Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 41 of 186
Found at i:12085578 original size:19 final size:19
Alignment explanation
Indices: 12085545--12085592 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
12085535 TAAAAAATTC
12085545 AATAATATAAA--TAATAT
1 AATAATATAAATTTAATAT
*
12085562 AA-AATATGAAATTTAATTT
1 AATAATAT-AAATTTAATAT
12085581 AATAATATAAAT
1 AATAATATAAAT
12085593 AGTAGATATA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 5 0.19
19 11 0.42
20 5 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (19 bp):
AATAATATAAATTTAATAT
Found at i:12089245 original size:26 final size:25
Alignment explanation
Indices: 12089172--12089418 Score: 128
Period size: 26 Copynumber: 9.6 Consensus size: 25
12089162 GATTATTAAC
* * *
12089172 TTTTATATATTATTTATCTTAGATTT
1 TTTTATATATTA-TTATTTTAAATTA
*
12089198 TTTTATATAAATTATTTGTTTTAAATTA
1 TTTTATAT--ATTA-TTATTTTAAATTA
*
12089226 TTTTACATATTATCTATTTTAAATT-
1 TTTTATATATTAT-TATTTTAAATTA
* * * * * *
12089251 TTCATGTGTAATATTTAATTTAAACTA
1 TT-TTATATATTA-TTATTTTAAATTA
*
12089278 TTTTATATGTTATTCATTTTAAATT-
1 TTTTATATATTATT-ATTTTAAATTA
* * *
12089303 TGTTTATATATTATTCTTTTTAAACTG
1 T-TTTATATATTATT-ATTTTAAATTA
* *
12089330 TTTTA-ATACATATTATTTTGAATTA
1 TTTTATATA-TTATTATTTTAAATTA
* * *
12089355 TTTTATATATTAATTACTTTACATTG
1 TTTTATATATT-ATTATTTTAAATTA
* *
12089381 CTTTATTTA-T-TTATTTTAAACTCT-
1 TTTTATATATTATTATTTTAAA-T-TA
12089405 TTTTATATATTATT
1 TTTTATATATTATT
12089419 TTTGAATTGT
Statistics
Matches: 166, Mismatches: 39, Indels: 32
0.70 0.16 0.14
Matches are distributed among these distances:
23 8 0.05
24 8 0.05
25 25 0.15
26 100 0.60
27 4 0.02
28 21 0.13
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.60
Consensus pattern (25 bp):
TTTTATATATTATTATTTTAAATTA
Found at i:12089515 original size:25 final size:25
Alignment explanation
Indices: 12089474--12089543 Score: 70
Period size: 25 Copynumber: 2.7 Consensus size: 25
12089464 AAATTTCTAT
*
12089474 TTTATACGGATTATTTATTTTCAAA-TT
1 TTTATAC--ATTATTTATTTT-AAACTC
* * *
12089501 TTTATATATTGTTTATCTTAAACTC
1 TTTATACATTATTTATTTTAAACTC
12089526 TTTATACATTATTTATTT
1 TTTATACATTATTTATTT
12089544 ATTTATTTTA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
24 3 0.09
25 26 0.74
27 6 0.17
ACGTcount: A:0.29, C:0.09, G:0.04, T:0.59
Consensus pattern (25 bp):
TTTATACATTATTTATTTTAAACTC
Found at i:12089543 original size:4 final size:4
Alignment explanation
Indices: 12089534--12089574 Score: 52
Period size: 4 Copynumber: 11.0 Consensus size: 4
12089524 TCTTTATACA
*
12089534 TTAT TTAT TTAT TTAT TT-T ATAT TTA- TTAT TTA- TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT
12089575 ATTAAAGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 8 0.25
4 24 0.75
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (4 bp):
TTAT
Found at i:12089564 original size:7 final size:7
Alignment explanation
Indices: 12089533--12089574 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
12089523 CTCTTTATAC
12089533 ATTATTT
1 ATTATTT
12089540 ATTTATTT
1 A-TTATTT
12089548 A-T-TTT
1 ATTATTT
12089553 A-TATTT
1 ATTATTT
12089559 ATTATTT
1 ATTATTT
12089566 ATTATTT
1 ATTATTT
12089573 AT
1 AT
12089575 ATTAAAGTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
5 5 0.16
6 5 0.16
7 15 0.47
8 7 0.22
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (7 bp):
ATTATTT
Found at i:12089566 original size:22 final size:22
Alignment explanation
Indices: 12089538--12089612 Score: 66
Period size: 22 Copynumber: 3.5 Consensus size: 22
12089528 TATACATTAT
12089538 TTATTTATTTATTTTATATTTA
1 TTATTTATTTATTTTATATTTA
*
12089560 TTATTTA-TTA-TTTATATTAAA
1 TTATTTATTTATTTTATATT-TA
* * *
12089581 GTT-TTTTTTTATTTTATGTATA
1 -TTATTTATTTATTTTATATTTA
*
12089603 CTATTTATTT
1 TTATTTATTT
12089613 TAAATTTCTT
Statistics
Matches: 41, Mismatches: 7, Indels: 10
0.71 0.12 0.17
Matches are distributed among these distances:
20 8 0.20
21 8 0.20
22 19 0.46
23 6 0.15
ACGTcount: A:0.27, C:0.01, G:0.03, T:0.69
Consensus pattern (22 bp):
TTATTTATTTATTTTATATTTA
Found at i:12089591 original size:25 final size:25
Alignment explanation
Indices: 12089533--12089593 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
12089523 CTCTTTATAC
* *
12089533 ATTATTTATTTATTTATTTTATATTT
1 ATTATTTA-TTATTTATATTAAATTT
12089559 ATTATTTATTATTTATATTAAAGTTT
1 ATTATTTATTATTTATATTAAA-TTT
*
12089585 -TTTTTTATT
1 ATTATTTATT
12089594 TTATGTATAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
25 20 0.65
26 11 0.35
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (25 bp):
ATTATTTATTATTTATATTAAATTT
Found at i:12089673 original size:20 final size:21
Alignment explanation
Indices: 12089632--12089680 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
12089622 TTTTACATAT
* *
12089632 TATTATTTTAGACTTTTTATA
1 TATTATTTTAGAATTGTTATA
*
12089653 TGTTATTTTA-AATTGTTATA
1 TATTATTTTAGAATTGTTATA
12089673 TATTATTT
1 TATTATTT
12089681 ATTTTAAGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.29, C:0.02, G:0.06, T:0.63
Consensus pattern (21 bp):
TATTATTTTAGAATTGTTATA
Found at i:12089682 original size:24 final size:24
Alignment explanation
Indices: 12089655--12089736 Score: 82
Period size: 24 Copynumber: 3.5 Consensus size: 24
12089645 TTTTTATATG
12089655 TTATTTTAAATTGTTATATATTAT
1 TTATTTTAAATTGTTATATATTAT
* *
12089679 TTATTTTAAGTTG--ATTTA-T-T
1 TTATTTTAAATTGTTATATATTAT
* *
12089699 TTATTTTAAATTGTTTTGTATATTAA
1 TTATTTTAAATTG--TTATATATTAT
12089725 TTATTTTAAATT
1 TTATTTTAAATT
12089737 ATTTTACACT
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
20 13 0.28
21 1 0.02
22 4 0.09
24 15 0.33
25 1 0.02
26 12 0.26
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.63
Consensus pattern (24 bp):
TTATTTTAAATTGTTATATATTAT
Found at i:12092247 original size:23 final size:23
Alignment explanation
Indices: 12092201--12092247 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
12092191 ATAATTACTT
*
12092201 TCTCTGTCTCTGGACACGCTTTC
1 TCTCTGTCTCTGGACACGCATTC
* * *
12092224 TCTCTGTCTTTTGACACTCATTC
1 TCTCTGTCTCTGGACACGCATTC
12092247 T
1 T
12092248 GTTTTTCTAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.32, G:0.13, T:0.45
Consensus pattern (23 bp):
TCTCTGTCTCTGGACACGCATTC
Found at i:12095767 original size:26 final size:26
Alignment explanation
Indices: 12095731--12095840 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
12095721 TGATACAAAT
12095731 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
12095757 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
12095783 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
12095809 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
12095835 TGATAA
1 TGATAA
12095841 GAATTTCATG
Statistics
Matches: 82, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 82 1.00
ACGTcount: A:0.34, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:12097722 original size:38 final size:40
Alignment explanation
Indices: 12097621--12097725 Score: 99
Period size: 38 Copynumber: 2.6 Consensus size: 40
12097611 GACCTCGAGT
* **
12097621 CGATGAGACACTGGGTGTC-ACTATATTTCTTCGGATAGATT
1 CGATGAGACACTGGGTGTCAAC--TATTACTTCGGATAGAGC
** ** *
12097662 CGATGAGGTACTGGGTACCAACT-TTACTTCGGCTAG-GC
1 CGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAGC
12097700 CGATGAGACACTGGGTGTCAACTATT
1 CGATGAGACACTGGGTGTCAACTATT
12097726 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
38 19 0.38
39 13 0.26
40 1 0.02
41 15 0.30
42 2 0.04
ACGTcount: A:0.24, C:0.20, G:0.27, T:0.30
Consensus pattern (40 bp):
CGATGAGACACTGGGTGTCAACTATTACTTCGGATAGAGC
Found at i:12103943 original size:26 final size:26
Alignment explanation
Indices: 12103907--12104016 Score: 175
Period size: 26 Copynumber: 4.2 Consensus size: 26
12103897 TGATACAAAT
*
12103907 TGATAAAAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
12103933 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
12103959 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
* *
12103985 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTCCA
12104011 TGATAA
1 TGATAA
12104017 GAATTTCATG
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:12113351 original size:22 final size:22
Alignment explanation
Indices: 12113321--12113365 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
12113311 TTTAGTTTAA
*
12113321 TTAATATAAA-ATTTCATCCTTT
1 TTAAAATAAATATTTCAT-CTTT
*
12113343 TTAAAATAAATTTTTCATCTTT
1 TTAAAATAAATATTTCATCTTT
12113365 T
1 T
12113366 GACCTATGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAAATAAATATTTCATCTTT
Found at i:12123870 original size:90 final size:89
Alignment explanation
Indices: 12123717--12123898 Score: 310
Period size: 90 Copynumber: 2.0 Consensus size: 89
12123707 ATCTGAACTT
* *
12123717 CGAATGTTAGACGGTCAACTCCAAGCTACTATCAATCAAACTAGATATTCACTCAATAACCCTTT
1 CGAATGTTACACGGTCAACTCCAAACTACTATCAATCAAACTAGATATTCACTCAATAACCC-TT
*
12123782 TTTTTCGGGCAATTTCAGTTTTCTA
65 TTTTTCAGGCAATTTCAGTTTTCTA
* *
12123807 CGAATGTTACACGGTCAACTCCAAACTATTATCGATCAAACTAGATATTCACTCAATAACCCTTT
1 CGAATGTTACACGGTCAACTCCAAACTACTATCAATCAAACTAGATATTCACTCAATAACCCTTT
12123872 TTTTCAGGCAATTTCAGTTTTCTA
66 TTTTCAGGCAATTTCAGTTTTCTA
12123896 CGA
1 CGA
12123899 TTCTAAAACC
Statistics
Matches: 87, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 29 0.33
90 58 0.67
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.34
Consensus pattern (89 bp):
CGAATGTTACACGGTCAACTCCAAACTACTATCAATCAAACTAGATATTCACTCAATAACCCTTT
TTTTCAGGCAATTTCAGTTTTCTA
Found at i:12129452 original size:45 final size:45
Alignment explanation
Indices: 12129403--12129618 Score: 220
Period size: 45 Copynumber: 4.8 Consensus size: 45
12129393 TTGGATTGAA
* * *
12129403 AAATGAAAAAGACCATGGTTGAAAGATACCATGGCATTATACCCG
1 AAATGAAAAAGACCATAGTTGAAAGATACTATGACATTATACCCG
* * * *
12129448 AAATGAGAAATACCATAGTTGAAAGATACTATGACATTA-AACTG
1 AAATGAAAAAGACCATAGTTGAAAGATACTATGACATTATACCCG
* * * * *
12129492 GAATGAATAAGACCATATTTGAAAGATACTATGAAATTATACCGG
1 AAATGAAAAAGACCATAGTTGAAAGATACTATGACATTATACCCG
* * * * * *
12129537 AAATGTATAAGACCATAGTTGAAAAATACTATGGCATTAAATCCG
1 AAATGAAAAAGACCATAGTTGAAAGATACTATGACATTATACCCG
* * *
12129582 ATA-CAAATAAGACCATAGTTGAAAGATACTATAACAT
1 AAATGAAA-AAGACCATAGTTGAAAGATACTATGACAT
12129619 CACTTTAGAA
Statistics
Matches: 138, Mismatches: 31, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
44 37 0.27
45 101 0.73
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (45 bp):
AAATGAAAAAGACCATAGTTGAAAGATACTATGACATTATACCCG
Found at i:12129555 original size:89 final size:89
Alignment explanation
Indices: 12129404--12129613 Score: 253
Period size: 89 Copynumber: 2.3 Consensus size: 89
12129394 TGGATTGAAA
* * * ** *
12129404 AATGAAAAAGACCATGGTTGAAAGATACCATGGCATTATACCCGAAATGAGAAATACCATAGTTG
1 AATGAATAAGACCATAGTTGAAAGATACTATGAAATTATACCCGAAATGAGAAAGACCATAGTTG
* *
12129469 AAAGATACTATGACATTAAA-CTGG
66 AAAAATACTATGACATTAAATC-CG
* * *
12129493 AATGAATAAGACCATATTTGAAAGATACTATGAAATTATACCGGAAATGTA-TAAGACCATAGTT
1 AATGAATAAGACCATAGTTGAAAGATACTATGAAATTATACCCGAAATG-AGAAAGACCATAGTT
*
12129557 GAAAAATACTATGGCATTAAATCCG
65 GAAAAATACTATGACATTAAATCCG
**
12129582 ATACAAATAAGACCATAGTTGAAAGATACTAT
1 A-ATGAATAAGACCATAGTTGAAAGATACTAT
12129614 AACATCACTT
Statistics
Matches: 103, Mismatches: 15, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
89 74 0.72
90 29 0.28
ACGTcount: A:0.45, C:0.13, G:0.17, T:0.25
Consensus pattern (89 bp):
AATGAATAAGACCATAGTTGAAAGATACTATGAAATTATACCCGAAATGAGAAAGACCATAGTTG
AAAAATACTATGACATTAAATCCG
Found at i:12134605 original size:38 final size:35
Alignment explanation
Indices: 12134535--12134609 Score: 96
Period size: 38 Copynumber: 2.1 Consensus size: 35
12134525 AGTCCAAACC
* * *
12134535 AAGCCCAAAGTATATCACCTAACCTAAAACCCTAA
1 AAGCCCAAACTATATCACCCAACCCAAAACCCTAA
12134570 AAGCCCAATACTATATCAACCCAAGCCCAAAACCCTAA
1 AAGCCCAA-ACTATATC-ACCCAA-CCCAAAACCCTAA
12134608 AA
1 AA
12134610 AACTAACAGA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
35 8 0.24
36 7 0.21
37 5 0.15
38 14 0.41
ACGTcount: A:0.47, C:0.33, G:0.05, T:0.15
Consensus pattern (35 bp):
AAGCCCAAACTATATCACCCAACCCAAAACCCTAA
Found at i:12141281 original size:23 final size:21
Alignment explanation
Indices: 12141255--12141298 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 21
12141245 TTACTTTAGT
12141255 AAGAAATTTACTGAATGTGAGAA
1 AAGAAATTTACT-AAT-TGAGAA
* *
12141278 AAGATATTTGCTAATTGAGAA
1 AAGAAATTTACTAATTGAGAA
12141299 GTTGTGTTGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 6 0.32
22 3 0.16
23 10 0.53
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (21 bp):
AAGAAATTTACTAATTGAGAA
Found at i:12145775 original size:44 final size:44
Alignment explanation
Indices: 12145570--12145918 Score: 140
Period size: 44 Copynumber: 7.7 Consensus size: 44
12145560 CTACCATAGT
* * *
12145570 GAATCTTATCTCTCTGAAGTTGCAGTGGAGCAAGATGAAGCTAC
1 GAATCTTATATCCCTGAAATTGCAGTGGAGCAAGATGAAGCTAC
* * * * *
12145614 AAATCCTATATCCAT-AAAGTTGCAATGGATC-AGATTGAAGCTAC
1 GAATCTTATATCCCTGAAA-TTGCAGTGGAGCAAGA-TGAAGCTAC
* *** *
12145658 -AATATT-TATACCTCT-AAAGTTGCAGTGG-GTTGGAATGAAACTACGATGGC
1 GAATCTTATAT-CC-CTGAAA-TTGCAGTGGAGCAAG-ATGAAGCT---A---C
* * *
12145708 GAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTAC
1 GAATCTTATATCCCTGAAATTGCAGTGGAGCAAGATGAAGCTAC
* * *
12145752 GAATCTTATATCCCTGAAATTGCAGTGGATCGAA-TTGAAGCCAC
1 GAATCTTATATCCCTGAAATTGCAGTGGAGC-AAGATGAAGCTAC
* * * * * ** **
12145796 -AATTTCTATACCCCT-AAAGTTGCAGTGGGTTGGAATAAAAATATAATGGC
1 GAATCT-TATATCCCTGAAA-TTGCAGT-GG-AGCAAGATGAAGCT-A---C
* * * * *
12145846 GAATCTTATCTCCCTGGAGTTGCAATGGAGCAATATGAAGCTAC
1 GAATCTTATATCCCTGAAATTGCAGTGGAGCAAGATGAAGCTAC
*
12145890 GAATCTTATATCCTTGAAATTGCAGTGGA
1 GAATCTTATATCCCTGAAATTGCAGTGGA
12145919 TCGGATTAAA
Statistics
Matches: 219, Mismatches: 58, Indels: 56
0.66 0.17 0.17
Matches are distributed among these distances:
42 3 0.01
43 18 0.08
44 125 0.57
45 7 0.03
46 2 0.01
47 4 0.02
48 8 0.04
49 2 0.01
50 32 0.15
51 16 0.07
52 2 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (44 bp):
GAATCTTATATCCCTGAAATTGCAGTGGAGCAAGATGAAGCTAC
Found at i:12145775 original size:138 final size:137
Alignment explanation
Indices: 12145570--12146042 Score: 689
Period size: 138 Copynumber: 3.4 Consensus size: 137
12145560 CTACCATAGT
* * *
12145570 GAATCTTATCTCTCTGAAGTTGCAGTGGAGCAAGATGAAGCTACAAATCCTATATCCAT-AAAGT
1 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACGAATCCTATATCCCTGAAA-T
* * *
12145634 TGCAATGGATCAGATTGAAGCTACAATATT-TATACCTCTAAAGTTGCAGTGGGTTGGAATGAAA
65 TGCAGTGGATC-GATTGAAGCCACAAT-TTCTATACCTCTAAAGTTGCAGTGGGTTGGAATAAAA
* **
12145698 CTACGATGGC
128 ATATAATGGC
* *
12145708 GAATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGATGAAGCTACGAATCTTATATCCCTGAAATT
1 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACGAATCCTATATCCCTGAAATT
*
12145773 GCAGTGGATCGAATTGAAGCCACAATTTCTATACCCCTAAAGTTGCAGTGGGTTGGAATAAAAAT
66 GCAGTGGATCG-ATTGAAGCCACAATTTCTATACCTCTAAAGTTGCAGTGGGTTGGAATAAAAAT
12145838 ATAATGGC
130 ATAATGGC
* * * * *
12145846 GAATCTTATCTCCCTGGAGTTGCAATGGAGCAATATGAAGCTACGAATCTTATATCCTTGAAATT
1 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACGAATCCTATATCCCTGAAATT
*
12145911 GCAGTGGATCGGATTAAAGCCACAATTTCTATACCTCTAAAGTTGCAGTGGGTTGGAATAAAAAT
66 GCAGTGGATC-GATTGAAGCCACAATTTCTATACCTCTAAAGTTGCAGTGGGTTGGAATAAAAAT
*
12145976 ATAATAGC
130 ATAATGGC
* * *
12145984 GAATCTTATCTCCCTGGAGTTGCAGTGGAGCAAGATGAAGCTATGAATCCTAAATCCCT
1 GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACGAATCCTATATCCCT
12146043 AATATGGTAA
Statistics
Matches: 305, Mismatches: 26, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
137 3 0.01
138 298 0.98
139 4 0.01
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (137 bp):
GAATCTTATCTCCCTGAAGTTGCAGTGGAGCAAGATGAAGCTACGAATCCTATATCCCTGAAATT
GCAGTGGATCGATTGAAGCCACAATTTCTATACCTCTAAAGTTGCAGTGGGTTGGAATAAAAATA
TAATGGC
Found at i:12147816 original size:13 final size:14
Alignment explanation
Indices: 12147788--12147817 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
12147778 CCTACTTTTT
12147788 TTTTATTTTGATTA
1 TTTTATTTTGATTA
12147802 TTTTATTTT-ATTA
1 TTTTATTTTGATTA
12147815 TTT
1 TTT
12147818 CAGACACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.20, C:0.00, G:0.03, T:0.77
Consensus pattern (14 bp):
TTTTATTTTGATTA
Found at i:12148042 original size:9 final size:9
Alignment explanation
Indices: 12148028--12148053 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
12148018 TTAAATTTTG
12148028 ATACTATTA
1 ATACTATTA
12148037 ATACTATTA
1 ATACTATTA
12148046 ATACTATT
1 ATACTATT
12148054 TGTATATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (9 bp):
ATACTATTA
Found at i:12148180 original size:22 final size:22
Alignment explanation
Indices: 12148147--12148193 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
12148137 ATTAATTGAA
12148147 TATTTTTCATTATTGTTATT-AT
1 TATTTTTCATTATTG-TATTCAT
12148169 TATTTCTT-ATTATTGTATTCAT
1 TATTT-TTCATTATTGTATTCAT
12148191 TAT
1 TAT
12148194 AGTATTGTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 4 0.17
22 17 0.74
23 2 0.09
ACGTcount: A:0.23, C:0.06, G:0.04, T:0.66
Consensus pattern (22 bp):
TATTTTTCATTATTGTATTCAT
Found at i:12148471 original size:21 final size:21
Alignment explanation
Indices: 12148445--12148486 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
12148435 ACATAGGATT
12148445 TAGGTAATAATCAAATGACGA
1 TAGGTAATAATCAAATGACGA
12148466 TAGGTAATAATCAAATGACGA
1 TAGGTAATAATCAAATGACGA
12148487 GTATTCTTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.10, G:0.19, T:0.24
Consensus pattern (21 bp):
TAGGTAATAATCAAATGACGA
Found at i:12153063 original size:5 final size:5
Alignment explanation
Indices: 12153053--12153084 Score: 64
Period size: 5 Copynumber: 6.4 Consensus size: 5
12153043 TATTATTTTT
12153053 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TAAAA TA
12153085 TAATTTTGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
TAAAA
Found at i:12154129 original size:2 final size:2
Alignment explanation
Indices: 12154122--12154156 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
12154112 TGAACATTTC
* *
12154122 TA TA TA TA TA CA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12154157 TTTTCATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
TA
Found at i:12155183 original size:17 final size:17
Alignment explanation
Indices: 12155124--12155183 Score: 54
Period size: 16 Copynumber: 3.6 Consensus size: 17
12155114 TTAAATTATA
*
12155124 TCTTCTTTTTTTGTATT
1 TCTTCTTTTTTTCTATT
*
12155141 TCTTCTTTTTTT-TCCTT
1 TCTTCTTTTTTTCT-ATT
* *
12155158 T-TACATTTTTTCTATT
1 TCTTCTTTTTTTCTATT
12155174 TCTT-TTTTTT
1 TCTTCTTTTTT
12155184 CCCTATTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 7
0.72 0.13 0.15
Matches are distributed among these distances:
16 17 0.50
17 17 0.50
ACGTcount: A:0.07, C:0.15, G:0.02, T:0.77
Consensus pattern (17 bp):
TCTTCTTTTTTTCTATT
Found at i:12157276 original size:24 final size:24
Alignment explanation
Indices: 12157243--12157289 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
12157233 TATAAAATAC
12157243 GCCACAAAGGTATTTACAGGATAT
1 GCCACAAAGGTATTTACAGGATAT
*
12157267 GCCACCAAGGTATTTACAGGATA
1 GCCACAAAGGTATTTACAGGATA
12157290 AACCGCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (24 bp):
GCCACAAAGGTATTTACAGGATAT
Found at i:12166125 original size:18 final size:18
Alignment explanation
Indices: 12166102--12166170 Score: 120
Period size: 18 Copynumber: 3.8 Consensus size: 18
12166092 CACAGCCTGG
12166102 CCACACGGGCGTGTGTAC
1 CCACACGGGCGTGTGTAC
*
12166120 CCACACAGGCGTGTGTAC
1 CCACACGGGCGTGTGTAC
*
12166138 CCACACGGGCTTGTGTAC
1 CCACACGGGCGTGTGTAC
12166156 CCACACGGGCGTGTG
1 CCACACGGGCGTGTG
12166171 AAATCTCCAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 47 1.00
ACGTcount: A:0.17, C:0.33, G:0.32, T:0.17
Consensus pattern (18 bp):
CCACACGGGCGTGTGTAC
Found at i:12166712 original size:20 final size:19
Alignment explanation
Indices: 12166663--12166723 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
12166653 TTAATATAAA
*
12166663 TAAATATTATTAAATTATTTT
1 TAAATATT-TTAAA-TATATT
** *
12166684 TTTATATTTTTAATAGTATT
1 TAAATATTTTAAATA-TATT
12166704 TAAATATTTTAAATATATT
1 TAAATATTTTAAATATATT
12166723 T
1 T
12166724 TATTTTATAA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
19 7 0.22
20 19 0.59
21 6 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (19 bp):
TAAATATTTTAAATATATT
Found at i:12166917 original size:44 final size:44
Alignment explanation
Indices: 12166866--12166956 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
12166856 AAAACATTTG
12166866 AAATAATATAATAAAATTAAAATAATTAAAAGCTAACAACTAAT
1 AAATAATATAATAAAATTAAAATAATTAAAAGCTAACAACTAAT
12166910 AAATAATATAATAAAATTAAAATAATTAAAAGCTAACAACTAAT
1 AAATAATATAATAAAATTAAAATAATTAAAAGCTAACAACTAAT
12166954 AAA
1 AAA
12166957 AAGAGAGAAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (44 bp):
AAATAATATAATAAAATTAAAATAATTAAAAGCTAACAACTAAT
Found at i:12169010 original size:42 final size:42
Alignment explanation
Indices: 12168814--12169008 Score: 230
Period size: 42 Copynumber: 4.6 Consensus size: 42
12168804 AAACGGCCAG
*
12168814 GGACATGAGCGTGTGCCCAGGCCGTGTGAGCCACACGGGCAA
1 GGACATGGGCGTGTGCCCAGGCCGTGTGAGCCACACGGGCAA
* * * * *
12168856 GGACATGGGCGCGTGCCCAAGCTGTGTGATCCACACAGGCAA
1 GGACATGGGCGTGTGCCCAGGCCGTGTGAGCCACACGGGCAA
* ** * * *
12168898 GGACATGGGCATGTGCCCAGTTCATGTGAGACACACGGGTAA
1 GGACATGGGCGTGTGCCCAGGCCGTGTGAGCCACACGGGCAA
* *
12168940 GGACATGGGTGTGTGCCCAGGCCGTGTAAGCCACACGGGTC-A
1 GGACATGGGCGTGTGCCCAGGCCGTGTGAGCCACACGGG-CAA
* *
12168982 GGACATGGGCGTGTGTCCAGGTCGTGT
1 GGACATGGGCGTGTGCCCAGGCCGTGT
12169009 AACTCATTGT
Statistics
Matches: 124, Mismatches: 28, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
42 124 1.00
ACGTcount: A:0.21, C:0.25, G:0.37, T:0.17
Consensus pattern (42 bp):
GGACATGGGCGTGTGCCCAGGCCGTGTGAGCCACACGGGCAA
Found at i:12169916 original size:5 final size:5
Alignment explanation
Indices: 12169906--12169938 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
12169896 ACATACATAC
*
12169906 TCTGT TCTGT TCTGT TCTGT T-TGT TATGT TCTG
1 TCTGT TCTGT TCTGT TCTGT TCTGT TCTGT TCTG
12169939 CTATATTCGG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
4 4 0.15
5 22 0.85
ACGTcount: A:0.03, C:0.15, G:0.21, T:0.61
Consensus pattern (5 bp):
TCTGT
Found at i:12173309 original size:3 final size:3
Alignment explanation
Indices: 12173301--12173337 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
12173291 TACTGATTTT
12173301 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
12173338 TATTATTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:12173342 original size:3 final size:3
Alignment explanation
Indices: 12173336--12173363 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
12173326 AATAATAATA
12173336 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT A
12173364 AGTTTTCTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12176269 original size:13 final size:13
Alignment explanation
Indices: 12176253--12176292 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
12176243 AGAGAACAGA
12176253 AAAGAAGAAAAAG
1 AAAGAAGAAAAAG
*
12176266 AAAGAAGAAGAAG
1 AAAGAAGAAAAAG
*
12176279 AAA-ATGAAAAAG
1 AAAGAAGAAAAAG
12176291 AA
1 AA
12176293 GAAATAGAGG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
12 9 0.38
13 15 0.62
ACGTcount: A:0.75, C:0.00, G:0.23, T:0.03
Consensus pattern (13 bp):
AAAGAAGAAAAAG
Found at i:12189544 original size:22 final size:22
Alignment explanation
Indices: 12189514--12189563 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 22
12189504 GAAAAGTGAA
12189514 ATTTGTAGGAATATTCTGTAAAT
1 ATTT-TAGGAATATTCTGTAAAT
* *
12189537 ATTTTAGGAATATTTTGTAGAT
1 ATTTTAGGAATATTCTGTAAAT
12189559 ATTTT
1 ATTTT
12189564 TTATTAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 21 0.84
23 4 0.16
ACGTcount: A:0.32, C:0.02, G:0.16, T:0.50
Consensus pattern (22 bp):
ATTTTAGGAATATTCTGTAAAT
Found at i:12192323 original size:22 final size:22
Alignment explanation
Indices: 12192295--12192339 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
12192285 AGGGGGAGTG
12192295 TAGGAATATTCTGTAAATATTT
1 TAGGAATATTCTGTAAATATTT
* *
12192317 TAGGAATATTTTGTAGATATTT
1 TAGGAATATTCTGTAAATATTT
12192339 T
1 T
12192340 TTTATTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (22 bp):
TAGGAATATTCTGTAAATATTT
Found at i:12197118 original size:13 final size:13
Alignment explanation
Indices: 12197100--12197124 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12197090 TTAATTTAAG
12197100 AATATTTTTAAAA
1 AATATTTTTAAAA
12197113 AATATTTTTAAA
1 AATATTTTTAAA
12197125 CTAATTCTTA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AATATTTTTAAAA
Found at i:12218185 original size:36 final size:36
Alignment explanation
Indices: 12218134--12218256 Score: 144
Period size: 35 Copynumber: 3.5 Consensus size: 36
12218124 TATAAGACCG
** **
12218134 AATATACAAGGTTCAATATATCATCACATATGGCTG
1 AATATACAAAATTCAATATATCATCACATATGGCCA
* **
12218170 ATTATACAAAATTCAATATATTC-TCACATATAACCA
1 AATATACAAAATTCAATATA-TCATCACATATGGCCA
*
12218206 AATATAC-AAATTCAATATATCATCACATATGGTCA
1 AATATACAAAATTCAATATATCATCACATATGGCCA
12218241 AATATAC-AAATTCAAT
1 AATATACAAAATTCAAT
12218257 TGATGTGCGT
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.03
35 38 0.51
36 32 0.43
37 2 0.03
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.32
Consensus pattern (36 bp):
AATATACAAAATTCAATATATCATCACATATGGCCA
Found at i:12220188 original size:50 final size:50
Alignment explanation
Indices: 12220090--12220238 Score: 135
Period size: 50 Copynumber: 3.0 Consensus size: 50
12220080 AAATATATAT
* * * *
12220090 ATACATACCTATGTAG-CCGAATTTACAA-GTTCAAT-TGGAACACCACATAA
1 ATACATACCTAT-AAGACCGAATATACAAGGTTCAATAT--ATCATCACATAA
* * ** * *
12220140 ATACTTACCTATATGACCGGTTATACCAA-GTTCATTATATCATTACATAA
1 ATACATACCTATAAGACCGAATATA-CAAGGTTCAATATATCATCACATAA
*
12220190 GTACATACCTATAAGACCGAATATACAAGGTTCAATATATCATCACATA
1 ATACATACCTATAAGACCGAATATACAAGGTTCAATATATCATCACATA
12220239 TGGCTGATTA
Statistics
Matches: 78, Mismatches: 17, Indels: 8
0.76 0.17 0.08
Matches are distributed among these distances:
49 4 0.05
50 64 0.82
51 9 0.12
52 1 0.01
ACGTcount: A:0.40, C:0.21, G:0.10, T:0.30
Consensus pattern (50 bp):
ATACATACCTATAAGACCGAATATACAAGGTTCAATATATCATCACATAA
Found at i:12220260 original size:36 final size:36
Alignment explanation
Indices: 12220209--12220331 Score: 144
Period size: 35 Copynumber: 3.5 Consensus size: 36
12220199 TATAAGACCG
** **
12220209 AATATACAAGGTTCAATATATCATCACATATGGCTG
1 AATATACAAAATTCAATATATCATCACATATGGCCA
* **
12220245 ATTATACAAAATTCAATATATTC-TCACATATAACCA
1 AATATACAAAATTCAATATA-TCATCACATATGGCCA
*
12220281 AATATAC-AAATTCAATATATCATCACATATGGTCA
1 AATATACAAAATTCAATATATCATCACATATGGCCA
12220316 AATATAC-AAATTCAAT
1 AATATACAAAATTCAAT
12220332 TGATGTGCGT
Statistics
Matches: 74, Mismatches: 11, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
34 2 0.03
35 38 0.51
36 32 0.43
37 2 0.03
ACGTcount: A:0.46, C:0.17, G:0.06, T:0.32
Consensus pattern (36 bp):
AATATACAAAATTCAATATATCATCACATATGGCCA
Found at i:12230089 original size:39 final size:42
Alignment explanation
Indices: 12230043--12230137 Score: 108
Period size: 42 Copynumber: 2.3 Consensus size: 42
12230033 CACCAGCATA
12230043 AAGCCTGCTAGGCAT-AGGTCTGA-A-TCACACACCGGCAC-
1 AAGCCTGCTAGGCATAAGGTCTGATATTCACACACCGGCACT
* * * **
12230081 AAGGCCTGCTAGACCTAAGGTCTGATATTTATTCACCGGCACT
1 AA-GCCTGCTAGGCATAAGGTCTGATATTCACACACCGGCACT
12230124 AAGCCTGCTAGGCA
1 AAGCCTGCTAGGCA
12230138 CAAAGCCCGA
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
38 2 0.04
39 11 0.24
40 8 0.18
41 1 0.02
42 21 0.47
43 2 0.04
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.21
Consensus pattern (42 bp):
AAGCCTGCTAGGCATAAGGTCTGATATTCACACACCGGCACT
Found at i:12230561 original size:11 final size:10
Alignment explanation
Indices: 12230519--12230557 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
12230509 TGAGCACTAC
12230519 TATATTTTAT
1 TATATTTTAT
*
12230529 TATATGTT-T
1 TATATTTTAT
12230538 TATATTTTTAT
1 TATA-TTTTAT
12230549 TATATTTTA
1 TATATTTTA
12230558 ATTAATTACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 5 0.20
10 15 0.60
11 5 0.20
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (10 bp):
TATATTTTAT
Found at i:12232769 original size:21 final size:21
Alignment explanation
Indices: 12232733--12232825 Score: 78
Period size: 21 Copynumber: 4.4 Consensus size: 21
12232723 TCTATTGAGC
*
12232733 TTCTGTTGAACCCTTATGGGT
1 TTCTGTTCAACCCTTATGGGT
* * * * *
12232754 TTTTGTTCAACTCTTACGAGC
1 TTCTGTTCAACCCTTATGGGT
*
12232775 TTCTGTTCAACCCTTATTGGT
1 TTCTGTTCAACCCTTATGGGT
* * * * *
12232796 TTCTGTTTAGCTCTTATGAGC
1 TTCTGTTCAACCCTTATGGGT
12232817 TTCTGTTCA
1 TTCTGTTCA
12232826 CCTTTCGGGC
Statistics
Matches: 53, Mismatches: 19, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 53 1.00
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTGTTCAACCCTTATGGGT
Found at i:12232824 original size:42 final size:42
Alignment explanation
Indices: 12232636--12232825 Score: 179
Period size: 42 Copynumber: 4.5 Consensus size: 42
12232626 CTTTCCATTT
* * * * * *
12232636 AGCTCTCACGAGCTTCTGTTTAACTCATATGAGTTTTC-GTTC
1 AGCTCTTATGAGCTTCTGTTCAACCCTTAT-AGGTTTCTGTTC
* * * *
12232678 AGTTC-TATTGAGCTTTTGTTTAACCCTTATAGGTTTCCGTTC
1 AGCTCTTA-TGAGCTTCTGTTCAACCCTTATAGGTTTCTGTTC
* * *
12232720 AGCTC-TATTGAGCTTCTGTTGAACCCTTATGGGTTTTTGTTC
1 AGCTCTTA-TGAGCTTCTGTTCAACCCTTATAGGTTTCTGTTC
* * * *
12232762 AACTCTTACGAGCTTCTGTTCAACCCTTATTGGTTTCTGTTT
1 AGCTCTTATGAGCTTCTGTTCAACCCTTATAGGTTTCTGTTC
12232804 AGCTCTTATGAGCTTCTGTTCA
1 AGCTCTTATGAGCTTCTGTTCA
12232826 CCTTTCGGGC
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
41 7 0.06
42 115 0.93
43 2 0.02
ACGTcount: A:0.17, C:0.22, G:0.17, T:0.44
Consensus pattern (42 bp):
AGCTCTTATGAGCTTCTGTTCAACCCTTATAGGTTTCTGTTC
Found at i:12235410 original size:16 final size:16
Alignment explanation
Indices: 12235386--12235418 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12235376 ATATGAAAAG
*
12235386 GAAATGTATACTTTGT
1 GAAAGGTATACTTTGT
12235402 GAAAGGTATACTTTGT
1 GAAAGGTATACTTTGT
12235418 G
1 G
12235419 TATACCACTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.39
Consensus pattern (16 bp):
GAAAGGTATACTTTGT
Found at i:12235499 original size:33 final size:33
Alignment explanation
Indices: 12235451--12235566 Score: 144
Period size: 33 Copynumber: 3.5 Consensus size: 33
12235441 TACACTATAT
* *
12235451 GTGTAC-ACTTGAAAAGGTTATGTGCACTTTGA
1 GTGTACAACTTGAAAAGGGTATGTGCACTTCGA
* * *
12235483 GTGTACAAATTGAAAAGGGTATGTACACTTCGT
1 GTGTACAACTTGAAAAGGGTATGTGCACTTCGA
* * *
12235516 GTGTACCACTTGAAAAGGGAATGTGCACCTCGA
1 GTGTACAACTTGAAAAGGGTATGTGCACTTCGA
*
12235549 GTGTACAACTAGAAAAGG
1 GTGTACAACTTGAAAAGG
12235567 AAAAGTCCAT
Statistics
Matches: 70, Mismatches: 13, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
32 6 0.09
33 64 0.91
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.27
Consensus pattern (33 bp):
GTGTACAACTTGAAAAGGGTATGTGCACTTCGA
Found at i:12239119 original size:17 final size:20
Alignment explanation
Indices: 12239099--12239140 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
12239089 TATACATATT
12239099 TTGTA-AAGA-TGA-AATGC
1 TTGTACAAGAGTGAGAATGC
12239116 TTGTACAAGAGTGATGAATGC
1 TTGTACAAGAGTGA-GAATGC
12239137 TTGT
1 TTGT
12239141 TGTAATCAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 5 0.24
18 4 0.19
19 3 0.14
21 9 0.43
ACGTcount: A:0.33, C:0.07, G:0.26, T:0.33
Consensus pattern (20 bp):
TTGTACAAGAGTGAGAATGC
Found at i:12243166 original size:31 final size:31
Alignment explanation
Indices: 12243131--12243190 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
12243121 TACACCATTA
* * *
12243131 GTCACTAAATTATTGGTAAGTTTTCATTTTG
1 GTCACTAAACTATTCGAAAGTTTTCATTTTG
*
12243162 GTCACTGAACTATTCGAAAGTTTTCATTT
1 GTCACTAAACTATTCGAAAGTTTTCATTT
12243191 AAGTCATTGA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.13, G:0.15, T:0.45
Consensus pattern (31 bp):
GTCACTAAACTATTCGAAAGTTTTCATTTTG
Found at i:12243202 original size:31 final size:32
Alignment explanation
Indices: 12243148--12243234 Score: 106
Period size: 31 Copynumber: 2.8 Consensus size: 32
12243138 AATTATTGGT
** *
12243148 AAGTTTTCATTTTGGTCACTGAACTATTC-GA
1 AAGTTTTCATTTAAGTCACTGAACTATTCAAA
*
12243179 AAGTTTTCATTTAAGTCATTGAACTATTCAAA
1 AAGTTTTCATTTAAGTCACTGAACTATTCAAA
**
12243211 AAAATTT-ATTTAAGTCACTGAACT
1 AAGTTTTCATTTAAGTCACTGAACT
12243235 GTTAAGTTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
31 42 0.88
32 6 0.12
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.40
Consensus pattern (32 bp):
AAGTTTTCATTTAAGTCACTGAACTATTCAAA
Found at i:12247459 original size:49 final size:48
Alignment explanation
Indices: 12247370--12247504 Score: 164
Period size: 49 Copynumber: 2.8 Consensus size: 48
12247360 GATCTCAATC
* * * *
12247370 GAAGTACCTATACCATGGCTCGAAACCAAATTAAGGTAACTTATCCCT
1 GAAGTACCTATACCATGGCCCGAAGCCAAATCAAGGTAACTCATCCCT
* * * *
12247418 -AGAGTAACTATACCATGGCCCTGTAGCCAAATCAATGTAACTCATCTCT
1 GA-AGTACCTATACCATGGCCC-GAAGCCAAATCAAGGTAACTCATCCCT
*
12247467 GAAATACCTATACCATGGCCCGAAGCCAAATCAAGGTA
1 GAAGTACCTATACCATGGCCCGAAGCCAAATCAAGGTA
12247505 TAATTCACAC
Statistics
Matches: 72, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
47 1 0.01
48 32 0.44
49 38 0.53
50 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.16, T:0.23
Consensus pattern (48 bp):
GAAGTACCTATACCATGGCCCGAAGCCAAATCAAGGTAACTCATCCCT
Found at i:12248363 original size:42 final size:42
Alignment explanation
Indices: 12248311--12248394 Score: 132
Period size: 42 Copynumber: 2.0 Consensus size: 42
12248301 GCAAGTCTCA
* *
12248311 AACCCTAAAACTCAATTAAAGGCTTTCTTGTTCATCAATATT
1 AACCCTAAAACTCAATCAAAGGCTTTCTTCTTCATCAATATT
* *
12248353 AACCTTAAAACTCAATCAAAGGCTTTTTTCTTCATCAATATT
1 AACCCTAAAACTCAATCAAAGGCTTTCTTCTTCATCAATATT
12248395 CGGCCAAAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.36, C:0.21, G:0.06, T:0.37
Consensus pattern (42 bp):
AACCCTAAAACTCAATCAAAGGCTTTCTTCTTCATCAATATT
Found at i:12249009 original size:16 final size:17
Alignment explanation
Indices: 12248983--12249016 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
12248973 AGAAAAAGGG
12248983 AGAAAAGAAAAAGAGAA
1 AGAAAAGAAAAAGAGAA
*
12249000 AGAAAA-AAAAGGAGAA
1 AGAAAAGAAAAAGAGAA
12249016 A
1 A
12249017 ATTAGGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (17 bp):
AGAAAAGAAAAAGAGAA
Found at i:12253530 original size:42 final size:43
Alignment explanation
Indices: 12253453--12253553 Score: 116
Period size: 42 Copynumber: 2.4 Consensus size: 43
12253443 TCCCGGACGC
* * **
12253453 GGTCTTACATGTAATTCAATATCGATGCCTCTGTCCCAAACAG
1 GGTCTTACACGTAAATCAATATCGATGCCGATGTCCCAAACAG
* *
12253496 GGTCTTACACG-AAATCAGATA-CGATGCCGATGTCCCAGACAT
1 GGTCTTACACGTAAATCA-ATATCGATGCCGATGTCCCAAACAG
*
12253538 GGTCTTATACGTAAAT
1 GGTCTTACACGTAAAT
12253554 ATCAATCGAG
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
42 32 0.65
43 17 0.35
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.28
Consensus pattern (43 bp):
GGTCTTACACGTAAATCAATATCGATGCCGATGTCCCAAACAG
Found at i:12262528 original size:13 final size:13
Alignment explanation
Indices: 12262512--12262538 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12262502 AGATTTAAAT
12262512 ATTAAATTTATTA
1 ATTAAATTTATTA
12262525 ATTAAATTTATTA
1 ATTAAATTTATTA
12262538 A
1 A
12262539 AAAAAAGCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTAAATTTATTA
Found at i:12264778 original size:16 final size:16
Alignment explanation
Indices: 12264744--12264813 Score: 59
Period size: 16 Copynumber: 4.2 Consensus size: 16
12264734 GTAGGTTTGA
*
12264744 TTTTAATATTTAATATAG
1 TTTTAAT-TTT-ATTTAG
*
12264762 TTTTAATTTTTTTTAG
1 TTTTAATTTTATTTAG
* * *
12264778 TCTCAATTTTATTTAA
1 TTTTAATTTTATTTAG
* *
12264794 TTTTAATGTTATTTAA
1 TTTTAATTTTATTTAG
12264810 TTTT
1 TTTT
12264814 TTTTCTCTAA
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
16 33 0.77
17 3 0.07
18 7 0.16
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (16 bp):
TTTTAATTTTATTTAG
Found at i:12265512 original size:23 final size:23
Alignment explanation
Indices: 12265484--12265527 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
12265474 ATTGTTGAGC
* *
12265484 TTGATATATCTCTTCACTTTTGT
1 TTGATATAACTCTTCAATTTTGT
12265507 TTGATATAACTCTTCAATTTT
1 TTGATATAACTCTTCAATTTT
12265528 TAAATATTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.55
Consensus pattern (23 bp):
TTGATATAACTCTTCAATTTTGT
Found at i:12266433 original size:25 final size:26
Alignment explanation
Indices: 12266385--12266451 Score: 68
Period size: 25 Copynumber: 2.7 Consensus size: 26
12266375 AACACCAAAC
*
12266385 ATAAATATAATTATAACCATAATA-A
1 ATAAATATAATTATAACCAAAATATA
*
12266410 ATAAATA-AATTATTAACTAAAATATA
1 ATAAATATAATTA-TAACCAAAATATA
* *
12266436 AT-ATTATAATTGTAAC
1 ATAAATATAATTATAAC
12266452 ATATGACAAC
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
24 5 0.14
25 23 0.66
26 7 0.20
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (26 bp):
ATAAATATAATTATAACCAAAATATA
Found at i:12267419 original size:15 final size:16
Alignment explanation
Indices: 12267396--12267429 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
12267386 ATTGAAAATA
12267396 TTAAATTTT-AATGAT
1 TTAAATTTTCAATGAT
*
12267411 TTAATTTTTCAATGAT
1 TTAAATTTTCAATGAT
12267427 TTA
1 TTA
12267430 TCAAGGCTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.35, C:0.03, G:0.06, T:0.56
Consensus pattern (16 bp):
TTAAATTTTCAATGAT
Found at i:12267979 original size:25 final size:24
Alignment explanation
Indices: 12267951--12268017 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 24
12267941 ACAGTTTTAA
12267951 TTAATAATAATTTTAAATAATATT
1 TTAATAATAATTTTAAATAATATT
*
12267975 CTTAAT-A-AATATTAAA-AATATT
1 -TTAATAATAATTTTAAATAATATT
*
12267997 TATATTAAT-ATTTT-AATAATA
1 T-TAATAATAATTTTAAATAATA
12268018 CAATTTATAA
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
21 1 0.03
22 11 0.31
23 17 0.49
24 1 0.03
25 5 0.14
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (24 bp):
TTAATAATAATTTTAAATAATATT
Found at i:12267980 original size:22 final size:22
Alignment explanation
Indices: 12267955--12267996 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
12267945 TTTTAATTAA
*
12267955 TAAT-AATTTTAAATAATATTCT
1 TAATAAATATTAAA-AATATTCT
12267977 TAATAAATATTAAAAATATT
1 TAATAAATATTAAAAATATT
12267997 TATATTAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 10 0.56
23 8 0.44
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATAAATATTAAAAATATTCT
Found at i:12272848 original size:16 final size:16
Alignment explanation
Indices: 12272827--12272866 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
12272817 GCTTACAGAA
12272827 AAAATAAAAAAAAAAC
1 AAAATAAAAAAAAAAC
**
12272843 AAAATAAATCAAAAAC
1 AAAATAAAAAAAAAAC
12272859 AAAA-AAAA
1 AAAATAAAA
12272867 CCAAAATAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 3 0.14
16 18 0.86
ACGTcount: A:0.85, C:0.07, G:0.00, T:0.07
Consensus pattern (16 bp):
AAAATAAAAAAAAAAC
Found at i:12272871 original size:16 final size:16
Alignment explanation
Indices: 12272837--12272872 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
12272827 AAAATAAAAA
* *
12272837 AAAAACAAAATAAATC
1 AAAAACAAAAAAAACC
12272853 AAAAACAAAAAAAACC
1 AAAAACAAAAAAAACC
12272869 AAAA
1 AAAA
12272873 TAGAAAAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.81, C:0.14, G:0.00, T:0.06
Consensus pattern (16 bp):
AAAAACAAAAAAAACC
Found at i:12280720 original size:19 final size:19
Alignment explanation
Indices: 12280637--12280703 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
12280627 AGGGAAATCT
12280637 AATGCAAATGATGCAATGC
1 AATGCAAATGATGCAATGC
*
12280656 AATGCAAATGATGCAATGT
1 AATGCAAATGATGCAATGC
*
12280675 AATGTAAATGATGCAATGC
1 AATGCAAATGATGCAATGC
12280694 AATGCAAATG
1 AATGCAAATG
12280704 CATGGGATGA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.43, C:0.12, G:0.21, T:0.24
Consensus pattern (19 bp):
AATGCAAATGATGCAATGC
Found at i:12284530 original size:10 final size:10
Alignment explanation
Indices: 12284515--12284549 Score: 52
Period size: 10 Copynumber: 3.3 Consensus size: 10
12284505 CCTTATTATA
12284515 ATATATATGT
1 ATATATATGT
12284525 ATATATATGT
1 ATATATATGT
12284535 ATATGATAATGT
1 ATAT-AT-ATGT
12284547 ATA
1 ATA
12284550 AAAAGAAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.61
11 2 0.09
12 7 0.30
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (10 bp):
ATATATATGT
Found at i:12285881 original size:27 final size:27
Alignment explanation
Indices: 12285821--12285883 Score: 67
Period size: 26 Copynumber: 2.3 Consensus size: 27
12285811 CTGTTATGGA
* *
12285821 TTGGGCTTTTTGGGCTAGGATATTGAGT
1 TTGGG-TTTTTGGGCTAAGATAATGAGT
*
12285849 TT-GGTTTTTGGGTCTAAG-TAATGATT
1 TTGGGTTTTTGGG-CTAAGATAATGAGT
12285875 TTGGGTTTT
1 TTGGGTTTT
12285884 AGGTTATTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
26 16 0.53
27 12 0.40
28 2 0.07
ACGTcount: A:0.14, C:0.05, G:0.32, T:0.49
Consensus pattern (27 bp):
TTGGGTTTTTGGGCTAAGATAATGAGT
Found at i:12291999 original size:3 final size:3
Alignment explanation
Indices: 12291991--12292030 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
12291981 TGTTAAAGGT
12291991 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12292031 AGGTAAATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12293227 original size:22 final size:22
Alignment explanation
Indices: 12293199--12293242 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
12293189 TTAATTTGTA
12293199 GATACCCTTTAATCTTACCAGT
1 GATACCCTTTAATCTTACCAGT
12293221 GATACCCTTTAATCTTACCAGT
1 GATACCCTTTAATCTTACCAGT
12293243 TGGTGTACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.27, G:0.09, T:0.36
Consensus pattern (22 bp):
GATACCCTTTAATCTTACCAGT
Found at i:12295548 original size:25 final size:25
Alignment explanation
Indices: 12295508--12295601 Score: 145
Period size: 25 Copynumber: 3.8 Consensus size: 25
12295498 CTCTTTTAAT
*
12295508 AACTGGGG-AAAGCCCTTTTTGATA
1 AACTGGGGCAAAGCCCTTTTTGGTA
* *
12295532 AACTAGGGCAAAGCCCTTTTCGGTA
1 AACTGGGGCAAAGCCCTTTTTGGTA
12295557 AACTGGGGCAAAGCCCTTTTTGGTA
1 AACTGGGGCAAAGCCCTTTTTGGTA
*
12295582 AACTGGGGCATAGCCCTTTT
1 AACTGGGGCAAAGCCCTTTT
12295602 GCACTTCTTC
Statistics
Matches: 63, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
24 7 0.11
25 56 0.89
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.28
Consensus pattern (25 bp):
AACTGGGGCAAAGCCCTTTTTGGTA
Found at i:12295551 original size:24 final size:24
Alignment explanation
Indices: 12295495--12295602 Score: 121
Period size: 25 Copynumber: 4.4 Consensus size: 24
12295485 CTGGAGGCCT
*
12295495 AGCCTCTTTTAAT-AACTGGGG-AA
1 AGCC-CTTTTGATAAACTGGGGCAA
*
12295518 AGCCCTTTTTGATAAACTAGGGCAA
1 AGCCC-TTTTGATAAACTGGGGCAA
*
12295543 AGCCCTTTTCGGTAAACTGGGGCAA
1 AGCCCTTTT-GATAAACTGGGGCAA
* *
12295568 AGCCCTTTTTGGTAAACTGGGGCAT
1 AGCCC-TTTTGATAAACTGGGGCAA
12295593 AGCCCTTTTG
1 AGCCCTTTTG
12295603 CACTTCTTCC
Statistics
Matches: 75, Mismatches: 5, Indels: 9
0.84 0.06 0.10
Matches are distributed among these distances:
22 1 0.01
23 10 0.13
24 16 0.21
25 44 0.59
26 4 0.05
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (24 bp):
AGCCCTTTTGATAAACTGGGGCAA
Found at i:12302845 original size:41 final size:43
Alignment explanation
Indices: 12302800--12302913 Score: 153
Period size: 43 Copynumber: 2.7 Consensus size: 43
12302790 TGTGTTATGG
* *
12302800 TGTAAGACCACGTCTAGGACATTGGCATC-A-ATTTGATTTCA
1 TGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTACA
*
12302841 TGTAAGACC-CGATCTGGGACAGTGGCATCGATATTTGATTACA
1 TGTAAGACCACG-TCTGGGACATTGGCATCGATATTTGATTACA
* *
12302884 TGTAACACCACGTCTGGGACATTGGTATCG
1 TGTAAGACCACGTCTGGGACATTGGCATCG
12302914 TAAGAGATTT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
40 2 0.03
41 24 0.38
42 1 0.02
43 34 0.54
44 2 0.03
ACGTcount: A:0.27, C:0.20, G:0.24, T:0.29
Consensus pattern (43 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATATTTGATTACA
Found at i:12318719 original size:3 final size:3
Alignment explanation
Indices: 12318704--12318739 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
12318694 AAGCATAAAC
* *
12318704 TAA TAA AAA TAA TAA TAA TAA TAA TAA TAA TGA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
12318740 CATTGGAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:12338044 original size:20 final size:20
Alignment explanation
Indices: 12338010--12338049 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
12338000 CTATTCAGAC
* *
12338010 AATATTATTTAAATAGTTAT
1 AATATTATATAAATAATTAT
*
12338030 AATATTATATGAATAATTAT
1 AATATTATATAAATAATTAT
12338050 TTGTCTTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.47
Consensus pattern (20 bp):
AATATTATATAAATAATTAT
Found at i:12339484 original size:34 final size:34
Alignment explanation
Indices: 12339437--12339507 Score: 133
Period size: 34 Copynumber: 2.1 Consensus size: 34
12339427 ACAAAGATAT
12339437 GATTAAAAACAATACTATCATATATTAGTTATCA
1 GATTAAAAACAATACTATCATATATTAGTTATCA
*
12339471 GATTAAAACCAATACTATCATATATTAGTTATCA
1 GATTAAAAACAATACTATCATATATTAGTTATCA
12339505 GAT
1 GAT
12339508 CAATTGTAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 36 1.00
ACGTcount: A:0.45, C:0.13, G:0.07, T:0.35
Consensus pattern (34 bp):
GATTAAAAACAATACTATCATATATTAGTTATCA
Found at i:12345684 original size:8 final size:8
Alignment explanation
Indices: 12345664--12345700 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
12345654 CTAAATTTAT
12345664 ATTTTTCA
1 ATTTTTCA
12345672 A-TTTTCA
1 ATTTTTCA
12345679 ATTTTTCA
1 ATTTTTCA
12345687 ATTTTTCA
1 ATTTTTCA
12345695 ATTTTT
1 ATTTTT
12345701 TAAATTAAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 7 0.25
8 21 0.75
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.65
Consensus pattern (8 bp):
ATTTTTCA
Found at i:12345714 original size:23 final size:24
Alignment explanation
Indices: 12345688--12345739 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 24
12345678 AATTTTTCAA
* *
12345688 TTTTTCAATTTTTTAA-ATTAAAC
1 TTTTTCAATTTCTAAACATTAAAC
*
12345711 TTTTTCAATTTCTAAACATTAAGC
1 TTTTTCAATTTCTAAACATTAAAC
12345735 TTTTT
1 TTTTT
12345740 TTAGCTAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 14 0.56
24 11 0.44
ACGTcount: A:0.31, C:0.12, G:0.02, T:0.56
Consensus pattern (24 bp):
TTTTTCAATTTCTAAACATTAAAC
Found at i:12345783 original size:16 final size:16
Alignment explanation
Indices: 12345762--12345794 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
12345752 TTTTTCCTAT
*
12345762 TTTTTGAATTTTTAAA
1 TTTTTGAATTTTGAAA
12345778 TTTTTGAATTTTGAAA
1 TTTTTGAATTTTGAAA
12345794 T
1 T
12345795 AAAAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (16 bp):
TTTTTGAATTTTGAAA
Found at i:12345877 original size:28 final size:28
Alignment explanation
Indices: 12345827--12345883 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
12345817 TTTGTACAAT
* *
12345827 ATATATTTTTTAATTTTCTAAAATTTAA
1 ATATATTTTTTAATTTTATAAAAATTAA
*
12345855 ATAT-TTTTTTATTTTTATAAAAAATTAA
1 ATATATTTTTTAATTTTAT-AAAAATTAA
12345883 A
1 A
12345884 ATTATATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
ATATATTTTTTAATTTTATAAAAATTAA
Found at i:12354519 original size:176 final size:176
Alignment explanation
Indices: 12354225--12354580 Score: 667
Period size: 176 Copynumber: 2.0 Consensus size: 176
12354215 CTCTTCACTT
*
12354225 TATAACTCTTTTGGCTTAATTTTTTTCGAAAAAATGAGCTCCACAAAATTTGACTAAATTGAAGG
1 TATAACTCTTTTGGCTTAATTTTTTTCGAAAAAATGAGATCCACAAAATTTGACTAAATTGAAGG
*
12354290 TTTAAACATGTAATTATATCATATTAGGGAAGATTAGGATTGAAATTAAGGTTTAGAAATAAAAT
66 TTTAAACATGTAATTATATCATATTAGGGAAGATTAGGATCGAAATTAAGGTTTAGAAATAAAAT
12354355 TTGAGTGGTGAAATCATATTTTCGACAAAACTAGTTAAGTTTTCGG
131 TTGAGTGGTGAAATCATATTTTCGACAAAACTAGTTAAGTTTTCGG
*
12354401 TATAACTCTTTTGGCTTAATTTTTTTCGAAGAAATGAGATCCACAAAATTTGACTAAATTGAAGG
1 TATAACTCTTTTGGCTTAATTTTTTTCGAAAAAATGAGATCCACAAAATTTGACTAAATTGAAGG
12354466 TTTAAACATGTAATTATATCATATTAGGGAAGATTAGGATCGAAATTAAGGTTTAGAAATAAAAT
66 TTTAAACATGTAATTATATCATATTAGGGAAGATTAGGATCGAAATTAAGGTTTAGAAATAAAAT
* *
12354531 TTGAGTGGTGAAATCGTATTTTCGACAAAACTGGTTAAGTTTTCGG
131 TTGAGTGGTGAAATCATATTTTCGACAAAACTAGTTAAGTTTTCGG
12354577 TATA
1 TATA
12354581 GAGATCTAGA
Statistics
Matches: 175, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
176 175 1.00
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (176 bp):
TATAACTCTTTTGGCTTAATTTTTTTCGAAAAAATGAGATCCACAAAATTTGACTAAATTGAAGG
TTTAAACATGTAATTATATCATATTAGGGAAGATTAGGATCGAAATTAAGGTTTAGAAATAAAAT
TTGAGTGGTGAAATCATATTTTCGACAAAACTAGTTAAGTTTTCGG
Found at i:12356918 original size:40 final size:39
Alignment explanation
Indices: 12356873--12357004 Score: 133
Period size: 40 Copynumber: 3.4 Consensus size: 39
12356863 AGTTTGGCAT
* *
12356873 CTAGTGCCTCATCGGATAATTCGAAGTAATAGATTAACAC
1 CTAGTGCCTCATCGGATAATCCAAAGTAATA-ATTAACAC
* * * *
12356913 CTAGTGTCTCATCGGCTAAACCAAAGT-A-AATTAGCAC
1 CTAGTGCCTCATCGGATAATCCAAAGTAATAATTAACAC
* * *
12356950 CTAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGACAC
1 CTAGTGCCTCATCGGA-TAATCCAAAGTAAT-AATTAACAC
*
12356991 CTAGTGTCTCATCG
1 CTAGTGCCTCATCG
12357005 CCTCGAAGTC
Statistics
Matches: 74, Mismatches: 14, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
37 20 0.27
38 11 0.15
39 1 0.01
40 22 0.30
41 20 0.27
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (39 bp):
CTAGTGCCTCATCGGATAATCCAAAGTAATAATTAACAC
Found at i:12356992 original size:41 final size:37
Alignment explanation
Indices: 12356873--12357004 Score: 106
Period size: 41 Copynumber: 3.4 Consensus size: 37
12356863 AGTTTGGCAT
* * *
12356873 CTAGTGCCTCATCGGATAATTCGAAGTAATAGATTAACAC
1 CTAGTGCCTCATC-GATAA-TCCAAGTAGTAAATT-ACAC
* * *
12356913 CTAGTGTCTCATCGGCTAAACCAA--AGTAAATTAGCAC
1 CTAGTGCCTCATC-GATAATCCAAGTAGTAAATTA-CAC
12356950 CTAGTGCCTCATCGAATTAATCCAAAGTAGTAAATTGACAC
1 CTAGTGCCTCATCG-A-TAATCC-AAGTAGTAAATT-ACAC
*
12356991 CTAGTGTCTCATCG
1 CTAGTGCCTCATCG
12357005 CCTCGAAGTC
Statistics
Matches: 75, Mismatches: 10, Indels: 13
0.77 0.10 0.13
Matches are distributed among these distances:
36 2 0.03
37 21 0.28
38 5 0.07
39 5 0.07
40 17 0.23
41 24 0.32
42 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (37 bp):
CTAGTGCCTCATCGATAATCCAAGTAGTAAATTACAC
Found at i:12366820 original size:13 final size:13
Alignment explanation
Indices: 12366802--12366828 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
12366792 GCTATCTCCA
12366802 TGATGCTGCTAGT
1 TGATGCTGCTAGT
12366815 TGATGCTGCTAGT
1 TGATGCTGCTAGT
12366828 T
1 T
12366829 CTTACAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.15, G:0.30, T:0.41
Consensus pattern (13 bp):
TGATGCTGCTAGT
Found at i:12368832 original size:24 final size:26
Alignment explanation
Indices: 12368757--12368840 Score: 68
Period size: 24 Copynumber: 3.2 Consensus size: 26
12368747 AAATTTAAAT
12368757 AATTTT-TAT-TTATTATAACATTTTTTCA
1 AATTTTATATATTATTATAA-A--TTTT-A
* *
12368785 ATTTTTATATATTATTTTAAATTTTA
1 AATTTTATATATTATTATAAATTTTA
*
12368811 AATTTTATA-ATTA-TATATATTTTA
1 AATTTTATATATTATTATAAATTTTA
*
12368835 CATTTT
1 AATTTT
12368841 TAGTCAATAT
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
24 14 0.29
25 4 0.08
26 9 0.19
27 4 0.08
28 5 0.10
29 4 0.08
30 8 0.17
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (26 bp):
AATTTTATATATTATTATAAATTTTA
Found at i:12374421 original size:31 final size:31
Alignment explanation
Indices: 12374386--12374451 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
12374376 AAAGAGGCGA
12374386 CACCCAATGGTCACGCCTTAGGCACAAGCAG
1 CACCCAATGGTCACGCCTTAGGCACAAGCAG
* * * *
12374417 CACCCACTGGTCACGCCTTTGGCAGAGGCAG
1 CACCCAATGGTCACGCCTTAGGCACAAGCAG
12374448 CACC
1 CACC
12374452 ATCAGTCATG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.24, C:0.38, G:0.24, T:0.14
Consensus pattern (31 bp):
CACCCAATGGTCACGCCTTAGGCACAAGCAG
Found at i:12374897 original size:31 final size:31
Alignment explanation
Indices: 12374859--12374920 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
12374849 TAGTAGTGCT
* *
12374859 GCCAAAGTGATAGGCGGCACCACTTTGTCCA
1 GCCAAAGTGATAGGCGACACCACTTAGTCCA
*
12374890 GCCAAAGTGATAGGCGACACTACTTAGTCCA
1 GCCAAAGTGATAGGCGACACCACTTAGTCCA
12374921 TTCTGGTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.29, C:0.27, G:0.24, T:0.19
Consensus pattern (31 bp):
GCCAAAGTGATAGGCGACACCACTTAGTCCA
Found at i:12377447 original size:21 final size:21
Alignment explanation
Indices: 12377378--12377448 Score: 63
Period size: 21 Copynumber: 3.4 Consensus size: 21
12377368 AAATTTAGAA
* *
12377378 AATTA-TGGTTGATTTTGATT
1 AATTATTGATTGACTTTGATT
* * * *
12377398 CATTATTGATTGGCATTGGTT
1 AATTATTGATTGACTTTGATT
* *
12377419 GATGATTGATTGACTTTGATT
1 AATTATTGATTGACTTTGATT
12377440 AATTATTGA
1 AATTATTGA
12377449 CGGATGTTGA
Statistics
Matches: 37, Mismatches: 13, Indels: 1
0.73 0.25 0.02
Matches are distributed among these distances:
20 4 0.11
21 33 0.89
ACGTcount: A:0.25, C:0.04, G:0.21, T:0.49
Consensus pattern (21 bp):
AATTATTGATTGACTTTGATT
Found at i:12377686 original size:22 final size:20
Alignment explanation
Indices: 12377646--12377687 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
12377636 TTTCTTTTGG
*
12377646 ATTTTTTTGAATTTTTAGAA
1 ATTTTATTGAATTTTTAGAA
12377666 ATTTTATTGATATATTTTAGAA
1 ATTTTATTGA-AT-TTTTAGAA
12377688 GTTCCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 2 0.11
22 8 0.42
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (20 bp):
ATTTTATTGAATTTTTAGAA
Found at i:12381721 original size:24 final size:24
Alignment explanation
Indices: 12381693--12381777 Score: 127
Period size: 24 Copynumber: 3.5 Consensus size: 24
12381683 CCCTCCTCGT
12381693 CCATTCCCTCCTCACCCACCGCGA
1 CCATTCCCTCCTCACCCACCGCGA
*
12381717 CCATTCCCTCCTCACCCGCCGCGA
1 CCATTCCCTCCTCACCCACCGCGA
* *
12381741 CCGA-TCCCTCCTCATCCACCACGA
1 CC-ATTCCCTCCTCACCCACCGCGA
12381765 CCATTCCCTCCTC
1 CCATTCCCTCCTC
12381778 CTCATCCTCA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
23 1 0.02
24 53 0.96
25 1 0.02
ACGTcount: A:0.15, C:0.58, G:0.08, T:0.19
Consensus pattern (24 bp):
CCATTCCCTCCTCACCCACCGCGA
Found at i:12384168 original size:18 final size:18
Alignment explanation
Indices: 12384126--12384169 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
12384116 CCTTTTTTTC
12384126 TTTATT-TTTATTTTAGT
1 TTTATTATTTATTTTAGT
*
12384143 TTTTTTATTTATTTTA-T
1 TTTATTATTTATTTTAGT
12384160 TCTTATTATT
1 T-TTATTATT
12384170 ACTATTTAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.77
Consensus pattern (18 bp):
TTTATTATTTATTTTAGT
Found at i:12384927 original size:34 final size:34
Alignment explanation
Indices: 12384888--12384952 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
12384878 ATTTAAAGGC
12384888 AAACTTGTTCTCGAATGTTCGAATGTCGCATCCT
1 AAACTTGTTCTCGAATGTTCGAATGTCGCATCCT
* *
12384922 AAACTTGTTCTCGAATTTTTGAATGTCGCAT
1 AAACTTGTTCTCGAATGTTCGAATGTCGCAT
12384953 TTCGTTATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (34 bp):
AAACTTGTTCTCGAATGTTCGAATGTCGCATCCT
Found at i:12385228 original size:153 final size:154
Alignment explanation
Indices: 12384944--12385246 Score: 536
Period size: 153 Copynumber: 2.0 Consensus size: 154
12384934 GAATTTTTGA
*
12384944 ATGTCGCATTTCGTTATCTCAGGACGAATAGGCCTTTGGTGTTCGTTTCAACTTAATTCAAGCTT
1 ATGTCGCATTTCGTTATCTCAGGACGAATAGGCCTTTGATGTTCGTTTCAACTTAATTCAAGCTT
**
12385009 TTTTTAAAAAAAAAAGCTTTAATAAAAAGGGATCGTATTTTAAATCTTTTCAAAATTTTAACTTT
66 TTTTTAAAAAAAAAAGCTTTAATAAAAAGGGATCGTATTTTAAATCTTTTCAAAATTGCAACTTT
12385074 CGCCATTAAGACATTAATTACGGG
131 CGCCATTAAGACATTAATTACGGG
* * * *
12385098 ATGTTGCATTTCGTTATCTCAGGACGAGTGGGCCTTTGATGTTTGTTTCAACTTAATTCAAGCTT
1 ATGTCGCATTTCGTTATCTCAGGACGAATAGGCCTTTGATGTTCGTTTCAACTTAATTCAAGCTT
12385163 TTTTT-AAAAAAAAAGCTTTAATAAAAAGGGATCGTATTTTAAATCTTTTCAAAATTGCAACTTT
66 TTTTTAAAAAAAAAAGCTTTAATAAAAAGGGATCGTATTTTAAATCTTTTCAAAATTGCAACTTT
12385227 CGCCATTAAGACATTAATTA
131 CGCCATTAAGACATTAATTA
12385247 ATTAATTGGA
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
153 77 0.54
154 65 0.46
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.38
Consensus pattern (154 bp):
ATGTCGCATTTCGTTATCTCAGGACGAATAGGCCTTTGATGTTCGTTTCAACTTAATTCAAGCTT
TTTTTAAAAAAAAAAGCTTTAATAAAAAGGGATCGTATTTTAAATCTTTTCAAAATTGCAACTTT
CGCCATTAAGACATTAATTACGGG
Found at i:12391956 original size:37 final size:37
Alignment explanation
Indices: 12391888--12391959 Score: 108
Period size: 37 Copynumber: 1.9 Consensus size: 37
12391878 TCTGTGCAAG
*
12391888 TATTCTTTTATTATTTTCATTCTATTCATAACCAAAA
1 TATTCTTTTATTATTTCCATTCTATTCATAACCAAAA
* * *
12391925 TATTCTTTTATTCTTTCCATTTTATTTATAACCAA
1 TATTCTTTTATTATTTCCATTCTATTCATAACCAA
12391960 TCATATGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (37 bp):
TATTCTTTTATTATTTCCATTCTATTCATAACCAAAA
Found at i:12396580 original size:44 final size:45
Alignment explanation
Indices: 12396514--12396850 Score: 183
Period size: 44 Copynumber: 7.5 Consensus size: 45
12396504 TACCATGGCG
* *
12396514 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATAGAAACCA-CT
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATAGAAAACAGCA
* * * * * *
12396558 AGTCTTATCTCCCTGAAATTGCA-AAGGAGCAGATTGAAAATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTA-GAGTAGATAGAAAACAGCA
* * *
12396603 AATCTTATCTCTCTGAAGTTGCAGTAGAGTAGATTAAAACTATAAACAACA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGA-T---A-GA-AAACAGCA
* * * * * * * **
12396654 AACCCTATCTCCCTAAAGTTACAGTAGAGCAGGTTGAAATTA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATAGAAAACAGCA
* * * *
12396698 AATCTAATTTCCCTGAAGTT---GTGGAGTAGATAGAAACCA-CA
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATAGAAAACAGCA
* * * *
12396739 AATCTTATCTCCAT-AATGTTGCAATGGAGTAGATTGAAGAA-AGCA
1 AATCTTATCTCCCTGAA-GTTGCAGTAGAGTAGATAGAA-AACAGCA
* * * * * *
12396784 AGTCTTATCTCCTTGAAGTT-CAGTGGAGTAGACTA-AAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGA-TAGAAAACAGCA
* *
12396828 AATATTATTTCCCTGAAGTTGCA
1 AATCTTATCTCCCTGAAGTTGCA
12396851 ATGGAACAGA
Statistics
Matches: 219, Mismatches: 55, Indels: 37
0.70 0.18 0.12
Matches are distributed among these distances:
40 2 0.01
41 29 0.13
43 2 0.01
44 96 0.44
45 51 0.23
46 5 0.02
50 2 0.01
51 32 0.15
ACGTcount: A:0.36, C:0.18, G:0.18, T:0.28
Consensus pattern (45 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAGTAGATAGAAAACAGCA
Found at i:12398663 original size:18 final size:19
Alignment explanation
Indices: 12398622--12398664 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
12398612 CTTTTTTTCT
12398622 TTATT-TTTATTTTAGTTA
1 TTATTATTTATTTTAGTTA
*
12398640 TT-TTATTTATTTTA-TTC
1 TTATTATTTATTTTAGTTA
12398657 TTATTATT
1 TTATTATT
12398665 ACTATTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 6 0.27
18 16 0.73
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.74
Consensus pattern (19 bp):
TTATTATTTATTTTAGTTA
Found at i:12398670 original size:24 final size:24
Alignment explanation
Indices: 12398621--12398672 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
12398611 CCTTTTTTTC
*
12398621 TTTATTTTTATTTTAGTTATTTTA
1 TTTATTTTTATTTTAGTTATTCTA
12398645 TTTA-TTTTATTCTTA-TTATTACTA
1 TTTATTTTTATT-TTAGTTATT-CTA
12398669 TTTA
1 TTTA
12398673 AAATTGTTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.23, C:0.04, G:0.02, T:0.71
Consensus pattern (24 bp):
TTTATTTTTATTTTAGTTATTCTA
Found at i:12398833 original size:13 final size:14
Alignment explanation
Indices: 12398815--12398856 Score: 52
Period size: 13 Copynumber: 3.1 Consensus size: 14
12398805 ATTTTCAATA
12398815 TTTTATA-AATTAT
1 TTTTATATAATTAT
*
12398828 TTTTATATATTTA-
1 TTTTATATAATTAT
*
12398841 TTTTATATATTTAT
1 TTTTATATAATTAT
12398855 TT
1 TT
12398857 AATTACTTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (14 bp):
TTTTATATAATTAT
Found at i:12398849 original size:15 final size:14
Alignment explanation
Indices: 12398813--12398856 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 14
12398803 TTATTTTCAA
12398813 TATTTTATA-A-AT
1 TATTTTATATATAT
12398825 TATTTT-TATATATT
1 TATTTTATATATA-T
12398839 TATTTTATATAT-T
1 TATTTTATATATAT
12398852 TATTT
1 TATTT
12398857 AATTACTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
11 2 0.07
12 7 0.25
13 7 0.25
14 7 0.25
15 5 0.18
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (14 bp):
TATTTTATATATAT
Found at i:12401232 original size:24 final size:25
Alignment explanation
Indices: 12401185--12401240 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 25
12401175 TATTCAATAC
** *
12401185 AATATATTATTTATATATTTTTTAA
1 AATATATTAAATATATATTGTTTAA
12401210 AATATATTAAATAT-TATTGTTTAA
1 AATATATTAAATATATATTGTTTAA
*
12401234 TATATAT
1 AATATAT
12401241 ATATGCTTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
24 15 0.56
25 12 0.44
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (25 bp):
AATATATTAAATATATATTGTTTAA
Found at i:12405292 original size:18 final size:18
Alignment explanation
Indices: 12405269--12405324 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
12405259 CCACCACCAA
12405269 CTCCACTAGCCACAATTG
1 CTCCACTAGCCACAATTG
*
12405287 CTCCACCA--C-CAA---
1 CTCCACTAGCCACAATTG
*
12405299 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACAATTG
12405317 CTCCACTA
1 CTCCACTA
12405325 CCTACTCCAC
Statistics
Matches: 29, Mismatches: 3, Indels: 12
0.66 0.07 0.27
Matches are distributed among these distances:
12 7 0.24
14 1 0.03
15 5 0.17
16 1 0.03
18 15 0.52
ACGTcount: A:0.27, C:0.46, G:0.07, T:0.20
Consensus pattern (18 bp):
CTCCACTAGCCACAATTG
Found at i:12405295 original size:30 final size:30
Alignment explanation
Indices: 12405259--12405357 Score: 171
Period size: 30 Copynumber: 3.3 Consensus size: 30
12405249 CTAGCATTTG
*
12405259 CCACCACCAACTCCACTAGCCACAATTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
12405289 CCACCACCAACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
* *
12405319 CCACTACCTACTCCACTAGCCACACTTGCT
1 CCACCACCAACTCCACTAGCCACACTTGCT
12405349 CCACCACCA
1 CCACCACCA
12405358 CTTGTACCTA
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 64 1.00
ACGTcount: A:0.27, C:0.49, G:0.06, T:0.17
Consensus pattern (30 bp):
CCACCACCAACTCCACTAGCCACACTTGCT
Found at i:12405352 original size:18 final size:18
Alignment explanation
Indices: 12405299--12405352 Score: 57
Period size: 18 Copynumber: 3.3 Consensus size: 18
12405289 CCACCACCAA
12405299 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
*
12405317 CTCCACT----AC-C-TA
1 CTCCACTAGCCACACTTG
12405329 CTCCACTAGCCACACTTG
1 CTCCACTAGCCACACTTG
12405347 CTCCAC
1 CTCCAC
12405353 CACCACTTGT
Statistics
Matches: 28, Mismatches: 2, Indels: 12
0.67 0.05 0.29
Matches are distributed among these distances:
12 8 0.29
13 1 0.04
14 2 0.07
16 2 0.07
17 1 0.04
18 14 0.50
ACGTcount: A:0.22, C:0.48, G:0.07, T:0.22
Consensus pattern (18 bp):
CTCCACTAGCCACACTTG
Found at i:12412890 original size:14 final size:13
Alignment explanation
Indices: 12412871--12412906 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
12412861 CGCTGAGGTA
12412871 TTTTCAAAATCTG
1 TTTTCAAAATCTG
*
12412884 TTTTTCAAATTCTG
1 -TTTTCAAAATCTG
12412898 TTTTCAAAA
1 TTTTCAAAA
12412907 ATCAACTCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.31, C:0.14, G:0.06, T:0.50
Consensus pattern (13 bp):
TTTTCAAAATCTG
Found at i:12413025 original size:75 final size:76
Alignment explanation
Indices: 12412946--12413208 Score: 255
Period size: 75 Copynumber: 3.3 Consensus size: 76
12412936 AGCCTCAAGA
* *
12412946 CACGT-TGAGGTATTTTCAATTTCTGTCTTTTAAAAAAATCAATTCATATTTCGAGAAGTGAGTT
1 CACGTCTGAGCTATGTTCAATTTCTGTCTTTTAAAAAAATCAATTCATATTTCGAGAAGTGAGTT
12413010 GAACCTTGGCT
66 GAACCTTGGCT
* * * *
12413021 CACGTGCTGAGCTATGTTCAATTTCTATTTTAATGTCTGTTTTTAAAGAATCAACTCATATTGCG
1 CACGT-CTGAGCTATGTTCAATTTC--------TGTC--TTTTAAAAAAATCAATTCATATTTCG
* * ** *
12413086 A-ATGGTGAGTTGAGCCTCAAG-A
55 AGA-AGTGAGTTGAACCT-TGGCT
* *
12413108 CACGT-TGAGGTATTTTCAATTTCTGTCTTTTAAAAAAATCAATTCATATTTCGAGAAGTGAGTT
1 CACGTCTGAGCTATGTTCAATTTCTGTCTTTTAAAAAAATCAATTCATATTTCGAGAAGTGAGTT
12413172 GAACCTTGGCT
66 GAACCTTGGCT
12413183 CACGTGCTGAGCTATGTTCAATTTCT
1 CACGT-CTGAGCTATGTTCAATTTCT
12413209 ATTTTAATGT
Statistics
Matches: 146, Mismatches: 24, Indels: 34
0.72 0.12 0.17
Matches are distributed among these distances:
74 1 0.01
75 45 0.31
76 1 0.01
77 37 0.25
85 20 0.14
86 1 0.01
87 40 0.27
88 1 0.01
ACGTcount: A:0.28, C:0.16, G:0.18, T:0.38
Consensus pattern (76 bp):
CACGTCTGAGCTATGTTCAATTTCTGTCTTTTAAAAAAATCAATTCATATTTCGAGAAGTGAGTT
GAACCTTGGCT
Found at i:12413104 original size:162 final size:161
Alignment explanation
Indices: 12412804--12413974 Score: 917
Period size: 162 Copynumber: 7.1 Consensus size: 161
12412794 TGATATTTTT
* * * * * * * *
12412804 ATTTCTATTTTCAAAAAAATCTACTCATATTGCGAGAGATGAGTTGAGCCTCGG-GCAC--GCTG
1 ATTTCTGTTTTTAAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACCTAGGCTCACGTGCTG
* * ** * * *
12412866 AGGTATTTTCAAAATCTGTTTTTCAAAT-TCTGTTTTCAAA-AATCAACTCATATTGCAAGGAGG
66 AGCTATGTTCAATTTCT-ATTTTC-AATGTCTGTTTTTAAAGAATCAACTCATATTGC--GAAGG
*
12412929 TGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
127 TGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
* * *
12412964 ATTTCTGTCTTTTAAAAAAATCAATTCATATTTCGAGAAGTGAGTTGAACCTTGGCTCACGTGCT
1 ATTTCTGT-TTTTAAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACCTAGGCTCACGTGCT
12413029 GAGCTATGTTCAATTTCTATTTT-AATGTCTGTTTTTAAAGAATCAACTCATATTGCGAATGGTG
65 GAGCTATGTTCAATTTCTATTTTCAATGTCTGTTTTTAAAGAATCAACTCATATTGCGAA-GGTG
*
12413093 AGTTGAGCCTCAAGACACGTTGAGGTATTTTCA
129 AGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
* * *
12413126 ATTTCTGTCTTTTAAAAAAATCAATTCATATTTCGAGAAGTGAGTTGAACCTTGGCTCACGTGCT
1 ATTTCTGT-TTTTAAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACCTAGGCTCACGTGCT
12413191 GAGCTATGTTCAATTTCTATTTT-AATGTCTGTTTTTAAAGAATCAACTCATATTGCGAATGGTG
65 GAGCTATGTTCAATTTCTATTTTCAATGTCTGTTTTTAAAGAATCAACTCATATTGCGAA-GGTG
12413255 AGTTGAGCCTCAAGACACGCTGAGGTAATTTT-A
129 AGTTGAGCCTCAAGACACGCTGAGGT-ATTTTCA
** * * * *
12413288 ATTTCAATTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACACGT--
1 ATTTCTGTTTTT-AAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACCT-AGGCTCACGTGC
* * ******* ** * *
12413350 TGAGGTATTTTCAATTTCTATCTTTCAA-AAAAAAATCAAAAAAATCAACTTATATTGCGAGAGG
64 TGAGCTATGTTCAATTTCTAT-TTTCAATGTCTGTTTTTAAAGAATCAACTCATATTGCGA-AGG
*
12413414 TGAGTTGAGCCTCAAG--ACGCTGAGGCATTTTCA
127 TGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
* * * *
12413447 ATTTCTATTTTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACGTGCT
1 ATTTCTGTTTTT-AAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACCTAGGCTCACGTGCT
* * * * *
12413512 GAGGTATTTTCAATTTCTACTTTTCAATTTCTATTTTTCAAAAGAATCAACTTATATTGCGAGAG
65 GAGCTATGTTCAATTTCTA-TTTTCAATGTCTGTTTTT--AAAGAATCAACTCATATTGCGA-AG
* *
12413577 GTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCA
126 GTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
* * * ** * ***
12413613 ATTTCTG-TTGTCAAAAAATCAACTT-GTATTGCGAGAGGTGAGTTGAGTCTCGGGC-CATACGC
1 ATTTCTGTTTTTAAAAAAATCAA-TTCATATTGCGAGAGGTGAGTTGAACCT-AGGCTCACGTGC
* * * * * * *
12413675 CGAGGTCTTTTCAAATTCCGTTTTCAATTTCCATTTTTTCAATTTATGCTTTTGAAAAAATTAAC
64 TGA-G-C---T---A-T--G--TTCAATTT-C-TATTTTCAATGTCTG-TTTTTAAAGAATCAAC
* * *
12413740 TCATATTGCGAATGGTGAGTTGAGCCTCATGACACACTGAGGTAATTTCA
113 TCATATTGCGAA-GGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
* * * * * * * ** *
12413790 ATTTATGCTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCAC--GCCG
1 ATTTCTGTTTTTAAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACCTAGGCTCACGTGCTG
* * *
12413852 AGGTATTTTTAATTTCTATTTTTCAATTTCTGCTTTTAATTTCTGTTTTTCAAA-AATCAACTCA
66 AGCTATGTTCAATTTCTA-TTTTCAA----TG---------TCTGTTTTT-AAAGAATCAACTCA
* * *
12413916 TATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGATATTTTCA
116 TATTGCGA-AGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCA
12413963 ATTTCTGTTTTT
1 ATTTCTGTTTTT
12413975 CAATTTTTGC
Statistics
Matches: 845, Mismatches: 105, Indels: 109
0.80 0.10 0.10
Matches are distributed among these distances:
158 7 0.01
159 65 0.08
160 27 0.03
161 123 0.15
162 265 0.31
163 26 0.03
164 95 0.11
165 9 0.01
166 22 0.03
167 1 0.00
169 1 0.00
170 1 0.00
172 1 0.00
173 64 0.08
174 8 0.01
175 5 0.01
176 4 0.00
177 101 0.12
178 15 0.02
179 5 0.01
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (161 bp):
ATTTCTGTTTTTAAAAAAATCAATTCATATTGCGAGAGGTGAGTTGAACCTAGGCTCACGTGCTG
AGCTATGTTCAATTTCTATTTTCAATGTCTGTTTTTAAAGAATCAACTCATATTGCGAAGGTGAG
TTGAGCCTCAAGACACGCTGAGGTATTTTCA
Found at i:12413330 original size:75 final size:75
Alignment explanation
Indices: 12413231--12413538 Score: 365
Period size: 75 Copynumber: 4.0 Consensus size: 75
12413221 GTTTTTAAAG
*
12413231 AATCAACTCATATTGCGA-ATGGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTT-AATTTCA
1 AATCAACTCATATTGCGAGA-GGTGAGTTGAGCCTCAAGACACGCTGAGGT-ATTTTCAATTTCT
12413294 ATTTTTCAAAAA
64 ATTTTTCAAAAA
*
12413306 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTAT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTAT
12413371 CTTTCAAAAAAAAATCAAAAA
66 -TTT----------TCAAAAA
* *
12413392 AATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAG--ACGCTGAGGCATTTTCAATTTCTAT
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTAT
*
12413455 TTTTCAAAAG
66 TTTTCAAAAA
* *
12413465 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AGGCTCACGTGCTGAGGTATTTTCAATTTC
1 AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAG-ACAC--GCTGAGGTATTTTCAATTTC
*
12413529 TACTTTTCAA
63 TATTTTTCAA
12413539 TTTCTATTTT
Statistics
Matches: 205, Mismatches: 10, Indels: 34
0.82 0.04 0.14
Matches are distributed among these distances:
72 2 0.01
73 39 0.19
74 5 0.02
75 57 0.28
76 4 0.02
77 28 0.14
83 3 0.01
84 23 0.11
86 44 0.21
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (75 bp):
AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGCTGAGGTATTTTCAATTTCTAT
TTTTCAAAAA
Found at i:12413471 original size:73 final size:74
Alignment explanation
Indices: 12413385--12413538 Score: 213
Period size: 73 Copynumber: 2.1 Consensus size: 74
12413375 CAAAAAAAAA
*
12413385 TCAAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCAAG-AC-GCTGAGGCATTTTCAA
1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT-AAGCACGGCTGAGGCATTTTCAA
*
12413448 TTTCTATTTT
65 TTTCTACTTT
* * *
12413458 TCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGCTCACGTGCTGAGGTATTTTC
1 TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAAG--CACG-GCTGAGGCATTTTC
12413523 AATTTCTACTTT
63 AATTTCTACTTT
12413535 TCAA
1 TCAA
12413539 TTTCTATTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
72 2 0.03
73 39 0.55
75 2 0.03
77 28 0.39
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (74 bp):
TCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAAGCACGGCTGAGGCATTTTCAAT
TTCTACTTT
Found at i:12413537 original size:14 final size:14
Alignment explanation
Indices: 12413518--12413552 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
12413508 TGCTGAGGTA
12413518 TTTTCAATTTCTAC
1 TTTTCAATTTCTAC
*
12413532 TTTTCAATTTCTAT
1 TTTTCAATTTCTAC
12413546 TTTTCAA
1 TTTTCAA
12413553 AAGAATCAAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTTCAATTTCTAC
Found at i:12413822 original size:177 final size:174
Alignment explanation
Indices: 12413518--12413973 Score: 557
Period size: 177 Copynumber: 2.6 Consensus size: 174
12413508 TGCTGAGGTA
* * *
12413518 TTTTCAATTTCTA-CTTTTCAATTTCTATTTTTCAAAAGAATCAACTTATATTGCGAGAGGTGAG
1 TTTTCAATTTCCATCTTTTCAATTTCT-GTTTTCAAAA-AATCAACTCATATTGCGAGAGGTGAG
* **
12413582 TTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTGTCAAAAAATCAACTTGTATTGCGA
64 TTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTC-AAAAATCAACTCATATTGCGA
* * * *
12413647 GAGGTGAGTTGAGTCTCGGGCCATACGCCGAGGTCTTTTCAAATTC-CG
128 GAGGTGAGCTGAGCCTCGGGCC--ACGCCGAGGTATTTTCAAATTCTAG
* * * *
12413695 TTTTCAATTTCCATTTTTTCAATTTATGCTTTTGAAAAAATTAACTCATATTGCGA-ATGGTGAG
1 TTTTCAATTTCCATCTTTTCAATTTCTG-TTTTCAAAAAATCAACTCATATTGCGAGA-GGTGAG
* * *
12413759 TTGAGCCTCATGACACACTGAGGTAATTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGA
64 TTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-TTTTCAAAAATCAACTCATATTGCGA
* * * *
12413824 GAGGTGAGCTGAGCCTCGGGGCACGCCGAGGTATTTTTAATTTCTAT
128 GAGGTGAGCTGAGCCTCGGGCCACGCCGAGGTATTTTCAAATTCTAG
12413871 TTTTCAATTT-C-TGCTTTT-AATTTCTGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAG
1 TTTTCAATTTCCAT-CTTTTCAATTTCTG-TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAG
* * *
12413932 TTGAGCCTCAGGGCACGCTGAGATATTTTCAATTTCTGTTTT
64 TTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTT
12413974 TCAATTTTTG
Statistics
Matches: 240, Mismatches: 32, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
172 4 0.02
173 58 0.24
174 13 0.05
175 24 0.10
176 11 0.05
177 107 0.45
178 23 0.10
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.38
Consensus pattern (174 bp):
TTTTCAATTTCCATCTTTTCAATTTCTGTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTT
GAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTGTTTTCAAAAATCAACTCATATTGCGAGAG
GTGAGCTGAGCCTCGGGCCACGCCGAGGTATTTTCAAATTCTAG
Found at i:12413855 original size:73 final size:74
Alignment explanation
Indices: 12413711--12413866 Score: 199
Period size: 73 Copynumber: 2.1 Consensus size: 74
12413701 ATTTCCATTT
* * *
12413711 TTTCAATTTATGCTTTTGAAAAAATTAACTCATATTGCGAATGGTGAGTTGAGCCTCATGACACA
1 TTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGAATGGTGAGCTGAGCCTCAGGACACA
*
12413776 CTGAGGTAA
66 CCGAGGTAA
* * *
12413785 TTTCAATTTATGCTTTT-CAAAAATCAACTCATATTGCGAGA-GGTGAGCTGAGCCTCGGGGCAC
1 TTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGA-ATGGTGAGCTGAGCCTCAGGACAC
* *
12413848 GCCGAGGTAT
65 ACCGAGGTAA
*
12413858 TTTTAATTT
1 TTTCAATTT
12413867 CTATTTTTCA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
73 53 0.75
74 18 0.25
ACGTcount: A:0.29, C:0.17, G:0.21, T:0.34
Consensus pattern (74 bp):
TTTCAATTTATGCTTTTGAAAAAATCAACTCATATTGCGAATGGTGAGCTGAGCCTCAGGACACA
CCGAGGTAA
Found at i:12413879 original size:14 final size:13
Alignment explanation
Indices: 12413855--12413901 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
12413845 CACGCCGAGG
12413855 TATTTTTAATTTC
1 TATTTTTAATTTC
12413868 TATTTTTCAATTTC
1 TATTTTT-AATTTC
**
12413882 TGCTTTTAATTTC
1 TATTTTTAATTTC
*
12413895 TGTTTTT
1 TATTTTT
12413902 CAAAAATCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.17, C:0.11, G:0.04, T:0.68
Consensus pattern (13 bp):
TATTTTTAATTTC
Found at i:12413966 original size:100 final size:99
Alignment explanation
Indices: 12413789--12414155 Score: 404
Period size: 100 Copynumber: 3.8 Consensus size: 99
12413779 AGGTAATTTC
* * * *
12413789 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGCTGAGCCTCGGGGCACGCCGAG
1 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
*
12413854 GTATTTTTAATTTCTATTTTTCAATTTCTGCTTTT
66 GTATTTTCAATTTCTATTTTTCAATTT-TGCTTTT
* * *
12413889 AATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAG
1 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
* * **
12413954 ATATTTTCAATTTCTGTTTTTCAATTTTTGCCTTAC
66 GTATTTTCAATTTCTATTTTTCAA-TTTTG-CTTTT
* * * *
12413990 AAATTCTGCTTTTC--AAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGATACGTTGAG
1 AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
12414053 GTATTTTC-A-----A-TTTTC-A-TTT--TTTT
66 GTATTTTCAATTTCTATTTTTCAATTTTGCTTTT
* *
12414076 AATTTATG--TTTCAAAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGT
1 AATTTATGCTTTTC----AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGC
12414139 TGAGGTATTTTCAATTT
62 TGAGGTATTTTCAATTT
12414156 TTGTCTTCCA
Statistics
Matches: 232, Mismatches: 23, Indels: 30
0.81 0.08 0.11
Matches are distributed among these distances:
84 4 0.02
86 8 0.03
89 3 0.01
90 55 0.24
91 2 0.01
92 5 0.02
98 1 0.00
99 53 0.23
100 83 0.36
101 18 0.08
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (99 bp):
AATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAG
GTATTTTCAATTTCTATTTTTCAATTTTGCTTTT
Found at i:12414264 original size:146 final size:146
Alignment explanation
Indices: 12414092--12414379 Score: 497
Period size: 146 Copynumber: 2.0 Consensus size: 146
12414082 TGTTTCAAAA
* *
12414092 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTT-
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTC
12414156 TTGTCTTCCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
66 TT-TCTTCCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAAT
12414221 TTCAATTTTTGTTTGTC
130 TTCAATTTTTGTTTGTC
*
12414238 AAAAATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTC
1 AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTC
* **
12414303 TTTCTTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGTTT
66 TTTCTTCCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAATT
*
12414368 TCCATTTTTGTT
131 TCAATTTTTGTT
12414380 CTTCAACTTC
Statistics
Matches: 134, Mismatches: 7, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
146 132 0.99
147 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.33
Consensus pattern (146 bp):
AAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATTTC
TTTCTTCCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAATT
TCAATTTTTGTTTGTC
Found at i:12414385 original size:73 final size:73
Alignment explanation
Indices: 12414090--12414385 Score: 404
Period size: 75 Copynumber: 4.0 Consensus size: 73
12414080 TATGTTTCAA
* * *
12414090 AAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAG--ACGCTGAGGTATTTTCAATT
12414155 TTTG-TCTTCC
64 TTTGTTCTT-C
*
12414165 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTAATTTCAATTTT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATTTTCAATTTT
12414230 TGTT-TGTC
66 TGTTCT-TC
* * *
12414238 --AAAAATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCAAGACACATTGAGGTATTTTCAATT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGC--TGAGGTATTTTCAATT
*
12414301 TCT-TTCTTTC
64 TTTGTTC-TTC
* *
12414311 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGTTTTCCATTTT
1 AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATTTTCAATTTT
12414376 TGTTCTTC
66 TGTTCTTC
12414384 AA
1 AA
12414386 CTTCTGTATT
Statistics
Matches: 197, Mismatches: 15, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
71 42 0.21
72 2 0.01
73 64 0.32
74 6 0.03
75 83 0.42
ACGTcount: A:0.30, C:0.17, G:0.20, T:0.32
Consensus pattern (73 bp):
AAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTATTTTCAATTTT
TGTTCTTC
Found at i:12415020 original size:18 final size:18
Alignment explanation
Indices: 12414997--12415051 Score: 59
Period size: 18 Copynumber: 3.4 Consensus size: 18
12414987 AAGAGGGGCA
12414997 GCTCCACTAGCCACACTT
1 GCTCCACTAGCCACACTT
12415015 GCTCCACT----AC-C-T
1 GCTCCACTAGCCACACTT
*
12415027 ACTCCACTAGCCACACTT
1 GCTCCACTAGCCACACTT
12415045 GCTCCAC
1 GCTCCAC
12415052 CACCACTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 12
0.67 0.05 0.28
Matches are distributed among these distances:
12 8 0.28
13 1 0.03
14 2 0.07
16 2 0.07
17 1 0.03
18 15 0.52
ACGTcount: A:0.22, C:0.47, G:0.09, T:0.22
Consensus pattern (18 bp):
GCTCCACTAGCCACACTT
Found at i:12423105 original size:11 final size:11
Alignment explanation
Indices: 12423062--12423113 Score: 52
Period size: 11 Copynumber: 4.5 Consensus size: 11
12423052 TTAATTAAAT
12423062 TTTATATTTTAA
1 TTTA-ATTTTAA
12423074 TATTACATTTTAA
1 T-TTA-ATTTTAA
*
12423087 -TTATTTTTAA
1 TTTAATTTTAA
*
12423097 TTTAATTTTTA
1 TTTAATTTTAA
12423108 TTTAAT
1 TTTAAT
12423114 GTTCAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
10 6 0.18
11 17 0.50
12 1 0.03
13 10 0.29
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (11 bp):
TTTAATTTTAA
Found at i:12423107 original size:22 final size:24
Alignment explanation
Indices: 12423063--12423105 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
12423053 TAATTAAATT
12423063 TTATATTTTAATATTACATTTTAA
1 TTATATTTTAATATTACATTTTAA
12423087 TTAT-TTTTAAT-TTA-ATTTT
1 TTATATTTTAATATTACATTTT
12423106 TATTTAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 7 0.37
24 4 0.21
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
TTATATTTTAATATTACATTTTAA
Found at i:12423359 original size:60 final size:60
Alignment explanation
Indices: 12423288--12423403 Score: 223
Period size: 60 Copynumber: 1.9 Consensus size: 60
12423278 TTATTTTTTT
12423288 AAATTTAAAAAATAATTTGATAAATACAAATAAAAATATGTTTTCAATGAAATATGAAAA
1 AAATTTAAAAAATAATTTGATAAATACAAATAAAAATATGTTTTCAATGAAATATGAAAA
*
12423348 AAATTTAAAAAATCATTTGATAAATACAAATAAAAATATGTTTTCAATGAAATATG
1 AAATTTAAAAAATAATTTGATAAATACAAATAAAAATATGTTTTCAATGAAATATG
12423404 TTTCGTACAT
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.56, C:0.04, G:0.07, T:0.33
Consensus pattern (60 bp):
AAATTTAAAAAATAATTTGATAAATACAAATAAAAATATGTTTTCAATGAAATATGAAAA
Found at i:12427550 original size:16 final size:16
Alignment explanation
Indices: 12427525--12427555 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12427515 CCTTCAACTC
*
12427525 TTATATGTAAAAAAAT
1 TTATAAGTAAAAAAAT
12427541 TTATAAGTAAAAAAA
1 TTATAAGTAAAAAAA
12427556 AAGAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.61, C:0.00, G:0.06, T:0.32
Consensus pattern (16 bp):
TTATAAGTAAAAAAAT
Done.