Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168026.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_28, 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: 15507587
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 97000 characters in sequence are not A, C, G, or T
File 57 of 91
Found at i:9467900 original size:6 final size:6
Alignment explanation
Indices: 9467885--9467950 Score: 79
Period size: 6 Copynumber: 11.7 Consensus size: 6
9467875 AGAAATCCAA
*
9467885 AAAAAT -AAAAT AAAAAT AAAAAT --AAAT AAAAAT AAAAA- AAAATT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT
9467929 AAAAAAT AAAAAT -AAAAT AAAA
1 -AAAAAT AAAAAT AAAAAT AAAA
9467951 TCTATACTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
4 4 0.08
5 14 0.27
6 29 0.56
7 5 0.10
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:9467901 original size:11 final size:11
Alignment explanation
Indices: 9467886--9467950 Score: 73
Period size: 11 Copynumber: 5.8 Consensus size: 11
9467876 GAAATCCAAA
9467886 AAAAT-AAAAT
1 AAAATAAAAAT
9467896 AAAAATAAAAAT
1 -AAAATAAAAAT
9467908 -AAATAAAAAT
1 AAAATAAAAAT
9467918 AAAA-AAAAATT
1 AAAATAAAAA-T
9467929 AAAAAATAAAAAT
1 --AAAATAAAAAT
9467942 AAAATAAAA
1 AAAATAAAA
9467951 TCTATACTAA
Statistics
Matches: 48, Mismatches: 0, Indels: 12
0.80 0.00 0.20
Matches are distributed among these distances:
10 15 0.31
11 18 0.38
12 5 0.10
13 5 0.10
14 5 0.10
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:9468854 original size:23 final size:23
Alignment explanation
Indices: 9468800--9468858 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 23
9468790 TAAAAATAAT
*
9468800 AATAAT-AATATGTTAATAGATA
1 AATAATAAATATATTAATAGATA
*
9468822 AA-AATAAATATATTAGTAGATA
1 AATAATAAATATATTAATAGATA
9468844 AATAATAAATATATT
1 AATAATAAATATATT
9468859 CAAAAAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 3 0.09
22 18 0.55
23 12 0.36
ACGTcount: A:0.58, C:0.00, G:0.07, T:0.36
Consensus pattern (23 bp):
AATAATAAATATATTAATAGATA
Found at i:9468880 original size:17 final size:17
Alignment explanation
Indices: 9468792--9468903 Score: 75
Period size: 17 Copynumber: 6.2 Consensus size: 17
9468782 ATAAATGATA
*
9468792 AAAATAATAATAATAAT
1 AAAATAATAATAAAAAT
***
9468809 ATGTTAATAGATAAAAAT
1 AAAATAATA-ATAAAAAT
9468827 AAATATATTAGTAGATAAATAAT
1 AAA-ATA--A-TA-ATAAA-AAT
* *
9468850 AAATATATTCA-AAAAAT
1 AAA-ATAATAATAAAAAT
9468867 AAAA-AATAATAAAAAT
1 AAAATAATAATAAAAAT
*
9468883 AAAATACTAATAAAAAT
1 AAAATAATAATAAAAAT
9468900 AAAA
1 AAAA
9468904 GCAAAAATGG
Statistics
Matches: 75, Mismatches: 12, Indels: 16
0.73 0.12 0.16
Matches are distributed among these distances:
15 3 0.04
16 11 0.15
17 27 0.36
18 11 0.15
19 3 0.04
20 1 0.01
21 1 0.01
22 8 0.11
23 10 0.13
ACGTcount: A:0.67, C:0.02, G:0.04, T:0.28
Consensus pattern (17 bp):
AAAATAATAATAAAAAT
Found at i:9470280 original size:8 final size:8
Alignment explanation
Indices: 9470263--9470312 Score: 54
Period size: 8 Copynumber: 6.6 Consensus size: 8
9470253 CTCCAAAATC
9470263 TATT-TTT
1 TATTATTT
9470270 TATTATTT
1 TATTATTT
9470278 TATTATTT
1 TATTATTT
*
9470286 TGTTATTT
1 TATTATTT
9470294 T-TT-TTT
1 TATTATTT
9470300 T-TTATTTT
1 TATTA-TTT
9470308 TATTA
1 TATTA
9470313 GATAAATTTT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
6 6 0.16
7 6 0.16
8 23 0.61
9 3 0.08
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (8 bp):
TATTATTT
Found at i:9471209 original size:23 final size:23
Alignment explanation
Indices: 9471183--9471242 Score: 57
Period size: 23 Copynumber: 2.6 Consensus size: 23
9471173 TCAATTTGGC
** *
9471183 CTTTCTTTTTTTTTTTTTTTTTG
1 CTTTCTTTTTTTTTTAATTTTAG
** *
9471206 CTTTGGTTATTTTTTAATTTTAG
1 CTTTCTTTTTTTTTTAATTTTAG
*
9471229 CTTTCTTGTTTTTT
1 CTTTCTTTTTTTTT
9471243 AATCCATCCA
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.07, C:0.08, G:0.08, T:0.77
Consensus pattern (23 bp):
CTTTCTTTTTTTTTTAATTTTAG
Found at i:9471757 original size:17 final size:17
Alignment explanation
Indices: 9471735--9471776 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
9471725 TACTTTTTAA
9471735 TTTTTC-TTTTCTTT-AT
1 TTTTTCATTTT-TTTCAT
9471751 CTTTTTCATTTTTTTCAT
1 -TTTTTCATTTTTTTCAT
9471769 TTTTTCAT
1 TTTTTCAT
9471777 ATTAAATAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 17 0.74
18 6 0.26
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (17 bp):
TTTTTCATTTTTTTCAT
Found at i:9471764 original size:25 final size:25
Alignment explanation
Indices: 9471717--9471763 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
9471707 ACCCAATGAG
*
9471717 TTTCTTTCTACTTTTTAATTTTTCT
1 TTTCTTTATACTTTTTAATTTTTCT
*
9471742 TTTCTTTAT-CTTTTTCATTTTT
1 TTTCTTTATACTTTTTAATTTTT
9471764 TTCATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.11, C:0.15, G:0.00, T:0.74
Consensus pattern (25 bp):
TTTCTTTATACTTTTTAATTTTTCT
Found at i:9472306 original size:9 final size:9
Alignment explanation
Indices: 9472286--9472314 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
9472276 GTTGCATTTA
9472286 TTTTTATC-
1 TTTTTATCT
9472294 TTTTTATCT
1 TTTTTATCT
9472303 TTTTTATCT
1 TTTTTATCT
9472312 TTT
1 TTT
9472315 CTTTTAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTTATCT
Found at i:9472999 original size:16 final size:15
Alignment explanation
Indices: 9472953--9473026 Score: 69
Period size: 16 Copynumber: 4.8 Consensus size: 15
9472943 TGTTTTTTAT
*
9472953 TTTTTTATTTTTTTG
1 TTTTTTCTTTTTTTG
* *
9472968 TTTTTGTCTATGTTTG
1 TTTTT-TCTTTTTTTG
9472984 TTTTTTCTTTTCTTTG
1 TTTTTTCTTTT-TTTG
*
9473000 TTTTTTGTTTTTTT-
1 TTTTTTCTTTTTTTG
*
9473014 TCTTTTTGTTTTT
1 T-TTTTTCTTTTT
9473027 CCTTTTCAGT
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
14 1 0.02
15 23 0.46
16 26 0.52
ACGTcount: A:0.03, C:0.05, G:0.09, T:0.82
Consensus pattern (15 bp):
TTTTTTCTTTTTTTG
Found at i:9473014 original size:20 final size:20
Alignment explanation
Indices: 9472961--9473018 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
9472951 ATTTTTTTAT
* *
9472961 TTTTTTG-TTTTTGTCTATG
1 TTTTTTGTTTTTTTTCTTTG
*
9472980 TTTGTTT-TTTCTTTTCTTTG
1 TTT-TTTGTTTTTTTTCTTTG
9473000 TTTTTTGTTTTTTTTCTTT
1 TTTTTTGTTTTTTTTCTTT
9473019 TTGTTTTTCC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
19 6 0.19
20 26 0.81
ACGTcount: A:0.02, C:0.07, G:0.10, T:0.81
Consensus pattern (20 bp):
TTTTTTGTTTTTTTTCTTTG
Found at i:9473413 original size:25 final size:24
Alignment explanation
Indices: 9473377--9473440 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 24
9473367 TATGAGCTCA
*
9473377 TTTTTCCTTTTTCTTAAATTCTCTC
1 TTTTTCC-TTTTCTTAAATTCTCCC
* *
9473402 TTTTTCGCTTTTCTTAATTTTTCCC
1 TTTTTC-CTTTTCTTAAATTCTCCC
*
9473427 TTTTTCATTTTCTT
1 TTTTTCCTTTTCTT
9473441 TTTTTTTTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.21
25 26 0.76
26 1 0.03
ACGTcount: A:0.09, C:0.22, G:0.02, T:0.67
Consensus pattern (24 bp):
TTTTTCCTTTTCTTAAATTCTCCC
Found at i:9473437 original size:24 final size:25
Alignment explanation
Indices: 9473385--9473456 Score: 74
Period size: 25 Copynumber: 2.9 Consensus size: 25
9473375 CATTTTTCCT
* * * *
9473385 TTTTCTTAAATTCTCTCTTTTTCGC
1 TTTTCTTAATTTTTCCCTTTTTCGA
9473410 TTTTCTTAATTTTTCCCTTTTTC-A
1 TTTTCTTAATTTTTCCCTTTTTCGA
**
9473434 TTTTCTTTTTTTTTTCCCTTTTT
1 TTTTC-TTAATTTTTCCCTTTTT
9473457 TTGGTTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 2
0.83 0.12 0.04
Matches are distributed among these distances:
24 5 0.12
25 35 0.88
ACGTcount: A:0.08, C:0.21, G:0.01, T:0.69
Consensus pattern (25 bp):
TTTTCTTAATTTTTCCCTTTTTCGA
Found at i:9474068 original size:18 final size:17
Alignment explanation
Indices: 9474039--9474084 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
9474029 TTTGATATTT
9474039 GTTTTT-TTTTTTTTCA
1 GTTTTTATTTTTTTTCA
*
9474055 GTTCTTTATTTTTTTTTA
1 GTT-TTTATTTTTTTTCA
*
9474073 GTTTTTCTTTTT
1 GTTTTTATTTTT
9474085 AAAAATCTAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 3 0.12
17 11 0.42
18 12 0.46
ACGTcount: A:0.07, C:0.07, G:0.07, T:0.80
Consensus pattern (17 bp):
GTTTTTATTTTTTTTCA
Found at i:9474517 original size:26 final size:24
Alignment explanation
Indices: 9474488--9474550 Score: 58
Period size: 25 Copynumber: 2.5 Consensus size: 24
9474478 ATGTGTAATT
*
9474488 AAATATAAAATTATAATATTCATAAA
1 AAATATAAAATTAT-AT-TTAATAAA
*
9474514 AAATA-ATATATGTATATTTAATAAA
1 AAATATA-AAAT-TATATTTAATAAA
9474539 AAA-ATAAAATTA
1 AAATATAAAATTA
9474551 CCTTATAATG
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
23 2 0.06
24 4 0.13
25 12 0.39
26 10 0.32
27 3 0.10
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
AAATATAAAATTATATTTAATAAA
Found at i:9476148 original size:16 final size:16
Alignment explanation
Indices: 9476127--9476178 Score: 68
Period size: 16 Copynumber: 3.2 Consensus size: 16
9476117 GAACTAAAGC
*
9476127 TTACTAAATATAGAAA
1 TTACTAAAAATAGAAA
*
9476143 TTACTAAAAATGGAAA
1 TTACTAAAAATAGAAA
*
9476159 GTTGCTAAAAATAGAAA
1 -TTACTAAAAATAGAAA
9476176 TTA
1 TTA
9476179 AACAATTAAG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 16 0.53
17 14 0.47
ACGTcount: A:0.54, C:0.06, G:0.12, T:0.29
Consensus pattern (16 bp):
TTACTAAAAATAGAAA
Found at i:9477515 original size:52 final size:52
Alignment explanation
Indices: 9477425--9477551 Score: 150
Period size: 52 Copynumber: 2.4 Consensus size: 52
9477415 TATAACCATA
* * **
9477425 CAAACTTGTCC-ATTAAGAATCCTTTTGCTCTTAAAATTCTTCTCCTGTAAGT
1 CAAACTTG-CCTATTAAGAATCCTTTTCCCCTTAAAATTCTTCTCCTACAAGT
* *
9477477 CAAACTTGCCTATTAAGAATACC-TTTCCCCTTAGAATTCTTCTCTTACAAGT
1 CAAACTTGCCTATTAAGAAT-CCTTTTCCCCTTAAAATTCTTCTCCTACAAGT
* *
9477529 CAAACTTACCTATTAAAAATCCT
1 CAAACTTGCCTATTAAGAATCCT
9477552 CTTTATTTTA
Statistics
Matches: 64, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
51 4 0.06
52 58 0.91
53 2 0.03
ACGTcount: A:0.31, C:0.25, G:0.07, T:0.37
Consensus pattern (52 bp):
CAAACTTGCCTATTAAGAATCCTTTTCCCCTTAAAATTCTTCTCCTACAAGT
Found at i:9477567 original size:52 final size:52
Alignment explanation
Indices: 9477454--9477581 Score: 141
Period size: 52 Copynumber: 2.5 Consensus size: 52
9477444 TCCTTTTGCT
* * * * *
9477454 CTTAAAATTCTTCTCCTGTAAGTCAAACTTGCCTATTAAGAATACCTTTCCC
1 CTTAAAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAAAATACCTTTCAC
* * * *
9477506 CTTAGAATTCTTCTCTTACAAGTCAAACTTACCTATTAAAAAT-CCTCTTTAT
1 CTTAAAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAAAATACCT-TTCAC
* *
9477558 TTTAAAATTCTTCTTTTGCAAGTC
1 CTTAAAATTCTTCTCTTGCAAGTC
9477582 TTCTTGTCCA
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
51 3 0.05
52 59 0.95
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (52 bp):
CTTAAAATTCTTCTCTTGCAAGTCAAACTTACCTATTAAAAATACCTTTCAC
Found at i:9479252 original size:49 final size:49
Alignment explanation
Indices: 9479184--9479280 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
9479174 TTTATAACTT
* * *
9479184 AATTTAAATATTAATATTTTAAACTCGATTTGGATGTTCATATAACAAC
1 AATTTAAAAATTAACATTTTAAACTCAATTTGGATGTTCATATAACAAC
9479233 AATTTAAAAATTAACATTTTAAACTCAATTTGGATGTTCATATAACAA
1 AATTTAAAAATTAACATTTTAAACTCAATTTGGATGTTCATATAACAA
9479281 GGATGATCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (49 bp):
AATTTAAAAATTAACATTTTAAACTCAATTTGGATGTTCATATAACAAC
Found at i:9484300 original size:16 final size:16
Alignment explanation
Indices: 9484279--9484309 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9484269 TTAATATTAA
9484279 TTTTCTTTTTTTTTTC
1 TTTTCTTTTTTTTTTC
9484295 TTTTCTTTTTTTTTT
1 TTTTCTTTTTTTTTT
9484310 TGTTAAGCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (16 bp):
TTTTCTTTTTTTTTTC
Found at i:9486050 original size:12 final size:11
Alignment explanation
Indices: 9486026--9486090 Score: 57
Period size: 11 Copynumber: 5.9 Consensus size: 11
9486016 TAAAGAAACA
*
9486026 ATAAAAATGAG
1 ATAAAAATAAG
9486037 ATAAAAATCAAG
1 ATAAAAAT-AAG
9486049 AT--AAAT-AG
1 ATAAAAATAAG
9486057 ATAAATAAGTAAG
1 ATAAA-AA-TAAG
9486070 ATAAAAATAA-
1 ATAAAAATAAG
9486080 ATATAAAATAA
1 ATA-AAAATAA
9486091 AAATAATGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 14
0.75 0.02 0.23
Matches are distributed among these distances:
8 4 0.09
10 8 0.17
11 20 0.43
12 7 0.15
13 7 0.15
ACGTcount: A:0.68, C:0.02, G:0.09, T:0.22
Consensus pattern (11 bp):
ATAAAAATAAG
Found at i:9486070 original size:21 final size:21
Alignment explanation
Indices: 9486030--9486082 Score: 60
Period size: 21 Copynumber: 2.6 Consensus size: 21
9486020 GAAACAATAA
9486030 AAATGAGATAAA-AATCAAGAT
1 AAAT-AGATAAATAATCAAGAT
9486051 AAATAGATAAATAAGT-AAGAT
1 AAATAGATAAATAA-TCAAGAT
9486072 AAA-A-ATAAATA
1 AAATAGATAAATA
9486083 TAAAATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
19 7 0.23
20 8 0.27
21 14 0.47
22 1 0.03
ACGTcount: A:0.66, C:0.02, G:0.11, T:0.21
Consensus pattern (21 bp):
AAATAGATAAATAATCAAGAT
Found at i:9487163 original size:2 final size:2
Alignment explanation
Indices: 9487156--9487182 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9487146 ATCTATAAAC
9487156 TA 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 TA T
9487183 TTGTGTGTGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9489592 original size:3 final size:3
Alignment explanation
Indices: 9489581--9489621 Score: 73
Period size: 3 Copynumber: 13.3 Consensus size: 3
9489571 ATTTACCTCC
9489581 TCT TGCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT T-CT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
9489622 GTGCCCCGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:9492619 original size:20 final size:21
Alignment explanation
Indices: 9492574--9492619 Score: 69
Period size: 20 Copynumber: 2.3 Consensus size: 21
9492564 TGAAATTAAC
9492574 ACAATAAAAATATATTAAAAT
1 ACAATAAAAATATATTAAAAT
*
9492595 A-AATAAAAATTTATTAAAA-
1 ACAATAAAAATATATTAAAAT
9492614 ACAATA
1 ACAATA
9492620 TAACTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.28
Consensus pattern (21 bp):
ACAATAAAAATATATTAAAAT
Found at i:9497142 original size:2 final size:2
Alignment explanation
Indices: 9497135--9497172 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
9497125 CCTCGGGGCC
9497135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9497173 AAACAAATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9497747 original size:2 final size:2
Alignment explanation
Indices: 9497740--9497788 Score: 71
Period size: 2 Copynumber: 24.5 Consensus size: 2
9497730 TACTCGAGGC
* * *
9497740 AT AT AT AT AA AA AT AT AT CT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9497782 AT AT AT A
1 AT AT AT A
9497789 ACAAAGCTAA
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:9498803 original size:21 final size:19
Alignment explanation
Indices: 9498770--9498813 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
9498760 TTCAGTGATG
*
9498770 TAATAATTGATTATATGAATA
1 TAATAATTAATTATA--AATA
*
9498791 TAATATTTAATTATAAATA
1 TAATAATTAATTATAAATA
9498810 TAAT
1 TAAT
9498814 TTCAAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
21 13 0.62
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (19 bp):
TAATAATTAATTATAAATA
Found at i:9500974 original size:173 final size:172
Alignment explanation
Indices: 9500650--9500979 Score: 531
Period size: 173 Copynumber: 1.9 Consensus size: 172
9500640 TTTTTTGTAG
9500650 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTCGATTATCAAGGAAAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTC-ATTATCAAGGAAAA
* *
9500715 TTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGAGGAAAATTGATAC
65 TTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTAAGGAAAATTGATAC
*
9500780 TTTCAACTTTTCCCCAAAATATTTTTTGGAAATTTATTTCTAA
130 TTTCAACTTTTCCCAAAAATATTTTTTGGAAATTTATTTCTAA
* * * *
9500823 GGAAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTTTTTGAAATTT-ATT-TCTGAGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAA-A-TATTTTTTGGAAATTTCATTATC-AAGGAA
9500886 AATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTGGAAATTTATTTCTAAGGAAAATTGAT
63 AATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTAAGGAAAATTGAT
9500950 ACTTTCAACTTTTCCCTAAAAATATTTTTT
128 ACTTTCAACTTTTCCC-AAAAATATTTTTT
9500980 TTGGAATTTT
Statistics
Matches: 146, Mismatches: 7, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
172 57 0.39
173 74 0.51
174 1 0.01
175 14 0.10
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (172 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTCATTATCAAGGAAAAT
TGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTAAGGAAAATTGATACT
TTCAACTTTTCCCAAAAATATTTTTTGGAAATTTATTTCTAA
Found at i:9500980 original size:59 final size:58
Alignment explanation
Indices: 9500650--9500985 Score: 529
Period size: 59 Copynumber: 5.8 Consensus size: 58
9500640 TTTTTTGTAG
*
9500650 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATA-TTTTTTGGAAATTTCGATTATC-AA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTT--ATT-TCTAA
* *
9500709 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTAA
*
9500767 GGAAAATTGATACTTTCAACTTTTCCC-CAAAATA-TTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTAA
* * *
9500823 GGAAAATTGATACTTTCAACTTTTCCCTAAAATATTTTTTTTTTGAAATTTATTTCTGA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAA-ATATTTTTTTGGAAATTTATTTCTAA
9500882 GGAAAATTGATACTTTCAACTTTTCCC-AAAAATATTTTTTTGGAAATTTATTTCTAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTAA
9500939 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAA
1 GGAAAATTGATACTTTCAACTTTTCCCTAAAAATA-TTTTTTTGGAA
9500986 TTTTTTATTT
Statistics
Matches: 257, Mismatches: 13, Indels: 14
0.90 0.05 0.05
Matches are distributed among these distances:
56 47 0.18
57 61 0.24
58 44 0.17
59 92 0.36
60 13 0.05
ACGTcount: A:0.34, C:0.13, G:0.09, T:0.44
Consensus pattern (58 bp):
GGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTGGAAATTTATTTCTAA
Found at i:9500982 original size:115 final size:114
Alignment explanation
Indices: 9500650--9500988 Score: 590
Period size: 116 Copynumber: 2.9 Consensus size: 114
9500640 TTTTTTGTAG
9500650 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTGGAAATTTCGATTATC-AAGGAAA
1 GGAAAATTGATACTTTCAACTTTT-CCCAAAAATATTTTTTGGAAATTT--ATT-TCTAAGGAAA
9500714 ATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGA
62 ATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGA
*
9500767 GGAAAATTGATACTTTCAACTTTTCCCCAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATTG
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATTG
*
9500832 ATACTTTCAACTTTTCCCTAAAATATTTTTTTTTTGAAATTTATTTCTGA
66 ATACTTTCAACTTTTCCCTAAAA-ATATTTTTTTTGAAATTTATTTCTGA
9500882 GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTTGGAAATTTATTTCTAAGGAAAATT
1 GGAAAATTGATACTTTCAACTTTTCCCAAAAATA-TTTTTTGGAAATTTATTTCTAAGGAAAATT
*
9500947 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGGAATTT
65 GATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTT
9500989 TTTATTTTTA
Statistics
Matches: 214, Mismatches: 5, Indels: 8
0.94 0.02 0.04
Matches are distributed among these distances:
113 2 0.01
114 37 0.17
115 74 0.35
116 77 0.36
117 24 0.11
ACGTcount: A:0.33, C:0.13, G:0.09, T:0.45
Consensus pattern (114 bp):
GGAAAATTGATACTTTCAACTTTTCCCAAAAATATTTTTTGGAAATTTATTTCTAAGGAAAATTG
ATACTTTCAACTTTTCCCTAAAAATATTTTTTTTGAAATTTATTTCTGA
Found at i:9501023 original size:11 final size:11
Alignment explanation
Indices: 9501007--9501116 Score: 54
Period size: 11 Copynumber: 9.6 Consensus size: 11
9500997 TATTTAAAGA
9501007 AAAAAAATAAT
1 AAAAAAATAAT
9501018 AAAAAAATAAAT
1 AAAAAAAT-AAT
*
9501030 AAAAAGAATATT
1 AAAAA-AATAAT
9501042 ACATAAACCTAATCTAAT
1 A-A-AAA---AA--TAAT
9501060 AAATAAAA-AAT
1 AAA-AAAATAAT
9501071 -AAAAAATAA-
1 AAAAAAATAAT
*
9501080 ACAAAAAAAAAT
1 A-AAAAAATAAT
9501092 AAAAAAA-AA-
1 AAAAAAATAAT
9501101 AAAAAAA-AA-
1 AAAAAAATAAT
9501110 AAAAAAA
1 AAAAAAA
9501117 AAAAAAACCT
Statistics
Matches: 82, Mismatches: 4, Indels: 28
0.72 0.04 0.25
Matches are distributed among these distances:
9 20 0.24
10 6 0.07
11 25 0.30
12 12 0.15
13 4 0.05
14 5 0.06
16 3 0.04
17 3 0.04
18 4 0.05
ACGTcount: A:0.80, C:0.05, G:0.01, T:0.15
Consensus pattern (11 bp):
AAAAAAATAAT
Found at i:9501075 original size:1 final size:1
Alignment explanation
Indices: 9501064--9501123 Score: 84
Period size: 1 Copynumber: 60.0 Consensus size: 1
9501054 TCTAATAAAT
* * * *
9501064 AAAAAATAAAAAATAAACAAAAAAAAATAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
9501124 CCTGGAGCGG
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 51 1.00
ACGTcount: A:0.93, C:0.02, G:0.00, T:0.05
Consensus pattern (1 bp):
A
Found at i:9501077 original size:14 final size:13
Alignment explanation
Indices: 9501060--9501123 Score: 96
Period size: 12 Copynumber: 4.9 Consensus size: 13
9501050 CTAATCTAAT
9501060 AAATAAAAAATAAA
1 AAATAAAAAA-AAA
9501074 AAATAAACAAAAAA
1 AAATAAA-AAAAAA
9501088 AAATAAAAAAAAA
1 AAATAAAAAAAAA
9501101 AAA-AAAAAAAAA
1 AAATAAAAAAAAA
9501113 AAA-AAAAAAAA
1 AAATAAAAAAAA
9501124 CCTGGAGCGG
Statistics
Matches: 49, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
12 20 0.41
13 9 0.18
14 17 0.35
15 3 0.06
ACGTcount: A:0.92, C:0.02, G:0.00, T:0.06
Consensus pattern (13 bp):
AAATAAAAAAAAA
Found at i:9501090 original size:21 final size:19
Alignment explanation
Indices: 9501064--9501123 Score: 95
Period size: 18 Copynumber: 3.1 Consensus size: 19
9501054 TCTAATAAAT
9501064 AAAAAATAAAAAATAAACAAA
1 AAAAAATAAAAAA-AAA-AAA
9501085 AAAAAATAAAAAAAAAAAA
1 AAAAAATAAAAAAAAAAAA
9501104 AAAAAA-AAAAAAAAAAAA
1 AAAAAATAAAAAAAAAAAA
9501122 AA
1 AA
9501124 CCTGGAGCGG
Statistics
Matches: 39, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
18 14 0.36
19 9 0.23
20 3 0.08
21 13 0.33
ACGTcount: A:0.93, C:0.02, G:0.00, T:0.05
Consensus pattern (19 bp):
AAAAAATAAAAAAAAAAAA
Found at i:9501569 original size:30 final size:31
Alignment explanation
Indices: 9501533--9501591 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 31
9501523 ACTGGGCAGG
*
9501533 TGCCGGAAACTTC-AATGTT-GCCGGAATTGT
1 TGCCGGAAAATTCAAAT-TTCGCCGGAATTGT
9501563 TGCCGGAAAATTCAAATTTCGCCGGAATT
1 TGCCGGAAAATTCAAATTTCGCCGGAATT
9501592 TTCGTCGGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 14 0.54
31 12 0.46
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (31 bp):
TGCCGGAAAATTCAAATTTCGCCGGAATTGT
Found at i:9501622 original size:11 final size:11
Alignment explanation
Indices: 9501607--9501657 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
9501597 CGGAATCTGG
*
9501607 AAATTTCCCAG
1 AAATTTCCCAA
*
9501618 AAATTTCCAAA
1 AAATTTCCCAA
9501629 AAATTTTCGCCAA
1 AAA-TTTC-CCAA
*
9501642 AAATTT-CTAA
1 AAATTTCCCAA
9501652 AAATTT
1 AAATTT
9501658 TTTCTCACTC
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 9 0.26
11 12 0.35
12 7 0.21
13 6 0.18
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (11 bp):
AAATTTCCCAA
Found at i:9501647 original size:24 final size:23
Alignment explanation
Indices: 9501610--9501659 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
9501600 AATCTGGAAA
*
9501610 TTTCCCAGAAATTTCCAAAAAAT
1 TTTCCCAAAAATTTCCAAAAAAT
* *
9501633 TTTCGCCAAAAATTTCTAAAAATT
1 TTTC-CCAAAAATTTCCAAAAAAT
9501657 TTT
1 TTT
9501660 TCTCACTCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.17
24 19 0.83
ACGTcount: A:0.40, C:0.18, G:0.04, T:0.38
Consensus pattern (23 bp):
TTTCCCAAAAATTTCCAAAAAAT
Found at i:9501978 original size:4 final size:4
Alignment explanation
Indices: 9501969--9502179 Score: 50
Period size: 4 Copynumber: 52.2 Consensus size: 4
9501959 ATATTATAGG
* * * * * *
9501969 ATAA ATAA AT-A AT-A ATAA AAAA ATAT ATCAG ATAT ATAA TTAG ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA ATAA ATAA ATAA ATAA
* * * *
9502016 GT-A A-AA ATACA A-AA ATGA ATAAA ATAA AAAA GATAA A-AA TAAAA
1 ATAA ATAA ATA-A ATAA ATAA AT-AA ATAA ATAA -ATAA ATAA -ATAA
* * *
9502060 ATAA ATAA TATAT ATAT ATAC ATAA AT-A ATAAA ATACA CATAA ATATTA
1 ATAA ATAA -ATAA ATAA ATAA ATAA ATAA AT-AA ATA-A -ATAA ATA--A
* * * *
9502109 ACAA A-AA ATAA ATAA ATAA ATAT ATACA TATTA ATAC AT-A AT-A AT-A
1 ATAA ATAA ATAA ATAA ATAA ATAA ATA-A -ATAA ATAA ATAA ATAA ATAA
*
9502155 ATAA ATAA AT-A ATACA ATAC ATAA A
1 ATAA ATAA ATAA ATA-A ATAA ATAA A
9502180 ATACAAAAGA
Statistics
Matches: 155, Mismatches: 29, Indels: 46
0.67 0.13 0.20
Matches are distributed among these distances:
3 30 0.19
4 91 0.59
5 26 0.17
6 8 0.05
ACGTcount: A:0.66, C:0.05, G:0.02, T:0.27
Consensus pattern (4 bp):
ATAA
Found at i:9502054 original size:15 final size:16
Alignment explanation
Indices: 9502017--9502060 Score: 56
Period size: 15 Copynumber: 2.8 Consensus size: 16
9502007 ATTAGATAAG
9502017 TAAAAATACAAAAATGA
1 TAAAAATA-AAAAATGA
9502034 -ATAAAATAAAAAA-GA
1 TA-AAAATAAAAAATGA
9502049 TAAAAATAAAAA
1 TAAAAATAAAAA
9502061 TAAATAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
15 12 0.48
16 7 0.28
17 6 0.24
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (16 bp):
TAAAAATAAAAAATGA
Found at i:9502081 original size:55 final size:55
Alignment explanation
Indices: 9502022--9502136 Score: 137
Period size: 55 Copynumber: 2.1 Consensus size: 55
9502012 ATAAGTAAAA
*
9502022 ATACAAAAATGAATAAAATA-A-A-AAAGATAAAAATAAAAATAAATAATATATATAT
1 ATACAAAAAT-AATAAAATACACATAAAGATAAAAA-AAAAATAAATAA-ATAAATAT
* * * *
9502077 ATACATAAATAATAAAATACACATAAATATTAACAAAAAATAAATAAATAAATAT
1 ATACAAAAATAATAAAATACACATAAAGATAAAAAAAAAATAAATAAATAAATAT
9502132 ATACA
1 ATACA
9502137 TATTAATACA
Statistics
Matches: 52, Mismatches: 5, Indels: 6
0.83 0.08 0.10
Matches are distributed among these distances:
54 9 0.17
55 22 0.42
56 13 0.25
57 8 0.15
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (55 bp):
ATACAAAAATAATAAAATACACATAAAGATAAAAAAAAAATAAATAAATAAATAT
Found at i:9502100 original size:18 final size:21
Alignment explanation
Indices: 9502060--9502105 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 21
9502050 AAAAATAAAA
*
9502060 ATAAATAATATATATATATAC
1 ATAAATAATATATATATACAC
9502081 ATAAATAATA-A-A-ATACAC
1 ATAAATAATATATATATACAC
9502099 ATAAATA
1 ATAAATA
9502106 TTAACAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 12 0.50
19 1 0.04
20 1 0.04
21 10 0.42
ACGTcount: A:0.63, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
ATAAATAATATATATATACAC
Found at i:9502124 original size:39 final size:39
Alignment explanation
Indices: 9502081--9502184 Score: 97
Period size: 39 Copynumber: 2.7 Consensus size: 39
9502071 ATATATATAC
*
9502081 ATAAATAATAAAATACACATAAATA-TTAACAAAAAATAA
1 ATAAATAATAAAATACACATAAATACATAA-AAAAAATAA
* * * * *
9502120 ATAAATAA-ATATATACATATTAATACATAATAATAATAA
1 ATAAATAATA-AAATACACATAAATACATAAAAAAAATAA
* *
9502159 ATAAATAATACAATACATA-AAATACA
1 ATAAATAATAAAATACACATAAATACA
9502185 AAAGAAGAAG
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
38 7 0.13
39 42 0.79
40 4 0.08
ACGTcount: A:0.65, C:0.08, G:0.00, T:0.27
Consensus pattern (39 bp):
ATAAATAATAAAATACACATAAATACATAAAAAAAATAA
Found at i:9502371 original size:1 final size:1
Alignment explanation
Indices: 9502365--9502459 Score: 136
Period size: 1 Copynumber: 95.0 Consensus size: 1
9502355 CAACTCAACA
* * * *
9502365 TTTTTTTTTTGTTTTTTTTTTTGTTTTTTTTTTTTTTGTTTTTTTGTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
9502430 TGTTTTTTTTTGTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
9502460 AAAGCTCCTC
Statistics
Matches: 82, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 82 1.00
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (1 bp):
T
Found at i:9502393 original size:21 final size:22
Alignment explanation
Indices: 9502366--9502459 Score: 156
Period size: 22 Copynumber: 4.3 Consensus size: 22
9502356 AACTCAACAT
9502366 TTTTTTTTTGTTTTTTTTTTTG
1 TTTTTTTTTGTTTTTTTTTTTG
*
9502388 TTTTTTTTTTTTTTGTTTTTTTG
1 TTTTTTTTTGTTTT-TTTTTTTG
9502411 TTTTTTTTT-TTTTTTTTTTTG
1 TTTTTTTTTGTTTTTTTTTTTG
9502432 TTTTTTTTTGTTTTTTTTTTT-
1 TTTTTTTTTGTTTTTTTTTTTG
9502453 TTTTTTT
1 TTTTTTT
9502460 AAAGCTCCTC
Statistics
Matches: 69, Mismatches: 1, Indels: 5
0.92 0.01 0.07
Matches are distributed among these distances:
21 24 0.35
22 28 0.41
23 17 0.25
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (22 bp):
TTTTTTTTTGTTTTTTTTTTTG
Found at i:9502408 original size:29 final size:28
Alignment explanation
Indices: 9502365--9502459 Score: 156
Period size: 29 Copynumber: 3.4 Consensus size: 28
9502355 CAACTCAACA
*
9502365 TTTTTTTTTTG-TTTTTTTTTTTGTTTT
1 TTTTTTTTTTGTTTTTTTTTTTTTTTTT
9502392 TTTTTTTTTTGTTTTTTTGTTTTTTTTTT
1 TTTTTTTTTTGTTTTTTT-TTTTTTTTTT
9502421 TTTTTTTTTTGTTTTTTTTTGTTTTTTTT
1 TTTTTTTTTTGTTTTTTTTT-TTTTTTTT
9502450 TTTTTTTTTT
1 TTTTTTTTTT
9502460 AAAGCTCCTC
Statistics
Matches: 64, Mismatches: 1, Indels: 4
0.93 0.01 0.06
Matches are distributed among these distances:
27 11 0.17
28 8 0.12
29 45 0.70
ACGTcount: A:0.00, C:0.00, G:0.06, T:0.94
Consensus pattern (28 bp):
TTTTTTTTTTGTTTTTTTTTTTTTTTTT
Found at i:9502629 original size:41 final size:41
Alignment explanation
Indices: 9502463--9502897 Score: 769
Period size: 41 Copynumber: 10.7 Consensus size: 41
9502453 TTTTTTTAAA
*
9502463 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
9502502 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
9502544 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
9502584 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
9502625 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATT
9502667 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
9502708 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
9502749 GCTCCTCTAAACAGAGGCA--ACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
9502788 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
9502829 GCTCCTCTAAACAGAGGCA--ACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
9502869 GCTCCTCTAAACAGAGGCACCACGACTTT
1 GCTCCTCTAAACAGAGGCACCACGACTTT
9502898 NNNNNNNNNN
Statistics
Matches: 384, Mismatches: 1, Indels: 20
0.95 0.00 0.05
Matches are distributed among these distances:
39 63 0.16
40 74 0.19
41 163 0.42
42 84 0.22
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:9502685 original size:83 final size:83
Alignment explanation
Indices: 9502463--9502897 Score: 775
Period size: 81 Copynumber: 5.3 Consensus size: 83
9502453 TTTTTTTAAA
9502463 GCTCCTCTAAACAGAGGCA--ACGACTTTGG-AAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
9502525 GACTTTGGAAAAGTAAATT
66 GACTTT-GAAAAGTAAATT
9502544 GCTCCTCTAAACAGAGGCA--ACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
9502607 GACTTTGAAAAGTAAATT
66 GACTTTGAAAAGTAAATT
9502625 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
9502690 GACTTTGAAAAGTAAATT
66 GACTTTGAAAAGTAAATT
9502708 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCA--AC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
9502770 GACTTTGAAAAGTAAATT
66 GACTTTGAAAAGTAAATT
9502788 GCTCCTCTAAACAGAGGCACCACGACTTT-GAAAAGTAAATTGCTCCTCTAAACAGAGGCA--AC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
9502850 GACTTTTGAAAAGTAAATT
66 GAC-TTTGAAAAGTAAATT
9502869 GCTCCTCTAAACAGAGGCACCACGACTTT
1 GCTCCTCTAAACAGAGGCACCACGACTTT
9502898 NNNNNNNNNN
Statistics
Matches: 350, Mismatches: 0, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
80 85 0.24
81 104 0.30
82 70 0.20
83 91 0.26
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (83 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC
GACTTTGAAAAGTAAATT
Found at i:9507468 original size:49 final size:49
Alignment explanation
Indices: 9507400--9507496 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
9507390 TTTATAACTT
* * *
9507400 AATTTAAATATTAATATTTTAAACTCGATTTGGATGTTCATATAACAAC
1 AATTTAAAAATTAACATTTTAAACTCAATTTGGATGTTCATATAACAAC
9507449 AATTTAAAAATTAACATTTTAAACTCAATTTGGATGTTCATATAACAA
1 AATTTAAAAATTAACATTTTAAACTCAATTTGGATGTTCATATAACAA
9507497 GGATGATCTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.43, C:0.10, G:0.07, T:0.39
Consensus pattern (49 bp):
AATTTAAAAATTAACATTTTAAACTCAATTTGGATGTTCATATAACAAC
Found at i:9514260 original size:12 final size:11
Alignment explanation
Indices: 9514236--9514313 Score: 60
Period size: 11 Copynumber: 7.3 Consensus size: 11
9514226 TAAAGAAACA
*
9514236 ATAAAAATGAG
1 ATAAAAATAAG
9514247 ATAAAAATCAAG
1 ATAAAAAT-AAG
9514259 AT--AAAT-AG
1 ATAAAAATAAG
9514267 ATAAATAAGTAAG
1 ATAAA-AA-TAAG
9514280 ATAAAAAT-A-
1 ATAAAAATAAG
*
9514289 A-AAAAATAAA
1 ATAAAAATAAG
9514299 ATAAAAATAATG
1 ATAAAAATAA-G
9514311 ATA
1 ATA
9514314 GATACAATTA
Statistics
Matches: 55, Mismatches: 2, Indels: 19
0.72 0.03 0.25
Matches are distributed among these distances:
8 10 0.18
9 2 0.04
10 7 0.13
11 19 0.35
12 10 0.18
13 7 0.13
ACGTcount: A:0.69, C:0.01, G:0.09, T:0.21
Consensus pattern (11 bp):
ATAAAAATAAG
Found at i:9514280 original size:21 final size:21
Alignment explanation
Indices: 9514240--9514284 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
9514230 GAAACAATAA
9514240 AAATGAGATAAAAATCAAGAT
1 AAATGAGATAAAAATCAAGAT
9514261 AAAT-AGATAAATAAGT-AAGAT
1 AAATGAGATAAA-AA-TCAAGAT
9514282 AAA
1 AAA
9514285 AATAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.32
21 14 0.64
22 1 0.05
ACGTcount: A:0.64, C:0.02, G:0.13, T:0.20
Consensus pattern (21 bp):
AAATGAGATAAAAATCAAGAT
Found at i:9514368 original size:42 final size:43
Alignment explanation
Indices: 9514287--9514369 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 43
9514277 AAGATAAAAA
** *
9514287 TAAAAAAATAAAATAAAAATAATGATAGATACAATTATAAAGG
1 TAAAAAAATAAAATAAAAATAAAAATAAATACAATTATAAAGG
* *
9514330 TAAAAAAA-CAAATAAAAATAAAAATATAATATAA-TATAAA
1 TAAAAAAATAAAATAAAAATAAAAATA-AATACAATTATAAA
9514370 ATTAGACATT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
42 21 0.62
43 13 0.38
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (43 bp):
TAAAAAAATAAAATAAAAATAAAAATAAATACAATTATAAAGG
Found at i:9524868 original size:24 final size:24
Alignment explanation
Indices: 9524840--9524886 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
9524830 TTTTCAAAAT
*
9524840 ATAATCCA-TACAAAGTAAAATTCC
1 ATAAT-CATTACAAAGCAAAATTCC
*
9524864 ATAATCATTCCAAAGCAAAATTC
1 ATAATCATTACAAAGCAAAATTC
9524887 ATATTTCGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.49, C:0.21, G:0.04, T:0.26
Consensus pattern (24 bp):
ATAATCATTACAAAGCAAAATTCC
Found at i:9525561 original size:20 final size:20
Alignment explanation
Indices: 9525526--9525576 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 20
9525516 ATAATATAAA
*
9525526 ATTAACATAA-TAAAAATAT-
1 ATTAAAATAATTAAAAAT-TC
9525545 ATTAAAATAATTAAAAATTC
1 ATTAAAATAATTAAAAATTC
9525565 ATTAAAAATAAT
1 ATT-AAAATAAT
9525577 ATAACTAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 10 0.36
20 10 0.36
21 8 0.29
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (20 bp):
ATTAAAATAATTAAAAATTC
Found at i:9528401 original size:2 final size:2
Alignment explanation
Indices: 9528394--9528438 Score: 54
Period size: 2 Copynumber: 22.5 Consensus size: 2
9528384 TACTCGAGGC
* * * *
9528394 AT AT AT AT AA AA AT AA AT AT GT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9528436 AT A
1 AT A
9528439 ACAAAGCTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (2 bp):
AT
Found at i:9533690 original size:98 final size:98
Alignment explanation
Indices: 9533521--9533716 Score: 392
Period size: 98 Copynumber: 2.0 Consensus size: 98
9533511 GGAGGACCTA
9533521 ATCATGGATAGTACTCCTCTGGACATCAGCTTTTTGGAAAGCATTGGTATCTTGACTTCTCTCAA
1 ATCATGGATAGTACTCCTCTGGACATCAGCTTTTTGGAAAGCATTGGTATCTTGACTTCTCTCAA
9533586 AACCTTGTCTTTGTATGATTGCAGTCTGGCTGG
66 AACCTTGTCTTTGTATGATTGCAGTCTGGCTGG
9533619 ATCATGGATAGTACTCCTCTGGACATCAGCTTTTTGGAAAGCATTGGTATCTTGACTTCTCTCAA
1 ATCATGGATAGTACTCCTCTGGACATCAGCTTTTTGGAAAGCATTGGTATCTTGACTTCTCTCAA
9533684 AACCTTGTCTTTGTATGATTGCAGTCTGGCTGG
66 AACCTTGTCTTTGTATGATTGCAGTCTGGCTGG
9533717 CACTTTACCT
Statistics
Matches: 98, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
98 98 1.00
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.37
Consensus pattern (98 bp):
ATCATGGATAGTACTCCTCTGGACATCAGCTTTTTGGAAAGCATTGGTATCTTGACTTCTCTCAA
AACCTTGTCTTTGTATGATTGCAGTCTGGCTGG
Found at i:9537016 original size:22 final size:22
Alignment explanation
Indices: 9536988--9537117 Score: 75
Period size: 22 Copynumber: 5.8 Consensus size: 22
9536978 TTGATAAACT
9536988 ATTAACTATTAAGTTATTAATG
1 ATTAACTATTAAGTTATTAATG
* * * *
9537010 ATTAACTACAACTAAATTA-TATTT
1 ATTAACT---ATTAAGTTATTAATG
* *
9537034 ATTTACTTTTAAGTT-TCTAATG
1 ATTAACTATTAAGTTAT-TAATG
* * *
9537056 ATTAACTATTAAATTATCATTG
1 ATTAACTATTAAGTTATTAATG
* * *
9537078 ATTGATTATTAAGTTATTTATG
1 ATTAACTATTAAGTTATTAATG
* *
9537100 ATTGACTACTAAGGTTAT
1 ATTAACTATTAA-GTTAT
9537118 CGATTAATTA
Statistics
Matches: 78, Mismatches: 23, Indels: 13
0.68 0.20 0.11
Matches are distributed among these distances:
21 5 0.06
22 51 0.65
23 6 0.08
24 9 0.12
25 7 0.09
ACGTcount: A:0.37, C:0.08, G:0.08, T:0.47
Consensus pattern (22 bp):
ATTAACTATTAAGTTATTAATG
Found at i:9537175 original size:22 final size:22
Alignment explanation
Indices: 9537143--9537206 Score: 85
Period size: 22 Copynumber: 2.9 Consensus size: 22
9537133 AAATTGAAAC
*
9537143 AATTTACTATTAAGTTATCATT
1 AATTTATTATTAAGTTATCATT
*
9537165 AATTTATTATTAA-TTGACCATT
1 AATTTATTATTAAGTT-ATCATT
*
9537187 GATTTATTATTAAGTTATCA
1 AATTTATTATTAAGTTATCA
9537207 ATGATTAACT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.36, C:0.08, G:0.06, T:0.50
Consensus pattern (22 bp):
AATTTATTATTAAGTTATCATT
Found at i:9537211 original size:22 final size:22
Alignment explanation
Indices: 9537034--9537269 Score: 81
Period size: 22 Copynumber: 10.8 Consensus size: 22
9537024 AATTATATTT
9537034 ATTTACTT-TTAAGTT-TCTAATG
1 ATTTA-TTATTAAGTTATC-AATG
* * * *
9537056 ATTAACTATTAAATTATCATTG
1 ATTTATTATTAAGTTATCAATG
* **
9537078 ATTGATTATTAAGTTATTTATG
1 ATTTATTATTAAGTTATCAATG
* * * * *
9537100 ATTGACTACTAAGGTTATCGATT
1 ATTTATTATTAA-GTTATCAATG
* * * **
9537123 AATTACTATTAAATTGA--AACA
1 ATTTATTATTAAGTT-ATCAATG
* * *
9537144 ATTTACTATTAAGTTATCATTA
1 ATTTATTATTAAGTTATCAATG
* *
9537166 ATTTATTATTAA-TTGACCATTG
1 ATTTATTATTAAGTT-ATCAATG
9537188 ATTTATTATTAAGTTATCAATG
1 ATTTATTATTAAGTTATCAATG
* * * * *
9537210 ATTAACTACTAAATTATCACTTG
1 ATTTATTATTAAGTTATCA-ATG
* **
9537233 -TTTTTTATTAACCTATC-ATG
1 ATTTATTATTAAGTTATCAATG
* *
9537253 ATTTATTAATATGTTAT
1 ATTTATTATTAAGTTAT
9537270 TATCTTTTTA
Statistics
Matches: 156, Mismatches: 48, Indels: 21
0.69 0.21 0.09
Matches are distributed among these distances:
20 3 0.02
21 28 0.18
22 102 0.65
23 23 0.15
ACGTcount: A:0.35, C:0.09, G:0.08, T:0.48
Consensus pattern (22 bp):
ATTTATTATTAAGTTATCAATG
Found at i:9537523 original size:22 final size:22
Alignment explanation
Indices: 9537495--9537616 Score: 86
Period size: 22 Copynumber: 5.5 Consensus size: 22
9537485 AGGTATAAAA
9537495 AAGTTATCAATGATTGACAATT
1 AAGTTATCAATGATTGACAATT
* * * *
9537517 AAGTTATCGATTG-TTTACTACT
1 AAGTTATC-AATGATTGACAATT
* * * * *
9537539 AAATTATTAATGATTTACTACT
1 AAGTTATCAATGATTGACAATT
* *
9537561 AATTTATGAATGATTTG-CAATT
1 AAGTTATCAATGA-TTGACAATT
* *
9537583 AAATTATGAATGATTTGACAATT
1 AAGTTATCAATGA-TTGACAATT
9537606 AAGTTATCAAT
1 AAGTTATCAAT
9537617 TGTTTACTAC
Statistics
Matches: 81, Mismatches: 15, Indels: 7
0.79 0.15 0.07
Matches are distributed among these distances:
21 3 0.04
22 59 0.73
23 19 0.23
ACGTcount: A:0.39, C:0.08, G:0.11, T:0.42
Consensus pattern (22 bp):
AAGTTATCAATGATTGACAATT
Found at i:9537647 original size:22 final size:22
Alignment explanation
Indices: 9537530--9537751 Score: 168
Period size: 22 Copynumber: 10.2 Consensus size: 22
9537520 TTATCGATTG
*
9537530 TTTACTACTAAATTATTAATGA
1 TTTACTACTAAATTATGAATGA
*
9537552 TTTACTACTAATTTATGAATGA
1 TTTACTACTAAATTATGAATGA
* * *
9537574 TTTGCAATTAAATTATGAATGA
1 TTTACTACTAAATTATGAATGA
* * * *
9537596 TTTGACAATTAAGTTATCAATTG-
1 TTT-ACTACTAAATTATGAA-TGA
* *
9537619 TTTACTACTAAATAATTAATGA
1 TTTACTACTAAATTATGAATGA
* *
9537641 TTTACTACTTATTTATGAATGA
1 TTTACTACTAAATTATGAATGA
* *
9537663 TTTGCTATTAAATTATGAATGA
1 TTTACTACTAAATTATGAATGA
* * * *
9537685 TTTACCATTAAGTTATAAATGA
1 TTTACTACTAAATTATGAATGA
* *
9537707 TTT--TA-TAAAATTGTTG-GTGA
1 TTTACTACT-AAATT-ATGAATGA
*
9537727 TTTACTACT-AATTATTAATGA
1 TTTACTACTAAATTATGAATGA
9537748 TTTA
1 TTTA
9537752 TTATAAAGTT
Statistics
Matches: 157, Mismatches: 34, Indels: 19
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.01
20 12 0.08
21 14 0.09
22 111 0.71
23 17 0.11
24 2 0.01
ACGTcount: A:0.37, C:0.07, G:0.10, T:0.45
Consensus pattern (22 bp):
TTTACTACTAAATTATGAATGA
Found at i:9537659 original size:89 final size:88
Alignment explanation
Indices: 9537498--9537700 Score: 334
Period size: 89 Copynumber: 2.3 Consensus size: 88
9537488 TATAAAAAAG
* * * *
9537498 TTATCAATGATTGACAATTAAGTTATCGATTGTTTACTACTAAATTATTAATGATTTACTACTAA
1 TTATGAATGATTTACAATTAAGTTATCAATTGTTTACTACTAAATAATTAATGATTTACTACTAA
9537563 TTTATGAATGATTTGCAATTAAA
66 TTTATGAATGATTTGCAATTAAA
*
9537586 TTATGAATGATTTGACAATTAAGTTATCAATTGTTTACTACTAAATAATTAATGATTTACTACTT
1 TTATGAATGATTT-ACAATTAAGTTATCAATTGTTTACTACTAAATAATTAATGATTTACTACTA
*
9537651 ATTTATGAATGATTTGCTATTAAA
65 ATTTATGAATGATTTGCAATTAAA
*
9537675 TTATGAATGATTTACCATTAAGTTAT
1 TTATGAATGATTTACAATTAAGTTAT
9537701 AAATGATTTT
Statistics
Matches: 107, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
88 23 0.21
89 84 0.79
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.44
Consensus pattern (88 bp):
TTATGAATGATTTACAATTAAGTTATCAATTGTTTACTACTAAATAATTAATGATTTACTACTAA
TTTATGAATGATTTGCAATTAAA
Found at i:9538106 original size:22 final size:22
Alignment explanation
Indices: 9537821--9538259 Score: 142
Period size: 22 Copynumber: 20.4 Consensus size: 22
9537811 TGATTAACTA
* * *
9537821 ATTTACTACTAAATTATCACTA
1 ATTTACTATTAAATTATCAATT
* **
9537843 ATTTACTATTATATT-TTTATAT
1 ATTTACTATTAAATTATCAAT-T
* ** *
9537865 ATTTACCATTATTTTAAC-ATT
1 ATTTACTATTAAATTATCAATT
* **
9537886 AATTTACTACTT-AATTTTTTATT
1 -ATTTACTA-TTAAATTATCAATT
* * ***
9537909 ATTCACTA-AAAATTATCACCA
1 ATTTACTATTAAATTATCAATT
* *
9537930 ATTTACTACTAAATTATCAATA
1 ATTTACTATTAAATTATCAATT
** * * * *
9537952 ATTCGCTATCAAGTTATTACTT
1 ATTTACTATTAAATTATCAATT
9537974 ATTTA-TATTAAATTATGCACA--
1 ATTTACTATTAAATTAT-CA-ATT
* * *
9537995 ATTTATTATTAAGTTATC-GTT
1 ATTTACTATTAAATTATCAATT
* *
9538016 GATTAACTATTATATTATCAATT
1 -ATTTACTATTAAATTATCAATT
**
9538039 ATTTACTACAAAATTAT--ATT
1 ATTTACTATTAAATTATCAATT
* * * *
9538059 GATTTA-TGTTCAAGTTTTTAATT
1 -ATTTACTATT-AAATTATCAATT
*
9538082 ATTAACTATTAAATTATCAATT
1 ATTTACTATTAAATTATCAATT
* *
9538104 ATTTACTATTAATTTAT-TATT
1 ATTTACTATTAAATTATCAATT
** ** *
9538125 AGTTTACTGCTAAATTATTTATG
1 A-TTTACTATTAAATTATCAATT
*
9538148 ATTTAC---T--ACTATCAATT
1 ATTTACTATTAAATTATCAATT
* * *
9538165 AATTACTATTAAATT-TAAAATG
1 ATTTACTATTAAATTAT-CAATT
* *
9538187 ATTTACTATTAAATTATCACTA
1 ATTTACTATTAAATTATCAATT
9538209 ATTTACTATTAAATTATC-ATT
1 ATTTACTATTAAATTATCAATT
* * * * *
9538230 AATTATTACTAAGTTATCAATA
1 ATTTACTATTAAATTATCAATT
*
9538252 ATTAACTA
1 ATTTACTA
9538260 CTAAGCTATG
Statistics
Matches: 296, Mismatches: 92, Indels: 58
0.66 0.21 0.13
Matches are distributed among these distances:
17 11 0.04
19 1 0.00
20 5 0.02
21 60 0.20
22 201 0.68
23 18 0.06
ACGTcount: A:0.38, C:0.11, G:0.03, T:0.48
Consensus pattern (22 bp):
ATTTACTATTAAATTATCAATT
Found at i:9538213 original size:61 final size:61
Alignment explanation
Indices: 9538096--9538216 Score: 138
Period size: 61 Copynumber: 2.0 Consensus size: 61
9538086 ACTATTAAAT
* ** * * * *
9538096 TATCAATTATTTACTATTAATTTATTATTAGTTTACTGCTAAATTATTTATGATTTACTAC
1 TATCAATTAATTACTATTAATTTAAAATGAGTTTACTACTAAATTATTCATAATTTACTAC
*
9538157 TATCAATTAATTACTATTAAATTTAAAATGA-TTTACTATTAAATTA-TCACTAATTTACTA
1 TATCAATTAATTACTATT-AATTTAAAATGAGTTTACTACTAAATTATTCA-TAATTTACTA
9538217 TTAAATTATC
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 2 0.04
61 39 0.78
62 9 0.18
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (61 bp):
TATCAATTAATTACTATTAATTTAAAATGAGTTTACTACTAAATTATTCATAATTTACTAC
Found at i:9538435 original size:22 final size:23
Alignment explanation
Indices: 9538382--9538438 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 23
9538372 ATATTATTAC
* *
9538382 TAATTTACTAAAAAATTATCAAT
1 TAATTTACTATAAAATAATCAAT
* *
9538405 T-ATTGACTATTAAATAATC-AT
1 TAATTTACTATAAAATAATCAAT
9538426 TAATTTACTATAA
1 TAATTTACTATAA
9538439 GTTATTACTA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
21 3 0.11
22 23 0.85
23 1 0.04
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATTTACTATAAAATAATCAAT
Found at i:9538481 original size:20 final size:20
Alignment explanation
Indices: 9538456--9538499 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
9538446 CTACACTAAT
*
9538456 TTACTACTAAGTTATGA-TGA
1 TTACTACTAAATTAT-ATTGA
*
9538476 TTACTATTAAATTATATTGA
1 TTACTACTAAATTATATTGA
9538496 TTAC
1 TTAC
9538500 ATTTAACTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 1 0.05
20 20 0.95
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (20 bp):
TTACTACTAAATTATATTGA
Found at i:9540349 original size:30 final size:33
Alignment explanation
Indices: 9540314--9540378 Score: 91
Period size: 33 Copynumber: 2.1 Consensus size: 33
9540304 TTCAATTTTC
**
9540314 TTTTATT-TA-AAAAAT-TTATTATACATAATT
1 TTTTATTATATAAAAATATTAAAATACATAATT
9540344 TTTTATTATATAAAAATATTAAAATACATAATT
1 TTTTATTATATAAAAATATTAAAATACATAATT
9540377 TT
1 TT
9540379 AGAAATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
30 7 0.23
31 2 0.07
32 6 0.20
33 15 0.50
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (33 bp):
TTTTATTATATAAAAATATTAAAATACATAATT
Found at i:9547100 original size:26 final size:26
Alignment explanation
Indices: 9547071--9547120 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
9547061 AATACCAAAA
9547071 CTCAACAAATATTACAAATTTTAGAG
1 CTCAACAAATATTACAAATTTTAGAG
9547097 CTCAACAAATATTACAAATTTTAG
1 CTCAACAAATATTACAAATTTTAG
9547121 TTTTATAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.46, C:0.16, G:0.06, T:0.32
Consensus pattern (26 bp):
CTCAACAAATATTACAAATTTTAGAG
Found at i:9548192 original size:19 final size:20
Alignment explanation
Indices: 9548164--9548209 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
9548154 ATACCATGAA
*
9548164 ATTAATATAG-TAAAAATGT-
1 ATTAAAATAGCTAAAAAT-TC
9548183 ATTAAAATAGCTAAAAATTC
1 ATTAAAATAGCTAAAAATTC
9548203 ATTAAAA
1 ATTAAAA
9548210 ATAATATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.57, C:0.04, G:0.07, T:0.33
Consensus pattern (20 bp):
ATTAAAATAGCTAAAAATTC
Found at i:9548340 original size:13 final size:13
Alignment explanation
Indices: 9548311--9548348 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
9548301 TAAAACTTTC
9548311 ATTTTTTGAA-TTT
1 ATTTTTT-AATTTT
9548324 -TTTTTTAATTTT
1 ATTTTTTAATTTT
9548336 ATTTTTTAATTTT
1 ATTTTTTAATTTT
9548349 TAAGCTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 9 0.39
13 12 0.52
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (13 bp):
ATTTTTTAATTTT
Found at i:9548432 original size:21 final size:22
Alignment explanation
Indices: 9548403--9548448 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 22
9548393 TATTTTTTAA
9548403 TTTTTTAAAA-CATTT-AAAAT
1 TTTTTTAAAATCATTTGAAAAT
*
9548423 TTTTTATAAAATTATTTGAAAAT
1 TTTTT-TAAAATCATTTGAAAAT
9548446 TTT
1 TTT
9548449 AGAAATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 5 0.23
21 5 0.23
22 4 0.18
23 8 0.36
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.54
Consensus pattern (22 bp):
TTTTTTAAAATCATTTGAAAAT
Found at i:9548468 original size:21 final size:21
Alignment explanation
Indices: 9548414--9548476 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
9548404 TTTTTAAAAC
* *
9548414 ATTTAAAATTTTTTATAAAATT
1 ATTTAAAATATTTTA-GAAATT
*
9548436 ATTTGAAA-ATTTTAGAAATT
1 ATTTAAAATATTTTAGAAATT
*
9548456 ATTTAAAATATTTTTGAAATT
1 ATTTAAAATATTTTAGAAATT
9548477 TTGAGTTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 12 0.34
21 16 0.46
22 7 0.20
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTAAAATATTTTAGAAATT
Found at i:9557283 original size:32 final size:32
Alignment explanation
Indices: 9557242--9557304 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
9557232 CTTTGATGAC
* *
9557242 GAGCTCAAGTTCTTGGAAATATCATTGTTTAT
1 GAGCTCAAGTTCTTAGAAACATCATTGTTTAT
9557274 GAGCTCAAGTTCTTAGAAACATCATTGTTTA
1 GAGCTCAAGTTCTTAGAAACATCATTGTTTA
9557305 CCGAGGACAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.30, C:0.14, G:0.17, T:0.38
Consensus pattern (32 bp):
GAGCTCAAGTTCTTAGAAACATCATTGTTTAT
Found at i:9559872 original size:25 final size:28
Alignment explanation
Indices: 9559846--9559899 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
9559836 TAATTTTTTA
9559846 TTCTTTT-AG-ACAAGAAAATGTGTTAT
1 TTCTTTTAAGAACAAGAAAATGTGTTAT
*
9559872 TTTTTTTAAAGAACAAGAAAATGTGTTA
1 TTCTTTT-AAGAACAAGAAAATGTGTTA
9559900 ATTATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 6 0.25
28 2 0.08
29 16 0.67
ACGTcount: A:0.39, C:0.06, G:0.15, T:0.41
Consensus pattern (28 bp):
TTCTTTTAAGAACAAGAAAATGTGTTAT
Found at i:9576149 original size:23 final size:23
Alignment explanation
Indices: 9576116--9576167 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
9576106 GATATCTTTA
* *
9576116 TTTCCATCTCAGCAAATAGTTTT
1 TTTCCAACTCAACAAATAGTTTT
9576139 TTTCCAACTCAACAAATAGTTTT
1 TTTCCAACTCAACAAATAGTTTT
9576162 TTTCCA
1 TTTCCA
9576168 GAAGGAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (23 bp):
TTTCCAACTCAACAAATAGTTTT
Found at i:9577362 original size:20 final size:21
Alignment explanation
Indices: 9577337--9577378 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
9577327 ATGACATACA
9577337 AATTAAATAT-CATTCTATTT
1 AATTAAATATGCATTCTATTT
9577357 AATTAAATATGGCATTCTATTT
1 AATTAAATAT-GCATTCTATTT
9577379 TATTCACTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 10 0.50
22 10 0.50
ACGTcount: A:0.38, C:0.10, G:0.05, T:0.48
Consensus pattern (21 bp):
AATTAAATATGCATTCTATTT
Found at i:9577519 original size:91 final size:91
Alignment explanation
Indices: 9577403--9577571 Score: 304
Period size: 91 Copynumber: 1.9 Consensus size: 91
9577393 ATTCTGTTAG
9577403 AAAAATTCTTAACAAATATGACATGCAAACTAAATATCATTCTATTTAACGGCGAGTGTTATTCA
1 AAAAATTCTTAACAAATATGACATGCAAACTAAATATCATTCTATTTAACGGCGAGTGTTATTCA
*
9577468 CTTATCTCATTCCATTTCAGTTAGAA
66 CTTAACTCATTCCATTTCAGTTAGAA
*
9577494 AAAAATTCTTAACAAATACT-ACATGCAAACTAAATATCATTCTATTTAACGGCGAGTGTTGTTC
1 AAAAATTCTTAACAAATA-TGACATGCAAACTAAATATCATTCTATTTAACGGCGAGTGTTATTC
9577558 ACTTAACTCATTCC
65 ACTTAACTCATTCC
9577572 GTTAGTAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
91 74 0.99
92 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.09, T:0.34
Consensus pattern (91 bp):
AAAAATTCTTAACAAATATGACATGCAAACTAAATATCATTCTATTTAACGGCGAGTGTTATTCA
CTTAACTCATTCCATTTCAGTTAGAA
Found at i:9579250 original size:27 final size:27
Alignment explanation
Indices: 9579197--9579250 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 27
9579187 TGTTTAAATC
* **
9579197 TAAATTTATGAGATATTTTTTATAAAA
1 TAAAATTATGAGATATTTTAAATAAAA
9579224 TAAAATTATGAGA-ATTTTAAATCAAAA
1 TAAAATTATGAGATATTTTAAAT-AAAA
9579251 CGAACAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 7 0.30
27 16 0.70
ACGTcount: A:0.50, C:0.02, G:0.07, T:0.41
Consensus pattern (27 bp):
TAAAATTATGAGATATTTTAAATAAAA
Found at i:9579668 original size:272 final size:272
Alignment explanation
Indices: 9579158--9579679 Score: 581
Period size: 272 Copynumber: 1.9 Consensus size: 272
9579148 CTGAAATATT
* * *
9579158 TTAAGAATTTATTATGATATTTAAATTAATGTTTAAATCTAAATTTATGAGATATTTTTTATAAA
1 TTAAGAATTTATTATGATATTTAAATTAATGCTTAAATCTAAACTTATAAGATATTTTTTATAAA
* * * * *
9579223 ATAAAATTATGAGAATTTTAAATCAAAACGAACAATATCTCACAAGTTTTATGCAGATGTCCACA
66 ATAAAATCATAAGAATTTTAAATCAAAACGAACAATACCTCACAAGTTGTATGCAGATCTCCACA
* * * *
9579288 AATAATATTAAAACAATCACCAGTCGAACGAAAGTTAAATGTTACATGATATAAGCTATCTCTAA
131 AATAATATTAAAACAATCACCAATCGAACGAAAGTTAAATGCTACATGATAGAACCTATCTCTAA
* * * * *
9579353 AATTTTACATGAGCTAAGTGTTGCACGTTAGACATCCCCAATATTTGATGTGATTAAGTGAATTT
196 AATCTTACATAAGCTAAGTGTTACACGTTAGACATACCCAATATTGGATGTGATTAAGTGAATTT
9579418 GTGTGTTTTGTA
261 GTGTGTTTTGTA
* * * *
9579430 TTAA-AATTTATTATGATATTTAAATTGATGCTTAAATCTAAACTTGTAAGGTATTTTTTTATAG
1 TTAAGAATTTATTATGATATTTAAATTAATGCTTAAATCTAAACTTATAAGATA-TTTTTTATAA
* * * * *
9579494 AATAAAATCATAAGATTTTTGAATCAAAACGGATAATACCTCACATGTTAGGTATG-A-ATCTCC
65 AATAAAATCATAAGAATTTTAAATCAAAACGAACAATACCTCACAAGTT--GTATGCAGATCTCC
* *** * ** *
9579557 ATAAATAATATTAAAGTGATCACTAATCG-ACGGGAGTTAAATGCTACACT-AGTGGGAACC-AT
128 ACAAATAATATTAAAACAATCACCAATCGAACGAAAGTTAAATGCTACA-TGA-T-AGAACCTAT
* * * * *
9579619 -TCTTAAAATCTTACGTAAGTTAAGTGTTACACGTTGGACGTATCCAATATTGGATGTGATT
190 CTC-TAAAATCTTACATAAGCTAAGTGTTACACGTTAGACATACCCAATATTGGATGTGATT
9579680 TGTATTAAGC
Statistics
Matches: 204, Mismatches: 39, Indels: 14
0.79 0.15 0.05
Matches are distributed among these distances:
271 62 0.30
272 134 0.66
273 4 0.02
274 4 0.02
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (272 bp):
TTAAGAATTTATTATGATATTTAAATTAATGCTTAAATCTAAACTTATAAGATATTTTTTATAAA
ATAAAATCATAAGAATTTTAAATCAAAACGAACAATACCTCACAAGTTGTATGCAGATCTCCACA
AATAATATTAAAACAATCACCAATCGAACGAAAGTTAAATGCTACATGATAGAACCTATCTCTAA
AATCTTACATAAGCTAAGTGTTACACGTTAGACATACCCAATATTGGATGTGATTAAGTGAATTT
GTGTGTTTTGTA
Found at i:9580198 original size:29 final size:29
Alignment explanation
Indices: 9580140--9580198 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
9580130 AAATTATATG
* * *
9580140 AAATATTTAATATAATATTTAAATTTTAA
1 AAATATTTAAAATAATATTTAAACTATAA
*
9580169 AAATTTTTAAAATAATATTTAAACTATAA
1 AAATATTTAAAATAATATTTAAACTATAA
9580198 A
1 A
9580199 TTTATTAATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (29 bp):
AAATATTTAAAATAATATTTAAACTATAA
Found at i:9580211 original size:27 final size:27
Alignment explanation
Indices: 9580140--9580213 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 27
9580130 AAATTATATG
* *
9580140 AAATATTTAATATAATATTTAAATTTTAA
1 AAATTTTTAAT-TAATATTTAAA-TCTAA
* *
9580169 AAATTTTTAAAATAATATTTAAA-CTAT
1 AAATTTTT-AATTAATATTTAAATCTAA
9580196 AAATTTATTAATTAATAT
1 AAATTT-TTAATTAATAT
9580214 AATAATTAGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
27 16 0.42
28 2 0.05
29 18 0.47
30 2 0.05
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (27 bp):
AAATTTTTAATTAATATTTAAATCTAA
Found at i:9580334 original size:29 final size:29
Alignment explanation
Indices: 9580297--9580356 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
9580287 TATTAATAAA
* * * *
9580297 TTTATAATTTAAATATTATAATAAATATT
1 TTTAAAATTTAAAAATCACAATAAATATT
*
9580326 TTTAAAATTTAAAAATCACATTAAATATT
1 TTTAAAATTTAAAAATCACAATAAATATT
9580355 TT
1 TT
9580357 ATTATAATTT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (29 bp):
TTTAAAATTTAAAAATCACAATAAATATT
Found at i:9580927 original size:16 final size:16
Alignment explanation
Indices: 9580906--9580939 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
9580896 TAATTTTTTA
*
9580906 TTTTTTTT-ATATAAT
1 TTTTTTTTGATAAAAT
9580921 TTTTTTTTGATAAAAT
1 TTTTTTTTGATAAAAT
9580937 TTT
1 TTT
9580940 AGTAACTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TTTTTTTTGATAAAAT
Found at i:9580981 original size:21 final size:21
Alignment explanation
Indices: 9580925--9581039 Score: 88
Period size: 21 Copynumber: 5.4 Consensus size: 21
9580915 TATAATTTTT
*
9580925 TTTTGATAAAATTTTAGTAAC
1 TTTTGATATAATTTTAGTAAC
* * *
9580946 TTTTTATATATTTTTGGTAAC
1 TTTTGATATAATTTTAGTAAC
* * * * *
9580967 TATTGATACAATTTTGGAAAT
1 TTTTGATATAATTTTAGTAAC
9580988 TTTTGATA-AACTTTTAGTAATC
1 TTTTGATATAA-TTTTAGTAA-C
* * *
9581010 TGTTGATATAATTTCAGTAATA
1 TTTTGATATAATTTTAGTAA-C
9581032 TTTTGATA
1 TTTTGATA
9581040 GCTTATGATA
Statistics
Matches: 73, Mismatches: 18, Indels: 5
0.76 0.19 0.05
Matches are distributed among these distances:
20 2 0.03
21 46 0.63
22 23 0.32
23 2 0.03
ACGTcount: A:0.33, C:0.05, G:0.11, T:0.50
Consensus pattern (21 bp):
TTTTGATATAATTTTAGTAAC
Found at i:9581016 original size:22 final size:22
Alignment explanation
Indices: 9580990--9581039 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
9580980 TTGGAAATTT
* *
9580990 TTGATA-AACTTTTAGTAATCTG
1 TTGATATAA-TTTCAGTAATATG
*
9581012 TTGATATAATTTCAGTAATATT
1 TTGATATAATTTCAGTAATATG
9581034 TTGATA
1 TTGATA
9581040 GCTTATGATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
22 22 0.92
23 2 0.08
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (22 bp):
TTGATATAATTTCAGTAATATG
Found at i:9581563 original size:21 final size:21
Alignment explanation
Indices: 9581539--9581579 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
9581529 ATGCAATATC
9581539 TTTAAAAAT-CAAATAAATAAG
1 TTTAAAAATACAAA-AAATAAG
*
9581560 TTTAAAAGTACAAAAAATAA
1 TTTAAAAATACAAAAAATAA
9581580 TATCATAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (21 bp):
TTTAAAAATACAAAAAATAAG
Found at i:9581796 original size:35 final size:35
Alignment explanation
Indices: 9581757--9581826 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
9581747 ATTGAAATAC
*
9581757 TTATAAACTTTGGTTTGAAAAAATAAAATATAAAA
1 TTATAAACTTTGGTTCGAAAAAATAAAATATAAAA
9581792 TTATAAACTTTGGTTCGAAAAAATAAAATATAAAA
1 TTATAAACTTTGGTTCGAAAAAATAAAATATAAAA
9581827 GAAAGCAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.54, C:0.04, G:0.09, T:0.33
Consensus pattern (35 bp):
TTATAAACTTTGGTTCGAAAAAATAAAATATAAAA
Found at i:9582163 original size:22 final size:22
Alignment explanation
Indices: 9582135--9582181 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
9582125 ACAATTATGG
9582135 TTATTAGCAATTTACTATTAAA
1 TTATTAGCAATTTACTATTAAA
*
9582157 TTATTAGTAATTTACTATTAAA
1 TTATTAGCAATTTACTATTAAA
9582179 TTA
1 TTA
9582182 ACATTAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.49
Consensus pattern (22 bp):
TTATTAGCAATTTACTATTAAA
Found at i:9582189 original size:22 final size:22
Alignment explanation
Indices: 9582143--9582195 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
9582133 GGTTATTAGC
**
9582143 AATTTACTATTAAATTATTAGT
1 AATTTACTATTAAATTAACAGT
*
9582165 AATTTACTATTAAATTAACATT
1 AATTTACTATTAAATTAACAGT
9582187 AATTTACTA
1 AATTTACTA
9582196 CCTATTTATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (22 bp):
AATTTACTATTAAATTAACAGT
Found at i:9582294 original size:22 final size:21
Alignment explanation
Indices: 9582225--9582296 Score: 56
Period size: 22 Copynumber: 3.3 Consensus size: 21
9582215 AAGTTATAAC
* * *
9582225 TGATTTAATATTAAATTATTGA
1 TGATTTATTA-TAAATTACTAA
* *
9582247 TGATTTACTTCTAAGTTACTAA
1 TGATTTA-TTATAAATTACTAA
9582269 TGATTTATTATAAAATTA-TAA
1 TGATTTATTAT-AAATTACTAA
9582290 CTGATTT
1 -TGATTT
9582297 GCTATTAATT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
21 6 0.15
22 33 0.82
23 1 0.03
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.49
Consensus pattern (21 bp):
TGATTTATTATAAATTACTAA
Found at i:9582295 original size:44 final size:44
Alignment explanation
Indices: 9582213--9582331 Score: 109
Period size: 44 Copynumber: 2.7 Consensus size: 44
9582203 ATAAATGATA
* *
9582213 CTAAGTTATAACTGATTTAATATTAAATTATTGATGATTTACTT
1 CTAAGTTATAACTGATTTAATATAAAATTATTAATGATTTACTT
* *
9582257 CTAAGTTACTAA-TGATTTATTATAAAATTA-TAACTGATTTGCTAT
1 CTAAGTTA-TAACTGATTTAATATAAAATTATTAA-TGATTTACT-T
* * * * *
9582302 -TAATTTATAAATAATTTACTACAAAATTAT
1 CTAAGTTATAACTGATTTAATATAAAATTAT
9582332 CAATAATTAG
Statistics
Matches: 62, Mismatches: 8, Indels: 9
0.78 0.10 0.11
Matches are distributed among these distances:
43 5 0.08
44 53 0.85
45 4 0.06
ACGTcount: A:0.40, C:0.08, G:0.07, T:0.45
Consensus pattern (44 bp):
CTAAGTTATAACTGATTTAATATAAAATTATTAATGATTTACTT
Found at i:9582371 original size:22 final size:22
Alignment explanation
Indices: 9582345--9582853 Score: 144
Period size: 22 Copynumber: 23.2 Consensus size: 22
9582335 TAATTAGCTA
*
9582345 ATTTACTACTAAATTATCACTT
1 ATTTACTACTAAATTATCAATT
* * *
9582367 ATTTACAACTAAATTATTAATG
1 ATTTACTACTAAATTATCAATT
*
9582389 ATTTACTACTAAATTATCAATA
1 ATTTACTACTAAATTATCAATT
*
9582411 ATTTAC-ATCTAAATTATCAATG
1 ATTTACTA-CTAAATTATCAATT
* * * *
9582433 ATTTACTATTATATCAT-TATAT
1 ATTTACTACTAAATTATCAAT-T
* * *
9582455 ATTTACTACTATATTATTATTT
1 ATTTACTACTAAATTATCAATT
* * * *
9582477 ATTTACTATTTAGTTTTCAATT
1 ATTTACTACTAAATTATCAATT
* * * *
9582499 GTTTACTACAAAATAATCACA-A
1 ATTTACTACTAAATTATCA-ATT
* * *
9582521 ATTTATTACAAAATTAGTC-ATA
1 ATTTACTACTAAATTA-TCAATT
* **
9582543 ATTTATTA-TCAAGGTATC-ATT
1 ATTTACTACT-AAATTATCAATT
* * *
9582564 GATTTA-TATTAAATTAACAATG
1 -ATTTACTACTAAATTATCAATT
* * *
9582586 ATTAACTATTAAATTAT-TATCT
1 ATTTACTACTAAATTATCAAT-T
* * * * * *
9582608 ATTAATTATTAAGTTATCGATG
1 ATTTACTACTAAATTATCAATT
* * * *
9582630 ATTAAATATTAAGTTAT--ATT
1 ATTTACTACTAAATTATCAATT
* ** * *
9582650 GATTTATTTTTAAATTTTCAATG
1 -ATTTACTACTAAATTATCAATT
* *
9582673 ATTAACTACTAAATTAT-TATT
1 ATTTACTACTAAATTATCAATT
* * * ** *
9582694 GGTTTATTATTAAATTATTTATA
1 -ATTTACTACTAAATTATCAATT
* *
9582717 ATTTATTACTAAATTTATTAATT
1 ATTTACTACTAAA-TTATCAATT
* * * *
9582740 AATTACTATTAAATTA-AAACTG
1 ATTTACTACTAAATTATCAA-TT
* * * * *
9582762 ATCTACTATTAAATTATTACTA
1 ATTTACTACTAAATTATCAATT
* * *
9582784 ATTTACTATTAAGTTATC-ATCG
1 ATTTACTACTAAATTATCAAT-T
* *
9582806 ATTTATTATTAAATTATCAATT
1 ATTTACTACTAAATTATCAATT
* * *
9582828 ATTAACTACTAAGTTATCATTT
1 ATTTACTACTAAATTATCAATT
9582850 ATTT
1 ATTT
9582854 TTTATTAATA
Statistics
Matches: 364, Mismatches: 99, Indels: 48
0.71 0.19 0.09
Matches are distributed among these distances:
20 2 0.01
21 38 0.10
22 292 0.80
23 32 0.09
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.48
Consensus pattern (22 bp):
ATTTACTACTAAATTATCAATT
Found at i:9582482 original size:66 final size:66
Alignment explanation
Indices: 9582343--9582471 Score: 163
Period size: 66 Copynumber: 2.0 Consensus size: 66
9582333 AATAATTAGC
* * *
9582343 TAATTTACTACTAAATTATCACTTATTTACAACTAAATTATTAATGATTTACTACTAAATTATCA
1 TAATTTACTACTAAATTATCAATGATTTACAACTAAATCATTAATGATTTACTACTAAATTATCA
9582408 A
66 A
* * * *
9582409 TAATTTAC-ATCTAAATTATCAATGATTTACTATTATATCATTATAT-ATTTACTACTATATTAT
1 TAATTTACTA-CTAAATTATCAATGATTTACAACTAAATCATTA-ATGATTTACTACTAAATTAT
9582472 TATTTATTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
65 1 0.02
66 51 0.94
67 2 0.04
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (66 bp):
TAATTTACTACTAAATTATCAATGATTTACAACTAAATCATTAATGATTTACTACTAAATTATCA
A
Found at i:9582604 original size:15 final size:14
Alignment explanation
Indices: 9582586--9582619 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
9582576 ATTAACAATG
9582586 ATTAACTATTAAATT
1 ATTAACTATT-AATT
*
9582601 ATTATCTATTAATT
1 ATTAACTATTAATT
9582615 ATTAA
1 ATTAA
9582620 GTTATCGATG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.44, C:0.06, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTAACTATTAATT
Found at i:9582700 original size:44 final size:44
Alignment explanation
Indices: 9582561--9582822 Score: 196
Period size: 44 Copynumber: 6.0 Consensus size: 44
9582551 TCAAGGTATC
*
9582561 ATTGATTTA-TATTAAATTAACAATGATTAACTATTAAATTATT
1 ATTGATTTATTATTAAATTATCAATGATTAACTATTAAATTATT
* * * * *
9582604 ATCT-ATTAATTATTAAGTTATCGATGATTAAATATTAAGTTA-T
1 AT-TGATTTATTATTAAATTATCAATGATTAACTATTAAATTATT
* * *
9582647 ATTGATTTATTTTTAAATTTTCAATGATTAACTACTAAATTATT
1 ATTGATTTATTATTAAATTATCAATGATTAACTATTAAATTATT
* ** * * * *
9582691 ATTGGTTTATTATTAAATTATTTATAATTTATTACTAAATTTATT
1 ATTGATTTATTATTAAATTATCAATGATTAACTATTAAA-TTATT
* * *
9582736 AATT-AATTACTATTAAATTA-AAACTGATCT-ACTATTAAATTATT
1 -ATTGATTTATTATTAAATTATCAA-TGAT-TAACTATTAAATTATT
* * * * * *
9582780 ACTAATTTACTATTAAGTTATC-ATCGATTTATTATTAAATTAT
1 ATTGATTTATTATTAAATTATCAAT-GATTAACTATTAAATTAT
9582823 CAATTATTAA
Statistics
Matches: 172, Mismatches: 35, Indels: 23
0.75 0.15 0.10
Matches are distributed among these distances:
42 1 0.01
43 43 0.25
44 96 0.56
45 28 0.16
46 4 0.02
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (44 bp):
ATTGATTTATTATTAAATTATCAATGATTAACTATTAAATTATT
Found at i:9582711 original size:11 final size:11
Alignment explanation
Indices: 9582682--9582822 Score: 54
Period size: 11 Copynumber: 12.7 Consensus size: 11
9582672 GATTAACTAC
9582682 TAAATTATTAT
1 TAAATTATTAT
***
9582693 TGGTTTATTAT
1 TAAATTATTAT
9582704 TAAATTATT-T
1 TAAATTATTAT
* *
9582714 ATAATTTATTAC
1 -TAAATTATTAT
9582726 TAAATTTATTAAT
1 TAAA-TTATT-AT
*
9582739 T-AATTACTAT
1 TAAATTATTAT
** *
9582749 TAAATTAAAAC
1 TAAATTATTAT
* *
9582760 T-GATCTACTAT
1 TAAAT-TATTAT
*
9582771 TAAATTATTAC
1 TAAATTATTAT
* *
9582782 TAATTTACTAT
1 TAAATTATTAT
* *
9582793 TAAGTTATCAT
1 TAAATTATTAT
** *
9582804 CGATTTATTAT
1 TAAATTATTAT
9582815 TAAATTAT
1 TAAATTAT
9582823 CAATTATTAA
Statistics
Matches: 89, Mismatches: 34, Indels: 14
0.65 0.25 0.10
Matches are distributed among these distances:
10 6 0.07
11 72 0.81
12 9 0.10
13 2 0.02
ACGTcount: A:0.40, C:0.06, G:0.04, T:0.50
Consensus pattern (11 bp):
TAAATTATTAT
Found at i:9582744 original size:20 final size:19
Alignment explanation
Indices: 9582710--9582747 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
9582700 TTATTAAATT
*
9582710 ATTTATAATTTATTACTAA
1 ATTTATAATTAATTACTAA
9582729 ATTTATTAATTAATTACTA
1 ATTTA-TAATTAATTACTA
9582748 TTAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (19 bp):
ATTTATAATTAATTACTAA
Found at i:9583191 original size:22 final size:21
Alignment explanation
Indices: 9583166--9583234 Score: 57
Period size: 22 Copynumber: 3.1 Consensus size: 21
9583156 TTAAGCTATC
9583166 AATGATGTGTTATTAATTTATG
1 AATGAT-TGTTATTAATTTATG
* * *
9583188 AATGATTTGCTACTAATTTATA
1 AATGA-TTGTTATTAATTTATG
* * *
9583210 AATTATTTTTCATTAAATTATG
1 AATGATTGTT-ATTAATTTATG
9583232 AAT
1 AAT
9583235 CATTTACCAA
Statistics
Matches: 36, Mismatches: 9, Indels: 4
0.73 0.18 0.08
Matches are distributed among these distances:
21 3 0.08
22 32 0.89
23 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.49
Consensus pattern (21 bp):
AATGATTGTTATTAATTTATG
Found at i:9583385 original size:22 final size:22
Alignment explanation
Indices: 9583353--9583445 Score: 87
Period size: 22 Copynumber: 4.2 Consensus size: 22
9583343 TGATTAACTA
* *
9583353 ATTTATTACTAAATTATTACTG
1 ATTTACTACTAAATTATTAGTG
* * * *
9583375 ATTTACAACTAAGTTCTTAGTA
1 ATTTACTACTAAATTATTAGTG
* *
9583397 ATTTACTATTACATTATTAGTG
1 ATTTACTACTAAATTATTAGTG
* * *
9583419 ATTCACTACTAAATTATCAATG
1 ATTTACTACTAAATTATTAGTG
9583441 ATTTA
1 ATTTA
9583446 ATATTATATA
Statistics
Matches: 53, Mismatches: 18, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
22 53 1.00
ACGTcount: A:0.37, C:0.12, G:0.06, T:0.45
Consensus pattern (22 bp):
ATTTACTACTAAATTATTAGTG
Found at i:9583569 original size:22 final size:22
Alignment explanation
Indices: 9583535--9583678 Score: 97
Period size: 22 Copynumber: 6.7 Consensus size: 22
9583525 ATTATCACTA
* *
9583535 ATTTACCACTAAATTATCTATG
1 ATTTACTATTAAATTATCTATG
*
9583557 ATTCACTATTAAATTAT-TACTG
1 ATTTACTATTAAATTATCTA-TG
9583579 -TTTA-TATTAAATTATAC-ATG
1 ATTTACTATTAAATTAT-CTATG
**
9583599 ATTTACTATTAAATTATAAATG
1 ATTTACTATTAAATTATCTATG
* *
9583621 -TTTAATTATTATATTAT-TGATG
1 ATTT-ACTATTAAATTATCT-ATG
* *
9583643 ATTTACTACTAAACTATGCTA-G
1 ATTTACTATTAAATTAT-CTATG
*
9583665 -TTTACTTTTAAATT
1 ATTTACTATTAAATT
9583679 TGCAATAGAT
Statistics
Matches: 96, Mismatches: 15, Indels: 23
0.72 0.11 0.17
Matches are distributed among these distances:
20 13 0.14
21 24 0.25
22 54 0.56
23 4 0.04
24 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.06, T:0.48
Consensus pattern (22 bp):
ATTTACTATTAAATTATCTATG
Found at i:9583588 original size:20 final size:20
Alignment explanation
Indices: 9583563--9583628 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 20
9583553 TATGATTCAC
9583563 TATTAAATTATTACTGTTTA
1 TATTAAATTATTACTGTTTA
9583583 TATTAAATTA-TACATGATTTA
1 TATTAAATTATTAC-TG-TTTA
* *
9583604 CTATTAAATTATAAATGTTTA
1 -TATTAAATTATTACTGTTTA
9583625 -ATTA
1 TATTA
9583629 TTATATTATT
Statistics
Matches: 40, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 7 0.17
20 12 0.30
21 8 0.20
22 12 0.30
23 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
TATTAAATTATTACTGTTTA
Found at i:9583592 original size:42 final size:44
Alignment explanation
Indices: 9583544--9583655 Score: 133
Period size: 42 Copynumber: 2.6 Consensus size: 44
9583534 AATTTACCAC
* * *
9583544 TAAATTATCTATGATTCACTATTAAATTATTACTGTTT-A-TAT
1 TAAATTATCTATGATTTACTATTAAATTATAAATGTTTAATTAT
9583586 TAAATTATAC-ATGATTTACTATTAAATTATAAATGTTTAATTAT
1 TAAATTAT-CTATGATTTACTATTAAATTATAAATGTTTAATTAT
* *
9583630 TATATTAT-TGATGATTTACTACTAAA
1 TAAATTATCT-ATGATTTACTATTAAA
9583656 CTATGCTAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 8
0.82 0.07 0.11
Matches are distributed among these distances:
42 33 0.55
43 2 0.03
44 25 0.42
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.48
Consensus pattern (44 bp):
TAAATTATCTATGATTTACTATTAAATTATAAATGTTTAATTAT
Found at i:9583736 original size:22 final size:22
Alignment explanation
Indices: 9583690--9583761 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
9583680 GCAATAGATA
* * *
9583690 ACTACTAAATTA-TCATTTTTT
1 ACTACTAAGTTATTTATTATTT
9583711 ACTACTAA-TT-TGTTATTGATTT
1 ACTACTAAGTTAT-TTATT-ATTT
9583733 ACTACTAAGTTATTTATTATTT
1 ACTACTAAGTTATTTATTATTT
9583755 ACTACTA
1 ACTACTA
9583762 TCAATTAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
20 2 0.05
21 12 0.27
22 22 0.50
23 7 0.16
24 1 0.02
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.51
Consensus pattern (22 bp):
ACTACTAAGTTATTTATTATTT
Found at i:9583788 original size:21 final size:22
Alignment explanation
Indices: 9583764--9583804 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
9583754 TACTACTATC
*
9583764 AATTAA-TTATTATTAAATTGA
1 AATTAATTTACTATTAAATTGA
9583785 AATTAATTTACTATTAAATT
1 AATTAATTTACTATTAAATT
9583805 ATCACTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (22 bp):
AATTAATTTACTATTAAATTGA
Found at i:9586393 original size:17 final size:17
Alignment explanation
Indices: 9586359--9586404 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
9586349 AAAATTTCCT
* *
9586359 TTATTTAAAAACTTTTA
1 TTATATAAAAATTTTTA
* *
9586376 TTTTATATAAATTTTTA
1 TTATATAAAAATTTTTA
9586393 TTATATAAAAAT
1 TTATATAAAAAT
9586405 ATTAAAATAT
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (17 bp):
TTATATAAAAATTTTTA
Found at i:9586673 original size:21 final size:21
Alignment explanation
Indices: 9586649--9586702 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
9586639 CACTAAAAAC
9586649 AATTAATTTTACTTTGTTGAT
1 AATTAATTTTACTTTGTTGAT
9586670 AATTAATTTTACTTTGTTGAT
1 AATTAATTTTACTTTGTTGAT
9586691 AATT--TTTTACTT
1 AATTAATTTTACTT
9586703 AAATAATTCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
19 8 0.24
21 25 0.76
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (21 bp):
AATTAATTTTACTTTGTTGAT
Found at i:9589884 original size:25 final size:22
Alignment explanation
Indices: 9589843--9589909 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 22
9589833 TTTTTATACT
*
9589843 TTAATTATATATTTATTTAA-AA
1 TTAA-TATATTTTTATTTAATAA
9589865 TTTAATAGTATTATTT-TATTAATAA
1 -TTAATA-TATT-TTTAT-TTAATAA
9589890 TTAATATATTTTTATTTAAT
1 TTAATATATTTTTATTTAAT
9589910 TATTTTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
22 10 0.26
23 13 0.34
24 13 0.34
25 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (22 bp):
TTAATATATTTTTATTTAATAA
Found at i:9589886 original size:24 final size:24
Alignment explanation
Indices: 9589854--9589909 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
9589844 TAATTATATA
9589854 TTTATTTAA-AATTTAATAGTATTAT
1 TTTATTTAATAA-TTAATA-TATTAT
9589879 TTTA-TTAATAATTAATATA-T-T
1 TTTATTTAATAATTAATATATTAT
9589900 TTTATTTAAT
1 TTTATTTAAT
9589910 TATTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
21 5 0.17
22 6 0.21
23 2 0.07
24 10 0.34
25 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (24 bp):
TTTATTTAATAATTAATATATTAT
Found at i:9589902 original size:21 final size:21
Alignment explanation
Indices: 9589844--9589905 Score: 58
Period size: 24 Copynumber: 2.9 Consensus size: 21
9589834 TTTTATACTT
*
9589844 TAATT-ATATATTTAT-TTAA
1 TAATTAATATATTTTTATTAA
9589863 -AATTTAATAGTATTATTTTATTAA
1 TAA-TTAATA-TA-T-TTTTATTAA
9589887 TAATTAATATATTTTTATT
1 TAATTAATATATTTTTATT
9589906 TAATTATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
18 2 0.06
19 2 0.06
20 3 0.09
21 9 0.26
22 2 0.06
23 5 0.14
24 10 0.29
25 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TAATTAATATATTTTTATTAA
Found at i:9589930 original size:12 final size:12
Alignment explanation
Indices: 9589913--9589948 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
9589903 ATTTAATTAT
*
9589913 TTTAAAAATATA
1 TTTAAAAATAAA
9589925 TTTAAAAAATAAA
1 TTT-AAAAATAAA
9589938 TTTAAAAATAA
1 TTTAAAAATAA
9589949 TAAATAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
TTTAAAAATAAA
Found at i:9589953 original size:15 final size:13
Alignment explanation
Indices: 9589911--9589945 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
9589901 TTATTTAATT
* *
9589911 ATTTTAAAAATAT
1 ATTTAAAAAATAA
9589924 ATTTAAAAAATAA
1 ATTTAAAAAATAA
9589937 ATTTAAAAA
1 ATTTAAAAA
9589946 TAATAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
ATTTAAAAAATAA
Found at i:9594785 original size:26 final size:24
Alignment explanation
Indices: 9594756--9594804 Score: 80
Period size: 26 Copynumber: 2.0 Consensus size: 24
9594746 AGTAAAGGGG
9594756 TAGGAGTGTATGACATCTTGTAAGGA
1 TAGGAGTGTATGACA--TTGTAAGGA
9594782 TAGGAGTGTATGACATTGTAAGG
1 TAGGAGTGTATGACATTGTAAGG
9594805 TATTTACCCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 8 0.35
26 15 0.65
ACGTcount: A:0.31, C:0.06, G:0.33, T:0.31
Consensus pattern (24 bp):
TAGGAGTGTATGACATTGTAAGGA
Found at i:9595368 original size:34 final size:34
Alignment explanation
Indices: 9595325--9595393 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
9595315 GTTGCTTAGA
9595325 AGCAAACATAAATAGTAAAAAGAGAAATCGTCAT
1 AGCAAACATAAATAGTAAAAAGAGAAATCGTCAT
*
9595359 AGCAAACATAAATGGTAAAAAGAGAAATCGTCAT
1 AGCAAACATAAATAGTAAAAAGAGAAATCGTCAT
9595393 A
1 A
9595394 CCATATGATA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.55, C:0.12, G:0.16, T:0.17
Consensus pattern (34 bp):
AGCAAACATAAATAGTAAAAAGAGAAATCGTCAT
Found at i:9599788 original size:30 final size:30
Alignment explanation
Indices: 9599754--9599812 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
9599744 TTAAACTTTA
* *
9599754 AATTTATTAATTA-AAATTTGATTCAAAATT
1 AATTT-TTAAATATAAATTTAATTCAAAATT
*
9599784 AATTTTTAAATATAAATTTAATTCGAAAT
1 AATTTTTAAATATAAATTTAATTCAAAAT
9599813 AAAAATTAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 6 0.24
30 19 0.76
ACGTcount: A:0.47, C:0.03, G:0.03, T:0.46
Consensus pattern (30 bp):
AATTTTTAAATATAAATTTAATTCAAAATT
Found at i:9599895 original size:22 final size:21
Alignment explanation
Indices: 9599869--9599910 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
9599859 ATTTCAATTT
*
9599869 TTATATCAGATTTGAAATTAAA
1 TTATATCAAATTTG-AATTAAA
*
9599891 TTATATTAAATTTGAATTAA
1 TTATATCAAATTTGAATTAA
9599911 TATGTATAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (21 bp):
TTATATCAAATTTGAATTAAA
Found at i:9600605 original size:2 final size:2
Alignment explanation
Indices: 9600598--9600641 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
9600588 TTGATCCAAA
9600598 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
9600640 AG
1 AG
9600642 GGTGATTTCA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9604905 original size:13 final size:13
Alignment explanation
Indices: 9604883--9604921 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
9604873 TTTTTTTTTA
*
9604883 ATTTTTATATATT
1 ATTTTAATATATT
**
9604896 ATTTTAATATAAA
1 ATTTTAATATATT
9604909 ATTTTAATATATT
1 ATTTTAATATATT
9604922 TAAGTAGATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
ATTTTAATATATT
Found at i:9604997 original size:19 final size:19
Alignment explanation
Indices: 9604958--9604997 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
9604948 ATTTTTATTT
* **
9604958 TATAAAAATTTAAAATCTA
1 TATAAAAATTAAAAAAATA
9604977 TATAAAAATTAAAAAAATA
1 TATAAAAATTAAAAAAATA
9604996 TA
1 TA
9604998 AAACTTGGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (19 bp):
TATAAAAATTAAAAAAATA
Found at i:9605091 original size:13 final size:13
Alignment explanation
Indices: 9605056--9605091 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
9605046 TTAAAATTCA
9605056 ATTTAAATTTAAT
1 ATTTAAATTTAAT
* *
9605069 ATATACATTTAAT
1 ATTTAAATTTAAT
9605082 ATTTAAATTT
1 ATTTAAATTT
9605092 GATTTGAATT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (13 bp):
ATTTAAATTTAAT
Found at i:9608658 original size:29 final size:29
Alignment explanation
Indices: 9608600--9608658 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
9608590 CATAGAAGAG
*
9608600 TGATAATAAAGAAATAACTGACAAATGAA
1 TGATAATAAAGAAATAACTGACAAAGGAA
*
9608629 TGATAATAAAGAAATAACTGACGAAGGAA
1 TGATAATAAAGAAATAACTGACAAAGGAA
9608658 T
1 T
9608659 TTTTAAGTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.56, C:0.07, G:0.17, T:0.20
Consensus pattern (29 bp):
TGATAATAAAGAAATAACTGACAAAGGAA
Done.