Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D11
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: 73211361
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1690000 characters in sequence are not A, C, G, or T
File 34 of 240
Found at i:11892098 original size:23 final size:23
Alignment explanation
Indices: 11892066--11892109 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
11892056 GAACATTTAA
11892066 TCGGGAAGCTCA-TAAAGAGCCTC
1 TCGGGAAGCTCACT-AAGAGCCTC
*
11892089 TCGGGTAGCTCACTAAGAGCC
1 TCGGGAAGCTCACTAAGAGCC
11892110 ATGTAACGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.18
Consensus pattern (23 bp):
TCGGGAAGCTCACTAAGAGCCTC
Found at i:11914120 original size:27 final size:27
Alignment explanation
Indices: 11914074--11914204 Score: 93
Period size: 27 Copynumber: 4.9 Consensus size: 27
11914064 ATAGTCCGAC
* * * *
11914074 AGGACATTAAACACTAGATTTTTCAAT
1 AGGACGTTAAACACGAGATTGTCCAAT
* *
11914101 GGGACGTTAAACACGGGATTGTCCAAT
1 AGGACGTTAAACACGAGATTGTCCAAT
* * ** *
11914128 AGGACGTTAAATACGAGATAGTCTGAC
1 AGGACGTTAAACACGAGATTGTCCAAT
* * *
11914155 AAGACATTAAGCACG-GAATTGTCCAAT
1 AGGACGTTAAACACGAG-ATTGTCCAAT
* * *
11914182 AGAAGGTTAAACACGGGATTGTC
1 AGGACGTTAAACACGAGATTGTC
11914205 TGACGAGATG
Statistics
Matches: 76, Mismatches: 26, Indels: 4
0.72 0.25 0.04
Matches are distributed among these distances:
26 1 0.01
27 74 0.97
28 1 0.01
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (27 bp):
AGGACGTTAAACACGAGATTGTCCAAT
Found at i:11914217 original size:27 final size:27
Alignment explanation
Indices: 11914187--11914261 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
11914177 CCAATAGAAG
*
11914187 GTTAAACACGGGATTG-TCTGACGAGAT
1 GTTAAACACGGGATAGTTC-GACGAGAT
* * *
11914214 GTTAAACACAGGATAGTTCGATGGGAT
1 GTTAAACACGGGATAGTTCGACGAGAT
*
11914241 GTTAAATACGGGATAGTTCGA
1 GTTAAACACGGGATAGTTCGA
11914262 TGGGACTCTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
27 39 0.95
28 2 0.05
ACGTcount: A:0.32, C:0.12, G:0.29, T:0.27
Consensus pattern (27 bp):
GTTAAACACGGGATAGTTCGACGAGAT
Found at i:11914262 original size:27 final size:27
Alignment explanation
Indices: 11914211--11914266 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
11914201 TGTCTGACGA
11914211 GATGTTAAACACAGGATAGTTCGATGG
1 GATGTTAAACACAGGATAGTTCGATGG
* *
11914238 GATGTTAAATACGGGATAGTTCGATGG
1 GATGTTAAACACAGGATAGTTCGATGG
11914265 GA
1 GA
11914267 CTCTATACAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.32, C:0.09, G:0.32, T:0.27
Consensus pattern (27 bp):
GATGTTAAACACAGGATAGTTCGATGG
Found at i:11923076 original size:20 final size:20
Alignment explanation
Indices: 11923045--11923096 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
11923035 TAAAAAGTTA
* *
11923045 AAAATGAATTATTTATAATTT
1 AAAAT-AATTATATAAAATTT
*
11923066 ATAATAATTATATAAAATTT
1 AAAATAATTATATAAAATTT
11923086 AAAATATATTA
1 AAAATA-ATTA
11923097 CAAAGTTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 18 0.69
21 8 0.31
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
AAAATAATTATATAAAATTT
Found at i:11923301 original size:25 final size:27
Alignment explanation
Indices: 11923256--11923322 Score: 77
Period size: 25 Copynumber: 2.5 Consensus size: 27
11923246 ATAACTTATT
*
11923256 ATTTTAATAAAAAATTAATA-TTA-AA
1 ATTTTAATAATAAATTAATATTTATAA
11923281 ATTTTAATAATAAA-TATATATTTATAA
1 ATTTTAATAATAAATTA-ATATTTATAA
*
11923308 ATATTTAGTAATAAA
1 AT-TTTAATAATAAA
11923323 AGGTTTATAT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
24 2 0.06
25 16 0.44
26 3 0.08
27 4 0.11
28 11 0.31
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.43
Consensus pattern (27 bp):
ATTTTAATAATAAATTAATATTTATAA
Found at i:11924338 original size:19 final size:20
Alignment explanation
Indices: 11924296--11924338 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
11924286 TCATGCTTTC
*
11924296 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
11924316 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
11924334 TATTC
1 TATTC
11924339 CACAATCATG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:11924519 original size:38 final size:37
Alignment explanation
Indices: 11924467--11924558 Score: 96
Period size: 38 Copynumber: 2.5 Consensus size: 37
11924457 ATCAGATTGG
* * *
11924467 CACCCAGTGCCTCATCGG-ATAGTTCGAAGCAAAGTTGA
1 CACCTAGTGTCTCATCGGCATAG-CCGAAGCAAAG-TGA
* *
11924505 CACCTAGTGTCTCATCGGCCTAGCCGAAGTAAAGTGA
1 CACCTAGTGTCTCATCGGCATAGCCGAAGCAAAGTGA
* *
11924542 TACCTAGTATCTCATCG
1 CACCTAGTGTCTCATCG
11924559 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
37 18 0.39
38 25 0.54
39 3 0.07
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (37 bp):
CACCTAGTGTCTCATCGGCATAGCCGAAGCAAAGTGA
Found at i:11924570 original size:38 final size:38
Alignment explanation
Indices: 11924491--11924601 Score: 107
Period size: 38 Copynumber: 2.9 Consensus size: 38
11924481 TCGGATAGTT
* * *
11924491 CGAAGCAAAGTTGACACCTAGTGTCTCATCGGCCTAGC
1 CGAAGTAAAGTTGACACCTAGTATCTCATCGACCTAGC
* * *
11924529 CGAAGTAAAG-TGATACCTAGTATCTCATCGAATCTATC
1 CGAAGTAAAGTTGACACCTAGTATCTCATCG-ACCTAGC
* * *
11924567 CGAAGTAAAATAGTGACACCCAGTGTCTCATCGAC
1 CGAAGTAAAGT--TGACACCTAGTATCTCATCGAC
11924602 TCAAGGTCGA
Statistics
Matches: 58, Mismatches: 11, Indels: 6
0.77 0.15 0.08
Matches are distributed among these distances:
37 18 0.31
38 22 0.38
40 1 0.02
41 17 0.29
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.23
Consensus pattern (38 bp):
CGAAGTAAAGTTGACACCTAGTATCTCATCGACCTAGC
Found at i:11924596 original size:41 final size:38
Alignment explanation
Indices: 11924491--11924600 Score: 114
Period size: 41 Copynumber: 2.8 Consensus size: 38
11924481 TCGGATAGTT
* *
11924491 CGAAGCAAAGTTGACACCTAGTGTCTCATCG-GCCTAGC
1 CGAAGTAAAG-TGACACCTAGTGTCTCATCGAACCTAGC
* * * *
11924529 CGAAGTAAAGTGATACCTAGTATCTCATCGAATCTATC
1 CGAAGTAAAGTGACACCTAGTGTCTCATCGAACCTAGC
*
11924567 CGAAGTAAAATAGTGACACCCAGTGTCTCATCGA
1 CGAAGT--AA-AGTGACACCTAGTGTCTCATCGA
11924601 CTCAAGGTCG
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
37 18 0.31
38 19 0.32
40 2 0.03
41 20 0.34
ACGTcount: A:0.32, C:0.25, G:0.20, T:0.24
Consensus pattern (38 bp):
CGAAGTAAAGTGACACCTAGTGTCTCATCGAACCTAGC
Found at i:11927879 original size:22 final size:24
Alignment explanation
Indices: 11927843--11927891 Score: 75
Period size: 22 Copynumber: 2.1 Consensus size: 24
11927833 AAAATTTTAA
11927843 TAATAATACAAATAATAATATGAT
1 TAATAATACAAATAATAATATGAT
*
11927867 TAATAA-A-AAATAATAATATTAT
1 TAATAATACAAATAATAATATGAT
11927889 TAA
1 TAA
11927892 ATTAATTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 17 0.71
23 1 0.04
24 6 0.25
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (24 bp):
TAATAATACAAATAATAATATGAT
Found at i:11929933 original size:25 final size:25
Alignment explanation
Indices: 11929904--11929955 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
11929894 CCTATTTCTC
* *
11929904 CTTTCTTTCTT-TCCCTTTTTCTTTT
1 CTTTCTTT-TTCTCCCTGTTTCGTTT
11929929 CTTTCTTTTTCTCCCTGTTTCGTTT
1 CTTTCTTTTTCTCCCTGTTTCGTTT
11929954 CT
1 CT
11929956 ATTTTGTTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 2 0.08
25 22 0.92
ACGTcount: A:0.00, C:0.29, G:0.04, T:0.67
Consensus pattern (25 bp):
CTTTCTTTTTCTCCCTGTTTCGTTT
Found at i:11929938 original size:10 final size:10
Alignment explanation
Indices: 11929905--11929990 Score: 55
Period size: 10 Copynumber: 8.3 Consensus size: 10
11929895 CTATTTCTCC
11929905 TTTCTTTCTT
1 TTTCTTTCTT
** *
11929915 TCCCTTTTTCT
1 TTTCTTTCT-T
11929926 TTTCTTTCTT
1 TTTCTTTCTT
** *
11929936 TTTCTCCCTG
1 TTTCTTTCTT
11929946 TTTCGTTTCTAT
1 TTTC-TTTCT-T
*
11929958 TTTGTTTCTT
1 TTTCTTTCTT
* *
11929968 TCTATTTCTT
1 TTTCTTTCTT
*
11929978 TTTGTTTCTT
1 TTTCTTTCTT
11929988 TTT
1 TTT
11929991 ATGCTTTCAT
Statistics
Matches: 56, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
10 38 0.68
11 15 0.27
12 3 0.05
ACGTcount: A:0.02, C:0.21, G:0.05, T:0.72
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:11929969 original size:15 final size:16
Alignment explanation
Indices: 11929944--11929974 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
11929934 TTTTTCTCCC
11929944 TGTTTCGTTTCTATTT
1 TGTTTCGTTTCTATTT
11929960 TGTTTC-TTTCTATTT
1 TGTTTCGTTTCTATTT
11929975 CTTTTTGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.60
16 6 0.40
ACGTcount: A:0.06, C:0.13, G:0.10, T:0.71
Consensus pattern (16 bp):
TGTTTCGTTTCTATTT
Found at i:11930470 original size:9 final size:9
Alignment explanation
Indices: 11930456--11930480 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11930446 AATTTATAAT
11930456 ATAATAACA
1 ATAATAACA
11930465 ATAATAACA
1 ATAATAACA
11930474 ATAATAA
1 ATAATAA
11930481 TATGTTTTAT
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:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (9 bp):
ATAATAACA
Found at i:11935213 original size:23 final size:26
Alignment explanation
Indices: 11935182--11935239 Score: 77
Period size: 23 Copynumber: 2.3 Consensus size: 26
11935172 ATTAACTCTT
11935182 ATGAGCTTACC-GT-TTCAGCTC-GA
1 ATGAGCTTACCAGTCTTCAGCTCGGA
* *
11935205 TTGAGCTTACCATTCTTCAGCTCGGA
1 ATGAGCTTACCAGTCTTCAGCTCGGA
11935231 ATGAGCTTA
1 ATGAGCTTA
11935240 TCGATCATGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 10 0.34
24 1 0.03
25 8 0.28
26 10 0.34
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (26 bp):
ATGAGCTTACCAGTCTTCAGCTCGGA
Found at i:11935825 original size:24 final size:24
Alignment explanation
Indices: 11935805--11935854 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
11935795 GCTAATAATA
11935805 AAATACATGTGTAATAAAATATAT
1 AAATACATGTGTAATAAAATATAT
* * * *
11935829 ACATACATTTGTAATAATATGTAT
1 AAATACATGTGTAATAAAATATAT
11935853 AA
1 AA
11935855 TTTACTTATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (24 bp):
AAATACATGTGTAATAAAATATAT
Found at i:11935946 original size:16 final size:17
Alignment explanation
Indices: 11935925--11935956 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
11935915 TATATAACAA
11935925 AAGAAAGAAA-AGAAAT
1 AAGAAAGAAACAGAAAT
11935941 AAGAAAGAAACAGAAA
1 AAGAAAGAAACAGAAA
11935957 GCTTAAAACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.75, C:0.03, G:0.19, T:0.03
Consensus pattern (17 bp):
AAGAAAGAAACAGAAAT
Found at i:11936956 original size:24 final size:22
Alignment explanation
Indices: 11936905--11936959 Score: 85
Period size: 22 Copynumber: 2.5 Consensus size: 22
11936895 AGCACGACAA
11936905 TGCTCTCTGTTTAGCACATCTG
1 TGCTCTCTGTTTAGCACATCTG
*
11936927 TGCTCTCTGTTTAGCAC-TTTAG
1 TGCTCTCTGTTTAGCACATCT-G
11936949 TGCTCTCTGTT
1 TGCTCTCTGTT
11936960 CATTAGTGCA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.11, C:0.25, G:0.18, T:0.45
Consensus pattern (22 bp):
TGCTCTCTGTTTAGCACATCTG
Found at i:11939150 original size:24 final size:24
Alignment explanation
Indices: 11939123--11939168 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
11939113 ATTGAAATGG
11939123 ATTG-ATTTAGTATGTGA-TGAATTT
1 ATTGAATTTA-TAT-TGATTGAATTT
11939147 ATTGAATTTATATTGATTGAAT
1 ATTGAATTTATATTGATTGAAT
11939169 GGGTATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 3 0.15
24 12 0.60
25 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.50
Consensus pattern (24 bp):
ATTGAATTTATATTGATTGAATTT
Found at i:11939449 original size:40 final size:40
Alignment explanation
Indices: 11939327--11939467 Score: 135
Period size: 40 Copynumber: 3.6 Consensus size: 40
11939317 CGATTTCGAG
* * *
11939327 CCGATGAGACATTGGGTGTCAATTTACTACTTCGGATTAAT
1 CCGATGAGACACTGGGTGTCAAATTATTACTTCGGATT-AT
* * * * * * *
11939368 TCAATGAGGCACTGGGTG-CCAA-T-TTACTTTGGTTTAG
1 CCGATGAGACACTGGGTGTCAAATTATTACTTCGGATTAT
*
11939405 CCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTAT
1 CCGATGAGACACTGGGTGTCAAATTATTACTTCGGATTAT
* *
11939445 CCGATGAGGCACTGGGTGCCAAA
1 CCGATGAGACACTGGGTGTCAAA
11939468 CTGGTGCGTT
Statistics
Matches: 77, Mismatches: 20, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
37 16 0.21
38 12 0.16
39 2 0.03
40 33 0.43
41 14 0.18
ACGTcount: A:0.26, C:0.18, G:0.25, T:0.30
Consensus pattern (40 bp):
CCGATGAGACACTGGGTGTCAAATTATTACTTCGGATTAT
Found at i:11939668 original size:11 final size:12
Alignment explanation
Indices: 11939654--11939697 Score: 54
Period size: 11 Copynumber: 3.7 Consensus size: 12
11939644 TTATATACTC
11939654 ATGAAATGAAT-
1 ATGAAATGAATA
11939665 ATGAAATGAATA
1 ATGAAATGAATA
**
11939677 ATGAAATTGTGTA
1 ATGAAA-TGAATA
11939690 ATGAAATG
1 ATGAAATG
11939698 TGAAATAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
11 11 0.38
12 8 0.28
13 10 0.34
ACGTcount: A:0.50, C:0.00, G:0.20, T:0.30
Consensus pattern (12 bp):
ATGAAATGAATA
Found at i:11939711 original size:12 final size:13
Alignment explanation
Indices: 11939676--11939714 Score: 55
Period size: 12 Copynumber: 3.2 Consensus size: 13
11939666 TGAAATGAAT
*
11939676 AATGAAATTGTGT
1 AATGAAATTGTGA
11939689 AATGAAA-TGTGA
1 AATGAAATTGTGA
11939701 AAT-AAATTGTGA
1 AATGAAATTGTGA
11939713 AA
1 AA
11939715 ATTTATTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 3 0.12
12 14 0.58
13 7 0.29
ACGTcount: A:0.49, C:0.00, G:0.21, T:0.31
Consensus pattern (13 bp):
AATGAAATTGTGA
Found at i:11947786 original size:8 final size:8
Alignment explanation
Indices: 11947773--11947802 Score: 60
Period size: 8 Copynumber: 3.8 Consensus size: 8
11947763 CATCATATCC
11947773 TTCATGTT
1 TTCATGTT
11947781 TTCATGTT
1 TTCATGTT
11947789 TTCATGTT
1 TTCATGTT
11947797 TTCATG
1 TTCATG
11947803 CTTTATTAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60
Consensus pattern (8 bp):
TTCATGTT
Found at i:11954483 original size:22 final size:23
Alignment explanation
Indices: 11954458--11954502 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
11954448 ATTAAGCTAT
*
11954458 TTAAAAGTTTTT-AATTTTTGAA
1 TTAAAACTTTTTAAATTTTTGAA
*
11954480 TTAAATCTTTTTAAATTTTTGAA
1 TTAAAACTTTTTAAATTTTTGAA
11954503 AATTTAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.56
Consensus pattern (23 bp):
TTAAAACTTTTTAAATTTTTGAA
Found at i:11961357 original size:16 final size:15
Alignment explanation
Indices: 11961331--11961374 Score: 56
Period size: 14 Copynumber: 3.0 Consensus size: 15
11961321 TGGTAGGGTG
11961331 AAGAG-AAAATTAGA
1 AAGAGAAAAATTAGA
11961345 AAGATGAAAAATTAG-
1 AAGA-GAAAAATTAGA
*
11961360 AAGAGAAAAAATAGA
1 AAGAGAAAAATTAGA
11961375 TTTTCCATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
14 13 0.50
15 5 0.19
16 8 0.31
ACGTcount: A:0.66, C:0.00, G:0.20, T:0.14
Consensus pattern (15 bp):
AAGAGAAAAATTAGA
Found at i:11962881 original size:18 final size:20
Alignment explanation
Indices: 11962836--11962888 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 20
11962826 ATATATAGTA
*
11962836 ATAAATGTTTTATAATAAGAT
1 ATAAATATTTT-TAATAAGAT
*
11962857 ATGAATATTTTTAAT-A-AT
1 ATAAATATTTTTAATAAGAT
*
11962875 ATAAATATGTTTAA
1 ATAAATATTTTTAA
11962889 ACTTTTCTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 14 0.50
19 1 0.04
20 4 0.14
21 9 0.32
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (20 bp):
ATAAATATTTTTAATAAGAT
Found at i:11970992 original size:17 final size:20
Alignment explanation
Indices: 11970960--11970997 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
11970950 TCAAAATCAA
11970960 TTTTTTTACAACATTT-ATT
1 TTTTTTTACAACATTTCATT
11970979 TTTTTTTA-AA-ATTTCATT
1 TTTTTTTACAACATTTCATT
11970997 T
1 T
11970998 CAAATTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 6 0.33
19 8 0.44
ACGTcount: A:0.26, C:0.08, G:0.00, T:0.66
Consensus pattern (20 bp):
TTTTTTTACAACATTTCATT
Found at i:11983054 original size:24 final size:24
Alignment explanation
Indices: 11983010--11983077 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
11983000 TATAAAGGGA
*
11983010 AGCTCACAAAGAGC-CTATAACGGGT
1 AGCTC-CAAAGAGCAAT-TAACGGGT
*
11983035 AGCTCCAAATAGCAATTAACGGGT
1 AGCTCCAAAGAGCAATTAACGGGT
* *
11983059 TGCTCCGAAGAGCAATTAA
1 AGCTCCAAAGAGCAATTAA
11983078 TGGGAAGCGC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 31 0.84
25 6 0.16
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.19
Consensus pattern (24 bp):
AGCTCCAAAGAGCAATTAACGGGT
Found at i:11987452 original size:102 final size:102
Alignment explanation
Indices: 11987276--11987540 Score: 356
Period size: 102 Copynumber: 2.6 Consensus size: 102
11987266 TAACCGTTAT
* * * * *
11987276 CGGTGGATTCCGCACTTAGCAACCACCAATAAATGAGGGAATCAGCACACAGCAATCCCTTGGGG
1 CGGTGGAATCAGCACTTAGCAACTACCAATGAATG-GGGAATCAGCACACAGCAATCCCTCGGGG
* * *
11987341 GAATCAGCACTTAGCAACCCCC-TTCACATTTCAGATG
65 GAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
**
11987378 CGGTGGAATCAGCACTTAGCAACTACCAATGAATAGGGGAATCAGCACTTAGCAA-CCACTCGGG
1 CGGTGGAATCAGCACTTAGCAACTACCAATGAAT-GGGGAATCAGCACACAGCAATCC-CTCGGG
11987442 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
64 GGAATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
* *
11987481 CGGTGGAATCAGCACTTAGCAACCT-CCAATGAATCGGGGAATCAACACACAGCAACCCCT
1 CGGTGGAATCAGCACTTAGCAA-CTACCAATGAAT-GGGGAATCAGCACACAGCAATCCCT
11987541 TTATATGCAA
Statistics
Matches: 144, Mismatches: 14, Indels: 9
0.86 0.08 0.05
Matches are distributed among these distances:
101 2 0.01
102 75 0.52
103 63 0.44
104 4 0.03
ACGTcount: A:0.32, C:0.29, G:0.20, T:0.19
Consensus pattern (102 bp):
CGGTGGAATCAGCACTTAGCAACTACCAATGAATGGGGAATCAGCACACAGCAATCCCTCGGGGG
AATCAGCACTTAGCAACCCCCTTTCACATTTAAAATA
Found at i:11987916 original size:30 final size:31
Alignment explanation
Indices: 11987867--11987924 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
11987857 TAAACCTCCA
11987867 CCAAACTTTTTGAATATTTACAATTTTGCCC
1 CCAAACTTTTTGAATATTTACAATTTTGCCC
*
11987898 CCAAAC-TTTT-ACATATTTACACTTTTG
1 CCAAACTTTTTGA-ATATTTACAATTTTG
11987925 TCCCTAAGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
29 1 0.04
30 18 0.72
31 6 0.24
ACGTcount: A:0.29, C:0.22, G:0.05, T:0.43
Consensus pattern (31 bp):
CCAAACTTTTTGAATATTTACAATTTTGCCC
Found at i:11995073 original size:114 final size:114
Alignment explanation
Indices: 11994859--11995073 Score: 358
Period size: 114 Copynumber: 1.9 Consensus size: 114
11994849 ATTGTTTTTG
**
11994859 GGGGGGCCGGAATTAAATTGTATATTTTTACGATAGTAAAAATGCAATTTCACCATTTTAATATC
1 GGGGGGCCAAAATTAAATTGTATATTTTTACGATAGTAAAAATGCAATTTCACCATTTTAATATC
* *
11994924 TATATATTTATAATTTTTAAATGATTAAATCAAAATTTTATCATTTTCA
66 TATATATTTATAATTTTTAAAAGATCAAATCAAAATTTTATCATTTTCA
*
11994973 GGGGGGCCAAAATTAAATTGTATATTTTTACGATAGTAAAAATGCGATTTCACCATTTTAATATC
1 GGGGGGCCAAAATTAAATTGTATATTTTTACGATAGTAAAAATGCAATTTCACCATTTTAATATC
* * *
11995038 TATATCTTTATGATTTTTAAAAGATCAAATTAAAAT
66 TATATATTTATAATTTTTAAAAGATCAAATCAAAAT
11995074 GCAATTTCAC
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 93 1.00
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (114 bp):
GGGGGGCCAAAATTAAATTGTATATTTTTACGATAGTAAAAATGCAATTTCACCATTTTAATATC
TATATATTTATAATTTTTAAAAGATCAAATCAAAATTTTATCATTTTCA
Found at i:12006375 original size:10 final size:9
Alignment explanation
Indices: 12006336--12006387 Score: 54
Period size: 9 Copynumber: 5.9 Consensus size: 9
12006326 TTATAAGTTC
*
12006336 AATTTTAAT
1 AATTTTTAT
12006345 -ATTTTTAT
1 AATTTTTAT
12006353 AATTTTTAT
1 AATTTTTAT
*
12006362 AATTCTTTAC
1 AATT-TTTAT
12006372 AATTTTT-T
1 AATTTTTAT
*
12006380 TATTTTTA
1 AATTTTTA
12006388 AGAATTCTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 13 0.36
9 15 0.42
10 8 0.22
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (9 bp):
AATTTTTAT
Found at i:12006375 original size:19 final size:17
Alignment explanation
Indices: 12006335--12006387 Score: 61
Period size: 17 Copynumber: 3.0 Consensus size: 17
12006325 TTTATAAGTT
*
12006335 CAATTTTAATATTTTTA
1 CAATTTTTATATTTTTA
*
12006352 TAATTTTTATAATTCTTTA
1 CAATTTTTAT-ATT-TTTA
*
12006371 CAATTTTTTTATTTTTA
1 CAATTTTTATATTTTTA
12006388 AGAATTCTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 12 0.40
18 6 0.20
19 12 0.40
ACGTcount: A:0.30, C:0.06, G:0.00, T:0.64
Consensus pattern (17 bp):
CAATTTTTATATTTTTA
Found at i:12027479 original size:17 final size:18
Alignment explanation
Indices: 12027448--12027486 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
12027438 TATTATATTT
*
12027448 TAAAAAATTATTTTTAAA
1 TAAAAAATTAATTTTAAA
12027466 TAAAAAA-TAATTTTAAA
1 TAAAAAATTAATTTTAAA
12027483 -AAAA
1 TAAAA
12027487 TCAAATATGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 4 0.20
17 9 0.45
18 7 0.35
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TAAAAAATTAATTTTAAA
Found at i:12034119 original size:4 final size:4
Alignment explanation
Indices: 12034110--12034134 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
12034100 TTAAATTTTT
12034110 TAAA TAAA TAAA TAAA TAAA TAAA T
1 TAAA TAAA TAAA TAAA TAAA TAAA T
12034135 GGTACCGTTT
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (4 bp):
TAAA
Found at i:12053988 original size:12 final size:13
Alignment explanation
Indices: 12053965--12053993 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
12053955 TATAGCATAA
12053965 AAATATAATAAAT
1 AAATATAATAAAT
12053978 AAATA-AATAAAT
1 AAATATAATAAAT
12053990 AAAT
1 AAAT
12053994 TTTTCCTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATATAATAAAT
Found at i:12060484 original size:46 final size:46
Alignment explanation
Indices: 12060427--12060609 Score: 294
Period size: 46 Copynumber: 4.0 Consensus size: 46
12060417 ACAATGCTAT
* * *
12060427 AACTCAGTATGGTTTCCTTCACTGGAATACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
*
12060473 AACACAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
12060519 AACTCTGTATGGTTTTCTTCACTGAAACACCATATCTACTTTTCAC
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
* *
12060565 AACTTAGTATGGCTTTCTTCACTGAAACACCATACCTACTTTTCA
1 AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCA
12060610 AAATTTTTCC
Statistics
Matches: 126, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
46 126 1.00
ACGTcount: A:0.28, C:0.27, G:0.09, T:0.36
Consensus pattern (46 bp):
AACTCAGTATGGTTTTCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:12061385 original size:17 final size:17
Alignment explanation
Indices: 12061355--12061402 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
12061345 AAATTCTTTT
*
12061355 TAAATTACAAAATTCAC
1 TAAATCACAAAATTCAC
*
12061372 TAAATCACAGAATTCAC
1 TAAATCACAAAATTCAC
*
12061389 TAATTCA-AAAATTC
1 TAAATCACAAAATTC
12061403 TTCTAAATTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.50, C:0.19, G:0.02, T:0.29
Consensus pattern (17 bp):
TAAATCACAAAATTCAC
Found at i:12064789 original size:20 final size:20
Alignment explanation
Indices: 12064764--12064801 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
12064754 AAAGGTTAAC
12064764 TTAGTAAAATAATAATAATG
1 TTAGTAAAATAATAATAATG
* *
12064784 TTAGTATAATGATAATAA
1 TTAGTAAAATAATAATAA
12064802 AATAAAACAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.37
Consensus pattern (20 bp):
TTAGTAAAATAATAATAATG
Found at i:12065740 original size:41 final size:41
Alignment explanation
Indices: 12065662--12065760 Score: 139
Period size: 41 Copynumber: 2.4 Consensus size: 41
12065652 CTATATGATT
* * *
12065662 AGCACTAAGTGTGCG-AATTAAATGATGAGGTTGAATAACG
1 AGCACTAGGTGTGCGAAATTAAATAATGAGGTTAAATAACG
*
12065702 AGCACTAGGTGTGCGAAATTAAATAATGATGTTAAATAACG
1 AGCACTAGGTGTGCGAAATTAAATAATGAGGTTAAATAACG
12065743 AGCACT-GAGTGTGCGAAA
1 AGCACTAG-GTGTGCGAAA
12065761 CCGAGATCAA
Statistics
Matches: 53, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
40 15 0.28
41 38 0.72
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.24
Consensus pattern (41 bp):
AGCACTAGGTGTGCGAAATTAAATAATGAGGTTAAATAACG
Found at i:12074445 original size:15 final size:15
Alignment explanation
Indices: 12074425--12074459 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
12074415 TGTTAATCAG
12074425 TATTAATCAGTATGT
1 TATTAATCAGTATGT
12074440 TATTAATCAGTATGT
1 TATTAATCAGTATGT
12074455 TATTA
1 TATTA
12074460 GAATAGTCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.34, C:0.06, G:0.11, T:0.49
Consensus pattern (15 bp):
TATTAATCAGTATGT
Found at i:12098176 original size:6 final size:6
Alignment explanation
Indices: 12098165--12098194 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
12098155 CAAACAACCG
*
12098165 CCTTCT CCTTCT CCTTCT GCTTCT CCTTCT
1 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT
12098195 TCTACTCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (6 bp):
CCTTCT
Found at i:12101925 original size:23 final size:23
Alignment explanation
Indices: 12101899--12101994 Score: 167
Period size: 23 Copynumber: 4.2 Consensus size: 23
12101889 AGTGCCACAT
12101899 TGATATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
12101922 TGATATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
12101945 TGATATGTAGCC-ATAGCTACCAC
1 TGATATGTAGCCGA-AGCTACCAC
*
12101968 TGAAATGTAGCCGAAGCTACCAC
1 TGATATGTAGCCGAAGCTACCAC
12101991 TGAT
1 TGAT
12101995 CAATAACACT
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
22 1 0.01
23 67 0.97
24 1 0.01
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (23 bp):
TGATATGTAGCCGAAGCTACCAC
Found at i:12102246 original size:18 final size:17
Alignment explanation
Indices: 12102220--12102258 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
12102210 ATTTTCCTTC
12102220 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
12102237 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
12102255 CACA
1 CACA
12102259 ATTTATACAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:12109947 original size:16 final size:16
Alignment explanation
Indices: 12109928--12109959 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
12109918 AATAATATTG
12109928 TAAAGAAAAAAGATGA
1 TAAAGAAAAAAGATGA
*
12109944 TAAAGAAAGAAGATGA
1 TAAAGAAAAAAGATGA
12109960 GATAAAAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.22, T:0.12
Consensus pattern (16 bp):
TAAAGAAAAAAGATGA
Found at i:12117317 original size:18 final size:18
Alignment explanation
Indices: 12117296--12117334 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
12117286 TTTCTTCAAC
* *
12117296 TTCTTTTTCAAATTTCTT
1 TTCTGTTTCAAATTCCTT
*
12117314 TTCTGTTTCACATTCCTT
1 TTCTGTTTCAAATTCCTT
12117332 TTC
1 TTC
12117335 ACTCTCAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.13, C:0.23, G:0.03, T:0.62
Consensus pattern (18 bp):
TTCTGTTTCAAATTCCTT
Found at i:12128920 original size:32 final size:32
Alignment explanation
Indices: 12128835--12128921 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
12128825 TTTCTGAAAA
* *
12128835 ATGATTTATTGAAAATATTTTTTGATGTTTGG
1 ATGATTTTTTGAAAATATTTTCTGATGTTTGG
* * * *
12128867 ATGAATCTGTGTAAAATATTTTCTGTTGTTTGG
1 ATGATTTTTTG-AAAATATTTTCTGATGTTTGG
12128900 CA-GATTTTTTGAAAATATTTTC
1 -ATGATTTTTTGAAAATATTTTC
12128922 CGAAAAAGTT
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
32 18 0.41
33 25 0.57
34 1 0.02
ACGTcount: A:0.28, C:0.05, G:0.17, T:0.51
Consensus pattern (32 bp):
ATGATTTTTTGAAAATATTTTCTGATGTTTGG
Found at i:12128965 original size:20 final size:20
Alignment explanation
Indices: 12128942--12128980 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
12128932 ATTTTTACAT
12128942 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
12128962 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
12128981 TTTTAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:12148036 original size:9 final size:9
Alignment explanation
Indices: 12148022--12148050 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
12148012 AGGTAAGTTA
12148022 TTTTATTTT
1 TTTTATTTT
12148031 TTTTA-TTT
1 TTTTATTTT
12148039 TTTTATTTT
1 TTTTATTTT
12148048 TTT
1 TTT
12148051 AATATCTTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
8 8 0.42
9 11 0.58
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (9 bp):
TTTTATTTT
Found at i:12148039 original size:8 final size:8
Alignment explanation
Indices: 12148022--12148051 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
12148012 AGGTAAGTTA
12148022 TTTTATTTT
1 TTTTA-TTT
12148031 TTTTATTT
1 TTTTATTT
12148039 TTTTATTT
1 TTTTATTT
12148047 TTTTA
1 TTTTA
12148052 ATATCTTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 16 0.76
9 5 0.24
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (8 bp):
TTTTATTT
Found at i:12148342 original size:16 final size:16
Alignment explanation
Indices: 12148321--12148357 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
12148311 TTGGTTCGCT
12148321 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
12148337 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGC
12148353 GTAAT
1 GTAAT
12148358 AGGTAATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.38, C:0.05, G:0.35, T:0.22
Consensus pattern (16 bp):
GTAATGGAATAGAGGC
Found at i:12148423 original size:44 final size:46
Alignment explanation
Indices: 12148337--12148424 Score: 144
Period size: 46 Copynumber: 2.0 Consensus size: 46
12148327 GAATAGAGGC
* *
12148337 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGACT
1 GTAATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTGACT
12148383 GTAATGGAATAGAGGCATAAT-GGT-ATTCTTGTGTTTGGTTGA
1 GTAATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTGA
12148425 ATGGAATAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
44 17 0.43
45 3 0.08
46 20 0.50
ACGTcount: A:0.26, C:0.06, G:0.30, T:0.39
Consensus pattern (46 bp):
GTAATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTGACT
Found at i:12148428 original size:39 final size:44
Alignment explanation
Indices: 12148337--12148436 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 44
12148327 GAATAGAGGC
* *
12148337 GTAATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGACT
1 GTAATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTT-A-T
12148383 GTAATGGAATAGAGGCATAAT-GGT-ATTCTTGTGTTTGG-T-T
1 GTAATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTAT
12148423 G-AATGGAATAGAGG
1 GTAATGGAATAGAGG
12148437 TGTAATAGCA
Statistics
Matches: 52, Mismatches: 2, Indels: 7
0.85 0.03 0.11
Matches are distributed among these distances:
39 13 0.25
40 2 0.04
43 1 0.02
44 13 0.25
45 3 0.06
46 20 0.38
ACGTcount: A:0.28, C:0.05, G:0.31, T:0.36
Consensus pattern (44 bp):
GTAATGGAATAGAGGCATAATAGGTAATTCTTGTGTTTGGTTAT
Found at i:12148595 original size:26 final size:27
Alignment explanation
Indices: 12148566--12148617 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
12148556 ATAATTTAAT
* *
12148566 TATATTTTAATATAACTGTT-ATAAAA
1 TATAATTTAATAAAACTGTTAATAAAA
*
12148592 TATAATTTAATAAAATTGTTAATAAA
1 TATAATTTAATAAAACTGTTAATAAA
12148618 TATTCTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (27 bp):
TATAATTTAATAAAACTGTTAATAAAA
Found at i:12148695 original size:26 final size:28
Alignment explanation
Indices: 12148665--12148728 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 28
12148655 TAATACTATA
*
12148665 AAATATAATTTAA-AATAAT-TATTATT
1 AAATATAATTTAATAATAATATATAATT
12148691 AAATATAATTTAATAATAATATATAATT
1 AAATATAATTTAATAATAATATATAATT
* *
12148719 TAATAAAATT
1 AAATATAATT
12148729 CTTATTATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
26 13 0.39
27 6 0.18
28 14 0.42
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (28 bp):
AAATATAATTTAATAATAATATATAATT
Found at i:12148761 original size:44 final size:41
Alignment explanation
Indices: 12148662--12148761 Score: 103
Period size: 44 Copynumber: 2.3 Consensus size: 41
12148652 ATATAATACT
12148662 ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTA
1 ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTA
* *
12148703 ATAATAATATATAATTTAATAA-AATTCTTATTATTATATGAATTTA
1 AT-A-AA-ATATAATTTAA-AATAATTATTATTA-AATAT-AATTTA
*
12148749 TTAAAATCATAAT
1 ATAAAAT-ATAAT
12148762 ATATAATACT
Statistics
Matches: 49, Mismatches: 3, Indels: 11
0.78 0.05 0.17
Matches are distributed among these distances:
41 2 0.04
42 1 0.02
43 4 0.08
44 28 0.57
45 7 0.14
46 7 0.14
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (41 bp):
ATAAAATATAATTTAAAATAATTATTATTAAATATAATTTA
Found at i:12150258 original size:49 final size:49
Alignment explanation
Indices: 12150186--12150289 Score: 145
Period size: 49 Copynumber: 2.1 Consensus size: 49
12150176 GAAAAAAAAC
* * ** * *
12150186 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
*
12150235 AAATTAAAATTGAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
1 AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
12150284 AAATTA
1 AAATTA
12150290 TAACACATGA
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.51, C:0.10, G:0.09, T:0.31
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATAAAAAACTCAACACTGTATA
Found at i:12152888 original size:18 final size:19
Alignment explanation
Indices: 12152855--12152895 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
12152845 ATATATAAAA
12152855 ATACCAATAAAAATTATCCT
1 ATACCAAT-AAAATTATCCT
12152875 ATACCAAT-AAATTATCCT
1 ATACCAATAAAATTATCCT
12152893 ATA
1 ATA
12152896 AAGTCCATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
18 13 0.62
20 8 0.38
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (19 bp):
ATACCAATAAAATTATCCT
Found at i:12153074 original size:25 final size:25
Alignment explanation
Indices: 12153040--12153101 Score: 106
Period size: 25 Copynumber: 2.5 Consensus size: 25
12153030 CAATTTACTA
*
12153040 GAATTGCAACTATAAAATACCTCTT
1 GAATTGCAACTATAAAACACCTCTT
12153065 GAATTGCAACTATAAAACACCTCTT
1 GAATTGCAACTATAAAACACCTCTT
*
12153090 GAAATGCAACTA
1 GAATTGCAACTA
12153102 GAGCTTCATC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 35 1.00
ACGTcount: A:0.42, C:0.21, G:0.10, T:0.27
Consensus pattern (25 bp):
GAATTGCAACTATAAAACACCTCTT
Found at i:12153361 original size:26 final size:26
Alignment explanation
Indices: 12153331--12153388 Score: 107
Period size: 26 Copynumber: 2.2 Consensus size: 26
12153321 CCGTAAAATA
12153331 CTGCAGCTAATACCAATGACAAAAAC
1 CTGCAGCTAATACCAATGACAAAAAC
*
12153357 CTGCAGCTAATATCAATGACAAAAAC
1 CTGCAGCTAATACCAATGACAAAAAC
12153383 CTGCAG
1 CTGCAG
12153389 GTAGAAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.43, C:0.26, G:0.14, T:0.17
Consensus pattern (26 bp):
CTGCAGCTAATACCAATGACAAAAAC
Found at i:12161771 original size:16 final size:16
Alignment explanation
Indices: 12161750--12161789 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
12161740 CATATATATT
12161750 TATTTTTAATCAAATA
1 TATTTTTAATCAAATA
* *
12161766 TATTTTTTATTAAATA
1 TATTTTTAATCAAATA
12161782 TATATTTT
1 TAT-TTTT
12161790 TTGGACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (16 bp):
TATTTTTAATCAAATA
Found at i:12161778 original size:20 final size:19
Alignment explanation
Indices: 12161733--12161791 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
12161723 CTGAATTGTA
12161733 TATTAAACATATATATTTATT
1 TATT-AACATATATATTT-TT
*
12161754 T-TTAATCAAATATATTTTT
1 TATTAA-CATATATATTTTT
12161773 TATTAA-ATATATATTTTT
1 TATTAACATATATATTTTT
12161791 T
1 T
12161792 GGACTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
18 12 0.35
19 5 0.15
20 16 0.47
21 1 0.03
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (19 bp):
TATTAACATATATATTTTT
Found at i:12168085 original size:18 final size:18
Alignment explanation
Indices: 12168062--12168104 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12168052 ACCCAATCTA
**
12168062 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
12168080 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
12168098 AACCCAA
1 AACCCAA
12168105 CCATAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:12168226 original size:9 final size:9
Alignment explanation
Indices: 12168212--12168305 Score: 125
Period size: 9 Copynumber: 10.4 Consensus size: 9
12168202 GTAGTGATTC
*
12168212 AATTTGGTT
1 AATTCGGTT
*
12168221 AATTTGGTT
1 AATTCGGTT
*
12168230 AATTCGGGT
1 AATTCGGTT
12168239 AATTCGGTT
1 AATTCGGTT
*
12168248 AATTCGGGT
1 AATTCGGTT
*
12168257 AATTCGGGT
1 AATTCGGTT
*
12168266 AATTCAGTT
1 AATTCGGTT
12168275 AATTCGGTT
1 AATTCGGTT
*
12168284 AATTCGGGT
1 AATTCGGTT
12168293 AATTCGGTT
1 AATTCGGTT
12168302 AATT
1 AATT
12168306 TTTAACCAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 76 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (9 bp):
AATTCGGTT
Found at i:12168247 original size:27 final size:27
Alignment explanation
Indices: 12168212--12168305 Score: 152
Period size: 27 Copynumber: 3.5 Consensus size: 27
12168202 GTAGTGATTC
* *
12168212 AATTTGGTTAATTTGGTTAATTCGGGT
1 AATTCGGTTAATTCGGTTAATTCGGGT
*
12168239 AATTCGGTTAATTCGGGTAATTCGGGT
1 AATTCGGTTAATTCGGTTAATTCGGGT
*
12168266 AATTCAGTTAATTCGGTTAATTCGGGT
1 AATTCGGTTAATTCGGTTAATTCGGGT
12168293 AATTCGGTTAATT
1 AATTCGGTTAATT
12168306 TTTAACCAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 61 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.43
Consensus pattern (27 bp):
AATTCGGTTAATTCGGTTAATTCGGGT
Found at i:12168763 original size:21 final size:21
Alignment explanation
Indices: 12168716--12168766 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
12168706 ATTTCAATGC
* * *
12168716 AACTACAAAAGGAGGTTACCC
1 AACTTCAAAAGGAGGTGACCA
* *
12168737 ATCTTCAACAGGAGGTGACCA
1 AACTTCAAAAGGAGGTGACCA
12168758 AACTTCAAA
1 AACTTCAAA
12168767 TTGAGTTATC
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.24, G:0.18, T:0.18
Consensus pattern (21 bp):
AACTTCAAAAGGAGGTGACCA
Found at i:12179145 original size:53 final size:53
Alignment explanation
Indices: 12179084--12179187 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
12179074 TATGTTCCCT
12179084 AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAATTA
1 AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAATTA
12179137 AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAAT
1 AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAAT
12179188 ATTTTCATGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.36, C:0.06, G:0.21, T:0.38
Consensus pattern (53 bp):
AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAATTA
Found at i:12179297 original size:18 final size:18
Alignment explanation
Indices: 12179259--12179297 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12179249 TTTACGTTAA
*
12179259 AAATTTTGAATTCTCCGT
1 AAATTTTGAATTCTCAGT
*
12179277 AAATTTTGAATTCTCATT
1 AAATTTTGAATTCTCAGT
12179295 AAA
1 AAA
12179298 CTATTAGCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (18 bp):
AAATTTTGAATTCTCAGT
Found at i:12206674 original size:29 final size:30
Alignment explanation
Indices: 12206627--12206685 Score: 111
Period size: 29 Copynumber: 2.0 Consensus size: 30
12206617 CTCCAACAGA
12206627 GTATGTACAAACTCTTTCCAAAAAAAATGG
1 GTATGTACAAACTCTTTCCAAAAAAAATGG
12206657 GTATGTAC-AACTCTTTCCAAAAAAAATGG
1 GTATGTACAAACTCTTTCCAAAAAAAATGG
12206686 ACGGGTAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.27
Consensus pattern (30 bp):
GTATGTACAAACTCTTTCCAAAAAAAATGG
Found at i:12223321 original size:53 final size:53
Alignment explanation
Indices: 12223241--12223344 Score: 208
Period size: 53 Copynumber: 2.0 Consensus size: 53
12223231 ACATGAAAAT
12223241 ATTTACATACAAATTGAACAAAGCCAATCAAACTTTCATTTTGCTTTCACTTA
1 ATTTACATACAAATTGAACAAAGCCAATCAAACTTTCATTTTGCTTTCACTTA
12223294 ATTTACATACAAATTGAACAAAGCCAATCAAACTTTCATTTTGCTTTCACT
1 ATTTACATACAAATTGAACAAAGCCAATCAAACTTTCATTTTGCTTTCACT
12223345 AGGGAACATA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.38, C:0.21, G:0.06, T:0.36
Consensus pattern (53 bp):
ATTTACATACAAATTGAACAAAGCCAATCAAACTTTCATTTTGCTTTCACTTA
Found at i:12245670 original size:51 final size:52
Alignment explanation
Indices: 12245615--12245717 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 52
12245605 TATGTTCCCT
12245615 AGTGAAAGCAAAATGAAAGTTTGATTGGC-TTGTTCAATTTGTATGTAAATA
1 AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAATA
12245666 AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAATA
1 AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAATA
12245718 TTTTCATGTT
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
51 29 0.57
52 22 0.43
ACGTcount: A:0.37, C:0.06, G:0.21, T:0.36
Consensus pattern (52 bp):
AGTGAAAGCAAAATGAAAGTTTGATTGGCTTTGTTCAATTTGTATGTAAATA
Found at i:12262174 original size:31 final size:31
Alignment explanation
Indices: 12262136--12262199 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
12262126 TGTTACCCCG
12262136 TCCATTTTTTTTGGAAAGAGTTTGTACATAC
1 TCCATTTTTTTTGGAAAGAGTTTGTACATAC
12262167 TCCATTTTTTTTGGAAAGAGTTTGTACATAC
1 TCCATTTTTTTTGGAAAGAGTTTGTACATAC
12262198 TC
1 TC
12262200 TGTTGGAGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.25, C:0.14, G:0.16, T:0.45
Consensus pattern (31 bp):
TCCATTTTTTTTGGAAAGAGTTTGTACATAC
Found at i:12267734 original size:12 final size:11
Alignment explanation
Indices: 12267704--12267758 Score: 56
Period size: 13 Copynumber: 4.6 Consensus size: 11
12267694 TTCTTTAAAT
12267704 TAAAAAAATTA
1 TAAAAAAATTA
**
12267715 TTTAAAAATTA
1 TAAAAAAATTA
12267726 TAAACAAAATTCA
1 TAAA-AAAATT-A
12267739 TAAAAAGAAGTTA
1 TAAAAA-AA-TTA
12267752 TAAAAAA
1 TAAAAAA
12267759 TATATTTTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 11 0.31
12 9 0.25
13 14 0.39
14 2 0.06
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (11 bp):
TAAAAAAATTA
Found at i:12267894 original size:11 final size:10
Alignment explanation
Indices: 12267872--12267915 Score: 63
Period size: 11 Copynumber: 4.3 Consensus size: 10
12267862 TTATTAATAA
12267872 TTTTATAA-T
1 TTTTATAATT
12267881 TTTTATAAGTT
1 TTTTATAA-TT
12267892 TTTTATAATTT
1 TTTTATAA-TT
12267903 TTTTATAATT
1 TTTTATAATT
12267913 TTT
1 TTT
12267916 ATGGTTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
9 8 0.25
10 5 0.16
11 19 0.59
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (10 bp):
TTTTATAATT
Found at i:12267914 original size:20 final size:20
Alignment explanation
Indices: 12267858--12267917 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
12267848 TGTTATTTTT
12267858 ATTTTTATTAATAA-TTTTATA
1 ATTTTT-TT-ATAATTTTTATA
12267879 A--TTTTTATAAGTTTTTTATA
1 ATTTTTTTATAA--TTTTTATA
12267899 ATTTTTTTATAATTTTTAT
1 ATTTTTTTATAATTTTTAT
12267918 GGTTTTTTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
17 4 0.12
18 2 0.06
19 3 0.09
20 15 0.44
21 1 0.03
22 9 0.26
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (20 bp):
ATTTTTTTATAATTTTTATA
Found at i:12268951 original size:24 final size:24
Alignment explanation
Indices: 12268924--12268969 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
12268914 TATTTTTAAC
12268924 AATTATATTTATATTTCGAATCAT
1 AATTATATTTATATTTCGAATCAT
12268948 AATTATATTTATATTTCGAATC
1 AATTATATTTATATTTCGAATC
12268970 TTAAACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.37, C:0.09, G:0.04, T:0.50
Consensus pattern (24 bp):
AATTATATTTATATTTCGAATCAT
Found at i:12270199 original size:21 final size:21
Alignment explanation
Indices: 12270173--12270213 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
12270163 TAGAAAGTAC
12270173 TTAAGAGAGGAGACATATTTT
1 TTAAGAGAGGAGACATATTTT
12270194 TTAAGAGAGGAGACATATTT
1 TTAAGAGAGGAGACATATTT
12270214 ATCTTTTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.05, G:0.24, T:0.32
Consensus pattern (21 bp):
TTAAGAGAGGAGACATATTTT
Found at i:12273391 original size:10 final size:9
Alignment explanation
Indices: 12273310--12273406 Score: 51
Period size: 10 Copynumber: 10.6 Consensus size: 9
12273300 TATTAAAAAT
12273310 TAAAATTGATA
1 TAAAATT-A-A
* *
12273321 TAAACTTAT
1 TAAAATTAA
12273330 TAAAATT-A
1 TAAAATTAA
*
12273338 TAAGTATT-A
1 TAA-AATTAA
12273347 TAAAATATAA
1 TAAAAT-TAA
*
12273357 AAAAATCTAA
1 TAAAAT-TAA
12273367 T-AAATT-A
1 TAAAATTAA
12273374 TAAAATTAA
1 TAAAATTAA
*
12273383 TAGAAATTATT
1 TA-AAATTA-A
12273394 TAAAATTAA
1 TAAAATTAA
12273403 -AAAA
1 TAAAA
12273407 AAACGTATTA
Statistics
Matches: 68, Mismatches: 11, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
7 2 0.03
8 15 0.22
9 21 0.31
10 22 0.32
11 8 0.12
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (9 bp):
TAAAATTAA
Found at i:12273459 original size:9 final size:9
Alignment explanation
Indices: 12273447--12273498 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
12273437 AAAATTGTAA
12273447 AAAAATTAT
1 AAAAATTAT
**
12273456 AAAAAAAAT
1 AAAAATTAT
*
12273465 TAAAATTGAT
1 AAAAATT-AT
*
12273475 ATAAACTTAT
1 A-AAAATTAT
12273485 AAAAATTAT
1 AAAAATTAT
12273494 AAAAA
1 AAAAA
12273499 AATCATAAAA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
9 23 0.70
10 5 0.15
11 5 0.15
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (9 bp):
AAAAATTAT
Found at i:12273466 original size:12 final size:11
Alignment explanation
Indices: 12273425--12273462 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
12273415 TAGAATACTT
*
12273425 AAAAAA-TAGA
1 AAAAAATTATA
*
12273435 AAAAAATTGTA
1 AAAAAATTATA
12273446 AAAAAATTATA
1 AAAAAATTATA
12273457 AAAAAA
1 AAAAAA
12273463 ATTAAAATTG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
10 6 0.25
11 18 0.75
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.18
Consensus pattern (11 bp):
AAAAAATTATA
Found at i:12273904 original size:10 final size:9
Alignment explanation
Indices: 12273892--12274123 Score: 118
Period size: 9 Copynumber: 24.6 Consensus size: 9
12273882 TATGAATTTT
12273892 TTTTTATAA
1 TTTTTATAA
12273901 TTTTTATAA
1 TTTTTATAA
*
12273910 GTTTATATTAA
1 -TTTTTA-TAA
* *
12273921 TTTTAATACTT
1 TTTTTATA--A
*
12273932 TTTTTATGA
1 TTTTTATAA
*
12273941 TTTTTATGA
1 TTTTTATAA
12273950 TTTTTATAGA
1 TTTTTATA-A
* * *
12273960 ATTTAATACG
1 TTTTTATA-A
12273970 TTTTTATAA
1 TTTTTATAA
*
12273979 TATTTTAAATA
1 T-TTTTATA-A
12273990 TGTTTTATTAA
1 T-TTTTA-TAA
12274001 -TTTTATAA
1 TTTTTATAA
12274009 TTTTTTATAA
1 -TTTTTATAA
*
12274019 TTTATTAGAA
1 TTT-TTATAA
12274029 TTTTTTATAA
1 -TTTTTATAA
*
12274039 TATTTAT-A
1 TTTTTATAA
12274047 TTTTTATAA
1 TTTTTATAA
12274056 TTTTTTAAATAA
1 -TTTTT--ATAA
*
12274068 TATTTATAA
1 TTTTTATAA
*
12274077 GTTTATATCAA
1 -TTTTTAT-AA
*
12274088 -TTTT-CAA
1 TTTTTATAA
12274095 TTTTT-TAA
1 TTTTTATAA
*
12274103 --TTAATAA
1 TTTTTATAA
12274110 TTTTTATAA
1 TTTTTATAA
12274119 TTTTT
1 TTTTT
12274124 TTCTGATTTT
Statistics
Matches: 171, Mismatches: 30, Indels: 44
0.70 0.12 0.18
Matches are distributed among these distances:
6 2 0.01
7 5 0.03
8 16 0.09
9 61 0.36
10 56 0.33
11 26 0.15
12 5 0.03
ACGTcount: A:0.34, C:0.02, G:0.03, T:0.61
Consensus pattern (9 bp):
TTTTTATAA
Found at i:12273944 original size:40 final size:38
Alignment explanation
Indices: 12273890--12274014 Score: 110
Period size: 40 Copynumber: 3.2 Consensus size: 38
12273880 TTTATGAATT
12273890 TTTTTTTATAATTTTTATAAGTTTATATTAATTTTAATAC
1 TTTTTTTAT-ATTTTTATAAGTTT-TATTAATTTTAATAC
* * *
12273930 TTTTTTTATGATTTTTATGATTTTTA-TAGAATTTAATAC
1 TTTTTTTAT-ATTTTTATAAGTTTTATTA-ATTTTAATAC
* * * *
12273969 GTTTTTATAATATTTTAAATATGTTTTATTAATTTT-ATAA
1 -TTTTT-TTATATTTT-TATAAGTTTTATTAATTTTAATAC
12274009 TTTTTT
1 TTTTTT
12274015 ATAATTTATT
Statistics
Matches: 69, Mismatches: 11, Indels: 12
0.75 0.12 0.13
Matches are distributed among these distances:
38 3 0.04
39 16 0.23
40 34 0.49
41 14 0.20
42 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.63
Consensus pattern (38 bp):
TTTTTTTATATTTTTATAAGTTTTATTAATTTTAATAC
Found at i:12274032 original size:20 final size:18
Alignment explanation
Indices: 12273891--12274065 Score: 90
Period size: 20 Copynumber: 9.1 Consensus size: 18
12273881 TTATGAATTT
12273891 TTTTTTATAATTTTTATAA
1 TTTTTTATAATTTTTA-AA
* *
12273910 GTTTATATTAA-TTTTAATA
1 TTTTTTA-TAATTTTTAA-A
* *
12273929 CTTTTTTTATGATTTTTATGA
1 --TTTTTTATAATTTTTA-AA
*
12273950 -TTTTTATAGA-ATTTAATA
1 TTTTTTATA-ATTTTTAA-A
*
12273968 CGTTTTTATAATATTTTAAA
1 -TTTTTTATAAT-TTTTAAA
12273988 TATGTTTTATTAA-TTTTATAA
1 T-T-TTTTA-TAATTTTTA-AA
12274009 TTTTTTATAATTTATTAGAA
1 TTTTTTATAATTT-TTA-AA
* *
12274029 TTTTTTATAATATTTATA
1 TTTTTTATAATTTTTAAA
12274047 -TTTTTATAATTTTTTAAA
1 TTTTTTATAA-TTTTTAAA
12274065 T
1 T
12274066 AATATTTATA
Statistics
Matches: 120, Mismatches: 16, Indels: 40
0.68 0.09 0.23
Matches are distributed among these distances:
17 9 0.08
18 23 0.19
19 23 0.19
20 38 0.32
21 24 0.20
22 3 0.03
ACGTcount: A:0.33, C:0.01, G:0.04, T:0.62
Consensus pattern (18 bp):
TTTTTTATAATTTTTAAA
Found at i:12274045 original size:29 final size:29
Alignment explanation
Indices: 12274001--12274082 Score: 96
Period size: 29 Copynumber: 2.8 Consensus size: 29
12273991 GTTTTATTAA
*
12274001 TTTTATAATTTTTTATAATTTATTAGAATT
1 TTTTATAA-TATTTATAATTTATTAGAATT
*
12274031 TTTTATAATATTTAT-ATTT-TTATAATT
1 TTTTATAATATTTATAATTTATTAGAATT
12274058 TTTTAAATAATATTTATAAGTTTAT
1 TTTT--ATAATATTTATAA-TTTAT
12274083 ATCAATTTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
27 11 0.24
28 4 0.09
29 17 0.38
30 9 0.20
31 3 0.07
32 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (29 bp):
TTTTATAATATTTATAATTTATTAGAATT
Found at i:12274166 original size:20 final size:20
Alignment explanation
Indices: 12274109--12274165 Score: 71
Period size: 20 Copynumber: 2.8 Consensus size: 20
12274099 TTAATTAATA
**
12274109 ATTTTTATAAT-TTTTTTCTG
1 ATTTTT-TAATATTTTTTAGG
12274129 ATTTTTTAATATTTTTTAGG
1 ATTTTTTAATATTTTTTAGG
12274149 ATTTTTTAATCATTTTT
1 ATTTTTTAAT-ATTTTT
12274166 ATGAGAAAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 4 0.12
20 23 0.70
21 6 0.18
ACGTcount: A:0.23, C:0.04, G:0.05, T:0.68
Consensus pattern (20 bp):
ATTTTTTAATATTTTTTAGG
Found at i:12278872 original size:42 final size:42
Alignment explanation
Indices: 12278825--12278909 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
12278815 GTGGATTGTT
12278825 GGTTTCTCACCTTTTCTCTTTGATGTAGGTTTTGAGACTTTG
1 GGTTTCTCACCTTTTCTCTTTGATGTAGGTTTTGAGACTTTG
12278867 GGTTTCTCACCTTTTCTCTTTGATGTAGGTTTTGAGACTTTG
1 GGTTTCTCACCTTTTCTCTTTGATGTAGGTTTTGAGACTTTG
12278909 G
1 G
12278910 TTGGAAAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.12, C:0.16, G:0.22, T:0.49
Consensus pattern (42 bp):
GGTTTCTCACCTTTTCTCTTTGATGTAGGTTTTGAGACTTTG
Found at i:12288556 original size:25 final size:24
Alignment explanation
Indices: 12288519--12288585 Score: 57
Period size: 25 Copynumber: 2.8 Consensus size: 24
12288509 GTCCTGATAT
**
12288519 TAGCTTTCATGAGCATCCCATTATA
1 TAGCTTTTGTGAGCATCCCATTA-A
** *
12288544 TAG-TTCTTGTGAGTTTCCCGTTAA
1 TAGCTT-TTGTGAGCATCCCATTAA
12288568 TAGCTTTTG-GAGCATCCC
1 TAGCTTTTGTGAGCATCCC
12288586 GATTGGTTCT
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
23 7 0.21
24 9 0.27
25 17 0.52
ACGTcount: A:0.21, C:0.22, G:0.18, T:0.39
Consensus pattern (24 bp):
TAGCTTTTGTGAGCATCCCATTAA
Found at i:12288777 original size:25 final size:23
Alignment explanation
Indices: 12288749--12288811 Score: 63
Period size: 25 Copynumber: 2.6 Consensus size: 23
12288739 TTCTCGATAT
12288749 TGGCTCGTATGAGCTTCCCGTTTTA
1 TGGCTCGTATGAGCTTCCCG--TTA
* * *
12288774 TGGCTTGAAAGAGCTTCCCGTTA
1 TGGCTCGTATGAGCTTCCCGTTA
*
12288797 AGTGCTCGTATGAGC
1 TG-GCTCGTATGAGC
12288812 ATTCGCGAAT
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
23 4 0.13
24 9 0.30
25 17 0.57
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.33
Consensus pattern (23 bp):
TGGCTCGTATGAGCTTCCCGTTA
Found at i:12294260 original size:5 final size:5
Alignment explanation
Indices: 12294252--12294302 Score: 57
Period size: 5 Copynumber: 9.6 Consensus size: 5
12294242 ACCTAATCTA
* *
12294252 ATAAT ATAAT ATAAT ATAAT ATAATTT ACAAT ATAAT AAAAT AATAAT
1 ATAAT ATAAT ATAAT ATAAT ATAA--T ATAAT ATAAT ATAAT -ATAAT
12294300 ATA
1 ATA
12294303 CTTCAAAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 31 0.79
6 4 0.10
7 4 0.10
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (5 bp):
ATAAT
Found at i:12294272 original size:15 final size:15
Alignment explanation
Indices: 12294252--12294302 Score: 57
Period size: 17 Copynumber: 3.2 Consensus size: 15
12294242 ACCTAATCTA
12294252 ATAATATAATATAAT
1 ATAATATAATATAAT
*
12294267 ATAATATAATTTACAAT
1 ATAATATAA--TATAAT
*
12294284 ATAATAAAATAATAAT
1 ATAATATAAT-ATAAT
12294300 ATA
1 ATA
12294303 CTTCAAAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
15 10 0.33
16 7 0.23
17 13 0.43
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
ATAATATAATATAAT
Found at i:12295199 original size:16 final size:16
Alignment explanation
Indices: 12295178--12295226 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
12295168 ATCATGTAAC
12295178 TATTTTCATATACATA
1 TATTTTCATATACATA
*
12295194 TATTTTCCACAT-CATA
1 TATTTT-CATATACATA
12295210 TA--TTCATATAACATA
1 TATTTTCATAT-ACATA
12295225 TA
1 TA
12295227 CATTGCCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
13 4 0.14
14 2 0.07
15 6 0.21
16 12 0.43
17 4 0.14
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (16 bp):
TATTTTCATATACATA
Found at i:12295560 original size:73 final size:74
Alignment explanation
Indices: 12295483--12295625 Score: 175
Period size: 73 Copynumber: 1.9 Consensus size: 74
12295473 TCTTAAGAGC
* * *
12295483 CATAT-TCAGGAAGCTCATGCGAGCCAATAACGGGTAGCTCTAAAGAGCCATTAATCA-GAAAGC
1 CATATATCAGGAAGCTCAAGCGAGCC-ATAACGGGAAGCTCCAAAGAGCCATTAATCATG-AAGC
12295546 TC-CAAATAGT
64 TCACAAATAGT
* * * **
12295556 CATATATCGGGAAGTTCAAGCGAGCCATATCGGGAAGCTCCGGAGAGCCATTAATCATGAAGCTC
1 CATATATCAGGAAGCTCAAGCGAGCCATAACGGGAAGCTCCAAAGAGCCATTAATCATGAAGCTC
12295621 ACAAA
66 ACAAA
12295626 GAGCCTTTAA
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
73 37 0.63
74 22 0.37
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (74 bp):
CATATATCAGGAAGCTCAAGCGAGCCATAACGGGAAGCTCCAAAGAGCCATTAATCATGAAGCTC
ACAAATAGT
Found at i:12295603 original size:23 final size:23
Alignment explanation
Indices: 12295559--12295606 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
12295549 AAATAGTCAT
* *
12295559 ATATCGGGAAGTTCAAGCGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
**
12295582 ATATCGGGAAGCTCCGGAGAGCC
1 ATATCGGGAAGCTCAAGAGAGCC
12295605 AT
1 AT
12295607 TAATCATGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.23, G:0.31, T:0.17
Consensus pattern (23 bp):
ATATCGGGAAGCTCAAGAGAGCC
Found at i:12295620 original size:25 final size:25
Alignment explanation
Indices: 12295589--12295657 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
12295579 GCCATATCGG
* *
12295589 GAAGCTCCGGAGAGCCATTAATCAT
1 GAAGCTCCGAAGAGCCATTAATCAA
* *
12295614 GAAGCTCACAAAGAGCCTTTAATCAA
1 GAAGCTC-CGAAGAGCCATTAATCAA
*
12295640 GAAGCTCCGAAAAGCCAT
1 GAAGCTCCGAAGAGCCAT
12295658 ATAACGGGAT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
25 15 0.42
26 21 0.58
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (25 bp):
GAAGCTCCGAAGAGCCATTAATCAA
Found at i:12300941 original size:50 final size:50
Alignment explanation
Indices: 12300831--12301081 Score: 281
Period size: 50 Copynumber: 4.9 Consensus size: 50
12300821 GACATTAAGA
*
12300831 AGATGAGA--TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGTG
1 AGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C----CG
* *
12300884 ATTATGAGAGGTCCTATGTAAGACCATGTCTGGGACATGGCATTGGCACCG
1 A-GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG
* **
12300935 AGATGAGAGGTCCCATGTAAGACCATGTCTAGGACATGGTGTTGGCACCG
1 AGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG
** * *
12300985 AGATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCT
1 AGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG
* ** * * * *
12301035 ATATGAGAACTCCCATGTAAGACCATATCTGAGATATGACATTGGCA
1 AGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
12301082 GTACAAGAAA
Statistics
Matches: 170, Mismatches: 25, Indels: 9
0.83 0.12 0.04
Matches are distributed among these distances:
50 124 0.73
51 2 0.01
53 1 0.01
54 6 0.04
55 1 0.01
56 36 0.21
ACGTcount: A:0.27, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
AGATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG
Found at i:12307108 original size:34 final size:35
Alignment explanation
Indices: 12307065--12307142 Score: 99
Period size: 35 Copynumber: 2.3 Consensus size: 35
12307055 ATAAATAGGA
*
12307065 AAAAATATAT-AATTTATTAAATATTA-AAAA-AGTT
1 AAAAATATATAAACTTA-TAAATATTATAAAATA-TT
*
12307099 AAAATTATATAAACTTATAAATATTATAAAATATT
1 AAAAATATATAAACTTATAAATATTATAAAATATT
12307134 AAAAATATA
1 AAAAATATA
12307143 AAAAACCTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
34 18 0.47
35 19 0.50
36 1 0.03
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (35 bp):
AAAAATATATAAACTTATAAATATTATAAAATATT
Found at i:12307227 original size:21 final size:20
Alignment explanation
Indices: 12307203--12307306 Score: 53
Period size: 20 Copynumber: 5.3 Consensus size: 20
12307193 AAAACACATT
*
12307203 TAAAATATTGAAAATTTTATA
1 TAAAATATT-AAAATTCTATA
*
12307224 TAAACCTATTAAAATTCTATA
1 TAAA-ATATTAAAATTCTATA
12307245 -AAAATCA-TATAAATTACT-TA
1 TAAAAT-ATTA-AAATT-CTATA
**
12307265 -AAAATA-TAAAA-AGTAT-
1 TAAAATATTAAAATTCTATA
*
12307281 TAAAAGTATTAAAATT-GATA
1 TAAAA-TATTAAAATTCTATA
12307301 TAAAAT
1 TAAAAT
12307307 TATAAAAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 22
0.69 0.07 0.23
Matches are distributed among these distances:
16 1 0.02
17 5 0.08
18 5 0.08
19 14 0.21
20 21 0.32
21 16 0.24
22 4 0.06
ACGTcount: A:0.56, C:0.05, G:0.04, T:0.36
Consensus pattern (20 bp):
TAAAATATTAAAATTCTATA
Found at i:12311198 original size:30 final size:31
Alignment explanation
Indices: 12311123--12311217 Score: 111
Period size: 32 Copynumber: 3.1 Consensus size: 31
12311113 TGAATTCAAA
* * *
12311123 TGTATATGTTTTATATATTGCCAAATTGATT
1 TGTATATGATATATATATTGCCGAATTGATT
* * *
12311154 TATATGTAGATATATACATTGCCGAATTGATT
1 TGTATAT-GATATATATATTGCCGAATTGATT
*
12311186 TGTATATG-TATATATATTACCGAATTGATT
1 TGTATATGATATATATATTGCCGAATTGATT
12311216 TG
1 TG
12311218 AGATCCTGTA
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
30 22 0.42
31 6 0.11
32 25 0.47
ACGTcount: A:0.32, C:0.07, G:0.15, T:0.46
Consensus pattern (31 bp):
TGTATATGATATATATATTGCCGAATTGATT
Found at i:12311326 original size:42 final size:43
Alignment explanation
Indices: 12311254--12311354 Score: 125
Period size: 42 Copynumber: 2.4 Consensus size: 43
12311244 ATATGACATC
* * *
12311254 GGCATCGATTTGAGATCCCGTATAAGACCATATCTGGGATA-T
1 GGCATCGATATGAGATCCCGTATAAAACCATAGCTGGGATATT
* * *
12311296 GGCATCGATATGAGA-CTTCGTGTAAAACCATAGCTGGGCTATT
1 GGCATCGATATGAGATC-CCGTATAAAACCATAGCTGGGATATT
12311339 GGCATCGATATGAGAT
1 GGCATCGATATGAGAT
12311355 TTCCATATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
41 1 0.02
42 33 0.66
43 16 0.32
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (43 bp):
GGCATCGATATGAGATCCCGTATAAAACCATAGCTGGGATATT
Found at i:12318178 original size:6 final size:6
Alignment explanation
Indices: 12318167--12318197 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
12318157 AAAAACATAT
12318167 ATATAC ATATAC ATATAC ATATAC ATATAC A
1 ATATAC ATATAC ATATAC ATATAC ATATAC A
12318198 ATCATTTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.16, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAC
Found at i:12320441 original size:5 final size:5
Alignment explanation
Indices: 12320431--12320458 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
12320421 TTCATGCATT
12320431 TAATA TAATA TAATA TAATA TAATA TAA
1 TAATA TAATA TAATA TAATA TAATA TAA
12320459 ATATTTACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAATA
Found at i:12322743 original size:3 final size:3
Alignment explanation
Indices: 12322735--12322764 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
12322725 TTGTGTTCTT
*
12322735 TTA TTA TTA TTA TTA TTA TTA TTA TGA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
12322765 ATAAGTTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:12333234 original size:6 final size:6
Alignment explanation
Indices: 12333223--12333257 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
12333213 GCCATCATCA
* *
12333223 CCACCT CCACCT CCACCT CCACCC CCCCCT CCACC
1 CCACCT CCACCT CCACCT CCACCT CCACCT CCACC
12333258 GCCTCCTCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.14, C:0.74, G:0.00, T:0.11
Consensus pattern (6 bp):
CCACCT
Found at i:12341329 original size:6 final size:6
Alignment explanation
Indices: 12341320--12341351 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
12341310 TCGCAACCAT
12341320 AGCCGC AGCCGC AGCCGC AGCCGC AGCCGC AG
1 AGCCGC AGCCGC AGCCGC AGCCGC AGCCGC AG
12341352 TAACAGCCGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.19, C:0.47, G:0.34, T:0.00
Consensus pattern (6 bp):
AGCCGC
Found at i:12341332 original size:18 final size:18
Alignment explanation
Indices: 12341311--12341350 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
12341301 TCCTCGCAAT
*
12341311 CGCAACCATAGCCGCAGC
1 CGCAACCACAGCCGCAGC
* *
12341329 CGCAGCCGCAGCCGCAGC
1 CGCAACCACAGCCGCAGC
12341347 CGCA
1 CGCA
12341351 GTAACAGCCG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.23, C:0.47, G:0.28, T:0.03
Consensus pattern (18 bp):
CGCAACCACAGCCGCAGC
Found at i:12341358 original size:18 final size:18
Alignment explanation
Indices: 12341320--12341361 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
12341310 TCGCAACCAT
**
12341320 AGCCGCAGCCGCAGCCGC
1 AGCCGCAGCCGCAGCAAC
*
12341338 AGCCGCAGCCGCAGTAAC
1 AGCCGCAGCCGCAGCAAC
12341356 AGCCGC
1 AGCCGC
12341362 CGTCGCAGTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.21, C:0.45, G:0.31, T:0.02
Consensus pattern (18 bp):
AGCCGCAGCCGCAGCAAC
Found at i:12342388 original size:16 final size:16
Alignment explanation
Indices: 12342367--12342418 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
12342357 TTTGGTTCGC
12342367 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
12342383 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
12342399 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
12342415 TGTA
1 TGTA
12342419 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:12342504 original size:39 final size:43
Alignment explanation
Indices: 12342399--12342508 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
12342389 GGATTAGAGG
12342399 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
12342444 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
12342484 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
12342509 TAATGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:12342662 original size:25 final size:25
Alignment explanation
Indices: 12342630--12342684 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 25
12342620 TAAGTTAATC
*
12342630 ATAT-TTAAACATAATTATTATT-AA
1 ATATATTAAACAT-ATTATAATTAAA
*
12342654 ATATATTAAATATATTATAATTAAA
1 ATATATTAAACATATTATAATTAAA
12342679 ATATAT
1 ATATAT
12342685 AATTTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
24 12 0.44
25 15 0.56
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (25 bp):
ATATATTAAACATATTATAATTAAA
Found at i:12342917 original size:88 final size:88
Alignment explanation
Indices: 12342825--12343038 Score: 279
Period size: 88 Copynumber: 2.4 Consensus size: 88
12342815 AATTTAAAAT
* * * *
12342825 AATTATAACTAATAAATTATCTTATATGAATTTGTATAATTTAAAATAATTATTATTACATATAA
1 AATTATAA-TAATAAATT-TCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
12342890 TTTAAT-A-ATATATAATTTCATAA
64 TTTAATAAGATATATAATTTCATAA
* *
12342913 AATTATTGATAATAATTTTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
1 AATTA-TAATAATAA-ATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAA
12342978 TTTAATAATGATATATAATTTCATAA
64 TTTAATAA-GATATATAATTTCATAA
*
12343004 AATTCTTAATAATAAAATGTTCTTATATGAATTTA
1 AATT-ATAATAAT-AAAT-TTCTTATATGAATTTA
12343039 CTAAAATCAA
Statistics
Matches: 109, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
88 59 0.54
89 5 0.05
91 27 0.25
92 18 0.17
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.46
Consensus pattern (88 bp):
AATTATAATAATAAATTTCTTATATGAATTTATACAATTTAAAATAATTAATATTAAATATAATT
TAATAAGATATATAATTTCATAA
Found at i:12342998 original size:44 final size:43
Alignment explanation
Indices: 12342859--12342998 Score: 115
Period size: 44 Copynumber: 3.2 Consensus size: 43
12342849 TATGAATTTG
* *
12342859 TATAATTTAAAATAATTATTATTACATATAATTTAATAATATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
* * * * ** *
12342902 TA-ATTTCATAAAATTATTGATAAT-AAT-TTTTCTTATATGAATTTA
1 TATAATT--TAAAATAATTAATATTAAATATAAT-TTA-AT-AATATA
*
12342947 TACAATTTAAAATAATTAATATTAAATATAATTTAATAATGATA
1 TATAATTTAAAATAATTAATATTAAATATAATTTAATAAT-ATA
12342991 TATAATTT
1 TATAATTT
12342999 CATAAAATTC
Statistics
Matches: 71, Mismatches: 17, Indels: 17
0.68 0.16 0.16
Matches are distributed among these distances:
42 5 0.07
43 10 0.14
44 38 0.54
45 13 0.18
46 5 0.07
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (43 bp):
TATAATTTAAAATAATTAATATTAAATATAATTTAATAATATA
Found at i:12347065 original size:40 final size:40
Alignment explanation
Indices: 12347020--12347100 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
12347010 ATTTAATGAT
12347020 TGAGAATAAATTCTCTCAATTTTTCAGCAGAGTAACAATC
1 TGAGAATAAATTCTCTCAATTTTTCAGCAGAGTAACAATC
12347060 TGAGAATAAATTCTCTCAATTTTTCAGCAGAGTAACAATC
1 TGAGAATAAATTCTCTCAATTTTTCAGCAGAGTAACAATC
12347100 T
1 T
12347101 CTTAAAGTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.33
Consensus pattern (40 bp):
TGAGAATAAATTCTCTCAATTTTTCAGCAGAGTAACAATC
Found at i:12348832 original size:28 final size:28
Alignment explanation
Indices: 12348783--12348842 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
12348773 ATGTAAAGAG
* * *
12348783 ATATATATGTATATTTTAAAATTGTGAA
1 ATATATATGTATATTATAAAATTATAAA
12348811 ATATATATGTATA-TATATAAATTATAAA
1 ATATATATGTATATTATA-AAATTATAAA
12348839 ATAT
1 ATAT
12348843 GTGTGCATCT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
27 3 0.11
28 25 0.89
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (28 bp):
ATATATATGTATATTATAAAATTATAAA
Found at i:12350142 original size:9 final size:9
Alignment explanation
Indices: 12350125--12350161 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12350115 TGAGTTTTCA
12350125 AATTCGAAT
1 AATTCGAAT
*
12350134 AACTCGAAT
1 AATTCGAAT
12350143 AATTCGAAT
1 AATTCGAAT
12350152 AATTCGAAT
1 AATTCGAAT
12350161 A
1 A
12350162 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12350410 original size:30 final size:31
Alignment explanation
Indices: 12350374--12350433 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
12350364 AAACCTTTTA
*
12350374 TTTTCCCCCAAAATTTTTACTCC-CTCCCAC
1 TTTTCCCCCAAAACTTTTACTCCTCTCCCAC
* *
12350404 TTTTCCCCTAAAACTTTTATTCCTCTCCCA
1 TTTTCCCCCAAAACTTTTACTCCTCTCCCA
12350434 TCCCACCTCT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 20 0.77
31 6 0.23
ACGTcount: A:0.20, C:0.40, G:0.00, T:0.40
Consensus pattern (31 bp):
TTTTCCCCCAAAACTTTTACTCCTCTCCCAC
Found at i:12351619 original size:12 final size:12
Alignment explanation
Indices: 12351595--12351644 Score: 55
Period size: 12 Copynumber: 4.1 Consensus size: 12
12351585 CCTTATAGAA
12351595 TCATTTCTCATTT
1 TCATTTC-CATTT
*
12351608 TCATTTTCATTT
1 TCATTTCCATTT
* *
12351620 CCATTTCCGTTT
1 TCATTTCCATTT
*
12351632 TAATTTCCATTT
1 TCATTTCCATTT
12351644 T
1 T
12351645 GAGAAAACTA
Statistics
Matches: 30, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 24 0.80
13 6 0.20
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.60
Consensus pattern (12 bp):
TCATTTCCATTT
Found at i:12351632 original size:18 final size:18
Alignment explanation
Indices: 12351595--12351643 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
12351585 CCTTATAGAA
*
12351595 TCATTTCTCATTTTCATTT
1 TCATTTC-CATTTCCATTT
*
12351614 TCATTTCCATTTCCGTTT
1 TCATTTCCATTTCCATTT
*
12351632 TAATTTCCATTT
1 TCATTTCCATTT
12351644 TGAGAAAACT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 20 0.74
19 7 0.26
ACGTcount: A:0.16, C:0.22, G:0.02, T:0.59
Consensus pattern (18 bp):
TCATTTCCATTTCCATTT
Found at i:12353137 original size:77 final size:77
Alignment explanation
Indices: 12353044--12353202 Score: 309
Period size: 77 Copynumber: 2.1 Consensus size: 77
12353034 ATGTGTTTTA
12353044 GTCCTAATGTGAAATATTTGAGTTTTAGCTATATCCACACTATTACAATGTCATAACTTTTCTAT
1 GTCCTAATGTGAAATATTTGAGTTTTAGCTATATCCACACTATTACAATGTCATAACTTTTCTAT
12353109 ACCTCATGTTCG
66 ACCTCATGTTCG
*
12353121 GTCCTTATGTGAAATATTTGAGTTTTAGCTATATCCACACTATTACAATGTCATAACTTTTCTAT
1 GTCCTAATGTGAAATATTTGAGTTTTAGCTATATCCACACTATTACAATGTCATAACTTTTCTAT
12353186 ACCTCATGTTCG
66 ACCTCATGTTCG
12353198 GTCCT
1 GTCCT
12353203 CCATAGTGAA
Statistics
Matches: 81, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
77 81 1.00
ACGTcount: A:0.27, C:0.20, G:0.12, T:0.41
Consensus pattern (77 bp):
GTCCTAATGTGAAATATTTGAGTTTTAGCTATATCCACACTATTACAATGTCATAACTTTTCTAT
ACCTCATGTTCG
Found at i:12358894 original size:58 final size:60
Alignment explanation
Indices: 12358825--12358940 Score: 166
Period size: 61 Copynumber: 1.9 Consensus size: 60
12358815 ATTACTTTAA
* *
12358825 TATTAAATTAATATAATACTTA-T-CAAGATAAATATTAGATTAAATT-TAATATTAAATC
1 TATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATT-AATTCTAATATTAAATC
*
12358883 TATTAAATTAATAGAATATTTATCTACAAGATAAATATTAAATTAATTCTAATATTAA
1 TATTAAATTAATAGAATACTTA-CTACAAGATAAATATTAAATTAATTCTAATATTAA
12358941 GATAATCACT
Statistics
Matches: 51, Mismatches: 3, Indels: 5
0.86 0.05 0.08
Matches are distributed among these distances:
58 20 0.39
60 5 0.10
61 26 0.51
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.41
Consensus pattern (60 bp):
TATTAAATTAATAGAATACTTACTACAAGATAAATATTAAATTAATTCTAATATTAAATC
Done.