Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032248.1 Gossypioides kirkii chromosome KI_06
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: 60359545
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 900 characters in sequence are not A, C, G, or T
File 156 of 193
Found at i:48275579 original size:17 final size:17
Alignment explanation
Indices: 48275554--48275601 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
48275544 AAATTTAGTT
*
48275554 AAATTTAAATTTAAAAC
1 AAATCTAAATTTAAAAC
48275571 AAATCTAAATTTAAAAC
1 AAATCTAAATTTAAAAC
* *
48275588 CAATCTAAACTTAA
1 AAATCTAAATTTAA
48275602 TTTAAAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATCTAAATTTAAAAC
Found at i:48276429 original size:24 final size:24
Alignment explanation
Indices: 48276384--48276429 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
48276374 TACAATAATG
* **
48276384 TTATTATAATTCTATTTTATTATA
1 TTATTACAATTCTATTCCATTATA
48276408 TTATTACAATTCTATTCCATTA
1 TTATTACAATTCTATTCCATTA
48276430 CATTCAACCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.11, G:0.00, T:0.57
Consensus pattern (24 bp):
TTATTACAATTCTATTCCATTATA
Found at i:48276458 original size:64 final size:64
Alignment explanation
Indices: 48276334--48276469 Score: 147
Period size: 64 Copynumber: 2.1 Consensus size: 64
48276324 ATTTTAATTT
* * * *
48276334 TTTTCTTATATTATTACAATATTTATTACATTCAACCAAATACAATAATGTTATTATAATT-CTA
1 TTTTATTATATTATTACAATATTCATTACATTCAACCAAATACAAT-ATGTAATTATAATTACAA
48276398 TTTTATTATATTATTACAATTCTATTCCATTACATTCAACC-AA-ACAAT-TG-AATTACTAATT
1 TTTTATTATATTATTACAA---TATT-CATTACATTCAACCAAATACAATATGTAATTA-TAATT
48276459 ACAA
61 ACAA
48276463 TTTTATT
1 TTTTATT
48276470 CCATTACAAT
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
63 4 0.06
64 25 0.40
65 9 0.15
66 5 0.08
67 6 0.10
68 13 0.21
ACGTcount: A:0.38, C:0.14, G:0.01, T:0.46
Consensus pattern (64 bp):
TTTTATTATATTATTACAATATTCATTACATTCAACCAAATACAATATGTAATTATAATTACAA
Found at i:48276530 original size:13 final size:13
Alignment explanation
Indices: 48276512--48276537 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
48276502 AACGTACCTC
48276512 AATATTTTTAAAT
1 AATATTTTTAAAT
48276525 AATATTTTTAAAT
1 AATATTTTTAAAT
48276538 TTAAAAATTG
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:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
AATATTTTTAAAT
Found at i:48280265 original size:11 final size:11
Alignment explanation
Indices: 48280249--48280311 Score: 73
Period size: 11 Copynumber: 6.1 Consensus size: 11
48280239 CAATCAAACC
48280249 ATTTTAAATTT
1 ATTTTAAATTT
48280260 ATTTTAAA---
1 ATTTTAAATTT
48280268 A--TTAAATTT
1 ATTTTAAATTT
48280277 ATTTTAAATTT
1 ATTTTAAATTT
*
48280288 AAATTTAAATTT
1 -ATTTTAAATTT
48280300 ATTTTAAATTT
1 ATTTTAAATTT
48280311 A
1 A
48280312 ATAAAATTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
6 5 0.11
8 1 0.02
9 1 0.02
11 27 0.61
12 10 0.23
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATTTTAAATTT
Found at i:48280288 original size:6 final size:6
Alignment explanation
Indices: 48280251--48280312 Score: 67
Period size: 6 Copynumber: 10.8 Consensus size: 6
48280241 ATCAAACCAT
* * *
48280251 TTTAAA TTT-AT TTTAAA ATTAAA TTT-AT TTTAAA TTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
*
48280297 TTT-AT TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAA
48280313 TAAAATTCCA
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
5 12 0.27
6 33 0.73
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:48280288 original size:23 final size:23
Alignment explanation
Indices: 48280262--48280312 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
48280252 TTAAATTTAT
48280262 TTTAAAATTAAATTTATTTTAAA
1 TTTAAAATTAAATTTATTTTAAA
*
48280285 TTTAAATTTAAATTTATTTTAAA
1 TTTAAAATTAAATTTATTTTAAA
48280308 TTTAA
1 TTTAA
48280313 TAAAATTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAAAATTAAATTTATTTTAAA
Found at i:48280312 original size:17 final size:17
Alignment explanation
Indices: 48280251--48280294 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
48280241 ATCAAACCAT
48280251 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
*
48280268 ATTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
48280285 TTTAAATTTA
1 TTTAAATTTA
48280295 AATTTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:48286189 original size:13 final size:13
Alignment explanation
Indices: 48286156--48286196 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
48286146 TGAATATCTC
48286156 TTTATTTAATTAATA
1 TTTATTT-ATT-ATA
*
48286171 TGTATTTATTATA
1 TTTATTTATTATA
48286184 TTTATTTATTATA
1 TTTATTTATTATA
48286197 CATTGAATGC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 15 0.62
14 3 0.12
15 6 0.25
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (13 bp):
TTTATTTATTATA
Found at i:48287693 original size:97 final size:97
Alignment explanation
Indices: 48287527--48287712 Score: 282
Period size: 97 Copynumber: 1.9 Consensus size: 97
48287517 AACCTTGGAA
* * * *
48287527 AAGGGTATTCGATTATCTCGATTTGAAGAAAAGTCATGCCTAGTAAGTTAAGGCACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAATAAGTTAAGGCACAAATTTTCA
48287592 AAACCAGAGATAAAGAAACATTGCCTCGATTT
66 AAACCAGAGATAAAGAAACATTGCCTCGATTT
* * *
48287624 AAGGGTATTCGATTATCCCGGTTTGAAGAAAAATCGCGCCTAATAAGTTAAGGTACAAATTTTCA
1 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAATAAGTTAAGGCACAAATTTTCA
* * *
48287689 AAACCCGAGATAAAGGAATATTGC
66 AAACCAGAGATAAAGAAACATTGC
48287713 TTCGTTTTTA
Statistics
Matches: 79, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
97 79 1.00
ACGTcount: A:0.38, C:0.16, G:0.19, T:0.27
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACGCCTAATAAGTTAAGGCACAAATTTTCA
AAACCAGAGATAAAGAAACATTGCCTCGATTT
Found at i:48288331 original size:29 final size:29
Alignment explanation
Indices: 48288281--48288461 Score: 120
Period size: 29 Copynumber: 6.2 Consensus size: 29
48288271 AATTTGGTAA
* *
48288281 TTTTGGATGTTCGAGGGTAAAATGATAAT
1 TTTTGAATGTTCGGGGGTAAAATGATAAT
* * *
48288310 TTTTGAATGTTCGGGGGCAAAATGGTGAT
1 TTTTGAATGTTCGGGGGTAAAATGATAAT
*
48288339 TTTTGAATGTTCGGGGGTAAAAAT-ATGAT
1 TTTTGAATGTTCGGGGGT-AAAATGATAAT
* ** * *
48288368 TTTAAGAA-GCACGGGAGTAAAAATG-TGAT
1 TTT-TGAATGTTCGGGGGT-AAAATGATAAT
* * **
48288397 TTTTGAAAGTTTGAGGGAAAAAATGA-AAT
1 TTTTGAATGTTCG-GGGGTAAAATGATAAT
* *
48288426 TTTTGAGAAGTTTGGGGGTCAAAATG-TAAT
1 TTTTGA-ATGTTCGGGGGT-AAAATGATAAT
48288456 TTTTGA
1 TTTTGA
48288462 GAAGTGTAGG
Statistics
Matches: 122, Mismatches: 21, Indels: 17
0.76 0.13 0.11
Matches are distributed among these distances:
28 3 0.02
29 87 0.71
30 32 0.26
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.35
Consensus pattern (29 bp):
TTTTGAATGTTCGGGGGTAAAATGATAAT
Found at i:48288370 original size:58 final size:56
Alignment explanation
Indices: 48288289--48288490 Score: 151
Period size: 58 Copynumber: 3.5 Consensus size: 56
48288279 AATTTTGGAT
* *
48288289 GTTCGAGGGT-AAAATGATAATTTTTGAATGTTCGGGGGCAAAATGGTGATTTTTGAAT
1 GTTCGAGGGTAAAAAT-ATGATTTTTGAA-GTTCGGGGGCAAAAT-GTGATTTTTGAAA
* * ** **
48288347 GTTCGGGGGTAAAAATATGATTTTAAGAAGCACGGGAGTAAAAATGTGATTTTTGAAA
1 GTTCGAGGGTAAAAATATGATTTT-TGAAGTTCGGG-GGCAAAATGTGATTTTTGAAA
* * *
48288405 GTTTGAGGG-AAAAA-ATGAAATTTTTGAGAAGTTTGGGGGTCAAAATGTAATTTTTGAGAA
1 GTTCGAGGGTAAAAATATG--ATTTTT--GAAGTTCGGGGG-CAAAATGTGATTTTTGA-AA
* *
48288465 GTGTAG-GGGTCAAAATATGATTTTTG
1 GT-TCGAGGGTAAAAATATGATTTTTG
48288491 GACAGTTCAG
Statistics
Matches: 113, Mismatches: 19, Indels: 24
0.72 0.12 0.15
Matches are distributed among these distances:
56 3 0.03
57 5 0.04
58 47 0.42
59 36 0.32
60 13 0.12
61 6 0.05
62 3 0.03
ACGTcount: A:0.34, C:0.04, G:0.29, T:0.34
Consensus pattern (56 bp):
GTTCGAGGGTAAAAATATGATTTTTGAAGTTCGGGGGCAAAATGTGATTTTTGAAA
Found at i:48288439 original size:30 final size:30
Alignment explanation
Indices: 48288386--48288466 Score: 110
Period size: 30 Copynumber: 2.7 Consensus size: 30
48288376 GCACGGGAGT
*
48288386 AAAAATGTGATTTTTGA-AAGTTTGAGGGA
1 AAAAATGTAATTTTTGAGAAGTTTGAGGGA
* * *
48288415 AAAAATGAAATTTTTGAGAAGTTTGGGGGT
1 AAAAATGTAATTTTTGAGAAGTTTGAGGGA
*
48288445 CAAAATGTAATTTTTGAGAAGT
1 AAAAATGTAATTTTTGAGAAGT
48288467 GTAGGGGTCA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
29 15 0.33
30 30 0.67
ACGTcount: A:0.38, C:0.01, G:0.26, T:0.35
Consensus pattern (30 bp):
AAAAATGTAATTTTTGAGAAGTTTGAGGGA
Found at i:48288474 original size:30 final size:30
Alignment explanation
Indices: 48288416--48288490 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
48288406 TTTGAGGGAA
* * *
48288416 AAAATGAAATTTTTGAGAAGTTTGGGGGTC
1 AAAATGTAATTTTTGAGAAGTGTAGGGGTC
48288446 AAAATGTAATTTTTGAGAAGTGTAGGGGTC
1 AAAATGTAATTTTTGAGAAGTGTAGGGGTC
* *
48288476 AAAATATGATTTTTG
1 AAAATGTAATTTTTG
48288491 GACAGTTCAG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.35, C:0.03, G:0.27, T:0.36
Consensus pattern (30 bp):
AAAATGTAATTTTTGAGAAGTGTAGGGGTC
Found at i:48289193 original size:3 final size:3
Alignment explanation
Indices: 48289180--48289246 Score: 55
Period size: 3 Copynumber: 22.0 Consensus size: 3
48289170 TTCTCTTTTT
* * * * *
48289180 TTA TTA ATA TTA TTTA ATA TTA ATA TTA TTA TTA ATA ATA -TA TTTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA
*
48289226 TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA
48289247 ATGTCATTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
2 2 0.04
3 45 0.87
4 5 0.10
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:48289905 original size:17 final size:17
Alignment explanation
Indices: 48289865--48289906 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
48289855 TTTTAATTTT
* *
48289865 AATTTAAAATAAATTTA
1 AATTTTAAATAAATTAA
*
48289882 AA-CTTAAATAAATTAA
1 AATTTTAAATAAATTAA
48289898 AATTTTAAA
1 AATTTTAAA
48289907 ATCTAAAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (17 bp):
AATTTTAAATAAATTAA
Found at i:48291982 original size:17 final size:18
Alignment explanation
Indices: 48291956--48292000 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
48291946 CAAATTTTTA
* *
48291956 AAATTTTTAAAAA-ATTT
1 AAATTATTAAAAATATTG
48291973 AAATTATTAAAAATATTG
1 AAATTATTAAAAATATTG
*
48291991 AAATAATTAA
1 AAATTATTAA
48292001 TTAATTATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (18 bp):
AAATTATTAAAAATATTG
Found at i:48295422 original size:407 final size:407
Alignment explanation
Indices: 48294667--48295479 Score: 1477
Period size: 407 Copynumber: 2.0 Consensus size: 407
48294657 GTTGAACTCT
*
48294667 AAGATCATGAGCAATCTGCCTCCGTTCCTCCTCCCCAGTATTGGAACTGAAAAACACTGTAGATT
1 AAGATCATGAGCAATCTGCCTCCGTTCCTCCTCCCCAGTATTGGAAATGAAAAACACTGTAGATT
*
48294732 TATTAAAGTTAACACAATGCCTAGAGTGCTTTTCGTATTCTTTCAAAATGGTCTTTAAAACTCGT
66 TATTAAAGTTAACACAATGCCCAGAGTGCTTTTCGTATTCTTTCAAAATGGTCTTTAAAACTCGT
*
48294797 ACCCCTTGGTTAGTAGCTTCTTCAAAAAGCACATAATTATCAGCAAATAACAAATGGGATATAGG
131 ACCCCTTGGTTAGTAGCTTCTTCAAAAAGCACATAATCATCAGCAAATAACAAATGGGATATAGG
* *
48294862 GGGCACTTCTACTTGCTTTAACCCCACTTAAAGACCCGTTATTAATGCTGATTCATAGTAATGAC
196 GGGCACTTCTACTTACTTTAACCCCACTTAAAGACCCGTTATTAATGCTAATTCATAGTAATGAC
48294927 GATAACCCCTCACTGCAAATAAGAAAAAGAAACAGGCTCAAAGGATCACCTTGTCGAAGCCCCTT
261 GATAACCCCTCACTGCAAATAAGAAAAAGAAACAGGCTCAAAGGATCACCTTGTCGAAGCCCCTT
*
48294992 GCTCGGTTTAAAAGGAATGCCAATACTTCCATTGAGACAAACGGAATATGAGACAGATGAAACAC
326 GCTCGATTTAAAAGGAATGCCAATACTTCCATTGAGACAAACGGAATATGAGACAGATGAAACAC
48295057 AATTCATAATCATCTCC
391 AATTCATAATCATCTCC
*
48295074 AAGATCATGAGCAATCTGCCTCCGTTCCTCCTCCCTAGTATTGGAAATGAAAAACACTGTAGATT
1 AAGATCATGAGCAATCTGCCTCCGTTCCTCCTCCCCAGTATTGGAAATGAAAAACACTGTAGATT
48295139 TATTAAAGTTAACACAATGCCCAGAGTG-TTCTTCGTATTCTTTC-AAATGGTCTTTAAAACTCG
66 TATTAAAGTTAACACAATGCCCAGAGTGCTT-TTCGTATTCTTTCAAAATGGTCTTTAAAACTCG
* *
48295202 TACCTCTTGGTTAGTAGCTTCTTCAAAAAGTACATAATCATCAGCAAATAACAAATGGGATATAG
130 TACCCCTTGGTTAGTAGCTTCTTCAAAAAGCACATAATCATCAGCAAATAACAAATGGGATATAG
48295267 GGGGCCACTTCTACTTACTTTAACCCCACTTAAAGACCCGTTATTAATGCTAATTCATAGTAATG
195 GGGG-CACTTCTACTTACTTTAACCCCACTTAAAGACCCGTTATTAATGCTAATTCATAGTAATG
* *
48295332 ACGATAACCCCTCACTGCAAATAAGAAAAAGAAACAGGCTCGAAGGATCACCTTGTCGAAGCCCT
259 ACGATAACCCCTCACTGCAAATAAGAAAAAGAAACAGGCTCAAAGGATCACCTTGTCGAAGCCCC
* *
48295397 TTGCTCGATTTAAAAGGAATGCCAATACTTCTATTGAGACAAATGGAATATGAGACAGATGAAAC
324 TTGCTCGATTTAAAAGGAATGCCAATACTTCCATTGAGACAAACGGAATATGAGACAGATGAAAC
48295462 ACAATTCATAATCATCTC
389 ACAATTCATAATCATCTC
48295480 TATCCATAAT
Statistics
Matches: 391, Mismatches: 13, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
406 87 0.22
407 304 0.78
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (407 bp):
AAGATCATGAGCAATCTGCCTCCGTTCCTCCTCCCCAGTATTGGAAATGAAAAACACTGTAGATT
TATTAAAGTTAACACAATGCCCAGAGTGCTTTTCGTATTCTTTCAAAATGGTCTTTAAAACTCGT
ACCCCTTGGTTAGTAGCTTCTTCAAAAAGCACATAATCATCAGCAAATAACAAATGGGATATAGG
GGGCACTTCTACTTACTTTAACCCCACTTAAAGACCCGTTATTAATGCTAATTCATAGTAATGAC
GATAACCCCTCACTGCAAATAAGAAAAAGAAACAGGCTCAAAGGATCACCTTGTCGAAGCCCCTT
GCTCGATTTAAAAGGAATGCCAATACTTCCATTGAGACAAACGGAATATGAGACAGATGAAACAC
AATTCATAATCATCTCC
Found at i:48299279 original size:13 final size:13
Alignment explanation
Indices: 48299261--48299285 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48299251 GAAATCAATT
48299261 TATAAATTATAAC
1 TATAAATTATAAC
48299274 TATAAATTATAA
1 TATAAATTATAA
48299286 TTAATATACC
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:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (13 bp):
TATAAATTATAAC
Found at i:48301841 original size:26 final size:25
Alignment explanation
Indices: 48301786--48301835 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
48301776 AGATGTGCTA
*
48301786 AAATTTAATTTCATTTTTTTTGAGG
1 AAATTTAATTTCATTTTCTTTGAGG
*
48301811 AAATTTAAATTTTATTATTCTTTGA
1 AAATTT-AATTTCATT-TTCTTTGA
48301836 TAAATTATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 6 0.29
26 8 0.38
27 7 0.33
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (25 bp):
AAATTTAATTTCATTTTCTTTGAGG
Found at i:48313226 original size:31 final size:31
Alignment explanation
Indices: 48313188--48313249 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
48313178 GAAATTTAAT
48313188 GTTGACATTATTGAAAGAGATATACTTAAAA
1 GTTGACATTATTGAAAGAGATATACTTAAAA
*
48313219 GTTGACATTATTGAAAGAGATCTACTTAAAA
1 GTTGACATTATTGAAAGAGATATACTTAAAA
48313250 TTTATGAATT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (31 bp):
GTTGACATTATTGAAAGAGATATACTTAAAA
Found at i:48313960 original size:2 final size:2
Alignment explanation
Indices: 48313953--48314043 Score: 182
Period size: 2 Copynumber: 45.5 Consensus size: 2
48313943 AATGATGATG
48313953 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
48313995 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
48314037 GA GA GA G
1 GA GA GA G
48314044 CAGTGGGTTA
Statistics
Matches: 89, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:48315000 original size:34 final size:34
Alignment explanation
Indices: 48314962--48315033 Score: 117
Period size: 34 Copynumber: 2.1 Consensus size: 34
48314952 AGTAAACAAC
* *
48314962 ATTTGGGTAAGGTAAAAGATAAAAAATTAAAAAT
1 ATTTGGATAAGATAAAAGATAAAAAATTAAAAAT
*
48314996 ATTTGGATAAGATAAAAGGTAAAAAATTAAAAAT
1 ATTTGGATAAGATAAAAGATAAAAAATTAAAAAT
48315030 ATTT
1 ATTT
48315034 AGGTTTAATT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.56, C:0.00, G:0.15, T:0.29
Consensus pattern (34 bp):
ATTTGGATAAGATAAAAGATAAAAAATTAAAAAT
Found at i:48315415 original size:33 final size:31
Alignment explanation
Indices: 48315372--48315440 Score: 77
Period size: 33 Copynumber: 2.1 Consensus size: 31
48315362 TTAAAGTATT
* *
48315372 AAATTTTTATT-TTTAATAATTAAATTTAAATA
1 AAATTTTTATTATTAAATAA-T-AATTCAAATA
48315404 AAATATTTTATTAATTAAATAATAATTCAAATA
1 AAAT-TTTTATT-ATTAAATAATAATTCAAATA
48315437 AAAT
1 AAAT
48315441 CAATCTACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 4 0.12
33 20 0.62
34 1 0.03
35 7 0.22
ACGTcount: A:0.52, C:0.01, G:0.00, T:0.46
Consensus pattern (31 bp):
AAATTTTTATTATTAAATAATAATTCAAATA
Found at i:48315642 original size:31 final size:31
Alignment explanation
Indices: 48315602--48315660 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
48315592 AAAAGATAAG
* **
48315602 TAAATTATTTAAAAGTTTTTATTTAAGTCAC
1 TAAACTATTTAAAAAATTTTATTTAAGTCAC
48315633 TAAACTATTTAAAAAATTTTATTTAAGT
1 TAAACTATTTAAAAAATTTTATTTAAGT
48315661 AATTGGGCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (31 bp):
TAAACTATTTAAAAAATTTTATTTAAGTCAC
Found at i:48324357 original size:2 final size:2
Alignment explanation
Indices: 48324350--48324378 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
48324340 TTATTCTTAT
48324350 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48324379 TTATGTAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:48324710 original size:3 final size:3
Alignment explanation
Indices: 48324702--48324727 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
48324692 TTTATCTTGT
48324702 ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA AT
48324728 TTCTTTAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
ATA
Found at i:48324812 original size:13 final size:14
Alignment explanation
Indices: 48324796--48324828 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
48324786 TTAATTCTTA
48324796 TATTTTAATTTA-G
1 TATTTTAATTTATG
*
48324809 TATTTTAGTTTATG
1 TATTTTAATTTATG
48324823 TATTTT
1 TATTTT
48324829 TAATGGATCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 11 0.61
14 7 0.39
ACGTcount: A:0.24, C:0.00, G:0.09, T:0.67
Consensus pattern (14 bp):
TATTTTAATTTATG
Found at i:48327418 original size:3 final size:3
Alignment explanation
Indices: 48327410--48327462 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
48327400 ACAAATAAAG
48327410 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
48327458 TAT TA
1 TAT TA
48327463 ATTTATTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:48335243 original size:25 final size:25
Alignment explanation
Indices: 48335205--48335256 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
48335195 CTCAAATGTT
48335205 TTTTAAAATATTAAATATTTTTATA
1 TTTTAAAATATTAAATATTTTTATA
*
48335230 TTTTAATAAT-TTAAATATTTTTTTA
1 TTTTAA-AATATTAAATATTTTTATA
48335255 TT
1 TT
48335257 AATGTATGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
25 22 0.88
26 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (25 bp):
TTTTAAAATATTAAATATTTTTATA
Found at i:48341532 original size:27 final size:26
Alignment explanation
Indices: 48341498--48341549 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
48341488 CTGTTTTCAG
48341498 AATAATATTTTCAT-TGATTTTAATCA
1 AATAATATTTTCATATGA-TTTAATCA
48341524 AATATATATTTTCATATGATTTAATC
1 AATA-ATATTTTCATATGATTTAATC
48341550 GTACTGTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.17
27 17 0.71
28 3 0.12
ACGTcount: A:0.38, C:0.08, G:0.04, T:0.50
Consensus pattern (26 bp):
AATAATATTTTCATATGATTTAATCA
Found at i:48344851 original size:19 final size:19
Alignment explanation
Indices: 48344827--48344901 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
48344817 AAATATATAA
48344827 AAAAATATTTTTAAAAATT
1 AAAAATATTTTTAAAAATT
48344846 AAAAATCATTAAATTATTAAAAAGTAT
1 AAAAAT-A-T---TT-TTAAAAA-T-T
*
48344873 AAAAATATTTTTAAAAAAT
1 AAAAATATTTTTAAAAATT
*
48344892 AAAAAAATTT
1 AAAAATATTT
48344902 AATTAAATAC
Statistics
Matches: 46, Mismatches: 2, Indels: 16
0.72 0.03 0.25
Matches are distributed among these distances:
19 16 0.35
20 1 0.02
21 8 0.17
22 2 0.04
24 2 0.04
25 8 0.17
26 2 0.04
27 7 0.15
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (19 bp):
AAAAATATTTTTAAAAATT
Found at i:48344907 original size:21 final size:21
Alignment explanation
Indices: 48344859--48344908 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
48344849 AATCATTAAA
*
48344859 TTATTAAAAAGTATAAAAATAT
1 TTATTAAAAAG-ATAAAAAAAT
48344881 TT-TTAAAAA-ATAAAAAAAT
1 TTATTAAAAAGATAAAAAAAT
48344900 TTAATTAAA
1 TT-ATTAAA
48344909 TACTGATGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 11 0.44
21 12 0.48
22 2 0.08
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (21 bp):
TTATTAAAAAGATAAAAAAAT
Found at i:48347055 original size:2 final size:2
Alignment explanation
Indices: 48347048--48347086 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
48347038 CCCTGGTATG
48347048 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
48347087 CCTCCCCCCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:48351105 original size:17 final size:17
Alignment explanation
Indices: 48351079--48351175 Score: 85
Period size: 17 Copynumber: 5.8 Consensus size: 17
48351069 AGCTTTTGAT
*
48351079 TTTAAATTAATTTTAAA
1 TTTAATTTAATTTTAAA
* *
48351096 TTTTATTTAAATTTAAA
1 TTTAATTTAATTTTAAA
*
48351113 TTTAAATTT-ATCTTAAA
1 TTT-AATTTAATTTTAAA
48351130 TTTAAATTT-A-TTTAAA
1 TTT-AATTTAATTTTAAA
*
48351146 TTT-ATCTTAAATTTAAA
1 TTTAAT-TTAATTTTAAA
*
48351163 TTTAATTAAATTT
1 TTTAATTTAATTT
48351176 AAAAGGATAT
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
14 2 0.03
15 2 0.03
16 9 0.14
17 47 0.71
18 6 0.09
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAATTTAATTTTAAA
Found at i:48351122 original size:6 final size:6
Alignment explanation
Indices: 48351079--48351178 Score: 94
Period size: 6 Copynumber: 18.0 Consensus size: 6
48351069 AGCTTTTGAT
* *
48351079 TTTAAA -TTAAT TTTAAA TTT-TA TTTAAA TTTAAA TTTAAA TTT--A
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
48351123 TCTTAAA TTTAAA TTT--A TTTAAA TTT--A TCTTAAA TTTAAA TTT-AA
1 T-TTAAA TTTAAA TTTAAA TTTAAA TTTAAA T-TTAAA TTTAAA TTTAAA
48351168 -TTAAA TTTAAA
1 TTTAAA TTTAAA
48351179 AGGATATTAA
Statistics
Matches: 78, Mismatches: 4, Indels: 24
0.74 0.04 0.23
Matches are distributed among these distances:
4 10 0.13
5 16 0.21
6 48 0.62
7 4 0.05
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (6 bp):
TTTAAA
Found at i:48351150 original size:27 final size:27
Alignment explanation
Indices: 48351100--48351176 Score: 127
Period size: 27 Copynumber: 2.8 Consensus size: 27
48351090 TTTAAATTTT
48351100 ATTTAAATTTAAATTTAAATTTATCTTAA
1 ATTTAAATTT--ATTTAAATTTATCTTAA
48351129 ATTTAAATTTATTTAAATTTATCTTAA
1 ATTTAAATTTATTTAAATTTATCTTAA
*
48351156 ATTTAAATTTAATTAAATTTA
1 ATTTAAATTTATTTAAATTTA
48351177 AAAGGATATT
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
27 37 0.79
29 10 0.21
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTTAAATTTATTTAAATTTATCTTAA
Found at i:48351169 original size:11 final size:11
Alignment explanation
Indices: 48351079--48351177 Score: 82
Period size: 11 Copynumber: 9.0 Consensus size: 11
48351069 AGCTTTTGAT
48351079 TTTAAA-TTAA
1 TTTAAATTTAA
*
48351089 TTTTAAATTTTA
1 -TTTAAATTTAA
48351101 TTTAAATTTAAA
1 TTTAAATTT-AA
48351113 TTTAAATTT-A
1 TTTAAATTTAA
48351123 TCTTAAATTTAAA
1 T-TTAAATTT-AA
48351136 TTT--ATTTAAA
1 TTTAAATTT-AA
** *
48351146 TTTATCTTAAA
1 TTTAAATTTAA
48351157 TTTAAATTTAA
1 TTTAAATTTAA
48351168 -TTAAATTTAA
1 TTTAAATTTAA
48351178 AAGGATATTA
Statistics
Matches: 74, Mismatches: 7, Indels: 15
0.77 0.07 0.16
Matches are distributed among these distances:
10 22 0.30
11 33 0.45
12 17 0.23
13 2 0.03
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:48353177 original size:30 final size:30
Alignment explanation
Indices: 48353143--48353243 Score: 88
Period size: 28 Copynumber: 3.5 Consensus size: 30
48353133 CGATTTCACC
*
48353143 AAAATTTACCGTTTTACCCTTGAACTTTCT
1 AAAATTTACCATTTTACCCTTGAACTTTCT
* * * *
48353173 AAAA-TT-CCATTTTAACCTCG--TTTTCACC
1 AAAATTTACCATTTTACCCTTGAACTTT--CT
*
48353201 AAAATTTACCATTTTACCCCTGAACTTTCT
1 AAAATTTACCATTTTACCCTTGAACTTTCT
48353231 AAAA-TT-CCATTTT
1 AAAATTTACCATTTT
48353244 TGACCCCGAT
Statistics
Matches: 55, Mismatches: 10, Indels: 14
0.70 0.13 0.18
Matches are distributed among these distances:
26 3 0.05
28 23 0.42
29 6 0.11
30 20 0.36
32 3 0.05
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.42
Consensus pattern (30 bp):
AAAATTTACCATTTTACCCTTGAACTTTCT
Found at i:48353357 original size:117 final size:116
Alignment explanation
Indices: 48353096--48353419 Score: 383
Period size: 117 Copynumber: 2.8 Consensus size: 116
48353086 GAAATTATAT
* *
48353096 TTTTACCCC-CGAACTTTCCAAAATTCCA-TTTTAAGCCCGATTTCACCAAAATT-TACCGTTTT
1 TTTTACCCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAATTATA--ATTTT
* * * *
48353158 ACCCTTGAACTTTCTAAAATTCCA-TTTTAACCTCGTTTTCACCAAAATTTACCA
64 ACCC-CGAAC-TTCCAAAATTCCATTTTTAACCTCGATTCCACCAAAATTTACCA
* *
48353212 TTTTACCCCT-GAACTTTCTAAAATTCCATTTTTGACCCCGATTTCACCAAAATTATAATTTTAC
1 TTTTACCCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAATTATAATTTTAC
*
48353276 TCCCGAATCTTCCAAAATTCCATTTTTGACCTCGATTCCACCAAAA-TTACCA
66 -CCCGAA-CTTCCAAAATTCCATTTTTAACCTCGATTCCACCAAAATTTACCA
* * * **
48353328 TTTTACCCCTCGAACTTTCCAAAACTCCATTTTTAACCTCGATTTCACTAAAAATTACCATTTTA
1 TTTTACCCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCAC-CAAAATTATAATTTTA
48353393 CCCCCGAACCTTCC-AAATTACCATTTT
65 -CCCCGAA-CTTCCAAAATT-CCATTTT
48353420 ATTCCCGAAT
Statistics
Matches: 181, Mismatches: 17, Indels: 18
0.84 0.08 0.08
Matches are distributed among these distances:
116 63 0.35
117 84 0.46
118 33 0.18
119 1 0.01
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.36
Consensus pattern (116 bp):
TTTTACCCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCACCAAAATTATAATTTTAC
CCCGAACTTCCAAAATTCCATTTTTAACCTCGATTCCACCAAAATTTACCA
Found at i:48353368 original size:59 final size:58
Alignment explanation
Indices: 48353096--48353419 Score: 397
Period size: 58 Copynumber: 5.6 Consensus size: 58
48353086 GAAATTATAT
*
48353096 TTTTACCCCCGAACTTTCCAAAATTCCA-TTTTAAGCC-CGATTTCACCAAAATTTACCG
1 TTTTACCCCCGAACTTTCCAAAATTCCATTTTTAA-CCTCGATTTCACCAAAA-TTACCA
** * *
48353154 TTTTACCCTTGAACTTTCTAAAATTCCA-TTTTAACCTCGTTTTCACCAAAATTTACCA
1 TTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAA-TTACCA
* * * * **
48353212 TTTTACCCCTGAACTTTCTAAAATTCCATTTTTGACCCCGATTTCACCAAAATTATAA
1 TTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAATTACCA
* * *
48353270 TTTTACTCCCGAA-TCTTCCAAAATTCCATTTTTGACCTCGATTCCACCAAAATTACCA
1 TTTTACCCCCGAACT-TTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAATTACCA
* *
48353328 TTTTACCCCTCGAACTTTCCAAAACTCCATTTTTAACCTCGATTTCACTAAAAATTACCA
1 TTTTACCCC-CGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCAC-CAAAATTACCA
*
48353388 TTTTACCCCCGAACCTTCC-AAATTACCATTTT
1 TTTTACCCCCGAACTTTCCAAAATT-CCATTTT
48353420 ATTCCCGAAT
Statistics
Matches: 234, Mismatches: 25, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
57 3 0.01
58 142 0.61
59 69 0.29
60 20 0.09
ACGTcount: A:0.30, C:0.29, G:0.05, T:0.36
Consensus pattern (58 bp):
TTTTACCCCCGAACTTTCCAAAATTCCATTTTTAACCTCGATTTCACCAAAATTACCA
Found at i:48355148 original size:17 final size:17
Alignment explanation
Indices: 48355128--48355160 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
48355118 ATTATTTTAA
48355128 TATT-TATATTATAGTAG
1 TATTATATATT-TAGTAG
48355145 TATTATATATTTAGTA
1 TATTATATATTTAGTA
48355161 TATGTTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (17 bp):
TATTATATATTTAGTAG
Found at i:48367872 original size:37 final size:37
Alignment explanation
Indices: 48367816--48367889 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
48367806 CATGTATAGC
*
48367816 TAAAATGAAAATTCTAAATTGTGGACTTCCATGCTCT
1 TAAAATGAAAATTCCAAATTGTGGACTTCCATGCTCT
* *
48367853 TAAATTGAAATTTCCAAATTGTGGACTTCCATGCTCT
1 TAAAATGAAAATTCCAAATTGTGGACTTCCATGCTCT
48367890 AATTACTGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.14, T:0.36
Consensus pattern (37 bp):
TAAAATGAAAATTCCAAATTGTGGACTTCCATGCTCT
Found at i:48373754 original size:10 final size:10
Alignment explanation
Indices: 48373722--48373754 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
48373712 CGTGAGGGCG
48373722 GAAAGAGAGA
1 GAAAGAGAGA
*
48373732 GAGAGAGAGA
1 GAAAGAGAGA
48373742 GAAAGAGAGA
1 GAAAGAGAGA
48373752 GAA
1 GAA
48373755 GTGATTAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.58, C:0.00, G:0.42, T:0.00
Consensus pattern (10 bp):
GAAAGAGAGA
Found at i:48376372 original size:9 final size:9
Alignment explanation
Indices: 48376350--48376407 Score: 66
Period size: 9 Copynumber: 6.2 Consensus size: 9
48376340 AAATTATTTT
48376350 TTAAAA-TA
1 TTAAAATTA
48376358 -TAAAATTA
1 TTAAAATTA
48376366 TTAAAATTA
1 TTAAAATTA
48376375 TTTTAAAATTAA
1 --TTAAAATT-A
48376387 TTTAAAATTA
1 -TTAAAATTA
48376397 TTAAAATTA
1 TTAAAATTA
48376406 TT
1 TT
48376408 TGTTTGAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
7 5 0.11
8 2 0.04
9 19 0.42
10 1 0.02
11 17 0.38
12 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
TTAAAATTA
Found at i:48376379 original size:40 final size:40
Alignment explanation
Indices: 48376329--48376407 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
48376319 ACATGTCAGC
*
48376329 AAATGATTTTAAAATTATTTTTTAAAA-TA-TAAAATTATTA
1 AAATGATTTTAAAATTA--ATTTAAAATTATTAAAATTATTA
*
48376369 AAATTATTTTAAAATTAATTTAAAATTATTAAAATTATT
1 AAATGATTTTAAAATTAATTTAAAATTATTAAAATTATT
48376408 TGTTTGAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
38 7 0.20
39 2 0.06
40 26 0.74
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (40 bp):
AAATGATTTTAAAATTAATTTAAAATTATTAAAATTATTA
Found at i:48376381 original size:20 final size:20
Alignment explanation
Indices: 48376338--48376408 Score: 69
Period size: 20 Copynumber: 3.5 Consensus size: 20
48376328 CAAATGATTT
48376338 TAAAATTATTTTTTAAAA-TA-
1 TAAAATTA--TTTTAAAATTAT
48376358 TAAAATTA--TTAAAATTATTT
1 TAAAATTATTTTAAAATTA--T
*
48376378 TAAAATTAATTTAAAATTAT
1 TAAAATTATTTTAAAATTAT
48376398 TAAAATTATTT
1 TAAAATTATTT
48376409 GTTTGAAATA
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
16 6 0.14
17 2 0.05
20 27 0.61
22 9 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TAAAATTATTTTAAAATTAT
Found at i:48376396 original size:31 final size:29
Alignment explanation
Indices: 48376337--48376441 Score: 104
Period size: 31 Copynumber: 3.5 Consensus size: 29
48376327 GCAAATGATT
**
48376337 TTAAAATTATTTTTTAAAATATAAAATTA
1 TTAAAATTATTTTAAAAAATATAAAATTA
*
48376366 TTAAAATTATTTTAAAATTAATTTAAAATTA
1 TTAAAATTATTTTAAAA--AATATAAAATTA
***
48376397 TTAAAATTATTTGTTTGAAATAATAAAATTA
1 TTAAAATTATTT-TAAAAAAT-ATAAAATTA
*
48376428 TT-AAATAATTTTAA
1 TTAAAATTATTTTAA
48376442 TTTCTAATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
29 16 0.26
30 11 0.18
31 33 0.53
32 2 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (29 bp):
TTAAAATTATTTTAAAAAATATAAAATTA
Found at i:48377512 original size:29 final size:29
Alignment explanation
Indices: 48377481--48377581 Score: 134
Period size: 29 Copynumber: 3.4 Consensus size: 29
48377471 ATTAAAATTA
48377481 TTTAATAATTTTATTATTTAAAAAAATAAT
1 TTTAATAATTTTATTATTT-AAAAAATAAT
* *
48377511 TTTAATAATTTTAATAATTT-TAAAATAAT
1 TTTAATAATTTT-ATTATTTAAAAAATAAT
*
48377540 TTTAACAATTTTA-TATTTTAAAAAATAAT
1 TTTAATAATTTTATTA-TTTAAAAAATAAT
48377569 TTTAATAATTTTA
1 TTTAATAATTTTA
48377582 AAATTATTTG
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
27 1 0.02
28 4 0.06
29 39 0.63
30 12 0.19
31 6 0.10
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
TTTAATAATTTTATTATTTAAAAAATAAT
Found at i:48377519 original size:9 final size:9
Alignment explanation
Indices: 48377505--48377586 Score: 81
Period size: 9 Copynumber: 9.8 Consensus size: 9
48377495 TATTTAAAAA
48377505 AATAATTTT
1 AATAATTTT
48377514 AATAATTTT
1 AATAATTTT
48377523 AATAATTTT
1 AATAATTTT
48377532 AAAATAATTTT
1 --AATAATTTT
*
48377543 AACAATTTT
1 AATAATTTT
48377552 -AT-ATTTT
1 AATAATTTT
48377559 AA-AA----
1 AATAATTTT
48377563 AATAATTTT
1 AATAATTTT
48377572 AATAATTTT
1 AATAATTTT
48377581 AA-AATT
1 AATAATT
48377587 ATTTGCTGAT
Statistics
Matches: 62, Mismatches: 2, Indels: 19
0.75 0.02 0.23
Matches are distributed among these distances:
4 2 0.03
5 2 0.03
7 5 0.08
8 7 0.11
9 37 0.60
11 9 0.15
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (9 bp):
AATAATTTT
Found at i:48377539 original size:20 final size:20
Alignment explanation
Indices: 48377503--48377590 Score: 80
Period size: 20 Copynumber: 4.5 Consensus size: 20
48377493 ATTATTTAAA
48377503 AAAATAATTTTAATAATTTT
1 AAAATAATTTTAATAATTTT
48377523 --AATAATTTTAAAATAATTTT
1 AAAATAATTTT--AATAATTTT
*
48377543 --AACAATTTT-AT-ATTTT
1 AAAATAATTTTAATAATTTT
48377559 AAAAAATAATTTTAATAATTTT
1 --AAAATAATTTTAATAATTTT
*
48377581 AAAATTATTT
1 AAAATAATTT
48377591 GCTGATGTGG
Statistics
Matches: 57, Mismatches: 3, Indels: 16
0.75 0.04 0.21
Matches are distributed among these distances:
16 5 0.09
17 2 0.04
18 9 0.16
20 34 0.60
21 2 0.04
22 5 0.09
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (20 bp):
AAAATAATTTTAATAATTTT
Found at i:48377564 original size:58 final size:57
Alignment explanation
Indices: 48377472--48377586 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 57
48377462 AAATTGGAAA
* *
48377472 TTAAAATTATTTAATAATTTTATTATTTAAAAAAATAATTTTAATAATTTTAATAATT
1 TTAAAATAATTTAACAATTTTATTATTTAAAAAAATAATTTTAATAATTTTAA-AATT
*
48377530 TTAAAATAATTTTAACAATTTTA-TATTTTAAAAAATAATTTTAATAATTTTAAAATT
1 TTAAAATAA-TTTAACAATTTTATTATTTAAAAAAATAATTTTAATAATTTTAAAATT
48377587 ATTTGCTGAT
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
57 4 0.08
58 37 0.70
59 12 0.23
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (57 bp):
TTAAAATAATTTAACAATTTTATTATTTAAAAAAATAATTTTAATAATTTTAAAATT
Found at i:48382019 original size:91 final size:90
Alignment explanation
Indices: 48381894--48382117 Score: 297
Period size: 91 Copynumber: 2.4 Consensus size: 90
48381884 ATAAAATGTT
* * *
48381894 CAATGTGATACCTGAACTATTAATTTGTATATTATTTGGTACTTGTACTTTCATAAAATGTTCAA
1 CAATGTGATA-CTGAACTATCAATTTGTGTATTATTTGGTACTTGTACTTTCATAAAATGTCCAA
48381959 TATGGTACTTATACTTTGAAAATATC
65 TATGGTACTTATACTTTGAAAATATC
* * * *
48381985 CAATATGATATCTGAACTATCAATTTGTGCATTATTTAGTACTTGTACTTTCATAAATTGTCCAA
1 CAATGTGATA-CTGAACTATCAATTTGTGTATTATTTGGTACTTGTACTTTCATAAAATGTCCAA
* * *
48382050 TGTGGTACTTATACTTTGAAAATGTT
65 TATGGTACTTATACTTTGAAAATATC
*
48382076 CAATGT-AGTACTTGAATTATCAATTTGTGTATTATTATGGTA
1 CAATGTGA-TAC-TGAACTATCAATTTGTGTATTATT-TGGTA
48382118 TCTAAAATTA
Statistics
Matches: 115, Mismatches: 15, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
90 2 0.02
91 109 0.95
92 4 0.03
ACGTcount: A:0.32, C:0.12, G:0.13, T:0.43
Consensus pattern (90 bp):
CAATGTGATACTGAACTATCAATTTGTGTATTATTTGGTACTTGTACTTTCATAAAATGTCCAAT
ATGGTACTTATACTTTGAAAATATC
Found at i:48382088 original size:29 final size:31
Alignment explanation
Indices: 48382021--48382088 Score: 86
Period size: 29 Copynumber: 2.3 Consensus size: 31
48382011 GTGCATTATT
*
48382021 TAGTACTTGTACTTTCATAAATTGTCCAATG
1 TAGTACTTATACTTTCATAAATTGTCCAATG
* * *
48382052 TGGTACTTATACTTTGA-AAA-TGTTCAATG
1 TAGTACTTATACTTTCATAAATTGTCCAATG
48382081 TAGTACTT
1 TAGTACTT
48382089 GAATTATCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
29 15 0.47
30 3 0.09
31 14 0.44
ACGTcount: A:0.29, C:0.13, G:0.15, T:0.43
Consensus pattern (31 bp):
TAGTACTTATACTTTCATAAATTGTCCAATG
Found at i:48383000 original size:30 final size:31
Alignment explanation
Indices: 48382947--48383028 Score: 101
Period size: 31 Copynumber: 2.6 Consensus size: 31
48382937 TATTTTTTTT
* * *
48382947 AGCTTTTAAGGGCTCAAAAAAAAATTTCACC
1 AGCTTTTAAGGGATCTAAAAAAATTTTCACC
*
48382978 AGCTTTTAAGGGATCTAAAAAAATTTTCTCC
1 AGCTTTTAAGGGATCTAAAAAAATTTTCACC
* * *
48383009 AACATTTAAGGAATCTAAAA
1 AGCTTTTAAGGGATCTAAAA
48383029 CCCATTTTAT
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.43, C:0.16, G:0.12, T:0.29
Consensus pattern (31 bp):
AGCTTTTAAGGGATCTAAAAAAATTTTCACC
Found at i:48387538 original size:58 final size:59
Alignment explanation
Indices: 48387476--48387611 Score: 213
Period size: 59 Copynumber: 2.3 Consensus size: 59
48387466 TTGGATACCC
* *
48387476 GGGGGCAAAATGGTAATTTTAGTTGGAATTG-GGTTAAAAATGGGATTTTTAAAAGTTT
1 GGGGGCAAAATGGTAATTTTAGGTGAAATTGAGGTTAAAAATGGGATTTTTAAAAGTTT
* * *
48387534 GGGGGTAAAATGGTAATTTTTGGTGAAATTGAGGTTAAAAATGGGATTTTTAGAAGTTT
1 GGGGGCAAAATGGTAATTTTAGGTGAAATTGAGGTTAAAAATGGGATTTTTAAAAGTTT
48387593 GGGGGCAAAAT-GTAATTTT
1 GGGGGCAAAATGGTAATTTT
48387612 TGAAAAGTTT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
58 35 0.49
59 36 0.51
ACGTcount: A:0.32, C:0.01, G:0.30, T:0.36
Consensus pattern (59 bp):
GGGGGCAAAATGGTAATTTTAGGTGAAATTGAGGTTAAAAATGGGATTTTTAAAAGTTT
Found at i:48387591 original size:59 final size:58
Alignment explanation
Indices: 48387476--48387613 Score: 215
Period size: 58 Copynumber: 2.4 Consensus size: 58
48387466 TTGGATACCC
* * *
48387476 GGGGGCAAAATGGTAATTTTAGTTGGAATTGGGTTAAAAATGGGATTTTTAAAAGTTT
1 GGGGGCAAAATGGTAATTTTTGGTGAAATTGGGTTAAAAATGGGATTTTTAAAAGTTT
* *
48387534 GGGGGTAAAATGGTAATTTTTGGTGAAATTGAGGTTAAAAATGGGATTTTTAGAAGTTT
1 GGGGGCAAAATGGTAATTTTTGGTGAAATTG-GGTTAAAAATGGGATTTTTAAAAGTTT
48387593 GGGGGCAAAAT-GTAATTTTTG
1 GGGGGCAAAATGGTAATTTTTG
48387614 AAAAGTTTAG
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
58 37 0.51
59 36 0.49
ACGTcount: A:0.32, C:0.01, G:0.30, T:0.36
Consensus pattern (58 bp):
GGGGGCAAAATGGTAATTTTTGGTGAAATTGGGTTAAAAATGGGATTTTTAAAAGTTT
Found at i:48387744 original size:30 final size:30
Alignment explanation
Indices: 48387579--48387733 Score: 172
Period size: 30 Copynumber: 5.1 Consensus size: 30
48387569 TAAAAATGGG
*
48387579 ATTTTTAG-AAG-TTTGGGGGCAAAATGTA
1 ATTTTTAGAAAGTTTTGGGGTCAAAATGTA
*
48387607 ATTTTT-GAAAAGTTTAGGGGGGATCAAAATGTA
1 ATTTTTAG-AAAGTTT--TGGGG-TCAAAATGTA
* * *
48387640 ATTTTTAGAAAGTATTGGGATCAAAATATA
1 ATTTTTAGAAAGTTTTGGGGTCAAAATGTA
* * *
48387670 ATTTTTAGGAAGTTTTGGTGTCAAAATGTG
1 ATTTTTAGAAAGTTTTGGGGTCAAAATGTA
*
48387700 ATTTTTAGAAAGTTTTGGGGTCAAAATATA
1 ATTTTTAGAAAGTTTTGGGGTCAAAATGTA
48387730 ATTT
1 ATTT
48387734 CTAAATAGTT
Statistics
Matches: 104, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.01
28 6 0.06
29 3 0.03
30 65 0.62
31 3 0.03
32 4 0.04
33 21 0.20
34 1 0.01
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (30 bp):
ATTTTTAGAAAGTTTTGGGGTCAAAATGTA
Found at i:48387744 original size:60 final size:61
Alignment explanation
Indices: 48387571--48387748 Score: 202
Period size: 60 Copynumber: 2.9 Consensus size: 61
48387561 ATTGAGGTTA
* * *
48387571 AAAATGGGATTTTTAG-AAG-TTTGGGGGCAAAATGTAATTTTTGAAAAGTTTAGGGGGGATC
1 AAAATGTGATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTT-AAAAGTTTA-GGGGGATC
* * * * * *
48387632 AAAATGTAATTTTTAGAAAGTATTGGGATCAAAATATAATTTTTAGGAAGTTT-TGGTG-TC
1 AAAATGTGATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTTA-AAAGTTTAGGGGGATC
*
48387692 AAAATGTGATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTCTAAATAGTTTAGGG
1 AAAATGTGATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTTAAA-AGTTTAGGG
48387749 ACCTATAAAA
Statistics
Matches: 97, Mismatches: 15, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
59 1 0.01
60 48 0.49
61 19 0.20
62 4 0.04
63 25 0.26
ACGTcount: A:0.35, C:0.03, G:0.24, T:0.37
Consensus pattern (61 bp):
AAAATGTGATTTTTAGAAAGTTTTGGGGTCAAAATATAATTTTTAAAAGTTTAGGGGGATC
Found at i:48389368 original size:19 final size:19
Alignment explanation
Indices: 48389324--48389374 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
48389314 AATTCAAATT
48389324 AAATTTAAACTT--AAGTA
1 AAATTTAAACTTAAAAGTA
48389341 AAATTTAAACTTAAAAG-A
1 AAATTTAAACTTAAAAGTA
48389359 AAAGTTTAAACTTAAA
1 AAA-TTTAAACTTAAA
48389375 CTAAATTAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
17 12 0.39
18 4 0.13
19 15 0.48
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (19 bp):
AAATTTAAACTTAAAAGTA
Found at i:48389405 original size:35 final size:35
Alignment explanation
Indices: 48389366--48389439 Score: 94
Period size: 35 Copynumber: 2.1 Consensus size: 35
48389356 AGAAAAGTTT
** * **
48389366 AAACTTAAACTAAATTAAAATTTAATCATGAATTA
1 AAACTTAAAAAAAATTAAAAGTTAAAAATGAATTA
*
48389401 AAACTTAAAAAAAATTAAAAGTTAAAAATGAATTT
1 AAACTTAAAAAAAATTAAAAGTTAAAAATGAATTA
48389436 AAAC
1 AAAC
48389440 ATTAGGCCCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.59, C:0.07, G:0.04, T:0.30
Consensus pattern (35 bp):
AAACTTAAAAAAAATTAAAAGTTAAAAATGAATTA
Found at i:48389418 original size:17 final size:17
Alignment explanation
Indices: 48389324--48389428 Score: 75
Period size: 17 Copynumber: 6.0 Consensus size: 17
48389314 AATTCAAATT
* **
48389324 AAATTTAAACTTAAGTA
1 AAATTAAAACTTAAAAA
*
48389341 AAATTTAAACTTAAAAGA
1 AAATTAAAACTTAAAA-A
* **
48389359 AAAGTTTAAACTTAAACT
1 AAA-TTAAAACTTAAAAA
* * *
48389377 AAATTAAAATTTAATCAT
1 AAATTAAAACTTAA-AAA
*
48389395 GAATTAAAACTTAAAAA
1 AAATTAAAACTTAAAAA
*
48389412 AAATTAAAAGTTAAAAA
1 AAATTAAAACTTAAAAA
48389429 TGAATTTAAA
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
17 39 0.55
18 20 0.28
19 12 0.17
ACGTcount: A:0.59, C:0.06, G:0.05, T:0.30
Consensus pattern (17 bp):
AAATTAAAACTTAAAAA
Found at i:48389434 original size:18 final size:18
Alignment explanation
Indices: 48389378--48389439 Score: 63
Period size: 18 Copynumber: 3.5 Consensus size: 18
48389368 ACTTAAACTA
* **
48389378 AATTAAAATTTAATCATG
1 AATTAAAACTTAAAAATG
*
48389396 AATTAAAACTTAAAAA-A
1 AATTAAAACTTAAAAATG
*
48389413 AATTAAAAGTTAAAAATG
1 AATTAAAACTTAAAAATG
*
48389431 AATTTAAAC
1 AATTAAAAC
48389440 ATTAGGCCCG
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
17 15 0.43
18 20 0.57
ACGTcount: A:0.60, C:0.05, G:0.05, T:0.31
Consensus pattern (18 bp):
AATTAAAACTTAAAAATG
Found at i:48391556 original size:2 final size:2
Alignment explanation
Indices: 48391549--48391585 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
48391539 TAAGTTCTTT
48391549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
48391586 TGTATGCATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:48401697 original size:24 final size:24
Alignment explanation
Indices: 48401666--48401715 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
48401656 TTTGATGAAG
48401666 TGTTGATCAAT-TTCTA-TGGGCTT
1 TGTTGATC-ATGTTCTATTGGGCTT
*
48401689 TGTTCGATCATGTTGTATTGGGCTT
1 TGTT-GATCATGTTCTATTGGGCTT
48401714 TG
1 TG
48401716 GGCTATACTG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
23 6 0.26
24 8 0.35
25 9 0.39
ACGTcount: A:0.14, C:0.12, G:0.26, T:0.48
Consensus pattern (24 bp):
TGTTGATCATGTTCTATTGGGCTT
Found at i:48425288 original size:2 final size:2
Alignment explanation
Indices: 48425281--48425328 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
48425271 TAACAAGACA
48425281 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
48425323 AT AT AT
1 AT AT AT
48425329 TAATAGTTTT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48426065 original size:23 final size:24
Alignment explanation
Indices: 48426031--48426080 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
48426021 TTCTTCTTGC
48426031 TTTCAATATTTT-TTTTAATTAAT
1 TTTCAATATTTTATTTTAATTAAT
* *
48426054 TTTCAAGT-TTTTATTTTATTTTAT
1 TTTCAA-TATTTTATTTTAATTAAT
48426078 TTT
1 TTT
48426081 TAGTTCACAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.24, C:0.04, G:0.02, T:0.70
Consensus pattern (24 bp):
TTTCAATATTTTATTTTAATTAAT
Found at i:48427372 original size:24 final size:23
Alignment explanation
Indices: 48427317--48427384 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 23
48427307 GTAAAAAATA
*
48427317 TTTAATATTTTTAAAAAAAGTACAGTT
1 TTTAATATTTTT---AAAA-TATAGTT
48427344 TTTAATATATTTTAAAATATAGTT
1 TTTAATAT-TTTTAAAATATAGTT
48427368 TTTAATATTTTTAAAAT
1 TTTAATATTTTTAAAAT
48427385 TTAAATATAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
23 9 0.23
24 14 0.36
25 4 0.10
27 8 0.21
28 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.51
Consensus pattern (23 bp):
TTTAATATTTTTAAAATATAGTT
Found at i:48427423 original size:19 final size:19
Alignment explanation
Indices: 48427367--48427428 Score: 74
Period size: 19 Copynumber: 3.3 Consensus size: 19
48427357 AAAATATAGT
48427367 TTTTAA-TATTTTT-AAAA
1 TTTTAATTATTTTTAAAAA
* * *
48427384 TTTAAATATATATTTACAAA
1 TTTTAAT-TATTTTTAAAAA
48427404 TTTTAATTATTTTTAAAAA
1 TTTTAATTATTTTTAAAAA
48427423 TTTTAA
1 TTTTAA
48427429 AAAATTACAA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
17 5 0.14
19 22 0.61
20 9 0.25
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTTTAATTATTTTTAAAAA
Found at i:48427462 original size:18 final size:18
Alignment explanation
Indices: 48427437--48427487 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
48427427 AAAAAATTAC
*
48427437 AATTTTTATAATTTTAAG
1 AATTTTTACAATTTTAAG
* *
48427455 ATTTTTTACAATTTGAAG
1 AATTTTTACAATTTTAAG
*
48427473 AATCTTTACAATTTT
1 AATTTTTACAATTTT
48427488 TTTGTATTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (18 bp):
AATTTTTACAATTTTAAG
Found at i:48427996 original size:16 final size:16
Alignment explanation
Indices: 48427975--48428013 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
48427965 GTTTGGTTCG
48427975 CTGTAATGGAATAGAA
1 CTGTAATGGAATAGAA
*
48427991 CTGTAATGGAATAGAG
1 CTGTAATGGAATAGAA
48428007 CTGTAAT
1 CTGTAAT
48428014 CAGTAATTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.26, T:0.28
Consensus pattern (16 bp):
CTGTAATGGAATAGAA
Found at i:48428249 original size:58 final size:56
Alignment explanation
Indices: 48428182--48428328 Score: 170
Period size: 59 Copynumber: 2.5 Consensus size: 56
48428172 AATTTTAATG
*
48428182 ATTATTATTAAATATAATTGAATAAAAATAT-TAATTTATTTAATTATATTTTAACATA
1 ATTATTATTAAATATAATT-AATAAAAATATGTAATTTA-ATAA-TATATTTTAACATA
* * *
48428240 ATTATTATTAAATACAATTTAATAAAATAATATGTAATTTAATAATATTTTTTAATATA
1 ATTATTATTAAATATAA-TTAAT-AAA-AATATGTAATTTAATAATATATTTTAACATA
*
48428299 ATTATTATTAAAATATGAATTAGTAAAAAT
1 ATTATTATT-AAATAT-AATTAATAAAAAT
48428329 TATAATATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 12
0.81 0.06 0.13
Matches are distributed among these distances:
58 22 0.29
59 29 0.38
60 17 0.22
61 9 0.12
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (56 bp):
ATTATTATTAAATATAATTAATAAAAATATGTAATTTAATAATATATTTTAACATA
Found at i:48433520 original size:35 final size:37
Alignment explanation
Indices: 48433481--48433556 Score: 102
Period size: 38 Copynumber: 2.1 Consensus size: 37
48433471 TGCAGCATAA
* *
48433481 CAATCCAAAA-TATC-CCTATCATTCATAAGTTTAGC
1 CAATCCAAAACTAACACCTAACATTCATAAGTTTAGC
*
48433516 CAATCCAAAAGCTAACAGCTAACATTCATAAGTTTAGC
1 CAATCCAAAA-CTAACACCTAACATTCATAAGTTTAGC
48433554 CAA
1 CAA
48433557 CCTTTTTTCC
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 10 0.29
37 3 0.09
38 22 0.63
ACGTcount: A:0.41, C:0.25, G:0.08, T:0.26
Consensus pattern (37 bp):
CAATCCAAAACTAACACCTAACATTCATAAGTTTAGC
Found at i:48446394 original size:2 final size:2
Alignment explanation
Indices: 48446387--48446413 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
48446377 CACAAAAGAA
48446387 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
48446414 ATTTAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:48449777 original size:24 final size:22
Alignment explanation
Indices: 48449722--48449763 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
48449712 GCTTCTTCAT
*
48449722 AAGCGTCGCTAATGCTCTGATG
1 AAGCGCCGCTAATGCTCTGATG
48449744 AAGCGCCGCTAATGCTCTGA
1 AAGCGCCGCTAATGCTCTGA
48449764 CCTTTAGCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (22 bp):
AAGCGCCGCTAATGCTCTGATG
Found at i:48449876 original size:40 final size:40
Alignment explanation
Indices: 48449744--48449968 Score: 180
Period size: 41 Copynumber: 5.8 Consensus size: 40
48449734 TGCTCTGATG
* * *
48449744 AAGCGCCGCTAATGCTCTGACCTTTAGCGGCGCTTACTCAT
1 AAGCGACGCTAATGCTCTGACCTTTAGCGGTGC-TCCTCAT
* ** *
48449785 AAG-TACTGCTAATGCTCTGACCTTTAATGGTGTTTCCTCAT
1 AAGCGAC-GCTAATGCTCTGACCTTTAGCGGTG-CTCCTCAT
* *
48449826 AAGCGCCGTTAATGCTCTGACCTTTAGCGGTGCTCCTCAT
1 AAGCGACGCTAATGCTCTGACCTTTAGCGGTGCTCCTCAT
* * *
48449866 AAGCGACGTTAATTCTCTGACCTTTAGCGGCGCT--T-AT
1 AAGCGACGCTAATGCTCTGACCTTTAGCGGTGCTCCTCAT
** *
48449903 ----GA-GCTAATATTCTGACCTTTAGCGGCGCTTCCTCAT
1 AAGCGACGCTAATGCTCTGACCTTTAGCGGTGC-TCCTCAT
* * * *
48449939 AAGCGCCGCTAGTGCTATGACTTTTAGCGG
1 AAGCGACGCTAATGCTCTGACCTTTAGCGG
48449969 CGTTTATTGA
Statistics
Matches: 147, Mismatches: 25, Indels: 24
0.75 0.13 0.12
Matches are distributed among these distances:
32 23 0.16
33 3 0.02
35 1 0.01
36 2 0.01
37 2 0.01
38 1 0.01
40 40 0.27
41 74 0.50
42 1 0.01
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.32
Consensus pattern (40 bp):
AAGCGACGCTAATGCTCTGACCTTTAGCGGTGCTCCTCAT
Found at i:48449965 original size:73 final size:72
Alignment explanation
Indices: 48449841--48449975 Score: 189
Period size: 73 Copynumber: 1.9 Consensus size: 72
48449831 CCGTTAATGC
* * * *
48449841 TCTGACCTTTAGCGGTGCTCCTCATAAGCGACGTTAATTCTCTGACCTTTAGCGGCGCTTATGAG
1 TCTGACCTTTAGCGGCGCTCCTCATAAGCGACGCTAATGCTATGACCTTTAGCGGCGCTTATGAG
48449906 CTAATAT
66 CTAATAT
* * * *
48449913 TCTGACCTTTAGCGGCGCTTCCTCATAAGCGCCGCTAGTGCTATGACTTTTAGCGGCGTTTAT
1 TCTGACCTTTAGCGGCGC-TCCTCATAAGCGACGCTAATGCTATGACCTTTAGCGGCGCTTAT
48449976 TGAAAAGCGC
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
72 17 0.31
73 37 0.69
ACGTcount: A:0.19, C:0.26, G:0.22, T:0.33
Consensus pattern (72 bp):
TCTGACCTTTAGCGGCGCTCCTCATAAGCGACGCTAATGCTATGACCTTTAGCGGCGCTTATGAG
CTAATAT
Found at i:48449984 original size:41 final size:40
Alignment explanation
Indices: 48449939--48450051 Score: 154
Period size: 40 Copynumber: 2.8 Consensus size: 40
48449929 GCTTCCTCAT
* * *
48449939 AAGCGCCGCTAGTGCTATGACTTTTAGCGGCGTTTATTGAA
1 AAGCGCCGCTATTGCT-TTACTTTTAGCGGCGTTAATTGAA
* * *
48449980 AAGCGCCACTATTGCTTTACCTTTAGCGGCATTAATTGAA
1 AAGCGCCGCTATTGCTTTACTTTTAGCGGCGTTAATTGAA
*
48450020 AAGCGCCGCTATTGCTTTACTTTTTGCGGCGT
1 AAGCGCCGCTATTGCTTTACTTTTAGCGGCGT
48450052 CTTCTTTCCA
Statistics
Matches: 62, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
40 48 0.77
41 14 0.23
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (40 bp):
AAGCGCCGCTATTGCTTTACTTTTAGCGGCGTTAATTGAA
Found at i:48451114 original size:28 final size:28
Alignment explanation
Indices: 48451082--48451144 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
48451072 ACCTAAATTT
48451082 TAAATTTTGAAAAAGTAAAA-TAAAAAAA
1 TAAATTTTGAAAAA-TAAAAGTAAAAAAA
* * *
48451110 TAAATTTTTAGAAATAAAAGTAAATAAA
1 TAAATTTTGAAAAATAAAAGTAAAAAAA
48451138 TAAATTT
1 TAAATTT
48451145 CTAGCGGACG
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (28 bp):
TAAATTTTGAAAAATAAAAGTAAAAAAA
Found at i:48458174 original size:28 final size:28
Alignment explanation
Indices: 48458132--48458194 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
48458122 CGTCCGCTAG
48458132 AAATTTATTTATTTACTTTTA-TTTCTAA
1 AAATTTATTTATTTA-TTTTACTTTCTAA
* * *
48458160 AAATTTATTTTTTTATTTTACTTTTTCA
1 AAATTTATTTATTTATTTTACTTTCTAA
48458188 AAATTTA
1 AAATTTA
48458195 AAATTTAGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.32, C:0.06, G:0.00, T:0.62
Consensus pattern (28 bp):
AAATTTATTTATTTATTTTACTTTCTAA
Found at i:48459281 original size:40 final size:40
Alignment explanation
Indices: 48459225--48459337 Score: 163
Period size: 40 Copynumber: 2.8 Consensus size: 40
48459215 TGGAAAGAAG
* *
48459225 ACGCCGCAAAAAGTAAAGCAATAGCGGCGCTTTTCAATTA
1 ACGCCGCTAAAAGTAAAGCAATAGCGGCGCTTTTCAATAA
* *
48459265 ACGCCGCTAAAGGTAAAGCAATAGTGGCGCTTTTCAATAA
1 ACGCCGCTAAAAGTAAAGCAATAGCGGCGCTTTTCAATAA
* *
48459305 ACGCCGCTAAAAGTCATAGCACTAGCGGCGCTT
1 ACGCCGCTAAAAGT-AAAGCAATAGCGGCGCTT
48459338 ATGAGGAAGC
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
40 49 0.77
41 15 0.23
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (40 bp):
ACGCCGCTAAAAGTAAAGCAATAGCGGCGCTTTTCAATAA
Found at i:48459482 original size:41 final size:41
Alignment explanation
Indices: 48459376--48459532 Score: 190
Period size: 41 Copynumber: 3.9 Consensus size: 41
48459366 ATTAGCTCAT
* * *
48459376 AAGCGCCGCTAAAGGTCAGAGAATTAACGTCGCTTATGAGG
1 AAGCACCGCTAAAGGTCAGAGCATTAACGGCGCTTATGAGG
48459417 -AGCACCGCTAAAGGTCAGAGCATTAACGGCGCTTATGAGG
1 AAGCACCGCTAAAGGTCAGAGCATTAACGGCGCTTATGAGG
* ** * * ** *
48459457 AAACACCATTAAAGGTCAGAGCATTAGCAGTACTTATGAGT
1 AAGCACCGCTAAAGGTCAGAGCATTAACGGCGCTTATGAGG
* *
48459498 AAGCGCCGCTAAAGGTCAGAGCATTAGCGGCGCTT
1 AAGCACCGCTAAAGGTCAGAGCATTAACGGCGCTT
48459533 CATCAGAGCA
Statistics
Matches: 97, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 37 0.38
41 60 0.62
ACGTcount: A:0.32, C:0.21, G:0.27, T:0.20
Consensus pattern (41 bp):
AAGCACCGCTAAAGGTCAGAGCATTAACGGCGCTTATGAGG
Found at i:48459531 original size:24 final size:22
Alignment explanation
Indices: 48459499--48459553 Score: 56
Period size: 22 Copynumber: 2.4 Consensus size: 22
48459489 CTTATGAGTA
*
48459499 AGCGCCGCTAAAGGTCAGAGCATT
1 AGCGACGCTAAA--TCAGAGCATT
* **
48459523 AGCGGCGCTTCATCAGAGCATT
1 AGCGACGCTAAATCAGAGCATT
48459545 AGCGACGCT
1 AGCGACGCT
48459554 TATGAAGAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 18 0.67
24 9 0.33
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.18
Consensus pattern (22 bp):
AGCGACGCTAAATCAGAGCATT
Found at i:48459541 original size:22 final size:22
Alignment explanation
Indices: 48459513--48459554 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
48459503 CCGCTAAAGG
*
48459513 TCAGAGCATTAGCGGCGCTTCA
1 TCAGAGCATTAGCGACGCTTCA
48459535 TCAGAGCATTAGCGACGCTT
1 TCAGAGCATTAGCGACGCTT
48459555 ATGAAGAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (22 bp):
TCAGAGCATTAGCGACGCTTCA
Found at i:48462880 original size:13 final size:13
Alignment explanation
Indices: 48462864--48462888 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
48462854 TATTTAAATT
48462864 ATATATATATATA
1 ATATATATATATA
48462877 ATATATATATAT
1 ATATATATATAT
48462889 TTCTTTTGTG
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:48471302 original size:24 final size:24
Alignment explanation
Indices: 48471252--48471303 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
48471242 AAAGTTCAAA
**
48471252 ATATTTATAAAAAAATCAAAATTT
1 ATATTTATAAAAAAATCAAAAAAT
*
48471276 ATATTT-TTAAAAAATCTAAAAAAT
1 ATATTTATAAAAAAATC-AAAAAAT
48471300 ATAT
1 ATAT
48471304 AAAGAAACTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 9 0.38
24 15 0.62
ACGTcount: A:0.58, C:0.04, G:0.00, T:0.38
Consensus pattern (24 bp):
ATATTTATAAAAAAATCAAAAAAT
Found at i:48475273 original size:15 final size:15
Alignment explanation
Indices: 48475253--48475281 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48475243 CAACTGTAAG
48475253 TTCTAGAAATAGTAT
1 TTCTAGAAATAGTAT
48475268 TTCTAGAAATAGTA
1 TTCTAGAAATAGTA
48475282 GTAGAATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (15 bp):
TTCTAGAAATAGTAT
Found at i:48479568 original size:15 final size:15
Alignment explanation
Indices: 48479548--48479576 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
48479538 TCCATTCTAC
48479548 TACTATTTCTAGAAA
1 TACTATTTCTAGAAA
48479563 TACTATTTCTAGAA
1 TACTATTTCTAGAA
48479577 CTTACAGTTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (15 bp):
TACTATTTCTAGAAA
Found at i:48488168 original size:22 final size:21
Alignment explanation
Indices: 48488143--48488183 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
48488133 TTTTTATAAA
48488143 TAAATAACACTTTTATAATATG
1 TAAATAA-ACTTTTATAATATG
* *
48488165 TAAATTAATTTTTATAATA
1 TAAATAAACTTTTATAATA
48488184 AGCTTTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 11 0.65
22 6 0.35
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (21 bp):
TAAATAAACTTTTATAATATG
Found at i:48492924 original size:17 final size:17
Alignment explanation
Indices: 48492902--48492940 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
48492892 CTCCACCTTC
* * *
48492902 ACAAGAATTCTCTACGA
1 ACAAGAACTCTCAACAA
48492919 ACAAGAACTCTCAACAA
1 ACAAGAACTCTCAACAA
48492936 ACAAG
1 ACAAG
48492941 TTCTCCACCT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.26, G:0.10, T:0.15
Consensus pattern (17 bp):
ACAAGAACTCTCAACAA
Found at i:48504033 original size:8 final size:8
Alignment explanation
Indices: 48504020--48504057 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
48504010 TATTTATAAA
48504020 ATATTATT
1 ATATTATT
*
48504028 ATATTATA
1 ATATTATT
48504036 ATATTATT
1 ATATTATT
48504044 A-ATTATT
1 ATATTATT
*
48504051 AAATTAT
1 ATATTAT
48504058 CTTTTGATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 7 0.26
8 20 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (8 bp):
ATATTATT
Found at i:48507625 original size:18 final size:21
Alignment explanation
Indices: 48507588--48507625 Score: 55
Period size: 18 Copynumber: 2.0 Consensus size: 21
48507578 AAATAAAAAA
48507588 ATATTATCGTAATAATATAAC
1 ATATTATCGTAATAATATAAC
48507609 ATATT-TCGT-AT-ATATAA
1 ATATTATCGTAATAATATAA
48507626 AAGAAATATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
18 6 0.35
19 2 0.12
20 4 0.24
21 5 0.29
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (21 bp):
ATATTATCGTAATAATATAAC
Found at i:48508789 original size:16 final size:17
Alignment explanation
Indices: 48508752--48508797 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
48508742 CTTCATTTAT
48508752 TTCCCCTTTTCTTCTTC
1 TTCCCCTTTTCTTCTTC
48508769 TTCCCC-TTTCATTCTTC
1 TTCCCCTTTTC-TTCTTC
*
48508786 -TCCCTTTTTCTT
1 TTCCCCTTTTCTT
48508798 TCACCAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (17 bp):
TTCCCCTTTTCTTCTTC
Found at i:48512707 original size:26 final size:26
Alignment explanation
Indices: 48512658--48512707 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
48512648 TATTAAGATA
* *
48512658 AATAATATTTATCTTTATGTTAATTG
1 AATAAGATTTATCTTTATGATAATTG
48512684 AATAAGATTTAT-TTTCATGATAAT
1 AATAAGATTTATCTTT-ATGATAAT
48512708 AGCATTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (26 bp):
AATAAGATTTATCTTTATGATAATTG
Found at i:48512736 original size:7 final size:7
Alignment explanation
Indices: 48512726--48512761 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
48512716 TTTTTTATAG
48512726 TAAATAT
1 TAAATAT
48512733 TAAATAT
1 TAAATAT
48512740 TAAATAT
1 TAAATAT
48512747 TAAAT-T
1 TAAATAT
48512753 T-AATAT
1 TAAATAT
48512759 TAA
1 TAA
48512762 GATAAATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 3 0.11
6 4 0.15
7 20 0.74
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (7 bp):
TAAATAT
Found at i:48512769 original size:12 final size:12
Alignment explanation
Indices: 48512726--48512772 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
48512716 TTTTTTATAG
48512726 TAAATATTAAATAT
1 TAAATATT-AA-AT
48512740 TAAATATTAAAT
1 TAAATATTAAAT
*
48512752 TTAATATTAAGA-
1 TAAATATTAA-AT
48512764 TAAATATTA
1 TAAATATTA
48512773 TTTAACTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
12 19 0.63
13 3 0.10
14 8 0.27
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (12 bp):
TAAATATTAAAT
Found at i:48516526 original size:3 final size:3
Alignment explanation
Indices: 48516518--48516553 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
48516508 GATTGAGGCT
48516518 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
48516554 AAAAGATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:48519272 original size:24 final size:24
Alignment explanation
Indices: 48519244--48519306 Score: 99
Period size: 24 Copynumber: 2.6 Consensus size: 24
48519234 AGAAATAATC
48519244 TTTCAGTTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
*
48519268 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTATTTG
* *
48519292 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
48519307 TATTACTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTATTTG
Found at i:48521261 original size:24 final size:24
Alignment explanation
Indices: 48521234--48521295 Score: 97
Period size: 24 Copynumber: 2.6 Consensus size: 24
48521224 AGAAATAATC
48521234 TTCAGTTAAACTCTGTTTATTTGT
1 TTCAGTTAAACTCTGTTTATTTGT
*
48521258 TTCAATTAAACTCTGTTTATTTGT
1 TTCAGTTAAACTCTGTTTATTTGT
* *
48521282 TTGAGTCAAACTCT
1 TTCAGTTAAACTCT
48521296 TATTACTCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.50
Consensus pattern (24 bp):
TTCAGTTAAACTCTGTTTATTTGT
Found at i:48522340 original size:18 final size:19
Alignment explanation
Indices: 48522317--48522371 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 19
48522307 TTGATTAACT
48522317 AAATAAAAT-TAATGTAAA
1 AAATAAAATATAATGTAAA
*
48522335 AAAT-AAATAAAAT-TAAA
1 AAATAAAATATAATGTAAA
48522352 AAATAGAAATACTAATGTAA
1 AAATA-AAATA-TAATGTAA
48522372 GGTTTAAGGT
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
17 12 0.40
18 7 0.23
19 5 0.17
20 3 0.10
21 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.25
Consensus pattern (19 bp):
AAATAAAATATAATGTAAA
Found at i:48524366 original size:140 final size:140
Alignment explanation
Indices: 48523940--48524618 Score: 787
Period size: 140 Copynumber: 5.0 Consensus size: 140
48523930 ATAGTCTTAA
* * *
48523940 GACACTTTTGGGCCGACACTTTTCTAAGTGTTCGGATAGACTTGCCAACATATGCTTTGGCCAAC
1 GACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACGCTTTGGCCAAC
* * * * *
48524005 TCTTTATATAAGGTTTGGGATATGCATGCCTAAGACAACGCTTAAATAACAGTTGGCTTTGTCCA
66 TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCA
*
48524070 ATACTATGCC
131 ACACTATGCC
* * * *
48524080 GACACTTTTGGGCCGACACTTTTCTAAGTGTTGGGATAGACTTGCCGACATACGCTTTGACTAAC
1 GACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACGCTTTGGCCAAC
** *
48524145 TCTTTTGTATAAGCATTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGCCTTTGTCC
66 TC-TTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCC
48524210 AACACTATGCC
130 AACACTATGCC
* * * *
48524221 TACACTTTTGGGCCGATACTTTCCAAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAAC
1 GACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACGCTTTGGCCAAC
* * *
48524286 TCTTTGTATAAGGGATGGGATATGCATGCCTAAGGCAATGCTTAAATAAGAGTTGGCTTTGT---
66 TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCA
48524348 ---CTA----
131 ACACTATGCC
* * * * * * **
48524351 -ACAC-TAT--GCCGACACTTTCCTAAATATTGGGATAGAGTTGCTAACATACGCTTAGAACAAC
1 GACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACGCTTTGGCCAAC
* * * **
48524412 TCTTTGTATAAGGGTTGGAATATCCATGCCTAAGGCAAGGCTTAAATAAGAGTCAACTTTG-CCT
66 TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCC-
** *
48524476 AGTATTATGCC
130 AACACTATGCC
* ** *
48524487 GACATTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTG-CGGCATACGCTTTGGCTAAC
1 GACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACGCTTTGGCCAAC
* * * * * *
48524551 TCTTTGTATAAGAGTTGGGATATGCATGCCTAAGACAACACTTAAATAAGAGTCAGTTTTGTTCA
66 TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCA
48524616 ACA
131 ACA
48524619 TTATAACGAC
Statistics
Matches: 453, Mismatches: 69, Indels: 35
0.81 0.12 0.06
Matches are distributed among these distances:
126 98 0.22
128 2 0.00
129 4 0.01
132 2 0.00
134 3 0.01
137 3 0.01
138 2 0.00
139 68 0.15
140 147 0.32
141 124 0.27
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (140 bp):
GACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATACGCTTTGGCCAAC
TCTTTGTATAAGGGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCA
ACACTATGCC
Found at i:48524457 original size:126 final size:126
Alignment explanation
Indices: 48524232--48524464 Score: 342
Period size: 126 Copynumber: 1.8 Consensus size: 126
48524222 ACACTTTTGG
* * * **
48524232 GCCGATACTTTCCAAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAACTCTTTGTATAA
1 GCCGACACTTTCCAAAGTATTGGGATAGACTTGCCAACATACACTTAGAACAACTCTTTGTATAA
* * *
48524297 GGGATGGGATATGCATGCCTAAGGCAATGCTTAAATAAGAGTTGGCTTTGTCTAACACTAT
66 GGGATGGAATATCCATGCCTAAGGCAAGGCTTAAATAAGAGTTGGCTTTGTCTAACACTAT
* * *
48524358 GCCGACACTTTCCTAAA-TATTGGGATAGAGTTGCTAACATACGCTTAGAACAACTCTTTGTATA
1 GCCGACACTTTCC-AAAGTATTGGGATAGACTTGCCAACATACACTTAGAACAACTCTTTGTATA
*
48524422 AGGGTTGGAATATCCATGCCTAAGGCAAGGCTTAAATAAGAGT
65 AGGGATGGAATATCCATGCCTAAGGCAAGGCTTAAATAAGAGT
48524465 CAACTTTGCC
Statistics
Matches: 94, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
126 91 0.97
127 3 0.03
ACGTcount: A:0.30, C:0.18, G:0.22, T:0.29
Consensus pattern (126 bp):
GCCGACACTTTCCAAAGTATTGGGATAGACTTGCCAACATACACTTAGAACAACTCTTTGTATAA
GGGATGGAATATCCATGCCTAAGGCAAGGCTTAAATAAGAGTTGGCTTTGTCTAACACTAT
Found at i:48524472 original size:126 final size:126
Alignment explanation
Indices: 48524232--48524490 Score: 331
Period size: 126 Copynumber: 2.1 Consensus size: 126
48524222 ACACTTTTGG
* * * **
48524232 GCCGATACTTTCCAAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAACTCTTTGTATAA
1 GCCGACACTTTCCAAAGTATTGGGATAGACTTGCCAACATACACTTAGAACAACTCTTTGTATAA
* * * *** *
48524297 GGGATGGGATATGCATGCCTAAGGCAATGCTTAAATAAGAGTTGGCTTTGTCTAACACTAT
66 GGGATGGAATATCCATGCCTAAGGCAAGGCTTAAATAAGAGTCAACTTTGCCTAACACTAT
* * *
48524358 GCCGACACTTTCCTAAA-TATTGGGATAGAGTTGCTAACATACGCTTAGAACAACTCTTTGTATA
1 GCCGACACTTTCC-AAAGTATTGGGATAGACTTGCCAACATACACTTAGAACAACTCTTTGTATA
* ** *
48524422 AGGGTTGGAATATCCATGCCTAAGGCAAGGCTTAAATAAGAGTCAACTTTGCCTAGTATTAT
65 AGGGATGGAATATCCATGCCTAAGGCAAGGCTTAAATAAGAGTCAACTTTGCCTAACACTAT
48524484 GCCGACA
1 GCCGACA
48524491 TTTTTGGGCC
Statistics
Matches: 113, Mismatches: 19, Indels: 2
0.84 0.14 0.01
Matches are distributed among these distances:
126 110 0.97
127 3 0.03
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.29
Consensus pattern (126 bp):
GCCGACACTTTCCAAAGTATTGGGATAGACTTGCCAACATACACTTAGAACAACTCTTTGTATAA
GGGATGGAATATCCATGCCTAAGGCAAGGCTTAAATAAGAGTCAACTTTGCCTAACACTAT
Found at i:48524650 original size:266 final size:267
Alignment explanation
Indices: 48523940--48524633 Score: 718
Period size: 281 Copynumber: 2.6 Consensus size: 267
48523930 ATAGTCTTAA
* * * **
48523940 GACACTTTTGGGCCGACACTTTTCTAAGTGTTCGGATAGACTTGCCAACATATGCTTTGGCCAAC
1 GACACTTTTGGGCCGACACTTTCCAAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAAC
* * * * ** *
48524005 TCTTTATATAAG-GTTTGGGATATGCATGCCTAAGACAACGCTTAAATAACAGTTGGCTTTGTCC
66 TCTTTGTATAAGAG-ATGGGATATGCATGCCTAAGACAACACTTAAATAAGAGTCAGCTTTGTCT
* * * *
48524069 AATACTATGCCGACACTTTTGGGCCGACACTTTTCT-AAGTGTTGGGATAGACTTGCCGACATAC
130 AACACTAT----A-A---------CGACACTTTCCTAAAG-ATTGGGATAGACTTGCCAACATAC
* * *
48524133 GCTTTGACTAACTCTTTTGTATAAGCATTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAG
180 GCTTAGACTAACTCTTTTGTATAAGCATTGGAATATCCATGCCTAAGGCAACGCTTAAATAAGAG
**
48524198 TCGCCTTTGTCCAACACTATGCC
245 TCAACTTTGTCCAACACTATGCC
* *
48524221 TACACTTTTGGGCCGATACTTTCCAAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAAC
1 GACACTTTTGGGCCGACACTTTCCAAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAAC
* * ** **
48524286 TCTTTGTATAAGGGATGGGATATGCATGCCTAAGGCAATGCTTAAATAAGAGTTGGCTTTGTCTA
66 TCTTTGTATAAGAGATGGGATATGCATGCCTAAGACAACACTTAAATAAGAGTCAGCTTTGTCTA
** * * *
48524351 ACACTATGCCGACACTTTCCTAAATATTGGGATAGAGTTGCTAACATACGCTTAGAAC-AACTC-
131 ACACTATAACGACACTTTCCTAAAGATTGGGATAGACTTGCCAACATACGCTTAG-ACTAACTCT
** * *
48524414 TTTGTATAAGGGTTGGAATATCCATGCCTAAGGCAAGGCTTAAATAAGAGTCAACTTTG-CCTAG
195 TTTGTATAAGCATTGGAATATCCATGCCTAAGGCAACGCTTAAATAAGAGTCAACTTTGTCC-AA
* *
48524478 TATTATGCC
259 CACTATGCC
* * ** * *
48524487 GACATTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTG-CGGCATACGCTTTGGCTAAC
1 GACACTTTTGGGCCGACACTTTCCAAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAAC
* *
48524551 TCTTTGTATAAGAGTTGGGATATGCATGCCTAAGACAACACTTAAATAAGAGTCAGTTTTGT-TC
66 TCTTTGTATAAGAGATGGGATATGCATGCCTAAGACAACACTTAAATAAGAGTCAGCTTTGTCT-
* *
48524615 AACATTATAACGACTCTTT
130 AACACTATAACGACACTTT
48524634 GTATAACGGA
Statistics
Matches: 355, Mismatches: 53, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
264 1 0.00
265 87 0.25
266 100 0.28
267 41 0.12
268 4 0.01
281 121 0.34
282 1 0.00
ACGTcount: A:0.28, C:0.20, G:0.21, T:0.31
Consensus pattern (267 bp):
GACACTTTTGGGCCGACACTTTCCAAAGTGTTGGGATAGACTTGCCAACATACACTTTGGCCAAC
TCTTTGTATAAGAGATGGGATATGCATGCCTAAGACAACACTTAAATAAGAGTCAGCTTTGTCTA
ACACTATAACGACACTTTCCTAAAGATTGGGATAGACTTGCCAACATACGCTTAGACTAACTCTT
TTGTATAAGCATTGGAATATCCATGCCTAAGGCAACGCTTAAATAAGAGTCAACTTTGTCCAACA
CTATGCC
Found at i:48524689 original size:78 final size:78
Alignment explanation
Indices: 48524549--48524701 Score: 220
Period size: 78 Copynumber: 2.0 Consensus size: 78
48524539 GCTTTGGCTA
* *
48524549 ACTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGACAACACTTAAATAAGAGTCAGTTTTGTT
1 ACTCTTTGTATAAGAGATGGGATATGCATGCCTAAGACAACACTTAAATAAGAGTCAGTTTTGTC
*
48524614 CAACATTATAACG
66 CAACAGTATAACG
* * *
48524627 ACTCTTTGTATAACG-GATGGGATATGCATGCCTAAGGCAACATTTAAATAAGAGT-TGATTTTG
1 ACTCTTTGTATAA-GAGATGGGATATGCATGCCTAAGACAACACTTAAATAAGAGTCAG-TTTTG
48524690 TCCAACAGTATA
64 TCCAACAGTATA
48524702 CTTAAGGCAA
Statistics
Matches: 67, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
77 1 0.01
78 65 0.97
79 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (78 bp):
ACTCTTTGTATAAGAGATGGGATATGCATGCCTAAGACAACACTTAAATAAGAGTCAGTTTTGTC
CAACAGTATAACG
Found at i:48525618 original size:16 final size:16
Alignment explanation
Indices: 48525597--48525635 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
48525587 AATTATATTT
48525597 TAATATTACCCTAAAA
1 TAATATTACCCTAAAA
*
48525613 TAATATATTCCCTAAAA
1 TAATAT-TACCCTAAAA
48525630 -AATATT
1 TAATATT
48525636 TTTATTGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 11 0.52
17 9 0.43
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.36
Consensus pattern (16 bp):
TAATATTACCCTAAAA
Found at i:48525627 original size:17 final size:17
Alignment explanation
Indices: 48525599--48525634 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
48525589 TTATATTTTA
48525599 ATATTACCCTAAAATAAT
1 ATATTACCCTAAAA-AAT
48525617 ATATT-CCCTAAAAAAT
1 ATATTACCCTAAAAAAT
48525633 AT
1 AT
48525635 TTTTATTGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 5 0.28
17 8 0.44
18 5 0.28
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (17 bp):
ATATTACCCTAAAAAAT
Found at i:48525795 original size:20 final size:20
Alignment explanation
Indices: 48525770--48525821 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
48525760 TTTTAAAATT
48525770 TTAAACCCTAAATCCT-AGA
1 TTAAACCCTAAATCCTAAGA
*
48525789 GTTAAACCCTAAATCTTAAGA
1 -TTAAACCCTAAATCCTAAGA
*
48525810 TTAAACCATAAA
1 TTAAACCCTAAA
48525822 CCCCAAACCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 26 0.90
21 3 0.10
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.27
Consensus pattern (20 bp):
TTAAACCCTAAATCCTAAGA
Found at i:48525848 original size:27 final size:27
Alignment explanation
Indices: 48525771--48525935 Score: 126
Period size: 27 Copynumber: 6.1 Consensus size: 27
48525761 TTTAAAATTT
*
48525771 TAAACCCTAAATCCT-AGAGTTAAACCC
1 TAAACCTTAAATCCTAAG-GTTAAACCC
* ***
48525798 TAAATCTTAAGAT--TAAACCATAAACCC
1 TAAACCTTAA-ATCCT-AAGGTTAAACCC
* * *
48525825 CAAACCTTAAATCCTAAGGCTAAACCT
1 TAAACCTTAAATCCTAAGGTTAAACCC
*
48525852 TAAGA-C-TAAATCTTAAGGTTAAACCC
1 TAA-ACCTTAAATCCTAAGGTTAAACCC
* *
48525878 TAAACACTTAAA-CCTAAAGTTAAATCC
1 TAAAC-CTTAAATCCTAAGGTTAAACCC
* *
48525905 TAAACCCTAAATTCTAAGGTTAAACCC
1 TAAACCTTAAATCCTAAGGTTAAACCC
48525932 TAAA
1 TAAA
48525936 TTATAGGGTT
Statistics
Matches: 106, Mismatches: 22, Indels: 20
0.72 0.15 0.14
Matches are distributed among these distances:
25 1 0.01
26 28 0.26
27 68 0.64
28 9 0.08
ACGTcount: A:0.44, C:0.24, G:0.07, T:0.25
Consensus pattern (27 bp):
TAAACCTTAAATCCTAAGGTTAAACCC
Found at i:48525888 original size:54 final size:53
Alignment explanation
Indices: 48525818--48525935 Score: 141
Period size: 54 Copynumber: 2.2 Consensus size: 53
48525808 GATTAAACCA
* * * *
48525818 TAAACCCCAAACCTTAAATCCTAAGGCTAAA-CCTTAAGACTAAA-TCTTAAGGT
1 TAAACCCTAAACCTTAAA-CCTAAAGCTAAATCCTAAACACTAAATTC-TAAGGT
* *
48525871 TAAACCCTAAACACTTAAACCTAAAGTTAAATCCTAAACCCTAAATTCTAAGGT
1 TAAACCCTAAAC-CTTAAACCTAAAGCTAAATCCTAAACACTAAATTCTAAGGT
48525925 TAAACCCTAAA
1 TAAACCCTAAA
48525936 TTATAGGGTT
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
53 21 0.38
54 33 0.59
55 2 0.04
ACGTcount: A:0.44, C:0.25, G:0.07, T:0.25
Consensus pattern (53 bp):
TAAACCCTAAACCTTAAACCTAAAGCTAAATCCTAAACACTAAATTCTAAGGT
Found at i:48525928 original size:20 final size:20
Alignment explanation
Indices: 48525905--48525955 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
48525895 AGTTAAATCC
*
48525905 TAAACCCTAAATTCTAAGGT
1 TAAACCCTAAATTATAAGGT
*
48525925 TAAACCCTAAATTATAGGGT
1 TAAACCCTAAATTATAAGGT
*
48525945 TAAATCCTAAA
1 TAAACCCTAAA
48525956 CCTTAAATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.43, C:0.18, G:0.10, T:0.29
Consensus pattern (20 bp):
TAAACCCTAAATTATAAGGT
Found at i:48528707 original size:18 final size:18
Alignment explanation
Indices: 48528684--48528720 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
48528674 TTTGTGATCA
48528684 AAATTGAAAGTGAAAGTG
1 AAATTGAAAGTGAAAGTG
* *
48528702 AAATTGGAATTGAAAGTG
1 AAATTGAAAGTGAAAGTG
48528720 A
1 A
48528721 TATGAATTGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.27, T:0.24
Consensus pattern (18 bp):
AAATTGAAAGTGAAAGTG
Found at i:48531292 original size:25 final size:27
Alignment explanation
Indices: 48531246--48531295 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
48531236 TATTATTGTA
*
48531246 TTTAAGATATATTATACTTTTATAAAT
1 TTTAAGATATATTATACATTTATAAAT
*
48531273 TTTAATATAT-TTATA-ATTTATAA
1 TTTAAGATATATTATACATTTATAA
48531296 TAAAATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 5 0.24
27 9 0.43
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (27 bp):
TTTAAGATATATTATACATTTATAAAT
Found at i:48535024 original size:6 final size:6
Alignment explanation
Indices: 48535006--48535113 Score: 71
Period size: 6 Copynumber: 18.0 Consensus size: 6
48534996 TTAAATTGAT
* * * *
48535006 TTTAAA TTT--A TTTAAA TTTAGA TTT-AT TTTAAA TTGAAAA TTAAATA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TT-TAAA TTTAA-A
* ** * *
48535053 TTTAAA TTT-AA TTTGAA TTTAAA TTTAAA TAAAAA TTAAAA CATTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA
48535101 TTTAACA TTTAAA
1 TTTAA-A TTTAAA
48535114 AGTCCAAATG
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
4 4 0.05
5 8 0.10
6 49 0.60
7 20 0.25
ACGTcount: A:0.49, C:0.02, G:0.03, T:0.46
Consensus pattern (6 bp):
TTTAAA
Found at i:48535030 original size:16 final size:17
Alignment explanation
Indices: 48535006--48535082 Score: 68
Period size: 17 Copynumber: 4.4 Consensus size: 17
48534996 TTAAATTGAT
48535006 TTTAAATTTA-TTTAAA
1 TTTAAATTTATTTTAAA
*
48535022 TTTAGATTTATTTTAAA
1 TTTAAATTTATTTTAAA
* *
48535039 TTGAAAATTAAATATTTAAA
1 TT-TAAATT-TAT-TTTAAA
*
48535059 TTT-AATTTGAATTTAAA
1 TTTAAATTT-ATTTTAAA
48535076 TTTAAAT
1 TTTAAAT
48535083 AAAAATTAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 10
0.74 0.11 0.15
Matches are distributed among these distances:
16 9 0.19
17 17 0.35
18 12 0.25
19 2 0.04
20 8 0.17
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:48535062 original size:31 final size:31
Alignment explanation
Indices: 48535021--48535083 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
48535011 ATTTATTTAA
* *
48535021 ATTTAGATTTATTTTAAATTGAAAATTAAAT
1 ATTTAAATTTAATTTAAATTGAAAATTAAAT
* * *
48535052 ATTTAAATTTAATTTGAATTTAAATTTAAAT
1 ATTTAAATTTAATTTAAATTGAAAATTAAAT
48535083 A
1 A
48535084 AAAATTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (31 bp):
ATTTAAATTTAATTTAAATTGAAAATTAAAT
Found at i:48535071 original size:11 final size:11
Alignment explanation
Indices: 48534996--48535082 Score: 52
Period size: 11 Copynumber: 7.5 Consensus size: 11
48534986 GACTCTTGAG
* *
48534996 TTAAATTGATT
1 TTAAATTTAAT
48535007 TTAAATTT-AT
1 TTAAATTTAAT
48535017 TTAAATTTAGAT
1 TTAAATTTA-AT
*
48535029 TT-ATTTTAAAT
1 TTAAATTT-AAT
* *
48535040 TGAAAATTAAATAT
1 T-TAAATT-TA-AT
48535054 TTAAATTTAAT
1 TTAAATTTAAT
*
48535065 TTGAATTTAAAT
1 TTAAATTT-AAT
48535077 TTAAAT
1 TTAAAT
48535083 AAAAATTAAA
Statistics
Matches: 58, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
10 9 0.16
11 23 0.40
12 14 0.24
13 9 0.16
14 3 0.05
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.52
Consensus pattern (11 bp):
TTAAATTTAAT
Found at i:48535161 original size:14 final size:14
Alignment explanation
Indices: 48535142--48535195 Score: 76
Period size: 14 Copynumber: 4.0 Consensus size: 14
48535132 CATGGCCCAC
48535142 GGCCCAATTACAAT
1 GGCCCAATTACAAT
*
48535156 GGCCCAATTACAAA
1 GGCCCAATTACAAT
*
48535170 GGCCCAATT--AAG
1 GGCCCAATTACAAT
48535182 GGCCCAATTACAAT
1 GGCCCAATTACAAT
48535196 AGTCTAAATC
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 11 0.31
14 24 0.69
ACGTcount: A:0.37, C:0.28, G:0.17, T:0.19
Consensus pattern (14 bp):
GGCCCAATTACAAT
Found at i:48535191 original size:26 final size:27
Alignment explanation
Indices: 48535142--48535194 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
48535132 CATGGCCCAC
*
48535142 GGCCCAATTACAATGGCCCAATTACAAA
1 GGCCCAATTA-AAGGGCCCAATTACAAA
48535170 GGCCCAATT-AAGGGCCCAATTACAA
1 GGCCCAATTAAAGGGCCCAATTACAA
48535195 TAGTCTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 15 0.62
28 9 0.38
ACGTcount: A:0.38, C:0.28, G:0.17, T:0.17
Consensus pattern (27 bp):
GGCCCAATTAAAGGGCCCAATTACAAA
Found at i:48537199 original size:30 final size:30
Alignment explanation
Indices: 48536883--48537192 Score: 478
Period size: 30 Copynumber: 10.3 Consensus size: 30
48536873 CCCTAAATTG
48536883 TCCAGAAATTATATTTTGACCCCAAAACTTT
1 TCCA-AAATTATATTTTGACCCCAAAACTTT
* * *
48536914 TCCAAAATCATATTTTAACCCTAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
48536944 TCCAAAATTATATTTTGACCCTAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
* * *
48536974 TCCAAAATCATATTTTAACCCCGAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
48537004 TCCAAAATTATATTTTAACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
48537034 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
48537064 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
* **
48537094 TCCAAAATCATATTTTGACCCTGAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
48537124 TCCAAAATTATATTTTGACCCCAAAACTTT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
48537154 TCCAAAATTACATTTTGACCCCAAAAC-TT
1 TCCAAAATTATATTTTGACCCCAAAACTTT
*
48537183 TCAAAAATTA
1 TCCAAAATTA
48537193 CCATTTTACC
Statistics
Matches: 257, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
29 11 0.04
30 242 0.94
31 4 0.02
ACGTcount: A:0.38, C:0.24, G:0.03, T:0.35
Consensus pattern (30 bp):
TCCAAAATTATATTTTGACCCCAAAACTTT
Done.