size:57
Alignment explanation
Indices: 12281641--12281956 Score: 335
Period size: 58 Copynumber: 5.6 Consensus size: 57
12281631 AAAAATATTT
* * * *
12281641 TTTTTGGGGAAAAGCTGAAAGTATCAATTTTCCTTGAAAATAAACTTTCTAAAAAATA
1 TTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTCAAAAAAATA
* * * * **
12281699 TTTTTGGAAAAAAGTTGAAAG--------TTCCTTAAAAATAAATTTTC-AAAAAACG
1 TTTTTGG-GAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTCAAAAAAATA
* *
12281748 TTTTTGAGGAAGAGTTGAAAGTATCAATTTTTCTTGAAATTAAAGTTTCAAAAAAATA
1 TTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTCAAAAAAATA
* *
12281806 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAACTTTCTAAAAAAAATA
1 TTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTC--AAAAAAATA
* * *
12281866 TTTTTTGGGAAAAGTTAAAAGTATTAATTTTCCTCGAAATTAAAGTTTCAAAAAAATA
1 -TTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTCAAAAAAATA
*
12281924 TTTTTGGAGAAATGTTGAAAGTATCAATTTTCC
1 TTTTTGG-GAAAAGTTGAAAGTATCAATTTTCC
12281957 CCTATACAAA
Statistics
Matches: 217, Mismatches: 26, Indels: 30
0.79 0.10 0.11
Matches are distributed among these distances:
49 23 0.11
50 19 0.09
57 25 0.12
58 98 0.45
60 46 0.21
61 6 0.03
ACGTcount: A:0.42, C:0.08, G:0.14, T:0.36
Consensus pattern (57 bp):
TTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTCAAAAAAATA
Found at i:12281925 original size:118 final size:116
Alignment explanation
Indices: 12281628--12281956 Score: 383
Period size: 118 Copynumber: 2.9 Consensus size: 116
12281618 AATAAAATCC
* * * *
12281628 AAAAAAAATATTTTTTTTGGGGAAAAGCTGAAAGTATCAATTTTCCTTGAAAATAAACTTTCTAA
1 AAAAAAAATA--TTTTTT-GGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTCAAA
*
12281693 AAAATATTTTTGGAAAAAAGTTGAAAG--------TTCCTTAAAAATAAATTTT
63 AAAATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
* ** * *
12281739 -CAAAAAA-CGTTTTTGAGGAAGAGTTGAAAGTATCAATTTTTCTTGAAATTAAAGTTTCAAAAA
1 AAAAAAAATATTTTTTG-GGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTCAAAAA
*
12281802 AATATTTTT-GAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAACTTTCT
65 AATATTTTTGGA-GAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTT-T
* * *
12281856 AAAAAAAATATTTTTTGGGAAAAGTTAAAAGTATTAATTTTCCTCGAAATTAAAGTTTCAAAAAA
1 AAAAAAAATATTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTCAAAAAA
*
12281921 ATATTTTTGGAGAAATGTTGAAAGTATCAATTTTCC
66 ATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCC
12281957 CCTATACAAA
Statistics
Matches: 183, Mismatches: 20, Indels: 23
0.81 0.09 0.10
Matches are distributed among these distances:
106 3 0.02
107 67 0.37
110 6 0.03
115 14 0.08
116 3 0.02
117 1 0.01
118 81 0.44
119 8 0.04
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (116 bp):
AAAAAAAATATTTTTTGGGAAAAGTTGAAAGTATCAATTTTCCTTGAAATTAAAGTTTCAAAAAA
ATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTT
Found at i:12289404 original size:12 final size:12
Alignment explanation
Indices: 12289387--12289411 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
12289377 TAGTACCTGT
12289387 TCTTAAGAAAGA
1 TCTTAAGAAAGA
12289399 TCTTAAGAAAGA
1 TCTTAAGAAAGA
12289411 T
1 T
12289412 GGAAAAGTAC
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:0.48, C:0.08, G:0.16, T:0.28
Consensus pattern (12 bp):
TCTTAAGAAAGA
Found at i:12291430 original size:9 final size:9
Alignment explanation
Indices: 12291379--12291429 Score: 84
Period size: 9 Copynumber: 5.6 Consensus size: 9
12291369 TTTATTGATT
12291379 ATGCTCGTAA
1 ATGC-CGTAA
12291389 ATGCCGTAA
1 ATGCCGTAA
12291398 ATGCCGTAA
1 ATGCCGTAA
12291407 ATGCCGTAA
1 ATGCCGTAA
*
12291416 ATGCCATAA
1 ATGCCGTAA
12291425 ATGCC
1 ATGCC
12291430 AGATATATGC
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
9 36 0.90
10 4 0.10
ACGTcount: A:0.33, C:0.24, G:0.20, T:0.24
Consensus pattern (9 bp):
ATGCCGTAA
Found at i:12292380 original size:17 final size:17
Alignment explanation
Indices: 12292354--12292393 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
12292344 ACTATGCTTG
12292354 AAAT-AAAAAA-AAATAA
1 AAATGAAAAAAGAAA-AA
12292370 AAATGAAAAAAGAAAAA
1 AAATGAAAAAAGAAAAA
12292387 AAATGAA
1 AAATGAA
12292394 TGAAAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.18
17 15 0.68
18 3 0.14
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.10
Consensus pattern (17 bp):
AAATGAAAAAAGAAAAA
Found at i:12293419 original size:42 final size:43
Alignment explanation
Indices: 12293367--12293452 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
12293357 TGATTGTCAA
* * *
12293367 GGAGCTATTTACTTTT-CAAAGTCGTTGAGCCTCTGATTAGAG
1 GGAGCCATTTACTTTTCCAAAATCATTGAGCCTCTGATTAGAG
* *
12293409 GGAGCCATTTATTTTTCCAAAATCATTGAGCCTCTGCTTAGAG
1 GGAGCCATTTACTTTTCCAAAATCATTGAGCCTCTGATTAGAG
12293452 G
1 G
12293453 AGCTTTGATA
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
42 14 0.37
43 24 0.63
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (43 bp):
GGAGCCATTTACTTTTCCAAAATCATTGAGCCTCTGATTAGAG
Found at i:12293468 original size:1 final size:1
Alignment explanation
Indices: 12293462--12293498 Score: 65
Period size: 1 Copynumber: 37.0 Consensus size: 1
12293452 GAGCTTTGAT
*
12293462 AAAAAAAAAAAAAAACAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
12293499 TTACCTCTGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.97, C:0.03, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:12293674 original size:45 final size:42
Alignment explanation
Indices: 12293509--12293691 Score: 217
Period size: 43 Copynumber: 4.2 Consensus size: 42
12293499 TTACCTCTGT
*
12293509 TTAGAGGAGCTTTGTTTA-TTTTCAAAAGTCATTGAGCCTCTA
1 TTAGAGGAGCTTTGTTTATTTTTC-AAAGTCATTGAGCCTTTA
*
12293551 TTTAGAGGAGCTTTATTTATTTTTCAAAGTCATTGAGCCTCTTA
1 -TTAGAGGAGCTTTGTTTATTTTTCAAAGTCATTGAGCCT-TTA
* * *
12293595 TTAGAGGAGCTTTATTCA-TTTTCAAAGTCGTTGAGCCTTTGA
1 TTAGAGGAGCTTTGTTTATTTTTCAAAGTCATTGAGCCTTT-A
* * *
12293637 TTAGAGGAGCATTGTTTATGTTTTTCAAAGTCGTTGAGCCTTTGC
1 TTAGAGGAGCTTTGTTTA--TTTTTCAAAGTCATTGAGCCTTT-A
12293682 TTAGAGGAGC
1 TTAGAGGAGC
12293692 CTTGATTAAA
Statistics
Matches: 126, Mismatches: 8, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
41 2 0.02
42 35 0.28
43 49 0.39
44 7 0.06
45 33 0.26
ACGTcount: A:0.24, C:0.14, G:0.21, T:0.41
Consensus pattern (42 bp):
TTAGAGGAGCTTTGTTTATTTTTCAAAGTCATTGAGCCTTTA
Found at i:12293886 original size:7 final size:7
Alignment explanation
Indices: 12293876--12293916 Score: 50
Period size: 7 Copynumber: 6.1 Consensus size: 7
12293866 CACTTTTTTT
*
12293876 TTTTGTA
1 TTTTATA
12293883 TTTTATA
1 TTTTATA
12293890 TTTTATA
1 TTTTATA
12293897 -TTT-TA
1 TTTTATA
12293902 TTTTATA
1 TTTTATA
*
12293909 TTATATA
1 TTTTATA
12293916 T
1 T
12293917 ATATTTTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 2 0.07
6 6 0.20
7 22 0.73
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (7 bp):
TTTTATA
Found at i:12293936 original size:24 final size:23
Alignment explanation
Indices: 12293872--12293923 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
12293862 GGTCCACTTT
* *
12293872 TTTTTTTTGTATTTTATATTTTATA
1 TTTTATTT-TATTTTATA-TATATA
*
12293897 TTTTATTTTATATTATATATATA
1 TTTTATTTTATTTTATATATATA
12293920 TTTT
1 TTTT
12293924 CTTTATCTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 8 0.33
25 7 0.29
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (23 bp):
TTTTATTTTATTTTATATATATA
Found at i:12293950 original size:15 final size:15
Alignment explanation
Indices: 12293938--12293988 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 15
12293928 ATCTTTTATG
12293938 TATTTATTATTTACT
1 TATTTATTATTTACT
12293953 TATTTATTA-TTAC-
1 TATTTATTATTTACT
12293966 TATTT-TTATTT--T
1 TATTTATTATTTACT
12293978 TA-TTATTATTT
1 TATTTATTATTT
12293989 TTCTTTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
11 2 0.06
12 11 0.33
13 7 0.21
14 4 0.12
15 9 0.27
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (15 bp):
TATTTATTATTTACT
Found at i:12293979 original size:21 final size:21
Alignment explanation
Indices: 12293925--12293986 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 21
12293915 ATATATTTTC
12293925 TTTATCTTTTATGTATT-TATTA
1 TTTAT-TTTTAT-TATTATATTA
12293947 TTTACTTATTTATTATTACTATT-
1 TTTA-TT-TTTATTATTA-TATTA
12293970 TTTATTTTTATTATTAT
1 TTTATTTTTATTATTAT
12293987 TTTTCTTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
20 1 0.03
21 10 0.28
22 11 0.31
23 10 0.28
24 4 0.11
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTATTTTTATTATTATATTA
Found at i:12293980 original size:18 final size:18
Alignment explanation
Indices: 12293952--12293996 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
12293942 TATTATTTAC
12293952 TTATTTATTATTACTATTT
1 TTATTT-TTATTACTATTT
*
12293971 TTATTTTTATTATTATTT
1 TTATTTTTATTACTATTT
*
12293989 TTCTTTTT
1 TTATTTTT
12293997 TTCTTTTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 18 0.75
19 6 0.25
ACGTcount: A:0.20, C:0.04, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATTTTTATTACTATTT
Found at i:12293981 original size:12 final size:12
Alignment explanation
Indices: 12293869--12293996 Score: 51
Period size: 15 Copynumber: 9.4 Consensus size: 12
12293859 GTTGGTCCAC
* *
12293869 TTTTTTTTTTTG
1 TTTTTATTTTTA
12293881 TATTTTATATTTTA
1 T-TTTTAT-TTTTA
12293895 TATTTTATTTTATA
1 T-TTTTATTTT-TA
*
12293909 TTATATATATATTT-
1 TT-T-T-TATTTTTA
*
12293923 TCTTTATCTTTTA
1 TTTTTAT-TTTTA
12293936 TGTATTTATTATTTA
1 T-T-TTTATT-TTTA
12293951 CTTATTTATTATTACTA
1 -TT-TTTATT-TT--TA
12293968 TTTTTATTTTTA
1 TTTTTATTTTTA
* *
12293980 TTATTATTTTTC
1 TTTTTATTTTTA
12293992 TTTTT
1 TTTTT
12293997 TTCTTTTTCT
Statistics
Matches: 93, Mismatches: 9, Indels: 28
0.72 0.07 0.22
Matches are distributed among these distances:
11 3 0.03
12 21 0.23
13 11 0.12
14 20 0.22
15 28 0.30
16 8 0.09
17 2 0.02
ACGTcount: A:0.22, C:0.04, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTTTATTTTTA
Found at i:12294005 original size:14 final size:15
Alignment explanation
Indices: 12293986--12294015 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
12293976 TTTATTATTA
12293986 TTTTTCTTT-TTTTC
1 TTTTTCTTTCTTTTC
12294000 TTTTTCTTTCTTTTC
1 TTTTTCTTTCTTTTC
12294015 T
1 T
12294016 GTTAATATTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTCTTTCTTTTC
Found at i:12294074 original size:14 final size:14
Alignment explanation
Indices: 12294036--12294080 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
12294026 ATATATATGT
12294036 TTATTTATCTAGTTA
1 TTATTTATCTA-TTA
*
12294051 -TA--TATTTATTA
1 TTATTTATCTATTA
12294062 TTATTTATCTATTA
1 TTATTTATCTATTA
12294076 TTATT
1 TTATT
12294081 GTTAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 7
0.74 0.06 0.21
Matches are distributed among these distances:
11 3 0.12
12 7 0.28
14 15 0.60
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.64
Consensus pattern (14 bp):
TTATTTATCTATTA
Found at i:12295009 original size:6 final size:6
Alignment explanation
Indices: 12294989--12295055 Score: 50
Period size: 6 Copynumber: 11.2 Consensus size: 6
12294979 TAGTTCCAAG
*
12294989 TTTT-T TTTTATT TTTTAT TTTTA- -TATAT TTTTAT ATATTTAT TTTTAT
1 TTTTAT TTTTA-T TTTTAT TTTTAT TTTTAT TTTTAT -T-TTTAT TTTTAT
* * *
12295037 TATTAT TATTAT TATTAT T
1 TTTTAT TTTTAT TTTTAT T
12295056 AGATTAGATT
Statistics
Matches: 53, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
4 3 0.06
5 4 0.08
6 33 0.62
7 8 0.15
8 5 0.09
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (6 bp):
TTTTAT
Found at i:12295041 original size:3 final size:3
Alignment explanation
Indices: 12295003--12295056 Score: 54
Period size: 3 Copynumber: 17.0 Consensus size: 3
12294993 TTTTTATTTT
* * *
12295003 TTA TTT TTA TATA TTT TTA TATA TTTA TTT TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA T-TA TTA TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA
12295051 TTA TTA
1 TTA TTA
12295057 GATTAGATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
3 34 0.81
4 7 0.17
5 1 0.02
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:12295118 original size:22 final size:21
Alignment explanation
Indices: 12295079--12295133 Score: 76
Period size: 22 Copynumber: 2.6 Consensus size: 21
12295069 TTAATATTCT
*
12295079 TTTATTTTTATTTTACTTTTC
1 TTTATTTTTATTTTACTTTTA
12295100 TTTATTTTTATTTTCACTTTTA
1 TTTATTTTTATTTT-ACTTTTA
12295122 TTT-TGTTTTATT
1 TTTAT-TTTTATT
12295134 ATTTTATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTATTTTTATTTTACTTTTA
Found at i:12295248 original size:34 final size:33
Alignment explanation
Indices: 12295210--12295286 Score: 118
Period size: 33 Copynumber: 2.3 Consensus size: 33
12295200 TCTCGAAATT
* *
12295210 AAAGTTTCAAAATAATATTTTTGAGAAAAAGTTA
1 AAAGTATCAAAA-AATATCTTTGAGAAAAAGTTA
*
12295244 AAAGTATCAAAAAATATCTTTGAGAAAAAGTTG
1 AAAGTATCAAAAAATATCTTTGAGAAAAAGTTA
12295277 AAAGTATCAA
1 AAAGTATCAA
12295287 TTTTCCTTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
33 29 0.73
34 11 0.28
ACGTcount: A:0.52, C:0.05, G:0.13, T:0.30
Consensus pattern (33 bp):
AAAGTATCAAAAAATATCTTTGAGAAAAAGTTA
Found at i:12295273 original size:90 final size:90
Alignment explanation
Indices: 12295162--12295341 Score: 236
Period size: 90 Copynumber: 2.0 Consensus size: 90
12295152 AAAATCCAAA
* * * * * *
12295162 AAAAAATATTTTTGGGGAAAAGTTGAAAGTATCAATTTT-CTCGAAATTAAAGTTTCAAAATAAT
1 AAAAAATATCTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTTTCAAAA-AAG
*
12295226 ATTTTTGAGAAAAAGTTAAAAGTATC
65 ATTTATGAGAAAAAGTTAAAAGTATC
* * *
12295252 AAAAAATATCTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGG
1 AAAAAATATCTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTTTCAAAAAAGA
* *
12295317 TTTATGAGGAAAAGTTGAAAGTATC
66 TTTATGAGAAAAAGTTAAAAGTATC
12295342 GATTTTCCTC
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
90 60 0.78
91 17 0.22
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (90 bp):
AAAAAATATCTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTCAAAAATAAAGTTTCAAAAAAGA
TTTATGAGAAAAAGTTAAAAGTATC
Found at i:12295333 original size:57 final size:57
Alignment explanation
Indices: 12295262--12295460 Score: 251
Period size: 57 Copynumber: 3.5 Consensus size: 57
12295252 AAAAAATATC
*
12295262 TTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTT
* * ** * * **
12295319 TATGAGGAAAAGTTGAAAGTATCGATTTTCCTCGAAATTAAAGTTTTAAAAAAATATT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTTCAAAAAAGGTT
* *
12295377 TTTG-GGAAAAAATTGAAAATATCAATTTT-CTTAAAAATAAATTTTC-AAAAAGGTT
1 TTTGAGG-AAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTT
*
12295432 TTTGAGGAAAAGTTGAAAGTATCGATTTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTT
12295461 TTCCTGTACA
Statistics
Matches: 117, Mismatches: 22, Indels: 8
0.80 0.15 0.05
Matches are distributed among these distances:
55 30 0.26
56 6 0.05
57 47 0.40
58 34 0.29
ACGTcount: A:0.44, C:0.06, G:0.15, T:0.36
Consensus pattern (57 bp):
TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGGTT
Found at i:12295455 original size:113 final size:115
Alignment explanation
Indices: 12295252--12295460 Score: 359
Period size: 113 Copynumber: 1.8 Consensus size: 115
12295242 TAAAAGTATC
* *
12295252 AAAAAATATCTTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGG
1 AAAAAATATCTTTGAGAAAAAATTGAAAATATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGG
12295317 TTTATGAGGAAAAGTTGAAAGTATCGATTTTCCTCGAAATTAAAGTTTTA
66 TTTATGAGGAAAAGTTGAAAGTATCGATTTTCCTCGAAATTAAAGTTTTA
* *
12295367 AAAAAATATTTTTGGGAAAAAATTGAAAATATCAATTTT-CTTAAAAATAAATTTTC-AAAAAGG
1 AAAAAATATCTTTGAGAAAAAATTGAAAATATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGG
*
12295430 TTTTTGAGGAAAAGTTGAAAGTATCGATTTT
66 TTTATGAGGAAAAGTTGAAAGTATCGATTTT
12295461 TTCCTGTACA
Statistics
Matches: 89, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
113 37 0.42
114 17 0.19
115 35 0.39
ACGTcount: A:0.45, C:0.06, G:0.14, T:0.35
Consensus pattern (115 bp):
AAAAAATATCTTTGAGAAAAAATTGAAAATATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGG
TTTATGAGGAAAAGTTGAAAGTATCGATTTTCCTCGAAATTAAAGTTTTA
Found at i:12296182 original size:27 final size:27
Alignment explanation
Indices: 12296152--12296204 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
12296142 CACATTCAGT
12296152 GTTTACTTTATTATTCACTTTATATTG
1 GTTTACTTTATTATTCACTTTATATTG
* *
12296179 GTTTACTTTGTTATTTACTTTATATT
1 GTTTACTTTATTATTCACTTTATATT
12296205 CATTGACTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.09, G:0.08, T:0.62
Consensus pattern (27 bp):
GTTTACTTTATTATTCACTTTATATTG
Found at i:12300914 original size:17 final size:17
Alignment explanation
Indices: 12300892--12300950 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
12300882 CAATATAAAA
12300892 TATAAATATTTTAATAT
1 TATAAATATTTTAATAT
* *
12300909 TATAAATATTTAAAATAA
1 TATAAATATTT-TAATAT
* *
12300927 TATTACTATTTTAATAT
1 TATAAATATTTTAATAT
12300944 TAATAAA
1 T-ATAAA
12300951 AATAATATTG
Statistics
Matches: 32, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
17 16 0.50
18 16 0.50
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (17 bp):
TATAAATATTTTAATAT
Found at i:12300944 original size:43 final size:46
Alignment explanation
Indices: 12300894--12300990 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 46
12300884 ATATAAAATA
**
12300894 TAAATATTTTAAT-ATTATAAATATT-TAA-AATAAT-ATTACTATTT
1 TAAATATTTTAATAAAAAT-AATATTGTAAGAATAATGA-TACTATTT
12300938 T-AATA--TTAATAAAAATAATATTGTAAGAATAATGATACTATTT
1 TAAATATTTTAATAAAAATAATATTGTAAGAATAATGATACTATTT
12300981 TAAATATTTT
1 TAAATATTTT
12300991 TAAAATATTA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
41 11 0.25
42 6 0.14
43 19 0.43
44 6 0.14
46 2 0.05
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.46
Consensus pattern (46 bp):
TAAATATTTTAATAAAAATAATATTGTAAGAATAATGATACTATTT
Found at i:12304360 original size:5 final size:5
Alignment explanation
Indices: 12304270--12304367 Score: 56
Period size: 5 Copynumber: 18.8 Consensus size: 5
12304260 CTATTAGCAT
* * * *
12304270 TATTA TATCA TGTTA TATAGTA TAATA TATTA TATTGA TATTA TAATA
1 TATTA TATTA TATTA TAT--TA TATTA TATTA TATT-A TATTA TATTA
* * **
12304318 TACTA GTATTA TCATTA TATTT TA-T- TATTA TACCA TATTA TATTA CTATT
1 TATTA -TATTA T-ATTA TATTA TATTA TATTA TATTA TATTA TATTA -TATT
12304368 GTAATAATAA
Statistics
Matches: 71, Mismatches: 14, Indels: 15
0.71 0.14 0.15
Matches are distributed among these distances:
3 2 0.03
4 2 0.03
5 45 0.63
6 18 0.25
7 4 0.06
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (5 bp):
TATTA
Found at i:12304377 original size:3 final size:3
Alignment explanation
Indices: 12304369--12304424 Score: 94
Period size: 3 Copynumber: 18.7 Consensus size: 3
12304359 ATTACTATTG
*
12304369 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA CAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
12304417 TAT TAA TA
1 TAA TAA TA
12304425 TTATTTTTTT
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12305659 original size:147 final size:144
Alignment explanation
Indices: 12305397--12305667 Score: 366
Period size: 147 Copynumber: 1.9 Consensus size: 144
12305387 AAAATCTTTT
* * **
12305397 CAAAATAGATTCATGAATTCTACCAAACTATTGGAAAGTTTCATGACTTGCTTTTTTAAATGAAA
1 CAAAATAAACTCATGAATTCTACCAAACTATTGGAAAGTTTCATGACTTAATTTTTTAAATGAAA
* *
12305462 TCCACTAAACTATTGAAAAATTCCATAAATCATTTTTTAAAAACATATAAATAAA-AAAATTTTC
66 TCCACCAAACTATTGAAAAATTCCATAAATCATTTTTTAAAAACAAATAAA-AAATAAAATTTTC
12305526 AAATAAAAATTCATG
130 AAATAAAAATTCATG
* *
12305541 CAAAATAAACTCATGAATTCTACCAAACTATTGGAGAATTTTCATGGATTTAATTTTCTTAAATG
1 CAAAATAAACTCATGAATTCTACCAAACTATTGGA-AAGTTTCAT-GACTTAATTTT-TTAAATG
* * ** *
12305606 GAGTCCACCAAACTATTGGGAAATTCCATGAATCATTTTTTAAGAAA-AAATAAAAAATAAAA
63 AAATCCACCAAACTATTGAAAAATTCCATAAATCATTTTTTAA-AAACAAATAAAAAATAAAA
12305668 GTAAATAAAA
Statistics
Matches: 109, Mismatches: 13, Indels: 7
0.84 0.10 0.05
Matches are distributed among these distances:
144 33 0.30
145 8 0.07
146 11 0.10
147 54 0.50
148 3 0.03
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (144 bp):
CAAAATAAACTCATGAATTCTACCAAACTATTGGAAAGTTTCATGACTTAATTTTTTAAATGAAA
TCCACCAAACTATTGAAAAATTCCATAAATCATTTTTTAAAAACAAATAAAAAATAAAATTTTCA
AATAAAAATTCATG
Found at i:12307656 original size:16 final size:16
Alignment explanation
Indices: 12307635--12307666 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12307625 TATCTTTAAT
*
12307635 AAAGTAAATTAAAATA
1 AAAGTAAAATAAAATA
12307651 AAAGTAAAATAAAATA
1 AAAGTAAAATAAAATA
12307667 GTCAAAGATG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.06, T:0.22
Consensus pattern (16 bp):
AAAGTAAAATAAAATA
Found at i:12311820 original size:17 final size:17
Alignment explanation
Indices: 12311794--12311827 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
12311784 AGCTTAGGTC
*
12311794 CTAAATGAATTATAAAT
1 CTAAAGGAATTATAAAT
*
12311811 CTAAAGGAATTTTAAAT
1 CTAAAGGAATTATAAAT
12311828 GTAATTATTC
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:0.50, C:0.06, G:0.09, T:0.35
Consensus pattern (17 bp):
CTAAAGGAATTATAAAT
Found at i:12316623 original size:45 final size:42
Alignment explanation
Indices: 12316570--12316653 Score: 105
Period size: 45 Copynumber: 1.9 Consensus size: 42
12316560 GCATTTTGGG
* ** *
12316570 TTTTTTTTTTATTTTTGTTCTCTATTTTATTTATATTTTTGTTA
1 TTTTTTTTTGATTTTTGTGATAT-TTTTATTT-TATTTTTGTTA
12316614 TTTTATTTTTGATTTTTGTGATATTTTTATTTTATTTTTG
1 TTTT-TTTTTGATTTTTGTGATATTTTTATTTTATTTTTG
12316654 CATGGACTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 8 0.23
44 12 0.34
45 15 0.43
ACGTcount: A:0.14, C:0.02, G:0.07, T:0.76
Consensus pattern (42 bp):
TTTTTTTTTGATTTTTGTGATATTTTTATTTTATTTTTGTTA
Found at i:12316714 original size:32 final size:32
Alignment explanation
Indices: 12316673--12316741 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
12316663 TTGGTGTAAG
12316673 AATAAAATAAATGTTAGAAAAAATTTAGGAAA
1 AATAAAATAAATGTTAGAAAAAATTTAGGAAA
* * *** *
12316705 AATAAAATAACTTTTAGTTGAAATTTAGTAAA
1 AATAAAATAAATGTTAGAAAAAATTTAGGAAA
12316737 AATAA
1 AATAA
12316742 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.58, C:0.01, G:0.10, T:0.30
Consensus pattern (32 bp):
AATAAAATAAATGTTAGAAAAAATTTAGGAAA
Found at i:12320639 original size:3 final size:3
Alignment explanation
Indices: 12320631--12320659 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12320621 CTGATCAATC
12320631 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
12320660 CAACCACTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:12324945 original size:23 final size:23
Alignment explanation
Indices: 12324910--12324953 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
12324900 CTAGGAGGGT
* *
12324910 TTTTTTGTTATTGATCTTATTTC
1 TTTTCTGTCATTGATCTTATTTC
12324933 TTTTCTGTCATTGATCTTATT
1 TTTTCTGTCATTGATCTTATT
12324954 GGACTTGAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.14, C:0.11, G:0.09, T:0.66
Consensus pattern (23 bp):
TTTTCTGTCATTGATCTTATTTC
Found at i:12328258 original size:31 final size:34
Alignment explanation
Indices: 12328206--12328272 Score: 97
Period size: 31 Copynumber: 2.1 Consensus size: 34
12328196 TTTTCAGGTC
12328206 TAATTTTTATATAAAATATATTTTTA-TATTTTA
1 TAATTTTTATATAAAATATATTTTTATTATTTTA
12328239 TAATTTTT-T-TAATAA-ATATTTTTATTATTTTA
1 TAATTTTTATATAA-AATATATTTTTATTATTTTA
12328271 TA
1 TA
12328273 TTTCTAGAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
31 12 0.38
32 12 0.38
33 8 0.25
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (34 bp):
TAATTTTTATATAAAATATATTTTTATTATTTTA
Found at i:12328273 original size:16 final size:16
Alignment explanation
Indices: 12328222--12328275 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
12328212 TTATATAAAA
12328222 TATATTTTTA-TATTT
1 TATATTTTTATTATTT
* *
12328237 TATAATTTTT-TTAATA
1 TAT-ATTTTTATTATTT
*
12328253 AATATTTTTATTATTT
1 TATATTTTTATTATTT
12328269 TATATTT
1 TATATTT
12328276 CTAGAAGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 9 0.30
16 21 0.70
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TATATTTTTATTATTT
Found at i:12330260 original size:3 final size:3
Alignment explanation
Indices: 12330252--12330286 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
12330242 TCCTGTAGCA
* *
12330252 GCT GCT GCT ACT GCT ACT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GCT GC
12330287 GATGGCAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.06, C:0.34, G:0.29, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:12355999 original size:19 final size:19
Alignment explanation
Indices: 12355960--12356008 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 19
12355950 TTGCTAGGAT
12355960 ATCTTACTTTAACTTGAAA
1 ATCTTACTTTAACTTGAAA
12355979 ATCTTCACTTTAACTTGAAA
1 ATCTT-ACTTTAACTTGAAA
* *
12355999 TTCCTACTTT
1 ATCTTACTTT
12356009 GACTAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 10 0.37
20 17 0.63
ACGTcount: A:0.31, C:0.20, G:0.04, T:0.45
Consensus pattern (19 bp):
ATCTTACTTTAACTTGAAA
Found at i:12356746 original size:11 final size:11
Alignment explanation
Indices: 12356719--12356772 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
12356709 TAGTCTTACG
*
12356719 TTTTCTTT-CA
1 TTTTCTTTAAA
12356729 TTGTTCTTTAAA
1 TT-TTCTTTAAA
12356741 TTTTCTTT-AA
1 TTTTCTTTAAA
* *
12356751 -TTGCTTTAAG
1 TTTTCTTTAAA
12356761 TTTTCTTTAAA
1 TTTTCTTTAAA
12356772 T
1 T
12356773 AGTTATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
9 6 0.17
10 5 0.14
11 21 0.60
12 3 0.09
ACGTcount: A:0.20, C:0.11, G:0.06, T:0.63
Consensus pattern (11 bp):
TTTTCTTTAAA
Found at i:12356759 original size:20 final size:21
Alignment explanation
Indices: 12356719--12356770 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
12356709 TAGTCTTACG
*
12356719 TTTTCTTTCATTGTTCTTTAAA
1 TTTTCTTTAATTG-TCTTTAAA
*
12356741 TTTTCTTTAATTG-CTTTAAG
1 TTTTCTTTAATTGTCTTTAAA
12356761 TTTTCTTTAA
1 TTTTCTTTAA
12356771 ATAGTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 16 0.57
22 12 0.43
ACGTcount: A:0.19, C:0.12, G:0.06, T:0.63
Consensus pattern (21 bp):
TTTTCTTTAATTGTCTTTAAA
Found at i:12356840 original size:21 final size:21
Alignment explanation
Indices: 12356816--12356865 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
12356806 ATTTGTTTAA
12356816 TTTTAAGT-CTAGTTTTAAGTT
1 TTTTAAGTACTAG-TTTAAGTT
* *
12356837 TTTTAATTACTTGTTTAAGTT
1 TTTTAAGTACTAGTTTAAGTT
*
12356858 TTTAAAGT
1 TTTTAAGT
12356866 TTCTACTTCA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.26, C:0.04, G:0.12, T:0.58
Consensus pattern (21 bp):
TTTTAAGTACTAGTTTAAGTT
Found at i:12358912 original size:20 final size:19
Alignment explanation
Indices: 12358877--12358927 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
12358867 TTTTACTTTC
*
12358877 AATAAAAAAAAGCCAAACA
1 AATAAAAAAAAACCAAACA
12358896 AATAAAAAACAAACCAAA-A
1 AATAAAAAA-AAACCAAACA
12358915 ACATAAAGAAAAA
1 A-ATAAA-AAAAA
12358928 TTTCATATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 11 0.39
20 14 0.50
21 3 0.11
ACGTcount: A:0.76, C:0.14, G:0.04, T:0.06
Consensus pattern (19 bp):
AATAAAAAAAAACCAAACA
Found at i:12363073 original size:13 final size:13
Alignment explanation
Indices: 12363028--12363066 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
12363018 CGATAAAATC
12363028 ATAAAAA-AATAAA
1 ATAAAAAGAA-AAA
*
12363041 AAAAAAAGAAAAA
1 ATAAAAAGAAAAA
12363054 ATAAAAAGAAAAA
1 ATAAAAAGAAAAA
12363067 TGAAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 21 0.91
14 2 0.09
ACGTcount: A:0.87, C:0.00, G:0.05, T:0.08
Consensus pattern (13 bp):
ATAAAAAGAAAAA
Found at i:12363075 original size:20 final size:18
Alignment explanation
Indices: 12363031--12363078 Score: 78
Period size: 18 Copynumber: 2.6 Consensus size: 18
12363021 TAAAATCATA
12363031 AAAAAATAAAAAAAAAAG
1 AAAAAATAAAAAAAAAAG
12363049 AAAAAATAAAAAGAAAAATG
1 AAAAAATAAAAA-AAAAA-G
12363069 AAAAAATAAA
1 AAAAAATAAA
12363079 GCTTTAGGGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 12 0.43
19 5 0.18
20 11 0.39
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.08
Consensus pattern (18 bp):
AAAAAATAAAAAAAAAAG
Found at i:12363079 original size:18 final size:18
Alignment explanation
Indices: 12363031--12363079 Score: 62
Period size: 20 Copynumber: 2.6 Consensus size: 18
12363021 TAAAATCATA
*
12363031 AAAAAATAAAAAAAAAAG
1 AAAAAATAAAGAAAAAAG
*
12363049 AAAAAATAAAAAGAAAAATG
1 AAAAAAT--AAAGAAAAAAG
12363069 AAAAAATAAAG
1 AAAAAATAAAG
12363080 CTTTAGGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 11 0.41
20 16 0.59
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (18 bp):
AAAAAATAAAGAAAAAAG
Found at i:12364140 original size:42 final size:42
Alignment explanation
Indices: 12364087--12364185 Score: 135
Period size: 42 Copynumber: 2.4 Consensus size: 42
12364077 CATTTATATT
* * *
12364087 TTCTTGGTGGTGATATCTGAGTGTTAAGGTTTTAATTACATC
1 TTCTTAGTGGTGATATCTGAGTGTCAAGGTTTGAATTACATC
* ** *
12364129 TTCTTAGTGGTGATATCTGATTGTCAAGGTTTGAATTTTATT
1 TTCTTAGTGGTGATATCTGAGTGTCAAGGTTTGAATTACATC
12364171 TTCTTAGTGGTGATA
1 TTCTTAGTGGTGATA
12364186 GCCAAGGCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.21, C:0.08, G:0.23, T:0.47
Consensus pattern (42 bp):
TTCTTAGTGGTGATATCTGAGTGTCAAGGTTTGAATTACATC
Found at i:12364353 original size:42 final size:42
Alignment explanation
Indices: 12364303--12364527 Score: 249
Period size: 42 Copynumber: 5.4 Consensus size: 42
12364293 GTTTTCTTGA
* *
12364303 TGGTGATATCCGAGTGTTAAGGTTTGAATTACATTTTCTCGG
1 TGGTGATATCCGAGTGTCAAGGTTTGAATTACATTTTCTCAG
* ** * *
12364345 TGGGGATATCTAAATGTCCAA-GTTTGAATTACATCTTCTC-G
1 TGGTGATATCCGAGTGT-CAAGGTTTGAATTACATTTTCTCAG
* * * *
12364386 ATGGTGATATTCGAGTGTCAAGGTTTGAATTGCATTTTTTTAG
1 -TGGTGATATCCGAGTGTCAAGGTTTGAATTACATTTTCTCAG
* *
12364429 TGGTGATATCCGAGTATCAAGGTTTGAATTGCATTTTCTCAG
1 TGGTGATATCCGAGTGTCAAGGTTTGAATTACATTTTCTCAG
* *
12364471 TGGTGATA-CCAGAGTGTCGAGGTTTGAATTACATTTTCTCAA
1 TGGTGATATCC-GAGTGTCAAGGTTTGAATTACATTTTCTCAG
* *
12364513 TGGTAATATTCGAGT
1 TGGTGATATCCGAGT
12364528 TTCCTTCGAT
Statistics
Matches: 152, Mismatches: 25, Indels: 12
0.80 0.13 0.06
Matches are distributed among these distances:
41 6 0.04
42 142 0.93
43 4 0.03
ACGTcount: A:0.24, C:0.12, G:0.24, T:0.39
Consensus pattern (42 bp):
TGGTGATATCCGAGTGTCAAGGTTTGAATTACATTTTCTCAG
Found at i:12364884 original size:99 final size:98
Alignment explanation
Indices: 12364650--12364898 Score: 252
Period size: 99 Copynumber: 2.5 Consensus size: 98
12364640 ATTTTCTTGG
* * * * *
12364650 TGGTGATATTTGAGTGTTAAAGCTTCAATTGCATTTTCTCGATAGTAATATTCGAGTTTCCTTCA
1 TGGTGATATTCGAGTATTAAGGCTTCAATTGCATTTTCTCGATAGTGATATTCAAGTTTCCTTCA
*
12364715 GTGGCAATATCCAAGTCATTTGCATATTCTCAA
66 GTGGCAATATCAAAGTCATTTGCATATTCTCAA
* *** * * *
12364748 TGGTGATA-TCTAAGTATTAAAGAAGTCATTTGCATTTTCTCGATAGTGATATTTAAGTTTCTTT
1 TGGTGATATTC-GAGTATT-AAGGCTTCAATTGCATTTTCTCGATAGTGATATTCAAGTTTCCTT
** *
12364812 C-GATGGTGATATCTAAAGTCATTTGCATATTTTCAGA
64 CAG-TGGCAATATC-AAAGTCATTTGCATATTCTCA-A
* * * *
12364849 -GGTGATATTCGAGTATTAAGGCTTGAATTGTATTTTTTCGATGGTGATAT
1 TGGTGATATTCGAGTATTAAGGCTTCAATTGCATTTTCTCGATAGTGATAT
12364899 CCGAGTGTTA
Statistics
Matches: 120, Mismatches: 25, Indels: 11
0.77 0.16 0.07
Matches are distributed among these distances:
97 1 0.01
98 14 0.12
99 70 0.58
100 32 0.27
101 3 0.03
ACGTcount: A:0.27, C:0.12, G:0.19, T:0.42
Consensus pattern (98 bp):
TGGTGATATTCGAGTATTAAGGCTTCAATTGCATTTTCTCGATAGTGATATTCAAGTTTCCTTCA
GTGGCAATATCAAAGTCATTTGCATATTCTCAA
Found at i:12364895 original size:42 final size:42
Alignment explanation
Indices: 12364834--12364946 Score: 129
Period size: 42 Copynumber: 2.7 Consensus size: 42
12364824 CTAAAGTCAT
* * *
12364834 TTGCATATTTTCAGA-GGTGATATTCGAGTATTAAGGCTTGAA
1 TTGCATTTTTTC-GATGGTGATATTCGAGTATTAAAGCTTCAA
* * * *
12364876 TTGTATTTTTTCGATGGTGATATCCGAGTGTTAAAGTTTCAA
1 TTGCATTTTTTCGATGGTGATATTCGAGTATTAAAGCTTCAA
* *
12364918 TTGCATTTTCTCGATGGTAATATTCGAGT
1 TTGCATTTTTTCGATGGTGATATTCGAGT
12364947 TTCCTTCAGT
Statistics
Matches: 59, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
41 2 0.03
42 57 0.97
ACGTcount: A:0.25, C:0.11, G:0.22, T:0.42
Consensus pattern (42 bp):
TTGCATTTTTTCGATGGTGATATTCGAGTATTAAAGCTTCAA
Found at i:12365077 original size:98 final size:99
Alignment explanation
Indices: 12364886--12365105 Score: 246
Period size: 98 Copynumber: 2.2 Consensus size: 99
12364876 TTGTATTTTT
*** * * *
12364886 TCGATGGTGATATCCGAGTGTTAAAGTTTCAATTGCATTTTCTCGATGGTAATATTCGAGTTTCC
1 TCGATGGTGATATCCGAGTGTTAAAAAATCAATTACATTTTCTCGATGGTAACATTCAAGTTTCC
* * *
12364951 TTCAGTAGTGATATCCAAAGTCATTTGCATATTC
66 TTCAATAGTAATATCCAAAGTCACTTGCATATTC
* * *
12364985 TCGATGGTGATATCTGAGTG-TAAAAAATCATTTACATTTTCTCGATGGTGACATTCAAGTTTCC
1 TCGATGGTGATATCCGAGTGTTAAAAAATCAATTACATTTTCTCGATGGTAACATTCAAGTTTCC
* * * * *
12365049 TTCAATGGTAATATTCGAAGTTACTTGCATCTTC
66 TTCAATAGTAATATCCAAAGTCACTTGCATATTC
* *
12365083 T-TAGTGGTGATATCCGAATGTTA
1 TCGA-TGGTGATATCCGAGTGTTA
12365106 CAATTTGATT
Statistics
Matches: 99, Mismatches: 20, Indels: 4
0.80 0.16 0.03
Matches are distributed among these distances:
97 1 0.01
98 77 0.78
99 21 0.21
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (99 bp):
TCGATGGTGATATCCGAGTGTTAAAAAATCAATTACATTTTCTCGATGGTAACATTCAAGTTTCC
TTCAATAGTAATATCCAAAGTCACTTGCATATTC
Found at i:12365132 original size:42 final size:40
Alignment explanation
Indices: 12365073--12365182 Score: 114
Period size: 42 Copynumber: 2.7 Consensus size: 40
12365063 TCGAAGTTAC
* * ** *
12365073 TTGCATCTTCTTAGTGGTGATATCCGAATGTTACAATTTGAT
1 TTGCATTTTCTCAGTGGTGATATCC-AATGTTA-AAAATCAT
*
12365115 TTGCATTTTCTCAGTGGTGATATCCAGTGTTAAAAATCAT
1 TTGCATTTTCTCAGTGGTGATATCCAATGTTAAAAATCAT
*
12365155 TTGCATTTTCTTC-GATGGCGATATCCAA
1 TTGCATTTTC-TCAG-TGGTGATATCCAA
12365183 AGTCATTCAC
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
40 16 0.28
41 19 0.33
42 23 0.40
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (40 bp):
TTGCATTTTCTCAGTGGTGATATCCAATGTTAAAAATCAT
Found at i:12365165 original size:40 final size:42
Alignment explanation
Indices: 12365073--12365165 Score: 118
Period size: 42 Copynumber: 2.3 Consensus size: 42
12365063 TCGAAGTTAC
* * ** *
12365073 TTGCATCTTCTTAGTGGTGATATCCGAATGTTACAATTTGAT
1 TTGCATTTTCTCAGTGGTGATATCCGAATGTTACAAAATCAT
*
12365115 TTGCATTTTCTCAGTGGTGATATCC-AGTGTTA-AAAATCAT
1 TTGCATTTTCTCAGTGGTGATATCCGAATGTTACAAAATCAT
12365155 TTGCATTTTCT
1 TTGCATTTTCT
12365166 TCGATGGCGA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
40 16 0.36
41 6 0.13
42 23 0.51
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (42 bp):
TTGCATTTTCTCAGTGGTGATATCCGAATGTTACAAAATCAT
Found at i:12365710 original size:9 final size:9
Alignment explanation
Indices: 12365684--12365733 Score: 64
Period size: 9 Copynumber: 5.2 Consensus size: 9
12365674 TTAATGTATT
12365684 AAATACAATA
1 AAATACAA-A
12365694 ATAATACAAA
1 A-AATACAAA
12365704 AAATACAAA
1 AAATACAAA
*
12365713 AAATAAAAA
1 AAATACAAA
12365722 AAATAGCAAA
1 AAATA-CAAA
12365732 AA
1 AA
12365734 GGGTTGATGG
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
9 21 0.58
10 8 0.22
11 7 0.19
ACGTcount: A:0.76, C:0.08, G:0.02, T:0.14
Consensus pattern (9 bp):
AAATACAAA
Found at i:12366043 original size:20 final size:19
Alignment explanation
Indices: 12366018--12366080 Score: 81
Period size: 20 Copynumber: 3.2 Consensus size: 19
12366008 GTTAACACAA
12366018 AAAAAACCTAAAATAAAACC
1 AAAAAACCTAAAA-AAAACC
*
12366038 AAAAAACCTAAAACAGAACC
1 AAAAAACCTAAAA-AAAACC
**
12366058 AAAAAACCTATCAAAAACC
1 AAAAAACCTAAAAAAAACC
12366077 AAAA
1 AAAA
12366081 GAAAAAACAC
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
19 9 0.24
20 29 0.76
ACGTcount: A:0.68, C:0.22, G:0.02, T:0.08
Consensus pattern (19 bp):
AAAAAACCTAAAAAAAACC
Found at i:12371383 original size:18 final size:18
Alignment explanation
Indices: 12371360--12371550 Score: 111
Period size: 18 Copynumber: 9.7 Consensus size: 18
12371350 ACTTTTACTT
*
12371360 ATAAATAATATCATATTA
1 ATAAATAATATAATATTA
12371378 ATAAATGAATAATATTATATTA
1 ATAAAT-AAT-ATA--ATATTA
12371400 ATAAATGATATTATTATATATTA
1 ATAAAT-A-A-TA-TA-ATATTA
*
12371423 ACAAATAATATAATATTA
1 ATAAATAATATAATATTA
*
12371441 ATAAATAATAT--TATAA
1 ATAAATAATATAATATTA
*
12371457 ATAAATATATACTAAATACTAA
1 ATAAATA-ATA-T-AATA-TTA
12371479 TATAAATAA-ATAATATTA
1 -ATAAATAATATAATATTA
* * *
12371497 TATTACTAA-ATCATATTA
1 -ATAAATAATATAATATTA
12371515 ATAAATAATATTATAATATATTA
1 ATAAAT-A-A-TAT-A-ATATTA
12371538 ATAAATAATATAA
1 ATAAATAATATAA
12371551 AGAATAATAA
Statistics
Matches: 142, Mismatches: 11, Indels: 40
0.74 0.06 0.21
Matches are distributed among these distances:
16 11 0.08
17 7 0.05
18 42 0.30
19 11 0.08
20 8 0.06
21 7 0.05
22 20 0.14
23 33 0.23
24 3 0.02
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.39
Consensus pattern (18 bp):
ATAAATAATATAATATTA
Found at i:12371453 original size:31 final size:31
Alignment explanation
Indices: 12371360--12371563 Score: 122
Period size: 31 Copynumber: 6.5 Consensus size: 31
12371350 ACTTTTACTT
*
12371360 ATAAATAATATCATATTAATAAATGAATAATATTA
1 ATAAATAATATAATATTAAT--A--AATAATATTA
* * *
12371395 TATTAATAA-ATGATATT-AT-TAT-ATATTA
1 -ATAAATAATATAATATTAATAAATAATATTA
*
12371423 ACAAATAATATAATATTAATAAATAATATT-
1 ATAAATAATATAATATTAATAAATAATATTA
* * *
12371453 ATAAATAA-ATATATACTAA-ATACTAATATAA
1 ATAAATAATATA-ATATTAATA-AATAATATTA
* * *
12371484 ATAAATAATATTATATTACTAAATCATATTA
1 ATAAATAATATAATATTAATAAATAATATTA
12371515 ATAAATAATATTATAATATATTAATAAATAATA-TA
1 ATAAAT-A-A-TAT-A-ATATTAATAAATAATATTA
12371550 A-AGAATAATA-AATA
1 ATA-AATAATATAATA
12371564 GTTTTATTTT
Statistics
Matches: 133, Mismatches: 20, Indels: 37
0.70 0.11 0.19
Matches are distributed among these distances:
27 6 0.05
28 13 0.10
29 11 0.08
30 23 0.17
31 31 0.23
32 6 0.05
33 2 0.02
34 7 0.05
35 13 0.10
36 21 0.16
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.38
Consensus pattern (31 bp):
ATAAATAATATAATATTAATAAATAATATTA
Found at i:12371472 original size:27 final size:26
Alignment explanation
Indices: 12371429--12371547 Score: 85
Period size: 27 Copynumber: 4.8 Consensus size: 26
12371419 ATTAACAAAT
*
12371429 AATATAATATTAATAAATAATATTATA
1 AATA-AATATTAATAAATAATAATATA
* *
12371456 AATAAATATATACTAAATACTAATATA
1 AATAAATAT-TAATAAATAATAATATA
* *
12371483 AAT-AA-A-TAAT--ATTATATTACTA
1 AATAAATATTAATAAATAATAATA-TA
* *
12371505 AAT-CATATTAATAAATAATATTAT-
1 AATAAATATTAATAAATAATAATATA
12371529 AAT--ATATTAATAAATAATA
1 AATAAATATTAATAAATAATA
12371548 TAAAGAATAA
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
21 6 0.08
22 6 0.08
23 20 0.26
24 7 0.09
25 2 0.03
26 15 0.19
27 21 0.27
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (26 bp):
AATAAATATTAATAAATAATAATATA
Found at i:12371563 original size:23 final size:23
Alignment explanation
Indices: 12371509--12371563 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
12371499 TTACTAAATC
* * *
12371509 ATATTAATAAATAATATTATAAT
1 ATATAAATAAATAATATAAGAAT
*
12371532 ATATTAATAAATAATATAAAGAAT
1 ATATAAATAAATAATAT-AAGAAT
12371556 A-ATAAATA
1 ATATAAATA
12371564 GTTTTATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 23 0.82
24 5 0.18
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
ATATAAATAAATAATATAAGAAT
Found at i:12371675 original size:25 final size:27
Alignment explanation
Indices: 12371647--12371720 Score: 75
Period size: 26 Copynumber: 2.9 Consensus size: 27
12371637 TTTGAATATT
12371647 AATAATTTTAATAA-TAAA-TAATTTC
1 AATAATTTTAATAATTAAATTAATTTC
* *
12371672 AATATATTTTAA-AATTAAATTATTTTT
1 AATA-ATTTTAATAATTAAATTAATTTC
* *
12371699 AAT-ATTTTAATAGTTATATTAA
1 AATAATTTTAATAATTAAATTAA
12371721 CATTATTTGA
Statistics
Matches: 40, Mismatches: 5, Indels: 7
0.77 0.10 0.13
Matches are distributed among these distances:
25 13 0.32
26 19 0.47
27 8 0.20
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (27 bp):
AATAATTTTAATAATTAAATTAATTTC
Found at i:12371829 original size:15 final size:14
Alignment explanation
Indices: 12371791--12371828 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
12371781 TAGAAAATAT
12371791 AAAT-ATTTTTCAA
1 AAATCATTTTTCAA
*
12371804 AAATCATTTTTCAT
1 AAATCATTTTTCAA
*
12371818 AAGTCATTTTT
1 AAATCATTTTT
12371829 TACGAAATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.50
Consensus pattern (14 bp):
AAATCATTTTTCAA
Found at i:12382605 original size:24 final size:23
Alignment explanation
Indices: 12382573--12382637 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 23
12382563 TATTATTTAT
12382573 TTATTATATAATAAAATTTATATA
1 TTATTATATAATAAAATTTAT-TA
***
12382597 TTATTATATAGGCAAATTTATTA
1 TTATTATATAATAAAATTTATTA
*
12382620 -TATTAAATCAATAAAATT
1 TTATTATAT-AATAAAATT
12382638 ATTTTAAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
22 7 0.21
23 8 0.24
24 18 0.55
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.46
Consensus pattern (23 bp):
TTATTATATAATAAAATTTATTA
Done.