Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 40 of 50
Found at i:17225687 original size:244 final size:242
Alignment explanation
Indices: 17225234--17225690 Score: 564
Period size: 244 Copynumber: 1.9 Consensus size: 242
17225224 CTTTTCTCAT
* * *
17225234 AAATTCATCATTCTGGACTTGGACTTGTTGGCATAAAGTTTATTTATTCAATTCTAGGCATCAAT
1 AAATTCATCATTCTGGACTTGAACTTGTAGGCATAAAGTTTATTCATTCAATTCTAGGCATCAAT
* * * *
17225299 AGAGATTTCAGCAGAGACAAAGAAAGGAACAAAACTTTTTGTGGCAGAGAACATAATTCCATGAA
66 AGAGATTTCAACAAAGACAAAGAAAGGAACAAAACTATTTGTGGCAAAGAACATAATTCCATGAA
* * * *
17225364 GTAACAATTGATCTTGGCAAGTCCAATGATCATAGGCTGGAATGGAAACCATCATAGAAGGATTG
131 GGAACAATTGATCTTGGCAAGTCCAATAATCATAGGCTGGAATGAAAACCATCATAGAAGAATTG
17225429 GAACCTTCTTGTGGAATCATAGTAGGGGAACGGGGAGATGATCCATC
196 GAACCTTCTTGTGGAATCATAGTAGGGGAACGGGGAGATGATCCATC
* **
17225476 AAATTCATTA-TCTTGGACTTGAACTTGTAGGCATAAAGTTTATACTCATTTTATGTCTAGGCAT
1 AAATTCATCATTC-TGGACTTGAACTTGTAGGCATAAAGTTTAT--TCATTCAAT-TCTAGGCAT
* * * *
17225540 C-ATAGGAGGTTTCAACAAAGATAAAGAAAGGAA-AAAACTATTTGTGGTAAAGAATATAATTCC
62 CAATA-GAGATTTCAACAAAGACAAAGAAAGGAACAAAACTATTTGTGGCAAAGAACATAATTCC
* ** * * * *
17225603 ATGAAGGAGCAATTGATC-TGAGTGAGTCCAGTAATCATAGGCTGG-ATCGAAAATCATTATAGG
126 ATGAAGGAACAATTGATCTTG-GCAAGTCCAATAATCATAGGCTGGAAT-GAAAACCATCATAGA
* * *
17225666 AGAATTGGAGCTTTTTTGTGGAATC
189 AGAATTGGAACCTTCTTGTGGAATC
17225691 TTGGTAAAAC
Statistics
Matches: 180, Mismatches: 28, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
241 2 0.01
242 37 0.21
243 4 0.02
244 103 0.57
245 34 0.19
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.29
Consensus pattern (242 bp):
AAATTCATCATTCTGGACTTGAACTTGTAGGCATAAAGTTTATTCATTCAATTCTAGGCATCAAT
AGAGATTTCAACAAAGACAAAGAAAGGAACAAAACTATTTGTGGCAAAGAACATAATTCCATGAA
GGAACAATTGATCTTGGCAAGTCCAATAATCATAGGCTGGAATGAAAACCATCATAGAAGAATTG
GAACCTTCTTGTGGAATCATAGTAGGGGAACGGGGAGATGATCCATC
Found at i:17242194 original size:23 final size:26
Alignment explanation
Indices: 17242149--17242225 Score: 74
Period size: 26 Copynumber: 3.1 Consensus size: 26
17242139 TAAAAATATC
* *
17242149 TTTTATTATATTTAATTATTTAATTA
1 TTTTATTATATTTAAATATTTAATAA
17242175 TTTTATT-T-TTTAAATA-TTAATAA
1 TTTTATTATATTTAAATATTTAATAA
*
17242198 TTTGTAATTA-ATTAAAATA-TTAATAA
1 TTT-T-ATTATATTTAAATATTTAATAA
17242224 TT
1 TT
17242226 AATAATTTAA
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
23 9 0.20
24 8 0.18
25 4 0.09
26 23 0.52
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (26 bp):
TTTTATTATATTTAAATATTTAATAA
Found at i:17242261 original size:52 final size:51
Alignment explanation
Indices: 17242205--17242329 Score: 121
Period size: 52 Copynumber: 2.4 Consensus size: 51
17242195 TAATTTGTAA
*
17242205 TTAATTAAAATATTAATAATTAA-TA-ATTTAAATATCAATATTTTAATATAAT
1 TTAATTAAAATATTAATAATTAATTATATTT---TATCAATAATTTAATATAAT
* * ** *
17242257 TTAATTACTAATATT-TTAATTAATTATATTTTATTTATAATTTAATATTAT
1 TTAATTA-AAATATTAATAATTAATTATATTTTATCAATAATTTAATATAAT
*
17242308 TATGATTAAAATATTAATAATT
1 T-TAATTAAAATATTAATAATT
17242330 TTTATTTTTA
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
51 23 0.39
52 24 0.41
53 8 0.14
54 4 0.07
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.51
Consensus pattern (51 bp):
TTAATTAAAATATTAATAATTAATTATATTTTATCAATAATTTAATATAAT
Found at i:17242269 original size:25 final size:25
Alignment explanation
Indices: 17242227--17242281 Score: 78
Period size: 25 Copynumber: 2.2 Consensus size: 25
17242217 TTAATAATTA
17242227 ATAATTTAAATATCAATATTTTAAT
1 ATAATTTAAATATCAATATTTTAAT
*
17242252 ATAATTTAATTA-CTAATATTTTAAT
1 ATAATTTAAATATC-AATATTTTAAT
17242277 -TAATT
1 ATAATT
17242282 ATATTTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 6 0.21
25 22 0.79
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (25 bp):
ATAATTTAAATATCAATATTTTAAT
Found at i:17242269 original size:40 final size:41
Alignment explanation
Indices: 17242225--17242302 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 41
17242215 TATTAATAAT
17242225 TAATAATTTAAAT-ATCAATATTTTA-ATATAATTTAATTAC
1 TAATAATTTAAATAAT-AATATTTTATATATAATTTAATTAC
* * * *
17242265 TAATATTTTAATTAATTATATTTTATTTATAATTTAAT
1 TAATAATTTAAATAATAATATTTTATATATAATTTAAT
17242303 ATTATTATGA
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
40 19 0.59
41 13 0.41
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (41 bp):
TAATAATTTAAATAATAATATTTTATATATAATTTAATTAC
Found at i:17242370 original size:16 final size:16
Alignment explanation
Indices: 17242345--17242430 Score: 65
Period size: 16 Copynumber: 5.4 Consensus size: 16
17242335 TTTTATATTC
*
17242345 ATTAAAAATTTAATAT
1 ATTAATAATTTAATAT
17242361 ATTAATAATTTAATA-
1 ATTAATAATTTAATAT
* *
17242376 AATAA-AACATTAATAGT
1 ATTAATAA-TTTAATA-T
17242393 -TTAA-AATATTAATAT
1 ATTAATAAT-TTAATAT
*
17242408 -TTAATATTTTAATCAT
1 ATTAATAATTTAAT-AT
17242424 ATTAATA
1 ATTAATA
17242431 TTAATAATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
14 2 0.04
15 20 0.35
16 29 0.51
17 6 0.11
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (16 bp):
ATTAATAATTTAATAT
Found at i:17242473 original size:15 final size:15
Alignment explanation
Indices: 17242182--17242473 Score: 64
Period size: 15 Copynumber: 19.5 Consensus size: 15
17242172 TTATTTTATT
17242182 TTTTAAATATTAATAA
1 TTTTAAATATTAAT-A
* *
17242198 TTTGTAATTAATTAAAA
1 TTT-TAAAT-ATTAATA
*
17242215 TATT-AATAATTAATA
1 TTTTAAAT-ATTAATA
* *
17242230 ATTTAAATATCAATA
1 TTTTAAATATTAATA
17242245 TTTT-AATA-T-A-A
1 TTTTAAATATTAATA
* *
17242256 -TTTAATTACTAATA
1 TTTTAAATATTAATA
*
17242270 TTTTAATTAATT-ATA
1 TTTTAAAT-ATTAATA
17242285 TTTT--AT-TT-ATA
1 TTTTAAATATTAATA
* *
17242296 ATTT-AATATTATTA
1 TTTTAAATATTAATA
*
17242310 TGATTAAAATATTAATAA
1 T--TTTAAATATTAAT-A
* * *
17242328 TTTT-TATTTTTATA
1 TTTTAAATATTAATA
*
17242342 TTCATTAAAAATTTAATA
1 TT--TTAAATA-TTAATA
*
17242360 TATT-AATAATTTAATA
1 TTTTAAAT-A-TTAATA
** * *
17242376 AATAAAACATTAATA
1 TTTTAAATATTAATA
*
17242391 GTTTAAAATATTAATA
1 -TTTTAAATATTAATA
*
17242407 -TTTAATATTTTAATCA
1 TTTTAA-ATATTAAT-A
*
17242423 TATT-AATATTAATAA
1 TTTTAAATATTAAT-A
17242438 TATTT-AA-ATT-ATA
1 T-TTTAAATATTAATA
* *
17242451 TATAAAATATTAATA
1 TTTTAAATATTAATA
17242466 TTTTAAAT
1 TTTTAAAT
17242474 TTTATAAATA
Statistics
Matches: 202, Mismatches: 44, Indels: 61
0.66 0.14 0.20
Matches are distributed among these distances:
10 3 0.01
11 12 0.06
12 5 0.02
13 8 0.04
14 19 0.09
15 76 0.38
16 46 0.23
17 20 0.10
18 13 0.06
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.50
Consensus pattern (15 bp):
TTTTAAATATTAATA
Found at i:17242522 original size:8 final size:8
Alignment explanation
Indices: 17242489--17242530 Score: 50
Period size: 8 Copynumber: 5.0 Consensus size: 8
17242479 AAATAATTTA
17242489 TTCTTTTT
1 TTCTTTTT
17242497 ATTCTATTATT
1 -TTCT-TT-TT
17242508 TTC-TTTT
1 TTCTTTTT
17242515 TTCTTTTT
1 TTCTTTTT
17242523 TTCTTTTT
1 TTCTTTTT
17242531 CATGGGCCAG
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
7 5 0.17
8 14 0.47
9 4 0.13
10 5 0.17
11 2 0.07
ACGTcount: A:0.07, C:0.12, G:0.00, T:0.81
Consensus pattern (8 bp):
TTCTTTTT
Found at i:17245510 original size:31 final size:31
Alignment explanation
Indices: 17245440--17245510 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
17245430 TTATTTGTTG
*
17245440 ATGTGTTTTAGTACAACTCCATTAAGAACTTG
1 ATGTG-TTTAGTACAACTCCATTAAGAACTTA
* * * * *
17245472 GTATGTTTAGTATAACTCTATTAAGAAGTTA
1 ATGTGTTTAGTACAACTCCATTAAGAACTTA
17245503 ATGTGTTT
1 ATGTGTTT
17245511 TAATATGTCT
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
31 28 0.90
32 3 0.10
ACGTcount: A:0.31, C:0.10, G:0.17, T:0.42
Consensus pattern (31 bp):
ATGTGTTTAGTACAACTCCATTAAGAACTTA
Found at i:17252882 original size:23 final size:23
Alignment explanation
Indices: 17252854--17252900 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
17252844 TTCTCTCTTC
*
17252854 TCTTTAATTGTTCTTTCAAGTTA
1 TCTTTAATTGTTATTTCAAGTTA
* *
17252877 TCTTTATTTGTTATTTTAAGTTA
1 TCTTTAATTGTTATTTCAAGTTA
17252900 T
1 T
17252901 ATTTTCGTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.21, C:0.09, G:0.09, T:0.62
Consensus pattern (23 bp):
TCTTTAATTGTTATTTCAAGTTA
Found at i:17253045 original size:23 final size:23
Alignment explanation
Indices: 17253019--17253075 Score: 55
Period size: 22 Copynumber: 2.5 Consensus size: 23
17253009 AGGTATTTTG
17253019 GATACTATTTTTCAAATCTTACA
1 GATACTATTTTTCAAATCTTACA
* * *
17253042 GATA-TCA-TTTGCAAATCTTGCT
1 GATACT-ATTTTTCAAATCTTACA
*
17253064 GGTACTATTTTT
1 GATACTATTTTT
17253076 TTTGAATCCT
Statistics
Matches: 26, Mismatches: 5, Indels: 6
0.70 0.14 0.16
Matches are distributed among these distances:
22 17 0.65
23 9 0.35
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.46
Consensus pattern (23 bp):
GATACTATTTTTCAAATCTTACA
Found at i:17255728 original size:20 final size:20
Alignment explanation
Indices: 17255705--17255745 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
17255695 ATGATATCCC
17255705 TCAATACTTTATCTGAATAT
1 TCAATACTTTATCTGAATAT
17255725 TCAATACTTTATCTGAATAT
1 TCAATACTTTATCTGAATAT
17255745 T
1 T
17255746 GTCTTTCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.15, G:0.05, T:0.46
Consensus pattern (20 bp):
TCAATACTTTATCTGAATAT
Found at i:17257076 original size:18 final size:18
Alignment explanation
Indices: 17257053--17257089 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
17257043 AATAAATATA
*
17257053 ATTACTATTACTACAACT
1 ATTACTAGTACTACAACT
*
17257071 ATTACTAGTACTACTACT
1 ATTACTAGTACTACAACT
17257089 A
1 A
17257090 GAGATAAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.03, T:0.38
Consensus pattern (18 bp):
ATTACTAGTACTACAACT
Found at i:17262961 original size:3 final size:3
Alignment explanation
Indices: 17262953--17262982 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
17262943 GTTCTTCATA
17262953 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
17262983 GGGCATTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:17275584 original size:27 final size:27
Alignment explanation
Indices: 17275550--17275614 Score: 98
Period size: 26 Copynumber: 2.5 Consensus size: 27
17275540 ATAATTTGTA
*
17275550 ATAA-TTTTTTTTTAATATGGCGTG-T
1 ATAACTTTTTTTTTAATATGGCATGTT
17275575 ATAACTTTTTTTTTAATATGGCATGTT
1 ATAACTTTTTTTTTAATATGGCATGTT
*
17275602 ATAACGTTTTTTT
1 ATAACTTTTTTTT
17275615 CAACGTGGTG
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 4 0.11
26 19 0.53
27 13 0.36
ACGTcount: A:0.25, C:0.06, G:0.12, T:0.57
Consensus pattern (27 bp):
ATAACTTTTTTTTTAATATGGCATGTT
Found at i:17275719 original size:25 final size:25
Alignment explanation
Indices: 17275690--17275746 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
17275680 ACAATAATAT
*
17275690 TTTTTTTAACATGACATTTAACAAC
1 TTTTTTTAACATGACATGTAACAAC
* ** *
17275715 TTTTTTTAATATGATGTGTAATAAC
1 TTTTTTTAACATGACATGTAACAAC
17275740 TTTTTTT
1 TTTTTTT
17275747 TAATATATGT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.54
Consensus pattern (25 bp):
TTTTTTTAACATGACATGTAACAAC
Found at i:17275751 original size:26 final size:26
Alignment explanation
Indices: 17275546--17275756 Score: 85
Period size: 27 Copynumber: 8.0 Consensus size: 26
17275536 CAACATAATT
* **
17275546 TGTAATAATTTTTTTTTAATATGGCG
1 TGTAATAACTTTTTTTTAATATGATG
17275572 TGT-ATAACTTTTTTTTTAATATGGCATG
1 TGTAATAAC-TTTTTTTTAATAT-G-ATG
* ** *
17275600 T-T-ATAACGTTTTTTTCAACGTGGTG
1 TGTAATAAC-TTTTTTTTAATATGATG
** * * * *
17275625 CATAACAAATTTATTTTCAATATGACG
1 TGTAATAACTTT-TTTTTAATATGATG
* *
17275652 TGTAATAAC--ATTTTAAATATGAAATG
1 TGTAATAACTTTTTTTTAATATG--ATG
** * * **
17275678 TAACAATAATATTTTTTTTAACATGACA
1 T-GTAATAA-CTTTTTTTTAATATGATG
* *
17275706 TTTAACAAC-TTTTTTTAATATGATG
1 TGTAATAACTTTTTTTTAATATGATG
17275731 TGTAATAACTTTTTTTTAATAT-ATG
1 TGTAATAACTTTTTTTTAATATGATG
17275756 T
1 T
17275757 AATTTTTTTT
Statistics
Matches: 133, Mismatches: 39, Indels: 27
0.67 0.20 0.14
Matches are distributed among these distances:
24 10 0.08
25 30 0.23
26 36 0.27
27 44 0.33
28 4 0.03
30 9 0.07
ACGTcount: A:0.33, C:0.08, G:0.11, T:0.48
Consensus pattern (26 bp):
TGTAATAACTTTTTTTTAATATGATG
Found at i:17279896 original size:16 final size:17
Alignment explanation
Indices: 17279875--17279910 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
17279865 TCTCCTTTTT
*
17279875 TTTTTCTTTTTTTC-CC
1 TTTTTCATTTTTTCTCC
17279891 TTTTTCATTTTTTCTCC
1 TTTTTCATTTTTTCTCC
17279908 TTT
1 TTT
17279911 ATATTTATAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.03, C:0.22, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTCATTTTTTCTCC
Found at i:17280185 original size:50 final size:50
Alignment explanation
Indices: 17280126--17280232 Score: 187
Period size: 50 Copynumber: 2.1 Consensus size: 50
17280116 CTTATATTTA
*
17280126 AATTATTAATGAAATTTTATGTTATAATTTAATTTTATTTCAAAAGTGATT
1 AATT-TTAATGAAATTTTATATTATAATTTAATTTTATTTCAAAAGTGATT
*
17280177 AATTTTAATGAAATTTTATATTATAATTTTATTTTATTTCAAAAGTGATT
1 AATTTTAATGAAATTTTATATTATAATTTAATTTTATTTCAAAAGTGATT
17280227 AATTTT
1 AATTTT
17280233 TTACTCTGAA
Statistics
Matches: 54, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
50 50 0.93
51 4 0.07
ACGTcount: A:0.38, C:0.02, G:0.07, T:0.53
Consensus pattern (50 bp):
AATTTTAATGAAATTTTATATTATAATTTAATTTTATTTCAAAAGTGATT
Found at i:17281069 original size:19 final size:20
Alignment explanation
Indices: 17281047--17281086 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
17281037 TCCATTGACT
17281047 TATTGGAGTATAATTT-AAG
1 TATTGGAGTATAATTTGAAG
*
17281066 TATTGGAGTATGATTTGAAG
1 TATTGGAGTATAATTTGAAG
17281086 T
1 T
17281087 TTAGAAGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 15 0.79
20 4 0.21
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (20 bp):
TATTGGAGTATAATTTGAAG
Found at i:17282380 original size:13 final size:13
Alignment explanation
Indices: 17282362--17282386 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17282352 GGAAAATGAG
17282362 ATTTTATAAAATA
1 ATTTTATAAAATA
17282375 ATTTTATAAAAT
1 ATTTTATAAAAT
17282387 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:17302150 original size:13 final size:12
Alignment explanation
Indices: 17302127--17302151 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17302117 GCTTTAGGTA
17302127 TGAAATTTTTTT
1 TGAAATTTTTTT
17302139 TGAAATTTTTTT
1 TGAAATTTTTTT
17302151 T
1 T
17302152 ATAGAAAGGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TGAAATTTTTTT
Found at i:17302841 original size:15 final size:16
Alignment explanation
Indices: 17302811--17302843 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
17302801 GTTTGGTACT
17302811 TTACAATGTAACGTGA
1 TTACAATGTAACGTGA
*
17302827 TTACAA-GTAATGTGA
1 TTACAATGTAACGTGA
17302842 TT
1 TT
17302844 GCAAACAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (16 bp):
TTACAATGTAACGTGA
Found at i:17303095 original size:71 final size:69
Alignment explanation
Indices: 17303020--17303163 Score: 177
Period size: 71 Copynumber: 2.1 Consensus size: 69
17303010 TTTAATTAAA
**
17303020 TATATTTTATTTTTCATTTCTTATT-ACAAG-TATATATTTTATTTTTATTT-TTAATATAATTT
1 TATATTTTATTTTAAATTTCTTATTCACAAGATA-ATATTTTATTTTTATTTCTTAATAT--TTT
17303082 CTTATATTG
63 -TTATA-TG
* * *
17303091 TATATTTTATTTTAAATTTTTTCTTCAGAAGATAATATTTTATTTTTATTTCTTAATATTTTTTA
1 TATATTTTATTTTAAATTTCTTATTCACAAGATAATATTTTATTTTTATTTCTTAATATTTTTTA
17303156 TATG
66 TATG
17303160 TATA
1 TATA
17303164 CATTAATGTG
Statistics
Matches: 65, Mismatches: 5, Indels: 8
0.83 0.06 0.10
Matches are distributed among these distances:
69 6 0.09
70 5 0.08
71 24 0.37
72 21 0.32
73 9 0.14
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.62
Consensus pattern (69 bp):
TATATTTTATTTTAAATTTCTTATTCACAAGATAATATTTTATTTTTATTTCTTAATATTTTTTA
TATG
Found at i:17308840 original size:24 final size:26
Alignment explanation
Indices: 17308790--17308844 Score: 78
Period size: 24 Copynumber: 2.2 Consensus size: 26
17308780 CTTCATGCTC
*
17308790 AAATATAAAAATAATTAAAAAATTAA
1 AAATATAAAAATAATTAAAAAAATAA
*
17308816 AAATAT-AACATAA-TAAAAAAATAA
1 AAATATAAAAATAATTAAAAAAATAA
17308840 AAATA
1 AAATA
17308845 CATTTAATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
24 15 0.56
25 6 0.22
26 6 0.22
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.24
Consensus pattern (26 bp):
AAATATAAAAATAATTAAAAAAATAA
Found at i:17314013 original size:31 final size:30
Alignment explanation
Indices: 17313978--17314035 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
17313968 TTTCCAATGA
17313978 AAGTATAACTAA-GCTTACTTTTTCAAGGCTT
1 AAGTATAACTAATG--TACTTTTTCAAGGCTT
*
17314009 AAGTATAACTTATGTACTTTTTCAAGG
1 AAGTATAACTAATGTACTTTTTCAAGG
17314036 AGGTATAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
30 13 0.52
31 11 0.44
32 1 0.04
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.40
Consensus pattern (30 bp):
AAGTATAACTAATGTACTTTTTCAAGGCTT
Found at i:17324801 original size:23 final size:24
Alignment explanation
Indices: 17324766--17324812 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
17324756 TTTAATTTTG
17324766 AAAATATACTTAA-ATATTAATAA
1 AAAATATACTTAATATATTAATAA
** *
17324789 AAAATATTTTTAATATTTTAATAA
1 AAAATATACTTAATATATTAATAA
17324813 TCAAAATTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAATATACTTAATATATTAATAA
Found at i:17325326 original size:2 final size:2
Alignment explanation
Indices: 17325315--17325345 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
17325305 GTATCAAATT
17325315 TA TA -A 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
17325346 ATTAGTTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:17326171 original size:34 final size:34
Alignment explanation
Indices: 17326133--17326197 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
17326123 TCTTACATGT
*
17326133 CAAGGTCAAAGCTTCAACACTAAATGTTACACTC
1 CAAGGTCAAAGCTTCAACACTAAATATTACACTC
** *
17326167 CAAGGTTGAAGCTTCAACACTAGATATTACA
1 CAAGGTCAAAGCTTCAACACTAAATATTACA
17326198 TGCCAAAGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (34 bp):
CAAGGTCAAAGCTTCAACACTAAATATTACACTC
Found at i:17326525 original size:20 final size:20
Alignment explanation
Indices: 17326500--17326555 Score: 58
Period size: 20 Copynumber: 2.8 Consensus size: 20
17326490 ATATATCGAT
*
17326500 ACATGTATTGATACATTTTG
1 ACATGTATAGATACATTTTG
* *
17326520 ACATGTAAAGATAGATTTTG
1 ACATGTATAGATACATTTTG
* * *
17326540 AAATCTATCGATACAT
1 ACATGTATAGATACAT
17326556 GTTCTTCAGA
Statistics
Matches: 28, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (20 bp):
ACATGTATAGATACATTTTG
Found at i:17326680 original size:21 final size:21
Alignment explanation
Indices: 17326651--17326690 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
17326641 CTCACTGCCT
17326651 CAAAAGTATCGATACATTTCA
1 CAAAAGTATCGATACATTTCA
*
17326672 CAAATGTATCGATACATTT
1 CAAAAGTATCGATACATTT
17326691 TCAACAGAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
CAAAAGTATCGATACATTTCA
Found at i:17326697 original size:61 final size:60
Alignment explanation
Indices: 17326596--17326751 Score: 168
Period size: 61 Copynumber: 2.6 Consensus size: 60
17326586 CAAACTCAAT
* * * * * ** *
17326596 CTATTGATACATTTTCAAATGTATTGATAAAATTGGAACAGATTGCTCACTGCCTCAAAA
1 CTATCGATACATTTACAAATGTATCGATACATTTTCAACAGAGTGCTCACTGCCTCAAAA
* * * * *
17326656 GTATCGATACATTTCACAAATGTATCGATACATTTTCAACAGAGTGCTTATTGTCTTAAAA
1 CTATCGATACATTT-ACAAATGTATCGATACATTTTCAACAGAGTGCTCACTGCCTCAAAA
* *
17326717 CTATCGATACATTTGCAAATGTATCGATACCTTTT
1 CTATCGATACATTTACAAATGTATCGATACATTTT
17326752 AAATAGAATG
Statistics
Matches: 79, Mismatches: 16, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
60 31 0.39
61 48 0.61
ACGTcount: A:0.34, C:0.17, G:0.13, T:0.36
Consensus pattern (60 bp):
CTATCGATACATTTACAAATGTATCGATACATTTTCAACAGAGTGCTCACTGCCTCAAAA
Found at i:17329543 original size:20 final size:20
Alignment explanation
Indices: 17329518--17329559 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
17329508 AGGTTCAACA
17329518 TAATGTGCAGAAGCATAAAC
1 TAATGTGCAGAAGCATAAAC
*
17329538 TAATGTGCGGAAGCATAAAC
1 TAATGTGCAGAAGCATAAAC
17329558 TA
1 TA
17329560 GTATGAGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.21, T:0.21
Consensus pattern (20 bp):
TAATGTGCAGAAGCATAAAC
Found at i:17331068 original size:28 final size:28
Alignment explanation
Indices: 17331015--17331077 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
17331005 CACTACAATA
* * *
17331015 CCTTTTCAAGGTTCAAGCATAGCCATTG
1 CCTTTTCAAGGCTCAAGCAAAACCATTG
17331043 CCTTTTCAAGGCTCGAA-CAAAACCATTG
1 CCTTTTCAAGGCTC-AAGCAAAACCATTG
*
17331071 TCTTTTC
1 CCTTTTC
17331078 GAGATTCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 28 0.93
29 2 0.07
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.33
Consensus pattern (28 bp):
CCTTTTCAAGGCTCAAGCAAAACCATTG
Found at i:17331195 original size:39 final size:39
Alignment explanation
Indices: 17331144--17331219 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
17331134 TGCCTTATCA
*
17331144 AAGAAATCAAGCACAACCTCTAAACACTACCTTTTGAAG
1 AAGAAATCAAGCACAACCTCTAAACAATACCTTTTGAAG
*
17331183 AAGAAATCAAGCACAACTTCTAAACAATACCTTTTGA
1 AAGAAATCAAGCACAACCTCTAAACAATACCTTTTGA
17331220 TGAGATGAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (39 bp):
AAGAAATCAAGCACAACCTCTAAACAATACCTTTTGAAG
Found at i:17331772 original size:93 final size:93
Alignment explanation
Indices: 17331640--17331819 Score: 288
Period size: 93 Copynumber: 1.9 Consensus size: 93
17331630 TGTGAGTTAA
* *
17331640 GGATTGATCCCTCCCATAGTGGGGATTGATCCCCGCAAGGCACCAAGAGATTTAGGCAATTTATT
1 GGATCGATCCCTCCCATAGTGGGGATTGATCCCCACAAGGCACCAAGAGATTTAGGCAATTTATT
17331705 TGATATGGATCAATCCTCAAACCCTTGG
66 TGATATGGATCAATCCTCAAACCCTTGG
* * * * * *
17331733 GGATCGATCCTTCCCATAGTGGGGATTGATCCCTACAAGGCAGCAAGGGATTTGGGCAATTTGTT
1 GGATCGATCCCTCCCATAGTGGGGATTGATCCCCACAAGGCACCAAGAGATTTAGGCAATTTATT
17331798 TGATATGGATCAATCCTCAAAC
66 TGATATGGATCAATCCTCAAAC
17331820 TCGAGGGAAT
Statistics
Matches: 79, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.27, C:0.22, G:0.24, T:0.27
Consensus pattern (93 bp):
GGATCGATCCCTCCCATAGTGGGGATTGATCCCCACAAGGCACCAAGAGATTTAGGCAATTTATT
TGATATGGATCAATCCTCAAACCCTTGG
Found at i:17331968 original size:21 final size:21
Alignment explanation
Indices: 17331944--17331987 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
17331934 TGAAGAACTT
*
17331944 AAGTTGAAAACTCATTCAAGC
1 AAGTTCAAAACTCATTCAAGC
17331965 AAGTTCAAAACTCATTCAAGC
1 AAGTTCAAAACTCATTCAAGC
17331986 AA
1 AA
17331988 TTTTGATTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.20, G:0.11, T:0.23
Consensus pattern (21 bp):
AAGTTCAAAACTCATTCAAGC
Found at i:17342151 original size:29 final size:28
Alignment explanation
Indices: 17342119--17342179 Score: 97
Period size: 29 Copynumber: 2.2 Consensus size: 28
17342109 GGGAATTCAA
*
17342119 GTTAAAATCAATAAAACTCAGTCAGCAAT
1 GTTAAAATCAATAAAACTCAATCAG-AAT
17342148 GTTAAAATCAATAAAACTCAATCAGAAT
1 GTTAAAATCAATAAAACTCAATCAGAAT
17342176 -TTAA
1 GTTAA
17342180 TCAGATTACA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 4 0.13
28 3 0.10
29 24 0.77
ACGTcount: A:0.51, C:0.15, G:0.08, T:0.26
Consensus pattern (28 bp):
GTTAAAATCAATAAAACTCAATCAGAAT
Found at i:17342224 original size:89 final size:88
Alignment explanation
Indices: 17342110--17342284 Score: 289
Period size: 89 Copynumber: 2.0 Consensus size: 88
17342100 ACAAAATCAG
**
17342110 GGAATTCAAGTTAAAATCAATAAAACTCAGTCAGCAATGTTAAAATCAATAAAACTCA-ATCAGA
1 GGAATTCAAGTTAAAATCAATAAAACTCAGTCAGCAACATTAAAATCAATAAAACTCATA-CAGA
17342174 ATTTAATCAGATTACATTGGTAGT
65 ATTTAATCAGATTACATTGGTAGT
* *
17342198 GGAATTCAACGTTAAAATCAATAAAACTTAGTCAGTAACATTAAAATCAATAAAACTCATACAGA
1 GGAATTCAA-GTTAAAATCAATAAAACTCAGTCAGCAACATTAAAATCAATAAAACTCATACAGA
17342263 ATTTAATCAGATTACATTGGTA
65 ATTTAATCAGATTACATTGGTA
17342285 ATGGTTGAGA
Statistics
Matches: 81, Mismatches: 4, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
88 9 0.11
89 71 0.88
90 1 0.01
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.29
Consensus pattern (88 bp):
GGAATTCAAGTTAAAATCAATAAAACTCAGTCAGCAACATTAAAATCAATAAAACTCATACAGAA
TTTAATCAGATTACATTGGTAGT
Found at i:17346618 original size:10 final size:11
Alignment explanation
Indices: 17346600--17346636 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
17346590 GTGGCTGAAA
17346600 TTGATGATATT
1 TTGATGATATT
17346611 TT-ATGATATT
1 TTGATGATATT
*
17346621 TTGGTGATA-T
1 TTGATGATATT
17346631 TTGATG
1 TTGATG
17346637 TTTGGTGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
10 16 0.70
11 7 0.30
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (11 bp):
TTGATGATATT
Found at i:17354266 original size:15 final size:15
Alignment explanation
Indices: 17354242--17354271 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
17354232 TGCTATCACA
*
17354242 ATAATTTCAAAAATG
1 ATAATCTCAAAAATG
17354257 ATAATCTCAAAAATG
1 ATAATCTCAAAAATG
17354272 GAAAGATGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.53, C:0.10, G:0.07, T:0.30
Consensus pattern (15 bp):
ATAATCTCAAAAATG
Found at i:17357008 original size:3 final size:3
Alignment explanation
Indices: 17356991--17357030 Score: 62
Period size: 3 Copynumber: 12.7 Consensus size: 3
17356981 ACTTATTATG
17356991 TAA TGAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA T-AA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
17357031 TCTTTGATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 29 0.83
4 6 0.17
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:17370692 original size:22 final size:22
Alignment explanation
Indices: 17370650--17370692 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
17370640 GATTGAAGGC
*
17370650 ATTGCTTGATTAGGTTTTAGGA
1 ATTGCTTGAGTAGGTTTTAGGA
17370672 ATTGCTTGAGTA-GTTTGTAGG
1 ATTGCTTGAGTAGGTTT-TAGG
17370693 CATTCCATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.21, C:0.05, G:0.30, T:0.44
Consensus pattern (22 bp):
ATTGCTTGAGTAGGTTTTAGGA
Found at i:17373381 original size:18 final size:20
Alignment explanation
Indices: 17373341--17373378 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
17373331 GTTTATCAAG
17373341 GATAATATCAAATTTAAAAAT
1 GATAATATCAAATTT-AAAAT
17373362 GATAATATC-AATTTAAA
1 GATAATATCAAATTTAAA
17373379 TGAAATTCTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 5 0.29
21 9 0.53
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (20 bp):
GATAATATCAAATTTAAAAT
Found at i:17382229 original size:29 final size:29
Alignment explanation
Indices: 17382186--17382245 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
17382176 ATGTGATTGG
17382186 ACTAAGATTAATGGATAGAGATGAAACTC
1 ACTAAGATTAATGGATAGAGATGAAACTC
*
17382215 ACTAAGATTAGTGGATAGAGATGAAACTC
1 ACTAAGATTAATGGATAGAGATGAAACTC
17382244 AC
1 AC
17382246 GTCAGTTTAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (29 bp):
ACTAAGATTAATGGATAGAGATGAAACTC
Found at i:17383574 original size:29 final size:30
Alignment explanation
Indices: 17383541--17383617 Score: 86
Period size: 30 Copynumber: 2.6 Consensus size: 30
17383531 ATTCAAAAAT
17383541 TTTAAATAAATTTTTA-ATCTTTTA-TTAAA
1 TTTAAATAAATTTTTATAT-TTTTATTTAAA
* * *
17383570 TTTAATTATATTTTTATATTTTTATTTTAA
1 TTTAAATAAATTTTTATATTTTTATTTAAA
* *
17383600 GTTAAATAAACTTTTATA
1 TTTAAATAAATTTTTATA
17383618 ATTAATGATT
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.58
Consensus pattern (30 bp):
TTTAAATAAATTTTTATATTTTTATTTAAA
Found at i:17384177 original size:20 final size:21
Alignment explanation
Indices: 17384152--17384191 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
17384142 TGACTTAAAA
*
17384152 TAAAAAT-ATAAAAATTTAAT
1 TAAAAATAATAAAAAATTAAT
17384172 TAAAAATAATAAAAAATTAA
1 TAAAAATAATAAAAAATTAA
17384192 AATTTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
TAAAAATAATAAAAAATTAAT
Found at i:17386337 original size:20 final size:20
Alignment explanation
Indices: 17386312--17386354 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
17386302 TCTCTCTGTG
*
17386312 CATATATATATATATAAATA
1 CATATATATATACATAAATA
*
17386332 CATATATATATACATACATA
1 CATATATATATACATAAATA
17386352 CAT
1 CAT
17386355 GCATGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (20 bp):
CATATATATATACATAAATA
Found at i:17386338 original size:16 final size:16
Alignment explanation
Indices: 17386317--17386351 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
17386307 CTGTGCATAT
17386317 ATATATATATAAATAC
1 ATATATATATAAATAC
*
17386333 ATATATATATACATAC
1 ATATATATATAAATAC
17386349 ATA
1 ATA
17386352 CATGCATGTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.54, C:0.09, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATATATATAAATAC
Found at i:17386771 original size:21 final size:20
Alignment explanation
Indices: 17386747--17386800 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
17386737 TTATTTATTT
*
17386747 TTAAAAATTACAAATTTAAAC
1 TTAAAAATTA-AAATTTAAAA
*
17386768 TTAAAAAATTAATATTTAAAA
1 TT-AAAAATTAAAATTTAAAA
17386789 TT-AAAATTAAAA
1 TTAAAAATTAAAA
17386801 AATTATTAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 9 0.31
21 12 0.41
22 8 0.28
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (20 bp):
TTAAAAATTAAAATTTAAAA
Found at i:17386801 original size:13 final size:13
Alignment explanation
Indices: 17386750--17386801 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
17386740 TTTATTTTTA
*
17386750 AAAATTACAAATTT
1 AAAATTA-AAAATT
*
17386764 AAACTTAAAAAATT
1 AAAATT-AAAAATT
* *
17386778 AATATTTAAAATT
1 AAAATTAAAAATT
17386791 AAAATTAAAAA
1 AAAATTAAAAA
17386802 ATTATTAATA
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
13 15 0.50
14 14 0.47
15 1 0.03
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (13 bp):
AAAATTAAAAATT
Found at i:17386885 original size:14 final size:16
Alignment explanation
Indices: 17386852--17386891 Score: 57
Period size: 15 Copynumber: 2.6 Consensus size: 16
17386842 ATTACAAATA
17386852 AAAAT-TTAATATTTT
1 AAAATATTAATATTTT
17386867 AAAATATTAAT-TTTT
1 AAAATATTAATATTTT
*
17386882 AAATTATTAA
1 AAAATATTAA
17386892 GTGAATTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 18 0.78
16 5 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (16 bp):
AAAATATTAATATTTT
Found at i:17387094 original size:19 final size:20
Alignment explanation
Indices: 17387058--17387096 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
17387048 ATTAAATTAC
17387058 CAATTAATAATATTTTAAAT
1 CAATTAATAATATTTTAAAT
17387078 CAATT-ATAA-ATTATTAAAT
1 CAATTAATAATATT-TTAAAT
17387097 ATTTAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 3 0.17
19 10 0.56
20 5 0.28
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (20 bp):
CAATTAATAATATTTTAAAT
Found at i:17387247 original size:23 final size:23
Alignment explanation
Indices: 17387190--17387263 Score: 80
Period size: 23 Copynumber: 3.3 Consensus size: 23
17387180 TAAATTACAA
* * *
17387190 ATAAAATATTAATACTTAAATA-
1 ATAAATTATTAATATTTAAAAAT
* *
17387212 ATCAACTATTAATATTTAAAAAT
1 ATAAATTATTAATATTTAAAAAT
17387235 ATAAATTATTAATATTTAAAAGAT
1 ATAAATTATTAATATTTAAAA-AT
17387259 A-AAAT
1 ATAAAT
17387264 AAAATAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
22 18 0.41
23 23 0.52
24 3 0.07
ACGTcount: A:0.57, C:0.04, G:0.01, T:0.38
Consensus pattern (23 bp):
ATAAATTATTAATATTTAAAAAT
Found at i:17387260 original size:22 final size:21
Alignment explanation
Indices: 17387188--17387264 Score: 91
Period size: 22 Copynumber: 3.5 Consensus size: 21
17387178 ATTAAATTAC
*
17387188 AAATAAAATATTAATACTTAA
1 AAATAAAATATTAATATTTAA
* *
17387209 ATAATCAACTATTAATATTTAA
1 A-AATAAAATATTAATATTTAA
17387231 AAATATAAATTATTAATATTTAA
1 AAATA-AAA-TATTAATATTTAA
17387254 AAGATAAAATA
1 AA-ATAAAATA
17387265 AAATAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
21 4 0.09
22 22 0.47
23 18 0.38
24 3 0.06
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.36
Consensus pattern (21 bp):
AAATAAAATATTAATATTTAA
Found at i:17387642 original size:20 final size:20
Alignment explanation
Indices: 17387575--17387646 Score: 67
Period size: 20 Copynumber: 3.5 Consensus size: 20
17387565 TTTAAATTAT
17387575 AAATAAAATATTAATATTTTA
1 AAATAAAATATTAATA-TTTA
* **
17387596 TAATATTCATGATTAA-A-TTA
1 AAATA-AAAT-ATTAATATTTA
17387616 TAAATAAAATATTAATATTTA
1 -AAATAAAATATTAATATTTA
17387637 AAATAAAATA
1 AAATAAAATA
17387647 AAATAATTAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
19 5 0.12
20 16 0.40
21 11 0.28
22 3 0.08
23 5 0.12
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.40
Consensus pattern (20 bp):
AAATAAAATATTAATATTTA
Found at i:17387651 original size:25 final size:25
Alignment explanation
Indices: 17387608--17387669 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
17387598 ATATTCATGA
*
17387608 TTAAATTATAAATAAAAT-ATTAATAT
1 TTAAAATA-AAATAAAATAATT-ATAT
17387634 TTAAAATAAAATAAAATAATTATAT
1 TTAAAATAAAATAAAATAATTATAT
* *
17387659 ATATAATAAAA
1 TTAAAATAAAA
17387670 GATTTTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 22 0.69
26 10 0.31
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (25 bp):
TTAAAATAAAATAAAATAATTATAT
Found at i:17391524 original size:67 final size:66
Alignment explanation
Indices: 17391423--17391607 Score: 262
Period size: 67 Copynumber: 2.8 Consensus size: 66
17391413 TTTTCGCAGG
* * * *
17391423 CTCAGCCACAACCTTTAGCAATGATTTTTTACGGGATCAATCAAAACCCAAAGTGGTTTTTCAAA
1 CTCAACCACAACCTTTAACAATG-GTTTTTACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAA
*
17391488 GA
65 AA
*
17391490 CTCAACCACAACCTTTAACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTTAAA
1 CTCAACCACAACCTTTAACAATGGTTTTT-ACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAA
17391555 AA
65 AA
** *
17391557 CTCAACCACAACCTACAACAATAGTTTTTACCGGGATCAACCAAAACCCAA
1 CTCAACCACAACCTTTAACAATGGTTTTTA-CGGGATCAACCAAAACCCAA
17391608 CAACCAACTT
Statistics
Matches: 107, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
66 6 0.06
67 101 0.94
ACGTcount: A:0.37, C:0.26, G:0.12, T:0.25
Consensus pattern (66 bp):
CTCAACCACAACCTTTAACAATGGTTTTTACGGGATCAACCAAAACCCAAAGTGGTTTTTCAAAA
A
Found at i:17391530 original size:35 final size:35
Alignment explanation
Indices: 17391432--17391537 Score: 94
Period size: 35 Copynumber: 3.1 Consensus size: 35
17391422 GCTCAGCCAC
* * * *
17391432 AACCTTTAGCAATGATTTTTTACGGGATCAATCAA
1 AACCTTTAACAATGGTTTTTCACGGGATCAACCAA
* * ** *
17391467 AACC--CAA-AGTGGTTTTTCA-AAGACTCAACCAC
1 AACCTTTAACAATGGTTTTTCACGGGA-TCAACCAA
17391499 AACCTTTAACAATGGTTTTTCACGGGATCAACCAA
1 AACCTTTAACAATGGTTTTTCACGGGATCAACCAA
17391534 AACC
1 AACC
17391538 CAAAGTGGTT
Statistics
Matches: 52, Mismatches: 14, Indels: 10
0.68 0.18 0.13
Matches are distributed among these distances:
31 2 0.04
32 19 0.37
33 1 0.02
34 2 0.04
35 26 0.50
36 2 0.04
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (35 bp):
AACCTTTAACAATGGTTTTTCACGGGATCAACCAA
Found at i:17391562 original size:32 final size:32
Alignment explanation
Indices: 17391459--17391569 Score: 98
Period size: 32 Copynumber: 3.4 Consensus size: 32
17391449 TTTTACGGGA
*
17391459 TCAATCAAAACCCAAAGTGGTTTTTCAAAGAC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGAC
* * * **
17391491 TCAACCACAACCTTTAACAATGGTTTTTCACGGGA-
1 TCAACCAAAACC--CAA-AGTGGTTTTTCA-AAGAC
* *
17391526 TCAACCAAAACCCAAAGTGGTTTTTTAAAAAC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGAC
*
17391558 TCAACCACAACC
1 TCAACCAAAACC
17391570 TACAACAATA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
31 1 0.02
32 31 0.52
33 2 0.03
34 2 0.03
35 22 0.37
36 2 0.03
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGAC
Found at i:17393835 original size:2 final size:2
Alignment explanation
Indices: 17393828--17393872 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
17393818 TTGTACAAAT
17393828 TA TA 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 TA TA
17393870 TA T
1 TA T
17393873 NNNNNNNNNN
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17393918 original size:2 final size:2
Alignment explanation
Indices: 17393911--17393955 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
17393901 ATGTATAAAT
17393911 TA TA 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 TA TA
17393953 TA T
1 TA T
17393956 CTTGTTAATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:17396831 original size:65 final size:65
Alignment explanation
Indices: 17396642--17396823 Score: 186
Period size: 65 Copynumber: 2.8 Consensus size: 65
17396632 TATGGTTATC
* * * * * *
17396642 CTCATCTCACATAGTATGTGGAAACAATATCACATACACAGTAACATAACATACATCATGTGTTC
1 CTCAACTCATATAGTATGTGGAAAC---ATCACATACATAGCAACATAACATACATCATATGCTC
17396707 ACT
63 ACT
* * * ** *
17396710 CTCAACTCATATAGTATGT-GACAACGTCATATACATAGCAATATAGTATACATCATATGCTCAT
1 CTCAACTCATATAGTATGTGGA-AACATCACATACATAGCAACATAACATACATCATATGCTCAC
17396774 T
65 T
* * *
17396775 CTTATCTCATTTAGTATGTGGAAACATCACATACATAGCAACATAACAT
1 CTCAACTCATATAGTATGTGGAAACATCACATACATAGCAACATAACAT
17396824 CTTTCATACA
Statistics
Matches: 92, Mismatches: 20, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
65 68 0.74
66 2 0.02
67 2 0.02
68 20 0.22
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.30
Consensus pattern (65 bp):
CTCAACTCATATAGTATGTGGAAACATCACATACATAGCAACATAACATACATCATATGCTCACT
Found at i:17408504 original size:16 final size:16
Alignment explanation
Indices: 17408481--17408513 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
17408471 TCAAATGACG
17408481 TTTAAGTG-TAAAAAA
1 TTTAAGTGTTAAAAAA
17408496 TTTATAGTGTTAAAAAA
1 TTTA-AGTGTTAAAAAA
17408513 T
1 T
17408514 ATTTATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.25
16 4 0.25
17 8 0.50
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.39
Consensus pattern (16 bp):
TTTAAGTGTTAAAAAA
Found at i:17412160 original size:214 final size:215
Alignment explanation
Indices: 17411872--17412321 Score: 656
Period size: 214 Copynumber: 2.1 Consensus size: 215
17411862 GAAACTTCAT
* *
17411872 CTTTAATTATATATATATATAAATAAATGATATAACTTATATGTTATAATATTTTACATCAAATT
1 CTTT-ATTATATATATATATAAATAAATGATATAACTTATATGTTAAAATATTTTACATCAAAGT
* * * **
17411937 TTATATAAATAATAATTAATTAAAAATAATATGTTATAAAATCTAAATTGATAGCT-AATAAACT
65 TTATATAAATAATAACTAATTAAAAACAATATGTTATAAAATCTAAAGTGA-AAATAAATAAACT
* *
17412001 TATTAAGTGTAATCATATAAATAAAGTTTATTATAAGTTATAATAATGCTTATGTATAAATTAAA
129 TATTAAATGTAATCATATAAATAAAGTCTATTATAAGTTATAATAATGCTTATGTATAAATTAAA
* *
17412066 TATATGTATATATAATATATTA
194 TATACGTATATATAATATATGA
* * *
17412088 CTTTATTATACATATATA-AAATTAATGATGCA-AAC-TATATGTTAAAATATTTTATATCAAAG
1 CTTTATTATATATATATATAAATAAATGAT--ATAACTTATATGTTAAAATATTTTACATCAAAG
* * * *
17412150 TTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGAAAATAAATAAAGT
64 TTTATATAAATAATAACTAATTAAAAACAATATGTTATAAAATCTAAAGTGAAAATAAATAAACT
*
17412215 TATTAAATGTAATCATATAAATAAAGTCTATTATAAGTTATAGTAATGCTTATGTATAAATTAAA
129 TATTAAATGTAATCATATAAATAAAGTCTATTATAAGTTATAATAATGCTTATGTATAAATTAAA
17412280 TATACGTATATATAATATATGA
194 TATACGTATATATAATATATGA
*
17412302 CTTTATTTTATATATATATA
1 CTTTATTATATATATATATA
17412322 TATATATATA
Statistics
Matches: 209, Mismatches: 21, Indels: 9
0.87 0.09 0.04
Matches are distributed among these distances:
213 2 0.01
214 185 0.89
215 17 0.08
216 5 0.02
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (215 bp):
CTTTATTATATATATATATAAATAAATGATATAACTTATATGTTAAAATATTTTACATCAAAGTT
TATATAAATAATAACTAATTAAAAACAATATGTTATAAAATCTAAAGTGAAAATAAATAAACTTA
TTAAATGTAATCATATAAATAAAGTCTATTATAAGTTATAATAATGCTTATGTATAAATTAAATA
TACGTATATATAATATATGA
Found at i:17412315 original size:2 final size:2
Alignment explanation
Indices: 17412310--17412342 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
17412300 GACTTTATTT
17412310 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
17412343 GAAATTAATG
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:17412382 original size:238 final size:237
Alignment explanation
Indices: 17412072--17412537 Score: 679
Period size: 238 Copynumber: 2.0 Consensus size: 237
17412062 TAAATATATG
*
17412072 TATATATAATATATTACTTTATTATACATATATAAAATTAATGATGCAAACTATATGTTAAAATA
1 TATATATAATATATTACTATATTATACATATATAAAATTAATGAT-CAAACTATATGTTAAAATA
* * * * *
17412137 TTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAACAATATGTTATAAAATCTAAGGTGA
65 CTTTATATCAAAATTTGAATAAATAATAACTAATTATAAACAATATATTAAAAAATCTAAGGTGA
* *
17412202 -AAATAAATAAAGTTATTAAATGTAATCATATAAATAAAGTCTATTATAAGTTATAGTAATGCTT
130 TAAAT-AATAAAGTTATTAAATATAATCATATAAATAAAGTCTATTATAAATTATAGTAATGCTT
17412266 ATGTATAAATTAAATATACGTATATATAATATATGACTTTATTT
194 ATGTATAAATTAAATATACGTATATATAATATATGACTTTATTT
* * *
17412310 TATATAT-ATATATATA-TATATATATATATATATGAAATTAATGAT-ATAACTGATATGTTATA
1 TATATATAATATAT-TACTATAT-TATACATATATAAAATTAATGATCA-AACT-ATATGTTAAA
* *
17412372 ATGCTTTATATCAAAATTTGAATAAATAATAACTAGTTATAAACAATATATTAAAAAATCTAAGG
62 ATACTTTATATCAAAATTTGAATAAATAATAACTAATTATAAACAATATATTAAAAAATCTAAGG
* * * * *
17412437 TGATAACTAATAAAGTTATTAAGTATAATCATATAAATAAATTTTATTATAAATTATAGTAATGT
127 TGATAAATAATAAAGTTATTAAATATAATCATATAAATAAAGTCTATTATAAATTATAGTAATGC
*
17412502 TTATGTATAAATTAAATATATGTATATATAATATAT
192 TTATGTATAAATTAAATATACGTATATATAATATAT
17412538 TTATACAATT
Statistics
Matches: 204, Mismatches: 19, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
236 1 0.00
237 14 0.07
238 186 0.91
239 3 0.01
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.41
Consensus pattern (237 bp):
TATATATAATATATTACTATATTATACATATATAAAATTAATGATCAAACTATATGTTAAAATAC
TTTATATCAAAATTTGAATAAATAATAACTAATTATAAACAATATATTAAAAAATCTAAGGTGAT
AAATAATAAAGTTATTAAATATAATCATATAAATAAAGTCTATTATAAATTATAGTAATGCTTAT
GTATAAATTAAATATACGTATATATAATATATGACTTTATTT
Found at i:17412494 original size:23 final size:23
Alignment explanation
Indices: 17412479--17412524 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
17412469 ATAAATAAAT
*
17412479 TTTAT-TATAAATTATAGTAATG
1 TTTATGTATAAATTATAATAATG
17412501 TTTATGTATAAATTA-AATATATG
1 TTTATGTATAAATTATAATA-ATG
17412524 T
1 T
17412525 ATATATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.41, C:0.00, G:0.09, T:0.50
Consensus pattern (23 bp):
TTTATGTATAAATTATAATAATG
Found at i:17412804 original size:16 final size:16
Alignment explanation
Indices: 17412783--17412816 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
17412773 CTAATAAATT
17412783 TTAAGTAAATTATTAA
1 TTAAGTAAATTATTAA
**
17412799 TTAAGTTTATTATTAA
1 TTAAGTAAATTATTAA
17412815 TT
1 TT
17412817 CTTCTTAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (16 bp):
TTAAGTAAATTATTAA
Found at i:17415489 original size:24 final size:24
Alignment explanation
Indices: 17415462--17415510 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
17415452 AAGTTAATAA
17415462 TTAAGTCAAATTAAAATATAAATT
1 TTAAGTCAAATTAAAATATAAATT
*
17415486 TTAAGTCAAATTAGAATATAAATT
1 TTAAGTCAAATTAAAATATAAATT
17415510 T
1 T
17415511 CAAATTTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.06, T:0.39
Consensus pattern (24 bp):
TTAAGTCAAATTAAAATATAAATT
Found at i:17416533 original size:81 final size:80
Alignment explanation
Indices: 17416425--17416652 Score: 314
Period size: 81 Copynumber: 2.8 Consensus size: 80
17416415 ATTTAAATTG
* *
17416425 GACCAATTAAAAATTAGTTATTGGTCATCTAATTTATCTCTAAATAAATCAAAATAATTTAGAGA
1 GACCAATCAAAATTTAGTTATTGGTCATCTAATTTATCTCTAAATAAAT-AAAATAATTTAGAGA
17416490 TAATATTCATATTTTT
65 TAATATTCATATTTTT
* * * * * *
17416506 GACCAATCAAAATTTAGTTATTAGTCATCCAATTTTTTTTTAAATAAAATAAGATAATTTAGAGA
1 GACCAATCAAAATTTAGTTATTGGTCATCTAATTTATCTCTAAAT-AAATAAAATAATTTAGAGA
17416571 TAATATTCATATTTTT
65 TAATATTCATATTTTT
* * * * *
17416587 GACCAATCAAAATTTAATTATTGGTCATGTAATTTATCTCT-AATAATTATACTAATTTAGAGAT
1 GACCAATCAAAATTTAGTTATTGGTCATCTAATTTATCTCTAAATAAATAAAATAATTTAGAGAT
17416651 AA
66 AA
17416653 AAATCAAATT
Statistics
Matches: 127, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
79 18 0.14
80 3 0.02
81 102 0.80
82 4 0.03
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (80 bp):
GACCAATCAAAATTTAGTTATTGGTCATCTAATTTATCTCTAAATAAATAAAATAATTTAGAGAT
AATATTCATATTTTT
Found at i:17416605 original size:41 final size:41
Alignment explanation
Indices: 17416471--17416605 Score: 101
Period size: 41 Copynumber: 3.4 Consensus size: 41
17416461 TCTCTAAATA
17416471 AATCAAAA--TAATTTAGAGATAATATTCATATTTTTGACC
1 AATCAAAATTTAATTTAGAGATAATATTCATATTTTTGACC
* **
17416510 AATCAAAATTTAGTTATTAGTCATCCAAT-TT--T-TTTTT-A--
1 AATCAAAATTTA-AT-TTAGAGAT--AATATTCATATTTTTGACC
*
17416548 AAT-AAAATAAGATAATTTAGAGATAATATTCATATTTTTGACC
1 AATCAAAAT---TTAATTTAGAGATAATATTCATATTTTTGACC
17416591 AATCAAAATTTAATT
1 AATCAAAATTTAATT
17416606 ATTGGTCATG
Statistics
Matches: 71, Mismatches: 8, Indels: 32
0.64 0.07 0.29
Matches are distributed among these distances:
36 3 0.04
37 7 0.10
38 9 0.13
39 10 0.14
40 8 0.11
41 13 0.18
42 2 0.03
43 9 0.13
44 7 0.10
45 3 0.04
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.41
Consensus pattern (41 bp):
AATCAAAATTTAATTTAGAGATAATATTCATATTTTTGACC
Found at i:17416920 original size:18 final size:19
Alignment explanation
Indices: 17416894--17416929 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17416884 TCATTCATTC
17416894 GAAAGCATTCAAAGATTGG
1 GAAAGCATTCAAAGATTGG
*
17416913 GAAA-CATTCTAAGATTG
1 GAAAGCATTCAAAGATTG
17416930 AGAGTATTGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.42, C:0.11, G:0.22, T:0.25
Consensus pattern (19 bp):
GAAAGCATTCAAAGATTGG
Found at i:17421198 original size:22 final size:22
Alignment explanation
Indices: 17421173--17421247 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
17421163 TGAACATGAT
**
17421173 GTGTAACAAATTTTTCACTTGC
1 GTGTAACAAATTTTGAACTTGC
** *
17421195 GTGTAACATGTTTTGAACATGGC
1 GTGTAACAAATTTTGAAC-TTGC
*
17421218 ATGTAACAAATTTTGAACTTGC
1 GTGTAACAAATTTTGAACTTGC
*
17421240 GTATAACA
1 GTGTAACA
17421248 TTTTCGAACA
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
22 23 0.56
23 18 0.44
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (22 bp):
GTGTAACAAATTTTGAACTTGC
Found at i:17421205 original size:45 final size:45
Alignment explanation
Indices: 17421148--17421269 Score: 140
Period size: 45 Copynumber: 2.7 Consensus size: 45
17421138 ATTTAACATA
* ** **
17421148 GCGTGCAACATGTTGTGAACATGATGTGTAACAAATTTTTCACTT
1 GCGTGTAACATGTTGTGAACATGACATGTAACAAATTTTGAACTT
* *
17421193 GCGTGTAACATGTTTTGAACATGGCATGTAACAAATTTTGAACTT
1 GCGTGTAACATGTTGTGAACATGACATGTAACAAATTTTGAACTT
* *
17421238 GCGTATAACAT-TT-TCGAACATGGCATGTAACA
1 GCGTGTAACATGTTGT-GAACATGACATGTAACA
17421270 TTTTCTAAAC
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
43 1 0.01
44 19 0.28
45 48 0.71
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (45 bp):
GCGTGTAACATGTTGTGAACATGACATGTAACAAATTTTGAACTT
Found at i:17421224 original size:23 final size:22
Alignment explanation
Indices: 17421196--17421315 Score: 116
Period size: 23 Copynumber: 5.3 Consensus size: 22
17421186 TTCACTTGCG
17421196 TGTAACATGTTTTGAACATGGCA
1 TGTAACAT-TTTTGAACATGGCA
* * *
17421219 TGTAACAAATTTTGAAC-TTGCG
1 TGTAAC-ATTTTTGAACATGGCA
* *
17421241 TATAACATTTTCGAACATGGCA
1 TGTAACATTTTTGAACATGGCA
* *
17421263 TGTAACATTTTCTAAACATGGCG
1 TGTAACATTTT-TGAACATGGCA
* *
17421286 TGTAACATTTTTTTAAAATGGCA
1 TGTAACA-TTTTTGAACATGGCA
17421309 TGTAACA
1 TGTAACA
17421316 ACATGACTGA
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
21 8 0.10
22 21 0.27
23 44 0.56
24 5 0.06
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (22 bp):
TGTAACATTTTTGAACATGGCA
Found at i:17424743 original size:86 final size:85
Alignment explanation
Indices: 17424590--17424919 Score: 416
Period size: 86 Copynumber: 3.9 Consensus size: 85
17424580 AAGCAAATGC
*
17424590 TTGTGGTGACA--CTGAGTGCATGCAGACTTCTGACGTGACA-GCTGACTTGTTACAGTATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCGTGACACGCTGACTTGTTACAGTATTGTG
17424652 GGGTGACACGGCACATGCCAA
66 GGGTGACACGG-ACATGCCAA
* * * *
17424673 TTGTGGTGACACGGTGAGTGCATGCAAACTTCTGGCGTGACACACTGACTTGTTACAGTATTATG
1 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCGTGACACGCTGACTTGTTACAGTATTGTG
* **
17424738 GGGTGACACGAAACGGGCCAA
66 GGGTGACACG-GACATGCCAA
* * * * *
17424759 TTGTGGTGACATGCTGAGTGCATGCAGACTTCTGGCGTGACATGTTGACTTGTTGCAGTTTTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCGTGACACGCTGACTTGTTACAGTATTGTG
*
17424824 GGGTGACAC-GTCATGCCCCAA
66 GGGTGACACGGACATG--CCAA
* * * * *
17424845 TTGTGGTGGCACGCTGAATGCATGCAGATTTCTGGCGTGACACGTTGACTTGTTACAATATTGTG
1 TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCGTGACACGCTGACTTGTTACAGTATTGTG
*
17424910 GGATGACACG
66 GGGTGACACG
17424920 CCACGTGGTT
Statistics
Matches: 210, Mismatches: 30, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
83 11 0.05
84 2 0.01
85 26 0.12
86 171 0.81
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (85 bp):
TTGTGGTGACACGCTGAGTGCATGCAGACTTCTGGCGTGACACGCTGACTTGTTACAGTATTGTG
GGGTGACACGGACATGCCAA
Found at i:17424886 original size:172 final size:169
Alignment explanation
Indices: 17424590--17424919 Score: 466
Period size: 172 Copynumber: 1.9 Consensus size: 169
17424580 AAGCAAATGC
17424590 TTGTGGTGACACTGAGTGCATGCAGACTTCTGACGTGACAGCTGACTTGTTACAGTATTGTGGGG
1 TTGTGGTGACACTGAGTGCATGCAGACTTCTGACGTGACAGCTGACTTGTTACAGTATTGTGGGG
* *
17424655 TGACACGGCACATGCCAATTGTGGTGACACGGTGAGTGCATGCAAACTTCTGGCGTGACACACTG
66 TGACACGGCACATGCCAATTGTGGTGACACGCTGAATGCATGCAAACTTCTGGCGTGACACACTG
* *
17424720 ACTTGTTACAGTATTATGGGGTGACACGAAACGGGCCAA
131 ACTTGTTACAATATTATGGGATGACACGAAACGGGCCAA
* * * *
17424759 TTGTGGTGACATGCTGAGTGCATGCAGACTTCTGGCGTGACATGTTGACTTGTTGCAGTTTTGTG
1 TTGTGGTGACA--CTGAGTGCATGCAGACTTCTGACGTGACA-GCTGACTTGTTACAGTATTGTG
* * * *
17424824 GGGTGACAC-G-TCATGCCCCAATTGTGGTGGCACGCTGAATGCATGCAGATTTCTGGCGTGACA
63 GGGTGACACGGCACATG--CCAATTGTGGTGACACGCTGAATGCATGCAAACTTCTGGCGTGACA
** *
17424887 CGTTGACTTGTTACAATATTGTGGGATGACACG
126 CACTGACTTGTTACAATATTATGGGATGACACG
17424920 CCACGTGGTT
Statistics
Matches: 141, Mismatches: 15, Indels: 7
0.87 0.09 0.04
Matches are distributed among these distances:
169 11 0.08
170 4 0.03
171 29 0.21
172 97 0.69
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (169 bp):
TTGTGGTGACACTGAGTGCATGCAGACTTCTGACGTGACAGCTGACTTGTTACAGTATTGTGGGG
TGACACGGCACATGCCAATTGTGGTGACACGCTGAATGCATGCAAACTTCTGGCGTGACACACTG
ACTTGTTACAATATTATGGGATGACACGAAACGGGCCAA
Found at i:17426501 original size:81 final size:81
Alignment explanation
Indices: 17426318--17426485 Score: 237
Period size: 81 Copynumber: 2.1 Consensus size: 81
17426308 GATGCTCTCC
* * * *
17426318 TTCAACCACGAGCTAGTGAAGGTCCCCCTCCCCTCTCGCAGATGCATCGATAACCGAATCAACCT
1 TTCAGCCACGAGCAAGTGAAGGTCCCCCTCCCCTCCCACAGATGCATCGATAACCGAATCAACCT
* *
17426383 CAGGAACGTGGACTAT
66 CAAGAACATGGACTAT
** * *
17426399 TTCAGCCACGAGCAAGTGAAGGTCCCTTTCCCCTCCCATAGATGCATCGATAACCGAATCAGCCT
1 TTCAGCCACGAGCAAGTGAAGGTCCCCCTCCCCTCCCACAGATGCATCGATAACCGAATCAACCT
*
17426464 CAAGAACATGGACTCT
66 CAAGAACATGGACTAT
17426480 TTCAGC
1 TTCAGC
17426486 ATCATCTGAT
Statistics
Matches: 76, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
81 76 1.00
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (81 bp):
TTCAGCCACGAGCAAGTGAAGGTCCCCCTCCCCTCCCACAGATGCATCGATAACCGAATCAACCT
CAAGAACATGGACTAT
Found at i:17428776 original size:31 final size:31
Alignment explanation
Indices: 17428740--17428859 Score: 177
Period size: 31 Copynumber: 3.9 Consensus size: 31
17428730 AGAAAGAAAT
* *
17428740 AAATGTTGTTACACGCTATGCATATCAAGAA
1 AAATGTTGTAACACGCCATGCATATCAAGAA
*
17428771 AAATGTTGTAACACGCTATGCATATCAAGAA
1 AAATGTTGTAACACGCCATGCATATCAAGAA
**
17428802 AAATGTTGTAACACGCCATGCATATCAAGTC
1 AAATGTTGTAACACGCCATGCATATCAAGAA
* *
17428833 AAATGTTGTGACATGCCATGCATATCA
1 AAATGTTGTAACACGCCATGCATATCA
17428860 GTGTCGTGAC
Statistics
Matches: 83, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 83 1.00
ACGTcount: A:0.38, C:0.18, G:0.17, T:0.28
Consensus pattern (31 bp):
AAATGTTGTAACACGCCATGCATATCAAGAA
Found at i:17428980 original size:55 final size:54
Alignment explanation
Indices: 17428904--17429172 Score: 299
Period size: 55 Copynumber: 4.9 Consensus size: 54
17428894 TCGTTACACC
* *
17428904 AACAGCTGTGACATGCCAAAAACCAAAAAAACCAGTTAACCCACAACACACCAGG
1 AACAGCTGTGACACGCTAAAAACC-AAAAAACCAGTTAACCCACAACACACCAGG
* * *
17428959 AACAGCTGTGACACGTTAAAAACTCAAAAAACCGGTTAACCCACAACACTCCAGG
1 AACAGCTGTGACACGCTAAAAAC-CAAAAAACCAGTTAACCCACAACACACCAGG
* * * * *
17429014 AACAGCCGTGACATGTTAAAAACTCAAAAAACCAGTTAACCCACAACACGCCAAG
1 AACAGCTGTGACACGCTAAAAAC-CAAAAAACCAGTTAACCCACAACACACCAGG
* * * * * *
17429069 AACAACCGTGACACGCTAAAAACCCATAAAACTAGTTAACCCACAACATGA-TAGG
1 AACAGCTGTGACACGCTAAAAA-CCAAAAAACCAGTTAACCCACAACA-CACCAGG
* *
17429124 AACAG-TCGTGACAAGCTAAAAACCCAAAAAACTAGTTAACCCACAACAC
1 AACAGCT-GTGACACGCTAAAAA-CCAAAAAACCAGTTAACCCACAACAC
17429173 GCCATATGTA
Statistics
Matches: 186, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
55 184 0.99
56 2 0.01
ACGTcount: A:0.46, C:0.29, G:0.13, T:0.13
Consensus pattern (54 bp):
AACAGCTGTGACACGCTAAAAACCAAAAAACCAGTTAACCCACAACACACCAGG
Found at i:17429100 original size:110 final size:109
Alignment explanation
Indices: 17428904--17429176 Score: 350
Period size: 110 Copynumber: 2.5 Consensus size: 109
17428894 TCGTTACACC
* * * * * *
17428904 AACAGCTGTGACATGCCAAAAACCAAAAAAACCAGTTAACCCACAACACACCAGGAACAGCTGTG
1 AACAGCCGTGACATGCTAAAAACC-AAAAAACCAGTTAACCCACAACACGCCAAGAACAACCGTG
* * * *
17428969 ACACGTTAAAAACTCAAAAAACCGGTTAACCCACAACACT-CCAGG
65 ACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACA-TGACAGG
*
17429014 AACAGCCGTGACATGTTAAAAACTCAAAAAACCAGTTAACCCACAACACGCCAAGAACAACCGTG
1 AACAGCCGTGACATGCTAAAAAC-CAAAAAACCAGTTAACCCACAACACGCCAAGAACAACCGTG
* * *
17429079 ACACGCTAAAAACCCATAAAACTAGTTAACCCACAACATGATAGG
65 ACACGCTAAAAACCCAAAAAACCAGTTAACCCACAACATGACAGG
* * *
17429124 AACAGTCGTGACAAGCTAAAAACCCAAAAAACTAGTTAACCCACAACACGCCA
1 AACAGCCGTGACATGCTAAAAA-CCAAAAAACCAGTTAACCCACAACACGCCA
17429177 TATGTAGACA
Statistics
Matches: 142, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
109 1 0.01
110 139 0.98
111 2 0.01
ACGTcount: A:0.45, C:0.29, G:0.13, T:0.12
Consensus pattern (109 bp):
AACAGCCGTGACATGCTAAAAACCAAAAAACCAGTTAACCCACAACACGCCAAGAACAACCGTGA
CACGCTAAAAACCCAAAAAACCAGTTAACCCACAACATGACAGG
Found at i:17429756 original size:47 final size:45
Alignment explanation
Indices: 17429698--17429853 Score: 145
Period size: 46 Copynumber: 3.4 Consensus size: 45
17429688 ATACATTATC
* *
17429698 ACCCTGGCGTGTCACAAATTTCCTTCATGGCGTGTCACACACTCTAA
1 ACCCTGCCGTGTCACACATTTCC--CATGGCGTGTCACACACTCTAA
* * * *
17429745 ACCCTGCCGTGTCACACATTATCACCATGCCATTTCACATA-T-TATA
1 ACCCTGCCGTGTCACACATT-TC-CCATGGCGTGTCACACACTCTA-A
* * * **
17429791 ACCCTGTCGGGTCACACGTCTAACCATGGCGTGTCACACACTCTAA
1 ACCCTGCCGTGTCACACAT-TTCCCATGGCGTGTCACACACTCTAA
17429837 ACCCTGCCGTGTCACAC
1 ACCCTGCCGTGTCACAC
17429854 CCCTGTCACA
Statistics
Matches: 86, Mismatches: 17, Indels: 13
0.74 0.15 0.11
Matches are distributed among these distances:
45 15 0.17
46 35 0.41
47 33 0.38
48 2 0.02
49 1 0.01
ACGTcount: A:0.24, C:0.35, G:0.15, T:0.26
Consensus pattern (45 bp):
ACCCTGCCGTGTCACACATTTCCCATGGCGTGTCACACACTCTAA
Found at i:17429759 original size:24 final size:23
Alignment explanation
Indices: 17429728--17429853 Score: 105
Period size: 23 Copynumber: 5.4 Consensus size: 23
17429718 TCCTTCATGG
17429728 CGTGTCACACACTCTAAACCCTGC
1 CGTGTCACACA-TCTAAACCCTGC
* *
17429752 CGTGTCACACAT-TATCACCATGC
1 CGTGTCACACATCTA-AACCCTGC
* * * *
17429775 CATTTCACATAT-TATAACCCTGT
1 CGTGTCACACATCTA-AACCCTGC
* * * *
17429798 CGGGTCACACGTCT-AACCATGG
1 CGTGTCACACATCTAAACCCTGC
17429820 CGTGTCACACACTCTAAACCCTGC
1 CGTGTCACACA-TCTAAACCCTGC
17429844 CGTGTCACAC
1 CGTGTCACAC
17429854 CCCTGTCACA
Statistics
Matches: 79, Mismatches: 19, Indels: 8
0.75 0.18 0.08
Matches are distributed among these distances:
22 17 0.22
23 34 0.43
24 28 0.35
ACGTcount: A:0.25, C:0.36, G:0.14, T:0.25
Consensus pattern (23 bp):
CGTGTCACACATCTAAACCCTGC
Found at i:17429815 original size:22 final size:23
Alignment explanation
Indices: 17429789--17429853 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 23
17429779 TCACATATTA
* * *
17429789 TAACCCTGTCGGGTCACAC-GTC
1 TAACCCTGCCGTGTCACACACTC
* *
17429811 TAACCATGGCGTGTCACACACTC
1 TAACCCTGCCGTGTCACACACTC
17429834 TAAACCCTGCCGTGTCACAC
1 T-AACCCTGCCGTGTCACAC
17429854 CCCTGTCACA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
22 16 0.46
23 3 0.09
24 16 0.46
ACGTcount: A:0.23, C:0.37, G:0.18, T:0.22
Consensus pattern (23 bp):
TAACCCTGCCGTGTCACACACTC
Found at i:17429840 original size:46 final size:46
Alignment explanation
Indices: 17429723--17429853 Score: 151
Period size: 46 Copynumber: 2.8 Consensus size: 46
17429713 AAATTTCCTT
17429723 CATGGCGTGTCACACACTCTAAACCCTGCCGTGTCACACATTATCAC
1 CATGGCGTGTCACACACTCTAAACCCTGCCGTGTCACACATTA-CAC
* * * * * * *
17429770 CATGCCATTTCACATA-T-TATAACCCTGTCGGGTCACACGTCTA-AC
1 CATGGCGTGTCACACACTCTA-AACCCTGCCGTGTCACACAT-TACAC
17429815 CATGGCGTGTCACACACTCTAAACCCTGCCGTGTCACAC
1 CATGGCGTGTCACACACTCTAAACCCTGCCGTGTCACAC
17429854 CCCTGTCACA
Statistics
Matches: 67, Mismatches: 13, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
45 16 0.24
46 35 0.52
47 16 0.24
ACGTcount: A:0.25, C:0.35, G:0.15, T:0.24
Consensus pattern (46 bp):
CATGGCGTGTCACACACTCTAAACCCTGCCGTGTCACACATTACAC
Found at i:17429979 original size:194 final size:194
Alignment explanation
Indices: 17429620--17429981 Score: 485
Period size: 194 Copynumber: 1.9 Consensus size: 194
17429610 ACATCTGATT
* * * * ** * *
17429620 ATGGCGTGTCACACACTTTAAACTCTGTCGTGTCACATCTGTCTCACATATTCTCACCGTGTCGT
1 ATGGCGTGTCACACACTCTAAACCCTGCCGTGTCACACCCCTCTCACA-ATTCTCACCGTGCCAT
* * * **
17429685 CTCATACATTATCACCCTGGCGTGTCACAAATTTCCTTCATGGCGTGTCACACACTCTAAACCCT
65 CTCACACATTATCACCCTGACGTGTCACAAATTCCCCCCATGGCGTGTCACACACTCTAAACCCT
*
17429750 GCCGTGTCACACATTATCACCATGCCATTTCACATATTATAACCCTGTCGGGTCACACGTCTAAC
130 ACCGTGTCACACATTATCACCATG-CATTTCACATATTATAACCCTGTCGGGTCACACGTCTAAC
17429815 C
194 C
*
17429816 ATGGCGTGTCACACACTCTAAACCCTGCCGTGTCACACCCCTGTCAC-ATTCTCACCGTGCCATC
1 ATGGCGTGTCACACACTCTAAACCCTGCCGTGTCACACCCCTCTCACAATTCTCACCGTGCCATC
* * *
17429880 TCACACATTATCATCCTGACGTGTCACATATTCCCCCCATGGTGTGTCACACACTCTAAACCCTA
66 TCACACATTATCACCCTGACGTGTCACAAATTCCCCCCATGGCGTGTCACACACTCTAAACCCTA
* * *
17429945 CCGTGTCACATATTCTCACTATG-ATGTGTCACATATT
131 CCGTGTCACACATTATCACCATGCAT-T-TCACATATT
17429982 CCCACCATGC
Statistics
Matches: 143, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
192 2 0.01
193 1 0.01
194 100 0.70
196 40 0.28
ACGTcount: A:0.23, C:0.33, G:0.14, T:0.29
Consensus pattern (194 bp):
ATGGCGTGTCACACACTCTAAACCCTGCCGTGTCACACCCCTCTCACAATTCTCACCGTGCCATC
TCACACATTATCACCCTGACGTGTCACAAATTCCCCCCATGGCGTGTCACACACTCTAAACCCTA
CCGTGTCACACATTATCACCATGCATTTCACATATTATAACCCTGTCGGGTCACACGTCTAACC
Found at i:17429998 original size:23 final size:23
Alignment explanation
Indices: 17429947--17429990 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
17429937 AAACCCTACC
* *
17429947 GTGTCACATATTCTCACTATGAT
1 GTGTCACATATTCCCACCATGAT
17429970 GTGTCACATATTCCCACCATG
1 GTGTCACATATTCCCACCATG
17429991 CCTTGTCATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.25, C:0.27, G:0.14, T:0.34
Consensus pattern (23 bp):
GTGTCACATATTCCCACCATGAT
Found at i:17430068 original size:23 final size:23
Alignment explanation
Indices: 17430028--17430071 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
17430018 TGTCACAACC
* **
17430028 GTGTCACATATTTTCACCATGAT
1 GTGTCACACATTCCCACCATGAT
17430051 GTGTCACACATTCCCACCATG
1 GTGTCACACATTCCCACCATG
17430072 CCATTTCACA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.32
Consensus pattern (23 bp):
GTGTCACACATTCCCACCATGAT
Found at i:17430085 original size:81 final size:81
Alignment explanation
Indices: 17429944--17430119 Score: 246
Period size: 81 Copynumber: 2.2 Consensus size: 81
17429934 TCTAAACCCT
* * * *
17429944 ACCGTGTCACATATTCTCACTATGATGTGTCACATATTCCCACCATGCCTTGTCATAAACTCTAT
1 ACCGTGTCACATATTCTCACCATGATGTGTCACACATTCCCACCATGCCTTGTCACAAACTCTAA
**
17430009 ATCCTACCATGTCACA
66 ATCCTACCATCACACA
* *
17430025 ACCGTGTCACATATTTTCACCATGATGTGTCACACATTCCCACCATGCCATT-TCACAAACTTTA
1 ACCGTGTCACATATTCTCACCATGATGTGTCACACATTCCCACCATGCC-TTGTCACAAACTCTA
*
17430089 AATCCTGCCATCACACA
65 AATCCTACCATCACACA
*
17430106 AACGTGTCACATAT
1 ACCGTGTCACATAT
17430120 GGCCTGCTGT
Statistics
Matches: 84, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
81 82 0.98
82 2 0.02
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.30
Consensus pattern (81 bp):
ACCGTGTCACATATTCTCACCATGATGTGTCACACATTCCCACCATGCCTTGTCACAAACTCTAA
ATCCTACCATCACACA
Found at i:17433110 original size:21 final size:21
Alignment explanation
Indices: 17433076--17433117 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17433066 TTGAATATAA
17433076 AATTTTTTAATAATTT-TTTT
1 AATTTTTTAATAATTTATTTT
*
17433096 AATTTGTTTGATAATTTATTTT
1 AATTT-TTTAATAATTTATTTT
17433118 TTGAAACCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 5 0.26
21 10 0.53
22 4 0.21
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.67
Consensus pattern (21 bp):
AATTTTTTAATAATTTATTTT
Found at i:17437833 original size:28 final size:29
Alignment explanation
Indices: 17437792--17437846 Score: 78
Period size: 28 Copynumber: 1.9 Consensus size: 29
17437782 AAGTCATCAA
17437792 TTTTTAATTATAATTTA-TTTATTTTTAGT
1 TTTTTAATTATAA-TTAGTTTATTTTTAGT
*
17437821 TTTTTTATT-TAATTAGTTTATTTTTA
1 TTTTTAATTATAATTAGTTTATTTTTA
17437847 ACTGAGTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 3 0.12
28 13 0.54
29 8 0.33
ACGTcount: A:0.25, C:0.00, G:0.04, T:0.71
Consensus pattern (29 bp):
TTTTTAATTATAATTAGTTTATTTTTAGT
Found at i:17439866 original size:24 final size:24
Alignment explanation
Indices: 17439839--17439890 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
17439829 CAACTCAAGT
17439839 TAAAAACTAAGTCAAATTAAAATA
1 TAAAAACTAAGTCAAATTAAAATA
*** *
17439863 TAAATTTTAAGTCAAATTAGAATA
1 TAAAAACTAAGTCAAATTAAAATA
17439887 TAAA
1 TAAA
17439891 TTTCAAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.58, C:0.06, G:0.06, T:0.31
Consensus pattern (24 bp):
TAAAAACTAAGTCAAATTAAAATA
Found at i:17439891 original size:24 final size:24
Alignment explanation
Indices: 17439846--17439893 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
17439836 AGTTAAAAAC
17439846 TAAGTCAAATTAAAATATAAATTT
1 TAAGTCAAATTAAAATATAAATTT
*
17439870 TAAGTCAAATTAGAATATAAATTT
1 TAAGTCAAATTAAAATATAAATTT
17439894 CAAATTTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.52, C:0.04, G:0.06, T:0.38
Consensus pattern (24 bp):
TAAGTCAAATTAAAATATAAATTT
Found at i:17449290 original size:18 final size:18
Alignment explanation
Indices: 17449267--17449304 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
17449257 GCATCTCATA
17449267 TCTTTTAGCTCAAGCACT
1 TCTTTTAGCTCAAGCACT
17449285 TCTTTTAGCTCAAGCACT
1 TCTTTTAGCTCAAGCACT
17449303 TC
1 TC
17449305 CTGCTCCATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.21, C:0.29, G:0.11, T:0.39
Consensus pattern (18 bp):
TCTTTTAGCTCAAGCACT
Found at i:17455362 original size:205 final size:203
Alignment explanation
Indices: 17455010--17455743 Score: 965
Period size: 205 Copynumber: 3.5 Consensus size: 203
17455000 TTGATATAAC
* * * *
17455010 TTATATGTTATAATATTTTATATCAAAATTTATATAAATAATAATTAATTATAAATAATATGTTA
1 TTATATGTTAAAATATTTTATATCAAAATTTGTATAAATAATAACTAATTATAAACAATATGTTA
* *** * *
17455075 TAAAATCTAAGATGATAGTTAATAAATTTATTAAGTGTAATCATATAAATAAATTTTATTATAAG
66 TAAAATCTAAGGTGATAACAAATAAAGTTATTAAATGTAATCATATAAATAAA-TTTATTATAAG
17455140 TTATAGTAATGCTTATGTATAAATTAAATATATATAATATTACTTTATTATATATATATAATTAA
130 TTATAGTAATGCTTATGTATAAATTAAATATATATAATATTACTTTATTATATATATATAATTAA
17455205 TTATACAAA
195 TTATACAAA
* *
17455214 TTATATGTTAAAATGTTTTATATCAAAGTTTTGTATAAATAATAACTAATTATAAACAATATGTT
1 TTATATGTTAAAATATTTTATATCAAA-ATTTGTATAAATAATAACTAATTATAAACAATATGTT
* *
17455279 ATAAAATCTAAGGTGATAACAAATAAAGTTATTAAATGTAATCATATAAATAAAGTCTAGTATAA
65 ATAAAATCTAAGGTGATAACAAATAAAGTTATTAAATGTAATCATATAAATAAA-TTTATTATAA
*
17455344 GTTATAGTAATTCTTATGTATAAATTAAATATATGTATATATAATATATGACTTTATTTTATATA
129 GTTATAGTAATGCTTATGTATAAATT--A-A-A--TATATATAATAT-T-ACTTTA--TTATATA
17455409 TATATATATATGAAATTAATGACATAA
184 TATATA-AT-T--AATT-AT-ACA-AA
* * * *
17455436 CTTATATGTTATAATATTTTATATCAAAATTTGTATAAATAATAATTAATTATAAGCAACATGTT
1 -TTATATGTTAAAATATTTTATATCAAAATTTGTATAAATAATAACTAATTATAAACAATATGTT
* * * * *
17455501 ATAAAATCTAAAGTGATAGCTAATAAACTTATTAAGTGTAATCATATAAATAAATTTATTATAAG
65 ATAAAATCTAAGGTGATAACAAATAAAGTTATTAAATGTAATCATATAAATAAATTTATTATAAG
*
17455566 TTATAGTAATGCTTATGTATAAATTAAATATATATAATATTATTTTA-T-TATATATATAATT-A
130 TTATAGTAATGCTTATGTATAAATTAAATATATATAATATTACTTTATTATATATATATAATTAA
*
17455628 --ATGCAAA
195 TTATACAAA
* * * *
17455635 TTATATGTTAAAATGTTTTATATCAAAGTTTTGTATAAATAATAACTAATTATAAACAAAATATT
1 TTATATGTTAAAATATTTTATATCAAA-ATTTGTATAAATAATAACTAATTATAAACAATATGTT
17455700 ATAAAATCTAAGGTGATAACAAATAAAGTTATTAAATGTAATCA
65 ATAAAATCTAAGGTGATAACAAATAAAGTTATTAAATGTAATCA
17455744 NNNNNNNNNN
Statistics
Matches: 466, Mismatches: 44, Indels: 45
0.84 0.08 0.08
Matches are distributed among these distances:
198 25 0.05
199 73 0.16
200 2 0.00
201 2 0.00
204 26 0.06
205 114 0.24
207 2 0.00
208 3 0.01
209 11 0.02
210 1 0.00
211 12 0.03
212 1 0.00
213 11 0.02
214 1 0.00
215 25 0.05
216 2 0.00
217 2 0.00
218 1 0.00
219 5 0.01
220 2 0.00
221 36 0.08
222 84 0.18
223 25 0.05
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.42
Consensus pattern (203 bp):
TTATATGTTAAAATATTTTATATCAAAATTTGTATAAATAATAACTAATTATAAACAATATGTTA
TAAAATCTAAGGTGATAACAAATAAAGTTATTAAATGTAATCATATAAATAAATTTATTATAAGT
TATAGTAATGCTTATGTATAAATTAAATATATATAATATTACTTTATTATATATATATAATTAAT
TATACAAA
Found at i:17473203 original size:21 final size:21
Alignment explanation
Indices: 17473183--17473260 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
17473173 AGAGAGAGAG
17473183 GAAA-AAAAGAAAAAAAAAGA
1 GAAAGAAAAGAAAAAAAAAGA
*** ** *
17473203 GGGGGAGCAGAAAAAGAAAGA
1 GAAAGAAAAGAAAAAAAAAGA
*
17473224 GAAAGAGAAGAAAAAAAAA-A
1 GAAAGAAAAGAAAAAAAAAGA
*
17473244 GAAATAAAAGAAAAAAA
1 GAAAGAAAAGAAAAAAA
17473261 GGAGAGAGGG
Statistics
Matches: 44, Mismatches: 13, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
20 17 0.39
21 27 0.61
ACGTcount: A:0.74, C:0.01, G:0.23, T:0.01
Consensus pattern (21 bp):
GAAAGAAAAGAAAAAAAAAGA
Found at i:17473246 original size:20 final size:20
Alignment explanation
Indices: 17473211--17473260 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
17473201 GAGGGGGAGC
* *
17473211 AGAAAAAGAAAGAGAAAGAGA
1 AGAAAAA-AAAAAGAAAGAAA
*
17473232 AGAAAAAAAAAAGAAATAAA
1 AGAAAAAAAAAAGAAAGAAA
17473252 AGAAAAAAA
1 AGAAAAAAA
17473261 GGAGAGAGGG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 19 0.73
21 7 0.27
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (20 bp):
AGAAAAAAAAAAGAAAGAAA
Found at i:17473365 original size:14 final size:14
Alignment explanation
Indices: 17473285--17473374 Score: 55
Period size: 14 Copynumber: 6.6 Consensus size: 14
17473275 CGACGACGAA
*
17473285 GAGAATAAGGAGAG
1 GAGAAAAAGGAGAG
*
17473299 G-GAAAAA--AGAA
1 GAGAAAAAGGAGAG
*
17473310 GAGAAAGAAAGAGAAG
1 GAGAAA-AAGGAG-AG
*
17473326 AAGAAAAA-GAGAGG
1 GAGAAAAAGGAGA-G
* **
17473340 GAGTAACGGGAGAG
1 GAGAAAAAGGAGAG
17473354 GAGAAAAAGGAGAG
1 GAGAAAAAGGAGAG
17473368 G-GAAAAA
1 GAGAAAAA
17473375 AGAAAAGAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 15
0.69 0.13 0.18
Matches are distributed among these distances:
11 4 0.07
12 4 0.07
13 14 0.24
14 22 0.38
15 8 0.14
16 6 0.10
ACGTcount: A:0.58, C:0.01, G:0.39, T:0.02
Consensus pattern (14 bp):
GAGAAAAAGGAGAG
Found at i:17473371 original size:69 final size:69
Alignment explanation
Indices: 17473283--17473466 Score: 228
Period size: 67 Copynumber: 2.7 Consensus size: 69
17473273 CACGACGACG
* * * *
17473283 AAGAGAATAAGGAGAGGGAAAAAAGAAGAGAAAGAAAGAGAAGAAGAAAAAGAGAGGGAGTAACG
1 AAGAGAAAAAGGAGAGGGAAAAAAGAAGAGAAAGAAAAAGAAGAAGAAAAAGAGAGAGAGCAACG
* *
17473348 GGAG
66 GCAA
* * *
17473352 AGGAGAAAAAGGAGAGGGAAAAAAGAAAAGAAAGAAAAAGAAGAAG--AAAGAGAGAGAGCAGCG
1 AAGAGAAAAAGGAGAGGGAAAAAAGAAGAGAAAGAAAAAGAAGAAGAAAAAGAGAGAGAGCAACG
17473415 GCAA
66 GCAA
* * * * *
17473419 AAGAGCAGAATGAGAGGGAAGAAAGAAGAAAAAGAAAAAGAAGAAGAA
1 AAGAGAAAAAGGAGAGGGAAAAAAGAAGAGAAAGAAAAAGAAGAAGAA
17473467 GGAGAGAAGG
Statistics
Matches: 97, Mismatches: 16, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
67 55 0.57
69 42 0.43
ACGTcount: A:0.61, C:0.03, G:0.35, T:0.02
Consensus pattern (69 bp):
AAGAGAAAAAGGAGAGGGAAAAAAGAAGAGAAAGAAAAAGAAGAAGAAAAAGAGAGAGAGCAACG
GCAA
Found at i:17473390 original size:16 final size:17
Alignment explanation
Indices: 17473369--17473402 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
17473359 AAAGGAGAGG
17473369 GAAAAAAGAA-AAGAAA
1 GAAAAAAGAAGAAGAAA
17473385 G-AAAAAGAAGAAGAAA
1 GAAAAAAGAAGAAGAAA
17473401 GA
1 GA
17473403 GAGAGAGCAG
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
GAAAAAAGAAGAAGAAA
Found at i:17474090 original size:60 final size:60
Alignment explanation
Indices: 17473997--17474300 Score: 353
Period size: 60 Copynumber: 5.0 Consensus size: 60
17473987 ATATTTGATT
* * *
17473997 GTAAAGGGGGACTTGAAGCCCTGATTTATATTTGGTGACGTGGGTAGTTCCTACGAGTAG
1 GTAAAAGGGGACCTGAAGCCCTGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAG
* *
17474057 GTAAAAGAGGACCTGAAGCCCTGATTTATATTTGGTGACGTGGGTAGTTCTCACGAGTAG
1 GTAAAAGGGGACCTGAAGCCCTGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAG
* * * * *
17474117 GTAAAGGGGGACTTGAAGCTCC-GTTTTATATTTGGTGGCGTGGATAGTTCCCACGAGTAG
1 GTAAAAGGGGACCTGAAGC-CCTGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAG
* ***
17474177 GTAAAAAGGGAGACCTGAAGCCCCGATTTATATTTGGTGGTATGGGTAGTTCCCACGAGTAG
1 GT-AAAAGGG-GACCTGAAGCCCTGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAG
* * * * * * *
17474239 GTAAAAAGGGAGACTTGAAGCCCCGA-TT-CATCTGGTGGCATTGGTAGTTCCCACGAGTAG
1 GT-AAAAGGG-GACCTGAAGCCCTGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAG
17474299 GT
1 GT
17474301 GATGATGTTT
Statistics
Matches: 217, Mismatches: 23, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
60 137 0.63
61 12 0.06
62 68 0.31
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.28
Consensus pattern (60 bp):
GTAAAAGGGGACCTGAAGCCCTGATTTATATTTGGTGACGTGGGTAGTTCCCACGAGTAG
Found at i:17474275 original size:122 final size:118
Alignment explanation
Indices: 17473997--17474300 Score: 385
Period size: 122 Copynumber: 2.5 Consensus size: 118
17473987 ATATTTGATT
* * *
17473997 GTAAAGGGGGACTTGAAGCCCTGATTTATATTTGGTGACGTGGGTAGTTCCTACGAGTAGGTAAA
1 GTAAAGGGGGACTTGAAGCCCCGA-TTATATTTGGTGGCGT-GGTAGTTCCCACGAGTAGGTAAA
* * *
17474062 AGAGGACCTGAAGCCCTGATTTATATTTGGTGACGTGGGTAGTTCTCACGAGTAG
64 AGAGGACCTGAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACGAGTAG
* *
17474117 GTAAAGGGGGACTTGAAGCTCCGTTTTATATTTGGTGGCGTGGATAGTTCCCACGAGTAGGTAAA
1 GTAAAGGGGGACTTGAAGCCCCG-ATTATATTTGGTGGCGTGG-TAGTTCCCACGAGTAGGT-AA
* **
17474182 AAGGGAGACCTGAAGCCCCGATTTATATTTGGTGGTATGGGTAGTTCCCACGAGTAG
63 AAGAG-GACCTGAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACGAGTAG
* * * *
17474239 GTAAAAAGGGAGACTTGAAGCCCCGATT-CATCTGGTGGCATTGGTAGTTCCCACGAGTAGGT
1 GT--AAAGGGGGACTTGAAGCCCCGATTATATTTGGTGGC-GTGGTAGTTCCCACGAGTAGGT
17474301 GATGATGTTT
Statistics
Matches: 160, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
119 2 0.01
120 53 0.33
121 6 0.04
122 75 0.47
123 5 0.03
124 19 0.12
ACGTcount: A:0.25, C:0.16, G:0.32, T:0.28
Consensus pattern (118 bp):
GTAAAGGGGGACTTGAAGCCCCGATTATATTTGGTGGCGTGGTAGTTCCCACGAGTAGGTAAAAG
AGGACCTGAAGCCCCGATTTATATTTGGTGACATGGGTAGTTCCCACGAGTAG
Found at i:17484738 original size:189 final size:190
Alignment explanation
Indices: 17484471--17484912 Score: 586
Period size: 189 Copynumber: 2.3 Consensus size: 190
17484461 ATGCATCGCC
* * ***
17484471 AGTCTCATAATA-TTAATAATAAGTCACTCAATGCCTAATATCCACTCATGTTATACCAAAATA-
1 AGTCTCATAATACTTAATAATAAGTCACTCAATGCCTAATATCTACTCACGTTATTGAAAAATAC
* * * **
17484534 ACCAATCCCGTATTGGCCCAACGTCATGCAATACATGACAACCAGTCACGCAATGCTTAAAAAGT
66 ACCAATCACGTATTGGCCCAACGTCACGCAATACATAACAACCAGTCACGCAATGCCAAAAAAGT
* * * **
17484599 AGTCAAAAAATGTCTCAAAATAAGATATGCATTGCATAATTCACGCAACGCTTATAAGCT
131 AGTCAAAAAATGTCTCAAAACAAGATATGCATTGCACAATTCACACAACGCCCATAAGCT
17484659 AGTCTCATAATACTTAATAATAAGTCACTCAATGCCTAATATCTACTCACGTTATTGAAAAATAC
1 AGTCTCATAATACTTAATAATAAGTCACTCAATGCCTAATATCTACTCACGTTATTGAAAAATAC
* * * * * * *
17484724 A-CAGTCATGTATTGGCTCAATGTCACGCAATACATAACAACCAGTTACGTATTGCCAAAAAAGT
66 ACCAATCACGTATTGGCCCAACGTCACGCAATACATAACAACCAGTCACGCAATGCCAAAAAAGT
* * *
17484788 AGTCAAGAAATGTCTCAAAACAAGATATGCATTGCACGATTCATACAACGCCCATAAGCT
131 AGTCAAAAAATGTCTCAAAACAAGATATGCATTGCACAATTCACACAACGCCCATAAGCT
* * * *
17484848 AGTCTTACAATACGTAATAATAAGTCACACAATGCCTAATATCTACTCACGTTA-TGCAAAAATA
1 AGTCTCATAATACTTAATAATAAGTCACTCAATGCCTAATATCTACTCACGTTATTG-AAAAATA
17484912 C
65 C
17484913 CTAAACACAT
Statistics
Matches: 222, Mismatches: 29, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
188 14 0.06
189 207 0.93
190 1 0.00
ACGTcount: A:0.40, C:0.22, G:0.12, T:0.26
Consensus pattern (190 bp):
AGTCTCATAATACTTAATAATAAGTCACTCAATGCCTAATATCTACTCACGTTATTGAAAAATAC
ACCAATCACGTATTGGCCCAACGTCACGCAATACATAACAACCAGTCACGCAATGCCAAAAAAGT
AGTCAAAAAATGTCTCAAAACAAGATATGCATTGCACAATTCACACAACGCCCATAAGCT
Found at i:17485710 original size:22 final size:22
Alignment explanation
Indices: 17485661--17485702 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
17485651 ATCAGACATG
*
17485661 CAATGCCTAATATCAATTCATA
1 CAATGCATAATATCAATTCATA
*
17485683 CAATGCATAATATCCATTCA
1 CAATGCATAATATCAATTCA
17485703 CTTAATGCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.24, G:0.05, T:0.31
Consensus pattern (22 bp):
CAATGCATAATATCAATTCATA
Found at i:17486969 original size:38 final size:38
Alignment explanation
Indices: 17486926--17487018 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 38
17486916 ATGGTGAGAA
*
17486926 AGTTGGAAGGCGAGATATAGACCCCAATGGTGTTGGAG
1 AGTTGGAAGGCGAGATATAGACCCCAATGGCGTTGGAG
* * * *
17486964 AGTTGGACGGTGAGATATAGACTCCGATGGCGTTGGAG
1 AGTTGGAAGGCGAGATATAGACCCCAATGGCGTTGGAG
** *
17487002 AGCGGGATGGCGAGATA
1 AGTTGGAAGGCGAGATA
17487019 GCTAAATCAA
Statistics
Matches: 46, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 46 1.00
ACGTcount: A:0.27, C:0.13, G:0.40, T:0.20
Consensus pattern (38 bp):
AGTTGGAAGGCGAGATATAGACCCCAATGGCGTTGGAG
Found at i:17489214 original size:33 final size:33
Alignment explanation
Indices: 17489153--17489215 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 33
17489143 GCATATTAAA
* * * *
17489153 ATATTATAATTGATGATGATGTGGTATACTGGC
1 ATATCATAATTGATAATGATATGATATACTGGC
*
17489186 ATATCATAATTGATAATTATATGATATACT
1 ATATCATAATTGATAATGATATGATATACT
17489216 AATTTGATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 25 1.00
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (33 bp):
ATATCATAATTGATAATGATATGATATACTGGC
Found at i:17489631 original size:319 final size:319
Alignment explanation
Indices: 17489043--17489667 Score: 1002
Period size: 319 Copynumber: 2.0 Consensus size: 319
17489033 GAACTAAATA
17489043 AATCCTCATATTTTTATTTTGAGTCAAATAAATTTTTATGACTAATGATTCACTTAGTTAAAATG
1 AATCCTCATATTTTTATTTTGAGTCAAATAAATTTTTATGACTAATGATTCACTTAGTTAAAATG
* * ** *
17489108 TCATTTATTATTTTATATCATATGATGTTGACGTGGCATATTAAAATATTATAATTGATGATGAT
66 TCATTTATTATTCTATATCATATGATGCTGACGTAACATACTAAAATATTATAATTGATGATGAT
* * *
17489173 GTGGTATACTGGCATATCATAATTGATAATTATATGATATACTAATTTGATATAATAACATGATC
131 GTGGTATACTGGCATATCATAATTGATAATTACATGACATACTAATTTGATATAATAACATGAAC
* * *
17489238 ATGTGGTATTTTTCACTTATCACATTAGTGTCATATTAGTACCATGTCGATATAAAATAATAAAT
196 ATGTGGTATTTTTCACTTATCACATCAATGTCATATTAGTACCATGTCGATATAAAATAACAAAT
*
17489303 GATATTTTTATTAATGACAATTAATCAATCATTAGTGAAAATGTCATTTATTATTAGTG
261 GACATTTTTATTAATGACAATTAATCAATCATTAGTGAAAATGTCATTTATTATTAGTG
* *
17489362 AATCCTTATATTTTTATTTTGAGTCAAATAAGTCTTTT-TGACTAATGATTCACTTAGTTAAAAT
1 AATCCTCATATTTTTATTTTGAGTCAAATAAAT-TTTTATGACTAATGATTCACTTAGTTAAAAT
* *
17489426 GTCATTTATTATTCTATATTATATGATGCTGACGTAACATACTAAAATATTATAATTGATTATGA
65 GTCATTTATTATTCTATATCATATGATGCTGACGTAACATACTAAAATATTATAATTGATGATGA
* * *
17489491 TGTGGTATTCTGGCATATCATAATTGATGATTACATGACATACTAATTTGATATAATAATATGAA
130 TGTGGTATACTGGCATATCATAATTGATAATTACATGACATACTAATTTGATATAATAACATGAA
* *
17489556 CATGTGGTATTTTTCACCTT-TTACATCAATGTCATATTAGTGCCATGTCGATATAAAATAACAA
195 CATGTGGTATTTTTCA-CTTATCACATCAATGTCATATTAGTACCATGTCGATATAAAATAACAA
* * *
17489620 ATGACATTTTTATTAATGACATTTAGTCAATCATTAGTTAAAATGTCA
259 ATGACATTTTTATTAATGACAATTAATCAATCATTAGTGAAAATGTCA
17489668 ATCATTAGTG
Statistics
Matches: 280, Mismatches: 24, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
319 273 0.98
320 7 0.03
ACGTcount: A:0.36, C:0.10, G:0.12, T:0.42
Consensus pattern (319 bp):
AATCCTCATATTTTTATTTTGAGTCAAATAAATTTTTATGACTAATGATTCACTTAGTTAAAATG
TCATTTATTATTCTATATCATATGATGCTGACGTAACATACTAAAATATTATAATTGATGATGAT
GTGGTATACTGGCATATCATAATTGATAATTACATGACATACTAATTTGATATAATAACATGAAC
ATGTGGTATTTTTCACTTATCACATCAATGTCATATTAGTACCATGTCGATATAAAATAACAAAT
GACATTTTTATTAATGACAATTAATCAATCATTAGTGAAAATGTCATTTATTATTAGTG
Found at i:17489811 original size:29 final size:30
Alignment explanation
Indices: 17489779--17489835 Score: 80
Period size: 29 Copynumber: 1.9 Consensus size: 30
17489769 TTTGATCAAA
* **
17489779 AATAAAAGTATAGGGACTTA-ATTGAATGC
1 AATAAAAGAATAAAGACTTATATTGAATGC
17489808 AATAAAAGAATAAAGACTTATATTGAAT
1 AATAAAAGAATAAAGACTTATATTGAAT
17489836 ATTCTTGCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 17 0.71
30 7 0.29
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (30 bp):
AATAAAAGAATAAAGACTTATATTGAATGC
Found at i:17504243 original size:93 final size:93
Alignment explanation
Indices: 17504084--17504269 Score: 336
Period size: 93 Copynumber: 2.0 Consensus size: 93
17504074 TCTTGTTAAT
*
17504084 AACTTGGTAGTTTGTGATGTTTGTGTGTTTAAGTTGCTTTGGGCACTAAAAATGGTTGAATATCC
1 AACTTGGTAGTTTGTGATGTTTGTGTGTTTAAGTTGCTTTGGGCACTAAAAATGGTTCAATATCC
17504149 CTTAGTTATTTTCGGTCATTGCCATATA
66 CTTAGTTATTTTCGGTCATTGCCATATA
*
17504177 AACTTGGTAGTTTGTGATGTTTGTGTGTTTAAGTTGCTTTGGGCACTGAAAATGGTTCAATATCC
1 AACTTGGTAGTTTGTGATGTTTGTGTGTTTAAGTTGCTTTGGGCACTAAAAATGGTTCAATATCC
* *
17504242 CTTGGTTATTTTTGGTCATTGCCATATA
66 CTTAGTTATTTTCGGTCATTGCCATATA
17504270 TTGAATATCC
Statistics
Matches: 89, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 89 1.00
ACGTcount: A:0.22, C:0.12, G:0.23, T:0.44
Consensus pattern (93 bp):
AACTTGGTAGTTTGTGATGTTTGTGTGTTTAAGTTGCTTTGGGCACTAAAAATGGTTCAATATCC
CTTAGTTATTTTCGGTCATTGCCATATA
Found at i:17506352 original size:23 final size:21
Alignment explanation
Indices: 17506308--17506352 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 21
17506298 TCACATGTTT
*
17506308 ATTTTTTTTATTTTTATCTTA
1 ATTTTTTTTATTTTTATATTA
*
17506329 ATTTTTTTCTCTTTTTATAATTA
1 ATTTTTTT-TATTTTTAT-ATTA
17506352 A
1 A
17506353 GTTAATACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 8 0.40
23 4 0.20
ACGTcount: A:0.22, C:0.07, G:0.00, T:0.71
Consensus pattern (21 bp):
ATTTTTTTTATTTTTATATTA
Found at i:17509439 original size:15 final size:15
Alignment explanation
Indices: 17509404--17509433 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
17509394 TTGGGCTTGG
17509404 TCGCTGGCTGGTGGT
1 TCGCTGGCTGGTGGT
17509419 TCGCTGGCTGGTGGT
1 TCGCTGGCTGGTGGT
17509434 GTGCTGTGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.00, C:0.20, G:0.47, T:0.33
Consensus pattern (15 bp):
TCGCTGGCTGGTGGT
Found at i:17511990 original size:2 final size:2
Alignment explanation
Indices: 17511979--17512007 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
17511969 TCGTGGCCTG
17511979 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
17512008 TTTGAATGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:17512976 original size:20 final size:18
Alignment explanation
Indices: 17512949--17512990 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
17512939 TACTTGAATA
17512949 AAAT-CTTTTTACTCTCTCT
1 AAATACTTTTT-CTC-CTCT
*
17512968 AAATACTTTTTTTCCTCT
1 AAATACTTTTTCTCCTCT
17512986 AAATA
1 AAATA
17512991 TTTCTCTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (18 bp):
AAATACTTTTTCTCCTCT
Found at i:17513342 original size:53 final size:54
Alignment explanation
Indices: 17513285--17513393 Score: 130
Period size: 53 Copynumber: 2.0 Consensus size: 54
17513275 ATGAAAAACC
*
17513285 ATGAACATCCATTCCCTGAAGTGAATGTGACAAACAAGCGACTAAT-AAAAATT
1 ATGAACATCCATTCCCTGAAGTAAATGTGACAAACAAGCGACTAATAAAAAATT
** * * * * **
17513338 ATGAATGTTCATTTCCTGAAGTAAATGTGGCAAATAAGTTACTAATAAAAAATT
1 ATGAACATCCATTCCCTGAAGTAAATGTGACAAACAAGCGACTAATAAAAAATT
17513392 AT
1 AT
17513394 AAATCTTTTA
Statistics
Matches: 46, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
53 37 0.80
54 9 0.20
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (54 bp):
ATGAACATCCATTCCCTGAAGTAAATGTGACAAACAAGCGACTAATAAAAAATT
Found at i:17513397 original size:25 final size:25
Alignment explanation
Indices: 17513369--17513422 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
17513359 TAAATGTGGC
17513369 AAATAAGTTACTAATAAAAAATTAT
1 AAATAAGTTACTAATAAAAAATTAT
***
17513394 AAATCTTTTACTAATAAAAAATTAT
1 AAATAAGTTACTAATAAAAAATTAT
17513419 AAAT
1 AAAT
17513423 CCTTTCATTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.57, C:0.06, G:0.02, T:0.35
Consensus pattern (25 bp):
AAATAAGTTACTAATAAAAAATTAT
Found at i:17513427 original size:26 final size:25
Alignment explanation
Indices: 17513376--17513423 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
17513366 GGCAAATAAG
17513376 TTACTAATAAAAAATTATAAATCTT
1 TTACTAATAAAAAATTATAAATCTT
17513401 TTACTAATAAAAAATTATAAATC
1 TTACTAATAAAAAATTATAAATC
17513424 CTTTCATTCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (25 bp):
TTACTAATAAAAAATTATAAATCTT
Found at i:17513591 original size:26 final size:26
Alignment explanation
Indices: 17513559--17513648 Score: 85
Period size: 26 Copynumber: 3.5 Consensus size: 26
17513549 TATTTTAATT
*
17513559 ATAATTTTACCACCAGAAGTAGATAG
1 ATAATTTTACCATCAGAAGTAGATAG
* * **
17513585 ATAATTTTATCATCTGAA-TTTA-AG
1 ATAATTTTACCATCAGAAGTAGATAG
* * *
17513609 AATAATTTTACCATTAGAAGTGGATAA
1 -ATAATTTTACCATCAGAAGTAGATAG
17513636 ATAATTTTACCAT
1 ATAATTTTACCAT
17513649 AAAAAATGGA
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
24 2 0.04
25 17 0.34
26 30 0.60
27 1 0.02
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.37
Consensus pattern (26 bp):
ATAATTTTACCATCAGAAGTAGATAG
Found at i:17513658 original size:26 final size:26
Alignment explanation
Indices: 17513609--17513659 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
17513599 TGAATTTAAG
* * *
17513609 AATAATTTTACCATTAGAAGTGGATA
1 AATAATTTTACCATAAAAAATGGATA
17513635 AATAATTTTACCATAAAAAATGGAT
1 AATAATTTTACCATAAAAAATGGAT
17513660 GGATGCCTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.47, C:0.08, G:0.12, T:0.33
Consensus pattern (26 bp):
AATAATTTTACCATAAAAAATGGATA
Found at i:17518747 original size:39 final size:39
Alignment explanation
Indices: 17518668--17518774 Score: 137
Period size: 38 Copynumber: 2.7 Consensus size: 39
17518658 GCACACCGGC
*
17518668 TCATGTACATCCCCCCACATCGTGCACATAGCCGACGTCA
1 TCATGTACATCCCCCCACATCGTGCACATA-CAGACGTCA
* *
17518708 TCATGTGCATCCCCCCCACATCGTGCACAGT-CAG-TGTCA
1 TCATGTACAT-CCCCCCACATCGTGCACA-TACAGACGTCA
*
17518747 TCGTGTACATCCCCCCACATCGTGCACA
1 TCATGTACATCCCCCCACATCGTGCACA
17518775 CGGGCACTAT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
38 18 0.30
39 12 0.20
40 11 0.18
41 18 0.30
42 1 0.02
ACGTcount: A:0.22, C:0.40, G:0.16, T:0.21
Consensus pattern (39 bp):
TCATGTACATCCCCCCACATCGTGCACATACAGACGTCA
Done.