Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, 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: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 71 of 106
Found at i:13052673 original size:14 final size:13
Alignment explanation
Indices: 13052654--13052707 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 13
13052644 TTTGACCATG
13052654 ATAAAAAATAATTA
1 ATAAAAAA-AATTA
13052668 ATAAAAGAAAATGTA
1 ATAAAA-AAAAT-TA
**
13052683 CATATGAAAAATTA
1 -ATAAAAAAAATTA
13052697 ATAAAAAAAAT
1 ATAAAAAAAAT
13052708 CTACATTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
13 9 0.27
14 11 0.33
15 9 0.27
16 4 0.12
ACGTcount: A:0.69, C:0.02, G:0.06, T:0.24
Consensus pattern (13 bp):
ATAAAAAAAATTA
Found at i:13052791 original size:26 final size:31
Alignment explanation
Indices: 13052748--13052812 Score: 86
Period size: 27 Copynumber: 2.3 Consensus size: 31
13052738 TGAATTTCCA
*
13052748 TTTTACTAATTTTCATATA-A-A-ATTTC-T
1 TTTTATTAATTTTCATATATAGATATTTCTT
13052775 TTTTATTAATTTT-ATATATAGATATTTCTT
1 TTTTATTAATTTTCATATATAGATATTTCTT
13052805 TTTTATTA
1 TTTTATTA
13052813 CATAAAGATT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
26 5 0.15
27 13 0.39
28 1 0.03
29 5 0.15
30 9 0.27
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.62
Consensus pattern (31 bp):
TTTTATTAATTTTCATATATAGATATTTCTT
Found at i:13052885 original size:13 final size:14
Alignment explanation
Indices: 13052869--13052919 Score: 52
Period size: 13 Copynumber: 3.8 Consensus size: 14
13052859 ATAAATATAA
13052869 ATAATTATTAT-TT
1 ATAATTATTATATT
13052882 ATAATTATT-TATT
1 ATAATTATTATATT
* * *
13052895 ATATTTATTAAAAT
1 ATAATTATTATATT
*
13052909 ATAAATATTAT
1 ATAATTATTAT
13052920 TTCTAACTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
12 1 0.03
13 19 0.63
14 10 0.33
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATAATTATTATATT
Found at i:13062845 original size:25 final size:26
Alignment explanation
Indices: 13062817--13062881 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
13062807 GAAATGTGAG
*
13062817 ATATATATTTAAATAT-AAATATTTT
1 ATATATATATAAATATCAAATATTTT
* * *
13062842 ATATAAATGTAAA-ATCATATATTTT
1 ATATATATATAAATATCAAATATTTT
13062867 AT-TATATATAAATAT
1 ATATATATATAAATAT
13062882 TATTTTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
24 10 0.30
25 23 0.70
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
ATATATATATAAATATCAAATATTTT
Found at i:13065486 original size:57 final size:57
Alignment explanation
Indices: 13065398--13065511 Score: 219
Period size: 57 Copynumber: 2.0 Consensus size: 57
13065388 CTCATTATAT
13065398 TTATCTTCCTTTGTCTCTCCTTTAAATCCCCATTTAATCTCTTCTTCTGGAACTTCA
1 TTATCTTCCTTTGTCTCTCCTTTAAATCCCCATTTAATCTCTTCTTCTGGAACTTCA
*
13065455 TTATCTTCCTTTGTCTCTTCTTTAAATCCCCATTTAATCTCTTCTTCTGGAACTTCA
1 TTATCTTCCTTTGTCTCTCCTTTAAATCCCCATTTAATCTCTTCTTCTGGAACTTCA
13065512 CAGCAGAAAA
Statistics
Matches: 56, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.18, C:0.29, G:0.05, T:0.48
Consensus pattern (57 bp):
TTATCTTCCTTTGTCTCTCCTTTAAATCCCCATTTAATCTCTTCTTCTGGAACTTCA
Found at i:13067812 original size:15 final size:15
Alignment explanation
Indices: 13067770--13068061 Score: 83
Period size: 15 Copynumber: 19.1 Consensus size: 15
13067760 TGGCCGCAAT
13067770 TTATGCAACTGCAGC
1 TTATGCAACTGCAGC
* **
13067785 TCATGCATTTGCAGC
1 TTATGCAACTGCAGC
* *
13067800 TTATGTAACTGCAGA
1 TTATGCAACTGCAGC
**
13067815 TCCTGCAACTGCAGC
1 TTATGCAACTGCAGC
* * **
13067830 TT-TTCTGACTGCAAT
1 TTATGC-AACTGCAGC
13067845 TTATGCAACTGCAACTGCAGC
1 TTAT------GCAACTGCAGC
* **
13067866 TCATGCATTTGCAGC
1 TTATGCAACTGCAGC
* *
13067881 TTATGTAACTGCAGA
1 TTATGCAACTGCAGC
**
13067896 TCCTGCAACTGCAGC
1 TTATGCAACTGCAGC
* **
13067911 TCT-T-CTGACTGCAAT
1 T-TATGC-AACTGCAGC
13067926 TTATGCAACTGCAGC
1 TTATGCAACTGCAGC
* **
13067941 TCATGCATTTGCAGC
1 TTATGCAACTGCAGC
* *
13067956 TTATGTAACTGCAGG
1 TTATGCAACTGCAGC
** *
13067971 TCCTACAACTGCAGC
1 TTATGCAACTGCAGC
*
13067986 TTAT-CTGACTGCAG-
1 TTATGC-AACTGCAGC
*
13068000 TTCATGCAAATGCAGC
1 TT-ATGCAACTGCAGC
* * * *
13068016 TCATCCGATTGCAG-
1 TTATGCAACTGCAGC
*
13068030 TTCATGCAAATGCAGC
1 TT-ATGCAACTGCAGC
* **
13068046 TCATGTGACTGCAGC
1 TTATGCAACTGCAGC
13068061 T
1 T
13068062 CATGTAAATG
Statistics
Matches: 189, Mismatches: 70, Indels: 36
0.64 0.24 0.12
Matches are distributed among these distances:
14 8 0.04
15 166 0.88
16 5 0.03
21 9 0.05
22 1 0.01
ACGTcount: A:0.25, C:0.26, G:0.20, T:0.30
Consensus pattern (15 bp):
TTATGCAACTGCAGC
Found at i:13067894 original size:81 final size:80
Alignment explanation
Indices: 13067772--13068013 Score: 377
Period size: 81 Copynumber: 3.1 Consensus size: 80
13067762 GCCGCAATTT
13067772 ATGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAACTGCAGCTTTTCTG
1 ATGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAACTGCAGCTTTTCTG
13067837 ACTGCAATTTATGCA
66 ACTGCAATTTATGCA
*
13067852 ACTGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAACTGCAGCTCTTCT
1 A-TGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAACTGCAGCTTTTCT
13067917 GACTGCAA-TT-T---
65 GACTGCAATTTATGCA
* * *
13067928 ATGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGGTCCTACAACTGCAGCTTATCTG
1 ATGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAACTGCAGCTTTTCTG
* *
13067993 ACTGCAGTTCATGCAA
66 ACTGCAATTTATGC-A
13068009 ATGCA
1 ATGCA
13068014 GCTCATCCGA
Statistics
Matches: 148, Mismatches: 7, Indels: 13
0.88 0.04 0.08
Matches are distributed among these distances:
75 66 0.45
76 2 0.01
77 1 0.01
79 1 0.01
80 3 0.02
81 75 0.51
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (80 bp):
ATGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAACTGCAGCTTTTCTG
ACTGCAATTTATGCA
Found at i:13067949 original size:75 final size:74
Alignment explanation
Indices: 13067765--13068019 Score: 384
Period size: 75 Copynumber: 3.3 Consensus size: 74
13067755 CTTTGTGGCC
13067765 GCAATTTATGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAACTGCAGC
1 GCAATTTATGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAACTGCAGC
13067830 TTTTCTGACT
66 -TTTCTGACT
13067840 GCAATTTATGCAACTGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAAC
1 GCAA-TT-T---A-TGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAAC
13067905 TGCAGCTCTTCTGACT
60 TGCAGCT-TTCTGACT
* *
13067921 GCAATTTATGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGGTCCTACAACTGCAGC
1 GCAATTTATGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAACTGCAGC
13067986 TTATCTGACT
66 TT-TCTGACT
* * *
13067996 GCAGTTCATGCAAATGCAGCTCAT
1 GCAATTTATGCAACTGCAGCTCAT
13068020 CCGATTGCAG
Statistics
Matches: 167, Mismatches: 5, Indels: 16
0.89 0.03 0.09
Matches are distributed among these distances:
74 1 0.01
75 88 0.53
76 3 0.02
77 1 0.01
79 1 0.01
80 4 0.02
81 69 0.41
ACGTcount: A:0.25, C:0.26, G:0.19, T:0.30
Consensus pattern (74 bp):
GCAATTTATGCAACTGCAGCTCATGCATTTGCAGCTTATGTAACTGCAGATCCTGCAACTGCAGC
TTTCTGACT
Found at i:13067960 original size:30 final size:30
Alignment explanation
Indices: 13067926--13068072 Score: 125
Period size: 30 Copynumber: 4.9 Consensus size: 30
13067916 TGACTGCAAT
* **
13067926 TTATGCAACTGCAGCTCATGCATTTGCAGC
1 TTATGCGACTGCAGCTCATGCAAATGCAGC
** * * * *
13067956 TTATGTAACTGCAGGTCCTACAACTGCAGC
1 TTATGCGACTGCAGCTCATGCAAATGCAGC
*
13067986 TTAT-CTGACTGCAGTTCATGCAAATGCAGC
1 TTATGC-GACTGCAGCTCATGCAAATGCAGC
* * * *
13068016 TCATCCGATTGCAGTTCATGCAAATGCAGC
1 TTATGCGACTGCAGCTCATGCAAATGCAGC
* * *
13068046 TCATGTGACTGCAGCTCATGTAAATGC
1 TTATGCGACTGCAGCTCATGCAAATGC
13068073 TATTCATGTA
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
30 95 0.99
31 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (30 bp):
TTATGCGACTGCAGCTCATGCAAATGCAGC
Found at i:13077353 original size:15 final size:15
Alignment explanation
Indices: 13077333--13077363 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13077323 GTTAGATATT
13077333 AATAAAGGAAAGAAA
1 AATAAAGGAAAGAAA
*
13077348 AATAAAGGTAAGAAA
1 AATAAAGGAAAGAAA
13077363 A
1 A
13077364 GGAAAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.19, T:0.10
Consensus pattern (15 bp):
AATAAAGGAAAGAAA
Found at i:13078325 original size:5 final size:5
Alignment explanation
Indices: 13078317--13078343 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
13078307 AACAATACAA
13078317 TTATT TTATT TTATT TTATT TTATT TT
1 TTATT TTATT TTATT TTATT TTATT TT
13078344 CTTACTCTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTATT
Found at i:13080830 original size:4 final size:4
Alignment explanation
Indices: 13080821--13080892 Score: 63
Period size: 4 Copynumber: 18.0 Consensus size: 4
13080811 ACTTTCGAGC
* * * * * * * *
13080821 ATAT ATAT ATGT ATAT GTAC ATGT ATAT GTAT ATAC ATAC ATAT ACAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
*
13080869 ATAT GTAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT
13080893 GTGTGTGTGT
Statistics
Matches: 52, Mismatches: 16, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (4 bp):
ATAT
Found at i:13080877 original size:6 final size:6
Alignment explanation
Indices: 13080821--13080892 Score: 63
Period size: 6 Copynumber: 12.0 Consensus size: 6
13080811 ACTTTCGAGC
* * * * * * * *
13080821 ATATAT ATATGT ATATGT ACATGT ATATGT ATATAC ATACAT ATACAT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
*
13080869 ATATGT ATATAT ATATAT ATATAT
1 ATATAT ATATAT ATATAT ATATAT
13080893 GTGTGTGTGT
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 56 1.00
ACGTcount: A:0.43, C:0.06, G:0.07, T:0.44
Consensus pattern (6 bp):
ATATAT
Found at i:13087805 original size:19 final size:18
Alignment explanation
Indices: 13087781--13087824 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
13087771 TACGTGTGAA
13087781 TTTAATTGT-TTAATTATAT
1 TTTAATT-TATTAATTA-AT
13087800 TTTAATTTATTAATTAAT
1 TTTAATTTATTAATTAAT
13087818 TATTAAT
1 T-TTAAT
13087825 GATATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTAATTTATTAATTAAT
Found at i:13089479 original size:16 final size:18
Alignment explanation
Indices: 13089452--13089484 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
13089442 TTGAATATAA
13089452 AGTAATTTTATT-ATTTT
1 AGTAATTTTATTCATTTT
13089469 AGTAA-TTTATTCATTT
1 AGTAATTTTATTCATTT
13089485 AATTAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (18 bp):
AGTAATTTTATTCATTTT
Found at i:13092470 original size:3 final size:3
Alignment explanation
Indices: 13092462--13092496 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
13092452 CCTATCCTTT
13092462 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13092497 TGTTGGGGAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13097539 original size:52 final size:52
Alignment explanation
Indices: 13097454--13097609 Score: 206
Period size: 52 Copynumber: 3.0 Consensus size: 52
13097444 ATAACCATAC
* * * *
13097454 AAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCTTGTAAGTT
1 AAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCTTGCAAGTT
* *
13097506 AAACTTGCCTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCTTGCAAGTC
1 AAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCTTGCAAGTT
* * * *
13097558 AAACTTACCTATTAAAAATCCTCTTT-CTCTTAGAATTATTCTTTTGCAAGTT
1 AAACTTGCCTATTAAGAAT-CTCTTTCCTCTTAGAATTCTTCTCTTGCAAGTT
13097610 TTCTTATCCA
Statistics
Matches: 91, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
52 85 0.93
53 6 0.07
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (52 bp):
AAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCTTGCAAGTT
Found at i:13097650 original size:11 final size:11
Alignment explanation
Indices: 13097634--13097683 Score: 64
Period size: 11 Copynumber: 4.5 Consensus size: 11
13097624 GTAATATCTG
13097634 ACAAATCCCAA
1 ACAAATCCCAA
* *
13097645 ACAAATCTCTA
1 ACAAATCCCAA
* *
13097656 ACAAATCTCTA
1 ACAAATCCCAA
13097667 ACAAATCCCAA
1 ACAAATCCCAA
13097678 ACAAAT
1 ACAAAT
13097684 TTCTTATGGG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 35 1.00
ACGTcount: A:0.52, C:0.30, G:0.00, T:0.18
Consensus pattern (11 bp):
ACAAATCCCAA
Found at i:13097990 original size:24 final size:24
Alignment explanation
Indices: 13097963--13098054 Score: 69
Period size: 25 Copynumber: 3.8 Consensus size: 24
13097953 TTTTCCCACA
13097963 TCTCGAACTTTCAGCTCTTTCACG
1 TCTCGAACTTTCAGCTCTTTCACG
* *
13097987 TCTCGAACCTTT-GGCTCTTTCCACA
1 TCTCGAA-CTTTCAGCTCTTT-CACG
* * * *
13098012 TCTTGAATTTTTAACTCTTCTCACG
1 TCTCGAACTTTCAGCTCTT-TCACG
* * *
13098037 TTTTGAACCTTCAGCTCT
1 TCTCGAACTTTCAGCTCT
13098055 GATACCACTT
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
24 17 0.33
25 34 0.65
26 1 0.02
ACGTcount: A:0.17, C:0.30, G:0.11, T:0.41
Consensus pattern (24 bp):
TCTCGAACTTTCAGCTCTTTCACG
Found at i:13098054 original size:50 final size:49
Alignment explanation
Indices: 13097958--13098054 Score: 113
Period size: 49 Copynumber: 2.0 Consensus size: 49
13097948 TTAGTTTTTC
* **
13097958 CCACATCTCGAACTTTCAGCTCTTTCACGTCTCGAACCTTTGGCTCTTT
1 CCACATCTCGAACTTTCAACTCTTTCACGTCTCGAACCTTCAGCTCTTT
* * * * *
13098007 CCACATCTTGAATTTTTAACTCTTCTCACGTTTTGAACCTTCAGCTCT
1 CCACATCTCGAACTTTCAACTCTT-TCACGTCTCGAACCTTCAGCTCT
13098055 GATACCACTT
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
49 20 0.51
50 19 0.49
ACGTcount: A:0.19, C:0.32, G:0.10, T:0.39
Consensus pattern (49 bp):
CCACATCTCGAACTTTCAACTCTTTCACGTCTCGAACCTTCAGCTCTTT
Found at i:13100291 original size:35 final size:35
Alignment explanation
Indices: 13100242--13100312 Score: 133
Period size: 35 Copynumber: 2.0 Consensus size: 35
13100232 TGTGGACCCT
*
13100242 CTCAGTCTCTTTTAGTCCACTCACAAACAAATATA
1 CTCAGTCTCCTTTAGTCCACTCACAAACAAATATA
13100277 CTCAGTCTCCTTTAGTCCACTCACAAACAAATATA
1 CTCAGTCTCCTTTAGTCCACTCACAAACAAATATA
13100312 C
1 C
13100313 GCACCCATAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.31, G:0.06, T:0.30
Consensus pattern (35 bp):
CTCAGTCTCCTTTAGTCCACTCACAAACAAATATA
Found at i:13100521 original size:52 final size:52
Alignment explanation
Indices: 13100435--13100539 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
13100425 TATAACTATA
* * *
13100435 CAAACTTGCCTATTAAGAATCTATTTCCTTTTAGAATTCTTCTCTTGCAAGT
1 CAAACTTACATATTAAGAATCTATTTCCTCTTAGAATTCTTCTCTTGCAAGT
* * * *
13100487 CAAACTTACATATTAAGAATCTTTTTTCTCTTAGAATTCTTCTTTTGTAAGT
1 CAAACTTACATATTAAGAATCTATTTCCTCTTAGAATTCTTCTCTTGCAAGT
13100539 C
1 C
13100540 TTCTTGTCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.45
Consensus pattern (52 bp):
CAAACTTACATATTAAGAATCTATTTCCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:13100582 original size:11 final size:11
Alignment explanation
Indices: 13100566--13100627 Score: 115
Period size: 11 Copynumber: 5.6 Consensus size: 11
13100556 AATATTTGAT
13100566 AAATCTCAAAC
1 AAATCTCAAAC
13100577 AAATCTCAAAC
1 AAATCTCAAAC
*
13100588 AAATCTCTAAC
1 AAATCTCAAAC
13100599 AAATCTCAAAC
1 AAATCTCAAAC
13100610 AAATCTCAAAC
1 AAATCTCAAAC
13100621 AAATCTC
1 AAATCTC
13100628 TTATGGGATT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 49 1.00
ACGTcount: A:0.52, C:0.27, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATCTCAAAC
Found at i:13101740 original size:23 final size:23
Alignment explanation
Indices: 13101714--13101758 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
13101704 AATAACTTTA
13101714 AAATATAAAAAAATAAAAATTTT
1 AAATATAAAAAAATAAAAATTTT
** *
13101737 AAATATTCAAAAATAATAATTT
1 AAATATAAAAAAATAAAAATTT
13101759 GAGACATTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (23 bp):
AAATATAAAAAAATAAAAATTTT
Found at i:13101772 original size:24 final size:24
Alignment explanation
Indices: 13101695--13101779 Score: 61
Period size: 23 Copynumber: 3.6 Consensus size: 24
13101685 TATCATGATT
*
13101695 TTAATAAAA-AATAACTTT-AAA-A
1 TTAAAAAAATAATAA-TTTGAAACA
* * *
13101717 TATAAAAAAATAAAAATTTTAAATA
1 T-TAAAAAAATAATAATTTGAAACA
* *
13101742 TT-CAAAAATAATAATTTGAGACA
1 TTAAAAAAATAATAATTTGAAACA
*
13101765 TTAAAAAAAGAATAA
1 TTAAAAAAATAATAA
13101780 AAAAAATGAG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
22 1 0.02
23 28 0.57
24 18 0.37
25 2 0.04
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (24 bp):
TTAAAAAAATAATAATTTGAAACA
Found at i:13104106 original size:4 final size:4
Alignment explanation
Indices: 13104097--13104121 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
13104087 AATTTGGGTT
13104097 TTTC TTTC TTTC TTTC TTTC TTTC T
1 TTTC TTTC TTTC TTTC TTTC TTTC T
13104122 GGGTTTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTC
Found at i:13106315 original size:59 final size:59
Alignment explanation
Indices: 13106223--13106341 Score: 202
Period size: 59 Copynumber: 2.0 Consensus size: 59
13106213 ATAGCTGATG
* * *
13106223 AGCTCACCTAGTATCCTTGTGTGGCATTCAAAACAACAGAATTTACGTTAAAGTTCATA
1 AGCTCACCAAGTATACATGTGTGGCATTCAAAACAACAGAATTTACGTTAAAGTTCATA
*
13106282 AGCTCACCAAGTATACATGTGTGGCATTCAAAACAACAGAATTTATGTTAAAGTTCATA
1 AGCTCACCAAGTATACATGTGTGGCATTCAAAACAACAGAATTTACGTTAAAGTTCATA
13106341 A
1 A
13106342 TGGCATCAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.29
Consensus pattern (59 bp):
AGCTCACCAAGTATACATGTGTGGCATTCAAAACAACAGAATTTACGTTAAAGTTCATA
Found at i:13110426 original size:52 final size:51
Alignment explanation
Indices: 13110271--13110427 Score: 170
Period size: 52 Copynumber: 3.0 Consensus size: 51
13110261 TATAATCATA
* * * * * * *
13110271 CAAACTTGCCCATTAAGAATCCCTCTCCTCTTAGAATTCTTCTCCTGTAAGT
1 CAAACTTACCTATTAAAAATCTCT-TTCTCTTAGAATTCTTCTCTTGCAAGT
* * *
13110323 CAAACTTGCCTATTAAAAATCTCTTTCCCTTTAGAATTCTTCTCTTACAAGT
1 CAAACTTACCTATTAAAAATCTCTTTCTC-TTAGAATTCTTCTCTTGCAAGT
* * *
13110375 CAAACTTACCTATTAAGAATTTTCTTTCTCTTAGAATTCTTCTTTTGCAAGT
1 CAAACTTACCTATTAA-AAATCTCTTTCTCTTAGAATTCTTCTCTTGCAAGT
13110427 C
1 C
13110428 TTCTTGTCCA
Statistics
Matches: 89, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
51 3 0.03
52 76 0.85
53 10 0.11
ACGTcount: A:0.27, C:0.25, G:0.08, T:0.40
Consensus pattern (51 bp):
CAAACTTACCTATTAAAAATCTCTTTCTCTTAGAATTCTTCTCTTGCAAGT
Found at i:13110746 original size:25 final size:25
Alignment explanation
Indices: 13110713--13110798 Score: 95
Period size: 25 Copynumber: 3.5 Consensus size: 25
13110703 AAACCATGCA
*
13110713 CTTCTCACATCTTAAACCTTTAGCT
1 CTTCTCACATCTCAAACCTTTAGCT
* *
13110738 CTTCCCACATCTCGAA-CTTTCAGCT
1 CTTCTCACATCTCAAACCTTT-AGCT
* *
13110763 CTT-TCACATCTCGAACCTTTGGCT
1 CTTCTCACATCTCAAACCTTTAGCT
*
13110787 CTTTTCACATCT
1 CTTCTCACATCT
13110799 TAAATCTATG
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
24 21 0.40
25 32 0.60
ACGTcount: A:0.20, C:0.35, G:0.07, T:0.38
Consensus pattern (25 bp):
CTTCTCACATCTCAAACCTTTAGCT
Found at i:13110875 original size:31 final size:31
Alignment explanation
Indices: 13110835--13110914 Score: 126
Period size: 31 Copynumber: 2.6 Consensus size: 31
13110825 GAACATTCAA
*
13110835 CTCTGATACCAATTGTT-AGGGAACACCACAG
1 CTCTGATACCATTTGTTGA-GGAACACCACAG
*
13110866 CTCTAATACCATTTGTTGAGGAACACCACAG
1 CTCTGATACCATTTGTTGAGGAACACCACAG
13110897 CTCTGATACCATTTGTTG
1 CTCTGATACCATTTGTTG
13110915 GGCCTAAAAG
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
31 44 0.98
32 1 0.02
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (31 bp):
CTCTGATACCATTTGTTGAGGAACACCACAG
Found at i:13111499 original size:52 final size:52
Alignment explanation
Indices: 13111408--13111552 Score: 184
Period size: 52 Copynumber: 2.8 Consensus size: 52
13111398 TATAACCATA
* * * * * **
13111408 CAAATTTGCCCATTAAGAATCCCTCTCCTCTTAGGATTCTTCTCCTGTAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTACAAGT
* *
13111460 CAAACTTGCCTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTCTTACAAGT
1 CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTACAAGT
*
13111512 CAAACTTACCTATTAAGAATCTTCTTT-CTCTTAGAATTCTT
1 CAAACTTGCCTATTAAGAATC-TCTTTCCTCTTAGAATTCTT
13111553 TTTTTGCAAG
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 76 0.94
53 5 0.06
ACGTcount: A:0.26, C:0.25, G:0.08, T:0.41
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTCCTACAAGT
Found at i:13113394 original size:15 final size:15
Alignment explanation
Indices: 13113361--13113410 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
13113351 TAAATCTCAT
*
13113361 AAAATAAT-ATATTTA
1 AAAATAATAATA-TAA
13113376 AAAATAATAATATAA
1 AAAATAATAATATAA
13113391 AAAATAAATTAAT-TAA
1 AAAAT-AA-TAATATAA
13113407 AAAA
1 AAAA
13113411 GATAATATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
15 15 0.48
16 12 0.39
17 4 0.13
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAAATAATAATATAA
Found at i:13126219 original size:25 final size:25
Alignment explanation
Indices: 13126172--13126219 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
13126162 ATATAATTAA
*
13126172 ATAAATAATTAAAATAAATAACAAC
1 ATAAATAATTAAAATAAAAAACAAC
*
13126197 ATAAATAA-TAAAGTAAACAAACA
1 ATAAATAATTAAAATAAA-AAACA
13126220 TACAAATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.69, C:0.08, G:0.02, T:0.21
Consensus pattern (25 bp):
ATAAATAATTAAAATAAAAAACAAC
Found at i:13127465 original size:5 final size:5
Alignment explanation
Indices: 13127455--13127479 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
13127445 ATATTCATAT
13127455 AATTA AATTA AATTA AATTA AATTA
1 AATTA AATTA AATTA AATTA AATTA
13127480 TCTTTTATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:13130947 original size:10 final size:10
Alignment explanation
Indices: 13130929--13130959 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
13130919 TGTAGGATAG
*
13130929 AAATCTATAT
1 AAATATATAT
13130939 AAATATATAT
1 AAATATATAT
13130949 AAATATATAT
1 AAATATATAT
13130959 A
1 A
13130960 TATTATATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (10 bp):
AAATATATAT
Found at i:13131110 original size:26 final size:26
Alignment explanation
Indices: 13131079--13131130 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
13131069 TCAAATAAAA
*
13131079 ATTTTTAATAAATTATTTAAATTGAAT
1 ATTTTGAAT-AATTATTTAAATTGAAT
*
13131106 ATTTTGGATAATTATTTAAATTGAA
1 ATTTTGAATAATTATTTAAATTGAA
13131131 ATCAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 16 0.70
27 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (26 bp):
ATTTTGAATAATTATTTAAATTGAAT
Found at i:13134198 original size:14 final size:15
Alignment explanation
Indices: 13134169--13134201 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
13134159 TTTTTAATAT
*
13134169 TTAAAATTGTTAAAA
1 TTAAAATTGATAAAA
13134184 TTAAAATT-ATAAAA
1 TTAAAATTGATAAAA
13134198 TTAA
1 TTAA
13134202 TATTCTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (15 bp):
TTAAAATTGATAAAA
Found at i:13149240 original size:12 final size:12
Alignment explanation
Indices: 13149223--13149273 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
13149213 TTCTGTTTTT
13149223 TATTTTTTAAAA
1 TATTTTTTAAAA
13149235 TA--TTTTAAAA
1 TATTTTTTAAAA
* **
13149245 -ATTATAAAAAA
1 TATTTTTTAAAA
13149256 TATTTTTTAAAA
1 TATTTTTTAAAA
13149268 TATTTT
1 TATTTT
13149274 ATTTTATTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 6
0.71 0.14 0.14
Matches are distributed among these distances:
9 1 0.03
10 8 0.27
11 5 0.17
12 16 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (12 bp):
TATTTTTTAAAA
Found at i:13149842 original size:8 final size:8
Alignment explanation
Indices: 13149810--13149840 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
13149800 TTCCATTTTT
13149810 TCTTTTCA
1 TCTTTTCA
13149818 TCTTTTCA
1 TCTTTTCA
*
13149826 TCTTTTCC
1 TCTTTTCA
13149834 TCTTTTC
1 TCTTTTC
13149841 CTTTTTTCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (8 bp):
TCTTTTCA
Found at i:13149847 original size:8 final size:8
Alignment explanation
Indices: 13149810--13149848 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
13149800 TTCCATTTTT
*
13149810 TCTTTTCA
1 TCTTTTCC
*
13149818 TCTTTTCA
1 TCTTTTCC
13149826 TCTTTTCC
1 TCTTTTCC
13149834 TCTTTTCC
1 TCTTTTCC
*
13149842 TTTTTTC
1 TCTTTTC
13149849 TTCCTTTCTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.05, C:0.28, G:0.00, T:0.67
Consensus pattern (8 bp):
TCTTTTCC
Found at i:13157009 original size:20 final size:21
Alignment explanation
Indices: 13156984--13157037 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
13156974 ATATTTTTTA
13156984 AATATTTATATTT-AAAAAAT
1 AATATTTATATTTAAAAAAAT
13157004 AATATTTTATATTTAAAAAAAAT
1 AATA-TTTATATTT-AAAAAAAT
13157027 AATATTT-TATT
1 AATATTTATATT
13157038 AATTTCGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.13
21 13 0.42
22 3 0.10
23 11 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
AATATTTATATTTAAAAAAAT
Found at i:13157014 original size:21 final size:22
Alignment explanation
Indices: 13156984--13157036 Score: 83
Period size: 23 Copynumber: 2.5 Consensus size: 22
13156974 ATATTTTTTA
13156984 AATA-TTTATATTT-AAAAAAT
1 AATATTTTATATTTAAAAAAAT
13157004 AATATTTTATATTTAAAAAAAAT
1 AATATTTTATATTT-AAAAAAAT
13157027 AATATTTTAT
1 AATATTTTAT
13157037 TAATTTCGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
20 4 0.13
21 9 0.30
23 17 0.57
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
AATATTTTATATTTAAAAAAAT
Found at i:13158714 original size:4 final size:4
Alignment explanation
Indices: 13158682--13158806 Score: 97
Period size: 4 Copynumber: 31.2 Consensus size: 4
13158672 GTCACATACG
* * * * * *
13158682 TATA TATA TGTA TATG TGTA CATA CATA TATA TATA TATA TTTA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * ** *
13158730 TATA TATA TGTA TACA TATA CATA TATA CATA CGTA TATA TATG TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
13158778 TGTG TACA TACA TATA TATA TATA TATA T
1 TATA TATA TATA TATA TATA TATA TATA T
13158807 TGTGAGGCCT
Statistics
Matches: 93, Mismatches: 28, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
4 93 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (4 bp):
TATA
Found at i:13158716 original size:6 final size:6
Alignment explanation
Indices: 13158682--13158806 Score: 97
Period size: 6 Copynumber: 20.8 Consensus size: 6
13158672 GTCACATACG
* * * * * *
13158682 TATATA TATGTA TATGTG TACATA CATATA TATATA TATATT TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * * ** *
13158730 TATATA TATGTA TACATA TACATA TATACA TACGTA TATATA TGTATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
13158778 TGTGTA CATACA TATATA TATATA TATAT
1 TATATA TATATA TATATA TATATA TATAT
13158807 TGTGAGGCCT
Statistics
Matches: 91, Mismatches: 28, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
6 91 1.00
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (6 bp):
TATATA
Found at i:13158803 original size:26 final size:26
Alignment explanation
Indices: 13158675--13158804 Score: 125
Period size: 26 Copynumber: 4.8 Consensus size: 26
13158665 TCTAATTGTC
* * *
13158675 ACATACGTATATATATGTATATGTGT
1 ACATACATATATATATATATATGTAT
*
13158701 ACATACATATATATATATATATTTAT
1 ACATACATATATATATATATATGTAT
* * * *
13158727 ATATATATATATGTATACATATACATATAT
1 ACATACATATA--TAT--ATATATATGTAT
* * *
13158757 ACATACGTATATATATGTATATGTGT
1 ACATACATATATATATATATATGTAT
13158783 ACATACATATATATATATATAT
1 ACATACATATATATATATATAT
13158805 ATTGTGAGGC
Statistics
Matches: 83, Mismatches: 17, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
26 59 0.71
28 6 0.07
30 18 0.22
ACGTcount: A:0.42, C:0.08, G:0.07, T:0.43
Consensus pattern (26 bp):
ACATACATATATATATATATATGTAT
Found at i:13186941 original size:18 final size:17
Alignment explanation
Indices: 13186914--13186947 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
13186904 TATTTTATTA
13186914 TTTTTTATTTAAATTTT
1 TTTTTTATTTAAATTTT
*
13186931 TTTTTTCATTTGAATTT
1 TTTTTT-ATTTAAATTT
13186948 ATATTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.74
Consensus pattern (17 bp):
TTTTTTATTTAAATTTT
Found at i:13194196 original size:23 final size:23
Alignment explanation
Indices: 13194150--13194197 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
13194140 CAAGTATGTT
* *
13194150 AAAATATTGTCTTAATTTTAATA
1 AAAATATTATCTTAATTTAAATA
13194173 AAAATA-TATCTTAATTTAACATA
1 AAAATATTATCTTAATTTAA-ATA
13194196 AA
1 AA
13194198 CAAATCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAATATTATCTTAATTTAAATA
Found at i:13194664 original size:23 final size:23
Alignment explanation
Indices: 13194638--13194702 Score: 67
Period size: 23 Copynumber: 2.8 Consensus size: 23
13194628 AATTTTTAAC
13194638 TTTTAATTTATATTTATATAAAT
1 TTTTAATTTATATTTATATAAAT
* * * *
13194661 TTTTAACTTGTATTTAAATAAGT
1 TTTTAATTTATATTTATATAAAT
* * *
13194684 TTTTGATATATATTAATAT
1 TTTTAATTTATATTTATAT
13194703 TTTATTTAAA
Statistics
Matches: 32, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.37, C:0.02, G:0.05, T:0.57
Consensus pattern (23 bp):
TTTTAATTTATATTTATATAAAT
Found at i:13197454 original size:2 final size:2
Alignment explanation
Indices: 13197447--13197476 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
13197437 TTTGGCCCTT
*
13197447 TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
13197477 CGGAGCAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:13198753 original size:2 final size:2
Alignment explanation
Indices: 13198741--13198775 Score: 61
Period size: 2 Copynumber: 17.0 Consensus size: 2
13198731 ATTTGCTAGT
13198741 TA TA GTA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13198776 ATCAAAACAA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:13199534 original size:2 final size:2
Alignment explanation
Indices: 13199527--13199554 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13199517 GAAGCATGTG
13199527 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13199555 AACTTAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:13208076 original size:23 final size:22
Alignment explanation
Indices: 13208046--13208090 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 22
13208036 AGTTACTTAA
13208046 AATTAAATTAAATTATTTTTATT
1 AATTAAATTAAATT-TTTTTATT
13208069 AATTAAATTAAATTTTTTTATT
1 AATTAAATTAAATTTTTTTATT
13208091 TCAAAAATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
22 8 0.36
23 14 0.64
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (22 bp):
AATTAAATTAAATTTTTTTATT
Found at i:13208245 original size:14 final size:14
Alignment explanation
Indices: 13208213--13208245 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
13208203 TAAAATAAAA
13208213 TAAATAAAAATAGT
1 TAAATAAAAATAGT
*
13208227 T-AATAAAAATATT
1 TAAATAAAAATAGT
13208240 TAAATA
1 TAAATA
13208246 TCCAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
TAAATAAAAATAGT
Found at i:13208454 original size:9 final size:9
Alignment explanation
Indices: 13208440--13208481 Score: 57
Period size: 9 Copynumber: 4.7 Consensus size: 9
13208430 TGATAGAATG
13208440 ATTAAATTA
1 ATTAAATTA
13208449 ATTAAATTA
1 ATTAAATTA
**
13208458 ATTTGATTA
1 ATTAAATTA
*
13208467 ATTAATTTA
1 ATTAAATTA
13208476 ATTAAA
1 ATTAAA
13208482 ACCAAAATTA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
9 27 1.00
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (9 bp):
ATTAAATTA
Found at i:13208469 original size:13 final size:13
Alignment explanation
Indices: 13208440--13208480 Score: 55
Period size: 13 Copynumber: 3.1 Consensus size: 13
13208430 TGATAGAATG
*
13208440 ATTAAATTAATTAA
1 ATTAATTTAATT-A
*
13208454 ATTAATTTGATTA
1 ATTAATTTAATTA
13208467 ATTAATTTAATTA
1 ATTAATTTAATTA
13208480 A
1 A
13208481 AACCAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 14 0.58
14 10 0.42
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (13 bp):
ATTAATTTAATTA
Found at i:13209512 original size:10 final size:10
Alignment explanation
Indices: 13209487--13209515 Score: 51
Period size: 9 Copynumber: 3.0 Consensus size: 10
13209477 AAACGAAAAA
13209487 TTAAAATATC
1 TTAAAATATC
13209497 -TAAAATATC
1 TTAAAATATC
13209506 TTAAAATATC
1 TTAAAATATC
13209516 AAGTTTTAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
9 9 0.50
10 9 0.50
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAAATATC
Found at i:13223656 original size:20 final size:20
Alignment explanation
Indices: 13223615--13223656 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
13223605 CTTAGAGGAG
*
13223615 ATAGATTCTGGATTACATAT
1 ATAGATTCTGGATTACACAT
*
13223635 ATAGATTCTGGATTATACAT
1 ATAGATTCTGGATTACACAT
13223655 AT
1 AT
13223657 CTTGTTTGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.14, T:0.40
Consensus pattern (20 bp):
ATAGATTCTGGATTACACAT
Found at i:13247681 original size:34 final size:34
Alignment explanation
Indices: 13247643--13247712 Score: 140
Period size: 34 Copynumber: 2.1 Consensus size: 34
13247633 AGAGCATACG
13247643 TTTGATTATGAAAATTAATTATGGCAAACATATA
1 TTTGATTATGAAAATTAATTATGGCAAACATATA
13247677 TTTGATTATGAAAATTAATTATGGCAAACATATA
1 TTTGATTATGAAAATTAATTATGGCAAACATATA
13247711 TT
1 TT
13247713 GGTAAAACAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.43, C:0.06, G:0.11, T:0.40
Consensus pattern (34 bp):
TTTGATTATGAAAATTAATTATGGCAAACATATA
Found at i:13248065 original size:15 final size:15
Alignment explanation
Indices: 13248045--13248076 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
13248035 ATAAAATTTA
*
13248045 AAATTTTATAGCAAT
1 AAATTTTATAACAAT
13248060 AAATTTTATAACAAT
1 AAATTTTATAACAAT
13248075 AA
1 AA
13248077 TTAGATTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.38
Consensus pattern (15 bp):
AAATTTTATAACAAT
Found at i:13248341 original size:19 final size:20
Alignment explanation
Indices: 13248301--13248343 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
13248291 ATTTTTTATA
13248301 TTAAATTACTATATCGTATT
1 TTAAATTACTATATCGTATT
*
13248321 TTAAATTATTATATC-TATT
1 TTAAATTACTATATCGTATT
13248340 TTAA
1 TTAA
13248344 TCTCATAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (20 bp):
TTAAATTACTATATCGTATT
Found at i:13251752 original size:29 final size:31
Alignment explanation
Indices: 13251703--13251772 Score: 90
Period size: 29 Copynumber: 2.3 Consensus size: 31
13251693 AAATGAGTCT
13251703 TAAATTATAATAAAATATTTAACATGATATC
1 TAAATTATAATAAAATATTTAACATGATATC
* * *
13251734 TAAATT-TAA-AAAATTTTTAATATGATATT
1 TAAATTATAATAAAATATTTAACATGATATC
*
13251763 TGAATTATAA
1 TAAATTATAA
13251773 ATCTATTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.65
30 6 0.18
31 6 0.18
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (31 bp):
TAAATTATAATAAAATATTTAACATGATATC
Found at i:13253914 original size:163 final size:165
Alignment explanation
Indices: 13253622--13253948 Score: 534
Period size: 163 Copynumber: 2.0 Consensus size: 165
13253612 CATTGTTACC
* *
13253622 TAAATGAGTGATATAAGAGTTATTTCCACTTGTCCCTCATGTCCTCTCCACAAGCAAACGCTAGT
1 TAAATAAGTGATATAAGAGTGATTTCCACTTGTCCCTCATGTCCTCTCCACAAGCAAACGCTAGT
*
13253687 GCCAGACAAACAGAAAAGGCCATTATTATGTACGGTTCAGACATCCCATGAGCATAAAAATTTTG
66 GCCAGACAAACAGAAAAGGCCATTATTATGTACGGTTCAAACATCCCATGAGCATAAAAATTTTG
13253752 TTCT-TTTT-TATAATTAGTGTTCAAACACACCAT
131 TTCTCTTTTCTATAATTAGTGTTCAAACACACCAT
* *
13253785 TAAATAAGTGATATAAGAGTGATTTCCACTTGTCCCTCATGTCCTTTCCACAAGCAAGCGCTAGT
1 TAAATAAGTGATATAAGAGTGATTTCCACTTGTCCCTCATGTCCTCTCCACAAGCAAACGCTAGT
* * * *
13253850 GCCAGACAAACAGAAAAGGCCATTATTATGTATGGTTCAAACA-CAGCATGAGTATAAGAATTTT
66 GCCAGACAAACAGAAAAGGCCATTATTATGTACGGTTCAAACATC-CCATGAGCATAAAAATTTT
13253914 GTTCTCCTTTTCTATAATTAGTGTTCAAACACACC
130 GTTCT-CTTTTCTATAATTAGTGTTCAAACACACC
13253949 CTTATTATGT
Statistics
Matches: 151, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
162 1 0.01
163 123 0.81
165 4 0.03
166 23 0.15
ACGTcount: A:0.33, C:0.21, G:0.15, T:0.31
Consensus pattern (165 bp):
TAAATAAGTGATATAAGAGTGATTTCCACTTGTCCCTCATGTCCTCTCCACAAGCAAACGCTAGT
GCCAGACAAACAGAAAAGGCCATTATTATGTACGGTTCAAACATCCCATGAGCATAAAAATTTTG
TTCTCTTTTCTATAATTAGTGTTCAAACACACCAT
Found at i:13254525 original size:107 final size:107
Alignment explanation
Indices: 13254337--13254562 Score: 353
Period size: 107 Copynumber: 2.1 Consensus size: 107
13254327 TTGGGAGTTC
* * *
13254337 ATATGATTTCTTTTCAACTTATAATTTGTACTTCCTTGTGCAATAGGTTATTGTTAGTTCAAAGC
1 ATATGATTTCTTTTAAACTTATAATTTGTACTTCCTTGTGCAATAGGTCATTGTTAGTGCAAAGC
* * *
13254402 TAAGGTAATAGTGTGCTAAATCTATGAAATTCAACAATGGAT
66 TAAGGGAACAGCGTGCTAAATCTATGAAATTCAACAATGGAT
*
13254444 ATATGATTTCTTTTAAACTTATAATTTGTACTTCCTTGTGCAATAGGTCATTGTTAGTGGAAAGC
1 ATATGATTTCTTTTAAACTTATAATTTGTACTTCCTTGTGCAATAGGTCATTGTTAGTGCAAAGC
* **
13254509 TAAGGGCACAGCGTGCTAAATCTATGAAATTCAAGGATGGAT
66 TAAGGGAACAGCGTGCTAAATCTATGAAATTCAACAATGGAT
*
13254551 ATATGATATCTT
1 ATATGATTTCTT
13254563 CCGGCCATCC
Statistics
Matches: 108, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
107 108 1.00
ACGTcount: A:0.31, C:0.12, G:0.18, T:0.38
Consensus pattern (107 bp):
ATATGATTTCTTTTAAACTTATAATTTGTACTTCCTTGTGCAATAGGTCATTGTTAGTGCAAAGC
TAAGGGAACAGCGTGCTAAATCTATGAAATTCAACAATGGAT
Found at i:13266663 original size:2 final size:2
Alignment explanation
Indices: 13266656--13266680 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
13266646 ACTATTTGAG
13266656 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
13266681 ATTCAACATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:13273695 original size:29 final size:28
Alignment explanation
Indices: 13273642--13273696 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
13273632 ATTGTTTCTA
*
13273642 GTTTTATATTTTATGTTTTTGAAATTTT
1 GTTTTATATTTTATGTTTTTAAAATTTT
*
13273670 GTTTTATTTTTTTAT-TTTATTAAAATT
1 GTTTTA-TATTTTATGTTT-TTAAAATT
13273697 AAAAATAGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (28 bp):
GTTTTATATTTTATGTTTTTAAAATTTT
Found at i:13275739 original size:11 final size:11
Alignment explanation
Indices: 13275700--13275755 Score: 55
Period size: 11 Copynumber: 5.4 Consensus size: 11
13275690 ATATTTTATA
*
13275700 ATGTTTTATGG
1 ATGTTTGATGG
*
13275711 ATG-TT-ATGT
1 ATGTTTGATGG
*
13275720 ATATTTGATGG
1 ATGTTTGATGG
13275731 ATGTTTGATGG
1 ATGTTTGATGG
*
13275742 ATGTTGGAT-G
1 ATGTTTGATGG
13275752 ATGT
1 ATGT
13275756 ATTTGACGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
9 5 0.13
10 9 0.24
11 24 0.63
ACGTcount: A:0.21, C:0.00, G:0.30, T:0.48
Consensus pattern (11 bp):
ATGTTTGATGG
Found at i:13275874 original size:19 final size:20
Alignment explanation
Indices: 13275852--13275889 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
13275842 AGAGTTTACA
13275852 AATAATTACAAAT-TTTTTG
1 AATAATTACAAATATTTTTG
*
13275871 AATAATTATAAATATTTTT
1 AATAATTACAAATATTTTT
13275890 ATTTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (20 bp):
AATAATTACAAATATTTTTG
Found at i:13276035 original size:20 final size:20
Alignment explanation
Indices: 13275997--13276034 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13275987 ATTTTCATGG
*
13275997 TTATTATCGATGAAATTTTA
1 TTATTACCGATGAAATTTTA
13276017 TTATTACCGATG-AATTTT
1 TTATTACCGATGAAATTTT
13276035 TTGACAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.32, C:0.08, G:0.11, T:0.50
Consensus pattern (20 bp):
TTATTACCGATGAAATTTTA
Found at i:13277096 original size:27 final size:27
Alignment explanation
Indices: 13277045--13277096 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
13277035 AAGCTCTGGA
** *
13277045 GACTTGAACAGATTTTTTTTTTCCAAT
1 GACTTGAACAGATTTAATTTATCCAAT
*
13277072 GACTTGAACAGGTTTAATTTATCCA
1 GACTTGAACAGATTTAATTTATCCA
13277097 GAAACGGGGG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (27 bp):
GACTTGAACAGATTTAATTTATCCAAT
Found at i:13278224 original size:2 final size:2
Alignment explanation
Indices: 13278217--13278247 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
13278207 AAAGCCCATT
13278217 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
13278248 TTCCTCTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13278456 original size:2 final size:2
Alignment explanation
Indices: 13278449--13278484 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
13278439 TCCATCAGCC
13278449 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13278485 GGTGGTGCAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13289225 original size:16 final size:16
Alignment explanation
Indices: 13289204--13289234 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
13289194 AATATATATC
*
13289204 ATAAATTTTATTTTAT
1 ATAAATTTTAATTTAT
13289220 ATAAATTTTAATTTA
1 ATAAATTTTAATTTA
13289235 ATATTTTTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
ATAAATTTTAATTTAT
Found at i:13289238 original size:17 final size:16
Alignment explanation
Indices: 13289204--13289238 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
13289194 AATATATATC
*
13289204 ATAAATTTTATTTTAT
1 ATAAATTTTATTTAAT
13289220 ATAAATTTTAATTTAAT
1 ATAAATTTT-ATTTAAT
13289237 AT
1 AT
13289239 TTTTAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 9 0.53
17 8 0.47
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATAAATTTTATTTAAT
Found at i:13290222 original size:28 final size:28
Alignment explanation
Indices: 13290191--13290245 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
13290181 TAAATAAAGG
**
13290191 AAAAGATAATTTTTTAAATATATTTTAT
1 AAAAGATAATAATTTAAATATATTTTAT
* * *
13290219 AAAATATTATAATTTAAATATTTTTTA
1 AAAAGATAATAATTTAAATATATTTTA
13290246 ATTTTTATTA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (28 bp):
AAAAGATAATAATTTAAATATATTTTAT
Found at i:13294876 original size:35 final size:35
Alignment explanation
Indices: 13294791--13294877 Score: 111
Period size: 35 Copynumber: 2.5 Consensus size: 35
13294781 GAACCTTCTG
*
13294791 AATTGATTGCTCTAAACCCCTAAGTTTAAACCCTA
1 AATTGATTGCTCTAAACCCCAAAGTTTAAACCCTA
* * * * *
13294826 AATTGATAGCCCTAAACCTCAAATTTTAAATCCTA
1 AATTGATTGCTCTAAACCCCAAAGTTTAAACCCTA
*
13294861 AATTCATTGCTCTAAAC
1 AATTGATTGCTCTAAAC
13294878 ACAAACCCCA
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.37, C:0.24, G:0.07, T:0.32
Consensus pattern (35 bp):
AATTGATTGCTCTAAACCCCAAAGTTTAAACCCTA
Found at i:13303510 original size:3 final size:3
Alignment explanation
Indices: 13303502--13303533 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
13303492 CTAAGTACTG
13303502 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
13303534 GCGAGTGGGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:13311329 original size:14 final size:15
Alignment explanation
Indices: 13311301--13311329 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
13311291 ATGAATTTAT
13311301 TAAATTTAGCTTAGA
1 TAAATTTAGCTTAGA
13311316 TAAATTTA-CTTAGA
1 TAAATTTAGCTTAGA
13311330 CAAACACAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.41
Consensus pattern (15 bp):
TAAATTTAGCTTAGA
Found at i:13313002 original size:11 final size:11
Alignment explanation
Indices: 13312986--13313015 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
13312976 TAATTATTCA
13312986 TATATTTATGT
1 TATATTTATGT
*
13312997 TATATTTATTT
1 TATATTTATGT
13313008 TATATTTA
1 TATATTTA
13313016 ATATATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (11 bp):
TATATTTATGT
Found at i:13313635 original size:1 final size:1
Alignment explanation
Indices: 13313629--13313653 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
13313619 ATCCCATAGG
13313629 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
13313654 CTTTCACTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:13323117 original size:21 final size:20
Alignment explanation
Indices: 13323064--13323117 Score: 65
Period size: 21 Copynumber: 2.7 Consensus size: 20
13323054 GAAACAAACA
13323064 AAATCATCATCAA-TTAGCC
1 AAATCATCATCAAGTTAGCC
** *
13323083 AAATCAAAACCAAGTATAGCC
1 AAATCATCATCAAGT-TAGCC
13323104 AAATCATCATCAAG
1 AAATCATCATCAAG
13323118 CAAAACCAAG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
19 10 0.37
20 1 0.04
21 16 0.59
ACGTcount: A:0.48, C:0.24, G:0.07, T:0.20
Consensus pattern (20 bp):
AAATCATCATCAAGTTAGCC
Found at i:13333617 original size:296 final size:296
Alignment explanation
Indices: 13333083--13333668 Score: 1136
Period size: 296 Copynumber: 2.0 Consensus size: 296
13333073 CATGTGGGTG
13333083 ACGATAACATCTATGGCAGTCACCACATTGCTTCATGTTGACCAACACACCAGCCAACGAGCAAA
1 ACGATAACATCTATGGCAGTCACCACATTGCTTCATGTTGACCAACACACCAGCCAACGAGCAAA
13333148 CTGTACAAATGGTGGTCGCAATTGCTATGCTTGTATGGTTGGCCCTGATTGGCATTGTCTTCTTA
66 CTGTACAAATGGTGGTCGCAATTGCTATGCTTGTATGGTTGGCCCTGATTGGCATTGTCTTCTTA
*
13333213 GCTCATACTGCCCGTTTTACTTTTATCGTTTGGATTGTCCATAGGGTAAGAAAACACATAAAGAA
131 GCTCATACTGCCCGTTTTACTTTTATCATTTGGATTGTCCATAGGGTAAGAAAACACATAAAGAA
*
13333278 GCGGCTTTCTAGGCGCAGAAAAGAAAGGCAAGATCAGGACCAAGGCAATGGCTGAATACATACGT
196 GCGGCTTTCTAGGCGCAGAAAAGAAAGGCAAGATCAGGACCAAGGCAATGCCTGAATACATACGT
13333343 CTTCAAGATCAAATCCTCAGTGGAAACCGATAACAT
261 CTTCAAGATCAAATCCTCAGTGGAAACCGATAACAT
*
13333379 ACGATAACATCTATGGCAGTCACCACATTGCTTCATGTTGACCATCACACCAGCCAACGAGCAAA
1 ACGATAACATCTATGGCAGTCACCACATTGCTTCATGTTGACCAACACACCAGCCAACGAGCAAA
13333444 CTGTACAAATGGTGGTCGCAATTGCTATGCTTGTATGGTTGGCCCTGATTGGCATTGTCTTCTTA
66 CTGTACAAATGGTGGTCGCAATTGCTATGCTTGTATGGTTGGCCCTGATTGGCATTGTCTTCTTA
13333509 GCTCATACTGCCCGTTTTACTTTTATCATTTGGATTGTCCATAGGGTAAGAAAACACATAAAGAA
131 GCTCATACTGCCCGTTTTACTTTTATCATTTGGATTGTCCATAGGGTAAGAAAACACATAAAGAA
*
13333574 GCGGCTTTCTAGGCGCAGAAAAGAAAGGCAAGATCAGGACCAAGGCAATGCCTGAATGCATACGT
196 GCGGCTTTCTAGGCGCAGAAAAGAAAGGCAAGATCAGGACCAAGGCAATGCCTGAATACATACGT
13333639 CTTCAAGATCAAATCCTCAGTGGAAACCGA
261 CTTCAAGATCAAATCCTCAGTGGAAACCGA
13333669 GCTGGTCATT
Statistics
Matches: 286, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
296 286 1.00
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (296 bp):
ACGATAACATCTATGGCAGTCACCACATTGCTTCATGTTGACCAACACACCAGCCAACGAGCAAA
CTGTACAAATGGTGGTCGCAATTGCTATGCTTGTATGGTTGGCCCTGATTGGCATTGTCTTCTTA
GCTCATACTGCCCGTTTTACTTTTATCATTTGGATTGTCCATAGGGTAAGAAAACACATAAAGAA
GCGGCTTTCTAGGCGCAGAAAAGAAAGGCAAGATCAGGACCAAGGCAATGCCTGAATACATACGT
CTTCAAGATCAAATCCTCAGTGGAAACCGATAACAT
Found at i:13340929 original size:14 final size:12
Alignment explanation
Indices: 13340903--13340958 Score: 55
Period size: 12 Copynumber: 4.8 Consensus size: 12
13340893 TGAATTTGAG
13340903 TTTAATTTTAAA
1 TTTAATTTTAAA
13340915 TTTAATATTTAAAA
1 TTTAAT-TTT-AAA
*
13340929 TTTGA-TTTAAA
1 TTTAATTTTAAA
13340940 TTTAA--TTAAA
1 TTTAATTTTAAA
*
13340950 TTTTATTTT
1 TTTAATTTT
13340959 TTAATTCGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
10 9 0.24
11 7 0.19
12 11 0.30
13 3 0.08
14 7 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (12 bp):
TTTAATTTTAAA
Found at i:13340944 original size:6 final size:6
Alignment explanation
Indices: 13340886--13340952 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
13340876 TAATACGTAA
* * * * *
13340886 TTAAAT TTGAAT TTGAGT TTAATT TTAAAT TTAATAT TTAAAAT TT-GAT
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA-AT TT-AAAT TTAAAT
13340935 TTAAAT TT-AA- TTAAAT TT
1 TTAAAT TTAAAT TTAAAT TT
13340953 TATTTTTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
4 2 0.04
5 8 0.16
6 29 0.59
7 8 0.16
8 2 0.04
ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54
Consensus pattern (6 bp):
TTAAAT
Found at i:13341047 original size:22 final size:25
Alignment explanation
Indices: 13341022--13341070 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
13341012 AACATATAAA
13341022 AATAAATA-T-GATT-CTTATATTT
1 AATAAATATTCGATTACTTATATTT
*
13341044 AATAAATATTCGATTATTTATATTT
1 AATAAATATTCGATTACTTATATTT
13341069 AA
1 AA
13341071 ATTCAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 8 0.35
23 1 0.04
24 4 0.17
25 10 0.43
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.49
Consensus pattern (25 bp):
AATAAATATTCGATTACTTATATTT
Found at i:13342037 original size:21 final size:20
Alignment explanation
Indices: 13342013--13342077 Score: 53
Period size: 20 Copynumber: 3.2 Consensus size: 20
13342003 TAATTCAAGC
13342013 TATTAATTTAATAAAAAACTA
1 TATTAATTTAATAAAAAA-TA
* * *
13342034 TATTTATGT-ATAATAAATA
1 TATTAATTTAATAAAAAATA
*
13342053 TA-TAATTTATATTAAAAATAA
1 TATTAATTTA-ATAAAAAAT-A
13342074 TATT
1 TATT
13342078 TTATAAATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 7
0.70 0.15 0.15
Matches are distributed among these distances:
18 4 0.12
19 4 0.12
20 14 0.42
21 10 0.30
22 1 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (20 bp):
TATTAATTTAATAAAAAATA
Found at i:13342068 original size:18 final size:19
Alignment explanation
Indices: 13342042--13342083 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
13342032 TATATTTATG
*
13342042 TATAATAAATAT-ATAATT
1 TATAATAAAAATAATAATT
* *
13342060 TATATTAAAAATAATATTT
1 TATAATAAAAATAATAATT
13342079 TATAA
1 TATAA
13342084 ATATTATACT
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TATAATAAAAATAATAATT
Found at i:13343355 original size:19 final size:19
Alignment explanation
Indices: 13343331--13343376 Score: 62
Period size: 17 Copynumber: 2.6 Consensus size: 19
13343321 TTTTAAATTA
13343331 AAATATATTAATTTTTAAT
1 AAATATATTAATTTTTAAT
13343350 AAATATA-T-ATTTTTAAT
1 AAATATATTAATTTTTAAT
*
13343367 CAAT-TATTAA
1 AAATATATTAA
13343377 AATTTTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
16 2 0.08
17 13 0.54
18 2 0.08
19 7 0.29
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (19 bp):
AAATATATTAATTTTTAAT
Found at i:13343357 original size:21 final size:22
Alignment explanation
Indices: 13343320--13343360 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
13343310 ATGTAAAATT
13343320 TTTTTAAATTAAAATATATTAA
1 TTTTTAAATTAAAATATATTAA
13343342 TTTTT-AA-TAAATATATATT
1 TTTTTAAATTAAA-ATATATT
13343361 TTTAATCAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
21 9 0.50
22 5 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTTTAAATTAAAATATATTAA
Found at i:13343953 original size:34 final size:35
Alignment explanation
Indices: 13343878--13343978 Score: 109
Period size: 34 Copynumber: 3.0 Consensus size: 35
13343868 ATTTATTGGA
* * * * *
13343878 TATAAAAATAAAATTTTGAAAAGTTATATGA-CTT
1 TATAAAAATAGATTTTTGATAAGTTATATAATTTT
**
13343912 TATAAAAATCTATTTTTGATAAGTTATATAATTTT
1 TATAAAAATAGATTTTTGATAAGTTATATAATTTT
*
13343947 TA-AAAAATAGATTTTCGATAAGTTA-ATAATTT
1 TATAAAAATAGATTTTTGATAAGTTATATAATTT
13343979 ATCAAATACG
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
33 7 0.12
34 46 0.81
35 4 0.07
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (35 bp):
TATAAAAATAGATTTTTGATAAGTTATATAATTTT
Found at i:13344350 original size:6 final size:6
Alignment explanation
Indices: 13344333--13344363 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
13344323 AATGAATAAA
13344333 TAAAATT TAAAAT TAAAAT TAAAAT TAAAAT
1 TAAAA-T TAAAAT TAAAAT TAAAAT TAAAAT
13344364 ATCTCATCAC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 19 0.79
7 5 0.21
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (6 bp):
TAAAAT
Found at i:13344436 original size:13 final size:15
Alignment explanation
Indices: 13344408--13344459 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 15
13344398 ATTTTTTTAT
13344408 ATATTTATTAAATAA
1 ATATTTATTAAATAA
*
13344423 ATATTT-TTAATAAAA
1 ATATTTATTAA-ATAA
13344438 ATATTTATAGTTAAATAA
1 ATA-TT-TA-TTAAATAA
13344456 ATAT
1 ATAT
13344460 CAATCAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 4 0.13
15 12 0.40
16 2 0.07
17 2 0.07
18 6 0.20
19 4 0.13
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (15 bp):
ATATTTATTAAATAA
Found at i:13356782 original size:54 final size:54
Alignment explanation
Indices: 13356720--13356829 Score: 220
Period size: 54 Copynumber: 2.0 Consensus size: 54
13356710 AATATGTCCA
13356720 TCTCTGTCCCTAAACTTATTACAACTATAAAATGATGGGATTTACAACTTACTT
1 TCTCTGTCCCTAAACTTATTACAACTATAAAATGATGGGATTTACAACTTACTT
13356774 TCTCTGTCCCTAAACTTATTACAACTATAAAATGATGGGATTTACAACTTACTT
1 TCTCTGTCCCTAAACTTATTACAACTATAAAATGATGGGATTTACAACTTACTT
13356828 TC
1 TC
13356830 CCTCCAAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 56 1.00
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.37
Consensus pattern (54 bp):
TCTCTGTCCCTAAACTTATTACAACTATAAAATGATGGGATTTACAACTTACTT
Found at i:13372151 original size:6 final size:6
Alignment explanation
Indices: 13372140--13372178 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
13372130 CAGGGCCCCT
13372140 CCAACC CCAACC CCAACC CCAACC CCAACC CCAACC CCA
1 CCAACC CCAACC CCAACC CCAACC CCAACC CCAACC CCA
13372179 TCATTACCGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (6 bp):
CCAACC
Found at i:13372773 original size:15 final size:15
Alignment explanation
Indices: 13372731--13372773 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
13372721 TTGAAAGACA
13372731 GAGGATGGTGGTGGAG
1 GAGG-TGGTGGTGGAG
*
13372747 GCA-GTGGCGGTGGAG
1 G-AGGTGGTGGTGGAG
13372762 GAGGTGGTGGTG
1 GAGGTGGTGGTG
13372774 ATGGTGGTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 1 0.04
15 19 0.83
16 2 0.09
17 1 0.04
ACGTcount: A:0.14, C:0.05, G:0.63, T:0.19
Consensus pattern (15 bp):
GAGGTGGTGGTGGAG
Found at i:13378414 original size:32 final size:32
Alignment explanation
Indices: 13378373--13378438 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
13378363 AACCAAGTCT
13378373 TAGTGCACAAAAGTATTATTTTCATTCATGAA
1 TAGTGCACAAAAGTATTATTTTCATTCATGAA
*
13378405 TAGTGCACAAAATTATTATTTTCATTCATGAA
1 TAGTGCACAAAAGTATTATTTTCATTCATGAA
13378437 TA
1 TA
13378439 ATACATCTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.11, T:0.39
Consensus pattern (32 bp):
TAGTGCACAAAAGTATTATTTTCATTCATGAA
Found at i:13384948 original size:23 final size:23
Alignment explanation
Indices: 13384874--13384948 Score: 55
Period size: 23 Copynumber: 3.3 Consensus size: 23
13384864 AAATTTTAAT
* * **
13384874 TATAATTAATTATTACATTTATA
1 TATAATAAATTATAACATAAATA
* * *
13384897 TATAATATATCACTAA-ATAATTA
1 TATAATAAATTA-TAACATAAATA
13384920 -ATTAATAAATTATAACATAAATA
1 TA-TAATAAATTATAACATAAATA
13384943 TATAAT
1 TATAAT
13384949 TAAACTCACG
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
22 4 0.11
23 31 0.82
24 3 0.08
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (23 bp):
TATAATAAATTATAACATAAATA
Found at i:13385255 original size:20 final size:21
Alignment explanation
Indices: 13385218--13385257 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
13385208 AAAAATGTAG
*
13385218 AAATTTAAATTTTAAATATTA
1 AAATTAAAATTTTAAATATTA
13385239 AAATTAAAATTTT-AATATT
1 AAATTAAAATTTTAAATATT
13385258 TCAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
AAATTAAAATTTTAAATATTA
Found at i:13385269 original size:21 final size:22
Alignment explanation
Indices: 13385223--13385269 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
13385213 TGTAGAAATT
*
13385223 TAAATTTTAAATATTAAAATTA
1 TAAATTTTAAATATTAAAATAA
**
13385245 -AAATTTT-AATATTTCAATAA
1 TAAATTTTAAATATTAAAATAA
13385265 TAAAT
1 TAAAT
13385270 AAATCGATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAAATTTTAAATATTAAAATAA
Found at i:13385640 original size:16 final size:17
Alignment explanation
Indices: 13385619--13385653 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
13385609 AAAAATTTTA
*
13385619 ATATATTTAAAA-AATT
1 ATATATATAAAATAATT
13385635 ATATATATAAAATAATT
1 ATATATATAAAATAATT
13385652 AT
1 AT
13385654 TTTTATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATATATAAAATAATT
Found at i:13389443 original size:21 final size:21
Alignment explanation
Indices: 13389419--13389461 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
13389409 AAAATATTAG
13389419 ATAAAAAT-AAATATTGTAATA
1 ATAAAAATAAAAT-TTGTAATA
*
13389440 ATAAAATTAAAATTTGTAATA
1 ATAAAAATAAAATTTGTAATA
13389461 A
1 A
13389462 AAATATATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (21 bp):
ATAAAAATAAAATTTGTAATA
Found at i:13390057 original size:41 final size:42
Alignment explanation
Indices: 13389992--13390071 Score: 126
Period size: 41 Copynumber: 1.9 Consensus size: 42
13389982 ATTCAATCCG
*
13389992 TTTTATATTTATAATAATTGAATTTGATTTAATTTAATAATT
1 TTTTATATTTATAATAATTAAATTTGATTTAATTTAATAATT
* *
13390034 TTTTAT-TTTTTAATATTTAAATTTGATTTAATTTAATA
1 TTTTATATTTATAATAATTAAATTTGATTTAATTTAATA
13390072 TTATAAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 29 0.83
42 6 0.17
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (42 bp):
TTTTATATTTATAATAATTAAATTTGATTTAATTTAATAATT
Found at i:13390072 original size:23 final size:23
Alignment explanation
Indices: 13390003--13390078 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
13389993 TTTATATTTA
* *
13390003 TAATAATTGAATTTGATTTAATT
1 TAATATTTAAATTTGATTTAATT
13390026 TAATAATTT---TTT-ATTT--TT
1 TAAT-ATTTAAATTTGATTTAATT
13390044 TAATATTTAAATTTGATTTAATT
1 TAATATTTAAATTTGATTTAATT
13390067 TAATATTATAAA
1 TAATATT-TAAA
13390079 AATTTATATT
Statistics
Matches: 44, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
17 4 0.09
18 6 0.14
20 7 0.16
21 7 0.16
23 13 0.30
24 7 0.16
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (23 bp):
TAATATTTAAATTTGATTTAATT
Found at i:13390137 original size:23 final size:23
Alignment explanation
Indices: 13390102--13390145 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
13390092 TTTAATTTAA
*
13390102 TTTAAAATTAATA-AAATATTATT
1 TTTAAAATAAATATAAA-ATTATT
*
13390125 TTTAATATAAATATAAAATTA
1 TTTAAAATAAATATAAAATTA
13390146 AATAATTAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 15 0.83
24 3 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TTTAAAATAAATATAAAATTATT
Found at i:13390732 original size:21 final size:22
Alignment explanation
Indices: 13390694--13390745 Score: 90
Period size: 21 Copynumber: 2.5 Consensus size: 22
13390684 CCTGAAATTA
13390694 ATAAAATATTATTTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
13390716 ATAAAATATTA-TTTTTAAAAT
1 ATAAAATATTATTTTTTAAAAT
13390737 AT-AAATATT
1 ATAAAATATT
13390746 TAAAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
20 7 0.23
21 12 0.40
22 11 0.37
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
ATAAAATATTATTTTTTAAAAT
Found at i:13390753 original size:16 final size:16
Alignment explanation
Indices: 13390732--13390781 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
13390722 TATTATTTTT
*
13390732 AAAATATAAATATTTA
1 AAAATATAAATATATA
* *
13390748 AAAATATTATTATATA
1 AAAATATAAATATATA
* *
13390764 AAAATATATATAAATA
1 AAAATATAAATATATA
13390780 AA
1 AA
13390782 TAATTAATTA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (16 bp):
AAAATATAAATATATA
Found at i:13390783 original size:30 final size:30
Alignment explanation
Indices: 13390718--13390783 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 30
13390708 TTTAAAATAT
* *
13390718 AAAATATTATTTTTAAAATATAAATATTTA
1 AAAATATTATTTATAAAATATAAATATTAA
*
13390748 AAAATATTATTATATAAAA-ATATATA-TAA
1 AAAATATTATT-TATAAAATATAAATATTAA
13390777 ATAAATA
1 A-AAATA
13390784 ATTAATTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 3 0.10
30 22 0.71
31 6 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (30 bp):
AAAATATTATTTATAAAATATAAATATTAA
Found at i:13391384 original size:26 final size:26
Alignment explanation
Indices: 13391307--13391384 Score: 63
Period size: 26 Copynumber: 3.0 Consensus size: 26
13391297 AGCTAAAATT
* * * *
13391307 TAAATTTTAATATTTATA-ATTTTTT
1 TAAAATTTAAAATTTATATATTTATA
* *
13391332 TAAAATTTTAGA-TTAT-TATTTTGATA
1 TAAAATTTAAAATTTATATA-TTT-ATA
13391358 TAAAATTTAAAATTTATATATTTATA
1 TAAAATTTAAAATTTATATATTTATA
13391384 T
1 T
13391385 TTATTTTGAA
Statistics
Matches: 41, Mismatches: 7, Indels: 9
0.72 0.12 0.16
Matches are distributed among these distances:
24 5 0.12
25 12 0.29
26 15 0.37
27 7 0.17
28 2 0.05
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (26 bp):
TAAAATTTAAAATTTATATATTTATA
Found at i:13397329 original size:23 final size:23
Alignment explanation
Indices: 13397303--13397361 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
13397293 CATATTAAAA
*
13397303 AAAAAAAATAGTTAAGTTTCTTC
1 AAAAAAAATAGTTAAATTTCTTC
* * *
13397326 AAAATAGAA-AGATAAATTTGTTC
1 AAAA-AAAATAGTTAAATTTCTTC
*
13397349 AAAATAAATAGTT
1 AAAAAAAATAGTT
13397362 TTAACTATTC
Statistics
Matches: 27, Mismatches: 7, Indels: 4
0.71 0.18 0.11
Matches are distributed among these distances:
22 2 0.07
23 22 0.81
24 3 0.11
ACGTcount: A:0.53, C:0.05, G:0.10, T:0.32
Consensus pattern (23 bp):
AAAAAAAATAGTTAAATTTCTTC
Found at i:13406321 original size:2 final size:2
Alignment explanation
Indices: 13406314--13406356 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
13406304 GCTTGGCATT
13406314 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
13406356 T
1 T
13406357 TTTTCTTCTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:13410955 original size:13 final size:13
Alignment explanation
Indices: 13410937--13410961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13410927 TGAAAAGCTC
13410937 TGGAAGCTCTGGT
1 TGGAAGCTCTGGT
13410950 TGGAAGCTCTGG
1 TGGAAGCTCTGG
13410962 AGGGGAGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.40, T:0.28
Consensus pattern (13 bp):
TGGAAGCTCTGGT
Found at i:13411564 original size:272 final size:274
Alignment explanation
Indices: 13411040--13411587 Score: 893
Period size: 272 Copynumber: 2.0 Consensus size: 274
13411030 CAAAAAACCC
13411040 TAACTACTATTCAGTTTTTAGAATTTTAACTACCTTCGTCATCTATGCAGATAAAGAGAAAGAAA
1 TAACTACTATTCAGTTTTTAGAATTTTAACTACCTTCGTCATCTATGCAGATAAAGAGAAAGAAA
* * *
13411105 AGAACATAAGAGTTATTTGATAAACCTCTGCTGGCCAAATTCTTCATCAGGCTTTTAAAAGAGTT
66 AGAACATAAGAGTTATTAGATAAACCTCTGCTAGCCAAATTATTCATCAGGCTTTT-AAAGAGTT
* * * * *
13411170 TCCACTATCAAAACCCCACAGACTCGAAAGTTGGTGAAATAATTGATTCTTGAGAGCATCAAAGA
130 TCCACTATCAAAACCCCACAGACTCAAAAGGTGGCGAAATAATTGATTCCTGAGAACATCAAAGA
* *
13411235 GAACACCCAAGCATATTTACCAGGAAGCAAAAGGACAAAGTACCCTGCCTCAATTTAGATGACAT
195 GAACAACCAAGCATATTTACCAGGAAGCAAAAGGACAAAGTACCCTGCCTCAATTTAGATAACAT
13411300 TCAACCACATGACAG
260 TCAACCACATGACAG
* * * *
13411315 TAACTGCTATTCAGTTTTTAGCATTTTAACTACCTTTGTCATCTATGCAGCTAAAGAGAAAGAAA
1 TAACTACTATTCAGTTTTTAGAATTTTAACTACCTTCGTCATCTATGCAGATAAAGAGAAAGAAA
*
13411380 AGAACATAAGAGTTATTAGATAAAGCTCTGCTAGCCAAATTATTCATCAGGC-TTT-AAGAGTTT
66 AGAACATAAGAGTTATTAGATAAACCTCTGCTAGCCAAATTATTCATCAGGCTTTTAAAGAGTTT
* * *
13411443 CCACTATCTAAACCCCAGAGACTCAAAAGGTGGCGAAATAATTGATTCCTGAGAACGTCAAAGAG
131 CCACTATCAAAACCCCACAGACTCAAAAGGTGGCGAAATAATTGATTCCTGAGAACATCAAAGAG
*
13411508 AACAACCAAGCATATTTACCAGGAAGCGAAAGGACAAAGTACCCTGCCTCAATTTAGATAACATT
196 AACAACCAAGCATATTTACCAGGAAGCAAAAGGACAAAGTACCCTGCCTCAATTTAGATAACATT
*
13411573 CAATCACATGACAG
261 CAACCACATGACAG
13411587 T
1 T
13411588 CATGGTGGAA
Statistics
Matches: 253, Mismatches: 20, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
272 141 0.56
274 3 0.01
275 109 0.43
ACGTcount: A:0.38, C:0.20, G:0.16, T:0.26
Consensus pattern (274 bp):
TAACTACTATTCAGTTTTTAGAATTTTAACTACCTTCGTCATCTATGCAGATAAAGAGAAAGAAA
AGAACATAAGAGTTATTAGATAAACCTCTGCTAGCCAAATTATTCATCAGGCTTTTAAAGAGTTT
CCACTATCAAAACCCCACAGACTCAAAAGGTGGCGAAATAATTGATTCCTGAGAACATCAAAGAG
AACAACCAAGCATATTTACCAGGAAGCAAAAGGACAAAGTACCCTGCCTCAATTTAGATAACATT
CAACCACATGACAG
Found at i:13412859 original size:2 final size:2
Alignment explanation
Indices: 13412852--13412879 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
13412842 CTTTGAAACA
13412852 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
13412880 GAAGCTGCCA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:13429897 original size:27 final size:27
Alignment explanation
Indices: 13429867--13429923 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
13429857 AAACTTACAT
13429867 TAATTCATTAAATAAGAAAAACCTTTC
1 TAATTCATTAAATAAGAAAAACCTTTC
*
13429894 TAATTCATTAAATAAGAAAACCCTTTC
1 TAATTCATTAAATAAGAAAAACCTTTC
13429921 TAA
1 TAA
13429924 ACCAATTTCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (27 bp):
TAATTCATTAAATAAGAAAAACCTTTC
Found at i:13431064 original size:7 final size:8
Alignment explanation
Indices: 13431041--13431074 Score: 52
Period size: 8 Copynumber: 4.2 Consensus size: 8
13431031 ATAAAAGATA
13431041 TAAATATTT
1 TAAA-ATTT
13431050 TAAAATTT
1 TAAAATTT
13431058 T-AAATTT
1 TAAAATTT
13431065 TAAAATTT
1 TAAAATTT
13431073 TA
1 TA
13431075 GTTCAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
7 7 0.29
8 13 0.54
9 4 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
TAAAATTT
Found at i:13431066 original size:15 final size:15
Alignment explanation
Indices: 13431046--13431074 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13431036 AGATATAAAT
13431046 ATTTTAAAATTTTAA
1 ATTTTAAAATTTTAA
13431061 ATTTTAAAATTTTA
1 ATTTTAAAATTTTA
13431075 GTTCAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTAAAATTTTAA
Found at i:13431218 original size:28 final size:26
Alignment explanation
Indices: 13431181--13431300 Score: 77
Period size: 28 Copynumber: 4.5 Consensus size: 26
13431171 AACATTTTAT
*
13431181 TAAATTATATTTTATATTTTAATAATTA
1 TAAATAATATTTTATA-TTTAATAA-TA
13431209 TAAATAATA-TTTATATTTAATAA-A
1 TAAATAATATTTTATATTTAATAATA
* ***
13431233 TAAATAA-ATAATTACTAACAAATAATTA
1 TAAATAATAT-TTTA-TATTTAATAA-TA
*
13431261 TAAATAATTATTTATATTTTTTAA-AATA
1 TAAATAA-TATTT-TA-TATTTAATAATA
*
13431289 TAAATATTATTT
1 TAAATAATATTT
13431301 ATTAATATAT
Statistics
Matches: 72, Mismatches: 12, Indels: 17
0.71 0.12 0.17
Matches are distributed among these distances:
23 1 0.01
24 8 0.11
25 3 0.04
26 15 0.21
27 11 0.15
28 24 0.33
29 3 0.04
30 7 0.10
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (26 bp):
TAAATAATATTTTATATTTAATAATA
Found at i:13431904 original size:17 final size:17
Alignment explanation
Indices: 13431879--13431913 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
13431869 TGATTTAAAG
* *
13431879 TGATTTAATTGTAAAAT
1 TGATCTAATTATAAAAT
13431896 TGATCTAATTATAAAAT
1 TGATCTAATTATAAAAT
13431913 T
1 T
13431914 AAATTGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.46
Consensus pattern (17 bp):
TGATCTAATTATAAAAT
Found at i:13444817 original size:25 final size:24
Alignment explanation
Indices: 13444794--13444839 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
13444784 TTTATTACAA
13444794 ATTAAA-AAAAATTAAAAAAATAC
1 ATTAAAGAAAAATTAAAAAAATAC
*
13444817 ATTAAATGCAAAATTAAAAAAAT
1 ATTAAA-GAAAAATTAAAAAAAT
13444840 TTCACTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
25 14 0.70
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.24
Consensus pattern (24 bp):
ATTAAAGAAAAATTAAAAAAATAC
Found at i:13446835 original size:43 final size:43
Alignment explanation
Indices: 13446773--13446870 Score: 151
Period size: 43 Copynumber: 2.3 Consensus size: 43
13446763 AGGCAGAGTG
* * *
13446773 TTCTTTCTTTCCTTTAGCGATAAAAGCCAAAATCCATAGTACA
1 TTCTTTCTTTCCATAAGCGATAAAAGCCAAAAGCCATAGTACA
13446816 TTCTTTCTTTCCATAAGCGATAAAAGCCAAAAGCCATAGTACA
1 TTCTTTCTTTCCATAAGCGATAAAAGCCAAAAGCCATAGTACA
* *
13446859 TTTTTTCCTTCC
1 TTCTTTCTTTCC
13446871 TTTAACGTCG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (43 bp):
TTCTTTCTTTCCATAAGCGATAAAAGCCAAAAGCCATAGTACA
Found at i:13447132 original size:16 final size:17
Alignment explanation
Indices: 13447106--13447142 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
13447096 ATATAATAAT
13447106 TATTATATTTTAAATTA
1 TATTATATTTTAAATTA
*
13447123 TATTAT-TTTTATATTA
1 TATTATATTTTAAATTA
13447139 TATT
1 TATT
13447143 CTTATAATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TATTATATTTTAAATTA
Done.