Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004823.1 Hibiscus syriacus cultivar Beakdansim tig00010868_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: 139299
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:443 original size:16 final size:16
Alignment explanation
Indices: 404--446 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
394 GTCATCAGTA
*
404 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
420 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
437 CTTATCAATC
1 CTTATCAATC
447 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:9211 original size:18 final size:17
Alignment explanation
Indices: 9157--9205 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
9147 TTGGACCCTT
* *
9157 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
9175 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
9193 AGTGCATTCGATG
1 AGTGCA-TCGATG
9206 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:9314 original size:64 final size:64
Alignment explanation
Indices: 9178--9315 Score: 174
Period size: 64 Copynumber: 2.2 Consensus size: 64
9168 GCACTAAGAG
* * **
9178 TGCATCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGTTGA
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGTAAA
* *
9242 TGCATCGATGCATCAAATGCATTCGATGTGTTCATAAA-ATCCTCAGTGCATCGATGCAT-G-AA
1 TGCATCGATGCATCAAATGCATTCGATGT-TTCA-AAATAGCCACAGTGCATCGATGCATGGTAA
9304 A
64 A
9305 TGCATTCGATG
1 TGCA-TCGATG
9316 TTCAATTTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
63 5 0.08
64 35 0.54
65 22 0.34
66 3 0.05
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (64 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCACAGTGCATCGATGCATGGTAAA
Found at i:9346 original size:45 final size:44
Alignment explanation
Indices: 9242--9346 Score: 124
Period size: 46 Copynumber: 2.3 Consensus size: 44
9232 GCATGGTTGA
*
9242 TGCATCGATGCATCAAATGCATTCGATGTGTTCATAAAATCCTCAG
1 TGCATCGATGCATGAAATGCATTCGA-GTGTTCATAAAAT-CTCAG
**
9288 TGCATCGATGCATGAAATGCATTCGA-TGTTCAATTTAAT-TCATGG
1 TGCATCGATGCATGAAATGCATTCGAGTGTTC-ATAAAATCTCA--G
9333 TGCATCGATGCATG
1 TGCATCGATGCATG
9347 GATTGGTGCA
Statistics
Matches: 53, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
43 3 0.06
44 5 0.09
45 20 0.38
46 25 0.47
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.32
Consensus pattern (44 bp):
TGCATCGATGCATGAAATGCATTCGAGTGTTCATAAAATCTCAG
Found at i:9673 original size:37 final size:38
Alignment explanation
Indices: 9630--9709 Score: 101
Period size: 37 Copynumber: 2.1 Consensus size: 38
9620 AAAATTGAAA
*
9630 AATAATTAACGTCTATTGGATTT-A-CCAAAAAAAATAT
1 AATAATTAACGTCTATTGCATTTAATCCAAAAAAAAT-T
* * *
9667 AATAATTAATGTTTATTGCATTTAATTCAAAAAAAATT
1 AATAATTAACGTCTATTGCATTTAATCCAAAAAAAATT
9705 AATAA
1 AATAA
9710 ATTTCTGGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
37 20 0.54
38 7 0.19
39 10 0.27
ACGTcount: A:0.50, C:0.07, G:0.06, T:0.36
Consensus pattern (38 bp):
AATAATTAACGTCTATTGCATTTAATCCAAAAAAAATT
Found at i:23463 original size:11 final size:11
Alignment explanation
Indices: 23449--23482 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
23439 TAATTAAAAG
23449 TTATTTTAAAT
1 TTATTTTAAAT
23460 TTATTTTAAA-
1 TTATTTTAAAT
23470 TTA-TTTAAAT
1 TTATTTTAAAT
23480 TTA
1 TTA
23483 CTTAAACTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 6 0.27
10 6 0.27
11 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTATTTTAAAT
Found at i:23495 original size:20 final size:20
Alignment explanation
Indices: 23453--23495 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
23443 TAAAAGTTAT
* *
23453 TTTAAATTTATTTTAAATTA
1 TTTAAATTTATCTTAAATAA
23473 TTTAAATTTA-CTTAAACTAA
1 TTTAAATTTATCTTAAA-TAA
23493 TTT
1 TTT
23496 TTAGTAAAGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAAATTTATCTTAAATAA
Found at i:24191 original size:20 final size:20
Alignment explanation
Indices: 24168--24399 Score: 197
Period size: 20 Copynumber: 11.5 Consensus size: 20
24158 CAGTTCCCAG
* *
24168 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATCTGTA
*
24188 AATCGCAACGCGAA-CATATA
1 AATCGCAACGCGAATC-TGTA
*
24208 AATCGCAACGCGATTCTG-A
1 AATCGCAACGCGAATCTGTA
* * *
24227 CTATCGCAACGAGTATCTGTAA
1 -AATCGCAACGCGAATCTGT-A
* *
24249 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATCTGTA
*
24269 AATCGCAACGAGAATAC-GTA
1 AATCGCAACGCGAAT-CTGTA
*
24289 AATCGCAACGCGTATCTGTA
1 AATCGCAACGCGAATCTGTA
*
24309 AATCGCAACGAGAATAC-GTA
1 AATCGCAACGCGAAT-CTGTA
* * *
24329 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATCTGTA
24349 AATCGCAACGAC-AATAC-GTAA
1 AATCGCAACG-CGAAT-CTGT-A
* *
24370 AATCGTAACGCGTATCTGTA
1 AATCGCAACGCGAATCTGTA
24390 AATCGCAACG
1 AATCGCAACG
24400 TGATTTTTAA
Statistics
Matches: 172, Mismatches: 26, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.02
20 133 0.77
21 35 0.20
22 1 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAATCTGTA
Found at i:24212 original size:40 final size:40
Alignment explanation
Indices: 24168--24399 Score: 236
Period size: 40 Copynumber: 5.8 Consensus size: 40
24158 CAGTTCCCAG
* * * * *
24168 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAACATGTA
* *
24208 AATCGCAACGCG-ATTCTG-ACTATCGCAACGAGTATC-TGTAA
1 AATCGCAACGCGTA-TCTGTA-AATCGCAACGAG-AACATGT-A
* * *
24249 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAACATGTA
* *
24289 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAACATGTA
* * * * *
24329 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAA
1 AATCGCAACGCGTATCTGTAAATCGCAACGAGAACATGT-A
*
24370 AATCGTAACGCGTATCTGTAAATCGCAACG
1 AATCGCAACGCGTATCTGTAAATCGCAACG
24400 TGATTTTTAA
Statistics
Matches: 167, Mismatches: 17, Indels: 15
0.84 0.09 0.08
Matches are distributed among these distances:
39 2 0.01
40 104 0.62
41 59 0.35
42 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGAGAACATGTA
Found at i:24272 original size:81 final size:80
Alignment explanation
Indices: 24168--24399 Score: 263
Period size: 81 Copynumber: 2.9 Consensus size: 80
24158 CAGTTCCCAG
* ** * * * *
24168 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACGCG-ATTCTG-ACTAT
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAACACATAAATCGCAACGCGTA-TCTGTA-AAT
*
24231 CGCAACGAGTAT-CTGTAA
64 CGCAACGAGAATAC-GT-A
* *
24249 AATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGTAAATCGCAACGCGTATCTGTAAATCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAACACATAAATCGCAACGCGTATCTGTAAATCG
24314 CAACGAGAATACGTA
66 CAACGAGAATACGTA
* * * * *
24329 AATCGCAATGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGTAACGCGTATCTGTAAATC
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGAACACAT-AAATCGCAACGCGTATCTGTAAATC
24394 GCAACG
65 GCAACG
24400 TGATTTTTAA
Statistics
Matches: 134, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
80 38 0.28
81 93 0.69
82 3 0.02
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (80 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGAACACATAAATCGCAACGCGTATCTGTAAATCG
CAACGAGAATACGTA
Found at i:24962 original size:19 final size:19
Alignment explanation
Indices: 24916--25028 Score: 83
Period size: 20 Copynumber: 6.1 Consensus size: 19
24906 GAAATGAAAA
**
24916 TCGCATTGCGATTTTGGTT
1 TCGCATTGCGATTTTCATT
*
24935 TCGCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
* *
24954 TTGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
**
24970 TCG--TTGCGATAGTCATT
1 TCGCATTGCGATTTTCATT
*
24987 TCCGCGTTGCGATTTTCATT
1 T-CGCATTGCGATTTTCATT
* *
25007 CTCTCGTTGCGATTTTCATT
1 -TCGCATTGCGATTTTCATT
25027 TC
1 TC
25029 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
14 6 0.08
16 5 0.07
17 5 0.07
18 2 0.03
19 27 0.36
20 29 0.39
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:28481 original size:14 final size:14
Alignment explanation
Indices: 28462--28497 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
28452 ATTGTTTAAT
28462 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
28476 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
28490 TGATTTGT
1 TGATTTGT
28498 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:28620 original size:19 final size:17
Alignment explanation
Indices: 28604--28701 Score: 64
Period size: 19 Copynumber: 5.8 Consensus size: 17
28594 AAAAATGACT
28604 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
28623 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
28637 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
**
28656 ATCGCAA--CG-AGGGA
1 ATCGCAATGCGAAATGA
28670 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
28689 ATCGCAACGCGAA
1 ATCGCAATGCGAA
28702 TTTAGTTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 16 0.26
16 9 0.15
17 9 0.15
19 28 0.45
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:28646 original size:33 final size:33
Alignment explanation
Indices: 28604--28697 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
28594 AAAAATGACT
28604 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
28637 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
28670 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
28698 CGAATTTAGT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:28751 original size:33 final size:33
Alignment explanation
Indices: 28697--28859 Score: 164
Period size: 33 Copynumber: 4.7 Consensus size: 33
28687 AAATCGCAAC
* * * * *
28697 GCGAATTTAGTTTCGCGTTGCGATTTTGTCGTT
1 GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
28730 GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
1 GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
* *
28763 GCGATTTTCATTTCGCATTGCGATAGTCATTTCCGCGTT
1 GCGATTTTAATTTCGCATTGCGAT--TC---T-CTCGTT
*
28802 GCGATTTTCATTTCGCATTGCGATTCTCTCGTT
1 GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
** *
28835 GCGATAGTAATTTCCGCGTTGCGAT
1 GCGATTTTAATTT-CGCATTGCGAT
28860 AGATATTAAG
Statistics
Matches: 111, Mismatches: 12, Indels: 13
0.82 0.09 0.10
Matches are distributed among these distances:
33 66 0.59
34 11 0.10
35 2 0.02
37 2 0.02
38 1 0.01
39 29 0.26
ACGTcount: A:0.15, C:0.21, G:0.22, T:0.42
Consensus pattern (33 bp):
GCGATTTTAATTTCGCATTGCGATTCTCTCGTT
Found at i:28752 original size:19 final size:19
Alignment explanation
Indices: 28728--28826 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
28718 GATTTTGTCG
*
28728 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
28747 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
28761 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
** *
28780 TTGCGATAGTCATTTCCGCG
1 TTGCGATTTTCATTT-CGCA
28800 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
28819 TTGCGATT
1 TTGCGATT
28827 CTCTCGTTGC
Statistics
Matches: 65, Mismatches: 9, Indels: 12
0.76 0.10 0.14
Matches are distributed among these distances:
14 6 0.09
16 7 0.11
17 6 0.09
19 30 0.46
20 16 0.25
ACGTcount: A:0.15, C:0.21, G:0.19, T:0.44
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:28805 original size:20 final size:19
Alignment explanation
Indices: 28759--28861 Score: 81
Period size: 20 Copynumber: 5.6 Consensus size: 19
28749 GCGATTCTCT
**
28759 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
28778 CATTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTT-CG
**
28798 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
28817 CATTGCGAT--TC---TCT
1 CGTTGCGATAGTCATTTCG
*
28831 CGTTGCGATAGTAATTTCCG
1 CGTTGCGATAGTCATTT-CG
28851 CGTTGCGATAG
1 CGTTGCGATAG
28862 ATATTAAGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 13
0.73 0.12 0.14
Matches are distributed among these distances:
14 10 0.15
16 1 0.02
17 2 0.03
19 25 0.38
20 28 0.42
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:28848 original size:72 final size:73
Alignment explanation
Indices: 28726--28861 Score: 220
Period size: 72 Copynumber: 1.9 Consensus size: 73
28716 GCGATTTTGT
** *
28726 CGTTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATAGT
1 CGTTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCGATAGT
28790 CATTTCCG
66 CATTTCCG
* *
28798 CGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCGTTGCGATAG
1 CGTTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCGATAG
28862 ATATTAAGAT
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
72 46 0.79
73 12 0.21
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.41
Consensus pattern (73 bp):
CGTTGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATAGTAATTTCCGCATTGCGATAGT
CATTTCCG
Found at i:31284 original size:24 final size:24
Alignment explanation
Indices: 31220--31287 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
31210 CTGAAAAATC
* *
31220 ATCAAAATCCAAGTATTGACCAAG
1 ATCAAAGTCCAAATATTGACCAAG
***
31244 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCAAATATTGACCAAG
* *
31268 ATCAAATTTCAAATATTGAC
1 ATCAAAGTCCAAATATTGAC
31288 TAGTACTCAC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.25
Consensus pattern (24 bp):
ATCAAAGTCCAAATATTGACCAAG
Found at i:32148 original size:20 final size:19
Alignment explanation
Indices: 32127--32365 Score: 140
Period size: 20 Copynumber: 11.9 Consensus size: 19
32117 GCGATAGTCA
*
32127 GAATCTCGTTGCGATTTAC
1 GAATCGCGTTGCGATTTAC
* *
32146 AGATTCGCATTGCGATTTAC
1 -GAATCGCGTTGCGATTTAC
**
32166 GTGTTCGCGTTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
* *
32186 GTATTCGCATTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
* *
32206 GGATACGCATTGCGATTTAC
1 GAAT-CGCGTTGCGATTTAC
* *
32226 GTATTCTCGTTGCGATTTAC
1 G-AATCGCGTTGCGATTTAC
*
32246 -AGATACGCATTGCGATTTAC
1 GA-AT-CGCGTTGCGATTTAC
* * *
32266 GTATTCTCGTTGCGATTTAT
1 G-AATCGCGTTGCGATTTAC
*
32286 GGATACGCGTTGCGATTTTAC
1 GAAT-CGCGTTGCGA-TTTAC
* *
32307 GTATTGTCGTTGCGATTTAC
1 GAATCG-CGTTGCGATTTAC
* * * *
32327 GGATACTCGTTGTGATAGT-C
1 GAAT-CGCGTTGCGAT-TTAC
32347 AGAATCGCGTTGCGATTTA
1 -GAATCGCGTTGCGATTTA
32366 TATGTTCACG
Statistics
Matches: 170, Mismatches: 35, Indels: 28
0.73 0.15 0.12
Matches are distributed among these distances:
18 1 0.01
19 5 0.03
20 142 0.84
21 21 0.12
22 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (19 bp):
GAATCGCGTTGCGATTTAC
Found at i:32177 original size:40 final size:40
Alignment explanation
Indices: 32133--32403 Score: 266
Period size: 40 Copynumber: 6.8 Consensus size: 40
32123 GTCAGAATCT
* *
32133 CGTTGCGATTTACAG-ATTCGCATTGCGATTTACGTG-TTCG
1 CGTTGCGATTTAC-GTATTCGCGTTGCGATTTACG-GATACG
*
32173 CGTTGCGATTTACGTATTCGCATTGCGATTTACGGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
* * *
32213 CATTGCGATTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
* * *
32253 CATTGCGATTTACGTATTCTCGTTGCGATTTATGGATACG
1 CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
*
32293 CGTTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATACT
1 CGTTGCGA-TTTACGTATTCG-CGTTGCGATTTACGGATACG
* * * ** * *
32334 CGTTGTGATAGT-CAG-AATCGCGTTGCGATTTATATG-TTCA
1 CGTTGCGAT-TTAC-GTATTCGCGTTGCGATTTA-CGGATACG
* *
32374 CGTTGCGATTTTCATATTCGCGTTGCGATT
1 CGTTGCGATTTACGTATTCGCGTTGCGATT
32404 CTGGAAAATC
Statistics
Matches: 199, Mismatches: 22, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
39 3 0.02
40 157 0.79
41 39 0.20
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCGCGTTGCGATTTACGGATACG
Found at i:32200 original size:60 final size:59
Alignment explanation
Indices: 32135--32327 Score: 221
Period size: 60 Copynumber: 3.2 Consensus size: 59
32125 CAGAATCTCG
32135 TTGCGATTTACAGATTCGCATTGCGATTTACGTGTTCGCGTTGCGATTTACGTATTCGCA
1 TTGCGATTTAC-GATTCGCATTGCGATTTACGTGTTCGCGTTGCGATTTACGTATTCGCA
* * * *
32195 TTGCGATTTACGGATACGCATTGCGATTTACGTATTCTCGTTGCGATTTACAG-ATACGCA
1 TTGCGATTTAC-GATTCGCATTGCGATTTACGTGTTCGCGTTGCGATTTAC-GTATTCGCA
* * * * *
32255 TTGCGATTTACGTATTCTCGTTGCGATTTATG-GATACGCGTTGCGATTTTACGTATT-GTCG
1 TTGCGATTTACG-ATTCGCATTGCGATTTACGTG-TTCGCGTTGCGA-TTTACGTATTCG-CA
32316 TTGCGATTTACG
1 TTGCGATTTACG
32328 GATACTCGTT
Statistics
Matches: 113, Mismatches: 14, Indels: 11
0.82 0.10 0.08
Matches are distributed among these distances:
59 1 0.01
60 91 0.81
61 21 0.19
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (59 bp):
TTGCGATTTACGATTCGCATTGCGATTTACGTGTTCGCGTTGCGATTTACGTATTCGCA
Found at i:32377 original size:20 final size:20
Alignment explanation
Indices: 32354--32403 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
32344 GTCAGAATCG
*
32354 CGTTGCGATTTAT-ATGTTCA
1 CGTTGCGATTT-TCATATTCA
*
32374 CGTTGCGATTTTCATATTCG
1 CGTTGCGATTTTCATATTCA
32394 CGTTGCGATT
1 CGTTGCGATT
32404 CTGGAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 1 0.04
20 26 0.96
ACGTcount: A:0.16, C:0.18, G:0.22, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTTTCATATTCA
Found at i:32421 original size:21 final size:21
Alignment explanation
Indices: 32397--32449 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
32387 ATATTCGCGT
32397 TGCGATTCTGGAAAATCGCAA
1 TGCGATTCTGGAAAATCGCAA
* ** *
32418 TGCGAATT-TGTACTATCGCAT
1 TGCG-ATTCTGGAAAATCGCAA
32439 TGCGATTCTGG
1 TGCGATTCTGG
32450 GAACTGATTT
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
20 3 0.12
21 19 0.76
22 3 0.12
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (21 bp):
TGCGATTCTGGAAAATCGCAA
Found at i:32481 original size:20 final size:20
Alignment explanation
Indices: 32391--32485 Score: 61
Period size: 20 Copynumber: 4.7 Consensus size: 20
32381 ATTTTCATAT
* *
32391 TCGCGTTGCGATTCTGGAAAA
1 TCGCATTGCGATTCTGG-AGA
* * *
32412 TCGCAATGCGAATT-TGTACTA
1 TCGCATTGCG-ATTCTGGA-GA
32433 TCGCATTGCGATTCTGG-GA
1 TCGCATTGCGATTCTGGAGA
*
32452 ACTG-ATTTGCGATTCTGGAGA
1 TC-GCA-TTGCGATTCTGGAGA
*
32473 TCGCGTTGCGATT
1 TCGCATTGCGATT
32486 TTTATTTCGC
Statistics
Matches: 57, Mismatches: 10, Indels: 15
0.70 0.12 0.18
Matches are distributed among these distances:
19 3 0.05
20 26 0.46
21 25 0.44
22 3 0.05
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
TCGCATTGCGATTCTGGAGA
Found at i:36301 original size:7 final size:7
Alignment explanation
Indices: 36289--36313 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
36279 ATCAGCTTTT
36289 ATGGAAG
1 ATGGAAG
36296 ATGGAAG
1 ATGGAAG
36303 ATGGAAG
1 ATGGAAG
36310 ATGG
1 ATGG
36314 TTGATTTTGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.44, T:0.16
Consensus pattern (7 bp):
ATGGAAG
Found at i:37766 original size:42 final size:41
Alignment explanation
Indices: 37719--38007 Score: 443
Period size: 42 Copynumber: 6.9 Consensus size: 41
37709 CTAGGAAAAT
*
37719 TGTAAGGTTTATCCTTGCACACAGCAAAGGGACCTGGGAAAC
1 TGTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAAC
* *
37761 TGTAAGGCTTACCCTTGCATACAGCAAAAGGGACCTGGTAAAC
1 TGTAAGGCTTA-CCTTGCACACAGC-AAAGGGACCTGGGAAAC
37804 TGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAAC
1 TGTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAAC
*
37846 TGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGTAAAC
1 TGTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAAC
*
37888 TGTAAGGCTTACCTTCGCACACAGCAAAGAGACCTGGGAAAC
1 TGTAAGGCTTACCTT-GCACACAGCAAAGGGACCTGGGAAAC
* *
37930 TGTAAGGCTTACCCTTGCACACAGCAAAGTGACCTGGTAAAC
1 TGTAAGGCTTA-CCTTGCACACAGCAAAGGGACCTGGGAAAC
37972 TGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
1 TGTAAGGCTTACCTT-GCACACAGCAAAGGGACCTG
38008 ATAATACTTC
Statistics
Matches: 229, Mismatches: 12, Indels: 12
0.91 0.05 0.05
Matches are distributed among these distances:
41 8 0.03
42 178 0.78
43 43 0.19
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.19
Consensus pattern (41 bp):
TGTAAGGCTTACCTTGCACACAGCAAAGGGACCTGGGAAAC
Found at i:37924 original size:84 final size:84
Alignment explanation
Indices: 37719--38007 Score: 517
Period size: 84 Copynumber: 3.4 Consensus size: 84
37709 CTAGGAAAAT
* *
37719 TGTAAGGTTTATCCTT-GCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCATAC
1 TGTAAGGCTTA-CCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCACAC
37783 AGCAAAAGGGACCTGGTAAAC
65 AGC-AAAGGGACCTGGTAAAC
37804 TGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCACACA
1 TGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCACACA
37869 GCAAAGGGACCTGGTAAAC
66 GCAAAGGGACCTGGTAAAC
*
37888 TGTAAGGCTTACCTTCGCACACAGCAAAGAGACCTGGGAAACTGTAAGGCTTACCCTTGCACACA
1 TGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCACACA
*
37953 GCAAAGTGACCTGGTAAAC
66 GCAAAGGGACCTGGTAAAC
37972 TGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
1 TGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTG
38008 ATAATACTTC
Statistics
Matches: 198, Mismatches: 5, Indels: 3
0.96 0.02 0.01
Matches are distributed among these distances:
84 138 0.70
85 60 0.30
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.19
Consensus pattern (84 bp):
TGTAAGGCTTACCTTCGCACACAGCAAAGGGACCTGGGAAACTGTAAGGCTTACCCTTGCACACA
GCAAAGGGACCTGGTAAAC
Found at i:38896 original size:30 final size:30
Alignment explanation
Indices: 38862--39016 Score: 108
Period size: 29 Copynumber: 5.3 Consensus size: 30
38852 TATTTTACAT
* *
38862 AAATAGCACCTTTTTTTTAAA-TAATTACCA
1 AAATAGCACC-TATTTTCAAATTAATTACCA
*
38892 AAATAGCA-CTATTTTCAAATTAATTCCCA
1 AAATAGCACCTATTTTCAAATTAATTACCA
* ** *
38921 AAATAGCACC-AATTTCGGATTAATTCCCA
1 AAATAGCACCTATTTTCAAATTAATTACCA
* * *
38950 TAATATCACCT-TTTTCGAACA-AAATTACCA
1 AAATAGCACCTATTTTC-AA-ATTAATTACCA
* * *
38980 AAATAGCACATA-TTTCGAA-TAATTTCCA
1 AAATAGCACCTATTTTCAAATTAATTACCA
*
39008 GAATAGCAC
1 AAATAGCAC
39017 TAAAACCGAA
Statistics
Matches: 99, Mismatches: 20, Indels: 14
0.74 0.15 0.11
Matches are distributed among these distances:
28 24 0.24
29 46 0.46
30 28 0.28
31 1 0.01
ACGTcount: A:0.41, C:0.21, G:0.06, T:0.32
Consensus pattern (30 bp):
AAATAGCACCTATTTTCAAATTAATTACCA
Found at i:39033 original size:87 final size:88
Alignment explanation
Indices: 38884--39046 Score: 213
Period size: 87 Copynumber: 1.9 Consensus size: 88
38874 TTTTTTAAAT
*** *
38884 AATTACCAAAATAGCACTATTTTCAAATTAATTCCCAAAATAGCACCAATTTCGGATTAATTCCC
1 AATTACCAAAATAGCACTATTTTCAAATTAATTCCCAAAATAGCACCAAAACCGAATTAATTCCC
* *
38949 ATAATATCACCTTTTTCGAACAA
66 AGAATAACACCTTTTTCGAACAA
* * * *
38972 AATTACCAAAATAGCAC-ATATTTCGAA-TAATTTCCAGAATAGCACTAAAACCGAATTAATTCC
1 AATTACCAAAATAGCACTAT-TTTCAAATTAATTCCCAAAATAGCACCAAAACCGAATTAATTCC
39035 CAGAATAACACC
65 CAGAATAACACC
39047 GGTCAACGGT
Statistics
Matches: 64, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
87 41 0.64
88 23 0.36
ACGTcount: A:0.42, C:0.23, G:0.07, T:0.28
Consensus pattern (88 bp):
AATTACCAAAATAGCACTATTTTCAAATTAATTCCCAAAATAGCACCAAAACCGAATTAATTCCC
AGAATAACACCTTTTTCGAACAA
Found at i:39118 original size:13 final size:13
Alignment explanation
Indices: 39064--39118 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
39054 GGTCAACGAC
39064 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
39077 AGGGT--A-GGGT
1 CGGGTCAACGGGT
**
39087 CGGGTCGTCGGGT
1 CGGGTCAACGGGT
39100 C-GGTCAACGGGT
1 CGGGTCAACGGGT
39112 CGGGTCA
1 CGGGTCA
39119 TGACCGGTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
10 8 0.24
11 1 0.03
12 10 0.30
13 14 0.42
ACGTcount: A:0.13, C:0.20, G:0.49, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:42704 original size:2 final size:2
Alignment explanation
Indices: 42697--42740 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
42687 CACTTTCAAA
42697 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
42739 AT
1 AT
42741 CTGCTTTGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:44432 original size:30 final size:30
Alignment explanation
Indices: 44396--44455 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
44386 TTACCGCCAT
*
44396 CATAATCTATTTGTTTCGATCAACAATTGA
1 CATAATCTATTTGTTTCCATCAACAATTGA
*
44426 CATAATCTATTTGTTTCCATCAATAATTGA
1 CATAATCTATTTGTTTCCATCAACAATTGA
44456 TATGATGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (30 bp):
CATAATCTATTTGTTTCCATCAACAATTGA
Found at i:48985 original size:67 final size:67
Alignment explanation
Indices: 48903--49037 Score: 261
Period size: 67 Copynumber: 2.0 Consensus size: 67
48893 GATCTTAATA
48903 ATGCAACCAATCAAAGAGAATTTTAGGGATTATGTCCACACACAAAAACTAAAATATAAAATAAA
1 ATGCAACCAATCAAAGAGAATTTTAGGGATTATGTCCACACACAAAAACTAAAATATAAAATAAA
48968 AT
66 AT
*
48970 ATGCAACCAATCAAAGAGAGTTTTAGGGATTATGTCCACACACAAAAACTAAAATATAAAATAAA
1 ATGCAACCAATCAAAGAGAATTTTAGGGATTATGTCCACACACAAAAACTAAAATATAAAATAAA
49035 AT
66 AT
49037 A
1 A
49038 AAGAGAAAAC
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
67 67 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (67 bp):
ATGCAACCAATCAAAGAGAATTTTAGGGATTATGTCCACACACAAAAACTAAAATATAAAATAAA
AT
Found at i:52099 original size:21 final size:22
Alignment explanation
Indices: 52073--52154 Score: 75
Period size: 21 Copynumber: 3.9 Consensus size: 22
52063 ATATCGATGG
52073 GATGTTAACATGAAAAGATATT
1 GATGTTAACATGAAAAGATATT
*
52095 G-TGTTAAAATGAAGAA-ATA-T
1 GATGTTAACATGAA-AAGATATT
* *
52115 GATGTTAACATG-AAAGGT-TA
1 GATGTTAACATGAAAAGATATT
* *
52135 GCTGTTAACATGAAGAGATA
1 GATGTTAACATGAAAAGATA
52155 AAGTTCTATC
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
19 2 0.04
20 15 0.32
21 27 0.57
22 3 0.06
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (22 bp):
GATGTTAACATGAAAAGATATT
Found at i:54825 original size:5 final size:5
Alignment explanation
Indices: 54807--54875 Score: 52
Period size: 5 Copynumber: 13.2 Consensus size: 5
54797 ATTTTTAGTA
* *
54807 ATTTC ATTTCT ATTTT ATTTT ATTTT AATTATT AATTT ATTTT ATTATGT
1 ATTTT ATTT-T ATTTT ATTTT ATTTT -ATT-TT ATTTT ATTTT ATT-T-T
*
54857 A-CTT ATTTT A-TTT ATTTT A
1 ATTTT ATTTT ATTTT ATTTT A
54876 AATTTTCTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
4 6 0.12
5 32 0.62
6 10 0.19
7 4 0.08
ACGTcount: A:0.26, C:0.04, G:0.01, T:0.68
Consensus pattern (5 bp):
ATTTT
Found at i:54847 original size:17 final size:16
Alignment explanation
Indices: 54825--54872 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
54815 TCTATTTTAT
54825 TTTATTTTAATTATTAA
1 TTTATTTTAATTATT-A
54842 TTTATTTT-ATTATGTA
1 TTTATTTTAATTAT-TA
* *
54858 CTTATTTTATTTATT
1 TTTATTTTAATTATT
54873 TTAAATTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTATTTTAATTATTA
Found at i:62009 original size:21 final size:20
Alignment explanation
Indices: 61983--62039 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 20
61973 ATATCGATGG
61983 GATGTTAACATGAAAAGATATT
1 GATGTTAACATGAAAA-ATA-T
*
62005 G-TGTTAAAATGAAGAAATAT
1 GATGTTAACATGAA-AAATAT
62025 GATGTTAACATGAAA
1 GATGTTAACATGAAA
62040 GGTTAGCTGT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
20 3 0.10
21 25 0.81
22 3 0.10
ACGTcount: A:0.47, C:0.04, G:0.19, T:0.30
Consensus pattern (20 bp):
GATGTTAACATGAAAAATAT
Found at i:62322 original size:42 final size:42
Alignment explanation
Indices: 62212--62568 Score: 442
Period size: 42 Copynumber: 8.6 Consensus size: 42
62202 TCATAATGTA
* *
62212 GTGGCGTTTTTATA-CAAACGCCGCTATAAACTA-GTA-TTTT
1 GTGGCGTTTTAATACCAAACGCCGCTATAGAC-ACGTACTTTT
* ** *
62252 AGTGGCGTTTTTATA-CAAACGCTACTATAGACACGCACTTTT
1 -GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
* * * *
62294 GTGGCGTTTTAATACCAAACGACGCTATAGACTCATACTTTA
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
*
62336 GTGGCATTTT--TACACAAACGCCGCTATAGACACGTACTTTT
1 GTGGCGTTTTAATAC-CAAACGCCGCTATAGACACGTACTTTT
*
62377 GTGGCGTTTTAATACCAAACGCCGCTATAGAAACGTACTTTT
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
** *
62419 GTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTACTTTA
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
62461 GTGGCGTTTT--TACACAAACGCCGCTATAGACACGTACTTTT
1 GTGGCGTTTTAATAC-CAAACGCCGCTATAGACACGTACTTTT
* * * * *
62502 GTGACGTTTTAATAACAAACGCCGCTGTAGACTCGTACTTTA
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
62544 GTGGCGTTTTAATACCAAACGCCGC
1 GTGGCGTTTTAATACCAAACGCCGC
62569 AATTGTCATA
Statistics
Matches: 275, Mismatches: 32, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
40 7 0.03
41 108 0.39
42 155 0.56
43 5 0.02
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (42 bp):
GTGGCGTTTTAATACCAAACGCCGCTATAGACACGTACTTTT
Found at i:62346 original size:83 final size:83
Alignment explanation
Indices: 62163--62568 Score: 448
Period size: 83 Copynumber: 4.9 Consensus size: 83
62153 GCAAAATACT
* * * * * *
62163 ATACTTTAGTGGCGTTTGT-ATAAAAACGCCGCTAAAGA-ATCATAATGTAGTGGCGTTTTTATA
1 ATACTTTAGTGGCGTTT-TAATACAAACGCCGCTATAGACA-CGTACTTTAGTGGCGTTTTAATA
62226 -CAAACGCCGCTATA-A-AC
64 CCAAACGCCGCTATAGACAC
* * ** * *
62243 TAGTATTTTAGTGGCGTTTTTATACAAACGCTACTATAGACACGCACTTTTGTGGCGTTTTAATA
1 -A-TACTTTAGTGGCGTTTTAATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATA
* *
62308 CCAAACGACGCTATAGACTC
64 CCAAACGCCGCTATAGACAC
* * * *
62328 ATACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACC
1 ATACTTTAGTGGCGTTTTAATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACC
*
62393 AAACGCCGCTATAGAAAC
66 AAACGCCGCTATAGACAC
* * **
62411 GTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGTGGCGTTTT--TAC
1 ATACTTTAGTGGCGTTTTAATA-CAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATAC
62474 ACAAACGCCGCTATAGACAC
65 -CAAACGCCGCTATAGACAC
* * * * *
62494 GTACTTTTGTGACGTTTTAATAACAAACGCCGCTGTAGACTCGTACTTTAGTGGCGTTTTAATAC
1 ATACTTTAGTGGCGTTTTAAT-ACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATAC
62559 CAAACGCCGC
65 CAAACGCCGC
62569 AATTGTCATA
Statistics
Matches: 280, Mismatches: 34, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
81 2 0.01
82 50 0.18
83 177 0.63
84 47 0.17
85 4 0.01
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (83 bp):
ATACTTTAGTGGCGTTTTAATACAAACGCCGCTATAGACACGTACTTTAGTGGCGTTTTAATACC
AAACGCCGCTATAGACAC
Found at i:62445 original size:125 final size:124
Alignment explanation
Indices: 62164--62568 Score: 548
Period size: 125 Copynumber: 3.3 Consensus size: 124
62154 CAAAATACTA
* * * * *
62164 TACTTTAGTGGCGTTTGT-ATA-AAAACGCCGCTAAAGAATCATAATGTAGTGGCGTTTTTATAC
1 TACTTTAGTGGCGTTT-TAATACCAAACGCCGCTATAGAATCATACTTTAGTGGCGTTTTTACAC
* * **
62227 AAACGCCGCTATAAACTA-GTA-TTTTAGTGGCGTTTTTATACAAACGCTACTATAGACACG
65 AAACGCCGCTATAGAC-ACGTACTTTT-GTGGCGTTTTAATACAAACGCCGCTATAGACACG
* * * * *
62287 CACTTTTGTGGCGTTTTAATACCAAACGACGCTATAGACTCATACTTTAGTGGCATTTTTACACA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAATCATACTTTAGTGGCGTTTTTACACA
*
62352 AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGAAACG
66 AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATA-CAAACGCCGCTATAGACACG
* * *
62412 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGTGGCGTTTTTACACA
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAATCATACTTTAGTGGCGTTTTTACACA
* * *
62477 AACGCCGCTATAGACACGTACTTTTGTGACGTTTTAATAACAAACGCCGCTGTAGACTCG
66 AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAAT-ACAAACGCCGCTATAGACACG
62537 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
1 TACTTTAGTGGCGTTTTAATACCAAACGCCGC
62569 AATTGTCATA
Statistics
Matches: 251, Mismatches: 25, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
122 1 0.00
123 18 0.07
124 65 0.26
125 166 0.66
126 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (124 bp):
TACTTTAGTGGCGTTTTAATACCAAACGCCGCTATAGAATCATACTTTAGTGGCGTTTTTACACA
AACGCCGCTATAGACACGTACTTTTGTGGCGTTTTAATACAAACGCCGCTATAGACACG
Found at i:64870 original size:46 final size:46
Alignment explanation
Indices: 64803--64899 Score: 185
Period size: 46 Copynumber: 2.1 Consensus size: 46
64793 ATGCATTGTA
*
64803 TCTATTGGTACATCTTTTTCCAACATTTTATGTATGGATAATATTC
1 TCTATTGATACATCTTTTTCCAACATTTTATGTATGGATAATATTC
64849 TCTATTGATACATCTTTTTCCAACATTTTATGTATGGATAATATTC
1 TCTATTGATACATCTTTTTCCAACATTTTATGTATGGATAATATTC
64895 TCTAT
1 TCTAT
64900 GCTCAAAATG
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.48
Consensus pattern (46 bp):
TCTATTGATACATCTTTTTCCAACATTTTATGTATGGATAATATTC
Found at i:66200 original size:21 final size:21
Alignment explanation
Indices: 66158--66216 Score: 64
Period size: 21 Copynumber: 2.8 Consensus size: 21
66148 TGATTTATTA
**
66158 TTATGGATTTCATTTTTCTTG
1 TTATGGATTTCAAGTTTCTTG
* *
66179 TTATGGATTTTAAGTTTGTTG
1 TTATGGATTTCAAGTTTCTTG
* *
66200 TTATCGATATCAAGTTT
1 TTATGGATTTCAAGTTT
66217 ATTGGAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.20, C:0.07, G:0.17, T:0.56
Consensus pattern (21 bp):
TTATGGATTTCAAGTTTCTTG
Found at i:66416 original size:43 final size:43
Alignment explanation
Indices: 66369--66550 Score: 242
Period size: 43 Copynumber: 4.3 Consensus size: 43
66359 ACCAGATCTT
* *
66369 TTGCGGTGTTTGTTGGAAAAACGCCGCTAAATATCAAGACCTA
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTA
*
66412 TTGCGGCGTTTG-TGGAAAAAACGCCGCTAAATCTCAACACCTA
1 TTGCGGCGTTTGTTGG-AAAAACGCCGCTAAATATCAACACCTA
* *
66455 TTGCGGCGTTTGTTGGAAAAA-GCCACCAAATATCAACACCTA
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTA
* * ***
66497 TTGCGGCGTTTGTTGGACAAACGCCGCTATATATCGTTACCTA
1 TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTA
*
66540 TTGTGGCGTTT
1 TTGCGGCGTTT
66551 TTTGTTACCA
Statistics
Matches: 122, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
42 41 0.34
43 78 0.64
44 3 0.02
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (43 bp):
TTGCGGCGTTTGTTGGAAAAACGCCGCTAAATATCAACACCTA
Found at i:66501 original size:85 final size:86
Alignment explanation
Indices: 66369--66525 Score: 246
Period size: 85 Copynumber: 1.8 Consensus size: 86
66359 ACCAGATCTT
* * * *
66369 TTGCGGTGTTTGTTGGAAAAACGCCGCTAAATATCAAGACCTATTGCGGCGTTTG-TGGAAAAAA
1 TTGCGGCGTTTGTTGGAAAAACGCCACCAAATATCAACACCTATTGCGGCGTTTGTTGG-AAAAA
66433 CGCCGCTAAATCTCAACACCTA
65 CGCCGCTAAATCTCAACACCTA
*
66455 TTGCGGCGTTTGTTGGAAAAA-GCCACCAAATATCAACACCTATTGCGGCGTTTGTTGGACAAAC
1 TTGCGGCGTTTGTTGGAAAAACGCCACCAAATATCAACACCTATTGCGGCGTTTGTTGGAAAAAC
66519 GCCGCTA
66 GCCGCTA
66526 TATATCGTTA
Statistics
Matches: 65, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
85 42 0.65
86 23 0.35
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (86 bp):
TTGCGGCGTTTGTTGGAAAAACGCCACCAAATATCAACACCTATTGCGGCGTTTGTTGGAAAAAC
GCCGCTAAATCTCAACACCTA
Found at i:66539 original size:85 final size:86
Alignment explanation
Indices: 66369--66550 Score: 242
Period size: 85 Copynumber: 2.1 Consensus size: 86
66359 ACCAGATCTT
* * * *
66369 TTGCGGTGTTTGTTGGAAAAACGCCGCTAAATATCAAGACCTATTGCGGCGTTTGTGGAAAAAAC
1 TTGCGGCGTTTGTTGGAAAAACGCCACCAAATATCAACACCTATTGCGGCGTTTGTGGAAAAAAC
*
66434 GCCGCTAAATCTCAACACCTA
66 GCCGCTAAATATCAACACCTA
*
66455 TTGCGGCGTTTGTTGGAAAAA-GCCACCAAATATCAACACCTATTGCGGCGTTTGTTGG-ACAAA
1 TTGCGGCGTTTGTTGGAAAAACGCCACCAAATATCAACACCTATTGCGGCGTTTG-TGGAAAAAA
* ***
66518 CGCCGCTATATATCGTTACCTA
65 CGCCGCTAAATATCAACACCTA
*
66540 TTGTGGCGTTT
1 TTGCGGCGTTT
66551 TTTGTTACCA
Statistics
Matches: 84, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
85 61 0.73
86 23 0.27
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.29
Consensus pattern (86 bp):
TTGCGGCGTTTGTTGGAAAAACGCCACCAAATATCAACACCTATTGCGGCGTTTGTGGAAAAAAC
GCCGCTAAATATCAACACCTA
Found at i:66596 original size:15 final size:15
Alignment explanation
Indices: 66576--66605 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
66566 CGCGAACTTT
66576 AGCGACGCTATTTGC
1 AGCGACGCTATTTGC
*
66591 AGCGACGCTTTTTGC
1 AGCGACGCTATTTGC
66606 GGCGTTTGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.30
Consensus pattern (15 bp):
AGCGACGCTATTTGC
Found at i:69387 original size:17 final size:16
Alignment explanation
Indices: 69367--69414 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
69357 TTTCTATTTT
69367 TTTATTTTAATTATTAA
1 TTTATTTTAATTATT-A
69384 TTTATTTT-ATTATGTA
1 TTTATTTTAATTAT-TA
* *
69400 CTTATTTTATTTATT
1 TTTATTTTAATTATT
69415 TAAATTTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 14 0.52
17 13 0.48
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (16 bp):
TTTATTTTAATTATTA
Found at i:83240 original size:21 final size:21
Alignment explanation
Indices: 83216--83257 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
83206 TTGAATTTAT
*
83216 TAATATTA-AATACTAATATTA
1 TAATATTATAA-AATAATATTA
83237 TAATATTATAAAATAATATTA
1 TAATATTATAAAATAATATTA
83258 GATTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 17 0.89
22 2 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (21 bp):
TAATATTATAAAATAATATTA
Found at i:94193 original size:71 final size:71
Alignment explanation
Indices: 94047--94193 Score: 154
Period size: 71 Copynumber: 2.1 Consensus size: 71
94037 TTTAAGGATT
* * * * * *
94047 AAAATGAAAATTAAAGCATTTTATTAACGTATTACATCATTAAACTAATGACATTCAATGTTTCA
1 AAAATAAAAATTAAAGCATTTTATTAACGTATTACACCATCAAACTAACGACATTCAACGTCTCA
* *
94112 GTGGTT
66 GTGATC
* * * *
94118 AAAATAAAAATTAAATCATTTTATTAATGTGA-TACGCCATCAAACTAACGACATTTAACGTC-C
1 AAAATAAAAATTAAAGCATTTTATTAACGT-ATTACACCATCAAACTAACGACATTCAACGTCTC
94181 TAGTGATC
65 -AGTGATC
94189 AAAAT
1 AAAAT
94194 TTAATAAAAT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
70 1 0.02
71 60 0.97
72 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.33
Consensus pattern (71 bp):
AAAATAAAAATTAAAGCATTTTATTAACGTATTACACCATCAAACTAACGACATTCAACGTCTCA
GTGATC
Found at i:101705 original size:14 final size:14
Alignment explanation
Indices: 101673--101707 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
101663 AATATGAATT
*
101673 ATATCTTTTAAAAA
1 ATATTTTTTAAAAA
*
101687 ATATTTTTTGAAAA
1 ATATTTTTTAAAAA
101701 ATATTTT
1 ATATTTT
101708 ACAGTATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (14 bp):
ATATTTTTTAAAAA
Found at i:102740 original size:31 final size:31
Alignment explanation
Indices: 102702--102763 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
102692 TTAAAAGTTA
102702 AACTATCATGCCGGCCCCTACATTAAGCTTT
1 AACTATCATGCCGGCCCCTACATTAAGCTTT
*
102733 AACTATCATGCTGGCCCCTACATTAAGCTTT
1 AACTATCATGCCGGCCCCTACATTAAGCTTT
102764 CCCTTTCCTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.31, G:0.13, T:0.31
Consensus pattern (31 bp):
AACTATCATGCCGGCCCCTACATTAAGCTTT
Found at i:108766 original size:23 final size:24
Alignment explanation
Indices: 108727--108774 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
108717 GTCCACTAAC
*
108727 AGAGGGATCAAATTATGCTGAACT
1 AGAGGGATCAAATTATGATGAACT
108751 AGAGGGAT-AAATTATGATGAACT
1 AGAGGGATCAAATTATGATGAACT
108774 A
1 A
108775 AAGTAGAGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 15 0.65
24 8 0.35
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (24 bp):
AGAGGGATCAAATTATGATGAACT
Found at i:118259 original size:16 final size:15
Alignment explanation
Indices: 118233--118266 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
118223 TTTCAATTGT
118233 AAATAAAAAAATATA
1 AAATAAAAAAATATA
*
118248 AAATATAAAAAATTTA
1 AAATA-AAAAAATATA
118264 AAA
1 AAA
118267 AAATTTAGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAATAAAAAAATATA
Found at i:122845 original size:30 final size:30
Alignment explanation
Indices: 122794--122850 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
122784 TCTGAATATC
*
122794 ATAAATAAAAAATTAAAATTAATAACAAAA
1 ATAAATAAAAAATTAAAATTAAAAACAAAA
* * *
122824 ATAAATACAAAATTTATATTAAAAACA
1 ATAAATAAAAAATTAAAATTAAAAACA
122851 TAATAGTAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.26
Consensus pattern (30 bp):
ATAAATAAAAAATTAAAATTAAAAACAAAA
Found at i:128621 original size:64 final size:63
Alignment explanation
Indices: 128535--128695 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
128525 ATTGTTTAAG
* * * *
128535 ATGCATCGATGTACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGA-TT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAAT-GCATTT
128598 T
63 T
* * *
128599 ATGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAAAAACATCGAATGCATTTT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATGCATTTT
* *
128663 ATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 ATGCATCGATGCACAAGCAGTGCATCGATGCAT
128696 ACATTCATTG
Statistics
Matches: 84, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
63 2 0.02
64 74 0.88
65 7 0.08
66 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.26
Consensus pattern (63 bp):
ATGCATCGATGCACAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATGCATTTT
Found at i:129419 original size:30 final size:30
Alignment explanation
Indices: 129370--129428 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
129360 GGAACATATG
* *
129370 GATAGTTGCCGAGGATCTTTATGACCTCTT
1 GATAGTTACCGAGGATCTTTATAACCTCTT
* * *
129400 GATAGTTACCGGGGTTCTTTGTAACCTCT
1 GATAGTTACCGAGGATCTTTATAACCTCT
129429 GGACAGGTCA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.19, C:0.20, G:0.24, T:0.37
Consensus pattern (30 bp):
GATAGTTACCGAGGATCTTTATAACCTCTT
Found at i:132860 original size:64 final size:65
Alignment explanation
Indices: 132784--132907 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 65
132774 ATGCATGAAT
* * *
132784 TTAAATAGAAAACATCGAATAGGA-TTTATGCATCGATGCATAAGGAGTGCATCGATGCATCCCC
1 TTAAATAGAAAACATCGAAT-GCATTTTATGCACCGATGCACAAGGAGTGCATCGATGCATCCCC
132848 A
65 A
*
132849 TTAAATA-AAAACATCGAATGCATTTTATGCACCGATGCACAAGTAGTGCATCGATGCAT
1 TTAAATAGAAAACATCGAATGCATTTTATGCACCGATGCACAAGGAGTGCATCGATGCAT
132908 ACATTCATTG
Statistics
Matches: 54, Mismatches: 4, Indels: 3
0.89 0.07 0.05
Matches are distributed among these distances:
63 2 0.04
64 45 0.83
65 7 0.13
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (65 bp):
TTAAATAGAAAACATCGAATGCATTTTATGCACCGATGCACAAGGAGTGCATCGATGCATCCCCA
Found at i:134558 original size:18 final size:18
Alignment explanation
Indices: 134535--134570 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
134525 AAGAAAAAGG
*
134535 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
134553 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
134571 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:136496 original size:21 final size:21
Alignment explanation
Indices: 136467--136547 Score: 144
Period size: 21 Copynumber: 3.8 Consensus size: 21
136457 GAACGGTGGG
*
136467 AGGGACCTCTTGAACAATGACA
1 AGGG-CCTCTTGAACGATGACA
136489 AGGGCCTCTTGAACGATGACA
1 AGGGCCTCTTGAACGATGACA
136510 AGGGCCTCTTGAACGATGACA
1 AGGGCCTCTTGAACGATGACA
136531 AGGGCCTCTTGAACGAT
1 AGGGCCTCTTGAACGAT
136548 AGGAGAGTCC
Statistics
Matches: 58, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
21 54 0.93
22 4 0.07
ACGTcount: A:0.30, C:0.23, G:0.27, T:0.20
Consensus pattern (21 bp):
AGGGCCTCTTGAACGATGACA
Found at i:136564 original size:42 final size:41
Alignment explanation
Indices: 136452--136572 Score: 143
Period size: 42 Copynumber: 2.9 Consensus size: 41
136442 ATGAATCGGG
* * *
136452 CTCTTGAACGGTGGGAGGGACCTCTTGAACAATGACAAGGGC
1 CTCTTGAACGATAGGA-GGACCTCTTGAACGATGACAAGGGC
** *
136494 CTCTTGAACGATGACAAGGGCCTCTTGAACGATGACAAGGGC
1 CTCTTGAACGAT-AGGAGGACCTCTTGAACGATGACAAGGGC
* *
136536 CTCTTGAACGATAGGAGAGTCCTATTGAACGATGACA
1 CTCTTGAACGATAGGAG-GACCTCTTGAACGATGACA
136573 GGTGAATCGA
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
41 3 0.04
42 63 0.94
43 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.29, T:0.21
Consensus pattern (41 bp):
CTCTTGAACGATAGGAGGACCTCTTGAACGATGACAAGGGC
Found at i:136878 original size:21 final size:21
Alignment explanation
Indices: 136854--136926 Score: 92
Period size: 21 Copynumber: 3.5 Consensus size: 21
136844 TACATCAATC
* * *
136854 TCACGTAGAGCGGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
*
136875 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGCAGATACCTCA
*
136896 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGCAGATACCTCA
*
136917 CCACGTAAAG
1 TCACGTAAAG
136927 TACCATTGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.34, C:0.27, G:0.18, T:0.21
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:136927 original size:21 final size:21
Alignment explanation
Indices: 136868--136928 Score: 113
Period size: 21 Copynumber: 2.9 Consensus size: 21
136858 GTAGAGCGGC
136868 TACCTCATCACGTAAAGTAGA
1 TACCTCATCACGTAAAGTAGA
136889 TACCTCATCACGTAAAGTAGA
1 TACCTCATCACGTAAAGTAGA
*
136910 TACCTCACCACGTAAAGTA
1 TACCTCATCACGTAAAGTA
136929 CCATTGTCAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (21 bp):
TACCTCATCACGTAAAGTAGA
Found at i:136965 original size:21 final size:21
Alignment explanation
Indices: 136867--136984 Score: 55
Period size: 21 Copynumber: 5.6 Consensus size: 21
136857 CGTAGAGCGG
* *
136867 CTACCTCATCACGTAAAGTA-G
1 CTACCTCACCACGTAAAG-ACC
* * *
136888 ATACCTCATCACGTAAAGTA-G
1 CTACCTCACCACGTAAAG-ACC
*
136909 ATACCTCACCACGTAAAGTACC
1 CTACCTCACCACGTAAAG-ACC
* ** * *
136931 AT-TGTCATCGCGTAAA-ACC
1 CTACCTCACCACGTAAAGACC
136950 TCTACCTCACCACGTAAAGACC
1 -CTACCTCACCACGTAAAGACC
* *
136972 GTACCTCATCACG
1 CTACCTCACCACG
136985 CCATGCACCA
Statistics
Matches: 79, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
19 3 0.04
20 1 0.01
21 70 0.89
22 5 0.06
ACGTcount: A:0.33, C:0.32, G:0.13, T:0.22
Consensus pattern (21 bp):
CTACCTCACCACGTAAAGACC
Found at i:138744 original size:19 final size:18
Alignment explanation
Indices: 138686--138737 Score: 77
Period size: 19 Copynumber: 2.8 Consensus size: 18
138676 AATAGTTTCT
138686 GAAACTAAAATCGCACGC
1 GAAACTAAAATCGCACGC
*
138704 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGC-ACGC
138724 GAAACTAAAATCGC
1 GAAACTAAAATCGC
138738 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 5 0.17
19 16 0.53
20 9 0.30
ACGTcount: A:0.48, C:0.23, G:0.17, T:0.12
Consensus pattern (18 bp):
GAAACTAAAATCGCACGC
Done.