Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007823.1 Hibiscus syriacus cultivar Beakdansim tig00110160_pilon, whole genome shotgun sequence
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: 6287495
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 33
Found at i:380592 original size:18 final size:18
Alignment explanation
Indices: 380569--380613 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
380559 TAGTTTGATT
380569 AATGAACTAACATTATTC
1 AATGAACTAACATTATTC
*
380587 AATGAACTAACTTTATTC
1 AATGAACTAACATTATTC
380605 AATGAACTA
1 AATGAACTA
380614 GATGCATGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.44, C:0.16, G:0.07, T:0.33
Consensus pattern (18 bp):
AATGAACTAACATTATTC
Found at i:383262 original size:21 final size:22
Alignment explanation
Indices: 383220--383262 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
383210 ATTAATGAAG
* *
383220 AAAATTTTGAGTTTTAAAAAAT
1 AAAATTTTGAATTCTAAAAAAT
*
383242 AAAA-TTTGAATTCTAAGAAAT
1 AAAATTTTGAATTCTAAAAAAT
383263 TTAGAGTGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.51, C:0.02, G:0.09, T:0.37
Consensus pattern (22 bp):
AAAATTTTGAATTCTAAAAAAT
Found at i:384928 original size:20 final size:20
Alignment explanation
Indices: 384899--384942 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
384889 AAATCCAGAA
*
384899 CCCC-AGGGGGGTATCGATT
1 CCCCTAGGGGGGAATCGATT
*
384918 CCCCTAGGGGGGAATCGGTT
1 CCCCTAGGGGGGAATCGATT
384938 CCCCT
1 CCCCT
384943 TTAAAGGGGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.18
20 18 0.82
ACGTcount: A:0.14, C:0.32, G:0.34, T:0.20
Consensus pattern (20 bp):
CCCCTAGGGGGGAATCGATT
Found at i:396047 original size:21 final size:21
Alignment explanation
Indices: 396009--396049 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
395999 TTTGCATTTT
*
396009 TTTAATTTAGCCTTTTTTAAG
1 TTTAATTTAGCCTCTTTTAAG
**
396030 TTTAATTTATTCTCTTTTAA
1 TTTAATTTAGCCTCTTTTAA
396050 TTTGATAATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.24, C:0.10, G:0.05, T:0.61
Consensus pattern (21 bp):
TTTAATTTAGCCTCTTTTAAG
Found at i:396116 original size:14 final size:13
Alignment explanation
Indices: 396092--396126 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
396082 CAATGCATGT
396092 TTATTTTATTTTA
1 TTATTTTATTTTA
396105 TTATTGTTATTTTA
1 TTATT-TTATTTTA
396119 TTATTTTA
1 TTATTTTA
396127 ATTATGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:404547 original size:66 final size:66
Alignment explanation
Indices: 404378--404616 Score: 354
Period size: 67 Copynumber: 3.6 Consensus size: 66
404368 TTCCTTTTTG
* * *
404378 AACAAATTTTGTCTCTTTTGAGACAGTTTCTCTTAAAACCAAAATATTTGCATATGTTTCCCTTG
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACCAAAATATTTGAATATGTTTCCCTTG
404443 A
66 A
* * *
404444 AACAAAATTTTGTCTATCTTGAGACAGTTTCTCTTGAAACCAAAATCTTTGAATCTGTTTCCCTT
1 AAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACCAAAATATTTGAATATGTTTCCCTT
404509 GA
65 GA
*
404511 AACAAATTTCGTCTCTCTTGAGACAGTTTCTCTTGAAACGCAAAATATTTGAATATGTTTCCCTT
1 AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-CAAAATATTTGAATATGTTTCCCTT
404576 GA
65 GA
* * *
404578 AACAAATTTTGTCT-TCCTTGAGATAGTCTCCCTTGAAAC
1 AACAAATTTTGTCTCT-CTTGAGACAGTTTCTCTTGAAAC
404617 AAATTTTGTC
Statistics
Matches: 156, Mismatches: 14, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
66 38 0.24
67 118 0.76
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (66 bp):
AACAAATTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACCAAAATATTTGAATATGTTTCCCTTG
A
Found at i:404617 original size:36 final size:36
Alignment explanation
Indices: 404567--404799 Score: 351
Period size: 36 Copynumber: 6.5 Consensus size: 36
404557 ATTTGAATAT
* *
404567 GTTTCCCTTGAAACAAATTTTGTCTTCCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
* * *
404603 GTCTCCCTTGAAACAAATTTTGTCTTCATTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
404639 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGATA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
* *
404675 GTTTCCCTTTAAACAAATTTTGTCTCCCTTGAGAAA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
* *
404711 GTTTCTCTTTAAACAAATTTTGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
*
404747 GTTTCCCTTGAAACAAA-TTTGCTCTCCCTCGAGACA
1 GTTTCCCTTGAAACAAATTTTG-TCTCCCTTGAGACA
404783 GTTTCCCTTGAAACAAA
1 GTTTCCCTTGAAACAAA
404800 CTTAGCTTGT
Statistics
Matches: 182, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
35 4 0.02
36 178 0.98
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
Found at i:404668 original size:21 final size:21
Alignment explanation
Indices: 404603--404670 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 21
404593 CCTTGAGATA
404603 GTCTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAAACAAATTTT
* * *
404624 GTCTTCATTGAGAC--A----
1 GTCTCCCTTGAAACAAATTTT
*
404639 GTTTCCCTTGAAACAAATTTT
1 GTCTCCCTTGAAACAAATTTT
404660 GTCTCCCTTGA
1 GTCTCCCTTGA
404671 GATAGTTTCC
Statistics
Matches: 33, Mismatches: 8, Indels: 12
0.62 0.15 0.23
Matches are distributed among these distances:
15 10 0.30
17 1 0.03
19 1 0.03
21 21 0.64
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (21 bp):
GTCTCCCTTGAAACAAATTTT
Found at i:404704 original size:21 final size:21
Alignment explanation
Indices: 404678--404740 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 21
404668 TGAGATAGTT
404678 TCCCTTTAAACAAATTTTGTC
1 TCCCTTTAAACAAATTTTGTC
* * *
404699 TCCC-TT-GAGAAA-GTT-TC
1 TCCCTTTAAACAAATTTTGTC
404716 T--CTTTAAACAAATTTTGTC
1 TCCCTTTAAACAAATTTTGTC
404735 TCCCTT
1 TCCCTT
404741 GAGACAGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 12
0.62 0.12 0.25
Matches are distributed among these distances:
15 1 0.03
16 2 0.07
17 7 0.23
18 4 0.13
19 7 0.23
20 2 0.07
21 7 0.23
ACGTcount: A:0.25, C:0.24, G:0.08, T:0.43
Consensus pattern (21 bp):
TCCCTTTAAACAAATTTTGTC
Found at i:406424 original size:21 final size:21
Alignment explanation
Indices: 406386--406425 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
406376 GTTTGCATTT
*
406386 TTTAATTTAGCCTTTTTTATG
1 TTTAATTTAGCCTCTTTTATG
**
406407 TTTAATTTATTCTCTTTTA
1 TTTAATTTAGCCTCTTTTA
406426 ACTTGGTAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.10, G:0.05, T:0.65
Consensus pattern (21 bp):
TTTAATTTAGCCTCTTTTATG
Found at i:406493 original size:14 final size:13
Alignment explanation
Indices: 406469--406503 Score: 61
Period size: 14 Copynumber: 2.6 Consensus size: 13
406459 CAATGCATGT
406469 TTATTTTATTTTA
1 TTATTTTATTTTA
406482 TTATTGTTATTTTA
1 TTATT-TTATTTTA
406496 TTATTTTA
1 TTATTTTA
406504 ATTATGTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TTATTTTATTTTA
Found at i:412047 original size:2 final size:2
Alignment explanation
Indices: 411957--412030 Score: 55
Period size: 2 Copynumber: 38.0 Consensus size: 2
411947 CTTTTAAATT
* * *
411957 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA AA T- TT TA TGA -A
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA
* * * *
411998 TT TA -A TT TT TA TA AA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
412031 AATTAAAAAT
Statistics
Matches: 57, Mismatches: 11, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
1 3 0.05
2 53 0.93
3 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (2 bp):
TA
Found at i:412316 original size:23 final size:23
Alignment explanation
Indices: 412290--412337 Score: 87
Period size: 23 Copynumber: 2.1 Consensus size: 23
412280 TGTTACATTC
*
412290 CATGAACCAACCAAACACTCCCT
1 CATGAACCAACCAAACACCCCCT
412313 CATGAACCAACCAAACACCCCCT
1 CATGAACCAACCAAACACCCCCT
412336 CA
1 CA
412338 AGTACATCCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.46, G:0.04, T:0.10
Consensus pattern (23 bp):
CATGAACCAACCAAACACCCCCT
Found at i:416355 original size:14 final size:13
Alignment explanation
Indices: 416333--416377 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 13
416323 ATTTAGATAT
416333 TAATATTTAGAATTA
1 TAAT-TTTA-AATTA
*
416348 TAATTTTAAATTT
1 TAATTTTAAATTA
416361 TAAATTTTAAATTA
1 T-AATTTTAAATTA
416375 TAA
1 TAA
416378 ATTATAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 7 0.26
14 16 0.59
15 4 0.15
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (13 bp):
TAATTTTAAATTA
Found at i:416361 original size:7 final size:7
Alignment explanation
Indices: 416349--416396 Score: 69
Period size: 7 Copynumber: 6.7 Consensus size: 7
416339 TTAGAATTAT
416349 AATTTTA
1 AATTTTA
416356 AATTTTA
1 AATTTTA
416363 AATTTTA
1 AATTTTA
*
416370 AATTATA
1 AATTTTA
*
416377 AATTATAA
1 AATT-TTA
416385 AATTTTA
1 AATTTTA
416392 AATTT
1 AATTT
416397 ATATAATAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
7 31 0.86
8 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (7 bp):
AATTTTA
Found at i:416373 original size:21 final size:21
Alignment explanation
Indices: 416316--416396 Score: 69
Period size: 21 Copynumber: 3.9 Consensus size: 21
416306 TTTTATGTTT
* *
416316 ATTTTAAA-TTTAGATATT-A
1 ATTTTAAATTTTAAATTTTAA
*
416335 ATATTTAGAATTAT-AATTTTAA
1 AT-TTTA-AATTTTAAATTTTAA
*
416357 ATTTTAAATTTTAAATTATAA
1 ATTTTAAATTTTAAATTTTAA
*
416378 ATTATAAAATTTTAAATTT
1 ATT-TTAAATTTTAAATTT
416397 ATATAATAAA
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
19 2 0.04
20 9 0.18
21 20 0.41
22 18 0.37
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
ATTTTAAATTTTAAATTTTAA
Found at i:416378 original size:14 final size:14
Alignment explanation
Indices: 416338--416396 Score: 66
Period size: 14 Copynumber: 4.1 Consensus size: 14
416328 GATATTAATA
416338 TTTAGAATTAT-AAT
1 TTTA-AATTATAAAT
*
416352 TTTAAATTTTAAAT
1 TTTAAATTATAAAT
416366 TTTAAATTATAAAT
1 TTTAAATTATAAAT
* *
416380 TATAAAATTTTAAAT
1 T-TTAAATTATAAAT
416395 TT
1 TT
416397 ATATAATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
13 5 0.13
14 22 0.56
15 12 0.31
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.53
Consensus pattern (14 bp):
TTTAAATTATAAAT
Found at i:416411 original size:22 final size:22
Alignment explanation
Indices: 416362--416411 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
416352 TTTAAATTTT
*
416362 AAATTTTAAATTATAAATTATA
1 AAATTTTAAATTATAAATAATA
*
416384 AAATTTTAAATT-TATATAATA
1 AAATTTTAAATTATAAATAATA
416405 AATATTT
1 AA-ATTT
416412 ATCATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
AAATTTTAAATTATAAATAATA
Found at i:416412 original size:21 final size:22
Alignment explanation
Indices: 416361--416412 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
416351 TTTTAAATTT
*
416361 TAAAT-TTTAAATTATAAATTA
1 TAAATATTTAAATTATAAATAA
*
416382 TAAA-ATTTTAAATT-TATATAA
1 TAAATA-TTTAAATTATAAATAA
416403 TAAATATTTA
1 TAAATATTTA
416413 TCATATATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 17 0.65
22 9 0.35
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATATTTAAATTATAAATAA
Found at i:428195 original size:23 final size:23
Alignment explanation
Indices: 428169--428254 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
428159 ATTATTATAT
* *
428169 GGCACTTCGGTGCATTTCTATTC
1 GGCACTACGGTGCATTTCTACTC
*
428192 GGCACTACGGTGCATTTCTACAC
1 GGCACTACGGTGCATTTCTACTC
*
428215 GGCACTACGGTGCAATTCTACGT-
1 GGCACTACGGTGCATTTCTAC-TC
**
428238 GGCACTTTGGTGCATTT
1 GGCACTACGGTGCATTT
428255 ATACGAGCTG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACTC
Found at i:430939 original size:16 final size:16
Alignment explanation
Indices: 430918--430960 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
430908 GAAAATTAAA
430918 GATTGATAAGGAATTT
1 GATTGATAAGGAATTT
* *
430934 GATTGATTAATGATTTT
1 GATTGA-TAAGGAATTT
*
430951 GAGTGATAAG
1 GATTGATAAG
430961 AACTGATGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.35, C:0.00, G:0.26, T:0.40
Consensus pattern (16 bp):
GATTGATAAGGAATTT
Found at i:431856 original size:22 final size:22
Alignment explanation
Indices: 431830--431872 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
431820 TTATGGGCTA
* *
431830 GGGGAATCGGTACCCATTCAAG
1 GGGGAACCGATACCCATTCAAG
*
431852 GGGGAACCGATACCCCTTCAA
1 GGGGAACCGATACCCATTCAA
431873 ACGAACAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.16
Consensus pattern (22 bp):
GGGGAACCGATACCCATTCAAG
Found at i:433302 original size:23 final size:23
Alignment explanation
Indices: 433276--433361 Score: 102
Period size: 23 Copynumber: 3.7 Consensus size: 23
433266 ATTATTATAT
* *
433276 GGCACTTCGGTGCATTTCTATTC
1 GGCACTACGGTGCATTTCTACTC
*
433299 GGCACTACGGTGCATTTCTACAC
1 GGCACTACGGTGCATTTCTACTC
*
433322 GGCACTACGGTGCAATTCTACGT-
1 GGCACTACGGTGCATTTCTAC-TC
**
433345 GGCACTTTGGTGCATTT
1 GGCACTACGGTGCATTT
433362 ATACGAGCTG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 54 1.00
ACGTcount: A:0.17, C:0.26, G:0.24, T:0.33
Consensus pattern (23 bp):
GGCACTACGGTGCATTTCTACTC
Found at i:436958 original size:22 final size:22
Alignment explanation
Indices: 436932--436974 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
436922 TTCTGGGCTA
436932 GGGGAATCGG-TACCCATTCAAG
1 GGGGAA-CGGATACCCATTCAAG
*
436954 GGGGAACGGATACCCCTTCAA
1 GGGGAACGGATACCCATTCAA
436975 ACGAACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 3 0.16
22 16 0.84
ACGTcount: A:0.28, C:0.26, G:0.30, T:0.16
Consensus pattern (22 bp):
GGGGAACGGATACCCATTCAAG
Found at i:438421 original size:23 final size:23
Alignment explanation
Indices: 438395--438508 Score: 156
Period size: 23 Copynumber: 5.0 Consensus size: 23
438385 ATTATTATAT
438395 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
*
438418 GGCACTACGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
438441 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
* * *
438464 GGCACTTCAGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
438487 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
438509 AGCTGTGGTG
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:443548 original size:24 final size:25
Alignment explanation
Indices: 443498--443595 Score: 64
Period size: 24 Copynumber: 4.0 Consensus size: 25
443488 ATAGTAAGTA
* *
443498 AAAAAACAAATAATAAAATATATAT
1 AAAAAAGAAATAAGAAAATATATAT
443523 AAAAAAGAAA-AAGAAAATA-ATAAT
1 AAAAAAGAAATAAGAAAATATAT-AT
* *
443547 AACAAAG---TACGAATAATATATAT
1 AAAAAAGAAATAAGAA-AATATATAT
* * *
443570 ATAAAATAAATAA-AAAAGTAAATAT
1 AAAAAAGAAATAAGAAAA-TATATAT
443595 A
1 A
443596 TAATTAATAA
Statistics
Matches: 56, Mismatches: 9, Indels: 16
0.69 0.11 0.20
Matches are distributed among these distances:
22 4 0.07
23 12 0.21
24 20 0.36
25 18 0.32
26 2 0.04
ACGTcount: A:0.70, C:0.03, G:0.05, T:0.21
Consensus pattern (25 bp):
AAAAAAGAAATAAGAAAATATATAT
Found at i:444042 original size:2 final size:2
Alignment explanation
Indices: 444035--444069 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
444025 ACATATGCAT
*
444035 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
444070 AAAATAATAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:444089 original size:12 final size:11
Alignment explanation
Indices: 444061--444099 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
444051 TATATATATA
* *
444061 AATAATATAAA
1 AATAATACAAG
444072 AATAATACAAG
1 AATAATACAAG
444083 TAATAATACAAG
1 -AATAATACAAG
444095 AATAA
1 AATAA
444100 AAGAAAGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.67, C:0.05, G:0.05, T:0.23
Consensus pattern (11 bp):
AATAATACAAG
Found at i:444195 original size:12 final size:12
Alignment explanation
Indices: 444173--444217 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
444163 GAATAAAAGG
444173 AAAATATAATAGT
1 AAAA-ATAATAGT
*
444186 AAAAATAATAAT
1 AAAAATAATAGT
*
444198 AAATATAATAGT
1 AAAAATAATAGT
*
444210 AATAATAA
1 AAAAATAA
444218 AAATGAAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:444821 original size:37 final size:37
Alignment explanation
Indices: 444780--444884 Score: 147
Period size: 37 Copynumber: 2.8 Consensus size: 37
444770 GTGCTTGTGG
* *
444780 ATCCTATCTTTAGGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
* * * *
444817 ATCCTATTTTTAGGAGTTTAAATCCTAGAAAAATTTT
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
*
444854 ATCCTATTTTTAGGAGTTTGAATCCTAGTAG
1 ATCCTATTTTTAGGAGTTTAAATCCTAGTAG
444885 GACGAAAAGG
Statistics
Matches: 59, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 59 1.00
ACGTcount: A:0.31, C:0.13, G:0.14, T:0.41
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTAAATCCTAGTAGAACTCT
Found at i:445940 original size:106 final size:106
Alignment explanation
Indices: 445615--446693 Score: 1595
Period size: 106 Copynumber: 10.3 Consensus size: 106
445605 GCATTGTTCT
* * * * ** *
445615 GAGTCCAATATCCTCCGTCGTGAAGTTGTAATTGGCTCTGGAACCGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * *
445680 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** * *
445721 GAGTCCAATATCCTTCACTGTGAAGTTGAAATTGACTCTG-AA-T--GAA-AT-TTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * * * * *
445780 TCAGCCG-CCTCTTCGTCGTAAAGTTGAGCTTGTGTTGCCTTG
66 CCAGCGGTCC-CTTCGTCGTGAAGTTGAACTTGCGTTGTC-TG
* * * * *
445822 G-GTTCAAGATCCTTCGCTGAGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
445886 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
445927 GAGTCCAATATCCTACGTTGTGAAGTTGAAATTGCCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
445992 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
446033 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
446098 CCAGCGGTCCCTTCGTCTTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
446139 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
446204 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
446245 GAGTCCAATATTCTTCATTGTAAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
446310 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
446351 GAGTCCAATATCCTACATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
446416 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
** *
446457 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGTTTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
446522 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
446563 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AATTAGGAAGTTGTTTATTG--AA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
446625 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
446666 GAGTCCAATATCCTTCGTTGTGAAGTTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTG
446694 TTTGTTGACA
Statistics
Matches: 887, Mismatches: 76, Indels: 23
0.90 0.08 0.02
Matches are distributed among these distances:
99 2 0.00
100 75 0.08
101 5 0.01
102 4 0.00
103 69 0.08
104 3 0.00
105 22 0.02
106 705 0.79
107 2 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:446244 original size:318 final size:318
Alignment explanation
Indices: 445605--447068 Score: 1930
Period size: 318 Copynumber: 4.7 Consensus size: 318
445595 CAAGTAAGTA
* * * * **
445605 GCATTGT-TCTGAGTCCAATATCCTCCGTCGTGAAGTTGTAATTGGCTCTGGAACCGGGAAATTG
1 GCATTGTCT-TGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTG
* * * * *
445669 TTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCC
65 TTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCC
** * * *
445734 TTCACTGTGAAGTTGAAATTGACTCT-GAA-TGA-AA--T-TTTGTTGACAATCAGCCG-CCTCT
130 TTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCC-CT
* * * * * * *
445792 TCGTCGTAAAGTTGAGCTTGTGTTGCCTTGG-GTTCAAGATCCTTCGCTGAGAAGTTGAAATTGG
194 TCGTCGTGAAGTTGAACTTGCGTTGTC-TGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGG
445856 CTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
258 CTCTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
* * *
445917 GCGTTGTCTTGAGTCCAATATCCTACGTTGTGAAGTTGAAATTGCCTCTGAAATTGGGAAATTGT
1 GCATTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGT
445982 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCT
66 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCT
*
446047 TCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTC
131 TCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTC
* *
446112 GTCTTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
196 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
446177 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
261 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
* * *
446235 GCATTGTCTTGAGTCCAATATTCTTCATTGTAAAGTTGAAATTGGCTCTGAAATTGGGAAATTGT
1 GCATTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGT
* *
446300 TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTGGAGTCCAATATCCT
66 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCT
* * * *
446365 ACATTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTC
131 TCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTC
* **
446430 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGTTTC
196 GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
* * *
446495 TGAAATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAACTT
261 TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
* * * * *
446553 GCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTG-AATTAGGAAGTTGT
1 GCATTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGT
446617 TTATTG--AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCT
66 TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCT
* * * ** * *
446680 TCGTTGTGAAGTTG---TTTG-T-TGACA---ACCAG-CG---G-T------C--CC-T--TTGT
131 TCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCT-T
446721 C---GTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT
195 CGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCT
* * *
446783 CTAAAAATGGAAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
260 CTGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
** * * *
446842 GTGTTGTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTAGATCTGAAATTGGGAAATT
1 G-CAT-TGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATT
* *
446907 GTTTATTGATAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGGAGTCCAATATC
64 GTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATC
* * *
446972 CTTCGCTGTGAAGTTGAAATTGGCTCCAAAATTG-GAAAATTG-TTGTTGACAACCAGCCGTCCC
129 CTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAG-AAGTTGTTTGTTGACAACCAGCCGTCCC
* * *
447035 TTCGTTGTGAAGTTGAACTTGTGTTGTCTTGAGT
193 TTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
447069 GGCACGATAT
Statistics
Matches: 1017, Mismatches: 93, Indels: 77
0.86 0.08 0.06
Matches are distributed among these distances:
289 112 0.11
290 1 0.00
291 44 0.04
292 20 0.02
293 1 0.00
294 70 0.07
296 1 0.00
297 3 0.00
298 1 0.00
299 2 0.00
302 2 0.00
303 2 0.00
305 1 0.00
306 2 0.00
307 3 0.00
310 4 0.00
311 1 0.00
312 141 0.14
313 3 0.00
314 5 0.00
315 71 0.07
316 2 0.00
317 22 0.02
318 475 0.47
319 28 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (318 bp):
GCATTGTCTTGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGT
TTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCT
TCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTTGTTGACAACCAGCCGTCCCTTC
GTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTC
TGAAATTGGGAAGTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTT
Found at i:446682 original size:43 final size:43
Alignment explanation
Indices: 446634--446775 Score: 122
Period size: 43 Copynumber: 3.4 Consensus size: 43
446624 ACCAGCGGTC
446634 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
* * * * ***
446677 CCTTCGTTGTGAAGTTG---TT-TGTTGAC---A-ACCAGCGGT
1 CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCA-ATAT
*
446713 CCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
1 -CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
446757 CCTTCG-CTGTGAAGTTGAA
1 CCTTCGTC-GTGAAGTTGAA
446776 ATTGGCTCTA
Statistics
Matches: 72, Mismatches: 16, Indels: 22
0.65 0.15 0.20
Matches are distributed among these distances:
35 3 0.04
36 2 0.03
37 15 0.21
39 5 0.07
40 4 0.06
41 5 0.07
42 1 0.01
43 32 0.44
44 2 0.03
45 3 0.04
ACGTcount: A:0.18, C:0.20, G:0.26, T:0.35
Consensus pattern (43 bp):
CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATAT
Found at i:446740 original size:80 final size:78
Alignment explanation
Indices: 446609--446773 Score: 285
Period size: 80 Copynumber: 2.1 Consensus size: 78
446599 TCTGAATTAG
446609 GAAGTTGTTTATTGAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
1 GAAGTTGTTTATTGAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
*
446674 TATCCTTCGTTGT
66 TATCCTTCGCTGT
* *
446687 GAAGTTGTTTGTTGACAACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
1 GAAGTTGTTTATTG--AACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCC
446752 AATATCCTTCGCTGT
64 AATATCCTTCGCTGT
446767 GAAGTTG
1 GAAGTTG
446774 AAATTGGCTC
Statistics
Matches: 82, Mismatches: 3, Indels: 2
0.94 0.03 0.02
Matches are distributed among these distances:
78 13 0.16
80 69 0.84
ACGTcount: A:0.18, C:0.20, G:0.27, T:0.35
Consensus pattern (78 bp):
GAAGTTGTTTATTGAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAA
TATCCTTCGCTGT
Found at i:446909 original size:108 final size:107
Alignment explanation
Indices: 446691--447068 Score: 550
Period size: 106 Copynumber: 3.6 Consensus size: 107
446681 CGTTGTGAAG
* * *
446691 TTGTTTGTTGACAACCAGCGGTCCCTTTGTCGTGAAGTTGAACTTGCG-TTGTCTGGAGTCCAAT
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTTGTCTGGAGTCCAAT
*
446755 ATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAAAT-GGAAA
66 ATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAA
446796 GTTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTGTCTGGAGTCCA
1 -TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTT-TGTCTGGAGTCCA
* * * *
446861 ATATCCTTCGTTGTGAAGTTGAAATTAGATCTGAAATTGGGAAA
64 ATATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAA
* **
446905 TTGTTTATTGATAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTG-CATTGTCTGGAGTCCAAT
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTTGTCTGGAGTCCAAT
* *
446969 ATCCTTCGCTGTGAAGTTGAAATTGGCTCCAAAATTGGAAAA
66 ATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAA
* * * *
447011 TTG-TTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTG-TTGTCTTGAGT
1 TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTTGTCTGGAGT
447069 GGCACGATAT
Statistics
Matches: 245, Mismatches: 23, Indels: 9
0.88 0.08 0.03
Matches are distributed among these distances:
105 48 0.20
106 99 0.40
107 2 0.01
108 91 0.37
109 5 0.02
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.35
Consensus pattern (107 bp):
TTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTTGTCTGGAGTCCAAT
ATCCTTCGCTGTGAAGTTGAAATTGGCTCTAAAATTGGGAAA
Found at i:447919 original size:22 final size:22
Alignment explanation
Indices: 447893--447962 Score: 115
Period size: 22 Copynumber: 3.2 Consensus size: 22
447883 TTATGTTTGG
447893 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGGCATTTGATGC
*
447915 TCAAAGGTTTGGCATGTGATGC
1 TCAAAGGTTTGGCATTTGATGC
447937 TCAATA-GTTTGGCATTTGATGC
1 TCAA-AGGTTTGGCATTTGATGC
447959 TCAA
1 TCAA
447963 CAGTTTGATG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
22 44 0.98
23 1 0.02
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTGATGC
Found at i:448602 original size:14 final size:14
Alignment explanation
Indices: 448585--448635 Score: 68
Period size: 13 Copynumber: 3.6 Consensus size: 14
448575 TTCTTTTTGA
448585 TTTTTGTTCTTTCT
1 TTTTTGTTCTTTCT
*
448599 TTTTTGTT-ATTCT
1 TTTTTGTTCTTTCT
448612 TTTTTGCTTCTTTTCT
1 TTTTTG-TTC-TTTCT
448628 TTTTTGTT
1 TTTTTGTT
448636 TTTGCCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 10 0.31
14 10 0.31
15 2 0.06
16 10 0.31
ACGTcount: A:0.02, C:0.12, G:0.08, T:0.78
Consensus pattern (14 bp):
TTTTTGTTCTTTCT
Found at i:453242 original size:24 final size:23
Alignment explanation
Indices: 453201--453251 Score: 59
Period size: 25 Copynumber: 2.2 Consensus size: 23
453191 ATAGTAAGTA
* *
453201 AAAAAATAAATAATAAAATATATAT
1 AAAAAAGAAATAAGAAAATA-A-AT
453226 AAAAAAGAAA-AAGAAAATAAAT
1 AAAAAAGAAATAAGAAAATAAAT
453248 AAAA
1 AAAA
453252 CAAATAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 6 0.25
23 1 0.04
24 8 0.33
25 9 0.38
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (23 bp):
AAAAAAGAAATAAGAAAATAAAT
Found at i:453599 original size:2 final size:2
Alignment explanation
Indices: 453558--453584 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
453548 TTTGTGTAGA
453558 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
453585 GTAAATGTGT
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:453651 original size:33 final size:31
Alignment explanation
Indices: 453606--453670 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 31
453596 TATAACAATA
453606 ATAATATCAATAAAAAATAAAATAAAATATAAT
1 ATAATATCAATAAAAAATAAAA-AAAAT-TAAT
*
453639 ATAATGAT-AATAAAAAATATAAAAAATTAAT
1 ATAAT-ATCAATAAAAAATAAAAAAAATTAAT
453670 A
1 A
453671 GAAAAATATA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 5 0.17
32 5 0.17
33 18 0.60
34 2 0.07
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.28
Consensus pattern (31 bp):
ATAATATCAATAAAAAATAAAAAAAATTAAT
Found at i:453829 original size:12 final size:11
Alignment explanation
Indices: 453801--453841 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
453791 TAACAAAATA
* *
453801 AATAATATAAA
1 AATAATACAAG
453812 AATAATACAAG
1 AATAATACAAG
453823 TAATAATACAAG
1 -AATAATACAAG
453835 AATAATA
1 AATAATA
453842 AAAAGAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.66, C:0.05, G:0.05, T:0.24
Consensus pattern (11 bp):
AATAATACAAG
Found at i:453945 original size:12 final size:12
Alignment explanation
Indices: 453923--453967 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
453913 GAATAAAAGG
453923 AAAATATAATAGT
1 AAAA-ATAATAGT
*
453936 AAAAATAATAAT
1 AAAAATAATAGT
*
453948 AAATATAATAGT
1 AAAAATAATAGT
*
453960 AATAATAA
1 AAAAATAA
453968 AAATAAAATG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 23 0.85
13 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (12 bp):
AAAAATAATAGT
Found at i:453951 original size:24 final size:24
Alignment explanation
Indices: 453924--453974 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
453914 AATAAAAGGA
*
453924 AAATATAATAGTAAAAATAATAAT
1 AAATATAATAGTAAAAATAAAAAT
*
453948 AAATATAATAGTAATAATAAAAAT
1 AAATATAATAGTAAAAATAAAAAT
453972 AAA
1 AAA
453975 ATGCAAAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.69, C:0.00, G:0.04, T:0.27
Consensus pattern (24 bp):
AAATATAATAGTAAAAATAAAAAT
Found at i:454617 original size:37 final size:37
Alignment explanation
Indices: 454519--454619 Score: 130
Period size: 37 Copynumber: 2.7 Consensus size: 37
454509 GTGTTTGTGG
* * *
454519 ATCCTATTTTTAAGAGTTTAAATCATAGTAGAACTCT
1 ATCCTATTTTTAAGAGTTTAAATCCTAGCAAAACTCT
* * *
454556 ATCCTATTTTTAGGAGTTTAAATCCTAGCAAAATTTT
1 ATCCTATTTTTAAGAGTTTAAATCCTAGCAAAACTCT
* *
454593 ATCCTATTTTTAAAAGTTTGAATCCTA
1 ATCCTATTTTTAAGAGTTTAAATCCTA
454620 ATAGGACGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.43
Consensus pattern (37 bp):
ATCCTATTTTTAAGAGTTTAAATCCTAGCAAAACTCT
Found at i:455099 original size:13 final size:13
Alignment explanation
Indices: 455081--455107 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
455071 TGTTCCAATA
455081 GATAGCTTACCCG
1 GATAGCTTACCCG
455094 GATAGCTTACCCG
1 GATAGCTTACCCG
455107 G
1 G
455108 TGCCCGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.22, C:0.30, G:0.26, T:0.22
Consensus pattern (13 bp):
GATAGCTTACCCG
Found at i:458675 original size:21 final size:20
Alignment explanation
Indices: 458647--458691 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
458637 TATCCATTCA
458647 ATTGGCAAGACTTATTTATT
1 ATTGGCAAGACTTATTTATT
* *
458667 ATTGTGCAATACTTGTTTATT
1 ATTG-GCAAGACTTATTTATT
458688 ATTG
1 ATTG
458692 ATGAAAGTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 4 0.18
21 18 0.82
ACGTcount: A:0.27, C:0.09, G:0.16, T:0.49
Consensus pattern (20 bp):
ATTGGCAAGACTTATTTATT
Found at i:458918 original size:15 final size:14
Alignment explanation
Indices: 458898--459015 Score: 70
Period size: 13 Copynumber: 8.6 Consensus size: 14
458888 CAATAATTAA
*
458898 AATAATGTATTTTAT
1 AATAATATA-TTTAT
458913 AATAATATATTTAT
1 AATAATATATTTAT
* *
458927 AATTATTTA-TTAT
1 AATAATATATTTAT
* *
458940 ATTTAA-ATTTTTA-
1 A-ATAATATATTTAT
458953 AATTAATATATTT-T
1 AA-TAATATATTTAT
*
458967 -ATAATATTTTTAT
1 AATAATATATTTAT
** *
458980 AATTTTTATAATTA-
1 AA-TAATATATTTAT
458994 AATAATATATTT-T
1 AATAATATATTTAT
459007 AATAATATA
1 AATAATATA
459016 AAATAAAAAT
Statistics
Matches: 77, Mismatches: 17, Indels: 20
0.68 0.15 0.18
Matches are distributed among these distances:
12 9 0.12
13 28 0.36
14 25 0.32
15 15 0.19
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (14 bp):
AATAATATATTTAT
Found at i:458939 original size:27 final size:27
Alignment explanation
Indices: 458909--459009 Score: 77
Period size: 27 Copynumber: 3.8 Consensus size: 27
458899 ATAATGTATT
458909 TTATAATAATATATTTATAATTATTTA
1 TTATAATAATATATTTATAATTATTTA
* * *
458936 TTATATTTAA-ATTTTTA-AATTAATATA
1 TTATA-ATAATATATTTATAATT-ATTTA
* *
458963 TT-TTATAATATTTTTATAATT-TTTA
1 TTATAATAATATATTTATAATTATTTA
*
458988 TAATTAAATAATATATTT-TAAT
1 TTA-T-AATAATATATTTATAAT
459010 AATATAAAAT
Statistics
Matches: 58, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
25 7 0.12
26 12 0.21
27 26 0.45
28 13 0.22
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (27 bp):
TTATAATAATATATTTATAATTATTTA
Found at i:458957 original size:19 final size:19
Alignment explanation
Indices: 458918--458952 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
458908 TTTATAATAA
458918 TATATTTATAATTATTTAT
1 TATATTTATAATTATTTAT
458937 TATATTTA-AATT-TTTA
1 TATATTTATAATTATTTA
458953 AATTAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.25
18 4 0.25
19 8 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (19 bp):
TATATTTATAATTATTTAT
Found at i:458986 original size:9 final size:9
Alignment explanation
Indices: 458922--458992 Score: 51
Period size: 9 Copynumber: 8.0 Consensus size: 9
458912 TAATAATATA
458922 TTTATAATT
1 TTTATAATT
* *
458931 ATTTATTATA
1 -TTTATAATT
458941 TTTA-AATT
1 TTTATAATT
458949 TTTA-AATT
1 TTTATAATT
**
458957 AATAT-A-T
1 TTTATAATT
458964 TTTATAATATT
1 TTTAT-A-ATT
458975 TTTATAATT
1 TTTATAATT
458984 TTTATAATT
1 TTTATAATT
458993 AAATAATATA
Statistics
Matches: 48, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
7 4 0.08
8 13 0.27
9 16 0.33
10 9 0.19
11 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (9 bp):
TTTATAATT
Found at i:458995 original size:41 final size:40
Alignment explanation
Indices: 458913--459014 Score: 118
Period size: 41 Copynumber: 2.5 Consensus size: 40
458903 TGTATTTTAT
**
458913 AATAATATA-TTTATAATTATTTATTATATTTAAATTTTTA
1 AATAATATATTTTATAA-TATTTATTATATTTAAATAATTA
**
458953 AATTAATATATTTTATAATATTT-TTATAATTTTTATAATTA
1 AA-TAATATATTTTATAATATTTATTAT-ATTTAAATAATTA
458994 AATAATATATTTTAATAATAT
1 AATAATATATTTT-ATAATAT
459015 AAAATAAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 17 0.31
41 30 0.56
42 7 0.13
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (40 bp):
AATAATATATTTTATAATATTTATTATATTTAAATAATTA
Found at i:459013 original size:53 final size:55
Alignment explanation
Indices: 458897--459015 Score: 131
Period size: 53 Copynumber: 2.2 Consensus size: 55
458887 ACAATAATTA
* * **
458897 AAATAATGTATTTTATAATAATATATTTATAATTATTTATTATATTTAAATTTTT
1 AAATAATATATTTTATAATAATATATTTATAATTATTTATAATAAATAAATTTTT
458952 AAATTAATATATTTTATAAT-AT-T-TTTATAATT-TTTATAATTAAATAATATATTTT
1 AAA-TAATATATTTTATAATAATATATTTATAATTATTTATAA-TAAATAA-AT-TTTT
459007 -AATAATATA
1 AAATAATATA
459016 AAATAAAAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
52 6 0.11
53 21 0.38
54 5 0.09
55 9 0.16
56 15 0.27
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.55
Consensus pattern (55 bp):
AAATAATATATTTTATAATAATATATTTATAATTATTTATAATAAATAAATTTTT
Found at i:461925 original size:22 final size:21
Alignment explanation
Indices: 461888--461928 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
461878 AATATTTAAT
*
461888 ATTTTTTGGTTTATTCGGTTA
1 ATTTTTTGGTTGATTCGGTTA
461909 ATTTTGTTGGTTGATTCGGT
1 ATTTT-TTGGTTGATTCGGT
461929 AAAAACCAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.05, G:0.24, T:0.59
Consensus pattern (21 bp):
ATTTTTTGGTTGATTCGGTTA
Found at i:466841 original size:17 final size:17
Alignment explanation
Indices: 466819--466861 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
466809 TCTCTCTTGA
466819 TTCTAGTTGCTTGTTGT
1 TTCTAGTTGCTTGTTGT
*
466836 TTCTAGTTTCTTGTTGT
1 TTCTAGTTGCTTGTTGT
*
466853 TTCTTGTTG
1 TTCTAGTTG
466862 TTGATCAATG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.05, C:0.12, G:0.21, T:0.63
Consensus pattern (17 bp):
TTCTAGTTGCTTGTTGT
Found at i:468140 original size:18 final size:19
Alignment explanation
Indices: 468119--468156 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
468109 GATCCTCTGG
468119 TTGTGCTTGTTCCT-TTGC
1 TTGTGCTTGTTCCTCTTGC
468137 TTGTGCTTGTTCCTCTTGC
1 TTGTGCTTGTTCCTCTTGC
468156 T
1 T
468157 GTTCTGGTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.00, C:0.24, G:0.21, T:0.55
Consensus pattern (19 bp):
TTGTGCTTGTTCCTCTTGC
Found at i:468166 original size:18 final size:18
Alignment explanation
Indices: 468119--468166 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
468109 GATCCTCTGG
*
468119 TTGTGCTTGTTCCTTTGC
1 TTGTGCTGGTTCCTTTGC
*
468137 TTGTGCTTGTTCCTCTTGC
1 TTGTGCTGGTTCCT-TTGC
*
468156 -TGTTCTGGTTC
1 TTGTGCTGGTTC
468167 ATCGTCGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
18 23 0.85
19 4 0.15
ACGTcount: A:0.00, C:0.23, G:0.23, T:0.54
Consensus pattern (18 bp):
TTGTGCTGGTTCCTTTGC
Found at i:469786 original size:22 final size:22
Alignment explanation
Indices: 469712--469792 Score: 78
Period size: 23 Copynumber: 3.7 Consensus size: 22
469702 TGAACCCTTG
*
469712 GGGGGTATCGATTCCCC-T-AA
1 GGGGGAATCGATTCCCCTTCAA
*
469732 GGGGGAATC-AGTTCCCATTCAAA
1 GGGGGAATCGA-TTCCCCTTC-AA
* *
469755 GGGGGAATCGGTTCCCCTTCAT
1 GGGGGAATCGATTCCCCTTCAA
*
469777 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
469793 TCTGCCCTAT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
19 1 0.02
20 13 0.27
21 1 0.02
22 15 0.31
23 19 0.39
ACGTcount: A:0.20, C:0.25, G:0.31, T:0.25
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Found at i:475952 original size:22 final size:21
Alignment explanation
Indices: 475910--475949 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
475900 GAGTTTATTT
*
475910 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
475931 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
475950 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:477916 original size:18 final size:18
Alignment explanation
Indices: 477893--477929 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
477883 GTGCACTAAG
477893 AGTGCATTCGATGTTTCA
1 AGTGCATTCGATGTTTCA
477911 AGTGCATTCGATGTTTCA
1 AGTGCATTCGATGTTTCA
477929 A
1 A
477930 AATAGCCAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (18 bp):
AGTGCATTCGATGTTTCA
Found at i:477985 original size:64 final size:63
Alignment explanation
Indices: 477894--478104 Score: 194
Period size: 65 Copynumber: 3.3 Consensus size: 63
477884 TGCACTAAGA
** * * *
477894 GTGCATTCGATGTTTCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATACATGGCTG
1 GTGCA-TCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGG-TG
** * *
477959 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATAGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
*
478023 T
63 G
* ** *
478024 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG--
478087 TG
62 TG
478089 GTGCATCGATGCATCA
1 GTGCATCGATGCATCA
478105 CTTTGATAAA
Statistics
Matches: 118, Mismatches: 20, Indels: 16
0.77 0.13 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 39 0.33
65 70 0.59
66 4 0.03
ACGTcount: A:0.27, C:0.18, G:0.23, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTG
Found at i:478529 original size:23 final size:23
Alignment explanation
Indices: 478503--478556 Score: 92
Period size: 23 Copynumber: 2.3 Consensus size: 23
478493 AGTTCCATAT
478503 AATTTTTAACCTT-GAAATTTTAA
1 AATTTTTAA-CTTCGAAATTTTAA
478526 AATTTTTAACTTCGAAATTTTAA
1 AATTTTTAACTTCGAAATTTTAA
478549 AATTTTTA
1 AATTTTTA
478557 TTTTTTTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 3 0.10
23 27 0.90
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.50
Consensus pattern (23 bp):
AATTTTTAACTTCGAAATTTTAA
Found at i:479428 original size:22 final size:22
Alignment explanation
Indices: 479397--479448 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
479387 AAAGATTAGA
479397 CAATCATAAATGTCTATTTTGC
1 CAATCATAAATGTCTATTTTGC
*
479419 CAATCGTAAATGTCTATTTTGC
1 CAATCATAAATGTCTATTTTGC
479441 CAATCATA
1 CAATCATA
479449 TATGAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.33, C:0.19, G:0.10, T:0.38
Consensus pattern (22 bp):
CAATCATAAATGTCTATTTTGC
Found at i:487195 original size:15 final size:15
Alignment explanation
Indices: 487177--487214 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
487167 AATGAATTTA
* *
487177 AAAAATAATTATAAT
1 AAAAATAAATAAAAT
487192 AAAAATAAATAAAAT
1 AAAAATAAATAAAAT
487207 -AAAATAAA
1 AAAAATAAA
487215 AAGAATATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAAATAAAAT
Found at i:487234 original size:2 final size:2
Alignment explanation
Indices: 487227--487256 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
487217 GAATATTTAA
487227 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
487257 TATTTAGGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:487511 original size:36 final size:35
Alignment explanation
Indices: 487432--487551 Score: 113
Period size: 38 Copynumber: 3.4 Consensus size: 35
487422 GATTTTTTAT
* *
487432 TATAT-ATATATATTT-AAAATG-TTTTCGAAAAT
1 TATATAATATATATTTCAAAATGTTTTTCAAAAAC
* **
487464 TATATTATATATATTTCAAAATGTTTTTTTTAAAAC
1 TATATAATATATATTTCAAAATG-TTTTTCAAAAAC
*
487500 TATATAATATATATGTTTTCAAAAAT-ATTTTCAAAAAC
1 TATATAATATATA---TTTC-AAAATGTTTTTCAAAAAC
487538 TATATAATATATAT
1 TATATAATATATAT
487552 GTTTTCAAAA
Statistics
Matches: 73, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
32 5 0.07
33 10 0.14
34 6 0.08
35 1 0.01
36 20 0.27
38 22 0.30
39 4 0.05
40 5 0.07
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.47
Consensus pattern (35 bp):
TATATAATATATATTTCAAAATGTTTTTCAAAAAC
Found at i:487574 original size:24 final size:26
Alignment explanation
Indices: 487524--487585 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
487514 GTTTTCAAAA
*
487524 ATATTTTCAAAAACTATATAATATAT
1 ATATTTTCAAAAACCATATAATATAT
*
487550 ATGTTTTCAAAAACCATAT-AT-TAT
1 ATATTTTCAAAAACCATATAATATAT
487574 ATATTTTCAAAA
1 ATATTTTCAAAA
487586 TGTTTTCCTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 14 0.42
25 2 0.06
26 17 0.52
ACGTcount: A:0.47, C:0.10, G:0.02, T:0.42
Consensus pattern (26 bp):
ATATTTTCAAAAACCATATAATATAT
Found at i:488446 original size:165 final size:164
Alignment explanation
Indices: 488251--489062 Score: 1160
Period size: 165 Copynumber: 4.9 Consensus size: 164
488241 TTTGCCTCTT
* * * *
488251 AGCTGAGTGTAATCGAACTC-AAATGTCTTTGGAAGATAGCCTTTCTCGACTTAAGTTATGCTGC
1 AGCTGAGTGTAATCGAACTCGAGA-GTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
* *
488315 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGGCAGATAACTATTC
65 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTGGCAGATAACCATTC
* *
488380 TAGCCTTGAGTTATGCTGTAAATGATGTGCGCTCGA
129 TAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGA
*
488416 AGCTGAGTGTAATCGAACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATACTGCA
1 AGCTGAGTGTAATCGAACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* ** * * * * *
488481 AATGATATGCCTCAGAGCTGAGCTTAGTCAAACTCAAAGGTCTTTGATTGGTAGATAACCCTTCT
66 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTG-GTGGCAGATAACCATTCT
* * *
488546 CGACTTAAGTTATGCTGCAAATGATGTGCCCTCGA
130 AGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGA
*
488581 AGCTGAGTGTAATCGAACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGTA
1 AGCTGAGTGTAATCGAACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* *
488646 AATGATGTGTCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTTGGAAGATAACCATTCT
66 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGG-TGGCAGATAACCATTCT
* * * * *
488711 TGACTTAAGTTATGCAGCAAATGAAGTGCCCTCGA
130 AGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGA
488746 AGCTGAGTGTAATCGAACTCGAG-GATCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
1 AGCTGAGTGTAATCGAACTCGAGAG-TCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC
* * ** *
488810 AAATGATGTGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTTTGGTTACAGATAACCTTTC
65 AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTC-TTTGGTGGCAGATAACCATTC
** *
488875 TAGCCTTGAGTTATGCTATAAATGATGTGCCCTCAA
129 TAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGA
* * * *
488911 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCATATAGCCCTTCTCGACTTAAGATATTCTGCA
1 AGCTGAGTGTAATCGAACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
* * * *
488976 AATGATATGCCTTGGAGCTGAACGTAGTCGAACTCAAAGGTCTTTGTTGGCAGATAACCCTTCTA
66 AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGGCAGATAACCATTCTA
489041 GCCTTGAGTTATGCTGCAAATG
131 GCCTTGAGTTATGCTGCAAATG
489063 TTATCTTTTA
Statistics
Matches: 578, Mismatches: 63, Indels: 13
0.88 0.10 0.02
Matches are distributed among these distances:
164 44 0.08
165 526 0.91
166 8 0.01
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.30
Consensus pattern (164 bp):
AGCTGAGTGTAATCGAACTCGAGAGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCA
AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGGTGGCAGATAACCATTCTA
GCCTTGAGTTATGCTGCAAATGATGTGCCCTCGA
Found at i:494328 original size:5 final size:5
Alignment explanation
Indices: 494295--494570 Score: 84
Period size: 5 Copynumber: 51.2 Consensus size: 5
494285 ATGTTAGTAA
*
494295 AAAAT AAAATT AAAATT AAAA- ACAAT AAAAT AAAAT -AAAT ACATGAAT
1 AAAAT AAAA-T AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT A-A--AAT
* * *
494343 AAAAT AATAAAT CAAGGAAA AAAAG AAAAT AAAAT -AAAT AAAAGA ATAAAT
1 AAAAT -A-AAAT -AA--AAT AAAAT AAAAT AAAAT AAAAT AAAA-T A-AAAT
* *
494394 CGAAAGA- AAAAT GAAAAAT AAAAT AAAAAT AAAAT AAAAT -AAAG GAAA-
1 --AAA-AT AAAAT --AAAAT AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT
* *
494442 AAAAT -AAAT TAAAT AGATAAGT AAAAT AATAAT AATGAT AACAAT GAAAA-
1 AAAAT AAAAT AAAAT A-A-AA-T AAAAT AA-AAT AA-AAT AA-AAT -AAAAT
** * * *
494492 AAAGC ACAAA- AAAAT AAAAT AAAATT TAATT AAAAT AAAAT AAAAG AAAAT
1 AAAAT A-AAAT AAAAT AAAAT AAAA-T AAAAT AAAAT AAAAT AAAAT AAAAT
* * *
494543 AAACT AAAAAT GAAAAG AAAAG AAAAT A
1 AAAAT -AAAAT -AAAAT AAAAT AAAAT A
494571 TTAACTATTT
Statistics
Matches: 211, Mismatches: 27, Indels: 66
0.69 0.09 0.22
Matches are distributed among these distances:
4 28 0.13
5 100 0.47
6 50 0.24
7 23 0.11
8 10 0.05
ACGTcount: A:0.72, C:0.03, G:0.07, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:494391 original size:39 final size:38
Alignment explanation
Indices: 494340--494454 Score: 117
Period size: 39 Copynumber: 2.9 Consensus size: 38
494330 TAAATACATG
494340 AATAAAATAATAAATCAAGGAAAAAAAGAAAATAAAATA
1 AATAAAA-AATAAATCAAGGAAAAAAAGAAAATAAAATA
* *
494379 AATAAAAGAATAAATCGAAAG-AAAAATGAAAAATAAAATA
1 AATAAAA-AATAAATC-AAGGAAAAAAAG-AAAATAAAATA
* * *
494419 AA-AATAAAATAAAATAAAGGAAAAAAATAAATTAAA
1 AATAA-AAAAT-AAATCAAGGAAAAAAAGAAAATAAA
494455 TAGATAAGTA
Statistics
Matches: 63, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
39 36 0.57
40 27 0.43
ACGTcount: A:0.75, C:0.02, G:0.08, T:0.16
Consensus pattern (38 bp):
AATAAAAAATAAATCAAGGAAAAAAAGAAAATAAAATA
Found at i:494401 original size:13 final size:12
Alignment explanation
Indices: 494375--494415 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
494365 AAGAAAATAA
*
494375 AATAAATAAAAG
1 AATAAATGAAAG
494387 AATAAATCGAAAG
1 AATAAAT-GAAAG
494400 AA-AAATGAAA-
1 AATAAATGAAAG
494410 AATAAA
1 AATAAA
494416 ATAAAAATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 2 0.08
11 7 0.27
12 11 0.42
13 6 0.23
ACGTcount: A:0.73, C:0.02, G:0.10, T:0.15
Consensus pattern (12 bp):
AATAAATGAAAG
Found at i:495826 original size:22 final size:22
Alignment explanation
Indices: 495792--495833 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
495782 CAGAAAAACC
*
495792 AAAAAGAACTAAATAAATAAGG
1 AAAAAGAAATAAATAAATAAGG
*
495814 AAAAATAAATAAATAAATAA
1 AAAAAGAAATAAATAAATAA
495834 TAAAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.74, C:0.02, G:0.07, T:0.17
Consensus pattern (22 bp):
AAAAAGAAATAAATAAATAAGG
Found at i:495942 original size:38 final size:37
Alignment explanation
Indices: 495854--496293 Score: 301
Period size: 38 Copynumber: 11.8 Consensus size: 37
495844 ATTAAAATAT
* * *
495854 TTTTCAAAAACTATTATATAATATATATTTTCCAAAATGAT
1 TTTT-AAAAACTA-TATATTATATATATTTT-CAAAA-AAA
* *
495895 TTTTTAAAACTATATAATATATATATTTTCAAAAAAA
1 TTTTAAAAACTATATATTATATATATTTTCAAAAAAA
*
495932 GTTTTAAAAACTATATA-T-TATATATTTTCAAAATAA
1 -TTTTAAAAACTATATATTATATATATTTTCAAAAAAA
**
495968 TTTTAAAAA--ACTATA-TAT-TATATTTTCAAAATATTT
1 TTTTAAAAACTA-TATATTATATATATTTTCAAAA-A-AA
* * *
496004 TTTTAAAAACTATATATTATATATATATTCCAAAATA
1 TTTTAAAAACTATATATTATATATATTTTCAAAAAAA
* * ** ****
496041 TTTTGAAAACTATATTTTATACGTATTTTCAAAGTGTT
1 TTTTAAAAACTATATATTATATATATTTTCAAA-AAAA
* * * ***
496079 TTTTGAAAACCATATAGTATATAT-TTTT-AAAATGT
1 TTTTAAAAACTATATATTATATATATTTTCAAAAAAA
* * ***
496114 TTTTCAAAATCTATATAATATATATATTTTCAAAATGT
1 TTTT-AAAAACTATATATTATATATATTTTCAAAAAAA
**
496152 TTTTCAAAAACTATATATTATATATATTTTTTC-AAAATG
1 TTTT-AAAAACTATATATTATATATA--TTTTCAAAAAAA
* *
496191 TTTTAAAAACTATATATTATATGTAAGTTTTCAAAAATA
1 TTTTAAAAACTATATATTATATAT-A-TTTTCAAAAAAA
* * *
496230 -TTTAAAAACCATATATTATATGTAAGTTTTCAAAAATA
1 TTTTAAAAACTATATATTATATAT-A-TTTTCAAAAAAA
*
496268 -TTTAAAAACCATATATTATATA-ATTT
1 TTTTAAAAACTATATATTATATATATTT
496294 CCGAAATGAT
Statistics
Matches: 338, Mismatches: 44, Indels: 40
0.80 0.10 0.09
Matches are distributed among these distances:
33 1 0.00
34 18 0.05
35 18 0.05
36 46 0.14
37 42 0.12
38 158 0.47
39 39 0.12
40 12 0.04
41 4 0.01
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTTAAAAACTATATATTATATATATTTTCAAAAAAA
Found at i:499370 original size:13 final size:13
Alignment explanation
Indices: 499337--499366 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
499327 TTCTAATCAT
499337 TTTCATTTCTTTA
1 TTTCATTTCTTTA
499350 TTTCATTTC-TTA
1 TTTCATTTCTTTA
499362 TTTCA
1 TTTCA
499367 ATTTAATCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.47
13 9 0.53
ACGTcount: A:0.17, C:0.17, G:0.00, T:0.67
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:499560 original size:6 final size:6
Alignment explanation
Indices: 499549--499589 Score: 57
Period size: 6 Copynumber: 6.7 Consensus size: 6
499539 GTGCTGCAAC
499549 AAAAGA AAAAGA AAGAAGA AAAACG- AAAAGA AAAAGA AAAA
1 AAAAGA AAAAGA AA-AAGA AAAA-GA AAAAGA AAAAGA AAAA
499590 ACTCCTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 1 0.03
6 24 0.75
7 7 0.22
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:503792 original size:16 final size:16
Alignment explanation
Indices: 503763--503795 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
503753 ATAGCATCTC
503763 TATCCATTTTATTTCT
1 TATCCATTTTATTTCT
503779 TATCC-TTTTCATTTCT
1 TATCCATTTT-ATTTCT
503795 T
1 T
503796 TATTTCATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 12 0.75
ACGTcount: A:0.15, C:0.21, G:0.00, T:0.64
Consensus pattern (16 bp):
TATCCATTTTATTTCT
Found at i:503812 original size:12 final size:13
Alignment explanation
Indices: 503785--503836 Score: 54
Period size: 12 Copynumber: 4.1 Consensus size: 13
503775 TTCTTATCCT
503785 TTTCATTTCTTTA
1 TTTCATTTCTTTA
503798 TTTCATTTC-TTA
1 TTTCATTTCTTTA
** *
503810 TTTCAATTTAATCA
1 TTTC-ATTTCTTTA
503824 TTT-ATTTCTTTA
1 TTTCATTTCTTTA
503836 T
1 T
503837 ATTGTGCAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
12 14 0.44
13 13 0.41
14 5 0.16
ACGTcount: A:0.21, C:0.13, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTCATTTCTTTA
Found at i:512682 original size:2 final size:2
Alignment explanation
Indices: 512675--512740 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
512665 AATACTACTT
512675 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
512717 TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
512741 ACTTTAATTT
Statistics
Matches: 64, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 64 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:513918 original size:31 final size:31
Alignment explanation
Indices: 513880--514004 Score: 198
Period size: 31 Copynumber: 4.0 Consensus size: 31
513870 CCCGAAGGAC
* *
513880 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
513911 CAGTCCATATGTCCCAAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
513942 CAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
513973 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
514004 C
1 C
514005 CCTCGACCCT
Statistics
Matches: 87, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
31 86 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.22, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:514767 original size:64 final size:64
Alignment explanation
Indices: 514659--514882 Score: 247
Period size: 64 Copynumber: 3.5 Consensus size: 64
514649 TAATGAAGGT
* * * * **
514659 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTGTTGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTT-TCATTATTAATGAG
* * ** *
514723 ATGTATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
* * *
514787 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTCATTATTAATGAG
** *
514850 AGTGCATCGATGCACTACCAATGCATCGGTGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
514883 CATTCAAACA
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
63 3 0.02
64 128 0.94
65 5 0.04
ACGTcount: A:0.27, C:0.19, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
Found at i:518083 original size:31 final size:31
Alignment explanation
Indices: 518059--518199 Score: 264
Period size: 31 Copynumber: 4.5 Consensus size: 31
518049 CATAGATTCT
* *
518059 GAAGAACCTAGGTAAATAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
518090 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
518121 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
518152 GAAGAACATAGGTAAACAGTCCATATGTCCC
1 GAAGAACATAGGTAAACAGTCCATATGTCCC
518183 GAAGAACATAGGTAAAC
1 GAAGAACATAGGTAAAC
518200 CCTCGACCCT
Statistics
Matches: 108, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 108 1.00
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (31 bp):
GAAGAACATAGGTAAACAGTCCATATGTCCC
Found at i:518961 original size:64 final size:64
Alignment explanation
Indices: 518853--519076 Score: 247
Period size: 64 Copynumber: 3.5 Consensus size: 64
518843 TAATGAAGGT
* * * * **
518853 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTGTTGAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTT-TCATTATTAATGAG
* * ** *
518917 ATGCATCGATACACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
* * *
518981 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-TTCATTATTAATGAG
** *
519044 AGTGCATCGATGCACTACCAATGCATCGGTGCA
1 A-TGCATCGATGCACTACTTATGCATCGATGCA
519077 CATTCAAACA
Statistics
Matches: 136, Mismatches: 21, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
63 3 0.02
64 128 0.94
65 5 0.04
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTTTCATTATTAATGAG
Found at i:520924 original size:22 final size:21
Alignment explanation
Indices: 520890--520941 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
520880 TCATAATAAA
* * *
520890 ATCGATACCCTAGTTCAGAAGT
1 ATCGATACTCTAGCT-AAAAGT
*
520912 ATTGATACTCTAGCTAAAAGT
1 ATCGATACTCTAGCTAAAAGT
520933 ATCGATACT
1 ATCGATACT
520942 ACCCATTCTT
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (21 bp):
ATCGATACTCTAGCTAAAAGT
Found at i:522116 original size:16 final size:16
Alignment explanation
Indices: 522081--522112 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
522071 TAACTTAACA
522081 TAATTTTATATTATTT
1 TAATTTTATATTATTT
522097 TAATTTTATA-TATTT
1 TAATTTTATATTATTT
522112 T
1 T
522113 TAATAAAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TAATTTTATATTATTT
Found at i:522685 original size:20 final size:19
Alignment explanation
Indices: 522642--522687 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
522632 TTTTCAGAGT
* *
522642 GATGCACCAATCATGCACC
1 GATGCACAAATCATCCACC
*
522661 GATGCACAAATCCATCCATC
1 GATGCACAAAT-CATCCACC
522681 GATGCAC
1 GATGCAC
522688 CATGAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.33, C:0.35, G:0.15, T:0.17
Consensus pattern (19 bp):
GATGCACAAATCATCCACC
Found at i:522851 original size:17 final size:19
Alignment explanation
Indices: 522824--522871 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
522814 ATTTTGAAAT
522824 ATCGAATGCACT-TGA-TGC
1 ATCG-ATGCACTCTGAGTGC
*
522842 ATCGATGCACTCTTAGTGC
1 ATCGATGCACTCTGAGTGC
*
522861 ACCGATGCACT
1 ATCGATGCACT
522872 GAGAGTCCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 7 0.27
18 6 0.23
19 13 0.50
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (19 bp):
ATCGATGCACTCTGAGTGC
Found at i:530313 original size:21 final size:21
Alignment explanation
Indices: 530271--530318 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
530261 ACCCCAGGAG
*
530271 CTAGCTCTTCACGAGCTGCTC
1 CTAGCTCTTCACGAGCTCCTC
* *
530292 CTAGCTCTTCATGTGCTCCTC
1 CTAGCTCTTCACGAGCTCCTC
530313 CT-GCTC
1 CTAGCTC
530319 CTACGGCACC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.10, C:0.40, G:0.17, T:0.33
Consensus pattern (21 bp):
CTAGCTCTTCACGAGCTCCTC
Found at i:549041 original size:20 final size:20
Alignment explanation
Indices: 549004--549053 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
548994 TGGTAAAACA
549004 CTACTTAAAATATTATTTTT
1 CTACTTAAAATATTATTTTT
* *
549024 CTAC-TAAAATGTTAATTTTG
1 CTACTTAAAATATT-ATTTTT
*
549044 CTATTTAAAA
1 CTACTTAAAA
549054 ACCGGTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 8 0.32
20 12 0.48
21 5 0.20
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (20 bp):
CTACTTAAAATATTATTTTT
Found at i:549042 original size:19 final size:20
Alignment explanation
Indices: 549004--549053 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
548994 TGGTAAAACA
*
549004 CTACTTAAAATATTATTTTT
1 CTACTTAAAATATTAATTTT
*
549024 CTAC-TAAAATGTTAATTTT
1 CTACTTAAAATATTAATTTT
*
549043 GCTATTTAAAA
1 -CTACTTAAAA
549054 ACCGGTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
19 13 0.52
20 7 0.28
21 5 0.20
ACGTcount: A:0.38, C:0.10, G:0.04, T:0.48
Consensus pattern (20 bp):
CTACTTAAAATATTAATTTT
Found at i:550666 original size:19 final size:18
Alignment explanation
Indices: 550642--550700 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 18
550632 CTTTTACTTT
550642 TAATATACTTATAATTAAA
1 TAATATACTT-TAATTAAA
*
550661 TAATAT-TTTTAATTAAAAA
1 TAATATACTTTAATT--AAA
550680 TAATAATTACTTTAATTAAA
1 TAAT-A-TACTTTAATTAAA
550700 T
1 T
550701 TAATTTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
17 5 0.15
18 2 0.06
19 13 0.39
20 5 0.15
21 1 0.03
22 7 0.21
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (18 bp):
TAATATACTTTAATTAAA
Found at i:551002 original size:88 final size:88
Alignment explanation
Indices: 550846--551022 Score: 284
Period size: 88 Copynumber: 2.0 Consensus size: 88
550836 GCCCAACAGT
* *
550846 TACCCAGCAGTCGAACAGTAGTCGGCTACCCAGAAAAAGCTGTGCAGCAAGTCCGCCGGTGCCTC
1 TACCCAGCAGTCGAACAGTAGTCGGCTACCCAGAAAAAGCTGCGCAGCAAGTCCGCCAGTGCCTC
550911 CCTGTTTCTATGCAAATTGCACG
66 CCTGTTTCTATGCAAATTGCACG
* * *
550934 TACCCAGCAGTCGTACAGTTGTCGGCTACCCAGAAAAAAGCTGCGCAGCAAGTCCGCCAGTTCC-
1 TACCCAGCAGTCGAACAGTAGTCGGCTACCCAG-AAAAAGCTGCGCAGCAAGTCCGCCAGTGCCT
*
550998 CCCTGTTTCTATTCAAATTGCACG
65 CCCTGTTTCTATGCAAATTGCACG
551022 T
1 T
551023 TGAGGTTTAG
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
88 55 0.67
89 27 0.33
ACGTcount: A:0.25, C:0.31, G:0.22, T:0.22
Consensus pattern (88 bp):
TACCCAGCAGTCGAACAGTAGTCGGCTACCCAGAAAAAGCTGCGCAGCAAGTCCGCCAGTGCCTC
CCTGTTTCTATGCAAATTGCACG
Found at i:553304 original size:40 final size:40
Alignment explanation
Indices: 553260--553352 Score: 95
Period size: 43 Copynumber: 2.3 Consensus size: 40
553250 TAAATAAAAT
553260 TTATTAATAAATAATAATAA-A-TAATAAGTTAACTAAT-CTA
1 TTATTAATAAATAATAA-AATATTAATAA-TTAA-TAATACTA
*
553300 TTATTTTTAATAAATAATAAAATATTAATAATTAATAATATTA
1 TTA---TTAATAAATAATAAAATATTAATAATTAATAATACTA
553343 TT-TTAATAAA
1 TTATTAATAAA
553353 AAAAACCCAA
Statistics
Matches: 46, Mismatches: 1, Indels: 13
0.77 0.02 0.22
Matches are distributed among these distances:
39 8 0.17
40 3 0.07
42 6 0.13
43 23 0.50
44 6 0.13
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (40 bp):
TTATTAATAAATAATAAAATATTAATAATTAATAATACTA
Found at i:553348 original size:21 final size:21
Alignment explanation
Indices: 553298--553352 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 21
553288 TTAACTAATC
553298 TATTATTTTTAATAAATAATAA
1 TATTA-TTTTAATAAATAATAA
* *
553320 -A--ATATTAATAATTAATAA
1 TATTATTTTAATAAATAATAA
553338 TATTATTTTAATAAA
1 TATTATTTTAATAAA
553353 AAAAACCCAA
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
18 14 0.54
19 2 0.08
21 10 0.38
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (21 bp):
TATTATTTTAATAAATAATAA
Found at i:553456 original size:21 final size:21
Alignment explanation
Indices: 553430--553471 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
553420 TTTTTTTAGT
553430 GAGCTTAACAAGCAACGAGTC
1 GAGCTTAACAAGCAACGAGTC
* *
553451 GAGCTTAACGAGCAATGAGTC
1 GAGCTTAACAAGCAACGAGTC
553472 AAGTTGAACG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (21 bp):
GAGCTTAACAAGCAACGAGTC
Found at i:553481 original size:21 final size:21
Alignment explanation
Indices: 553431--553486 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
553421 TTTTTTAGTG
* * *
553431 AGCTTAACAAGCAACGAGTCG
1 AGCTTAACGAGCAATGAGTCA
553452 AGCTTAACGAGCAATGAGTCA
1 AGCTTAACGAGCAATGAGTCA
553473 AG-TTGAACGA-CAAT
1 AGCTT-AACGAGCAAT
553487 TTTTTTTAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.19
21 25 0.81
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (21 bp):
AGCTTAACGAGCAATGAGTCA
Found at i:558394 original size:12 final size:12
Alignment explanation
Indices: 558369--558407 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
558359 ATTAAAATTA
*
558369 AATAA-ATAAGT
1 AATAATATAAAT
558380 AATAATATAAAT
1 AATAATATAAAT
*
558392 AATAATAAAAAT
1 AATAATATAAAT
558404 AATA
1 AATA
558408 TTATTTAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 5 0.20
12 20 0.80
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (12 bp):
AATAATATAAAT
Found at i:558405 original size:16 final size:16
Alignment explanation
Indices: 558368--558401 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
558358 AATTAAAATT
558368 AAATAAATAAGTAATA
1 AAATAAATAAGTAATA
*
558384 ATATAAATAA-TAATA
1 AAATAAATAAGTAATA
558399 AAA
1 AAA
558402 ATAATATTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (16 bp):
AAATAAATAAGTAATA
Found at i:558503 original size:28 final size:26
Alignment explanation
Indices: 558443--558507 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
558433 ATTTTCAAAA
* *
558443 ATATTTTC-AAAACTGTATATTATAT
1 ATATTTTCAAAAACTATACATTATAT
*
558468 ATGTTTTCAAAAACTATACATTATAT
1 ATATTTTCAAAAACTATACATTATAT
558494 ATACATTTTCAAAA
1 AT--ATTTTCAAAA
558508 TGTTTTCAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 7 0.21
26 17 0.52
28 9 0.27
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (26 bp):
ATATTTTCAAAAACTATACATTATAT
Found at i:558516 original size:39 final size:38
Alignment explanation
Indices: 558468--558798 Score: 354
Period size: 37 Copynumber: 9.0 Consensus size: 38
558458 TATATTATAT
*
558468 ATGTTTTCAAAAACTATACATTATATATACATTTTCAAA
1 ATGTTTTCAAAAACTATATATTATATATA-ATTTTCAAA
*
558507 ATGTTTTCAAAAACTATATATTATATAT--GTTTCAAAA
1 ATGTTTTCAAAAACTATATATTATATATAATTTTC-AAA
* *
558544 ATGTTTTC-AAAACTATATATTATATA-AGTTTTTAAA
1 ATGTTTTCAAAAACTATATATTATATATAATTTTCAAA
* *
558580 ATGTTTTCAAAAAC--TATATTATATAT-A-TAT--AT
1 ATGTTTTCAAAAACTATATATTATATATAATTTTCAAA
* * * * *
558612 AT-ATAT-ATATA-TATATATATATATATATATATTCAAA
1 ATGTTTTCAAAAACTATATAT-TATATATA-ATTTTCAAA
* *
558649 ATGTTTTCAAAAACTATATATTATATAT-GTTTTTAAA
1 ATGTTTTCAAAAACTATATATTATATATAATTTTCAAA
*
558686 ATGTTTTCAAAAACTATATATTATATAT-GTTTTCAAA
1 ATGTTTTCAAAAACTATATATTATATATAATTTTCAAA
* *
558723 ATGTTTTCAAAAACTATACATTATATATATTTTTTCAAA
1 ATGTTTTCAAAAACTATATATTATATATA-ATTTTCAAA
558762 ATGTTTTCAAAAACTATATATTATATAT-A-TTTCAAA
1 ATGTTTTCAAAAACTATATATTATATATAATTTTCAAA
558798 A
1 A
558799 ACCGATTAAA
Statistics
Matches: 248, Mismatches: 26, Indels: 39
0.79 0.08 0.12
Matches are distributed among these distances:
30 3 0.01
31 7 0.03
32 10 0.04
34 3 0.01
35 12 0.05
36 41 0.17
37 91 0.37
38 2 0.01
39 72 0.29
40 7 0.03
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.45
Consensus pattern (38 bp):
ATGTTTTCAAAAACTATATATTATATATAATTTTCAAA
Found at i:558606 original size:2 final size:2
Alignment explanation
Indices: 558594--558643 Score: 93
Period size: 2 Copynumber: 25.5 Consensus size: 2
558584 TTTCAAAAAC
558594 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
558635 TA TA TA TA T
1 TA TA TA TA T
558644 TCAAAATGTT
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 46 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:558647 original size:142 final size:144
Alignment explanation
Indices: 558489--558752 Score: 451
Period size: 142 Copynumber: 1.8 Consensus size: 144
558479 AACTATACAT
*
558489 TATATATACATTTTCAAAATGTTTTCAAAAACTATATATTATATATGTTTCAAAAATGTTTTC-A
1 TATATATACATATTCAAAATGTTTTCAAAAACTATATATTATATATGTTTCAAAAATGTTTTCAA
*
558553 AAACTATATATTATATAAGTTTTTAAAATGTTTTCAAAAACTAT-ATTATATATATATATATATA
66 AAACTATATATTATATAAGTTTTCAAAATGTTTTCAAAAACTATAATTATATATATATATATATA
558617 TATATATATATATA
131 TATATATATATATA
* **
558631 TATATATATATATTCAAAATGTTTTCAAAAACTATATATTATATATGTTTTTAAAATGTTTTCAA
1 TATATATACATATTCAAAATGTTTTCAAAAACTATATATTATATATGTTTCAAAAATGTTTTCAA
*
558696 AAACTATATATTATATATGTTTTCAAAATGTTTTCAAAAACTATACATTATATATAT
66 AAACTATATATTATATAAGTTTTCAAAATGTTTTCAAAAACTATA-ATTATATATAT
558753 TTTTTCAAAA
Statistics
Matches: 113, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
142 59 0.52
143 43 0.38
145 11 0.10
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.46
Consensus pattern (144 bp):
TATATATACATATTCAAAATGTTTTCAAAAACTATATATTATATATGTTTCAAAAATGTTTTCAA
AAACTATATATTATATAAGTTTTCAAAATGTTTTCAAAAACTATAATTATATATATATATATATA
TATATATATATATA
Found at i:558671 original size:106 final size:102
Alignment explanation
Indices: 558521--558713 Score: 316
Period size: 106 Copynumber: 1.9 Consensus size: 102
558511 TTTCAAAAAC
*
558521 TATATATTATATATGTTTCAAAAATGTTTTCAAAACTATATATTATATAAGTTTTTAAAATGTTT
1 TATATATTATATATATTTCAAAAATGTTTTCAAAACTATATATTATATAAGTTTTTAAAATGTTT
558586 TCAAAAACTATATTATATATATATATATATATATATATA
66 TCAAAAACTATA-TAT-TATATATATATATATATATATA
*
558625 TATATATATATATATATATTC-AAAATGTTTTCAAAAACTATATATTATATATGTTTTTAAAATG
1 TATATAT-TATATATAT-TTCAAAAATGTTTTC-AAAACTATATATTATATAAGTTTTTAAAATG
558689 TTTTCAAAAACTATATATTATATAT
63 TTTTCAAAAACTATATATTATATAT
558714 GTTTTCAAAA
Statistics
Matches: 84, Mismatches: 2, Indels: 6
0.91 0.02 0.07
Matches are distributed among these distances:
104 14 0.17
105 22 0.26
106 48 0.57
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (102 bp):
TATATATTATATATATTTCAAAAATGTTTTCAAAACTATATATTATATAAGTTTTTAAAATGTTT
TCAAAAACTATATATTATATATATATATATATATATA
Found at i:558835 original size:76 final size:76
Alignment explanation
Indices: 558468--558837 Score: 211
Period size: 76 Copynumber: 5.0 Consensus size: 76
558458 TATATTATAT
* * * * *
558468 ATGTTTTCAAAAACTATACATTATATATACATTTTCAAAATGTTTTCAAAAACTATATATTAT--
1 ATGTTTTCAAAAACTATATATTATATAT-GA-TTTCAAAACGTATTCAAAAACTATACATTATAA
* *
558531 ATA-TGTTTCAAAA
64 AAATTCTTTC-AAA
* * * * * * *
558544 ATGTTTTC-AAAACTATATATTATATAAGTTTTTAAAATGTTTTCAAAAACTAT--ATTATATAT
1 ATGTTTTCAAAAACTATATATTATATATGATTTCAAAACGTATTCAAAAACTATACATTATAAAA
* * *
558606 A-TATAT--AT
66 ATTCTTTCAAA
* * * * * * * *
558614 AT-ATAT-ATATA-TATATATATATATAT-ATATTCAAAATGTTTTCAAAAACTATATATTATAT
1 ATGTTTTCAAAAACTATATAT-TATATATGAT-TTCAAAACGTATTCAAAAACTATACATTATAA
**
558675 ATGTT-TTT-AAA
64 AAATTCTTTCAAA
* * * * *
558686 ATGTTTTCAAAAACTATATATTATATATGTTTTCAAAATGTTTTCAAAAACTATACATTATATAT
1 ATGTTTTCAAAAACTATATATTATATATGATTTCAAAACGTATTCAAAAACTATACATTATAAAA
*
558751 ATTTTTTCAAA
66 ATTCTTTCAAA
**
558762 ATGTTTTCAAAAACTATATATTATATAT-ATTTCAAAAACCG-ATT-AAAAACTATATGTT-TCA
1 ATGTTTTCAAAAACTATATATTATATATGATTTC-AAAA-CGTATTCAAAAACTATACATTAT--
558823 AAAAATTCTTTCAAA
62 AAAAATTCTTTCAAA
558838 GACTATGATA
Statistics
Matches: 242, Mismatches: 33, Indels: 38
0.77 0.11 0.12
Matches are distributed among these distances:
68 8 0.03
69 32 0.13
70 3 0.01
71 16 0.07
72 4 0.02
73 31 0.13
74 46 0.19
75 44 0.18
76 57 0.24
77 1 0.00
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (76 bp):
ATGTTTTCAAAAACTATATATTATATATGATTTCAAAACGTATTCAAAAACTATACATTATAAAA
ATTCTTTCAAA
Found at i:562250 original size:19 final size:20
Alignment explanation
Indices: 562206--562250 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
562196 ACTTGTTTTT
*
562206 AATAAATTTTTATCTGTGAA
1 AATAAATTTTTATCTGTCAA
* *
562226 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTGTCAA
562245 AATAAA
1 AATAAA
562251 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTGTCAA
Found at i:566161 original size:19 final size:19
Alignment explanation
Indices: 566137--566185 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
566127 TTTAGAATTG
* *
566137 AGTTTGAATTTGTGACTGT
1 AGTTTGAATTGGTGACCGT
566156 AGTTTGAATTGGTGACCGT
1 AGTTTGAATTGGTGACCGT
566175 AGTTTGAATTG
1 AGTTTGAATTG
566186 TAAATCATGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.22, C:0.06, G:0.29, T:0.43
Consensus pattern (19 bp):
AGTTTGAATTGGTGACCGT
Found at i:568909 original size:15 final size:15
Alignment explanation
Indices: 568889--568925 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
568879 TGAGACCTTA
*
568889 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
568904 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
568919 CCCGCCC
1 CCCGCCC
568926 ACTAAATACC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.08, C:0.70, G:0.16, T:0.05
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:570808 original size:2 final size:2
Alignment explanation
Indices: 570769--570795 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
570759 GATGTGTAAG
570769 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
570796 CAAAAGTATA
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:592257 original size:19 final size:19
Alignment explanation
Indices: 592233--592270 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
592223 GAGAATAAAG
*
592233 GAATGAAGAAGAGAAGAGA
1 GAATGAAAAAGAGAAGAGA
*
592252 GAATGAAAAAGTGAAGAGA
1 GAATGAAAAAGAGAAGAGA
592271 AGAAGATGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.34, T:0.08
Consensus pattern (19 bp):
GAATGAAAAAGAGAAGAGA
Found at i:595945 original size:16 final size:16
Alignment explanation
Indices: 595926--595963 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
595916 CGAAAAATAT
595926 GATATCTGAAAATTCA
1 GATATCTGAAAATTCA
*
595942 GATATCTGAAAATTCG
1 GATATCTGAAAATTCA
595958 GATATC
1 GATATC
595964 CAAATATCCG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.39, C:0.13, G:0.16, T:0.32
Consensus pattern (16 bp):
GATATCTGAAAATTCA
Found at i:599797 original size:21 final size:20
Alignment explanation
Indices: 599712--599868 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
599702 AAATGACCAA
**
599712 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
***
599731 -AAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
599750 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
599770 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
599791 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
599812 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
599832 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
599853 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
599869 ACACATAAAT
Statistics
Matches: 104, Mismatches: 27, Indels: 13
0.72 0.19 0.09
Matches are distributed among these distances:
18 15 0.14
19 1 0.01
20 41 0.39
21 47 0.45
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:599900 original size:20 final size:20
Alignment explanation
Indices: 599835--600084 Score: 229
Period size: 20 Copynumber: 12.5 Consensus size: 20
599825 CGATTTTCCA
* ** *
599835 AAATCGCAACGCGAATATGA
1 AAATCGCAACGTGAATCCGT
* *
599855 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGTGAATC-CGT
*
599875 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
599895 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
599915 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
* * *
599935 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGTGAATCCGT
599955 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
599975 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
599995 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
600015 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
600035 AAATCGCAACGAT-AATCCGT
1 AAATCGCAACG-TGAATCCGT
* *
600055 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGTGAATCCGT
*
600075 AAATCACAAC
1 AAATCGCAAC
600085 ACTGAAATTT
Statistics
Matches: 195, Mismatches: 27, Indels: 16
0.82 0.11 0.07
Matches are distributed among these distances:
20 194 0.99
21 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGTGAATCCGT
Found at i:603349 original size:19 final size:19
Alignment explanation
Indices: 603309--603404 Score: 134
Period size: 19 Copynumber: 5.4 Consensus size: 19
603299 GATTCTCTCG
603309 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
603329 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
603348 TTGCGA--TTC---TCG--
1 TTGCGATTTTCATTTCGCA
603360 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
603379 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
603398 TTGCGAT
1 TTGCGAT
603405 AGTCAATTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 15
0.82 0.00 0.18
Matches are distributed among these distances:
12 6 0.09
14 6 0.09
17 6 0.09
19 36 0.52
20 15 0.22
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:603395 original size:50 final size:52
Alignment explanation
Indices: 603290--603404 Score: 207
Period size: 50 Copynumber: 2.2 Consensus size: 52
603280 GAAATGAAAA
603290 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
603343 TCGCATTGCGAT-TCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
603393 TCGCATTGCGAT
1 TCGCATTGCGAT
603405 AGTCAATTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
50 30 0.48
51 20 0.32
52 1 0.02
53 11 0.18
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:603518 original size:19 final size:19
Alignment explanation
Indices: 603462--603648 Score: 215
Period size: 19 Copynumber: 10.6 Consensus size: 19
603452 CCATTACATT
603462 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
603482 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
603496 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
603515 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
603534 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
603548 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
603567 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
603586 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
603605 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
*
603619 TCGCAATGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
603638 TCGCATTGCGA
1 TCGCAATGCGA
603649 TTCTCCCATT
Statistics
Matches: 144, Mismatches: 8, Indels: 31
0.79 0.04 0.17
Matches are distributed among these distances:
14 30 0.21
15 3 0.02
16 6 0.04
17 5 0.03
18 4 0.03
19 90 0.62
20 6 0.04
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:603541 original size:52 final size:52
Alignment explanation
Indices: 603462--603642 Score: 251
Period size: 52 Copynumber: 3.5 Consensus size: 52
603452 CCATTACATT
603462 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
603515 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
* * * * *
603567 TCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AA
*
603619 TCGCAATGCGAAATTAAAATCGCA
1 TCGCAATGCGAAATGAAAATCGCA
603643 TTGCGATTCT
Statistics
Matches: 119, Mismatches: 6, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
50 7 0.06
51 7 0.06
52 96 0.81
53 9 0.08
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.14
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:603550 original size:33 final size:33
Alignment explanation
Indices: 603513--603642 Score: 197
Period size: 33 Copynumber: 3.8 Consensus size: 33
603503 GCGAAATGAA
603513 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
603546 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAG
603584 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
603617 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
603643 TTGCGATTCT
Statistics
Matches: 89, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
33 54 0.61
34 1 0.01
35 2 0.02
36 2 0.02
37 1 0.01
38 29 0.33
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:603574 original size:71 final size:71
Alignment explanation
Indices: 603494--603648 Score: 292
Period size: 71 Copynumber: 2.2 Consensus size: 71
603484 GCAACGAGAG
603494 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
603559 AATGAA
66 AATGAA
603565 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
*
603630 AATTAA
66 AATGAA
*
603636 AATCGCATTGCGA
1 AATCGCAATGCGA
603649 TTCTCCCATT
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
71 82 1.00
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
AATGAA
Found at i:603697 original size:19 final size:19
Alignment explanation
Indices: 603655--603754 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
603645 GCGATTCTCC
603655 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
603675 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
603694 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
603710 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
603727 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
603746 CATTGCGAT
1 CATTGCGAT
603755 AGTCAATTTG
Statistics
Matches: 73, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:603751 original size:52 final size:53
Alignment explanation
Indices: 603638--603754 Score: 209
Period size: 53 Copynumber: 2.2 Consensus size: 53
603628 GAAATTAAAA
603638 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
603691 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
603743 TCGCATTGCGAT
1 TCGCATTGCGAT
603755 AGTCAATTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 30 0.48
53 32 0.52
ACGTcount: A:0.15, C:0.25, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:605051 original size:22 final size:22
Alignment explanation
Indices: 605020--605084 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
605010 GTGAATCGGG
605020 CTCTTGAATGGTGGGAGGGGAC
1 CTCTTGAATGGTGGGAGGGGAC
* * ** *
605042 CTCTTCAATGATGACAGTGG-C
1 CTCTTGAATGGTGGGAGGGGAC
*
605063 CTCTTGAACGGTGGGAGGGGAC
1 CTCTTGAATGGTGGGAGGGGAC
605085 TCTCGAGGAA
Statistics
Matches: 31, Mismatches: 11, Indels: 2
0.70 0.25 0.05
Matches are distributed among these distances:
21 15 0.48
22 16 0.52
ACGTcount: A:0.20, C:0.18, G:0.38, T:0.23
Consensus pattern (22 bp):
CTCTTGAATGGTGGGAGGGGAC
Found at i:605087 original size:21 final size:21
Alignment explanation
Indices: 605020--605087 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
605010 GTGAATCGGG
605020 CTCTTGAATGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
* * ** * *
605041 CCTCTTCAATGATGACAGTGGC
1 -CTCTTGAATGGTGGGAGGGGA
*
605063 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAATGGTGGGAGGGGA
605084 CTCT
1 CTCT
605088 CGAGGAATGA
Statistics
Matches: 33, Mismatches: 13, Indels: 1
0.70 0.28 0.02
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.19, C:0.19, G:0.37, T:0.25
Consensus pattern (21 bp):
CTCTTGAATGGTGGGAGGGGA
Done.