Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold439
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: 1094049
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
File 2 of 7
Found at i:144317 original size:10 final size:11
Alignment explanation
Indices: 144281--144322 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
144271 TGTTTTTGTT
**
144281 TTTTTTTTGTT
1 TTTTTTTTGAC
144292 TTTTTTTTGAC
1 TTTTTTTTGAC
144303 TTTTTTTTGAC
1 TTTTTTTTGAC
*
144314 TTTTGTTTG
1 TTTTTTTTG
144323 TGTGTTTACT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.05, C:0.05, G:0.12, T:0.79
Consensus pattern (11 bp):
TTTTTTTTGAC
Found at i:151072 original size:9 final size:9
Alignment explanation
Indices: 151055--151090 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
151045 GAGATAAGGT
*
151055 TTGGCAGCC
1 TTGGAAGCC
151064 TTGGAAGCC
1 TTGGAAGCC
151073 TTGGAAGCC
1 TTGGAAGCC
*
151082 TTGGGAGCC
1 TTGGAAGCC
151091 AATGAACTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.17, C:0.25, G:0.36, T:0.22
Consensus pattern (9 bp):
TTGGAAGCC
Found at i:151404 original size:52 final size:52
Alignment explanation
Indices: 151256--151384 Score: 249
Period size: 52 Copynumber: 2.5 Consensus size: 52
151246 CAAAATATGA
*
151256 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATATGGGC
151308 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATATGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATATGGGC
151360 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
151385 AAGATCAGTG
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
52 76 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATATGGGC
Found at i:151411 original size:13 final size:13
Alignment explanation
Indices: 151393--151417 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
151383 CAAAGATCAG
151393 TGTATCGATACAA
1 TGTATCGATACAA
151406 TGTATCGATACA
1 TGTATCGATACA
151418 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:151498 original size:32 final size:33
Alignment explanation
Indices: 151458--151523 Score: 107
Period size: 32 Copynumber: 2.0 Consensus size: 33
151448 AGTAGCTTAA
*
151458 ATTGTATCGATACAAAAC-TTATGTGTCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
*
151490 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAACTTTATGTATCGATAC
151523 A
1 A
151524 AATCGTTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 17 0.55
33 14 0.45
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.35
Consensus pattern (33 bp):
ATTGTATCGATACAAAACTTTATGTATCGATAC
Found at i:152669 original size:13 final size:14
Alignment explanation
Indices: 152646--152694 Score: 50
Period size: 13 Copynumber: 3.6 Consensus size: 14
152636 GTATAATCTA
152646 GAAATAGAG-AAAGT
1 GAAA-AGAGAAAAGT
*
152660 GAAAAGAGAAAAGG
1 GAAAAGAGAAAAGT
152674 GAAAA-AGAAAAG-
1 GAAAAGAGAAAAGT
*
152686 GGAAAGAGA
1 GAAAAGAGA
152695 CATGAAAAGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
12 4 0.13
13 14 0.45
14 13 0.42
ACGTcount: A:0.63, C:0.00, G:0.33, T:0.04
Consensus pattern (14 bp):
GAAAAGAGAAAAGT
Found at i:160452 original size:19 final size:20
Alignment explanation
Indices: 160430--160479 Score: 66
Period size: 19 Copynumber: 2.5 Consensus size: 20
160420 ATTTTTTATT
160430 TAAATTTAAATT-TGATTTA
1 TAAATTTAAATTATGATTTA
*
160449 TAAATTTAAATTATTATTTA
1 TAAATTTAAATTATGATTTA
*
160469 AAAATATTAAA
1 TAAAT-TTAAA
160480 AATTATTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 12 0.44
20 10 0.37
21 5 0.19
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (20 bp):
TAAATTTAAATTATGATTTA
Found at i:160508 original size:22 final size:22
Alignment explanation
Indices: 160483--160524 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
160473 TATTAAAAAT
160483 TATTTTTAT-ATTAATATTTATA
1 TATTTTTATAATTAA-ATTTATA
160505 TATTTTTATAATTAAATTTA
1 TATTTTTATAATTAAATTTA
160525 AATAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TATTTTTATAATTAAATTTATA
Found at i:165498 original size:22 final size:22
Alignment explanation
Indices: 165473--165514 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
165463 TTCCAAATTG
165473 AATTATA-AAACTATAAAAAAGT
1 AATTATAGAAAC-ATAAAAAAGT
*
165495 AATTCTAGAAACATAAAAAA
1 AATTATAGAAACATAAAAAA
165515 TAGATTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.64, C:0.07, G:0.05, T:0.24
Consensus pattern (22 bp):
AATTATAGAAACATAAAAAAGT
Found at i:168670 original size:20 final size:20
Alignment explanation
Indices: 168642--168691 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
168632 ACTCAAAATA
*
168642 TATCAATACATTCTATAT-TG
1 TATCGATACATT-TATATGTG
*
168662 TATCGATACATTTTTATGTG
1 TATCGATACATTTATATGTG
*
168682 TATTGATACA
1 TATCGATACA
168692 AATGAGGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.15
20 22 0.85
ACGTcount: A:0.32, C:0.12, G:0.10, T:0.46
Consensus pattern (20 bp):
TATCGATACATTTATATGTG
Found at i:168758 original size:21 final size:21
Alignment explanation
Indices: 168726--168787 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
168716 GCTACTACCA
* *
168726 ACATGATGTATCAATACATTC
1 ACATAATGTATCGATACATTC
* *
168747 ACATAATTTATCGATATATTC
1 ACATAATGTATCGATACATTC
*
168768 ATATAATGTATCGATACATT
1 ACATAATGTATCGATACATT
168788 TTCACTTGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.15, G:0.08, T:0.39
Consensus pattern (21 bp):
ACATAATGTATCGATACATTC
Found at i:168881 original size:113 final size:114
Alignment explanation
Indices: 168635--168881 Score: 261
Period size: 113 Copynumber: 2.2 Consensus size: 114
168625 CATTGTAACT
* * * * * * *
168635 CAAAATATATCAATACATTC-TATATTGTATCGATACATTTTTATGTGTATTGATACAAATGAGG
1 CAAAATTTATCGATACATTCATATAATGTATCGATACATTTTCATGTGTATCGATAAAAATAAGG
* * * * *
168699 GTTTTAGGAATTGCTTAGCTACTACCAACATGATGTATCAATACATTCA
66 ATTTCAGGAATTGCGTAGCTACTACCAACATGATATATCAATAAATTCA
* *
168748 CATAATTTATCGATATATTCATATAATGTATCGATACATTTTCACT-TGTATCGATAAAAATAAG
1 CAAAATTTATCGATACATTCATATAATGTATCGATACATTTTCA-TGTGTATCGATAAAAATAAG
* * * *
168812 GATTTCA-GCATTTCGTAGCTACTGCCAACCAT-ATATATCGATAAATTCA
65 GATTTCAGGAATTGCGTAGCTACTACCAA-CATGATATATCAATAAATTCA
*
168861 CAAAATGTT-TTGATACATTCA
1 CAAAAT-TTATCGATACATTCA
168882 ATCCTAAACT
Statistics
Matches: 109, Mismatches: 21, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
113 62 0.57
114 46 0.42
115 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.37
Consensus pattern (114 bp):
CAAAATTTATCGATACATTCATATAATGTATCGATACATTTTCATGTGTATCGATAAAAATAAGG
ATTTCAGGAATTGCGTAGCTACTACCAACATGATATATCAATAAATTCA
Found at i:169788 original size:20 final size:21
Alignment explanation
Indices: 169743--169798 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 21
169733 AAAACCCTTG
169743 TTTGTATCGATACA-TATCCA
1 TTTGTATCGATACATTATCCA
** *
169763 GATGTATCGATACATTATGC-
1 TTTGTATCGATACATTATCCA
169783 TTTGTATCGATACATT
1 TTTGTATCGATACATT
169799 GTATCGATAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.29, C:0.16, G:0.14, T:0.41
Consensus pattern (21 bp):
TTTGTATCGATACATTATCCA
Found at i:169802 original size:13 final size:13
Alignment explanation
Indices: 169784--169810 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
169774 ACATTATGCT
169784 TTGTATCGATACA
1 TTGTATCGATACA
169797 TTGTATCGATACA
1 TTGTATCGATACA
169810 T
1 T
169811 GCACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:170536 original size:9 final size:9
Alignment explanation
Indices: 170524--170557 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
170514 TACATCATAG
170524 AGAAAAACA
1 AGAAAAACA
170533 AGAAAAACA
1 AGAAAAACA
*
170542 AGATAAACA
1 AGAAAAACA
170551 AGAAAAA
1 AGAAAAA
170558 TAAGCCTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.76, C:0.09, G:0.12, T:0.03
Consensus pattern (9 bp):
AGAAAAACA
Found at i:176383 original size:3 final size:3
Alignment explanation
Indices: 176377--176409 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
176367 CTCCTCCTCC
176377 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
176410 CTTTGAGTAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:178035 original size:20 final size:19
Alignment explanation
Indices: 177991--178079 Score: 90
Period size: 20 Copynumber: 4.5 Consensus size: 19
177981 GTAACTCAAA
*
177991 GTATCGATACATTTAAGGATT
1 GTATCGATACATTT--TGATT
178012 -TATCGATACATTTTGTATT
1 GTATCGATACATTTTG-ATT
*
178031 GTATCGATATATTTTGATGT
1 GTATCGATACATTTTGAT-T
*
178051 GTATCGATACATTTTCACTT
1 GTATCGATACATTTTGA-TT
*
178071 GTATAGATA
1 GTATCGATA
178080 AAAATAAGGG
Statistics
Matches: 59, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
18 1 0.02
19 5 0.08
20 52 0.88
21 1 0.02
ACGTcount: A:0.29, C:0.10, G:0.16, T:0.45
Consensus pattern (19 bp):
GTATCGATACATTTTGATT
Found at i:179177 original size:20 final size:19
Alignment explanation
Indices: 179154--179203 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
179144 ACACTCAGAT
*
179154 GTATTGATACATATTGCTTA
1 GTATTGATACATATT-CATA
*
179174 GTATCGATACATATTCATA
1 GTATTGATACATATTCATA
*
179193 GTATTAATACA
1 GTATTGATACA
179204 CTTTGAATTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (19 bp):
GTATTGATACATATTCATA
Found at i:179944 original size:20 final size:21
Alignment explanation
Indices: 179921--179960 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
179911 AAGAGTGAAT
179921 AAAATCG-AAA-AAGACTTTGA
1 AAAATCGTAAACAAG-CTTTGA
179941 AAAATCGTAAACAAGCTTTG
1 AAAATCGTAAACAAGCTTTG
179961 TTCGTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 8 0.44
22 3 0.17
ACGTcount: A:0.50, C:0.12, G:0.15, T:0.23
Consensus pattern (21 bp):
AAAATCGTAAACAAGCTTTGA
Found at i:180233 original size:20 final size:20
Alignment explanation
Indices: 180208--180279 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
180198 GATACTTTGC
180208 ATCGATACATGAACAAATGT
1 ATCGATACATGAACAAATGT
** *
180228 ATCGATACATGTTC-ATTGT
1 ATCGATACATGAACAAATGT
*
180247 ATCGATACATGAACAAAAGT
1 ATCGATACATGAACAAATGT
180267 ATCGATACATGAA
1 ATCGATACATGAA
180280 ATCGGCAGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 16 0.36
20 28 0.64
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.28
Consensus pattern (20 bp):
ATCGATACATGAACAAATGT
Found at i:180345 original size:13 final size:13
Alignment explanation
Indices: 180327--180351 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
180317 CATTGCACAT
180327 TGTATCGATACAA
1 TGTATCGATACAA
180340 TGTATCGATACA
1 TGTATCGATACA
180352 TGGAGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:180349 original size:33 final size:33
Alignment explanation
Indices: 180307--180371 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
180297 TACCACTATT
*
180307 TGTATCGATACATTGCA-CATTGTATCGATACAA
1 TGTATCGATACA-TGCAGAATTGTATCGATACAA
*
180340 TGTATCGATACATGGAGAATTGTATCGATACA
1 TGTATCGATACATGCAGAATTGTATCGATACA
180372 TTGTCCTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 3 0.10
33 26 0.90
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.32
Consensus pattern (33 bp):
TGTATCGATACATGCAGAATTGTATCGATACAA
Found at i:187967 original size:33 final size:33
Alignment explanation
Indices: 187930--187998 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
187920 AGTTGATCAC
* * * *
187930 TTCACTTTCGCAGTGCATGGATGAGCATTTTAG
1 TTCACTTTCCCAGCGCATGGATGAGAACTTTAG
187963 TTCACTTTCCCAGCGCATGGATGAGAACTTTAG
1 TTCACTTTCCCAGCGCATGGATGAGAACTTTAG
187996 TTC
1 TTC
187999 TCTTAACCGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.22, C:0.22, G:0.22, T:0.35
Consensus pattern (33 bp):
TTCACTTTCCCAGCGCATGGATGAGAACTTTAG
Found at i:188971 original size:13 final size:13
Alignment explanation
Indices: 188953--188979 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
188943 ACATTATGCT
188953 TTGTATCGATACA
1 TTGTATCGATACA
188966 TTGTATCGATACA
1 TTGTATCGATACA
188979 T
1 T
188980 GAACAAATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:192237 original size:13 final size:13
Alignment explanation
Indices: 192219--192245 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
192209 ACATTATGCT
192219 TTGTATCGATACA
1 TTGTATCGATACA
192232 TTGTATCGATACA
1 TTGTATCGATACA
192245 T
1 T
192246 GCACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:192334 original size:13 final size:13
Alignment explanation
Indices: 192316--192340 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
192306 CATGGCGTAT
192316 TGTATCGATACAA
1 TGTATCGATACAA
192329 TGTATCGATACA
1 TGTATCGATACA
192341 TGATGAATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:192351 original size:33 final size:33
Alignment explanation
Indices: 192296--192358 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
192286 TACCATTGTT
* *
192296 TGTAACGATACATGGCGTATTGTATCGATACAA
1 TGTAACGATACATGACGAATTGTATCGATACAA
* * *
192329 TGTATCGATACATGATGAATTGTATTGATA
1 TGTAACGATACATGACGAATTGTATCGATA
192359 TATTGTCCCA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.33, C:0.11, G:0.21, T:0.35
Consensus pattern (33 bp):
TGTAACGATACATGACGAATTGTATCGATACAA
Found at i:200371 original size:19 final size:19
Alignment explanation
Indices: 200347--200411 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 19
200337 TAGCCAAACT
200347 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
200366 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
200379 TGTATCGATACACAAAAAATA
1 TGTATCGATACAC--AAAATA
200400 TGTATCGATACA
1 TGTATCGATACA
200412 TTGGCTTGTA
Statistics
Matches: 38, Mismatches: 0, Indels: 14
0.73 0.00 0.27
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
19 9 0.24
20 1 0.03
21 13 0.34
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:200383 original size:13 final size:13
Alignment explanation
Indices: 200365--200390 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
200355 TACACAAAAT
200365 ATGTATCGATACA
1 ATGTATCGATACA
200378 ATGTATCGATACA
1 ATGTATCGATACA
200391 CAAAAAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:200388 original size:32 final size:33
Alignment explanation
Indices: 200347--200411 Score: 114
Period size: 34 Copynumber: 2.0 Consensus size: 33
200337 TAGCCAAACT
200347 TGTATCGATACAC-AAAATATGTATCGATACAA
1 TGTATCGATACACAAAAATATGTATCGATACAA
200379 TGTATCGATACACAAAAAATATGTATCGATACA
1 TGTATCGATACAC-AAAAATATGTATCGATACA
200412 TTGGCTTGTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
32 13 0.42
34 18 0.58
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAATATGTATCGATACAA
Found at i:202640 original size:21 final size:21
Alignment explanation
Indices: 202607--202656 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
202597 TTGCAAGTTG
*
202607 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
202629 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
202650 AAATAAA
1 AAATAAA
202657 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:204474 original size:15 final size:15
Alignment explanation
Indices: 204454--204484 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
204444 TAAAAATATC
*
204454 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
204469 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
204484 C
1 C
204485 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:206583 original size:13 final size:13
Alignment explanation
Indices: 206565--206602 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
206555 ACATTTTTTT
206565 TGTATCGATATAA
1 TGTATCGATATAA
* *
206578 TGTATCGATACAC
1 TGTATCGATATAA
206591 TGTATCGATATA
1 TGTATCGATATA
206603 GGGGATTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATATAA
Found at i:206756 original size:20 final size:20
Alignment explanation
Indices: 206713--206758 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
206703 AAATCTTTTG
206713 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
206734 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
206754 CAAAA
1 CAAAA
206759 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:209151 original size:19 final size:19
Alignment explanation
Indices: 209127--209189 Score: 84
Period size: 19 Copynumber: 3.6 Consensus size: 19
209117 TAGCCAAACT
209127 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
209146 TGTATCGAT--AC---A-A
1 TGTATCGATACACAAAATA
209159 TGTATCGATACACAAAATA
1 TGTATCGATACACAAAATA
209178 TGTATCGATACA
1 TGTATCGATACA
209190 ATGTATCGAT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 10 0.26
14 1 0.03
15 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.29
Consensus pattern (19 bp):
TGTATCGATACACAAAATA
Found at i:209163 original size:13 final size:13
Alignment explanation
Indices: 209145--209202 Score: 62
Period size: 13 Copynumber: 4.0 Consensus size: 13
209135 TACACAAAAT
209145 ATGTATCGATACA
1 ATGTATCGATACA
209158 ATGTATCGATACACAAAA
1 ATGTATCGAT--AC---A
209176 TATGTATCGATACA
1 -ATGTATCGATACA
209190 ATGTATCGATACA
1 ATGTATCGATACA
209203 CAAAAAATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.59
14 1 0.03
15 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.41, C:0.16, G:0.14, T:0.29
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:209168 original size:32 final size:32
Alignment explanation
Indices: 209127--209223 Score: 167
Period size: 32 Copynumber: 3.0 Consensus size: 32
209117 TAGCCAAACT
209127 TGTATCGATACACAAAATATGTATCGATACAA
1 TGTATCGATACACAAAATATGTATCGATACAA
209159 TGTATCGATACACAAAATATGTATCGATACAA
1 TGTATCGATACACAAAATATGTATCGATACAA
*
209191 TGTATCGATACACAAAAAATATGTATTGATACA
1 TGTATCGATACAC--AAAATATGTATCGATACA
209224 TTGGCTTGTA
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 45 0.73
34 17 0.27
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.29
Consensus pattern (32 bp):
TGTATCGATACACAAAATATGTATCGATACAA
Found at i:221259 original size:374 final size:374
Alignment explanation
Indices: 220748--221457 Score: 1269
Period size: 374 Copynumber: 1.9 Consensus size: 374
220738 GACGTTGCTC
220748 CCATCCACATGAGCATCTACACAACTCTGGTCCATTGTCATAGTGTTGAAGAAGAGAAAGATGGC
1 CCATCCACATGAGCATCTACACAACTCTGGTCCATTGTCATAGTGTTGAAGAAGAGAAAGATGGC
* *
220813 CTACCATGGTACTATAACATCCTTCGCTATATCAAGGATCAGCAATATCCGAAAGATGCAACTAA
66 CAACCATGGTACTATAACATCCTTCACTATATCAAGGATCAGCAATATCCGAAAGATGCAACTAA
* * *
220878 GACTGATAAAAAGG-CCATCAGAAAATTGGCTATAGGATTTGTTCTTGACAGAGAAATTTTATAC
131 AACTGAT-AAAAGGACCATCAAAAAACTGGCTATAGGATTTGTTCTTGACAGAGAAATTTTATAC
*
220942 AAGAGGAGTTACGTCTAAGTGCTACTCAGATGCATCGACATTCTTAAAGCCAAAAAGATCTTAAA
195 AAGAGGAGTTACGACTAAGTGCTACTCAGATGCATCGACATTCTTAAAGCCAAAAAGATCTTAAA
221007 AGAAGTTCATAATGGGATTTGCGGCATGCATGCTAATGGACATCGAATGACCAAGCAAATCATGA
260 AGAAGTTCATAATGGGATTTGCGGCATGCATGCTAATGGACATCGAATGACCAAGCAAATCATGA
221072 AAGTAGTTATTACTAGTTGAGCATCTACATGAGCATGAGCATCGAATGGT
325 AAGTAGTTATTACTAGTTGAGCATCTACATGAGCATGAGCATCGAATGGT
221122 CCATCCACATGAGCATCTACACAACTCTGGTCCATTGTCATAGTGTTGAAGAAGAGAAAGATGGC
1 CCATCCACATGAGCATCTACACAACTCTGGTCCATTGTCATAGTGTTGAAGAAGAGAAAGATGGC
* * *
221187 CAACTATGGTACTATGACATCTTTCACTATATCAAGGATCAGCAATATCCGAAAGATGCAACTAA
66 CAACCATGGTACTATAACATCCTTCACTATATCAAGGATCAGCAATATCCGAAAGATGCAACTAA
221252 AACTGATAAAAGGACCATCAAAAAACTGGCTATAGGATTTGTTCTTGACAGAGAAATTTTATACA
131 AACTGATAAAAGGACCATCAAAAAACTGGCTATAGGATTTGTTCTTGACAGAGAAATTTTATACA
*
221317 AGAGGAGTTACGACTAAGTGCTACTCATATGCATCGACATTCTTAAAGCCAAAAAGATCTTAAAA
196 AGAGGAGTTACGACTAAGTGCTACTCAGATGCATCGACATTCTTAAAGCCAAAAAGATCTTAAAA
* * * *
221382 GAAGTTCATGATGGGATTTGTGGCATGCATGCTAATGGACATCGGATGGCCAAGCAAATCATGAA
261 GAAGTTCATAATGGGATTTGCGGCATGCATGCTAATGGACATCGAATGACCAAGCAAATCATGAA
*
221447 AGTGGTTATTA
326 AGTAGTTATTA
221458 TTATTTGACC
Statistics
Matches: 320, Mismatches: 15, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
373 6 0.02
374 314 0.98
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.26
Consensus pattern (374 bp):
CCATCCACATGAGCATCTACACAACTCTGGTCCATTGTCATAGTGTTGAAGAAGAGAAAGATGGC
CAACCATGGTACTATAACATCCTTCACTATATCAAGGATCAGCAATATCCGAAAGATGCAACTAA
AACTGATAAAAGGACCATCAAAAAACTGGCTATAGGATTTGTTCTTGACAGAGAAATTTTATACA
AGAGGAGTTACGACTAAGTGCTACTCAGATGCATCGACATTCTTAAAGCCAAAAAGATCTTAAAA
GAAGTTCATAATGGGATTTGCGGCATGCATGCTAATGGACATCGAATGACCAAGCAAATCATGAA
AGTAGTTATTACTAGTTGAGCATCTACATGAGCATGAGCATCGAATGGT
Found at i:222494 original size:22 final size:21
Alignment explanation
Indices: 222469--222519 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
222459 CATCCTTCGC
222469 AAAAAAAAAACAACAAAAAACA
1 AAAAAAAAAACAAC-AAAAACA
*
222491 AAAAAACAAACAACAAAAACA
1 AAAAAAAAAACAACAAAAACA
*
222512 ACAAAAAA
1 AAAAAAAA
222520 TAATGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.84, C:0.16, G:0.00, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAACAACAAAAACA
Found at i:223822 original size:52 final size:52
Alignment explanation
Indices: 223744--223861 Score: 137
Period size: 52 Copynumber: 2.3 Consensus size: 52
223734 CTTGCCAAAA
* ** * * * *
223744 TTTATCATCTTTCATTCCAATATTGCTAACCTTGGATTAGCACGTTGGCACC
1 TTTATCATCTTTAAGGCCAATATTGCTAACCTCGAATTAGAACATTGGCACC
* * *
223796 TTTATCATCTTTAAGGCCAATGTTGCTAGCCTCGAATTAGAACATTGGTACC
1 TTTATCATCTTTAAGGCCAATATTGCTAACCTCGAATTAGAACATTGGCACC
*
223848 TTCATCATCTTTAA
1 TTTATCATCTTTAA
223862 ATTCAATTCA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
52 55 1.00
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (52 bp):
TTTATCATCTTTAAGGCCAATATTGCTAACCTCGAATTAGAACATTGGCACC
Found at i:224187 original size:32 final size:33
Alignment explanation
Indices: 224104--224190 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 33
224094 TCATCCTTTT
** *
224104 AAGCCCACACAAGTTGGTGGCATTTTTTCTCAA
1 AAGCCCACACAAGTTGGTGGCAACTTTCCTCAA
* * * * *
224137 AAACCCATACAAGCTGGTGGTAACTTTCCT-TA
1 AAGCCCACACAAGTTGGTGGCAACTTTCCTCAA
224169 AAGCCCACACAAGTTGGTGGCA
1 AAGCCCACACAAGTTGGTGGCA
224191 TCCTCTTCCA
Statistics
Matches: 42, Mismatches: 12, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
32 19 0.45
33 23 0.55
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (33 bp):
AAGCCCACACAAGTTGGTGGCAACTTTCCTCAA
Found at i:224412 original size:52 final size:52
Alignment explanation
Indices: 224334--224914 Score: 558
Period size: 52 Copynumber: 11.2 Consensus size: 52
224324 ATGTCGCTAA
* * *
224334 CCTTGAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAATATTGCTGG
1 CCTTGAATCAGCATATTGGCACCTTTATCATTTTTAAGTCCAATATCGCTGG
* * * * * * *
224386 CCTTGAATTAGCATATTGACACCTTTACCATTCTTAAGCCCAATATCACTAG
1 CCTTGAATCAGCATATTGGCACCTTTATCATTTTTAAGTCCAATATCGCTGG
* * * * *
224438 CCTTGAATCAACATATTGGCACCTTTATCATCTTTAAGTCTAATGTCGCTAG
1 CCTTGAATCAGCATATTGGCACCTTTATCATTTTTAAGTCCAATATCGCTGG
* * ** *
224490 CCTTGAATTAGCACATTAACACCTTT-TCTTTTCTTAAGTCCAATATCGCTGG
1 CCTTGAATCAGCATATTGGCACCTTTATCATTT-TTAAGTCCAATATCGCTGG
* * * * *
224542 CCTTGAATCAGCACATTGGCACCTTT-TTATTTCTTAAATCCAATATTGTTGG
1 CCTTGAATCAGCATATTGGCACCTTTATCATTT-TTAAGTCCAATATCGCTGG
* * * * * **
224594 CCTTGAATCAACATATTGGCGCCTTTATCATCTTTAAGTCAAATGTCATTGG
1 CCTTGAATCAGCATATTGGCACCTTTATCATTTTTAAGTCCAATATCGCTGG
* ** * * * * *
224646 CCTTGACTCAATATATTGGCGCCTTTATCATTTTTAGGTCCAATGTCACTAG
1 CCTTGAATCAGCATATTGGCACCTTTATCATTTTTAAGTCCAATATCGCTGG
* * *
224698 CCTTGAATTAGCATATTGGCACCTTTTTC-TTTCTTAAGTCCAATATCG-TTG
1 CCTTGAATCAGCATATTGGCACCTTTATCATTT-TTAAGTCCAATATCGCTGG
* * * * * *
224749 CCTTGAATCAGCATATTAGCACCTTTGTCATCTTTAAGTCTAATGTCGCTAG
1 CCTTGAATCAGCATATTGGCACCTTTATCATTTTTAAGTCCAATATCGCTGG
* * * * *
224801 CCTTGAATCAGCATATTAGCACTTTTGTCATCTTTAAGTTCAATATCGCTGG
1 CCTTGAATCAGCATATTGGCACCTTTATCATTTTTAAGTCCAATATCGCTGG
* * * * ** *
224853 CCTTGAATCAGCATATTAGCACTTTTGTCATCTTTAAGTCTGATATCGCTAG
1 CCTTGAATCAGCATATTGGCACCTTTATCATTTTTAAGTCCAATATCGCTGG
224905 CCTTGAATCA
1 CCTTGAATCA
224915 ACGTATCGGT
Statistics
Matches: 447, Mismatches: 77, Indels: 10
0.84 0.14 0.02
Matches are distributed among these distances:
51 48 0.11
52 395 0.88
53 4 0.01
ACGTcount: A:0.25, C:0.23, G:0.14, T:0.38
Consensus pattern (52 bp):
CCTTGAATCAGCATATTGGCACCTTTATCATTTTTAAGTCCAATATCGCTGG
Found at i:224549 original size:156 final size:155
Alignment explanation
Indices: 224317--224935 Score: 679
Period size: 156 Copynumber: 4.0 Consensus size: 155
224307 TTCCTTTTCA
* * * * *
224317 AAGTCTAATGTCGCTAACCTTGAATCAGCATATTGGCACCTTTACCATTTTTAAGCCCAATATTG
1 AAGTCTAATGTCGCTAGCCTTGAATCAGCATATTAGCACCTTTATCATTTTTAAGTCCAATATCG
* * * *
224382 CTGGCCTTGAATTAGCATATTGACACCTTTACCATTCTTAAGCCCAATATCACTAGCCTTGAATC
66 CTGGCCTTGAATCAGCATATTGACACCTTT-TCATTCTTAAGTCCAATATCGCTAGCCTTGAATC
224447 AACATATTGGCACCTTTATCATCTTT
130 AACATATTGGCACCTTTATCATCTTT
* * * *
224473 AAGTCTAATGTCGCTAGCCTTGAATTAGCACATTAACACCTTT-TCTTTTCTTAAGTCCAATATC
1 AAGTCTAATGTCGCTAGCCTTGAATCAGCATATTAGCACCTTTATCATTT-TTAAGTCCAATATC
* * * * * * *
224537 GCTGGCCTTGAATCAGCACATTGGCACCTTTTTATTTCTTAAATCCAATATTGTTGGCCTTGAAT
65 GCTGGCCTTGAATCAGCATATTGACACCTTTTCA-TTCTTAAGTCCAATATCGCTAGCCTTGAAT
*
224602 CAACATATTGGCGCCTTTATCATCTTT
129 CAACATATTGGCACCTTTATCATCTTT
* ** * * ** * * * * *
224629 AAGTCAAATGTCATTGGCCTTGACTCAATATATTGGCGCCTTTATCATTTTTAGGTCCAATGTCA
1 AAGTCTAATGTCGCTAGCCTTGAATCAGCATATTAGCACCTTTATCATTTTTAAGTCCAATATCG
* * * * *
224694 CTAGCCTTGAATTAGCATATTGGCACCTTTTTCTTTCTTAAGTCCAATATCG-TTGCCTTGAATC
66 CTGGCCTTGAATCAGCATATTGACACC-TTTTCATTCTTAAGTCCAATATCGCTAGCCTTGAATC
* * *
224758 AGCATATTAGCACCTTTGTCATCTTT
130 AACATATTGGCACCTTTATCATCTTT
* * * *
224784 AAGTCTAATGTCGCTAGCCTTGAATCAGCATATTAGCACTTTTGTCATCTTTAAGTTCAATATCG
1 AAGTCTAATGTCGCTAGCCTTGAATCAGCATATTAGCACCTTTATCATTTTTAAGTCCAATATCG
* **
224849 CTGGCCTTGAATCAGCATATT-AGCACTTTTGTCA-TCTTTAAGTCTGATATCGCTAGCCTTGAA
66 CTGGCCTTGAATCAGCATATTGA-CACCTTT-TCATTC-TTAAGTCCAATATCGCTAGCCTTGAA
* * * *
224912 TCAACGTATCGGTATCTTTATCAT
128 TCAACATATTGGCACCTTTATCAT
224936 TCTTCTCATC
Statistics
Matches: 375, Mismatches: 80, Indels: 16
0.80 0.17 0.03
Matches are distributed among these distances:
154 5 0.01
155 124 0.33
156 237 0.63
157 9 0.02
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (155 bp):
AAGTCTAATGTCGCTAGCCTTGAATCAGCATATTAGCACCTTTATCATTTTTAAGTCCAATATCG
CTGGCCTTGAATCAGCATATTGACACCTTTTCATTCTTAAGTCCAATATCGCTAGCCTTGAATCA
ACATATTGGCACCTTTATCATCTTT
Found at i:225114 original size:113 final size:112
Alignment explanation
Indices: 224828--225213 Score: 384
Period size: 113 Copynumber: 3.4 Consensus size: 112
224818 AGCACTTTTG
* * * *
224828 TCATCTTTAAGTTCAATATCGCTGGCCTTGAATCAGCATATTAGCACTTTTGTCATCTTTAAGTC
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCAC-TTTGTTATCTTTAAGCC
* * * *
224893 TGATATCGCTAGCCTTGAATCAACGTATCGGTATCTTTATCATTCTTC
65 TGATATCACTAGCCTTGAATCAGCATATTGGTATCTTTATCATTCTTC
* * * * * * * *
224941 TCATCTTTAAGTCTAATGTCGTTGGTCGTGAATCAGCACATTGGCATTCTTCG-TACCTTTAAGC
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCA--CTTTGTTATCTTTAAGC
* * * *
225005 CTGATATTACT-GATCGTGAATCAGCATATTAGTA-CTTTTATCATTCTTC
64 CTGATATCACTAG-CCTTGAATCAGCATATTGGTATC-TTTATCATTCTTC
* * *
225054 TCAT-TTTCAAGTCCAATGTCGCTGGTCTTGAATCAACACATTAGCACATTTGTTATCTTTAAGC
1 TCATCTTT-AAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCAC-TTTGTTATCTTTAAGC
** * * *
225118 CAAATATCACCAGCCTTGAATCAGTATATTGGCATCTTTATCATTCTTC
64 CTGATATCACTAGCCTTGAATCAGCATATTGGTATCTTTATCATTCTTC
* * * * *
225167 TCATCTTCAAGCCCGATATCGCTGGCCATGAATCAGCATATTAGCAC
1 TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCAC
225214 CTTTATCATT
Statistics
Matches: 219, Mismatches: 44, Indels: 20
0.77 0.16 0.07
Matches are distributed among these distances:
111 1 0.00
112 8 0.04
113 202 0.92
114 7 0.03
115 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.15, T:0.37
Consensus pattern (112 bp):
TCATCTTTAAGTCCAATATCGCTGGCCTTGAATCAGCACATTAGCACTTTGTTATCTTTAAGCCT
GATATCACTAGCCTTGAATCAGCATATTGGTATCTTTATCATTCTTC
Found at i:225250 original size:61 final size:61
Alignment explanation
Indices: 225134--225251 Score: 141
Period size: 61 Copynumber: 1.9 Consensus size: 61
225124 TCACCAGCCT
* * * * *
225134 TGAATCAGTATATTGGCATCTTTATCATTCTTCTCATCTTCAAGCCCGATATCGCTGGCCA
1 TGAATCAGCATATTAGCACCTTTATCATTCTTCTCATCTTCAAACCCAATATCGCTGGCCA
* *
225195 TGAATCAGCATATTAGCACCTTTATCATTCTT-TGCATCCTT-AAATCCAATGTCGCTG
1 TGAATCAGCATATTAGCACCTTTATCATTCTTCT-CAT-CTTCAAACCCAATATCGCTG
225252 ACCTAGAATT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
60 1 0.02
61 44 0.92
62 3 0.06
ACGTcount: A:0.25, C:0.25, G:0.14, T:0.36
Consensus pattern (61 bp):
TGAATCAGCATATTAGCACCTTTATCATTCTTCTCATCTTCAAACCCAATATCGCTGGCCA
Found at i:226163 original size:20 final size:19
Alignment explanation
Indices: 226133--226171 Score: 69
Period size: 20 Copynumber: 2.0 Consensus size: 19
226123 TGAGTTTTTG
226133 TTCTTAATGTATCGATACA
1 TTCTTAATGTATCGATACA
226152 TTCTTCAATGTATCGATACA
1 TTCTT-AATGTATCGATACA
226172 AGCAAGCGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 5 0.26
20 14 0.74
ACGTcount: A:0.31, C:0.18, G:0.10, T:0.41
Consensus pattern (19 bp):
TTCTTAATGTATCGATACA
Found at i:235044 original size:26 final size:27
Alignment explanation
Indices: 235006--235056 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
234996 GAACTTTTTA
*
235006 TTTTCAAA-ATTTTTTGTTTTAAAAAG
1 TTTTCAAATATTTTTTATTTTAAAAAG
* *
235032 TTTTTAAATTTTTTTTATTTTAAAA
1 TTTTCAAATATTTTTTATTTTAAAA
235057 TATTAATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 7 0.33
27 14 0.67
ACGTcount: A:0.33, C:0.02, G:0.04, T:0.61
Consensus pattern (27 bp):
TTTTCAAATATTTTTTATTTTAAAAAG
Found at i:240601 original size:13 final size:13
Alignment explanation
Indices: 240585--240609 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
240575 TCTTTTTCTT
240585 TTTTTTTTTTAAA
1 TTTTTTTTTTAAA
240598 TTTTTTTTTTAA
1 TTTTTTTTTTAA
240610 GTATCATTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTTTTTTAAA
Found at i:242243 original size:2 final size:2
Alignment explanation
Indices: 242236--242263 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
242226 CGCATATCAA
242236 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
242264 CAGATAACAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:243592 original size:22 final size:23
Alignment explanation
Indices: 243566--243612 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
243556 TTGAACAATA
243566 TTTTT-CTTTTAATTTTGTTACT
1 TTTTTCCTTTTAATTTTGTTACT
* *
243588 TTTTTCCTTTTATTTTTGTTCCT
1 TTTTTCCTTTTAATTTTGTTACT
243611 TT
1 TT
243613 CTGCTAAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 5 0.23
23 17 0.77
ACGTcount: A:0.09, C:0.13, G:0.04, T:0.74
Consensus pattern (23 bp):
TTTTTCCTTTTAATTTTGTTACT
Found at i:244385 original size:31 final size:32
Alignment explanation
Indices: 244316--244385 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 32
244306 TTAATTATAA
* *
244316 AATAAATAAAATATTAAATATATTATTTTGAT
1 AATAAATAAAATATTAAATATATGATTTAGAT
* *
244348 ATTAAAT-AAATATTAAATATAGTGA-TTAGTT
1 AATAAATAAAATATTAAATATA-TGATTTAGAT
244379 AATAAAT
1 AATAAAT
244386 TTTCTAAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
31 24 0.75
32 8 0.25
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (32 bp):
AATAAATAAAATATTAAATATATGATTTAGAT
Found at i:245233 original size:15 final size:16
Alignment explanation
Indices: 245206--245236 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
245196 TTAAATAATT
245206 ATATTATTTTTAAAAA
1 ATATTATTTTTAAAAA
245222 ATATTA-TTTTAAAAA
1 ATATTATTTTTAAAAA
245237 TTTTTAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTATTTTTAAAAA
Found at i:245893 original size:38 final size:39
Alignment explanation
Indices: 245850--245942 Score: 113
Period size: 38 Copynumber: 2.4 Consensus size: 39
245840 TTTGTAAACT
245850 TTATTTATAATTTTTTTCATTATCA-ATATATGA-A-ATAA
1 TTATTTATAATTTTTTT-ATTATCATA-ATATGATATATAA
245888 TTATTTGA-ATATTTTTTTATTATCATAATATGATATTATAA
1 TTATTT-ATA-ATTTTTTTATTATCATAATATGATA-TATAA
245929 TTATTTATAATTTT
1 TTATTTATAATTTT
245943 AATTTTTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
38 20 0.42
39 11 0.23
40 6 0.12
41 11 0.23
ACGTcount: A:0.37, C:0.03, G:0.03, T:0.57
Consensus pattern (39 bp):
TTATTTATAATTTTTTTATTATCATAATATGATATATAA
Found at i:246400 original size:18 final size:16
Alignment explanation
Indices: 246377--246410 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
246367 AGAGCTTCTC
246377 TCCTTTTACTTTCTCTTT
1 TCCTTTT-CTTT-TCTTT
246395 TCCTTTTCTTTTCTTT
1 TCCTTTTCTTTTCTTT
246411 GCTTTACGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.03, C:0.26, G:0.00, T:0.71
Consensus pattern (16 bp):
TCCTTTTCTTTTCTTT
Found at i:247837 original size:20 final size:20
Alignment explanation
Indices: 247798--247838 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
247788 ATTAAATAAG
*
247798 TAATTCAAATCACATTAAAT
1 TAATTCAAATCACATAAAAT
247818 TAATTCAAATTCA-ATAAAAT
1 TAATTCAAA-TCACATAAAAT
247838 T
1 T
247839 TTATCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 16 0.84
21 3 0.16
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (20 bp):
TAATTCAAATCACATAAAAT
Found at i:249550 original size:20 final size:20
Alignment explanation
Indices: 249512--249552 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
249502 AAAATTAGAT
249512 ATAAGTTTAATTGATAAAAA
1 ATAAGTTTAATTGATAAAAA
249532 ATAA-TTTAATTGATAAAAA
1 ATAAGTTTAATTGATAAAAA
249551 AT
1 AT
249553 CATTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.56, C:0.00, G:0.07, T:0.37
Consensus pattern (20 bp):
ATAAGTTTAATTGATAAAAA
Found at i:249561 original size:19 final size:19
Alignment explanation
Indices: 249520--249561 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
249510 ATATAAGTTT
*
249520 AATTGATAAAAAATAATTT
1 AATTGATAAAAAATAATTA
*
249539 AATTGATAAAAAATCATTA
1 AATTGATAAAAAATAATTA
249558 AATT
1 AATT
249562 AGAGTGATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.57, C:0.02, G:0.05, T:0.36
Consensus pattern (19 bp):
AATTGATAAAAAATAATTA
Found at i:250052 original size:14 final size:15
Alignment explanation
Indices: 250033--250064 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
250023 ACCCAATAAA
250033 TTTAATATTCA-AAT
1 TTTAATATTCACAAT
250047 TTTAATATTCACAAT
1 TTTAATATTCACAAT
250062 TTT
1 TTT
250065 TTTCTAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (15 bp):
TTTAATATTCACAAT
Found at i:250622 original size:17 final size:17
Alignment explanation
Indices: 250602--250659 Score: 73
Period size: 19 Copynumber: 3.2 Consensus size: 17
250592 TTAAAACACG
250602 ATATAAAATAAAT-TATA
1 ATATAAAA-AAATATATA
250619 ATATAAAAAAATAATATGA
1 ATATAAAAAAAT-ATAT-A
250638 ATATAAAAAAAATATATA
1 ATAT-AAAAAAATATATA
250656 ATAT
1 ATAT
250660 GAATTTATGG
Statistics
Matches: 37, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
16 4 0.11
17 8 0.22
18 8 0.22
19 9 0.24
20 8 0.22
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (17 bp):
ATATAAAAAAATATATA
Found at i:251690 original size:19 final size:19
Alignment explanation
Indices: 251666--251729 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
251656 CTTTATTATT
251666 ATAAAAAAATTAGAAATAA
1 ATAAAAAAATTAGAAATAA
* **
251685 AT-AAAAAATATCG-AATGTG
1 ATAAAAAAAT-TAGAAAT-AA
*
251704 ATGAAAAAATTAGAAATAA
1 ATAAAAAAATTAGAAATAA
251723 ATAAAAA
1 ATAAAAA
251730 TTATTAAATA
Statistics
Matches: 34, Mismatches: 7, Indels: 8
0.69 0.14 0.16
Matches are distributed among these distances:
18 10 0.29
19 14 0.41
20 10 0.29
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (19 bp):
ATAAAAAAATTAGAAATAA
Found at i:251692 original size:18 final size:18
Alignment explanation
Indices: 251669--251729 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
251659 TATTATTATA
251669 AAAAAATTAGAAATAAAT
1 AAAAAATTAGAAATAAAT
* **
251687 AAAAAATATCG-AATGTGAT
1 AAAAAAT-TAGAAAT-AAAT
251706 GAAAAAATTAGAAATAAAT
1 -AAAAAATTAGAAATAAAT
251725 AAAAA
1 AAAAA
251730 TTATTAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
18 15 0.45
19 8 0.24
20 10 0.30
ACGTcount: A:0.67, C:0.02, G:0.10, T:0.21
Consensus pattern (18 bp):
AAAAAATTAGAAATAAAT
Found at i:253564 original size:25 final size:25
Alignment explanation
Indices: 253536--253586 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
253526 TTTTGAGATC
*
253536 TTCAAATTACACTTTCAAGCTCCAA
1 TTCAAATTAAACTTTCAAGCTCCAA
*
253561 TTCAAATTAAAGTTTCAAGCTCCAA
1 TTCAAATTAAACTTTCAAGCTCCAA
253586 T
1 T
253587 AATTTAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.06, T:0.33
Consensus pattern (25 bp):
TTCAAATTAAACTTTCAAGCTCCAA
Found at i:256717 original size:2 final size:2
Alignment explanation
Indices: 256710--256743 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
256700 ATTGTAGTAA
256710 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
256744 TGGTATTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:263691 original size:51 final size:52
Alignment explanation
Indices: 263636--263754 Score: 170
Period size: 51 Copynumber: 2.3 Consensus size: 52
263626 TATGGAAAGA
* *
263636 AAATGTATCGATACATTTTTCATTGTATCGATACATT-TTGGGTTTT-AGCCC
1 AAATGTATCGATACATTTTTCATTATATCGATACATTCTAGGGTTTTGA-CCC
* * *
263687 AAATGTATCGACACAGTTTTCATTATATCGATATATTCTAGGGTTTTGACCC
1 AAATGTATCGATACATTTTTCATTATATCGATACATTCTAGGGTTTTGACCC
263739 AAATGTATCGATACAT
1 AAATGTATCGATACAT
263755 ACAGGTTATT
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
51 33 0.56
52 25 0.42
53 1 0.02
ACGTcount: A:0.29, C:0.16, G:0.15, T:0.39
Consensus pattern (52 bp):
AAATGTATCGATACATTTTTCATTATATCGATACATTCTAGGGTTTTGACCC
Found at i:266062 original size:43 final size:43
Alignment explanation
Indices: 266001--266306 Score: 216
Period size: 52 Copynumber: 6.6 Consensus size: 43
265991 TCGATTAGCC
* *
266001 TCAAGGCCAGTGATATTGGACTTAAAGGTGCCAATGTGCTGAT
1 TCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGAT
* * *
266044 TCAAGGCCAGCGACATTGGTCTTAAAGATGACAAAGGCGCTAATATGCTGAT
1 TCAAGGCCAGCGATATTGGACTTAAAG--G-----TGC-C-AATATGCTGAT
* *
266096 TTAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGAT
1 TCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGAT
** * * * * *
266139 TCAAGGCTTGCCACACTAGACTTAAAGATGACAAAGGCGCCAATATGCTGAT
1 TCAAGGCCAGCGATATTGGAC-T-----T---AAAGGTGCCAATATGCTGAT
* *
266191 TCAAGGCCAGCGATATTGGACTTAAAGGTGTCCAATGTGCTAAT
1 TCAAGGCCAGCGATATTGGACTTAAAGGTG-CCAATATGCTGAT
* * *
266235 TTAAGGCCAGCGACATTGGTCTTAAAGACAAGGTGCCAATATGCTGAT
1 TCAAGGCCAGCGATATTGGACTT----A-AAGGTGCCAATATGCTGAT
*
266283 TCAAGGCCAGCAATATTGGACTTA
1 TCAAGGCCAGCGATATTGGACTTA
266307 GAAGAAGACG
Statistics
Matches: 202, Mismatches: 37, Indels: 47
0.71 0.13 0.16
Matches are distributed among these distances:
43 54 0.27
44 34 0.17
45 3 0.01
46 1 0.00
48 31 0.15
49 7 0.03
50 3 0.01
51 2 0.01
52 67 0.33
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (43 bp):
TCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATATGCTGAT
Found at i:266166 original size:95 final size:95
Alignment explanation
Indices: 266001--266306 Score: 458
Period size: 95 Copynumber: 3.3 Consensus size: 95
265991 TCGATTAGCC
*
266001 TCAAGGCCAGTGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCT
1 TCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCT
*
266066 TAAAGATGACAAAGGCGCTAATATGCTGAT
66 TAAAGATGACAAAGGCGCCAATATGCTGAT
* ** * * * *
266096 TTAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCTTGCCACACTAGACT
1 TCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCT
266161 TAAAGATGACAAAGGCGCCAATATGCTGAT
66 TAAAGATGACAAAGGCGCCAATATGCTGAT
* *
266191 TCAAGGCCAGCGATATTGGACTTAAAGGTGTCCAATGTGCTAATTTAAGGCCAGCGACATTGGTC
1 TCAAGGCCAGCGATATTGGACTTAAAGGTG-CCAATGTGCTGATTCAAGGCCAGCGACATTGGTC
*
266256 TT-AA-A-GAC-AAGGTGCCAATATGCTGAT
65 TTAAAGATGACAAAGGCGCCAATATGCTGAT
*
266283 TCAAGGCCAGCAATATTGGACTTA
1 TCAAGGCCAGCGATATTGGACTTA
266307 GAAGAAGACG
Statistics
Matches: 190, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
92 41 0.22
93 3 0.02
94 1 0.01
95 117 0.62
96 28 0.15
ACGTcount: A:0.31, C:0.19, G:0.25, T:0.25
Consensus pattern (95 bp):
TCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCGACATTGGTCT
TAAAGATGACAAAGGCGCCAATATGCTGAT
Found at i:266241 original size:44 final size:45
Alignment explanation
Indices: 266177--266311 Score: 157
Period size: 44 Copynumber: 2.9 Consensus size: 45
266167 TGACAAAGGC
266177 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT-AA-AGGT
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGGT
* * * * *
266220 GTCCAATGTGCTAATTTAAGGCCAGCGACATTGGTCTTAAAGACAAGGT
1 G-CCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG---AGGT
*
266269 GCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAGAAGA
1 GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTA-AAGA
266312 AGACGCCACC
Statistics
Matches: 74, Mismatches: 11, Indels: 11
0.77 0.11 0.11
Matches are distributed among these distances:
43 1 0.01
44 31 0.42
45 2 0.03
46 1 0.01
48 31 0.42
49 8 0.11
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (45 bp):
GCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGAGGT
Found at i:266444 original size:27 final size:28
Alignment explanation
Indices: 266406--266611 Score: 143
Period size: 27 Copynumber: 7.0 Consensus size: 28
266396 GAGGAGAAGA
*
266406 TGCCACAGAGTTGTGGAC-TTAAAAGGG
1 TGCCACAGAGTTGTGGGCTTTAAAAGGG
*
266433 TGCCACAGAGTTGTGGAC-TTAAAAGGAAAAAAAG
1 TGCCACAGAGTTGTGGGCTTTAAAAGG-------G
266467 TGCCAC-GAAGTTGTGGGCTTTAAAAAGAAAAAGG
1 TGCCACAG-AGTTGTGGGCTTT-AAAAG-----GG
* *
266501 TGCCACGGAGTTGTGGGCTTTAAAAGAG
1 TGCCACAGAGTTGTGGGCTTTAAAAGGG
* * * *
266529 TGACAC-GGGATTATGGGCTTTAAAAGAG
1 TGCCACAGAG-TTGTGGGCTTTAAAAGGG
* * *
266557 TGCCACGGAGTTGTGGAC-TTAAAAGGA
1 TGCCACAGAGTTGTGGGCTTTAAAAGGG
266584 TGCCACAGAGTTGTGGGCTTTAAAAGGG
1 TGCCACAGAGTTGTGGGCTTTAAAAGGG
266612 GAAATGGTGC
Statistics
Matches: 146, Mismatches: 14, Indels: 37
0.74 0.07 0.19
Matches are distributed among these distances:
27 51 0.35
28 42 0.29
29 2 0.01
33 6 0.04
34 36 0.25
35 3 0.02
36 5 0.03
41 1 0.01
ACGTcount: A:0.33, C:0.13, G:0.32, T:0.22
Consensus pattern (28 bp):
TGCCACAGAGTTGTGGGCTTTAAAAGGG
Found at i:266497 original size:35 final size:34
Alignment explanation
Indices: 266432--266525 Score: 120
Period size: 34 Copynumber: 2.8 Consensus size: 34
266422 ACTTAAAAGG
* *
266432 GTGCCAC-AGAGTTGTGGAC-TTAAAAGGAAAAAAA
1 GTGCCACGA-AGTTGTGGGCTTTAAAAAG-AAAAAA
*
266466 GTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAG
1 GTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAA
*
266500 GTGCCACGGAGTTGTGGGCTTTAAAA
1 GTGCCACGAAGTTGTGGGCTTTAAAA
266526 GAGTGACACG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
34 46 0.85
35 8 0.15
ACGTcount: A:0.36, C:0.13, G:0.30, T:0.21
Consensus pattern (34 bp):
GTGCCACGAAGTTGTGGGCTTTAAAAAGAAAAAA
Found at i:266536 original size:28 final size:27
Alignment explanation
Indices: 266495--266610 Score: 146
Period size: 28 Copynumber: 4.2 Consensus size: 27
266485 TTTAAAAAGA
266495 AAAAGGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGTGCCACGGAGTTGTGGGCTTT
* *
266522 AAAAGAGTGACACGG-GATTATGGGCTTT
1 AAAAG-GTGCCACGGAG-TTGTGGGCTTT
*
266550 AAAAGAGTGCCACGGAGTTGTGGAC-TT
1 AAAAG-GTGCCACGGAGTTGTGGGCTTT
*
266577 AAAAGGATGCCACAGAGTTGTGGGCTTT
1 AAAAGG-TGCCACGGAGTTGTGGGCTTT
266605 AAAAGG
1 AAAAGG
266611 GGAAATGGTG
Statistics
Matches: 77, Mismatches: 7, Indels: 9
0.83 0.08 0.10
Matches are distributed among these distances:
26 1 0.01
27 29 0.38
28 46 0.60
29 1 0.01
ACGTcount: A:0.30, C:0.13, G:0.34, T:0.23
Consensus pattern (27 bp):
AAAAGGTGCCACGGAGTTGTGGGCTTT
Found at i:266578 original size:151 final size:150
Alignment explanation
Indices: 266402--266672 Score: 375
Period size: 151 Copynumber: 1.8 Consensus size: 150
266392 TTTTGAGGAG
*
266402 AAGATGCCACAGAGTTGTGGACTTAAAAGGGTGCCACAGAGTTGTGGAC-TTAAAAGGAAAAAAA
1 AAGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGAAAAAAA
* * * * *
266466 GTGCCACGA-AGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGAGT
66 GTGCCA-GAGAGTCGTGGAC-TTAAAAAGAAAAAGATGCCACGAAGTTGTGGACTTTAAAAGAGT
266530 GACACGGGATTATGGGCTTTAA
129 GACACGGGATTATGGGCTTTAA
* * ** *
266552 AAGAGTGCCACGGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGGCTTTAAAAGGGGAAAT
1 AAGA-TGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGAAAAAA
* * *
266617 GGTGCCAGAGAGTCGTGGACTTAAAAGGGAAAAGATGCCACGAAGTTGTGGACTTT
65 AGTGCCAGAGAGTCGTGGACTTAAAAAGAAAAAGATGCCACGAAGTTGTGGACTTT
266673 GAAGAAAAGA
Statistics
Matches: 104, Mismatches: 14, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
150 4 0.04
151 75 0.72
152 25 0.24
ACGTcount: A:0.33, C:0.13, G:0.32, T:0.22
Consensus pattern (150 bp):
AAGATGCCACAGAGTTGTGGACTTAAAAGGATGCCACAGAGTTGTGGACTTTAAAAGGAAAAAAA
GTGCCAGAGAGTCGTGGACTTAAAAAGAAAAAGATGCCACGAAGTTGTGGACTTTAAAAGAGTGA
CACGGGATTATGGGCTTTAA
Found at i:266623 original size:35 final size:34
Alignment explanation
Indices: 266577--266862 Score: 118
Period size: 31 Copynumber: 9.0 Consensus size: 34
266567 TTGTGGACTT
*
266577 AAAAGGATGCCACAGAGTTGTGGGCTTTAAAAGGGG
1 AAAA-GATGCCACAGAGTTGTGGACTTTAAAA-GGG
* * * *
266613 AAATGGTGCCAGAGAGTCGTGGAC-TTAAAAGGG
1 AAAAGATGCCACAGAGTTGTGGACTTTAAAAGGG
*
266646 AAAAGATGCCAC-GAAGTTGTGGACTTT-GAA--G
1 AAAAGATGCCACAG-AGTTGTGGACTTTAAAAGGG
* *
266677 AAAAGATGCCACTGAG-TGCGGACTTT----GGG
1 AAAAGATGCCACAGAGTTGTGGACTTTAAAAGGG
* * *
266706 AAGAGATGCCACTGAGTCGTGGACTTT-----GG
1 AAAAGATGCCACAGAGTTGTGGACTTTAAAAGGG
* ** *
266735 AAAGAGATGCCACTGAGTCATGGACTTT-GAA--G
1 AAA-AGATGCCACAGAGTTGTGGACTTTAAAAGGG
* ** *
266767 AAAAGATGCCACTGAGTCATGGACTTT-GAA--G
1 AAAAGATGCCACAGAGTTGTGGACTTTAAAAGGG
* * * *
266798 AAAAGATGCCACTGAGTCGTGGGCTTT----GAG
1 AAAAGATGCCACAGAGTTGTGGACTTTAAAAGGG
* *
266828 AAGAGATTGCCACTGAGTTGTGGACTTTAAGAAGG
1 AAAAGA-TGCCACAGAGTTGTGGACTTTAA-AAGG
266863 TATTTGAAGA
Statistics
Matches: 210, Mismatches: 22, Indels: 36
0.78 0.08 0.13
Matches are distributed among these distances:
29 20 0.10
30 46 0.22
31 87 0.41
32 6 0.03
33 23 0.11
34 8 0.04
35 16 0.08
36 4 0.02
ACGTcount: A:0.31, C:0.14, G:0.32, T:0.22
Consensus pattern (34 bp):
AAAAGATGCCACAGAGTTGTGGACTTTAAAAGGG
Found at i:266647 original size:33 final size:34
Alignment explanation
Indices: 266577--266671 Score: 104
Period size: 33 Copynumber: 2.8 Consensus size: 34
266567 TTGTGGACTT
* *
266577 AAAAGGATGCCACAGAGTTGTGGGCTTTAAAAGGGG
1 AAAA-GATGCCAGAGAGTTGTGGAC-TTAAAAGGGG
* * *
266613 AAATGGTGCCAGAGAGTCGTGGACTTAAAA-GGG
1 AAAAGATGCCAGAGAGTTGTGGACTTAAAAGGGG
266646 AAAAGATGCCACGA-AGTTGTGGACTT
1 AAAAGATGCCA-GAGAGTTGTGGACTT
266672 TGAAGAAAAG
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
33 23 0.46
34 8 0.16
35 16 0.32
36 3 0.06
ACGTcount: A:0.34, C:0.13, G:0.34, T:0.20
Consensus pattern (34 bp):
AAAAGATGCCAGAGAGTTGTGGACTTAAAAGGGG
Found at i:266683 original size:31 final size:31
Alignment explanation
Indices: 266626--266860 Score: 277
Period size: 31 Copynumber: 7.6 Consensus size: 31
266616 TGGTGCCAGA
**
266626 GAGTCGTGGACTTAAAAGGGAAAAGATGCCAC-
1 GAGTCGTGGACTTTGAA--GAAAAGATGCCACT
*
266658 GAAGTTGTGGACTTTGAAGAAAAGATGCCACT
1 G-AGTCGTGGACTTTGAAGAAAAGATGCCACT
* * *
266690 GAGT-GCGGACTTTG-GGAAGAGATGCCACT
1 GAGTCGTGGACTTTGAAGAAAAGATGCCACT
266719 GAGTCGTGGACTTTG--GAAAGAGATGCCACT
1 GAGTCGTGGACTTTGAAGAAA-AGATGCCACT
*
266749 GAGTCATGGACTTTGAAGAAAAGATGCCACT
1 GAGTCGTGGACTTTGAAGAAAAGATGCCACT
*
266780 GAGTCATGGACTTTGAAGAAAAGATGCCACT
1 GAGTCGTGGACTTTGAAGAAAAGATGCCACT
* *
266811 GAGTCGTGGGCTTTG-AGAAGAGATTGCCACT
1 GAGTCGTGGACTTTGAAGAAAAGA-TGCCACT
*
266842 GAGTTGTGGACTTT-AAGAA
1 GAGTCGTGGACTTTGAAGAA
266861 GGTATTTGAA
Statistics
Matches: 181, Mismatches: 14, Indels: 17
0.85 0.07 0.08
Matches are distributed among these distances:
29 20 0.11
30 49 0.27
31 93 0.51
32 6 0.03
33 13 0.07
ACGTcount: A:0.31, C:0.15, G:0.31, T:0.23
Consensus pattern (31 bp):
GAGTCGTGGACTTTGAAGAAAAGATGCCACT
Found at i:270007 original size:13 final size:13
Alignment explanation
Indices: 269989--270014 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
269979 TACAGCAAGT
269989 ATGTATCGATACA
1 ATGTATCGATACA
270002 ATGTATCGATACA
1 ATGTATCGATACA
270015 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:270535 original size:34 final size:35
Alignment explanation
Indices: 270472--270538 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
270462 CTAAGTGATT
270472 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
270508 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
270539 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:272221 original size:84 final size:84
Alignment explanation
Indices: 272061--272221 Score: 186
Period size: 84 Copynumber: 1.9 Consensus size: 84
272051 ACTCAAAGAA
* * * *
272061 GAAAATAAATCAATAAGTGTAGAGAATCATATTCTTGAAAAGAAATTAAGTGAATTAGAGAAGAG
1 GAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
* *
272126 TATGAAAGAGTTACAAAAT
66 AAAGAAAGAGTTACAAAAT
* *
272145 GAAAATAAATCAATGAGTTTAGAAAAT-A-ATTCTTTTAAAAAGAAAATAAATGAATT--AGAAG
1 GAAAATAAATCAATAAGTGTAGAAAATCATATTC--TTAAAAAGAAAATAAATGAATTAGAGAAG
272206 AGAAAAGAAATGAGTT
64 AG-AAAGAAA-GAGTT
272222 GCAAGTCGAA
Statistics
Matches: 65, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
82 11 0.17
83 6 0.09
84 48 0.74
ACGTcount: A:0.53, C:0.04, G:0.17, T:0.25
Consensus pattern (84 bp):
GAAAATAAATCAATAAGTGTAGAAAATCATATTCTTAAAAAGAAAATAAATGAATTAGAGAAGAG
AAAGAAAGAGTTACAAAAT
Found at i:273757 original size:13 final size:13
Alignment explanation
Indices: 273739--273763 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
273729 TTTTCCAGAT
273739 TGTATCGATACAA
1 TGTATCGATACAA
273752 TGTATCGATACA
1 TGTATCGATACA
273764 TTGCTTCAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:274522 original size:21 final size:21
Alignment explanation
Indices: 274498--274540 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
274488 TTGGTATAAA
274498 TTTGGTTTTATCAACTTAGCT
1 TTTGGTTTTATCAACTTAGCT
274519 TTTGGTTTTATCAACTTAGCT
1 TTTGGTTTTATCAACTTAGCT
274540 T
1 T
274541 ATGATCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.14, G:0.14, T:0.53
Consensus pattern (21 bp):
TTTGGTTTTATCAACTTAGCT
Found at i:274649 original size:31 final size:30
Alignment explanation
Indices: 274594--274660 Score: 82
Period size: 29 Copynumber: 2.2 Consensus size: 30
274584 GGGTGACAAC
*
274594 GTATTAAGGGAGAGAGTTGGTAAACATTT-
1 GTATTAAGGGAGAGAGTTGATAAACATTTG
* *
274623 GTATTAAGGGGGAGAGTTTGCATAAACTTTTG
1 GTATTAAGGGAGAGAG-TTG-ATAAACATTTG
274655 GTATTA
1 GTATTA
274661 GTTGCATGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 15 0.47
30 3 0.09
31 8 0.25
32 6 0.19
ACGTcount: A:0.31, C:0.04, G:0.30, T:0.34
Consensus pattern (30 bp):
GTATTAAGGGAGAGAGTTGATAAACATTTG
Found at i:275577 original size:13 final size:13
Alignment explanation
Indices: 275559--275584 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
275549 TACAGCAAGT
275559 ATGTATCGATACA
1 ATGTATCGATACA
275572 ATGTATCGATACA
1 ATGTATCGATACA
275585 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:276105 original size:34 final size:35
Alignment explanation
Indices: 276042--276108 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
276032 CTAAGTGATT
276042 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
276078 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
276109 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:281885 original size:13 final size:13
Alignment explanation
Indices: 281867--281893 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
281857 ACAAAGATCA
281867 AATGTATCGATAC
1 AATGTATCGATAC
281880 AATGTATCGATAC
1 AATGTATCGATAC
281893 A
1 A
281894 TTGAGTAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:281969 original size:19 final size:19
Alignment explanation
Indices: 281945--281994 Score: 82
Period size: 19 Copynumber: 2.6 Consensus size: 19
281935 AGCGATACAT
281945 TGTATCGATACAAAACTTA
1 TGTATCGATACAAAACTTA
*
281964 TGTATCGATACAACACTTA
1 TGTATCGATACAAAACTTA
*
281983 TGTACCGATACA
1 TGTATCGATACA
281995 TTGTATCGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.38, C:0.20, G:0.12, T:0.30
Consensus pattern (19 bp):
TGTATCGATACAAAACTTA
Found at i:288812 original size:42 final size:42
Alignment explanation
Indices: 288742--288872 Score: 165
Period size: 42 Copynumber: 3.1 Consensus size: 42
288732 AAATCTCACT
* * * *
288742 AAACTTCTTCATCTTTTTGTTTGCCCATCGGTTCAAACCTAGG
1 AAACTTTTTCA-CTTTTTATTTTCCCATCGATTCAAACCTAGG
*
288785 AAACTTTTTCACTTTCTATTTTCCCATCGATT-AAGACCTAGG
1 AAACTTTTTCACTTTTTATTTTCCCATCGATTCAA-ACCTAGG
* **
288827 AAACTTTTTCACTTTTTATTTTCCTATCGATTCAGCCCTAGG
1 AAACTTTTTCACTTTTTATTTTCCCATCGATTCAAACCTAGG
288869 AAAC
1 AAAC
288873 AACCTTTTAT
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
41 2 0.03
42 64 0.83
43 11 0.14
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.40
Consensus pattern (42 bp):
AAACTTTTTCACTTTTTATTTTCCCATCGATTCAAACCTAGG
Found at i:289205 original size:42 final size:41
Alignment explanation
Indices: 289158--290091 Score: 202
Period size: 42 Copynumber: 22.1 Consensus size: 41
289148 TCCTACCCTC
* *
289158 AGTCTACCTATCAGCTTTGACTTTGGAGACTGCCTTATCTAA
1 AGTCTACCTGTC-GCTTTGACCTTGGAGACTGCCTTATCTAA
* * * * *
289200 AGTCTACCTGTTGGCTTTGACCTTGGAAACTTTCC-TACCCT-C
1 AGTCTACCTG-TCGCTTTGACCTTGGAGAC-TGCCTTA-TCTAA
* * * * *
289242 AGTCTGCTTGTCGACTTTAACTTTAGAGACTGCCTTATCTAA
1 AGTCTACCTGTCG-CTTTGACCTTGGAGACTGCCTTATCTAA
* * *** * *
289284 AGTCTACTTGTCGCTTTGACCCTGGAGACTTTTTTACCCT-T
1 AGTCTACCTGTCGCTTTGACCTTGGAGACTGCCTTA-TCTAA
* * * * * *
289325 AGTATCCCTATCGGCCTTGACCCTGAAGACTGCCTTATCTAA
1 AGTCTACCTGTC-GCTTTGACCTTGGAGACTGCCTTATCTAA
* * * * * ** **
289367 ATTTTTCCTGTTGGCTTTAACCTTGGAGACTTTCTTACTCTTC
1 AGTCTACCTG-TCGCTTTGACCTTGGAGACTGCCTTA-TCTAA
* * * * * **
289410 ATTCGACCAGTCAGGCTTTGACCCTAGAGACTATCTTATCTAA
1 AGTCTACCTGTC--GCTTTGACCTTGGAGACTGCCTTATCTAA
* * ** * ** * **
289453 AGTCTGCCTATTAACTTTGACCTTAGAGACTTTCTTACCTTT
1 AGTCTACCT-GTCGCTTTGACCTTGGAGACTGCCTTATCTAA
* * * * *
289495 AGTCTGCCTGTCAGCTTTGACCTTAGAGCCTGTCTCATCTAA
1 AGTCTACCTGTC-GCTTTGACCTTGGAGACTGCCTTATCTAA
* * * * *** *
289537 AGTCTGCCTATCGGATTTGACATTGGAGACTTTTTTACATCTGA
1 AGTCTACCTGTC-GCTTTGACCTTGGAGACTGCCTT--ATCTAA
* * *
289581 A-TCTGCCTGTCGGCTTTGAACC-TAGAGACTAG-TTTATCTAA
1 AGTCTACCTGTC-GCTTTG-ACCTTGGAGACT-GCCTTATCTAA
* * ** * * ** * **
289622 AGTTTGCCTAACGACTTTGACCCTAGAGACTTTTCTTACCCTTC
1 AGTCTACCTGTCG-CTTTGACCTTGGAGAC-TGCCTTA-TCTAA
** * * * * ** * **
289666 AGTCTGTC-ATCAGCTTTGACCCTGTAAACTTTCTTACCCTTT
1 AGTCTACCTGTC-GCTTTGACCTTGGAGACTGCCTTA-TCTAA
* * * * *
289708 AGTCTGCCTGTCAACTTTGACCCTAGAGACTACCTTATCTAA
1 AGTCTACCTGTC-GCTTTGACCTTGGAGACTGCCTTATCTAA
*
289750 AGAT-TACCTGTCAGCTTTGACCTTGGAGAGTGCCTTATCTAA
1 AG-TCTACCTGTC-GCTTTGACCTTGGAGACTGCCTTATCTAA
* * * * *
289792 AGTCTGCCTATCGACTTTGATCC-TGGAAACTACCTTCTCTAA
1 AGTCTACCTGTCG-CTTTGA-CCTTGGAGACTGCCTTATCTAA
* * ** ** * *
289834 AGTCTGCCTAGTCAGCTTTGACCCTACAGACTTTCTTACCCT-T
1 AGTCTACCT-GTC-GCTTTGACCTTGGAGACTGCCTTA-TCTAA
* * * * * * *
289877 AGTTTGCCTATCGATTTTGACCCTAGAGACTGCTTTATCTAA
1 AGTCTACCTGTCG-CTTTGACCTTGGAGACTGCCTTATCTAA
* * * * * * ** * *
289919 AGTTTGCTTGTCGAATTTGACCCTAGAGACTTTCTTACACT-C
1 AGTCTACCTGTCG-CTTTGACCTTGGAGACTGCCTTA-TCTAA
* * *
289961 AGTCTGCTTGTCAGCTTTGACCTTGGAGACTACCTTATCTAA
1 AGTCTACCTGTC-GCTTTGACCTTGGAGACTGCCTTATCTAA
* * * *
290003 AGTCTGCCTGTCGGTTTTGACCTTGGAGACTTTCC-TATCCT-C
1 AGTCTACCTGTC-GCTTTGACCTTGGAGAC-TGCCTTAT-CTAA
* * *
290045 AGTCTATCTGTTGGCTTTGACATTGGAGACTGCCTTATCTAA
1 AGTCTACCTG-TCGCTTTGACCTTGGAGACTGCCTTATCTAA
290087 AGTCT
1 AGTCT
290092 TTTGACCTGA
Statistics
Matches: 664, Mismatches: 183, Indels: 90
0.71 0.20 0.10
Matches are distributed among these distances:
41 56 0.08
42 442 0.67
43 125 0.19
44 41 0.06
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.37
Consensus pattern (41 bp):
AGTCTACCTGTCGCTTTGACCTTGGAGACTGCCTTATCTAA
Found at i:289539 original size:84 final size:84
Alignment explanation
Indices: 289072--289865 Score: 442
Period size: 84 Copynumber: 9.4 Consensus size: 84
289062 TTTCCTATCG
* * * * ** * * * *
289072 TCAGTCTACTTGTCGGCTTTGACCCTAGAGACTACCACATCTAAAGTCTGCTTGTCGACTTTTAC
1 TCAGTCTGCCTGTCAGCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTGCCTATTGACTTTGAC
* ** * *
289137 CCTAAAGACTTTCCTACCC
66 CTTGGAGACTTTCTTACCT
* * ** * * * *
289156 TCAGTCTACCTATCAGCTTTGACTTTGGAGACTGCCTTATCTAAAGTCTACCTGTTGGCTTTGAC
1 TCAGTCTGCCTGTCAGCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTGCCTATTGACTTTGAC
* * *
289221 CTTGGAAACTTTCCTACCC
66 CTTGGAGACTTTCTTACCT
* * ** * * * *
289240 TCAGTCTGCTTGTC-GACTTTAACTTTAGAGACTGCCTTATCTAAAGTCTACTTGTCG-CTTTGA
1 TCAGTCTGCCTGTCAG-CTTTGACCCTAGAGACTGCCTTATCTAAAGTCTGCCTATTGACTTTGA
* *
289303 CCCTGGAGACTTTTTTACCCT
65 CCTTGGAGACTTTCTTA-CCT
* * * * * * * * * * *
289324 T-AGTATCCCTATCGGCCTTGACCCT-GAAGACTGCCTTATCTAAATTTTTCCTGTTGGCTTTAA
1 TCAGTCTGCCTGTCAGCTTTGACCCTAG-AGACTGCCTTATCTAAAGTCTGCCTATTGACTTTGA
289387 CCTTGGAGACTTTCTTACTCT
65 CCTTGGAGACTTTCTTAC-CT
* * ** *
289408 TCATTC-GACCAGTCAGGCTTTGACCCTAGAGACTATCTTATCTAAAGTCTGCCTATTAACTTTG
1 TCAGTCTG-CCTGTCA-GCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTGCCTATTGACTTTG
*
289472 ACCTTAGAGACTTTCTTACCT
64 ACCTTGGAGACTTTCTTACCT
* * * * * *
289493 TTAGTCTGCCTGTCAGCTTTGACCTTAGAGCCTGTCTCATCTAAAGTCTGCCTATCGGA-TTTGA
1 TCAGTCTGCCTGTCAGCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTGCCTAT-TGACTTTGA
* * *
289557 CATTGGAGACTTTTTTACAT
65 CCTTGGAGACTTTCTTACCT
* * * * * * **
289577 CTGAATCTGCCTGTCGGCTTTGAACCTAGAGACTAG-TTTATCTAAAGTTTGCCTAACGACTTTG
1 -TCAGTCTGCCTGTCAGCTTTGACCCTAGAGACT-GCCTTATCTAAAGTCTGCCTATTGACTTTG
* *
289641 ACCCTAGAGACTTTTCTTACCCT
64 ACCTTGGAGAC-TTTCTTA-CCT
* * * ** * ** * **
289664 TCAGTCTGTC-ATCAGCTTTGACCCT-GTAAACTTTCTTACCCTTTAGTCTGCCTGTCAACTTTG
1 TCAGTCTGCCTGTCAGCTTTGACCCTAG-AGACTGCCTTA-TCTAAAGTCTGCCTATTGACTTTG
* * ** *
289727 ACCCTAGAGACTACCTTATCT
64 ACCTTGGAGACTTTCTTACCT
** * * * * *
289748 AAAGAT-TACCTGTCAGCTTTGACCTTGGAGAGTGCCTTATCTAAAGTCTGCCTATCGACTTTGA
1 TCAG-TCTGCCTGTCAGCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTGCCTATTGACTTTGA
* **
289812 TCC-TGGAAACTACCTT-CTCT
65 -CCTTGGAGACTTTCTTAC-CT
** *
289832 AAAGTCTGCCTAGTCAGCTTTGACCCTACAGACT
1 TCAGTCTGCCT-GTCAGCTTTGACCCTAGAGACT
289866 TTCTTACCCT
Statistics
Matches: 549, Mismatches: 134, Indels: 53
0.75 0.18 0.07
Matches are distributed among these distances:
82 1 0.00
83 60 0.11
84 248 0.45
85 139 0.25
86 98 0.18
87 3 0.01
ACGTcount: A:0.22, C:0.27, G:0.16, T:0.36
Consensus pattern (84 bp):
TCAGTCTGCCTGTCAGCTTTGACCCTAGAGACTGCCTTATCTAAAGTCTGCCTATTGACTTTGAC
CTTGGAGACTTTCTTACCT
Found at i:289697 original size:43 final size:43
Alignment explanation
Indices: 289626--289734 Score: 123
Period size: 43 Copynumber: 2.5 Consensus size: 43
289616 ATCTAAAGTT
* * *
289626 TGCCTAACGACTTTGACCCTAGAGACTTTTCTTACCCTTCAGTC
1 TGCCTATCAACTTTGACCCTAGAAAC-TTTCTTACCCTTCAGTC
* * *
289670 TGTC-ATCAGCTTTGACCCT-GTAAACTTTCTTACCCTTTAGTC
1 TGCCTATCAACTTTGACCCTAG-AAACTTTCTTACCCTTCAGTC
*
289712 TGCCTGTCAACTTTGACCCTAGA
1 TGCCTATCAACTTTGACCCTAGA
289735 GACTACCTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
42 20 0.38
43 29 0.55
44 4 0.08
ACGTcount: A:0.20, C:0.30, G:0.14, T:0.36
Consensus pattern (43 bp):
TGCCTATCAACTTTGACCCTAGAAACTTTCTTACCCTTCAGTC
Found at i:289918 original size:85 final size:83
Alignment explanation
Indices: 289419--290578 Score: 523
Period size: 84 Copynumber: 13.9 Consensus size: 83
289409 CATTCGACCA
* * * ** * *
289419 GTCAGGCTTTGACCCTAGAGACTATCTTA-TCTAAAGTCTGCCTATTAACTTTGACCTTAGAGAC
1 GTCA-GCTTTGACCCTAGAGACTTTCTTACCCT-TAGTCTGCCTATCGACTTTGACCCTGGAGAC
** * **
289483 TTTCTTACCTTTAGTCTGCCT
64 TACCTTATCTAAAGTCTG-CT
* * * * * * **
289504 GTCAGCTTTGACCTTAGAGCCTGTCTCA-TCTAAAGTCTGCCTATCGGA-TTTGACATTGGAGAC
1 GTCAGCTTTGACCCTAGAGACTTTCTTACCCT-TAGTCTGCCTATC-GACTTTGACCCTGGAGAC
*** *
289567 TTTTTTACATCTGAA-TCTGCCT
64 TACCTT--ATCTAAAGTCTG-CT
* * * * * * * *
289589 GTCGGCTTTGAACCTAGAGACTAGT-TTA-TCTAAAGTTTGCCTAACGACTTTGACCCTAGAGAC
1 GTCAGCTTTGACCCTAGAGACT-TTCTTACCCT-TAGTCTGCCTATCGACTTTGACCCTGGAGAC
** * **
289652 TTTTCTTACCCTTCAGTCTG-T
64 -TACCTTA-TCTAAAGTCTGCT
* * * * *
289673 CATCAGCTTTGACCCT-GTAAACTTTCTTACCCTTTAGTCTGCCTGTCAACTTTGACCCTAGAGA
1 -GTCAGCTTTGACCCTAG-AGACTTTCTTACCC-TTAGTCTGCCTATCGACTTTGACCCTGGAGA
*
289737 CTACCTTATCTAAAGAT-TACCT
63 CTACCTTATCTAAAG-TCT-GCT
* * * ** * * * *
289759 GTCAGCTTTGACCTTGGAGAGTGCCTTA-TCTAAAGTCTGCCTATCGACTTTGATCCTGGAAACT
1 GTCAGCTTTGACCCTAGAGACTTTCTTACCCT-TAGTCTGCCTATCGACTTTGACCCTGGAGACT
*
289823 ACCTTCTCTAAAGTCTGCCT
65 ACCTTATCTAAAGTCTG-CT
* * * *
289843 AGTCAGCTTTGACCCTACAGACTTTCTTACCCTTAGTTTGCCTATCGATTTTGACCCTAGAGACT
1 -GTCAGCTTTGACCCTAGAGACTTTCTTACCCTTAGTCTGCCTATCGACTTTGACCCTGGAGACT
* * *
289908 GCTTTATCTAAAGTTTGCTT
65 ACCTTATCTAAAGTCTGC-T
* * * * * *
289928 GTC-GAATTTGACCCTAGAGACTTTCTTACACTCAGTCTGCTTGTC-AGCTTTGACCTTGGAGAC
1 GTCAG-CTTTGACCCTAGAGACTTTCTTACCCTTAGTCTGCCTATCGA-CTTTGACCCTGGAGAC
289991 TACCTTATCTAAAGTCTGCCT
64 TACCTTATCTAAAGTCTG-CT
* * * * * * * ** * * * ** *
290012 GTCGGTTTTGACCTTGGAGACTTTCCTATCCTCAGTCTATCTGTTGGCTTTGACATTGGAGACTG
1 GTCAGCTTTGACCCTAGAGACTTTCTTACCCTTAGTCTGCCTATCGACTTTGACCCTGGAGACTA
290077 CCTTATCTAAAG--T-C-
66 CCTTATCTAAAGTCTGCT
* * * * *
290091 -T----TTTGA-CCT-GAAGACTTTTTTACATCTTAGTTTGCCTAT-TAGCTTTGACACTGGAGA
1 GTCAGCTTTGACCCTAG-AGACTTTCTTAC-CCTTAGTCTGCCTATCGA-CTTTGACCCTGGAGA
*
290148 CTACCTTATCTAAAGTCCGCTT
63 CTACCTTATCTAAAGTCTGC-T
* * * * * * * * * *
290170 GGCGGCTTTGACCTTGGAGACTTTTTTTACCTTTTAGTTTACCTATTGACTTTGACCCTAGAGAC
1 GTCAGCTTTGACCCTAGAGAC-TTTCTTACC-CTTAGTCTGCCTATCGACTTTGACCCTGGAGAC
*
290235 T-GCTTATCTAAAGTCTGCCT
64 TACCTTATCTAAAGTCTG-CT
* * * * * * *
290255 AT-TGACTTTGACCTTGGAGAATTTCTTACCCTCAGTCTGCCTATCGACTTTGACCCTAGAGACT
1 GTCAG-CTTTGACCCTAGAGACTTTCTTACCCTTAGTCTGCCTATCGACTTTGACCCTGGAGACT
*** * **
290319 TTTTTATATTTCAGTCTGCT
65 ACCTTAT-CTAAAGTCTGCT
* * * * * *
290339 GTCGGCTTTGACCTTTGAGACTTTCTTACCTTTCAGTCTG-GT-T----TTTGACCTTGGAGACT
1 GTCAGCTTTGACCCTAGAGACTTTCTTACCCTT-AGTCTGCCTATCGACTTTGACCCTGGAGACT
* *
290398 ACTTTATCTAAAGTTTGCTT
65 ACCTTATCTAAAGTCTGC-T
* * * * * * * *
290418 GTC-GACTTTAACCCTAGAAACTTTCTTACCTTTCAGTCTACCTGTTGGCTTTGACCCTTGAGAC
1 GTCAG-CTTTGACCCTAGAGACTTTCTTACCCTT-AGTCTGCCTATCGACTTTGACCCTGGAGAC
*
290482 TATCTTATCTAAAGTCTGCTT
64 TACCTTATCTAAAGTCTGC-T
* * * * * * * *
290503 GTCAGCTTTGACCCTAGAGACTTTCCTACCCTCAGTCTGCTTGTCGATTTTTACCTTGGAGACTG
1 GTCAGCTTTGACCCTAGAGACTTTCTTACCCTTAGTCTGCCTATCGACTTTGACCCTGGAGACTA
290568 CCTTATCTAAA
66 CCTTATCTAAA
290579 ATCTACCTAT
Statistics
Matches: 832, Mismatches: 182, Indels: 123
0.73 0.16 0.11
Matches are distributed among these distances:
72 1 0.00
73 11 0.01
74 42 0.05
77 1 0.00
78 9 0.01
79 53 0.06
80 2 0.00
81 1 0.00
82 1 0.00
83 34 0.04
84 313 0.38
85 278 0.33
86 84 0.10
87 2 0.00
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.38
Consensus pattern (83 bp):
GTCAGCTTTGACCCTAGAGACTTTCTTACCCTTAGTCTGCCTATCGACTTTGACCCTGGAGACTA
CCTTATCTAAAGTCTGCT
Found at i:290207 original size:86 final size:83
Alignment explanation
Indices: 290092--290249 Score: 210
Period size: 86 Copynumber: 1.9 Consensus size: 83
290082 TCTAAAGTCT
* *
290092 TTTGACCTGAAGACTTTTTTACATCTTAGTTTGCCTATT-AGCTTTGACACTGGAGACTACCTTA
1 TTTGACCTGAAGACTTTTTTACATCTTAGTTTACCTATTGA-CTTTGACACTAGAGACT-CCTTA
290156 TCTAAAGTCCGCTTGGCGGC
64 TCTAAAGTCCGCTTGGCGGC
* * * * *
290176 TTTGACCTTGGAGACTTTTTTTACCTTTTAGTTTACCTATTGACTTTGACCCTAGAGACTGCTTA
1 TTTGACC-TGAAGAC-TTTTTTACATCTTAGTTTACCTATTGACTTTGACACTAGAGACTCCTTA
290241 TCTAAAGTC
64 TCTAAAGTC
290250 TGCCTATTGA
Statistics
Matches: 64, Mismatches: 7, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
84 7 0.11
85 19 0.30
86 37 0.58
87 1 0.02
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.40
Consensus pattern (83 bp):
TTTGACCTGAAGACTTTTTTACATCTTAGTTTACCTATTGACTTTGACACTAGAGACTCCTTATC
TAAAGTCCGCTTGGCGGC
Found at i:290304 original size:42 final size:42
Alignment explanation
Indices: 290175--290779 Score: 185
Period size: 42 Copynumber: 14.4 Consensus size: 42
290165 CGCTTGGCGG
* * * * * *
290175 CTTTGACCTTGGAGACTTTTTTTACCTTTTAGTTTACCTATTGA
1 CTTTGACCTTAGAGAC-TTTCTTACC-TTCAGTCTGCCTATCGA
* * * ** *
290219 CTTTGACCCTAGAGAC-TGCTTATCTAAAGTCTGCCTATTGA
1 CTTTGACCTTAGAGACTTTCTTACCTTCAGTCTGCCTATCGA
* * *
290260 CTTTGACCTTGGAGAATTTCTTACCCTCAGTCTGCCTATCGA
1 CTTTGACCTTAGAGACTTTCTTACCTTCAGTCTGCCTATCGA
* * ** * *
290302 CTTTGACCCTAGAGACTTTTTTATATTTCAGTCTG-CTGTCGG
1 CTTTGACCTTAGAGACTTTCTTA-CCTTCAGTCTGCCTATCGA
* *
290344 CTTTGACCTTTGAGACTTTCTTACCTTTCAGTCTG-GT-T---
1 CTTTGACCTTAGAGACTTTCTTACC-TTCAGTCTGCCTATCGA
* * * ** * * *
290382 -TTTGACCTTGGAGAC-TACTTTATCTAAAGTTTGCTTGTCGA
1 CTTTGACCTTAGAGACTTTC-TTACCTTCAGTCTGCCTATCGA
* * * * * * *
290423 CTTTAACCCTAGAAACTTTCTTACCTTTCAGTCTACCTGTTGG
1 CTTTGACCTTAGAGACTTTCTTACC-TTCAGTCTGCCTATCGA
* * ** * *
290466 CTTTGACCCTT-GAGACTATCTTATCTAAAGTCTGCTTGTC-A
1 CTTTGA-CCTTAGAGACTTTCTTACCTTCAGTCTGCCTATCGA
* * * * *
290507 GCTTTGACCCTAGAGACTTTCCTACCCTCAGTCTGCTTGTCGA
1 -CTTTGACCTTAGAGACTTTCTTACCTTCAGTCTGCCTATCGA
* * * ** * ** * *
290550 TTTTTACCTTGGAGACTGCCTTATCTAAAATCTACCTATCGA
1 CTTTGACCTTAGAGACTTTCTTACCTTCAGTCTGCCTATCGA
* * ** * ** * *
290592 TTTTGACCCT-GAAGACTACCTTATCTAAAGTCTGCCTGTCGG
1 CTTTGACCTTAG-AGACTTTCTTACCTTCAGTCTGCCTATCGA
* * * *
290634 CTTTGACCCTAGAGACTTTTTTTACCCTTTAGTCTG-C-AGTTGA
1 CTTTGACCTTAGAGAC-TTTCTTA-CCTTCAGTCTGCCTA-TCGA
* * * * * * **
290677 CTTTGACCTTGGAGACTTTCTCACCCTTTAGTCTACTTGTTAA
1 CTTTGACCTTAGAGACTTTCTTA-CCTTCAGTCTGCCTATCGA
* * * * * **
290720 CTTTAACCCTAGAGACTTTTTTACCTTTTAGTCTACCTATAAA
1 CTTTGACCTTAGAGACTTTCTTACC-TTCAGTCTGCCTATCGA
* *
290763 CTTTGACCCTGGAGACT
1 CTTTGACCTTAGAGACT
290780 GCCTTATTTA
Statistics
Matches: 416, Mismatches: 121, Indels: 49
0.71 0.21 0.08
Matches are distributed among these distances:
36 8 0.02
37 19 0.05
38 1 0.00
41 31 0.07
42 223 0.54
43 109 0.26
44 25 0.06
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (42 bp):
CTTTGACCTTAGAGACTTTCTTACCTTCAGTCTGCCTATCGA
Found at i:290421 original size:79 final size:80
Alignment explanation
Indices: 290134--290546 Score: 248
Period size: 85 Copynumber: 5.0 Consensus size: 80
290124 GCCTATTAGC
* * * * * * * *
290134 TTTGACACTGGAGACTACCTTATCTAAAGTCCGCTTGGCGGCTTTGACCTTGGAGACTTTTTTTA
1 TTTGACCCTTGAGACTATCTTATCTAAAGTCTGCTTGTCGGCTTTGACCCTAGAGAC-TTTCTTA
* *
290199 CCTTTTAGTTTACCT-ATTG
65 CCTTTCAG--T--CTGGTTG
* * * * * * * * *
290218 ACTTTGACCCTAGAGACT-GCTTATCTAAAGTCTGCCTATTGACTTTGACCTTGGAGAATTTCTT
1 --TTTGACCCTTGAGACTATCTTATCTAAAGTCTGCTTGTCGGCTTTGACCCTAGAGACTTTCTT
* *
290282 ACC-CTCAGTCTGCCTATCG
64 ACCTTTCAGTCTG-GT-T-G
* * * * ** * *
290301 ACTTTGACCCTAGAGACTTTTTTATATTTCAGTCTGC-TGTCGGCTTTGACCTTTGAGACTTTCT
1 --TTTGACCCTTGAGACTATCTTAT-CTAAAGTCTGCTTGTCGGCTTTGACCCTAGAGACTTTCT
290365 TACCTTTCAGTCTGGTT-
63 TACCTTTCAGTCTGGTTG
* * * *
290382 TTTGA-CCTTGGAGACTA-CTTTATCTAAAGTTTGCTTGTCGACTTTAACCCTAGAAACTTTCTT
1 TTTGACCCTT-GAGACTATC-TTATCTAAAGTCTGCTTGTCGGCTTTGACCCTAGAGACTTTCTT
*
290445 ACCTTTCAGTCTACCTGTTGG
64 ACCTTTCAGTCT---GGTT-G
* *
290466 CTTTGACCCTTGAGACTATCTTATCTAAAGTCTGCTTGTCAGCTTTGACCCTAGAGACTTTCCTA
1 -TTTGACCCTTGAGACTATCTTATCTAAAGTCTGCTTGTCGGCTTTGACCCTAGAGACTTTCTTA
* *
290531 CC-CTCAGTCTGCTTG
65 CCTTTCAGTCTGGTTG
290546 T
1 T
290547 CGATTTTTAC
Statistics
Matches: 261, Mismatches: 48, Indels: 43
0.74 0.14 0.12
Matches are distributed among these distances:
78 10 0.04
79 53 0.20
80 1 0.00
81 4 0.02
82 4 0.02
83 23 0.09
84 46 0.18
85 101 0.39
86 19 0.07
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.39
Consensus pattern (80 bp):
TTTGACCCTTGAGACTATCTTATCTAAAGTCTGCTTGTCGGCTTTGACCCTAGAGACTTTCTTAC
CTTTCAGTCTGGTTG
Found at i:290683 original size:43 final size:43
Alignment explanation
Indices: 290634--290779 Score: 161
Period size: 43 Copynumber: 3.4 Consensus size: 43
290624 TGCCTGTCGG
* *
290634 CTTTGACCCTAGAGACTTTTTTTACCCTTTAGTCTGC-AGTTGA
1 CTTTGACCCTAGAGAC-TTTTTTACCCTTTAGTCTACTAGTTAA
* * * * *
290677 CTTTGACCTTGGAGACTTTCTCACCCTTTAGTCTACTTGTTAA
1 CTTTGACCCTAGAGACTTTTTTACCCTTTAGTCTACTAGTTAA
* * *
290720 CTTTAACCCTAGAGACTTTTTTACCTTTTAGTCTACCTA-TAAA
1 CTTTGACCCTAGAGACTTTTTTACCCTTTAGTCTA-CTAGTTAA
*
290763 CTTTGACCCTGGAGACT
1 CTTTGACCCTAGAGACT
290780 GCCTTATTTA
Statistics
Matches: 84, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
42 17 0.20
43 65 0.77
44 2 0.02
ACGTcount: A:0.21, C:0.25, G:0.14, T:0.40
Consensus pattern (43 bp):
CTTTGACCCTAGAGACTTTTTTACCCTTTAGTCTACTAGTTAA
Found at i:290818 original size:42 final size:42
Alignment explanation
Indices: 290763--290863 Score: 130
Period size: 42 Copynumber: 2.4 Consensus size: 42
290753 TACCTATAAA
* * *
290763 CTTTGACCCTGGAGACTGCCTTATTTAAAGACTGCCTATCGG
1 CTTTGACCTTGGAGACTGCCTTATCTAAAGACTCCCTATCGG
* * ** *
290805 CTTTAACCTTGGAGATTGCCTTATCTAAAGTTTCCCTGTCGG
1 CTTTGACCTTGGAGACTGCCTTATCTAAAGACTCCCTATCGG
290847 CTTTGACCTTGGAGACT
1 CTTTGACCTTGGAGACT
290864 TTTCTACCCT
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.20, C:0.25, G:0.21, T:0.35
Consensus pattern (42 bp):
CTTTGACCTTGGAGACTGCCTTATCTAAAGACTCCCTATCGG
Found at i:291012 original size:85 final size:83
Alignment explanation
Indices: 290823--291036 Score: 214
Period size: 85 Copynumber: 2.5 Consensus size: 83
290813 TTGGAGATTG
* * * * * *
290823 CCTTATCTAAAGTTTCCCTGTCGGCTTTGACCTTGGAGACTTTTCTACCCTCAGTATACCCGTCA
1 CCTTATCTAAAGTCTGCCTGTCAGCTTTGACC-TGGAGACTTTTTTACCCTCAGTAGACACGTCA
*
290888 GCCTTGACCTTAAAGACTA
65 GCCTTGAACTTAAAGACTA
* * * * * * *
290907 CCTCATTTAAATTCTGCCTGTCAGCTTTAATCCTGGAGACTTTTTTACCCTTCAGTCGGCATGTC
1 CCTTATCTAAAGTCTGCCTGTCAGCTTTGA-CCTGGAGACTTTTTTACCC-TCAGTAGACACGTC
* * *
290972 AGCTTTGAACTTGAAGACTG
64 AGCCTTGAACTTAAAGACTA
* *
290992 CTTTATCTAAAGTCTGCCTGTCAGCTTTGACCCTAGAGA-TTTTTT
1 CCTTATCTAAAGTCTGCCTGTCAGCTTTGA-CCTGGAGACTTTTTT
291037 CACATTTTGT
Statistics
Matches: 104, Mismatches: 24, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
84 45 0.43
85 59 0.57
ACGTcount: A:0.21, C:0.26, G:0.16, T:0.36
Consensus pattern (83 bp):
CCTTATCTAAAGTCTGCCTGTCAGCTTTGACCTGGAGACTTTTTTACCCTCAGTAGACACGTCAG
CCTTGAACTTAAAGACTA
Found at i:291572 original size:17 final size:16
Alignment explanation
Indices: 291548--291604 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 16
291538 ATAAGTAAAG
291548 TCAAAAATTAAAAAAA
1 TCAAAAATTAAAAAAA
291564 TCTAAAAATT-AAAAAA
1 TC-AAAAATTAAAAAAA
*
291580 TCAAAGAAATAAAAAAA
1 TCAAA-AATTAAAAAAA
291597 TTCAAAAA
1 -TCAAAAA
291605 ATTCAAAGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
15 3 0.08
16 13 0.36
17 15 0.42
18 5 0.14
ACGTcount: A:0.72, C:0.07, G:0.02, T:0.19
Consensus pattern (16 bp):
TCAAAAATTAAAAAAA
Found at i:291606 original size:17 final size:16
Alignment explanation
Indices: 291548--291606 Score: 73
Period size: 16 Copynumber: 3.6 Consensus size: 16
291538 ATAAGTAAAG
*
291548 TCAAAAATTAAAAAAA
1 TCAAAAAATAAAAAAA
* *
291564 TCTAAAAATTAAAAAA
1 TCAAAAAATAAAAAAA
291580 TCAAAGAAATAAAAAAA
1 TCAAA-AAATAAAAAAA
291597 TTCAAAAAAT
1 -TCAAAAAAT
291607 TCAAAGAAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
16 17 0.47
17 14 0.39
18 5 0.14
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (16 bp):
TCAAAAAATAAAAAAA
Found at i:291608 original size:9 final size:9
Alignment explanation
Indices: 291550--291611 Score: 60
Period size: 9 Copynumber: 7.2 Consensus size: 9
291540 AAGTAAAGTC
291550 AAAAATT-A
1 AAAAATTCA
* *
291558 AAAAAATCT
1 AAAAATTCA
291567 AAAAATT-A
1 AAAAATTCA
291575 AAAAA-TCA
1 AAAAATTCA
*
291583 AAGAAA-TAA
1 AA-AAATTCA
291592 AAAAATTCA
1 AAAAATTCA
291601 AAAAATTCA
1 AAAAATTCA
291610 AA
1 AA
291612 GAAGAAAGAA
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
7 1 0.02
8 17 0.39
9 26 0.59
ACGTcount: A:0.73, C:0.06, G:0.02, T:0.19
Consensus pattern (9 bp):
AAAAATTCA
Found at i:291798 original size:30 final size:29
Alignment explanation
Indices: 291742--291812 Score: 90
Period size: 30 Copynumber: 2.4 Consensus size: 29
291732 TATACATAAA
*
291742 CATTTCATGC-TTCATGCATGCATATGTT
1 CATTTCATGCATACATGCATGCATATGTT
*
291770 CATTTCATGCATACATGCATTTCATATGTT
1 CATTTCATGCATACATGCA-TGCATATGTT
*
291800 CATCTCATTGCAT
1 CATTTCA-TGCAT
291813 CGCTTTCATT
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 10 0.27
29 7 0.19
30 15 0.41
31 5 0.14
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (29 bp):
CATTTCATGCATACATGCATGCATATGTT
Found at i:297700 original size:19 final size:18
Alignment explanation
Indices: 297676--297738 Score: 73
Period size: 19 Copynumber: 3.7 Consensus size: 18
297666 AATGTATAAC
297676 TGTATCGATACATAAGTGT
1 TGTATCGATACATAAGT-T
297695 TGTATCGATAC--AA---
1 TGTATCGATACATAAGTT
297708 TGTATCGATACATAAGTTT
1 TGTATCGATACATAAG-TT
297727 TGTATCGATACA
1 TGTATCGATACA
297739 ATGTATCGCG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 11 0.29
15 2 0.05
17 2 0.05
19 23 0.61
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
TGTATCGATACATAAGTT
Found at i:297713 original size:13 final size:13
Alignment explanation
Indices: 297695--297719 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
297685 ACATAAGTGT
297695 TGTATCGATACAA
1 TGTATCGATACAA
297708 TGTATCGATACA
1 TGTATCGATACA
297720 TAAGTTTTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:297717 original size:32 final size:32
Alignment explanation
Indices: 297676--297746 Score: 133
Period size: 32 Copynumber: 2.2 Consensus size: 32
297666 AATGTATAAC
297676 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
297708 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
297740 TGTATCG
1 TGTATCG
297747 CGACAAAACT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:301027 original size:8 final size:8
Alignment explanation
Indices: 301014--301044 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
301004 TTTTTTGACT
301014 AAAAAAAC
1 AAAAAAAC
*
301022 AAAAAAAT
1 AAAAAAAC
301030 AAAAAAAC
1 AAAAAAAC
301038 AAAAAAA
1 AAAAAAA
301045 AAGGAAAAGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.90, C:0.06, G:0.00, T:0.03
Consensus pattern (8 bp):
AAAAAAAC
Found at i:301034 original size:16 final size:16
Alignment explanation
Indices: 301013--301044 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
301003 TTTTTTTGAC
301013 TAAAAAAACAAAAAAA
1 TAAAAAAACAAAAAAA
301029 TAAAAAAACAAAAAAA
1 TAAAAAAACAAAAAAA
301045 AAGGAAAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.88, C:0.06, G:0.00, T:0.06
Consensus pattern (16 bp):
TAAAAAAACAAAAAAA
Found at i:302167 original size:63 final size:62
Alignment explanation
Indices: 302042--302219 Score: 218
Period size: 63 Copynumber: 2.9 Consensus size: 62
302032 TAGGACACAG
* * * * * * *
302042 TTTTC-TTTTTAAAAGCCA-ATAAGTTAGTAGCATCTTTTAGTCCTTAAAGAGTAGGATACC
1 TTTTCTTTTTTAAAAGCCACACAAGCTAGTGGCACCTTTTAGTCCTCAAAGAGCAAGATACC
*
302102 TTTTCTTTTTTAAAAGCCCACACAAGCTAGTGGCACCTTTTAGTCCTCAAAGAGCAAGATGCC
1 TTTTCTTTTTTAAAAG-CCACACAAGCTAGTGGCACCTTTTAGTCCTCAAAGAGCAAGATACC
* *
302165 TTTTCCTCTTTT-AAAGTCCACACAAGCTAGTGGCACCTTTTAGTCCTCAGAGAGC
1 TTTT-CTTTTTTAAAAG-CCACACAAGCTAGTGGCACCTTTTAGTCCTCAAAGAGC
302220 CAAACACCTT
Statistics
Matches: 103, Mismatches: 11, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
60 5 0.05
61 10 0.10
62 3 0.03
63 79 0.77
64 6 0.06
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (62 bp):
TTTTCTTTTTTAAAAGCCACACAAGCTAGTGGCACCTTTTAGTCCTCAAAGAGCAAGATACC
Found at i:302230 original size:63 final size:63
Alignment explanation
Indices: 302013--302231 Score: 214
Period size: 63 Copynumber: 3.5 Consensus size: 63
302003 AACCTTTTAT
* * * * * * * *
302013 CCTTTAAGTTCTCAAAGAGTAGGACACAGTTTTCT-TTTTAAAAG-CCA-ATAAGTTAGTAGCA
1 CCTTTTAGTCCTCAAAGAGCAAGACAC-CTTTTCTCTTTTAAAAGCCCACACAAGCTAGTGGCA
* * * * * *
302074 TCTTTTAGTCCTTAAAGAGTAGGATACCTTTTCTTTTTTAAAAGCCCACACAAGCTAGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAAGACACCTTTTCTCTTTTAAAAGCCCACACAAGCTAGTGGCA
** *
302137 CCTTTTAGTCCTCAAAGAGCAAGATGCCTTTTCCTCTTTT-AAAGTCCACACAAGCTAGTGGCA
1 CCTTTTAGTCCTCAAAGAGCAAGACACCTTTT-CTCTTTTAAAAGCCCACACAAGCTAGTGGCA
*
302200 CCTTTTAGTCCTCAGAGAGCCAA-ACACCTTTT
1 CCTTTTAGTCCTCAAAGAG-CAAGACACCTTTT
302232 TTTCTTTTTC
Statistics
Matches: 134, Mismatches: 19, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
60 6 0.04
61 31 0.23
62 3 0.02
63 85 0.63
64 9 0.07
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (63 bp):
CCTTTTAGTCCTCAAAGAGCAAGACACCTTTTCTCTTTTAAAAGCCCACACAAGCTAGTGGCA
Found at i:303333 original size:13 final size:13
Alignment explanation
Indices: 303315--303340 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
303305 TACACCAAGT
303315 ATGTATCGATACA
1 ATGTATCGATACA
303328 ATGTATCGATACA
1 ATGTATCGATACA
303341 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:307333 original size:15 final size:15
Alignment explanation
Indices: 307313--307343 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
307303 TAAAAATGTC
*
307313 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
307328 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
307343 C
1 C
307344 CAAACGTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:309416 original size:13 final size:13
Alignment explanation
Indices: 309398--309435 Score: 76
Period size: 13 Copynumber: 2.9 Consensus size: 13
309388 GGAAATTCAA
309398 TGTATCGATACAT
1 TGTATCGATACAT
309411 TGTATCGATACAT
1 TGTATCGATACAT
309424 TGTATCGATACA
1 TGTATCGATACA
309436 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.37
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:309599 original size:20 final size:20
Alignment explanation
Indices: 309556--309601 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
309546 AAATCTTTTG
309556 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
309577 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
309597 CAAAA
1 CAAAA
309602 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:311976 original size:215 final size:215
Alignment explanation
Indices: 311605--312035 Score: 826
Period size: 215 Copynumber: 2.0 Consensus size: 215
311595 AGGGGGAGAT
311605 TGTTAGGATCTTGGTTTTGATATAACAAAGGATTGAATAAAACCAGAAATTATTTTGAAAATAAC
1 TGTTAGGATCTTGGTTTTGATATAACAAAGGATTGAATAAAACCAGAAATTATTTTGAAAATAAC
* *
311670 ATTAATATGTTTTATTCAATTAAGTGCTTTATAAATTTTGTACCAAATGATTTTTGATTCACCAA
66 AATAATATGTTTTATTCAACTAAGTGCTTTATAAATTTTGTACCAAATGATTTTTGATTCACCAA
311735 ATGTTTTCTAGTTAAGGATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGTTAAAATATA
131 ATGTTTTCTAGTTAAGGATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGTTAAAATATA
311800 TCAAAGTATCGATACATAGG
196 TCAAAGTATCGATACATAGG
*
311820 TGTTAGGATCTTGGTTTTGATATAACAAAGGATTGAATAAAACCGGAAATTATTTTGAAAATAAC
1 TGTTAGGATCTTGGTTTTGATATAACAAAGGATTGAATAAAACCAGAAATTATTTTGAAAATAAC
*
311885 AATAATATGTTTTATTCAACTAAGTGCTTTATAAATTTTGTACCAAATGATTTTTGATTTACCAA
66 AATAATATGTTTTATTCAACTAAGTGCTTTATAAATTTTGTACCAAATGATTTTTGATTCACCAA
311950 ATGTTTTCTAGTTAAGGATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGTTAAAATATA
131 ATGTTTTCTAGTTAAGGATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGTTAAAATATA
312015 TCAAAGTATCGATACATAGG
196 TCAAAGTATCGATACATAGG
312035 T
1 T
312036 ATTTGTATCG
Statistics
Matches: 212, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
215 212 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (215 bp):
TGTTAGGATCTTGGTTTTGATATAACAAAGGATTGAATAAAACCAGAAATTATTTTGAAAATAAC
AATAATATGTTTTATTCAACTAAGTGCTTTATAAATTTTGTACCAAATGATTTTTGATTCACCAA
ATGTTTTCTAGTTAAGGATAAATGTTTTCAAGGCTTAAAATGATTGATTTTTAAGTTAAAATATA
TCAAAGTATCGATACATAGG
Found at i:312134 original size:20 final size:20
Alignment explanation
Indices: 312111--312163 Score: 106
Period size: 20 Copynumber: 2.6 Consensus size: 20
312101 ACAATTCAAA
312111 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
312131 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
312151 GTATCGATACATG
1 GTATCGATACATG
312164 AAAAAGATGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:312240 original size:13 final size:13
Alignment explanation
Indices: 312222--312247 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
312212 TACACCAAGT
312222 ATGTATCGATACA
1 ATGTATCGATACA
312235 ATGTATCGATACA
1 ATGTATCGATACA
312248 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:312245 original size:32 final size:33
Alignment explanation
Indices: 312204--312267 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
312194 TAGCCAAACT
* **
312204 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
312236 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
312268 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:314500 original size:21 final size:21
Alignment explanation
Indices: 314467--314511 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
314457 TTGCAAGTTG
*
314467 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
314489 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
314509 AAA
1 AAA
314512 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:316334 original size:15 final size:15
Alignment explanation
Indices: 316323--316352 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
316313 CCAAAATGTG
316323 GAAGCTCAAAATGAA
1 GAAGCTCAAAATGAA
*
316338 GAAGCTCCAAATGAA
1 GAAGCTCAAAATGAA
316353 ATTGATGAAC
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:0.50, C:0.17, G:0.20, T:0.13
Consensus pattern (15 bp):
GAAGCTCAAAATGAA
Found at i:320970 original size:13 final size:13
Alignment explanation
Indices: 320952--320977 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
320942 TACACCAAGT
320952 ATGTATCGATACA
1 ATGTATCGATACA
320965 ATGTATCGATACA
1 ATGTATCGATACA
320978 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:320975 original size:32 final size:33
Alignment explanation
Indices: 320934--320997 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
320924 TAGCCAAACT
* **
320934 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
320966 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
320998 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:321921 original size:13 final size:13
Alignment explanation
Indices: 321903--321928 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
321893 TACACCAAGT
321903 ATGTATCGATACA
1 ATGTATCGATACA
321916 ATGTATCGATACA
1 ATGTATCGATACA
321929 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:321926 original size:32 final size:33
Alignment explanation
Indices: 321885--321948 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
321875 TAGCCAAACT
* **
321885 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
321917 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
321949 TTGGTTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Done.