Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008985.1 Hibiscus syriacus cultivar Beakdansim tig00112349_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1528252
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
File 5 of 9
Found at i:692244 original size:27 final size:27
Alignment explanation
Indices: 692173--692258 Score: 91
Period size: 27 Copynumber: 3.1 Consensus size: 27
692163 AATGGAATAC
* * *
692173 ATAACCAGATTAAATAAATAAGTATAATAC
1 ATAACCAAATAAAATAAATAA--ATAA-AA
* * *
692203 ATAACCATATTAAATAAATACATAAAA
1 ATAACCAAATAAAATAAATAAATAAAA
692230 ATAACCAAATAAAATAAATAAATAAAA
1 ATAACCAAATAAAATAAATAAATAAAA
692257 AT
1 AT
692259 TACCTCTGGA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
27 27 0.54
28 4 0.08
30 19 0.38
ACGTcount: A:0.64, C:0.09, G:0.02, T:0.24
Consensus pattern (27 bp):
ATAACCAAATAAAATAAATAAATAAAA
Found at i:692673 original size:39 final size:37
Alignment explanation
Indices: 692612--693051 Score: 271
Period size: 37 Copynumber: 11.8 Consensus size: 37
692602 AATGTGTTAA
* **
692612 TTTTTGAAAATATTTTTTTATATAGTTTTTAGAAAACAGT
1 TTTTTGAAAATA-TATAATATATAGTTTTT-GAAAACA-T
* * *
692652 TTTTTGAAAACATATAATATATACTTTTT-AAAAAAT
1 TTTTTGAAAATATATAATATATAGTTTTTGAAAACAT
* * *
692688 CGGTTTTCGAAAATATATATTATATAG-TTTTGAAAACGGT
1 ---TTTTTGAAAATATATAATATATAGTTTTTGAAAAC-AT
* *** *
692728 ATTCAAAAAATATATATTATATAG-TTTTGAAAACA-
1 TTTTTGAAAATATATAATATATAGTTTTTGAAAACAT
692763 -TTTTGAAAATATATATAATATATAG-TTTTGAAAACA-
1 TTTTTG-AAA-ATATATAATATATAGTTTTTGAAAACAT
* * * *
692799 TTTTTGAATATATATATTATAT-GGTTTTGAAAATAT
1 TTTTTGAAAATATATAATATATAGTTTTTGAAAACAT
***
692835 TTTGAAAACATATATATAATATATAGTTTTTGAAAACA-
1 TTTTTGAA-A-ATATATAATATATAGTTTTTGAAAACAT
** * *
692873 TTTTAAAAAATATATATATAATATATATTTTTTAAAA-AT
1 TTTTTGAAAATATATA-AT-ATATA-GTTTTTGAAAACAT
* *
692912 ATTTTGAAAATATATATAATATATAG-TTTTGAAAATAT
1 TTTTTG-AAA-ATATATAATATATAGTTTTTGAAAACAT
* * *
692950 ATTTTTGAAAATATATATTATATAG-TTGT-AAAACAA
1 -TTTTTGAAAATATATAATATATAGTTTTTGAAAACAT
* * *
692986 TTTTTGAAAATATA-CATATTATA-TGTTTTGAAAAAAA
1 TTTTTGAAAATATATAATA-TATAGT-TTTTGAAAACAT
* **
693023 ATTTAAAAACATATATAATATATAGTTTT
1 TTTTTGAAA-ATATATAATATATAGTTTT
693052 AAAAATGAAT
Statistics
Matches: 320, Mismatches: 52, Indels: 58
0.74 0.12 0.13
Matches are distributed among these distances:
34 5 0.02
35 43 0.13
36 48 0.15
37 80 0.25
38 46 0.14
39 74 0.23
40 17 0.05
41 7 0.02
ACGTcount: A:0.45, C:0.03, G:0.08, T:0.44
Consensus pattern (37 bp):
TTTTTGAAAATATATAATATATAGTTTTTGAAAACAT
Found at i:692738 original size:37 final size:36
Alignment explanation
Indices: 692697--693056 Score: 325
Period size: 37 Copynumber: 9.8 Consensus size: 36
692687 TCGGTTTTCG
* * *
692697 AAAATATATATTATATAGTTTTGAAAACGGTATTCAA
1 AAAATATATATTATATAGTTTTGAAAAC-ATTTTGAA
692734 AAAATATATATTATATAGTTTTGAAAACATTTTGAA
1 AAAATATATATTATATAGTTTTGAAAACATTTTGAA
* *
692770 AATATATATAATATATAGTTTTGAAAACATTTTTG--
1 AAAATATATATTATATAGTTTTGAAAACA-TTTTGAA
* * *
692805 AATATATATATTATATGGTTTTGAAAATATTTTGAA
1 AAAATATATATTATATAGTTTTGAAAACATTTTGAA
* *
692841 AACATATATATAATATATAGTTTTTGAAAACATTTTAAA
1 AA-A-ATATATATTATATAG-TTTTGAAAACATTTTGAA
* * *
692880 AAATATATATATAATATATATTTTTTAAAAATATTTTGAA
1 AAA-ATATATAT--TATATA-GTTTTGAAAACATTTTGAA
* * * ***
692920 AATATATATAATATATAGTTTTGAAAATATATTTTTG
1 AAAATATATATTATATAGTTTTGAAAACAT-TTTGAA
*
692957 AAAATATATATTATATAGTTGT-AAAACAATTTTTGAA
1 AAAATATATATTATATAGTTTTGAAAAC-A-TTTTGAA
* * * *
692994 AATATACATATTATAT-GTTTTGAAAAAAAATTT-AA
1 AAAATATATATTATATAGTTTTG-AAAACATTTTGAA
* *
693029 AAACATATATAATATATAGTTTTAAAAA
1 AAA-ATATATATTATATAGTTTTGAAAA
693057 TGAATTATTT
Statistics
Matches: 266, Mismatches: 41, Indels: 33
0.78 0.12 0.10
Matches are distributed among these distances:
34 5 0.02
35 30 0.11
36 71 0.27
37 85 0.32
38 27 0.10
39 25 0.09
40 23 0.09
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (36 bp):
AAAATATATATTATATAGTTTTGAAAACATTTTGAA
Found at i:692796 original size:73 final size:72
Alignment explanation
Indices: 692691--693056 Score: 384
Period size: 73 Copynumber: 5.0 Consensus size: 72
692681 AAAAAATCGG
* *
692691 TTTTCGAAAATATATAT--TATATAGTTTTGAAAACGGTATTCAAAAAATATATATTATATAGTT
1 TTTT-GAAAATATATATAATATATAGTTTTGAAAAC-ATATTTAAAAAATATATATTATATAGTT
*
692754 TTGAAAACA
64 TTAAAAACA
** * *
692763 TTTTGAAAATATATATAATATATAGTTTTGAAAACAT-TTTTGAATATATATATTATATGGTTTT
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACATATTTAAAAAATATATATTATATAGTTTT
* *
692827 GAAAATA
66 AAAAACA
692834 TTTTGAAAACATATATATAATATATAGTTTTTGAAAACAT-TTTAAAAAATATATATATAATATA
1 TTTTG-AAA-ATATATATAATATATAG-TTTTGAAAACATATTT-AAAAA-ATATATAT--TATA
* *
692898 TATTTTTTAAAAATA
59 TA-GTTTTAAAAACA
* ** *
692913 TTTTGAAAATATATATAATATATAGTTTTGAAAATATATTTTTGAAAATATATATTATATAGTTG
1 TTTTGAAAATATATATAATATATAGTTTTGAAAACATA-TTTAAAAAATATATATTATATAGTTT
692978 T-AAAACAA
65 TAAAAAC-A
* * * * *
692986 TTTTTGAAAATATACATATTATAT-GTTTTGAAAAAAAATTTAAAAACATATATAATATATAGTT
1 -TTTTGAAAATATATATAATATATAGTTTTGAAAACATATTTAAAAA-ATATATATTATATAGTT
693050 TTAAAAA
64 TTAAAAA
693057 TGAATTATTT
Statistics
Matches: 251, Mismatches: 27, Indels: 30
0.81 0.09 0.10
Matches are distributed among these distances:
71 45 0.18
72 18 0.07
73 67 0.27
74 46 0.18
75 2 0.01
76 27 0.11
77 20 0.08
78 11 0.04
79 15 0.06
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.43
Consensus pattern (72 bp):
TTTTGAAAATATATATAATATATAGTTTTGAAAACATATTTAAAAAATATATATTATATAGTTTT
AAAAACA
Found at i:692950 original size:16 final size:15
Alignment explanation
Indices: 692929--692968 Score: 64
Period size: 14 Copynumber: 2.7 Consensus size: 15
692919 AAATATATAT
692929 AATATATAGTTTTGAA
1 AATATATA-TTTTGAA
692945 AATATAT-TTTTGAA
1 AATATATATTTTGAA
692959 AATATATATT
1 AATATATATT
692969 ATATAGTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.61
15 2 0.09
16 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
AATATATATTTTGAA
Found at i:694319 original size:29 final size:29
Alignment explanation
Indices: 694255--694323 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
694245 TTGCAGCTCC
694255 TTTTTA-TTATCAATTTGAACCATAAATT
1 TTTTTAGTTATCAATTTGAACCATAAATT
** *
694283 TCAATTAGTT-TCAATTTGACCCTATAAATT
1 T-TTTTAGTTATCAATTTGAACC-ATAAATT
694313 TTTTTAGTTAT
1 TTTTTAGTTAT
694324 TCATTTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
28 1 0.03
29 20 0.62
30 11 0.34
ACGTcount: A:0.32, C:0.12, G:0.06, T:0.51
Consensus pattern (29 bp):
TTTTTAGTTATCAATTTGAACCATAAATT
Found at i:699720 original size:85 final size:85
Alignment explanation
Indices: 699575--699737 Score: 220
Period size: 85 Copynumber: 1.9 Consensus size: 85
699565 GAATCCAGTA
* * * *
699575 AGCATAACTCAAGGCGAGAAGGGTTGTCTGTCAACAAAAACCTTTGAGTTCGATTTCATTCAGCT
1 AGCATAACTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTTGAGTTCGATTCCATTCAGCT
699640 CAAGGGCATATCAAATTTAC
66 CAAGGGCATATCAAATTTAC
* ** *
699660 AGCATAGCTCAAGGCGAGAAGGGCTATCTATCAATGAAGA-CTTTCGAGTTCGATTCCATTCAGC
1 AGCATAACTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTT-GAGTTCGATTCCATTCAGC
* *
699724 TCGAGGGCGTATCA
65 TCAAGGGCATATCA
699738 GCCACATTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
84 4 0.06
85 63 0.94
ACGTcount: A:0.31, C:0.21, G:0.23, T:0.26
Consensus pattern (85 bp):
AGCATAACTCAAGGCGAGAAGGGCTATCTATCAACAAAAACCTTTGAGTTCGATTCCATTCAGCT
CAAGGGCATATCAAATTTAC
Found at i:700397 original size:19 final size:19
Alignment explanation
Indices: 700360--700399 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
700350 TTTCGTCCGG
*
700360 AATTTTTTTTATATGTTTT
1 AATTTTTTTAATATGTTTT
*
700379 AATTTTTTATAATATTTTTT
1 AATTTTTT-TAATATGTTTT
700399 A
1 A
700400 TATAGTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
AATTTTTTTAATATGTTTT
Found at i:700440 original size:37 final size:38
Alignment explanation
Indices: 700398--700491 Score: 104
Period size: 39 Copynumber: 2.4 Consensus size: 38
700388 TAATATTTTT
*
700398 TATATAGTTTTTAGAAAAT-GGTTTTTTGAAAACATATAA
1 TATATA-TTTTTAGAAAATCGG-TTTTCGAAAACATATAA
* *
700437 TATATACTTTTTAAAAAATCGGTTTTCGAAAATATAT-A
1 TATATA-TTTTTAGAAAATCGGTTTTCGAAAACATATAA
700475 T-TATATTGTTTAGAAAA
1 TATATATT-TTTAGAAAA
700492 CAATATTCAA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
36 2 0.04
37 12 0.25
38 2 0.04
39 30 0.62
40 2 0.04
ACGTcount: A:0.41, C:0.04, G:0.11, T:0.44
Consensus pattern (38 bp):
TATATATTTTTAGAAAATCGGTTTTCGAAAACATATAA
Found at i:700441 original size:39 final size:37
Alignment explanation
Indices: 700398--700621 Score: 107
Period size: 36 Copynumber: 6.1 Consensus size: 37
700388 TAATATTTTT
*
700398 TATATAGTTTTTAGAAAAT-GGTTTTTTGAAAACATATAA
1 TATATA-TTTTTAGAAAATCGG-TTTTCGAAAACATAT-A
* *
700437 TATATACTTTTTAAAAAATCGGTTTTCGAAAATATATA
1 TATATA-TTTTTAGAAAATCGGTTTTCGAAAACATATA
** * * *
700475 T-TATATTGTTTAGAAAA-CAATATTCAAAAATATATA
1 TATATATT-TTTAGAAAATCGGTTTTCGAAAACATATA
* * *
700511 TTATATAGTTTT-GAAAA-C-ATTTT-GAAAATATATA
1 -TATATATTTTTAGAAAATCGGTTTTCGAAAACATATA
* * *
700545 TAATATATACTTTT-G-AAAT-GTTTTTTGAAAATATATA
1 T-ATATAT--TTTTAGAAAATCGGTTTTCGAAAACATATA
*
700582 TATTATATGGTTTT-GAAAAT--ATTTT-GAAAACATATA
1 TA-TATAT--TTTTAGAAAATCGGTTTTCGAAAACATATA
700618 TATA
1 TATA
700622 ATATATAGTT
Statistics
Matches: 155, Mismatches: 18, Indels: 28
0.77 0.09 0.14
Matches are distributed among these distances:
33 1 0.01
34 15 0.10
35 9 0.06
36 45 0.29
37 42 0.27
38 11 0.07
39 30 0.19
40 2 0.01
ACGTcount: A:0.43, C:0.04, G:0.09, T:0.44
Consensus pattern (37 bp):
TATATATTTTTAGAAAATCGGTTTTCGAAAACATATA
Found at i:700510 original size:36 final size:35
Alignment explanation
Indices: 700465--700664 Score: 132
Period size: 36 Copynumber: 5.5 Consensus size: 35
700455 TCGGTTTTCG
*
700465 AAAATATATATTATATTGTTTAGAAAACAATATTCA
1 AAAATATATATTATATAGTTTAGAAAAC-ATATTCA
* * *
700501 AAAATATATATTATATAGTTTTGAAAACATTTTGA
1 AAAATATATATTATATAGTTTAGAAAACATATTCA
* * * *** * *
700536 AAATATATATAATATATACTTTTGAAATGTTTTTTGA
1 AAA-ATATATATTATATAGTTTAGAAA-ACATATTCA
* * * * *
700573 AAATATATATATTATATGGTTTTGAAAATATTTTGA
1 AAA-ATATATATTATATAGTTTAGAAAACATATTCA
* *
700609 AAACATATATATAATATATAGTTTTTGAAAACAT-TTTA
1 AAA-ATATATAT--TATATAG-TTTAGAAAACATATTCA
*
700647 AATATATATATATATATA
1 AAAATATATAT-TATATA
700665 TATAATATAT
Statistics
Matches: 140, Mismatches: 19, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
35 8 0.06
36 72 0.51
37 38 0.27
38 11 0.08
39 11 0.08
ACGTcount: A:0.46, C:0.03, G:0.07, T:0.44
Consensus pattern (35 bp):
AAAATATATATTATATAGTTTAGAAAACATATTCA
Found at i:700628 original size:47 final size:45
Alignment explanation
Indices: 700574--700791 Score: 161
Period size: 40 Copynumber: 5.2 Consensus size: 45
700564 GTTTTTTGAA
*
700574 AATATATATATTATATGGTTTTGAAAATATTTTGAAAAC----ATAT
1 AATATATATA-TATATGTTTTTGAAAATATTTT-AAAACATATATAT
* *
700617 -ATATA-ATATATA-GTTTTTGAAAACATTTT-AAATATATATAT
1 AATATATATATATATGTTTTTGAAAATATTTTAAAACATATATAT
* *
700658 ATATATATATAATATATAGTTTTTAAAAATATTTT-AAA-A-ACATAT
1 A-ATATATAT-ATATAT-GTTTTTGAAAATATTTTAAAACATATATAT
**
700703 -ATATA-ATATATA-GTTTTTGAAACCATTTTAAAA-A-ATATAT
1 AATATATATATATATGTTTTTGAAAATATTTTAAAACATATATAT
* * *
700743 -ATATA-ATATATA-GTTTTTAAAAATATATTGAAA-ATATATAT
1 AATATATATATATATGTTTTTGAAAATATTTTAAAACATATATAT
700784 AATATATA
1 AATATATA
700792 GTTTTGAAAA
Statistics
Matches: 146, Mismatches: 15, Indels: 28
0.77 0.08 0.15
Matches are distributed among these distances:
37 3 0.02
39 29 0.20
40 42 0.29
41 18 0.12
42 12 0.08
43 11 0.08
44 2 0.01
45 10 0.07
46 1 0.01
47 18 0.12
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (45 bp):
AATATATATATATATGTTTTTGAAAATATTTTAAAACATATATAT
Found at i:700638 original size:28 final size:26
Alignment explanation
Indices: 700603--700654 Score: 77
Period size: 28 Copynumber: 1.9 Consensus size: 26
700593 TTTGAAAATA
700603 TTTTGAAAACATATATATAATATATAGT
1 TTTTGAAAACAT-TATA-AATATATAGT
*
700631 TTTTGAAAACATTTTAAATATATA
1 TTTTGAAAACATTATAAATATATA
700655 TATATATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.35
27 3 0.13
28 12 0.52
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (26 bp):
TTTTGAAAACATTATAAATATATAGT
Found at i:700662 original size:111 final size:110
Alignment explanation
Indices: 700459--701019 Score: 458
Period size: 111 Copynumber: 4.9 Consensus size: 110
700449 AAAAAATCGG
* * * * * *
700459 TTTTCGAAAATATATATTATATTGTTTAGAAAACAATATTCAAAAATATATAT--TATATAG-TT
1 TTTTTGAATATATATATTATATGGTTTTGAAAA-AATTTTGAAAAATATATATAATATATAGTTT
* *
700521 TTGAAAACATTTTGAAAATATATATAATATATACTTTTG-AAAT-GT
65 TTGAAAACATTTT-AAAATATATATAATATATAGTTTTGTAAATATT
*
700566 TTTTTGAAAATATATATATTATATGGTTTTGAAAATATTTTGAAAACATATATATAATATATAGT
1 TTTTTG--AATATATATATTATATGGTTTTGAAAAAATTTTGAAAA-ATATATATAATATATAGT
*
700631 TTTTGAAAACATTTTAAATATATATATATATATATA-TAATATATAGTTTTTAAAAATAT
63 TTTTGAAAACATTTTAAA-ATATATATA-ATATATAGT--T-T-T-G----TAAATAT-T
*** * * * ** *
700690 TTTAAAAACATATATATAATATATAGTTTTTGAAACCATTTTAAAAAATATATATATAATATATA
1 TTTTTGAATATATATATTATA--T-GGTTTTGAAAAAATTTT-GAAAA-ATATATATAATATATA
* * * *
700755 GTTTTTAAAAATATATTGAAAATATATATAATATATAGTTTTGAAAATATT
61 GTTTTTGAAAACAT-TTTAAAATATATATAATATATAGTTTTGTAAATATT
* * *
700806 TTTTTGAATATATATATTATATAGTTTTTAAAAATATATTG-AAAATATATATAATATATAGTTT
1 TTTTTGAATATATATATTATATGGTTTTGAAAAA-ATTTTGAAAAATATATATAATATATAGTTT
* * * *
700870 TTAAAAATATATTGAAAATATATATAATATATAGTTTTGAAAATATT
65 TTGAAAACAT-TTTAAAATATATATAATATATAGTTTTGTAAATATT
* * * * *
700917 TTTTTGAATATATATATTATATAGTTGTAAAAACAATTTTTG-AATATATATATATTATAT-G-T
1 TTTTTGAATATATATATTATATGGTTTTGAAAA-AA-TTTTGAAAAATATATATAATATATAGTT
*
700979 TTTGAAAACAATTTTTAAAAGCATATATAATATATAGTTTT
64 TTTGAAAAC-A-TTTTAAAA-TATATATAATATATAGTTTT
701020 AAAAATGAAT
Statistics
Matches: 377, Mismatches: 45, Indels: 59
0.78 0.09 0.12
Matches are distributed among these distances:
107 5 0.01
108 8 0.02
109 32 0.08
110 8 0.02
111 117 0.31
112 69 0.18
113 14 0.04
114 6 0.02
115 1 0.00
116 18 0.05
117 6 0.02
121 1 0.00
122 17 0.05
123 1 0.00
124 6 0.02
125 21 0.06
126 42 0.11
127 5 0.01
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.45
Consensus pattern (110 bp):
TTTTTGAATATATATATTATATGGTTTTGAAAAAATTTTGAAAAATATATATAATATATAGTTTT
TGAAAACATTTTAAAATATATATAATATATAGTTTTGTAAATATT
Found at i:700705 original size:37 final size:37
Alignment explanation
Indices: 700660--701025 Score: 370
Period size: 37 Copynumber: 9.8 Consensus size: 37
700650 ATATATATAT
*
700660 ATATATATAATATATAGTTTTTAAAAATATTTTAAAAA
1 ATATATATAATATATAGTTTTTAAAAATATTTT-GAAA
* ** *
700698 CATATATATAATATATAGTTTTTGAAACCATTTTAAAAAA
1 -ATATATATAATATATAGTTTTTAAAAATATTTT--GAAA
*
700738 TATATATATAATATATAGTTTTTAAAAATATATTGAAA
1 -ATATATATAATATATAGTTTTTAAAAATATTTTGAAA
* *
700776 ATATATATAATATATAGTTTTGAAAATATTTTTTTG--A
1 ATATATATAATATATAGTTTTTAAAA-A-TATTTTGAAA
* *
700813 ATATATATATTATATAGTTTTTAAAAATATATTGAAA
1 ATATATATAATATATAGTTTTTAAAAATATTTTGAAA
*
700850 ATATATATAATATATAGTTTTTAAAAATATATTGAAA
1 ATATATATAATATATAGTTTTTAAAAATATTTTGAAA
* *
700887 ATATATATAATATATAGTTTTGAAAATATTTTTTTG--A
1 ATATATATAATATATAGTTTTTAAAA-A-TATTTTGAAA
* * * *
700924 ATATATATATTATATAG-TTGTAAAAACAATTTTTGAAT
1 ATATATATAATATATAGTTTTTAAAAA-TA-TTTTGAAA
* * *
700962 ATATATATATTATAT-GTTTTGAAAACA-ATTTTTAAA
1 ATATATATAATATATAGTTTTTAAAA-ATATTTTGAAA
*
700998 AGCATATATAATATATAG-TTTTAAAAAT
1 A-TATATATAATATATAGTTTTTAAAAAT
701026 GAATTTTTAT
Statistics
Matches: 278, Mismatches: 34, Indels: 32
0.81 0.10 0.09
Matches are distributed among these distances:
35 6 0.02
36 20 0.07
37 150 0.54
38 27 0.10
39 41 0.15
40 34 0.12
ACGTcount: A:0.47, C:0.02, G:0.06, T:0.45
Consensus pattern (37 bp):
ATATATATAATATATAGTTTTTAAAAATATTTTGAAA
Found at i:701049 original size:10 final size:10
Alignment explanation
Indices: 701032--701085 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
701022 AAATGAATTT
701032 TTATTTA-T-
1 TTATTTATTA
701040 TTA-TTATTA
1 TTATTTATTA
701049 TTATTTATTA
1 TTATTTATTA
701059 TTA-TTATTTA
1 TTATTTA-TTA
701069 TTATCTTATTA
1 TTAT-TTATTA
*
701080 ATATTT
1 TTATTT
701086 TTTCTTTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
7 3 0.08
8 4 0.10
9 6 0.15
10 17 0.44
11 6 0.15
12 3 0.08
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (10 bp):
TTATTTATTA
Found at i:701054 original size:13 final size:13
Alignment explanation
Indices: 701036--701072 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
701026 GAATTTTTAT
701036 TTATTTATTATTA
1 TTATTTATTATTA
701049 TTATTTATTATTA
1 TTATTTATTATTA
701062 TTATTTATTAT
1 TTATTTATTAT
701073 CTTATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
TTATTTATTATTA
Found at i:701091 original size:16 final size:16
Alignment explanation
Indices: 701040--701091 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
701030 TTTTATTTAT
* *
701040 TTATTATTATTATTTA
1 TTATTATTATTTTTTC
701056 TTATTATTATTTATTATC
1 TTATTATTATTT-TT-TC
*
701074 TTATTAATATTTTTTC
1 TTATTATTATTTTTTC
701090 TT
1 TT
701092 TTTCTGATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
16 15 0.48
17 4 0.13
18 12 0.39
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (16 bp):
TTATTATTATTTTTTC
Found at i:702476 original size:3 final size:3
Alignment explanation
Indices: 702470--702495 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
702460 ATTATTATTA
702470 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
702496 TTTCTAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:703706 original size:3 final size:3
Alignment explanation
Indices: 703698--703778 Score: 162
Period size: 3 Copynumber: 27.0 Consensus size: 3
703688 ATAAGAAAAA
703698 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
703746 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG
703779 AAAGGTTAAC
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 78 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:703827 original size:54 final size:54
Alignment explanation
Indices: 703777--703936 Score: 257
Period size: 54 Copynumber: 3.0 Consensus size: 54
703767 GAGGAGGAGG
* * * *
703777 AGAAAGGTTAACGAGAGGTAACATGCCATGTCAGATAAAACTTATGGGAGGTGA
1 AGAAAGGTTAATGGGAGGTAACATGCCACGTCAGATAAAACTTACGGGAGGTGA
703831 AGAAAGGTTAATGGGAGGTAACATGCCACGTCAGATAAAACTTACGGGAGGTGA
1 AGAAAGGTTAATGGGAGGTAACATGCCACGTCAGATAAAACTTACGGGAGGTGA
* * *
703885 AGAAAGGTTAATGGGAGGTAACATGCCACGTAAGATAAAACTGACAGGAGGT
1 AGAAAGGTTAATGGGAGGTAACATGCCACGTCAGATAAAACTTACGGGAGGT
703937 AACGTCAGAG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 99 1.00
ACGTcount: A:0.39, C:0.12, G:0.31, T:0.19
Consensus pattern (54 bp):
AGAAAGGTTAATGGGAGGTAACATGCCACGTCAGATAAAACTTACGGGAGGTGA
Found at i:704189 original size:31 final size:31
Alignment explanation
Indices: 704154--704233 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
704144 CGATTTTATC
704154 CTTGAAGTCATTTAATTACATTAATTCTATT
1 CTTGAAGTCATTTAATTACATTAATTCTATT
*
704185 CTTGAAGTCATTTAATTACATTAATTTTATT
1 CTTGAAGTCATTTAATTACATTAATTCTATT
*
704216 CTCGAAGTCATTTAATTA
1 CTTGAAGTCATTTAATTA
704234 AATCAAATTT
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.47
Consensus pattern (31 bp):
CTTGAAGTCATTTAATTACATTAATTCTATT
Found at i:708191 original size:3 final size:3
Alignment explanation
Indices: 708183--708208 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
708173 AGTTACAAAG
708183 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
708209 TTAATAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:711768 original size:21 final size:21
Alignment explanation
Indices: 711739--711813 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
711729 ATTCTGACTA
711739 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
* *
711760 TCGCGTTGCGATTTTCCGAAT
1 TCGCATTGCGATTTTCCAAAT
* * ** *
711781 TCGTAATGCGATAGTCCAAAA
1 TCGCATTGCGATTTTCCAAAT
711802 TCGCATTGCGAT
1 TCGCATTGCGAT
711814 AGCACTGTTC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 43 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:712539 original size:21 final size:21
Alignment explanation
Indices: 712513--712565 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
712503 TTTTTGATCA
712513 CTATCGCAATGGTGAACAGTG
1 CTATCGCAATGGTGAACAGTG
*
712534 CTATCGCAACGGTGAACAGTG
1 CTATCGCAATGGTGAACAGTG
712555 CTATCGCAATG
1 CTATCGCAATG
712566 CGATTTTGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (21 bp):
CTATCGCAATGGTGAACAGTG
Found at i:712579 original size:21 final size:21
Alignment explanation
Indices: 712555--712608 Score: 72
Period size: 21 Copynumber: 2.6 Consensus size: 21
712545 GTGAACAGTG
*
712555 CTATCGCAATGCGATTTTGGA
1 CTATCGCAATGCGAATTTGGA
*
712576 CTATCGCATTGCGAATTTGGA
1 CTATCGCAATGCGAATTTGGA
**
712597 AAATCGCAATGC
1 CTATCGCAATGC
712609 AATAGTCAGA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (21 bp):
CTATCGCAATGCGAATTTGGA
Found at i:721753 original size:20 final size:22
Alignment explanation
Indices: 721728--721767 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
721718 TCAAAATAGA
721728 AGTAAATA-AAAAG-TTTAATG
1 AGTAAATAGAAAAGATTTAATG
721748 AGTAAATAGAAAAGATTTAA
1 AGTAAATAGAAAAGATTTAA
721768 ACTTTAATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.44
21 5 0.28
22 5 0.28
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (22 bp):
AGTAAATAGAAAAGATTTAATG
Found at i:723721 original size:12 final size:12
Alignment explanation
Indices: 723685--723787 Score: 63
Period size: 12 Copynumber: 8.7 Consensus size: 12
723675 TATTGGAAAA
723685 TATTGATAATGG
1 TATTGATAATGG
*
723697 T-TTGAT-GTGGG
1 TATTGATAAT-GG
723708 TATTGATAATGG
1 TATTGATAATGG
**
723720 TATTGAT-GCGG
1 TATTGATAATGG
* *
723731 ATATTGATACTAG
1 -TATTGATAATGG
*
723744 TATTGAT-GTGAG
1 TATTGATAATG-G
*
723756 TATTGATACTGG
1 TATTGATAATGG
*
723768 TATTGATGCA-GG
1 TATTGAT-AATGG
723780 TATTGATA
1 TATTGATA
723788 CGAGTATCGT
Statistics
Matches: 70, Mismatches: 13, Indels: 17
0.70 0.13 0.17
Matches are distributed among these distances:
10 1 0.01
11 11 0.16
12 54 0.77
13 4 0.06
ACGTcount: A:0.27, C:0.04, G:0.28, T:0.41
Consensus pattern (12 bp):
TATTGATAATGG
Found at i:723759 original size:48 final size:49
Alignment explanation
Indices: 723684--723794 Score: 156
Period size: 48 Copynumber: 2.3 Consensus size: 49
723674 GTATTGGAAA
* * *
723684 ATATTGATAATGGT-TTGATGTGGGTATTGATAATGGTATTGATGC-GG
1 ATATTGATACTAGTATTGATGTGAGTATTGATAATGGTATTGATGCAGG
*
723731 ATATTGATACTAGTATTGATGTGAGTATTGATACTGGTATTGATGCAGG
1 ATATTGATACTAGTATTGATGTGAGTATTGATAATGGTATTGATGCAGG
*
723780 -TATTGATACGAGTAT
1 ATATTGATACTAGTAT
723795 CGTTGATTCG
Statistics
Matches: 57, Mismatches: 5, Indels: 3
0.88 0.08 0.05
Matches are distributed among these distances:
47 12 0.21
48 43 0.75
49 2 0.04
ACGTcount: A:0.28, C:0.05, G:0.28, T:0.40
Consensus pattern (49 bp):
ATATTGATACTAGTATTGATGTGAGTATTGATAATGGTATTGATGCAGG
Found at i:723788 original size:24 final size:23
Alignment explanation
Indices: 723685--723788 Score: 120
Period size: 24 Copynumber: 4.4 Consensus size: 23
723675 TATTGGAAAA
* *
723685 TATTGATAATGGT-TTGATGTGGG
1 TATTGATACTGGTATTGATG-CGG
*
723708 TATTGATAATGGTATTGATGCGG
1 TATTGATACTGGTATTGATGCGG
* *
723731 ATATTGATACTAGTATTGATGTGAG
1 -TATTGATACTGGTATTGATGCG-G
723756 TATTGATACTGGTATTGATGCAGG
1 TATTGATACTGGTATTGATGC-GG
723780 TATTGATAC
1 TATTGATAC
723789 GAGTATCGTT
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
23 15 0.21
24 54 0.76
25 2 0.03
ACGTcount: A:0.27, C:0.05, G:0.28, T:0.40
Consensus pattern (23 bp):
TATTGATACTGGTATTGATGCGG
Found at i:724103 original size:18 final size:18
Alignment explanation
Indices: 724080--724117 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
724070 AAATCTTCAT
724080 ACTTATGAAAGCCTTAAC
1 ACTTATGAAAGCCTTAAC
724098 ACTTATGAAAGCCTTAAC
1 ACTTATGAAAGCCTTAAC
724116 AC
1 AC
724118 CACAATGTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (18 bp):
ACTTATGAAAGCCTTAAC
Found at i:726861 original size:17 final size:19
Alignment explanation
Indices: 726834--726881 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
726824 ATTTTGAAAT
726834 ATCGAATGCACT-TCA-TGC
1 ATCG-ATGCACTCTCAGTGC
*
726852 ATCGATGCACTCTTAGTGC
1 ATCGATGCACTCTCAGTGC
*
726871 ACCGATGCACT
1 ATCGATGCACT
726882 AAGGGTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 7 0.27
18 6 0.23
19 13 0.50
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (19 bp):
ATCGATGCACTCTCAGTGC
Found at i:726881 original size:64 final size:65
Alignment explanation
Indices: 726702--726861 Score: 202
Period size: 65 Copynumber: 2.5 Consensus size: 65
726692 GAATAAATTG
* * * *
726702 AACATCGAATGCA-TTATATGCATCGATCCACATA-CCATGCATCGATGCACTCAGGTTTTTATG
1 AACATCGAATGCACTT-CATGCATCGATGCACA-AGACATGCATCGATGCACTCAGGTATTTATG
726765 AA
64 AA
* *
726767 AACATCGAATGCATTTGATGCATCGATGCACAAGACATGCATCGATGCACTCAGGCTATTT-TG-
1 AACATCGAATGCACTTCATGCATCGATGCACAAGACATGCATCGATGCACTCAGG-TATTTATGA
726830 A
65 A
*
726831 AATATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCACTTCATGCATCGATGCAC
726862 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
64 30 0.35
65 49 0.58
66 6 0.07
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCACTTCATGCATCGATGCACAAGACATGCATCGATGCACTCAGGTATTTATGAA
Found at i:735018 original size:21 final size:22
Alignment explanation
Indices: 734990--735044 Score: 67
Period size: 25 Copynumber: 2.4 Consensus size: 22
734980 ATTTAACAAA
734990 AAGGGGGAG-AAGTGTTAAAGT
1 AAGGGGGAGAAAGTGTTAAAGT
*
735011 AAGTGGGAGTAATAAGTGTTAAAGT
1 AAGGGGGAG--A-AAGTGTTAAAGT
735036 AAGGGGGAG
1 AAGGGGGAG
735045 TAATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 8 0.29
25 20 0.71
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (22 bp):
AAGGGGGAGAAAGTGTTAAAGT
Found at i:735027 original size:25 final size:25
Alignment explanation
Indices: 734999--735049 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
734989 AAAGGGGGAG
*
734999 AAGTGTTAAAGTAAGTGGGAGTAAT
1 AAGTGTTAAAGTAAGGGGGAGTAAT
735024 AAGTGTTAAAGTAAGGGGGAGTAAT
1 AAGTGTTAAAGTAAGGGGGAGTAAT
735049 A
1 A
735050 TTTTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.25
Consensus pattern (25 bp):
AAGTGTTAAAGTAAGGGGGAGTAAT
Found at i:735430 original size:65 final size:63
Alignment explanation
Indices: 735356--735515 Score: 180
Period size: 65 Copynumber: 2.5 Consensus size: 63
735346 GAATAAATTG
* * * * *
735356 AACATCGAATGCATTATATGCATCCATGCACATA-CCATGCATCGATGCACTCA-GGTTTTTATG
1 AACATCGAATGCATT-TATGCATCGATGCACA-AGACATACATCGATGCACTCATGCTATTT-TG
735419 AA
63 -A
*
735421 AACATCGAATGTATTTGATGCATCGATGCACAAGACATACATCGATGCACTCATGCTATTTTGA
1 AACATCGAATGCATTT-ATGCATCGATGCACAAGACATACATCGATGCACTCATGCTATTTTGA
* *
735485 AATATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCA-TTTATGCATCGATGCAC
735516 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 9, Indels: 9
0.82 0.09 0.09
Matches are distributed among these distances:
64 28 0.34
65 49 0.60
66 5 0.06
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACAAGACATACATCGATGCACTCATGCTATTTTGA
Found at i:735515 original size:17 final size:19
Alignment explanation
Indices: 735488--735535 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
735478 ATTTTGAAAT
735488 ATCGAATGCACT-TCA-TGC
1 ATCG-ATGCACTCTCAGTGC
*
735506 ATCGATGCACTCTTAGTGC
1 ATCGATGCACTCTCAGTGC
*
735525 ACCGATGCACT
1 ATCGATGCACT
735536 AAATGTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 7 0.27
18 6 0.23
19 13 0.50
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (19 bp):
ATCGATGCACTCTCAGTGC
Found at i:749411 original size:18 final size:18
Alignment explanation
Indices: 749377--749411 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
749367 CACGGAAGGT
*
749377 AAGATTACCTGGAAATAA
1 AAGATTACCAGGAAATAA
*
749395 AAGATTACCAGGGAATA
1 AAGATTACCAGGAAATA
749412 GGATTACCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.11, G:0.20, T:0.20
Consensus pattern (18 bp):
AAGATTACCAGGAAATAA
Found at i:749425 original size:15 final size:16
Alignment explanation
Indices: 749397--749426 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
749387 GGAAATAAAA
749397 GATTACCAGGGAATAG
1 GATTACCAGGGAATAG
749413 GATTACC-GGGAATA
1 GATTACCAGGGAATA
749427 TTGTATTTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.13, G:0.30, T:0.20
Consensus pattern (16 bp):
GATTACCAGGGAATAG
Found at i:765334 original size:2 final size:2
Alignment explanation
Indices: 765327--765360 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
765317 TTGATCGACA
765327 AT 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 AT
765361 GGTTTTGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:768391 original size:45 final size:44
Alignment explanation
Indices: 768294--768393 Score: 103
Period size: 45 Copynumber: 2.2 Consensus size: 44
768284 CACATTCAAT
* * *
768294 GTGTATCGATGCACTCTTTAAAGAAGAAACATCGAATGCAATTA
1 GTGTATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTA
* * ** *
768338 GTGCATCGATGCACCCCCTTAAA-ATGAAAACATCGAAGGTGATTG
1 GTGTATCGATGCA-CCCCTTAAAGAAG-AAACATCGAAGGCAATTA
768383 GTGTATCGATG
1 GTGTATCGATG
768394 GATGGGTAGT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
44 14 0.31
45 31 0.69
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.26
Consensus pattern (44 bp):
GTGTATCGATGCACCCCTTAAAGAAGAAACATCGAAGGCAATTA
Found at i:768448 original size:20 final size:20
Alignment explanation
Indices: 768403--768460 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
768393 GGATGGGTAG
768403 TGCATCGATGCACATGTTAAAGAA
1 TGCATCGATGCAC-TG-T--AGAA
*
768427 TGCATTGATGCACTGTAGAA
1 TGCATCGATGCACTGTAGAA
*
768447 TGTATCGATGCACT
1 TGCATCGATGCACT
768461 TCAAAGGGGA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 16 0.52
22 1 0.03
23 2 0.06
24 12 0.39
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.29
Consensus pattern (20 bp):
TGCATCGATGCACTGTAGAA
Found at i:770041 original size:23 final size:23
Alignment explanation
Indices: 770015--770082 Score: 82
Period size: 23 Copynumber: 3.0 Consensus size: 23
770005 AAAATTATAT
*
770015 GGCACTTCGGTGCATTTCTATGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
770038 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* *
770061 GGCACTTCGGTGTATTTATACG
1 GGCACTTCGGTGCATTTCTACG
770083 AGCTGTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.18, C:0.24, G:0.26, T:0.32
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:771453 original size:29 final size:23
Alignment explanation
Indices: 771385--771464 Score: 142
Period size: 23 Copynumber: 3.5 Consensus size: 23
771375 TTCCATAGAT
771385 AACAGAAACATCTTAAGTCTAAG
1 AACAGAAACATCTTAAGTCTAAG
771408 AACAGAAACATCTTAAGTCTAAG
1 AACAGAAACATCTTAAGTCTAAG
*
771431 AACAGAAACATCTTAAGTGTAAG
1 AACAGAAACATCTTAAGTCTAAG
*
771454 AACATAAACAT
1 AACAGAAACAT
771465 TATGTTTCTG
Statistics
Matches: 55, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.50, C:0.16, G:0.12, T:0.21
Consensus pattern (23 bp):
AACAGAAACATCTTAAGTCTAAG
Found at i:783246 original size:19 final size:19
Alignment explanation
Indices: 783207--783246 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
783197 GGATGCCCCA
* *
783207 TTTTGTTTTTTTTTCTCTT
1 TTTTGTATTTTTTTCTATT
*
783226 TTTTGTATTTTTTTGTATT
1 TTTTGTATTTTTTTCTATT
783245 TT
1 TT
783247 ATTTTCATGC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.05, G:0.07, T:0.82
Consensus pattern (19 bp):
TTTTGTATTTTTTTCTATT
Found at i:784107 original size:2 final size:2
Alignment explanation
Indices: 784100--784124 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
784090 AGCAAAACTA
784100 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
784125 AACAAAGACT
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:785729 original size:19 final size:19
Alignment explanation
Indices: 785705--785741 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
785695 TATCTTGAAC
*
785705 CCTTTTTTATTTATTTTTT
1 CCTTTTTTATTCATTTTTT
*
785724 CCTTTTTTCTTCATTTTT
1 CCTTTTTTATTCATTTTT
785742 CTTCTTTTTC
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:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (19 bp):
CCTTTTTTATTCATTTTTT
Found at i:789858 original size:16 final size:16
Alignment explanation
Indices: 789827--789860 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
789817 GAGTAGGATT
*
789827 AAAATATAAACTACTA
1 AAAATATAAACGACTA
*
789843 AAAATATAAAGGACTA
1 AAAATATAAACGACTA
789859 AA
1 AA
789861 TGTATGATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.09, G:0.06, T:0.21
Consensus pattern (16 bp):
AAAATATAAACGACTA
Found at i:789920 original size:15 final size:17
Alignment explanation
Indices: 789902--789934 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
789892 TATAATAAGG
789902 ACTAAAA-TAAAA-ATA
1 ACTAAAATTAAAAGATA
789917 ACTAAAATTAAAAGATA
1 ACTAAAATTAAAAGATA
789934 A
1 A
789935 AATTGAAATG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 5 0.31
17 4 0.25
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (17 bp):
ACTAAAATTAAAAGATA
Found at i:791682 original size:96 final size:90
Alignment explanation
Indices: 791516--791725 Score: 276
Period size: 96 Copynumber: 2.3 Consensus size: 90
791506 TGGATTACTC
* * * * * *
791516 CACTACTCTTCTGTGAAGTTCTCATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGA
1 CACTACTCTTCCGTGAAGTT-TGATACTTTGCTGAAAAATCCATTCCACTACTCTTCCATGAAAA
* *
791581 CTGAATTTTATTCTGGTTCTTTCTTTCTGCTT
65 CTGAATTTTA------TTCTTGCTTTCTGCAT
*
791613 TACTACTCTTCCGTGAAGTTTGATACTTTGCTGAAAAATCCATTCCACTACTCTTCCATGAAAAC
1 CACTACTCTTCCGTGAAGTTTGATACTTTGCTGAAAAATCCATTCCACTACTCTTCCATGAAAAC
791678 TGAATTTTATTCTTGCTTTCTGCAT
66 TGAATTTTATTCTTGCTTTCTGCAT
791703 CACTACTCTTCCGTGAAGTTTGA
1 CACTACTCTTCCGTGAAGTTTGA
791726 AAATGATTGA
Statistics
Matches: 103, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
90 36 0.35
96 49 0.48
97 18 0.17
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.40
Consensus pattern (90 bp):
CACTACTCTTCCGTGAAGTTTGATACTTTGCTGAAAAATCCATTCCACTACTCTTCCATGAAAAC
TGAATTTTATTCTTGCTTTCTGCAT
Found at i:791896 original size:20 final size:20
Alignment explanation
Indices: 791871--791933 Score: 90
Period size: 20 Copynumber: 3.1 Consensus size: 20
791861 ACTCAAAGAA
*
791871 TTTACAAATTACCCGAAGGC
1 TTTACAAATTACCCGGAGGC
* *
791891 TTTACAAATTACTCGGAGGA
1 TTTACAAATTACCCGGAGGC
*
791911 TTTACAAATGACCCGGAGGC
1 TTTACAAATTACCCGGAGGC
791931 TTT
1 TTT
791934 TAATTTTCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (20 bp):
TTTACAAATTACCCGGAGGC
Found at i:792035 original size:19 final size:19
Alignment explanation
Indices: 792011--792047 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
792001 ACCCTAAGGC
*
792011 TTTACAGATGACCCGAAGA
1 TTTACAAATGACCCGAAGA
*
792030 TTTACAAATTACCCGAAG
1 TTTACAAATGACCCGAAG
792048 GCTTTAATTT
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:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (19 bp):
TTTACAAATGACCCGAAGA
Found at i:792074 original size:118 final size:119
Alignment explanation
Indices: 791879--792146 Score: 421
Period size: 118 Copynumber: 2.3 Consensus size: 119
791869 AATTTACAAA
* * * * * *
791879 TTACCCGAAGGCTTTACAAATTACTCGGAGGATTTACAAATGACCCGGAGGCTTTTAATTTTCTA
1 TTACCCTAAGGCTTTACAGATGAC-CCGAAGATTTACAAATGACCCGAAGGCTTTTAATTTTCTA
* *
791944 GAATATTAAATGAGAAGCTTTGAAAATGGCTTTCTCATTTTCATGCGAAAACATC
65 GAACATTAAATGAGAAACTTTGAAAATGGCTTTCTCATTTTCATGCGAAAACATC
*
791999 TTACCCTAAGGCTTTACAGATGACCCGAAGATTTACAAATTACCCGAAGGC-TTTAATTTTCTAG
1 TTACCCTAAGGCTTTACAGATGACCCGAAGATTTACAAATGACCCGAAGGCTTTTAATTTTCTAG
792063 AACATTAAATGAGAAACTTTGAAAATGGCTTTCTCATTTTCATGCGAAAACATC
66 AACATTAAATGAGAAACTTTGAAAATGGCTTTCTCATTTTCATGCGAAAACATC
* *
792117 TTACCCTGAGGCTTTACAGATGATCCGAAG
1 TTACCCTAAGGCTTTACAGATGACCCGAAG
792147 GATATAAACA
Statistics
Matches: 137, Mismatches: 11, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
118 93 0.68
119 23 0.17
120 21 0.15
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (119 bp):
TTACCCTAAGGCTTTACAGATGACCCGAAGATTTACAAATGACCCGAAGGCTTTTAATTTTCTAG
AACATTAAATGAGAAACTTTGAAAATGGCTTTCTCATTTTCATGCGAAAACATC
Found at i:792814 original size:22 final size:22
Alignment explanation
Indices: 792789--792837 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
792779 GATAAAACTT
792789 TCATCTTTGAAAAGAGAATCTA
1 TCATCTTTGAAAAGAGAATCTA
*
792811 TCATCTTTGAAAAGATAATCTA
1 TCATCTTTGAAAAGAGAATCTA
792833 TCATC
1 TCATC
792838 CTTGCAGAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.10, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAGAATCTA
Found at i:792998 original size:54 final size:54
Alignment explanation
Indices: 792933--793036 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
792923 GCACATTACA
792933 AAAAGGATTTATCATAATTACTTTCATGTCTCAACATCTAATAATTTCTTTCAT
1 AAAAGGATTTATCATAATTACTTTCATGTCTCAACATCTAATAATTTCTTTCAT
* * * * * *
792987 AAAAGGTTTTATCCTAATTCCTTTCATGTCTCCATATCTAATCATTTCTT
1 AAAAGGATTTATCATAATTACTTTCATGTCTCAACATCTAATAATTTCTT
793037 GAACAAGGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (54 bp):
AAAAGGATTTATCATAATTACTTTCATGTCTCAACATCTAATAATTTCTTTCAT
Found at i:799221 original size:15 final size:15
Alignment explanation
Indices: 799185--799223 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
799175 TATTACGGGT
*
799185 AGGATTAAAATATAA
1 AGGACTAAAATATAA
**
799200 ACTACTAAAATATAA
1 AGGACTAAAATATAA
799215 AGGACTAAA
1 AGGACTAAA
799224 TGTATGATTT
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:0.59, C:0.08, G:0.10, T:0.23
Consensus pattern (15 bp):
AGGACTAAAATATAA
Found at i:799302 original size:17 final size:16
Alignment explanation
Indices: 799265--799304 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
799255 TATAATAAGG
799265 ACTAAAA-TAAAAATA
1 ACTAAAATTAAAAATA
799280 ACTAAAATTAAAAGATA
1 ACTAAAATTAAAA-ATA
*
799297 ATTAAAAT
1 ACTAAAAT
799305 ACGTGAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.32
16 5 0.23
17 10 0.45
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.25
Consensus pattern (16 bp):
ACTAAAATTAAAAATA
Found at i:803699 original size:21 final size:21
Alignment explanation
Indices: 803669--803718 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
803659 CATAGCCCTG
803669 ATTTCCTCTTCTAATTGTTTCT
1 ATTT-CTCTTCTAATTGTTTCT
* *
803691 ATTTCTCTTCTAGTTGTTTGT
1 ATTTCTCTTCTAATTGTTTCT
*
803712 TTTTCTC
1 ATTTCTC
803719 CAACCTGGCT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 21 0.84
22 4 0.16
ACGTcount: A:0.10, C:0.20, G:0.08, T:0.62
Consensus pattern (21 bp):
ATTTCTCTTCTAATTGTTTCT
Found at i:804251 original size:20 final size:20
Alignment explanation
Indices: 804203--804255 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
804193 GAATGAATAT
*
804203 AATGTAATGCG-AAAGATAA
1 AATGCAATGCGAAAAGATAA
804222 AATGCAATGCGAAAAG-TAA
1 AATGCAATGCGAAAAGATAA
804241 AATGCAGATGC-AAAA
1 AATGCA-ATGCGAAAA
804256 TGCAAGGTGT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 23 0.74
20 8 0.26
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.17
Consensus pattern (20 bp):
AATGCAATGCGAAAAGATAA
Found at i:810087 original size:119 final size:119
Alignment explanation
Indices: 809876--810099 Score: 412
Period size: 119 Copynumber: 1.9 Consensus size: 119
809866 CAGTAGCGAG
* *
809876 TCCAAAAATATTTTTAGAGTAAATACAAATATATCAATTACACGAATTTTATAATAAATATAGAT
1 TCCAAAAATATTTTTAGAGTAAAAACAAATATATCAATTACACAAATTTTATAATAAATATAGAT
* *
809941 ATAAATAAATTTTCAAGTGGGCACAATCAATAAAATAAATAATTAATAGAAGGA
66 ATAAACAAATTTTCAAGTGGACACAATCAATAAAATAAATAATTAATAGAAGGA
809995 TCCAAAAATATTTTTAGAGTAAAAACAAATATATCAATTACACAAATTTTATAATAAATATAGAT
1 TCCAAAAATATTTTTAGAGTAAAAACAAATATATCAATTACACAAATTTTATAATAAATATAGAT
810060 ATAAACAAATTTTCAAGTGGACACAATCAATAAAATAAAT
66 ATAAACAAATTTTCAAGTGGACACAATCAATAAAATAAAT
810100 CACTAATTAT
Statistics
Matches: 101, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
119 101 1.00
ACGTcount: A:0.52, C:0.09, G:0.08, T:0.31
Consensus pattern (119 bp):
TCCAAAAATATTTTTAGAGTAAAAACAAATATATCAATTACACAAATTTTATAATAAATATAGAT
ATAAACAAATTTTCAAGTGGACACAATCAATAAAATAAATAATTAATAGAAGGA
Found at i:813872 original size:19 final size:20
Alignment explanation
Indices: 813848--813897 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
813838 GATAAATTTA
*
813848 TTAATAATTTTATAA-TCTT
1 TTAATAATTTTATAAGTATT
*
813867 TTAATAAATTTAATAAGTATT
1 TTAAT-AATTTTATAAGTATT
813888 TT-ATAATTTT
1 TTAATAATTTT
813898 TTAAACTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
19 10 0.38
20 11 0.42
21 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (20 bp):
TTAATAATTTTATAAGTATT
Found at i:813874 original size:31 final size:30
Alignment explanation
Indices: 813816--813898 Score: 96
Period size: 31 Copynumber: 2.7 Consensus size: 30
813806 GTTTGATAAT
* *
813816 ATAATAATTTTTATAGTATTTAGATAAATTTA
1 ATAATAA-TTTTATAATTTTTA-ATAAATTTA
*
813848 TTAATAATTTTATAATCTTTTAATAAATTTA
1 ATAATAATTTTATAAT-TTTTAATAAATTTA
813879 ATAAGT-ATTTTATAATTTTT
1 ATAA-TAATTTTATAATTTTT
813899 TAAACTTTAT
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
30 4 0.09
31 30 0.67
32 11 0.24
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (30 bp):
ATAATAATTTTATAATTTTTAATAAATTTA
Found at i:814644 original size:31 final size:30
Alignment explanation
Indices: 814609--814695 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 30
814599 GTCAATAAGT
*
814609 TTAAAAAATTATAAAATACTTATTAAATTTA
1 TTAAAATATTATAAAATA-TTATTAAATTTA
*
814640 TTAAAATATTATAAAAATATTAATAAATTTA
1 TTAAAATATTAT-AAAATATTATTAAATTTA
* *
814671 TCAAAATACTATAAAATAATTATTA
1 TTAAAATATTATAAAAT-ATTATTA
814696 TATTATCGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
30 5 0.10
31 38 0.78
32 6 0.12
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (30 bp):
TTAAAATATTATAAAATATTATTAAATTTA
Found at i:814651 original size:11 final size:11
Alignment explanation
Indices: 814609--814695 Score: 69
Period size: 11 Copynumber: 8.3 Consensus size: 11
814599 GTCAATAAGT
*
814609 TTAAAAAATTA
1 TTAAAATATTA
814620 -TAAAATACTTA
1 TTAAAATA-TTA
814631 TT-AAAT-TTA
1 TTAAAATATTA
814640 TTAAAATATTA
1 TTAAAATATTA
*
814651 TAAAAATATTA
1 TTAAAATATTA
*
814662 AT-AAAT-TTA
1 TTAAAATATTA
* *
814671 TCAAAATACTA
1 TTAAAATATTA
814682 -TAAAATAATTA
1 TTAAAAT-ATTA
814693 TTA
1 TTA
814696 TATTATCGAA
Statistics
Matches: 59, Mismatches: 9, Indels: 15
0.71 0.11 0.18
Matches are distributed among these distances:
9 8 0.14
10 23 0.39
11 25 0.42
12 3 0.05
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (11 bp):
TTAAAATATTA
Found at i:814687 original size:20 final size:21
Alignment explanation
Indices: 814641--814693 Score: 56
Period size: 20 Copynumber: 2.5 Consensus size: 21
814631 TTAAATTTAT
*
814641 TAAAATATTATAAAAATATTA
1 TAAAATATTATAAAAATACTA
*
814662 -ATAAAT-TTATCAAAATACTA
1 TA-AAATATTATAAAAATACTA
814682 TAAAATAATTAT
1 TAAAAT-ATTAT
814694 TATATTATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
20 17 0.65
21 5 0.19
22 4 0.15
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (21 bp):
TAAAATATTATAAAAATACTA
Found at i:816545 original size:2 final size:2
Alignment explanation
Indices: 816538--816580 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
816528 AAGAAATAAC
816538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
816579 AT
1 AT
816581 TACCATAAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:817345 original size:2 final size:2
Alignment explanation
Indices: 817340--817379 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
817330 TTAATCATAA
817340 AT AT AT AT 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 AT AT AT AT
817380 TTAAATGAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:818085 original size:17 final size:17
Alignment explanation
Indices: 818059--818096 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
818049 ACTATAAATG
*
818059 TTAAAAAAAATAATATT
1 TTAAAAAAAAAAATATT
*
818076 TTAAATAAAAAAATATT
1 TTAAAAAAAAAAATATT
818093 TTAA
1 TTAA
818097 GTATTTTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTAAAAAAAAAAATATT
Found at i:822522 original size:3 final size:3
Alignment explanation
Indices: 822514--822562 Score: 80
Period size: 3 Copynumber: 16.3 Consensus size: 3
822504 AACAATTGTT
* *
822514 TTA TTA TTA TTA GTG TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
822562 T
1 T
822563 ATTTTGTGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:829723 original size:13 final size:14
Alignment explanation
Indices: 829724--829757 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
829714 TAAACGAAGA
829724 AAAC-AACGAACAT
1 AAACGAACGAACAT
829737 -AACGAACGAACAT
1 AAACGAACGAACAT
829750 AAACGAAC
1 AAACGAAC
829758 ATATTACCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 3 0.16
13 9 0.47
14 7 0.37
ACGTcount: A:0.59, C:0.24, G:0.12, T:0.06
Consensus pattern (14 bp):
AAACGAACGAACAT
Found at i:832458 original size:12 final size:12
Alignment explanation
Indices: 832441--832465 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
832431 ACTTTTGAAC
832441 AATGATGGTTGA
1 AATGATGGTTGA
832453 AATGATGGTTGA
1 AATGATGGTTGA
832465 A
1 A
832466 GCTCAAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (12 bp):
AATGATGGTTGA
Found at i:837475 original size:17 final size:17
Alignment explanation
Indices: 837439--837477 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
837429 TAATTAAGTA
837439 AAATA-TTAAAAAAATT
1 AAATACTTAAAAAAATT
*
837455 AAATACTTAAATAAATT
1 AAATACTTAAAAAAATT
837472 AAATAC
1 AAATAC
837478 AAAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATACTTAAAAAAATT
Found at i:838056 original size:19 final size:19
Alignment explanation
Indices: 838020--838057 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
838010 ATTTTTAAAT
*
838020 TAAAATAAAATAATAAAAA
1 TAAAATAAAATAAGAAAAA
838039 TAAAATAAAAGT-AGAAAAA
1 TAAAATAAAA-TAAGAAAAA
838058 AGGGAATTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.94
20 1 0.06
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (19 bp):
TAAAATAAAATAAGAAAAA
Found at i:840932 original size:47 final size:45
Alignment explanation
Indices: 840862--840986 Score: 173
Period size: 47 Copynumber: 2.8 Consensus size: 45
840852 TATAAAATCT
*
840862 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTATCAAAATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTATCAAAATA
*
840907 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCATTT--ATTCCATAAGCTCGTAAGCTTATTTTATCAAAATA
* * *
840954 CTTGCCA-TCATT-CATAAGCTTGTAAGCTTATTT
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTT
840987 GCATACTTGC
Statistics
Matches: 73, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
43 20 0.27
44 3 0.04
45 10 0.14
46 1 0.01
47 39 0.53
ACGTcount: A:0.31, C:0.21, G:0.08, T:0.40
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTATCAAAATA
Found at i:842130 original size:14 final size:14
Alignment explanation
Indices: 842111--842149 Score: 69
Period size: 14 Copynumber: 2.8 Consensus size: 14
842101 AGTTGACCAA
*
842111 CAGAATCTGTTTTG
1 CAGAATCTGCTTTG
842125 CAGAATCTGCTTTG
1 CAGAATCTGCTTTG
842139 CAGAATCTGCT
1 CAGAATCTGCT
842150 GTCCGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.36
Consensus pattern (14 bp):
CAGAATCTGCTTTG
Found at i:842432 original size:30 final size:30
Alignment explanation
Indices: 842375--842438 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 30
842365 TCTTCATCAA
* * *
842375 TTTTCCAAAATTTACGAATTTATCCCAAAC
1 TTTTCCAAAACTTACGAAATGATCCCAAAC
* *
842405 TTTT-CAAAACTTACGAAATGATCCCCAAT
1 TTTTCCAAAACTTACGAAATGATCCCAAAC
842434 TTTTC
1 TTTTC
842439 TAAGGCTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
29 24 0.86
30 4 0.14
ACGTcount: A:0.34, C:0.23, G:0.05, T:0.38
Consensus pattern (30 bp):
TTTTCCAAAACTTACGAAATGATCCCAAAC
Found at i:845360 original size:2 final size:2
Alignment explanation
Indices: 845353--845440 Score: 176
Period size: 2 Copynumber: 44.0 Consensus size: 2
845343 TTACAGGGAG
845353 AT AT AT AT AT 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 AT AT AT AT AT
845395 AT AT AT AT AT 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 AT AT AT AT AT
845437 AT AT
1 AT AT
845441 TGGTAATGGA
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 86 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:847331 original size:6 final size:6
Alignment explanation
Indices: 847308--847342 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
847298 TTATTTCACT
847308 TATATG TTATAT- TATATG TATATG TATATG TATAT
1 TATATG -TATATG TATATG TATATG TATATG TATAT
847343 ACGTACACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 17 0.63
7 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (6 bp):
TATATG
Found at i:855818 original size:49 final size:49
Alignment explanation
Indices: 855746--855840 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
855736 AATACTTCGC
* * *
855746 TTAGGATGAAAACCCGAGAGGGCATCCTAAGTTAAAAAAAAAAAAACGT
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTAAAAAAAAAAAAACGT
* * *
855795 TTAGGGTGAAAACCCGAAAGGGCACCCTAAATTGAAAAAAGAAAAA
1 TTAGGATGAAAACCCGAAAGGGCACCCTAAATTAAAAAAAAAAAAA
855841 GAGGAAAGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 40 1.00
ACGTcount: A:0.49, C:0.15, G:0.21, T:0.15
Consensus pattern (49 bp):
TTAGGATGAAAACCCGAAAGGGCACCCTAAATTAAAAAAAAAAAAACGT
Found at i:856756 original size:105 final size:105
Alignment explanation
Indices: 856570--857272 Score: 1217
Period size: 105 Copynumber: 6.7 Consensus size: 105
856560 AGGTTTTACC
*
856570 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
856635 ACGAAGGGACCACTGGTTGTCAACAAACGTTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
856675 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
856740 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
856780 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
856845 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
*
856885 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGGAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
856950 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
856990 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
857055 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
* *
857095 CAGAGCCAATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCATG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * * * *
857160 ACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCCAACTT
66 ACGAAGGGACCGCTGGTTGTCAACAAA-CATTTCTCAATTT
* * **** *
857201 CAGAGCCAATTTCAACTTCACAACGAGGGATATTGGACTCAAGACAGTATAAGTTCAACTTCGCG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
857266 ACGAAGG
66 ACGAAGG
857273 AGCTATATAC
Statistics
Matches: 573, Mismatches: 24, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
105 501 0.87
106 72 0.13
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAATTT
Found at i:858920 original size:6 final size:6
Alignment explanation
Indices: 858897--858931 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
858887 TTATTTCACT
858897 TATATG TTATAT- TATATG TATATG TATATG TATAT
1 TATATG -TATATG TATATG TATATG TATATG TATAT
858932 ACGTACACAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
5 5 0.19
6 17 0.63
7 5 0.19
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (6 bp):
TATATG
Found at i:863987 original size:20 final size:20
Alignment explanation
Indices: 863964--864019 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
863954 GTTTTACATT
863964 TTTTTATTGAATTTTATT-CA
1 TTTTTATTG-ATTTTATTGCA
* *
863984 TTTTTAATTCATTTTTTTGCA
1 TTTTT-ATTGATTTTATTGCA
864005 TTTTTATTGATTTTA
1 TTTTTATTGATTTTA
864020 AATATATGAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 20 0.67
21 10 0.33
ACGTcount: A:0.21, C:0.05, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTATTGATTTTATTGCA
Found at i:863993 original size:11 final size:10
Alignment explanation
Indices: 863964--864018 Score: 58
Period size: 10 Copynumber: 5.4 Consensus size: 10
863954 GTTTTACATT
*
863964 TTTTTATTGA
1 TTTTTATTCA
*
863974 ATTTTATTCA
1 TTTTTATTCA
863984 TTTTTAATTCA
1 TTTTT-ATTCA
863995 TTTTT-TTGCA
1 TTTTTATT-CA
*
864005 TTTTTATTGA
1 TTTTTATTCA
864015 TTTT
1 TTTT
864019 AAATATATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
9 2 0.05
10 24 0.63
11 12 0.32
ACGTcount: A:0.20, C:0.05, G:0.05, T:0.69
Consensus pattern (10 bp):
TTTTTATTCA
Found at i:864344 original size:14 final size:14
Alignment explanation
Indices: 864325--864351 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
864315 TTTTTTTTTA
864325 AATAATAATTAATG
1 AATAATAATTAATG
864339 AATAATAATTAAT
1 AATAATAATTAAT
864352 TTGATCCCTC
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:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (14 bp):
AATAATAATTAATG
Found at i:865144 original size:17 final size:17
Alignment explanation
Indices: 865124--865161 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
865114 GGAAATAATA
*
865124 AAAAT-GAAATTTAAAAG
1 AAAATGGAAAATT-AAAG
865141 AAAATGGAAAATTAAAG
1 AAAATGGAAAATTAAAG
865158 AAAA
1 AAAA
865162 AAACAACATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.13, T:0.18
Consensus pattern (17 bp):
AAAATGGAAAATTAAAG
Found at i:866715 original size:49 final size:49
Alignment explanation
Indices: 866658--866878 Score: 189
Period size: 49 Copynumber: 4.6 Consensus size: 49
866648 CTCTTCGCTC
* *
866658 TCAAATCTGGAAAACCTTGATGATTCATTCCATCATCTCTTCATGGAAA
1 TCAAATCTGGAAAACCTTGATGATTCATCCCACCATCTCTTCATGGAAA
* * * * * *
866707 TCAAATCTGAAAAACCTTGATGATTTACCCCACCATCACTTCGTGGAGA
1 TCAAATCTGGAAAACCTTGATGATTCATCCCACCATCTCTTCATGGAAA
* ** * * * *
866756 TCAAATCT--AAAACTTTTGGCGACTT-GTCCCACCATCTCTTCGTAGAGA
1 TCAAATCTGGAAAAC-CTTGATGA-TTCATCCCACCATCTCTTCATGGAAA
* * * * * * *
866804 TTAAATAT-GAAAACTTTGATGATTCATTCCATCACCCCTTCATGGAAA
1 TCAAATCTGGAAAACCTTGATGATTCATCCCACCATCTCTTCATGGAAA
*
866852 TCAAATTTGGAAAACCTTGATGATTCA
1 TCAAATCTGGAAAACCTTGATGATTCA
866879 CTCCTCCTGT
Statistics
Matches: 137, Mismatches: 30, Indels: 10
0.77 0.17 0.06
Matches are distributed among these distances:
47 7 0.05
48 57 0.42
49 73 0.53
ACGTcount: A:0.33, C:0.23, G:0.13, T:0.31
Consensus pattern (49 bp):
TCAAATCTGGAAAACCTTGATGATTCATCCCACCATCTCTTCATGGAAA
Found at i:867845 original size:20 final size:20
Alignment explanation
Indices: 867820--867868 Score: 80
Period size: 20 Copynumber: 2.5 Consensus size: 20
867810 TATACGATGG
867820 TATCGATACTGATCCCTTAA
1 TATCGATACTGATCCCTTAA
* *
867840 TATCGATATTGATCCCTTAG
1 TATCGATACTGATCCCTTAA
867860 TATCGATAC
1 TATCGATAC
867869 CTCACCTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.29, C:0.22, G:0.12, T:0.37
Consensus pattern (20 bp):
TATCGATACTGATCCCTTAA
Found at i:869160 original size:48 final size:48
Alignment explanation
Indices: 869104--869229 Score: 139
Period size: 50 Copynumber: 2.6 Consensus size: 48
869094 TCTATTTATC
* *
869104 CCACCATCTCTTCGCGAAGATCAAATCT-AAAAACTTTGATGATTCGTT
1 CCACCATCTCTTCG-GAAGATCAAATCTAAAAAACCTTGATGATTCGCT
* *
869152 CCATCATCTCTTCATGGAA-ATCAAATATGAAAAAACCTTGATGATTCGCT
1 CCACCATCTCTTC--GGAAGATCAAATCT-AAAAAACCTTGATGATTCGCT
* *
869202 CCACCATCACTTCGTGAAGATCCAATCT
1 CCACCATCTCTTCG-GAAGATCAAATCT
869230 GGAAATTTTG
Statistics
Matches: 64, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
48 21 0.33
49 6 0.09
50 37 0.58
ACGTcount: A:0.33, C:0.26, G:0.12, T:0.29
Consensus pattern (48 bp):
CCACCATCTCTTCGGAAGATCAAATCTAAAAAACCTTGATGATTCGCT
Found at i:874629 original size:21 final size:21
Alignment explanation
Indices: 874605--874656 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
874595 TTCAAGAGTG
874605 AATGATGATCATCAAAAGAAA
1 AATGATGATCATCAAAAGAAA
874626 AATGATGATCATCAAAAGAAA
1 AATGATGATCATCAAAAGAAA
*
874647 ATTGATGATC
1 AATGATGATC
874657 TTAAAGCTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.52, C:0.10, G:0.15, T:0.23
Consensus pattern (21 bp):
AATGATGATCATCAAAAGAAA
Found at i:875483 original size:16 final size:16
Alignment explanation
Indices: 875458--875488 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
875448 AGAGGGTTGC
*
875458 CAAAGCTAAAATTTGG
1 CAAAGATAAAATTTGG
875474 CAAAGATAAAATTTG
1 CAAAGATAAAATTTG
875489 TGATACATGT
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:0.48, C:0.10, G:0.16, T:0.26
Consensus pattern (16 bp):
CAAAGATAAAATTTGG
Found at i:880725 original size:14 final size:14
Alignment explanation
Indices: 880693--880728 Score: 58
Period size: 12 Copynumber: 2.7 Consensus size: 14
880683 AGGGGGAGTA
880693 ATTTTTCAAAAATG
1 ATTTTTCAAAAATG
880707 A--TTTCAAAAATG
1 ATTTTTCAAAAATG
880719 ATTTTTCAAA
1 ATTTTTCAAA
880729 TAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
12 12 0.60
14 8 0.40
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (14 bp):
ATTTTTCAAAAATG
Found at i:884602 original size:18 final size:17
Alignment explanation
Indices: 884576--884615 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
884566 AGGAAACAAT
*
884576 AAAAATGAAATTTAAAAG
1 AAAAATGAAAATT-AAAG
*
884594 AAAATTGAAAATTAAAG
1 AAAAATGAAAATTAAAG
884611 AAAAA
1 AAAAA
884616 ATCAACATAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (17 bp):
AAAAATGAAAATTAAAG
Found at i:884892 original size:2 final size:2
Alignment explanation
Indices: 884885--884919 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
884875 AATTGAATAG
884885 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
884920 TAAAATGTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:885296 original size:9 final size:9
Alignment explanation
Indices: 885274--885310 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
885264 ATGAACAATG
*
885274 AAAAAGCAAG
1 AAAAAG-AAA
885284 AAAAAGAAA
1 AAAAAGAAA
885293 AAAAAGAAA
1 AAAAAGAAA
885302 AAAAAGAAA
1 AAAAAGAAA
885311 TACCTTTAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 20 0.77
10 6 0.23
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (9 bp):
AAAAAGAAA
Found at i:891797 original size:31 final size:31
Alignment explanation
Indices: 891729--891820 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 31
891719 CAAAATCTTA
* *
891729 TCTCACTTGAAATTATCTTTT-TAAAACAATTTCG
1 TCTCACTTGAAATTGT-TTTTCTTAAA-AA-TT-G
*
891763 TCTCAC-TGAGATTGTTTTTCTTTAAAAATTG
1 TCTCACTTGAAATTGTTTTTC-TTAAAAATTG
891794 TCTCACTTGAAATTGTTTTTCTTAAAA
1 TCTCACTTGAAATTGTTTTTCTTAAAA
891821 TAAATTTCGA
Statistics
Matches: 51, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
31 13 0.25
32 19 0.37
33 9 0.18
34 10 0.20
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (31 bp):
TCTCACTTGAAATTGTTTTTCTTAAAAATTG
Found at i:891800 original size:65 final size:66
Alignment explanation
Indices: 891729--891856 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 66
891719 CAAAATCTTA
* *
891729 TCTCACTTGAAATTATCTTT-TTAAAA-CAATTTCGTCTCACTGAGA-TTGTTTTTCTTTAAAAA
1 TCTCACTTGAAATTATCTTTCTTAAAATAAATTTCGACTCACT-A-ATTTGTTTTTCTTTAAAAA
891791 TTG
64 TTG
* * *
891794 TCTCACTTGAAATTGTTTTTCTTAAAATAAATTTCGACTCACTAATTTTTTTTTCTTTAAAAA
1 TCTCACTTGAAATTATCTTTCTTAAAATAAATTTCGACTCACTAATTTGTTTTTCTTTAAAAA
891857 AATCATCTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
65 19 0.35
66 23 0.42
67 13 0.24
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (66 bp):
TCTCACTTGAAATTATCTTTCTTAAAATAAATTTCGACTCACTAATTTGTTTTTCTTTAAAAATT
G
Found at i:891812 original size:32 final size:34
Alignment explanation
Indices: 891729--891960 Score: 140
Period size: 35 Copynumber: 6.9 Consensus size: 34
891719 CAAAATCTTA
* * *
891729 TCTCACTTGAAATTATCTTT-TTAAAACAATTTCG
1 TCTCACTTGAAATTGTTTTTCTTTAAA-AATTTCG
*
891763 TCTCAC-TGAGATTGTTTTTCTTTAAAAA-TT-G
1 TCTCACTTGAAATTGTTTTTCTTTAAAAATTTCG
*
891794 TCTCACTTGAAATTGTTTTTCTTAAAATAAATTTCG
1 TCTCACTTGAAATTGTTTTTCTT-TAA-AAATTTCG
* * * ** *
891830 ACTCAC-T-AATTTTTTTTTCTTTAAAAAAATCA
1 TCTCACTTGAAATTGTTTTTCTTTAAAAATTTCG
* * * *
891862 TCTTACTTGATATTGTTTTTTCTTAAAACAAATTTCA
1 TCTCACTTGAAATTG-TTTTTCTT-TAA-AAATTTCG
* * * *
891899 TCTCACTTGAGATT-CTTTTCTTAAAACAAATTTCA
1 TCTCACTTGAAATTGTTTTTCTT-TAA-AAATTTCG
* *
891934 TCTCACTTGAGATT-CTTTTC-TTAAAAA
1 TCTCACTTGAAATTGTTTTTCTTTAAAAA
891961 CAAAGTTTAT
Statistics
Matches: 162, Mismatches: 25, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
31 7 0.04
32 29 0.18
33 19 0.12
34 30 0.19
35 51 0.31
36 8 0.05
37 18 0.11
ACGTcount: A:0.31, C:0.16, G:0.06, T:0.47
Consensus pattern (34 bp):
TCTCACTTGAAATTGTTTTTCTTTAAAAATTTCG
Found at i:891923 original size:69 final size:68
Alignment explanation
Indices: 891728--891982 Score: 213
Period size: 69 Copynumber: 3.7 Consensus size: 68
891718 ACAAAATCTT
* * * *
891728 ATCTCACTTGAAATT-ATCTTT-TTAAAAC-AATTTCGTCTCACTGAGATTGTTTTTCTT-TAAA
1 ATCTCACTTGAAATTGTTTTTTCTTAAAACAAATTTCATCTCACTGAGATT-TTTTTCTTAAAAA
*
891789 AATT
65 AATC
* * * **
891793 GTCTCACTTGAAATTG-TTTTTCTTAAAATAAATTTCGA-CTCACTAATTTTTTTTTCTTTAAAA
1 ATCTCACTTGAAATTGTTTTTTCTTAAAACAAATTTC-ATCTCACTGAGATTTTTTTC-TTAAAA
891856 AAATC
64 AAATC
* * *
891861 ATCTTACTTGATATTGTTTTTTCTTAAAACAAATTTCATCTCACTTGAGATTCTTTTCTTAAAAC
1 ATCTCACTTGAAATTGTTTTTTCTTAAAACAAATTTCATCTCAC-TGAGATTTTTTTCTTAAAA-
891926 AAATTTC
64 AAA--TC
* * *
891933 ATCTCACTTGAGA-T-TCTTTTCTTAAAAACAAAGTTT-ATCTCGCATGAGAT
1 ATCTCACTTGAAATTGTTTTTTCTT-AAAACAAA-TTTCATCTCAC-TGAGAT
891983 AATATCCTTT
Statistics
Matches: 154, Mismatches: 22, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
65 18 0.12
66 12 0.08
67 17 0.11
68 20 0.13
69 30 0.19
70 20 0.13
71 21 0.14
72 16 0.10
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.45
Consensus pattern (68 bp):
ATCTCACTTGAAATTGTTTTTTCTTAAAACAAATTTCATCTCACTGAGATTTTTTTCTTAAAAAA
ATC
Found at i:891962 original size:36 final size:35
Alignment explanation
Indices: 891728--892213 Score: 217
Period size: 36 Copynumber: 14.0 Consensus size: 35
891718 ACAAAATCTT
* *
891728 ATCTCACTTGAAATTATCTTT-TTAAAAC-AATTTC
1 ATCTCACTTGAGATTCT-TTTCTTAAAACAAATTTC
* * *
891762 GTCTCAC-TGAGATTGTTTTTCTT-TAA-AAA-TT-
1 ATCTCACTTGAGATT-CTTTTCTTAAAACAAATTTC
* * * *
891793 GTCTCACTTGAAATTGTTTTTCTTAAAATAAATTTC
1 ATCTCACTTGAGATT-CTTTTCTTAAAACAAATTTC
* ** *
891829 GA-CTCAC-TAATTTTTTTTTCTTTAAAA-AAA--TC
1 -ATCTCACTTGAGATTCTTTTC-TTAAAACAAATTTC
* * *
891861 ATCTTACTTGATATTGTTTTTTCTTAAAACAAATTTC
1 ATCTCACTTGAGA-T-TCTTTTCTTAAAACAAATTTC
891898 ATCTCACTTGAGATTCTTTTCTTAAAACAAATTTC
1 ATCTCACTTGAGATTCTTTTCTTAAAACAAATTTC
891933 ATCTCACTTGAGATTCTTTTCTTAAAAACAAAGTTT-
1 ATCTCACTTGAGATTCTTTTCTT-AAAACAAA-TTTC
* * ** * * *
891969 ATCTCGCATGAGATAATATCCTTTGAAACACAA----
1 ATCTCACTTGAGATTCTTTTC-TTAAAACA-AATTTC
* * * *
892002 A-CT---TT-AAAATCATTTCACTTAAAAGAAATATT-
1 ATCTCACTTGAGATTC-TTT-TCTTAAAACAAAT-TTC
* * *
892034 ATCTCAATTGAGATTATTTTTCTTAAAATAAATTTC
1 ATCTCACTTGAGATT-CTTTTCTTAAAACAAATTTC
* * *
892070 GTCTCACTTGAGATTGTTATTCTTAAAATAAATTTC
1 ATCTCACTTGAGATTCTT-TTCTTAAAACAAATTTC
* * * ** *
892106 GTCTCGCTTGAGATTGTTTTTCTTAAAATGAGTTTC
1 ATCTCACTTGAGATT-CTTTTCTTAAAACAAATTTC
* * * * *
892142 ATCTAACTTGAGATTTTTTTTCTAAAAACACATTTT
1 ATCTCACTTGAGA-TTCTTTTCTTAAAACAAATTTC
* *
892178 ATCTCACTTGAGATTGTTTTCCTTGAACACAAATTT
1 ATCTCACTTGAGATTCTTTT-CTT-AAAACAAATTT
892214 TAAGATCAGT
Statistics
Matches: 355, Mismatches: 58, Indels: 75
0.73 0.12 0.15
Matches are distributed among these distances:
28 4 0.01
29 9 0.03
30 1 0.00
31 8 0.02
32 26 0.07
33 21 0.06
34 28 0.08
35 75 0.21
36 144 0.41
37 39 0.11
ACGTcount: A:0.32, C:0.15, G:0.08, T:0.44
Consensus pattern (35 bp):
ATCTCACTTGAGATTCTTTTCTTAAAACAAATTTC
Found at i:892375 original size:67 final size:67
Alignment explanation
Indices: 892279--892586 Score: 280
Period size: 66 Copynumber: 4.7 Consensus size: 67
892269 GAAACAAAAA
* * * *
892279 TTTTATCTCGCCTGAAATAGTTTCGCTTGAAATACAAACTTTGAAAAGTTTTACTCGAAAGAAAT
1 TTTTATCTCGCTTGAGATAGTTTCCCTTGAAATACAAACTTTGAAAAGTTTCACTCGAAAGAAAT
892344 AT
66 AT
* * *
892346 TTTTATCTCGCTTGAGATAGTTTCCCTTGAAACATAAAATTTGAAATCA-TTTCACTC----GAA
1 TTTTATCTCGCTTGAGATAGTTTCCCTTGAAATACAAACTTTGAAA--AGTTTCACTCGAAAGAA
892406 A-AT
64 ATAT
** * * * *
892409 TTTTATCTCG-TCTGAGATAGTTTATCTTGTAGTACAAACTTTGAAAACTTTCACTTGAAAG-AA
1 TTTTATCTCGCT-TGAGATAGTTTCCCTTGAAATACAAACTTTGAAAAGTTTCACTCGAAAGAAA
*
892472 TTT
65 TAT
* * ** * *
892475 TTTTGTCTCGCTTGAGATAATTTCCCTTGAAATACAAA-TATTGAGATTGTTTCACTTGAAATAA
1 TTTTATCTCGCTTGAGATAGTTTCCCTTGAAATACAAACT-TTGA-AAAGTTTCACTCGAAAGAA
892539 A-A-
64 ATAT
* *
892541 TTTTATCTC-TTCTGAGATAATTTCCCTTGAAATACAAACTTTGAAA
1 TTTTATCTCGCT-TGAGATAGTTTCCCTTGAAATACAAACTTTGAAA
892587 TTGTTTTACT
Statistics
Matches: 196, Mismatches: 30, Indels: 32
0.76 0.12 0.12
Matches are distributed among these distances:
61 1 0.01
62 8 0.04
63 39 0.20
64 4 0.02
65 5 0.03
66 74 0.38
67 55 0.28
68 9 0.05
69 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.39
Consensus pattern (67 bp):
TTTTATCTCGCTTGAGATAGTTTCCCTTGAAATACAAACTTTGAAAAGTTTCACTCGAAAGAAAT
AT
Found at i:892448 original size:130 final size:131
Alignment explanation
Indices: 892274--892606 Score: 386
Period size: 130 Copynumber: 2.5 Consensus size: 131
892264 CTGTCGAAAC
* * * *
892274 AAAAATTTTATCTCGCCTGAAATAGTTTCGCTTGAAATACAAACTTTGAAAAGTTTTACTCGAAA
1 AAAAATTTTATCTCGTCTGAGATAGTTTCCCTTGAAATACAAACTTTGAAAAGTTTTACTAGAAA
*
892339 GAAATATTTTTATCTCGCTTGAGATAGTTTCCCTTGAAACATA-AAAT-TTGAAATCATTTCACT
66 GAAATATTTTTATCTCGCTTGAGATAATTTCCCTTG-AA-ATACAAATATTGAAATCATTTCACT
892402 CG-
129 CGA
* ** * * * * *
892404 AAAATTTTTATCTCGTCTGAGATAGTTTATCTTGTAGTACAAACTTTGAAAACTTTCACTTGAAA
1 AAAAATTTTATCTCGTCTGAGATAGTTTCCCTTGAAATACAAACTTTGAAAAGTTTTACTAGAAA
* * * ** *
892469 G-AATTTTTTTGTCTCGCTTGAGATAATTTCCCTTGAAATACAAATATTGAGATTGTTTCACTTG
66 GAAATATTTTTATCTCGCTTGAGATAATTTCCCTTGAAATACAAATATTGAAATCATTTCACTCG
892533 AA
131 -A
* * *
892535 ATAAAATTTTATCTCTTCTGAGATAATTTCCCTTGAAATACAAACTTTGAAATTGTTTTACTAGA
1 A-AAAATTTTATCTCGTCTGAGATAGTTTCCCTTGAAATACAAACTTTGAAA-AGTTTTACTAGA
*
892600 AAAAAAT
64 AAGAAAT
892607 CATCTCACTT
Statistics
Matches: 167, Mismatches: 29, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
127 3 0.02
128 6 0.04
129 45 0.27
130 56 0.34
131 1 0.01
132 43 0.26
133 10 0.06
134 3 0.02
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (131 bp):
AAAAATTTTATCTCGTCTGAGATAGTTTCCCTTGAAATACAAACTTTGAAAAGTTTTACTAGAAA
GAAATATTTTTATCTCGCTTGAGATAATTTCCCTTGAAATACAAATATTGAAATCATTTCACTCG
A
Found at i:892532 original size:29 final size:28
Alignment explanation
Indices: 892486--892541 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
892476 TTTGTCTCGC
*
892486 TTGAGATAATTTCCCTTGAAATACAAATA
1 TTGAGATAATTTCACTTGAAATA-AAATA
**
892515 TTGAGATTGTTTCACTTGAAATAAAAT
1 TTGAGATAATTTCACTTGAAATAAAAT
892542 TTTATCTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.39, C:0.11, G:0.12, T:0.38
Consensus pattern (28 bp):
TTGAGATAATTTCACTTGAAATAAAATA
Found at i:893769 original size:27 final size:27
Alignment explanation
Indices: 893731--893785 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
893721 CTAACGAAGG
893731 TAACAATTTCATTTCCCCGAGTAATTT
1 TAACAATTTCATTTCCCCGAGTAATTT
* *
893758 TAACAATTTCATTTCCCTGATTAATTT
1 TAACAATTTCATTTCCCCGAGTAATTT
893785 T
1 T
893786 GCCTTCATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.05, T:0.45
Consensus pattern (27 bp):
TAACAATTTCATTTCCCCGAGTAATTT
Found at i:895043 original size:18 final size:18
Alignment explanation
Indices: 895000--895037 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
894990 GTGAAGTATG
*
895000 AATGGCGTTGTCGTGGCA
1 AATGGTGTTGTCGTGGCA
*
895018 AATGGTGTTGTTGTGGCA
1 AATGGTGTTGTCGTGGCA
895036 AA
1 AA
895038 GTGTGTAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.21, C:0.11, G:0.37, T:0.32
Consensus pattern (18 bp):
AATGGTGTTGTCGTGGCA
Found at i:900818 original size:18 final size:18
Alignment explanation
Indices: 900784--900819 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
900774 CCCTCTTTAA
*
900784 ACTTTTTTTTTCTTTTTG
1 ACTTTTTTTTTCATTTTG
*
900802 ACTTTTTTTTTGATTTTG
1 ACTTTTTTTTTCATTTTG
900820 TACTGACCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.08, G:0.08, T:0.75
Consensus pattern (18 bp):
ACTTTTTTTTTCATTTTG
Found at i:903294 original size:20 final size:20
Alignment explanation
Indices: 903269--903308 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
903259 GACTTCTTTC
903269 TATACGAAAATAGAAATTAG
1 TATACGAAAATAGAAATTAG
903289 TATACGAAAATAGAAATTAG
1 TATACGAAAATAGAAATTAG
903309 AAAGAGGCCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.25
Consensus pattern (20 bp):
TATACGAAAATAGAAATTAG
Found at i:911161 original size:16 final size:17
Alignment explanation
Indices: 911140--911171 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
911130 TTTATCTATC
911140 TAAATGTCAT-GAAAAG
1 TAAATGTCATGGAAAAG
911156 TAAATGTCATGGAAAA
1 TAAATGTCATGGAAAA
911172 ATTGAATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.50, C:0.06, G:0.19, T:0.25
Consensus pattern (17 bp):
TAAATGTCATGGAAAAG
Found at i:923233 original size:2 final size:2
Alignment explanation
Indices: 923226--923258 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
923216 TTAACATCAA
923226 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 A
923259 AAGATTTGGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:939068 original size:21 final size:19
Alignment explanation
Indices: 939031--939087 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
939021 GAACGCTGGA
939031 AACCGGTTTTGACCGGTTT
1 AACCGGTTTTGACCGGTTT
939050 AACCGGGTTTTGAACCGGTTTT
1 AACC-GGTTTTG-ACCGG-TTT
*
939072 GACCGG-TTTGACCGGT
1 AACCGGTTTTGACCGGT
939088 CACGACCCGT
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 1 0.03
19 9 0.26
20 11 0.32
21 7 0.21
22 6 0.18
ACGTcount: A:0.16, C:0.21, G:0.30, T:0.33
Consensus pattern (19 bp):
AACCGGTTTTGACCGGTTT
Found at i:939083 original size:9 final size:10
Alignment explanation
Indices: 939032--939087 Score: 71
Period size: 9 Copynumber: 5.6 Consensus size: 10
939022 AACGCTGGAA
939032 ACCGGTTTTG
1 ACCGGTTTTG
*
939042 ACCGG-TTTA
1 ACCGGTTTTG
939051 ACCGGGTTTTG
1 ACC-GGTTTTG
939062 AACCGGTTTTG
1 -ACCGGTTTTG
939073 ACCGG-TTTG
1 ACCGGTTTTG
939082 ACCGGT
1 ACCGGT
939088 CACGACCCGT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
9 15 0.38
10 12 0.30
11 10 0.25
12 3 0.08
ACGTcount: A:0.14, C:0.21, G:0.30, T:0.34
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:939141 original size:13 final size:13
Alignment explanation
Indices: 939100--939130 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
939090 CGACCCGTTT
*
939100 ACCCGTTTACCCG
1 ACCCGTTGACCCG
939113 ACCCGTTGACCCG
1 ACCCGTTGACCCG
939126 ACCCG
1 ACCCG
939131 ACCCGTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.48, G:0.19, T:0.16
Consensus pattern (13 bp):
ACCCGTTGACCCG
Found at i:939210 original size:29 final size:29
Alignment explanation
Indices: 939149--939215 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
939139 ACCGTTGACC
*****
939149 GGTGCTATTCTGGGAATTAATTCAGTTTT
1 GGTGCTATTCTGGGAATTAATTCAAAAAG
939178 GGTGCTATTCTGGGAATTAATTCAAAAAG
1 GGTGCTATTCTGGGAATTAATTCAAAAAG
939207 GGTGCTATT
1 GGTGCTATT
939216 TGTGTAAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.25, C:0.10, G:0.25, T:0.39
Consensus pattern (29 bp):
GGTGCTATTCTGGGAATTAATTCAAAAAG
Found at i:944509 original size:15 final size:15
Alignment explanation
Indices: 944491--944521 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
944481 AAATTCTAAA
944491 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
944506 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
944521 T
1 T
944522 CTATTTGTTG
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:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:946362 original size:15 final size:15
Alignment explanation
Indices: 946342--946372 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
946332 CAACAAATAG
946342 AATTTTTATATAAAT
1 AATTTTTATATAAAT
*
946357 AATTTTTATTTAAAT
1 AATTTTTATATAAAT
946372 A
1 A
946373 TTTAGAATTT
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:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATTTTTATATAAAT
Found at i:951737 original size:13 final size:13
Alignment explanation
Indices: 951721--951751 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
951711 GTCAACGGGT
*
951721 CGGGTCGGGTCAA
1 CGGGTCGGGTAAA
951734 CGGGTCGGGTAAA
1 CGGGTCGGGTAAA
951747 CGGGT
1 CGGGT
951752 AAACGGGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.19, G:0.48, T:0.16
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:951774 original size:19 final size:20
Alignment explanation
Indices: 951763--951819 Score: 75
Period size: 19 Copynumber: 2.9 Consensus size: 20
951753 AACGGGTCGT
951763 AACCGGTC-AAACCGG-TCAA
1 AACCGGTCAAAACCGGTTC-A
951782 AACCGGTTCAAAACCGGTT-A
1 AACCGG-TCAAAACCGGTTCA
951802 AACCGGTCAAAACCGGTT
1 AACCGGTCAAAACCGGTT
951820 TCCAGCGTTC
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
19 18 0.51
20 9 0.26
21 7 0.20
22 1 0.03
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (20 bp):
AACCGGTCAAAACCGGTTCA
Found at i:951777 original size:9 final size:10
Alignment explanation
Indices: 951763--951818 Score: 80
Period size: 9 Copynumber: 5.7 Consensus size: 10
951753 AACGGGTCGT
951763 AACCGGTC-A
1 AACCGGTCAA
951772 AACCGGTCAA
1 AACCGGTCAA
951782 AACCGGTTCAA
1 AACCGG-TCAA
*
951793 AACCGGT-TA
1 AACCGGTCAA
951802 AACCGGTCAA
1 AACCGGTCAA
951812 AACCGGT
1 AACCGGT
951819 TTCCAGCGTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
9 16 0.38
10 16 0.38
11 10 0.24
ACGTcount: A:0.36, C:0.29, G:0.21, T:0.14
Consensus pattern (10 bp):
AACCGGTCAA
Found at i:951797 original size:30 final size:30
Alignment explanation
Indices: 951763--951819 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
951753 AACGGGTCGT
951763 AACCGGTCAAACCGGTCAAAACCGGTTCAA
1 AACCGGTCAAACCGGTCAAAACCGGTTCAA
*
951793 AACCGGTTAAACCGGTCAAAACCGGTT
1 AACCGGTCAAACCGGTCAAAACCGGTT
951820 TCCAGCGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (30 bp):
AACCGGTCAAACCGGTCAAAACCGGTTCAA
Found at i:960163 original size:13 final size:13
Alignment explanation
Indices: 960145--960183 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
960135 ACCGGTCAAC
960145 GGTCAACGGGTCG
1 GGTCAACGGGTCG
960158 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
960171 GGTAAACGGGTCG
1 GGTCAACGGGTCG
960184 TGACCGGTCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.18, C:0.21, G:0.46, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:960206 original size:10 final size:10
Alignment explanation
Indices: 960186--960240 Score: 78
Period size: 10 Copynumber: 5.6 Consensus size: 10
960176 ACGGGTCGTG
960186 ACCGGTC-AA
1 ACCGGTCAAA
960195 ACCGGTCAAA
1 ACCGGTCAAA
960205 ACCGGTTCAAA
1 ACCGG-TCAAA
*
960216 ACCGGT-TAA
1 ACCGGTCAAA
960225 ACCGGTCAAA
1 ACCGGTCAAA
960235 ACCGGT
1 ACCGGT
960241 TTCCAGCGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
9 15 0.37
10 16 0.39
11 10 0.24
ACGTcount: A:0.35, C:0.29, G:0.22, T:0.15
Consensus pattern (10 bp):
ACCGGTCAAA
Done.