Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007731.1 Hibiscus syriacus cultivar Beakdansim tig00109983_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: 835416
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:438963 original size:19 final size:19
Alignment explanation
Indices: 438871--438984 Score: 59
Period size: 19 Copynumber: 6.5 Consensus size: 19
438861 GCGATTCCCT
*
438871 CATTGCGATTTTTATTTCG
1 CATTGCGATTTTCATTTCG
* *
438890 CGTTGCGA--TTC---TCT
1 CATTGCGATTTTCATTTCG
*
438904 CATTGCAATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
** *
438923 CATTATGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
438939 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
**
438956 CATTGCGATAGTCATTTCCG
1 CATTGCGATTTTCATTT-CG
*
438976 CGTTGCGAT
1 CATTGCGAT
438985 AGACATTAAG
Statistics
Matches: 68, Mismatches: 16, Indels: 21
0.65 0.15 0.20
Matches are distributed among these distances:
14 12 0.18
16 10 0.15
17 9 0.13
19 27 0.40
20 10 0.15
ACGTcount: A:0.16, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:438983 original size:20 final size:20
Alignment explanation
Indices: 438937--439030 Score: 68
Period size: 20 Copynumber: 4.7 Consensus size: 20
438927 ATGATTCTCT
**
438937 CGTTGCGATTTTCATTT-CG
1 CGTTGCGATAGTCATTTCCG
*
438956 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* **
438976 CGTTGCGATAGACA-TTAAG
1 CGTTGCGATAGTCATTTCCG
*
438995 ATGATTGCGA-ACGTCATTTCCG
1 -CG-TTGCGATA-GTCATTTCCG
*
439017 TGTTGCGATAGTCA
1 CGTTGCGATAGTCA
439031 AATGATTGCC
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
19 17 0.29
20 26 0.45
21 12 0.21
22 3 0.05
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:441309 original size:12 final size:12
Alignment explanation
Indices: 441292--441316 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
441282 TCTTCGGGGA
441292 CTTTTTCTTCTT
1 CTTTTTCTTCTT
441304 CTTTTTCTTCTT
1 CTTTTTCTTCTT
441316 C
1 C
441317 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:441525 original size:24 final size:24
Alignment explanation
Indices: 441491--441544 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
441481 CTGAAACATC
*
441491 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
441515 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
441539 ATCAAA
1 ATCAAA
441545 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:442356 original size:60 final size:60
Alignment explanation
Indices: 442289--442437 Score: 174
Period size: 60 Copynumber: 2.5 Consensus size: 60
442279 TGTATTATCT
* *
442289 CGTTGCGATAGTCAGAATCTCATTGCGAAAGTCAGAATCACATTGCGA-AAGTCAGAATCG
1 CGTTGCGATAGTCAGTATCGCATTGCGAAAGTCAGAATCACATTGCGATAAGT-AGAATCG
* * * * * ** **
442349 CGTTGCGAAAGTCAGTATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATTATCG
1 CGTTGCGATAGTCAGTATCGCATTGCGAAAGTCAGAATCACATTGCGA-TAAGTAGAATCG
442410 CGTTGCGATAGTCAGTATCGCATTGCGA
1 CGTTGCGATAGTCAGTATCGCATTGCGA
442438 TTTTCCAAAT
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
60 41 0.55
61 31 0.42
62 2 0.03
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.28
Consensus pattern (60 bp):
CGTTGCGATAGTCAGTATCGCATTGCGAAAGTCAGAATCACATTGCGATAAGTAGAATCG
Found at i:442438 original size:20 final size:20
Alignment explanation
Indices: 442284--442437 Score: 157
Period size: 20 Copynumber: 7.7 Consensus size: 20
442274 GATTCTGTAT
* *
442284 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
442304 AATCTCATTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
442324 AATCACATTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
442344 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
442364 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
** *
442384 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
*
442405 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
442425 TATCGCATTGCGA
1 TATCGCGTTGCGA
442438 TTTTCCAAAT
Statistics
Matches: 118, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
19 3 0.03
20 99 0.84
21 14 0.12
22 2 0.02
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:442457 original size:41 final size:41
Alignment explanation
Indices: 442264--442459 Score: 128
Period size: 40 Copynumber: 4.8 Consensus size: 41
442254 AACTTTGAAA
* ** * * *
442264 ATCGCATTGCGATTCTGTATTATCTCGTTGCGATAGTCAGA
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
* *** * * * * *
442305 ATCTCATTGCGAAAGTCAGA-ATCACATTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
* *** * *
442345 ATCGCGTTGCGAAAGTC-AGTATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
* ** *
442385 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
*
442426 ATCGCATTGCGATTTTCCAAAT-TCGCATTGCGAT
1 ATCGCATTGCGATTTT-CAAATATCGCGTTGCGAT
442460 TTACTTATTC
Statistics
Matches: 123, Mismatches: 29, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
40 62 0.50
41 59 0.48
42 2 0.02
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCAAATATCGCGTTGCGATAGTCAGT
Found at i:442471 original size:20 final size:21
Alignment explanation
Indices: 442427--442478 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
442417 ATAGTCAGTA
*
442427 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
442448 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
442468 TCGCATTGCGA
1 TCGCATTGCGA
442479 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:442520 original size:21 final size:22
Alignment explanation
Indices: 442468--442520 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
442458 ATTTACTTAT
442468 TCGCATTGCG-AATTGGGAAAA
1 TCGCATTGCGAAATTGGGAAAA
**
442489 TCGCAACGCGAAATT-GGAAAA
1 TCGCATTGCGAAATTGGGAAAA
442510 TCGCATTGCGA
1 TCGCATTGCGA
442521 TAGTAATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTGGGAAAA
Found at i:446731 original size:52 final size:52
Alignment explanation
Indices: 446670--446768 Score: 171
Period size: 52 Copynumber: 1.9 Consensus size: 52
446660 ATAAAGGTGA
*
446670 AACGATGATTCATGGTACTTAAGATTCATGTCTATTTATCAGGATATTGAGT
1 AACGATGATTCATGGTACTTAAGATTCATGTCGATTTATCAGGATATTGAGT
* *
446722 AACGATGATTCATGGTATTTAAGATTCCTGTCGATTTATCAGGATAT
1 AACGATGATTCATGGTACTTAAGATTCATGTCGATTTATCAGGATAT
446769 CAAGTCAACT
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 44 1.00
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.38
Consensus pattern (52 bp):
AACGATGATTCATGGTACTTAAGATTCATGTCGATTTATCAGGATATTGAGT
Found at i:447377 original size:27 final size:27
Alignment explanation
Indices: 447325--447387 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
447315 ATGTACTTTA
* *
447325 GGTCATTTTACTCATTAGGGGTATTTT
1 GGTCATTTTACTAATTAGGGGCATTTT
*
447352 GGTCATTTTAC-AATTTGAGGGCATTTT
1 GGTCATTTTACTAATTAG-GGGCATTTT
* *
447379 AGTTATTTT
1 GGTCATTTT
447388 CTTCAATCCA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
26 4 0.13
27 26 0.87
ACGTcount: A:0.21, C:0.10, G:0.21, T:0.49
Consensus pattern (27 bp):
GGTCATTTTACTAATTAGGGGCATTTT
Found at i:453842 original size:20 final size:21
Alignment explanation
Indices: 453813--453875 Score: 60
Period size: 20 Copynumber: 3.1 Consensus size: 21
453803 AATAGTATGA
*
453813 ACTGGATGAA-TAGTATCAAT
1 ACTGGATGAAGAAGTATCAAT
* *
453833 ACTGGTTGAAGAAGTATCGAT
1 ACTGGATGAAGAAGTATCAAT
*
453854 ACT-GATGTAA-AGGTATCAAT
1 ACTGGATG-AAGAAGTATCAAT
453874 AC
1 AC
453876 CAAGAATAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 22 0.63
21 13 0.37
ACGTcount: A:0.38, C:0.11, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTGGATGAAGAAGTATCAAT
Found at i:454760 original size:21 final size:22
Alignment explanation
Indices: 454710--454782 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 22
454700 GTCGAGGGTT
*
454710 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCATTCGGGAC-AAA
454733 CTATGTGGTCATTCGGGACAAA
1 CTATGTGGTCATTCGGGACAAA
454755 -TATGTGG-CACTTCGGTG-CAAA
1 CTATGTGGTCA-TTCGG-GACAAA
*
454776 TTATGTG
1 CTATGTG
454783 AGTTGTGGTG
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
20 2 0.04
21 16 0.35
22 10 0.22
23 18 0.39
ACGTcount: A:0.25, C:0.18, G:0.27, T:0.30
Consensus pattern (22 bp):
CTATGTGGTCATTCGGGACAAA
Found at i:455765 original size:21 final size:20
Alignment explanation
Indices: 455727--455771 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
455717 TGAATGTTTG
*
455727 AAAAATAATTTCAAATGAACA
1 AAAAATAAATTCAAATGAA-A
**
455748 AAAAATAAATTCCCATGAAA
1 AAAAATAAATTCAAATGAAA
455768 AAAA
1 AAAA
455772 TATCAACAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 5 0.24
21 16 0.76
ACGTcount: A:0.64, C:0.11, G:0.04, T:0.20
Consensus pattern (20 bp):
AAAAATAAATTCAAATGAAA
Found at i:458182 original size:24 final size:24
Alignment explanation
Indices: 458155--458205 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
458145 ACAAATTCAA
458155 TTCTTCCTATATTTACTTCACCAG
1 TTCTTCCTATATTTACTTCACCAG
* *
458179 TTCTTCCTATATTTGCTTGACCAG
1 TTCTTCCTATATTTACTTCACCAG
458203 TTC
1 TTC
458206 GATCGATATT
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:0.18, C:0.27, G:0.08, T:0.47
Consensus pattern (24 bp):
TTCTTCCTATATTTACTTCACCAG
Found at i:461823 original size:3 final size:3
Alignment explanation
Indices: 461817--461863 Score: 58
Period size: 3 Copynumber: 15.7 Consensus size: 3
461807 TCATCATCAT
* * * *
461817 CAC CAC CAC TAC TAC CAC CAC CAC CAC TAC TAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
461864 TCATCATCAT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.34, C:0.57, G:0.00, T:0.09
Consensus pattern (3 bp):
CAC
Found at i:461835 original size:15 final size:15
Alignment explanation
Indices: 461817--461863 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
461807 TCATCATCAT
*
461817 CACCACCACTACTAC
1 CACCACCACCACTAC
461832 CACCACCACCACTAC
1 CACCACCACCACTAC
* *
461847 TACCACCACCACCAC
1 CACCACCACCACTAC
461862 CA
1 CA
461864 TCATCATCAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.34, C:0.57, G:0.00, T:0.09
Consensus pattern (15 bp):
CACCACCACCACTAC
Found at i:461840 original size:18 final size:18
Alignment explanation
Indices: 461817--461861 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
461807 TCATCATCAT
461817 CACCACCACTACTACCAC
1 CACCACCACTACTACCAC
461835 CACCACCACTACTACCAC
1 CACCACCACTACTACCAC
461853 CACCACCAC
1 CACCACCAC
461862 CATCATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.33, C:0.58, G:0.00, T:0.09
Consensus pattern (18 bp):
CACCACCACTACTACCAC
Found at i:465258 original size:2 final size:2
Alignment explanation
Indices: 465251--465275 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
465241 AGAAAAATGT
465251 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 T
465276 TATTTTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:468514 original size:5 final size:5
Alignment explanation
Indices: 468504--468540 Score: 74
Period size: 5 Copynumber: 7.4 Consensus size: 5
468494 TAACAAAAAT
468504 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AA
1 AATTA AATTA AATTA AATTA AATTA AATTA AATTA AA
468541 GGGGTGGATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
AATTA
Found at i:470714 original size:23 final size:22
Alignment explanation
Indices: 470683--470765 Score: 112
Period size: 23 Copynumber: 3.6 Consensus size: 22
470673 CTTGATGGGT
* * *
470683 TTATAGAAGAAAAAGAAATGTG
1 TTATGGAAGAAGAAGAAATGAG
470705 CTTATGGAAGAAGAAGAAATGAG
1 -TTATGGAAGAAGAAGAAATGAG
470728 TTTATGGAAGAAGAAGAAATGAG
1 -TTATGGAAGAAGAAGAAATGAG
470751 TATATGGAAGAAGAA
1 T-TATGGAAGAAGAA
470766 TAATAATTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
22 1 0.02
23 54 0.98
ACGTcount: A:0.51, C:0.01, G:0.28, T:0.20
Consensus pattern (22 bp):
TTATGGAAGAAGAAGAAATGAG
Found at i:471664 original size:22 final size:23
Alignment explanation
Indices: 471631--471674 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
471621 GAAAAGGGGA
471631 GGAGGAGAG-AAAAAAAGGAAAG
1 GGAGGAGAGAAAAAAAAGGAAAG
471653 GGAGG-GATGAAAAAAAAGGAAA
1 GGAGGAGA-GAAAAAAAAGGAAA
471675 ACGGGGAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 2 0.10
22 6 0.30
23 12 0.60
ACGTcount: A:0.59, C:0.00, G:0.39, T:0.02
Consensus pattern (23 bp):
GGAGGAGAGAAAAAAAAGGAAAG
Found at i:475037 original size:24 final size:23
Alignment explanation
Indices: 474985--475047 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
474975 CTCTTGATGG
*
474985 GTTTATGGAAGAAAAAGAAATAT
1 GTTTATGGAAGAAGAAGAAATAT
*
475008 GCTTATGGAAGATAGAAGAAATGA-
1 GTTTATGGAAGA-AGAAGAAAT-AT
475032 GTTTATGGAAGAAGAA
1 GTTTATGGAAGAAGAA
475048 TAATAGTTTA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 15 0.43
24 19 0.54
25 1 0.03
ACGTcount: A:0.48, C:0.02, G:0.27, T:0.24
Consensus pattern (23 bp):
GTTTATGGAAGAAGAAGAAATAT
Found at i:475884 original size:19 final size:20
Alignment explanation
Indices: 475862--475901 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
475852 AAGGGGAGGA
*
475862 GGAGAGAA-AAAAAGGAAAG
1 GGAGAGAAGAAAAAAGAAAG
*
475881 GGAGGGAAGAAAAAAGAAAG
1 GGAGAGAAGAAAAAAGAAAG
475901 G
1 G
475902 AAAAGAGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (20 bp):
GGAGAGAAGAAAAAAGAAAG
Found at i:475906 original size:26 final size:26
Alignment explanation
Indices: 475849--475906 Score: 66
Period size: 25 Copynumber: 2.2 Consensus size: 26
475839 CAACAACACA
* *
475849 GAAAAGGGGAGGAGGAGAGAAAAAAAG
1 GAAAA-GGGAGGAGAAGAAAAAAAAAG
475876 G-AAAGGGAGG-GAAGAAAAAAGAAAG
1 GAAAAGGGAGGAGAAGAAAAAA-AAAG
475901 GAAAAG
1 GAAAAG
475907 AGGGATTTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 8 0.30
25 11 0.41
26 7 0.26
27 1 0.04
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (26 bp):
GAAAAGGGAGGAGAAGAAAAAAAAAG
Found at i:484794 original size:16 final size:16
Alignment explanation
Indices: 484759--484794 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
484749 AAATAGAAGG
* *
484759 AGTTAATAGATTTTGG
1 AGTTAATAGATATTGA
484775 AGTTAATAGATATTGA
1 AGTTAATAGATATTGA
484791 AGTT
1 AGTT
484795 GAATTTGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (16 bp):
AGTTAATAGATATTGA
Found at i:485183 original size:20 final size:20
Alignment explanation
Indices: 485158--485213 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
485148 AAATTTTTGA
485158 AGGTGCATCGATGCATTAAG
1 AGGTGCATCGATGCATTAAG
*
485178 AGGTGCATCGATGCATTCAG
1 AGGTGCATCGATGCATTAAG
*
485198 GGGTGCATCGATGCAT
1 AGGTGCATCGATGCAT
485214 GAATATTTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (20 bp):
AGGTGCATCGATGCATTAAG
Found at i:486276 original size:2 final size:2
Alignment explanation
Indices: 486269--486334 Score: 132
Period size: 2 Copynumber: 33.0 Consensus size: 2
486259 ATTGCATAAG
486269 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
486311 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
486335 TCATATGATT
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):
AT
Found at i:486721 original size:23 final size:23
Alignment explanation
Indices: 486688--486755 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
486678 CATATTATAT
486688 GGCACTTCGGTGCATTTCTACGC
1 GGCACTTCGGTGCATTTCTACGC
* * *
486711 GGCACTACGGTGCAATTCTACGT
1 GGCACTTCGGTGCATTTCTACGC
*
486734 GGCACTTCGGTGCATTTATACG
1 GGCACTTCGGTGCATTTCTACG
486756 AGCTGTGGTG
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.18, C:0.26, G:0.26, T:0.29
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACGC
Found at i:488790 original size:20 final size:20
Alignment explanation
Indices: 488753--488791 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
488743 GATTTCAATT
* *
488753 TGGAATGAATAAAGGAAAAA
1 TGGAATAAAGAAAGGAAAAA
*
488773 TGGAATAAAGAAATGAAAA
1 TGGAATAAAGAAAGGAAAA
488792 TGATTGAGTT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.23, T:0.15
Consensus pattern (20 bp):
TGGAATAAAGAAAGGAAAAA
Found at i:491173 original size:2 final size:2
Alignment explanation
Indices: 491166--491227 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
491156 ATTGCATAAG
491166 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
491208 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
491228 CATGATTTGG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:493000 original size:42 final size:42
Alignment explanation
Indices: 492897--493015 Score: 141
Period size: 42 Copynumber: 2.8 Consensus size: 42
492887 TGGTAAGTTC
* ** *
492897 TTCGGGCCATTAGTAAGTCTTTAAAGAATGATGATTAAATCA
1 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCA
*
492939 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCC
1 TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCA
* * * *
492981 TTTGGGTCATCTA-TCAGTCTTTCGAGCAAGATGAT
1 TTCGGGCCATC-AGTAAGTCTTTCGAGCATGATGAT
493016 AAGTCCTACG
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 66 0.99
43 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (42 bp):
TTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCA
Found at i:493259 original size:299 final size:299
Alignment explanation
Indices: 492652--493265 Score: 921
Period size: 299 Copynumber: 2.1 Consensus size: 299
492642 TCCAAAATTG
* *
492652 GTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGTTCATCTGTCAGACTTTCGAGCAAGATGAT
1 GTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGACTTTCGAGCAAGATGAT
* * *
492717 AAGTCATTCGGGCCCTCTATAAGACCTTCAGGCAGGATGTTTTCACATGATTTTCAAAAAATGAG
66 AAGTCATACGAGCCATCTATAAGACCTTCAGGCAGGATGTTTTCACATGATTTTCAAAAAATGAG
*
492782 AAAGCGATTTCCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATTTTTGAAAAGTATGAAAG
131 AAAGCGATTTCCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTATGAAAG
* * * *
492847 TGATTTCCAAAGTTTCTTACCTAGTAAATTTTTCCAAAATTGGTAAGTTCTTCGGGCCATTAGTA
196 TGATTTCCAAAGTTTCTTACCCAGTAAATATTTCCAAAATTGGTAAGTCCTTCGGGCCACTAGTA
* *
492912 AGTCTTTAAAGAATGATGATTAAATCATTCGGGCCATCA
261 AGTCGTTAAAGAATGATGATTAAATCATTCAGGCCATCA
* *
492951 GTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTATCAGTCTTTCGAGCAAGATGAT
1 GTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGACTTTCGAGCAAGATGAT
* * *
493016 AAGTCCTACGAGCCATCTATAAGACCTTCGGGCATGATGTTTTCACATGATTTTCAAAAAATGAG
66 AAGTCATACGAGCCATCTATAAGACCTTCAGGCAGGATGTTTTCACATGATTTTCAAAAAATGAG
*
493081 AAATCGATTTCCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAATG-AA
131 AAAGCGATTTCCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGT-ATGAAA
* *
493145 GTGATTTCCAAAGTTTCTTACCCGGTAGACA-ATTTCCAAAATTGGTAAGTCCTTCGGGTCACTA
195 GTGATTTCCAAAGTTTCTTACCCAGTA-A-ATATTTCCAAAATTGGTAAGTCCTTCGGGCCACTA
** * * * *
493209 GTAAGTCGTTCGAGCAA-GATGATTAAA-CCTTTAGGTCATCT
258 GTAAGTCGTTAAAG-AATGATGATTAAATCATTCAGGCCATCA
*
493250 GTCAGTCTTTCGAGCA
1 GTAAGTCTTTCGAGCA
493266 AGATTATAAG
Statistics
Matches: 284, Mismatches: 27, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
299 227 0.80
300 54 0.19
301 3 0.01
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (299 bp):
GTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATCTATCAGACTTTCGAGCAAGATGAT
AAGTCATACGAGCCATCTATAAGACCTTCAGGCAGGATGTTTTCACATGATTTTCAAAAAATGAG
AAAGCGATTTCCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTATGAAAG
TGATTTCCAAAGTTTCTTACCCAGTAAATATTTCCAAAATTGGTAAGTCCTTCGGGCCACTAGTA
AGTCGTTAAAGAATGATGATTAAATCATTCAGGCCATCA
Found at i:493315 original size:257 final size:258
Alignment explanation
Indices: 492950--493459 Score: 774
Period size: 257 Copynumber: 2.0 Consensus size: 258
492940 TCGGGCCATC
* * *
492950 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTTGGGTCATCTATCAGTCTTTCGAGCAAGATGA
1 AGTAAGTCGTTCGAGCAAGATGATTAAATCCTTTAGGTCATCTATCAGTCTTTCGAGCAAGATGA
* * *
493015 TAAGTCCTACGAGCCATCTATAAGACCTTCGGGCATGATGTTTTCACATGATTTTCAAAAAATGA
66 TAAGTCATACGAGCCATCCATAAGACCTTCAGGCATGATGTTTTCACATGATTTTCAAAAAATGA
* *
493080 GAAA-TCGATTTCCAAAGTTTCTCATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAATGA
131 GAAAGT-GATTTCCAAAGTTTATCATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAAGGA
** * *
493144 AGTGATTTCCAAAGTTTCTTACCCGGTAGACAATTTCCAAAATTGGTAAGTCCTTCGGGTCACT
195 AGAAATTTCCAAAGTTTCTTACACAGTAGACAATTTCCAAAATTGGTAAGTCCTTCGGGTCACT
* *
493208 AGTAAGTCGTTCGAGCAAGATGATTAAA-CCTTTAGGTCATCTGTCAGTCTTTCGAGCAAGATTA
1 AGTAAGTCGTTCGAGCAAGATGATTAAATCCTTTAGGTCATCTATCAGTCTTTCGAGCAAGATGA
* * * * **
493272 TAAGTCATTCGGGCCATCCATAATACCTTTAGGCA-GAATGTTTTCACATGATTTTTGAAAAATG
66 TAAGTCATACGAGCCATCCATAAGACCTTCAGGCATG-ATGTTTTCACATGATTTTCAAAAAATG
*
493336 AGAAAGTGATTTCCAAATTTTATCATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAAGGA
130 AGAAAGTGATTTCCAAAGTTTATCATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAAGGA
* *
493401 AGAAATTTCCAAAGTTTCTTACATAGTAGACTATTTCCAAAATTGGTAAGTCCTTCGGG
195 AGAAATTTCCAAAGTTTCTTACACAGTAGACAATTTCCAAAATTGGTAAGTCCTTCGGG
493460 CCATCTGTTG
Statistics
Matches: 227, Mismatches: 23, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
256 1 0.00
257 199 0.88
258 27 0.12
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (258 bp):
AGTAAGTCGTTCGAGCAAGATGATTAAATCCTTTAGGTCATCTATCAGTCTTTCGAGCAAGATGA
TAAGTCATACGAGCCATCCATAAGACCTTCAGGCATGATGTTTTCACATGATTTTCAAAAAATGA
GAAAGTGATTTCCAAAGTTTATCATTTAATATTTTCAGAAAATGAAATCTTTGAAAAGTAAGGAA
GAAATTTCCAAAGTTTCTTACACAGTAGACAATTTCCAAAATTGGTAAGTCCTTCGGGTCACT
Found at i:493808 original size:45 final size:46
Alignment explanation
Indices: 493759--493846 Score: 142
Period size: 45 Copynumber: 1.9 Consensus size: 46
493749 GAACATCGAA
* *
493759 TGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTTAG
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
*
493804 TGCATTTGATGCATCGATGCACAAGACTATGCATCGATGCACT
1 TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACT
493847 CAGGCTTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
45 21 0.54
46 18 0.46
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTTAG
Found at i:501366 original size:21 final size:21
Alignment explanation
Indices: 501324--501367 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
501314 ACTCCGGGAA
* *
501324 CTAGTTCCTCACGAGCTGCTC
1 CTAGCTCCTCACGAGCTCCTC
* *
501345 CTAGCTCCTCTCGTGCTCCTC
1 CTAGCTCCTCACGAGCTCCTC
501366 CT
1 CT
501368 CCTCCTCCGG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.43, G:0.16, T:0.32
Consensus pattern (21 bp):
CTAGCTCCTCACGAGCTCCTC
Found at i:502460 original size:20 final size:20
Alignment explanation
Indices: 502422--502460 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
502412 TTTTGGAGGG
*
502422 CATGCACCGATGTACCAATC
1 CATGCACCGATGCACCAATC
* *
502442 CATGCATCGATGCATCAAT
1 CATGCACCGATGCACCAAT
502461 TAATTTCTTG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.31, C:0.31, G:0.15, T:0.23
Consensus pattern (20 bp):
CATGCACCGATGCACCAATC
Found at i:502529 original size:45 final size:46
Alignment explanation
Indices: 502480--502570 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 46
502470 GAACATCGAA
* * * *
502480 TGCATTTTATGCATCGATGTAC-ATACCATGCATCGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATACATCGATGCACTCAG
* *
502525 TGCATTTGATGCATCGATGCACAAGACTATACATTGATGCACTCAG
1 TGCATTTGATGCATCGATGCACAAGACCATACATCGATGCACTCAG
502571 GTTTTTTCAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
45 20 0.51
46 19 0.49
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (46 bp):
TGCATTTGATGCATCGATGCACAAGACCATACATCGATGCACTCAG
Found at i:503525 original size:19 final size:19
Alignment explanation
Indices: 503503--503543 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
503493 AAAATAAAAA
503503 GAAAATATCAAAAAAAGGG
1 GAAAATATCAAAAAAAGGG
503522 GAAAATATCAAAAAAAGGG
1 GAAAATATCAAAAAAAGGG
503541 GAA
1 GAA
503544 GATCTTTTCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.63, C:0.05, G:0.22, T:0.10
Consensus pattern (19 bp):
GAAAATATCAAAAAAAGGG
Found at i:506984 original size:9 final size:9
Alignment explanation
Indices: 506966--506996 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
506956 GGTAAGTAAT
*
506966 ATATACATA
1 ATATATATA
506975 ATATATATA
1 ATATATATA
506984 ATATATATA
1 ATATATATA
506993 ATAT
1 ATAT
506997 TTAAAATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (9 bp):
ATATATATA
Found at i:508869 original size:27 final size:29
Alignment explanation
Indices: 508837--508901 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 29
508827 TTAGAATTTA
*
508837 GGATTTTTAGGAATTTAT-GAG-TTTTTG
1 GGATTTTTAGAAATTTATGGAGTTTTTTG
*
508864 GGATTTTCT-GAAATTTATGGCGTTTTTTG
1 GGATTTT-TAGAAATTTATGGAGTTTTTTG
*
508893 GGAATTTTA
1 GGATTTTTA
508902 ATAATTTCAT
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
27 15 0.48
28 4 0.13
29 12 0.39
ACGTcount: A:0.22, C:0.03, G:0.25, T:0.51
Consensus pattern (29 bp):
GGATTTTTAGAAATTTATGGAGTTTTTTG
Found at i:508907 original size:29 final size:30
Alignment explanation
Indices: 508858--508921 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
508848 AATTTATGAG
* *
508858 TTTTTGGGATTTTCTGAAATTT-ATGGCGT-
1 TTTTTGGGAATTTCTAAAATTTCATGG-GTA
508887 TTTTTGGGAATTT-TAATAATTTCATGGGTA
1 TTTTTGGGAATTTCTAA-AATTTCATGGGTA
508917 TTTTT
1 TTTTT
508922 AGTAAATAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 2 0.07
29 19 0.63
30 9 0.30
ACGTcount: A:0.20, C:0.05, G:0.20, T:0.55
Consensus pattern (30 bp):
TTTTTGGGAATTTCTAAAATTTCATGGGTA
Found at i:510343 original size:2 final size:2
Alignment explanation
Indices: 510323--510387 Score: 107
Period size: 2 Copynumber: 33.5 Consensus size: 2
510313 TTGTAATAAT
*
510323 TA TA TC TA T- TA TA -A 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
510363 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 T
510388 TAAAATTTTG
Statistics
Matches: 59, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 57 0.97
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:511555 original size:3 final size:3
Alignment explanation
Indices: 511537--511605 Score: 59
Period size: 3 Copynumber: 23.0 Consensus size: 3
511527 TGTCTCGTGT
* * * * *
511537 TTA TTA TT- TTA ATA TTA TTA CTA TTA TTA GTA TTA TTA TTA ATA ATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
511584 ATA ATA TTA TTTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA
511606 ATAATAAATA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
2 2 0.04
3 51 0.91
4 3 0.05
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:512565 original size:30 final size:30
Alignment explanation
Indices: 512531--512595 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
512521 GTAATTTTAT
512531 ATTTTCTGAGTACTTTAATTTGGTCTCATA
1 ATTTTCTGAGTACTTTAATTTGGTCTCATA
* * *
512561 ATTTTTTTAGTACTTTAATTTGGTCTCGTA
1 ATTTTCTGAGTACTTTAATTTGGTCTCATA
512591 ATTTT
1 ATTTT
512596 ATTTTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.22, C:0.11, G:0.12, T:0.55
Consensus pattern (30 bp):
ATTTTCTGAGTACTTTAATTTGGTCTCATA
Found at i:512858 original size:22 final size:21
Alignment explanation
Indices: 512830--512870 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
512820 CAATTTAATT
512830 TAATTTTATATATTTAATTTAG
1 TAATTTTAT-TATTTAATTTAG
*
512852 TAATTTTATTATTTTATTT
1 TAATTTTATTATTTAATTT
512871 CAATCATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TAATTTTATTATTTAATTTAG
Found at i:513096 original size:2 final size:2
Alignment explanation
Indices: 513084--513159 Score: 143
Period size: 2 Copynumber: 38.0 Consensus size: 2
513074 AGTCATATTA
*
513084 AT AT AT GT 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
513126 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
513160 GAAAGATTAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 72 1.00
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (2 bp):
AT
Found at i:519771 original size:19 final size:19
Alignment explanation
Indices: 519747--519787 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
519737 TGTATTTGTA
519747 AAGCTTTCTTATGCAACGT
1 AAGCTTTCTTATGCAACGT
519766 AAGCTTTCTTATGCAACGT
1 AAGCTTTCTTATGCAACGT
519785 AAG
1 AAG
519788 TAGAAGTAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.34
Consensus pattern (19 bp):
AAGCTTTCTTATGCAACGT
Found at i:520681 original size:19 final size:19
Alignment explanation
Indices: 520659--520707 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
520649 GAGGTGGCTA
520659 ACGGTTGTCAATGTGGTTG
1 ACGGTTGTCAATGTGGTTG
520678 ACGGTTGTCAATGTGGTTG
1 ACGGTTGTCAATGTGGTTG
*
520697 ACGGCTGTCAA
1 ACGGTTGTCAA
520708 CGTAGACAGC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.18, C:0.14, G:0.35, T:0.33
Consensus pattern (19 bp):
ACGGTTGTCAATGTGGTTG
Found at i:523282 original size:20 final size:20
Alignment explanation
Indices: 523259--523310 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
523249 AACGCGATCC
523259 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
523279 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
523299 CCAAAATCGCAA
1 CCAGAATCGCAA
523311 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:523327 original size:21 final size:20
Alignment explanation
Indices: 523300--523398 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
523290 AATCAGTTTC
523300 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
523321 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
523342 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
523362 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
523383 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
523399 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:523427 original size:20 final size:20
Alignment explanation
Indices: 523365--523558 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
523355 CGATTTTCCA
* ** *
523365 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
523385 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
523405 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
523425 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
523445 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
523465 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
523485 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
523505 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
523525 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
523546 AAATCGCAACGCG
1 AAATCGCAACGCG
523559 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:523449 original size:60 final size:60
Alignment explanation
Indices: 523365--523558 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
523355 CGATTTTCCA
* ** * *
523365 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
523425 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
523485 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
523546 AAATCGCAACGCG
1 AAATCGCAACGCG
523559 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:523978 original size:33 final size:33
Alignment explanation
Indices: 523939--524009 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
523929 TTCACTTAGA
523939 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
523972 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
524005 TTTCA
1 TTTCA
524010 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:524148 original size:14 final size:14
Alignment explanation
Indices: 524129--524183 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
524119 AGAATGACTG
524129 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
524143 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
524162 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
524176 TCGCAACG
1 TCGCAACG
524184 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:524196 original size:33 final size:33
Alignment explanation
Indices: 524129--524199 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
524119 AGAATGACTG
***
524129 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
524162 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
524195 TCGCA
1 TCGCA
524200 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:524217 original size:19 final size:19
Alignment explanation
Indices: 524195--524292 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
524185 GAAACCAAAA
*
524195 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
524214 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
524228 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
524247 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
524261 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
524280 TCGCGTTGCGATT
1 TCGCGTTGCGATT
524293 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:524236 original size:14 final size:14
Alignment explanation
Indices: 524217--524306 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
524207 TTTCATTTCG
524217 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
524231 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
524250 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
524264 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
524281 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
524297 CGTTGCGATT
1 CGTTGCGATT
524307 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:524242 original size:33 final size:33
Alignment explanation
Indices: 524200--524314 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
524190 CAAAATCGCA
524200 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
524233 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
524266 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
524299 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
524315 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:526239 original size:185 final size:186
Alignment explanation
Indices: 526010--526389 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
526000 TAGATTGCTT
526010 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
526075 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
526140 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
526195 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
526260 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
526325 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
526381 AGTAAATTT
1 AGTAAATTT
526390 ATCCATTCAA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:526324 original size:93 final size:93
Alignment explanation
Indices: 526010--526389 Score: 753
Period size: 93 Copynumber: 4.1 Consensus size: 93
526000 TAGATTGCTT
526010 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
526075 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
526103 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
526167 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
526195 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
526260 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
526288 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
526353 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
526381 AGTAAATTT
1 AGTAAATTT
526390 ATCCATTCAA
Statistics
Matches: 286, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.32
93 194 0.68
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:526491 original size:33 final size:32
Alignment explanation
Indices: 526448--526540 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
526438 ACGAAACTTA
**
526448 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
526480 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
526513 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
526541 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:526540 original size:19 final size:19
Alignment explanation
Indices: 526431--526540 Score: 87
Period size: 19 Copynumber: 6.3 Consensus size: 19
526421 AAGTTTACTT
* *
526431 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
**
526451 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
526470 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
526484 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
526503 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
526517 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
526536 TCGCA
1 TCGCA
526541 TTGCGATTTT
Statistics
Matches: 72, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.26
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 29 0.40
20 12 0.17
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:526558 original size:19 final size:19
Alignment explanation
Indices: 526536--526670 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
526526 GAAACCAAAA
*
526536 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
526555 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
526571 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
526588 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
526604 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
526621 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
526640 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
526660 TCGTGTTGCGA
1 TCGCGTTGCGA
526671 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:526577 original size:14 final size:14
Alignment explanation
Indices: 526558--526614 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
526548 TTTCATTTCG
526558 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
526572 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
526589 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
526605 CGTTGCGATT
1 CGTTGCGATT
526615 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:526583 original size:33 final size:33
Alignment explanation
Indices: 526541--526633 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
526531 CAAAATCGCA
*
526541 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
526574 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
526607 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
526634 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:528531 original size:38 final size:38
Alignment explanation
Indices: 528488--528560 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
528478 AATTGATTGT
*
528488 TTTTTGATTGTTTAATTGATTTGTAAAAGTTGATTCAA
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
528526 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
1 TTTTTGATTGTTTAATTGATTTGTAAAAGATGATT
528561 TGTAAAAGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.53
Consensus pattern (38 bp):
TTTTTGATTGTTTAATTGATTTGTAAAAGATGATTCAA
Found at i:528547 original size:19 final size:19
Alignment explanation
Indices: 528483--528547 Score: 51
Period size: 19 Copynumber: 3.4 Consensus size: 19
528473 AGTTTAATTG
*
528483 ATTGTTTTTTGATTGTTTA
1 ATTGATTTTTGATTGTTTA
* * ** *
528502 ATTGATTTGTAAAAG-TTG
1 ATTGATTTTTGATTGTTTA
*
528520 ATTCAATTTTTGATTGTTTA
1 ATT-GATTTTTGATTGTTTA
528540 ATTGATTT
1 ATTGATTT
528548 GTAAAAGATG
Statistics
Matches: 31, Mismatches: 13, Indels: 4
0.65 0.27 0.08
Matches are distributed among these distances:
18 5 0.16
19 21 0.68
20 5 0.16
ACGTcount: A:0.25, C:0.02, G:0.15, T:0.58
Consensus pattern (19 bp):
ATTGATTTTTGATTGTTTA
Found at i:528561 original size:14 final size:14
Alignment explanation
Indices: 528542--528577 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
528532 ATTGTTTAAT
528542 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
528556 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
528570 TGATTTGT
1 TGATTTGT
528578 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:528700 original size:19 final size:19
Alignment explanation
Indices: 528684--528785 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
528674 AAAAATGACT
528684 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
528703 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
528722 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
528736 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
528755 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
528775 ATCGCAATGCG
1 ATCGCAATGCG
528786 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:528838 original size:19 final size:19
Alignment explanation
Indices: 528814--529120 Score: 349
Period size: 19 Copynumber: 17.4 Consensus size: 19
528804 GATTATCTCG
528814 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
528833 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
528852 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
528866 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
528885 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
528904 TTGCGATTTTCATTTTGTA
1 TTGCGATTTTCATTTCGCA
*
528923 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
528942 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
528957 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
528975 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
528994 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
529008 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
529027 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
529046 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
529060 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
529080 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
529094 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
529113 TTGCGATT
1 TTGCGATT
529121 GTATTTTCCG
Statistics
Matches: 247, Mismatches: 15, Indels: 52
0.79 0.05 0.17
Matches are distributed among these distances:
14 32 0.13
15 2 0.01
16 31 0.13
17 28 0.11
18 5 0.02
19 137 0.55
20 12 0.05
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:528889 original size:71 final size:71
Alignment explanation
Indices: 528814--529053 Score: 346
Period size: 71 Copynumber: 3.4 Consensus size: 71
528804 GATTATCTCG
528814 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
528879 TTCGCA
66 TTCGCA
* * *
528885 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTTGTATTGCGATTTTAATTTCGCATTGCGA--
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TT-CTTTCG--TTGCGATT
* *
528948 TT-ATGTCG-G
61 TTCATTTCGCA
*
528957 TT-CGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCAT
1 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
529021 TTCGCA
66 TTCGCA
529027 TTGCGATTTTCATTTCGCATTGCGATT
1 TTGCGATTTTCATTTCGCATTGCGATT
529054 CTCTCGTTGC
Statistics
Matches: 148, Mismatches: 11, Indels: 20
0.83 0.06 0.11
Matches are distributed among these distances:
66 6 0.04
68 6 0.04
69 7 0.05
70 2 0.01
71 105 0.71
72 2 0.01
73 7 0.05
74 7 0.05
76 6 0.04
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (71 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCAT
TTCGCA
Found at i:528973 original size:142 final size:136
Alignment explanation
Indices: 528782--529120 Score: 495
Period size: 142 Copynumber: 2.4 Consensus size: 136
528772 AAAATCGCAA
528782 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTAT-TCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
*
528846 TTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-
* *
528911 TTTCATTTTGTAT
128 -TTC-TCTCG--T
528924 TGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTAT-TC-GTTGCGATTTTCATTTCGCATTGCGATTTTCAT
528988 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
64 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
529053 TCTCTCGT
129 TCTCTCGT
* * *
529061 TGCGATTTTCATTTCCGCATTGCGATT-TTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTAATTT-CGCATTGCGATTATTC--GTTGCGATTTTCATTTCGCATTGCGATT
529121 GTATTTTCCG
Statistics
Matches: 184, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 34 0.18
139 3 0.02
140 3 0.02
142 118 0.64
143 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (136 bp):
TGCGATTTTAATTTCGCATTGCGATTATTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTC
TCTCGT
Found at i:529059 original size:52 final size:52
Alignment explanation
Indices: 528814--529092 Score: 345
Period size: 52 Copynumber: 5.2 Consensus size: 52
528804 GATTATCTCG
*
528814 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
528866 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTTGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
528923 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
528975 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
529027 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
529080 TTGCGATTTTCAT
1 TTGCGATTTTCAT
529093 GTTGGGATTT
Statistics
Matches: 210, Mismatches: 9, Indels: 15
0.90 0.04 0.06
Matches are distributed among these distances:
51 3 0.01
52 151 0.72
53 19 0.09
54 6 0.03
55 7 0.03
57 24 0.11
ACGTcount: A:0.15, C:0.20, G:0.17, T:0.48
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:531443 original size:12 final size:12
Alignment explanation
Indices: 531426--531450 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
531416 TTCTTCGGGA
531426 CTTTTTCTTCTT
1 CTTTTTCTTCTT
531438 CTTTTTCTTCTT
1 CTTTTTCTTCTT
531450 C
1 C
531451 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:531659 original size:24 final size:24
Alignment explanation
Indices: 531625--531671 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
531615 CTGAAACATC
531625 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
531649 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
531672 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:532373 original size:20 final size:20
Alignment explanation
Indices: 532345--532713 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
532335 AAATTTCAGT
* * * *
532345 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
532365 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
532385 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
532405 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
532425 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
532445 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
532465 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
532485 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
532505 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
532525 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
532545 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
532565 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
532585 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
532605 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
532625 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
532645 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
532665 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
532685 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
532705 GTTGCGATT
1 GTTGCGATT
532714 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:542285 original size:29 final size:29
Alignment explanation
Indices: 542230--542294 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
542220 GAATTTCTAA
**
542230 AAAATTTAGGGTCCAAATTATA-TTTTTT
1 AAAATTTAGGGTCCAAATTATAGTTTTCC
* *
542258 AAAATTTAATGGTCCAAATTTTAGTTTTCC
1 AAAATTT-AGGGTCCAAATTATAGTTTTCC
542288 AAAATTT
1 AAAATTT
542295 TAGTGGACAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 7 0.23
29 13 0.42
30 11 0.35
ACGTcount: A:0.37, C:0.09, G:0.09, T:0.45
Consensus pattern (29 bp):
AAAATTTAGGGTCCAAATTATAGTTTTCC
Found at i:546594 original size:2 final size:2
Alignment explanation
Indices: 546583--546622 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
546573 CAAGCTTAAT
546583 TA TA -A 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 TA TA T
546623 TTATTTATTT
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:546627 original size:4 final size:4
Alignment explanation
Indices: 546620--546645 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
546610 TATATATATA
546620 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
546646 CAGGGACACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:548757 original size:37 final size:37
Alignment explanation
Indices: 548698--549463 Score: 531
Period size: 37 Copynumber: 20.2 Consensus size: 37
548688 GTCAGACTCG
* * * *
548698 AGATTGATTTGCATCACCACTCTTCGGTGAAGGCTTG
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*
548735 AGATGGATTTGCTTTACTACTCTTCGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * *
548772 AAATAGATTTGATTCACTACTCTTCGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * * *
548809 AGATTGATTTGATTCAATACTCTTTGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
**** **** * * *
548846 AGA-GGGCCCGAAGAACTTAATCATCATGCTCGGAAGGCTTA
1 AGATGGATTTGCTTCAC-TACTCTTC--GGT--GAAGGCTTA
* * * *
548887 CTGATGGATTTTCTTCACTACTATTCGATGAAGGCTTA
1 -AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*
548925 AGATTGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * *
548962 AGATTGATTTGATTCACTACTCTTTGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*** **** * * *
548999 AGATGG-CCCGAAGGACTTAATCATCATGCTCGAAAGGCTTA
1 AGATGGATTTGCTTCAC-TACTCTTC--GGT-G-AAGGCTTA
*
549040 CTGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
1 -AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* *
549078 AGATTGATTTGGTTCACTACTCTTCGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* *
549115 AGATTGATTTGCTTCACTACTCTTTGGTGAAGGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
**** * * *
549152 AGATGGCCCGGAGGATTTAAT-CGTCATGCTC-G-GAAGGCTTA
1 AGATGG---ATTTGCTTCACTAC-TC-T--TCGGTGAAGGCTTA
* *
549193 CTGATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTA
1 -AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* *
549231 AGATGAATTTGCTTCACTACTCTTCGGTGAAGGCTTT
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * * *
549268 AGATTGATTTACTTCACTACTCTTTGGTGAAAGCTTA
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
*** *** * * *
549305 AGATGGCCCTG-AGGACTTAATCATCATGCTCAGAAGGCTTA
1 AGATGGATTTGCTTCAC-TACTCTTC--GGT--GAAGGCTTA
* *
549346 CTA-ATGGATTTGCTTCACTACTATTTGGTGAAGGCTTA
1 --AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* *
549384 AGATGAATTTGCTTCACTACTCTTCGGTGAAGGCTTT
1 AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
* * *
549421 AGATTGATTTGCTTCACGACTTTTTC-GTGAAGGCTTA
1 AGATGGATTTGCTTCACTAC-TCTTCGGTGAAGGCTTA
549458 AGATGG
1 AGATGG
549464 CCCTGAGGAC
Statistics
Matches: 558, Mismatches: 136, Indels: 70
0.73 0.18 0.09
Matches are distributed among these distances:
36 12 0.02
37 396 0.71
38 40 0.07
39 15 0.03
40 15 0.03
41 35 0.06
42 34 0.06
43 11 0.02
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (37 bp):
AGATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTA
Found at i:549017 original size:153 final size:152
Alignment explanation
Indices: 548736--549503 Score: 1191
Period size: 153 Copynumber: 5.0 Consensus size: 152
548726 GAAGGCTTGA
* * * *
548736 GATGGATTTGCTTTACTACTCTTCGGTGAAGGCTTAAAATAGATTTGATTCACTACTCTTCGGTG
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTG
* * *
548801 AAGGCTTAAGATTGATTTGATTCAATACTCTTTGGTGAAGGCTTAAGAGGGCCCGAAGAACTTAA
66 AAGGCTTAAGATTGATTTGATTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCG-AGGACTTAA
548866 TCATCATGCTCGGAAGGCTTACT
130 TCATCATGCTCGGAAGGCTTACT
* * *
548889 GATGGATTTTCTTCACTACTATTCGATGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTG
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTG
548954 AAGGCTTAAGATTGATTTGATTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGAAGGACTTAA
66 AAGGCTTAAGATTGATTTGATTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCG-AGGACTTAA
*
549019 TCATCATGCTCGAAAGGCTTACT
130 TCATCATGCTCGGAAGGCTTACT
*
549042 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGGTTCACTACTCTTCGGTG
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTG
* *
549107 AAGGCTTAAGATTGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGGAGGATTTAA
66 AAGGCTTAAGATTGATTTGATTCACTACTCTTTGGTGAAGGCTTAAGATGGCCC-GAGGACTTAA
*
549172 TCGTCATGCTCGGAAGGCTTACT
130 TCATCATGCTCGGAAGGCTTACT
*
549195 GATGGATTTGCTTCACTACTCTTTGGTGAAGGCTTAAGA-TGAATTTGCTTCACTACTCTTCGGT
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTG-ATTTGCTTCACTACTCTTCGGT
* *
549259 GAAGGCTTTAGATTGATTT-ACTTCACTACTCTTTGGTGAAAGCTTAAGATGGCCCTGAGGACTT
65 GAAGGCTTAAGATTGATTTGA-TTCACTACTCTTTGGTGAAGGCTTAAGATGGCCC-GAGGACTT
*
549323 AATCATCATGCTCAGAAGGCTTACT
128 AATCATCATGCTCGGAAGGCTTACT
* * *
549348 AATGGATTTGCTTCACTACTATTTGGTGAAGGCTTAAGA-TGAATTTGCTTCACTACTCTTCGGT
1 GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTG-ATTTGCTTCACTACTCTTCGGT
* * * * *
549412 GAAGGCTTTAGATTGATTTGCTTCACGACTTTTTCGTGAAGGCTTAAGATGGCCCTGAGGACTTA
65 GAAGGCTTAAGATTGATTTGATTCACTACTCTTTGGTGAAGGCTTAAGATGGCCC-GAGGACTTA
*
549477 ATCATCATGCTCAGAAGGCTTACT
129 ATCATCATGCTCGGAAGGCTTACT
549501 GAT
1 GAT
549504 TAGCATCATG
Statistics
Matches: 575, Mismatches: 36, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
152 2 0.00
153 572 0.99
154 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.23, T:0.35
Consensus pattern (152 bp):
GATGGATTTGCTTCACTACTCTTCGGTGAAGGCTTAAGATTGATTTGCTTCACTACTCTTCGGTG
AAGGCTTAAGATTGATTTGATTCACTACTCTTTGGTGAAGGCTTAAGATGGCCCGAGGACTTAAT
CATCATGCTCGGAAGGCTTACT
Found at i:549914 original size:234 final size:235
Alignment explanation
Indices: 549505--550110 Score: 934
Period size: 234 Copynumber: 2.6 Consensus size: 235
549495 CTTACTGATT
*
549505 AGCATCATGCTCGGAAGACTTACTGATGG-CTCGAAAGACTTATAAATTTTGGAAATAGTTTACT
1 AGCATCATGCTCGGAAGACTTACTGATGGCCT-GAAGGACTTATAAATTTTGGAAATAGTTTACT
* * *
549569 AGGTAAGAAACCTTTCTTACTTTTCAAAAATTTTAATTTTCAGATTTAAATGAGAAACCTTTCTT
65 AGGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTC
* * *
549634 A-TTTTTTGATAGACATGTGAAAAACATCCTGCCCGAATAACTTATGGATGGTCCAAAGGACTTA
130 ATTTTTTTGATAGACATGTGAAAAACATCCTACCCGAAGAACTTATGGATGGCCCAAAGGACTTA
549698 TCATCTTGCTCA-AAAGACTTACAGATGAACTAG-AGGATTTA
195 TCATCTTGCT-AGAAAGACTTACAGATG-ACTAGAAGGATTTA
* * *
549739 AGCATCATGCTCGGAAGACTTACTGGTGGCCTGCAGGAGTTATAAATTTTGGAAATAGTTTACTA
1 AGCATCATGCTCGGAAGACTTACTGATGGCCTGAAGGACTTATAAATTTTGGAAATAGTTTACTA
*
549804 GGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCACA
66 GGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCA
* ** *
549869 TTTTTTTGATAGACATGTGAAAGA-ATCCTACCCGAAGGTCTTATGGATGGCCCGAAGGACTTAT
131 TTTTTTTGATAGACATGTGAAAAACATCCTACCCGAAGAACTTATGGATGGCCCAAAGGACTTAT
** *
549933 CATCTTGCTAGAAAGGTTTACAGATGACTCGAAGGATTTA
196 CATCTTGCTAGAAAGACTTACAGATGACTAGAAGGATTTA
* * *
549973 AGCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTATAAATTTTGGAAATATTTTACTA
1 AGCATCATGCTCGGAAGACTTACTGATGGCCTGAAGGACTTATAAATTTTGGAAATAGTTTACTA
* *
550038 GGTAAGAAACCTTTCTTATTTTTCAAAAAATTTCAATTTTCAAATTTGAATGAGAAACCTTTCTC
66 GGTAAGAAACCTTTCTTACTTTTC-AAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTC
550103 ATTTTTTT
130 ATTTTTTT
550111 AACATATAAA
Statistics
Matches: 340, Mismatches: 27, Indels: 9
0.90 0.07 0.02
Matches are distributed among these distances:
233 5 0.01
234 265 0.78
235 70 0.21
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Consensus pattern (235 bp):
AGCATCATGCTCGGAAGACTTACTGATGGCCTGAAGGACTTATAAATTTTGGAAATAGTTTACTA
GGTAAGAAACCTTTCTTACTTTTCAAAAATTTCAATTTTCAAATTTAAATGAGAAACCTTTCTCA
TTTTTTTGATAGACATGTGAAAAACATCCTACCCGAAGAACTTATGGATGGCCCAAAGGACTTAT
CATCTTGCTAGAAAGACTTACAGATGACTAGAAGGATTTA
Found at i:550008 original size:42 final size:41
Alignment explanation
Indices: 549914--550014 Score: 112
Period size: 42 Copynumber: 2.4 Consensus size: 41
549904 AGGTCTTATG
* * **
549914 GATGGCCCGAAGGACTTATCATCTTGCTAGAAAGGTTTACA
1 GATGGCCCGAAGGACTTAGCATCATGCTAGAAAGACTTACA
* * * * *
549955 GATGACTCGAAGGATTTAAGCATCATGCTCGAAAGACTTACT
1 GATGGCCCGAAGGACTT-AGCATCATGCTAGAAAGACTTACA
549997 GATGGCCCGAAGGACTTA
1 GATGGCCCGAAGGACTTA
550015 TAAATTTTGG
Statistics
Matches: 47, Mismatches: 12, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
41 15 0.32
42 32 0.68
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.25
Consensus pattern (41 bp):
GATGGCCCGAAGGACTTAGCATCATGCTAGAAAGACTTACA
Found at i:555576 original size:12 final size:13
Alignment explanation
Indices: 555549--555573 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
555539 ATTAAATCAA
555549 AAAATCAAATTTT
1 AAAATCAAATTTT
555562 AAAATCAAATTT
1 AAAATCAAATTT
555574 AAATTTTCAA
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:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAATCAAATTTT
Found at i:556035 original size:23 final size:22
Alignment explanation
Indices: 556005--556086 Score: 76
Period size: 23 Copynumber: 3.6 Consensus size: 22
555995 GCATGGTAAT
556005 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
556027 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
*
556049 GTGTATCGATGCACATTCAAAGG
1 GTGCATCGATGCACATTC-AAGG
* *
556072 GATACATCTATGCAC
1 G-TGCATCGATGCAC
556087 TGTTAAGTGT
Statistics
Matches: 46, Mismatches: 10, Indels: 5
0.75 0.16 0.08
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 19 0.41
24 10 0.22
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:556061 original size:21 final size:22
Alignment explanation
Indices: 556005--556067 Score: 74
Period size: 21 Copynumber: 2.9 Consensus size: 22
555995 GCATGGTAAT
556005 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTC-AGGC
* * *
556028 GTGCATCGGTGCACCTTCATG-
1 GTGCATCGATGCACATTCAGGC
*
556049 GTGTATCGATGCACATTCA
1 GTGCATCGATGCACATTCA
556068 AAGGGATACA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 16 0.47
22 2 0.06
23 16 0.47
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.27
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGC
Found at i:563018 original size:17 final size:18
Alignment explanation
Indices: 562993--563027 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
562983 ATGTTCAAAC
*
562993 AAAATGTTTCA-AATGAA
1 AAAAAGTTTCACAATGAA
563010 AAAAAGTTTCACAATGAA
1 AAAAAGTTTCACAATGAA
563028 TGAAATGATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.09, G:0.11, T:0.26
Consensus pattern (18 bp):
AAAAAGTTTCACAATGAA
Found at i:566293 original size:4 final size:4
Alignment explanation
Indices: 566284--566309 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
566274 AATAATAGCA
566284 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
566310 GCTAATGTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:568843 original size:2 final size:2
Alignment explanation
Indices: 568832--568887 Score: 105
Period size: 2 Copynumber: 28.5 Consensus size: 2
568822 CAAGCTTAAT
568832 TA TA -A 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
568873 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
568888 TTACAGGGAC
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 52 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:576327 original size:21 final size:21
Alignment explanation
Indices: 576301--576345 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
576291 GATTTCTGGG
* *
576301 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
576322 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
576343 CAA
1 CAA
576346 ACGATAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:577022 original size:23 final size:24
Alignment explanation
Indices: 576979--577025 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
576969 ATATGGCATG
*
576979 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
577003 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
577026 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:577395 original size:31 final size:31
Alignment explanation
Indices: 577241--577383 Score: 241
Period size: 31 Copynumber: 4.6 Consensus size: 31
577231 AGGGTCGAGG
577241 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
577272 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
577303 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
577334 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
577365 GATTACCTAGGTTCTTCGG
1 GTTTACCTATGTTCTTCGG
577384 AATCTATGGA
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 104 1.00
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:580553 original size:21 final size:21
Alignment explanation
Indices: 580527--580571 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
580517 GATTTCTGGG
* *
580527 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
580548 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
580569 CAA
1 CAA
580572 ACGATAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:581248 original size:23 final size:24
Alignment explanation
Indices: 581205--581251 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
581195 ATATGGCATG
*
581205 TGATATGAAAGTGTATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
581229 TGATATGAAA-TATATATGTGAAA
1 TGATATGAAAGTATATATGTGAAA
581252 ACAAGTATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.45, C:0.00, G:0.21, T:0.34
Consensus pattern (24 bp):
TGATATGAAAGTATATATGTGAAA
Found at i:581505 original size:31 final size:31
Alignment explanation
Indices: 581467--581622 Score: 242
Period size: 31 Copynumber: 5.0 Consensus size: 31
581457 AGGGTCGAGG
581467 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
581498 GTTTACCTATGTTCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* *
581529 GTTTACCTATGTTCTTCGGAACATACGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
*
581560 GTTTACCTATGTCCTTCGGGACATATGGACT
1 GTTTACCTATGTTCTTCGGGACATATGGACT
* * *
581591 GATTACCTAGGTTCTTCGGAATC-TATGGACT
1 GTTTACCTATGTTCTTCGGGA-CATATGGACT
581622 G
1 G
581623 GTCCTTCGGG
Statistics
Matches: 115, Mismatches: 9, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
31 114 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.37
Consensus pattern (31 bp):
GTTTACCTATGTTCTTCGGGACATATGGACT
Found at i:589592 original size:18 final size:17
Alignment explanation
Indices: 589558--589604 Score: 53
Period size: 18 Copynumber: 2.8 Consensus size: 17
589548 GCAAATGTAA
589558 AATAA-AATAAT-TATT
1 AATAATAATAATATATT
589573 AATAATAATAATATATTT
1 AATAATAATAATATA-TT
* *
589591 AATATTTATAATAT
1 AATAATAATAATAT
589605 TTTTTAAGCC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
15 5 0.19
16 6 0.22
17 2 0.07
18 14 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATAATAATAATATATT
Found at i:602746 original size:325 final size:325
Alignment explanation
Indices: 602156--602811 Score: 1120
Period size: 325 Copynumber: 2.0 Consensus size: 325
602146 TGACTAGACC
602156 TTTGACCGGCGTTGACCGGGCGTTGAACGACCTTTGACTTTGACCGAGTATACCTATTCTGACAT
1 TTTGACCGGCGTTGACCGGGCGTTGAACGACCTTTGACTTTGACCGAGTATACCTATTCTGACAT
*
602221 TTTTGATGTCCTGAATCTTTTTTGGGGTCCGTTTTTCCAAATTCGAACCCAGTAAGTTGGTTTTC
66 TTTTGATGTCCTGAATCTATTTTGGGGTCCGTTTTTCCAAATTCGAACCCAGTAAGTTGGTTTTC
*
602286 ACTGACTAATCACCCGATTCGATCCGTTTTTAAGAATTAAGCCCCGTTTTTTATAAAATGTTTAT
131 ACTGACTAATCACCCGATTCGATCCGTTTTTAAGAATTAAGCCCCGTTTTTTACAAAATGTTTAT
*
602351 TGTTATGTATCTGAGGAATTATTGGAAGATGATTTCAAGATCGAGGGAGGTTGAATGGAATTTAA
196 TGTTATGTATCTGAGGAATTATTGGAAGATGATTTCAAGATCGAGAGAGGTTGAATGGAATTTAA
*
602416 TGGTCGATCAGTATGGCAC-AGAAATCGAGGTAATACATTACGACCTATTTATGCTTTATGGAAC
261 TGGTCGATCAGTATGACACGA-AAATCGAGGTAATACATTACGACCTATTTATGCTTTATGGAAC
602480 A
325 A
*
602481 TTTGACCGGCGTTGACCGGGCGTTGAACGACCTTTGACTTTGACCGAGTATACCTATTCTGACGT
1 TTTGACCGGCGTTGACCGGGCGTTGAACGACCTTTGACTTTGACCGAGTATACCTATTCTGACAT
* * * *
602546 TTTTGATGTCTTGAATCTATTTTGGGGTCCGTTTTTCCAAATTCGAA-TCTGATATGTTGGTTTT
66 TTTTGATGTCCTGAATCTATTTTGGGGTCCGTTTTTCCAAATTCGAACCCAG-TAAGTTGGTTTT
* * *
602610 CACTGATTAATCACCCGATTTC-ATCCGTTTTTCAGAATTAAGCCCCGTTTTTTACGAAATGTTT
130 CACTGACTAATCACCCGA-TTCGATCCGTTTTTAAGAATTAAGCCCCGTTTTTTACAAAATGTTT
602674 ATTGTTATGTATCTGAGGAATTATTGGAAGATGATTTCAAGATCGAGAGAGGTTGAATGGAATTT
194 ATTGTTATGTATCTGAGGAATTATTGGAAGATGATTTCAAGATCGAGAGAGGTTGAATGGAATTT
** *
602739 AATGGTCGATCAGTATGACACGAAAATCGAGGTAATACATTATTACCTCTTTATGCTTTATGGAA
259 AATGGTCGATCAGTATGACACGAAAATCGAGGTAATACATTACGACCTATTTATGCTTTATGGAA
602804 CA
324 CA
602806 TGTTGA
1 T-TTGA
602812 TAATGGATAA
Statistics
Matches: 312, Mismatches: 15, Indels: 7
0.93 0.04 0.02
Matches are distributed among these distances:
324 2 0.01
325 302 0.97
326 8 0.03
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.36
Consensus pattern (325 bp):
TTTGACCGGCGTTGACCGGGCGTTGAACGACCTTTGACTTTGACCGAGTATACCTATTCTGACAT
TTTTGATGTCCTGAATCTATTTTGGGGTCCGTTTTTCCAAATTCGAACCCAGTAAGTTGGTTTTC
ACTGACTAATCACCCGATTCGATCCGTTTTTAAGAATTAAGCCCCGTTTTTTACAAAATGTTTAT
TGTTATGTATCTGAGGAATTATTGGAAGATGATTTCAAGATCGAGAGAGGTTGAATGGAATTTAA
TGGTCGATCAGTATGACACGAAAATCGAGGTAATACATTACGACCTATTTATGCTTTATGGAACA
Found at i:610415 original size:325 final size:325
Alignment explanation
Indices: 609825--610480 Score: 1102
Period size: 325 Copynumber: 2.0 Consensus size: 325
609815 TGACTAGACC
*
609825 TTTGACCGGCGTTGACCGGGCGTTGAACGACCTTTGACTTTGACCGAGTATACCTATTCTGACAT
1 TTTGACCGACGTTGACCGGGCGTTGAACGACCTTTGACTTTGACCGAGTATACCTATTCTGACAT
*
609890 TTTTGATGTCCTGAATCTTTTTTGGGGTCCGTTTTTCCAAATTCGAACCCAGTAAGTTGGTTTTC
66 TTTTGATGTCCTGAATCTATTTTGGGGTCCGTTTTTCCAAATTCGAACCCAGTAAGTTGGTTTTC
*
609955 ACTGACTAATCACCCGATTCGATCCGTTTTTAAGAATTAAGCCCCGTTTTTTATAAAATGTTTAT
131 ACTGACTAATCACCCGATTCGATCCGTTTTTAAGAATTAAGCCCCGTTTTTTACAAAATGTTTAT
*
610020 TGTTATGTATCTGAGGAATTATTGGAAGATGATTTCAAGATCGAGGGAGGTTGAATGGAATTTAA
196 TGTTATGTATCTGAGGAATTATTGGAAGATGATTTCAAGATCGAGAGAGGTTGAATGGAATTTAA
* *
610085 TGGTCGATCAGTATGGCAC-AGAAATCGAGGTAATATATTACGACCTATTTATGCTTTATGGAAC
261 TGGTCGATCAGTATGACACGA-AAATCGAGGTAATACATTACGACCTATTTATGCTTTATGGAAC
610149 A
325 A
*
610150 TTTGACCGACGTTGACCGGGCGTTGAACGACCTTTGACTTTGACCGAGTATACCTATTCTGACGT
1 TTTGACCGACGTTGACCGGGCGTTGAACGACCTTTGACTTTGACCGAGTATACCTATTCTGACAT
* * * *
610215 TTTTGATGTCTTGAATCTATTTTGGGGTCCGTTTTTCCAAATTCGAA-TCTGATATGTTGGTTTT
66 TTTTGATGTCCTGAATCTATTTTGGGGTCCGTTTTTCCAAATTCGAACCCAG-TAAGTTGGTTTT
* * *
610279 CACTGATTAATCACCCGATTTC-ATCCGTTTTTCAGAATTAAGCCCCGTTTTTTACGAAATGTTT
130 CACTGACTAATCACCCGA-TTCGATCCGTTTTTAAGAATTAAGCCCCGTTTTTTACAAAATGTTT
610343 ATTGTTATGTATCTGAGGAATTATTGGAAGATGATTTCAAGATCGAGAGAGGTTGAATGGAATTT
194 ATTGTTATGTATCTGAGGAATTATTGGAAGATGATTTCAAGATCGAGAGAGGTTGAATGGAATTT
** *
610408 AATGGTCGATCAGTATGACACGAAAATCGAGGTAATACATTATTACCTCTTTATGCTTTATGGAA
259 AATGGTCGATCAGTATGACACGAAAATCGAGGTAATACATTACGACCTATTTATGCTTTATGGAA
610473 CA
324 CA
610475 TGTTGA
1 T-TTGA
610481 TAATGGATAA
Statistics
Matches: 310, Mismatches: 17, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
324 2 0.01
325 300 0.97
326 8 0.03
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (325 bp):
TTTGACCGACGTTGACCGGGCGTTGAACGACCTTTGACTTTGACCGAGTATACCTATTCTGACAT
TTTTGATGTCCTGAATCTATTTTGGGGTCCGTTTTTCCAAATTCGAACCCAGTAAGTTGGTTTTC
ACTGACTAATCACCCGATTCGATCCGTTTTTAAGAATTAAGCCCCGTTTTTTACAAAATGTTTAT
TGTTATGTATCTGAGGAATTATTGGAAGATGATTTCAAGATCGAGAGAGGTTGAATGGAATTTAA
TGGTCGATCAGTATGACACGAAAATCGAGGTAATACATTACGACCTATTTATGCTTTATGGAACA
Found at i:617462 original size:36 final size:36
Alignment explanation
Indices: 617422--617491 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
617412 CGGGATGAGA
* * *
617422 AAAAATCGTTTATGTTAAACGGGGACGGGGACGGGG
1 AAAAACCGTTTATGTTAAACGGAGACGGAGACGGGG
617458 AAAAACCGTTTATGTTAAACGGAGACGGAGACGG
1 AAAAACCGTTTATGTTAAACGGAGACGGAGACGG
617492 ATTTGGTAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.19
Consensus pattern (36 bp):
AAAAACCGTTTATGTTAAACGGAGACGGAGACGGGG
Found at i:617601 original size:2 final size:2
Alignment explanation
Indices: 617588--617644 Score: 55
Period size: 2 Copynumber: 29.5 Consensus size: 2
617578 TTTAATTTAA
* * *
617588 AT AT AA AT AT AT AT AT AT AT AT AT A- AT AT TT AT AT AT TT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
617628 AT TT AA AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
617645 CCCGACCCGA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
1 2 0.05
2 41 0.95
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:617601 original size:40 final size:40
Alignment explanation
Indices: 617557--617644 Score: 112
Period size: 40 Copynumber: 2.2 Consensus size: 40
617547 TAATTATTAT
617557 TATATATATA-ATAT-TAATAAATTTA-AT-TTAAATATAAA
1 TATATATATATATATATAAT--ATTTATATATTAAATATAAA
* *
617595 TATATATATATATATATAATATTTATATATTTAATTTAAA
1 TATATATATATATATATAATATTTATATATTAAATATAAA
617635 TATATATATA
1 TATATATATA
617645 CCCGACCCGA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
38 15 0.34
39 6 0.14
40 23 0.52
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (40 bp):
TATATATATATATATATAATATTTATATATTAAATATAAA
Found at i:617617 original size:46 final size:46
Alignment explanation
Indices: 617557--617644 Score: 149
Period size: 46 Copynumber: 1.9 Consensus size: 46
617547 TAATTATTAT
617557 TATATATATAATATTAATAAATTTAATTTAAATATAAATATATATA
1 TATATATATAATATTAATAAATTTAATTTAAATATAAATATATATA
* * *
617603 TATATATATAATATTTATATATTTAATTTAAATATATATATA
1 TATATATATAATATTAATAAATTTAATTTAAATATAAATATA
617645 CCCGACCCGA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (46 bp):
TATATATATAATATTAATAAATTTAATTTAAATATAAATATATATA
Found at i:618680 original size:42 final size:42
Alignment explanation
Indices: 618632--618731 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
618622 AAACTTTGGG
618632 TCTAGTTTCAAAACTCGAAGGTAGAATTTCAAAACTCTTCCC
1 TCTAGTTTCAAAACTCGAAGGTAGAATTTCAAAACTCTTCCC
** * * *
618674 TCTAGTTTTGAAACTTGTAGGTAGAGTTTCAAAACTCTTCCC
1 TCTAGTTTCAAAACTCGAAGGTAGAATTTCAAAACTCTTCCC
*
618716 TCTAATTTCAAAACTC
1 TCTAGTTTCAAAACTC
618732 TTTGTAAGAG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (42 bp):
TCTAGTTTCAAAACTCGAAGGTAGAATTTCAAAACTCTTCCC
Found at i:627661 original size:49 final size:49
Alignment explanation
Indices: 627584--627873 Score: 235
Period size: 49 Copynumber: 5.9 Consensus size: 49
627574 TACATGTGTA
* * *
627584 TGAATGATATTGAATCACATGTTGTGGTAAATCAGAAGTTTACAAGTTT
1 TGAATGAAATTAAATCACATGTTATGGTAAATCAGAAGTTTACAAGTTT
* * * * **
627633 TGAATGAAATTAAATCACAAGTTATGGTAAACCAAAAATTTACGCGTTT
1 TGAATGAAATTAAATCACATGTTATGGTAAATCAGAAGTTTACAAGTTT
* ** * * * * *
627682 TAAATCTAATTAAATCATATATTGTGTTAAA-CTACAAG-TTACAAGTTT
1 TGAATGAAATTAAATCACATGTTATGGTAAATC-AGAAGTTTACAAGTTT
* * ** *
627730 TGAATGACATTGAATCACATGTTATAATAAATAAGAAGTTTACAAGTTT
1 TGAATGAAATTAAATCACATGTTATGGTAAATCAGAAGTTTACAAGTTT
* * * * *
627779 TGAATAAAATTAAATCACGTGGTATCGTAAATCA-AATGTTCACAAGTTTT
1 TGAATGAAATTAAATCACATGTTATGGTAAATCAGAA-GTTTACAAG-TTT
* ** * * *
627829 TGAATGAGATTGTATCACATGTTACGGTAAACCATAAGTTTACAA
1 TGAATGAAATTAAATCACATGTTATGGTAAATCAGAAGTTTACAA
627874 CTTCGAAAAT
Statistics
Matches: 183, Mismatches: 52, Indels: 11
0.74 0.21 0.04
Matches are distributed among these distances:
48 36 0.20
49 110 0.60
50 35 0.19
51 2 0.01
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (49 bp):
TGAATGAAATTAAATCACATGTTATGGTAAATCAGAAGTTTACAAGTTT
Found at i:630939 original size:33 final size:33
Alignment explanation
Indices: 630902--630979 Score: 156
Period size: 33 Copynumber: 2.4 Consensus size: 33
630892 ATTTTATTTT
630902 AATTTAGTCACTATTATTATTCTGATTTGTTTG
1 AATTTAGTCACTATTATTATTCTGATTTGTTTG
630935 AATTTAGTCACTATTATTATTCTGATTTGTTTG
1 AATTTAGTCACTATTATTATTCTGATTTGTTTG
630968 AATTTAGTCACT
1 AATTTAGTCACT
630980 GATTTTTACG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.26, C:0.10, G:0.12, T:0.53
Consensus pattern (33 bp):
AATTTAGTCACTATTATTATTCTGATTTGTTTG
Found at i:631236 original size:4 final size:5
Alignment explanation
Indices: 631212--631262 Score: 50
Period size: 5 Copynumber: 10.0 Consensus size: 5
631202 GTCCTTGTAC
* * *
631212 TTATGT TTATT TTATT TTA-T TTATT TTATG TTGTT TTCACT TTATT TTATT
1 TTAT-T TTATT TTATT TTATT TTATT TTATT TTATT TT-ATT TTATT TTATT
631263 ATTGTTATTT
Statistics
Matches: 37, Mismatches: 6, Indels: 5
0.77 0.12 0.10
Matches are distributed among these distances:
4 4 0.11
5 26 0.70
6 7 0.19
ACGTcount: A:0.18, C:0.04, G:0.06, T:0.73
Consensus pattern (5 bp):
TTATT
Found at i:631236 original size:14 final size:13
Alignment explanation
Indices: 631217--631279 Score: 63
Period size: 14 Copynumber: 4.5 Consensus size: 13
631207 TGTACTTATG
631217 TTTATTTTATTTT
1 TTTATTTTATTTT
631230 ATTTATTTTATGTTGT
1 -TTTATTTTAT-TT-T
*
631246 TTTCACTTTATTTT
1 TTT-ATTTTATTTT
*
631260 ATTATTGTTATTTT
1 TTTATT-TTATTTT
631274 TTTATT
1 TTTATT
631280 AAGTTTATTA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
13 2 0.05
14 25 0.61
15 7 0.17
16 7 0.17
ACGTcount: A:0.17, C:0.03, G:0.05, T:0.75
Consensus pattern (13 bp):
TTTATTTTATTTT
Found at i:635751 original size:34 final size:34
Alignment explanation
Indices: 635713--635832 Score: 118
Period size: 34 Copynumber: 3.4 Consensus size: 34
635703 AAGATAGCAT
635713 AAAAAG-AAAAAAATGAAAAAAATGAAAAAAAGAA
1 AAAAAGAAAAAAAATGAAAAAAATGAAAAAAA-AA
**
635747 AAAAAGAAAGAAAAATGAAGGAAA-GAAAAAAAAA
1 AAAAAGAAA-AAAAATGAAAAAAATGAAAAAAAAA
* * *
635781 AAGAAGAAAAACAAATGAAAAAAATACGAAAGAAATA
1 AAAAAGAAAAA-AAATGAAAAAAAT--GAAAAAAAAA
* *
635818 TAAAAGAAAACAAAT
1 AAAAAGAAAAAAAAT
635833 CAAATACTTC
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
33 2 0.03
34 26 0.37
35 10 0.14
36 16 0.23
37 16 0.23
ACGTcount: A:0.78, C:0.03, G:0.13, T:0.07
Consensus pattern (34 bp):
AAAAAGAAAAAAAATGAAAAAAATGAAAAAAAAA
Found at i:635760 original size:27 final size:27
Alignment explanation
Indices: 635713--635785 Score: 96
Period size: 27 Copynumber: 2.7 Consensus size: 27
635703 AAGATAGCAT
635713 AAAAAGAAAAAAATG-AA-AAAAATGAA
1 AAAAAGAAAAAAA-GAAAGAAAAATGAA
635739 AAAAAGAAAAAAAGAAAGAAAAATGAA
1 AAAAAGAAAAAAAGAAAGAAAAATGAA
** *
635766 GGAAAGAAAAAAAAAAAGAA
1 AAAAAGAAAAAAAGAAAGAA
635786 GAAAAACAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
25 1 0.02
26 15 0.36
27 26 0.62
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (27 bp):
AAAAAGAAAAAAAGAAAGAAAAATGAA
Found at i:635805 original size:9 final size:8
Alignment explanation
Indices: 635713--635791 Score: 79
Period size: 8 Copynumber: 9.4 Consensus size: 8
635703 AAGATAGCAT
635713 AAAAAGAA
1 AAAAAGAA
635721 AAAAATGAA
1 AAAAA-GAA
635730 AAAAATGAA
1 AAAAA-GAA
635739 AAAAAGAA
1 AAAAAGAA
635747 AAAAAGAAA
1 AAAAAG-AA
635756 GAAAAATGAA
1 -AAAAA-GAA
**
635766 GGAAAGAA
1 AAAAAGAA
635774 AAAAA-AA
1 AAAAAGAA
*
635781 AAGAAGAA
1 AAAAAGAA
635789 AAA
1 AAA
635792 CAAATGAAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
7 6 0.10
8 24 0.40
9 22 0.37
10 7 0.12
11 1 0.02
ACGTcount: A:0.81, C:0.00, G:0.15, T:0.04
Consensus pattern (8 bp):
AAAAAGAA
Found at i:635812 original size:41 final size:39
Alignment explanation
Indices: 635737--635815 Score: 97
Period size: 41 Copynumber: 2.0 Consensus size: 39
635727 GAAAAAAATG
* * *
635737 AAAAAAAGAAAAAAAGAAAGAAAAATGAAGGAAAGAAAA
1 AAAAAAAGAAAAAAACAAAGAAAAATAAACGAAAGAAAA
635776 AAAAAAAGAAGAAAAACAAATGAAAAA-AATACGAAAGAAA
1 AAAAAAAGAA-AAAAACAAA-GAAAAATAA-ACGAAAGAAA
635816 TATAAAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 10 0.29
40 9 0.26
41 15 0.44
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.04
Consensus pattern (39 bp):
AAAAAAAGAAAAAAACAAAGAAAAATAAACGAAAGAAAA
Found at i:637585 original size:83 final size:83
Alignment explanation
Indices: 637488--637657 Score: 295
Period size: 83 Copynumber: 2.0 Consensus size: 83
637478 GTCATGCATT
* * * *
637488 ACATTTAGATACATATTGCATTCATATTTCATGCATCAAAACATATTTTTATAGATATTTTAAGA
1 ACATTTAGATACATATCGCATTCACATTTCATGCATAAAAACATATTTTTACAGATATTTTAAGA
637553 AAAGAAGAGAAGGAAAAG
66 AAAGAAGAGAAGGAAAAG
*
637571 ACATTTTGATACATATCGCATTCACATTTCATGCATAAAAACATATTTTTACAGATATTTTAAGA
1 ACATTTAGATACATATCGCATTCACATTTCATGCATAAAAACATATTTTTACAGATATTTTAAGA
637636 AAAGAAGAGAAGGAAAAG
66 AAAGAAGAGAAGGAAAAG
637654 ACAT
1 ACAT
637658 AACTCAAGCC
Statistics
Matches: 82, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 82 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (83 bp):
ACATTTAGATACATATCGCATTCACATTTCATGCATAAAAACATATTTTTACAGATATTTTAAGA
AAAGAAGAGAAGGAAAAG
Found at i:637875 original size:59 final size:59
Alignment explanation
Indices: 637771--637892 Score: 147
Period size: 59 Copynumber: 2.1 Consensus size: 59
637761 CCCAAACAAC
* * * *
637771 ATGATATTTTTCAAAGCAATTTTTAAAAGAAGTTAAGCCTGATTTTCAGGGGTTTCTTA
1 ATGATAATTTTCAAAGCAATTTTTAAAAGAAGCTAAGCCTAATTTTCAGGGGTTCCTTA
* * * * *
637830 ATGATAATTTTCAATG-ATTTTTTAAAAGGAAGCTAAGTCTAATTTTTAGGGGTTCCTTG
1 ATGATAATTTTCAAAGCAATTTTTAAAA-GAAGCTAAGCCTAATTTTCAGGGGTTCCTTA
637889 ATGA
1 ATGA
637893 CAACTAAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
58 10 0.19
59 43 0.81
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (59 bp):
ATGATAATTTTCAAAGCAATTTTTAAAAGAAGCTAAGCCTAATTTTCAGGGGTTCCTTA
Found at i:638027 original size:41 final size:41
Alignment explanation
Indices: 637936--638028 Score: 109
Period size: 41 Copynumber: 2.3 Consensus size: 41
637926 TCTTGATTTG
* *
637936 TAAGTCATTCGGGCCATCAGTAAGTCTTTCGAGCATATGCT
1 TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATATGCA
** *
637977 TAAACCCTTCGGGTCATCTA-TAAGTCTTTCGAGCATGATG-A
1 TAAGTCCTTCGGGCCATC-AGTAAGTCTTTCGAGCAT-ATGCA
638018 TAAGTCCTTCG
1 TAAGTCCTTCG
638029 ACCCATCCTA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
41 39 0.91
42 4 0.09
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (41 bp):
TAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCATATGCA
Found at i:639081 original size:91 final size:89
Alignment explanation
Indices: 638903--639166 Score: 368
Period size: 91 Copynumber: 2.9 Consensus size: 89
638893 CTTGAGAGAG
*
638903 TAACATTTCAGTGGAGAG-TCAATAATGAGTAGAACTCATCCAACGAGGGAGAAGAAGTTCATAA
1 TAACATTTCAGTGG-GAGTTC-ATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAA
* * *
638967 CGAGAGGAACTTGTTCAACCTTGGAT
64 TGAGAAGAACTTGTTCAAACTTGGAT
638993 TAACATTTCAAGTGTGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAA
1 TAACATTTC-AGTG-GGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAA
639058 TGAGAAGAACTTGTTCAAACTTGGAT
64 TGAGAAGAACTTGTTCAAACTTGGAT
* * * * ** *
639084 CAACATTTCCAGTAGAGAGTTCATAATGAAAAGAACTCATCCGATAAGGGAGAAGAAGTTCCTAA
1 TAACATTT-CAGT-GGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAA
639149 TGAGAAGAACTTGTTCAA
64 TGAGAAGAACTTGTTCAA
639167 CCTTAGCTTG
Statistics
Matches: 158, Mismatches: 11, Indels: 9
0.89 0.06 0.05
Matches are distributed among these distances:
90 9 0.06
91 144 0.91
92 5 0.03
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.24
Consensus pattern (89 bp):
TAACATTTCAGTGGGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAAACTTGGAT
Found at i:639223 original size:115 final size:114
Alignment explanation
Indices: 639080--639428 Score: 497
Period size: 115 Copynumber: 3.0 Consensus size: 114
639070 GTTCAAACTT
* * *
639080 GGATCAACATTTCCAGTAGAGAGTTCATAATGAAAAGAACTCATCCGATAAGGGAGAAGAAGTTC
1 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
* *
639145 CTAATGAGAAGAACTTGTTCAACCTTAGCTTGATTCCATCACAGAATGAAG
66 ATAATGAGAAGAACTTGTTCAACCTTAG-TCGATTCCATCACAGAAT-AAG
* * *
639196 GG-TCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCA-CTTGATGAGGGAGAAAAAATT
1 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATC-CGATGAGGGAGAAGAAGTT
* *
639259 CATAATGAGAAGAACTTGGTCAACCCTTTGTCGATTCCATCACAGAATAAG
65 CATAATGAGAAGAACTTGTTCAA-CCTTAGTCGATTCCATCACAGAATAAG
*
639310 GGATCAACATTTCCAGTGGAGAGTTTATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
1 GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
* * *
639375 ATAATGAGAAGAACTTGTTCAACCTTTGT-GATTCTATCATAGAAGTAAG
66 ATAATGAGAAGAACTTGTTCAACCTTAGTCGATTCCATCACAGAA-TAAG
639424 TGGAT
1 -GGAT
639429 TGACATCCCA
Statistics
Matches: 210, Mismatches: 17, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
113 13 0.06
114 17 0.08
115 172 0.82
116 8 0.04
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (114 bp):
GGATCAACATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCGATGAGGGAGAAGAAGTTC
ATAATGAGAAGAACTTGTTCAACCTTAGTCGATTCCATCACAGAATAAG
Found at i:640642 original size:51 final size:50
Alignment explanation
Indices: 640581--640710 Score: 133
Period size: 51 Copynumber: 2.6 Consensus size: 50
640571 TGATATTTGC
* **
640581 AATTTATTCATTTTAGTCACTTTTTAATTTCTGA-TTAGCTACTATTA-TTTT
1 AATTTTTTCATTTTAGTCACTTTTT-ATTTCTGATTTAAATACTA--ACTTTT
* * *
640632 AATTTTTTCATTTTGGTCACTATTTATTTCTTATTTAAATACTAACTTTT
1 AATTTTTTCATTTTAGTCACTTTTTATTTCTGATTTAAATACTAACTTTT
640682 -ATTTTCTTACATTTTAGTCAC-TTTTATTT
1 AATTTT-TT-CATTTTAGTCACTTTTTATTT
640711 TATTTCATGC
Statistics
Matches: 67, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
49 6 0.09
50 20 0.30
51 41 0.61
ACGTcount: A:0.25, C:0.12, G:0.05, T:0.58
Consensus pattern (50 bp):
AATTTTTTCATTTTAGTCACTTTTTATTTCTGATTTAAATACTAACTTTT
Found at i:641115 original size:15 final size:15
Alignment explanation
Indices: 641091--641124 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
641081 TTTTAGTCTC
641091 TTAGAACTTGATATT
1 TTAGAACTTGATATT
* *
641106 TTAGAGCTTGATCTT
1 TTAGAACTTGATATT
641121 TTAG
1 TTAG
641125 TCCCCGAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.26, C:0.09, G:0.18, T:0.47
Consensus pattern (15 bp):
TTAGAACTTGATATT
Found at i:642911 original size:2 final size:2
Alignment explanation
Indices: 642904--642960 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
642894 ATATGAAGTT
642904 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
642946 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
642961 CATGGGAAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.