Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold223
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: 4172444
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 17292 characters in sequence are not A, C, G, or T
File 10 of 26
Found at i:1727095 original size:86 final size:85
Alignment explanation
Indices: 1726995--1727191 Score: 211
Period size: 86 Copynumber: 2.3 Consensus size: 85
1726985 TTTTTATATA
* * *
1726995 AATATATAAATAATATATGATATATTATAAATAAAATTATACTAACAGTTTTAAC-TTTTTCATA
1 AATATATAAATAATATATAATATATTATAAATAAAACTATACTAACAGTTTT-ACTTTTTTAATA
*
1727059 TACTAAAATAATATATCAAAAT
65 TAAT-AAATAATATATCAAAAT
* * * ** *
1727081 AATAT-TAATATAATATGTAATATATTATAAATGAAACTATTCTAATGGTTTTTCTTTTTTAATA
1 AATATATAA-ATAATATATAATATATTATAAATAAAACTATACTAACAGTTTTACTTTTTTAATA
*
1727145 TAATAAATAATATATTAAAAT
65 TAATAAATAATATATCAAAAT
*
1727166 AATGATATATTATTAATAT-TAATATA
1 AAT-ATATA--AATAATATATAATATA
1727192 ATGTATAATA
Statistics
Matches: 93, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
85 23 0.25
86 54 0.58
87 9 0.10
88 6 0.06
89 1 0.01
ACGTcount: A:0.49, C:0.05, G:0.04, T:0.43
Consensus pattern (85 bp):
AATATATAAATAATATATAATATATTATAAATAAAACTATACTAACAGTTTTACTTTTTTAATAT
AATAAATAATATATCAAAAT
Found at i:1727202 original size:12 final size:12
Alignment explanation
Indices: 1727140--1727212 Score: 53
Period size: 12 Copynumber: 6.0 Consensus size: 12
1727130 TTTTCTTTTT
1727140 TAATATAATAA-A
1 TAATAT-ATAATA
*
1727152 TAATATATTAAAA
1 TAATATA-TAATA
*
1727165 TAATGATATATTA
1 TAAT-ATATAATA
1727178 TTAATAT-TAATA
1 -TAATATATAATA
*
1727190 TAATGTATAATA
1 TAATATATAATA
*
1727202 TATTATA-AATA
1 TAATATATAATA
1727213 AAAATATGCT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
11 10 0.20
12 23 0.46
13 10 0.20
14 7 0.14
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (12 bp):
TAATATATAATA
Found at i:1727295 original size:24 final size:23
Alignment explanation
Indices: 1727266--1727327 Score: 72
Period size: 24 Copynumber: 2.7 Consensus size: 23
1727256 ATAATAAAAA
1727266 AATATATTAAAATAATATTTATAT
1 AATATATTAAAATAATA-TTATAT
*
1727290 AATATATTATAAATTATATTATAT
1 AATATATTA-AAATAATATTATAT
* *
1727314 TATA-AATAAAATAA
1 AATATATTAAAATAA
1727328 ATAATTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 5 0.15
23 3 0.09
24 18 0.55
25 7 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
AATATATTAAAATAATATTATAT
Found at i:1727306 original size:99 final size:98
Alignment explanation
Indices: 1727056--1727307 Score: 251
Period size: 99 Copynumber: 2.6 Consensus size: 98
1727046 TAACTTTTTC
* * * * * *
1727056 ATATACTAAAATAATATATCAAAATAATATTAATATAATATGTAATATATTATAAATGAAACTAT
1 ATATAATAAAAAAATATATTAAAATAATATTAATATAATATATAATATATTATAAATAAAAATAT
* *** * *
1727121 TCTAATGGTTTTTCTTTTTTAATATAATAAATA
66 GCTAACAATTTTTCTTATATAATATAATAAATA
* * *
1727154 ATATATTAAAATAATGATATATT--ATTAATATTAATATAATGTATAATATATTATAAATAAAAA
1 ATATAATAAAA-AA--ATATATTAAAATAATATTAATATAATATATAATATATTATAAATAAAAA
1727217 TATGCTAACAATTTTT-TTATATAA-ATAATATAATA
63 TATGCTAACAATTTTTCTTATATAATATAATA-AATA
* * * *
1727252 TGTTATAATAAAAAAATATATTAAAATAATATTTATATAATATATTATAAATTATA
1 --ATATAATAAAAAAATATATTAAAATAATATTAATATAATATATAATATATTATA
1727308 TTATATTATA
Statistics
Matches: 125, Mismatches: 21, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
97 13 0.10
98 20 0.16
99 77 0.62
100 9 0.07
101 6 0.05
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (98 bp):
ATATAATAAAAAAATATATTAAAATAATATTAATATAATATATAATATATTATAAATAAAAATAT
GCTAACAATTTTTCTTATATAATATAATAAATA
Found at i:1727307 original size:17 final size:17
Alignment explanation
Indices: 1727287--1727320 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1727277 ATAATATTTA
1727287 TATAATATATTATAAAT
1 TATAATATATTATAAAT
*
1727304 TATATTATATTATAAAT
1 TATAATATATTATAAAT
1727321 AAAATAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
TATAATATATTATAAAT
Found at i:1727757 original size:13 final size:13
Alignment explanation
Indices: 1727739--1727774 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
1727729 AATATTTATT
1727739 TTTTAAAATTAAA
1 TTTTAAAATTAAA
*
1727752 TTTTAAATTTAAA
1 TTTTAAAATTAAA
1727765 TTTTATAAAT
1 TTTTA-AAAT
1727775 AAAAAATTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 17 0.85
14 3 0.15
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTTTAAAATTAAA
Found at i:1728472 original size:26 final size:24
Alignment explanation
Indices: 1728436--1728485 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
1728426 ATTTTATTTT
*
1728436 ATTTTATATATTATTTTAAGATATTA
1 ATTTTATATATT-TTATAA-ATATTA
*
1728462 ATTTTTTATATTTTATAAATATTA
1 ATTTTATATATTTTATAAATATTA
1728486 TAAAAGTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.27
25 5 0.23
26 11 0.50
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
ATTTTATATATTTTATAAATATTA
Found at i:1729608 original size:17 final size:17
Alignment explanation
Indices: 1729572--1729609 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
1729562 AATTAAATTT
*
1729572 AATAATTTTTTATGAAA
1 AATAATTTTTTATAAAA
1729589 AATAATTTTTTA-AAATA
1 AATAATTTTTTATAAA-A
1729606 AATA
1 AATA
1729610 TAATAATAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 2 0.11
17 17 0.89
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (17 bp):
AATAATTTTTTATAAAA
Found at i:1729633 original size:19 final size:20
Alignment explanation
Indices: 1729600--1729683 Score: 73
Period size: 19 Copynumber: 4.1 Consensus size: 20
1729590 ATAATTTTTT
*
1729600 AAAATAAATATA-ATAATAA
1 AAAATAAATAAATATAATAA
* *
1729619 AAAATAATTAAAATACGACATAA
1 AAAATAAAT-AAATA-TA-ATAA
1729642 AAAATAATATAAATATAAT-A
1 AAAATAA-ATAAATATAATAA
* *
1729662 TAAATAAATAAATATATTAA
1 AAAATAAATAAATATAATAA
1729682 AA
1 AA
1729684 TCTATAAAAA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
19 18 0.35
20 11 0.22
21 3 0.06
22 2 0.04
23 16 0.31
24 1 0.02
ACGTcount: A:0.69, C:0.02, G:0.01, T:0.27
Consensus pattern (20 bp):
AAAATAAATAAATATAATAA
Found at i:1729664 original size:23 final size:23
Alignment explanation
Indices: 1729603--1729677 Score: 82
Period size: 23 Copynumber: 3.1 Consensus size: 23
1729593 ATTTTTTAAA
1729603 ATAAATATAATAATAAAAAATAAT
1 ATAAATATAAT-ATAAAAAATAAT
*
1729627 -TAAA-ATACGACATAAAAAATAAT
1 ATAAATATA--ATATAAAAAATAAT
1729650 ATAAATATAATATAAATAAATAAAT
1 ATAAATATAATATAAA-AAAT-AAT
1729675 ATA
1 ATA
1729678 TTAAAATCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 11
0.77 0.04 0.20
Matches are distributed among these distances:
22 3 0.07
23 22 0.51
24 9 0.21
25 9 0.21
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.28
Consensus pattern (23 bp):
ATAAATATAATATAAAAAATAAT
Found at i:1731878 original size:22 final size:25
Alignment explanation
Indices: 1731836--1731884 Score: 77
Period size: 22 Copynumber: 2.1 Consensus size: 25
1731826 ACGTAACCTT
1731836 AAAAAAATAATTAAATCATAACATA
1 AAAAAAATAATTAAATCATAACATA
1731861 AAAAAAAT-A-TAAAT-ATAACATA
1 AAAAAAATAATTAAATCATAACATA
1731883 AA
1 AA
1731885 TAAATGAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
22 10 0.42
23 5 0.21
24 1 0.04
25 8 0.33
ACGTcount: A:0.71, C:0.06, G:0.00, T:0.22
Consensus pattern (25 bp):
AAAAAAATAATTAAATCATAACATA
Found at i:1731882 original size:27 final size:25
Alignment explanation
Indices: 1731836--1731888 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
1731826 ACGTAACCTT
*
1731836 AAAAAAATAATTAAATCATAACATAA
1 AAAAAAATAAATAAATCATAA-ATAA
1731862 AAAAAATATAAATATAA-CATAAATAA
1 AAAAAA-ATAAATA-AATCATAAATAA
1731888 A
1 A
1731889 TGAATATATC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 11 0.46
27 11 0.46
28 2 0.08
ACGTcount: A:0.72, C:0.06, G:0.00, T:0.23
Consensus pattern (25 bp):
AAAAAAATAAATAAATCATAAATAA
Found at i:1732028 original size:16 final size:17
Alignment explanation
Indices: 1731985--1732031 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
1731975 TAGATAATAT
1731985 AATTTATATA-ATATTA
1 AATTTATATATATATTA
1732001 AA-TTAT-TAATATATTTA
1 AATTTATAT-ATATA-TTA
1732018 AATTTATATATATA
1 AATTTATATATATA
1732032 ATAATCTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
14 1 0.04
15 5 0.19
16 5 0.19
17 5 0.19
18 9 0.35
19 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
AATTTATATATATATTA
Found at i:1733419 original size:47 final size:44
Alignment explanation
Indices: 1733335--1733426 Score: 123
Period size: 47 Copynumber: 2.0 Consensus size: 44
1733325 TATGATAAAG
* *
1733335 CAATAAAATAAAATTTTAATTATTTATTAATTTTAATTATAAATAT
1 CAATAAAATAAAATTTTAATTATATATAAATTTTAATT-T-AATAT
1733381 CAATAAAATTTAAAATTTT-ATTATATATAAATTTTAATTTAATAT
1 CAATAAAA--TAAAATTTTAATTATATATAAATTTTAATTTAATAT
1733426 C
1 C
1733427 TTTAATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
45 6 0.14
46 9 0.21
47 18 0.43
48 9 0.21
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (44 bp):
CAATAAAATAAAATTTTAATTATATATAAATTTTAATTTAATAT
Found at i:1733923 original size:40 final size:40
Alignment explanation
Indices: 1733868--1733950 Score: 148
Period size: 40 Copynumber: 2.1 Consensus size: 40
1733858 TCCTAGAAAT
* *
1733868 GGATCGAATGTAGAGGGATGACATGTAGGTGGGCATCGTA
1 GGATCAAATGCAGAGGGATGACATGTAGGTGGGCATCGTA
1733908 GGATCAAATGCAGAGGGATGACATGTAGGTGGGCATCGTA
1 GGATCAAATGCAGAGGGATGACATGTAGGTGGGCATCGTA
1733948 GGA
1 GGA
1733951 GGAGGTTCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.29, C:0.11, G:0.40, T:0.20
Consensus pattern (40 bp):
GGATCAAATGCAGAGGGATGACATGTAGGTGGGCATCGTA
Found at i:1734038 original size:11 final size:11
Alignment explanation
Indices: 1734020--1734069 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
1734010 TATAATTATT
1734020 TAATATAAATA
1 TAATATAAATA
*
1734031 TTATATAAAATA
1 TAATAT-AAATA
1734043 TAATATAAATA
1 TAATATAAATA
1734054 TGAA-ATAAATA
1 T-AATATAAATA
*
1734065 AAATA
1 TAATA
1734070 ATTTATCAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 2 0.06
11 19 0.58
12 12 0.36
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (11 bp):
TAATATAAATA
Found at i:1735930 original size:18 final size:18
Alignment explanation
Indices: 1735907--1735941 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1735897 TCAAGAAAAG
*
1735907 CTTTATTTAGTATTTAAT
1 CTTTATTTAATATTTAAT
1735925 CTTTATTTAATATTTAA
1 CTTTATTTAATATTTAA
1735942 ATTTATGTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.60
Consensus pattern (18 bp):
CTTTATTTAATATTTAAT
Found at i:1739579 original size:2 final size:2
Alignment explanation
Indices: 1739572--1739611 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1739562 ATATGGTGGT
1739572 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1739612 AATTCGTAGC
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):
TA
Found at i:1739976 original size:16 final size:16
Alignment explanation
Indices: 1739945--1739991 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
1739935 TTTAATATTT
*
1739945 ATAAAATTTTTAATTAA
1 ATAAAA-TTATAATTAA
1739962 ATAAAATTATAATT-A
1 ATAAAATTATAATTAA
1739977 ATAAAA-TAT-ATTAA
1 ATAAAATTATAATTAA
1739991 A
1 A
1739992 ATATTTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
13 3 0.11
14 5 0.18
15 7 0.25
16 7 0.25
17 6 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAAAATTATAATTAA
Found at i:1743501 original size:14 final size:14
Alignment explanation
Indices: 1743482--1743511 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
1743472 TTATACTTTA
1743482 GAGGTGTGGTGGGT
1 GAGGTGTGGTGGGT
1743496 GAGGTGTGGTGGGT
1 GAGGTGTGGTGGGT
1743510 GA
1 GA
1743512 TTAGTCAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.00, G:0.63, T:0.27
Consensus pattern (14 bp):
GAGGTGTGGTGGGT
Found at i:1743556 original size:27 final size:26
Alignment explanation
Indices: 1743525--1743599 Score: 98
Period size: 27 Copynumber: 2.9 Consensus size: 26
1743515 GTCAATAAAA
1743525 ATTATTTTTTATTTGTCAAAAATAAT
1 ATTATTTTTTATTTGTCAAAAATAAT
* * *
1743551 AGTTATTTTGTGTTTGTCAAAAATGAT
1 A-TTATTTTTTATTTGTCAAAAATAAT
*
1743578 ATT-TTTTTTATTTGTAAAAAAT
1 ATTATTTTTTATTTGTCAAAAAT
1743600 GATGACATAT
Statistics
Matches: 42, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
25 16 0.38
26 3 0.07
27 23 0.55
ACGTcount: A:0.35, C:0.03, G:0.09, T:0.53
Consensus pattern (26 bp):
ATTATTTTTTATTTGTCAAAAATAAT
Found at i:1744729 original size:17 final size:17
Alignment explanation
Indices: 1744694--1744740 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
1744684 ATAATTACAT
*
1744694 AATATAAATATCATATAA
1 AATAT-AATATTATATAA
*
1744712 AATATAATATTATGTAA
1 AATATAATATTATATAA
1744729 AA-A-AATATTATA
1 AATATAATATTATA
1744741 AATATTAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 8 0.31
16 1 0.04
17 12 0.46
18 5 0.19
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
AATATAATATTATATAA
Found at i:1744753 original size:20 final size:20
Alignment explanation
Indices: 1744696--1744760 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
1744686 AATTACATAA
*
1744696 TATAAATATCATATAAAATAT
1 TATAAATATTA-ATAAAATAT
* * *
1744717 AAT-ATTATGTAAAAAAATAT
1 TATAAATAT-TAATAAAATAT
*
1744737 TATAAATATTAATAAAATAA
1 TATAAATATTAATAAAATAT
1744757 TATA
1 TATA
1744761 TAAAATTTTA
Statistics
Matches: 34, Mismatches: 8, Indels: 5
0.72 0.17 0.11
Matches are distributed among these distances:
20 27 0.79
21 7 0.21
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
TATAAATATTAATAAAATAT
Found at i:1744772 original size:20 final size:23
Alignment explanation
Indices: 1744717--1744764 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
1744707 TATAAAATAT
* *
1744717 AATATTATGTAAAAAAATATTATA
1 AATATTA-ATAAAATAATATTATA
1744741 AATATTAATAAAATAATA-TATA
1 AATATTAATAAAATAATATTATA
1744763 AA
1 AA
1744765 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.27
23 9 0.41
24 7 0.32
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (23 bp):
AATATTAATAAAATAATATTATA
Found at i:1745309 original size:24 final size:23
Alignment explanation
Indices: 1745266--1745310 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
1745256 TAATATATTT
1745266 ATTTATTTTTTAAATATATATAA
1 ATTTATTTTTTAAATATATATAA
* *
1745289 ATTTATATTTTTATATCTATAT
1 ATTTAT-TTTTTAAATATATAT
1745311 TTAAATATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTATTTTTTAAATATATATAA
Found at i:1748889 original size:25 final size:25
Alignment explanation
Indices: 1748857--1748906 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1748847 GATGAATCCA
1748857 GGCCAAATTAAGCAGATCATGACTT
1 GGCCAAATTAAGCAGATCATGACTT
1748882 GGCCAAATTAAGCAGATCATGACTT
1 GGCCAAATTAAGCAGATCATGACTT
1748907 TCTAACACAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (25 bp):
GGCCAAATTAAGCAGATCATGACTT
Found at i:1751495 original size:42 final size:45
Alignment explanation
Indices: 1751449--1751536 Score: 103
Period size: 47 Copynumber: 2.0 Consensus size: 45
1751439 ATTTAGTTTG
*
1751449 AATTAT-TATT-TATATAATAAAATA-ATATTTTTA-TTTAAATTT
1 AATTATATATTATATAAAATAAAATATA-ATTTTTATTTTAAATTT
1751491 AATTATAAATATTAATATAAAATAAAATATAATTTTTATTTTAAAT
1 AATTAT--ATATT-ATATAAAATAAAATATAATTTTTATTTTAAAT
1751537 AATAATATAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
42 6 0.16
45 4 0.11
47 20 0.53
48 8 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (45 bp):
AATTATATATTATATAAAATAAAATATAATTTTTATTTTAAATTT
Found at i:1753108 original size:2 final size:2
Alignment explanation
Indices: 1753101--1753139 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
1753091 AACCTTAATC
* *
1753101 TA TA TA TA TA TA TA TA TA TA TA CA TA TA TT TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1753140 TGGTAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1758932 original size:2 final size:2
Alignment explanation
Indices: 1758925--1758957 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1758915 CTAAAACAGT
1758925 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 T
1758958 GTGACACCCA
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1765962 original size:77 final size:77
Alignment explanation
Indices: 1765870--1766040 Score: 200
Period size: 77 Copynumber: 2.2 Consensus size: 77
1765860 ATTACTTTAG
* * * *
1765870 ATGAATTGGTATATAGACTGTTGTAATTTTA-TTAAATGATAAATTACAAATTTATAATCATCCA
1 ATGAAATGGTGTATAGACTGTTGTAATTCTACCT-AATGATAAATTACAAATTTATAATCATCCA
1765934 ATAATCACCTTAA
65 ATAATCACCTTAA
* * * * * *
1765947 ATGAAATGGTGTATAGATTGTTGTAATTCTACCTAGTGGTAGATTATAAATTTATAATCATTCAA
1 ATGAAATGGTGTATAGACTGTTGTAATTCTACCTAATGATAAATTACAAATTTATAATCATCCAA
* **
1766012 TAATTACCTTTG
66 TAATCACCTTAA
*
1766024 ATGAAATGGTGAATAGA
1 ATGAAATGGTGTATAGA
1766041 TATCATTTTT
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
77 78 0.99
78 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (77 bp):
ATGAAATGGTGTATAGACTGTTGTAATTCTACCTAATGATAAATTACAAATTTATAATCATCCAA
TAATCACCTTAA
Found at i:1766845 original size:102 final size:101
Alignment explanation
Indices: 1766669--1766872 Score: 302
Period size: 102 Copynumber: 2.0 Consensus size: 101
1766659 GGTTCAGTCT
* * *
1766669 GGGCTAAGAATGCCATGAGTATCACGCTCACAAATGTTGTAGATACAGTCGTTGGTAGCATTCCT
1 GGGCTAACAATGCCATGAATATCACGCTCACAAATCTTGTAGATACAGTCGTTGGTAGCATTCCT
*
1766734 TACTATCTATTTGGCTTCACCTTTGCATTTGGTGATA
66 TACTATCTATTTGGCTTCACC-TTGCATTCGGTGATA
* * * *
1766771 GGGCTAACAATGCCATGAATATTATGCTCACAAATCTTGTAGATGCTGTCGTTGGTAGCA-TCTC
1 GGGCTAACAATGCCATGAATATCACGCTCACAAATCTTGTAGATACAGTCGTTGGTAGCATTC-C
*
1766835 TTACTATCTATTTGGCTTCGCCTTGCATTCGGTGATA
65 TTACTATCTATTTGGCTTCACCTTGCATTCGGTGATA
1766872 G
1 G
1766873 CTGCCTCCAA
Statistics
Matches: 92, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
101 17 0.18
102 75 0.82
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.35
Consensus pattern (101 bp):
GGGCTAACAATGCCATGAATATCACGCTCACAAATCTTGTAGATACAGTCGTTGGTAGCATTCCT
TACTATCTATTTGGCTTCACCTTGCATTCGGTGATA
Found at i:1769004 original size:2 final size:2
Alignment explanation
Indices: 1768997--1769045 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
1768987 AAATAGTTAA
1768997 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
1769039 AG AG AG A
1 AG AG AG A
1769046 ACAGAGAATA
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:1771338 original size:25 final size:28
Alignment explanation
Indices: 1771274--1771344 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 28
1771264 TATTTTGTAA
1771274 AATTAATTAATATATATTATATATGATAAT
1 AATTAATT-AT-TATATTATATATGATAAT
*
1771304 AA-TATGTTATTATATTA-A-AT-ATAAT
1 AATTA-ATTATTATATTATATATGATAAT
1771329 AATTAATTATTATATT
1 AATTAATTATTATATT
1771345 TTTTAAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
25 17 0.46
26 4 0.11
27 1 0.03
28 7 0.19
29 4 0.11
30 4 0.11
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (28 bp):
AATTAATTATTATATTATATATGATAAT
Found at i:1771341 original size:28 final size:28
Alignment explanation
Indices: 1771274--1771341 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
1771264 TATTTTGTAA
* * *
1771274 AATTAATTAATA-TATATTATATATGAT
1 AATTAATTATTATTATATTAAATATAAT
*
1771301 AA-TAATATGTTATTATATTAAATATAAT
1 AATTAAT-TATTATTATATTAAATATAAT
1771329 AATTAATTATTAT
1 AATTAATTATTAT
1771342 ATTTTTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
26 4 0.12
27 5 0.15
28 20 0.61
29 4 0.12
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (28 bp):
AATTAATTATTATTATATTAAATATAAT
Found at i:1771780 original size:25 final size:24
Alignment explanation
Indices: 1771752--1771802 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
1771742 ATTTAAATTT
1771752 TTTTATACATATATAAAAATATATA
1 TTTTATACATAT-TAAAAATATATA
** *
1771777 TTTTATATTTATTTAAAATATATA
1 TTTTATACATATTAAAAATATATA
1771801 TT
1 TT
1771803 AAATATAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (24 bp):
TTTTATACATATTAAAAATATATA
Found at i:1771798 original size:34 final size:35
Alignment explanation
Indices: 1771738--1771809 Score: 85
Period size: 35 Copynumber: 2.1 Consensus size: 35
1771728 TTTAAAGGAA
* *
1771738 ATATATTTAAATTTTTTTATACATATATA-AAAAT
1 ATATATTTAAATTTATTTATAAATATATATAAAAT
* *
1771772 ATATATTTTATATTTATTTA-AAATATATATTAAAT
1 ATATA-TTTAAATTTATTTATAAATATATATAAAAT
1771807 ATA
1 ATA
1771810 AATATCATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
34 13 0.41
35 19 0.59
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (35 bp):
ATATATTTAAATTTATTTATAAATATATATAAAAT
Found at i:1773022 original size:25 final size:25
Alignment explanation
Indices: 1772972--1773057 Score: 63
Period size: 24 Copynumber: 3.5 Consensus size: 25
1772962 TATTTTTATG
*
1772972 TTTTTATATTTATGTCATATTTATT
1 TTTTTATATTTATGTCATATTAATT
* *
1772997 TTTTTATATTTTATTTTA-ATTAA-T
1 TTTTTATA-TTTATGTCATATTAATT
* * *
1773021 TTTTAATA-TTATGTTCGTACT-ATT
1 TTTTTATATTTATG-TCATATTAATT
1773045 TTTTATATATTTA
1 TTTT-TATATTTA
1773058 AAATATTAAA
Statistics
Matches: 46, Mismatches: 9, Indels: 11
0.70 0.14 0.17
Matches are distributed among these distances:
22 4 0.09
23 2 0.04
24 15 0.33
25 15 0.33
26 10 0.22
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.66
Consensus pattern (25 bp):
TTTTTATATTTATGTCATATTAATT
Found at i:1773280 original size:17 final size:18
Alignment explanation
Indices: 1773250--1773283 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1773240 AAAATTCGTA
*
1773250 TTTATATCTTATTCATGT
1 TTTATATCTGATTCATGT
1773268 TTTATAT-TGATTCATG
1 TTTATATCTGATTCATG
1773284 AATATTTTGC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.59
Consensus pattern (18 bp):
TTTATATCTGATTCATGT
Found at i:1773936 original size:16 final size:16
Alignment explanation
Indices: 1773890--1773936 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1773880 TTTACTTCAA
*
1773890 ATTTAATTAAATAAAAT
1 ATTTAAATAAA-AAAAT
*
1773907 -TTTAAATTATAAAAAT
1 ATTTAAA-TAAAAAAAT
1773923 ATTTAAATAAAAAA
1 ATTTAAATAAAAAA
1773937 TAAATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
16 16 0.64
17 9 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATTTAAATAAAAAAAT
Found at i:1773970 original size:27 final size:28
Alignment explanation
Indices: 1773950--1774004 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
1773940 ATATTTAATA
*
1773950 TAATTTAATTTAA-ATTTATATAATTAT
1 TAATTTAATTAAATATTTATATAATTAT
1773977 TAATTTAATTAAATATTTATA-AA-TAT
1 TAATTTAATTAAATATTTATATAATTAT
1774003 TA
1 TA
1774005 CAAATATGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 5 0.19
27 14 0.54
28 7 0.27
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
TAATTTAATTAAATATTTATATAATTAT
Found at i:1773982 original size:22 final size:21
Alignment explanation
Indices: 1773942--1773992 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 21
1773932 AAAAATAAAT
1773942 ATTTAATATAATTTAATTTAA
1 ATTTAATATAATTTAATTTAA
1773963 ATTT-ATATAATTATTAATTT-A
1 ATTTAATATAA-T-TTAATTTAA
*
1773984 ATTAAATAT
1 ATTTAATAT
1773993 TTATAAATAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.23
21 9 0.35
22 11 0.42
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (21 bp):
ATTTAATATAATTTAATTTAA
Found at i:1773997 original size:26 final size:27
Alignment explanation
Indices: 1773946--1774004 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 27
1773936 ATAAATATTT
1773946 AATA-TAATTTAATTTAAATTTATATA
1 AATATTAATTTAATTTAAATTTATATA
*
1773972 ATTATTAATTTAA-TTAAATATT-TATA
1 AATATTAATTTAATTTAAAT-TTATATA
1773998 AATATTA
1 AATATTA
1774005 CAAATATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (27 bp):
AATATTAATTTAATTTAAATTTATATA
Found at i:1775517 original size:13 final size:13
Alignment explanation
Indices: 1775499--1775532 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
1775489 ATATCAAAAT
*
1775499 ATTTTAGATACAA
1 ATTTTAAATACAA
*
1775512 ATTTTAAATATAA
1 ATTTTAAATACAA
1775525 ATTTTAAA
1 ATTTTAAA
1775533 AAAATAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (13 bp):
ATTTTAAATACAA
Found at i:1781168 original size:9 final size:8
Alignment explanation
Indices: 1781153--1781178 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1781143 AATTGCATAG
1781153 ATTTTTTT
1 ATTTTTTT
1781161 ATTTTTTT
1 ATTTTTTT
1781169 ATTTTTTT
1 ATTTTTTT
1781177 AT
1 AT
1781179 AATTTTGTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (8 bp):
ATTTTTTT
Found at i:1781534 original size:27 final size:28
Alignment explanation
Indices: 1781472--1781537 Score: 75
Period size: 27 Copynumber: 2.4 Consensus size: 28
1781462 ACATGTCAAT
1781472 TTTGATTTAAATTTTAAAAATTTAATTAA
1 TTTGATTTAAATTTT-AAAATTTAATTAA
* *
1781501 -TTAATTTAAA-TTT-AAATTTGATATAA
1 TTTGATTTAAATTTTAAAATTTAAT-TAA
1781527 TTTGATTTAAA
1 TTTGATTTAAA
1781538 CAAAAAAATT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
25 8 0.25
26 3 0.09
27 12 0.38
28 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (28 bp):
TTTGATTTAAATTTTAAAATTTAATTAA
Found at i:1781604 original size:16 final size:16
Alignment explanation
Indices: 1781579--1781617 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1781569 CTTGAATTAA
*
1781579 AAAATTACTTGAATCC
1 AAAATAACTTGAATCC
* *
1781595 AAAATAACTTGATTCT
1 AAAATAACTTGAATCC
1781611 AAAATAA
1 AAAATAA
1781618 TCCGAACTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (16 bp):
AAAATAACTTGAATCC
Found at i:1781655 original size:16 final size:16
Alignment explanation
Indices: 1781634--1781680 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
1781624 CTTATAACCC
1781634 AAACTTAAAATGATCA
1 AAACTTAAAATGATCA
* * *
1781650 AAACTTGAAATAATCC
1 AAACTTAAAATGATCA
1781666 AAA-TTCAAAATGATC
1 AAACTT-AAAATGATC
1781681 GAACTTAATA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.53, C:0.15, G:0.06, T:0.26
Consensus pattern (16 bp):
AAACTTAAAATGATCA
Found at i:1782081 original size:21 final size:22
Alignment explanation
Indices: 1782056--1782099 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
1782046 AATAATTTTT
**
1782056 AATTTTACTTGTAATAT-TAAA
1 AATTTTACTAATAATATATAAA
1782077 AATTTTACTAATAATATATAAA
1 AATTTTACTAATAATATATAAA
1782099 A
1 A
1782100 TAATAAATAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (22 bp):
AATTTTACTAATAATATATAAA
Found at i:1782113 original size:16 final size:16
Alignment explanation
Indices: 1782085--1782121 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
1782075 AAAATTTTAC
*
1782085 TAAT-AATATATAAAA
1 TAATAAATACATAAAA
1782100 TAATAAATACATAAAA
1 TAATAAATACATAAAA
1782116 T-ATAAA
1 TAATAAA
1782122 CTCTAATTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
TAATAAATACATAAAA
Found at i:1786198 original size:62 final size:62
Alignment explanation
Indices: 1786127--1786245 Score: 157
Period size: 62 Copynumber: 1.9 Consensus size: 62
1786117 TTAAATCTAC
** * * *
1786127 AATTTAATTTGGTTTAATTTATTATTTAAAATAATTAAAATTTAAATTTAATATTATTATAA
1 AATTTAATTTAATTCAATTTATTATTTAAAATAATTAAAATTTAAAATTAACATTATTATAA
* * * *
1786189 AATTTAATTTAATTCATTTTATTATTTAAAATGATTAGAGTTTAAAATTAACATTAT
1 AATTTAATTTAATTCAATTTATTATTTAAAATAATTAAAATTTAAAATTAACATTAT
1786246 AAATATTAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
62 48 1.00
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (62 bp):
AATTTAATTTAATTCAATTTATTATTTAAAATAATTAAAATTTAAAATTAACATTATTATAA
Found at i:1790590 original size:16 final size:16
Alignment explanation
Indices: 1790569--1790616 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
1790559 TTATGGACTT
1790569 TTTTTATCATACCATA
1 TTTTTATCATACCATA
1790585 TTTTTATCATACCATA
1 TTTTTATCATACCATA
1790601 TTTTTATCATACCATA
1 TTTTTATCATACCATA
1790617 CAAAAGTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.31, C:0.19, G:0.00, T:0.50
Consensus pattern (16 bp):
TTTTTATCATACCATA
Found at i:1791511 original size:14 final size:14
Alignment explanation
Indices: 1791494--1791523 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1791484 ACTTAATGCT
1791494 AATAAAGACAATGA
1 AATAAAGACAATGA
*
1791508 AATAAAGATAATGA
1 AATAAAGACAATGA
1791522 AA
1 AA
1791524 AGCAATAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.67, C:0.03, G:0.13, T:0.17
Consensus pattern (14 bp):
AATAAAGACAATGA
Found at i:1792099 original size:26 final size:22
Alignment explanation
Indices: 1792043--1792084 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
1792033 TTTGGTTCTT
1792043 ATGATTAATCAACCCAACTTGA
1 ATGATTAATCAACCCAACTTGA
1792065 ATGATTAATCAACCCAACTT
1 ATGATTAATCAACCCAACTT
1792085 TATATTAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.40, C:0.24, G:0.07, T:0.29
Consensus pattern (22 bp):
ATGATTAATCAACCCAACTTGA
Found at i:1792747 original size:18 final size:18
Alignment explanation
Indices: 1792726--1792760 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1792716 ATATAAAAAA
1792726 TAATTTTTTTTAATTTTT
1 TAATTTTTTTTAATTTTT
*
1792744 TAATTTTTTTTCATTTT
1 TAATTTTTTTTAATTTT
1792761 ATTCGTTAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (18 bp):
TAATTTTTTTTAATTTTT
Found at i:1795315 original size:26 final size:26
Alignment explanation
Indices: 1795252--1795303 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
1795242 ATGTTTAATT
* *
1795252 AAATCAGACTGATTTTAATTTATAAA
1 AAATTAGACTGATCTTAATTTATAAA
1795278 AAATTAGACTGATCTTAATTTATAAA
1 AAATTAGACTGATCTTAATTTATAAA
1795304 GACTTTATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (26 bp):
AAATTAGACTGATCTTAATTTATAAA
Found at i:1798229 original size:47 final size:47
Alignment explanation
Indices: 1798177--1798275 Score: 180
Period size: 47 Copynumber: 2.1 Consensus size: 47
1798167 ATAAATATGA
* *
1798177 ATATGAATATAAATATGAATGTCATAATTTTATTCAATAATTAATAC
1 ATATGAATATAAATATAAATGTAATAATTTTATTCAATAATTAATAC
1798224 ATATGAATATAAATATAAATGTAATAATTTTATTCAATAATTAATAC
1 ATATGAATATAAATATAAATGTAATAATTTTATTCAATAATTAATAC
1798271 ATATG
1 ATATG
1798276 GAAAATGAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.48, C:0.05, G:0.06, T:0.40
Consensus pattern (47 bp):
ATATGAATATAAATATAAATGTAATAATTTTATTCAATAATTAATAC
Found at i:1806216 original size:16 final size:17
Alignment explanation
Indices: 1806197--1806228 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
1806187 AACTAATAAA
1806197 TAAAAGTA-TTGGTCAG
1 TAAAAGTAGTTGGTCAG
1806213 TAAAAGTAGTTGGTCA
1 TAAAAGTAGTTGGTCA
1806229 AGATAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.38, C:0.06, G:0.25, T:0.31
Consensus pattern (17 bp):
TAAAAGTAGTTGGTCAG
Found at i:1806360 original size:13 final size:12
Alignment explanation
Indices: 1806317--1806421 Score: 60
Period size: 13 Copynumber: 8.6 Consensus size: 12
1806307 AATTAAATAT
1806317 AATATAATATAA
1 AATATAATATAA
*
1806329 AATTTTAATATAA
1 AA-TATAATATAA
1806342 AA-ATAATATAA
1 AATATAATATAA
1806353 ATATATAA-ATAA
1 A-ATATAATATAA
*
1806365 ATTA-AATTCATAA
1 AATATAA-T-ATAA
*
1806378 AATAAAAACTACTAA
1 AAT-ATAA-TA-TAA
*
1806393 CATATAA-A-AA
1 AATATAATATAA
1806403 AATATAA-ATAA
1 AATATAATATAA
1806414 ATATATAA
1 A-ATATAA
1806422 CAAATTAATT
Statistics
Matches: 74, Mismatches: 8, Indels: 22
0.71 0.08 0.21
Matches are distributed among these distances:
10 11 0.15
11 14 0.19
12 15 0.20
13 21 0.28
14 5 0.07
15 8 0.11
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.31
Consensus pattern (12 bp):
AATATAATATAA
Found at i:1807647 original size:26 final size:24
Alignment explanation
Indices: 1807617--1807667 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 24
1807607 TATCAAACAA
*
1807617 TAAAACATAAATATTATTAATTATAT
1 TAAAA-AT-AATAATATTAATTATAT
*
1807643 T-AAAATAATAATATTCATTATAT
1 TAAAAATAATAATATTAATTATAT
1807666 TA
1 TA
1807668 TGATCAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
23 16 0.73
24 2 0.09
25 3 0.14
26 1 0.05
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (24 bp):
TAAAAATAATAATATTAATTATAT
Found at i:1816135 original size:8 final size:8
Alignment explanation
Indices: 1816107--1816135 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
1816097 AATCTTGACG
1816107 TTTTTCTT
1 TTTTTCTT
1816115 TTTTT-TT
1 TTTTTCTT
1816122 TTTTTCTT
1 TTTTTCTT
1816130 TTTTTC
1 TTTTTC
1816136 ATGTTAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTCTT
Found at i:1822922 original size:2 final size:2
Alignment explanation
Indices: 1822915--1822939 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1822905 ATTATCCTTT
1822915 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
1822940 TTAAATATAG
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:1823221 original size:25 final size:25
Alignment explanation
Indices: 1823148--1823222 Score: 73
Period size: 25 Copynumber: 3.0 Consensus size: 25
1823138 CAAATCCAAA
*
1823148 AAAATTACTTTATTATTTAAA-ATATT
1 AAAATTA-TTTATTAATTAAATA-ATT
**
1823174 AAAATTATTT-TTATATTTTATAATT
1 AAAATTATTTATTA-ATTAAATAATT
*
1823199 AAATTTATTTATTAATTAAATAAT
1 AAAATTATTTATTAATTAAATAAT
1823223 AATTAAAGTC
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
24 3 0.08
25 26 0.65
26 11 0.28
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.53
Consensus pattern (25 bp):
AAAATTATTTATTAATTAAATAATT
Found at i:1823722 original size:2 final size:2
Alignment explanation
Indices: 1823710--1823738 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1823700 TAATAAAAGA
1823710 AT AT AT A- 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
1823739 GCTTATTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1824397 original size:17 final size:18
Alignment explanation
Indices: 1824369--1824402 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
1824359 TATAGATATT
*
1824369 ATTATCATATTACTTTAA
1 ATTATCATATTAATTTAA
1824387 ATTAT-ATATTAATTTA
1 ATTATCATATTAATTTA
1824403 TATTTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTATCATATTAATTTAA
Found at i:1825189 original size:24 final size:25
Alignment explanation
Indices: 1825152--1825201 Score: 77
Period size: 24 Copynumber: 2.0 Consensus size: 25
1825142 ATTTTTTATT
1825152 TAAATTTAATTATAAAAA-TATTTA
1 TAAATTTAATTATAAAAATTATTTA
1825176 TAAATATTAA-TATAAAAATTATTTA
1 TAAAT-TTAATTATAAAAATTATTTA
1825201 T
1 T
1825202 TTTTTAACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (25 bp):
TAAATTTAATTATAAAAATTATTTA
Found at i:1825769 original size:17 final size:17
Alignment explanation
Indices: 1825749--1825787 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1825739 AAATTATTTA
1825749 AATATAAAATA-TAATAT
1 AATATAAAATATTAA-AT
*
1825766 AATATAAATTATTAAAT
1 AATATAAAATATTAAAT
1825783 AATAT
1 AATAT
1825788 TTAATAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 17 0.85
18 3 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
AATATAAAATATTAAAT
Found at i:1827421 original size:26 final size:28
Alignment explanation
Indices: 1827378--1827431 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1827368 TTAATTATAA
1827378 TTAAATTTTAAATTA-TTT-TTTAAAAT
1 TTAAATTTTAAATTATTTTATTTAAAAT
*
1827404 TTAAA-TTTAAGTTAATTTTATTTAAAAT
1 TTAAATTTTAAATT-ATTTTATTTAAAAT
1827432 ATTTTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 7 0.29
26 6 0.25
27 3 0.12
28 8 0.33
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (28 bp):
TTAAATTTTAAATTATTTTATTTAAAAT
Found at i:1827437 original size:14 final size:15
Alignment explanation
Indices: 1827418--1827446 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1827408 ATTTAAGTTA
1827418 ATTTT-ATTTAAAAT
1 ATTTTAATTTAAAAT
1827432 ATTTTAATTTAAAAT
1 ATTTTAATTTAAAAT
1827447 GAAAATACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTTAATTTAAAAT
Found at i:1828056 original size:20 final size:21
Alignment explanation
Indices: 1828011--1828056 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
1828001 AATAAATAGT
*
1828011 AAAA-ATATGTTTTTAATTTAA
1 AAAATATATATTTTTAA-TTAA
*
1828032 TAAATATATATTTTTAA-TAA
1 AAAATATATATTTTTAATTAA
1828052 AAAAT
1 AAAAT
1828057 TAAAAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 7 0.33
21 3 0.14
22 11 0.52
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (21 bp):
AAAATATATATTTTTAATTAA
Found at i:1828990 original size:18 final size:20
Alignment explanation
Indices: 1828904--1828991 Score: 55
Period size: 18 Copynumber: 4.7 Consensus size: 20
1828894 TGTGAGTAAG
*
1828904 ATAATTTATTTATTTTG-AT
1 ATAATTTAATTATTTTGAAT
* * *
1828923 A-AATTTTATTAGTAT--AT
1 ATAATTTAATTATTTTGAAT
*
1828940 AT-ATTAAATTATGTTTGAAT
1 ATAATTTAATTAT-TTTGAAT
**
1828960 ATAATTTTTTTATTTT-AAT
1 ATAATTTAATTATTTTGAAT
1828979 -TAATTTAATTATT
1 ATAATTTAATTATT
1828992 ATTTAAATAA
Statistics
Matches: 51, Mismatches: 13, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
17 10 0.20
18 23 0.45
19 4 0.08
20 7 0.14
21 7 0.14
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (20 bp):
ATAATTTAATTATTTTGAAT
Found at i:1830144 original size:18 final size:17
Alignment explanation
Indices: 1830118--1830179 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
1830108 AATAAAAATA
1830118 TTTTT-TAATAATTTAT
1 TTTTTATAATAATTTAT
*
1830134 GTTTTTATAATATAATTA-
1 -TTTTTATAATA-ATTTAT
* *
1830152 TATTTATAATATTTTAT
1 TTTTTATAATAATTTAT
1830169 TTATTTATAAT
1 TT-TTTATAAT
1830180 TTTAAAATAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
16 3 0.08
17 16 0.44
18 13 0.36
19 4 0.11
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (17 bp):
TTTTTATAATAATTTAT
Found at i:1830171 original size:14 final size:16
Alignment explanation
Indices: 1830137--1830211 Score: 51
Period size: 18 Copynumber: 4.3 Consensus size: 16
1830127 AATTTATGTT
1830137 TTTATAATATAATTATA
1 TTTATAATAT-ATTATA
*
1830154 TTTATAATATTTTATTTA
1 TTTATAATATATTA--TA
* **
1830172 TTTATAATTTTAAAATAA
1 TTTATAA-TATATTAT-A
*
1830190 TTTTATATTATATTATA
1 -TTTATAATATATTATA
1830207 TTTAT
1 TTTAT
1830212 TTATTTTTTA
Statistics
Matches: 44, Mismatches: 9, Indels: 11
0.69 0.14 0.17
Matches are distributed among these distances:
16 8 0.18
17 12 0.27
18 15 0.34
19 9 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTTATAATATATTATA
Found at i:1830183 original size:43 final size:43
Alignment explanation
Indices: 1830136--1830217 Score: 114
Period size: 43 Copynumber: 1.9 Consensus size: 43
1830126 TAATTTATGT
1830136 TTTTATAATATAATTATAT-TTATAATAT-TTTATTTATTTATAA
1 TTTTA-AA-ATAATTATATATTATAATATATTTATTTATTTATAA
* *
1830179 TTTTAAAATAATTTTATATTATATTATATTTATTTATTT
1 TTTTAAAATAATTATATATTATAATATATTTATTTATTT
1830218 TTTATATATT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
41 9 0.26
42 10 0.29
43 16 0.46
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (43 bp):
TTTTAAAATAATTATATATTATAATATATTTATTTATTTATAA
Found at i:1830230 original size:24 final size:25
Alignment explanation
Indices: 1830189--1830235 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
1830179 TTTTAAAATA
*
1830189 ATTTTATATTATATTATATTTATTT
1 ATTTTATATTATATTATAATTATTT
*
1830214 ATTTTTTA-TATATTATAATTAT
1 ATTTTATATTATATTATAATTAT
1830236 GTTTGGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (25 bp):
ATTTTATATTATATTATAATTATTT
Found at i:1830294 original size:2 final size:2
Alignment explanation
Indices: 1830277--1830312 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
1830267 TATTTATTAC
*
1830277 AT AT AA AT AT -T 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
1830313 GAAATCTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1832544 original size:3 final size:3
Alignment explanation
Indices: 1832536--1832560 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1832526 TAATGGGTCT
1832536 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
1832561 TGGTTGTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:1839765 original size:25 final size:27
Alignment explanation
Indices: 1839715--1839773 Score: 79
Period size: 25 Copynumber: 2.3 Consensus size: 27
1839705 ATCTAATCTT
*
1839715 TTTTAAATAAAATTTTTAATTAATTAA
1 TTTTAAATAAAATTTATAATTAATTAA
1839742 TTTTAAAT-AAA-TTATAA-TACATTAA
1 TTTTAAATAAAATTTATAATTA-ATTAA
1839767 TTTTAAA
1 TTTTAAA
1839774 GTTAATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
24 2 0.07
25 17 0.57
26 3 0.10
27 8 0.27
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTTAAATAAAATTTATAATTAATTAA
Found at i:1839782 original size:25 final size:25
Alignment explanation
Indices: 1839715--1839791 Score: 75
Period size: 25 Copynumber: 3.0 Consensus size: 25
1839705 ATCTAATCTT
* *
1839715 TTTTAAATAAAATTTTTAATTAATTAA
1 TTTTAAAT-AAA-TTATAATAAATTAA
*
1839742 TTTTAAATAAATTATAATACATTAA
1 TTTTAAATAAATTATAATAAATTAA
* *
1839767 TTTTAAAGTTAA-TATATTAAATTAA
1 TTTTAAA-TAAATTATAATAAATTAA
1839792 AAATAATTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
25 29 0.67
26 6 0.14
27 8 0.19
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (25 bp):
TTTTAAATAAATTATAATAAATTAA
Found at i:1839932 original size:13 final size:13
Alignment explanation
Indices: 1839916--1839958 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1839906 TTGAATAAAA
1839916 AATAAAATAGATG
1 AATAAAATAGATG
*
1839929 AAT-AAATA-ATT
1 AATAAAATAGATG
*
1839940 AATATAATAGATG
1 AATAAAATAGATG
1839953 AATAAA
1 AATAAA
1839959 TAATTAATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 5 0.21
12 9 0.38
13 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.09, T:0.28
Consensus pattern (13 bp):
AATAAAATAGATG
Found at i:1839937 original size:24 final size:24
Alignment explanation
Indices: 1839909--1839961 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
1839899 AAAAGTCTTG
1839909 AATAAAAAATAAAATAGATGAATA
1 AATAAAAAATAAAATAGATGAATA
** *
1839933 AATAATTAATATAATAGATGAATA
1 AATAAAAAATAAAATAGATGAATA
1839957 AATAA
1 AATAA
1839962 TTAATATACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.08, T:0.26
Consensus pattern (24 bp):
AATAAAAAATAAAATAGATGAATA
Found at i:1839962 original size:24 final size:24
Alignment explanation
Indices: 1839916--1839969 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
1839906 TTGAATAAAA
*
1839916 AATAAAATAGATGAATAAATAATT
1 AATATAATAGATGAATAAATAATT
1839940 AATATAATAGATGAATAAATAATT
1 AATATAATAGATGAATAAATAATT
1839964 AATATA
1 AATATA
1839970 CAGTAATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.31
Consensus pattern (24 bp):
AATATAATAGATGAATAAATAATT
Found at i:1841244 original size:5 final size:5
Alignment explanation
Indices: 1841202--1841341 Score: 100
Period size: 5 Copynumber: 29.2 Consensus size: 5
1841192 ATTATTTAAT
* *
1841202 TATAA TATAA -ATAA AATAA T-TAA AATAA T-TAA -ATAA TATAA TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* * * *
1841248 TATAA -ATAT TTTAA TAT-A TATAA TATAA -ATTA T-TAA TATAT TATAA
1 TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA TATAA
* * * *
1841294 T-TTA TATAAA TATAA AATAA TTTAAA TAGTAT TATAA TATAA TATAA
1 TATAA TAT-AA TATAA TATAA TAT-AA TA-TAA TATAA TATAA TATAA
1841341 T
1 T
1841342 TCACGAATTT
Statistics
Matches: 104, Mismatches: 19, Indels: 24
0.71 0.13 0.16
Matches are distributed among these distances:
4 29 0.28
5 64 0.62
6 10 0.10
7 1 0.01
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (5 bp):
TATAA
Found at i:1841268 original size:23 final size:22
Alignment explanation
Indices: 1841235--1841294 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 22
1841225 AATAATTAAA
*
1841235 TAATATAATATAATATAAATATTT
1 TAATAT-ATATAATATAAAT-TAT
1841259 TAATATATATAATATAAATTAT
1 TAATATATATAATATAAATTAT
1841281 TAATATATTATAAT
1 TAATATA-TATAAT
1841295 TTATATAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 9 0.26
23 19 0.56
24 6 0.18
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
TAATATATATAATATAAATTAT
Found at i:1841301 original size:60 final size:58
Alignment explanation
Indices: 1841186--1841342 Score: 144
Period size: 60 Copynumber: 2.6 Consensus size: 58
1841176 GCTTGGTATA
*
1841186 AATATAATTA-TTTAATTATAATATAA-ATAAAATAATTAAAATAATTAAATAATATAATAT
1 AATATAAATATTTTAA-TAT-ATATAATAT-AAATAATTAAAATAATTAAATAATATAA-AT
* * *
1841246 AATATAAATATTTTAATATATATAATATAAATTATTAATAT-ATTATAATTTATATAAAT
1 AATATAAATATTTTAATATATATAATATAAATAATTAAAATAATTA-AA-TAATATAAAT
*
1841305 -ATA-AAATAATTTAAATAGTATTATAATATAATATAATT
1 AATATAAAT-ATTTTAATA-TA-TATAATATAA-ATAATT
1841343 CACGAATTTA
Statistics
Matches: 83, Mismatches: 6, Indels: 15
0.80 0.06 0.14
Matches are distributed among these distances:
57 4 0.05
58 15 0.18
59 23 0.28
60 31 0.37
61 10 0.12
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (58 bp):
AATATAAATATTTTAATATATATAATATAAATAATTAAAATAATTAAATAATATAAAT
Found at i:1847750 original size:2 final size:2
Alignment explanation
Indices: 1847743--1847782 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1847733 GAAGTTGCAA
1847743 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
1847783 GGCGGGATTT
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1848676 original size:22 final size:22
Alignment explanation
Indices: 1848646--1848689 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1848636 TAAATAATTT
* *
1848646 AAATTTATTTTATGTTTTTTAA
1 AAATATATTTTATATTTTTTAA
*
1848668 AAATATATTTTTTATTTTTTAA
1 AAATATATTTTATATTTTTTAA
1848690 TATTTATATT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (22 bp):
AAATATATTTTATATTTTTTAA
Found at i:1848775 original size:12 final size:12
Alignment explanation
Indices: 1848744--1848784 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
1848734 ATGATATAAT
1848744 TTATATAATATA
1 TTATATAATATA
* * *
1848756 TAAAATAAAATA
1 TTATATAATATA
1848768 TTATATAATATA
1 TTATATAATATA
1848780 TTATA
1 TTATA
1848785 ATTGAAAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
TTATATAATATA
Found at i:1853474 original size:193 final size:193
Alignment explanation
Indices: 1853145--1853526 Score: 710
Period size: 193 Copynumber: 2.0 Consensus size: 193
1853135 TCTATTTTAA
*
1853145 CATCATCAGGTCCTGTTTAAAGTAAAAGAGCACCTTCAAATTATGTAGCATCATAAATTCTACTT
1 CATCATCAGGTCCTATTTAAAGTAAAAGAGCACCTTCAAATTATGTAGCATCATAAATTCTACTT
1853210 CAAGTAAGTGATAGAAAGAAATCTTCTCTGTTTTCTCCAGAAGTGCTCTTACTTTCCATATTTTA
66 CAAGTAAGTGATAGAAAGAAATCTTCTCTGTTTTCTCCAGAAGTGCTCTTACTTTCCATATTTTA
* *
1853275 TATCCCCATATTCTATATCAACTAGATAAAAACAGGAAATGAGTTAGCACAAGGCATACTTTC
131 TATCCCCATATTCTATATCAACTAGACAAAAACAGGAAATGAGTTAGCACAAGACATACTTTC
*
1853338 CATCATCGGGTCCTATTTAAAGTAAAAGAGCACCTTCAAATTATGTAGCATCATAAATTCTACTT
1 CATCATCAGGTCCTATTTAAAGTAAAAGAGCACCTTCAAATTATGTAGCATCATAAATTCTACTT
1853403 CAAGTAAGTGATAGAAAGAAATCTTCTCTGTTTTCTCCAGAAGTGCTCTTACTTTCCATATTTTA
66 CAAGTAAGTGATAGAAAGAAATCTTCTCTGTTTTCTCCAGAAGTGCTCTTACTTTCCATATTTTA
* *
1853468 TATCCCCATATTCTATATCAATTAGACAAAAACATGAAATGAGTTAGCACAAGACATAC
131 TATCCCCATATTCTATATCAACTAGACAAAAACAGGAAATGAGTTAGCACAAGACATAC
1853527 CTTCACGCAA
Statistics
Matches: 183, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
193 183 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (193 bp):
CATCATCAGGTCCTATTTAAAGTAAAAGAGCACCTTCAAATTATGTAGCATCATAAATTCTACTT
CAAGTAAGTGATAGAAAGAAATCTTCTCTGTTTTCTCCAGAAGTGCTCTTACTTTCCATATTTTA
TATCCCCATATTCTATATCAACTAGACAAAAACAGGAAATGAGTTAGCACAAGACATACTTTC
Found at i:1855969 original size:15 final size:16
Alignment explanation
Indices: 1855946--1855979 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
1855936 TTTTAATTTA
1855946 TTAAGTATATTAA-AT
1 TTAAGTATATTAATAT
*
1855961 TTAATTATATTAATAT
1 TTAAGTATATTAATAT
1855977 TTA
1 TTA
1855980 TTTAAATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTAAGTATATTAATAT
Found at i:1856020 original size:11 final size:11
Alignment explanation
Indices: 1856004--1856056 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
1855994 TAGGCTTAAT
1856004 TAAATTTAAAA
1 TAAATTTAAAA
*
1856015 TAAATTTAAATT
1 TAAATTTAAA-A
*
1856027 TAAATTT-AAT
1 TAAATTTAAAA
1856037 TAAA---AAAA
1 TAAATTTAAAA
1856045 TAAATTTAAAA
1 TAAATTTAAAA
1856056 T
1 T
1856057 TGAACATAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
8 6 0.17
10 5 0.14
11 17 0.49
12 7 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:1856025 original size:17 final size:17
Alignment explanation
Indices: 1856003--1856054 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
1855993 ATAGGCTTAA
1856003 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
* *
1856020 TTAAATTTAAATTTAA-
1 TTAAATTTAAAATAAAT
1856036 TTAAA---AAAATAAAT
1 TTAAATTTAAAATAAAT
1856050 TTAAA
1 TTAAA
1856055 ATTGAACATA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
13 6 0.20
14 5 0.17
16 5 0.17
17 14 0.47
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:1856054 original size:6 final size:6
Alignment explanation
Indices: 1856003--1856035 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
1855993 ATAGGCTTAA
*
1856003 TTAAAT TTAAA- ATAAAT TTAAAT TTAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
1856036 TTAAAAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (6 bp):
TTAAAT
Found at i:1857838 original size:20 final size:20
Alignment explanation
Indices: 1857810--1857848 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1857800 CGTATATTTA
*
1857810 AATATAAATATAAAAATATT
1 AATAAAAATATAAAAATATT
*
1857830 AATAAAAATTTAAAAATAT
1 AATAAAAATATAAAAATAT
1857849 AAAATATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AATAAAAATATAAAAATATT
Found at i:1859637 original size:93 final size:91
Alignment explanation
Indices: 1859458--1859638 Score: 276
Period size: 93 Copynumber: 1.9 Consensus size: 91
1859448 ATAACGAAAC
*
1859458 AAATGTTAAAGGTCCAAATTGTATAGCAGGTGAGGAACAAGACATCACATTCACGAGATGTACCA
1 AAATGTTAAAGGTCCAAATTGTATAGCAGGTGAGGAACAAGACATCACATTCACAAGATGTACCA
1859523 TTTACCTGGATGACGATGATGATCGTAA
66 TTTACCTGGATGAC-A-GATGATCGTAA
*
1859551 AAATGTTAAAGGTTCAAATTGTATAGCAGGTGAGGAACAAAGACATCACATATTCACAAGA-GTT
1 AAATGTTAAAGGTCCAAATTGTATAGCAGGTGAGGAAC-AAGACATCAC--ATTCACAAGATG-T
1859615 ACCATTTACCTGGATGAC-GATGAT
62 ACCATTTACCTGGATGACAGATGAT
1859639 GATCTCGAAG
Statistics
Matches: 82, Mismatches: 2, Indels: 8
0.89 0.02 0.09
Matches are distributed among these distances:
93 43 0.52
94 10 0.12
95 1 0.01
96 28 0.34
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (91 bp):
AAATGTTAAAGGTCCAAATTGTATAGCAGGTGAGGAACAAGACATCACATTCACAAGATGTACCA
TTTACCTGGATGACAGATGATCGTAA
Found at i:1860788 original size:15 final size:15
Alignment explanation
Indices: 1860755--1860801 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
1860745 CATCTTAAAA
* *
1860755 ATATTCATATTATATT
1 ATATT-ATATTTTAAT
1860771 ATATTATATTTTAAT
1 ATATTATATTTTAAT
*
1860786 ATATTA-AATTTAAT
1 ATATTATATTTTAAT
1860800 AT
1 AT
1860802 GAGGATGCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
14 9 0.32
15 14 0.50
16 5 0.18
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTATATTTTAAT
Found at i:1861465 original size:13 final size:13
Alignment explanation
Indices: 1861449--1861476 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1861439 AAAAATTAAT
1861449 AATTTAAATTTTA
1 AATTTAAATTTTA
1861462 AATTTAAATTTTA
1 AATTTAAATTTTA
1861475 AA
1 AA
1861477 ATTTTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTTAAATTTTA
Found at i:1862646 original size:29 final size:29
Alignment explanation
Indices: 1862606--1862698 Score: 125
Period size: 30 Copynumber: 3.1 Consensus size: 29
1862596 ATAAATATAA
* *
1862606 AAATTTTAAATTTTTTATTATACTTAAAT
1 AAATTTTTAATTTTTAATTATACTTAAAT
*
1862635 AAATTTTTAATTTTTAATTAATATTTAAAT
1 AAATTTTTAATTTTTAATT-ATACTTAAAT
1862665 AAATTTTTTAATTTTTAATT-TATCTTAAAT
1 AAA-TTTTTAATTTTTAATTATA-CTTAAAT
1862695 AAAT
1 AAAT
1862699 ATTAACTTAA
Statistics
Matches: 57, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
29 20 0.35
30 21 0.37
31 16 0.28
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (29 bp):
AAATTTTTAATTTTTAATTATACTTAAAT
Found at i:1862735 original size:60 final size:60
Alignment explanation
Indices: 1862609--1862732 Score: 153
Period size: 59 Copynumber: 2.1 Consensus size: 60
1862599 AATATAAAAA
* * * * **
1862609 TTTTAAATTTTTTATTATACTTAAATAAATTTTTAATTTTTAATTAATATTTAAATAAAT
1 TTTTTAATTTTTAATTATACTTAAATAAATTATTAACTTAAAATTAATATTTAAATAAAT
* *
1862669 TTTTTAATTTTTAATT-TATCTTAAATAAA-TATTAACTTAAAATTTATATTTAAATAACT
1 TTTTTAATTTTTAATTATA-CTTAAATAAATTATTAACTTAAAATTAATATTTAAATAAAT
1862728 TTTTT
1 TTTTT
1862733 TAAAATATAT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
59 31 0.56
60 24 0.44
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.56
Consensus pattern (60 bp):
TTTTTAATTTTTAATTATACTTAAATAAATTATTAACTTAAAATTAATATTTAAATAAAT
Found at i:1867950 original size:18 final size:20
Alignment explanation
Indices: 1867908--1867952 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
1867898 GATTTAGATT
1867908 TAAAATT-TATTGAATCTTAA
1 TAAAATTATATTGAATC-TAA
1867928 T-AAATTATA-TGAATC-AA
1 TAAAATTATATTGAATCTAA
1867945 TAAAATTA
1 TAAAATTA
1867953 AAATTCAAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
17 3 0.13
18 6 0.26
19 11 0.48
20 3 0.13
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (20 bp):
TAAAATTATATTGAATCTAA
Found at i:1869018 original size:3 final size:3
Alignment explanation
Indices: 1869010--1869040 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1869000 TAATGGTTGT
1869010 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1869041 CAAAATTCAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1869324 original size:20 final size:21
Alignment explanation
Indices: 1869275--1869313 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1869265 AAAAGCCTTT
*
1869275 AAATTATT-TACTTTTAAAGC
1 AAATTTTTATACTTTTAAAGC
1869295 AAATTTTTATACTTTTAAA
1 AAATTTTTATACTTTTAAA
1869314 TAATTTTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.03, T:0.49
Consensus pattern (21 bp):
AAATTTTTATACTTTTAAAGC
Found at i:1869454 original size:30 final size:29
Alignment explanation
Indices: 1869420--1869513 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 29
1869410 AGCTGAAAGT
1869420 TTTATTTGGAAACAATTAAAAAATTAAAAA
1 TTTATTT-GAAACAATTAAAAAATTAAAAA
* *
1869450 TTTATTTGAATATAATTAAAAAATTAAAAT
1 TTTATTTGAA-ACAATTAAAAAATTAAAAA
*
1869480 TTTATTTG-AACAA-AATAAAAATATAAAAA
1 TTTATTTGAAACAATTA-AAAAAT-TAAAAA
1869509 TTTAT
1 TTTAT
1869514 ACAAATAAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
27 1 0.02
28 9 0.16
29 14 0.25
30 32 0.57
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.38
Consensus pattern (29 bp):
TTTATTTGAAACAATTAAAAAATTAAAAA
Found at i:1870086 original size:18 final size:20
Alignment explanation
Indices: 1870050--1870094 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
1870040 AACACATAAA
1870050 TTTTTTTCCTTCCTCCTTTC
1 TTTTTTTCCTTCCTCCTTTC
*
1870070 TTTTTTT-CTTTCT-CTTTC
1 TTTTTTTCCTTCCTCCTTTC
1870088 TTTTTTT
1 TTTTTTT
1870095 TTTTAAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 12 0.50
19 5 0.21
20 7 0.29
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTCCTTCCTCCTTTC
Found at i:1870094 original size:19 final size:20
Alignment explanation
Indices: 1870050--1870095 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1870040 AACACATAAA
*
1870050 TTTTTTTCCTTCCTCCTTTC
1 TTTTTTTTCTTCCTCCTTTC
*
1870070 -TTTTTTTCTTTCT-CTTTC
1 TTTTTTTTCTTCCTCCTTTC
1870088 TTTTTTTT
1 TTTTTTTT
1870096 TTTAAATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 18 0.78
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTTTTCTTCCTCCTTTC
Found at i:1870476 original size:16 final size:16
Alignment explanation
Indices: 1870455--1870485 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1870445 TAAATAAAAT
*
1870455 AAATTATTAAAACTTA
1 AAATTAATAAAACTTA
1870471 AAATTAATAAAACTT
1 AAATTAATAAAACTT
1870486 TATAATATTT
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:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (16 bp):
AAATTAATAAAACTTA
Found at i:1876499 original size:19 final size:18
Alignment explanation
Indices: 1876465--1876500 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
1876455 CAAGTAGTTA
1876465 TATTTTAATATAAATAAT
1 TATTTTAATATAAATAAT
*
1876483 TATTTTATATATTAATAA
1 TATTTTA-ATATAAATAA
1876501 AAAATTTTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATTTTAATATAAATAAT
Found at i:1877465 original size:33 final size:32
Alignment explanation
Indices: 1877428--1877509 Score: 100
Period size: 32 Copynumber: 2.7 Consensus size: 32
1877418 TGAAGTTAAG
* *
1877428 ATAAATATATGATTATTTTAATATTTATATAAA
1 ATAAAT-TATGAATATTTTAAAATTTATATAAA
*
1877461 ATAAATTATTAATATTTTAAAATTTATATAAA
1 ATAAATTATGAATATTTTAAAATTTATATAAA
1877493 AT--A-TAT-AATATTTTAAA
1 ATAAATTATGAATATTTTAAA
1877510 TATAATTATA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
28 11 0.24
29 3 0.07
30 1 0.02
32 25 0.54
33 6 0.13
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (32 bp):
ATAAATTATGAATATTTTAAAATTTATATAAA
Found at i:1877522 original size:27 final size:28
Alignment explanation
Indices: 1877470--1877527 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 28
1877460 AATAAATTAT
* *
1877470 TAATATTTTAAAATTTATATAAAATATA
1 TAATATTTTAAAATTAATATAAAATACA
*
1877498 TAATATTTT-AAATATAAT-TATAATACA
1 TAATATTTTAAAAT-TAATATAAAATACA
1877525 TAA
1 TAA
1877528 AATAATACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 14 0.54
28 12 0.46
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (28 bp):
TAATATTTTAAAATTAATATAAAATACA
Found at i:1877565 original size:20 final size:20
Alignment explanation
Indices: 1877548--1877611 Score: 64
Period size: 19 Copynumber: 3.2 Consensus size: 20
1877538 ACATAATATC
1877548 AAAATT-TTAAAAATAATAA
1 AAAATTATTAAAAATAATAA
*
1877567 AAAATTATT-AAAATTATAA
1 AAAATTATTAAAAATAATAA
1877586 AATAATTA--AAAAATACATAA
1 AA-AATTATTAAAAATA-ATAA
1877606 ACAAAT
1 A-AAAT
1877612 AATATATCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 22 0.58
20 15 0.39
21 1 0.03
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATTATTAAAAATAATAA
Found at i:1880532 original size:24 final size:23
Alignment explanation
Indices: 1880498--1880557 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 23
1880488 AAATTATATT
* * *
1880498 TAAATTATAAATATTGAAATAAAA
1 TAAATTTTAAATAGTAAAAT-AAA
* *
1880522 TAATTTTTAAATAGTAAAATCAA
1 TAAATTTTAAATAGTAAAATAAA
1880545 TAAATTTTAAATA
1 TAAATTTTAAATA
1880558 AATTTTATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 14 0.47
24 16 0.53
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (23 bp):
TAAATTTTAAATAGTAAAATAAA
Found at i:1882311 original size:15 final size:13
Alignment explanation
Indices: 1882284--1882329 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
1882274 ATTTAAATTT
1882284 AAATT-ATT-TAA
1 AAATTAATTATAA
1882295 AAATTAATATATAA
1 AAATTAAT-TATAA
*
1882309 AAATTTATTATAA
1 AAATTAATTATAA
1882322 TAAATTAA
1 -AAATTAA
1882330 AACAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
11 5 0.17
12 2 0.07
13 6 0.21
14 16 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AAATTAATTATAA
Found at i:1882420 original size:2 final size:2
Alignment explanation
Indices: 1882413--1882440 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1882403 CAATATCATT
1882413 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1882441 GACCCCGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1883268 original size:18 final size:18
Alignment explanation
Indices: 1883245--1883279 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
1883235 GTAATTTTTA
1883245 ATATAATATAAAA-ATATG
1 ATATAA-ATAAAATATATG
1883263 ATATAAATAAAATATAT
1 ATATAAATAAAATATAT
1883280 TTAATAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (18 bp):
ATATAAATAAAATATATG
Found at i:1883356 original size:18 final size:19
Alignment explanation
Indices: 1883335--1883379 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
1883325 AATATACACT
1883335 ATTTTATTTATATTTAA-A
1 ATTTTATTTATATTTAATA
*
1883353 ATTTTA-ATATATTTAATA
1 ATTTTATTTATATTTAATA
1883371 ATTTATATT
1 ATTT-TATT
1883380 ATGTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 9 0.41
18 11 0.50
19 2 0.09
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (19 bp):
ATTTTATTTATATTTAATA
Found at i:1887336 original size:25 final size:25
Alignment explanation
Indices: 1887282--1887330 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1887272 ATAAGATAAA
1887282 ATTAATAAATATTAATAATTTTATT
1 ATTAATAAATATTAATAATTTTATT
*
1887307 TTTAATAAA-A-TAAT-ATTTT-TT
1 ATTAATAAATATTAATAATTTTATT
1887328 ATT
1 ATT
1887331 CATTAACAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 4 0.18
22 5 0.23
23 4 0.18
24 1 0.05
25 8 0.36
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (25 bp):
ATTAATAAATATTAATAATTTTATT
Found at i:1890973 original size:33 final size:32
Alignment explanation
Indices: 1890909--1890979 Score: 88
Period size: 33 Copynumber: 2.2 Consensus size: 32
1890899 AAAAATAATT
* * * *
1890909 AAAATATAATATTAATATTAAATATGTATATA
1 AAAATACAATATAAATAATAAATATGAATATA
*
1890941 TAAATACAATATAAATTAATAAATATGAATATA
1 AAAATACAATATAAA-TAATAAATATGAATATA
1890974 AAAATA
1 AAAATA
1890980 TATTAAAATT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 12 0.38
33 20 0.62
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (32 bp):
AAAATACAATATAAATAATAAATATGAATATA
Found at i:1893762 original size:2 final size:2
Alignment explanation
Indices: 1893755--1893794 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1893745 GAAACAAGTT
1893755 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
1893795 TATGTGTAAA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1894455 original size:18 final size:18
Alignment explanation
Indices: 1894434--1894486 Score: 62
Period size: 16 Copynumber: 3.2 Consensus size: 18
1894424 TAAAATATTT
1894434 ATATTTATATAAATTTTA
1 ATATTTATATAAATTTTA
1894452 ATATGTTA-AT-AA-TTT-
1 ATAT-TTATATAAATTTTA
1894467 ATA-TTATATAAATTTTA
1 ATATTTATATAAATTTTA
1894484 ATA
1 ATA
1894487 CATATATTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 11
0.73 0.00 0.27
Matches are distributed among these distances:
13 3 0.10
14 2 0.07
15 5 0.17
16 6 0.20
17 5 0.17
18 6 0.20
19 3 0.10
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (18 bp):
ATATTTATATAAATTTTA
Found at i:1895807 original size:14 final size:14
Alignment explanation
Indices: 1895788--1895838 Score: 57
Period size: 14 Copynumber: 3.4 Consensus size: 14
1895778 AAATATATAA
1895788 ATATATTAAAATTT
1 ATATATTAAAATTT
1895802 ATATATTATAAATTATT
1 ATATATTA-AAA-T-TT
*
1895819 AATATTTTAAAATTT
1 -ATATATTAAAATTT
1895834 ATATA
1 ATATA
1895839 AATATAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
14 12 0.39
15 5 0.16
16 2 0.06
17 5 0.16
18 7 0.23
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
ATATATTAAAATTT
Found at i:1895813 original size:16 final size:16
Alignment explanation
Indices: 1895794--1895838 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
1895784 ATAAATATAT
1895794 TAAAATTTATATATTA
1 TAAAATTTATATATTA
* *
1895810 TAAATTATTA-ATATTT
1 TAAAAT-TTATATATTA
1895826 TAAAATTTATATA
1 TAAAATTTATATA
1895839 AATATAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.12
16 18 0.75
17 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TAAAATTTATATATTA
Done.