Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 13 of 204
Found at i:5090201 original size:21 final size:20
Alignment explanation
Indices: 5090164--5090203 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
5090154 TTTAATTGGG
*
5090164 CTGTTCATTTTTTTTTAATT
1 CTGTTCATTTTTATTTAATT
*
5090184 CTGTTGATTTTTAATTTAAT
1 CTGTTCATTTTT-ATTTAAT
5090204 CCTTAATCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.20, C:0.07, G:0.07, T:0.65
Consensus pattern (20 bp):
CTGTTCATTTTTATTTAATT
Found at i:5090286 original size:15 final size:13
Alignment explanation
Indices: 5090233--5090286 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 13
5090223 GTTTTTAGTC
5090233 TATTTTATTAATT-
1 TATTTTATT-ATTA
*
5090246 T-TTCTATTATTA
1 TATTTTATTATTA
5090258 T-TTTTATTATTA
1 TATTTTATTATTA
5090270 TATTATATATTATTA
1 TATT-T-TATTATTA
5090285 TA
1 TA
5090287 CCTACATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.51
13 3 0.09
14 1 0.03
15 10 0.29
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTATTATTA
Found at i:5090375 original size:29 final size:31
Alignment explanation
Indices: 5090313--5090375 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
5090303 CATATGCATG
* **
5090313 TTAATATATATACATATATATTTTAAATGTT
1 TTAATATATATACATATATATTATAAATACT
*
5090344 TTAATATATATACATAT-TA-TATACATACT
1 TTAATATATATACATATATATTATAAATACT
5090373 TTA
1 TTA
5090376 TTATTATTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 9 0.32
30 2 0.07
31 17 0.61
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (31 bp):
TTAATATATATACATATATATTATAAATACT
Found at i:5090661 original size:51 final size:52
Alignment explanation
Indices: 5090547--5090668 Score: 135
Period size: 51 Copynumber: 2.4 Consensus size: 52
5090537 ATTTTTCACG
* **
5090547 TTTT-TATAT-TATACTTATATATTTCATTTTTTTGTAAATGCATGAATATA
1 TTTTATATATATATATTTATATATTTCATTTTTTCATAAATGCATGAATATA
* * * *
5090597 TTTTATATGTATATATTTATAT-TTTCCTTGTTTTCATAAATGCAT-TATGTA
1 TTTTATATATATATATTTATATATTTCATT-TTTTCATAAATGCATGAATATA
*
5090648 TTTTATATATATATATATATA
1 TTTTATATATATATATTTATA
5090669 AAAGTTTTAT
Statistics
Matches: 60, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
50 4 0.07
51 33 0.55
52 23 0.38
ACGTcount: A:0.32, C:0.06, G:0.06, T:0.57
Consensus pattern (52 bp):
TTTTATATATATATATTTATATATTTCATTTTTTCATAAATGCATGAATATA
Found at i:5094803 original size:2 final size:2
Alignment explanation
Indices: 5094798--5094823 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5094788 ATAAATATGA
5094798 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
5094824 GAACTCTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5096268 original size:30 final size:30
Alignment explanation
Indices: 5096234--5096290 Score: 114
Period size: 30 Copynumber: 1.9 Consensus size: 30
5096224 ATATTTGTTT
5096234 AGTAATTTAATCTCGTATCTTATTAATGAG
1 AGTAATTTAATCTCGTATCTTATTAATGAG
5096264 AGTAATTTAATCTCGTATCTTATTAAT
1 AGTAATTTAATCTCGTATCTTATTAAT
5096291 AATGAGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.46
Consensus pattern (30 bp):
AGTAATTTAATCTCGTATCTTATTAATGAG
Found at i:5097866 original size:16 final size:16
Alignment explanation
Indices: 5097845--5097877 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5097835 AAATAGATAT
5097845 TTTATTTCTCAAAAGC
1 TTTATTTCTCAAAAGC
5097861 TTTATTTCTCAAAAGC
1 TTTATTTCTCAAAAGC
5097877 T
1 T
5097878 AAAATCTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.18, G:0.06, T:0.45
Consensus pattern (16 bp):
TTTATTTCTCAAAAGC
Found at i:5108225 original size:26 final size:25
Alignment explanation
Indices: 5108196--5108259 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 25
5108186 AATTAAATTT
5108196 AATACTTATTTATTATAATAAAAATA
1 AATA-TTATTTATTATAATAAAAATA
* * *
5108222 AATATTATTTAATTATTATGAAGATA
1 AATATTATTT-ATTATAATAAAAATA
*
5108248 AATAATATTTAT
1 AATATTATTTAT
5108260 CTTAATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
25 8 0.24
26 25 0.76
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (25 bp):
AATATTATTTATTATAATAAAAATA
Found at i:5108662 original size:31 final size:33
Alignment explanation
Indices: 5108597--5108706 Score: 95
Period size: 31 Copynumber: 3.5 Consensus size: 33
5108587 ATTCTAAATT
* *
5108597 ATTAAAATAATAATTTATTTTAATTATACTTAA
1 ATTAAATTAATAATTTATTCTAATTATACTTAA
* *
5108630 ATTAAATTATTAATTT-TTCTATTTA-ACTTAA
1 ATTAAATTAATAATTTATTCTAATTATACTTAA
* ** * *
5108661 ATTAAA-TGATAATAAATTCTAAATATA-ATAA
1 ATTAAATTAATAATTTATTCTAATTATACTTAA
5108692 ATATAAA-TAATAATT
1 AT-TAAATTAATAATT
5108707 GAATAGAAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
30 5 0.08
31 24 0.39
32 18 0.30
33 14 0.23
ACGTcount: A:0.50, C:0.04, G:0.01, T:0.45
Consensus pattern (33 bp):
ATTAAATTAATAATTTATTCTAATTATACTTAA
Found at i:5108704 original size:16 final size:14
Alignment explanation
Indices: 5108658--5108705 Score: 51
Period size: 16 Copynumber: 3.1 Consensus size: 14
5108648 CTATTTAACT
5108658 TAAATTAAATGATAA
1 TAAATTAAAT-ATAA
5108673 TAAATTCTAAATATAA
1 TAAA-T-TAAATATAA
5108689 TAAATATAAATAATAA
1 TAAAT-TAAAT-ATAA
5108705 T
1 T
5108706 TGAATAGAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
15 10 0.34
16 14 0.48
17 5 0.17
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (14 bp):
TAAATTAAATATAA
Found at i:5109585 original size:23 final size:21
Alignment explanation
Indices: 5109543--5109591 Score: 55
Period size: 23 Copynumber: 2.2 Consensus size: 21
5109533 TTAGTTTATA
5109543 ATATTTTATTTGATTTTTTAGT
1 ATATTTTATTT-ATTTTTTAGT
5109565 GATATTTTA-TTATTTTATTTAGT
1 -ATATTTTATTTA-TTT-TTTAGT
5109588 ATAT
1 ATAT
5109592 ATATGTAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 1 0.04
22 9 0.38
23 14 0.58
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (21 bp):
ATATTTTATTTATTTTTTAGT
Found at i:5111549 original size:11 final size:13
Alignment explanation
Indices: 5111525--5111556 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
5111515 TAGTTTATTA
5111525 ATATTTTAATATG
1 ATATTTTAATATG
5111538 AT-TTTTAA-ATG
1 ATATTTTAATATG
5111549 ATATTTTA
1 ATATTTTA
5111557 TTAATTTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 5 0.28
12 11 0.61
13 2 0.11
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (13 bp):
ATATTTTAATATG
Found at i:5113439 original size:123 final size:120
Alignment explanation
Indices: 5113216--5113457 Score: 358
Period size: 123 Copynumber: 2.0 Consensus size: 120
5113206 AATGTTTTGA
*
5113216 TTTTGATTGGTTATAAATATGAATGTTTGATGAAATGAAATGTCTGAAAATGAATTTGTAAACTC
1 TTTTGATTGGTTATAAATATGAATGCTTGATGAAATGAAATGTCTGAAAATGAATTTGTAAACTC
* * ** *
5113281 CGGTAATGCTCTATAACCCTATTTTGGGGAAGGATACGGGTTAGGGGTGTTACAT
66 CGGTAATGCCCTATAACCCTATTCTGACGAAGGATACAGGTTAGGGGTGTTACAT
* * *
5113336 TTTTGATTGGTTATAAATATGAATGCTTGATGAAATAATGAAATGTTTGTAAATTAATTTGTAAA
1 TTTTGATTGGTTATAAATATGAATGCTTGATG--A-AATGAAATGTCTGAAAATGAATTTGTAAA
* *
5113401 CTCCGGTAATGCCCTATAACCCTATTCTGACGATGGATATAGGTTAGGGGTGTTACA
63 CTCCGGTAATGCCCTATAACCCTATTCTGACGAAGGATACAGGTTAGGGGTGTTACA
5113458 AGTCTAGTAC
Statistics
Matches: 108, Mismatches: 11, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
120 31 0.29
122 1 0.01
123 76 0.70
ACGTcount: A:0.31, C:0.10, G:0.22, T:0.36
Consensus pattern (120 bp):
TTTTGATTGGTTATAAATATGAATGCTTGATGAAATGAAATGTCTGAAAATGAATTTGTAAACTC
CGGTAATGCCCTATAACCCTATTCTGACGAAGGATACAGGTTAGGGGTGTTACAT
Found at i:5113786 original size:13 final size:13
Alignment explanation
Indices: 5113747--5113789 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
5113737 AGTTCTTCAT
*
5113747 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
* *
5113760 TGCTATGGAAAAG
1 TGCTTTTGAAAAG
*
5113773 TGCTTTTGAGAAG
1 TGCTTTTGAAAAG
5113786 TGCT
1 TGCT
5113790 GTAACACCCC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.30, C:0.09, G:0.26, T:0.35
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:5114507 original size:51 final size:51
Alignment explanation
Indices: 5114431--5114549 Score: 193
Period size: 51 Copynumber: 2.3 Consensus size: 51
5114421 ATCACATTTA
* *
5114431 TCACTTGTCACTGATCAGATTAGTGTAGCTAAAGCTACCACTCATCACTTG
1 TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTCATCACTTG
* * *
5114482 TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTATCACTTATTACTTG
1 TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTCATCACTTG
5114533 TCACTTGTCACTGATCA
1 TCACTTGTCACTGATCA
5114550 GAAGTACTCA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 63 1.00
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.34
Consensus pattern (51 bp):
TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTCATCACTTG
Found at i:5116264 original size:2 final size:2
Alignment explanation
Indices: 5116257--5116291 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5116247 TTTCTTCCAC
5116257 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5116292 CTAAATAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5138684 original size:81 final size:81
Alignment explanation
Indices: 5138544--5138785 Score: 412
Period size: 81 Copynumber: 3.0 Consensus size: 81
5138534 CTAAACTGAG
* * * *
5138544 TGAATTAGAAAATAGTATGATATAGTTAATGCATGATATGTGATATGAATCTAAAATGAACCATG
1 TGAAATAGAAAATAGTATGATATAGTTGATGCATGATATGTGATATGAATATAGAATGAACCATG
5138609 CTATGTGATATTGGGA
66 CTATGTGATATTGGGA
*
5138625 TGAAATAGAAAATAGTATGATATAGTTGATGCATGATATGTGATATGAATATAGAATGAACCGTG
1 TGAAATAGAAAATAGTATGATATAGTTGATGCATGATATGTGATATGAATATAGAATGAACCATG
5138690 CTATGTGATATTGGGA
66 CTATGTGATATTGGGA
* * *
5138706 TGAAGTAGAAAATAGTATGATGTAGTTGATGCATGATATGTGATATGAATATAGCATGAACCATG
1 TGAAATAGAAAATAGTATGATATAGTTGATGCATGATATGTGATATGAATATAGAATGAACCATG
5138771 CTATGTGATATTGGG
66 CTATGTGATATTGGG
5138786 GATATATGAA
Statistics
Matches: 152, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
81 152 1.00
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.33
Consensus pattern (81 bp):
TGAAATAGAAAATAGTATGATATAGTTGATGCATGATATGTGATATGAATATAGAATGAACCATG
CTATGTGATATTGGGA
Found at i:5144547 original size:29 final size:31
Alignment explanation
Indices: 5144501--5144563 Score: 112
Period size: 29 Copynumber: 2.1 Consensus size: 31
5144491 ATTTCTTATG
5144501 CCAATATTTCGATACCCATATCTTTGACTTT
1 CCAATATTTCGATACCCATATCTTTGACTTT
5144532 CCAATA-TT-GATACCCATATCTTTGACTTT
1 CCAATATTTCGATACCCATATCTTTGACTTT
5144561 CCA
1 CCA
5144564 TAATATGGAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 24 0.75
30 2 0.06
31 6 0.19
ACGTcount: A:0.27, C:0.27, G:0.06, T:0.40
Consensus pattern (31 bp):
CCAATATTTCGATACCCATATCTTTGACTTT
Found at i:5147181 original size:8 final size:8
Alignment explanation
Indices: 5147178--5147203 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5147168 TATATTGTTA
5147178 TATTATAT
1 TATTATAT
5147186 TATTATAT
1 TATTATAT
5147194 TATTATAT
1 TATTATAT
5147202 TA
1 TA
5147204 ATAAAATAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (8 bp):
TATTATAT
Found at i:5148186 original size:25 final size:25
Alignment explanation
Indices: 5148152--5148310 Score: 190
Period size: 25 Copynumber: 6.6 Consensus size: 25
5148142 CTTTAGCGCA
5148152 CTCTCTGATTATTAGCACATCAGTG
1 CTCTCTGATTATTAGCACATCAGTG
5148177 CTCTCTGATTATTAGCACATCAGTG
1 CTCTCTGATTATTAGCACATCAGTG
* *
5148202 CTCTTTGATTATTAGCACGTCAGTG
1 CTCTCTGATTATTAGCACATCAGTG
*
5148227 CTCTCTGATTACTAGCACATCAGTG
1 CTCTCTGATTATTAGCACATCAGTG
* *
5148252 CTCTCCG--T-TTAGCACA-AATGTG
1 CTCTCTGATTATTAGCACATCA-GTG
*
5148274 CTCTCTG--TA-TAGCACTTCAGTG
1 CTCTCTGATTATTAGCACATCAGTG
5148296 CTCTCTG-TTCATTAG
1 CTCTCTGATT-ATTAG
5148311 TGCATAACAA
Statistics
Matches: 117, Mismatches: 11, Indels: 12
0.84 0.08 0.09
Matches are distributed among these distances:
21 1 0.01
22 33 0.28
23 3 0.03
24 1 0.01
25 79 0.68
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.36
Consensus pattern (25 bp):
CTCTCTGATTATTAGCACATCAGTG
Found at i:5151488 original size:30 final size:31
Alignment explanation
Indices: 5151429--5151488 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
5151419 TTTCTTATGC
*
5151429 CAATATTTCGATACCCATATTTTTAACTTTT
1 CAATATTTCGATACCCATATCTTTAACTTTT
* *
5151460 CAATATTT-GATACCTATATCTTTGACTTT
1 CAATATTTCGATACCCATATCTTTAACTTT
5151489 CCATAATATG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.28, C:0.18, G:0.05, T:0.48
Consensus pattern (31 bp):
CAATATTTCGATACCCATATCTTTAACTTTT
Found at i:5154681 original size:1 final size:1
Alignment explanation
Indices: 5154645--5154671 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5154635 TGGAAAATAG
5154645 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
5154672 GGGAAAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:5164163 original size:15 final size:14
Alignment explanation
Indices: 5164136--5164163 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5164126 AATTAGTGTT
5164136 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
5164150 GAAAACTAAAAAAA
1 GAAAACTAAAAAAA
5164164 TGGGGGAGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.79, C:0.07, G:0.07, T:0.07
Consensus pattern (14 bp):
GAAAACTAAAAAAA
Found at i:5172311 original size:19 final size:20
Alignment explanation
Indices: 5172287--5172325 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5172277 AGTGTAAAAT
5172287 TATATAAAATTA-AAATTAA
1 TATATAAAATTACAAATTAA
*
5172306 TATATATAATTACAAATTAA
1 TATATAAAATTACAAATTAA
5172326 ACCTAAATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (20 bp):
TATATAAAATTACAAATTAA
Found at i:5172922 original size:17 final size:19
Alignment explanation
Indices: 5172890--5172924 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
5172880 TTTTGCTCTG
5172890 TTTGTTGATTCAATGTGTT
1 TTTGTTGATTCAATGTGTT
5172909 TTTGTT-ATTC-ATGTGT
1 TTTGTTGATTCAATGTGT
5172925 CTTCTTTGTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 4 0.25
19 6 0.38
ACGTcount: A:0.14, C:0.06, G:0.20, T:0.60
Consensus pattern (19 bp):
TTTGTTGATTCAATGTGTT
Found at i:5184855 original size:14 final size:14
Alignment explanation
Indices: 5184830--5184862 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
5184820 TCAAATCAGC
5184830 TTTAAAACT-AAAA
1 TTTAAAACTAAAAA
5184843 TTTAAATACTAAAAA
1 TTTAAA-ACTAAAAA
5184858 TTTAA
1 TTTAA
5184863 CACAATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.33
14 3 0.17
15 9 0.50
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (14 bp):
TTTAAAACTAAAAA
Found at i:5184990 original size:20 final size:22
Alignment explanation
Indices: 5184959--5184999 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
5184949 ATGTTATTTT
5184959 AACATGAAATTTG-ATTATAAC
1 AACATGAAATTTGAATTATAAC
5184980 AACAT-AAATTTGAATTATAA
1 AACATGAAATTTGAATTATAA
5185000 AATTATTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.51, C:0.07, G:0.07, T:0.34
Consensus pattern (22 bp):
AACATGAAATTTGAATTATAAC
Found at i:5186681 original size:21 final size:21
Alignment explanation
Indices: 5186645--5186718 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 21
5186635 ACAAGTGCTA
* *
5186645 AACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGGGTTG
* * *
5186666 AACGGAAGCTCATAAGAGCTG
1 AACAGAAGCTCATAAGGGTTG
*
5186687 AACAGAA-CCCATAAGGGTT-
1 AACAGAAGCTCATAAGGGTTG
*
5186706 AAGCTGAAGCTCA
1 AA-CAGAAGCTCA
5186719 AAAGAGCTAA
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 2 0.05
20 13 0.32
21 25 0.62
ACGTcount: A:0.41, C:0.20, G:0.24, T:0.15
Consensus pattern (21 bp):
AACAGAAGCTCATAAGGGTTG
Found at i:5186703 original size:41 final size:41
Alignment explanation
Indices: 5186641--5186762 Score: 149
Period size: 41 Copynumber: 2.9 Consensus size: 41
5186631 GCACACAAGT
*
5186641 GCTAAACAGAAACCCATAAGGGTTGAACGGAAGCTCATAAGA
1 GCTAAACAGAAACCCATAAGGGTT-AACTGAAGCTCATAAGA
* *
5186683 GCTGAACAG-AACCCATAAGGGTTAAGCTGAAGCTCAAAAGA
1 GCTAAACAGAAACCCATAAGGGTTAA-CTGAAGCTCATAAGA
* *
5186724 GCTAAACGGAAACCCAATAA-GGTTAAACTGAAACTCATA
1 GCTAAACAGAAACCC-ATAAGGGTT-AACTGAAGCTCATA
5186763 TGAATTAACT
Statistics
Matches: 69, Mismatches: 7, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
40 2 0.03
41 34 0.49
42 27 0.39
43 6 0.09
ACGTcount: A:0.43, C:0.20, G:0.21, T:0.16
Consensus pattern (41 bp):
GCTAAACAGAAACCCATAAGGGTTAACTGAAGCTCATAAGA
Found at i:5186756 original size:21 final size:21
Alignment explanation
Indices: 5186692--5186757 Score: 55
Period size: 21 Copynumber: 3.1 Consensus size: 21
5186682 AGCTGAACAG
*
5186692 AACCC-ATAAGGGTTAAGCTGA
1 AACCCAATAA-GGTTAAACTGA
* * * *
5186713 AGCTCAA-AAGAGCTAAACGGA
1 AACCCAATAAG-GTTAAACTGA
5186734 AACCCAATAAGGTTAAACTGA
1 AACCCAATAAGGTTAAACTGA
5186755 AAC
1 AAC
5186758 TCATATGAAT
Statistics
Matches: 33, Mismatches: 9, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
20 1 0.03
21 28 0.85
22 4 0.12
ACGTcount: A:0.45, C:0.20, G:0.20, T:0.15
Consensus pattern (21 bp):
AACCCAATAAGGTTAAACTGA
Found at i:5190409 original size:25 final size:24
Alignment explanation
Indices: 5190364--5190411 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 24
5190354 TTAATATTAT
*
5190364 ATATTATATATTTATAAGCCCAAC
1 ATATTATATATATATAAGCCCAAC
5190388 ATATTATATTATATATAAGCCCAA
1 ATATTATA-TATATATAAGCCCAA
5190412 TGCATGACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 8 0.36
25 14 0.64
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.38
Consensus pattern (24 bp):
ATATTATATATATATAAGCCCAAC
Found at i:5194380 original size:23 final size:23
Alignment explanation
Indices: 5194352--5194397 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
5194342 CTTTTAATTT
*
5194352 CTTATTTTAGTAAGTGTTATCTC
1 CTTATTTTACTAAGTGTTATCTC
5194375 CTTATTTTACTAAGTGTTATCTC
1 CTTATTTTACTAAGTGTTATCTC
5194398 GATTGACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.15, G:0.11, T:0.52
Consensus pattern (23 bp):
CTTATTTTACTAAGTGTTATCTC
Found at i:5199205 original size:5 final size:6
Alignment explanation
Indices: 5199192--5199216 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5199182 AAAACAAATT
5199192 AAATAA AAATAA AAATAA AAATAA A
1 AAATAA AAATAA AAATAA AAATAA A
5199217 GAAGAAGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:5220076 original size:22 final size:23
Alignment explanation
Indices: 5220034--5220076 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5220024 AAATCAAATC
5220034 TCTAAGATTACAAAATCATATTT
1 TCTAAGATTACAAAATCATATTT
*
5220057 TCTAAGATTAC-ATATCATAT
1 TCTAAGATTACAAAATCATAT
5220077 CTACGATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (23 bp):
TCTAAGATTACAAAATCATATTT
Found at i:5225193 original size:22 final size:23
Alignment explanation
Indices: 5225166--5225210 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5225156 AGGTATCTAC
5225166 AAATCA-AATCTCTAAGATTACA
1 AAATCATAATCTCTAAGATTACA
* *
5225188 AAATCATATTTTCTAAGATTACA
1 AAATCATAATCTCTAAGATTACA
5225211 TATCATATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 6 0.30
23 14 0.70
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (23 bp):
AAATCATAATCTCTAAGATTACA
Found at i:5225204 original size:23 final size:22
Alignment explanation
Indices: 5225163--5225218 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
5225153 GAAAGGTATC
* *
5225163 TACAAATCA-AATCTCTAAGAT
1 TACAAATCATATTTTCTAAGAT
5225184 TACAAAATCATATTTTCTAAGAT
1 TAC-AAATCATATTTTCTAAGAT
*
5225207 TACATATCATAT
1 TACAAATCATAT
5225219 CTGCGATTGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.10
22 14 0.47
23 13 0.43
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.36
Consensus pattern (22 bp):
TACAAATCATATTTTCTAAGAT
Found at i:5225218 original size:22 final size:23
Alignment explanation
Indices: 5225176--5225218 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
5225166 AAATCAAATC
5225176 TCTAAGATTACAAAATCATATTT
1 TCTAAGATTACAAAATCATATTT
*
5225199 TCTAAGATTAC-ATATCATAT
1 TCTAAGATTACAAAATCATAT
5225219 CTGCGATTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.42, C:0.14, G:0.05, T:0.40
Consensus pattern (23 bp):
TCTAAGATTACAAAATCATATTT
Found at i:5234765 original size:26 final size:26
Alignment explanation
Indices: 5234736--5234794 Score: 118
Period size: 26 Copynumber: 2.3 Consensus size: 26
5234726 AAAAGAAAGA
5234736 AAGCCATTAGACAAGCAGCAAAGGAG
1 AAGCCATTAGACAAGCAGCAAAGGAG
5234762 AAGCCATTAGACAAGCAGCAAAGGAG
1 AAGCCATTAGACAAGCAGCAAAGGAG
5234788 AAGCCAT
1 AAGCCAT
5234795 AAACGAGTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.46, C:0.20, G:0.25, T:0.08
Consensus pattern (26 bp):
AAGCCATTAGACAAGCAGCAAAGGAG
Found at i:5238036 original size:27 final size:27
Alignment explanation
Indices: 5237995--5238124 Score: 208
Period size: 27 Copynumber: 4.8 Consensus size: 27
5237985 TAGTATTGGC
*
5237995 GCCTATCTGGAAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
*
5238022 GCCTATTTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
5238049 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
5238076 GCCTATCTGGGAGGCGCCAATGGTGGT
1 GCCTATCTGGGAGGCGCCAATGGTGGT
**
5238103 GCC-ATACTGAAAGGCGCCAATG
1 GCCTAT-CTGGGAGGCGCCAATG
5238125 CTGTGATTTT
Statistics
Matches: 97, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
26 2 0.02
27 95 0.98
ACGTcount: A:0.18, C:0.22, G:0.38, T:0.22
Consensus pattern (27 bp):
GCCTATCTGGGAGGCGCCAATGGTGGT
Found at i:5238228 original size:18 final size:20
Alignment explanation
Indices: 5238186--5238232 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 20
5238176 GAAACGGAAG
5238186 AAAGAAGAAGGAAGGAAGCA
1 AAAGAAGAAGGAAGGAAGCA
* *
5238206 GAAGAA-AA-GAAGGAAGGA
1 AAAGAAGAAGGAAGGAAGCA
5238224 AAAGAAGAA
1 AAAGAAGAA
5238233 AAAAATTAGG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 14 0.61
19 4 0.17
20 5 0.22
ACGTcount: A:0.64, C:0.02, G:0.34, T:0.00
Consensus pattern (20 bp):
AAAGAAGAAGGAAGGAAGCA
Found at i:5238235 original size:22 final size:23
Alignment explanation
Indices: 5238182--5238235 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
5238172 TACAGAAACG
*
5238182 GAAGAAAGAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
5238206 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
5238227 GAAGAAAAA
1 GAAGAAAAA
5238236 AATTAGGTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:5241560 original size:6 final size:6
Alignment explanation
Indices: 5241549--5241605 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
5241539 AGAATGTAGT
5241549 TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC
1 TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC TCTGGC
5241597 TCTGGC TCT
1 TCTGGC TCT
5241606 TGTGCATGAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.00, C:0.33, G:0.32, T:0.35
Consensus pattern (6 bp):
TCTGGC
Found at i:5243260 original size:16 final size:15
Alignment explanation
Indices: 5243229--5243270 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
5243219 ACAAAATCAA
*
5243229 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
5243244 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
5243260 ATAAAAATTAA
1 ATAAAAGTTAA
5243271 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:5243350 original size:38 final size:39
Alignment explanation
Indices: 5243307--5243389 Score: 150
Period size: 38 Copynumber: 2.2 Consensus size: 39
5243297 AAAAAGTCAG
5243307 TTATAATTAAACTTTTAATAAAATGATTTTTAA-TTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
*
5243345 TTATAATTAAACTTTTAATGAAATGATTTTTAATTTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
5243384 TTATAA
1 TTATAA
5243390 ACTTTATATA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
38 32 0.74
39 11 0.26
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (39 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTTT
Found at i:5243835 original size:22 final size:22
Alignment explanation
Indices: 5243803--5244039 Score: 162
Period size: 22 Copynumber: 11.0 Consensus size: 22
5243793 ACAAAATTAC
5243803 AAAATTACAATATTCATACAAA
1 AAAATTACAATATTCATACAAA
*
5243825 AAAATTGCAATATTCATACAAAA
1 AAAATTACAATATTCATAC-AAA
5243848 CTATAATATTACAATATTCATACAAA
1 --A-AA-ATTACAATATTCATACAAA
* *
5243874 AAATTTATAATATTCATAC---
1 AAAATTACAATATTCATACAAA
5243893 AAAATTACAATATTCATAC-AA
1 AAAATTACAATATTCATACAAA
* *
5243914 AAAATTACTA-ATCCA-A-AACTA
1 AAAATTACAATATTCATACAA--A
* * *
5243935 TAAA-TACAA-ATTTAATTATAAA
1 AAAATTACAATA-TTCA-TACAAA
* *
5243957 ATAATTACAATATCCATAC---
1 AAAATTACAATATTCATACAAA
*
5243976 AACATTACAATATTCAT--AAA
1 AAAATTACAATATTCATACAAA
*
5243996 AAAA-TATAATATTCATACAAA
1 AAAATTACAATATTCATACAAA
* *
5244017 AAATTTAAAATATTCATACAAA
1 AAAATTACAATATTCATACAAA
5244039 A
1 A
5244040 TTCTAATCTA
Statistics
Matches: 169, Mismatches: 24, Indels: 44
0.71 0.10 0.19
Matches are distributed among these distances:
19 44 0.26
20 12 0.07
21 21 0.12
22 54 0.32
23 13 0.08
24 4 0.02
25 1 0.01
26 5 0.03
27 15 0.09
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (22 bp):
AAAATTACAATATTCATACAAA
Found at i:5243857 original size:41 final size:42
Alignment explanation
Indices: 5243800--5244039 Score: 144
Period size: 41 Copynumber: 5.6 Consensus size: 42
5243790 CATACAAAAT
*
5243800 TACAAAATTACAATATTCATACAAAAAAA-TTGCAATATTCA
1 TACAAAATTACAATATTCATACAAAAAAATTTACAATATTCA
*
5243841 TACAAAACTATAATATTACAATATTCATAC-AAAAAATTTATAATATTCA
1 T-----AC-A-AA-ATTACAATATTCATACAAAAAAATTTACAATATTCA
* *
5243890 TACAAAATTACAATATTCATAC-AAAAAA-TTACTA-ATCCAA
1 TACAAAATTACAATATTCATACAAAAAAATTTACAATATTC-A
* * * * *
5243930 AACTATAAA-TACAA-ATTTAATTATAAAATAA-TTACAATATCCA
1 TAC-A-AAATTACAATA-TTCA-TACAAAAAAATTTACAATATTCA
* *
5243973 TACAACATTACAATATTCAT--AAAAAAA--TATAATATTCA
1 TACAAAATTACAATATTCATACAAAAAAATTTACAATATTCA
*
5244011 TACAAAAAATTTAAAATATTCATACAAAA
1 TAC--AAAA-TTACAATATTCATACAAAA
5244040 TTCTAATCTA
Statistics
Matches: 158, Mismatches: 18, Indels: 44
0.72 0.08 0.20
Matches are distributed among these distances:
38 12 0.08
39 9 0.06
40 11 0.07
41 47 0.30
42 16 0.10
43 19 0.12
44 6 0.04
46 2 0.01
47 1 0.01
48 8 0.05
49 27 0.17
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.31
Consensus pattern (42 bp):
TACAAAATTACAATATTCATACAAAAAAATTTACAATATTCA
Found at i:5243862 original size:49 final size:49
Alignment explanation
Indices: 5243790--5243906 Score: 180
Period size: 49 Copynumber: 2.4 Consensus size: 49
5243780 NNNNNNNNNN
* *
5243790 CATACAAAATTACAAAATTACAATATTCATACAAAAAAATTGCAATATT
1 CATACAAAATTACAATATTACAATATTCATACAAAAAAATTACAATATT
* * * *
5243839 CATACAAAACTATAATATTACAATATTCATACAAAAAATTTATAATATT
1 CATACAAAATTACAATATTACAATATTCATACAAAAAAATTACAATATT
5243888 CATACAAAATTACAATATT
1 CATACAAAATTACAATATT
5243907 CATACAAAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
49 60 1.00
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.32
Consensus pattern (49 bp):
CATACAAAATTACAATATTACAATATTCATACAAAAAAATTACAATATT
Found at i:5243870 original size:27 final size:25
Alignment explanation
Indices: 5243790--5243906 Score: 111
Period size: 22 Copynumber: 4.7 Consensus size: 25
5243780 NNNNNNNNNN
*
5243790 CATACAAAATTACAAAATTACAATATT
1 CATACAAAA-TA-AATATTACAATATT
*
5243817 CATAC-AAA-AAA-ATTGCAATATT
1 CATACAAAATAAATATTACAATATT
5243839 CATACAAAACTATAATATTACAATATT
1 CATACAAAA-TA-AATATTACAATATT
*
5243866 CATAC-AAA-AAAT-TTATAATATT
1 CATACAAAATAAATATTACAATATT
5243888 CATACAAAATTACAATATT
1 CATACAAAA-TA-AATATT
5243907 CATACAAAAA
Statistics
Matches: 77, Mismatches: 3, Indels: 20
0.77 0.03 0.20
Matches are distributed among these distances:
22 29 0.38
23 11 0.14
24 2 0.03
25 2 0.03
26 11 0.14
27 22 0.29
ACGTcount: A:0.54, C:0.14, G:0.01, T:0.32
Consensus pattern (25 bp):
CATACAAAATAAATATTACAATATT
Found at i:5244517 original size:25 final size:25
Alignment explanation
Indices: 5244467--5244518 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 25
5244457 TTTTAAAAAA
5244467 TATTAAAAAATTATTAAAATTATATTT
1 TATTAAAAAATTATT--AATTATATTT
*
5244494 TATTCAAAAAATTATT-ATTTTATTT
1 TATT-AAAAAATTATTAATTATATTT
5244519 ATTGGCGCCT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 8 0.35
27 4 0.17
28 11 0.48
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TATTAAAAAATTATTAATTATATTT
Found at i:5245544 original size:16 final size:15
Alignment explanation
Indices: 5245489--5245545 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
5245479 AAAAGATATT
* *
5245489 TTTTAAATCAATAGA
1 TTTTAATTCAATTGA
* *
5245504 TTTTAACTCAATTAA
1 TTTTAATTCAATTGA
*
5245519 TTTAATATTCAATTTGA
1 TTTTA-ATTCAA-TTGA
5245536 TTTTAATTCA
1 TTTTAATTCA
5245546 GTGTTTTAGA
Statistics
Matches: 33, Mismatches: 7, Indels: 3
0.77 0.16 0.07
Matches are distributed among these distances:
15 16 0.48
16 10 0.30
17 7 0.21
ACGTcount: A:0.39, C:0.09, G:0.04, T:0.49
Consensus pattern (15 bp):
TTTTAATTCAATTGA
Found at i:5247433 original size:21 final size:20
Alignment explanation
Indices: 5247382--5247433 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
5247372 TTTTTATCAT
5247382 AATTTTATTATAATATTTTGA
1 AATTTT-TTATAATATTTTGA
*
5247403 AATGTATTTATATATATTTTTG-
1 AAT-TTTTTATA-ATA-TTTTGA
5247425 AATTTTTTA
1 AATTTTTTA
5247434 AAATTATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
21 13 0.50
22 8 0.31
23 5 0.19
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (20 bp):
AATTTTTTATAATATTTTGA
Found at i:5247856 original size:22 final size:21
Alignment explanation
Indices: 5247831--5247883 Score: 60
Period size: 19 Copynumber: 2.7 Consensus size: 21
5247821 ATAAATATTT
5247831 TTTAAAAAAATATTATAATAAA
1 TTTAAAAAAATATTATAA-AAA
5247853 TTT--AAAAATA-TATAAAAA
1 TTTAAAAAAATATTATAAAAA
*
5247871 -TGAAAAAAATATT
1 TTTAAAAAAATATT
5247884 GTTGACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
17 1 0.04
18 3 0.11
19 12 0.44
20 8 0.30
22 3 0.11
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (21 bp):
TTTAAAAAAATATTATAAAAA
Found at i:5247876 original size:17 final size:19
Alignment explanation
Indices: 5247836--5247882 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 19
5247826 TATTTTTTAA
*
5247836 AAAAATATTATAATAAATTT
1 AAAAATA-TATAATAAATTG
5247856 AAAAATATATAA-AAA-TG
1 AAAAATATATAATAAATTG
*
5247873 AAAAAAATAT
1 AAAAATATAT
5247883 TGTTGACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 10 0.40
18 3 0.12
19 5 0.20
20 7 0.28
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAAATATATAATAAATTG
Found at i:5247957 original size:17 final size:15
Alignment explanation
Indices: 5247929--5247968 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 15
5247919 GACATAAAAT
5247929 AAATAAATAATTTAA
1 AAATAAATAATTTAA
5247944 AAATATAATAAATTT-A
1 AAATA-AAT-AATTTAA
5247960 AAATAAATA
1 AAATAAATA
5247969 TTAAATTAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 1 0.04
15 8 0.35
16 9 0.39
17 5 0.22
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATAAATAATTTAA
Found at i:5247977 original size:17 final size:17
Alignment explanation
Indices: 5247923--5247977 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
5247913 TCACAAGACA
*
5247923 TAAAATAAATAAATAATT
1 TAAAATAAAT-AATAAAT
*
5247941 TAAAA-ATATAATAAATT
1 TAAAATAAATAATAAA-T
*
5247958 TAAAATAAATATTAAAT
1 TAAAATAAATAATAAAT
5247975 TAA
1 TAA
5247978 TAAAATTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
16 5 0.16
17 13 0.42
18 13 0.42
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAAAATAAATAATAAAT
Found at i:5248493 original size:22 final size:21
Alignment explanation
Indices: 5248468--5248539 Score: 71
Period size: 22 Copynumber: 3.4 Consensus size: 21
5248458 TTATTTAATA
5248468 TTATTATTATTTTAAAATTATT
1 TTATTATT-TTTTAAAATTATT
*
5248490 TTATT-TTTTTTTAAATTGATT
1 TTATTATTTTTTAAAATT-ATT
5248511 ATTA-TATTTTTTAAAA-TA-T
1 -TTATTATTTTTTAAAATTATT
5248530 TTATGTATTT
1 TTAT-TATTT
5248540 ATATACATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
18 3 0.07
19 1 0.02
20 15 0.35
21 7 0.16
22 17 0.40
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
TTATTATTTTTTAAAATTATT
Found at i:5248496 original size:16 final size:16
Alignment explanation
Indices: 5248450--5248496 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
5248440 ATATTAATAT
5248450 AATTATATTTA-TTTAA
1 AATTAT-TTTATTTTAA
*
5248466 TATTATTATTATTTTAA
1 AATTATT-TTATTTTAA
5248483 AATTATTTTATTTT
1 AATTATTTTATTTT
5248497 TTTTTAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 1 0.04
16 15 0.56
17 11 0.41
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
AATTATTTTATTTTAA
Found at i:5248497 original size:17 final size:17
Alignment explanation
Indices: 5248461--5248496 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
5248451 ATTATATTTA
*
5248461 TTTAATATTATTATTAT
1 TTTAAAATTATTATTAT
5248478 TTTAAAATTATT-TTAT
1 TTTAAAATTATTATTAT
5248494 TTT
1 TTT
5248497 TTTTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTAAAATTATTATTAT
Found at i:5248533 original size:21 final size:19
Alignment explanation
Indices: 5248464--5248530 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 19
5248454 ATATTTATTT
*
5248464 AATATTATTATTATTTTAA
1 AATATTATTATTTTTTTAA
5248483 AATTATT-TTATTTTTTTTTAA
1 AA-TATTATTA--TTTTTTTAA
*
5248504 ATTGATTATTATATTTTTTAA
1 AAT-ATTATTAT-TTTTTTAA
5248525 AATATT
1 AATATT
5248531 TATGTATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
19 5 0.13
20 9 0.23
21 22 0.56
22 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.01, T:0.63
Consensus pattern (19 bp):
AATATTATTATTTTTTTAA
Found at i:5259531 original size:27 final size:27
Alignment explanation
Indices: 5259469--5259551 Score: 78
Period size: 27 Copynumber: 3.1 Consensus size: 27
5259459 GAAAAATAAG
*
5259469 ACCATTGGCGCCTCTCA-ACATGGCACC
1 ACCATTGGCGCCTCTCAGATA-GGCACC
** * *
5259496 ATTAATGGCGCCTGTCAGATAGGCACC
1 ACCATTGGCGCCTCTCAGATAGGCACC
* * *
5259523 ACCATTGGCGCTTCTGAGATAGGCGCC
1 ACCATTGGCGCCTCTCAGATAGGCACC
5259550 AC
1 AC
5259552 TACTTTTTAT
Statistics
Matches: 43, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
27 41 0.95
28 2 0.05
ACGTcount: A:0.23, C:0.33, G:0.24, T:0.20
Consensus pattern (27 bp):
ACCATTGGCGCCTCTCAGATAGGCACC
Found at i:5277703 original size:21 final size:21
Alignment explanation
Indices: 5277675--5277723 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
5277665 AATTAAGCTT
5277675 AATA-TTA-TTATATTTTTAA
1 AATATTTATTTATATTTTTAA
* *
5277694 TAATTTTTATTTTTATTTTTAA
1 -AATATTTATTTATATTTTTAA
5277716 AATATTTA
1 AATATTTA
5277724 AAATATTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 3 0.12
21 10 0.42
22 11 0.46
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
AATATTTATTTATATTTTTAA
Found at i:5277940 original size:15 final size:15
Alignment explanation
Indices: 5277920--5277976 Score: 60
Period size: 15 Copynumber: 3.5 Consensus size: 15
5277910 CATTCAATTT
5277920 AATATTTTAATAATA
1 AATATTTTAATAATA
*
5277935 AATATTCTCTACAATTATA
1 AATATT-T-T--AATAATA
*
5277954 AATATATTAATAATA
1 AATATTTTAATAATA
5277969 AATATTTT
1 AATATTTT
5277977 GTAGTATAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
15 19 0.56
16 1 0.03
17 2 0.06
18 1 0.03
19 11 0.32
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:5283168 original size:49 final size:50
Alignment explanation
Indices: 5283111--5283224 Score: 198
Period size: 49 Copynumber: 2.3 Consensus size: 50
5283101 TAGTTTGCCC
5283111 TTATTAGTATTGGTTACAACATATTTGTCTTGAAA-TTTTTAGCTAATTA
1 TTATTAGTATTGGTTACAACATATTTGTCTTGAAAGTTTTTAGCTAATTA
5283160 TTATTAGTATTGGTTACAACATATTTGTCTTGAAAGTTTTTAGCTAATTA
1 TTATTAGTATTGGTTACAACATATTTGTCTTGAAAGTTTTTAGCTAATTA
*
5283210 TTA--AGTATTTGTTAC
1 TTATTAGTATTGGTTAC
5283225 TCAACTCAGA
Statistics
Matches: 63, Mismatches: 1, Indels: 3
0.94 0.01 0.04
Matches are distributed among these distances:
48 11 0.17
49 35 0.56
50 17 0.27
ACGTcount: A:0.30, C:0.08, G:0.13, T:0.49
Consensus pattern (50 bp):
TTATTAGTATTGGTTACAACATATTTGTCTTGAAAGTTTTTAGCTAATTA
Found at i:5286358 original size:331 final size:331
Alignment explanation
Indices: 5285751--5286407 Score: 1163
Period size: 331 Copynumber: 2.0 Consensus size: 331
5285741 GGAAGCTTTC
5285751 TAAGCTGCTTATTACTTCTCAACTTAACTCCGCAGAGCAATTCTTCGCTTAAACCCCTACTTCCA
1 TAAGCTGCTTATTACTTCTCAACTTAACTCCGCAGAGCAATTCTTCGCTTAAACCCCTACTTCCA
*
5285816 TAGCTTTTATGGGTGATTCACCCTTTCTTATTGATGCTTTTCCTATTGGGATACCAATCTAAGTT
66 CAGCTTTTATGGGTGATTCACCCTTTCTTATTGATGCTTTTCCTATTGGGATACCAATCTAAGTT
* * *
5285881 AATAGATTGACTATGGGGATATCTTTATTCGGGGCTATTCGCCTTTTGAATCAAACAAAGTAAGT
131 AATAAATTGACTATGAGGATATCTTTATTCGGGGCTATTCGCATTTTGAATCAAACAAAGTAAGT
*
5285946 AATAGGGGCTTCATAGCTACTTTCATTCTAAAGGAAACCTAAAAACCAATCTTCAGTCAATAGGA
196 AATAGGGGCTTCATAGCTACTTTCATTCTAAAGGAAACCTAAAAACCAACCTTCAGTCAATAGGA
* *
5286011 GCCCTACTTCCCTCTTTGCGACCTCATCACTTTAATTTAAGCGCAAACTCATTTCTTTTTTAGAG
261 GCCCTACTTCCCTCTTTGCGACCTCATCACTTCAATTTAAGCGCAAACCCATTTCTTTTTTAGAG
5286076 TCAATT
326 TCAATT
* *
5286082 TAAGTTGCTTATTACTTCTCAACTTAACTCCGCAG-GACCATTCTTCGCTTAAACCCCTACTTCC
1 TAAGCTGCTTATTACTTCTCAACTTAACTCCGCAGAG-CAATTCTTCGCTTAAACCCCTACTTCC
*
5286146 ACAGCTTTTATTGGTGATTCACCCTTTCTTATTGATGCTTTTCCTATTGGGATACCAATCTAAGT
65 ACAGCTTTTATGGGTGATTCACCCTTTCTTATTGATGCTTTTCCTATTGGGATACCAATCTAAGT
* * *
5286211 TAATAAATTGACTATGAGGATATCTTTATTGGGGGTTGTTCGCATTTTGAATCAAACAAAGTAAG
130 TAATAAATTGACTATGAGGATATCTTTATTCGGGGCTATTCGCATTTTGAATCAAACAAAGTAAG
* *
5286276 TAGTAGGGGCTTCATAGCTACTTTCATTCTAAAGGAGACCTAAAAACCAACCTTCAGTCAATAGG
195 TAATAGGGGCTTCATAGCTACTTTCATTCTAAAGGAAACCTAAAAACCAACCTTCAGTCAATAGG
5286341 AGCCCTACTTCCCTCTTTGCGACCTCATCACTTCAATTTAAGCGCAAACCCATTTCTTTTTTAGA
260 AGCCCTACTTCCCTCTTTGCGACCTCATCACTTCAATTTAAGCGCAAACCCATTTCTTTTTTAGA
5286406 GT
325 GT
5286408 GAGTTTGGAT
Statistics
Matches: 310, Mismatches: 15, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
330 1 0.00
331 309 1.00
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.35
Consensus pattern (331 bp):
TAAGCTGCTTATTACTTCTCAACTTAACTCCGCAGAGCAATTCTTCGCTTAAACCCCTACTTCCA
CAGCTTTTATGGGTGATTCACCCTTTCTTATTGATGCTTTTCCTATTGGGATACCAATCTAAGTT
AATAAATTGACTATGAGGATATCTTTATTCGGGGCTATTCGCATTTTGAATCAAACAAAGTAAGT
AATAGGGGCTTCATAGCTACTTTCATTCTAAAGGAAACCTAAAAACCAACCTTCAGTCAATAGGA
GCCCTACTTCCCTCTTTGCGACCTCATCACTTCAATTTAAGCGCAAACCCATTTCTTTTTTAGAG
TCAATT
Found at i:5289534 original size:3 final size:3
Alignment explanation
Indices: 5289521--5289572 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
5289511 ATTACCAATC
*
5289521 TCA TTA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
5289569 TCA T
1 TCA T
5289573 TAAAACTATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.33, C:0.31, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:5298752 original size:21 final size:20
Alignment explanation
Indices: 5298727--5298782 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
5298717 CTTAGATTTT
*
5298727 TATATTATTTATTTATATAAA
1 TATATTATTTAATTATA-AAA
* * *
5298748 TATATAAATTAATTATAAAG
1 TATATTATTTAATTATAAAA
*
5298768 TATATTATTAAATTA
1 TATATTATTTAATTA
5298783 ATTATATTAT
Statistics
Matches: 28, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATTATTTAATTATAAAA
Found at i:5298766 original size:11 final size:11
Alignment explanation
Indices: 5298750--5298788 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
5298740 TATATAAATA
5298750 TATAAATTAAT
1 TATAAATTAAT
*
5298761 TATAAAGTATAT
1 TATAAATTA-AT
5298773 TATTAAATTAAT
1 TA-TAAATTAAT
5298785 TATA
1 TATA
5298789 TTATAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 10 0.42
12 8 0.33
13 6 0.25
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (11 bp):
TATAAATTAAT
Found at i:5298777 original size:19 final size:20
Alignment explanation
Indices: 5298727--5298778 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
5298717 CTTAGATTTT
*
5298727 TATATTATTTATTTATATAAA
1 TATATTA-TTAATTATATAAA
* *
5298748 TATATAAATTAATTATA-AAG
1 TATAT-TATTAATTATATAAA
5298768 TATATTATTAA
1 TATATTATTAA
5298779 ATTAATTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.19
20 7 0.27
21 13 0.50
22 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TATATTATTAATTATATAAA
Found at i:5298800 original size:14 final size:16
Alignment explanation
Indices: 5298768--5298808 Score: 59
Period size: 14 Copynumber: 2.6 Consensus size: 16
5298758 AATTATAAAG
5298768 TATATTATTAAATTAAT
1 TATATTA-TAAATTAAT
5298785 TATATTATAAA-T-AT
1 TATATTATAAATTAAT
5298799 TATATTATAA
1 TATATTATAA
5298809 GAAATAAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
14 12 0.50
15 1 0.04
16 4 0.17
17 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
TATATTATAAATTAAT
Found at i:5299092 original size:16 final size:17
Alignment explanation
Indices: 5299073--5299132 Score: 52
Period size: 16 Copynumber: 3.5 Consensus size: 17
5299063 AAAAGGAAAT
5299073 AAAAACAAAGCAAA-AG
1 AAAAACAAAGCAAACAG
* * *
5299089 AAAAAAAAAACAGAATAG
1 AAAAACAAAGCA-AACAG
5299107 AAAGAACAAAG-AAACAG
1 AAA-AACAAAGCAAACAG
*
5299124 AGAAACAAA
1 AAAAACAAA
5299133 CGGAACAGGG
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
16 16 0.46
17 8 0.23
18 6 0.17
19 5 0.14
ACGTcount: A:0.75, C:0.10, G:0.13, T:0.02
Consensus pattern (17 bp):
AAAAACAAAGCAAACAG
Found at i:5299162 original size:13 final size:14
Alignment explanation
Indices: 5299144--5299174 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
5299134 GGAACAGGGG
5299144 AAAGAAAGAAA-AA
1 AAAGAAAGAAAGAA
5299157 AAAGAAAGAAAGAA
1 AAAGAAAGAAAGAA
5299171 AAAG
1 AAAG
5299175 GGGAAAATAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAGAAAGAAAGAA
Found at i:5299180 original size:17 final size:17
Alignment explanation
Indices: 5299139--5299180 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
5299129 CAAACGGAAC
5299139 AGGGGAAAGAAAGAAAA
1 AGGGGAAAGAAAGAAAA
***
5299156 AAAAGAAAGAAAGAAAA
1 AGGGGAAAGAAAGAAAA
5299173 AGGGGAAA
1 AGGGGAAA
5299181 ATAGATTTTT
Statistics
Matches: 19, Mismatches: 6, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (17 bp):
AGGGGAAAGAAAGAAAA
Found at i:5299822 original size:3 final size:3
Alignment explanation
Indices: 5299808--5299893 Score: 154
Period size: 3 Copynumber: 28.7 Consensus size: 3
5299798 GTGAGGTAAA
*
5299808 TAT TAG TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
5299856 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT CAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
5299894 AGATGAGTGG
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 79 1.00
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:5304906 original size:31 final size:31
Alignment explanation
Indices: 5304832--5304913 Score: 87
Period size: 31 Copynumber: 2.7 Consensus size: 31
5304822 AGAAAGAAAA
** *
5304832 AAAAACCTT--AATAACCCAATCACTTAAAT
1 AAAAACCTTCAAATAATTCAATAACTTAAAT
5304861 AAAAACCTTCAAATAATTCAATAACTTAAAT
1 AAAAACCTTCAAATAATTCAATAACTTAAAT
* ** *
5304892 GAAAATTTTTAAATAATTCAAT
1 AAAAACCTTCAAATAATTCAAT
5304914 GATAATTTTG
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 9 0.20
31 35 0.80
ACGTcount: A:0.52, C:0.16, G:0.01, T:0.30
Consensus pattern (31 bp):
AAAAACCTTCAAATAATTCAATAACTTAAAT
Found at i:5304920 original size:22 final size:23
Alignment explanation
Indices: 5304880--5304922 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
5304870 CAAATAATTC
5304880 AATAACTTAAATGAAAATTTTTA
1 AATAACTTAAATGAAAATTTTTA
* *
5304903 AATAA-TTCAATGATAATTTT
1 AATAACTTAAATGAAAATTTT
5304923 GTAACTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.42
Consensus pattern (23 bp):
AATAACTTAAATGAAAATTTTTA
Found at i:5316294 original size:132 final size:132
Alignment explanation
Indices: 5316057--5316314 Score: 349
Period size: 132 Copynumber: 2.0 Consensus size: 132
5316047 CTTTCCCACC
* * * *
5316057 GATTCGGATTTCACCTTGCTCGAATCATAATAGTGTACACCAGGCACAGTTTTTTCAGATTGCAA
1 GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
* * * *
5316122 TGAACGAAAGGAGTTAGAACTCTTATGATCATCAATGGGATG-TTTGAAGGAAGATTTGCTTCTC
66 CGAACGAAAGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTG-AGGAAGACTTGCTTCTC
5316186 ACT
130 ACT
* * *
5316189 GATTCAGATTTTACCTTACTCGAATCATAATAGTGTGCACCAGGCACAGGTTTTTCATATTCCAA
1 GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
* * * *
5316254 CGAA-GCAATGGAATCAGAAGTTTTATGATCATCGATGGGATGCTTTGAGGAAGACTTGCTT
66 CGAACG-AAAGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGCTT
5316315 GCAGTTGTCA
Statistics
Matches: 109, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
131 1 0.01
132 104 0.95
133 4 0.04
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.32
Consensus pattern (132 bp):
GATTCAGATTTCACCTTACTCGAATCATAATAGTGTACACCAGGCACAGGTTTTTCAGATTCCAA
CGAACGAAAGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGCTTCTCA
CT
Found at i:5316463 original size:150 final size:150
Alignment explanation
Indices: 5316189--5316524 Score: 399
Period size: 150 Copynumber: 2.2 Consensus size: 150
5316179 GCTTCTCACT
* * *
5316189 GATTCAGATTTTACCTTACTCGAATCATAATAGTGTGCACCAGGCACAGGTTTTTCATATTCCAA
1 GATTCAGATTTTACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTTTTCATATTCCAA
* * *
5316254 CGAAGCAATGGAATCAGAAGTTTTATGATCATCGATGGGATGCTTTGAGGAAGACTTGCTTG-CA
66 CGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGCTTGCCA
* * *
5316318 GTTGTCAGAATCTTTCCCACC
131 -CTGCCAAAATCTTTCCCACC
* * *
5316339 GATTCGGATTTTACCTTACTAGAATCATAATAGTGTACACCAGATACA-GTTTGTTCGTATTCCA
1 GATTCAGATTTTACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTT-TTCATATTCCA
* * ** * *
5316403 ATGAAGCAGTGGAATTGGAACTCTTATGGTCATCAATGGGATG-TTTGAAGGAAGATTTGCTTGC
65 ACGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTG-AGGAAGACTTGCTTGC
**
5316467 CACTGCCAAAATCTTTCCCGTC
129 CACTGCCAAAATCTTTCCCACC
* * * * *
5316489 AATTCAGATTTCATCTTGCTTGAATCATAATAGTGT
1 GATTCAGATTTTACCTTACTAGAATCATAATAGTGT
5316525 TTTGCCATAT
Statistics
Matches: 157, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
149 8 0.05
150 147 0.94
151 2 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (150 bp):
GATTCAGATTTTACCTTACTAGAATCATAATAGTGTACACCAGACACAGGTTTTTCATATTCCAA
CGAAGCAATGGAATCAGAACTCTTATGATCATCAATGGGATGCTTTGAGGAAGACTTGCTTGCCA
CTGCCAAAATCTTTCCCACC
Found at i:5317124 original size:2 final size:2
Alignment explanation
Indices: 5317117--5317149 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5317107 AACAATCTTA
5317117 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5317150 ATCCTTGGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5321096 original size:23 final size:24
Alignment explanation
Indices: 5321046--5321097 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
5321036 CTAAATATAC
*
5321046 ATATTTGATTAAAAAGTTAAAAAGT
1 ATATTTGATTAAAAAG-TAAAAAAT
5321071 ATATTTGATTAAAAA-TAAAAAAT
1 ATATTTGATTAAAAAGTAAAAAAT
5321094 ATAT
1 ATAT
5321098 ATTTAATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 11 0.42
25 15 0.58
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.37
Consensus pattern (24 bp):
ATATTTGATTAAAAAGTAAAAAAT
Found at i:5326396 original size:18 final size:18
Alignment explanation
Indices: 5326373--5326433 Score: 54
Period size: 18 Copynumber: 3.4 Consensus size: 18
5326363 TTAAAATAAT
5326373 TAAAAATTAAAATATTTA
1 TAAAAATTAAAATATTTA
*
5326391 TAAAAATTCCAAAT-TTTA
1 TAAAAATT-AAAATATTTA
***
5326409 TATATTTTTAAAATA-TTA
1 TA-AAAATTAAAATATTTA
5326427 TAAAAAT
1 TAAAAAT
5326434 CTTAAAAAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 7
0.68 0.17 0.15
Matches are distributed among these distances:
17 2 0.06
18 23 0.72
19 7 0.22
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (18 bp):
TAAAAATTAAAATATTTA
Found at i:5328537 original size:98 final size:98
Alignment explanation
Indices: 5328359--5328556 Score: 387
Period size: 98 Copynumber: 2.0 Consensus size: 98
5328349 AAGATAGCAA
5328359 CCTGTGCAGATGATTTCACGGTCAGTGTTGAGCTTGTTATATTTGCGTCTAAAATCTGTGTGAAA
1 CCTGTGCAGATGATTTCACGGTCAGTGTTGAGCTTGTTATATTTGCGTCTAAAATCTGTGTGAAA
5328424 TTTCAAAAAGAAAAAAAACTTGCATGTTTTAAG
66 TTTCAAAAAGAAAAAAAACTTGCATGTTTTAAG
5328457 CCTGTGCAGATGATTTCACGGTCAGTGTTGAGCTTGTTATATTTGCGTCTAAAATCTGTGTGAAA
1 CCTGTGCAGATGATTTCACGGTCAGTGTTGAGCTTGTTATATTTGCGTCTAAAATCTGTGTG-AA
5328522 ATTTCAAAAAGAAAAAAAACTTGCATGTTTTAAG
65 ATTTCAAAAAGAAAAAAAACTTGCATGTTTTAAG
5328556 C
1 C
5328557 ATGTTTGTAT
Statistics
Matches: 99, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
98 62 0.63
99 37 0.37
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.34
Consensus pattern (98 bp):
CCTGTGCAGATGATTTCACGGTCAGTGTTGAGCTTGTTATATTTGCGTCTAAAATCTGTGTGAAA
TTTCAAAAAGAAAAAAAACTTGCATGTTTTAAG
Found at i:5336915 original size:33 final size:33
Alignment explanation
Indices: 5336878--5336942 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
5336868 ATTTAAAATA
*
5336878 TATATT-ATATATTATGTTTACTTA-AATAATAAG
1 TATATTGATATATTAT-ATTA-TTATAATAATAAG
*
5336911 TATATTGTTATATTATATTATTATAATAATAA
1 TATATTGATATATTATATTATTATAATAATAA
5336943 AACAAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 3 0.11
33 17 0.61
34 8 0.29
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (33 bp):
TATATTGATATATTATATTATTATAATAATAAG
Found at i:5345226 original size:2 final size:2
Alignment explanation
Indices: 5345221--5345255 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5345211 GACACATTCA
5345221 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5345256 NNNNNNNNNN
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5347513 original size:14 final size:14
Alignment explanation
Indices: 5347490--5347530 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 14
5347480 GGTTATAATG
*
5347490 TTTAGATATTTTAT
1 TTTAAATATTTTAT
*
5347504 TTTAATTATTTTA-
1 TTTAAATATTTTAT
5347517 TTTAAATATTTTAT
1 TTTAAATATTTTAT
5347531 ATAAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTAAATATTTTAT
Found at i:5347526 original size:13 final size:13
Alignment explanation
Indices: 5347490--5347535 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
5347480 GGTTATAATG
*
5347490 TTTAGATATTTTA
1 TTTAAATATTTTA
*
5347503 TTTTAATTATTTTA
1 -TTTAAATATTTTA
5347517 TTTAAATATTTTA
1 TTTAAATATTTTA
*
5347530 TATAAA
1 TTTAAA
5347536 AATAATAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (13 bp):
TTTAAATATTTTA
Found at i:5353388 original size:5 final size:6
Alignment explanation
Indices: 5353371--5353395 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
5353361 AATTATTAAA
5353371 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
5353396 TTATATTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:5357240 original size:35 final size:35
Alignment explanation
Indices: 5357201--5357270 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
5357191 AGTAAATCAA
*
5357201 GTTGGTCTTCTTCAAGAGCTAACTCATACAAGTCT
1 GTTGGTCTTCTTCAAGAACTAACTCATACAAGTCT
5357236 GTTGGTCTTCTTCAAGAACTAACTCATACAAGTCT
1 GTTGGTCTTCTTCAAGAACTAACTCATACAAGTCT
5357271 ATTGAGATGG
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:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (35 bp):
GTTGGTCTTCTTCAAGAACTAACTCATACAAGTCT
Found at i:5357815 original size:136 final size:136
Alignment explanation
Indices: 5357571--5357845 Score: 523
Period size: 136 Copynumber: 2.0 Consensus size: 136
5357561 ACGCTTTCAC
5357571 TCTAGATGTTGGAGATGGACTATGCTCTGAAACTTCAGCTAAATACTTATGCTCCACAAAACTCT
1 TCTAGATGTTGGAGATGGACTATGCTCTGAAACTTCAGCTAAATACTTATGCTCCACAAAACTCT
5357636 TTACATCAGAATTCTTAGATTCCCCATCATCTGACGCAACTTCTTGGGAGATGCTGCATGCTAAT
66 TTACATCAGAATTCTTAGATTCCCCATCATCTGACGCAACTTCTTGGGAGATGCTGCATGCTAAT
5357701 TTTTCT
131 TTTTCT
**
5357707 TCTAGATGTTGGAGATGGACTATGCTCTGAAACTTCAGCTAAATACTTATGCTTTACAAAACTCT
1 TCTAGATGTTGGAGATGGACTATGCTCTGAAACTTCAGCTAAATACTTATGCTCCACAAAACTCT
*
5357772 TTACATCAGAATTCTTAGGTTCCCCATCATCTGACGCAACTTCTTGGGAGATGCTGCATGCTAAT
66 TTACATCAGAATTCTTAGATTCCCCATCATCTGACGCAACTTCTTGGGAGATGCTGCATGCTAAT
5357837 TTTTCT
131 TTTTCT
5357843 TCT
1 TCT
5357846 GTCTGGATAT
Statistics
Matches: 136, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 136 1.00
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (136 bp):
TCTAGATGTTGGAGATGGACTATGCTCTGAAACTTCAGCTAAATACTTATGCTCCACAAAACTCT
TTACATCAGAATTCTTAGATTCCCCATCATCTGACGCAACTTCTTGGGAGATGCTGCATGCTAAT
TTTTCT
Found at i:5363639 original size:25 final size:25
Alignment explanation
Indices: 5363611--5363660 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
5363601 CAGGTAAGGC
5363611 TCCTTCTCCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
* *
5363636 TCCTTTTTCTTCTTCCGTTCTTCAT
1 TCCTTCTCCTTCTTCCGTTCTTCAT
5363661 CTTCTCTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.04, C:0.36, G:0.04, T:0.56
Consensus pattern (25 bp):
TCCTTCTCCTTCTTCCGTTCTTCAT
Found at i:5365930 original size:12 final size:12
Alignment explanation
Indices: 5365900--5365932 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
5365890 TTGTAACAGG
5365900 AAACCAGCA-GC
1 AAACCAGCATGC
5365911 AAACCAGCATGC
1 AAACCAGCATGC
*
5365923 AGACCAGCAT
1 AAACCAGCAT
5365933 CCTAGCTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.42, C:0.33, G:0.18, T:0.06
Consensus pattern (12 bp):
AAACCAGCATGC
Found at i:5366605 original size:21 final size:21
Alignment explanation
Indices: 5366579--5366631 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5366569 TGCTGTTTCT
* *
5366579 AATCTCACTGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
* *
5366600 AATCTCACCGTTACAGTAACT
1 AATCTCACCGCTACAGTAACC
5366621 AATCTCACCGC
1 AATCTCACCGC
5366632 CACCGCTGTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.09, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:5371658 original size:96 final size:96
Alignment explanation
Indices: 5371494--5371687 Score: 280
Period size: 96 Copynumber: 2.0 Consensus size: 96
5371484 GGGATGTTGC
* * * * * *
5371494 TGCTGTGTAGGAGGCATTGGGAAGTGTTGACTTGGAGCCTCCTGAGTTTGGCCAGGCGGTGGATA
1 TGCTGAGTAGGAGGCATCGAGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGCGGAGGATA
5371559 GTAAGCATCTCGCTGAGGGACAGAAGGAACT
66 GTAAGCATCTCGCTGAGGGACAGAAGGAACT
* * * * *
5371590 TGCTGAGTAGGAGGCATCGAGAATTGCTGACTTGGAATCTCCTGAGTTTGGGCAGGGGGAGTATA
1 TGCTGAGTAGGAGGCATCGAGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGCGGAGGATA
*
5371655 GTAAGCATCTCGTTGAGGGACAGAAGGAACT
66 GTAAGCATCTCGCTGAGGGACAGAAGGAACT
5371686 TG
1 TG
5371688 GCTCTGACGG
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
96 86 1.00
ACGTcount: A:0.24, C:0.15, G:0.37, T:0.24
Consensus pattern (96 bp):
TGCTGAGTAGGAGGCATCGAGAAGTGCTGACTTGGAACCTCCTGAGTTTGGCCAGGCGGAGGATA
GTAAGCATCTCGCTGAGGGACAGAAGGAACT
Found at i:5375691 original size:17 final size:16
Alignment explanation
Indices: 5375669--5375705 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
5375659 ATAAGAATTT
5375669 TATTTTTTACTTTTTGC
1 TATTTTTTACTTTTT-C
*
5375686 TATTTTTTAGTTTTTC
1 TATTTTTTACTTTTTC
5375702 TATT
1 TATT
5375706 CTATCACTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.73
Consensus pattern (16 bp):
TATTTTTTACTTTTTC
Found at i:5376220 original size:32 final size:33
Alignment explanation
Indices: 5376158--5376227 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 33
5376148 CATCGATAAT
*
5376158 TTTTTATTTTTTTAAATTTAACTATATTTTT-A
1 TTTTTATTTTTTTAAATTTAACCATATTTTTAA
**
5376190 TTTTTATTTTTTTAATATTTTCCCAT-TTTTTAA
1 TTTTTATTTTTTTAA-ATTTAACCATATTTTTAA
5376223 TTTTT
1 TTTTT
5376228 TGAAATATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
32 20 0.61
33 13 0.39
ACGTcount: A:0.23, C:0.06, G:0.00, T:0.71
Consensus pattern (33 bp):
TTTTTATTTTTTTAAATTTAACCATATTTTTAA
Found at i:5378213 original size:26 final size:25
Alignment explanation
Indices: 5378162--5378215 Score: 63
Period size: 25 Copynumber: 2.1 Consensus size: 25
5378152 CAAAAATTTT
** **
5378162 AATTTTTTAACCATTAATTGAATTA
1 AATTTTTTAAAAATTAACCGAATTA
5378187 AATTTTTTAAAAATTAACCGAACTTA
1 AATTTTTTAAAAATTAACCGAA-TTA
5378213 AAT
1 AAT
5378216 ATTTCGATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.44, C:0.09, G:0.04, T:0.43
Consensus pattern (25 bp):
AATTTTTTAAAAATTAACCGAATTA
Found at i:5381206 original size:58 final size:58
Alignment explanation
Indices: 5381141--5381258 Score: 236
Period size: 58 Copynumber: 2.0 Consensus size: 58
5381131 GATCATAATA
5381141 AATTACATAAATAAATAAGCAAATGTCTGTCTCTTTCGGCGTACCTATTTTAGTTTTG
1 AATTACATAAATAAATAAGCAAATGTCTGTCTCTTTCGGCGTACCTATTTTAGTTTTG
5381199 AATTACATAAATAAATAAGCAAATGTCTGTCTCTTTCGGCGTACCTATTTTAGTTTTG
1 AATTACATAAATAAATAAGCAAATGTCTGTCTCTTTCGGCGTACCTATTTTAGTTTTG
5381257 AA
1 AA
5381259 ACAAGGGTAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 60 1.00
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (58 bp):
AATTACATAAATAAATAAGCAAATGTCTGTCTCTTTCGGCGTACCTATTTTAGTTTTG
Found at i:5381862 original size:17 final size:17
Alignment explanation
Indices: 5381836--5381869 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5381826 ATATTTAATT
*
5381836 TTTAAGATTAAATTTTA
1 TTTAAAATTAAATTTTA
5381853 TTTAAAATTAAATTTTA
1 TTTAAAATTAAATTTTA
5381870 AAAAAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAAATTAAATTTTA
Found at i:5383519 original size:17 final size:19
Alignment explanation
Indices: 5383497--5383541 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
5383487 TAAATTTCAA
*
5383497 AAATATAA-ATAAC-ATTT
1 AAATATAATATAACAAGTT
*
5383514 AAATATAATATACCAAGTT
1 AAATATAATATAACAAGTT
5383533 AAATATAAT
1 AAATATAAT
5383542 CAAATTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 8 0.33
18 4 0.17
19 12 0.50
ACGTcount: A:0.58, C:0.07, G:0.02, T:0.33
Consensus pattern (19 bp):
AAATATAATATAACAAGTT
Found at i:5384811 original size:11 final size:11
Alignment explanation
Indices: 5384791--5384840 Score: 57
Period size: 11 Copynumber: 4.5 Consensus size: 11
5384781 TTTAAATTTT
* *
5384791 TTATTCCGTTA
1 TTATTTCGTTG
5384802 TTATTTCGTTG
1 TTATTTCGTTG
5384813 TTGATTT-GTTG
1 TT-ATTTCGTTG
5384824 TTATTTCGTTG
1 TTATTTCGTTG
*
5384835 CTATTT
1 TTATTT
5384841 TGCTGTCATT
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 4 0.12
11 26 0.76
12 4 0.12
ACGTcount: A:0.12, C:0.10, G:0.16, T:0.62
Consensus pattern (11 bp):
TTATTTCGTTG
Found at i:5384842 original size:22 final size:22
Alignment explanation
Indices: 5384802--5384852 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5384792 TATTCCGTTA
* *
5384802 TTATTTCGTTGTTGATTTGTTG
1 TTATTTCGTTGCTGATTTGCTG
5384824 TTATTTCGTTGCT-ATTTTGCTG
1 TTATTTCGTTGCTGA-TTTGCTG
*
5384846 TCATTTC
1 TTATTTC
5384853 ATTATTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 1 0.04
22 24 0.96
ACGTcount: A:0.10, C:0.12, G:0.18, T:0.61
Consensus pattern (22 bp):
TTATTTCGTTGCTGATTTGCTG
Found at i:5386133 original size:27 final size:28
Alignment explanation
Indices: 5386031--5386128 Score: 164
Period size: 28 Copynumber: 3.5 Consensus size: 28
5386021 AAAAATAAAA
5386031 ATTTACCAAAATATTACAACTTTTTTTTT
1 ATTTACCAAAATATTACAAC-TTTTTTTT
5386060 ATTTACCAAAATATTACAACTTTTTTTT
1 ATTTACCAAAATATTACAACTTTTTTTT
5386088 ATTTACCAAAATATATA-AAC-TTTTTTT
1 ATTTACCAAAATAT-TACAACTTTTTTTT
5386115 ATTTACCAAAATAT
1 ATTTACCAAAATAT
5386129 ATAAAAAACA
Statistics
Matches: 68, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
27 21 0.31
28 25 0.37
29 22 0.32
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (28 bp):
ATTTACCAAAATATTACAACTTTTTTTT
Found at i:5386727 original size:19 final size:18
Alignment explanation
Indices: 5386703--5386763 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
5386693 TCTAATTAAG
5386703 TAATAATTCTATTTTAATT
1 TAATAA-TCTATTTTAATT
* * *
5386722 TAATAAACTATTCTCATT
1 TAATAATCTATTTTAATT
* *
5386740 TAATAACTATATTTTAAAT
1 TAATAA-TCTATTTTAATT
5386759 TAATA
1 TAATA
5386764 GAAATATCAG
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
18 15 0.45
19 18 0.55
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (18 bp):
TAATAATCTATTTTAATT
Found at i:5386732 original size:18 final size:18
Alignment explanation
Indices: 5386711--5386763 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
5386701 AGTAATAATT
5386711 CTATTTTAATTTAATAAA
1 CTATTTTAATTTAATAAA
* *
5386729 CTATTCTCATTTAAT-AA
1 CTATTTTAATTTAATAAA
*
5386746 CTATATTTTAAATTAATA
1 C--TATTTTAATTTAATA
5386764 GAAATATCAG
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
17 3 0.11
18 13 0.48
19 11 0.41
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (18 bp):
CTATTTTAATTTAATAAA
Found at i:5387292 original size:27 final size:26
Alignment explanation
Indices: 5387254--5387310 Score: 87
Period size: 27 Copynumber: 2.2 Consensus size: 26
5387244 TTTTAGTCCT
*
5387254 TTGGCACATTGGTGCCGTCAATGGCA
1 TTGGCACATTGGTGCCGCCAATGGCA
*
5387280 TTGGCACCTTTGGTGCCGCCAATGGCA
1 TTGGCA-CATTGGTGCCGCCAATGGCA
5387307 TTGG
1 TTGG
5387311 GGTGATCAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
26 6 0.21
27 22 0.79
ACGTcount: A:0.16, C:0.25, G:0.32, T:0.28
Consensus pattern (26 bp):
TTGGCACATTGGTGCCGCCAATGGCA
Found at i:5387390 original size:29 final size:30
Alignment explanation
Indices: 5387349--5387422 Score: 134
Period size: 29 Copynumber: 2.5 Consensus size: 30
5387339 GTTTTTTTTA
5387349 ATATATTTTGGTAAATAAAAAAAAAGTT-T
1 ATATATTTTGGTAAATAAAAAAAAAGTTGT
5387378 ATATATTTTGGTAAATAAAAAAAAAGTTGT
1 ATATATTTTGGTAAATAAAAAAAAAGTTGT
5387408 A-ATATTTTGGTAAAT
1 ATATATTTTGGTAAAT
5387423 TTTTATTTTT
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 42 0.95
30 2 0.05
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (30 bp):
ATATATTTTGGTAAATAAAAAAAAAGTTGT
Found at i:5387697 original size:31 final size:29
Alignment explanation
Indices: 5387655--5387718 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 29
5387645 TTACAATTTG
* *
5387655 GTCACTAAACTATTTAAATGTTTTCATTTAA
1 GTCACTAAACTATTCAAA--ATTTCATTTAA
*
5387686 GTCACTGAACTATTCAAAATTTCATTTAA
1 GTCACTAAACTATTCAAAATTTCATTTAA
5387715 GTCA
1 GTCA
5387719 TTGGGCTATG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 14 0.47
31 16 0.53
ACGTcount: A:0.36, C:0.16, G:0.08, T:0.41
Consensus pattern (29 bp):
GTCACTAAACTATTCAAAATTTCATTTAA
Found at i:5398727 original size:29 final size:28
Alignment explanation
Indices: 5398695--5398771 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
5398685 TTTTTTTTAG
*
5398695 GTTACATTTTAGTCATTTATGTTTGAAAT
1 GTTACATTTTAGTCATTTACG-TTGAAAT
* * *
5398724 GTTACGTTTTAGTCACTTACGTTGACAT
1 GTTACATTTTAGTCATTTACGTTGAAAT
5398752 GTTGTAACATTTTAGTCATT
1 G-T-T-ACATTTTAGTCATT
5398772 AAGTTGTTAA
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
28 7 0.18
29 19 0.49
30 1 0.03
31 12 0.31
ACGTcount: A:0.25, C:0.12, G:0.16, T:0.48
Consensus pattern (28 bp):
GTTACATTTTAGTCATTTACGTTGAAAT
Found at i:5400428 original size:3 final size:3
Alignment explanation
Indices: 5400420--5400456 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
5400410 TAGATTTGAG
5400420 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5400457 GTACAGATAG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5409801 original size:14 final size:14
Alignment explanation
Indices: 5409782--5409811 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5409772 ATCATTGTCC
5409782 CACACATACTTAGG
1 CACACATACTTAGG
5409796 CACACATACTTAGG
1 CACACATACTTAGG
5409810 CA
1 CA
5409812 TTGGTGTAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.20
Consensus pattern (14 bp):
CACACATACTTAGG
Found at i:5413382 original size:2 final size:2
Alignment explanation
Indices: 5413375--5413407 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5413365 TAATTTTTAT
5413375 TA TA TA 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 TA TA TA T
5413408 TGGGTTTGAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5415802 original size:21 final size:19
Alignment explanation
Indices: 5415773--5415817 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
5415763 TATAAAAAAC
*
5415773 TCTAAGATTTTATCAAAATT
1 TCTAAGA-TTTACCAAAATT
5415793 TCTAATGATTTACCAAAATT
1 TCTAA-GATTTACCAAAATT
5415813 TCTAA
1 TCTAA
5415818 AAGTATACCT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.40, C:0.13, G:0.04, T:0.42
Consensus pattern (19 bp):
TCTAAGATTTACCAAAATT
Found at i:5415912 original size:20 final size:20
Alignment explanation
Indices: 5415895--5415959 Score: 80
Period size: 20 Copynumber: 3.2 Consensus size: 20
5415885 CTAGAATTCT
*
5415895 TAAGATTATACCAAAATTTA
1 TAAGATTATACAAAAATTTA
*
5415915 TAAGGTTATACAAAAATTTA
1 TAAGATTATACAAAAATTTA
5415935 TAATGATTA-AGC-AAAATTTA
1 TAA-GATTATA-CAAAAATTTA
5415955 TAAGA
1 TAAGA
5415960 ATTTATTAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
19 2 0.05
20 33 0.82
21 5 0.12
ACGTcount: A:0.51, C:0.06, G:0.09, T:0.34
Consensus pattern (20 bp):
TAAGATTATACAAAAATTTA
Found at i:5416326 original size:17 final size:17
Alignment explanation
Indices: 5416296--5416329 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5416286 ATATTGGTTG
**
5416296 ATATATTTTTTATAAAT
1 ATATATTTAATATAAAT
5416313 ATATATTTAATATAAAT
1 ATATATTTAATATAAAT
5416330 TATTTTTGTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATATATTTAATATAAAT
Found at i:5416637 original size:5 final size:5
Alignment explanation
Indices: 5416619--5416651 Score: 57
Period size: 5 Copynumber: 6.4 Consensus size: 5
5416609 TCGATATTTT
5416619 TAATA TATATA TAATA TAATA TAATA TAATA TA
1 TAATA TA-ATA TAATA TAATA TAATA TAATA TA
5416652 TATTTAAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 22 0.81
6 5 0.19
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TAATA
Found at i:5442362 original size:126 final size:126
Alignment explanation
Indices: 5442205--5442501 Score: 488
Period size: 126 Copynumber: 2.4 Consensus size: 126
5442195 AGTGTTAATT
* **
5442205 TAAAA-AAGCTCCCACATGGACGCTTTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAG
1 TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAG
* *
5442269 ACGTTTCTGAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGTAAAAGTAC
66 ACGTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTAC
* * * *
5442330 TAAAAGAAGCTCCCACGTGGTCGCGCTTTTGCTACAATAGCTCCTGAAAAAATAATTTTGAGTAG
1 TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAG
5442395 ACGTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTAC
66 ACGTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTAC
* *
5442456 TGAAAGAAGCTCCCACGTGGACGCGCTTTTGTTACAGTAGCTCCTG
1 TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTG
5442502 TTTGGCTTGA
Statistics
Matches: 158, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
125 5 0.03
126 153 0.97
ACGTcount: A:0.33, C:0.20, G:0.21, T:0.27
Consensus pattern (126 bp):
TAAAAGAAGCTCCCACGTGGACGCGCTTTTGCTACAGTAGCTCCTGAAAAAATAATTTCGAGAAG
ACGTTTCTAAGCAAATAGTGTCAAAAACGCTTTAAGCAGGATGCTTTGTCAGCAAAAGTAC
Found at i:5443961 original size:22 final size:24
Alignment explanation
Indices: 5443931--5443975 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
5443921 AAAAAATAAA
5443931 AAAATAAAA-TTAAAGCTTTTTTT
1 AAAATAAAATTTAAAGCTTTTTTT
5443954 AAAA-AAAATTTAAAGCTTTTTT
1 AAAATAAAATTTAAAGCTTTTTT
5443976 AAGAGGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (24 bp):
AAAATAAAATTTAAAGCTTTTTTT
Found at i:5443991 original size:11 final size:11
Alignment explanation
Indices: 5443977--5444057 Score: 94
Period size: 11 Copynumber: 7.4 Consensus size: 11
5443967 AGCTTTTTTA
5443977 AGAGGAATTTG
1 AGAGGAATTTG
*
5443988 AGAGGAAATTG
1 AGAGGAATTTG
* *
5443999 AAAGGATTTTG
1 AGAGGAATTTG
5444010 AGAGGAATTTG
1 AGAGGAATTTG
5444021 AGAGGAATTTG
1 AGAGGAATTTG
5444032 AGA-GAATATTG
1 AGAGGAAT-TTG
*
5444043 -GAGAGAAATTG
1 AGAG-GAATTTG
5444054 AGAG
1 AGAG
5444058 AAAGGATTTA
Statistics
Matches: 59, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
10 6 0.10
11 47 0.80
12 6 0.10
ACGTcount: A:0.41, C:0.00, G:0.35, T:0.25
Consensus pattern (11 bp):
AGAGGAATTTG
Found at i:5446029 original size:20 final size:19
Alignment explanation
Indices: 5445975--5446030 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 19
5445965 AAATTTATAT
5445975 ATAATTAAT-TATTATTTA
1 ATAATTAATATATTATTTA
5445993 ACTAAATCTAA-AT-TTATTTA
1 A-T-AAT-TAATATATTATTTA
5446013 ATAATATAATATATTATT
1 ATAAT-TAATATATTATT
5446031 ATTTACGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
18 7 0.23
19 4 0.13
20 16 0.52
21 4 0.13
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (19 bp):
ATAATTAATATATTATTTA
Found at i:5450041 original size:41 final size:42
Alignment explanation
Indices: 5449996--5450152 Score: 223
Period size: 41 Copynumber: 3.8 Consensus size: 42
5449986 TTGTATATAA
** * *
5449996 CACCGGCATAAAGCCTGCTAGGCACCAAGCTC-GATACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCTCTGATATAATT
* *
5450037 CACCGGCACAAAGCCTGCTAGACATAAAG-TCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCTCTGATATAATT
*
5450078 CACCGGCATAAAGCCTGCTAGGCATAAAGC-CTGACATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCTCTGATATAATT
5450119 CACCGGCATAAAGCCTGCTAGGCATAAAGC-CTGA
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCTCTGA
5450153 ACTTACAAAA
Statistics
Matches: 105, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.02
41 103 0.98
ACGTcount: A:0.33, C:0.28, G:0.20, T:0.19
Consensus pattern (42 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAGCTCTGATATAATT
Found at i:5450103 original size:16 final size:16
Alignment explanation
Indices: 5450082--5450151 Score: 59
Period size: 16 Copynumber: 3.8 Consensus size: 16
5450072 ATAATTCACC
5450082 GGCATAAAGCCTGCTA
1 GGCATAAAGCCTGCTA
5450098 GGCATAAAGCCTGACATAATTCA
1 GGCATAAAGCCTG-C-----T-A
5450121 CCGGCATAAAGCCTGCTA
1 --GGCATAAAGCCTGCTA
5450139 GGCATAAAGCCTG
1 GGCATAAAGCCTG
5450152 AACTTACAAA
Statistics
Matches: 45, Mismatches: 0, Indels: 18
0.71 0.00 0.29
Matches are distributed among these distances:
16 26 0.58
17 1 0.02
18 1 0.02
19 1 0.02
22 1 0.02
23 1 0.02
24 1 0.02
25 13 0.29
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (16 bp):
GGCATAAAGCCTGCTA
Done.