Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A05
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: 100714657
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 3970000 characters in sequence are not A, C, G, or T
File 2 of 318
Found at i:287961 original size:35 final size:35
Alignment explanation
Indices: 287922--288034 Score: 92
Period size: 35 Copynumber: 3.3 Consensus size: 35
287912 TAATCGTTTA
287922 ATGTTTGTGAATATATTTGATTAAGTTAAATAAAC
1 ATGTTTGTGAATATATTTGATTAAGTTAAATAAAC
* * ** * **
287957 ATGTTCGT-AA-ACATTAAATAAACG--AACATGTA-
1 ATGTTTGTGAATATATTTGATTAA-GTTAA-ATAAAC
* *
287989 ATGTTTGTAAATATATTTGATTAAATTAAATAAAC
1 ATGTTTGTGAATATATTTGATTAAGTTAAATAAAC
288024 ATGTTTGTGAA
1 ATGTTTGTGAA
288035 CATTAAATAA
Statistics
Matches: 55, Mismatches: 16, Indels: 14
0.65 0.19 0.16
Matches are distributed among these distances:
32 9 0.16
33 13 0.24
34 14 0.25
35 19 0.35
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (35 bp):
ATGTTTGTGAATATATTTGATTAAGTTAAATAAAC
Found at i:288002 original size:67 final size:67
Alignment explanation
Indices: 287920--288053 Score: 232
Period size: 67 Copynumber: 2.0 Consensus size: 67
287910 CATAATCGTT
* *
287920 TAATGTTTGTGAATATATTTGATTAAGTTAAATAAACATGTTCGTAAACATTAAATAAACGAACA
1 TAATGTTTGTAAATATATTTGATTAAATTAAATAAACATGTTCGTAAACATTAAATAAACGAACA
287985 TG
66 TG
* *
287987 TAATGTTTGTAAATATATTTGATTAAATTAAATAAACATGTTTGTGAACATTAAATAAACGAACA
1 TAATGTTTGTAAATATATTTGATTAAATTAAATAAACATGTTCGTAAACATTAAATAAACGAACA
288052 TG
66 TG
288054 GAACACATGT
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.37
Consensus pattern (67 bp):
TAATGTTTGTAAATATATTTGATTAAATTAAATAAACATGTTCGTAAACATTAAATAAACGAACA
TG
Found at i:290662 original size:26 final size:24
Alignment explanation
Indices: 290633--290724 Score: 75
Period size: 26 Copynumber: 3.8 Consensus size: 24
290623 GAGTAAGATC
290633 AAATTAATAAAAATTATAAATATAAA
1 AAATTAATAAAAATTATAAATAT--A
* *
290659 AAATTATTAAAAATCA-AAAT-T-
1 AAATTAATAAAAATTATAAATATA
290680 AAATTAAT-AAAATATATAAACTATA
1 AAATTAATAAAAAT-TATAAA-TATA
* *
290705 CCAATTAAAAAAAATTATAA
1 -AAATTAATAAAAATTATAA
290725 TCTATAACCA
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
20 5 0.09
21 8 0.15
22 3 0.06
23 1 0.02
24 2 0.04
25 4 0.08
26 25 0.47
27 5 0.09
ACGTcount: A:0.65, C:0.04, G:0.00, T:0.30
Consensus pattern (24 bp):
AAATTAATAAAAATTATAAATATA
Found at i:320277 original size:3 final size:3
Alignment explanation
Indices: 320269--320301 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
320259 ATCAAGAATA
320269 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
320302 GCTAAATCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:320659 original size:23 final size:21
Alignment explanation
Indices: 320633--320678 Score: 65
Period size: 23 Copynumber: 2.1 Consensus size: 21
320623 ATGTTAAATA
320633 AATATATTATAATATTGTATAAT
1 AATATATTATAATA-T-TATAAT
*
320656 AATATATTATATTATTATAAT
1 AATATATTATAATATTATAAT
320677 AA
1 AA
320679 AACAAAACAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 8 0.36
22 1 0.05
23 13 0.59
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AATATATTATAATATTATAAT
Found at i:321061 original size:30 final size:28
Alignment explanation
Indices: 321007--321063 Score: 71
Period size: 30 Copynumber: 2.0 Consensus size: 28
320997 AATTGTAGAA
*
321007 TAAATTGTAAATTTTGAGTATTAGGGAC
1 TAAATTGTAAATTTTGAATATTAGGGAC
321035 TAAATTGTGAAAATTTTAGAAT-TTAGGGA
1 TAAATTGT--AAATTTT-GAATATTAGGGA
321064 TTTAAGTGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
28 8 0.32
30 14 0.56
31 3 0.12
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.39
Consensus pattern (28 bp):
TAAATTGTAAATTTTGAATATTAGGGAC
Found at i:322490 original size:21 final size:22
Alignment explanation
Indices: 322465--322511 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
322455 TTAGGATGAT
322465 TGTTTTGA-CATGTTTTGGATG
1 TGTTTTGATCATGTTTTGGATG
**
322486 TG-TTTGATTGTGTTTTGGATG
1 TGTTTTGATCATGTTTTGGATG
322507 TGTTT
1 TGTTT
322512 GAGTTGCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 15 0.68
22 2 0.09
ACGTcount: A:0.11, C:0.02, G:0.30, T:0.57
Consensus pattern (22 bp):
TGTTTTGATCATGTTTTGGATG
Found at i:322502 original size:11 final size:11
Alignment explanation
Indices: 322475--322511 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
322465 TGTTTTGACA
322475 TGTTTTGGATG
1 TGTTTTGGATG
322486 TG-TTT-GATTG
1 TGTTTTGGA-TG
322496 TGTTTTGGATG
1 TGTTTTGGATG
322507 TGTTT
1 TGTTT
322512 GAGTTGCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
9 2 0.09
10 7 0.30
11 12 0.52
12 2 0.09
ACGTcount: A:0.08, C:0.00, G:0.32, T:0.59
Consensus pattern (11 bp):
TGTTTTGGATG
Found at i:323668 original size:41 final size:40
Alignment explanation
Indices: 323561--323809 Score: 284
Period size: 41 Copynumber: 6.1 Consensus size: 40
323551 GCAAAAATTG
323561 TAAAATACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
1 TAAAA-ACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* *
323602 TAAAAACAAAGCAATAGCGGCGCTTTTGGTAAAACGCCAC
1 TAAAAACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* * *
323642 TAAAAGACGGAGCAATAGCAGCGCTTTTGGTAAAACGTCGC
1 TAAAA-ACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
*** * * * *
323683 TAAAAGTTGGAGCATTAGCAGCGCTTTTTGTAAAACACCGC
1 TAAAA-ACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* * *
323724 TAAAAACCGGAGCATTAGCGGCGCTTTT-GTAAAACACCGC
1 TAAAAA-CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
* * *
323764 TAAAAATCAGAGCATTAGCGGCACTTTTTGTAAAACGCCGC
1 TAAAAA-CAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
323805 TAAAA
1 TAAAA
323810 GTCATATAAC
Statistics
Matches: 185, Mismatches: 20, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
40 75 0.41
41 110 0.59
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (40 bp):
TAAAAACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGC
Found at i:323756 original size:81 final size:81
Alignment explanation
Indices: 323561--323810 Score: 315
Period size: 81 Copynumber: 3.1 Consensus size: 81
323551 GCAAAAATTG
* * * * *
323561 TAAAATACAGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAAACAAAGCAATAGCGGCGCT
1 TAAAAGACGGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAATCAGAGCATTAGCGGCGCT
* *
323626 TTTGGTAAAACGCCAC
66 TTTTGTAAAACGCCGC
* * ** *
323642 TAAAAGACGGAGCAATAGCAGCGCTTTTGGTAAAACGTCGCTAAAAGTTGGAGCATTAGCAGCGC
1 TAAAAGACGGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAA-TCAGAGCATTAGCGGCGC
*
323707 TTTTTGTAAAACACCGC
65 TTTTTGTAAAACGCCGC
* * *
323724 TAAAA-ACCGGAGCATTAGCGGCGCTTTT-GTAAAACACCGCTAAAAATCAGAGCATTAGCGGCA
1 TAAAAGA-CGGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCT-AAAATCAGAGCATTAGCGGCG
323787 CTTTTTGTAAAACGCCGC
64 CTTTTTGTAAAACGCCGC
323805 TAAAAG
1 TAAAAG
323811 TCATATAACC
Statistics
Matches: 143, Mismatches: 22, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
81 89 0.62
82 54 0.38
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.21
Consensus pattern (81 bp):
TAAAAGACGGAGCAATAGCGGCGCTTTTGGTAAAACGCCGCTAAAATCAGAGCATTAGCGGCGCT
TTTTGTAAAACGCCGC
Found at i:323996 original size:7 final size:7
Alignment explanation
Indices: 323980--324009 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
323970 TTATTTTTGA
*
323980 GTTTAGG
1 GTTTAAG
323987 GTTTAAG
1 GTTTAAG
323994 GTTTAAG
1 GTTTAAG
324001 GTTTAAG
1 GTTTAAG
324008 GT
1 GT
324010 CTGTGGTCCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.33, T:0.43
Consensus pattern (7 bp):
GTTTAAG
Found at i:324319 original size:21 final size:21
Alignment explanation
Indices: 324278--324321 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
324268 TTTAATCATT
* *
324278 TAAAGTTTAGATGATAGGGGG
1 TAAAGGTTAGATGATAAGGGG
324299 TAAAGGTTAGA-GATTAAGGGG
1 TAAAGGTTAGATGA-TAAGGGG
324320 TA
1 TA
324322 GACGTTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.36, C:0.00, G:0.36, T:0.27
Consensus pattern (21 bp):
TAAAGGTTAGATGATAAGGGG
Found at i:324399 original size:7 final size:7
Alignment explanation
Indices: 324325--324435 Score: 62
Period size: 7 Copynumber: 15.3 Consensus size: 7
324315 AGGGGTAGAC
324325 GTTTAGG
1 GTTTAGG
*
324332 GTTTATG
1 GTTTAGG
*
324339 GTTTATG
1 GTTTAGG
* *
324346 GCTTAAG
1 GTTTAGG
324353 GTTTAGG
1 GTTTAGG
* *
324360 GGTTAAG
1 GTTTAGG
*
324367 ATTTATGG
1 GTTTA-GG
*
324375 GTTTATAG
1 GTTTA-GG
*
324383 GTTATGGG
1 GTT-TAGG
324391 GTTTAGG
1 GTTTAGG
324398 GTTTAGG
1 GTTTAGG
* *
324405 ATATA-G
1 GTTTAGG
324411 GTGTTAGGG
1 GT-TTA-GG
324420 GTTTAGG
1 GTTTAGG
*
324427 TTTTAGG
1 GTTTAGG
324434 GT
1 GT
324436 AATTAGTGTG
Statistics
Matches: 78, Mismatches: 21, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
6 2 0.03
7 55 0.71
8 17 0.22
9 4 0.05
ACGTcount: A:0.19, C:0.01, G:0.37, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:324563 original size:17 final size:17
Alignment explanation
Indices: 324537--324589 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
324527 AATCTATATA
*
324537 TTAAATAATTTCAAATT
1 TTAAAAAATTTCAAATT
* *
324554 TTAAAGAA-TTAAAATT
1 TTAAAAAATTTCAAATT
324570 TTAAAAAAATTTCAAGATT
1 TT-AAAAAATTTCAA-ATT
324589 T
1 T
324590 CAGATTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 9 0.31
17 12 0.41
18 4 0.14
19 4 0.14
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (17 bp):
TTAAAAAATTTCAAATT
Found at i:324816 original size:14 final size:14
Alignment explanation
Indices: 324787--324837 Score: 59
Period size: 13 Copynumber: 3.6 Consensus size: 14
324777 CTTGTTTTTT
*
324787 TTTATAAAAATTTAA
1 TTTATAAAAA-ATAA
324802 TTTATAAAAAATAA
1 TTTATAAAAAATAA
* *
324816 -TAATAAAAAATAT
1 TTTATAAAAAATAA
324829 TTTATAAAA
1 TTTATAAAA
324838 TTATGTAGCT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 11 0.35
14 10 0.32
15 10 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TTTATAAAAAATAA
Found at i:332095 original size:93 final size:92
Alignment explanation
Indices: 331936--332159 Score: 288
Period size: 93 Copynumber: 2.4 Consensus size: 92
331926 TTCGACATGA
* * * * * *
331936 TGCCATAGTGTCTTTCAACTATAGTCTTACTCATTTTC-TGTCATGTTGCCATGGTATCATTCAA
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGTCACGTTGCCATGGTATCATTCAA
** * *
332000 CCATGGTCTTATTCATTTTCCCGTCACGT
65 CCATGGTCTTACACA-TTTCACATCACGT
* *
332029 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATGTCACGTTGCCATGGTATCTTTCAAC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCACGTTGCCATGGTATCATTCAAC
* *
332094 CATGGTCTTACACATTTCATATCAGGT
66 CATGGTCTTACACATTTCACATCACGT
*
332121 TGCCGTGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
332160 ATCAGAGAGT
Statistics
Matches: 114, Mismatches: 16, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
92 50 0.44
93 64 0.56
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (92 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCACGTTGCCATGGTATCATTCAAC
CATGGTCTTACACATTTCACATCACGT
Found at i:332164 original size:46 final size:46
Alignment explanation
Indices: 331936--332159 Score: 288
Period size: 46 Copynumber: 4.8 Consensus size: 46
331926 TTCGACATGA
* * * * * *
331936 TGCCATAGTGTCTTTCAACTATAGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGTCACGT
* ** **
331982 TGCCATGGTATCATTCAACCATGGTCTTATTCATTTTCCCGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATGTCACGT
*
332029 TGCCATGGTATCTTTCAACCATGGTCTTACACGTTTCATGTCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCACGT
* *
332075 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCACGT
*
332121 TGCCGTGGTATCTTTCAACCATGGTCTTACACATTTCAT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCAT
332160 ATCAGAGAGT
Statistics
Matches: 159, Mismatches: 18, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
46 124 0.78
47 35 0.22
ACGTcount: A:0.21, C:0.25, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATGTCACGT
Found at i:334298 original size:11 final size:11
Alignment explanation
Indices: 334282--334333 Score: 52
Period size: 11 Copynumber: 4.7 Consensus size: 11
334272 TATACTAAAT
334282 AAATAATAATA
1 AAATAATAATA
*
334293 AAATAAT-ATT
1 AAATAATAATA
* *
334303 AAATATCTCATA
1 AAATA-ATAATA
*
334315 AAATATTAATA
1 AAATAATAATA
334326 AAATAATA
1 AAATAATA
334334 TTTATCTAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
10 7 0.21
11 19 0.58
12 7 0.21
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (11 bp):
AAATAATAATA
Found at i:335810 original size:45 final size:45
Alignment explanation
Indices: 335610--336126 Score: 272
Period size: 45 Copynumber: 11.6 Consensus size: 45
335600 TAATTTCAAC
* * * * * *
335610 CTGCTCCACTGCATCTTTAGGGAGATGAGGTTTGCGA-CTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGT
* * *
335654 CTGCTCCACTGCAACTTCAGGGAGATGAGATTCGCCATAGTAACTTGA-T
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTG-C-TA-T--CTTCAGT
* * * * * * * *
335703 CCGAC-CTACTGCAACTTCAGAGG-TATAGGATTT-ATAGCTTTAAT
1 CTG-CTCCACTGCAACTTCAG-GGAGATAAGATTTGCTATCTTCAGT
* * * *
335747 CTGCTCTACTGCAACTTCAGAGAGATAAGATTTGCTATTTTGAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGT
* * * *
335792 CTGCTCCGCTGCAACTTCAAGGAAATGAGATTTGCTATCTTCAGT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGT
* * * * * **
335837 CTACTCCATTGCAAGTTCAGGGAGATAAGACTTG-TA-CTTTAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGT
* * *
335880 CTG-TCCTACTGCAACTTCAGGGGGATAAGGTTTGTTATCTTCAGT
1 CTGCTCC-ACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGT
* * * * **
335925 CTACTCCACTGCAAGTTCAGGGAGATAAGACTTG-TA-CTTTAAC
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGT
* * *
335968 CTGCCCCACTGCAACTTCAGGGGGATAATG-TTTGTTATCTTC-GAT
1 CTGCTCCACTGCAACTTCAGGGAGATAA-GATTTGCTATCTTCAG-T
*** * * * *
336013 CCATTCCACTGCAACTTTAGGGAGATAAGATCTG-TAACTTCAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGT
* ** * * * * * *
336057 CTACTCTGCTGAAACTTCAGAGAGACAAGATTTG--AGGCTTAAAAT
1 CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTA-TCTT-CAGT
*
336102 CTTCTCCACTGCAACTTCAGGGAGA
1 CTGCTCCACTGCAACTTCAGGGAGA
336127 CAAAATCTAC
Statistics
Matches: 356, Mismatches: 93, Indels: 47
0.72 0.19 0.09
Matches are distributed among these distances:
42 3 0.01
43 66 0.19
44 101 0.28
45 150 0.42
46 6 0.02
49 23 0.06
50 7 0.02
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.31
Consensus pattern (45 bp):
CTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAGT
Found at i:335899 original size:43 final size:42
Alignment explanation
Indices: 335841--335995 Score: 157
Period size: 43 Copynumber: 3.6 Consensus size: 42
335831 TTCAGTCTAC
* *
335841 TCCATTGCAAGTTCAGGGAGATAAGACTTGTACTTTAACCTG
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTACTTTAACCTG
* ** * ** *
335883 TCCTACTGCAACTTCAGGGGGATAAGGTTTGTTATCTTCAGTCTAC
1 TCC-ACTGCAACTTCAGGGAGATAAGACTTG-TA-CTTTAACCT-G
*
335929 TCCACTGCAAGTTCAGGGAGATAAGACTTGTACTTTAACCTG
1 TCCACTGCAACTTCAGGGAGATAAGACTTGTACTTTAACCTG
* *
335971 CCCCACTGCAACTTCAGGGGGATAA
1 -TCCACTGCAACTTCAGGGAGATAA
335996 TGTTTGTTAT
Statistics
Matches: 88, Mismatches: 20, Indels: 9
0.75 0.17 0.08
Matches are distributed among these distances:
42 3 0.03
43 49 0.56
44 4 0.05
45 29 0.33
46 3 0.03
ACGTcount: A:0.26, C:0.23, G:0.22, T:0.29
Consensus pattern (42 bp):
TCCACTGCAACTTCAGGGAGATAAGACTTGTACTTTAACCTG
Found at i:335922 original size:88 final size:88
Alignment explanation
Indices: 335754--336042 Score: 346
Period size: 88 Copynumber: 3.3 Consensus size: 88
335744 AATCTGCTCT
* * * * ** * * * ** *
335754 ACTGCAACTTCAGAGAGATAAGATTTGCTATTTTGAGTCTGCTCCGCTGCAACTTCAAGGAAATG
1 ACTGCAAGTTCAGGGAGATAAGACTTG-TACTTT-AACCTGCCCCACTGCAACTTCAGGGGGATA
* *
335819 AGATTTGCTATCTTCAGTCTACTCC
64 AGGTTTGTTATCTTCAGTCTACTCC
* * *
335844 ATTGCAAGTTCAGGGAGATAAGACTTGTACTTTAACCTGTCCTACTGCAACTTCAGGGGGATAAG
1 ACTGCAAGTTCAGGGAGATAAGACTTGTACTTTAACCTGCCCCACTGCAACTTCAGGGGGATAAG
335909 GTTTGTTATCTTCAGTCTACTCC
66 GTTTGTTATCTTCAGTCTACTCC
*
335932 ACTGCAAGTTCAGGGAGATAAGACTTGTACTTTAACCTGCCCCACTGCAACTTCAGGGGGATAAT
1 ACTGCAAGTTCAGGGAGATAAGACTTGTACTTTAACCTGCCCCACTGCAACTTCAGGGGGATAAG
* *
335997 GTTTGTTATCTTC-GATCCATTCC
66 GTTTGTTATCTTCAG-TCTACTCC
* *
336020 ACTGCAACTTTAGGGAGATAAGA
1 ACTGCAAGTTCAGGGAGATAAGA
336043 TCTGTAACTT
Statistics
Matches: 173, Mismatches: 25, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
87 1 0.01
88 144 0.83
89 5 0.03
90 23 0.13
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (88 bp):
ACTGCAAGTTCAGGGAGATAAGACTTGTACTTTAACCTGCCCCACTGCAACTTCAGGGGGATAAG
GTTTGTTATCTTCAGTCTACTCC
Found at i:340291 original size:29 final size:29
Alignment explanation
Indices: 340258--340320 Score: 99
Period size: 29 Copynumber: 2.2 Consensus size: 29
340248 TTTCCCAGCC
340258 TTGGGGCAAAAGTGTAAATATGTAAAAGT
1 TTGGGGCAAAAGTGTAAATATGTAAAAGT
* * *
340287 TTGGGGCAAAAGTGTAATTTTGTCAAAGT
1 TTGGGGCAAAAGTGTAAATATGTAAAAGT
340316 TTGGG
1 TTGGG
340321 TCAAGGATTG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.05, G:0.30, T:0.32
Consensus pattern (29 bp):
TTGGGGCAAAAGTGTAAATATGTAAAAGT
Found at i:340850 original size:53 final size:52
Alignment explanation
Indices: 340655--340860 Score: 200
Period size: 55 Copynumber: 3.8 Consensus size: 52
340645 ATTAGGGTTT
* *
340655 AAGGATACCATGTAAGCCCGTGCCAAGGCATGGCAATTGGTAAGGTTTC-TAAGGC
1 AAGGATACCATGTAAGACCATGCCAA-GCATGGC-ATTGGTAA-G-TTCATAAGGC
* * * *
340710 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAG-CATGGCATTGGTAAGTT-C-ATAAGGC
* *
340765 AAAGG-TCCCATGTAAGACCATGCCAAAGCATGGCATTGGTGAGTTCATAAGGC
1 -AAGGATACCATGTAAGACCATGCC-AAGCATGGCATTGGTAAGTTCATAAGGC
* * * *
340818 AAGGATACCACGTAAGACCATGACAAGTCATGGAAGTGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAG-CATGGCATTGGTAAG
340861 GTACCCGTGT
Statistics
Matches: 125, Mismatches: 18, Indels: 18
0.78 0.11 0.11
Matches are distributed among these distances:
52 9 0.07
53 37 0.30
54 9 0.07
55 63 0.50
56 7 0.06
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (52 bp):
AAGGATACCATGTAAGACCATGCCAAGCATGGCATTGGTAAGTTCATAAGGC
Found at i:351494 original size:27 final size:25
Alignment explanation
Indices: 351430--351546 Score: 114
Period size: 25 Copynumber: 4.7 Consensus size: 25
351420 TTATTATGCA
*
351430 CTAATGAA-CAGAGAGCACT-GACATG
1 CTAAT-AATCAGAGAGCACTAGA-GTG
*
351455 CTAA-ATATCAGAGAGCACTAGCGTG
1 CTAATA-ATCAGAGAGCACTAGAGTG
*
351480 CTAATAATCAGAGAGCACTGGAGTG
1 CTAATAATCAGAGAGCACTAGAGTG
* **
351505 CTAATATTCAGAGAGCACCGGAGTG
1 CTAATAATCAGAGAGCACTAGAGTG
* *
351530 CTAATATTCATAGAGCA
1 CTAATAATCAGAGAGCA
351547 TGCTGAGGTC
Statistics
Matches: 81, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
23 1 0.01
24 1 0.01
25 77 0.95
26 2 0.02
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.21
Consensus pattern (25 bp):
CTAATAATCAGAGAGCACTAGAGTG
Found at i:351531 original size:50 final size:50
Alignment explanation
Indices: 351430--351546 Score: 132
Period size: 50 Copynumber: 2.3 Consensus size: 50
351420 TTATTATGCA
* *
351430 CTAATGAA-CAGAGAGCACTGACATGCTAAATATCAGAGAGCACTAGCGTG
1 CTAAT-AATCAGAGAGCACTGACATGCTAAATATCAGAGAGCACCAGAGTG
* *
351480 CTAATAATCAGAGAGCACTGGA-GTGCT-AATATTCAGAGAGCACCGGAGTG
1 CTAATAATCAGAGAGCACT-GACATGCTAAATA-TCAGAGAGCACCAGAGTG
* *
351530 CTAATATTCATAGAGCA
1 CTAATAATCAGAGAGCA
351547 TGCTGAGGTC
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
49 6 0.10
50 50 0.86
51 2 0.03
ACGTcount: A:0.37, C:0.19, G:0.24, T:0.21
Consensus pattern (50 bp):
CTAATAATCAGAGAGCACTGACATGCTAAATATCAGAGAGCACCAGAGTG
Found at i:359734 original size:30 final size:30
Alignment explanation
Indices: 359693--359753 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
359683 TTTCCGAGCC
*
359693 TTGGGGTAAAAGTGTAAATATGTAAAAGTT
1 TTGGGGCAAAAGTGTAAATATGTAAAAGTT
* * *
359723 TTGGGGCAAAAGTGTAATTTTGTCAAAGTT
1 TTGGGGCAAAAGTGTAAATATGTAAAAGTT
359753 T
1 T
359754 GAGTCAAGGA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.34, C:0.03, G:0.26, T:0.36
Consensus pattern (30 bp):
TTGGGGCAAAAGTGTAAATATGTAAAAGTT
Found at i:360178 original size:55 final size:53
Alignment explanation
Indices: 360091--360296 Score: 193
Period size: 55 Copynumber: 3.8 Consensus size: 53
360081 ATTAGGGTTT
* * *
360091 AAGGATACCATGTAAGCCCGTGCCAAGGCATGGCAATTGGTAAGGTTTCTAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGC-ATTGGTAA-GTTTCTAAGGC
* * * * *
360146 AAGGAAATCATGTAAGACCATGTCAAGACATGGCATTGATAAGTTACTATAAGGC
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTT--TCTAAGGC
* *
360201 AAAGG-TCCCATGTAAGACCATGCCAA-AGCATGGCATTGGTGAG-TTCGTAAGGC
1 -AAGGATACCATGTAAGACCATGCCAAGA-CATGGCATTGGTAAGTTTC-TAAGGC
* * * * *
360254 AAGGATACCACGTAAGACCATGACAAGTCATGGAAATGGTAAG
1 AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAG
360297 GTACCCGTGT
Statistics
Matches: 122, Mismatches: 22, Indels: 16
0.76 0.14 0.10
Matches are distributed among these distances:
52 5 0.04
53 39 0.32
54 9 0.07
55 65 0.53
56 4 0.03
ACGTcount: A:0.35, C:0.18, G:0.26, T:0.21
Consensus pattern (53 bp):
AAGGATACCATGTAAGACCATGCCAAGACATGGCATTGGTAAGTTTCTAAGGC
Found at i:361551 original size:12 final size:13
Alignment explanation
Indices: 361524--361557 Score: 52
Period size: 12 Copynumber: 2.6 Consensus size: 13
361514 CCAATACAAA
361524 CCCAAAACCTTTAG
1 CCCAAAA-CTTTAG
361538 CCCAAAAC-TTAG
1 CCCAAAACTTTAG
361550 CCCAAAAC
1 CCCAAAAC
361558 ACTAACCCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 12 0.60
13 1 0.05
14 7 0.35
ACGTcount: A:0.41, C:0.38, G:0.06, T:0.15
Consensus pattern (13 bp):
CCCAAAACTTTAG
Found at i:361632 original size:22 final size:22
Alignment explanation
Indices: 361607--361669 Score: 101
Period size: 22 Copynumber: 2.9 Consensus size: 22
361597 AAATATCTTT
*
361607 ACTCCACTAAACTACTCCAACC
1 ACTCCACTAAACCACTCCAACC
361629 ACTCCACTAAACCACTCCAACC
1 ACTCCACTAAACCACTCCAACC
361651 AC-CCTACTAAACCACTCCA
1 ACTCC-ACTAAACCACTCCA
361670 CTAAACCACC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
21 2 0.05
22 37 0.95
ACGTcount: A:0.37, C:0.48, G:0.00, T:0.16
Consensus pattern (22 bp):
ACTCCACTAAACCACTCCAACC
Found at i:361641 original size:13 final size:13
Alignment explanation
Indices: 361625--361693 Score: 66
Period size: 13 Copynumber: 5.9 Consensus size: 13
361615 AAACTACTCC
361625 AACCACTCCACTA
1 AACCACTCCACTA
361638 AACCACT-C-C--
1 AACCACTCCACTA
361647 AACCAC-CCTACTA
1 AACCACTCC-ACTA
361660 AACCACTCCACTA
1 AACCACTCCACTA
361673 AACCAC-CC-C--
1 AACCACTCCACTA
361682 AACCACTCCACT
1 AACCACTCCACT
361694 TGCCTACAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 19
0.71 0.00 0.29
Matches are distributed among these distances:
9 13 0.28
10 2 0.04
11 4 0.09
12 3 0.06
13 23 0.49
14 2 0.04
ACGTcount: A:0.36, C:0.51, G:0.00, T:0.13
Consensus pattern (13 bp):
AACCACTCCACTA
Found at i:362116 original size:3 final size:3
Alignment explanation
Indices: 362081--362174 Score: 56
Period size: 3 Copynumber: 31.3 Consensus size: 3
362071 GAGCTTTGTT
* * *
362081 TTA TTT TTA TT- TTA TT- TTA TTA TTT TTA CTA TTA TT- TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
*
362124 TTA TTA TTA TT- TCTCA TGTA TATA TTA TTA TT- TATA CTA TTA TTA
1 TTA TTA TTA TTA T-T-A T-TA T-TA TTA TTA TTA T-TA TTA TTA TTA
362169 -TA TTA T
1 TTA TTA T
362175 ATATGCCCTC
Statistics
Matches: 71, Mismatches: 10, Indels: 20
0.70 0.10 0.20
Matches are distributed among these distances:
2 9 0.13
3 54 0.76
4 6 0.08
5 2 0.03
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:362149 original size:21 final size:18
Alignment explanation
Indices: 362081--362178 Score: 82
Period size: 18 Copynumber: 5.6 Consensus size: 18
362071 GAGCTTTGTT
*
362081 TTATTTTTATT-TTATT-
1 TTATTTATATTATTATTA
*
362097 TTA-TTAT-TT-TTACTA
1 TTATTTATATTATTATTA
362112 TTATTTATATTATTATTA
1 TTATTTATATTATTATTA
*
362130 TTATTTCTCATGTATATATTA
1 TTATTTAT-AT-TAT-TATTA
*
362151 TTATTTATACTATTATTA
1 TTATTTATATTATTATTA
362169 -TATTATATAT
1 TTATT-TATAT
362179 GCCCTCTCCA
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
14 6 0.09
15 6 0.09
16 7 0.10
17 6 0.09
18 21 0.31
19 5 0.07
20 4 0.06
21 12 0.18
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.65
Consensus pattern (18 bp):
TTATTTATATTATTATTA
Found at i:362420 original size:18 final size:19
Alignment explanation
Indices: 362379--362441 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 19
362369 CTATTACTAT
* *
362379 TATTATTATATATTAGTGTA
1 TATTTTTATATA-TAGTATA
*
362399 TATTTTTATGTATA-TATA
1 TATTTTTATATATAGTATA
362417 TA--TTTATATATAGTAT-
1 TATTTTTATATATAGTATA
362433 TATTTTTAT
1 TATTTTTAT
362442 TACTTTAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
16 11 0.31
17 3 0.08
18 10 0.28
19 2 0.06
20 10 0.28
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.60
Consensus pattern (19 bp):
TATTTTTATATATAGTATA
Found at i:364462 original size:40 final size:37
Alignment explanation
Indices: 364391--364525 Score: 143
Period size: 35 Copynumber: 3.7 Consensus size: 37
364381 CATGGCAAAG
*
364391 TGTGAAATGTAAGTATGGTA--TCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
364426 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATT-TC--ATCCATACTGAGT
** * * * *
364466 TAAGAAACGTAGGTATTGCATTTC-T-CATAATGAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
*
364501 TGTAAAATGTAGGTATGGTATTTCA
1 TGTGAAATGTAGGTATGGTATTTCA
364526 ATGAGGAAAA
Statistics
Matches: 81, Mismatches: 13, Indels: 11
0.77 0.12 0.10
Matches are distributed among these distances:
35 46 0.57
36 1 0.01
38 2 0.02
39 2 0.02
40 30 0.37
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.36
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
Found at i:371360 original size:40 final size:37
Alignment explanation
Indices: 371289--371423 Score: 136
Period size: 35 Copynumber: 3.7 Consensus size: 37
371279 CATGGCAAAG
*
371289 TGTGAAATGTAAGTATGGTA--TCATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
371324 TGTGAAATGTAGGTATGGTATTATCAAATCCATACTGAGT
1 TGTGAAATGTAGGTATGGTATT-TC--ATCCATACTGAGT
** * *
371364 TAAGAAACGTAGGTATGGCATTTC-T-CATAAC-GAGT
1 TGTGAAATGTAGGTATGGTATTTCATCCAT-ACTGAGT
* *
371399 TGTAAAATGTAGATATGGTATTTCA
1 TGTGAAATGTAGGTATGGTATTTCA
371424 ATGAGGAAAA
Statistics
Matches: 82, Mismatches: 11, Indels: 13
0.77 0.10 0.12
Matches are distributed among these distances:
35 44 0.54
36 3 0.04
38 2 0.02
39 2 0.02
40 31 0.38
ACGTcount: A:0.33, C:0.10, G:0.22, T:0.34
Consensus pattern (37 bp):
TGTGAAATGTAGGTATGGTATTTCATCCATACTGAGT
Found at i:374963 original size:50 final size:50
Alignment explanation
Indices: 374909--375085 Score: 293
Period size: 50 Copynumber: 3.5 Consensus size: 50
374899 CCATGGCAAC
*
374909 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGGCAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
*
374959 AAGTGATAAGT-AGTAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGA-TAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
375009 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
375059 CAAGTGAAAAGTGGTAGCTTCGGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
375086 CTGATCAGTG
Statistics
Matches: 119, Mismatches: 5, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
49 1 0.01
50 93 0.78
51 25 0.21
ACGTcount: A:0.34, C:0.16, G:0.24, T:0.25
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:375099 original size:31 final size:31
Alignment explanation
Indices: 375061--375209 Score: 228
Period size: 31 Copynumber: 4.8 Consensus size: 31
375051 ACAAATGACA
375061 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
375092 AGTGAAAAGTTGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
*
375123 AGTGAAAAGTGGTAGC-TCTTGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTC-GGCTACCTGATC
* *
375154 AATGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
375185 AATGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTTCGGCTAC
375210 AAGTGACAAG
Statistics
Matches: 108, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
30 2 0.02
31 105 0.97
32 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:375313 original size:47 final size:46
Alignment explanation
Indices: 375229--375349 Score: 143
Period size: 47 Copynumber: 2.6 Consensus size: 46
375219 GTGATTTCCG
* * * *
375229 TATAAGACCATATCTGGGATATGGCACCGGTGTGATATATGCTACTA
1 TATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATAC-A
* * *
375276 TATAAGACCATATCTGGGATATGGCATCAGTGAGATATGTGATTCG
1 TATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACA
* * *
375322 TGTAAGACCATAGCTGGGTTATGGCATC
1 TATAAGACCATATCTGGGATATGGCATC
375350 GATATATGAA
Statistics
Matches: 64, Mismatches: 10, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
46 25 0.39
47 39 0.61
ACGTcount: A:0.29, C:0.16, G:0.26, T:0.30
Consensus pattern (46 bp):
TATAAGACCATATCTGGGATATGGCATCAGTGAGATATATGATACA
Found at i:375387 original size:42 final size:42
Alignment explanation
Indices: 375328--375435 Score: 121
Period size: 42 Copynumber: 2.6 Consensus size: 42
375318 TTCGTGTAAG
* *
375328 ACCATAGCTGGGTTATGGCATCGATATAT-GAATATGTATAAA
1 ACCATAGCTGGGCTATGGCATCGAT-TATCGAAGATGTATAAA
* *
375370 ACCATAGCTGGGCTATGGCATC-ATTATGCGAAGATGTGTAAG
1 ACCATAGCTGGGCTATGGCATCGATTAT-CGAAGATGTATAAA
* **
375412 ACCATAGTTGAACTATGGCATCGA
1 ACCATAGCTGGGCTATGGCATCGA
375436 GAAAACGAAG
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
40 3 0.05
41 2 0.04
42 50 0.89
43 1 0.02
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.28
Consensus pattern (42 bp):
ACCATAGCTGGGCTATGGCATCGATTATCGAAGATGTATAAA
Found at i:380764 original size:6 final size:6
Alignment explanation
Indices: 380753--380778 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
380743 AAAAATGCAA
380753 GATATG GATATG GATATG GATATG GA
1 GATATG GATATG GATATG GATATG GA
380779 AGTACGGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.31
Consensus pattern (6 bp):
GATATG
Found at i:383683 original size:18 final size:18
Alignment explanation
Indices: 383656--383748 Score: 132
Period size: 18 Copynumber: 5.2 Consensus size: 18
383646 TACGACCGTT
383656 TACGGTACTATTCACGTA
1 TACGGTACTATTCACGTA
* *
383674 TACGGCACTATTCACATA
1 TACGGTACTATTCACGTA
* *
383692 TACGGTACTATTTACGCA
1 TACGGTACTATTCACGTA
*
383710 TACGATACTATTCACGTA
1 TACGGTACTATTCACGTA
*
383728 TACGGTACTGTTCACGTA
1 TACGGTACTATTCACGTA
383746 TAC
1 TAC
383749 AGTAGTTGGG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (18 bp):
TACGGTACTATTCACGTA
Found at i:389617 original size:29 final size:29
Alignment explanation
Indices: 389579--389653 Score: 78
Period size: 29 Copynumber: 2.6 Consensus size: 29
389569 AACTTTAATT
389579 AAAATAATAAAACAATCATTAAATTTTAA
1 AAAATAATAAAACAATCATTAAATTTTAA
* ** * *
389608 AAAATTATAACTCAGTCATTAAATTTTACG
1 AAAATAATAAAACAATCATTAAATTTTA-A
* *
389638 GAAATAACAAAACAAT
1 AAAATAATAAAACAAT
389654 TACTAATAAC
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
29 24 0.71
30 10 0.29
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (29 bp):
AAAATAATAAAACAATCATTAAATTTTAA
Found at i:405317 original size:24 final size:23
Alignment explanation
Indices: 405290--405344 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
405280 TGACGTACAA
*
405290 AAATTAATTTTTAACCATAAAAAT
1 AAATTAATTTTTAA-CAAAAAAAT
*
405314 AAATGAAATTTTTAACAAAAAAAT
1 AAAT-TAATTTTTAACAAAAAAAT
*
405338 TAATTAA
1 AAATTAA
405345 CATGTAAATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
23 2 0.08
24 15 0.58
25 9 0.35
ACGTcount: A:0.58, C:0.05, G:0.02, T:0.35
Consensus pattern (23 bp):
AAATTAATTTTTAACAAAAAAAT
Found at i:414590 original size:2 final size:2
Alignment explanation
Indices: 414583--414612 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
414573 CTATCATTAA
414583 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
414613 GCATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:418741 original size:48 final size:48
Alignment explanation
Indices: 418683--418774 Score: 166
Period size: 48 Copynumber: 1.9 Consensus size: 48
418673 CACCTCGGCT
*
418683 TCTTTTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTACCA
1 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTACCA
*
418731 TCTTCTATCCCTATCATGATCATCATCACTTTTAGTTCTCCGGT
1 TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGT
418775 GCCTATCTGT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.20, C:0.30, G:0.09, T:0.41
Consensus pattern (48 bp):
TCTTCTATCCCTATCATGATCATCATCACTTTCAGTTCTCCGGTACCA
Found at i:427362 original size:14 final size:14
Alignment explanation
Indices: 427343--427375 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
427333 TGATATGTTG
427343 CTAGTGGAACTCTA
1 CTAGTGGAACTCTA
427357 CTAGTGGAACTCTA
1 CTAGTGGAACTCTA
427371 CTAGT
1 CTAGT
427376 AAAGTTACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.30
Consensus pattern (14 bp):
CTAGTGGAACTCTA
Found at i:427413 original size:6 final size:6
Alignment explanation
Indices: 427402--427431 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
427392 CACGGGTCTC
427402 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT
427432 GCTATAACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (6 bp):
ATTTTT
Found at i:427644 original size:22 final size:19
Alignment explanation
Indices: 427619--427659 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 19
427609 TGAAATTTGG
427619 TTAAATGATTTTCATCTAAAAT
1 TTAAAT-ATTTT-AT-TAAAAT
427641 TTAAATATTTTATTAAAAT
1 TTAAATATTTTATTAAAAT
427660 AATATATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.32
20 2 0.11
21 5 0.26
22 6 0.32
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAAATATTTTATTAAAAT
Found at i:429510 original size:21 final size:21
Alignment explanation
Indices: 429453--429510 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
429443 TTTTTCTCCT
* * *
429453 CAGCTGCAGGAGCTTCAGCGG
1 CAGCGGCAGCAGCTCCAGCGG
429474 CAGCGGCAGC-GCCTCCAGCCGG
1 CAGCGGCAGCAG-CTCCAG-CGG
429496 -AGCGGCAGCAGCTCC
1 CAGCGGCAGCAGCTCC
429511 TCCACCCCCG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 26 0.84
22 4 0.13
ACGTcount: A:0.17, C:0.38, G:0.36, T:0.09
Consensus pattern (21 bp):
CAGCGGCAGCAGCTCCAGCGG
Found at i:430430 original size:97 final size:99
Alignment explanation
Indices: 430322--430522 Score: 300
Period size: 103 Copynumber: 2.0 Consensus size: 99
430312 TTTTTTATCA
* *
430322 TTTTATTTTACCCTTTCTACTATTCATCATTTTCTGAAC-C-T-AATTTTCTATTTAAATCTTTT
1 TTTTATTTTACCCTTTCTACTATTCATCATTTTCCG-ACTCTTAAAATTTCTATTTAAATCTTTT
430384 AAAAATTTTAAATTAATAAAAATAAAATTATATTT
65 AAAAATTTTAAATTAATAAAAATAAAATTATATTT
*
430419 TTTTATTTTACCCTTTTTACTATTCATCATTTTCCGACTCTTAAAAAAAATTTCTATTTAAATCT
1 TTTTATTTTACCCTTTCTACTATTCATCATTTTCCGACTCTT----AAAATTTCTATTTAAATCT
*
430484 TTTAAAAATTTTAAATTGATAAAAATAAAATTATATTT
62 TTTAAAAATTTTAAATTAATAAAAATAAAATTATATTT
430522 T
1 T
430523 AATTTCATTA
Statistics
Matches: 93, Mismatches: 4, Indels: 8
0.89 0.04 0.08
Matches are distributed among these distances:
96 2 0.02
97 35 0.38
98 1 0.01
103 55 0.59
ACGTcount: A:0.37, C:0.12, G:0.01, T:0.50
Consensus pattern (99 bp):
TTTTATTTTACCCTTTCTACTATTCATCATTTTCCGACTCTTAAAATTTCTATTTAAATCTTTTA
AAAATTTTAAATTAATAAAAATAAAATTATATTT
Found at i:430555 original size:31 final size:32
Alignment explanation
Indices: 430510--430573 Score: 78
Period size: 30 Copynumber: 2.0 Consensus size: 32
430500 TGATAAAAAT
*
430510 AAAATTATATTTTAATTTCATTAAAAATAATAA
1 AAAATTATATTTTAA-TACATTAAAAATAATAA
* *
430543 AAAATTA-A-TTTAATACTTTAAAAATTATAA
1 AAAATTATATTTTAATACATTAAAAATAATAA
430573 A
1 A
430574 TACATAAACT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 15 0.54
31 5 0.18
32 1 0.04
33 7 0.25
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (32 bp):
AAAATTATATTTTAATACATTAAAAATAATAA
Found at i:443835 original size:21 final size:23
Alignment explanation
Indices: 443793--443836 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
443783 TAATAAATGA
*
443793 AAATTATAAAACTATTAAATATT
1 AAATTATAAAACTACTAAATATT
*
443816 AAATTA-AAAA-TACTATATATT
1 AAATTATAAAACTACTAAATATT
443837 TTCTAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 9 0.47
22 4 0.21
23 6 0.32
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (23 bp):
AAATTATAAAACTACTAAATATT
Found at i:447288 original size:28 final size:29
Alignment explanation
Indices: 447257--447318 Score: 74
Period size: 28 Copynumber: 2.1 Consensus size: 29
447247 AAGTATTTCA
*
447257 AAAAATAT-AAAAACATTTAAT-TTATTTT
1 AAAAAT-TCAAAAACAATTAATATTATTTT
*
447285 AAAAATTCAAAAATAATTAATAATTATTTT
1 AAAAATTCAAAAACAATTAAT-ATTATTTT
447315 AAAA
1 AAAA
447319 TTTTAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 1 0.03
28 17 0.59
30 11 0.38
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (29 bp):
AAAAATTCAAAAACAATTAATATTATTTT
Found at i:448732 original size:20 final size:19
Alignment explanation
Indices: 448700--448752 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 19
448690 ATTTAATGGT
* *
448700 TATATTTAAATATTTAAAA
1 TATATTTATATATTCAAAA
*
448719 TATAGTTTATATATTCAAAT
1 TATA-TTTATATATTCAAAA
*
448739 TAAAATTTATATAT
1 T-ATATTTATATAT
448753 AATTAATATT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.14
20 22 0.79
21 2 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
TATATTTATATATTCAAAA
Found at i:449169 original size:31 final size:31
Alignment explanation
Indices: 449134--449202 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
449124 TTAATGGCGG
*
449134 GTGACTAAAAAAG-AAAAATTCAAATAATTGA
1 GTGACTAAAAAAGAAAAAATT-AAAGAATTGA
* *
449165 GTGACCAAAAAAGAAAAAATTGAAGAATTGA
1 GTGACTAAAAAAGAAAAAATTAAAGAATTGA
449196 GTGACTA
1 GTGACTA
449203 TTTTATAACT
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.20
Consensus pattern (31 bp):
GTGACTAAAAAAGAAAAAATTAAAGAATTGA
Found at i:455136 original size:46 final size:45
Alignment explanation
Indices: 455061--455236 Score: 162
Period size: 46 Copynumber: 3.8 Consensus size: 45
455051 TGTAACCCGC
* *
455061 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTT-GCAT
* * *
455107 CCATGAGTGAACTCGGACTCAACTCAACGAGCTCGAATGCCTAGTTACAT
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCG---GAC--GTTGCAT
* * * *
455157 CTC-TCA---AACTCGGACTCAACTCAACGAGTTCAGACATTTGCAT
1 C-CATAAGTGAACTCGGACTCAACTCAACGAGCTCGGAC-GTTGCAT
*
455200 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGA
455237 TGCCCAAACA
Statistics
Matches: 108, Mismatches: 12, Indels: 20
0.77 0.09 0.14
Matches are distributed among these distances:
42 1 0.01
43 9 0.08
44 2 0.02
46 60 0.56
47 24 0.22
49 2 0.02
50 6 0.06
51 4 0.04
ACGTcount: A:0.30, C:0.30, G:0.20, T:0.21
Consensus pattern (45 bp):
CCATAAGTGAACTCGGACTCAACTCAACGAGCTCGGACGTTGCAT
Found at i:455229 original size:93 final size:93
Alignment explanation
Indices: 455070--455240 Score: 270
Period size: 93 Copynumber: 1.8 Consensus size: 93
455060 CCCATAAGCG
* * * *
455070 AACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATGAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
455135 GAGCTCGAATGCCTAGTTACATCTCTCA
66 GAGCTCGAATGCCTAGTTACATCTCTCA
* *
455163 AACTCGGACTCAACTCAACGAGTTCAGACATTTGCATCCATAAGTGAACTCGGACTCAACTCAAC
1 AACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
* *
455228 GAGTTCGGATGCC
66 GAGCTCGAATGCC
455241 CAAACATCCT
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 70 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.22
Consensus pattern (93 bp):
AACTCGGACTCAACTCAACGAGCTCAGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAAC
GAGCTCGAATGCCTAGTTACATCTCTCA
Found at i:457510 original size:15 final size:15
Alignment explanation
Indices: 457481--457530 Score: 66
Period size: 15 Copynumber: 3.4 Consensus size: 15
457471 CAAAGATAAC
*
457481 AAGAAAACC-GAATA
1 AAGAAATCCAGAATA
457495 AAGAAATCCAGAATA
1 AAGAAATCCAGAATA
* *
457510 AAGAGATCCAGGATA
1 AAGAAATCCAGAATA
457525 AAGAAA
1 AAGAAA
457531 CCCAAGATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
14 8 0.26
15 23 0.74
ACGTcount: A:0.60, C:0.12, G:0.18, T:0.10
Consensus pattern (15 bp):
AAGAAATCCAGAATA
Found at i:457539 original size:15 final size:15
Alignment explanation
Indices: 457492--457539 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
457482 AGAAAACCGA
457492 ATAAAGAAATCC-AG
1 ATAAAGAAATCCAAG
* *
457506 AATAAAGAGATCCAGG
1 -ATAAAGAAATCCAAG
*
457522 ATAAAGAAACCCAAG
1 ATAAAGAAATCCAAG
457537 ATA
1 ATA
457540 TGATACTATG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 26 0.96
16 1 0.04
ACGTcount: A:0.56, C:0.15, G:0.17, T:0.12
Consensus pattern (15 bp):
ATAAAGAAATCCAAG
Found at i:464781 original size:38 final size:38
Alignment explanation
Indices: 464725--464804 Score: 124
Period size: 38 Copynumber: 2.1 Consensus size: 38
464715 TATGTGTATT
* * *
464725 CGGGTTAAATCCCGCAGGCTTCGTGCTGGTATTATATC
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
*
464763 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATT
1 CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
464801 CGGG
1 CGGG
464805 CCTTCGTGCC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.29
Consensus pattern (38 bp):
CGGGATAAATCCCGCAGGCCTAGTGCTGGTATTATATC
Found at i:464852 original size:43 final size:43
Alignment explanation
Indices: 464776--465050 Score: 374
Period size: 43 Copynumber: 6.4 Consensus size: 43
464766 GATAAATCCC
* * *
464776 GCAGGCCTAGTGCTGGT-AT-TATATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
*
464817 GCAGGCTTAGTGCCGGTGATGTGTATTCTGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
464860 GCAGGATTAGTGCCGATGATGTGTATTCGGGCCTTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * *
464903 GCAGACTTCGTGCCGGTGATGTGTATTCGGGCATTCGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* * * * *
464946 ACAGGCTTCGTGCTGGTGATGTGTATTCGGGCATTCTTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
464989 GCAGGCTTCGTGCCGGTGATGTGTATTCGGGCCTTTGTGCCTA
1 GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
* *
465032 GCAGGCGTAATGCCGGTGA
1 GCAGGCTTAGTGCCGGTGA
465051 AATGATATGT
Statistics
Matches: 208, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
41 15 0.07
42 2 0.01
43 191 0.92
ACGTcount: A:0.14, C:0.23, G:0.33, T:0.31
Consensus pattern (43 bp):
GCAGGCTTAGTGCCGGTGATGTGTATTCGGGCCTTCGTGCCTA
Found at i:465441 original size:45 final size:44
Alignment explanation
Indices: 465367--465493 Score: 136
Period size: 45 Copynumber: 2.9 Consensus size: 44
465357 TTGACTTGAT
* * **
465367 TATTCGGGCCTTTGAGCTTAGCAAACTATAATGCCGGTGAGATAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGA-AC
* *
465412 TATTCGGGCCTTCGAGCCTAGTAGGCTATAATGCTGGT--GAAC
1 TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGAAC
*
465454 TGATATCGGGCC-TCGAGCCTAACAGGCTA-AATGCCGGTGA
1 T-AT-TCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGA
465494 TTTGAGAAAA
Statistics
Matches: 69, Mismatches: 9, Indels: 9
0.79 0.10 0.10
Matches are distributed among these distances:
42 11 0.16
43 19 0.28
44 7 0.10
45 32 0.46
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (44 bp):
TATTCGGGCCTTCGAGCCTAGCAGGCTATAATGCCGGTGAGAAC
Found at i:468785 original size:46 final size:46
Alignment explanation
Indices: 468725--468998 Score: 424
Period size: 46 Copynumber: 6.0 Consensus size: 46
468715 TTTGACATGA
* * * * * * *
468725 TGCCATAGTGTCTTTTAACTATGGTCTTACTCATTTTC-TGTCATGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACA-TTTCATATCAGGT
*** *
468771 TGCCATGGTATCTTTCAACCATGGTCTTGTTCATTTCATATCACGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
468817 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
468863 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
*
468909 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGC
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
468955 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
1 TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAG
468999 AGAGCACACT
Statistics
Matches: 214, Mismatches: 13, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
45 4 0.02
46 210 0.98
ACGTcount: A:0.22, C:0.24, G:0.15, T:0.39
Consensus pattern (46 bp):
TGCCATGGTATCTTTCAACCATGGTCTTACACATTTCATATCAGGT
Found at i:469822 original size:16 final size:16
Alignment explanation
Indices: 469801--469832 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
469791 GAGTTACCGA
*
469801 TTCATTTATCCGATAT
1 TTCATTAATCCGATAT
469817 TTCATTAATCCGATAT
1 TTCATTAATCCGATAT
469833 CTTTTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (16 bp):
TTCATTAATCCGATAT
Found at i:479042 original size:13 final size:13
Alignment explanation
Indices: 479009--479053 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
478999 TAGCCTATTC
479009 TAAATTAAT-AAAA
1 TAAA-TAATAAAAA
479022 TAAA-AATAAAAA
1 TAAATAATAAAAA
*
479034 TAAATAATAAAAC
1 TAAATAATAAAAA
479047 TAAATAA
1 TAAATAA
479054 AACAAAGTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 3 0.10
12 8 0.28
13 18 0.62
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.24
Consensus pattern (13 bp):
TAAATAATAAAAA
Found at i:480131 original size:21 final size:21
Alignment explanation
Indices: 480105--480160 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
480095 AACAGCGGTG
480105 GCGGTGAGATTA-ATTACTGTA
1 GCGGTGAGATTAGA-TACTGTA
480126 GCGGTGAGATTAGATACTGTA
1 GCGGTGAGATTAGATACTGTA
480147 GCGGTGAGATTAGA
1 GCGGTGAGATTAGA
480161 AACAGCGGTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.29, C:0.09, G:0.34, T:0.29
Consensus pattern (21 bp):
GCGGTGAGATTAGATACTGTA
Found at i:480169 original size:18 final size:19
Alignment explanation
Indices: 480124--480170 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 19
480114 TTAATTACTG
*
480124 TAGCGGTGAGATTAGATAC
1 TAGCGGTGAGATTAGAAAC
480143 TGTAGCGGTGAGATTAGAAAC
1 --TAGCGGTGAGATTAGAAAC
480164 -AGCGGTG
1 TAGCGGTG
480171 GAATGTGTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 7 0.28
21 18 0.72
ACGTcount: A:0.30, C:0.11, G:0.36, T:0.23
Consensus pattern (19 bp):
TAGCGGTGAGATTAGAAAC
Found at i:480400 original size:18 final size:18
Alignment explanation
Indices: 480377--480459 Score: 70
Period size: 18 Copynumber: 4.8 Consensus size: 18
480367 TATTTTAATG
480377 AATTATATAATCAATTTA
1 AATTATATAATCAATTTA
* *
480395 AATTAT-TTATTAGA--TA
1 AATTATATAATCA-ATTTA
*
480411 AA--ATGATAAT-AATTTTT
1 AATTAT-ATAATCAA-TTTA
480428 AATTATATAATCAATTTA
1 AATTATATAATCAATTTA
480446 AATTATATAATCAA
1 AATTATATAATCAA
480460 CAGGCCAGGG
Statistics
Matches: 51, Mismatches: 5, Indels: 18
0.69 0.07 0.24
Matches are distributed among these distances:
14 3 0.06
15 1 0.02
16 7 0.14
17 7 0.14
18 29 0.57
19 4 0.08
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (18 bp):
AATTATATAATCAATTTA
Found at i:484153 original size:25 final size:25
Alignment explanation
Indices: 484122--484171 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
484112 CATGATGATT
484122 TTATTTTTCAATTTTCTGTCACTTA
1 TTATTTTTCAATTTTCTGTCACTTA
484147 TTATTTTTCAATTTTCTGTCACTTA
1 TTATTTTTCAATTTTCTGTCACTTA
484172 CATTTAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.60
Consensus pattern (25 bp):
TTATTTTTCAATTTTCTGTCACTTA
Found at i:485946 original size:3 final size:3
Alignment explanation
Indices: 485938--485964 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
485928 CACACTCGAG
485938 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
485965 TATCTATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:491132 original size:25 final size:25
Alignment explanation
Indices: 491104--491151 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
491094 TAATAGAATT
491104 GATCAATTTGCTATTTGATCTAATA
1 GATCAATTTGCTATTTGATCTAATA
*
491129 GATCAATTTGCTCTTTGATCTAA
1 GATCAATTTGCTATTTGATCTAA
491152 CTTGTAAGGA
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:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (25 bp):
GATCAATTTGCTATTTGATCTAATA
Found at i:493545 original size:13 final size:13
Alignment explanation
Indices: 493527--493552 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
493517 TAACATGTAC
493527 ATTTCTGCTACTA
1 ATTTCTGCTACTA
493540 ATTTCTGCTACTA
1 ATTTCTGCTACTA
493553 GTTATGCTTC
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:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTTCTGCTACTA
Found at i:503640 original size:19 final size:20
Alignment explanation
Indices: 503601--503646 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
503591 CTACACTTAC
503601 TTTAAATTAAAATTTACA-T
1 TTTAAATTAAAATTTACATT
*
503620 TTTAAATTAATTATTTA-ATT
1 TTTAAATTAA-AATTTACATT
503640 TTTAAAT
1 TTTAAAT
503647 ACATAATATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (20 bp):
TTTAAATTAAAATTTACATT
Found at i:505159 original size:12 final size:13
Alignment explanation
Indices: 505137--505163 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
505127 TGTTTCTTTC
505137 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
505150 TTTCTTTTTTTTT
1 TTTCTTTTTTTTT
505163 T
1 T
505164 GCTCTTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (13 bp):
TTTCTTTTTTTTT
Found at i:507074 original size:18 final size:18
Alignment explanation
Indices: 506988--507074 Score: 61
Period size: 18 Copynumber: 4.7 Consensus size: 18
506978 AAATGAATAT
506988 AAATTATGT-AAATTATAA
1 AAATTAT-TAAAATTATAA
* *
507006 AAATTTTCTGAAAAATACTAA
1 AAATTAT-T-AAAATTA-TAA
* * *
507027 AATTTATTAACATGATAA
1 AAATTATTAAAATTATAA
*
507045 AAATT-TTAAAAATTATAT
1 AAATTATT-AAAATTATAA
507063 AAATTATTAAAA
1 AAATTATTAAAA
507075 CAATGAAAAA
Statistics
Matches: 52, Mismatches: 12, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
17 2 0.04
18 30 0.58
19 6 0.12
20 6 0.12
21 8 0.15
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.38
Consensus pattern (18 bp):
AAATTATTAAAATTATAA
Found at i:527490 original size:19 final size:19
Alignment explanation
Indices: 527456--527502 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
527446 TGGCACAAGC
* * *
527456 AGAAAAAAAAGGAAAATTG
1 AGAAAATAAGGGAAAAATG
*
527475 AGGAAATAAGGGAAAAATG
1 AGAAAATAAGGGAAAAATG
527494 AGAAAATAA
1 AGAAAATAA
527503 CAAAATTTAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.66, C:0.00, G:0.23, T:0.11
Consensus pattern (19 bp):
AGAAAATAAGGGAAAAATG
Found at i:530476 original size:42 final size:42
Alignment explanation
Indices: 530422--530567 Score: 172
Period size: 42 Copynumber: 3.5 Consensus size: 42
530412 GATTTACATA
*
530422 TAAGACCATGTCTGAGACATCGGCATCGTATCTGATTTCGTG
1 TAAGACCATGTCTGGGACATCGGCATCGTATCTGATTTCGTG
* * *
530464 TAAGACCGTGTCTGGGACA-CAGGCCTCG-AT-TGAGATTTACGTA
1 TAAGACCATGTCTGGGACATC-GGCATCGTATCT--GATTT-CGTG
* *
530507 TAAGACCATGTCTGGGATATTGGCATCGTATCTGATTTCGTG
1 TAAGACCATGTCTGGGACATCGGCATCGTATCTGATTTCGTG
*
530549 TAAGACCCTGTCTGGGACA
1 TAAGACCATGTCTGGGACA
530568 GAGGTATCGA
Statistics
Matches: 86, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 48 0.56
43 31 0.36
44 2 0.02
45 1 0.01
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACATCGGCATCGTATCTGATTTCGTG
Found at i:530519 original size:43 final size:42
Alignment explanation
Indices: 530392--530567 Score: 146
Period size: 42 Copynumber: 4.1 Consensus size: 42
530382 TGGTGGTTTC
* *
530392 GGGACATAGGCCTCGATTAAGATTTACATATAAGACCATGTCT
1 GGGACACAGGCCTCGATT-AGATTTACGTATAAGACCATGTCT
* * * *
530435 GAGACATC-GGCATCGTATCT-GATTT-CGTGTAAGACCGTGTCT
1 GGGACA-CAGGCCTCG-AT-TAGATTTACGTATAAGACCATGTCT
530477 GGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCT
1 GGGACACAGGCCTCGATT-AGATTTACGTATAAGACCATGTCT
* ** * * *
530520 GGGATATTGGCATCGTATCT-GATTT-CGTGTAAGACCCTGTCT
1 GGGACACAGGCCTCG-AT-TAGATTTACGTATAAGACCATGTCT
530562 GGGACA
1 GGGACA
530568 GAGGTATCGA
Statistics
Matches: 107, Mismatches: 17, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
40 1 0.01
41 3 0.03
42 50 0.47
43 47 0.44
44 4 0.04
45 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (42 bp):
GGGACACAGGCCTCGATTAGATTTACGTATAAGACCATGTCT
Found at i:530535 original size:85 final size:85
Alignment explanation
Indices: 530392--530567 Score: 289
Period size: 85 Copynumber: 2.1 Consensus size: 85
530382 TGGTGGTTTC
*
530392 GGGACATAGGCCTCGATTAAGATTTACATATAAGACCATGTCTGAGACATCGGCATCGTATCTGA
1 GGGACACAGGCCTCGATTAAGATTTACATATAAGACCATGTCTGAGACATCGGCATCGTATCTGA
*
530457 TTTCGTGTAAGACCGTGTCT
66 TTTCGTGTAAGACCCTGTCT
* * * * *
530477 GGGACACAGGCCTCGATTGAGATTTACGTATAAGACCATGTCTGGGATATTGGCATCGTATCTGA
1 GGGACACAGGCCTCGATTAAGATTTACATATAAGACCATGTCTGAGACATCGGCATCGTATCTGA
530542 TTTCGTGTAAGACCCTGTCT
66 TTTCGTGTAAGACCCTGTCT
530562 GGGACA
1 GGGACA
530568 GAGGTATCGA
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (85 bp):
GGGACACAGGCCTCGATTAAGATTTACATATAAGACCATGTCTGAGACATCGGCATCGTATCTGA
TTTCGTGTAAGACCCTGTCT
Found at i:532352 original size:13 final size:13
Alignment explanation
Indices: 532336--532360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
532326 CTTTTCTCCT
532336 TTTCTTTCTTTTC
1 TTTCTTTCTTTTC
532349 TTTCTTTCTTTT
1 TTTCTTTCTTTT
532361 TCTCCCCTGC
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:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTCTTTCTTTTC
Found at i:542572 original size:41 final size:41
Alignment explanation
Indices: 542514--542752 Score: 290
Period size: 41 Copynumber: 5.8 Consensus size: 41
542504 TTAAACAGAT
** * * *
542514 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTG-ATTCAGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAAT--GTA
* *
542556 -CACCGGCACTT-AGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCA-TTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
* *
542596 TCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
542637 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
*
542678 TCACCGGCATTTAGCCTGCTAGACTTAAAGTCTG-AAT-TA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
* *
542717 CTTCACCGGCATTAAGCCTGCTAGACGTAACGTCTG
1 --TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTG
542753 TATTATATTC
Statistics
Matches: 179, Mismatches: 12, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
39 2 0.01
40 8 0.04
41 165 0.92
42 4 0.02
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (41 bp):
TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAAATGTA
Found at i:542752 original size:123 final size:122
Alignment explanation
Indices: 542514--542742 Score: 320
Period size: 123 Copynumber: 1.9 Consensus size: 122
542504 TTAAACAGAT
** * *
542514 TCACCGGCATTTTGCCTGCTAGGCTTAAAGCCTGATTCAGTACACCGGCACTTAGCCTGCTAGAC
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGCCTGAAT-AGTACACCGGCACTTAGCCTGCTAGAC
*
542579 ATATAGTCTGAAATGTATCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA
65 ATAAAGTCTGAAATGTATCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA
* *
542637 TCACCGGCATTAAGCCTGCTAGACTTAAAGTCTGAA-ATGTATCACCGGCATTTAGCCTGCTAGA
1 TCACCGGCATTAAGCCTGCTAGACTTAAAGCCTGAATA-GTA-CACCGGCACTTAGCCTGCTAGA
*
542701 CTTAAAGTCTG-AAT-TACTTCACCGGCATTAAGCCTGCTAGAC
64 CATAAAGTCTGAAATGTA--TCACCGGCATTAAGCCTGCTAGAC
542743 GTAACGTCTG
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
121 3 0.03
122 6 0.06
123 85 0.90
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.28
Consensus pattern (122 bp):
TCACCGGCATTAAGCCTGCTAGACTTAAAGCCTGAATAGTACACCGGCACTTAGCCTGCTAGACA
TAAAGTCTGAAATGTATCACCGGCATTAAGCCTGCTAGACATATAGTCTGAAATGTA
Found at i:549921 original size:41 final size:41
Alignment explanation
Indices: 549714--549910 Score: 326
Period size: 41 Copynumber: 4.8 Consensus size: 41
549704 TTTATCGTTA
* * * *
549714 GTGACATAATTCAGACTTTACGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
549755 GTGA-A-ATTATTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACA-T-TTCAGACTATAAGTCTAGCAGGCTTAATGCCG
549796 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
549837 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
549878 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
1 GTGACACATTTCAGACTATAAGTCTAGCAGGCT
549911 AAGAGCCGGT
Statistics
Matches: 149, Mismatches: 3, Indels: 8
0.93 0.02 0.05
Matches are distributed among these distances:
39 1 0.01
40 1 0.01
41 144 0.97
42 2 0.01
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (41 bp):
GTGACACATTTCAGACTATAAGTCTAGCAGGCTTAATGCCG
Found at i:550181 original size:33 final size:32
Alignment explanation
Indices: 550125--550188 Score: 101
Period size: 33 Copynumber: 2.0 Consensus size: 32
550115 ATAGATATGT
550125 ATATATATATATGTTGCATTCGGCATAGGTGG
1 ATATATATATATGTTGCATTCGGCATAGGTGG
* *
550157 ATATATTTATGTGTATGCATTCGGCATAGGTG
1 ATATATATATATGT-TGCATTCGGCATAGGTG
550189 AAAATAAGTG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 12 0.41
33 17 0.59
ACGTcount: A:0.27, C:0.09, G:0.25, T:0.39
Consensus pattern (32 bp):
ATATATATATATGTTGCATTCGGCATAGGTGG
Found at i:550205 original size:33 final size:33
Alignment explanation
Indices: 550132--550205 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 33
550122 TGTATATATA
* * **
550132 TATATGT-TGCATTCGGCATAGGTGGATATATT
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
550164 TATGTGTATGCATTCGGCATAGGTGAAAATAAG
1 TATATGTATGCATTCGGCATAGGTGAAAATAAG
*
550197 TGTATGTAT
1 TATATGTAT
550206 CTATGCATTC
Statistics
Matches: 34, Mismatches: 7, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
32 6 0.18
33 28 0.82
ACGTcount: A:0.28, C:0.08, G:0.26, T:0.38
Consensus pattern (33 bp):
TATATGTATGCATTCGGCATAGGTGAAAATAAG
Found at i:551217 original size:23 final size:24
Alignment explanation
Indices: 551191--551285 Score: 93
Period size: 28 Copynumber: 3.6 Consensus size: 24
551181 AAATGTCCAA
551191 CCAAAACACACCAG-TATAATCCT
1 CCAAAACACACCAGATATAATCCT
551214 CCAAAACACACCAGTATCATATAATCCT
1 CCAAAACACACCAG----ATATAATCCT
*
551242 CCCAAACACACCAGAATAATATAATCCAT
1 CCAAAACACACCAG----ATATAATCC-T
551271 CCAAAACACACCAGA
1 CCAAAACACACCAGA
551286 ATAGCACAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 10
0.82 0.05 0.13
Matches are distributed among these distances:
23 14 0.23
25 1 0.02
28 33 0.53
29 14 0.23
ACGTcount: A:0.46, C:0.34, G:0.04, T:0.16
Consensus pattern (24 bp):
CCAAAACACACCAGATATAATCCT
Found at i:551287 original size:29 final size:28
Alignment explanation
Indices: 551205--551288 Score: 132
Period size: 28 Copynumber: 3.0 Consensus size: 28
551195 AACACACCAG
* *
551205 TATAATCCTCCAAAACACACCAGTATCA
1 TATAATCCTCCAAAACACACCAGAATAA
*
551233 TATAATCCTCCCAAACACACCAGAATAA
1 TATAATCCTCCAAAACACACCAGAATAA
551261 TATAATCCATCCAAAACACACCAGAATA
1 TATAATCC-TCCAAAACACACCAGAATA
551289 GCACAAAGTG
Statistics
Matches: 51, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
28 33 0.65
29 18 0.35
ACGTcount: A:0.46, C:0.31, G:0.04, T:0.19
Consensus pattern (28 bp):
TATAATCCTCCAAAACACACCAGAATAA
Found at i:553841 original size:17 final size:16
Alignment explanation
Indices: 553809--553842 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
553799 TTGGCTATTC
*
553809 TGTTTCTTTCTTCTTT
1 TGTTTCTTTATTCTTT
553825 TGTTTCTTTTATTCTTT
1 TGTTTC-TTTATTCTTT
553842 T
1 T
553843 ATTTTAACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.03, C:0.15, G:0.06, T:0.76
Consensus pattern (16 bp):
TGTTTCTTTATTCTTT
Found at i:553890 original size:14 final size:14
Alignment explanation
Indices: 553831--553881 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
553821 CTTTTGTTTC
*
553831 TTTTA-TTCTTTTA
1 TTTTATTTCCTTTA
* *
553844 TTTTAACTTACTTTA
1 TTTT-ATTTCCTTTA
*
553859 CTTTATTTCCTTTA
1 TTTTATTTCCTTTA
553873 TTTTATTTC
1 TTTTATTTC
553882 TTTTGTTTTC
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
13 4 0.13
14 17 0.57
15 9 0.30
ACGTcount: A:0.18, C:0.14, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATTTCCTTTA
Found at i:554050 original size:14 final size:17
Alignment explanation
Indices: 554031--554067 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
554021 ATTTATTTCT
554031 TAATATAA-T-ATTT-A
1 TAATATAATTAATTTAA
554045 TAATATAATTAATTTAA
1 TAATATAATTAATTTAA
554062 TAATAT
1 TAATAT
554068 CCTTTATAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 8 0.40
15 1 0.05
16 4 0.20
17 7 0.35
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATATAATTAATTTAA
Found at i:554650 original size:16 final size:16
Alignment explanation
Indices: 554629--554662 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
554619 GAGTTACCAA
*
554629 TTCATTTATCAGATAT
1 TTCATTAATCAGATAT
*
554645 TTCATTAATCCGATAT
1 TTCATTAATCAGATAT
554661 TT
1 TT
554663 TTTCTTTTCC
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:0.29, C:0.15, G:0.06, T:0.50
Consensus pattern (16 bp):
TTCATTAATCAGATAT
Found at i:555655 original size:23 final size:22
Alignment explanation
Indices: 555625--555668 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
555615 AAAATAAAGT
* *
555625 AAATAAAAGAATAAAAAGAATG
1 AAATAAAAAAACAAAAAGAATG
555647 AAATAAAAAAAACAAAAAGAAT
1 AAAT-AAAAAAACAAAAAGAAT
555669 AAGAAACAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.77, C:0.02, G:0.09, T:0.11
Consensus pattern (22 bp):
AAATAAAAAAACAAAAAGAATG
Found at i:556689 original size:23 final size:23
Alignment explanation
Indices: 556654--556718 Score: 121
Period size: 23 Copynumber: 2.8 Consensus size: 23
556644 GATTTATAAT
556654 ATTCTGGGTGTGTTTGGGTTGGAC
1 ATTCT-GGTGTGTTTGGGTTGGAC
556678 ATTCTGGTGTGTTTGGGTTGGAC
1 ATTCTGGTGTGTTTGGGTTGGAC
556701 ATTCTGGTGTGTTTGGGT
1 ATTCTGGTGTGTTTGGGT
556719 GGAATCCGCG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
23 36 0.88
24 5 0.12
ACGTcount: A:0.08, C:0.08, G:0.40, T:0.45
Consensus pattern (23 bp):
ATTCTGGTGTGTTTGGGTTGGAC
Found at i:562628 original size:20 final size:20
Alignment explanation
Indices: 562599--562651 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
562589 ATTATATATA
*
562599 TTAA-AATTATTATTATGAT
1 TTAATAATTATTATGATGAT
*
562618 TTAATAATTATTATGATTAT
1 TTAATAATTATTATGATGAT
562638 TTAATGAA-TATTAT
1 TTAAT-AATTATTAT
562652 ATTTTAAATA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 4 0.13
20 24 0.80
21 2 0.07
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (20 bp):
TTAATAATTATTATGATGAT
Found at i:563670 original size:25 final size:24
Alignment explanation
Indices: 563624--563670 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
563614 ATAAAAATTC
*
563624 AATTAATTATTAAATTAATATTGT
1 AATTAATAATTAAATTAATATTGT
*
563648 AATTAATAATGTAAATTATTATT
1 AATTAATAAT-TAAATTAATATT
563671 ATTTTTTTCG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 9 0.45
25 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (24 bp):
AATTAATAATTAAATTAATATTGT
Found at i:566509 original size:54 final size:53
Alignment explanation
Indices: 566342--566511 Score: 211
Period size: 53 Copynumber: 3.2 Consensus size: 53
566332 GGCCGTTACA
* * *
566342 GTCTTACACGGG-AGCACTTATCACTTTTCTCCGATGCCATAGCCCAGCTATG
1 GTCTTATACGGGAATCACTTATCACTTTTATCCGATGCCATAGCCCAGCTATG
* *
566394 GTCTTATAC--GAATCACTTGTATCACTTTAATCCGAAGCCATAGCCCAGCTATG
1 GTCTTATACGGGAATCAC-T-TATCACTTTTATCCGATGCCATAGCCCAGCTATG
* * * *
566447 GTCTTATACGGGAATCACTTATCACTTGTTTTCTGATGTCATAGCCCAACTATG
1 GTCTTATACGGGAATCACTTATCACTT-TTATCCGATGCCATAGCCCAGCTATG
566501 GTCTTATACGG
1 GTCTTATACGG
566512 ATATTGCTTA
Statistics
Matches: 101, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
50 1 0.01
51 4 0.04
52 9 0.09
53 48 0.48
54 32 0.32
55 7 0.07
ACGTcount: A:0.24, C:0.26, G:0.18, T:0.32
Consensus pattern (53 bp):
GTCTTATACGGGAATCACTTATCACTTTTATCCGATGCCATAGCCCAGCTATG
Found at i:567773 original size:183 final size:183
Alignment explanation
Indices: 567447--567805 Score: 628
Period size: 183 Copynumber: 2.0 Consensus size: 183
567437 TGACAGATAT
* *
567447 GGGTTAGGGGTGTTACAATTATTATTGAGCTCATTCACATGAATCTGTCATTTGAAATTGTGATA
1 GGGTTAAGGGTATTACAATTATTATTGAGCTCATTCACATGAATCTGTCATTTGAAATTGTGATA
* * *
567512 GACAATAAGAAATAGTGAATGGCATGCTTATGCATGGTTATATGTATTTATCTAAAACACAAGAA
66 GACAAGAAGAAATAGAGAATGGCATGCTTATGCATGGTTATATATATTTATCTAAAACACAAGAA
567577 AATGATGGTTATATATTTGATAGATGGAGACACGAGACTATGATATGGGTTAG
131 AATGATGGTTATATATTTGATAGATGGAGACACGAGACTATGATATGGGTTAG
*
567630 GGGTTAAGGGTATTACAGTTATTATTGAGCTCATTCACATGAATCTGTCATTTGAAATTGTGATA
1 GGGTTAAGGGTATTACAATTATTATTGAGCTCATTCACATGAATCTGTCATTTGAAATTGTGATA
* *
567695 GACAAGAAGAAATAGAGAATGGCATGCTTATGTATGGTTATATATATTTATCTGAAACACAAGAA
66 GACAAGAAGAAATAGAGAATGGCATGCTTATGCATGGTTATATATATTTATCTAAAACACAAGAA
* *
567760 AATGATGGTTATATATTTGATATATGGAGACATGAGACTATGATAT
131 AATGATGGTTATATATTTGATAGATGGAGACACGAGACTATGATAT
567806 ATGAATATTT
Statistics
Matches: 166, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
183 166 1.00
ACGTcount: A:0.35, C:0.09, G:0.22, T:0.34
Consensus pattern (183 bp):
GGGTTAAGGGTATTACAATTATTATTGAGCTCATTCACATGAATCTGTCATTTGAAATTGTGATA
GACAAGAAGAAATAGAGAATGGCATGCTTATGCATGGTTATATATATTTATCTAAAACACAAGAA
AATGATGGTTATATATTTGATAGATGGAGACACGAGACTATGATATGGGTTAG
Found at i:568472 original size:7 final size:8
Alignment explanation
Indices: 568447--568479 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
568437 AAAGGGGAGG
568447 AAAATAAA
1 AAAATAAA
568455 GAAAATAAA
1 -AAAATAAA
568464 AAAATAAA
1 AAAATAAA
568472 AAAATAAA
1 AAAATAAA
568480 TTGTTCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.85, C:0.00, G:0.03, T:0.12
Consensus pattern (8 bp):
AAAATAAA
Found at i:570434 original size:23 final size:23
Alignment explanation
Indices: 570404--570450 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
570394 ACTGAAACGT
570404 AAATTTATTAATAGTTTAGTCAC
1 AAATTTATTAATAGTTTAGTCAC
570427 AAATTTATTAATAGTTTAGTCAC
1 AAATTTATTAATAGTTTAGTCAC
570450 A
1 A
570451 TTTAGTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.43
Consensus pattern (23 bp):
AAATTTATTAATAGTTTAGTCAC
Found at i:574638 original size:15 final size:14
Alignment explanation
Indices: 574618--574666 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 14
574608 GTTAATAGGG
*
574618 AAGAAAAAAAGGGAA
1 AAGAAAAAAA-AGAA
574633 AAGAAAAGAAAAGAA
1 AAGAAAA-AAAAGAA
574648 AAGAAAAAGAAAGAA
1 AAGAAAAA-AAAGAA
574663 AAGA
1 AAGA
574667 GACGAGACGA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
14 1 0.03
15 27 0.87
16 3 0.10
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (14 bp):
AAGAAAAAAAAGAA
Found at i:574640 original size:5 final size:5
Alignment explanation
Indices: 574630--574666 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
574620 GAAAAAAAGG
574630 GAAAA GAAAA GAAAA GAAAA GAAAA -AGAAA GAAAA GA
1 GAAAA GAAAA GAAAA GAAAA GAAAA GA-AAA GAAAA GA
574667 GACGAGACGA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 1 0.03
5 28 0.93
6 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
GAAAA
Found at i:590541 original size:106 final size:106
Alignment explanation
Indices: 590405--590605 Score: 366
Period size: 106 Copynumber: 1.9 Consensus size: 106
590395 AAAATTTTTC
590405 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
* *
590470 TTCTTGTTCGACCAAATAGCCAAATATCCTTTTTAAACTTT
66 TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
*
590511 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGGAAACGTGCCCTAACGTGCTGGGTTTCGAT
1 TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
*
590576 TTCTCGTTCGACTAAACAGCCAAATATCCT
66 TTCTCGTTCGACCAAACAGCCAAATATCCT
590606 CTTAGAGCTT
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
106 91 1.00
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (106 bp):
TAAATAAGGCAATATTTCGCGTTTGGAAAATCGAGAAAACGTGCCCTAACGTGCTGGGTTTCGAT
TTCTCGTTCGACCAAACAGCCAAATATCCTTTTTAAACTTT
Found at i:598217 original size:54 final size:54
Alignment explanation
Indices: 598135--598290 Score: 183
Period size: 54 Copynumber: 2.8 Consensus size: 54
598125 ATAGATAGAC
* * * *
598135 AGAGCGTTAAGACTATGAACTATCATCAGTTTTGCTCTACAGCTGAA-CCAAAGT
1 AGAGC-TTAAGACTACGAACTAACATCAGTTTTGCTCTAAAGCTGAAGCAAAAGT
598189 AGAGCATTAAGACTACGAACTAACATCAGTTTTGCTCTAAAGCTGAAGCAAAAGT
1 AGAGC-TTAAGACTACGAACTAACATCAGTTTTGCTCTAAAGCTGAAGCAAAAGT
* *
598244 AGAGC--AAGACTACAATGAACTAACATCAGTTTAGCTCCAAAGACTGA
1 AGAGCTTAAGACTAC---GAACTAACATCAGTTTTGCTCTAAAG-CTGA
598291 CAGATTACTT
Statistics
Matches: 90, Mismatches: 7, Indels: 8
0.86 0.07 0.08
Matches are distributed among these distances:
52 8 0.09
54 43 0.48
55 35 0.39
56 4 0.04
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.24
Consensus pattern (54 bp):
AGAGCTTAAGACTACGAACTAACATCAGTTTTGCTCTAAAGCTGAAGCAAAAGT
Found at i:603286 original size:15 final size:16
Alignment explanation
Indices: 603255--603295 Score: 66
Period size: 15 Copynumber: 2.6 Consensus size: 16
603245 ACAATAGAAC
603255 AATCTATTTACCATTTT
1 AATC-ATTTACCATTTT
603272 AATCATTTA-CATTTT
1 AATCATTTACCATTTT
603287 AATCATTTA
1 AATCATTTA
603296 ACTATTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
15 15 0.62
16 5 0.21
17 4 0.17
ACGTcount: A:0.34, C:0.15, G:0.00, T:0.51
Consensus pattern (16 bp):
AATCATTTACCATTTT
Found at i:604822 original size:15 final size:14
Alignment explanation
Indices: 604782--604818 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
604772 TAATTAGATC
604782 TAAAATTTAAAATA
1 TAAAATTTAAAATA
*
604796 TAATAAATTAAAATA
1 TAA-AATTTAAAATA
604811 TAAAATTT
1 TAAAATTT
604819 TAAAGAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAATTTAAAATA
Found at i:606884 original size:53 final size:58
Alignment explanation
Indices: 606818--606944 Score: 149
Period size: 58 Copynumber: 2.3 Consensus size: 58
606808 TAATTTGCCT
606818 TAGTCA-TTCAATTATT-ACAA-TTTTTT-ATAATTTAATCAT-AAAAAA-TTATAAAA
1 TAGTCACTT-AATTATTAACAATTTTTTTGATAATTTAATCATGAAAAAAGTTATAAAA
* * *
606871 TAGTCACTTAATTATTAATAATTTTTTTGATATTTTAATTATGAAAAAAGTTATAAAA
1 TAGTCACTTAATTATTAACAATTTTTTTGATAATTTAATCATGAAAAAAGTTATAAAA
* * *
606929 TATTTACCTAATTATT
1 TAGTCACTTAATTATT
606945 TAATTTTATC
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
53 13 0.21
54 5 0.08
55 6 0.10
56 11 0.18
57 6 0.10
58 21 0.34
ACGTcount: A:0.43, C:0.06, G:0.04, T:0.46
Consensus pattern (58 bp):
TAGTCACTTAATTATTAACAATTTTTTTGATAATTTAATCATGAAAAAAGTTATAAAA
Found at i:610122 original size:20 final size:20
Alignment explanation
Indices: 610097--610146 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
610087 TGGCTTAAAA
610097 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
610117 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
610134 GTGGTAGTGGATT
1 TTGGTAGTGGATT
610147 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:614762 original size:20 final size:20
Alignment explanation
Indices: 614737--614786 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
614727 TGGCTTAAAA
614737 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
614757 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
614774 GTGGTAGTGGATT
1 TTGGTAGTGGATT
614787 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:621224 original size:28 final size:28
Alignment explanation
Indices: 621176--621230 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
621166 ACTATGTCAA
*
621176 TTTTTAATAGTAAAAATGATTAATTTAC
1 TTTTTAATACTAAAAATGATTAATTTAC
*
621204 TTTTTAAT-CTAAATATAGATTAATTTA
1 TTTTTAATACTAAAAAT-GATTAATTTA
621231 ACTATTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (28 bp):
TTTTTAATACTAAAAATGATTAATTTAC
Found at i:626960 original size:21 final size:22
Alignment explanation
Indices: 626923--626980 Score: 59
Period size: 22 Copynumber: 2.6 Consensus size: 22
626913 TTACCCGTAT
*
626923 ATAAATATAA-ATATTTTAAA-A
1 ATAAAAATAATAT-TTTTAAACA
626944 ATAAAAATAATATTTTTTAAACA
1 ATAAAAATAATA-TTTTTAAACA
626967 A-AAAAATTAATATT
1 ATAAAAA-TAATATT
626981 AAAAAAATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 9 0.28
22 15 0.47
23 8 0.25
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
ATAAAAATAATATTTTTAAACA
Found at i:626969 original size:20 final size:20
Alignment explanation
Indices: 626932--626970 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
626922 TATAAATATA
*
626932 AATATTTTAAAAATAAAAAT
1 AATATTTTAAAAACAAAAAT
**
626952 AATATTTTTTAAACAAAAA
1 AATATTTTAAAAACAAAAA
626971 AATTAATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.36
Consensus pattern (20 bp):
AATATTTTAAAAACAAAAAT
Found at i:626972 original size:23 final size:22
Alignment explanation
Indices: 626936--626980 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
626926 AATATAAATA
*
626936 TTTTAAAAATAAAAATAATATT
1 TTTTAAAAAAAAAAATAATATT
*
626958 TTTTAAACAAAAAAATTAATATT
1 TTTTAAA-AAAAAAAATAATATT
626981 AAAAAAATAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 7 0.35
23 13 0.65
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTTAAAAAAAAAAATAATATT
Found at i:628833 original size:16 final size:17
Alignment explanation
Indices: 628812--628845 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
628802 TTCTTTAGTA
*
628812 TTTTTGTTA-TTTTATT
1 TTTTTGGTATTTTTATT
628828 TTTTTGGTATTTTTATT
1 TTTTTGGTATTTTTATT
628845 T
1 T
628846 AACAAATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.12, C:0.00, G:0.09, T:0.79
Consensus pattern (17 bp):
TTTTTGGTATTTTTATT
Found at i:629030 original size:17 final size:17
Alignment explanation
Indices: 629008--629041 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
628998 TATCTATTGG
629008 ATTAAATTAAAAGTAAA
1 ATTAAATTAAAAGTAAA
*
629025 ATTAAATTAACAGTAAA
1 ATTAAATTAAAAGTAAA
629042 TTTATTTTAT
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:0.62, C:0.03, G:0.06, T:0.29
Consensus pattern (17 bp):
ATTAAATTAAAAGTAAA
Found at i:630323 original size:45 final size:45
Alignment explanation
Indices: 630236--630358 Score: 144
Period size: 45 Copynumber: 2.8 Consensus size: 45
630226 GTTTGTACAT
* * * * *
630236 AGTTTCAGCCTC-AACATTATTTAAAATGGGTTTTTGTTTATAAGA
1 AGTTTCAGCTTCAAACATTCTTGAAAAT-AGTTTATGTTTATAAGA
*
630281 AG-TTCTAGCTTCAAATATTCTTGAAAATAGTTTATGTTTATAAGA
1 AGTTTC-AGCTTCAAACATTCTTGAAAATAGTTTATGTTTATAAGA
*
630326 AGTTTCAGCTTCAAACATTCTTGTAAATA-TTTA
1 AGTTTCAGCTTCAAACATTCTTGAAAATAGTTTA
630359 ATGAAGCTTT
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
44 7 0.10
45 45 0.67
46 15 0.22
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.42
Consensus pattern (45 bp):
AGTTTCAGCTTCAAACATTCTTGAAAATAGTTTATGTTTATAAGA
Found at i:645957 original size:32 final size:32
Alignment explanation
Indices: 645917--645985 Score: 122
Period size: 32 Copynumber: 2.2 Consensus size: 32
645907 ATGTGAAGGT
645917 AGGT-TATAGGGTTTTTCTTTTATATAATAGG
1 AGGTATATAGGGTTTTTCTTTTATATAATAGG
*
645948 AGGTATATAGGGTTTTTCTTTTATATAATTGG
1 AGGTATATAGGGTTTTTCTTTTATATAATAGG
645980 AGGTAT
1 AGGTAT
645986 TGTTAAGATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
31 4 0.11
32 32 0.89
ACGTcount: A:0.26, C:0.03, G:0.23, T:0.48
Consensus pattern (32 bp):
AGGTATATAGGGTTTTTCTTTTATATAATAGG
Found at i:653633 original size:12 final size:12
Alignment explanation
Indices: 653616--653640 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
653606 TCGATTAAAT
653616 TAAATAATAATA
1 TAAATAATAATA
653628 TAAATAATAATA
1 TAAATAATAATA
653640 T
1 T
653641 TTTTAATTAT
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TAAATAATAATA
Found at i:655401 original size:29 final size:28
Alignment explanation
Indices: 655366--655452 Score: 79
Period size: 30 Copynumber: 3.0 Consensus size: 28
655356 CCATTTGAAT
655366 TTAATTTTAAAATTTTAAAAATAAAAAA
1 TTAATTTTAAAATTTTAAAAATAAAAAA
*
655394 TTATATTTTTAAAA--ATAAAAATATAAAAA
1 TTA-A-TTTTAAAATTTTAAAAATA-AAAAA
* * *
655423 TTAAATTTCAATTTTATAAAAAGTAAAAAA
1 TTAATTTTAAAATTT-TAAAAA-TAAAAAA
655453 AAAACTTATA
Statistics
Matches: 47, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
27 5 0.11
28 12 0.26
29 9 0.19
30 19 0.40
31 2 0.04
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (28 bp):
TTAATTTTAAAATTTTAAAAATAAAAAA
Found at i:656897 original size:19 final size:19
Alignment explanation
Indices: 656875--656915 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
656865 TCTCACACTT
*
656875 AAAATTT-ATATATTTTTCA
1 AAAATTTAAAATATTTTT-A
656894 AAAATTTAAAATATTTTTA
1 AAAATTTAAAATATTTTTA
656913 AAA
1 AAA
656916 GTGTCTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (19 bp):
AAAATTTAAAATATTTTTA
Found at i:665954 original size:14 final size:16
Alignment explanation
Indices: 665924--665976 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
665914 TTATGTATAT
665924 AATT-ATATTAAATTAA
1 AATTCATATT-AATTAA
665940 AATTCATA-T-ATT-A
1 AATTCATATTAATTAA
665953 AATTACATATTAATTAA
1 AATT-CATATTAATTAA
665970 AATTCAT
1 AATTCAT
665977 GTATAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
13 5 0.16
14 7 0.22
15 1 0.03
16 11 0.34
17 8 0.25
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (16 bp):
AATTCATATTAATTAA
Done.