Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D08
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: 65987480
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 223646 characters in sequence are not A, C, G, or T
File 169 of 211
Found at i:52665138 original size:13 final size:13
Alignment explanation
Indices: 52665120--52665162 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
52665110 TAAGTATAAT
52665120 TAAGTTATGTATG
1 TAAGTTATGTATG
*
52665133 TAAGTTATGTATAAT
1 TAAGTTATGTAT--G
52665148 TAAGTTATGTATG
1 TAAGTTATGTATG
52665161 TA
1 TA
52665163 TGTATGTGAG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 14 0.54
15 12 0.46
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.47
Consensus pattern (13 bp):
TAAGTTATGTATG
Found at i:52665143 original size:9 final size:9
Alignment explanation
Indices: 52665129--52665466 Score: 150
Period size: 9 Copynumber: 37.4 Consensus size: 9
52665119 TTAAGTTATG
52665129 TATGTAAGT
1 TATGTAAGT
52665138 TATGT-A-T
1 TATGTAAGT
*
52665145 AAT-TAAGT
1 TATGTAAGT
*
52665153 TATGTATGTAT
1 TATGTAAG--T
*
52665164 GTATGTGAGT
1 -TATGTAAGT
52665174 TAT-TAAGT
1 TATGTAAGT
52665182 TATGTAAGT
1 TATGTAAGT
*
52665191 TATGTGAGT
1 TATGTAAGT
* *
52665200 TATGATATGA
1 TATG-TAAGT
52665210 TATG--A-T
1 TATGTAAGT
*
52665216 ATATATAAGT
1 -TATGTAAGT
52665226 TAT-TAAGT
1 TATGTAAGT
*
52665234 TATGTATG-
1 TATGTAAGT
*
52665242 TATGTGAGT
1 TATGTAAGT
52665251 TATGTAAGT
1 TATGTAAGT
* **
52665260 AATG-ACCT
1 TATGTAAGT
* * *
52665268 GATATATATT
1 TATGTA-AGT
52665278 TATGT-A-T
1 TATGTAAGT
52665285 TATGTAAGT
1 TATGTAAGT
**
52665294 TATGTGTCTGT
1 TA--TGTAAGT
*
52665305 TTTGTAAGT
1 TATGTAAGT
*
52665314 TATGGTATGAT
1 TAT-GTAAG-T
*
52665325 ATATATAAGT
1 -TATGTAAGT
52665335 TAT-TAAGT
1 TATGTAAGT
52665343 TATGTAAGT
1 TATGTAAGT
*
52665352 TATGTGAGT
1 TATGTAAGT
*
52665361 TATGATATGAT
1 TATG-TAAG-T
*
52665372 ATATATAAGT
1 -TATGTAAGT
*
52665382 TAT-TATGT
1 TATGTAAGT
52665390 TATGTAAGT
1 TATGTAAGT
*
52665399 TATGTGAGT
1 TATGTAAGT
*
52665408 TATGATATGAT
1 TATG-TAAG-T
*
52665419 ATATATAAGT
1 -TATGTAAGT
52665429 TAT-TAAGT
1 TATGTAAGT
*
52665437 TATGTATG-
1 TATGTAAGT
*
52665445 TATGTCAGT
1 TATGTAAGT
52665454 TATGTAAGT
1 TATGTAAGT
52665463 TATG
1 TATG
52665467 ATCTGATATA
Statistics
Matches: 245, Mismatches: 51, Indels: 66
0.68 0.14 0.18
Matches are distributed among these distances:
6 1 0.00
7 13 0.05
8 60 0.24
9 114 0.47
10 23 0.09
11 19 0.08
12 15 0.06
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (9 bp):
TATGTAAGT
Found at i:52665153 original size:15 final size:15
Alignment explanation
Indices: 52665113--52665159 Score: 71
Period size: 15 Copynumber: 3.3 Consensus size: 15
52665103 TTAGGGATAA
52665113 GTATAATTAAGTTAT
1 GTATAATTAAGTTAT
*
52665128 GTAT--GTAAGTTAT
1 GTATAATTAAGTTAT
52665141 GTATAATTAAGTTAT
1 GTATAATTAAGTTAT
52665156 GTAT
1 GTAT
52665160 GTATGTATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 12 0.43
15 16 0.57
ACGTcount: A:0.36, C:0.00, G:0.17, T:0.47
Consensus pattern (15 bp):
GTATAATTAAGTTAT
Found at i:52665153 original size:28 final size:27
Alignment explanation
Indices: 52665113--52665187 Score: 105
Period size: 28 Copynumber: 2.7 Consensus size: 27
52665103 TTAGGGATAA
52665113 GTATAATTAAGTTATGTATGTAAGTTAT
1 GTATAATTAAGTTATGTATGTAAG-TAT
*
52665141 GTATAATTAAGTTATGTATGTATGTAT
1 GTATAATTAAGTTATGTATGTAAGTAT
*
52665168 GTGAGTTATTAAGTTATGTA
1 GT-A-TAATTAAGTTATGTA
52665188 AGTTATGTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
27 5 0.12
28 24 0.56
29 14 0.33
ACGTcount: A:0.33, C:0.00, G:0.20, T:0.47
Consensus pattern (27 bp):
GTATAATTAAGTTATGTATGTAAGTAT
Found at i:52665191 original size:17 final size:17
Alignment explanation
Indices: 52665165--52665465 Score: 84
Period size: 17 Copynumber: 17.7 Consensus size: 17
52665155 TGTATGTATG
* *
52665165 TATGTGAGTTATTAAGT
1 TATGTAAGTTATTGAGT
52665182 TATGTAAGTTATGTGAGT
1 TATGTAAGTTAT-TGAGT
* *
52665200 TATGATATGATA-TGA-T
1 TATG-TAAGTTATTGAGT
* *
52665216 ATATATAAGTTATTAAGT
1 -TATGTAAGTTATTGAGT
*
52665234 TATGTATG-TATGTGAGT
1 TATGTAAGTTAT-TGAGT
* *
52665251 TATGTAAG-TAATGACCT
1 TATGTAAGTTATTGA-GT
* * *
52665268 GATATATATTTA-TGTA-T
1 TATGTA-AGTTATTG-AGT
*
52665285 TATGTAAGTTATGTGTCTGT
1 TATGTAAGTTAT-TG--AGT
* *
52665305 TTTGTAAGTTATGGTATGAT
1 TATGTAAGTTATTG-A-G-T
* *
52665325 ATATATAAGTTATTAAGT
1 -TATGTAAGTTATTGAGT
52665343 TATGTAAGTTATGTGAGT
1 TATGTAAGTTAT-TGAGT
52665361 TATG--A--TA-TGA-T
1 TATGTAAGTTATTGAGT
*
52665372 ATATATAAGTTATT-ATGT
1 -TATGTAAGTTATTGA-GT
52665390 TATGTAAGTTATGTGAGT
1 TATGTAAGTTAT-TGAGT
52665408 TATG--A--TA-TGA-T
1 TATGTAAGTTATTGAGT
* *
52665419 ATATATAAGTTATTAAGT
1 -TATGTAAGTTATTGAGT
* *
52665437 TATGTATG-TATGTCAGT
1 TATGTAAGTTAT-TGAGT
52665454 TATGTAAGTTAT
1 TATGTAAGTTAT
52665466 GATCTGATAT
Statistics
Matches: 207, Mismatches: 40, Indels: 73
0.65 0.12 0.23
Matches are distributed among these distances:
11 2 0.01
12 12 0.06
14 6 0.03
16 26 0.13
17 90 0.43
18 35 0.17
19 12 0.06
20 14 0.07
21 10 0.05
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (17 bp):
TATGTAAGTTATTGAGT
Found at i:52665242 original size:47 final size:46
Alignment explanation
Indices: 52665191--52665445 Score: 188
Period size: 47 Copynumber: 5.1 Consensus size: 46
52665181 TTATGTAAGT
*
52665191 TATGTGAGTTATGATATGATATGATATATATAAGTTATTAAGTTATG
1 TATGTGAGTTA-GTTATGATATGATATATATAAGTTATTAAGTTATG
*
52665238 TATGT-ATGTGAGTTATGTAAGTAATGACCTGATATATATTTATGTATTATGTAAGTTATGTG
1 TATGTGA-GTTAGTTATG--A-T-ATGA--T-ATATATA---A-G--TTAT-TAAGTTA--TG
* ** * *
52665300 TCTGTTTTGTAAGTTATGGTATGATATATATAAGTTATTAAGTTATG
1 TATG-TGAGTTAGTTATGATATGATATATATAAGTTATTAAGTTATG
* * * *
52665347 TAAGTTATGTGAGTTATGATATGATATATATAAGTTATTATGTTATG
1 TATGTGA-GTTAGTTATGATATGATATATATAAGTTATTAAGTTATG
* * *
52665394 TAAGTTATGTGAGTTATGATATGATATATATAAGTTATTAAGTTATG
1 TATGTGA-GTTAGTTATGATATGATATATATAAGTTATTAAGTTATG
52665441 TATGT
1 TATGT
52665446 ATGTCAGTTA
Statistics
Matches: 174, Mismatches: 14, Indels: 40
0.76 0.06 0.18
Matches are distributed among these distances:
46 8 0.05
47 98 0.56
48 1 0.01
49 8 0.05
50 8 0.05
52 2 0.01
53 8 0.05
56 8 0.05
57 2 0.01
59 8 0.05
60 8 0.05
62 5 0.03
63 10 0.06
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (46 bp):
TATGTGAGTTAGTTATGATATGATATATATAAGTTATTAAGTTATG
Found at i:52665252 original size:60 final size:59
Alignment explanation
Indices: 52665182--52665364 Score: 163
Period size: 60 Copynumber: 3.2 Consensus size: 59
52665172 GTTATTAAGT
* *
52665182 TATGTAAGTTATGTGAGTTATGATATGATATGATATATATAAGTTATTAAGTTATGTATG
1 TATGTGAGTTATGTAAGTTATGATATGATAT-ATATATATAAGTTATTAAGTTATGTATG
* ** * *
52665242 TATGTGAGTTATGTAAGTAATGACCTGATATATATTTATGTA-TTATGTAAGTTATG--TG
1 TATGTGAGTTATGTAAGTTATGATATGATATATATATAT-AAGTTAT-TAAGTTATGTATG
* * *
52665300 TCTGT---TT-TGTAAGTTATGGTATG----ATATATATAAGTTATTAAGTTATGTAAG
1 TATGTGAGTTATGTAAGTTATGATATGATATATATATATAAGTTATTAAGTTATGTATG
52665351 TTATGTGAGTTATG
1 -TATGTGAGTTATG
52665365 ATATGATATA
Statistics
Matches: 97, Mismatches: 16, Indels: 24
0.71 0.12 0.18
Matches are distributed among these distances:
49 10 0.10
50 11 0.11
51 1 0.01
52 4 0.04
54 12 0.12
55 4 0.04
56 2 0.02
58 6 0.06
59 11 0.11
60 36 0.37
ACGTcount: A:0.32, C:0.02, G:0.21, T:0.46
Consensus pattern (59 bp):
TATGTGAGTTATGTAAGTTATGATATGATATATATATATAAGTTATTAAGTTATGTATG
Found at i:52665464 original size:55 final size:51
Alignment explanation
Indices: 52665341--52665495 Score: 192
Period size: 47 Copynumber: 3.0 Consensus size: 51
52665331 AAGTTATTAA
52665341 GTTATGTAAGTTATGTGAGTTATGATATGATATATATAAG--TT-A-TTAT
1 GTTATGTAAGTTATGTGAGTTATGATATGATATATATAAGTATTAAGTTAT
52665388 GTTATGTAAGTTATGTGAGTTATGATATGATATATATAAGTTATTAAGTTAT
1 GTTATGTAAGTTATGTGAGTTATGATATGATATATATAAG-TATTAAGTTAT
* * *
52665440 GTATGTATGTCAGTTATGTAAGTTATGATCTGATATATATATAAGGTATTAAGTTA
1 G--T-TATGTAAGTTATGTGAGTTATGATATG--ATATATATAA-GTATTAAGTTA
52665496 AGATCCAAAG
Statistics
Matches: 94, Mismatches: 3, Indels: 12
0.86 0.03 0.11
Matches are distributed among these distances:
47 40 0.43
50 2 0.02
51 1 0.01
52 5 0.05
54 1 0.01
55 24 0.26
57 20 0.21
58 1 0.01
ACGTcount: A:0.34, C:0.01, G:0.19, T:0.45
Consensus pattern (51 bp):
GTTATGTAAGTTATGTGAGTTATGATATGATATATATAAGTATTAAGTTAT
Found at i:52665542 original size:9 final size:9
Alignment explanation
Indices: 52665528--52665648 Score: 66
Period size: 9 Copynumber: 13.3 Consensus size: 9
52665518 TCTTTAAAGG
52665528 TATGTAAAT
1 TATGTAAAT
*
52665537 TATGTAAGT
1 TATGTAAAT
* **
52665546 TGTGATATGGT
1 TATG-TA-AAT
52665557 TAT-TAAAT
1 TATGTAAAT
*
52665565 TATGTAAGT
1 TATGTAAAT
* *
52665574 TATGTGAGT
1 TATGTAAAT
52665583 TATGTAAAT
1 TATGTAAAT
*
52665592 TATATAAAT
1 TATGTAAAT
*
52665601 TATGTAATT
1 TATGTAAAT
* *
52665610 TTTG-ATAT
1 TATGTAAAT
* * *
52665618 GATATATATT
1 TATGTA-AAT
*
52665628 TATGTAAGT
1 TATGTAAAT
52665637 TATGTAAAT
1 TATGTAAAT
52665646 TAT
1 TAT
52665649 ATATTCATTT
Statistics
Matches: 82, Mismatches: 25, Indels: 10
0.70 0.21 0.09
Matches are distributed among these distances:
8 7 0.09
9 64 0.78
10 7 0.09
11 4 0.05
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (9 bp):
TATGTAAAT
Found at i:52668176 original size:23 final size:24
Alignment explanation
Indices: 52668133--52668192 Score: 95
Period size: 23 Copynumber: 2.5 Consensus size: 24
52668123 GAAAAACTAG
52668133 ATTGCTTCATTTGTTAATGGACAA
1 ATTGCTTCATTTGTTAATGGACAA
* *
52668157 ATTTCTTCATTT-TTAATGGACAG
1 ATTGCTTCATTTGTTAATGGACAA
52668180 ATTGCTTCATTTG
1 ATTGCTTCATTTG
52668193 AATTGATCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
23 21 0.66
24 11 0.34
ACGTcount: A:0.25, C:0.13, G:0.15, T:0.47
Consensus pattern (24 bp):
ATTGCTTCATTTGTTAATGGACAA
Found at i:52670136 original size:7 final size:7
Alignment explanation
Indices: 52670124--52670370 Score: 79
Period size: 7 Copynumber: 34.7 Consensus size: 7
52670114 CTAATTAATT
52670124 TAAACCC
1 TAAACCC
52670131 TAAACCTC
1 TAAACC-C
52670139 T-AACCC
1 TAAACCC
52670145 TTAAATCCTC
1 -TAAA-CC-C
52670155 TAAACCC
1 TAAACCC
*
52670162 TGAACCC
1 TAAACCC
*
52670169 -AAA-AC
1 TAAACCC
* *
52670174 TCAACTTC
1 TAAAC-CC
*
52670182 TAAACCT
1 TAAACCC
*
52670189 TAAACTC
1 TAAACCC
*
52670196 TAACCCC
1 TAAACCC
52670203 TAAACCC
1 TAAACCC
**
52670210 TAAATAC
1 TAAACCC
52670217 TAAACCC
1 TAAACCC
*
52670224 TTAAATCC
1 -TAAACCC
**
52670232 TAAACTA
1 TAAACCC
*
52670239 TAAACCA
1 TAAACCC
*
52670246 TAATCCC
1 TAAACCC
52670253 TAAACCC
1 TAAACCC
* *
52670260 ATAATCCA
1 -TAAACCC
*
52670268 TAAACCT
1 TAAACCC
***
52670275 TAAATAG
1 TAAACCC
52670282 T-AACTCC
1 TAAAC-CC
*
52670289 TAAACCA
1 TAAACCC
*
52670296 TAAACCA
1 TAAACCC
*
52670303 TAAACCA
1 TAAACCC
****
52670310 TAATTTA
1 TAAACCC
52670317 TAAACCC
1 TAAACCC
***
52670324 TAAATTT
1 TAAACCC
*
52670331 TAAAACC
1 TAAACCC
*
52670338 TAAACCA
1 TAAACCC
*
52670345 TCAACCC
1 TAAACCC
*
52670352 TAAACCA
1 TAAACCC
*
52670359 TCAACCC
1 TAAACCC
52670366 TAAAC
1 TAAAC
52670371 TATAATGATA
Statistics
Matches: 170, Mismatches: 58, Indels: 24
0.67 0.23 0.10
Matches are distributed among these distances:
5 1 0.01
6 7 0.04
7 130 0.76
8 25 0.15
9 6 0.04
10 1 0.01
ACGTcount: A:0.44, C:0.32, G:0.01, T:0.23
Consensus pattern (7 bp):
TAAACCC
Found at i:52670156 original size:16 final size:16
Alignment explanation
Indices: 52670124--52670162 Score: 55
Period size: 17 Copynumber: 2.5 Consensus size: 16
52670114 CTAATTAATT
52670124 TAAACCC-TAAACCTC
1 TAAACCCTTAAACCTC
52670139 T-AACCCTTAAATCCTC
1 TAAACCCTTAAA-CCTC
52670155 TAAACCCT
1 TAAACCCT
52670163 GAACCCAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.24
15 5 0.24
16 5 0.24
17 6 0.29
ACGTcount: A:0.36, C:0.38, G:0.00, T:0.26
Consensus pattern (16 bp):
TAAACCCTTAAACCTC
Found at i:52670219 original size:14 final size:15
Alignment explanation
Indices: 52670202--52670236 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
52670192 ACTCTAACCC
52670202 CTAAACCC-TAAATA
1 CTAAACCCTTAAATA
*
52670216 CTAAACCCTTAAATC
1 CTAAACCCTTAAATA
52670231 CTAAAC
1 CTAAAC
52670237 TATAAACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (15 bp):
CTAAACCCTTAAATA
Found at i:52670263 original size:15 final size:15
Alignment explanation
Indices: 52670238--52670273 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
52670228 ATCCTAAACT
52670238 ATAAA-CCATAATCC
1 ATAAACCCATAATCC
*
52670252 CTAAACCCATAATCC
1 ATAAACCCATAATCC
52670267 ATAAACC
1 ATAAACC
52670274 TTAAATAGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
14 4 0.21
15 15 0.79
ACGTcount: A:0.47, C:0.33, G:0.00, T:0.19
Consensus pattern (15 bp):
ATAAACCCATAATCC
Found at i:52670276 original size:50 final size:50
Alignment explanation
Indices: 52670200--52670357 Score: 126
Period size: 49 Copynumber: 3.2 Consensus size: 50
52670190 AAACTCTAAC
* *
52670200 CCCTAAACCC-TAAATAC-TAAACCCTTAAATCCTAAACT-ATAAACCATAAT
1 CCCTAAACCCAT-AATACATAAA-CCTTAAATACT-AACTCATAAACCATAAA
* * *
52670250 CCCTAAACCCATAATCCATAAACCTTAAATAGTAACTCCTAAACCATAAA
1 CCCTAAACCCATAATACATAAACCTTAAATACTAACTCATAAACCATAAA
* ** * ** ** * *
52670300 CCATAAA-CCATAATTTATAAACCCTAAATTTTAAAACCTAAACCATCAA
1 CCCTAAACCCATAATACATAAACCTTAAATACTAACTCATAAACCATAAA
52670349 CCCTAAACC
1 CCCTAAACC
52670358 ATCAACCCTA
Statistics
Matches: 89, Mismatches: 15, Indels: 8
0.79 0.13 0.07
Matches are distributed among these distances:
49 44 0.49
50 40 0.45
51 5 0.06
ACGTcount: A:0.46, C:0.30, G:0.01, T:0.23
Consensus pattern (50 bp):
CCCTAAACCCATAATACATAAACCTTAAATACTAACTCATAAACCATAAA
Found at i:52670340 original size:49 final size:49
Alignment explanation
Indices: 52670239--52670359 Score: 143
Period size: 49 Copynumber: 2.4 Consensus size: 49
52670229 TCCTAAACTA
* * **
52670239 TAAACCATAATCCCTAAACCCATAATCCATAAACCTTAAATAGTAACTCC
1 TAAACCATAAACCCTAAA-CCATAATCCATAAACCCTAAATAGTAAAACC
* ** **
52670289 TAAACCATAAACCATAAACCATAATTTATAAACCCTAAATTTTAAAACC
1 TAAACCATAAACCCTAAACCATAATCCATAAACCCTAAATAGTAAAACC
*
52670338 TAAACCATCAACCCTAAACCAT
1 TAAACCATAAACCCTAAACCAT
52670360 CAACCCTAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
49 44 0.73
50 16 0.27
ACGTcount: A:0.47, C:0.28, G:0.01, T:0.24
Consensus pattern (49 bp):
TAAACCATAAACCCTAAACCATAATCCATAAACCCTAAATAGTAAAACC
Found at i:52670707 original size:40 final size:39
Alignment explanation
Indices: 52670651--52670756 Score: 149
Period size: 40 Copynumber: 2.6 Consensus size: 39
52670641 TTCTTTACTA
52670651 CGTTTTTCAAAGAGCGCCGCTAATGCTCGACCTATAGCGG
1 CGTTTTTCAAA-AGCGCCGCTAATGCTCGACCTATAGCGG
** * *
52670691 CGTTTTTCAACAAGCGCAACTAATGATCGACCTATAGTGG
1 CGTTTTTCAA-AAGCGCCGCTAATGCTCGACCTATAGCGG
52670731 CGTTTTTCAAAAAGCGCCGCTAATGC
1 CGTTTTTC-AAAAGCGCCGCTAATGC
52670757 CACTAAAGCT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
40 54 0.95
41 3 0.05
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.26
Consensus pattern (39 bp):
CGTTTTTCAAAAGCGCCGCTAATGCTCGACCTATAGCGG
Found at i:52673890 original size:24 final size:25
Alignment explanation
Indices: 52673845--52673902 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
52673835 TAAAAATACT
*
52673845 AAAAATATTAAAATACATGTTTTCC
1 AAAAATATTAAAATACAAGTTTTCC
**
52673870 AAAAA-ATTGAAAATA-AAGTTTTTT
1 AAAAATATT-AAAATACAAGTTTTCC
52673894 AAAAATATT
1 AAAAATATT
52673903 TATACTTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (25 bp):
AAAAATATTAAAATACAAGTTTTCC
Found at i:52677751 original size:19 final size:21
Alignment explanation
Indices: 52677706--52677751 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
52677696 CATGATGAAT
52677706 TGATGTTGAATTGAGAATGATG
1 TGATGTTGAATT-AGAATGATG
* *
52677728 GGATG-TGAATT-GAATTATG
1 TGATGTTGAATTAGAATGATG
52677747 TGATG
1 TGATG
52677752 ATATTGCAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
19 11 0.52
21 6 0.29
22 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.33, T:0.37
Consensus pattern (21 bp):
TGATGTTGAATTAGAATGATG
Found at i:52678003 original size:138 final size:138
Alignment explanation
Indices: 52677753--52678031 Score: 540
Period size: 138 Copynumber: 2.0 Consensus size: 138
52677743 TATGTGATGA
52677753 TATTGCAAATTGGTTACTCTATTAAATGTACAGGGCTATATTTCGGGTTAACTGATGATACATTA
1 TATTGCAAATTGGTTACTCTATTAAATGTACAGGGCTATATTTCGGGTTAACTGATGATACATTA
* *
52677818 CGGGTACCAGTTTGAAATGCAGATTGACTAATTCTAGTATCCTTCTTGAAAGCCCGATTCAGGTT
66 CGGGTACCAGTTTGAAATGCAGATTGACTAATTCTAGTATCCGTCTTGAAAGCCCGATTCAAGTT
52677883 AATAGGAT
131 AATAGGAT
52677891 TATTGCAAATTGGTTACTCTATTAAATGTACAGGGCTATATTTCGGGTTAACTGATGATACATTA
1 TATTGCAAATTGGTTACTCTATTAAATGTACAGGGCTATATTTCGGGTTAACTGATGATACATTA
52677956 CGGGTACCAGTTTGAAATGCAGATTGACTAATTCTAGTATCCGTCTTGAAAGCCCGATTCAAGTT
66 CGGGTACCAGTTTGAAATGCAGATTGACTAATTCTAGTATCCGTCTTGAAAGCCCGATTCAAGTT
52678021 AATAGGAT
131 AATAGGAT
52678029 TAT
1 TAT
52678032 ATCAATGTGT
Statistics
Matches: 139, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 139 1.00
ACGTcount: A:0.30, C:0.15, G:0.20, T:0.35
Consensus pattern (138 bp):
TATTGCAAATTGGTTACTCTATTAAATGTACAGGGCTATATTTCGGGTTAACTGATGATACATTA
CGGGTACCAGTTTGAAATGCAGATTGACTAATTCTAGTATCCGTCTTGAAAGCCCGATTCAAGTT
AATAGGAT
Found at i:52688551 original size:158 final size:158
Alignment explanation
Indices: 52688365--52688661 Score: 429
Period size: 158 Copynumber: 1.9 Consensus size: 158
52688355 AATATGAAAA
52688365 AAAATAAAAAAAACAAAAATAGTATATTTACTGAAAGTAATAAAATCCAGAAAA-AAGAAAAATA
1 AAAATAAAAAAAACAAAAATAGTATATTTACTGAAAGTAATAAAATCC-GAAAATAAGAAAAATA
* * * *
52688429 CGAACAAAGGGCCAAAAT-AAGGGTTTTTCACTAAATTTATAT-AAAAAATACATTAAAATAATA
65 CGAACAAAGAGCCAAAATGAA-GATTTTTCACTAAATTTATATAAAAAAACACACTAAAATAATA
52688492 AATTTCAAACATTATGTACTAAAATAATAT
129 AATTTCAAACATTATGTACTAAAATAATAT
* * **
52688522 AAAATAATAAAATACGAAAATAGTATATTTTTTGAAAGTAATAAAATCCGAAAATAAGAAAAATA
1 AAAATAA-AAAAAACAAAAATAGTATATTTACTGAAAGTAATAAAATCCGAAAATAAGAAAAATA
* * * *
52688587 CGAACAAATAGCCAAAATGAAGATTTTTTACTAAATTTATATAAAAAAACACACTAAATTAATAC
65 CGAACAAAGAGCCAAAATGAAGATTTTTCACTAAATTTATATAAAAAAACACACTAAAATAATAA
*
52688652 ATTTTAAACA
130 ATTTCAAACA
52688662 CACTAAATTA
Statistics
Matches: 123, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
157 12 0.10
158 82 0.67
159 29 0.24
ACGTcount: A:0.57, C:0.09, G:0.08, T:0.27
Consensus pattern (158 bp):
AAAATAAAAAAAACAAAAATAGTATATTTACTGAAAGTAATAAAATCCGAAAATAAGAAAAATAC
GAACAAAGAGCCAAAATGAAGATTTTTCACTAAATTTATATAAAAAAACACACTAAAATAATAAA
TTTCAAACATTATGTACTAAAATAATAT
Found at i:52688664 original size:24 final size:25
Alignment explanation
Indices: 52688633--52688682 Score: 93
Period size: 24 Copynumber: 2.0 Consensus size: 25
52688623 TTATATAAAA
52688633 AAACACACTAAATTAATAC-ATTTT
1 AAACACACTAAATTAATACTATTTT
52688657 AAACACACTAAATTAATACTATTTT
1 AAACACACTAAATTAATACTATTTT
52688682 A
1 A
52688683 TTATTTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 19 0.76
25 6 0.24
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (25 bp):
AAACACACTAAATTAATACTATTTT
Found at i:52688917 original size:158 final size:154
Alignment explanation
Indices: 52688676--52688996 Score: 459
Period size: 158 Copynumber: 2.1 Consensus size: 154
52688666 AAATTAATAC
* *
52688676 TATTTTATTATTTTATATTATTTTATTACATAAAGTTTGAAATGTATTAATTTAGTGTGTGTTTT
1 TATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTCTTTT
*
52688741 TATATAAATTTAGTAAAAAACCCTCATTTTGGCCATTTG-TTCGTATTTTTCTTATTCTCGGATT
66 TATATAAATTTAGT-AAAAACCCTCATTTTGGCCATTTGTTTC-TA-TTTT-TT-TTC-CGAATT
52688805 TTATTACTTTCA-AAAATATACTATTTTCG
125 TTATTACTTTCAGAAAATATACTATTTTCG
* *
52688834 TATTTTATTATTTTATATTATTTTAGTACATAATGTTTGAAATGTATTATTTTAGTGTG-CTTTT
1 TATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTCTTTT
* * *
52688898 TATATAAATTTAGTGAAAAACCTTTATTTTGGCCCTTTGTTTCTATTTTTTTTCCGAATTTTATT
66 TATATAAATTTAGT-AAAAACCCTCATTTTGGCCATTTGTTTCTATTTTTTTTCCGAATTTTATT
* *
52688963 ACTTTCAGTAAATATCCTATTTTCG
130 ACTTTCAGAAAATATACTATTTTCG
*
52688988 TAATTTATT
1 TATTTTATT
52688997 TCTTTTCGTA
Statistics
Matches: 149, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
153 17 0.11
154 26 0.17
155 2 0.01
156 4 0.03
157 41 0.28
158 59 0.40
ACGTcount: A:0.28, C:0.09, G:0.09, T:0.54
Consensus pattern (154 bp):
TATTTTATTATTTTATATTATTTTAGTACATAAAGTTTGAAATGTATTAATTTAGTGTGTCTTTT
TATATAAATTTAGTAAAAACCCTCATTTTGGCCATTTGTTTCTATTTTTTTTCCGAATTTTATTA
CTTTCAGAAAATATACTATTTTCG
Found at i:52689592 original size:18 final size:18
Alignment explanation
Indices: 52689569--52689604 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
52689559 ATTGATAAAA
52689569 ATTAAAAATTATTACTTT
1 ATTAAAAATTATTACTTT
52689587 ATTAAAAATTATTACTTT
1 ATTAAAAATTATTACTTT
52689605 TAAATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTAAAAATTATTACTTT
Found at i:52711703 original size:6 final size:6
Alignment explanation
Indices: 52711692--52711731 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
52711682 AAATAATTAT
52711692 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTTA TATT
52711732 AAATCACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
TATTTA
Found at i:52712461 original size:45 final size:46
Alignment explanation
Indices: 52712404--52712494 Score: 130
Period size: 45 Copynumber: 2.0 Consensus size: 46
52712394 CATTTTAATT
*
52712404 TATTAATATTTAAATAAATTACATAGTATTTAATACAAATTATTTA
1 TATTAATATTTAAATAAATTACATAATATTTAATACAAATTATTTA
* * **
52712450 TATTAAT-TTTAACTAAATTACATAATATTTATTATTAATTATTTA
1 TATTAATATTTAAATAAATTACATAATATTTAATACAAATTATTTA
52712495 AACTTTGTTG
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 33 0.82
46 7 0.17
ACGTcount: A:0.45, C:0.04, G:0.01, T:0.49
Consensus pattern (46 bp):
TATTAATATTTAAATAAATTACATAATATTTAATACAAATTATTTA
Found at i:52713925 original size:23 final size:21
Alignment explanation
Indices: 52713883--52713925 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
52713873 AATCTAACAA
*
52713883 TAATATAAATAATATGTATAG
1 TAATATAAATAAAATGTATAG
52713904 TAATATATAATAAAATGCTATA
1 TAATATA-AATAAAATG-TATA
52713926 AACAGAGTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 7 0.37
22 8 0.42
23 4 0.21
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.37
Consensus pattern (21 bp):
TAATATAAATAAAATGTATAG
Found at i:52715778 original size:21 final size:20
Alignment explanation
Indices: 52715737--52715787 Score: 50
Period size: 20 Copynumber: 2.5 Consensus size: 20
52715727 ACTTGTGTAG
**
52715737 ATTGATTTTTTTCAAGGATT
1 ATTGATTTTTTTCAAAAATT
*
52715757 ATTGCTTTTTTTACAAAAATT
1 ATTGATTTTTTT-CAAAAATT
*
52715778 AAT-ATTTTTT
1 ATTGATTTTTT
52715788 AGAATTTAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 17 0.68
21 8 0.32
ACGTcount: A:0.29, C:0.06, G:0.08, T:0.57
Consensus pattern (20 bp):
ATTGATTTTTTTCAAAAATT
Found at i:52727366 original size:41 final size:42
Alignment explanation
Indices: 52727305--52727389 Score: 129
Period size: 41 Copynumber: 2.0 Consensus size: 42
52727295 CAAAAAAAAA
*
52727305 TTCAAAAATCCCAAAAATATTTTCCATT-TTCGTTTTTAATTT
1 TTCAAAAATCCCAAAAATATTTTCC-TTCTTCATTTTTAATTT
*
52727347 TTCAAAAAT-CCAAAAATATTTTCCTTCTTTATTTTTAATTT
1 TTCAAAAATCCCAAAAATATTTTCCTTCTTCATTTTTAATTT
52727388 TT
1 TT
52727390 GTTATTGCAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
40 2 0.05
41 29 0.73
42 9 0.22
ACGTcount: A:0.33, C:0.15, G:0.01, T:0.51
Consensus pattern (42 bp):
TTCAAAAATCCCAAAAATATTTTCCTTCTTCATTTTTAATTT
Found at i:52730594 original size:13 final size:13
Alignment explanation
Indices: 52730557--52730607 Score: 57
Period size: 13 Copynumber: 3.9 Consensus size: 13
52730547 TTTAGCAATG
*
52730557 CTTTTGAAAAGTG
1 CTTTTGAAAAGTA
* *
52730570 CTGTGGAAAAGTA
1 CTTTTGAAAAGTA
* *
52730583 CTTTTGAGAAGTC
1 CTTTTGAAAAGTA
52730596 CTTTTGAAAAGT
1 CTTTTGAAAAGT
52730608 TTGGTTTAAG
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (13 bp):
CTTTTGAAAAGTA
Found at i:52730604 original size:26 final size:26
Alignment explanation
Indices: 52730557--52730607 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 26
52730547 TTTAGCAATG
*
52730557 CTTTTGAAAAGTGCTGTGGAAAAGTA
1 CTTTTGAAAAGTCCTGTGGAAAAGTA
* * *
52730583 CTTTTGAGAAGTCCTTTTGAAAAGT
1 CTTTTGAAAAGTCCTGTGGAAAAGT
52730608 TTGGTTTAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.31, C:0.10, G:0.24, T:0.35
Consensus pattern (26 bp):
CTTTTGAAAAGTCCTGTGGAAAAGTA
Found at i:52731112 original size:13 final size:13
Alignment explanation
Indices: 52731065--52731111 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
52731055 TAGCTTATCC
*
52731065 TTTTCAGAAGTGT
1 TTTTCAAAAGTGT
52731078 TTTTCAAAAGTGT
1 TTTTCAAAAGTGT
*
52731091 TTTTCAAAAGTGC
1 TTTTCAAAAGTGT
52731104 TTTT-AAAA
1 TTTTCAAAA
52731112 AACCAAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
12 4 0.12
13 28 0.88
ACGTcount: A:0.32, C:0.09, G:0.15, T:0.45
Consensus pattern (13 bp):
TTTTCAAAAGTGT
Found at i:52731707 original size:21 final size:19
Alignment explanation
Indices: 52731683--52731724 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 19
52731673 ATAACTTTTA
52731683 ATGTTTACATTATAATATTAT
1 ATGTTTA-ATT-TAATATTAT
*
52731704 ATGTTTAATTTAATTTTAT
1 ATGTTTAATTTAATATTAT
52731723 AT
1 AT
52731725 AAATTACATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 10 0.50
20 3 0.15
21 7 0.35
ACGTcount: A:0.36, C:0.02, G:0.05, T:0.57
Consensus pattern (19 bp):
ATGTTTAATTTAATATTAT
Found at i:52736355 original size:2 final size:2
Alignment explanation
Indices: 52736348--52736394 Score: 76
Period size: 2 Copynumber: 23.5 Consensus size: 2
52736338 TCATCTTTCT
* *
52736348 TC TC TC TC TC TC TC TC TC TC TC GC TC TC TC TC GC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
52736390 TC TC T
1 TC TC T
52736395 GTCACTAAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.04, T:0.47
Consensus pattern (2 bp):
TC
Found at i:52741206 original size:3 final size:3
Alignment explanation
Indices: 52741200--52741230 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
52741190 CGAAAGAAGA
*
52741200 AGG AGG AGG AGG AGG AGG AGG AGG TGG AGG A
1 AGG AGG AGG AGG AGG AGG AGG AGG AGG AGG A
52741231 TAGTATAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.65, T:0.03
Consensus pattern (3 bp):
AGG
Found at i:52744285 original size:9 final size:9
Alignment explanation
Indices: 52744193--52744406 Score: 101
Period size: 9 Copynumber: 22.2 Consensus size: 9
52744183 ATCATTTAAT
52744193 AATTATAAAA
1 AATTAT-AAA
* *
52744203 AATCAAAAA
1 AATTATAAA
52744212 AATTATAAGA
1 AATTATAA-A
**
52744222 AGGTATAAA
1 AATTATAAA
* *
52744231 TATTAT-TA
1 AATTATAAA
52744239 AATGT-TAAA
1 AAT-TATAAA
*
52744248 AATATATTAA
1 AAT-TATAAA
*
52744258 TATTAATATAA
1 AATT-ATA-AA
*
52744269 ACTTATAAA
1 AATTATAAA
52744278 AATTATAATA
1 AATTATAA-A
52744288 AATTATAAA
1 AATTATAAA
52744297 AATTATAAA
1 AATTATAAA
52744306 AATTAT-AA
1 AATTATAAA
52744314 AATTAATAAA
1 AATT-ATAAA
*
52744324 ATATATTTAAA
1 A-AT-TATAAA
*
52744335 ATTTTATAAAAA
1 A-ATTAT--AAA
*
52744347 AATGTATTAA
1 AAT-TATAAA
*
52744357 ATTCTATAAA
1 AAT-TATAAA
*
52744367 AATCATAAA
1 AATTATAAA
* *
52744376 AAGTATTAA
1 AATTATAAA
52744385 AATTAATATAA
1 AATT-ATA-AA
*
52744396 ACTTATAAA
1 AATTATAAA
52744405 AA
1 AA
52744407 CATATATAAA
Statistics
Matches: 152, Mismatches: 36, Indels: 33
0.69 0.16 0.15
Matches are distributed among these distances:
8 10 0.07
9 64 0.42
10 51 0.34
11 19 0.12
12 8 0.05
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (9 bp):
AATTATAAA
Found at i:52744295 original size:19 final size:19
Alignment explanation
Indices: 52744265--52744315 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
52744255 TAATATTAAT
52744265 ATAAACTTATAAAAATTATA
1 ATAAA-TTATAAAAATTATA
52744285 ATAAATTATAAAAATTATA
1 ATAAATTATAAAAATTATA
52744304 A-AAATTATAAAA
1 ATAAATTATAAAA
52744316 TTAATAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.35
19 15 0.48
20 5 0.16
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATAAATTATAAAAATTATA
Found at i:52744354 original size:24 final size:22
Alignment explanation
Indices: 52744321--52744368 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
52744311 TAAAATTAAT
*
52744321 AAAATATATTTAAAATTTTATAAA
1 AAAATATA-TT-AAATTCTATAAA
*
52744345 AAAATGTATTAAATTCTATAAA
1 AAAATATATTAAATTCTATAAA
52744367 AA
1 AA
52744369 TCATAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
22 13 0.59
23 2 0.09
24 7 0.32
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (22 bp):
AAAATATATTAAATTCTATAAA
Found at i:52744878 original size:9 final size:9
Alignment explanation
Indices: 52744869--52744967 Score: 62
Period size: 9 Copynumber: 10.8 Consensus size: 9
52744859 AATTTAAATT
52744869 ATTTTTATTA
1 ATTTTTA-TA
*
52744879 A-TTTTACA
1 ATTTTTATA
52744887 ATTAATTTATA
1 ATT--TTTATA
*
52744898 ATTTATTA-G
1 ATTT-TTATA
52744907 ATTTTTAT-
1 ATTTTTATA
52744915 ATTTTTATA
1 ATTTTTATA
*
52744924 ATATTTATA
1 ATTTTTATA
*
52744933 ATTTTAATA
1 ATTTTTATA
*
52744942 AGTTTATATCA
1 A-TTTTTAT-A
*
52744953 ATTTTAAT-
1 ATTTTTATA
52744961 ATTTTTA
1 ATTTTTA
52744968 AATATTTAAT
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
8 19 0.27
9 27 0.39
10 14 0.20
11 10 0.14
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (9 bp):
ATTTTTATA
Found at i:52744967 original size:20 final size:19
Alignment explanation
Indices: 52744930--52744983 Score: 58
Period size: 20 Copynumber: 2.9 Consensus size: 19
52744920 TATAATATTT
** *
52744930 ATAATTTTAATAAGTTTAT
1 ATAATTTTAATATTTTTAA
52744949 ATCAATTTTAATATTTTTAA
1 AT-AATTTTAATATTTTTAA
52744969 AT-A-TTTAATATTTTT
1 ATAATTTTAATATTTTT
52744984 TTTCTATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
17 12 0.39
18 1 0.03
19 2 0.06
20 16 0.52
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
ATAATTTTAATATTTTTAA
Found at i:52750601 original size:27 final size:27
Alignment explanation
Indices: 52750552--52750603 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
52750542 CGAGATTTGA
**
52750552 GATTCGAGTTTAAAGTTTGGGGTTTAT
1 GATTCGAGTTTAAAGTTCAGGGTTTAT
*
52750579 GATTCGGGTTTAAAGTTCAGGGTTT
1 GATTCGAGTTTAAAGTTCAGGGTTT
52750604 TAGGATTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.21, C:0.06, G:0.31, T:0.42
Consensus pattern (27 bp):
GATTCGAGTTTAAAGTTCAGGGTTTAT
Found at i:52754665 original size:6 final size:6
Alignment explanation
Indices: 52754654--52754679 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
52754644 ATTATAAGTC
52754654 AAAGCT AAAGCT AAAGCT AAAGCT AA
1 AAAGCT AAAGCT AAAGCT AAAGCT AA
52754680 GATAATGTCT
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:0.54, C:0.15, G:0.15, T:0.15
Consensus pattern (6 bp):
AAAGCT
Found at i:52764568 original size:51 final size:51
Alignment explanation
Indices: 52764486--52764607 Score: 201
Period size: 51 Copynumber: 2.4 Consensus size: 51
52764476 TCTAATCCTC
52764486 TCAATTTCCT-TCCAATTTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
1 TCAATTTCCTCT-CAA-TTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
*
52764538 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAATCCATATTTAATT
1 TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
*
52764589 TCAATTTCCCCTCAATTTC
1 TCAATTTCCTCTCAATTTC
52764608 ATTTTTTAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 3
0.93 0.03 0.04
Matches are distributed among these distances:
51 53 0.79
52 13 0.19
53 1 0.01
ACGTcount: A:0.28, C:0.30, G:0.00, T:0.43
Consensus pattern (51 bp):
TCAATTTCCTCTCAATTTCCTTCCAAAATTCTCTCAAACCCATATTTAATT
Found at i:52764635 original size:10 final size:10
Alignment explanation
Indices: 52764608--52764674 Score: 53
Period size: 10 Copynumber: 6.5 Consensus size: 10
52764598 CCTCAATTTC
*
52764608 ATTTTTTAAA
1 ATTTTTTTAA
**
52764618 ATAATTTTAA
1 ATTTTTTTAA
52764628 ATTTTTTTATA
1 ATTTTTTTA-A
*
52764639 TTTTTTTTAAA
1 ATTTTTTT-AA
**
52764650 ATAATTTTAA
1 ATTTTTTTAA
*
52764660 ATTTTTTTAT
1 ATTTTTTTAA
52764670 ATTTT
1 ATTTT
52764675 CATCAATGGC
Statistics
Matches: 43, Mismatches: 12, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
10 28 0.65
11 14 0.33
12 1 0.02
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (10 bp):
ATTTTTTTAA
Found at i:52764650 original size:32 final size:32
Alignment explanation
Indices: 52764609--52764674 Score: 132
Period size: 32 Copynumber: 2.1 Consensus size: 32
52764599 CTCAATTTCA
52764609 TTTTTTAAAATAATTTTAAATTTTTTTATATT
1 TTTTTTAAAATAATTTTAAATTTTTTTATATT
52764641 TTTTTTAAAATAATTTTAAATTTTTTTATATT
1 TTTTTTAAAATAATTTTAAATTTTTTTATATT
52764673 TT
1 TT
52764675 CATCAATGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (32 bp):
TTTTTTAAAATAATTTTAAATTTTTTTATATT
Found at i:52764651 original size:22 final size:21
Alignment explanation
Indices: 52764622--52764667 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
52764612 TTTAAAATAA
** *
52764622 TTTTAAATTTTTTTATATTTT
1 TTTTAAATAATTTTAAATTTT
52764643 TTTTAAAATAATTTTAAATTTT
1 TTTT-AAATAATTTTAAATTTT
52764665 TTT
1 TTT
52764668 ATATTTTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTAAATAATTTTAAATTTT
Found at i:52765767 original size:7 final size:7
Alignment explanation
Indices: 52765755--52765779 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52765745 AGTCGATTGA
52765755 TATTTAG
1 TATTTAG
52765762 TATTTAG
1 TATTTAG
52765769 TATTTAG
1 TATTTAG
52765776 TATT
1 TATT
52765780 ATGTATATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.60
Consensus pattern (7 bp):
TATTTAG
Found at i:52766457 original size:18 final size:18
Alignment explanation
Indices: 52766431--52766465 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
52766421 AAGTGTGTTT
* *
52766431 CCTAGCCCTTATATGTAC
1 CCTAACCCTTACATGTAC
52766449 CCTAACCCTTACATGTA
1 CCTAACCCTTACATGTA
52766466 TCCTTTTCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.34, G:0.09, T:0.31
Consensus pattern (18 bp):
CCTAACCCTTACATGTAC
Found at i:52766955 original size:71 final size:71
Alignment explanation
Indices: 52766867--52767051 Score: 325
Period size: 71 Copynumber: 2.6 Consensus size: 71
52766857 TATTTAAATT
52766867 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
52766932 TTTTGA
66 TTTTGA
* * *
52766938 TATTATTTGATGTAATAAAATATAAGTTTATTTGATATAATAGGCATAGAAATTTTTTCGAGTTA
1 TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
52767003 TTTTGA
66 TTTTGA
*
52767009 TATTATTTGATATAATAAAATAGAAGTTCTATTTGATGTAATA
1 TATTATTTGATGTAATAAAATAGAAGTT-TATTTGATGTAATA
52767052 AAAACCCTAA
Statistics
Matches: 107, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
71 94 0.88
72 13 0.12
ACGTcount: A:0.37, C:0.03, G:0.14, T:0.45
Consensus pattern (71 bp):
TATTATTTGATGTAATAAAATAGAAGTTTATTTGATGTAATACGCATAGAAATTTTTTCGAGTTA
TTTTGA
Found at i:52767090 original size:29 final size:29
Alignment explanation
Indices: 52767054--52767149 Score: 156
Period size: 29 Copynumber: 3.3 Consensus size: 29
52767044 ATGTAATAAA
*
52767054 AACCCTAACTTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
52767083 AATCCTAACCTAATTTAATTAAAAACCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
*
52767112 AACCCTAACCTAATTTAATTAAAAATCCT
1 AACCCTAACCTAATTTAATTAAAAACCCT
52767141 AAACCCTAA
1 -AACCCTAA
52767150 ACCCTAAAAG
Statistics
Matches: 62, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 54 0.87
30 8 0.13
ACGTcount: A:0.46, C:0.25, G:0.00, T:0.29
Consensus pattern (29 bp):
AACCCTAACCTAATTTAATTAAAAACCCT
Found at i:52769205 original size:14 final size:15
Alignment explanation
Indices: 52769174--52769224 Score: 50
Period size: 14 Copynumber: 3.3 Consensus size: 15
52769164 AAAAAGTAAA
**
52769174 AAAAATTAAAATTTT
1 AAAAATTAAAATAAT
52769189 AAAAA-TAAAATAAT
1 AAAAATTAAAATAAT
52769203 AAAGAATTACAAATATAT
1 AAA-AATTA-AAATA-AT
52769221 AAAA
1 AAAA
52769225 TAATACCAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
14 10 0.33
15 7 0.23
16 2 0.07
17 6 0.20
18 5 0.17
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (15 bp):
AAAAATTAAAATAAT
Found at i:52784722 original size:40 final size:38
Alignment explanation
Indices: 52784677--52784754 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 38
52784667 TTGTCATATG
**
52784677 ACATTAATTTAAAATATGATTATTGTAGCTTAAAAAACTT
1 ACATTAATGCAAAATA--ATTATTGTAGCTTAAAAAACTT
* *
52784717 ACATTAATGCGACATAATTATTGTAGCTTAAAAAACTT
1 ACATTAATGCAAAATAATTATTGTAGCTTAAAAAACTT
52784755 GACCTACAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 22 0.65
40 12 0.35
ACGTcount: A:0.44, C:0.10, G:0.09, T:0.37
Consensus pattern (38 bp):
ACATTAATGCAAAATAATTATTGTAGCTTAAAAAACTT
Found at i:52792345 original size:13 final size:13
Alignment explanation
Indices: 52792327--52792352 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
52792317 GTTCAATTTT
52792327 TTTACTAGAAAAC
1 TTTACTAGAAAAC
52792340 TTTACTAGAAAAC
1 TTTACTAGAAAAC
52792353 AAATCTCTTT
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:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:52794219 original size:5 final size:5
Alignment explanation
Indices: 52794209--52794237 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
52794199 GAGAATTGTG
52794209 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAA
52794238 GTGAAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:52804583 original size:129 final size:129
Alignment explanation
Indices: 52804344--52804632 Score: 470
Period size: 129 Copynumber: 2.2 Consensus size: 129
52804334 AATTCTTCGG
* * * *
52804344 TCTATTCCACTGTAATCTTAGGGAGATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGA
1 TCTACTCCGCTGTAATCTCAGGGAGATAAGACCTGATGCGATATACTCTACTGTAACTTCAGAGA
52804409 GATAAAATCCTTTATTTTAATCCGTTCCACTGTAATATCAGGGAAATAAGATTACTGGCTTCAA
66 GATAAAATCCTTTATTTTAATCCGTTCCACTGTAATATCAGGGAAATAAGATTACTGGCTTCAA
* * *
52804473 TCTGCTCCGCTGTAATCTCAGAGCGATAAGACCTGATGCGATATACTCTACTGTAACTTCAGAGA
1 TCTACTCCGCTGTAATCTCAGGGAGATAAGACCTGATGCGATATACTCTACTGTAACTTCAGAGA
* * * *
52804538 GATAAGATTCTTTATTTTAATTCGTTCCACTGTAATATCAGGGAAATAGGATTACTGGCTTCAA
66 GATAAAATCCTTTATTTTAATCCGTTCCACTGTAATATCAGGGAAATAAGATTACTGGCTTCAA
*
52804602 TCTACTCCGCTGTAATCTCAGGGGGATAAGA
1 TCTACTCCGCTGTAATCTCAGGGAGATAAGA
52804633 TCTGTAATTC
Statistics
Matches: 146, Mismatches: 14, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
129 146 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (129 bp):
TCTACTCCGCTGTAATCTCAGGGAGATAAGACCTGATGCGATATACTCTACTGTAACTTCAGAGA
GATAAAATCCTTTATTTTAATCCGTTCCACTGTAATATCAGGGAAATAAGATTACTGGCTTCAA
Found at i:52820892 original size:15 final size:15
Alignment explanation
Indices: 52820883--52820915 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
52820873 CAAATGCTAT
52820883 AATAATAAATACAAC
1 AATAATAAATACAAC
*
52820898 AATAATAAATACATC
1 AATAATAAATACAAC
52820913 AAT
1 AAT
52820916 GTCATATCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (15 bp):
AATAATAAATACAAC
Found at i:52821124 original size:28 final size:27
Alignment explanation
Indices: 52821088--52821148 Score: 70
Period size: 26 Copynumber: 2.2 Consensus size: 27
52821078 GAAGGCACAT
* *
52821088 AATATATACATTAATATGAATATAAAAAA
1 AATATATACACT--TATGAACATAAAAAA
*
52821117 AATA-ATACACTTATGAACATAAGAAA
1 AATATATACACTTATGAACATAAAAAA
52821143 AATATA
1 AATATA
52821149 AAAATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 17 0.61
27 1 0.04
28 6 0.21
29 4 0.14
ACGTcount: A:0.61, C:0.07, G:0.05, T:0.28
Consensus pattern (27 bp):
AATATATACACTTATGAACATAAAAAA
Found at i:52821387 original size:3 final size:3
Alignment explanation
Indices: 52821368--52821414 Score: 58
Period size: 3 Copynumber: 15.3 Consensus size: 3
52821358 GTGCATGAAT
* * *
52821368 ATA AAA ATA AAA ATA ATA ATAA ATA ATA ATA ATA ATA ATG ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
52821414 A
1 A
52821415 ATAACAATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (3 bp):
ATA
Found at i:52821393 original size:16 final size:16
Alignment explanation
Indices: 52821368--52821405 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
52821358 GTGCATGAAT
52821368 ATAA-AAATAAAAATA
1 ATAATAAATAAAAATA
*
52821383 ATAATAAATAATAATA
1 ATAATAAATAAAAATA
52821399 ATAATAA
1 ATAATAA
52821406 TGATAATAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (16 bp):
ATAATAAATAAAAATA
Found at i:52821396 original size:25 final size:25
Alignment explanation
Indices: 52821368--52821418 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
52821358 GTGCATGAAT
52821368 ATAAAAATAAAAATAATAATAAATA
1 ATAAAAATAAAAATAATAATAAATA
* * *
52821393 ATAATAATAATAATGATAATAAATA
1 ATAAAAATAAAAATAATAATAAATA
52821418 A
1 A
52821419 CAATTTTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (25 bp):
ATAAAAATAAAAATAATAATAAATA
Found at i:52821398 original size:22 final size:22
Alignment explanation
Indices: 52821368--52821415 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
52821358 GTGCATGAAT
52821368 ATAAAAATAAAAATAATAATAA
1 ATAAAAATAAAAATAATAATAA
* * *
52821390 ATAATAATAATAATAATGAT-A
1 ATAAAAATAAAAATAATAATAA
52821411 ATAAA
1 ATAAA
52821416 TAACAATTTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (22 bp):
ATAAAAATAAAAATAATAATAA
Found at i:52821552 original size:63 final size:63
Alignment explanation
Indices: 52821453--52821579 Score: 254
Period size: 63 Copynumber: 2.0 Consensus size: 63
52821443 AATTGCAAAG
52821453 AAAACGTAATTAAAACAAAATGGAGGGCCGAATTGCGATGCGCGCATTATATGAGGGTCCTAA
1 AAAACGTAATTAAAACAAAATGGAGGGCCGAATTGCGATGCGCGCATTATATGAGGGTCCTAA
52821516 AAAACGTAATTAAAACAAAATGGAGGGCCGAATTGCGATGCGCGCATTATATGAGGGTCCTAA
1 AAAACGTAATTAAAACAAAATGGAGGGCCGAATTGCGATGCGCGCATTATATGAGGGTCCTAA
52821579 A
1 A
52821580 TGGAAATAAT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.20
Consensus pattern (63 bp):
AAAACGTAATTAAAACAAAATGGAGGGCCGAATTGCGATGCGCGCATTATATGAGGGTCCTAA
Found at i:52822110 original size:6 final size:6
Alignment explanation
Indices: 52822075--52822103 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
52822065 TTTGTTTGTA
52822075 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
52822104 AATAAAAGCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:52823618 original size:19 final size:20
Alignment explanation
Indices: 52823560--52823619 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
52823550 CAACTCTTTA
52823560 AAAAACAATTTAACTTGATTG
1 AAAAA-AATTTAACTTGATTG
*
52823581 AAAAAAATTCTAACATGATTG
1 AAAAAAATT-TAACTTGATTG
**
52823602 -AAATCATTTAACTTGATT
1 AAAAAAATTTAACTTGATT
52823620 TGGAAATTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 9 0.26
20 10 0.29
21 15 0.44
ACGTcount: A:0.47, C:0.10, G:0.08, T:0.35
Consensus pattern (20 bp):
AAAAAAATTTAACTTGATTG
Found at i:52823959 original size:14 final size:14
Alignment explanation
Indices: 52823940--52823986 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
52823930 TCCATTTGAT
*
52823940 TTCTTTCTTTCTTC
1 TTCTTTTTTTCTTC
52823954 TTCTTTTTTTCTTCC
1 TTCTTTTTTTCTT-C
* *
52823969 TTATTTTTTTCATC
1 TTCTTTTTTTCTTC
52823983 TTCT
1 TTCT
52823987 CCTTAACCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 16 0.57
15 12 0.43
ACGTcount: A:0.04, C:0.23, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCTTTTTTTCTTC
Found at i:52825840 original size:22 final size:24
Alignment explanation
Indices: 52825814--52825857 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
52825804 GAAAAATATT
52825814 AAATAT-ATA-TTTTTTATTTTTA
1 AAATATAATAGTTTTTTATTTTTA
52825836 AAATATAATAGTTTTTTATTTT
1 AAATATAATAGTTTTTTATTTT
52825858 AAGTTTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 3 0.15
24 11 0.55
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.61
Consensus pattern (24 bp):
AAATATAATAGTTTTTTATTTTTA
Found at i:52825987 original size:59 final size:59
Alignment explanation
Indices: 52825924--52826100 Score: 273
Period size: 66 Copynumber: 2.9 Consensus size: 59
52825914 TCAAGTTTGT
*
52825924 TTTACTAATCAAATGTTAGATTTTGTTACAACAATTAATACAATTAATAATTTGATAAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
52825983 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATTAATAATTTGATAA
1 TTTACTAATCAAATGTTAGATTTTATTACAACAA-T--T--AA-T-ACAATTAATAATTTGATAA
52826048 A
59 A
*
52826049 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAACAATT
1 TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATT
52826101 AATAATTTGA
Statistics
Matches: 109, Mismatches: 2, Indels: 14
0.87 0.02 0.11
Matches are distributed among these distances:
59 45 0.41
60 2 0.02
61 2 0.02
62 1 0.01
63 1 0.01
64 2 0.02
65 2 0.02
66 54 0.50
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (59 bp):
TTTACTAATCAAATGTTAGATTTTATTACAACAATTAATACAATTAATAATTTGATAAA
Found at i:52826037 original size:66 final size:66
Alignment explanation
Indices: 52825954--52826122 Score: 311
Period size: 66 Copynumber: 2.5 Consensus size: 66
52825944 TTTTGTTACA
52825954 ACAATTAATACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
1 ACAATT-A-ACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATT
52826019 AAT
64 AAT
52826022 ACAATTAACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAA
1 ACAATTAACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAA
52826087 T
66 T
*
52826088 ACAATTAACAATTAATAATTTGATAATTTTACTAA
1 ACAATTAACAATTAATAATTTGATAAATTTACTAA
52826123 CAATTAATTT
Statistics
Matches: 100, Mismatches: 1, Indels: 2
0.97 0.01 0.02
Matches are distributed among these distances:
66 93 0.93
67 1 0.01
68 6 0.06
ACGTcount: A:0.47, C:0.09, G:0.04, T:0.40
Consensus pattern (66 bp):
ACAATTAACAATTAATAATTTGATAAATTTACTAATCAAATGTTAGATTTTATTACAACAATTAA
T
Found at i:52826132 original size:16 final size:16
Alignment explanation
Indices: 52826111--52826152 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
52826101 AATAATTTGA
*
52826111 TAATTTTACTAACAAT
1 TAATTTTAATAACAAT
52826127 TAATTTTAATAACAAT
1 TAATTTTAATAACAAT
*
52826143 TAGTTTTAAT
1 TAATTTTAAT
52826153 TTTATTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.43, C:0.07, G:0.02, T:0.48
Consensus pattern (16 bp):
TAATTTTAATAACAAT
Found at i:52826136 original size:22 final size:23
Alignment explanation
Indices: 52826126--52826181 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
52826116 TTACTAACAA
* * *
52826126 TTAATTTTAAT-AACAATTAGTT
1 TTAATTTTAATAAAAAAATAATT
*
52826148 TTAATTTTATTAAAAAAATAATT
1 TTAATTTTAATAAAAAAATAATT
52826171 TTAATTTTAAT
1 TTAATTTTAAT
52826182 TTTAATTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TTAATTTTAATAAAAAAATAATT
Found at i:52827590 original size:14 final size:15
Alignment explanation
Indices: 52827571--52827599 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
52827561 TAAACTTAAA
52827571 TAAAGTAAA-ATCTT
1 TAAAGTAAATATCTT
52827585 TAAAGTAAATATCTT
1 TAAAGTAAATATCTT
52827600 GTCTCTTTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (15 bp):
TAAAGTAAATATCTT
Found at i:52829636 original size:17 final size:17
Alignment explanation
Indices: 52829592--52829648 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 17
52829582 AAGGTGATAC
*
52829592 TTTCATTT-TATTTCATT
1 TTTCATTTAT-TTTTATT
**
52829609 TTTGTTTTA-TTTTATT
1 TTTCATTTATTTTTATT
52829625 TTATCATTTATTTTTATT
1 TT-TCATTTATTTTTATT
52829643 TTTCAT
1 TTTCAT
52829649 CTCGAAACAA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
16 8 0.25
17 15 0.47
18 9 0.28
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.74
Consensus pattern (17 bp):
TTTCATTTATTTTTATT
Found at i:52829641 original size:18 final size:16
Alignment explanation
Indices: 52829592--52829648 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
52829582 AAGGTGATAC
*
52829592 TTTCATTTTATTTCATT
1 TTTCA-TTTATTTTATT
**
52829609 TTTGTTTTATTTTATT
1 TTTCATTTATTTTATT
52829625 TTATCATTTATTTTTATT
1 TT-TCATTTA-TTTTATT
52829643 TTTCAT
1 TTTCAT
52829649 CTCGAAACAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
16 12 0.36
17 12 0.36
18 9 0.27
ACGTcount: A:0.18, C:0.07, G:0.02, T:0.74
Consensus pattern (16 bp):
TTTCATTTATTTTATT
Found at i:52833125 original size:14 final size:14
Alignment explanation
Indices: 52833106--52833135 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
52833096 AACTGGAAAG
*
52833106 GACCTTATGTGGAA
1 GACCTTATCTGGAA
52833120 GACCTTATCTGGAA
1 GACCTTATCTGGAA
52833134 GA
1 GA
52833136 GTGTTGATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.27
Consensus pattern (14 bp):
GACCTTATCTGGAA
Found at i:52834358 original size:132 final size:132
Alignment explanation
Indices: 52834116--52834657 Score: 755
Period size: 132 Copynumber: 4.1 Consensus size: 132
52834106 TGAAGTCATC
* * * *
52834116 ACGGCGAATCTTATCTTTTCAAGGTAGTAGAGAAGCAGATTTAAGCCACTAGATCCTATCTTCCT
1 ACGGCGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAG-TCCTATCTCCCT
* *
52834181 GGGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCC-GTCTCCCTAAGTAGTAGTGGAGCAGATCG
65 GAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGTAGTAGTGGAGCAGATCG
*
52834245 AAT
130 AAG
* * * * * *
52834248 ACGGTGAATCTTATCTTTCCAAGGTAGTAGGGAAACAAATTTAAGCCACTAGTCTTATCTCTCTG
1 ACGGCGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTG
* * *
52834313 AGCAGCAGTGGAGTAGGTTAAAGATTGTAGATCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGA
66 AGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGTAGTAGTGGAGCAGATCGA
52834378 AG
131 AG
* * **
52834380 ACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAGCAGATTTAAAACACCAG-CCTTATCTCCCT
1 ACGGCGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCC-TATCTCCCT
* * * * *
52834444 GAGCAGCAGTGGAGTAGGTTGAAGATTGAAGATCCTGTCTCCCAAAGTAGTTGTGGAGTAGATCA
65 GAGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGTAGTAGTGGAGCAGATCG
52834509 AAG
130 AAG
* * * *
52834512 ACGACAAATCTTATCTTTCCAATGTAGTAGGGAAGCAGATTTAAGTCACCAGTCCTATCTCCCTG
1 ACGGCGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTG
* * *
52834577 AGCAGTAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGTTGTAGTGGAGCGGATCGA
66 AGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGTAGTAGTGGAGCAGATCGA
52834642 AG
131 AG
*
52834644 ACAGCGAATCTTAT
1 ACGGCGAATCTTAT
52834658 TTCCCTAGCT
Statistics
Matches: 359, Mismatches: 48, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
131 42 0.12
132 315 0.88
133 2 0.01
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.27
Consensus pattern (132 bp):
ACGGCGAATCTTATCTTTCCAAGGTAGTAGGGAAGCAGATTTAAGCCACCAGTCCTATCTCCCTG
AGCAGCAGTGGAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGTAGTAGTGGAGCAGATCGA
AG
Found at i:52834899 original size:181 final size:180
Alignment explanation
Indices: 52834648--52835130 Score: 668
Period size: 181 Copynumber: 2.7 Consensus size: 180
52834638 TCGAAGACAG
* * * *
52834648 CGAATCTTATTTCCCT--AGCTTTGCAGTGGAACAGATTGAAGCTATAAATTACAGATATTATAT
1 CGAATCTTATTTCCCTGAAG--GTGCAGTGGAACAGATCGAAGCTATAAATTACAGATCTTATCT
*
52834711 TTCTGAAGTTGCAGTAGAGCAGATCATATCAAACCTCATCTCCCTGAAGTTGCAGTGTGGCAGGT
64 CTCTGAAGTTGCAGTAGAGCAGATCATATCAAACCTCATCTCCCTGAAGTTGCAGTG-GGCAGGT
* * * * * *
52834776 TGAAATTATGTGTCTTATCTT-CCTAAAGTTGCAGTGGAGCAGATTGGAGATAA
128 TGAAATAACGAGTCATAT-TTCCCTAAAGTTGCAGTGGAACAGACTGGAGATAA
* *
52834829 CGAATCTTATTTCTCTGAAGGTGCAGT-GAATTAGATCGAAGCTATAAATTACAGATCTTATCTC
1 CGAATCTTATTTCCCTGAAGGTGCAGTGGAA-CAGATCGAAGCTATAAATTACAGATCTTATCTC
* *
52834893 TCTGAAGTTGCAGTAGAGCAGATCATATCAAACATCATCTCCCTGAAGTTACAGTAGGGCAGGTT
65 TCTGAAGTTGCAGTAGAGCAGATCATATCAAACCTCATCTCCCTGAAGTTGCAGT-GGGCAGGTT
* *
52834958 GAAATAACGAGTCATATTTCCCTGAAGTTGCAGTGGAACAGACTGGAGATAG
129 GAAATAACGAGTCATATTTCCCTAAAGTTGCAGTGGAACAGACTGGAGATAA
* * *
52835010 CGAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATCGAAGCTATAAGTAACAGATCTTATCTCT
1 CGAATCTTATTTCCCTGAAGGTGCAGTGGAACAGATCGAAGCTATAAATTACAGATCTTATCTCT
* ** *
52835075 CTGAAGTTGCAGTAGAGCAGGTCATATCAAGTCTTATCTCCCTGAAGTTGCAGTGG
66 CTGAAGTTGCAGTAGAGCAGATCATATCAAACCTCATCTCCCTGAAGTTGCAGTGG
52835131 AGCAAATTAA
Statistics
Matches: 268, Mismatches: 28, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
180 7 0.03
181 255 0.95
182 4 0.01
183 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.30
Consensus pattern (180 bp):
CGAATCTTATTTCCCTGAAGGTGCAGTGGAACAGATCGAAGCTATAAATTACAGATCTTATCTCT
CTGAAGTTGCAGTAGAGCAGATCATATCAAACCTCATCTCCCTGAAGTTGCAGTGGGCAGGTTGA
AATAACGAGTCATATTTCCCTAAAGTTGCAGTGGAACAGACTGGAGATAA
Found at i:52834912 original size:96 final size:94
Alignment explanation
Indices: 52834788--52835094 Score: 255
Period size: 96 Copynumber: 3.3 Consensus size: 94
52834778 AAATTATGTG
* * * *
52834788 TCTTATCT-TCCTAAAGTTGCAGTGGAGCAGATTGGAGATAACGAATCTTATTTCTCTGAAGGTG
1 TCTTATCTCT-CTGAAGTTGCAGTAGAGCAGA-TGGAGATAACGAATCTTATTTCCCTGAAGTTG
*
52834852 CAGTGAATTAGATCGAAGCTATAAATTACAGA
64 CAGTGAA-TAGATCGAAGCTATAAATAACAGA
* * * *
52834884 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGAT-CATATCAA--ACATC--ATCTCCCTGAAGTTA
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATGGAGAT-AACGA-ATCTTATTTCCCTGAAGTTG
* * *
52834944 CA--G--TAG--GGCAGGT-TGAAATAAC-GA
64 CAGTGAATAGATCGAAGCTAT-AAATAACAGA
* * * * * *
52834968 GTCATATTTCCCTGAAGTTGCAGTGGAACAGACTGGAGATAGCGAATCTTATTTCCCTGAAGTTG
1 -TCTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TGGAGATAACGAATCTTATTTCCCTGAAGTTG
* *
52835033 CAGTGGAACAGATCGAAGCTATAAGTAACAGA
64 CAGT-GAATAGATCGAAGCTATAAATAACAGA
52835065 TCTTATCTCTCTGAAGTTGCAGTAGAGCAG
1 TCTTATCTCTCTGAAGTTGCAGTAGAGCAG
52835095 GTCATATCAA
Statistics
Matches: 159, Mismatches: 32, Indels: 40
0.69 0.14 0.17
Matches are distributed among these distances:
84 3 0.02
85 36 0.23
86 2 0.01
87 9 0.06
88 1 0.01
89 15 0.09
90 1 0.01
92 14 0.09
93 1 0.01
94 8 0.05
95 3 0.02
96 62 0.39
97 4 0.03
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.29
Consensus pattern (94 bp):
TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATGGAGATAACGAATCTTATTTCCCTGAAGTTGCA
GTGAATAGATCGAAGCTATAAATAACAGA
Found at i:52835779 original size:21 final size:21
Alignment explanation
Indices: 52835753--52835799 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
52835743 TGATACTTTC
*
52835753 ATTTTATTTCAT-TTTTGTTTT
1 ATTTTATTTCATCATTT-TTTT
*
52835774 ATTTTATTTTATCATTTTTTT
1 ATTTTATTTCATCATTTTTTT
52835795 ATTTT
1 ATTTT
52835800 TCATTTCGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.17, C:0.04, G:0.02, T:0.77
Consensus pattern (21 bp):
ATTTTATTTCATCATTTTTTT
Found at i:52835794 original size:16 final size:15
Alignment explanation
Indices: 52835749--52835805 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 15
52835739 AAGGTGATAC
52835749 TTTCATTTTATTTCATT
1 TTTCATTTT-TTT-ATT
**
52835766 TTTGTTTTATTTTATT
1 TTTCATTT-TTTTATT
52835782 TTATCATTTTTTTATT
1 TT-TCATTTTTTTATT
52835798 TTTCATTT
1 TTTCATTT
52835806 CGAAACAACA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
15 6 0.18
16 14 0.41
17 13 0.38
18 1 0.03
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (15 bp):
TTTCATTTTTTTATT
Found at i:52837461 original size:20 final size:20
Alignment explanation
Indices: 52837436--52837475 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
52837426 CGTAAAATGA
*
52837436 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
52837456 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
52837476 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:52837465 original size:34 final size:35
Alignment explanation
Indices: 52837421--52837487 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
52837411 TAGTAAAATA
*
52837421 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
52837455 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
52837488 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:52837491 original size:14 final size:15
Alignment explanation
Indices: 52837415--52837491 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
52837405 GATTGGTAGT
* *
52837415 AAAAT-ATTTTCCGT
1 AAAATGATTTTCTGG
52837429 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
52837443 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
52837463 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
52837478 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
52837492 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 24 0.48
15 12 0.24
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.34, C:0.09, G:0.14, T:0.43
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:52838203 original size:9 final size:9
Alignment explanation
Indices: 52838184--52838220 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
52838174 TGAGTTTTCG
*
52838184 AATTTGAAT
1 AATTCGAAT
*
52838193 AACTCGAAT
1 AATTCGAAT
52838202 AATTCGAAT
1 AATTCGAAT
52838211 AATTCGAAT
1 AATTCGAAT
52838220 A
1 A
52838221 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:52841105 original size:18 final size:19
Alignment explanation
Indices: 52841082--52841120 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
52841072 ATGGACTTTG
52841082 TAGGATAA-TTTATTGGTA
1 TAGGATAATTTTATTGGTA
52841100 TAGGATAATTTTTATTGGTA
1 TAGGATAA-TTTTATTGGTA
52841120 T
1 T
52841121 TTTTATATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 8 0.42
20 11 0.58
ACGTcount: A:0.31, C:0.00, G:0.21, T:0.49
Consensus pattern (19 bp):
TAGGATAATTTTATTGGTA
Found at i:52843889 original size:49 final size:49
Alignment explanation
Indices: 52843834--52843937 Score: 154
Period size: 49 Copynumber: 2.1 Consensus size: 49
52843824 TCATGTGTTA
* * ** *
52843834 TAATTTTATACAGTGTTGAGTTTTTGATTCATGATATTGAACTCAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
*
52843883 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTTAATTT
1 TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
52843932 TAATTT
1 TAATTT
52843938 GTTTTTTTCT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.31, C:0.09, G:0.11, T:0.50
Consensus pattern (49 bp):
TAATTTTATAAAGTGTTCACCTTTTGATTCATGATATTAAACTCAATTT
Found at i:52845783 original size:44 final size:46
Alignment explanation
Indices: 52845720--52845817 Score: 155
Period size: 44 Copynumber: 2.2 Consensus size: 46
52845710 CTATTACACC
* *
52845720 TCTATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTAT
1 TCTATTACATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
52845764 TCTATTACATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
1 TCTATTACATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
*
52845810 TCCATTAC
1 TCTATTAC
52845818 GCTTCTATTC
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
44 25 0.51
45 4 0.08
46 20 0.41
ACGTcount: A:0.37, C:0.30, G:0.04, T:0.30
Consensus pattern (46 bp):
TCTATTACATTCAACCAAACAAAAGAATTACCTATTACGCCTCTAT
Found at i:52845817 original size:46 final size:44
Alignment explanation
Indices: 52845727--52845817 Score: 146
Period size: 46 Copynumber: 2.0 Consensus size: 44
52845717 ACCTCTATTC
* *
52845727 CATTCAACCAAACACAAGAATACCATTACGCCTCTATTCTATTA
1 CATTCAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTA
52845771 CATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACAAAAGAA-TACC-ATTACGCCTCTATTCCATTA
52845817 C
1 C
52845818 GCTTCTATTC
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 19 0.44
45 4 0.09
46 20 0.47
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.27
Consensus pattern (44 bp):
CATTCAACCAAACAAAAGAATACCATTACGCCTCTATTCCATTA
Found at i:52845818 original size:16 final size:16
Alignment explanation
Indices: 52845797--52845849 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
52845787 AGAATTACCT
52845797 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
52845813 ATTACGCTTCTATTCC
1 ATTACGCCTCTATTCC
*
52845829 ATTACGCCTTTATTCC
1 ATTACGCCTCTATTCC
52845845 ATTAC
1 ATTAC
52845850 AGCGAACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.21, C:0.32, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:52848136 original size:36 final size:36
Alignment explanation
Indices: 52848049--52848265 Score: 172
Period size: 36 Copynumber: 5.9 Consensus size: 36
52848039 TTGTGCCAAA
* *
52848049 GTTTTGCGCCCAGCGCTAGT-TGAATAAACCGACGAT
1 GTTTTGCGCCCAGCACTAGTCAG-ATAAACCGACGAT
* * * * *
52848085 AGGTGTGC-CTC-GCACTAGTCAGATAATCCGATGAT
1 -GTTTTGCGCCCAGCACTAGTCAGATAAACCGACGAT
* * * *
52848120 GTTTTGCGCCTAGCACTAGTCGGATAAATCGATGAT
1 GTTTTGCGCCCAGCACTAGTCAGATAAACCGACGAT
* * **
52848156 ATCAATTATGTGCCCAGCACTAGTTGGATAAACCGACGAT
1 GT---TT-TGCGCCCAGCACTAGTCAGATAAACCGACGAT
* *
52848196 GTTTTGCACCCAGCATTAGT-AGGATAAACCGACGAT
1 GTTTTGCGCCCAGCACTAGTCA-GATAAACCGACGAT
*
52848232 GTTTTGCGCCCAGCACTAGTCAAATAAAACCGAC
1 GTTTTGCGCCCAGCACTAGTCAGAT-AAACCGAC
52848266 AAATACATAT
Statistics
Matches: 142, Mismatches: 28, Indels: 20
0.75 0.15 0.11
Matches are distributed among these distances:
34 5 0.04
35 19 0.13
36 72 0.51
37 16 0.11
39 2 0.01
40 28 0.20
ACGTcount: A:0.29, C:0.24, G:0.23, T:0.25
Consensus pattern (36 bp):
GTTTTGCGCCCAGCACTAGTCAGATAAACCGACGAT
Found at i:52848259 original size:112 final size:111
Alignment explanation
Indices: 52848056--52848259 Score: 268
Period size: 112 Copynumber: 1.8 Consensus size: 111
52848046 AAAGTTTTGC
* * * *
52848056 GCCCAGCGCTAGTTGAATAAACCGACGATAGGTGTGCCTCGCACTAGTCAGATAATCCGATGATG
1 GCCCAGCACTAGTTGAATAAACCGACGATAGGTGTGCCCCGCACTAGTCAGATAAACCGACGATG
* **
52848121 TTTTGCGCCTAGCACTAGTCGGATAAATCGATGATATCAATTATGT
66 TTTTGCGCCCAGCACTAGTCAAATAAATCGATGATATCAATTATGT
* * * *
52848167 GCCCAGCACTAGTTGGATAAACCGACGAT-GTTTTGCACCCAGCATTAGT-AGGATAAACCGACG
1 GCCCAGCACTAGTTGAATAAACCGACGATAGGTGTGC-CCC-GCACTAGTCA-GATAAACCGACG
52848230 ATGTTTTGCGCCCAGCACTAGTCAAATAAA
63 ATGTTTTGCGCCCAGCACTAGTCAAATAAA
52848260 ACCGACAAAT
Statistics
Matches: 79, Mismatches: 11, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
110 5 0.06
111 30 0.38
112 44 0.56
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (111 bp):
GCCCAGCACTAGTTGAATAAACCGACGATAGGTGTGCCCCGCACTAGTCAGATAAACCGACGATG
TTTTGCGCCCAGCACTAGTCAAATAAATCGATGATATCAATTATGT
Found at i:52859717 original size:13 final size:13
Alignment explanation
Indices: 52859699--52859741 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
52859689 CTTTTACTAT
52859699 GAGAAACAAAAGA
1 GAGAAACAAAAGA
*
52859712 GAG-AA-AAAGGA
1 GAGAAACAAAAGA
*
52859723 TAGAAACAAAAGA
1 GAGAAACAAAAGA
52859736 GAGAAA
1 GAGAAA
52859742 AAGGATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
11 7 0.29
12 4 0.17
13 13 0.54
ACGTcount: A:0.67, C:0.05, G:0.26, T:0.02
Consensus pattern (13 bp):
GAGAAACAAAAGA
Found at i:52859727 original size:24 final size:24
Alignment explanation
Indices: 52859700--52859757 Score: 107
Period size: 24 Copynumber: 2.4 Consensus size: 24
52859690 TTTTACTATG
52859700 AGAAACAAAAGAGAGAAAAAGGAT
1 AGAAACAAAAGAGAGAAAAAGGAT
52859724 AGAAACAAAAGAGAGAAAAAGGAT
1 AGAAACAAAAGAGAGAAAAAGGAT
*
52859748 AAAAACAAAA
1 AGAAACAAAA
52859758 AGCATCTGTG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.71, C:0.05, G:0.21, T:0.03
Consensus pattern (24 bp):
AGAAACAAAAGAGAGAAAAAGGAT
Found at i:52860113 original size:168 final size:168
Alignment explanation
Indices: 52859831--52860168 Score: 649
Period size: 168 Copynumber: 2.0 Consensus size: 168
52859821 TACTGCTTAA
*
52859831 AACAACAAAATGCCAAATTCAATTAAAAGATAAAAAGAGATTTTTTCCATGTTATGGAAATCGAA
1 AACAACAAAATGCCAAAGTCAATTAAAAGATAAAAAGAGATTTTTTCCATGTTATGGAAATCGAA
52859896 ACCCACATAATATATAGATTTTACATCACAGGCTCGATTGTCCAGCCCTCACAACCTCATTCAAG
66 ACCCACATAATATATAGATTTTACATCACAGGCTCGATTGTCCAGCCCTCACAACCTCATTCAAG
52859961 TTAGCTGATCATGGACCAAACTTTCATCAAGTATAGGT
131 TTAGCTGATCATGGACCAAACTTTCATCAAGTATAGGT
*
52859999 AACAACAAAATGCCAAAGTCAATTAAAAGATAAAAAGAGATTTTTTCCATGTTATGGAAATGGAA
1 AACAACAAAATGCCAAAGTCAATTAAAAGATAAAAAGAGATTTTTTCCATGTTATGGAAATCGAA
*
52860064 ACCCACATAATATATAGATTTTACATCACAGGCTCGATTGTCTAGCCCTCACAACCTCATTCAAG
66 ACCCACATAATATATAGATTTTACATCACAGGCTCGATTGTCCAGCCCTCACAACCTCATTCAAG
52860129 TTAGCTGATCATGGACCAAACTTTCATCAAGTATAGGT
131 TTAGCTGATCATGGACCAAACTTTCATCAAGTATAGGT
52860167 AA
1 AA
52860169 ACAAGTTTTA
Statistics
Matches: 167, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
168 167 1.00
ACGTcount: A:0.39, C:0.20, G:0.14, T:0.27
Consensus pattern (168 bp):
AACAACAAAATGCCAAAGTCAATTAAAAGATAAAAAGAGATTTTTTCCATGTTATGGAAATCGAA
ACCCACATAATATATAGATTTTACATCACAGGCTCGATTGTCCAGCCCTCACAACCTCATTCAAG
TTAGCTGATCATGGACCAAACTTTCATCAAGTATAGGT
Found at i:52874901 original size:23 final size:23
Alignment explanation
Indices: 52874873--52874966 Score: 134
Period size: 23 Copynumber: 4.1 Consensus size: 23
52874863 ATGTGTGTAT
* *
52874873 CTTTTCATATTCAAGCCTCTTAA
1 CTTTTCATATTCAAGTCTCTTCA
*
52874896 CTTTTCATCTTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
* * *
52874919 CTATTCATATTCAAGTTTTTTCA
1 CTTTTCATATTCAAGTCTCTTCA
52874942 CTTTTCATATTCAAGTCTCTTCA
1 CTTTTCATATTCAAGTCTCTTCA
52874965 CT
1 CT
52874967 CTTCTAATTT
Statistics
Matches: 61, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 61 1.00
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (23 bp):
CTTTTCATATTCAAGTCTCTTCA
Found at i:52875956 original size:30 final size:30
Alignment explanation
Indices: 52875922--52875984 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
52875912 ACTTATTTTA
52875922 TTGTTAATTTTGTTATTATTTTA-ATGACAT
1 TTGTTAATTTTGTTATTATTTTAGA-GACAT
52875952 TTGTTAATTTTGTTATTATTTTAGAGACAT
1 TTGTTAATTTTGTTATTATTTTAGAGACAT
52875982 TTG
1 TTG
52875985 CTTGTTAAGT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.25, C:0.03, G:0.13, T:0.59
Consensus pattern (30 bp):
TTGTTAATTTTGTTATTATTTTAGAGACAT
Found at i:52876102 original size:17 final size:17
Alignment explanation
Indices: 52876065--52876103 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
52876055 GGGAAATATT
*
52876065 TATTTTGATGTTTTTAG
1 TATTTTGATGTTTGTAG
52876082 TATTTTGATGTATTGTA-
1 TATTTTGATGT-TTGTAG
52876099 TATTT
1 TATTT
52876104 AAAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 16 0.80
18 4 0.20
ACGTcount: A:0.21, C:0.00, G:0.15, T:0.64
Consensus pattern (17 bp):
TATTTTGATGTTTGTAG
Found at i:52877087 original size:21 final size:20
Alignment explanation
Indices: 52877047--52877094 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
52877037 ATATTTAAAT
*
52877047 ATTATTTTGATAACTTTGTA
1 ATTATTTTGATAACTATGTA
52877067 ATTATTTTGGATAA-TCATGTA
1 ATTATTTT-GATAACT-ATGTA
*
52877088 GTTATTT
1 ATTATTT
52877095 GGGGTGAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 9 0.38
21 15 0.62
ACGTcount: A:0.29, C:0.04, G:0.12, T:0.54
Consensus pattern (20 bp):
ATTATTTTGATAACTATGTA
Found at i:52879793 original size:28 final size:26
Alignment explanation
Indices: 52879746--52879813 Score: 86
Period size: 25 Copynumber: 2.6 Consensus size: 26
52879736 AATAAAAAAA
52879746 TTACCAAAATAT-TATAAATTTTTTTTAT
1 TTACCAAAATATATATAAA---TTTTTAT
*
52879774 TTACCAATATATATAT-AATTTTTAT
1 TTACCAAAATATATATAAATTTTTAT
52879799 TTACCAAAATATATA
1 TTACCAAAATATATA
52879814 AAAAAACAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
25 21 0.57
28 13 0.35
29 3 0.08
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (26 bp):
TTACCAAAATATATATAAATTTTTAT
Found at i:52879909 original size:27 final size:27
Alignment explanation
Indices: 52879879--52879955 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
52879869 ACGCCAATGG
*
52879879 CATTGGCGGCACCAAAGGTGCCAAAAC
1 CATTGGCGGCACCAATGGTGCCAAAAC
**
52879906 CATTGGCGGCACCAATGGTGCCAATGC
1 CATTGGCGGCACCAATGGTGCCAAAAC
*
52879933 CATTGGAGGCACCAATGGTGCCA
1 CATTGGCGGCACCAATGGTGCCA
52879956 TATTGATTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 46 1.00
ACGTcount: A:0.27, C:0.29, G:0.29, T:0.16
Consensus pattern (27 bp):
CATTGGCGGCACCAATGGTGCCAAAAC
Found at i:52879964 original size:27 final size:25
Alignment explanation
Indices: 52879871--52879971 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 25
52879861 CCTTTGTCAC
*
52879871 GCCAATGGCATTGGCGGCACCAAAGGT
1 GCCAAT-G-ATTGGCGGCACCAATGGT
**
52879898 GCCAAAACCATTGGCGGCACCAATGGT
1 GCC--AATGATTGGCGGCACCAATGGT
*
52879925 GCCAATGCCATTGGAGGCACCAATGGT
1 GCCAATG--ATTGGCGGCACCAATGGT
52879952 GCCATATTGATTGGCGGCAC
1 GCCA-A-TGATTGGCGGCAC
52879972 TATTTGTATT
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
25 2 0.03
27 54 0.89
28 1 0.02
29 4 0.07
ACGTcount: A:0.26, C:0.27, G:0.30, T:0.18
Consensus pattern (25 bp):
GCCAATGATTGGCGGCACCAATGGT
Found at i:52880136 original size:19 final size:21
Alignment explanation
Indices: 52880098--52880136 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
52880088 AAATTTTGAT
*
52880098 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
52880119 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
52880137 TTGTTTTAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:52880218 original size:3 final size:3
Alignment explanation
Indices: 52880212--52880249 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
52880202 ATTATTATTA
52880212 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
52880250 AGTATTAAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:52903195 original size:17 final size:17
Alignment explanation
Indices: 52903165--52903205 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
52903155 ATACACTAGT
*
52903165 AAAAATTTATAAAATA-
1 AAAAATTTAAAAAATAG
52903181 AAAATATTTAAAAAATAG
1 AAAA-ATTTAAAAAATAG
52903199 AAAAATT
1 AAAAATT
52903206 CGGCTTACTC
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
16 4 0.18
17 14 0.64
18 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (17 bp):
AAAAATTTAAAAAATAG
Found at i:52904901 original size:22 final size:20
Alignment explanation
Indices: 52904868--52904973 Score: 77
Period size: 22 Copynumber: 4.9 Consensus size: 20
52904858 TAATAGAGCA
*
52904868 ATAAGCATCAAAGTGCAAATC
1 ATAAGCACCAAAGTGCAAA-C
52904889 ACTAAGCACCAAAGTGCAAAAC
1 A-TAAGCACCAAAGTGC-AAAC
* *
52904911 AATAGGCACCGAAGTGCAGAAC
1 -ATAAGCACCAAAGTGCA-AAC
* *
52904933 GATAAGCACCGAAGTGCGAGAC
1 -ATAAGCACCAAAGTGC-AAAC
* *
52904955 AGTAAGCGCTAAAGTGCAA
1 A-TAAGCACCAAAGTGCAA
52904974 GACAATAAAC
Statistics
Matches: 69, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
21 4 0.06
22 60 0.87
23 5 0.07
ACGTcount: A:0.43, C:0.22, G:0.23, T:0.12
Consensus pattern (20 bp):
ATAAGCACCAAAGTGCAAAC
Found at i:52905498 original size:19 final size:19
Alignment explanation
Indices: 52905462--52905500 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
52905452 GACTACAATA
52905462 TTCATATATTCTTATATTT
1 TTCATATATTCTTATATTT
52905481 TTCACTATATTCTT-TATTT
1 TTCA-TATATTCTTATATTT
52905500 T
1 T
52905501 CCAATATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.23, C:0.13, G:0.00, T:0.64
Consensus pattern (19 bp):
TTCATATATTCTTATATTT
Found at i:52908509 original size:10 final size:12
Alignment explanation
Indices: 52908486--52908518 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
52908476 TTGCATTTTT
52908486 TATATACATATA
1 TATATACATATA
*
52908498 TATATACTTATA
1 TATATACATATA
52908510 TATATACAT
1 TATATACAT
52908519 GTATTTTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (12 bp):
TATATACATATA
Found at i:52921434 original size:18 final size:19
Alignment explanation
Indices: 52921411--52921448 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
52921401 TTTAAAAAAA
52921411 TATAAAT-TTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
52921429 TATAAATATTTTGAATTTT
1 TATAAATATTTGGAATTTT
52921448 T
1 T
52921449 TTGAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.34, C:0.00, G:0.08, T:0.58
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:52921458 original size:19 final size:19
Alignment explanation
Indices: 52921414--52921458 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 19
52921404 AAAAAAATAT
52921414 AAATTTTGGAATTTTTATA
1 AAATTTTGGAATTTTTATA
*
52921433 AATATTTT-GAATTTTTTTGA
1 AA-ATTTTGGAATTTTTAT-A
52921453 AAATTT
1 AAATTT
52921459 GAAAATTATT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 15 0.65
20 8 0.35
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.56
Consensus pattern (19 bp):
AAATTTTGGAATTTTTATA
Found at i:52924667 original size:45 final size:45
Alignment explanation
Indices: 52924618--52924881 Score: 420
Period size: 45 Copynumber: 5.9 Consensus size: 45
52924608 TCGGCCATGG
* * * * *
52924618 TGCTTCCTCAATTTGTTCCTTAAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
52924663 TGCTTCCTTAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
*
52924708 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGCCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
52924753 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
52924798 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
* * * **
52924843 TGCTTCCTTAATTTGTTCCACAAATTATGCATGATGTTG
1 TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTG
52924882 TCCACCTCTT
Statistics
Matches: 205, Mismatches: 14, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 205 1.00
ACGTcount: A:0.26, C:0.20, G:0.16, T:0.39
Consensus pattern (45 bp):
TGCTTCCTCAAATTCTTCCATGAATTATGCATGATGTTGGTCAAA
Found at i:52925016 original size:16 final size:16
Alignment explanation
Indices: 52924995--52925026 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52924985 CATTCTGCAT
52924995 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
52925011 TTAAACAACAGCAGCA
1 TTAAACAACAGCAGCA
52925027 AAACACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.25, G:0.12, T:0.12
Consensus pattern (16 bp):
TTAAACAACAGCAGCA
Found at i:52933576 original size:15 final size:15
Alignment explanation
Indices: 52933556--52933585 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
52933546 TGATAGTATT
*
52933556 TACAGTCTTGAACTC
1 TACAGTCTTAAACTC
52933571 TACAGTCTTAAACTC
1 TACAGTCTTAAACTC
52933586 ACATACTCGT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (15 bp):
TACAGTCTTAAACTC
Found at i:52935939 original size:9 final size:9
Alignment explanation
Indices: 52935925--52935961 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
52935915 TATAGTTTGA
52935925 TATTCGAAT
1 TATTCGAAT
52935934 TATTCGAAT
1 TATTCGAAT
*
52935943 TATTCGAGT
1 TATTCGAAT
52935952 TATTCGAAT
1 TATTCGAAT
52935961 T
1 T
52935962 CGAAAACCCA
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:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:52936717 original size:7 final size:7
Alignment explanation
Indices: 52936705--52936729 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
52936695 TTTTGACATT
52936705 AAATTTA
1 AAATTTA
52936712 AAATTTA
1 AAATTTA
52936719 AAATTTA
1 AAATTTA
52936726 AAAT
1 AAAT
52936730 GATAAATGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (7 bp):
AAATTTA
Found at i:52937385 original size:20 final size:19
Alignment explanation
Indices: 52937362--52937402 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
52937352 AAAAATAGGG
52937362 CTTTTATGTGTAATTTGCCC
1 CTTTTATG-GTAATTTGCCC
* *
52937382 CTTTTTTGGTATTTTGCCC
1 CTTTTATGGTAATTTGCCC
52937401 CT
1 CT
52937403 AATAATACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 12 0.63
20 7 0.37
ACGTcount: A:0.10, C:0.22, G:0.15, T:0.54
Consensus pattern (19 bp):
CTTTTATGGTAATTTGCCC
Found at i:52939503 original size:5 final size:5
Alignment explanation
Indices: 52939477--52939681 Score: 87
Period size: 5 Copynumber: 40.8 Consensus size: 5
52939467 GTTTTTAAAC
*
52939477 TGTTA TG-TA TATTA TG-TA TGTTA TGTTTAA TGTTA TGTT- TGTATA
1 TGTTA TGTTA TGTTA TGTTA TGTTA TG-TT-A TGTTA TGTTA TGT-TA
* *
52939522 TTTTTA TG-TA TGTTA TGTACTA TTATTA TG-TA TGTTA TGTTTA CTGTTA
1 -TGTTA TGTTA TGTTA TGT--TA -TGTTA TGTTA TGTTA TG-TTA -TGTTA
* * *
52939571 TGTT- TGTATA TTTGTA TG-TA TGTTA TGTTA TGTTA TG-TA CCGTCA
1 TGTTA TGT-TA TGT-TA TGTTA TGTTA TGTTA TGTTA TGTTA -TGTTA
* *
52939616 TG-TA TATTA TG-TA TGTT- TGTTA TGTGTTA TATTA CTGTTA TGTT-
1 TGTTA TGTTA TGTTA TGTTA TGTTA --TGTTA TGTTA -TGTTA TGTTA
* *
52939660 TG-TA TATTA TG-TA TGTCA TGTT
1 TGTTA TGTTA TGTTA TGTTA TGTT
52939682 TAATGTATAT
Statistics
Matches: 151, Mismatches: 21, Indels: 56
0.66 0.09 0.25
Matches are distributed among these distances:
3 1 0.01
4 44 0.29
5 66 0.44
6 24 0.16
7 14 0.09
8 2 0.01
ACGTcount: A:0.22, C:0.03, G:0.18, T:0.57
Consensus pattern (5 bp):
TGTTA
Found at i:52939545 original size:22 final size:21
Alignment explanation
Indices: 52939486--52939561 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
52939476 CTGTTATGTA
52939486 TATTATGTATGTTATG--T-T
1 TATTATGTATGTTATGTATAT
52939504 TA--ATGTTATGTT-TGTATAT
1 TATTATG-TATGTTATGTATAT
*
52939523 TTTTATGTATGTTATGTACTAT
1 TATTATGTATGTTATGTA-TAT
52939545 TATTATGTATGTTATGT
1 TATTATGTATGTTATGT
52939562 TTACTGTTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
16 5 0.10
17 6 0.12
18 3 0.06
19 2 0.04
20 6 0.12
21 7 0.15
22 19 0.40
ACGTcount: A:0.24, C:0.01, G:0.16, T:0.59
Consensus pattern (21 bp):
TATTATGTATGTTATGTATAT
Found at i:52939570 original size:59 final size:59
Alignment explanation
Indices: 52939486--52939598 Score: 208
Period size: 59 Copynumber: 1.9 Consensus size: 59
52939476 CTGTTATGTA
*
52939486 TATTATGTATGTTATGTTTAATGTTATGTTTGTATATTTTTATGTATGTTATGTACTAT
1 TATTATGTATGTTATGTTTAATGTTATGTTTGTATATTTGTATGTATGTTATGTACTAT
*
52939545 TATTATGTATGTTATGTTTACTGTTATGTTTGTATATTTGTATGTATGTTATGT
1 TATTATGTATGTTATGTTTAATGTTATGTTTGTATATTTGTATGTATGTTATGT
52939599 TATGTTATGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 52 1.00
ACGTcount: A:0.22, C:0.02, G:0.17, T:0.59
Consensus pattern (59 bp):
TATTATGTATGTTATGTTTAATGTTATGTTTGTATATTTGTATGTATGTTATGTACTAT
Found at i:52939656 original size:18 final size:19
Alignment explanation
Indices: 52939633--52939668 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
52939623 TATGTATGTT
52939633 TGTTATGTGT-TATATTAC
1 TGTTATGTGTGTATATTAC
*
52939651 TGTTATGTTTGTATATTA
1 TGTTATGTGTGTATATTA
52939669 TGTATGTCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.22, C:0.03, G:0.17, T:0.58
Consensus pattern (19 bp):
TGTTATGTGTGTATATTAC
Found at i:52939665 original size:44 final size:42
Alignment explanation
Indices: 52939530--52939681 Score: 149
Period size: 44 Copynumber: 3.6 Consensus size: 42
52939520 TATTTTTATG
52939530 TATGTTATGTACTATTAT-TATGTATGTTATG---T-TTACTGT
1 TATGTT-TGTA-TATTATGTATGTATGTTATGTTATATTACTGT
*
52939569 TATGTTTGTATATT-TGTATGTATGTTATGTTATGTTA-TG-
1 TATGTTTGTATATTATGTATGTATGTTATGTTATATTACTGT
* * *
52939608 TACCGTCATGTATATTATGTATGTTTGTTATGTGTTATATTACTGT
1 TA-TGT-TTGTATATTATGTATGTATGTTA--TGTTATATTACTGT
52939654 TATGTTTGTATATTATGTATGTCATGTT
1 TATGTTTGTATATTATGTATGT-ATGTT
52939682 TAATGTATAT
Statistics
Matches: 93, Mismatches: 7, Indels: 20
0.77 0.06 0.17
Matches are distributed among these distances:
36 1 0.01
37 17 0.18
38 4 0.04
39 8 0.09
40 5 0.05
41 11 0.12
42 12 0.13
44 25 0.27
45 8 0.09
46 2 0.02
ACGTcount: A:0.22, C:0.05, G:0.18, T:0.56
Consensus pattern (42 bp):
TATGTTTGTATATTATGTATGTATGTTATGTTATATTACTGT
Found at i:52953671 original size:14 final size:15
Alignment explanation
Indices: 52953654--52953686 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
52953644 CAAAAAAAAT
52953654 AGAAAGAAAAGA-AA
1 AGAAAGAAAAGAGAA
52953668 AGAAAGAAAAGAGAA
1 AGAAAGAAAAGAGAA
52953683 AGAA
1 AGAA
52953687 GAATGCACGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 12 0.67
15 6 0.33
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (15 bp):
AGAAAGAAAAGAGAA
Done.