Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 137 of 144
Found at i:35316508 original size:309 final size:311
Alignment explanation
Indices: 35315949--35316602 Score: 1100
Period size: 309 Copynumber: 2.1 Consensus size: 311
35315939 TAAACCTACC
*
35315949 GTTATTGAAGATGAATCAATAAATAAACCTACTGCTGAAAACAAACAGCTGAAGGTATTGTTAGA
1 GTTATTGAAGATGAATCAATGAATAAACCTACTGCTGAAAACAAACAGCTGAAGGTATTGTTAGA
35316014 CATTTGTTGCTTCGAATACTATCTTAAGTTTGACTAAAGGCTTTCTTGATGTCATTTGAAAAAAA
66 CATTTGTTGCTTCGAATACTATCTTAAGTTTGACTAAAGGCTTTCTTGATGTCATTTGAAAAAAA
*
35316079 GATTTTGAACATGGGAGCTGAGGACCAGAAACCACAGCAGCAGGCCATGTCGAGTTCACCGAATA
131 GATTTTGAACATGGGAACTGAGGACCAGAAACCACAGCAGCAGGCCATGTCGAGTTCACCGAATA
35316144 CAAACATGTCAGAGGTGACATCTGCAGTAAGATACATCTCAACATTCTTTCCTTATTTTTATTGA
196 CAAACATGTCAGAGGTGACATCTGCAGTAAGATACATCTCAACATTCTTTCCTTATTTTTATTGA
* *
35316209 GT-G-GATTCTTTCCTTATCTCAACAAGTTCCTGTGGTTCAGGAGATCCCT
261 GTAGAAATTCTTTCCTTATCTCAACAAGTTCCTGTGGTTCAGGAAATCCCT
* * **
35316258 GTTATTGATGATGAATCAATGAATAAACTTACTGCTGAAAATGAACAGCTGAAGGTATTGTTAGA
1 GTTATTGAAGATGAATCAATGAATAAACCTACTGCTGAAAACAAACAGCTGAAGGTATTGTTAGA
*
35316323 CATTTGTTGCTTCGAATACTATCTTAAGTTTGACTAAAGGCTTTCTTGATGTCATTTGGAAAAAA
66 CATTTGTTGCTTCGAATACTATCTTAAGTTTGACTAAAGGCTTTCTTGATGTCATTTGAAAAAAA
* * * *
35316388 GATTTTGGACTTGGGAACTGAGGACCAGAAACCACAGCTGCAGGCCATG-CTGAGTTCACCGAGT
131 GATTTTGAACATGGGAACTGAGGACCAGAAACCACAGCAGCAGGCCATGTC-GAGTTCACCGAAT
*
35316452 ACAAACATGTCAGAGGTGACATCTGCAGTAAGATATATCTCAACATTCTTTCCTTATTTTTATTG
195 ACAAACATGTCAGAGGTGACATCTGCAGTAAGATACATCTCAACATTCTTTCCTTATTTTTATTG
35316517 AGTAGAATAATTCTTTCCTTATCTCAACAAGTTCCTGTGGTTCAGGAAATCCCT
260 AGTAG-A-AATTCTTTCCTTATCTCAACAAGTTCCTGTGGTTCAGGAAATCCCT
* *
35316571 GCTATTGACA-ATAAATCAATGAATAAACCTAC
1 GTTATTGA-AGATGAATCAATGAATAAACCTAC
35316603 CGTTATTGAC
Statistics
Matches: 321, Mismatches: 18, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
308 1 0.00
309 248 0.77
310 1 0.00
313 71 0.22
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (311 bp):
GTTATTGAAGATGAATCAATGAATAAACCTACTGCTGAAAACAAACAGCTGAAGGTATTGTTAGA
CATTTGTTGCTTCGAATACTATCTTAAGTTTGACTAAAGGCTTTCTTGATGTCATTTGAAAAAAA
GATTTTGAACATGGGAACTGAGGACCAGAAACCACAGCAGCAGGCCATGTCGAGTTCACCGAATA
CAAACATGTCAGAGGTGACATCTGCAGTAAGATACATCTCAACATTCTTTCCTTATTTTTATTGA
GTAGAAATTCTTTCCTTATCTCAACAAGTTCCTGTGGTTCAGGAAATCCCT
Found at i:35324395 original size:29 final size:29
Alignment explanation
Indices: 35324363--35324439 Score: 70
Period size: 29 Copynumber: 2.6 Consensus size: 29
35324353 TTTATGTGTT
*
35324363 TTTTGAAATTTTAAAATTTAATTTC-TTTA-
1 TTTT-AAATTTTAAAATTTAA-TTCATCTAC
*
35324392 TTTT-TATTTTCAATAATTTAATTCATCTAC
1 TTTTAAATTTT-AA-AATTTAATTCATCTAC
35324422 TTTTAAAATTTTAAAATT
1 TTTT-AAATTTTAAAATT
35324440 CAGATTCTAC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
27 5 0.13
28 5 0.13
29 14 0.36
30 8 0.21
31 2 0.05
32 5 0.13
ACGTcount: A:0.35, C:0.06, G:0.01, T:0.57
Consensus pattern (29 bp):
TTTTAAATTTTAAAATTTAATTCATCTAC
Found at i:35336263 original size:29 final size:29
Alignment explanation
Indices: 35336230--35336299 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
35336220 TATTTAGGCA
* *
35336230 ATTTTTGAAGTTCTGATTTTTTA-TTTTTT
1 ATTTTTGAA-TTCTGAATTTTGACTTTTTT
*
35336259 ATTTTTGAATTTTGAATTTTGACTTTTTT
1 ATTTTTGAATTCTGAATTTTGACTTTTTT
* *
35336288 GTTTTTGGATTC
1 ATTTTTGAATTC
35336300 GTTTTGGTAG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 10 0.29
29 24 0.71
ACGTcount: A:0.17, C:0.04, G:0.13, T:0.66
Consensus pattern (29 bp):
ATTTTTGAATTCTGAATTTTGACTTTTTT
Found at i:35347402 original size:16 final size:16
Alignment explanation
Indices: 35347381--35347433 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
35347371 GCGAGTGACC
*
35347381 AAAATAAAAATTATCT
1 AAAATAAAAATGATCT
****
35347397 AAAATATGCGTGATC-
1 AAAATAAAAATGATCT
35347412 AAAATAAAAATGATCT
1 AAAATAAAAATGATCT
35347428 AAAATA
1 AAAATA
35347434 CTAGCGACTA
Statistics
Matches: 27, Mismatches: 9, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
15 11 0.41
16 16 0.59
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (16 bp):
AAAATAAAAATGATCT
Found at i:35347418 original size:31 final size:31
Alignment explanation
Indices: 35347375--35347433 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
35347365 AATGGAGCGA
*
35347375 GTGACCAAAATAAAAATTATCTAAAATATGC
1 GTGACCAAAATAAAAATGATCTAAAATATGC
*
35347406 GTGATCAAAATAAAAATGATCTAAAATA
1 GTGACCAAAATAAAAATGATCTAAAATA
35347434 CTAGCGACTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.54, C:0.10, G:0.10, T:0.25
Consensus pattern (31 bp):
GTGACCAAAATAAAAATGATCTAAAATATGC
Found at i:35353792 original size:3 final size:3
Alignment explanation
Indices: 35353786--35353811 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
35353776 CTAGAAGAAA
35353786 CTG CTG CTG CTG CTG CTG CTG CTG CT
1 CTG CTG CTG CTG CTG CTG CTG CTG CT
35353812 TCTAGACCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (3 bp):
CTG
Found at i:35361414 original size:16 final size:15
Alignment explanation
Indices: 35361392--35361428 Score: 56
Period size: 16 Copynumber: 2.4 Consensus size: 15
35361382 AGGTATACAC
35361392 ACATACATGCATGCAT
1 ACATACATGCAT-CAT
*
35361408 GCATACATGCATCAT
1 ACATACATGCATCAT
35361423 ACATAC
1 ACATAC
35361429 TTTCTGATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
15 8 0.42
16 11 0.58
ACGTcount: A:0.38, C:0.27, G:0.11, T:0.24
Consensus pattern (15 bp):
ACATACATGCATCAT
Found at i:35363806 original size:28 final size:27
Alignment explanation
Indices: 35363727--35363806 Score: 74
Period size: 26 Copynumber: 3.0 Consensus size: 27
35363717 CAATCAGTCC
*
35363727 AATTCTACTTGGACTAAATATGATCAG
1 AATTCTACTTGAACTAAATATGATCAG
* * *
35363754 --TTCTTACTTGAATTAAATCTAATCAG
1 AATTC-TACTTGAACTAAATATGATCAG
* *
35363780 TAATTCTACTTAAAGTAAATATGATCA
1 -AATTCTACTTGAACTAAATATGATCA
35363807 ACAAATAAGT
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
25 3 0.07
26 18 0.44
28 17 0.41
29 3 0.07
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.38
Consensus pattern (27 bp):
AATTCTACTTGAACTAAATATGATCAG
Found at i:35369507 original size:2 final size:2
Alignment explanation
Indices: 35369502--35369538 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35369492 TTTTTGTTAT
35369502 TA TA 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 TA TA T
35369539 TTCACTATAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35379108 original size:27 final size:28
Alignment explanation
Indices: 35379056--35379108 Score: 72
Period size: 28 Copynumber: 1.9 Consensus size: 28
35379046 TTTATAAGTG
**
35379056 AAAGAAAATACATGCACTGTGATGGTGA
1 AAAGAAAATACATGCACAATGATGGTGA
*
35379084 AAAGCAAATACATGCACAATG-TGGT
1 AAAGAAAATACATGCACAATGATGGT
35379109 CAATGACTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.43, C:0.13, G:0.23, T:0.21
Consensus pattern (28 bp):
AAAGAAAATACATGCACAATGATGGTGA
Found at i:35386649 original size:1 final size:1
Alignment explanation
Indices: 35386643--35386667 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
35386633 CTATATGCTT
35386643 CCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCC
35386668 GGTATTTGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:35389415 original size:17 final size:17
Alignment explanation
Indices: 35389393--35389431 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
35389383 CAAATTAACG
35389393 GCTATGGATATGTTTTA
1 GCTATGGATATGTTTTA
35389410 GCTATGGATATGTTTTA
1 GCTATGGATATGTTTTA
35389427 GCTAT
1 GCTAT
35389432 TGTCCTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.08, G:0.23, T:0.46
Consensus pattern (17 bp):
GCTATGGATATGTTTTA
Found at i:35399549 original size:24 final size:24
Alignment explanation
Indices: 35399521--35399575 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
35399511 AGTTTGACTC
35399521 ATTGAAACAAATAAACAGAGTTTA
1 ATTGAAACAAATAAACAGAGTTTA
35399545 ATTGAAACAAATAAACAGAGTTTA
1 ATTGAAACAAATAAACAGAGTTTA
*
35399569 ACTGAAA
1 ATTGAAA
35399576 GATTATTTCT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.55, C:0.09, G:0.13, T:0.24
Consensus pattern (24 bp):
ATTGAAACAAATAAACAGAGTTTA
Found at i:35401424 original size:32 final size:32
Alignment explanation
Indices: 35401364--35401426 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
35401354 ATTAATCAAT
* *
35401364 ATGAGTTATCAAATTAAATTAATTAATTTATC
1 ATGAGTTATCAAATTAAAGTAATCAATTTATC
* * *
35401396 ATGATTTATTAAATTCAAGTAATCAATTTAT
1 ATGAGTTATCAAATTAAAGTAATCAATTTAT
35401427 AAGTTTATGA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.44
Consensus pattern (32 bp):
ATGAGTTATCAAATTAAAGTAATCAATTTATC
Found at i:35403408 original size:3 final size:3
Alignment explanation
Indices: 35403400--35403449 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
35403390 AACTTTTGCA
35403400 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
35403448 AA
1 AA
35403450 ACCACCTTAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:35408559 original size:15 final size:15
Alignment explanation
Indices: 35408535--35408565 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
35408525 TATTTAGTCT
35408535 TTAAAAGAAAAAAAG
1 TTAAAAGAAAAAAAG
*
35408550 TTAAAGGAAAAAAAG
1 TTAAAAGAAAAAAAG
35408565 T
1 T
35408566 AGCCAATTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.16, T:0.16
Consensus pattern (15 bp):
TTAAAAGAAAAAAAG
Found at i:35426021 original size:162 final size:159
Alignment explanation
Indices: 35425745--35426041 Score: 393
Period size: 162 Copynumber: 1.8 Consensus size: 159
35425735 TAGAAAAACG
* * *
35425745 AGCCCGTACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCGCAATGGAGACCAGGTACGAGACT
1 AGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCACAATGAAGACCAGGTACGAGACT
* * *
35425810 GCCTTGTTGACCCTCTCTGCATAAGCAAAGAATAATGTTACAGGAGGAACTTACACAAATTCTTA
66 GCCGTGTTGACCCTCTCTGCAGAAGCAAAGAATAA--TTACAGGAGGAACTTACACAAATTC-AA
35425875 AAGAAAGGGACTCCAGCAGAAGTACGAGAACA
128 AAGAAAGGGACTCCAGCAGAAGTACGAGAACA
* * * *
35425907 AGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCACACTGAAGA-CTGAGTACGGGAT
1 AGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCACAATGAAGACCAG-GTACGAGAC
* *
35425971 TGCCGTGTTGGA-CCTCTCTGCGTTAGAAGCAAAGAATAA-TACATGAGGAACTTATACAAATTC
65 TGCCGTGTT-GACCCTCTCTGC---AGAAGCAAAGAATAATTACAGGAGGAACTTACACAAATTC
35426034 AAAAGAAA
126 AAAAGAAA
35426042 AGCATCAAGT
Statistics
Matches: 118, Mismatches: 12, Indels: 11
0.84 0.09 0.08
Matches are distributed among these distances:
161 9 0.08
162 93 0.79
163 2 0.02
165 14 0.12
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (159 bp):
AGCCCATACTCCTCTCCTATTTGAAGAATTCTGAGAAGTCCACAATGAAGACCAGGTACGAGACT
GCCGTGTTGACCCTCTCTGCAGAAGCAAAGAATAATTACAGGAGGAACTTACACAAATTCAAAAG
AAAGGGACTCCAGCAGAAGTACGAGAACA
Found at i:35437872 original size:10 final size:10
Alignment explanation
Indices: 35437848--35437899 Score: 52
Period size: 10 Copynumber: 5.0 Consensus size: 10
35437838 ATAAAATCTA
35437848 TATTT-ATTT
1 TATTTAATTT
35437857 TAATTTAATTT
1 T-ATTTAATTT
*
35437868 GATTTAAATTT
1 TATTT-AATTT
*
35437879 TAATTAATTT
1 TATTTAATTT
35437889 TATTTATATTT
1 TATTTA-ATTT
35437900 ATAAATAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 1 0.03
10 18 0.51
11 16 0.46
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (10 bp):
TATTTAATTT
Found at i:35465893 original size:28 final size:28
Alignment explanation
Indices: 35465862--35465961 Score: 78
Period size: 30 Copynumber: 3.4 Consensus size: 28
35465852 ACTTATTTAT
35465862 ATTATAAAAATCTAATAAATTATTAAAA
1 ATTATAAAAATCTAATAAATTATTAAAA
*
35465890 ATTAT-AAAAT-TAATAACATTTATTTGAAAT
1 ATTATAAAAATCTAATAA-A-TTA-TT-AAAA
* *** *
35465920 TTTATAAAAGGGTATATAAATTCTTAAAA
1 ATTATAAAAATCTA-ATAAATTATTAAAA
35465949 ACTTATAAAAATC
1 A-TTATAAAAATC
35465962 ATTAAAAATC
Statistics
Matches: 54, Mismatches: 10, Indels: 14
0.69 0.13 0.18
Matches are distributed among these distances:
26 6 0.11
27 6 0.11
28 8 0.15
29 5 0.09
30 17 0.31
31 5 0.09
32 3 0.06
33 4 0.07
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.38
Consensus pattern (28 bp):
ATTATAAAAATCTAATAAATTATTAAAA
Found at i:35466219 original size:3 final size:3
Alignment explanation
Indices: 35466211--35466245 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
35466201 ATAACAAAAT
35466211 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
35466246 GTATTTGTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:35471801 original size:16 final size:17
Alignment explanation
Indices: 35471765--35471804 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
35471755 ATAGAATAAA
*
35471765 AAAATATGCAATTATAT
1 AAAATATGCAATTACAT
*
35471782 AAAATATGTAA-TACAT
1 AAAATATGCAATTACAT
35471798 AAAATAT
1 AAAATAT
35471805 TACATTTTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.52
17 10 0.48
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.33
Consensus pattern (17 bp):
AAAATATGCAATTACAT
Found at i:35472348 original size:17 final size:17
Alignment explanation
Indices: 35472326--35472390 Score: 55
Period size: 17 Copynumber: 3.9 Consensus size: 17
35472316 GATTATTTTT
*
35472326 TAAAAATATTTTTGGGA
1 TAAAAATATTTTTGAGA
35472343 TAAAAAGTA-TTTTGAGA
1 TAAAAA-TATTTTTGAGA
* ** *
35472360 TAAAAGTATTACT-AAA
1 TAAAAATATTTTTGAGA
35472376 T-AAAATATTTTTGAG
1 TAAAAATATTTTTGAG
35472391 TTTTTTAAAA
Statistics
Matches: 36, Mismatches: 9, Indels: 7
0.69 0.17 0.13
Matches are distributed among these distances:
15 8 0.22
16 6 0.17
17 20 0.56
18 2 0.06
ACGTcount: A:0.46, C:0.02, G:0.14, T:0.38
Consensus pattern (17 bp):
TAAAAATATTTTTGAGA
Found at i:35472364 original size:16 final size:17
Alignment explanation
Indices: 35472326--35472369 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
35472316 GATTATTTTT
*
35472326 TAAAAA-TATTTTTGGGA
1 TAAAAAGTA-TTTTGAGA
35472343 TAAAAAGTATTTTGAGA
1 TAAAAAGTATTTTGAGA
35472360 T-AAAAGTATT
1 TAAAAAGTATT
35472370 ACTAAATAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
16 9 0.36
17 14 0.56
18 2 0.08
ACGTcount: A:0.45, C:0.00, G:0.16, T:0.39
Consensus pattern (17 bp):
TAAAAAGTATTTTGAGA
Found at i:35474663 original size:36 final size:38
Alignment explanation
Indices: 35474611--35474684 Score: 102
Period size: 36 Copynumber: 2.0 Consensus size: 38
35474601 GAGTAATTTC
35474611 ATATGACAAATTCATATGATA-AAAT-TTTAAATTATTAA
1 ATATGACAAATTCATAT-ATATAAATGTTTAAA-TATTAA
35474649 ATATGA-AAA-TCATATATATAAATGTTTAAATATTAA
1 ATATGACAAATTCATATATATAAATGTTTAAATATTAA
35474685 TTAATAAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
35 3 0.09
36 16 0.47
37 9 0.26
38 6 0.18
ACGTcount: A:0.51, C:0.04, G:0.05, T:0.39
Consensus pattern (38 bp):
ATATGACAAATTCATATATATAAATGTTTAAATATTAA
Found at i:35474811 original size:23 final size:22
Alignment explanation
Indices: 35474752--35474823 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 22
35474742 GAGAGTACCG
* *
35474752 AAGTACTATACAGAGAGCACAT
1 AAGTACTAAACAGAGAGCACAC
*
35474774 AAGTGCTAGGCAACAGAGAGCACAC
1 AAGTACTA---AACAGAGAGCACAC
*
35474799 AGAGTACTAAACAGAGAGTACAC
1 A-AGTACTAAACAGAGAGCACAC
35474822 AA
1 AA
35474824 AGTATTGAGC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
22 8 0.20
23 14 0.34
25 13 0.32
26 6 0.15
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (22 bp):
AAGTACTAAACAGAGAGCACAC
Found at i:35474827 original size:23 final size:23
Alignment explanation
Indices: 35474742--35474827 Score: 70
Period size: 23 Copynumber: 3.7 Consensus size: 23
35474732 TTCGATATTG
* *
35474742 GAGAGTAC-CGAAGTACTATACA
1 GAGAGTACACAAAGTACTAAACA
*
35474764 GAGAG--CACATAAGTGCTAGGCAACA
1 GAGAGTACACA-AAGTACTA---AACA
* *
35474789 GAGAGCACACAGAGTACTAAACA
1 GAGAGTACACAAAGTACTAAACA
35474812 GAGAGTACACAAAGTA
1 GAGAGTACACAAAGTA
35474828 TTGAGCATAC
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
20 1 0.02
21 1 0.02
22 12 0.24
23 18 0.36
25 8 0.16
26 6 0.12
27 4 0.08
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (23 bp):
GAGAGTACACAAAGTACTAAACA
Found at i:35474859 original size:16 final size:16
Alignment explanation
Indices: 35474818--35474861 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
35474808 AACAGAGAGT
**
35474818 ACACAAAGTATTGAGC
1 ACACAAAGTGCTGAGC
*
35474834 ATACAAAGTGCTGAGC
1 ACACAAAGTGCTGAGC
35474850 ACACAAAGTGCT
1 ACACAAAGTGCT
35474862 AATCGGAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.41, C:0.20, G:0.20, T:0.18
Consensus pattern (16 bp):
ACACAAAGTGCTGAGC
Found at i:35474876 original size:23 final size:23
Alignment explanation
Indices: 35474846--35474895 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
35474836 ACAAAGTGCT
35474846 GAGCACACAAAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCGGA
*
35474869 GAGCACACACAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCGGA
35474892 GAGC
1 GAGC
35474896 GCGCTAGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.36, C:0.24, G:0.28, T:0.12
Consensus pattern (23 bp):
GAGCACACAAAGTGCTAATCGGA
Found at i:35476988 original size:14 final size:14
Alignment explanation
Indices: 35476969--35477030 Score: 66
Period size: 14 Copynumber: 4.9 Consensus size: 14
35476959 AGAATAGATT
35476969 TTTAATTAAATAAA
1 TTTAATTAAATAAA
*
35476983 TTTAATTAATTAAA
1 TTTAATTAAATAAA
35476997 -TT--TT--A-AAA
1 TTTAATTAAATAAA
35477005 TTTAA-TAAATAAA
1 TTTAATTAAATAAA
35477018 TTTAATTAAATAA
1 TTTAATTAAATAA
35477031 GATACAGCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 14
0.71 0.04 0.25
Matches are distributed among these distances:
8 3 0.08
9 2 0.05
10 1 0.03
11 2 0.05
12 1 0.03
13 10 0.26
14 20 0.51
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (14 bp):
TTTAATTAAATAAA
Found at i:35477017 original size:21 final size:22
Alignment explanation
Indices: 35476980--35477020 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
35476970 TTAATTAAAT
*
35476980 AAATTTAATTAATTAAATTTTA
1 AAATTTAATTAAATAAATTTTA
35477002 AAATTTAA-TAAATAAATTT
1 AAATTTAATTAAATAAATTT
35477021 AATTAAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAATTTAATTAAATAAATTTTA
Found at i:35482813 original size:28 final size:30
Alignment explanation
Indices: 35482748--35482814 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 30
35482738 GGACTCTTGA
35482748 GGGTAAAAATGACAATTTTGGGAAAATTTGG
1 GGGTAAAAATGACAATTTT-GGAAAATTTGG
* * *
35482779 GGCTAAAAATGA-TATTTT-GAATATTTGG
1 GGGTAAAAATGACAATTTTGGAAAATTTGG
35482807 GGGTAAAA
1 GGGTAAAA
35482815 CGATAATCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 16 0.50
30 5 0.16
31 11 0.34
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31
Consensus pattern (30 bp):
GGGTAAAAATGACAATTTTGGAAAATTTGG
Found at i:35482903 original size:29 final size:28
Alignment explanation
Indices: 35482865--35482970 Score: 90
Period size: 29 Copynumber: 3.7 Consensus size: 28
35482855 TGGACATTCG
35482865 AGGGT-AAAATGATAATTTTGAAAGTTTT
1 AGGGTCAAAATG-TAATTTTGAAAGTTTT
* *
35482893 TGGGTCAAAATGGAATTTCT-AGAAGTTTT
1 AGGGTCAAAATGTAATTT-TGA-AAGTTTT
* * *
35482922 GGGGGCAAAAATGTAATTTTTGGAAGTTTT
1 AGGGTC-AAAATGTAA-TTTTGAAAGTTTT
* *
35482952 AGGGTTAAAATGGAATTTT
1 AGGGTCAAAATGTAATTTT
35482971 TGGAAGTTAG
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
28 14 0.23
29 26 0.42
30 19 0.31
31 3 0.05
ACGTcount: A:0.34, C:0.03, G:0.25, T:0.38
Consensus pattern (28 bp):
AGGGTCAAAATGTAATTTTGAAAGTTTT
Found at i:35482971 original size:29 final size:29
Alignment explanation
Indices: 35482880--35483073 Score: 149
Period size: 29 Copynumber: 6.6 Consensus size: 29
35482870 AAAATGATAA
* * *
35482880 TTTTGAAAGTTTTTGGGTCAAAATGGAAT
1 TTTTGGAAGTTTTAGGGTAAAAATGGAAT
* * * * *
35482909 TTCTAGAAGTTTTGGGGGCAAAAATGTAAT
1 TTTTGGAAGTTTT-AGGGTAAAAATGGAAT
*
35482939 TTTTGGAAGTTTTAGGGTTAAAATGGAAT
1 TTTTGGAAGTTTTAGGGTAAAAATGGAAT
** * *
35482968 TTTTGGAAGTTAGAGGGAAAAAATAGAAT
1 TTTTGGAAGTTTTAGGGTAAAAATGGAAT
* * *
35482997 TTTTGGAA--TTTCGGAGACAAAAATGTAAT
1 TTTTGGAAGTTTTAGG-G-TAAAAATGGAAT
* * * *
35483026 TTTGGGGAGTTCTGAGGTTAAAAATGGAAT
1 TTTTGGAAGTT-TTAGGGTAAAAATGGAAT
*
35483056 TTTTGGAAGTTTGAGGGT
1 TTTTGGAAGTTTTAGGGT
35483074 TTAGGGTTTA
Statistics
Matches: 125, Mismatches: 34, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
27 3 0.02
28 1 0.01
29 75 0.60
30 42 0.34
31 1 0.01
32 3 0.02
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.36
Consensus pattern (29 bp):
TTTTGGAAGTTTTAGGGTAAAAATGGAAT
Found at i:35483127 original size:29 final size:29
Alignment explanation
Indices: 35483094--35483230 Score: 150
Period size: 29 Copynumber: 4.7 Consensus size: 29
35483084 AAATTTTTGG
35483094 AATTTTTGGAAGTTTAGGGGCAAAAATGT
1 AATTTTTGGAAGTTTAGGGGCAAAAATGT
* *
35483123 AATTTTTGTG-AGTTTCGAGGTCAAAAATGT
1 AATTTTTG-GAAGTTTAG-GGGCAAAAATGT
* *
35483153 AATTTTTGGAAGTTCAGGGGTAAAAATGT
1 AATTTTTGGAAGTTTAGGGGCAAAAATGT
* * * * *
35483182 AATTTTTAGAAGTTTCGAGGCCAAAATAT
1 AATTTTTGGAAGTTTAGGGGCAAAAATGT
*
35483211 AATTTTTGGGCAGTTTAGGG
1 AATTTTT-GGAAGTTTAGGG
35483231 ACCTCCAATG
Statistics
Matches: 87, Mismatches: 17, Indels: 7
0.78 0.15 0.06
Matches are distributed among these distances:
29 54 0.62
30 33 0.38
ACGTcount: A:0.32, C:0.06, G:0.26, T:0.36
Consensus pattern (29 bp):
AATTTTTGGAAGTTTAGGGGCAAAAATGT
Found at i:35483127 original size:129 final size:130
Alignment explanation
Indices: 35482962--35483201 Score: 328
Period size: 129 Copynumber: 1.9 Consensus size: 130
35482952 AGGGTTAAAA
35482962 TGGAATTTTTGGAAGTTAGAGGGAAAAAATAGAATTTTTG-GAATTTCG-GAGACAAAAATGTAA
1 TGGAATTTTTGGAAGTTAGAGGGAAAAAATAGAATTTTTGTGAATTTCGAG-GACAAAAATGTAA
* * * *
35483025 TTTTGGGGAGTTCTGAGGTTAAAAATGGAATTTTTGGAAGTTT-GAGGGTTTAGGGTTTAAAATT
65 TTTTGGGAAGTTCAG-GGGTAAAAATGGAATTTTTAGAAGTTTCGAGGGTTTAGGGTTTAAAATT
35483089 TT
129 TT
* * *
35483091 TGGAATTTTTGGAAGTTTAG-GGGCAAAAAT-GTAATTTTTGTGAGTTTCGAGGTCAAAAATGTA
1 TGGAATTTTTGGAAG-TTAGAGGGAAAAAATAG-AATTTTTGTGAATTTCGAGGACAAAAATGTA
* *
35483154 ATTTTTGGAAGTTCAGGGGTAAAAATGTAATTTTTAGAAGTTTCGAGG
64 ATTTTGGGAAGTTCAGGGGTAAAAATGGAATTTTTAGAAGTTTCGAGG
35483202 CCAAAATATA
Statistics
Matches: 97, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
128 1 0.01
129 56 0.58
130 39 0.40
131 1 0.01
ACGTcount: A:0.33, C:0.03, G:0.28, T:0.37
Consensus pattern (130 bp):
TGGAATTTTTGGAAGTTAGAGGGAAAAAATAGAATTTTTGTGAATTTCGAGGACAAAAATGTAAT
TTTGGGAAGTTCAGGGGTAAAAATGGAATTTTTAGAAGTTTCGAGGGTTTAGGGTTTAAAATTTT
Found at i:35483186 original size:59 final size:58
Alignment explanation
Indices: 35483094--35483219 Score: 182
Period size: 59 Copynumber: 2.2 Consensus size: 58
35483084 AAATTTTTGG
* * *
35483094 AATTTTTGGAAGTTTAGGGGCAAAAATGTAATTTTT-GTGAGTTTCGAGGTCAAAAATGT
1 AATTTTTGGAAGTTCAGGGGCAAAAATGTAATTTTTAG-AAGTTTCGAGG-CAAAAATAT
* *
35483153 AATTTTTGGAAGTTCAGGGGTAAAAATGTAATTTTTAGAAGTTTCGAGGCCAAAATAT
1 AATTTTTGGAAGTTCAGGGGCAAAAATGTAATTTTTAGAAGTTTCGAGGCAAAAATAT
35483211 AATTTTTGG
1 AATTTTTGG
35483220 GCAGTTTAGG
Statistics
Matches: 61, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
58 16 0.26
59 44 0.72
60 1 0.02
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.37
Consensus pattern (58 bp):
AATTTTTGGAAGTTCAGGGGCAAAAATGTAATTTTTAGAAGTTTCGAGGCAAAAATAT
Found at i:35484862 original size:6 final size:6
Alignment explanation
Indices: 35484792--35484878 Score: 54
Period size: 6 Copynumber: 14.7 Consensus size: 6
35484782 AATATTTATA
* * * * *
35484792 TTAAAT CTTAAAG TTAAAT ATAAA- TTAAAA TTAAAA TTAAATT TTAATT
1 TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA-T TTAAAT
* * * *
35484841 TTAATT TTAAA- ATAAAT TTAAAC TTAAA- ATAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
35484879 TCTTTAAAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 9
0.75 0.14 0.11
Matches are distributed among these distances:
5 12 0.19
6 43 0.67
7 9 0.14
ACGTcount: A:0.54, C:0.02, G:0.01, T:0.43
Consensus pattern (6 bp):
TTAAAT
Found at i:35484868 original size:12 final size:11
Alignment explanation
Indices: 35484779--35484868 Score: 63
Period size: 12 Copynumber: 7.5 Consensus size: 11
35484769 ATTATTGGAC
*
35484779 ATTAATATTTAT
1 ATTAA-ATTTAA
35484791 ATTAAATCTTAA
1 ATTAAAT-TTAA
*
35484803 AGTTAAATATAA
1 A-TTAAATTTAA
*
35484815 ATTAAAATTAAA
1 ATT-AAATTTAA
35484827 ATTAAATTTTAA
1 ATTAAA-TTTAA
* *
35484839 TTTTAATTTTAA
1 -ATTAAATTTAA
*
35484851 AATAAATTTAA
1 ATTAAATTTAA
35484862 ACTTAAA
1 A-TTAAA
35484869 ATAAATTTAA
Statistics
Matches: 61, Mismatches: 11, Indels: 12
0.73 0.13 0.14
Matches are distributed among these distances:
11 16 0.26
12 35 0.57
13 10 0.16
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.44
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:35484887 original size:18 final size:18
Alignment explanation
Indices: 35484840--35484897 Score: 84
Period size: 17 Copynumber: 3.3 Consensus size: 18
35484830 AAATTTTAAT
35484840 TTTAAT-TTTAAAATAAA
1 TTTAATCTTTAAAATAAA
*
35484857 TTTAAAC-TTAAAATAAA
1 TTTAATCTTTAAAATAAA
35484874 TTTAATCTTTAAAATAAA
1 TTTAATCTTTAAAATAAA
35484892 TCTTAA
1 T-TTAA
35484898 AAATGAGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
17 21 0.58
18 11 0.31
19 4 0.11
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (18 bp):
TTTAATCTTTAAAATAAA
Found at i:35489014 original size:17 final size:18
Alignment explanation
Indices: 35488977--35489014 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
35488967 ATTACAATTA
* *
35488977 TTAATTTTAAAAATTGTG
1 TTAATTTTAAAAATAGAG
35488995 TTAATTTT-AAAATAGAG
1 TTAATTTTAAAAATAGAG
35489012 TTA
1 TTA
35489015 TTATTTGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (18 bp):
TTAATTTTAAAAATAGAG
Found at i:35493264 original size:29 final size:30
Alignment explanation
Indices: 35493232--35493291 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
35493222 TTTAACTTGT
35493232 AATCAAATCTA-TTTTTATATTACTATTGA
1 AATCAAATCTATTTTTTATATTACTATTGA
35493261 AATCAAATCTATTTTTTATATTACTATTGA
1 AATCAAATCTATTTTTTATATTACTATTGA
35493291 A
1 A
35493292 GGGATTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 11 0.37
30 19 0.63
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.48
Consensus pattern (30 bp):
AATCAAATCTATTTTTTATATTACTATTGA
Found at i:35496033 original size:15 final size:14
Alignment explanation
Indices: 35496013--35496052 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
35496003 TTTAAATTAC
35496013 ATAATATATATGAAA
1 ATAATATATAT-AAA
35496028 ATAATATAATATAAA
1 ATAATAT-ATATAAA
*
35496043 ATATTATATA
1 ATAATATATA
35496053 CTTAAAAACA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 3 0.13
15 16 0.70
16 4 0.17
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.38
Consensus pattern (14 bp):
ATAATATATATAAA
Found at i:35497754 original size:32 final size:32
Alignment explanation
Indices: 35497699--35497760 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
35497689 TTTTTTTAAT
*
35497699 ATTTTAATATTTTATCAGTAATTTTATTTTGA
1 ATTTTAATATTTTATCAGTAATTTAATTTTGA
**
35497731 ATTTTAATATTTTTATTTG-AATTTAATTTT
1 ATTTTAATA-TTTTATCAGTAATTTAATTTT
35497761 TTTAAAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 19 0.73
33 7 0.27
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (32 bp):
ATTTTAATATTTTATCAGTAATTTAATTTTGA
Found at i:35497763 original size:20 final size:21
Alignment explanation
Indices: 35497720--35497764 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
35497710 TTATCAGTAA
35497720 TTTTATTTTGAATTTTAATAT
1 TTTTATTTTGAATTTTAATAT
*
35497741 TTTTA-TTTGAA-TTTAATTT
1 TTTTATTTTGAATTTTAATAT
35497760 TTTTA
1 TTTTA
35497765 AAATAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.52
20 6 0.26
21 5 0.22
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (21 bp):
TTTTATTTTGAATTTTAATAT
Found at i:35499208 original size:37 final size:38
Alignment explanation
Indices: 35499174--35499250 Score: 93
Period size: 40 Copynumber: 2.0 Consensus size: 38
35499164 TTTAAATATA
35499174 AATTATTAAAATATAACCTA-ATAAAAATAAAAATAAT
1 AATTATTAAAATATAACCTATATAAAAATAAAAATAAT
* * * *
35499211 TATTTTTATAATTTAACCTACTTATAAAAATAAAAATAAT
1 AATTATTAAAATATAACCTA--TATAAAAATAAAAATAAT
35499251 TATTTTTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
37 16 0.48
40 17 0.52
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (38 bp):
AATTATTAAAATATAACCTATATAAAAATAAAAATAAT
Found at i:35499245 original size:40 final size:40
Alignment explanation
Indices: 35499194--35499278 Score: 152
Period size: 40 Copynumber: 2.1 Consensus size: 40
35499184 ATATAACCTA
35499194 ATAAAAATAAAAATAATTATTTTTATAATTTAACCTACTT
1 ATAAAAATAAAAATAATTATTTTTATAATTTAACCTACTT
* *
35499234 ATAAAAATAAAAATAATTATTTTTGTAGTTTAACCTACTT
1 ATAAAAATAAAAATAATTATTTTTATAATTTAACCTACTT
35499274 ATAAA
1 ATAAA
35499279 TATGGTCGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (40 bp):
ATAAAAATAAAAATAATTATTTTTATAATTTAACCTACTT
Found at i:35508128 original size:22 final size:22
Alignment explanation
Indices: 35508102--35508172 Score: 79
Period size: 22 Copynumber: 3.2 Consensus size: 22
35508092 ATATCCAAAC
*
35508102 AATAACAACAAAATAGTTACAA
1 AATAACAACAAAATAGTAACAA
* * *
35508124 TATAATAACAAAATGGTAACAA
1 AATAACAACAAAATAGTAACAA
* * *
35508146 AACAACAACATAACAGTAACAA
1 AATAACAACAAAATAGTAACAA
35508168 AATAA
1 AATAA
35508173 TAGTAAACAC
Statistics
Matches: 38, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 38 1.00
ACGTcount: A:0.63, C:0.14, G:0.06, T:0.17
Consensus pattern (22 bp):
AATAACAACAAAATAGTAACAA
Found at i:35512823 original size:9 final size:9
Alignment explanation
Indices: 35512787--35512848 Score: 54
Period size: 9 Copynumber: 6.6 Consensus size: 9
35512777 TAAATATATA
35512787 TTTTATAAT
1 TTTTATAAT
* *
35512796 ATTTGTAAGT
1 TTTTATAA-T
35512806 TTTTAATAAT
1 TTTT-ATAAT
35512816 TTTTATAAT
1 TTTTATAAT
35512825 TTTATATCAAT
1 TTT-TAT-AAT
*
35512836 TTTAAT-AT
1 TTTTATAAT
35512844 TTTTA
1 TTTTA
35512849 GTATCTCATA
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
8 6 0.14
9 14 0.33
10 14 0.33
11 9 0.21
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTATAAT
Found at i:35512838 original size:20 final size:21
Alignment explanation
Indices: 35512813--35512853 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
35512803 AGTTTTTAAT
*
35512813 AATTTTTATAATTTTA-TATC
1 AATTTTAATAATTTTAGTATC
*
35512833 AATTTTAATATTTTTAGTATC
1 AATTTTAATAATTTTAGTATC
35512854 TCATAATTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.34, C:0.05, G:0.02, T:0.59
Consensus pattern (21 bp):
AATTTTAATAATTTTAGTATC
Found at i:35523893 original size:31 final size:31
Alignment explanation
Indices: 35523832--35523910 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
35523822 AGATTTTTTA
*
35523832 TAATTTATAAAATTTTAAATAATAATAAAA-T
1 TAATTT-TAATATTTTAAATAATAATAAAATT
35523863 TACATTTTAATATTTTAAA-AATAATAAAAATT
1 TA-ATTTTAATATTTTAAATAATAAT-AAAATT
*
35523895 TAATTTAAAT-TTTTAA
1 TAATTTTAATATTTTAA
35523911 TTGTAAGAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
30 12 0.28
31 24 0.56
32 7 0.16
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (31 bp):
TAATTTTAATATTTTAAATAATAATAAAATT
Found at i:35523902 original size:30 final size:30
Alignment explanation
Indices: 35523841--35523907 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 30
35523831 ATAATTTATA
35523841 AAATTTTAAATAATAATAAAATTACATTTT
1 AAATTTTAAATAATAATAAAATTACATTTT
35523871 AATATTTTAAA-AATAATAAAAATTTA-A-TTT
1 AA-ATTTTAAATAATAAT-AAAA-TTACATTTT
35523901 AAATTTT
1 AAATTTT
35523908 TAATTGTAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
29 5 0.15
30 13 0.38
31 13 0.38
32 3 0.09
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (30 bp):
AAATTTTAAATAATAATAAAATTACATTTT
Found at i:35542525 original size:2 final size:2
Alignment explanation
Indices: 35542513--35542563 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
35542503 CGTGAAAGAA
*
35542513 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
35542555 GT AT AT AT A
1 AT AT AT AT A
35542564 AATGTTAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
AT
Found at i:35548500 original size:92 final size:92
Alignment explanation
Indices: 35548372--35548715 Score: 512
Period size: 92 Copynumber: 3.8 Consensus size: 92
35548362 AGTTGCCTAA
* * *
35548372 AAATTAATTTAGATAACTTTATTAAATATGATTGATTAGATTTAGTTTTTTTATTATAAATATTT
1 AAATTAATTTAAATAATTTTATTAAATATGATTGATTAGATTTAGTTTTTTTATGATAAATATTT
*
35548437 TTTTAAATGATTGATTAAATAAAGAAT
66 TTTTAAATGATTGATTAAATAAACAAT
* * * *
35548464 AAATTAATTTAAATAATTTTATTAAATATAATTGATTGGATTTAATATTTTTATGATAAATA--T
1 AAATTAATTTAAATAATTTTATTAAATATGATTGATTAGATTTAGTTTTTTTATGATAAATATTT
* *
35548527 TTTTAAATGATTGATTGAATAAATAAT
66 TTTTAAATGATTGATTAAATAAACAAT
* *
35548554 AAATTAATTTAAACAATTTTATTAAATATGATTGATTAGGTTTAGTTTTTTTATGATAAATATTT
1 AAATTAATTTAAATAATTTTATTAAATATGATTGATTAGATTTAGTTTTTTTATGATAAATATTT
35548619 TTTTAAATGATTGATTAAATAAACAAT
66 TTTTAAATGATTGATTAAATAAACAAT
* * * * *
35548646 AAATTAATTTAAATAATTTTATTAAATATGATTGATTGGATTTAATATTTCTACGATAAATATAT
1 AAATTAATTTAAATAATTTTATTAAATATGATTGATTAGATTTAGTTTTTTTATGATAAATAT-T
35548711 TTTTT
65 TTTTT
35548716 CTTGAATGGT
Statistics
Matches: 225, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
90 82 0.36
92 137 0.61
93 6 0.03
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (92 bp):
AAATTAATTTAAATAATTTTATTAAATATGATTGATTAGATTTAGTTTTTTTATGATAAATATTT
TTTTAAATGATTGATTAAATAAACAAT
Found at i:35548682 original size:182 final size:183
Alignment explanation
Indices: 35548372--35548713 Score: 596
Period size: 182 Copynumber: 1.9 Consensus size: 183
35548362 AGTTGCCTAA
* * *
35548372 AAATTAATTTAGATAACTTTATTAAATATGATTGATTAGATTTAGTTTTTTTATTATAAATATTT
1 AAATTAATTTAAACAACTTTATTAAATATGATTGATTAGATTTAGTTTTTTTATGATAAATATTT
*
35548437 TTTTAAATGATTGATTAAATAAAGAATAAATTAATTTAAATAATTTTATTAAATATAATTGATTG
66 TTTTAAATGATTGATTAAATAAACAATAAATTAATTTAAATAATTTTATTAAATATAATTGATTG
* *
35548502 GATTTAATATTTTTATGATAAATAT-TTTTAAATGATTGATTGAATAAATAAT
131 GATTTAATATTTCTACGATAAATATATTTTAAATGATTGATTGAATAAATAAT
* *
35548554 AAATTAATTTAAACAATTTTATTAAATATGATTGATTAGGTTTAGTTTTTTTATGATAAATATTT
1 AAATTAATTTAAACAACTTTATTAAATATGATTGATTAGATTTAGTTTTTTTATGATAAATATTT
*
35548619 TTTTAAATGATTGATTAAATAAACAATAAATTAATTTAAATAATTTTATTAAATATGATTGATTG
66 TTTTAAATGATTGATTAAATAAACAATAAATTAATTTAAATAATTTTATTAAATATAATTGATTG
35548684 GATTTAATATTTCTACGATAAATATATTTT
131 GATTTAATATTTCTACGATAAATATATTTT
35548714 TTCTTGAATG
Statistics
Matches: 150, Mismatches: 9, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
182 146 0.97
183 4 0.03
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.48
Consensus pattern (183 bp):
AAATTAATTTAAACAACTTTATTAAATATGATTGATTAGATTTAGTTTTTTTATGATAAATATTT
TTTTAAATGATTGATTAAATAAACAATAAATTAATTTAAATAATTTTATTAAATATAATTGATTG
GATTTAATATTTCTACGATAAATATATTTTAAATGATTGATTGAATAAATAAT
Found at i:35563061 original size:2 final size:2
Alignment explanation
Indices: 35563056--35563080 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
35563046 CCCCCCCCCC
35563056 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
35563081 AATATCTCAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:35567264 original size:2 final size:2
Alignment explanation
Indices: 35567257--35567300 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
35567247 AACCCTCAAA
35567257 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A- AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
35567298 AG A
1 AG A
35567301 TAGGGTTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:35583443 original size:15 final size:15
Alignment explanation
Indices: 35583423--35583466 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 15
35583413 TGATCTAAAT
35583423 ATTGTAAATATTTAA
1 ATTGTAAATATTTAA
*
35583438 ATTGTAAAT-TTT-T
1 ATTGTAAATATTTAA
*
35583451 ATTTTAAATATTTAA
1 ATTGTAAATATTTAA
35583466 A
1 A
35583467 ATAAAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
13 8 0.33
14 6 0.25
15 10 0.42
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (15 bp):
ATTGTAAATATTTAA
Found at i:35583474 original size:28 final size:28
Alignment explanation
Indices: 35583422--35583479 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
35583412 ATGATCTAAA
* **
35583422 TATTGTAAATATTTAAATTGTAAATTTT
1 TATTGTAAATATTTAAAATAAAAATTTT
*
35583450 TATTTTAAATATTTAAAATAAAAATTTT
1 TATTGTAAATATTTAAAATAAAAATTTT
35583478 TA
1 TA
35583480 ATAATTAAGT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (28 bp):
TATTGTAAATATTTAAAATAAAAATTTT
Found at i:35591577 original size:12 final size:12
Alignment explanation
Indices: 35591560--35591584 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35591550 TTCAAGGGGG
35591560 AATGTATTAGAA
1 AATGTATTAGAA
35591572 AATGTATTAGAA
1 AATGTATTAGAA
35591584 A
1 A
35591585 CAATGAATAA
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:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
AATGTATTAGAA
Found at i:35593924 original size:31 final size:31
Alignment explanation
Indices: 35593877--35593937 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
35593867 TTGATCATTA
*
35593877 AATTGTTCAAAAGTTTTTATTTAAGTCACTG
1 AATTATTCAAAAGTTTTTATTTAAGTCACTG
*
35593908 AATTATTCGAAAGTTTTTATTTAAGTCACT
1 AATTATTCAAAAGTTTTTATTTAAGTCACT
35593938 AGGCTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (31 bp):
AATTATTCAAAAGTTTTTATTTAAGTCACTG
Found at i:35597640 original size:6 final size:6
Alignment explanation
Indices: 35597629--35597660 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
35597619 TAAGCTATTG
35597629 TATTTT TATTTT TATTTT TATTTT TATTTT TA
1 TATTTT TATTTT TATTTT TATTTT TATTTT TA
35597661 AGAATTTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
TATTTT
Found at i:35600445 original size:2 final size:2
Alignment explanation
Indices: 35600438--35600463 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35600428 TGTAGCAAAG
35600438 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
35600464 CTTTGGACTG
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:35607531 original size:15 final size:15
Alignment explanation
Indices: 35607513--35607545 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35607503 TTATCATTAT
*
35607513 TAATTTAAAATTTTA
1 TAATTTAAAACTTTA
35607528 TAATTTAAAACTTTA
1 TAATTTAAAACTTTA
35607543 TAA
1 TAA
35607546 AATGTTTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (15 bp):
TAATTTAAAACTTTA
Found at i:35615056 original size:22 final size:23
Alignment explanation
Indices: 35615019--35615062 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
35615009 AACATCAAAT
35615019 TATTTTTTAAA-ATTTTAATAAA
1 TATTTTTTAAATATTTTAATAAA
* *
35615041 TATTTTTTATATTTTTTAATAA
1 TATTTTTTAAATATTTTAATAA
35615063 TTTTAATGAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (23 bp):
TATTTTTTAAATATTTTAATAAA
Found at i:35617963 original size:47 final size:48
Alignment explanation
Indices: 35617912--35618014 Score: 110
Period size: 45 Copynumber: 2.2 Consensus size: 48
35617902 CTATTTTAAG
*
35617912 ATTTTTTAAAT-AATTTTTTGAG-TATTGA-GATTTTTTAGGCTTTTATT
1 ATTTTTTAAATGAATTTTTTGAGATATTAATGATTTTTTA-G-TTTTATT
* *
35617959 A-TTTTT--ATGAATTTTTTGAGATTTTAATGATTTTTTAGTTTTGTT
1 ATTTTTTAAATGAATTTTTTGAGATATTAATGATTTTTTAGTTTTATT
35618004 ATATTTTTAAA
1 AT-TTTTTAAA
35618015 AATATATGTG
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
44 2 0.04
45 18 0.39
46 10 0.22
47 15 0.33
49 1 0.02
ACGTcount: A:0.26, C:0.01, G:0.12, T:0.61
Consensus pattern (48 bp):
ATTTTTTAAATGAATTTTTTGAGATATTAATGATTTTTTAGTTTTATT
Found at i:35637853 original size:19 final size:19
Alignment explanation
Indices: 35637815--35637853 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
35637805 ATAATATATA
* *
35637815 TATATATATATAGCTGGAT
1 TATAGATATATAGCTAGAT
*
35637834 TATAGATATATTGCTAGAT
1 TATAGATATATAGCTAGAT
35637853 T
1 T
35637854 TATTGCAATG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.05, G:0.15, T:0.44
Consensus pattern (19 bp):
TATAGATATATAGCTAGAT
Found at i:35643804 original size:28 final size:29
Alignment explanation
Indices: 35643746--35643832 Score: 86
Period size: 28 Copynumber: 3.0 Consensus size: 29
35643736 TCGAGTTCTT
* * *
35643746 AAAATTTAATAAATTTAATTTTTAATGTTTA
1 AAAAATTAATACATTTAA--TTTAATTTTTA
* *
35643777 CAAAATTTAT-CATTTAATTTAATTTTTA
1 AAAAATTAATACATTTAATTTAATTTTTA
* *
35643805 AAAAATTAATAGATTTAATTTATTTTTT
1 AAAAATTAATACATTTAATTTAATTTTT
35643833 TCACTGAATC
Statistics
Matches: 46, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
28 18 0.39
29 15 0.33
30 6 0.13
31 7 0.15
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (29 bp):
AAAAATTAATACATTTAATTTAATTTTTA
Found at i:35653887 original size:29 final size:30
Alignment explanation
Indices: 35653854--35653912 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
35653844 TTTAATTTAA
*
35653854 TATGTAATATTATATAT-AAATTTTGATTT
1 TATGTAATATTATACATGAAATTTTGATTT
*
35653883 TATGTAATTTTATACATGAAATTTTGATTT
1 TATGTAATATTATACATGAAATTTTGATTT
35653913 CATATAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 15 0.56
30 12 0.44
ACGTcount: A:0.36, C:0.02, G:0.08, T:0.54
Consensus pattern (30 bp):
TATGTAATATTATACATGAAATTTTGATTT
Found at i:35653907 original size:30 final size:29
Alignment explanation
Indices: 35653854--35653932 Score: 95
Period size: 30 Copynumber: 2.7 Consensus size: 29
35653844 TTTAATTTAA
* *
35653854 TATGTAATATTATATATAAATTTTGATTT
1 TATGTAATTTTATACATAAATTTTGATTT
35653883 TATGTAATTTTATACATGAAATTTTGATTT
1 TATGTAATTTTATACAT-AAATTTTGATTT
* * *
35653913 CATATAAGTTTTATAAATAA
1 TATGTAA-TTTTATACATAA
35653933 TTAATATAAC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
29 15 0.35
30 19 0.44
31 9 0.21
ACGTcount: A:0.39, C:0.03, G:0.08, T:0.51
Consensus pattern (29 bp):
TATGTAATTTTATACATAAATTTTGATTT
Found at i:35666182 original size:6 final size:6
Alignment explanation
Indices: 35666171--35666200 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
35666161 TACCTTGACT
35666171 TAACCC TAACCC TAACCC TAACCC TAACCC
1 TAACCC TAACCC TAACCC TAACCC TAACCC
35666201 CACAAACCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.50, G:0.00, T:0.17
Consensus pattern (6 bp):
TAACCC
Found at i:35674517 original size:22 final size:22
Alignment explanation
Indices: 35674482--35674532 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
35674472 TACTTACCTT
* *
35674482 ATTTTTATGTAAAAATTTTTCAA
1 ATTTTTATGAAAAAATATTT-AA
35674505 ATTTTTAT-AAAAAATATTTAA
1 ATTTTTATGAAAAAATATTTAA
35674526 AGTTTTT
1 A-TTTTT
35674533 TTTTTACATT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.12
22 14 0.56
23 8 0.32
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTTTATGAAAAAATATTTAA
Found at i:35677442 original size:18 final size:17
Alignment explanation
Indices: 35677416--35677449 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
35677406 TTTTTTTCTC
35677416 TCTTTTCCTTGTCCTTG
1 TCTTTTCCTTGTCCTTG
35677433 TCTTTGTCCTTGTCCTT
1 TCTTT-TCCTTGTCCTT
35677450 CTTCTCCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.00, C:0.29, G:0.12, T:0.59
Consensus pattern (17 bp):
TCTTTTCCTTGTCCTTG
Found at i:35685607 original size:23 final size:23
Alignment explanation
Indices: 35685548--35685694 Score: 143
Period size: 23 Copynumber: 6.3 Consensus size: 23
35685538 ACACTAGCGC
* *
35685548 GCTCTCTATTTAGCAC-GTCTCGT
1 GCTCTCTAATTAGCACTGTGT-GT
* *
35685571 GCTCTCTGTTATTAGTACTGTGTGT
1 GCTCTC--TAATTAGCACTGTGTGT
*
35685596 GCTCTCTAATTAGCACTCTGTGT
1 GCTCTCTAATTAGCACTGTGTGT
* *
35685619 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTAATTAGCACTGTGTGT
* ** *
35685642 GCTCTCTGATTAATACTTTGTGT
1 GCTCTCTAATTAGCACTGTGTGT
* *
35685665 ACTCTCTATTTAGCACTGTGTGT
1 GCTCTCTAATTAGCACTGTGTGT
35685688 GCTCTCT
1 GCTCTCT
35685695 GTTGCCCAGC
Statistics
Matches: 103, Mismatches: 18, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
23 85 0.83
25 15 0.15
26 3 0.03
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (23 bp):
GCTCTCTAATTAGCACTGTGTGT
Found at i:35685648 original size:46 final size:46
Alignment explanation
Indices: 35685548--35685694 Score: 163
Period size: 46 Copynumber: 3.2 Consensus size: 46
35685538 ACACTAGCGC
* * *
35685548 GCTCTCTATTTAGCACGTCT-CGTGCTCTCTGTTATTAGTACTGTGTGT
1 GCTCTCTAATTAGCAC-TCTGTGTGCTCTCTG--ATTAGCACTGTGTGT
*
35685596 GCTCTCTAATTAGCACTCTGTGTGCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTAATTAGCACTCTGTGTGCTCTCTGATTAGCACTGTGTGT
* ** * *
35685642 GCTCTCTGATTAATACTTTGTGTACTCTCT-ATTTAGCACTGTGTGT
1 GCTCTCTAATTAGCACTCTGTGTGCTCTCTGA-TTAGCACTGTGTGT
35685688 GCTCTCT
1 GCTCTCT
35685695 GTTGCCCAGC
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
45 1 0.01
46 58 0.67
47 3 0.03
48 25 0.29
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.44
Consensus pattern (46 bp):
GCTCTCTAATTAGCACTCTGTGTGCTCTCTGATTAGCACTGTGTGT
Found at i:35685739 original size:69 final size:69
Alignment explanation
Indices: 35685569--35685740 Score: 208
Period size: 69 Copynumber: 2.5 Consensus size: 69
35685559 AGCACGTCTC
*
35685569 GTGCTCTCTGTTATTAGTACTGTGTGTGCTCTCTAATTAGCACTCTGTGTGCTCTCTGATTAGCA
1 GTGCTCTCTG--ATTAGTACTTTGTGTGCTCTCTAATTAGCACTCTGTGTGCTCTCTGATTAGCA
*
35685634 CTTTGT
64 CTTTAT
* * * *
35685640 GTGCTCTCTGATTAATACTTTGTGTACTCTCTATTTAGCACTGTGTGTGCTCTCTG-TTGCCCAG
1 GTGCTCTCTGATTAGTACTTTGTGTGCTCTCTAATTAGCACTCTGTGTGCTCTCTGATT----AG
35685704 CAC-TTAT
62 CACTTTAT
35685711 GTGCTCTCTG-TTAGTACTTTG-GTGCTCTCT
1 GTGCTCTCTGATTAGTACTTTGTGTGCTCTCT
35685741 GTTTGTTCCG
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
68 2 0.02
69 49 0.55
70 10 0.11
71 23 0.26
72 5 0.06
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (69 bp):
GTGCTCTCTGATTAGTACTTTGTGTGCTCTCTAATTAGCACTCTGTGTGCTCTCTGATTAGCACT
TTAT
Found at i:35690405 original size:4 final size:4
Alignment explanation
Indices: 35690396--35690438 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
35690386 ATAAGTTTAA
* *
35690396 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT ATAT ATAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
35690439 ATTAATTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
AAAT
Found at i:35699591 original size:26 final size:26
Alignment explanation
Indices: 35699548--35699601 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
35699538 ATAAATTATA
* *
35699548 ATTTTATTTTTTCATAGAATGTTTTAAT
1 ATTTTATTCTTT-ATAGAAT-TATTAAT
35699576 ATTTTATTCTTT-TAGAATTATTAAT
1 ATTTTATTCTTTATAGAATTATTAAT
35699601 A
1 A
35699602 CAATAGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 7 0.29
26 6 0.25
28 11 0.46
ACGTcount: A:0.31, C:0.04, G:0.06, T:0.59
Consensus pattern (26 bp):
ATTTTATTCTTTATAGAATTATTAAT
Found at i:35720515 original size:21 final size:20
Alignment explanation
Indices: 35720477--35720527 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
35720467 CCAGTCATTC
*
35720477 AAATATAATTAT--TTAAAT
1 AAATAAAATTATAATTAAAT
*
35720495 AAAATAAATTTATAATTAAAT
1 -AAATAAAATTATAATTAAAT
35720516 AAATAAAATTAT
1 AAATAAAATTAT
35720528 GAGTAGCAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.37
20 11 0.41
21 6 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (20 bp):
AAATAAAATTATAATTAAAT
Found at i:35722281 original size:28 final size:28
Alignment explanation
Indices: 35722228--35722288 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
35722218 TTTGTTTTTA
* *
35722228 TTTTATTTTAAATTTATTATGGTTTGAT
1 TTTTTTTTTAAATATATTATGGTTTGAT
*
35722256 TTTTTTTTTGAATATATTATGGTTTGAT
1 TTTTTTTTTAAATATATTATGGTTTGAT
*
35722284 CTTTT
1 TTTTT
35722289 AATCTATTTG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.21, C:0.02, G:0.11, T:0.66
Consensus pattern (28 bp):
TTTTTTTTTAAATATATTATGGTTTGAT
Found at i:35722296 original size:23 final size:22
Alignment explanation
Indices: 35722260--35722336 Score: 59
Period size: 23 Copynumber: 3.4 Consensus size: 22
35722250 TTTGATTTTT
35722260 TTTTTGAATATATTATGGTTTGA
1 TTTTT-AATATATTATGGTTTGA
*
35722283 TCTTTTAATCTATT-TGTGTTT-A
1 T-TTTTAATATATTATG-GTTTGA
* * *
35722305 TTTTAAATTTATTATGGTATGA
1 TTTTTAATATATTATGGTTTGA
*
35722327 TGTCTTAATA
1 T-TTTTAATA
35722337 AAGTATGAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
21 13 0.31
22 8 0.19
23 17 0.40
24 4 0.10
ACGTcount: A:0.26, C:0.04, G:0.13, T:0.57
Consensus pattern (22 bp):
TTTTTAATATATTATGGTTTGA
Found at i:35724063 original size:60 final size:59
Alignment explanation
Indices: 35723990--35724158 Score: 185
Period size: 60 Copynumber: 2.8 Consensus size: 59
35723980 TTAACTTAAT
35723990 ACTTTTTCCTAATTTGGTACCTAAACACTTTTTTGATCCAATTTGGTACATGAACTTGAC
1 ACTTTTTCCTAATTTGGTACCTAAAC-CTTTTTTGATCCAATTTGGTACATGAACTTGAC
* * * * * * * *
35724050 ACTTTTTCCTAATTCGGTACTTAAACCTTTTTGGACCCATTTTGATACTTGAACTTGGC
1 ACTTTTTCCTAATTTGGTACCTAAACCTTTTTTGATCCAATTTGGTACATGAACTTGAC
* * * * * *
35724109 ATTTTTTTCTTATTTTGGTACCTAAGCTTTTTTTAGATTCAATTTGGTAC
1 A-CTTTTTCCTAATTTGGTACCTAAACCTTTTTT-GATCCAATTTGGTAC
35724159 CTAAATTTAT
Statistics
Matches: 87, Mismatches: 20, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
59 28 0.32
60 48 0.55
61 11 0.13
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.46
Consensus pattern (59 bp):
ACTTTTTCCTAATTTGGTACCTAAACCTTTTTTGATCCAATTTGGTACATGAACTTGAC
Found at i:35724377 original size:59 final size:59
Alignment explanation
Indices: 35724303--35724415 Score: 145
Period size: 59 Copynumber: 1.9 Consensus size: 59
35724293 TTAATATTAA
* * * *
35724303 AAAAAGATTAGGTACCAAATTAGGAAAAAGAGTCAAGTTCAGGTACCAAATTAGATCCC
1 AAAAAGATTAAGTACCAAATTAGAAAAAAGAGTCAAATTCAGGTACAAAATTAGATCCC
* * * * *
35724362 AAAAAGTTTAAGTACCAACTTATAAAAAAGTGTCAAATTTAGGTACAAAATTAG
1 AAAAAGATTAAGTACCAAATTAGAAAAAAGAGTCAAATTCAGGTACAAAATTAG
35724416 GAAAAAGTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
59 45 1.00
ACGTcount: A:0.48, C:0.12, G:0.16, T:0.24
Consensus pattern (59 bp):
AAAAAGATTAAGTACCAAATTAGAAAAAAGAGTCAAATTCAGGTACAAAATTAGATCCC
Found at i:35724543 original size:3 final size:3
Alignment explanation
Indices: 35724537--35724566 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
35724527 ATATTATTTT
35724537 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35724567 TCAATCTCGA
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:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35726482 original size:24 final size:22
Alignment explanation
Indices: 35726411--35726482 Score: 60
Period size: 21 Copynumber: 3.2 Consensus size: 22
35726401 TTAATTTATT
35726411 TTAAATTTATTATGGGTTGATCTC
1 TTAAATTTATTAT-GGTTGAT-TC
* *
35726435 TT-AATCTATT-TGTGTTTATT-
1 TTAAATTTATTATG-GTTGATTC
35726455 TTAAATTTATTATGGTATGATGTC
1 TTAAATTTATTATGGT-TGAT-TC
35726479 TTAA
1 TTAA
35726483 TAAAGTATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 2 0.05
21 11 0.29
22 11 0.29
23 8 0.21
24 6 0.16
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (22 bp):
TTAAATTTATTATGGTTGATTC
Found at i:35727769 original size:3 final size:3
Alignment explanation
Indices: 35727761--35727800 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
35727751 AATACGTTGC
35727761 ATA 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 ATA A
35727801 CTACTTAATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:35729647 original size:46 final size:46
Alignment explanation
Indices: 35729591--35729683 Score: 143
Period size: 47 Copynumber: 2.0 Consensus size: 46
35729581 TGTTAGGTAT
* **
35729591 TTTTTTTAA-TTTTATTTTTGCTACAATTACGATTTAGGGAAAGGGA
1 TTTTTTTAATTTTTATTTTTGATACAATTAAAATTTA-GGAAAGGGA
35729637 TTTTTTTAATTTTTATTTTTGATACAATTAAAATTTAGGAAAGGGA
1 TTTTTTTAATTTTTATTTTTGATACAATTAAAATTTAGGAAAGGGA
35729683 T
1 T
35729684 GTTAATACAT
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 19 0.44
47 24 0.56
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.49
Consensus pattern (46 bp):
TTTTTTTAATTTTTATTTTTGATACAATTAAAATTTAGGAAAGGGA
Found at i:35729696 original size:47 final size:47
Alignment explanation
Indices: 35729600--35729696 Score: 124
Period size: 47 Copynumber: 2.1 Consensus size: 47
35729590 TTTTTTTTAA
* ** * **
35729600 TTTTATTTTTGCTACAATTACGATTTAGGGAAAGGGATTTTTTTAAT
1 TTTTATTTTTGATACAATTAAAATTTAGGGAAAGGGATGTTAATAAT
35729647 TTTTATTTTTGATACAATTAAAATTTA-GGAAAGGGATGTTAATACAT
1 TTTTATTTTTGATACAATTAAAATTTAGGGAAAGGGATGTTAATA-AT
35729694 TTT
1 TTT
35729697 AGGATTACAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
46 14 0.33
47 29 0.67
ACGTcount: A:0.32, C:0.05, G:0.15, T:0.47
Consensus pattern (47 bp):
TTTTATTTTTGATACAATTAAAATTTAGGGAAAGGGATGTTAATAAT
Found at i:35733379 original size:21 final size:21
Alignment explanation
Indices: 35733353--35733393 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
35733343 ACTCGATTTG
35733353 AAATTTTCTCGAATCAAGTTA
1 AAATTTTCTCGAATCAAGTTA
35733374 AAATTTTCTCGAATCAAGTT
1 AAATTTTCTCGAATCAAGTT
35733394 GAGTGAGATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
AAATTTTCTCGAATCAAGTTA
Found at i:35735778 original size:30 final size:31
Alignment explanation
Indices: 35735711--35735779 Score: 88
Period size: 31 Copynumber: 2.3 Consensus size: 31
35735701 ACTGTTAATC
*
35735711 AGTGACTATTTTGTCACTTTTTAATAACGTT
1 AGTGACTATTTTGTCACATTTTAATAACGTT
* *
35735742 AGTGACTGTTTTGTCACATTTTCA-AA-GTT
1 AGTGACTATTTTGTCACATTTTAATAACGTT
35735771 GAGTGACTA
1 -AGTGACTA
35735780 AAATGTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.09
30 9 0.27
31 21 0.64
ACGTcount: A:0.26, C:0.13, G:0.17, T:0.43
Consensus pattern (31 bp):
AGTGACTATTTTGTCACATTTTAATAACGTT
Found at i:35736086 original size:30 final size:31
Alignment explanation
Indices: 35736025--35736087 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
35736015 TGGGGGTGGG
*
35736025 ATGAGAGAGGAGTAAAAGTTTTTGGAGGAAA
1 ATGAGAGAGGAGTAAAAGTTTTTGAAGGAAA
35736056 ATGAGAGA-GAGTAAAAG-TTTTGAAGAGAAA
1 ATGAGAGAGGAGTAAAAGTTTTTGAAG-GAAA
35736086 AT
1 AT
35736088 AAAAAGGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 7 0.23
30 15 0.50
31 8 0.27
ACGTcount: A:0.46, C:0.00, G:0.32, T:0.22
Consensus pattern (31 bp):
ATGAGAGAGGAGTAAAAGTTTTTGAAGGAAA
Found at i:35738562 original size:21 final size:22
Alignment explanation
Indices: 35738526--35738566 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
35738516 CGTAAGGGTC
*
35738526 AAAACTTCTTAAAATTTTTATT
1 AAAACTTCTCAAAATTTTTATT
35738548 AAAACTT-TCAAAATTTTTA
1 AAAACTTCTCAAAATTTTTA
35738567 GAATATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 11 0.61
22 7 0.39
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAACTTCTCAAAATTTTTATT
Found at i:35748050 original size:31 final size:28
Alignment explanation
Indices: 35747998--35748054 Score: 69
Period size: 31 Copynumber: 1.9 Consensus size: 28
35747988 TTGAATATTC
35747998 AATTTAGAATGGGTAAAAGTTTAGGGACT
1 AATTTAGAATGGGTAAAAGTTT-GGGACT
**
35748027 AATTTAAGATATGGGTATTAGTTTGGGA
1 AATTT-AGA-ATGGGTAAAAGTTTGGGA
35748055 TGTTTAGTAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 5 0.21
30 7 0.29
31 12 0.50
ACGTcount: A:0.35, C:0.02, G:0.28, T:0.35
Consensus pattern (28 bp):
AATTTAGAATGGGTAAAAGTTTGGGACT
Found at i:35748439 original size:70 final size:71
Alignment explanation
Indices: 35748275--35748453 Score: 252
Period size: 70 Copynumber: 2.5 Consensus size: 71
35748265 ATCATTTATA
* * * * *
35748275 ATAGCTATGGATATGTCAATAATTATGTAAATGGTGGTAATTTGTTGTCAATCTCTAATAATTTA
1 ATAGCTATGGATATGTCAATAGTTATGTCAATGATGGTAATTCGTTGTCAATCTATAATAATTTA
*
35748340 AAATCG
66 AAATAG
* * *
35748346 ATAGCTATGGATATGTCAGTAGTTATTTCCATGATGGTAATTCGTTGTC-ATCTATAATAATTTA
1 ATAGCTATGGATATGTCAATAGTTATGTCAATGATGGTAATTCGTTGTCAATCTATAATAATTTA
*
35748410 TAATAG
66 AAATAG
*
35748416 ATAGCTATGGATATGTCAATAGTTATGTCGATGATGGT
1 ATAGCTATGGATATGTCAATAGTTATGTCAATGATGGT
35748454 TATGTATATA
Statistics
Matches: 95, Mismatches: 13, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
70 53 0.56
71 42 0.44
ACGTcount: A:0.32, C:0.09, G:0.19, T:0.40
Consensus pattern (71 bp):
ATAGCTATGGATATGTCAATAGTTATGTCAATGATGGTAATTCGTTGTCAATCTATAATAATTTA
AAATAG
Found at i:35749230 original size:23 final size:23
Alignment explanation
Indices: 35749204--35749276 Score: 70
Period size: 23 Copynumber: 3.5 Consensus size: 23
35749194 GAAGTTAAAT
35749204 TGTAATTTTTACGATAGTAAAAG
1 TGTAATTTTTACGATAGTAAAAG
35749227 TGTAATTTTTA--A-A-T--AA-
1 TGTAATTTTTACGATAGTAAAAG
**
35749243 TTAAATTTTTACGATAGTAAAAG
1 TGTAATTTTTACGATAGTAAAAG
*
35749266 TGCAATTTTTA
1 TGTAATTTTTA
35749277 AATGGTCAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
16 9 0.23
17 2 0.05
18 1 0.03
19 2 0.05
20 2 0.05
21 1 0.03
22 2 0.05
23 20 0.51
ACGTcount: A:0.40, C:0.04, G:0.12, T:0.44
Consensus pattern (23 bp):
TGTAATTTTTACGATAGTAAAAG
Found at i:35753023 original size:294 final size:290
Alignment explanation
Indices: 35752454--35753035 Score: 1083
Period size: 294 Copynumber: 2.0 Consensus size: 290
35752444 GATTATAACA
35752454 ATAAACCAACATAACTTCTACTTTGAGATTTTGAGATTCCATAGCTTCTCTACATTTTATAAGGA
1 ATAAACCAACATAACTTCTACTTTGAGATTTTGAGATTCCATAGCTTCTCTACATTTTATAAGGA
35752519 TATTATATATTGCATATTTGTAAAACCATATACCATGAATGTACATTTTATTGTTAATGCATTGT
66 TATTATATATTGCATATTTGTAAAACCATATACCATGAATGTACATTTTATTGTTAATGCATTGT
* *
35752584 TGATGTAGTTAGATTAAATTGTAAAAATATGATATTTAACGAATTCAAGCATATGATTTTACAGA
131 TGATGTAGTTAGATTAAATTGTAAAAATATGATATTTAACGAACTCAAGCATATGATTTCACAGA
35752649 TCAAATCATCAGATAAATTTGTAATTCGGGTTTAACATTTTTATATTAAAAATAAGCATGTTCAA
196 TCAAATCATCAGATAAATTTGTAATTCGGGTTTAACATTTTTATATTAAAAATAAGCATGTTCAA
35752714 GAATCGAGTTATCTGTTCAAGCTCAAAGCC
261 GAATCGAGTTATCTGTTCAAGCTCAAAGCC
35752744 ATAAACCAACATAACTTCTACTTTGAGATTTTGAGATTCCATAGCTTCTCTACATTTTATAAGGA
1 ATAAACCAACATAACTTCTACTTTGAGATTTTGAGATTCCATAGCTTCTCTACATTTTATAAGGA
35752809 TATTATATATTGCATATTTGTAAAACCATATACCATGAATGTACATTTTATTGTTAATGCATTGT
66 TATTATATATTGCATATTTGTAAAACCATATACCATGAATGTACATTTTATTGTTAATGCATTGT
35752874 TGATGTGGTGAGTTAGATTAAATTGTAAAAATATGATATTTAACGAACTCAAGCATATGATTTCA
131 TGA--T-GT-AGTTAGATTAAATTGTAAAAATATGATATTTAACGAACTCAAGCATATGATTTCA
*
35752939 CAGATCAAATCATCAGATAAATTTGTAATTCGGGTTTAACATTTTTATATTAAAAATAGGCATGT
192 CAGATCAAATCATCAGATAAATTTGTAATTCGGGTTTAACATTTTTATATTAAAAATAAGCATGT
* *
35753004 TTAAGAATCGAGTTATCTGTTCAAGCTTAAAG
257 TCAAGAATCGAGTTATCTGTTCAAGCTCAAAG
35753036 ATTTATACAA
Statistics
Matches: 283, Mismatches: 5, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
290 133 0.47
292 1 0.00
293 2 0.01
294 147 0.52
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.38
Consensus pattern (290 bp):
ATAAACCAACATAACTTCTACTTTGAGATTTTGAGATTCCATAGCTTCTCTACATTTTATAAGGA
TATTATATATTGCATATTTGTAAAACCATATACCATGAATGTACATTTTATTGTTAATGCATTGT
TGATGTAGTTAGATTAAATTGTAAAAATATGATATTTAACGAACTCAAGCATATGATTTCACAGA
TCAAATCATCAGATAAATTTGTAATTCGGGTTTAACATTTTTATATTAAAAATAAGCATGTTCAA
GAATCGAGTTATCTGTTCAAGCTCAAAGCC
Found at i:35757629 original size:21 final size:21
Alignment explanation
Indices: 35757605--35757650 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
35757595 TTCCATCACT
*
35757605 AGAACTTGAATTTCCTCCACC
1 AGAACTTGAAGTTCCTCCACC
*
35757626 AGAACTTGAAGTTCCTCCACT
1 AGAACTTGAAGTTCCTCCACC
35757647 AGAA
1 AGAA
35757651 ACACTAGGAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (21 bp):
AGAACTTGAAGTTCCTCCACC
Found at i:35767185 original size:22 final size:22
Alignment explanation
Indices: 35767160--35767207 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
35767150 TTTATAACGA
35767160 AAAGATCTAATTT-TAATAATTT
1 AAAGATCTAATTTGT-ATAATTT
*
35767182 AAAGATGTAATTTGTATAATTT
1 AAAGATCTAATTTGTATAATTT
35767204 AAAG
1 AAAG
35767208 TTTAGGGATC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.46, C:0.02, G:0.10, T:0.42
Consensus pattern (22 bp):
AAAGATCTAATTTGTATAATTT
Found at i:35775001 original size:32 final size:29
Alignment explanation
Indices: 35774935--35775012 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 29
35774925 TATTATAAGG
* *
35774935 ATTAAATTAAATTAATTTTTTATTATTAA
1 ATTAAATTAATTTAATTTTTTACTATTAA
35774964 A-TAAATTAATTTAATTTTTATACTATTAAAA
1 ATTAAATTAATTTAATTTTT-TACTATT--AA
*
35774995 ATTAAATAAATTTAATTT
1 ATTAAATTAATTTAATTT
35775013 ATAACAGAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
28 17 0.40
29 7 0.17
31 3 0.07
32 15 0.36
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (29 bp):
ATTAAATTAATTTAATTTTTTACTATTAA
Found at i:35786487 original size:423 final size:423
Alignment explanation
Indices: 35785701--35786551 Score: 1666
Period size: 423 Copynumber: 2.0 Consensus size: 423
35785691 GAAAGCATAA
35785701 AGATAACATAAATTTGTGTGAATACATTCGAAAGAAAAAATGTACTCCATAGGAATAACTTTTAT
1 AGATAACATAAATTTGTGTGAATACATTCGAAAGAAAAAATGTACTCCATAGGAATAACTTTTAT
35785766 GTATAAAAGATCACTTTTTAACCAATTGCTGAAGTAAATGCACTGACATCAAATGCTAATCAAAC
66 GTATAAAAGATCACTTTTTAACCAATTGCTGAAGTAAATGCACTGACATCAAATGCTAATCAAAC
35785831 AGAAAACTGGGTTTTAAACATGGCTCTGTTTTGTACTACAATGGGCACCAGTGTTGTGCTCTAAT
131 AGAAAACTGGGTTTTAAACATGGCTCTGTTTTGTACTACAATGGGCACCAGTGTTGTGCTCTAAT
35785896 TACAAAGAGTTTTGCTTCTTTTTGGATGCCTGCAGTTTTTTACATTATTTACAAAAGAAACATGC
196 TACAAAGAGTTTTGCTTCTTTTTGGATGCCTGCAGTTTTTTACATTATTTACAAAAGAAACATGC
35785961 ACCAATATAACAATGATATATCACTGAATAGAACTTTCAGGATGGCAACAAATATAAAGGTCATA
261 ACCAATATAACAATGATATATCACTGAATAGAACTTTCAGGATGGCAACAAATATAAAGGTCATA
35786026 CTACATACAAGTTATAACAAACCATATCCAGCTCAACCATCTAATCCATGTTACTTGGAATTGGG
326 CTACATACAAGTTATAACAAACCATATCCAGCTCAACCATCTAATCCATGTTACTTGGAATTGGG
35786091 AAAGAGTGTTGGACATTAATACATGTCCAATAC
391 AAAGAGTGTTGGACATTAATACATGTCCAATAC
35786124 AGATAACATAAATTTGTGTGAATACATTCGAAAGAAAAAATGTACTCCATAGGAATAACTTTTAT
1 AGATAACATAAATTTGTGTGAATACATTCGAAAGAAAAAATGTACTCCATAGGAATAACTTTTAT
35786189 GTATAAAAGATCACTTTTTAACCAATTGCTGAAGTAAATGCACTGACATCAAATGCTAATCAAAC
66 GTATAAAAGATCACTTTTTAACCAATTGCTGAAGTAAATGCACTGACATCAAATGCTAATCAAAC
35786254 AGAAAACTGGGTTTTAAACATGGCTCTGTTTTGTACTACAATGGGCACCAGTGTTGTGCTCTAAT
131 AGAAAACTGGGTTTTAAACATGGCTCTGTTTTGTACTACAATGGGCACCAGTGTTGTGCTCTAAT
35786319 TACAAAGAGTTTTGCTTCTTTTTGGATGCCTGCAGTTTTTTACATTATTTACAAAAGAAACATGC
196 TACAAAGAGTTTTGCTTCTTTTTGGATGCCTGCAGTTTTTTACATTATTTACAAAAGAAACATGC
* *
35786384 ACCAATATAACAATGATGTATCATTGAATAGAACTTTCAGGATGGCAACAAATATAAAGGTCATA
261 ACCAATATAACAATGATATATCACTGAATAGAACTTTCAGGATGGCAACAAATATAAAGGTCATA
35786449 CTACATACAAGTTATAACAAACCATATCCAGCTCAACCATCTAATCCATGTTACTTGGAATTGGG
326 CTACATACAAGTTATAACAAACCATATCCAGCTCAACCATCTAATCCATGTTACTTGGAATTGGG
**
35786514 TCAGAGTGTTGGACATTAATACATGTCCAATAC
391 AAAGAGTGTTGGACATTAATACATGTCCAATAC
35786547 AGATA
1 AGATA
35786552 GTTCATTTAT
Statistics
Matches: 424, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
423 424 1.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (423 bp):
AGATAACATAAATTTGTGTGAATACATTCGAAAGAAAAAATGTACTCCATAGGAATAACTTTTAT
GTATAAAAGATCACTTTTTAACCAATTGCTGAAGTAAATGCACTGACATCAAATGCTAATCAAAC
AGAAAACTGGGTTTTAAACATGGCTCTGTTTTGTACTACAATGGGCACCAGTGTTGTGCTCTAAT
TACAAAGAGTTTTGCTTCTTTTTGGATGCCTGCAGTTTTTTACATTATTTACAAAAGAAACATGC
ACCAATATAACAATGATATATCACTGAATAGAACTTTCAGGATGGCAACAAATATAAAGGTCATA
CTACATACAAGTTATAACAAACCATATCCAGCTCAACCATCTAATCCATGTTACTTGGAATTGGG
AAAGAGTGTTGGACATTAATACATGTCCAATAC
Found at i:35787892 original size:11 final size:11
Alignment explanation
Indices: 35787876--35787901 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
35787866 TTTTGGGGAA
35787876 TTTTCAATTTT
1 TTTTCAATTTT
35787887 TTTTCAATTTT
1 TTTTCAATTTT
35787898 TTTT
1 TTTT
35787902 GGTGATTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.08, G:0.00, T:0.77
Consensus pattern (11 bp):
TTTTCAATTTT
Found at i:35790768 original size:13 final size:13
Alignment explanation
Indices: 35790750--35790776 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35790740 CGTTAATTCT
35790750 TTTTATTGGTTAC
1 TTTTATTGGTTAC
35790763 TTTTATTGGTTAC
1 TTTTATTGGTTAC
35790776 T
1 T
35790777 GACTTTTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (13 bp):
TTTTATTGGTTAC
Found at i:35794776 original size:46 final size:46
Alignment explanation
Indices: 35794707--35794818 Score: 188
Period size: 46 Copynumber: 2.4 Consensus size: 46
35794697 CGTCACTCCA
* * * *
35794707 GGTTGCTCGGCAACGATGATGCTAACATGTTCATACTACCACCCTG
1 GGTTGCTTGGCAACGCTGGTGCTAACATGTACATACTACCACCCTG
35794753 GGTTGCTTGGCAACGCTGGTGCTAACATGTACATACTACCACCCTG
1 GGTTGCTTGGCAACGCTGGTGCTAACATGTACATACTACCACCCTG
35794799 GGTTGCTTGGCAACGCTGGT
1 GGTTGCTTGGCAACGCTGGT
35794819 TTTCAATCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
46 62 1.00
ACGTcount: A:0.21, C:0.27, G:0.26, T:0.27
Consensus pattern (46 bp):
GGTTGCTTGGCAACGCTGGTGCTAACATGTACATACTACCACCCTG
Found at i:35795675 original size:11 final size:11
Alignment explanation
Indices: 35795661--35795706 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
35795651 TTTATATATG
*
35795661 TTTAATTAAGC
1 TTTAATTAATC
*
35795672 TTTAGTTAATC
1 TTTAATTAATC
35795683 -TTAATTAA-C
1 TTTAATTAATC
35795692 TTTTAATTAATC
1 -TTTAATTAATC
35795704 TTT
1 TTT
35795707 TCTTATAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
9 1 0.03
10 7 0.24
11 20 0.69
12 1 0.03
ACGTcount: A:0.33, C:0.09, G:0.04, T:0.54
Consensus pattern (11 bp):
TTTAATTAATC
Found at i:35795686 original size:21 final size:21
Alignment explanation
Indices: 35795662--35795705 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35795652 TTATATATGT
*
35795662 TTAATTAAGC-TTTAGTTAATC
1 TTAATTAA-CTTTTAATTAATC
35795683 TTAATTAACTTTTAATTAATC
1 TTAATTAACTTTTAATTAATC
35795704 TT
1 TT
35795706 TTCTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (21 bp):
TTAATTAACTTTTAATTAATC
Found at i:35798704 original size:444 final size:445
Alignment explanation
Indices: 35797832--35798730 Score: 1367
Period size: 444 Copynumber: 2.0 Consensus size: 445
35797822 ATCACATTTC
* *
35797832 AATTTC-ATTTCATTCATCATTTAATCAATTTATATGTTTATACCCTATTAACCAAAAACGGACT
1 AATTTCGATTTCAATCATCATTTAATCAATTTATATGTTTATACCCTATTAACCAAAAACAGACT
* *
35797896 CAAAATGGATACACGAATTCGTCACCCAGGGTTGCTCGGCAACGATGACGCTAACATGTACATAC
66 CAAAATGGATACACGAATTCGTCACCCAGAGTTGCTCGACAACGATGACGCTAACATGTACATAC
* * * * * *
35797961 TACCACCCAGGGTTGCATGGCAATGCTGGTTTTTAATCAATAATCTGACGCTATGGCATGCCAAC
131 TACCACCCAGGGTTGCATGACAACGCTAGTTTTCAATCAATAATCTAACGCTATGCCATGCCAAC
* * *
35798026 TATATTCGATTCAATTTGAACAGCTAACAGGGGTAACCAAATTTTTTATTCATTATAAACAATTC
196 TATATCCGATTCAATTCGAACAGCTAACAGAGGTAACCAAATTTTTTATTCATTATAAACAATTC
* * * *
35798091 AAATCATACTTTATGATATCAATTAATCATCAATTCATCTTATAATACAAATTGTTTCAACTTAA
261 AAACCATACTTTATAATATCAATTAATCATCAATTCATCTTATAATACAAACTGTTTCAACTCAA
*
35798156 TTTCATACCAATTATCATATATAAATTAAATAATTAAATCTCTATACTATTCAATTTAGTCCTTG
326 TTTCATACCAATTATCATATATAAATTAAATAATGAAATCTCTATACTATTCAATTTAGTCCTTG
* *
35798221 TCTCGATAATCAATCTCGAAAAATTTAATTCAATTCAAATATGTACTCACCAACG
391 TCTCGATAATCAATCTCGAAAAATGTAATTCAATTCAAATATCTACTCACCAACG
* * * *
35798276 AATTTCGATTTCAATCATCATTTAATCAGTTTGTATGTTTTTAACCCTATTAACCAAACACAGAC
1 AATTTCGATTTCAATCATCATTTAATCAATTTATATGTTTAT-ACCCTATTAACCAAAAACAGAC
* * * *
35798341 TCAGAATTGATACACGGATTCGTCACCCCA-AGTTGCTCGACAATGATGACGCTAACATGTACAT
65 TCAAAATGGATACACGAATTCGTCA-CCCAGAGTTGCTCGACAACGATGACGCTAACATGTACAT
* *
35798405 ACTACCACCCTGGGTTGTC-TGACAACGCTAGTTTTCAATCAATAGTCTAACGCTATGCCATGCC
129 ACTACCACCCAGGGTTG-CATGACAACGCTAGTTTTCAATCAATAATCTAACGCTATGCCATGCC
**
35798469 AACTATATCCGATTCTGTTCGAACAGCTAACA-AGGTAACCAAATTTTTT-TTCATTATAAACAA
193 AACTATATCCGATTCAATTCGAACAGCTAACAGAGGTAACCAAATTTTTTATTCATTATAAACAA
* *
35798532 TTCAAACCATACTTTATAATATTAATTAATCGTCAATTCATCTTATAATACAAACTGTTTCAACT
258 TTCAAACCATACTTTATAATATCAATTAATCATCAATTCATCTTATAATACAAACTGTTTCAACT
* * *
35798597 CAATTTCATACCAATTATCATATATAAATTAAATCATGAGATTTCTATACTATTCAATTTAGTCC
323 CAATTTCATACCAATTATCATATATAAATTAAATAATGAAATCTCTATACTATTCAATTTAGTCC
* **
35798662 TTGTCTCGATAATCAATCTCGACAAATGTAATTCAATTCAAATATCTACTCGTCAACG
388 TTGTCTCGATAATCAATCTCGAAAAATGTAATTCAATTCAAATATCTACTCACCAACG
*
35798720 ACTTTCGATTT
1 AATTTCGATTT
35798731 TTCTTTCCCT
Statistics
Matches: 410, Mismatches: 41, Indels: 8
0.89 0.09 0.02
Matches are distributed among these distances:
444 203 0.50
445 47 0.11
446 155 0.38
447 5 0.01
ACGTcount: A:0.35, C:0.21, G:0.10, T:0.34
Consensus pattern (445 bp):
AATTTCGATTTCAATCATCATTTAATCAATTTATATGTTTATACCCTATTAACCAAAAACAGACT
CAAAATGGATACACGAATTCGTCACCCAGAGTTGCTCGACAACGATGACGCTAACATGTACATAC
TACCACCCAGGGTTGCATGACAACGCTAGTTTTCAATCAATAATCTAACGCTATGCCATGCCAAC
TATATCCGATTCAATTCGAACAGCTAACAGAGGTAACCAAATTTTTTATTCATTATAAACAATTC
AAACCATACTTTATAATATCAATTAATCATCAATTCATCTTATAATACAAACTGTTTCAACTCAA
TTTCATACCAATTATCATATATAAATTAAATAATGAAATCTCTATACTATTCAATTTAGTCCTTG
TCTCGATAATCAATCTCGAAAAATGTAATTCAATTCAAATATCTACTCACCAACG
Found at i:35800240 original size:21 final size:21
Alignment explanation
Indices: 35800216--35800259 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35800206 TTATATATGT
*
35800216 TTAATTAAGC-TTTAGTTAATC
1 TTAATTAA-CTTTTAATTAATC
35800237 TTAATTAACTTTTAATTAATC
1 TTAATTAACTTTTAATTAATC
35800258 TT
1 TT
35800260 TTCTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (21 bp):
TTAATTAACTTTTAATTAATC
Found at i:35803198 original size:21 final size:21
Alignment explanation
Indices: 35803164--35803217 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
35803154 ATAAATAAGC
35803164 TTAATTAAGT-TTAATTAAGC-T
1 TTAATTAA-TCTTAATTAA-CTT
*
35803185 TTAGTTAATCTTAATTAACTT
1 TTAATTAATCTTAATTAACTT
35803206 TTAATTAATCTT
1 TTAATTAATCTT
35803218 TTCTTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 2 0.07
21 27 0.93
ACGTcount: A:0.35, C:0.07, G:0.06, T:0.52
Consensus pattern (21 bp):
TTAATTAATCTTAATTAACTT
Found at i:35806130 original size:10 final size:10
Alignment explanation
Indices: 35806112--35806166 Score: 58
Period size: 10 Copynumber: 5.3 Consensus size: 10
35806102 AATTTATAAA
*
35806112 TAAGCTTAAT
1 TAAGTTTAAT
35806122 TAAGTTTAAT
1 TAAGTTTAAT
*
35806132 TAAGCTTTAGT
1 TAAG-TTTAAT
35806143 TAA-TCTTAAT
1 TAAGT-TTAAT
35806153 TAAGTTTTAAT
1 TAAG-TTTAAT
35806164 TAA
1 TAA
35806167 TCTTTTCTTA
Statistics
Matches: 38, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
9 1 0.03
10 20 0.53
11 16 0.42
12 1 0.03
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.47
Consensus pattern (10 bp):
TAAGTTTAAT
Found at i:35806151 original size:21 final size:21
Alignment explanation
Indices: 35806112--35806170 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
35806102 AATTTATAAA
35806112 TAAGC-TTAATTAAGT-TTAAT
1 TAAGCTTTAATTAA-TCTTAAT
*
35806132 TAAGCTTTAGTTAATCTTAAT
1 TAAGCTTTAATTAATCTTAAT
*
35806153 TAAGTTTTAATTAATCTT
1 TAAGCTTTAATTAATCTT
35806171 TTCTTATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.36, C:0.07, G:0.08, T:0.49
Consensus pattern (21 bp):
TAAGCTTTAATTAATCTTAAT
Found at i:35806162 original size:11 final size:11
Alignment explanation
Indices: 35806117--35806166 Score: 59
Period size: 11 Copynumber: 4.7 Consensus size: 11
35806107 ATAAATAAGC
35806117 TTAATTAAG-T
1 TTAATTAAGTT
*
35806127 TTAATTAAGCT
1 TTAATTAAGTT
* *
35806138 TTAGTTAA-TC
1 TTAATTAAGTT
35806148 TTAATTAAGTT
1 TTAATTAAGTT
35806159 TTAATTAA
1 TTAATTAA
35806167 TCTTTTCTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
10 16 0.48
11 17 0.52
ACGTcount: A:0.38, C:0.04, G:0.08, T:0.50
Consensus pattern (11 bp):
TTAATTAAGTT
Found at i:35809347 original size:21 final size:21
Alignment explanation
Indices: 35809323--35809366 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
35809313 TTATATATGT
*
35809323 TTAATTAAGC-TTTAGTTAATC
1 TTAATTAA-CTTTTAATTAATC
35809344 TTAATTAACTTTTAATTAATC
1 TTAATTAACTTTTAATTAATC
35809365 TT
1 TT
35809367 TTCTTATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (21 bp):
TTAATTAACTTTTAATTAATC
Found at i:35811799 original size:24 final size:24
Alignment explanation
Indices: 35811770--35811844 Score: 123
Period size: 24 Copynumber: 3.1 Consensus size: 24
35811760 AGAAATAATC
*
35811770 TTTCAATTAAACTCTGTTTAATTG
1 TTTCAATTAAACTCTGTTTATTTG
* *
35811794 TTTCAAATAAACTTTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
35811818 TTTCAATTAAACTCTGTTTATTTG
1 TTTCAATTAAACTCTGTTTATTTG
35811842 TTT
1 TTT
35811845 GAGTCAAACT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.27, C:0.11, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTCTGTTTATTTG
Found at i:35814585 original size:69 final size:66
Alignment explanation
Indices: 35814505--35814644 Score: 192
Period size: 69 Copynumber: 2.0 Consensus size: 66
35814495 CTCTCTATTA
*
35814505 TTAGCACTGTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACTC
1 TTAGCACTGTGTGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACTTTG-GTACTC
*
35814569 TTTGT
62 TCTGT
35814574 TTAGCACTGTGTGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCT
1 TTAGCACTGTGTGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCT
35814639 CTGT
63 CTGT
35814643 TT
1 TT
35814645 GTTCCGTATA
Statistics
Matches: 65, Mismatches: 2, Indels: 8
0.87 0.03 0.11
Matches are distributed among these distances:
68 2 0.03
69 34 0.52
70 11 0.17
71 13 0.20
72 5 0.08
ACGTcount: A:0.12, C:0.21, G:0.21, T:0.45
Consensus pattern (66 bp):
TTAGCACTGTGTGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTG
T
Found at i:35814597 original size:23 final size:23
Alignment explanation
Indices: 35814471--35814644 Score: 140
Period size: 23 Copynumber: 7.5 Consensus size: 23
35814461 ACACTAGCGC
*
35814471 GCTCTCTGTTTAGCAC-GTCTCGT
1 GCTCTCTGTTTAGCACTGTGT-GT
*
35814494 GCTCTCTATTATTAGCACTGTGTGT
1 GCTCTCT-GT-TTAGCACTGTGTGT
* *
35814519 GCTCTCTGATTAGCACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* * *
35814542 GCTCTCTGATTAGTACTTTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
35814565 ACTCTTTGTTTAGCACTGTGTGT
1 GCTCTCTGTTTAGCACTGTGTGT
* *
35814588 GCTCTCTGTTGCCCAGCACT-TATGT
1 GCTCTCTGTT---TAGCACTGTGTGT
* *
35814613 GCTCTCTG-TTAGTACTTTG-GT
1 GCTCTCTGTTTAGCACTGTGTGT
*
35814634 ACTCTCTGTTT
1 GCTCTCTGTTT
35814645 GTTCCGTATA
Statistics
Matches: 124, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
21 14 0.11
22 3 0.02
23 68 0.55
24 2 0.02
25 28 0.23
26 9 0.07
ACGTcount: A:0.12, C:0.23, G:0.21, T:0.44
Consensus pattern (23 bp):
GCTCTCTGTTTAGCACTGTGTGT
Found at i:35815585 original size:24 final size:24
Alignment explanation
Indices: 35815557--35815619 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
35815547 AGAAATAATC
35815557 TTTCAGTTAAACTCTGTTTAATTG
1 TTTCAGTTAAACTCTGTTTAATTG
** *
35815581 TTTCAAATAAACTCTGTTTATTTG
1 TTTCAGTTAAACTCTGTTTAATTG
* *
35815605 TTTGAGTCAAACTCT
1 TTTCAGTTAAACTCT
35815620 TATTAGTGTA
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.14, G:0.11, T:0.48
Consensus pattern (24 bp):
TTTCAGTTAAACTCTGTTTAATTG
Found at i:35821046 original size:32 final size:30
Alignment explanation
Indices: 35821009--35821083 Score: 87
Period size: 32 Copynumber: 2.4 Consensus size: 30
35820999 ATCATAAATT
*
35821009 TATAAATTAATTACTTAAATTTAATAACTCA
1 TATAAATTAATTAATT-AATTTAATAACTCA
* *
35821040 TGATAAATTAATCAAATTAGTTTAATAACTCA
1 T-ATAAATTAAT-TAATTAATTTAATAACTCA
*
35821072 TATCAATTAATT
1 TATAAATTAATT
35821084 GAGATTGTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
31 10 0.27
32 24 0.65
33 3 0.08
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (30 bp):
TATAAATTAATTAATTAATTTAATAACTCA
Found at i:35821795 original size:41 final size:41
Alignment explanation
Indices: 35821750--35821833 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
35821740 CGTCGGAAGA
35821750 TAATTATAGTTATTGATCAAAAACAAGAATACAAAGGTAAT
1 TAATTATAGTTATTGATCAAAAACAAGAATACAAAGGTAAT
35821791 TAATTATAGTTATTGATCAAAAACAAGAATACAAAGGTAAT
1 TAATTATAGTTATTGATCAAAAACAAGAATACAAAGGTAAT
35821832 TA
1 TA
35821834 TACCCCATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.51, C:0.07, G:0.12, T:0.30
Consensus pattern (41 bp):
TAATTATAGTTATTGATCAAAAACAAGAATACAAAGGTAAT
Found at i:35824909 original size:32 final size:33
Alignment explanation
Indices: 35824873--35824947 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 33
35824863 CATTTAATTG
35824873 TTAATAAATTTATAATTCAAATCA-CTCAAT-AA
1 TTAATAAATTTATAATT-AAATCACCTCAATCAA
*
35824905 TTAATAAATTTATAATTTAATCACGCTCAATCAA
1 TTAATAAATTTATAATTAAATCAC-CTCAATCAA
35824939 TTAAATAAA
1 TT-AATAAA
35824948 AGGTGCTATT
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
31 5 0.13
32 17 0.45
33 6 0.16
34 4 0.11
35 6 0.16
ACGTcount: A:0.49, C:0.12, G:0.01, T:0.37
Consensus pattern (33 bp):
TTAATAAATTTATAATTAAATCACCTCAATCAA
Found at i:35848801 original size:26 final size:28
Alignment explanation
Indices: 35848739--35848802 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
35848729 AACTATCACA
35848739 TAAATTATGAAAATAACTCATTTTAATTT
1 TAAATTATGAAAATAACTCATTTT-ATTT
**
35848768 TAAATTATGAAAATAGTTCATTTT-TTT
1 TAAATTATGAAAATAACTCATTTTATTT
35848795 T-AATTATG
1 TAAATTATG
35848803 TACCTAAATG
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
26 7 0.21
27 4 0.12
29 22 0.67
ACGTcount: A:0.41, C:0.05, G:0.06, T:0.48
Consensus pattern (28 bp):
TAAATTATGAAAATAACTCATTTTATTT
Found at i:35849280 original size:25 final size:24
Alignment explanation
Indices: 35849228--35849273 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
35849218 AATAGATAAT
35849228 AAAAAATAAAGAGAAAAAAATTAA
1 AAAAAATAAAGAGAAAAAAATTAA
35849252 AAAAACATAAA-A-AAAAAAATTA
1 AAAAA-ATAAAGAGAAAAAAATTA
35849274 CTCAAAACAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 10 0.48
24 6 0.29
25 5 0.24
ACGTcount: A:0.80, C:0.02, G:0.04, T:0.13
Consensus pattern (24 bp):
AAAAAATAAAGAGAAAAAAATTAA
Done.