Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold206
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: 2736418
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.34
Warning! 22040 characters in sequence are not A, C, G, or T
File 17 of 20
Found at i:2268468 original size:21 final size:21
Alignment explanation
Indices: 2268444--2268500 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2268434 AAAAAATTTA
2268444 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2268465 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
2268486 AATGTATCGATACAT
1 AATGTATCGATACAT
2268501 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:2268580 original size:19 final size:19
Alignment explanation
Indices: 2268556--2268623 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2268546 AATTCAACAA
2268556 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2268575 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2268590 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2268607 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2268624 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:2268595 original size:13 final size:13
Alignment explanation
Indices: 2268577--2268601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2268567 ACATAAGTTT
2268577 TGTATCGATACAA
1 TGTATCGATACAA
2268590 TGTATCGATACA
1 TGTATCGATACA
2268602 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:2268599 original size:32 final size:32
Alignment explanation
Indices: 2268558--2268620 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2268548 TTCAACAATT
*
2268558 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2268590 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2268621 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:2268681 original size:13 final size:13
Alignment explanation
Indices: 2268663--2268688 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2268653 CATTTTTCTG
2268663 TGTATCGATACAT
1 TGTATCGATACAT
2268676 TGTATCGATACAT
1 TGTATCGATACAT
2268689 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:2268685 original size:33 final size:33
Alignment explanation
Indices: 2268643--2268709 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2268633 GCCAAGGAAA
***
2268643 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2268676 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2268709 T
1 T
2268710 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:2271231 original size:52 final size:52
Alignment explanation
Indices: 2271158--2271539 Score: 261
Period size: 52 Copynumber: 7.3 Consensus size: 52
2271148 TTATTTTCGA
*
2271158 GGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTAT-GTTCAAAACACCAATTTTTCCACAATC
* * **
2271210 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATGTTCAAAACACCAATTTTTCC-ACAATC
* *
2271262 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATGTT-C-AAAACACCAATTTTTCCACAATC
* * *** * * *** **
2271314 GAGGATACTCCAAC-CTCGTTATTTCATCG-GGGATACTCCAACCCCGTT--ACTTTC
1 GGGGATACTCCAACTC-CGGT-TTT-AT-GTTCAAAACACCAA--TTTTTCCACAATC
*
2271368 GAGGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 --GGGGATACTCCAACTCCGGTTTTAT-GTTCAAAACACCAATTTTTCCACAATC
* * **
2271422 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATGTTCAAAACACCAATTTTTCC-ACAATC
* *
2271474 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATGTT-C-AAAACACCAATTTTTCCACAATC
*
2271526 GAGGATACTCCAAC
1 GGGGATACTCCAAC
2271540 CTCGTTATTT
Statistics
Matches: 257, Mismatches: 46, Indels: 54
0.72 0.13 0.15
Matches are distributed among these distances:
51 27 0.11
52 147 0.57
53 33 0.13
54 28 0.11
55 5 0.02
56 16 0.06
57 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACTCCGGTTTTATGTTCAAAACACCAATTTTTCCACAATC
Found at i:2271311 original size:104 final size:103
Alignment explanation
Indices: 2271158--2271538 Score: 402
Period size: 104 Copynumber: 3.6 Consensus size: 103
2271148 TTATTTTCGA
* * *
2271158 GGGGATACTCCAACTCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATC-TTAAAACACCAATTTTTCCACAATCGAGGATACTCCAA
2271223 TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
65 TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
*
2271262 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATCGAGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATCTT---AAAACACCAATTTTTCCACAATCGAGGATACTCC
* * * * ** * *
2271325 AA-CCTCG--TTATTTCATCGGGGATACTCCAA--CCCCGTTACTTTC
63 AATCCTGGTTTTATTT--TC---AAAACGCCAATTTTCCTTTA--ATC
* * *
2271368 GAGGGGATACTCCAACTCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCC
1 --GGGGATACTCCAACTCCGATTTTATC-TTAAAACACCAATTTTTCCACAATCGAGGATACTCC
2271433 AATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
63 AATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
*
2271474 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATCGAGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATCTT---AAAACACCAATTTTTCCACAATCGAGGATACTCC
2271537 AA
63 AA
2271539 CCTCGTTATT
Statistics
Matches: 226, Mismatches: 28, Indels: 46
0.75 0.09 0.15
Matches are distributed among these distances:
101 6 0.03
102 4 0.02
103 6 0.03
104 91 0.40
105 26 0.12
106 18 0.08
107 13 0.06
108 48 0.21
109 6 0.03
110 2 0.01
111 6 0.03
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (103 bp):
GGGGATACTCCAACTCCGATTTTATCTTAAAACACCAATTTTTCCACAATCGAGGATACTCCAAT
CCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
Found at i:2271347 original size:28 final size:30
Alignment explanation
Indices: 2271311--2271383 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 30
2271301 ATTTTTCACA
* *
2271311 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
2271339 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
2271369 A--GGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
2271384 TCCGGTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCGTTACTTTCG
Found at i:2271425 original size:212 final size:212
Alignment explanation
Indices: 2271043--2271606 Score: 1004
Period size: 212 Copynumber: 2.6 Consensus size: 212
2271033 AATTCTCCAC
* * *
2271043 AATCGAGGATATTCCAACTCCGATTTTATTTCCAAAAAAAATACCAATTTCTTCACAATCGGGGA
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC---AAAAATACCAATTT-TTCACAATCGAGGA
* * *
2271108 TACTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAAC
62 TACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAAC
2271172 TCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTT
127 TCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTT
2271237 TCAAAACGCCAATTTTCCTTT
192 TCAAAACGCCAATTTTCCTTT
2271258 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
2271323 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
66 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
2271388 GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
131 GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
2271453 AACGCCAATTTTCCTTT
196 AACGCCAATTTTCCTTT
2271470 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
* *
2271535 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCG
66 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
*
2271600 GCTTTAT
131 GTTTTAT
2271607 TCCCAAAATA
Statistics
Matches: 339, Mismatches: 9, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
211 28 0.08
212 280 0.83
215 31 0.09
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (212 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
AACGCCAATTTTCCTTT
Found at i:2271559 original size:28 final size:28
Alignment explanation
Indices: 2271523--2271599 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
2271513 ATTTTTCACA
* * *
2271523 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2271551 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
2271579 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2271600 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2284139 original size:1 final size:1
Alignment explanation
Indices: 2284133--2284206 Score: 94
Period size: 1 Copynumber: 74.0 Consensus size: 1
2284123 CCTTCTCTTC
* * * * *
2284133 AAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAACAAAAAAACAAAAAAAAAAAGAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
*
2284198 AAGAAAAAA
1 AAAAAAAAA
2284207 CCTACTTAAG
Statistics
Matches: 61, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 61 1.00
ACGTcount: A:0.92, C:0.04, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:2285488 original size:54 final size:56
Alignment explanation
Indices: 2285162--2286326 Score: 1401
Period size: 53 Copynumber: 21.4 Consensus size: 56
2285152 TCTCCTTCCG
* *
2285162 CTTTTAGTCCTC-AAGAGCAGGACACCTCTT-AAAGACCCACCCAAGTGTGGT-GCA-
1 CTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAAG-CCCACACAAGT-TGGTGGCAC
* *
2285216 TTTTGCCAGTCCTCAAAGAGCAGGACAAC-CTTCAAAGCCCACACAAGTTGGTGGGCA-
1 CTTT--CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGT-GGCAC
* *
2285273 TTTTCCAGTCCTCAACG-GCAGGACACCTCTT-AAAGCCCACACACAGTTTTGGTGGCAC
1 CTTT-CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACA-AG--TTGGTGGCAC
2285331 CTTTCAGTCC-CAAAGAGCAGGACACCGTC-TC--AG-CCACACAAGTTGGTGGGCAAC
1 CTTTCAGTCCTCAAAGAGCAGGACACC-TCTTCAAAGCCCACACAAGTTGGT-GGC-AC
*
2285385 CTTTTCAAGTCCCCAAAGAGCAGGACCACCTC-TCAAAGCCCACAC-AGTTGGT-GCAC
1 C-TTTC-AGTCCTCAAAGAGCAGGA-CACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
** * *
2285441 CTTTCAGTCCTCAAAGCTCA-GACACCTCTTAAAAGCCCACACAAGTTGGGTGGCGC
1 CTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTT-GGTGGCAC
*
2285497 C-TTCTAGTCCTCAAAGAGCAGGACACCTCGTCAAAAGGGCCCCCACACAAGTT-GTGGCAC
1 CTTTC-AGTCCTCAAAGAGCAGGACACCTCTTC-AAA--G--CCCACACAAGTTGGTGGCAC
*
2285557 CTTTCAATCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
2285612 CTTTCAGTCCTCAAAGAGCAGGACA-C-CTTCAAAGCCCACACAAGTTGGTGGCA-
1 CTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
*
2285665 TTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCA-
1 CTTT-CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
2285720 -TTTCCAGTCCTCAAAGAGCAGGACA-C-CTTCAAAGCCCACACAAGTTGGTGGCA-
1 CTTT-CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
*
2285773 TTTTCAGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
2285828 CTTT---TCCCTCAAAGAGCAGGACACCT-TT-AAAGCCCACACAAGTTGGTGGCA-
1 CTTTCAGT-CCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
*
2285879 TTTTCAGTCCTCAAAGAGCAGGACA-C-CTTCAAAGCCCACACAAGTTGGTGGCA-
1 CTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
*
2285932 -TTTCAGTCCCCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
2285986 CTTTCAGTCC-CAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGG---
1 CTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
2286037 CTTTCCAGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACAC-AGTTGGTGGCA-
1 CTTT-CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
2286091 -TTTCCAGTCCTCAAAGA-CAGGACACCT-TTCAAAGCCCACAC-AGTTGGTGGCA-
1 CTTT-CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
*
2286143 TTTTCCAGT-CTCAAAGAGCAGGACACCTCTT-AAAGCCCACAC-AGTTGGTGGCAC
1 CTTT-CAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
* * *
2286197 C-TTCATTCCCCAAAGAGCAGGACA-CT-TTCAAAG-CCACACAAGTGGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
* *
2286249 CTTTCAGTCCTCAAAGAGCAGGACGCCT-TTCAAAGCCCACACGAGTTGGTGGCAC
1 CTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
* * * *
2286304 TTTTTACTCCTCAATGAGCAGGA
1 CTTTCAGTCCTCAAAGAGCAGGA
2286327 TACAATTTAT
Statistics
Matches: 1003, Mismatches: 38, Indels: 139
0.85 0.03 0.12
Matches are distributed among these distances:
51 15 0.01
52 144 0.14
53 277 0.28
54 189 0.19
55 155 0.15
56 69 0.07
57 72 0.07
58 20 0.02
59 9 0.01
60 38 0.04
61 3 0.00
62 12 0.01
ACGTcount: A:0.29, C:0.31, G:0.21, T:0.20
Consensus pattern (56 bp):
CTTTCAGTCCTCAAAGAGCAGGACACCTCTTCAAAGCCCACACAAGTTGGTGGCAC
Found at i:2285639 original size:26 final size:26
Alignment explanation
Indices: 2285554--2285640 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
2285544 CAAGTTGTGG
*
2285554 CACCTTTCAATCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
* * * * **
2285580 CACCTCTTAAAGCCCACACAAGTTGGTGG-
1 CACCT-TT-CAGTCCTCA-AAG-AGCAGGA
2285609 CACCTTTCAGTCCTCAAAGAGCAGGA
1 CACCTTTCAGTCCTCAAAGAGCAGGA
2285635 CACCTT
1 CACCTT
2285641 CAAAGCCCAC
Statistics
Matches: 43, Mismatches: 13, Indels: 10
0.65 0.20 0.15
Matches are distributed among these distances:
25 3 0.07
26 14 0.33
27 8 0.19
28 7 0.16
29 8 0.19
30 3 0.07
ACGTcount: A:0.30, C:0.32, G:0.17, T:0.21
Consensus pattern (26 bp):
CACCTTTCAGTCCTCAAAGAGCAGGA
Found at i:2292583 original size:7 final size:6
Alignment explanation
Indices: 2292520--2292589 Score: 50
Period size: 5 Copynumber: 12.8 Consensus size: 6
2292510 CCTTCTCTTC
2292520 AAAAA- AAAAA- AAAAA- AAAAA- AAAAA- AAAAA- AAAAA- AACAAA-
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AA-AAAG
*
2292561 AAAAAC AAAAA- AAAAAG AGAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG A-AAAAG AAAAA
2292590 CCTACTTAGC
Statistics
Matches: 61, Mismatches: 0, Indels: 7
0.90 0.00 0.10
Matches are distributed among these distances:
5 40 0.66
6 15 0.25
7 6 0.10
ACGTcount: A:0.93, C:0.03, G:0.04, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2292589 original size:1 final size:1
Alignment explanation
Indices: 2292520--2292576 Score: 96
Period size: 1 Copynumber: 57.0 Consensus size: 1
2292510 CCTTCTCTTC
* *
2292520 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2292577 GAGAAAAGAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:2300966 original size:1 final size:1
Alignment explanation
Indices: 2300960--2301036 Score: 100
Period size: 1 Copynumber: 77.0 Consensus size: 1
2300950 CCTTCTCTTC
* * * *
2300960 AAAAAAAAAAAAAAAAAAAAAAAAAAAAACAAAAAAAAAAAACAAAAAAAACAAAAAAAAAAAGA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
2301025 GAAAAGAAAAAA
1 AAAAAAAAAAAA
2301037 CCTACTTAAG
Statistics
Matches: 64, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 64 1.00
ACGTcount: A:0.92, C:0.04, G:0.04, T:0.00
Consensus pattern (1 bp):
A
Found at i:2302086 original size:55 final size:56
Alignment explanation
Indices: 2302001--2302846 Score: 1249
Period size: 55 Copynumber: 15.3 Consensus size: 56
2301991 TCCGCTTTTT
*
2302001 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
*
2302056 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
*
2302111 AGTCCTCAACGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
* * *
2302166 AGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
* *
2302222 AGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
* *
2302278 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCGCC-TTCT
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
*
2302333 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
* *
2302388 AATCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
* *
2302444 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCGCC-TTCT
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
* * *
2302499 AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCA-TTTTTC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
*
2302554 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
* *
2302609 AGTCCTCAAAGAACAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
2302664 AGTCCTCAAAGAGCAGGACACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCT-TTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
* * * *
2302719 ATTCCCCAAAGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTT-C
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
* * **
2302774 AGTCCTCAAAGAGCAGGACGCCTTTCAAAGCCCACACGAGTTGGTGGCA-CTTTTT
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
* *
2302829 ACTCCTCAATGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
2302847 TACAATTTAT
Statistics
Matches: 734, Mismatches: 41, Indels: 32
0.91 0.05 0.04
Matches are distributed among these distances:
54 11 0.01
55 560 0.76
56 161 0.22
57 2 0.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (56 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCC
Found at i:2302244 original size:27 final size:26
Alignment explanation
Indices: 2302158--2302244 Score: 70
Period size: 26 Copynumber: 3.2 Consensus size: 26
2302148 AAGTTGGTGG
2302158 CACCTTTCAGTCCCCAAAGAGCAGGA
1 CACCTTTCAGTCCCCAAAGAGCAGGA
* * **
2302184 CACCTCTCAAAG-CCCACACAAGTTGGTGG-
1 CACCTTTC--AGTCCC-CA-AAG-AGCAGGA
2302213 CACCTTTTCAGTCCCCAAAGAGCAGGA
1 CACC-TTTCAGTCCCCAAAGAGCAGGA
2302240 CACCT
1 CACCT
2302245 CTCAAAGCCC
Statistics
Matches: 45, Mismatches: 8, Indels: 16
0.65 0.12 0.23
Matches are distributed among these distances:
26 11 0.24
27 10 0.22
28 8 0.18
29 10 0.22
30 6 0.13
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.17
Consensus pattern (26 bp):
CACCTTTCAGTCCCCAAAGAGCAGGA
Found at i:2302400 original size:166 final size:166
Alignment explanation
Indices: 2302000--2302846 Score: 1339
Period size: 166 Copynumber: 5.1 Consensus size: 166
2301990 TTCCGCTTTT
* *
2302000 TAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCA
1 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTT-CAGTCCTCA
* *
2302064 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAACGAGCAGG
65 AAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAGG
2302128 ACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTT-
130 ACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
* *
2302164 TCAGTCCCCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTTCAGTCCCC
1 T-AGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACC-TTTCAGTCCTC
*
2302229 AAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAG
64 AAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAG
*
2302294 GACACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTC
129 GACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
*
2302332 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCAATCCTCAA
1 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
*
2302397 AGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAGGA
66 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAGGA
*
2302462 CACCTCTTAAAGCCCACACAAGTTGGTGGCGCCTTC
131 CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
**
2302498 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCATTTTTCAGTCCTCAA
1 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
* *
2302563 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCA-TTTTCCAGTCCTCAAAGAACAGGA
66 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAGGA
**
2302627 CACCT-TTCAAAGCCCACACAAGTTGGTGGCATTTTC
131 CACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTC
* * * *
2302663 CAGTCCTCAAAGAGCAGGACACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTTCATTCCCCAA
1 TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
* *
2302728 AGAGCAGGACACTTTTCAAAGCCCACACAAGTGGGTGGCACCTTT-CAGTCCTCAAAGAGCAGGA
66 AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAGGA
* * * *
2302792 CGCCT-TTCAAAGCCCACACGAGTTGGTGGCACTTTT
131 CACCTCTT-AAAGCCCACACAAGTTGGTGGCACCTTC
* *
2302828 TACTCCTCAATGAGCAGGA
1 TAGTCCTCAAAGAGCAGGA
2302847 TACAATTTAT
Statistics
Matches: 639, Mismatches: 37, Indels: 13
0.93 0.05 0.02
Matches are distributed among these distances:
164 3 0.00
165 262 0.41
166 264 0.41
167 109 0.17
168 1 0.00
ACGTcount: A:0.29, C:0.31, G:0.20, T:0.20
Consensus pattern (166 bp):
TAGTCCTCAAAGAGCAGGACACCTCTCAAAGCCCACACAAGTTGGTGGCACCTTTCAGTCCTCAA
AGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACCTTTCCAGTCCTCAAAGAGCAGGA
CACCTCTTAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:2302774 original size:29 final size:29
Alignment explanation
Indices: 2302627--2302774 Score: 71
Period size: 29 Copynumber: 5.3 Consensus size: 29
2302617 AAGAACAGGA
*
2302627 CACCTTTCAAAGCCCACACAAGTTGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
* * * * * * *
2302656 CA-TTTTC-CAGTCCTCA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
2302682 CACCTCTT-AAAGCCCACACAAGTTGGTGG
1 CACCT-TTCAAAGCCCACACAAGTGGGTGG
** * * *
2302711 CACCTTTC-ATTCCC-CA-AAGAGCAG-GA
1 CACCTTTCAAAGCCCACACAAGTG-GGTGG
*
2302737 CACTTTTCAAAGCCCACACAAGTGGGTGG
1 CACCTTTCAAAGCCCACACAAGTGGGTGG
2302766 CACCTTTCA
1 CACCTTTCA
2302775 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:2303449 original size:1 final size:1
Alignment explanation
Indices: 2303443--2303485 Score: 59
Period size: 1 Copynumber: 43.0 Consensus size: 1
2303433 AAAGTGTTTG
***
2303443 AAAAAAAAAAAAAAAATTGAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
2303486 TTTAAATGTA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.93, C:0.00, G:0.02, T:0.05
Consensus pattern (1 bp):
A
Found at i:2303464 original size:19 final size:19
Alignment explanation
Indices: 2303440--2303477 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
2303430 GATAAAGTGT
2303440 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
2303459 TTGAAAAAAAAAAAAAAAA
1 TTGAAAAAAAAAAAAAAAA
2303478 AAAAAAAATT
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:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (19 bp):
TTGAAAAAAAAAAAAAAAA
Found at i:2303514 original size:21 final size:21
Alignment explanation
Indices: 2303490--2303546 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
2303480 AAAAAATTTA
2303490 AATGTATCGATACATTTGTAG
1 AATGTATCGATACATTTGTAG
*
2303511 AATGTATCGATACATTTGTGG
1 AATGTATCGATACATTTGTAG
2303532 AATGTATCGATACAT
1 AATGTATCGATACAT
2303547 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:2303626 original size:19 final size:19
Alignment explanation
Indices: 2303602--2303669 Score: 85
Period size: 19 Copynumber: 3.9 Consensus size: 19
2303592 AATTCAACAA
2303602 TTTGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
2303621 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
2303636 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
2303653 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
2303670 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:2303641 original size:13 final size:13
Alignment explanation
Indices: 2303623--2303647 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2303613 ACATAAGTTT
2303623 TGTATCGATACAA
1 TGTATCGATACAA
2303636 TGTATCGATACA
1 TGTATCGATACA
2303648 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:2303645 original size:32 final size:32
Alignment explanation
Indices: 2303604--2303666 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2303594 TTCAACAATT
*
2303604 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
2303636 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
2303667 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:2303727 original size:13 final size:13
Alignment explanation
Indices: 2303709--2303734 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2303699 CATTTTTCTG
2303709 TGTATCGATACAT
1 TGTATCGATACAT
2303722 TGTATCGATACAT
1 TGTATCGATACAT
2303735 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:2303731 original size:33 final size:33
Alignment explanation
Indices: 2303689--2303755 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2303679 GCCAAGGAAA
***
2303689 TGTATCGATACATTTTTCTGTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
*
2303722 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACATGGATCTGTGTATCGATACAT
2303755 T
1 T
2303756 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:2306277 original size:52 final size:52
Alignment explanation
Indices: 2306204--2306585 Score: 261
Period size: 52 Copynumber: 7.3 Consensus size: 52
2306194 TTATTTTCGA
*
2306204 GGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 GGGGATACTCCAACTCCGGTTTTAT-GTTCAAAACACCAATTTTTCCACAATC
* * **
2306256 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATGTTCAAAACACCAATTTTTCC-ACAATC
* *
2306308 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATGTT-C-AAAACACCAATTTTTCCACAATC
* * *** * * *** **
2306360 GAGGATACTCCAAC-CTCGTTATTTCATCG-GGGATACTCCAACCCCGTT--ACTTTC
1 GGGGATACTCCAACTC-CGGT-TTT-AT-GTTCAAAACACCAA--TTTTTCCACAATC
*
2306414 GAGGGGATACTCCAACTCCGGTTTTATCGTT-AAAACACTAATTTTTCCACAATC
1 --GGGGATACTCCAACTCCGGTTTTAT-GTTCAAAACACCAATTTTTCCACAATC
* * **
2306468 GGGGATACTCCAA-TCCTGGTTTTATTTTCAAAACGCCAA-TTTTCCTTTAATC
1 GGGGATACTCCAACTCC-GGTTTTATGTTCAAAACACCAATTTTTCC-ACAATC
* *
2306520 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATC
1 GGGGATACTCCAACTCCGGTTTTATGTT-C-AAAACACCAATTTTTCCACAATC
*
2306572 GAGGATACTCCAAC
1 GGGGATACTCCAAC
2306586 CTCGTTATTT
Statistics
Matches: 257, Mismatches: 46, Indels: 54
0.72 0.13 0.15
Matches are distributed among these distances:
51 27 0.11
52 147 0.57
53 33 0.13
54 28 0.11
55 5 0.02
56 16 0.06
57 1 0.00
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (52 bp):
GGGGATACTCCAACTCCGGTTTTATGTTCAAAACACCAATTTTTCCACAATC
Found at i:2306357 original size:104 final size:103
Alignment explanation
Indices: 2306204--2306584 Score: 402
Period size: 104 Copynumber: 3.6 Consensus size: 103
2306194 TTATTTTCGA
* * *
2306204 GGGGATACTCCAACTCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAA
1 GGGGATACTCCAACTCCGATTTTATC-TTAAAACACCAATTTTTCCACAATCGAGGATACTCCAA
2306269 TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
65 TCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
*
2306308 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATCGAGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATCTT---AAAACACCAATTTTTCCACAATCGAGGATACTCC
* * * * ** * *
2306371 AA-CCTCG--TTATTTCATCGGGGATACTCCAA--CCCCGTTACTTTC
63 AATCCTGGTTTTATTT--TC---AAAACGCCAATTTTCCTTTA--ATC
* * *
2306414 GAGGGGATACTCCAACTCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCC
1 --GGGGATACTCCAACTCCGATTTTATC-TTAAAACACCAATTTTTCCACAATCGAGGATACTCC
2306479 AATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
63 AATCCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
*
2306520 GGGGATACTCCAACTCCGATTTTAT-TTCCAAAAATACCAATTTTT-CACAATCGAGGATACTCC
1 GGGGATACTCCAACTCCGATTTTATCTT---AAAACACCAATTTTTCCACAATCGAGGATACTCC
2306583 AA
63 AA
2306585 CCTCGTTATT
Statistics
Matches: 226, Mismatches: 28, Indels: 46
0.75 0.09 0.15
Matches are distributed among these distances:
101 6 0.03
102 4 0.02
103 6 0.03
104 91 0.40
105 26 0.12
106 18 0.08
107 13 0.06
108 48 0.21
109 6 0.03
110 2 0.01
111 6 0.03
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (103 bp):
GGGGATACTCCAACTCCGATTTTATCTTAAAACACCAATTTTTCCACAATCGAGGATACTCCAAT
CCTGGTTTTATTTTCAAAACGCCAATTTTCCTTTAATC
Found at i:2306393 original size:28 final size:30
Alignment explanation
Indices: 2306357--2306429 Score: 100
Period size: 28 Copynumber: 2.6 Consensus size: 30
2306347 ATTTTTCACA
* *
2306357 ATCGAGGATACTCCAACCTCGTTA-TTTC-
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
2306385 ATCGGGGATACTCCAACCCCGTTACTTTCG
1 ATCGGGGATACTCCAACCCCGTTACTTTCG
2306415 A--GGGGATACTCCAAC
1 ATCGGGGATACTCCAAC
2306430 TCCGGTTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
28 36 0.88
29 4 0.10
30 1 0.02
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (30 bp):
ATCGGGGATACTCCAACCCCGTTACTTTCG
Found at i:2306471 original size:212 final size:212
Alignment explanation
Indices: 2306089--2306652 Score: 1004
Period size: 212 Copynumber: 2.6 Consensus size: 212
2306079 AATTCTCCAC
* * *
2306089 AATCGAGGATATTCCAACTCCGATTTTATTTCCAAAAAAAATACCAATTTCTTCACAATCGGGGA
1 AATCGGGGATACTCCAACTCCGATTTTATTTCC---AAAAATACCAATTT-TTCACAATCGAGGA
* * *
2306154 TACTCCAACCCCGTTA-ATCATCGGGGATACTCCAACCCCGTTATTTTCGAGGGGATACTCCAAC
62 TACTCCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAAC
2306218 TCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTT
127 TCCGGTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTT
2306283 TCAAAACGCCAATTTTCCTTT
192 TCAAAACGCCAATTTTCCTTT
2306304 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
2306369 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
66 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
2306434 GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
131 GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
2306499 AACGCCAATTTTCCTTT
196 AACGCCAATTTTCCTTT
2306516 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
1 AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
* *
2306581 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTCCGAGGGGATACTCCAACCCCG
66 CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
*
2306646 GCTTTAT
131 GTTTTAT
2306653 TCCCAAAATA
Statistics
Matches: 339, Mismatches: 9, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
211 28 0.08
212 280 0.83
215 31 0.09
ACGTcount: A:0.28, C:0.27, G:0.14, T:0.32
Consensus pattern (212 bp):
AATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAATACCAATTTTTCACAATCGAGGATACT
CCAACCTCGTTATTTCATCGGGGATACTCCAACCCCGTTACTTTCGAGGGGATACTCCAACTCCG
GTTTTATCGTTAAAACACTAATTTTTCCACAATCGGGGATACTCCAATCCTGGTTTTATTTTCAA
AACGCCAATTTTCCTTT
Found at i:2306605 original size:28 final size:28
Alignment explanation
Indices: 2306569--2306645 Score: 100
Period size: 28 Copynumber: 2.8 Consensus size: 28
2306559 ATTTTTCACA
* * *
2306569 ATCGAGGATACTCCAACCTCGTTATTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
2306597 ATCGGGGATACTCCAACCCCGTTACTTC
1 ATCGGGGATACTCCAACCCCGTTACTTC
***
2306625 CGAGGGGATACTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
2306646 GCTTTATTCC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 43 1.00
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTACTTC
Found at i:2308777 original size:13 final size:13
Alignment explanation
Indices: 2308759--2308784 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2308749 ACAAAGATCC
2308759 ATGTATCGATACA
1 ATGTATCGATACA
2308772 ATGTATCGATACA
1 ATGTATCGATACA
2308785 CAGAAAAATG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:2308780 original size:33 final size:33
Alignment explanation
Indices: 2308738--2308804 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2308728 AAAATTTCCA
***
2308738 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
2308771 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
2308804 A
1 A
2308805 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:2308848 original size:19 final size:19
Alignment explanation
Indices: 2308824--2308910 Score: 123
Period size: 19 Copynumber: 4.9 Consensus size: 19
2308814 CAGTAGCTAA
*
2308824 TTATGTATCGATACAATAC
1 TTATGTATCGATACAAAAC
2308843 TTATGTATCGATAC---A-
1 TTATGTATCGATACAAAAC
2308858 -T-TGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
2308875 TTATGTATCGATACAAAAC
1 TTATGTATCGATACAAAAC
2308894 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
2308911 TCGTTGAATT
Statistics
Matches: 62, Mismatches: 0, Indels: 12
0.84 0.00 0.16
Matches are distributed among these distances:
13 11 0.18
14 1 0.02
16 2 0.03
18 1 0.02
19 47 0.76
ACGTcount: A:0.39, C:0.15, G:0.11, T:0.34
Consensus pattern (19 bp):
TTATGTATCGATACAAAAC
Found at i:2308864 original size:13 final size:13
Alignment explanation
Indices: 2308846--2308870 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2308836 ACAATACTTA
2308846 TGTATCGATACAT
1 TGTATCGATACAT
2308859 TGTATCGATACA
1 TGTATCGATACA
2308871 AAACTTATGT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2308868 original size:32 final size:32
Alignment explanation
Indices: 2308827--2308889 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
2308817 TAGCTAATTA
*
2308827 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
2308859 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
2308890 AAACTTATGT
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:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:2317587 original size:17 final size:17
Alignment explanation
Indices: 2317565--2317598 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
2317555 ACGTCCTCTC
2317565 TCCTCAACACTTTCTTG
1 TCCTCAACACTTTCTTG
*
2317582 TCCTCAACATTTTCTTG
1 TCCTCAACACTTTCTTG
2317599 CCGAGTGTAT
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:0.18, C:0.32, G:0.06, T:0.44
Consensus pattern (17 bp):
TCCTCAACACTTTCTTG
Found at i:2317885 original size:34 final size:35
Alignment explanation
Indices: 2317816--2317888 Score: 105
Period size: 34 Copynumber: 2.1 Consensus size: 35
2317806 CTGGTGTTTA
*
2317816 TGAAAGAATAAGCACAAAGGAATACAAATGAGCTT
1 TGAAAGAATAAGCACAAAGGAATACAAAAGAGCTT
*
2317851 TGAAAGAATAA-CAACAAA-GAATACAAAAGCGCTT
1 TGAAAGAATAAGC-ACAAAGGAATACAAAAGAGCTT
2317885 TGAA
1 TGAA
2317889 GTGTAGACAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
34 19 0.54
35 16 0.46
ACGTcount: A:0.53, C:0.12, G:0.18, T:0.16
Consensus pattern (35 bp):
TGAAAGAATAAGCACAAAGGAATACAAAAGAGCTT
Found at i:2318246 original size:20 final size:19
Alignment explanation
Indices: 2318201--2318252 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
2318191 CTATCAGTTT
**
2318201 CATGTATCGATACTATGAA
1 CATGTATCGATACTAACAA
2318220 CATGTATCGATACTAAACAA
1 CATGTATCGATACT-AACAA
*
2318240 TATGTATCGATAC
1 CATGTATCGATAC
2318253 ATCTGGGTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 14 0.48
20 15 0.52
ACGTcount: A:0.38, C:0.17, G:0.13, T:0.31
Consensus pattern (19 bp):
CATGTATCGATACTAACAA
Found at i:2325490 original size:3 final size:3
Alignment explanation
Indices: 2325482--2325525 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
2325472 TGAATCAACT
2325482 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
2325526 TTTGATGGTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.32, C:0.34, G:0.00, T:0.34
Consensus pattern (3 bp):
TCA
Found at i:2331453 original size:35 final size:35
Alignment explanation
Indices: 2331407--2331520 Score: 126
Period size: 35 Copynumber: 3.2 Consensus size: 35
2331397 AGGTGAGAGC
2331407 TTTAGTTGAAACCAGGGAGTTTGTAAATACTTGAT
1 TTTAGTTGAAACCAGGGAGTTTGTAAATACTTGAT
* ** *
2331442 TTTAGTTGAAACCAGAGGTGTTGATGTAGGTGA---GAGC
1 TTTAGTTGAAACCAG-GGAGTT--TGTAAAT-ACTTGA-T
2331479 TTTAGTTGAAACCAGGGAGTTTGTAAATACTTGAT
1 TTTAGTTGAAACCAGGGAGTTTGTAAATACTTGAT
2331514 TTTAGTT
1 TTTAGTT
2331521 TTTAAAATAT
Statistics
Matches: 63, Mismatches: 8, Indels: 16
0.72 0.09 0.18
Matches are distributed among these distances:
33 1 0.02
34 5 0.08
35 22 0.35
36 14 0.22
37 15 0.24
38 5 0.08
39 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.26, T:0.37
Consensus pattern (35 bp):
TTTAGTTGAAACCAGGGAGTTTGTAAATACTTGAT
Found at i:2331469 original size:72 final size:72
Alignment explanation
Indices: 2331383--2331520 Score: 276
Period size: 72 Copynumber: 1.9 Consensus size: 72
2331373 ATCGGCGGTG
2331383 AGAGGTGTTGATGTAGGTGAGAGCTTTAGTTGAAACCAGGGAGTTTGTAAATACTTGATTTTAGT
1 AGAGGTGTTGATGTAGGTGAGAGCTTTAGTTGAAACCAGGGAGTTTGTAAATACTTGATTTTAGT
2331448 TGAAACC
66 TGAAACC
2331455 AGAGGTGTTGATGTAGGTGAGAGCTTTAGTTGAAACCAGGGAGTTTGTAAATACTTGATTTTAGT
1 AGAGGTGTTGATGTAGGTGAGAGCTTTAGTTGAAACCAGGGAGTTTGTAAATACTTGATTTTAGT
2331520 T
66 T
2331521 TTTAAAATAT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 66 1.00
ACGTcount: A:0.28, C:0.07, G:0.30, T:0.35
Consensus pattern (72 bp):
AGAGGTGTTGATGTAGGTGAGAGCTTTAGTTGAAACCAGGGAGTTTGTAAATACTTGATTTTAGT
TGAAACC
Found at i:2331492 original size:37 final size:37
Alignment explanation
Indices: 2331383--2331493 Score: 124
Period size: 37 Copynumber: 3.1 Consensus size: 37
2331373 ATCGGCGGTG
2331383 AGAGGTGTTGATGTAGGTGAGAGCTTTAGTTGAAACC
1 AGAGGTGTTGATGTAGGTGAGAGCTTTAGTTGAAACC
* ** *
2331420 AG-GGAGTT--TGTAAAT-ACTTGA-TTTTAGTTGAAACC
1 AGAGGTGTTGATGTAGGTGA---GAGCTTTAGTTGAAACC
2331455 AGAGGTGTTGATGTAGGTGAGAGCTTTAGTTGAAACC
1 AGAGGTGTTGATGTAGGTGAGAGCTTTAGTTGAAACC
2331492 AG
1 AG
2331494 GGAGTTTGTA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
33 1 0.02
34 5 0.09
35 15 0.26
36 14 0.24
37 17 0.29
38 5 0.09
39 1 0.02
ACGTcount: A:0.29, C:0.08, G:0.32, T:0.32
Consensus pattern (37 bp):
AGAGGTGTTGATGTAGGTGAGAGCTTTAGTTGAAACC
Found at i:2331672 original size:15 final size:16
Alignment explanation
Indices: 2331640--2331675 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
2331630 TTACTTTATC
2331640 AAATATTATTATTAAA
1 AAATATTATTATTAAA
*
2331656 AAATATT-TTATTTAA
1 AAATATTATTATTAAA
2331671 AAATA
1 AAATA
2331676 ATTGATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.63
16 7 0.37
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
AAATATTATTATTAAA
Found at i:2331696 original size:48 final size:48
Alignment explanation
Indices: 2331640--2331748 Score: 125
Period size: 48 Copynumber: 2.3 Consensus size: 48
2331630 TTACTTTATC
* * * *
2331640 AAAT-ATTATTATTAAAAA-ATATTTTATTTAAAAATAATTGA-TGTTTA
1 AAATAATTATTATTAAAAATAAATTTCACTT-AAAATAATT-ATTATTTA
* *
2331687 GAATAATTATTGTTAAAAATAAATTTCACTTAAAATAATTATTATTTA
1 AAATAATTATTATTAAAAATAAATTTCACTTAAAATAATTATTATTTA
2331735 AAATAATTATTATT
1 AAATAATTATTATT
2331749 CAGTACAATT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
47 4 0.08
48 39 0.76
49 8 0.16
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (48 bp):
AAATAATTATTATTAAAAATAAATTTCACTTAAAATAATTATTATTTA
Found at i:2331700 original size:16 final size:16
Alignment explanation
Indices: 2331640--2331772 Score: 96
Period size: 16 Copynumber: 8.4 Consensus size: 16
2331630 TTACTTTATC
2331640 AAAT-ATTATTA-TTA
1 AAATAATTATTATTTA
*
2331654 AAA-AATATTTTATTTAA
1 AAATAAT-TATTATTT-A
*
2331671 AAATAATTGA-TGTTTA
1 AAATAATT-ATTATTTA
* * *
2331687 GAATAATTATTGTTAA
1 AAATAATTATTATTTA
* *
2331703 AAATAAATT-TCACTTA
1 AAAT-AATTATTATTTA
2331719 AAATAATTATTATTTA
1 AAATAATTATTATTTA
*
2331735 AAATAATTATTATTCA
1 AAATAATTATTATTTA
** *
2331751 GTACAATTATTATTTA
1 AAATAATTATTATTTA
2331767 AAATAA
1 AAATAA
2331773 ATTTAGTGTA
Statistics
Matches: 90, Mismatches: 20, Indels: 16
0.71 0.16 0.13
Matches are distributed among these distances:
14 5 0.06
15 9 0.10
16 60 0.67
17 13 0.14
18 3 0.03
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (16 bp):
AAATAATTATTATTTA
Found at i:2331875 original size:17 final size:16
Alignment explanation
Indices: 2331839--2331871 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2331829 CATAGTAGTC
*
2331839 TTATTATTTTACCTTT
1 TTATTACTTTACCTTT
2331855 TTATTACTTTA-CTTT
1 TTATTACTTTACCTTT
2331870 TT
1 TT
2331872 TTATGATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.18, C:0.12, G:0.00, T:0.70
Consensus pattern (16 bp):
TTATTACTTTACCTTT
Found at i:2332456 original size:16 final size:17
Alignment explanation
Indices: 2332413--2332456 Score: 56
Period size: 16 Copynumber: 2.7 Consensus size: 17
2332403 TAATTACTAT
2332413 TTAAATTAAA-ATAAAA
1 TTAAATTAAATATAAAA
* *
2332429 TTTAATTCAATA-AAAA
1 TTAAATTAAATATAAAA
2332445 TTAAATTAAATA
1 TTAAATTAAATA
2332457 CTATAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 22 0.96
17 1 0.04
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TTAAATTAAATATAAAA
Found at i:2332462 original size:21 final size:21
Alignment explanation
Indices: 2332420--2332462 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2332410 TATTTAAATT
* *
2332420 AAAATAAAATTTAATTCAATA
1 AAAATAAAATTAAATACAATA
* *
2332441 AAAATTAAATTAAATACTATA
1 AAAATAAAATTAAATACAATA
2332462 A
1 A
2332463 TTTAAATAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.33
Consensus pattern (21 bp):
AAAATAAAATTAAATACAATA
Found at i:2334538 original size:2 final size:2
Alignment explanation
Indices: 2334531--2334566 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2334521 TTATATTTAC
*
2334531 AT AT AT AT AT AT AT AT AT AT AT A- AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2334567 ATGAAAGTAT
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2335319 original size:17 final size:17
Alignment explanation
Indices: 2335292--2335326 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
2335282 ATTTTTTACC
2335292 TAAAATA-TTTTAATTA
1 TAAAATATTTTTAATTA
2335308 TAAAATTATTTTTAATTA
1 TAAAA-TATTTTTAATTA
2335326 T
1 T
2335327 TATTGAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.29
17 2 0.12
18 10 0.59
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAAATATTTTTAATTA
Found at i:2335869 original size:16 final size:16
Alignment explanation
Indices: 2335850--2335887 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
2335840 TAGAAATAAC
2335850 TTAATAAAAATTTAAT
1 TTAATAAAAATTTAAT
**
2335866 TTAATAGTAATTTAAT
1 TTAATAAAAATTTAAT
2335882 TTAATA
1 TTAATA
2335888 GTAATTAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (16 bp):
TTAATAAAAATTTAAT
Found at i:2335888 original size:16 final size:16
Alignment explanation
Indices: 2335858--2335893 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
2335848 ACTTAATAAA
2335858 AATTTAATTTAATAGT
1 AATTTAATTTAATAGT
2335874 AATTTAATTTAATAGT
1 AATTTAATTTAATAGT
2335890 AATT
1 AATT
2335894 AAATATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (16 bp):
AATTTAATTTAATAGT
Found at i:2336276 original size:47 final size:48
Alignment explanation
Indices: 2336188--2336283 Score: 131
Period size: 48 Copynumber: 2.0 Consensus size: 48
2336178 TAATAAAAAT
*
2336188 ATTAAAATTTTTAAATAATTATTATAATATCATATTATTATTATTTAA
1 ATTAAAATTTATAAATAATTATTATAATATCATATTATTATTATTTAA
* *
2336236 ATTAAAA-TTATAAATATATTTTTAATTATATCATATTTATTATTATTT
1 ATTAAAATTTATAAATA-ATTATT-ATAATATCATA-TTATTATTATTT
2336284 TCAATAATAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
47 8 0.19
48 12 0.29
49 10 0.24
50 12 0.29
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (48 bp):
ATTAAAATTTATAAATAATTATTATAATATCATATTATTATTATTTAA
Found at i:2336317 original size:27 final size:27
Alignment explanation
Indices: 2336287--2336344 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
2336277 ATTATTTTCA
* * *
2336287 ATAATATAATTATTAATTAT-AATAAAT
1 ATAATAAAAATATTAATAATGAA-AAAT
2336314 ATAATAAAAATATTAATAATGAAAAAT
1 ATAATAAAAATATTAATAATGAAAAAT
2336341 ATAA
1 ATAA
2336345 AATCATACAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
27 25 0.93
28 2 0.07
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (27 bp):
ATAATAAAAATATTAATAATGAAAAAT
Found at i:2337267 original size:42 final size:42
Alignment explanation
Indices: 2337208--2337292 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
2337198 AATAAGATAC
2337208 TATAATGTCTTAGACATTTAATAAAGATGAACTTTTTTTAAT
1 TATAATGTCTTAGACATTTAATAAAGATGAACTTTTTTTAAT
2337250 TATAATGTCTTAGACATTTAATAAAGATGAACTTTTTTTAAT
1 TATAATGTCTTAGACATTTAATAAAGATGAACTTTTTTTAAT
2337292 T
1 T
2337293 TATTTCGGGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.38, C:0.07, G:0.09, T:0.46
Consensus pattern (42 bp):
TATAATGTCTTAGACATTTAATAAAGATGAACTTTTTTTAAT
Found at i:2345043 original size:15 final size:16
Alignment explanation
Indices: 2344995--2345043 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
2344985 TTTAAAATTT
2344995 TAAACTTAATAAAAAT-
1 TAAACTTAA-AAAAATA
* *
2345011 TAAATTTAAACAAA-A
1 TAAACTTAAAAAAATA
2345026 TAAA-TTAAAAAAATA
1 TAAACTTAAAAAAATA
2345041 TAA
1 TAA
2345044 TATAAATAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 8 0.29
15 12 0.43
16 8 0.29
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (16 bp):
TAAACTTAAAAAAATA
Found at i:2345837 original size:33 final size:34
Alignment explanation
Indices: 2345764--2345874 Score: 90
Period size: 33 Copynumber: 3.4 Consensus size: 34
2345754 CGATTACATG
* * *
2345764 AATA-AAATATA-AAAAATAATTAAAATGTGATACA
1 AATATAAATATATAAACAT-ATTAAAAT-TTATATA
* *
2345798 AA-ATAAATATATAAATATTTTAAAATTTATAT-
1 AATATAAATATATAAACATATTAAAATTTATATA
* * *
2345830 AATATAAAT-TATTAACGTATTAATATTTATATA
1 AATATAAATATATAAACATATTAAAATTTATATA
2345863 AATATAAA-ATAT
1 AATATAAATATAT
2345875 TTTAAATATA
Statistics
Matches: 63, Mismatches: 9, Indels: 11
0.76 0.11 0.13
Matches are distributed among these distances:
32 20 0.32
33 22 0.35
34 16 0.25
35 5 0.08
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.38
Consensus pattern (34 bp):
AATATAAATATATAAACATATTAAAATTTATATA
Found at i:2346481 original size:6 final size:6
Alignment explanation
Indices: 2346470--2346496 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2346460 AATAAAATAA
2346470 AATATT AATATT AATATT AATATT AAT
1 AATATT AATATT AATATT AATATT AAT
2346497 TATATAAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
AATATT
Found at i:2346528 original size:23 final size:23
Alignment explanation
Indices: 2346502--2346546 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
2346492 TTAATTATAT
*
2346502 AAATAAATTTTAAATGATCTATC
1 AAATAAATTTCAAATGATCTATC
*
2346525 AAATAAGTTTCAAATGATCTAT
1 AAATAAATTTCAAATGATCTAT
2346547 AAACAAGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.38
Consensus pattern (23 bp):
AAATAAATTTCAAATGATCTATC
Found at i:2347154 original size:15 final size:15
Alignment explanation
Indices: 2347110--2347161 Score: 52
Period size: 15 Copynumber: 3.4 Consensus size: 15
2347100 TTTATTTGAT
*
2347110 ATTTATAAATTTTA-A
1 ATTT-TAAAATTTATA
*
2347125 ATATTAAATATTTATA
1 ATTTTAAA-ATTTATA
2347141 ATTTTAAAATTTATA
1 ATTTTAAAATTTATA
*
2347156 TTTTTA
1 ATTTTA
2347162 TATATATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 4 0.13
15 19 0.61
16 8 0.26
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATTTTAAAATTTATA
Found at i:2347525 original size:10 final size:10
Alignment explanation
Indices: 2347510--2347569 Score: 52
Period size: 10 Copynumber: 6.1 Consensus size: 10
2347500 TTTATTATGA
2347510 TAATATATTT
1 TAATATATTT
*
2347520 TAATATATTA
1 TAATATATTT
*
2347530 TAAT-TATAGT
1 TAATATAT-TT
* *
2347540 TAAAATATTA
1 TAATATATTT
*
2347550 T-ATAAATTT
1 TAATATATTT
2347559 TAATATATTT
1 TAATATATTT
2347569 T
1 T
2347570 TAAATTTATA
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
9 9 0.24
10 25 0.68
11 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
TAATATATTT
Found at i:2347562 original size:29 final size:29
Alignment explanation
Indices: 2347534--2347589 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2347524 ATATTATAAT
2347534 TATA-GTTAAAATATTATA-TAAATTTTAA
1 TATATGTTAAAAT-TTATATTAAATTTTAA
* *
2347562 TATATTTTTAAATTTATATTAAATTTTA
1 TATATGTTAAAATTTATATTAAATTTTA
2347590 TTTTAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 9 0.38
29 15 0.62
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.54
Consensus pattern (29 bp):
TATATGTTAAAATTTATATTAAATTTTAA
Found at i:2349450 original size:21 final size:21
Alignment explanation
Indices: 2349403--2349455 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 21
2349393 AGATAAAATA
*
2349403 TATTTTTTATATTTTTTTATTC
1 TATTTTTT-TATTTTTTTATAC
2349425 T-TTTTTTTATTTTTTTA-AC
1 TATTTTTTTATTTTTTTATAC
*
2349444 TAATTTTATTAT
1 T-ATTTTTTTAT
2349456 CACTAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 2 0.07
20 10 0.37
21 14 0.52
22 1 0.04
ACGTcount: A:0.21, C:0.04, G:0.00, T:0.75
Consensus pattern (21 bp):
TATTTTTTTATTTTTTTATAC
Found at i:2349508 original size:28 final size:30
Alignment explanation
Indices: 2349477--2349532 Score: 71
Period size: 28 Copynumber: 1.9 Consensus size: 30
2349467 TCAATAATAG
*
2349477 TAATTAATTAATT-T-AAGTAAAAATATTT
1 TAATAAATTAATTGTAAAGTAAAAATATTT
* *
2349505 TAATAAATTCATTGTAAAGTTAAAATAT
1 TAATAAATTAATTGTAAAGTAAAAATAT
2349533 AATTGAATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 11 0.48
29 1 0.04
30 11 0.48
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (30 bp):
TAATAAATTAATTGTAAAGTAAAAATATTT
Found at i:2349866 original size:21 final size:21
Alignment explanation
Indices: 2349842--2349882 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
2349832 CATAAAAATT
2349842 TAAAAAATAAAATTTTTATCC
1 TAAAAAATAAAATTTTTATCC
* *
2349863 TAAAAAATATATTTTTTATC
1 TAAAAAATAAAATTTTTATC
2349883 ACAATTTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (21 bp):
TAAAAAATAAAATTTTTATCC
Found at i:2351023 original size:12 final size:12
Alignment explanation
Indices: 2351018--2351044 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
2351008 ATATTTCATA
2351018 TTATATTATATT
1 TTATATTATATT
2351030 TTATATTATATT
1 TTATATTATATT
2351042 TTA
1 TTA
2351045 ATTTTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TTATATTATATT
Found at i:2351028 original size:17 final size:18
Alignment explanation
Indices: 2351003--2351041 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
2350993 ATCATATGTG
2351003 TATTAATATTTCATATTA
1 TATTAATATTTCATATTA
*
2351021 TATT-ATATTTTATATTA
1 TATTAATATTTCATATTA
2351038 TATT
1 TATT
2351042 TTAATTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (18 bp):
TATTAATATTTCATATTA
Found at i:2352496 original size:24 final size:24
Alignment explanation
Indices: 2352452--2352507 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
2352442 TAATTAGATC
*
2352452 AAATAATATTAAATATAATATAAAT
1 AAATAATATCAAATATAATAT-AAT
*
2352477 AAATAAT-TCAAATATGATATAAT
1 AAATAATATCAAATATAATATAAT
2352500 AAA-AATAT
1 AAATAATAT
2352508 TAAAAACGTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
22 3 0.11
23 7 0.25
24 11 0.39
25 7 0.25
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (24 bp):
AAATAATATCAAATATAATATAAT
Found at i:2353096 original size:21 final size:21
Alignment explanation
Indices: 2353055--2353096 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
2353045 CTGAATTTAA
* *
2353055 TTAAATTTAATATATGTTATT
1 TTAAATTTAACATATGCTATT
2353076 TTAAATTTGAACATAT-CTATT
1 TTAAATTT-AACATATGCTATT
2353097 GATATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.38, C:0.05, G:0.05, T:0.52
Consensus pattern (21 bp):
TTAAATTTAACATATGCTATT
Found at i:2353697 original size:20 final size:20
Alignment explanation
Indices: 2353674--2353712 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2353664 TAAATTATTT
2353674 ATATATCAA-AATTTAAATAA
1 ATATAT-AATAATTTAAATAA
*
2353694 ATATATAATATTTTAAATA
1 ATATATAATAATTTAAATA
2353713 TGATTATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
ATATATAATAATTTAAATAA
Found at i:2354653 original size:24 final size:25
Alignment explanation
Indices: 2354615--2354678 Score: 78
Period size: 26 Copynumber: 2.6 Consensus size: 25
2354605 TTATTATTTT
* *
2354615 ATTAA-AATATTTATA-TTTAATAC
1 ATTAATAATATATATATTTTAATAA
2354638 ATTAATAATATATATATTTTTAATAA
1 ATTAATAATATATATA-TTTTAATAA
*
2354664 AATAATAATATATAT
1 ATTAATAATATATAT
2354679 TATTAGAGAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
23 5 0.14
24 9 0.26
26 21 0.60
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (25 bp):
ATTAATAATATATATATTTTAATAA
Found at i:2356753 original size:2 final size:2
Alignment explanation
Indices: 2356746--2356793 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
2356736 TAATTATTTG
*
2356746 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2356788 AT AT AT
1 AT AT AT
2356794 GTAGCATGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2357050 original size:34 final size:34
Alignment explanation
Indices: 2357012--2357080 Score: 111
Period size: 34 Copynumber: 2.0 Consensus size: 34
2357002 GGAGGGTCAG
* *
2357012 TTATGGTGGGTCTTGACCCTTGATTGTTGGGTTA
1 TTATGGTGGGTCGTGACCCTTGAGTGTTGGGTTA
*
2357046 TTATGGTGGGTCGTGACTCTTGAGTGTTGGGTTA
1 TTATGGTGGGTCGTGACCCTTGAGTGTTGGGTTA
2357080 T
1 T
2357081 GAGATTATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.12, C:0.10, G:0.35, T:0.43
Consensus pattern (34 bp):
TTATGGTGGGTCGTGACCCTTGAGTGTTGGGTTA
Found at i:2357173 original size:19 final size:19
Alignment explanation
Indices: 2357149--2357209 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
2357139 GTTAAAAATT
*
2357149 TATATTATATAAATTTTAA
1 TATATTATATATATTTTAA
*
2357168 TATATT-TATATTATTTTTA
1 TATATTATATA-TATTTTAA
*
2357187 TATTTTA-ATATATTTTAA
1 TATATTATATATATTTTAA
2357205 T-TATT
1 TATATT
2357210 TTTATATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 3 0.09
18 12 0.34
19 20 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATATTATATATATTTTAA
Found at i:2357174 original size:25 final size:26
Alignment explanation
Indices: 2357146--2357209 Score: 78
Period size: 27 Copynumber: 2.5 Consensus size: 26
2357136 TATGTTAAAA
2357146 ATTTATATTA-TATAAATTTTAATAT
1 ATTTATATTATTATAAATTTTAATAT
* *
2357171 ATTTATATTATTTTTATATTTTAATAT
1 ATTTATATTA-TTATAAATTTTAATAT
2357198 ATTT-TAATTATT
1 ATTTAT-ATTATT
2357210 TTTATATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 10 0.29
26 3 0.09
27 21 0.62
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTATATTATTATAAATTTTAATAT
Found at i:2357188 original size:11 final size:11
Alignment explanation
Indices: 2357172--2357227 Score: 52
Period size: 10 Copynumber: 5.6 Consensus size: 11
2357162 TTTTAATATA
2357172 TTTATATTA-T
1 TTTATATTATT
2357182 TTT-TA-TATT
1 TTTATATTATT
*
2357191 TTAATA-TA-T
1 TTTATATTATT
2357200 TTTA-ATTATT
1 TTTATATTATT
*
2357210 TTTATATTATA
1 TTTATATTATT
2357221 TTTATAT
1 TTTATAT
2357228 AATATAATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
8 3 0.08
9 11 0.29
10 12 0.32
11 12 0.32
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TTTATATTATT
Found at i:2357199 original size:27 final size:27
Alignment explanation
Indices: 2357161--2357217 Score: 98
Period size: 27 Copynumber: 2.1 Consensus size: 27
2357151 TATTATATAA
2357161 ATTTTAATATA-TTTATATTATTTTTAT
1 ATTTTAATATATTTTA-ATTATTTTTAT
2357188 ATTTTAATATATTTTAATTATTTTTAT
1 ATTTTAATATATTTTAATTATTTTTAT
2357215 ATT
1 ATT
2357218 ATATTTATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
27 25 0.86
28 4 0.14
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
ATTTTAATATATTTTAATTATTTTTAT
Found at i:2357225 original size:38 final size:36
Alignment explanation
Indices: 2357146--2357234 Score: 115
Period size: 38 Copynumber: 2.4 Consensus size: 36
2357136 TATGTTAAAA
2357146 ATTTATATTATATAAATTTTAATATATTTATATTAT
1 ATTTATATTATATAAATTTTAATATATTTATATTAT
* * * *
2357182 TTTTATATTTTAATATATTTTAATTATTTTTATATTAT
1 ATTTATATTAT-ATAAATTTTAA-TATATTTATATTAT
*
2357220 ATTTATATAATATAA
1 ATTTATATTATATAA
2357235 TTATTTTATA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
36 9 0.21
37 13 0.30
38 21 0.49
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (36 bp):
ATTTATATTATATAAATTTTAATATATTTATATTAT
Found at i:2357236 original size:30 final size:28
Alignment explanation
Indices: 2357162--2357247 Score: 88
Period size: 27 Copynumber: 3.1 Consensus size: 28
2357152 ATTATATAAA
*
2357162 TTTTAATAT-ATTTATATTATTTTTATA-
1 TTTTAATATAATATA-ATTATTTTTATAT
* *
2357189 TTTTAATATATTTTAATTATTTTTATAT
1 TTTTAATATAATATAATTATTTTTATAT
*
2357217 TATATTTATATAATATAATTA-TTTTATAT
1 T-T-TTAATATAATATAATTATTTTTATAT
2357246 TT
1 TT
2357248 AAAATTATCA
Statistics
Matches: 51, Mismatches: 4, Indels: 7
0.82 0.06 0.11
Matches are distributed among these distances:
27 21 0.41
28 6 0.12
29 10 0.20
30 14 0.27
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (28 bp):
TTTTAATATAATATAATTATTTTTATAT
Found at i:2357595 original size:20 final size:19
Alignment explanation
Indices: 2357531--2357595 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
2357521 ATTTAATTAA
*
2357531 AATAAAT-TAAATATTAAAT
1 AATAAATAT-AATATTAAGT
* *
2357550 ATATAATTTTAATATTAAGT
1 A-ATAAATATAATATTAAGT
* *
2357570 ATTAAATATAATAATTAATT
1 AATAAATATAAT-ATTAAGT
2357590 AATAAA
1 AATAAA
2357596 AATATATTTG
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
19 9 0.25
20 26 0.72
21 1 0.03
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AATAAATATAATATTAAGT
Found at i:2357697 original size:16 final size:16
Alignment explanation
Indices: 2357664--2357697 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2357654 TTTCATAACT
**
2357664 TAAAAAATAATTTTAA
1 TAAAAAATAATTAAAA
2357680 TAAAAAATAATTAAAA
1 TAAAAAATAATTAAAA
2357696 TA
1 TA
2357698 GTAAAAACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAAAATAATTAAAA
Found at i:2358581 original size:2 final size:2
Alignment explanation
Indices: 2358574--2358600 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2358564 TGGTAATTTG
2358574 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2358601 ATTTCATTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2358842 original size:31 final size:33
Alignment explanation
Indices: 2358802--2358877 Score: 93
Period size: 31 Copynumber: 2.3 Consensus size: 33
2358792 TAATTTCATT
* * *
2358802 TAATATTTAAAAATATTTGAGTAAAAAA-AAATA
1 TAAT-TTTAAAAAAATTTAAATAAAAAATAAATA
*
2358835 -AGTTTTAAAAAAATTTAAATAAAAAATAAATA
1 TAATTTTAAAAAAATTTAAATAAAAAATAAATA
2358867 TAATTTTAAAA
1 TAATTTTAAAA
2358878 CATCAAAACT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 20 0.56
32 7 0.19
33 9 0.25
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (33 bp):
TAATTTTAAAAAAATTTAAATAAAAAATAAATA
Found at i:2359153 original size:2 final size:2
Alignment explanation
Indices: 2359146--2359181 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2359136 TATGCTTGAA
2359146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2359182 GCTTGGAGTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2359993 original size:18 final size:18
Alignment explanation
Indices: 2359970--2360047 Score: 57
Period size: 18 Copynumber: 4.0 Consensus size: 18
2359960 AAAATTAAAA
* *
2359970 TTTTAATATTTATAATTT
1 TTTTAAAATTTAAAATTT
2359988 TTTTAAAATTTAAAATTT
1 TTTTAAAATTTAAAATTT
*
2360006 AATTTTATTAAATTATATAATTAT
1 --TTTTA--AAATT-TAAAATT-T
* *
2360030 TTTTAAAAATTAATATTT
1 TTTTAAAATTTAAAATTT
2360048 AACCTATTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
18 17 0.35
19 5 0.10
20 9 0.19
22 10 0.21
23 6 0.12
24 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TTTTAAAATTTAAAATTT
Found at i:2360018 original size:22 final size:21
Alignment explanation
Indices: 2359986--2360072 Score: 63
Period size: 22 Copynumber: 4.0 Consensus size: 21
2359976 TATTTATAAT
2359986 TTTTTTAAAATTTAAAATTTAA
1 TTTTTT-AAATTTAAAATTTAA
*
2360008 TTTTATTAAATTATATAA-TT-A
1 TTTT-TTAAATT-TAAAATTTAA
* * *
2360029 TTTTTAAAAATTAATATTTAA
1 TTTTTTAAATTTAAAATTTAA
*
2360050 CCTATTTTAAATTT-AAATTTAA
1 --TTTTTTAAATTTAAAATTTAA
2360072 T
1 T
2360073 ATTTACAAGC
Statistics
Matches: 50, Mismatches: 9, Indels: 14
0.68 0.12 0.19
Matches are distributed among these distances:
19 3 0.06
20 8 0.16
21 6 0.12
22 18 0.36
23 15 0.30
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (21 bp):
TTTTTTAAATTTAAAATTTAA
Found at i:2360027 original size:23 final size:23
Alignment explanation
Indices: 2359963--2360017 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
2359953 AAATTTTAAA
*
2359963 ATTAAAATTTTAATATTTATAATTTT
1 ATTAAAA-TTTAA-AATT-TAATTTT
*
2359989 TTTAAAATTTAAAATTTAATTTT
1 ATTAAAATTTAAAATTTAATTTT
2360012 ATTAAA
1 ATTAAA
2360018 TTATATAATT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
23 12 0.46
24 3 0.12
25 5 0.19
26 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
ATTAAAATTTAAAATTTAATTTT
Found at i:2360060 original size:43 final size:39
Alignment explanation
Indices: 2359948--2360069 Score: 122
Period size: 41 Copynumber: 3.0 Consensus size: 39
2359938 AAAAATAATA
*
2359948 TTTAAAAATTTTAAAA-TTAAAATTTTAATATTTATAATTTT
1 TTTAAAAA--TTAAAATTTAATATTTTAA-ATTTATAATTTT
* *
2359989 TTTAAAATTTAAAATTTAATTTTATTAAATTATATAATTATT
1 TTTAAAAATTAAAATTTAATATT-TTAAATT-TATAATT-TT
*
2360031 TTTAAAAATTAATATTTAACCTATTTTAAATTTA-AATTT
1 TTTAAAAATTAAAATTTAA--TATTTTAAATTTATAATTT
2360070 AATATTTACA
Statistics
Matches: 69, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
39 6 0.09
40 10 0.14
41 22 0.32
42 21 0.30
43 7 0.10
44 3 0.04
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (39 bp):
TTTAAAAATTAAAATTTAATATTTTAAATTTATAATTTT
Found at i:2361301 original size:12 final size:12
Alignment explanation
Indices: 2361286--2361310 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2361276 TAAATTACTA
2361286 AAAAAATATCTT
1 AAAAAATATCTT
2361298 AAAAAATATCTT
1 AAAAAATATCTT
2361310 A
1 A
2361311 GATTTAAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (12 bp):
AAAAAATATCTT
Found at i:2361414 original size:24 final size:24
Alignment explanation
Indices: 2361387--2361456 Score: 70
Period size: 24 Copynumber: 2.8 Consensus size: 24
2361377 GGTTTTTTTA
*
2361387 AAAATAAATTATT-TATATTACTAT
1 AAAATAAATAATTGTATATTA-TAT
*
2361411 AAAAGAAATAATTGTATATTATAT
1 AAAATAAATAATTGTATATTATAT
* *
2361435 AATATAAACTACATAGTATATT
1 AAAATAAA-TA-ATTGTATATT
2361457 GAATAACTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
24 20 0.53
25 9 0.24
26 9 0.24
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.40
Consensus pattern (24 bp):
AAAATAAATAATTGTATATTATAT
Found at i:2361862 original size:35 final size:33
Alignment explanation
Indices: 2361809--2361918 Score: 84
Period size: 35 Copynumber: 3.2 Consensus size: 33
2361799 ATATAAAGAT
2361809 AAATAT-TTATAA-TATTATAATGTAAATATTAAA
1 AAATATATTA-AATTATTATAAT-TAAATATTAAA
* *
2361842 AAATATATTAAGTTATTTATATTTTAAA-ATTTAATA
1 AAATATATTAAATTA-TTATA-ATTAAATA-TTAA-A
*
2361878 AAAAATTATTAAATTATTATAGATTAAAT-TTAAA
1 AAATA-TATTAAATTATTATA-ATTAAATATTAAA
2361912 AACATAT
1 AA-ATAT
2361919 TTTTAATAAA
Statistics
Matches: 61, Mismatches: 7, Indels: 17
0.72 0.08 0.20
Matches are distributed among these distances:
33 7 0.11
34 10 0.16
35 19 0.31
36 16 0.26
37 9 0.15
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.44
Consensus pattern (33 bp):
AAATATATTAAATTATTATAATTAAATATTAAA
Found at i:2363647 original size:16 final size:14
Alignment explanation
Indices: 2363613--2363642 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2363603 AAAATGTGCG
*
2363613 TTAAATATGAATAT
1 TTAAATATAAATAT
2363627 TTAAATATAAATAT
1 TTAAATATAAATAT
2363641 TT
1 TT
2363643 TTAAAAAATA
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (14 bp):
TTAAATATAAATAT
Found at i:2365139 original size:16 final size:18
Alignment explanation
Indices: 2365120--2365152 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2365110 CTCAATTTCT
2365120 TTTCT-TTTGAG-TCCAG
1 TTTCTGTTTGAGCTCCAG
2365136 TTTCTGTTTGAGCTCCA
1 TTTCTGTTTGAGCTCCA
2365153 ACCTAGAGAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 6 0.40
18 4 0.27
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.48
Consensus pattern (18 bp):
TTTCTGTTTGAGCTCCAG
Found at i:2366276 original size:18 final size:18
Alignment explanation
Indices: 2366253--2366337 Score: 52
Period size: 17 Copynumber: 4.7 Consensus size: 18
2366243 ATTTATATTT
2366253 AATATATATTTAAATATA
1 AATATATATTTAAATATA
*
2366271 AATATAATTTTTTAAAAATATA
1 AATAT-A-TATTT--AAATATA
* * *
2366293 AA-AAAT-TTTAAAAAATT
1 AATATATATTT-AAATATA
*
2366310 AA-ATATATTCAAAT-TA
1 AATATATATTTAAATATA
2366326 AATATATATTTA
1 AATATATATTTA
2366338 TATAACATTA
Statistics
Matches: 52, Mismatches: 9, Indels: 13
0.70 0.12 0.18
Matches are distributed among these distances:
16 3 0.06
17 22 0.42
18 10 0.19
19 2 0.04
20 5 0.10
21 1 0.02
22 9 0.17
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.42
Consensus pattern (18 bp):
AATATATATTTAAATATA
Found at i:2366307 original size:20 final size:22
Alignment explanation
Indices: 2366264--2366316 Score: 60
Period size: 22 Copynumber: 2.6 Consensus size: 22
2366254 ATATATATTT
**
2366264 AAATATAAATATAATTTTTTAA
1 AAATATAAATATAATTTTAAAA
2366286 AAATATAAA-A-AATTTT-AAA
1 AAATATAAATATAATTTTAAAA
2366305 AAAT-TAAATATA
1 AAATATAAATATA
2366317 TTCAAATTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 4 0.14
19 7 0.25
20 7 0.25
21 1 0.04
22 9 0.32
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATATAAATATAATTTTAAAA
Found at i:2366691 original size:18 final size:18
Alignment explanation
Indices: 2366668--2366709 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
2366658 ATTAAATATG
* *
2366668 AATATTTTTATATTTTTA
1 AATATTTTTATATATTAA
2366686 AATATTTTTATATATTAA
1 AATATTTTTATATATTAA
2366704 AATATT
1 AATATT
2366710 ATATTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATATTTTTATATATTAA
Found at i:2366753 original size:39 final size:39
Alignment explanation
Indices: 2366652--2366757 Score: 110
Period size: 39 Copynumber: 2.7 Consensus size: 39
2366642 TGGAATATAG
* *
2366652 ATATGTATTAAATATGAATATTTTTATATTTTTAAATATTT
1 ATATATATTAAATATAAATATTTTTATA-TTTT-AATATTT
* *
2366693 TTATATATTAAA-ATATTATATTTTTATA-TTT-ATATTT
1 ATATATATTAAATATA-AATATTTTTATATTTTAATATTT
2366730 AAATATATATTAAATATAAATATTTTTA
1 --ATATATATTAAATATAAATATTTTTA
2366758 AAAAAATAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
37 6 0.11
39 23 0.42
40 5 0.09
41 21 0.38
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (39 bp):
ATATATATTAAATATAAATATTTTTATATTTTAATATTT
Found at i:2369334 original size:23 final size:23
Alignment explanation
Indices: 2369291--2369337 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
2369281 TAGATGTATT
*
2369291 TAAATTTATTCATTTAAATTAAA
1 TAAATTTATTCATTAAAATTAAA
*
2369314 TAAATTTATTTA-TAAATATTAAA
1 TAAATTTATTCATTAAA-ATTAAA
2369337 T
1 T
2369338 GAACGTGTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 3 0.14
23 18 0.86
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAATTTATTCATTAAAATTAAA
Found at i:2374014 original size:24 final size:25
Alignment explanation
Indices: 2373987--2374035 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
2373977 AATCCAAAGG
2373987 AAAT-CACCATTTTTGACAAACACA
1 AAATACACCATTTTTGACAAACACA
2374011 AAATAACCACCATTTTTGACAAACA
1 AAAT-A-CACCATTTTTGACAAACA
2374036 AATGGGTGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 4 0.18
27 18 0.82
ACGTcount: A:0.47, C:0.24, G:0.04, T:0.24
Consensus pattern (25 bp):
AAATACACCATTTTTGACAAACACA
Found at i:2379006 original size:21 final size:21
Alignment explanation
Indices: 2378969--2379022 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
2378959 TAAACATATT
* * *
2378969 TTTTTAT-TATGTAATTATAA
1 TTTTTATATATATTATTAAAA
2378989 TTTTTATATATATTATTAAAA
1 TTTTTATATATATTATTAAAA
*
2379010 TATTTATAT-TATT
1 TTTTTATATATATT
2379023 TATATTTAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
20 11 0.38
21 18 0.62
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTTATATATATTATTAAAA
Found at i:2379039 original size:24 final size:26
Alignment explanation
Indices: 2378992--2379039 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
2378982 ATTATAATTT
*
2378992 TTATATATATTATTAAAATATTTATA
1 TTATATATATTATAAAAATATTTATA
*
2379018 TTATTTATATT-TAAAAAT-TTTA
1 TTATATATATTATAAAAATATTTA
2379040 AGATTTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 4 0.20
25 6 0.30
26 10 0.50
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (26 bp):
TTATATATATTATAAAAATATTTATA
Found at i:2379427 original size:20 final size:20
Alignment explanation
Indices: 2379402--2379444 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
2379392 ATAATAATTA
2379402 TTTTTAAAAA-TTTAAGAAAT
1 TTTTTAAAAATTTTAA-AAAT
2379422 TTTTTAAAAATTTTAAAAAT
1 TTTTTAAAAATTTTAAAAAT
2379442 TTT
1 TTT
2379445 ATTTTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (20 bp):
TTTTTAAAAATTTTAAAAAT
Found at i:2379444 original size:9 final size:9
Alignment explanation
Indices: 2379403--2379445 Score: 52
Period size: 9 Copynumber: 4.6 Consensus size: 9
2379393 TAATAATTAT
2379403 TTTTAAAAA
1 TTTTAAAAA
2379412 -TTTAAGAAA
1 TTTTAA-AAA
2379421 TTTTTTAAAAA
1 --TTTTAAAAA
2379432 TTTTAAAAA
1 TTTTAAAAA
2379441 TTTTA
1 TTTTA
2379446 TTTTTTTTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
8 5 0.17
9 17 0.57
11 3 0.10
12 5 0.17
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:2379472 original size:32 final size:33
Alignment explanation
Indices: 2379434--2379500 Score: 109
Period size: 33 Copynumber: 2.1 Consensus size: 33
2379424 TTTAAAAATT
**
2379434 TTAAAAATTTTATTT-TTTTTAATATTATTAAA
1 TTAAAAATGATATTTATTTTTAATATTATTAAA
2379466 TTAAAAATGATATTTATTTTTAATATTATTAAA
1 TTAAAAATGATATTTATTTTTAATATTATTAAA
2379499 TT
1 TT
2379501 TAAGATATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (33 bp):
TTAAAAATGATATTTATTTTTAATATTATTAAA
Found at i:2379508 original size:30 final size:31
Alignment explanation
Indices: 2379444--2379513 Score: 99
Period size: 33 Copynumber: 2.3 Consensus size: 31
2379434 TTAAAAATTT
2379444 TATTTTTTTTAATATTATTAAATTAAAAATGA
1 TATTTTTTTTAATATTATTAAATT-AAAATGA
*
2379476 TATTTATTTTTAATATTATTAAATT-TAA-GA
1 TATTT-TTTTTAATATTATTAAATTAAAATGA
2379506 TATTTTTT
1 TATTTTTT
2379514 AATAGTGTGA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
29 3 0.08
30 7 0.19
31 2 0.06
32 5 0.14
33 19 0.53
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.59
Consensus pattern (31 bp):
TATTTTTTTTAATATTATTAAATTAAAATGA
Found at i:2379881 original size:15 final size:14
Alignment explanation
Indices: 2379841--2379900 Score: 54
Period size: 13 Copynumber: 4.2 Consensus size: 14
2379831 TTTTAATTGA
2379841 TTTATATAA-TTATTT
1 TTTA-ATAATTTA-TT
2379856 TTTAA-AATTTATT
1 TTTAATAATTTATT
*
2379869 TTTAATAATTTTAAAT
1 TTTAATAA-TTT-ATT
2379885 TTT-ATAATTTATT
1 TTTAATAATTTATT
2379898 TTT
1 TTT
2379901 TTATTTTTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
13 14 0.36
14 9 0.23
15 11 0.28
16 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TTTAATAATTTATT
Found at i:2379887 original size:29 final size:28
Alignment explanation
Indices: 2379855--2379913 Score: 82
Period size: 29 Copynumber: 2.1 Consensus size: 28
2379845 TATAATTATT
2379855 TTTTAAAATTTATTTTTAATAATTTTAAA
1 TTTTAAAATTTATTTTT-ATAATTTTAAA
* * *
2379884 TTTTATAATTTATTTTTTTATTTTTAAA
1 TTTTAAAATTTATTTTTATAATTTTAAA
2379912 TT
1 TT
2379914 ACTATTTGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (28 bp):
TTTTAAAATTTATTTTTATAATTTTAAA
Found at i:2379904 original size:15 final size:14
Alignment explanation
Indices: 2379845--2379901 Score: 62
Period size: 14 Copynumber: 4.1 Consensus size: 14
2379835 AATTGATTTA
2379845 TATAA-TTATTTTT
1 TATAATTTATTTTT
*
2379858 TAAAATTTATTTTT
1 TATAATTTATTTTT
* **
2379872 AATAATTTTAAATTT
1 TATAA-TTTATTTTT
2379887 TATAATTTATTTTT
1 TATAATTTATTTTT
2379901 T
1 T
2379902 TATTTTTAAA
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
13 4 0.12
14 19 0.56
15 11 0.32
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (14 bp):
TATAATTTATTTTT
Found at i:2380071 original size:16 final size:16
Alignment explanation
Indices: 2380012--2380069 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
2380002 ATCAAAATTT
2380012 TAAATATTAAATAT-A
1 TAAATATTAAATATAA
* * *
2380027 T-GATTTTAATATTTAA
1 TAAATATTAA-ATATAA
2380043 TAAATATTAAATATAA
1 TAAATATTAAATATAA
2380059 TAAATAATTAA
1 TAAAT-ATTAA
2380070 TAAAAATAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
14 6 0.18
15 4 0.12
16 12 0.36
17 11 0.33
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TAAATATTAAATATAA
Found at i:2380073 original size:20 final size:20
Alignment explanation
Indices: 2380050--2380090 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
2380040 TAATAAATAT
* * *
2380050 TAAATATAATAAATAATTAA
1 TAAAAATAAAAAAAAATTAA
2380070 TAAAAATAAAAAAAAATTAA
1 TAAAAATAAAAAAAAATTAA
2380090 T
1 T
2380091 TTAATAATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAAAATAAAAAAAAATTAA
Found at i:2380777 original size:24 final size:24
Alignment explanation
Indices: 2380750--2380813 Score: 75
Period size: 22 Copynumber: 2.9 Consensus size: 24
2380740 TTATATTACT
2380750 ATTTAATTAATAAAAAATATTTAA
1 ATTTAATTAATAAAAAATATTTAA
*
2380774 ATTTAATT-AT-AAAAATATATAA
1 ATTTAATTAATAAAAAATATTTAA
*
2380796 A---AATTAATATAAAATATT
1 ATTTAATTAATAAAAAATATT
2380814 AAGCCAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
19 4 0.11
20 2 0.06
21 7 0.20
22 12 0.34
23 2 0.06
24 8 0.23
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (24 bp):
ATTTAATTAATAAAAAATATTTAA
Found at i:2383223 original size:2 final size:2
Alignment explanation
Indices: 2383216--2383249 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2383206 ACGCACATAA
2383216 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2383250 TACTAGTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2385139 original size:32 final size:31
Alignment explanation
Indices: 2385079--2385139 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
2385069 AAATATTTAT
* * *
2385079 TTAATTTTTAAAAAAGATTTGAACAAAAATA
1 TTAAATTTTAAAAAAAATTTAAACAAAAATA
*
2385110 TTAAATTTTAAAAACAAATTTAAATAAAAA
1 TTAAATTTTAAAAA-AAATTTAAACAAAAA
2385140 AATTTCAGTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 13 0.52
32 12 0.48
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (31 bp):
TTAAATTTTAAAAAAAATTTAAACAAAAATA
Found at i:2390493 original size:20 final size:20
Alignment explanation
Indices: 2390468--2390541 Score: 96
Period size: 20 Copynumber: 3.7 Consensus size: 20
2390458 TACCCGAATG
2390468 TATCGATACATTTTTCAATA
1 TATCGATACATTTTTCAATA
* * *
2390488 TATCGATACATGTATGAA-A
1 TATCGATACATTTTTCAATA
*
2390507 GTATCGATACATTTTTCAATG
1 -TATCGATACATTTTTCAATA
2390528 TATCGATACATTTT
1 TATCGATACATTTT
2390542 ATCTTTTTAC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
19 1 0.02
20 44 0.98
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.42
Consensus pattern (20 bp):
TATCGATACATTTTTCAATA
Found at i:2393865 original size:27 final size:27
Alignment explanation
Indices: 2393826--2393877 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
2393816 ATTAACTCAT
2393826 ATAATTATCATAAAAAGA-TAATATTAA
1 ATAATTATCATAAAAA-ATTAATATTAA
*
2393853 ATAATTATTATAAAAAATTAATATT
1 ATAATTATCATAAAAAATTAATATT
2393878 GATTAAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (27 bp):
ATAATTATCATAAAAAATTAATATTAA
Found at i:2393946 original size:20 final size:19
Alignment explanation
Indices: 2393914--2393952 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
2393904 CAATTATAAT
2393914 TATTTTTATATTAATATTTA
1 TATTTTTATATTAA-ATTTA
2393934 TATTTGTTA-ATTAAATTTA
1 TATTT-TTATATTAAATTTA
2393953 AATAAAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.28
20 10 0.56
21 3 0.17
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (19 bp):
TATTTTTATATTAAATTTA
Done.