Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008570.1 Hibiscus syriacus cultivar Beakdansim tig00111495_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: 912507
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
File 4 of 5
Found at i:555642 original size:40 final size:40
Alignment explanation
Indices: 555558--555728 Score: 193
Period size: 40 Copynumber: 4.2 Consensus size: 40
555548 TTAAAAATCG
* *
555558 CGTTGCGATTTACGGATACGCGTTGCAATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
*
555599 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* ** *
555639 CGTTGTGATTTACATATACGCGTTGCGATTTACGTATACT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* * * * *
555679 CGTTGCGATAGT-CAGA-ATCGCGTTGCGATTTTCATATTCG
1 CGTTGCGAT-TTACGGATA-CGCGTTGCGATTTACGTATTCT
555719 CGTTGCGATT
1 CGTTGCGATT
555729 CTTGAAAATC
Statistics
Matches: 112, Mismatches: 16, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.01
40 84 0.75
41 27 0.24
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:555781 original size:21 final size:21
Alignment explanation
Indices: 555694--555791 Score: 76
Period size: 21 Copynumber: 4.7 Consensus size: 21
555684 CGATAGTCAG
555694 AATCGCGTTGCGA-TTTTCAT
1 AATCGCGTTGCGATTTTTCAT
* * * *
555714 ATTCGCGTTGCGATTCTTGAA
1 AATCGCGTTGCGATTTTTCAT
* ** *
555735 AATCACAATGCGAATTTGT-ACT
1 AATCGCGTTGCG-ATTTTTCA-T
*
555757 -ATCGCATTGCGATTTTTCAT
1 AATCGCGTTGCGATTTTTCAT
555777 AATCGCGTTGCGATT
1 AATCGCGTTGCGATT
555792 CTGGGAACTG
Statistics
Matches: 58, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
20 18 0.31
21 36 0.62
22 4 0.07
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.38
Consensus pattern (21 bp):
AATCGCGTTGCGATTTTTCAT
Found at i:555827 original size:20 final size:19
Alignment explanation
Indices: 555778--555831 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
555768 ATTTTTCATA
555778 ATCGCGTTGCGATTCTGGG
1 ATCGCGTTGCGATTCTGGG
* **
555797 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGG-G
555818 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
555832 TTTATTTCGT
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 22 0.81
21 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.31, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGGG
Found at i:556542 original size:21 final size:21
Alignment explanation
Indices: 556425--556562 Score: 77
Period size: 21 Copynumber: 6.7 Consensus size: 21
556415 ACGCGAAATA
**
556425 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
556445 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* *
556465 AAAATCACAACGCGATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
556486 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
556507 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * *
556528 AAAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
556548 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
556563 ACACATAAAT
Statistics
Matches: 87, Mismatches: 27, Indels: 8
0.71 0.22 0.07
Matches are distributed among these distances:
19 1 0.01
20 38 0.44
21 46 0.53
22 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (21 bp):
AAAATCGCAACGCGATTTTCC
Found at i:556591 original size:20 final size:20
Alignment explanation
Indices: 556529--556721 Score: 210
Period size: 20 Copynumber: 9.7 Consensus size: 20
556519 CGATTTTCCA
* ** *
556529 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
556549 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
556569 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
556589 AAATCACAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
556609 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
556629 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
556649 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
556669 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
556689 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
556709 AAATCGCAACGCG
1 AAATCGCAACGCG
556722 ATATTTAAAG
Statistics
Matches: 143, Mismatches: 26, Indels: 7
0.81 0.15 0.04
Matches are distributed among these distances:
19 1 0.01
20 140 0.98
21 2 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:557142 original size:33 final size:33
Alignment explanation
Indices: 557103--557173 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
557093 TTCACTTCGA
* *
557103 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
557136 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
557169 TTTCA
1 TTTCA
557174 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:557297 original size:20 final size:20
Alignment explanation
Indices: 557266--557329 Score: 92
Period size: 20 Copynumber: 3.1 Consensus size: 20
557256 CAATGAGATA
*
557266 AATGAAAATCGCAACGAGAG
1 AATGACAATCGCAACGAGAG
**
557286 AATGACTGTCGCAACGAGAG
1 AATGACAATCGCAACGAGAG
557306 AAATGACAATCGCAACGAGAG
1 -AATGACAATCGCAACGAGAG
557327 AAT
1 AAT
557330 CGCAACGCGA
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
20 20 0.53
21 18 0.47
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.12
Consensus pattern (20 bp):
AATGACAATCGCAACGAGAG
Found at i:557310 original size:41 final size:38
Alignment explanation
Indices: 557246--557362 Score: 127
Period size: 41 Copynumber: 3.1 Consensus size: 38
557236 TTCAATTTGC
* * *
557246 AGAAGAGTCGCAATGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
557284 AGAATGACTGTCGCAACGAGAGAAATGACAATCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
557325 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
557358 AGAAT
1 AGAAT
557363 CGCAACGCGA
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
33 22 0.32
34 1 0.01
35 7 0.10
38 5 0.07
39 1 0.01
40 1 0.01
41 31 0.46
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.12
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:557326 original size:21 final size:21
Alignment explanation
Indices: 557253--557328 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
557243 TGCAGAAGAG
* * *
557253 TCGCAATGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGACAA
**
557274 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGACAA
557294 TCGCAACGAGAGAAATGACAA
1 TCGCAACGAGAGAAATGACAA
557315 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
557329 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGACAA
Found at i:557332 original size:14 final size:14
Alignment explanation
Indices: 557313--557369 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
557303 GAGAAATGAC
557313 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
557327 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
557346 AATCGCAACGAGAG
1 AATCGCAACGAGAG
557360 AATCGCAACG
1 AATCGCAACG
557370 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:557350 original size:33 final size:33
Alignment explanation
Indices: 557305--557385 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
557295 CGCAACGAGA
*
557305 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
557338 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
557371 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
557386 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.46, C:0.23, G:0.22, T:0.09
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:557403 original size:19 final size:19
Alignment explanation
Indices: 557381--557478 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
557371 GAAACCAAAA
*
557381 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
557400 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
557414 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
557433 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
557447 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
557466 TCGCGTTGCGATT
1 TCGCGTTGCGATT
557479 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 20 0.33
16 4 0.07
17 5 0.08
19 32 0.52
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:557422 original size:14 final size:14
Alignment explanation
Indices: 557403--557492 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
557393 TTTCATTTCG
557403 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
557417 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
557436 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
557450 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
557467 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
557483 CGTTGCGATT
1 CGTTGCGATT
557493 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 2 0.03
16 7 0.11
17 7 0.11
18 2 0.03
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.24, T:0.41
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:557432 original size:33 final size:33
Alignment explanation
Indices: 557386--557500 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
557376 CAAAATCGCA
*
557386 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
557419 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
557452 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
*
557485 TTGCGATTTTCATTTC
1 TTGCGATTGTCATTTC
557501 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.44
Consensus pattern (33 bp):
TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
Found at i:559357 original size:93 final size:93
Alignment explanation
Indices: 559198--559671 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
559188 TAGATTGCTT
*
559198 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
559263 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
559291 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
559356 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
559384 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
559449 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
559477 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
559542 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
559570 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
559635 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
559663 AGTAAATTT
1 AGTAAATTT
559672 ATCCATTCAA
Statistics
Matches: 378, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 378 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:559755 original size:19 final size:19
Alignment explanation
Indices: 559715--559824 Score: 87
Period size: 19 Copynumber: 6.3 Consensus size: 19
559705 TAGTTTACTT
* *
559715 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
559735 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
559754 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
559768 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
559787 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
**
559801 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
559820 TCGCA
1 TCGCA
559825 TTGCGATTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
14 16 0.21
16 11 0.15
17 10 0.13
19 26 0.35
20 12 0.16
ACGTcount: A:0.46, C:0.25, G:0.18, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:559771 original size:14 final size:14
Alignment explanation
Indices: 559752--559808 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
559742 GCGAAATGAA
*
559752 AATCGCAACGACAG
1 AATCGCAACGAAAG
559766 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
559783 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
559799 AATCGCAACG
1 AATCGCAACG
559809 CGAAACCAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:559779 original size:33 final size:33
Alignment explanation
Indices: 559733--559824 Score: 148
Period size: 33 Copynumber: 2.8 Consensus size: 33
559723 CGAAACTTAA
*
559733 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
559766 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
**
559799 AATCGCAACGCGAAACCAAAATCGCA
1 AATCGCAACGCGAAATGAAAATCGCA
559825 TTGCGATTTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 54 1.00
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.10
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:559842 original size:19 final size:19
Alignment explanation
Indices: 559820--559954 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
559810 GAAACCAAAA
*
559820 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
559839 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
559855 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
559872 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
*
559888 T--CGTTGTGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
559905 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
559924 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
559944 TCGTGTTGCGA
1 TCGCGTTGCGA
559955 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 12, Indels: 21
0.74 0.10 0.17
Matches are distributed among these distances:
14 14 0.15
16 11 0.12
17 11 0.12
19 45 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:559861 original size:14 final size:14
Alignment explanation
Indices: 559842--559898 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
559832 TTTCATTTCG
559842 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
559856 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
559873 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
*
559889 CGTTGTGATT
1 CGTTGCGATT
559899 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 15 0.42
16 7 0.19
17 8 0.22
19 6 0.17
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:559867 original size:33 final size:33
Alignment explanation
Indices: 559825--559917 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
559815 CAAAATCGCA
*
559825 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
559858 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
559891 TTGTGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
559918 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.11, C:0.19, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:561901 original size:14 final size:14
Alignment explanation
Indices: 561882--561917 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
561872 ATTGTTTAAT
561882 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
561896 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
561910 TGATTTGT
1 TGATTTGT
561918 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:562092 original size:20 final size:19
Alignment explanation
Indices: 562024--562104 Score: 109
Period size: 19 Copynumber: 4.5 Consensus size: 19
562014 AAAATTGACT
562024 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
562043 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
562057 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
562076 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
562096 ATCGCAATG
1 ATCGCAATG
562105 GGAGAATCGC
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 10 0.19
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 20 0.37
20 18 0.33
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:562139 original size:19 final size:19
Alignment explanation
Indices: 562111--562259 Score: 139
Period size: 19 Copynumber: 8.6 Consensus size: 19
562101 AATGGGAGAA
* *
562111 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
562130 TCGCATTGCGA--TT-ATC
1 TCGCATTGCGATTTTCATT
562146 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
562163 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
562182 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
562198 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
562215 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
562231 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
562248 TCCGCATTGCGA
1 T-CGCATTGCGA
562260 AATGTAATGG
Statistics
Matches: 107, Mismatches: 7, Indels: 31
0.74 0.05 0.21
Matches are distributed among these distances:
14 18 0.17
16 21 0.20
17 19 0.18
18 2 0.02
19 41 0.38
20 6 0.06
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:562174 original size:52 final size:52
Alignment explanation
Indices: 562111--562227 Score: 207
Period size: 52 Copynumber: 2.2 Consensus size: 52
562101 AATGGGAGAA
*
562111 TCGCAATGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
* *
562163 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
562215 TCGCATTGCGATT
1 TCGCATTGCGATT
562228 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 62 1.00
ACGTcount: A:0.16, C:0.21, G:0.18, T:0.44
Consensus pattern (52 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATT
Found at i:562205 original size:33 final size:33
Alignment explanation
Indices: 562168--562259 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
562158 TCATTTCGCA
562168 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
562201 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
562234 TTGCGATTTTCATTTCCGCATTGCGA
1 TTGCGATTTTCATTT-CGCATTGCGA
562260 AATGTAATGG
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 48 0.83
34 10 0.17
ACGTcount: A:0.13, C:0.24, G:0.18, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:562206 original size:14 final size:14
Alignment explanation
Indices: 562187--562241 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
562177 TCATTTCGCA
562187 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
562201 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
562218 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
562234 TTGCGATT
1 TTGCGATT
562242 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:562342 original size:19 final size:19
Alignment explanation
Indices: 562318--562487 Score: 225
Period size: 19 Copynumber: 9.4 Consensus size: 19
562308 AAAATTGACT
562318 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
562337 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
562356 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
562370 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
562389 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
562408 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
562422 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
562441 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
562461 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
*
562481 ATTGCAA
1 ATCGCAA
562488 CGAGAGAATC
Statistics
Matches: 135, Mismatches: 5, Indels: 21
0.84 0.03 0.13
Matches are distributed among these distances:
14 20 0.15
15 2 0.01
16 4 0.03
17 4 0.03
18 2 0.01
19 68 0.50
20 35 0.26
ACGTcount: A:0.46, C:0.16, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:562396 original size:52 final size:52
Alignment explanation
Indices: 562318--562467 Score: 291
Period size: 52 Copynumber: 2.9 Consensus size: 52
562308 AAAATTGACT
562318 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
562370 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
562422 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAA
562468 TGCGGAAATG
Statistics
Matches: 97, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
52 81 0.84
53 16 0.16
ACGTcount: A:0.46, C:0.17, G:0.23, T:0.14
Consensus pattern (52 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:562425 original size:33 final size:33
Alignment explanation
Indices: 562388--562506 Score: 157
Period size: 33 Copynumber: 3.4 Consensus size: 33
562378 GCGAAATGAA
562388 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
562421 AATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--C-G--A-GAG
*
562460 AATCGCAATGCGGAAATGAAAATTGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAG
562494 AATCGCAATGCGA
1 AATCGCAATGCGA
562507 TTTTCATTTC
Statistics
Matches: 76, Mismatches: 3, Indels: 14
0.82 0.03 0.15
Matches are distributed among these distances:
33 29 0.38
34 13 0.17
35 2 0.03
36 1 0.01
37 1 0.01
38 2 0.03
39 13 0.17
40 15 0.20
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:562519 original size:73 final size:72
Alignment explanation
Indices: 562318--562506 Score: 260
Period size: 73 Copynumber: 2.6 Consensus size: 72
562308 AAAATTGACT
* * * * *
562318 ATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-CGCAACGAGAGAATCGCAATGC
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-CAATGCGAAATGA-A-AATCGCAATGC
562380 -GAAATGAAA
63 GGAAATGAAA
562389 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGGA
562454 AATGAAA
66 AATGAAA
*
562461 ATCGCAATGCGGAAATGAAAATTGCAACGAGAGAATCGCAATGCGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
562507 TTTTCATTTC
Statistics
Matches: 107, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
71 40 0.37
72 26 0.24
73 41 0.38
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (72 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGGA
AATGAAA
Found at i:564842 original size:12 final size:12
Alignment explanation
Indices: 564825--564849 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
564815 TCTTCGGGGA
564825 CTTTTTCTTCTT
1 CTTTTTCTTCTT
564837 CTTTTTCTTCTT
1 CTTTTTCTTCTT
564849 C
1 C
564850 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:565062 original size:24 final size:23
Alignment explanation
Indices: 565023--565068 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
565013 CTGAAACATC
565023 ATCAAATCCGTGTATTGACCAAT
1 ATCAAATCCGTGTATTGACCAAT
565046 ATCAAAGTCCG-GATATTGACCAA
1 ATCAAA-TCCGTG-TATTGACCAA
565069 GACCAAATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 14 0.67
ACGTcount: A:0.37, C:0.22, G:0.15, T:0.26
Consensus pattern (23 bp):
ATCAAATCCGTGTATTGACCAAT
Found at i:566000 original size:20 final size:20
Alignment explanation
Indices: 565750--565999 Score: 261
Period size: 20 Copynumber: 12.5 Consensus size: 20
565740 AAATTTCAGT
* * *
565750 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
565770 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
565790 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
565810 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
565830 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
*
565850 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
565870 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* **
565890 ATTGCGATTTACCCATAT-GC
1 GTTGCGATTTACGGAT-TCGC
*
565910 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
565930 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
565950 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
565970 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
565990 GTTGCGATTT
1 GTTGCGATTT
566000 TAGAAAATCG
Statistics
Matches: 198, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
20 197 0.99
21 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:566051 original size:21 final size:21
Alignment explanation
Indices: 565966--566063 Score: 74
Period size: 21 Copynumber: 4.7 Consensus size: 21
565956 ATTTATGTGT
* *
565966 TCGCGTTGCGATTTTC-ATAT
1 TCGCGTTGCGATTTTCAAAAA
565986 TCGCGTTGCGATTTT-AGAAAA
1 TCGCGTTGCGATTTTCA-AAAA
** * ** **
566007 TCGCAATGCGAATTTGTACTA
1 TCGCGTTGCGATTTTCAAAAA
* *
566028 TCGCATTGCGATTTTCAAGAA
1 TCGCGTTGCGATTTTCAAAAA
566049 TCGCGTTGCGATTTT
1 TCGCGTTGCGATTTT
566064 GGAAACTGAT
Statistics
Matches: 60, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 15 0.25
21 45 0.75
ACGTcount: A:0.22, C:0.18, G:0.21, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTTTCAAAAA
Found at i:566059 original size:42 final size:43
Alignment explanation
Indices: 565966--566064 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
565956 ATTTATGTGT
*
565966 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTAGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTAGAAAA
** *
566007 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTTCA-AGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTT-AGAAAA
*
566049 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
566065 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 8 0.17
42 35 0.74
43 4 0.09
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTAGAAAA
Found at i:570626 original size:20 final size:20
Alignment explanation
Indices: 570603--570677 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
570593 CAGGTTCCAA
*
570603 ATTCGCAACACGATTTTAGG
1 ATTCGCAACGCGATTTTAGG
** * *
570623 ATTCGCAACGCGATAGTCGAA
1 ATTCGCAACGCGATTTTAG-G
*
570644 ATTCGCAACGCGATTTTAAG
1 ATTCGCAACGCGATTTTAGG
*
570664 ATTCGCAATGCGAT
1 ATTCGCAACGCGAT
570678 AGTCGAAATT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (20 bp):
ATTCGCAACGCGATTTTAGG
Found at i:570649 original size:21 final size:21
Alignment explanation
Indices: 570623--570713 Score: 105
Period size: 21 Copynumber: 4.4 Consensus size: 21
570613 CGATTTTAGG
570623 ATTCGCAACGCGATAGTCGAA
1 ATTCGCAACGCGATAGTCGAA
**
570644 ATTCGCAACGCGAT--TTTAA
1 ATTCGCAACGCGATAGTCGAA
*
570663 GATTCGCAATGCGATAGTCGAA
1 -ATTCGCAACGCGATAGTCGAA
* *
570685 ATTCGCAACGCGATACTCCAA
1 ATTCGCAACGCGATAGTCGAA
*
570706 AATCGCAA
1 ATTCGCAA
570714 TGCATTTGTT
Statistics
Matches: 58, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
19 3 0.05
20 13 0.22
21 39 0.67
22 3 0.05
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (21 bp):
ATTCGCAACGCGATAGTCGAA
Found at i:570651 original size:41 final size:41
Alignment explanation
Indices: 570601--570698 Score: 169
Period size: 41 Copynumber: 2.4 Consensus size: 41
570591 CTCAGGTTCC
* *
570601 AAATTCGCAACACGATTTTAGGATTCGCAACGCGATAGTCG
1 AAATTCGCAACGCGATTTTAAGATTCGCAACGCGATAGTCG
*
570642 AAATTCGCAACGCGATTTTAAGATTCGCAATGCGATAGTCG
1 AAATTCGCAACGCGATTTTAAGATTCGCAACGCGATAGTCG
570683 AAATTCGCAACGCGAT
1 AAATTCGCAACGCGAT
570699 ACTCCAAAAT
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.24
Consensus pattern (41 bp):
AAATTCGCAACGCGATTTTAAGATTCGCAACGCGATAGTCG
Found at i:571379 original size:25 final size:25
Alignment explanation
Indices: 571345--571403 Score: 118
Period size: 25 Copynumber: 2.4 Consensus size: 25
571335 TGTTCACTTG
571345 GTTAAATGTGTTCCAACTTCCAAAT
1 GTTAAATGTGTTCCAACTTCCAAAT
571370 GTTAAATGTGTTCCAACTTCCAAAT
1 GTTAAATGTGTTCCAACTTCCAAAT
571395 GTTAAATGT
1 GTTAAATGT
571404 TAAATGTTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (25 bp):
GTTAAATGTGTTCCAACTTCCAAAT
Found at i:571700 original size:21 final size:21
Alignment explanation
Indices: 571674--571762 Score: 92
Period size: 21 Copynumber: 4.3 Consensus size: 21
571664 AAGAAATGCA
*
571674 TTGCGATTTTGGAGTATCGCG
1 TTGCGATTTTGGACTATCGCG
* *
571695 TTGCGAATTTCGACTATCGCG
1 TTGCGATTTTGGACTATCGCG
* **
571716 TTGCGAATCTT--AAAATCGCG
1 TTGCG-ATTTTGGACTATCGCG
*
571736 TTGCAATTTTGGACTATCGCG
1 TTGCGATTTTGGACTATCGCG
571757 TTGCGA
1 TTGCGA
571763 ATCTTAAAAT
Statistics
Matches: 53, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 4 0.08
20 11 0.21
21 35 0.66
22 3 0.06
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (21 bp):
TTGCGATTTTGGACTATCGCG
Found at i:571735 original size:20 final size:20
Alignment explanation
Indices: 571710--571784 Score: 80
Period size: 20 Copynumber: 3.7 Consensus size: 20
571700 AATTTCGACT
571710 ATCGCGTTGCGAATCTTAAA
1 ATCGCGTTGCGAATCTTAAA
* **
571730 ATCGCGTTGC-AATTTTGGACT
1 ATCGCGTTGCGAATCTT--AAA
571751 ATCGCGTTGCGAATCTTAAA
1 ATCGCGTTGCGAATCTTAAA
* *
571771 ATTGTGTTGCGAAT
1 ATCGCGTTGCGAAT
571785 TTCAACTTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
19 5 0.11
20 23 0.52
21 11 0.25
22 5 0.11
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGAATCTTAAA
Found at i:571735 original size:41 final size:41
Alignment explanation
Indices: 571689--571805 Score: 173
Period size: 41 Copynumber: 2.9 Consensus size: 41
571679 ATTTTGGAGT
571689 ATCGCGTTGCGAATTTCGACTATCGCGTTGCGAATCTTAAA
1 ATCGCGTTGCGAATTTCGACTATCGCGTTGCGAATCTTAAA
*
571730 ATCGCGTTGC-AATTTTGGACTATCGCGTTGCGAATCTTAAA
1 ATCGCGTTGCGAA-TTTCGACTATCGCGTTGCGAATCTTAAA
* * * *
571771 ATTGTGTTGCGAATTTCAACTTTCGCGTTGCGAAT
1 ATCGCGTTGCGAATTTCGACTATCGCGTTGCGAAT
571806 TTGGAACATG
Statistics
Matches: 68, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
40 2 0.03
41 64 0.94
42 2 0.03
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGAATTTCGACTATCGCGTTGCGAATCTTAAA
Found at i:571802 original size:21 final size:20
Alignment explanation
Indices: 571688--571807 Score: 102
Period size: 21 Copynumber: 5.8 Consensus size: 20
571678 GATTTTGGAG
*
571688 TATCGCGTTGCGAATTTCGAC
1 TATCGCGTTGCGAATTT-AAC
571709 TATCGCGTTGCGAATCTTAA-
1 TATCGCGTTGCGAAT-TTAAC
* *
571729 AATCGCGTTGC-AATTTTGGAC
1 TATCGCGTTGCGAA-TTT-AAC
571750 TATCGCGTTGCGAATCTTAA-
1 TATCGCGTTGCGAAT-TTAAC
* * *
571770 AATTGTGTTGCGAATTTCAAC
1 TATCGCGTTGCGAATTT-AAC
*
571791 TTTCGCGTTGCGAATTT
1 TATCGCGTTGCGAATTT
571808 GGAACATGGG
Statistics
Matches: 79, Mismatches: 12, Indels: 16
0.74 0.11 0.15
Matches are distributed among these distances:
19 6 0.08
20 26 0.33
21 41 0.52
22 6 0.08
ACGTcount: A:0.23, C:0.19, G:0.22, T:0.37
Consensus pattern (20 bp):
TATCGCGTTGCGAATTTAAC
Found at i:572483 original size:20 final size:18
Alignment explanation
Indices: 572446--572489 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
572436 CCTATTTCTT
572446 AATATTAAAAAATAAATA
1 AATATTAAAAAATAAATA
*
572464 AATATTAATAAAATGTAATA
1 AATATTAA-AAAAT-AAATA
572484 AATATT
1 AATATT
572490 CCTAAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 5 0.22
20 10 0.43
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
AATATTAAAAAATAAATA
Found at i:572644 original size:2 final size:2
Alignment explanation
Indices: 572637--572668 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
572627 ATTTAAACAA
572637 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
572669 GACTAATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:572699 original size:11 final size:11
Alignment explanation
Indices: 572679--572712 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
572669 GACTAATATG
572679 AAAATAATAAT
1 AAAATAATAAT
572690 AAAATAATAATT
1 AAAATAATAA-T
*
572702 AAAGTAATAAT
1 AAAATAATAAT
572713 TTAAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:572709 original size:12 final size:12
Alignment explanation
Indices: 572679--572713 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
572669 GACTAATATG
572679 AAAATAATAA-T
1 AAAATAATAATT
572690 AAAATAATAATT
1 AAAATAATAATT
*
572702 AAAGTAATAATT
1 AAAATAATAATT
572714 TAAACATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:573939 original size:3 final size:3
Alignment explanation
Indices: 573931--573990 Score: 70
Period size: 3 Copynumber: 20.0 Consensus size: 3
573921 ATTATTTATT
* *
573931 TAA TAA TAA T-A TATA TAA T-A TATA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
573976 TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA
573991 AAAAAATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:573957 original size:18 final size:18
Alignment explanation
Indices: 573931--573990 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
573921 ATTATTTATT
573931 TAATAATAATATATATAA
1 TAATAATAATATATATAA
*
573949 T-ATATATAATATTTATAA
1 TAATA-ATAATATATATAA
573967 TAATAATAATA-ATAATAA
1 TAATAATAATATAT-ATAA
573985 TAATAA
1 TAATAA
573991 AAAAAATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
17 4 0.11
18 30 0.81
19 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATAATAATATATATAA
Found at i:574433 original size:44 final size:45
Alignment explanation
Indices: 574295--574433 Score: 199
Period size: 45 Copynumber: 3.1 Consensus size: 45
574285 GAGGTATTAT
* *
574295 CATCTTGCACTGTAGGTCTTACAGATAACCCGAAGGCTTTGAAAA
1 CATCATGCACTGTAGGACTTACAGATAACCCGAAGGCTTTGAAAA
* *
574340 CATCATGCATTGTAGGACTTACAGATAACCCGAAGGTTTTGAAAA
1 CATCATGCACTGTAGGACTTACAGATAACCCGAAGGCTTTGAAAA
* * * *
574385 CATCATGCACTGAAGGGCTTACAGAT-ACACGAAGGCTTGGAAAA
1 CATCATGCACTGTAGGACTTACAGATAACCCGAAGGCTTTGAAAA
574429 CATCA
1 CATCA
574434 AAAAGCTCCC
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
44 20 0.24
45 64 0.76
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (45 bp):
CATCATGCACTGTAGGACTTACAGATAACCCGAAGGCTTTGAAAA
Found at i:574726 original size:17 final size:17
Alignment explanation
Indices: 574699--574737 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
574689 AATTTACAAT
574699 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
574715 TAATTATAAATAATATC
1 TAATTATAAATAATATC
574732 TAATTA
1 TAATTA
574738 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:575172 original size:45 final size:45
Alignment explanation
Indices: 575113--575216 Score: 163
Period size: 45 Copynumber: 2.3 Consensus size: 45
575103 CCTGAAGGCT
* *
575113 TTTTGAAAACATCATGCCCTGAAGGGCTTACAGATGACCCGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACACGAAGG
* *
575158 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACACGAAGG
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACACGAAGG
*
575203 CTTTGAAAACATCA
1 TTTTGAAAACATCA
575217 AAAAGCTCCC
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 54 1.00
ACGTcount: A:0.34, C:0.20, G:0.21, T:0.25
Consensus pattern (45 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACACGAAGG
Found at i:575238 original size:121 final size:121
Alignment explanation
Indices: 575024--575413 Score: 613
Period size: 121 Copynumber: 3.2 Consensus size: 121
575014 AGGTCTTATG
* *
575024 GATGACCCGAAGGTTTTGAAAACGTCATGCACTGTAGGACTTAGAGATGACCCGAAGGCTTTGAA
1 GATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAA
* * *
575089 AACATCAAAAATCTCCTGAAGGCTTTTTGAAAACATCATGCCCTGAAGGGCTTACA
66 AACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACA
* *
575145 GATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACACGAAGGCTTTGAA
1 GATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAA
* * * *
575210 AACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATTC-TGCACTGTACGTCTTA-T
66 AACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACA-TCATGCACTGAAGGGCTTACA
* * *
575265 GTATGACCCAAATGTTTTGAAAATATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGA
1 G-ATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGA
575330 AAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACA
65 AAACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACA
*
575387 GATGACCCGAAGGCTTTGAAAACATCA
1 GATGACCCGAAGGTTTTGAAAACATCA
575414 AAAAGCTCCC
Statistics
Matches: 241, Mismatches: 24, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
120 3 0.01
121 235 0.98
122 3 0.01
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.25
Consensus pattern (121 bp):
GATGACCCGAAGGTTTTGAAAACATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAA
AACATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACA
Found at i:575405 original size:76 final size:76
Alignment explanation
Indices: 575279--575488 Score: 366
Period size: 76 Copynumber: 2.8 Consensus size: 76
575269 GACCCAAATG
* * *
575279 TTTTGAAAATATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
575344 TCCCGAAGGCT
66 TCCCGAAGGCT
575355 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
575420 TCCCGAAGGCT
66 TCCCGAAGGCT
* * *
575431 TTTTTAAAACATCATGCACTGAAGGGCTTACAGATGACACGAAGGCTTTAAAAACATC
1 TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATC
575489 CTGCACTGAA
Statistics
Matches: 128, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
76 128 1.00
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (76 bp):
TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGC
TCCCGAAGGCT
Found at i:575496 original size:197 final size:195
Alignment explanation
Indices: 575150--575511 Score: 521
Period size: 197 Copynumber: 1.8 Consensus size: 195
575140 TTACAGATGA
* *
575150 CCCGAAGGTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACACGAAGGCTTTGAAAACAT
1 CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACACGAAGGCTTTGAAAACAT
* * * * * *
575215 CAAAAAGCTCCCGAAGGCTTTTTGAAAACATTCTGCACTGTACGTCTTATGTATGACCCAAATGT
66 CAAAAAGCTCCCGAAGGCTTTTTGAAAACATTCTGCACTGAACGGCTTAAGTATGACACAAAGGC
* * *
575280 TTTGAAAATATCATGCACTGTAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
131 TTTAAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
575345 CCCGAAGGCTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGCTTTGAAAAC
1 CCCGAAGG--TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACACGAAGGCTTTGAAAAC
* * *
575410 ATCAAAAAGCTCCCGAAGGCTTTTTTAAAACA-TCATGCACTGAAGGGCTTACAG-ATGACACGA
64 ATCAAAAAGCTCCCGAAGGCTTTTTGAAAACATTC-TGCACTGAACGGCTTA-AGTATGACACAA
* *
575473 AGGCTTTAAAAACATCCTGCACTGAAGGTCTTACAGATG
127 AGGCTTTAAAAACATCATGCACTGAAGGACTTACAGATG
575512 TGGGAAATAG
Statistics
Matches: 146, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
195 8 0.05
196 2 0.01
197 135 0.92
198 1 0.01
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (195 bp):
CCCGAAGGTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGACACGAAGGCTTTGAAAACAT
CAAAAAGCTCCCGAAGGCTTTTTGAAAACATTCTGCACTGAACGGCTTAAGTATGACACAAAGGC
TTTAAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
Found at i:576235 original size:22 final size:22
Alignment explanation
Indices: 576180--576236 Score: 96
Period size: 22 Copynumber: 2.6 Consensus size: 22
576170 AATAAAGCTT
* *
576180 TCATCTTTGAAAAGAGAATTTA
1 TCATCTTTGAAGAGAGAATCTA
576202 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
576224 TCATCTTTGAAGA
1 TCATCTTTGAAGA
576237 ATGTAGATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:576711 original size:54 final size:54
Alignment explanation
Indices: 576604--576711 Score: 146
Period size: 54 Copynumber: 2.0 Consensus size: 54
576594 ATAATTACTG
* *
576604 GTTCGTAAAACATTTGACAACACGTTCATCTTTTACTATGGCTTCTGCACAGAT
1 GTTCGTAAAACATTTGACAACACATTCATCTTTTACTATGGCTTCTACACAGAT
* * * *
576658 GTTCGTAAAATATTTGACAACACATTTATCTTTTTA-TGTGGCTTCTACCCAGAT
1 GTTCGTAAAACATTTGACAACACATTCATC-TTTTACTATGGCTTCTACACAGAT
576712 TTCTCATCAA
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 42 0.89
55 5 0.11
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCTTTTACTATGGCTTCTACACAGAT
Found at i:577636 original size:66 final size:69
Alignment explanation
Indices: 577553--577709 Score: 178
Period size: 75 Copynumber: 2.2 Consensus size: 69
577543 ACAGGATGAT
* * *
577553 ATGAGCCTTCAGCATGCCCCAACATTTG-T-T-GTTCAAAATGCATCAACATTCCT-ATTTCTGA
1 ATGAGCTTTCAGCATGCCCCAACATTTGCTATAATTCAAAATACATCAACATTCCTGATTT-TGA
577614 TTGAA
65 TTGAA
*
577619 ATGAGCTTTCAGCATGCCCTAACATTTGCTGATACAAACATTCAAAATACATCAACATTCCTGAT
1 ATGAGCTTTCAGCATGCCCCAACATTTGCT-AT----A-ATTCAAAATACATCAACATTCCTGAT
577684 TTTGATTGAA
60 TTTGATTGAA
*
577694 ATGGGCTTTCAGCATG
1 ATGAGCTTTCAGCATG
577710 TTCCAGCATT
Statistics
Matches: 76, Mismatches: 5, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
66 26 0.34
67 1 0.01
69 1 0.01
75 44 0.58
76 4 0.05
ACGTcount: A:0.31, C:0.22, G:0.15, T:0.32
Consensus pattern (69 bp):
ATGAGCTTTCAGCATGCCCCAACATTTGCTATAATTCAAAATACATCAACATTCCTGATTTTGAT
TGAA
Found at i:582962 original size:24 final size:22
Alignment explanation
Indices: 582930--582991 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 22
582920 TTGATGCATA
*
582930 AGGAGTGCATCGATGCACACGTT
1 AGGA-TGCATCGATGCACACGAT
582953 AAGGGATGCATCGAT--ACACGAT
1 -A-GGATGCATCGATGCACACGAT
582975 AGGATGCATCGATGCAC
1 AGGATGCATCGATGCAC
582992 TTCAAGGGGA
Statistics
Matches: 34, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 12 0.35
21 1 0.03
22 8 0.24
24 10 0.29
25 3 0.09
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (22 bp):
AGGATGCATCGATGCACACGAT
Found at i:586714 original size:24 final size:24
Alignment explanation
Indices: 586686--586749 Score: 66
Period size: 24 Copynumber: 2.8 Consensus size: 24
586676 CATTGATGCA
*
586686 TAAGGAGTGCATCGATGCACACGT
1 TAAGGAGTGCATCGATGCACACGG
*
586710 TAAGG-GATACATCGAT--ACACGG
1 TAAGGAG-TGCATCGATGCACACGG
586732 T-AGGA-TGCATCGATGCAC
1 TAAGGAGTGCATCGATGCAC
586750 TTCAAGGGGA
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
20 8 0.24
21 3 0.09
22 8 0.24
23 1 0.03
24 13 0.39
ACGTcount: A:0.31, C:0.20, G:0.28, T:0.20
Consensus pattern (24 bp):
TAAGGAGTGCATCGATGCACACGG
Found at i:587124 original size:21 final size:21
Alignment explanation
Indices: 587098--587137 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
587088 ATATGTGAAC
*
587098 ATATGAATTATATGAAAAGTT
1 ATATGAATTACATGAAAAGTT
587119 ATATGAATTACATGAAAAG
1 ATATGAATTACATGAAAAG
587138 AAGCTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.03, G:0.15, T:0.33
Consensus pattern (21 bp):
ATATGAATTACATGAAAAGTT
Found at i:587447 original size:27 final size:27
Alignment explanation
Indices: 587394--587448 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
587384 CTTAAGAAGT
* * *
587394 GGTCATTCGGGACAAATACAGTACATA
1 GGTCATTCGGGACAAAAAAAATACATA
* *
587421 GGTCCTTCGGGACAAAAAAAATTCATA
1 GGTCATTCGGGACAAAAAAAATACATA
587448 G
1 G
587449 CCCCTAGTGG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.22
Consensus pattern (27 bp):
GGTCATTCGGGACAAAAAAAATACATA
Found at i:588738 original size:43 final size:43
Alignment explanation
Indices: 588690--588774 Score: 125
Period size: 43 Copynumber: 2.0 Consensus size: 43
588680 CGGTGCATCA
* *
588690 AACAAAACTTTACATATAGGGGACATCTTTCAGTCCTAACTTC
1 AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
* * *
588733 AACAAAACTTTACATATATGGGATAACTTTCCCTCCTAACTT
1 AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTT
588775 ATCTAAAGCC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.35, C:0.24, G:0.09, T:0.32
Consensus pattern (43 bp):
AACAAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTC
Found at i:590698 original size:2 final size:2
Alignment explanation
Indices: 590685--590726 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
590675 ATAAAAGTAA
*
590685 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
590727 TTAAGTTATT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:591044 original size:11 final size:11
Alignment explanation
Indices: 591024--591057 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
591014 GACTAATATG
591024 AAAATAATAAT
1 AAAATAATAAT
591035 AAAATAATAATT
1 AAAATAATAA-T
*
591047 AAAGTAATAAT
1 AAAATAATAAT
591058 TTAAACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (11 bp):
AAAATAATAAT
Found at i:591054 original size:12 final size:12
Alignment explanation
Indices: 591024--591058 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
591014 GACTAATATG
591024 AAAATAATAA-T
1 AAAATAATAATT
591035 AAAATAATAATT
1 AAAATAATAATT
*
591047 AAAGTAATAATT
1 AAAATAATAATT
591059 TAAACATATC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (12 bp):
AAAATAATAATT
Found at i:592274 original size:3 final size:3
Alignment explanation
Indices: 592266--592346 Score: 76
Period size: 3 Copynumber: 27.0 Consensus size: 3
592256 ATTATTTATT
* * * *
592266 TAA TAA TAA TAA T-A TATA TTA TATA TAG TAT TAA TAA TAA TAA TTA
1 TAA TAA TAA TAA TAA TA-A TAA TA-A TAA TAA TAA TAA TAA TAA TAA
* *
592312 TTA TAA TTA TAA TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
592347 AATGAAAAAA
Statistics
Matches: 65, Mismatches: 9, Indels: 8
0.79 0.11 0.10
Matches are distributed among these distances:
2 4 0.06
3 56 0.86
4 5 0.08
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (3 bp):
TAA
Found at i:595207 original size:32 final size:32
Alignment explanation
Indices: 595169--595245 Score: 95
Period size: 31 Copynumber: 2.4 Consensus size: 32
595159 TGGGGCTGTG
*
595169 GGGCCTACCTAAGAACAT-ATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ATGATCTCAGGGCCGCA
**
595201 GGGCCTACCCGAG-AATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAATGATCTCAGGGCCGCA
*
595232 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
595246 GTCACATTAG
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
30 2 0.05
31 24 0.65
32 11 0.30
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (32 bp):
GGGCCTACCTAAGAAATGATCTCAGGGCCGCA
Found at i:596705 original size:26 final size:26
Alignment explanation
Indices: 596675--596737 Score: 99
Period size: 26 Copynumber: 2.4 Consensus size: 26
596665 GGTGAAATTC
*
596675 TTGGTCATTTGCATACCAGGGGTATT
1 TTGGTCATTTCCATACCAGGGGTATT
* *
596701 TTGGTTATTTCCATACTAGGGGTATT
1 TTGGTCATTTCCATACCAGGGGTATT
596727 TTGGTCATTTC
1 TTGGTCATTTC
596738 ACAGATCTAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.17, C:0.14, G:0.24, T:0.44
Consensus pattern (26 bp):
TTGGTCATTTCCATACCAGGGGTATT
Found at i:599930 original size:20 final size:20
Alignment explanation
Indices: 599905--599962 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
599895 ATTCTATTCC
599905 CTGGTAATCTTTCATTCCCA
1 CTGGTAATCTTTCATTCCCA
* *
599925 CTGGTAATCTTTTATTCTCA
1 CTGGTAATCTTTCATTCCCA
*
599945 CTGGTAATCTTACATTCC
1 CTGGTAATCTTTCATTCC
599963 GTGAACCAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.21, C:0.26, G:0.10, T:0.43
Consensus pattern (20 bp):
CTGGTAATCTTTCATTCCCA
Found at i:607448 original size:2 final size:2
Alignment explanation
Indices: 607443--607484 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
607433 TGGTTTTGAG
*
607443 GA GA GA GA GA GA GA GA GA GA GA GA AA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
607485 AGGGGGTTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:607615 original size:21 final size:22
Alignment explanation
Indices: 607578--607629 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
607568 TCTTTCAAAT
**
607578 TTTATTTTTTGATATTTTTCATC
1 TTTATTTTTTGA-ATTTAACATC
607601 TTTATTTTTTG-ATTTAACATC
1 TTTATTTTTTGAATTTAACATC
607622 TTTATTTT
1 TTTATTTT
607630 AACGCGACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 16 0.59
23 11 0.41
ACGTcount: A:0.19, C:0.08, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTATTTTTTGAATTTAACATC
Found at i:607946 original size:32 final size:31
Alignment explanation
Indices: 607910--607985 Score: 80
Period size: 32 Copynumber: 2.3 Consensus size: 31
607900 ATTATTATTT
*
607910 TTAAATTAAATAAAAATGCAATAAAAAAAGAA
1 TTAAAGTAAAT-AAAATGCAATAAAAAAAGAA
** *
607942 TTAAAAGTGTATAAAATTCAATAAAAAAAGAA
1 TT-AAAGTAAATAAAATGCAATAAAAAAAGAA
607974 TGTAAAGCTAAA
1 T-TAAAG-TAAA
607986 AAATATCACC
Statistics
Matches: 35, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
32 26 0.74
33 9 0.26
ACGTcount: A:0.63, C:0.04, G:0.09, T:0.24
Consensus pattern (31 bp):
TTAAAGTAAATAAAATGCAATAAAAAAAGAA
Found at i:608406 original size:20 final size:21
Alignment explanation
Indices: 608362--608403 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
608352 ATGTATTGTG
608362 TAATTTCATGAAAAAATCAAAA
1 TAATTTCATGAAAAAAT-AAAA
* *
608384 TAATTTTATTAAAAAATAAA
1 TAATTTCATGAAAAAATAAA
608404 TAAACATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 3 0.17
22 15 0.83
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (21 bp):
TAATTTCATGAAAAAATAAAA
Found at i:610700 original size:85 final size:85
Alignment explanation
Indices: 610558--611227 Score: 736
Period size: 85 Copynumber: 7.9 Consensus size: 85
610548 ATCTTCCAGT
* * * *
610558 AAATTTATAGTATAGCTCAAGGCGAGAAGGACTATCTGTTAACAAAGACCTTCGAGTTCGATTAC
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTAC
* * * *
610623 ATTCATCTAAAAGTCATATT
66 ATTCAGCTCAAAGGCATATC
* * * * * * *
610643 AAATTTATAGCATAGCTCAAGGCGAGAAGGACTATCTATTAACCAAGATCTTTGAGTTCGATTAC
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTAC
610708 ATTCAGCTCAAAGGCATATC
66 ATTCAGCTCAAAGGCATATC
* * * *
610728 AAATTTACAACATAGCTCAAGGCGAGAAGGGGTATCTATCAACAAAAGACCTTCGAGTTTGATTA
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAGACCTTCGAGTTCGATTA
* *
610793 CATTCAGCTCAAAGACACATC
65 CATTCAGCTCAAAGGCATATC
* * * *
610814 AAACTTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTAC
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTAC
*
610879 ATTCAGCT-AAATGACATATC
66 ATTCAGCTCAAA-GGCATATC
* * * * * *
610899 AAATTTGA-AGCATAACTCAAGGCGATAAGGGTTATCTGTGAACCAAGACCTTTGAGTTCGATTA
1 AAATTT-ACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTA
* *
610963 TATTTAGCTCAAAGGCATATC
65 CATTCAGCTCAAAGGCATATC
* * * * *
610984 AAATTTGCAGTATAGCTCAAGGTGAGAAGGTCTATCTGTCAACAAAAGACCTTCGATTTCGATTA
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAAC-AAAGACCTTCGAGTTCGATTA
*
611049 CATTCAGCTCAAAGGCACATC
65 CATTCAGCTCAAAGGCATATC
* * * * * * *
611070 AAATTTACAGAATAGCTCAAGTCAAGAAGAGTTATCTGTCAACAAATACCTTCGAGTTTGATT-C
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTAC
*
611134 TATTCAGCTCAAAGGCATGTC
66 -ATTCAGCTCAAAGGCATATC
* * * *** * ** *
611155 AAATTTACAGTATAGCTTAAGTCGAGAAAAACTATCTATCAACAAA-AATTGTCGAGTTCGATTC
1 AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCT-TCGAGTTCGATTA
611219 CATTCAGCT
65 CATTCAGCT
611228 TGACGACATA
Statistics
Matches: 501, Mismatches: 75, Indels: 18
0.84 0.13 0.03
Matches are distributed among these distances:
84 6 0.01
85 346 0.69
86 149 0.30
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (85 bp):
AAATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAGACCTTCGAGTTCGATTAC
ATTCAGCTCAAAGGCATATC
Found at i:610842 original size:171 final size:170
Alignment explanation
Indices: 610569--611227 Score: 743
Period size: 171 Copynumber: 3.9 Consensus size: 170
610559 AATTTATAGT
** * * *
610569 ATAGCTCAAGGCGAGAAGGACTATCTGTTAACAAAGACCTTCGAGTTCGATTACATTCATCTAAA
1 ATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAA
* * * * * * *
610634 AGTCATATTAAATTTATAGCATAGCTCAAGGCGAGAAGGACTATCTATTAACCAAGATCTTTGAG
66 AGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGACTATCTATCAACAAAGACCTTCGAG
610699 TTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAAC
131 TTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAAC
* * *
610739 ATAGCTCAAGGCGAGAAGGGGTATCTATCAACAAAAGACCTTCGAGTTTGATTACATTCAGCTCA
1 ATAGCTCAAGGCGAGAAGGGTTATCTGTCAAC-AAAGACCTTCGAGTTCGATTACATTCAGCTCA
* * * * ** * *
610804 AAGACACATCAAACTTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGA
65 AAGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGACTATCTATCAACAAAGACCTTCGA
* *
610869 GTTCGATTACATTCAGCT-AAATGACATATCAAATTTGA-AGC
130 GTTCGATTACATTCAGCTCAAA-GGCATATCAAATTT-ACAAC
* * * * * * *
610910 ATAACTCAAGGCGATAAGGGTTATCTGTGAACCAAGACCTTTGAGTTCGATTATATTTAGCTCAA
1 ATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAA
* * * * *
610975 AGGCATATCAAATTTGCAGTATAGCTCAAGGTGAGAAGGTCTATCTGTCAACAAAAGACCTTCGA
66 AGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGACTATCTATCAAC-AAAGACCTTCGA
* *
611040 TTTCGATTACATTCAGCTCAAAGGCACATCAAATTTACAGA-
130 GTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACA-AC
* * * * *
611081 ATAGCTCAAGTCAAGAAGAGTTATCTGTCAACAAATACCTTCGAGTTTGATT-CTATTCAGCTCA
1 ATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTAC-ATTCAGCTCA
* * * * ** **
611145 AAGGCATGTCAAATTTACAGTATAGCTTAAGTCGAGAAAAACTATCTATCAACAAA-AATTGTCG
65 AAGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGACTATCTATCAACAAAGACCT-TCG
*
611209 AGTTCGATTCCATTCAGCT
129 AGTTCGATTACATTCAGCT
611228 TGACGACATA
Statistics
Matches: 410, Mismatches: 70, Indels: 18
0.82 0.14 0.04
Matches are distributed among these distances:
169 2 0.00
170 125 0.30
171 279 0.68
172 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (170 bp):
ATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTCAGCTCAA
AGGCATATCAAATTTACAGCATAGCTCAAGGCGAGAAGGACTATCTATCAACAAAGACCTTCGAG
TTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAAC
Found at i:611028 original size:256 final size:255
Alignment explanation
Indices: 610562--611227 Score: 811
Period size: 256 Copynumber: 2.6 Consensus size: 255
610552 TCCAGTAAAT
* ** *
610562 TTATAGTATAGCTCAAGGCGAGAAGGACTATCTGTTAACAAAGACCTTCGAGTTCGATTACATTC
1 TTATAGAATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
* * * * * *
610627 ATCTAAAAGTCATATTAAATTTATAGCATAGCTCAAGGCGAGAAGGACTATCTATTAACCAAGAT
66 AGCT-AAAGACATATCAAATTTATAGCATAACTCAAGGCGAGAAGGACTATCTATGAACCAAGAC
610692 CTTTGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAG
130 CTTTGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAG
*
610757 GGGTATCTATCAACAAAAGACCTTCGAGTTT-GATTACATTCAGCTCAAAGACACATCAAAC
195 GGCTATCTATCAACAAAAGACCTTCGA-TTTCGATTACATTCAGCTCAAAGACACATCAAAC
* *
610818 TTATAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAATAAAGACCTTCGAGTTCGATTACATTC
1 TTATAGAATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
* ** *
610883 AGCTAAATGACATATCAAATTTGA-AGCATAACTCAAGGCGATAAGGGTTATCTGTGAACCAAGA
66 AGCTAAA-GACATATCAAATTT-ATAGCATAACTCAAGGCGAGAAGGACTATCTATGAACCAAGA
* * * ** *
610947 CCTTTGAGTTCGATTATATTTAGCTCAAAGGCATATCAAATTTGCAGTATAGCTCAAGGTGAGAA
129 CCTTTGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCGAGAA
* * * *
611012 GGTCTATCTGTCAACAAAAGACCTTCGATTTCGATTACATTCAGCTCAAAGGCACATCAAAT
194 GGGCTATCTATCAACAAAAGACCTTCGATTTCGATTACATTCAGCTCAAAGACACATCAAAC
* * * * * *
611074 TTACAGAATAGCTCAAGTCAAGAAGAGTTATCTGTCAACAAATACCTTCGAGTTTGATT-CTATT
1 TTATAGAATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTAC-ATT
* * * * * * * ** *
611138 CAGCTCAAAGGCATGTCAAATTTACAGTATAGCTTAAGTCGAGAAAAACTATCTATCAA-CAA-A
65 CAGCT-AAAGACATATCAAATTTATAGCATAACTCAAGGCGAGAAGGACTATCTATGAACCAAGA
** *
611201 AATTGTCGAGTTCGATTCCATTCAGCT
129 CCTT-T-GAGTTCGATTACATTCAGCT
611228 TGACGACATA
Statistics
Matches: 350, Mismatches: 52, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
254 3 0.01
255 12 0.03
256 331 0.95
257 4 0.01
ACGTcount: A:0.36, C:0.19, G:0.18, T:0.28
Consensus pattern (255 bp):
TTATAGAATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAAGACCTTCGAGTTCGATTACATTC
AGCTAAAGACATATCAAATTTATAGCATAACTCAAGGCGAGAAGGACTATCTATGAACCAAGACC
TTTGAGTTCGATTACATTCAGCTCAAAGGCATATCAAATTTACAACATAGCTCAAGGCGAGAAGG
GCTATCTATCAACAAAAGACCTTCGATTTCGATTACATTCAGCTCAAAGACACATCAAAC
Found at i:613409 original size:19 final size:17
Alignment explanation
Indices: 613387--613430 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 17
613377 TTCTTACTTA
613387 ATTTTATTTATCTTTATCT
1 ATTTTATTTAT-TTTAT-T
613406 ATTTTATTTATTTTATT
1 ATTTTATTTATTTTATT
613423 ATTATTAT
1 ATT-TTAT
613431 ATTAATATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.17
18 9 0.38
19 11 0.46
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTATTTATTTTATT
Found at i:613417 original size:9 final size:9
Alignment explanation
Indices: 613387--613422 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
613377 TTCTTACTTA
613387 ATTTTATTT
1 ATTTTATTT
*
613396 ATCTTTATCT
1 AT-TTTATTT
613406 ATTTTATTT
1 ATTTTATTT
613415 ATTTTATT
1 ATTTTATT
613423 ATTATTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.72
Consensus pattern (9 bp):
ATTTTATTT
Found at i:616459 original size:18 final size:18
Alignment explanation
Indices: 616436--616471 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
616426 AGGGATTTTC
*
616436 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
*
616454 AGTGGTTATTCGGGACAT
1 AGTGGTCATTCGGGACAT
616472 TTCATAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.17, G:0.33, T:0.31
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:618653 original size:11 final size:12
Alignment explanation
Indices: 618613--618676 Score: 85
Period size: 12 Copynumber: 5.4 Consensus size: 12
618603 TATTTAAACA
618613 GGTATTGGGTCG
1 GGTATTGGGTCG
618625 GGTATTGGGTCG
1 GGTATTGGGTCG
618637 GGTATTGGGTC-
1 GGTATTGGGTCG
*
618648 GGTATTGGGCCG
1 GGTATTGGGTCG
* * *
618660 GGAATCGGGCCG
1 GGTATTGGGTCG
618672 GGTAT
1 GGTAT
618677 ATATATATAT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
11 10 0.21
12 37 0.79
ACGTcount: A:0.11, C:0.12, G:0.48, T:0.28
Consensus pattern (12 bp):
GGTATTGGGTCG
Found at i:618655 original size:23 final size:24
Alignment explanation
Indices: 618613--618676 Score: 85
Period size: 23 Copynumber: 2.7 Consensus size: 24
618603 TATTTAAACA
*
618613 GGTATTGGGTCGGGTATTGGGTCG
1 GGTATTGGGTCGGGTATTGGGCCG
618637 GGTATTGGGTC-GGTATTGGGCCG
1 GGTATTGGGTCGGGTATTGGGCCG
* * *
618660 GGAATCGGGCCGGGTAT
1 GGTATTGGGTCGGGTAT
618677 ATATATATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 19 0.54
24 16 0.46
ACGTcount: A:0.11, C:0.12, G:0.48, T:0.28
Consensus pattern (24 bp):
GGTATTGGGTCGGGTATTGGGCCG
Found at i:618734 original size:24 final size:25
Alignment explanation
Indices: 618674--618734 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
618664 TCGGGCCGGG
618674 TATATA-TATA-TATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
*
618697 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
618721 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
618735 ATATATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 8 0.25
24 20 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:623074 original size:10 final size:10
Alignment explanation
Indices: 623059--623098 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
623049 TTTATCACAC
623059 CAAATTCTCT
1 CAAATTCTCT
623069 CAAATTCTCT
1 CAAATTCTCT
623079 -AAATTTCTCT
1 CAAA-TTCTCT
*
623089 CAAATACTCT
1 CAAATTCTCT
623099 ATTTTAAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 3 0.11
10 21 0.78
11 3 0.11
ACGTcount: A:0.33, C:0.28, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:623416 original size:111 final size:111
Alignment explanation
Indices: 623222--623443 Score: 354
Period size: 111 Copynumber: 2.0 Consensus size: 111
623212 TGGAAATCAT
* * * * *
623222 ATATCTCTACACTTTGCTAATACGATAATATTTTAACGTTTTAGTTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTAATACGACAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* * *
623287 TATTTAGTTGATTGATTTAATGCATGACTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGACTATTAGATTAAAAATTAA
623333 ATATCTCGACACTTTACTAATACGACAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTAATACGACAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
623398 TAATTAGTTGATTCATTTAATGCATGATTATTATATTAAAAATTAA
66 TAATTAGTTGATTCATTTAATGCATGACTATTAGATTAAAAATTAA
623444 TTTTTGTAAT
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (111 bp):
ATATCTCGACACTTTACTAATACGACAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGACTATTAGATTAAAAATTAA
Found at i:624973 original size:18 final size:18
Alignment explanation
Indices: 624950--624988 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
624940 CCAACAGCCA
624950 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
624968 CCGCAACCATATATGATG
1 CCGCAACCATATATGATG
624986 CCG
1 CCG
624989 ACATCGCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.31, C:0.31, G:0.18, T:0.21
Consensus pattern (18 bp):
CCGCAACCATATATGATG
Found at i:625343 original size:6 final size:6
Alignment explanation
Indices: 625328--625390 Score: 57
Period size: 6 Copynumber: 11.5 Consensus size: 6
625318 ACCTGCTCAG
* *
625328 GACGAC GACGAT GACGAT GAC--- GACGAT GACGAT G--G-T GACGAC
1 GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT GACGAT
*
625370 GACGAT GACGAT GATGAT GAC
1 GACGAT GACGAT GACGAT GAC
625391 AGCGATGAGT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
3 5 0.11
4 1 0.02
5 1 0.02
6 39 0.85
ACGTcount: A:0.32, C:0.19, G:0.35, T:0.14
Consensus pattern (6 bp):
GACGAT
Found at i:625351 original size:15 final size:15
Alignment explanation
Indices: 625331--625386 Score: 76
Period size: 15 Copynumber: 3.7 Consensus size: 15
625321 TGCTCAGGAC
625331 GACGACGATGACGAT
1 GACGACGATGACGAT
625346 GACGACGATGACGAT
1 GACGACGATGACGAT
** *
625361 GGTGACGACGACGAT
1 GACGACGATGACGAT
*
625376 GACGATGATGA
1 GACGACGATGA
625387 TGACAGCGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.32, C:0.18, G:0.36, T:0.14
Consensus pattern (15 bp):
GACGACGATGACGAT
Found at i:625358 original size:21 final size:21
Alignment explanation
Indices: 625328--625398 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
625318 ACCTGCTCAG
* *
625328 GACGACGACGATGACGATGAC
1 GACGATGACGATGATGATGAC
* *
625349 GACGATGACGATGGTGACGAC
1 GACGATGACGATGATGATGAC
625370 GACGATGACGATGATGATGAC
1 GACGATGACGATGATGATGAC
625391 -AGCGATGA
1 GA-CGATGA
625399 GTCAGAACCA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 1 0.02
21 42 0.98
ACGTcount: A:0.32, C:0.18, G:0.35, T:0.14
Consensus pattern (21 bp):
GACGATGACGATGATGATGAC
Found at i:625386 original size:9 final size:9
Alignment explanation
Indices: 625328--625383 Score: 58
Period size: 9 Copynumber: 6.2 Consensus size: 9
625318 ACCTGCTCAG
*
625328 GACGACGAC
1 GACGACGAT
*
625337 GATGACGAT
1 GACGACGAT
625346 GACGACGAT
1 GACGACGAT
* *
625355 GACGATGGT
1 GACGACGAT
*
625364 GACGACGAC
1 GACGACGAT
*
625373 GATGACGAT
1 GACGACGAT
625382 GA
1 GA
625384 TGATGACAGC
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.32, C:0.20, G:0.36, T:0.12
Consensus pattern (9 bp):
GACGACGAT
Found at i:625615 original size:35 final size:33
Alignment explanation
Indices: 625576--625660 Score: 82
Period size: 35 Copynumber: 2.5 Consensus size: 33
625566 ATATTTTAGT
625576 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
* *
625611 TAATTTGGTTATCATTTACCATTTTATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
625646 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
625661 TAAATATCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.57
36 1 0.02
37 3 0.07
38 11 0.26
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.56
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:628169 original size:50 final size:50
Alignment explanation
Indices: 628085--628215 Score: 124
Period size: 51 Copynumber: 2.6 Consensus size: 50
628075 CTACGTGTCG
* * * * *
628085 TATAGCGC-GTATCAGGGGGCGCGCTATACC-CCACGTGTAC-CCAGTCAGCG
1 TATAGCGCGGT-TCAAGGGGCGCGCT-TTCCTCCACGTG-ACGCAAATCAGCA
* * *
628135 TATAGCGCGGTTCAAGGGGTGCGTTTTCCTCCACGTGGCGTCAAATCAGCA
1 TATAGCGCGGTTCAAGGGGCGCGCTTTCCTCCACGTGACG-CAAATCAGCA
*
628186 TATAGCGCGGTTCAGGGGGCGCGCTTTCCT
1 TATAGCGCGGTTCAAGGGGCGCGCTTTCCT
628216 GCTAAGCGTG
Statistics
Matches: 66, Mismatches: 11, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
49 4 0.06
50 26 0.39
51 36 0.55
ACGTcount: A:0.18, C:0.28, G:0.31, T:0.23
Consensus pattern (50 bp):
TATAGCGCGGTTCAAGGGGCGCGCTTTCCTCCACGTGACGCAAATCAGCA
Found at i:629995 original size:21 final size:21
Alignment explanation
Indices: 629966--630005 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
629956 TGGCCTGTCA
*
629966 TCTACTGGTGTCACTTTTAAG
1 TCTACTGGTGTCACATTTAAG
* *
629987 TCTAGTGGTTTCACATTTA
1 TCTACTGGTGTCACATTTA
630006 GTAGTGGAGG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.17, T:0.45
Consensus pattern (21 bp):
TCTACTGGTGTCACATTTAAG
Found at i:630849 original size:28 final size:29
Alignment explanation
Indices: 630816--630876 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
630806 GTTCCTATCA
630816 TGAAA-CAAGAAATACAATATAATCAAGG
1 TGAAACCAAGAAATACAATATAATCAAGG
** *
630844 TGAAACCTTGAAATTCAATATAATCAAGG
1 TGAAACCAAGAAATACAATATAATCAAGG
630873 TGAA
1 TGAA
630877 GGAACATTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.51, C:0.11, G:0.15, T:0.23
Consensus pattern (29 bp):
TGAAACCAAGAAATACAATATAATCAAGG
Found at i:631301 original size:81 final size:81
Alignment explanation
Indices: 631159--631308 Score: 201
Period size: 81 Copynumber: 1.9 Consensus size: 81
631149 AACAATTTTA
* * * * * *
631159 ATGGATCATCAGGCATTTTTGGTTCACTCACTTCTCATCCTGATTCGGATTGAAAAAAAGCAGCA
1 ATGGATCATCAGACATTTTTGGTTCACTCACTTCTCAGCCTGATCCAGATTCAAAAAAAGCAACA
631224 CAAAATCCAACTAATG
66 CAAAATCCAACTAATG
* * * * *
631240 ATGGATCATCAGATATTTTTGGTTCATTCGCTTCTCAGCCTGATCCAGCTTCAAAAGAAGCAACA
1 ATGGATCATCAGACATTTTTGGTTCACTCACTTCTCAGCCTGATCCAGATTCAAAAAAAGCAACA
631305 CAAA
66 CAAA
631309 GTCCGACCTC
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
81 58 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (81 bp):
ATGGATCATCAGACATTTTTGGTTCACTCACTTCTCAGCCTGATCCAGATTCAAAAAAAGCAACA
CAAAATCCAACTAATG
Found at i:633703 original size:17 final size:17
Alignment explanation
Indices: 633681--633739 Score: 52
Period size: 18 Copynumber: 3.5 Consensus size: 17
633671 ATCGAAAACT
633681 AATAATA-ATATAATTAA
1 AATAATACAT-TAATTAA
633698 AATAATTACATTAATTAA
1 AATAA-TACATTAATTAA
* *
633716 AAAAATAGA-TAA-TAA
1 AATAATACATTAATTAA
633731 TAATAATAC
1 -AATAATAC
633740 TAACAAGTCC
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.09
16 9 0.26
17 8 0.23
18 13 0.37
19 2 0.06
ACGTcount: A:0.63, C:0.03, G:0.02, T:0.32
Consensus pattern (17 bp):
AATAATACATTAATTAA
Found at i:635098 original size:31 final size:31
Alignment explanation
Indices: 635058--635130 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
635048 AGTTGAATCT
* *
635058 GTCAGAAATTTGTGACGGATCCACATATTCC
1 GTCACAAATTTGTGACGGATCCACATATCCC
* *
635089 GTCACAAATTTGTGATGGGTCCACATATCCC
1 GTCACAAATTTGTGACGGATCCACATATCCC
*
635120 ATCACAAATTT
1 GTCACAAATTT
635131 AAAAAATTGT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (31 bp):
GTCACAAATTTGTGACGGATCCACATATCCC
Found at i:636154 original size:51 final size:52
Alignment explanation
Indices: 636096--636199 Score: 147
Period size: 51 Copynumber: 2.0 Consensus size: 52
636086 GTTGAACAAA
* * * *
636096 ATTTCCGACGGAATCATTATCCCGTCATAAATTAAATTGATAT-TTTTTTTT
1 ATTTCCGACGAAATCATTATCCCATCACAAATTAAATTGATATATTTTATTT
* *
636147 ATTTCCGACGAAATGATTATTCCATCACAAATTAAATTGATATATTTTATTT
1 ATTTCCGACGAAATCATTATCCCATCACAAATTAAATTGATATATTTTATTT
636199 A
1 A
636200 AAGTTGAACA
Statistics
Matches: 46, Mismatches: 6, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
51 38 0.83
52 8 0.17
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (52 bp):
ATTTCCGACGAAATCATTATCCCATCACAAATTAAATTGATATATTTTATTT
Found at i:636168 original size:116 final size:116
Alignment explanation
Indices: 636025--636261 Score: 395
Period size: 116 Copynumber: 2.0 Consensus size: 116
636015 TTAATGTATA
* * *
636025 TTTTTTATTTCCGACAGAATGACTATTCTATCGCAAATTAAATTGGTATATTTTAATTAAAGTTG
1 TTTTTTATTTCCGACAGAATGACTATTCCATCACAAATTAAATTGATATATTTTAATTAAAGTTG
636090 AACAAAATTTCCGACGGAATCATTATCCCGTCATAAATTAAATTGATATTT
66 AACAAAATTTCCGACGGAATCATTATCCCGTCATAAATTAAATTGATATTT
* *
636141 TTTTTTATTTCCGAC-GAAATGATTATTCCATCACAAATTAAATTGATATATTTTATTTAAAGTT
1 TTTTTTATTTCCGACAG-AATGACTATTCCATCACAAATTAAATTGATATATTTTAATTAAAGTT
* *
636205 GAACACAATTTCCGACGGAATCATTGTCCCGTCATAAATTAAATTGATATTT
65 GAACAAAATTTCCGACGGAATCATTATCCCGTCATAAATTAAATTGATATTT
636257 TTTTT
1 TTTTT
636262 ATTGAAATGA
Statistics
Matches: 113, Mismatches: 7, Indels: 2
0.93 0.06 0.02
Matches are distributed among these distances:
115 1 0.01
116 112 0.99
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (116 bp):
TTTTTTATTTCCGACAGAATGACTATTCCATCACAAATTAAATTGATATATTTTAATTAAAGTTG
AACAAAATTTCCGACGGAATCATTATCCCGTCATAAATTAAATTGATATTT
Found at i:639378 original size:20 final size:20
Alignment explanation
Indices: 639349--639387 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
639339 AGAGCTCATA
*
639349 TAAGATCATATAGGTGCATT
1 TAAGAGCATATAGGTGCATT
*
639369 TAAGAGCATATAGTTGCAT
1 TAAGAGCATATAGGTGCAT
639388 GTGGTGGAAA
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:0.36, C:0.10, G:0.21, T:0.33
Consensus pattern (20 bp):
TAAGAGCATATAGGTGCATT
Found at i:644351 original size:24 final size:24
Alignment explanation
Indices: 644306--644383 Score: 77
Period size: 24 Copynumber: 3.2 Consensus size: 24
644296 CAGATAAGCT
* * *
644306 ATCAGAACAAAATCCAAGTCAGGA
1 ATCAGAACAGAATTCAAATCAGGA
* *
644330 ATCAGAACAGATTTCATATCA-GA
1 ATCAGAACAGAATTCAAATCAGGA
* *
644353 TGTCAGAACAGAATTCAAATCAGAA
1 -ATCAGAACAGAATTCAAATCAGGA
644378 ATCAGA
1 ATCAGA
644384 TAAAATATTC
Statistics
Matches: 42, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
23 2 0.05
24 39 0.93
25 1 0.02
ACGTcount: A:0.47, C:0.18, G:0.15, T:0.19
Consensus pattern (24 bp):
ATCAGAACAGAATTCAAATCAGGA
Found at i:645757 original size:11 final size:11
Alignment explanation
Indices: 645741--645769 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
645731 CAAAGTCAAT
645741 GGTCAACAGTC
1 GGTCAACAGTC
645752 GGTCAACAGTC
1 GGTCAACAGTC
645763 GGTCAAC
1 GGTCAAC
645770 GGGTCAGGTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.28, T:0.17
Consensus pattern (11 bp):
GGTCAACAGTC
Found at i:647385 original size:55 final size:55
Alignment explanation
Indices: 647294--647403 Score: 166
Period size: 55 Copynumber: 2.0 Consensus size: 55
647284 CAAAACCATA
*
647294 CACCCCCTACACAACAGTAAGGCCCTGAGCACAAAGCCGAGGAACCTGCAAATAT
1 CACCCCCTACACAACAGTAAGGCCCTAAGCACAAAGCCGAGGAACCTGCAAATAT
* * * * *
647349 CACCCCCTGCACAACATTAAGTCCCTAAGCATAAAGCCGAGGAACCTGCATATAT
1 CACCCCCTACACAACAGTAAGGCCCTAAGCACAAAGCCGAGGAACCTGCAAATAT
647404 AAACCCTTCA
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 49 1.00
ACGTcount: A:0.35, C:0.34, G:0.16, T:0.15
Consensus pattern (55 bp):
CACCCCCTACACAACAGTAAGGCCCTAAGCACAAAGCCGAGGAACCTGCAAATAT
Found at i:647496 original size:24 final size:24
Alignment explanation
Indices: 647469--647551 Score: 80
Period size: 24 Copynumber: 3.5 Consensus size: 24
647459 CAGGAAACAA
*
647469 AACATAATTCAGATCAGATATCTG
1 AACATAATTCAGATCAGATATCAG
* *
647493 AACAGAATCCA-AGTCAGGA-ATCAG
1 AACATAATTCAGA-TCA-GATATCAG
* * *
647517 AACATATTTCAGATAAGATGTCAG
1 AACATAATTCAGATCAGATATCAG
647541 AACATAATTCA
1 AACATAATTCA
647552 AATAAAAAAT
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
23 3 0.07
24 40 0.87
25 3 0.07
ACGTcount: A:0.45, C:0.17, G:0.14, T:0.24
Consensus pattern (24 bp):
AACATAATTCAGATCAGATATCAG
Found at i:648897 original size:17 final size:16
Alignment explanation
Indices: 648867--648913 Score: 76
Period size: 16 Copynumber: 2.8 Consensus size: 16
648857 TAAAAAACAT
648867 AAAATATGACTTTTTGA
1 AAAAT-TGACTTTTTGA
648884 AAAATTGACTTTTTGA
1 AAAATTGACTTTTTGA
648900 AAAATTTGACTTTT
1 AAAA-TTGACTTTT
648914 CGATCAATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
16 15 0.52
17 14 0.48
ACGTcount: A:0.38, C:0.06, G:0.11, T:0.45
Consensus pattern (16 bp):
AAAATTGACTTTTTGA
Found at i:648954 original size:23 final size:24
Alignment explanation
Indices: 648928--648973 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
648918 CAATGACAAC
*
648928 GGTC-AACGGGTCGGGTCAAACCT
1 GGTCAAACGGGTCGGGCCAAACCT
648951 GGTCAAACGGGTCGGGCCAAACC
1 GGTCAAACGGGTCGGGCCAAACC
648974 GGGTTAACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 4 0.19
24 17 0.81
ACGTcount: A:0.24, C:0.28, G:0.35, T:0.13
Consensus pattern (24 bp):
GGTCAAACGGGTCGGGCCAAACCT
Found at i:655021 original size:24 final size:23
Alignment explanation
Indices: 654960--655025 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
654950 GCAAGAAACC
*
654960 AAACAGCAAGCAGACAGCAGAAAA
1 AAACAGCAAGCA-ATAGCAGAAAA
*
654984 AAACAAC-AGACAATAG-AGAAAAA
1 AAACAGCAAG-CAATAGCAG-AAAA
655007 GAAACAGCAAGCAATAGCA
1 -AAACAGCAAGCAATAGCA
655026 AACGAAGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 9
0.74 0.07 0.20
Matches are distributed among these distances:
22 2 0.06
23 9 0.26
24 20 0.59
25 3 0.09
ACGTcount: A:0.61, C:0.18, G:0.18, T:0.03
Consensus pattern (23 bp):
AAACAGCAAGCAATAGCAGAAAA
Found at i:660477 original size:11 final size:12
Alignment explanation
Indices: 660451--660481 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
660441 ACAACAATTA
660451 AGTTAGGTGAAG
1 AGTTAGGTGAAG
660463 AGTTAGGTG-AG
1 AGTTAGGTGAAG
660474 AGTTAGGT
1 AGTTAGGT
660482 ATTTATCTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.29, C:0.00, G:0.42, T:0.29
Consensus pattern (12 bp):
AGTTAGGTGAAG
Found at i:668166 original size:13 final size:13
Alignment explanation
Indices: 668148--668175 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
668138 GAATATTAAT
668148 AATTAAATTAAAA
1 AATTAAATTAAAA
668161 AATTAAATTAAAA
1 AATTAAATTAAAA
668174 AA
1 AA
668176 ATATTATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATTAAATTAAAA
Found at i:668783 original size:64 final size:64
Alignment explanation
Indices: 668675--668817 Score: 223
Period size: 64 Copynumber: 2.2 Consensus size: 64
668665 GTAGCACGGG
* * * *
668675 GTCACCATAGCATCACATAATACATACCCTATTTACTTATTGAAGGTATCTTGGGTAGGATCTGA
1 GTCA-CATAGCATCACATAATACACACCCTATTTACTTACTGAAGGTACCTTGGGTAAGATCTGA
* *
668740 GTCACATAGCATCACATAATACACACCCTATTTGCTTACTGAAGGTACCTTGGGTAAGATCTGG
1 GTCACATAGCATCACATAATACACACCCTATTTACTTACTGAAGGTACCTTGGGTAAGATCTGA
668804 GTCACATAGCATCA
1 GTCACATAGCATCA
668818 TCATCTTATA
Statistics
Matches: 72, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
64 68 0.94
65 4 0.06
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.29
Consensus pattern (64 bp):
GTCACATAGCATCACATAATACACACCCTATTTACTTACTGAAGGTACCTTGGGTAAGATCTGA
Found at i:669218 original size:20 final size:20
Alignment explanation
Indices: 669193--669245 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
669183 AACCTCAAAC
669193 GAGTATCGATACTCAAAGGT
1 GAGTATCGATACTCAAAGGT
*
669213 GAGTATCGATACTCAAAGTT
1 GAGTATCGATACTCAAAGGT
669233 GAGTATCGATACT
1 GAGTATCGATACT
669246 TCTTCCTTAC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (20 bp):
GAGTATCGATACTCAAAGGT
Found at i:673423 original size:16 final size:15
Alignment explanation
Indices: 673404--673452 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
673394 ATGATATCTC
673404 TAGGGTATAGTTAGGT
1 TAGGGTATA-TTAGGT
*
673420 TAGGGTTATATTGGGT
1 TAGGG-TATATTAGGT
*
673436 TAGGGTTATATTGGGT
1 TAGGG-TATATTAGGT
673452 T
1 T
673453 TGAATATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
16 27 0.87
17 4 0.13
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.43
Consensus pattern (15 bp):
TAGGGTATATTAGGT
Found at i:674098 original size:105 final size:105
Alignment explanation
Indices: 673961--674230 Score: 425
Period size: 105 Copynumber: 2.6 Consensus size: 105
673951 TTTGTCGGAT
673961 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAA
* * *
674026 GGAATGA-GCTCTTCTCATTACGAATATTCTCCTTTAAGAC
66 AGAA-CATGCTCTTCTCATTACGAACATTCTCCTTTAAGAC
** * * *
674066 GAGTTCTTCTCATTATGAACTCTTCTAAAAATGTTGGTTCACCTCCTTCTGCGGTGGATTTGAAA
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAA
* *
674131 AGAACATGCTCTTCTCATTACGAACCTTCTCCTTTAGGAC
66 AGAACATGCTCTTCTCATTACGAACATTCTCCTTTAAGAC
*
674171 GAGTTCTTCTCATTATGAACTATTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATT
1 GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATT
674231 ATAGTTGTTG
Statistics
Matches: 148, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
104 1 0.01
105 147 0.99
ACGTcount: A:0.24, C:0.21, G:0.18, T:0.37
Consensus pattern (105 bp):
GAGTTCTTCTCATTATGAACTCTTCTGGAAATGTTGATTCACCTCCTTCTGGGGTGAATTTGAAA
AGAACATGCTCTTCTCATTACGAACATTCTCCTTTAAGAC
Found at i:675188 original size:18 final size:19
Alignment explanation
Indices: 675154--675192 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
675144 GAACTCTCAT
675154 TTTTCTTTTCTTATTTTCA
1 TTTTCTTTTCTTATTTTCA
675173 TTTT-TTTTCATT-TTTTCA
1 TTTTCTTTTC-TTATTTTCA
675191 TT
1 TT
675193 CATTCATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTCTTATTTTCA
Found at i:680096 original size:3 final size:3
Alignment explanation
Indices: 680090--680116 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
680080 GATGATGATG
680090 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
680117 TTACAATATT
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:692392 original size:23 final size:23
Alignment explanation
Indices: 692357--692404 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
692347 ATCAAGTACA
*
692357 ATAATATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
692380 ATAATGTAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
692403 AT
1 AT
692405 TGACCTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.08, G:0.19, T:0.38
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:693336 original size:182 final size:182
Alignment explanation
Indices: 693027--693477 Score: 753
Period size: 182 Copynumber: 2.5 Consensus size: 182
693017 TTTATACTAT
* * *
693027 CGATTTTGTCATTTCGAGATCGGTTTTGTTATATTTTTACCTGTTATATTATTATGGATCGATAC
1 CGATTTTGTCATTTCGAGATCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
* *
693092 ATTTTTATAAAGTATCGACACTTTATTGGCGCTATAACTTCTTTTCTTTTAAATTCCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
*
693157 CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCTCTTTAC
131 CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
* *
693209 CGATTTTGTCATTTCGAGACCGGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATAC
1 CGATTTTGTCATTTCGAGATCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
*
693274 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTTCAAAAGTGT
66 ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
*
693339 CGATACTTATAATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTAC
131 CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
** *
693391 CTG-TTTTGTCATTTATAGATCGGTTTTATCAGT-TTTTTACCTGTTTTATTGTTATGGATCGAT
1 C-GATTTTGTCATTTCGAGATCGGTTTTATCA-TATTTTTACCTGTTATATTGTTATGGATCGAT
693454 ACATTTTTATAAAGTATCGACACT
64 ACATTTTTATAAAGTATCGACACT
693478 ATCAACATAT
Statistics
Matches: 252, Mismatches: 15, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
182 250 0.99
183 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.14, T:0.43
Consensus pattern (182 bp):
CGATTTTGTCATTTCGAGATCGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATAC
ATTTTTATAAAGTATCGACACTTTATTAGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGT
CGATACTTATAATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTAC
Found at i:693701 original size:113 final size:112
Alignment explanation
Indices: 693350--693813 Score: 714
Period size: 112 Copynumber: 4.1 Consensus size: 112
693340 GATACTTATA
* *
693350 ATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * *
693415 TTTATCAGTTTTTTACCTGTTTTATTGTTATGGATCGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
693462 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGAT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
693527 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
66 TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * *
693574 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
*
693639 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
* * * * *
693687 ATAAAGTATCGACACTTTCAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCAGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
* * * *
693752 TTTGT-ATTTTTTTTACTTGTTATATTGTTATCGATCAATATATTTTT
66 TTTGTCA-TTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
*
693799 ATAAAGTATGGACAC
1 ATAAAGTATCGACAC
693814 AAACCGATAA
Statistics
Matches: 330, Mismatches: 21, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
112 224 0.68
113 106 0.32
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (112 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCGGT
TTTGTCATTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
Found at i:693740 original size:225 final size:224
Alignment explanation
Indices: 693350--693813 Score: 734
Period size: 225 Copynumber: 2.1 Consensus size: 224
693340 GATACTTATA
*
693350 ATAAAGTATCGACACTATCAACATATCTGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
*
693415 TTTATCAGTTTTTTACCTGTTTTATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
66 TTTATCAGTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
693480 CAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACC-GATTTTGTCA-TTTTTTTAC
131 CAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAG-TTTTGT-ATTTTTTTTAC
* **
693543 CTGTTATATTGTTATGGATTGATACATTTTT
194 CTGTTATATTGTTATCGATCAATACATTTTT
* *
693574 ATAAAGTATCGACACTTTCAATATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
1 ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
* * * *
693639 TTTGTCATTTTTTTTACCTGTTATATTGTTATGGATTGATACATTTTTATAAAGTATCGACACTT
66 TTTATCA-GTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTA
* * * *
693704 TCAATATATCTGGTAGCGTTTTACCTGTTTTGTCATTTATAGACCAGTTTTGTATTTTTTTTACT
130 TCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGTTTTGTATTTTTTTTACC
*
693769 TGTTATATTGTTATCGATCAATATATTTTT
195 TGTTATATTGTTATCGATCAATACATTTTT
*
693799 ATAAAGTATGGACAC
1 ATAAAGTATCGACAC
693814 AAACCGATAA
Statistics
Matches: 220, Mismatches: 17, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
224 69 0.31
225 150 0.68
226 1 0.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (224 bp):
ATAAAGTATCGACACTATCAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGATCGGT
TTTATCAGTTTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACTAT
CAACATATCCGGTAGCGCTTTACCTGTTTTGTCATTTATAGACCAGTTTTGTATTTTTTTTACCT
GTTATATTGTTATCGATCAATACATTTTT
Done.