Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167871.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_14, 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: 22631831
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 114000 characters in sequence are not A, C, G, or T
File 14 of 125
Found at i:2263747 original size:17 final size:17
Alignment explanation
Indices: 2263725--2263768 Score: 79
Period size: 17 Copynumber: 2.6 Consensus size: 17
2263715 TATACATTTT
2263725 TAATACAATTATACTTC
1 TAATACAATTATACTTC
2263742 TAATACAATTATACTTC
1 TAATACAATTATACTTC
*
2263759 TAGTACAATT
1 TAATACAATT
2263769 GGATAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.02, T:0.41
Consensus pattern (17 bp):
TAATACAATTATACTTC
Found at i:2267848 original size:13 final size:15
Alignment explanation
Indices: 2267832--2267863 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
2267822 TGATTTATAT
2267832 AATTATT-TTTAA-A
1 AATTATTATTTAATA
2267845 AATTATTATTTAATA
1 AATTATTATTTAATA
2267860 AATT
1 AATT
2267864 TAGAATTTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 7 0.41
14 5 0.29
15 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTATTATTTAATA
Found at i:2270057 original size:17 final size:17
Alignment explanation
Indices: 2270031--2270064 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2270021 GTTTATGTTT
*
2270031 TTATTTATTATATTAAA
1 TTATTAATTATATTAAA
*
2270048 TTATTAATTATTTTAAA
1 TTATTAATTATATTAAA
2270065 CATCTTCAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATTAATTATATTAAA
Found at i:2270512 original size:2 final size:2
Alignment explanation
Indices: 2270507--2270532 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2270497 AGATAAATAA
2270507 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
2270533 TCTAAAAGAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2271010 original size:22 final size:22
Alignment explanation
Indices: 2270972--2271025 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
2270962 TTATTTATTT
2270972 ATTT-TTTATATTATTTTATATA
1 ATTTATTT-TATTATTTTATATA
* *
2270994 ATTTATATTTATT-TTTTTTGTA
1 ATTTAT-TTTATTATTTTATATA
2271016 ATTTATTTTA
1 ATTTATTTTA
2271026 AAATTTTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
21 4 0.14
22 17 0.61
23 5 0.18
24 2 0.07
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
ATTTATTTTATTATTTTATATA
Found at i:2279584 original size:24 final size:24
Alignment explanation
Indices: 2279520--2279585 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
2279510 AAAAAATCAT
2279520 AAAAA-ATAATTTTAA-ACT-ATAA
1 AAAAATATAATTTTAAGA-TAATAA
*
2279542 AAAAATAAGAATTTT-AGATAATAA
1 AAAAAT-ATAATTTTAAGATAATAA
2279566 AAAAATATAATTTTAAGATA
1 AAAAATATAATTTTAAGATA
2279586 TCCCAAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
22 5 0.14
23 9 0.24
24 23 0.62
ACGTcount: A:0.62, C:0.02, G:0.05, T:0.32
Consensus pattern (24 bp):
AAAAATATAATTTTAAGATAATAA
Found at i:2284788 original size:6 final size:6
Alignment explanation
Indices: 2284773--2284802 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
2284763 TCTTTTCACC
*
2284773 TCATCG TCATCT TCATCT TCATCT TCATCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT
2284803 GCTTGATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.33, G:0.03, T:0.47
Consensus pattern (6 bp):
TCATCT
Found at i:2285894 original size:26 final size:27
Alignment explanation
Indices: 2285872--2285925 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
2285862 AAAATTACAT
2285872 ATAAA-TTAATATTTTAAATATTAAAA
1 ATAAATTTAATATTTTAAATATTAAAA
2285898 ATAAATTTAATATTTTAAATATTAAAA
1 ATAAATTTAATATTTTAAATATTAAAA
2285925 A
1 A
2285926 AAAACCTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 5 0.19
27 22 0.81
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (27 bp):
ATAAATTTAATATTTTAAATATTAAAA
Found at i:2287899 original size:24 final size:24
Alignment explanation
Indices: 2287856--2287919 Score: 74
Period size: 24 Copynumber: 2.7 Consensus size: 24
2287846 TTTTTTAATT
* * *
2287856 TACATTTGATATATTGATAATATA
1 TACATTTCATATACTAATAATATA
* *
2287880 TACGTTTCATATACTAATAATGTA
1 TACATTTCATATACTAATAATATA
*
2287904 TACATTTTATATACTA
1 TACATTTCATATACTA
2287920 TCAATTAATT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.39, C:0.09, G:0.06, T:0.45
Consensus pattern (24 bp):
TACATTTCATATACTAATAATATA
Found at i:2288142 original size:2 final size:2
Alignment explanation
Indices: 2288135--2288166 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2288125 GTTTTTGCTC
2288135 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2288167 AAAGGAAAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2291205 original size:13 final size:13
Alignment explanation
Indices: 2291187--2291211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2291177 AATTTTTGAA
2291187 TTAAAAAATATAT
1 TTAAAAAATATAT
2291200 TTAAAAAATATA
1 TTAAAAAATATA
2291212 ATAAAAAAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
TTAAAAAATATAT
Found at i:2291326 original size:24 final size:24
Alignment explanation
Indices: 2291264--2291327 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
2291254 AAAAAATATG
* *
2291264 TAAATAATTGAAATATTTAAATATA
1 TAAATAA-TGAAATATTGAAACATA
*
2291289 TATAATAATAAAATATTGGAAACATA
1 TA-AATAATGAAATATT-GAAACATA
2291315 -AAATAATGAAATA
1 TAAATAATGAAATA
2291328 ATTTTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
24 11 0.33
25 11 0.33
26 11 0.33
ACGTcount: A:0.59, C:0.02, G:0.06, T:0.33
Consensus pattern (24 bp):
TAAATAATGAAATATTGAAACATA
Found at i:2297020 original size:3 final size:3
Alignment explanation
Indices: 2297012--2297037 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2297002 TATTGCTTAA
2297012 GTT GTT GTT GTT GTT GTT GTT GTT GT
1 GTT GTT GTT GTT GTT GTT GTT GTT GT
2297038 CGCGACCGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.35, T:0.65
Consensus pattern (3 bp):
GTT
Found at i:2301019 original size:29 final size:29
Alignment explanation
Indices: 2300977--2301040 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
2300967 CTCAATTCAT
* *
2300977 ACTTAGTTGGTTAGAGTAATTGAGTTATA
1 ACTTAGTTGGTTAGAATAATTAAGTTATA
* *
2301006 ACTTGGTTTGTTAGAATAATTAAGTTATA
1 ACTTAGTTGGTTAGAATAATTAAGTTATA
2301035 ACTTAG
1 ACTTAG
2301041 AAGTGATATA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.33, C:0.05, G:0.20, T:0.42
Consensus pattern (29 bp):
ACTTAGTTGGTTAGAATAATTAAGTTATA
Found at i:2312718 original size:35 final size:35
Alignment explanation
Indices: 2312679--2312750 Score: 126
Period size: 35 Copynumber: 2.1 Consensus size: 35
2312669 CTCTTTATAT
*
2312679 AGAAACTCTGAACTTAAAATTTACTCGTGTAAGAA
1 AGAAACTCTGAACTTAAAATTTACTCATGTAAGAA
*
2312714 AGAAACTCTGAACTTGAAATTTACTCATGTAAGAA
1 AGAAACTCTGAACTTAAAATTTACTCATGTAAGAA
2312749 AG
1 AG
2312751 TGCACAGCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (35 bp):
AGAAACTCTGAACTTAAAATTTACTCATGTAAGAA
Found at i:2327487 original size:23 final size:23
Alignment explanation
Indices: 2327461--2327528 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
2327451 TCACTAATGG
*
2327461 ATAAAAAATGATAAGAGAAAAAA
1 ATAAAAAATGAGAAGAGAAAAAA
*
2327484 ATAAAAAATAAGAAGAGAAAAAA
1 ATAAAAAATGAGAAGAGAAAAAA
*
2327507 ATAAAAAAAGAGAAGA-AAAAAA
1 ATAAAAAATGAGAAGAGAAAAAA
2327529 TGAAAAGGAG
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 6 0.15
23 35 0.85
ACGTcount: A:0.78, C:0.00, G:0.13, T:0.09
Consensus pattern (23 bp):
ATAAAAAATGAGAAGAGAAAAAA
Found at i:2327496 original size:20 final size:21
Alignment explanation
Indices: 2327473--2327572 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 21
2327463 AAAAAATGAT
2327473 AAGAGAAAAAAATAAAAAATAA
1 AAGAGAAAAAAATAAAAAA-AA
2327495 GAAGAGAAAAAAAT-AAAAAAA
1 -AAGAGAAAAAAATAAAAAAAA
*
2327516 GAGAAGAAAAAAATGAAAAGGAGAAA
1 AAG-AGAAAAAAAT-AAAA--A-AAA
2327542 AA-ATGAAAAAAATAAAAAAAA
1 AAGA-GAAAAAAATAAAAAAAA
2327563 AAGAGAAAAA
1 AAGAGAAAAA
2327573 TGAGAGAAAA
Statistics
Matches: 67, Mismatches: 2, Indels: 18
0.77 0.02 0.21
Matches are distributed among these distances:
20 2 0.03
21 23 0.34
22 7 0.10
23 16 0.24
24 5 0.07
25 10 0.15
26 4 0.06
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (21 bp):
AAGAGAAAAAAATAAAAAAAA
Found at i:2327504 original size:21 final size:21
Alignment explanation
Indices: 2327471--2327573 Score: 81
Period size: 23 Copynumber: 4.8 Consensus size: 21
2327461 ATAAAAAATG
2327471 ATAAG-AGAAAAAAATAAAAA
1 ATAAGAAGAAAAAAATAAAAA
2327491 ATAAGAAGAGAAAAAAATAAAAA
1 ATAAG-A-AGAAAAAAATAAAAA
2327514 A-AGAGAAGAAAAAAATGAAAAGGA
1 ATA-AGAAGAAAAAAAT-AAAA--A
*
2327538 GA-AAAAATGAAAAAAATAAAAA
1 -ATAAGAA-GAAAAAAATAAAAA
*
2327560 A-AA-AAGAGAAAAAT
1 ATAAGAAGAAAAAAAT
2327574 GAGAGAAAAG
Statistics
Matches: 72, Mismatches: 2, Indels: 19
0.77 0.02 0.20
Matches are distributed among these distances:
19 8 0.11
20 7 0.10
21 13 0.18
22 7 0.10
23 18 0.25
24 8 0.11
25 11 0.15
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.08
Consensus pattern (21 bp):
ATAAGAAGAAAAAAATAAAAA
Found at i:2327544 original size:29 final size:30
Alignment explanation
Indices: 2327501--2327582 Score: 75
Period size: 29 Copynumber: 2.9 Consensus size: 30
2327491 ATAAGAAGAG
*
2327501 AAAAAAATA-AAAAAAGAGAAGAAAA-AAA
1 AAAAAAAGAGAAAAAAGAGAAGAAAATAAA
** *
2327529 TGAAAAGGAGAAAAAATGA-AA-AAAATAAA
1 AAAAAAAGAGAAAAAA-GAGAAGAAAATAAA
*
2327558 AAAAAAAGAGAAAAATGAG-AGAAAA
1 AAAAAAAGAGAAAAAAGAGAAGAAAA
2327583 GGAAGACTCA
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
28 12 0.29
29 27 0.66
30 2 0.05
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (30 bp):
AAAAAAAGAGAAAAAAGAGAAGAAAATAAA
Found at i:2327579 original size:60 final size:60
Alignment explanation
Indices: 2327463--2327582 Score: 142
Period size: 60 Copynumber: 2.0 Consensus size: 60
2327453 ACTAATGGAT
* *
2327463 AAAAAATGATAAGAGAAAAAAATAAAAAATAAGAAGAGAAAAAAATAAAAAAAGAGAAGA
1 AAAAAATGAAAAGAGAAAAAAATAAAAAATAAGAAGAGAAAAAAAGAAAAAAAGAGAAGA
* * *
2327523 AAAAAATGAAAAG-GAGAAAAAATGAAAAA-AATAA-A-AAAAAAAGAGAAAAATGAG-AGA
1 AAAAAATGAAAAGAGA-AAAAAATAAAAAATAAGAAGAGAAAAAAAGA-AAAAAAGAGAAGA
2327580 AAA
1 AAA
2327583 GGAAGACTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
57 14 0.26
58 9 0.17
59 6 0.11
60 24 0.45
ACGTcount: A:0.77, C:0.00, G:0.16, T:0.07
Consensus pattern (60 bp):
AAAAAATGAAAAGAGAAAAAAATAAAAAATAAGAAGAGAAAAAAAGAAAAAAAGAGAAGA
Found at i:2328798 original size:21 final size:22
Alignment explanation
Indices: 2328746--2328807 Score: 90
Period size: 21 Copynumber: 2.9 Consensus size: 22
2328736 TTATGAATCC
*
2328746 TCAAATGAGAATCTTTGAGTTT
1 TCAAATGAGAATCTTTAAGTTT
* *
2328768 TTAGATGAGAATCTTTAAG-TT
1 TCAAATGAGAATCTTTAAGTTT
2328789 TCAAATGAGAATCTTTAAG
1 TCAAATGAGAATCTTTAAG
2328808 ATGTGAAGCC
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
21 19 0.54
22 16 0.46
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (22 bp):
TCAAATGAGAATCTTTAAGTTT
Found at i:2329324 original size:40 final size:40
Alignment explanation
Indices: 2329240--2329617 Score: 379
Period size: 40 Copynumber: 9.3 Consensus size: 40
2329230 TTAAGAAGCC
* * * * *
2329240 TTTATTTTTTAAAGTTGTTATGCCTATGTTTAAAGGAG-TC
1 TTTA-TTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTT
* *
2329280 TTTATTTTCAAAGTTGTTGTGCCTCTATTTAGAAGAGCTT
1 TTTATTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTT
* * *
2329320 TTTATTTTCAAAGTTGTTGTGCTTTTGTTTAGAGGAGC-C
1 TTTATTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTT
* * * *
2329359 TTTATTTTTCAAAGTTATTGTGCCTCTGTTTAAAGAAGCCT
1 TTTA-TTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTT
* * * *
2329400 TTTATTTTTAAAGTTGTTGTGCTTCTATTTAGAGGTGCCTT
1 TTTATTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAG-CTT
* * * *
2329441 TATT-TTTT-AAAGTTATTGTGCCTCTGTTTAAAGAAGCCT
1 T-TTATTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTT
* * *
2329480 TTTATTTTCAAAGTTGTTATGCCTCTGTTTAGTGGAGCCT
1 TTTATTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTT
*
2329520 TTTATTTTTCTAAAGTTGTTGTGCCTTTGTTTAGAGGAGCTTT
1 TTTA-TTTTC-AAAGTTGTTGTGCCTCTGTTTAGAGGAGC-TT
* *
2329563 GTTTATTTTCAAAAGTTGTTGAGCCTCTGTCTAGAGGAG-TT
1 -TTTATTTTC-AAAGTTGTTGTGCCTCTGTTTAGAGGAGCTT
2329604 TTTATTATTCAAAG
1 TTTATT-TTCAAAG
2329618 AGTCTGTAAA
Statistics
Matches: 280, Mismatches: 46, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
38 2 0.01
39 38 0.14
40 156 0.56
41 21 0.08
42 28 0.10
43 31 0.11
44 4 0.01
ACGTcount: A:0.21, C:0.11, G:0.19, T:0.48
Consensus pattern (40 bp):
TTTATTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCTT
Found at i:2329385 original size:80 final size:80
Alignment explanation
Indices: 2329232--2329617 Score: 445
Period size: 80 Copynumber: 4.8 Consensus size: 80
2329222 CAAGATTGTT
* * * * *
2329232 AAGAAGCC-TTTATTTTTTAAAGTTGTTATGCCTATGTTTAAAGGAGTCTTTA-TTTTCAAAGTT
1 AAGAAGCCTTTTA-TTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCCTTTATTTTTCAAAGTT
* *
2329295 GTTGTGCCTCTATTTA
65 ATTGTGCCTCTGTTTA
* * *
2329311 GAAG-AGCTTTTTATTTTCAAAGTTGTTGTGCTTTTGTTTAGAGGAGCCTTTATTTTTCAAAGTT
1 -AAGAAGCCTTTTATTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCCTTTATTTTTCAAAGTT
2329375 ATTGTGCCTCTGTTTA
65 ATTGTGCCTCTGTTTA
* * * * *
2329391 AAGAAGCCTTTTATTTTTAAAGTTGTTGTGCTTCTATTTAGAGGTGCCTTTATTTTTTAAAGTTA
1 AAGAAGCCTTTTATTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCCTTTATTTTTCAAAGTTA
2329456 TTGTGCCTCTGTTTA
66 TTGTGCCTCTGTTTA
* *
2329471 AAGAAGCCTTTTATTTTCAAAGTTGTTATGCCTCTGTTTAGTGGAGCCTTTTATTTTTCTAAAGT
1 AAGAAGCCTTTTATTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCC-TTTATTTTTC-AAAGT
* *
2329536 TGTTGTGCCTTTGTTTA
64 TATTGTGCCTCTGTTTA
* * * * * ** *
2329553 GAGGAGCTTTGTTTATTTTCAAAAGTTGTTGAGCCTCTGTCTAGAGGAGTTTTTATTATTCAAAG
1 AAGAAGC-CT-TTTATTTTC-AAAGTTGTTGTGCCTCTGTTTAGAGGAGCCTTTATTTTTCAAAG
2329618 AGTCTGTAAA
Statistics
Matches: 264, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
79 39 0.15
80 144 0.55
81 9 0.03
82 25 0.09
83 5 0.02
84 18 0.07
85 24 0.09
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (80 bp):
AAGAAGCCTTTTATTTTCAAAGTTGTTGTGCCTCTGTTTAGAGGAGCCTTTATTTTTCAAAGTTA
TTGTGCCTCTGTTTA
Found at i:2329460 original size:120 final size:120
Alignment explanation
Indices: 2329232--2329592 Score: 426
Period size: 120 Copynumber: 3.0 Consensus size: 120
2329222 CAAGATTGTT
* * * *
2329232 AAGAAGCCTTTATTTTTTAAAGTTGTTATGCCTATGTTTAAAGGAGTC-TTTATTTTCAAAGTTG
1 AAGAAGCCTTTATTTTTCAAAGTTGTTATGCCTCTGTTTAAAGGAGCCTTTTATTTTTAAAGTTG
* * * * *
2329296 TTGTGCCTCTATTTAGAAGAGCTTTTTATTTTCAAAGTTGTTGTGCTTTTGTTTA
66 TTGTGCTTCTATTTAGAGGAGCTTTTTATTTTCAAAGTTATTGTGCCTCTGTTTA
* * * * *
2329351 GAGGAGCCTTTATTTTTCAAAGTTATTGTGCCTCTGTTTAAAGAAGCCTTTTATTTTTAAAGTTG
1 AAGAAGCCTTTATTTTTCAAAGTTGTTATGCCTCTGTTTAAAGGAGCCTTTTATTTTTAAAGTTG
*
2329416 TTGTGCTTCTATTTAGAGGTGCCTTTATT-TTTT-AAAGTTATTGTGCCTCTGTTTA
66 TTGTGCTTCTATTTAGAGGAG-CTTT-TTATTTTCAAAGTTATTGTGCCTCTGTTTA
**
2329471 AAGAAGCCTTT-TATTTTCAAAGTTGTTATGCCTCTGTTTAGTGGAGCCTTTTATTTTTCTAAAG
1 AAGAAGCCTTTAT-TTTTCAAAGTTGTTATGCCTCTGTTTAAAGGAGCCTTTTA-TTTT-TAAAG
* * *
2329535 TTGTTGTGCCTT-TGTTTAGAGGAGCTTTGTTTATTTTCAAAAGTTGTTGAGCCTCTGT
63 TTGTTGTG-CTTCTATTTAGAGGAGC-TT-TTTATTTTC-AAAGTTATTGTGCCTCTGT
2329593 CTAGAGGAGT
Statistics
Matches: 204, Mismatches: 26, Indels: 18
0.82 0.10 0.07
Matches are distributed among these distances:
119 41 0.20
120 96 0.47
121 13 0.06
122 29 0.14
123 8 0.04
125 17 0.08
ACGTcount: A:0.21, C:0.12, G:0.19, T:0.48
Consensus pattern (120 bp):
AAGAAGCCTTTATTTTTCAAAGTTGTTATGCCTCTGTTTAAAGGAGCCTTTTATTTTTAAAGTTG
TTGTGCTTCTATTTAGAGGAGCTTTTTATTTTCAAAGTTATTGTGCCTCTGTTTA
Found at i:2330303 original size:32 final size:32
Alignment explanation
Indices: 2330261--2330322 Score: 88
Period size: 32 Copynumber: 1.9 Consensus size: 32
2330251 ATTCTTTAAT
* *
2330261 TAATTATTTATTCATTTATTTTGTTTTATGCA
1 TAATTATTTATTCATTCAATTTGTTTTATGCA
* *
2330293 TAATTGTTTATTTATTCAATTTGTTTTATG
1 TAATTATTTATTCATTCAATTTGTTTTATG
2330323 GCTTTCATTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.63
Consensus pattern (32 bp):
TAATTATTTATTCATTCAATTTGTTTTATGCA
Found at i:2331036 original size:16 final size:16
Alignment explanation
Indices: 2331017--2331050 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
2331007 AAATCCAAGA
*
2331017 AAATAAAAAGGAAAAG
1 AAATAAAAAGAAAAAG
*
2331033 AAATAAAACGAAAAAG
1 AAATAAAAAGAAAAAG
2331049 AA
1 AA
2331051 GAAAAAAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.76, C:0.03, G:0.15, T:0.06
Consensus pattern (16 bp):
AAATAAAAAGAAAAAG
Found at i:2331181 original size:60 final size:58
Alignment explanation
Indices: 2331113--2331241 Score: 186
Period size: 60 Copynumber: 2.2 Consensus size: 58
2331103 TGCTTTTGTA
* *
2331113 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAACTTTTTTTTTGAAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTT-CTCAAAAAA-TATTTTTTAGAAAACTTATTTT
* * *
2331173 TAAGAAAAATTGATACTTTTAACTTTTTTCAAAAAATATTTTTTAGAAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCTCAAAAAATATTTTTTAGAAAACTTATTTT
2331231 CAAGGAAAAAT
1 CAA-GAAAAAT
2331242 ATTTTTTAGA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
58 22 0.35
59 15 0.24
60 25 0.40
ACGTcount: A:0.41, C:0.11, G:0.06, T:0.42
Consensus pattern (58 bp):
CAAGAAAAATTGATACTTTCAACTTTTCTCAAAAAATATTTTTTAGAAAACTTATTTT
Found at i:2331222 original size:16 final size:16
Alignment explanation
Indices: 2331203--2331253 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 16
2331193 AACTTTTTTC
2331203 AAAAAATATTTTTTAG
1 AAAAAATATTTTTTAG
** **
2331219 AAAACTTATTTTCAAG
1 AAAAAATATTTTTTAG
*
2331235 GAAAAATATTTTTTAG
1 AAAAAATATTTTTTAG
2331251 AAA
1 AAA
2331254 GCTTATTTTC
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (16 bp):
AAAAAATATTTTTTAG
Found at i:2331242 original size:32 final size:32
Alignment explanation
Indices: 2331204--2331271 Score: 127
Period size: 32 Copynumber: 2.1 Consensus size: 32
2331194 ACTTTTTTCA
2331204 AAAAATATTTTTTAGAAAACTTATTTTCAAGG
1 AAAAATATTTTTTAGAAAACTTATTTTCAAGG
*
2331236 AAAAATATTTTTTAGAAAGCTTATTTTCAAGG
1 AAAAATATTTTTTAGAAAACTTATTTTCAAGG
2331268 AAAA
1 AAAA
2331272 TTGATACTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (32 bp):
AAAAATATTTTTTAGAAAACTTATTTTCAAGG
Found at i:2331348 original size:13 final size:12
Alignment explanation
Indices: 2331321--2331381 Score: 56
Period size: 13 Copynumber: 5.0 Consensus size: 12
2331311 AATTTTATTT
2331321 AAAGAAATAATAAA
1 AAAG-AATAA-AAA
2331335 AAAGAATAAGAAA
1 AAAGAATAA-AAA
2331348 AAA-AATAAAAA
1 AAAGAATAAAAA
*
2331359 TAAAGAA-AAAAT
1 -AAAGAATAAAAA
2331371 AAA-AATAAAAA
1 AAAGAATAAAAA
2331382 TAAACTAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
10 2 0.05
11 10 0.24
12 12 0.29
13 13 0.32
14 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.07, T:0.11
Consensus pattern (12 bp):
AAAGAATAAAAA
Found at i:2331353 original size:25 final size:23
Alignment explanation
Indices: 2331325--2331385 Score: 79
Period size: 23 Copynumber: 2.6 Consensus size: 23
2331315 TTATTTAAAG
2331325 AAATAATAAA-AAAGAATAAGAAAAA
1 AAATAA-AAATAAAGAA-AA-AAAAA
*
2331350 AAATAAAAATAAAGAAAAAATAA
1 AAATAAAAATAAAGAAAAAAAAA
2331373 AAATAAAAATAAA
1 AAATAAAAATAAA
2331386 CTAAAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
23 17 0.50
24 5 0.15
25 12 0.35
ACGTcount: A:0.82, C:0.00, G:0.05, T:0.13
Consensus pattern (23 bp):
AAATAAAAATAAAGAAAAAAAAA
Found at i:2331356 original size:22 final size:23
Alignment explanation
Indices: 2331348--2331400 Score: 79
Period size: 23 Copynumber: 2.2 Consensus size: 23
2331338 GAATAAGAAA
2331348 AAAAATAAAAATAAAGAAAAAAT
1 AAAAATAAAAATAAAGAAAAAAT
*
2331371 AAAAATAAAAATAAACTAAAAATAT
1 AAAAATAAAAATAAA-GAAAAA-AT
2331396 AAAAA
1 AAAAA
2331401 AAGAAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 15 0.56
24 5 0.19
25 7 0.26
ACGTcount: A:0.81, C:0.02, G:0.02, T:0.15
Consensus pattern (23 bp):
AAAAATAAAAATAAAGAAAAAAT
Found at i:2331357 original size:6 final size:6
Alignment explanation
Indices: 2331325--2331399 Score: 68
Period size: 6 Copynumber: 12.5 Consensus size: 6
2331315 TTATTTAAAG
*
2331325 AAATAA TAAA-AA AGAATAA GAAA-AA AAATAA AAATAA AGA-AA AAATAA
1 AAATAA -AAATAA A-AATAA -AAATAA AAATAA AAATAA AAATAA AAATAA
*
2331373 AAATAA AAAT-A AACTAA AAATATA AAA
1 AAATAA AAATAA AAATAA AAATA-A AAA
2331400 AAAGAAAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
5 12 0.21
6 33 0.58
7 11 0.19
8 1 0.02
ACGTcount: A:0.80, C:0.01, G:0.04, T:0.15
Consensus pattern (6 bp):
AAATAA
Found at i:2331367 original size:17 final size:16
Alignment explanation
Indices: 2331345--2331409 Score: 85
Period size: 17 Copynumber: 3.9 Consensus size: 16
2331335 AAAGAATAAG
2331345 AAAAAAAATAAAAATA
1 AAAAAAAATAAAAATA
2331361 AAGAAAAAATAAAAATA
1 AA-AAAAAATAAAAATA
*
2331378 AAAATAAACTAAAAATA
1 AAAA-AAAATAAAAATA
* *
2331395 TAAAAAAAGAAAAAT
1 AAAAAAAATAAAAAT
2331410 TACTAAACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
16 13 0.30
17 30 0.70
ACGTcount: A:0.82, C:0.02, G:0.03, T:0.14
Consensus pattern (16 bp):
AAAAAAAATAAAAATA
Found at i:2331369 original size:12 final size:11
Alignment explanation
Indices: 2331329--2331407 Score: 65
Period size: 11 Copynumber: 7.2 Consensus size: 11
2331319 TTAAAGAAAT
*
2331329 AATAAAAA-AG
1 AATAAAAATAA
*
2331339 AATAAGAAAAAA
1 AATAA-AAATAA
2331351 AATAAAAATAA
1 AATAAAAATAA
2331362 AGA-AAAAATAAA
1 A-ATAAAAAT-AA
2331374 AATAAAAATAA
1 AATAAAAATAA
* *
2331385 ACTAAAAATAT
1 AATAAAAATAA
*
2331396 AA-AAAAAGAA
1 AATAAAAATAA
2331406 AA
1 AA
2331408 ATTACTAAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
10 13 0.23
11 28 0.49
12 16 0.28
ACGTcount: A:0.81, C:0.01, G:0.05, T:0.13
Consensus pattern (11 bp):
AATAAAAATAA
Found at i:2331374 original size:23 final size:23
Alignment explanation
Indices: 2331325--2331400 Score: 82
Period size: 25 Copynumber: 3.1 Consensus size: 23
2331315 TTATTTAAAG
*
2331325 AAATAATAAA-AAAGAATAAGAAAAA
1 AAATAA-AAATAAAGAA-AA-AATAA
2331350 AAATAAAAATAAAGAAAAAATAA
1 AAATAAAAATAAAGAAAAAATAA
*
2331373 AAATAAAAATAAACTAAAAATATAA
1 AAATAAAAATAAA-GAAAAA-ATAA
2331398 AAA
1 AAA
2331401 AAGAAAAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
23 17 0.37
24 10 0.22
25 19 0.41
ACGTcount: A:0.80, C:0.01, G:0.04, T:0.14
Consensus pattern (23 bp):
AAATAAAAATAAAGAAAAAATAA
Found at i:2331441 original size:3 final size:3
Alignment explanation
Indices: 2331428--2331467 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
2331418 AATTTTAATC
*
2331428 TAA TAAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2331468 ATAAATACAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2331494 original size:13 final size:14
Alignment explanation
Indices: 2331466--2331496 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
2331456 TAATAATAAT
2331466 AAATAAATACAAAA
1 AAATAAATACAAAA
2331480 AAATAAATA-AAAA
1 AAATAAATACAAAA
2331493 AAAT
1 AAAT
2331497 TAGGAATGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (14 bp):
AAATAAATACAAAA
Found at i:2332328 original size:4 final size:4
Alignment explanation
Indices: 2332291--2332461 Score: 70
Period size: 4 Copynumber: 42.5 Consensus size: 4
2332281 AGTTAAAAGG
* * * * *
2332291 AAAT AATT AGAT AAAT AAA- AATAT TAAT AGAT AAAT -AAT -AAT ATAT
1 AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT AAAT
* * * *
2332337 AAAT AGAT AAAT -AAT -AAT AAAT ACAT ATAT ATAAT -AAT ATAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
* * * *
2332383 ATATAT TAAC AGAT AAAT AATAA AAAT AAAT AAAT AAAT ATTAAT AAAT
1 A-A-AT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT A--AAT AAAT
* *
2332432 AGTAAT -AGT AAAT AAAT -AAT AAAT ACAT AA
1 A--AAT AAAT AAAT AAAT AAAT AAAT AAAT AA
2332462 GATACACAAA
Statistics
Matches: 123, Mismatches: 29, Indels: 30
0.68 0.16 0.16
Matches are distributed among these distances:
3 22 0.18
4 84 0.68
5 8 0.07
6 9 0.07
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.31
Consensus pattern (4 bp):
AAAT
Found at i:2332332 original size:14 final size:14
Alignment explanation
Indices: 2332315--2332461 Score: 81
Period size: 14 Copynumber: 10.2 Consensus size: 14
2332305 ATAAAAATAT
2332315 TAATAGATAAAT-AA
1 TAATA-ATAAATAAA
*
2332329 TAATATATAAATAGA
1 TAATA-ATAAATAAA
2332344 TAAATAAT-AATAAA
1 T-AATAATAAATAAA
*
2332358 TACAT-ATATAT-AA
1 TA-ATAATAAATAAA
*
2332371 TAATATATAAATATA
1 TAATA-ATAAATAAA
* * *
2332386 TATTAACAGATAAA
1 TAATAATAAATAAA
2332400 TAATAA-AAATAAA
1 TAATAATAAATAAA
2332413 TAAATAAATATTAATAAA
1 T-AAT-AATA--AATAAA
* *
2332431 TAGTAAT-AGTAAA
1 TAATAATAAATAAA
*
2332444 TAAATAATAAATACA
1 T-AATAATAAATAAA
2332459 TAA
1 TAA
2332462 GATACACAAA
Statistics
Matches: 102, Mismatches: 17, Indels: 28
0.69 0.12 0.19
Matches are distributed among these distances:
12 2 0.02
13 20 0.20
14 47 0.46
15 16 0.16
16 8 0.08
17 2 0.02
18 7 0.07
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.31
Consensus pattern (14 bp):
TAATAATAAATAAA
Found at i:2332344 original size:42 final size:42
Alignment explanation
Indices: 2332293--2332383 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
2332283 TTAAAAGGAA
* *
2332293 ATAATTAGATAAATAAAAATATTAATAGATA-A-ATAATAATAT
1 ATAAATAGATAAATAAAAATA--AATACATATATATAATAATAT
*
2332335 ATAAATAGATAAATAATAATAAATACATATATATAATAATAT
1 ATAAATAGATAAATAAAAATAAATACATATATATAATAATAT
2332377 ATAAATA
1 ATAAATA
2332384 TATATTAACA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
40 7 0.16
41 1 0.02
42 36 0.82
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (42 bp):
ATAAATAGATAAATAAAAATAAATACATATATATAATAATAT
Found at i:2332372 original size:20 final size:20
Alignment explanation
Indices: 2332325--2332456 Score: 89
Period size: 20 Copynumber: 6.7 Consensus size: 20
2332315 TAATAGATAA
* *
2332325 ATAATAATATATAAATAGATAA
1 ATAATAATAAATAAAT--ATAT
*
2332347 ATAATAATAAATACATATAT
1 ATAATAATAAATAAATATAT
*
2332367 ATAATAATATATAAATATAT
1 ATAATAATAAATAAATATAT
* *
2332387 AT--TAACAGATAAATA-AT
1 ATAATAATAAATAAATATAT
2332404 A-AA-AATAAATAAATA-A-
1 ATAATAATAAATAAATATAT
* *
2332420 ATATTAATAAATAGTAATAGTAA
1 ATAATAATAAATA--AATA-TAT
2332443 ATAAATAATAAATA
1 AT-AATAATAAATA
2332457 CATAAGATAC
Statistics
Matches: 89, Mismatches: 11, Indels: 18
0.75 0.09 0.15
Matches are distributed among these distances:
16 1 0.01
17 15 0.17
18 19 0.21
20 27 0.30
22 15 0.17
23 2 0.02
24 10 0.11
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.32
Consensus pattern (20 bp):
ATAATAATAAATAAATATAT
Found at i:2332386 original size:18 final size:17
Alignment explanation
Indices: 2332301--2332453 Score: 125
Period size: 18 Copynumber: 8.9 Consensus size: 17
2332291 AAATAATTAG
*
2332301 ATAAATAAA-AATATTA
1 ATAAATAAATAATAATA
*
2332317 ATAGATAAATAATAATA
1 ATAAATAAATAATAATA
*
2332334 TATAAATAGATAAATAATA
1 -ATAAATAAAT-AATAATA
2332353 ATAAATACATATATATAATA
1 ATAAATA-A-ATA-ATAATA
* *
2332373 ATATATAAATATATATTA
1 ATAAATAAATA-ATAATA
* * *
2332391 ACAGATAAATAATAAAA
1 ATAAATAAATAATAATA
2332408 ATAAATAAAT-A-AAT-
1 ATAAATAAATAATAATA
* *
2332422 ATTAATAAATAGTAATA
1 ATAAATAAATAATAATA
*
2332439 GTAAATAAATAATAA
1 ATAAATAAATAATAA
2332454 ATACATAAGA
Statistics
Matches: 109, Mismatches: 19, Indels: 17
0.75 0.13 0.12
Matches are distributed among these distances:
14 9 0.08
15 2 0.02
16 12 0.11
17 30 0.28
18 33 0.30
19 9 0.08
20 14 0.13
ACGTcount: A:0.64, C:0.01, G:0.03, T:0.31
Consensus pattern (17 bp):
ATAAATAAATAATAATA
Found at i:2332415 original size:42 final size:42
Alignment explanation
Indices: 2332293--2332411 Score: 111
Period size: 42 Copynumber: 2.9 Consensus size: 42
2332283 TTAAAAGGAA
* * *
2332293 ATAATTAGATAAATAAAAAT-ATTA-ATAGATAAATAATAATAT
1 ATAAATAGATAAATAACAATAAATACATA-A-AAATAATAATAT
* * *
2332335 ATAAATAGATAAATAATAATAAATACATATATATAATAATAT
1 ATAAATAGATAAATAACAATAAATACATAAAAATAATAATAT
* *
2332377 ATAAATATAT-ATTAACAGATAAATA-ATAAAAATAA
1 ATAAATAGATAAATAACA-ATAAATACATAAAAATAA
2332412 ATAAATAAAT
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
41 13 0.20
42 45 0.70
43 3 0.05
44 3 0.05
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (42 bp):
ATAAATAGATAAATAACAATAAATACATAAAAATAATAATAT
Found at i:2332493 original size:7 final size:7
Alignment explanation
Indices: 2332483--2332521 Score: 55
Period size: 7 Copynumber: 5.9 Consensus size: 7
2332473 CAAAAAAGAA
2332483 AAAATAT
1 AAAATAT
2332490 AAAATAT
1 AAAATAT
*
2332497 AAAATAC
1 AAAATAT
2332504 AAAATA-
1 AAAATAT
2332510 AAAA-AT
1 AAAATAT
2332516 AAAATA
1 AAAATA
2332522 GGCCTACCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
5 1 0.03
6 8 0.28
7 20 0.69
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.21
Consensus pattern (7 bp):
AAAATAT
Found at i:2332493 original size:14 final size:14
Alignment explanation
Indices: 2332476--2332516 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
2332466 CACAAAACAA
* *
2332476 AAAAGAAAAAATAT
1 AAAATAAAAAATAC
*
2332490 AAAATATAAAATAC
1 AAAATAAAAAATAC
2332504 AAAATAAAAAATA
1 AAAATAAAAAATA
2332517 AAATAGGCCT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (14 bp):
AAAATAAAAAATAC
Found at i:2332500 original size:21 final size:19
Alignment explanation
Indices: 2332476--2332519 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
2332466 CACAAAACAA
2332476 AAAAGAAAAAATATAAAATAT
1 AAAAGAAAAAATA-AAAA-AT
* *
2332497 AAAATACAAAATAAAAAAT
1 AAAAGAAAAAATAAAAAAT
2332516 AAAA
1 AAAA
2332520 TAGGCCTACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 6 0.29
20 4 0.19
21 11 0.52
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (19 bp):
AAAAGAAAAAATAAAAAAT
Found at i:2332849 original size:46 final size:45
Alignment explanation
Indices: 2332700--2333050 Score: 339
Period size: 46 Copynumber: 7.9 Consensus size: 45
2332690 AAATTTTGAT
* *
2332700 CAAAGCTCTTCTAAGT-AGAGGCTCAATGACTTT-AAAAAACATAAA
1 CAAAGCTCCTCTAA-TCAGAGGCTCAACGACTTTGAAAAAA-ATAAA
* * * * *
2332745 CAAAGCTCCTCTAATAAAATGTTCAACGACTTTGAAAAACATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAAATAAA
*
2332790 CAAAGCTCCTCTAATCAGAGGCTCAACGAATTTGAAAATAAATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAA-AAATAAA
* * *
2332836 CAAAGCTCCTCTAATTAAAGGCTCAACGACTTTGAAAATAAACAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAA-AAATAAA
2332882 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTG---AAAATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAAATAAA
* * * * ** *
2332924 C-GA-TTCCTCTAATCAGAGGCTCAATGACTTT-TAGGAAGT-AA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAAATAAA
** * * * *
2332965 -ATTGCTCATCTAATAAGAGGTTCTACGACTTTG--AAAAATAAA
1 CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAAATAAA
*
2333007 CAAAGCTCCTCTAATCAGAGGCTCAATGACTTTTGAAAATAAAT
1 CAAAGCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAAA-AAAT
2333051 TACTTCTCTA
Statistics
Matches: 249, Mismatches: 42, Indels: 28
0.78 0.13 0.09
Matches are distributed among these distances:
40 26 0.10
41 6 0.02
42 34 0.14
43 23 0.09
44 5 0.02
45 64 0.26
46 87 0.35
47 4 0.02
ACGTcount: A:0.42, C:0.20, G:0.13, T:0.25
Consensus pattern (45 bp):
CAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAAAAATAAA
Found at i:2333036 original size:85 final size:82
Alignment explanation
Indices: 2332886--2333040 Score: 229
Period size: 85 Copynumber: 1.9 Consensus size: 82
2332876 AACAAACAAA
* * * *
2332886 GCTCCTCTAATCAGAGGCTCAACGACTTTGAAAATAAACGATTCCTCTAATCAGAGGCTCAATGA
1 GCTCATCTAATAAGAGGCTCAACGACTTTGAAAATAAACAACTCCTCTAATCAGAGGCTCAATGA
2332951 CTTTTAGGAAGTAAATT
66 CTTTTAGGAAGTAAATT
* *
2332968 GCTCATCTAATAAGAGGTTCTACGACTTTGAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAA
1 GCTCATCTAATAAGAGGCTCAACGACTTTG-AAAATAAAC-AA-CTCCTCTAATCAGAGGCTCAA
2333033 TGACTTTT
63 TGACTTTT
2333041 GAAAATAAAT
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
82 26 0.41
83 9 0.14
84 1 0.02
85 28 0.44
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.28
Consensus pattern (82 bp):
GCTCATCTAATAAGAGGCTCAACGACTTTGAAAATAAACAACTCCTCTAATCAGAGGCTCAATGA
CTTTTAGGAAGTAAATT
Found at i:2333121 original size:125 final size:125
Alignment explanation
Indices: 2332716--2333110 Score: 330
Period size: 125 Copynumber: 3.0 Consensus size: 125
2332706 TCTTCTAAGT
* * * * * *
2332716 AGAGGCTCAATGACTTTAAAAAACATAAACAAAGCTCCTCTAATAAAATGTTCAACGACTTTGAA
1 AGAGGCTCAACGACTTT-GAAAA-ATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTG--
* * * * * * * * **
2332781 AAACATAAACAAAGCTCCTCTAATCAGAGGCTCAACGAATTTGAAAATAAATAAACAAAGCTCCT
62 AAA-ATAAAC-GA-TTCCTCTAAACAAAGGATCAATGACTTTG-AGA-AAAT-AA-ATTGCTCCT
2332846 CTAATTA
120 CTAA-TA
*
2332853 A-AGGCTCAACGACTTTGAAAATAAACAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGA
1 AGAGGCTCAACGACTTTG--AA-AAATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGA
* * * * * * *
2332917 AAATAAACGATTCCTCTAATCAGAGGCTCAATGACTTTTAGGAAGTAAATTGCTCATCTAATA
63 AAATAAACGATTCCTCTAAACAAAGGATCAATGACTTTGAGAAAATAAATTGCTCCTCTAATA
* * *
2332980 AGAGGTTCTACGACTTTGAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAATGACTTTTGAAA
1 AGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACGAC-TTTGAAA
** *
2333045 ATAAATTACTT-CTCTAAACAAAGGTATC-ATGACTTTGA-AAAATAGATTGCTCCTCTAATA
65 ATAAACGA-TTCCTCTAAACAAAGG-ATCAATGACTTTGAGAAAATAAATTGCTCCTCTAATA
2333105 AGAGGC
1 AGAGGC
2333111 ATCACAACTT
Statistics
Matches: 218, Mismatches: 33, Indels: 26
0.79 0.12 0.09
Matches are distributed among these distances:
125 58 0.27
126 35 0.16
127 7 0.03
128 24 0.11
129 2 0.01
130 3 0.01
131 1 0.00
132 25 0.11
133 1 0.00
134 6 0.03
135 3 0.01
136 14 0.06
137 37 0.17
138 2 0.01
ACGTcount: A:0.42, C:0.19, G:0.14, T:0.26
Consensus pattern (125 bp):
AGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAATCAGAGGCTCAACGACTTTGAAAA
TAAACGATTCCTCTAAACAAAGGATCAATGACTTTGAGAAAATAAATTGCTCCTCTAATA
Found at i:2333178 original size:41 final size:41
Alignment explanation
Indices: 2332992--2333180 Score: 170
Period size: 41 Copynumber: 4.6 Consensus size: 41
2332982 AGGTTCTACG
** * *
2332992 ACTTTGAAAAATAAACAAAGCTCCTCTAATCAGAGGC-TCAATG
1 ACTTTGAAAAAT-AA-ATTGCTCCTCTAAACAGAGGCATC-ATA
* * * * *
2333035 ACTTTTG-AAAATAAATTACTTCTCTAAACAAAGGTATCATG
1 AC-TTTGAAAAATAAATTGCTCCTCTAAACAGAGGCATCATA
* *
2333076 ACTTTGAAAAATAGATTGCTCCTCTAATA-AGAGGCATCACA
1 ACTTTGAAAAATAAATTGCTCCTCTAA-ACAGAGGCATCATA
* *
2333117 ACTTT-AAAGAATAGATTGCTCTTCTAAACAGAGGCATCATA
1 ACTTTGAAA-AATAAATTGCTCCTCTAAACAGAGGCATCATA
*
2333158 ATTTTGAAAAATAAATTGCTCCT
1 ACTTTGAAAAATAAATTGCTCCT
2333181 TGACAATCAT
Statistics
Matches: 120, Mismatches: 19, Indels: 16
0.77 0.12 0.10
Matches are distributed among these distances:
40 8 0.07
41 93 0.77
42 8 0.07
43 7 0.06
44 4 0.03
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (41 bp):
ACTTTGAAAAATAAATTGCTCCTCTAAACAGAGGCATCATA
Found at i:2344615 original size:19 final size:19
Alignment explanation
Indices: 2344572--2344616 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
2344562 AAAATTCAAG
* *
2344572 AAAATAAAAAAAAAGAAAT
1 AAAATGAAAAAAAAGAAAA
*
2344591 AAAATGAAAAAGAAGAAAA
1 AAAATGAAAAAAAAGAAAA
2344610 AAAATGA
1 AAAATGA
2344617 TTTAGTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.80, C:0.00, G:0.11, T:0.09
Consensus pattern (19 bp):
AAAATGAAAAAAAAGAAAA
Found at i:2344818 original size:30 final size:29
Alignment explanation
Indices: 2344729--2344820 Score: 80
Period size: 30 Copynumber: 3.1 Consensus size: 29
2344719 TAATTTCGAG
2344729 AAAAATTGATACTTTCAACTTTTCCTCAA
1 AAAAATTGATACTTTCAACTTTTCCTCAA
* ** * **
2344758 AAAACTT--TTTTTTAGAAAGCTTTTTTTCAA
1 AAAAATTGATACTTT--CAA-CTTTTCCTCAA
2344788 AGAAAATTGATACTTTCAACTTTTCCTCAA
1 A-AAAATTGATACTTTCAACTTTTCCTCAA
2344818 AAA
1 AAA
2344821 TATTTTTTAG
Statistics
Matches: 45, Mismatches: 12, Indels: 12
0.65 0.17 0.17
Matches are distributed among these distances:
27 4 0.09
29 10 0.22
30 20 0.44
31 7 0.16
33 4 0.09
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.40
Consensus pattern (29 bp):
AAAAATTGATACTTTCAACTTTTCCTCAA
Found at i:2344853 original size:59 final size:58
Alignment explanation
Indices: 2344668--2344941 Score: 365
Period size: 59 Copynumber: 4.7 Consensus size: 58
2344658 TGTTTTTGTA
* * *
2344668 CAAGAAAAATTGATACTTTTAACTTTTTCTC-AAAATATTTTTTA-AAAACTTTAATTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAAC-TTATTTT
* * * *
2344725 CGAGAAAAATTGATACTTTCAACTTTTCCTCAAAAAACTTTTTTTTAGAAAGCTTTTTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTC-AAAAA-TATTTTTTAGAAAACTTATTTT
*
2344785 CAA-AGAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAAACTTAGTTT
1 CAAGA-AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAG-AAAACTTATTTT
2344844 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTTAGAAAACTTATTTT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTAGAAAACTTATTTT
* * * *
2344903 TAAGGAAAATTGATACTTTCAACTTTTTCTTAAAAATAT
1 CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATAT
2344942 ATATATTTAA
Statistics
Matches: 192, Mismatches: 17, Indels: 15
0.86 0.08 0.07
Matches are distributed among these distances:
57 28 0.15
58 10 0.05
59 100 0.52
60 50 0.26
61 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.06, T:0.42
Consensus pattern (58 bp):
CAAGAAAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAACTTATTTT
Found at i:2344924 original size:118 final size:117
Alignment explanation
Indices: 2344673--2344941 Score: 402
Period size: 118 Copynumber: 2.3 Consensus size: 117
2344663 TTGTACAAGA
* *
2344673 AAAATTGATACTTTTAACTTTTTCTC-AAAATATTTTTTAAAAACTTTAATTTCGAGAAAAATTG
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAACTTTAATTTCAAGAAAAATTG
*
2344737 ATACTTTCAACTTTTCCTCAAAAAACTTTTTTTTAGAAAGCTTTTTTTCAAAG
66 ATACTTTCAACTTTTCCTCAAAAAAC-TTTTTTTAGAAAACTTTTTTTCAAAG
* *
2344790 AAAATTGATACTTTCAACTTTTCCTCAAAAATATTTTTTAGAAAAAC-TTAGTTTCAAGAAAAAT
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTT--AAAAACTTTAATTTCAAGAAAAAT
*
2344854 TGATACTTTCAACTTTTCCTCAAAAATA-TTTTTTTAGAAAACTTATTTTT-AAGG
64 TGATACTTTCAACTTTTCCTCAAAAA-ACTTTTTTTAGAAAACTT-TTTTTCAAAG
*
2344908 AAAATTGATACTTTCAACTTTTTCTTAAAAATAT
1 AAAATTGATACTTTCAACTTTTTCTCAAAAATAT
2344942 ATATATTTAA
Statistics
Matches: 139, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
117 24 0.17
118 62 0.45
119 46 0.33
120 7 0.05
ACGTcount: A:0.38, C:0.13, G:0.06, T:0.43
Consensus pattern (117 bp):
AAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTAAAAACTTTAATTTCAAGAAAAATTG
ATACTTTCAACTTTTCCTCAAAAAACTTTTTTTAGAAAACTTTTTTTCAAAG
Found at i:2345003 original size:30 final size:31
Alignment explanation
Indices: 2344968--2345030 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 31
2344958 TTAAAGAAAT
2344968 AATAAA-AAAAGAATA-AGAAAAAAAAATAAA
1 AATAAACAAAA-AATATAGAAAAAAAAATAAA
* * *
2344998 AATAAACTAAAAATATATAAAAAAAGATAAA
1 AATAAACAAAAAATATAGAAAAAAAAATAAA
2345029 AA
1 AA
2345031 GTACTAAACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (31 bp):
AATAAACAAAAAATATAGAAAAAAAAATAAA
Found at i:2345018 original size:10 final size:10
Alignment explanation
Indices: 2344968--2345117 Score: 62
Period size: 10 Copynumber: 14.2 Consensus size: 10
2344958 TTAAAGAAAT
*
2344968 AATAAAAAAA
1 AATAAATAAA
2344978 GAATAAGA-AAA
1 -AATAA-ATAAA
2344989 AA-AAATAAA
1 AATAAATAAA
2344998 AATAAACTAAA
1 AATAAA-TAAA
*
2345009 AATATATAAA
1 AATAAATAAA
2345019 AA-AAGATAAA
1 AATAA-ATAAA
*
2345029 AAGT-ACTAAA
1 AA-TAAATAAA
*
2345039 CAATTCTAATCTAATA
1 -AA---TAA-ATAA-A
*
2345055 AATAAATAAT
1 AATAAATAAA
2345065 AATAAAT--A
1 AATAAATAAA
2345073 AATAAAT-AA
1 AATAAATAAA
*
2345082 AATAATAATAAT
1 AAT-A-AATAAA
2345094 AATAAATAAATA
1 AATAAAT-AA-A
2345106 AATAAATAAA
1 AATAAATAAA
2345116 AA
1 AA
2345118 CCTGGGAACG
Statistics
Matches: 111, Mismatches: 9, Indels: 39
0.70 0.06 0.25
Matches are distributed among these distances:
8 8 0.07
9 12 0.11
10 36 0.32
11 31 0.28
12 15 0.14
13 1 0.01
14 1 0.01
15 6 0.05
16 1 0.01
ACGTcount: A:0.72, C:0.03, G:0.03, T:0.22
Consensus pattern (10 bp):
AATAAATAAA
Found at i:2345060 original size:4 final size:4
Alignment explanation
Indices: 2345051--2345115 Score: 79
Period size: 4 Copynumber: 17.5 Consensus size: 4
2345041 ATTCTAATCT
2345051 AATA AATA AAT- AAT- AATA AATA AATA AATA AA-A TAAT- AAT- AAT-
1 AATA AATA AATA AATA AATA AATA AATA AATA AATA -AATA AATA AATA
2345094 AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AA
2345116 AACCTGGGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
3 16 0.28
4 41 0.72
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:2346009 original size:42 final size:41
Alignment explanation
Indices: 2345951--2346077 Score: 134
Period size: 42 Copynumber: 3.0 Consensus size: 41
2345941 AAATCAAATC
* *
2345951 AAATAAAAAATGTTAATAGATAATTAA-AATAAAATA-ATTAGAT
1 AAAT-AAAAATATTAATAGATAAATAATAATAAAATACA-T--AT
2345994 AAATAAAAATATTAATAGATAAATAATAAT-AAATACATAT
1 AAATAAAAATATTAATAGATAAATAATAATAAAATACATAT
* *
2346034 AAATAATAATATATAAATAGATAAATAATAATAAATATATATAT
1 AAATAA-AA-ATATTAATAGATAAATAATAATAAA-ATACATAT
2346078 TAACAGATAA
Statistics
Matches: 74, Mismatches: 4, Indels: 11
0.83 0.04 0.12
Matches are distributed among these distances:
40 8 0.11
41 2 0.03
42 47 0.64
43 10 0.14
44 7 0.09
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (41 bp):
AAATAAAAATATTAATAGATAAATAATAATAAAATACATAT
Found at i:2346014 original size:20 final size:20
Alignment explanation
Indices: 2345951--2346066 Score: 83
Period size: 20 Copynumber: 5.5 Consensus size: 20
2345941 AAATCAAATC
*
2345951 AAATAAAAAATGTTAATAGAT
1 AAAT-AAAAATATTAATAGAT
* * *
2345972 AATTAAAATAAAATAATTAGAT
1 AAATAAAA-ATATTAA-TAGAT
2345994 AAATAAAAATATTAATAGAT
1 AAATAAAAATATTAATAGAT
* *
2346014 AAATAATAATA--AATACATAT
1 AAATAAAAATATTAAT--AGAT
*
2346034 AAATAATAATATATAAATAGAT
1 AAATAA-AA-ATATTAATAGAT
*
2346056 AAATAATAATA
1 AAATAAAAATA
2346067 AATATATATA
Statistics
Matches: 75, Mismatches: 12, Indels: 17
0.72 0.12 0.16
Matches are distributed among these distances:
18 3 0.04
20 31 0.41
21 14 0.19
22 24 0.32
24 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.04, T:0.30
Consensus pattern (20 bp):
AAATAAAAATATTAATAGAT
Found at i:2346019 original size:4 final size:4
Alignment explanation
Indices: 2345977--2346146 Score: 72
Period size: 4 Copynumber: 43.5 Consensus size: 4
2345967 TAGATAATTA
* * * *
2345977 AAAT AAAAT AATT AGAT AAAT AAA- AATAT TAAT AGAT AAAT -AAT -AAT
1 AAAT -AAAT AAAT AAAT AAAT AAAT AA-AT AAAT AAAT AAAT AAAT AAAT
* *
2346024 AAAT ACATAT AAAT -AAT -AAT ATAT AAAT AGAT AAAT -AAT -AAT AAAT
1 AAAT A-A-AT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
* * * * * * * * *
2346070 ATAT ATAT TAAC AGAT AAAT AAAA AAAT AAA- ATAT ATAT TAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
*
2346117 AGTAAT -AAT AAAT AAAT -AAT AAAT ACAT AA
1 A--AAT AAAT AAAT AAAT AAAT AAAT AAAT AA
2346147 GATACACAAA
Statistics
Matches: 125, Mismatches: 28, Indels: 25
0.70 0.16 0.14
Matches are distributed among these distances:
3 28 0.22
4 84 0.67
5 7 0.06
6 6 0.05
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (4 bp):
AAAT
Found at i:2346023 original size:14 final size:13
Alignment explanation
Indices: 2345964--2346146 Score: 85
Period size: 14 Copynumber: 13.5 Consensus size: 13
2345954 TAAAAAATGT
*
2345964 TAATAGATAATTAA
1 TAATA-ATAATAAA
*
2345978 -AATAA-AATAAT
1 TAATAATAATAAA
2345989 TAGATAAATAA-AAA
1 TA-AT-AATAATAAA
*
2346003 TATTAATAGATAAA
1 TAATAATA-ATAAA
*
2346017 TAATAATAAATACA
1 TAATAAT-AATAAA
2346031 T-ATAAATAAT-AA
1 TAAT-AATAATAAA
2346043 TATATAAATAGATAAA
1 TA-AT-AATA-ATAAA
2346059 TAATAATAAATATATA
1 TAATAAT-AATA-A-A
* *
2346075 TATTAACAGATAAA
1 TAATAATA-ATAAA
*
2346089 TAA-AAAAATAAAA
1 TAATAATAAT-AAA
*
2346102 TATATATTAATAAA
1 TA-ATAATAATAAA
*
2346116 TAGTAATAATAAA
1 TAATAATAATAAA
2346129 T-A-AATAATAAA
1 TAATAATAATAAA
2346140 TACATAA
1 TA-ATAA
2346147 GATACACAAA
Statistics
Matches: 131, Mismatches: 16, Indels: 44
0.69 0.08 0.23
Matches are distributed among these distances:
11 14 0.11
12 10 0.08
13 32 0.24
14 47 0.36
15 15 0.11
16 13 0.10
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (13 bp):
TAATAATAATAAA
Found at i:2346092 original size:42 final size:41
Alignment explanation
Indices: 2345965--2346146 Score: 130
Period size: 42 Copynumber: 4.4 Consensus size: 41
2345955 AAAAAATGTT
*
2345965 AATAGATAATTA-A-AATAAAATAAT-TAGATAAATAA-AAATA
1 AATAGATAAATACATAAT-AAATAATATA-AT-AATAATAAATA
*
2346005 TTAATAGATAAATA-ATAATAAATACATATAAATAATAATATATA
1 --AATAGATAAATACATAATAAATA-ATAT-AATAATAATAAATA
* *
2346049 AATAGATAAATA-ATAATAAATATATATATTAACAGATAAATA
1 AATAGATAAATACATAATAAATA-ATATAATAATA-ATAAATA
* * * * *
2346091 AAAAAATAAA-ATATATATTAATAA-ATAGTAATAATAAATA
1 AATAGATAAATACATA-ATAAATAATATAATAATAATAAATA
2346131 AATA-ATAAATACATAA
1 AATAGATAAATACATAA
2346147 GATACACAAA
Statistics
Matches: 118, Mismatches: 13, Indels: 21
0.78 0.09 0.14
Matches are distributed among these distances:
39 6 0.05
40 14 0.12
41 13 0.11
42 61 0.52
43 16 0.14
44 7 0.06
45 1 0.01
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (41 bp):
AATAGATAAATACATAATAAATAATATAATAATAATAAATA
Found at i:2346134 original size:31 final size:29
Alignment explanation
Indices: 2346032--2346131 Score: 87
Period size: 31 Copynumber: 3.3 Consensus size: 29
2346022 ATAAATACAT
*
2346032 ATAAATAATAATATATAAATAGATAAATAATA
1 ATAAATAAT-ATATATTAATAGAT--ATAATA
*
2346064 ATAAAT-ATATATATTAACAGATA-AATAA
1 ATAAATAATATATATTAATAGATATAAT-A
* *
2346092 AAAAATAAAATATATATTAATAAATAGTAATA
1 ATAAAT--AATATATATTAATAGATA-TAATA
2346124 ATAAATAA
1 ATAAATAA
2346132 ATAATAAATA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
27 3 0.05
28 7 0.12
30 14 0.25
31 17 0.30
32 12 0.21
33 3 0.05
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (29 bp):
ATAAATAATATATATTAATAGATATAATA
Found at i:2346137 original size:20 final size:19
Alignment explanation
Indices: 2345977--2346146 Score: 85
Period size: 20 Copynumber: 8.9 Consensus size: 19
2345967 TAGATAATTA
*
2345977 AAATAAAATAATTAGATAAAT
1 AAATAATATAA-TA-ATAAAT
2345998 AAA-AATATTAATAGATAAAT
1 AAATAATA-TAATA-ATAAAT
2346018 -AATAATA-AATACAT--AT
1 AAATAATATAATA-ATAAAT
2346034 AAAT-A-ATAATATATAAAT
1 AAATAATATAATA-ATAAAT
*
2346052 AGATAA-ATAATAATAAAT
1 AAATAATATAATAATAAAT
* *
2346070 ATAT-ATATTAACAGATAAAT
1 AAATAATA-TAATA-ATAAAT
*
2346090 AAA-AAAATAA-AATATATAT
1 AAATAATATAATAATA-A-AT
*
2346109 TAATAAATAGTAATAATAAAT
1 AAAT-AATA-TAATAATAAAT
2346130 AAATAATA-AATACATAA
1 AAATAATATAATA-ATAA
2346147 GATACACAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 38
0.71 0.07 0.22
Matches are distributed among these distances:
15 1 0.01
16 9 0.08
17 7 0.06
18 27 0.22
19 24 0.20
20 30 0.25
21 14 0.12
22 4 0.03
23 4 0.03
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.30
Consensus pattern (19 bp):
AAATAATATAATAATAAAT
Found at i:2349874 original size:13 final size:13
Alignment explanation
Indices: 2349856--2349881 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2349846 GACCAGGAAA
2349856 CCCATTACATGTG
1 CCCATTACATGTG
2349869 CCCATTACATGTG
1 CCCATTACATGTG
2349882 ATGGATTTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.15, T:0.31
Consensus pattern (13 bp):
CCCATTACATGTG
Found at i:2351738 original size:48 final size:48
Alignment explanation
Indices: 2351667--2351763 Score: 194
Period size: 48 Copynumber: 2.0 Consensus size: 48
2351657 AGGTGATCCA
2351667 GCCGCCTTGTTTACGACCTGAATTTGGGGTTTGGATTTCTCTATCAAG
1 GCCGCCTTGTTTACGACCTGAATTTGGGGTTTGGATTTCTCTATCAAG
2351715 GCCGCCTTGTTTACGACCTGAATTTGGGGTTTGGATTTCTCTATCAAG
1 GCCGCCTTGTTTACGACCTGAATTTGGGGTTTGGATTTCTCTATCAAG
2351763 G
1 G
2351764 GTATCCATTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 49 1.00
ACGTcount: A:0.16, C:0.21, G:0.26, T:0.37
Consensus pattern (48 bp):
GCCGCCTTGTTTACGACCTGAATTTGGGGTTTGGATTTCTCTATCAAG
Found at i:2361694 original size:26 final size:26
Alignment explanation
Indices: 2361661--2361711 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
2361651 TTTTGATTTG
2361661 TAATGATGTAAAAATTTAATGAAATT
1 TAATGATGTAAAAATTTAATGAAATT
2361687 TAATGATGTAAAAATTTAATGAAAT
1 TAATGATGTAAAAATTTAATGAAAT
2361712 ATAAATGTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.12, T:0.37
Consensus pattern (26 bp):
TAATGATGTAAAAATTTAATGAAATT
Found at i:2361717 original size:16 final size:16
Alignment explanation
Indices: 2361682--2361747 Score: 53
Period size: 16 Copynumber: 4.0 Consensus size: 16
2361672 AAATTTAATG
** *
2361682 AAATTTAATGATGTAA
1 AAATTTAATGAAATAT
2361698 AAATTTAATGAAATAT
1 AAATTTAATGAAATAT
*
2361714 AAATGTATCAATCAAATAT
1 AAAT-T-T-AATGAAATAT
*
2361733 AAA-TTAATAAAATAT
1 AAATTTAATGAAATAT
2361748 TTTATTCCAT
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
15 9 0.21
16 18 0.43
17 2 0.05
18 1 0.02
19 12 0.29
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (16 bp):
AAATTTAATGAAATAT
Found at i:2374402 original size:31 final size:32
Alignment explanation
Indices: 2374367--2374440 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 32
2374357 TAAAACGTTA
2374367 CAAATGAAATCCAAA-TGCATTAATATTTTAC
1 CAAATGAAATCCAAAGTGCATTAATATTTTAC
2374398 CAAATGAAAT-CAAATGTGCATTAATATTTTAC
1 CAAATGAAATCCAAA-GTGCATTAATATTTTAC
*
2374430 CATATGAAATC
1 CAAATGAAATC
2374441 ATATTTAATG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 4 0.10
31 10 0.26
32 25 0.64
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (32 bp):
CAAATGAAATCCAAAGTGCATTAATATTTTAC
Found at i:2374473 original size:19 final size:21
Alignment explanation
Indices: 2374431--2374479 Score: 66
Period size: 19 Copynumber: 2.4 Consensus size: 21
2374421 ATATTTTACC
*
2374431 ATATGAAATCATATTTAATGAA
1 ATAT-AAATCATATTTAATCAA
2374453 ATATAAATC-TA-TTAATCAA
1 ATATAAATCATATTTAATCAA
2374472 ATATAAAT
1 ATATAAAT
2374480 TAATAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 15 0.58
20 2 0.08
21 5 0.19
22 4 0.15
ACGTcount: A:0.53, C:0.06, G:0.04, T:0.37
Consensus pattern (21 bp):
ATATAAATCATATTTAATCAA
Found at i:2374730 original size:8 final size:9
Alignment explanation
Indices: 2374704--2374728 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
2374694 TCAAATTAAG
2374704 AAATTTTTA
1 AAATTTTTA
2374713 AAATTTTTA
1 AAATTTTTA
2374722 AAATTTT
1 AAATTTT
2374729 AATATGAATT
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AAATTTTTA
Found at i:2375752 original size:19 final size:19
Alignment explanation
Indices: 2375701--2375752 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
2375691 TAATTTTTTT
*
2375701 AAAT-TATTT-TTAAATTA
1 AAATATATTTATTAAAATA
*
2375718 AGAATATA-TTAATAAAATA
1 A-AATATATTTATTAAAATA
2375737 AAATATATTTATTAAA
1 AAATATATTTATTAAA
2375753 TATCATGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 1 0.04
18 11 0.39
19 16 0.57
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (19 bp):
AAATATATTTATTAAAATA
Found at i:2375753 original size:18 final size:18
Alignment explanation
Indices: 2375701--2375754 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
2375691 TAATTTTTTT
2375701 AAAT-TATTT-TTAAATTA
1 AAATATATTTATTAAA-TA
* *
2375718 AGAATATATTAATAAAATA
1 A-AATATATTTATTAAATA
2375737 AAATATATTTATTAAATA
1 AAATATATTTATTAAATA
2375755 TCATGTGACT
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.03
18 18 0.60
19 7 0.23
20 4 0.13
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (18 bp):
AAATATATTTATTAAATA
Found at i:2375901 original size:5 final size:5
Alignment explanation
Indices: 2375893--2375917 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
2375883 ATAGATTAGA
2375893 TTTAT TTTAT TTTAT TTTAT TTTAT
1 TTTAT TTTAT TTTAT TTTAT TTTAT
2375918 GTACTTTGTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTAT
Found at i:2376262 original size:18 final size:18
Alignment explanation
Indices: 2376221--2376263 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2376211 TGTTAGTTTT
* * *
2376221 TTAATAATATTTTTTATG
1 TTAAAAATATTTTTAATA
*
2376239 TCAAAAATATTTTTAATA
1 TTAAAAATATTTTTAATA
2376257 TTAAAAA
1 TTAAAAA
2376264 AAACTAAAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAAAAATATTTTTAATA
Found at i:2377527 original size:20 final size:20
Alignment explanation
Indices: 2377502--2377544 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
2377492 TATTTAACCA
2377502 AAAATTGGAAA-AGTACATTG
1 AAAATTGGAAATA-TACATTG
2377522 AAAATTGGAAATATACATTG
1 AAAATTGGAAATATACATTG
2377542 AAA
1 AAA
2377545 TCTGGGTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 21 0.95
21 1 0.05
ACGTcount: A:0.53, C:0.05, G:0.16, T:0.26
Consensus pattern (20 bp):
AAAATTGGAAATATACATTG
Found at i:2378493 original size:87 final size:86
Alignment explanation
Indices: 2378250--2378514 Score: 395
Period size: 87 Copynumber: 3.1 Consensus size: 86
2378240 TTCTCTAAGT
* *
2378250 AGAGGCTCAATGACTTTGGATAAATAAACAAAGCTCCTCTAAATAGAGGCTCAAAGACTTTGAAA
1 AGAGGCTCAATGACTTTGGA-AAATAAACAAAGCTCCTCTAAGTAGAGGCTTAAAGACTTTGAAA
**
2378315 AATAAACAAAGCTCCCCTAAAC
65 AATAAACAAAGCTCCTTTAAAC
* * * *
2378337 AGAGGCTTAATGACTTTAGAAAATAAACAAAGCTCCTCTAAGCAGAGGCTTAACGACTTTGAAAA
1 AGAGGCTCAATGACTTTGGAAAATAAACAAAGCTCCTCTAAGTAGAGGCTTAAAGACTTTGAAAA
2378402 ATAAACAAAGCTCCTTTAAAC
66 ATAAACAAAGCTCCTTTAAAC
* * *
2378423 AGAGGCTCAATGACTTTGGACAAATAAATAAAGCTTCTCTAAGTAGAGGCTTAATGACTTTGAAA
1 AGAGGCTCAATGACTTTGGA-AAATAAACAAAGCTCCTCTAAGTAGAGGCTTAAAGACTTTGAAA
* *
2378488 AATAAACAAAGCTCTTTTAAAT
65 AATAAACAAAGCTCCTTTAAAC
2378510 AGAGG
1 AGAGG
2378515 TACCATAACT
Statistics
Matches: 161, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
86 78 0.48
87 83 0.52
ACGTcount: A:0.43, C:0.17, G:0.16, T:0.24
Consensus pattern (86 bp):
AGAGGCTCAATGACTTTGGAAAATAAACAAAGCTCCTCTAAGTAGAGGCTTAAAGACTTTGAAAA
ATAAACAAAGCTCCTTTAAAC
Found at i:2378513 original size:43 final size:43
Alignment explanation
Indices: 2378189--2378514 Score: 359
Period size: 43 Copynumber: 7.5 Consensus size: 43
2378179 AAATCTTGAT
* *
2378189 CAAAGCTCCTC-CAATAAGAGGCTCAATGACTTTTTAAAAAATAAA
1 CAAAGCTCCTCTAAAT-AGAGGCTCAATGAC--TTTGAAAAATAAA
* * * * * *
2378234 TAAGGTTTCTCTAAGTAGAGGCTCAATGACTTTGGATAAATAAA
1 CAAAGCTCCTCTAAATAGAGGCTCAATGACTTT-GAAAAATAAA
*
2378278 CAAAGCTCCTCTAAATAGAGGCTCAAAGACTTTGAAAAATAAA
1 CAAAGCTCCTCTAAATAGAGGCTCAATGACTTTGAAAAATAAA
* * *
2378321 CAAAGCTCCCCTAAACAGAGGCTTAATGACTTT-AGAAAATAAA
1 CAAAGCTCCTCTAAATAGAGGCTCAATGACTTTGA-AAAATAAA
** * *
2378364 CAAAGCTCCTCTAAGCAGAGGCTTAACGACTTTGAAAAATAAA
1 CAAAGCTCCTCTAAATAGAGGCTCAATGACTTTGAAAAATAAA
* * *
2378407 CAAAGCTCCTTTAAACAGAGGCTCAATGACTTTGGACAAATAAA
1 CAAAGCTCCTCTAAATAGAGGCTCAATGACTTT-GAAAAATAAA
* * * *
2378451 TAAAGCTTCTCTAAGTAGAGGCTTAATGACTTTGAAAAATAAA
1 CAAAGCTCCTCTAAATAGAGGCTCAATGACTTTGAAAAATAAA
* *
2378494 CAAAGCTCTTTTAAATAGAGG
1 CAAAGCTCCTCTAAATAGAGG
2378515 TACCATAACT
Statistics
Matches: 237, Mismatches: 39, Indels: 12
0.82 0.14 0.04
Matches are distributed among these distances:
42 1 0.00
43 141 0.59
44 72 0.30
45 21 0.09
46 2 0.01
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.25
Consensus pattern (43 bp):
CAAAGCTCCTCTAAATAGAGGCTCAATGACTTTGAAAAATAAA
Found at i:2389943 original size:8 final size:8
Alignment explanation
Indices: 2389930--2389968 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
2389920 AAAAAAATTC
2389930 AAGAATAA
1 AAGAATAA
2389938 AAGAATAA
1 AAGAATAA
2389946 AAGAATAA
1 AAGAATAA
*
2389954 AATAA-AA
1 AAGAATAA
*
2389961 AGGAATAA
1 AAGAATAA
2389969 TGATTCAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 5 0.19
8 22 0.81
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (8 bp):
AAGAATAA
Found at i:2390163 original size:58 final size:60
Alignment explanation
Indices: 2390032--2390188 Score: 210
Period size: 58 Copynumber: 2.6 Consensus size: 60
2390022 TTTGTACAAA
* * * * * *
2390032 AAAAATTAATACTTTCAACTTTTTCTTAAAATGTTTTTCTTGATAATTTTTATTTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTTGATAATTTTTAATTTTAAG
* *
2390092 AAAAATTGGTACTTCCAACTTTTCCTAAAAATATTTTTTTTGA-AA-TTTTAATTTTAAG
1 AAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTTGATAATTTTTAATTTTAAG
* *
2390150 AAAAATTGATACTTTCAACTTTTCTTCAAAATATTTTTT
1 AAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTT
2390189 GAAAAATTTA
Statistics
Matches: 85, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
58 47 0.55
59 2 0.02
60 36 0.42
ACGTcount: A:0.35, C:0.10, G:0.05, T:0.50
Consensus pattern (60 bp):
AAAAATTGATACTTTCAACTTTTCCTAAAAATATTTTTTTTGATAATTTTTAATTTTAAG
Found at i:2390194 original size:72 final size:72
Alignment explanation
Indices: 2390118--2390255 Score: 206
Period size: 71 Copynumber: 1.9 Consensus size: 72
2390108 AACTTTTCCT
* * ** *
2390118 AAAAATATTTTTTTTGAAATTTTAATTTTAAGAAAAATTGATACTTTCAAC-TTTTCTTCAAAAT
1 AAAAAT-TTATTTATGAAATTTTAATTCCAAGAAAAATTGATACTTTCAACTTTTTCTTAAAAAT
2390182 ATTTTTTG
65 ATTTTTTG
*
2390190 AAAAATTTATTTATGAAATTTTACTTCCAAGAAAAATTGATACTTTCAACTTTTTCTTAAAAATA
1 AAAAATTTATTTATGAAATTTTAATTCCAAGAAAAATTGATACTTTCAACTTTTTCTTAAAAATA
2390255 T
66 T
2390256 ATATGTTTTT
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
71 39 0.66
72 20 0.34
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (72 bp):
AAAAATTTATTTATGAAATTTTAATTCCAAGAAAAATTGATACTTTCAACTTTTTCTTAAAAATA
TTTTTTG
Found at i:2390312 original size:5 final size:5
Alignment explanation
Indices: 2390304--2390337 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
2390294 AATATATATA
2390304 AAAAT AAAAAT AAAAT AAAAT AAAAT AAAAT AAA
1 AAAAT -AAAAT AAAAT AAAAT AAAAT AAAAT AAA
2390338 GAATACCAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAAAT
Found at i:2390330 original size:15 final size:16
Alignment explanation
Indices: 2390285--2390337 Score: 63
Period size: 15 Copynumber: 3.2 Consensus size: 16
2390275 AATTTTAAGA
*
2390285 AAAATAAAAAATATATAT
1 AAAAT-AAAAATA-AAAT
2390303 AAAAATAAAAATAAAAT
1 -AAAATAAAAATAAAAT
2390320 AAAAT-AAAATAAAAT
1 AAAATAAAAATAAAAT
2390335 AAA
1 AAA
2390338 GAATACCAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
15 13 0.39
16 5 0.15
17 3 0.09
18 7 0.21
19 5 0.15
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (16 bp):
AAAATAAAAATAAAAT
Found at i:2390382 original size:4 final size:4
Alignment explanation
Indices: 2390373--2390397 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
2390363 AAATAATAAT
2390373 AATA AATA AATA AATA AATA AATA A
1 AATA AATA AATA AATA AATA AATA A
2390398 CCTTAACGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AATA
Found at i:2390685 original size:16 final size:17
Alignment explanation
Indices: 2390653--2390685 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2390643 AACAGAGGCG
*
2390653 TCTTTTTTTTCTCTCTT
1 TCTTTCTTTTCTCTCTT
2390670 TCTTTCTTTT-TCTCTT
1 TCTTTCTTTTCTCTCTT
2390686 ATTTCTCTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (17 bp):
TCTTTCTTTTCTCTCTT
Found at i:2390857 original size:20 final size:21
Alignment explanation
Indices: 2390820--2390859 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
2390810 AAATTTGGCC
*
2390820 AAAAAATTTCATCGAATTTTG
1 AAAAAATTTCATCAAATTTTG
*
2390841 AAAAATTTTCAT-AAATTTT
1 AAAAAATTTCATCAAATTTT
2390860 TCAGAAAAGA
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:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
AAAAAATTTCATCAAATTTTG
Found at i:2391196 original size:3 final size:3
Alignment explanation
Indices: 2391188--2391264 Score: 79
Period size: 3 Copynumber: 25.7 Consensus size: 3
2391178 AATCAATCAA
* * *
2391188 AAT AAT AAT AAT AAT AAT -AT AAT AGCA- AAT AAT AAA AAT AAA AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT A--AT AAT AAT AAT AAT AAT AAT
2391233 AAT AAT AAAT AAT AAT -AT AAT AAT AAT AAT AA
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AA
2391265 AAAAAGGGTC
Statistics
Matches: 64, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
2 5 0.08
3 54 0.84
4 4 0.06
5 1 0.02
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:2391218 original size:21 final size:18
Alignment explanation
Indices: 2391188--2391266 Score: 85
Period size: 17 Copynumber: 4.4 Consensus size: 18
2391178 AATCAATCAA
2391188 AATAATAATAATAATAATAT
1 AATAA-AATAATAATAA-AT
2391208 AATAGCAAATAATAA-AAAT
1 AATA--AAATAATAATAAAT
2391227 AA-AAAA-AATAATAAAT
1 AATAAAATAATAATAAAT
*
2391243 AATAATATAATAAT-AAT
1 AATAAAATAATAATAAAT
2391260 AATAAAA
1 AATAAAA
2391267 AAAGGGTCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 13
0.78 0.03 0.19
Matches are distributed among these distances:
15 5 0.10
16 9 0.17
17 12 0.23
18 7 0.13
19 4 0.08
20 6 0.12
21 8 0.15
22 1 0.02
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (18 bp):
AATAAAATAATAATAAAT
Found at i:2391237 original size:36 final size:35
Alignment explanation
Indices: 2391177--2391269 Score: 105
Period size: 36 Copynumber: 2.6 Consensus size: 35
2391167 AGAAAAAATA
* * * *
2391177 AAATCAATCAAAATAATAATAATAATAATATAATAGC
1 AAAT-AATAAAAATAAAAAAAATAATAA-ATAATAAC
*
2391214 AAATAATAAAAATAAAAAAAATAATAAATAATAAT
1 AAATAATAAAAATAAAAAAAATAATAAATAATAAC
*
2391249 ATAATAATAATAATAAAAAAA
1 A-AATAATAAAAATAAAAAAA
2391270 GGGTCAATCT
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
35 7 0.14
36 38 0.78
37 4 0.08
ACGTcount: A:0.71, C:0.03, G:0.01, T:0.25
Consensus pattern (35 bp):
AAATAATAAAAATAAAAAAAATAATAAATAATAAC
Found at i:2391856 original size:20 final size:22
Alignment explanation
Indices: 2391831--2391871 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2391821 AATATGTATT
2391831 AAAA-TTTATATTT-ATATTAA
1 AAAATTTTATATTTGATATTAA
2391851 AAAATTTTTATATTTGATATT
1 AAAA-TTTTATATTTGATATT
2391872 TTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
AAAATTTTATATTTGATATTAA
Found at i:2397073 original size:5 final size:6
Alignment explanation
Indices: 2397056--2397080 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
2397046 AATTCTATTG
2397056 TCTTTT TCTTTT TCTTTT TCTTTT T
1 TCTTTT TCTTTT TCTTTT TCTTTT T
2397081 TTATCAATTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TCTTTT
Found at i:2397215 original size:34 final size:34
Alignment explanation
Indices: 2397176--2397242 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 34
2397166 CAATAAATTT
* *
2397176 TAAATTCAATTTTAAATATTTATAATTTTTTTTA
1 TAAATTCAAATTTAAATATTTATAATTTCTTTTA
*
2397210 TAAATTTAAATTTAAATATTTATAATTTCTTTT
1 TAAATTCAAATTTAAATATTTATAATTTCTTTT
2397243 CATATTTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (34 bp):
TAAATTCAAATTTAAATATTTATAATTTCTTTTA
Found at i:2399117 original size:22 final size:21
Alignment explanation
Indices: 2399069--2399117 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 21
2399059 ATAAAATTTA
**
2399069 TATAATTTTTTAATAAAAAAT
1 TATAATTTTAAAATAAAAAAT
2399090 TCATAATTTTAAAATAAAAAAAT
1 T-ATAATTTTAAAAT-AAAAAAT
2399113 TATAA
1 TATAA
2399118 ATGTTAAGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 1 0.04
22 15 0.62
23 8 0.33
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (21 bp):
TATAATTTTAAAATAAAAAAT
Found at i:2399839 original size:17 final size:18
Alignment explanation
Indices: 2399819--2399853 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
2399809 GTAATAAAAT
2399819 AATTAAGTTAA-TATTAA
1 AATTAAGTTAATTATTAA
*
2399836 AATTAATTTAATTATTAA
1 AATTAAGTTAATTATTAA
2399854 TCCAATTTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (18 bp):
AATTAAGTTAATTATTAA
Found at i:2400357 original size:17 final size:17
Alignment explanation
Indices: 2400337--2400372 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
2400327 AAACTCAAAC
2400337 TCAAATTTAATAATCTA
1 TCAAATTTAATAATCTA
2400354 TCAAATTTAATAATCTA
1 TCAAATTTAATAATCTA
2400371 TC
1 TC
2400373 GATTTAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.14, G:0.00, T:0.42
Consensus pattern (17 bp):
TCAAATTTAATAATCTA
Found at i:2402187 original size:12 final size:12
Alignment explanation
Indices: 2402169--2402217 Score: 55
Period size: 12 Copynumber: 4.0 Consensus size: 12
2402159 GGAAGGTTTG
2402169 GGAGGAAGAGAT
1 GGAGGAAGAGAT
* *
2402181 AGAGGAAGGGAT
1 GGAGGAAGAGAT
2402193 GGAGGAA-AGGAT
1 GGAGGAAGA-GAT
2402205 GGAGGAAAGAGAT
1 GGAGG-AAGAGAT
2402218 TGATGGATGA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
12 24 0.80
13 5 0.17
14 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.49, T:0.08
Consensus pattern (12 bp):
GGAGGAAGAGAT
Found at i:2406362 original size:24 final size:24
Alignment explanation
Indices: 2406335--2406388 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2406325 GAGATCCTTT
2406335 AATTTAGAACAATAAAACAAATTA
1 AATTTAGAACAATAAAACAAATTA
* *
2406359 AATTTAGAATAATAAAACAAATTG
1 AATTTAGAACAATAAAACAAATTA
2406383 AATTTA
1 AATTTA
2406389 TTGTATTTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.30
Consensus pattern (24 bp):
AATTTAGAACAATAAAACAAATTA
Found at i:2406511 original size:31 final size:32
Alignment explanation
Indices: 2406476--2406549 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 32
2406466 TAAAACGTTA
2406476 CAAATGAAATCCAAA-TACATTAATATTTTAC
1 CAAATGAAATCCAAAGTACATTAATATTTTAC
*
2406507 CAAATGAAAT-CAAATGTGCATTAATATTTTAC
1 CAAATGAAATCCAAA-GTACATTAATATTTTAC
*
2406539 CATATGAAATC
1 CAAATGAAATC
2406550 ATATTTAATG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
30 4 0.11
31 10 0.26
32 24 0.63
ACGTcount: A:0.46, C:0.15, G:0.07, T:0.32
Consensus pattern (32 bp):
CAAATGAAATCCAAAGTACATTAATATTTTAC
Found at i:2418258 original size:17 final size:18
Alignment explanation
Indices: 2418218--2418259 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
2418208 AAATGATAAT
*
2418218 AATAAAA-TTAAATAATA
1 AATAAAATTTAAAGAATA
*
2418235 AAAAAAATTTAAAGAA-A
1 AATAAAATTTAAAGAATA
2418252 AATAAAAT
1 AATAAAAT
2418260 GTGTGCATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 14 0.67
18 7 0.33
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
AATAAAATTTAAAGAATA
Found at i:2420743 original size:24 final size:24
Alignment explanation
Indices: 2420710--2420763 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
2420700 GAGATCCTTT
*
2420710 AATTTAGAACAATAAAATAAATTA
1 AATTTAGAACAATAAAACAAATTA
*
2420734 AATTTGGAACAATAAAACAAATTA
1 AATTTAGAACAATAAAACAAATTA
2420758 AATTTA
1 AATTTA
2420764 TTGTATTTAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.30
Consensus pattern (24 bp):
AATTTAGAACAATAAAACAAATTA
Found at i:2420886 original size:31 final size:32
Alignment explanation
Indices: 2420851--2420924 Score: 116
Period size: 32 Copynumber: 2.3 Consensus size: 32
2420841 TAAAACGTTA
2420851 CAAATGAAATCCAAA-TGCATTAATATTTTAC
1 CAAATGAAATCCAAAGTGCATTAATATTTTAC
2420882 CAAATGAAAT-CAAATGTGCATTAATATTTTAC
1 CAAATGAAATCCAAA-GTGCATTAATATTTTAC
*
2420914 CATATGAAATC
1 CAAATGAAATC
2420925 TTATTTAATG
Statistics
Matches: 39, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
30 4 0.10
31 10 0.26
32 25 0.64
ACGTcount: A:0.45, C:0.15, G:0.08, T:0.32
Consensus pattern (32 bp):
CAAATGAAATCCAAAGTGCATTAATATTTTAC
Found at i:2422060 original size:23 final size:23
Alignment explanation
Indices: 2422020--2422070 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
2422010 ATTAATTAGA
* * *
2422020 ATTTATAATTGTAGTATTTATTT
1 ATTTATAATTATAGTATTGATTG
2422043 ATTTATTAATTATA-TATTGATTG
1 ATTTA-TAATTATAGTATTGATTG
2422066 ATTTA
1 ATTTA
2422071 ATTTGTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (23 bp):
ATTTATAATTATAGTATTGATTG
Found at i:2422226 original size:18 final size:18
Alignment explanation
Indices: 2422174--2422227 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 18
2422164 TTAATTTTTT
2422174 AAAT-TATTT-TTAAATTAA
1 AAATATATTTATTAAA-T-A
* *
2422192 AAATATATTAATAAAATA
1 AAATATATTTATTAAATA
2422210 AAATATATTTATTAAATA
1 AAATATATTTATTAAATA
2422228 TCACGTGATG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
18 21 0.70
19 5 0.17
20 4 0.13
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATATATTTATTAAATA
Found at i:2422738 original size:18 final size:18
Alignment explanation
Indices: 2422697--2422739 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
2422687 TGTTAGTTTT
* * *
2422697 TTAATAATATTTTTTATG
1 TTAAAAATATTTTTAATA
*
2422715 TCAAAAATATTTTTAATA
1 TTAAAAATATTTTTAATA
2422733 TTAAAAA
1 TTAAAAA
2422740 AATAACTAAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAAAAATATTTTTAATA
Found at i:2423497 original size:60 final size:58
Alignment explanation
Indices: 2423427--2423614 Score: 241
Period size: 60 Copynumber: 3.2 Consensus size: 58
2423417 GCTTTTGTAC
*
2423427 AAGGAAAATTGATACTTTCAACTTTTTCTTAAAATGTTTTTCTTGATAATTTTTAATTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCTTAAAATGTTTTTATTGA-AA-TTTTAATTTT
* * *
2423487 AAGGAAAATTGGTACTTCCAACTTTTTCTCAAAATGTTTTTATTGAAATTTTAATTTT
1 AAGGAAAATTGATACTTTCAACTTTTTCTTAAAATGTTTTTATTGAAATTTTAATTTT
* * * * *
2423545 AAGAAAAATTGATACTTTCAACTTTTTCCTAAAAATATATATTTTTTGAAACTTTAATTTT
1 AAGGAAAATTGATACTTTCAACTTTTT-CTTAAAATGT-T-TTTATTGAAATTTTAATTTT
*
2423606 AAAGAAAAT
1 AAGGAAAAT
2423615 AAATAAAATA
Statistics
Matches: 112, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
58 34 0.30
59 10 0.09
60 43 0.38
61 25 0.22
ACGTcount: A:0.37, C:0.09, G:0.08, T:0.46
Consensus pattern (58 bp):
AAGGAAAATTGATACTTTCAACTTTTTCTTAAAATGTTTTTATTGAAATTTTAATTTT
Found at i:2424489 original size:3 final size:3
Alignment explanation
Indices: 2424449--2424478 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
2424439 AATCAATCAA
2424449 AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2424479 GCAAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2424544 original size:19 final size:18
Alignment explanation
Indices: 2424500--2424536 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
2424490 AAATAAATGG
2424500 AAAAAAATAATAAATAAA
1 AAAAAAATAATAAATAAA
2424518 AAACAAAATAATAAA-AAA
1 AAA-AAAATAATAAATAAA
2424536 A
1 A
2424537 GAGAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.14
Consensus pattern (18 bp):
AAAAAAATAATAAATAAA
Found at i:2424907 original size:43 final size:43
Alignment explanation
Indices: 2424721--2424929 Score: 222
Period size: 44 Copynumber: 4.8 Consensus size: 43
2424711 AATATTGATT
* * * *
2424721 AAAGCTCCTCTAATC-ACGGCTCAATGACTTTTTAAAAAAATAAAT
1 AAAGCTCCTCTAAACAAAGGCTCAATGAC--TTT-GAAAAATAAAC
* * * *
2424766 AAGGCTCCTCTAAGCAAAGGCTCAATGACTTCGTACAAATAAAC
1 AAAGCTCCTCTAAACAAAGGCTCAATGACTTTG-AAAAATAAAC
* * * *
2424810 AAAACTCCTCTAAACAAAGGCTCAACGATTTTGGATAAATAAAC
1 AAAGCTCCTCTAAACAAAGGCTCAATGACTTT-GAAAAATAAAC
* *
2424854 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAAC
1 AAAGCTCCTCTAAACAAAGGCTCAATGACTTTGAAAAATAAAC
* *
2424897 AAAGCTCCTCTAAACAGAGGTTCAATGACTTTG
1 AAAGCTCCTCTAAACAAAGGCTCAATGACTTTG
2424930 GATAGCTTAA
Statistics
Matches: 141, Mismatches: 20, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
43 41 0.29
44 74 0.52
45 14 0.10
46 12 0.09
ACGTcount: A:0.41, C:0.22, G:0.13, T:0.23
Consensus pattern (43 bp):
AAAGCTCCTCTAAACAAAGGCTCAATGACTTTGAAAAATAAAC
Found at i:2424932 original size:87 final size:88
Alignment explanation
Indices: 2424758--2424933 Score: 237
Period size: 87 Copynumber: 2.0 Consensus size: 88
2424748 CTTTTTAAAA
* * * * *
2424758 AAATAAATAAGGCTCCTCTAAGCAAAGGCTCAATGACTTCGTACAAATAAACAAAACTCCTCTAA
1 AAATAAACAAAGCTCCTCTAAACAAAGGCTCAACGACTTCGTAAAAATAAACAAAACTCCTCTAA
*
2424823 ACAAAGGCTCAACGATTTTGGAT
66 ACAAAGGCTCAACGACTTTGGAT
* * *
2424846 AAATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTG-AAAAATAAACAAAGCTCCTCTAA
1 AAATAAACAAAGCTCCTCTAAACAAAGGCTCAACGACTTCGTAAAAATAAACAAAACTCCTCTAA
* * *
2424910 ACAGAGGTTCAATGACTTTGGAT
66 ACAAAGGCTCAACGACTTTGGAT
2424933 A
1 A
2424934 GCTTAATGAC
Statistics
Matches: 76, Mismatches: 12, Indels: 1
0.85 0.13 0.01
Matches are distributed among these distances:
87 41 0.54
88 35 0.46
ACGTcount: A:0.43, C:0.21, G:0.14, T:0.22
Consensus pattern (88 bp):
AAATAAACAAAGCTCCTCTAAACAAAGGCTCAACGACTTCGTAAAAATAAACAAAACTCCTCTAA
ACAAAGGCTCAACGACTTTGGAT
Found at i:2424999 original size:43 final size:43
Alignment explanation
Indices: 2424938--2425177 Score: 315
Period size: 43 Copynumber: 5.6 Consensus size: 43
2424928 TGGATAGCTT
* *
2424938 AATGACTTTGGACAAATAAACAAAGCTCCTCTAAGCAAAGGCTC
1 AATGACTTT-GAAAAATAAACAAAGCTCCTCTAAGCAGAGGCTC
* * * *
2424982 AACGA-TTTTAGAAAATAAACAAAGCTCCTCTAAACAGAGGCTT
1 AATGACTTTGA-AAAATAAACAAAGCTCCTCTAAGCAGAGGCTC
*
2425025 AATGACTTTGAAAAATAAGCAAAGCTCCTCT-AGACAGAGGCTC
1 AATGACTTTGAAAAATAAACAAAGCTCCTCTAAG-CAGAGGCTC
* * *
2425068 AATGACTTTGAAAAATAAACAAAGCTCTTCTAAACAGAGGCTT
1 AATGACTTTGAAAAATAAACAAAGCTCCTCTAAGCAGAGGCTC
* *
2425111 AATGACTTTGAAAAATAAGCAAAGCTCCTCT-AGACAGAAGCTC
1 AATGACTTTGAAAAATAAACAAAGCTCCTCTAAG-CAGAGGCTC
2425154 AATGACTTTGAAAAATAAACAAAG
1 AATGACTTTGAAAAATAAACAAAG
2425178 ACAAACAAAT
Statistics
Matches: 170, Mismatches: 21, Indels: 11
0.84 0.10 0.05
Matches are distributed among these distances:
42 3 0.02
43 158 0.93
44 9 0.05
ACGTcount: A:0.44, C:0.19, G:0.15, T:0.22
Consensus pattern (43 bp):
AATGACTTTGAAAAATAAACAAAGCTCCTCTAAGCAGAGGCTC
Found at i:2425021 original size:105 final size:105
Alignment explanation
Indices: 2424839--2425034 Score: 324
Period size: 105 Copynumber: 1.9 Consensus size: 105
2424829 GCTCAACGAT
* *
2424839 TTTGGATAAATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTC
1 TTTGGACAAATAAACAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGAAAAATAAACAAAGCTC
2424904 CTCTAAACAGAGG-TTCAATGACTTTGGATAGCTTAATGAC
66 CTCTAAACAGAGGCTT-AATGACTTTGGATAGCTTAATGAC
* *
2424944 TTTGGACAAATAAACAAAGCTCCTCTAAGCAAAGGCTCAACGA-TTTTAGAAAATAAACAAAGCT
1 TTTGGACAAATAAACAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGA-AAAATAAACAAAGCT
2425008 CCTCTAAACAGAGGCTTAATGACTTTG
65 CCTCTAAACAGAGGCTTAATGACTTTG
2425035 AAAAATAAGC
Statistics
Matches: 85, Mismatches: 4, Indels: 4
0.91 0.04 0.04
Matches are distributed among these distances:
104 4 0.05
105 79 0.93
106 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.24
Consensus pattern (105 bp):
TTTGGACAAATAAACAAAGCTCCTCTAAACAAAGGCTCAACGACTTTGAAAAATAAACAAAGCTC
CTCTAAACAGAGGCTTAATGACTTTGGATAGCTTAATGAC
Found at i:2425056 original size:86 final size:86
Alignment explanation
Indices: 2424934--2425177 Score: 377
Period size: 86 Copynumber: 2.8 Consensus size: 86
2424924 ACTTTGGATA
* * * *
2424934 GCTTAATGACTTTGGACAAATAAACAAAGCTCCTCTA-AGCAAAGGCTCAACGA-TTTTAGAAAA
1 GCTTAATGACTTT-GAAAAATAAGCAAAGCTCCTCTAGA-CAAAGGCTCAATGACTTTGA-AAAA
2424997 TAAACAAAGCTCCTCTAAACAGAG
63 TAAACAAAGCTCCTCTAAACAGAG
*
2425021 GCTTAATGACTTTGAAAAATAAGCAAAGCTCCTCTAGACAGAGGCTCAATGACTTTGAAAAATAA
1 GCTTAATGACTTTGAAAAATAAGCAAAGCTCCTCTAGACAAAGGCTCAATGACTTTGAAAAATAA
*
2425086 ACAAAGCTCTTCTAAACAGAG
66 ACAAAGCTCCTCTAAACAGAG
2425107 GCTTAATGACTTTGAAAAATAAGCAAAGCTCCTCTAGACAGAA-GCTCAATGACTTTGAAAAATA
1 GCTTAATGACTTTGAAAAATAAGCAAAGCTCCTCTAGACA-AAGGCTCAATGACTTTGAAAAATA
2425171 AACAAAG
65 AACAAAG
2425178 ACAAACAAAT
Statistics
Matches: 147, Mismatches: 7, Indels: 7
0.91 0.04 0.04
Matches are distributed among these distances:
86 128 0.87
87 19 0.13
ACGTcount: A:0.43, C:0.19, G:0.16, T:0.23
Consensus pattern (86 bp):
GCTTAATGACTTTGAAAAATAAGCAAAGCTCCTCTAGACAAAGGCTCAATGACTTTGAAAAATAA
ACAAAGCTCCTCTAAACAGAG
Found at i:2425062 original size:148 final size:149
Alignment explanation
Indices: 2424789--2425077 Score: 481
Period size: 148 Copynumber: 1.9 Consensus size: 149
2424779 GCAAAGGCTC
* *
2424789 AATGACTTCGTACAAATAAACAAAACTCCTCTAAACAAAGGCTCAACGATTTTGGATAAATAAAC
1 AATGACTTCGGACAAATAAACAAAACTCCTCTAAACAAAGGCTCAACGATTTTAGATAAATAAAC
*
2424854 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAAACAGAGGTT
66 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAAACAGAGGCT
2424919 CAATGACTTTGGATAGCTT
131 CAATGACTTTGGATAGCTT
* * *
2424938 AATGACTTTGGACAAATAAACAAAGCTCCTCTAAGCAAAGGCTCAACGATTTTAGA-AAATAAAC
1 AATGACTTCGGACAAATAAACAAAACTCCTCTAAACAAAGGCTCAACGATTTTAGATAAATAAAC
* * * *
2425002 AAAGCTCCTCTAAACAGAGGCTTAATGACTTTGAAAAATAAGCAAAGCTCCTCTAGACAGAGGCT
66 AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAAACAGAGGCT
2425067 CAATGACTTTG
131 CAATGACTTTG
2425078 AAAAATAAAC
Statistics
Matches: 130, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
148 79 0.61
149 51 0.39
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.23
Consensus pattern (149 bp):
AATGACTTCGGACAAATAAACAAAACTCCTCTAAACAAAGGCTCAACGATTTTAGATAAATAAAC
AAAGCTCCTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAAACAGAGGCT
CAATGACTTTGGATAGCTT
Found at i:2425084 original size:191 final size:193
Alignment explanation
Indices: 2424758--2425120 Score: 545
Period size: 191 Copynumber: 1.9 Consensus size: 193
2424748 CTTTTTAAAA
* * * *
2424758 AAATAAATAAGGCTCCTCTAAGCAAAGGCTCAATGACTTCGTACAAATAAACAAAACTCCTCTAA
1 AAATAAACAAAGCTCCTCTAAGCAAAGGCTCAACGACTTCGTAAAAATAAACAAAACTCCTCTAA
* *
2424823 ACAAAGGCTCAACGATTTTGGATAAATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGA
66 ACAAAGGCTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGA
2424888 AAAATAAACAAAGCTCCTCTAAACAGAGG-TTCAATGACTTTGGATAGCTTAATGACTTTGGAC
131 AAAATAAACAAAGCTCCTCTAAACAGAGGCTT-AATGACTTTGGATAGCTTAATGACTTTGGAC
* *
2424951 AAATAAACAAAGCTCCTCTAAGCAAAGGCTCAACGA-TT-TTAGAAAATAAACAAAGCTCCTCTA
1 AAATAAACAAAGCTCCTCTAAGCAAAGGCTCAACGACTTCGTA-AAAATAAACAAAACTCCTCTA
* * * * * *
2425014 AACAGAGGCTTAATGACTTT-GAAAAATAAGCAAAGCTCCTCTAGACAGAGGCTCAATGACTTTG
65 AACAAAGGCTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTG
*
2425078 AAAAATAAACAAAGCTCTTCTAAACAGAGGCTTAATGACTTTG
130 AAAAATAAACAAAGCTCCTCTAAACAGAGGCTTAATGACTTTG
2425121 AAAAATAAGC
Statistics
Matches: 153, Mismatches: 15, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
191 81 0.53
192 39 0.25
193 33 0.22
ACGTcount: A:0.42, C:0.20, G:0.15, T:0.23
Consensus pattern (193 bp):
AAATAAACAAAGCTCCTCTAAGCAAAGGCTCAACGACTTCGTAAAAATAAACAAAACTCCTCTAA
ACAAAGGCTCAACGACTTTGGAAAAATAAACAAAGCTCCTCTAAACAGAGGCTCAACGACTTTGA
AAAATAAACAAAGCTCCTCTAAACAGAGGCTTAATGACTTTGGATAGCTTAATGACTTTGGAC
Found at i:2425262 original size:100 final size:101
Alignment explanation
Indices: 2425088--2425268 Score: 249
Period size: 100 Copynumber: 1.8 Consensus size: 101
2425078 AAAAATAAAC
* * * *
2425088 AAAGCTCTTCTAAACAGAGGCTTAATGACTTTGAAAAATAAGCAAAGCTCCTCTAGACAGAAGCT
1 AAAGCTCTTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAAACAGAAGCT
*
2425153 CAATGAC-TTTGAAAAATAAACAAAGACAAACAAAT
66 CAATAACTTTTGAAAAATAAACAAAGACAAACAAAT
** * *
2425188 AAAGCTCTTCTAAGTAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTTTAAACAG-AGGT
1 AAAGCTCTTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAAACAGAAGCT
*
2425252 ACCATAACTTTTGAAAA
66 -CAATAACTTTTGAAAA
2425269 TGAATTGCTC
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
99 3 0.04
100 58 0.84
101 8 0.12
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (101 bp):
AAAGCTCTTCTAAACAGAGGCTCAACGACTTTGAAAAATAAACAAAGCTCCTCTAAACAGAAGCT
CAATAACTTTTGAAAAATAAACAAAGACAAACAAAT
Found at i:2426301 original size:15 final size:16
Alignment explanation
Indices: 2426283--2426312 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2426273 TTTTTTTTGT
2426283 TTTTTTTAT-TTTTTA
1 TTTTTTTATCTTTTTA
2426298 TTTTTTTATCTTTTT
1 TTTTTTTATCTTTTT
2426313 TTTCAAGTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.10, C:0.03, G:0.00, T:0.87
Consensus pattern (16 bp):
TTTTTTTATCTTTTTA
Found at i:2430119 original size:15 final size:15
Alignment explanation
Indices: 2430101--2430129 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2430091 TTAAATGTAT
2430101 TGAATGAAAATGCAA
1 TGAATGAAAATGCAA
2430116 TGAATGAAAATGCA
1 TGAATGAAAATGCA
2430130 TGCATGAAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.21
Consensus pattern (15 bp):
TGAATGAAAATGCAA
Found at i:2435006 original size:20 final size:22
Alignment explanation
Indices: 2434981--2435021 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2434971 AATATGTATT
2434981 AAAA-TTTATATTT-ATATTAA
1 AAAATTTTATATTTGATATTAA
2435001 AAAATTTTTATATTTGATATT
1 AAAA-TTTTATATTTGATATT
2435022 TTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (22 bp):
AAAATTTTATATTTGATATTAA
Found at i:2440368 original size:34 final size:34
Alignment explanation
Indices: 2440329--2440395 Score: 116
Period size: 34 Copynumber: 2.0 Consensus size: 34
2440319 CAATAAATTT
*
2440329 TAAATTCAAATTTAAATATTTATAATTTTTTTTA
1 TAAATTCAAATTTAAATATTTATAATTTCTTTTA
*
2440363 TAAATTTAAATTTAAATATTTATAATTTCTTTT
1 TAAATTCAAATTTAAATATTTATAATTTCTTTT
2440396 CATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (34 bp):
TAAATTCAAATTTAAATATTTATAATTTCTTTTA
Done.