Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, 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: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 103 of 129
Found at i:17093985 original size:66 final size:66
Alignment explanation
Indices: 17093879--17094009 Score: 217
Period size: 66 Copynumber: 2.0 Consensus size: 66
17093869 CTAGACAGAC
*
17093879 GTGTTTTATGCCAACTTCTACAACCATTCCCTGAAAAATATAAATGAACCATGCAATTTTTTTTT
1 GTGTTTTATGCCAACTTCTACAACCAATCCCTGAAAAATATAAATGAACCATGCAATTTTTTTTT
17093944 T
66 T
* * * *
17093945 GTGTTTTATGTCAACTTCTCCAACCAATCCCTGGAAAATATAAATGAGCCATGCAATTTTTTTTT
1 GTGTTTTATGCCAACTTCTACAACCAATCCCTGAAAAATATAAATGAACCATGCAATTTTTTTTT
17094010 AAAATCTTCC
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 60 1.00
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.39
Consensus pattern (66 bp):
GTGTTTTATGCCAACTTCTACAACCAATCCCTGAAAAATATAAATGAACCATGCAATTTTTTTTT
T
Found at i:17095543 original size:10 final size:10
Alignment explanation
Indices: 17095519--17095548 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
17095509 TATTTTATCA
17095519 ATTAAAATA-
1 ATTAAAATAT
17095528 ATTAAAATAT
1 ATTAAAATAT
17095538 ATTAAAATAT
1 ATTAAAATAT
17095548 A
1 A
17095549 AAAGTTCAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:17098008 original size:22 final size:21
Alignment explanation
Indices: 17097941--17098008 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 21
17097931 ATTATTTTTT
17097941 ATTAAATTAAATTTTAAATCAA
1 ATTAAATTAAATTTTAAAT-AA
* * *
17097963 ATCAAATTAAATTTAAAAAAA
1 ATTAAATTAAATTTTAAATAA
*
17097984 ATTAAAGTTGAATTTTAAATAA
1 ATTAAA-TTAAATTTTAAATAA
17098006 ATT
1 ATT
17098009 CATCCTACCC
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 7 0.18
22 31 0.82
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (21 bp):
ATTAAATTAAATTTTAAATAA
Found at i:17098092 original size:20 final size:20
Alignment explanation
Indices: 17098058--17098111 Score: 99
Period size: 20 Copynumber: 2.6 Consensus size: 20
17098048 TTAATTATTT
17098058 AATTATATATTTATATTTAAA
1 AATTATAT-TTTATATTTAAA
17098079 AATTATATTTTATATTTAAA
1 AATTATATTTTATATTTAAA
17098099 AATTATATTTTAT
1 AATTATATTTTAT
17098112 TAATTTCATC
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 25 0.76
21 8 0.24
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
AATTATATTTTATATTTAAA
Found at i:17098480 original size:31 final size:32
Alignment explanation
Indices: 17098419--17098482 Score: 85
Period size: 31 Copynumber: 2.0 Consensus size: 32
17098409 TTTTCATTTC
* *
17098419 AATTTTTTATTATATAATAAACTAATAAATAA
1 AATTTATTATTATATAATAAACTAAAAAATAA
* *
17098451 AATTTATTATTAT-TGATAAATTAAAAAATAA
1 AATTTATTATTATATAATAAACTAAAAAATAA
17098482 A
1 A
17098483 TAAATTTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 16 0.57
32 12 0.43
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (32 bp):
AATTTATTATTATATAATAAACTAAAAAATAA
Found at i:17098574 original size:17 final size:17
Alignment explanation
Indices: 17098544--17098579 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
17098534 ATTATTTAAA
17098544 ATAAATTTATAAATTTT
1 ATAAATTTATAAATTTT
17098561 ATAATATTTA-AAATTTT
1 ATAA-ATTTATAAATTTT
17098578 AT
1 AT
17098580 TTTAATACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATAAATTTATAAATTTT
Found at i:17099426 original size:9 final size:9
Alignment explanation
Indices: 17099414--17099443 Score: 60
Period size: 9 Copynumber: 3.3 Consensus size: 9
17099404 TATAAAAAAT
17099414 TATGTTAAA
1 TATGTTAAA
17099423 TATGTTAAA
1 TATGTTAAA
17099432 TATGTTAAA
1 TATGTTAAA
17099441 TAT
1 TAT
17099444 ATATTCGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (9 bp):
TATGTTAAA
Found at i:17099851 original size:24 final size:24
Alignment explanation
Indices: 17099818--17099866 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
17099808 ATCTCACTCG
*
17099818 TGCTATTCAATTTTACCGCTGTTT
1 TGCTAATCAATTTTACCGCTGTTT
17099842 TGCTAATCAATTTTACCGCTGTTT
1 TGCTAATCAATTTTACCGCTGTTT
17099866 T
1 T
17099867 ACTCCCACTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.18, C:0.20, G:0.12, T:0.49
Consensus pattern (24 bp):
TGCTAATCAATTTTACCGCTGTTT
Found at i:17103369 original size:25 final size:26
Alignment explanation
Indices: 17103341--17103391 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
17103331 GAGTATAATT
*
17103341 TCATTTTTAA-CTTTTTAGTAAAAGC
1 TCATTTTTAATCTTTTTAATAAAAGC
*
17103366 TCATTTTTAATTTTTTTAATAAAAGC
1 TCATTTTTAATCTTTTTAATAAAAGC
17103392 AATAAGTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 10 0.43
26 13 0.57
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.51
Consensus pattern (26 bp):
TCATTTTTAATCTTTTTAATAAAAGC
Found at i:17103579 original size:23 final size:24
Alignment explanation
Indices: 17103535--17103579 Score: 56
Period size: 23 Copynumber: 1.9 Consensus size: 24
17103525 TAGATAATTA
***
17103535 AAAAAATAAAAGAAAGCTAAAACT
1 AAAAAATAAAAGAAAAAAAAAACT
17103559 AAAAAA-AAAAGAAAAAAAAAA
1 AAAAAATAAAAGAAAAAAAAAA
17103580 AACGTCCATG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 12 0.67
24 6 0.33
ACGTcount: A:0.82, C:0.04, G:0.07, T:0.07
Consensus pattern (24 bp):
AAAAAATAAAAGAAAAAAAAAACT
Found at i:17103852 original size:28 final size:29
Alignment explanation
Indices: 17103817--17103896 Score: 76
Period size: 29 Copynumber: 2.8 Consensus size: 29
17103807 ATAAATGACA
17103817 TATT-AATTATATATAAATATAAT-ATTT
1 TATTAAATTATATATAAATATAATAATTT
* *
17103844 TATTAAATTAAAGTATTAA-ATAATAATTT
1 TATTAAATTATA-TATAAATATAATAATTT
* * *
17103873 TATTAATATAATACATACATATAA
1 TATTAA-ATTATATATAAATATAA
17103897 ATATAAAATT
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
27 4 0.10
28 11 0.27
29 18 0.44
30 8 0.20
ACGTcount: A:0.51, C:0.03, G:0.01, T:0.45
Consensus pattern (29 bp):
TATTAAATTATATATAAATATAATAATTT
Found at i:17105945 original size:2 final size:2
Alignment explanation
Indices: 17105938--17105969 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17105928 AGTCAATAAG
17105938 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17105970 GATGTTCTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17106070 original size:31 final size:31
Alignment explanation
Indices: 17106005--17106070 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
17105995 ATAAATTATC
* * *
17106005 AATAAATAAGATGATTTCATCTAATTAATGA
1 AATAAATAAGATGATATCACCTAATGAATGA
*
17106036 AATAAATTAGATGATATCACCTTAATGAAT-A
1 AATAAATAAGATGATATCACC-TAATGAATGA
17106067 AATA
1 AATA
17106071 TTTTAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 23 0.77
32 7 0.23
ACGTcount: A:0.50, C:0.08, G:0.09, T:0.33
Consensus pattern (31 bp):
AATAAATAAGATGATATCACCTAATGAATGA
Found at i:17106665 original size:16 final size:15
Alignment explanation
Indices: 17106626--17106656 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
17106616 ATATACTCAC
17106626 ATAAAATAATTTTTT
1 ATAAAATAATTTTTT
17106641 ATAATAATAATTTTTT
1 ATAA-AATAATTTTTT
17106657 CTTAAAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATAAAATAATTTTTT
Found at i:17107106 original size:252 final size:258
Alignment explanation
Indices: 17106834--17107336 Score: 806
Period size: 254 Copynumber: 2.0 Consensus size: 258
17106824 TAATAAGAAC
*
17106834 ATGTAACATATAATAAGCAAATATTCACAT-GAAATAATTATTTATAATAAT-AA-TTTTTTCTT
1 ATGTAACATATAATAAGCAAATACTCACATAG-AATAATTATTTATAATAATGAATTTTTTTCTT
* *
17106896 AAAATATACAAAATATCTTAATAATATATAAAAAAGATTTTTAGGTGC-AATATATAAAAACAAA
65 AAAATATACAAAATATATTAATAATATATAAAAAAGATTTTTAGGTACAAATATATAAAAACAAA
*
17106960 ATTCAAAATTATAATAAGCAAAAATTGTTATAATAAAAACACGTAACATACAAT-A-AAAAAATA
130 ATTCAAAATTATAATAAG-AAAAAATGTTATAATAAAAACACGTAACATACAATAAGAAAAAATA
* **
17107023 TTTGGTTGA-AAAAATGTTA-TTATAATTGTGAATTTTTTTTTTATATATTGCACCTATAAAAAT
194 TTTGGTTGAGAAAAATATTATTTATAATTGTGAATTTTGCTTTTATATATTGCACCTATAAAAAT
*
17107086 ATGTAACATATAATAAGCAAATACTCACATAGAATAATTATTTATAATTATGAATTTTTTTCTTA
1 ATGTAACATATAATAAGCAAATACTCACATAGAATAATTATTTATAATAATGAATTTTTTTCTTA
* *
17107151 AAATATATAAAATATATTAATAATATATAAAAAATATTTTTAGGTACAAATATATAAAAACAAAA
66 AAATATACAAAATATATTAATAATATATAAAAAAGATTTTTAGGTACAAATATATAAAAACAAAA
* * *
17107216 TTCAAAATTATAATAAGAAAAAATGTTATAATAAGAACATGTAACATATAATAAGAAAAAATATT
131 TTCAAAATTATAATAAGAAAAAATGTTATAATAAAAACACGTAACATACAATAAGAAAAAATATT
*
17107281 TGGTTGAGAAAAATATTATTTATAGTTGTGAATTTTGCTTTTATATATTGCACCTA
196 TGGTTGAGAAAAATATTATTTATAATTGTGAATTTTGCTTTTATATATTGCACCTA
17107337 ATTTTTTTTA
Statistics
Matches: 229, Mismatches: 14, Indels: 10
0.91 0.06 0.04
Matches are distributed among these distances:
252 47 0.21
253 3 0.01
254 84 0.37
255 35 0.15
256 17 0.07
257 9 0.04
258 34 0.15
ACGTcount: A:0.49, C:0.07, G:0.07, T:0.37
Consensus pattern (258 bp):
ATGTAACATATAATAAGCAAATACTCACATAGAATAATTATTTATAATAATGAATTTTTTTCTTA
AAATATACAAAATATATTAATAATATATAAAAAAGATTTTTAGGTACAAATATATAAAAACAAAA
TTCAAAATTATAATAAGAAAAAATGTTATAATAAAAACACGTAACATACAATAAGAAAAAATATT
TGGTTGAGAAAAATATTATTTATAATTGTGAATTTTGCTTTTATATATTGCACCTATAAAAAT
Found at i:17107163 original size:9 final size:9
Alignment explanation
Indices: 17107149--17107187 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
17107139 ATTTTTTTCT
17107149 TAAAATATA
1 TAAAATATA
17107158 TAAAATATA
1 TAAAATATA
17107167 TTAATAATATA
1 -TAA-AATATA
*
17107178 TAAAAAATA
1 TAAAATATA
17107187 T
1 T
17107188 TTTTAGGTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 15 0.56
10 6 0.22
11 6 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (9 bp):
TAAAATATA
Found at i:17107177 original size:20 final size:19
Alignment explanation
Indices: 17107148--17107188 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
17107138 AATTTTTTTC
*
17107148 TTAAAATATATAAAATATA
1 TTAAAATATATAAAAAATA
17107167 TTAATAATATATAAAAAATA
1 TTAA-AATATATAAAAAATA
17107187 TT
1 TT
17107189 TTTAGGTACA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TTAAAATATATAAAAAATA
Found at i:17109499 original size:27 final size:27
Alignment explanation
Indices: 17109462--17109524 Score: 108
Period size: 27 Copynumber: 2.3 Consensus size: 27
17109452 TTGAGAGGAT
17109462 TTTTTTTATATAAAATGATTTACTCAA
1 TTTTTTTATATAAAATGATTTACTCAA
* *
17109489 TTTTTTTATATAAAATGATTTATTCAT
1 TTTTTTTATATAAAATGATTTACTCAA
17109516 TTTTTTTAT
1 TTTTTTTAT
17109525 GGTGTCAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.32, C:0.05, G:0.03, T:0.60
Consensus pattern (27 bp):
TTTTTTTATATAAAATGATTTACTCAA
Found at i:17112651 original size:3 final size:3
Alignment explanation
Indices: 17112643--17112671 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
17112633 TTTTTCGTGG
17112643 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
17112672 TGGCCTTTAA
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:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:17115827 original size:27 final size:28
Alignment explanation
Indices: 17115775--17115829 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
17115765 TTATATATAA
* **
17115775 ATATATGTTTTATTATTAATTTAATTAT
1 ATATATGTATTATTATTAATAAAATTAT
17115803 ATATATGTATTA-TATTAATAAAATTAT
1 ATATATGTATTATTATTAATAAAATTAT
17115830 TCTTAAATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 13 0.54
28 11 0.46
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.55
Consensus pattern (28 bp):
ATATATGTATTATTATTAATAAAATTAT
Found at i:17116189 original size:17 final size:17
Alignment explanation
Indices: 17116169--17116227 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
17116159 TGTATATATG
17116169 TATTATATTAATAAAAT
1 TATTATATTAATAAAAT
*
17116186 TATTAT-TTAAT-TAAT
1 TATTATATTAATAAAAT
* *
17116201 ATCTTA-ATTTAATAAAAA
1 -TATTATA-TTAATAAAAT
17116219 TATTATATT
1 TATTATATT
17116228 TATCCATAAC
Statistics
Matches: 32, Mismatches: 5, Indels: 10
0.68 0.11 0.21
Matches are distributed among these distances:
15 3 0.09
16 9 0.28
17 17 0.53
18 3 0.09
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (17 bp):
TATTATATTAATAAAAT
Found at i:17116555 original size:15 final size:14
Alignment explanation
Indices: 17116526--17116562 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
17116516 TCAAATGAGC
17116526 TTTCTTTT-A-CTT
1 TTTCTTTTAACCTT
17116538 TTTACTTTTAACCTT
1 TTT-CTTTTAACCTT
17116553 TTTCTTTTAA
1 TTTCTTTTAA
17116563 TTTTTGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
12 3 0.14
13 5 0.23
14 8 0.36
15 6 0.27
ACGTcount: A:0.16, C:0.16, G:0.00, T:0.68
Consensus pattern (14 bp):
TTTCTTTTAACCTT
Found at i:17116559 original size:14 final size:13
Alignment explanation
Indices: 17116526--17116572 Score: 53
Period size: 12 Copynumber: 3.6 Consensus size: 13
17116516 TCAAATGAGC
17116526 TTTCTTTT-ACTT
1 TTTCTTTTAACTT
17116538 TTTACTTTTAACCTT
1 TTT-CTTTTAA-CTT
17116553 TTTCTTTTAA-TT
1 TTTCTTTTAACTT
*
17116565 TTTGTTTT
1 TTTCTTTT
17116573 TTCTTTTTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
12 12 0.39
13 5 0.16
14 8 0.26
15 6 0.19
ACGTcount: A:0.13, C:0.13, G:0.02, T:0.72
Consensus pattern (13 bp):
TTTCTTTTAACTT
Found at i:17116586 original size:26 final size:26
Alignment explanation
Indices: 17116557--17116612 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
17116547 AACCTTTTTC
** **
17116557 TTTTAATTTTTGTTTTTTCTTTTTGT
1 TTTTAATTTTCATTTTTTTGTTTTGT
*
17116583 TTTTCATTTTCATTTTTTTGTTTTGT
1 TTTTAATTTTCATTTTTTTGTTTTGT
17116609 TTTT
1 TTTT
17116613 TATTAAAGTA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.07, C:0.05, G:0.07, T:0.80
Consensus pattern (26 bp):
TTTTAATTTTCATTTTTTTGTTTTGT
Found at i:17117711 original size:15 final size:15
Alignment explanation
Indices: 17117693--17117741 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
17117683 CTTTTCTCAA
17117693 TTTTCATTTTTTATT
1 TTTTCATTTTTTATT
**
17117708 TTTTCATTTTCCACTT
1 TTTTCATTTTTTA-TT
* *
17117724 TTTTTATTTTTTGTT
1 TTTTCATTTTTTATT
17117739 TTT
1 TTT
17117742 GATAATTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.10, C:0.10, G:0.02, T:0.78
Consensus pattern (15 bp):
TTTTCATTTTTTATT
Found at i:17119475 original size:15 final size:15
Alignment explanation
Indices: 17119452--17119486 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
17119442 CGGGACCCAA
*
17119452 GCATTCACCTTTCCG
1 GCATCCACCTTTCCG
*
17119467 GCATCCACCTTTTCG
1 GCATCCACCTTTCCG
17119482 GCATC
1 GCATC
17119487 TCAGATCAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.14, C:0.40, G:0.14, T:0.31
Consensus pattern (15 bp):
GCATCCACCTTTCCG
Found at i:17119989 original size:21 final size:22
Alignment explanation
Indices: 17119965--17120005 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
17119955 TATTAACATA
17119965 ATTAAATATT-AAATTTAAAAT
1 ATTAAATATTAAAATTTAAAAT
* *
17119986 ATTAATTTTTAAAATTTAAA
1 ATTAAATATTAAAATTTAAA
17120006 TTTTAATAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
ATTAAATATTAAAATTTAAAAT
Found at i:17120009 original size:14 final size:15
Alignment explanation
Indices: 17119968--17120011 Score: 65
Period size: 14 Copynumber: 3.1 Consensus size: 15
17119958 TAACATAATT
17119968 AAATATTAAA-TTTA
1 AAATATTAAATTTTA
*
17119982 AAATATTAATTTTTA
1 AAATATTAAATTTTA
17119997 AAAT-TTAAATTTTA
1 AAATATTAAATTTTA
17120011 A
1 A
17120012 TAATGAGGTG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
14 19 0.70
15 8 0.30
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATATTAAATTTTA
Found at i:17120594 original size:19 final size:20
Alignment explanation
Indices: 17120562--17120600 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
17120552 TTATTTTTTA
17120562 TTTAAAAATATTAAAATAAT
1 TTTAAAAATATTAAAATAAT
* *
17120582 TTTAATAAT-TTAATATAAT
1 TTTAAAAATATTAAAATAAT
17120601 AAATAAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (20 bp):
TTTAAAAATATTAAAATAAT
Found at i:17120626 original size:27 final size:26
Alignment explanation
Indices: 17120575--17120638 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 26
17120565 AAAAATATTA
*
17120575 AAATAATTTTAATAATTTAATATAAT
1 AAATAATTTTAATAATATAATATAAT
*
17120601 AAATAAATTTT-ATTATAT-A-ATAAT
1 AAAT-AATTTTAATAATATAATATAAT
* *
17120625 AAATTATATTAATA
1 AAATAATTTTAATA
17120639 GGTATTAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
23 4 0.13
24 11 0.35
25 1 0.03
26 9 0.29
27 6 0.19
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
AAATAATTTTAATAATATAATATAAT
Found at i:17120627 original size:20 final size:21
Alignment explanation
Indices: 17120594--17120635 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
17120584 TAATAATTTA
*
17120594 ATATAATAAATAAATTTTATT
1 ATATAATAAATAAATTATATT
17120615 ATATAAT-AATAAATTATATT
1 ATATAATAAATAAATTATATT
17120635 A
1 A
17120636 ATAGGTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATAATAAATAAATTATATT
Found at i:17120884 original size:143 final size:143
Alignment explanation
Indices: 17120602--17120882 Score: 467
Period size: 143 Copynumber: 2.0 Consensus size: 143
17120592 TAATATAATA
* *
17120602 AATAAATTTTATTATATAATAATAAATTATATTAATAGGTATTAATATTTTGACTGAATAAATAC
1 AATAAATTTTATTATATAATAATAAATAATATTAATAGGTATTAATATTTTGACTAAATAAATAC
* * *
17120667 TAAATTTTATAATCAAATAAATATTTAGGAAATTAAAAAATAAAATATTTTGTTATTAATATGAC
66 TAAATTTTATAATCAAATAAATATTTAAGAAATTAAAAAATAAAATAATTTGTAATTAATATGAC
17120732 TTAACAAAATTTT
131 TTAACAAAATTTT
* *
17120745 AATAAATTTTATTATATAATAATAAATAATATTAGT-GTGTATTAATATTTTGATTAAATAAATA
1 AATAAATTTTATTATATAATAATAAATAATATTAATAG-GTATTAATATTTTGACTAAATAAATA
*
17120809 CTAAATTTTATAATCAAATAAATATTTAATAAATTAAAAAAT-AAATAATTTGTAATTAATATGA
65 CTAAATTTTATAATCAAATAAATATTTAAGAAATTAAAAAATAAAATAATTTGTAATTAATATGA
17120873 CTTAACAAAA
130 CTTAACAAAA
17120883 ATATATAATT
Statistics
Matches: 129, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
142 31 0.24
143 98 0.76
ACGTcount: A:0.51, C:0.03, G:0.05, T:0.41
Consensus pattern (143 bp):
AATAAATTTTATTATATAATAATAAATAATATTAATAGGTATTAATATTTTGACTAAATAAATAC
TAAATTTTATAATCAAATAAATATTTAAGAAATTAAAAAATAAAATAATTTGTAATTAATATGAC
TTAACAAAATTTT
Found at i:17122816 original size:52 final size:53
Alignment explanation
Indices: 17122715--17122817 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 53
17122705 GATAAGAAAA
* *
17122715 CTTGCAAAAGAAGAATTCTAAAAGAAAAGAGGATTTTTAATAGGTAAGTTTGG
1 CTTGCAAAAGAAGAATTCTAAAAGAAAAGAGGATTCTTAATAGGCAAGTTTGG
* *
17122768 CTTGCAAGAGAATAATTCTAAAA-AGAAAG-GGATTCTTAATAGGCAAGTTT
1 CTTGCAAAAGAAGAATTCTAAAAGA-AAAGAGGATTCTTAATAGGCAAGTTT
17122818 ATATGGTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
52 20 0.44
53 25 0.56
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (53 bp):
CTTGCAAAAGAAGAATTCTAAAAGAAAAGAGGATTCTTAATAGGCAAGTTTGG
Found at i:17126809 original size:52 final size:53
Alignment explanation
Indices: 17126708--17126810 Score: 147
Period size: 53 Copynumber: 2.0 Consensus size: 53
17126698 GATAAGAAAA
* *
17126708 CTTGCAAAAGAAGAATTCTAAAAGAAAAGAGGATTTTTAATAGGTAAGTTTGG
1 CTTGCAAAAGAAGAATTCTAAAAGAAAAGAGGATTCTTAATAGGCAAGTTTGG
* *
17126761 CTTGCAAGAGAATAATTCTAAAA-AGAAAG-GGATTCTTAATAGGCAAGTTT
1 CTTGCAAAAGAAGAATTCTAAAAGA-AAAGAGGATTCTTAATAGGCAAGTTT
17126811 ATATGGTATA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
52 20 0.44
53 25 0.56
ACGTcount: A:0.43, C:0.08, G:0.21, T:0.28
Consensus pattern (53 bp):
CTTGCAAAAGAAGAATTCTAAAAGAAAAGAGGATTCTTAATAGGCAAGTTTGG
Found at i:17140696 original size:9 final size:9
Alignment explanation
Indices: 17140682--17140728 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
17140672 ACTTTTTGAA
17140682 AAAATTTTG
1 AAAATTTTG
*
17140691 AAAATTTTT
1 AAAATTTTG
*
17140700 TAAATTTTG
1 AAAATTTTG
17140709 AAAA-TTTG
1 AAAATTTTG
17140717 AAAATTTT-
1 AAAATTTTG
17140725 AAAA
1 AAAA
17140729 CATATGAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
8 12 0.36
9 21 0.64
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (9 bp):
AAAATTTTG
Found at i:17140766 original size:19 final size:19
Alignment explanation
Indices: 17140744--17140785 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
17140734 GAAGTATTCT
* *
17140744 AAAAATTTTTTAAAAATTA
1 AAAAATTTCTCAAAAATTA
17140763 AAAAATTTCTCAAAAATTA
1 AAAAATTTCTCAAAAATTA
17140782 AAAA
1 AAAA
17140786 TTTAATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (19 bp):
AAAAATTTCTCAAAAATTA
Found at i:17140795 original size:18 final size:17
Alignment explanation
Indices: 17140743--17140795 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 17
17140733 TGAAGTATTC
*
17140743 TAAAAATTTTTTAAAAAT
1 TAAAAA-TTTATAAAAAT
*
17140761 TAAAAAATTTCTCAAAAAT
1 T-AAAAATTTAT-AAAAAT
17140780 TAAAAATTTAATAAAA
1 TAAAAATTT-ATAAAA
17140796 GTCCAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
18 17 0.57
19 13 0.43
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAAATTTATAAAAAT
Found at i:17140824 original size:19 final size:19
Alignment explanation
Indices: 17140801--17140848 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
17140791 TAAAAGTCCA
17140801 AAAAATTAAAAAAATATAT
1 AAAAATTAAAAAAATATAT
*
17140820 CAAAATT-AAAAAATATAT
1 AAAAATTAAAAAAATATAT
*
17140838 AAAAAATAAAA
1 AAAAATTAAAA
17140849 TCTTAAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 16 0.64
19 9 0.36
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAATTAAAAAAATATAT
Found at i:17140824 original size:29 final size:25
Alignment explanation
Indices: 17140774--17140846 Score: 65
Period size: 27 Copynumber: 2.7 Consensus size: 25
17140764 AAAATTTCTC
**
17140774 AAAAATTAAAAATTTAATAAAAGTCCA
1 AAAAATTAAAAAAATAATAAAA-T-CA
*
17140801 AAAAATTAAAAAAATATATCAAAATTA
1 AAAAATTAAAAAAATA-AT-AAAATCA
17140828 AAAAATATATAAAAAATAA
1 AAAAAT-TA-AAAAAATAA
17140847 AATCTTAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
27 21 0.54
28 6 0.15
29 12 0.31
ACGTcount: A:0.70, C:0.04, G:0.01, T:0.25
Consensus pattern (25 bp):
AAAAATTAAAAAAATAATAAAATCA
Found at i:17141067 original size:26 final size:27
Alignment explanation
Indices: 17141022--17141099 Score: 81
Period size: 25 Copynumber: 3.0 Consensus size: 27
17141012 ATTTTTTTGA
*
17141022 ATTTTTTGAGATTTTATAAAATTTTAGG
1 ATTTTTTTA-ATTTTATAAAATTTTAGG
**
17141050 ATTTTTTTAATTTT-T-AAATTTTAAT
1 ATTTTTTTAATTTTATAAAATTTTAGG
* *
17141075 AATTTTTT-ATTTTAAAAAATTTTAG
1 ATTTTTTTAATTTTATAAAATTTTAG
17141100 TTTTTAATTT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
24 5 0.12
25 15 0.36
26 9 0.21
27 5 0.12
28 8 0.19
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.59
Consensus pattern (27 bp):
ATTTTTTTAATTTTATAAAATTTTAGG
Found at i:17141098 original size:33 final size:33
Alignment explanation
Indices: 17141061--17141127 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
17141051 TTTTTTTAAT
17141061 TTTTAAATTTTAATAATTTTT-T-ATTTTAAAAAA
1 TTTTAAATTTTAAT--TTTTTATAATTTTAAAAAA
**
17141094 TTTTAGTTTTTAATTTTTTATAATTTTAAAAAA
1 TTTTAAATTTTAATTTTTTATAATTTTAAAAAA
17141127 T
1 T
17141128 ATTTTAGATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
31 5 0.17
32 1 0.03
33 24 0.80
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TTTTAAATTTTAATTTTTTATAATTTTAAAAAA
Found at i:17141159 original size:19 final size:20
Alignment explanation
Indices: 17141109--17141159 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
17141099 GTTTTTAATT
*
17141109 TTTTATAATTTTAAAAAATA
1 TTTTAAAATTTTAAAAAATA
* *
17141129 TTTTAGATTTTTAAAAAA-A
1 TTTTAAAATTTTAAAAAATA
17141148 TTTTAAAATTTT
1 TTTTAAAATTTT
17141160 TTGAAACTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (20 bp):
TTTTAAAATTTTAAAAAATA
Found at i:17141160 original size:9 final size:9
Alignment explanation
Indices: 17141143--17141199 Score: 51
Period size: 10 Copynumber: 6.0 Consensus size: 9
17141133 AGATTTTTAA
*
17141143 AAAAATTTT
1 AAAATTTTT
17141152 AAAATTTTTT
1 AAAA-TTTTT
*
17141162 GAAACTTTTT
1 -AAAATTTTT
**
17141172 GTAATTTTT
1 AAAATTTTT
17141181 AAAATTTTT
1 AAAATTTTT
17141190 GAAAATTTTT
1 -AAAATTTTT
17141200 TTTAATATTG
Statistics
Matches: 38, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
9 17 0.45
10 18 0.47
11 3 0.08
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (9 bp):
AAAATTTTT
Found at i:17142230 original size:2 final size:2
Alignment explanation
Indices: 17142219--17142258 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
17142209 ACCACAGCCT
17142219 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
17142259 TAATCGCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:17145726 original size:26 final size:29
Alignment explanation
Indices: 17145690--17145753 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
17145680 ATATTTTAAA
* *
17145690 AATTTTATATT-TTATTGAT-AG-AAAAT
1 AATTTTTTATTATGATTGATGAGTAAAAT
*
17145716 AATTTTTTATTATGATTTATGAGTAAAAT
1 AATTTTTTATTATGATTGATGAGTAAAAT
*
17145745 AATATTTTA
1 AATTTTTTA
17145754 ATAGAAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
26 10 0.32
27 6 0.19
28 2 0.06
29 13 0.42
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.52
Consensus pattern (29 bp):
AATTTTTTATTATGATTGATGAGTAAAAT
Found at i:17145797 original size:22 final size:21
Alignment explanation
Indices: 17145763--17145839 Score: 70
Period size: 22 Copynumber: 3.8 Consensus size: 21
17145753 AATAGAAAAC
* *
17145763 AAATTTTTTAAAAATGATATTG
1 AAATTTTTAAAAAATAAT-TTG
*
17145785 AAGTTTTTAAAAAATAATTTG
1 AAATTTTTAAAAAATAATTTG
* *
17145806 AAA-TTTT--AAATTAATTTT
1 AAATTTTTAAAAAATAATTTG
*
17145824 AATTTTTTAAAAAATA
1 AAATTTTTAAAAAATA
17145840 TTTTTTGTTA
Statistics
Matches: 44, Mismatches: 8, Indels: 7
0.75 0.14 0.12
Matches are distributed among these distances:
18 11 0.25
19 4 0.09
20 4 0.09
21 10 0.23
22 15 0.34
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (21 bp):
AAATTTTTAAAAAATAATTTG
Found at i:17151996 original size:31 final size:31
Alignment explanation
Indices: 17151945--17152005 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
17151935 AAAAACATAT
*
17151945 TCATTAATGAAGTTTTATCATATGATTCACC
1 TCATTAATGAAGTTTCATCATATGATTCACC
* *
17151976 TCATTAATG-AGTTATCATCATTTGGTTCAC
1 TCATTAATGAAGTT-TCATCATATGATTCAC
17152006 TGATAGTGTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 4 0.15
31 22 0.85
ACGTcount: A:0.30, C:0.16, G:0.11, T:0.43
Consensus pattern (31 bp):
TCATTAATGAAGTTTCATCATATGATTCACC
Found at i:17152656 original size:18 final size:18
Alignment explanation
Indices: 17152630--17152670 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
17152620 TATATAATAT
*
17152630 GTTACTATTTTATCAAAA
1 GTTATTATTTTATCAAAA
17152648 GTTATTATTTTATCAAAA
1 GTTATTATTTTATCAAAA
17152666 GTTAT
1 GTTAT
17152671 AAAAGTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (18 bp):
GTTATTATTTTATCAAAA
Found at i:17153222 original size:15 final size:15
Alignment explanation
Indices: 17153202--17153274 Score: 51
Period size: 15 Copynumber: 4.9 Consensus size: 15
17153192 TTAAAAGATT
17153202 TGGGTTTGAAGTTTC
1 TGGGTTTGAAGTTTC
* *
17153217 TGGGTTTAAAGATTC
1 TGGGTTTGAAGTTTC
* * *
17153232 TGAG-ATGCAAGTTTG
1 TGGGTTTG-AAGTTTC
* *
17153247 AGAGTTTGAAGTTTC
1 TGGGTTTGAAGTTTC
*
17153262 TAGGTTT-AAGTTT
1 TGGGTTTGAAGTTT
17153275 GAATTTTTGG
Statistics
Matches: 43, Mismatches: 13, Indels: 5
0.70 0.21 0.08
Matches are distributed among these distances:
14 7 0.16
15 34 0.79
16 2 0.05
ACGTcount: A:0.23, C:0.05, G:0.29, T:0.42
Consensus pattern (15 bp):
TGGGTTTGAAGTTTC
Found at i:17153661 original size:18 final size:17
Alignment explanation
Indices: 17153635--17153675 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 17
17153625 TGATCGCGAG
17153635 TTTTTTTTTTCATTTTA
1 TTTTTTTTTTCATTTTA
*
17153652 TTTTTATTTTTTATTTTA
1 TTTTT-TTTTTCATTTTA
17153670 TTTTTT
1 TTTTTT
17153676 CATTTTATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.12, C:0.02, G:0.00, T:0.85
Consensus pattern (17 bp):
TTTTTTTTTTCATTTTA
Found at i:17153663 original size:13 final size:13
Alignment explanation
Indices: 17153653--17153703 Score: 68
Period size: 13 Copynumber: 3.8 Consensus size: 13
17153643 TTCATTTTAT
17153653 TTTTATTTTTT-A
1 TTTTATTTTTTCA
17153665 TTTTATTTTTTCA
1 TTTTATTTTTTCA
17153678 TTTTATTTTTTGCCA
1 TTTTATTTTTT--CA
17153693 TTTTTATTTTT
1 -TTTTATTTTT
17153704 AAGCTTTTTT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
12 11 0.31
13 12 0.34
15 2 0.06
16 10 0.29
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTATTTTTTCA
Found at i:17153681 original size:18 final size:18
Alignment explanation
Indices: 17153641--17153686 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
17153631 CGAGTTTTTT
*
17153641 TTTTCATTTTATTTTTATT
1 TTTT-ATTTTATTTTTATA
17153660 TTTTATTTTATTTTT-TCA
1 TTTTATTTTATTTTTAT-A
17153678 TTTTATTTT
1 TTTTATTTT
17153687 TTGCCATTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 1 0.04
18 20 0.80
19 4 0.16
ACGTcount: A:0.15, C:0.04, G:0.00, T:0.80
Consensus pattern (18 bp):
TTTTATTTTATTTTTATA
Found at i:17155938 original size:61 final size:61
Alignment explanation
Indices: 17155742--17156127 Score: 261
Period size: 62 Copynumber: 6.3 Consensus size: 61
17155732 TTTTTTATAA
* * * * ** *
17155742 AAAAAAGCCTTGAATAATCTTTAAAAAAAATT-AGAGGGGATTATTGAAGGCGTTTTTAGCC
1 AAAAACGCCTTGAATAATCTCTAAAAAAAATTGA-AAGGGATTATTCAAGGTATTTTTAGTC
* * *
17155803 AAAAACCACCTTGAATAATCCCTAAAAAAAATTGAAGGGGATTATTCAAGGTATTTTTAG-C
1 AAAAA-CGCCTTGAATAATCTCTAAAAAAAATTGAAAGGGATTATTCAAGGTATTTTTAGTC
* *
17155864 ATAAAAACGCCTTGAATAATCTCTAAAAAAAATTGAAAGGGATTATTGAAGGTATTTTTAGTT
1 --AAAAACGCCTTGAATAATCTCTAAAAAAAATTGAAAGGGATTATTCAAGGTATTTTTAGTC
* * ** * ** *
17155927 AAAAACGCCTTGAAAAAT-AC-AAAAAAAA-AAAAATGAGATTATTCAAGACATTTTTTA-CC
1 AAAAACGCCTTGAATAATCTCTAAAAAAAATTGAAA-GGGATTATTCAAGGTA-TTTTTAGTC
* * ** ** **** * * *
17155986 AAGAACGCCTTGAATAACCAATTTAATTTTTTGTAAA-GGATTATTCAATGTGTTTTCTAGTT
1 AAAAACGCCTTGAATAATCTCTAAAAAAAATTG-AAAGGGATTATTCAAGGTATTTT-TAGTC
* * * *
17156048 AAAAGCGCCTTAAATAATCT-TCAAAAAAAATTGAAAGAGATTATTGAAGACGT-TTTTT-GTC
1 AAAAACGCCTTGAATAATCTCT-AAAAAAAATTGAAAGGGATTATTCAAG--GTATTTTTAGTC
*
17156109 AGAAACGCCTTGAATAATC
1 AAAAACGCCTTGAATAATC
17156128 CCAAAAGCCT
Statistics
Matches: 249, Mismatches: 59, Indels: 34
0.73 0.17 0.10
Matches are distributed among these distances:
58 3 0.01
59 35 0.14
60 12 0.05
61 59 0.24
62 125 0.50
63 13 0.05
64 2 0.01
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (61 bp):
AAAAACGCCTTGAATAATCTCTAAAAAAAATTGAAAGGGATTATTCAAGGTATTTTTAGTC
Found at i:17156116 original size:123 final size:120
Alignment explanation
Indices: 17155903--17156125 Score: 272
Period size: 123 Copynumber: 1.8 Consensus size: 120
17155893 AAATTGAAAG
*
17155903 GGATTATTGAAGGTATTTTTAGTTAAAAACGCCTTGAAAAATACAAAAAAAAAAAAATGAGATTA
1 GGATTATTCAAGGTATTTTTAGTTAAAAACGCCTTGAAAAATACAAAAAAAAAAAAATGAGATTA
17155968 TTCAAGACATTTTTTACCAAGAACGCCTTGAATAACCAATTTAATTTTTTGTAAA
66 TTCAAGACATTTTTTACCAAGAACGCCTTGAATAACCAATTTAATTTTTTGTAAA
* * * * **
17156023 GGATTATTCAATGTGTTTTCTAGTTAAAAGCGCCTT-AAATAATCTTCAAAAAAAATTGAAA-GA
1 GGATTATTCAAGGTATTTT-TAGTTAAAAACGCCTTGAAA-AA--TACAAAAAAAA-AAAAATGA
* * **
17156086 GATTATTGAAGACGTTTTTTGTC-AGAAACGCCTTGAATAA
61 GATTATTCAAGACATTTTTTACCAAG-AACGCCTTGAATAA
17156126 TCCCAAAAGC
Statistics
Matches: 86, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
120 19 0.22
121 17 0.20
122 2 0.02
123 45 0.52
124 3 0.03
ACGTcount: A:0.41, C:0.11, G:0.14, T:0.33
Consensus pattern (120 bp):
GGATTATTCAAGGTATTTTTAGTTAAAAACGCCTTGAAAAATACAAAAAAAAAAAAATGAGATTA
TTCAAGACATTTTTTACCAAGAACGCCTTGAATAACCAATTTAATTTTTTGTAAA
Found at i:17156139 original size:19 final size:19
Alignment explanation
Indices: 17156115--17156152 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
17156105 TGTCAGAAAC
17156115 GCCTTGAATAATCCCAAAA
1 GCCTTGAATAATCCCAAAA
17156134 GCCTTGAATAATCCCAAAA
1 GCCTTGAATAATCCCAAAA
17156153 AAAATTTGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.11, T:0.21
Consensus pattern (19 bp):
GCCTTGAATAATCCCAAAA
Found at i:17156477 original size:30 final size:31
Alignment explanation
Indices: 17156411--17156477 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 31
17156401 TTCTTGCATT
17156411 TTGAGTCAAATCCCTAAACTTCTTATTTGATATG
1 TTGAGTCAAATCCCTAAACTTC---TTTGATATG
*
17156445 TTGAGTCAAATCCCTAAACTTC-TTGATTTG
1 TTGAGTCAAATCCCTAAACTTCTTTGATATG
17156475 TTG
1 TTG
17156478 CTTTTCTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 10 0.31
34 22 0.69
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (31 bp):
TTGAGTCAAATCCCTAAACTTCTTTGATATG
Found at i:17158713 original size:17 final size:17
Alignment explanation
Indices: 17158685--17158733 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
17158675 TAAATTAAGG
*
17158685 TATAAA-ATAATAATTT
1 TATAAATATAATAATTA
* *
17158701 TATTAATATAATAAATA
1 TATAAATATAATAATTA
17158718 TATAAATATAA-AATTA
1 TATAAATATAATAATTA
17158734 AATACATAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
16 9 0.33
17 18 0.67
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TATAAATATAATAATTA
Found at i:17160152 original size:17 final size:19
Alignment explanation
Indices: 17160130--17160170 Score: 59
Period size: 17 Copynumber: 2.2 Consensus size: 19
17160120 TGAATTTAAT
17160130 AAAAAATTA-AAATATA-A
1 AAAAAATTATAAATATATA
17160147 AAAAAATTATTAAATATATA
1 AAAAAATTA-TAAATATATA
17160167 AAAA
1 AAAA
17160171 GAAAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
19 7 0.33
20 5 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AAAAAATTATAAATATATA
Found at i:17160190 original size:16 final size:16
Alignment explanation
Indices: 17160166--17160196 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
17160156 TTAAATATAT
17160166 AAAAAGAAAAAAAAGG
1 AAAAAGAAAAAAAAGG
*
17160182 AAAAGGAAAAAAAAG
1 AAAAAGAAAAAAAAG
17160197 TTACATAACT
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:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGG
Found at i:17163681 original size:52 final size:50
Alignment explanation
Indices: 17163560--17163697 Score: 152
Period size: 52 Copynumber: 2.7 Consensus size: 50
17163550 CTTAAATCTA
*
17163560 TAATTGATTCTGAAATCAAATCCCAAAAATCTCTCCCTATCATTTTAATG
1 TAATTGATTCTGAAATTAAATCCCAAAAATCTCTCCCTATCATTTTAATG
* * * * * *
17163610 TGAATTAATTATGAAATTAAATCTCTATAATTTCTCCAC-ATCATTTTTAATG
1 T-AATTGATTCTGAAATTAAATCCCAAAAATCTCTCC-CTATCA-TTTTAATG
* *
17163662 CTAATTGATTCCGAAATTAAATTCCAAAAATCTCTC
1 -TAATTGATTCTGAAATTAAATCCCAAAAATCTCTC
17163698 AATTATGGTT
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
50 1 0.01
51 32 0.46
52 35 0.51
53 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.06, T:0.38
Consensus pattern (50 bp):
TAATTGATTCTGAAATTAAATCCCAAAAATCTCTCCCTATCATTTTAATG
Found at i:17164243 original size:25 final size:25
Alignment explanation
Indices: 17164209--17164259 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
17164199 ATTCTGAAAG
17164209 TACCTATAATTTCATTTATTAATCC
1 TACCTATAATTTCATTTATTAATCC
17164234 TACCTATAATTTCATTTATTAATCC
1 TACCTATAATTTCATTTATTAATCC
17164259 T
1 T
17164260 TGATTAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (25 bp):
TACCTATAATTTCATTTATTAATCC
Found at i:17167565 original size:14 final size:15
Alignment explanation
Indices: 17167535--17167567 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
17167525 TTTCTAGAAT
17167535 TTCTTTCTATCTCTC
1 TTCTTTCTATCTCTC
*
17167550 TTCTTTC-ATCTTTC
1 TTCTTTCTATCTCTC
17167564 TTCT
1 TTCT
17167568 CTCCTTATCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.06, C:0.30, G:0.00, T:0.64
Consensus pattern (15 bp):
TTCTTTCTATCTCTC
Found at i:17170236 original size:33 final size:33
Alignment explanation
Indices: 17170196--17170273 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
17170186 AAAATTTCAC
*
17170196 GCATTTTCTCACTTGACTAGGAA-AATTTCCTAA
1 GCATTTTCTCACTTGACTA-AAATAATTTCCTAA
* * *
17170229 GCATTTTCTCACTTTACTAAAATAATTTTCTAG
1 GCATTTTCTCACTTGACTAAAATAATTTCCTAA
*
17170262 GCATTCTCTCAC
1 GCATTTTCTCAC
17170274 ACGACTATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 2 0.05
33 37 0.95
ACGTcount: A:0.28, C:0.23, G:0.09, T:0.40
Consensus pattern (33 bp):
GCATTTTCTCACTTGACTAAAATAATTTCCTAA
Found at i:17170466 original size:26 final size:25
Alignment explanation
Indices: 17170419--17170467 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
17170409 TTCTCAGAAC
*
17170419 ATTTTCTCACTTGACTATGAAACAT
1 ATTTTCTCACTTGACTAGGAAACAT
* *
17170444 ATTTTTTCATTTGACTAGGGAAAC
1 ATTTTCTCACTTGACTA-GGAAAC
17170468 TTTCTGCGCA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 15 0.75
26 5 0.25
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (25 bp):
ATTTTCTCACTTGACTAGGAAACAT
Found at i:17170584 original size:33 final size:32
Alignment explanation
Indices: 17170477--17170586 Score: 116
Period size: 33 Copynumber: 3.4 Consensus size: 32
17170467 CTTTCTGCGC
*
17170477 ATTCTCT-ACTTCACTAAGAAAATTTTTCTTGT
1 ATTCTCTCACTTCACTAAGAAAATTTTTC-AGT
* * * * *
17170509 ATTTTCTTACTTTACTAAAAAAATTTTTCATGC
1 ATTCTCTCACTTCACTAAGAAAATTTTTCA-GT
17170542 ATTCTCTCACTTCACT-AGAAAATTTTTCGGAGT
1 ATTCTCTCACTTCACTAAGAAAATTTTTC--AGT
17170575 ATTCTCTCACTT
1 ATTCTCTCACTT
17170587 GATTACGAAA
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
32 17 0.27
33 46 0.72
34 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.06, T:0.45
Consensus pattern (32 bp):
ATTCTCTCACTTCACTAAGAAAATTTTTCAGT
Found at i:17170669 original size:156 final size:155
Alignment explanation
Indices: 17170107--17170852 Score: 521
Period size: 156 Copynumber: 4.8 Consensus size: 155
17170097 GTTTTAGGTT
* ** * *
17170107 ATTCTCTCACTTGACTATGAAACACATTCTTTCACTTGATTAGATAAA-TTTC-CCAAGCATTCT
1 ATTCTCTCACTTGACTATGAAACACATTCTTTCACTTGACTAGGGAAACTTTCTGC--G-ATTTT
* * * * * * ** * *
17170170 CTATTTCATTAAAAAAAAAATTT--CACGCATTTTCTCACTTGACTAGGAAAATTTCCTAAGCAT
63 CTACTTCACT---AAGAAAATTTCCCATGTATTTTCTTACTTGACTAAAAAAATTTCCCATGCAT
* * *
17170233 TTTCTCACTTTACTAA-AATA-ATTTTC-TAGGC
125 TCTCTCACTTCAC-AAGAA-ACATTTTCGGA-GC
** * * * *
17170264 ATTCTCTCACACGACTATAAAACACATTCTTTCACTTGACTAGAGAAA-TTTC-CCTATATTCTC
1 ATTCTCTCACTTGACTATGAAACACATTCTTTCACTTGACTAGGGAAACTTTCTGCGAT-TT-TC
* * * * * ****
17170327 TACTTCACTAAAAAAATTTCTCACGCATTTTCTCA-TTGGACTGGGGAAATTTCCCATGCATTCT
64 TACTTCACTAAGAAAATTTCCCATGTATTTTCTTACTT-GACTAAAAAAATTTCCCATGCATTCT
*** * ** * * *
17170391 CTTGTTTGATTAGAAA-AGTTCTCAGAAC
128 CTCACTTCACAAGAAACA-TTTTCGGAGC
* * * * *
17170419 ATTTTCTCACTTGACTATGAAACATATTTTTTCATTTGACTAGGGAAACTTTCTGCGCATTCTCT
1 ATTCTCTCACTTGACTATGAAACACATTCTTTCACTTGACTAGGGAAACTTTCTGCG-ATTTTCT
** * * **
17170484 ACTTCACTAAGAAAATTTTTCTTGTATTTTCTTACTTTACTAAAAAAATTTTTCATGCATTCTCT
65 ACTTCACTAAGAAAATTTCCCATGTATTTTCTTACTTGACTAAAAAAATTTCCCATGCATTCTCT
* *
17170549 CACTTCACTAGAAA-ATTTTTCGGAGT
130 CACTTCACAAGAAACA-TTTTCGGAGC
* * * *
17170575 ATTCTCTCACTTGATTACGAAATACATTCTTTCACTTGACTAGGGAAACTTCTTATGCG-TTTTC
1 ATTCTCTCACTTGACTATGAAACACATTCTTTCACTTGACTAGGGAAAC-T-TTCTGCGATTTTC
* * * * ** *
17170639 TGCTTCACTAAGAAAATTTCCCACGCATTTTCTCACTTGAC-AAGGGAAATTTCCCGTGCATTCT
64 TACTTCACTAAGAAAATTTCCCATGTATTTTCTTACTTGACTAA-AAAAATTTCCCATGCATTCT
* * *
17170703 CTCACTTGACAAGAAACATTTTGGGGGC
128 CTCACTTCACAAGAAACATTTTCGGAGC
* * * * *
17170731 ATTCTCTTATTTGACTATGAAACACATTCTTTCACTTGAATAGGGAAACTTTCCGCGCATTTTTT
1 ATTCTCTCACTTGACTATGAAACACATTCTTTCACTTGACTAGGGAAACTTTCTGCG-A-TTTTC
* * *
17170796 TACTTTACTAAGAAAATTTCCCATGTATTTTCTTACTTGATTAGAAAAATTTCCCAT
64 TACTTCACTAAGAAAATTTCCCATGTATTTTCTTACTTGACTAAAAAAATTTCCCAT
17170853 ACTTCCCACG
Statistics
Matches: 466, Mismatches: 103, Indels: 40
0.77 0.17 0.07
Matches are distributed among these distances:
153 10 0.02
154 12 0.03
155 91 0.20
156 240 0.52
157 104 0.22
158 9 0.02
ACGTcount: A:0.29, C:0.21, G:0.11, T:0.39
Consensus pattern (155 bp):
ATTCTCTCACTTGACTATGAAACACATTCTTTCACTTGACTAGGGAAACTTTCTGCGATTTTCTA
CTTCACTAAGAAAATTTCCCATGTATTTTCTTACTTGACTAAAAAAATTTCCCATGCATTCTCTC
ACTTCACAAGAAACATTTTCGGAGC
Found at i:17170690 original size:33 final size:33
Alignment explanation
Indices: 17170652--17170715 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
17170642 TTCACTAAGA
*
17170652 AAATTTCCCACGCATTTTCTCACTTGACAAGGG
1 AAATTTCCCACGCATTCTCTCACTTGACAAGGG
**
17170685 AAATTTCCCGTGCATTCTCTCACTTGACAAG
1 AAATTTCCCACGCATTCTCTCACTTGACAAG
17170716 AAACATTTTG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.31
Consensus pattern (33 bp):
AAATTTCCCACGCATTCTCTCACTTGACAAGGG
Found at i:17170826 original size:33 final size:33
Alignment explanation
Indices: 17170789--17170852 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
17170779 CTTTCCGCGC
* *
17170789 ATTTTTTTACTTTACTAAG-AAAATTTCCCATGT
1 ATTTTCTTACTTGA-TAAGAAAAATTTCCCATGT
*
17170822 ATTTTCTTACTTGATTAGAAAAATTTCCCAT
1 ATTTTCTTACTTGATAAGAAAAATTTCCCAT
17170853 ACTTCCCACG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
32 3 0.11
33 24 0.89
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (33 bp):
ATTTTCTTACTTGATAAGAAAAATTTCCCATGT
Found at i:17172552 original size:5 final size:5
Alignment explanation
Indices: 17172538--17172582 Score: 65
Period size: 5 Copynumber: 9.2 Consensus size: 5
17172528 AAAGAAAAAA
* *
17172538 ATTAT ATTAT GTTAT ATTAT ATTAT ATTAT ATTAT TTTA- ATTAT A
1 ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT ATTAT A
17172583 CTCTTTTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
4 3 0.09
5 32 0.91
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (5 bp):
ATTAT
Found at i:17176607 original size:19 final size:19
Alignment explanation
Indices: 17176585--17176621 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
17176575 ATATGATTTT
17176585 TTTTTCAAAATAATAATAA
1 TTTTTCAAAATAATAATAA
* *
17176604 TTTTTTAAAATATTAATA
1 TTTTTCAAAATAATAATA
17176622 TATCTATACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTTTCAAAATAATAATAA
Found at i:17176680 original size:35 final size:35
Alignment explanation
Indices: 17176639--17176711 Score: 128
Period size: 35 Copynumber: 2.1 Consensus size: 35
17176629 ACATCTTAAA
*
17176639 ATAAAACAACAAATATTTATGTGCTTTGTATTTAT
1 ATAAAACAACAAATATTTATGTACTTTGTATTTAT
*
17176674 ATAAAACAACAAATATTTATTTACTTTGTATTTAT
1 ATAAAACAACAAATATTTATGTACTTTGTATTTAT
17176709 ATA
1 ATA
17176712 GATATCTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.42, C:0.08, G:0.05, T:0.44
Consensus pattern (35 bp):
ATAAAACAACAAATATTTATGTACTTTGTATTTAT
Found at i:17177071 original size:15 final size:15
Alignment explanation
Indices: 17177034--17177072 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
17177024 ATATATGAAA
17177034 ATAAATATAATTTAT
1 ATAAATATAATTTAT
* * *
17177049 TTATATATATTTTAT
1 ATAAATATAATTTAT
17177064 ATAAATATA
1 ATAAATATA
17177073 CAAAAGTCAA
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATAAATATAATTTAT
Found at i:17178581 original size:13 final size:13
Alignment explanation
Indices: 17178563--17178588 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17178553 ATTATGTGGG
17178563 ATATGATATAAAA
1 ATATGATATAAAA
17178576 ATATGATATAAAA
1 ATATGATATAAAA
17178589 GCATTATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.08, T:0.31
Consensus pattern (13 bp):
ATATGATATAAAA
Found at i:17181411 original size:7 final size:7
Alignment explanation
Indices: 17181399--17181426 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
17181389 ATGCGGGTTT
17181399 TGGATAG
1 TGGATAG
17181406 TGGATAG
1 TGGATAG
17181413 TGGATAG
1 TGGATAG
17181420 TGGATAG
1 TGGATAG
17181427 GTTGCAAGCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.00, G:0.43, T:0.29
Consensus pattern (7 bp):
TGGATAG
Found at i:17189719 original size:21 final size:20
Alignment explanation
Indices: 17189681--17189721 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
17189671 ATAAAAAATT
17189681 ATTTTTTAATTAATTATTTA
1 ATTTTTTAATTAATTATTTA
17189701 ATTTTTT-ATTATATATATTTA
1 ATTTTTTAATTA-AT-TATTTA
17189722 TATAATGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 9 0.47
21 6 0.32
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
ATTTTTTAATTAATTATTTA
Found at i:17189735 original size:30 final size:30
Alignment explanation
Indices: 17189701--17189771 Score: 88
Period size: 30 Copynumber: 2.3 Consensus size: 30
17189691 TAATTATTTA
* * * *
17189701 ATTTTTTATTATATATATTTATATAATGAT
1 ATTTTTTAATATATATATTTAAAAAATAAT
*
17189731 ATTTTTTAATATTTATATTTAAAAAATAAT
1 ATTTTTTAATATATATATTTAAAAAATAAT
17189761 ATTTTATTAAT
1 ATTTT-TTAAT
17189772 TTCGGATCGG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
30 30 0.86
31 5 0.14
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (30 bp):
ATTTTTTAATATATATATTTAAAAAATAAT
Found at i:17191295 original size:3 final size:3
Alignment explanation
Indices: 17191289--17191315 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
17191279 TCCTCCTCCC
17191289 CTT CTT CTT CTT CTT CTT CTT CTT CTT
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT
17191316 TTTGGACTCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
CTT
Found at i:17206726 original size:3 final size:3
Alignment explanation
Indices: 17206718--17206770 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
17206708 ACGTGGAGCC
* *
17206718 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TTT TCT TTT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
17206766 TCT TC
1 TCT TC
17206771 ATGCTCACTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:17206782 original size:24 final size:24
Alignment explanation
Indices: 17206732--17206782 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
17206722 CTTCTTCTTC
* ** **
17206732 TTCTTCTTCTTCTTCTTTTTCTTT
1 TTCTTCTTCTTCTTCATGCTCACT
17206756 TTCTTCTTCTTCTTCATGCTCACT
1 TTCTTCTTCTTCTTCATGCTCACT
17206780 TTC
1 TTC
17206783 ACCGTTCAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.04, C:0.29, G:0.02, T:0.65
Consensus pattern (24 bp):
TTCTTCTTCTTCTTCATGCTCACT
Found at i:17207652 original size:14 final size:14
Alignment explanation
Indices: 17207633--17207659 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
17207623 TTAATTTTTT
17207633 TTTAAAATTATAAA
1 TTTAAAATTATAAA
17207647 TTTAAAATTATAA
1 TTTAAAATTATAA
17207660 TTACACCCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
TTTAAAATTATAAA
Found at i:17208505 original size:5 final size:5
Alignment explanation
Indices: 17208495--17208524 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
17208485 AGTGATATTA
17208495 TCTTT TCTTT TCTTT TCTTT TCTTT T-TTT T
1 TCTTT TCTTT TCTTT TCTTT TCTTT TCTTT T
17208525 GAGGTACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TCTTT
Found at i:17208798 original size:151 final size:150
Alignment explanation
Indices: 17208625--17208909 Score: 437
Period size: 151 Copynumber: 1.9 Consensus size: 150
17208615 TACGTAAATC
* * * *
17208625 AATTAAATTAAATTTTAAATTCATCTTTTTTAAAATATTGAA-TAAAAATTATTAAATGTTTTAC
1 AATTAAATTAAATTTCAAATTCATATTTTTTAAAACATT-AAGTAAAAATTATTAAATGTCTTAC
* *
17208689 TAATAAAAGTCCATGAATAAAACTTGAAATAGTGAACAATTTTACTAGTAAAAATATAAAAATTC
65 TAACAAAAGTCCATGAATAAAACTTGAAATAGTGAACAATGTTACTAG-AAAAATATAAAAATTC
17208754 ATTTCATGTGACTACATGAACT
129 ATTTCATGTGACTACATGAACT
* * *
17208776 AATTAAATTAAATTTCGAATTCATATTTTTTACAACATTAAGTAAAAATTGTTAAATGTCTTACT
1 AATTAAATTAAATTTCAAATTCATATTTTTTAAAACATTAAGTAAAAATTATTAAATGTCTTACT
* * *
17208841 AACAAAAGTCCATGAATATAATTTGAAATAGTGAACAATGTTATTAGAAAAATATAAAAATTCAT
66 AACAAAAGTCCATGAATAAAACTTGAAATAGTGAACAATGTTACTAGAAAAATATAAAAATTCAT
17208906 TTCA
131 TTCA
17208910 CTTATTACTC
Statistics
Matches: 121, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
150 24 0.20
151 97 0.80
ACGTcount: A:0.46, C:0.09, G:0.08, T:0.37
Consensus pattern (150 bp):
AATTAAATTAAATTTCAAATTCATATTTTTTAAAACATTAAGTAAAAATTATTAAATGTCTTACT
AACAAAAGTCCATGAATAAAACTTGAAATAGTGAACAATGTTACTAGAAAAATATAAAAATTCAT
TTCATGTGACTACATGAACT
Found at i:17214796 original size:4 final size:4
Alignment explanation
Indices: 17214787--17214812 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
17214777 AGAAGTACAA
17214787 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
17214813 AGTCTGCAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:17219086 original size:49 final size:49
Alignment explanation
Indices: 17219011--17219106 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 49
17219001 ACCAGTCTAA
* *
17219011 TAGTGTCACAATTGTCTATCAAGGTTAGTAGAAACATAAATATTATGCT
1 TAGTGTCACAACTGGCTATCAAGGTTAGTAGAAACATAAATATTATGCT
* * * *
17219060 TAGTGTCATAACTGGCTATCATGGTTAGTAGAGACATAAGTATTATG
1 TAGTGTCACAACTGGCTATCAAGGTTAGTAGAAACATAAATATTATG
17219107 TTCTTTGCAT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 41 1.00
ACGTcount: A:0.34, C:0.11, G:0.20, T:0.34
Consensus pattern (49 bp):
TAGTGTCACAACTGGCTATCAAGGTTAGTAGAAACATAAATATTATGCT
Found at i:17221654 original size:28 final size:27
Alignment explanation
Indices: 17221597--17221648 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
17221587 TTTAATTTTA
17221597 AAATAATTTTTTATTTAAATACTAATTT
1 AAATAATTTTTTATTTAAATAC-AATTT
17221625 AAAT-ATTTTTTATTTAAATA-AATT
1 AAATAATTTTTTATTTAAATACAATT
17221649 GATTAATCAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
25 4 0.17
27 16 0.67
28 4 0.17
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (27 bp):
AAATAATTTTTTATTTAAATACAATTT
Found at i:17222240 original size:17 final size:17
Alignment explanation
Indices: 17222218--17222250 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
17222208 ATCTTTTGAA
17222218 TTAAAAA-AAATGACATT
1 TTAAAAATAAAT-ACATT
17222235 TTAAAAATAAATACAT
1 TTAAAAATAAATACAT
17222251 GATTTTTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.61, C:0.06, G:0.03, T:0.30
Consensus pattern (17 bp):
TTAAAAATAAATACATT
Found at i:17222457 original size:20 final size:19
Alignment explanation
Indices: 17222442--17222479 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
17222432 TAAAATAATT
17222442 TAACAAA-ATATTAAATGAA
1 TAACAAACATATTAAAT-AA
*
17222461 TAACAAACATGTTAAATAA
1 TAACAAACATATTAAATAA
17222480 ATAAAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.61, C:0.08, G:0.05, T:0.26
Consensus pattern (19 bp):
TAACAAACATATTAAATAA
Found at i:17222466 original size:19 final size:20
Alignment explanation
Indices: 17222442--17222483 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
17222432 TAAAATAATT
*
17222442 TAACAAA-ATATTAAATGAA
1 TAACAAACATATTAAATAAA
*
17222461 TAACAAACATGTTAAATAAA
1 TAACAAACATATTAAATAAA
17222481 TAA
1 TAA
17222484 AATTTTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.62, C:0.07, G:0.05, T:0.26
Consensus pattern (20 bp):
TAACAAACATATTAAATAAA
Found at i:17223796 original size:12 final size:12
Alignment explanation
Indices: 17223767--17223805 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
17223757 TTAGGTTTTG
17223767 AATTTAAATATTT
1 AATTTAAA-ATTT
* *
17223780 TATTTAAGATTT
1 AATTTAAAATTT
17223792 AATTTAAAATTT
1 AATTTAAAATTT
17223804 AA
1 AA
17223806 ATGCATTTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
12 16 0.73
13 6 0.27
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (12 bp):
AATTTAAAATTT
Found at i:17224712 original size:8 final size:8
Alignment explanation
Indices: 17224701--17224749 Score: 53
Period size: 8 Copynumber: 6.0 Consensus size: 8
17224691 TAATATTATT
*
17224701 TAATTTAA
1 TAATTTTA
17224709 TAATATTTA
1 TAAT-TTTA
17224718 TAATTTTA
1 TAATTTTA
17224726 TAATTTTA
1 TAATTTTA
** *
17224734 TTGTATTA
1 TAATTTTA
17224742 TAATTTTA
1 TAATTTTA
17224750 CATAATAAAT
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
8 26 0.79
9 7 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (8 bp):
TAATTTTA
Found at i:17225087 original size:4 final size:4
Alignment explanation
Indices: 17225078--17225110 Score: 57
Period size: 4 Copynumber: 8.2 Consensus size: 4
17225068 AATCATTTCA
*
17225078 ACAT ACAT ACAT ATAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
17225111 TATATATATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.21, G:0.00, T:0.27
Consensus pattern (4 bp):
ACAT
Found at i:17225095 original size:8 final size:8
Alignment explanation
Indices: 17225078--17225134 Score: 60
Period size: 8 Copynumber: 7.1 Consensus size: 8
17225068 AATCATTTCA
*
17225078 ACATACAT
1 ACATATAT
17225086 ACATATAT
1 ACATATAT
*
17225094 ACATACAT
1 ACATATAT
*
17225102 ACATACAT
1 ACATATAT
*
17225110 ATATATAT
1 ACATATAT
*
17225118 ATATATAT
1 ACATATAT
*
17225126 ATATATAT
1 ACATATAT
17225134 A
1 A
17225135 TAGGTTTTGC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 45 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (8 bp):
ACATATAT
Found at i:17225115 original size:4 final size:4
Alignment explanation
Indices: 17225088--17225136 Score: 62
Period size: 4 Copynumber: 12.2 Consensus size: 4
17225078 ACATACATAC
* * * *
17225088 ATAT ATAC ATAC ATAC ATAC ATAT ATAT ATAT ATAT ATAT ATAT ATAT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
17225136 A
1 A
17225137 GGTTTTGCAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 43 1.00
ACGTcount: A:0.51, C:0.08, G:0.00, T:0.41
Consensus pattern (4 bp):
ATAT
Found at i:17225131 original size:12 final size:12
Alignment explanation
Indices: 17225080--17225136 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
17225070 TCATTTCAAC
*
17225080 ATACATACATAT
1 ATACATATATAT
* *
17225092 ATACATACATAC
1 ATACATATATAT
17225104 ATACATATATAT
1 ATACATATATAT
*
17225116 ATATATATATAT
1 ATACATATATAT
*
17225128 ATATATATA
1 ATACATATA
17225137 GGTTTTGCAG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.39
Consensus pattern (12 bp):
ATACATATATAT
Found at i:17227870 original size:2 final size:2
Alignment explanation
Indices: 17227863--17227893 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17227853 ATCTTGCCTT
17227863 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
17227894 GAGAAGAAAG
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:17228243 original size:2 final size:2
Alignment explanation
Indices: 17228236--17228260 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
17228226 TGAAATGATT
17228236 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 T
17228261 TGATCCTTAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:17230180 original size:12 final size:13
Alignment explanation
Indices: 17230154--17230178 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17230144 TTCTTTAAAA
17230154 CTTCTTTTTTTTT
1 CTTCTTTTTTTTT
17230167 CTTCTTTTTTTT
1 CTTCTTTTTTTT
17230179 CTAAATTGAA
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (13 bp):
CTTCTTTTTTTTT
Found at i:17240083 original size:72 final size:72
Alignment explanation
Indices: 17239963--17240103 Score: 194
Period size: 72 Copynumber: 2.0 Consensus size: 72
17239953 ATATGGATGC
*
17239963 AGCAATACGGAAAACTGGTGTTTAAGCTAACTCGCTGCTTGCTAGTGATCT-CTTCGGCCACAAG
1 AGCAATACGGAAAACTGGTGTTTAAGATAACTCGCTGCTTGCTAGTGAT-TGCTTCGGCCACAAG
17240027 TAATAAGA
65 TAATAAGA
* ** * * * *
17240035 AGCAATACTGAAAACTGGTGTTTCGGATGACTCTCTGCTTGCTGGTGATTGCTTTGGCCACAAGT
1 AGCAATACGGAAAACTGGTGTTTAAGATAACTCGCTGCTTGCTAGTGATTGCTTCGGCCACAAGT
17240100 AATA
66 AATA
17240104 TCATCCTTCA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 1 0.02
72 59 0.98
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (72 bp):
AGCAATACGGAAAACTGGTGTTTAAGATAACTCGCTGCTTGCTAGTGATTGCTTCGGCCACAAGT
AATAAGA
Found at i:17247882 original size:2 final size:2
Alignment explanation
Indices: 17247875--17247911 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
17247865 CTGCTAGAGG
17247875 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
17247912 GAGAGAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17247967 original size:2 final size:2
Alignment explanation
Indices: 17247911--17247959 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
17247901 ATATATATAT
17247911 AG AG AG 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 AG AG AG
17247953 AG AG AG A
1 AG AG AG A
17247960 TTGAGAGAAG
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:17266030 original size:41 final size:41
Alignment explanation
Indices: 17265969--17266048 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 41
17265959 AGTTACAGTT
* * * *
17265969 AATCTCAAGCGTACACAAGAAGACGCATTTATATCGAGATC
1 AATCTCAAGCATACACAAGAAGACACATTCACATCGAGATC
* *
17266010 AATCTGAAGCATACATAAGAAGACACATTCACATCGAGA
1 AATCTCAAGCATACACAAGAAGACACATTCACATCGAGA
17266049 AAAAGAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.20
Consensus pattern (41 bp):
AATCTCAAGCATACACAAGAAGACACATTCACATCGAGATC
Found at i:17276115 original size:20 final size:20
Alignment explanation
Indices: 17276087--17276156 Score: 72
Period size: 20 Copynumber: 3.6 Consensus size: 20
17276077 TAAAAATAAT
*
17276087 TTTTTTAATTATTTATTTAA
1 TTTTATAATTATTTATTTAA
*
17276107 TTTTATAATTATTTATAT-A
1 TTTTATAATTATTTATTTAA
* * *
17276126 TTTTTTTA-TATATATTTAA
1 TTTTATAATTATTTATTTAA
*
17276145 TTTTATATTTAT
1 TTTTATAATTAT
17276157 ATTTAAATTA
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
18 7 0.18
19 13 0.33
20 19 0.49
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (20 bp):
TTTTATAATTATTTATTTAA
Found at i:17276134 original size:16 final size:16
Alignment explanation
Indices: 17276115--17276161 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 16
17276105 AATTTTATAA
17276115 TTATTTATATATT-TTT
1 TTATTTATAT-TTATTT
*
17276131 TTATATATATTTAATTT
1 TTATTTATATTT-ATTT
17276148 TATATTTATATTTA
1 T-TATTTATATTTA
17276162 AATTAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
15 2 0.08
16 9 0.35
17 5 0.19
18 10 0.38
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATTTATATTTATTT
Found at i:17276139 original size:14 final size:15
Alignment explanation
Indices: 17276120--17276152 Score: 50
Period size: 14 Copynumber: 2.2 Consensus size: 15
17276110 TATAATTATT
17276120 TATATATTT-TTTTA
1 TATATATTTATTTTA
17276134 TATATATTTAATTTTA
1 TATATATTT-ATTTTA
17276150 TAT
1 TAT
17276153 TTATATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 9 0.53
16 8 0.47
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATATATTTATTTTA
Found at i:17276151 original size:12 final size:12
Alignment explanation
Indices: 17276090--17276160 Score: 56
Period size: 12 Copynumber: 5.7 Consensus size: 12
17276080 AAATAATTTT
17276090 TTTAATTATT-TA
1 TTTAATT-TTATA
17276102 TTTAATTTTATA
1 TTTAATTTTATA
*
17276114 ATT-ATTTATATA
1 TTTAATTT-TATA
**
17276126 TTTTTTTATATATA
1 TTTAATT-T-TATA
17276140 TTTAATTTTATA
1 TTTAATTTTATA
17276152 TTTATATTT
1 TTTA-ATTT
17276161 AAATTAAAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
11 6 0.12
12 25 0.51
13 7 0.14
14 11 0.22
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAATTTTATA
Found at i:17276161 original size:12 final size:11
Alignment explanation
Indices: 17276100--17276161 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
17276090 TTTAATTATT
17276100 TATTTAATTTTA
1 TATTT-ATTTTA
*
17276112 TAATTATTTATA
1 TATTTATTT-TA
17276124 TATTT-TTTTA
1 TATTTATTTTA
* *
17276134 TATATATTTAA
1 TATTTATTTTA
17276145 T-TTTATATTTA
1 TATTTAT-TTTA
17276156 TATTTA
1 TATTTA
17276162 AATTAAAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
10 10 0.25
11 16 0.40
12 14 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (11 bp):
TATTTATTTTA
Found at i:17277050 original size:39 final size:39
Alignment explanation
Indices: 17276980--17277100 Score: 127
Period size: 39 Copynumber: 3.1 Consensus size: 39
17276970 TCTAAGAGAT
* *** * *
17276980 GATGAAGATGGTTTAGATGGCATTGGAGGTTTAGGTGAT
1 GATGAAGATGGTTTAGAAGATGTTGGAGGTTTAGGGGAA
*
17277019 GAT-AGAGATGGTTTAGAAGATGTTGGGGGTTTAGGGGAA
1 GATGA-AGATGGTTTAGAAGATGTTGGAGGTTTAGGGGAA
** * *
17277058 GATGAAGATGGTTTAGAAGATGGAGGTGGTTTAGGAGAA
1 GATGAAGATGGTTTAGAAGATGTTGGAGGTTTAGGGGAA
17277097 GATG
1 GATG
17277101 TTGGGGGTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
38 1 0.01
39 67 0.97
40 1 0.01
ACGTcount: A:0.29, C:0.01, G:0.41, T:0.29
Consensus pattern (39 bp):
GATGAAGATGGTTTAGAAGATGTTGGAGGTTTAGGGGAA
Found at i:17277058 original size:21 final size:21
Alignment explanation
Indices: 17277034--17277171 Score: 90
Period size: 21 Copynumber: 6.9 Consensus size: 21
17277024 AGATGGTTTA
*
17277034 GAAGATGTTGGGGGTTTAGGG
1 GAAGATGTAGGGGGTTTAGGG
* **
17277055 GAAGATGAAGATGGTTTA---
1 GAAGATGTAGGGGGTTTAGGG
* * *
17277073 GAAGATGGAGGTGGTTTAGGA
1 GAAGATGTAGGGGGTTTAGGG
*
17277094 GAAGATGTTGGGGGTTTAGGG
1 GAAGATGTAGGGGGTTTAGGG
* **
17277115 GAAGATGAAGATGGTTTA---
1 GAAGATGTAGGGGGTTTAGGG
* * *
17277133 GAAGATGGAGGTGGTTTAGGA
1 GAAGATGTAGGGGGTTTAGGG
* *
17277154 GAAGAAGTTGGGGGTTTA
1 GAAGATGTAGGGGGTTTA
17277172 AAGGATGATG
Statistics
Matches: 91, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
18 32 0.35
21 59 0.65
ACGTcount: A:0.28, C:0.00, G:0.45, T:0.27
Consensus pattern (21 bp):
GAAGATGTAGGGGGTTTAGGG
Found at i:17277073 original size:60 final size:59
Alignment explanation
Indices: 17277019--17277171 Score: 204
Period size: 60 Copynumber: 2.6 Consensus size: 59
17277009 TTTAGGTGAT
17277019 GATAGAGATGGTTT-AGAAGATGTTGGGGGTTTAGGGGAAGATGAAGATGGTTTA-GAA
1 GATAGAGATGGTTTGAGAAGATGTTGGGGGTTTAGGGGAAGATGAAGATGGTTTAGGAA
* *
17277076 GATGGAGGTGGTTTAGGAGAAGATGTTGGGGGTTTAGGGGAAGATGAAGATGGTTTA-GAA
1 GATAGAGATGGTTT--GAGAAGATGTTGGGGGTTTAGGGGAAGATGAAGATGGTTTAGGAA
* * *
17277136 GATGGAGGTGGTTTAGGAGAAGAAGTTGGGGGTTTA
1 GATAGAGATGGTTT--GAGAAGATGTTGGGGGTTTA
17277172 AAGGATGATG
Statistics
Matches: 90, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
57 12 0.13
60 78 0.87
ACGTcount: A:0.29, C:0.00, G:0.44, T:0.27
Consensus pattern (59 bp):
GATAGAGATGGTTTGAGAAGATGTTGGGGGTTTAGGGGAAGATGAAGATGGTTTAGGAA
Found at i:17280450 original size:14 final size:14
Alignment explanation
Indices: 17280431--17280458 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17280421 CGGCAATAAA
17280431 ATTCAAACAGAAAT
1 ATTCAAACAGAAAT
17280445 ATTCAAACAGAAAT
1 ATTCAAACAGAAAT
17280459 CAGGACCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
ATTCAAACAGAAAT
Found at i:17285201 original size:19 final size:20
Alignment explanation
Indices: 17285174--17285215 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
17285164 ATTGAAATAT
* *
17285174 ATATTTTTTTAAGTTTTA-A
1 ATATATTTTAAAGTTTTATA
*
17285193 ATATATTTTAAATTTTTATA
1 ATATATTTTAAAGTTTTATA
17285213 ATA
1 ATA
17285216 AATAAAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (20 bp):
ATATATTTTAAAGTTTTATA
Found at i:17285269 original size:12 final size:12
Alignment explanation
Indices: 17285231--17285274 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
17285221 AAATAATAAT
17285231 TTTATATTAAAA
1 TTTATATTAAAA
17285243 -TT-TATT-AAA
1 TTTATATTAAAA
17285252 --TATATTAAAA
1 TTTATATTAAAA
17285262 TTTATATTAAAA
1 TTTATATTAAAA
17285274 T
1 T
17285275 AATCTATAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
8 1 0.04
9 7 0.25
10 7 0.25
11 2 0.07
12 11 0.39
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
TTTATATTAAAA
Found at i:17285295 original size:23 final size:22
Alignment explanation
Indices: 17285268--17285329 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
17285258 AAAATTTATA
17285268 TTAAAAT-AATCTATAAAAATAAT
1 TTAAAATAAATC-A-AAAAATAAT
*
17285291 TTAAATTCAAATCAAAAAATAAT
1 TTAAAAT-AAATCAAAAAATAAT
*
17285314 TTAAATTCAAATCAAA
1 TTAAAAT-AAATCAAA
17285330 TTTTAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
23 31 0.86
24 1 0.03
25 4 0.11
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (22 bp):
TTAAAATAAATCAAAAAATAAT
Found at i:17285334 original size:18 final size:20
Alignment explanation
Indices: 17285283--17285338 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 20
17285273 ATAATCTATA
17285283 AAAATAATTTAAATTCAAATC
1 AAAAT-ATTTAAATTCAAATC
17285304 AAAAAATAATTTAAATTCAAATC
1 --AAAAT-ATTTAAATTCAAATC
17285327 -AAAT-TTTAAATT
1 AAAATATTTAAATT
17285339 TTTATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.24
20 4 0.12
23 21 0.64
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAATATTTAAATTCAAATC
Found at i:17289355 original size:33 final size:33
Alignment explanation
Indices: 17289313--17289379 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
17289303 AAGGAAATAG
*
17289313 ATGAATAATGACTGAATCAACATTCAGAATCTA
1 ATGAATAATGACTGAATCAACACTCAGAATCTA
*
17289346 ATGAATAATGACTGAGTCAACACTCAGAATCTA
1 ATGAATAATGACTGAATCAACACTCAGAATCTA
17289379 A
1 A
17289380 CGGTTAGCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.45, C:0.16, G:0.13, T:0.25
Consensus pattern (33 bp):
ATGAATAATGACTGAATCAACACTCAGAATCTA
Found at i:17292933 original size:16 final size:17
Alignment explanation
Indices: 17292914--17292951 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
17292904 ACTAAAGAAT
17292914 TATATTAAAATTTAT-A
1 TATATTAAAATTTATAA
*
17292930 TATAATAAAATTTATAA
1 TATATTAAAATTTATAA
17292947 TATAT
1 TATAT
17292952 ATTTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TATATTAAAATTTATAA
Found at i:17292955 original size:29 final size:29
Alignment explanation
Indices: 17292923--17293016 Score: 86
Period size: 29 Copynumber: 3.2 Consensus size: 29
17292913 TTATATTAAA
17292923 ATTTATATATAATAA-AATTTATAATATAT
1 ATTTATATA-AATAATAATTTATAATATAT
* *
17292952 ATTTA-ATAAATTAATAAATTATTAAAAT-T
1 ATTTATATAAA-TAATAATTTA-TAATATAT
* *
17292981 ATTTATATAAATAATACTTTTATAAATAAAT
1 ATTTATATAAATAATA-ATTTAT-AATATAT
17293012 ATTTA
1 ATTTA
17293017 AATATATTTA
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
27 2 0.04
28 6 0.12
29 22 0.42
30 16 0.31
31 6 0.12
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.47
Consensus pattern (29 bp):
ATTTATATAAATAATAATTTATAATATAT
Found at i:17295025 original size:88 final size:88
Alignment explanation
Indices: 17294876--17295052 Score: 354
Period size: 88 Copynumber: 2.0 Consensus size: 88
17294866 TGGCTTCAGC
17294876 TCGTCCACACTTAGGTTTTATTTAGATAGATGATGAGATTAAAAATAATAATAAAATTTACTGTA
1 TCGTCCACACTTAGGTTTTATTTAGATAGATGATGAGATTAAAAATAATAATAAAATTTACTGTA
17294941 ATTATGATGAAAAAAAGTTATTA
66 ATTATGATGAAAAAAAGTTATTA
17294964 TCGTCCACACTTAGGTTTTATTTAGATAGATGATGAGATTAAAAATAATAATAAAATTTACTGTA
1 TCGTCCACACTTAGGTTTTATTTAGATAGATGATGAGATTAAAAATAATAATAAAATTTACTGTA
17295029 ATTATGATGAAAAAAAGTTATTA
66 ATTATGATGAAAAAAAGTTATTA
17295052 T
1 T
17295053 AGTTGCGATT
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
88 89 1.00
ACGTcount: A:0.43, C:0.07, G:0.14, T:0.37
Consensus pattern (88 bp):
TCGTCCACACTTAGGTTTTATTTAGATAGATGATGAGATTAAAAATAATAATAAAATTTACTGTA
ATTATGATGAAAAAAAGTTATTA
Found at i:17296940 original size:16 final size:14
Alignment explanation
Indices: 17296918--17296954 Score: 56
Period size: 16 Copynumber: 2.5 Consensus size: 14
17296908 TGTGTTCATA
17296918 TTTAAATTTTAAATT
1 TTTAAATTTT-AATT
17296933 TATTAAATTTTAATT
1 T-TTAAATTTTAATT
17296948 TTTAAAT
1 TTTAAAT
17296955 ATAATTATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TTTAAATTTTAATT
Found at i:17298528 original size:14 final size:12
Alignment explanation
Indices: 17298507--17298545 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
17298497 TTATATCATG
17298507 AAAAAAAAAATT
1 AAAAAAAAAATT
*
17298519 AATTAAAAAAAATG
1 AA--AAAAAAAATT
17298533 AAAAAAAAAATT
1 AAAAAAAAAATT
17298545 A
1 A
17298546 TGTGAATAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
12 12 0.52
14 11 0.48
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (12 bp):
AAAAAAAAAATT
Done.