Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 117 of 187
Found at i:35222423 original size:33 final size:33
Alignment explanation
Indices: 35222386--35222455 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 33
35222376 ACTCTTTATT
35222386 TGGTGTGTTGGTTGGACTAGCTCTTATGAGCAC
1 TGGTGTGTTGGTTGGACTAGCTCTTATGAGCAC
* * *
35222419 TGGTGTGTTGGTTGGATTAGCTCTTCTGAGCAT
1 TGGTGTGTTGGTTGGACTAGCTCTTATGAGCAC
35222452 TGGT
1 TGGT
35222456 ATGCTGGAGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.13, C:0.13, G:0.34, T:0.40
Consensus pattern (33 bp):
TGGTGTGTTGGTTGGACTAGCTCTTATGAGCAC
Found at i:35222469 original size:33 final size:33
Alignment explanation
Indices: 35222403--35222474 Score: 81
Period size: 33 Copynumber: 2.2 Consensus size: 33
35222393 TTGGTTGGAC
* * **
35222403 TAGCTCTTATGAGCACTGGTGTGTTGGTTGGAT
1 TAGCTCTTATGAGCACTGGTATGCTGGAGGGAT
* *
35222436 TAGCTCTTCTGAGCATTGGTATGCTGGAGGGAT
1 TAGCTCTTATGAGCACTGGTATGCTGGAGGGAT
*
35222469 TGGCTC
1 TAGCTC
35222475 GTGTGAGTTT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.15, C:0.15, G:0.33, T:0.36
Consensus pattern (33 bp):
TAGCTCTTATGAGCACTGGTATGCTGGAGGGAT
Found at i:35226768 original size:27 final size:27
Alignment explanation
Indices: 35226709--35226773 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 27
35226699 AATTTTGTTT
* * *
35226709 CATTCTTTTATTAGTTTATTTTTTTTA
1 CATTATTTTATTAGTTAATTTCTTTTA
* * *
35226736 CTTTATTTTATTTGTTAATTTCTTTTC
1 CATTATTTTATTAGTTAATTTCTTTTA
*
35226763 CATTATCTTAT
1 CATTATTTTAT
35226774 ATTGCATATT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.18, C:0.11, G:0.03, T:0.68
Consensus pattern (27 bp):
CATTATTTTATTAGTTAATTTCTTTTA
Found at i:35230355 original size:420 final size:427
Alignment explanation
Indices: 35229536--35230381 Score: 1086
Period size: 420 Copynumber: 2.0 Consensus size: 427
35229526 TTAATCAAAC
*
35229536 GATTATGCTTCCAATAGCTAAAATGTGGATACAGTTTATTTGCACTAGAATTACACAAGCTCTAA
1 GATTATGCTTCCAATAGCAAAAATGTGGATACAGTTTATTTGCACTAGAATTACACAAGCTCTAA
*
35229601 ATATCTCTAATGTCAATACTTTTCGAGCTATGTTGCTATGTGGAATTTTGTAAAAAAAAAAACAA
66 ATATCTCTAATGTCAATACTTTTCGAGCTATGTTGCTATATGGAATTTTGTAAAAAAAAAAACAA
* * * * *
35229666 CTATGCATTGTAGAATGGATCTATCAAAATATGAAACAATGAGTTCGCATCCAGAAGCTCGATAT
131 CTATGCATTGGAGAATAGATCCATCAAAATATGAAACAATGACTTCGCAGCCAGAAGCTCGATAT
* * * *
35229731 TTTCTTTCCCCATCTTGTGACGACATCATGCAAATAGGCTAGAGTCCCTATGGAAGAGAATGAAA
196 TTTCTTTCACCATCTTGTGACAACATCATGCAAACAGGCTAGAGTCCCTATGGAAAAGAATGAAA
** ** * *
35229796 AGTTTATGTGATTGACAAAGAGCCTAATAGGCGACTCTATGTACATATAGTACGTAGAGCACAAT
261 AGTTTATACGACCGACAAAGAGCCTAATAGGCGACTCTATGTACACACAGTACGTAGAGCACAAT
* * * * * *
35229861 TGGAAACAAATTAAAGATTGGAACCAAATGAGAAAAGTAAAGATAGACATCCCGACTTTGCTTAA
326 CGAAAACAAATTAAAGATTGGAACCAAAGGAGAAAAGAAAAGATAGACATCCAGACTTTGCATAA
35229926 ACAAAAAGTAAGA-CTAACGCCTCAAAAAGAAATTAGT
391 ACAAAAAGTAAGATC-AACGCCTCAAAAAGAAATTAGT
* * *
35229963 GATTAT-CTTCCAATAGCAAAAATGTGGATGCAGTTTGTTTGCACTAGAATTACACCAGCTCTAA
1 GATTATGCTTCCAATAGCAAAAATGTGGATACAGTTTATTTGCACTAGAATTACACAAGCTCTAA
* * * * *
35230027 ATGTCTCTAATGTCAATACTTTTCGAGCTATTTTGCTATATGGGA-TTT-T-ACAGAAAAAA-AA
66 ATATCTCTAATGTCAATACTTTTCGAGCTATGTTGCTATATGGAATTTTGTAAAAAAAAAAACAA
* *
35230088 -TATGCATTGGAGAATAGATCCATCAAAATATGAAACAATG-CTTCATCAGCCAGAAGGTCGA-A
131 CTATGCATTGGAGAATAGATCCATCAAAATATGAAACAATGACTTC-GCAGCCAGAAGCTCGATA
* * *
35230150 TTTTCTTTCATCATCTTGTGACAACA-CTATGCAAACATGCTAGAGTTCCTATGGAAAAGAAT-A
195 TTTTCTTTCACCATCTTGTGACAACATC-ATGCAAACAGGCTAGAGTCCCTATGGAAAAGAATGA
* * *
35230213 AGCAGTTTATACGGCCGACAAAGAGCCTAATAGGCGACTCTATGTACACACAGTACGTAGAGCTC
259 A-AAGTTTATACGACCGACAAAGAGCCTAATAGGCGACTCTATGTACACACAGTACGTAGAGCAC
* * * * * ** * *
35230278 AATCGAAAACATATTAAATATTGGTACTAGAGGAGAAGCGAAAAGATGGACGTCCTAG-CTTTGC
323 AATCGAAAACAAATTAAAGATTGGAACCAAAGGAGAAAAGAAAAGATAGACATCC-AGACTTTGC
** * **
35230342 ATAAATGAAAAGTAAGATCGACGCCTTGAAAAGAAATTAG
387 ATAAACAAAAAGTAAGATCAACGCCTCAAAAAGAAATTAG
35230382 CGAGAGTAGC
Statistics
Matches: 361, Mismatches: 53, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
419 3 0.01
420 191 0.53
421 52 0.14
422 2 0.01
423 8 0.02
424 1 0.00
425 3 0.01
426 95 0.26
427 6 0.02
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.27
Consensus pattern (427 bp):
GATTATGCTTCCAATAGCAAAAATGTGGATACAGTTTATTTGCACTAGAATTACACAAGCTCTAA
ATATCTCTAATGTCAATACTTTTCGAGCTATGTTGCTATATGGAATTTTGTAAAAAAAAAAACAA
CTATGCATTGGAGAATAGATCCATCAAAATATGAAACAATGACTTCGCAGCCAGAAGCTCGATAT
TTTCTTTCACCATCTTGTGACAACATCATGCAAACAGGCTAGAGTCCCTATGGAAAAGAATGAAA
AGTTTATACGACCGACAAAGAGCCTAATAGGCGACTCTATGTACACACAGTACGTAGAGCACAAT
CGAAAACAAATTAAAGATTGGAACCAAAGGAGAAAAGAAAAGATAGACATCCAGACTTTGCATAA
ACAAAAAGTAAGATCAACGCCTCAAAAAGAAATTAGT
Found at i:35231439 original size:48 final size:48
Alignment explanation
Indices: 35231365--35231463 Score: 162
Period size: 48 Copynumber: 2.1 Consensus size: 48
35231355 ATAAAATATG
* * *
35231365 ATAGAACCACCAGTCTACATAGTAATCTCGGTGCAGTGCACTGACTAT
1 ATAGAACCACCAGTCTACACACTAATCTCAGTGCAGTGCACTGACTAT
*
35231413 ATAGAACCGCCAGTCTACACACTAATCTCAGTGCAGTGCACTGACTAT
1 ATAGAACCACCAGTCTACACACTAATCTCAGTGCAGTGCACTGACTAT
35231461 ATA
1 ATA
35231464 TAAATGCAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (48 bp):
ATAGAACCACCAGTCTACACACTAATCTCAGTGCAGTGCACTGACTAT
Found at i:35231876 original size:12 final size:12
Alignment explanation
Indices: 35231855--35231888 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
35231845 TCATATTAGT
*
35231855 ACCAAACAGTCA
1 ACCATACAGTCA
*
35231867 ACCATTCAGTCA
1 ACCATACAGTCA
35231879 ACCATACAGT
1 ACCATACAGT
35231889 TTTGCAAACA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.32, G:0.09, T:0.18
Consensus pattern (12 bp):
ACCATACAGTCA
Found at i:35233907 original size:8 final size:8
Alignment explanation
Indices: 35233891--35233920 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
35233881 ATTTCTGGTG
35233891 TTTGAAAGT
1 TTTG-AAGT
35233900 TTTGAAGT
1 TTTGAAGT
35233908 TTTGAAGT
1 TTTGAAGT
35233916 TTTGA
1 TTTGA
35233921 TAGATGGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (8 bp):
TTTGAAGT
Found at i:35235122 original size:15 final size:15
Alignment explanation
Indices: 35235098--35235130 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
35235088 CTAAATTTTG
*
35235098 AAATTTAAAAAATTA
1 AAATTAAAAAAATTA
35235113 AAATTAAAAAAATTA
1 AAATTAAAAAAATTA
35235128 AAA
1 AAA
35235131 AGACTAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
AAATTAAAAAAATTA
Found at i:35235301 original size:25 final size:25
Alignment explanation
Indices: 35235264--35235312 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
35235254 TACATGGACA
35235264 ACTAATAAGCATAGATTAAATTTTC
1 ACTAATAAGCATAGATTAAATTTTC
* *
35235289 ACTATTAATCATAGATTAAATTTT
1 ACTAATAAGCATAGATTAAATTTT
35235313 TACTGTACAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.06, T:0.41
Consensus pattern (25 bp):
ACTAATAAGCATAGATTAAATTTTC
Found at i:35235556 original size:107 final size:105
Alignment explanation
Indices: 35235344--35235558 Score: 270
Period size: 105 Copynumber: 2.0 Consensus size: 105
35235334 TTTTTAATTA
* * * * * * **
35235344 TATCTATATTATTATTTAAGTGTTTGATTGAGTTAGTGTCGCAAGTTAATTCAATATCAATTTAG
1 TATCTATACTATTATTTAAGTGTGTGATTGAGTTAGTGTCACAAGTCAACTCAACATCAACCTAG
*
35235409 TTAAAAAATACTAAAATAACCTTATATATTTAAAATAAAT
66 TCAAAAAATACTAAAATAACCTTATATATTTAAAATAAAT
* * *
35235449 TATCTATACTATTATTTAAGTGTGTGATTGAGTT-GATGTCACGAGTCAACTCGACATTAACCTA
1 TATCTATACTATTATTTAAGTGTGTGATTGAGTTAG-TGTCACAAGTCAACTCAACATCAACCTA
* *
35235513 GTCAAGAAAATTACTAAAATAATCTTATATATTTAAGATAAAT
65 GTCAA-AAAA-TACTAAAATAACCTTATATATTTAAAATAAAT
35235556 TAT
1 TAT
35235559 ATTATTACGA
Statistics
Matches: 93, Mismatches: 14, Indels: 4
0.84 0.13 0.04
Matches are distributed among these distances:
104 1 0.01
105 55 0.59
106 4 0.04
107 33 0.35
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.40
Consensus pattern (105 bp):
TATCTATACTATTATTTAAGTGTGTGATTGAGTTAGTGTCACAAGTCAACTCAACATCAACCTAG
TCAAAAAATACTAAAATAACCTTATATATTTAAAATAAAT
Found at i:35235696 original size:2 final size:2
Alignment explanation
Indices: 35235689--35235714 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
35235679 CCGTAAGACT
35235689 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
35235715 CATTTCAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:35236828 original size:24 final size:24
Alignment explanation
Indices: 35236792--35236837 Score: 67
Period size: 23 Copynumber: 1.9 Consensus size: 24
35236782 GGTTTGTATA
35236792 ATTTTTAATATTT-TTTACTTTTG
1 ATTTTTAATATTTATTTACTTTTG
*
35236815 ATTTTTAATAATTTATTTGCTTT
1 ATTTTTAAT-ATTTATTTACTTT
35236838 GAATTAGTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
24 4 0.20
25 7 0.35
ACGTcount: A:0.24, C:0.04, G:0.04, T:0.67
Consensus pattern (24 bp):
ATTTTTAATATTTATTTACTTTTG
Found at i:35237741 original size:16 final size:15
Alignment explanation
Indices: 35237717--35237757 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
35237707 AAATAATAAA
* *
35237717 TAATTTAATTATATTT
1 TAATATAATTAT-TAT
35237733 TAATATAATTATTAT
1 TAATATAATTATTAT
35237748 TAATATAATT
1 TAATATAATT
35237758 TAATAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
TAATATAATTATTAT
Found at i:35238579 original size:12 final size:12
Alignment explanation
Indices: 35238562--35238586 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35238552 GGTGTTCATT
35238562 CGGTTAACCGAC
1 CGGTTAACCGAC
35238574 CGGTTAACCGAC
1 CGGTTAACCGAC
35238586 C
1 C
35238587 CGAAATTACT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:35238759 original size:9 final size:9
Alignment explanation
Indices: 35238745--35238812 Score: 91
Period size: 9 Copynumber: 7.4 Consensus size: 9
35238735 TTTGATTAAA
35238745 AATTACCCG
1 AATTACCCG
35238754 AATTACCCG
1 AATTACCCG
35238763 AATTACCCG
1 AATTACCCG
*
35238772 AATTAACCG
1 AATTACCCG
**
35238781 AATTACCAAA
1 AATTACC-CG
*
35238791 AAATACCCG
1 AATTACCCG
35238800 AATTACCCG
1 AATTACCCG
35238809 AATT
1 AATT
35238813 TTTTTATTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
9 44 0.88
10 6 0.12
ACGTcount: A:0.41, C:0.28, G:0.09, T:0.22
Consensus pattern (9 bp):
AATTACCCG
Found at i:35238968 original size:13 final size:13
Alignment explanation
Indices: 35238950--35238979 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
35238940 TTTTAGTTTT
35238950 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
35238963 ATTGGGTTGGGTA
1 ATTGGGTTGGGTA
35238976 ATTG
1 ATTG
35238980 AGTTTGGGCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.17, C:0.00, G:0.43, T:0.40
Consensus pattern (13 bp):
ATTGGGTTGGGTA
Found at i:35245140 original size:19 final size:18
Alignment explanation
Indices: 35245098--35245140 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 18
35245088 GGAAAAGGGA
35245098 AATGAGAGAGAGAATGAT
1 AATGAGAGAGAGAATGAT
35245116 AGATGAGAGA-ATGAATGAT
1 A-ATGAGAGAGA-GAATGAT
35245135 GAATGA
1 -AATGA
35245141 CTGTTGAGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
18 2 0.09
19 19 0.86
20 1 0.05
ACGTcount: A:0.49, C:0.00, G:0.33, T:0.19
Consensus pattern (18 bp):
AATGAGAGAGAGAATGAT
Found at i:35246686 original size:19 final size:19
Alignment explanation
Indices: 35246659--35246700 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
35246649 ATGATTTATT
* *
35246659 ATAATATTTGTCTACCCAA
1 ATAAGATTTATCTACCCAA
*
35246678 ATAAGATTTATCTACCTAA
1 ATAAGATTTATCTACCCAA
35246697 ATAA
1 ATAA
35246701 CTTTAAAATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.17, G:0.05, T:0.36
Consensus pattern (19 bp):
ATAAGATTTATCTACCCAA
Found at i:35257864 original size:15 final size:13
Alignment explanation
Indices: 35257823--35257870 Score: 64
Period size: 13 Copynumber: 3.7 Consensus size: 13
35257813 AGTTTCTTTG
35257823 AAAAAAATAT-GAA
1 AAAAAAAT-TCGAA
35257836 AAAAAAATTCGAA
1 AAAAAAATTCGAA
35257849 AAAAAAATTC-AA
1 AAAAAAATTCGAA
35257861 GAAAAAAATT
1 -AAAAAAATT
35257871 TAGTTTACAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
12 3 0.09
13 30 0.91
ACGTcount: A:0.73, C:0.04, G:0.06, T:0.17
Consensus pattern (13 bp):
AAAAAAATTCGAA
Found at i:35257929 original size:13 final size:13
Alignment explanation
Indices: 35257911--35257944 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
35257901 ATCAAGCAAA
35257911 AAAAAAAATCGTG
1 AAAAAAAATCGTG
*
35257924 AAAAAAAATTGTG
1 AAAAAAAATCGTG
35257937 AAAAAAAA
1 AAAAAAAA
35257945 AAGAAAAGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.71, C:0.03, G:0.12, T:0.15
Consensus pattern (13 bp):
AAAAAAAATCGTG
Found at i:35264679 original size:21 final size:20
Alignment explanation
Indices: 35264655--35264722 Score: 64
Period size: 21 Copynumber: 3.3 Consensus size: 20
35264645 TTCATTGCTG
35264655 TTTTGAATCGATTGTTTGTT
1 TTTTGAATCGATTGTTTGTT
* * * * *
35264675 ATTTTAAATTGATTCTCTGCT
1 -TTTTGAATCGATTGTTTGTT
*
35264696 TTTTGAATCGATTGTTTATT
1 TTTTGAATCGATTGTTTGTT
35264716 GTTTTGA
1 -TTTTGA
35264723 CTTGACTCTT
Statistics
Matches: 35, Mismatches: 11, Indels: 2
0.73 0.23 0.04
Matches are distributed among these distances:
20 14 0.40
21 21 0.60
ACGTcount: A:0.19, C:0.07, G:0.16, T:0.57
Consensus pattern (20 bp):
TTTTGAATCGATTGTTTGTT
Found at i:35266475 original size:20 final size:20
Alignment explanation
Indices: 35266438--35266477 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
35266428 CCACTCATTG
* *
35266438 CTTGTATTATTAGAAATGTT
1 CTTGTATTACTACAAATGTT
*
35266458 CTTGTATTACTACTAATGTT
1 CTTGTATTACTACAAATGTT
35266478 ACAAGAACCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
CTTGTATTACTACAAATGTT
Found at i:35267653 original size:31 final size:29
Alignment explanation
Indices: 35267618--35267688 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
35267608 AACGGCTCAA
* *
35267618 TGACTAAAATGTTACAACATGATAACTTAAG
1 TGACTAAAATGTAAC-ACATGA-AACATAAG
* **
35267649 TGACTAAAACGTAACATTTGAAACATAAG
1 TGACTAAAATGTAACACATGAAACATAAG
35267678 TGACTAAAATG
1 TGACTAAAATG
35267689 CAACCTGGGG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 17 0.50
30 4 0.12
31 13 0.38
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (29 bp):
TGACTAAAATGTAACACATGAAACATAAG
Found at i:35270796 original size:6 final size:6
Alignment explanation
Indices: 35270780--35270809 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
35270770 TTATTCCTGG
*
35270780 GCACAC ACACAC GCACAC GCACAC GCACAC
1 GCACAC GCACAC GCACAC GCACAC GCACAC
35270810 ATGCACATAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.37, C:0.50, G:0.13, T:0.00
Consensus pattern (6 bp):
GCACAC
Found at i:35272261 original size:72 final size:72
Alignment explanation
Indices: 35272163--35272328 Score: 183
Period size: 72 Copynumber: 2.3 Consensus size: 72
35272153 GTTCAACTTT
* * * * *
35272163 TAGGACAGCTTGCTGTCCATCTGAATGGA-TAACATCCATCATCTGAACGACGTTTT-AGTATAA
1 TAGGACAGTTTGCTCTCCATCCGAAT-GACTAACATCCACCATCCGAACGACGTTTTGA-TATAA
*
35272226 CTCAAGTAC
64 CTCAACTAC
* * * * * *
35272235 TAGGAAAGTTTGCTCTCCATCCGAATGACTAATATTCGCCATCCGAATGGCGTTTTGATATAACT
1 TAGGACAGTTTGCTCTCCATCCGAATGACTAACATCCACCATCCGAACGACGTTTTGATATAACT
35272300 CAACTAC
66 CAACTAC
*
35272307 TAGGACATTTTGCTCTCCATCC
1 TAGGACAGTTTGCTCTCCATCC
35272329 AGATGGCTTT
Statistics
Matches: 78, Mismatches: 14, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
71 2 0.03
72 75 0.96
73 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (72 bp):
TAGGACAGTTTGCTCTCCATCCGAATGACTAACATCCACCATCCGAACGACGTTTTGATATAACT
CAACTAC
Found at i:35272547 original size:40 final size:39
Alignment explanation
Indices: 35272461--35272557 Score: 99
Period size: 40 Copynumber: 2.5 Consensus size: 39
35272451 GCGTTTGCAT
*
35272461 AAAAAATGCCGCTAAAAATCGAGCATTAGCGGCGCTTTA
1 AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTA
* * * *
35272500 AGGAAAACGCCGCTAATAAT-GAGTATTAGCGGCGTTTTTA
1 A-AAAAACGCCGCTAAAAATCGAGCATTAGCGGCG-CTTTA
*
35272540 CAAAAAACACCG-TAAAAA
1 -AAAAAACGCCGCTAAAAA
35272558 ACCTAAACCC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
39 19 0.40
40 27 0.57
41 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.20, T:0.21
Consensus pattern (39 bp):
AAAAAACGCCGCTAAAAATCGAGCATTAGCGGCGCTTTA
Found at i:35272696 original size:42 final size:41
Alignment explanation
Indices: 35272590--35272788 Score: 319
Period size: 41 Copynumber: 4.9 Consensus size: 41
35272580 TTCTTACCTT
* *
35272590 TCAGGGCTTTAGCGGCATTTTTGTAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
*
35272631 TTAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
*
35272672 TCAGGGACTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATAC
1 TCAGGG-CTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
*
35272714 TCAGGGCTTTAGCGGCGTTTTTGGAAAAGCGCCGCTAATGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
* *
35272755 TCA-GGCTTTAGCGGCGTTTTTGTAAAAGCGCCGC
1 TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGC
35272789 AAAAACATTT
Statistics
Matches: 149, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
40 30 0.20
41 79 0.53
42 40 0.27
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (41 bp):
TCAGGGCTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATGC
Found at i:35272735 original size:83 final size:82
Alignment explanation
Indices: 35272590--35272788 Score: 328
Period size: 83 Copynumber: 2.4 Consensus size: 82
35272580 TTCTTACCTT
* * *
35272590 TCAGGGCTTTAGCGGCATTTTTGTAGAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGG
1 TCAGGGCTTTAGCGGCGTTTTTGTAGAAGCGCCGCTAATACTCAGGGCTTTAGCGGCGTTTTTGG
*
35272655 AGAAGCGCCGCTAATGC
66 AAAAGCGCCGCTAATGC
*
35272672 TCAGGGACTTTAGCGGCGTTTTTGGAGAAGCGCCGCTAATACTCAGGGCTTTAGCGGCGTTTTTG
1 TCAGGG-CTTTAGCGGCGTTTTTGTAGAAGCGCCGCTAATACTCAGGGCTTTAGCGGCGTTTTTG
35272737 GAAAAGCGCCGCTAATGC
65 GAAAAGCGCCGCTAATGC
*
35272755 TCA-GGCTTTAGCGGCGTTTTTGTAAAAGCGCCGC
1 TCAGGGCTTTAGCGGCGTTTTTGTAGAAGCGCCGC
35272789 AAAAACATTT
Statistics
Matches: 109, Mismatches: 7, Indels: 3
0.92 0.06 0.03
Matches are distributed among these distances:
81 27 0.25
82 8 0.07
83 74 0.68
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (82 bp):
TCAGGGCTTTAGCGGCGTTTTTGTAGAAGCGCCGCTAATACTCAGGGCTTTAGCGGCGTTTTTGG
AAAAGCGCCGCTAATGC
Found at i:35273141 original size:7 final size:7
Alignment explanation
Indices: 35273109--35273326 Score: 129
Period size: 7 Copynumber: 31.0 Consensus size: 7
35273099 TAAGGTTTTT
35273109 GGTTTAG
1 GGTTTAG
* *
35273116 GGTATAT
1 GGTTTAG
*
35273123 GGTATAG
1 GGTTTAG
* *
35273130 AGTTTAA
1 GGTTTAG
*
35273137 GGTTTAT
1 GGTTTAG
*
35273144 GGATTATG
1 GGTTTA-G
35273152 GGTTTAG
1 GGTTTAG
* *
35273159 GGGTTAT
1 GGTTTAG
*
35273166 GGTTTAA
1 GGTTTAG
35273173 GGTTTAG
1 GGTTTAG
35273180 GGTTTAG
1 GGTTTAG
*
35273187 GGTTTAT
1 GGTTTAG
*
35273194 GGTTTAT
1 GGTTTAG
35273201 GGTTTAG
1 GGTTTAG
35273208 GGTTTAG
1 GGTTTAG
* *
35273215 GGGTTAC
1 GGTTTAG
*
35273222 GGTTTAT
1 GGTTTAG
*
35273229 GGTTTAA
1 GGTTTAG
35273236 GGTTATA-
1 GGTT-TAG
* *
35273243 GATTAAG
1 GGTTTAG
*
35273250 GG-TTGG
1 GGTTTAG
*
35273256 GGTTTAA
1 GGTTTAG
35273263 GGTTTAG
1 GGTTTAG
35273270 GAG-TTAG
1 G-GTTTAG
*
35273277 GGGTTAGG
1 GGTTTA-G
*
35273285 GGTTGAG
1 GGTTTAG
*
35273292 GGTTAAG
1 GGTTTAG
* *
35273299 AG-TCAGG
1 GGTTTA-G
35273306 GGTTTAG
1 GGTTTAG
*
35273313 GATTTAG
1 GGTTTAG
35273320 GGTTTAG
1 GGTTTAG
35273327 ATTAATTAGT
Statistics
Matches: 162, Mismatches: 40, Indels: 18
0.74 0.18 0.08
Matches are distributed among these distances:
6 8 0.05
7 139 0.86
8 15 0.09
ACGTcount: A:0.21, C:0.01, G:0.39, T:0.40
Consensus pattern (7 bp):
GGTTTAG
Found at i:35273151 original size:28 final size:28
Alignment explanation
Indices: 35273137--35273239 Score: 152
Period size: 28 Copynumber: 3.6 Consensus size: 28
35273127 TAGAGTTTAA
*
35273137 GGTTTATGGATTATGGGTTTAGGGGTTAT
1 GGTTTATGGTTTA-GGGTTTAGGGGTTAT
* *
35273166 GGTTTAAGGTTTAGGGTTTAGGGTTTAT
1 GGTTTATGGTTTAGGGTTTAGGGGTTAT
*
35273194 GGTTTATGGTTTAGGGTTTAGGGGTTAC
1 GGTTTATGGTTTAGGGTTTAGGGGTTAT
*
35273222 GGTTTATGGTTTAAGGTT
1 GGTTTATGGTTTAGGGTT
35273240 ATAGATTAAG
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
28 56 0.84
29 11 0.16
ACGTcount: A:0.17, C:0.01, G:0.37, T:0.46
Consensus pattern (28 bp):
GGTTTATGGTTTAGGGTTTAGGGGTTAT
Found at i:35273263 original size:27 final size:29
Alignment explanation
Indices: 35273201--35273288 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 29
35273191 TATGGTTTAT
* * * * *
35273201 GGTTTAGGGTTTAGGGGTTACGGTTTA-T
1 GGTTTAAGGTTTAGGAGTTAAGGGTTAGG
35273229 GGTTTAAGGTTATA-GA-TTAAGGGTT-GG
1 GGTTTAAGGTT-TAGGAGTTAAGGGTTAGG
*
35273256 GGTTTAAGGTTTAGGAGTTAGGGGTTAGG
1 GGTTTAAGGTTTAGGAGTTAAGGGTTAGG
35273285 GGTT
1 GGTT
35273289 GAGGGTTAAG
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
26 2 0.04
27 20 0.41
28 19 0.39
29 8 0.16
ACGTcount: A:0.19, C:0.01, G:0.41, T:0.39
Consensus pattern (29 bp):
GGTTTAAGGTTTAGGAGTTAAGGGTTAGG
Found at i:35273451 original size:15 final size:16
Alignment explanation
Indices: 35273389--35273457 Score: 59
Period size: 17 Copynumber: 4.0 Consensus size: 16
35273379 GAGATAATAT
35273389 TAAATTGATATATTAAA
1 TAAATT-ATATATTAAA
*
35273406 -ATTATTATTATAGTTTAAA
1 TA-AATTA-TATA--TTAAA
35273425 TAAATTATATATTAAA
1 TAAATTATATATTAAA
*
35273441 TAATTTAATATATTAAA
1 TAAATT-ATATATTAAA
35273458 ATAATGATTA
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
16 12 0.28
17 17 0.40
18 4 0.09
19 9 0.21
20 1 0.02
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TAAATTATATATTAAA
Found at i:35273453 original size:17 final size:16
Alignment explanation
Indices: 35273420--35273462 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
35273410 TTATTATAGT
*
35273420 TTAAATAAATTATATA
1 TTAAATAATTTATATA
35273436 TTAAATAATTTAATATA
1 TTAAATAATTT-ATATA
35273453 TTAAAATAAT
1 TT-AAATAAT
35273463 GATTATAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 7 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAATAATTTATATA
Found at i:35273469 original size:17 final size:17
Alignment explanation
Indices: 35273397--35273469 Score: 69
Period size: 17 Copynumber: 4.2 Consensus size: 17
35273387 ATTAAATTGA
*
35273397 TATATTAAAATTATTAT
1 TATATTAAAATAATTAT
*
35273414 TATAGTTTAAATAAATTA-
1 TATA-TTAAAAT-AATTAT
*
35273432 TATATT-AAATAATTTAA
1 TATATTAAAATAA-TTAT
*
35273449 TATATTAAAATAATGAT
1 TATATTAAAATAATTAT
35273466 TATA
1 TATA
35273470 GTGCTCTTGG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
15 2 0.04
16 7 0.15
17 18 0.38
18 16 0.34
19 4 0.09
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
TATATTAAAATAATTAT
Found at i:35273593 original size:7 final size:7
Alignment explanation
Indices: 35273569--35273644 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 7
35273559 GGATTTAAAT
35273569 TTTAGGG
1 TTTAGGG
*
35273576 GTTAGGAG
1 TTTAGG-G
35273584 TTTAGGG
1 TTTAGGG
35273591 TTTTAGGG
1 -TTTAGGG
* *
35273599 -TTATGT
1 TTTAGGG
* *
35273605 TTTATGA
1 TTTAGGG
*
35273612 TTTATGG
1 TTTAGGG
35273619 TTTAGGG
1 TTTAGGG
**
35273626 GATAGGG
1 TTTAGGG
35273633 TTTAGGG
1 TTTAGGG
35273640 TTTAG
1 TTTAG
35273645 ATTAATTAGT
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
6 4 0.07
7 38 0.69
8 13 0.24
ACGTcount: A:0.18, C:0.00, G:0.37, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:35279296 original size:43 final size:42
Alignment explanation
Indices: 35279247--35279472 Score: 253
Period size: 43 Copynumber: 5.3 Consensus size: 42
35279237 ACGGTATTTT
* *
35279247 TAGCGGCGTTTGTAATCAAAGCGTCGCTAAAGGTCTTGAGCTA
1 TAGCGGCGTTTGTAA-AAAAGCGTCGCTAAAGGTCTTGATCTA
* *
35279290 TAGCGGCGTTTTTGAAAAAAGCGTCGCTAAAGAT-TATGATCTA
1 TAGCGGCGTTTGT-AAAAAAGCGTCGCTAAAGGTCT-TGATCTA
*
35279333 TAGCGGCGTTTGTGAGAAAAGC--CGCTAAAGGTCTTGATCTA
1 TAGCGGCGTTTGT-AAAAAAGCGTCGCTAAAGGTCTTGATCTA
* * * *
35279374 TAGCGGCGTTTGTAAAAAAGTGCCGCTAAA-GTTTATGATTTA
1 TAGCGGCGTTTGTAAAAAAGCGTCGCTAAAGGTCT-TGATCTA
* ***
35279416 TAGCGGCGTTTGTGGAAAAAGCGTCGCTAAAGGTCCAAATCTA
1 TAGCGGCGTTTGT-AAAAAAGCGTCGCTAAAGGTCTTGATCTA
35279459 TAGCGGCGTTTGTA
1 TAGCGGCGTTTGTA
35279473 GGAAAAAATG
Statistics
Matches: 155, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
40 6 0.04
41 32 0.21
42 28 0.18
43 85 0.55
44 4 0.03
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (42 bp):
TAGCGGCGTTTGTAAAAAAGCGTCGCTAAAGGTCTTGATCTA
Found at i:35279728 original size:35 final size:35
Alignment explanation
Indices: 35279682--35279754 Score: 119
Period size: 35 Copynumber: 2.1 Consensus size: 35
35279672 AGCTTCAACC
*
35279682 GAGCAACTGGTGTGCTAGATGGTAATGGCTCTTAT
1 GAGCAACTGGTGTGCTAGATGGTAATGACTCTTAT
* *
35279717 GAGCAACTGGTGTGCTGGATGGTACTGACTCTTAT
1 GAGCAACTGGTGTGCTAGATGGTAATGACTCTTAT
35279752 GAG
1 GAG
35279755 TATTTGATGT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.22, C:0.15, G:0.33, T:0.30
Consensus pattern (35 bp):
GAGCAACTGGTGTGCTAGATGGTAATGACTCTTAT
Found at i:35279771 original size:35 final size:35
Alignment explanation
Indices: 35279682--35279774 Score: 105
Period size: 35 Copynumber: 2.7 Consensus size: 35
35279672 AGCTTCAACC
* * *
35279682 GAGCAACTGGTGTGCTAGATGGTAATGGCTCTTAT
1 GAGCAACTGATGTGCTGGATGGTAATGACTCTTAT
* *
35279717 GAGCAACTGGTGTGCTGGATGGTACTGACTCTTAT
1 GAGCAACTGATGTGCTGGATGGTAATGACTCTTAT
* ** *
35279752 GAGTATTTGATGTGTTGGATGGT
1 GAGCAACTGATGTGCTGGATGGT
35279775 TAACCGTGTG
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 50 1.00
ACGTcount: A:0.20, C:0.12, G:0.33, T:0.34
Consensus pattern (35 bp):
GAGCAACTGATGTGCTGGATGGTAATGACTCTTAT
Found at i:35280085 original size:60 final size:60
Alignment explanation
Indices: 35279991--35280112 Score: 226
Period size: 60 Copynumber: 2.0 Consensus size: 60
35279981 TTATTAACCG
* *
35279991 AATTATTATGCGTAATTTAGTAAGATTTAGTATTTAATCGATGAACTTACTAAGCTTTAT
1 AATTATTATGCGTAATTTAGTAAGATTTACTATTTAATCGATGAACTTACTAAGATTTAT
35280051 AATTATTATGCGTAATTTAGTAAGATTTACTATTTAATCGATGAACTTACTAAGATTTAT
1 AATTATTATGCGTAATTTAGTAAGATTTACTATTTAATCGATGAACTTACTAAGATTTAT
35280111 AA
1 AA
35280113 AAGCTTACTC
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 60 1.00
ACGTcount: A:0.37, C:0.08, G:0.12, T:0.43
Consensus pattern (60 bp):
AATTATTATGCGTAATTTAGTAAGATTTACTATTTAATCGATGAACTTACTAAGATTTAT
Found at i:35280107 original size:30 final size:29
Alignment explanation
Indices: 35280011--35280111 Score: 107
Period size: 30 Copynumber: 3.4 Consensus size: 29
35280001 CGTAATTTAG
35280011 TAAGATTTAGTATTTAATCGATGAACTTAC
1 TAAGATTTA-TATTTAATCGATGAACTTAC
* * * *
35280041 TAAGCTTTATAATTATTATGCG-T-AATTTAG
1 TAAGATTTAT-ATT-TAAT-CGATGAACTTAC
35280071 TAAGATTTACTATTTAATCGATGAACTTAC
1 TAAGATTTA-TATTTAATCGATGAACTTAC
35280101 TAAGATTTATA
1 TAAGATTTATA
35280112 AAAGCTTACT
Statistics
Matches: 57, Mismatches: 8, Indels: 13
0.73 0.10 0.17
Matches are distributed among these distances:
28 2 0.04
29 7 0.12
30 41 0.72
31 5 0.09
32 2 0.04
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.43
Consensus pattern (29 bp):
TAAGATTTATATTTAATCGATGAACTTAC
Found at i:35283354 original size:70 final size:70
Alignment explanation
Indices: 35283236--35283372 Score: 256
Period size: 70 Copynumber: 2.0 Consensus size: 70
35283226 TTGCATGCCC
35283236 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
35283301 TGTTG
66 TGTTG
* *
35283306 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
35283371 TG
66 TG
35283373 ATTTAATTCA
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 65 1.00
ACGTcount: A:0.27, C:0.26, G:0.12, T:0.34
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
TGTTG
Found at i:35285393 original size:33 final size:35
Alignment explanation
Indices: 35285350--35285420 Score: 92
Period size: 33 Copynumber: 2.1 Consensus size: 35
35285340 TCAATATCAA
35285350 TCTCAATCTCAAATTCTTTTT-TCTT-TTTCTTTT
1 TCTCAATCTCAAATTCTTTTTCTCTTATTTCTTTT
* ** *
35285383 TCTCACTCTCATTTTCTTTTTCTTTTATTTCTTTT
1 TCTCAATCTCAAATTCTTTTTCTCTTATTTCTTTT
35285418 TCT
1 TCT
35285421 TTTTCTCTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 18 0.56
34 3 0.09
35 11 0.34
ACGTcount: A:0.11, C:0.23, G:0.00, T:0.66
Consensus pattern (35 bp):
TCTCAATCTCAAATTCTTTTTCTCTTATTTCTTTT
Found at i:35285413 original size:15 final size:14
Alignment explanation
Indices: 35285394--35285444 Score: 66
Period size: 15 Copynumber: 3.5 Consensus size: 14
35285384 CTCACTCTCA
35285394 TTTTCTTTTTCTTT
1 TTTTCTTTTTCTTT
35285408 TATTTCTTTTTCTTT
1 T-TTTCTTTTTCTTT
* *
35285423 TTCTCTCATTTCTTT
1 TTTTCT-TTTTCTTT
35285438 TTTTCTT
1 TTTTCTT
35285445 CTCTCAATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 5 0.16
15 26 0.84
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (14 bp):
TTTTCTTTTTCTTT
Found at i:35285449 original size:22 final size:21
Alignment explanation
Indices: 35285369--35285455 Score: 97
Period size: 21 Copynumber: 4.2 Consensus size: 21
35285359 CAAATTCTTT
*
35285369 TTTCTTTTTCTTTTTCTCAC-
1 TTTCTTTTTCTTTTTCTCTCA
* * * *
35285389 TCTCATTTTCTTTTTCTTTTA
1 TTTCTTTTTCTTTTTCTCTCA
35285410 TTTCTTTTTCTTTTTCTCTCA
1 TTTCTTTTTCTTTTTCTCTCA
*
35285431 TTTCTTTTT-TTCTTCTCTCAA
1 TTTCTTTTTCTTTTTCTCTC-A
35285452 TTTC
1 TTTC
35285456 ATTCAAGATT
Statistics
Matches: 55, Mismatches: 10, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
20 24 0.44
21 31 0.56
ACGTcount: A:0.07, C:0.23, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTCTTTTTCTTTTTCTCTCA
Found at i:35286328 original size:28 final size:29
Alignment explanation
Indices: 35286274--35286345 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
35286264 TTTCAATCAC
* * *
35286274 TCTTTTTTTTTTTCAATTTCGATTTTTTT
1 TCTTCTTTTTTTTCAATTCCGAATTTTTT
35286303 TCTTCTTTTTTTT-AATTCCGAATTTTTT
1 TCTTCTTTTTTTTCAATTCCGAATTTTTT
35286331 TCTTCCTTTTTTTTC
1 TCTT-CTTTTTTTTC
35286346 TTCAATACTA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 17 0.45
29 21 0.55
ACGTcount: A:0.10, C:0.15, G:0.03, T:0.72
Consensus pattern (29 bp):
TCTTCTTTTTTTTCAATTCCGAATTTTTT
Found at i:35286406 original size:12 final size:12
Alignment explanation
Indices: 35286389--35286443 Score: 69
Period size: 13 Copynumber: 4.6 Consensus size: 12
35286379 GAATACAAAC
35286389 TTTTTTTTTGAA
1 TTTTTTTTTGAA
35286401 TTTTTTTTTCGAA
1 TTTTTTTTT-GAA
*
35286414 TTTTTTTTTCAA
1 TTTTTTTTTGAA
35286426 GTTTTTTTTT--A
1 -TTTTTTTTTGAA
35286437 TTTTTTT
1 TTTTTTT
35286444 ACAATACCGT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
10 7 0.17
11 1 0.03
12 11 0.28
13 21 0.52
ACGTcount: A:0.13, C:0.04, G:0.05, T:0.78
Consensus pattern (12 bp):
TTTTTTTTTGAA
Found at i:35287707 original size:70 final size:70
Alignment explanation
Indices: 35287589--35287725 Score: 247
Period size: 70 Copynumber: 2.0 Consensus size: 70
35287579 TTGCATGCCC
35287589 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTACTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTACTTTATTGCTGC
35287654 TGTTG
66 TGTTG
* * *
35287659 AACATCACCTTAAATGCATGTCTATGCTTTACATTAAATTCGGCCAACACCTCCTTTATTGCTGC
1 AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTACTTTATTGCTGC
35287724 TG
66 TG
35287726 ATTTAATTCA
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 64 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (70 bp):
AACAGCACCTTAAATACATGTCTATGCTTTACATTAAATTCGGCCAACACCTACTTTATTGCTGC
TGTTG
Found at i:35288251 original size:20 final size:19
Alignment explanation
Indices: 35288216--35288253 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
35288206 AGCTAATAAC
35288216 GAGCTCAATGAACTGAATT
1 GAGCTCAATGAACTGAATT
*
35288235 GAGCTCGAATGAGCTGAAT
1 GAGCTC-AATGAACTGAAT
35288254 CAAAAATGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.34, C:0.16, G:0.26, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAACTGAATT
Found at i:35294153 original size:56 final size:58
Alignment explanation
Indices: 35294072--35294194 Score: 162
Period size: 57 Copynumber: 2.2 Consensus size: 58
35294062 AAATGAATAG
* *
35294072 AAATGGAGAAATAGAAAATATTTGGAAATG-ATAAGGTTTTCTCCAAATTGAAAATGA
1 AAATGGAAAAATAGAAAATATTTGGAAATGAATAAGGTTTTCTCCAAAATGAAAATGA
** * *
35294129 AAATGGAAAAAT-G-AAATCATTTGGAAATGAATTTGGTTTTCTCCAAAATGGAAATGG
1 AAATGGAAAAATAGAAAAT-ATTTGGAAATGAATAAGGTTTTCTCCAAAATGAAAATGA
35294186 AAATGGAAA
1 AAATGGAAA
35294195 TGGAAATGAA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
55 4 0.07
56 12 0.21
57 42 0.72
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (58 bp):
AAATGGAAAAATAGAAAATATTTGGAAATGAATAAGGTTTTCTCCAAAATGAAAATGA
Found at i:35294185 original size:6 final size:6
Alignment explanation
Indices: 35294174--35294220 Score: 60
Period size: 6 Copynumber: 7.7 Consensus size: 6
35294164 GTTTTCTCCA
*
35294174 AAATGG AAATGG AAATGG AAATGG AAAT-G AAAGTGA AAATGAG AAAT
1 AAATGG AAATGG AAATGG AAATGG AAATGG AAA-TGG AAATG-G AAAT
35294221 CAATTCATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
5 4 0.11
6 25 0.69
7 7 0.19
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (6 bp):
AAATGG
Found at i:35302680 original size:12 final size:12
Alignment explanation
Indices: 35302663--35302726 Score: 76
Period size: 12 Copynumber: 5.4 Consensus size: 12
35302653 ATACAAACTC
*
35302663 TTTTTTTGAATT
1 TTTTTTTCAATT
*
35302675 TTTTTTTCAAAT
1 TTTTTTTCAATT
35302687 TTTTTTTCAATT
1 TTTTTTTCAATT
**
35302699 TTTTTTTCAAAA
1 TTTTTTTCAATT
*
35302711 TTTTTTT-GATT
1 TTTTTTTCAATT
35302722 TTTTT
1 TTTTT
35302727 ACAATACCGT
Statistics
Matches: 44, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
11 6 0.14
12 38 0.86
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (12 bp):
TTTTTTTCAATT
Found at i:35302690 original size:24 final size:24
Alignment explanation
Indices: 35302663--35302726 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
35302653 ATACAAACTC
*
35302663 TTTTTTTGAATTTTTTTTTCAAAT
1 TTTTTTTGAATTTTTTTTTCAAAA
*
35302687 TTTTTTTCAATTTTTTTTTCAAAA
1 TTTTTTTGAATTTTTTTTTCAAAA
35302711 TTTTTTTG-ATTTTTTT
1 TTTTTTTGAATTTTTTT
35302727 ACAATACCGT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 8 0.22
24 29 0.78
ACGTcount: A:0.19, C:0.05, G:0.03, T:0.73
Consensus pattern (24 bp):
TTTTTTTGAATTTTTTTTTCAAAA
Found at i:35319730 original size:13 final size:13
Alignment explanation
Indices: 35319712--35319736 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35319702 TCTGATGCTT
35319712 ACACAACTCATGG
1 ACACAACTCATGG
35319725 ACACAACTCATG
1 ACACAACTCATG
35319737 AAGGAGTTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.32, G:0.12, T:0.16
Consensus pattern (13 bp):
ACACAACTCATGG
Found at i:35321904 original size:22 final size:22
Alignment explanation
Indices: 35321879--35321950 Score: 117
Period size: 22 Copynumber: 3.3 Consensus size: 22
35321869 TTAATTAACC
35321879 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
35321901 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
35321923 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
35321945 CTCATG
1 CTCATG
35321951 TTTGAACAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 47 1.00
ACGTcount: A:0.25, C:0.28, G:0.17, T:0.31
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:35325059 original size:20 final size:20
Alignment explanation
Indices: 35325034--35325071 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
35325024 CCAGTTTTTA
*
35325034 TTTTTATTTTAATATTTATG
1 TTTTTAATTTAATATTTATG
*
35325054 TTTTTAATTTAATTTTTA
1 TTTTTAATTTAATATTTA
35325072 CATTCTAATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (20 bp):
TTTTTAATTTAATATTTATG
Found at i:35327573 original size:27 final size:27
Alignment explanation
Indices: 35327335--35327562 Score: 323
Period size: 27 Copynumber: 8.5 Consensus size: 27
35327325 ACCCTAAAAC
* * *
35327335 AGGGTAAAATGATCGAAATGCCCCCAT
1 AGGGTAAAATGACCAAAATACCCCCAT
35327362 AGGGTAAAATGACCAAAATACCCCCAT
1 AGGGTAAAATGACCAAAATACCCCCAT
* *
35327389 AGGATAAAATGACCAAAATACTCCCAT
1 AGGGTAAAATGACCAAAATACCCCCAT
** *
35327416 AGGGTAAAATGACTGAAATAGCCCCAT
1 AGGGTAAAATGACCAAAATACCCCCAT
* *
35327443 AGGGTAAAATGATCGAAATACCCCCAT
1 AGGGTAAAATGACCAAAATACCCCCAT
*
35327470 AGGGTAAAATGACAAAAATACCCCCAT
1 AGGGTAAAATGACCAAAATACCCCCAT
*
35327497 AGGGTAAAATGACAAAAATA-CCCCAT
1 AGGGTAAAATGACCAAAATACCCCCAT
*
35327523 AGGGTAAAATGACCGAAATACCCCCAT
1 AGGGTAAAATGACCAAAATACCCCCAT
*
35327550 AAGGTAAAATGAC
1 AGGGTAAAATGAC
35327563 TGTTATACCC
Statistics
Matches: 181, Mismatches: 19, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
26 24 0.13
27 157 0.87
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.17
Consensus pattern (27 bp):
AGGGTAAAATGACCAAAATACCCCCAT
Found at i:35335357 original size:66 final size:66
Alignment explanation
Indices: 35335251--35335386 Score: 200
Period size: 66 Copynumber: 2.1 Consensus size: 66
35335241 ATTGATACAA
* *
35335251 TGATTGGATGATGCATATACATATTGAGCATCGATTATATAATCCCATGGGGCCAATACAGAAAT
1 TGATTGGATGATGCATATACATATTGAGCATCGATTATATAAGCCCATGGGACCAATACAGAAAT
35335316 G
66 G
* *** **
35335317 TGATTGGATGATGCATATACATATTTAGCATTTTTTATATAAGCCCATGGGACCAATATGGAAAT
1 TGATTGGATGATGCATATACATATTGAGCATCGATTATATAAGCCCATGGGACCAATACAGAAAT
35335382 G
66 G
35335383 TGAT
1 TGAT
35335387 AAATTGATGA
Statistics
Matches: 62, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
66 62 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.32
Consensus pattern (66 bp):
TGATTGGATGATGCATATACATATTGAGCATCGATTATATAAGCCCATGGGACCAATACAGAAAT
G
Found at i:35342904 original size:12 final size:12
Alignment explanation
Indices: 35342887--35342928 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
35342877 AAGGCTTCCA
35342887 AAAATGGAAATG
1 AAAATGGAAATG
*
35342899 AAAATGAAAATG
1 AAAATGGAAATG
*
35342911 GAAATGGAAATGG
1 AAAATGGAAAT-G
35342924 AAAAT
1 AAAAT
35342929 TGCAATCTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
12 20 0.80
13 5 0.20
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.17
Consensus pattern (12 bp):
AAAATGGAAATG
Found at i:35342910 original size:18 final size:19
Alignment explanation
Indices: 35342887--35342928 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 19
35342877 AAGGCTTCCA
35342887 AAAATGGAAATGAAAAT-G
1 AAAATGGAAATGAAAATGG
*
35342905 AAAATGGAAATGGAAATGG
1 AAAATGGAAATGAAAATGG
35342924 AAAAT
1 AAAAT
35342929 TGCAATCTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.60, C:0.00, G:0.24, T:0.17
Consensus pattern (19 bp):
AAAATGGAAATGAAAATGG
Found at i:35349725 original size:252 final size:252
Alignment explanation
Indices: 35349280--35349770 Score: 752
Period size: 252 Copynumber: 1.9 Consensus size: 252
35349270 AAGTATGTAT
* *
35349280 ACCTTATGCACCACAAGAGTGAAACCTTCAATAAGTTCTAAAAGTTTTGTGCAAAAGTTGAGAAA
1 ACCTTATGCACCACAAGAGTGAAACCTTCAATAAGTTCAAAAAGTTTTGTGCAAAAGTGGAGAAA
*
35349345 CAACTAGGTTTAACCATAAAGACACTTCAGTCTGGTCGAGGTGGGGAATATTTATCTAATTAGTT
66 CAACTAGGTTTAACCATAAAGACACTTCAGTCTGGTCGAGGTGGGGAATATTGATCTAATTAGTT
* *
35349410 CTTAGGATACCTCATAGAGAATGTGATTCTATCCCAGTTGACTGCACTGGGCACTCCACAATAGA
131 CTTAGGATACCTCATAGAGAATGAGATTCTATCCCAGTTGACTGCACTAGGCACTCCACAATAGA
* * *
35349475 ATGGCATGGAAGAGAGAAGGAATCGAATGTTATTAGACATGGTACGTTTGATGTTAA
196 ATGACATGGAAGAGAGAAAGAATCAAATGTTATTAGACATGGTACGTTTGATGTTAA
** * * *
35349532 ACCTTATGCACTGCAATAGTGAAACC-TCTGATTAGTTCAAAAAGTTTTGTGCAGAAA-TGGAGA
1 ACCTTATGCACCACAAGAGTGAAACCTTC-AATAAGTTCAAAAAGTTTTGTGCA-AAAGTGGAGA
* * * *
35349595 AACAACTAGGTTTACCCATAAAGATACTTCGGTCTGGTTGAGGTGGGGAATATTGATCTAATTAG
64 AACAACTAGGTTTAACCATAAAGACACTTCAGTCTGGTCGAGGTGGGGAATATTGATCTAATTAG
* *
35349660 TTTTTAGGGTACCTCATAGAGAATGAGATTCTATCCCAGTTGACTGCACTAGGCACTCCACAATA
129 TTCTTAGGATACCTCATAGAGAATGAGATTCTATCCCAGTTGACTGCACTAGGCACTCCACAATA
** *
35349725 GAATGATGTGGAAGAGAGAAAGAATCAAATGTTATTCGACATGGTA
194 GAATGACATGGAAGAGAGAAAGAATCAAATGTTATTAGACATGGTA
35349771 TGTTCAATGT
Statistics
Matches: 215, Mismatches: 22, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
251 2 0.01
252 210 0.98
253 3 0.01
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.28
Consensus pattern (252 bp):
ACCTTATGCACCACAAGAGTGAAACCTTCAATAAGTTCAAAAAGTTTTGTGCAAAAGTGGAGAAA
CAACTAGGTTTAACCATAAAGACACTTCAGTCTGGTCGAGGTGGGGAATATTGATCTAATTAGTT
CTTAGGATACCTCATAGAGAATGAGATTCTATCCCAGTTGACTGCACTAGGCACTCCACAATAGA
ATGACATGGAAGAGAGAAAGAATCAAATGTTATTAGACATGGTACGTTTGATGTTAA
Found at i:35356789 original size:17 final size:17
Alignment explanation
Indices: 35356767--35356799 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35356757 TGGGGGTCGC
35356767 TAGAATTAAATTAATTA
1 TAGAATTAAATTAATTA
*
35356784 TAGAATTAACTTAATT
1 TAGAATTAAATTAATT
35356800 CGGTAATCAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (17 bp):
TAGAATTAAATTAATTA
Found at i:35371441 original size:15 final size:16
Alignment explanation
Indices: 35371421--35371450 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35371411 TAACAACTAA
35371421 TATATAAT-TATATTT
1 TATATAATATATATTT
35371436 TATATAATATATATT
1 TATATAATATATATT
35371451 AATTGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
TATATAATATATATTT
Found at i:35386343 original size:45 final size:45
Alignment explanation
Indices: 35386264--35386397 Score: 166
Period size: 45 Copynumber: 3.0 Consensus size: 45
35386254 TATTCGTCCG
*
35386264 ATTCATGATGCCATTAA-AGTCTTTTAGCTATGGTCTTACTCGTTACA
1 ATTCATGATGCCA-TAACA-TCTTTCAGCTATGGTCTTACTCGTTA-A
* * *
35386311 A-TCATGATACCATAACATCTTTCAGTTATGGTCTTACTCATTAA
1 ATTCATGATGCCATAACATCTTTCAGCTATGGTCTTACTCGTTAA
*
35386355 ATTCATGATGCCATAACGTCTTTC-GACTATGGTCTTACTCGTT
1 ATTCATGATGCCATAACATCTTTCAG-CTATGGTCTTACTCGTT
35386398 TTTGGTATGA
Statistics
Matches: 76, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
44 3 0.04
45 61 0.80
46 11 0.14
47 1 0.01
ACGTcount: A:0.26, C:0.21, G:0.13, T:0.40
Consensus pattern (45 bp):
ATTCATGATGCCATAACATCTTTCAGCTATGGTCTTACTCGTTAA
Found at i:35387907 original size:24 final size:24
Alignment explanation
Indices: 35387880--35387928 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
35387870 GGAACACATT
35387880 GCCTTTATTTAAATGCTTTTTTAG
1 GCCTTTATTTAAATGCTTTTTTAG
*
35387904 GCCTTTATTTAAATGTTTTTTTAG
1 GCCTTTATTTAAATGCTTTTTTAG
35387928 G
1 G
35387929 AACATGCCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.20, C:0.10, G:0.14, T:0.55
Consensus pattern (24 bp):
GCCTTTATTTAAATGCTTTTTTAG
Found at i:35391708 original size:13 final size:13
Alignment explanation
Indices: 35391687--35391750 Score: 85
Period size: 13 Copynumber: 4.9 Consensus size: 13
35391677 ACACTCAAAT
35391687 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
* *
35391700 TTCTCAAAAGCAT
1 TTTTCAAAAGCAC
*
35391713 TTTTCCACAA-CAC
1 TTTT-CAAAAGCAC
35391726 TTTTCAAAAGCAC
1 TTTTCAAAAGCAC
35391739 TTTTCAAAAGCA
1 TTTTCAAAAGCA
35391751 ATAGAGAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
12 4 0.09
13 35 0.81
14 4 0.09
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (13 bp):
TTTTCAAAAGCAC
Found at i:35393419 original size:5 final size:5
Alignment explanation
Indices: 35393409--35393469 Score: 122
Period size: 5 Copynumber: 12.2 Consensus size: 5
35393399 GTTATAACTT
35393409 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
35393459 ATATA ATATA A
1 ATATA ATATA A
35393470 GTGTAGAAAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 56 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATATA
Found at i:35395072 original size:9 final size:9
Alignment explanation
Indices: 35395058--35395094 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
35395048 TATAGTTTGA
35395058 TATTCGAAT
1 TATTCGAAT
35395067 TATTCGAAT
1 TATTCGAAT
* *
35395076 TATTTGAGT
1 TATTCGAAT
35395085 TATTCGAAT
1 TATTCGAAT
35395094 T
1 T
35395095 CGAAAACTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.30, C:0.08, G:0.14, T:0.49
Consensus pattern (9 bp):
TATTCGAAT
Found at i:35404745 original size:41 final size:41
Alignment explanation
Indices: 35404700--35404806 Score: 108
Period size: 42 Copynumber: 2.6 Consensus size: 41
35404690 CAGGCTCTGT
* *
35404700 GCCTAGCAAGCCTCGTGCTGGTG-TGATATATCAGGCTAAAA
1 GCCTAGCAAGCCTAGTGCCGGTGAT-ATATATCAGGCTAAAA
* * * *
35404741 GCCTAGTAGGCGTAGTGCCGGTGAATTTATATCAGGCTAAAA
1 GCCTAGCAAGCCTAGTGCCGGTG-ATATATATCAGGCTAAAA
* **
35404783 GCCTAGCAGGTGTAGTGCCGGTGA
1 GCCTAGCAAGCCTAGTGCCGGTGA
35404807 ATTTTTATTA
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
41 19 0.34
42 36 0.64
43 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (41 bp):
GCCTAGCAAGCCTAGTGCCGGTGATATATATCAGGCTAAAA
Found at i:35404777 original size:42 final size:42
Alignment explanation
Indices: 35404726--35404820 Score: 154
Period size: 42 Copynumber: 2.3 Consensus size: 42
35404716 GCTGGTGTGA
*
35404726 TATATCAGGCTAAAAGCCTAGTAGGCGTAGTGCCGGTGAATT
1 TATATCAGGCTAAAAGCCTAGCAGGCGTAGTGCCGGTGAATT
*
35404768 TATATCAGGCTAAAAGCCTAGCAGGTGTAGTGCCGGTGAATT
1 TATATCAGGCTAAAAGCCTAGCAGGCGTAGTGCCGGTGAATT
* *
35404810 TTTATTAGGCT
1 TATATCAGGCT
35404821 TGTGCCTAGC
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.29
Consensus pattern (42 bp):
TATATCAGGCTAAAAGCCTAGCAGGCGTAGTGCCGGTGAATT
Found at i:35404964 original size:34 final size:34
Alignment explanation
Indices: 35404921--35404988 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
35404911 TCAGAATTAT
35404921 GTATGTGATTTGATACCTATTACAAATTATGTAC
1 GTATGTGATTTGATACCTATTACAAATTATGTAC
35404955 GTATGTGATTTGATACCTATTACAAATTATGTAC
1 GTATGTGATTTGATACCTATTACAAATTATGTAC
35404989 TCTGTTAACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.41
Consensus pattern (34 bp):
GTATGTGATTTGATACCTATTACAAATTATGTAC
Found at i:35410807 original size:19 final size:19
Alignment explanation
Indices: 35410783--35410826 Score: 63
Period size: 19 Copynumber: 2.3 Consensus size: 19
35410773 ATTTTGAAGT
35410783 TGAAAATACA-TGTTTGTTA
1 TGAAAA-ACAGTGTTTGTTA
*
35410802 TGAAAAACAGTGTTTGTTG
1 TGAAAAACAGTGTTTGTTA
35410821 TGAAAA
1 TGAAAA
35410827 CTTATTTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (19 bp):
TGAAAAACAGTGTTTGTTA
Found at i:35411187 original size:28 final size:31
Alignment explanation
Indices: 35411115--35411193 Score: 83
Period size: 33 Copynumber: 2.6 Consensus size: 31
35411105 CTTTTAGTAT
* *
35411115 CAGTGTGGGCCTCAGCCCAATATAATTTAAGTA
1 CAGTGTGGGCCTAAGCCCAATATAA-TGAAG-A
* *
35411148 CAGTGCGGGCCTTAGCCCAATAT-A-GAA-A
1 CAGTGTGGGCCTAAGCCCAATATAATGAAGA
35411176 CAGTGTGGGCCTAAGCCC
1 CAGTGTGGGCCTAAGCCC
35411194 GTTACAGTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 17 0.41
30 2 0.05
32 1 0.02
33 21 0.51
ACGTcount: A:0.28, C:0.25, G:0.25, T:0.22
Consensus pattern (31 bp):
CAGTGTGGGCCTAAGCCCAATATAATGAAGA
Found at i:35411400 original size:27 final size:27
Alignment explanation
Indices: 35411368--35411446 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
35411358 GTACAATATA
35411368 TGTGGCAAAGCCACCAGTAACAGTAAT
1 TGTGGCAAAGCCACCAGTAACAGTAAT
35411395 TGTGGCAAAGCCACCAGTAACAGTAAT
1 TGTGGCAAAGCCACCAGTAACAGTAAT
* *
35411422 TGTTGCAAAACCACCAGTAACAGTA
1 TGTGGCAAAGCCACCAGTAACAGTA
35411447 CTTTCTCCAT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 50 1.00
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (27 bp):
TGTGGCAAAGCCACCAGTAACAGTAAT
Found at i:35411645 original size:26 final size:26
Alignment explanation
Indices: 35411616--35411667 Score: 77
Period size: 26 Copynumber: 2.0 Consensus size: 26
35411606 ACGGTCATTC
* *
35411616 TACCCTTCGGGGGTATTTCAATAATT
1 TACCCATCGAGGGTATTTCAATAATT
*
35411642 TACCCATCGAGGGTATTTCGATAATT
1 TACCCATCGAGGGTATTTCAATAATT
35411668 AAGGCCCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.37
Consensus pattern (26 bp):
TACCCATCGAGGGTATTTCAATAATT
Found at i:35415065 original size:21 final size:20
Alignment explanation
Indices: 35415021--35415065 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
35415011 GGGGCCTCAG
*
35415021 TCAAAACTTTCTTCAGCTTC
1 TCAAAACTTTCTTCAGCTTA
*
35415041 TCAAAACTTTCTTGCTGCTTA
1 TCAAAACTTTCTT-CAGCTTA
35415062 TCAA
1 TCAA
35415066 TCCTGTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (20 bp):
TCAAAACTTTCTTCAGCTTA
Found at i:35418298 original size:20 final size:19
Alignment explanation
Indices: 35418273--35418314 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
35418263 TTTAAAGTTG
35418273 AAAATACGTGTTTGTTATGA
1 AAAATA-GTGTTTGTTATGA
*
35418293 AAAATAGTGTTTGTTGTGA
1 AAAATAGTGTTTGTTATGA
35418312 AAA
1 AAA
35418315 CCTATTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.38, C:0.02, G:0.21, T:0.38
Consensus pattern (19 bp):
AAAATAGTGTTTGTTATGA
Found at i:35418833 original size:26 final size:26
Alignment explanation
Indices: 35418798--35418847 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
35418788 CCCACACACC
* *
35418798 AATATTGCAGCAGAGTTGCCAGTAAT
1 AATATCGCAGCAGAGCTGCCAGTAAT
*
35418824 AATATCGCAGTAGAGCTGCCAGTA
1 AATATCGCAGCAGAGCTGCCAGTA
35418848 GAGTATATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (26 bp):
AATATCGCAGCAGAGCTGCCAGTAAT
Found at i:35418906 original size:27 final size:27
Alignment explanation
Indices: 35418849--35418906 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
35418839 CTGCCAGTAG
* * *
35418849 AGTATATGTGTCAAAGCCACCAGTAAT
1 AGTATATGTGGCAAAGCCACCAGCAAC
* *
35418876 AGTATTTGTGGCAGAGCCACCAGCAAC
1 AGTATATGTGGCAAAGCCACCAGCAAC
35418903 AGTA
1 AGTA
35418907 CTGCCTCCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.34, C:0.21, G:0.22, T:0.22
Consensus pattern (27 bp):
AGTATATGTGGCAAAGCCACCAGCAAC
Found at i:35423194 original size:25 final size:25
Alignment explanation
Indices: 35423166--35423213 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
35423156 GTTTGCTCTC
* * *
35423166 CCAATCTGAATTATGGTAAGCTCCT
1 CCAAGCTGAATAACGGTAAGCTCCT
35423191 CCAAGCTGAATAACGGTAAGCTC
1 CCAAGCTGAATAACGGTAAGCTC
35423214 ATACGAGCTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (25 bp):
CCAAGCTGAATAACGGTAAGCTCCT
Found at i:35423222 original size:25 final size:25
Alignment explanation
Indices: 35423171--35423258 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 25
35423161 CTCTCCCAAT
* * * * *
35423171 CTGAATTATGGTAAGCTCCTCCAAG
1 CTGAATAACGGTAAGCTCATACGAG
35423196 CTGAATAACGGTAAGCTCATACGAG
1 CTGAATAACGGTAAGCTCATACGAG
* * * *
35423221 CTGAGTATCAGTAAGCTCATAAGAG
1 CTGAATAACGGTAAGCTCATACGAG
*
35423246 CTGAA-ATCGGTAA
1 CTGAATAACGGTAA
35423259 CCCTAATGAC
Statistics
Matches: 52, Mismatches: 11, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
24 7 0.13
25 45 0.87
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (25 bp):
CTGAATAACGGTAAGCTCATACGAG
Found at i:35433834 original size:33 final size:30
Alignment explanation
Indices: 35433789--35433882 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 30
35433779 GGTAGCAGTC
*
35433789 TGGGCCTGAGCCCTATTCAGTAACAGTACAATG
1 TGGGCCTTAGCCC-A-TCA-TAACAGTACAATG
*
35433822 TGGGCCTTAGCCCA--AT-ACAATAACAATG
1 TGGGCCTTAGCCCATCATAACAGT-ACAATG
*
35433850 TGGGCCTTAGCCCGATACAATATCAGTACAATG
1 TGGGCCTTAGCCC-AT-C-ATAACAGTACAATG
35433883 CAGTAATGCA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
27 4 0.08
28 20 0.40
29 2 0.04
32 1 0.02
33 20 0.40
34 3 0.06
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.23
Consensus pattern (30 bp):
TGGGCCTTAGCCCATCATAACAGTACAATG
Found at i:35433856 original size:28 final size:28
Alignment explanation
Indices: 35433816--35433871 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
35433806 CAGTAACAGT
35433816 ACAATGTGGGCCTTAGCCCAATACAATA
1 ACAATGTGGGCCTTAGCCCAATACAATA
*
35433844 ACAATGTGGGCCTTAGCCCGATACAATA
1 ACAATGTGGGCCTTAGCCCAATACAATA
35433872 TCAGTACAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.20, T:0.21
Consensus pattern (28 bp):
ACAATGTGGGCCTTAGCCCAATACAATA
Found at i:35434043 original size:26 final size:26
Alignment explanation
Indices: 35433979--35434055 Score: 100
Period size: 26 Copynumber: 3.0 Consensus size: 26
35433969 AACACACCAA
* *
35433979 TATCGTAGCAAAGCTGTCAGTAATAG
1 TATCGTAGCAAAGCTGCCAGTAACAG
* * *
35434005 TATTGCAGTAAAGCTGCCAGTAACAG
1 TATCGTAGCAAAGCTGCCAGTAACAG
*
35434031 TATCGTAGCAAAGCTGCCAGCAACA
1 TATCGTAGCAAAGCTGCCAGTAACA
35434056 TTATACTTCC
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.35, C:0.21, G:0.22, T:0.22
Consensus pattern (26 bp):
TATCGTAGCAAAGCTGCCAGTAACAG
Found at i:35436565 original size:3 final size:3
Alignment explanation
Indices: 35436557--35436586 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
35436547 TGTCCCCAAA
35436557 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
35436587 CACTCTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:35453229 original size:16 final size:16
Alignment explanation
Indices: 35453175--35453231 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
35453165 AAGGTGATAC
35453175 TTTCA-TTTTTTTCATT
1 TTTCATTTTTTTTC-TT
* *
35453191 TTT-GTTTTATTTTATT
1 TTTCATTTT-TTTTCTT
35453207 TTATCATTTTTTTTCTT
1 TT-TCATTTTTTTTCTT
35453224 TTTCATTT
1 TTTCATTT
35453232 CGAAATAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 16 0.48
17 13 0.39
18 4 0.12
ACGTcount: A:0.12, C:0.09, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTCATTTTTTTTCTT
Found at i:35459423 original size:25 final size:24
Alignment explanation
Indices: 35459378--35459470 Score: 62
Period size: 25 Copynumber: 3.6 Consensus size: 24
35459368 ACTTCATTTT
* *
35459378 AAAAAAAAGAAAAATGTAAAATGC
1 AAAAAAAAGAAAAATGGAAAAAGC
35459402 AAAATAAAACGAAAAA-GGAAAAAGC
1 AAAA-AAAA-GAAAAATGGAAAAAGC
** *
35459427 AACGAAGAGAAAGAAAAGAAAGAAAAAGA
1 AA--AA-A-AAAGAAAA-ATGGAAAAAGC
35459456 AAAGAAAAAGAAAAA
1 AAA-AAAAAGAAAAA
35459471 GGAGAGGCTA
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
24 4 0.07
25 14 0.25
26 14 0.25
27 10 0.18
28 5 0.09
29 9 0.16
ACGTcount: A:0.74, C:0.04, G:0.17, T:0.04
Consensus pattern (24 bp):
AAAAAAAAGAAAAATGGAAAAAGC
Found at i:35459440 original size:6 final size:6
Alignment explanation
Indices: 35459381--35459471 Score: 55
Period size: 6 Copynumber: 15.0 Consensus size: 6
35459371 TCATTTTAAA
* * * * *
35459381 AAAAAG AAAAATG TAAAATG CAAAAT AAAACG AAAAAGG AAAAAG CAACGAAG
1 AAAAAG AAAAA-G -AAAAAG AAAAAG AAAAAG AAAAA-G AAAAAG -AA-AAAG
*
35459434 AGAAAG -AAAAG --AAAG AAAAAG -AAAAG AAAAAG AAAAAG
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG
35459472 GAGAGGCTAG
Statistics
Matches: 65, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
4 4 0.06
5 9 0.14
6 34 0.52
7 11 0.17
8 7 0.11
ACGTcount: A:0.73, C:0.04, G:0.19, T:0.04
Consensus pattern (6 bp):
AAAAAG
Found at i:35459454 original size:15 final size:15
Alignment explanation
Indices: 35459431--35459462 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
35459421 AAAAGCAACG
*
35459431 AAGAGAAAGAAAAGA
1 AAGAAAAAGAAAAGA
35459446 AAGAAAAAGAAAAGA
1 AAGAAAAAGAAAAGA
35459461 AA
1 AA
35459463 AAGAAAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (15 bp):
AAGAAAAAGAAAAGA
Found at i:35459459 original size:11 final size:11
Alignment explanation
Indices: 35459431--35459469 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
35459421 AAAAGCAACG
35459431 AAGAGAAAG-AA
1 AAGA-AAAGAAA
35459442 AAG-AAAGAAA
1 AAGAAAAGAAA
35459452 AAGAAAAGAAA
1 AAGAAAAGAAA
35459463 AAGAAAA
1 AAGAAAA
35459470 AGGAGAGGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 4 0.15
10 5 0.19
11 17 0.65
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (11 bp):
AAGAAAAGAAA
Found at i:35459916 original size:143 final size:143
Alignment explanation
Indices: 35459650--35460317 Score: 971
Period size: 143 Copynumber: 4.7 Consensus size: 143
35459640 AAGCATTCTG
* * *
35459650 AATCTTATCTTCCTAAAGTTGCAATGGAGCAGATTGAAGCCACCAGTCTTATCT-CCTAGAAGTT
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTA-AAGTT
* * * * *
35459714 GCAGCGGGGCAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTAGAACAGATTAAAGC
65 GCAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCATTACAGTGGAACAGATTAAAGC
*
35459779 TACAAGTTATGGCG
130 TACAAGTTATGGCA
* *
35459793 GATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTTAAGTTG
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTG
* * *
35459858 CAGCGGAACAGACTGAAGACAACGAATCTTATTTCCCTGGCATTACAGTGGAATAGATTAAAGCT
66 CAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCATTACAGTGGAACAGATTAAAGCT
*
35459923 ACAAGTTATGGAA
131 ACAAGTTATGGCA
* * *
35459936 AATATTGTCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTG
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTG
* * * *
35460001 TAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCCGGCA-TACAATGGAACAAATTAAAGCT
66 CAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCATTACAGTGGAACAGATTAAAGCT
35460065 ACAAGTTATGGCA
131 ACAAGTTATGGCA
* * *
35460078 GATCTTATCTTCCTGAAGTTGCAGTGGATCAGATTGAAGCCACCAGCCTTATCTCCCTGAAGTTG
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTG
* * * * *
35460143 CAGTGGAGCAGACTGAAGACAGCGAATATTAGTTCCCTGGCATTGCAGTGGAACAGGTTAAAGCT
66 CAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCATTACAGTGGAACAGATTAAAGCT
*
35460208 ACAAATTATGGCA
131 ACAAGTTATGGCA
* * *
35460221 AATATTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCCTAAAGTTG
1 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTG
* * * *
35460286 TAGCAGAGCAGACTGAAGATAGTGAATCTTAT
66 CAGCGGAGCAGACTGAAGACAGCGAATCTTAT
35460318 CTCTCTAAAG
Statistics
Matches: 466, Mismatches: 57, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
142 127 0.27
143 336 0.72
144 3 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.26
Consensus pattern (143 bp):
AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTG
CAGCGGAGCAGACTGAAGACAGCGAATCTTATTTCCCTGGCATTACAGTGGAACAGATTAAAGCT
ACAAGTTATGGCA
Found at i:35460181 original size:285 final size:286
Alignment explanation
Indices: 35459654--35460317 Score: 1026
Period size: 285 Copynumber: 2.3 Consensus size: 286
35459644 ATTCTGAATC
* * *
35459654 TTATCTTCCTAAAGTTGCAATGGAGCAGATTGAAGCCACCAGTCTTATCT-CCTAGAAGTTGCAG
1 TTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTA-AAGTTGTAG
* * * * * * *
35459718 CGGGGCAGACTAAAGACAGCGAATCTTATTTCCCTGGCGTTGCAGTAGAACAGATTAAAGCTACA
65 CGGAGCAGACTGAAGACAGCGAATCTTATTTCCCCGGCGATACAATAGAACAAATTAAAGCTACA
*
35459783 AGTTATGGCGGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTC
130 AGTTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTC
* * * *
35459848 CCTTAAGTTGCAGCGGAACAGACTGAAGACAACGAATCTTATTTCCCTGGCATTACAGTGGAATA
195 CCTGAAGTTGCAGCGGAACAGACTGAAGACAACGAATATTAGTTCCCTGGCATTACAGTGGAACA
*
35459913 GATTAAAGCTACAAGTTATGGAAAATA
260 GATTAAAGCTACAAATTATGGAAAATA
* * *
35459940 TTGTCTTCTTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTGTAGC
1 TTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTGTAGC
*
35460005 GGAGCAGACTGAAGACAGCGAATCTTATTTCCCCGGC-ATACAATGGAACAAATTAAAGCTACAA
66 GGAGCAGACTGAAGACAGCGAATCTTATTTCCCCGGCGATACAATAGAACAAATTAAAGCTACAA
*
35460069 GTTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGATCAGATTGAAGCCACCAGCCTTATCTCC
131 GTTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
* * * *
35460134 CTGAAGTTGCAGTGGAGCAGACTGAAGACAGCGAATATTAGTTCCCTGGCATTGCAGTGGAACAG
196 CTGAAGTTGCAGCGGAACAGACTGAAGACAACGAATATTAGTTCCCTGGCATTACAGTGGAACAG
* *
35460199 GTTAAAGCTACAAATTATGGCAAATA
261 ATTAAAGCTACAAATTATGGAAAATA
*
35460225 TTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACTAGCCTTATCTCCCTAAAGTTGTAGC
1 TTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTGTAGC
* * *
35460290 AGAGCAGACTGAAGATAGTGAATCTTAT
66 GGAGCAGACTGAAGACAGCGAATCTTAT
35460318 CTCTCTAAAG
Statistics
Matches: 343, Mismatches: 34, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
285 251 0.73
286 88 0.26
287 4 0.01
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (286 bp):
TTATCTTCCTAAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCCCTAAAGTTGTAGC
GGAGCAGACTGAAGACAGCGAATCTTATTTCCCCGGCGATACAATAGAACAAATTAAAGCTACAA
GTTATGGCAGATCTTATCTTCCTGAAGTTGCAGTGGAGCAGATTGAAGCCACCAGCCTTATCTCC
CTGAAGTTGCAGCGGAACAGACTGAAGACAACGAATATTAGTTCCCTGGCATTACAGTGGAACAG
ATTAAAGCTACAAATTATGGAAAATA
Found at i:35468969 original size:25 final size:25
Alignment explanation
Indices: 35468941--35468989 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
35468931 TATAGTTTTT
35468941 ATATTAT-TTATAAAGGTTATAATAC
1 ATATTATATTAT-AAGGTTATAATAC
*
35468966 ATATTATATTATAATGTTATAATA
1 ATATTATATTATAAGGTTATAATA
35468990 AAACAAATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (25 bp):
ATATTATATTATAAGGTTATAATAC
Found at i:35474732 original size:15 final size:15
Alignment explanation
Indices: 35474708--35474737 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35474698 GATTTCTTGT
35474708 TTTTCATTTATTTAC
1 TTTTCATTTATTTAC
*
35474723 TTTTCTTTTATTTAC
1 TTTTCATTTATTTAC
35474738 CTCCTTATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTCATTTATTTAC
Found at i:35477649 original size:29 final size:29
Alignment explanation
Indices: 35477546--35477812 Score: 204
Period size: 29 Copynumber: 9.1 Consensus size: 29
35477536 TGAAGTGGAA
*
35477546 AATTGATGGTCGTCACCATCCCTTTTCAT
1 AATTGATGGTCCTCACCATCCCTTTTCAT
* * ** * *
35477575 AATCGATAG-CCAAAGCTATCCGTTTTCAT
1 AATTGATGGTCCTCA-CCATCCCTTTTCAT
35477604 AATTCGATGG-CCTTCACCATCCCTTTTCAT
1 AATT-GATGGTCC-TCACCATCCCTTTTCAT
* *
35477634 AGTTGATGGTCCTCACGATCCCTTTTCAT
1 AATTGATGGTCCTCACCATCCCTTTTCAT
* * *
35477663 AGTTAATGGTCGTCACCATCCCCTTTT-AT
1 AATTGATGGTCCTCACCAT-CCCTTTTCAT
* *
35477692 AATTCGATGTTCGTCACCATCCCTTTTCAT
1 AATT-GATGGTCCTCACCATCCCTTTTCAT
* * * *
35477722 AATCGATAG--CTAAATCTATCCCTTTTCAT
1 AATTGATGGTCCT-CA-CCATCCCTTTTCAT
*
35477751 AATTCGATGGTCGTCACCATCCCTTTTCAT
1 AATT-GATGGTCCTCACCATCCCTTTTCAT
* * * *
35477781 AGTTGATAGTAGC-CACTATCCCTTTTCAT
1 AATTGATGGT-CCTCACCATCCCTTTTCAT
35477810 AAT
1 AAT
35477813 CGATAGCCAA
Statistics
Matches: 187, Mismatches: 38, Indels: 26
0.75 0.15 0.10
Matches are distributed among these distances:
27 1 0.01
28 3 0.02
29 112 0.60
30 68 0.36
31 2 0.01
32 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.37
Consensus pattern (29 bp):
AATTGATGGTCCTCACCATCCCTTTTCAT
Found at i:35477660 original size:59 final size:59
Alignment explanation
Indices: 35477558--35477781 Score: 208
Period size: 59 Copynumber: 3.8 Consensus size: 59
35477548 TTGATGGTCG
* *** * *
35477558 TCACCATCCCTTTTCATAA-TCGATAG-CCAAAGCTATCCGTTTTCATAATTCGATGGCCT
1 TCACCATCCCTTTTCATAATTCGATGGTCGTCA-CCATCCCTTTTCATAATTCGATGG-CT
* * * * * *
35477617 TCACCATCCCTTTTCATAGTT-GATGGTCCTCACGATCCCTTTTCATAGTT-AATGGTCG
1 TCACCATCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAATTCGATGG-CT
* *
35477675 TCACCATCCCCTTTT-ATAATTCGATGTTCGTCACCATCCCTTTTCATAA-TCGATAGCT
1 TCACCAT-CCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAATTCGATGGCT
** *
35477733 AAATCTATCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATA
1 TCA-CCATCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATA
35477782 GTTGATAGTA
Statistics
Matches: 136, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
58 27 0.20
59 105 0.77
60 4 0.03
ACGTcount: A:0.23, C:0.29, G:0.11, T:0.37
Consensus pattern (59 bp):
TCACCATCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAATTCGATGGCT
Found at i:35477789 original size:59 final size:58
Alignment explanation
Indices: 35477622--35477816 Score: 211
Period size: 59 Copynumber: 3.3 Consensus size: 58
35477612 GGCCTTCACC
* * * * * *
35477622 ATCCCTTTTCATAGTT-GATGGTCCTCACGATCCCTTTTCATAGTTAATGGTCGT-CACC
1 ATCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAGTTGATAG-C-TACACT
* * * *
35477680 ATCCCCTTTT-ATAATTCGATGTTCGTCACCATCCCTTTTCATAATCGATAGCTAAATCT
1 AT-CCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAGTTGATAGCTACA-CT
35477739 ATCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAGTTGATAG-TAGCCACT
1 ATCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAGTTGATAGCTA--CACT
35477798 ATCCCTTTTCATAA-TCGAT
1 ATCCCTTTTCATAATTCGAT
35477817 AGCCAAAACT
Statistics
Matches: 116, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
57 1 0.01
58 23 0.20
59 91 0.78
60 1 0.01
ACGTcount: A:0.23, C:0.27, G:0.12, T:0.38
Consensus pattern (58 bp):
ATCCCTTTTCATAATTCGATGGTCGTCACCATCCCTTTTCATAGTTGATAGCTACACT
Found at i:35477827 original size:29 final size:29
Alignment explanation
Indices: 35477710--35477838 Score: 107
Period size: 29 Copynumber: 4.4 Consensus size: 29
35477700 GTTCGTCACC
* *
35477710 ATCCCTTTTCATAATCGATAGCTAAATCT
1 ATCCCTTTTCATAATCGATAGCCAAAACT
* * *** *
35477739 ATCCCTTTTCATAATTCGATGGTCGTCACC
1 ATCCCTTTTCATAA-TCGATAGCCAAAACT
* * * **
35477769 ATCCCTTTTCATAGTTGATAG-TAGCCACT
1 ATCCCTTTTCATAATCGATAGCCA-AAACT
35477798 ATCCCTTTTCATAATCGATAGCCAAAACT
1 ATCCCTTTTCATAATCGATAGCCAAAACT
*
35477827 ATCCATTTTCAT
1 ATCCCTTTTCAT
35477839 TAGTCGATGA
Statistics
Matches: 76, Mismatches: 21, Indels: 6
0.74 0.20 0.06
Matches are distributed among these distances:
29 55 0.72
30 21 0.28
ACGTcount: A:0.27, C:0.26, G:0.09, T:0.37
Consensus pattern (29 bp):
ATCCCTTTTCATAATCGATAGCCAAAACT
Found at i:35477846 original size:88 final size:89
Alignment explanation
Indices: 35477651--35477854 Score: 254
Period size: 88 Copynumber: 2.3 Consensus size: 89
35477641 GGTCCTCACG
** * *
35477651 ATCCCTTTTCA-TAGTTAATGGTCGTCACCATCCCCTTTTATAATTCGATGTTCGTCACCATCCC
1 ATCCCTTTTCATTAGTCGATGGTCGTCACCATCCCCTTTTATAATTCGATGTTAGCCACCATCCC
* *
35477715 TTTTCATAATCGATAGCTAAATCT
66 TTTTCATAATCGATAGCCAAAACT
* * * *
35477739 ATCCCTTTTCATAATTCGATGGTCGTCACCAT-CCCTTTTCATAGTT-GATAG-TAGCCACTATC
1 ATCCCTTTTCATTAGTCGATGGTCGTCACCATCCCCTTTT-ATAATTCGAT-GTTAGCCACCATC
35477801 CCTTTTCATAATCGATAGCCAAAACT
64 CCTTTTCATAATCGATAGCCAAAACT
* *
35477827 ATCCATTTTCATTAGTCGATGATCGTCA
1 ATCCCTTTTCATTAGTCGATGGTCGTCA
35477855 ATATGCCGTT
Statistics
Matches: 99, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
88 77 0.78
89 22 0.22
ACGTcount: A:0.25, C:0.26, G:0.11, T:0.37
Consensus pattern (89 bp):
ATCCCTTTTCATTAGTCGATGGTCGTCACCATCCCCTTTTATAATTCGATGTTAGCCACCATCCC
TTTTCATAATCGATAGCCAAAACT
Found at i:35477846 original size:147 final size:147
Alignment explanation
Indices: 35477550--35477854 Score: 380
Period size: 147 Copynumber: 2.1 Consensus size: 147
35477540 GTGGAAAATT
* *
35477550 GATGGTCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCCGTTTTCATAATTCGATGGC
1 GATGATCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATTCGATGGC
* * * * * * ***
35477615 CTTCACCATCCCTTTTCATAGTTGATGGTCCTCACGATCCCTTTTCATAGTTAATGGTCGTCACC
66 CGTCACCATCCCTTTTCATAGTTGATAGTCCTCACGATCCCTTTTCATAATCAATAGCCAAAACC
* *
35477680 ATCCCCTTTTATAATTC
131 ATCCCATTTTATAAGTC
* * * *
35477697 GATGTTCGTCACCATCCCTTTTCATAATCGATAGCTAAATCTATCCCTTTTCATAATTCGATGGT
1 GATGATCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATTCGATGGC
* * *
35477762 CGTCACCATCCCTTTTCATAGTTGATAGTAGC-CACTATCCCTTTTCATAATCGATAGCCAAAAC
66 CGTCACCATCCCTTTTCATAGTTGATAGT-CCTCACGATCCCTTTTCATAATCAATAGCCAAAAC
* *
35477826 TAT-CCATTTTCATTAGTC
130 CATCCCATTTT-ATAAGTC
35477844 GATGATCGTCA
1 GATGATCGTCA
35477855 ATATGCCGTT
Statistics
Matches: 134, Mismatches: 22, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
146 6 0.04
147 127 0.95
148 1 0.01
ACGTcount: A:0.24, C:0.27, G:0.13, T:0.36
Consensus pattern (147 bp):
GATGATCGTCACCATCCCTTTTCATAATCGATAGCCAAAGCTATCCCTTTTCATAATTCGATGGC
CGTCACCATCCCTTTTCATAGTTGATAGTCCTCACGATCCCTTTTCATAATCAATAGCCAAAACC
ATCCCATTTTATAAGTC
Found at i:35482066 original size:27 final size:27
Alignment explanation
Indices: 35482025--35482407 Score: 466
Period size: 27 Copynumber: 14.2 Consensus size: 27
35482015 GTAATGGGCC
*
35482025 TAAAATGACCAAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
** * *
35482052 TAAAATGATTGAAATACTCTCAAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*
35482079 TAAAATGACTGAAATACCCT-GAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
35482105 TAAAATGACCAAAATACCCCCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
35482132 TAAAATGACCAAAATACCCCCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * * *
35482159 TAAAATAACTGAAATTCCCCCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
35482186 TAAAATAACTGAAATTCCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*
35482213 TAAAATGACTGAAATACCAC-CGAAGGG
1 TAAAATGACCGAAATACC-CTCGAAGGG
* *
35482240 TAAAATGATCGAAATGCCCTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
35482267 TAAAATGACCGAAATGCCCTTGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
*
35482294 TAAAATGACTGAAATACCC-CTGAAGGG
1 TAAAATGACCGAAATACCCTC-GAAGGG
*
35482321 TAAAATGACCGAAATACCTTCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* *
35482348 TAAAATGACCGAAGTACCCCCGAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
* * *
35482375 TAAAATGATCGAAATACCCCCAAAGGG
1 TAAAATGACCGAAATACCCTCGAAGGG
35482402 TAAAAT
1 TAAAAT
35482408 AACTGTTATA
Statistics
Matches: 317, Mismatches: 34, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
26 23 0.07
27 292 0.92
28 2 0.01
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.17
Consensus pattern (27 bp):
TAAAATGACCGAAATACCCTCGAAGGG
Found at i:35482614 original size:26 final size:26
Alignment explanation
Indices: 35482585--35482661 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
35482575 TTGCCACATA
*
35482585 TACTGTTACTGGCAGCTTTGCTGCGT
1 TACTATTACTGGCAGCTTTGCTGCGT
*
35482611 TACTATTACTGGCAGCTTTGCTGCAT
1 TACTATTACTGGCAGCTTTGCTGCGT
* *
35482637 CACTATTACTGGTAGCTTTGCTGCG
1 TACTATTACTGGCAGCTTTGCTGCG
35482662 ATTTTGGTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 46 1.00
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.38
Consensus pattern (26 bp):
TACTATTACTGGCAGCTTTGCTGCGT
Found at i:35486673 original size:32 final size:30
Alignment explanation
Indices: 35486622--35486691 Score: 86
Period size: 32 Copynumber: 2.3 Consensus size: 30
35486612 CATGCTCAAC
* *
35486622 CTTTACTTTTCAGATTTTAAGCAAACTTTACT
1 CTTTATTTTTCAGAATTTAAGCAAACTTT--T
* *
35486654 CTTTATTTTTGAGAATTTAAGCAATCTTTT
1 CTTTATTTTTCAGAATTTAAGCAAACTTTT
35486684 CTTTATTT
1 CTTTATTT
35486692 ATTATTCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 9 0.26
32 25 0.74
ACGTcount: A:0.26, C:0.14, G:0.07, T:0.53
Consensus pattern (30 bp):
CTTTATTTTTCAGAATTTAAGCAAACTTTT
Found at i:35488016 original size:88 final size:89
Alignment explanation
Indices: 35487866--35488055 Score: 233
Period size: 88 Copynumber: 2.2 Consensus size: 89
35487856 TCAACTATCG
* * * *
35487866 ACTATGAAAAGGGA-TAGTTTCGACTATCGACTATGAAAAGGGATGGTGGCGACCATCAACTATG
1 ACTATGAAAAGGGATTAGTTTCGACTATAGACTATGAAAAGGGATAGTGGCAACCATCAACTATA
*
35487930 AAAAGGGATGGTGACCACCAGC-A
66 AAAAGGGATGGTGACAACCAGCGA
** ** ** * *
35487953 ACTATGAAAAGGGATTTTTTTTTACTATAGACTATGAAAAGGGATAGTTTCAACTATCGACTATA
1 ACTATGAAAAGGGATTAGTTTCGACTATAGACTATGAAAAGGGATAGTGGCAACCATCAACTATA
*
35488018 AAAAGGGATGGTGACAACCATCGA
66 AAAAGGGATGGTGACAACCAGCGA
35488042 A-TATGAAAAGGGAT
1 ACTATGAAAAGGGAT
35488056 GGTTACGACC
Statistics
Matches: 87, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
87 14 0.16
88 71 0.82
89 2 0.02
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (89 bp):
ACTATGAAAAGGGATTAGTTTCGACTATAGACTATGAAAAGGGATAGTGGCAACCATCAACTATA
AAAAGGGATGGTGACAACCAGCGA
Found at i:35488035 original size:29 final size:29
Alignment explanation
Indices: 35487814--35488059 Score: 197
Period size: 29 Copynumber: 8.4 Consensus size: 29
35487804 CGATCAATGA
** * *
35487814 AAAAGGGATGGTTTTGACCATCGTA-TATA
1 AAAAGGGATGGTTTCAACTATCG-ACTATG
* *
35487843 AAAAGGTATAGTTTCAACTATCGACTATG
1 AAAAGGGATGGTTTCAACTATCGACTATG
* *
35487872 AAAAGGGATAGTTTCGACTATCGACTATG
1 AAAAGGGATGGTTTCAACTATCGACTATG
** * * *
35487901 AAAAGGGATGGTGGCGACCATCAACTATG
1 AAAAGGGATGGTTTCAACTATCGACTATG
** * * * *
35487930 AAAAGGGATGGTGACCACCAGCAACTATG
1 AAAAGGGATGGTTTCAACTATCGACTATG
** ** *
35487959 AAAAGGGATTTTTTTTTACTATAGACTATG
1 AAAAGGGA-TGGTTTCAACTATCGACTATG
* *
35487989 AAAAGGGATAGTTTCAACTATCGACTATA
1 AAAAGGGATGGTTTCAACTATCGACTATG
** * *
35488018 AAAAGGGATGGTGACAACCATCGAATATG
1 AAAAGGGATGGTTTCAACTATCGACTATG
35488047 AAAAGGGATGGTT
1 AAAAGGGATGGTT
35488060 ACGACCATTT
Statistics
Matches: 176, Mismatches: 39, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
28 1 0.01
29 156 0.89
30 19 0.11
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (29 bp):
AAAAGGGATGGTTTCAACTATCGACTATG
Found at i:35489050 original size:12 final size:12
Alignment explanation
Indices: 35489033--35489059 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
35489023 AGGCAGTTAA
35489033 ACGGCCTAGCAC
1 ACGGCCTAGCAC
35489045 ACGGCCTAGCAC
1 ACGGCCTAGCAC
35489057 ACG
1 ACG
35489060 AGAGTGTGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.26, C:0.41, G:0.26, T:0.07
Consensus pattern (12 bp):
ACGGCCTAGCAC
Found at i:35493331 original size:21 final size:21
Alignment explanation
Indices: 35493302--35493342 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
35493292 TAGTCAAGAT
*
35493302 ATTAGTAAATTTTAAATGTTG
1 ATTAGTAAATGTTAAATGTTG
*
35493323 ATTATTAAATGTTAAATGTT
1 ATTAGTAAATGTTAAATGTT
35493343 AAATGTTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.49
Consensus pattern (21 bp):
ATTAGTAAATGTTAAATGTTG
Found at i:35493337 original size:7 final size:7
Alignment explanation
Indices: 35493307--35493354 Score: 51
Period size: 7 Copynumber: 6.9 Consensus size: 7
35493297 AAGATATTAG
*
35493307 TAAATTT
1 TAAATGT
35493314 TAAATGT
1 TAAATGT
* * *
35493321 TGATTAT
1 TAAATGT
35493328 TAAATGT
1 TAAATGT
35493335 TAAATGT
1 TAAATGT
35493342 TAAATGT
1 TAAATGT
*
35493349 TCAATG
1 TAAATG
35493355 AATTACTTGA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.40, C:0.02, G:0.12, T:0.46
Consensus pattern (7 bp):
TAAATGT
Found at i:35500447 original size:36 final size:36
Alignment explanation
Indices: 35500400--35500473 Score: 121
Period size: 36 Copynumber: 2.1 Consensus size: 36
35500390 AATAAACTCT
*
35500400 ATTCAATTCAGCAGCCTTTCGGATCTATTCTGACTG
1 ATTCAATTCAGCACCCTTTCGGATCTATTCTGACTG
* *
35500436 ATTCAGTTCAGCACCCTTTTGGATCTATTCTGACTG
1 ATTCAATTCAGCACCCTTTCGGATCTATTCTGACTG
35500472 AT
1 AT
35500474 GCACTCCTCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.38
Consensus pattern (36 bp):
ATTCAATTCAGCACCCTTTCGGATCTATTCTGACTG
Found at i:35500648 original size:21 final size:21
Alignment explanation
Indices: 35500602--35500649 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
35500592 CAATGGAAGG
*
35500602 AAAAGGGAAATGGAATGTAAA
1 AAAATGGAAATGGAATGTAAA
*
35500623 AAAATGGAAATGGAATGTAGA
1 AAAATGGAAATGGAATGTAAA
35500644 AAAATG
1 AAAATG
35500650 CTAATGAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.56, C:0.00, G:0.27, T:0.17
Consensus pattern (21 bp):
AAAATGGAAATGGAATGTAAA
Found at i:35500655 original size:21 final size:21
Alignment explanation
Indices: 35500609--35500655 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
35500599 AGGAAAAGGG
*
35500609 AAATGGAATGTAAAAAAATGG
1 AAATGGAATGTAAAAAAATGC
*
35500630 AAATGGAATGTAGAAAAATGC
1 AAATGGAATGTAAAAAAATGC
*
35500651 TAATG
1 AAATG
35500656 AAAGAAGAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.53, C:0.02, G:0.23, T:0.21
Consensus pattern (21 bp):
AAATGGAATGTAAAAAAATGC
Found at i:35506388 original size:26 final size:26
Alignment explanation
Indices: 35506353--35506405 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
35506343 TCAAGATTCA
35506353 TCACTAATAAGCATTCTCACTTTTTT
1 TCACTAATAAGCATTCTCACTTTTTT
35506379 TCACTAATAAGCATTCTCACTTTTTT
1 TCACTAATAAGCATTCTCACTTTTTT
35506405 T
1 T
35506406 GGCTGAGTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.23, G:0.04, T:0.47
Consensus pattern (26 bp):
TCACTAATAAGCATTCTCACTTTTTT
Found at i:35508775 original size:47 final size:46
Alignment explanation
Indices: 35508679--35508776 Score: 124
Period size: 47 Copynumber: 2.1 Consensus size: 46
35508669 GTTGAATTGG
* * * *
35508679 ATATATGTGGTCAAGCCACTATATTGCAGCCAAGCTACCAGAACAA
1 ATATATGTGATCAAGCCACTATATTGCAGACAAACTACCAGAAAAA
* * *
35508725 ATATATGTGATCGAGCCACTATAATTGCAGACAAACTGCTAGAAAAA
1 ATATATGTGATCAAGCCACTAT-ATTGCAGACAAACTACCAGAAAAA
35508772 ATATA
1 ATATA
35508777 GATGAACCAC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
46 20 0.45
47 24 0.55
ACGTcount: A:0.41, C:0.19, G:0.16, T:0.23
Consensus pattern (46 bp):
ATATATGTGATCAAGCCACTATATTGCAGACAAACTACCAGAAAAA
Found at i:35511228 original size:3 final size:3
Alignment explanation
Indices: 35511220--35511250 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
35511210 GAAAATTCTC
*
35511220 ATA ATA ATA GTA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
35511251 ATCTATATGG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:35512256 original size:4 final size:4
Alignment explanation
Indices: 35512249--35512274 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
35512239 TATATATATA
35512249 TATT TATT TATT TATT TATT TATT TA
1 TATT TATT TATT TATT TATT TATT TA
35512275 AGAGTATACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:35512378 original size:3 final size:3
Alignment explanation
Indices: 35512372--35512428 Score: 105
Period size: 3 Copynumber: 18.7 Consensus size: 3
35512362 CTTGTGTTCT
35512372 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
35512420 TTA TATA TT
1 TTA T-TA TT
35512429 GCATATTTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 50 0.94
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35513521 original size:2 final size:2
Alignment explanation
Indices: 35513509--35513544 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
35513499 TAATCTGCTA
35513509 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
35513545 GCACACAGCA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:35521907 original size:62 final size:62
Alignment explanation
Indices: 35521795--35521922 Score: 141
Period size: 62 Copynumber: 2.1 Consensus size: 62
35521785 TCCTAAATAT
* ** ** ** * * *
35521795 AAAAAATTCAATAAATTTAGCCCTCAATGTTTATGAAATTTTTCATTTTAGT-TCTAATTCTA
1 AAAAAACTCAATAAATTTAGCCCTCAACATTTACAAAACCTGTCAATTTAGTCT-TAACTCTA
*
35521857 AAAAAACTCAATAAATTTGGCCCTCAACATTTACAAAACCTGTCAATTTAGTCTTAACTCTA
1 AAAAAACTCAATAAATTTAGCCCTCAACATTTACAAAACCTGTCAATTTAGTCTTAACTCTA
35521919 AAAA
1 AAAA
35521923 TTAAAAAATA
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
62 53 0.98
63 1 0.02
ACGTcount: A:0.41, C:0.17, G:0.06, T:0.36
Consensus pattern (62 bp):
AAAAAACTCAATAAATTTAGCCCTCAACATTTACAAAACCTGTCAATTTAGTCTTAACTCTA
Found at i:35526251 original size:152 final size:153
Alignment explanation
Indices: 35525637--35526379 Score: 811
Period size: 153 Copynumber: 4.9 Consensus size: 153
35525627 AAGATGTATT
* * * * *
35525637 TTTGAGAACTTATAGCTTAACCCAATCGATTCATGCAACTAGCTAATCAATATAGCAGTTGGACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTAATGCAACTAGCTAATAAATATAGCAATTGGACT
* * * * * * *
35525702 TCCCCTAAATCTTAATTTGTTACC-CTTTTATTAAAAAAATAAACCATCGCCAACAAAATCAAGA
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
35525766 TTAATGTGCTGCTAATATGCGTC
131 TTAATGTGCTGCTAATATGCGTC
* *
35525789 TTTGAGAACTTACAGCTTAACTCGATCGA-TACATGCAACTAGCTAATAAATGTAGCAATTGGAC
1 TTTGAGAACTTATAGCTTAACTCGATCGATTA-ATGCAACTAGCTAATAAATATAGCAATTGGAC
* *
35525853 TTCCCCTTAATCTCAAAGTATTACCTCTTTTATTAAAAATATAAACCATCACCCACAAAATCAAG
65 TTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAG
* ** ***
35525918 ATTAATGTACTATTAATATTTATC
130 ATTAATGTGCTGCTAATATGCGTC
* * ** * ** *
35525942 TTTGAGAATTTATAGCTTAAATCGATCGATTCTTACAACTATTTAATAAATA-ATGCAATTGAAC
1 TTTGAGAACTTATAGCTTAACTCGATCGATTAATGCAACTAGCTAATAAATATA-GCAATTGGAC
* * * * *
35526006 TTCCCCTTAATATGAAATCATTACCTCTTTTGTTAAAAATATAAACCATCACCGTCAAAATCAAG
65 TTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAG
35526071 ATTAATGTGCTGCTAATATGCGTC
130 ATTAATGTGCTGCTAATATGCGTC
* * *
35526095 TTTGAGAAATTATAACTTAACTCGATCGATTAATGCAACTAGCTAATAAATATAGCAGTTGGACT
1 TTTGAGAACTTATAGCTTAACTCGATCGATTAATGCAACTAGCTAATAAATATAGCAATTGGACT
* * * * *
35526160 T-CCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATCTAAACCATCGCCGACATATTCAATA
66 TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
* * * ** *
35526224 TCAATGTGCTGCAAATGTTTGTA
131 TTAATGTGCTGCTAATATGCGTC
* * * * * * * *
35526247 TTTGAGAACTTATAGTTTAACTCGATCCATT-TTG--ACTACCTAATAAGTATATCATTTGAACC
1 TTTGAGAACTTATAGCTTAACTCGATCGATTAATGCAACTAGCTAATAAATATAGCAATTG---G
* ** * * *
35526309 ACTT-CCCTTAATATCAAATTACGA-CTTTTTTATTAAAAATATAAACTATCACCGGCAAAATCA
63 ACTTCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCA
35526372 AGATTAAT
128 AGATTAAT
35526380 ATGCGACTAA
Statistics
Matches: 491, Mismatches: 92, Indels: 17
0.82 0.15 0.03
Matches are distributed among these distances:
149 20 0.04
151 41 0.08
152 194 0.40
153 234 0.48
154 2 0.00
ACGTcount: A:0.37, C:0.19, G:0.10, T:0.34
Consensus pattern (153 bp):
TTTGAGAACTTATAGCTTAACTCGATCGATTAATGCAACTAGCTAATAAATATAGCAATTGGACT
TCCCCTTAATCTCAAATTATTACCTCTTTTATTAAAAATATAAACCATCACCGACAAAATCAAGA
TTAATGTGCTGCTAATATGCGTC
Found at i:35527664 original size:3 final size:3
Alignment explanation
Indices: 35527658--35527719 Score: 61
Period size: 3 Copynumber: 20.7 Consensus size: 3
35527648 ACCAGAGCAG
* * * * * *
35527658 GAT GAT GAT GAT GAA GAT GAT GAT GAT GAC GAC GAT GAT GGT GCT GCT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
*
35527706 GCT GAT GAT GAT GA
1 GAT GAT GAT GAT GA
35527720 GGACGATAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.29, C:0.08, G:0.35, T:0.27
Consensus pattern (3 bp):
GAT
Found at i:35531174 original size:135 final size:132
Alignment explanation
Indices: 35531010--35531278 Score: 411
Period size: 135 Copynumber: 2.0 Consensus size: 132
35531000 GTTATTGAAT
35531010 TCATTGAGTCGAATCAATAATCATATAACTTTTATCGCTTATATCTTCATTTATCATAACACTTA
1 TCATTGAGTCGAATCAATAATCATATAACTTTTATCGCTTATATCTTCATTTATCATAACACTTA
*
35531075 CGTGTGATTTTTTTTATCT-AAGCATT-TTTGTCGTTTATACGTTAATTTCTTAGATAACATTTA
66 CGTGTGA-TTTTTTTATCTGAA-CATTATTT-TCGTTTATACCTTAATTTCTT--ATAACATTTA
35531138 CATGTGA
126 CATGTGA
* *
35531145 TCATTGAGTC-ACATCAATAATCAGT-TAACTTTTATCGTTTATATCTTCATTTATTATAACACT
1 TCATTGAGTCGA-ATCAATAATCA-TATAACTTTTATCGCTTATATCTTCATTTATCATAACACT
*
35531208 TATGTGTGATTTTTTTATCTGAACATTATTTTCGTTTATACCTTAATTTCTTATAACATTTACAT
64 TACGTGTGATTTTTTTATCTGAACATTATTTTCGTTTATACCTTAATTTCTTATAACATTTACAT
35531273 GTGA
129 GTGA
35531277 TC
1 TC
35531279 TTTTTACCTA
Statistics
Matches: 126, Mismatches: 4, Indels: 11
0.89 0.03 0.08
Matches are distributed among these distances:
132 19 0.15
134 36 0.29
135 70 0.56
136 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (132 bp):
TCATTGAGTCGAATCAATAATCATATAACTTTTATCGCTTATATCTTCATTTATCATAACACTTA
CGTGTGATTTTTTTATCTGAACATTATTTTCGTTTATACCTTAATTTCTTATAACATTTACATGT
GA
Done.