Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000073.1 Hibiscus syriacus cultivar Beakdansim tig00000132_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: 1402814
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 7 of 7
Found at i:1289501 original size:20 final size:20
Alignment explanation
Indices: 1289476--1289522 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
1289466 CTTTTGCCAC
*
1289476 GTGGAAGTCTCTGGTTCGAG
1 GTGGAAATCTCTGGTTCGAG
1289496 GTGGAAATCTCTGGTTCGAG
1 GTGGAAATCTCTGGTTCGAG
*
1289516 ATGGAAA
1 GTGGAAA
1289523 GAAACGGCGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (20 bp):
GTGGAAATCTCTGGTTCGAG
Found at i:1293736 original size:15 final size:15
Alignment explanation
Indices: 1293716--1293747 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1293706 GAATTTTATC
1293716 AAGAGTCAAAGTTTG
1 AAGAGTCAAAGTTTG
*
1293731 AAGAGTTAAAGTTTG
1 AAGAGTCAAAGTTTG
1293746 AA
1 AA
1293748 AAGTTAATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.03, G:0.25, T:0.28
Consensus pattern (15 bp):
AAGAGTCAAAGTTTG
Found at i:1293752 original size:15 final size:15
Alignment explanation
Indices: 1293723--1293754 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1293713 ATCAAGAGTC
*
1293723 AAAGTTTGAAGAGTT
1 AAAGTTTGAAAAGTT
1293738 AAAGTTTGAAAAGTT
1 AAAGTTTGAAAAGTT
1293753 AA
1 AA
1293755 TGTGACACCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.47, C:0.00, G:0.22, T:0.31
Consensus pattern (15 bp):
AAAGTTTGAAAAGTT
Found at i:1295429 original size:7 final size:7
Alignment explanation
Indices: 1295411--1295444 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
1295401 TCTAAAGTTC
1295411 TCTTCTCT
1 TCTTC-CT
1295419 TCTTCCT
1 TCTTCCT
1295426 TCTTCCT
1 TCTTCCT
1295433 TCTTCCT
1 TCTTCCT
1295440 TCTTC
1 TCTTC
1295445 ATACGTGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 21 0.81
8 5 0.19
ACGTcount: A:0.00, C:0.41, G:0.00, T:0.59
Consensus pattern (7 bp):
TCTTCCT
Found at i:1299774 original size:5 final size:5
Alignment explanation
Indices: 1299764--1299788 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1299754 CACACACATG
1299764 AGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA
1299789 CCTTGGTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:1301092 original size:5 final size:5
Alignment explanation
Indices: 1301082--1301110 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
1301072 GGTTGAAAAA
1301082 CTTCC CTTCC CTTCC CTTCC CTTCC CTTC
1 CTTCC CTTCC CTTCC CTTCC CTTCC CTTC
1301111 AAGTAATGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.59, G:0.00, T:0.41
Consensus pattern (5 bp):
CTTCC
Found at i:1301419 original size:21 final size:21
Alignment explanation
Indices: 1301302--1301439 Score: 77
Period size: 21 Copynumber: 6.7 Consensus size: 21
1301292 ACGCGAAATA
**
1301302 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGATTTTCC
* ** *
1301322 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGATTTTCC
* *
1301342 AAAATCGCAACGCAATTCTT-G
1 AAAATCGCAACGCGATT-TTCC
* ** *
1301363 AAAATCGCAATGCGATAGTAC
1 AAAATCGCAACGCGATTTTCC
* **
1301384 AAATTCGCATTGCGATTTTCC
1 AAAATCGCAACGCGATTTTCC
* * *
1301405 AAAATCGCAACGCGAATAT-G
1 AAAATCGCAACGCGATTTTCC
1301425 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
1301440 ACACATAAAT
Statistics
Matches: 88, Mismatches: 26, Indels: 8
0.72 0.21 0.07
Matches are distributed among these distances:
19 1 0.01
20 39 0.44
21 46 0.52
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:1301449 original size:20 final size:20
Alignment explanation
Indices: 1301406--1301599 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
1301396 CGATTTTCCA
* ** *
1301406 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
1301426 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
1301446 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1301466 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
1301486 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
1301506 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
1301526 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
1301546 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
1301566 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
1301587 AAATCGCAACGCG
1 AAATCGCAACGCG
1301600 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 124 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:1301490 original size:60 final size:60
Alignment explanation
Indices: 1301406--1301599 Score: 237
Period size: 60 Copynumber: 3.2 Consensus size: 60
1301396 CGATTTTCCA
* ** * *
1301406 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACTCGTATCCGT
* * ***
1301466 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAA-TGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACT-CGTATCCGT
* ** *
1301526 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACTCGTATCCGT
1301587 AAATCGCAACGCG
1 AAATCGCAACGCG
1301600 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 20, Indels: 5
0.82 0.15 0.04
Matches are distributed among these distances:
59 1 0.01
60 80 0.72
61 30 0.27
ACGTcount: A:0.36, C:0.26, G:0.19, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACTCGTATCCGT
Found at i:1302021 original size:33 final size:33
Alignment explanation
Indices: 1301982--1302052 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1301972 TTCACTTAGA
*
1301982 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* * *
1302015 TTTCATTTTGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1302048 TTTCA
1 TTTCA
1302053 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:0.21, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:1302189 original size:41 final size:41
Alignment explanation
Indices: 1302131--1302208 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
1302121 TTGCAGAAGA
*
1302131 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
1302172 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1302209 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:1302205 original size:21 final size:21
Alignment explanation
Indices: 1302132--1302207 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
1302122 TGCAGAAGAG
*
1302132 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
1302153 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
1302173 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
1302194 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
1302208 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:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:1302211 original size:14 final size:14
Alignment explanation
Indices: 1302192--1302248 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1302182 GAGAAATGAA
1302192 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1302206 AATCGCAACGCGATATGAA
1 AATCGCAA--CG--A-GAG
1302225 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1302239 AATCGCAACG
1 AATCGCAACG
1302249 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:0.42, C:0.23, G:0.25, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1302227 original size:33 final size:33
Alignment explanation
Indices: 1302187--1302251 Score: 130
Period size: 33 Copynumber: 2.0 Consensus size: 33
1302177 AACGAGAGAA
1302187 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
1302220 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1 ATGAAAATCGCAACGAGAGAATCGCAACGCGA
1302252 AACCAAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.11
Consensus pattern (33 bp):
ATGAAAATCGCAACGAGAGAATCGCAACGCGAT
Found at i:1302260 original size:33 final size:33
Alignment explanation
Indices: 1302190--1302264 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 33
1302180 GAGAGAAATG
* **
1302190 AAAATCGCAACGAGAGAATCGCAACGCGATATG
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1302223 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1 AAAATCGCAACGAGAGAATCGCAACGCGAAACC
1302256 AAAATCGCA
1 AAAATCGCA
1302265 TTGCGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 39 1.00
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.09
Consensus pattern (33 bp):
AAAATCGCAACGAGAGAATCGCAACGCGAAACC
Found at i:1302282 original size:19 final size:19
Alignment explanation
Indices: 1302260--1302376 Score: 84
Period size: 19 Copynumber: 6.9 Consensus size: 19
1302250 GAAACCAAAA
* *
1302260 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATC
1302279 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
*
1302295 T--CGTTGCGATTTTCATA
1 TCGCGTTGCGATTTTCATC
1302312 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
* *
1302328 T--CGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATC
1302345 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATC
1302361 T--CGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
1302377 TTCAACCAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 28
0.68 0.07 0.25
Matches are distributed among these distances:
14 24 0.31
16 14 0.18
17 13 0.17
19 26 0.34
ACGTcount: A:0.11, C:0.24, G:0.21, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATC
Found at i:1302301 original size:14 final size:14
Alignment explanation
Indices: 1302282--1302371 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
1302272 TTTCATTTCG
1302282 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1302296 CGTTGCGATTTTCATATCG
1 CGTTGCGA--TTC---TCT
1302315 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1302329 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
1302348 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1302362 CGTTGCGATT
1 CGTTGCGATT
1302372 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.32
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1302307 original size:33 final size:33
Alignment explanation
Indices: 1302265--1302379 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1302255 CAAAATCGCA
1302265 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1302298 TTGCGATTTTCATATCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
1302331 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1302364 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
1302380 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:0.23, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:1304320 original size:93 final size:93
Alignment explanation
Indices: 1304078--1304878 Score: 1566
Period size: 93 Copynumber: 8.6 Consensus size: 93
1304068 TAGATTGCTT
*
1304078 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
1304143 TTTGTCTTTGTTTTTTCTTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTC-TTTTGGTTGAA
1304172 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1304237 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1304265 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1304330 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1304358 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1304423 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1304451 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1304516 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1304544 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1304609 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1304637 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1304702 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
1304730 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1304795 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
1304823 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTGT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGT
1304879 CATCATTGAA
Statistics
Matches: 704, Mismatches: 3, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
93 624 0.89
94 80 0.11
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:1306337 original size:14 final size:14
Alignment explanation
Indices: 1306318--1306353 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1306308 ATTGTTTAAT
1306318 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
1306332 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
1306346 TGATTTGT
1 TGATTTGT
1306354 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:1306476 original size:19 final size:20
Alignment explanation
Indices: 1306460--1306505 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
1306450 AAAAATGACT
1306460 ATCGCAATGC-GAAATGAAA
1 ATCGCAATGCGGAAATGAAA
1306479 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGCGGAAATGAAA
1306499 ATCGCAA
1 ATCGCAA
1306506 CGAGAGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAATGCGGAAATGAAA
Found at i:1306567 original size:33 final size:33
Alignment explanation
Indices: 1306530--1306820 Score: 238
Period size: 33 Copynumber: 8.5 Consensus size: 33
1306520 TGCGTTTATA
1306530 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
1306563 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * *
1306603 -TTT-GCGATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGC-A-TTGCGATTCTCTCGTTGCGATTTTC
1306634 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
1306667 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * * *
1306707 GTTGCG-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCGTTGCGATTTTC
1306738 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
1306771 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
*
1306805 ATTTCGCGTTGCGATT
1 ATTTCGCATTGCGATT
1306821 GTAATTTCCG
Statistics
Matches: 209, Mismatches: 23, Indels: 52
0.74 0.08 0.18
Matches are distributed among these distances:
31 14 0.07
32 13 0.06
33 89 0.43
34 29 0.14
35 11 0.05
36 8 0.04
37 4 0.02
38 18 0.09
39 9 0.04
40 14 0.07
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.46
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:1306576 original size:19 final size:19
Alignment explanation
Indices: 1306552--1306820 Score: 291
Period size: 19 Copynumber: 15.4 Consensus size: 19
1306542 GATTCTCTCG
1306552 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1306571 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
1306590 TTGCGA--TTC---TCTCT
1 TTGCGATTTTCATTTCGCA
1306604 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1306623 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1306642 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1306656 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1306675 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1306694 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1306708 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1306727 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1306746 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1306760 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1306780 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
1306794 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
1306813 TTGCGATT
1 TTGCGATT
1306821 GTAATTTCCG
Statistics
Matches: 212, Mismatches: 12, Indels: 52
0.77 0.04 0.19
Matches are distributed among these distances:
14 38 0.18
16 26 0.12
17 23 0.11
18 3 0.01
19 110 0.52
20 12 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:1306587 original size:52 final size:52
Alignment explanation
Indices: 1306530--1306792 Score: 508
Period size: 52 Copynumber: 5.0 Consensus size: 52
1306520 TGCGTTTATA
1306530 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
1306582 ATTTCGCATTGCGATTCTCTCTTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1306634 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1306686 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1306738 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTC
1306791 AT
1 AT
1306793 GTTGGGATTT
Statistics
Matches: 208, Mismatches: 2, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
52 191 0.92
53 17 0.08
ACGTcount: A:0.14, C:0.23, G:0.17, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:1309121 original size:12 final size:12
Alignment explanation
Indices: 1309104--1309128 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1309094 TCTTCGGGGA
1309104 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1309116 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1309128 C
1 C
1309129 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:1310060 original size:20 final size:20
Alignment explanation
Indices: 1310032--1310261 Score: 228
Period size: 20 Copynumber: 11.5 Consensus size: 20
1310022 AAATTTCAGT
* * *
1310032 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1310052 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
1310072 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
1310092 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
1310112 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
1310132 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
1310152 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
1310172 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
* *
1310192 GTTGCGATTTACGGATACGA
1 GTTGCGATTTACGGATTCGC
*
1310212 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
1310232 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
1310252 GTTGCGATTT
1 GTTGCGATTT
1310262 TGGAAAATCG
Statistics
Matches: 180, Mismatches: 28, Indels: 4
0.85 0.13 0.02
Matches are distributed among these distances:
20 179 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:1310278 original size:21 final size:21
Alignment explanation
Indices: 1310248--1310330 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
1310238 ATTTTCATAT
*
1310248 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1310269 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
1310290 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1310311 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1310331 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1310321 original size:42 final size:43
Alignment explanation
Indices: 1310228--1310326 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
1310218 ATTTATGTGT
* *
1310228 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
1310269 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
1310311 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
1310327 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:1319809 original size:8 final size:8
Alignment explanation
Indices: 1319798--1319822 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1319788 AGGATGAAAG
1319798 GGTAAAAT
1 GGTAAAAT
1319806 GGTAAAAT
1 GGTAAAAT
1319814 GGTAAAAT
1 GGTAAAAT
1319822 G
1 G
1319823 ATCATTTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (8 bp):
GGTAAAAT
Found at i:1322306 original size:20 final size:20
Alignment explanation
Indices: 1322281--1322334 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1322271 AATTGGGAAA
1322281 ATCGCAATACGATACTGACT
1 ATCGCAATACGATACTGACT
*
1322301 ATCGCAATGA-GATACTTACT
1 ATCGCAAT-ACGATACTGACT
*
1322321 ATCGCAATGCGATA
1 ATCGCAATACGATA
1322335 ATACAAAATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 29 0.97
21 1 0.03
ACGTcount: A:0.35, C:0.22, G:0.17, T:0.26
Consensus pattern (20 bp):
ATCGCAATACGATACTGACT
Found at i:1322343 original size:61 final size:62
Alignment explanation
Indices: 1322278--1322395 Score: 152
Period size: 61 Copynumber: 1.9 Consensus size: 62
1322268 GCGAATTGGG
* * *
1322278 AAAATCGCAA-TACGATACTGACTATCGCAATGAGATACTTAC-T-ATCGCAATGCGATAATAC
1 AAAATCGCAACGA-GATACTGACTATCGCAACGAGATA-ATACATAATCGCAATGCGATAATAC
* *
1322339 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATAATCGCAATGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGAGATAATACATAATCGCAATGCGAT
1322396 TTTCAAAGCG
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
60 3 0.06
61 32 0.65
62 14 0.29
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (62 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGAGATAATACATAATCGCAATGCGATAATAC
Found at i:1322346 original size:41 final size:41
Alignment explanation
Indices: 1322301--1322391 Score: 137
Period size: 41 Copynumber: 2.2 Consensus size: 41
1322291 GATACTGACT
* *
1322301 ATCGCAATGAGATACTTACTATCGCAATGCGATAATACAAA
1 ATCGCAATGAGATACTGACTATCGCAACGCGATAATACAAA
* * *
1322342 ATCGCAACGAGATACTGACTTTCGCAACGCGATAATACATA
1 ATCGCAATGAGATACTGACTATCGCAACGCGATAATACAAA
1322383 ATCGCAATG
1 ATCGCAATG
1322392 CGATTTTCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.23
Consensus pattern (41 bp):
ATCGCAATGAGATACTGACTATCGCAACGCGATAATACAAA
Found at i:1322347 original size:21 final size:20
Alignment explanation
Indices: 1322321--1322395 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
1322311 GATACTTACT
*
1322321 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATAATAC-AA
* * *
1322342 ATCGCAACGAGATACTGAC-T
1 ATCGCAACGCGATAAT-ACAA
*
1322362 TTCGCAACGCGATAATACATA
1 ATCGCAACGCGATAATACA-A
*
1322383 ATCGCAATGCGAT
1 ATCGCAACGCGAT
1322396 TTTCAAAGCG
Statistics
Matches: 41, Mismatches: 10, Indels: 6
0.72 0.18 0.11
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 24 0.59
22 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGCAACGCGATAATACAA
Found at i:1322591 original size:22 final size:22
Alignment explanation
Indices: 1322563--1322606 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
1322553 CACTCTCTCA
1322563 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
1322585 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
1322607 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:1322923 original size:20 final size:20
Alignment explanation
Indices: 1322869--1322927 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
1322859 GCGATTCTCT
**
1322869 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
1322889 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
1322909 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
1322928 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:1323118 original size:25 final size:24
Alignment explanation
Indices: 1323064--1323118 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
1323054 TGTTTATTAT
* *
1323064 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
1323088 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
1323114 TGTTT
1 TGTTT
1323119 ATTCCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:1324267 original size:18 final size:18
Alignment explanation
Indices: 1324246--1324290 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
1324236 TCCACTTCGG
*
1324246 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
1324264 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
1324282 GAGCCATCA
1 GAGCCATCA
1324291 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:1324797 original size:20 final size:20
Alignment explanation
Indices: 1324772--1324817 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1324762 TAGTTTACTT
*
1324772 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
1324792 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
1324812 TCGCAA
1 TCGCAA
1324818 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:1324826 original size:19 final size:20
Alignment explanation
Indices: 1324783--1324838 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
1324773 CGCAACATGA
1324783 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
1324803 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
**
1324822 AAATGAAAATCGCAACG
1 AAATGACTATCGCAACG
1324839 ACAAAATCGC
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.39, C:0.21, G:0.23, T:0.16
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:1324869 original size:19 final size:18
Alignment explanation
Indices: 1324811--1324874 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
1324801 GGAAATGGCT
1324811 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG-AA
*
1324830 ATCGCAA--CGACA--AA
1 ATCGCAATGCGAAATGAA
1324844 ATCGCAATGCGAAATGAA
1 ATCGCAATGCGAAATGAA
1324862 AGTCGCAATGCGA
1 A-TCGCAATGCGA
1324875 TTTGTGTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 9 0.24
16 4 0.11
17 4 0.11
18 3 0.08
19 18 0.47
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.14
Consensus pattern (18 bp):
ATCGCAATGCGAAATGAA
Found at i:1324905 original size:14 final size:14
Alignment explanation
Indices: 1324886--1324975 Score: 63
Period size: 14 Copynumber: 5.8 Consensus size: 14
1324876 TTGTGTTTCA
*
1324886 CGTTGCGATTTTGT
1 CGTTGCGATTTTTT
1324900 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TTT
**
1324916 CGCATTTTGATTTTTT
1 CG--TTGCGATTTTTT
1324932 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TTT
*
1324949 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTTT
1324965 CGTTGCGATTT
1 CGTTGCGATTT
1324976 GCATTTCGCA
Statistics
Matches: 61, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 24 0.39
15 3 0.05
16 13 0.21
17 5 0.08
18 10 0.16
19 6 0.10
ACGTcount: A:0.11, C:0.17, G:0.21, T:0.51
Consensus pattern (14 bp):
CGTTGCGATTTTTT
Found at i:1324950 original size:33 final size:33
Alignment explanation
Indices: 1324888--1324992 Score: 167
Period size: 33 Copynumber: 3.2 Consensus size: 33
1324878 GTGTTTCACG
1324888 TTGCGATTTTGTCGTTGCGA-TTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
** *
1324920 TTTTGATTTTTTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
*
1324953 TTGCGATTTTGTCGTTGCGATTTGCATTTCGCA
1 TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
1324986 TTGCGAT
1 TTGCGAT
1324993 AGCCATTTCC
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
32 17 0.26
33 48 0.74
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (33 bp):
TTGCGATTTTGTCGTTGCGATTTTCATTTCGCA
Found at i:1325011 original size:20 final size:19
Alignment explanation
Indices: 1324977--1325032 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
1324967 TTGCGATTTG
*
1324977 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
1324996 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
1325016 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
1325033 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:1326933 original size:14 final size:14
Alignment explanation
Indices: 1326899--1326937 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1326889 TTGATTGTTT
1326899 AATTGATTTGTAAA
1 AATTGATTTGTAAA
*
1326913 AAATGATTTGTAAA
1 AATTGATTTGTAAA
**
1326927 TGTTGATTTGT
1 AATTGATTTGT
1326938 TTAATTGGTG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (14 bp):
AATTGATTTGTAAA
Found at i:1327098 original size:19 final size:19
Alignment explanation
Indices: 1327074--1327160 Score: 139
Period size: 19 Copynumber: 4.8 Consensus size: 19
1327064 ATCGCAACGA
1327074 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1327093 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1327112 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
1327131 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
1327145 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
1327161 TTTTCATTTC
Statistics
Matches: 65, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
14 11 0.17
15 1 0.02
16 2 0.03
17 2 0.03
19 49 0.75
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:1327118 original size:38 final size:33
Alignment explanation
Indices: 1327064--1327160 Score: 149
Period size: 38 Copynumber: 2.8 Consensus size: 33
1327054 GAAACTGACT
1327064 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1327097 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAAATCGCAATGCGAAATGAAA
1327135 ATCGCAACGAGAAAATCGCAATGCGA
1 ATCGCAACGAGAAAATCGCAATGCGA
1327161 TTTTCATTTC
Statistics
Matches: 59, Mismatches: 0, Indels: 10
0.86 0.00 0.14
Matches are distributed among these distances:
33 23 0.39
34 1 0.02
35 2 0.03
36 2 0.03
37 1 0.02
38 30 0.51
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:1327204 original size:20 final size:20
Alignment explanation
Indices: 1327187--1327274 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
1327177 CGATTTTCTA
1327187 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
* *** *
1327207 GTTGTGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
*
1327227 ATTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1327247 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
1327267 GTTGCGAT
1 GTTGCGAT
1327275 TTCCCCGTTG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 3 0.06
20 48 0.89
21 3 0.06
ACGTcount: A:0.16, C:0.20, G:0.24, T:0.40
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:1327216 original size:34 final size:37
Alignment explanation
Indices: 1327167--1327254 Score: 101
Period size: 40 Copynumber: 2.4 Consensus size: 37
1327157 GCGATTTTCA
* *
1327167 TTTCGCATTGCGA-TTTTC-T-AGTTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTTCTTCAATTGCGATAGCCAT
*
1327201 TTTCGCGTTGTGATTTTTCATTTCGAATTGCGATAGCCAT
1 TTTCGCGTTGCGATTTTTC--TTC-AATTGCGATAGCCAT
1327241 TTTCGCGTTGCGAT
1 TTTCGCGTTGCGAT
1327255 AGCCATTTTC
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
34 11 0.25
35 5 0.11
38 1 0.02
40 27 0.61
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.43
Consensus pattern (37 bp):
TTTCGCGTTGCGATTTTTCTTCAATTGCGATAGCCAT
Found at i:1327513 original size:20 final size:20
Alignment explanation
Indices: 1327488--1327537 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
1327478 TTGAAGATGA
1327488 TTGCGATTTTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
***
1327508 TTGCGAAAGTCAGAATCTCG
1 TTGCGATTTTCAGAATCTCG
1327528 TTGCGATTTT
1 TTGCGATTTT
1327538 GTATTATCTC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (20 bp):
TTGCGATTTTCAGAATCTCG
Found at i:1327608 original size:20 final size:21
Alignment explanation
Indices: 1327564--1327615 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1327554 ATAGTCAGTA
*
1327564 TCGCATTGCGATTTTTCAAAT
1 TCGCATTGCGATTTTACAAAT
**
1327585 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
1327605 TCGCATTGCGA
1 TCGCATTGCGA
1327616 ATTAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.21, G:0.17, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:1328427 original size:24 final size:24
Alignment explanation
Indices: 1328400--1328453 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
1328390 GTATTCGAAA
*
1328400 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
1328424 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
1328448 TTTGAT
1 TTTGAT
1328454 GATGTTTCAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:1328645 original size:12 final size:12
Alignment explanation
Indices: 1328628--1328664 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
1328618 ATATAATCCT
1328628 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1328640 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1328652 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1328664 G
1 G
1328665 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1331003 original size:33 final size:33
Alignment explanation
Indices: 1330956--1331082 Score: 168
Period size: 33 Copynumber: 3.8 Consensus size: 33
1330946 GGAAATTACT
*
1330956 ATCGTAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGAAATGCGAAATGAAAATCGCAACGAGAGA
*
1330989 ATCGAAATGCGAAATGAAAATCGCAACGCGA-A
1 ATCGAAATGCGAAATGAAAATCGCAACGAGAGA
* * *
1331021 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGAAATGCGAAATGAAAATCGCAACGAGAGA
*
1331055 ATC-ACAATACGAAATGAAAATCGCAACG
1 ATCGA-AATGCGAAATGAAAATCGCAACG
1331083 CGAATTTAAT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
32 1 0.01
33 80 0.98
34 1 0.01
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (33 bp):
ATCGAAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:1331019 original size:19 final size:19
Alignment explanation
Indices: 1330936--1331049 Score: 59
Period size: 19 Copynumber: 6.5 Consensus size: 19
1330926 CTTAATGTCT
* **
1330936 ATCGCAACGCGGAAATTACT
1 ATCGCAACGC-GAAATGAAA
* *
1330956 ATCGTAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
1330975 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
* *
1330989 ATCGAAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1331008 ATCGCAACGCG-AAT----
1 ATCGCAACGCGAAATGAAA
* *
1331022 TTCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
1331041 ATCGCAACG
1 ATCGCAACG
1331050 AGGGAATCAC
Statistics
Matches: 69, Mismatches: 15, Indels: 21
0.66 0.14 0.20
Matches are distributed among these distances:
14 18 0.26
15 4 0.06
16 2 0.03
17 2 0.03
18 4 0.06
19 31 0.45
20 8 0.12
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.17
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:1331068 original size:66 final size:66
Alignment explanation
Indices: 1330961--1331089 Score: 224
Period size: 66 Copynumber: 2.0 Consensus size: 66
1330951 TTACTATCGT
*
1330961 AATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGCGAAATGAAAATCGCAACGCGAATTTCG
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGAAATACGAAATGAAAATCGCAACGCGAATTTCG
1331026 C
66 C
*
1331027 AATGCGAAATGAAAATCGCAACGAGGGAATC-ACAATACGAAATGAAAATCGCAACGCGAATTT
1 AATGCGAAATGAAAATCGCAACGAGAGAATCGA-AATACGAAATGAAAATCGCAACGCGAATTT
1331090 AATTTCTCGT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
65 1 0.02
66 59 0.98
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.16
Consensus pattern (66 bp):
AATGCGAAATGAAAATCGCAACGAGAGAATCGAAATACGAAATGAAAATCGCAACGCGAATTTCG
C
Found at i:1331104 original size:19 final size:19
Alignment explanation
Indices: 1331082--1331123 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
1331072 AAATCGCAAC
*
1331082 GCGAATTTAATTTCTCGTT
1 GCGAATTTAATTTCGCGTT
* *
1331101 GCGATTTTCATTTCGCGTT
1 GCGAATTTAATTTCGCGTT
1331120 GCGA
1 GCGA
1331124 TTCTCTCGTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.17, C:0.19, G:0.21, T:0.43
Consensus pattern (19 bp):
GCGAATTTAATTTCGCGTT
Found at i:1331124 original size:19 final size:19
Alignment explanation
Indices: 1331091--1331157 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
1331081 CGCGAATTTA
*
1331091 ATTTCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
1331110 ATTTCGCGTTGCGA--TTC
1 ATTTCGCGTTGCGATTTTC
*
1331127 ---TCTCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
*
1331143 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
1331158 AGTACTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
14 10 0.26
16 3 0.08
17 3 0.08
19 23 0.59
ACGTcount: A:0.12, C:0.22, G:0.19, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:1331133 original size:33 final size:33
Alignment explanation
Indices: 1331094--1331157 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
1331084 GAATTTAATT
*
1331094 TCTCGTTGCGATTTTCATTTCGCGTTGCGATTC
1 TCTCGTTGCGATTTTCATTTCGCATTGCGATTC
1331127 TCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCTCGTTGCGATTTTCATTTCGCATTGCGAT
1331158 AGTACTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.11, C:0.23, G:0.20, T:0.45
Consensus pattern (33 bp):
TCTCGTTGCGATTTTCATTTCGCATTGCGATTC
Found at i:1331283 original size:14 final size:14
Alignment explanation
Indices: 1331264--1331300 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1331254 CATCAATTAA
1331264 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1331278 ACAAATCACCTTTT
1 ACAAATCAACTTTT
1331292 ACAAATCAA
1 ACAAATCAA
1331301 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1332722 original size:21 final size:21
Alignment explanation
Indices: 1332656--1332722 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1332646 GTGAATCGGG
*
1332656 CTCTTGAAAGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1332676 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1332698 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1332719 CTCT
1 CTCT
1332723 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.21, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1332741 original size:42 final size:41
Alignment explanation
Indices: 1332656--1332778 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1332646 GTGAATCGGG
* * * *
1332656 CTCTTGAAAGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1332698 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1332740 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1332779 CGAGTCGAGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.24, C:0.19, G:0.37, T:0.21
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:1333171 original size:91 final size:90
Alignment explanation
Indices: 1332996--1333180 Score: 300
Period size: 91 Copynumber: 2.0 Consensus size: 90
1332986 ATTTCAAACT
*
1332996 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
1333061 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
1333089 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTCACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
*
1333153 GTATTGGCAGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
1333180 T
1 T
1333181 AAGCAATCTA
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
91 42 0.48
93 19 0.22
95 27 0.31
ACGTcount: A:0.47, C:0.19, G:0.12, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:1334935 original size:14 final size:14
Alignment explanation
Indices: 1334916--1334971 Score: 58
Period size: 14 Copynumber: 3.6 Consensus size: 14
1334906 GGAAATGACT
1334916 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
1334930 ATCGCAACGCAAAATGA
1 ATCGCAACG--AGA-GA
1334947 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
1334963 ATCGCAACG
1 ATCGCAACG
1334972 CGAAATGAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
14 18 0.51
16 4 0.11
17 4 0.11
19 9 0.26
ACGTcount: A:0.41, C:0.25, G:0.23, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:1334950 original size:33 final size:33
Alignment explanation
Indices: 1334892--1334990 Score: 162
Period size: 33 Copynumber: 3.0 Consensus size: 33
1334882 ACGAGATAAT
1334892 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
*
1334926 GAGAATCGCAACGCAAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
**
1334959 GAGAATCGCAACGCGAAATGAAAATCGCAACG
1 GAGAATCGCAACGCGAAATGACTATCGCAACG
1334991 CGAAATGAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 47 0.77
34 14 0.23
ACGTcount: A:0.41, C:0.23, G:0.24, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:1334997 original size:52 final size:52
Alignment explanation
Indices: 1334929--1335045 Score: 198
Period size: 52 Copynumber: 2.2 Consensus size: 52
1334919 GCAACGAGAG
* **
1334929 AATCGCAACGCAAAATGACTATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
1334981 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
*
1335033 AATCGCAATGCGA
1 AATCGCAACGCGA
1335046 TTTTGGTTTC
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.11
Consensus pattern (52 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAA
Found at i:1335038 original size:19 final size:19
Alignment explanation
Indices: 1334867--1335045 Score: 136
Period size: 19 Copynumber: 10.1 Consensus size: 19
1334857 TCTTTTGGTT
*
1334867 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
1334886 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
1334906 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
1334924 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
* **
1334940 AAAATGACTATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1334957 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1334973 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
1334992 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
1335009 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
1335025 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
1335044 GA
1 GA
1335046 TTTTGGTTTC
Statistics
Matches: 127, Mismatches: 16, Indels: 34
0.72 0.09 0.19
Matches are distributed among these distances:
14 28 0.22
15 3 0.02
16 5 0.04
17 4 0.03
18 4 0.03
19 54 0.43
20 27 0.21
21 2 0.02
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:1335670 original size:21 final size:20
Alignment explanation
Indices: 1335621--1335672 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
1335611 GCTATGTAAA
*
1335621 TCACATTGCGATTTACGTAT
1 TCACATTGCGATTTACCTAT
* * *
1335641 TCGCGTTGCGATTTTCCTAAT
1 TCACATTGCGATTTACCT-AT
1335662 TCACATTGCGA
1 TCACATTGCGA
1335673 ATTATGAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (20 bp):
TCACATTGCGATTTACCTAT
Found at i:1335695 original size:21 final size:21
Alignment explanation
Indices: 1335669--1335724 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
1335659 AATTCACATT
*
1335669 GCGAATTATGAAAATCGCAAC
1 GCGAATTACGAAAATCGCAAC
* *
1335690 GCGAA-TACGTAAATCGCAAT
1 GCGAATTACGAAAATCGCAAC
*
1335710 GCGAATTAGGAAAAT
1 GCGAATTACGAAAAT
1335725 TGCATTGCGA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
20 17 0.59
21 12 0.41
ACGTcount: A:0.43, C:0.16, G:0.21, T:0.20
Consensus pattern (21 bp):
GCGAATTACGAAAATCGCAAC
Found at i:1335733 original size:21 final size:21
Alignment explanation
Indices: 1335668--1335734 Score: 73
Period size: 21 Copynumber: 3.2 Consensus size: 21
1335658 TAATTCACAT
*
1335668 TGCGAATTATGAAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
* *
1335689 CGCGAA-TACGTAAATCGCAA
1 TGCGAATTACGAAAATCGCAA
* * *
1335709 TGCGAATTAGGAAAATTGCAT
1 TGCGAATTACGAAAATCGCAA
1335730 TGCGA
1 TGCGA
1335735 TAGTCAGTAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.22
Consensus pattern (21 bp):
TGCGAATTACGAAAATCGCAA
Found at i:1335866 original size:21 final size:21
Alignment explanation
Indices: 1335826--1335866 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1335816 ACTGTAGACC
** *
1335826 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGCAACT
1335847 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATGCAAC
1335867 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.29, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAAATGCAACT
Found at i:1347850 original size:9 final size:9
Alignment explanation
Indices: 1347816--1347931 Score: 63
Period size: 9 Copynumber: 12.6 Consensus size: 9
1347806 TATATATTAG
1347816 TTTTGTTTTA
1 TTTT-TTTTA
*
1347826 TTTTTTATA
1 TTTTTTTTA
*
1347835 TTGTTTTTTT
1 TT-TTTTTTA
*
1347845 TATTTTTTTC
1 T-TTTTTTTA
*
1347855 TTATTTTTA
1 TTTTTTTTA
** *
1347864 TTTGCTTTG
1 TTTTTTTTA
*
1347873 TTTTATTTA
1 TTTTTTTTA
* *
1347882 TGTTATTTA
1 TTTTTTTTA
*
1347891 TCTTGTTTTA
1 T-TTTTTTTA
**
1347901 TTTTACTTA
1 TTTTTTTTA
*
1347910 TTTTTTATA
1 TTTTTTTTA
1347919 -TTTTTTTA
1 TTTTTTTTA
1347927 TTTTT
1 TTTTT
1347932 CTTTTCTCTT
Statistics
Matches: 78, Mismatches: 24, Indels: 9
0.70 0.22 0.08
Matches are distributed among these distances:
8 7 0.09
9 47 0.60
10 23 0.29
11 1 0.01
ACGTcount: A:0.14, C:0.03, G:0.05, T:0.78
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:1347853 original size:29 final size:31
Alignment explanation
Indices: 1347821--1347889 Score: 72
Period size: 31 Copynumber: 2.3 Consensus size: 31
1347811 ATTAGTTTTG
*
1347821 TTTTA-TTTTTTATATTG-TTTTTTTTATTT-
1 TTTTATTTTTTTAT-TTGCTTTGTTTTATTTA
*
1347850 TTTTCTTATTTTTATTTGCTTTGTTTTATTTA
1 TTTTATT-TTTTTATTTGCTTTGTTTTATTTA
*
1347882 TGTTATTT
1 TTTTATTT
1347890 ATCTTGTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
29 4 0.12
30 4 0.12
31 19 0.59
32 5 0.16
ACGTcount: A:0.13, C:0.03, G:0.06, T:0.78
Consensus pattern (31 bp):
TTTTATTTTTTTATTTGCTTTGTTTTATTTA
Found at i:1347859 original size:23 final size:23
Alignment explanation
Indices: 1347808--1347852 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
1347798 ATTATATATA
1347808 TATATTAGTTTTGTTTTATTTTT
1 TATATTAGTTTTGTTTTATTTTT
1347831 TATATT-GTTTT-TTTTATTTTT
1 TATATTAGTTTTGTTTTATTTTT
1347852 T
1 T
1347853 TCTTATTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 11 0.50
22 5 0.23
23 6 0.27
ACGTcount: A:0.16, C:0.00, G:0.07, T:0.78
Consensus pattern (23 bp):
TATATTAGTTTTGTTTTATTTTT
Found at i:1347925 original size:26 final size:26
Alignment explanation
Indices: 1347839--1347949 Score: 75
Period size: 26 Copynumber: 4.2 Consensus size: 26
1347829 TTTATATTGT
*
1347839 TTTTTTTATTTTTTTCTTA-TTTTTAT-
1 TTTTTTTA--TTTTACTTATTTTTTATA
** * * *
1347865 TTGCTTTGTTTTATTTATGTTATTTATC
1 TTTTTTTATTTTACTTAT-TT-TTTATA
*
1347893 TTGTTTTATTTTACTTATTTTTTATA
1 TTTTTTTATTTTACTTATTTTTTATA
* *
1347919 TTTTTTTATTTTTCTT-TTCTCTTATA
1 TTTTTTTATTTTACTTATT-TTTTATA
1347945 TTTTT
1 TTTTT
1347950 AGATTAGTCC
Statistics
Matches: 68, Mismatches: 12, Indels: 10
0.76 0.13 0.11
Matches are distributed among these distances:
24 7 0.10
25 2 0.03
26 37 0.54
27 7 0.10
28 15 0.22
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.77
Consensus pattern (26 bp):
TTTTTTTATTTTACTTATTTTTTATA
Found at i:1351529 original size:18 final size:18
Alignment explanation
Indices: 1351506--1351540 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1351496 TCGATTCTTC
1351506 CGACCGATAAAACCGATT
1 CGACCGATAAAACCGATT
*
1351524 CGACCGATTAAACCGAT
1 CGACCGATAAAACCGAT
1351541 AGCATGACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.29, G:0.17, T:0.17
Consensus pattern (18 bp):
CGACCGATAAAACCGATT
Found at i:1366360 original size:29 final size:29
Alignment explanation
Indices: 1366328--1366421 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
1366318 GATATTATTG
1366328 GAATGTTCAAAAGTTTGGGGACTAATTTA
1 GAATGTTCAAAAGTTTGGGGACTAATTTA
* * * *
1366357 GAATAAATATC-ATAGTTT-GAGAATGAATTT-
1 GAAT--GT-TCAAAAGTTTGGGGACT-AATTTA
*
1366387 GAAATGTTCAAAAGTTTGGGGACCAATTTA
1 G-AATGTTCAAAAGTTTGGGGACTAATTTA
1366417 GAATG
1 GAATG
1366422 GGAGTCATAG
Statistics
Matches: 48, Mismatches: 9, Indels: 16
0.66 0.12 0.22
Matches are distributed among these distances:
28 2 0.04
29 20 0.42
30 9 0.19
31 15 0.31
32 2 0.04
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.33
Consensus pattern (29 bp):
GAATGTTCAAAAGTTTGGGGACTAATTTA
Found at i:1366477 original size:29 final size:29
Alignment explanation
Indices: 1366329--1366477 Score: 74
Period size: 29 Copynumber: 5.0 Consensus size: 29
1366319 ATATTATTGG
*
1366329 AATGTTCAAAAGTTTGGGGACTAATTTAGA
1 AATGTTCAAAAGTTTAGGGACTAATTTA-A
** * * * *
1366359 ATAAATATC-ATAGTTT-GAGAATGAATTTGA
1 A-ATGT-TCAAAAGTTTAGGGACT-AATTTAA
* * *
1366389 AATGTTCAAAAGTTTGGGGACCAATTTAG
1 AATGTTCAAAAGTTTAGGGACTAATTTAA
* *
1366418 AATGGGAGTC-ATAGTTTAGGGA-TGGAA-TTAA
1 AAT--G-TTCAAAAGTTTAGGGACT--AATTTAA
1366449 AATGTTCAAAAGTTTAGGGACTAATTTAA
1 AATGTTCAAAAGTTTAGGGACTAATTTAA
1366478 TATAAGAGTC
Statistics
Matches: 85, Mismatches: 21, Indels: 27
0.64 0.16 0.20
Matches are distributed among these distances:
28 6 0.07
29 32 0.38
30 11 0.13
31 30 0.35
32 6 0.07
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.33
Consensus pattern (29 bp):
AATGTTCAAAAGTTTAGGGACTAATTTAA
Found at i:1366487 original size:60 final size:60
Alignment explanation
Indices: 1366329--1366495 Score: 207
Period size: 60 Copynumber: 2.8 Consensus size: 60
1366319 ATATTATTGG
* *
1366329 AATGTTCAAAAGTTTGGGGACTAATTTAGAATAA-ATATCATAGTTTGAGAATGAATTTGA
1 AATGTTCAAAAGTTTGGGGACTAATTTAGAATAAGA-GTCATAGTTTGAGAATGAATTTAA
* ** *
1366389 AATGTTCAAAAGTTTGGGGACCAATTTAGAATGGGAGTCATAGTTT-AGGGATGGAA-TTAA
1 AATGTTCAAAAGTTTGGGGACTAATTTAGAATAAGAGTCATAGTTTGA-GAAT-GAATTTAA
*
1366449 AATGTTCAAAAGTTTAGGGACTAATTTA-ATATAAGAGTCATAGTTTG
1 AATGTTCAAAAGTTTGGGGACTAATTTAGA-ATAAGAGTCATAGTTTG
1366496 GGCATGTATG
Statistics
Matches: 92, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
59 2 0.02
60 86 0.93
61 4 0.04
ACGTcount: A:0.38, C:0.06, G:0.23, T:0.34
Consensus pattern (60 bp):
AATGTTCAAAAGTTTGGGGACTAATTTAGAATAAGAGTCATAGTTTGAGAATGAATTTAA
Found at i:1383159 original size:23 final size:23
Alignment explanation
Indices: 1383133--1383193 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
1383123 CTCATATAAA
*
1383133 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
1383156 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
1383179 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
1383194 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:1383380 original size:103 final size:103
Alignment explanation
Indices: 1383216--1383416 Score: 375
Period size: 103 Copynumber: 2.0 Consensus size: 103
1383206 CATAAAGACC
* *
1383216 ACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
1383281 CACATGTTCCAAAGAATACATATATGTCCCGAATGACT
66 CACATGTTCCAAAGAATACATATATGTCCCGAATGACT
*
1383319 ACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
1383384 CACATGTTCCAAAGAATACATATATGTCCCGAA
66 CACATGTTCCAAAGAATACATATATGTCCCGAA
1383417 GGACCACAAA
Statistics
Matches: 95, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 95 1.00
ACGTcount: A:0.36, C:0.23, G:0.12, T:0.28
Consensus pattern (103 bp):
ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
CACATGTTCCAAAGAATACATATATGTCCCGAATGACT
Found at i:1384523 original size:20 final size:20
Alignment explanation
Indices: 1384486--1384523 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1384476 ATTCATATAA
*
1384486 TTTATTATCATATCATATGG
1 TTTATTATCATATAATATGG
1384506 TTTA-TATCATCATAATAT
1 TTTATTATCAT-ATAATAT
1384524 ATCACACATT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.34, C:0.11, G:0.05, T:0.50
Consensus pattern (20 bp):
TTTATTATCATATAATATGG
Found at i:1388240 original size:23 final size:23
Alignment explanation
Indices: 1388222--1388274 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
1388212 AATGCATCGA
1388222 AGTGCCACATAGAATTGCACCGT
1 AGTGCCACATAGAATTGCACCGT
* *
1388245 AGTGCCGCGTAGAATTGCACCGT
1 AGTGCCACATAGAATTGCACCGT
1388268 AGTGCCA
1 AGTGCCA
1388275 TATAATATGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.26, C:0.26, G:0.26, T:0.21
Consensus pattern (23 bp):
AGTGCCACATAGAATTGCACCGT
Found at i:1388454 original size:103 final size:97
Alignment explanation
Indices: 1388292--1388499 Score: 353
Period size: 103 Copynumber: 2.1 Consensus size: 97
1388282 TGTCCATAAA
1388292 GACCACAATCATTCCTTAAGAATCATATACATAGGGATCAAGTATGTGTCTCACCAGACTTCACA
1 GACCACAATCATTCCTTAAGAATCATATACATAGGGATCAAGTATGTGTCTCACCAGACTTCACA
*
1388357 CATGTTCCAAAGAATACATATATGTCCCGAAT
66 CATGTTCCAAAGAATACATATATGTCCCGAAG
1388389 GACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGAC
1 GACCACA-ATCATTCCTTAAGAATCATATACATA-G----GGATCAAGTATGTGTCTCACCAGAC
1388454 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
60 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
1388492 GACCACAA
1 GACCACAA
1388500 AGACCCTCGA
Statistics
Matches: 104, Mismatches: 1, Indels: 7
0.93 0.01 0.06
Matches are distributed among these distances:
97 7 0.07
98 26 0.25
99 1 0.01
102 1 0.01
103 69 0.66
ACGTcount: A:0.37, C:0.25, G:0.13, T:0.25
Consensus pattern (97 bp):
GACCACAATCATTCCTTAAGAATCATATACATAGGGATCAAGTATGTGTCTCACCAGACTTCACA
CATGTTCCAAAGAATACATATATGTCCCGAAG
Found at i:1389579 original size:20 final size:19
Alignment explanation
Indices: 1389556--1389594 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
1389546 TCTTTTATAT
1389556 TCATATAATTTATTATCATA
1 TCATATAATTTA-TATCATA
**
1389576 TCATATGGTTTATATCATA
1 TCATATAATTTATATCATA
1389595 ATATATCACA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.36, C:0.10, G:0.05, T:0.49
Consensus pattern (19 bp):
TCATATAATTTATATCATA
Found at i:1391306 original size:22 final size:21
Alignment explanation
Indices: 1391259--1391311 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
1391249 TTATATCATT
1391259 TATTAAATATTTTAAAATATC
1 TATTAAATATTTTAAAATATC
** *
1391280 T-TTAAATATATTTTCATTATC
1 TATTAAATAT-TTTAAAATATC
1391301 TATTAAA-ATTT
1 TATTAAATATTT
1391312 ATATTACAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
20 10 0.37
21 12 0.44
22 5 0.19
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.53
Consensus pattern (21 bp):
TATTAAATATTTTAAAATATC
Found at i:1402652 original size:21 final size:22
Alignment explanation
Indices: 1402628--1402678 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
1402618 TGTAATATAA
1402628 ATTTTAATAGATA-ATGAAAAT
1 ATTTTAATAGATATATGAAAAT
* *
1402649 ATTTTAA-AGATATTTTAAAAT
1 ATTTTAATAGATATATGAAAAT
1402670 ATTTTAATA
1 ATTTTAATA
1402679 ATGATATACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 5 0.19
21 20 0.77
22 1 0.04
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (22 bp):
ATTTTAATAGATATATGAAAAT
Found at i:1402673 original size:10 final size:10
Alignment explanation
Indices: 1402644--1402676 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
1402634 ATAGATAATG
1402644 AAAATATTTT
1 AAAATATTTT
1402654 AAAGATATTTT
1 AAA-ATATTTT
1402665 AAAATATTTT
1 AAAATATTTT
1402675 AA
1 AA
1402677 TAATGATATA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.45
Consensus pattern (10 bp):
AAAATATTTT
Done.