Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008721.1 Hibiscus syriacus cultivar Beakdansim tig00111779_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2464137
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 12
Found at i:398453 original size:18 final size:19
Alignment explanation
Indices: 398343--398485 Score: 66
Period size: 18 Copynumber: 7.6 Consensus size: 19
398333 ATTATATTTT
*
398343 TATT-TTAATAATATATAA
1 TATTATTAATAATATTTAA
*
398361 TAAATTATTAATAAAATTT-A
1 T--ATTATTAATAATATTTAA
* * *
398381 TATTATTTATTA-ATTTCA
1 TATTATTAATAATATTTAA
** * * *
398399 TAGAAATACTATTA-TTAA
1 TATTATTAATAATATTTAA
*
398417 -ATTATTAATAATATATAA
1 TATTATTAATAATATTTAA
*
398435 TATTATTTAT-ATATTTAA
1 TATTATTAATAATATTTAA
* *
398453 TATTAATATAATAATCTAATAA
1 TATT-AT-TAATAATAT-TTAA
398475 TATT-TTAATAA
1 TATTATTAATAA
398486 AGATATTTAA
Statistics
Matches: 91, Mismatches: 23, Indels: 21
0.67 0.17 0.16
Matches are distributed among these distances:
17 12 0.13
18 33 0.36
19 17 0.19
20 9 0.10
21 13 0.14
22 7 0.08
ACGTcount: A:0.48, C:0.02, G:0.01, T:0.49
Consensus pattern (19 bp):
TATTATTAATAATATTTAA
Found at i:398506 original size:23 final size:22
Alignment explanation
Indices: 398480--398523 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
398470 AATAATATTT
398480 TAATAAAGATATTTAAAATATAC
1 TAATAAA-ATATTTAAAATATAC
* * *
398503 TAATTAATTTTTTAAAATATA
1 TAATAAAATATTTAAAATATA
398524 ATATAAACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAATAAAATATTTAAAATATAC
Found at i:398632 original size:30 final size:34
Alignment explanation
Indices: 398562--398633 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 34
398552 AATATAATTT
*
398562 ATAATA-TTTTTATTTCAATAAAATATACTAATA
1 ATAATATTTTTTATTTCAATAAAATATACTAAAA
*
398595 TTAATATTTTTTA-TT-AATAAAAT-TA-TAAAA
1 ATAATATTTTTTATTTCAATAAAATATACTAAAA
398625 ATAATATTT
1 ATAATATTT
398634 AGTAATAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
30 12 0.34
31 2 0.06
32 8 0.23
33 7 0.20
34 6 0.17
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (34 bp):
ATAATATTTTTTATTTCAATAAAATATACTAAAA
Found at i:398850 original size:14 final size:14
Alignment explanation
Indices: 398828--398866 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
398818 ATATAATTCA
*
398828 TTTTACGGAAAACG
1 TTTTCCGGAAAACG
398842 TTTTCCGGAAAACG
1 TTTTCCGGAAAACG
*
398856 TTTTCCAGAAA
1 TTTTCCGGAAA
398867 TGTAATTCAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (14 bp):
TTTTCCGGAAAACG
Found at i:398889 original size:14 final size:14
Alignment explanation
Indices: 398870--398928 Score: 64
Period size: 14 Copynumber: 4.1 Consensus size: 14
398860 CCAGAAATGT
* *
398870 AATTCATTTTCTAG
1 AATTCAATTTCCAG
* *
398884 AATTCAAATTACAG
1 AATTCAATTTCCAG
*
398898 TAATTCATTTTCCAG
1 -AATTCAATTTCCAG
398913 AATTCAATTTCCAG
1 AATTCAATTTCCAG
398927 AA
1 AA
398929 AACCAATTAC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
14 25 0.69
15 11 0.31
ACGTcount: A:0.37, C:0.17, G:0.07, T:0.39
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:399738 original size:6 final size:6
Alignment explanation
Indices: 399727--399782 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
399717 AGATGATGGC
* * * *
399727 GAAGAT GAAGAT GAATAT GAAGAT GATGAT GGAA-AT GGAGAT GAGGAT
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGAT -GAAGAT GAAGAT GAAGAT
*
399775 GGAGAT GA
1 GAAGAT GA
399783 TGAAGAATAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
5 2 0.05
6 34 0.89
7 2 0.05
ACGTcount: A:0.43, C:0.00, G:0.38, T:0.20
Consensus pattern (6 bp):
GAAGAT
Found at i:399776 original size:18 final size:19
Alignment explanation
Indices: 399727--399788 Score: 65
Period size: 18 Copynumber: 3.3 Consensus size: 19
399717 AGATGATGGC
399727 GAAGATGAAGAT-GAATAT
1 GAAGATGAAGATGGAATAT
*
399745 GAAGATGATGATGGAA-AT
1 GAAGATGAAGATGGAATAT
* *
399763 GGAGATGAGGATGGAGATGAT
1 GAAGATGAAGATGGA-AT-AT
399784 GAAGA
1 GAAGA
399789 ATAAGAGGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
18 26 0.72
19 4 0.11
21 6 0.17
ACGTcount: A:0.44, C:0.00, G:0.37, T:0.19
Consensus pattern (19 bp):
GAAGATGAAGATGGAATAT
Found at i:400535 original size:460 final size:461
Alignment explanation
Indices: 399663--400568 Score: 1593
Period size: 460 Copynumber: 2.0 Consensus size: 461
399653 ACCCCGACGA
*
399663 ACTTCTTGAAGGTTCTCATTTGCTAGATAAGGCTAAGACTGAAGGTGGAACTGAAGATGATGGCG
1 ACTTCCTGAAGGTTCTCATTTGCTAGATAAGGCTAAGACTGAAGGTGGAACTGAAGATGATGGC-
* * *
399728 AAGATGAAGATGAATATGAAGATGATGATGGAAATGGAGATGAGGATGGAGATGATGAAGAATAA
65 ---A-GAAGATGAATATGAAGATGATGATGGAAATAGAGATGAGGATGGAGATGACGAAGAAGAA
*
399793 GAGGAACTGACGATGAGAAACAGATTGAAGAGAAGGTCGTTCAATCTAAACAGGTTTGTCTTCTC
126 GAGGAACTGACGATGAGAAACAGATTGAAGAGAAGGTCGTTCAATCTAAAAAGGTTTGTCTTCTC
* * *
399858 CCTTTCTTATATTTATTGAAGTCCTGACATTAGATTGATTCATTGATTGTGAATTTGGTTGCAGA
191 CCTTTCTTATATTGATTAAAGTCCTGACATTAGATTGATTCATCGATTGTGAATTTGGTTGCAGA
*
399923 TAACATTGTGCGTAGGATTTGGTAGATTTTCTGACCCTCCTGAAGCGTAGGGTCTCGCTCATTTT
256 TAACATTGTGCGTAGGATTTGGAAGATTTTCTGACCCTCCTGAAGCGTAGGGTCTCGCTCATTTT
*
399988 CTAGGTTTCGTTACTTTCAGCTCTATTCATTCTGCTCAACTGCACTAATTTCTTCTCTGCTTAAT
321 CTAGGTTTCGTTACTTTCAGCTCTATTCATTCTGCTCAACTGCACTAATTTCTGCTCTGCTTAAT
400053 ATTCGTGAGTTTTAAAAGTCCGTTTGCAAGGTTCTCAAGGGAAGCCAGAGTTTAAGCCAGTGTTT
386 ATTCGTGAGTTTTAAAAGTCCGTTTGCAAGGTTCTCAAGGGAAGCCAGAGTTTAAGCCAGTGTTT
400118 AAAATGTCAGG
451 AAAATGTCAGG
400129 ACTTCCTGAAGGTTCTCATTTGCTAGATAAGGCTAAGACTGAAGGTGGAACTGAAGATGATGGC-
1 ACTTCCTGAAGGTTCTCATTTGCTAGATAAGGCTAAGACTGAAGGTGGAACTGAAGATGATGGCA
400193 GAAGATGAATATGAAGATGATGATGGAAATAGAGATGAGGATGGAGATGACGAAGAAGAAGAGGA
66 GAAGATGAATATGAAGATGATGATGGAAATAGAGATGAGGATGGAGATGACGAAGAAGAAGAGGA
** *
400258 ACTGATTATGAGAAACAGATTGAAGAGAAGGTCGTTCAGTCTAAAAAGGTTTGTCTTCTCCCTTT
131 ACTGACGATGAGAAACAGATTGAAGAGAAGGTCGTTCAATCTAAAAAGGTTTGTCTTCTCCCTTT
400323 CTTATATTGATTAAAGTCCTGACATTAGATTGATTCATCGATTGTGAATTTGGTTGCAGGCAT-A
196 CTTATATTGATTAAAGTCCTGACATTAGATTGATTCATCGATTGTGAATTTGGTTGCA-G-ATAA
* *
400387 -ATTGTGCGTAGGATTTGGAAGCTTTTCTGACCCTCTTGAAGCGTAGGGTCTCGCTCATTTTCTA
259 CATTGTGCGTAGGATTTGGAAGATTTTCTGACCCTCCTGAAGCGTAGGGTCTCGCTCATTTTCTA
400451 GGTTTCGTTACTTTCAGCTCTATTCATTCTGCTCAACTGCACTAATTTCTGCTCTGCTTAATATT
324 GGTTTCGTTACTTTCAGCTCTATTCATTCTGCTCAACTGCACTAATTTCTGCTCTGCTTAATATT
400516 CGTGAGTTTTAAAAGTCCGTTTGCAAGGTTCTCAAGGGAAGCCAGAGTTTAAG
389 CGTGAGTTTTAAAAGTCCGTTTGCAAGGTTCTCAAGGGAAGCCAGAGTTTAAG
400569 GTGAGAATTT
Statistics
Matches: 423, Mismatches: 15, Indels: 10
0.94 0.03 0.02
Matches are distributed among these distances:
460 356 0.84
461 2 0.00
462 2 0.00
466 63 0.15
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.32
Consensus pattern (461 bp):
ACTTCCTGAAGGTTCTCATTTGCTAGATAAGGCTAAGACTGAAGGTGGAACTGAAGATGATGGCA
GAAGATGAATATGAAGATGATGATGGAAATAGAGATGAGGATGGAGATGACGAAGAAGAAGAGGA
ACTGACGATGAGAAACAGATTGAAGAGAAGGTCGTTCAATCTAAAAAGGTTTGTCTTCTCCCTTT
CTTATATTGATTAAAGTCCTGACATTAGATTGATTCATCGATTGTGAATTTGGTTGCAGATAACA
TTGTGCGTAGGATTTGGAAGATTTTCTGACCCTCCTGAAGCGTAGGGTCTCGCTCATTTTCTAGG
TTTCGTTACTTTCAGCTCTATTCATTCTGCTCAACTGCACTAATTTCTGCTCTGCTTAATATTCG
TGAGTTTTAAAAGTCCGTTTGCAAGGTTCTCAAGGGAAGCCAGAGTTTAAGCCAGTGTTTAAAAT
GTCAGG
Found at i:404810 original size:64 final size:63
Alignment explanation
Indices: 404735--404855 Score: 179
Period size: 64 Copynumber: 1.9 Consensus size: 63
404725 ATGGTTCAAG
* * * *
404735 GTGTATCGATGCACATGAAGTGCATCGATGCACTCCTTTAAAATAAAAACATTGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTT-AAATAAAAACATCGAATGCCATCA
* *
404799 GTGTATCGATGCACAAGTAGTGCATCGATGCACCCCCTTAAATACAAACATCGAATG
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATG
404856 GGATTTATGC
Statistics
Matches: 51, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
63 16 0.31
64 35 0.69
ACGTcount: A:0.35, C:0.22, G:0.18, T:0.25
Consensus pattern (63 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCTTAAATAAAAACATCGAATGCCATCA
Found at i:406262 original size:85 final size:84
Alignment explanation
Indices: 406164--406325 Score: 243
Period size: 85 Copynumber: 1.9 Consensus size: 84
406154 TGAGGGTGTT
* *
406164 ACACAATGTGTGTCATCTTCATTTATGACGAGGGCTTCGATGACACACAATGTAAGTCATATATG
1 ACACAATGTGTGTCATCTTCATTTATGACGAGGGCTTCAATGACACACAATGTAAGTCATAAATG
*
406229 TGTATCATAAATTTATGAC
66 AGTATCATAAATTTATGAC
* * **
406248 ACACAAATGTGTGTCATCTTCATTTATGACGGGGGCTTCAATGACACGCAATGTGCGTCATAAAT
1 ACAC-AATGTGTGTCATCTTCATTTATGACGAGGGCTTCAATGACACACAATGTAAGTCATAAAT
*
406313 GAGTGTCATAAAT
65 GAGTATCATAAAT
406326 GCACGTCATC
Statistics
Matches: 69, Mismatches: 8, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
84 4 0.06
85 65 0.94
ACGTcount: A:0.31, C:0.17, G:0.20, T:0.31
Consensus pattern (84 bp):
ACACAATGTGTGTCATCTTCATTTATGACGAGGGCTTCAATGACACACAATGTAAGTCATAAATG
AGTATCATAAATTTATGAC
Found at i:409187 original size:210 final size:208
Alignment explanation
Indices: 408705--409204 Score: 633
Period size: 210 Copynumber: 2.4 Consensus size: 208
408695 TTTTTTCTAT
* * *
408705 GCATTGTAATGCATTTAATCTTTT-TTAACGTCTCCGGGATTGAATTAC-A-AA---CGATATTT
1 GCATTATAATGCATTTAATCTTTTGTTAACGTCTTCTGGATTGAATTACAAGAAGTTCGATATTT
* * * *
408764 CTTAAATAAGACATTAAAATTTAATTCGATGGATATAGAACAAAGTTACGAGAAAGCTTAGCTTA
66 TTTAAATAAGATATT-AAGTTTAATTCGATGGATATAGAACAAAGTTACGAGAAAGCTTACCTTA
* * *
408829 CCGAAAGGTTCTCGAACGGATTCGACTCTGGACTTTCGAGACTTTCATCTCGATATTTCTCTTTT
130 CCGAAAGGTTCTCGAACCGATTCGACTATGGACTTTCGAGACTTTCATCTCGATATATCTCTTTT
*
408894 TTCTCACTTTTTAA
195 TTCACACTTTTTAA
* * * * *
408908 GCATTATAATGCATTTAGTCTTTTGTTAACCTCTTCTAGATTGAATTATAAGAAGTTTGATATTT
1 GCATTATAATGCATTTAATCTTTTGTTAACGTCTTCTGGATTGAATTACAAGAAGTTCGATA-TT
* *
408973 TTTTAAATAAGATATTAAGTTTCAATAT-GATGGATATGGAA-AAAGGTTACGGGAAAGCTTACC
65 TTTTAAATAAGATATTAAGTTT-AAT-TCGATGGATATAGAACAAA-GTTACGAGAAAGCTTACC
* * ** *
409036 TTA-CGAAAAGGTTCTCGAACCTATTCGACTATGGACTTTTGAGACTTTCATCTCTTTCTATCT-
127 TTACCG-AAAGGTTCTCGAACCGATTCGACTATGGACTTTCGAGACTTTCATCTCGATATATCTC
409099 TTCTCTTTCACACTTTTTAA
191 TT-T-TTTCACACTTTTTAA
* *
409119 GCATTATAATGCGTTTAATCTTTTGTTAACGTCTTCTGGATTGAATTACAAGAAGTTCGACATTT
1 GCATTATAATGCATTTAATCTTTTGTTAACGTCTTCTGGATTGAATTACAAGAAGTTCGATATTT
409184 TTTAAATAAGATATTAAGTTT
66 TTTAAATAAGATATTAAGTTT
409205 GATATTTGAT
Statistics
Matches: 254, Mismatches: 30, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
203 22 0.09
204 19 0.07
205 1 0.00
206 2 0.01
209 16 0.06
210 124 0.49
211 70 0.28
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (208 bp):
GCATTATAATGCATTTAATCTTTTGTTAACGTCTTCTGGATTGAATTACAAGAAGTTCGATATTT
TTTAAATAAGATATTAAGTTTAATTCGATGGATATAGAACAAAGTTACGAGAAAGCTTACCTTAC
CGAAAGGTTCTCGAACCGATTCGACTATGGACTTTCGAGACTTTCATCTCGATATATCTCTTTTT
TCACACTTTTTAA
Found at i:414652 original size:20 final size:21
Alignment explanation
Indices: 414606--414659 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
414596 TTTCTATAAG
*
414606 GGTACCGATACCCTAGGGGGA
1 GGTACCGATACCCTAGGAGGA
*
414627 GATACCGATACCCTA-GAGGA
1 GGTACCGATACCCTAGGAGGA
414647 GGTACCGATACCC
1 GGTACCGATACCC
414660 CCTAATATAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.53
21 14 0.47
ACGTcount: A:0.28, C:0.28, G:0.30, T:0.15
Consensus pattern (21 bp):
GGTACCGATACCCTAGGAGGA
Found at i:414934 original size:20 final size:20
Alignment explanation
Indices: 414909--414958 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
414899 GATGAACAGT
414909 GGGGGAATCGATTCCCTGTA
1 GGGGGAATCGATTCCCTGTA
414929 GGGGGAATCGATTCCCTGTA
1 GGGGGAATCGATTCCCTGTA
414949 GGGGGAATCG
1 GGGGGAATCG
414959 GTACCCCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.20, C:0.18, G:0.40, T:0.22
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTGTA
Found at i:415491 original size:44 final size:46
Alignment explanation
Indices: 415372--415495 Score: 146
Period size: 47 Copynumber: 2.7 Consensus size: 46
415362 TATAAAATCT
* *
415372 CTTACCATTT-ATCCCATAAGCTCGCAAGCTTATTTTACCAAAATA
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
* *
415417 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTTCCAATATA
1 CTTACCATTT-AATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
** * *
415464 CTTGTCA-TT-ATTCCGTAAGCTCATAAGCTTAT
1 CTTACCATTTAATTCCATAAGCTCGTAAGCTTAT
415496 ATGCATGATT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
44 21 0.30
45 10 0.14
46 2 0.03
47 36 0.52
ACGTcount: A:0.31, C:0.23, G:0.08, T:0.38
Consensus pattern (46 bp):
CTTACCATTTAATTCCATAAGCTCGTAAGCTTATTTTACCAAAATA
Found at i:415646 original size:40 final size:40
Alignment explanation
Indices: 415602--415763 Score: 297
Period size: 40 Copynumber: 4.0 Consensus size: 40
415592 ACCGTAGTAC
415602 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
415642 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
* *
415682 TACACATAAAGTCGTGCCCACCATATACACTGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
*
415722 TACATATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
1 TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
415762 TA
1 TA
415764 TAAACCTGCA
Statistics
Matches: 117, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 117 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (40 bp):
TACACATAAGGTCGTGCCCACCATATACACCGAAGTGTAT
Found at i:420431 original size:22 final size:22
Alignment explanation
Indices: 420390--420470 Score: 144
Period size: 22 Copynumber: 3.6 Consensus size: 22
420380 CTCGTATAAA
420390 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
420413 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
420435 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
420457 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
420471 ATATAATGAT
Statistics
Matches: 57, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
22 45 0.79
23 12 0.21
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:420466 original size:13 final size:13
Alignment explanation
Indices: 420404--420466 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
420394 CCGAAGTGCC
420404 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
420417 CC---GAAGTGC-
1 CCGTAGAATTGCA
420426 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
420439 CC---GAAGTGC-
1 CCGTAGAATTGCA
420448 CCGTAGAATTGCA
1 CCGTAGAATTGCA
420461 CCGTAG
1 CCGTAG
420467 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:421128 original size:2 final size:2
Alignment explanation
Indices: 421121--421174 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
421111 TCTCTTAAAC
421121 AT AT AT 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
421163 AT AT AT AT AT AT
1 AT AT AT AT AT AT
421175 TCACATGTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:422215 original size:21 final size:21
Alignment explanation
Indices: 422191--422235 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
422181 TCTTGTTCGT
*
422191 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
422212 TTGAATGGGTATCGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
422233 TTG
1 TTG
422236 CCCAGAAATC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Found at i:423174 original size:19 final size:19
Alignment explanation
Indices: 423151--423196 Score: 67
Period size: 18 Copynumber: 2.5 Consensus size: 19
423141 TTTTTTATAC
*
423151 ATTTTTAGAAATTTT-AAT
1 ATTTTTACAAATTTTAAAT
423169 ATTTTTACAAATTTTAAAT
1 ATTTTTACAAATTTTAAAT
*
423188 ATTTATACA
1 ATTTTTACA
423197 TTCTTTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 14 0.56
19 11 0.44
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.52
Consensus pattern (19 bp):
ATTTTTACAAATTTTAAAT
Found at i:434855 original size:2 final size:2
Alignment explanation
Indices: 434836--434936 Score: 75
Period size: 2 Copynumber: 57.0 Consensus size: 2
434826 TTTATATTTA
*
434836 AT AT -T AT A- AT AT -T AT AT AT AT AT AT A- AT TT A- AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
434872 AC A- AT AT -T AT AT AT AT AT A- AT TT A- AT AT -T AC A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
434908 -T 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
434937 TATTTAATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 26
0.71 0.05 0.23
Matches are distributed among these distances:
1 13 0.16
2 67 0.84
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:434868 original size:31 final size:31
Alignment explanation
Indices: 434831--434921 Score: 159
Period size: 29 Copynumber: 3.0 Consensus size: 31
434821 TAAAATTTAT
*
434831 ATTTAATATTATAATATTATATATATATATA
1 ATTTAATATTACAATATTATATATATATATA
434862 ATTTAATATTACAATA-T-TATATATATATA
1 ATTTAATATTACAATATTATATATATATATA
434891 ATTTAATATTACAATATTATATATATATATA
1 ATTTAATATTACAATATTATATATATATATA
434922 TATATATATA
Statistics
Matches: 57, Mismatches: 1, Indels: 4
0.92 0.02 0.06
Matches are distributed among these distances:
29 28 0.49
30 2 0.04
31 27 0.47
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (31 bp):
ATTTAATATTACAATATTATATATATATATA
Found at i:434928 original size:29 final size:30
Alignment explanation
Indices: 434828--434930 Score: 145
Period size: 31 Copynumber: 3.4 Consensus size: 30
434818 TTTTAAAATT
* *
434828 TATATTTAATATTATAATATTATATATATA
1 TATATATAATATTACAATATTATATATATA
*
434858 TATAATTTAATATTACAATATTATATATATA
1 TAT-ATATAATATTACAATATTATATATATA
*
434889 TA-ATTTAATATTACAATATTATATATATA
1 TATATATAATATTACAATATTATATATATA
434918 TATATATATATAT
1 TATATATA-ATAT
434931 ATATATTATT
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
29 29 0.43
30 7 0.10
31 32 0.47
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (30 bp):
TATATATAATATTACAATATTATATATATA
Found at i:434936 original size:29 final size:28
Alignment explanation
Indices: 434827--434948 Score: 82
Period size: 29 Copynumber: 4.5 Consensus size: 28
434817 CTTTTAAAAT
*
434827 TTATATTTAATATTATA-ATAT-TATATA
1 TTATATAT-ATATTATATATATATATATA
*
434854 -TATATATA-ATT-TA-ATAT-TACAATA
1 TTATATATATATTATATATATATA-TATA
* * *
434878 TTATATATATATAATTTA-ATATTACAATA
1 TTATATATATATTATATATATA-TA-TATA
434907 TTATATATATATATATATATATATATATA
1 TTATATATATAT-TATATATATATATATA
*
434936 TTATTTA-ATATTA
1 TTATATATATATTA
434949 CAATTTTAAC
Statistics
Matches: 78, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
23 8 0.10
24 6 0.08
25 9 0.12
26 8 0.10
27 5 0.06
28 5 0.06
29 28 0.36
30 6 0.08
31 3 0.04
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
TTATATATATATTATATATATATATATA
Found at i:435586 original size:34 final size:35
Alignment explanation
Indices: 435548--435620 Score: 139
Period size: 34 Copynumber: 2.1 Consensus size: 35
435538 TGTTCAATGA
435548 AATGTTCGACGTAAAGTTCATTTATTTATTAAAC-
1 AATGTTCGACGTAAAGTTCATTTATTTATTAAACG
435582 AATGTTCGACGTAAAGTTCATTTATTTATTAAACG
1 AATGTTCGACGTAAAGTTCATTTATTTATTAAACG
435617 AATG
1 AATG
435621 AACATGAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 34 0.89
35 4 0.11
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (35 bp):
AATGTTCGACGTAAAGTTCATTTATTTATTAAACG
Found at i:436123 original size:53 final size:50
Alignment explanation
Indices: 435986--436124 Score: 134
Period size: 53 Copynumber: 2.7 Consensus size: 50
435976 ACAGTGACAC
* *
435986 AGAACTCGTCACGTCGAGGTGATGAGTTCTAATAAAAAATATATTTTTATT
1 AGAACTCGTCAC-TCGACGTGATGAGTTCTAATAAAAAAAATATTTTTATT
** ** * * * * *
436037 CTAACTTTTTACCTCGATGTGATAAATTTTAATAAAAAAAATTATATTTTATT
1 AGAACTCGTCA-CTCGACGTGATGAGTTCTAATAAAAAAAA-TAT-TTTTATT
436090 AGAACTCGTCATCTCGACGTGATGAGTTCTAATAA
1 AGAACTCGTCA-CTCGACGTGATGAGTTCTAATAA
436125 CACTGTAAAA
Statistics
Matches: 65, Mismatches: 20, Indels: 4
0.73 0.22 0.04
Matches are distributed among these distances:
51 29 0.45
52 4 0.06
53 32 0.49
ACGTcount: A:0.36, C:0.13, G:0.14, T:0.37
Consensus pattern (50 bp):
AGAACTCGTCACTCGACGTGATGAGTTCTAATAAAAAAAATATTTTTATT
Found at i:436766 original size:14 final size:14
Alignment explanation
Indices: 436747--436774 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
436737 ACAGAAATGT
436747 AAAACATTTTCCAG
1 AAAACATTTTCCAG
436761 AAAACATTTTCCAG
1 AAAACATTTTCCAG
436775 TGTTTGAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.21, G:0.07, T:0.29
Consensus pattern (14 bp):
AAAACATTTTCCAG
Found at i:439946 original size:197 final size:197
Alignment explanation
Indices: 439611--440006 Score: 792
Period size: 197 Copynumber: 2.0 Consensus size: 197
439601 CCAATGCTGA
439611 AGCAACAACTCCCACTATTGTTTTATGAATAGAATTATGTTACATCTACAAAGAAATGATCGTAA
1 AGCAACAACTCCCACTATTGTTTTATGAATAGAATTATGTTACATCTACAAAGAAATGATCGTAA
439676 TAATTTATGAATACTTGAACTGTAAAATAAATACTTGAGGCAGTTATGGAAAGACTATCTCGCAT
66 TAATTTATGAATACTTGAACTGTAAAATAAATACTTGAGGCAGTTATGGAAAGACTATCTCGCAT
439741 TATTCTTGAGGTAGTTGATAATGGTGATTGAAAAGTTTTAAAATTATCTAGAAGAAACACTAATG
131 TATTCTTGAGGTAGTTGATAATGGTGATTGAAAAGTTTTAAAATTATCTAGAAGAAACACTAATG
439806 TT
196 TT
439808 AGCAACAACTCCCACTATTGTTTTATGAATAGAATTATGTTACATCTACAAAGAAATGATCGTAA
1 AGCAACAACTCCCACTATTGTTTTATGAATAGAATTATGTTACATCTACAAAGAAATGATCGTAA
439873 TAATTTATGAATACTTGAACTGTAAAATAAATACTTGAGGCAGTTATGGAAAGACTATCTCGCAT
66 TAATTTATGAATACTTGAACTGTAAAATAAATACTTGAGGCAGTTATGGAAAGACTATCTCGCAT
439938 TATTCTTGAGGTAGTTGATAATGGTGATTGAAAAGTTTTAAAATTATCTAGAAGAAACACTAATG
131 TATTCTTGAGGTAGTTGATAATGGTGATTGAAAAGTTTTAAAATTATCTAGAAGAAACACTAATG
440003 TT
196 TT
440005 AG
1 AG
440007 TCATCTATTT
Statistics
Matches: 199, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
197 199 1.00
ACGTcount: A:0.39, C:0.12, G:0.16, T:0.33
Consensus pattern (197 bp):
AGCAACAACTCCCACTATTGTTTTATGAATAGAATTATGTTACATCTACAAAGAAATGATCGTAA
TAATTTATGAATACTTGAACTGTAAAATAAATACTTGAGGCAGTTATGGAAAGACTATCTCGCAT
TATTCTTGAGGTAGTTGATAATGGTGATTGAAAAGTTTTAAAATTATCTAGAAGAAACACTAATG
TT
Found at i:442036 original size:32 final size:32
Alignment explanation
Indices: 441995--442101 Score: 94
Period size: 31 Copynumber: 3.4 Consensus size: 32
441985 AGTCGAGGGT
*
441995 TTACCTATGTTCTACGAAACATATAGACTGAA
1 TTACCTATGTTCTACGAAACATATAGACAGAA
* * * *
442027 TTACCTATG-TCTTTCGAGACATATGGACAGTA
1 TTACCTATGTTC-TACGAAACATATAGACAGAA
* * * *
442059 -TACCTATGTTCTAAGGAACATATGGACA-AT
1 TTACCTATGTTCTACGAAACATATAGACAGAA
*
442089 TTACCTAGGTTCT
1 TTACCTATGTTCT
442102 TCGAGACCTA
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
31 34 0.57
32 26 0.43
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.34
Consensus pattern (32 bp):
TTACCTATGTTCTACGAAACATATAGACAGAA
Found at i:442066 original size:31 final size:31
Alignment explanation
Indices: 442028--442119 Score: 89
Period size: 31 Copynumber: 3.0 Consensus size: 31
442018 TAGACTGAAT
442028 TACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTCTTTCGAGACATATGGACAGTA
*** * *
442059 TACCTATGTTCTAAGGA-ACATATGGACAATT
1 TACCTATG-TCTTTCGAGACATATGGACAGTA
* *
442090 TACCTAGGT-TCTTCGAGACCTATGGACAGT
1 TACCTATGTCT-TTCGAGACATATGGACAGT
442120 TGTTGAGGTT
Statistics
Matches: 47, Mismatches: 11, Indels: 6
0.73 0.17 0.09
Matches are distributed among these distances:
29 1 0.02
30 3 0.06
31 38 0.81
32 5 0.11
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.32
Consensus pattern (31 bp):
TACCTATGTCTTTCGAGACATATGGACAGTA
Found at i:442114 original size:62 final size:62
Alignment explanation
Indices: 441996--442119 Score: 162
Period size: 62 Copynumber: 2.0 Consensus size: 62
441986 GTCGAGGGTT
* *
441996 TACCTATGTTCTACGAAACATATAGACTGAATTACCTATGTCTTTCGAGACATATGGACAGTA
1 TACCTATGTTCTAAGAAACATATAGAC-GAATTACCTAGGTCTTTCGAGACATATGGACAGTA
* * *
442059 TACCTATGTTCTAAGGAACATATGGAC-AATTTACCTAGGT-TCTTCGAGACCTATGGACAGT
1 TACCTATGTTCTAAGAAACATATAGACGAA-TTACCTAGGTCT-TTCGAGACATATGGACAGT
442120 TGTTGAGGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
61 3 0.06
62 27 0.50
63 24 0.44
ACGTcount: A:0.31, C:0.19, G:0.18, T:0.31
Consensus pattern (62 bp):
TACCTATGTTCTAAGAAACATATAGACGAATTACCTAGGTCTTTCGAGACATATGGACAGTA
Found at i:444730 original size:63 final size:61
Alignment explanation
Indices: 444614--444732 Score: 157
Period size: 63 Copynumber: 1.9 Consensus size: 61
444604 AACCTCGGCA
* * * *
444614 ACTGTCCATAGGTCCCAAGAACCTAGGTAAATTGTCCATATGTTCCTTAGAACATAAGTAT
1 ACTGTCCATAGATCCCAAAAACATAGGTAAATTGTCCATATGTTCCGTAGAACATAAGTAT
* * *
444675 ACTGTCCATATATCCCAAAAAACATAGGTAATTCTGTCTATATGTTCCGTAGAACATA
1 ACTGTCCATAGATCCC-AAAAACATAGGTAAAT-TGTCCATATGTTCCGTAGAACATA
444733 GGTAAACCCT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
61 14 0.29
62 13 0.27
63 22 0.45
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.30
Consensus pattern (61 bp):
ACTGTCCATAGATCCCAAAAACATAGGTAAATTGTCCATATGTTCCGTAGAACATAAGTAT
Found at i:444731 original size:32 final size:32
Alignment explanation
Indices: 444615--444737 Score: 108
Period size: 31 Copynumber: 3.9 Consensus size: 32
444605 ACCTCGGCAA
* * * *
444615 CTGTCCATAGGTCCCA-AGAACCTAGGTAAAT
1 CTGTCCATATGTTCCATAGAACATAGGTAATT
* * *
444646 -TGTCCATATGTTCCTTAGAACATAAGT-ATA
1 CTGTCCATATGTTCCATAGAACATAGGTAATT
* * * *
444676 CTGTCCATATATCCCAAAAAACATAGGTAATT
1 CTGTCCATATGTTCCATAGAACATAGGTAATT
* *
444708 CTGTCTATATGTTCCGTAGAACATAGGTAA
1 CTGTCCATATGTTCCATAGAACATAGGTAA
444738 ACCCTCGACT
Statistics
Matches: 69, Mismatches: 20, Indels: 5
0.73 0.21 0.05
Matches are distributed among these distances:
30 13 0.19
31 30 0.43
32 26 0.38
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.30
Consensus pattern (32 bp):
CTGTCCATATGTTCCATAGAACATAGGTAATT
Found at i:445069 original size:24 final size:25
Alignment explanation
Indices: 445036--445082 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
445026 ACATGGTCAC
445036 AATTCATATAA-CACTTATATTATA
1 AATTCATATAATCACTTATATTATA
* *
445060 AATTCCTATAATTACTTATATTA
1 AATTCATATAATCACTTATATTA
445083 ATATCACATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.43, C:0.13, G:0.00, T:0.45
Consensus pattern (25 bp):
AATTCATATAATCACTTATATTATA
Found at i:445657 original size:64 final size:65
Alignment explanation
Indices: 445578--445716 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 65
445568 TCCCTTAACA
445578 TGTGCATCGATGCACTACC-CATGCATCGATACACAAATCACCTTCGATGTTT-TAATCTTAAGG
1 TGTGCATCGATGCACT-CCTCATGCATCGATACACAAATCACCTTCGATGTTTATAATCTTAAGG
445641 G
65 G
* * * * ** * * *
445642 TGTGTATCGATGCACTCCTTATGCATCGATGCACTAATTGCTTTCGATGTTTATATTTTTAAGGG
1 TGTGCATCGATGCACTCCTCATGCATCGATACACAAATCACCTTCGATGTTTATAATCTTAAGGG
445707 -GTGCATCGAT
1 TGTGCATCGAT
445717 ACACACTGAA
Statistics
Matches: 63, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
63 2 0.03
64 51 0.81
65 10 0.16
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.35
Consensus pattern (65 bp):
TGTGCATCGATGCACTCCTCATGCATCGATACACAAATCACCTTCGATGTTTATAATCTTAAGGG
Found at i:451769 original size:20 final size:20
Alignment explanation
Indices: 451715--451769 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
451705 TTAAGTATAC
*
451715 GGAATGTAAGATTACTAATG
1 GGAATGTAAGATTATTAATG
*
451735 AGAATGTAAGATTATTAATG
1 GGAATGTAAGATTATTAATG
*
451755 GGAATATAAGATTAT
1 GGAATGTAAGATTAT
451770 CAGGGAATAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.44, C:0.02, G:0.22, T:0.33
Consensus pattern (20 bp):
GGAATGTAAGATTATTAATG
Found at i:457895 original size:32 final size:33
Alignment explanation
Indices: 457854--457934 Score: 101
Period size: 32 Copynumber: 2.5 Consensus size: 33
457844 ATATTGTGCT
* ** *
457854 TAAGAGCCTACCCAATAGTGTACCTT-GGGGCC
1 TAAGAGCCTACCCAAGAGAATACCTTAGAGGCC
*
457886 TAAGAGCCTACCCAAGGGAATACCTTAGAGGCC
1 TAAGAGCCTACCCAAGAGAATACCTTAGAGGCC
*
457919 TTAGAGCCTACCCAAG
1 TAAGAGCCTACCCAAG
457935 TATCACCTTA
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
32 22 0.52
33 20 0.48
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (33 bp):
TAAGAGCCTACCCAAGAGAATACCTTAGAGGCC
Found at i:459011 original size:26 final size:26
Alignment explanation
Indices: 458976--459030 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
458966 TTCAAGGTAG
*
458976 ATTCATTCATTCCAGAGCTTAAGGGT
1 ATTCAATCATTCCAGAGCTTAAGGGT
* * **
459002 ATTCAATCATTTCAGGGCTTGTGGGT
1 ATTCAATCATTCCAGAGCTTAAGGGT
459028 ATT
1 ATT
459031 TTAGGTTATT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.16, G:0.22, T:0.38
Consensus pattern (26 bp):
ATTCAATCATTCCAGAGCTTAAGGGT
Found at i:459085 original size:27 final size:27
Alignment explanation
Indices: 459024--459086 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
459014 CAGGGCTTGT
*
459024 GGGTATTTTAGGTTATTTTACACTTCA
1 GGGTATTTTAGGTCATTTTACACTTCA
*
459051 GGGATATTTT-TGTCATTTTACAAC-TCAA
1 GGG-TATTTTAGGTCATTTTAC-ACTTC-A
459079 GGGTATTT
1 GGGTATTT
459087 CACTCATTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
27 19 0.61
28 12 0.39
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (27 bp):
GGGTATTTTAGGTCATTTTACACTTCA
Found at i:459956 original size:26 final size:26
Alignment explanation
Indices: 459927--459981 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
459917 TTCAAGGTAG
*
459927 ATTCATTCATTCCAGAGCTTATGGGT
1 ATTCAATCATTCCAGAGCTTATGGGT
* * *
459953 ATTCAATCATTTCAGGGCTTGTGGGT
1 ATTCAATCATTCCAGAGCTTATGGGT
459979 ATT
1 ATT
459982 TTAGGTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.40
Consensus pattern (26 bp):
ATTCAATCATTCCAGAGCTTATGGGT
Found at i:460036 original size:27 final size:27
Alignment explanation
Indices: 459975--460037 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
459965 CAGGGCTTGT
459975 GGGTATTTTAGGTCATTTTACACTTCA
1 GGGTATTTTAGGTCATTTTACACTTCA
*
460002 GGGATATTTT-TGTCATTTTACAAC-TCAA
1 GGG-TATTTTAGGTCATTTTAC-ACTTC-A
460030 GGGTATTT
1 GGGTATTT
460038 CACTCATTTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
27 20 0.62
28 12 0.38
ACGTcount: A:0.24, C:0.13, G:0.19, T:0.44
Consensus pattern (27 bp):
GGGTATTTTAGGTCATTTTACACTTCA
Found at i:460521 original size:951 final size:951
Alignment explanation
Indices: 458681--460583 Score: 3689
Period size: 951 Copynumber: 2.0 Consensus size: 951
458671 TATGTAGGTA
458681 GAGAAACTTCACGAATATTCATTTATTAGAACTGGGTACACTGCAGAATCGAACTGATCACCTTC
1 GAGAAACTTCACGAATATTCATTTATTAGAACTGGGTACACTGCAGAATCGAACTGATCACCTTC
*
458746 AGAACCATCTTTGGATGGATCATGAGGAGACAAATATGTATTTAAGCCGTATTTATTTACTTCTC
66 AGAACCATCTTTGGATGGATCATGAGGAGACAAATATGTATTTAAGCCGTATTTATTTACTTCCC
458811 GTATTGTAATAGTATTATGGATGGTCGACCTACTTAGGTCGTACTCCATAAACCTCAAAGGCGTT
131 GTATTGTAATAGTATTATGGATGGTCGACCTACTTAGGTCGTACTCCATAAACCTCAAAGGCGTT
*
458876 ACAATATTTAAAGATTCACTGATATCTTCCGAAGTTATCCAAAGGCATTTGCTTAATCCAAGTCA
196 ACAATATTTAAAGATTCACCGATATCTTCCGAAGTTATCCAAAGGCATTTGCTTAATCCAAGTCA
*
458941 TGAGGATATTCAAATTATTCTAGTATTCAAGGTAGATTCATTCATTCCAGAGCTTAAGGGTATTC
261 TGAGGATATTAAAATTATTCTAGTATTCAAGGTAGATTCATTCATTCCAGAGCTTAAGGGTATTC
*
459006 AATCATTTCAGGGCTTGTGGGTATTTTAGGTTATTTTACACTTCAGGGATATTTTTGTCATTTTA
326 AATCATTTCAGGGCTTGTGGGTATTTTAGGTCATTTTACACTTCAGGGATATTTTTGTCATTTTA
*
459071 CAACTCAAGGGTATTTCACTCATTTACTTCTGTCCAATATTTCCATTTAATTCAAACTTGTCATT
391 CAACTCAAGGGTATTTCACTCATTTACTTCTGTCCAATATTTCCATTTAACTCAAACTTGTCATT
459136 TATTTCAGTTATTTCAAACAATTCTGACAATAATGGCACTTCTGATAAGTTAGTATTCAGGTGTT
456 TATTTCAGTTATTTCAAACAATTCTGACAATAATGGCACTTCTGATAAGTTAGTATTCAGGTGTT
459201 TGCTCATAAAACATAAATTCTAGGTCAAGTGATTTCTCAAAGGAACGAACTAATTCTAAATTCTT
521 TGCTCATAAAACATAAATTCTAGGTCAAGTGATTTCTCAAAGGAACGAACTAATTCTAAATTCTT
459266 TTCAAACAAATCAAGAATTTAATAGGTGAATTAGTAATATATAAGATTAAATACGAATTCTCAGG
586 TTCAAACAAATCAAGAATTTAATAGGTGAATTAGTAATATATAAGATTAAATACGAATTCTCAGG
* *
459331 ATACTTTCACTATCATTGTCAATTCGGGTCATTTTTTCTTCTCAATGGTAATTTCGTAATTTATT
651 ATACTTTCACTATCATGGTCAATTCGGGTCATTTTTTCTTCACAATGGTAATTTCGTAATTTATT
459396 AATCGATATTAAAACTTTTAACGAAGATAAATAAAAGTTTAAGATTATGAGGTTAATTGTTTTTC
716 AATCGATATTAAAACTTTTAACGAAGATAAATAAAAGTTTAAGATTATGAGGTTAATTGTTTTTC
459461 TGGATAATCATTAAACTTGAAATTATTTTTATCAGTTTTCTAGTGTCTTATACGTATAATCTGAG
781 TGGATAATCATTAAACTTGAAATTATTTTTATCAGTTTTCTAGTGTCTTATACGTATAATCTGAG
459526 TCTTATTTAGTTTAATACTTTATATAGCATACAGATTAAGTTTAGAAATATTAACTACACTCATG
846 TCTTATTTAGTTTAATACTTTATATAGCATACAGATTAAGTTTAGAAATATTAACTACACTCATG
459591 TGACCAAACATAATCATTCATGCATTAACAAACACCAACAT
911 TGACCAAACATAATCATTCATGCATTAACAAACACCAACAT
459632 GAGAAACTTCACGAATATTCATTTATTAGAACTGGGTACACTGCAGAATCGAACTGATCACCTTC
1 GAGAAACTTCACGAATATTCATTTATTAGAACTGGGTACACTGCAGAATCGAACTGATCACCTTC
459697 AGAACCATCTTTGGATGGATCATGAGGAGACAAATATGTATTTAAGCCGTATTTATTTACTTCCC
66 AGAACCATCTTTGGATGGATCATGAGGAGACAAATATGTATTTAAGCCGTATTTATTTACTTCCC
*
459762 GTATTGTAATAGTATTATGGATGGTCGACCTACTTAGGTCGTACTCTATAAACCTCAAAGGCGTT
131 GTATTGTAATAGTATTATGGATGGTCGACCTACTTAGGTCGTACTCCATAAACCTCAAAGGCGTT
459827 ACAATATTTAAAGATTCACCGATATCTTCCGAAGTTATCCAAAGGCATTTGCTTAATCCAAGTCA
196 ACAATATTTAAAGATTCACCGATATCTTCCGAAGTTATCCAAAGGCATTTGCTTAATCCAAGTCA
*
459892 TGAGGATATTAAAATTATTCTAGTATTCAAGGTAGATTCATTCATTCCAGAGCTTATGGGTATTC
261 TGAGGATATTAAAATTATTCTAGTATTCAAGGTAGATTCATTCATTCCAGAGCTTAAGGGTATTC
459957 AATCATTTCAGGGCTTGTGGGTATTTTAGGTCATTTTACACTTCAGGGATATTTTTGTCATTTTA
326 AATCATTTCAGGGCTTGTGGGTATTTTAGGTCATTTTACACTTCAGGGATATTTTTGTCATTTTA
460022 CAACTCAAGGGTATTTCACTCATTTACTTCTGTCCAATATTTCCATTTAACTCAAACTTGTCATT
391 CAACTCAAGGGTATTTCACTCATTTACTTCTGTCCAATATTTCCATTTAACTCAAACTTGTCATT
460087 TATTTCAGTTATTTCAAACAATTCTGACAATAATGGCACTTCTGATAAGTTAGTATTCAGGTGTT
456 TATTTCAGTTATTTCAAACAATTCTGACAATAATGGCACTTCTGATAAGTTAGTATTCAGGTGTT
*
460152 TGCTCATAAAACATAAATTCTAGGTCTAGTGATTTCTCAAAGGAACGAACTAATTCTAAATTCTT
521 TGCTCATAAAACATAAATTCTAGGTCAAGTGATTTCTCAAAGGAACGAACTAATTCTAAATTCTT
460217 TTCAAACAAATCAAGAATTTAATAGGTGAATTAGTAATATATAAGATTAAATACGAATTCTCAGG
586 TTCAAACAAATCAAGAATTTAATAGGTGAATTAGTAATATATAAGATTAAATACGAATTCTCAGG
460282 ATACTTTCACTATCATGGTCAATTCGGGTCATTTTTTCTTCACAATGGTAATTTCGTAATTTATT
651 ATACTTTCACTATCATGGTCAATTCGGGTCATTTTTTCTTCACAATGGTAATTTCGTAATTTATT
*
460347 AATCGATATTAAAACTTTTAATGAAGATAAATAAAAGTTTAAGATTATGAGGTTAATTGTTTTTC
716 AATCGATATTAAAACTTTTAACGAAGATAAATAAAAGTTTAAGATTATGAGGTTAATTGTTTTTC
460412 TGGATAATCATTAAACTTGAAATTATTTTTATCAGTTTTCTAGTGTCTTATACGTATAATCTGAG
781 TGGATAATCATTAAACTTGAAATTATTTTTATCAGTTTTCTAGTGTCTTATACGTATAATCTGAG
*
460477 TCTTATTTAGTTTAATACTTTATATAGCATACAGATTGAGTTTAGAAATATTAACTACACTCATG
846 TCTTATTTAGTTTAATACTTTATATAGCATACAGATTAAGTTTAGAAATATTAACTACACTCATG
*
460542 TGACCAAACATAATCATTCATGCATTAATAAACACCAACAT
911 TGACCAAACATAATCATTCATGCATTAACAAACACCAACAT
460583 G
1 G
460584 TTCCATAAAG
Statistics
Matches: 939, Mismatches: 13, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
951 939 1.00
ACGTcount: A:0.33, C:0.15, G:0.14, T:0.37
Consensus pattern (951 bp):
GAGAAACTTCACGAATATTCATTTATTAGAACTGGGTACACTGCAGAATCGAACTGATCACCTTC
AGAACCATCTTTGGATGGATCATGAGGAGACAAATATGTATTTAAGCCGTATTTATTTACTTCCC
GTATTGTAATAGTATTATGGATGGTCGACCTACTTAGGTCGTACTCCATAAACCTCAAAGGCGTT
ACAATATTTAAAGATTCACCGATATCTTCCGAAGTTATCCAAAGGCATTTGCTTAATCCAAGTCA
TGAGGATATTAAAATTATTCTAGTATTCAAGGTAGATTCATTCATTCCAGAGCTTAAGGGTATTC
AATCATTTCAGGGCTTGTGGGTATTTTAGGTCATTTTACACTTCAGGGATATTTTTGTCATTTTA
CAACTCAAGGGTATTTCACTCATTTACTTCTGTCCAATATTTCCATTTAACTCAAACTTGTCATT
TATTTCAGTTATTTCAAACAATTCTGACAATAATGGCACTTCTGATAAGTTAGTATTCAGGTGTT
TGCTCATAAAACATAAATTCTAGGTCAAGTGATTTCTCAAAGGAACGAACTAATTCTAAATTCTT
TTCAAACAAATCAAGAATTTAATAGGTGAATTAGTAATATATAAGATTAAATACGAATTCTCAGG
ATACTTTCACTATCATGGTCAATTCGGGTCATTTTTTCTTCACAATGGTAATTTCGTAATTTATT
AATCGATATTAAAACTTTTAACGAAGATAAATAAAAGTTTAAGATTATGAGGTTAATTGTTTTTC
TGGATAATCATTAAACTTGAAATTATTTTTATCAGTTTTCTAGTGTCTTATACGTATAATCTGAG
TCTTATTTAGTTTAATACTTTATATAGCATACAGATTAAGTTTAGAAATATTAACTACACTCATG
TGACCAAACATAATCATTCATGCATTAACAAACACCAACAT
Found at i:461956 original size:30 final size:31
Alignment explanation
Indices: 461921--462008 Score: 117
Period size: 31 Copynumber: 2.9 Consensus size: 31
461911 GAAGGACCTA
* *
461921 TCCATATGTTTCGAATAG-CATAGGTAA-TTG
1 TCCATATGTCTCGAA-AGACATAGGTAAGCTG
*
461951 TCCATATGTCCCGAAAGACATAGGTAAGCTG
1 TCCATATGTCTCGAAAGACATAGGTAAGCTG
*
461982 TTCATATGTCTCGAAAGACATAGGTAA
1 TCCATATGTCTCGAAAGACATAGGTAA
462009 CCCTCGACTC
Statistics
Matches: 51, Mismatches: 5, Indels: 3
0.86 0.08 0.05
Matches are distributed among these distances:
29 2 0.04
30 22 0.43
31 27 0.53
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.30
Consensus pattern (31 bp):
TCCATATGTCTCGAAAGACATAGGTAAGCTG
Found at i:464087 original size:18 final size:18
Alignment explanation
Indices: 464064--464162 Score: 97
Period size: 18 Copynumber: 5.9 Consensus size: 18
464054 CGTAGAACAC
*
464064 ATGTCCCATAGGACCACT
1 ATGTCCCGTAGGACCACT
464082 ATGTCCCGTAGGACCACT
1 ATGTCCCGTAGGACCACT
* *
464100 ATATCCCGTAGAACCAC-
1 ATGTCCCGTAGGACCACT
* *
464117 --GT--AG-AGCA-CA-T
1 ATGTCCCGTAGGACCACT
464128 ATGTCCCGTAGGACCACT
1 ATGTCCCGTAGGACCACT
464146 ATGTCCCGTAGGACCAC
1 ATGTCCCGTAGGACCAC
464163 GTAGAACACA
Statistics
Matches: 65, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
11 2 0.03
12 3 0.05
13 3 0.05
15 2 0.03
16 3 0.05
17 2 0.03
18 50 0.77
ACGTcount: A:0.27, C:0.32, G:0.20, T:0.20
Consensus pattern (18 bp):
ATGTCCCGTAGGACCACT
Found at i:464118 original size:62 final size:63
Alignment explanation
Indices: 464021--464162 Score: 214
Period size: 64 Copynumber: 2.3 Consensus size: 63
464011 GCGTAGAGTT
* * * *
464021 TGTCCCGTAGGACCATTATGTCTCGTAGGACCACGTAGA-ACACATGTCCCATAGGACCACTA
1 TGTCCCGTAGGACCACTATATCCCGTAGAACCACGTAGACACACATGTCCCATAGGACCACTA
* *
464083 TGTCCCGTAGGACCACTATATCCCGTAGAACCACGTAGAGCACATATGTCCCGTAGGACCACTA
1 TGTCCCGTAGGACCACTATATCCCGTAGAACCACGTAGA-CACACATGTCCCATAGGACCACTA
464147 TGTCCCGTAGGACCAC
1 TGTCCCGTAGGACCAC
464163 GTAGAACACA
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
62 35 0.49
64 37 0.51
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.21
Consensus pattern (63 bp):
TGTCCCGTAGGACCACTATATCCCGTAGAACCACGTAGACACACATGTCCCATAGGACCACTA
Found at i:464137 original size:46 final size:46
Alignment explanation
Indices: 464081--464282 Score: 298
Period size: 46 Copynumber: 4.4 Consensus size: 46
464071 ATAGGACCAC
* * *
464081 TATGTCCCGTAGGACCACTATATCCCGTAGAACCACGTAGAGCACA
1 TATGTCCCGTAGGACCACTATGTCCCGTAGGACCACGTAGAACACA
464127 TATGTCCCGTAGGACCACTATGTCCCGTAGGACCACGTAGAACACA
1 TATGTCCCGTAGGACCACTATGTCCCGTAGGACCACGTAGAACACA
* ** * *
464173 TATGTCCCATATAACCACTATGTCCCGTAGGGCCATGTAGAACACA
1 TATGTCCCGTAGGACCACTATGTCCCGTAGGACCACGTAGAACACA
* *
464219 TATGTCCCGTAGGACCATTATGTCCCGTAGGACCACGT-GAAACAAA
1 TATGTCCCGTAGGACCACTATGTCCCGTAGGACCACGTAG-AACACA
464265 TATGTCCCGTAGGACCAC
1 TATGTCCCGTAGGACCAC
464283 GTAAAACCCT
Statistics
Matches: 139, Mismatches: 16, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
45 1 0.01
46 138 0.99
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.21
Consensus pattern (46 bp):
TATGTCCCGTAGGACCACTATGTCCCGTAGGACCACGTAGAACACA
Found at i:464195 original size:64 final size:64
Alignment explanation
Indices: 464064--464203 Score: 158
Period size: 64 Copynumber: 2.2 Consensus size: 64
464054 CGTAGAACAC
* * * * * * *
464064 ATGTCCCATAGGACCACTATGTCCCGTAGGACCACTATATCCCGTAGAACCACGTAGAGCACAT
1 ATGTCCCGTAGGACCACTATGTCCCGTAGGACCACTAGAACACATAGAACCACATAGACCACAT
** *
464128 ATGTCCCGTAGGACCACTATGTCCCGTAGGACCACGTAGAACACATATGTCCCATATA-ACCAC-
1 ATGTCCCGTAGGACCACTATGTCCCGTAGGACCAC-TAGAACACATA-GAACCACATAGACCACA
464191 T
64 T
464192 ATGTCCCGTAGG
1 ATGTCCCGTAGG
464204 GCCATGTAGA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
64 47 0.73
65 11 0.17
66 6 0.09
ACGTcount: A:0.29, C:0.31, G:0.19, T:0.21
Consensus pattern (64 bp):
ATGTCCCGTAGGACCACTATGTCCCGTAGGACCACTAGAACACATAGAACCACATAGACCACAT
Found at i:464240 original size:18 final size:18
Alignment explanation
Indices: 464219--464253 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
464209 GTAGAACACA
464219 TATGTCCCGTAGGACCAT
1 TATGTCCCGTAGGACCAT
464237 TATGTCCCGTAGGACCA
1 TATGTCCCGTAGGACCA
464254 CGTGAAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.26
Consensus pattern (18 bp):
TATGTCCCGTAGGACCAT
Found at i:467660 original size:3 final size:3
Alignment explanation
Indices: 467652--467717 Score: 64
Period size: 3 Copynumber: 22.0 Consensus size: 3
467642 TATAAATGAG
* * *
467652 TAT TAT TA- TAT TAT TAT TAT TAA TAT TAAT TAT TAA TAT TAAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT T-AT TAT
*
467698 TGT TAT TA- TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT
467718 CCAATCATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
2 4 0.08
3 41 0.80
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:467685 original size:13 final size:13
Alignment explanation
Indices: 467653--467696 Score: 63
Period size: 13 Copynumber: 3.3 Consensus size: 13
467643 ATAAATGAGT
467653 ATTATT-ATATTA
1 ATTATTAATATTA
467665 TTATTATTAATATTA
1 --ATTATTAATATTA
467680 ATTATTAATATTA
1 ATTATTAATATTA
467693 ATTA
1 ATTA
467697 GTGTTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
13 17 0.59
14 6 0.21
15 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTATTAATATTA
Found at i:469097 original size:34 final size:34
Alignment explanation
Indices: 469058--469122 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 34
469048 AGTTGTTCTA
*
469058 AGATAAATATTATAAT-TATCTCTTATATATTTAG
1 AGATAAATATAATAATATATCTC-TATATATTTAG
*
469092 AGATAATTATAATAATATATCTCTATATATT
1 AGATAAATATAATAATATATCTCTATATATT
469123 ATTATTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 22 0.79
35 6 0.21
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (34 bp):
AGATAAATATAATAATATATCTCTATATATTTAG
Found at i:471802 original size:8 final size:8
Alignment explanation
Indices: 471783--471841 Score: 64
Period size: 8 Copynumber: 7.4 Consensus size: 8
471773 ATCATTTTGC
*
471783 ATACATGT
1 ATACATAT
*
471791 ATACATAC
1 ATACATAT
*
471799 ATACATAC
1 ATACATAT
*
471807 ATATATAT
1 ATACATAT
*
471815 ATATATAT
1 ATACATAT
*
471823 ATATATAT
1 ATACATAT
471831 ATACATAT
1 ATACATAT
471839 ATA
1 ATA
471842 TTGAACTTGA
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
8 46 1.00
ACGTcount: A:0.49, C:0.10, G:0.02, T:0.39
Consensus pattern (8 bp):
ATACATAT
Found at i:471814 original size:2 final size:2
Alignment explanation
Indices: 471807--471842 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
471797 ACATACATAC
*
471807 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
471843 TGAACTTGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:471842 original size:12 final size:12
Alignment explanation
Indices: 471783--471842 Score: 66
Period size: 12 Copynumber: 5.0 Consensus size: 12
471773 ATCATTTTGC
* *
471783 ATACATGTATAC
1 ATACATATATAT
* *
471795 ATACATACATAC
1 ATACATATATAT
*
471807 ATATATATATAT
1 ATACATATATAT
*
471819 ATATATATATAT
1 ATACATATATAT
471831 ATACATATATAT
1 ATACATATATAT
471843 TGAACTTGAA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 42 1.00
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (12 bp):
ATACATATATAT
Found at i:472007 original size:14 final size:14
Alignment explanation
Indices: 471985--472015 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
471975 CTACAGGGAA
*
471985 ATATGCATATATAC
1 ATATACATATATAC
471999 ATATACATATATAC
1 ATATACATATATAC
472013 ATA
1 ATA
472016 GTTATTTCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.13, G:0.03, T:0.35
Consensus pattern (14 bp):
ATATACATATATAC
Found at i:472548 original size:4 final size:4
Alignment explanation
Indices: 472539--472600 Score: 65
Period size: 4 Copynumber: 16.0 Consensus size: 4
472529 AGAGTGGGCT
* * * *
472539 CATA CATA CATA CATA CATA CATA CATA TAT- CAAA GATT CAT- CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
*
472585 CATA CATA TATA CATA
1 CATA CATA CATA CATA
472601 TAATCTTCGG
Statistics
Matches: 47, Mismatches: 9, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
3 4 0.09
4 43 0.91
ACGTcount: A:0.48, C:0.21, G:0.02, T:0.29
Consensus pattern (4 bp):
CATA
Found at i:473999 original size:14 final size:13
Alignment explanation
Indices: 473977--474024 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
473967 TTTGACATTG
473977 TTTTTAAAAAGTA
1 TTTTTAAAAAGTA
*
473990 TTTTTGAAAAGTGA
1 TTTTTAAAAAGT-A
*
474004 TTTTGAAAAA-TA
1 TTTTTAAAAAGTA
474016 TTTTTAAAA
1 TTTTTAAAA
474025 GGTTGAATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
12 9 0.30
13 12 0.40
14 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (13 bp):
TTTTTAAAAAGTA
Found at i:474820 original size:23 final size:23
Alignment explanation
Indices: 474794--474841 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
474784 ATAAAGTACA
*
474794 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
474817 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
474840 AT
1 AT
474842 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:475313 original size:23 final size:23
Alignment explanation
Indices: 475278--475350 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
475268 ATACTTTACA
*
475278 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
475301 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
475324 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
475347 ATAT
1 ATAT
475351 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:475803 original size:23 final size:23
Alignment explanation
Indices: 475768--475840 Score: 119
Period size: 23 Copynumber: 3.2 Consensus size: 23
475758 ATACTTTACA
*
475768 ATATAAGCACTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
475791 ATATAAACGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
*
475814 ATATAAGCGCTACCTATTACATC
1 ATATAAGCGCTACCTATTACATT
475837 ATAT
1 ATAT
475841 TTTTACCTAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.38, C:0.22, G:0.05, T:0.34
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:476214 original size:25 final size:25
Alignment explanation
Indices: 476186--476250 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
476176 ACTCAAAAGA
*
476186 TGTATATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
476211 TGTACATACCTAAATATGTAGTTAT
1 TGTACATACCTAAATATGTAGTTAT
476236 TGTACATACCTAAAT
1 TGTACATACCTAAAT
476251 TTAATGATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (25 bp):
TGTACATACCTAAATATGTAGTTAT
Found at i:479021 original size:183 final size:183
Alignment explanation
Indices: 478712--480019 Score: 2280
Period size: 183 Copynumber: 7.1 Consensus size: 183
478702 TACTTAAAAT
* *
478712 TACCGACACAATATTAAAACGTGTCGATATAGGTTGTAAGACATATTCGCTCATAAAACCGGTAT
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGT-AGACCTATTCGCTCATAAAACCGGTAT
478777 ATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATC
65 ATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATC
*
478842 TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGATATAAAG
130 TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
478896 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
*
478961 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATCT
*
479026 CGATACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
479079 TACCGACATAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
479144 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATCT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATCT
*
479209 CGACATTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
479262 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
479327 TTTATACCGGTTATATTACAAAATTATCTATTTCATTATAAATCTGGGTTCCGATGTGTAAATAT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATCT
479392 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
479445 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
479510 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATCT
*
479575 CGACACTTTTTGACAAT-GTATCGACACATTTTTCTTCCAATCTGGACATAAAG
131 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
479628 TACCGACACAATATTAGAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
1 TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
* *
479693 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGT
66 TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATCT
* * *
479758 CGACAATTTTTGACAAT-GTATCGACACATTTTTCTTCTAATCTGGACATAAAG
131 CGACACTTTTTTA-AATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
479811 TACCGACACAATATTAAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCAGTAT
1 TACCGACACAATATT-AAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTAT
* * ***
479876 ATTTATACTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGT-TTTTTC
65 ATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATC
* * *
479940 AATCGACAGTTTTTTAAATGGTATCGACACATTTTTCTTTCATTCTGGACATAAAG
130 --TCGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
*
479996 TACAGACACAATATTAAAAAGTGT
1 TACCGACACAATATTAAAAAGTGT
480020 GAAAACTTTG
Statistics
Matches: 1084, Mismatches: 35, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
183 870 0.80
184 155 0.14
185 59 0.05
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (183 bp):
TACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATA
TTTATACCGGTTATATTACAAAATTATCTATTACATTATAAATCTGGGTTCCGATGTGTAAATCT
CGACACTTTTTTAAATGGTATCGACACATTTTTCTTCCAATCTGGACATAAAG
Found at i:480647 original size:200 final size:200
Alignment explanation
Indices: 480303--481279 Score: 1830
Period size: 200 Copynumber: 4.9 Consensus size: 200
480293 TTTAAATTAG
480303 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
*
480368 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATAATTTTGGGTTTT-GATGTTTTTGGG
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTT-GGTTTTCGATGTTTTTGGG
* *
480432 ATCGACACATTTTATATATGGATCGACACTTTATGGTTGCACCTTGTTTTCCATTCATTCTGGAC
130 ATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGAC
480497 CAAAAA
195 CAAAAA
480503 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
480568 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
*
480633 TCGACTCTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
480698 AAAAA
196 AAAAA
480703 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
* *
480768 CTTGTACAGGTTAGATTGAAAACTTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
480833 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
480898 AAAAA
196 AAAAA
*
480903 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACAGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
480968 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
481033 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
481098 AAAAA
196 AAAAA
** *
481103 TATCGACACAAACTAAAGCAGTGTCGACACATTATTTAGGCATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
481168 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
66 CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
* *
481233 TCGACACTTTTTATATATGGTTCGACACTTTATTGTTGCACCCTGTT
131 TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTT
481280 GGCCATATTG
Statistics
Matches: 760, Mismatches: 16, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
199 6 0.01
200 754 0.99
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.37
Consensus pattern (200 bp):
TATCGACACAAACTAAAAAAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
CTTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGTTTTCGATGTTTTTGGGA
TCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTTCCATTCATTCTGGACC
AAAAA
Found at i:481409 original size:18 final size:18
Alignment explanation
Indices: 481386--481446 Score: 59
Period size: 19 Copynumber: 3.3 Consensus size: 18
481376 TCTCATTCAT
*
481386 AATTATATTCACATACAA
1 AATTATAATCACATACAA
**
481404 AATTATAAATCGTATACAA
1 AATTAT-AATCACATACAA
**
481423 AATTATAAATCTTATACAA
1 AATTAT-AATCACATACAA
481442 AATTA
1 AATTA
481447 ACCCTACATT
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
18 6 0.16
19 32 0.84
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTATAATCACATACAA
Found at i:481422 original size:19 final size:19
Alignment explanation
Indices: 481398--481446 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
481388 TTATATTCAC
481398 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
481417 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
481436 ATACAAAATTA
1 ATACAAAATTA
481447 ACCCTACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:483275 original size:33 final size:33
Alignment explanation
Indices: 483238--483303 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
483228 CATCTTAATA
*
483238 TCACCCCTTAACACCCCAACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
* *
483271 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCCCAACTTCTTTCACCACT
483304 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCCCAACTTCTTTCACCACT
Found at i:483362 original size:21 final size:21
Alignment explanation
Indices: 483337--483401 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
483327 CCCCTTATGC
*
483337 CTCTCAAGTGTATCTTCGACT
1 CTCTCAAGTTTATCTTCGACT
*
483358 CTCTCAAGTTTCTCTTCGACT
1 CTCTCAAGTTTATCTTCGACT
*
483379 CTATCAAGTTTATCTTCGACT
1 CTCTCAAGTTTATCTTCGACT
483400 CT
1 CT
483402 TGATTGTCTT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.18, C:0.29, G:0.11, T:0.42
Consensus pattern (21 bp):
CTCTCAAGTTTATCTTCGACT
Found at i:485638 original size:17 final size:18
Alignment explanation
Indices: 485616--485658 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 18
485606 ATATATCCGG
485616 TATCATTT-TACCGGTTT
1 TATCATTTATACCGGTTT
485633 TATCATTTTGATACCGGTTT
1 TATCA-TTT-ATACCGGTTT
485653 TATCAT
1 TATCAT
485659 ATTTTTACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
17 5 0.22
18 3 0.13
19 1 0.04
20 14 0.61
ACGTcount: A:0.21, C:0.16, G:0.12, T:0.51
Consensus pattern (18 bp):
TATCATTTATACCGGTTT
Found at i:485676 original size:20 final size:19
Alignment explanation
Indices: 485621--485667 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
485611 TCCGGTATCA
485621 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
485640 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
485661 TTTTACC
1 TTTTACC
485668 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:485847 original size:20 final size:19
Alignment explanation
Indices: 485801--485847 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
485791 TCCGGTAACG
*
485801 TTTTACCGGTTTTATCATT
1 TTTTACCGATTTTATCATT
*
485820 TTGATACCGATTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
485841 TTTTACC
1 TTTTACC
485848 TGGTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:486074 original size:182 final size:180
Alignment explanation
Indices: 485588--486059 Score: 721
Period size: 180 Copynumber: 2.6 Consensus size: 180
485578 CGTACTTACG
* * *
485588 AAAGTATCGACACTTTCAATATATCCGGTATCATTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
485653 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTAAAGTATCGACACATTATA
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATA
* *
485718 GGCGCTAAAACTGTTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
485768 AAAGTATCGACACTTTTAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
485833 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTT-AAAGTATCGACACATTAT
** *
485898 AGGATTTAAAACTGCTTCTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
130 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * *
485950 AAAGTACCGACACTTTAAATGTATCCGGTAGCGCTTTACCGGTTTTATCATTTCT-ATACCGGTT
1 AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTT-TGATACCGGTT
* * *
486014 TTGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
65 TTATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
486060 AATTTGGATC
Statistics
Matches: 266, Mismatches: 23, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
180 104 0.39
181 62 0.23
182 99 0.37
183 1 0.00
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (180 bp):
AAAGTATCGACACTTTAAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAGTATCGACACATTATA
GGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:488085 original size:30 final size:31
Alignment explanation
Indices: 488042--488110 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
488032 GTAACGGGTT
*
488042 AAACGGACGGTTACGTC-GGGACCATATTGC
1 AAACGGACAGTTACGTCAGGGACCATATTGC
*
488072 AAACGGCCAGTTACGTCAGGGACCATATTGC
1 AAACGGACAGTTACGTCAGGGACCATATTGC
488103 AAACGGAC
1 AAACGGAC
488111 TAAATGATGG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 15 0.43
31 20 0.57
ACGTcount: A:0.30, C:0.25, G:0.28, T:0.17
Consensus pattern (31 bp):
AAACGGACAGTTACGTCAGGGACCATATTGC
Found at i:493711 original size:3 final size:3
Alignment explanation
Indices: 493703--493757 Score: 51
Period size: 3 Copynumber: 18.0 Consensus size: 3
493693 TGTGGGCATG
*
493703 TAA TAA TAA T-T TAA TTAA TTAA TAA TAA TAA TAA GTAA TAA -AA TAA
1 TAA TAA TAA TAA TAA -TAA -TAA TAA TAA TAA TAA -TAA TAA TAA TAA
*
493749 TAA GAA TAA
1 TAA TAA TAA
493758 AAAATAAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
2 3 0.07
3 31 0.70
4 10 0.23
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:493749 original size:21 final size:21
Alignment explanation
Indices: 493723--493781 Score: 61
Period size: 21 Copynumber: 3.0 Consensus size: 21
493713 TTAATTAATT
* **
493723 AATAATAATAATAAGTAATAA
1 AATAATAAGAATAAAAAATAA
493744 AATAATAAGAATAAAAAATAA
1 AATAATAAGAATAAAAAATAA
*
493765 AA-AAT--GGATAAAAAATA
1 AATAATAAGAATAAAAAATA
493782 GTATCTTCAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.32
20 3 0.09
21 20 0.59
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.22
Consensus pattern (21 bp):
AATAATAAGAATAAAAAATAA
Found at i:493749 original size:24 final size:25
Alignment explanation
Indices: 493703--493757 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
493693 TGTGGGCATG
* * *
493703 TAATAATAATTTAATTAATTAATAA
1 TAATAATAATGTAATAAAATAATAA
493728 TAATAATAA-GTAATAAAATAATAA
1 TAATAATAATGTAATAAAATAATAA
*
493752 GAATAA
1 TAATAA
493758 AAAATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 17 0.65
25 9 0.35
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (25 bp):
TAATAATAATGTAATAAAATAATAA
Found at i:494673 original size:195 final size:193
Alignment explanation
Indices: 494281--494690 Score: 757
Period size: 195 Copynumber: 2.1 Consensus size: 193
494271 TCTTCAGATG
494281 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAAAAAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAAAAAG
*
494346 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATCTTTAGATAAATTCTTCTCATTATGAA
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATCTTCAGATAAATTCTTCTCATTATGAA
*
494411 CACTTCTGGAAATGTTGGTGTTGATCTATCTCCTTCTGGATAGAATCAAACAAAGGTTGAACA
131 CACTTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGGATAGAATCAAACAAAGGTTGAACA
494474 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAAAAAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAAAAAG
* * *
494539 GTTGAACAAATTCTTCTCATTATGAATTTTTTTTCTTCATCTTCAGATGAGTTCTTCTCATTATG
66 GTTGAACAAATTCTTCTCATTATGAA--TTTCTTCTTCATCTTCAGATAAATTCTTCTCATTATG
494604 AACACTTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGGATAGAATCAAACAAAGGTTGAACA
129 AACACTTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGGATAGAATCAAACAAAGGTTGAACA
494669 AGTTCTTCTCATTATGAACTTC
1 AGTTCTTCTCATTATGAACTTC
494691 TTCTTCCTCT
Statistics
Matches: 210, Mismatches: 5, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
193 91 0.43
195 119 0.57
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.37
Consensus pattern (193 bp):
AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAAAAAG
GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATCTTCAGATAAATTCTTCTCATTATGAA
CACTTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGGATAGAATCAAACAAAGGTTGAACA
Found at i:494788 original size:112 final size:112
Alignment explanation
Indices: 494657--495071 Score: 534
Period size: 112 Copynumber: 3.6 Consensus size: 112
494647 AGAATCAAAC
*
494657 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
*
494722 TGAACTTCCTCTGGAAAAATTGATCCATCGAGTGATGAATTCAAGAA
66 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAA
* *
494769 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTA
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
* * * * * *
494834 TGAAC-ACTTCTGGAAATGTTGGTGCCGATATATCTCCTTA-TGGATAGAA-TCAA-AC
66 TGAACTTCCTCTGGAAAAGTTGAT-CC-----A--T-C-GAGT-GAT-GAATTCAAGAA
* *
494889 AAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTG
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
*
494954 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGAGATG-ATTCAAGAA
66 TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAA
* * *
495000 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTTTTCAGATGAGTTCTTCTCATT
1 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC-CTCTTCAGATGAGTTCTTCTCATT
495065 ATGAACT
65 ATGAACT
495072 CTACCTAGCA
Statistics
Matches: 260, Mismatches: 26, Indels: 34
0.81 0.08 0.11
Matches are distributed among these distances:
109 1 0.00
110 5 0.02
111 56 0.22
112 98 0.38
113 1 0.00
115 1 0.00
117 1 0.00
119 1 0.00
120 71 0.27
121 22 0.08
122 3 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (112 bp):
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATGAGTTCTTCTCATTA
TGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAA
Found at i:494901 original size:232 final size:232
Alignment explanation
Indices: 494474--495070 Score: 1088
Period size: 232 Copynumber: 2.6 Consensus size: 232
494464 AGGTTGAACA
494474 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAAAAAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAAAAAG
*
494539 GTTGAACAAATTCTTCTCATTATGAATTTTTTTTCTTCATCTTCAGATGAGTTCTTCTCATTATG
66 GTTGAACAAATTCTTCTCATTATGAA--TTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTATG
* * *
494604 AACACTTCTGGAAATGTTGGTGCTGATCTATCTCCTTCTGGATAGAATCAAACAAAGGTTGAACA
129 AACACTTCTGGAAATGTTGGTGCCGATATATCTCCTTATGGATAGAATCAAACAAAGGTTGAACA
494669 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
194 AGTTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
*
494708 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAATTGATCCATCGAGTGATGAATTCAAGAAAAAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAAAAAG
494773 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTATGAA
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTATGAA
494838 CACTTCTGGAAATGTTGGTGCCGATATATCTCCTTATGGATAGAATCAAACAAAGGTTGAACAAG
131 CACTTCTGGAAATGTTGGTGCCGATATATCTCCTTATGGATAGAATCAAACAAAGGTTGAACAAG
494903 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
196 TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
* *
494940 AGTTCTTCTCATTGTGAACTTCCTCTGGAAAAGTTGATCCATCGAGAGATG-ATTCAAGAAAAAG
1 AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAAAAAG
*
495004 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATTTTTCAGATGAGTTCTTCTCATTATGA
66 GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCA-TCTTCAGATGAGTTCTTCTCATTATGA
495069 AC
130 AC
495071 TCTACCTAGC
Statistics
Matches: 353, Mismatches: 9, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
231 50 0.14
232 213 0.60
234 90 0.25
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (232 bp):
AGTTCTTCTCATTATGAACTTCCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCAAGAAAAAG
GTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCATCTTCAGATGAGTTCTTCTCATTATGAA
CACTTCTGGAAATGTTGGTGCCGATATATCTCCTTATGGATAGAATCAAACAAAGGTTGAACAAG
TTCTTCTCATTATGAACTTCTTCTTCCTCTTCAGATG
Found at i:496923 original size:33 final size:33
Alignment explanation
Indices: 496886--496998 Score: 84
Period size: 33 Copynumber: 3.2 Consensus size: 33
496876 AACATACCCT
*
496886 AACATTTGCTGATACAGACGTTCAAAATGCACC
1 AACATTTGCTGATAAAGACGTTCAAAATGCACC
* ** *
496919 AACATTCTTGATTCTGATTAAAAGGGA-TTTCAGCATGCCCC
1 AACA-T-TTG---CTGA-T-AAA--GACGTTCAAAATGCACC
*
496960 AACATTTGCTGATATAGACGTTCAAAATGCACC
1 AACATTTGCTGATAAAGACGTTCAAAATGCACC
496993 AACATT
1 AACATT
496999 CTATTTTTGG
Statistics
Matches: 60, Mismatches: 10, Indels: 20
0.67 0.11 0.22
Matches are distributed among these distances:
32 2 0.03
33 20 0.33
34 3 0.05
35 4 0.07
36 4 0.07
38 4 0.07
39 4 0.07
40 3 0.05
41 14 0.23
42 2 0.03
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (33 bp):
AACATTTGCTGATAAAGACGTTCAAAATGCACC
Found at i:499617 original size:32 final size:32
Alignment explanation
Indices: 499560--499621 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
499550 GAAGAAATTA
* * *
499560 TTGTTATGCTTATCTGGTAGGGATACTTCTCG
1 TTGTTATACTCATCTGGTAGAGATACTTCTCG
*
499592 TTGTTATACTCATCTTGTAGAGATACTTCT
1 TTGTTATACTCATCTGGTAGAGATACTTCT
499622 TATTTCTAGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.19, C:0.16, G:0.19, T:0.45
Consensus pattern (32 bp):
TTGTTATACTCATCTGGTAGAGATACTTCTCG
Found at i:503474 original size:7 final size:7
Alignment explanation
Indices: 503440--503475 Score: 56
Period size: 7 Copynumber: 5.1 Consensus size: 7
503430 TAAAAGTACG
503440 AATGCAA
1 AATGCAA
503447 AATG-AA
1 AATGCAA
503453 AATGCAA
1 AATGCAA
503460 AGATGCAA
1 A-ATGCAA
503468 AATGCAA
1 AATGCAA
503475 A
1 A
503476 TGTATATATG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 6 0.22
7 14 0.52
8 7 0.26
ACGTcount: A:0.58, C:0.11, G:0.17, T:0.14
Consensus pattern (7 bp):
AATGCAA
Found at i:503625 original size:43 final size:43
Alignment explanation
Indices: 503557--503638 Score: 119
Period size: 43 Copynumber: 1.9 Consensus size: 43
503547 TGCATCAAAG
*
503557 AAAACTTTACATATAGGGGACAACTTTCAGTCCTAACTTCAAC
1 AAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTCAAC
* * * *
503600 AAAACTTTATATATATGGGATAACTTTCCCTCCTAACTT
1 AAAACTTTACATATAGGGGACAACTTTCACTCCTAACTT
503639 TTCTAAAGCC
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.10, T:0.33
Consensus pattern (43 bp):
AAAACTTTACATATAGGGGACAACTTTCACTCCTAACTTCAAC
Found at i:504998 original size:28 final size:28
Alignment explanation
Indices: 504959--505042 Score: 91
Period size: 28 Copynumber: 3.0 Consensus size: 28
504949 TAAAAACATT
*
504959 AATAATATATATATATAAATATTATGAA
1 AATAATAAATATATATAAATATTATGAA
*
504987 AATAATAAATATATATATAA-ATTTTGAA
1 AATAATAAATATATATA-AATATTATGAA
* *
505015 AATAAAAAATTATAAATTAAATA-TATGA
1 AATAATAAA-TATATA-TAAATATTATGA
505043 TTTTTTTTAA
Statistics
Matches: 47, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
28 31 0.66
29 13 0.28
30 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.37
Consensus pattern (28 bp):
AATAATAAATATATATAAATATTATGAA
Found at i:505791 original size:13 final size:14
Alignment explanation
Indices: 505775--505805 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
505765 ACATATTTCT
505775 TAAAATT-AATTTA
1 TAAAATTAAATTTA
505788 TAAAATTAAATTTA
1 TAAAATTAAATTTA
505802 TAAA
1 TAAA
505806 TAGGATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (14 bp):
TAAAATTAAATTTA
Found at i:505977 original size:24 final size:24
Alignment explanation
Indices: 505916--505978 Score: 60
Period size: 24 Copynumber: 2.7 Consensus size: 24
505906 ATTTAAAAGT
* *
505916 ATTAA-AAAATAAAGTACAATACA
1 ATTAATAAAATAAATTACAATAAA
*
505939 A--AATATAAATAAAATTGCAATAAA
1 ATTAATA-AAAT-AAATTACAATAAA
505963 ATTAATAAAATAAATT
1 ATTAATAAAATAAATT
505979 TAAAAACTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 9
0.73 0.07 0.20
Matches are distributed among these distances:
21 2 0.06
22 1 0.03
23 5 0.16
24 16 0.50
25 4 0.12
26 4 0.12
ACGTcount: A:0.65, C:0.05, G:0.03, T:0.27
Consensus pattern (24 bp):
ATTAATAAAATAAATTACAATAAA
Found at i:506952 original size:22 final size:22
Alignment explanation
Indices: 506924--506982 Score: 109
Period size: 22 Copynumber: 2.7 Consensus size: 22
506914 GGGAAGCTTC
506924 GGTGAGTCACCATAGCTATGGT
1 GGTGAGTCACCATAGCTATGGT
506946 GGTGAGTCACCATAGCTATGGT
1 GGTGAGTCACCATAGCTATGGT
*
506968 GGTGACTCACCATAG
1 GGTGAGTCACCATAG
506983 GGCTTCGACG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.24, C:0.20, G:0.31, T:0.25
Consensus pattern (22 bp):
GGTGAGTCACCATAGCTATGGT
Found at i:507257 original size:15 final size:15
Alignment explanation
Indices: 507233--507276 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
507223 TAATTTAATT
*
507233 AATAATAATAATAAGT
1 AATAA-AATAATAAGA
*
507249 TATAAAATAATAAGA
1 AATAAAATAATAAGA
*
507264 AAAAAAATAATAA
1 AATAAAATAATAA
507277 ATGGATAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 20 0.83
16 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (15 bp):
AATAAAATAATAAGA
Found at i:507257 original size:18 final size:21
Alignment explanation
Indices: 507217--507261 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
507207 CGTGGGCTTG
*
507217 TAATAATAATTTAATTAATAA
1 TAATAATAAGTTAATTAATAA
507238 TAATAATAAGTT-A-TAA-AA
1 TAATAATAAGTTAATTAATAA
507256 TAATAA
1 TAATAA
507262 GAAAAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 3 0.13
20 1 0.04
21 11 0.48
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (21 bp):
TAATAATAAGTTAATTAATAA
Found at i:516382 original size:20 final size:19
Alignment explanation
Indices: 516347--516394 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
516337 ATAAATTGTT
516347 TATA-AAATTTAATTTAAA
1 TATATAAATTTAATTTAAA
* *
516365 TATATAAATTATATTTTAGA
1 TATATAAATT-TAATTTAAA
*
516385 TATTTAAATT
1 TATATAAATT
516395 GTATAGATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.16
19 5 0.20
20 16 0.64
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
TATATAAATTTAATTTAAA
Found at i:530641 original size:47 final size:47
Alignment explanation
Indices: 530583--530674 Score: 132
Period size: 47 Copynumber: 2.0 Consensus size: 47
530573 ATCATTTAAT
*
530583 ATAAAACTTTACATAC-ATCTATATACTCGTGTTATATATATATATAC
1 ATAAAAATTTACAT-CTATCTATATACTCGTGTTATATATATATATAC
* * *
530630 ATAAAAATTTACGTCTATCTCTATATTCGTGTTATATATATATAT
1 ATAAAAATTTACATCTATCTATATACTCGTGTTATATATATATAT
530675 GTAGATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 1 0.03
47 39 0.98
ACGTcount: A:0.38, C:0.13, G:0.05, T:0.43
Consensus pattern (47 bp):
ATAAAAATTTACATCTATCTATATACTCGTGTTATATATATATATAC
Found at i:543296 original size:3 final size:3
Alignment explanation
Indices: 543278--543325 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
543268 AATATGAATA
* * *
543278 AAT AAT ATAT ATT AAT AAT AAT AAT ACT AAT ACT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
543324 AA
1 AA
543326 AATGAGTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:543703 original size:17 final size:16
Alignment explanation
Indices: 543678--543737 Score: 59
Period size: 17 Copynumber: 3.6 Consensus size: 16
543668 AAGTTGAACA
543678 AATTCTTCTCATTATG
1 AATTCTTCTCATTATG
*
543694 AATCTCTTCTTTCA-GATG
1 AAT-TCTTC--TCATTATG
*
543712 AGTTCTTCTCATTATG
1 AATTCTTCTCATTATG
543728 AACTTCTTCT
1 AA-TTCTTCT
543738 TCTTTCTTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 9
0.73 0.08 0.19
Matches are distributed among these distances:
15 3 0.09
16 7 0.20
17 17 0.49
18 5 0.14
19 3 0.09
ACGTcount: A:0.22, C:0.22, G:0.08, T:0.48
Consensus pattern (16 bp):
AATTCTTCTCATTATG
Found at i:543719 original size:34 final size:38
Alignment explanation
Indices: 543680--543775 Score: 139
Period size: 40 Copynumber: 2.6 Consensus size: 38
543670 GTTGAACAAA
543680 TTCTTCTCATTATGAA-TC-TCTTC-T-TTCAGATGAG
1 TTCTTCTCATTATGAACTCTTCTTCTTCTTCAGATGAG
543714 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAG
1 TTCTTCTCATTATGAAC-TCTTCTTC-TTCTTCAGATGAG
543754 TTCTTCTCATTATGAACT-TTCT
1 TTCTTCTCATTATGAACTCTTCT
543776 CTGGAAAAGC
Statistics
Matches: 56, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
34 16 0.29
36 2 0.04
37 5 0.09
38 4 0.07
39 2 0.04
40 27 0.48
ACGTcount: A:0.19, C:0.22, G:0.09, T:0.50
Consensus pattern (38 bp):
TTCTTCTCATTATGAACTCTTCTTCTTCTTCAGATGAG
Found at i:543915 original size:113 final size:112
Alignment explanation
Indices: 543714--544259 Score: 1002
Period size: 113 Copynumber: 4.8 Consensus size: 112
543704 TTCAGATGAG
* * *
543714 TTCTTCTCATTATGAACTTCTTCTTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
543779 GAAAAGCTGATCCATCGAATGATGGATTTGAGCATAAGGTTGAACAAA
66 GAAAAGCTGATCCATC-AATGATGGATTTGAGCATAAGGTTGAACAAA
543827 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
543892 GAAAAGCTGATCCATCAAGTGATGGATTTGAGCCTAAGGTTGAACAAA
66 GAAAAGCTGATCCATCAA-TGATGGATTTGAGCATAAGGTTGAACAAA
*
543940 TTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
544005 GAAAAGCTGATCCATCGAATGATGGATTTGAGCATAAGGTTGAACAAA
66 GAAAAGCTGATCCATC-AATGATGGATTTGAGCATAAGGTTGAACAAA
544053 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
544118 GAAAAGCTGATCCATCAAATGATGGATTTGAGCATAAGGTTGAACAAA
66 GAAAAGCTGATCCATC-AATGATGGATTTGAGCATAAGGTTGAACAAA
544166 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
544231 GAAAAGCTGATCCATCAAGTGATGGATTT
66 GAAAAGCTGATCCATCAA-TGATGGATTT
544260 AAATCTTTGC
Statistics
Matches: 422, Mismatches: 8, Indels: 6
0.97 0.02 0.01
Matches are distributed among these distances:
112 4 0.01
113 416 0.99
114 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (112 bp):
TTCTTCTCATTATGAATTTCTTCTTCCTCCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGCTGATCCATCAATGATGGATTTGAGCATAAGGTTGAACAAA
Found at i:545248 original size:115 final size:115
Alignment explanation
Indices: 545027--545468 Score: 778
Period size: 115 Copynumber: 3.9 Consensus size: 115
545017 TCAGAAGATG
* * * * * * *
545027 CTATTAGCACATTCCTCTTCCAAATTCAATAACTGGTTCTGTGG-TTCATACCAAACCAGATCAG
1 CTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
*
545091 ATAACTCAAAGAATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTA
66 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTA
545141 CTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
1 CTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
*
545206 ATAACTCAAAGAATACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTA
66 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTA
*
545256 CTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCTGTGGTTTCATATCAAACCAGATCAG
1 CTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
545321 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTA
66 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTA
*
545371 CTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCTGTGGTTTCATATCAAACCAGATCAG
1 CTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
545436 ATAACTCAAAGAACACTTCCAGAAGATGCTATT
66 ATAACTCAAAGAACACTTCCAGAAGATGCTATT
545469 AGCACATTCC
Statistics
Matches: 318, Mismatches: 9, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
114 37 0.12
115 281 0.88
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (115 bp):
CTATGAGCAAATTCATCTTTCAAATTTAATGATTGGTTCTGTGGTTTCATACCAAACCAGATCAG
ATAACTCAAAGAACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTA
Found at i:545562 original size:83 final size:83
Alignment explanation
Indices: 545423--545808 Score: 637
Period size: 83 Copynumber: 4.7 Consensus size: 83
545413 GGTTTCATAT
* *
545423 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
*
545488 TTCAATAACTGGTTTTAC
66 TTCAATAATTGGTTTTAC
* * *
545506 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATACTATTAGCACATTCCTCTTCCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
545571 TTCAATAATTGGTTTTAC
66 TTCAATAATTGGTTTTAC
* * *
545589 CAAACCAGATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGAGGACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
*
545654 TTCAATGATTGGTTTTAC
66 TTCAATAATTGGTTTTAC
* *
545672 CAAACCAGATCAGATAACTCAAATAACACTTCCAGAAGATGCTATGAGCACATTCATCTTTCAAA
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
*
545737 TTCAATGATTGGTTTTAC
66 TTCAATAATTGGTTTTAC
* *
545755 CAAACCAGATCAGATAAATCAAAGAACACTTCCAGAAGATGCTATGAGTACATT
1 CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATT
545809 GTATTTGTTC
Statistics
Matches: 288, Mismatches: 15, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
83 288 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.27
Consensus pattern (83 bp):
CAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAA
TTCAATAATTGGTTTTAC
Found at i:546979 original size:23 final size:22
Alignment explanation
Indices: 546954--547016 Score: 76
Period size: 22 Copynumber: 2.8 Consensus size: 22
546944 CTTGACCCCC
546954 TTTTTTTTTTTTTCTC-TTTTC
1 TTTTTTTTTTTTTCTCTTTTTC
*
546975 TCTTTTTTCTTTTTCTCTTTTT-
1 T-TTTTTTTTTTTTCTCTTTTTC
546997 TTTTCTTTTCTTTTTCTCTT
1 TTTT-TTTT-TTTTTCTCTT
547017 CAAGCATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 4 0.11
22 18 0.50
23 14 0.39
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (22 bp):
TTTTTTTTTTTTTCTCTTTTTC
Found at i:546980 original size:15 final size:14
Alignment explanation
Indices: 546962--547016 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 14
546952 CCTTTTTTTT
546962 TTTTTCTCTTTTCTC
1 TTTTT-TCTTTTCTC
546977 TTTTTTCTTTTTCTC
1 TTTTTTC-TTTTCTC
* *
546992 TTTTTTTTTCTTTTC
1 TTTTTTCTT-TTCTC
547007 TTTTTCTCTT
1 TTTTT-TCTT
547017 CAAGCATAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 4 0.12
15 27 0.79
16 3 0.09
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TTTTTTCTTTTCTC
Found at i:559761 original size:3 final size:3
Alignment explanation
Indices: 559743--559814 Score: 99
Period size: 3 Copynumber: 23.7 Consensus size: 3
559733 AATATGAATA
* *
559743 AAT AAT ATAT ATT AAT AAT AAT AAT AAT AAT TAT AAT AAT AAT AAT
1 AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
559789 TAT AAT AAT ACT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
559815 AATGAGTAAA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
3 57 0.95
4 3 0.05
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:562308 original size:148 final size:154
Alignment explanation
Indices: 562110--562664 Score: 524
Period size: 148 Copynumber: 3.6 Consensus size: 154
562100 TTTTTATATT
* * * * * *
562110 TTTATAAATAAGATATTTAATTACTTAGAAATATCAGAAAAGGACTTCTAGTTACTTTAAAACAA
1 TTTATAAATAGGATATTTATTTATTTAAAAATATCAGAAAAGGACATCTAGTTACTTTAAGAC--
*
562175 CCCTTTTCTTAATATTAAAAAATAAATAAATATTAAT-A-AA-A-CAT-TTTT-CT-AAAAATAA
64 CCCTTTTCTTAATATTAAAAAATAAATAAATATTAATAATAATATAATATTTTCCTAAAAAATAA
*
562233 TTAAAAAAT-AG--ATTAATATATA-A
129 TTAAAAAATAAGTAAAT-ATATATACA
562256 TTTATAAAAATAGGATATTTATTTATTTAAAAATATCAGAAAAGGACATCTAGTTACTTTAAGAC
1 TTTAT--AAATAGGATATTTATTTATTTAAAAATATCAGAAAAGGACATCTAGTTACTTTAAGAC
* * * *
562321 TGCTTTTTCTTTAATATTAATAAAGAAATAAATATTAATAATAATATAATAATTTTCCTAAAAAA
64 -CCCTTTTC-TTAATATTAAAAAATAAATAAATATTAATAATAATATAAT-ATTTTCCTAAAAAA
*
562386 TAATTAAAAACTAAGTAAATATATATACA
126 TAATTAAAAAATAAGTAAATATATATACA
** * * *
562415 TTTATAAGCAGGATATTTATTTATTTATTAAAATATCAGAATAGGACGTCTAGTTATTTTAAGAC
1 TTTATAAATAGGATATTTATTTATTTA--AAAATATCAGAAAAGGACATCTAGTTACTTTAAGAC
* * * *
562480 CGCTCTTTCTTAATATTAAAAAAATAAATAAATATTAAAAAT-GTGATAAT-TTTTCATAAAAAA
64 CCCT-TTTCTTAATATT-AAAAAATAAATAAATATTAATAATAAT-ATAATATTTTCCT-AAAAA
* *
562543 ATAATT-AAAATTAAATTAAATATATATA-A
125 ATAATTAAAAAAT-AAGTAAATATATATACA
* * * *
562572 TTT-T-TATA--ATATTTATTTATTT-AAAATACCAGAATAGAACATCTAGTTA-TATTAAGACT
1 TTTATAAATAGGATATTTATTTATTTAAAAATATCAGAAAAGGACATCTAGTTACT-TTAAGAC-
** *
562631 GTCATTTCTTAATA-TAAAAAATAAATAAATATTA
64 CCCTTTTCTTAATATTAAAAAATAAATAAATATTA
562665 TTATTTAAAC
Statistics
Matches: 347, Mismatches: 38, Indels: 46
0.81 0.09 0.11
Matches are distributed among these distances:
146 5 0.01
147 6 0.02
148 98 0.28
149 3 0.01
150 43 0.12
151 2 0.01
152 2 0.01
153 14 0.04
154 4 0.01
155 3 0.01
156 17 0.05
157 37 0.11
158 42 0.12
159 71 0.20
ACGTcount: A:0.48, C:0.07, G:0.06, T:0.38
Consensus pattern (154 bp):
TTTATAAATAGGATATTTATTTATTTAAAAATATCAGAAAAGGACATCTAGTTACTTTAAGACCC
CTTTTCTTAATATTAAAAAATAAATAAATATTAATAATAATATAATATTTTCCTAAAAAATAATT
AAAAAATAAGTAAATATATATACA
Found at i:562696 original size:2 final size:2
Alignment explanation
Indices: 562689--562744 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
562679 AAATAAATAA
562689 AT AT AT 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
*
562731 AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT
562745 GACTAAGATG
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:564201 original size:3 final size:3
Alignment explanation
Indices: 564186--564233 Score: 62
Period size: 3 Copynumber: 16.0 Consensus size: 3
564176 AATTATTTAT
* *
564186 TAA TAA TATA TAA TAA T-A TAA TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
564231 TAA
1 TAA
564234 AATGAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 34 0.87
4 3 0.08
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:564210 original size:21 final size:21
Alignment explanation
Indices: 564186--564233 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
564176 AATTATTTAT
564186 TAATAATATATAATAAT-ATAA
1 TAATAATAT-TAATAATAATAA
*
564207 TAATAATATTTATAATAATAA
1 TAATAATATTAATAATAATAA
564228 TAATAA
1 TAATAA
564234 AATGAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 6 0.24
21 19 0.76
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATAATATTAATAATAATAA
Found at i:564548 original size:45 final size:45
Alignment explanation
Indices: 564484--564580 Score: 151
Period size: 45 Copynumber: 2.2 Consensus size: 45
564474 TAAAATCTCA
** *
564484 TTTGAAAACATCTTGCACTGTAGGTCTTATGGATGACCCGAAGGT
1 TTTGAAAACATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGC
564529 TTTGAAAACAT-TATGCACTGTAGGTCTTACAGATGACCCGAAGGC
1 TTTGAAAACATCT-TGCACTGTAGGTCTTACAGATGACCCGAAGGC
564574 TTTGAAA
1 TTTGAAA
564581 TATCAAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
44 1 0.02
45 47 0.98
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.30
Consensus pattern (45 bp):
TTTGAAAACATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGC
Found at i:564760 original size:120 final size:120
Alignment explanation
Indices: 564484--565016 Score: 740
Period size: 120 Copynumber: 4.5 Consensus size: 120
564474 TAAAATCTCA
* * * * *
564484 TTTGAAAACATCTTGCACTGTAGGTCTTATGGATGACCC-GAAGGTTTTGAAAACATTATGCACT
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTG-AGGTCTTAAAAACATCATGCACT
564548 GTAGGTCTTACAGATGACCCGAAGGCTTTGAAATATCAAAAAA-CTCCCGAAGGCTT
65 GTAGGTCTTACAGATGACCCGAAGGCTTTGAAATAT-AAAAAAGCTCCCGAAGGCTT
* *
564604 GTTTGAACACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTAAAAAACATCATGCACT
1 -TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTAAAAACATCATGCACT
* *
564669 GTAGGTCTTACAGATGACCTGGAGGCTTT-AAATATAAAAAAGCTCCCGAAGGCTT
65 GTAGGTCTTACAGATGACCCGAAGGCTTTGAAATATAAAAAAGCTCCCGAAGGCTT
* * * * * *
564724 GTTTGAACACTTTCTGCATTGTAAGTCTTATGGATGGCCCTGAGGTCTTGAAAACATCATGCACT
1 -TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTAAAAACATCATGCACT
* * *
564789 GTAGGTCTTACAGATGACCCGGAGGCTTT-AAATATCAAAAAGCTCTCGAAGGCTT
65 GTAGGTCTTACAGATGACCCGAAGGCTTTGAAATATAAAAAAGCTCCCGAAGGCTT
* * *
564844 TTTGAAAACATCATGCACTGTAGGTCTTATGGATGGTCCC-GAGGTCTT---ATCATCTTGCACT
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGG-CCCTGAGGTCTTAAAAACATCATGCACT
* * *
564905 GTAGGTCTTATAGATGACCCGAAGGCTTTGAAATATCAAAAAGCTCCCGAAAGCTT
65 GTAGGTCTTACAGATGACCCGAAGGCTTTGAAATATAAAAAAGCTCCCGAAGGCTT
*
564961 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGACCCTGAGGTCTTAAAAACAT
1 TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTAAAAACAT
565017 TAAAAATCTC
Statistics
Matches: 371, Mismatches: 33, Indels: 17
0.88 0.08 0.04
Matches are distributed among these distances:
116 41 0.11
117 66 0.18
119 44 0.12
120 137 0.37
121 82 0.22
122 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (120 bp):
TTTGAAAACATCCTGCACTGTAGGTCTTATGGATGGCCCTGAGGTCTTAAAAACATCATGCACTG
TAGGTCTTACAGATGACCCGAAGGCTTTGAAATATAAAAAAGCTCCCGAAGGCTT
Found at i:565044 original size:76 final size:76
Alignment explanation
Indices: 564894--565558 Score: 797
Period size: 76 Copynumber: 8.7 Consensus size: 76
564884 GAGGTCTTAT
* * * *
564894 CATCTTGCACTGTAGGTCTTATAGATGACCCGAAGG-CTTTG-AAATATCAAAAAGCTCCCGAAA
1 CATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTC-TTGAAAACATCAAAAAGCTCCCGAAG
564957 GCTTTTTGAAAA
65 GCTTTTTGAAAA
** * * *
564969 CATCCTGCACTGTAGGTCTTATGGATGACCCTG-AGGTCTTAAAAACATTAAAAATCTCCCGAAG
1 CATCCTGCACTGTAGGTCTTACAGATGACCC-GAAGGTCTTGAAAACATCAAAAAGCTCCCGAAG
565033 GCTTTTTGAAAA
65 GCTTTTTGAAAA
* * * * * *
565045 CATCTTGCACTGTAGGTCTTACAGATGACCCGAAGGATCATGCACTGAAAGGC-TTACAGATGAT
1 CATCCTGCACTGTAGGTCTTACAGATGACCCGAAGG-TC-T----TGAAA-ACATCA-AAAAGCT
*
565109 -CCGAAGACTTTTTGAAAAA
58 CCCGAAGGCTTTTTG-AAAA
* * * *
565128 AATCCTGCACTGTAGGTCTTACAGATGATCCGAAGGTTTTGAAAACATCAAAAAGCTCCTGAAGG
1 CATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTCTTGAAAACATCAAAAAGCTCCCGAAGG
565193 CTTTTTGAAAA
66 CTTTTTGAAAA
* * *
565204 CATCCTGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGAAAACATCAAAAAGCTCCCGAAGG
1 CATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTCTTGAAAACATCAAAAAGCTCCCGAAGG
565269 CTTTTTGAAAA
66 CTTTTTGAAAA
* * * * *
565280 CACCCTGCACTGTAGGTCTTACAGATGACCAGAAGGTTTTGAAAACATCAAAAATCTCCTGAAGG
1 CATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTCTTGAAAACATCAAAAAGCTCCCGAAGG
565345 CTTTTTGAAAA
66 CTTTTTGAAAA
* * * *
565356 CATCATGCACTGAAGGGCTTAAAGATGACCCGAAGG-CTTTGAAAACATCAAAAAGCTCCCGAAG
1 CATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTC-TTGAAAACATCAAAAAGCTCCCGAAG
565420 GCTTTTTGAAAA
65 GCTTTTTGAAAA
* * *
565432 TATCCTGCACTGAAGGGT-TTACAAATGACCCGAAGG-CTTTGAAAACATCAAAAAGCTCCCGAA
1 CATCCTGCACTGTA-GGTCTTACAGATGACCCGAAGGTC-TTGAAAACATCAAAAAGCTCCCGAA
565495 GGCTTTTTTGAAAA
64 GGC-TTTTTGAAAA
* * *
565509 CATCCTGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTGAAAACATCA
1 CATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTCTTGAAAACATCA
565559 TGCACTGTAG
Statistics
Matches: 513, Mismatches: 57, Indels: 38
0.84 0.09 0.06
Matches are distributed among these distances:
75 35 0.07
76 339 0.66
77 75 0.15
78 1 0.00
81 1 0.00
82 21 0.04
83 41 0.08
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (76 bp):
CATCCTGCACTGTAGGTCTTACAGATGACCCGAAGGTCTTGAAAACATCAAAAAGCTCCCGAAGG
CTTTTTGAAAA
Found at i:566211 original size:22 final size:22
Alignment explanation
Indices: 566183--566239 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
566173 AATAAAGCTT
566183 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
566205 TCATCTTTGAAGAGAGAATCTA
1 TCATCTTTGAAGAGAGAATCTA
566227 TCATCTTTGAAGA
1 TCATCTTTGAAGA
566240 ATGTAAATGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (22 bp):
TCATCTTTGAAGAGAGAATCTA
Found at i:566705 original size:54 final size:54
Alignment explanation
Indices: 566609--566713 Score: 147
Period size: 54 Copynumber: 1.9 Consensus size: 54
566599 TAACTGGTTC
* * * * *
566609 GTAAAATATTTGACAACACATTTATCATCTCATGTGGTTTCTGTTCAGATGCTA
1 GTAAAACATTTGACAACACATTCATCATCTCACGTGGCTTCTGGTCAGATGCTA
* *
566663 GTAAAACATTTGACAACACATTCATCATTTCCCGTGGCTTCTGGTCAGATG
1 GTAAAACATTTGACAACACATTCATCATCTCACGTGGCTTCTGGTCAGATG
566714 TTCTCCAGTG
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 44 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.35
Consensus pattern (54 bp):
GTAAAACATTTGACAACACATTCATCATCTCACGTGGCTTCTGGTCAGATGCTA
Found at i:568571 original size:45 final size:45
Alignment explanation
Indices: 568520--568662 Score: 250
Period size: 45 Copynumber: 3.2 Consensus size: 45
568510 CAATTTAATC
*
568520 CCATAAGCTTGTAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
568565 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
* * *
568610 CCATAAACTCGTAAGCTTATTTTACCAACACACATACCATTTATT
1 CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
568655 CCATAAGC
1 CCATAAGC
568663 ATACTTGCCA
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 93 1.00
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.36
Consensus pattern (45 bp):
CCATAAGCTCGTAAGCTTATTTTACCAACATACTTACCATTTATT
Found at i:568690 original size:68 final size:68
Alignment explanation
Indices: 568593--568729 Score: 204
Period size: 68 Copynumber: 2.0 Consensus size: 68
568583 ATTTTACCAA
568593 CATACTTACCATTTATTCCATAAACTCGTAAGCTTATTTTACCAACACACATACCATTTATTCCA
1 CATACTTACCATTTATTCCATAAACTCGTAAGCTTATTTTACCAACACACATACCA-TTATTCCA
568658 TAAG
65 TAAG
* * * * * *
568662 CATACTTGCCA-TTATTCCATAAGCTCGTAATCTTATTTTACCAACATACTTGCCATTATTCCAT
1 CATACTTACCATTTATTCCATAAACTCGTAAGCTTATTTTACCAACACACATACCATTATTCCAT
568726 AAG
66 AAG
568729 C
1 C
568730 TCGTAAGCTT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
67 13 0.21
68 39 0.63
69 10 0.16
ACGTcount: A:0.32, C:0.26, G:0.06, T:0.36
Consensus pattern (68 bp):
CATACTTACCATTTATTCCATAAACTCGTAAGCTTATTTTACCAACACACATACCATTATTCCAT
AAG
Found at i:572672 original size:65 final size:64
Alignment explanation
Indices: 572532--572735 Score: 277
Period size: 65 Copynumber: 3.1 Consensus size: 64
572522 GTGCACTAAG
*
572532 TGTGCATCGATGCATAAAATGCATTCGATGTTTTAAAAAAGT-CTGAGTGCATCGATGCATGGCT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTATAAAA-TCCTGAGTGCATCGATGCATGGCT
* * *
572596 GGTGCATCGATGCATCAAATGCATTCTATGTTTTCATAAAATCCTGAGTGCATCGATGCATGG-T
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTT-ATAAAATCCTGAGTGCATCGATGCATGGCT
* * * *
572660 ATGTGCATCGATGCTTGAAATGCATTCGATGTTTTTATAAAACCCTGAGTGCATCGATGCATGGA
1 -TGTGCATCGATGCATAAAATGCATTCGATG-TTTTATAAAATCCTGAGTGCATCGATGCATGGC
572725 T
64 T
572726 TGGTGCATCG
1 T-GTGCATCG
572736 GTGTATCACT
Statistics
Matches: 125, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
64 33 0.26
65 79 0.63
66 13 0.10
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (64 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTTATAAAATCCTGAGTGCATCGATGCATGGCT
Found at i:574305 original size:20 final size:21
Alignment explanation
Indices: 574268--574307 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
574258 AAATTAAGTT
574268 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
574289 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
574308 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:574701 original size:65 final size:63
Alignment explanation
Indices: 574562--574764 Score: 282
Period size: 65 Copynumber: 3.1 Consensus size: 63
574552 GTGCACTAAG
*
574562 TGTGCATCGATGCATAAAATGCATTCGATGTTTTAAAAAAGT-CTGAGTGCATCGATGCATGGT
1 TGTGCATCGATGCATAAAATGCATTCGATGTTTTATAAAA-TCCTGAGTGCATCGATGCATGGT
* *
574625 TGGTGCATCGATGCATCAAATGCATTCTATGTTTTCATAAAATCCTGAGTGCATCGATGCATGGT
1 T-GTGCATCGATGCATAAAATGCATTCGATGTTTT-ATAAAATCCTGAGTGCATCGATGCATGGT
* * * *
574690 ATGTGCATCGATGCTTGAAATACATTCGATGTTTTATAAAACCCTGAGTGCATCGATGCATGGAT
1 -TGTGCATCGATGCATAAAATGCATTCGATGTTTTATAAAATCCTGAGTGCATCGATGCATGG-T
574755 TGGTGCATCG
1 T-GTGCATCG
574765 GTGTATCACT
Statistics
Matches: 126, Mismatches: 8, Indels: 10
0.88 0.06 0.07
Matches are distributed among these distances:
63 1 0.01
64 60 0.48
65 64 0.51
66 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (63 bp):
TGTGCATCGATGCATAAAATGCATTCGATGTTTTATAAAATCCTGAGTGCATCGATGCATGGT
Found at i:582238 original size:148 final size:153
Alignment explanation
Indices: 582058--582615 Score: 485
Period size: 148 Copynumber: 3.6 Consensus size: 153
582048 TTTTTATATT
* * * * * *
582058 TTTATAAATAAGATATTTATTTACTTAGAAATATCAGAAAATGACTTCTAGTTGCTTTAAGACAG
1 TTTATAAATATGATATTTATTTATTTAAAAATATCATAAAA-GACATCTAGTTACTTTAAGACAG
*
582123 TCCCTTTCTTAATATTAAAAAATAAATAAATATTAATA-AA-AT-AT-TTTT-CTAA-AAATAAT
65 -CACTTTCTTAATATTAAAAAATAAATAAATATTAATATAATATAATATTTTCCTAACAAATAAT
*
582182 TAAAAAAT-AG--ATTAATATATA-A
129 TAAAAAATAAGTAAAT-ATATATACA
582204 TTTATAAAAATATGATATTTATTTATTTAAAAATATCATAAAAGGACATCTAGTTACTTTAAGAC
1 TTTAT--AAATATGATATTTATTTATTTAAAAATATCATAAAA-GACATCTAGTTACTTTAAGAC
* * * *
582269 TGCATTTTCTTTAATATTAATAAAGAAATAAATATTAATATAATATAATAATTTTCCTAACAAAT
63 AGCACTTTC-TTAATATTAAAAAATAAATAAATATTAATATAATATAAT-ATTTTCCTAACAAAT
*
582334 AATTAAAAACTAAGTAAATATATATACA
126 AATTAAAAAATAAGTAAATATATATACA
** * * *
582362 TTTATAAGCATGATATTTATTTATTTTTTAAAATATCATAATAAGACGTCTAGTTATTTTAAGAC
1 TTTATAAATATGATATTTATTTA--TTTAAAAATATCATAA-AAGACATCTAGTTACTTTAAGAC
* * * *
582427 CGCTCTTTCTTAATATTAAAAAAATAAATAAATATTGAAAAT-GTGATAAT-TTTTCCTAA-ATA
63 AGCACTTTCTTAATATT-AAAAAATAAATAAATATT-AATATAAT-ATAATATTTTCCTAACA-A
*
582489 ATAATTTAAATAAAATAAAATTAAATATATATA-A
124 ATAA-TT-AA-AAAAT--AAGTAAATATATATACA
* * * * * * *
582523 TTT-T---TATAATTTTTATTTATTT-AAAATACCAGAATTAGACATCTAATTA-TATTAAGACT
1 TTTATAAATATGATATTTATTTATTTAAAAATATCATAA-AAGACATCTAGTTACT-TTAAGACA
582582 GTCA-TTTCTTAATA-TAAAAAATAAATAAATATTA
64 G-CACTTTCTTAATATTAAAAAATAAATAAATATTA
582616 TTATTTAAAC
Statistics
Matches: 346, Mismatches: 38, Indels: 51
0.80 0.09 0.12
Matches are distributed among these distances:
146 5 0.01
147 5 0.01
148 80 0.23
149 2 0.01
150 2 0.01
151 3 0.01
152 18 0.05
153 6 0.02
154 44 0.13
155 18 0.05
156 19 0.05
157 41 0.12
158 67 0.19
159 13 0.04
160 5 0.01
161 4 0.01
162 14 0.04
ACGTcount: A:0.47, C:0.07, G:0.06, T:0.40
Consensus pattern (153 bp):
TTTATAAATATGATATTTATTTATTTAAAAATATCATAAAAGACATCTAGTTACTTTAAGACAGC
ACTTTCTTAATATTAAAAAATAAATAAATATTAATATAATATAATATTTTCCTAACAAATAATTA
AAAAATAAGTAAATATATATACA
Found at i:582498 original size:158 final size:153
Alignment explanation
Indices: 582071--582615 Score: 465
Period size: 158 Copynumber: 3.6 Consensus size: 153
582061 ATAAATAAGA
* * * * * *
582071 TATTTATTTACTTAGAAATATCAGAAAATGACTTCTAGTTGCTTTAAGACAGTCCCTTTCTTAAT
1 TATTTATTTATTTA-AAATATCAGAAAAGGACATCTAGTTACTTTAAGACTG-CTCTTTCTTAAT
*
582136 ATTAAAAAATAAATAAATATTAATAA--AAT-ATTTTT-CTAAAAATAATT-AAAA-AA-TAGAT
64 ATTAAAAAATAAATAAATATTAATAATTAATAATTTTTCCTAAAAATAATTAAAAATAAGTA-AA
582194 TAATATATAATTTATAAAAATATGATATT
128 T-ATATATAATTTAT--AAATATGATATT
*
582223 TATTTATTTA---AAAATATCATAAAAGGACATCTAGTTACTTTAAGACTGCAT-TTTCTTTAAT
1 TATTTATTTATTTAAAATATCAGAAAAGGACATCTAGTTACTTTAAGACTGC-TCTTTC-TTAAT
* *
582284 ATTAATAAAGAAATAAATATTAATATAATATAATAA-TTTTCCTAACAAATAATTAAAAACTAAG
64 ATTAAAAAATAAATAAATATT-A-ATAAT-TAATAATTTTTCCTAA-AAATAATTAAAAA-TAAG
**
582348 TAAATATATATACATTTATAAGCATGATATT
124 TAAATATATATA-ATTTATAAATATGATATT
* * * *
582379 TATTTATTT-TTTAAAATATCATAATAA-GACGTCTAGTTATTTTAAGACCGCTCTTTCTTAATA
1 TATTTATTTATTTAAAATATCAGAA-AAGGACATCTAGTTACTTTAAGACTGCTCTTTCTTAATA
*
582442 TTAAAAAAATAAATAAATATTGAA-AATGTGATAATTTTTCCTAAATAATAATTTAAATAA-AA-
65 TT-AAAAAATAAATAAATATT-AATAAT-TAATAATTTTTCCTAAA-AATAA-TTAAA-AATAAG
* * * *
582504 TAAA-AT-TA-AATATATATAATTTTTATAAT
124 TAAATATATATAAT-T-TATAAATATGATATT
* * *
582533 T-TTTATTTATTTAAAATACCAGAATTA-GACATCTAATTA-TATTAAGACTG-TCATTTCTTAA
1 TATTTATTTATTTAAAATATCAGAA-AAGGACATCTAGTTACT-TTAAGACTGCTC-TTTCTTAA
582594 TA-TAAAAAATAAATAAATATTA
63 TATTAAAAAATAAATAAATATTA
582616 TTATTTAAAC
Statistics
Matches: 333, Mismatches: 30, Indels: 61
0.79 0.07 0.14
Matches are distributed among these distances:
147 5 0.02
148 56 0.17
149 2 0.01
150 4 0.01
151 1 0.00
152 30 0.09
153 20 0.06
154 61 0.18
155 10 0.03
156 36 0.11
157 33 0.10
158 69 0.21
159 6 0.02
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.40
Consensus pattern (153 bp):
TATTTATTTATTTAAAATATCAGAAAAGGACATCTAGTTACTTTAAGACTGCTCTTTCTTAATAT
TAAAAAATAAATAAATATTAATAATTAATAATTTTTCCTAAAAATAATTAAAAATAAGTAAATAT
ATATAATTTATAAATATGATATT
Found at i:582514 original size:15 final size:17
Alignment explanation
Indices: 582484--582515 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
582474 AATTTTTCCT
582484 AAATAATAATTTAAATA
1 AAATAATAATTTAAATA
582501 AAATAA-AA-TTAAATA
1 AAATAATAATTTAAATA
582516 TATATAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 2 0.13
17 6 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAATAATAATTTAAATA
Found at i:582635 original size:2 final size:2
Alignment explanation
Indices: 582628--582659 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
582618 ATTTAAACAA
582628 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
582660 GACTAAGATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:584076 original size:3 final size:3
Alignment explanation
Indices: 584061--584117 Score: 80
Period size: 3 Copynumber: 19.0 Consensus size: 3
584051 AATTATTTAT
* *
584061 TAA TAA TATA TAA TAA T-A TAA TAA TAA TAT TTA TAA TAA TAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
584106 TAA TAA TAA TAA
1 TAA TAA TAA TAA
584118 AATGAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 2 0.04
3 43 0.90
4 3 0.06
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:587084 original size:16 final size:17
Alignment explanation
Indices: 587056--587087 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
587046 TATATTAATA
587056 TAATAATAATAAATTAT
1 TAATAATAATAAATTAT
587073 TAATAA-AATAAATTA
1 TAATAATAATAAATTA
587088 GAGTGATTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAATAAATTAT
Found at i:589561 original size:34 final size:34
Alignment explanation
Indices: 589513--589585 Score: 119
Period size: 34 Copynumber: 2.1 Consensus size: 34
589503 AACAAAAATG
*
589513 ATAATTATGTTATTTACCAATATTAAATTACTTT
1 ATAATTATGCTATTTACCAATATTAAATTACTTT
* *
589547 ATAATTATGCTATTTACCTATATTAAATTGCTTT
1 ATAATTATGCTATTTACCAATATTAAATTACTTT
589581 ATAAT
1 ATAAT
589586 CATCTACAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.37, C:0.10, G:0.04, T:0.49
Consensus pattern (34 bp):
ATAATTATGCTATTTACCAATATTAAATTACTTT
Done.