Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015188.1 Kokia drynarioides strain JFW-HI SEQ_130232, 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: 508151
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 585 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:216559 original size:201 final size:191
Alignment explanation
Indices: 216195--216567 Score: 478
Period size: 201 Copynumber: 1.9 Consensus size: 191
216185 CTATACTATA
* * * *
216195 AACTGTTCCCTAATGATGTTGCTCACACGAGCTATCGAGAGTATGCAATAAGCATAATCTCAGCC
1 AACTATTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCAATAAGCATAATCTCAGCC
* * * *
216260 ATCGTAGGGCCTGTAATCCATTTAGGATTCATATCTCTTTCCCAAGTCACAATGTTGCTCACACG
66 ATCGTAGGACCTGTAATCCATTTAGGATTCATATCTCTTTCCCAACTCACAATGCTACTCACACG
* *
216325 AACTGTCGAAGACTCGTAACATATGCAGTACCTCAGCCATCGATACGGTATCTGTGCATAT
131 AACTATCGAAGACTCGTAACATATACAGTACCTCAGCCATCGATACGGTATCTGTGCATAT
* * *
216386 AACTATTCCCTGACGATGCTGCTCACACGAGCTATCGAGAATATGCACTTATGCATAAATCTCAG
1 AACTATTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCA-ATAAGCAT-AATCTCAG
* *
216451 CCATCGTAGGACCTGTAATCCATTTAGGATCCGTATTTCTTTTCTCATTTCCCAACTCACAATGC
64 CCATCGTAGGACCTGTAATCCATTTA-G----G-A-TTCATATCTC-TTTCCCAACTCACAATGC
* * *
216516 TACTCGCAC-AAGCTATCGAGGACTCGTAACATATACGGTACCTCAGCCATCG
121 TACTCACACGAA-CTATCGAAGACTCGTAACATATACAGTACCTCAGCCATCG
216568 CGTTGGTTTC
Statistics
Matches: 153, Mismatches: 18, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
191 42 0.27
192 6 0.04
193 33 0.22
194 1 0.01
198 1 0.01
199 1 0.01
200 10 0.07
201 59 0.39
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (191 bp):
AACTATTCCCTAACGATGCTGCTCACACGAGCTATCGAGAATATGCAATAAGCATAATCTCAGCC
ATCGTAGGACCTGTAATCCATTTAGGATTCATATCTCTTTCCCAACTCACAATGCTACTCACACG
AACTATCGAAGACTCGTAACATATACAGTACCTCAGCCATCGATACGGTATCTGTGCATAT
Found at i:220578 original size:15 final size:15
Alignment explanation
Indices: 220560--220608 Score: 57
Period size: 15 Copynumber: 3.3 Consensus size: 15
220550 TAGCTTATTT
220560 TTATTTATTAAATTA
1 TTATTTATTAAATTA
*
220575 TTATTTAATT-AATTT
1 TTATTT-ATTAAATTA
*
220590 TTATTT-TAAAATTA
1 TTATTTATTAAATTA
220604 TTATT
1 TTATT
220609 ATTTTTCATC
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
13 1 0.03
14 9 0.31
15 16 0.55
16 3 0.10
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
TTATTTATTAAATTA
Found at i:220790 original size:15 final size:18
Alignment explanation
Indices: 220770--220805 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
220760 TCGATGGTGA
220770 ATAT-AAGATT-TTGG-C
1 ATATAAAGATTATTGGAC
220785 ATATAAAGATTATTGGAC
1 ATATAAAGATTATTGGAC
220803 ATA
1 ATA
220806 AGGATGACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 4 0.22
16 6 0.33
17 4 0.22
18 4 0.22
ACGTcount: A:0.42, C:0.06, G:0.17, T:0.36
Consensus pattern (18 bp):
ATATAAAGATTATTGGAC
Found at i:221351 original size:29 final size:29
Alignment explanation
Indices: 221272--221368 Score: 77
Period size: 30 Copynumber: 3.2 Consensus size: 29
221262 GGCCCAAAAA
*
221272 TTTTTTAACTTTTTAAAGGCCAAAATTTTT
1 TTTTTTAA-TTTTTAAGGGCCAAAATTTTT
** * ***
221302 TTTTACCAATTTGTAAGGGGCCTCCATTTTT
1 TTTT-TTAATTTTTAA-GGGCCAAAATTTTT
*
221333 TTTTTTAATTTTTAAGGGCCCAAAAATTTT
1 TTTTTTAATTTTTAAGGG-CCAAAATTTTT
*
221363 GTTTTT
1 TTTTTT
221369 GTTTTTTGTT
Statistics
Matches: 49, Mismatches: 15, Indels: 6
0.70 0.21 0.09
Matches are distributed among these distances:
29 3 0.06
30 30 0.61
31 16 0.33
ACGTcount: A:0.25, C:0.12, G:0.11, T:0.52
Consensus pattern (29 bp):
TTTTTTAATTTTTAAGGGCCAAAATTTTT
Found at i:221377 original size:13 final size:13
Alignment explanation
Indices: 221359--221383 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
221349 GGCCCAAAAA
221359 TTTTGTTTTTGTT
1 TTTTGTTTTTGTT
221372 TTTTGTTTTTGT
1 TTTTGTTTTTGT
221384 ATAATGTGTT
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:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (13 bp):
TTTTGTTTTTGTT
Found at i:221775 original size:17 final size:17
Alignment explanation
Indices: 221753--221789 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
221743 AATTCTTAAT
*
221753 GTATTAGGATTATGGGA
1 GTATTAGGATTAAGGGA
221770 GTATTAGGATTAAGGGA
1 GTATTAGGATTAAGGGA
221787 GTA
1 GTA
221790 AAGTGGATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.35, T:0.32
Consensus pattern (17 bp):
GTATTAGGATTAAGGGA
Found at i:222457 original size:33 final size:33
Alignment explanation
Indices: 222419--222508 Score: 123
Period size: 33 Copynumber: 2.8 Consensus size: 33
222409 CTAATAATTA
*
222419 TATTAAAATATAATTAAATTATTTATTTATTTT
1 TATTAAAATATAATTAAAATATTTATTTATTTT
*
222452 TATTAAATTAT-ATTAAAATATTT-TTTATTTT
1 TATTAAAATATAATTAAAATATTTATTTATTTT
222483 TATATAAAATA-ATATTAAAATATTTA
1 TAT-TAAAATATA-ATTAAAATATTTA
222509 AAATATTTTA
Statistics
Matches: 50, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
31 11 0.22
32 17 0.34
33 22 0.44
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (33 bp):
TATTAAAATATAATTAAAATATTTATTTATTTT
Found at i:226577 original size:25 final size:24
Alignment explanation
Indices: 226528--226578 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
226518 GTTATGTATT
*
226528 ATTTTTCTAATATTATATATTATA
1 ATTTTTCTAATATCATATATTATA
*
226552 ATTTTTACTAAT-TCATATTTTAATA
1 ATTTTT-CTAATATCATATATT-ATA
226577 AT
1 AT
226579 AATTATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (24 bp):
ATTTTTCTAATATCATATATTATA
Found at i:226708 original size:58 final size:58
Alignment explanation
Indices: 226547--226713 Score: 205
Period size: 58 Copynumber: 2.9 Consensus size: 58
226537 ATATTATATA
* * * *
226547 TTATAATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATGTTATTAAATTAT
1 TTATTATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAT
* * *
226607 ATATTA-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAT
1 TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
*
226664 TTATTATTTTTATTAAATTATATTTAATAATAATCT-TATTAAAATTTAAT
1 TTATTATTTTTATTAAATTATATTTAATAATAAT-TATATTAAAATATAAT
226714 AACAATNNNN
Statistics
Matches: 93, Mismatches: 11, Indels: 8
0.83 0.10 0.07
Matches are distributed among these distances:
57 21 0.23
58 55 0.59
59 9 0.10
60 8 0.09
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (58 bp):
TTATTATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAT
Found at i:227577 original size:17 final size:17
Alignment explanation
Indices: 227552--227612 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 17
227542 TAAATAGATT
*
227552 TAAACTTAAACTTATAG
1 TAAATTTAAACTTATAG
*
227569 TAAATTTAAA-TTTTAAG
1 TAAATTTAAACTTAT-AG
* *
227586 TAAATTTAAACTTAAAA
1 TAAATTTAAACTTATAG
227603 TAAATTTAAA
1 TAAATTTAAA
227613 TTCTGTTGGG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
16 3 0.08
17 32 0.86
18 2 0.05
ACGTcount: A:0.52, C:0.05, G:0.03, T:0.39
Consensus pattern (17 bp):
TAAATTTAAACTTATAG
Found at i:228295 original size:47 final size:47
Alignment explanation
Indices: 228226--228344 Score: 229
Period size: 47 Copynumber: 2.5 Consensus size: 47
228216 ATTTGGTCCA
*
228226 CTTCTCAGTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGCCCTG
1 CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGCCCTG
228273 CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGCCCTG
1 CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGCCCTG
228320 CTTCTCAGTATCTCATCAGGAAGCT
1 CTTCTCAGTATCTCATCAGGAAGCT
228345 GGGATTCGAA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
47 71 1.00
ACGTcount: A:0.21, C:0.29, G:0.15, T:0.35
Consensus pattern (47 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGCCCTG
Found at i:228474 original size:115 final size:114
Alignment explanation
Indices: 228273--228486 Score: 358
Period size: 115 Copynumber: 1.9 Consensus size: 114
228263 CTTCGCCCTG
* *
228273 CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGCCCTGCTTCTCAGTATCTCATCA
1 CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGACCTGCTTCTCAGTAACTCATCA
228338 GGAAGCTGGGATTCGAAGATTTGCTCACATCGAGTCCTGAGTTGGTACA
66 GGAAGCTGGGATTCGAAGATTTGCTCACATCGAGTCCTGAGTTGGTACA
* *
228387 CTTCTCTGTATCTCATCAGGAAGCTAACCATTTTATTTCTTCGACCTGCTTCTCAGTAACTCATC
1 CTTCTCAGTATCTCATCAGGAAGCTAA-CATTTTATTGCTTCGACCTGCTTCTCAGTAACTCATC
*
228452 AGGAAGCT-GGAGTTCGAAGATTTGCTCGCATCGAG
65 AGGAAGCTGGGA-TTCGAAGATTTGCTCACATCGAG
228487 CATGGGTTTG
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
114 29 0.31
115 64 0.69
ACGTcount: A:0.23, C:0.25, G:0.20, T:0.33
Consensus pattern (114 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACATTTTATTGCTTCGACCTGCTTCTCAGTAACTCATCA
GGAAGCTGGGATTCGAAGATTTGCTCACATCGAGTCCTGAGTTGGTACA
Found at i:239652 original size:30 final size:29
Alignment explanation
Indices: 239609--239983 Score: 311
Period size: 30 Copynumber: 12.7 Consensus size: 29
239599 TTAGAGGTCG
**
239609 AAAATGGGGTTTTTGGACA-TTCGAGGGTA
1 AAAATGGAATTTTTGGA-AGTTCGAGGGTA
* * *
239638 AAAATTGTAATTTTT-AAAGTTTCGA-GGTCT
1 AAAA-TGGAATTTTTGGAAG-TTCGAGGGT-A
**
239668 AAAATGGAATTTTTGGAAGTTTAAGGGTA
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
***
239697 AAAATGGAATTTTTGGAAGTTTTTGGGTTA
1 AAAATGGAATTTTTGGAAGTTCGAGGG-TA
239727 AAAATGGAATTTTTGGAAGTTCGAGGGT-
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
* *
239755 AAAATGGAATTTTTGGAAGTTTTGAGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGTA
* *
239785 AAAATGGAATTTTTTTGAAGTTTG-GGGTA
1 AAAATGGAA-TTTTTGGAAGTTCGAGGGTA
* * *
239814 AGAATGAAATTTTTGGAAGTTTTG-GGGTCA
1 AAAATGGAATTTTTGGAAG-TTCGAGGGT-A
** *
239844 AAAATGGAATTTTTAAAAG-TCTAGGGGTA
1 AAAATGGAATTTTTGGAAGTTCGA-GGGTA
* * * *
239873 AAAATGTATTTTTTTTGAAAGTTTTG-GGGTTA
1 AAAATGGA--ATTTTTGGAAG-TTCGAGGG-TA
*
239905 AGAATGGAATTTTTGGAAGTTTCG-GGGTTA
1 AAAATGGAATTTTTGGAAG-TTCGAGGG-TA
239935 AAAATGGAATTTTTGGAAGTTCGAGGGT-
1 AAAATGGAATTTTTGGAAGTTCGAGGGTA
239963 AAAATGGAATTTTTGGAAGTT
1 AAAATGGAATTTTTGGAAGTT
239984 TCGGAGTCAA
Statistics
Matches: 287, Mismatches: 39, Indels: 41
0.78 0.11 0.11
Matches are distributed among these distances:
28 51 0.18
29 85 0.30
30 121 0.42
31 21 0.07
32 8 0.03
33 1 0.00
ACGTcount: A:0.32, C:0.02, G:0.27, T:0.38
Consensus pattern (29 bp):
AAAATGGAATTTTTGGAAGTTCGAGGGTA
Found at i:239672 original size:59 final size:57
Alignment explanation
Indices: 239544--239983 Score: 331
Period size: 59 Copynumber: 7.5 Consensus size: 57
239534 GGGAAAATTC
* * * * * * *
239544 GAGGCTAAAAAGGACATTTTTAGACA-TTCGGGGGTAAAAGGGTAA-TTTTGAGAGTTTA
1 GAGGTTAAAATGGA-ATTTTTGGA-AGTTCGAGGGTAAAATGG-AATTTTTGAAAGTTTT
* ** * *
239602 GAGGTCGAAAATGGGGTTTTTGGACA-TTCGAGGGTAAAAATTGTAATTTTT-AAAGTTTC
1 GAGGT-TAAAATGGAATTTTTGGA-AGTTCGAGGGT-AAAA-TGGAATTTTTGAAAGTTTT
** *
239661 GAGGTCTAAAATGGAATTTTTGGAAGTTTAAGGGTAAAAATGGAATTTTTGGAAGTTTTT
1 GAGGT-TAAAATGGAATTTTTGGAAGTTCGAGGGT-AAAATGGAATTTTTGAAAG-TTTT
*
239721 G-GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGAATTTTTGGAAGTTTT
1 GAGGTT-AAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGAATTTTTGAAAGTTTT
* * * *
239778 GAGGTTAAAAATGGAATTTTTTTGAAGTTTG-GGGTAAGAATGAAATTTTTGGAAGTTTT
1 GAGGTT-AAAATGGAA-TTTTTGGAAGTTCGAGGGTAA-AATGGAATTTTTGAAAGTTTT
* * ** * * *
239837 GGGGTCAAAAATGGAATTTTTAAAAG-TCTAGGGGTAAAAATGTATTTTTTTTGAAAGTTTT
1 GAGGT-TAAAATGGAATTTTTGGAAGTTCGA-GGGT-AAAATGGA--ATTTTTGAAAGTTTT
* * *
239898 GGGGTTAAGAATGGAATTTTTGGAAGTTTCG-GGGTTAAAAATGGAATTTTTGGAAG-TTC
1 GAGGTTAA-AATGGAATTTTTGGAAG-TTCGAGGG-T-AAAATGGAATTTTTGAAAGTTTT
*
239957 GAGGGTAAAATGGAATTTTTGGAAGTT
1 GAGGTTAAAATGGAATTTTTGGAAGTT
239984 TCGGAGTCAA
Statistics
Matches: 318, Mismatches: 43, Indels: 43
0.79 0.11 0.11
Matches are distributed among these distances:
57 8 0.03
58 96 0.30
59 145 0.46
60 22 0.07
61 36 0.11
62 9 0.03
63 2 0.01
ACGTcount: A:0.32, C:0.03, G:0.28, T:0.36
Consensus pattern (57 bp):
GAGGTTAAAATGGAATTTTTGGAAGTTCGAGGGTAAAATGGAATTTTTGAAAGTTTT
Found at i:241111 original size:18 final size:18
Alignment explanation
Indices: 241072--241111 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
241062 TTCATTATTA
* *
241072 ATTAATGTTATTATTACC
1 ATTAATGTCATTATGACC
*
241090 ATTAATGTCATTATGACT
1 ATTAATGTCATTATGACC
241108 ATTA
1 ATTA
241112 TTAATACTGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.10, G:0.07, T:0.47
Consensus pattern (18 bp):
ATTAATGTCATTATGACC
Found at i:241889 original size:17 final size:17
Alignment explanation
Indices: 241864--241924 Score: 61
Period size: 17 Copynumber: 3.6 Consensus size: 17
241854 TAAATAGATT
*
241864 TAAACTTAAACTTATAG
1 TAAATTTAAACTTATAG
*
241881 TAAATTTAAA-TTTTAAG
1 TAAATTTAAACTTAT-AG
* * *
241898 TAAATTTAAGCTTAAAA
1 TAAATTTAAACTTATAG
241915 TAAATTTAAA
1 TAAATTTAAA
241925 TTCTGTTAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
16 3 0.09
17 30 0.86
18 2 0.06
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (17 bp):
TAAATTTAAACTTATAG
Found at i:244474 original size:29 final size:27
Alignment explanation
Indices: 244424--244506 Score: 82
Period size: 29 Copynumber: 3.1 Consensus size: 27
244414 AATATAGATT
* *
244424 ATTTAAATTAAAAT-TT-ATATTATAT
1 ATTTAAATAAAAATATTAATATTATAA
* * *
244449 TTTTAAATTTAATATCATTAATATTATAA
1 ATTTAAA-TAAAAAT-ATTAATATTATAA
244478 ATTTAAATAAAAATATTAATATTA-AA
1 ATTTAAATAAAAATATTAATATTATAA
244504 ATT
1 ATT
244507 GAATTTTAAT
Statistics
Matches: 48, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
25 6 0.12
26 11 0.23
27 10 0.21
28 7 0.15
29 14 0.29
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (27 bp):
ATTTAAATAAAAATATTAATATTATAA
Found at i:244607 original size:23 final size:22
Alignment explanation
Indices: 244581--244626 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
244571 ATTTAATAAA
* *
244581 AATATGAATAATATTTAAATATT
1 AATATAAATAATACTTAAA-ATT
*
244604 AATATAAATATTACTTAAAATT
1 AATATAAATAATACTTAAAATT
244626 A
1 A
244627 TTTTAATTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (22 bp):
AATATAAATAATACTTAAAATT
Found at i:244735 original size:18 final size:18
Alignment explanation
Indices: 244708--244742 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
244698 CTTTTATGGG
244708 TAAATAAAATATTCTATT
1 TAAATAAAATATTCTATT
* *
244726 TAAATTAAATTTTCTAT
1 TAAATAAAATATTCTAT
244743 AAAACTTTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.49
Consensus pattern (18 bp):
TAAATAAAATATTCTATT
Found at i:259938 original size:17 final size:17
Alignment explanation
Indices: 259916--259963 Score: 78
Period size: 17 Copynumber: 2.8 Consensus size: 17
259906 TTCCATGCTT
259916 ATCCCTTTCAAGTTCCA
1 ATCCCTTTCAAGTTCCA
*
259933 ATCCCTTTCAAGTTTCA
1 ATCCCTTTCAAGTTCCA
*
259950 ATCCCTTTAAAGTT
1 ATCCCTTTCAAGTT
259964 GTAGTTTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.25, C:0.29, G:0.06, T:0.40
Consensus pattern (17 bp):
ATCCCTTTCAAGTTCCA
Found at i:269352 original size:68 final size:68
Alignment explanation
Indices: 269236--269378 Score: 232
Period size: 68 Copynumber: 2.1 Consensus size: 68
269226 TGCCATGAAT
*
269236 AAAGAGGATACGAAGCCAGAAAGTGAGGCTTTAAAGCTTGATTCTATGATACTCAATTATGTTAA
1 AAAGAGGATACGAAGCCAAAAAGTGAGGCTTTAAAGCTTGATTCTATGATACTCAATTATGTTAA
*
269301 GAC
66 GAA
* * * *
269304 AAAGAGTATACGAAGCCAAAAAGTGAGGCTTTAAAGCTTGGTTTTATGATACTCAATTCTGTTAA
1 AAAGAGGATACGAAGCCAAAAAGTGAGGCTTTAAAGCTTGATTCTATGATACTCAATTATGTTAA
269369 GAA
66 GAA
269372 AAAGAGG
1 AAAGAGG
269379 GGTTGACAAT
Statistics
Matches: 68, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.27
Consensus pattern (68 bp):
AAAGAGGATACGAAGCCAAAAAGTGAGGCTTTAAAGCTTGATTCTATGATACTCAATTATGTTAA
GAA
Found at i:277329 original size:25 final size:25
Alignment explanation
Indices: 277276--277381 Score: 106
Period size: 25 Copynumber: 4.2 Consensus size: 25
277266 TATTCCAGAA
* * *
277276 TTTAGCTCATACGAGTCCAGA-CAG
1 TTTAGCTCTTACGAGCCCAGATAAG
277300 ATTTAGCTCTTACGAGCCCAGATAAG
1 -TTTAGCTCTTACGAGCCCAGATAAG
* * *
277326 TTTAGCTCTAATGAAGCCCAGATAGG
1 TTTAGCTCTTACG-AGCCCAGATAAG
* *
277352 GTTAGCTCTTACGAGCCCAAATAGAG
1 TTTAGCTCTTACGAGCCCAGATA-AG
277378 TTTA
1 TTTA
277382 ACCGGTATAC
Statistics
Matches: 66, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
25 39 0.59
26 27 0.41
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (25 bp):
TTTAGCTCTTACGAGCCCAGATAAG
Found at i:278465 original size:15 final size:15
Alignment explanation
Indices: 278445--278476 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
278435 TTAGGTTTTG
*
278445 TTTATAATTATTATT
1 TTTATAATTACTATT
278460 TTTATAATTACTATT
1 TTTATAATTACTATT
278475 TT
1 TT
278477 CCCTTAAGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (15 bp):
TTTATAATTACTATT
Found at i:282618 original size:275 final size:275
Alignment explanation
Indices: 282120--282674 Score: 1038
Period size: 275 Copynumber: 2.0 Consensus size: 275
282110 AACATGCAGA
*
282120 AAATGCATACTATGTCAATAACATCCGAAAGGGGATCATTTGGTAATTCATATAATAATCGTTCT
1 AAATGCATACTATGTCAATAACATCCGAAAAGGGATCATTTGGTAATTCATATAATAATCGTTCT
*
282185 CAACAACCTTGGGGGAATCATAATACTTCCACGTATAGATATGAAAATTTCTCAAATCAAGGGGG
66 CAACAACCTTGGGGGAATCATAATACTTCCACGTATAGATATGAAAATTCCTCAAATCAAGGGGG
*
282250 TTATAAACAAAGAGGTTACAATTTGCCAATTCACAGTAGAATTATCATTAGAATTCACAGATAAA
131 TTATAAACAAAGAGGTTACAATTTACCAATTCACAGTAGAATTATCATTAGAATTCACAGATAAA
*
282315 TTCTCGTTCTAACCAGGTGCAGTCACATAATCTAATGCAACCACAATCACAATTACAACCACAAT
196 TTCTCGTTCTAACCAGGTGCAATCACATAATCTAATGCAACCACAATCACAATTACAACCACAAT
282380 AGTCTGTACCACCAC
261 AGTCTGTACCACCAC
282395 AAATGCATACTATGTCAATAACATCCGAAAAGGGATCATTTGGTAATTCATATAATAATCGTTCT
1 AAATGCATACTATGTCAATAACATCCGAAAAGGGATCATTTGGTAATTCATATAATAATCGTTCT
282460 CAACAACCTTGGGGGAATCATAATACTTCCACGTATAGATATGAAAATTCCTCAAATCAAGGGGG
66 CAACAACCTTGGGGGAATCATAATACTTCCACGTATAGATATGAAAATTCCTCAAATCAAGGGGG
* *
282525 TTATAGACAAGGAGGTTACAATTTACCAATTCACAGTAGAATTATCATTAGAATTCACAGATAAA
131 TTATAAACAAAGAGGTTACAATTTACCAATTCACAGTAGAATTATCATTAGAATTCACAGATAAA
* *
282590 TTCTCGTTCTAACCAGGTTCAATCACATAATCTAATGCAACCACAATCACGATTACAACCACAAT
196 TTCTCGTTCTAACCAGGTGCAATCACATAATCTAATGCAACCACAATCACAATTACAACCACAAT
282655 AGTCTGTACCACCAC
261 AGTCTGTACCACCAC
282670 AAATG
1 AAATG
282675 TAAGGATAAC
Statistics
Matches: 272, Mismatches: 8, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
275 272 1.00
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.27
Consensus pattern (275 bp):
AAATGCATACTATGTCAATAACATCCGAAAAGGGATCATTTGGTAATTCATATAATAATCGTTCT
CAACAACCTTGGGGGAATCATAATACTTCCACGTATAGATATGAAAATTCCTCAAATCAAGGGGG
TTATAAACAAAGAGGTTACAATTTACCAATTCACAGTAGAATTATCATTAGAATTCACAGATAAA
TTCTCGTTCTAACCAGGTGCAATCACATAATCTAATGCAACCACAATCACAATTACAACCACAAT
AGTCTGTACCACCAC
Found at i:293255 original size:20 final size:22
Alignment explanation
Indices: 293215--293255 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
293205 TCTAGGATGA
*
293215 TTATAGTTAGAAAATTTTAAAC
1 TTATAGTTAGAAAATTCTAAAC
293237 TTATA-TTAG-AAATTCTAAA
1 TTATAGTTAGAAAATTCTAAA
293256 AAATTATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 4 0.22
22 5 0.28
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.41
Consensus pattern (22 bp):
TTATAGTTAGAAAATTCTAAAC
Found at i:294284 original size:39 final size:38
Alignment explanation
Indices: 294239--294313 Score: 141
Period size: 39 Copynumber: 1.9 Consensus size: 38
294229 GAAAAGTGAG
294239 AAAATATACATGTGATTTTGCAAAAAAAAAAAAAAAAA
1 AAAATATACATGTGATTTTGCAAAAAAAAAAAAAAAAA
294277 NAAAATATACATGTGATTTTGCAAAAAAAAAAAAAAA
1 -AAAATATACATGTGATTTTGCAAAAAAAAAAAAAAA
294314 TGACAAGATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.21
Consensus pattern (38 bp):
AAAATATACATGTGATTTTGCAAAAAAAAAAAAAAAAA
Found at i:294624 original size:59 final size:59
Alignment explanation
Indices: 294538--294726 Score: 141
Period size: 59 Copynumber: 3.2 Consensus size: 59
294528 AAAAATTTTA
* * **
294538 GAGGCTAAAATGTAACTTTTCAAAAAGTTCGAAGGTCAAAATGTAATTTAAAAAAGGTTT
1 GAGGTTAAAATG-AAATTTTCAAAAAGTTCGAAGGTCAAAATAAAATTTAAAAAAGGTTT
* * * * ** *
294598 GGGGGTTAAAATGAAATTTT-AGAAAGTTTGAGGGTCAAAATAAAATTTTTAGAAGGTTT
1 -GAGGTTAAAATGAAATTTTCAAAAAGTTCGAAGGTCAAAATAAAATTTAAAAAAGGTTT
* * * * * * * * *
294657 GAGGTTAAAAT-AAAATTTCTAAAAAATTTGAGGGTAAAAATGAAATTTTAGAAA-GTTC
1 GAGGTTAAAATGAAATTTTC-AAAAAGTTCGAAGGTCAAAATAAAATTTAAAAAAGGTTT
294715 GAGGTTTAAAAT
1 GAGG-TTAAAAT
294727 ATCGTTTTTA
Statistics
Matches: 104, Mismatches: 21, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
57 6 0.06
58 17 0.16
59 65 0.62
60 6 0.06
61 10 0.10
ACGTcount: A:0.43, C:0.04, G:0.21, T:0.32
Consensus pattern (59 bp):
GAGGTTAAAATGAAATTTTCAAAAAGTTCGAAGGTCAAAATAAAATTTAAAAAAGGTTT
Found at i:294637 original size:29 final size:29
Alignment explanation
Indices: 294561--294718 Score: 147
Period size: 29 Copynumber: 5.4 Consensus size: 29
294551 AACTTTTCAA
* * * * *
294561 AAAGTTCGAAGGTCAAAATGTAATTTAAA
1 AAAGTTTGAGGGTCAAAATGAAATTTTAG
* *
294590 AAAGGTTTGGGGGTTAAAATGAAATTTTAG
1 AAA-GTTTGAGGGTCAAAATGAAATTTTAG
*
294620 AAAGTTTGAGGGTCAAAATAAAATTTTTAG
1 AAAGTTTGAGGGTCAAAATGAAA-TTTTAG
* * * *
294650 AAGGTTTGA-GGTTAAAATAAAATTTCTAA
1 AAAGTTTGAGGGTCAAAATGAAATTT-TAG
* *
294679 AAAATTTGAGGGTAAAAATGAAATTTTAG
1 AAAGTTTGAGGGTCAAAATGAAATTTTAG
*
294708 AAAGTTCGAGG
1 AAAGTTTGAGG
294719 TTTAAAATAT
Statistics
Matches: 105, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
28 3 0.03
29 52 0.50
30 50 0.48
ACGTcount: A:0.44, C:0.03, G:0.22, T:0.31
Consensus pattern (29 bp):
AAAGTTTGAGGGTCAAAATGAAATTTTAG
Found at i:303692 original size:21 final size:21
Alignment explanation
Indices: 303668--303709 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
303658 TTCTAGCTCC
303668 ACTATTCTA-GCTTCCAATTCA
1 ACTATT-TAGGCTTCCAATTCA
*
303689 ACTATTTAGGCTTTCAATTCA
1 ACTATTTAGGCTTCCAATTCA
303710 GCCTTCTTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 2 0.11
21 17 0.89
ACGTcount: A:0.29, C:0.24, G:0.07, T:0.40
Consensus pattern (21 bp):
ACTATTTAGGCTTCCAATTCA
Found at i:304290 original size:20 final size:21
Alignment explanation
Indices: 304254--304304 Score: 54
Period size: 20 Copynumber: 2.5 Consensus size: 21
304244 ATTGGTATGG
*
304254 TTTATATTAAGTGTAAATA-GA
1 TTTA-ATTAAGTGTAAAAATGA
304275 TTTAATTAAGAT-TAAAAATGA
1 TTTAATTAAG-TGTAAAAATGA
304296 -TTAATTAAG
1 TTTAATTAAG
304305 GCTTAATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 20 0.74
21 7 0.26
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.41
Consensus pattern (21 bp):
TTTAATTAAGTGTAAAAATGA
Found at i:308964 original size:29 final size:28
Alignment explanation
Indices: 308918--309030 Score: 100
Period size: 29 Copynumber: 3.9 Consensus size: 28
308908 CAGAATGTTC
*
308918 AGGGGTCAAAATGCAATTTTAAAAAGGTT
1 AGGGGTCAAAATGAAATTTTAAAAA-GTT
* * *
308947 AGGGGTTAAAATTAAATTTTTAGAAAGTT
1 AGGGGTCAAAATGAAA-TTTTAAAAAGTT
* * *
308976 TGGGCTCAAAATGAAATTTTCAAAAAATT
1 AGGGGTCAAAATGAAATTTT-AAAAAGTT
* *
309005 GAAGGGTTAAAAATGAAATTTTAAAA
1 --AGGGGTCAAAATGAAATTTTAAAA
309031 TATTCGAGGG
Statistics
Matches: 67, Mismatches: 13, Indels: 7
0.77 0.15 0.08
Matches are distributed among these distances:
28 4 0.06
29 34 0.51
30 12 0.18
31 17 0.25
ACGTcount: A:0.45, C:0.04, G:0.19, T:0.31
Consensus pattern (28 bp):
AGGGGTCAAAATGAAATTTTAAAAAGTT
Found at i:309043 original size:30 final size:31
Alignment explanation
Indices: 308983--309046 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
308973 GTTTGGGCTC
308983 AAAATGAAATTTTCAAAAAATTGAAGGGTTA
1 AAAATGAAATTTTCAAAAAATTGAAGGGTTA
*
309014 AAAATGAAATTTT-AAAATATTCG-AGGGTTA
1 AAAATGAAATTTTCAAAAAATT-GAAGGGTTA
309044 AAA
1 AAA
309047 TATAGTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.52, C:0.03, G:0.16, T:0.30
Consensus pattern (31 bp):
AAAATGAAATTTTCAAAAAATTGAAGGGTTA
Found at i:310752 original size:41 final size:41
Alignment explanation
Indices: 310649--310806 Score: 181
Period size: 41 Copynumber: 3.8 Consensus size: 41
310639 GGTGTATAAA
* * * * ** *
310649 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTAT
1 AAGGAAGACTCATATCTCGAGATGAGAATGAGATTTTGAAT
* *
310690 AAGTAGAAGACTAATGTCTCGAGATGAGAATGAGATTTTGAAT
1 AAG--GAAGACTCATATCTCGAGATGAGAATGAGATTTTGAAT
* *
310733 AAGGAAGACTCATATCTCGAAATGAGAATGAGATTTTGATT
1 AAGGAAGACTCATATCTCGAGATGAGAATGAGATTTTGAAT
* *
310774 AAAGAAGACTCATATCTCGAGTTGAGAATGAGA
1 AAGGAAGACTCATATCTCGAGATGAGAATGAGA
310807 ATATGGTTAA
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
41 67 0.66
43 34 0.34
ACGTcount: A:0.38, C:0.10, G:0.25, T:0.27
Consensus pattern (41 bp):
AAGGAAGACTCATATCTCGAGATGAGAATGAGATTTTGAAT
Found at i:310817 original size:41 final size:41
Alignment explanation
Indices: 310694--310825 Score: 156
Period size: 41 Copynumber: 3.2 Consensus size: 41
310684 TTGTATAAGT
* * * * *
310694 AGAAGACTAATGTCTCGAGATGAGAATGAGATTTTGAATAA
1 AGAAGACTCATATCTCGAGATGAGAATGAGAATATGATTAA
* * * *
310735 GGAAGACTCATATCTCGAAATGAGAATGAGATTTTGATTAA
1 AGAAGACTCATATCTCGAGATGAGAATGAGAATATGATTAA
* *
310776 AGAAGACTCATATCTCGAGTTGAGAATGAGAATATGGTTAA
1 AGAAGACTCATATCTCGAGATGAGAATGAGAATATGATTAA
310817 AGGAAGACT
1 A-GAAGACT
310826 TATGACTCGA
Statistics
Matches: 79, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
41 72 0.91
42 7 0.09
ACGTcount: A:0.40, C:0.09, G:0.24, T:0.27
Consensus pattern (41 bp):
AGAAGACTCATATCTCGAGATGAGAATGAGAATATGATTAA
Found at i:311409 original size:24 final size:24
Alignment explanation
Indices: 311377--311426 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
311367 GACTTGAGTT
311377 GTATTGACCACATTTGTATCAGTA
1 GTATTGACCACATTTGTATCAGTA
311401 GTATTGACCACATTTGTATCAGTA
1 GTATTGACCACATTTGTATCAGTA
311425 GT
1 GT
311427 TAGAATATTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (24 bp):
GTATTGACCACATTTGTATCAGTA
Found at i:317731 original size:43 final size:42
Alignment explanation
Indices: 317676--317822 Score: 154
Period size: 43 Copynumber: 3.5 Consensus size: 42
317666 TGGTGTATAA
* * *
317676 AAAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTAT
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAAATTGTAT
** *
317718 AAATGGAAGACTCATGTCTCGAGATGAGAATGAGATTTTGAAT
1 AAA-GGAAGACTCATGTCTCGAGATGAGAATGAGAAATTGTAT
* * * *
317761 -AAGGAAGACTCATATCTTGAAATGAGAATGAGAATATGGT-T
1 AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAA-ATTGTAT
* *
317802 AAAGGAAGACTTATGACTCGA
1 AAAGGAAGACTCATGTCTCGA
317823 AAGAGCATAA
Statistics
Matches: 85, Mismatches: 17, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
41 29 0.34
42 23 0.27
43 33 0.39
ACGTcount: A:0.38, C:0.10, G:0.26, T:0.26
Consensus pattern (42 bp):
AAAGGAAGACTCATGTCTCGAGATGAGAATGAGAAATTGTAT
Found at i:327720 original size:54 final size:53
Alignment explanation
Indices: 327656--327814 Score: 174
Period size: 54 Copynumber: 2.9 Consensus size: 53
327646 CAAAAGATTT
*
327656 GAATGGATCTTAACGAACAAGGGGCTTACCATCAGCTTGTTTACTATCGGACTG
1 GAATGGATCTTAACGAA-AAGGGGCTTACCATCAGCTTGTTTACTATCGGACTA
* * * * * *
327710 GAATGGATCTTAATGTATAGGGGGCTTACCATCAGCTTGTTTACTACCAGATTA
1 GAATGGATCTTAACG-AAAAGGGGCTTACCATCAGCTTGTTTACTATCGGACTA
* * ** * *
327764 GAATGGATCTTAACGGATAGGATACTTACCATCAACTTGTTTACTGTCGGA
1 GAATGGATCTTAACGAAAAGG-GGCTTACCATCAGCTTGTTTACTATCGGA
327815 TACTTTTGCC
Statistics
Matches: 85, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
53 2 0.02
54 82 0.96
55 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (53 bp):
GAATGGATCTTAACGAAAAGGGGCTTACCATCAGCTTGTTTACTATCGGACTA
Found at i:329674 original size:898 final size:900
Alignment explanation
Indices: 328222--330025 Score: 2612
Period size: 898 Copynumber: 2.0 Consensus size: 900
328212 ACTAGTGCTG
* *
328222 TAGTTTACCCAAAATAAGTGACAATAACTAAATGAAGAGAGCTAAATGTTTGAAGAAACCCCTAA
1 TAGTTTACCC-AAATAAGCGACAATAACGAAATGAAGAGAGCTAAATGTTTGAAGAAACCCCTAA
*
328287 CATAAGATAAAGCCTCGAAATTATCATTTTGAAAAAAAATAGATATTGGGCTTTAATAATTATTT
65 CATAAGATAAAGCCTCGAAATTATCATTTTGAAAAAAAATAGATATTGGGCTTTAATAATTATCT
* * *
328352 GGGCAGATGCTCACCTTTTAAGGCAGAACTCTGGGGTAGGCGAACTTCTCATTTTATTAAATAAA
130 GGACAGATGCTCACCTTTTAAGGCAGAACTCCGGGATAGGCGAACTTCTCATTTTATTAAATAAA
* * * * * *
328417 GGATATAAGAGAGCCACAATTCAGATAGACTACCTAGATGTGGTTAAAGTTTTGTTCATGAAGGA
195 GGATATAAGAGAGACACAATTCAGACAGACAACCTAAAGGTGGTTAAAGTTTTGTCCATGAAGGA
* * * *
328482 GTCTGTAAACTCAAGTATTACCTTGCTCAAAAGGATTCAACGACTTATGAGTTTTGAAGGATAGT
260 GTCTGTAAACTCAAGTATTACATTGCTCAAAAGGATTCAACGACTTACGAGTTTTGAAGGACAAT
* * **
328547 GGGAGATCAAACACGTACCTAATGATTGCAATTTAATTTCTGGTCAACTGGCAAAGATTAGCCTT
325 GGGAGATCAAACACGTACCTAATGATTGCAATTTAATTACTGATCAACAAGCAAAGATTAGCCTT
* **
328612 ACATGGCAGACAAGCTTACAGATTTTCGAAGTGCCTCTTGATATTGTGTCTATGGCTCTTCAACA
390 ACATGGCAGACAAACTTACAGATTTTCGAAGTGCCTCTAAATATTGTGTCTATGGCTCTTCAACA
* * * *
328677 AGACAAAGCATTTAGCGCTTTTTAGCATTTGATTTGATGTAACTTTGTTTTATTTTTCACCAAAA
455 AGACAAAACATTTAGCGATTTTTAACATTTGATTTGATGTAACTTTGATTTATTTTTCACC-AAA
*
328742 AAAATTATAAAATTTTATAGAATGTTTTGAATATTAGGGATAAATCTCAAAATTATACATGAATT
519 AAAATTATAAAATTTTATAGAATGTTTTGAATATTAGGGATAAATATCAAAATTATACATGAATT
*
328807 ATGGTTTAATGTGCAATTGTATACATGAAATTTTGATTTGATCCAATTCTTGTAAATTATTAACA
584 ATGGTTTAATGTGCAATTGTATACATAAAATTTTGATTTGATCCAATTCTTGTAAATTATTAACA
* * * *
328872 CAATTATTGATATAACATCTTTTTATGTTTATATATTACATAC-ATAAT-TTATATTTGTCCAAT
649 CAATTATTGATATAACACCCTTTTATGTTTATATATTAAATACAATAATATTATATTTATCCAAT
* * * *
328935 ATAAAAATAAATTGATGTATTTATTTCTTTACATGTGTATGATTAAA-CTAAAATTAAAGTTTCA
714 ATAAAAATAAATTGATGTATTTATTTCTTTAAATGTATATAAATAAATC-AAAATTAAAGTTTCA
* * * * ** * *
328999 AGTATACATTTGAACCACAATTAGAG-TTTCACATTTATAATTGTATCAAATTAATGTTCATGTA
778 AGGATACATTTAAACCACAATTAAAGTTTTCACATGTATAATTAAATAAAATTAAAGTTCATGTA
** * * * *
329063 TACAATTGGATATTAAATCAAAGCTCA-TGTATTTTTTAAATTTATCCCTGAATATTATA
843 TA-AATTAAATA-TAAATCAAAGCTAAGTGTATTTTTGAAATTTATCCCAGAATATGATA
*
329122 TAGTTTACCC-AATAAGCGACAATAACGAAATGAAGAGAGCTAAATGTTTGAAGAAACCCCTAGC
1 TAGTTTACCCAAATAAGCGACAATAACGAAATGAAGAGAGCTAAATGTTTGAAGAAACCCCTAAC
* * * *
329186 ATAAGATAAAGCCTTGAAATTATCATTTTGAAAAAAAATGGATATTGGGTTTTAATCATTATCTG
66 ATAAGATAAAGCCTCGAAATTATCATTTTGAAAAAAAATAGATATTGGGCTTTAATAATTATCTG
*
329251 GACAGATGCTCACCTTTTGAA-GTAGAACTCCGGGATATTTTGGACGAACTTCTCATTTTATTAA
131 GACAGATGCTCACCTTTT-AAGGCAGAACTCCGGGATA----GG-CGAACTTCTCATTTTATTAA
* *
329315 ATAAGGGACT-TAAGAGAGACACAATTTAGACAGACAACCTAAAGGTGGTTAAAGTTTTGTCCAT
190 ATAAAGGA-TATAAGAGAGACACAATTCAGACAGACAACCTAAAGGTGGTTAAAGTTTTGTCCAT
* *
329379 GAAGGAGTC-GATAGACTC-AGTATTACATTGCTCAAAAGGATTCAATGACTTACGAGTTTTGAA
254 GAAGGAGTCTG-TAAACTCAAGTATTACATTGCTCAAAAGGATTCAACGACTTACGAGTTTTGAA
*
329442 GGACAATGGGAGATCAAACACGTGCC-AATGATTGCAATTTAATTACTGATCAACAAGCAAAGAT
318 GGACAATGGGAGATCAAACACGTACCTAATGATTGCAATTTAATTACTGATCAACAAGCAAAGAT
* * * *
329506 TAGTCTTACATGGTAGACAAACTTACAGATTTTTG-AGATGCCT-TCAAATATTGTGTTTATGGC
383 TAGCCTTACATGGCAGACAAACTTACAGATTTTCGAAG-TGCCTCT-AAATATTGTGTCTATGGC
*
329569 TCTTCAACAAGACAAAATATTTAGC-ATTTTTAACATTTGATTTGATGTAACTTTGATTTATTTT
446 TCTTCAACAAGACAAAACATTTAGCGATTTTTAACATTTGATTTGATGTAACTTTGATTTATTTT
*
329633 TCACC-AAAAAATTATAAAATTTTATATAATGTTTTGAATATTAGGGATAAATATCAAAATTATA
511 TCACCAAAAAAATTATAAAATTTTATAGAATGTTTTGAATATTAGGGATAAATATCAAAATTATA
* * * *
329697 CATGAATTATGGTTTAATGTGTAGTTTTATACATAAAATTTTGATTTGATTCAATTCTTGTAAAT
576 CATGAATTATGGTTTAATGTGCAATTGTATACATAAAATTTTGATTTGATCCAATTCTTGTAAAT
*
329762 TATTAACATAATTATTGATATAACACCCTTTTATGTTTATATATTAAATACAATAATAATTATAT
641 TATTAACACAATTATTGATATAACACCCTTTTATGTTTATATATTAAATACAATAAT-ATTATAT
* *
329827 TTATCCAATATACAAATAAATTGATGTATTTATTTCTTTAAATGTATATAAATATATCAAAATTA
705 TTATCCAATATAAAAATAAATTGATGTATTTATTTCTTTAAATGTATATAAATAAATCAAAATTA
* * * *
329892 AAGTTTTAAGGATGCATTTAAACCATAATTAAAGTTTTCACGTGTATAATTAAATAAAATTAAAG
770 AAGTTTCAAGGATACATTTAAACCACAATTAAAGTTTTCACATGTATAATTAAATAAAATTAAAG
* * *
329957 TTCATGTATATATTAAATATAAATTAAAGTTAATGTGTATTTTTGAAATTTATCCCAGAATATGA
835 TTCATGTATAAATTAAATATAAATCAAAGCTAA-GTGTATTTTTGAAATTTATCCCAGAATATGA
330022 TA
899 TA
330024 TA
1 TA
330026 CATATTTTGA
Statistics
Matches: 805, Mismatches: 82, Indels: 32
0.88 0.09 0.03
Matches are distributed among these distances:
898 305 0.38
899 7 0.01
900 65 0.08
901 204 0.25
902 134 0.17
903 89 0.11
904 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (900 bp):
TAGTTTACCCAAATAAGCGACAATAACGAAATGAAGAGAGCTAAATGTTTGAAGAAACCCCTAAC
ATAAGATAAAGCCTCGAAATTATCATTTTGAAAAAAAATAGATATTGGGCTTTAATAATTATCTG
GACAGATGCTCACCTTTTAAGGCAGAACTCCGGGATAGGCGAACTTCTCATTTTATTAAATAAAG
GATATAAGAGAGACACAATTCAGACAGACAACCTAAAGGTGGTTAAAGTTTTGTCCATGAAGGAG
TCTGTAAACTCAAGTATTACATTGCTCAAAAGGATTCAACGACTTACGAGTTTTGAAGGACAATG
GGAGATCAAACACGTACCTAATGATTGCAATTTAATTACTGATCAACAAGCAAAGATTAGCCTTA
CATGGCAGACAAACTTACAGATTTTCGAAGTGCCTCTAAATATTGTGTCTATGGCTCTTCAACAA
GACAAAACATTTAGCGATTTTTAACATTTGATTTGATGTAACTTTGATTTATTTTTCACCAAAAA
AATTATAAAATTTTATAGAATGTTTTGAATATTAGGGATAAATATCAAAATTATACATGAATTAT
GGTTTAATGTGCAATTGTATACATAAAATTTTGATTTGATCCAATTCTTGTAAATTATTAACACA
ATTATTGATATAACACCCTTTTATGTTTATATATTAAATACAATAATATTATATTTATCCAATAT
AAAAATAAATTGATGTATTTATTTCTTTAAATGTATATAAATAAATCAAAATTAAAGTTTCAAGG
ATACATTTAAACCACAATTAAAGTTTTCACATGTATAATTAAATAAAATTAAAGTTCATGTATAA
ATTAAATATAAATCAAAGCTAAGTGTATTTTTGAAATTTATCCCAGAATATGATA
Found at i:329953 original size:31 final size:31
Alignment explanation
Indices: 329918--329987 Score: 94
Period size: 29 Copynumber: 2.3 Consensus size: 31
329908 TTTAAACCAT
329918 AATTAAAGTTTTCACGTGTATA-ATTAAATA-A
1 AATTAAAGTTTTCA--TGTATATATTAAATATA
329949 AATTAAAG--TTCATGTATATATTAAATATA
1 AATTAAAGTTTTCATGTATATATTAAATATA
329978 AATTAAAGTT
1 AATTAAAGTT
329988 AATGTGTATT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
27 6 0.17
28 8 0.23
29 13 0.37
31 8 0.23
ACGTcount: A:0.47, C:0.04, G:0.09, T:0.40
Consensus pattern (31 bp):
AATTAAAGTTTTCATGTATATATTAAATATA
Found at i:329968 original size:29 final size:29
Alignment explanation
Indices: 329934--329992 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
329924 AGTTTTCACG
329934 TGTATA-ATTAAATA-AAATTAAAGTTCA
1 TGTATATATTAAATATAAATTAAAGTTCA
*
329961 TGTATATATTAAATATAAATTAAAGTTAA
1 TGTATATATTAAATATAAATTAAAGTTCA
329990 TGT
1 TGT
329993 GTATTTTTGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 6 0.21
28 8 0.28
29 15 0.52
ACGTcount: A:0.49, C:0.02, G:0.08, T:0.41
Consensus pattern (29 bp):
TGTATATATTAAATATAAATTAAAGTTCA
Found at i:330454 original size:5 final size:5
Alignment explanation
Indices: 330444--330473 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
330434 ATTTGGATCT
330444 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC
330474 TCTATCACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
CTCTC
Found at i:334950 original size:30 final size:30
Alignment explanation
Indices: 334893--334951 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
334883 TGTATGATTG
*
334893 TATATAAGATTTTGATTTTGTGTAATTTTA
1 TATATAAGATTTTGATTTTGTGCAATTTTA
334923 TATATGAA-ATTTTGA-TTTGATGCAATTTT
1 TATAT-AAGATTTTGATTTTG-TGCAATTTT
334952 TGTAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 4 0.15
30 20 0.77
31 2 0.08
ACGTcount: A:0.31, C:0.02, G:0.14, T:0.54
Consensus pattern (30 bp):
TATATAAGATTTTGATTTTGTGCAATTTTA
Found at i:337690 original size:13 final size:13
Alignment explanation
Indices: 337654--337704 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
337644 ATTAGGAGTT
*
337654 GATTAAAAGAATA
1 GATTAAAAGAAAA
* * *
337667 CAATAAGAGAAAA
1 GATTAAAAGAAAA
337680 GATTAAAAGAAAA
1 GATTAAAAGAAAA
*
337693 -TTTAAAAGAAAA
1 GATTAAAAGAAAA
337705 ATCTTGTGCC
Statistics
Matches: 30, Mismatches: 8, Indels: 1
0.77 0.21 0.03
Matches are distributed among these distances:
12 11 0.37
13 19 0.63
ACGTcount: A:0.67, C:0.02, G:0.14, T:0.18
Consensus pattern (13 bp):
GATTAAAAGAAAA
Found at i:341858 original size:17 final size:17
Alignment explanation
Indices: 341832--341864 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
341822 ACTAGACCTT
341832 TTATAAAACAACTTAAG
1 TTATAAAACAACTTAAG
*
341849 TTATAGAACAACTTAA
1 TTATAAAACAACTTAA
341865 TGGTTGTTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.12, G:0.06, T:0.30
Consensus pattern (17 bp):
TTATAAAACAACTTAAG
Found at i:355214 original size:41 final size:44
Alignment explanation
Indices: 355169--355251 Score: 109
Period size: 44 Copynumber: 2.0 Consensus size: 44
355159 ATGTTTCAGG
*
355169 ATGAGAATGAG-A-A-TGTGATAAAGGAAGACTTATGACTCGAA
1 ATGAGAATGAGAATATTGTGAAAAAGGAAGACTTATGACTCGAA
** *
355210 ATGAGCGTGAGAATATTGTTAAAAAGGAAGACTTATGACTCG
1 ATGAGAATGAGAATATTGTGAAAAAGGAAGACTTATGACTCG
355252 GTTGAGCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 9 0.26
42 1 0.03
43 1 0.03
44 24 0.69
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (44 bp):
ATGAGAATGAGAATATTGTGAAAAAGGAAGACTTATGACTCGAA
Found at i:355285 original size:40 final size:40
Alignment explanation
Indices: 355228--355313 Score: 145
Period size: 40 Copynumber: 2.1 Consensus size: 40
355218 GAGAATATTG
*
355228 TTAAAAAGGAAGACTTATGACTCGGTTGAGCATAAGATTA
1 TTAAAAAGGAAGACTTATGACTCAGTTGAGCATAAGATTA
* *
355268 TTAAAAAGGAAGGCTTATGACTCAGTTGAGCATAAGATTG
1 TTAAAAAGGAAGACTTATGACTCAGTTGAGCATAAGATTA
355308 TTAAAA
1 TTAAAA
355314 GTAAGACACA
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.28
Consensus pattern (40 bp):
TTAAAAAGGAAGACTTATGACTCAGTTGAGCATAAGATTA
Found at i:356042 original size:21 final size:21
Alignment explanation
Indices: 355988--356042 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
355978 AAGTAAGACA
*
355988 TGTATCGGTAAAACTGTCACT
1 TGTATCGGTAGAACTGTCACT
*** *
356009 TGTATCAACAGAACTGTGACT
1 TGTATCGGTAGAACTGTCACT
356030 TGTATCGGTAGAA
1 TGTATCGGTAGAA
356043 ATTTGCACAT
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (21 bp):
TGTATCGGTAGAACTGTCACT
Found at i:356319 original size:29 final size:29
Alignment explanation
Indices: 356286--356341 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
356276 CCTAACCAAT
*
356286 GATAGTTTTTAG-GTTTTGGGTGTTACAAC
1 GATAG-TTTTAGAGTTTTAGGTGTTACAAC
*
356315 GATAGTTTTCGAGTTTTAGGTGTTACA
1 GATAGTTTTAGAGTTTTAGGTGTTACA
356342 CTTTTAATGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.21, C:0.07, G:0.27, T:0.45
Consensus pattern (29 bp):
GATAGTTTTAGAGTTTTAGGTGTTACAAC
Found at i:360629 original size:41 final size:41
Alignment explanation
Indices: 360567--360720 Score: 236
Period size: 41 Copynumber: 3.8 Consensus size: 41
360557 TTGTATAAAT
* * * *
360567 GGAATACTCATGTCTCAAAATGAGAACGAGATTATGAATAA
1 GGAAGACTCATATCTCGAAATGAGAATGAGATTATGAATAA
360608 GGAAGACTCATATCTCGAAATGAGAATGAGATTATGAATAA
1 GGAAGACTCATATCTCGAAATGAGAATGAGATTATGAATAA
* *
360649 GGAAGACTCATATCTCGAAATGAGAATGAGATTTTGATTAA
1 GGAAGACTCATATCTCGAAATGAGAATGAGATTATGAATAA
* *
360690 GGAAGACTCATGTCTCGAGATGAGAATGAGA
1 GGAAGACTCATATCTCGAAATGAGAATGAGA
360721 ATACGGTTAA
Statistics
Matches: 105, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 105 1.00
ACGTcount: A:0.41, C:0.11, G:0.23, T:0.25
Consensus pattern (41 bp):
GGAAGACTCATATCTCGAAATGAGAATGAGATTATGAATAA
Found at i:360763 original size:82 final size:82
Alignment explanation
Indices: 360572--360764 Score: 192
Period size: 82 Copynumber: 2.4 Consensus size: 82
360562 TAAATGGAAT
* * ** *
360572 ACTCATGTCTCAAAATGAGAACGAGATTATGAATAAGGAAGACTCATATCTCGAAATGAGAATGA
1 ACTCATATCTCGAAATGAGAATAAGATTTTGAATAAGGAAGACTCATATCTCGAAATGAGAATGA
* * **
360637 GATTATGAATAAGGAAG
66 GAATACGAATAAAAAAG
* * * *
360654 ACTCATATCTCGAAATGAGAATGAGATTTTGATTAAGGAAGACTCATGTCTCGAGATGAGAATGA
1 ACTCATATCTCGAAATGAGAATAAGATTTTGAATAAGGAAGACTCATATCTCGAAATGAGAATGA
**
360719 GAATACGGTTAAAAAAAG
66 GAATACGAAT-AAAAAAG
* * *
360737 ACTTATGA-CTCGATA-GAGCATAAGATTT
1 ACTCAT-ATCTCGAAATGAGAATAAGATTT
360765 GTTGAAGAGA
Statistics
Matches: 92, Mismatches: 17, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
82 75 0.82
83 16 0.17
84 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.22, T:0.25
Consensus pattern (82 bp):
ACTCATATCTCGAAATGAGAATAAGATTTTGAATAAGGAAGACTCATATCTCGAAATGAGAATGA
GAATACGAATAAAAAAG
Found at i:367765 original size:43 final size:40
Alignment explanation
Indices: 367691--367877 Score: 146
Period size: 41 Copynumber: 4.5 Consensus size: 40
367681 GGTGTACAAA
*** *
367691 AAGGAAGACTCATGTCTCGGGTTGAGCATGAGAAATTGTAT
1 AAGGAAGACTCATGTCTCGAAATGAGAATGAGAAATTG-AT
*
367732 AAATGGAATACTCATGTCTCGAAATGAGAATGAG--ATTACGAAT
1 -AA-GGAAGACTCATGTCTCGAAATGAGAATGAGAAATT--G-AT
* * **
367775 AAGGAAGACTCATATCTCGAAATGAGAATGGGATTTTGATT
1 AAGGAAGACTCATGTCTCGAAATGAGAATGAGAAATTGA-T
* *
367816 AAGGAAGACTCATGTCTC-AAGATGAGAATGAGAATATGGTT
1 AAGGAAGACTCATGTCTCGAA-ATGAGAATGAGAA-ATTGAT
* *
367857 AAAGGAAGACTTATGGCTCGA
1 -AAGGAAGACTCATGTCTCGA
367878 TAGAGCATAA
Statistics
Matches: 117, Mismatches: 18, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
40 3 0.03
41 61 0.52
42 22 0.19
43 31 0.26
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (40 bp):
AAGGAAGACTCATGTCTCGAAATGAGAATGAGAAATTGAT
Found at i:367795 original size:41 final size:41
Alignment explanation
Indices: 367736--367848 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 41
367726 TTGTATAAAT
*
367736 GGAATACTCATGTCTCGAAATGAGAATGAGATTACGAATAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTACGAATAA
* * ** *
367777 GGAAGACTCATATCTCGAAATGAGAATGGGATTTTGATTAA
1 GGAAGACTCATGTCTCGAAATGAGAATGAGATTACGAATAA
367818 GGAAGACTCATGTCTC-AAGATGAGAATGAGA
1 GGAAGACTCATGTCTCGAA-ATGAGAATGAGA
367849 ATATGGTTAA
Statistics
Matches: 63, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 2 0.03
41 61 0.97
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.25
Consensus pattern (41 bp):
GGAAGACTCATGTCTCGAAATGAGAATGAGATTACGAATAA
Found at i:367892 original size:82 final size:82
Alignment explanation
Indices: 367736--367892 Score: 174
Period size: 82 Copynumber: 1.9 Consensus size: 82
367726 TTGTATAAAT
* * *
367736 GGAATACTCATGTCTCGAAATGAGAATGAGATTACGAATAAGGAAGACTCATATCTCGAAATGAG
1 GGAAGACTCATGTCTCGAAATGAGAATGAGAATACGAATAAGGAAGACTCATAGCTCGAAATGAG
**
367801 AATGGGATTTTGATTAA
66 AATAAGATTTTGATTAA
* ** * * *
367818 GGAAGACTCATGTCTC-AAGATGAGAATGAGAATATGGTTAAAGGAAGACTTATGGCTCGATA-G
1 GGAAGACTCATGTCTCGAA-ATGAGAATGAGAATACGAAT-AAGGAAGACTCATAGCTCGAAATG
*
367881 AGCATAAGATTT
64 AGAATAAGATTT
367893 GTTGAAGAGA
Statistics
Matches: 61, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
81 2 0.03
82 41 0.67
83 18 0.30
ACGTcount: A:0.38, C:0.11, G:0.25, T:0.26
Consensus pattern (82 bp):
GGAAGACTCATGTCTCGAAATGAGAATGAGAATACGAATAAGGAAGACTCATAGCTCGAAATGAG
AATAAGATTTTGATTAA
Found at i:369654 original size:158 final size:158
Alignment explanation
Indices: 369366--369687 Score: 520
Period size: 158 Copynumber: 2.0 Consensus size: 158
369356 TAAGTCAGCC
* * *
369366 TAACTCTCGCAAAGTGAGAATTCTCAATAGAAATTCTCTTCAAGTACCGAAAATAAAGCTGAAGC
1 TAACTCTCGCAAAGTGAGAATTCTCAATAGAAATTCTCTTCAAGCACCGAAAAAAAAGCGGAAGC
*
369431 ACCTCGAAATGAAAGAGCAACGAGAGAACTAAAAAGCAATAAGGAAGCAATGCAAACTAAGTGTT
66 AACTCGAAATGAAAGAGCAACGAGAGAACTAAAAAGCAATAAGGAAGCAATGCAAACTAAGTGTT
* * *
369496 TGAGTAAATGCTCTCAATATATATTCTT
131 TAAGTAAATACTCTCAATATATAGTCTT
369524 TAACTCTCGCAAAGTGAGAATTCTCAATAGAAATTCTCTTCAAGCACCGAAAAAAAAGCGGAAGC
1 TAACTCTCGCAAAGTGAGAATTCTCAATAGAAATTCTCTTCAAGCACCGAAAAAAAAGCGGAAGC
* * ** *
369589 AACTCGAAATGAAATAGCAACGAGAGAACTGAAAAGCGGTAAGGAAGTAATGCACAAC-AAGTGT
66 AACTCGAAATGAAAGAGCAACGAGAGAACTAAAAAGCAATAAGGAAGCAATGCA-AACTAAGTGT
369653 TTAAGTAAATACTCTCAATATATAGTCTT
130 TTAAGTAAATACTCTCAATATATAGTCTT
369682 TAACTC
1 TAACTC
369688 AAGAATAAAA
Statistics
Matches: 151, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
158 148 0.98
159 3 0.02
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.23
Consensus pattern (158 bp):
TAACTCTCGCAAAGTGAGAATTCTCAATAGAAATTCTCTTCAAGCACCGAAAAAAAAGCGGAAGC
AACTCGAAATGAAAGAGCAACGAGAGAACTAAAAAGCAATAAGGAAGCAATGCAAACTAAGTGTT
TAAGTAAATACTCTCAATATATAGTCTT
Found at i:371387 original size:84 final size:84
Alignment explanation
Indices: 371269--371476 Score: 210
Period size: 84 Copynumber: 2.5 Consensus size: 84
371259 TGATTTCTAG
* * * *
371269 TTGAGCTATTCAATCTTCTATTTAGTTGAAATCTTTAATT-CCAGCAAAAGGAGGATCTGACGTT
1 TTGAACTATACAATCTTCTATTTAGTTGAAATCTTAAATTCCCA-CAAAAGGAGAATCTGACGTT
371333 GATAG-CCTCCAATCTTTGGT
65 GATAGTCC-CCAATCTTTGGT
* ** *
371353 TTGAACTATACAATCTTCTATTTA-TATGAGATCTTAAATTCCCACAGTAGGAGAATCTGAGGTT
1 TTGAACTATACAATCTTCTATTTAGT-TGAAATCTTAAATTCCCACAAAAGGAGAATCTGACGTT
* *
371417 GATAGTCCCCAATTTTTTG-
65 GATAGTCCCCAATCTTTGGT
* * * * *
371436 TTGAGCTAT-CTAATCTACTATTCAGCTGAAATATTAAATTC
1 TTGAACTATAC-AATCTTCTATTTAGTTGAAATCTTAAATTC
371477 TGACTGTAGG
Statistics
Matches: 103, Mismatches: 16, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
82 1 0.01
83 33 0.32
84 64 0.62
85 5 0.05
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (84 bp):
TTGAACTATACAATCTTCTATTTAGTTGAAATCTTAAATTCCCACAAAAGGAGAATCTGACGTTG
ATAGTCCCCAATCTTTGGT
Found at i:377961 original size:642 final size:635
Alignment explanation
Indices: 376735--378209 Score: 1982
Period size: 642 Copynumber: 2.3 Consensus size: 635
376725 TATATGGTTG
* * *
376735 AAGACAAGAATGGATATGGATGAAATGAGC-AAGAAAAGGGATTTGGGGCAGATTCAAGCAAGAA
1 AAGAAAAGAATGGATATGGATGAAAGGAGCGAA-AAAAGGGATTT-TGGCAGATTCAAGCAAGAA
* * * *
376799 TGCCTATCCAGTTTAGAGAAAAAGGGATGACGTTTAATCCAATTAGGGAGATAAAAAAAAGAGGT
64 TGCCTGTTCAGTTTAGAGAAAGAGGGATGACG-TTAATCCAAGTAGGG-GATAAAAAAAAGAGGT
*
376864 CAAA-AAGCGAAGAACTGAGTCGAAGAC-A-AGGAGGACTAGATCATATTAAATAAAAAGAGGTG
127 CAAACAAGCGAAGAACTGAGTCGAAGACAAGAGGAGGACTAGATCATATTAAATAAAATGAGGTG
* * *
376926 AATCAGGAGCTGGAAGACAACTCGATAGGGCTAGTGGAAGGAAAGAAAAAACAAACGGTGCAACA
192 AATCAGGAGCTAGAAGACAACTCGATAGGGCTAATGGAAGGAAACAAAAAACAAACGGTGCAACA
* *
376991 AACGGATTACACAAATAACAATGTCTCAATGGATACAAAGTTGGATAATGAAATATCGACGACCG
257 AACGAATTACACAAATAACAATCTCTCAATGGATACAAAGTTGGATAATGAAATATCGACGACCG
* * * * *
377056 CTAATAAGCAGTTCAACTGGTCACAATAAAAATCTTAAGCTAGAATGTCCGTGGCCTGAGGCAAC
322 CTAATAAGCAGCTCAACCGATCACAATAAAAACCTTAAGCTAGAATATCCGTGGCCTGAGGCAAC
* * * * * ***
377121 CACGGACAGTTAGACGTCTGAAATACAAATTTTTACAAATTCAGCCTCAACTATTGTTTCTTATA
387 CACAGACAATTAGACATCTCAAACACAAATTAAGACAAATTCAGCCTCAACTATTGTTTCTTATA
* * *
377186 GAAACAAAAGTTAGTATGAAAAGTATAGAAATAATAAGAAGGAAGTGTGGCTATGTGAATGGGAT
452 GAAACAAAAGTTAGTATGAAAAGTAGAGAAAAAATAAGAAGGAAGTGTGGCTACGTGAATGGGAT
* *
377251 TGATGTGAGTGATGAAGGATCGAGAGGAGGTTTGTCGTTAGGCTAGAAGGATAACTTAAACATTA
517 TGATATGAGTGATGAAGGATCGAGAAGAGGTTTGTCGTTAGGCTAGAAGGATAACTTAAACATTA
* *
377316 GTTTAAAATTTCTAAATCGCATGTAAATGGCTGAGGGATGAACCGAGAGAAGGAGGT
582 GTTTAAAATTTCTAAATCGCATGTAAATGGATGAGGGATGAA-C-AGAG-AGGAGGC
* * * * *
377373 GAGATAGGAATGGATATGGATGAAGGGAGCGAAAAAAGGGATTTTAGGTAGATTCAAGCAAGAAT
1 AAGAAAAGAATGGATATGGATGAAAGGAGCGAAAAAAGGGATTTT-GGCAGATTCAAGCAAGAAT
* *
377438 GCCTGTTCAGTTTAGAGAAAGAGGGATGACGTTAAATCCAAGTAGGGCGATCAAAAAAAGAGGTT
65 GCCTGTTCAGTTTAGAGAAAGAGGGATGACGTT-AATCCAAGTAGGG-GATAAAAAAAAGAGGTC
* *
377503 AAACAAGCAAAGAACTAAGTCGAAGACAACGAGGAGGACTAGATCATATTAAATAAAATGAGGTG
128 AAACAAGCGAAGAACTGAGTCGAAGACAA-GAGGAGGACTAGATCATATTAAATAAAATGAGGTG
* *
377568 AATTAGGAGCTAGAAGACAAGC-CGAT-GGGACTAATGGAAGGAAACAAAAGA-AAACGAGTGCA
192 AATCAGGAGCTAGAAGACAA-CTCGATAGGG-CTAATGGAAGGAAACAAAAAACAAACG-GTGCA
* * ** *
377630 ACAAACGAATTACACAAATAACAATCTCTCAATGGATACAGAGTTGGATAATGAAATATTGGTGG
254 ACAAACGAATTACACAAATAACAATCTCTCAATGGATACAAAGTTGGATAATGAAATATCGACGA
** * * * * *
377695 TTGCTAATAAGCAAGCT-GACCGATCA-AGATGAAAACCTTAAGTTGGAATATCTGTGGCCTGAG
319 CCGCTAATAAGC-AGCTCAACCGATCACA-ATAAAAACCTTAAGCTAGAATATCCGTGGCCTGAG
* *
377758 GCAACCACAGACAATTAGACATCTCAAACACAAATTAAGACAAATTTAGCCTCAGCTATTGTTTC
382 GCAACCACAGACAATTAGACATCTCAAACACAAATTAAGACAAATTCAGCCTCAACTATTGTTTC
377823 TTATAGAAACAAAAGTTAGTATGAAAAGTACGA-AAAAAATAAGAAGGAAGTGTGGCTACGTGAA
447 TTATAGAAACAAAAGTTAGTATGAAAAGTA-GAGAAAAAATAAGAAGGAAGTGTGGCTACGTGAA
* * * *
377887 TGGGATTGATATGGGTGTTGAAGGATTGAGAAGAGGTTTGTCGTTAGGCTGGAAGGATAACTTAA
511 TGGGATTGATATGAGTGATGAAGGATCGAGAAGAGGTTTGTCGTTAGGCTAGAAGGATAACTTAA
*
377952 ACATTAGTTTAAAATTTCTAAATCGCATGTAAATGGATGAGGGATGAACTGAGAGGAGGC
576 ACATTAGTTTAAAATTTCTAAATCGCATGTAAATGGATGAGGGATGAACAGAGAGGAGGC
* * * *
378012 AAGAAAAAAATGGATATGGATGAAAGGAGCGAGAAAATGGATTTTGGACATATTCAAGCAAGAAT
1 AAGAAAAGAATGGATATGGATGAAAGGAGCGAAAAAAGGGATTTTGG-CAGATTCAAGCAAGAAT
* * * *
378077 GCATG-TCTAGTTTACAGAAAGAGGGATGACGATTAATCCAAGTACGATGGTAAAAAAAAAAGGA
65 GCCTGTTC-AGTTTAGAGAAAGAGGGATGACG-TTAATCCAAGTA-G--GGGATAAAAAAAA-GA
* * *
378141 GGTCAAACAAGCGAAGAATTGAGTCGAAGGCAAGGAGGAGGACTAGATCATATTAAATCAAATGA
124 GGTCAAACAAGCGAAGAACTGAGTCGAAGACAA-GAGGAGGACTAGATCATATTAAATAAAATGA
378206 GGTG
188 GGTG
378210 TGTCGAAACA
Statistics
Matches: 733, Mismatches: 84, Indels: 36
0.86 0.10 0.04
Matches are distributed among these distances:
637 2 0.00
638 116 0.16
639 118 0.16
640 7 0.01
641 18 0.02
642 467 0.64
643 5 0.01
ACGTcount: A:0.41, C:0.12, G:0.26, T:0.22
Consensus pattern (635 bp):
AAGAAAAGAATGGATATGGATGAAAGGAGCGAAAAAAGGGATTTTGGCAGATTCAAGCAAGAATG
CCTGTTCAGTTTAGAGAAAGAGGGATGACGTTAATCCAAGTAGGGGATAAAAAAAAGAGGTCAAA
CAAGCGAAGAACTGAGTCGAAGACAAGAGGAGGACTAGATCATATTAAATAAAATGAGGTGAATC
AGGAGCTAGAAGACAACTCGATAGGGCTAATGGAAGGAAACAAAAAACAAACGGTGCAACAAACG
AATTACACAAATAACAATCTCTCAATGGATACAAAGTTGGATAATGAAATATCGACGACCGCTAA
TAAGCAGCTCAACCGATCACAATAAAAACCTTAAGCTAGAATATCCGTGGCCTGAGGCAACCACA
GACAATTAGACATCTCAAACACAAATTAAGACAAATTCAGCCTCAACTATTGTTTCTTATAGAAA
CAAAAGTTAGTATGAAAAGTAGAGAAAAAATAAGAAGGAAGTGTGGCTACGTGAATGGGATTGAT
ATGAGTGATGAAGGATCGAGAAGAGGTTTGTCGTTAGGCTAGAAGGATAACTTAAACATTAGTTT
AAAATTTCTAAATCGCATGTAAATGGATGAGGGATGAACAGAGAGGAGGC
Found at i:383637 original size:35 final size:35
Alignment explanation
Indices: 383598--383665 Score: 91
Period size: 35 Copynumber: 1.9 Consensus size: 35
383588 TCTTCTTCTC
383598 CATTGTTTCTCACAATCATTAATCATCATCACCTT
1 CATTGTTTCTCACAATCATTAATCATCATCACCTT
** * * *
383633 CATTGTTTCTTTCCATCGTTCATCATCATCACC
1 CATTGTTTCTCACAATCATTAATCATCATCACC
383666 CTCTCTATTG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.24, C:0.31, G:0.04, T:0.41
Consensus pattern (35 bp):
CATTGTTTCTCACAATCATTAATCATCATCACCTT
Found at i:385699 original size:29 final size:29
Alignment explanation
Indices: 385654--385722 Score: 93
Period size: 29 Copynumber: 2.4 Consensus size: 29
385644 CATATTCATT
*
385654 CACAAAGGCTCTCATATAATAGAATCAAC
1 CACAAAGGCTCTCATATAACAGAATCAAC
* * * *
385683 CATAAAGGCTCTTATATAACAGAATTAGC
1 CACAAAGGCTCTCATATAACAGAATCAAC
385712 CACAAAGGCTC
1 CACAAAGGCTC
385723 CTTTTTTAGA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.42, C:0.23, G:0.13, T:0.22
Consensus pattern (29 bp):
CACAAAGGCTCTCATATAACAGAATCAAC
Found at i:389953 original size:34 final size:35
Alignment explanation
Indices: 389914--389988 Score: 102
Period size: 34 Copynumber: 2.2 Consensus size: 35
389904 TTATGTTATA
*
389914 ATTTATGCTAATTA-GATTTTTTTATT-ATAAGAATT
1 ATTTATGCTAA-TAGGA-TTTTGTATTAATAAGAATT
389949 -TTTATGCTAATAGGATTTTGTATTAATAAGAATT
1 ATTTATGCTAATAGGATTTTGTATTAATAAGAATT
389983 ATTTAT
1 ATTTAT
389989 AGGATTGAGA
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
33 10 0.28
34 21 0.58
35 5 0.14
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.52
Consensus pattern (35 bp):
ATTTATGCTAATAGGATTTTGTATTAATAAGAATT
Found at i:403539 original size:127 final size:127
Alignment explanation
Indices: 403313--403567 Score: 368
Period size: 127 Copynumber: 2.0 Consensus size: 127
403303 TGTGAACCTT
* * * *
403313 GCTGTAAAAGTGTGAAAAATTCCCTGAAGGCAATTTTTGTTTGTTGCTTTATTACATTATTTAGA
1 GCTGTAAAAGTGTGAAAAATTCCCTGAAGGCAATTTTTGTTAGTTACTTCATTACACTATTTAGA
* * *
403378 AAGCAAATATTTTGTGATTTTGACACATACCTTAGTTGCAATAACTCCTGTTGTCCATTGTG
66 AAGCAAATATTTTGTGAGTTTGACACATACCTTAGTTACAATAACTCCTGTTGTCCATGGTG
* * * * * *
403440 GCTGTAAAAGTGTGGAAACTTTCCTGAAGGCAATTTTTGTTAGTTACTTCCTTATACTGTTTAGA
1 GCTGTAAAAGTGTGAAAAATTCCCTGAAGGCAATTTTTGTTAGTTACTTCATTACACTATTTAGA
*
403505 AAGCAAATAGTTTTGTG-GTTTGACACATATCTTAGTTACAATAACTCCTGTTGTCCATGGTG
66 AAGCAAATA-TTTTGTGAGTTTGACACATACCTTAGTTACAATAACTCCTGTTGTCCATGGTG
403567 G
1 G
403568 AGCCCTCAAG
Statistics
Matches: 113, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
127 106 0.94
128 7 0.06
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.39
Consensus pattern (127 bp):
GCTGTAAAAGTGTGAAAAATTCCCTGAAGGCAATTTTTGTTAGTTACTTCATTACACTATTTAGA
AAGCAAATATTTTGTGAGTTTGACACATACCTTAGTTACAATAACTCCTGTTGTCCATGGTG
Found at i:423308 original size:3 final size:3
Alignment explanation
Indices: 423263--423296 Score: 50
Period size: 3 Copynumber: 11.0 Consensus size: 3
423253 CATTTCATTC
*
423263 TCT TCT TTT TCT TCT TCT TCAT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT
423297 GGCCATCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 25 0.89
4 3 0.11
ACGTcount: A:0.03, C:0.29, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:433809 original size:25 final size:25
Alignment explanation
Indices: 433768--433816 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
433758 AATGCATTTT
*
433768 GTTTTAGTGAAATGGGGCACTTTGA
1 GTTTTAGTGAAACGGGGCACTTTGA
*
433793 GTTTTAGT-AATACGGGGCATTTTG
1 GTTTTAGTGAA-ACGGGGCACTTTG
433817 TTGTTAGTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 19 0.90
ACGTcount: A:0.22, C:0.08, G:0.31, T:0.39
Consensus pattern (25 bp):
GTTTTAGTGAAACGGGGCACTTTGA
Found at i:441896 original size:35 final size:35
Alignment explanation
Indices: 441837--441919 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 35
441827 TAGAAGTTGT
* * * *
441837 GTCTCGAGGCAGGGTTCCTAATGTCCCGAGACTAG
1 GTCTCGAGGTAGAGTCCCTAATGTCCCGAAACTAG
* *
441872 GTCTCGAGGTAGAGTCCCTCATGTCTCGAAACTAG
1 GTCTCGAGGTAGAGTCCCTAATGTCCCGAAACTAG
* *
441907 ATCTCGAGATAGA
1 GTCTCGAGGTAGA
441920 CCTCTCTTTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.24, C:0.24, G:0.28, T:0.24
Consensus pattern (35 bp):
GTCTCGAGGTAGAGTCCCTAATGTCCCGAAACTAG
Found at i:442052 original size:22 final size:22
Alignment explanation
Indices: 442024--442074 Score: 102
Period size: 22 Copynumber: 2.3 Consensus size: 22
442014 GTTCGATGTT
442024 TACTTGTCTCAAGACCATGGGG
1 TACTTGTCTCAAGACCATGGGG
442046 TACTTGTCTCAAGACCATGGGG
1 TACTTGTCTCAAGACCATGGGG
442068 TACTTGT
1 TACTTGT
442075 GTCGAGGCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (22 bp):
TACTTGTCTCAAGACCATGGGG
Found at i:444431 original size:18 final size:18
Alignment explanation
Indices: 444405--444442 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
444395 TAAATTTTTG
*
444405 AATTTGAAT-AACTCGAAT
1 AATTCGAATAAAC-CGAAT
444423 AATTCGAATAAACCGAAT
1 AATTCGAATAAACCGAAT
444441 AA
1 AA
444443 AACTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (18 bp):
AATTCGAATAAACCGAAT
Found at i:448964 original size:21 final size:21
Alignment explanation
Indices: 448938--448979 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
448928 GGAGATCAAC
448938 TTGAAAATAATATTTTAGTTA
1 TTGAAAATAATATTTTAGTTA
448959 TTGAAAATAATATTTTAGTTA
1 TTGAAAATAATATTTTAGTTA
448980 AGGGGAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (21 bp):
TTGAAAATAATATTTTAGTTA
Found at i:450616 original size:16 final size:17
Alignment explanation
Indices: 450597--450663 Score: 70
Period size: 16 Copynumber: 4.2 Consensus size: 17
450587 AAATTGTTTT
450597 AAATACA-AATTATTCC
1 AAATACATAATTATTCC
450613 AAATA-ATAATTATT-C
1 AAATACATAATTATTCC
*
450628 TAA-ACATAATTATTCC
1 AAATACATAATTATTCC
* * *
450644 AAAAACGTTATTATTCC
1 AAATACATAATTATTCC
450661 AAA
1 AAA
450664 CAATAATTGT
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
14 1 0.02
15 13 0.30
16 15 0.35
17 14 0.33
ACGTcount: A:0.49, C:0.15, G:0.01, T:0.34
Consensus pattern (17 bp):
AAATACATAATTATTCC
Found at i:450638 original size:15 final size:16
Alignment explanation
Indices: 450604--450671 Score: 68
Period size: 16 Copynumber: 4.2 Consensus size: 16
450594 TTTAAATACA
450604 AATTATTCCAAATAAT
1 AATTATTCCAAATAAT
* *
450620 AATTATTCTAAA-CAT
1 AATTATTCCAAATAAT
450635 AATTATTCCAAA-AACGT
1 AATTATTCCAAATAA--T
* *
450652 TATTATTCCAAACAAT
1 AATTATTCCAAATAAT
450668 AATT
1 AATT
450672 GTTTCAAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
15 14 0.33
16 15 0.35
17 12 0.28
18 2 0.05
ACGTcount: A:0.47, C:0.15, G:0.01, T:0.37
Consensus pattern (16 bp):
AATTATTCCAAATAAT
Found at i:455782 original size:17 final size:18
Alignment explanation
Indices: 455760--455795 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
455750 AAATAACATA
*
455760 ATTA-TTTATTATAAAAT
1 ATTATTTTAGTATAAAAT
455777 ATTATTTTAGTATAAAAT
1 ATTATTTTAGTATAAAAT
455795 A
1 A
455796 AATTTCGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (18 bp):
ATTATTTTAGTATAAAAT
Found at i:456593 original size:7 final size:7
Alignment explanation
Indices: 456564--456605 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
456554 ACTTGTAATA
456564 AATATTT
1 AATATTT
*
456571 ATTA-TT
1 AATATTT
*
456577 AAAATATT
1 AATAT-TT
456585 AATATTT
1 AATATTT
456592 AATATTT
1 AATATTT
456599 AATATTT
1 AATATTT
456606 TCAATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
6 4 0.14
7 19 0.66
8 6 0.21
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (7 bp):
AATATTT
Found at i:456655 original size:16 final size:16
Alignment explanation
Indices: 456624--456660 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
456614 ATGTGAAGAA
456624 TATTATTTAAAATTAT
1 TATTATTTAAAATTAT
456640 TATT-TTTAAAATTTAT
1 TATTATTTAAAA-TTAT
456656 TATTA
1 TATTA
456661 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTTAAAATTAT
Found at i:458090 original size:42 final size:42
Alignment explanation
Indices: 458029--458110 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
458019 TTATATAACC
* * *
458029 AAACTATTTGATTGCATCATTAGAATGAAGATTCCAACTTCA
1 AAACTATTCGATTACATCATTAGAACGAAGATTCCAACTTCA
* *
458071 AAACTCTTCGATTACATCATTAGAACGAGGATTCCAACTT
1 AAACTATTCGATTACATCATTAGAACGAAGATTCCAACTT
458111 TGAAAAGCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.32
Consensus pattern (42 bp):
AAACTATTCGATTACATCATTAGAACGAAGATTCCAACTTCA
Found at i:459126 original size:17 final size:17
Alignment explanation
Indices: 459104--459136 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
459094 ATTATGTAAA
459104 GAAACTAAAACTAAATT
1 GAAACTAAAACTAAATT
*
459121 GAAACTAAAATTAAAT
1 GAAACTAAAACTAAAT
459137 ATTTAAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.61, C:0.09, G:0.06, T:0.24
Consensus pattern (17 bp):
GAAACTAAAACTAAATT
Found at i:466330 original size:22 final size:23
Alignment explanation
Indices: 466283--466330 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
466273 TTTTGAACAA
* *
466283 TTTAATTTTTTTTTTTATGTTCT
1 TTTAACTTTTTTTTTTATGTTAT
*
466306 TTTAACTTTTTTTTTTCT-TTAT
1 TTTAACTTTTTTTTTTATGTTAT
466328 TTT
1 TTT
466331 CTATTCTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 6 0.27
23 16 0.73
ACGTcount: A:0.12, C:0.06, G:0.02, T:0.79
Consensus pattern (23 bp):
TTTAACTTTTTTTTTTATGTTAT
Found at i:483786 original size:2 final size:2
Alignment explanation
Indices: 483779--483803 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
483769 GTTCAATAAG
483779 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
483804 TATTTTAGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:485665 original size:16 final size:16
Alignment explanation
Indices: 485644--485677 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
485634 TTGACCTTCC
485644 TTTTGCATGGATTGAG
1 TTTTGCATGGATTGAG
485660 TTTTGCATGGATTGAG
1 TTTTGCATGGATTGAG
485676 TT
1 TT
485678 GTGGAATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.18, C:0.06, G:0.29, T:0.47
Consensus pattern (16 bp):
TTTTGCATGGATTGAG
Found at i:486307 original size:19 final size:20
Alignment explanation
Indices: 486270--486316 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
486260 TGAAAACATG
* *
486270 TTTATTTATTTTATAAATAT
1 TTTAATTATTTTATAAATAA
486290 TTTAATTATTTT-TAAATAA
1 TTTAATTATTTTATAAATAA
486309 TTTAATTA
1 TTTAATTA
486317 AAATTAAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 14 0.56
20 11 0.44
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAATTATTTTATAAATAA
Found at i:487167 original size:16 final size:15
Alignment explanation
Indices: 487143--487187 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
487133 AAAATTGTTT
487143 TATTATTATTTTAATA
1 TATTATTA-TTTAATA
*
487159 TATTTTTATTTAATA
1 TATTATTATTTAATA
*
487174 TAATATT-TTTAATA
1 TATTATTATTTAATA
487188 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
14 7 0.27
15 12 0.46
16 7 0.27
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTATTTAATA
Found at i:489389 original size:25 final size:25
Alignment explanation
Indices: 489360--489407 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
489350 AATTATTAAA
*
489360 GTTTACTCACTTTTATCTTTAAATT
1 GTTTACTCACTTTAATCTTTAAATT
489385 GTTTACTCACTTTAATCTTTAAA
1 GTTTACTCACTTTAATCTTTAAA
489408 GTTTTTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.27, C:0.17, G:0.04, T:0.52
Consensus pattern (25 bp):
GTTTACTCACTTTAATCTTTAAATT
Found at i:489588 original size:19 final size:19
Alignment explanation
Indices: 489566--489618 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
489556 AAAAAAAATA
489566 AAAAATTATTTAAAATTAC
1 AAAAATTATTTAAAATTAC
* * **
489585 AAAACTTA-CTAAAATTGT
1 AAAAATTATTTAAAATTAC
489603 AAAATATTATTTAAAA
1 AAAA-ATTATTTAAAA
489619 ATCTAAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 11 0.42
19 10 0.38
20 5 0.19
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAAATTATTTAAAATTAC
Found at i:490567 original size:14 final size:14
Alignment explanation
Indices: 490548--490588 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
490538 AAGTTTCACT
*
490548 GAAAATGGTTTTTG
1 GAAAATGATTTTTG
490562 GAAAATGATTTTTG
1 GAAAATGATTTTTG
*
490576 AAAAATGATTTTT
1 GAAAATGATTTTT
490589 TTTTAGAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.20, T:0.44
Consensus pattern (14 bp):
GAAAATGATTTTTG
Found at i:491813 original size:17 final size:18
Alignment explanation
Indices: 491780--491815 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
491770 ATAGAATATG
491780 AATATAGTTACAAATACA
1 AATATAGTTACAAATACA
*
491798 AATATA-TTACAGATACA
1 AATATAGTTACAAATACA
491815 A
1 A
491816 TTACAAATGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.56, C:0.11, G:0.06, T:0.28
Consensus pattern (18 bp):
AATATAGTTACAAATACA
Found at i:495174 original size:28 final size:28
Alignment explanation
Indices: 495120--495177 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
495110 CATTTTTCAC
*
495120 TTGGAATTAATTAAGTTTATGAATGAAT
1 TTGGAATTAATTAAGTTTATAAATGAAT
*
495148 TTGGAATTAATTATGTTTA-AAATTGAAT
1 TTGGAATTAATTAAGTTTATAAA-TGAAT
495176 TT
1 TT
495178 AATTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 2 0.07
28 25 0.93
ACGTcount: A:0.38, C:0.00, G:0.16, T:0.47
Consensus pattern (28 bp):
TTGGAATTAATTAAGTTTATAAATGAAT
Found at i:495408 original size:20 final size:21
Alignment explanation
Indices: 495365--495415 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
495355 ATTATTAGTA
* *
495365 TTTAGGG-TTATGGTTTTGAT
1 TTTAGGGTTTATGGTTTTAAG
495385 TTTAGGGTTTATGG-TTTAAG
1 TTTAGGGTTTATGGTTTTAAG
495405 TTTAGGGTTTA
1 TTTAGGGTTTA
495416 AAATTATAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 22 0.79
21 6 0.21
ACGTcount: A:0.18, C:0.00, G:0.29, T:0.53
Consensus pattern (21 bp):
TTTAGGGTTTATGGTTTTAAG
Found at i:495495 original size:14 final size:15
Alignment explanation
Indices: 495472--495505 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
495462 AGGTCTTGAT
495472 TTTAAGGTTTAAGGC
1 TTTAAGGTTTAAGGC
*
495487 TTTAA-GTTTAAGGT
1 TTTAAGGTTTAAGGC
495501 TTTAA
1 TTTAA
495506 ATATGAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (15 bp):
TTTAAGGTTTAAGGC
Found at i:495562 original size:6 final size:6
Alignment explanation
Indices: 495551--495587 Score: 65
Period size: 6 Copynumber: 6.2 Consensus size: 6
495541 CCCTAAATAC
*
495551 AAACAT AAACAT AAGCAT AAACAT AAACAT AAACAT A
1 AAACAT AAACAT AAACAT AAACAT AAACAT AAACAT A
495588 TTTAATTCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.65, C:0.16, G:0.03, T:0.16
Consensus pattern (6 bp):
AAACAT
Found at i:496024 original size:27 final size:27
Alignment explanation
Indices: 495974--496026 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
495964 GACCACGATG
**
495974 GAACGTATCCATCACCTGGCCACCCTA
1 GAACGTATCCATCACCTGAACACCCTA
496001 GAACGTATCCATCACCTGAACACCCT
1 GAACGTATCCATCACCTGAACACCCT
496027 GGATGATACG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.40, G:0.13, T:0.19
Consensus pattern (27 bp):
GAACGTATCCATCACCTGAACACCCTA
Found at i:497918 original size:33 final size:33
Alignment explanation
Indices: 497881--497976 Score: 104
Period size: 36 Copynumber: 2.8 Consensus size: 33
497871 ATAAATATCG
*
497881 AATATAAATTATTACTTTTTATATTATTAATAT
1 AATATAAATTATTACTTTTAATATTATTAATAT
*
497914 AATATTTTATATTATTACTTTTAATATTATTAATAT
1 AATA---TAAATTATTACTTTTAATATTATTAATAT
** *
497950 AATAT-TTTATATTACTTTTAAAATTAT
1 AATATAAAT-TATTACTTTTAATATTAT
497977 ATTTTATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
32 2 0.04
33 22 0.40
36 31 0.56
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (33 bp):
AATATAAATTATTACTTTTAATATTATTAATAT
Found at i:497921 original size:21 final size:21
Alignment explanation
Indices: 497897--497963 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 21
497887 AATTATTACT
497897 TTTTATATTATTAATATAATA
1 TTTTATATTATTAATATAATA
*
497918 -TTT-TA-TATT-AT-TACT-
1 TTTTATATTATTAATATAATA
*
497933 TTTAATATTATTAATATAATA
1 TTTTATATTATTAATATAATA
497954 TTTTATATTA
1 TTTTATATTA
497964 CTTTTAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 12
0.69 0.08 0.23
Matches are distributed among these distances:
16 5 0.14
17 4 0.11
18 8 0.22
19 4 0.11
20 6 0.17
21 9 0.25
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.60
Consensus pattern (21 bp):
TTTTATATTATTAATATAATA
Found at i:497933 original size:36 final size:36
Alignment explanation
Indices: 497888--497963 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
497878 TCGAATATAA
*
497888 ATTATTACTTTTTATATTATTAATATAATATTTTAT
1 ATTATTACTTTTAATATTATTAATATAATATTTTAT
497924 ATTATTACTTTTAATATTATTAATATAATATTTTAT
1 ATTATTACTTTTAATATTATTAATATAATATTTTAT
497960 ATTA
1 ATTA
497964 CTTTTAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (36 bp):
ATTATTACTTTTAATATTATTAATATAATATTTTAT
Found at i:501009 original size:21 final size:21
Alignment explanation
Indices: 500983--501032 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
500973 ACTTGTATCG
*
500983 GTAGAAATAAGAATTTTACCA
1 GTAGAAATAAGAATTGTACCA
*
501004 GTAGAAATAAGAATTGTATCA
1 GTAGAAATAAGAATTGTACCA
501025 GTAGAAAT
1 GTAGAAAT
501033 CCTAGTTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.28
Consensus pattern (21 bp):
GTAGAAATAAGAATTGTACCA
Found at i:501504 original size:5 final size:5
Alignment explanation
Indices: 501491--501529 Score: 53
Period size: 5 Copynumber: 7.8 Consensus size: 5
501481 TAAATGGATG
*
501491 AAAAC AAAAA AAAAC AAAAC AATAA- AAAAC AAAAC AAAA
1 AAAAC AAAAC AAAAC AAAAC AA-AAC AAAAC AAAAC AAAA
501530 TTTCAAGAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
4 2 0.07
5 26 0.87
6 2 0.07
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.03
Consensus pattern (5 bp):
AAAAC
Found at i:501511 original size:15 final size:15
Alignment explanation
Indices: 501491--501529 Score: 69
Period size: 15 Copynumber: 2.6 Consensus size: 15
501481 TAAATGGATG
501491 AAAACAAAAAAAAAC
1 AAAACAAAAAAAAAC
*
501506 AAAACAATAAAAAAC
1 AAAACAAAAAAAAAC
501521 AAAACAAAA
1 AAAACAAAA
501530 TTTCAAGAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.85, C:0.13, G:0.00, T:0.03
Consensus pattern (15 bp):
AAAACAAAAAAAAAC
Found at i:501730 original size:15 final size:15
Alignment explanation
Indices: 501710--501763 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
501700 CAATTACAAA
501710 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
501725 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
501742 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
501759 ATATT
1 ATATT
501764 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:501960 original size:26 final size:26
Alignment explanation
Indices: 501905--501962 Score: 68
Period size: 25 Copynumber: 2.3 Consensus size: 26
501895 ATGATTAAAT
*
501905 ATAA-ATAAATAAATATGTATGTTTA
1 ATAATATAAATAAATATATATGTTTA
501930 ATAATATAAA-AAATATAATAT-TTTA
1 ATAATATAAATAAATAT-ATATGTTTA
501955 ATTAATAT
1 A-TAATAT
501963 TTTAATAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 15 0.52
26 14 0.48
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.41
Consensus pattern (26 bp):
ATAATATAAATAAATATATATGTTTA
Found at i:501981 original size:12 final size:12
Alignment explanation
Indices: 501944--501993 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 12
501934 TATAAAAAAT
501944 ATAATATTTTAA
1 ATAATATTTTAA
*
501956 TTAATATTTT-A
1 ATAATATTTTAA
*
501967 ATAATTTTTTAA
1 ATAATATTTTAA
501979 AT-AT-TTTTAA
1 ATAATATTTTAA
501989 A-AATA
1 ATAATA
501994 AAAAAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
10 9 0.28
11 11 0.34
12 12 0.38
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
ATAATATTTTAA
Found at i:501985 original size:9 final size:11
Alignment explanation
Indices: 501944--501978 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
501934 TATAAAAAAT
501944 ATAATATTTTA
1 ATAATATTTTA
501955 ATTAATATTTTA
1 A-TAATATTTTA
*
501967 ATAATTTTTTA
1 ATAATATTTTA
501978 A
1 A
501979 ATATTTTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (11 bp):
ATAATATTTTA
Done.