Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 147 of 161
Found at i:45849982 original size:21 final size:21
Alignment explanation
Indices: 45849956--45849998 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
45849946 CAACGTGGCA
45849956 AGTTAACTGGCCACATCAGCT
1 AGTTAACTGGCCACATCAGCT
* **
45849977 AGTTAATTGGCCATGTCAGCT
1 AGTTAACTGGCCACATCAGCT
45849998 A
1 A
45849999 TCCCGTTAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.23, G:0.21, T:0.28
Consensus pattern (21 bp):
AGTTAACTGGCCACATCAGCT
Found at i:45850262 original size:196 final size:195
Alignment explanation
Indices: 45849924--45850446 Score: 920
Period size: 196 Copynumber: 2.7 Consensus size: 195
45849914 TCTTTTCTTC
*
45849924 TTTGACCTTTTGACTACTCGTCCAACGTGGCAAGTTAACTGGCCACATCAGCTAGTTAATTGGCC
1 TTTGACCCTTTGACTACTCGTCCAACGTGGCAAGTTAACTGGCCACATCAGCTAGTTAATTGGCC
* * * *
45849989 ATGTCAGCTATCCCGTTAAGTTTGTGACGGAAAATGTTAATGAGTGACTGATTTGTATCTTTTCA
66 ACGTTAGCTATCCCGTTAAGCTTGTGACGGAAAATGTTAATGAGTGACTGATTTGCA-CTTTTCA
45850054 ATAACATTAGTGACTGTTTTGTTATTTTTCCAAAGTTGAGTGACTGAAATGAAACCTAGGTGACT
130 ATAACATTAGTGACTGTTTTGTTATTTTTCCAAAGTTGAGTGACTGAAATGAAACCTAGGTGACT
45850119 G
195 G
* *
45850120 TTTGACCCTTTGACTACTCGTCCCACGTGGCAAGTTAACTGGCCACAGCAGCTAGTTAATTGGCC
1 TTTGACCCTTTGACTACTCGTCCAACGTGGCAAGTTAACTGGCCACATCAGCTAGTTAATTGGCC
*
45850185 ACGTTAGCTATCCCGTTAAGCTTGTGACGGAAAATGTTAATGAGTGACTAATTTGCCACTTTTCA
66 ACGTTAGCTATCCCGTTAAGCTTGTGACGGAAAATGTTAATGAGTGACTGATTTG-CACTTTTCA
*
45850250 ATAACGTTAGTGACTGTTTTGTTATTTTTCCAAAGTTGAGTGACTGAAATGAAACCTAGGTGACT
130 ATAACATTAGTGACTGTTTTGTTATTTTTCCAAAGTTGAGTGACTGAAATGAAACCTAGGTGACT
45850315 G
195 G
*
45850316 CTTGACCCTTTGACTACTCGTCCAACGTGGCAAGTTAACTGGCCACATCAGCTAGTTAATTGGCC
1 TTTGACCCTTTGACTACTCGTCCAACGTGGCAAGTTAACTGGCCACATCAGCTAGTTAATTGGCC
*
45850381 ACGTTAGCTATCCCGTTAAGCTTGTGACGGAAAATGTTAATGAGTGATTGATTTGTCACTTTTCA
66 ACGTTAGCTATCCCGTTAAGCTTGTGACGGAAAATGTTAATGAGTGACTGATTTG-CACTTTTCA
45850446 A
130 A
45850447 NNNNNNNNNN
Statistics
Matches: 311, Mismatches: 15, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
196 310 1.00
197 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.33
Consensus pattern (195 bp):
TTTGACCCTTTGACTACTCGTCCAACGTGGCAAGTTAACTGGCCACATCAGCTAGTTAATTGGCC
ACGTTAGCTATCCCGTTAAGCTTGTGACGGAAAATGTTAATGAGTGACTGATTTGCACTTTTCAA
TAACATTAGTGACTGTTTTGTTATTTTTCCAAAGTTGAGTGACTGAAATGAAACCTAGGTGACTG
Found at i:45851262 original size:17 final size:18
Alignment explanation
Indices: 45851231--45851264 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
45851221 CTCTAATTTA
*
45851231 CATTATAATTTAGTAAAC
1 CATTATAATTAAGTAAAC
45851249 CATTA-AATTAAGTAAA
1 CATTATAATTAAGTAAA
45851265 TAGTTAAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.50, C:0.09, G:0.06, T:0.35
Consensus pattern (18 bp):
CATTATAATTAAGTAAAC
Found at i:45852325 original size:24 final size:24
Alignment explanation
Indices: 45852293--45852361 Score: 66
Period size: 24 Copynumber: 2.9 Consensus size: 24
45852283 GGGTAGGCTT
*
45852293 TGTGACTGCATCTGTATCTGAATC
1 TGTGTCTGCATCTGTATCTGAATC
*** *
45852317 TGTGTCTGCATCCACATTTGAATC
1 TGTGTCTGCATCTGTATCTGAATC
* * *
45852341 TGCGTCTACATTTGTATCTGA
1 TGTGTCTGCATCTGTATCTGA
45852362 TTCTAAATAT
Statistics
Matches: 33, Mismatches: 12, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.20, C:0.22, G:0.19, T:0.39
Consensus pattern (24 bp):
TGTGTCTGCATCTGTATCTGAATC
Found at i:45852342 original size:18 final size:18
Alignment explanation
Indices: 45852321--45852360 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
45852311 TGAATCTGTG
45852321 TCTGCATCCACATTTGAA
1 TCTGCATCCACATTTGAA
* * *
45852339 TCTGCGTCTACATTTGTA
1 TCTGCATCCACATTTGAA
45852357 TCTG
1 TCTG
45852361 ATTCTAAATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.20, C:0.25, G:0.15, T:0.40
Consensus pattern (18 bp):
TCTGCATCCACATTTGAA
Found at i:45852415 original size:24 final size:24
Alignment explanation
Indices: 45852387--45852442 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
45852377 CGTATCTAAT
*
45852387 TATGAAAATACATTTGACTCTGTA
1 TATGAAAATACATTTGAATCTGTA
* **
45852411 TATGAGAATATGTTTGAATCTGTA
1 TATGAAAATACATTTGAATCTGTA
*
45852435 TCTGAAAA
1 TATGAAAA
45852443 CATATATGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.38
Consensus pattern (24 bp):
TATGAAAATACATTTGAATCTGTA
Found at i:45854922 original size:12 final size:12
Alignment explanation
Indices: 45854905--45854929 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45854895 CTCACGTCAG
45854905 TTTTCTTTCTTT
1 TTTTCTTTCTTT
45854917 TTTTCTTTCTTT
1 TTTTCTTTCTTT
45854929 T
1 T
45854930 CCTCTTTTGA
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTCTTTCTTT
Found at i:45855535 original size:41 final size:41
Alignment explanation
Indices: 45855477--45855554 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
45855467 GTGTAGTAGG
* *
45855477 TCGTGTGGTTCACATGAGCTTGTGTTAGGCCATGTGGAAGC
1 TCGTGTGGGTCACATGAGCTTATGTTAGGCCATGTGGAAGC
*
45855518 TCGTGTGGGTCATATGAGCTTATGTTAGGCCATGTGG
1 TCGTGTGGGTCACATGAGCTTATGTTAGGCCATGTGG
45855555 GCCACACGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.17, C:0.15, G:0.35, T:0.33
Consensus pattern (41 bp):
TCGTGTGGGTCACATGAGCTTATGTTAGGCCATGTGGAAGC
Found at i:45855567 original size:29 final size:29
Alignment explanation
Indices: 45855535--45855590 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
45855525 GGTCATATGA
45855535 GCTTATGTTAGGCCATGTGGGCCACACGG
1 GCTTATGTTAGGCCATGTGGGCCACACGG
* ***
45855564 GCTTGTGTTAGGTTGTGTGGGCCACAC
1 GCTTATGTTAGGCCATGTGGGCCACAC
45855591 AGACTGGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.14, C:0.21, G:0.36, T:0.29
Consensus pattern (29 bp):
GCTTATGTTAGGCCATGTGGGCCACACGG
Found at i:45859822 original size:18 final size:17
Alignment explanation
Indices: 45859793--45859835 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
45859783 TTGTTAACTT
45859793 TGTTGATGTCACATACA
1 TGTTGATGTCACATACA
*
45859810 TGTTGATTGTCACATAGA
1 TGTTGA-TGTCACATACA
45859828 TGTT-ATGT
1 TGTTGATGT
45859836 AAGCAATTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 3 0.12
17 7 0.29
18 14 0.58
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.42
Consensus pattern (17 bp):
TGTTGATGTCACATACA
Found at i:45874937 original size:40 final size:40
Alignment explanation
Indices: 45874860--45874937 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
45874850 ACAAATTCAG
*
45874860 AATAAATAATCAAAATTTAAATTTAAAATATTTTTTTACA
1 AATAAATAATCAAAATTTAAATTTAAAATATTATTTTACA
* *
45874900 AATAAATAATTAATAA-TTAATATTTTAAATA-TATTTTA
1 AATAAATAATCAA-AATTTAA-ATTTAAAATATTATTTTA
45874938 AATTTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 22 0.67
41 11 0.33
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (40 bp):
AATAAATAATCAAAATTTAAATTTAAAATATTATTTTACA
Found at i:45879984 original size:44 final size:42
Alignment explanation
Indices: 45879921--45880037 Score: 130
Period size: 44 Copynumber: 2.7 Consensus size: 42
45879911 TATGTGTTGT
* *
45879921 CGTGTAAGACCACATCTGGGACGTTGGCATCGACT-TGTGATTTA
1 CGTGTAAGACCACGTCTGGGACG-TGGCATC-AATATGTGA-TTA
*
45879965 CGTGTAAGACC-CTGTCTGGGATAGTGGCATCAATATGTGATTA
1 CGTGTAAGACCAC-GTCTGGGA-CGTGGCATCAATATGTGATTA
*
45880008 CATGTAAGACCACGTCTGGGACGATGGCAT
1 CGTGTAAGACCACGTCTGGGACG-TGGCAT
45880038 TGTACGAAAC
Statistics
Matches: 63, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
42 1 0.02
43 30 0.48
44 31 0.49
45 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (42 bp):
CGTGTAAGACCACGTCTGGGACGTGGCATCAATATGTGATTA
Found at i:45880028 original size:43 final size:44
Alignment explanation
Indices: 45879923--45880037 Score: 121
Period size: 43 Copynumber: 2.6 Consensus size: 44
45879913 TGTGTTGTCG
* * * *
45879923 TGTAAGACCACATCTGGGACGTTGGCATCGACTTGTGATTTACG
1 TGTAAGACCACGTCTGGGAAGTTGGCATCGAATTGTGATTTACA
45879967 TGTAAGACC-CTGTCTGGGATAG-TGGCATC-AATATGTGA-TTACA
1 TGTAAGACCAC-GTCTGGGA-AGTTGGCATCGAAT-TGTGATTTACA
* *
45880010 TGTAAGACCACGTCTGGGACGATGGCAT
1 TGTAAGACCACGTCTGGGAAGTTGGCAT
45880038 TGTACGAAAC
Statistics
Matches: 61, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
42 1 0.02
43 30 0.49
44 29 0.48
45 1 0.02
ACGTcount: A:0.25, C:0.19, G:0.28, T:0.28
Consensus pattern (44 bp):
TGTAAGACCACGTCTGGGAAGTTGGCATCGAATTGTGATTTACA
Found at i:45881580 original size:23 final size:23
Alignment explanation
Indices: 45881545--45881735 Score: 195
Period size: 23 Copynumber: 8.2 Consensus size: 23
45881535 TGGTGCATAA
*
45881545 ATGCTGTCCAATTTTGTATATAT
1 ATGCTGTCAAATTTTGTATATAT
* * * *
45881568 TTGCTGTCAAATTTAGTGTATAA
1 ATGCTGTCAAATTTTGTATATAT
*
45881591 ATGCTGTCCAATTTTGTATATAT
1 ATGCTGTCAAATTTTGTATATAT
* * *
45881614 ATGCTGTCAAATCTTGGTGTATAA
1 ATGCTGTCAAAT-TTTGTATATAT
*
45881638 ATGCTGTCCAAA-TTGGTATATAT
1 ATGCTGT-CAAATTTTGTATATAT
** * * * *
45881661 ATGCTACCCAATTTGGTGTATAA
1 ATGCTGTCAAATTTTGTATATAT
*
45881684 ATGCTGTCCAATTTTGTATATAT
1 ATGCTGTCAAATTTTGTATATAT
45881707 ATGCTGTCAAATTTTGGTATATAT
1 ATGCTGTCAAATTTT-GTATATAT
45881731 ATGCT
1 ATGCT
45881736 CGCAACTCAA
Statistics
Matches: 137, Mismatches: 27, Indels: 7
0.80 0.16 0.04
Matches are distributed among these distances:
22 3 0.02
23 102 0.74
24 28 0.20
25 4 0.03
ACGTcount: A:0.28, C:0.13, G:0.16, T:0.43
Consensus pattern (23 bp):
ATGCTGTCAAATTTTGTATATAT
Found at i:45881591 original size:46 final size:46
Alignment explanation
Indices: 45881533--45881735 Score: 298
Period size: 46 Copynumber: 4.4 Consensus size: 46
45881523 GTTATCCAAT
* *
45881533 TTTGGTGCATAAATGCTGTCCAATTTTGTATATATTTGCTGTCAAA
1 TTTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
*
45881579 TTTAGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
1 TTTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
* * ** *
45881625 TCTTGGTGTATAAATGCTGTCCAAATTGGTATATATATGCTACCCAA
1 T-TTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
45881672 TTTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
1 TTTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
* *
45881718 TTTTGGTATATATATGCT
1 -TTTGGTGTATAAATGCT
45881736 CGCAACTCAA
Statistics
Matches: 139, Mismatches: 16, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
46 84 0.60
47 55 0.40
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (46 bp):
TTTGGTGTATAAATGCTGTCCAATTTTGTATATATATGCTGTCAAA
Found at i:45881693 original size:93 final size:93
Alignment explanation
Indices: 45881534--45881735 Score: 305
Period size: 93 Copynumber: 2.2 Consensus size: 93
45881524 TTATCCAATT
* * * * **
45881534 TTGGTGCATAAATGCTGTCCAATTTTGTATATATTTGCTGTCAAATTTAGTGTATAAATGCTGTC
1 TTGGTGTATAAATGCTGTCCAAATTGGTATATATATGCTACCAAATTTAGTGTATAAATGCTGTC
45881599 CAATTTTGTATATATATGCTGTCAAATC
66 CAATTTTGTATATATATGCTGTCAAATC
* *
45881627 TTGGTGTATAAATGCTGTCCAAATTGGTATATATATGCTACCCAATTTGGTGTATAAATGCTGTC
1 TTGGTGTATAAATGCTGTCCAAATTGGTATATATATGCTACCAAATTTAGTGTATAAATGCTGTC
*
45881692 CAATTTTGTATATATATGCTGTCAAATT
66 CAATTTTGTATATATATGCTGTCAAATC
* *
45881720 TTGGTATATATATGCT
1 TTGGTGTATAAATGCT
45881736 CGCAACTCAA
Statistics
Matches: 98, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 98 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.43
Consensus pattern (93 bp):
TTGGTGTATAAATGCTGTCCAAATTGGTATATATATGCTACCAAATTTAGTGTATAAATGCTGTC
CAATTTTGTATATATATGCTGTCAAATC
Found at i:45882853 original size:24 final size:25
Alignment explanation
Indices: 45882820--45882868 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
45882810 TGATAATTAT
*
45882820 TTTAGGATTTAATA-TTAAGATTTA
1 TTTAGAATTTAATATTTAAGATTTA
*
45882844 TTTAGAATTTAATATTTACGATTTA
1 TTTAGAATTTAATATTTAAGATTTA
45882869 AAATTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 13 0.59
25 9 0.41
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (25 bp):
TTTAGAATTTAATATTTAAGATTTA
Found at i:45887249 original size:27 final size:27
Alignment explanation
Indices: 45887210--45887267 Score: 66
Period size: 27 Copynumber: 2.1 Consensus size: 27
45887200 AAAGGTTTTT
45887210 AAATGACCGAAATACCCTCGAAG-GGTA
1 AAATGACCGAAATACCCT-GAAGAGGTA
* *
45887237 AAATGA-CGAAAATATCCTTAAGAGGTA
1 AAATGACCG-AAATACCCTGAAGAGGTA
45887264 AAAT
1 AAAT
45887268 TACCATTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.47, C:0.16, G:0.19, T:0.19
Consensus pattern (27 bp):
AAATGACCGAAATACCCTGAAGAGGTA
Found at i:45892705 original size:30 final size:30
Alignment explanation
Indices: 45892671--45892730 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
45892661 TCTTTCATTC
* * *
45892671 TTTGTATATTATTGTCTGGTGTGAACTTTA
1 TTTGTATACTATTGCCTGGTATGAACTTTA
*
45892701 TTTGTATACTATTGCCTGTTATGAACTTTA
1 TTTGTATACTATTGCCTGGTATGAACTTTA
45892731 GTCCAAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.22, C:0.10, G:0.17, T:0.52
Consensus pattern (30 bp):
TTTGTATACTATTGCCTGGTATGAACTTTA
Found at i:45893077 original size:32 final size:33
Alignment explanation
Indices: 45893037--45893109 Score: 89
Period size: 33 Copynumber: 2.2 Consensus size: 33
45893027 CAGTTTTTAT
45893037 AAAATATTTT-CAGAAAAT-T-TGCCAAACACTAG
1 AAAATATTTTACAG-AAATCTAT-CCAAACACTAG
* *
45893069 AAATTATTTTACAGAGATCTATCCAAACACTAG
1 AAAATATTTTACAGAAATCTATCCAAACACTAG
45893102 AAAATATT
1 AAAATATT
45893110 AACAGTTATA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 12 0.34
33 22 0.63
34 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.08, T:0.30
Consensus pattern (33 bp):
AAAATATTTTACAGAAATCTATCCAAACACTAG
Found at i:45898032 original size:3 final size:3
Alignment explanation
Indices: 45898024--45898110 Score: 88
Period size: 3 Copynumber: 29.0 Consensus size: 3
45898014 CAAAATTTAG
* *
45898024 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT GTT ATT ATC ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * * *
45898072 GTT ATT -TAT ATT ATT GTT -TT CATC ATC ATT ATT ATT ATT
1 ATT ATT AT-T ATT ATT ATT ATT -ATT ATT ATT ATT ATT ATT
45898111 GTTTATGCAT
Statistics
Matches: 71, Mismatches: 9, Indels: 8
0.81 0.10 0.09
Matches are distributed among these distances:
2 3 0.04
3 66 0.93
4 2 0.03
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:45899386 original size:30 final size:31
Alignment explanation
Indices: 45899341--45899409 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 31
45899331 CCAAATCGGG
* *
45899341 ATAACTCCACAATCTCATATTTTCTTCCTAAA
1 ATAACT-CACAATCTCACATTTTCCTCCTAAA
45899373 ATAACTC-CAATCTCACATTTTCCTCCTAAA
1 ATAACTCACAATCTCACATTTTCCTCCTAAA
*
45899403 ATCACTC
1 ATAACTC
45899410 GAGCACTCCC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 27 0.79
31 1 0.03
32 6 0.18
ACGTcount: A:0.33, C:0.32, G:0.00, T:0.35
Consensus pattern (31 bp):
ATAACTCACAATCTCACATTTTCCTCCTAAA
Found at i:45924700 original size:42 final size:42
Alignment explanation
Indices: 45924653--45924738 Score: 172
Period size: 42 Copynumber: 2.0 Consensus size: 42
45924643 AAGTAAATTT
45924653 AAATAAAATAATAATATTATTAATATGAATCAAACTACTTTC
1 AAATAAAATAATAATATTATTAATATGAATCAAACTACTTTC
45924695 AAATAAAATAATAATATTATTAATATGAATCAAACTACTTTC
1 AAATAAAATAATAATATTATTAATATGAATCAAACTACTTTC
45924737 AA
1 AA
45924739 TTATAAGCTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.53, C:0.09, G:0.02, T:0.35
Consensus pattern (42 bp):
AAATAAAATAATAATATTATTAATATGAATCAAACTACTTTC
Found at i:45926627 original size:15 final size:18
Alignment explanation
Indices: 45926586--45926627 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
45926576 TCTTTAATTT
45926586 TTTTGTA-AT-TTTATTA
1 TTTTGTATATATTTATTA
45926602 TTTTGTATATATTTATTA
1 TTTTGTATATATTTATTA
45926620 TTTT-TATA
1 TTTTGTATA
45926628 ATTCTATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.29
17 6 0.25
18 11 0.46
ACGTcount: A:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (18 bp):
TTTTGTATATATTTATTA
Found at i:45926884 original size:32 final size:31
Alignment explanation
Indices: 45926848--45926907 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
45926838 AACCGTTAAA
* *
45926848 TTTTAACGGTCAAAAGTTCTAATTGGGTGTAT
1 TTTTAAAGGTCAAAAGTGC-AATTGGGTGTAT
* *
45926880 TTTTAAAGTTCAATAGTGCAATTGGGTG
1 TTTTAAAGGTCAAAAGTGCAATTGGGTG
45926908 CAAAAAAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 9 0.38
32 15 0.62
ACGTcount: A:0.28, C:0.08, G:0.23, T:0.40
Consensus pattern (31 bp):
TTTTAAAGGTCAAAAGTGCAATTGGGTGTAT
Found at i:45931384 original size:5 final size:5
Alignment explanation
Indices: 45931370--45931452 Score: 58
Period size: 5 Copynumber: 15.8 Consensus size: 5
45931360 GGCATATCTT
* * * * *
45931370 ATATC GTATC TTATC ATATC ATATTTC ATATA ATGTC ATATCAC ATTTC
1 ATATC ATATC ATATC ATATC ATA--TC ATATC ATATC ATAT--C ATATC
* * *
45931419 ATATC TTATC ATATC ATATC TTAAC ATATC ATAT
1 ATATC ATATC ATATC ATATC ATATC ATATC ATAT
45931453 TCTAACCCCA
Statistics
Matches: 59, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
5 50 0.85
7 9 0.15
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (5 bp):
ATATC
Found at i:45931408 original size:22 final size:22
Alignment explanation
Indices: 45931381--45931437 Score: 78
Period size: 22 Copynumber: 2.6 Consensus size: 22
45931371 TATCGTATCT
45931381 TATCATATCATATTTCATATAA
1 TATCATATCATATTTCATATAA
* * **
45931403 TGTCATATCACATTTCATATCT
1 TATCATATCATATTTCATATAA
45931425 TATCATATCATAT
1 TATCATATCATAT
45931438 CTTAACATAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.46
Consensus pattern (22 bp):
TATCATATCATATTTCATATAA
Found at i:45931437 original size:15 final size:15
Alignment explanation
Indices: 45931370--45931452 Score: 73
Period size: 15 Copynumber: 5.6 Consensus size: 15
45931360 GGCATATCTT
*
45931370 ATATCGTATCTTATC
1 ATATCATATCTTATC
45931385 ATATCATA--TT-TC
1 ATATCATATCTTATC
* * *
45931397 ATATAATGTCATATCAC
1 ATATCATATCTTAT--C
*
45931414 ATTTCATATCTTATC
1 ATATCATATCTTATC
*
45931429 ATATCATATCTTAAC
1 ATATCATATCTTATC
45931444 ATATCATAT
1 ATATCATAT
45931453 TCTAACCCCA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
12 8 0.15
13 2 0.04
14 1 0.02
15 31 0.58
17 11 0.21
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (15 bp):
ATATCATATCTTATC
Found at i:45935037 original size:27 final size:27
Alignment explanation
Indices: 45934985--45935037 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
45934975 TTATTTACAA
* *
45934985 TATTTTTATAATATTTTTATAGTTTCT
1 TATTTTTATAATATTTTCATACTTTCT
*
45935012 TATTTTT-TAATAATTTTCCTACTTTC
1 TATTTTTATAAT-ATTTTCATACTTTC
45935038 ATATCATACG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.25, C:0.09, G:0.02, T:0.64
Consensus pattern (27 bp):
TATTTTTATAATATTTTCATACTTTCT
Found at i:45935187 original size:9 final size:9
Alignment explanation
Indices: 45935173--45935253 Score: 50
Period size: 9 Copynumber: 9.4 Consensus size: 9
45935163 AATCGATATG
45935173 TTTTATAAT
1 TTTTATAAT
45935182 TTTTAT-AT
1 TTTTATAAT
45935190 TAATTT-TAAT
1 T--TTTATAAT
45935200 TTTTA-AAT
1 TTTTATAAT
45935208 TTTTA-AAT
1 TTTTATAAT
45935216 TTTT-T-AT
1 TTTTATAAT
**
45935223 TTACA-ATAT
1 TTTTATA-AT
*
45935232 TTTTATAGT
1 TTTTATAAT
*
45935241 TTTTATAGT
1 TTTTATAAT
45935250 TTTT
1 TTTT
45935254 TTTTATTTTT
Statistics
Matches: 58, Mismatches: 5, Indels: 18
0.72 0.06 0.22
Matches are distributed among these distances:
7 4 0.07
8 21 0.36
9 26 0.45
10 7 0.12
ACGTcount: A:0.30, C:0.01, G:0.02, T:0.67
Consensus pattern (9 bp):
TTTTATAAT
Found at i:45935303 original size:244 final size:248
Alignment explanation
Indices: 45934865--45935311 Score: 581
Period size: 244 Copynumber: 1.8 Consensus size: 248
45934855 TACAACAACA
*
45934865 TAAATATGATATGAAGTTATATAAATTGCAATTATAAACTATGAGTTAATTGACATGTTTATAAT
1 TAAATATGATATGAAGTTATATAAATTGCAATTATAAACTATGAGTTAATCGACATGTTTATAAT
* * *
45934930 TTATAGCTTTTATTAGTTTTATATTAATTGTAATTTTTTAATTTTTTATTTACAATATTTTTATA
66 TTATA--TTATATTAATTTTATATT-ATTGTAATTTTTAAATTTTTTATTTACAATATTTTTATA
* * * *
45934995 ATATTTTTATAGTTTCTTATTTTTTAATAATTTTCCTACTTTCATATCATACGCCCCTTCTTTTA
128 ATATTTTTATAGTTTCTTATTTTTCAATAATTTTCCAACTCTCATATCATACGCCCCATCTTTTA
45935060 CCTAGTTAACATAGTTAATATCAGTAACTAATTGATTTTAGTTTCAATCAGTAACT
193 CCTAGTTAACATAGTTAATATCAGTAACTAATTGATTTTAGTTTCAATCAGTAACT
* * * * * *
45935116 TAAATATGATTTGTAGTTATATGAATTGCAATTATAAATTTTGAGTTAATCGATATGTTTTATAA
1 TAAATATGATATGAAGTTATATAAATTGCAATTATAAACTATGAGTTAATCGACATG-TTTATAA
45935181 -TT-T-TTATATTAATTTTA-ATT-TT-TAAATTTTTAAATTTTTTATTTACAATATTTTTAT-A
65 TTTATATTATATTAATTTTATATTATTGT-AATTTTTAAATTTTTTATTTACAATATTTTTATAA
* * * *
45935239 -GTTTTTATAGTTTTTTTTTATTTTTCAAT-ATTTTCCAAC-CTCATATCATGTCGCCTCATCTT
129 TATTTTTATAG---TTTCTTATTTTTCAATAATTTTCCAACTCTCATATCAT-ACGCCCCATCTT
45935301 TTACCTAGTTA
190 TTACCTAGTTA
45935312 GCACAAAGTT
Statistics
Matches: 172, Mismatches: 18, Indels: 19
0.82 0.09 0.09
Matches are distributed among these distances:
242 9 0.05
243 11 0.06
244 63 0.37
245 14 0.08
246 3 0.02
247 12 0.07
250 1 0.01
251 52 0.30
252 7 0.04
ACGTcount: A:0.31, C:0.09, G:0.07, T:0.52
Consensus pattern (248 bp):
TAAATATGATATGAAGTTATATAAATTGCAATTATAAACTATGAGTTAATCGACATGTTTATAAT
TTATATTATATTAATTTTATATTATTGTAATTTTTAAATTTTTTATTTACAATATTTTTATAATA
TTTTTATAGTTTCTTATTTTTCAATAATTTTCCAACTCTCATATCATACGCCCCATCTTTTACCT
AGTTAACATAGTTAATATCAGTAACTAATTGATTTTAGTTTCAATCAGTAACT
Found at i:45940451 original size:17 final size:16
Alignment explanation
Indices: 45940429--45940500 Score: 81
Period size: 17 Copynumber: 4.1 Consensus size: 16
45940419 ATTTGAATCT
45940429 TTTTTTATTTATTTATG
1 TTTTTT-TTTATTTATG
45940446 TTTTTTTATTATTTATG
1 TTTTTTT-TTATTTATG
*
45940463 TTATTTTTTATTTGATG
1 TTTTTTTTTATTT-ATG
45940480 TTTTTTCTTATATTCTATG
1 TTTTTT-TT-TATT-TATG
45940499 TT
1 TT
45940501 GTATTAACAG
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
16 7 0.15
17 29 0.60
18 2 0.04
19 9 0.19
20 1 0.02
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.74
Consensus pattern (16 bp):
TTTTTTTTTATTTATG
Found at i:45940457 original size:21 final size:20
Alignment explanation
Indices: 45940428--45940471 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 20
45940418 GATTTGAATC
45940428 TTTTTTTATTTAT-TTATGTT
1 TTTTTTTATTTATGTTAT-TT
45940448 TTTTTATTATTTATGTTATTT
1 TTTTT-TTATTTATGTTATTT
45940469 TTT
1 TTT
45940472 ATTTGATGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 5 0.23
21 13 0.59
22 4 0.18
ACGTcount: A:0.16, C:0.00, G:0.05, T:0.80
Consensus pattern (20 bp):
TTTTTTTATTTATGTTATTT
Found at i:45949158 original size:125 final size:124
Alignment explanation
Indices: 45948760--45949326 Score: 744
Period size: 125 Copynumber: 4.5 Consensus size: 124
45948750 GATAAAATCA
* * * * * * *
45948760 AAGCAGGATGATTTATCAGAAGGATTTTTGAAGTCGCGCCCACGTGTACGCGCTTTTGCTAGAGT
1 AAGCA-GATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * *
45948825 ATGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTTTAAAAAATGCTTC
65 AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * *
45948885 AAGCAGGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGTTTTTACTACAGT
1 AAGCA-GATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * * * *
45948950 TGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTTTGAGCAAATAGTTTTAAAAAACGCTTC
65 AGGTCCT-GAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAG-TATAAAAAACGCTTC
* *
45949012 AAGCAAGATGCTTTATAAGAAGAATTTGTGAAGTCGCGCCCACGTGGACGCGCTTTTGCTACAGT
1 AAGC-AGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGT
* * *
45949077 AGGTCCT-AAAAAATAATTTTGAGTTGACGTTTCTGAGCAAATAGTATAAAACAACGCTGC
65 AGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAA-AACGCTTC
* *
45949137 AAGCAGCATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAG
1 AAGCAG-ATGCT-TTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAG
* *
45949201 TAGGTCCTGGAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTAT-AAAATCGCTTC
64 TAGGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
* * * * *
45949261 TAGCAGATGTTTTATGAGAAGAATTTGTGAAATCGTGCCCATGTGGACTCGCTTTTGCTACAGTA
1 AAGCAGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
45949326 G
66 G
45949327 CATGCTTAGG
Statistics
Matches: 390, Mismatches: 44, Indels: 18
0.86 0.10 0.04
Matches are distributed among these distances:
122 2 0.01
123 51 0.13
124 19 0.05
125 166 0.43
126 73 0.19
127 78 0.20
128 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (124 bp):
AAGCAGATGCTTTATGAGAAGAATTTGTGAAATCGCGCCCACGTGGACGCGCTTTTGCTACAGTA
GGTCCTGAAAAAATAATTTCGACTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTC
Found at i:45950546 original size:22 final size:22
Alignment explanation
Indices: 45950497--45951280 Score: 1060
Period size: 22 Copynumber: 36.0 Consensus size: 22
45950487 TCAAATTATA
*
45950497 TTTAAGTTAAGGG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
45950518 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * * *
45950540 TTAAATTTAAGTG-CTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
*
45950560 TTTAAGTTAAGGG-TTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
45950581 TTTAAGTTAAGGGTTTATGGAT
1 TTTAAGTTAAGGGTTTAGGGTT
*
45950603 TTTAATTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
*
45950624 TTTAATGTTAATGG-TTAGGGTT
1 TTTAA-GTTAAGGGTTTAGGGTT
45950646 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
45950668 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
45950690 TTTAAGTTACA-GGTTTAGGGTT
1 TTTAAGTTA-AGGGTTTAGGGTT
45950712 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
45950734 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
45950756 TTTAAGTTACA-GGTTTAGGGTT
1 TTTAAGTTA-AGGGTTTAGGGTT
45950778 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
45950800 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
45950822 TTTAAGTTACA-GGTTTAGGGTT
1 TTTAAGTTA-AGGGTTTAGGGTT
45950844 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
45950866 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
45950888 TTTAAGTTACA-GGTTTAGGGTT
1 TTTAAGTTA-AGGGTTTAGGGTT
45950910 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
45950932 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
45950954 TTTAAGTTACA-GGTTTAGGGTT
1 TTTAAGTTA-AGGGTTTAGGGTT
45950976 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
45950998 TTTAAGTTAAGGGGTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
45951020 TTTAAGTTACA-GGTTTAGGGTT
1 TTTAAGTTA-AGGGTTTAGGGTT
45951042 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
45951064 TTAAAGTTAAGGG-TTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
*
45951085 TTTAGGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
45951107 TTTAATTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
45951129 TTTAATTTAAGAG-TTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
45951150 TTTAAGTTAAGGGTTTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
45951172 TTAAAGTCAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* **
45951193 TTTAGGTTAAGGGGCTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
45951215 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * * **
45951237 TTTAGGTTTAGAGTTTAAGTTTT
1 TTTAAGTTAAGGGTTT-AGGGTT
*
45951260 TTTAATTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
45951281 AGGGGTAGGG
Statistics
Matches: 677, Mismatches: 64, Indels: 44
0.86 0.08 0.06
Matches are distributed among these distances:
20 15 0.02
21 113 0.17
22 530 0.78
23 19 0.03
ACGTcount: A:0.24, C:0.01, G:0.30, T:0.45
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:45951597 original size:21 final size:21
Alignment explanation
Indices: 45951573--45951619 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
45951563 GCGGCGGTTG
*
45951573 TGGTTCTCCCAGT-GGGGATT
1 TGGTTCTCCCAGTAGGGCATT
*
45951593 CTGGTTCTTCCAGTAGGGCATT
1 -TGGTTCTCCCAGTAGGGCATT
45951615 TGGTT
1 TGGTT
45951620 GTCGGAGTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 17 0.74
22 6 0.26
ACGTcount: A:0.11, C:0.19, G:0.32, T:0.38
Consensus pattern (21 bp):
TGGTTCTCCCAGTAGGGCATT
Found at i:45952531 original size:7 final size:7
Alignment explanation
Indices: 45952521--45952546 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
45952511 TTATATACAT
45952521 AATACTA
1 AATACTA
45952528 AATACTA
1 AATACTA
45952535 AATACTA
1 AATACTA
45952542 AATAC
1 AATAC
45952547 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:45952752 original size:20 final size:20
Alignment explanation
Indices: 45952715--45952752 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
45952705 TTTATTTTTA
*
45952715 AAAATCTACATAATAATTGC
1 AAAATCTACATAAAAATTGC
45952735 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
45952753 TACATCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.11, G:0.03, T:0.32
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGC
Found at i:45953787 original size:12 final size:11
Alignment explanation
Indices: 45953751--45953805 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
45953741 ATAAATATGG
45953751 ATTTGAGAGAA
1 ATTTGAGAGAA
*
45953762 ATTTTGA-AGGA
1 A-TTTGAGAGAA
45953773 ATTTGAGAGCAA
1 ATTTGAGAG-AA
45953785 A-TTGAGAGGAA
1 ATTTGAGA-GAA
*
45953796 ATTTAAGAGA
1 ATTTGAGAGA
45953806 GGATTAGTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
10 5 0.14
11 18 0.50
12 13 0.36
ACGTcount: A:0.44, C:0.02, G:0.27, T:0.27
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:45953794 original size:22 final size:22
Alignment explanation
Indices: 45953751--45953805 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
45953741 ATAAATATGG
45953751 ATTTGAGAGAAATTTTGAAGG-A
1 ATTTGAGAGAAA-TTTGAAGGAA
45953773 ATTTGAGAGCAAA-TTGAGAGGAA
1 ATTTGAGAG-AAATTTGA-AGGAA
*
45953796 ATTTAAGAGA
1 ATTTGAGAGA
45953806 GGATTAGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
21 4 0.14
22 13 0.45
23 12 0.41
ACGTcount: A:0.44, C:0.02, G:0.27, T:0.27
Consensus pattern (22 bp):
ATTTGAGAGAAATTTGAAGGAA
Found at i:45967294 original size:24 final size:23
Alignment explanation
Indices: 45967264--45967321 Score: 73
Period size: 22 Copynumber: 2.5 Consensus size: 23
45967254 TATTAATTAA
*
45967264 TTAAAATTTAAAGTTTTTATATAT
1 TTAAAATTTAAA-TTCTTATATAT
*
45967288 TTAAAATTT-AATTCTTATATTT
1 TTAAAATTTAAATTCTTATATAT
*
45967310 TTTAAATTTAAA
1 TTAAAATTTAAA
45967322 AATTGGCCCT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
22 17 0.57
23 4 0.13
24 9 0.30
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (23 bp):
TTAAAATTTAAATTCTTATATAT
Found at i:45981190 original size:40 final size:41
Alignment explanation
Indices: 45981130--45981210 Score: 110
Period size: 40 Copynumber: 2.0 Consensus size: 41
45981120 GTAACAGTTT
* * *
45981130 GGGCCTTAGCTCATCTCAGTA-CAATATCAAACATGCAGTA
1 GGGCCTTAGCCCATCACAGTATCAATAGCAAACATGCAGTA
**
45981170 GGGCCTTAGCCCATCACAGTATCAATAGCAGTCATGCAGTA
1 GGGCCTTAGCCCATCACAGTATCAATAGCAAACATGCAGTA
45981211 TTCAGTATCA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
40 19 0.54
41 16 0.46
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (41 bp):
GGGCCTTAGCCCATCACAGTATCAATAGCAAACATGCAGTA
Found at i:45988723 original size:265 final size:261
Alignment explanation
Indices: 45988218--45989031 Score: 1147
Period size: 265 Copynumber: 3.1 Consensus size: 261
45988208 TGCGCGCAAC
45988218 AAACACAACCCTCTTTGAAGTGCATTTTTTTTATAAAAGTTTTATTATTTTTCAAGAAAAAAATA
1 AAACACAACCCTCTTTGAAGTGCATTTTTTTTATAAAAGTTTTATTATTTTTCAAG-AAAAAATA
* *
45988283 AAATCTTTAAACTATTTATTTTTTCAGTTTTACTGTTCCAAAAAATCTGGAATTGGAATATTTTT
65 AAAT-TTTAAACTATTTATTTTTCCAGTTTTACTGTTCCGAAAAATCTGGAATTGGAATA--TTT
* **
45988348 TTTGGCTATTGGGGCAGAAATAGTGGGGCAATTTTTTGTG-TTTTTTACTTCTTTGCCCCTACTT
127 TTTGGCTGTT-GGGCAGAAATAGTGGGGCAA-TTTCAGTGCTTTTTTACTTCTTTGCCCCTACTT
* *
45988412 ATTTATCATTTTGCCCTTCTATTACTAGTATAAATAGA-TAGTTGATTTCTTCATTCTTTTCACA
190 ATTTACCATTTTTCCCTTCTATTACTAGTATAAATAGAGT-GTTGATTTCTTCATTCTTTTCACA
45988476 CTGAACA-
254 CTGAACAG
* *
45988483 AAGACACAACTCTTTTTGAAGTGCA-TTTTTTTATAAAAGTTTTATTATTTTTCAAGAAAGAAAT
1 AA-ACACAACCCTCTTTGAAGTGCATTTTTTTTATAAAAGTTTTATTATTTTTCAAGAAA-AAAT
* * *
45988547 AAAATGTTTAAATTATTTATTTTTCCAGTTTTACTGTTTCGAAAAATCTGGAACTGGAATATTTT
64 AAAAT-TTTAAACTATTTATTTTTCCAGTTTTACTGTTCCGAAAAATCTGGAATTGGAATATTTT
45988612 TTGGCTGTTGGAGCAGAAATAGTGGGGCAATTTCAGTGCATTTTTTACTTCTTTGCCCCTACTTA
128 TTGGCTGTTGG-GCAGAAATAGTGGGGCAATTTCAGTGC-TTTTTTACTTCTTTGCCCCTACTTA
45988677 TTTACCATTTTTCCCTTCTATTACTAGTATAAGATAGAGTGTTGATTTCTTCATTCTTTTCACAC
191 TTTACCATTTTTCCCTTCTATTACTAGTATAA-ATAGAGTGTTGATTTCTTCATTCTTTTCACAC
45988742 TGAACAG
255 TGAACAG
*
45988749 AAACACAACCCTCTCTGAAGTGCATATTTTTTTTATAAAA-TTTTAATTATTTTTCAA-AAAAAA
1 AAACACAACCCTCTTTGAAGTGC--ATTTTTTTTATAAAAGTTTT-ATTATTTTTCAAGAAAAAA
* * *
45988812 TAAAAATTTTAAACTATTTATTTTTCTAGTTTTACTGTTCCGAAAAATCTGAAATTGGAATTTTT
63 T-AAAATTTTAAACTATTTATTTTTCCAGTTTTACTGTTCCGAAAAATCTGGAATTGGAATATTT
* * ** * *
45988877 TTTTGTTGTTGGGCAGAAATAGTAAGGCAATTTCAGTGCGTTTTTCACTTCTTTTCCCCTACTTA
127 TTTGGCTGTTGGGCAGAAATAGTGGGGCAATTTCAGTGC-TTTTTTACTTCTTTGCCCCTACTTA
* * *
45988942 TTTACCGTTTTGT-CCTTCTGTTACTAGTATAAATAGAGGGTTGATTTCTTCATTCTTTTCACAC
191 TTTACCATTTT-TCCCTTCTATTACTAGTATAAATAGAGTGTTGATTTCTTCATTCTTTTCACAC
*
45989006 TGAATAG
255 TGAACAG
* * *
45989013 AAATACAACCTTCTCTGAA
1 AAACACAACCCTCTTTGAA
45989032 AATATTTTTC
Statistics
Matches: 500, Mismatches: 35, Indels: 29
0.89 0.06 0.05
Matches are distributed among these distances:
262 8 0.02
263 30 0.06
264 112 0.22
265 222 0.44
266 90 0.18
267 13 0.03
268 25 0.05
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.43
Consensus pattern (261 bp):
AAACACAACCCTCTTTGAAGTGCATTTTTTTTATAAAAGTTTTATTATTTTTCAAGAAAAAATAA
AATTTTAAACTATTTATTTTTCCAGTTTTACTGTTCCGAAAAATCTGGAATTGGAATATTTTTTG
GCTGTTGGGCAGAAATAGTGGGGCAATTTCAGTGCTTTTTTACTTCTTTGCCCCTACTTATTTAC
CATTTTTCCCTTCTATTACTAGTATAAATAGAGTGTTGATTTCTTCATTCTTTTCACACTGAACA
G
Found at i:45990348 original size:17 final size:19
Alignment explanation
Indices: 45990326--45990369 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
45990316 AATTATTAAA
45990326 ATATTTA-AAAT-AAAATC
1 ATATTTATAAATAAAAATC
* *
45990343 ATATTTATATATAAAAATT
1 ATATTTATAAATAAAAATC
45990362 ATATTTAT
1 ATATTTAT
45990370 GTTATTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 7 0.30
18 3 0.13
19 13 0.57
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (19 bp):
ATATTTATAAATAAAAATC
Found at i:45993157 original size:20 final size:20
Alignment explanation
Indices: 45993132--45993175 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
45993122 AAATAATATG
*
45993132 AAAAAA-AAGAAAAAACCTTT
1 AAAAAACAA-AAAAAACATTT
*
45993152 AAAAAACAAATAAAACATTT
1 AAAAAACAAAAAAAACATTT
45993172 AAAA
1 AAAA
45993176 TAAATAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAACAAAAAAAACATTT
Found at i:45995345 original size:44 final size:45
Alignment explanation
Indices: 45995242--45995356 Score: 153
Period size: 44 Copynumber: 2.6 Consensus size: 45
45995232 TTAATTCGCT
* * * *
45995242 CCACTGCAACTTCAGAGAGATAGGA-TTAGTAGCTTCAATCTGCT
1 CCACTGCAACTTCAGGGAGATAAGACTTAGTAGCCTCAATCTGCC
*
45995286 CCACTGCAACTTCAGGGAGATAAGACTT-GTATCCTCAATCTGCC
1 CCACTGCAACTTCAGGGAGATAAGACTTAGTAGCCTCAATCTGCC
* *
45995330 CCACTGCAACTTCAGGGGGATCAGACT
1 CCACTGCAACTTCAGGGAGATAAGACT
45995357 GGTGGCTTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
44 61 0.97
45 2 0.03
ACGTcount: A:0.28, C:0.27, G:0.21, T:0.24
Consensus pattern (45 bp):
CCACTGCAACTTCAGGGAGATAAGACTTAGTAGCCTCAATCTGCC
Found at i:45995686 original size:45 final size:45
Alignment explanation
Indices: 45995626--45996049 Score: 455
Period size: 45 Copynumber: 9.4 Consensus size: 45
45995616 ACCAGCTTTT
* * * * *
45995626 GATCTGCTTCACTGCCAGTACAAGAAGACAAGATTTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
*
45995671 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCT-ATAATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCT-ATCTTC
* * * *** * *
45995716 GACCTACTCCACTGCTGCT-CAGGGAGACAAGATCTGCTATCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * *
45995760 GATATACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* *
45995805 GACCTACTTCGCTGCCAATACAAGAAGACAAGATCTGCTATCTTC
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
** * *
45995850 -AGTCTACTTCGCTATCAATACAGGAAGACAAGACCTGTTATCTTC
1 GA-TCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * * * *
45995895 GATCTACTTCGCTACCAATATAGGAAGATAAGATCTGTTATCTTT
1 GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* * * *
45995940 GA-CTTACTTTGCTGCTAATACAGGAAGATAAGATCTACTATCTTC
1 GATC-TACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
* *
45995985 -AGTCTACTTCGCTGTCAATACAGGAAGACAAGA-CTTACTATCTTC
1 GA-TCTACTTCGCTGCCAATACAGGAAGACAAGATC-TGCTATCTTC
45996030 GATCTACTTCGCTGCCAATA
1 GATCTACTTCGCTGCCAATA
45996050 TAGAAAGATA
Statistics
Matches: 317, Mismatches: 52, Indels: 20
0.81 0.13 0.05
Matches are distributed among these distances:
44 37 0.12
45 277 0.87
46 3 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (45 bp):
GATCTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTC
Found at i:45995937 original size:135 final size:134
Alignment explanation
Indices: 45995626--45996057 Score: 512
Period size: 135 Copynumber: 3.2 Consensus size: 134
45995616 ACCAGCTTTT
* * * * * * * *
45995626 GATCTGCTTCACTGCCAGTACAAGAAGACAAGATTTGCTATCTTCGATCTACTTCGCTGCCAATA
1 GATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTTGACCTACTTCGCTGCCAATA
* * * * * * *
45995691 CAGGAAGACAAGATCTATAATCTTC-GACCTACTCCACTGCTGC--T-CAGGGAGACAAGATCTG
66 CAGGAAGACAAGATCTCT-ATCTTCAG-TCTACTTCGCT-AT-CAATACAGGAAGACAAGACCTG
*
45995752 CTATCTTT
127 CTATCTTC
*
45995760 GATATACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTTGACCTACTTCGCTGCCAATA
1 GATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTTGACCTACTTCGCTGCCAATA
* *
45995825 CAAGAAGACAAGATCTGCTATCTTCAGTCTACTTCGCTATCAATACAGGAAGACAAGACCTGTTA
66 CAGGAAGACAAGATCT-CTATCTTCAGTCTACTTCGCTATCAATACAGGAAGACAAGACCTGCTA
45995890 TCTTC
130 TCTTC
* * * * * *
45995895 GATCTACTTCGCTACCAATATAGGAAGATAAGATCTGTTATCTTTGACTTACTTTGCTGCTAATA
1 GATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTTGACCTACTTCGCTGCCAATA
* * * *
45995960 CAGGAAGATAAGATCTACTATCTTCAGTCTACTTCGCTGTCAATACAGGAAGACAAGACTTACTA
66 CAGGAAGACAAGATCT-CTATCTTCAGTCTACTTCGCTATCAATACAGGAAGACAAGACCTGCTA
45996025 TCTTC
130 TCTTC
*
45996030 GATCTACTTCGCTGCCAATATAGAAAGA
1 GATCTACTTCGCTGCCAATATAGGAAGA
45996058 TAATGCTATT
Statistics
Matches: 258, Mismatches: 35, Indels: 9
0.85 0.12 0.03
Matches are distributed among these distances:
132 1 0.00
133 1 0.00
134 86 0.33
135 170 0.66
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.29
Consensus pattern (134 bp):
GATCTACTTCGCTGCCAATATAGGAAGACAAGATCTGCTATCTTTGACCTACTTCGCTGCCAATA
CAGGAAGACAAGATCTCTATCTTCAGTCTACTTCGCTATCAATACAGGAAGACAAGACCTGCTAT
CTTC
Found at i:45999796 original size:18 final size:18
Alignment explanation
Indices: 45999775--45999810 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
45999765 TCTGTTATTT
45999775 TATTT-TTTTGTATATATG
1 TATTTGTTTT-TATATATG
45999793 TATTTGTTTTTATATATG
1 TATTTGTTTTTATATATG
45999811 ATTAACTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.76
19 4 0.24
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (18 bp):
TATTTGTTTTTATATATG
Found at i:46013865 original size:14 final size:14
Alignment explanation
Indices: 46013848--46013892 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
46013838 AAATATGTAT
*
46013848 ATACATATATTTAA
1 ATACATATATATAA
*
46013862 ATACGTATATATAA
1 ATACATATATATAA
46013876 GTATACATATATATAA
1 --ATACATATATATAA
46013892 A
1 A
46013893 AAATGAATGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
14 13 0.50
16 13 0.50
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (14 bp):
ATACATATATATAA
Found at i:46015898 original size:129 final size:130
Alignment explanation
Indices: 46015612--46015901 Score: 343
Period size: 130 Copynumber: 2.2 Consensus size: 130
46015602 TTATCTCTAG
* ** *
46015612 TCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGATGCAGTCTGCTCTACTGCAACTTCAGAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCGGATGCAGTCTACTCTACTGCAACTTCAGAGA
** * * * * * * **
46015677 GATAAGATCTGTGATTTTTAATCCACTCCACTGCAACCTCAAGGAGATAGGATTGGTTTCTTCTG
66 GATAAGATCCATCATTTTTAATCCACTCCACTACAACCTCAAGGAGATAGAATTGATTGCCTCAA
* *
46015742 TCTGCTCCACTGCAACTTCAGGGAGATAGGACCGGATGC-GATCTACTCTACTGCACCTTCAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCGGATGCAG-TCTACTCTACTGCAACTTCAGAG
* * *
46015806 AGATAAGATCCATCA-TTTTAATCCGCTCCACTACAACTTCAGGGAGATAGAATT-ATTGGCCTC
65 AGATAAGATCCATCATTTTTAATCCACTCCACTACAACCTCAAGGAGATAGAATTGATT-GCCTC
46015869 AA
129 AA
* * *
46015871 TCTGCTCCGCTGCATCTCCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
46015902 TTCATCGTCG
Statistics
Matches: 135, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
128 2 0.01
129 65 0.48
130 68 0.50
ACGTcount: A:0.27, C:0.25, G:0.21, T:0.28
Consensus pattern (130 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACCGGATGCAGTCTACTCTACTGCAACTTCAGAGA
GATAAGATCCATCATTTTTAATCCACTCCACTACAACCTCAAGGAGATAGAATTGATTGCCTCAA
Found at i:46016017 original size:99 final size:99
Alignment explanation
Indices: 46015906--46016086 Score: 267
Period size: 99 Copynumber: 1.8 Consensus size: 99
46015896 ATAAGATTCA
46015906 TCGTCGTAGCTTCAATCTGCTCCACTACACCGCCAAGA-AAGTAAGATT-AGCCATTGTGGATTC
1 TCGTCGTAGCTTCAATCTGCTCCACTACACCG-CAAGAGAAGTAAGATTCA-CCATTGTGGATTC
*
46015969 AATCTTTTCAATTGCAATGTCGGGAAACAAGATCCG
64 AATCTATTCAATTGCAATGTCGGGAAACAAGATCCG
* * * *
46016005 TCGTCGTGGCTTCAATCTGTTCCACTACACCGCTAGAGAAGTAAGATTCACCATTGTGGCTTCAA
1 TCGTCGTAGCTTCAATCTGCTCCACTACACCGCAAGAGAAGTAAGATTCACCATTGTGGATTCAA
* *
46016070 TCTATTCCATTGTAATG
66 TCTATTCAATTGCAATG
46016087 CCAAAGAGAT
Statistics
Matches: 73, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
98 4 0.05
99 68 0.93
100 1 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (99 bp):
TCGTCGTAGCTTCAATCTGCTCCACTACACCGCAAGAGAAGTAAGATTCACCATTGTGGATTCAA
TCTATTCAATTGCAATGTCGGGAAACAAGATCCG
Found at i:46021438 original size:37 final size:37
Alignment explanation
Indices: 46021388--46021462 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
46021378 CACTATCTTG
46021388 CACGGAGGTGAAAACCTCACTAAGGACTAGTTTCTCA
1 CACGGAGGTGAAAACCTCACTAAGGACTAGTTTCTCA
46021425 CACGGAGGTGAAAACCTCACTAAGGACTAGTTTCTCA
1 CACGGAGGTGAAAACCTCACTAAGGACTAGTTTCTCA
46021462 C
1 C
46021463 TCTCACTTAG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (37 bp):
CACGGAGGTGAAAACCTCACTAAGGACTAGTTTCTCA
Found at i:46022915 original size:9 final size:9
Alignment explanation
Indices: 46022901--46022925 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
46022891 TATAGAAATA
46022901 ATAATAATG
1 ATAATAATG
46022910 ATAATAATG
1 ATAATAATG
46022919 ATAATAA
1 ATAATAA
46022926 CATTAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.00, G:0.08, T:0.32
Consensus pattern (9 bp):
ATAATAATG
Found at i:46024665 original size:32 final size:32
Alignment explanation
Indices: 46024629--46024692 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
46024619 GCAGTCATAA
*
46024629 TTCCAAGGAACCCTTTTGCTATCCTTGTAGGG
1 TTCCAAGGAACCCTTTTGCTATCCTTGCAGGG
46024661 TTCCAAGGAACCCTTTTGCTATCCTTGCAGGG
1 TTCCAAGGAACCCTTTTGCTATCCTTGCAGGG
46024693 AAAGGATACA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.19, C:0.27, G:0.22, T:0.33
Consensus pattern (32 bp):
TTCCAAGGAACCCTTTTGCTATCCTTGCAGGG
Found at i:46030675 original size:20 final size:20
Alignment explanation
Indices: 46030650--46030693 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
46030640 AAATAATATG
*
46030650 AAAAAA-AAGAAAAAACCTTT
1 AAAAAACAA-AAAAAACATTT
*
46030670 AAAAAACAAATAAAACATTT
1 AAAAAACAAAAAAAACATTT
46030690 AAAA
1 AAAA
46030694 TAAATAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.73, C:0.09, G:0.02, T:0.16
Consensus pattern (20 bp):
AAAAAACAAAAAAAACATTT
Found at i:46031872 original size:6 final size:6
Alignment explanation
Indices: 46031863--46031900 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
46031853 ATTTTCATTT
46031863 ATAAAA ATAAAA A-ACAATA ATAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA ATA-AA-A ATAAAA ATAAAA ATAAAA A
46031901 AATAGAAAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
5 1 0.03
6 23 0.79
7 4 0.14
8 1 0.03
ACGTcount: A:0.82, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:46033021 original size:31 final size:31
Alignment explanation
Indices: 46032959--46033021 Score: 74
Period size: 31 Copynumber: 2.0 Consensus size: 31
46032949 TAAAATTTAA
*
46032959 TAAATGAAAAATATACAAAAATTTTAAATAT
1 TAAATGAAAAATATACAAAAATTATAAATAT
* * *
46032990 TAAATTAAAAATA-ACATAAATATATATATAT
1 TAAATGAAAAATATACAAAAAT-TATAAATAT
46033021 T
1 T
46033022 TTTTAAATAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 7 0.26
31 20 0.74
ACGTcount: A:0.60, C:0.03, G:0.02, T:0.35
Consensus pattern (31 bp):
TAAATGAAAAATATACAAAAATTATAAATAT
Found at i:46035080 original size:8 final size:8
Alignment explanation
Indices: 46035067--46035092 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
46035057 CACGTTTGCA
46035067 GAATTCTT
1 GAATTCTT
46035075 GAATTCTT
1 GAATTCTT
46035083 GAATTCTT
1 GAATTCTT
46035091 GA
1 GA
46035093 GACCAAGTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (8 bp):
GAATTCTT
Found at i:46038047 original size:14 final size:14
Alignment explanation
Indices: 46038030--46038067 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
46038020 ATTTATATAT
46038030 AAATATAAATTTTA
1 AAATATAAATTTTA
46038044 AAATTATAAATTTTA
1 AAA-TATAAATTTTA
*
46038059 AAAAATAAA
1 AAATATAAA
46038068 AAAATAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATATAAATTTTA
Found at i:46042366 original size:6 final size:6
Alignment explanation
Indices: 46042349--46042378 Score: 51
Period size: 6 Copynumber: 4.8 Consensus size: 6
46042339 CAAGGTTCGG
46042349 GATTTAA GATTTA GATTTA GATTTA GATTT
1 GATTT-A GATTTA GATTTA GATTTA GATTT
46042379 GAGGTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 18 0.78
7 5 0.22
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (6 bp):
GATTTA
Found at i:46043536 original size:28 final size:28
Alignment explanation
Indices: 46043492--46043552 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
46043482 AGTAGAAAAG
46043492 AAAAAGAAACAATAGAAAA-AAAAGGTGAA
1 AAAAAGAAACAATAGAAAATAAAA--TGAA
*
46043521 AAAAAGAAAGAA-AGAAAATAAAATGAA
1 AAAAAGAAACAATAGAAAATAAAATGAA
46043548 AAAAA
1 AAAAA
46043553 TATGGGTGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 9 0.30
28 6 0.20
29 15 0.50
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.07
Consensus pattern (28 bp):
AAAAAGAAACAATAGAAAATAAAATGAA
Found at i:46044118 original size:19 final size:21
Alignment explanation
Indices: 46044082--46044120 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
46044072 AGATAATAAT
46044082 ATTTATTATTTTTGTAAAATA
1 ATTTATTATTTTTGTAAAATA
46044103 ATTT-TTATTTTT-TAAAAT
1 ATTTATTATTTTTGTAAAAT
46044121 GACATTGACG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.33
20 8 0.44
21 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
ATTTATTATTTTTGTAAAATA
Found at i:46046111 original size:21 final size:21
Alignment explanation
Indices: 46046085--46046126 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
46046075 ACGAGATAGG
*
46046085 TGACGTGACCCGTTAACTAGC
1 TGACGTGACCAGTTAACTAGC
*
46046106 TGACGTGGCCAGTTAACTAGC
1 TGACGTGACCAGTTAACTAGC
46046127 CACAGTGGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (21 bp):
TGACGTGACCAGTTAACTAGC
Found at i:46047900 original size:22 final size:23
Alignment explanation
Indices: 46047872--46047915 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
46047862 CCTATGTGTC
*
46047872 ATAC-TTTTTAATTCCCTCTTTA
1 ATACTTTTTTAATTCCCGCTTTA
46047894 ATACTTTTTTAATTCCCGCTTT
1 ATACTTTTTTAATTCCCGCTTT
46047916 CCCTTTGCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.20, C:0.23, G:0.02, T:0.55
Consensus pattern (23 bp):
ATACTTTTTTAATTCCCGCTTTA
Found at i:46050495 original size:20 final size:20
Alignment explanation
Indices: 46050470--46050509 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
46050460 CGGAAAATAA
*
46050470 TTTTTGGAGAATAATTTACT
1 TTTTTGGAAAATAATTTACT
*
46050490 TTTTTGGAAAATGATTTACT
1 TTTTTGGAAAATAATTTACT
46050510 GAAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.15, T:0.50
Consensus pattern (20 bp):
TTTTTGGAAAATAATTTACT
Found at i:46051923 original size:32 final size:32
Alignment explanation
Indices: 46051872--46051932 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
46051862 TGTCAATCAT
*
46051872 TTCAATATCCAACAGGCTTAAAACATAATTAA
1 TTCAATATCCAACAAGCTTAAAACATAATTAA
*
46051904 TTCAATATCTAACAAGCTTAAAACATAAT
1 TTCAATATCCAACAAGCTTAAAACATAAT
46051933 CAATATCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.48, C:0.18, G:0.05, T:0.30
Consensus pattern (32 bp):
TTCAATATCCAACAAGCTTAAAACATAATTAA
Found at i:46051940 original size:27 final size:30
Alignment explanation
Indices: 46051872--46051945 Score: 91
Period size: 32 Copynumber: 2.5 Consensus size: 30
46051862 TGTCAATCAT
* *
46051872 TTCAATATCCAACAGGCTTAAAACATAATTAA
1 TTCAATATCTAACAAGCTTAAAAC--AATTAA
46051904 TTCAATATCTAACAAGCTTAAAAC-A-TAA
1 TTCAATATCTAACAAGCTTAAAACAATTAA
46051932 -TCAATATCTAACAA
1 TTCAATATCTAACAA
46051946 ATTCAAGACA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.35
28 3 0.08
29 1 0.03
32 22 0.55
ACGTcount: A:0.49, C:0.19, G:0.04, T:0.28
Consensus pattern (30 bp):
TTCAATATCTAACAAGCTTAAAACAATTAA
Found at i:46051956 original size:27 final size:27
Alignment explanation
Indices: 46051905--46051958 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
46051895 CATAATTAAT
*
46051905 TCAATATCTAACAAGCTTAAAACATAA
1 TCAATATCTAACAAGATTAAAACATAA
*
46051932 TCAATATCTAACAA-ATTCAAGACATAA
1 TCAATATCTAACAAGATT-AAAACATAA
46051959 AAATTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 2 0.08
27 22 0.92
ACGTcount: A:0.52, C:0.19, G:0.04, T:0.26
Consensus pattern (27 bp):
TCAATATCTAACAAGATTAAAACATAA
Found at i:46056993 original size:30 final size:30
Alignment explanation
Indices: 46056959--46057197 Score: 211
Period size: 30 Copynumber: 8.0 Consensus size: 30
46056949 ATTTTACATG
* *
46056959 TTATTTTATTGTCAGCTTGTGTGAGCAATC
1 TTATTATAATGTCAGCTTGTGTGAGCAATC
*
46056989 TTATTATAATGTCAGCTTGTGTGAACAATAC
1 TTATTATAATGTCAGCTTGTGTGAGCAAT-C
* * *
46057020 -TATTATAATGTCAACTTGTGTGAGTAAAGC
1 TTATTATAATGTCAGCTTGTGTGAG-CAATC
* * *
46057050 -TATTATAATATTAGCTTGTATGAGCAAT-
1 TTATTATAATGTCAGCTTGTGTGAGCAATC
* *
46057078 TCTATCATAATGTCAGCTTGTGTGAGTAAT-
1 T-TATTATAATGTCAGCTTGTGTGAGCAATC
* * *
46057108 TCCATCATAATGTCAGCTTGTGTAAGC-AT-
1 T-TATTATAATGTCAGCTTGTGTGAGCAATC
* * *
46057137 TTCCATCATAATGTCAGCTTGTGTGAGAAACC
1 TT--ATTATAATGTCAGCTTGTGTGAGCAATC
* *
46057169 TTATTATAATGTCAACTTGTCTGAGCAAT
1 TTATTATAATGTCAGCTTGTGTGAGCAAT
46057198 GTATTCACTT
Statistics
Matches: 171, Mismatches: 30, Indels: 16
0.79 0.14 0.07
Matches are distributed among these distances:
29 5 0.03
30 160 0.94
31 4 0.02
32 2 0.01
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (30 bp):
TTATTATAATGTCAGCTTGTGTGAGCAATC
Found at i:46057042 original size:60 final size:60
Alignment explanation
Indices: 46056968--46057197 Score: 250
Period size: 60 Copynumber: 3.8 Consensus size: 60
46056958 GTTATTTTAT
* * *
46056968 TGTCAGCTTGTGTGAGCAATCTTATTATAATGTCAGCTTGTGTGAACAATACTATTATAA
1 TGTCAGCTTGTGTGAGAAATCTTATTATAATGTCAGCTTGTGTGAACAATTCTATCATAA
* * * * * *
46057028 TGTCAACTTGTGTGAGTAAAGC-TATTATAATATTAGCTTGTATGAGCAATTCTATCATAA
1 TGTCAGCTTGTGTGAG-AAATCTTATTATAATGTCAGCTTGTGTGAACAATTCTATCATAA
* * * * *
46057088 TGTCAGCTTGTGTGAGTAAT-TCCATCATAATGTCAGCTTGTGT-AAGCATTTCCATCATAA
1 TGTCAGCTTGTGTGAGAAATCT-TATTATAATGTCAGCTTGTGTGAA-CAATTCTATCATAA
* * * *
46057148 TGTCAGCTTGTGTGAGAAACCTTATTATAATGTCAACTTGTCTGAGCAAT
1 TGTCAGCTTGTGTGAGAAATCTTATTATAATGTCAGCTTGTGTGAACAAT
46057198 GTATTCACTT
Statistics
Matches: 136, Mismatches: 28, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
59 3 0.02
60 128 0.94
61 5 0.04
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (60 bp):
TGTCAGCTTGTGTGAGAAATCTTATTATAATGTCAGCTTGTGTGAACAATTCTATCATAA
Found at i:46057148 original size:90 final size:90
Alignment explanation
Indices: 46056970--46057197 Score: 233
Period size: 90 Copynumber: 2.5 Consensus size: 90
46056960 TATTTTATTG
* * *
46056970 TCAGCTTGTGTGAGCAATCTTATTATAATGTCAGCTTGTGTGAACAATACTATTATAATGTCAAC
1 TCAGCTTGTGTGAGCAATCTTATCATAATGTCAGCTTGTGTGAACAATACCATCATAATGTCAAC
* * * *
46057035 TTGTGTGAGTAAAGCTATTATAATA
66 TTGTGTAAGCAAAGCCATCATAATA
* * ** * *
46057060 TTAGCTTGTATGAGCAAT-TCTATCATAATGTCAGCTTGTGTGAGTAATTCCATCATAATGTCAG
1 TCAGCTTGTGTGAGCAATCT-TATCATAATGTCAGCTTGTGTGAACAATACCATCATAATGTCAA
*** *
46057124 CTTGTGTAAGCATTTCCATCATAATG
65 CTTGTGTAAGCAAAGCCATCATAATA
* * * * * *
46057150 TCAGCTTGTGTGAGAAACCTTATTATAATGTCAACTTGTCTGAGCAAT
1 TCAGCTTGTGTGAGCAATCTTATCATAATGTCAGCTTGTGTGAACAAT
46057198 GTATTCACTT
Statistics
Matches: 111, Mismatches: 25, Indels: 4
0.79 0.18 0.03
Matches are distributed among these distances:
89 1 0.01
90 109 0.98
91 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.18, T:0.37
Consensus pattern (90 bp):
TCAGCTTGTGTGAGCAATCTTATCATAATGTCAGCTTGTGTGAACAATACCATCATAATGTCAAC
TTGTGTAAGCAAAGCCATCATAATA
Found at i:46058021 original size:19 final size:20
Alignment explanation
Indices: 46057987--46058027 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
46057977 TTTAAAGCTT
46057987 AATTAACTAATGTTTAATTA
1 AATTAACTAATGTTTAATTA
*
46058007 AATTAATTAAT-TTTAATTA
1 AATTAACTAATGTTTAATTA
46058026 AA
1 AA
46058028 GTGAAACATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
AATTAACTAATGTTTAATTA
Found at i:46058618 original size:71 final size:70
Alignment explanation
Indices: 46058538--46058685 Score: 244
Period size: 71 Copynumber: 2.1 Consensus size: 70
46058528 GGAAGGGATA
* * *
46058538 AATTGAATTGAATTATTATATAAATCTTAAATTGGACCAAATCAGAAATAATCAGGGAAAATAAA
1 AATTGAATTGAATTATTATATAAATCATAAATTGGACCAAATAAAAAATAATCAGGGAAAATAAA
46058603 AAATT
66 AAATT
*
46058608 GAATTGAATTGAATTATTATATAGATCATAAATTGGACCAAATAAAAAATAATCAGGGAAAATAA
1 -AATTGAATTGAATTATTATATAAATCATAAATTGGACCAAATAAAAAATAATCAGGGAAAATAA
46058673 AAAATT
65 AAAATT
46058679 -ATTGAAT
1 AATTGAAT
46058686 AGCCCCTGAA
Statistics
Matches: 73, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
69 7 0.10
71 66 0.90
ACGTcount: A:0.52, C:0.06, G:0.12, T:0.30
Consensus pattern (70 bp):
AATTGAATTGAATTATTATATAAATCATAAATTGGACCAAATAAAAAATAATCAGGGAAAATAAA
AAATT
Found at i:46061009 original size:22 final size:21
Alignment explanation
Indices: 46060981--46061056 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 21
46060971 AGGGGAGCCA
46060981 TGTCTCGAGATAATTATGTATT
1 TGTCTCGAGA-AATTATGTATT
** *
46061003 TGTCTCGAGAAAACAGTGTATG
1 TGTCTCGAGAAATTA-TGTATT
* *
46061025 TGTCTCAAGAAAATTGTGTATT
1 TGTCTCGAG-AAATTATGTATT
* *
46061047 TTTCTTGAGA
1 TGTCTCGAGA
46061057 CATATACCTT
Statistics
Matches: 41, Mismatches: 11, Indels: 5
0.72 0.19 0.09
Matches are distributed among these distances:
21 4 0.10
22 34 0.83
23 3 0.07
ACGTcount: A:0.29, C:0.11, G:0.21, T:0.39
Consensus pattern (21 bp):
TGTCTCGAGAAATTATGTATT
Found at i:46062977 original size:15 final size:15
Alignment explanation
Indices: 46062957--46062987 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
46062947 TAACTTGTGA
46062957 AACTATTAAAAGTTT
1 AACTATTAAAAGTTT
46062972 AACTATTAAAAGTTT
1 AACTATTAAAAGTTT
46062987 A
1 A
46062988 GGGACATACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (15 bp):
AACTATTAAAAGTTT
Found at i:46073954 original size:15 final size:15
Alignment explanation
Indices: 46073934--46073965 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
46073924 TCCCTTAAAG
*
46073934 TTAACTCGATTTCAA
1 TTAACTCAATTTCAA
46073949 TTAACTCAATTTCAA
1 TTAACTCAATTTCAA
46073964 TT
1 TT
46073966 CAAAAAGCGC
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:0.34, C:0.19, G:0.03, T:0.44
Consensus pattern (15 bp):
TTAACTCAATTTCAA
Found at i:46074397 original size:16 final size:17
Alignment explanation
Indices: 46074371--46074407 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
46074361 TTATTTCCCA
46074371 ATTTAATTTAATTTTTG
1 ATTTAATTTAATTTTTG
*
46074388 ATTT-ATTTAATTTTTT
1 ATTTAATTTAATTTTTG
46074404 ATTT
1 ATTT
46074408 CTGCTATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 15 0.79
17 4 0.21
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
ATTTAATTTAATTTTTG
Found at i:46077710 original size:126 final size:126
Alignment explanation
Indices: 46077573--46077950 Score: 533
Period size: 126 Copynumber: 3.0 Consensus size: 126
46077563 AGTAGTTTTA
* * * *
46077573 GAAAAATTAATTTTGAGAAGATGATTTTGAAAAGATAATGTCAAAAACGCTTCAAGCAGAATGCA
1 GAAAAAATAATTTTGAGAAGATGATTTTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCA
* * *
46077638 CTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGTTATTTTTCTATAATAGTTCCT
66 CTGTTAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAATAGTTCCT
* *
46077699 GAAAAAATAATTCTGAGAAGATGATTTTGAAAAAATAGTGTCAAAAACGCTTCAAACAGGATGCA
1 GAAAAAATAATTTTGAGAAGATGATTTTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCA
* * * ** *
46077764 CTGTTAACAAAATTACTAAAAAAAGCTCCCACGTGGACGCTCTTTTACTACGATAGTTCTT
66 CTGTTAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAATAGTTCCT
* * *
46077825 G-AAAAATAATTTTGGGAAGATGGTTTTGAAAAAATAGTGTAAAAAACGCTTCAAGCAGGATGCA
1 GAAAAAATAATTTTGAGAAGATGATTTTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCA
* * * * * *
46077889 CTATTAGCAAAATTACTGAAAAGAGCTCCTACGTGAACACTCTTTTTCTATAGTAGTTCCT
66 CTGTTAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAATAGTTCCT
46077950 G
1 G
46077951 CTTGGCCTTA
Statistics
Matches: 220, Mismatches: 32, Indels: 1
0.87 0.13 0.00
Matches are distributed among these distances:
125 108 0.49
126 112 0.51
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (126 bp):
GAAAAAATAATTTTGAGAAGATGATTTTGAAAAAATAGTGTCAAAAACGCTTCAAGCAGGATGCA
CTGTTAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAATAGTTCCT
Found at i:46081500 original size:18 final size:18
Alignment explanation
Indices: 46081474--46081516 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
46081464 GACTGGAAAA
* *
46081474 AGGAAACATATAAGGGTT
1 AGGATACATATAAGGGCT
46081492 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
46081510 AGGATAC
1 AGGATAC
46081517 GCAGCTGACA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.42, C:0.09, G:0.28, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:46083284 original size:32 final size:32
Alignment explanation
Indices: 46083237--46083303 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
46083227 GGAAATAATT
46083237 AATTAAAGAGA-TTTTTGAGAAATTTT-GAGAGA
1 AATTAAAGAGATTTTTTGAG-AATTTTGGA-AGA
* *
46083269 AATTTAAGAGCTTTTTTGAGAATTTTGGAAGA
1 AATTAAAGAGATTTTTTGAGAATTTTGGAAGA
46083301 AAT
1 AAT
46083304 GTTTGTGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
32 21 0.68
33 10 0.32
ACGTcount: A:0.40, C:0.01, G:0.21, T:0.37
Consensus pattern (32 bp):
AATTAAAGAGATTTTTTGAGAATTTTGGAAGA
Found at i:46086069 original size:16 final size:16
Alignment explanation
Indices: 46086050--46086081 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
46086040 TTTTGATTTG
46086050 GAGCAATTATACAACT
1 GAGCAATTATACAACT
46086066 GAGCAATTATACAACT
1 GAGCAATTATACAACT
46086082 TTTGTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.19, G:0.12, T:0.25
Consensus pattern (16 bp):
GAGCAATTATACAACT
Found at i:46087986 original size:70 final size:70
Alignment explanation
Indices: 46087911--46088049 Score: 269
Period size: 70 Copynumber: 2.0 Consensus size: 70
46087901 CAGTAAGTTT
*
46087911 GGACACGATTCTTTTTTAATTCCCGATATCGTTTAAAACTTGAGTTTGAAAAGATTCGTGTAATA
1 GGACACGATCCTTTTTTAATTCCCGATATCGTTTAAAACTTGAGTTTGAAAAGATTCGTGTAATA
46087976 AAGTA
66 AAGTA
46087981 GGACACGATCCTTTTTTAATTCCCGATATCGTTTAAAACTTGAGTTTGAAAAGATTCGTGTAATA
1 GGACACGATCCTTTTTTAATTCCCGATATCGTTTAAAACTTGAGTTTGAAAAGATTCGTGTAATA
46088046 AAGT
66 AAGT
46088050 TTAAGAGAAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
70 68 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (70 bp):
GGACACGATCCTTTTTTAATTCCCGATATCGTTTAAAACTTGAGTTTGAAAAGATTCGTGTAATA
AAGTA
Found at i:46089917 original size:20 final size:20
Alignment explanation
Indices: 46089876--46089931 Score: 53
Period size: 20 Copynumber: 2.8 Consensus size: 20
46089866 ATGTAAAAGG
*
46089876 AAAAATGAAATAAAATAGAA
1 AAAAATGAAATAAAATACAA
*
46089896 AAAAATGAAA-AAAGATTCAA
1 AAAAATGAAATAAA-ATACAA
*
46089916 AACAA-GAAAATAAAAT
1 AAAAATG-AAATAAAAT
46089932 CCTCTCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
19 4 0.13
20 23 0.77
21 3 0.10
ACGTcount: A:0.73, C:0.04, G:0.09, T:0.14
Consensus pattern (20 bp):
AAAAATGAAATAAAATACAA
Found at i:46090582 original size:22 final size:22
Alignment explanation
Indices: 46090550--46090606 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 22
46090540 AGGATATCCA
* *
46090550 ATATAGTTGCAGAATAGATCGG
1 ATATAGATGCAAAATAGATCGG
**
46090572 ATATAGATGCAAAATAGATCAA
1 ATATAGATGCAAAATAGATCGG
*
46090594 ATACAGATGCAAA
1 ATATAGATGCAAA
46090607 TTCCTAACTC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (22 bp):
ATATAGATGCAAAATAGATCGG
Found at i:46090889 original size:15 final size:16
Alignment explanation
Indices: 46090853--46090882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
46090843 CAACCCAATG
46090853 CAGATA-CAGATTTAA
1 CAGATATCAGATTTAA
46090868 CAGATATCAGATTTA
1 CAGATATCAGATTTA
46090883 CATATATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.30
Consensus pattern (16 bp):
CAGATATCAGATTTAA
Found at i:46100132 original size:20 final size:22
Alignment explanation
Indices: 46100073--46100133 Score: 83
Period size: 22 Copynumber: 2.9 Consensus size: 22
46100063 AAATTAATTC
*
46100073 AATCGTAATCAACGTATAAACT
1 AATCGTAATCAACATATAAACT
46100095 AATCGTAATCAACATATAAACT
1 AATCGTAATCAACATATAAACT
46100117 AA-C-TAATC-ACATTATAA
1 AATCGTAATCAACA-TATAA
46100134 TATGCAAGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
19 3 0.08
20 10 0.27
21 1 0.03
22 23 0.62
ACGTcount: A:0.49, C:0.18, G:0.05, T:0.28
Consensus pattern (22 bp):
AATCGTAATCAACATATAAACT
Found at i:46108758 original size:213 final size:213
Alignment explanation
Indices: 46108391--46108814 Score: 839
Period size: 213 Copynumber: 2.0 Consensus size: 213
46108381 ATAAGTTCGA
*
46108391 TAAACCATATATTTATTTGAATTCTTATGCTAACCAAATTCATGTCCTCACTATACGTACAACAA
1 TAAACCATATATTTATTTGAATTCTTATGCTAACCAAATTCATGTCCTCACTATACATACAACAA
46108456 CCTTGTACATAATGTGTTGGAAATTTGATTACCGAATTAAATTAATTCTATAATTAATTTAATTC
66 CCTTGTACATAATGTGTTGGAAATTTGATTACCGAATTAAATTAATTCTATAATTAATTTAATTC
46108521 AAGCGACCCCAAAAACAATACCAACTATGGTTTATTCCGTTCATTTCAACTATAGGGTGTGACCC
131 AAGCGACCCCAAAAACAATACCAACTATGGTTTATTCCGTTCATTTCAACTATAGGGTGTGACCC
46108586 TGTAGGTTCTTGTAACGG
196 TGTAGGTTCTTGTAACGG
46108604 TAAACCATATATTTATTTGAATTCTTATGCTAACCAAATTCATGTCCTCACTATACATACAACAA
1 TAAACCATATATTTATTTGAATTCTTATGCTAACCAAATTCATGTCCTCACTATACATACAACAA
46108669 CCTTGTACATAATGTGTTGGAAATTTGATTACCGAATTAAATTAATTCTATAATTAATTTAATTC
66 CCTTGTACATAATGTGTTGGAAATTTGATTACCGAATTAAATTAATTCTATAATTAATTTAATTC
46108734 AAGCGACCCCAAAAACAATACCAACTATGGTTTATTCCGTTCATTTCAACTATAGGGTGTGACCC
131 AAGCGACCCCAAAAACAATACCAACTATGGTTTATTCCGTTCATTTCAACTATAGGGTGTGACCC
46108799 TGTAGGTTCTTGTAAC
196 TGTAGGTTCTTGTAAC
46108815 ATTAGCAGTA
Statistics
Matches: 210, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
213 210 1.00
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.35
Consensus pattern (213 bp):
TAAACCATATATTTATTTGAATTCTTATGCTAACCAAATTCATGTCCTCACTATACATACAACAA
CCTTGTACATAATGTGTTGGAAATTTGATTACCGAATTAAATTAATTCTATAATTAATTTAATTC
AAGCGACCCCAAAAACAATACCAACTATGGTTTATTCCGTTCATTTCAACTATAGGGTGTGACCC
TGTAGGTTCTTGTAACGG
Found at i:46122045 original size:12 final size:12
Alignment explanation
Indices: 46122028--46122069 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
46122018 TATTAATTAA
46122028 TCATTTCATATT
1 TCATTTCATATT
46122040 TCATTTCAT-TT
1 TCATTTCATATT
*
46122051 CTCATCTCATA-T
1 -TCATTTCATATT
46122063 TCATTTC
1 TCATTTC
46122070 TCCTCTTTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 8 0.31
12 18 0.69
ACGTcount: A:0.21, C:0.24, G:0.00, T:0.55
Consensus pattern (12 bp):
TCATTTCATATT
Found at i:46126694 original size:20 final size:20
Alignment explanation
Indices: 46126658--46126695 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46126648 TATATATAGA
*
46126658 TATGTAAACAAATTATAAAC
1 TATGTAAACAAAATATAAAC
46126678 TATGTATAA-AAAATATAA
1 TATGTA-AACAAAATATAA
46126696 GGGTGCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
TATGTAAACAAAATATAAAC
Found at i:46126776 original size:10 final size:10
Alignment explanation
Indices: 46126761--46126794 Score: 50
Period size: 10 Copynumber: 3.2 Consensus size: 10
46126751 AAAATGTATG
46126761 TATGTATATA
1 TATGTATATA
46126771 TATGTATGTATA
1 TATGTA--TATA
46126783 TATGTATATA
1 TATGTATATA
46126793 TA
1 TA
46126795 AATTACAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
10 12 0.55
12 10 0.45
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (10 bp):
TATGTATATA
Found at i:46126776 original size:14 final size:14
Alignment explanation
Indices: 46126757--46126785 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46126747 TATAAAAATG
46126757 TATGTATGTATATA
1 TATGTATGTATATA
46126771 TATGTATGTATATA
1 TATGTATGTATATA
46126785 T
1 T
46126786 GTATATATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (14 bp):
TATGTATGTATATA
Found at i:46126917 original size:3 final size:3
Alignment explanation
Indices: 46126893--46126947 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
46126883 TAAATGAGTA
* * *
46126893 AAT AAC AAT AAT GAT GAT -AT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
46126940 AAT AAT AA
1 AAT AAT AA
46126948 GATTAAAAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:46147697 original size:15 final size:15
Alignment explanation
Indices: 46147674--46147709 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
46147664 ATATATCTCC
*
46147674 AAACTATTAAACTAT
1 AAACAATTAAACTAT
46147689 AAACAATTAAACTAT
1 AAACAATTAAACTAT
46147704 AAACAA
1 AAACAA
46147710 GGCCTTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.61, C:0.14, G:0.00, T:0.25
Consensus pattern (15 bp):
AAACAATTAAACTAT
Found at i:46155585 original size:12 final size:12
Alignment explanation
Indices: 46155568--46155592 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
46155558 GAATGTTAAT
46155568 AATAATAATAAC
1 AATAATAATAAC
46155580 AATAATAATAAC
1 AATAATAATAAC
46155592 A
1 A
46155593 CAAAAGATAT
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAATAATAAC
Found at i:46155763 original size:20 final size:20
Alignment explanation
Indices: 46155729--46155770 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
46155719 AACTATTTAA
** *
46155729 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
46155749 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
46155769 AT
1 AT
46155771 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Found at i:46167127 original size:13 final size:13
Alignment explanation
Indices: 46167109--46167136 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
46167099 ACAATAACAG
46167109 GGATAGCAGGAAT
1 GGATAGCAGGAAT
46167122 GGATAGCAGGAAT
1 GGATAGCAGGAAT
46167135 GG
1 GG
46167137 TTTTTTAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.36, C:0.07, G:0.43, T:0.14
Consensus pattern (13 bp):
GGATAGCAGGAAT
Found at i:46168855 original size:54 final size:54
Alignment explanation
Indices: 46168608--46168863 Score: 200
Period size: 54 Copynumber: 4.7 Consensus size: 54
46168598 ATTACCATGC
* * * * *
46168608 ATGTAGGAAGTCCGTTAGGACAAT-TGCAATATGGAAGTCCGTCAGAATAATCTTA
1 ATGT-GGAAGTCCGTCAGGACAATCT-TAATGTGGAAGTCCGTCAGGACAATCTTA
* * * *
46168663 ATGTGGGAAGTCTGTCAGGACTATCTTAA-GTGGGAAGTCCCTCAGGACAATCGTA
1 ATGT-GGAAGTCCGTCAGGACAATCTTAATGT-GGAAGTCCGTCAGGACAATCTTA
** * * * ** * *
46168718 ATGTGGAAGTCCACCAGAACAATCATAATGTGAAAGTTTGCCAAGACAAT-TATA
1 ATGTGGAAGTCCGTCAGGACAATCTTAATGTGGAAGTCCGTCAGGACAATCT-TA
* *
46168772 ATGTGGAAGTCTG-CTAGGTA-AAT-TGTAATGTGGAAGTCCGTTAGGACAATCTTA
1 ATGTGGAAGTCCGTC-AGG-ACAATCT-TAATGTGGAAGTCCGTCAGGACAATCTTA
* *
46168826 ATGTGGCAGTCCGTCAGGACAATCTTAATGTAGAAGTC
1 ATGTGGAAGTCCGTCAGGACAATCTTAATGTGGAAGTC
46168864 TGCTAGGACG
Statistics
Matches: 154, Mismatches: 36, Indels: 23
0.72 0.17 0.11
Matches are distributed among these distances:
53 2 0.01
54 100 0.65
55 51 0.33
56 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (54 bp):
ATGTGGAAGTCCGTCAGGACAATCTTAATGTGGAAGTCCGTCAGGACAATCTTA
Found at i:46168871 original size:27 final size:27
Alignment explanation
Indices: 46168656--46168872 Score: 160
Period size: 27 Copynumber: 8.0 Consensus size: 27
46168646 CCGTCAGAAT
46168656 AATCTTAATGTGGGAAGTCTG-TCAGGAC
1 AATCTTAATGT-GGAAGTCTGCT-AGGAC
* *
46168684 TATCTTAA-GTGGGAAGTC-CCTCAGGAC
1 AATCTTAATGT-GGAAGTCTGCT-AGGAC
* ** * *
46168711 AATCGTAATGTGGAAGTCCACCAGAAC
1 AATCTTAATGTGGAAGTCTGCTAGGAC
* * * * *
46168738 AATCATAATGTGAAAGTTTGCCAAGAC
1 AATCTTAATGTGGAAGTCTGCTAGGAC
46168765 AAT-TATAATGTGGAAGTCTGCTAGGTA-
1 AATCT-TAATGTGGAAGTCTGCTAGG-AC
* *
46168792 AAT-TGTAATGTGGAAGTCCGTTAGGAC
1 AATCT-TAATGTGGAAGTCTGCTAGGAC
* *
46168819 AATCTTAATGTGGCAGTCCG-TCAGGAC
1 AATCTTAATGTGGAAGTCTGCT-AGGAC
*
46168846 AATCTTAATGTAGAAGTCTGCTAGGAC
1 AATCTTAATGTGGAAGTCTGCTAGGAC
46168873 GATTGTATTT
Statistics
Matches: 154, Mismatches: 26, Indels: 19
0.77 0.13 0.10
Matches are distributed among these distances:
26 2 0.01
27 139 0.90
28 13 0.08
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (27 bp):
AATCTTAATGTGGAAGTCTGCTAGGAC
Found at i:46168878 original size:81 final size:81
Alignment explanation
Indices: 46168608--46168879 Score: 264
Period size: 81 Copynumber: 3.3 Consensus size: 81
46168598 ATTACCATGC
* * * * *
46168608 ATGTAGGAAGTCCGTTAGGACAATTGCAATATGGAAGTCCGTCAGAATAATCTTAATGTGGGAAG
1 ATGTA-GAAGTCTGCTAGGACAATTGTAATGTGGAAGTCCGTCAGAACAATCTTAATGT-GGAAG
*
46168673 TCTGTCAGGACTATCTTA
64 TCTGTCAGGACAATCTTA
* * * ** * *
46168691 A-GTGGGAAGTC-CCTCAGGACAATCGTAATGTGGAAGTCCACCAGAACAATCATAATGTGAAAG
1 ATGT-AGAAGTCTGCT-AGGACAATTGTAATGTGGAAGTCCGTCAGAACAATCTTAATGTGGAAG
* * *
46168754 TTTGCCAAGACAAT-TATA
64 TCTGTCAGGACAATCT-TA
* * * *
46168772 ATGTGGAAGTCTGCTAGGTA-AATTGTAATGTGGAAGTCCGTTAGGACAATCTTAATGTGGCAGT
1 ATGTAGAAGTCTGCTAGG-ACAATTGTAATGTGGAAGTCCGTCAGAACAATCTTAATGTGGAAGT
*
46168836 CCGTCAGGACAATCTTA
65 CTGTCAGGACAATCTTA
*
46168853 ATGTAGAAGTCTGCTAGGACGATTGTA
1 ATGTAGAAGTCTGCTAGGACAATTGTA
46168880 TTTGTGAAGT
Statistics
Matches: 151, Mismatches: 30, Indels: 18
0.76 0.15 0.09
Matches are distributed among these distances:
80 2 0.01
81 98 0.65
82 50 0.33
83 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (81 bp):
ATGTAGAAGTCTGCTAGGACAATTGTAATGTGGAAGTCCGTCAGAACAATCTTAATGTGGAAGTC
TGTCAGGACAATCTTA
Found at i:46169972 original size:9 final size:9
Alignment explanation
Indices: 46169958--46170033 Score: 91
Period size: 9 Copynumber: 8.4 Consensus size: 9
46169948 GTAGTGATTC
*
46169958 AATTCGATT
1 AATTCGGTT
46169967 AATTCGAG-T
1 AATTCG-GTT
*
46169976 AATTTGGTT
1 AATTCGGTT
*
46169985 AATTTGGTT
1 AATTCGGTT
*
46169994 AATTCGGGT
1 AATTCGGTT
46170003 AATTCGGTT
1 AATTCGGTT
46170012 AATTCGGTT
1 AATTCGGTT
*
46170021 AATTCAGTT
1 AATTCGGTT
46170030 AATT
1 AATT
46170034 TTTAACCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
8 1 0.02
9 58 0.98
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:46169996 original size:27 final size:27
Alignment explanation
Indices: 46169958--46170034 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
46169948 GTAGTGATTC
*
46169958 AATTCGATTAATTCGAGTAATTTGGTT
1 AATTCGGTTAATTCGAGTAATTTGGTT
* * *
46169985 AATTTGGTTAATTCGGGTAATTCGGTT
1 AATTCGGTTAATTCGAGTAATTTGGTT
46170012 AATTCGGTTAATTC-AGTTAATTT
1 AATTCGGTTAATTCGAG-TAATTT
46170035 TTAACCAAAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
26 1 0.02
27 41 0.98
ACGTcount: A:0.27, C:0.08, G:0.19, T:0.45
Consensus pattern (27 bp):
AATTCGGTTAATTCGAGTAATTTGGTT
Found at i:46170845 original size:44 final size:46
Alignment explanation
Indices: 46170755--46170846 Score: 161
Period size: 46 Copynumber: 2.0 Consensus size: 46
46170745 TTTGGATCGC
*
46170755 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
46170801 TGTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
46170845 TG
1 TG
46170847 GAATAGAGGT
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
44 20 0.44
45 3 0.07
46 22 0.49
ACGTcount: A:0.26, C:0.04, G:0.30, T:0.39
Consensus pattern (46 bp):
TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAA
Found at i:46170847 original size:39 final size:44
Alignment explanation
Indices: 46170755--46170863 Score: 147
Period size: 46 Copynumber: 2.5 Consensus size: 44
46170745 TTTGGATCGC
*
46170755 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--A
46170801 TGTAATGGAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTA
*
46170841 TG-AATGGAATAGAGGTGTAATAG
1 TGTAATGGAATAGAGGCGTAATAG
46170864 CATAAGGAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
39 18 0.30
40 3 0.05
43 1 0.02
44 13 0.22
45 3 0.05
46 22 0.37
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.37
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTA
Found at i:46171123 original size:122 final size:110
Alignment explanation
Indices: 46171006--46171251 Score: 296
Period size: 110 Copynumber: 2.1 Consensus size: 110
46170996 ATAATTGTTG
46171006 TAAAATATAATTTAATAAAAATATATAATTTAATAAAATGATTAATAAATATTCTTAAATATGAA
1 TAAAATATAATTTAATAAAAATATATAATTTAAT-AAA--ATT-AT---TATTCTT--ATATGAA
*
46171071 TTTACTAATAAAATCATAATATATAACACTATAAAATATAATTTAAAATAATTATAA
57 TTTAC---TAAAATCATAATATATAACAATATAAAATATAATTTAAAATAATTATAA
* * *
46171128 TTAAATATAATTTAATAATAATATATAATTTAATAAAATTCTTATTCTTATATGAATTTACTAAA
1 TAAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTATTCTTATATGAATTTACTAAA
* * *
46171193 ATCATAATATATAATAATATAAAATATAATTT-AACTAATTATTAT
66 ATCATAATATATAACAATATAAAATATAATTTAAAATAATTA-TAA
*
46171238 TAAATTATAATTTA
1 TAAAATATAATTTA
46171252 TAATCTACTT
Statistics
Matches: 114, Mismatches: 9, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
109 8 0.07
110 48 0.42
113 12 0.11
115 7 0.06
118 1 0.01
119 3 0.03
121 3 0.03
122 32 0.28
ACGTcount: A:0.53, C:0.04, G:0.01, T:0.41
Consensus pattern (110 bp):
TAAAATATAATTTAATAAAAATATATAATTTAATAAAATTATTATTCTTATATGAATTTACTAAA
ATCATAATATATAACAATATAAAATATAATTTAAAATAATTATAA
Found at i:46171128 original size:16 final size:17
Alignment explanation
Indices: 46171107--46171161 Score: 55
Period size: 18 Copynumber: 3.4 Consensus size: 17
46171097 CACTATAAAA
46171107 TATAATTTAAA-ATAAT
1 TATAATTTAAATATAAT
46171123 TATAA-TTAAATATAAT
1 TATAATTTAAATATAAT
*
46171139 T-TAATAATAATATATAAT
1 TATAAT-TTAA-ATATAAT
46171157 T-TAAT
1 TATAAT
46171162 AAAATTCTTA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
15 8 0.24
16 11 0.32
17 3 0.09
18 12 0.35
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
TATAATTTAAATATAAT
Found at i:46171134 original size:26 final size:28
Alignment explanation
Indices: 46171104--46171167 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
46171094 TAACACTATA
46171104 AAATATAATTTAA-AATAAT-TATAATT
1 AAATATAATTTAATAATAATATATAATT
46171130 AAATATAATTTAATAATAATATATAATT
1 AAATATAATTTAATAATAATATATAATT
* *
46171158 TAATAAAATT
1 AAATATAATT
46171168 CTTATTCTTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 13 0.38
27 6 0.18
28 15 0.44
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
AAATATAATTTAATAATAATATATAATT
Found at i:46173820 original size:22 final size:22
Alignment explanation
Indices: 46173795--46173836 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
46173785 TTTGCTGCAC
*
46173795 TAAATAAGAACACATTCAAATT
1 TAAATAAGAACACATCCAAATT
46173817 TAAATAAGAACACATCCAAA
1 TAAATAAGAACACATCCAAA
46173837 CGCAAGCCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.17, G:0.05, T:0.21
Consensus pattern (22 bp):
TAAATAAGAACACATCCAAATT
Found at i:46174072 original size:24 final size:25
Alignment explanation
Indices: 46174044--46174104 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
46174034 ATTCAAACCA
46174044 GAATTGCAACTATAAAA-ACCTCTT
1 GAATTGCAACTATAAAATACCTCTT
46174068 GAATTGCAACTATAAAATACCTCTT
1 GAATTGCAACTATAAAATACCTCTT
*
46174093 AAATTGCAACTA
1 GAATTGCAACTA
46174105 AAGCTTTAGC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
24 17 0.49
25 18 0.51
ACGTcount: A:0.43, C:0.20, G:0.08, T:0.30
Consensus pattern (25 bp):
GAATTGCAACTATAAAATACCTCTT
Found at i:46175718 original size:12 final size:12
Alignment explanation
Indices: 46175701--46175741 Score: 82
Period size: 12 Copynumber: 3.4 Consensus size: 12
46175691 AAACAGAGTG
46175701 TTATTATTTATT
1 TTATTATTTATT
46175713 TTATTATTTATT
1 TTATTATTTATT
46175725 TTATTATTTATT
1 TTATTATTTATT
46175737 TTATT
1 TTATT
46175742 TTTTCTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (12 bp):
TTATTATTTATT
Found at i:46183118 original size:20 final size:20
Alignment explanation
Indices: 46183081--46183118 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46183071 TCCCCCCGAA
**
46183081 TCTTTTTCTTTTCATTTTTT
1 TCTTTTTCTCCTCATTTTTT
46183101 TCTTTTTCTCCTC-TTTTT
1 TCTTTTTCTCCTCATTTTT
46183119 GTTGTCGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (20 bp):
TCTTTTTCTCCTCATTTTTT
Found at i:46183763 original size:44 final size:44
Alignment explanation
Indices: 46183715--46183820 Score: 108
Period size: 44 Copynumber: 2.4 Consensus size: 44
46183705 TGTTCTACTG
* * *
46183715 CAACTTCAGAGAGATAAGATCTAT-TACTTTAATCTGCTCCACTA
1 CAACTTCAGAGAGATAAGAT-TATCGAATTCAATCTGCTCCACTA
* * * *
46183759 CAACTTCAGGGGGATAGGATTATCGAATTCAATCTGCTCCACTG
1 CAACTTCAGAGAGATAAGATTATCGAATTCAATCTGCTCCACTA
*
46183803 CAACCTCA-AGGAGATAAG
1 CAACTTCAGA-GAGATAAG
46183821 TTTTGCTTCT
Statistics
Matches: 49, Mismatches: 11, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
43 3 0.06
44 46 0.94
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.26
Consensus pattern (44 bp):
CAACTTCAGAGAGATAAGATTATCGAATTCAATCTGCTCCACTA
Found at i:46184106 original size:87 final size:86
Alignment explanation
Indices: 46184004--46184269 Score: 397
Period size: 87 Copynumber: 3.1 Consensus size: 86
46183994 ACCTGTAATC
* ** * **
46184004 TTCGATCTGCCTTACTGTCGACGCAGGAGGGTAAGATCTGCTATCTTTAACCAGCTCCACTGGAA
1 TTCGATCTGCTTTACTGTTAACGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTACAA
46184069 CCGATGGAGGCAATGCTTTGTT
66 CCGATGGAGGCAA-GCTTTGTT
*
46184091 TTCGATCTGCTTTACTGTTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTCCACTACAA
1 TTCGATCTGCTTTACTGTTAACGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTACAA
*
46184156 CCGATGGAGGCAAGGTTTTGTT
66 CCGATGGAGGCAA-GCTTTGTT
* * * * *
46184178 TTCGATCTGCTTCACTGTTAATGTAGGAAGGTAAGATTTGCTATCTTTAATCAGCTCCACTACAA
1 TTCGATCTGCTTTACTGTTAACGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTACAA
46184243 CCGATGGAGGCAAGCTTTGTT
66 CCGATGGAGGCAAGCTTTGTT
46184264 TTCGAT
1 TTCGAT
46184270 TTTGACTGAT
Statistics
Matches: 163, Mismatches: 16, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
86 13 0.08
87 150 0.92
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.31
Consensus pattern (86 bp):
TTCGATCTGCTTTACTGTTAACGCAGGAAGGTAAGATCTGCTATCTTTAACCAGCTCCACTACAA
CCGATGGAGGCAAGCTTTGTT
Found at i:46185965 original size:26 final size:26
Alignment explanation
Indices: 46185936--46185995 Score: 79
Period size: 26 Copynumber: 2.3 Consensus size: 26
46185926 TTTACTTTGA
46185936 TTGA-TTTCTCTTTTTTGCTTTTGAC-T
1 TTGATTTTCT-TTTTTTGCTTTTG-CTT
*
46185962 TTGATTTTCTTTTTTTGTTTTTGCTT
1 TTGATTTTCTTTTTTTGCTTTTGCTT
46185988 TTGATTTT
1 TTGATTTT
46185996 GAGTTTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
25 1 0.03
26 25 0.81
27 5 0.16
ACGTcount: A:0.07, C:0.10, G:0.12, T:0.72
Consensus pattern (26 bp):
TTGATTTTCTTTTTTTGCTTTTGCTT
Found at i:46185987 original size:32 final size:31
Alignment explanation
Indices: 46185947--46186007 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 31
46185937 TGATTTCTCT
*
46185947 TTTTTGCTTTTGACTTTGATTTTCTTTTTTTG
1 TTTTTGCTTTTGACTTTGAGTTT-TTTTTTTG
*
46185979 TTTTTGCTTTTGATTTTGAGTTTTTTTTT
1 TTTTTGCTTTTGACTTTGAGTTTTTTTTT
46186008 ACTGAACCCT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
31 6 0.22
32 21 0.78
ACGTcount: A:0.07, C:0.07, G:0.13, T:0.74
Consensus pattern (31 bp):
TTTTTGCTTTTGACTTTGAGTTTTTTTTTTG
Found at i:46186002 original size:26 final size:26
Alignment explanation
Indices: 46185947--46186007 Score: 63
Period size: 26 Copynumber: 2.4 Consensus size: 26
46185937 TGATTTCTCT
* **
46185947 TTTTTGCTTTTGACTTTGATTTTCTT
1 TTTTTGTTTTTGACTTTGATTTTCAG
*
46185973 TTTTTGTTTTTG-CTTTTGATTTTGAG
1 TTTTTGTTTTTGAC-TTTGATTTTCAG
46185999 TTTTT-TTTT
1 TTTTTGTTTT
46186008 ACTGAACCCT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 5 0.17
26 25 0.83
ACGTcount: A:0.07, C:0.07, G:0.13, T:0.74
Consensus pattern (26 bp):
TTTTTGTTTTTGACTTTGATTTTCAG
Found at i:46193753 original size:31 final size:31
Alignment explanation
Indices: 46193715--46193776 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
46193705 ATTTTATCTA
*
46193715 ACCGCTCTTGCATTTGTACTTGTAACCGTTC
1 ACCGCTCTTGCATTTGCACTTGTAACCGTTC
46193746 ACCGCTCTTGCATTTGCACTTGTAACCGTTC
1 ACCGCTCTTGCATTTGCACTTGTAACCGTTC
46193777 TTGCATATCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.16, C:0.31, G:0.16, T:0.37
Consensus pattern (31 bp):
ACCGCTCTTGCATTTGCACTTGTAACCGTTC
Found at i:46196535 original size:20 final size:20
Alignment explanation
Indices: 46196498--46196535 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
46196488 TCCCCCCAAA
**
46196498 TCTTTTTCTTTTCATTTTTT
1 TCTTTTTCTCCTCATTTTTT
46196518 TCTTTTTCTCCTC-TTTTT
1 TCTTTTTCTCCTCATTTTT
46196536 GCTGTCGATT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 5 0.31
20 11 0.69
ACGTcount: A:0.03, C:0.21, G:0.00, T:0.76
Consensus pattern (20 bp):
TCTTTTTCTCCTCATTTTTT
Found at i:46207238 original size:23 final size:25
Alignment explanation
Indices: 46207208--46207259 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 25
46207198 TATCAGATTT
*
46207208 TATAAAATAT-ATTTGT-CCAAATA
1 TATAAAATATAATTTATACCAAATA
*
46207231 TATAAAATATAATTTATATCAAATA
1 TATAAAATATAATTTATACCAAATA
46207256 TATA
1 TATA
46207260 GAAAAGTATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.40
24 5 0.20
25 10 0.40
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (25 bp):
TATAAAATATAATTTATACCAAATA
Found at i:46209773 original size:22 final size:22
Alignment explanation
Indices: 46209745--46209787 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
46209735 AATATACATT
46209745 CTTAATGATCTAAGAAAGGTTG
1 CTTAATGATCTAAGAAAGGTTG
* *
46209767 CTTAATGATGTAAGAAGGGTT
1 CTTAATGATCTAAGAAAGGTT
46209788 ACTAGAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.07, G:0.26, T:0.33
Consensus pattern (22 bp):
CTTAATGATCTAAGAAAGGTTG
Done.