Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000761.1 Hibiscus syriacus cultivar Beakdansim tig00001478_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: 5609167
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 14 of 23
Found at i:3471383 original size:21 final size:21
Alignment explanation
Indices: 3471322--3471400 Score: 94
Period size: 20 Copynumber: 3.9 Consensus size: 21
3471312 TTCTAAACTT
3471322 AAAATCGCAAC-ATGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
3471342 AAAATCGCAAC-ACGA-AAATG
1 AAAATCGCAACGA-GAGAAATG
**
3471362 ATTATCGCAACGAGAGAAATG
1 AAAATCGCAACGAGAGAAATG
3471383 AAAATCGCAACGAGAGAA
1 AAAATCGCAACGAGAGAA
3471401 TCGCAACGCG
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
20 30 0.58
21 22 0.42
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (21 bp):
AAAATCGCAACGAGAGAAATG
Found at i:3471404 original size:14 final size:14
Alignment explanation
Indices: 3471385--3471441 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
3471375 GAGAAATGAA
3471385 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
3471399 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
3471418 AATCGCAACGAGAG
1 AATCGCAACGAGAG
3471432 AATCGCAACG
1 AATCGCAACG
3471442 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:3471418 original size:33 final size:33
Alignment explanation
Indices: 3471377--3471457 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
3471367 CGCAACGAGA
3471377 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
3471410 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
3471443 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
3471458 GTGCGATTTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.47, C:0.22, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:3471475 original size:19 final size:19
Alignment explanation
Indices: 3471459--3471545 Score: 103
Period size: 19 Copynumber: 4.8 Consensus size: 19
3471449 AAAATCGCAG
3471459 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
3471478 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
*
3471492 TGCGATTTTAATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
3471511 TGCGATTTTCATTCTCTCGT
1 TGCGATTTTCATT-TCGCGT
3471531 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
3471546 AACCAAAAGA
Statistics
Matches: 57, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
14 10 0.18
16 2 0.04
17 3 0.05
19 24 0.42
20 18 0.32
ACGTcount: A:0.11, C:0.22, G:0.18, T:0.48
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:3471533 original size:20 final size:20
Alignment explanation
Indices: 3471482--3471543 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
3471472 TCGCGTTGCG
*
3471482 ATTCTCTCGTTGCGATTTTA
1 ATTCTCTCGTTGCGATTTTC
*
3471502 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
3471521 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
3471541 ATT
1 ATT
3471544 TCAACCAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 17 0.45
20 21 0.55
ACGTcount: A:0.13, C:0.21, G:0.16, T:0.50
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:3473362 original size:94 final size:94
Alignment explanation
Indices: 3473201--3473580 Score: 620
Period size: 94 Copynumber: 4.1 Consensus size: 94
3473191 TAGATTGCTT
* * *
3473201 AGTAAATTTATTCGGTTGCTGTCAATACTGCTAAACTGTTTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
3473266 ATTTGTTTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTG-TCTTTGTTTTGTCTTTTGGTTGAA
* *
3473295 AGTAAATTTATTCGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAATTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3473360 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
3473389 AGTAAATTTGTTCGGTTGCTGCCAATGCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3473454 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* * * * *
3473483 AGTAAATTTGTTCGGTTGTTGTCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
3473548 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
3473576 AGTAA
1 AGTAA
3473581 TGCAATCTAT
Statistics
Matches: 270, Mismatches: 15, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
93 27 0.10
94 243 0.90
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.48
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:3473705 original size:33 final size:33
Alignment explanation
Indices: 3473668--3473785 Score: 119
Period size: 33 Copynumber: 3.4 Consensus size: 33
3473658 AAAAATGACT
* * *
3473668 ATCGCAACGAGAGAATCGTAACGAGAAATGAAA
1 ATCGCAACGAGAAAATCGCAACGCGAAATGAAA
3473701 ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAAAATCGCAACGCGAAATGAAA
* * **
3473739 ATCGCAATGACAAAATCGCAACGCGAAACCAAA
1 ATCGCAACGAGAAAATCGCAACGCGAAATGAAA
*
3473772 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
3473786 CTATAATCGC
Statistics
Matches: 70, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
33 38 0.54
34 1 0.01
35 2 0.03
36 1 0.01
37 1 0.01
38 27 0.39
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.10
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAACGCGAAATGAAA
Found at i:3473709 original size:19 final size:19
Alignment explanation
Indices: 3473681--3473785 Score: 121
Period size: 19 Copynumber: 5.8 Consensus size: 19
3473671 GCAACGAGAG
* *
3473681 AATCGTAACGAGAAATGAA
1 AATCGCAACGCGAAATGAA
3473700 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
3473719 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
* *
3473738 AATCGCAA--TG--A-CAA
1 AATCGCAACGCGAAATGAA
**
3473752 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAATGAA
3473771 AATCGCAACGCGAAA
1 AATCGCAACGCGAAA
3473786 CTATAATCGC
Statistics
Matches: 76, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 62 0.82
ACGTcount: A:0.49, C:0.22, G:0.19, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:3473724 original size:52 final size:51
Alignment explanation
Indices: 3473668--3473785 Score: 121
Period size: 52 Copynumber: 2.3 Consensus size: 51
3473658 AAAAATGACT
* * **
3473668 ATCGCAACGAGAGAATCGTAACGAGAAATG-AAAATCGCAACGCGAAATGAAA
1 ATCGCAACGAGA-AAT-GAAAAGAGAAATGAAAAATCGCAACGCGAAACCAAA
* ** *
3473720 ATCGCAACGCGAAATGAAAATCGCAATGACAAAATCGCAACGCGAAACCAAA
1 ATCGCAACGAGAAATGAAAAGAGAAATGA-AAAATCGCAACGCGAAACCAAA
*
3473772 ATCGCAACGCGAAA
1 ATCGCAACGAGAAA
3473786 CTATAATCGC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
50 8 0.14
51 3 0.05
52 45 0.80
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.10
Consensus pattern (51 bp):
ATCGCAACGAGAAATGAAAAGAGAAATGAAAAATCGCAACGCGAAACCAAA
Found at i:3473793 original size:19 final size:19
Alignment explanation
Indices: 3473698--3473795 Score: 102
Period size: 19 Copynumber: 5.4 Consensus size: 19
3473688 ACGAGAAATG
3473698 AAAATCGCAACGCGAAA-T
1 AAAATCGCAACGCGAAACT
3473716 GAAAATCGCAACGCGAAA-T
1 -AAAATCGCAACGCGAAACT
*
3473735 GAAAATCGCAA--TG--AC-
1 -AAAATCGCAACGCGAAACT
*
3473750 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACT
3473769 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
3473788 ATAATCGC
1 AAAATCGC
3473796 GTTGCGATTT
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 1 0.01
17 1 0.01
18 2 0.03
19 54 0.78
ACGTcount: A:0.47, C:0.24, G:0.17, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:3473860 original size:20 final size:20
Alignment explanation
Indices: 3473844--3473916 Score: 146
Period size: 20 Copynumber: 3.6 Consensus size: 20
3473834 AATAGTCAAA
3473844 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
3473864 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
3473884 TTCGCATTGCGATAGTCATT
1 TTCGCATTGCGATAGTCATT
3473904 TTCGCATTGCGAT
1 TTCGCATTGCGAT
3473917 TTTAAGTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.40
Consensus pattern (20 bp):
TTCGCATTGCGATAGTCATT
Found at i:3473890 original size:40 final size:40
Alignment explanation
Indices: 3473835--3473916 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
3473825 TCTCGTTACA
3473835 ATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCG
1 ATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCG
**
3473875 ATAGTCATTTTCGCATTGCGATAGTCATTTTCGCATTGCG
1 ATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCG
3473915 AT
1 AT
3473917 TTTAAGTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (40 bp):
ATAGTCAAATTCGCATTGCGATAGTCATTTTCGCATTGCG
Found at i:3475844 original size:14 final size:14
Alignment explanation
Indices: 3475825--3475860 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3475815 ATTGTTTAAT
3475825 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
3475839 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
3475853 TGATTTGT
1 TGATTTGT
3475861 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3475999 original size:33 final size:34
Alignment explanation
Indices: 3475962--3476037 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
3475952 AAAACAGACT
3475962 ATCGCAACGAGAAAATCGCAATGCG-AAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATGAAA
**
3475995 ATCGCAACGAGTGAATCGCAATGCGAAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAAATGAAA
3476029 ATCGCAACG
1 ATCGCAACG
3476038 CAAAACTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 23 0.57
34 17 0.43
ACGTcount: A:0.45, C:0.20, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAACGAGAAAATCGCAATGCGAAAATGAAA
Found at i:3476068 original size:19 final size:19
Alignment explanation
Indices: 3476046--3476133 Score: 105
Period size: 19 Copynumber: 4.8 Consensus size: 19
3476036 CGCAAAACTA
*
3476046 ATTTCGCGTTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
*
3476065 ATTTTCTCATTGCGA--TTC
1 A-TTTCGCATTGCGATTTTC
*
3476083 A-CTCG--TTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
3476099 ATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTTTC
3476118 ATTTCGCATTGCGATT
1 ATTTCGCATTGCGATT
3476134 CTCTCGTTGT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
14 6 0.10
16 6 0.10
17 3 0.05
18 4 0.07
19 28 0.48
20 11 0.19
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.47
Consensus pattern (19 bp):
ATTTCGCATTGCGATTTTC
Found at i:3476339 original size:20 final size:20
Alignment explanation
Indices: 3476310--3476499 Score: 161
Period size: 20 Copynumber: 9.4 Consensus size: 20
3476300 CAAAATCTCG
3476310 TTGCGATTTACAG-ATTCGCA
1 TTGCGATTTAC-GTATTCGCA
*
3476330 TTGTGATTTACGTATTCGCA
1 TTGCGATTTACGTATTCGCA
* *
3476350 TTGCGATTTATGTATTTGCA
1 TTGCGATTTACGTATTCGCA
* *
3476370 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGTATTCGCA
* * *
3476390 TTGCAATTTACAG-ATACGCG
1 TTGCGATTTAC-GTATTCGCA
* *
3476410 TTGCGATTTACGTATTCTCG
1 TTGCGATTTACGTATTCGCA
* * *
3476430 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATTCGCA
**
3476450 TTGCGATTTTACGTATT-GTTG
1 TTGCGA-TTTACGTATTCG-CA
* * *
3476471 TTGCGATTTACGGATACGCG
1 TTGCGATTTACGTATTCGCA
3476491 TTGCGATTT
1 TTGCGATTT
3476500 TACGGATACT
Statistics
Matches: 141, Mismatches: 23, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
19 2 0.01
20 122 0.87
21 17 0.12
ACGTcount: A:0.19, C:0.17, G:0.23, T:0.41
Consensus pattern (20 bp):
TTGCGATTTACGTATTCGCA
Found at i:3476371 original size:40 final size:40
Alignment explanation
Indices: 3476305--3476559 Score: 235
Period size: 40 Copynumber: 6.3 Consensus size: 40
3476295 ATAGTCAAAA
*
3476305 TCTCGTTGCGATTTACAGATTCGCATTGTGATTTACGTAT
1 TCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTAT
* * * *
3476345 TCGCATTGCGATTTA-TGTATTTGCATTGCGATTTACGTAT
1 TCTCGTTGCGATTTACAG-ATTCGCATTGCGATTTACGTAT
* * *
3476385 TCTCGTTGCAATTTACAGATACGCGTTGCGATTTACGTAT
1 TCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTAT
* * *
3476425 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
1 TCTCGTTGCGATTTACAGATTCGCATTGCGA-TTTACGTAT
* * * * * *
3476466 TGTTGTTGCGATTTACGGATACGCGTTGCGATTTTACGGAT
1 TCTCGTTGCGATTTACAGATTCGCATTGCGA-TTTACGTAT
* * * * ** *
3476507 ACTCGTTGCGATAGT-CAGAATCGCGTTGCGATTTATATGT
1 TCTCGTTGCGAT-TTACAGATTCGCATTGCGATTTACGTAT
*
3476547 TCGCGTTGCGATT
1 TCTCGTTGCGATT
3476560 CTGAAAAATC
Statistics
Matches: 180, Mismatches: 31, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 108 0.60
41 70 0.39
42 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.40
Consensus pattern (40 bp):
TCTCGTTGCGATTTACAGATTCGCATTGCGATTTACGTAT
Found at i:3476535 original size:61 final size:60
Alignment explanation
Indices: 3476406--3476541 Score: 157
Period size: 61 Copynumber: 2.2 Consensus size: 60
3476396 TTTACAGATA
* * * * * *
3476406 CGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATGTCACGAAT
* * *
3476466 TGTTGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATACTCGTTGCGATAGTCA-GAAT
1 CG-CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGGATACGCGTTGCGAT-GTCACGAAT
3476528 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
3476542 TATGTTCGCG
Statistics
Matches: 62, Mismatches: 11, Indels: 5
0.79 0.14 0.06
Matches are distributed among these distances:
60 1 0.02
61 35 0.56
62 24 0.39
63 2 0.03
ACGTcount: A:0.18, C:0.18, G:0.26, T:0.37
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATGTCACGAAT
Found at i:3476540 original size:41 final size:41
Alignment explanation
Indices: 3476305--3476518 Score: 254
Period size: 40 Copynumber: 5.3 Consensus size: 41
3476295 ATAGTCAAAA
* * * *
3476305 TCTCGTTGCGATTTACAGATTCGCATTGTGA-TTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
* * * * ** *
3476345 TCGCATTGCGATTTATGTATTTGCATTGCGA-TTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
* *
3476385 TCTCGTTGCAATTTACAGATACGCGTTGCGA-TTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
3476425 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
* * *
3476466 TGTTGTTGCGATTTACGGATACGCGTTGCGATTTTACGGAT
1 TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
*
3476507 ACTCGTTGCGAT
1 TCTCGTTGCGAT
3476519 AGTCAGAATC
Statistics
Matches: 149, Mismatches: 24, Indels: 1
0.86 0.14 0.01
Matches are distributed among these distances:
40 93 0.62
41 56 0.38
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.40
Consensus pattern (41 bp):
TCTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGTAT
Found at i:3476658 original size:20 final size:20
Alignment explanation
Indices: 3476608--3476662 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
3476598 GATTCTTCAT
3476608 AATCGCGTTGCGATTCTGAG
1 AATCGCGTTGCGATTCTGAG
* **
3476628 AATTGATTTGCGATTCT-AG
1 AATCGCGTTGCGATTCTGAG
3476647 AGATCGCGTTGCGATT
1 A-ATCGCGTTGCGATT
3476663 TTTATTTCGC
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.35
Consensus pattern (20 bp):
AATCGCGTTGCGATTCTGAG
Found at i:3476785 original size:13 final size:13
Alignment explanation
Indices: 3476763--3476807 Score: 83
Period size: 13 Copynumber: 3.5 Consensus size: 13
3476753 GGCGATTTTC
3476763 TCTT-AAATAATT
1 TCTTCAAATAATT
3476775 TCTTCAAATAATT
1 TCTTCAAATAATT
3476788 TCTTCAAATAATT
1 TCTTCAAATAATT
3476801 TCTTCAA
1 TCTTCAA
3476808 GCTCTTCAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
12 4 0.12
13 28 0.88
ACGTcount: A:0.38, C:0.16, G:0.00, T:0.47
Consensus pattern (13 bp):
TCTTCAAATAATT
Found at i:3485366 original size:35 final size:35
Alignment explanation
Indices: 3485327--3485394 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
3485317 ATAAACCCCC
*
3485327 AAAATACTACTGTTAGGAATGACTTATTACCCCAT
1 AAAATACTACTGTTAGAAATGACTTATTACCCCAT
*
3485362 AAAATATTACTGTTAGAAATGACTTATTACCCC
1 AAAATACTACTGTTAGAAATGACTTATTACCCC
3485395 TTACTAAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.38, C:0.19, G:0.10, T:0.32
Consensus pattern (35 bp):
AAAATACTACTGTTAGAAATGACTTATTACCCCAT
Found at i:3492261 original size:21 final size:22
Alignment explanation
Indices: 3492236--3492278 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
3492226 GATTTCAAAA
* *
3492236 TTTAAAATCGAAAAT-GATTTT
1 TTTAAAAACAAAAATAGATTTT
3492257 TTTAAAAACAAAAATAGATTTT
1 TTTAAAAACAAAAATAGATTTT
3492279 GAAAGCTAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.40
Consensus pattern (22 bp):
TTTAAAAACAAAAATAGATTTT
Found at i:3492982 original size:57 final size:56
Alignment explanation
Indices: 3492876--3492982 Score: 144
Period size: 57 Copynumber: 1.9 Consensus size: 56
3492866 TTAAAATTGG
* *
3492876 TTTTAATGAAAATTATATCTATCTAAAAATTGATATCAACTTTTCAAATTCTTTGA
1 TTTTAATGAAAATGATATCTATCTAAAAATTGATATCAAATTTTCAAATTCTTTGA
* * *
3492932 TTTTAAATGCAAATGATATCTCTCTAACAATTGATATCAAAATTTT-AAATT
1 TTTT-AATGAAAATGATATCTATCTAAAAATTGATATC-AAATTTTCAAATT
3492983 TTTTTAACTA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
56 4 0.09
57 34 0.77
58 6 0.14
ACGTcount: A:0.40, C:0.11, G:0.06, T:0.43
Consensus pattern (56 bp):
TTTTAATGAAAATGATATCTATCTAAAAATTGATATCAAATTTTCAAATTCTTTGA
Found at i:3493456 original size:18 final size:18
Alignment explanation
Indices: 3493433--3493490 Score: 80
Period size: 18 Copynumber: 3.1 Consensus size: 18
3493423 CAACAATTGG
3493433 TAACAATTGGTATCTTTT
1 TAACAATTGGTATCTTTT
3493451 TAACAATTGGTATCCTTTTGT
1 TAACAATTGGTAT-C-TTT-T
*
3493472 TAACAATTAGTATCTTTT
1 TAACAATTGGTATCTTTT
3493490 T
1 T
3493491 CATTAAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
18 15 0.42
19 4 0.11
20 4 0.11
21 13 0.36
ACGTcount: A:0.28, C:0.12, G:0.10, T:0.50
Consensus pattern (18 bp):
TAACAATTGGTATCTTTT
Found at i:3494269 original size:33 final size:34
Alignment explanation
Indices: 3494225--3494295 Score: 99
Period size: 33 Copynumber: 2.1 Consensus size: 34
3494215 CATTGTAAAG
* *
3494225 GGGAAATGTTCTAGCTGATCCCGTG-AAAAACTA
1 GGGAAAGGTTCTAGCTGAGCCCGTGAAAAAACTA
* *
3494258 GGGAAAGGTTCTAGTTTAGCCCGTGAAAAAACTA
1 GGGAAAGGTTCTAGCTGAGCCCGTGAAAAAACTA
3494292 GGGA
1 GGGA
3494296 GTTTGTAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
33 21 0.64
34 12 0.36
ACGTcount: A:0.34, C:0.15, G:0.28, T:0.23
Consensus pattern (34 bp):
GGGAAAGGTTCTAGCTGAGCCCGTGAAAAAACTA
Found at i:3498589 original size:15 final size:15
Alignment explanation
Indices: 3498569--3498656 Score: 51
Period size: 15 Copynumber: 5.9 Consensus size: 15
3498559 ATTGAAAAAA
3498569 ATATATTATATATAT
1 ATATATTATATATAT
*
3498584 ATATATAATATA-AGT
1 ATATATTATATATA-T
* *
3498599 TTATA-TATAAACTAT
1 ATATATTATATA-TAT
*
3498614 ATATA-TAAACTATAT
1 ATATATTATA-TATAT
* *
3498629 TTATATTATAAACTAT
1 ATATATTATATA-TAT
3498645 ATA-ATTAT-TATA
1 ATATATTATATATA
3498657 AGTTATATAT
Statistics
Matches: 55, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
13 2 0.04
14 6 0.11
15 37 0.67
16 10 0.18
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (15 bp):
ATATATTATATATAT
Found at i:3498615 original size:30 final size:30
Alignment explanation
Indices: 3498581--3498671 Score: 107
Period size: 31 Copynumber: 3.0 Consensus size: 30
3498571 ATATTATATA
3498581 TATATATATAATATAAGTTTATATATAAAC
1 TATATATATAATATAAGTTTATATATAAAC
3498611 TATATATATAA-ACTATA-TTTATATTATAAAC
1 TATATATATAATA-TA-AGTTTATA-TATAAAC
*
3498642 TATATA-ATTATTATAAGTTATATATATAAA
1 TATATATA-TAATATAAGTT-TATATATAAA
3498672 TTATGTTTAT
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
29 1 0.02
30 21 0.40
31 26 0.49
32 5 0.09
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.45
Consensus pattern (30 bp):
TATATATATAATATAAGTTTATATATAAAC
Found at i:3498653 original size:18 final size:18
Alignment explanation
Indices: 3498611--3498669 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
3498601 ATATATAAAC
3498611 TATATA-TATAAACTATA
1 TATATATTATAAACTATA
*
3498628 TTTATATTATAAACTATA
1 TATATATTATAAACTATA
**
3498646 TA-ATTATTATAAGTTATA
1 TATA-TATTATAAACTATA
3498664 TATATA
1 TATATA
3498670 AATTATGTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
17 6 0.17
18 28 0.80
19 1 0.03
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (18 bp):
TATATATTATAAACTATA
Found at i:3498727 original size:13 final size:13
Alignment explanation
Indices: 3498575--3498745 Score: 97
Period size: 13 Copynumber: 13.3 Consensus size: 13
3498565 AAAAATATAT
*
3498575 TATATATATATA-
1 TATATATATAAAC
*
3498587 TATA-ATAT-AAG
1 TATATATATAAAC
*
3498598 TTTATATATAAAC
1 TATATATATAAAC
3498611 TATATATATAAAC
1 TATATATATAAAC
* *
3498624 TATAT-T-TATAT
1 TATATATATAAAC
*
3498635 TATAAACTATATAA-
1 TATATA-TATA-AAC
**
3498649 T-TAT-TATAAGT
1 TATATATATAAAC
*
3498660 TATATATATAAAT
1 TATATATATAAAC
* *
3498673 TATGTTTATATGAAC
1 TA--TATATATAAAC
*
3498688 TATATATATAAAT
1 TATATATATAAAC
** *
3498701 TATATAGGTTAAC
1 TATATATATAAAC
3498714 TATATATATAAAC
1 TATATATATAAAC
3498727 TATATATGTATAAAC
1 TATATA--TATAAAC
3498742 TATA
1 TATA
3498746 AAAAAAATAT
Statistics
Matches: 121, Mismatches: 24, Indels: 25
0.71 0.14 0.15
Matches are distributed among these distances:
10 2 0.02
11 19 0.16
12 12 0.10
13 63 0.52
14 3 0.02
15 22 0.18
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.44
Consensus pattern (13 bp):
TATATATATAAAC
Found at i:3498781 original size:25 final size:25
Alignment explanation
Indices: 3498747--3498798 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
3498737 TAAACTATAA
3498747 AAAAAATATATAGTTTATAAACCAT
1 AAAAAATATATAGTTTATAAACCAT
* *
3498772 AAAAAGTATATAGTTTATAAACTAT
1 AAAAAATATATAGTTTATAAACCAT
3498797 AA
1 AA
3498799 TTTATATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (25 bp):
AAAAAATATATAGTTTATAAACCAT
Found at i:3498833 original size:29 final size:29
Alignment explanation
Indices: 3498779--3498834 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
3498769 CATAAAAAGT
* *
3498779 ATATAGTTTATAAACTATAATTTATATTA
1 ATATAGTATATAAACTATAATATATATTA
*
3498808 ATATAGTATATATA-TATATATATATAT
1 ATATAGTATATAAACTATA-ATATATAT
3498835 ATTATTCAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (29 bp):
ATATAGTATATAAACTATAATATATATTA
Found at i:3498929 original size:19 final size:19
Alignment explanation
Indices: 3498907--3499013 Score: 100
Period size: 19 Copynumber: 5.8 Consensus size: 19
3498897 TTTATTTTAT
3498907 TTGA-AAATTTAGAGGAAAA
1 TTGAGAAATTTAGA-GAAAA
* *
3498926 TTGAGAAATTTTGAGAATA
1 TTGAGAAATTTAGAGAAAA
*
3498945 TAGAGAAA-TT-GAGAAAA
1 TTGAGAAATTTAGAGAAAA
*
3498962 TTTGAG-AATATAGAG-AAA
1 -TTGAGAAATTTAGAGAAAA
*
3498980 TTGAG-AATTTAGAGGGAAA
1 TTGAGAAATTTAGA-GAAAA
3498999 TTGAGAAATTTAGAG
1 TTGAGAAATTTAGAG
3499014 GGAATAAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
17 20 0.27
18 11 0.15
19 27 0.36
20 16 0.22
ACGTcount: A:0.48, C:0.00, G:0.24, T:0.28
Consensus pattern (19 bp):
TTGAGAAATTTAGAGAAAA
Found at i:3498959 original size:27 final size:27
Alignment explanation
Indices: 3498905--3498986 Score: 119
Period size: 27 Copynumber: 3.0 Consensus size: 27
3498895 TTTTTATTTT
* *
3498905 ATTTGAAAATTTAGAGGAAAATTGAGAAA
1 ATTTGAGAATATAGA-G-AAATTGAGAAA
*
3498934 TTTTGAGAATATAGAGAAATTGAGAAA
1 ATTTGAGAATATAGAGAAATTGAGAAA
3498961 ATTTGAGAATATAGAGAAATTGAGAA
1 ATTTGAGAATATAGAGAAATTGAGAA
3498987 TTTAGAGGGA
Statistics
Matches: 49, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
27 36 0.73
28 1 0.02
29 12 0.24
ACGTcount: A:0.50, C:0.00, G:0.22, T:0.28
Consensus pattern (27 bp):
ATTTGAGAATATAGAGAAATTGAGAAA
Found at i:3498981 original size:46 final size:47
Alignment explanation
Indices: 3498909--3499014 Score: 130
Period size: 46 Copynumber: 2.3 Consensus size: 47
3498899 TATTTTATTT
*
3498909 GAAAATTTAGAGGAAAATTGAGAAATTTTGAGAATATAGA-GAAATTGA
1 GAAAATTTAGAGGAAAATAGAGAAA--TTGAGAATATAGAGGAAATTGA
* *
3498957 GAAAATTT-GA-GAATATAGAGAAATTGAGAATTTAGAGGGAAATTGA
1 GAAAATTTAGAGGAAAATAGAGAAATTGAGAATATAGA-GGAAATTGA
3499003 G-AAATTTAGAGG
1 GAAAATTTAGAGG
3499015 GAATAAAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
44 12 0.24
45 6 0.12
46 22 0.43
47 3 0.06
48 8 0.16
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.26
Consensus pattern (47 bp):
GAAAATTTAGAGGAAAATAGAGAAATTGAGAATATAGAGGAAATTGA
Found at i:3499046 original size:19 final size:19
Alignment explanation
Indices: 3498907--3499046 Score: 87
Period size: 19 Copynumber: 7.5 Consensus size: 19
3498897 TTTATTTTAT
* *
3498907 TTGAAAATTTAGAGGAAAA
1 TTGAGAATTTAGAGGGAAA
*
3498926 TTGAGAAATTTTGA--GAATA
1 TTGAG-AATTTAGAGGGAA-A
* * *
3498945 TAGAGAAATT-GA-GAAAA
1 TTGAGAATTTAGAGGGAAA
*
3498962 TTTGAGAATATAGA--GAAA
1 -TTGAGAATTTAGAGGGAAA
3498980 TTGAGAATTTAGAGGGAAA
1 TTGAGAATTTAGAGGGAAA
3498999 TTGAGAAATTTAGAGGG-AA
1 TTGAG-AATTTAGAGGGAAA
** * *
3499018 TAAAAAAATTTGGAGGGAAA
1 T-TGAGAATTTAGAGGGAAA
3499038 TTGAGAATT
1 TTGAGAATT
3499047 AAGATTTTAT
Statistics
Matches: 93, Mismatches: 18, Indels: 20
0.71 0.14 0.15
Matches are distributed among these distances:
17 15 0.16
18 18 0.19
19 38 0.41
20 22 0.24
ACGTcount: A:0.48, C:0.00, G:0.25, T:0.27
Consensus pattern (19 bp):
TTGAGAATTTAGAGGGAAA
Found at i:3499257 original size:2 final size:2
Alignment explanation
Indices: 3499250--3499284 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
3499240 ATCTATAGAT
3499250 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3499285 GAAATACTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3499449 original size:20 final size:19
Alignment explanation
Indices: 3499417--3499466 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
3499407 CTTATAGTAC
* *
3499417 ATATATGTATAAACCATGT
1 ATATATATATAAACCATAT
*
3499436 ATAGTATATATAAACTATAT
1 ATA-TATATATAAACCATAT
3499456 ATATATATATA
1 ATATATATATA
3499467 TATATAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.40
Consensus pattern (19 bp):
ATATATATATAAACCATAT
Found at i:3499565 original size:14 final size:14
Alignment explanation
Indices: 3499542--3499572 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3499532 TCATAACCCC
*
3499542 AAATCCTAAACTTT
1 AAATCATAAACTTT
3499556 AAATCATAAACTTT
1 AAATCATAAACTTT
3499570 AAA
1 AAA
3499573 CCCTAAACCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (14 bp):
AAATCATAAACTTT
Found at i:3499579 original size:14 final size:14
Alignment explanation
Indices: 3499546--3499580 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
3499536 AACCCCAAAT
*
3499546 CCTAAACTTTAAAT
1 CCTAAACTTTAAAC
*
3499560 CATAAACTTTAAAC
1 CCTAAACTTTAAAC
3499574 CCTAAAC
1 CCTAAAC
3499581 CATAAACCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.46, C:0.26, G:0.00, T:0.29
Consensus pattern (14 bp):
CCTAAACTTTAAAC
Found at i:3499919 original size:25 final size:22
Alignment explanation
Indices: 3499881--3499938 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 22
3499871 ATTAATCATG
3499881 TTTTATATAATTTACATTTAAATAA
1 TTTTATATAATTT--A-TTAAATAA
3499906 TTTTAT-TAATTTTATTAAATAA
1 TTTTATATAA-TTTATTAAATAA
*
3499928 TTTCATATAAT
1 TTTTATATAAT
3499939 ATGTATGTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 14 0.47
23 4 0.13
24 3 0.10
25 9 0.30
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTATATAATTTATTAAATAA
Found at i:3499980 original size:13 final size:13
Alignment explanation
Indices: 3499962--3500006 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
3499952 CCATGTATAG
3499962 TATATATAAACTA
1 TATATATAAACTA
*
3499975 TATATATAACCTATA
1 TATATATAAAC--TA
3499990 TATATATAAACTA
1 TATATATAAACTA
3500003 TATA
1 TATA
3500007 AAGTAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 16 0.57
15 12 0.43
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.40
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:3499980 original size:20 final size:20
Alignment explanation
Indices: 3499931--3499980 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
3499921 TAAATAATTT
*
3499931 CATATAATATGTATGTATAAAC
1 CATAT-ATA-GTATATATAAAC
*
3499953 CATGTATAGTATATATAAAC
1 CATATATAGTATATATAAAC
*
3499973 TATATATA
1 CATATATA
3499981 TAACCTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 17 0.71
21 3 0.12
22 4 0.17
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (20 bp):
CATATATAGTATATATAAAC
Found at i:3499982 original size:15 final size:15
Alignment explanation
Indices: 3499957--3500006 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
3499947 ATAAACCATG
3499957 TATAGTATATATAAAC
1 TATA-TATATATAAAC
*
3499973 --TATATATATAACC
1 TATATATATATAAAC
3499986 TATATATATATAAAC
1 TATATATATATAAAC
3500001 TATATA
1 TATATA
3500007 AAGTAAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 10 0.33
14 2 0.07
15 18 0.60
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (15 bp):
TATATATATATAAAC
Found at i:3500104 original size:7 final size:7
Alignment explanation
Indices: 3500094--3500124 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3500084 CCAAAACCTG
3500094 AAATCCT
1 AAATCCT
3500101 AAATCCT
1 AAATCCT
3500108 AAATCCT
1 AAATCCT
*
3500115 AAACCCT
1 AAATCCT
3500122 AAA
1 AAA
3500125 CTTTAAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.48, C:0.29, G:0.00, T:0.23
Consensus pattern (7 bp):
AAATCCT
Found at i:3500111 original size:14 final size:14
Alignment explanation
Indices: 3500094--3500165 Score: 58
Period size: 14 Copynumber: 5.1 Consensus size: 14
3500084 CCAAAACCTG
*
3500094 AAATCCTAAATCCT
1 AAATCCTAAACCCT
3500108 AAATCCTAAACCCT
1 AAATCCTAAACCCT
* *
3500122 AAA-CTTTAAACCAT
1 AAATC-CTAAACCCT
* * *
3500136 AAATACTAAATCAT
1 AAATCCTAAACCCT
3500150 AAA-CCATAAACCCT
1 AAATCC-TAAACCCT
3500164 AA
1 AA
3500166 TATATGTATT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
13 2 0.04
14 44 0.96
ACGTcount: A:0.50, C:0.26, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATCCTAAACCCT
Found at i:3500138 original size:21 final size:21
Alignment explanation
Indices: 3500098--3500165 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
3500088 AACCTGAAAT
*
3500098 CCTAAATCCTAAATCC-TAAAC
1 CCTAAATCATAAA-CCATAAAC
* *
3500119 CCTAAA-CTTTAAACCATAAAT
1 CCTAAATC-ATAAACCATAAAC
*
3500140 ACTAAATCATAAACCATAAAC
1 CCTAAATCATAAACCATAAAC
3500161 CCTAA
1 CCTAA
3500166 TATATGTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
20 3 0.08
21 34 0.89
22 1 0.03
ACGTcount: A:0.49, C:0.28, G:0.00, T:0.24
Consensus pattern (21 bp):
CCTAAATCATAAACCATAAAC
Found at i:3500187 original size:17 final size:16
Alignment explanation
Indices: 3500165--3500204 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
3500155 ATAAACCCTA
3500165 ATATATGTATTACATGC
1 ATATATGTA-TACATGC
*
3500182 ATATATGTATATATGC
1 ATATATGTATACATGC
3500198 ATA-ATGT
1 ATATATGT
3500205 GTGTATTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 4 0.18
16 9 0.41
17 9 0.41
ACGTcount: A:0.38, C:0.07, G:0.12, T:0.42
Consensus pattern (16 bp):
ATATATGTATACATGC
Found at i:3500941 original size:20 final size:20
Alignment explanation
Indices: 3500916--3500967 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
3500906 AACGCGATCT
*
3500916 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTC
*
3500936 CTAGAATCGCAAATCAGTTC
1 CCAGAATCGCAAATCAGTTC
3500956 CCAGAATCGCAA
1 CCAGAATCGCAA
3500968 CGCGATTATG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.37, C:0.27, G:0.15, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTC
Found at i:3501051 original size:20 final size:20
Alignment explanation
Indices: 3501023--3501075 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3501013 GATTTTCCAT
*
3501023 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACAT-ATA
*
3501043 AATCACAACGCGAACATATA
1 AATCGCAACGCGAACATATA
3501063 AATCGCAACGCGA
1 AATCGCAACGCGA
3501076 TTCTGACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.45, C:0.25, G:0.17, T:0.13
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:3501131 original size:20 final size:20
Alignment explanation
Indices: 3501084--3501256 Score: 159
Period size: 20 Copynumber: 8.6 Consensus size: 20
3501074 GATTCTGACT
* *
3501084 ATCGCAATGAGTATCCGTAAA
1 ATCGCAACGCGTATCCGT-AA
3501105 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* * * **
3501125 ATTGCAACGAGAATATGTAA
1 ATCGCAACGCGTATCCGTAA
* *
3501145 ATCGTAACGCGTATCTGTAA
1 ATCGCAACGCGTATCCGTAA
* * *
3501165 ATCGCAACGAGAATACGTAA
1 ATCGCAACGCGTATCCGTAA
* *
3501185 ATCGTAATGCGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
* *
3501205 ATCGCAACGAC-AATACGTAAA
1 ATCGCAACG-CGTATCCGT-AA
*
3501226 ATCGCAACACGTATCCGTAA
1 ATCGCAACGCGTATCCGTAA
3501246 ATCGCAACGCG
1 ATCGCAACGCG
3501257 ATTTTTAAAG
Statistics
Matches: 119, Mismatches: 30, Indels: 7
0.76 0.19 0.04
Matches are distributed among these distances:
20 87 0.73
21 32 0.27
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGTATCCGTAA
Found at i:3501133 original size:81 final size:80
Alignment explanation
Indices: 3501023--3501254 Score: 218
Period size: 81 Copynumber: 2.9 Consensus size: 80
3501013 GATTTTCCAT
* ** * * * *
3501023 AATCGCAACGCGAATATGAAAATCACAACGCGAACATATAAATCGCAACGCG-ATTCTG-ACTAT
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAACATATAAATCGCAACGCGTA-TCTGTA-AAT
* * *
3501086 CGCAATGAGTATCCGTAA
64 CGCAACGAGAATACGT-A
* * * *
3501104 AATCGCAACGCGTATCCGTAAATTGCAACGAGAATATGTAAATCGTAACGCGTATCTGTAAATCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAACATATAAATCGCAACGCGTATCTGTAAATCG
3501169 CAACGAGAATACGTA
66 CAACGAGAATACGTA
* * * * * *
3501184 AATCGTAATGCGTATCCGTAAATCGCAACGACAATACGTA-AAATCGCAACACGTATCCGTAAAT
1 AATCGCAACGCGTATCCGTAAATCGCAACGA-GA-ACATATAAATCGCAACGCGTATCTGTAAAT
3501248 CGCAACG
64 CGCAACG
3501255 CGATTTTTAA
Statistics
Matches: 123, Mismatches: 24, Indels: 8
0.79 0.15 0.05
Matches are distributed among these distances:
80 29 0.24
81 90 0.73
82 4 0.03
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.21
Consensus pattern (80 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAACATATAAATCGCAACGCGTATCTGTAAATCG
CAACGAGAATACGTA
Found at i:3501156 original size:40 final size:40
Alignment explanation
Indices: 3501084--3501254 Score: 225
Period size: 40 Copynumber: 4.2 Consensus size: 40
3501074 GATTCTGACT
* * *
3501084 ATCGCAATGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
* * * *
3501125 ATTGCAACGAGAATATGTAAATCGTAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* *
3501165 ATCGCAACGAGAATACGTAAATCGTAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
* *
3501205 ATCGCAACGACAATACGTAAAATCGCAACACGTATCCGTAA
1 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCCGTAA
3501246 ATCGCAACG
1 ATCGCAACG
3501255 CGATTTTTAA
Statistics
Matches: 114, Mismatches: 15, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
40 73 0.64
41 41 0.36
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.22
Consensus pattern (40 bp):
ATCGCAACGAGAATACGTAAATCGCAACGCGTATCCGTAA
Found at i:3501880 original size:41 final size:36
Alignment explanation
Indices: 3501832--3501927 Score: 108
Period size: 33 Copynumber: 2.6 Consensus size: 36
3501822 CGCAACATGA
3501832 AAATGAAAATCGCAACACGAAAATGACTATCGCAACGCAAG
1 AAATGAAAATCGCAACACGAAAA-GA--ATCGCAACGC--G
*
3501873 AAATGAAAATCGC-A-ACG-AGAGAATCGCAACGCG
1 AAATGAAAATCGCAACACGAAAAGAATCGCAACGCG
*
3501906 AAATGAAAATCGCAACGCGAAA
1 AAATGAAAATCGCAACACGAAA
3501928 CCAAAATCGC
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
33 14 0.29
34 1 0.02
35 12 0.24
36 1 0.02
37 2 0.04
38 2 0.04
39 3 0.06
40 1 0.02
41 13 0.27
ACGTcount: A:0.49, C:0.21, G:0.20, T:0.10
Consensus pattern (36 bp):
AAATGAAAATCGCAACACGAAAAGAATCGCAACGCG
Found at i:3501918 original size:19 final size:19
Alignment explanation
Indices: 3501817--3501938 Score: 101
Period size: 20 Copynumber: 6.5 Consensus size: 19
3501807 TTCTAAACTT
**
3501817 AAAATCGCAACATGAAAATG
1 AAAATCGCAACGCG-AAATG
*
3501837 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCG-AAATG
**
3501857 ACTATCGCAACGCAAGAAATG
1 AAAATCGCAACGC--GAAATG
3501878 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
*
3501892 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
3501911 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATG
3501930 AAAATCGCA
1 AAAATCGCA
3501939 TTGCGATTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 15
0.77 0.09 0.14
Matches are distributed among these distances:
14 10 0.12
15 1 0.01
16 2 0.02
17 1 0.01
18 1 0.01
19 27 0.32
20 29 0.34
21 13 0.15
22 1 0.01
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.11
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:3501956 original size:19 final size:19
Alignment explanation
Indices: 3501934--3502079 Score: 78
Period size: 19 Copynumber: 8.1 Consensus size: 19
3501924 GAAACCAAAA
*
3501934 TCGCATTGCGATTTTAATT
1 TCGCGTTGCGATTTTAATT
*
3501953 TCGCGTTGCGA---T--TC
1 TCGCGTTGCGATTTTAATT
*
3501967 TCTCGTTGCGATTTTAATT
1 TCGCGTTGCGATTTTAATT
*
3501986 TCGCGTTGCGA---T--TC
1 TCGCGTTGCGATTTTAATT
* * *
3502000 TCTCGTTACGATTTTCATT
1 TCGCGTTGCGATTTTAATT
* ** *
3502019 TCACGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTAATT
*
3502038 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTAATT
* *
3502058 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTAATT
3502078 TC
1 TC
3502080 AACCAAAAGA
Statistics
Matches: 98, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
14 21 0.21
16 2 0.02
17 2 0.02
19 40 0.41
20 32 0.33
21 1 0.01
ACGTcount: A:0.14, C:0.23, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTAATT
Found at i:3501981 original size:33 final size:33
Alignment explanation
Indices: 3501939--3502030 Score: 157
Period size: 33 Copynumber: 2.8 Consensus size: 33
3501929 CAAAATCGCA
3501939 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
3501972 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
* * *
3502005 TTACGATTTTCATTTCACGTTGCGAT
1 TTGCGATTTTAATTTCGCGTTGCGAT
3502031 AGTCATTTCC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTAATTTCGCGTTGCGATTCTCTCG
Found at i:3502056 original size:20 final size:20
Alignment explanation
Indices: 3502003--3502079 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
3501993 GCGATTCTCT
*
3502003 CGTTACGATTTTCATTT-CA
1 CGTTGCGATTTTCATTTCCA
** *
3502022 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCA
*
3502042 CGTTGCGATTTTCA-TTCTCT
1 CGTTGCGATTTTCATTTC-CA
3502062 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
3502080 AACCAAAAGA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
19 17 0.35
20 28 0.58
21 3 0.06
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCA
Found at i:3502077 original size:40 final size:39
Alignment explanation
Indices: 3502003--3502079 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 39
3501993 GCGATTCTCT
3502003 CGTTACGATTTTCATTTCACGTTGCGATAGTCATTTCCG
1 CGTTACGATTTTCATTTCACGTTGCGATAGTCATTTCCG
* * **
3502042 CGTTGCGATTTTCATTCTCTCGTTGCGATTTTCATTTC
1 CGTTACGATTTTCATT-TCACGTTGCGATAGTCATTTC
3502080 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
39 15 0.45
40 18 0.55
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.45
Consensus pattern (39 bp):
CGTTACGATTTTCATTTCACGTTGCGATAGTCATTTCCG
Found at i:3504127 original size:21 final size:21
Alignment explanation
Indices: 3504103--3504169 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
3504093 TCATTCTTTG
3504103 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
3504124 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
3504145 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
3504166 AGAG
1 AGAG
3504170 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:3504127 original size:42 final size:42
Alignment explanation
Indices: 3504060--3504169 Score: 116
Period size: 42 Copynumber: 2.6 Consensus size: 42
3504050 GTCATCTCTC
* * * * * *
3504060 AAGAGTCCACTCCTATCGTTGAAGAGGCCCCTATCATTCTTTG
1 AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCA-TCGTTG
*
3504103 -AGAGTCCCCTCCCACCGTTCAAGAGGCCACTGTCATCGTTG
1 AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCGTTG
*
3504144 AAGAGGT-CCCTCCCACCATTCAAGAG
1 AAGA-GTCCCCTCCCACCGTTCAAGAG
3504170 CCCGATTCAC
Statistics
Matches: 57, Mismatches: 8, Indels: 5
0.81 0.11 0.07
Matches are distributed among these distances:
41 5 0.09
42 50 0.88
43 2 0.04
ACGTcount: A:0.24, C:0.33, G:0.20, T:0.24
Consensus pattern (42 bp):
AAGAGTCCCCTCCCACCGTTCAAGAGGCCACTATCATCGTTG
Found at i:3505529 original size:14 final size:14
Alignment explanation
Indices: 3505510--3505545 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
3505500 ATTGTTTAAT
3505510 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
3505524 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
3505538 TGATTTGT
1 TGATTTGT
3505546 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:3505668 original size:19 final size:17
Alignment explanation
Indices: 3505652--3505702 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
3505642 AAAAATGACT
3505652 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
3505671 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
3505685 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
3505702 A
1 A
3505703 AATCGCAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
16 5 0.19
17 7 0.26
19 7 0.26
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:3505694 original size:33 final size:33
Alignment explanation
Indices: 3505652--3505745 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
3505642 AAAAATGACT
3505652 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
3505685 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
3505718 ATCACAATGCGAAATAAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
3505746 CGAATTTAGT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:3505708 original size:19 final size:19
Alignment explanation
Indices: 3505652--3505710 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 19
3505642 AAAAATGACT
3505652 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
3505671 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
3505685 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
3505704 ATCGCAA
1 ATCGCAA
3505711 CGAGGGAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 10 0.30
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 17 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:3505779 original size:14 final size:13
Alignment explanation
Indices: 3505755--3505785 Score: 53
Period size: 14 Copynumber: 2.3 Consensus size: 13
3505745 GCGAATTTAG
3505755 TTTTGCGTTGCGA
1 TTTTGCGTTGCGA
3505768 TTTTGTCGTTGCGA
1 TTTTG-CGTTGCGA
3505782 TTTT
1 TTTT
3505786 AATTTCGCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.06, C:0.13, G:0.26, T:0.55
Consensus pattern (13 bp):
TTTTGCGTTGCGA
Found at i:3505798 original size:19 final size:19
Alignment explanation
Indices: 3505776--3505859 Score: 79
Period size: 19 Copynumber: 4.6 Consensus size: 19
3505766 GATTTTGTCG
*
3505776 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
3505795 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
3505809 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
3505828 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
3505848 TTGCGATTTTCA
1 TTGCGATTTTCA
3505860 CGTTGTGATT
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
14 6 0.12
16 7 0.14
17 6 0.12
19 19 0.37
20 13 0.25
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:3505810 original size:33 final size:33
Alignment explanation
Indices: 3505762--3505834 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
3505752 TAGTTTTGCG
* *
3505762 TTGCGATTTTGTCGTTGCGATTTTAATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTAATTTCGCA
*
3505795 TTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTCTCTCGTTGCGATTTTAATTTCGCA
3505828 TTGCGAT
1 TTGCGAT
3505835 AGTCATTTCC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTCTCTCGTTGCGATTTTAATTTCGCA
Found at i:3505870 original size:86 final size:87
Alignment explanation
Indices: 3505759--3505928 Score: 225
Period size: 86 Copynumber: 2.0 Consensus size: 87
3505749 ATTTAGTTTT
** * ** *
3505759 GCGTTGCGATTTTGTCGTTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT
1 GCGTTGCGATTTTCACGTTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATAGTAATTT
*
3505824 -CGCATTGCGATAGTCATTTCC
66 CCGCATTGCGATAGACATTTCC
* * * *
3505845 GCGTTGCGATTTTCACGTTGTGATTTTTATTTCGCATTGTGATTATCTCGTTTCGATAGTAATTT
1 GCGTTGCGATTTTCACGTTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATAGTAATTT
*
3505910 CCGCGTTGCGATAGACATT
66 CCGCATTGCGATAGACATT
3505929 AAGAGTCCCA
Statistics
Matches: 71, Mismatches: 12, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
86 55 0.77
87 16 0.23
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (87 bp):
GCGTTGCGATTTTCACGTTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATAGTAATTT
CCGCATTGCGATAGACATTTCC
Found at i:3509285 original size:20 final size:20
Alignment explanation
Indices: 3509260--3509466 Score: 202
Period size: 20 Copynumber: 10.2 Consensus size: 20
3509250 GTCAGAATCT
*
3509260 CGTTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATACG
* *
3509280 CATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGTATACG
* *
3509300 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATACG
* *
3509320 CATTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATACG
* * *
3509340 CATTGCAATTTACAG-ATACA
1 CGTTGCGATTTAC-GTATACG
* *
3509360 CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGTATACG
* *
3509380 CGTTGCAATTTACGGATACG
1 CGTTGCGATTTACGTATACG
* *
3509400 CGTTGCGATTTTACGTATTCT
1 CGTTGCGA-TTTACGTATACG
3509421 CGTTGCGATTTACAG-ATACG
1 CGTTGCGATTTAC-GTATACG
* *
3509441 CGTTGCGATTTTACGGATACT
1 CGTTGCGA-TTTACGTATACG
3509462 CGTTG
1 CGTTG
3509467 TGATAGTCAG
Statistics
Matches: 161, Mismatches: 20, Indels: 11
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.01
20 127 0.79
21 33 0.20
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTTACGTATACG
Found at i:3509326 original size:60 final size:60
Alignment explanation
Indices: 3509260--3509460 Score: 242
Period size: 60 Copynumber: 3.3 Consensus size: 60
3509250 GTCAGAATCT
* * * *
3509260 CGTTGCGATTTACGTATTCGCATTGCGATTTACGTATTCGCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCACGTTGCGATTTACGGATACG
* * * * * *
3509320 CATTGCGATTTACGGATACGCATTGCAATTTACAG-ATACACGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCATTGCGATTTAC-GTATTCACGTTGCGATTTACGGATACG
* * * *
3509380 CGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCACGTTGCGATTTACGGATACG
3509441 CGTTGCGATTTTACGGATAC
1 CGTTGCGA-TTTACGGATAC
3509461 TCGTTGTGAT
Statistics
Matches: 116, Mismatches: 21, Indels: 6
0.81 0.15 0.04
Matches are distributed among these distances:
60 73 0.63
61 32 0.28
62 11 0.09
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (60 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCACGTTGCGATTTACGGATACG
Found at i:3509484 original size:41 final size:41
Alignment explanation
Indices: 3509258--3509492 Score: 185
Period size: 40 Copynumber: 5.8 Consensus size: 41
3509248 TAGTCAGAAT
* * * * *
3509258 CTCGTTGCGATTTAC-GTATTCGCATTGCGA-TTTACGTATT
1 CTCGTTGCGATGTACAG-ATACGCGTTGCGATTTTACGGATA
* * * * *
3509298 CGCATTGCGATTTACGGATACGCATTGCGA-TTTACGGATA
1 CTCGTTGCGATGTACAGATACGCGTTGCGATTTTACGGATA
* * * * * * *
3509338 CGCATTGCAATTTACAGATACACGTTGCGA-TTTACGTATT
1 CTCGTTGCGATGTACAGATACGCGTTGCGATTTTACGGATA
* * * * *
3509378 CTCGTTGCAATTTACGGATACGCGTTGCGATTTTACGTATT
1 CTCGTTGCGATGTACAGATACGCGTTGCGATTTTACGGATA
*
3509419 CTCGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATA
1 CTCGTTGCGATGTACAGATACGCGTTGCGATTTTACGGATA
*
3509460 CTCGTTGTGATAGT-CAGA-ATCGCGTTGCGATTT
1 CTCGTTGCGAT-GTACAGATA-CGCGTTGCGATTT
3509493 ATATGTTCGC
Statistics
Matches: 170, Mismatches: 21, Indels: 7
0.86 0.11 0.04
Matches are distributed among these distances:
40 94 0.55
41 75 0.44
42 1 0.01
ACGTcount: A:0.22, C:0.20, G:0.23, T:0.36
Consensus pattern (41 bp):
CTCGTTGCGATGTACAGATACGCGTTGCGATTTTACGGATA
Found at i:3509502 original size:20 final size:20
Alignment explanation
Indices: 3509479--3509531 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
3509469 ATAGTCAGAA
*
3509479 TCGCGTTGCGATTTAT-ATGT
1 TCGCGTTGCGATTT-TCATAT
*
3509499 TCGCATTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
3509519 TCGCGTTGCGATT
1 TCGCGTTGCGATT
3509532 ATGGAAAATC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 1 0.03
20 28 0.97
ACGTcount: A:0.15, C:0.19, G:0.23, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:3509508 original size:81 final size:81
Alignment explanation
Indices: 3509315--3509531 Score: 201
Period size: 81 Copynumber: 2.7 Consensus size: 81
3509305 CGATTTACGG
* * * * * * *
3509315 ATACGCATTGCGA-TTTACGGATACGCATTGCAATTTACAGATACACGTTGCGA-TTTACGTATT
1 ATACGCGTTGCGATTTTAC-TATTCGCATTGCGATTTACAGATACGCGTTGCGATTTTACGGATA
* * *
3509378 CTCGTTGCAATTTACGG
65 CTCGTTGCAAGTCACGA
* *
3509395 ATACGCGTTGCGATTTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTTACGGATA
1 ATACGCGTTGCGATTTTAC-TATTCGCATTGCGATTTACAGATACGCGTTGCGATTTTACGGATA
*
3509460 CTCGTTGTGATAGTCA-GA
65 CTCGTTG-CA-AGTCACGA
* * * *
3509478 AT-CGCGTTGCGATTTATA-TGTTCGCATTGCGATTTTCATATTCGCGTTGCGATT
1 ATACGCGTTGCGATTT-TACTATTCGCATTGCGATTTACAGATACGCGTTGCGATT
3509532 ATGGAAAATC
Statistics
Matches: 113, Mismatches: 19, Indels: 9
0.80 0.13 0.06
Matches are distributed among these distances:
80 12 0.11
81 64 0.57
82 28 0.25
83 6 0.05
84 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (81 bp):
ATACGCGTTGCGATTTTACTATTCGCATTGCGATTTACAGATACGCGTTGCGATTTTACGGATAC
TCGTTGCAAGTCACGA
Found at i:3509584 original size:21 final size:20
Alignment explanation
Indices: 3509477--3509594 Score: 71
Period size: 21 Copynumber: 5.8 Consensus size: 20
3509467 TGATAGTCAG
*
3509477 AATCGCGTTGCGATTTAT-AT
1 AATCGCATTGCGATTT-TCAT
**
3509497 GTTCGCATTGCGATTTTCAT
1 AATCGCATTGCGATTTTCAT
* * ** *
3509517 ATTCGCGTTGCGATTATGGAA
1 AATCGCATTGCGATT-TTCAT
*
3509538 AATCGCAATGCGAATTTGT-ACT
1 AATCGCATTGCG-ATTT-TCA-T
3509560 -ATCGCATTGCGATTCTTCAT
1 AATCGCATTGCGATT-TTCAT
*
3509580 AATCGCGTTGCGATT
1 AATCGCATTGCGATT
3509595 CTGGGAACTG
Statistics
Matches: 75, Mismatches: 15, Indels: 15
0.71 0.14 0.14
Matches are distributed among these distances:
19 1 0.01
20 33 0.44
21 38 0.51
22 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.37
Consensus pattern (20 bp):
AATCGCATTGCGATTTTCAT
Found at i:3511834 original size:14 final size:14
Alignment explanation
Indices: 3511713--3511836 Score: 87
Period size: 14 Copynumber: 8.7 Consensus size: 14
3511703 GTACTTTTTT
* *
3511713 TATAAAGTATAAAA
1 TATAAAGTATTAAG
*
3511727 TATATAA-TATAAAG
1 TATA-AAGTATTAAG
*
3511741 TAATAAAGTGTTTGAA-
1 T-ATAAAGT-ATT-AAG
3511757 TAT-AAGTATTAAAG
1 TATAAAGTATT-AAG
*
3511771 TAT-AAGTATTAAA
1 TATAAAGTATTAAG
*
3511784 TATAAAGTATAAAG
1 TATAAAGTATTAAG
3511798 TATTAAAGTATATAAG
1 TA-TAAAGTAT-TAAG
*
3511814 TAT-AAGTATTAAT
1 TATAAAGTATTAAG
3511827 TATAAAGTAT
1 TATAAAGTAT
3511837 ATTAATTATC
Statistics
Matches: 90, Mismatches: 10, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
13 15 0.17
14 49 0.54
15 17 0.19
16 7 0.08
17 2 0.02
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.36
Consensus pattern (14 bp):
TATAAAGTATTAAG
Found at i:3511835 original size:57 final size:58
Alignment explanation
Indices: 3511712--3511837 Score: 161
Period size: 57 Copynumber: 2.2 Consensus size: 58
3511702 GGTACTTTTT
* *
3511712 TTATAAAGTATAAAATATATAATATAAAGTAATAAAGTGTTTGAATATAAGTATTAAA
1 TTATAAAGTATAAAATATATAATATAAAGTAATAAAGTATATGAATATAAGTATTAAA
* * *
3511770 GTAT-AAGTATTAAATATA-AAGTATAAAGTATTAAAGTATAT-AAGTATAAGTATT-AA
1 TTATAAAGTATAAAATATATAA-TATAAAGTAATAAAGTATATGAA-TATAAGTATTAAA
3511826 TTATAAAGTATA
1 TTATAAAGTATA
3511838 TTAATTATCA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
56 9 0.16
57 46 0.79
58 3 0.05
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (58 bp):
TTATAAAGTATAAAATATATAATATAAAGTAATAAAGTATATGAATATAAGTATTAAA
Found at i:3513069 original size:29 final size:29
Alignment explanation
Indices: 3513037--3513136 Score: 164
Period size: 29 Copynumber: 3.4 Consensus size: 29
3513027 TGGTTAGTGA
3513037 CAAAATATAAAATGTGAAAGTTTATTGGC
1 CAAAATATAAAATGTGAAAGTTTATTGGC
3513066 CAAAATATAAAATGTGAAAGTTTATTGGC
1 CAAAATATAAAATGTGAAAGTTTATTGGC
* *
3513095 CAAAAAATAAAATTTGAAAGTTTATTGGC
1 CAAAATATAAAATGTGAAAGTTTATTGGC
* *
3513124 CAAAGTAAAAAAT
1 CAAAATATAAAAT
3513137 TGAGAAAATT
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 66 1.00
ACGTcount: A:0.49, C:0.07, G:0.15, T:0.29
Consensus pattern (29 bp):
CAAAATATAAAATGTGAAAGTTTATTGGC
Found at i:3525814 original size:15 final size:16
Alignment explanation
Indices: 3525794--3525824 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3525784 TATTTTCTTC
3525794 AAAAAAAC-AAAAAAA
1 AAAAAAACGAAAAAAA
3525809 AAAAAAACGAAAAAAA
1 AAAAAAACGAAAAAAA
3525825 GGCCAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.90, C:0.06, G:0.03, T:0.00
Consensus pattern (16 bp):
AAAAAAACGAAAAAAA
Found at i:3525836 original size:15 final size:15
Alignment explanation
Indices: 3525818--3525849 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3525808 AAAAAAAACG
3525818 AAAAAAAG--GCCAA
1 AAAAAAAGAAGCCAA
3525831 AAAAAAAGAAGCCAA
1 AAAAAAAGAAGCCAA
3525846 AAAA
1 AAAA
3525850 GCCAAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
15 9 0.53
ACGTcount: A:0.75, C:0.12, G:0.12, T:0.00
Consensus pattern (15 bp):
AAAAAAAGAAGCCAA
Found at i:3534206 original size:83 final size:82
Alignment explanation
Indices: 3534104--3534345 Score: 350
Period size: 83 Copynumber: 3.0 Consensus size: 82
3534094 GGAAATATGT
3534104 TTTTAATA-TATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
1 TTTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
3534168 TTCGAGTAAAACTCTCAG
66 TT-GAGTAAAACTCTCAG
* *
3534186 TTTTAATATTATAAATTTAAAAGATATTATAATATGTTTAAATTTAGATATTAAAAGAGTTTTGG
1 TTTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
3534251 TTAGAGTAAAACTCTCAG
66 TT-GAGTAAAACTCTCAG
* * * * * *
3534269 ATTTAATATTTTAAATTTAAGAGATATTTTAATCTA-TT---TTTAGATATTAAAAGTGTTTTAG
1 TTTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
3534330 TTGTAGTAAAACTCTC
66 TTG-AGTAAAACTCTC
3534346 TCGAAATTCC
Statistics
Matches: 147, Mismatches: 11, Indels: 7
0.89 0.07 0.04
Matches are distributed among these distances:
78 1 0.01
79 35 0.24
82 10 0.07
83 101 0.69
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (82 bp):
TTTTAATATTATAAATTTAAAAGATATTATAATCTATTTAAATTTAGATATTAAAAGAGTTTTGG
TTGAGTAAAACTCTCAG
Found at i:3535061 original size:14 final size:14
Alignment explanation
Indices: 3535038--3535071 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3535028 TTTCATTCAA
*
3535038 TTTATTTATTTACT
1 TTTATCTATTTACT
*
3535052 TTTATCTATTTATT
1 TTTATCTATTTACT
3535066 TTTATC
1 TTTATC
3535072 AAGTATTTTT
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:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATCTATTTACT
Found at i:3535573 original size:20 final size:20
Alignment explanation
Indices: 3535550--3535589 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3535540 AATTTGTAAA
3535550 TCGCAACAC-AGAAGTCAAAT
1 TCGCAACACGA-AAGTCAAAT
*
3535570 TCGCAACGCGAAAGTCAAAT
1 TCGCAACACGAAAGTCAAAT
3535590 GTTTTTACGC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 17 0.94
21 1 0.06
ACGTcount: A:0.42, C:0.25, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAGTCAAAT
Found at i:3536104 original size:20 final size:19
Alignment explanation
Indices: 3536067--3536118 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
3536057 ATTCGCAACA
*
3536067 CGATTTTAGTTTCGCGTTG
1 CGATTTTAGTTTCACGTTG
*
3536086 CGATTTTCATTTTCACGTTG
1 CGATTTT-AGTTTCACGTTG
*
3536106 CGAATTTAAGTTT
1 CG-ATTTTAGTTT
3536119 TAGAAACTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 16 0.59
21 4 0.15
ACGTcount: A:0.17, C:0.15, G:0.19, T:0.48
Consensus pattern (19 bp):
CGATTTTAGTTTCACGTTG
Found at i:3537847 original size:21 final size:21
Alignment explanation
Indices: 3537803--3537848 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
3537793 GTTAGGGGAA
* **
3537803 TTACGTGATGAGGTCGGTGTT
1 TTACGTCATGAGGTCGGTACT
*
3537824 TTACGTCATGAGTTCGGTACT
1 TTACGTCATGAGGTCGGTACT
3537845 TTAC
1 TTAC
3537849 ATGAAGATAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.17, C:0.15, G:0.28, T:0.39
Consensus pattern (21 bp):
TTACGTCATGAGGTCGGTACT
Found at i:3538288 original size:21 final size:20
Alignment explanation
Indices: 3538262--3538374 Score: 77
Period size: 21 Copynumber: 5.4 Consensus size: 20
3538252 CCTATCATCA
3538262 TTCAAGAGGCGCCTCCTATCG
1 TTCAAGAGGC-CCTCCTATCG
*
3538283 TTCAAGAGGCCCCCCTCAT--
1 TTCAAGAGGCCCTCCT-ATCG
* * *
3538302 TATCGAAGAAGCCCCTCCCACCG
1 T-TC-AAG-AGGCCCTCCTATCG
**
3538325 TTCAAGAGGCCCTTGTCATCG
1 TTCAAGAGGCCCTCCT-ATCG
* *
3538346 TTCAAGAGGTCCCGCCTGTCG
1 TTCAAGAGG-CCCTCCTATCG
3538367 TTCAAGAG
1 TTCAAGAG
3538375 CCCAATTCAC
Statistics
Matches: 70, Mismatches: 14, Indels: 16
0.70 0.14 0.16
Matches are distributed among these distances:
19 1 0.01
20 13 0.19
21 42 0.60
22 13 0.19
23 1 0.01
ACGTcount: A:0.21, C:0.35, G:0.22, T:0.22
Consensus pattern (20 bp):
TTCAAGAGGCCCTCCTATCG
Found at i:3539831 original size:65 final size:65
Alignment explanation
Indices: 3539745--3539879 Score: 193
Period size: 66 Copynumber: 2.1 Consensus size: 65
3539735 ACTTGATTTG
* *
3539745 TTGTTTAATTGATGAGGAAATAAGATTTA-TTTTTTGGTTGATTAATTGATTTCTAAAAGTTGAT
1 TTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGATTAATTGATTTCTAAAAGTTGAT
* * *
3539809 TTGTTTAATTTGATGTA-TAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGTAAAAGTTG
1 TTGTTTAA-TTGATG-AGGAAATAAGAATTATTTTTTTGCTTGATTAATTGATTTCTAAAAGTTG
3539873 AT
64 AT
3539875 TTGTT
1 TTGTT
3539880 GTTTCTAAAA
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
64 8 0.13
65 17 0.27
66 38 0.60
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.52
Consensus pattern (65 bp):
TTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGCTTGATTAATTGATTTCTAAAAGTTGAT
Found at i:3540008 original size:20 final size:20
Alignment explanation
Indices: 3539985--3540029 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
3539975 AATAAGCGTT
*
3539985 GCGATACTCAAATTCGCAAC
1 GCGATACTCAAATTCACAAC
* *
3540005 GCGAAAGTCAAATTCACAAC
1 GCGATACTCAAATTCACAAC
3540025 GCGAT
1 GCGAT
3540030 TTTCGGTTTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
GCGATACTCAAATTCACAAC
Found at i:3540078 original size:20 final size:20
Alignment explanation
Indices: 3540037--3540079 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3540027 GATTTTCGGT
**
3540037 TTGCGAATTTGACTTTTGCG
1 TTGCGAATTTGACTTTCACG
3540057 TTGCGAATTTGACTTTCACG
1 TTGCGAATTTGACTTTCACG
3540077 TTG
1 TTG
3540080 ATCGCAACAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.16, G:0.23, T:0.44
Consensus pattern (20 bp):
TTGCGAATTTGACTTTCACG
Found at i:3540309 original size:39 final size:39
Alignment explanation
Indices: 3540255--3540341 Score: 156
Period size: 39 Copynumber: 2.2 Consensus size: 39
3540245 TCAAGTTGTA
*
3540255 GATTTTGATTTCCTTTTGCTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTACTTGGCACCATATGAGATTTG
*
3540294 GATTTTGATTTCCTTTTACTTGGCACCATATGAGCTTTG
1 GATTTTGATTTCCTTTTACTTGGCACCATATGAGATTTG
3540333 GATTTTGAT
1 GATTTTGAT
3540342 GAGCATTGGA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.18, C:0.15, G:0.20, T:0.47
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTACTTGGCACCATATGAGATTTG
Found at i:3541530 original size:18 final size:18
Alignment explanation
Indices: 3541507--3541542 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3541497 AAGCCGGTTG
*
3541507 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3541525 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
3541543 CCTTTTGGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3543821 original size:24 final size:24
Alignment explanation
Indices: 3543794--3543872 Score: 104
Period size: 24 Copynumber: 3.2 Consensus size: 24
3543784 ATTTCATTAT
3543794 ACAAATTGCAAATTAATTTACTAA
1 ACAAATTGCAAATTAATTTACTAA
* **
3543818 ACAAATGAGCTTTATTAATTTACTAA
1 ACAAAT-TGC-AAATTAATTTACTAA
*
3543844 ACAAATTGTAAATTAATTTACTAA
1 ACAAATTGCAAATTAATTTACTAA
3543868 ACAAA
1 ACAAA
3543873 CCTAGAGAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
24 24 0.52
25 3 0.07
26 19 0.41
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.34
Consensus pattern (24 bp):
ACAAATTGCAAATTAATTTACTAA
Found at i:3543955 original size:16 final size:15
Alignment explanation
Indices: 3543933--3543971 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
3543923 GAAATCATTG
3543933 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
3543949 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
3543964 AAAAATTA
1 AAAAATTA
3543972 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:3544197 original size:39 final size:40
Alignment explanation
Indices: 3544129--3544213 Score: 154
Period size: 39 Copynumber: 2.1 Consensus size: 40
3544119 CTAAAACCTA
*
3544129 TTGCGAATTTGACTTTTGTGTTGCGAATTTGTCTATCGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCG
3544169 TTGCGAATTTGAC-TTTGTGTTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCG
3544208 TTGCGA
1 TTGCGA
3544214 TTTACAAATT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 31 0.70
40 13 0.30
ACGTcount: A:0.16, C:0.15, G:0.26, T:0.42
Consensus pattern (40 bp):
TTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCG
Found at i:3544212 original size:20 final size:20
Alignment explanation
Indices: 3544129--3544213 Score: 109
Period size: 20 Copynumber: 4.3 Consensus size: 20
3544119 CTAAAACCTA
* * *
3544129 TTGCGAATTTGACTTTTGTG
1 TTGCGAATTTGACTATCGCG
*
3544149 TTGCGAATTTGTCTATCGCG
1 TTGCGAATTTGACTATCGCG
* *
3544169 TTGCGAATTTGACT-TTGTG
1 TTGCGAATTTGACTATCGCG
3544188 TTGCGAATTTGACTATCGCG
1 TTGCGAATTTGACTATCGCG
3544208 TTGCGA
1 TTGCGA
3544214 TTTACAAATT
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
19 17 0.31
20 38 0.69
ACGTcount: A:0.16, C:0.15, G:0.26, T:0.42
Consensus pattern (20 bp):
TTGCGAATTTGACTATCGCG
Found at i:3544226 original size:20 final size:20
Alignment explanation
Indices: 3544203--3544313 Score: 177
Period size: 20 Copynumber: 5.5 Consensus size: 20
3544193 AATTTGACTA
*
3544203 TCGCGTTGCGATTTACAAAT
1 TCGCGTTGCGATTTACAGAT
*
3544223 TCGCGTAGCGATTTACAGAT
1 TCGCGTTGCGATTTACAGAT
*
3544243 TCGCGTAGCGATTTACAGAT
1 TCGCGTTGCGATTTACAGAT
*
3544263 TCGCGTTGCGAATTACAGAT
1 TCGCGTTGCGATTTACAGAT
*
3544283 TCGCGTTGCGAATTACAGAT
1 TCGCGTTGCGATTTACAGAT
3544303 TCGCGTTGCGA
1 TCGCGTTGCGA
3544314 ATTTGGAAAA
Statistics
Matches: 87, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 87 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.31
Consensus pattern (20 bp):
TCGCGTTGCGATTTACAGAT
Found at i:3544346 original size:41 final size:41
Alignment explanation
Indices: 3544301--3544404 Score: 156
Period size: 41 Copynumber: 2.5 Consensus size: 41
3544291 CGAATTACAG
*
3544301 ATTCGCGTTGCGAATTTGGAAAATCGCAATGCGATTTACT-T
1 ATTCGCGTTGCGAAATTGGAAAATCGCAATGCGATTTA-TAT
* * *
3544342 ATTCGCGTTGCAAAATTGGAAAATTGGAATGCGATTTATAT
1 ATTCGCGTTGCGAAATTGGAAAATCGCAATGCGATTTATAT
3544383 ATTCGCGTTGCGAAATTGGAAA
1 ATTCGCGTTGCGAAATTGGAAA
3544405 CTGGGTTGCG
Statistics
Matches: 57, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 1 0.02
41 56 0.98
ACGTcount: A:0.31, C:0.13, G:0.23, T:0.33
Consensus pattern (41 bp):
ATTCGCGTTGCGAAATTGGAAAATCGCAATGCGATTTATAT
Found at i:3544432 original size:20 final size:19
Alignment explanation
Indices: 3544383--3544436 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
3544373 CGATTTATAT
3544383 ATTCGCGTTGCGAAATTGG
1 ATTCGCGTTGCGAAATTGG
** *
3544402 AAACTGGGTTGCGAAATTGG
1 ATTC-GCGTTGCGAAATTGG
3544422 AGTTCGCGTTGCGAA
1 A-TTCGCGTTGCGAA
3544437 TTTGTTGGTC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 24 0.89
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.33, T:0.28
Consensus pattern (19 bp):
ATTCGCGTTGCGAAATTGG
Found at i:3545551 original size:29 final size:31
Alignment explanation
Indices: 3545501--3545560 Score: 72
Period size: 30 Copynumber: 2.0 Consensus size: 31
3545491 AGGAAAACAG
*
3545501 TGCAGTTTGATTCGAATGAGCA-TA-AAAAA
1 TGCAGTTTGATTCGAATCAGCAGTAGAAAAA
*
3545530 TGCAGTTTTGATTTGAA-CAGCAGTAGAAAAA
1 TGCAG-TTTGATTCGAATCAGCAGTAGAAAAA
3545561 ACAGATTCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
29 9 0.35
30 12 0.46
31 5 0.19
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (31 bp):
TGCAGTTTGATTCGAATCAGCAGTAGAAAAA
Found at i:3552778 original size:6 final size:6
Alignment explanation
Indices: 3552767--3552791 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3552757 TGGACTATGT
3552767 CTTTTC CTTTTC CTTTTC CTTTTC C
1 CTTTTC CTTTTC CTTTTC CTTTTC C
3552792 GCTACAAGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (6 bp):
CTTTTC
Found at i:3564847 original size:14 final size:15
Alignment explanation
Indices: 3564828--3564858 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
3564818 AAATATATAA
3564828 ACTTGTTCAC-ATTC
1 ACTTGTTCACAATTC
3564842 ACTTGTTCACAATTC
1 ACTTGTTCACAATTC
3564857 AC
1 AC
3564859 ATTTTCATAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 10 0.62
15 6 0.38
ACGTcount: A:0.26, C:0.29, G:0.06, T:0.39
Consensus pattern (15 bp):
ACTTGTTCACAATTC
Found at i:3565317 original size:54 final size:54
Alignment explanation
Indices: 3565242--3565367 Score: 173
Period size: 54 Copynumber: 2.3 Consensus size: 54
3565232 GATACTTCTC
* * *
3565242 TTCAAGGGTATCGATACCTCCTCAAAGTA-TCAATACCAATTTTACATTCGATGT
1 TTCAAGGGTATCGATACCTCCTCAAAGTACT-AATACCAATATGACATTCGAGGT
* *
3565296 TTCAAGGGTATCGATACCTCCTCAAGGTACTAATACCAATATGGCATTCGAGGT
1 TTCAAGGGTATCGATACCTCCTCAAAGTACTAATACCAATATGACATTCGAGGT
* *
3565350 TTTAAGGGTGTCGATACC
1 TTCAAGGGTATCGATACC
3565368 ATCACTCAGG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
54 63 0.98
55 1 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.31
Consensus pattern (54 bp):
TTCAAGGGTATCGATACCTCCTCAAAGTACTAATACCAATATGACATTCGAGGT
Found at i:3569661 original size:6 final size:6
Alignment explanation
Indices: 3569654--3569694 Score: 73
Period size: 6 Copynumber: 6.8 Consensus size: 6
3569644 TTGATTTCTT
*
3569654 CCTCTT CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCT
1 CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCTA CCTCT
3569695 CATCGGTGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.12, C:0.51, G:0.00, T:0.37
Consensus pattern (6 bp):
CCTCTA
Found at i:3576137 original size:20 final size:20
Alignment explanation
Indices: 3576114--3576160 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3576104 GAGTTGAATG
3576114 CGAAAAAATA-GTAGTTCGAA
1 CGAAAAAA-AGGTAGTTCGAA
*
3576134 CGAAAAAAAGGTTGTTCGAA
1 CGAAAAAAAGGTAGTTCGAA
*
3576154 AGAAAAA
1 CGAAAAA
3576161 GAAAAAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 1 0.04
20 23 0.96
ACGTcount: A:0.53, C:0.09, G:0.21, T:0.17
Consensus pattern (20 bp):
CGAAAAAAAGGTAGTTCGAA
Found at i:3581561 original size:27 final size:28
Alignment explanation
Indices: 3581519--3581599 Score: 96
Period size: 27 Copynumber: 2.8 Consensus size: 28
3581509 AATGTTGAAT
3581519 GAAAGAAAGAAG-AAAAAAAAAGCA-GTTC
1 GAAAGAAA-AAGAAAAAAAAAAG-ATGTTC
3581547 GAAA-AAAAAGAAAAAAAAAAGATGTTC
1 GAAAGAAAAAGAAAAAAAAAAGATGTTC
3581574 GAAAGAAAAAGAGAGAAGAAAAAAGA
1 GAAAGAAAAAGA-A-AA-AAAAAAGA
3581600 CATGAAAGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 9
0.84 0.00 0.16
Matches are distributed among these distances:
26 4 0.09
27 21 0.45
28 11 0.23
29 1 0.02
30 2 0.04
31 8 0.17
ACGTcount: A:0.69, C:0.04, G:0.21, T:0.06
Consensus pattern (28 bp):
GAAAGAAAAAGAAAAAAAAAAGATGTTC
Found at i:3585601 original size:20 final size:20
Alignment explanation
Indices: 3585572--3585610 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3585562 AGAGCTCATA
*
3585572 TAGGATCATATAGATGCATT
1 TAGGAGCATATAGATGCATT
*
3585592 TAGGAGCATATAGTTGCAT
1 TAGGAGCATATAGATGCAT
3585611 GAGGTGGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (20 bp):
TAGGAGCATATAGATGCATT
Found at i:3586462 original size:21 final size:20
Alignment explanation
Indices: 3586427--3586465 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
3586417 TAATGGATTG
3586427 TTGTTTTTGTATGATGTTAT
1 TTGTTTTTGTATGATGTTAT
*
3586447 TTGTTTTGTTTATGATGTT
1 TTGTTTT-TGTATGATGTT
3586466 TAATGCCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.13, C:0.00, G:0.21, T:0.67
Consensus pattern (20 bp):
TTGTTTTTGTATGATGTTAT
Found at i:3587117 original size:20 final size:22
Alignment explanation
Indices: 3587088--3587131 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
3587078 CATTACACCA
3587088 TCATTCCA-TTT-CCACAACAT
1 TCATTCCATTTTGCCACAACAT
*
3587108 TCATTTCATTTTGCCACAACAT
1 TCATTCCATTTTGCCACAACAT
3587130 TC
1 TC
3587132 TCATTTGTAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 7 0.33
21 3 0.14
22 11 0.52
ACGTcount: A:0.27, C:0.32, G:0.02, T:0.39
Consensus pattern (22 bp):
TCATTCCATTTTGCCACAACAT
Found at i:3591647 original size:2 final size:2
Alignment explanation
Indices: 3591640--3591671 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3591630 AAAATTACTC
*
3591640 AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3591672 TTAATTTTGC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:3592195 original size:4 final size:4
Alignment explanation
Indices: 3592186--3592210 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
3592176 GAATATAATC
3592186 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
3592211 ATTTCTGAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:3608692 original size:43 final size:43
Alignment explanation
Indices: 3608605--3608725 Score: 179
Period size: 43 Copynumber: 2.8 Consensus size: 43
3608595 ACACCGTAAT
* *
3608605 AGGTCAAGATATATAGCGGCCTTTTTTGGAACAAATGCCACAAA
1 AGGTCAAGATCTATAGCGG-CATTTTTGGAACAAATGCCACAAA
* **
3608649 AGGTCGAGATCTATAGCGGCATTTTTGGAACAAATGCTGCAAA
1 AGGTCAAGATCTATAGCGGCATTTTTGGAACAAATGCCACAAA
*
3608692 AGGTCAAGATCTATAGCGGCGTTTTTGGAACAAA
1 AGGTCAAGATCTATAGCGGCATTTTTGGAACAAA
3608726 CACCGCTAAT
Statistics
Matches: 70, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
43 53 0.76
44 17 0.24
ACGTcount: A:0.34, C:0.17, G:0.24, T:0.26
Consensus pattern (43 bp):
AGGTCAAGATCTATAGCGGCATTTTTGGAACAAATGCCACAAA
Found at i:3611366 original size:46 final size:45
Alignment explanation
Indices: 3611244--3611422 Score: 286
Period size: 45 Copynumber: 4.0 Consensus size: 45
3611234 TATAACATTT
* * * *
3611244 CTTATCATTTATCCTATAAACTCATAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3611289 CTTAACATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
3611334 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3611380 CTTACCATTTATTCCATAAGCTCGTAAGATTATTTTACCAATA
1 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATA
3611423 CAGTTGCCAT
Statistics
Matches: 126, Mismatches: 7, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
45 81 0.64
46 45 0.36
ACGTcount: A:0.34, C:0.22, G:0.06, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:3611433 original size:45 final size:45
Alignment explanation
Indices: 3611244--3611442 Score: 276
Period size: 45 Copynumber: 4.4 Consensus size: 45
3611234 TATAACATTT
* * *
3611244 CTTATCATTTA-TCCTATAAACTCATAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCC-ATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3611289 CTTAACATTTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
3611334 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3611380 CTTACCATTTATTCCATAAGCTCGTAAGATTATTTTACCAATACA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* *
3611425 GTTGCCA-TTATTCCATAA
1 CTTACCATTTATTCCATAA
3611443 CCATATACCA
Statistics
Matches: 142, Mismatches: 10, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
44 11 0.08
45 84 0.59
46 47 0.33
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:3611433 original size:91 final size:90
Alignment explanation
Indices: 3611244--3611442 Score: 283
Period size: 91 Copynumber: 2.2 Consensus size: 90
3611234 TATAACATTT
* *
3611244 CTTATCATTTATCCTATAAACTCATAAGCTTATTTTACCAATATACTTAACATTTATCCCATAAG
1 CTTACCATTTATCCCATAAACTCATAAGCTTATTTTACCAATATACTTAACATTTATCCCATAAG
* *
3611309 CTCGTAAGCTTATTTTACCAATATA
66 CTCGTAAGATTATTTTACCAATACA
* * * *
3611334 CTTACCATTTAATCCCATAAGCTCGTAAGCTTATTTTACCAATATACTTACCATTTATTCCATAA
1 CTTACCATTT-ATCCCATAAACTCATAAGCTTATTTTACCAATATACTTAACATTTATCCCATAA
3611399 GCTCGTAAGATTATTTTACCAATACA
65 GCTCGTAAGATTATTTTACCAATACA
* * *
3611425 GTTGCCA-TTATTCCATAA
1 CTTACCATTTATCCCATAA
3611443 CCATATACCA
Statistics
Matches: 97, Mismatches: 11, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
89 8 0.08
90 11 0.11
91 78 0.80
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (90 bp):
CTTACCATTTATCCCATAAACTCATAAGCTTATTTTACCAATATACTTAACATTTATCCCATAAG
CTCGTAAGATTATTTTACCAATACA
Found at i:3611670 original size:59 final size:59
Alignment explanation
Indices: 3611543--3611671 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 59
3611533 CATAGTGCAA
* * ** *
3611543 TCCCGAATATGACACATAAGGTCATGTCCACCATCTGTACTAGGTATCCTTAAGTACAG
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGCATCCTTAAGTACAG
* * * ** *
3611602 TCCCAAATATGACACATAAGGTCGTGCCCACCATATACACTAGGCATCCTTTAGTGTAT
1 TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGCATCCTTAAGTACAG
3611661 TCCCGAATATG
1 TCCCGAATATG
3611672 CAGCCTGCTG
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.30, C:0.26, G:0.16, T:0.27
Consensus pattern (59 bp):
TCCCGAATATGACACATAAGGTCATGCCCACCATATACACTAGGCATCCTTAAGTACAG
Found at i:3614471 original size:42 final size:42
Alignment explanation
Indices: 3614412--3614681 Score: 251
Period size: 42 Copynumber: 6.5 Consensus size: 42
3614402 CAAGACGGTA
* * *
3614412 TTTTAATAACAAACGCCACTAAGGTACAGATCTATTACGGCG
1 TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
*
3614454 TTTTAATAACAAACGCCACTAAGGTTC-GCCTCTATTGTGGCG
1 TTTTAATAACAAACGCCACTAAGGTTCAG-CTCTATTGCGGCG
* * * * * * *
3614496 TTTTTATAATAAACACCACTAAGGTACGGCTCTATAGCGGCA
1 TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
* * ** * * *
3614538 TTTTAGTGACAAATTCCACTAAGGTTCACCTCTACTGCGGTG
1 TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
* * * *
3614580 TTTTAGTAACAAACGCCACTAAGGTTCACCTTTATTGTGGCG
1 TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
* * * *
3614622 TTTTTATAACAAATGCGACTAAGGTTC--CTCTACTGCGGCG
1 TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
* *
3614662 TTTTCATAA-AAATGCCACTA
1 TTTTAATAACAAACGCCACTA
3614682 CGGGACGGAT
Statistics
Matches: 186, Mismatches: 40, Indels: 7
0.80 0.17 0.03
Matches are distributed among these distances:
39 10 0.05
40 18 0.10
41 1 0.01
42 156 0.84
43 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.17, T:0.31
Consensus pattern (42 bp):
TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
Found at i:3615431 original size:21 final size:21
Alignment explanation
Indices: 3615407--3615455 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
3615397 CTCTCTGATG
3615407 AACACTCTTCATGCTATTCAC
1 AACACTCTTCATGCTATTCAC
* *
3615428 AACACTCTTCATGTTGTTCAC
1 AACACTCTTCATGCTATTCAC
3615449 ATACACT
1 A-ACACT
3615456 AACATTCCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.80
22 5 0.20
ACGTcount: A:0.29, C:0.31, G:0.06, T:0.35
Consensus pattern (21 bp):
AACACTCTTCATGCTATTCAC
Found at i:3617128 original size:6 final size:6
Alignment explanation
Indices: 3617128--3617153 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
3617118 AAATAATAAT
3617128 ATATTA ATATTA ATATTA ATATTA AT
1 ATATTA ATATTA ATATTA ATATTA AT
3617154 CACACTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
ATATTA
Found at i:3622917 original size:42 final size:42
Alignment explanation
Indices: 3622858--3623128 Score: 260
Period size: 42 Copynumber: 6.5 Consensus size: 42
3622848 CAAGACGGTA
* * *
3622858 TTTTAATAACAAACGCCACTAAGGTACAGATCTATTACGGCG
1 TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
*
3622900 TTTTAATAACAAACGCCACTAAGGTTC-GCCTCTATTGTGGCG
1 TTTTAATAACAAACGCCACTAAGGTTCAG-CTCTATTGCGGCG
* * * * * * *
3622942 TTTTTATAATAAACACCACTAAGGTACGGCTCTATAGCGGCA
1 TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
* * * * * *
3622984 TTTTAGTGACAAATGCCACTAAGGTTCACCTCTACTGCGGTG
1 TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
* * * *
3623026 TTTTAGTAACAAACGCCACTAAGGTTCACCTTTATTGTGGCG
1 TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
* * * *
3623068 TTTTTATAACAAATGCGACTAAGGTTC--CTCTACTGCGGCG
1 TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
* * *
3623108 TTTTCATAAAAAATGCCACTA
1 TTTTAATAACAAACGCCACTA
3623129 CGGGACGGAT
Statistics
Matches: 187, Mismatches: 40, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
40 28 0.15
41 1 0.01
42 157 0.84
43 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.31
Consensus pattern (42 bp):
TTTTAATAACAAACGCCACTAAGGTTCAGCTCTATTGCGGCG
Found at i:3623204 original size:73 final size:73
Alignment explanation
Indices: 3623085--3623226 Score: 223
Period size: 73 Copynumber: 1.9 Consensus size: 73
3623075 AACAAATGCG
* * *
3623085 ACTAAGGTTCCTCTACTGCGGCGTTTTCATAAAAAATGCCACTACGGGACG-GATCTATAGTGGT
1 ACTAAGGTTCCTCTACTGCGGCATTTTCATAAAAAACGCCACTACGGGA-GAGATCTATAGTGGA
3623149 GTTTTTTCC
65 GTTTTTTCC
* *
3623158 ACTAAGGTTCCTCTATTGCGGCATTTTCATAACAAACGCCACTACGGGAGAGATCTATAGTGGAG
1 ACTAAGGTTCCTCTACTGCGGCATTTTCATAAAAAACGCCACTACGGGAGAGATCTATAGTGGAG
3623223 TTTT
66 TTTT
3623227 ACTGAAAAAC
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
72 1 0.02
73 62 0.98
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (73 bp):
ACTAAGGTTCCTCTACTGCGGCATTTTCATAAAAAACGCCACTACGGGAGAGATCTATAGTGGAG
TTTTTTCC
Done.