Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006907.1 Hibiscus syriacus cultivar Beakdansim tig00017647_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: 557747
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 3 of 3
Found at i:339233 original size:38 final size:38
Alignment explanation
Indices: 339190--339871 Score: 609
Period size: 38 Copynumber: 17.2 Consensus size: 38
339180 TAGAAACTTT
339190 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
1 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
* * * * *
339228 GATCTTTGTTATTCTTAACTTCATCATGAAGAAAAGTC
1 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
* *
339266 AATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTC
1 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
* * *
339304 AATATTTCAATGTTATTCTTGACTTCCTCGTGAAGAGAGGTT
1 AAT-CTT---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
* * *
339346 AATCTTTGTAATTCTTAACTTCCTCGTGACGAGAAGTC
1 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
*
339384 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAGGTC
1 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
* * * *
339422 AATATTTGTTATTCTTCACTTTCTCGTGAAGAGAAATC
1 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
* * * *
339460 AATCTTTTTTATTCTTAACTCCCTCGTGAAGAGGAGTC
1 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
*
339498 AATCTTTTAATGTTATTCTTGACTTCCTCATGAAGAGAAGGT-
1 AATC--TT--TGTTATTCTTGACTTCCTCGTGAAGAGAA-GTC
* * * *
339540 AATCTTTCGGTATTGTCTTTCTTGACTCCCTCGTGAAGAGGATTC
1 AATCTTT--G---T-T-ATTCTTGACTTCCTCGTGAAGAGAAGTC
* * * *
339585 AATCTTTCAATGTTATTCTCGACTTCTTTGTGAAGAGAAGTA
1 AATC-TT---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
* *
339627 AAT-TTTGTTATTCTTGACTCCCTCGTAAAGA-AGAGTC
1 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGA-AGTC
*
339664 AATCTTTCAATATTATTCTTGACTTCCTCGTGAAGATG-AGTC
1 AATC-TT---TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTC
* * * *
339706 AATTTGTCAATGTTATTATTGACTTCCTCGTGAAGAGAATTT
1 AATCT-T---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
* * *
339748 GATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTT
1 AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
* *
339786 AATCTTTGTTATTATTGACTCCCTCGTGAAGACGAA-TC
1 AATCTTTGTTATTCTTGACTTCCTCGTGAAGA-GAAGTC
* *
339824 AATATTTCAATGTTATTCTTGACTTTCTCGTGAAGAGAAGTC
1 AAT-CTT---TGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
339866 AATCTT
1 AATCTT
339872 CAGTGATGCC
Statistics
Matches: 521, Mismatches: 86, Indels: 71
0.77 0.13 0.10
Matches are distributed among these distances:
36 1 0.00
37 27 0.05
38 258 0.50
39 9 0.02
40 7 0.01
41 10 0.02
42 173 0.33
43 4 0.01
44 3 0.01
45 25 0.05
46 2 0.00
47 1 0.00
49 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (38 bp):
AATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAGTC
Found at i:339409 original size:118 final size:117
Alignment explanation
Indices: 339196--339871 Score: 611
Period size: 118 Copynumber: 5.6 Consensus size: 117
339186 CTTTAATCTT
* * * *
339196 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCGATCTTTGTTATTCTTAACTTCATCATGAAGAA
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTAACTTCCTCGTGAAGAG
*
339261 AAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATATTTCAA
66 AAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGGAGTCAATATTTC-A
* * * *
339314 TGTTATTCTTGACTTCCTCGTGAAGAGAGGTTAATCTTTGTAATTCTTAACTTCCTCGTGACGAG
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTAACTTCCTCGTGAAGAG
339379 AAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGA-GAGGTCAATA-TT--
66 AAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGGA-GTCAATATTTCA
* * * * *
339428 TGTTATTCTTCACTTTCTCGTGAAGAGAAATCAATCTTTTTTATTCTTAACTCCCTCGTGAAGAG
1 TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTAACTTCCTCGTGAAGAG
* * * *
339493 GAGTCAATCTTTTAATGTTATTCTTGACTTCCTCATGAAGAGAAGGT-AATCTTTCGGTA
66 AAGTCAATC--TT--TGTTATTCTTGACTTCCTCGTGAAGAGGA-GTCAATATTTC---A
* * * ** * *
339552 TTGTCT-TTCTTGACTCCCTCGTGAAGAGGATTCAATCTTTCAATGTTATTCTCGACTTCTTTGT
1 -TGT-TATTCTTGACTTCCTCGTGAAGAGAAGTCAATC-TT---TGTTATTCTTAACTTCCTCGT
* * * * *
339616 GAAGAGAAGTAAAT-TTTGTTATTCTTGACTCCCTCGTAAAGAAGAGTCAATCTTTCAA
60 GAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGGAGTCAATATTTC-A
* * * *
339674 TATTATTCTTGACTTCCTCGTGAAGATG-AGTCAATTTGTCAATGTTATTATTGACTTCCTCGTG
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAATCT-T---TGTTATTCTTAACTTCCTCGTG
* ** * * * *
339738 AAGAGAATTTGATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTTAAT-CTT--
61 AAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGGAGTCAATATTTCA
* * * * *
339792 TGTTATTATTGACTCCCTCGTGAAGACGAA-TCAATATTTCAATGTTATTCTTGACTTTCTCGTG
1 TGTTATTCTTGACTTCCTCGTGAAGA-GAAGTCAAT-CTT---TGTTATTCTTAACTTCCTCGTG
339856 AAGAGAAGTCAATCTT
61 AAGAGAAGTCAATCTT
339872 CAGTGATGCC
Statistics
Matches: 465, Mismatches: 68, Indels: 50
0.80 0.12 0.09
Matches are distributed among these distances:
114 64 0.14
116 2 0.00
117 4 0.01
118 194 0.42
119 9 0.02
120 2 0.00
121 62 0.13
122 33 0.07
123 2 0.00
124 32 0.07
125 29 0.06
126 5 0.01
129 27 0.06
ACGTcount: A:0.26, C:0.17, G:0.17, T:0.40
Consensus pattern (117 bp):
TGTTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTAACTTCCTCGTGAAGAG
AAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGGAGTCAATATTTCA
Found at i:339901 original size:44 final size:44
Alignment explanation
Indices: 339195--339984 Score: 219
Period size: 38 Copynumber: 19.5 Consensus size: 44
339185 ACTTTAATCT
* * *
339195 TTGTTATTCTTGACTTCCTCGTGAAGAGAAGTCGATCTT---TG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTCAGTG
* * *
339236 -T-T-ATTCTTAAC-TTCATCATGAAGAAAAGTCAATCTT---TG
1 TTGTCATTCTTGACTTTC-TCGTGAAGAGAAGTCAATCTTCAGTG
** * * *
339274 -T-T-ATTCTTGACTCCCTCGTGAAGAGGAGTCAATATTTCAATG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAAT-CTTCAGTG
* * *
339316 -T-T-ATTCTTGACTTCCTCGTGAAGAGAGGTTAA---TC--T-
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTCAGTG
* * * *
339351 TTGTAATTCTTAACTTCCTCGTGACGAGAAGTCAATCTT---TG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTCAGTG
* *
339392 -T-T-ATTCTTGACTTCCTCGTGAAGAGAGGTCAA---T-A-T-
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTCAGTG
* * *
339427 TTGTTATTCTTCACTTTCTCGTGAAGAGAAATCAATCTT---T-
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTCAGTG
* ** * * *
339467 TT-T-ATTCTTAACTCCCTCGTGAAGAGGAGTCAATCTTTTAATG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATC-TTCAGTG
* * * *
339510 -T-T-ATTCTTGACTTCCTCATGAAGAGAAGGT-AATCTTTCGGTA
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAA-GTCAATC-TTCAGTG
* ** * * *
339552 TTGTCTTTCTTGACTCCCTCGTGAAGAGGATTCAATCTTTCAATG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATC-TTCAGTG
* * *
339597 -T-T-ATTCTCGAC-TTCTTTGTGAAGAGAAGTAAAT-TT---TG
1 TTGTCATTCTTGACTTTC-TCGTGAAGAGAAGTCAATCTTCAGTG
** * *
339634 -T-T-ATTCTTGACTCCCTCGTAAAGA-AGAGTCAATCTTTCAAT-
1 TTGTCATTCTTGACTTTCTCGTGAAGAGA-AGTCAATC-TTCAGTG
* * * *
339675 AT-T-ATTCTTGACTTCCTCGTGAAGATG-AGTCAATTTGTCAATG
1 TTGTCATTCTTGACTTTCTCGTGAAGA-GAAGTCAATCT-TCAGTG
* * * **
339718 -T-T-ATTATTGACTTCCTCGTGAAGAGAATTTGATCTT---TG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTCAGTG
* * *
339756 -T-T-ATTCTTGACTTCCTCATGAAGAGAAGTTAATCTT---TG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTCAGTG
* ** * *
339794 -T-T-ATTATTGACTCCCTCGTGAAGACGAA-TCAATATTTCAATG
1 TTGTCATTCTTGACTTTCTCGTGAAGA-GAAGTCAAT-CTTCAGTG
339836 -T-T-ATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTCAGTG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTCAGTG
* * * * * * * *
339877 ATGCCATTCTTTACTTTCTCGTGAAG-GGAGTCGACCTTTATTG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTCAGTG
* * *
339920 TTGTCATTATTGAATTTCTCATGAAGAGAAGTCAATCTTTCAGTG
1 TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATC-TTCAGTG
*
339965 TTGTGATTCTTGACTTTCTC
1 TTGTCATTCTTGACTTTCTC
339985 AGAAAGAGGA
Statistics
Matches: 589, Mismatches: 105, Indels: 106
0.74 0.13 0.13
Matches are distributed among these distances:
35 1 0.00
36 5 0.01
37 29 0.05
38 223 0.38
39 15 0.03
40 8 0.01
41 15 0.03
42 175 0.30
43 36 0.06
44 30 0.05
45 52 0.09
ACGTcount: A:0.25, C:0.17, G:0.17, T:0.40
Consensus pattern (44 bp):
TTGTCATTCTTGACTTTCTCGTGAAGAGAAGTCAATCTTCAGTG
Found at i:339983 original size:45 final size:45
Alignment explanation
Indices: 339838--340058 Score: 180
Period size: 45 Copynumber: 4.9 Consensus size: 45
339828 TTTCAATGTT
* * * *
339838 ATTCTTGACTTTCTCGTGAAGAGAAGTCAATC-TTCAGTGATGCC
1 ATTCTTGACTTTCTCATGAAGAGAAGTCAACCTTTCAGTGTTGTC
* * * * *
339882 ATTCTTTACTTTCTCGTGAAG-GGAGTCGACCTTT-ATTGTTGTC
1 ATTCTTGACTTTCTCATGAAGAGAAGTCAACCTTTCAGTGTTGTC
* * * *
339925 ATTATTGAATTTCTCATGAAGAGAAGTCAATCTTTCAGTGTTGTG
1 ATTCTTGACTTTCTCATGAAGAGAAGTCAACCTTTCAGTGTTGTC
* * *
339970 ATTCTTGACTTTCTCA-GAAAGAGGAGTCAACCTTTTAGTGATGTC
1 ATTCTTGACTTTCTCATG-AAGAGAAGTCAACCTTTCAGTGTTGTC
* * * *
340015 ATTTTCAATTTGACTTTCTCGTGGAGAGGAGTCAACTTTTCAGT
1 A--TTC---TTGACTTTCTCATGAAGAGAAGTCAACCTTTCAGT
340059 AGTATCTTTC
Statistics
Matches: 140, Mismatches: 27, Indels: 14
0.77 0.15 0.08
Matches are distributed among these distances:
43 30 0.21
44 33 0.24
45 44 0.31
47 3 0.02
50 29 0.21
51 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (45 bp):
ATTCTTGACTTTCTCATGAAGAGAAGTCAACCTTTCAGTGTTGTC
Found at i:340854 original size:134 final size:134
Alignment explanation
Indices: 340659--341219 Score: 739
Period size: 134 Copynumber: 4.2 Consensus size: 134
340649 AACCACGTTC
* * * * * * * *
340659 GATTCAATCTTTCCTGAAGAGAATTGAAGTATATCAAAGATTTCTTGAATCTAATCTCCCCTAAA
1 GATTCAATCTTCCCTGAAGAGTAGTGAAGTAGATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAA
* * * * *
340724 GAGTAGTGGAGCAGATTTTTGTTCTTTCAGATTTGGTTTTCCTGAAGAGAAGTGAAACAAATTGA
66 GAGTAGTGGAGCAGATTCTTCTTCTTTTAGATTTGGTCTTCCTGAAGAGAAGTGAAACAAATCGA
340789 TTAT
131 TTAT
*
340793 GATTCAATCTTCCCTGAAGAGTAGTGAAGTAGATCAAAGTTTTCTCGAGTCTGATATCCCCTAAA
1 GATTCAATCTTCCCTGAAGAGTAGTGAAGTAGATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAA
* * ** *
340858 GAGTAGTGGAGCAGATTCTTCTTCTTTTAGATTTGGTCTTCTTGAAGAGCAGTGAAGTAAATCAA
66 GAGTAGTGGAGCAGATTCTTCTTCTTTTAGATTTGGTCTTCCTGAAGAGAAGTGAAACAAATCGA
340923 TTAT
131 TTAT
* * **
340927 GATTCAATCTTCCGTGAAGAGCAGTGAAGTCTATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAA
1 GATTCAATCTTCCCTGAAGAGTAGTGAAGTAGATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAA
** *
340992 GAGTAGTGGAGCAGACGCTTCTTCTTTTAGATTTGGTCTTCCTGAAGAGAAGTGAAGCAAATCGA
66 GAGTAGTGGAGCAGATTCTTCTTCTTTTAGATTTGGTCTTCCTGAAGAGAAGTGAAACAAATCGA
341057 TTAT
131 TTAT
** * * * *
341061 GATTCAATCTTCTATGAAGAATAGTAAAGTGGATCAAAGTTTTCTCGAGTCTGATCTTCCCTAAA
1 GATTCAATCTTCCCTGAAGAGTAGTGAAGTAGATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAA
* * * *
341126 AAGTAATGGAGCATATTCTTCTTCTTTTAGATTTGGTCTTCTTGAAGAGCAA-TGAAA-AAATCG
66 GAGTAGTGGAGCAGATTCTTCTTCTTTTAGATTTGGTCTTCCTGAAGAG-AAGTGAAACAAATCG
**
341189 ATTCC
130 ATTAT
* *
341194 GATTCAATATTCCCTGAAGAATAGTG
1 GATTCAATCTTCCCTGAAGAGTAGTG
341220 GAATGAATCA
Statistics
Matches: 375, Mismatches: 51, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
133 31 0.08
134 342 0.91
135 2 0.01
ACGTcount: A:0.30, C:0.16, G:0.20, T:0.34
Consensus pattern (134 bp):
GATTCAATCTTCCCTGAAGAGTAGTGAAGTAGATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAA
GAGTAGTGGAGCAGATTCTTCTTCTTTTAGATTTGGTCTTCCTGAAGAGAAGTGAAACAAATCGA
TTAT
Found at i:346484 original size:33 final size:33
Alignment explanation
Indices: 346447--346514 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
346437 CAGGTGATCG
346447 TTGGTGGTCATACGATGGGTATGTTCGTGAAGA
1 TTGGTGGTCATACGATGGGTATGTTCGTGAAGA
346480 TTGGTGGTCATACGATGGGTATGTTCGTGAAGA
1 TTGGTGGTCATACGATGGGTATGTTCGTGAAGA
346513 TT
1 TT
346515 ATTTTCTTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.21, C:0.09, G:0.35, T:0.35
Consensus pattern (33 bp):
TTGGTGGTCATACGATGGGTATGTTCGTGAAGA
Found at i:353136 original size:18 final size:18
Alignment explanation
Indices: 353113--353165 Score: 63
Period size: 18 Copynumber: 3.0 Consensus size: 18
353103 TATTAATATG
353113 TATCTGATAACTGTAAAA
1 TATCTGATAACTGTAAAA
** *
353131 TATCTGATATTTGT-AAT
1 TATCTGATAACTGTAAAA
*
353148 TATCTGATAACTGGAAAA
1 TATCTGATAACTGTAAAA
353166 ATCATCCGAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.40, C:0.09, G:0.13, T:0.38
Consensus pattern (18 bp):
TATCTGATAACTGTAAAA
Found at i:353548 original size:2 final size:2
Alignment explanation
Indices: 353541--353565 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
353531 TAAATTCCAA
353541 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
353566 ACTAAATCGT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:355592 original size:17 final size:17
Alignment explanation
Indices: 355570--355612 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
355560 GATTGTGATC
355570 GAGCTATTCTTTTAGAG
1 GAGCTATTCTTTTAGAG
355587 GAGCTATTCTTTTAGAG
1 GAGCTATTCTTTTAGAG
*
355604 GAGCAATTC
1 GAGCTATTC
355613 ATATATGTGC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.37
Consensus pattern (17 bp):
GAGCTATTCTTTTAGAG
Found at i:369785 original size:7 final size:7
Alignment explanation
Indices: 369773--369823 Score: 70
Period size: 7 Copynumber: 7.4 Consensus size: 7
369763 TTACCTAAAG
369773 AAAGAAA
1 AAAGAAA
369780 AAAGAAA
1 AAAGAAA
369787 AAAG-AA
1 AAAGAAA
369793 AAAGAAA
1 AAAGAAA
369800 AAAGAAA
1 AAAGAAA
369807 TAAA-AAA
1 -AAAGAAA
*
369814 GAAGAAA
1 AAAGAAA
369821 AAA
1 AAA
369824 TAATAATGAT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
6 8 0.21
7 28 0.72
8 3 0.08
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (7 bp):
AAAGAAA
Found at i:369785 original size:11 final size:11
Alignment explanation
Indices: 369769--369823 Score: 71
Period size: 10 Copynumber: 5.3 Consensus size: 11
369759 TATTTTACCT
369769 AAAGAAAGAAA
1 AAAGAAAGAAA
369780 AAAGAAA-AAA
1 AAAGAAAGAAA
*
369790 GAA-AAAGAAA
1 AAAGAAAGAAA
*
369800 AAAGAAATAAA
1 AAAGAAAGAAA
369811 AAAG-AAGAAA
1 AAAGAAAGAAA
369821 AAA
1 AAA
369824 TAATAATGAT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
9 3 0.08
10 18 0.47
11 17 0.45
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (11 bp):
AAAGAAAGAAA
Found at i:369796 original size:24 final size:24
Alignment explanation
Indices: 369769--369816 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
369759 TATTTTACCT
369769 AAAGAAAGAAA-AAAGAAAAAAGAA
1 AAAGAAA-AAAGAAAGAAAAAAGAA
*
369793 AAAGAAAAAAGAAATAAAAAAGAA
1 AAAGAAAAAAGAAAGAAAAAAGAA
369817 GAAAAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (24 bp):
AAAGAAAAAAGAAAGAAAAAAGAA
Found at i:369798 original size:20 final size:20
Alignment explanation
Indices: 369773--369855 Score: 78
Period size: 20 Copynumber: 3.9 Consensus size: 20
369763 TTACCTAAAG
369773 AAAGAAAAAAGAAA-AAAGAA
1 AAAGAAAAAAGAAATAAA-AA
369793 AAAGAAAAAAGAAATAAAAA
1 AAAGAAAAAAGAAATAAAAA
* *
369813 AGAAGAAAAAATAATAATGATAAA
1 A-AAGAAAAAA-GA-AAT-AAAAA
*
369837 AAAGAAAATAAAAAATAAA
1 AAAGAAAA-AAGAAATAAA
369856 TAAAGGGGTT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
20 17 0.31
21 14 0.26
22 4 0.07
23 12 0.22
24 7 0.13
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (20 bp):
AAAGAAAAAAGAAATAAAAA
Found at i:369835 original size:26 final size:25
Alignment explanation
Indices: 369784--369854 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 25
369774 AAGAAAAAAG
* *
369784 AAAAAAGAAAAAGAAAAAAGAA--AT
1 AAAAAAG-AAAATAAAAAATAATGAT
369808 AAAAAAGAAGAA-AAAATAATAATGAT
1 AAAAAAGAA-AATAAAA-AATAATGAT
369834 AAAAAAGAAAATAAAAAATAA
1 AAAAAAGAAAATAAAAAATAA
369855 ATAAAGGGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
23 6 0.15
24 13 0.32
25 7 0.17
26 15 0.37
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (25 bp):
AAAAAAGAAAATAAAAAATAATGAT
Found at i:369851 original size:14 final size:13
Alignment explanation
Indices: 369773--369851 Score: 68
Period size: 14 Copynumber: 5.8 Consensus size: 13
369763 TTACCTAAAG
369773 AAAGAAAAAAGAAA
1 AAAGAAAAAA-AAA
*
369787 AAAGAAAAAGAAA
1 AAAGAAAAAAAAA
369800 AAAGAAATAAAAAA
1 AAAGAAA-AAAAAA
* *
369814 GAAGAAAAAATAAT
1 AAAGAAAAAA-AAA
* *
369828 AATGATAAAAAAGA
1 AAAGA-AAAAAAAA
*
369842 AAATAAAAAA
1 AAAGAAAAAA
369852 TAAATAAAGG
Statistics
Matches: 52, Mismatches: 10, Indels: 7
0.75 0.14 0.10
Matches are distributed among these distances:
13 18 0.35
14 29 0.56
15 5 0.10
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.08
Consensus pattern (13 bp):
AAAGAAAAAAAAA
Found at i:371427 original size:41 final size:42
Alignment explanation
Indices: 371381--371573 Score: 106
Period size: 46 Copynumber: 4.5 Consensus size: 42
371371 CTTCCTGGAT
371381 AGCAGTGAAGCAAATC-AAGTTCGATTCAATCTTCCCTAAAG
1 AGCAGTGAAGCAAATCAAAGTTCGATTCAATCTTCCCTAAAG
*** * *
371422 AGCAGTGAAGTGGATCAAAGTTTTTCGAGTCTAATCTCCCCTAAAG
1 AGCAGTGAAGCAAATCAAAG---TTCGATTC-AATCTTCCCTAAAG
* * * **** *
371468 AGTAGTGGAGAATATACTCCTTCTTTCAGAATT-GATCTT-CCTAAAG
1 AGCAGTGAAGCA-A-A-T-CAAAGTTC-G-ATTCAATCTTCCCTAAAG
**
371514 ATAAGTGAAGCAAATC-AAGTTCGATTCAATCTTCCCTAAAG
1 AGCAGTGAAGCAAATCAAAGTTCGATTCAATCTTCCCTAAAG
* **
371555 AGCAGCGAAGTGAATCAAA
1 AGCAGTGAAGCAAATCAAA
371574 TTCTTTTCCG
Statistics
Matches: 108, Mismatches: 30, Indels: 27
0.65 0.18 0.16
Matches are distributed among these distances:
39 3 0.03
40 6 0.06
41 34 0.31
42 6 0.06
43 1 0.01
44 1 0.01
45 8 0.07
46 36 0.33
47 7 0.06
48 2 0.02
49 3 0.03
50 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (42 bp):
AGCAGTGAAGCAAATCAAAGTTCGATTCAATCTTCCCTAAAG
Found at i:371432 original size:133 final size:132
Alignment explanation
Indices: 371195--371573 Score: 483
Period size: 133 Copynumber: 2.9 Consensus size: 132
371185 ATTTGGTTTT
* * * * *
371195 CCCTAAAGAGTAGCGGAGCATATCATTATT-TTTTAGATTTGGTCTGCCTGAATACCAGTGAAGC
1 CCCTAAAGAGTAGTGGAGCATATCCTCATTCTTTTAGATTTGGTCTTCCTGGATA-CAGTGAAGC
* * ** * * * *
371259 AAATCAAGTACGATTAAATCTTCGTTGAAGAGCAATGAAGTGGGTCAAAGTTTTTCAAGTATGAT
65 AAATCAAGTTCGATTCAATCTTCCCTAAAGAGCAGTGAAGTGGATCAAAGTTTTTCAAGTATAAT
371324 CTC
130 CTC
*
371327 CCCTAAATAGTAGTGGAGCATATCCTCATTCTTTTAGATTTGGTCTTCCTGGATAGCAGTGAAGC
1 CCCTAAAGAGTAGTGGAGCATATCCTCATTCTTTTAGATTTGGTCTTCCTGGATA-CAGTGAAGC
* *
371392 AAATCAAGTTCGATTCAATCTTCCCTAAAGAGCAGTGAAGTGGATCAAAGTTTTTCGAGTCTAAT
65 AAATCAAGTTCGATTCAATCTTCCCTAAAGAGCAGTGAAGTGGATCAAAGTTTTTCAAGTATAAT
371457 CTC
130 CTC
* * * * * * *
371460 CCCTAAAGAGTAGTGGAGAATATACTCCTTCTTTCAGAATTGATCTTCCTAAAGATA-AGTGAAG
1 CCCTAAAGAGTAGTGGAGCATATCCTCATTCTTTTAGATTTGGTCTTCCT--GGATACAGTGAAG
* *
371524 CAAATCAAGTTCGATTCAATCTTCCCTAAAGAGCAGCGAAGTGAATCAAA
64 CAAATCAAGTTCGATTCAATCTTCCCTAAAGAGCAGTGAAGTGGATCAAA
371574 TTCTTTTCCG
Statistics
Matches: 217, Mismatches: 27, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
132 26 0.12
133 187 0.86
135 4 0.02
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (132 bp):
CCCTAAAGAGTAGTGGAGCATATCCTCATTCTTTTAGATTTGGTCTTCCTGGATACAGTGAAGCA
AATCAAGTTCGATTCAATCTTCCCTAAAGAGCAGTGAAGTGGATCAAAGTTTTTCAAGTATAATC
TC
Found at i:377319 original size:10 final size:10
Alignment explanation
Indices: 377290--377358 Score: 72
Period size: 10 Copynumber: 7.1 Consensus size: 10
377280 GCTGCTGGAA
377290 AACCGGTTTG
1 AACCGGTTTG
*
377300 -ACCAGTTTTG
1 AACC-GGTTTG
377310 AACCGGTTTG
1 AACCGGTTTG
*
377320 -ACCGGTCTG
1 AACCGGTTTG
377329 AACCGGTTTG
1 AACCGGTTTG
*
377339 -ACCGGTCTG
1 AACCGGTTTG
*
377348 AACCGGGTTG
1 AACCGGTTTG
377358 A
1 A
377359 CCTGACCCGA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
9 19 0.40
10 26 0.54
11 3 0.06
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:377332 original size:19 final size:19
Alignment explanation
Indices: 377290--377360 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
377280 GCTGCTGGAA
* *
377290 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
377310 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
377329 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
377348 AACCGGGTTGACC
1 AACCGGTTTGACC
377361 TGACCCGACT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
19 35 0.73
20 13 0.27
ACGTcount: A:0.18, C:0.25, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:377376 original size:17 final size:17
Alignment explanation
Indices: 377354--377411 Score: 73
Period size: 17 Copynumber: 3.4 Consensus size: 17
377344 TCTGAACCGG
*
377354 GTTGACCTGACCCGACT
1 GTTGACCCGACCCGACT
*
377371 GTTGACCCGACCTGACCT
1 GTTGACCCGACCCGA-CT
*
377389 -TTGACCCGACCCGACC
1 GTTGACCCGACCCGACT
377405 GTTGACC
1 GTTGACC
377412 GTGACCGTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 1 0.03
17 32 0.91
18 2 0.06
ACGTcount: A:0.17, C:0.40, G:0.22, T:0.21
Consensus pattern (17 bp):
GTTGACCCGACCCGACT
Found at i:377411 original size:7 final size:7
Alignment explanation
Indices: 377401--377443 Score: 63
Period size: 7 Copynumber: 6.4 Consensus size: 7
377391 GACCCGACCC
377401 GACCGTT
1 GACCGTT
377408 GACCG-T
1 GACCGTT
377414 GACCGTT
1 GACCGTT
*
377421 GACTG-T
1 GACCGTT
377427 GACCGTT
1 GACCGTT
377434 GACCGTT
1 GACCGTT
377441 GAC
1 GAC
377444 TTTCTTTGAC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 11 0.34
7 21 0.66
ACGTcount: A:0.16, C:0.28, G:0.30, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:377419 original size:13 final size:13
Alignment explanation
Indices: 377401--377439 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
377391 GACCCGACCC
377401 GACCGTTGACCGT
1 GACCGTTGACCGT
*
377414 GACCGTTGACTGT
1 GACCGTTGACCGT
377427 GACCGTTGACCGT
1 GACCGTTGACCGT
377440 TGACTTTCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.15, C:0.28, G:0.31, T:0.26
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:377438 original size:20 final size:19
Alignment explanation
Indices: 377407--377444 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 19
377397 ACCCGACCGT
377407 TGACCGTGACCGTTGACTG
1 TGACCGTGACCGTTGACTG
377426 TGACCGTTGACCGTTGACT
1 TGACCG-TGACCGTTGACT
377445 TTCTTTGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.16, C:0.26, G:0.29, T:0.29
Consensus pattern (19 bp):
TGACCGTGACCGTTGACTG
Found at i:378387 original size:32 final size:31
Alignment explanation
Indices: 378311--378432 Score: 113
Period size: 31 Copynumber: 3.9 Consensus size: 31
378301 CTAATGTGAC
* *
378311 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
* *
378342 TCTCAGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
** * *
378374 TCTTAGGTAGGCCCCACGGCCCCAAAATCTA-
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
* *
378405 TCTTGGGTAGGCTCT-CAGGCCCTAAGAT
1 TCTTAGGTAGGCCCTGC-GGCCCTAAGAT
378433 GTTCCCTTAG
Statistics
Matches: 73, Mismatches: 16, Indels: 4
0.78 0.17 0.04
Matches are distributed among these distances:
30 1 0.01
31 46 0.63
32 26 0.36
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.26
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:384675 original size:10 final size:10
Alignment explanation
Indices: 384646--384733 Score: 94
Period size: 10 Copynumber: 9.1 Consensus size: 10
384636 GCTGCTGGAA
384646 AACCGGTTTG
1 AACCGGTTTG
*
384656 -ACCAGTTTTG
1 AACC-GGTTTG
384666 AACCGGTTTG
1 AACCGGTTTG
*
384676 -ACCGGTTCG
1 AACCGGTTTG
384685 AACCGGTTTG
1 AACCGGTTTG
*
384695 -ACCGGTCTG
1 AACCGGTTTG
384704 AACCGGTTTG
1 AACCGGTTTG
*
384714 -ACCGGTCTG
1 AACCGGTTTG
*
384723 AACCGGGTTG
1 AACCGGTTTG
384733 A
1 A
384734 CCCGACCCGA
Statistics
Matches: 64, Mismatches: 9, Indels: 10
0.77 0.11 0.12
Matches are distributed among these distances:
9 27 0.42
10 34 0.53
11 3 0.05
ACGTcount: A:0.18, C:0.24, G:0.31, T:0.27
Consensus pattern (10 bp):
AACCGGTTTG
Found at i:384689 original size:19 final size:19
Alignment explanation
Indices: 384646--384735 Score: 128
Period size: 19 Copynumber: 4.7 Consensus size: 19
384636 GCTGCTGGAA
* *
384646 AACCGGTTTGACCAGTTTTG
1 AACCGGTTTGACC-GGTCTG
384666 AACCGGTTTGACCGGT-TCG
1 AACCGGTTTGACCGGTCT-G
384685 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
384704 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
*
384723 AACCGGGTTGACC
1 AACCGGTTTGACC
384736 CGACCCGACT
Statistics
Matches: 66, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
18 1 0.02
19 51 0.77
20 14 0.21
ACGTcount: A:0.18, C:0.26, G:0.30, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:384751 original size:17 final size:17
Alignment explanation
Indices: 384729--384786 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
384719 TCTGAACCGG
*
384729 GTTGACCCGACCCGACT
1 GTTGACCCGACCCGACC
384746 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
384763 GTTGACCCGACCCGACC
1 GTTGACCCGACCCGACC
384780 GTTGACC
1 GTTGACC
384787 GTGACCGTTG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GTTGACCCGACCCGACC
Found at i:384786 original size:7 final size:7
Alignment explanation
Indices: 384776--384818 Score: 72
Period size: 7 Copynumber: 6.4 Consensus size: 7
384766 GACCCGACCC
384776 GACCGTT
1 GACCGTT
384783 GACCG-T
1 GACCGTT
384789 GACCGTT
1 GACCGTT
384796 GACCG-T
1 GACCGTT
384802 GACCGTT
1 GACCGTT
384809 GACCGTT
1 GACCGTT
384816 GAC
1 GAC
384819 TTTCTTTGAC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
6 12 0.35
7 22 0.65
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:384794 original size:13 final size:13
Alignment explanation
Indices: 384776--384814 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
384766 GACCCGACCC
384776 GACCGTTGACCGT
1 GACCGTTGACCGT
384789 GACCGTTGACCGT
1 GACCGTTGACCGT
384802 GACCGTTGACCGT
1 GACCGTTGACCGT
384815 TGACTTTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.15, C:0.31, G:0.31, T:0.23
Consensus pattern (13 bp):
GACCGTTGACCGT
Found at i:384801 original size:20 final size:20
Alignment explanation
Indices: 384776--384818 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
384766 GACCCGACCC
384776 GACCGTTGACCGTGACCGTT
1 GACCGTTGACCGTGACCGTT
384796 GACCG-TGACCGTTGACCGTT
1 GACCGTTGACCG-TGACCGTT
384816 GAC
1 GAC
384819 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.16, C:0.30, G:0.30, T:0.23
Consensus pattern (20 bp):
GACCGTTGACCGTGACCGTT
Found at i:385772 original size:32 final size:31
Alignment explanation
Indices: 385688--385764 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
385678 CTAATGTGAC
* *
385688 TCTTAGGTAGGCTCTGCGGCCCTGAGATTAT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
** *
385719 TCTCGGGTAGGCCCTGCGGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCTGCGGCCCTAAGAT-TAT
385751 TCTTAGGTAGGCCC
1 TCTTAGGTAGGCCC
385765 CACGGCCCCG
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
31 24 0.63
32 14 0.37
ACGTcount: A:0.14, C:0.26, G:0.31, T:0.29
Consensus pattern (31 bp):
TCTTAGGTAGGCCCTGCGGCCCTAAGATTAT
Found at i:385790 original size:63 final size:63
Alignment explanation
Indices: 385688--385811 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
385678 CTAATGTGAC
* ** * *
385688 TCTTAGGTAGGCTCTGCGGCCCTGAGATTATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
385751 TCTTAGGTAGGCCCCACGGCCCCGAAATCTA-TCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCCCACGGCCCCGAAAT-TATTCTCGGGTAGGCCCTCAGGCCCTAAGATGT
385812 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 49 0.94
64 2 0.04
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCCCACGGCCCCGAAATTATTCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:400520 original size:27 final size:27
Alignment explanation
Indices: 400482--400545 Score: 128
Period size: 27 Copynumber: 2.4 Consensus size: 27
400472 ACATCCTTAA
400482 AAATTCACATGGACTCAACTTAAATCC
1 AAATTCACATGGACTCAACTTAAATCC
400509 AAATTCACATGGACTCAACTTAAATCC
1 AAATTCACATGGACTCAACTTAAATCC
400536 AAATTCACAT
1 AAATTCACAT
400546 TGACACGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (27 bp):
AAATTCACATGGACTCAACTTAAATCC
Found at i:401489 original size:14 final size:15
Alignment explanation
Indices: 401456--401494 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
401446 TCCAGTCATC
401456 GAGTCAACCCGATAT
1 GAGTCAACCCGATAT
* *
401471 GAGTCAACTCG-TCT
1 GAGTCAACCCGATAT
401485 GAGTCAACCC
1 GAGTCAACCC
401495 ATTGACTTTG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.28, C:0.31, G:0.21, T:0.21
Consensus pattern (15 bp):
GAGTCAACCCGATAT
Found at i:401513 original size:13 final size:13
Alignment explanation
Indices: 401495--401519 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
401485 GAGTCAACCC
401495 ATTGACTTTGACT
1 ATTGACTTTGACT
401508 ATTGACTTTGAC
1 ATTGACTTTGAC
401520 CGTTACCATT
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:0.24, C:0.16, G:0.16, T:0.44
Consensus pattern (13 bp):
ATTGACTTTGACT
Found at i:407555 original size:23 final size:21
Alignment explanation
Indices: 407486--407565 Score: 81
Period size: 20 Copynumber: 3.7 Consensus size: 21
407476 AAAACCCGTG
* *
407486 GGGGGTATCGATTCCC-TCAA
1 GGGGGAATCGGTTCCCTTCAA
*
407506 GGGGGAATCGGTTCCCATTTAAA
1 GGGGGAATCGGTTCCC--TTCAA
407529 GGGGGAATCGGTTTCCCTTCAA
1 GGGGGAATCGG-TTCCCTTCAA
* *
407551 GGGGGTATCGATTCC
1 GGGGGAATCGGTTCC
407566 TCCTGCACTA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
20 14 0.28
21 4 0.08
22 13 0.26
23 14 0.28
24 5 0.10
ACGTcount: A:0.20, C:0.21, G:0.33, T:0.26
Consensus pattern (21 bp):
GGGGGAATCGGTTCCCTTCAA
Found at i:418619 original size:22 final size:19
Alignment explanation
Indices: 418594--418656 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
418584 AAAATAAGAG
418594 AGAAAAGAAAGCAAAAGAAACA
1 AGAAAAGAAAG--AAAGAAA-A
*
418616 AGAAAA-AAAGAGA-AAAA
1 AGAAAAGAAAGAAAGAAAA
418633 AGAAAAGAAAGAAAGAAAA
1 AGAAAAGAAAGAAAGAAAA
418652 AGAAA
1 AGAAA
418657 TAAAATCGAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
17 7 0.19
18 9 0.24
19 11 0.30
21 4 0.11
22 6 0.16
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (19 bp):
AGAAAAGAAAGAAAGAAAA
Found at i:418629 original size:17 final size:16
Alignment explanation
Indices: 418583--418661 Score: 61
Period size: 17 Copynumber: 4.4 Consensus size: 16
418573 GAAAAAACAT
418583 AAAAATAAGAGAGAAAAG
1 AAAAA-AAGAGA-AAAAG
*
418601 AAAGCAAAAGA-AACAAG
1 AAA--AAAAGAGAAAAAG
418618 AAAAAAAGAGAAAAAAG
1 AAAAAAAGAG-AAAAAG
418635 AAAAGAAAGAAAGAAAAAG
1 AAAA-AAAG--AGAAAAAG
418654 AAATAAAA
1 AAA-AAAA
418662 TCGATCAAGT
Statistics
Matches: 51, Mismatches: 2, Indels: 15
0.75 0.03 0.22
Matches are distributed among these distances:
15 6 0.12
17 16 0.31
18 8 0.16
19 16 0.31
20 5 0.10
ACGTcount: A:0.77, C:0.03, G:0.18, T:0.03
Consensus pattern (16 bp):
AAAAAAAGAGAAAAAG
Found at i:418661 original size:9 final size:8
Alignment explanation
Indices: 418572--418661 Score: 56
Period size: 9 Copynumber: 10.1 Consensus size: 8
418562 GAATATATAT
418572 AGAAAAAA
1 AGAAAAAA
*
418580 CATAAAAATA
1 -AGAAAAA-A
*
418590 AGAGAGAAA
1 AGA-AAAAA
418599 AGAAAGCAAA
1 AGAAA--AAA
*
418609 AG-AAACA
1 AGAAAAAA
418616 AGAAAAAA
1 AGAAAAAA
418624 AGAGAAAAA
1 AGA-AAAAA
418633 AGAAAAGAA
1 AGAAAA-AA
418642 AGAAAGAAAA
1 AG-AA-AAAA
418652 AGAAATAAA
1 AGAAA-AAA
418661 A
1 A
418662 TCGATCAAGT
Statistics
Matches: 65, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
7 4 0.06
8 12 0.18
9 32 0.49
10 15 0.23
11 2 0.03
ACGTcount: A:0.77, C:0.03, G:0.17, T:0.03
Consensus pattern (8 bp):
AGAAAAAA
Found at i:418661 original size:29 final size:30
Alignment explanation
Indices: 418601--418661 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 30
418591 GAGAGAAAAG
*
418601 AAAGCAAAAGAAACAAGAAAAAAAGAGAAA
1 AAAGCAAAAGAAACAAGAAAAAAAGAAAAA
* * *
418631 AAAG-AAAAGAAAGAA-AGAAAAAGAAATA
1 AAAGCAAAAGAAACAAGAAAAAAAGAAAAA
418659 AAA
1 AAA
418662 TCGATCAAGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 13 0.48
29 10 0.37
30 4 0.15
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.02
Consensus pattern (30 bp):
AAAGCAAAAGAAACAAGAAAAAAAGAAAAA
Found at i:427819 original size:112 final size:112
Alignment explanation
Indices: 427607--427819 Score: 273
Period size: 112 Copynumber: 1.9 Consensus size: 112
427597 AATGAGGGGA
* * * * *
427607 ATCAACATTTCCAGTGAATAGTTTATAATGAGAAGAACTCATCCGATGAAGTAGAAGAAGTTCAT
1 ATCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACGAAGGAGAAGAAGTTCAT
* * * **** * *
427672 AATGAGAAGAACTTGTTTAATCTTGGTTTGGTTCCAAAAGGAGGTGG
66 AATAAGAAGAACTTGTTCAACCTCAACTCGATTCCAAAAGGAGGTGG
* * *
427719 ATCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCGTCCGACGAGGGAGAAGAAGTTCAT
1 ATCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACGAAGGAGAAGAAGTTCAT
427784 AATAAGAAGAACTTGTTCAACCTCAACTCGATTCCA
66 AATAAGAAGAACTTGTTCAACCTCAACTCGATTCCA
427820 TCACATAAGG
Statistics
Matches: 84, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
112 84 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (112 bp):
ATCAACATTTCCAATGAAGAGTTCATAATGAGAAGAACTCATCCGACGAAGGAGAAGAAGTTCAT
AATAAGAAGAACTTGTTCAACCTCAACTCGATTCCAAAAGGAGGTGG
Found at i:427911 original size:42 final size:42
Alignment explanation
Indices: 427816--428089 Score: 177
Period size: 40 Copynumber: 6.7 Consensus size: 42
427806 TCAACTCGAT
* * * * *
427816 TCCATCACATAAGGAGTTGGAACAGCACCGA-C-CTTGGCTCA
1 TCCATCACATAAGGAGTTGGATCAACATC-ATCATTTCGCTCA
*
427857 TCCATCACATAAGGAGTTGGGTCAACATCATCATTTCGCTCA
1 TCCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCA
* * ** *
427899 TCCATCATATAAGGACTTGGATCAACATCATCATTTTACTCG
1 TCCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCA
* * * * **
427941 TCCATTACATAAGGAGTTGGATTAGCATCA-C-TTTCGATTT
1 TCCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCA
* * * * * ** *
427981 TCTATCACATAAGAAGTTGTATTAAAATCAT--TTTTACTCG
1 TCCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCA
* * * * * *
428021 TCCATCATATAAGCAATTGAATCAACATCA-C-CTTGGCTCA
1 TCCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCA
* * *
428061 TCCATCAGATAAAGAGTTGGATCAGCATC
1 TCCATCACATAAGGAGTTGGATCAACATC
428090 GCCTCGTGCC
Statistics
Matches: 179, Mismatches: 50, Indels: 9
0.75 0.21 0.04
Matches are distributed among these distances:
40 84 0.47
41 27 0.15
42 68 0.38
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.30
Consensus pattern (42 bp):
TCCATCACATAAGGAGTTGGATCAACATCATCATTTCGCTCA
Found at i:430430 original size:2 final size:2
Alignment explanation
Indices: 430423--430486 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
430413 CAAATGGACT
430423 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
430465 TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA
430487 AATGTACATA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:432633 original size:8 final size:8
Alignment explanation
Indices: 432620--432666 Score: 85
Period size: 8 Copynumber: 5.9 Consensus size: 8
432610 TCATTTCCTT
432620 TTTTTCTC
1 TTTTTCTC
432628 TTTTTCTC
1 TTTTTCTC
432636 TTTTTCTC
1 TTTTTCTC
432644 TTTTTCTC
1 TTTTTCTC
432652 TTTTTCTC
1 TTTTTCTC
*
432660 TTCTTCT
1 TTTTTCT
432667 TTTATTTTCT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 38 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (8 bp):
TTTTTCTC
Found at i:432677 original size:24 final size:24
Alignment explanation
Indices: 432617--432678 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
432607 TATTCATTTC
*
432617 CTTTTTTTCTCTTTTTCTCTTTTT
1 CTTTTTTTCTCTTTTTCTCTTCTT
*
432641 CTCTTTTTCTCTTTTTCTCTTCTT
1 CTTTTTTTCTCTTTTTCTCTTCTT
432665 CTTTTATTT-TCTTT
1 CTTTT-TTTCTCTTT
432679 CTTTAAGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 31 0.91
25 3 0.09
ACGTcount: A:0.02, C:0.23, G:0.00, T:0.76
Consensus pattern (24 bp):
CTTTTTTTCTCTTTTTCTCTTCTT
Found at i:439460 original size:40 final size:40
Alignment explanation
Indices: 439398--439560 Score: 247
Period size: 40 Copynumber: 4.1 Consensus size: 40
439388 GCTGCAGGTT
*
439398 TGTAATACACTT-TGTGTATATGGTGGGCACGACCTTATG
1 TGTAATACACTTCGGTGTATATGGTGGGCACGACCTTATG
* *
439437 TGTAATACACATCGGTGTATATGGTTGGCACGACCTTATG
1 TGTAATACACTTCGGTGTATATGGTGGGCACGACCTTATG
* * *
439477 TGTAATACACTTCGGTGTGTATGGAGGGCACAACCTTATG
1 TGTAATACACTTCGGTGTATATGGTGGGCACGACCTTATG
* *
439517 TGTAATACACTTCGTTGTATATGGTCGGCACGACCTTATG
1 TGTAATACACTTCGGTGTATATGGTGGGCACGACCTTATG
439557 TGTA
1 TGTA
439561 GCACTACGGT
Statistics
Matches: 110, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
39 11 0.10
40 99 0.90
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (40 bp):
TGTAATACACTTCGGTGTATATGGTGGGCACGACCTTATG
Found at i:439712 original size:44 final size:44
Alignment explanation
Indices: 439637--439919 Score: 442
Period size: 44 Copynumber: 6.4 Consensus size: 44
439627 TGGTATATGG
* *
439637 TTATGGA-ATAATGGCAAGTGTATTGGTAAAATAAGCTTATGAGC
1 TTATGGATA-AATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
* ** *
439681 CTATCTATAAATGGTAAGTGTATTGGGAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
439725 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
439769 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
* *
439813 TTATGGAGAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
* * *
439857 TTATGGTATTAATGATAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGG-ATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
439902 TTATGGATAAATGGTAAG
1 TTATGGATAAATGGTAAG
439920 AGATTTTATA
Statistics
Matches: 220, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
44 178 0.81
45 42 0.19
ACGTcount: A:0.37, C:0.07, G:0.24, T:0.32
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
Found at i:439736 original size:24 final size:24
Alignment explanation
Indices: 439709--439780 Score: 59
Period size: 24 Copynumber: 3.2 Consensus size: 24
439699 TGTATTGGGA
439709 AAATAAGCTTACGAGCTTATGGAT
1 AAATAAGCTTACGAGCTTATGGAT
*
439733 AAAT--G-GTA--AG-TGTATTGG-T
1 AAATAAGCTTACGAGCT-TA-TGGAT
439752 AAAATAAGCTTACGAGCTTATGGAT
1 -AAATAAGCTTACGAGCTTATGGAT
439777 AAAT
1 AAAT
439781 GGTAAGTGTA
Statistics
Matches: 36, Mismatches: 2, Indels: 20
0.62 0.03 0.34
Matches are distributed among these distances:
18 1 0.03
19 5 0.14
20 7 0.19
21 2 0.06
22 2 0.06
23 2 0.06
24 11 0.31
25 5 0.14
26 1 0.03
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (24 bp):
AAATAAGCTTACGAGCTTATGGAT
Found at i:444497 original size:40 final size:40
Alignment explanation
Indices: 444433--444554 Score: 208
Period size: 40 Copynumber: 3.0 Consensus size: 40
444423 TGCAGGTTTA
444433 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
* * *
444473 TAATTCACTTCGGTGTATACGGTGGGCACGACCTTATGTG
1 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
*
444513 TAATACACTTTGGTGTATATGGTGGGTACGACCTTATGTG
1 TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
444553 TA
1 TA
444555 GCTCTACGGT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
40 75 1.00
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (40 bp):
TAATACACTTTGGTGTATATGGTGGGCACGACCTTATGTG
Found at i:444694 original size:44 final size:44
Alignment explanation
Indices: 444631--444913 Score: 442
Period size: 44 Copynumber: 6.4 Consensus size: 44
444621 TGGTATATGG
* **
444631 TTATGGA-ATAATGGCAAGTGTATTGGTAAAATAAGCTTGTGAGC
1 TTATGGATA-AATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
* * *
444675 TTATGGATAAATTGAAAGTGTATTGGTAAAATAAGGTTACGAGC
1 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
* *
444719 TTATGGATAAATGGTAAGTGTATTGGTAAATTTAGCTTACGAGC
1 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
444763 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
*
444807 TTATGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
* *
444851 TTATGGTATTAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGG-ATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
444896 TTATGGATAAATGGTAAG
1 TTATGGATAAATGGTAAG
444914 AGATTTTATA
Statistics
Matches: 222, Mismatches: 15, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
44 178 0.80
45 44 0.20
ACGTcount: A:0.36, C:0.06, G:0.25, T:0.33
Consensus pattern (44 bp):
TTATGGATAAATGGTAAGTGTATTGGTAAAATAAGCTTACGAGC
Found at i:447697 original size:43 final size:47
Alignment explanation
Indices: 447649--447754 Score: 121
Period size: 50 Copynumber: 2.3 Consensus size: 47
447639 ATAACTAATG
** *
447649 AATAAAATAATAACAA-ACTAAAT-ATGTTTTAACT-A-TAATTCGT
1 AATAAAATAATAACAACAAAAAATAATGTTTTAACTAACTAATTCCT
*
447692 AATAAAATAATAATAACAAAAAATAATGTTTTAACTCAAACTTAATTCCT
1 AATAAAATAATAACAACAAAAAATAATGTTTTAACT--AAC-TAATTCCT
447742 AATAAAATAATAA
1 AATAAAATAATAA
447755 ATCTAATCCT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
43 15 0.29
44 5 0.10
45 11 0.21
48 1 0.02
50 20 0.38
ACGTcount: A:0.56, C:0.09, G:0.03, T:0.32
Consensus pattern (47 bp):
AATAAAATAATAACAACAAAAAATAATGTTTTAACTAACTAATTCCT
Found at i:453013 original size:19 final size:19
Alignment explanation
Indices: 452958--453001 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
452948 AATTAATGAA
* *
452958 TAAAATACAATGCGGAAAG
1 TAAAATACATTGCGAAAAG
452977 TAAAATACATTGCGAAAAG
1 TAAAATACATTGCGAAAAG
452996 TAAAAT
1 TAAAAT
453002 GCATATGCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.55, C:0.09, G:0.16, T:0.20
Consensus pattern (19 bp):
TAAAATACATTGCGAAAAG
Found at i:461207 original size:27 final size:27
Alignment explanation
Indices: 461169--461236 Score: 136
Period size: 27 Copynumber: 2.5 Consensus size: 27
461159 ACATCCTTAA
461169 AAATTCACATTGACTCAACTTAAGTCC
1 AAATTCACATTGACTCAACTTAAGTCC
461196 AAATTCACATTGACTCAACTTAAGTCC
1 AAATTCACATTGACTCAACTTAAGTCC
461223 AAATTCACATTGAC
1 AAATTCACATTGAC
461237 ACGAATACAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.38, C:0.25, G:0.07, T:0.29
Consensus pattern (27 bp):
AAATTCACATTGACTCAACTTAAGTCC
Found at i:463224 original size:18 final size:18
Alignment explanation
Indices: 463201--463241 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
463191 ACCGGTCACA
* * *
463201 ACCCGACCCGTTGACTCG
1 ACCCGAACCATTGACCCG
463219 ACCCGAACCATTGACCCG
1 ACCCGAACCATTGACCCG
463237 ACCCG
1 ACCCG
463242 TTGACTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.22, C:0.46, G:0.20, T:0.12
Consensus pattern (18 bp):
ACCCGAACCATTGACCCG
Found at i:465756 original size:24 final size:24
Alignment explanation
Indices: 465729--465796 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
465719 TCAAATTTGA
* *
465729 ATTCTGTTATGATACCTGACCTGG
1 ATTCTGATATGATACATGACCTGG
*
465753 ATTCTGATCTGATACATGACCTGG
1 ATTCTGATATGATACATGACCTGG
*
465777 ATTCTGATATGATACTTGAC
1 ATTCTGATATGATACATGAC
465797 TTGAATTATG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (24 bp):
ATTCTGATATGATACATGACCTGG
Found at i:474574 original size:20 final size:20
Alignment explanation
Indices: 474549--474597 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
474539 TTTATTGACC
474549 TGCATATTATGATTTGAAGG
1 TGCATATTATGATTTGAAGG
*
474569 TGCATATTATGATTTGCAGG
1 TGCATATTATGATTTGAAGG
474589 TGCATATTA
1 TGCATATTA
474598 ATTTATTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.29, C:0.08, G:0.22, T:0.41
Consensus pattern (20 bp):
TGCATATTATGATTTGAAGG
Found at i:478948 original size:24 final size:24
Alignment explanation
Indices: 478895--478945 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
478885 TAAAATATAA
478895 TAAATATATTATTATTATTATTAT
1 TAAATATATTATTATTATTATTAT
478919 TAAATATATTATT-TTAATTATT-T
1 TAAATATATTATTATT-ATTATTAT
478942 TAAA
1 TAAA
478946 ATACTAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 7 0.27
24 19 0.73
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (24 bp):
TAAATATATTATTATTATTATTAT
Found at i:484614 original size:62 final size:59
Alignment explanation
Indices: 484547--484819 Score: 278
Period size: 62 Copynumber: 4.5 Consensus size: 59
484537 GATTTTCAAG
* * * *
484547 AATCGCAACGTGATTCTTACTATCGCAACGAGTATCCGTAAAATCGCAACGACAATACGTAA
1 AATCGCAACGTGATCCGTA-AATCGCAACGAGAATCCGT-AAATCGCAACGACAATACGT-A
* * * **
484609 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGACAATATTTAA
1 AATCGCAACGTG-ATCCGTAAATCGCAACGAGAATCCGT-AAATCGCAACGACAATACGT-A
* * * *
484671 AATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAAT-CTGTA
1 AATCGCAACGTG-ATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGACAATAC-GTA
* * * *
484731 AATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAAATCGCAACGATAATCCGTA
1 AATCGCAACG-TGATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGACAATACGTA
* *
484791 AATCGCAACGAGAATCTGTAAATCGCAAC
1 AATCGCAACGTG-ATCCGTAAATCGCAAC
484820 ACTGAAATTT
Statistics
Matches: 180, Mismatches: 26, Indels: 12
0.83 0.12 0.06
Matches are distributed among these distances:
60 77 0.43
61 17 0.09
62 81 0.45
63 5 0.03
ACGTcount: A:0.40, C:0.23, G:0.16, T:0.20
Consensus pattern (59 bp):
AATCGCAACGTGATCCGTAAATCGCAACGAGAATCCGTAAATCGCAACGACAATACGTA
Found at i:484633 original size:20 final size:20
Alignment explanation
Indices: 484568--484819 Score: 306
Period size: 20 Copynumber: 12.4 Consensus size: 20
484558 GATTCTTACT
*
484568 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGAATCCGT-AA
* *
484589 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGAATCCGT-AA
* *
484610 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATCCGTAA
* *
484630 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGAATCCGT-AA
* ***
484651 ATCGCAACGACAATATTTAAA
1 ATCGCAACGAGAATCCGT-AA
*
484672 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGAATCCGTAA
*
484692 ATCGCAACGATAATCCGTAA
1 ATCGCAACGAGAATCCGTAA
*
484712 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGAATCCGTAA
*
484732 ATCGCAACGATAATCCGTAA
1 ATCGCAACGAGAATCCGTAA
*
484752 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGAATCCGTAA
*
484772 ATCGCAACGATAATCCGTAA
1 ATCGCAACGAGAATCCGTAA
*
484792 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGAATCCGTAA
484812 ATCGCAAC
1 ATCGCAAC
484820 ACTGAAATTT
Statistics
Matches: 202, Mismatches: 28, Indels: 3
0.87 0.12 0.01
Matches are distributed among these distances:
20 134 0.66
21 68 0.34
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAGAATCCGTAA
Found at i:484723 original size:40 final size:40
Alignment explanation
Indices: 484568--484819 Score: 341
Period size: 40 Copynumber: 6.2 Consensus size: 40
484558 GATTCTTACT
*
484568 ATCGCAACGAGT-ATCCGTAAAATCGCAACGACAATAC-GTAAA
1 ATCGCAACGA-TAATCCGT-AAATCGCAACGAGAAT-CTGT-AA
* *
484610 ATCGCAACGCGT-ATCCGTAAATCGCAACGACAATAC-GTAAA
1 ATCGCAACG-ATAATCCGTAAATCGCAACGAGAAT-CTGT-AA
* ***
484651 ATCGCAACGACAATATTTAAAATCGCAACGAGAATCTGTAA
1 ATCGCAACGATAATCCGT-AAATCGCAACGAGAATCTGTAA
484692 ATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAA
1 ATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAA
484732 ATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAA
1 ATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAA
484772 ATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAA
1 ATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAA
484812 ATCGCAAC
1 ATCGCAAC
484820 ACTGAAATTT
Statistics
Matches: 195, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
40 110 0.56
41 52 0.27
42 33 0.17
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (40 bp):
ATCGCAACGATAATCCGTAAATCGCAACGAGAATCTGTAA
Found at i:485532 original size:24 final size:24
Alignment explanation
Indices: 485505--485558 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
485495 GTATTCGAAA
*
485505 TTTGATCTTGGTCAATACTCGGAC
1 TTTGATATTGGTCAATACTCGGAC
*
485529 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACTCGGAC
485553 TTTGAT
1 TTTGAT
485559 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.22, C:0.15, G:0.20, T:0.43
Consensus pattern (24 bp):
TTTGATATTGGTCAATACTCGGAC
Found at i:485750 original size:12 final size:12
Alignment explanation
Indices: 485733--485757 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
485723 ATATAATCCT
485733 GAAGAAGAAAAA
1 GAAGAAGAAAAA
485745 GAAGAAGAAAAA
1 GAAGAAGAAAAA
485757 G
1 G
485758 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:488164 original size:20 final size:19
Alignment explanation
Indices: 488092--488158 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 19
488082 GCAACGAGAG
*
488092 AATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAA
488111 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAA-ATGAA
488131 AATCGCAACGCGGAAATGAA
1 AATCGCAACGC-GAAATGAA
488151 AATCGCAA
1 AATCGCAA
488159 TGCGGAGCAT
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
19 13 0.29
20 29 0.64
21 3 0.07
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:488265 original size:53 final size:52
Alignment explanation
Indices: 488185--488312 Score: 220
Period size: 53 Copynumber: 2.4 Consensus size: 52
488175 TCTCTCGTTG
*
488185 CGATTTTCATTTCGAATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTA
1 CGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTA
* *
488238 CGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCTCATTG
1 CGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTA
488290 CGATTTTCATTTCGCATTGCGAT
1 CGATTTTCATTTCGCATTGCGAT
488313 AGTCATTTTT
Statistics
Matches: 72, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
52 28 0.39
53 44 0.61
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.46
Consensus pattern (52 bp):
CGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTA
Found at i:488320 original size:19 final size:19
Alignment explanation
Indices: 488182--488312 Score: 138
Period size: 19 Copynumber: 7.4 Consensus size: 19
488172 GATTCTCTCG
*
488182 TTGCGATTTTCATTTCGAA
1 TTGCGATTTTCATTTCGCA
*
488201 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
488215 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
*
488235 TTACGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
488254 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
488268 TTGCGATTTTCATTTCTCA
1 TTGCGATTTTCATTTCGCA
488287 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
488306 TTGCGAT
1 TTGCGAT
488313 AGTCATTTTT
Statistics
Matches: 93, Mismatches: 8, Indels: 22
0.76 0.07 0.18
Matches are distributed among these distances:
14 12 0.13
16 14 0.15
17 11 0.12
18 2 0.02
19 40 0.43
20 14 0.15
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:488438 original size:14 final size:14
Alignment explanation
Indices: 488419--488452 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
488409 CATCAATTAA
488419 ACAAATAAACTTTT
1 ACAAATAAACTTTT
* *
488433 ACAAATCATCTTTT
1 ACAAATAAACTTTT
488447 ACAAAT
1 ACAAAT
488453 CAATTAAACA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.47, C:0.18, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATAAACTTTT
Found at i:488453 original size:14 final size:14
Alignment explanation
Indices: 488428--488454 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
488418 AACAAATAAA
488428 CTTTTACAAATCAT
1 CTTTTACAAATCAT
488442 CTTTTACAAATCA
1 CTTTTACAAATCA
488455 ATTAAACAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.22, G:0.00, T:0.41
Consensus pattern (14 bp):
CTTTTACAAATCAT
Found at i:488521 original size:84 final size:84
Alignment explanation
Indices: 488426--488600 Score: 341
Period size: 84 Copynumber: 2.1 Consensus size: 84
488416 TAAACAAATA
*
488426 AACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTTTTTT
1 AACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTTATTT
488491 CCTCATCTACTATTGAATC
66 CCTCATCTACTATTGAATC
488510 AACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTTATTT
1 AACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTTATTT
488575 CCTCATCTACTATTGAATC
66 CCTCATCTACTATTGAATC
488594 AACTTTT
1 AACTTTT
488601 GCAGGCATAC
Statistics
Matches: 90, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 90 1.00
ACGTcount: A:0.42, C:0.19, G:0.02, T:0.37
Consensus pattern (84 bp):
AACTTTTACAAATCATCTTTTACAAATCAATTAAACAATCAAAAAATAAGCAATAATTCTTATTT
CCTCATCTACTATTGAATC
Found at i:488529 original size:14 final size:14
Alignment explanation
Indices: 488506--488539 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
488496 TCTACTATTG
488506 AATCAACTTTTACA
1 AATCAACTTTTACA
*
488520 AATCATCTTTTACA
1 AATCAACTTTTACA
488534 AATCAA
1 AATCAA
488540 TTAAACAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.35
Consensus pattern (14 bp):
AATCAACTTTTACA
Found at i:489914 original size:21 final size:20
Alignment explanation
Indices: 489884--489944 Score: 68
Period size: 21 Copynumber: 3.0 Consensus size: 20
489874 GTGAATCGGG
489884 CTCTTGAATGGTGGGAGGGAC
1 CTCTTGAATGGTGGGAGGG-C
* * *
489905 CTCTTCAATGATGGAAGTGGC
1 CTCTTGAATGGTGGGAG-GGC
*
489926 CTCTTGAACGGTGGGAGGG
1 CTCTTGAATGGTGGGAGGG
489945 GACTCTCGAG
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
20 2 0.06
21 28 0.88
22 2 0.06
ACGTcount: A:0.20, C:0.16, G:0.39, T:0.25
Consensus pattern (20 bp):
CTCTTGAATGGTGGGAGGGC
Found at i:489969 original size:42 final size:42
Alignment explanation
Indices: 489923--490002 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
489913 TGATGGAAGT
* * *
489923 GGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
* * *
489965 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGATGA
1 GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGA
490003 CAGGCGAGTC
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.23, C:0.17, G:0.39, T:0.21
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTCTCGAGGAATGATAGG
Found at i:490439 original size:19 final size:18
Alignment explanation
Indices: 490415--490566 Score: 121
Period size: 19 Copynumber: 8.8 Consensus size: 18
490405 CACGAAACTT
490415 AAAATCGCAACGCGAAATG
1 AAAATCGCAA-GCGAAATG
490434 AAAATCGCAA-CG--A-G
1 AAAATCGCAAGCGAAATG
* **
490448 AGAATCGCAACGCGAAACC
1 AAAATCGCAA-GCGAAATG
490467 AAAATCGCAACGCGAAATG
1 AAAATCGCAA-GCGAAATG
490486 AAAATCGCAA-CG--A-G
1 AAAATCGCAAGCGAAATG
*
490500 AGAATCGCAATGCGAAATG
1 AAAATCGCAA-GCGAAATG
490519 AAAATCGCAA-CG--A-G
1 AAAATCGCAAGCGAAATG
*
490533 AGAATCGCAATGCGAAATG
1 AAAATCGCAA-GCGAAATG
490552 AAAATCGCAATGCGA
1 AAAATCGCAA-GCGA
490567 TTTTGGTTTC
Statistics
Matches: 109, Mismatches: 9, Indels: 30
0.74 0.06 0.20
Matches are distributed among these distances:
14 30 0.28
15 3 0.03
16 6 0.06
17 6 0.06
18 3 0.03
19 61 0.56
ACGTcount: A:0.46, C:0.21, G:0.22, T:0.11
Consensus pattern (18 bp):
AAAATCGCAAGCGAAATG
Found at i:490486 original size:52 final size:52
Alignment explanation
Indices: 490415--490530 Score: 205
Period size: 52 Copynumber: 2.2 Consensus size: 52
490405 CACGAAACTT
490415 AAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAACC
* **
490467 AAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAACC
490519 AAAATCGCAACG
1 AAAATCGCAACG
490531 AGAGAATCGC
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (52 bp):
AAAATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:490506 original size:33 final size:33
Alignment explanation
Indices: 490469--490561 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
490459 GCGAAACCAA
*
490469 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
490502 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
490535 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
490562 TGCGATTTTG
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:490507 original size:14 final size:14
Alignment explanation
Indices: 490488--490542 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
490478 GCGAAATGAA
490488 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
490502 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
490521 AATCGCAACGAGAG
1 AATCGCAACGAGAG
490535 AATCGCAA
1 AATCGCAA
490543 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:490615 original size:33 final size:33
Alignment explanation
Indices: 490562--490653 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
490552 AAAATCGCAA
**
490562 TGCGATTTTGGTTTCGCGTTGCGATTCTATCAT
1 TGCGATTTTCATTTCGCGTTGCGATTCTATCAT
* * *
490595 TGCGATTTTCATTTCTCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTATCAT
490628 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTCATTTCGCGTTGCGATT
490654 TTAAGTTTCG
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTATCAT
Found at i:490618 original size:19 final size:19
Alignment explanation
Indices: 490594--490655 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
490584 GATTCTATCA
490594 TTGCGATTTTCATTTCTCG
1 TTGCGATTTTCATTTCTCG
490613 TTGCGA--TTC---TCTCG
1 TTGCGATTTTCATTTCTCG
*
490627 TTGCGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCTCG
490646 TTGCGATTTT
1 TTGCGATTTT
490656 AAGTTTCGTG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 11 0.30
16 3 0.08
17 3 0.08
19 20 0.54
ACGTcount: A:0.10, C:0.21, G:0.19, T:0.50
Consensus pattern (19 bp):
TTGCGATTTTCATTTCTCG
Found at i:490622 original size:12 final size:13
Alignment explanation
Indices: 490605--490635 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
490595 TGCGATTTTC
490605 ATTTCTCGTTGCG
1 ATTTCTCGTTGCG
490618 ATTCTCTCGTTGCG
1 ATT-TCTCGTTGCG
490632 ATTT
1 ATTT
490636 TCATTTCGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 4 0.24
14 13 0.76
ACGTcount: A:0.10, C:0.23, G:0.19, T:0.48
Consensus pattern (13 bp):
ATTTCTCGTTGCG
Found at i:490627 original size:14 final size:14
Alignment explanation
Indices: 490608--490634 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
490598 GATTTTCATT
490608 TCTCGTTGCGATTC
1 TCTCGTTGCGATTC
490622 TCTCGTTGCGATT
1 TCTCGTTGCGATT
490635 TTCATTTCGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.26, G:0.22, T:0.44
Consensus pattern (14 bp):
TCTCGTTGCGATTC
Found at i:490668 original size:20 final size:19
Alignment explanation
Indices: 490625--490671 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
490615 GCGATTCTCT
*
490625 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTAATTTCG
490644 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTAA-TTTCG
*
490664 TGTTGCGA
1 CGTTGCGA
490672 AAGTAAACTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 13 0.52
20 12 0.48
ACGTcount: A:0.13, C:0.17, G:0.26, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAATTTCG
Found at i:490835 original size:83 final size:86
Alignment explanation
Indices: 490719--490992 Score: 297
Period size: 94 Copynumber: 3.1 Consensus size: 86
490709 ATGGATTGCA
* **
490719 TTACTTCAACCAATAGACAAAACAAAGACAAATACTAACTTCAG-G-G-TA-TTAGTTTAGCAGA
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGTGAGATACACAGTTTAGCAGA
490780 ATTGGCAGCAACCGAACAAAT
66 ATTGGCAGCAACCGAACAAAT
*
490801 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACT-ATTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTT--CAGTG----AG-ATACACAGT
*
490865 TTAGCAGAATTGGCAGCAACCGAATAAAT
58 TTAGCAGAATTGGCAGCAACCGAACAAAT
*
490894 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCATAGTGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTC--AGTG----AG-ATACACAGT
* *
490959 TTAGCAGTATTGGCAGCAACCGAATAAAT
58 TTAGCAGAATTGGCAGCAACCGAACAAAT
490988 TTACT
1 TTACT
490993 AAGCAATCTA
Statistics
Matches: 168, Mismatches: 8, Indels: 20
0.86 0.04 0.10
Matches are distributed among these distances:
82 7 0.04
83 31 0.18
84 3 0.02
85 1 0.01
90 1 0.01
92 22 0.13
93 48 0.29
94 55 0.33
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.23
Consensus pattern (86 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGTGAGATACACAGTTTAGCAGA
ATTGGCAGCAACCGAACAAAT
Found at i:490928 original size:93 final size:93
Alignment explanation
Indices: 490769--490992 Score: 378
Period size: 94 Copynumber: 2.4 Consensus size: 93
490759 TCAGGGTATT
*
490769 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTAC-TTCAACCAAAAGACAAAACAAAGACAAA
* *
490834 TACT-ATTTCACAGTGTTAAAGAATACAC
65 TACTAACTTCACAGTGTTAAAGAATAAAC
490862 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAAC-AAAGACAAA
*
490927 TACTAACTTCATAGTGTTAAAGAATAAAC
65 TACTAACTTCACAGTGTTAAAGAATAAAC
*
490956 AGTTTAGCAGTATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
490993 AAGCAATCTA
Statistics
Matches: 124, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
92 19 0.15
93 48 0.39
94 57 0.46
ACGTcount: A:0.46, C:0.18, G:0.14, T:0.23
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACTTCAACCAAAAGACAAAACAAAGACAAAT
ACTAACTTCACAGTGTTAAAGAATAAAC
Found at i:495521 original size:27 final size:27
Alignment explanation
Indices: 495486--495552 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 27
495476 TGAACGAAAG
* *
495486 GACTGAAATACCCTTGAAA-TCTAAAAT
1 GACTAAAATACCCTT-AAACACTAAAAT
495513 GACTAAAATACCCTTAAACACTAAAAT
1 GACTAAAATACCCTTAAACACTAAAAT
* *
495540 AACGAAAATACCC
1 GACTAAAATACCC
495553 CAAGCTTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
26 3 0.09
27 32 0.91
ACGTcount: A:0.49, C:0.22, G:0.07, T:0.21
Consensus pattern (27 bp):
GACTAAAATACCCTTAAACACTAAAAT
Found at i:496695 original size:38 final size:39
Alignment explanation
Indices: 496663--496768 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 39
496653 TCTTACATAA
*
496663 GCTCATTTGCTTCGTGCATAGGGGAAAATCTTATCGCAT
1 GCTCATTTGCTTCGTGCATAGGGGAAAATCTTATCGTAT
* * *
496702 GCCCATTTTGCATCATGCATAGGGGAAAAT-TTATCGTAT
1 GCTCA-TTTGCTTCGTGCATAGGGGAAAATCTTATCGTAT
* *
496741 GCTCCTTTGCTTTGTGCATA-GGGAAAAT
1 GCTCATTTGCTTCGTGCATAGGGGAAAAT
496769 TTTCTAGACC
Statistics
Matches: 57, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
37 8 0.14
38 12 0.21
39 15 0.26
40 22 0.39
ACGTcount: A:0.25, C:0.19, G:0.23, T:0.34
Consensus pattern (39 bp):
GCTCATTTGCTTCGTGCATAGGGGAAAATCTTATCGTAT
Found at i:500141 original size:39 final size:39
Alignment explanation
Indices: 500092--500183 Score: 139
Period size: 39 Copynumber: 2.3 Consensus size: 39
500082 CCATCTTCCA
* *
500092 AGAACTCTTAAATTCATAATAAAATACTCTAACTCCCAAG
1 AGAA-TCTTAAATTCACAATAAAACACTCTAACTCCCAAG
*
500132 AGAATCTTAATTTCACAATAAAACACTCTAACTCCCAAG
1 AGAATCTTAAATTCACAATAAAACACTCTAACTCCCAAG
*
500171 AGACTCTTAAATT
1 AGAATCTTAAATT
500184 ACCCCATTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 43 0.91
40 4 0.09
ACGTcount: A:0.43, C:0.23, G:0.05, T:0.28
Consensus pattern (39 bp):
AGAATCTTAAATTCACAATAAAACACTCTAACTCCCAAG
Found at i:504227 original size:19 final size:20
Alignment explanation
Indices: 504191--504228 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
504181 CACGGAATGT
504191 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
504211 AAGATTACCAG-GGGAATA
1 AAGATTACCAGTGGGAATA
504229 GGATTACTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.45, C:0.11, G:0.26, T:0.18
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:505867 original size:32 final size:32
Alignment explanation
Indices: 505825--505955 Score: 118
Period size: 32 Copynumber: 4.1 Consensus size: 32
505815 TAAGGTGACA
* * * * *
505825 CTTGGGTAGGCTCTGAGGCCCTAAGTTATTTC
1 CTTGGGTAGGCTATAAGGCCCCAAGGTATTCC
*
505857 CTTGAGTAGGCTATAAGGCCCCAAGGTATTCC
1 CTTGGGTAGGCTATAAGGCCCCAAGGTATTCC
* * * ** *
505889 CTTGGGTAGGCTTTTAGGACCCAAGGTACACT
1 CTTGGGTAGGCTATAAGGCCCCAAGGTATTCC
* * * *
505921 CTTGGGTAGGCTCTCAGGCCCCAAGATAATCC
1 CTTGGGTAGGCTATAAGGCCCCAAGGTATTCC
505953 CTT
1 CTT
505956 AGGTTGGTTC
Statistics
Matches: 79, Mismatches: 20, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
32 79 1.00
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (32 bp):
CTTGGGTAGGCTATAAGGCCCCAAGGTATTCC
Found at i:507029 original size:98 final size:99
Alignment explanation
Indices: 506851--507032 Score: 294
Period size: 98 Copynumber: 1.8 Consensus size: 99
506841 CTGTAATAAG
* * *
506851 TATAACAAAGTATCTTATCTGTTATGACTCAATGTGAGCAAAAAAAGGGAATATTGTTAGTATTC
1 TATAACAAAGTATCTTATCTGTTATGAATCAATATGAGCAAAAAAAGGGAATATTGTCAGTATTC
506916 ATCCCAATTTTGGAAGTTATCATACGAGTAAAAT
66 ATCCCAATTTTGGAAGTTATCATACGAGTAAAAT
* * *
506950 TATACCAAAGTATCTTATTTGTTATGAATCAATATGTGC-AAAAAAGGGAATATTGTCAGTATTC
1 TATAACAAAGTATCTTATCTGTTATGAATCAATATGAGCAAAAAAAGGGAATATTGTCAGTATTC
*
507014 GTCCCAATTTTGGAAGTTA
66 ATCCCAATTTTGGAAGTTA
507033 CCCCGCACGT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
98 42 0.55
99 34 0.45
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (99 bp):
TATAACAAAGTATCTTATCTGTTATGAATCAATATGAGCAAAAAAAGGGAATATTGTCAGTATTC
ATCCCAATTTTGGAAGTTATCATACGAGTAAAAT
Found at i:508006 original size:16 final size:18
Alignment explanation
Indices: 507971--508007 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
507961 ACTATTATTG
507971 ATATTTTTAAGTAAATAT
1 ATATTTTTAAGTAAATAT
507989 ATATTTTTAAGTAAATAT
1 ATATTTTTAAGTAAATAT
508007 A
1 A
508008 CACTTGTCCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (18 bp):
ATATTTTTAAGTAAATAT
Found at i:510045 original size:30 final size:29
Alignment explanation
Indices: 510006--510086 Score: 71
Period size: 30 Copynumber: 2.9 Consensus size: 29
509996 ATTAAAACTA
*
510006 ATTTCTTATTTATATTTTAATAATATTTAT
1 ATTTATTATTTATATTTTAATAATA-TTAT
* *
510036 ATTTATTATTAATAATTTT-A-GA-ATTAT
1 ATTTATTATTTAT-ATTTTAATAATATTAT
* *
510063 -TTTATTATGTATATTCTAATAATA
1 ATTTATTATTTATATTTTAATAATA
510087 GTTTTTAAAC
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
25 4 0.10
26 11 0.28
27 5 0.12
28 2 0.05
29 1 0.03
30 12 0.30
31 5 0.12
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.58
Consensus pattern (29 bp):
ATTTATTATTTATATTTTAATAATATTAT
Found at i:510463 original size:8 final size:8
Alignment explanation
Indices: 510450--510476 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
510440 AGAATCATGT
510450 ATGCCATA
1 ATGCCATA
510458 ATGCCATA
1 ATGCCATA
510466 ATGCCATA
1 ATGCCATA
510474 ATG
1 ATG
510477 TAAGAATCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (8 bp):
ATGCCATA
Found at i:513870 original size:15 final size:15
Alignment explanation
Indices: 513850--513879 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
513840 TGTCAAAGTT
513850 AGTAGATCACGTGAA
1 AGTAGATCACGTGAA
513865 AGTAGATCACGTGAA
1 AGTAGATCACGTGAA
513880 CATATTGATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.27, T:0.20
Consensus pattern (15 bp):
AGTAGATCACGTGAA
Found at i:513963 original size:2 final size:2
Alignment explanation
Indices: 513952--513991 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
513942 AATTATAAAT
513952 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
513992 GTTTATTTAC
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:515518 original size:6 final size:6
Alignment explanation
Indices: 515516--515618 Score: 79
Period size: 6 Copynumber: 17.2 Consensus size: 6
515506 TTGTTTTATT
* *
515516 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTCATT- TTTTT- GTTTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTTA TTTTTA TTTTTA
* * * *
515563 TTTCTA -TTTTG TTTTTC TTTGTTA TTTTT- TGTTTTG TTTATTA TTTTTA
1 TTTTTA TTTTTA TTTTTA TTT-TTA TTTTTA T-TTTTA TTT-TTA TTTTTA
*
515612 TATTTA T
1 TTTTTA T
515619 GCATTTTCTA
Statistics
Matches: 79, Mismatches: 11, Indels: 14
0.76 0.11 0.13
Matches are distributed among these distances:
5 10 0.13
6 56 0.71
7 13 0.16
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.79
Consensus pattern (6 bp):
TTTTTA
Found at i:515525 original size:18 final size:17
Alignment explanation
Indices: 515499--515612 Score: 72
Period size: 18 Copynumber: 6.4 Consensus size: 17
515489 TTAATTTTTG
*
515499 TTTTGTTTTGTTTTATTT
1 TTTTATTTT-TTTTATTT
515517 TTTTATTTTTATTT-TTAT
1 TTTTATTTTT-TTTATT-T
*
515535 TTTTATTTTTATTCATTT
1 TTTTATTTTT-TTTATTT
*
515553 TTTTGTTTTATTTCTATTT
1 TTTTATTTT-TTT-TATTT
*
515572 TGTTT-TTCTTTGTTA-TT
1 T-TTTATT-TTTTTTATTT
* *
515589 TTTTGTTTTGTTTATTAT
1 TTTTATTTTTTTTATT-T
515607 TTTTAT
1 TTTTAT
515613 ATTTATGCAT
Statistics
Matches: 78, Mismatches: 8, Indels: 20
0.74 0.08 0.19
Matches are distributed among these distances:
16 8 0.10
17 9 0.12
18 44 0.56
19 12 0.15
20 5 0.06
ACGTcount: A:0.11, C:0.03, G:0.06, T:0.80
Consensus pattern (17 bp):
TTTTATTTTTTTTATTT
Found at i:518440 original size:95 final size:95
Alignment explanation
Indices: 518266--518525 Score: 317
Period size: 95 Copynumber: 2.7 Consensus size: 95
518256 TTATAATATT
* * * * * *
518266 TTAT-ATATACCATAAAGCTTGAGCTGTCCCTGTAAAGCAATTGGTTAAAAGCCCTGGCTTTATG
1 TTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
*
518330 GATAAGATTCTGCTAGCCTGATAAAGGTGA
66 GATAAGATTCAGCTAGCCTGATAAAGGTGA
* * **
518360 TTATAATATACAATAAAGCCTGAGTTGTCCCTCTAGAGCAATTAGTTAAACGCCCCAACTTTATG
1 TTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
*
518425 GATAATATTCAGCTAGCCTGATAAAGGTGA
66 GATAAGATTCAGCTAGCCTGATAAAGGTGA
* * * * *
518455 TTATAATAT-CTATACAATGATATTAAGTTATCCCTCTAGAGCAATTGGTTAAACTCCCCGGCTT
1 TTATAATATACAATA-AA-G--CTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTT
518519 TATGGAT
62 TATGGAT
518526 TCAGCTAGTC
Statistics
Matches: 140, Mismatches: 21, Indels: 6
0.84 0.13 0.04
Matches are distributed among these distances:
94 8 0.06
95 89 0.64
96 1 0.01
98 42 0.30
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (95 bp):
TTATAATATACAATAAAGCTTGAGTTGTCCCTCTAGAGCAATTGGTTAAACGCCCCGGCTTTATG
GATAAGATTCAGCTAGCCTGATAAAGGTGA
Found at i:524228 original size:33 final size:32
Alignment explanation
Indices: 524175--524246 Score: 74
Period size: 33 Copynumber: 2.2 Consensus size: 32
524165 AACAGTGGAG
* * * *
524175 GTTAGAG-CTCAGGACGGAAAGGGATCGTCGA
1 GTTAGAGACTCAGGACAGAAAGAGAACGCCGA
*
524206 GTTAGAGACGTCAGGGCAGAAAGAGAACGCCGA
1 GTTAGAGAC-TCAGGACAGAAAGAGAACGCCGA
*
524239 GTCAGAGA
1 GTTAGAGA
524247 GGAAGAGGCA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 7 0.21
32 1 0.03
33 25 0.76
ACGTcount: A:0.33, C:0.17, G:0.38, T:0.12
Consensus pattern (32 bp):
GTTAGAGACTCAGGACAGAAAGAGAACGCCGA
Found at i:529618 original size:51 final size:51
Alignment explanation
Indices: 529544--530143 Score: 787
Period size: 51 Copynumber: 11.8 Consensus size: 51
529534 TGACGTTATC
* * * *
529544 CGAGTTCCATACTTCC-TAGAGAAAGAGGGAGCGAACCC-TCTTGAAGATATC
1 CGAGTTCCATAC-TCCTTAAAGAAAGAAGGAGCGAACCCGT-TTGAAGATGTT
*
529595 CGAGTTCCATAATCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * * *
529646 TGAGTTCTATACTCCTTAAAGAGAGAAGGAGCAAACCCGTTTGAAGATGTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * * *
529697 CGAGTTCCATACTCCCTAGAGATAGAGGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* *
529748 CGAGTTCTATACTCCTTAAAGAGAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * * * * * *
529799 TGAGTTCTATACTCCTTAAAGAGAGAATGAGCGAACCCGTGTGAAGATATC
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* *
529850 CGAGTTCCATACTCCTTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* *
529901 CGAGTTCTATACTCCTTAAAGAGAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * * * * *
529952 CGAGTTCCATACTCCCTAGAGAAAGAGGGAGCGAACCCGCTTGAAGATATC
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
530003 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * *
530054 TGAGTTCTATACTCCTTAAAG--AG-AGGAGCGAACCCGTTTGAAGATTTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
* * * * *
530102 CGAGTTCTATACTCCCTGAAGAAAGAGGGACCGAACCCGTTT
1 CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTT
530144 CCAAAAGATT
Statistics
Matches: 482, Mismatches: 62, Indels: 10
0.87 0.11 0.02
Matches are distributed among these distances:
48 42 0.09
49 2 0.00
50 5 0.01
51 432 0.90
52 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (51 bp):
CGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTT
Found at i:530152 original size:153 final size:153
Alignment explanation
Indices: 529540--530143 Score: 896
Period size: 153 Copynumber: 4.0 Consensus size: 153
529530 ATGGTGACGT
* * *
529540 TATCCGAGTTCCATACTTCC-TAGAGAAAGAGGGAGCGAACCC-TCTTGAAGATATCCGAGTTCC
1 TATCCGAGTTCCATAC-TCCTTAGAGAAAGAGGGAGCGAACCCGT-TTGAAGATGTTCGAGTTCT
* * *
529603 ATAATCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTTGAGTTCTATACTCCTTAAAGA
64 ATACTCCTTAAAGAGAGAAGGAGCGAACCCGTTTGAAGATGTTTGAGTTCTATACTCCCTAAAGA
* *
529668 GAGAAGGAGCAAACCCGTTTGAAGA
129 AAGAAGGAGCGAACCCGTTTGAAGA
* * * *
529693 TGTTCGAGTTCCATACTCCCTAGAGATAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTAT
1 TATCCGAGTTCCATACTCCTTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTAT
* *
529758 ACTCCTTAAAGAGAGAAGGAGCGAACCCGTTTGAAGATGTTTGAGTTCTATACTCCTTAAAGAGA
66 ACTCCTTAAAGAGAGAAGGAGCGAACCCGTTTGAAGATGTTTGAGTTCTATACTCCCTAAAGAAA
* *
529823 GAATGAGCGAACCCGTGTGAAGA
131 GAAGGAGCGAACCCGTTTGAAGA
529846 TATCCGAGTTCCATACTCCTTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTAT
1 TATCCGAGTTCCATACTCCTTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTAT
* * *
529911 ACTCCTTAAAGAGAGAAGGAGCGAACCCGTTTGAAGATGTTCGAGTTCCATACTCCCTAGAGAAA
66 ACTCCTTAAAGAGAGAAGGAGCGAACCCGTTTGAAGATGTTTGAGTTCTATACTCCCTAAAGAAA
* *
529976 GAGGGAGCGAACCCGCTTGAAGA
131 GAAGGAGCGAACCCGTTTGAAGA
* * *
529999 TATCCGAGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTTTGAGTTCTAT
1 TATCCGAGTTCCATACTCCTTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTAT
*
530064 ACTCCTT-AA-AGAG-AGGAGCGAACCCGTTTGAAGAT-TTTCGAGTTCTATACTCCCTGAAGAA
66 ACTCCTTAAAGAGAGAAGGAGCGAACCCGTTTGAAGATGTTT-GAGTTCTATACTCCCTAAAGAA
* *
530125 AGAGGGACCGAACCCGTTT
130 AGAAGGAGCGAACCCGTTT
530144 CCAAAAGATT
Statistics
Matches: 415, Mismatches: 33, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
149 2 0.00
150 58 0.14
151 4 0.01
152 5 0.01
153 345 0.83
154 1 0.00
ACGTcount: A:0.31, C:0.20, G:0.25, T:0.24
Consensus pattern (153 bp):
TATCCGAGTTCCATACTCCTTAGAGAAAGAGGGAGCGAACCCGTTTGAAGATGTTCGAGTTCTAT
ACTCCTTAAAGAGAGAAGGAGCGAACCCGTTTGAAGATGTTTGAGTTCTATACTCCCTAAAGAAA
GAAGGAGCGAACCCGTTTGAAGA
Found at i:530274 original size:55 final size:54
Alignment explanation
Indices: 530148--530275 Score: 143
Period size: 55 Copynumber: 2.3 Consensus size: 54
530138 CCGTTTCCAA
* * *
530148 AAGATTGTTCGAGTCTCATACTCTATGAATAAATAGAGAGCAGACAAGATTATTG
1 AAGATTGTTCAAGTCTCATACTCTATGAAGAAATAGAGAGAAGACAAGATTA-TG
* * * *
530203 AAGATTGTTCATGTCTCATACTCTCTGAAGAAATAGGGAGAAGACACATATTCA-G
1 AAGATTGTTCAAGTCTCATACTCTATGAAGAAATAGAGAGAAGACA-AGATT-ATG
530258 AAGAGTT-TTCAAGTCTCA
1 AAGA-TTGTTCAAGTCTCA
530276 CTCACCCTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
55 55 0.89
56 6 0.10
57 1 0.02
ACGTcount: A:0.37, C:0.15, G:0.20, T:0.29
Consensus pattern (54 bp):
AAGATTGTTCAAGTCTCATACTCTATGAAGAAATAGAGAGAAGACAAGATTATG
Found at i:534180 original size:124 final size:124
Alignment explanation
Indices: 533475--534150 Score: 1025
Period size: 124 Copynumber: 5.5 Consensus size: 124
533465 TTCAGAACAA
* ** *
533475 ATCCAATTCATGGCTCAACTTCACAACGAAATGGCCATCCACGGTTTCAACTTCACGATAAAGGG
1 ATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACAAAGGG
* *
533540 AATCGTGCTCACCGGTAACATTCATCTTTAGATTGGATTTCAACTTCAAGATGAAGGAT
66 AATCGTGCTCACCAGTAACATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGAT
* *
533599 ATCCAATTTAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGATGAAA-G
1 ATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGA-CAAAGG
* *
533663 GTATCGTGCTCACCAGTAACATTCATCTTTAGATTGGATTT-ACACTTCACGAAGAAGGAT
65 GAATCGTGCTCACCAGTAACATTCATCTTTAGATTGGATTTCA-ACTTCACGATGAAGGAT
* * * *
533723 ATCCAATTCAAGCCTCAACTTCACAATGAATGGGCCATCCAGGGTTTCAACTTCACGACAAAGGG
1 ATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACAAAGGG
*
533788 AATCGTGCTCACCAGCAACATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGAT
66 AATCGTGCTCACCAGTAACATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGAT
* *
533847 ATCAAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACGAAGGG
1 ATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACAAAGGG
* *
533912 AATCGTGCTCACCAGTAACATTCATCTTTATATTGGATTTCAACTTCATGATGAAGGAT
66 AATCGTGCTCACCAGTAACATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGAT
* *
533971 ATCAAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTAAACTTCACGACAAAGGG
1 ATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACAAAGGG
** * * *
534036 AATCGTGC-CTACCAACAACATTCATCTTCAGATTGGATTTCAACTTCAGGACGAAGGAT
66 AATCGTGCTC-ACCAGTAACATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGAT
* * * * *
534095 ATCCAATTCAAGGCTCAACTGCACAATGAAGGGGCCCTCCATGATTTCAACTTCAC
1 ATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTCAC
534151 AACGAAGGAT
Statistics
Matches: 505, Mismatches: 42, Indels: 10
0.91 0.08 0.02
Matches are distributed among these distances:
123 5 0.01
124 496 0.98
125 4 0.01
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.26
Consensus pattern (124 bp):
ATCCAATTCAAGGCTCAACTTCACAACGAAGGGGCCATCCACGGTTTCAACTTCACGACAAAGGG
AATCGTGCTCACCAGTAACATTCATCTTTAGATTGGATTTCAACTTCACGATGAAGGAT
Found at i:534309 original size:84 final size:84
Alignment explanation
Indices: 534168--534560 Score: 441
Period size: 84 Copynumber: 4.7 Consensus size: 84
534158 GATATCGTGT
* *
534168 TCATTTGTAACATATCTCAAGGCAAGAA-GGTCTATTTGCCAACAAAAGACCTTCGAGTTCGACT
1 TCATTTGTAACATAACTCAAGGCAAGAAGGGT-TATCTGCCAACAAAAGACCTTCGAGTTCGACT
*
534232 ATGCTCAGCTCCAAGGCACA
65 ACGCTCAGCTCCAAGGCACA
** * * *
534252 TCATTTGTAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAATACCTTCGAGTTTGACTA
1 TCATTTGTAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* *
534317 CGCTAAGCTCCAAGGCATA
66 CGCTCAGCTCCAAGGCACA
* * * * * * *
534336 TCATTTGCAACATAGCTCAAGCCAAAAAGGGCTATTTGCC-ACAAAAGACCTTTGAGTTCGACTA
1 TCATTTGTAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
534400 CGCTCAGCTCCAAGGCACA
66 CGCTCAGCTCCAAGGCACA
* * * * * * * * *
534419 ACATTTGTAGCATAGCTGAAGGCGAGAAGGGTTATCTGCCAACAGACGACCTTCGGGTTCGATTA
1 TCATTTGTAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
* * * *
534484 CACTCAGCTCAAAAGCATA
66 CGCTCAGCTCCAAGGCACA
** * * *
534503 TCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAATAAAA-ACCTTCGAGTT
1 TCATTTGTAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTT
534561 TGATTCCATT
Statistics
Matches: 253, Mismatches: 54, Indels: 5
0.81 0.17 0.02
Matches are distributed among these distances:
83 79 0.31
84 171 0.68
85 3 0.01
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (84 bp):
TCATTTGTAACATAACTCAAGGCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACA
Found at i:534395 original size:167 final size:168
Alignment explanation
Indices: 534168--534560 Score: 493
Period size: 167 Copynumber: 2.4 Consensus size: 168
534158 GATATCGTGT
* * * * *
534168 TCATTTGTAACATATCTCAAGGCAAGAAGGTCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
1 TCATTTGCAACATAACTCAAGCCAAAAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* * * *
534233 TGCTCAGCTCCAAGGCACATCATTTGTAGTATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAA
66 CGCTCAGCTCCAAGGCACAACATTTGTAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAA
* * * * *
534298 ATACCTTCGAGTTTGACTACGCTAAGCTCCAAGGCATA
131 AGACCTTCGAGTTCGACTACACTAAGCTCAAAAGCATA
* *
534336 TCATTTGCAACATAGCTCAAGCCAAAAAGGGCTATTTGCC-ACAAAAGACCTTTGAGTTCGACTA
1 TCATTTGCAACATAACTCAAGCCAAAAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
* * *
534400 CGCTCAGCTCCAAGGCACAACATTTGTAGCATAGCTGAAGGCGAGAAGGGTTATCTGCCAACAGA
66 CGCTCAGCTCCAAGGCACAACATTTGTAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAA
* * * *
534465 CGACCTTCGGGTTCGATTACACTCAGCTCAAAAGCATA
131 AGACCTTCGAGTTCGACTACACTAAGCTCAAAAGCATA
* * * * * * * *
534503 TCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTGTCAATAAAA-ACCTTCGAGTT
1 TCATTTGCAACATAACTCAAGCCAAAAAGGGCTATTTGCCAACAAAAGACCTTCGAGTT
534561 TGATTCCATT
Statistics
Matches: 192, Mismatches: 32, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
167 152 0.79
168 40 0.21
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (168 bp):
TCATTTGCAACATAACTCAAGCCAAAAAGGGCTATTTGCCAACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCCAAGGCACAACATTTGTAGCATAACTCAAGGCGAGAAGGGTTATCTGCCAACAAA
AGACCTTCGAGTTCGACTACACTAAGCTCAAAAGCATA
Found at i:535116 original size:2 final size:2
Alignment explanation
Indices: 535105--535182 Score: 126
Period size: 2 Copynumber: 40.5 Consensus size: 2
535095 AATTATAAAT
535105 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
*
535146 TA TA TA TA TA T- TA TA AA T- 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 T
535183 TATTTACATG
Statistics
Matches: 71, Mismatches: 2, Indels: 6
0.90 0.03 0.08
Matches are distributed among these distances:
1 3 0.04
2 68 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:535899 original size:13 final size:13
Alignment explanation
Indices: 535881--535906 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
535871 AGATTTACTC
535881 CCTGAGGCTTGTT
1 CCTGAGGCTTGTT
535894 CCTGAGGCTTGTT
1 CCTGAGGCTTGTT
535907 TTCTTAAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.08, C:0.23, G:0.31, T:0.38
Consensus pattern (13 bp):
CCTGAGGCTTGTT
Found at i:538529 original size:7 final size:7
Alignment explanation
Indices: 538517--538542 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
538507 ACAAAAAAAG
538517 TGGTTGA
1 TGGTTGA
538524 TGGTTGA
1 TGGTTGA
538531 TGGTTGA
1 TGGTTGA
538538 TGGTT
1 TGGTT
538543 TTAATTTATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (7 bp):
TGGTTGA
Found at i:539756 original size:3 final size:3
Alignment explanation
Indices: 539748--539774 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
539738 GATAATTATT
539748 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
539775 ATATAATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:540209 original size:127 final size:127
Alignment explanation
Indices: 540046--540350 Score: 538
Period size: 127 Copynumber: 2.4 Consensus size: 127
540036 GAATTCTGGA
*
540046 CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTGAGTTGACACAACT
1 CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTGAGTTGACACAACT
*
540111 CCTTACATAATGAGGAGATCTGGTCATGTGATGACACTTCTCATTTGTTCATGAGTCTTGGC
66 CCTTACATAATGAGGAGATCTGGTCATGTGATGACACTGCTCATTTGTTCATGAGTCTTGGC
* * *
540173 CATCTAAAAGTGATAACACGGTTCCTATGTGATGAGGACAACTGGTTATCTGAGTTGACACAACT
1 CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTGAGTTGACACAACT
540238 CCTTACATAATGAGGAGATCTGGTCATGTGATGACACTGCTCATTTGTTCATGAGTCTTGGC
66 CCTTACATAATGAGGAGATCTGGTCATGTGATGACACTGCTCATTTGTTCATGAGTCTTGGC
** *
540300 CATCTATGGGTGATATCACGGTTCCTACGTGATGAGGACGACTGGTTATCT
1 CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCT
540351 ATAAGTGATA
Statistics
Matches: 167, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
127 167 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (127 bp):
CATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTGAGTTGACACAACT
CCTTACATAATGAGGAGATCTGGTCATGTGATGACACTGCTCATTTGTTCATGAGTCTTGGC
Found at i:540351 original size:46 final size:46
Alignment explanation
Indices: 540301--540434 Score: 125
Period size: 46 Copynumber: 3.0 Consensus size: 46
540291 AGTCTTGGCC
540301 ATCTATGGGTGATATCACGGTTCCTACGTGATGAGGACGACT-GGTT
1 ATCTATGGGTGATATCACGGTTCCTACGTGATGAGGACGA-TAGGTT
** * ** *
540347 ATCTATAAGTGATAACACAATTCCTACGTGATGAGGATGATAGGTT
1 ATCTATGGGTGATATCACGGTTCCTACGTGATGAGGACGATAGGTT
* * * *
540393 ATCAAAGGTTGAT-T--CGGCTCCTACGTGATGAGGA-GATCAGGT
1 ATCTATGGGTGATATCACGGTTCCTACGTGATGAGGACGAT-AGGT
540435 CGAATGATGA
Statistics
Matches: 71, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
42 3 0.04
43 21 0.30
45 1 0.01
46 46 0.65
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (46 bp):
ATCTATGGGTGATATCACGGTTCCTACGTGATGAGGACGATAGGTT
Found at i:541195 original size:91 final size:91
Alignment explanation
Indices: 541020--541188 Score: 268
Period size: 91 Copynumber: 1.9 Consensus size: 91
541010 CGTTTTTGGA
* * ** *
541020 TTGAACAAGTTCTTCTAATTATGAACTTCTTCTCTTTTGTTGGATGAGTTCTTCTCATTATGAAC
1 TTGAACAAGTTCTTATAATTATGAACTTCTTCTCTCTCATTGGATGAGTTCATCTCATTATGAAC
541085 TCTCCACTGGAAACATTGATGTAAGG
66 TCTCCACTGGAAACATTGATGTAAGG
*
541111 TTGAACAAGTTCTTATCATTATGAACTTCTTCT-TCCTCATTGGATGAGTTCATCTCATTATGAA
1 TTGAACAAGTTCTTATAATTATGAACTTCTTCTCT-CTCATTGGATGAGTTCATCTCATTATGAA
541175 CTCTCCACTGGAAA
65 CTCTCCACTGGAAA
541189 TGTTGATCCT
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
90 1 0.01
91 70 0.99
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.40
Consensus pattern (91 bp):
TTGAACAAGTTCTTATAATTATGAACTTCTTCTCTCTCATTGGATGAGTTCATCTCATTATGAAC
TCTCCACTGGAAACATTGATGTAAGG
Found at i:541505 original size:117 final size:118
Alignment explanation
Indices: 541299--541676 Score: 483
Period size: 117 Copynumber: 3.3 Consensus size: 118
541289 TAGATTTGAG
* * *
541299 TGAAAATGTTGATCCACCTCCTTCTGCGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATT
1 TGAAAACGTTGATCCACATCCTTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATT
*
541364 ATGAACTTCTTCTTCCTCGTTGGATGAGTTATTCTCACTATGAACTCTCCA-T
66 ATGAACTTCTTCTTCCTCATTGGATGAGTTATTCTCACTATGAACTCTCCACT
* * * * * *
541416 TGAAAACGTTGATTCATATCCTTCTATGATGGAATCAAACCAAAGTTGAACAAGTTCTTCTTATT
1 TGAAAACGTTGATCCACATCCTTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATT
* *
541481 ATGAACTTCTTCTTCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACT
66 ATGAACTTCTTCTTCCTCATTGGATGAGTTATTCTCACTATGAACTCTCCACT
*
541534 T-AAAACGTTGATCCACATCTTTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATT
1 TGAAAACGTTGATCCACATCCTTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATT
* *
541598 ATGAAC-T-TTC-TCCT--TTAGGACGAGATT-TTCTCATTATGAA--CT-CA-T
66 ATGAACTTCTTCTTCCTCATT-GGATGAG-TTATTCTCACTATGAACTCTCCACT
* * *
541643 ATGGAAATGTTGATCCACCTCCTTCTGTGATGGA
1 -TGAAAACGTTGATCCACATCCTTCTGTGATGGA
541677 TCATGATCTT
Statistics
Matches: 232, Mismatches: 24, Indels: 16
0.85 0.09 0.06
Matches are distributed among these distances:
109 1 0.00
110 3 0.01
111 29 0.12
112 2 0.01
113 19 0.08
114 6 0.03
115 3 0.01
116 1 0.00
117 166 0.72
118 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (118 bp):
TGAAAACGTTGATCCACATCCTTCTGTGATGGAATCGAACCAAGGTTGAACAAGTTCTTCTCATT
ATGAACTTCTTCTTCCTCATTGGATGAGTTATTCTCACTATGAACTCTCCACT
Found at i:544729 original size:25 final size:24
Alignment explanation
Indices: 544700--544778 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 24
544690 CTTGATTCAA
544700 TTTCTTTTCTTTTTTCATCTCTTCT
1 TTTCTTTTCTTTTTTC-TCTCTTCT
*
544725 TTTCTTTTATTTTTT-T-TCTTC-
1 TTTCTTTTCTTTTTTCTCTCTTCT
*
544746 TTTCTTTTCTTTTTT-TCTTCTTTAT
1 TTTCTTTTCTTTTTTCTC-TC-TTCT
544771 TTTCTTTT
1 TTTCTTTT
544779 TGTCTTTATT
Statistics
Matches: 47, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
21 15 0.32
22 5 0.11
23 3 0.06
24 2 0.04
25 22 0.47
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (24 bp):
TTTCTTTTCTTTTTTCTCTCTTCT
Found at i:544748 original size:17 final size:18
Alignment explanation
Indices: 544700--544800 Score: 72
Period size: 17 Copynumber: 5.7 Consensus size: 18
544690 CTTGATTCAA
544700 TTTCTTTTCTT-TTTTCA-
1 TTTCTTTTCTTCTTTT-AT
*
544717 TCTCTTCTT-TTCTTTTAT
1 TTTCTT-TTCTTCTTTTAT
*
544735 TTT-TTTTCTTC-TTTCT
1 TTTCTTTTCTTCTTTTAT
*
544751 TTTCTTTTTTTCTTCTTTAT
1 TTTCTTTTCTTC-T-TTTAT
544771 TTTCTTTT-TGTC-TTTAT
1 TTTCTTTTCT-TCTTTTAT
*
544788 TTTCTTTTTTTCT
1 TTTCTTTTCTTCT
544801 GATCGACGAG
Statistics
Matches: 68, Mismatches: 5, Indels: 21
0.72 0.05 0.22
Matches are distributed among these distances:
16 9 0.13
17 35 0.51
18 9 0.13
19 1 0.01
20 14 0.21
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (18 bp):
TTTCTTTTCTTCTTTTAT
Found at i:544760 original size:20 final size:20
Alignment explanation
Indices: 544700--544800 Score: 91
Period size: 20 Copynumber: 4.9 Consensus size: 20
544690 CTTGATTCAA
544700 TTTCTTTTCTTTTTTCATCTCTTC
1 TTTCTTTTC-TTTTT--T-TCTTC
*
544724 TTTTCTTTTATTTTTTTTCTTC
1 -TTTCTTTT-CTTTTTTTCTTC
544746 TTTCTTTTCTTTTTTTCTTC
1 TTTCTTTTCTTTTTTTCTTC
* *
544766 TTTATTTTC--TTTTT-GTC
1 TTTCTTTTCTTTTTTTCTTC
*
544783 TTTATTTTCTTTTTTTCT
1 TTTCTTTTCTTTTTTTCT
544801 GATCGACGAG
Statistics
Matches: 67, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
17 11 0.16
18 5 0.07
19 5 0.07
20 19 0.28
21 8 0.12
22 5 0.07
23 1 0.01
25 13 0.19
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (20 bp):
TTTCTTTTCTTTTTTTCTTC
Found at i:544767 original size:37 final size:37
Alignment explanation
Indices: 544730--544800 Score: 110
Period size: 37 Copynumber: 1.9 Consensus size: 37
544720 CTTCTTTTCT
*
544730 TTTATTTT-TTTTCT-TCTTTCTTTTCTTTTTTTCTTC
1 TTTATTTTCTTTT-TGTCTTTATTTTCTTTTTTTCTTC
544766 TTTATTTTCTTTTTGTCTTTATTTTCTTTTTTTCT
1 TTTATTTTCTTTTTGTCTTTATTTTCTTTTTTTCT
544801 GATCGACGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
36 9 0.28
37 23 0.72
ACGTcount: A:0.04, C:0.14, G:0.01, T:0.80
Consensus pattern (37 bp):
TTTATTTTCTTTTTGTCTTTATTTTCTTTTTTTCTTC
Found at i:544774 original size:12 final size:11
Alignment explanation
Indices: 544735--544800 Score: 55
Period size: 12 Copynumber: 5.8 Consensus size: 11
544725 TTTCTTTTAT
544735 TTTTTTTCTTC
1 TTTTTTTCTTC
*
544746 -TTTCTT-TTC
1 TTTTTTTCTTC
544755 TTTTTTTCTTC
1 TTTTTTTCTTC
*
544766 TTTATTTTCTTT
1 TTT-TTTTCTTC
*
544778 TTGTCTTTATTTTC
1 TT-T-TTT-TCTTC
544792 TTTTTTTCT
1 TTTTTTTCT
544801 GATCGACGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 10
0.72 0.12 0.17
Matches are distributed among these distances:
9 3 0.07
10 10 0.23
11 8 0.19
12 12 0.28
13 5 0.12
14 5 0.12
ACGTcount: A:0.03, C:0.15, G:0.02, T:0.80
Consensus pattern (11 bp):
TTTTTTTCTTC
Found at i:553941 original size:18 final size:18
Alignment explanation
Indices: 553918--553957 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
553908 GGAGGGTTTT
553918 TTAATCAAATTAAATGAA
1 TTAATCAAATTAAATGAA
553936 TTAATCAAATTAAATGAA
1 TTAATCAAATTAAATGAA
553954 TTAA
1 TTAA
553958 CCGAAAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (18 bp):
TTAATCAAATTAAATGAA
Done.