Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397256.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_56.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 13963513
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 99179 characters in sequence are not A, C, G, or T
File 9 of 29
Found at i:3165021 original size:21 final size:22
Alignment explanation
Indices: 3164977--3165022 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
3164967 TATTATTACT
*
3164977 AATAAATTTTATGTTTAGTAAA
1 AATAAATTTTATATTTAGTAAA
* *
3164999 AATACATTTTATATTT-TTAAA
1 AATAAATTTTATATTTAGTAAA
3165020 AAT
1 AAT
3165023 TTGTTTTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 7 0.33
22 14 0.67
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (22 bp):
AATAAATTTTATATTTAGTAAA
Found at i:3170103 original size:21 final size:22
Alignment explanation
Indices: 3170074--3170115 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
3170064 AAGATAAATA
* *
3170074 GATTATTTTTTTTCTCAAATTT
1 GATTATTTTTTATCTAAAATTT
3170096 GATT-TTTTTTATCTAAAATT
1 GATTATTTTTTATCTAAAATT
3170116 AAAAATTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.62
Consensus pattern (22 bp):
GATTATTTTTTATCTAAAATTT
Found at i:3180292 original size:195 final size:195
Alignment explanation
Indices: 3180033--3180565 Score: 643
Period size: 194 Copynumber: 2.7 Consensus size: 195
3180023 TATTATTATA
* *
3180033 AAAAAGTTTGAAA-TTTTAATTATATATTATAAAAATATAATATTTTAAATTTAAAAATTAATTA
1 AAAAAGTTT-AAATTTTTAATGATATGTTAT-AAAA-ATAATATTTTAAATTTAAAAATTAATTA
* *
3180097 AAATTATTAATATTTTAATCATAATAACATTGAAATTACAAATAAAATGTTAATATTTTAAAATG
63 AAATTATTAATATTTTAATCATAATAACATTGAAATTATAAATAAAATGTTAATA-TTTAAAATA
* ** *
3180162 TTAATGATTAAATTATTA-ATAAAATATTAATATTTAAATGATTCAAGTATTTAATATTATTGTA
127 TTAATAATTAAATTATTATATAAAATATTAATATACAAATGA-TCAAGTA-TTAATATTATTATA
3180226 -AAAAG
190 CAAAAG
* **
3180231 AAAAACGTTTAAATTTTTAATGATATGTTAT-AAAAT-GTATTTTAAATTTAAATGTTAATTAAA
1 AAAAA-GTTTAAATTTTTAATGATATGTTATAAAAATAATATTTTAAATTTAAAAATTAATTAAA
* * *
3180294 ATTATTAATATTTTAATCATAATAACATTTAAATTTTAAAT--AATG-TAATTACATTAAAAATA
65 ATTATTAATATTTTAATCATAATAACATTGAAATTATAAATAAAATGTTAA-T--ATTTAAAATA
* * * * * * *
3180356 TTAATAATTTAATTA-TATGTGAAATATTAATATACAAATTATCAATTATTAATTTTATTATACC
127 TTAATAATTAAATTATTATATAAAATATTAATATACAAATGATCAAGTATTAATATTATTATACA
3180420 AAAG
192 AAAG
* * * * * * *
3180424 AGAAATTTTTAATTTTTAATTATTTTTTATAAAAATAATATTTTAAATTTAAAAATTAATAAAAA
1 AAAAAGTTTAAATTTTTAATGATATGTTATAAAAATAATATTTTAAATTTAAAAATTAATTAAAA
* *
3180489 TTATTAATATTTTAATCATAATAACATTGAAATTATAAATAAAATATTAATATCTAAAATATTAA
66 TTATTAATATTTTAATCATAATAACATTGAAATTATAAATAAAATGTTAATATTTAAAATATTAA
3180554 TAATTAAATTAT
131 TAATTAAATTAT
3180566 CAATTATTAA
Statistics
Matches: 285, Mismatches: 37, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
192 35 0.12
193 26 0.09
194 122 0.43
195 63 0.22
196 6 0.02
197 6 0.02
198 8 0.03
199 19 0.07
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.44
Consensus pattern (195 bp):
AAAAAGTTTAAATTTTTAATGATATGTTATAAAAATAATATTTTAAATTTAAAAATTAATTAAAA
TTATTAATATTTTAATCATAATAACATTGAAATTATAAATAAAATGTTAATATTTAAAATATTAA
TAATTAAATTATTATATAAAATATTAATATACAAATGATCAAGTATTAATATTATTATACAAAAG
Found at i:3180347 original size:26 final size:26
Alignment explanation
Indices: 3180332--3180387 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
3180322 TTAAATTTTA
3180332 AATAATGTAATTACATTAAAAATATT
1 AATAATGTAATTACATTAAAAATATT
* * *
3180358 AATAATTTAATTATATGT-GAAATATT
1 AATAATGTAATTACAT-TAAAAATATT
3180384 AATA
1 AATA
3180388 TACAAATTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (26 bp):
AATAATGTAATTACATTAAAAATATT
Found at i:3180548 original size:15 final size:14
Alignment explanation
Indices: 3180528--3180610 Score: 78
Period size: 15 Copynumber: 5.6 Consensus size: 14
3180518 AAATTATAAA
3180528 TAAAATATTAATAT
1 TAAAATATTAATAT
3180542 CTAAAATATTAATAAT
1 -TAAAATATTAAT-AT
* *
3180558 TAAATTATCAATTAT
1 TAAAATATTAA-TAT
*
3180573 TAATATATTAAATTAT
1 TAAAATATT-AA-TAT
*
3180589 TAAAAT-TTAATAA
1 TAAAATATTAATAT
3180602 TAAAATATT
1 TAAAATATT
3180611 CTATTCCATT
Statistics
Matches: 57, Mismatches: 7, Indels: 9
0.78 0.10 0.12
Matches are distributed among these distances:
13 8 0.14
14 4 0.07
15 31 0.54
16 14 0.25
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.43
Consensus pattern (14 bp):
TAAAATATTAATAT
Found at i:3180598 original size:23 final size:22
Alignment explanation
Indices: 3180543--3180607 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
3180533 TATTAATATC
3180543 TAAAATATTAATAATTAAATTA
1 TAAAATATTAATAATTAAATTA
* *
3180565 TCAATTATTAATATATTAAATTA
1 TAAAATATTAATA-ATTAAATTA
*
3180588 TTAAAAT-TTAATAATAAAAT
1 -TAAAATATTAATAATTAAAT
3180608 ATTCTATTCC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
22 17 0.47
23 15 0.42
24 4 0.11
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAAATATTAATAATTAAATTA
Found at i:3185156 original size:3 final size:3
Alignment explanation
Indices: 3185148--3185182 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
3185138 AACTAATTTT
*
3185148 TAA TAA TAA TAA TAA CAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
3185183 TCATGGGTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:3187850 original size:34 final size:35
Alignment explanation
Indices: 3187766--3187880 Score: 164
Period size: 33 Copynumber: 3.4 Consensus size: 35
3187756 CCAAGATTTT
* * *
3187766 ACAATGGCTTTTCACAGGCTCAGCCACAA-CTTCA
1 ACAATGGTTTTTCAAAGGCTCAACCACAACCTTCA
3187800 ACAATGG-TTTTCAAAGGCTCAACCA-AACCTTCA
1 ACAATGGTTTTTCAAAGGCTCAACCACAACCTTCA
*
3187833 ACAATGGTTTTTCAAAGGCTCAACCACAACCTTAA
1 ACAATGGTTTTTCAAAGGCTCAACCACAACCTTCA
*
3187868 ACAATGATTTTTC
1 ACAATGGTTTTTC
3187881 TCGGGATCAA
Statistics
Matches: 74, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
32 2 0.03
33 28 0.38
34 25 0.34
35 19 0.26
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (35 bp):
ACAATGGTTTTTCAAAGGCTCAACCACAACCTTCA
Found at i:3187891 original size:35 final size:34
Alignment explanation
Indices: 3187799--3187895 Score: 106
Period size: 35 Copynumber: 2.9 Consensus size: 34
3187789 CCACAACTTC
* * *
3187799 AACAATG-GTTTTCAAAGGCTCAACCAAACCTTC
1 AACAATGATTTTTCAAAGGATCAACCAAACCTTA
* *
3187832 AACAATGGTTTTTCAAAGGCTCAACCACAACCTTA
1 AACAATGATTTTTCAAAGGATCAACCA-AACCTTA
***
3187867 AACAATGATTTTTCTCGGGATCAACCAAA
1 AACAATGATTTTTCAAAGGATCAACCAAA
3187896 ACCCAAAAAC
Statistics
Matches: 55, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
33 7 0.13
34 20 0.36
35 28 0.51
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.26
Consensus pattern (34 bp):
AACAATGATTTTTCAAAGGATCAACCAAACCTTA
Found at i:3189890 original size:90 final size:90
Alignment explanation
Indices: 3189727--3189903 Score: 221
Period size: 90 Copynumber: 2.0 Consensus size: 90
3189717 CAACGTGCTC
* * *
3189727 TTGTGAGTTGTATATCAACCTCATCAACAATATTTGAGCGGTCCCGCCCCACTCAAGCAAATAGA
1 TTGTGAGTGGCATATCAACCTCATCAACAATATTTGAGCGGTCCCACCCCACTCAAGCAAATAGA
*
3189792 GATTAATCCCCACTATCATCATCAT
66 GATCAATCCCCACTATCATCATCAT
* * * ** * **
3189817 TTGTGAGTGGCATATTAACCTCATCCACAATCTTTGAGCGGTTTCACCCCACTCAGGCGGATA-A
1 TTGTGAGTGGCATATCAACCTCATCAACAATATTTGAGCGGTCCCACCCCACTCAAGCAAATAGA
*
3189881 TGATCAATCCCCACTATCGTCAT
66 -GATCAATCCCCACTATCATCAT
3189904 AAAATCCCTT
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
89 1 0.01
90 72 0.99
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.28
Consensus pattern (90 bp):
TTGTGAGTGGCATATCAACCTCATCAACAATATTTGAGCGGTCCCACCCCACTCAAGCAAATAGA
GATCAATCCCCACTATCATCATCAT
Found at i:3190081 original size:80 final size:80
Alignment explanation
Indices: 3189987--3190196 Score: 251
Period size: 80 Copynumber: 2.6 Consensus size: 80
3189977 CATTGTGTAT
* * * * * * *
3189987 ATGAAATTTTCAACACATACATCTCATGGTATACATTTCGTAATCTTATAAATCATTTCCATGCT
1 ATGATATTCTCAACACATACATCTCATGGCATACATATCATAATCTCATAAATCATTCCCATGCT
* *
3190052 TCGCCCATAGTGGAC
66 TAGCCCATAGTAGAC
*
3190067 ATGATATTCTCAACACATACATCTCTTGGCATACATATCATAATCTCATAAATCATTCCCATGCT
1 ATGATATTCTCAACACATACATCTCATGGCATACATATCATAATCTCATAAATCATTCCCATGCT
* *
3190132 TATCCCATAGTATAC
66 TAGCCCATAGTAGAC
* * * * *
3190147 ATGATATTCTCAACACATGCATCTTAAGGCAT-CTATGTCATAATTTCATA
1 ATGATATTCTCAACACATACATCTCATGGCATAC-ATATCATAATCTCATA
3190197 GATGGAACTC
Statistics
Matches: 111, Mismatches: 18, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
79 1 0.01
80 110 0.99
ACGTcount: A:0.33, C:0.23, G:0.09, T:0.35
Consensus pattern (80 bp):
ATGATATTCTCAACACATACATCTCATGGCATACATATCATAATCTCATAAATCATTCCCATGCT
TAGCCCATAGTAGAC
Found at i:3190561 original size:17 final size:18
Alignment explanation
Indices: 3190535--3190572 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
3190525 TTTTATGATG
* *
3190535 TTTTATTTTAGGTTTAGT
1 TTTTATTTTAAGTTAAGT
3190553 TTTTA-TTTAAGTTAAGT
1 TTTTATTTTAAGTTAAGT
3190570 TTT
1 TTT
3190573 ATGCTTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 13 0.72
18 5 0.28
ACGTcount: A:0.21, C:0.00, G:0.13, T:0.66
Consensus pattern (18 bp):
TTTTATTTTAAGTTAAGT
Found at i:3197130 original size:15 final size:15
Alignment explanation
Indices: 3197110--3197140 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
3197100 AGTTTCGTCT
3197110 TAAAGCTTATAAGAA
1 TAAAGCTTATAAGAA
*
3197125 TAAAGCTTATGAGAA
1 TAAAGCTTATAAGAA
3197140 T
1 T
3197141 GCAAGCATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.06, G:0.16, T:0.29
Consensus pattern (15 bp):
TAAAGCTTATAAGAA
Found at i:3206924 original size:36 final size:36
Alignment explanation
Indices: 3206849--3206937 Score: 99
Period size: 36 Copynumber: 2.5 Consensus size: 36
3206839 CTTGATAGAG
* * * *
3206849 GTTACGCCTGATCTTG-TAAAAGGCATATTATGAAG
1 GTTACACCTGATCTTGTTAAAAGGCATACTATAAAA
* *
3206884 GTTACACCTGATCTTGTTAAAGGGCATGCTATAAAA
1 GTTACACCTGATCTTGTTAAAAGGCATACTATAAAA
* *
3206920 GTTACATCTAATCTTGTT
1 GTTACACCTGATCTTGTT
3206938 GGAAAAACAA
Statistics
Matches: 45, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
35 15 0.33
36 30 0.67
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (36 bp):
GTTACACCTGATCTTGTTAAAAGGCATACTATAAAA
Found at i:3213472 original size:14 final size:15
Alignment explanation
Indices: 3213446--3213474 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3213436 ACCAAAATTA
3213446 GAGTCTGTTCTTAAT
1 GAGTCTGTTCTTAAT
3213461 GAGTCT-TTCTTAAT
1 GAGTCTGTTCTTAAT
3213475 TTCAATTTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (15 bp):
GAGTCTGTTCTTAAT
Found at i:3225424 original size:15 final size:15
Alignment explanation
Indices: 3225400--3225433 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3225390 AATGCACCTA
* *
3225400 ATGAATGACATTATT
1 ATGAAGGACATTAAT
3225415 ATGAAGGACATTAAT
1 ATGAAGGACATTAAT
3225430 ATGA
1 ATGA
3225434 GTAATTGTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.06, G:0.18, T:0.32
Consensus pattern (15 bp):
ATGAAGGACATTAAT
Found at i:3225547 original size:29 final size:29
Alignment explanation
Indices: 3225509--3225579 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 29
3225499 AGACGTGAAA
*
3225509 AGGTATAAGAAAAGAAGCTGTAAGAGAAC
1 AGGTACAAGAAAAGAAGCTGTAAGAGAAC
* *
3225538 AGGTACAAGAGAAGAAGCTGTACGAGAAC
1 AGGTACAAGAAAAGAAGCTGTAAGAGAAC
*
3225567 AGGGACAAGAAAA
1 AGGTACAAGAAAA
3225580 ACAAGTGTAT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.51, C:0.10, G:0.30, T:0.10
Consensus pattern (29 bp):
AGGTACAAGAAAAGAAGCTGTAAGAGAAC
Found at i:3225913 original size:35 final size:34
Alignment explanation
Indices: 3225843--3225940 Score: 117
Period size: 35 Copynumber: 2.8 Consensus size: 34
3225833 GTAGTGCTCT
* *
3225843 ACTTATACTAGTTGTTCTGCAT-TAAATAGTGCTTC
1 ACTTATTCTAGTTGTTCT--ATGTAAATAGTACTTC
*
3225878 ACTTGTTCTAGTTGTTCTATGTAAAGTAGTACTTC
1 ACTTATTCTAGTTGTTCTATGTAAA-TAGTACTTC
*
3225913 ACTTATTCTAATTGTTCTATGTACAATA
1 ACTTATTCTAGTTGTTCTATGTA-AATA
3225941 TTATGTTGTA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
33 2 0.04
34 4 0.07
35 47 0.85
36 2 0.04
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (34 bp):
ACTTATTCTAGTTGTTCTATGTAAATAGTACTTC
Found at i:3237171 original size:22 final size:21
Alignment explanation
Indices: 3237145--3237185 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
3237135 CTTCCTCAAT
3237145 TTTGTGGAGATTAAGAAGATAA
1 TTTGTGGAGATTAA-AAGATAA
*
3237167 TTTGTGGATATTAAAAGAT
1 TTTGTGGAGATTAAAAGAT
3237186 TGAAAAGGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.39, C:0.00, G:0.24, T:0.37
Consensus pattern (21 bp):
TTTGTGGAGATTAAAAGATAA
Found at i:3238564 original size:21 final size:20
Alignment explanation
Indices: 3238538--3238577 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
3238528 AAAAACTAAT
*
3238538 AAATAACAATCAAATTAAAAG
1 AAATAA-AATAAAATTAAAAG
*
3238559 AAATAATATAAAATTAAAA
1 AAATAAAATAAAATTAAAA
3238578 TAACTCACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.70, C:0.05, G:0.03, T:0.23
Consensus pattern (20 bp):
AAATAAAATAAAATTAAAAG
Found at i:3238594 original size:15 final size:16
Alignment explanation
Indices: 3238574--3238616 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
3238564 ATATAAAATT
*
3238574 AAAATAACTCACT-TA
1 AAAATAACTAACTATA
*
3238589 AAAATAAACTAATTATA
1 AAAAT-AACTAACTATA
3238606 AAAATAACTAA
1 AAAATAACTAA
3238617 AAATAAGTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAATAACTAACTATA
Found at i:3244584 original size:19 final size:20
Alignment explanation
Indices: 3244549--3244587 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
3244539 AAAAACTAAT
*
3244549 AAATAACAATCAAATTAAAA
1 AAATAACAATAAAATTAAAA
3244569 AAATAAC-ATAAAATTAAAA
1 AAATAACAATAAAATTAAAA
3244588 TAACTCACTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.72, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAACAATAAAATTAAAA
Found at i:3244604 original size:15 final size:15
Alignment explanation
Indices: 3244583--3244625 Score: 52
Period size: 15 Copynumber: 2.8 Consensus size: 15
3244573 AACATAAAAT
*
3244583 TAAAATAACTCACTTA
1 TAAAATAACT-AATTA
3244599 -AAAATAAACTAATTA
1 TAAAAT-AACTAATTA
3244614 TAAAATAACTAA
1 TAAAATAACTAA
3244626 AATTAAGTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
15 15 0.62
16 9 0.38
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (15 bp):
TAAAATAACTAATTA
Found at i:3257480 original size:15 final size:15
Alignment explanation
Indices: 3257460--3257503 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 15
3257450 TTAATTATAT
3257460 TATTATTTAATAAAA
1 TATTATTTAATAAAA
3257475 TATTATTT--TAAAA
1 TATTATTTAATAAAA
*
3257488 AATTA-TTAA-AAAA
1 TATTATTTAATAAAA
3257501 TAT
1 TAT
3257504 ATAATATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
12 2 0.08
13 15 0.60
15 8 0.32
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTATTTAATAAAA
Found at i:3257484 original size:16 final size:16
Alignment explanation
Indices: 3257442--3257495 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
3257432 AAATTATTTT
*
3257442 AATATT-TTTTAATTAT
1 AATATTATTTTAA-TAA
*
3257458 ATTATTA-TTTAATAA
1 AATATTATTTTAATAA
3257473 AATATTATTTTAA-AA
1 AATATTATTTTAATAA
3257488 AATTATTA
1 AA-TATTA
3257496 AAAAATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
15 12 0.38
16 20 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
AATATTATTTTAATAA
Found at i:3257505 original size:28 final size:28
Alignment explanation
Indices: 3257461--3257527 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 28
3257451 TAATTATATT
* * *
3257461 ATTATTTAATAAAATATTAT-TTTAAAAA
1 ATTA-TTAAAAAAATATAATATATAAAAA
3257489 ATTATTAAAAAATATATAATATATAAAAA
1 ATTATTAAAAAA-ATATAATATATAAAAA
3257518 ATT-TTAAAAA
1 ATTATTAAAAA
3257528 TCTTGAAGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
27 7 0.21
28 17 0.50
29 10 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (28 bp):
ATTATTAAAAAAATATAATATATAAAAA
Found at i:3260117 original size:17 final size:18
Alignment explanation
Indices: 3260074--3260120 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
3260064 TGAAAGAGAA
3260074 TAGATAGAGAAATAGAAAG
1 TAGA-AGAGAAATAGAAAG
*
3260093 TAGAAGAGAATTAG-AAG
1 TAGAAGAGAAATAGAAAG
3260110 TTAG-AGAGAAA
1 -TAGAAGAGAAA
3260121 AGCTTTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 9 0.36
18 12 0.48
19 4 0.16
ACGTcount: A:0.55, C:0.00, G:0.28, T:0.17
Consensus pattern (18 bp):
TAGAAGAGAAATAGAAAG
Found at i:3265801 original size:28 final size:28
Alignment explanation
Indices: 3265761--3265840 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
3265751 GGTAGAAAGG
3265761 TTATGCTTAATCCTTGAAAATGCAGAGA
1 TTATGCTTAATCCTTGAAAATGCAGAGA
* * * * *
3265789 TTATGCTTCATCCTTTAAATTACAGAGG
1 TTATGCTTAATCCTTGAAAATGCAGAGA
*
3265817 TTATGCTTGATCCTTGAAAA-GCAG
1 TTATGCTTAATCCTTGAAAATGCAG
3265841 TTTTTTGTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
27 3 0.07
28 40 0.93
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.35
Consensus pattern (28 bp):
TTATGCTTAATCCTTGAAAATGCAGAGA
Found at i:3268818 original size:34 final size:34
Alignment explanation
Indices: 3268780--3268845 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
3268770 TGAAATTTTT
*
3268780 AAGCTT-CCACCAAGCTTTT-ATAATGGTTTTTCAC
1 AAGCTTGCCA-CAA-CTTTTAACAATGGTTTTTCAC
3268814 AAGCTTGGCCACAACTTTTAACAATGGTTTTT
1 AAGCTT-GCCACAACTTTTAACAATGGTTTTT
3268846 GGCAAGATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
34 11 0.39
35 14 0.50
36 3 0.11
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (34 bp):
AAGCTTGCCACAACTTTTAACAATGGTTTTTCAC
Found at i:3271766 original size:38 final size:38
Alignment explanation
Indices: 3271688--3271766 Score: 95
Period size: 38 Copynumber: 2.1 Consensus size: 38
3271678 CTAAATCTAC
* * * ** *
3271688 AAATGCATGGGCTAGTTATCCATCACATTCATTACTAT
1 AAATGCATAGGCTACTCATCCATCACATTCACAACCAT
*
3271726 AAATGCATAGGCTACTCATCCATCGCATTCACAACCAT
1 AAATGCATAGGCTACTCATCCATCACATTCACAACCAT
3271764 AAA
1 AAA
3271767 CTTATCCATA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.28
Consensus pattern (38 bp):
AAATGCATAGGCTACTCATCCATCACATTCACAACCAT
Found at i:3274036 original size:19 final size:20
Alignment explanation
Indices: 3273996--3274038 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3273986 AACTCTCCCC
*
3273996 TTAATCGATTAACAAAAGCT
1 TTAATCAATTAACAAAAGCT
*
3274016 TTAATCAATTAA-AAAATCT
1 TTAATCAATTAACAAAAGCT
3274035 TTAA
1 TTAA
3274039 ATTTTGAACT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.48
20 11 0.52
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.35
Consensus pattern (20 bp):
TTAATCAATTAACAAAAGCT
Found at i:3274688 original size:29 final size:29
Alignment explanation
Indices: 3274647--3274703 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
3274637 ATATTTTTAT
3274647 AATATCCACAGTAGCTAAACAAGATATAC
1 AATATCCACAGTAGCTAAACAAGATATAC
* * *
3274676 AATATCTATAGTAGCTAAGCAAGATATA
1 AATATCCACAGTAGCTAAACAAGATATA
3274704 TGGAATACCC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.16, G:0.12, T:0.25
Consensus pattern (29 bp):
AATATCCACAGTAGCTAAACAAGATATAC
Found at i:3281100 original size:18 final size:19
Alignment explanation
Indices: 3281065--3281117 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
3281055 ACTTTTAGAC
*
3281065 TATTAATTTTAACATATTTA-
1 TATT-ATTTTAA-TTATTTAT
*
3281085 TATTTTTTTAATTA-TTAT
1 TATTATTTTAATTATTTAT
3281103 TATTATTTTAATTAT
1 TATTATTTTAATTAT
3281118 GACACTACTT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
17 3 0.11
18 15 0.54
19 6 0.21
20 4 0.14
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTATTTTAATTATTTAT
Found at i:3293930 original size:18 final size:19
Alignment explanation
Indices: 3293893--3293933 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
3293883 AACTAGAAGG
*
3293893 AAATTAAAACTATAAAATA
1 AAATCAAAACTATAAAATA
*
3293912 AAATCAAAAC-ATAATATA
1 AAATCAAAACTATAAAATA
3293930 AAAT
1 AAAT
3293934 GATATTAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.68, C:0.07, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATCAAAACTATAAAATA
Found at i:3299979 original size:75 final size:74
Alignment explanation
Indices: 3299887--3300029 Score: 196
Period size: 75 Copynumber: 1.9 Consensus size: 74
3299877 AAACCTATAC
* * * *
3299887 TTATAAATATGTATTCATTAAATAACAATTATTGAAATATTTTTTTATTATAATTATTAGTATGA
1 TTATAAATATGTATTCATCAAATAACAATCATTGAAATA-TTTTTTATTATAATTATTAGGAAGA
3299952 TTTAAACTTA
65 TTTAAACTTA
* * * **
3299962 TTATAAATGTGTTTTCATCAAATGAGGATCATTGAAATATTTTTTATTATAATTATTAGGAAGAT
1 TTATAAATATGTATTCATCAAATAACAATCATTGAAATATTTTTTATTATAATTATTAGGAAGAT
3300027 TTA
66 TTA
3300030 TTCCATTTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
74 27 0.46
75 32 0.54
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.48
Consensus pattern (74 bp):
TTATAAATATGTATTCATCAAATAACAATCATTGAAATATTTTTTATTATAATTATTAGGAAGAT
TTAAACTTA
Found at i:3300151 original size:35 final size:38
Alignment explanation
Indices: 3300112--3300195 Score: 95
Period size: 35 Copynumber: 2.3 Consensus size: 38
3300102 GTCGTATAAT
3300112 TTAAATATTAATTA-TTTTAATTATTT-AT-TTTAAAG
1 TTAAATATTAATTATTTTTAATTATTTAATATTTAAAG
* * * *
3300147 TTAAATATT-TTTATTTTTATTTTTTTAATATTTTAAG
1 TTAAATATTAATTATTTTTAATTATTTAATATTTAAAG
*
3300184 GTAAATATTAAT
1 TTAAATATTAAT
3300196 ATTGATTAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
34 3 0.08
35 19 0.49
36 2 0.05
37 14 0.36
38 1 0.03
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (38 bp):
TTAAATATTAATTATTTTTAATTATTTAATATTTAAAG
Found at i:3300324 original size:26 final size:26
Alignment explanation
Indices: 3300269--3300324 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
3300259 CTTATGCCTT
* * * **
3300269 TTAAGGGTATACGACATTTTTTGTGT
1 TTAAGAGTATAAGACATTTTATGTAA
3300295 TTAAGAGTATAAGACATTTTATGTAA
1 TTAAGAGTATAAGACATTTTATGTAA
3300321 TTAA
1 TTAA
3300325 CCTTATTGAC
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.34, C:0.05, G:0.18, T:0.43
Consensus pattern (26 bp):
TTAAGAGTATAAGACATTTTATGTAA
Found at i:3307493 original size:7 final size:7
Alignment explanation
Indices: 3307466--3307496 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
3307456 TAAAGAGGAA
*
3307466 AAGGGAA
1 AAGGGAG
3307473 AAGGGAG
1 AAGGGAG
3307480 AAGGGAG
1 AAGGGAG
3307487 AAGGGAG
1 AAGGGAG
3307494 AAG
1 AAG
3307497 TGAGGGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (7 bp):
AAGGGAG
Found at i:3309702 original size:105 final size:105
Alignment explanation
Indices: 3309498--3309704 Score: 249
Period size: 105 Copynumber: 2.0 Consensus size: 105
3309488 TTGTTGATTA
* * * * *
3309498 TGTTAAATGGAGTTCAATAGTTTTGGTGATTTTTAGGCCTTGCATAATTGATTTTTGGGCTTTGA
1 TGTTAAATGAAATTCAATAGTTTTAGTGATTTTTAGGCCTTACATAATTGATTTTTGGGATTTGA
* * * * *
3309563 GTGACTAGTTTTTAGGTGTATCGTTAGAAGTTTTTAATCT
66 GTGACTAGTTTTTAAGTATATCATGACAAGTTTTTAATCT
* *
3309603 TGTTAAATGAAATTCAATAGTTTTAGTGGTTTTTAGGCCTTACGTAATTGATTTTT-GGATATTG
1 TGTTAAATGAAATTCAATAGTTTTAGTGATTTTTAGGCCTTACATAATTGATTTTTGGGAT-TTG
*
3309667 TGTGACTAGTTTTTAAGTAT-TGCATGATCAA-TTTTTAA
65 AGTGACTAGTTTTTAAGTATAT-CATGA-CAAGTTTTTAA
3309705 GTATTGAGTG
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
104 4 0.05
105 80 0.93
106 2 0.02
ACGTcount: A:0.25, C:0.07, G:0.21, T:0.47
Consensus pattern (105 bp):
TGTTAAATGAAATTCAATAGTTTTAGTGATTTTTAGGCCTTACATAATTGATTTTTGGGATTTGA
GTGACTAGTTTTTAAGTATATCATGACAAGTTTTTAATCT
Found at i:3309883 original size:22 final size:22
Alignment explanation
Indices: 3309858--3309910 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 22
3309848 ACGTAATTCT
3309858 TAAAAACTAGTTACAGAATGCC
1 TAAAAACTAGTTACAGAATGCC
* * *
3309880 T-AAAACCAATTACAGAATGCT
1 TAAAAACTAGTTACAGAATGCC
3309901 TAAAAACTAG
1 TAAAAACTAG
3309911 ATATGTAATG
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
21 18 0.72
22 7 0.28
ACGTcount: A:0.49, C:0.17, G:0.11, T:0.23
Consensus pattern (22 bp):
TAAAAACTAGTTACAGAATGCC
Found at i:3336104 original size:18 final size:18
Alignment explanation
Indices: 3336081--3336117 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3336071 TTGAATTGAT
3336081 TAGGTAATTTAGAGAGAA
1 TAGGTAATTTAGAGAGAA
3336099 TAGGTAATTTAGAGAGAA
1 TAGGTAATTTAGAGAGAA
3336117 T
1 T
3336118 CTACAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (18 bp):
TAGGTAATTTAGAGAGAA
Found at i:3337727 original size:7 final size:7
Alignment explanation
Indices: 3337708--3337821 Score: 60
Period size: 7 Copynumber: 16.4 Consensus size: 7
3337698 TCTTTCCGGC
3337708 CTTC-TT
1 CTTCTTT
*
3337714 CTCCTTT
1 CTTCTTT
3337721 CTTCTTT
1 CTTCTTT
* *
3337728 TTTCTTC
1 CTTCTTT
*
3337735 CTTTTTT
1 CTTCTTT
3337742 GC-TCTTT
1 -CTTCTTT
3337749 CTT-TCTT
1 CTTCT-TT
*
3337756 CTTCCTTC
1 CTT-CTTT
*
3337764 CTT-TCT
1 CTTCTTT
3337770 CTTTCTTT
1 C-TTCTTT
3337778 CTTCTTT
1 CTTCTTT
3337785 CTTCTTT
1 CTTCTTT
3337792 -TTCTTT
1 CTTCTTT
3337798 -TTCCTTT
1 CTT-CTTT
* *
3337805 CGTCTTC
1 CTTCTTT
*
3337812 CCTCTTT
1 CTTCTTT
3337819 CTT
1 CTT
3337822 GGCCGGCCTC
Statistics
Matches: 81, Mismatches: 17, Indels: 19
0.69 0.15 0.16
Matches are distributed among these distances:
6 15 0.19
7 56 0.69
8 9 0.11
9 1 0.01
ACGTcount: A:0.00, C:0.32, G:0.02, T:0.67
Consensus pattern (7 bp):
CTTCTTT
Found at i:3337750 original size:25 final size:25
Alignment explanation
Indices: 3337722--3337818 Score: 106
Period size: 25 Copynumber: 3.8 Consensus size: 25
3337712 TTCTCCTTTC
*
3337722 TTCTTTTTTCTTCCTT-TTTTGCTCT
1 TTCTTTCTTCTTCCTTCTTTT-CTCT
*
3337747 TTCTTTCTTCTTCCTTCCTTTCTCT
1 TTCTTTCTTCTTCCTTCTTTTCTCT
* *
3337772 TTCTTTCTTCTTTCTTCTTTTTCTTT
1 TTCTTTCTTCTTCCTTC-TTTTCTCT
* *
3337798 TTCCTTTCGTCTTCCCTCTTT
1 TT-CTTTCTTCTTCCTTCTTT
3337819 CTTGGCCGGC
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
25 35 0.57
26 14 0.23
27 12 0.20
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (25 bp):
TTCTTTCTTCTTCCTTCTTTTCTCT
Found at i:3337790 original size:10 final size:10
Alignment explanation
Indices: 3337709--3337811 Score: 68
Period size: 11 Copynumber: 9.9 Consensus size: 10
3337699 CTTTCCGGCC
*
3337709 TTCTTCTCCT
1 TTCTTCTTCT
*
3337719 TTCTTCTTTT
1 TTCTTCTTCT
*
3337729 TTCTTCCTTTT
1 TTCTT-CTTCT
3337740 TTGC-TCTTTCT
1 TT-CTTC-TTCT
3337751 TTCTTCTTCCT
1 TTCTTCTT-CT
*
3337762 TCCTT-TCTCT
1 TTCTTCT-TCT
3337772 TTCTTTCTTCT
1 TTC-TTCTTCT
3337783 TTCTTCTT-T
1 TTCTTCTTCT
*
3337792 TTCTTTTTCCT
1 TTCTTCTT-CT
*
3337803 TTCGTCTTC
1 TTCTTCTTC
3337812 CCTCTTTCTT
Statistics
Matches: 75, Mismatches: 8, Indels: 20
0.73 0.08 0.19
Matches are distributed among these distances:
9 8 0.11
10 28 0.37
11 37 0.49
12 2 0.03
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.68
Consensus pattern (10 bp):
TTCTTCTTCT
Found at i:3338708 original size:59 final size:59
Alignment explanation
Indices: 3338635--3338909 Score: 340
Period size: 60 Copynumber: 4.6 Consensus size: 59
3338625 ATGAAATTCT
* *
3338635 TAGGCTTGACCTATCTCAAAACA-GTTCAACTTAAAAATTAAAATTTTTCAGACTTGATC
1 TAGGCTCGACCTATCTCAAAACAGGTTCAACTTAAAAATTAAAATTTTT-AGACTTGTTC
* * * *
3338694 TAGGCTCGACCTATCTTAAAACAGGTTCAAATTTAAAAATTGAAATTTTTATTAC-TGTTC
1 TAGGCTCGACCTATCTCAAAACAGGTTC-AACTTAAAAATTAAAATTTTTA-GACTTGTTC
* * * *
3338754 TAGGCTCGACCTATCT-AAAACAGGTTCGATTTAAAAATTAAAATTCTCAGACTTGTTC
1 TAGGCTCGACCTATCTCAAAACAGGTTCAACTTAAAAATTAAAATTTTTAGACTTGTTC
* * * *
3338812 TAGGCTTGACCTATTTCAAAACAGGTTCGACTTAAAAATTAAAAATTCTTAGACTTGTTC
1 TAGGCTCGACCTATCTCAAAACAGGTTCAACTTAAAAATT-AAAATTTTTAGACTTGTTC
* * *
3338872 TAGGCTCGACCTATCTCAAAATAGGCTCGACTTAAAAA
1 TAGGCTCGACCTATCTCAAAACAGGTTCAACTTAAAAA
3338910 GTGAAATGCC
Statistics
Matches: 191, Mismatches: 19, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
57 2 0.01
58 37 0.19
59 54 0.28
60 77 0.40
61 21 0.11
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (59 bp):
TAGGCTCGACCTATCTCAAAACAGGTTCAACTTAAAAATTAAAATTTTTAGACTTGTTC
Found at i:3338824 original size:118 final size:120
Alignment explanation
Indices: 3338635--3338909 Score: 364
Period size: 118 Copynumber: 2.3 Consensus size: 120
3338625 ATGAAATTCT
* * *
3338635 TAGGCTTGACCTATCTCAAAACA-GTTCAACTTAAAAATTAAAATTTTTCAGACTTGATCTAGGC
1 TAGGCTCGACCTATCTCAAAACAGGTTCGACTTAAAAATTAAAATTTCTCAGACTTGATCTAGGC
* * * *
3338699 TCGACCTATCTT-AAAACAGGTTCAAATTTAAAAATT-GAAATTTTTATTAC-TGTTC
66 TCGACCTAT-TTCAAAACAGGTTC-AACTTAAAAATTAAAAATTCTTA-GACTTGTTC
* *
3338754 TAGGCTCGACCTATCT-AAAACAGGTTCGATTTAAAAATTAAAA-TTCTCAGACTTGTTCTAGGC
1 TAGGCTCGACCTATCTCAAAACAGGTTCGACTTAAAAATTAAAATTTCTCAGACTTGATCTAGGC
* *
3338817 TTGACCTATTTCAAAACAGGTTCGACTTAAAAATTAAAAATTCTTAGACTTGTTC
66 TCGACCTATTTCAAAACAGGTTCAACTTAAAAATTAAAAATTCTTAGACTTGTTC
* *
3338872 TAGGCTCGACCTATCTCAAAATAGGCTCGACTTAAAAA
1 TAGGCTCGACCTATCTCAAAACAGGTTCGACTTAAAAA
3338910 GTGAAATGCC
Statistics
Matches: 137, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
117 14 0.10
118 72 0.53
119 51 0.37
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (120 bp):
TAGGCTCGACCTATCTCAAAACAGGTTCGACTTAAAAATTAAAATTTCTCAGACTTGATCTAGGC
TCGACCTATTTCAAAACAGGTTCAACTTAAAAATTAAAAATTCTTAGACTTGTTC
Found at i:3342014 original size:21 final size:22
Alignment explanation
Indices: 3341979--3342022 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
3341969 CTCTTAAAGT
3341979 AATTTAAAATAAAATAACCTAA
1 AATTTAAAATAAAATAACCTAA
* *
3342001 AATTT-AACTAAAATAACTTAA
1 AATTTAAAATAAAATAACCTAA
3342022 A
1 A
3342023 TTAATCACTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.61, C:0.09, G:0.00, T:0.30
Consensus pattern (22 bp):
AATTTAAAATAAAATAACCTAA
Found at i:3352313 original size:21 final size:21
Alignment explanation
Indices: 3352266--3352316 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
3352256 CATTACATAT
**
3352266 CTGGTTTTTAGGCATTTTGTAA
1 CTGG-TTTTAGGCATTCCGTAA
* *
3352288 TTGGTTTTAGGCATTCCGTGA
1 CTGGTTTTAGGCATTCCGTAA
3352309 CTGGTTTT
1 CTGGTTTT
3352317 TAAGAATTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 21 0.88
22 3 0.12
ACGTcount: A:0.14, C:0.12, G:0.25, T:0.49
Consensus pattern (21 bp):
CTGGTTTTAGGCATTCCGTAA
Found at i:3352447 original size:22 final size:22
Alignment explanation
Indices: 3352416--3352535 Score: 91
Period size: 22 Copynumber: 5.5 Consensus size: 22
3352406 CATATCAACC
*
3352416 AATCATGCAATACTTAAAAACT
1 AATCACGCAATACTTAAAAACT
* ** *
3352438 AATCACGCAATGC--CCAAAGT
1 AATCACGCAATACTTAAAAACT
* *
3352458 AAATCAAGCAATACTTAAAAATT
1 -AATCACGCAATACTTAAAAACT
* * *
3352481 GATCACACAATACTTAAAAATT
1 AATCACGCAATACTTAAAAACT
** *
3352503 GGTCATGCAATACTTAAAAACT
1 AATCACGCAATACTTAAAAACT
*
3352525 AGTCACGCAAT
1 AATCACGCAAT
3352536 GCCCAAAGTC
Statistics
Matches: 76, Mismatches: 19, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
20 4 0.05
21 11 0.14
22 57 0.75
23 4 0.05
ACGTcount: A:0.47, C:0.20, G:0.09, T:0.24
Consensus pattern (22 bp):
AATCACGCAATACTTAAAAACT
Found at i:3352469 original size:43 final size:43
Alignment explanation
Indices: 3352416--3352571 Score: 141
Period size: 43 Copynumber: 3.6 Consensus size: 43
3352406 CATATCAACC
3352416 AATCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTA
1 AATCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTA
* * * * * ** * *
3352459 AATCAAGCAATACTTAAAAATTGATCACACAATACTTAAAAATT
1 AATCATGCAATACTTAAAAACTAATCACGCAATGC-CCAAAGTA
** * *
3352503 GGTCATGCAATACTTAAAAACTAGTCACGCAATGCCCAAAGTC
1 AATCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTA
* * * * *
3352546 AGTCACGCAATGCCTAAAAACCAATC
1 AATCATGCAATACTTAAAAACTAATC
3352572 CCACAATGTT
Statistics
Matches: 85, Mismatches: 27, Indels: 2
0.75 0.24 0.02
Matches are distributed among these distances:
43 54 0.64
44 31 0.36
ACGTcount: A:0.45, C:0.23, G:0.10, T:0.22
Consensus pattern (43 bp):
AATCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTA
Found at i:3352588 original size:87 final size:87
Alignment explanation
Indices: 3352418--3352578 Score: 232
Period size: 87 Copynumber: 1.9 Consensus size: 87
3352408 TATCAACCAA
* ***
3352418 TCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTAAATCAAGCAATACTTAAAAATTGA
1 TCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTAAATCAAGCAATACCTAAAAACCAA
3352483 TCACACAATACTTAAAAATTGG
66 TCACACAATACTTAAAAATTGG
* * * * *
3352505 TCATGCAATACTTAAAAACTAGTCACGCAATGCCCAAAGTCAGTCACGCAATGCCTAAAAACCAA
1 TCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTAAATCAAGCAATACCTAAAAACCAA
*
3352570 TCCCACAAT
66 TCACACAAT
3352579 GTTCAAAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
87 64 1.00
ACGTcount: A:0.44, C:0.24, G:0.10, T:0.22
Consensus pattern (87 bp):
TCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTAAATCAAGCAATACCTAAAAACCAA
TCACACAATACTTAAAAATTGG
Found at i:3352596 original size:87 final size:87
Alignment explanation
Indices: 3352417--3352596 Score: 227
Period size: 87 Copynumber: 2.1 Consensus size: 87
3352407 ATATCAACCA
* ***
3352417 ATCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTAAATCAAGCAATACTTAAAAATTG
1 ATCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTAAATCAAGCAATACCTAAAAACCA
*
3352482 ATCACACAATACTTAAAAATTG
66 ATCACACAATACTTAAAAATCG
* * * * * *
3352504 GTCATGCAATACTTAAAAACTAGTCACGCAATGCCCAAAGTCAGTCACGCAATGCCTAAAAACCA
1 ATCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTAAATCAAGCAATACCTAAAAACCA
* *
3352569 ATCCCACAAT-GTTCAAAAATCG
66 ATCACACAATACTT-AAAAATCG
3352591 ATCATG
1 ATCATG
3352597 TAAGGCCTAA
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
86 2 0.03
87 76 0.97
ACGTcount: A:0.44, C:0.23, G:0.11, T:0.22
Consensus pattern (87 bp):
ATCATGCAATACTTAAAAACTAATCACGCAATGCCCAAAGTAAATCAAGCAATACCTAAAAACCA
ATCACACAATACTTAAAAATCG
Found at i:3358912 original size:9 final size:9
Alignment explanation
Indices: 3358898--3358935 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
3358888 GCCCAAAGTT
3358898 TTTTTTTTA
1 TTTTTTTTA
3358907 TTTTTTTTA
1 TTTTTTTTA
**
3358916 -TTTCCTTA
1 TTTTTTTTA
3358924 TTTTTTTTA
1 TTTTTTTTA
3358933 TTT
1 TTT
3358936 CATAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
8 6 0.25
9 18 0.75
ACGTcount: A:0.11, C:0.05, G:0.00, T:0.84
Consensus pattern (9 bp):
TTTTTTTTA
Found at i:3358926 original size:17 final size:17
Alignment explanation
Indices: 3358904--3358936 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
3358894 AGTTTTTTTT
3358904 TTATTTTTTTTATTTCC
1 TTATTTTTTTTATTTCC
3358921 TTATTTTTTTTATTTC
1 TTATTTTTTTTATTTC
3358937 ATAATCATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.12, C:0.09, G:0.00, T:0.79
Consensus pattern (17 bp):
TTATTTTTTTTATTTCC
Found at i:3363836 original size:59 final size:59
Alignment explanation
Indices: 3363689--3363964 Score: 363
Period size: 60 Copynumber: 4.6 Consensus size: 59
3363679 GGCATTTCAC
* * *
3363689 TTTTTAAGTCGAGCCTATTTTGAGATAGGTCGAGCCTAGAACAAGTCTAAGAATTTTTAA
1 TTTTTAAGTCGAACCTGTTTTGAGATAGGTCGAGCCTAGAACAAGTCTAA-AAATTTTAA
* * * * *
3363749 TTTTTAAGTCGAACCTGTTTTGAAATAGGTCAAGCCTATAACAAGTCTGAGAATTTTAA
1 TTTTTAAGTCGAACCTGTTTTGAGATAGGTCGAGCCTAGAACAAGTCTAAAAATTTTAA
* * *
3363808 TTTTTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGAACAAGTATAAAAATTTCAA
1 TTTTTAAGTCGAACCTGTTTTGAGATAGGTCGAGCCTAGAACAAGTCTAAAAATTTTAA
* * * * *
3363867 TTTTTAAATTTGAACCTGTTTTAAGATAGGTCGAGCCTAGATCAAGTCTGAAAATTTTAA
1 TTTTT-AAGTCGAACCTGTTTTGAGATAGGTCGAGCCTAGAACAAGTCTAAAAATTTTAA
* * *
3363927 TTTTTAAGTTGAACTTGTTTTGAGATAGGTCAAGCCTA
1 TTTTTAAGTCGAACCTGTTTTGAGATAGGTCGAGCCTA
3363965 AGAATTTCAT
Statistics
Matches: 188, Mismatches: 27, Indels: 3
0.86 0.12 0.01
Matches are distributed among these distances:
59 92 0.49
60 96 0.51
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (59 bp):
TTTTTAAGTCGAACCTGTTTTGAGATAGGTCGAGCCTAGAACAAGTCTAAAAATTTTAA
Found at i:3363904 original size:119 final size:119
Alignment explanation
Indices: 3363689--3363964 Score: 385
Period size: 119 Copynumber: 2.3 Consensus size: 119
3363679 GGCATTTCAC
* * * * *
3363689 TTTTTAAGTCGAGCCTATTTTGAGATAGGTCGAGCCTAGAACAAGTCTAAGAATTTTTAATTTTT
1 TTTTTAAGTCGAACCTGTTTTGAGATAGGTCGAGCCTAGAACAAGTATAAGAAATTTCAATTTTT
* *
3363754 AAGTCGAACCTGTTTTGAAATAGGTCAAGCCTATAACAAGTCTGAGAATTTTAA
66 AAGTCGAACCTGTTTTGAAATAGGTCAAGCCTAGAACAAGTCTGAAAATTTTAA
*
3363808 TTTTTAAATCGAACCTGTTTTGAGATAGGTCGAGCCTAGAACAAGTATAA-AAATTTCAATTTTT
1 TTTTTAAGTCGAACCTGTTTTGAGATAGGTCGAGCCTAGAACAAGTATAAGAAATTTCAATTTTT
* * * *
3363872 AAATTTGAACCTGTTTT-AAGATAGGTCGAGCCTAGATCAAGTCTGAAAATTTTAA
66 -AAGTCGAACCTGTTTTGAA-ATAGGTCAAGCCTAGAACAAGTCTGAAAATTTTAA
* * *
3363927 TTTTTAAGTTGAACTTGTTTTGAGATAGGTCAAGCCTA
1 TTTTTAAGTCGAACCTGTTTTGAGATAGGTCGAGCCTA
3363965 AGAATTTCAT
Statistics
Matches: 139, Mismatches: 16, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
118 14 0.10
119 125 0.90
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (119 bp):
TTTTTAAGTCGAACCTGTTTTGAGATAGGTCGAGCCTAGAACAAGTATAAGAAATTTCAATTTTT
AAGTCGAACCTGTTTTGAAATAGGTCAAGCCTAGAACAAGTCTGAAAATTTTAA
Found at i:3366295 original size:18 final size:18
Alignment explanation
Indices: 3366272--3366308 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3366262 TTGAATTGAT
3366272 TAGGTAATTTAGAGAGAA
1 TAGGTAATTTAGAGAGAA
3366290 TAGGTAATTTAGAGAGAA
1 TAGGTAATTTAGAGAGAA
3366308 T
1 T
3366309 CTACAAAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (18 bp):
TAGGTAATTTAGAGAGAA
Found at i:3370804 original size:59 final size:59
Alignment explanation
Indices: 3370671--3371058 Score: 388
Period size: 59 Copynumber: 6.7 Consensus size: 59
3370661 AATTTGTTGT
* * *
3370671 TCTAGGCTTGACCTATCTTAAAACAGGTTCGACTTCAAAAATTGAAAACTTCT-AGACTTGA
1 TCTAGGCTCGACCTATCTCAAAACAGGTTCGA-TTTAAAAATT-AAAA-TTCTCAGACTTGA
*
3370732 TCTAGGCTCGACCTATCTCAAAACAGATTCGATTTAAAAATTAAAATTCTCAGACTTGA
1 TCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTAAAATTCTCAGACTTGA
* * * *
3370791 TCTAGGCTTGACCTATCTCAAAATAGGTTCGAATTAAAAA-T----TTCT-AGACTTGT
1 TCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTAAAATTCTCAGACTTGA
* * *
3370844 TCTAGGCTCGACCTATCTCAAAATAGGTTCGACTTT--AAA--AAAATTCTTAGACTTGT
1 TCTAGGCTCGACCTATCTCAAAACAGGTTCGA-TTTAAAAATTAAAATTCTCAGACTTGA
* * * ** * *
3370900 TCTAGGCTCGACCTATCTCAAAATAGGTTTGACTCCAAAATTGAAATTC-CTAGGCTTGA
1 TCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTAAAATTCTC-AGACTTGA
* * * *
3370959 TCTAGGCTTGACCTATTTCAAAACAGGTTCGATTTAGAAATTAAAAATT-TCTAGACTTGT
1 TCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATT-AAAATTCTC-AGACTTGA
* * * *
3371019 TCTAAGCTCGACCTATCTCAAAATAGGCTCGACTTAAAAA
1 TCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAA
3371059 GTGAAATGCT
Statistics
Matches: 277, Mismatches: 36, Indels: 29
0.81 0.11 0.08
Matches are distributed among these distances:
52 3 0.01
53 38 0.14
54 6 0.02
55 5 0.02
56 39 0.14
57 3 0.01
58 5 0.02
59 94 0.34
60 55 0.20
61 29 0.10
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (59 bp):
TCTAGGCTCGACCTATCTCAAAACAGGTTCGATTTAAAAATTAAAATTCTCAGACTTGA
Found at i:3370849 original size:53 final size:53
Alignment explanation
Indices: 3370770--3371058 Score: 267
Period size: 53 Copynumber: 5.2 Consensus size: 53
3370760 TCGATTTAAA
* *
3370770 AATT-AAAA-TTCTCAGACTTGATCTAGGCTTGACCTATCTCAAAATAGGTTCG
1 AATTAAAAATTTCT-AGACTTGTTCTAGGCTCGACCTATCTCAAAATAGGTTCG
3370822 AATTAAAAATTTCTAGACTTGTTCTAGGCTCGACCTATCTCAAAATAGGTTCG
1 AATTAAAAATTTCTAGACTTGTTCTAGGCTCGACCTATCTCAAAATAGGTTCG
* * *
3370875 ACTTTAAAAAAATTCTTAGACTTGTTCTAGGCTCGACCTATCTCAAAATAGGTTTG
1 A-ATT-AAAAATTTC-TAGACTTGTTCTAGGCTCGACCTATCTCAAAATAGGTTCG
* * * * * * * *
3370931 ACTCCAAAATTGAAATTCCTAGGCTTGATCTAGGCTTGACCTATTTCAAAACAGGTTCGATTTAG
1 AAT---TAA---AAATTTCTAGACTTGTTCTAGGCTCGACCTATCTCAAAATAGGTTC------G
* *
3370996 AAATTAAAAATTTCTAGACTTGTTCTAAGCTCGACCTATCTCAAAATAGGCTCG
1 -AATTAAAAATTTCTAGACTTGTTCTAGGCTCGACCTATCTCAAAATAGGTTCG
*
3371050 ACTTAAAAA
1 AATTAAAAA
3371059 GTGAAATGCT
Statistics
Matches: 193, Mismatches: 26, Indels: 35
0.76 0.10 0.14
Matches are distributed among these distances:
52 4 0.02
53 50 0.26
54 7 0.04
55 9 0.05
56 40 0.21
57 2 0.01
59 33 0.17
60 43 0.22
63 2 0.01
65 1 0.01
66 2 0.01
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (53 bp):
AATTAAAAATTTCTAGACTTGTTCTAGGCTCGACCTATCTCAAAATAGGTTCG
Found at i:3370960 original size:168 final size:170
Alignment explanation
Indices: 3370667--3371058 Score: 488
Period size: 168 Copynumber: 2.3 Consensus size: 170
3370657 GAATAATTTG
* * * *
3370667 TTGTTCTAGGCTTGACCTATCTTAAAACAGGTTCGACTTCAAAAATTGAAAACTTCTAGACTTGA
1 TTGTTCTAGGCTCGACCTATCTCAAAATAGGTTCGACTT--TAAA---AAAACTTCTAGACTTGA
* *
3370732 TCTAGGCTCGACCTATCTCAAAACAGATTCGATTTAAAAATTAAAATTCTCAGACTTGATCTAGG
61 TCTAGGCTCGACCTATCTCAAAACAGATTCGACTCAAAAATTAAAATTCTCAGACTTGATCTAGG
*
3370797 CTTGACCTATCTCAAAATAGGTTC-G-AATTAAAAATTTCTAGAC
126 CTTGACCTATCTCAAAACAGGTTCTGAAATTAAAAATTTCTAGAC
*
3370840 TTGTTCTAGGCTCGACCTATCTCAAAATAGGTTCGACTTTAAAAAAA-TTCTTAGACTTGTTCTA
1 TTGTTCTAGGCTCGACCTATCTCAAAATAGGTTCGACTTTAAAAAAACTTC-TAGACTTGATCTA
* * * * * *
3370904 GGCTCGACCTATCTCAAAATAGGTTTGACTCCAAAATTGAAATTC-CTAGGCTTGATCTAGGCTT
65 GGCTCGACCTATCTCAAAACAGATTCGACTCAAAAATTAAAATTCTC-AGACTTGATCTAGGCTT
*
3370968 GACCTATTTCAAAACAGGTTCGATTTAGAAATTAAAAATTTCTAGAC
129 GACCTATCTCAAAACAGGTTC----T-GAAATTAAAAATTTCTAGAC
* *
3371015 TTGTTCTAAGCTCGACCTATCTCAAAATAGGCTCGAC-TTAAAAA
1 TTGTTCTAGGCTCGACCTATCTCAAAATAGGTTCGACTTTAAAAA
3371059 GTGAAATGCT
Statistics
Matches: 193, Mismatches: 17, Indels: 17
0.85 0.07 0.07
Matches are distributed among these distances:
167 4 0.02
168 89 0.46
171 3 0.02
173 36 0.19
174 8 0.04
175 53 0.27
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Consensus pattern (170 bp):
TTGTTCTAGGCTCGACCTATCTCAAAATAGGTTCGACTTTAAAAAAACTTCTAGACTTGATCTAG
GCTCGACCTATCTCAAAACAGATTCGACTCAAAAATTAAAATTCTCAGACTTGATCTAGGCTTGA
CCTATCTCAAAACAGGTTCTGAAATTAAAAATTTCTAGAC
Found at i:3378812 original size:21 final size:21
Alignment explanation
Indices: 3378786--3378845 Score: 66
Period size: 21 Copynumber: 2.8 Consensus size: 21
3378776 CATAACTGAT
*
3378786 TTTTAGGCATTATGTGATTGG
1 TTTTAGGCATTACGTGATTGG
* *
3378807 TTTTAGGTATTGCGTGATTGG
1 TTTTAGGCATTACGTGATTGG
* *
3378828 TTTTTAAGCATTGCGTGA
1 -TTTTAGGCATTACGTGA
3378846 CTAATTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
21 18 0.55
22 15 0.45
ACGTcount: A:0.18, C:0.07, G:0.28, T:0.47
Consensus pattern (21 bp):
TTTTAGGCATTACGTGATTGG
Found at i:3378840 original size:22 final size:22
Alignment explanation
Indices: 3378785--3378859 Score: 71
Period size: 22 Copynumber: 3.5 Consensus size: 22
3378775 GCATAACTGA
* **
3378785 TTTTTAGGCATTATGTGATTGG
1 TTTTTAAGCATTGCGTGATTGG
* *
3378807 -TTTTAGGTATTGCGTGATTGG
1 TTTTTAAGCATTGCGTGATTGG
* **
3378828 TTTTTAAGCATTGCGTGACTAA
1 TTTTTAAGCATTGCGTGATTGG
3378850 TTTTTAAGCA
1 TTTTTAAGCA
3378860 ATATTTAAGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
21 18 0.41
22 26 0.59
ACGTcount: A:0.21, C:0.08, G:0.24, T:0.47
Consensus pattern (22 bp):
TTTTTAAGCATTGCGTGATTGG
Found at i:3378932 original size:22 final size:23
Alignment explanation
Indices: 3378904--3378957 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
3378894 ATGCCTTACT
*
3378904 AACTAGTCACCCAATA-CTTATC
1 AACTAGTCACCCAATATCATATC
* *
3378926 AATTAGTCACGCAATATCATATC
1 AACTAGTCACCCAATATCATATC
3378949 AACTAGTCA
1 AACTAGTCA
3378958 TGCAATATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.39, C:0.26, G:0.07, T:0.28
Consensus pattern (23 bp):
AACTAGTCACCCAATATCATATC
Found at i:3378955 original size:23 final size:23
Alignment explanation
Indices: 3378904--3378965 Score: 81
Period size: 23 Copynumber: 2.7 Consensus size: 23
3378894 ATGCCTTACT
* *
3378904 AACTAGTCACCCAATA-CTTATC
1 AACTAGTCACGCAATATCATATC
*
3378926 AATTAGTCACGCAATATCATATC
1 AACTAGTCACGCAATATCATATC
*
3378949 AACTAGTCATGCAATAT
1 AACTAGTCACGCAATAT
3378966 TGAAAAATTA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
22 14 0.41
23 20 0.59
ACGTcount: A:0.39, C:0.24, G:0.08, T:0.29
Consensus pattern (23 bp):
AACTAGTCACGCAATATCATATC
Found at i:3382911 original size:20 final size:20
Alignment explanation
Indices: 3382882--3382920 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3382872 AGTTGTAGGT
3382882 ATTATAGACAGAATTCATCC
1 ATTATAGACAGAATTCATCC
*
3382902 ATTATTGACAGAATTCATC
1 ATTATAGACAGAATTCATC
3382921 AGTTACCAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (20 bp):
ATTATAGACAGAATTCATCC
Found at i:3383595 original size:21 final size:20
Alignment explanation
Indices: 3383556--3383595 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3383546 TTTCTTTAAA
**
3383556 AAATATATAAAAATTTAATT
1 AAATATATAAAAAAATAATT
3383576 AAATATAATAAAAAAATAAT
1 AAATAT-ATAAAAAAATAAT
3383596 AATTTATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATATATAAAAAAATAATT
Found at i:3386392 original size:38 final size:38
Alignment explanation
Indices: 3386343--3386418 Score: 134
Period size: 38 Copynumber: 2.0 Consensus size: 38
3386333 ACAAATAAAT
*
3386343 AACAAACCAACTTAAATTTGCTCCACCACCTGGTTGCA
1 AACAAACCAACTTAAATTTGCTCCACCACCTGCTTGCA
*
3386381 AACAAACCAACTTATATTTGCTCCACCACCTGCTTGCA
1 AACAAACCAACTTAAATTTGCTCCACCACCTGCTTGCA
3386419 TTTATGCGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 36 1.00
ACGTcount: A:0.33, C:0.33, G:0.09, T:0.25
Consensus pattern (38 bp):
AACAAACCAACTTAAATTTGCTCCACCACCTGCTTGCA
Found at i:3388595 original size:20 final size:20
Alignment explanation
Indices: 3388570--3388618 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
3388560 TTTCGGCGCC
3388570 TCTTTCTCTCTCTTTCTTTT
1 TCTTTCTCTCTCTTTCTTTT
*
3388590 TCTTTCTCTCTCTTTTTTTT
1 TCTTTCTCTCTCTTTCTTTT
3388610 TCTTTCTCT
1 TCTTTCTCT
3388619 TTTGTCATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (20 bp):
TCTTTCTCTCTCTTTCTTTT
Found at i:3388597 original size:16 final size:16
Alignment explanation
Indices: 3388572--3388621 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
3388562 TCGGCGCCTC
*
3388572 TTTCTCTCTCTTTCTT
1 TTTCTTTCTCTTTCTT
*
3388588 TTTCTTTCTCTCTCTT
1 TTTCTTTCTCTTTCTT
3388604 TTT-TTT-TCTTTCTCT
1 TTTCTTTCTCTTTCT-T
3388619 TTT
1 TTT
3388622 GTCATTTCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 6 0.20
15 7 0.23
16 17 0.57
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTCTTTCTCTTTCTT
Found at i:3393927 original size:23 final size:23
Alignment explanation
Indices: 3393897--3393942 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
3393887 TAGAATAGCG
3393897 TATGATCCAATACACTTAGTTAT
1 TATGATCCAATACACTTAGTTAT
3393920 TATGATCCAATACACTTAGTTAT
1 TATGATCCAATACACTTAGTTAT
3393943 GTAAGTGGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.39
Consensus pattern (23 bp):
TATGATCCAATACACTTAGTTAT
Found at i:3399713 original size:16 final size:16
Alignment explanation
Indices: 3399692--3399740 Score: 52
Period size: 16 Copynumber: 3.3 Consensus size: 16
3399682 TAACAAATAA
3399692 ATAAATTACATCAAAC
1 ATAAATTACATCAAAC
*
3399708 ATAAA-TA-AGC-AA-
1 ATAAATTACATCAAAC
*
3399720 ATACATTACATCAAAC
1 ATAAATTACATCAAAC
3399736 ATAAA
1 ATAAA
3399741 CAAAATTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
12 4 0.16
13 4 0.16
14 4 0.16
15 4 0.16
16 9 0.36
ACGTcount: A:0.59, C:0.16, G:0.02, T:0.22
Consensus pattern (16 bp):
ATAAATTACATCAAAC
Found at i:3399713 original size:24 final size:25
Alignment explanation
Indices: 3399686--3399746 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 25
3399676 AACATATAAC
3399686 AAAT-AAATAAATTACATCAAACAT
1 AAATAAAATAAATTACATCAAACAT
*
3399710 AAATAAGCAAATACATTACATCAAACAT
1 AAAT-A--AAATAAATTACATCAAACAT
*
3399738 AAACAAAAT
1 AAATAAAAT
3399747 TTCAAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
24 4 0.13
25 4 0.13
27 1 0.03
28 22 0.71
ACGTcount: A:0.62, C:0.15, G:0.02, T:0.21
Consensus pattern (25 bp):
AAATAAAATAAATTACATCAAACAT
Found at i:3411824 original size:18 final size:18
Alignment explanation
Indices: 3411794--3411844 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 18
3411784 AAGTATTAAT
3411794 TATTTTTTAATTTATGAA-A
1 TATTTTTT-ATTTAT-AACA
3411813 TATTTTTTATTTATAACA
1 TATTTTTTATTTATAACA
3411831 T-TTTTATTATTTAT
1 TATTTT-TTATTTAT
3411845 TTTACTATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
17 6 0.20
18 16 0.53
19 8 0.27
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (18 bp):
TATTTTTTATTTATAACA
Found at i:3414205 original size:72 final size:72
Alignment explanation
Indices: 3414106--3414243 Score: 177
Period size: 72 Copynumber: 1.9 Consensus size: 72
3414096 AATAATCATC
* * * * **
3414106 AGCTCTCTCAACTCTCTAAACTGTATTAGCTTTATCAATTCTTTGATGAGCACCATTGTCATCAT
1 AGCTCTCTCAACTCACTAAACTATATTAGCTCTATCAACTCTTTGATGAGCACCATCATCATCAT
3414171 GTCTCTT
66 GTCTCTT
* * * * *
3414178 AGCTTTCTCATCTCACTGAACTATATTAGCTCTGTCAACTCTTTGTTGAGCACCATCATCATCAT
1 AGCTCTCTCAACTCACTAAACTATATTAGCTCTATCAACTCTTTGATGAGCACCATCATCATCAT
3414243 G
66 G
3414244 CTATGGTCTA
Statistics
Matches: 55, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
72 55 1.00
ACGTcount: A:0.24, C:0.26, G:0.12, T:0.38
Consensus pattern (72 bp):
AGCTCTCTCAACTCACTAAACTATATTAGCTCTATCAACTCTTTGATGAGCACCATCATCATCAT
GTCTCTT
Found at i:3417772 original size:8 final size:9
Alignment explanation
Indices: 3417754--3417778 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3417744 ATATTATGAG
3417754 TTTTTATTT
1 TTTTTATTT
3417763 TTTTTATTT
1 TTTTTATTT
3417772 TTTTTAT
1 TTTTTAT
3417779 AGATATATTA
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTTTATTT
Found at i:3418237 original size:76 final size:76
Alignment explanation
Indices: 3418141--3418511 Score: 444
Period size: 76 Copynumber: 4.9 Consensus size: 76
3418131 CACACCACAC
* * * * *
3418141 TTGTTAGATGTTGTTGACATCTTGTGGTGACATGGTGACTCATTGCAGTATTATGGGGTGACATG
1 TTGTTAGATGTCGTTGACATCTTGTGGTGACACGTTGAGTCGTTGCAGTATTATGGGGTGACATG
3418206 CCACGCT-TCAA
66 CCACGCTCT-AA
* *
3418217 TTGTTAGATGTCGTTGACATCTTGTGGTGACACGTTGAGTGGTTGCAGTATTATAGGGTGACATG
1 TTGTTAGATGTCGTTGACATCTTGTGGTGACACGTTGAGTCGTTGCAGTATTATGGGGTGACATG
* *
3418282 TCACGCTTTAA
66 CCACGCTCTAA
* * * * * *
3418293 TTGTAAGATGTCATTGACATCTTATGATGACACGTTGAGTTGTTGCAGTATTATGGGTTGACATG
1 TTGTTAGATGTCGTTGACATCTTGTGGTGACACGTTGAGTCGTTGCAGTATTATGGGGTGACATG
*
3418358 CCACACTCTAA
66 CCACGCTCTAA
* * *
3418369 TTGTTAAATATCGTTGACATCTTGTGGTGACACGTTGAGTCGTTACAGTATTATGGGGTGACACT
1 TTGTTAGATGTCGTTGACATCTTGTGGTGACACGTTGAGTCGTTGCAGTATTATGGGGTGACA-T
* * *
3418434 -TCATGCTCTGA
65 GCCACGCTCTAA
* * * * * *
3418445 TTGTTTGATGTTGTTGAAATCTTGTGGTGGCATGTTGAGTCGTTGCAATATTAT--GGTGACATG
1 TTGTTAGATGTCGTTGACATCTTGTGGTGACACGTTGAGTCGTTGCAGTATTATGGGGTGACATG
3418508 CCAC
66 CCAC
3418512 ACTTGTTAAA
Statistics
Matches: 250, Mismatches: 42, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
73 1 0.00
74 9 0.04
76 238 0.95
77 2 0.01
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (76 bp):
TTGTTAGATGTCGTTGACATCTTGTGGTGACACGTTGAGTCGTTGCAGTATTATGGGGTGACATG
CCACGCTCTAA
Found at i:3421742 original size:31 final size:31
Alignment explanation
Indices: 3421706--3421820 Score: 95
Period size: 31 Copynumber: 3.5 Consensus size: 31
3421696 AGAAAGAAAT
*
3421706 AAATGTTGTTACACGTTATGCATACCAAGTG
1 AAATGTTGTTACACGTTATGCATACCAAGTA
* *
3421737 AAATGTTGTTACATGTTAACACGCTAAGCATACCAAGCA
1 AAATGTTGTTACACGTT---A---T--GCATACCAAGTA
* * *
3421776 AAATGTTGTTACACGCTAAGCATACCAAGTC
1 AAATGTTGTTACACGTTATGCATACCAAGTA
*
3421807 AAATATTGTTACAC
1 AAATGTTGTTACAC
3421821 ACCAATGCTG
Statistics
Matches: 67, Mismatches: 9, Indels: 16
0.73 0.10 0.17
Matches are distributed among these distances:
31 39 0.58
34 1 0.01
36 1 0.01
37 1 0.01
39 25 0.37
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.29
Consensus pattern (31 bp):
AAATGTTGTTACACGTTATGCATACCAAGTA
Found at i:3421759 original size:39 final size:38
Alignment explanation
Indices: 3421712--3421788 Score: 109
Period size: 39 Copynumber: 2.0 Consensus size: 38
3421702 AAATAAATGT
* * **
3421712 TGTTACACGTTATGCATACCAAGTGAAATGTTGTTACA
1 TGTTACACGCTAAGCATACCAAGCAAAATGTTGTTACA
3421750 TGTTAACACGCTAAGCATACCAAGCAAAATGTTGTTACA
1 TGTT-ACACGCTAAGCATACCAAGCAAAATGTTGTTACA
3421789 CGCTAAGCAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
38 4 0.12
39 30 0.88
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (38 bp):
TGTTACACGCTAAGCATACCAAGCAAAATGTTGTTACA
Found at i:3421840 original size:23 final size:25
Alignment explanation
Indices: 3421813--3421873 Score: 63
Period size: 26 Copynumber: 2.5 Consensus size: 25
3421803 AGTCAAATAT
*
3421813 TGTTA-CACAC-CAATGCTGAGCCA
1 TGTTATCACACGCAACGCTGAGCCA
*
3421836 TGTTATGACACGTCAACGCTGAGCCA
1 TGTTATCACACG-CAACGCTGAGCCA
* *
3421862 TGTCATGACACG
1 TGTTATCACACG
3421874 TAATCATACT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.16
24 4 0.12
26 23 0.72
ACGTcount: A:0.28, C:0.28, G:0.21, T:0.23
Consensus pattern (25 bp):
TGTTATCACACGCAACGCTGAGCCA
Found at i:3422542 original size:23 final size:23
Alignment explanation
Indices: 3422510--3422573 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
3422500 TTTTTCTATT
*
3422510 TCAAGCCATGGCGTGTCACATAC
1 TCAAGCCATGGTGTGTCACATAC
*
3422533 TCAAGACATGGTGTGTCACATAC
1 TCAAGCCATGGTGTGTCACATAC
3422556 TCAAGCCATGGTGTGTCA
1 TCAAGCCATGGTGTGTCA
3422574 TAAATTCTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (23 bp):
TCAAGCCATGGTGTGTCACATAC
Found at i:3422611 original size:46 final size:46
Alignment explanation
Indices: 3422561--3422734 Score: 172
Period size: 46 Copynumber: 3.8 Consensus size: 46
3422551 CATACTCAAG
* *
3422561 CCATGGTGTGTCATAAATTCTCACCACGCCATGTCACACATTCTCA
1 CCATGGTGTGTCACAAATTCTCACCATGCCATGTCACACATTCTCA
* * * * * * *
3422607 CCATGCTGTGTCATACATTCTTACTATGCCGTCTCACACAATT-TCA
1 CCATGGTGTGTCACAAATTCTCACCATGCCATGTCACAC-ATTCTCA
* *** *
3422653 ACAT-GTGTGTCACAAATTCTCACCATGGTGTGTCACACATTCCCA
1 CCATGGTGTGTCACAAATTCTCACCATGCCATGTCACACATTCTCA
* *
3422698 CCATGGTGTGTCACAAACTCTAAACCATGCCATGTCA
1 CCATGGTGTGTCACAAATTCT-CACCATGCCATGTCA
3422735 TAGTCGTGTC
Statistics
Matches: 101, Mismatches: 23, Indels: 7
0.77 0.18 0.05
Matches are distributed among these distances:
44 3 0.03
45 31 0.31
46 53 0.52
47 14 0.14
ACGTcount: A:0.26, C:0.30, G:0.14, T:0.29
Consensus pattern (46 bp):
CCATGGTGTGTCACAAATTCTCACCATGCCATGTCACACATTCTCA
Found at i:3422635 original size:23 final size:23
Alignment explanation
Indices: 3422561--3422712 Score: 137
Period size: 23 Copynumber: 6.7 Consensus size: 23
3422551 CATACTCAAG
* * *
3422561 CCATGGTGTGTCATAAATTCTCA
1 CCATGCTGTGTCACACATTCTCA
* **
3422584 CCACGCCATGTCACACATTCTCA
1 CCATGCTGTGTCACACATTCTCA
* *
3422607 CCATGCTGTGTCATACATTCTTA
1 CCATGCTGTGTCACACATTCTCA
* * *
3422630 CTATGCCGTCTCACACAATT-TCA
1 CCATGCTGTGTCACAC-ATTCTCA
* *
3422653 ACATG-TGTGTCACAAATTCTCA
1 CCATGCTGTGTCACACATTCTCA
* *
3422675 CCATGGTGTGTCACACATTCCCA
1 CCATGCTGTGTCACACATTCTCA
*
3422698 CCATGGTGTGTCACA
1 CCATGCTGTGTCACA
3422713 AACTCTAAAC
Statistics
Matches: 102, Mismatches: 24, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
21 3 0.03
22 14 0.14
23 82 0.80
24 3 0.03
ACGTcount: A:0.25, C:0.30, G:0.14, T:0.30
Consensus pattern (23 bp):
CCATGCTGTGTCACACATTCTCA
Found at i:3422848 original size:104 final size:104
Alignment explanation
Indices: 3422662--3422849 Score: 286
Period size: 104 Copynumber: 1.8 Consensus size: 104
3422652 AACATGTGTG
* * * * *
3422662 TCACAAATTCTCACCATGGTGTGTCACACATTCCCACCATGGTGTGTCACAAACTCTAAACCATG
1 TCACAAATTCTCACCATGCTGTGTCACACAATCCCACCATGGCGTGCCACAAACTCTAAACCATA
*
3422727 CCATGTCATAGTCGTGTCATAGATTTTTACCATGCCATC
66 CCATGTCACAGTCGTGTCATAGATTTTTACCATGCCATC
* *
3422766 TCACAAATTCTCACCATGCTGTGTCACATAATCCCACCATGGCGTGCCACAAACTCTAAACCCTA
1 TCACAAATTCTCACCATGCTGTGTCACACAATCCCACCATGGCGTGCCACAAACTCTAAACCATA
* *
3422831 CCGTGTCACAGTTGTGTCA
66 CCATGTCACAGTCGTGTCA
3422850 CATACTCTCA
Statistics
Matches: 74, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
104 74 1.00
ACGTcount: A:0.27, C:0.31, G:0.14, T:0.28
Consensus pattern (104 bp):
TCACAAATTCTCACCATGCTGTGTCACACAATCCCACCATGGCGTGCCACAAACTCTAAACCATA
CCATGTCACAGTCGTGTCATAGATTTTTACCATGCCATC
Found at i:3422887 original size:23 final size:23
Alignment explanation
Indices: 3422861--3422913 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
3422851 ATACTCTCAC
* * *
3422861 CATATTCACGCCATAGCGTGTCA
1 CATATTCACACCATAACATGTCA
*
3422884 CATATTCACATCATAACATGTCA
1 CATATTCACACCATAACATGTCA
3422907 CATATTC
1 CATATTC
3422914 CCTCCATGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.28, G:0.09, T:0.30
Consensus pattern (23 bp):
CATATTCACACCATAACATGTCA
Found at i:3422950 original size:23 final size:23
Alignment explanation
Indices: 3422924--3422982 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
3422914 CCTCCATGTT
* *
3422924 GTGTCATATATTTTGATCCTGCC
1 GTGTCATATATTCTGACCCTGCC
* *
3422947 GTGTCACATATTCTGACCCTGTC
1 GTGTCATATATTCTGACCCTGCC
3422970 GTGTCATATATTC
1 GTGTCATATATTC
3422983 CCTTCATAGC
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.41
Consensus pattern (23 bp):
GTGTCATATATTCTGACCCTGCC
Found at i:3423063 original size:23 final size:23
Alignment explanation
Indices: 3423031--3423089 Score: 64
Period size: 23 Copynumber: 2.6 Consensus size: 23
3423021 ATCAGCCGTG
* * *
3423031 TCACATATTCTCACAATGTTGCA
1 TCACACATTCCCACAATGTCGCA
* **
3423054 TCACACATTCCCACCATGTCGTG
1 TCACACATTCCCACAATGTCGCA
3423077 TCACACATTCCCA
1 TCACACATTCCCA
3423090 TCATGGCATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.36, G:0.08, T:0.29
Consensus pattern (23 bp):
TCACACATTCCCACAATGTCGCA
Found at i:3423103 original size:23 final size:23
Alignment explanation
Indices: 3423054--3423104 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
3423044 CAATGTTGCA
* *
3423054 TCACACATTCCCACCATGTCGTG
1 TCACACATTCCCACCATGGCATG
* *
3423077 TCACACATTCCCATCATGGCATT
1 TCACACATTCCCACCATGGCATG
3423100 TCACA
1 TCACA
3423105 AACTTTGAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.25, C:0.37, G:0.10, T:0.27
Consensus pattern (23 bp):
TCACACATTCCCACCATGGCATG
Found at i:3424021 original size:24 final size:24
Alignment explanation
Indices: 3423989--3424036 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
3423979 ATAAATTACT
3423989 TTTACTTTTGA-ATATTAATTATAA
1 TTTACTTTTGATATATTAA-TATAA
* *
3424013 TTTATTTTTGATTTATTAATATAA
1 TTTACTTTTGATATATTAATATAA
3424037 AAAATAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.58
Consensus pattern (24 bp):
TTTACTTTTGATATATTAATATAA
Found at i:3429823 original size:1 final size:1
Alignment explanation
Indices: 3429817--3429847 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
3429807 TATTTTGGCC
3429817 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3429848 GTCTATACAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:3444717 original size:28 final size:30
Alignment explanation
Indices: 3444672--3444727 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
3444662 ATTTGACTAA
3444672 AAATAAAAACATATAAAT-TTAATTAAAAG
1 AAATAAAAACATATAAATCTTAATTAAAAG
*
3444701 AAATAAAAGA-ATA-AAATCTTATTTAAA
1 AAATAAAA-ACATATAAATCTTAATTAAA
3444728 TATTTTTGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 4 0.17
29 19 0.79
30 1 0.04
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.29
Consensus pattern (30 bp):
AAATAAAAACATATAAATCTTAATTAAAAG
Found at i:3455798 original size:22 final size:20
Alignment explanation
Indices: 3455773--3455834 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
3455763 TTTCACTACT
*
3455773 TTTTAGGTATTGCGTGACTAG
1 TTTTATGTATTGCGTGACT-G
* *
3455794 ATTTTATATATTGTGTGACCTG
1 -TTTTATGTATTGCGTGA-CTG
3455816 TTGTTATGTATTGCGTGAC
1 TT-TTATGTATTGCGTGAC
3455835 ATTATGCCAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 3 0.09
22 28 0.85
23 2 0.06
ACGTcount: A:0.19, C:0.10, G:0.24, T:0.47
Consensus pattern (20 bp):
TTTTATGTATTGCGTGACTG
Found at i:3456184 original size:203 final size:203
Alignment explanation
Indices: 3455725--3456184 Score: 566
Period size: 203 Copynumber: 2.3 Consensus size: 203
3455715 ACTAGTGGTG
* * * * * * *
3455725 CGTGACTTGTGTAGTTCATCTCTTATTTTGAGG-TTATTTTTCACTACTTTTTAGGTATTGCGTG
1 CGTGACTTGTGTAATTCATCTCTTGTTTTGAGGCTT-TTGTTCACTAATTTTTAGATATTACATG
* * * *
3455789 ACTAGATTTTATATATTGTGTGACCTGTTGTTATGTATTGCGTGACATTATGCCAATACGTGACT
65 ACTAGATTTTATATATTGCGTGACATGTTGTTATGTATTGCGTGACATTAGGCCAATACGTAACT
* * *
3455854 GGTTATGTTGACATAATGTGAGTGGATATTAGGTATTGAGTGACTTATTATTTAGTATTGCGAGA
130 GGTTATGTTGACATAATGTGAGTGGATATTAGATATAGAGTGACTTATTATTTAGTATTACGAGA
* *
3455919 CTGGCGGTG
195 CTGGCCGTA
* * * * * *
3455928 TGTGACTTATGCAATTCATCTCTTGTTTTGAGGCTTTCGTTTATTAATTTTTAGATATTACATGA
1 CGTGACTTGTGTAATTCATCTCTTGTTTTGAGGCTTTTGTTCACTAATTTTTAGATATTACATGA
* * * * * *
3455993 CTAG-TTTTGATGTATTGCGTGACATGTTGTTATGTGTTGCGTGACATTGGGCTAGTACGTAATT
66 CTAGATTTT-ATATATTGCGTGACATGTTGTTATGTATTGCGTGACATTAGGCCAATACGTAACT
* * *
3456057 GGTTATGTTGGCATAGTGTGAGTGGATATTAGATATAGAGTGACTTATTA-TTAGGTATTATGAG
130 GGTTATGTTGACATAATGTGAGTGGATATTAGATATAGAGTGACTTATTATTTA-GTATTACGAG
*
3456121 ATTGGCCGTA
194 ACTGGCCGTA
* *
3456131 CGTGACTTGTGTAATTCATCTCTTGTTTTAAGGCTTTTGTTCACTAGTTTTTAG
1 CGTGACTTGTGTAATTCATCTCTTGTTTTGAGGCTTTTGTTCACTAATTTTTAG
3456185 GCATTGCATG
Statistics
Matches: 214, Mismatches: 40, Indels: 6
0.82 0.15 0.02
Matches are distributed among these distances:
202 7 0.03
203 205 0.96
204 2 0.01
ACGTcount: A:0.22, C:0.11, G:0.24, T:0.44
Consensus pattern (203 bp):
CGTGACTTGTGTAATTCATCTCTTGTTTTGAGGCTTTTGTTCACTAATTTTTAGATATTACATGA
CTAGATTTTATATATTGCGTGACATGTTGTTATGTATTGCGTGACATTAGGCCAATACGTAACTG
GTTATGTTGACATAATGTGAGTGGATATTAGATATAGAGTGACTTATTATTTAGTATTACGAGAC
TGGCCGTA
Found at i:3459970 original size:69 final size:69
Alignment explanation
Indices: 3459854--3460086 Score: 222
Period size: 69 Copynumber: 3.4 Consensus size: 69
3459844 CATATAAAAA
* * * * * * * *
3459854 AGTCACGCGATTCCAT-ATCAACTAGTAACACGATTCCATAATAACTACTCACGTGATTCCATAA
1 AGTCACGCGATTCCATAAT-AACTAGTAACGCCACTCCATATTTACTACTCACGCGACTCAAT-A
3459918 T-AA-T
64 TCAACT
* *
3459922 TGCTCACGCGATTCCATAATAACTAGTAATGCCACTCCATATTTACTACTCACGCGACTCAATAT
1 AG-TCACGCGATTCCATAATAACTAGTAACGCCACTCCATATTTACTACTCACGCGACTCAATAT
3459987 CAACT
65 CAACT
** ** * *
3459992 AGTCACGTAATTTTATAATAACTAGTAACGCCACTCTATATTTATTACTCACGAC-ACTCAATAT
1 AGTCACGCGATTCCATAATAACTAGTAACGCCACTCCATATTTACTACTCACG-CGACTCAATAT
3460056 CAACT
65 CAACT
* ***
3460061 AGTCACGTGATTTTTTAATAACTAGT
1 AGTCACGCGATTCCATAATAACTAGT
3460087 CACTCAATTC
Statistics
Matches: 140, Mismatches: 20, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
68 3 0.02
69 132 0.94
70 5 0.04
ACGTcount: A:0.34, C:0.24, G:0.10, T:0.31
Consensus pattern (69 bp):
AGTCACGCGATTCCATAATAACTAGTAACGCCACTCCATATTTACTACTCACGCGACTCAATATC
AACT
Found at i:3460119 original size:69 final size:69
Alignment explanation
Indices: 3459937--3460112 Score: 183
Period size: 69 Copynumber: 2.6 Consensus size: 69
3459927 ACGCGATTCC
* * * * *
3459937 ATAATAACTAGTAATGCCACTCCATATTTACTACTCACG-CGACTCAATATCAACTAGTCACGTA
1 ATAATAACTAGTAACGCAACTCCATAATAACTACTAACGAC-ACTCAATATCAACTAGTCACGTA
3460001 ATTTT
65 ATTTT
* * * * * * *
3460006 ATAATAACTAGTAACGCCACTCTATATTTATTACTCACGACACTCAATATCAACTAGTCACGTGA
1 ATAATAACTAGTAACGCAACTCCATAATAACTACTAACGACACTCAATATCAACTAGTCACGTAA
3460071 TTTT
66 TTTT
* * * * *
3460075 TTAATAACTAGTCACTCAATTCCATAATAACTATTAAC
1 ATAATAACTAGTAACGCAACTCCATAATAACTACTAAC
3460113 TTCACTCCAT
Statistics
Matches: 91, Mismatches: 15, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
69 90 0.99
70 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.07, T:0.33
Consensus pattern (69 bp):
ATAATAACTAGTAACGCAACTCCATAATAACTACTAACGACACTCAATATCAACTAGTCACGTAA
TTTT
Found at i:3460172 original size:92 final size:91
Alignment explanation
Indices: 3459856--3460178 Score: 256
Period size: 92 Copynumber: 3.5 Consensus size: 91
3459846 TATAAAAAAG
* * * * *
3459856 TCACGCGATTCCATATCAACTAGTAACACGATTCCATAATAACTACTCACGTGATTCCATAATAA
1 TCACGCGACTCAATATCAACTAGTCACACGATTCCATAATAACTAGTCACGTAATTCCATAATAA
* * * * * * * *
3459921 TTGCTCACGCGATTCCATAATAACTAG
66 CTACTAAC-CCACTCCATATTTACTAC
* * * * ** * * * * **
3459948 TAATGCCACTCCATATTTACTACTCACGCGACTCAAT-ATCAACTAGTCACGTAATTTTATAATA
1 TCACGCGACTCAATATCAACTAGTCACACGATTCCATAAT-AACTAGTCACGTAATTCCATAATA
* * *
3460012 ACTAGTAACGCCACTCTATATTTATTAC
65 ACTACTAAC-CCACTCCATATTTACTAC
** ***
3460040 TCACGAC-ACTCAATATCAACTAGTCACGTGATTTTTTAATAACTAGTCAC-TCAATTCCATAAT
1 TCACG-CGACTCAATATCAACTAGTCACACGATTCCATAATAACTAGTCACGT-AATTCCATAAT
* *
3460103 AACTATTAACTTCACTCCATATTTACTAC
64 AACTACTAAC-CCACTCCATATTTACTAC
3460132 TCACGCGACTCAATATCAACTAGTCACACGATTCCATAATAACTAGT
1 TCACGCGACTCAATATCAACTAGTCACACGATTCCATAATAACTAGT
3460179 AACGACACTT
Statistics
Matches: 177, Mismatches: 49, Indels: 10
0.75 0.21 0.04
Matches are distributed among these distances:
91 4 0.02
92 170 0.96
93 3 0.02
ACGTcount: A:0.35, C:0.26, G:0.08, T:0.31
Consensus pattern (91 bp):
TCACGCGACTCAATATCAACTAGTCACACGATTCCATAATAACTAGTCACGTAATTCCATAATAA
CTACTAACCCACTCCATATTTACTAC
Found at i:3460227 original size:23 final size:23
Alignment explanation
Indices: 3459854--3460236 Score: 164
Period size: 23 Copynumber: 16.7 Consensus size: 23
3459844 CATATAAAAA
*
3459854 AGTCACGCGATTCCATATCAACT
1 AGTCACGCGATTCCATATTAACT
* * *
3459877 AGTAACACGATTCCATAATAACT
1 AGTCACGCGATTCCATATTAACT
* * *
3459900 ACTCACGTGATTCCATAATAA-T
1 AGTCACGCGATTCCATATTAACT
* *
3459922 TGCTCACGCGATTCCATAATAACT
1 AG-TCACGCGATTCCATATTAACT
* * * * *
3459946 AGTAATGCCACTCCATATTTACT
1 AGTCACGCGATTCCATATTAACT
* * * *
3459969 ACTCACGCGACTCAATATCAACT
1 AGTCACGCGATTCCATATTAACT
** ** *
3459992 AGTCACGTAATTTTATAATAACT
1 AGTCACGCGATTCCATATTAACT
* * * * * *
3460015 AGTAACGCCACTCTATATTTATT
1 AGTCACGCGATTCCATATTAACT
* * * *
3460038 ACTCACGAC-ACTCAATATCAACT
1 AGTCACG-CGATTCCATATTAACT
* *** *
3460061 AGTCACGTGATTTTTTAATAACT
1 AGTCACGCGATTCCATATTAACT
* * *
3460084 AGTCACTCAATTCCATAATAACT
1 AGTCACGCGATTCCATATTAACT
* * * * *
3460107 ATTAACTTC-ACTCCATATTTACT
1 AGTCAC-GCGATTCCATATTAACT
* * * *
3460130 ACTCACGCGACTCAATATCAACT
1 AGTCACGCGATTCCATATTAACT
* *
3460153 AGTCACACGATTCCATAATAACT
1 AGTCACGCGATTCCATATTAACT
* *
3460176 AGTAACGAC-ACTT-CATATTTACT
1 AGTCACG-CGA-TTCCATATTAACT
**
3460199 TCTCACGCGATTCCATATTAACT
1 AGTCACGCGATTCCATATTAACT
**
3460222 AGTCACATGATTCCA
1 AGTCACGCGATTCCA
3460237 AATTTAGTAG
Statistics
Matches: 260, Mismatches: 90, Indels: 20
0.70 0.24 0.05
Matches are distributed among these distances:
22 5 0.02
23 247 0.95
24 8 0.03
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (23 bp):
AGTCACGCGATTCCATATTAACT
Found at i:3460262 original size:69 final size:69
Alignment explanation
Indices: 3460080--3460236 Score: 215
Period size: 69 Copynumber: 2.3 Consensus size: 69
3460070 ATTTTTTAAT
* * * ** *
3460080 AACTAGTCACTCAATTCCATAATAACTATTAACTTCACTCCATATTTACTACTCACGCGACTCAA
1 AACTAGTCACACGATTCCATAATAACTAGTAACGACACTTCATATTTACTACTCACGCGACTCAA
3460145 TATC
66 TATC
* * *
3460149 AACTAGTCACACGATTCCATAATAACTAGTAACGACACTTCATATTTACTTCTCACGCGATTCCA
1 AACTAGTCACACGATTCCATAATAACTAGTAACGACACTTCATATTTACTACTCACGCGACTCAA
*
3460214 TATT
66 TATC
*
3460218 AACTAGTCACATGATTCCA
1 AACTAGTCACACGATTCCA
3460237 AATTTAGTAG
Statistics
Matches: 77, Mismatches: 11, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
69 77 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.31
Consensus pattern (69 bp):
AACTAGTCACACGATTCCATAATAACTAGTAACGACACTTCATATTTACTACTCACGCGACTCAA
TATC
Found at i:3460585 original size:26 final size:26
Alignment explanation
Indices: 3460548--3460613 Score: 96
Period size: 26 Copynumber: 2.5 Consensus size: 26
3460538 TGCCCTTCTT
3460548 TTTGTTAAATGATACAAAAAAGAATAA
1 TTTG-TAAATGATACAAAAAAGAATAA
*
3460575 TTTGTAAATGATACAACAAAGAATAA
1 TTTGTAAATGATACAAAAAAGAATAA
* *
3460601 TTTGGAGATGATA
1 TTTGTAAATGATA
3460614 ATGAACAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
26 32 0.89
27 4 0.11
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (26 bp):
TTTGTAAATGATACAAAAAAGAATAA
Found at i:3465782 original size:236 final size:236
Alignment explanation
Indices: 3465369--3465840 Score: 632
Period size: 236 Copynumber: 2.0 Consensus size: 236
3465359 GACAATCATT
*
3465369 ATCATTCAACATGTCATCAAATCATTCATGAATATTAAGTACACTTTTTTATGCTTTATACCATT
1 ATCATTCAACATGTCATCAAATCATTCATGAATATTAAGTACACTTTTCTATGCTTTATACCATT
* * * *
3465434 CCTATGTGAGTGGATCTACCTCATTTCGACAAATAGTGATTTAAACCTCCATTATTTTGTGTTTC
66 CCTATGTGAGTGCATCTACCTCATTTCGACAAATAGTGATTTAAACCTCCACTATTTTGAGTTCC
* **
3465499 TAAGGTGCTCTCATGAATAACACATTGGTCTTATCCATGACCTATTGAGTGGTCCCACCCCACTT
131 TAAGGTGCTCTCATGAATAACACATTGGTCTCATCCACAACCTATTGAGTGGTCCCACCCCACTT
*
3465564 GGGCCAA-TAAAGGACAAAGTTCTCACTACCGTCTAGTTCAC
196 AGG-CAAGTAAAGGACAAAGTTCTCACTACCGTCTAGTTCAC
* * *
3465605 ATCATTCAACATGTCATTAAATCATTCATGAATATTGCA-TACACTTTTCTATGCTTTATAGCAT
1 ATCATTCAACATGTCATCAAATCATTCATGAATATT-AAGTACACTTTTCTATGCTTTATACCAT
* *
3465669 TCCTATGTGAGTGCATCTACCTCA-TTCTGACGAATAGTGGTTTAAACAC-CCACTATTTTGAGT
65 TCCTATGTGAGTGCATCTACCTCATTTC-GACAAATAGTGATTTAAAC-CTCCACTATTTTGAGT
* * * ***
3465732 TCCT-A-GTGCGTTGTCGTTAATGGTACATTGGTCTCATCCACAACCTATTGAGTGGTCCCACCC
128 TCCTAAGGTGC--TCTCATGAATAACACATTGGTCTCATCCACAACCTATTGAGTGGTCCCACCC
* * * *
3465795 CACTTAGGCAAGTAGAGGAGAAAGTTCTCACTATCGTCTGGTTCAC
191 CACTTAGGCAAGTAAAGGACAAAGTTCTCACTACCGTCTAGTTCAC
3465841 TTCACGTGAA
Statistics
Matches: 206, Mismatches: 24, Indels: 12
0.85 0.10 0.05
Matches are distributed among these distances:
234 4 0.02
235 7 0.03
236 193 0.94
237 2 0.01
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (236 bp):
ATCATTCAACATGTCATCAAATCATTCATGAATATTAAGTACACTTTTCTATGCTTTATACCATT
CCTATGTGAGTGCATCTACCTCATTTCGACAAATAGTGATTTAAACCTCCACTATTTTGAGTTCC
TAAGGTGCTCTCATGAATAACACATTGGTCTCATCCACAACCTATTGAGTGGTCCCACCCCACTT
AGGCAAGTAAAGGACAAAGTTCTCACTACCGTCTAGTTCAC
Found at i:3488595 original size:17 final size:17
Alignment explanation
Indices: 3488573--3488605 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3488563 TTTGTAAGTG
3488573 TTTAATGAAAGAAGAAT
1 TTTAATGAAAGAAGAAT
*
3488590 TTTAATGGAAGAAGAA
1 TTTAATGAAAGAAGAA
3488606 GAGCAATTTC
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:0.52, C:0.00, G:0.21, T:0.27
Consensus pattern (17 bp):
TTTAATGAAAGAAGAAT
Found at i:3491099 original size:21 final size:21
Alignment explanation
Indices: 3491073--3491134 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
3491063 GGATTTCGTG
*
3491073 ACAAAGACTGATGCATTCATA
1 ACAAAGATTGATGCATTCATA
* *
3491094 ACAAAGATTGATGCATTTATG
1 ACAAAGATTGATGCATTCATA
* *
3491115 ACAAGGATTGATGCCTTCAT
1 ACAAAGATTGATGCATTCAT
3491135 TCAAAATTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (21 bp):
ACAAAGATTGATGCATTCATA
Found at i:3493109 original size:13 final size:12
Alignment explanation
Indices: 3493088--3493121 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3493078 AAGTTTCAAG
3493088 ATTTCTTTTATTT
1 ATTTCTTTTA-TT
*
3493101 ATTTATTTTATT
1 ATTTCTTTTATT
3493113 ATTTCTTTT
1 ATTTCTTTT
3493122 TCTTTTTCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (12 bp):
ATTTCTTTTATT
Found at i:3502369 original size:23 final size:24
Alignment explanation
Indices: 3502339--3502387 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
3502329 TGCTAATTAG
*
3502339 TAATTCTTTCATAATA-TTTGTTT
1 TAATTCTTTAATAATACTTTGTTT
3502362 TAATTCTTTAATAATACTTTTGTTT
1 TAATTCTTTAATAATAC-TTTGTTT
3502387 T
1 T
3502388 TTCTATTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 15 0.65
25 8 0.35
ACGTcount: A:0.27, C:0.08, G:0.04, T:0.61
Consensus pattern (24 bp):
TAATTCTTTAATAATACTTTGTTT
Found at i:3503561 original size:23 final size:24
Alignment explanation
Indices: 3503510--3503593 Score: 109
Period size: 23 Copynumber: 3.5 Consensus size: 24
3503500 GTTTAGCATT
* *
3503510 TTTATTGAACATGGTATGTAACAG
1 TTTATTGAACATGATGTGTAACAG
3503534 TTTTATTGAACATGATGTGTAACA-
1 -TTTATTGAACATGATGTGTAACAG
* *
3503558 TTTATTGAACATGACGTGTACCAG
1 TTTATTGAACATGATGTGTAACAG
3503582 TTT-TTGAACATG
1 TTTATTGAACATG
3503594 GCTTGCAATA
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
23 30 0.56
24 3 0.06
25 21 0.39
ACGTcount: A:0.31, C:0.11, G:0.19, T:0.39
Consensus pattern (24 bp):
TTTATTGAACATGATGTGTAACAG
Found at i:3507716 original size:23 final size:23
Alignment explanation
Indices: 3507688--3507755 Score: 104
Period size: 21 Copynumber: 3.0 Consensus size: 23
3507678 TTTTTTCTAT
*
3507688 TTCAAGCCATGGTGTGTCACATA
1 TTCAAGCCATGGCGTGTCACATA
*
3507711 TTCAAGCCATGGCATGT--CATA
1 TTCAAGCCATGGCGTGTCACATA
3507732 TTCAAGCCATGGCGTGTCACATA
1 TTCAAGCCATGGCGTGTCACATA
3507755 T
1 T
3507756 ATGCTTACCA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
21 20 0.50
23 20 0.50
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (23 bp):
TTCAAGCCATGGCGTGTCACATA
Found at i:3508129 original size:21 final size:21
Alignment explanation
Indices: 3508105--3508156 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 21
3508095 CATCATGATG
*
3508105 TGTCACATTCTCACATTGACA
1 TGTCACATTCTCACAATGACA
*
3508126 TGTCACATATTCTCACAATGTCA
1 TGTCAC--ATTCTCACAATGACA
*
3508149 TCTCACAT
1 TGTCACAT
3508157 ATTCCCTCCA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
21 8 0.31
23 18 0.69
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.35
Consensus pattern (21 bp):
TGTCACATTCTCACAATGACA
Found at i:3508154 original size:23 final size:23
Alignment explanation
Indices: 3508111--3508187 Score: 86
Period size: 23 Copynumber: 3.3 Consensus size: 23
3508101 GATGTGTCAC
* *
3508111 ATTCTCACATTGACATGTCACAT
1 ATTCTCACAATGTCATGTCACAT
*
3508134 ATTCTCACAATGTCATCTCACAT
1 ATTCTCACAATGTCATGTCACAT
*
3508157 ATTCCCTC-CAA-GTCGTGTCACAT
1 ATT--CTCACAATGTCATGTCACAT
3508180 ATTCTCAC
1 ATTCTCAC
3508188 CCTGCTGTGT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
21 3 0.07
22 1 0.02
23 36 0.78
24 3 0.07
25 3 0.07
ACGTcount: A:0.27, C:0.31, G:0.08, T:0.34
Consensus pattern (23 bp):
ATTCTCACAATGTCATGTCACAT
Found at i:3508349 original size:23 final size:23
Alignment explanation
Indices: 3508271--3508354 Score: 88
Period size: 23 Copynumber: 3.7 Consensus size: 23
3508261 ATGCTTACCT
3508271 TGTCATCTCACATATTCTCACCA
1 TGTCATCTCACATATTCTCACCA
* *
3508294 TGGCATGTCAC--ATTCTCA-CA
1 TGTCATCTCACATATTCTCACCA
3508314 CTAG-CAT-TGCACATATTCTCACCA
1 -T-GTCATCT-CACATATTCTCACCA
3508338 TGTCATCTCACATATTC
1 TGTCATCTCACATATTC
3508355 CTTTCAAACC
Statistics
Matches: 51, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
20 3 0.06
21 14 0.27
22 2 0.04
23 29 0.57
24 3 0.06
ACGTcount: A:0.26, C:0.32, G:0.08, T:0.33
Consensus pattern (23 bp):
TGTCATCTCACATATTCTCACCA
Found at i:3508395 original size:217 final size:217
Alignment explanation
Indices: 3507995--3508400 Score: 468
Period size: 217 Copynumber: 1.9 Consensus size: 217
3507985 GATTTCCTCC
* * **
3507995 ATGGCATGTCATAAACTCTAAACCCTACCATGTCATAGCCGTGTCACATATGCTCTCCATGTGGT
1 ATGGCATGTCATAAACTCTAAACCCTACCATGTCATAGCCATGTCACAAATGCTCTCCATGTCAT
* * *
3508060 CTCACACATTCTCACCTTGGCGTGTCATATATTCACATCATGATGTGTCACATTCTCACATTGAC
66 CTCACACATTCTCACCATGGCATGTCACATATTCACATCATGATGTGTCACATTCTCACATTGAC
* ** * *
3508125 ATGTCACATATTCTCACAATGTCATCTCACATATTCCCTCCAAGTCGTGTCACATATTCTCACCC
131 ATCTCACATATTCTCACAATACCATCTCACATATTCCCACCAAGTCATGTCACATATTCTCACCC
3508190 TGCTGTGTGACATAGTCCTTCT
196 TGCTGTGTGACATAGTCCTTCT
* * *
3508212 ATGGCATGTCATAAACTCTAAACCCTACTATGTCATAGCCATGTTACAAATGCT-TACCTTGTCA
1 ATGGCATGTCATAAACTCTAAACCCTACCATGTCATAGCCATGTCACAAATGCTCT-CCATGTCA
*
3508276 TCTCACATATTCTCACCATGGCATGTCACAT-TCTCACA-C-TAGCAT-TG-CACATATTCTCAC
65 TCTCACACATTCTCACCATGGCATGTCACATAT-TCACATCAT-G-ATGTGTCAC--ATTCTCA-
* ** * * ***
3508336 CA-TGTCATCTCACATATTCCTTTCAA-ACCATGTCACATATTCTCACTTTGTCATGTCACATAT
124 CATTGACATCTCACATATT-CTCACAATACCATCTCACATATTCCCACCAAGTCATGTCACATAT
3508399 TC
188 TC
3508401 CCTCTATAGC
Statistics
Matches: 157, Mismatches: 24, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
215 4 0.03
216 6 0.04
217 140 0.89
218 7 0.04
ACGTcount: A:0.26, C:0.29, G:0.11, T:0.33
Consensus pattern (217 bp):
ATGGCATGTCATAAACTCTAAACCCTACCATGTCATAGCCATGTCACAAATGCTCTCCATGTCAT
CTCACACATTCTCACCATGGCATGTCACATATTCACATCATGATGTGTCACATTCTCACATTGAC
ATCTCACATATTCTCACAATACCATCTCACATATTCCCACCAAGTCATGTCACATATTCTCACCC
TGCTGTGTGACATAGTCCTTCT
Found at i:3516057 original size:12 final size:12
Alignment explanation
Indices: 3516027--3516064 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
3516017 GTTACTGGAA
* *
3516027 ATATATGTATAC
1 ATATATTTATAT
3516039 ATATATTTATAT
1 ATATATTTATAT
3516051 ATATATTTAT-T
1 ATATATTTATAT
3516062 ATA
1 ATA
3516065 ATACTTCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
11 4 0.17
12 20 0.83
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (12 bp):
ATATATTTATAT
Found at i:3517264 original size:9 final size:9
Alignment explanation
Indices: 3517234--3517266 Score: 52
Period size: 8 Copynumber: 3.9 Consensus size: 9
3517224 GAGCTCGGTC
3517234 GGGGGT-GG
1 GGGGGTGGG
3517242 GGGGG-GGG
1 GGGGGTGGG
3517250 GGGGGTGGG
1 GGGGGTGGG
3517259 GGGGGTGG
1 GGGGGTGG
3517267 AAGTGGTGTG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 12 0.52
9 11 0.48
ACGTcount: A:0.00, C:0.00, G:0.91, T:0.09
Consensus pattern (9 bp):
GGGGGTGGG
Found at i:3521762 original size:22 final size:23
Alignment explanation
Indices: 3521737--3521780 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
3521727 GCTACAAACC
*
3521737 TATTTATAAAA-TAGAAAAAATA
1 TATTAATAAAATTAGAAAAAATA
*
3521759 TATTAATAAAATTAGATAAAAT
1 TATTAATAAAATTAGAAAAAAT
3521781 TTATACAGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (23 bp):
TATTAATAAAATTAGAAAAAATA
Found at i:3522188 original size:83 final size:84
Alignment explanation
Indices: 3522038--3522194 Score: 244
Period size: 83 Copynumber: 1.9 Consensus size: 84
3522028 CTGCCCTTTT
*
3522038 AGGGACAGGTGGTGTCTATTGATACAGCCACATAGGCACCTCACCATATGTGGGTTTCATGGCCT
1 AGGGACAGGTGGTGTCTATTGATA-AGCCACATAGGCACCTCACCATATGTGCGTTTCATGGCCT
3522103 TCTTAGATGACTGGCCGTTC
65 TCTTAGATGACTGGCCGTTC
* * * * *
3522123 AGGGACAGGTGGTGTCTATTGAT-AGCCACGTAGGCGCCTCGCCATATGTGCGTTTTATGGGCTT
1 AGGGACAGGTGGTGTCTATTGATAAGCCACATAGGCACCTCACCATATGTGCGTTTCATGGCCTT
3522187 CTTAGATG
66 CTTAGATG
3522195 GTTGGGCCTT
Statistics
Matches: 66, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
83 43 0.65
85 23 0.35
ACGTcount: A:0.20, C:0.22, G:0.29, T:0.29
Consensus pattern (84 bp):
AGGGACAGGTGGTGTCTATTGATAAGCCACATAGGCACCTCACCATATGTGCGTTTCATGGCCTT
CTTAGATGACTGGCCGTTC
Found at i:3550523 original size:21 final size:21
Alignment explanation
Indices: 3550499--3550546 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 21
3550489 TGATTGATCA
3550499 TCTATCGATAGATAAATGATG
1 TCTATCGATAGATAAATGATG
**
3550520 TCTATCGATAGATGCATGATG
1 TCTATCGATAGATAAATGATG
3550541 TGCTAT
1 T-CTAT
3550547 GCTACCCTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.35
Consensus pattern (21 bp):
TCTATCGATAGATAAATGATG
Found at i:3552217 original size:21 final size:21
Alignment explanation
Indices: 3552159--3552209 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
3552149 TTGAACGGAG
3552159 GCATCAGTCATTATCATAAAT
1 GCATCAGTCATTATCATAAAT
*
3552180 GCATCAATCATTATCATAAAT
1 GCATCAGTCATTATCATAAAT
3552201 GCATCAGTC
1 GCATCAGTC
3552210 TTTGTCATGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (21 bp):
GCATCAGTCATTATCATAAAT
Found at i:3554285 original size:9 final size:9
Alignment explanation
Indices: 3554271--3554307 Score: 56
Period size: 9 Copynumber: 3.9 Consensus size: 9
3554261 CAAATCGAAC
3554271 TAAAAAAAA
1 TAAAAAAAA
3554280 TAAAAAAAA
1 TAAAAAAAA
3554289 TAACAAAAAGA
1 TAA-AAAAA-A
3554300 TAAAAAAA
1 TAAAAAAA
3554308 CTCAAGAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
9 12 0.46
10 10 0.38
11 4 0.15
ACGTcount: A:0.84, C:0.03, G:0.03, T:0.11
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:3556962 original size:31 final size:31
Alignment explanation
Indices: 3556926--3557027 Score: 100
Period size: 31 Copynumber: 3.3 Consensus size: 31
3556916 AAAAGTGCCT
**
3556926 AATTTAATCTTTAAATGATAAAATTTTATTC
1 AATTTAATCCCTAAATGATAAAATTTTATTC
* *
3556957 AATTTAATCCCTACATGATAAAATTTTATTT
1 AATTTAATCCCTAAATGATAAAATTTTATTC
* * * *
3556988 AATTCAATTCCCGT-ACT-CTATAATTTTATTC
1 AATTTAA-TCCC-TAAATGATAAAATTTTATTC
3557019 AATTTAATC
1 AATTTAATC
3557028 TTTATACTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 5
0.78 0.15 0.07
Matches are distributed among these distances:
30 2 0.03
31 50 0.86
32 5 0.09
33 1 0.02
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (31 bp):
AATTTAATCCCTAAATGATAAAATTTTATTC
Found at i:3565470 original size:19 final size:20
Alignment explanation
Indices: 3565426--3565470 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
3565416 TTAATTATTT
* *
3565426 ATTAATTAAAAATGTATAAT
1 ATTAATTAAAAATGTACAAA
*
3565446 ATTAATTCAAAATG-ACAAA
1 ATTAATTAAAAATGTACAAA
3565465 ATTAAT
1 ATTAAT
3565471 AAACACATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 9 0.41
20 13 0.59
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.36
Consensus pattern (20 bp):
ATTAATTAAAAATGTACAAA
Found at i:3567800 original size:11 final size:11
Alignment explanation
Indices: 3567784--3567817 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3567774 ATCTTAAATT
3567784 TAAGACACAAA
1 TAAGACACAAA
3567795 TAAGACACAAA
1 TAAGACACAAA
* *
3567806 AAAAACACAAA
1 TAAGACACAAA
3567817 T
1 T
3567818 CGTAATCTGC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.68, C:0.18, G:0.06, T:0.09
Consensus pattern (11 bp):
TAAGACACAAA
Found at i:3569880 original size:2 final size:2
Alignment explanation
Indices: 3569873--3569900 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3569863 TAGTCCAAGG
3569873 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3569901 GCGCATAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.