Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 ID=Chr11-JGI_221_v2.0
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: 62681010
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1052928 characters in sequence are not A, C, G, or T
File 55 of 210
Found at i:16796214 original size:41 final size:41
Alignment explanation
Indices: 16796144--16796464 Score: 333
Period size: 41 Copynumber: 7.8 Consensus size: 41
16796134 AATTCTTTGG
*** * *
16796144 CCTTTAGCGGCGTTTTTGGTTATGTGCCGCTAATGCTCGGA
1 CCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAATGCTCGGA
* *
16796185 CCTTTAGCGGCGTTTTTTAGTAAGCGCCGCTAACGCTCGGA
1 CCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAATGCTCGGA
* *
16796226 CCTTTAGCAGCGTTTTTTACTAAGCGCCGCTAACGCTCGGA
1 CCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAATGCTCGGA
* * *
16796267 CCTTTAGCGGCGTTTTTTACTAAGCGTCGCTAAAGCTTGGA
1 CCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAATGCTCGGA
* * *
16796308 ACTTTAGCGGCGGTTTTATT--TAAGTGCCGCTAATGCTCGGG
1 CCTTTAGCGGC-GTTTT-TTACTAAGCGCCGCTAATGCTCGGA
* * *
16796349 CCTTTAGTGGCGTTTTTAATTAAGCGCCGCTAATGCTCTGG-
1 CCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAATGCTC-GGA
* * * **** * **
16796390 CCTTTAGAGGTGCTTTCGGGTAAGCGTCGCTAATGCTCTTA
1 CCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAATGCTCGGA
*
16796431 CCTTTAGCGGCGTTTTTGACTAAGCGCCGCTAAT
1 CCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAAT
16796465 AGTAACAAAA
Statistics
Matches: 235, Mismatches: 39, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.00
40 5 0.02
41 220 0.94
42 7 0.03
43 2 0.01
ACGTcount: A:0.17, C:0.24, G:0.26, T:0.33
Consensus pattern (41 bp):
CCTTTAGCGGCGTTTTTTACTAAGCGCCGCTAATGCTCGGA
Found at i:16797050 original size:15 final size:16
Alignment explanation
Indices: 16797016--16797053 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
16797006 TTTAAGGTTA
16797016 ATTTAGGGGTTAGAGG
1 ATTTAGGGGTTAGAGG
*
16797032 -TTTAGGGGTTTG-GG
1 ATTTAGGGGTTAGAGG
16797046 ATTTAGGG
1 ATTTAGGG
16797054 TTTCAACGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 2 0.10
15 18 0.90
ACGTcount: A:0.18, C:0.00, G:0.45, T:0.37
Consensus pattern (16 bp):
ATTTAGGGGTTAGAGG
Found at i:16797410 original size:15 final size:16
Alignment explanation
Indices: 16797390--16797426 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
16797380 TATAGGACCA
*
16797390 AAATAATAT-TAAAAT
1 AAATAATATAAAAAAT
16797405 AAATAA-ATAAAAAAT
1 AAATAATATAAAAAAT
16797420 AAATAAT
1 AAATAAT
16797427 TATACAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
14 2 0.11
15 17 0.89
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAATATAAAAAAT
Found at i:16801196 original size:19 final size:19
Alignment explanation
Indices: 16801169--16801213 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
16801159 TTATATACAG
16801169 TTTTAATATATATATT-AAAA
1 TTTT-ATATATAT-TTGAAAA
16801189 TTTTATATATATTTGAAAA
1 TTTTATATATATTTGAAAA
*
16801208 ATTTAT
1 TTTTAT
16801214 CAATCATATC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 2 0.09
19 17 0.74
20 4 0.17
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTATATATATTTGAAAA
Found at i:16801292 original size:12 final size:12
Alignment explanation
Indices: 16801275--16801344 Score: 51
Period size: 12 Copynumber: 6.1 Consensus size: 12
16801265 TGCACAACAC
16801275 ATAACTTAAATA
1 ATAACTTAAATA
*
16801287 ATAACTT--A-C
1 ATAACTTAAATA
*
16801296 ATAACTTATAT-
1 ATAACTTAAATA
*
16801307 ATAAACTTATA-A
1 AT-AACTTAAATA
*
16801319 ATAACTTACATA
1 ATAACTTAAATA
16801331 CATAACTTAAATA
1 -ATAACTTAAATA
16801344 A
1 A
16801345 AATTTATATA
Statistics
Matches: 48, Mismatches: 3, Indels: 14
0.74 0.05 0.22
Matches are distributed among these distances:
9 7 0.15
10 1 0.02
11 10 0.21
12 19 0.40
13 11 0.23
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (12 bp):
ATAACTTAAATA
Found at i:16801297 original size:21 final size:21
Alignment explanation
Indices: 16801275--16801344 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
16801265 TGCACAACAC
*
16801275 ATAACTTAAATAATAACTTAC
1 ATAACTTAAATAATAACTTAA
*
16801296 ATAACTTATAT-ATAAACTTATAA
1 ATAACTTAAATAAT-AAC-T-TAA
*
16801319 ATAACTTACATACATAACTTAA
1 ATAACTTAAATA-ATAACTTAA
16801341 ATAA
1 ATAA
16801345 AATTTATATA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
20 2 0.05
21 13 0.32
22 8 0.20
23 13 0.32
24 3 0.07
25 2 0.05
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (21 bp):
ATAACTTAAATAATAACTTAA
Found at i:16801305 original size:49 final size:48
Alignment explanation
Indices: 16801223--16801411 Score: 197
Period size: 49 Copynumber: 3.9 Consensus size: 48
16801213 TCAATCATAT
* * * *
16801223 CATAATTTACATACATAACATATATAAATTTATATATAAACTTGCACAACA
1 CATAACTTACATA-ATAACTTACAT-AACTTATATATAAACTTGCACAA-A
* *
16801274 CATAACTTAAATAATAACTTACATAACTTATATATAAACTT--A-TAA
1 CATAACTTACATAATAACTTACATAACTTATATATAAACTTGCACAAA
* * *
16801319 -ATAACTTACATACATAACTTAAATAAAATTTATATATAAACTTACACAAAA
1 CATAACTTACATA-ATAACTTACAT--AACTTATATATAAACTTGCAC-AAA
*
16801370 CATAACTTACACAATAACTTACATAACTTATATATAAACTTG
1 CATAACTTACATAATAACTTACATAACTTATATATAAACTTG
16801412 TATATAACTT
Statistics
Matches: 116, Mismatches: 14, Indels: 18
0.78 0.09 0.12
Matches are distributed among these distances:
44 11 0.09
45 11 0.09
46 1 0.01
47 17 0.15
49 33 0.28
50 9 0.08
51 23 0.20
52 11 0.09
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.33
Consensus pattern (48 bp):
CATAACTTACATAATAACTTACATAACTTATATATAAACTTGCACAAA
Found at i:16801322 original size:23 final size:23
Alignment explanation
Indices: 16801296--16801362 Score: 73
Period size: 23 Copynumber: 2.9 Consensus size: 23
16801286 AATAACTTAC
16801296 ATAACTTATATATAAACTTATAA-
1 ATAACTTATATATAAACTTA-AAT
* *
16801319 ATAACTTACATACATAACTTAAAT
1 ATAACTTATATATA-AACTTAAAT
* *
16801343 AAAATTTATATATAAACTTA
1 ATAACTTATATATAAACTTA
16801363 CACAAAACAT
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
23 20 0.56
24 16 0.44
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.37
Consensus pattern (23 bp):
ATAACTTATATATAAACTTAAAT
Found at i:16801324 original size:32 final size:32
Alignment explanation
Indices: 16801277--16801431 Score: 115
Period size: 32 Copynumber: 4.8 Consensus size: 32
16801267 CACAACACAT
*
16801277 AACTTAAATAATAACTTACATAACTTATATATA
1 AACTTATA-AATAACTTACATAACTTATATATA
*
16801310 AACTTATAAATAACTTACATACATAACTTAAATA-A
1 AACTTATAAATAAC-T---TACATAACTTATATATA
* * * *
16801345 AATTTATATATAAACTTACACAA---A-ACAT-
1 AACTTATAAAT-AACTTACATAACTTATATATA
*
16801373 AACTTACACAATAACTTACATAACTTATATATA
1 AACTTATA-AATAACTTACATAACTTATATATA
* * *
16801406 AACTTGTATATAACTTTCATAACTTA
1 AACTTATAAATAACTTACATAACTTA
16801432 CTTATAATAA
Statistics
Matches: 95, Mismatches: 15, Indels: 25
0.70 0.11 0.19
Matches are distributed among these distances:
28 18 0.19
29 3 0.03
31 1 0.01
32 31 0.33
33 14 0.15
35 11 0.12
36 17 0.18
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.35
Consensus pattern (32 bp):
AACTTATAAATAACTTACATAACTTATATATA
Found at i:16801337 original size:57 final size:58
Alignment explanation
Indices: 16801234--16801344 Score: 147
Period size: 57 Copynumber: 1.9 Consensus size: 58
16801224 ATAATTTACA
* *
16801234 TACATAACATATATAAATTTATATATAAACTTGCACAACACATAACTTAAATAATAACT
1 TACATAACATATATAAACTTATAAATAAACTT-CACAACACATAACTTAAATAATAACT
*
16801293 TACATAACTTATATATAAACTTATAAAT-AACTT-AC-ATACATAACTTAAATAA
1 TACATAAC--ATATATAAACTTATAAATAAACTTCACAACACATAACTTAAATAA
16801345 AATTTATATA
Statistics
Matches: 47, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
57 16 0.34
58 2 0.04
59 8 0.17
60 5 0.11
61 16 0.34
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.33
Consensus pattern (58 bp):
TACATAACATATATAAACTTATAAATAAACTTCACAACACATAACTTAAATAATAACT
Found at i:16801397 original size:9 final size:9
Alignment explanation
Indices: 16801369--16802223 Score: 201
Period size: 9 Copynumber: 100.1 Consensus size: 9
16801359 CTTACACAAA
16801369 ACATAACTT
1 ACATAACTT
16801378 ACACAATAACTT
1 --AC-ATAACTT
16801390 ACATAACTTAT
1 ACATAAC-T-T
*
16801401 ATATAAACTTGT
1 ACAT-AAC-T-T
*
16801413 ATATAACTT
1 ACATAACTT
*
16801422 TCATAACTT
1 ACATAACTT
*
16801431 AC-TTA--T
1 ACATAACTT
16801437 A-ATAACTT
1 ACATAACTT
*
16801445 CCATAAC--
1 ACATAACTT
*
16801452 ACATAGCTT
1 ACATAACTT
*
16801461 ACATGACTT
1 ACATAACTT
16801470 ACATAA--T
1 ACATAACTT
*
16801477 ACACAACTT
1 ACATAACTT
* *
16801486 AAATAATTT
1 ACATAACTT
*
16801495 AAATAACTT
1 ACATAACTT
16801504 ACATAA--T
1 ACATAACTT
16801511 ACATAACTT
1 ACATAACTT
*
16801520 ACATTAC--
1 ACATAACTT
*
16801527 ACACAACTT
1 ACATAACTT
16801536 ACATAACTT
1 ACATAACTT
16801545 AC---A-TT
1 ACATAACTT
16801550 -CATAACTT
1 ACATAACTT
*
16801558 GA-ATAAAATTTAT
1 -ACAT--AA-CT-T
*
16801571 ATATAAACTT
1 ACAT-AACTT
*
16801581 ACAAAAC--
1 ACATAACTT
16801588 ACATAACTT
1 ACATAACTT
16801597 ACAT-A--T
1 ACATAACTT
16801603 --ATAACTT
1 ACATAACTT
16801610 ACATAACTTAT
1 ACATAAC-T-T
*
16801621 ATATAAACTTAT
1 ACAT-AAC-T-T
*
16801633 ATATAACTT
1 ACATAACTT
*
16801642 TCATAACTT
1 ACATAACTT
*
16801651 AC-TTA-TT
1 ACATAACTT
16801658 --ATAACTT
1 ACATAACTT
16801665 ACATAAC--
1 ACATAACTT
* *
16801672 ACATAGCCT
1 ACATAACTT
*
16801681 ACATGACTT
1 ACATAACTT
16801690 ACATAA--T
1 ACATAACTT
*
16801697 ACACAACTT
1 ACATAACTT
*
16801706 AAATAACTT
1 ACATAACTT
*
16801715 AAATAACTT
1 ACATAACTT
16801724 ACATAA--T
1 ACATAACTT
16801731 ACATAACTT
1 ACATAACTT
*
16801740 ACATTAC--
1 ACATAACTT
*
16801747 ACACAACTT
1 ACATAACTT
16801756 ACATAACTT
1 ACATAACTT
16801765 AC---A-TT
1 ACATAACTT
16801770 -CATAACTT
1 ACATAACTT
*
16801778 GA-ATAAAATTTAT
1 -ACAT--AA-CT-T
*
16801791 ATATAAACTT
1 ACAT-AACTT
*
16801801 ACACAAC--
1 ACATAACTT
16801808 ACATAACTT
1 ACATAACTT
16801817 ACAT-A--T
1 ACATAACTT
16801823 --ATAACTT
1 ACATAACTT
16801830 ACATAACTTAT
1 ACATAAC-T-T
*
16801841 ATATAAACTTAT
1 ACAT-AAC-T-T
*
16801853 ATATAACTT
1 ACATAACTT
*
16801862 TCATAACTT
1 ACATAACTT
*
16801871 AC-TTA-TT
1 ACATAACTT
16801878 --ATAACTT
1 ACATAACTT
16801885 ACATAAC--
1 ACATAACTT
* *
16801892 ACATAGCCT
1 ACATAACTT
*
16801901 ACATGACTT
1 ACATAACTT
16801910 ACATAA--T
1 ACATAACTT
*
16801917 ACACAACTT
1 ACATAACTT
*
16801926 AAATAACTT
1 ACATAACTT
16801935 ACATAACTT
1 ACATAACTT
16801944 ACATAA--T
1 ACATAACTT
16801951 ACATAACTT
1 ACATAACTT
*
16801960 ACATTAC--
1 ACATAACTT
*
16801967 ACACAACTT
1 ACATAACTT
16801976 ACATAACTT
1 ACATAACTT
16801985 AC---A-TT
1 ACATAACTT
16801990 -CATAACTT
1 ACATAACTT
*
16801998 GA-ATAAAATTTAT
1 -ACAT--AA-CT-T
*
16802011 ATATAAACTT
1 ACAT-AACTT
*
16802021 ACACAAC--
1 ACATAACTT
16802028 ACATAACTT
1 ACATAACTT
16802037 ACAT-A--T
1 ACATAACTT
16802043 --ATAACTT
1 ACATAACTT
16802050 ACATAACTTAT
1 ACATAAC-T-T
*
16802061 ATATAAACTTAT
1 ACAT-AAC-T-T
*
16802073 ATATAACTT
1 ACATAACTT
*
16802082 TCATAACTT
1 ACATAACTT
*
16802091 AC-TTA-TT
1 ACATAACTT
16802098 --ATAACTT
1 ACATAACTT
16802105 ACATAAC--
1 ACATAACTT
* *
16802112 ACATAGCCT
1 ACATAACTT
*
16802121 ACATGACTT
1 ACATAACTT
16802130 ACATAA--T
1 ACATAACTT
*
16802137 ACACAACTT
1 ACATAACTT
*
16802146 AAATAACTT
1 ACATAACTT
16802155 ACATAA--T
1 ACATAACTT
16802162 ACATAACTT
1 ACATAACTT
*
16802171 TCATAACTT
1 ACATAACTT
*
16802180 ACATTA--T
1 ACATAACTT
*
16802187 ACACAACTT
1 ACATAACTT
*
16802196 ATATAACTT
1 ACATAACTT
16802205 ACATAACTT
1 ACATAACTT
*
16802214 ACATAGCTT
1 ACATAACTT
16802223 A
1 A
16802224 ATTATACTTA
Statistics
Matches: 629, Mismatches: 100, Indels: 232
0.65 0.10 0.24
Matches are distributed among these distances:
4 9 0.01
5 9 0.01
6 16 0.03
7 131 0.21
8 18 0.03
9 314 0.50
10 19 0.03
11 39 0.06
12 65 0.10
13 9 0.01
ACGTcount: A:0.45, C:0.19, G:0.02, T:0.34
Consensus pattern (9 bp):
ACATAACTT
Found at i:16801435 original size:96 final size:97
Alignment explanation
Indices: 16801224--16801441 Score: 309
Period size: 96 Copynumber: 2.3 Consensus size: 97
16801214 CAATCATATC
* * * * *
16801224 ATAATTTACATACATAACATAT-AT-AAATTTATATATAAACTTGCACAACACATAACTTAAATA
1 ATAACTTACATACATAACTTATAATAAAATTTATATATAAACTTACACAAAACATAACTTAAACA
16801287 ATAACTTACATAACTTATATATAAACTTATAA
66 ATAACTTACATAACTTATATATAAACTTATAA
*
16801319 ATAACTTACATACATAACTTA-AATAAAATTTATATATAAACTTACACAAAACATAACTTACACA
1 ATAACTTACATACATAACTTATAATAAAATTTATATATAAACTTACACAAAACATAACTTAAACA
* *
16801383 ATAACTTACATAACTTATATATAAACTTGTAT
66 ATAACTTACATAACTTATATATAAACTTATAA
* *
16801415 ATAACTTTCATA-ACTTACTTATAATAA
1 ATAACTTACATACA-TAACTTATAATAA
16801442 CTTCCATAAC
Statistics
Matches: 109, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
95 22 0.20
96 82 0.75
97 5 0.05
ACGTcount: A:0.50, C:0.15, G:0.01, T:0.35
Consensus pattern (97 bp):
ATAACTTACATACATAACTTATAATAAAATTTATATATAAACTTACACAAAACATAACTTAAACA
ATAACTTACATAACTTATATATAAACTTATAA
Found at i:16801485 original size:16 final size:16
Alignment explanation
Indices: 16801466--16801541 Score: 80
Period size: 16 Copynumber: 4.6 Consensus size: 16
16801456 AGCTTACATG
16801466 ACTTACATAATACACA
1 ACTTACATAATACACA
* * *
16801482 ACTTAAATAATTTAAATA
1 ACTTACATAA--TACACA
*
16801500 ACTTACATAATACATA
1 ACTTACATAATACACA
* *
16801516 ACTTACATTACACACA
1 ACTTACATAATACACA
16801532 ACTTACATAA
1 ACTTACATAA
16801542 CTTACATTCA
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
16 36 0.73
18 13 0.27
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
ACTTACATAATACACA
Found at i:16801549 original size:25 final size:25
Alignment explanation
Indices: 16801438--16801548 Score: 100
Period size: 25 Copynumber: 4.4 Consensus size: 25
16801428 CTTACTTATA
* * *
16801438 ATAACTTCCATAACACATAGCTTAC
1 ATAACTTACATAACACACAACTTAC
* * *
16801463 ATGACTTACATAATACACAACTTAA
1 ATAACTTACATAACACACAACTTAC
* * *
16801488 ATAATTTAAATAACTTACATAA--TAC
1 ATAACTTACATAAC--ACACAACTTAC
*
16801513 ATAACTTACATTACACACAACTTAC
1 ATAACTTACATAACACACAACTTAC
16801538 ATAACTTACAT
1 ATAACTTACAT
16801549 TCATAACTTG
Statistics
Matches: 66, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
23 5 0.08
25 56 0.85
27 5 0.08
ACGTcount: A:0.46, C:0.22, G:0.02, T:0.31
Consensus pattern (25 bp):
ATAACTTACATAACACACAACTTAC
Found at i:16801608 original size:13 final size:13
Alignment explanation
Indices: 16801590--16801614 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16801580 TACAAAACAC
16801590 ATAACTTACATAT
1 ATAACTTACATAT
16801603 ATAACTTACATA
1 ATAACTTACATA
16801615 ACTTATATAT
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAACTTACATAT
Found at i:16801616 original size:22 final size:21
Alignment explanation
Indices: 16801588--16801631 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
16801578 CTTACAAAAC
16801588 ACATAACTTACATATATAACTT
1 ACATAACTTACATATA-AACTT
*
16801610 ACATAACTTATATATAAACTT
1 ACATAACTTACATATAAACTT
16801631 A
1 A
16801632 TATATAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (21 bp):
ACATAACTTACATATAAACTT
Found at i:16801635 original size:10 final size:11
Alignment explanation
Indices: 16801599--16801641 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 11
16801589 CATAACTTAC
16801599 ATATATAAC-T
1 ATATATAACTT
*
16801609 -TACATAACTT
1 ATATATAACTT
16801619 ATATATAAACTT
1 ATATAT-AACTT
16801631 ATATATAACTT
1 ATATATAACTT
16801642 TCATAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 7 0.25
10 1 0.04
11 9 0.32
12 11 0.39
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATATAACTT
Found at i:16801660 original size:23 final size:24
Alignment explanation
Indices: 16801627--16801671 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
16801617 TTATATATAA
*
16801627 ACTTATATATAACTTTCATAACTT
1 ACTTATATATAACTTACATAACTT
16801651 ACTTAT-TATAACTTACATAAC
1 ACTTATATATAACTTACATAAC
16801672 ACATAGCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (24 bp):
ACTTATATATAACTTACATAACTT
Found at i:16801664 original size:34 final size:31
Alignment explanation
Indices: 16801590--16801665 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 31
16801580 TACAAAACAC
16801590 ATAACTTACATATATAACTTACATAACTTATAT
1 ATAACTT--ATATATAACTTACATAACTTATAT
*
16801623 ATAAACTTATATATAACTTTCATAACTTACTTATT
1 AT-AACTTATATATAACTTACATAACTTA--TA-T
16801658 ATAACTTA
1 ATAACTTA
16801666 CATAACACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
32 20 0.53
33 2 0.05
34 13 0.34
35 3 0.08
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.42
Consensus pattern (31 bp):
ATAACTTATATATAACTTACATAACTTATAT
Found at i:16801664 original size:220 final size:220
Alignment explanation
Indices: 16801319--16802208 Score: 1590
Period size: 220 Copynumber: 4.0 Consensus size: 220
16801309 AAACTTATAA
* * *
16801319 ATAACTTACATACATAACTTAAATAAAATTTATATATAAACTTACACAAA-ACATAACTTACACA
1 ATAACTTACATTCATAACTTGAATAAAATTTATATATAAACTTACA-AAACACATAACTTACATA
* * *
16801383 -ATAACTTACATAACTTATATATAAACTTGTATATAACTTTCATAACTTACTTATAATAACTTCC
65 TATAACTTACATAACTTATATATAAACTTATATATAACTTTCATAACTTACTTATTATAACTTAC
* *
16801447 ATAACACATAGCTTACATGACTTACATAATACACAACTTAAATAATTTAAATAACTTACATAATA
130 ATAACACATAGCCTACATGACTTACATAATACACAACTTAAATAACTTAAATAACTTACATAATA
16801512 CATAACTTACATTACACACAACTTAC
195 CATAACTTACATTACACACAACTTAC
16801538 ATAACTTACATTCATAACTTGAATAAAATTTATATATAAACTTACAAAACACATAACTTACATAT
1 ATAACTTACATTCATAACTTGAATAAAATTTATATATAAACTTACAAAACACATAACTTACATAT
16801603 ATAACTTACATAACTTATATATAAACTTATATATAACTTTCATAACTTACTTATTATAACTTACA
66 ATAACTTACATAACTTATATATAAACTTATATATAACTTTCATAACTTACTTATTATAACTTACA
16801668 TAACACATAGCCTACATGACTTACATAATACACAACTTAAATAACTTAAATAACTTACATAATAC
131 TAACACATAGCCTACATGACTTACATAATACACAACTTAAATAACTTAAATAACTTACATAATAC
16801733 ATAACTTACATTACACACAACTTAC
196 ATAACTTACATTACACACAACTTAC
*
16801758 ATAACTTACATTCATAACTTGAATAAAATTTATATATAAACTTACACAACACATAACTTACATAT
1 ATAACTTACATTCATAACTTGAATAAAATTTATATATAAACTTACAAAACACATAACTTACATAT
16801823 ATAACTTACATAACTTATATATAAACTTATATATAACTTTCATAACTTACTTATTATAACTTACA
66 ATAACTTACATAACTTATATATAAACTTATATATAACTTTCATAACTTACTTATTATAACTTACA
*
16801888 TAACACATAGCCTACATGACTTACATAATACACAACTTAAATAACTTACATAACTTACATAATAC
131 TAACACATAGCCTACATGACTTACATAATACACAACTTAAATAACTTAAATAACTTACATAATAC
16801953 ATAACTTACATTACACACAACTTAC
196 ATAACTTACATTACACACAACTTAC
*
16801978 ATAACTTACATTCATAACTTGAATAAAATTTATATATAAACTTACACAACACATAACTTACATAT
1 ATAACTTACATTCATAACTTGAATAAAATTTATATATAAACTTACAAAACACATAACTTACATAT
16802043 ATAACTTACATAACTTATATATAAACTTATATATAACTTTCATAACTTACTTATTATAACTTACA
66 ATAACTTACATAACTTATATATAAACTTATATATAACTTTCATAACTTACTTATTATAACTTACA
*
16802108 TAACACATAGCCTACATGACTTACATAATACACAACTTAAATAACTTACATAA--TACATAACTT
131 TAACACATAGCCTACATGACTTACATAATACACAACTTAAATAACTTAAATAACTTACATAA--T
* * *
16802171 TCATAACTTACATTATACACAACTTAT
194 ACATAACTTACATTACACACAACTTAC
16802198 ATAACTTACAT
1 ATAACTTACAT
16802209 AACTTACATA
Statistics
Matches: 654, Mismatches: 13, Indels: 7
0.97 0.02 0.01
Matches are distributed among these distances:
218 10 0.02
219 57 0.09
220 587 0.90
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (220 bp):
ATAACTTACATTCATAACTTGAATAAAATTTATATATAAACTTACAAAACACATAACTTACATAT
ATAACTTACATAACTTATATATAAACTTATATATAACTTTCATAACTTACTTATTATAACTTACA
TAACACATAGCCTACATGACTTACATAATACACAACTTAAATAACTTAAATAACTTACATAATAC
ATAACTTACATTACACACAACTTAC
Found at i:16801754 original size:16 final size:16
Alignment explanation
Indices: 16801686--16801762 Score: 73
Period size: 16 Copynumber: 4.7 Consensus size: 16
16801676 AGCCTACATG
*
16801686 ACTTACATAATACACA
1 ACTTACATAACACACA
* * *
16801702 ACTTAAATAACTTAAATA
1 ACTTACATAAC--ACACA
* *
16801720 ACTTACATAATACATA
1 ACTTACATAACACACA
*
16801736 ACTTACATTACACACA
1 ACTTACATAACACACA
16801752 ACTTACATAAC
1 ACTTACATAAC
16801763 TTACATTCAT
Statistics
Matches: 48, Mismatches: 11, Indels: 4
0.76 0.17 0.06
Matches are distributed among these distances:
16 36 0.75
18 12 0.25
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.29
Consensus pattern (16 bp):
ACTTACATAACACACA
Found at i:16801769 original size:25 final size:25
Alignment explanation
Indices: 16801658--16801768 Score: 109
Period size: 25 Copynumber: 4.4 Consensus size: 25
16801648 CTTACTTATT
* * *
16801658 ATAACTTACATAACACATAGCCTAC
1 ATAACTTACATAACACACAACTTAC
* * *
16801683 ATGACTTACATAATACACAACTTAA
1 ATAACTTACATAACACACAACTTAC
* *
16801708 ATAACTTAAATAACTTACATAA--TAC
1 ATAACTTACATAAC--ACACAACTTAC
*
16801733 ATAACTTACATTACACACAACTTAC
1 ATAACTTACATAACACACAACTTAC
16801758 ATAACTTACAT
1 ATAACTTACAT
16801769 TCATAACTTG
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
23 5 0.07
25 58 0.85
27 5 0.07
ACGTcount: A:0.47, C:0.23, G:0.02, T:0.29
Consensus pattern (25 bp):
ATAACTTACATAACACACAACTTAC
Found at i:16801828 original size:13 final size:13
Alignment explanation
Indices: 16801810--16801834 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16801800 TACACAACAC
16801810 ATAACTTACATAT
1 ATAACTTACATAT
16801823 ATAACTTACATA
1 ATAACTTACATA
16801835 ACTTATATAT
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAACTTACATAT
Found at i:16801836 original size:22 final size:21
Alignment explanation
Indices: 16801808--16801851 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
16801798 CTTACACAAC
16801808 ACATAACTTACATATATAACTT
1 ACATAACTTACATATA-AACTT
*
16801830 ACATAACTTATATATAAACTT
1 ACATAACTTACATATAAACTT
16801851 A
1 A
16801852 TATATAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (21 bp):
ACATAACTTACATATAAACTT
Found at i:16801844 original size:50 final size:51
Alignment explanation
Indices: 16801747--16802111 Score: 212
Period size: 52 Copynumber: 6.7 Consensus size: 51
16801737 CTTACATTAC
*
16801747 ACACAACTTACATAACTTACAT-TCATAACTTGA-ATAAAATTTATATATAAACTT
1 ACACAAC-TACATAACTTACATAT-ATAACTT-ACAT--AACTTATATATAAACTT
16801801 ACACAAC-ACATAACTTACATATATAACTTACATAACTTATATATAAACTTAT
1 ACACAACTACATAACTTACATATATAACTTACATAACTTATATATAAAC-T-T
* * * * ** * *
16801853 ATATAACTTTCATAACTTACTTATTATAACTTACATAACACATAGCCTACATGACTT
1 ACACAAC-TACATAACTTACATA-TATAACTTACATAACTTATA---TATA-AACTT
* *
16801910 ACATAA-TACACAACTT--A-A-ATAACTTACATAACTTACATAATACATAACTTACATT
1 ACACAACTACATAACTTACATATATAACTTACATAACTT--AT-AT--ATAA---AC-TT
*
16801965 ACACACAACTTACATAACTTACAT-TCATAACTTGA-ATAAAATTTATATATAAACTT
1 --ACACAAC-TACATAACTTACATAT-ATAACTT-ACAT--AACTTATATATAAACTT
16802021 ACACAAC-ACATAACTTACATATATAACTTACATAACTTATATATAAACTTAT
1 ACACAACTACATAACTTACATATATAACTTACATAACTTATATATAAAC-T-T
* * * *
16802073 ATATAACTTTCATAACTTACTTATTATAACTTACATAAC
1 ACACAAC-TACATAACTTACATA-TATAACTTACATAAC
16802112 ACATAGCCTA
Statistics
Matches: 247, Mismatches: 25, Indels: 77
0.71 0.07 0.22
Matches are distributed among these distances:
50 43 0.17
51 4 0.02
52 61 0.25
53 3 0.01
54 40 0.16
55 43 0.17
56 2 0.01
57 13 0.05
58 4 0.02
59 11 0.04
60 4 0.02
61 1 0.00
62 2 0.01
63 11 0.04
64 1 0.00
65 4 0.02
ACGTcount: A:0.45, C:0.19, G:0.01, T:0.35
Consensus pattern (51 bp):
ACACAACTACATAACTTACATATATAACTTACATAACTTATATATAAACTT
Found at i:16801855 original size:10 final size:11
Alignment explanation
Indices: 16801819--16801861 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 11
16801809 CATAACTTAC
16801819 ATATATAAC-T
1 ATATATAACTT
*
16801829 -TACATAACTT
1 ATATATAACTT
16801839 ATATATAAACTT
1 ATATAT-AACTT
16801851 ATATATAACTT
1 ATATATAACTT
16801862 TCATAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 7 0.25
10 1 0.04
11 9 0.32
12 11 0.39
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATATAACTT
Found at i:16801861 original size:61 final size:60
Alignment explanation
Indices: 16801733--16801861 Score: 147
Period size: 61 Copynumber: 2.1 Consensus size: 60
16801723 TACATAATAC
** * *
16801733 ATAACTTACATTACACACAACTTACATAACTTACATTCATAACTTGAATAAAATTTATAT
1 ATAACTTACACAACACACAACTTACATAACTAACATTCATAACTTGAATAAAACTTATAT
*
16801793 ATAAACTTACACAACACATAACTTACATATA-TAAC-TTACATAACTT-ATATATAAACTTATAT
1 AT-AACTTACACAACACACAACTTACATA-ACTAACATT-CATAACTTGA-ATA-AAACTTATAT
16801855 ATAACTT
1 ATAACTT
16801862 TCATAACTTA
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
60 5 0.08
61 42 0.71
62 12 0.20
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.35
Consensus pattern (60 bp):
ATAACTTACACAACACACAACTTACATAACTAACATTCATAACTTGAATAAAACTTATAT
Found at i:16801880 original size:23 final size:24
Alignment explanation
Indices: 16801847--16801891 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
16801837 TTATATATAA
*
16801847 ACTTATATATAACTTTCATAACTT
1 ACTTATATATAACTTACATAACTT
16801871 ACTTAT-TATAACTTACATAAC
1 ACTTATATATAACTTACATAAC
16801892 ACATAGCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (24 bp):
ACTTATATATAACTTACATAACTT
Found at i:16801884 original size:34 final size:31
Alignment explanation
Indices: 16801810--16801885 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 31
16801800 TACACAACAC
16801810 ATAACTTACATATATAACTTACATAACTTATAT
1 ATAACTT--ATATATAACTTACATAACTTATAT
*
16801843 ATAAACTTATATATAACTTTCATAACTTACTTATT
1 AT-AACTTATATATAACTTACATAACTTA--TA-T
16801878 ATAACTTA
1 ATAACTTA
16801886 CATAACACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
32 20 0.53
33 2 0.05
34 13 0.34
35 3 0.08
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.42
Consensus pattern (31 bp):
ATAACTTATATATAACTTACATAACTTATAT
Found at i:16801974 original size:16 final size:16
Alignment explanation
Indices: 16801906--16801982 Score: 82
Period size: 16 Copynumber: 4.7 Consensus size: 16
16801896 AGCCTACATG
*
16801906 ACTTACATAATACACA
1 ACTTACATAACACACA
* *
16801922 ACTTAAATAACTTACATA
1 ACTTACATAAC--ACACA
* *
16801940 ACTTACATAATACATA
1 ACTTACATAACACACA
*
16801956 ACTTACATTACACACA
1 ACTTACATAACACACA
16801972 ACTTACATAAC
1 ACTTACATAAC
16801983 TTACATTCAT
Statistics
Matches: 50, Mismatches: 9, Indels: 4
0.79 0.14 0.06
Matches are distributed among these distances:
16 37 0.74
18 13 0.26
ACGTcount: A:0.48, C:0.23, G:0.00, T:0.29
Consensus pattern (16 bp):
ACTTACATAACACACA
Found at i:16801989 original size:25 final size:25
Alignment explanation
Indices: 16801878--16801988 Score: 118
Period size: 25 Copynumber: 4.4 Consensus size: 25
16801868 CTTACTTATT
* * *
16801878 ATAACTTACATAACACATAGCCTAC
1 ATAACTTACATAACACACAACTTAC
* * *
16801903 ATGACTTACATAATACACAACTTAA
1 ATAACTTACATAACACACAACTTAC
*
16801928 ATAACTTACATAACTTACATAA--TAC
1 ATAACTTACATAAC--ACACAACTTAC
*
16801953 ATAACTTACATTACACACAACTTAC
1 ATAACTTACATAACACACAACTTAC
16801978 ATAACTTACAT
1 ATAACTTACAT
16801989 TCATAACTTG
Statistics
Matches: 70, Mismatches: 12, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
23 5 0.07
25 60 0.86
27 5 0.07
ACGTcount: A:0.46, C:0.23, G:0.02, T:0.29
Consensus pattern (25 bp):
ATAACTTACATAACACACAACTTAC
Found at i:16802048 original size:13 final size:13
Alignment explanation
Indices: 16802030--16802054 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16802020 TACACAACAC
16802030 ATAACTTACATAT
1 ATAACTTACATAT
16802043 ATAACTTACATA
1 ATAACTTACATA
16802055 ACTTATATAT
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:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAACTTACATAT
Found at i:16802055 original size:61 final size:62
Alignment explanation
Indices: 16801955--16802078 Score: 148
Period size: 61 Copynumber: 2.0 Consensus size: 62
16801945 CATAATACAT
** * *
16801955 AACTTACATTACACACAACTTACATAACTTACATTCATAACTTGA-ATA-AAATTTATATATA
1 AACTTACACAACACACAACTTACATAACTAACATTCATAACTT-ATATATAAACTTATATATA
*
16802016 AACTTACACAACACATAACTTACATATA-TAAC-TTACATAACTTATATATAAACTTATATATA
1 AACTTACACAACACACAACTTACATA-ACTAACATT-CATAACTTATATATAAACTTATATATA
16802078 A
1 A
16802079 CTTTCATAAC
Statistics
Matches: 54, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
60 3 0.06
61 37 0.69
62 14 0.26
ACGTcount: A:0.48, C:0.18, G:0.01, T:0.34
Consensus pattern (62 bp):
AACTTACACAACACACAACTTACATAACTAACATTCATAACTTATATATAAACTTATATATA
Found at i:16802075 original size:10 final size:11
Alignment explanation
Indices: 16802039--16802081 Score: 54
Period size: 12 Copynumber: 4.0 Consensus size: 11
16802029 CATAACTTAC
16802039 ATATATAAC-T
1 ATATATAACTT
*
16802049 -TACATAACTT
1 ATATATAACTT
16802059 ATATATAAACTT
1 ATATAT-AACTT
16802071 ATATATAACTT
1 ATATATAACTT
16802082 TCATAACTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
9 7 0.25
10 1 0.04
11 9 0.32
12 11 0.39
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.42
Consensus pattern (11 bp):
ATATATAACTT
Found at i:16802100 original size:23 final size:24
Alignment explanation
Indices: 16802067--16802111 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
16802057 TTATATATAA
*
16802067 ACTTATATATAACTTTCATAACTT
1 ACTTATATATAACTTACATAACTT
16802091 ACTTAT-TATAACTTACATAAC
1 ACTTATATATAACTTACATAAC
16802112 ACATAGCCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (24 bp):
ACTTATATATAACTTACATAACTT
Found at i:16802104 original size:34 final size:31
Alignment explanation
Indices: 16802030--16802105 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 31
16802020 TACACAACAC
16802030 ATAACTTACATATATAACTTACATAACTTATAT
1 ATAACTT--ATATATAACTTACATAACTTATAT
*
16802063 ATAAACTTATATATAACTTTCATAACTTACTTATT
1 AT-AACTTATATATAACTTACATAACTTA--TA-T
16802098 ATAACTTA
1 ATAACTTA
16802106 CATAACACAT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
32 20 0.53
33 2 0.05
34 13 0.34
35 3 0.08
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.42
Consensus pattern (31 bp):
ATAACTTATATATAACTTACATAACTTATAT
Found at i:16802154 original size:25 final size:25
Alignment explanation
Indices: 16802098--16802210 Score: 136
Period size: 25 Copynumber: 4.5 Consensus size: 25
16802088 CTTACTTATT
* * * *
16802098 ATAACTTACATAACACATAGCCTAC
1 ATAACTTACATAATACACAACTTAC
* *
16802123 ATGACTTACATAATACACAACTTAA
1 ATAACTTACATAATACACAACTTAC
* *
16802148 ATAACTTACATAATACATAACTTTC
1 ATAACTTACATAATACACAACTTAC
* *
16802173 ATAACTTACATTATACACAACTTAT
1 ATAACTTACATAATACACAACTTAC
16802198 ATAACTTACATAA
1 ATAACTTACATAA
16802211 CTTACATAGC
Statistics
Matches: 73, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 73 1.00
ACGTcount: A:0.46, C:0.21, G:0.02, T:0.31
Consensus pattern (25 bp):
ATAACTTACATAATACACAACTTAC
Found at i:16802166 original size:50 final size:50
Alignment explanation
Indices: 16802098--16802220 Score: 165
Period size: 50 Copynumber: 2.4 Consensus size: 50
16802088 CTTACTTATT
* *
16802098 ATAACTTACATAACACATAGCCTACATGACTTACATAATACACAACTTAA
1 ATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTAA
* * * * *
16802148 ATAACTTACATAATACATAACTTTCATAACTTACATTATACACAACTTAT
1 ATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTAA
16802198 ATAACTTACATAACTTACATAGC
1 ATAACTTACATAA--TACATAGC
16802221 TTAATTATAC
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 56 0.89
52 7 0.11
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.31
Consensus pattern (50 bp):
ATAACTTACATAATACATAGCCTACATAACTTACATAATACACAACTTAA
Found at i:16807758 original size:66 final size:66
Alignment explanation
Indices: 16807687--16807833 Score: 201
Period size: 66 Copynumber: 2.2 Consensus size: 66
16807677 GAGGCAACAT
16807687 CGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCCAGCTA-CAACTTAAAGCAGATGC-A
1 CGAGAGAAGCTGAGGTTCAACAAAAG-TATGAAGAACTCCAGC-AGCAACTTAAAGCAGATGCGA
16807749 GCAG
64 -CAG
* * * *
16807753 CGAGAGAAGATGAGGTTCAACGAAAGTATGAAGAACTCCAGCAGTAGCTTAAAGCAGATGCGACA
1 CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTTAAAGCAGATGCGACA
16807818 G
66 G
*
16807819 CGAGAGAAGCAGAGG
1 CGAGAGAAGCTGAGG
16807834 CTGCAGCGAG
Statistics
Matches: 72, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
65 1 0.01
66 66 0.92
67 5 0.07
ACGTcount: A:0.41, C:0.17, G:0.29, T:0.14
Consensus pattern (66 bp):
CGAGAGAAGCTGAGGTTCAACAAAAGTATGAAGAACTCCAGCAGCAACTTAAAGCAGATGCGACA
G
Found at i:16807830 original size:21 final size:21
Alignment explanation
Indices: 16807816--16807874 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
16807806 GCAGATGCGA
16807816 CAGCGAGAGAAGCAGAGGCTG
1 CAGCGAGAGAAGCAGAGGCTG
* *
16807837 CAGCGAGGGAAGTAGAGGCTG
1 CAGCGAGAGAAGCAGAGGCTG
*
16807858 CAGTGA-AGGAAGCAGAG
1 CAGCGAGA-GAAGCAGAG
16807875 TAGCGTAAAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.34, C:0.15, G:0.44, T:0.07
Consensus pattern (21 bp):
CAGCGAGAGAAGCAGAGGCTG
Found at i:16808266 original size:43 final size:43
Alignment explanation
Indices: 16808217--16808720 Score: 404
Period size: 43 Copynumber: 11.7 Consensus size: 43
16808207 TTAAAAAAAT
*
16808217 GCCGCTAAAGTTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
1 GCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
* *
16808260 GCCGCTAAATATCATGGTCTTTAGCGGCGTTTGTGGAAAAAAC
1 GCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
* *
16808303 GCCGCTAACGATCATGGTCTTTAGTGGCGTTTGTGGAAAAA-C
1 GCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
* * * * *
16808345 GCCGCTAAAGATCATGGTATTTAGTGGCGTTTATGGGAAAATC
1 GCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
* * * * * * *
16808388 ACCGCTAAAGTTCATGGTTTTTTGCTGCGTTTGTGGGAAAATC
1 GCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
* * * *
16808431 GCCGTTAAAAATCATGGTCTTTAGCGGCGTTTTTTGG-AGAAGC
1 GCCGCTAAAGATCATGGTCTTTAGCGGCG-TTTGTGGAAAAAGC
* * * ** * * **
16808474 GCTGCTAAAGGTCATTGTCTTTAGCAACATTTTTTGG-GTAAGC
1 GCCGCTAAAGATCATGGTCTTTAGCGGC-GTTTGTGGAAAAAGC
* *** *
16808517 GCCGCTAAAGGTCATGGTCTTTAGCGGCGTTTGTCTCAAAGGC
1 GCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
* * ** * * * *
16808560 GCCGCTAAAAACCATGACCTTTAGCAGCGTTTATGGTACAAGC
1 GCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
* * ** * * * **
16808603 GCCG-TACAAGACCGTGACCTTTAGCAGCGTTTATGGTACGAGC
1 GCCGCTA-AAGATCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
* * ** *
16808646 GCCGCTAAAGACCGTGACCTTTAGCGGCGTTTGTGGTAAAAGC
1 GCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
* ** *
16808689 GCCGCTAAAGACCATGACCTTTTGCGGCGTTT
1 GCCGCTAAAGATCATGGTCTTTAGCGGCGTTT
16808721 ATTTCTAAAA
Statistics
Matches: 386, Mismatches: 69, Indels: 12
0.83 0.15 0.03
Matches are distributed among these distances:
42 44 0.11
43 334 0.87
44 8 0.02
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.29
Consensus pattern (43 bp):
GCCGCTAAAGATCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
Found at i:16808423 original size:128 final size:128
Alignment explanation
Indices: 16808195--16808462 Score: 340
Period size: 128 Copynumber: 2.1 Consensus size: 128
16808185 TCTGCCAAAA
* * * * *
16808195 TTAGTGGCGTTTTTAAAAAAATGCCGCTAAAGTTCATGGTCTTTAGCGGCGTTTGTGGAAAAAGC
1 TTAGTGGCGTTTGTAAAAAAACGCCGCTAAAGATCATGGTATTTAGCGGCGTTTATGGAAAAAGC
* **
16808260 GCCGCTAAATATCATGGTCTTTAGCGGCGTTTGTGGAAAAAACGCCGCTAACGATCATGGTCT
66 ACCGCTAAATATCATGGTCTTTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAAATCATGGTCT
** * * *
16808323 TTAGTGGCGTTTGTGGAAAAACGCCGCTAAAGATCATGGTATTTAGTGGCGTTTATGGGAAAATC
1 TTAGTGGCGTTTGTAAAAAAACGCCGCTAAAGATCATGGTATTTAGCGGCGTTTATGGAAAAAGC
* * * * * *
16808388 ACCGCTAAAGT-TCATGGTTTTTTGCTGCGTTTGTGGGAAAATCGCCGTTAAAAATCATGGTCT
66 ACCGCTAAA-TATCATGGTCTTTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAAATCATGGTCT
*
16808451 TTAGCGGCGTTT
1 TTAGTGGCGTTT
16808463 TTTGGAGAAG
Statistics
Matches: 119, Mismatches: 20, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
128 118 0.99
129 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.26, T:0.32
Consensus pattern (128 bp):
TTAGTGGCGTTTGTAAAAAAACGCCGCTAAAGATCATGGTATTTAGCGGCGTTTATGGAAAAAGC
ACCGCTAAATATCATGGTCTTTAGCGGCGTTTGTGGAAAAAACGCCGCTAAAAATCATGGTCT
Found at i:16812015 original size:11 final size:11
Alignment explanation
Indices: 16811999--16812061 Score: 56
Period size: 11 Copynumber: 5.5 Consensus size: 11
16811989 CCTGCTATTC
16811999 TTTTCTTTTAT
1 TTTTCTTTTAT
16812010 TTTTCTTTT-T
1 TTTTCTTTTAT
16812020 TCCTTTCTTTTACCT
1 T--TTTCTTTTA--T
*
16812035 TTTTCTTTTCT
1 TTTTCTTTTAT
*
16812046 TTTTCTGTTAT
1 TTTTCTTTTAT
*
16812057 CTTTC
1 TTTTC
16812062 AAATCACATT
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
10 2 0.05
11 23 0.53
12 8 0.19
13 8 0.19
15 2 0.05
ACGTcount: A:0.05, C:0.19, G:0.02, T:0.75
Consensus pattern (11 bp):
TTTTCTTTTAT
Found at i:16812030 original size:18 final size:18
Alignment explanation
Indices: 16811999--16812051 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
16811989 CCTGCTATTC
*
16811999 TTTTCTTTTATTTTTCTT
1 TTTTCTTTTCTTTTTCTT
* * *
16812017 TTTTCCTTTCTTTTACCT
1 TTTTCTTTTCTTTTTCTT
16812035 TTTTCTTTTCTTTTTCT
1 TTTTCTTTTCTTTTTCT
16812052 GTTATCTTTC
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTCTT
Found at i:16816747 original size:6 final size:6
Alignment explanation
Indices: 16816715--16816746 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
16816705 TCTGCCATTC
16816715 TTTTG- TTTTGT TTTTGT TTTTGT TTTT-T TTTT
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT TTTT
16816747 TATGTTATCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTGT
Found at i:16818061 original size:57 final size:57
Alignment explanation
Indices: 16818000--16818107 Score: 198
Period size: 57 Copynumber: 1.9 Consensus size: 57
16817990 AAATTAATTG
*
16818000 TTCAAGTTATTGTTACACACTGAGTTTCGAAAACTCATATTCTGTTTGACTGATATT
1 TTCAAGTTATTGTTACACACTGAGTTTCGAAAACTCATATTCTATTTGACTGATATT
*
16818057 TTCAAGTTATTGTTACACACTGAGTTTCGTAAACTCATATTCTATTTGACT
1 TTCAAGTTATTGTTACACACTGAGTTTCGAAAACTCATATTCTATTTGACT
16818108 CAGTTACAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (57 bp):
TTCAAGTTATTGTTACACACTGAGTTTCGAAAACTCATATTCTATTTGACTGATATT
Found at i:16818766 original size:189 final size:189
Alignment explanation
Indices: 16818446--16818824 Score: 650
Period size: 189 Copynumber: 2.0 Consensus size: 189
16818436 GACATTTTTC
*
16818446 AAAGGTTTTGAAAACTGAATTTACAACTGCTTTACGTAACATCTCCAGATTTGGACATAACGTCG
1 AAAGGTTTTGAAAACTGAATTTACAACTGCTTTACGTAACAACTCCAGATTTGGACATAACGTCG
*
16818511 AGGTTGAGTTTGGGGTGCTACATATTGACTTGAAATGCTATGGTTGAAATTGAATATTGAGATAG
66 AGGTTGAGTTTGGGGTGCTACATATTGACTTGAAATGCTATGGTTGAAATTGAATATTCAGATAG
* * *
16818576 GGACAAAATTGAATAGAAATTTGTATGTCTTAGCTGATATAAGGAATTAGTATAAAATG
131 GGACAAAATTGAATAGAAATTTGTATGTCTAAGCTAATATAAGAAATTAGTATAAAATG
* * *
16818635 AAAGGTTTTGAAAACTGGATTTACAACTGCTTTACGTAACAACTCCAGATTTGGCCATAACGTCT
1 AAAGGTTTTGAAAACTGAATTTACAACTGCTTTACGTAACAACTCCAGATTTGGACATAACGTCG
* *
16818700 AGGTTGAGTTTGGGGTGTTACATATTGACTTGAAATGCTATGGTTGAAATTTAATATTCAGATAG
66 AGGTTGAGTTTGGGGTGCTACATATTGACTTGAAATGCTATGGTTGAAATTGAATATTCAGATAG
* *
16818765 GGACTAAATTGAATAGAAATTTGTATGTCTAAGCTAATATAAGAAATTGGTATAAAATG
131 GGACAAAATTGAATAGAAATTTGTATGTCTAAGCTAATATAAGAAATTAGTATAAAATG
16818824 A
1 A
16818825 GCTTATGTTA
Statistics
Matches: 178, Mismatches: 12, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
189 178 1.00
ACGTcount: A:0.35, C:0.10, G:0.21, T:0.33
Consensus pattern (189 bp):
AAAGGTTTTGAAAACTGAATTTACAACTGCTTTACGTAACAACTCCAGATTTGGACATAACGTCG
AGGTTGAGTTTGGGGTGCTACATATTGACTTGAAATGCTATGGTTGAAATTGAATATTCAGATAG
GGACAAAATTGAATAGAAATTTGTATGTCTAAGCTAATATAAGAAATTAGTATAAAATG
Found at i:16819185 original size:42 final size:41
Alignment explanation
Indices: 16819082--16819191 Score: 98
Period size: 43 Copynumber: 2.6 Consensus size: 41
16819072 TCAACTTATT
* * *
16819082 CGATGATGCACAATGCGTGCTAGTATAATTACTTCGGTTCATC
1 CGATGATGCACTATGTGTGC-AGTATAATTACTTCGCTTCA-C
* * *
16819125 TGATGATGTACCT-TGTGTGTCAGTATAATTGCTTCGACTTC-C
1 CGATGATGCA-CTATGTGTG-CAGTATAATTACTTCG-CTTCAC
16819167 CGATGATGCACTATGTGTGCCAGTA
1 CGATGATGCACTATGTGTG-CAGTA
16819192 ACTTTTATTG
Statistics
Matches: 54, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
41 2 0.04
42 20 0.37
43 27 0.50
44 5 0.09
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.35
Consensus pattern (41 bp):
CGATGATGCACTATGTGTGCAGTATAATTACTTCGCTTCAC
Found at i:16828453 original size:50 final size:50
Alignment explanation
Indices: 16828369--16828469 Score: 132
Period size: 50 Copynumber: 2.0 Consensus size: 50
16828359 GGTCATACAC
** * *
16828369 CTTATAATCCCCGTGTTTACTATTTTGAATAACTCTATCAGTTTTCATAG
1 CTTATAATCCCCGTGTTTACTACCTCGAATAACTCTATCAGTTGTCATAG
* *
16828419 CTTATAATCCCCGTGTTTACTGCCTCG-ATAAACTCTATTAGTTGTCATAG
1 CTTATAATCCCCGTGTTTACTACCTCGAAT-AACTCTATCAGTTGTCATAG
16828469 C
1 C
16828470 AGAGCTATGG
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
49 2 0.05
50 42 0.95
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.41
Consensus pattern (50 bp):
CTTATAATCCCCGTGTTTACTACCTCGAATAACTCTATCAGTTGTCATAG
Found at i:16828530 original size:69 final size:69
Alignment explanation
Indices: 16828419--16828562 Score: 211
Period size: 69 Copynumber: 2.1 Consensus size: 69
16828409 GTTTTCATAG
16828419 CTTATAATCCCCGTGTTTACTGCCTCGATAAACTCTATTAGTTGT-CATAGCAGAGCTATGGTCT
1 CTTATAATCCCCGTGTTTACTGCCTCGATAAACTCTATTAGTT-TCCATAGCAGAGCTATGGTCT
16828483 TACAC
65 TACAC
* * * *
16828488 CTTATAATCCCCGTGTTTACTATCCT-GATGAACTTTATTAGTTTCCATAGCTGAGCTATGGTCT
1 CTTATAATCCCCGTGTTTACT-GCCTCGATAAACTCTATTAGTTTCCATAGCAGAGCTATGGTCT
*
16828552 TATAC
65 TACAC
16828557 CTTATA
1 CTTATA
16828563 CCTCATTGGA
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
68 1 0.01
69 64 0.94
70 3 0.04
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (69 bp):
CTTATAATCCCCGTGTTTACTGCCTCGATAAACTCTATTAGTTTCCATAGCAGAGCTATGGTCTT
ACAC
Found at i:16830515 original size:23 final size:22
Alignment explanation
Indices: 16830475--16830543 Score: 79
Period size: 23 Copynumber: 3.1 Consensus size: 22
16830465 AGGAAGTAAA
16830475 ATAAAA-ATA-AAAACATATGT
1 ATAAAATATATAAAACATATGT
16830495 ATAAAATATATATAAACATATGT
1 ATAAAATATATA-AAACATATGT
** *
16830518 ATACTATATATAAAACAATATAT
1 ATAAAATATATAAAAC-ATATGT
16830541 ATA
1 ATA
16830544 TATATTACAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
20 6 0.14
21 3 0.07
22 5 0.12
23 28 0.67
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.32
Consensus pattern (22 bp):
ATAAAATATATAAAACATATGT
Found at i:16830520 original size:12 final size:12
Alignment explanation
Indices: 16830485--16830520 Score: 56
Period size: 12 Copynumber: 3.1 Consensus size: 12
16830475 ATAAAAATAA
16830485 AAACATATGTAT
1 AAACATATGTAT
*
16830497 AAA-ATATATAT
1 AAACATATGTAT
16830508 AAACATATGTAT
1 AAACATATGTAT
16830520 A
1 A
16830521 CTATATATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
11 10 0.48
12 11 0.52
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (12 bp):
AAACATATGTAT
Found at i:16830614 original size:6 final size:6
Alignment explanation
Indices: 16830577--16830610 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
16830567 GCGCATGAAT
*
16830577 ATAAAA ATAAAA ATAAAA ATAAAA ATAATA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAAAA ATAA
16830611 TAATGATACA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (6 bp):
ATAAAA
Found at i:16830868 original size:23 final size:23
Alignment explanation
Indices: 16830842--16830886 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
16830832 AAGAGATTTG
* *
16830842 AAATCAACAATATACAAATCAAT
1 AAATAAACAATACACAAATCAAT
**
16830865 AAATAAATTATACACAAATCAA
1 AAATAAACAATACACAAATCAA
16830887 CAAAATAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAACAATACACAAATCAAT
Found at i:16831116 original size:24 final size:23
Alignment explanation
Indices: 16831069--16831135 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
16831059 CAAATTAAAT
* *
16831069 TTCTAAGATTACAAAATCATATC
1 TTCTAAGATTGCAATATCATATC
16831092 TTCTAAGATTGCATATATCATA--
1 TTCTAAGATTGCA-ATATCATATC
16831114 -TCTAAGATTGC-ATATCATATC
1 TTCTAAGATTGCAATATCATATC
16831135 T
1 T
16831136 AAGATTACAT
Statistics
Matches: 38, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 8 0.21
21 11 0.29
23 12 0.32
24 7 0.18
ACGTcount: A:0.37, C:0.16, G:0.07, T:0.39
Consensus pattern (23 bp):
TTCTAAGATTGCAATATCATATC
Found at i:16831128 original size:19 final size:20
Alignment explanation
Indices: 16831070--16831141 Score: 83
Period size: 19 Copynumber: 3.5 Consensus size: 20
16831060 AAATTAAATT
* *
16831070 TCTAAGATTACAAAATCATA
1 TCTAAGATTGCAATATCATA
16831090 TCTTCTAAGATTGCATATATCATA
1 ---TCTAAGATTGCA-ATATCATA
16831114 TCTAAGATTGC-ATATCATA
1 TCTAAGATTGCAATATCATA
16831133 TCTAAGATT
1 TCTAAGATT
16831142 ACATGTCCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
19 17 0.37
21 11 0.24
23 11 0.24
24 7 0.15
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.38
Consensus pattern (20 bp):
TCTAAGATTGCAATATCATA
Found at i:16834069 original size:51 final size:51
Alignment explanation
Indices: 16833992--16834274 Score: 480
Period size: 51 Copynumber: 5.6 Consensus size: 51
16833982 CGGATCACAT
*
16833992 TTATCACTTGTCACTTGTCCCTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* *
16834043 CTATCACTTGTTACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
*
16834094 TTATCACTTGTTACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
16834145 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
* * *
16834196 TTATCACTTGTCAATTGT-ACTGATCATATAACTGTAGCTAAAGCTACTC-C
1 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTAC-CAC
16834246 TTATCACTTGTCACTTGTCACTGATCAGA
1 TTATCACTTGTCACTTGTCACTGATCAGA
16834275 AGTACTCAAA
Statistics
Matches: 220, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
50 45 0.20
51 175 0.80
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (51 bp):
TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
Found at i:16836478 original size:12 final size:12
Alignment explanation
Indices: 16836448--16836481 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
16836438 AACACTCCAT
*
16836448 AAATATCTATAA
1 AAATATTTATAA
16836460 AAATATTTATAA
1 AAATATTTATAA
16836472 AAATATTTAT
1 AAATATTTAT
16836482 GGCTCGGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (12 bp):
AAATATTTATAA
Found at i:16840637 original size:203 final size:202
Alignment explanation
Indices: 16840276--16840677 Score: 635
Period size: 203 Copynumber: 2.0 Consensus size: 202
16840266 TTGTCCTGAT
*
16840276 AGCTAAGCATGACAACCATTTATCGGTTAAACTAAATGTGTTCAACCCTTAAAAACATAGAATCC
1 AGCTAAGCATGACAACCATTTATCGGTTAAACTAAATGTGTTCAACCCTTAAAAACACAGAATCC
16840341 ATAATTATATAGAAGCTTTTAAGAGGTTTTACTCTACTTCTCTCTTCAATCCACAAGTACAGAGA
66 ATAATTATATAGAAGCTTTTAAGA-GTTTTACTCTACTTCTCTCTTCAATCCACAAGTACAGAGA
* * * * *
16840406 GGTAAGGAAGTTTACCAGTTCCTCAACTTATCTAATACCAGACTTCAGTTCTCATGATGGTTGTG
130 GGTAAGGAAGTTTACCAGTTCATCAACTTATCTAATACCAGACTACAATTCTCATGACGATTGTG
16840471 ACATGCAA
195 ACATGCAA
* * *
16840479 AGCTAAGCATGACAACCATTTATTGGTTAAACTAAATGTGTTCAACCCTTAAAAACCCATAATCC
1 AGCTAAGCATGACAACCATTTATCGGTTAAACTAAATGTGTTCAACCCTTAAAAACACAGAATCC
* * *
16840544 ATAATTATATAGAAGCTTTTAAGTA-TTCTTACTCTACTTCTCTCTTCAATCTATAAGTACATAG
66 ATAATTATATAGAAGCTTTTAAG-AGTT-TTACTCTACTTCTCTCTTCAATCCACAAGTACAGAG
* * *
16840608 AGGTAAGGAAGTTTATCAGTTCATCAACTTTTCTACTACCAGACTACAATTCTCATGACGATTGT
129 AGGTAAGGAAGTTTACCAGTTCATCAACTTATCTAATACCAGACTACAATTCTCATGACGATTGT
16840673 GACAT
194 GACAT
16840678 CTAGAGCTTT
Statistics
Matches: 182, Mismatches: 15, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
202 2 0.01
203 179 0.98
204 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.13, T:0.33
Consensus pattern (202 bp):
AGCTAAGCATGACAACCATTTATCGGTTAAACTAAATGTGTTCAACCCTTAAAAACACAGAATCC
ATAATTATATAGAAGCTTTTAAGAGTTTTACTCTACTTCTCTCTTCAATCCACAAGTACAGAGAG
GTAAGGAAGTTTACCAGTTCATCAACTTATCTAATACCAGACTACAATTCTCATGACGATTGTGA
CATGCAA
Found at i:16846503 original size:16 final size:16
Alignment explanation
Indices: 16846482--16846549 Score: 127
Period size: 16 Copynumber: 4.2 Consensus size: 16
16846472 TTTGGTTCGC
16846482 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
*
16846498 TGTATTGGATTAGAAG
1 TGTATTGGATTAGAGG
16846514 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
16846530 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
16846546 TGTA
1 TGTA
16846550 ATAGCAAATC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.26, C:0.00, G:0.35, T:0.38
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:16846802 original size:16 final size:16
Alignment explanation
Indices: 16846765--16846806 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
16846755 TTAATCATAT
*
16846765 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
16846781 TT-AAATATATTATAA
1 TTAAAATATATTATAA
16846796 TTAAAATATAT
1 TTAAAATATAT
16846807 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:16846813 original size:14 final size:15
Alignment explanation
Indices: 16846774--16846815 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
16846764 TTTAAACATA
*
16846774 ATTATTATTAAATAT
1 ATTATAATTAAATAT
16846789 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
16846803 A-TATAATTTAATA
1 ATTATAATTAAATA
16846816 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:16847010 original size:26 final size:28
Alignment explanation
Indices: 16846981--16847041 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
16846971 TATGAATTTG
*
16846981 TATAATTTAA-AATAAT-TATTATTACA
1 TATAATTTAATAATAATATATAATTACA
*
16847007 TATAATTTAATAATAATATATAATTTCA
1 TATAATTTAATAATAATATATAATTACA
*
16847035 TAAAATT
1 TATAATT
16847042 CTTGATAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
26 10 0.33
27 6 0.20
28 14 0.47
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (28 bp):
TATAATTTAATAATAATATATAATTACA
Found at i:16865745 original size:12 final size:13
Alignment explanation
Indices: 16865722--16865774 Score: 56
Period size: 12 Copynumber: 3.9 Consensus size: 13
16865712 TTTAAGAGCA
16865722 AATATGGTTAAAT
1 AATATGGTTAAAT
16865735 AATAT-GTTAAATTT
1 AATATGGTTAAA--T
16865749 AACATATGGTTAAA-
1 -A-ATATGGTTAAAT
16865763 AATATGGTTAAA
1 AATATGGTTAAA
16865775 CATATTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
12 17 0.49
13 6 0.17
14 1 0.03
15 1 0.03
16 4 0.11
17 6 0.17
ACGTcount: A:0.47, C:0.02, G:0.13, T:0.38
Consensus pattern (13 bp):
AATATGGTTAAAT
Found at i:16865779 original size:12 final size:12
Alignment explanation
Indices: 16865749--16865779 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
16865739 TGTTAAATTT
16865749 AACATATGGTTA
1 AACATATGGTTA
*
16865761 AAAATATGGTTA
1 AACATATGGTTA
16865773 AACATAT
1 AACATAT
16865780 TATTTAACTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.48, C:0.06, G:0.13, T:0.32
Consensus pattern (12 bp):
AACATATGGTTA
Found at i:16868592 original size:15 final size:16
Alignment explanation
Indices: 16868572--16868601 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
16868562 AAATATAATA
16868572 AAATA-TTAAAAAAAT
1 AAATATTTAAAAAAAT
16868587 AAATATTTAAAAAAA
1 AAATATTTAAAAAAA
16868602 GAGATATACA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATATTTAAAAAAAT
Found at i:16870833 original size:18 final size:18
Alignment explanation
Indices: 16870810--16870845 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
16870800 TCACAAATTT
*
16870810 TAAATATAAACAGTAAAA
1 TAAATATAAACAATAAAA
16870828 TAAATATAAACAATAAAA
1 TAAATATAAACAATAAAA
16870846 AAACTACTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.22
Consensus pattern (18 bp):
TAAATATAAACAATAAAA
Found at i:16871392 original size:23 final size:25
Alignment explanation
Indices: 16871361--16871425 Score: 66
Period size: 23 Copynumber: 2.7 Consensus size: 25
16871351 AGAGAGAATC
16871361 TTATATTAAATAAT-AATTTAAT-TT
1 TTATATT-AATAATAAATTTAATGTT
*
16871385 TTAT-TTAATATTAAATTTAATGTTT
1 TTATATTAATAATAAATTTAATG-TT
*
16871410 TTATATTACTAA-AAAT
1 TTATATTAATAATAAAT
16871426 GTGACGTGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
22 5 0.15
23 10 0.29
24 4 0.12
25 10 0.29
26 5 0.15
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (25 bp):
TTATATTAATAATAAATTTAATGTT
Found at i:16873841 original size:22 final size:21
Alignment explanation
Indices: 16873796--16873841 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
16873786 CACTATTTCA
* *
16873796 TTAAAAATTAATTTTAGTCCT
1 TTAAAAATTAATTTTAATCAT
*
16873817 TTAAAAAGTTAATTTTAATTAT
1 TTAAAAA-TTAATTTTAATCAT
16873839 TTA
1 TTA
16873842 GAGAATACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.41, C:0.04, G:0.04, T:0.50
Consensus pattern (21 bp):
TTAAAAATTAATTTTAATCAT
Found at i:16881544 original size:36 final size:36
Alignment explanation
Indices: 16881493--16881563 Score: 115
Period size: 36 Copynumber: 2.0 Consensus size: 36
16881483 GATTATGTAA
*
16881493 TCTTAGAGTTCTAATTGTATACAGCTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
* *
16881529 TCTTAGAGTTTTAATTGTATACAACTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGT
16881564 AGCCCTTGAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.27, C:0.11, G:0.14, T:0.48
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
Found at i:16886624 original size:36 final size:36
Alignment explanation
Indices: 16886573--16886643 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
16886563 GATTATGTAA
16886573 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
* * * * *
16886609 TCTTAGCGTTTTAATTGTATATAGCTTTTAATTGT
1 TCTTAGAGTTCTAATTGTATACAACTTCTAATTGT
16886644 AGCCCTTGAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.25, C:0.11, G:0.14, T:0.49
Consensus pattern (36 bp):
TCTTAGAGTTCTAATTGTATACAACTTCTAATTGTG
Found at i:16886639 original size:17 final size:17
Alignment explanation
Indices: 16886584--16886644 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
16886574 CTTAGAGTTC
* * *
16886584 TAATTGTATACAACTTC
1 TAATTGTATATAGCTTT
* *
16886601 TAATTGTGTCTTAGCGTTT
1 TAATTGTAT-ATAGC-TTT
16886620 TAATTGTATATAGCTTT
1 TAATTGTATATAGCTTT
16886637 TAATTGTA
1 TAATTGTA
16886645 GCCCTTGATG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
17 19 0.54
18 6 0.17
19 10 0.29
ACGTcount: A:0.28, C:0.10, G:0.13, T:0.49
Consensus pattern (17 bp):
TAATTGTATATAGCTTT
Found at i:16887105 original size:5 final size:5
Alignment explanation
Indices: 16887088--16887125 Score: 67
Period size: 5 Copynumber: 7.6 Consensus size: 5
16887078 TAAAAACTAG
*
16887088 AAAAT AAAGT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAA
16887126 GTTCTAATGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:16894477 original size:70 final size:68
Alignment explanation
Indices: 16894352--16894499 Score: 172
Period size: 70 Copynumber: 2.1 Consensus size: 68
16894342 ATGTTACATT
* ** * *
16894352 TTAATTTTAATCCCACATTGACTAGAGAATACTCTCATTGCTCATTTCTTCACTATTTTCATTAG
1 TTAATTTTAATCCCACATTAACTAGAGAATACTCTCATAACTCACTTATTCACTATTTTCATTA-
16894417 AAAA
65 AAAA
** * *
16894421 GTTAATTTTAATCTTATATTAACTAGAGAATACT-TCTATAACTCACTTATTTACTATTTTCATT
1 -TTAATTTTAATCCCACATTAACTAGAGAATACTCTC-ATAACTCACTTATTCACTATTTTCATT
16894485 AAAAA
64 AAAAA
*
16894490 TTAATATTAA
1 TTAATTTTAA
16894500 GAAGTTAATT
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
68 9 0.13
69 6 0.09
70 52 0.78
ACGTcount: A:0.36, C:0.16, G:0.05, T:0.43
Consensus pattern (68 bp):
TTAATTTTAATCCCACATTAACTAGAGAATACTCTCATAACTCACTTATTCACTATTTTCATTAA
AAA
Found at i:16896476 original size:20 final size:19
Alignment explanation
Indices: 16896447--16896495 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 19
16896437 ATCAAATTGA
* *
16896447 ATTATCATTGAATGGATTT
1 ATTATAATTGAATGCATTT
*
16896466 GATTATAATTGGATGCATTT
1 -ATTATAATTGAATGCATTT
16896486 A-TATAATTGA
1 ATTATAATTGA
16896496 TGATAAAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
18 8 0.32
19 1 0.04
20 16 0.64
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (19 bp):
ATTATAATTGAATGCATTT
Found at i:16898729 original size:17 final size:17
Alignment explanation
Indices: 16898707--16898756 Score: 82
Period size: 17 Copynumber: 2.9 Consensus size: 17
16898697 ATAGAAAGTC
16898707 AAAGATATGGGTATCAG
1 AAAGATATGGGTATCAG
* *
16898724 AAAGATATTGGTAACAG
1 AAAGATATGGGTATCAG
16898741 AAAGATATGGGTATCA
1 AAAGATATGGGTATCA
16898757 AAATCTGAGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.26, T:0.24
Consensus pattern (17 bp):
AAAGATATGGGTATCAG
Found at i:16917704 original size:24 final size:24
Alignment explanation
Indices: 16917677--16917818 Score: 73
Period size: 24 Copynumber: 5.8 Consensus size: 24
16917667 TGGCTCTCCG
16917677 GAGCTTCTCGATATTGGCTCGTAT
1 GAGCTTCTCGATATTGGCTCGTAT
* * *
16917701 GAGCTT-TCCA-ATTACAGCTCTTAT
1 GAGCTTCTCGATATT--GGCTCGTAT
* *
16917725 GAGCTTC-CTGATTAATGGC-CCTCAT
1 GAGCTTCTC-GA-TATTGGCTCGT-AT
*
16917750 GAGCTT-TCTGATATTTGGCTC-TCTT
1 GAGCTTCTC-GATA-TTGGCTCGT-AT
* *
16917775 GAGCTTCCCG-TTTATGGCTCGTAT
1 GAGCTTCTCGATAT-TGGCTCGTAT
16917799 GAGCTTCTCGATAATTGGCT
1 GAGCTTCTCGAT-ATTGGCT
16917819 TGCAAGAGCT
Statistics
Matches: 89, Mismatches: 14, Indels: 29
0.67 0.11 0.22
Matches are distributed among these distances:
22 3 0.03
23 4 0.04
24 41 0.46
25 36 0.40
26 3 0.03
27 2 0.02
ACGTcount: A:0.18, C:0.23, G:0.21, T:0.38
Consensus pattern (24 bp):
GAGCTTCTCGATATTGGCTCGTAT
Found at i:16917792 original size:49 final size:50
Alignment explanation
Indices: 16917724--16917818 Score: 115
Period size: 49 Copynumber: 1.9 Consensus size: 50
16917714 ACAGCTCTTA
* *
16917724 TGAGCTTCCTGATTAATGGC-CCTCATGAGCTT-TCTGATATTTGGCTCTCT
1 TGAGCTTCCCGATTAATGGCTCCT-ATGAGCTTCTC-GATAATTGGCTCTCT
* *
16917774 TGAGCTTCCCG-TTTATGGCTCGTATGAGCTTCTCGATAATTGGCT
1 TGAGCTTCCCGATTAATGGCTCCTATGAGCTTCTCGATAATTGGCT
16917819 TGCAAGAGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
49 25 0.64
50 14 0.36
ACGTcount: A:0.16, C:0.23, G:0.22, T:0.39
Consensus pattern (50 bp):
TGAGCTTCCCGATTAATGGCTCCTATGAGCTTCTCGATAATTGGCTCTCT
Found at i:16919797 original size:14 final size:14
Alignment explanation
Indices: 16919778--16919820 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
16919768 CATATAACAC
16919778 TTCATATAATTATT
1 TTCATATAATTATT
* *
16919792 TTCATATAATCA-A
1 TTCATATAATTATT
16919805 TTCATATAATTATT
1 TTCATATAATTATT
16919819 TT
1 TT
16919821 GTTCATCTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.37, C:0.09, G:0.00, T:0.53
Consensus pattern (14 bp):
TTCATATAATTATT
Found at i:16919814 original size:13 final size:13
Alignment explanation
Indices: 16919755--16919957 Score: 88
Period size: 13 Copynumber: 15.5 Consensus size: 13
16919745 CATATCTATC
*
16919755 CATATAAACATTT
1 CATATAATCATTT
*
16919768 CATATAA-CACTT
1 CATATAATCATTT
*
16919780 CATATAATTATTTT
1 CATATAATCA-TTT
*
16919794 CATATAATCAATT
1 CATATAATCATTT
*
16919807 CATATAATTATTT
1 CATATAATCATTT
** * *
16919820 TGT-TCATCTGTTT
1 CATATAATC-ATTT
* *
16919833 CCGTATAATTGA-TT
1 -CATATAA-TCATTT
*
16919847 CATATAAGCATTT
1 CATATAATCATTT
* * *
16919860 CGTATATTTATTT
1 CATATAATCATTT
* *
16919873 CTATATAACCAATT
1 C-ATATAATCATTT
*
16919887 CTTATAATCATTT
1 CATATAATCATTT
* * *
16919900 TACATAACCATTT
1 CATATAATCATTT
** *
16919913 CATATAAAAAATT
1 CATATAATCATTT
*
16919926 CATATAACCATTT
1 CATATAATCATTT
* **
16919939 CGTATAGCCATTT
1 CATATAATCATTT
16919952 CATATA
1 CATATA
16919958 GCCATTTCAA
Statistics
Matches: 136, Mismatches: 46, Indels: 16
0.69 0.23 0.08
Matches are distributed among these distances:
12 15 0.11
13 95 0.70
14 23 0.17
15 2 0.01
16 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.04, T:0.44
Consensus pattern (13 bp):
CATATAATCATTT
Found at i:16919814 original size:27 final size:26
Alignment explanation
Indices: 16919765--16919820 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 26
16919755 CATATAAACA
*
16919765 TTTCATATAACACTTCATATAATTAT
1 TTTCATATAACAATTCATATAATTAT
16919791 TTTCATATAATCAATTCATATAATTAT
1 TTTCATATAA-CAATTCATATAATTAT
16919818 TTT
1 TTT
16919821 GTTCATCTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
26 10 0.36
27 18 0.64
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (26 bp):
TTTCATATAACAATTCATATAATTAT
Found at i:16919932 original size:39 final size:39
Alignment explanation
Indices: 16919869--16919957 Score: 97
Period size: 39 Copynumber: 2.3 Consensus size: 39
16919859 TCGTATATTT
** * * *
16919869 ATTTCTATATAACCAATTCTTATAATCATTTTACATAACC
1 ATTTC-ATATAAAAAATTCATATAACCATTTCACATAACC
** *
16919909 ATTTCATATAAAAAATTCATATAACCATTTCGTATAGCC
1 ATTTCATATAAAAAATTCATATAACCATTTCACATAACC
16919948 ATTTCATATA
1 ATTTCATATA
16919958 GCCATTTCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 36 0.88
40 5 0.12
ACGTcount: A:0.39, C:0.18, G:0.02, T:0.40
Consensus pattern (39 bp):
ATTTCATATAAAAAATTCATATAACCATTTCACATAACC
Found at i:16919953 original size:26 final size:26
Alignment explanation
Indices: 16919845--16919965 Score: 107
Period size: 26 Copynumber: 4.6 Consensus size: 26
16919835 GTATAATTGA
* * *
16919845 TTCATATAAGCATTTCGTATATTTAT
1 TTCATATAACCATTTCGTATAATCAT
* *
16919871 TTCTATATAACCAATTCTTATAATCAT
1 TTC-ATATAACCATTTCGTATAATCAT
* * * ** *
16919898 TTTACATAACCATTTCATATAAAAAA
1 TTCATATAACCATTTCGTATAATCAT
**
16919924 TTCATATAACCATTTCGTATAGCCAT
1 TTCATATAACCATTTCGTATAATCAT
*
16919950 TTCATATAGCCATTTC
1 TTCATATAACCATTTC
16919966 AAAGTGTTAA
Statistics
Matches: 74, Mismatches: 20, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
26 54 0.73
27 20 0.27
ACGTcount: A:0.36, C:0.18, G:0.04, T:0.42
Consensus pattern (26 bp):
TTCATATAACCATTTCGTATAATCAT
Found at i:16919958 original size:13 final size:13
Alignment explanation
Indices: 16919924--16919966 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
16919914 ATATAAAAAA
*
16919924 TTCATATAACCAT
1 TTCATATAGCCAT
*
16919937 TTCGTATAGCCAT
1 TTCATATAGCCAT
16919950 TTCATATAGCCAT
1 TTCATATAGCCAT
16919963 TTCA
1 TTCA
16919967 AAGTGTTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 27 1.00
ACGTcount: A:0.30, C:0.23, G:0.07, T:0.40
Consensus pattern (13 bp):
TTCATATAGCCAT
Found at i:16922952 original size:26 final size:26
Alignment explanation
Indices: 16922899--16922979 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
16922889 AACACACTAA
*
16922899 TATCGCAGCAAAGCTGCCAGTAAT-AG
1 TATCGCAGCAAAGCTGCCAAT-ATCAG
* * **
16922925 TATTGTAGTGAAGCTGCCAATATCAG
1 TATCGCAGCAAAGCTGCCAATATCAG
*
16922951 TATCGCAGCAAAGCTGCCAATAACAG
1 TATCGCAGCAAAGCTGCCAATATCAG
16922977 TAT
1 TAT
16922980 ATGTGGCAAA
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
25 2 0.05
26 42 0.95
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.23
Consensus pattern (26 bp):
TATCGCAGCAAAGCTGCCAATATCAG
Found at i:16923004 original size:52 final size:52
Alignment explanation
Indices: 16922899--16923005 Score: 117
Period size: 52 Copynumber: 2.1 Consensus size: 52
16922889 AACACACTAA
* * ** * **
16922899 TATCGCAGCAAAGCTGCCAGTAATAGTATTGTAGTGAAGCTGCCAATATCAG
1 TATCGCAGCAAAGCTGCCAATAACAGTATTGTAGCAAAACCACCAATATCAG
* *
16922951 TATCGCAGCAAAGCTGCCAATAACAGTATATGTGGCAAAACCACCAGTA-CAG
1 TATCGCAGCAAAGCTGCCAATAACAGTAT-TGTAGCAAAACCACCAATATCAG
16923003 TAT
1 TAT
16923006 ACTTCCTCCA
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
52 33 0.73
53 12 0.27
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.22
Consensus pattern (52 bp):
TATCGCAGCAAAGCTGCCAATAACAGTATTGTAGCAAAACCACCAATATCAG
Found at i:16932211 original size:20 final size:20
Alignment explanation
Indices: 16932185--16932268 Score: 90
Period size: 20 Copynumber: 4.3 Consensus size: 20
16932175 AGATTCGGCT
16932185 GAAGGAGAAGATAGAAAAGGA
1 GAAGGAGAAGA-AGAAAAGGA
16932206 -AAGGAGAAGAAAGAAAA--A
1 GAAGGAGAAG-AAGAAAAGGA
16932224 GAA--AGAA-AAGAAAAGGA
1 GAAGGAGAAGAAGAAAAGGA
*
16932241 GAAGAAGAAGAAGAAGAAGGA
1 GAAGGAGAAGAAGAA-AAGGA
16932262 GAAGGAG
1 GAAGGAG
16932269 GCGCAGGAAA
Statistics
Matches: 54, Mismatches: 1, Indels: 16
0.76 0.01 0.23
Matches are distributed among these distances:
15 7 0.13
17 8 0.15
18 1 0.02
19 6 0.11
20 20 0.37
21 12 0.22
ACGTcount: A:0.63, C:0.00, G:0.36, T:0.01
Consensus pattern (20 bp):
GAAGGAGAAGAAGAAAAGGA
Found at i:16932231 original size:30 final size:29
Alignment explanation
Indices: 16932192--16932255 Score: 92
Period size: 30 Copynumber: 2.2 Consensus size: 29
16932182 GCTGAAGGAG
* *
16932192 AAGATAGAAAAGGAAAGGAGAAGAAAGAAA
1 AAGAAAGAAAAGAAAAGGAGAAG-AAGAAA
*
16932222 AAGAAAGAAAAGAAAAGGAGAAGAAGAAG
1 AAGAAAGAAAAGAAAAGGAGAAGAAGAAA
16932251 AAGAA
1 AAGAA
16932256 GAAGGAGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
29 10 0.32
30 21 0.68
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.02
Consensus pattern (29 bp):
AAGAAAGAAAAGAAAAGGAGAAGAAGAAA
Found at i:16932248 original size:3 final size:3
Alignment explanation
Indices: 16932210--16932265 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
16932200 AAAGGAAAGG
* *
16932210 AGA AGAA AGA AAA AGAA AGA A-A AGA A-A AGG AGA AGA AGA AGA AGA
1 AGA AG-A AGA AGA AG-A AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
*
16932255 AGA AGG AGA AG
1 AGA AGA AGA AG
16932266 GAGGCGCAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
2 4 0.09
3 33 0.77
4 6 0.14
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:16932264 original size:15 final size:15
Alignment explanation
Indices: 16932185--16932265 Score: 57
Period size: 15 Copynumber: 5.7 Consensus size: 15
16932175 AGATTCGGCT
16932185 GAAGGAGAAGATAGAA
1 GAAGGAGAAGA-AGAA
*
16932201 -AAGGA-AAGGAGAA
1 GAAGGAGAAGAAGAA
*
16932214 GAA--AGAAAAAGAAA
1 GAAGGAGAAGAAG-AA
* *
16932228 GAA-AAGAA-AAGGA
1 GAAGGAGAAGAAGAA
*
16932241 GAAGAAGAAGAAGAA
1 GAAGGAGAAGAAGAA
16932256 GAAGGAGAAG
1 GAAGGAGAAG
16932266 GAGGCGCAGG
Statistics
Matches: 53, Mismatches: 6, Indels: 13
0.74 0.08 0.18
Matches are distributed among these distances:
12 1 0.02
13 12 0.23
14 18 0.34
15 22 0.42
ACGTcount: A:0.64, C:0.00, G:0.35, T:0.01
Consensus pattern (15 bp):
GAAGGAGAAGAAGAA
Found at i:16932583 original size:16 final size:16
Alignment explanation
Indices: 16932562--16932611 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
16932552 AAATAGGATT
16932562 AAAAATAAAATACTGA
1 AAAAATAAAATACTGA
***
16932578 AAAAATATGTTTA-TGA
1 AAAAATA-AAATACTGA
16932594 AAAAATAAAATAC-GA
1 AAAAATAAAATACTGA
16932609 AAA
1 AAA
16932612 TAAACGAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 5
0.70 0.16 0.14
Matches are distributed among these distances:
15 7 0.27
16 17 0.65
17 2 0.08
ACGTcount: A:0.66, C:0.04, G:0.08, T:0.22
Consensus pattern (16 bp):
AAAAATAAAATACTGA
Found at i:16932729 original size:13 final size:13
Alignment explanation
Indices: 16932708--16932758 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
16932698 TAAATTTATT
16932708 TAAAA-AATACAC
1 TAAAATAATACAC
*
16932720 TAAAATAATACATT
1 TAAAATAATACA-C
*
16932734 TCAAACATAATGCAC
1 T-AAA-ATAATACAC
16932749 TAAAATAATA
1 TAAAATAATA
16932759 TAAAATAATA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
12 5 0.16
13 11 0.35
14 4 0.13
15 4 0.13
16 7 0.23
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.25
Consensus pattern (13 bp):
TAAAATAATACAC
Found at i:16932842 original size:159 final size:157
Alignment explanation
Indices: 16932593--16933318 Score: 890
Period size: 148 Copynumber: 4.7 Consensus size: 157
16932583 TATGTTTATG
** ** *
16932593 AAAA-AATAAAATACGAAAATAAACGAAAATAGTATATTTACTGAAAGTAATAAAA-TC-CGAAA
1 AAAATAATAAAATAATAAAAT-AA-GAAAATAGTATATTTTTTGAAAGTAATAAAATTCGGGAAA
* *
16932655 ATAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATTTAAAAAATACAC
64 A-AAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACAC
* *
16932720 TAAAATAATACATTTCAAACATAATGCACT
128 TAAATTAATACATTTCAAACATAATGTACT
*
16932750 AAAATAATATAAAATAATAAAATAATAAAATAGTATATTTTTTGAAAGTAATAAAATTCGGGAAA
1 AAAAT-A-ATAAAATAATAAAATAAGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGGGAAA
* * * *
16932815 AAAGAAAAATACGAATAAATGGCCAAAATAA-GATTTTTTACTAAATTCATATAAAAAA-ATACT
64 AAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACT
* * *
16932878 AAATTAATATACTTCAAACATAATGTAAT
129 AAATTAATACATTTCAAACATAATGTACT
* * * * *
16932907 AAAATAATATAAAATAATAAAATACGAAAATAGTATTTTTTTTTTAAAGTAATAAAATCCGAGAA
1 AAAAT-A-ATAAAATAATAAAATAAGAAAATAGTA-TATTTTTTGAAAGTAATAAAATTCGGGAA
* * *
16932972 AAAAGAAAAATACAAACAAAGGGCCAAAATAAGGGTTTTTTACTAAATTTATAT-AAAAACGCAC
63 AAAAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACAC
*
16933036 TAAATTAATACATTTCAAACATTATGTACT
128 TAAATTAATACATTTCAAACATAATGTACT
* *
16933066 AAAATAATAAAATACA-AAAAT-AG----TA-TAT-TTTTTT-AAAGTAATAAAATCCAGGAAAA
1 AAAATAATAAAATA-ATAAAATAAGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGGGAAAA
16933122 AAGAAAAATACGAACAAATGGCCAAAATAAGGG-TTTTTACTAAATTTATATAAAAAACACACTA
65 AAGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTA
*
16933186 AATTAATACATTTCAAACATTATGTAC-
130 AATTAATACATTTCAAACATAATGTACT
*
16933213 -------TAAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAA-TCTGGGAAAA
1 AAAATAATAAAATAATAAAATAAGAAAATAGTATATTTTTTGAAAGTAATAAAATTC-GGGAAAA
* *
16933270 AAGAAAAATACGAACAAAGGGCCAAAATAAGAGTTTTTTTACTAAATTT
65 AAGAAAAATACGAACAAATGGCCAAAATAAG-GGTTTTTTACTAAATTT
16933319 GTTTTGAAGT
Statistics
Matches: 503, Mismatches: 44, Indels: 51
0.84 0.07 0.09
Matches are distributed among these distances:
139 1 0.00
140 12 0.02
141 1 0.00
145 2 0.00
146 3 0.01
147 25 0.05
148 137 0.27
149 7 0.01
150 15 0.03
151 2 0.00
152 2 0.00
156 1 0.00
157 78 0.16
158 113 0.22
159 86 0.17
160 18 0.04
ACGTcount: A:0.54, C:0.09, G:0.09, T:0.28
Consensus pattern (157 bp):
AAAATAATAAAATAATAAAATAAGAAAATAGTATATTTTTTGAAAGTAATAAAATTCGGGAAAAA
AGAAAAATACGAACAAATGGCCAAAATAAGGGTTTTTTACTAAATTTATATAAAAAACACACTAA
ATTAATACATTTCAAACATAATGTACT
Found at i:16935632 original size:8 final size:8
Alignment explanation
Indices: 16935619--16935660 Score: 59
Period size: 8 Copynumber: 5.4 Consensus size: 8
16935609 GGGTGTTACA
16935619 ACAACATT
1 ACAACATT
16935627 ACAACATT
1 ACAACATT
16935635 ACAACATT
1 ACAACATT
*
16935643 AC-ACATA
1 ACAACATT
*
16935650 ACAACTTT
1 ACAACATT
16935658 ACA
1 ACA
16935661 GCATAAGCTC
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (8 bp):
ACAACATT
Found at i:16938598 original size:40 final size:43
Alignment explanation
Indices: 16938528--16938614 Score: 119
Period size: 40 Copynumber: 2.1 Consensus size: 43
16938518 CTAATTCTAA
**
16938528 TAACTAACACAATAATAATAGTTTTCTTACTAAAAATAAT-AC
1 TAACTAACACAATAATAATAGGGTTCTTACTAAAAATAATAAC
16938570 TAACTAACA-AA-AATAATTAGGGTT-TTACTAAAAATAATAAC
1 TAACTAACACAATAATAA-TAGGGTTCTTACTAAAAATAATAAC
16938611 TAAC
1 TAAC
16938615 AATAATCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
40 19 0.46
41 13 0.32
42 9 0.22
ACGTcount: A:0.52, C:0.13, G:0.05, T:0.31
Consensus pattern (43 bp):
TAACTAACACAATAATAATAGGGTTCTTACTAAAAATAATAAC
Found at i:16938672 original size:76 final size:76
Alignment explanation
Indices: 16938556--16938696 Score: 203
Period size: 76 Copynumber: 1.9 Consensus size: 76
16938546 TAGTTTTCTT
16938556 ACTAAAAATAATACTAACTAACAAAAATAATTAGGGTTTTACTAAAAATAATAACTAACAATAAT
1 ACTAAAAATAATACTAACTAACAAAAATAATTAGGGTTTTACTAAAAATAATAACTAACAATAAT
16938621 CTAATATAAAA
66 CTAATATAAAA
* * * *** *
16938632 ACTAACAATCATACTAACTAA-AATAATAATTAGGGTTTTTACTAATCCTAATAACTAACCATAA
1 ACTAAAAATAATACTAACTAACAAAAATAATTAGGG-TTTTACTAAAAATAATAACTAACAATAA
16938696 T
65 T
16938697 AATAATATTA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
75 13 0.23
76 44 0.77
ACGTcount: A:0.52, C:0.13, G:0.04, T:0.30
Consensus pattern (76 bp):
ACTAAAAATAATACTAACTAACAAAAATAATTAGGGTTTTACTAAAAATAATAACTAACAATAAT
CTAATATAAAA
Found at i:16938951 original size:20 final size:20
Alignment explanation
Indices: 16938917--16938978 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 20
16938907 TACCTTATTT
* *
16938917 TTTCTATTTTTTTTCTTCTC
1 TTTCTATTCTCTTTCTTCTC
*
16938937 TTTCT-TTCTCCTTTCTCCT-
1 TTTCTATTCT-CTTTCTTCTC
16938956 TTCTCTATTCTCTTTC-TCTC
1 TT-TCTATTCTCTTTCTTCTC
16938976 TTT
1 TTT
16938979 TCCTTCCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
19 8 0.24
20 22 0.65
21 4 0.12
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (20 bp):
TTTCTATTCTCTTTCTTCTC
Found at i:16939008 original size:3 final size:3
Alignment explanation
Indices: 16939000--16939036 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
16938990 CTGCACGGCT
16939000 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
16939037 NNNNNNNNNN
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.32, G:0.00, T:0.35
Consensus pattern (3 bp):
TCA
Found at i:16939148 original size:6 final size:6
Alignment explanation
Indices: 16939141--16939341 Score: 217
Period size: 6 Copynumber: 33.5 Consensus size: 6
16939131 NNNNNNTCTC
* * * * *
16939141 CTTCTC CTTCTT CTCCTT CTTCTC CTTCTC CTTCTT CTCCTT CTTC-T
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
* * * *
16939188 CTTTCTT CTCCTT CTTCTT CTTCTT CTTCTC CTTCTC CTTCTT CTTTTT
1 C-TTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
* * * * * * *
16939237 CTCCTT CTTCTT CCTCTC CTTCTT CTCCTC CTTCTT CTCCTT CTTCTC
1 CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
*
16939285 CTTC-T CTTTCTC CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
1 CTTCTT C-TTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT CTTCTT
16939333 CTTCTT CTT
1 CTTCTT CTT
16939342 AAGTGAATTG
Statistics
Matches: 162, Mismatches: 29, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
5 3 0.02
6 156 0.96
7 3 0.02
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (6 bp):
CTTCTT
Found at i:16939341 original size:9 final size:9
Alignment explanation
Indices: 16939141--16939341 Score: 217
Period size: 9 Copynumber: 22.3 Consensus size: 9
16939131 NNNNNNTCTC
*
16939141 CTTCTCCTT
1 CTTCTTCTT
*
16939150 CTTCTCCTT
1 CTTCTTCTT
*
16939159 CTTCTCCTT
1 CTTCTTCTT
*
16939168 CTCCTTCTT
1 CTTCTTCTT
*
16939177 CTCCTTCTT
1 CTTCTTCTT
16939186 C-TCTTTCTT
1 CTTC-TTCTT
*
16939195 CTCCTTCTT
1 CTTCTTCTT
16939204 CTTCTTCTT
1 CTTCTTCTT
*
16939213 CTTCTCCTT
1 CTTCTTCTT
*
16939222 CTCCTTCTT
1 CTTCTTCTT
* *
16939231 CTTTTTCTC
1 CTTCTTCTT
16939240 CTTCTTCTT
1 CTTCTTCTT
* *
16939249 CCTCTCCTT
1 CTTCTTCTT
* *
16939258 CTTCTCCTC
1 CTTCTTCTT
*
16939267 CTTCTTCTC
1 CTTCTTCTT
*
16939276 CTTCTTCTC
1 CTTCTTCTT
16939285 CTTC-TCTTT
1 CTTCTTC-TT
*
16939294 CTCCTTCTT
1 CTTCTTCTT
16939303 CTTCTTCTT
1 CTTCTTCTT
16939312 CTTCTTCTT
1 CTTCTTCTT
16939321 CTTCTTCTT
1 CTTCTTCTT
16939330 CTTCTTCTT
1 CTTCTTCTT
16939339 CTT
1 CTT
16939342 AAGTGAATTG
Statistics
Matches: 167, Mismatches: 21, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
8 3 0.02
9 161 0.96
10 3 0.02
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (9 bp):
CTTCTTCTT
Found at i:16939341 original size:15 final size:15
Alignment explanation
Indices: 16939141--16939341 Score: 217
Period size: 15 Copynumber: 13.4 Consensus size: 15
16939131 NNNNNNTCTC
* *
16939141 CTTCTCCTTCTTCTC
1 CTTCTTCTTCTTCTT
* *
16939156 CTTCTTCTCCTTCTC
1 CTTCTTCTTCTTCTT
*
16939171 CTTCTTCTCCTTCTT
1 CTTCTTCTTCTTCTT
*
16939186 C-TCTTTCTTCTCCTT
1 CTTC-TTCTTCTTCTT
16939201 CTTCTTCTTCTTCTT
1 CTTCTTCTTCTTCTT
* *
16939216 CTCCTTCTCCTTCTT
1 CTTCTTCTTCTTCTT
* *
16939231 CTTTTTCTCCTTCTT
1 CTTCTTCTTCTTCTT
* *
16939246 CTTCCTCTCCTTCTT
1 CTTCTTCTTCTTCTT
* * *
16939261 CTCCTCCTTCTTCTC
1 CTTCTTCTTCTTCTT
*
16939276 CTTCTTCTCCTTC-T
1 CTTCTTCTTCTTCTT
*
16939290 CTTTCTCCTTCTTCTT
1 C-TTCTTCTTCTTCTT
16939306 CTTCTTCTTCTTCTT
1 CTTCTTCTTCTTCTT
16939321 CTTCTTCTTCTTCTT
1 CTTCTTCTTCTTCTT
16939336 CTTCTT
1 CTTCTT
16939342 AAGTGAATTG
Statistics
Matches: 158, Mismatches: 24, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
14 3 0.02
15 151 0.96
16 4 0.03
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (15 bp):
CTTCTTCTTCTTCTT
Found at i:16943429 original size:9 final size:9
Alignment explanation
Indices: 16943415--16943445 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
16943405 GTTAAATGAA
16943415 TCGAGTTAT
1 TCGAGTTAT
*
16943424 TCGAGTTAA
1 TCGAGTTAT
16943433 TCGAGTTAT
1 TCGAGTTAT
16943442 TCGA
1 TCGA
16943446 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:16943515 original size:9 final size:9
Alignment explanation
Indices: 16943498--16943534 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
16943488 TAAGTTTTCG
16943498 AATTCGAAT
1 AATTCGAAT
*
16943507 AACTCGAAT
1 AATTCGAAT
16943516 AATTCGAAT
1 AATTCGAAT
16943525 AATTCGAAT
1 AATTCGAAT
16943534 A
1 A
16943535 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:16944571 original size:8 final size:8
Alignment explanation
Indices: 16944558--16944587 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
16944548 AGCTCATTTT
16944558 ATCACATC
1 ATCACATC
16944566 ATCACATC
1 ATCACATC
16944574 ATCACATC
1 ATCACATC
16944582 ATCACA
1 ATCACA
16944588 AAACATATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.40, C:0.37, G:0.00, T:0.23
Consensus pattern (8 bp):
ATCACATC
Found at i:16945501 original size:15 final size:15
Alignment explanation
Indices: 16945454--16945502 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 15
16945444 TATGTTTCCT
*
16945454 TTATTTTAA-TGTTA
1 TTATTTTAATTTTTA
16945468 TTATTTTAACCTTTATTA
1 TTATTTTAA--TTT-TTA
16945486 TTATTTTAATTTTTA
1 TTATTTTAATTTTTA
16945501 TT
1 TT
16945503 TAATATAAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 9 0.30
15 5 0.17
16 3 0.10
17 1 0.03
18 12 0.40
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (15 bp):
TTATTTTAATTTTTA
Found at i:16947050 original size:4 final size:4
Alignment explanation
Indices: 16947041--16947070 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
16947031 TTAGTAGACT
16947041 TAAC TAAC TAAC TAAC TAAC TAAC TTAAC T
1 TAAC TAAC TAAC TAAC TAAC TAAC -TAAC T
16947071 TAAACCAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (4 bp):
TAAC
Found at i:16947058 original size:12 final size:13
Alignment explanation
Indices: 16947038--16947070 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
16947028 CGCTTAGTAG
16947038 ACTTAACTAACTA
1 ACTTAACTAACTA
16947051 AC-TAACTAACTA
1 ACTTAACTAACTA
16947063 ACTTAACT
1 ACTTAACT
16947071 TAAACCAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.30
Consensus pattern (13 bp):
ACTTAACTAACTA
Found at i:16960070 original size:25 final size:25
Alignment explanation
Indices: 16960052--16960099 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
16960042 CCACATAGTC
*
16960052 TTTACAGGTAACCTACCACAAAGAA
1 TTTACAGATAACCTACCACAAAGAA
16960077 TTTACAGATAACCTACCACAAAG
1 TTTACAGATAACCTACCACAAAG
16960100 GCTTACCAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.44, C:0.25, G:0.10, T:0.21
Consensus pattern (25 bp):
TTTACAGATAACCTACCACAAAGAA
Found at i:16960112 original size:25 final size:25
Alignment explanation
Indices: 16960060--16960112 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
16960050 TCTTTACAGG
* *
16960060 TAACCTACCACAAAGAATTTACAGA
1 TAACCTACCACAAAGAACTTACAAA
*
16960085 TAACCTACCACAAAG-GCTTACCAAA
1 TAACCTACCACAAAGAACTTA-CAAA
16960110 TAA
1 TAA
16960113 ATCGCCACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 3 0.12
25 21 0.88
ACGTcount: A:0.47, C:0.26, G:0.08, T:0.19
Consensus pattern (25 bp):
TAACCTACCACAAAGAACTTACAAA
Found at i:16974190 original size:9 final size:9
Alignment explanation
Indices: 16974161--16974190 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16974151 TTCGCATCAT
16974161 TTTCTCTTA
1 TTTCTCTTA
*
16974170 TTGCTCTTA
1 TTTCTCTTA
16974179 TTTCTCTTA
1 TTTCTCTTA
16974188 TTT
1 TTT
16974191 AGCGACAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.67
Consensus pattern (9 bp):
TTTCTCTTA
Found at i:16977716 original size:43 final size:43
Alignment explanation
Indices: 16977655--16977897 Score: 291
Period size: 43 Copynumber: 5.7 Consensus size: 43
16977645 GATATGATTT
*
16977655 CGTGTAAGACCACGTCTGGGACGTTGGCATCAACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
*
16977698 CGTGTAAGACCACGTCTGGGACATTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
*
16977741 CGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
* * * *
16977784 CGTGTAAGACCATGTCAGGGACATTGGCATCGTA-TT-TGATT-
1 CGTGTAAGACCACGTCTGGGACGTTGGCATCG-ACTTGTGTTTA
* * * * *
16977825 CGTATAAGACC-CTGTCTGGGACAG-TGGAATTGA-TATATGATTA
1 CGTGTAAGACCAC-GTCTGGGAC-GTTGGCATCGACT-TGTGTTTA
*
16977868 CATGTAAGACCACGTCTGGGACGTTGGCAT
1 CGTGTAAGACCACGTCTGGGACGTTGGCAT
16977898 TGTACGAGAT
Statistics
Matches: 174, Mismatches: 18, Indels: 16
0.84 0.09 0.08
Matches are distributed among these distances:
40 2 0.01
41 25 0.14
42 10 0.06
43 135 0.78
44 2 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (43 bp):
CGTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTA
Found at i:16977886 original size:127 final size:129
Alignment explanation
Indices: 16977655--16977897 Score: 307
Period size: 127 Copynumber: 1.9 Consensus size: 129
16977645 GATATGATTT
* * * *
16977655 CGTGTAAGACCACGTCTGGGACGTTGGCATCAACTTGTGTTTACGTGTAAGACCACGTCTGGGAC
1 CGTGTAAGACCACGTCAGGGACATTGGCATCAACTTGTGATTACGTATAAGACCACGTCTGGGAC
* * * * *
16977720 ATTGGCATCGACTTGTGTTTACGTGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
66 AGTGGAATCGACTTATGATTACATGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
* *
16977784 CGTGTAAGACCATGTCAGGGACATTGGCATCGTA-TT-TGATT-CGTATAAGACC-CTGTCTGGG
1 CGTGTAAGACCACGTCAGGGACATTGGCATC-AACTTGTGATTACGTATAAGACCAC-GTCTGGG
* *
16977845 ACAGTGGAATTGA-TATATGATTACATGTAAGACCACGTCTGGGACGTTGGCAT
64 ACAGTGGAATCGACT-TATGATTACATGTAAGACCACATCTGGGACGTTGGCAT
16977898 TGTACGAGAT
Statistics
Matches: 98, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
126 2 0.02
127 61 0.62
128 4 0.04
129 30 0.31
130 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.28, T:0.30
Consensus pattern (129 bp):
CGTGTAAGACCACGTCAGGGACATTGGCATCAACTTGTGATTACGTATAAGACCACGTCTGGGAC
AGTGGAATCGACTTATGATTACATGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGTTTA
Found at i:16981619 original size:49 final size:47
Alignment explanation
Indices: 16981534--16981637 Score: 126
Period size: 49 Copynumber: 2.2 Consensus size: 47
16981524 TGCTCTCCCA
16981534 TCCCTCT--CCCTCTTCTCCACCATTCCTCCCCCTACTCTGATTCTCT
1 TCCCTCTCCCCCTCTTCTCCACCATTCCTCCCCCTACTCTGATTCT-T
* *
16981580 CTCCCTCTCCCCCTCTTC-CCTACCA-TCACTCCTCTTACTCTGATTCTT
1 -TCCCTCTCCCCCTCTTCTCC-ACCATTC-CTCCCCCTACTCTGATTCTT
16981628 TCCCTCTCCC
1 TCCCTCTCCC
16981638 ACACCGTCCC
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
47 17 0.33
48 5 0.10
49 29 0.57
ACGTcount: A:0.09, C:0.53, G:0.02, T:0.37
Consensus pattern (47 bp):
TCCCTCTCCCCCTCTTCTCCACCATTCCTCCCCCTACTCTGATTCTT
Found at i:16983593 original size:29 final size:30
Alignment explanation
Indices: 16983536--16983592 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
16983526 TTCAATAAAA
16983536 ATATAAGAAAATAATATTATTAATATTTTG
1 ATATAAGAAAATAATATTATTAATATTTTG
*
16983566 ATATATGAAATATAAT-TT-TTAA-ATTTT
1 ATATAAGAAA-ATAATATTATTAATATTTT
16983593 TAAGCAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 5 0.20
29 4 0.16
30 11 0.44
31 5 0.20
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (30 bp):
ATATAAGAAAATAATATTATTAATATTTTG
Found at i:16983869 original size:9 final size:9
Alignment explanation
Indices: 16983823--16983855 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
16983813 ATTTGATTTG
16983823 ACTCGAATA
1 ACTCGAATA
*
16983832 ATTCGAATA
1 ACTCGAATA
16983841 ACTCGAATA
1 ACTCGAATA
16983850 ACTCGA
1 ACTCGA
16983856 TTCGATTAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.42, C:0.21, G:0.12, T:0.24
Consensus pattern (9 bp):
ACTCGAATA
Found at i:16990767 original size:21 final size:21
Alignment explanation
Indices: 16990727--16990767 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
16990717 AATAACTACC
*
16990727 CAGCTAACAACCAACTAACTT
1 CAGCTAACAACCAACAAACTT
* *
16990748 CAGCTAACTACTAACAAACT
1 CAGCTAACAACCAACAAACT
16990768 AACTGACTTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.44, C:0.32, G:0.05, T:0.20
Consensus pattern (21 bp):
CAGCTAACAACCAACAAACTT
Found at i:16991494 original size:18 final size:18
Alignment explanation
Indices: 16991471--16991508 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
16991461 AATATATCAA
16991471 AAAGACTCTTTCACCATT
1 AAAGACTCTTTCACCATT
16991489 AAAGACTCTTTCACCATT
1 AAAGACTCTTTCACCATT
16991507 AA
1 AA
16991509 CTTTAATAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.26, G:0.05, T:0.32
Consensus pattern (18 bp):
AAAGACTCTTTCACCATT
Found at i:16991625 original size:9 final size:9
Alignment explanation
Indices: 16991599--16991630 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
16991589 GATATGACAA
16991599 AAAAATTAT
1 AAAAATTAT
16991608 AAAAA--AT
1 AAAAATTAT
16991615 AAAAATTAT
1 AAAAATTAT
16991624 AAAAATT
1 AAAAATT
16991631 TTTTATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.33
9 14 0.67
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (9 bp):
AAAAATTAT
Found at i:16991678 original size:23 final size:23
Alignment explanation
Indices: 16991639--16991685 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
16991629 TTTTTTATTG
**
16991639 AATTTTATTAATTTTTAATAAAA
1 AATTTTATTAAAATTTAATAAAA
*
16991662 AATTTTATTAAAATTTATTAAAA
1 AATTTTATTAAAATTTAATAAAA
16991685 A
1 A
16991686 TTATAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTTTATTAAAATTTAATAAAA
Found at i:16991694 original size:9 final size:9
Alignment explanation
Indices: 16991670--16991749 Score: 88
Period size: 9 Copynumber: 8.6 Consensus size: 9
16991660 AAAATTTTAT
*
16991670 TAAAATTTA
1 TAAAAATTA
16991679 TTAAAAATTA
1 -TAAAAATTA
*
16991689 TAAAAATTT
1 TAAAAATTA
*
16991698 TAAAAAATCA
1 T-AAAAATTA
16991708 TAAAAATTA
1 TAAAAATTA
*
16991717 TAAAATTTTA
1 TAAAA-ATTA
*
16991727 TAAAAATCA
1 TAAAAATTA
16991736 TAAAAATTA
1 TAAAAATTA
16991745 TAAAA
1 TAAAA
16991750 TACATCAAAA
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
9 36 0.61
10 23 0.39
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAAATTA
Done.