Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold43
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: 2559314
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 13088 characters in sequence are not A, C, G, or T
File 1 of 19
Found at i:8408 original size:14 final size:14
Alignment explanation
Indices: 8389--8437 Score: 73
Period size: 14 Copynumber: 3.6 Consensus size: 14
8379 CCTTCTCTTC
8389 AAAAAAAAAAAA-A
1 AAAAAAAAAAAACA
8402 AAAAAAAAAAAACA
1 AAAAAAAAAAAACA
*
8416 AAAAAAACAAAACA
1 AAAAAAAAAAAACA
*
8430 AAGAAAAA
1 AAAAAAAA
8438 GAGAGAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
13 12 0.38
14 20 0.62
ACGTcount: A:0.92, C:0.06, G:0.02, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAACA
Found at i:8453 original size:1 final size:1
Alignment explanation
Indices: 8389--8437 Score: 62
Period size: 1 Copynumber: 49.0 Consensus size: 1
8379 CCTTCTCTTC
* * * *
8389 AAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAACAAAACAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
8438 GAGAGAAAAG
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
1 40 1.00
ACGTcount: A:0.92, C:0.06, G:0.02, T:0.00
Consensus pattern (1 bp):
A
Found at i:9670 original size:55 final size:55
Alignment explanation
Indices: 9419--10154 Score: 1092
Period size: 55 Copynumber: 13.3 Consensus size: 55
9409 TCCGCTTTTT
* *
9419 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
*
9474 AGTCCTCAAAGAGCAGGACCACCTTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGA-CACCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
9531 AGTCCTCAAAGAGCAGGACACC-TTTAAAGCCCACACAAGTTGGTGGCACCTTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACC-TTT-C
*
9587 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
9642 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
9698 AGTCCTCAAAGAGCAGGACACC-TTTCAAGCCCACACAAGTTGGTGGCA--TTGTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTT-T-C
*
9752 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
9807 AGTCCCCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTTGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
9862 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
* * *
9917 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-C
*
9972 AGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* * *
10027 ATTCCCCAAAGAGCAGGACA-CTTTTCAAAGCCCACACAAGTGGGTGGCACCTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTC
* * * * *
10082 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCACTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
* *
10137 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
10155 TACAATTTAT
Statistics
Matches: 631, Mismatches: 35, Indels: 30
0.91 0.05 0.04
Matches are distributed among these distances:
53 2 0.00
54 55 0.09
55 428 0.68
56 75 0.12
57 71 0.11
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTC
Found at i:10082 original size:29 final size:29
Alignment explanation
Indices: 9935--10082 Score: 71
Period size: 29 Copynumber: 5.3 Consensus size: 29
9925 AAGAACAGGA
*
9935 CACCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
* * * * * * *
9964 CA-TTTTC-CAGTCCTCA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
9990 CACCTCTT-AAAGCCCACACAAGTTGGTGG
1 CACCT-TTCAAAGCCCACACAAGTGGGTGG
** * * *
10019 CACCTTTC-ATTCCC-CA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
10045 CACTTTTCAAAGCCCACACAAGTGGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
10074 CACCTTTCA
1 CACCTTTCA
10083 GTCCTCAAAG
Statistics
Matches: 78, Mismatches: 29, Indels: 24
0.60 0.22 0.18
Matches are distributed among these distances:
26 17 0.22
27 15 0.19
28 22 0.28
29 24 0.31
ACGTcount: A:0.28, C:0.31, G:0.19, T:0.22
Consensus pattern (29 bp):
CACCTTTCAAAGCCCACACAAGTGGGTGG
Found at i:10756 original size:1 final size:1
Alignment explanation
Indices: 10750--10789 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
10740 AAAGTGTTTG
***
10750 AAAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
10790 TTAAATGTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.93, C:0.00, G:0.03, T:0.05
Consensus pattern (1 bp):
A
Found at i:10772 original size:20 final size:20
Alignment explanation
Indices: 10747--10786 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
10737 GATAAAGTGT
10747 TTGAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAA
10767 TTGAAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAAA
10787 AAATTAAATG
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:0.85, C:0.00, G:0.05, T:0.10
Consensus pattern (20 bp):
TTGAAAAAAAAAAAAAAAAA
Found at i:10819 original size:21 final size:21
Alignment explanation
Indices: 10793--10849 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
10783 AAAAAAATTA
10793 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
10814 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
10835 AATGTATCGATACAT
1 AATGTATCGATACAT
10850 CCTACAAATG
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.37
Consensus pattern (21 bp):
AATGTATCGATACATTTGTAG
Found at i:10929 original size:19 final size:19
Alignment explanation
Indices: 10905--10972 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
10895 AATTCAACAA
10905 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
10924 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
10939 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
10956 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
10973 TTAGCTACTG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 28 0.65
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:10944 original size:13 final size:13
Alignment explanation
Indices: 10926--10950 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10916 ACATAAGTTT
10926 TGTATCGATACAA
1 TGTATCGATACAA
10939 TGTATCGATACA
1 TGTATCGATACA
10951 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:10948 original size:32 final size:32
Alignment explanation
Indices: 10907--10969 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
10897 TTCAACAATT
*
10907 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
10939 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
10970 TAATTAGCTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.35, C:0.13, G:0.16, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:11030 original size:13 final size:13
Alignment explanation
Indices: 11012--11037 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
11002 CATTTTTCTG
11012 TGTATCGATACAT
1 TGTATCGATACAT
11025 TGTATCGATACAT
1 TGTATCGATACAT
11038 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:11034 original size:33 final size:33
Alignment explanation
Indices: 10992--11058 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
10982 GCCAAGGAAA
***
10992 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
11025 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
11058 T
1 T
11059 TGGAAATTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.43
Consensus pattern (33 bp):
TGTATCGATACATGGATCTGTGTATCGATACAT
Found at i:13575 original size:28 final size:27
Alignment explanation
Indices: 13508--13580 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
13498 CTTCACAATC
* *
13508 GGGGACACTCCAACCCCGTTAATCATC
1 GGGGATACTCCAACCCCGTTAATCATA
*
13535 GGGGATACTCCAACCCCGTTATTTC-TGA
1 GGGGATACTCCAACCCCGTTA-ATCAT-A
13563 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
13581 ACTTTATTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
27 21 0.51
28 20 0.49
ACGTcount: A:0.23, C:0.34, G:0.22, T:0.21
Consensus pattern (27 bp):
GGGGATACTCCAACCCCGTTAATCATA
Found at i:13625 original size:51 final size:51
Alignment explanation
Indices: 13563--13733 Score: 198
Period size: 51 Copynumber: 3.3 Consensus size: 51
13553 TTATTTCTGA
* * *
13563 GGGGATACTCCAACCCCGACTTTATTTTCAAAATATCGATTTTTCATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
* * * * *
13614 GGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTT-TTC-ATAATC
** * *
13667 GGGGATACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAATACCAATTTTTCATAATC
*
13719 GAGGATACTCCAACC
1 GGGGATACTCCAACC
13734 TCGTTATTTC
Statistics
Matches: 97, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
51 36 0.37
52 18 0.19
53 32 0.33
54 11 0.11
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAATACCAATTTTTCATAATC
Found at i:13726 original size:105 final size:105
Alignment explanation
Indices: 13394--13733 Score: 273
Period size: 105 Copynumber: 3.2 Consensus size: 105
13384 CTCAATTCTC
* * * * ** *
13394 CACAATCGAGGATATTCCAACTCCGATTTTACTTTCAAAACATTAATTT-T-CTATAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
*
13457 TACTCCAACTCCGATTTTATTTCCAAAAAAAACACCAATTTCTT
66 TACTCCAACTCCGATTTTATTTCC---AAAAATACCAATTT-TT
* * * ** * * * * * *
13501 CACAATCGGGGACACTCCAACCCC-G-TTAATCATCGGGGATACTCCAA---CCCCGTTATTTCT
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTC---AAAACACCAATTTCTCCTTTA-ATC-
* * * * *
13561 GAGGGGATACTCCAACCCCGACTTTATTTTC-AAAATATCGATTTTT
61 --GGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
* * *
13607 CATAATCGGGGATACTCCAACCCCGGTTTTATTTTCACAACACCAATTTCTCCTTTAATCGGGGA
1 CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
*
13672 TACTCCAATTCCGATTTTATTTCCAAAAATACCAATTTTT
66 TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
13712 CACAATCGAGGATACTCCAACC
1 CACAATCGAGGATACTCCAACC
13734 TCGTTATTTC
Statistics
Matches: 174, Mismatches: 44, Indels: 32
0.70 0.18 0.13
Matches are distributed among these distances:
104 25 0.14
105 44 0.25
106 24 0.14
107 36 0.21
108 19 0.11
111 26 0.15
ACGTcount: A:0.30, C:0.27, G:0.12, T:0.31
Consensus pattern (105 bp):
CACAATCGAGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTCTCCTTTAATCGGGGA
TACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTT
Found at i:13752 original size:28 final size:28
Alignment explanation
Indices: 13716--13798 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 28
13706 ATTTTTCACA
*
13716 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
* *
13744 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCTCGTTATTTC
*
13772 --CGAAGGGAACACTCCAACCTCGTTATT
1 ATCG--GGG-ATACTCCAACCTCGTTATT
13799 ATCTCCAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
26 2 0.04
28 28 0.61
29 16 0.35
ACGTcount: A:0.25, C:0.31, G:0.17, T:0.27
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCTCGTTATTTC
Found at i:17991 original size:13 final size:13
Alignment explanation
Indices: 17973--17998 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
17963 CAATTATTTG
17973 TGTATCGATACAT
1 TGTATCGATACAT
17986 TGTATCGATACAT
1 TGTATCGATACAT
17999 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:18013 original size:32 final size:33
Alignment explanation
Indices: 17953--18016 Score: 96
Period size: 32 Copynumber: 2.0 Consensus size: 33
17943 TACAAGCCAA
*
17953 TGTATCGATACAATTATTTGTGTATCGATACAT
1 TGTATCGATACAATTATTGGTGTATCGATACAT
17986 TGTATCGATAC-A-TACTTGGTGTATCGATACA
1 TGTATCGATACAATTA-TTGGTGTATCGATACA
18017 AATTTGGCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
31 2 0.07
32 16 0.55
33 11 0.38
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATTATTGGTGTATCGATACAT
Found at i:18023 original size:19 final size:19
Alignment explanation
Indices: 17986--18023 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
17976 ATCGATACAT
*
17986 TGTATCGATACATACTTGG
1 TGTATCGATACAAACTTGG
*
18005 TGTATCGATACAAATTTGG
1 TGTATCGATACAAACTTGG
18024 CTACTGCCAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (19 bp):
TGTATCGATACAAACTTGG
Found at i:21381 original size:9 final size:10
Alignment explanation
Indices: 21327--21383 Score: 71
Period size: 10 Copynumber: 5.6 Consensus size: 10
21317 GTTCTAGGAA
*
21327 AAAAAAAAAG
1 AAAAAAATAG
*
21337 AAAAAAAAAG
1 AAAAAAATAG
21347 AAAAAAATAG
1 AAAAAAATAG
21357 AAGAAAATATAG
1 AA-AAAA-ATAG
21369 AAAAAAATA-
1 AAAAAAATAG
21378 AAAAAA
1 AAAAAA
21384 CTAGGCTAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
9 6 0.14
10 24 0.55
11 8 0.18
12 6 0.14
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (10 bp):
AAAAAAATAG
Found at i:22436 original size:157 final size:157
Alignment explanation
Indices: 22150--22759 Score: 839
Period size: 157 Copynumber: 3.9 Consensus size: 157
22140 ATTTTAACAA
* ** * *
22150 TAATTTTTTCTAATCTTTTATATTCCTATGGGCATTCGTAAAGGTATAAAAGACTTCAAAAATGT
1 TAATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTCAAAAATAT
*
22215 TTTCGTATCCTTTCGGGCTTCCATTAGGGTATGAAATAGTATTTTCAAAAATAAATAAAATTAAA
66 TTTCGTATCCTTTCGGGCTTCCATTAAGGTATGAAATAGTATTTTCAAAAATAAATAAAATTAAA
*
22280 TTGAATTAATACTTTCAGATTAAATTG
131 TTGAATTAATACTTTCAGATTAAATTT
* **
22307 TAATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGATATAAAAGATTTCAAAAACGT
1 TAATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTCAAAAATAT
* * * * * * *
22372 TTTTGTATCCTTTTGGG-TCTCTATTAGGGTACGAAATAATATTTTCGAAAATAAATAAAATTAA
66 TTTCGTATCCTTTCGGGCT-TCCATTAAGGTATGAAATAGTATTTTCAAAAATAAATAAAATTAA
**
22436 ATTGAATTAATTTTTTCAGATTAAATTT
130 ATTGAATTAATACTTTCAGATTAAATTT
* * *
22464 TAATTTTTTTTAATCTTTTATATTCCTATGGGCATCCATAGGGGTATAAAATATTTCAAAAATAT
1 TAATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTCAAAAATAT
* *
22529 TTTCGTATCCTTTCAGGCTTCCATTAAGGTATGAAATAGTATTTTTAAAAATAAATAAAATTAAA
66 TTTCGTATCCTTTCGGGCTTCCATTAAGGTATGAAATAGTATTTTCAAAAATAAATAAAATTAAA
*
22594 TTGAATTAATACTTT-TGAATTAAATTT
131 TTGAATTAATACTTTCAG-ATTAAATTT
*** *
22621 TAATTTTTTCTAATCTTTTATATTCCTATAACCATTCGTAGGGGTATAAAAGATTTCAAAAATAT
1 TAATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTCAAAAATAT
* * * * * * *
22686 TTTCGTATCCTTTCGAGCTTCTATGAAGGTA-GATATTGTATTTTCGAGAATAAATAAAATTAAA
66 TTTCGTATCCTTTCGGGCTTCCATTAAGGTATGAAATAGTATTTTCAAAAATAAATAAAATTAAA
**
22750 CCGAATTAAT
131 TTGAATTAAT
22760 GTTCTCGAGA
Statistics
Matches: 399, Mismatches: 51, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
156 38 0.10
157 360 0.90
158 1 0.00
ACGTcount: A:0.36, C:0.11, G:0.12, T:0.42
Consensus pattern (157 bp):
TAATTTTTTCTAATCTTTTATATTCCTATGGGCATCCGTAGGGGTATAAAAGATTTCAAAAATAT
TTTCGTATCCTTTCGGGCTTCCATTAAGGTATGAAATAGTATTTTCAAAAATAAATAAAATTAAA
TTGAATTAATACTTTCAGATTAAATTT
Found at i:27890 original size:33 final size:32
Alignment explanation
Indices: 27853--27914 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 32
27843 TGTATTTACT
27853 ATTAC-AAA-AAAATAACAATCAATATTTTAACAA
1 ATTACAAAATAAAATAA-AAT-AA-ATTTTAACAA
27886 ATTACAAAATAAAATAAAATAAATTTTAA
1 ATTACAAAATAAAATAAAATAAATTTTAA
27915 AACTATCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
32 7 0.26
33 7 0.26
34 6 0.22
35 7 0.26
ACGTcount: A:0.63, C:0.08, G:0.00, T:0.29
Consensus pattern (32 bp):
ATTACAAAATAAAATAAAATAAATTTTAACAA
Found at i:28993 original size:20 final size:19
Alignment explanation
Indices: 28950--29002 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
28940 ACATTATGCT
* *
28950 TTGTATCGATACATGCTCA
1 TTGTATCAATACATACTCA
*
28969 TTGTATCAATATATACTCAA
1 TTGTATCAATACATACTC-A
*
28989 TTGTATCGATACAT
1 TTGTATCAATACAT
29003 GAAACTGGTA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.54
20 13 0.46
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (19 bp):
TTGTATCAATACATACTCA
Found at i:32760 original size:68 final size:68
Alignment explanation
Indices: 32688--32818 Score: 181
Period size: 68 Copynumber: 1.9 Consensus size: 68
32678 TTTTTTAGTT
* * * ** *
32688 TAGGGTTTAGAGTAACCATGTTTTAGTTTGGGTGTCGTTCAAATTAACCCGTTTGATTTTTGGGA
1 TAGGGTTTAGAGTAACCATATTCTAGTTTGGGTATCGTTCAAAGCAACCCATTTGATTTTTGGGA
32753 ACG
66 ACG
* * *
32756 TAGGGTTTAGGGTAACCTTATTCTAGTTTGGGTATCGTTTAAAGCAACCCATTTGATTTTTGG
1 TAGGGTTTAGAGTAACCATATTCTAGTTTGGGTATCGTTCAAAGCAACCCATTTGATTTTTGG
32819 ATATGTGATT
Statistics
Matches: 54, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
68 54 1.00
ACGTcount: A:0.22, C:0.12, G:0.25, T:0.40
Consensus pattern (68 bp):
TAGGGTTTAGAGTAACCATATTCTAGTTTGGGTATCGTTCAAAGCAACCCATTTGATTTTTGGGA
ACG
Found at i:37498 original size:16 final size:16
Alignment explanation
Indices: 37479--37512 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
37469 AAATTTTAAT
37479 TAATTATATTAATAAA
1 TAATTATATTAATAAA
37495 TAATTATATTAATAAA
1 TAATTATATTAATAAA
37511 TA
1 TA
37513 TTAAGTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATTATATTAATAAA
Found at i:38481 original size:15 final size:15
Alignment explanation
Indices: 38453--38491 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
38443 AGGTAAACAG
* *
38453 GTGGTCGATGAACGA
1 GTGGTGGATAAACGA
38468 GTGGTGGATAAACGA
1 GTGGTGGATAAACGA
38483 GTGGTGGAT
1 GTGGTGGAT
38492 GAATAGGATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.26, C:0.08, G:0.44, T:0.23
Consensus pattern (15 bp):
GTGGTGGATAAACGA
Found at i:41297 original size:21 final size:21
Alignment explanation
Indices: 41271--41315 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
41261 TGAAAAAGTC
*
41271 ACATTTTTTAAATGTATCGAT
1 ACATTTCTTAAATGTATCGAT
*
41292 ACATTTCTTGAATGTATCGAT
1 ACATTTCTTAAATGTATCGAT
41313 ACA
1 ACA
41316 AAGTCCCAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.42
Consensus pattern (21 bp):
ACATTTCTTAAATGTATCGAT
Found at i:45605 original size:22 final size:22
Alignment explanation
Indices: 45548--45609 Score: 63
Period size: 24 Copynumber: 2.7 Consensus size: 22
45538 AGTAATATAA
*
45548 ATATACAA-ATATATTAAAATTT
1 ATATA-AATATATAATAAAATTT
* *
45570 TTATAATTTAATATAATAAAATTT
1 ATATAA-AT-ATATAATAAAATTT
45594 ATATAAATATATAATA
1 ATATAAATATATAATA
45610 TTTTAAATAC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
21 1 0.03
22 12 0.38
23 1 0.03
24 18 0.56
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATATAAATATATAATAAAATTT
Found at i:46734 original size:164 final size:162
Alignment explanation
Indices: 46542--46855 Score: 452
Period size: 164 Copynumber: 1.9 Consensus size: 162
46532 TAATAACAAA
* *
46542 TATATTAAAATTTAATAAATAGAAAAGTAATGAATTAAATTGTAATTTACATTACAAAGACTTGC
1 TATATTAAAATTTAATAAATAAAAAAGTAATGAATTAAATTGTAATTTACATAACAAAGACTTGC
* *
46607 TTATC-GA-ATATTTTGTGGTTGAAATATTAAAAAAGCTTTGAATTATTTTTTAAATAAATACTT
66 TTATCAGACACATTTTGTGGTTAAAATATTAAAAAAGCTTTGAATTATTTTTTAAATAAATA-TT
*
46670 ATATTTTTATTATATTGAAATAAGAAAAATTGTTT
130 -TA-TATTATTATATTGAAATAAGAAAAATTGTTT
* * *
46705 TATATTAAAATTTTAATAAATAAAAAAGTAATGAATTAAATTGTGATTTATATAATAAAGACTTG
1 TATATTAAAA-TTTAATAAATAAAAAAGTAATGAATTAAATTGTAATTTACATAACAAAGACTTG
* * ** *
46770 TTTATCATACACATTTTGTGGTTAAAATATTATTAAAGTTTTGAATTATTTTTTAAATAAATATT
65 CTTATCAGACACATTTTGTGGTTAAAATATTAAAAAAGCTTTGAATTATTTTTTAAATAAATATT
*
46835 TATATTATTGTATTGAAATAA
130 TATATTATTATATTGAAATAA
46856 ATTTTATTTT
Statistics
Matches: 134, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
163 27 0.20
164 56 0.42
165 3 0.02
166 48 0.36
ACGTcount: A:0.44, C:0.04, G:0.09, T:0.44
Consensus pattern (162 bp):
TATATTAAAATTTAATAAATAAAAAAGTAATGAATTAAATTGTAATTTACATAACAAAGACTTGC
TTATCAGACACATTTTGTGGTTAAAATATTAAAAAAGCTTTGAATTATTTTTTAAATAAATATTT
ATATTATTATATTGAAATAAGAAAAATTGTTT
Found at i:47269 original size:74 final size:74
Alignment explanation
Indices: 47173--47344 Score: 301
Period size: 74 Copynumber: 2.3 Consensus size: 74
47163 TCGCAAAGCA
*
47173 AATCCATCTC-TCAACTCAGGTTTGCTTCCCTGCATTACCATTTCGCTCAAGTTTTCAAGATCAG
1 AATCCATCTCTTTAACTCAGGTTTGCTTCCCTGCATTACCATTTCGCTCAAGTTTTCAAGATCAG
47237 AGGCCACGC
66 AGGCCACGC
* * *
47246 AATCCATCTCTTTAACTCAGGTTTGCTTCCCTGTATTACCATTTCGTTGAAGTTTTCAAGATCAG
1 AATCCATCTCTTTAACTCAGGTTTGCTTCCCTGCATTACCATTTCGCTCAAGTTTTCAAGATCAG
47311 AGGCCACGC
66 AGGCCACGC
47320 AATCCATCTCTTTAACTCAGGTTTG
1 AATCCATCTCTTTAACTCAGGTTTG
47345 TTTCATGTCC
Statistics
Matches: 94, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
73 10 0.11
74 84 0.89
ACGTcount: A:0.23, C:0.28, G:0.15, T:0.34
Consensus pattern (74 bp):
AATCCATCTCTTTAACTCAGGTTTGCTTCCCTGCATTACCATTTCGCTCAAGTTTTCAAGATCAG
AGGCCACGC
Found at i:47579 original size:68 final size:68
Alignment explanation
Indices: 47507--47637 Score: 201
Period size: 68 Copynumber: 1.9 Consensus size: 68
47497 TTTTATAGTT
* * * * *
47507 TAGGGTTTAGAGTAACCTTGTTTTAGTTTGGGTGTCGTTCT-AATTAACCCATTTGATTTTTGGG
1 TAGGGTTTAGAGTAACCTTATTCTAGTTTGGGTGTCGTT-TAAAGTAACCCATTTAAATTTTGGG
47571 AATG
65 AATG
47575 TAGGGTTTAGAGTAACCTTATTCTAGTTTGGGTGTCGTTTAAAGTAACCCATTTAAATTTTGG
1 TAGGGTTTAGAGTAACCTTATTCTAGTTTGGGTGTCGTTTAAAGTAACCCATTTAAATTTTGG
47638 ATATGTGATT
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
67 1 0.02
68 56 0.98
ACGTcount: A:0.23, C:0.11, G:0.24, T:0.43
Consensus pattern (68 bp):
TAGGGTTTAGAGTAACCTTATTCTAGTTTGGGTGTCGTTTAAAGTAACCCATTTAAATTTTGGGA
ATG
Found at i:50559 original size:30 final size:30
Alignment explanation
Indices: 50525--50584 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
50515 TACGTTATCC
*
50525 GGACTAAGAGGTTAAGTGTATGATGAGTAT
1 GGACTAAAAGGTTAAGTGTATGATGAGTAT
50555 GGACTAAAAGGTTAAGTGTATGATGAGTAT
1 GGACTAAAAGGTTAAGTGTATGATGAGTAT
50585 ATATCAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.03, G:0.32, T:0.30
Consensus pattern (30 bp):
GGACTAAAAGGTTAAGTGTATGATGAGTAT
Found at i:51815 original size:16 final size:16
Alignment explanation
Indices: 51773--51816 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
51763 GCTTTGAAAT
51773 AAATA-AAATTAATTA
1 AAATATAAATTAATTA
*
51788 AAATATATATTAATTA
1 AAATATAAATTAATTA
*
51804 AAATTTAAATTAA
1 AAATATAAATTAA
51817 ACATAAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
15 5 0.20
16 20 0.80
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATAAATTAATTA
Found at i:52578 original size:2 final size:2
Alignment explanation
Indices: 52571--52598 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
52561 CACCTAATTT
52571 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
52599 ATGTTCATTT
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:53365 original size:31 final size:28
Alignment explanation
Indices: 53307--53383 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 28
53297 ATTTAAAATT
53307 TTATTTAAATATAAATAAAAAATAAAAAA
1 TTATTTAAATAT-AATAAAAAATAAAAAA
53336 TTATTTAAATATAATAAAAATATAAAAAAAA
1 TTATTTAAATATAATAAAAA-AT--AAAAAA
* *
53367 TAATTTATATATAATAA
1 TTATTTAAATATAATAA
53384 TTTTTTACAT
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
28 8 0.19
29 14 0.33
31 21 0.49
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (28 bp):
TTATTTAAATATAATAAAAAATAAAAAA
Found at i:55495 original size:19 final size:19
Alignment explanation
Indices: 55471--55508 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55461 TAACTAGAAG
55471 ACTCTAGGTGAAACATTTA
1 ACTCTAGGTGAAACATTTA
55490 ACTCTAGGTGAAACATTTA
1 ACTCTAGGTGAAACATTTA
55509 CTAATAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.32
Consensus pattern (19 bp):
ACTCTAGGTGAAACATTTA
Found at i:56886 original size:2 final size:2
Alignment explanation
Indices: 56879--56920 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
56869 GATGAAGATG
56879 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56920 T
1 T
56921 TGGCATATGT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:58081 original size:165 final size:165
Alignment explanation
Indices: 57894--58220 Score: 618
Period size: 165 Copynumber: 2.0 Consensus size: 165
57884 ACCCAATGGT
57894 TGAGCTTGGCTAGATATTTCCAATATCCAAACTGATAACGTCACCATTTCTAAAAGTATCATATT
1 TGAGCTTGGCTAGATATTTCCAATATCCAAACTGATAACGTCACCATTTCTAAAAGTATCATATT
57959 ATCACCACATATCCTACATACATATATGTATGACTGGCTGCCTTATTGGATCCCCAACAAAATAT
66 ATCACCACATATCCTACATACATATATGTATGACTGGCTGCCTTATTGGATCCCCAACAAAATAT
* *
58024 AGGTAAGCTTACAGAAACTCCAAGGATGTAATAGC
131 AGATAAGCTTACAGAAACTCCAAAGATGTAATAGC
*
58059 TGAGCTTGGCTAGATATTTCCAATATCCAAACTGATAACGTCACCATTTCTAAAATTATCATATT
1 TGAGCTTGGCTAGATATTTCCAATATCCAAACTGATAACGTCACCATTTCTAAAAGTATCATATT
*
58124 ATCACCACATATTCTACATACATATATGTATGACTGGCTGCCTTATTGGATCCCCAACAAAATAT
66 ATCACCACATATCCTACATACATATATGTATGACTGGCTGCCTTATTGGATCCCCAACAAAATAT
58189 AGATAAGCTTACAGAAACTCCAAAGATGTAAT
131 AGATAAGCTTACAGAAACTCCAAAGATGTAAT
58221 GAATGTGACC
Statistics
Matches: 158, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
165 158 1.00
ACGTcount: A:0.36, C:0.21, G:0.13, T:0.30
Consensus pattern (165 bp):
TGAGCTTGGCTAGATATTTCCAATATCCAAACTGATAACGTCACCATTTCTAAAAGTATCATATT
ATCACCACATATCCTACATACATATATGTATGACTGGCTGCCTTATTGGATCCCCAACAAAATAT
AGATAAGCTTACAGAAACTCCAAAGATGTAATAGC
Found at i:61897 original size:12 final size:11
Alignment explanation
Indices: 61875--61950 Score: 52
Period size: 12 Copynumber: 6.9 Consensus size: 11
61865 AAAGAAAGAA
*
61875 GAGAGAGGAGG
1 GAGATAGGAGG
61886 GATGATAGGAGG
1 GA-GATAGGAGG
*
61898 AGAGACAGGA--
1 -GAGATAGGAGG
*
61908 GAGATAGTA--
1 GAGATAGGAGG
61917 GAGATAGGAGG
1 GAGATAGGAGG
61928 GATGATAGGAGG
1 GA-GATAGGAGG
*
61940 AGAGACAGGAG
1 -GAGATAGGAG
61951 AGATAATAGA
Statistics
Matches: 53, Mismatches: 6, Indels: 11
0.76 0.09 0.16
Matches are distributed among these distances:
9 15 0.28
11 4 0.08
12 30 0.57
13 4 0.08
ACGTcount: A:0.39, C:0.03, G:0.49, T:0.09
Consensus pattern (11 bp):
GAGATAGGAGG
Found at i:61907 original size:24 final size:24
Alignment explanation
Indices: 61874--61959 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
61864 AAAAGAAAGA
*
61874 AGAGAGAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
*
61898 AGAGACAGGA--GA-GAT---AGT
1 AGAGACAGGAGGGATGATAGGAGG
*
61916 AGAGATAGGAGGGATGATAGGAGG
1 AGAGACAGGAGGGATGATAGGAGG
* *
61940 AGAGACAGGAGAGATAATAG
1 AGAGACAGGAGGGATGATAG
61960 AGAGAGGAGG
Statistics
Matches: 49, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.22
20 2 0.04
21 6 0.12
22 2 0.04
24 28 0.57
ACGTcount: A:0.42, C:0.02, G:0.45, T:0.10
Consensus pattern (24 bp):
AGAGACAGGAGGGATGATAGGAGG
Found at i:61933 original size:42 final size:42
Alignment explanation
Indices: 61874--61983 Score: 193
Period size: 42 Copynumber: 2.6 Consensus size: 42
61864 AAAAGAAAGA
*
61874 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAGT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
61916 AGAGATAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
1 AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
*
61958 AGAGAGAGGAGGGATGACAGGAGGAG
1 AGAGAGAGGAGGGATGATAGGAGGAG
61984 GAGAGAAGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 64 1.00
ACGTcount: A:0.41, C:0.03, G:0.47, T:0.09
Consensus pattern (42 bp):
AGAGAGAGGAGGGATGATAGGAGGAGAGACAGGAGAGATAAT
Found at i:62604 original size:11 final size:12
Alignment explanation
Indices: 62577--62609 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
62567 TACAACTCTA
*
62577 AAGGATGGAAGG
1 AAGGAGGGAAGG
62589 AAGGAGGGAA-G
1 AAGGAGGGAAGG
62600 AAGGAGGGAA
1 AAGGAGGGAA
62610 CTTCAGCGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 11 0.55
12 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.03
Consensus pattern (12 bp):
AAGGAGGGAAGG
Found at i:69902 original size:12 final size:13
Alignment explanation
Indices: 69885--69913 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
69875 CCAAAAACAT
69885 AAAAGGA-AAAAA
1 AAAAGGAGAAAAA
69897 AAAAGGAGAAAAA
1 AAAAGGAGAAAAA
69910 AAAA
1 AAAA
69914 AAGAAACAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAGGAGAAAAA
Found at i:70842 original size:11 final size:11
Alignment explanation
Indices: 70826--70859 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
70816 TTAATAATTA
70826 TATATTTATAT
1 TATATTTATAT
70837 TATATTT-TAT
1 TATATTTATAT
*
70847 TATTTTTATAT
1 TATATTTATAT
70858 TA
1 TA
70860 ATTATGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TATATTTATAT
Found at i:70849 original size:15 final size:15
Alignment explanation
Indices: 70835--70903 Score: 59
Period size: 14 Copynumber: 4.3 Consensus size: 15
70825 ATATATTTAT
*
70835 ATTATATTTTATTATT
1 ATTATATTTTATTA-A
*
70851 TTTATATTAATTATGTAA
1 ATTATATT--TTAT-TAA
70869 ATATATATTTTATTAA
1 AT-TATATTTTATTAA
*
70885 A-TATTTTTTATTAA
1 ATTATATTTTATTAA
70899 ATTAT
1 ATTAT
70904 TATGATACAG
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
14 13 0.30
15 3 0.07
16 11 0.25
17 4 0.09
18 5 0.11
19 8 0.18
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (15 bp):
ATTATATTTTATTAA
Found at i:70893 original size:14 final size:16
Alignment explanation
Indices: 70837--70900 Score: 60
Period size: 16 Copynumber: 3.9 Consensus size: 16
70827 ATATTTATAT
** *
70837 TATATTTTATTATTTT
1 TATATTTTATTAAATA
70853 TATATTAATTATGTAAATA
1 TATATT--TTAT-TAAATA
70872 TATATTTTATTAAATA
1 TATATTTTATTAAATA
70888 T-T-TTTTATTAAAT
1 TATATTTTATTAAAT
70901 TATTATGATA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
14 11 0.26
15 1 0.02
16 13 0.31
17 4 0.10
18 4 0.10
19 9 0.21
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (16 bp):
TATATTTTATTAAATA
Found at i:71027 original size:21 final size:20
Alignment explanation
Indices: 71001--71040 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
70991 TTAAAAAGAA
71001 ATATATAAATTAATTTATATT
1 ATATATAAATTAA-TTATATT
*
71022 ATATATATATTAATTATAT
1 ATATATAAATTAATTATAT
71041 GATGTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
ATATATAAATTAATTATATT
Found at i:71039 original size:15 final size:15
Alignment explanation
Indices: 71019--71070 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
71009 ATTAATTTAT
71019 ATTATATATATATTA
1 ATTATATATATATTA
* *
71034 ATTATATGATGT-TTG
1 ATTATAT-ATATATTA
*
71049 TTTATATATATATTA
1 ATTATATATATATTA
71064 ATTATAT
1 ATTATAT
71071 TGATGTTTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
14 3 0.10
15 23 0.79
16 3 0.10
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (15 bp):
ATTATATATATATTA
Found at i:71054 original size:30 final size:31
Alignment explanation
Indices: 71020--71079 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 31
71010 TTAATTTATA
71020 TTATATATATATTAATTATA-TGATGTTTGT
1 TTATATATATATTAATTATATTGATGTTTGT
71050 TTATATATATATTAATTATATTGATGTTTG
1 TTATATATATATTAATTATATTGATGTTTG
71080 AGGGATATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 20 0.69
31 9 0.31
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (31 bp):
TTATATATATATTAATTATATTGATGTTTGT
Found at i:71286 original size:14 final size:15
Alignment explanation
Indices: 71263--71293 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
71253 AAGTTTTTAT
71263 TTTAATTTTTTAATA
1 TTTAATTTTTTAATA
71278 TTTAA-TTTTTAATA
1 TTTAATTTTTTAATA
71292 TT
1 TT
71294 AAAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTTAATTTTTTAATA
Found at i:71498 original size:12 final size:12
Alignment explanation
Indices: 71483--71519 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
71473 AATATTAATA
71483 TAAAAATATTTT
1 TAAAAATATTTT
71495 T--AAATATTTT
1 TAAAAATATTTT
*
71505 TAATAATATTTT
1 TAAAAATATTTT
71517 TAA
1 TAA
71520 TTTTTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
10 10 0.45
12 12 0.55
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TAAAAATATTTT
Found at i:71501 original size:10 final size:10
Alignment explanation
Indices: 71486--71528 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
71476 ATTAATATAA
71486 AAATATTTTT
1 AAATATTTTT
71496 AAATATTTTT
1 AAATATTTTT
71506 AATAATATTTTT
1 -A-AATATTTTT
*
71518 -AATTTTTTT
1 AAATATTTTT
71527 AA
1 AA
71529 TTGAATCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
9 8 0.28
10 11 0.38
11 1 0.03
12 9 0.31
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
AAATATTTTT
Found at i:71515 original size:22 final size:21
Alignment explanation
Indices: 71487--71529 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
71477 TTAATATAAA
71487 AATATTTTTAAATATTTTTAAT
1 AATATTTTT-AATATTTTTAAT
*
71509 AATATTTTTAATTTTTTTAAT
1 AATATTTTTAATATTTTTAAT
71530 TGAATCATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AATATTTTTAATATTTTTAAT
Found at i:71520 original size:12 final size:12
Alignment explanation
Indices: 71487--71520 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
71477 TTAATATAAA
71487 AATATTTTT-A-
1 AATATTTTTAAT
71497 AATATTTTTAAT
1 AATATTTTTAAT
71509 AATATTTTTAAT
1 AATATTTTTAAT
71521 TTTTTTAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 9 0.41
11 1 0.05
12 12 0.55
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (12 bp):
AATATTTTTAAT
Found at i:71982 original size:21 final size:22
Alignment explanation
Indices: 71949--71993 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
71939 ATTTCTATTT
71949 TAAATATTATTAAATATAA-TAA
1 TAAATATTATT-AATATAATTAA
*
71971 TAAA-ATTCTTAATATAATTAA
1 TAAATATTATTAATATAATTAA
71992 TA
1 TA
71994 TTACTTATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.33
21 10 0.48
22 4 0.19
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (22 bp):
TAAATATTATTAATATAATTAA
Found at i:73689 original size:2 final size:2
Alignment explanation
Indices: 73682--73722 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
73672 GAATTACCAG
* * *
73682 TA TA TA TA TA TG TG TA TA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
73723 GCTTTGCTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:73701 original size:12 final size:12
Alignment explanation
Indices: 73681--73722 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
73671 AGAATTACCA
73681 GTATATATATAT
1 GTATATATATAT
*
73693 GTGTATATATA-
1 GTATATATATAT
73704 -TATATATATAT
1 GTATATATATAT
73715 GTATATAT
1 GTATATAT
73723 GCTTTGCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 9 0.35
12 17 0.65
ACGTcount: A:0.40, C:0.00, G:0.10, T:0.50
Consensus pattern (12 bp):
GTATATATATAT
Found at i:75092 original size:3 final size:3
Alignment explanation
Indices: 75084--75109 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
75074 ATATATATAG
75084 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
75110 AGTACCATGA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:78093 original size:31 final size:30
Alignment explanation
Indices: 78044--78113 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 30
78034 TGGTGGAATT
* * * *
78044 TTTTTTTTTTAAATCTTCAATGGAGAAATA
1 TTTTCTTTTTAAAACTTCAATGAAAAAATA
*
78074 TTTTCTTTTTAAGAACTTCAGTGAAAAAATA
1 TTTTCTTTTTAA-AACTTCAATGAAAAAATA
78105 TTTCTCTTT
1 TTT-TCTTT
78114 AGATTGATGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 11 0.33
31 17 0.52
32 5 0.15
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (30 bp):
TTTTCTTTTTAAAACTTCAATGAAAAAATA
Found at i:78390 original size:20 final size:20
Alignment explanation
Indices: 78367--78404 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
78357 TGGCTTATGC
*
78367 CCATTTCATTTCATTTTATT
1 CCATTCCATTTCATTTTATT
*
78387 CCATTCCATTTTATTTTA
1 CCATTCCATTTCATTTTA
78405 CCTTTACATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.58
Consensus pattern (20 bp):
CCATTCCATTTCATTTTATT
Found at i:79010 original size:18 final size:18
Alignment explanation
Indices: 78984--79020 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
78974 ATAAATTGTG
*
78984 TATTAATTTTTATAAAAA
1 TATTAATTTATATAAAAA
*
79002 TATTTATTTATATAAAAA
1 TATTAATTTATATAAAAA
79020 T
1 T
79021 TCTTACCGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTAATTTATATAAAAA
Found at i:79325 original size:21 final size:20
Alignment explanation
Indices: 79279--79325 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 20
79269 TAAAATATAA
*
79279 AAAAAATACTTTGATATGAT
1 AAAAAATACTTTGAAATGAT
79299 ATAAAAATA-TTGTGAAATTGAT
1 A-AAAAATACTT-TGAAA-TGAT
79321 AAAAA
1 AAAAA
79326 TTGATGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 3 0.13
21 15 0.65
22 5 0.22
ACGTcount: A:0.55, C:0.02, G:0.11, T:0.32
Consensus pattern (20 bp):
AAAAAATACTTTGAAATGAT
Found at i:79796 original size:46 final size:43
Alignment explanation
Indices: 79706--79829 Score: 153
Period size: 46 Copynumber: 2.8 Consensus size: 43
79696 ATTTTACATC
* *
79706 TAATTAAATTAAATTAATTTTAAAAAT-AA-AAAAAATTATTTT
1 TAATTAAATTAAATTAA-TTAAAAAATAAATAAAAAATTATCTT
79748 TAATTAAATTAAATTAATTAAAAAATAAATATAAAAATTTTATCTT
1 TAATTAAATTAAATTAATTAAAAAATAAATA-AAAAA--TTATCTT
* * *
79794 TAATTAAATTAAATTAATTGAGACATAAATAAAAAA
1 TAATTAAATTAAATTAATTAAAAAATAAATAAAAAA
79830 GATAAGTTAT
Statistics
Matches: 72, Mismatches: 5, Indels: 7
0.86 0.06 0.08
Matches are distributed among these distances:
41 8 0.11
42 19 0.26
43 1 0.01
44 5 0.07
45 5 0.07
46 34 0.47
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (43 bp):
TAATTAAATTAAATTAATTAAAAAATAAATAAAAAATTATCTT
Found at i:80678 original size:23 final size:23
Alignment explanation
Indices: 80638--80683 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
80628 AATCTCACTA
*
80638 TTTATTTATTTATTTATAAAAAT
1 TTTATTTATTTATATATAAAAAT
*
80661 TTTATTT-TTTATAATATATAAAT
1 TTTATTTATTTAT-ATATAAAAAT
80684 CCAATTCATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 5 0.25
23 15 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TTTATTTATTTATATATAAAAAT
Found at i:80769 original size:12 final size:12
Alignment explanation
Indices: 80750--80785 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
80740 AATATAAAAT
80750 AAAA-TAATATA
1 AAAATTAATATA
80761 AAAATTAATATA
1 AAAATTAATATA
80773 AAAATT-ATATA
1 AAAATTAATATA
80784 AA
1 AA
80786 TATATAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.46
12 13 0.54
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAAATTAATATA
Found at i:80784 original size:28 final size:27
Alignment explanation
Indices: 80740--80811 Score: 76
Period size: 28 Copynumber: 2.6 Consensus size: 27
80730 CATGATATAG
* *
80740 AATAT-AAAATAAAATAATATAAAAATT
1 AATATAAAAATTATATAATATAAAAA-T
*
80767 AATATAAAAATTATATAAATATATAAAT
1 AATATAAAAATTATAT-AATATAAAAAT
80795 -ATATTAAAAATTATATA
1 AATA-TAAAAATTATATA
80812 TCACAAATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
27 9 0.23
28 21 0.54
29 9 0.23
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (27 bp):
AATATAAAAATTATATAATATAAAAAT
Found at i:80791 original size:8 final size:8
Alignment explanation
Indices: 80741--80798 Score: 52
Period size: 8 Copynumber: 7.5 Consensus size: 8
80731 ATGATATAGA
80741 ATATAAA-
1 ATATAAAT
80748 ATA-AAAT
1 ATATAAAT
80755 AATATAAA-
1 -ATATAAAT
*
80763 A-ATTAAT
1 ATATAAAT
*
80770 ATAAAAATT
1 ATATAAA-T
80779 ATATAAAT
1 ATATAAAT
80787 ATATAAAT
1 ATATAAAT
80795 ATAT
1 ATAT
80799 TAAAAATTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
6 7 0.17
7 5 0.12
8 19 0.46
9 10 0.24
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (8 bp):
ATATAAAT
Found at i:86590 original size:19 final size:19
Alignment explanation
Indices: 86568--86606 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
86558 TAAAAATTAC
*
86568 TTAATGATT-TTTTATTTAA
1 TTAATAATTATTTT-TTTAA
86587 TTAATAATTATTTTTTTAA
1 TTAATAATTATTTTTTTAA
86606 T
1 T
86607 ATTAAATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (19 bp):
TTAATAATTATTTTTTTAA
Found at i:97870 original size:54 final size:53
Alignment explanation
Indices: 97802--97961 Score: 223
Period size: 54 Copynumber: 3.0 Consensus size: 53
97792 CCCAGATTCA
*
97802 AACACTAAGTGATGCCAAGTCATTCAAACTCGGATTGCCACCAGAGTGACCCCT
1 AACACTAAGTGATGCCAAGTCA-TCAAACTCGGATCGCCACCAGAGTGACCCCT
* * *
97856 ACCACTAAGTGATGCCAAGTCACCAAAACTCGGATCGCCACCAGAGTGATCCCT
1 AACACTAAGTGATGCCAAGTCATC-AAACTCGGATCGCCACCAGAGTGACCCCT
* *
97910 AACA-TAAAGTGATGCCAAGTCACTCAAACTCGGATCGCCACCAAAGCGACCC
1 AACACT-AAGTGATGCCAAGTCA-TCAAACTCGGATCGCCACCAGAGTGACCC
97962 TTATCCAAAC
Statistics
Matches: 94, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
53 2 0.02
54 91 0.97
55 1 0.01
ACGTcount: A:0.33, C:0.32, G:0.18, T:0.17
Consensus pattern (53 bp):
AACACTAAGTGATGCCAAGTCATCAAACTCGGATCGCCACCAGAGTGACCCCT
Found at i:99237 original size:60 final size:60
Alignment explanation
Indices: 99144--99270 Score: 218
Period size: 60 Copynumber: 2.1 Consensus size: 60
99134 ACTGTAGAGT
* *
99144 CAGACACAATAAACCCCTAAGTAAAAACCAAACAGAAATGCGACTAATACTTACCTCCAC
1 CAGACACAATAAACCCCTAAGTAAAAACCAAACAAAAAGGCGACTAATACTTACCTCCAC
* *
99204 CAGACACAATAAACCCCTAAGTAAAAACCAAACAAAAAGGTGACTAATACTTACCTCCGC
1 CAGACACAATAAACCCCTAAGTAAAAACCAAACAAAAAGGCGACTAATACTTACCTCCAC
99264 CAGACAC
1 CAGACAC
99271 GTCATGCCTG
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.46, C:0.30, G:0.09, T:0.14
Consensus pattern (60 bp):
CAGACACAATAAACCCCTAAGTAAAAACCAAACAAAAAGGCGACTAATACTTACCTCCAC
Found at i:103363 original size:38 final size:38
Alignment explanation
Indices: 103321--103398 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
103311 GTCCCATTAG
103321 TTGCTATTTGATCTTGACACTGATCAGGCCATTCTAGC
1 TTGCTATTTGATCTTGACACTGATCAGGCCATTCTAGC
* *
103359 TTGCTATTTGATCTTGACAGTGATCATGCCATTCTAGC
1 TTGCTATTTGATCTTGACACTGATCAGGCCATTCTAGC
103397 TT
1 TT
103399 ATCTGGACTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.40
Consensus pattern (38 bp):
TTGCTATTTGATCTTGACACTGATCAGGCCATTCTAGC
Found at i:106434 original size:24 final size:24
Alignment explanation
Indices: 106407--106476 Score: 77
Period size: 30 Copynumber: 2.7 Consensus size: 24
106397 TAGACATAAC
106407 CAAAGGCCTTGTGTTGAACAATGG
1 CAAAGGCCTTGTGTTGAACAATGG
*
106431 CAAAGGCATTGTTCATTGATTGAACAATGG
1 CAAAGGCCTTG-----TG-TTGAACAATGG
106461 CAAAGGCCTTGTGTTG
1 CAAAGGCCTTGTGTTG
106477 CGTATACTCT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
24 13 0.34
25 2 0.05
29 2 0.05
30 21 0.55
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (24 bp):
CAAAGGCCTTGTGTTGAACAATGG
Found at i:111158 original size:15 final size:15
Alignment explanation
Indices: 111138--111171 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
111128 ATTTTTAATA
111138 AATAAAAAATAATTC
1 AATAAAAAATAATTC
* *
111153 AATAAAATATAATTT
1 AATAAAAAATAATTC
111168 AATA
1 AATA
111172 TGCTTAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAAAAATAATTC
Found at i:111884 original size:29 final size:29
Alignment explanation
Indices: 111833--111909 Score: 93
Period size: 29 Copynumber: 2.6 Consensus size: 29
111823 CTACTAATAT
*
111833 ATTTGATATTTTAAAATAATTTTTTATACTTTT
1 ATTT-ATATTTT--AATAATTTTTTAT-CTTTA
111866 A-TTATATTTTAATAATTTTTTATCTTTA
1 ATTTATATTTTAATAATTTTTTATCTTTA
*
111894 ATTTATATTTAAATAA
1 ATTTATATTTTAATAA
111910 AATCTTATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
28 5 0.12
29 26 0.63
31 7 0.17
32 2 0.05
33 1 0.02
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (29 bp):
ATTTATATTTTAATAATTTTTTATCTTTA
Found at i:112151 original size:23 final size:22
Alignment explanation
Indices: 112116--112161 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 22
112106 TAATTATACG
112116 ATATAAAAATAAT-TAAAATATA
1 ATATAAAAATAATGT-AAATATA
112138 ATATAAAAATTAATGTAAATATA
1 ATATAAAAA-TAATGTAAATATA
112161 A
1 A
112162 ACGAACACGT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 12 0.55
24 1 0.05
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
ATATAAAAATAATGTAAATATA
Found at i:112319 original size:24 final size:24
Alignment explanation
Indices: 112274--112319 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
112264 ACACGAATAT
*
112274 AATATAAATATATGAATGTATTTA
1 AATATAAATATACGAATGTATTTA
*
112298 AATATATATAATACGAAT-TATT
1 AATATAAAT-ATACGAATGTATT
112320 AATTTATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (24 bp):
AATATAAATATACGAATGTATTTA
Found at i:112419 original size:114 final size:113
Alignment explanation
Indices: 112200--112422 Score: 265
Period size: 114 Copynumber: 2.0 Consensus size: 113
112190 AAAAATATAT
* * * *
112200 ATTATTAATGTATTAAGATTTATATAAATATATATCATTTTAATTATAATTATGACATAAAAATA
1 ATTATTAATGTATCAAAATTTATATAAATATATATCATTTTAAATATAATTATAACATAAAAATA
* ** * *
112265 CACGAATATAATATAAATATATGAATGTATTTAAATATATATAATACGA
66 CAC-AATATAATATAAATACACAAATGAATTGAAATATATATAATACGA
*
112314 ATTATTAATTTATCAAAATTTATATAAATATATAAT-ATTTTAAATATAATTATAACATATAAAA
1 ATTATTAATGTATCAAAATTTATATAAATATAT-ATCATTTTAAATATAATTATAAC--ATAAAA
*
112378 ATACA-AATATAACT-TAAATACACAAAT-AATTGAATTAATATATAA
63 ATACACAATATAA-TATAAATACACAAATGAATTGAAAT-ATATATAA
112423 CAATGTAAAC
Statistics
Matches: 93, Mismatches: 11, Indels: 10
0.82 0.10 0.09
Matches are distributed among these distances:
113 6 0.06
114 73 0.78
115 3 0.03
116 11 0.12
ACGTcount: A:0.52, C:0.05, G:0.04, T:0.39
Consensus pattern (113 bp):
ATTATTAATGTATCAAAATTTATATAAATATATATCATTTTAAATATAATTATAACATAAAAATA
CACAATATAATATAAATACACAAATGAATTGAAATATATATAATACGA
Found at i:115051 original size:16 final size:16
Alignment explanation
Indices: 115030--115081 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
115020 ATAAATATTT
115030 TAAATTTTATATAATA
1 TAAATTTTATATAATA
115046 TAAATTATTA-AT-ATA
1 TAAATT-TTATATAATA
115061 TCAAATTTT-TATAAATA
1 T-AAATTTTATAT-AATA
115078 TAAA
1 TAAA
115082 ATGTTTTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
15 8 0.26
16 16 0.52
17 7 0.23
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (16 bp):
TAAATTTTATATAATA
Found at i:115067 original size:32 final size:33
Alignment explanation
Indices: 115005--115081 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
114995 ATAAAATATA
* * *
115005 ATATGATATAAATATATAAATATTTTAAATTTT
1 ATATAATATAAATATATAAATATATCAAATTTT
*
115038 ATATAATATAAAT-TATTAATATATCAAATTTT
1 ATATAATATAAATATATAAATATATCAAATTTT
115070 -TATAAATATAAA
1 ATAT-AATATAAA
115082 ATGTTTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
31 3 0.08
32 24 0.62
33 12 0.31
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.45
Consensus pattern (33 bp):
ATATAATATAAATATATAAATATATCAAATTTT
Found at i:115077 original size:19 final size:18
Alignment explanation
Indices: 115058--115095 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
115048 AATTATTAAT
*
115058 ATATCAAAT-TTTTATAA
1 ATATAAAATGTTTTATAA
115075 ATATAAAATGTTTTA-AA
1 ATATAAAATGTTTTATAA
115092 ATAT
1 ATAT
115096 GATATTATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (18 bp):
ATATAAAATGTTTTATAA
Found at i:117590 original size:39 final size:40
Alignment explanation
Indices: 117521--117599 Score: 99
Period size: 39 Copynumber: 2.0 Consensus size: 40
117511 ATCGATCCAC
* *
117521 AATTTTATTTTAATACTTAAAATTATATTAAA-AAATTTT
1 AATTTTATATTAATACTTAAAATTAAATTAAATAAATTTT
**
117560 AATTTTATATTAATA-TTTTAATTAAAATTAAATAAATTTT
1 AATTTTATATTAATACTTAAAATT-AAATTAAATAAATTTT
117600 TTTTATTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
38 6 0.18
39 21 0.62
40 7 0.21
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (40 bp):
AATTTTATATTAATACTTAAAATTAAATTAAATAAATTTT
Found at i:118193 original size:2 final size:2
Alignment explanation
Indices: 118186--118210 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
118176 CATAGGTATG
118186 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
118211 ATTTTTTATT
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:118633 original size:33 final size:35
Alignment explanation
Indices: 118594--118664 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
118584 AATTATAATA
* * **
118594 AAATAATA-TTTAATATTTAATATTTTAA-TTTTT
1 AAATAATATTTTAAAATTAAATAAATTAACTTTTT
118627 AAATAATATTTTAAAATTAAATAAATTAACTTTTT
1 AAATAATATTTTAAAATTAAATAAATTAACTTTTT
118662 AAA
1 AAA
118665 ATTATCATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 8 0.25
34 16 0.50
35 8 0.25
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (35 bp):
AAATAATATTTTAAAATTAAATAAATTAACTTTTT
Found at i:118648 original size:18 final size:19
Alignment explanation
Indices: 118588--118650 Score: 57
Period size: 19 Copynumber: 3.6 Consensus size: 19
118578 AAATTAAATT
*
118588 ATAATAAAATAATA-TTTA
1 ATAATTAAATAATATTTTA
118606 AT-ATT---TAATATTTTA
1 ATAATTAAATAATATTTTA
**
118621 ATTTTTAAATAATATTTTA
1 ATAATTAAATAATATTTTA
118640 A-AATTAAATAA
1 ATAATTAAATAA
118651 ATTAACTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 10
0.72 0.08 0.20
Matches are distributed among these distances:
14 5 0.14
15 6 0.17
16 2 0.06
17 2 0.06
18 10 0.28
19 11 0.31
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATAATTAAATAATATTTTA
Found at i:118684 original size:23 final size:23
Alignment explanation
Indices: 118635--118685 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
118625 TTAAATAATA
*
118635 TTTTAAAATTAAATAAATTAACT
1 TTTTAAAATTAAATAAATAAACT
* *
118658 TTTTAAAATTATCATAAGTAAACT
1 TTTTAAAATTA-AATAAATAAACT
118682 TTTT
1 TTTT
118686 TTTCTTTCAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (23 bp):
TTTTAAAATTAAATAAATAAACT
Found at i:118847 original size:17 final size:16
Alignment explanation
Indices: 118817--118858 Score: 59
Period size: 17 Copynumber: 2.6 Consensus size: 16
118807 TAACATTTCT
118817 CTTTA-TTTTTTTTTA
1 CTTTATTTTTTTTTTA
118832 CTTTATTTTTTATTTTA
1 CTTTATTTTTT-TTTTA
*
118849 TTTTATTTTT
1 CTTTATTTTT
118859 AATAATATTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
15 5 0.21
16 5 0.21
17 14 0.58
ACGTcount: A:0.14, C:0.05, G:0.00, T:0.81
Consensus pattern (16 bp):
CTTTATTTTTTTTTTA
Found at i:119201 original size:21 final size:22
Alignment explanation
Indices: 119175--119227 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
119165 TTAAGTTGAT
*
119175 TAATTTAAATTA-TTATTTTAA
1 TAATTTAAATTATTTATTTAAA
*
119196 TAATTTAAATAATTTATTTAAA
1 TAATTTAAATTATTTATTTAAA
*
119218 T-ATATAAATT
1 TAATTTAAATT
119228 TAATATAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 18 0.67
22 9 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TAATTTAAATTATTTATTTAAA
Found at i:121213 original size:20 final size:22
Alignment explanation
Indices: 121190--121231 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
121180 TATTAAAATT
*
121190 ATTTTAATTTT-TA-TAATTAA
1 ATTTAAATTTTGTACTAATTAA
121210 ATTTAAATTTTGTACTAATTAA
1 ATTTAAATTTTGTACTAATTAA
121232 CAGTGATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 2 0.11
22 7 0.37
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
ATTTAAATTTTGTACTAATTAA
Found at i:121677 original size:21 final size:22
Alignment explanation
Indices: 121620--121679 Score: 59
Period size: 21 Copynumber: 2.6 Consensus size: 22
121610 AATAAAATAG
121620 ATAAAATAGAAATTTTAACTTTTTA
1 ATAAAATA-AAA--TTAACTTTTTA
* * *
121645 ACAACATTAAATTAA-TTTTTA
1 ATAAAATAAAATTAACTTTTTA
121666 ATAAAATAAAATTA
1 ATAAAATAAAATTA
121680 CAAAAAAAAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
21 17 0.59
22 4 0.14
24 3 0.10
25 5 0.17
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
ATAAAATAAAATTAACTTTTTA
Found at i:125252 original size:20 final size:19
Alignment explanation
Indices: 125214--125252 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
125204 AAAGTTTTAA
*
125214 TTTAATTTAATTCATAAAT
1 TTTAATTTAATTAATAAAT
*
125233 TTTAATTATTATTAATAAAT
1 TTTAATT-TAATTAATAAAT
125253 ATAAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTAATTTAATTAATAAAT
Found at i:131687 original size:16 final size:16
Alignment explanation
Indices: 131650--131687 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
131640 GAGTTCATAT
131650 TATA-TTCATATTTAA
1 TATATTTCATATTTAA
* *
131665 CACATTTCATATTTAA
1 TATATTTCATATTTAA
131681 TATATTT
1 TATATTT
131688 TTAAATATAA
Statistics
Matches: 18, Mismatches: 4, Indels: 1
0.78 0.17 0.04
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.53
Consensus pattern (16 bp):
TATATTTCATATTTAA
Found at i:138806 original size:16 final size:16
Alignment explanation
Indices: 138787--138819 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
138777 AAAAATATGA
138787 TATTAAA-ATTTATATT
1 TATTAAATA-TTATATT
138803 TATTAAATATTATATT
1 TATTAAATATTATATT
138819 T
1 T
138820 TAAAAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 15 0.94
17 1 0.06
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (16 bp):
TATTAAATATTATATT
Found at i:144486 original size:20 final size:17
Alignment explanation
Indices: 144443--144487 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 17
144433 TATTATTAAA
144443 ATATTAAATATTATTTTT
1 ATATT-AATATTATTTTT
144461 ATATTAATATTAATATTTT
1 ATATTAATATT-AT-TTTT
144480 ATAATTAA
1 AT-ATTAA
144488 ATTTCAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.25
18 7 0.29
19 6 0.25
20 5 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
ATATTAATATTATTTTT
Found at i:145581 original size:27 final size:27
Alignment explanation
Indices: 145533--145584 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
145523 AAAATTTATA
*
145533 TAATATAAATTATTAATATATTAAAAT
1 TAATATAAATTATAAATATATTAAAAT
*
145560 TAATATAAATCTA-AAATCTATTAAA
1 TAATATAAAT-TATAAATATATTAAA
145585 CATAATTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
27 20 0.91
28 2 0.09
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (27 bp):
TAATATAAATTATAAATATATTAAAAT
Found at i:145590 original size:27 final size:26
Alignment explanation
Indices: 145532--145590 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 26
145522 AAAAATTTAT
*
145532 ATAATATAAATTATTAATATATTAAA
1 ATAATATAAATTATAAATATATTAAA
*
145558 ATTAATATAAATCTA-AAATCTATTAAA
1 A-TAATATAAAT-TATAAATATATTAAA
145585 CATAAT
1 -ATAAT
145591 TATGATATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
26 1 0.04
27 24 0.86
28 3 0.11
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (26 bp):
ATAATATAAATTATAAATATATTAAA
Found at i:146410 original size:24 final size:26
Alignment explanation
Indices: 146367--146415 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
146357 CATGTATTTA
146367 ATATAATTTTAAATATAAATATAAAT
1 ATATAATTTTAAATATAAATATAAAT
*
146393 ATATAATTTTTAA-A-AAATATAAA
1 ATATAATTTTAAATATAAATATAAA
146416 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
25 1 0.05
26 12 0.55
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (26 bp):
ATATAATTTTAAATATAAATATAAAT
Found at i:147304 original size:30 final size:30
Alignment explanation
Indices: 147240--147307 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
147230 TAAACTTATT
*
147240 CATATT-AAATATATATTCATATCAGATAC
1 CATATTCAAATATATATTCATATCAAATAC
* *
147269 TCATATTCAAATCTCTATCTCATATCAAATA-
1 -CATATTCAAATATATAT-TCATATCAAATAC
147300 CATATTCA
1 CATATTCA
147308 TATCGATGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 14 0.42
31 8 0.24
32 11 0.33
ACGTcount: A:0.41, C:0.19, G:0.01, T:0.38
Consensus pattern (30 bp):
CATATTCAAATATATATTCATATCAAATAC
Found at i:150369 original size:29 final size:29
Alignment explanation
Indices: 150302--150370 Score: 74
Period size: 29 Copynumber: 2.4 Consensus size: 29
150292 CATTGCTATT
* *
150302 AGAT-ATGATAAAAAAATATAATATATTT
1 AGATAATGATAAAAAAATATAATATAATA
150330 A-ATAAAT-ATAAAAATAATATAATA-AATA
1 AGAT-AATGATAAAAA-AATATAATATAATA
150358 AGATAATGATAAA
1 AGATAATGATAAA
150371 TTTAAATATA
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
27 2 0.06
28 14 0.41
29 18 0.53
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (29 bp):
AGATAATGATAAAAAAATATAATATAATA
Found at i:151917 original size:26 final size:25
Alignment explanation
Indices: 151871--151946 Score: 66
Period size: 25 Copynumber: 3.0 Consensus size: 25
151861 TTTAATTTAT
151871 TATTTTTTATATAATTAAAAA-ATTA
1 TATTTTTTATATAATTAAAAATA-TA
*
151896 TATTTTTATATTTATATT-AAAATATA
1 TATTTTT-TATATA-ATTAAAAATATA
** * *
151922 TATTAATTAAATATTTAAAAATATA
1 TATTTTTTATATAATTAAAAATATA
151947 AAAATTTAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
24 2 0.05
25 19 0.46
26 16 0.39
27 4 0.10
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (25 bp):
TATTTTTTATATAATTAAAAATATA
Found at i:152292 original size:8 final size:8
Alignment explanation
Indices: 152279--152374 Score: 67
Period size: 8 Copynumber: 12.0 Consensus size: 8
152269 GAAACTGATC
152279 ATTTATAT
1 ATTTATAT
152287 ATTTATATT
1 ATTTATA-T
152296 ATATTATAT
1 AT-TTATAT
152305 ATATT-TATT
1 AT-TTATA-T
152314 ATTT-TAT
1 ATTTATAT
*
152321 AATTATAT
1 ATTTATAT
* *
152329 -TTAAAAT
1 ATTTATAT
152336 ATTT-TAT
1 ATTTATAT
152343 ATTTATAT
1 ATTTATAT
*
152351 TTTTAATAT
1 ATTT-ATAT
*
152360 ATTAATA-
1 ATTTATAT
152367 ATTTATAT
1 ATTTATAT
152375 TATAAAAATT
Statistics
Matches: 70, Mismatches: 10, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
7 20 0.29
8 27 0.39
9 18 0.26
10 5 0.07
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTATAT
Found at i:152327 original size:22 final size:22
Alignment explanation
Indices: 152281--152375 Score: 81
Period size: 22 Copynumber: 4.4 Consensus size: 22
152271 AACTGATCAT
* *
152281 TTATATATTT-ATATTATATTA
1 TTATATATTTAATATTTTATAA
*
152302 -TATATATTTATTATTTTATAA
1 TTATATATTTAATATTTTATAA
* *
152323 TTATAT-TTAAAATATTTTATAT
1 TTATATATT-TAATATTTTATAA
* *
152345 TTATATTTTTAATATATTAATAA
1 TTATATATTTAATAT-TTTATAA
152368 TT-TATATT
1 TTATATATT
152376 ATAAAAATTA
Statistics
Matches: 59, Mismatches: 10, Indels: 9
0.76 0.13 0.12
Matches are distributed among these distances:
20 9 0.15
21 10 0.17
22 31 0.53
23 9 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATATATTTAATATTTTATAA
Found at i:152337 original size:29 final size:28
Alignment explanation
Indices: 152279--152378 Score: 97
Period size: 28 Copynumber: 3.7 Consensus size: 28
152269 GAAACTGATC
*
152279 ATTTATATATTTATATTATATTATATAT
1 ATTTATATATTTATATTATATTATAAAT
152307 ATTTAT-TATTTTATAATTATATT-TAAAAT
1 ATTTATATA-TTTAT-ATTATATTAT-AAAT
*
152336 ATTT-TATATTTATATT-T-TTA-ATAT
1 ATTTATATATTTATATTATATTATAAAT
*
152360 ATTAATA-ATTTATATTATA
1 ATTTATATATTTATATTATA
152379 AAAATTATAT
Statistics
Matches: 61, Mismatches: 3, Indels: 18
0.74 0.04 0.22
Matches are distributed among these distances:
24 15 0.25
25 5 0.08
26 1 0.02
27 5 0.08
28 18 0.30
29 17 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTATATATTTATATTATATTATAAAT
Found at i:152373 original size:30 final size:33
Alignment explanation
Indices: 152279--152375 Score: 92
Period size: 30 Copynumber: 2.9 Consensus size: 33
152269 GAAACTGATC
* * *
152279 ATTTATATATTTATATTATATTATATATATTTATT
1 ATTT-TATAATTATATTA-ATAATTTATATTTATT
*
152314 ATTTTATAATTATATTTAAAATATTTTATATTTA-T
1 ATTTTATAATTATA-TT--AATAATTTATATTTATT
152349 ATTTT-TAA-TATATTAATAATTTATATT
1 ATTTTATAATTATATTAATAATTTATATT
152376 ATAAAAATTA
Statistics
Matches: 54, Mismatches: 5, Indels: 11
0.77 0.07 0.16
Matches are distributed among these distances:
30 12 0.22
32 2 0.04
33 4 0.07
34 12 0.22
35 12 0.22
36 11 0.20
37 1 0.02
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (33 bp):
ATTTTATAATTATATTAATAATTTATATTTATT
Found at i:152392 original size:22 final size:22
Alignment explanation
Indices: 152318--152401 Score: 64
Period size: 23 Copynumber: 3.7 Consensus size: 22
152308 TTTATTATTT
* *
152318 TATAATTATATT-TAAAATATTT
1 TATATTTATATTATAAAA-ATTA
* *
152340 TATATTTATATTTTTAATATATTA
1 TATATTTATA-TTATAA-AAATTA
152364 -ATAATTTATATTATAAAAATTA
1 TAT-ATTTATATTATAAAAATTA
*
152386 TATATTTTTTATTATA
1 TATA-TTTATATTATA
152402 TAATCATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
22 15 0.30
23 21 0.42
24 13 0.26
25 1 0.02
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (22 bp):
TATATTTATATTATAAAAATTA
Found at i:152721 original size:17 final size:18
Alignment explanation
Indices: 152699--152732 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
152689 CACACATCAA
152699 ATTATA-AAAAAATAAAT
1 ATTATATAAAAAATAAAT
*
152716 ATTATATTAAAAATAAA
1 ATTATATAAAAAATAAA
152733 ATGAACAAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (18 bp):
ATTATATAAAAAATAAAT
Found at i:152846 original size:30 final size:28
Alignment explanation
Indices: 152812--152876 Score: 85
Period size: 28 Copynumber: 2.2 Consensus size: 28
152802 TCATCAAATT
*
152812 ATAAAAAATAATAGAATATTACATTAAAAA
1 ATAAAAAAT-AT-GAATATGACATTAAAAA
* *
152842 ATAAAAAATATGATTATGATATTAAAAA
1 ATAAAAAATATGAATATGACATTAAAAA
152870 ATAAAAA
1 ATAAAAA
152877 TAAAAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
28 21 0.66
29 2 0.06
30 9 0.28
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (28 bp):
ATAAAAAATATGAATATGACATTAAAAA
Found at i:152883 original size:113 final size:108
Alignment explanation
Indices: 152693--152912 Score: 253
Period size: 113 Copynumber: 2.0 Consensus size: 108
152683 AAATATCACA
* * *
152693 CATCAAATTATAAAAAAATAAATATTATATTAAAAATAAAATGAACAAGAATATGATATACAAAG
1 CATCAAATTATAAAAAAATAAATATTACATTAAAAATAAAA-GAACAAGAATATGATATAAAAAA
** * *
152758 TGGAAACCAAAATAGAAAATTTTCCTAAAATTACAATATGTTACT
65 TAAAAACAAAAATAGAAAATTTTACTAAAATTACAA-ATGTTACT
* * *
152803 CATCAAATTATAAAAAATAATAGAATATTACATTAAAAAATAAAA-AATATGATTATGATATTAA
1 CATCAAATTAT-AAAAA-AATA-AATATTACATT-AAAAATAAAAGAACAAGAATATGATA-TAA
* * *
152867 AAAATAAAAATAAAAATATAAAATTTTACTAAAATTTCAAATGTTA
61 AAAATAAAAACAAAAATAGAAAATTTTACTAAAATTACAAATGTTA
152913 TTAACATGAA
Statistics
Matches: 92, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
110 11 0.12
111 5 0.05
112 22 0.24
113 44 0.48
114 10 0.11
ACGTcount: A:0.58, C:0.07, G:0.05, T:0.30
Consensus pattern (108 bp):
CATCAAATTATAAAAAAATAAATATTACATTAAAAATAAAAGAACAAGAATATGATATAAAAAAT
AAAAACAAAAATAGAAAATTTTACTAAAATTACAAATGTTACT
Found at i:154802 original size:21 final size:21
Alignment explanation
Indices: 154778--154846 Score: 50
Period size: 25 Copynumber: 3.1 Consensus size: 21
154768 TTATAATTAA
154778 TATTATTATTATTATTTTATT
1 TATTATTATTATTATTTTATT
* **
154799 TATTTATAATATAATTAATAATATT
1 TA-TTAT--TATTATT-ATTTTATT
*
154824 TATATTTTATTATT-TTTTATT
1 TAT-TATTATTATTATTTTATT
154845 TA
1 TA
154847 AATTAAAACT
Statistics
Matches: 36, Mismatches: 7, Indels: 10
0.68 0.13 0.19
Matches are distributed among these distances:
21 9 0.25
22 4 0.11
23 6 0.17
24 7 0.19
25 10 0.28
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TATTATTATTATTATTTTATT
Found at i:154851 original size:36 final size:38
Alignment explanation
Indices: 154767--154852 Score: 99
Period size: 39 Copynumber: 2.3 Consensus size: 38
154757 TAATAAATTG
*
154767 TTTATAATTAATATTATTATTATTATTTTATTTATTTA
1 TTTATAATTAATAATATTATTATTATTTTATTTATTTA
*
154805 TAATATAATTAATAATATT-TATATT-TTATTATTT-TTTA
1 T-TTATAATTAATAATATTAT-TATTATT-TTATTTATTTA
154843 TTTA-AATTAA
1 TTTATAATTAA
154853 AACTAATAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
36 6 0.14
37 2 0.05
38 9 0.21
39 25 0.60
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (38 bp):
TTTATAATTAATAATATTATTATTATTTTATTTATTTA
Found at i:156840 original size:13 final size:14
Alignment explanation
Indices: 156811--156843 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
156801 TATAATTTAA
*
156811 AAAATACAAATTTT
1 AAAATTCAAATTTT
156825 AAAATTCAAA-TTT
1 AAAATTCAAATTTT
156838 AAAATT
1 AAAATT
156844 TATTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATTCAAATTTT
Found at i:158498 original size:11 final size:11
Alignment explanation
Indices: 158482--158506 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
158472 AAATAAAACA
158482 AATAAATAAAT
1 AATAAATAAAT
158493 AATAAATAAAT
1 AATAAATAAAT
158504 AAT
1 AAT
158507 TCTGCAGACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:158861 original size:26 final size:27
Alignment explanation
Indices: 158827--158888 Score: 74
Period size: 26 Copynumber: 2.3 Consensus size: 27
158817 AATCTAAATG
*
158827 ATTTTAAAAGGATAAAA-TTATA-TCAA
1 ATTTTAAAA-GATAAAATTTATATTAAA
**
158853 ATTTTAAAATTTAAAATTTATATTAAA
1 ATTTTAAAAGATAAAATTTATATTAAA
158880 ATTTTAAAA
1 ATTTTAAAA
158889 ATTTAGATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.16
26 14 0.45
27 12 0.39
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (27 bp):
ATTTTAAAAGATAAAATTTATATTAAA
Found at i:158880 original size:19 final size:19
Alignment explanation
Indices: 158856--158925 Score: 63
Period size: 19 Copynumber: 3.6 Consensus size: 19
158846 ATATCAAATT
*
158856 TTAAAATTTAAAATTTATA
1 TTAAAATTTAAAATTTAAA
*
158875 TTAAAATTTTAAAAATTTAGA
1 TTAAAA-TTT-AAAATTTAAA
* *
158896 -TAAAA-TCAGAATTTAAA
1 TTAAAATTTAAAATTTAAA
158913 TTTAAAATTTAAA
1 -TTAAAATTTAAA
158926 TTAGATAACT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
17 8 0.20
18 1 0.03
19 11 0.28
20 11 0.28
21 9 0.22
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.41
Consensus pattern (19 bp):
TTAAAATTTAAAATTTAAA
Found at i:158899 original size:20 final size:20
Alignment explanation
Indices: 158856--158901 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
158846 ATATCAAATT
*
158856 TTAAAA-TTTAAAATTTATA
1 TTAAAATTTTAAAATTTAGA
158875 TTAAAATTTTAAAAATTTAGA
1 TTAAAATTTT-AAAATTTAGA
158896 -TAAAAT
1 TTAAAAT
158902 CAGAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
TTAAAATTTTAAAATTTAGA
Found at i:159191 original size:20 final size:21
Alignment explanation
Indices: 159162--159220 Score: 70
Period size: 21 Copynumber: 2.9 Consensus size: 21
159152 TCTTTATTAC
159162 CTTTTCTTTTTCCCTTTTTCT
1 CTTTTCTTTTTCCCTTTTTCT
159183 CTTTT-TTTTT-CCTTTTT-T
1 CTTTTCTTTTTCCCTTTTTCT
* *
159201 CTTCTCTTTTCCTCCTTTTT
1 CTTTTCTTTTTC-CCTTTTT
159221 TTTTCCTCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 5 0.15
19 11 0.33
20 5 0.15
21 12 0.36
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (21 bp):
CTTTTCTTTTTCCCTTTTTCT
Found at i:159193 original size:12 final size:12
Alignment explanation
Indices: 159176--159210 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
159166 TCTTTTTCCC
159176 TTTTTCTCTTTT
1 TTTTTCTCTTTT
159188 TTTTTC-CTTTT
1 TTTTTCTCTTTT
*
159199 TTCTTCTCTTTT
1 TTTTTCTCTTTT
159211 CCTCCTTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:159197 original size:11 final size:11
Alignment explanation
Indices: 159176--159241 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
159166 TCTTTTTCCC
159176 TTTTTCTCTTTT
1 TTTTTC-CTTTT
159188 TTTTTCCTTTT
1 TTTTTCCTTTT
* *
159199 TTCTT-CTCTT
1 TTTTTCCTTTT
**
159209 TTCCTCCTTTT
1 TTTTTCCTTTT
**
159220 TTTTTCCTCCT
1 TTTTTCCTTTT
159231 TTTTTCTCTTT
1 TTTTTC-CTTT
159242 CTCCCGACCA
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
10 8 0.19
11 26 0.62
12 8 0.19
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTTCCTTTT
Found at i:159219 original size:32 final size:30
Alignment explanation
Indices: 159168--159241 Score: 94
Period size: 32 Copynumber: 2.4 Consensus size: 30
159158 TTACCTTTTC
* *
159168 TTTTTCCCTTTTTCTCTTTTTTTTTCCTTT
1 TTTTTCTCTTTTCCTCTTTTTTTTTCCTTT
*
159198 TTTCTTCTCTTTTCCTCCTTTTTTTTTCCTCCT
1 TTT-TTCTCTTTTCCT-CTTTTTTTTTCCT-TT
159231 TTTTTCTCTTT
1 TTTTTCTCTTT
159242 CTCCCGACCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
30 3 0.08
31 10 0.26
32 21 0.55
33 4 0.11
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (30 bp):
TTTTTCTCTTTTCCTCTTTTTTTTTCCTTT
Found at i:159226 original size:14 final size:14
Alignment explanation
Indices: 159207--159235 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
159197 TTTTCTTCTC
159207 TTTTCCTCCTTTTT
1 TTTTCCTCCTTTTT
159221 TTTTCCTCCTTTTT
1 TTTTCCTCCTTTTT
159235 T
1 T
159236 CTCTTTCTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTCCTCCTTTTT
Found at i:160450 original size:16 final size:17
Alignment explanation
Indices: 160429--160461 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
160419 TCGATAGTGG
160429 AGTTTTTTT-TATTTTT
1 AGTTTTTTTGTATTTTT
160445 AGTTTTTTTGTATTTTT
1 AGTTTTTTTGTATTTTT
160462 TATGTTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (17 bp):
AGTTTTTTTGTATTTTT
Done.