Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11
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: 47972186
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2603476 characters in sequence are not A, C, G, or T
File 128 of 145
Found at i:42055929 original size:28 final size:28
Alignment explanation
Indices: 42055897--42055962 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
42055887 TTAGGTAACC
*
42055897 TAATTAGGTTAGGTTAGTGTTTTTAATT
1 TAATTAGGTTAGGTTAGGGTTTTTAATT
**
42055925 TAATTAAATTAGGTTAGGGTTTTTAATT
1 TAATTAGGTTAGGTTAGGGTTTTTAATT
*
42055953 AAATTAGGTT
1 TAATTAGGTT
42055963 CCATAGGATT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.30, C:0.00, G:0.20, T:0.50
Consensus pattern (28 bp):
TAATTAGGTTAGGTTAGGGTTTTTAATT
Found at i:42062397 original size:19 final size:19
Alignment explanation
Indices: 42062360--42062398 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
42062350 ATTGATTTTT
42062360 TAAATTTTGAATTAAAATGA
1 TAAATTTTGAA-TAAAATGA
42062380 TAAATTTTGTAA-AAAATGA
1 TAAATTTTG-AATAAAATGA
42062399 GGGCTAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 9 0.50
21 2 0.11
ACGTcount: A:0.51, C:0.00, G:0.10, T:0.38
Consensus pattern (19 bp):
TAAATTTTGAATAAAATGA
Found at i:42067191 original size:18 final size:17
Alignment explanation
Indices: 42067147--42067198 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
42067137 ATCATTATTA
*
42067147 AAAATCATT-AAAAATAT
1 AAAAT-ATTCAAAAAAAT
*
42067164 ATAATATTCAAAAAAAT
1 AAAATATTCAAAAAAAT
42067181 AAAATATTTCAAAGAAAA
1 AAAATA-TTCAAA-AAAA
42067199 ATATAAGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 3 0.10
17 16 0.55
18 6 0.21
19 4 0.14
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATATTCAAAAAAAT
Found at i:42068557 original size:18 final size:17
Alignment explanation
Indices: 42068513--42068564 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 17
42068503 ATCATTATTA
*
42068513 AAAATCATT-AAAAATAT
1 AAAAT-ATTCAAAAAAAT
*
42068530 ATAATATTCAAAAAAAT
1 AAAATATTCAAAAAAAT
42068547 AAAATATTTCAAAGAAAA
1 AAAATA-TTCAAA-AAAA
42068565 ATATAAGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 3 0.10
17 16 0.55
18 6 0.21
19 4 0.14
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (17 bp):
AAAATATTCAAAAAAAT
Found at i:42068684 original size:19 final size:18
Alignment explanation
Indices: 42068658--42068708 Score: 50
Period size: 19 Copynumber: 2.8 Consensus size: 18
42068648 TTAAAATTAT
*
42068658 TTAA-TTAATTTTTAATT
1 TTAATTTAATTTTTAATC
**
42068675 TTAATTTTAATGTTAAAATC
1 TTAA-TTTAAT-TTTTAATC
42068695 TTAATTTAATTTTT
1 TTAATTTAATTTTT
42068709 TAGTTTTANN
Statistics
Matches: 26, Mismatches: 5, Indels: 5
0.72 0.14 0.14
Matches are distributed among these distances:
17 4 0.15
18 2 0.08
19 11 0.42
20 9 0.35
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (18 bp):
TTAATTTAATTTTTAATC
Found at i:42070432 original size:28 final size:29
Alignment explanation
Indices: 42070367--42070432 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
42070357 AATGTTTAGG
42070367 TTAT-ATTATATCAAATAATAATTATTTA
1 TTATAATTATATCAAATAATAATTATTTA
* *
42070395 TTA-ATTTTATATCAAATAA-AATTATTTT
1 TTATA-ATTATATCAAATAATAATTATTTA
42070423 TTATAATTAT
1 TTATAATTAT
42070433 TGAACTCAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
28 18 0.56
29 14 0.44
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (29 bp):
TTATAATTATATCAAATAATAATTATTTA
Found at i:42070964 original size:14 final size:14
Alignment explanation
Indices: 42070945--42070971 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42070935 TTATTTAGTT
42070945 GTAGAATCAAAATA
1 GTAGAATCAAAATA
42070959 GTAGAATCAAAAT
1 GTAGAATCAAAAT
42070972 TTAAGATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.56, C:0.07, G:0.15, T:0.22
Consensus pattern (14 bp):
GTAGAATCAAAATA
Found at i:42079609 original size:39 final size:39
Alignment explanation
Indices: 42079555--42079632 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
42079545 ATAAGTCGCC
*
42079555 GGCACTCGGGGATGCGTAGGTTATATCCATTCCCGCACT
1 GGCACTCGAGGATGCGTAGGTTATATCCATTCCCGCACT
*
42079594 GGCACTCGAGGATGCGTAGGTTATCTCCATTCCCGCACT
1 GGCACTCGAGGATGCGTAGGTTATATCCATTCCCGCACT
42079633 ATCGGAGCAT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.18, C:0.29, G:0.27, T:0.26
Consensus pattern (39 bp):
GGCACTCGAGGATGCGTAGGTTATATCCATTCCCGCACT
Found at i:42086066 original size:21 final size:21
Alignment explanation
Indices: 42086042--42086111 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 21
42086032 AATTTAATTT
42086042 TTTATTTTAATATTATATATA
1 TTTATTTTAATATTATATATA
*
42086063 TTTAATGTGTTATTATTA-ATA-A
1 TTT-AT-T-TTAATATTATATATA
*
42086085 TTAATTTTAA-ATTATATAT-
1 TTTATTTTAATATTATATATA
*
42086104 TTCATTTT
1 TTTATTTT
42086112 TTATTGTATG
Statistics
Matches: 40, Mismatches: 4, Indels: 12
0.71 0.07 0.21
Matches are distributed among these distances:
18 4 0.10
19 13 0.32
20 1 0.03
21 5 0.12
22 5 0.12
23 4 0.10
24 8 0.20
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (21 bp):
TTTATTTTAATATTATATATA
Found at i:42088972 original size:14 final size:14
Alignment explanation
Indices: 42088953--42088984 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
42088943 TAAAATCTTC
*
42088953 GATTCCAACTACAG
1 GATTCCAACTAAAG
42088967 GATTCCAACTAAAG
1 GATTCCAACTAAAG
42088981 GATT
1 GATT
42088985 TCTCCACTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.25
Consensus pattern (14 bp):
GATTCCAACTAAAG
Found at i:42090708 original size:26 final size:26
Alignment explanation
Indices: 42090679--42090730 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
42090669 ATAAGAAAGT
42090679 GACACGTTGATGAAAGAAACATTAGG
1 GACACGTTGATGAAAGAAACATTAGG
42090705 GACACGTTGATGAAAGAAACATTAGG
1 GACACGTTGATGAAAGAAACATTAGG
42090731 AGGTGCCACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.27, T:0.19
Consensus pattern (26 bp):
GACACGTTGATGAAAGAAACATTAGG
Found at i:42094636 original size:14 final size:14
Alignment explanation
Indices: 42094617--42094647 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42094607 TTCTAGTTTG
42094617 TTTTGTTCTAATAT
1 TTTTGTTCTAATAT
*
42094631 TTTTGTTGTAATAT
1 TTTTGTTCTAATAT
42094645 TTT
1 TTT
42094648 AGTTTATGCG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.10, T:0.68
Consensus pattern (14 bp):
TTTTGTTCTAATAT
Found at i:42097645 original size:15 final size:15
Alignment explanation
Indices: 42097600--42097645 Score: 53
Period size: 15 Copynumber: 3.1 Consensus size: 15
42097590 AAGTTGTGGA
42097600 TTTAATC-TATATTT
1 TTTAATCTTATATTT
42097614 TTTAAT-TTGAT-TATT
1 TTTAATCTT-ATAT-TT
42097629 TTTAATCTTATATTT
1 TTTAATCTTATATTT
42097644 TT
1 TT
42097646 CAAAATTTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 9
0.75 0.00 0.25
Matches are distributed among these distances:
14 8 0.30
15 16 0.59
16 3 0.11
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.67
Consensus pattern (15 bp):
TTTAATCTTATATTT
Found at i:42104671 original size:252 final size:253
Alignment explanation
Indices: 42104215--42104719 Score: 1003
Period size: 252 Copynumber: 2.0 Consensus size: 253
42104205 TATTGTTAAT
42104215 TTTACTACTATTTTAGAGACATTTGCTTGTTAAGCTATACCTATCTTAGCGTTATTTAAATATAA
1 TTTACTACTATTTTAGAGACATTTGCTTGTTAAGCTATACCTATCTTAGCGTTATTTAAATATAA
42104280 AATCTTTTTTTAATTTATTTTTAATTTTATTGGGAAACATTTAATTTAATTATTTAGTATTTTTG
66 AATCTTTTTTTAATTTATTTTTAATTTTATTGGGAAACATTTAATTTAATTATTTAGTATTTTTG
42104345 ATGTATTTTATTATTTATATAAAAATAAAATAAAAAAATTAATATGGGCCGAACCCAGATTTAAC
131 ATGTATTTTATTATTTATATAAAAATAAAATAAAAAAATTAATATGGGCCGAACCCAGATTTAAC
42104410 ATCTATAATCTAAGTCAAGCTTGAATAAAAATTTAAACTCATTTTTCAAATCGATCTC
196 ATCTATAATCTAAGTCAAGCTTGAATAAAAATTTAAACTCATTTTTCAAATCGATCTC
42104468 TTTACTACTA-TTTAGAGACATTTGCTTGTTAAGCTATACCTATCTTAGCGTTATTTAAATATAA
1 TTTACTACTATTTTAGAGACATTTGCTTGTTAAGCTATACCTATCTTAGCGTTATTTAAATATAA
42104532 AATCTTTTTTTAATTTATTTTTAATTTTATTGGGAAACATTTAATTTAATTATTTAGTATTTTTG
66 AATCTTTTTTTAATTTATTTTTAATTTTATTGGGAAACATTTAATTTAATTATTTAGTATTTTTG
42104597 ATGTATTTTATTATTTATATAAAAATAAAATAAAAAAATTAATATGGGCCGAACCCAGATTTAAC
131 ATGTATTTTATTATTTATATAAAAATAAAATAAAAAAATTAATATGGGCCGAACCCAGATTTAAC
42104662 ATCTATAATCTAAGTCAAGCTTGAATAAAAATTTAAACTCATTTTTCAAATCGATCTC
196 ATCTATAATCTAAGTCAAGCTTGAATAAAAATTTAAACTCATTTTTCAAATCGATCTC
42104720 GTATCTATCA
Statistics
Matches: 252, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
252 242 0.96
253 10 0.04
ACGTcount: A:0.37, C:0.11, G:0.09, T:0.44
Consensus pattern (253 bp):
TTTACTACTATTTTAGAGACATTTGCTTGTTAAGCTATACCTATCTTAGCGTTATTTAAATATAA
AATCTTTTTTTAATTTATTTTTAATTTTATTGGGAAACATTTAATTTAATTATTTAGTATTTTTG
ATGTATTTTATTATTTATATAAAAATAAAATAAAAAAATTAATATGGGCCGAACCCAGATTTAAC
ATCTATAATCTAAGTCAAGCTTGAATAAAAATTTAAACTCATTTTTCAAATCGATCTC
Found at i:42114157 original size:39 final size:39
Alignment explanation
Indices: 42114114--42114195 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 39
42114104 TTGAGGAAGG
*
42114114 ATTATTGTAAATTCTAAACATTATATCAA-AAAAGTAAAA
1 ATTATGGTAAATTCTAAACATTATATCAAGAAAA-TAAAA
* * *
42114153 ATTATGGTAAATTTTAAACATTATATTAAGAAAATAAAG
1 ATTATGGTAAATTCTAAACATTATATCAAGAAAATAAAA
42114192 ATTA
1 ATTA
42114196 AGAGAGTAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 34 0.89
40 4 0.11
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.35
Consensus pattern (39 bp):
ATTATGGTAAATTCTAAACATTATATCAAGAAAATAAAA
Found at i:42116571 original size:25 final size:27
Alignment explanation
Indices: 42116521--42116571 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 27
42116511 ACAAATAATT
*
42116521 AAAAAATTATAATAAAATATTAAAAAC
1 AAAAAATTATAATAAAATATCAAAAAC
42116548 AAAAAA-TAT-ATAAAAT-TCATAAAA
1 AAAAAATTATAATAAAATATCA-AAAA
42116572 ATTTAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
24 2 0.09
25 11 0.50
26 3 0.14
27 6 0.27
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (27 bp):
AAAAAATTATAATAAAATATCAAAAAC
Found at i:42117302 original size:19 final size:19
Alignment explanation
Indices: 42117280--42117318 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
42117270 ATCTTCATAA
42117280 AAGCTTCCACAAAAAAAAT
1 AAGCTTCCACAAAAAAAAT
42117299 AAGCTTCCACAAAAAAAAT
1 AAGCTTCCACAAAAAAAAT
42117318 A
1 A
42117319 TCCACACTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.59, C:0.21, G:0.05, T:0.15
Consensus pattern (19 bp):
AAGCTTCCACAAAAAAAAT
Found at i:42122121 original size:11 final size:10
Alignment explanation
Indices: 42122099--42122129 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
42122089 TCTTGTGTCG
42122099 AAAATTAAAA
1 AAAATTAAAA
*
42122109 AAACTTAAAA
1 AAAATTAAAA
42122119 AAAATTAAAA
1 AAAATTAAAA
42122129 A
1 A
42122130 TACGATCCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.77, C:0.03, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:42124533 original size:44 final size:43
Alignment explanation
Indices: 42124470--42124851 Score: 296
Period size: 46 Copynumber: 9.0 Consensus size: 43
42124460 TCATTAATCC
*
42124470 GCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT
* *
42124514 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGTACTT-TTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGA--T-TACTTCTTT-GATCT
* * * * *
42124560 GCTCCACTGTAATTTCAGGGAGATAAGACCTAATAC---GATCC
1 GCTCCACTGTAATCTCAGGGAGATAAGA-TTACTTCTTTGATCT
* * * *
42124601 ACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C--CTTTAATC-
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTTCTTTGATCT
42124639 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT
* * *
42124683 GCTCCGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT-T--ACTTCTTTGATCT
* * ** * *
42124729 GTTCCACTGTAATCTCAGGGAGATAAGA--CCTGATATGATCC
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACTTCTTTGATCT
* * * *
42124770 ACTCTACTGTAA-CTTCAGAGAGATAAGA-T-C--CTTTAATC-
1 GCTCCACTGTAATC-TCAGGGAGATAAGATTACTTCTTTGATCT
42124808 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
1 GCTCCACTGTAATCTCAGGGAGATAAGATTACT-TCTTTGATCT
42124852 ACTTCACTTA
Statistics
Matches: 267, Mismatches: 43, Indels: 56
0.73 0.12 0.15
Matches are distributed among these distances:
36 1 0.00
38 46 0.17
39 13 0.05
40 3 0.01
41 55 0.21
43 14 0.05
44 57 0.21
45 5 0.02
46 66 0.25
47 7 0.03
ACGTcount: A:0.27, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATTACTTCTTTGATCT
Found at i:42124662 original size:38 final size:39
Alignment explanation
Indices: 42124560--42124836 Score: 190
Period size: 38 Copynumber: 6.7 Consensus size: 39
42124550 TTTTCGGTCT
* *
42124560 GCTCCACTGTAATTTCAGGGAGATAAGA-CCTAATACGATCC
1 GCTCCACTGTAATCTCAGGGAGATAAGATCCTATTA--AT-C
* * *
42124601 ACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTAATC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATCCTATTAATC
* *
42124639 GCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATC
1 GCTCCACTGTAATCTCAGGGAGATAAGA-TCCTA---TTAATC
* **
42124682 TGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTGCACTTCTTC
1 -GCTCCACTGTAATCTCAGGGAGATAAGATCCT--A-TTAATC
*
42124724 GGTCTGTTCCACTGTAATCTCAGGGAGATAAGA-CCTGATATGATCC
1 -G-C---TCCACTGTAATCTCAGGGAGATAAGATCCT-AT-TAAT-C
* * *
42124770 ACTCTACTGTAA-CTTCAGAGAGATAAGATCCT-TTAATC
1 GCTCCACTGTAATC-TCAGGGAGATAAGATCCTATTAATC
42124808 GCTCCACTGTAATCTCAGGGAGATAAGAT
1 GCTCCACTGTAATCTCAGGGAGATAAGAT
42124837 TACTATCTTT
Statistics
Matches: 189, Mismatches: 26, Indels: 45
0.73 0.10 0.17
Matches are distributed among these distances:
38 49 0.26
39 10 0.05
40 2 0.01
41 47 0.25
42 13 0.07
43 7 0.04
44 30 0.16
45 3 0.02
46 28 0.15
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.29
Consensus pattern (39 bp):
GCTCCACTGTAATCTCAGGGAGATAAGATCCTATTAATC
Found at i:42124737 original size:169 final size:169
Alignment explanation
Indices: 42124454--42124851 Score: 708
Period size: 169 Copynumber: 2.4 Consensus size: 169
42124444 CTCTGTTGTA
* *
42124454 ATAAGAT-CATTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTATCTTTGATCTGCTC
1 ATAAGATCCTTTAAT-CGCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCTGCTC
* * *
42124518 CGCTGTAATCTCAGGGAGATAAGATCTGTACTTTTTCGGTCTGCTCCACTGTAATTTCAGGGAGA
65 CGCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGA
42124583 TAAGACCTAATACGATCCACTCTACTGTAACTTCAGAGAG
130 TAAGACCTAATACGATCCACTCTACTGTAACTTCAGAGAG
42124623 ATAAGATCCTTTAATCGCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCTGCTCC
1 ATAAGATCCTTTAATCGCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCTGCTCC
*
42124688 GCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGTTCCACTGTAATCTCAGGGAGAT
66 GCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGAT
* *
42124753 AAGACCTGATATGATCCACTCTACTGTAACTTCAGAGAG
131 AAGACCTAATACGATCCACTCTACTGTAACTTCAGAGAG
42124792 ATAAGATCCTTTAATCGCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
1 ATAAGATCCTTTAATCGCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCT
42124852 ACTTCACTTA
Statistics
Matches: 220, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
169 214 0.97
170 6 0.03
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (169 bp):
ATAAGATCCTTTAATCGCTCCACTGTAATCTCAGGGAGATAAGATTACTATCTTTGATCTGCTCC
GCTGTAATCTCAGGGAGATAAGATCTGCACTTCTTCGGTCTGCTCCACTGTAATCTCAGGGAGAT
AAGACCTAATACGATCCACTCTACTGTAACTTCAGAGAG
Found at i:42136647 original size:9 final size:10
Alignment explanation
Indices: 42136628--42136659 Score: 55
Period size: 10 Copynumber: 3.1 Consensus size: 10
42136618 CTTGATGTCG
42136628 AAAATTAAAA
1 AAAATTAAAA
42136638 AAAATTAAAAA
1 AAAATT-AAAA
42136649 AAAATTAAAA
1 AAAATTAAAA
42136659 A
1 A
42136660 TACGATCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 11 0.52
11 10 0.48
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAATTAAAA
Found at i:42136650 original size:11 final size:11
Alignment explanation
Indices: 42136628--42136659 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
42136618 CTTGATGTCG
42136628 AAAATT-AAAA
1 AAAATTAAAAA
42136638 AAAATTAAAAA
1 AAAATTAAAAA
42136649 AAAATTAAAAA
1 AAAATTAAAAA
42136660 TACGATCCTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAATTAAAAA
Found at i:42137721 original size:29 final size:28
Alignment explanation
Indices: 42137659--42137723 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 28
42137649 ATAAAATTGC
* *
42137659 TAAAATATGGGCTAAATCGAAATAAAAA
1 TAAAATATGGGCGAAATCGAAAGAAAAA
* *
42137687 TGAAAATGTAGGGCGAAATTGAAAGAAAAA
1 T-AAAATAT-GGGCGAAATCGAAAGAAAAA
42137717 TAAAATA
1 TAAAATA
42137724 AAAGGGACTA
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
28 1 0.03
29 11 0.37
30 18 0.60
ACGTcount: A:0.57, C:0.05, G:0.18, T:0.20
Consensus pattern (28 bp):
TAAAATATGGGCGAAATCGAAAGAAAAA
Found at i:42139207 original size:12 final size:12
Alignment explanation
Indices: 42139190--42139216 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
42139180 AATAAATCAT
42139190 ATATGTATATTA
1 ATATGTATATTA
42139202 ATATGTATATTA
1 ATATGTATATTA
42139214 ATA
1 ATA
42139217 GAAAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (12 bp):
ATATGTATATTA
Found at i:42139390 original size:21 final size:21
Alignment explanation
Indices: 42139366--42139421 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
42139356 CACTATTATT
* * *
42139366 TCTAATTTCACTGCTATAGTA
1 TCTAATCTCACCGCTACAGTA
42139387 TCTAATCTCACCGCTACAGTA
1 TCTAATCTCACCGCTACAGTA
*
42139408 ACTAATCTCACCGC
1 TCTAATCTCACCGC
42139422 CACCGCTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.29, C:0.30, G:0.09, T:0.32
Consensus pattern (21 bp):
TCTAATCTCACCGCTACAGTA
Found at i:42140249 original size:23 final size:23
Alignment explanation
Indices: 42140192--42140236 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
42140182 CATATAATCA
42140192 AATCAAACTAAAAATGATAAATG
1 AATCAAACTAAAAATGATAAATG
42140215 AATCAAACTAAAAATGATAAAT
1 AATCAAACTAAAAATGATAAAT
42140237 TATAGTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.09, G:0.07, T:0.22
Consensus pattern (23 bp):
AATCAAACTAAAAATGATAAATG
Found at i:42141682 original size:14 final size:14
Alignment explanation
Indices: 42141658--42141691 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
42141648 TTTATTTTCC
*
42141658 CCCTCTTTTTCTCT
1 CCCTCTCTTTCTCT
*
42141672 CTCTCTCTTTCTCT
1 CCCTCTCTTTCTCT
42141686 CCCTCT
1 CCCTCT
42141692 TCAGTTTCAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (14 bp):
CCCTCTCTTTCTCT
Found at i:42153168 original size:42 final size:42
Alignment explanation
Indices: 42153072--42153174 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 42
42153062 GTTTTCGAAC
* *
42153072 CTTGGTCAAAATGGCTATGGCACTAGTCAAAATAATTTTTCT
1 CTTGGTCAAAATTGCTATGGCACTAGTCAAAATAATTTTGCT
* *
42153114 -TCTGGTCAAAATTGCTATGG-ATTTGGTCAAAATAATTTTGCT
1 CT-TGGTCAAAATTGCTATGGCA-CTAGTCAAAATAATTTTGCT
*
42153156 CTTGGTCAAAATTGTTATG
1 CTTGGTCAAAATTGCTATG
42153175 CTGATGGATA
Statistics
Matches: 53, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
41 2 0.04
42 50 0.94
43 1 0.02
ACGTcount: A:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (42 bp):
CTTGGTCAAAATTGCTATGGCACTAGTCAAAATAATTTTGCT
Found at i:42153176 original size:21 final size:20
Alignment explanation
Indices: 42153116--42153176 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
42153106 ATTTTTCTTC
* *
42153116 TGGTCAAAATTGCTATGGATT
1 TGGTCAAAATTGTTAT-GCTT
** *
42153137 TGGTCAAAATAATTTTGCTCT
1 TGGTCAAAATTGTTATGCT-T
42153158 TGGTCAAAATTGTTATGCT
1 TGGTCAAAATTGTTATGCT
42153177 GATGGATATA
Statistics
Matches: 31, Mismatches: 8, Indels: 2
0.76 0.20 0.05
Matches are distributed among these distances:
20 2 0.06
21 29 0.94
ACGTcount: A:0.28, C:0.11, G:0.20, T:0.41
Consensus pattern (20 bp):
TGGTCAAAATTGTTATGCTT
Found at i:42160958 original size:42 final size:43
Alignment explanation
Indices: 42160906--42161008 Score: 131
Period size: 42 Copynumber: 2.4 Consensus size: 43
42160896 TATCCATCAG
* *
42160906 CATAACAATTTTGACCAAG-AGCAAAATTATTTTGACCAAAT-C
1 CATAGCAATTTTGACCAAGAAGAAAAATTATTTTGA-CAAATGC
* *
42160948 CATAGCAATTTTGACC-AGAAGAAAAATTATTTTGACTAGTGC
1 CATAGCAATTTTGACCAAGAAGAAAAATTATTTTGACAAATGC
*
42160990 CATAGCCATTTTGACCAAG
1 CATAGCAATTTTGACCAAG
42161009 GTTCGAAAAC
Statistics
Matches: 53, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
41 5 0.09
42 46 0.87
43 2 0.04
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (43 bp):
CATAGCAATTTTGACCAAGAAGAAAAATTATTTTGACAAATGC
Found at i:42169456 original size:20 final size:19
Alignment explanation
Indices: 42169416--42169467 Score: 65
Period size: 19 Copynumber: 2.9 Consensus size: 19
42169406 AATTTATTTG
42169416 TATATA-TATATACATACT
1 TATATATTATATACATACT
* *
42169434 TATATATTATTTATATACT
1 TATATATTATATACATACT
42169453 T-TATA-TATATACATA
1 TATATATTATATACATA
42169468 TATGTGTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
17 8 0.28
18 10 0.34
19 11 0.38
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (19 bp):
TATATATTATATACATACT
Found at i:42170408 original size:21 final size:21
Alignment explanation
Indices: 42170384--42170424 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42170374 TAATGCATTG
42170384 GATATG-GCATTTTATTTTCTC
1 GATATGAGCATTTT-TTTTCTC
*
42170405 GATATGAGGATTTTTTTTCT
1 GATATGAGCATTTTTTTTCT
42170425 AAAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.54
Consensus pattern (21 bp):
GATATGAGCATTTTTTTTCTC
Found at i:42172749 original size:22 final size:22
Alignment explanation
Indices: 42172698--42172742 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
42172688 TAGTTTAAAC
**
42172698 TTTAAATTCCTTTATCCTTTAT
1 TTTAAATTTATTTATCCTTTAT
42172720 TTTAAATTTATTTAT-CTTTAT
1 TTTAAATTTATTTATCCTTTAT
42172741 TT
1 TT
42172743 ATGAATTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTAAATTTATTTATCCTTTAT
Found at i:42173416 original size:40 final size:41
Alignment explanation
Indices: 42173349--42173430 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
42173339 AAATGTGAAG
* * *
42173349 CTGCCGACTATTTGGCGGATTGAAGACATGT-GGATTGAATT
1 CTGCCGAATATTTGACGGATTAAAGACATGTAGG-TTGAATT
42173390 CTGCCGAATATTT-ACGGATTAAAGACATGTAGGTTGAATT
1 CTGCCGAATATTTGACGGATTAAAGACATGTAGGTTGAATT
42173430 C
1 C
42173431 GACAATTGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 23 0.62
41 14 0.38
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (41 bp):
CTGCCGAATATTTGACGGATTAAAGACATGTAGGTTGAATT
Found at i:42180602 original size:21 final size:21
Alignment explanation
Indices: 42180578--42180618 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
42180568 TAATGCATTG
42180578 GATATG-GCATTTTATTTTCTC
1 GATATGAGCATTTT-TTTTCTC
*
42180599 GATATGAGGATTTTTTTTCT
1 GATATGAGCATTTTTTTTCT
42180619 AAAAAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.20, C:0.10, G:0.17, T:0.54
Consensus pattern (21 bp):
GATATGAGCATTTTTTTTCTC
Found at i:42182943 original size:22 final size:22
Alignment explanation
Indices: 42182892--42182936 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
42182882 TAGTTTAAAC
**
42182892 TTTAAATTCCTTTATCCTTTAT
1 TTTAAATTTATTTATCCTTTAT
42182914 TTTAAATTTATTTAT-CTTTAT
1 TTTAAATTTATTTATCCTTTAT
42182935 TT
1 TT
42182937 ATGAATTCTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.24, C:0.11, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTAAATTTATTTATCCTTTAT
Found at i:42183610 original size:40 final size:41
Alignment explanation
Indices: 42183543--42183624 Score: 114
Period size: 40 Copynumber: 2.0 Consensus size: 41
42183533 AAATGTGAAG
* * *
42183543 CTGCCGACTATTTGGCGGATTGAAGACATGT-GGATTGAATT
1 CTGCCGAATATTTGACGGATTAAAGACATGTAGG-TTGAATT
42183584 CTGCCGAATATTT-ACGGATTAAAGACATGTAGGTTGAATT
1 CTGCCGAATATTTGACGGATTAAAGACATGTAGGTTGAATT
42183624 C
1 C
42183625 GACAATTGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
40 23 0.62
41 14 0.38
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (41 bp):
CTGCCGAATATTTGACGGATTAAAGACATGTAGGTTGAATT
Found at i:42186406 original size:236 final size:236
Alignment explanation
Indices: 42185842--42186548 Score: 1180
Period size: 236 Copynumber: 3.0 Consensus size: 236
42185832 AGAGTTGTGT
* * * *
42185842 GCTATATATAGAGAGGTTGACATGCAGCAACCAAGGGCCACAGAGAAGTGGAATGGTCAATTGTA
1 GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAA-TG-C
* * * *
42185907 TAGTAAATAAGTCTTGGTGATTTACGAGTGTGATACTTCCCAATGATCTATATATCGACCACTGG
64 TAGTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGG
*
42185972 CCTCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGGGAATTCAATAAT
129 CCTCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAAT
*
42186037 CGATAATTATCTCTTATTTTACTTATGAGGTTACATATATCAGT
194 CGATAATTATCTCTTA-TTTACTTATGAGGTTACATATATCAGC
* *
42186081 GCTATATATAGAGAGGTTAATATGCAGTAAACAAGGGCCACAGAGAAGTGGAATGGTAAATGCTA
1 GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA
*
42186146 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATGTATCTACAACTGGCC
66 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC
* * **
42186211 TCCAACATTTGACTAGGAACTGATAACTAATGCTAATAATTTGTGTCTTGAGAATTCAATAATCG
131 TCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAATCG
* *
42186276 ATAATTATCTCTTATTTACCTATGAGGTTAAATATATCAGC
196 ATAATTATCTCTTATTTACTTATGAGGTTACATATATCAGC
*
42186317 GGTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA
1 GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA
42186382 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC
66 GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC
* * *
42186447 TCCAACATTTGTCCAGGAACTGATAACTAATGCTGATAATTACTATCTTGAGACTTCAATAATCG
131 TCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAATCG
42186512 ATAATTATCTCTTATTTACTTATGAGGTTACATATAT
196 ATAATTATCTCTTATTTACTTATGAGGTTACATATAT
42186549 ACGTGATATG
Statistics
Matches: 436, Mismatches: 32, Indels: 3
0.93 0.07 0.01
Matches are distributed among these distances:
236 243 0.56
237 136 0.31
238 2 0.00
239 55 0.13
ACGTcount: A:0.34, C:0.16, G:0.19, T:0.32
Consensus pattern (236 bp):
GCTATATATAGAGAGGTTAATATGCAGTAACCAAGGGCCACAGAGAAGTGGAATGGTCAATGCTA
GTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCAATGATCTATATATCTACAACTGGCC
TCCAACATTTGTCCAGGAACTGATAACTAATGCTAATAATTACTGTCTTGAGAATTCAATAATCG
ATAATTATCTCTTATTTACTTATGAGGTTACATATATCAGC
Found at i:42189218 original size:236 final size:237
Alignment explanation
Indices: 42188798--42189226 Score: 743
Period size: 236 Copynumber: 1.8 Consensus size: 237
42188788 GTTCTCCTAT
*
42188798 AGAGAAGTGGAATGGTCAATGCTATAGTAAATAAGTCTTGGTGATTTACGAGGGTGATACTTCCC
1 AGAGAAGTGGAATGGTCAATGC-ATAGTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCC
* * *
42188863 AATGATCTATATATCGACCACTGGCCTCCAACATTTGACTAGGAACTGATAACTAATGCTAATAA
65 AATGATCTATATATCGACAACTGGCCTCCAACATTTGACCAGGAACTGACAACTAATGCTAATAA
* *
42188928 TTTCTGTCTTGAGAATTCAATAATCGATAATTATCTCTTATTTACTTGTGAGGTTAAATATATCA
130 TTACTGTCTTGAGAATTCAATAATCGATAATTATCTCTTATTTACTTATGAGGTTAAATATATCA
42188993 GCGCTATATATAGAGAGGTTAATATGCAGAAACCAAGGGCAAC
195 GCGCTATATATAGAGAGGTTAATATGCAGAAACCAAGGGCAAC
42189036 AGAGAAGTGGAATGGTCAATGC-TAGTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCA
1 AGAGAAGTGGAATGGTCAATGCATAGTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCA
* * *
42189100 ATGATCTATATATCTACAACTGGCCTCCAACATTTGTCCAGGAACTGACAACTAATGCTGATAAT
66 ATGATCTATATATCGACAACTGGCCTCCAACATTTGACCAGGAACTGACAACTAATGCTAATAAT
* *
42189165 TACTGTCTTGAGACTTCAATAATCGATAATTATCTCTTATTTACTTATGAGGTTACATATAT
131 TACTGTCTTGAGAATTCAATAATCGATAATTATCTCTTATTTACTTATGAGGTTAAATATAT
42189227 AAGTGATATG
Statistics
Matches: 180, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
236 158 0.88
238 22 0.12
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.32
Consensus pattern (237 bp):
AGAGAAGTGGAATGGTCAATGCATAGTAAATAAGTCTTGGTGATTTACAAGGGTGATACTTCCCA
ATGATCTATATATCGACAACTGGCCTCCAACATTTGACCAGGAACTGACAACTAATGCTAATAAT
TACTGTCTTGAGAATTCAATAATCGATAATTATCTCTTATTTACTTATGAGGTTAAATATATCAG
CGCTATATATAGAGAGGTTAATATGCAGAAACCAAGGGCAAC
Found at i:42198262 original size:31 final size:31
Alignment explanation
Indices: 42198220--42198296 Score: 120
Period size: 31 Copynumber: 2.5 Consensus size: 31
42198210 ACTATAAAAA
42198220 TAGTCA-TTTTGTTTGCCTCAGGTTACATTT
1 TAGTCACTTTTGTTTGCCTCAGGTTACATTT
* *
42198250 TAGTCACTTTTGTTTGTCTTAGGTTACATTT
1 TAGTCACTTTTGTTTGCCTCAGGTTACATTT
*
42198281 TAGTCACTTATGTTTG
1 TAGTCACTTTTGTTTG
42198297 AAATGTTACG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 6 0.14
31 37 0.86
ACGTcount: A:0.17, C:0.14, G:0.17, T:0.52
Consensus pattern (31 bp):
TAGTCACTTTTGTTTGCCTCAGGTTACATTT
Found at i:42198492 original size:13 final size:15
Alignment explanation
Indices: 42198452--42198490 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
42198442 AATAGATTTT
42198452 TAAATTTTTAATTAA
1 TAAATTTTTAATTAA
42198467 TAAATTTAATTAATTAA
1 TAAATTT--TTAATTAA
42198484 -AAATTTT
1 TAAATTTT
42198491 AAACCCTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 1 0.05
15 7 0.32
16 6 0.27
17 8 0.36
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
TAAATTTTTAATTAA
Found at i:42200733 original size:18 final size:18
Alignment explanation
Indices: 42200710--42200748 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
42200700 TTTACCAACT
42200710 CCATTCTCCAAATTACCA
1 CCATTCTCCAAATTACCA
42200728 CCATTCTCCAAATTACCA
1 CCATTCTCCAAATTACCA
42200746 CCA
1 CCA
42200749 AGTCCGATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.33, C:0.41, G:0.00, T:0.26
Consensus pattern (18 bp):
CCATTCTCCAAATTACCA
Found at i:42209645 original size:51 final size:51
Alignment explanation
Indices: 42209569--42209669 Score: 177
Period size: 51 Copynumber: 2.0 Consensus size: 51
42209559 GGCTTCAAAA
42209569 GGGTGTCTTTGTTTACTGTTGGCTGAAT-TTAGGTATCATTCATATTCTCAT
1 GGGTGTCTTTGTTTACTGTTGGCTGAATGTT-GGTATCATTCATATTCTCAT
*
42209620 GGGTGTCTTTGTTTGCTGTTGGCTGAATGTTGGTATCATTCATATTCTCA
1 GGGTGTCTTTGTTTACTGTTGGCTGAATGTTGGTATCATTCATATTCTCA
42209670 AGGCTGTCAT
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
51 46 0.96
52 2 0.04
ACGTcount: A:0.16, C:0.14, G:0.24, T:0.47
Consensus pattern (51 bp):
GGGTGTCTTTGTTTACTGTTGGCTGAATGTTGGTATCATTCATATTCTCAT
Found at i:42209961 original size:1 final size:1
Alignment explanation
Indices: 42209955--42209991 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
42209945 CTTTGGCAGC
42209955 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
42209992 CTGAAGAACC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:42220455 original size:24 final size:23
Alignment explanation
Indices: 42220418--42220463 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
42220408 TGAAGTTAAA
42220418 TAAATGAATGATTAAATTAAAATT
1 TAAATGAATGATTAAA-TAAAATT
*
42220442 TAAAT-AATGAATTATATAAAAT
1 TAAATGAATG-ATTAAATAAAAT
42220464 AAATAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (23 bp):
TAAATGAATGATTAAATAAAATT
Found at i:42220467 original size:27 final size:28
Alignment explanation
Indices: 42220413--42220466 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
42220403 AGGTGTGAAG
*
42220413 TTAAATAAATGAATGATTAAATTAAAAT
1 TTAAATAAATGAATGATTAAAATAAAAT
*
42220441 TTAAAT-AATGAATTATATAAAATAAA
1 TTAAATAAATGAATGAT-TAAAATAAA
42220467 TAAATAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 9 0.39
28 14 0.61
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (28 bp):
TTAAATAAATGAATGATTAAAATAAAAT
Found at i:42220469 original size:4 final size:4
Alignment explanation
Indices: 42220460--42220493 Score: 50
Period size: 4 Copynumber: 8.0 Consensus size: 4
42220450 GAATTATATA
42220460 AAAT AAAT AAAT AAAT AAAT AAAT CAAAGT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAA-T AAAT
42220494 GACTAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 21 0.75
5 6 0.21
6 1 0.04
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:42224360 original size:119 final size:119
Alignment explanation
Indices: 42224149--42224389 Score: 473
Period size: 119 Copynumber: 2.0 Consensus size: 119
42224139 ACTTTTTCTT
42224149 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA
1 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA
42224214 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
66 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
42224268 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA
1 CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA
*
42224333 GGAGTAATTGTTAGATGATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
66 GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
42224387 CCA
1 CCA
42224390 CCCTCATTTG
Statistics
Matches: 121, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
119 121 1.00
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Consensus pattern (119 bp):
CCAATGCATCAAGCTGTTTAATGTTGAACTTATAGAGCAAATTTATGCTCGAAATAGTTGACATA
GGAGTAATTGTTAGATCATCCATGACCGTGTATGTAATGACCCCTTTTACGTAA
Found at i:42237891 original size:4 final size:4
Alignment explanation
Indices: 42237884--42237917 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
42237874 AGCTGTTTTT
* *
42237884 TTTA TTTA TTTA TCTA TTCA TTTA TTTA TTTA TT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT
42237918 ACCTTTTTTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:42238020 original size:17 final size:16
Alignment explanation
Indices: 42237968--42238027 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 16
42237958 TTTATGCATT
*
42237968 TTTTTATTATTGTCATTA
1 TTTTT-TTATT-TTATTA
42237986 TTATTTTTA-TTTATTTA
1 TT-TTTTTATTTTA-TTA
42238003 TTTTTGTTATTTTATTA
1 TTTTT-TTATTTTATTA
42238020 TTTCTTTT
1 TTT-TTTT
42238028 TGATATTTTC
Statistics
Matches: 36, Mismatches: 1, Indels: 11
0.75 0.02 0.23
Matches are distributed among these distances:
16 5 0.14
17 17 0.47
18 11 0.31
19 3 0.08
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.75
Consensus pattern (16 bp):
TTTTTTTATTTTATTA
Found at i:42238022 original size:21 final size:22
Alignment explanation
Indices: 42237990--42238036 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
42237980 TCATTATTAT
*
42237990 TTTTATTTATTTATTTTTGTTA
1 TTTTATTTATTTATTTTTGATA
*
42238012 TTTTA-TTATTTCTTTTTGATA
1 TTTTATTTATTTATTTTTGATA
42238033 TTTT
1 TTTT
42238037 CATGTTACGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.17, C:0.02, G:0.04, T:0.77
Consensus pattern (22 bp):
TTTTATTTATTTATTTTTGATA
Found at i:42240068 original size:13 final size:13
Alignment explanation
Indices: 42240041--42240087 Score: 76
Period size: 13 Copynumber: 3.5 Consensus size: 13
42240031 TTTTTAAGTT
42240041 TTTATTTATTTTTC
1 TTTATTTA-TTTTC
42240055 TTTATTTATTTTC
1 TTTATTTATTTTC
*
42240068 TTTATTTGTTTTC
1 TTTATTTATTTTC
42240081 TTTATTT
1 TTTATTT
42240088 GTTTATTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
13 24 0.75
14 8 0.25
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTATTTATTTTC
Found at i:42240079 original size:37 final size:36
Alignment explanation
Indices: 42240012--42240103 Score: 91
Period size: 37 Copynumber: 2.5 Consensus size: 36
42240002 TGATTTGTCC
*
42240012 TTTTTCATTTCTTT-TTTTCTTTTTAAGTTTTTATTTA
1 TTTTTC-TTTATTTATTTTCTTTTTAAG-TTTTATTTA
* *
42240049 TTTTTCTTTATTTATTTTCTTTATT-TGTTTTCTTTA
1 TTTTTCTTTATTTATTTTCTTT-TTAAGTTTTATTTA
42240085 TTTGTT-TATTATTTATTTT
1 TTT-TTCT-TTATTTATTTT
42240104 ATAAAATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
36 18 0.38
37 28 0.58
38 2 0.04
ACGTcount: A:0.13, C:0.07, G:0.03, T:0.77
Consensus pattern (36 bp):
TTTTTCTTTATTTATTTTCTTTTTAAGTTTTATTTA
Found at i:42240183 original size:13 final size:13
Alignment explanation
Indices: 42240167--42240191 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42240157 TTAAATATAT
42240167 TTTTTTAAAATTA
1 TTTTTTAAAATTA
42240180 TTTTTTAAAATT
1 TTTTTTAAAATT
42240192 TAAATATACA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTTTTAAAATTA
Found at i:42240186 original size:35 final size:34
Alignment explanation
Indices: 42240132--42240199 Score: 91
Period size: 35 Copynumber: 2.0 Consensus size: 34
42240122 ATTTGAAATG
* *
42240132 TTTTATAATATTATCTTTTACAATTTTAAATATAT
1 TTTTATAAAATTATCTTTTA-AAATTTAAATATAT
* *
42240167 TTTTTTAAAATTATTTTTTAAAATTTAAATATA
1 TTTTATAAAATTATCTTTTAAAATTTAAATATA
42240200 CAATATTTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 12 0.41
35 17 0.59
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (34 bp):
TTTTATAAAATTATCTTTTAAAATTTAAATATAT
Found at i:42240208 original size:50 final size:46
Alignment explanation
Indices: 42240154--42240245 Score: 112
Period size: 46 Copynumber: 1.9 Consensus size: 46
42240144 ATCTTTTACA
* *
42240154 ATTTTAAATATATTTTTTTAAAATTATTTTTTAAAATTTAAATATACAAT
1 ATTTTAAATATA-TATTTT-AAA-TATTCTTT-AAATTTAAATATACAAT
* *
42240204 ATTTTAAATGTATATTTTAAATATTCTTTAATTTTAAATATA
1 ATTTTAAATATATATTTTAAATATTCTTTAAATTTAAATATA
42240246 ATTTTTATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
46 12 0.32
47 7 0.18
48 3 0.08
49 5 0.13
50 11 0.29
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (46 bp):
ATTTTAAATATATATTTTAAATATTCTTTAAATTTAAATATACAAT
Found at i:42240226 original size:22 final size:22
Alignment explanation
Indices: 42240098--42240228 Score: 59
Period size: 22 Copynumber: 5.6 Consensus size: 22
42240088 GTTTATTATT
*
42240098 TATTTTATAAAATTTTAAATGTA
1 TATTTTA-AATATTTTAAATGTA
* * *
42240121 TATTTGAAATGTTTTATAATATTA
1 TATTTTAAATATTTTA-AAT-GTA
* * *
42240145 TCTTTTACA-ATTTTAAATATA
1 TATTTTAAATATTTTAAATGTA
* *
42240166 TTTTTTTAAAATTATTTTTTAAAATTTA
1 -TATTTT-AAA-TA--TTTT-AAATGTA
* *
42240194 -AATATACAATATTTTAAATGTA
1 TATTTTA-AATATTTTAAATGTA
42240216 TATTTTAAATATT
1 TATTTTAAATATT
42240229 CTTTAATTTT
Statistics
Matches: 79, Mismatches: 18, Indels: 23
0.66 0.15 0.19
Matches are distributed among these distances:
21 2 0.03
22 27 0.34
23 24 0.30
24 8 0.10
25 4 0.05
26 4 0.05
27 4 0.05
28 6 0.08
ACGTcount: A:0.40, C:0.02, G:0.03, T:0.54
Consensus pattern (22 bp):
TATTTTAAATATTTTAAATGTA
Found at i:42240252 original size:30 final size:28
Alignment explanation
Indices: 42240204--42240282 Score: 88
Period size: 30 Copynumber: 2.7 Consensus size: 28
42240194 AATATACAAT
* * *
42240204 ATTTTAAATGTATATTTTAAATATTCTTTA
1 ATTTTAAATATAT-TTTTAAA-ATTATTAA
42240234 ATTTTAAATATAATTTTTATAAATTATTAA
1 ATTTTAAATAT-ATTTTTA-AAATTATTAA
42240264 ATTTTAAA-ATATTTTTAAA
1 ATTTTAAATATATTTTTAAA
42240283 GATATTCAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
27 2 0.05
28 7 0.16
29 2 0.05
30 29 0.66
31 4 0.09
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (28 bp):
ATTTTAAATATATTTTTAAAATTATTAA
Found at i:42240317 original size:19 final size:21
Alignment explanation
Indices: 42240293--42240332 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 21
42240283 GATATTCAAA
42240293 AAAATTTT-AAATT-ATATTT
1 AAAATTTTAAAATTAATATTT
42240312 AAAATTTTAAAATTAATATTT
1 AAAATTTTAAAATTAATATTT
42240333 TATTTGGTGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 5 0.26
21 6 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AAAATTTTAAAATTAATATTT
Found at i:42240567 original size:16 final size:16
Alignment explanation
Indices: 42240543--42240573 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42240533 ATGAATAATG
42240543 ATGTGTTTTTTTATGT
1 ATGTGTTTTTTTATGT
*
42240559 ATGTTTTTTTTTATG
1 ATGTGTTTTTTTATG
42240574 GTGAAATTGT
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:0.13, C:0.00, G:0.16, T:0.71
Consensus pattern (16 bp):
ATGTGTTTTTTTATGT
Found at i:42245019 original size:25 final size:25
Alignment explanation
Indices: 42244991--42245053 Score: 67
Period size: 25 Copynumber: 2.6 Consensus size: 25
42244981 TACCGATTCG
42244991 CAGCTCATATGAGCTTACCG-TTATT
1 CAGCTCATATGAGCTTACCGTTTA-T
* * *
42245016 CAGCTCAAAAGAGTTTACCGTTTAT
1 CAGCTCATATGAGCTTACCGTTTAT
*
42245041 C-GCTCGTATGAGC
1 CAGCTCATATGAGC
42245054 ATACATGTAC
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
24 8 0.27
25 19 0.63
26 3 0.10
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.32
Consensus pattern (25 bp):
CAGCTCATATGAGCTTACCGTTTAT
Found at i:42249348 original size:21 final size:21
Alignment explanation
Indices: 42249301--42249349 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
42249291 GTTATAGTAT
**
42249301 ATATTTTTAATTTTTTAATTT
1 ATATTTTTAATTTTTTAATAC
* *
42249322 AAATTTTTACTTTTTTAATAC
1 ATATTTTTAATTTTTTAATAC
42249343 ATATTTT
1 ATATTTT
42249350 AAAAAAGTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (21 bp):
ATATTTTTAATTTTTTAATAC
Found at i:42249464 original size:23 final size:23
Alignment explanation
Indices: 42249438--42249481 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
42249428 TAAAATATTG
* *
42249438 TTTTTTTAAAATTTTAAATATAA
1 TTTTTTAAAAAGTTTAAATATAA
*
42249461 TTTTTTAAAAAGTTTGAATAT
1 TTTTTTAAAAAGTTTAAATAT
42249482 CTTTAAAAGT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTTTTAAAAAGTTTAAATATAA
Found at i:42249511 original size:25 final size:25
Alignment explanation
Indices: 42249483--42249530 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
42249473 TTTGAATATC
42249483 TTTAAAAGTAATT-TAAAA-AAATACA
1 TTTAAAA-T-ATTATAAAACAAATACA
42249508 TTTAAAATATTATAAAACAAATA
1 TTTAAAATATTATAAAACAAATA
42249531 ATAAATTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 6 0.29
25 12 0.57
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (25 bp):
TTTAAAATATTATAAAACAAATACA
Found at i:42249719 original size:22 final size:21
Alignment explanation
Indices: 42249694--42249760 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 21
42249684 AAAAACAATC
42249694 TAAAAGATATATATTTAAAATT
1 TAAAA-ATATATATTTAAAATT
42249716 TAAAAA-ATTATATTATAAAATAT
1 TAAAAATA-TATATT-TAAAAT-T
** *
42249739 TTCAAATATACATTTAAAATT
1 TAAAAATATATATTTAAAATT
42249760 T
1 T
42249761 TATAAAACAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
20 1 0.03
21 9 0.24
22 17 0.45
23 10 0.26
24 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (21 bp):
TAAAAATATATATTTAAAATT
Found at i:42259589 original size:10 final size:9
Alignment explanation
Indices: 42259560--42259589 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
42259550 TGTATATGCT
42259560 AAATAAGAA
1 AAATAAGAA
42259569 AAATAAGAA
1 AAATAAGAA
*
42259578 AAATATGAA
1 AAATAAGAA
42259587 AAA
1 AAA
42259590 CAGTACTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.77, C:0.00, G:0.10, T:0.13
Consensus pattern (9 bp):
AAATAAGAA
Found at i:42261166 original size:44 final size:44
Alignment explanation
Indices: 42261103--42261483 Score: 564
Period size: 44 Copynumber: 8.7 Consensus size: 44
42261093 TCATCTTCAA
* * * * *
42261103 CCTATTCCACTGCTAGTCAGGGAGCTAGGATTTACAGTCTTCTT
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCTT
* * * **
42261147 CCTATTCCATTGTTGGTCAGGGAGCTAGGACTTATAATCTTCTT
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCTT
**
42261191 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCCG
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCTT
* *
42261235 CCTATTCCACTGCTGGTCAGGGAACCAGGGCTTGCAATCTTCTT
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCTT
* *
42261279 CCTATTTCACTGCTGGTCAGGGAACTAGGTCTTGCAATCTTCTT
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCTT
* *
42261323 CCTATTCCACTGCTGGCCAGGGAACTAGGGCTTGCAATCTTCTT
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCTT
42261367 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCTT
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCTT
**
42261411 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCCA
1 CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCTT
* *
42261455 CCTATTCCACTGTTGGTCAGAGAACTAGG
1 CCTATTCCACTGCTGGTCAGGGAACTAGG
42261484 GCTTATAGTT
Statistics
Matches: 308, Mismatches: 29, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 308 1.00
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (44 bp):
CCTATTCCACTGCTGGTCAGGGAACTAGGACTTGCAATCTTCTT
Found at i:42272178 original size:10 final size:11
Alignment explanation
Indices: 42272110--42272176 Score: 54
Period size: 11 Copynumber: 6.4 Consensus size: 11
42272100 TAAAAATTAA
42272110 AAAAAGTATTTT
1 AAAAA-TATTTT
42272122 AAAAATATTTT
1 AAAAATATTTT
42272133 --AAA-A--TT
1 AAAAATATTTT
* **
42272139 AAAAAAATTAA
1 AAAAATATTTT
42272150 AAAAAGTATTTT
1 AAAAA-TATTTT
42272162 AAAAATATTTT
1 AAAAATATTTT
42272173 AAAA
1 AAAA
42272177 TAAAAAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
6 2 0.05
8 4 0.09
9 4 0.09
11 21 0.48
12 13 0.30
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:42272181 original size:39 final size:40
Alignment explanation
Indices: 42272083--42272225 Score: 207
Period size: 40 Copynumber: 3.5 Consensus size: 40
42272073 ACCAAAAATT
42272083 TATTTTAAAAATTAAAATAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATT--AA-AAAAATTAAAAAAAGTATTTTAAAAA
42272127 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
* * *
42272167 TATTTTAAAATAAAAAAAATT-AAAAAAGTATGTAAAAAA
1 TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
*
42272206 TATTTTAAAATTTAAAAAAT
1 TATTTTAAAATTAAAAAAAT
42272226 AAATATATTT
Statistics
Matches: 94, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
39 34 0.36
40 46 0.49
41 2 0.02
43 6 0.06
44 6 0.06
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (40 bp):
TATTTTAAAATTAAAAAAATTAAAAAAAGTATTTTAAAAA
Found at i:42281270 original size:15 final size:15
Alignment explanation
Indices: 42281246--42281281 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
42281236 TGTAAGGAGG
42281246 AAGAAATACAGTGTA
1 AAGAAATACAGTGTA
*
42281261 AAGAAGTACAGTGTA
1 AAGAAATACAGTGTA
*
42281276 AGGAAA
1 AAGAAA
42281282 GGAATAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.53, C:0.06, G:0.25, T:0.17
Consensus pattern (15 bp):
AAGAAATACAGTGTA
Found at i:42294109 original size:4 final size:4
Alignment explanation
Indices: 42294100--42294148 Score: 77
Period size: 4 Copynumber: 13.0 Consensus size: 4
42294090 AATATTGAGA
42294100 TAAT TAAT TAAT TAAT TAAT TAAT TAA- TAAT TAA- TAAT TAA- TAAT
1 TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT TAAT
42294145 TAAT
1 TAAT
42294149 GGTAAAATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
3 9 0.21
4 33 0.79
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (4 bp):
TAAT
Found at i:42294113 original size:8 final size:8
Alignment explanation
Indices: 42294100--42294148 Score: 77
Period size: 7 Copynumber: 6.5 Consensus size: 8
42294090 AATATTGAGA
42294100 TAATTAAT
1 TAATTAAT
42294108 TAATTAAT
1 TAATTAAT
42294116 TAATTAAT
1 TAATTAAT
42294124 TAA-TAAT
1 TAATTAAT
42294131 TAA-TAAT
1 TAATTAAT
42294138 TAA-TAAT
1 TAATTAAT
42294145 TAAT
1 TAAT
42294149 GGTAAAATTA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 21 0.52
8 19 0.47
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
TAATTAAT
Found at i:42305215 original size:42 final size:42
Alignment explanation
Indices: 42305151--42305302 Score: 202
Period size: 42 Copynumber: 3.6 Consensus size: 42
42305141 CAAACAAAAA
* *
42305151 CGCCGCTAAAGACCATGATCTTTAGCAGTGTTTCTTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGCAGTGTTTCTTTCTAAG
*
42305193 CGCCGCTAAAGAACATGGTCTTTAACGACGT-TTT-TTTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAGC-A-GTGTTTCTTTCTAAG
* *
42305235 CGCCGCTAAAGAACATGGTCTTTAGTGAGCGTTTC-TTCTAAG
1 CGCCGCTAAAGAACATGGTCTTTAG-CAGTGTTTCTTTCTAAG
*
42305277 CGCCGCTAAAGAACATAGTCTTTAGC
1 CGCCGCTAAAGAACATGGTCTTTAGC
42305303 GGCGTTTTAT
Statistics
Matches: 97, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
41 1 0.01
42 90 0.93
43 4 0.04
44 2 0.02
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (42 bp):
CGCCGCTAAAGAACATGGTCTTTAGCAGTGTTTCTTTCTAAG
Found at i:42305292 original size:84 final size:84
Alignment explanation
Indices: 42305151--42305310 Score: 241
Period size: 84 Copynumber: 1.9 Consensus size: 84
42305141 CAAACAAAAA
* * *
42305151 CGCCGCTAAAGACCATGATCTTTAGCAGTGTTTCTTTCTAAGCGCCGCTAAAGAACATGGTCTTT
1 CGCCGCTAAAGAACATGATCTTTAGCAGCGTTTCTTTCTAAGCGCCGCTAAAGAACATAGTCTTT
42305216 AACGACGTTTTTTTCTAAG
66 AACGACGTTTTTTTCTAAG
* *
42305235 CGCCGCTAAAGAACATGGTCTTTAGTGAGCGTTTC-TTCTAAGCGCCGCTAAAGAACATAGTCTT
1 CGCCGCTAAAGAACATGATCTTTAG-CAGCGTTTCTTTCTAAGCGCCGCTAAAGAACATAGTCTT
* *
42305299 TAGCGGCGTTTT
65 TAACGACGTTTT
42305311 ATACAAAAAC
Statistics
Matches: 68, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
84 61 0.90
85 7 0.10
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.32
Consensus pattern (84 bp):
CGCCGCTAAAGAACATGATCTTTAGCAGCGTTTCTTTCTAAGCGCCGCTAAAGAACATAGTCTTT
AACGACGTTTTTTTCTAAG
Found at i:42311731 original size:14 final size:14
Alignment explanation
Indices: 42311709--42311804 Score: 59
Period size: 14 Copynumber: 6.6 Consensus size: 14
42311699 CTTATCCGAC
42311709 CCCTGAAATCCTAAA
1 CCCT-AAATCCTAAA
42311724 CCCTAAATCCTAAA
1 CCCTAAATCCTAAA
* *
42311738 CCACT-AACCCTTAA
1 CC-CTAAATCCTAAA
* * *
42311752 CCCGTAACTCGTAAC
1 CCC-TAAATCCTAAA
*
42311767 CCCTAAACCCCTAAA
1 CCCTAAA-TCCTAAA
* * *
42311782 CCTTATATCCCAAA
1 CCCTAAATCCTAAA
*
42311796 CCTTAAATC
1 CCCTAAATC
42311805 AATACCCCCT
Statistics
Matches: 61, Mismatches: 16, Indels: 9
0.71 0.19 0.10
Matches are distributed among these distances:
13 1 0.02
14 38 0.62
15 22 0.36
ACGTcount: A:0.36, C:0.39, G:0.03, T:0.22
Consensus pattern (14 bp):
CCCTAAATCCTAAA
Found at i:42311990 original size:16 final size:16
Alignment explanation
Indices: 42311965--42311995 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42311955 AACCCCCTAA
*
42311965 CCCCTTACCCCTAAAT
1 CCCCTAACCCCTAAAT
42311981 CCCCTAACCCCTAAA
1 CCCCTAACCCCTAAA
42311996 GCATAACCTT
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:0.29, C:0.52, G:0.00, T:0.19
Consensus pattern (16 bp):
CCCCTAACCCCTAAAT
Found at i:42312372 original size:30 final size:30
Alignment explanation
Indices: 42312336--42312393 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
42312326 GGTATTTTTG
42312336 CGGCGCTTTCCCAAAAACGCCGCTAAATAA
1 CGGCGCTTTCCCAAAAACGCCGCTAAATAA
*
42312366 CGGCGCTTTCCTAAAAACGCCGCTAAAT
1 CGGCGCTTTCCCAAAAACGCCGCTAAAT
42312394 CCCCGACAGC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.31, C:0.33, G:0.17, T:0.19
Consensus pattern (30 bp):
CGGCGCTTTCCCAAAAACGCCGCTAAATAA
Found at i:42312439 original size:103 final size:103
Alignment explanation
Indices: 42312260--42312465 Score: 394
Period size: 103 Copynumber: 2.0 Consensus size: 103
42312250 CCTTGAGCAT
42312260 TAACGGCGCTTTCCTAAAAACGCCGCTAAATCCCCGACAGCTCAGAAAACGGCGTCGTTGGTCTT
1 TAACGGCGCTTTCCTAAAAACGCCGCTAAATCCCCGACAGCTCAGAAAACGGCGTCGTTGGTCTT
42312325 AGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAA
66 AGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAA
42312363 TAACGGCGCTTTCCTAAAAACGCCGCTAAATCCCCGACAGCTCAGAAAACGGCGTCGTTGGTCTT
1 TAACGGCGCTTTCCTAAAAACGCCGCTAAATCCCCGACAGCTCAGAAAACGGCGTCGTTGGTCTT
* *
42312428 AGGTATTTTTGCGGTGTTTTCCCAAAAACGCCGCTAAA
66 AGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAA
42312466 GCCCTGAGCA
Statistics
Matches: 101, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 101 1.00
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.24
Consensus pattern (103 bp):
TAACGGCGCTTTCCTAAAAACGCCGCTAAATCCCCGACAGCTCAGAAAACGGCGTCGTTGGTCTT
AGGTATTTTTGCGGCGCTTTCCCAAAAACGCCGCTAAA
Found at i:42312637 original size:40 final size:38
Alignment explanation
Indices: 42312551--42312637 Score: 97
Period size: 40 Copynumber: 2.2 Consensus size: 38
42312541 TAGGTATTTT
* *
42312551 GCGGCGTTTTCTGGAAACGCCGCTAATGTTTATTTTCA
1 GCGGCGTTTTCTGGAAACGCCACTAATGTCTATTTTCA
*
42312589 GCGGCGTTTTCCAT-GAAGCGCCACTAATGATCTATCTTT-A
1 GCGGCGTTTT-C-TGGAAACGCCACTAATG-TCTAT-TTTCA
42312629 GCGGCGTTT
1 GCGGCGTTT
42312638 GTTATCCAAC
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
38 10 0.24
39 14 0.33
40 15 0.36
41 3 0.07
ACGTcount: A:0.18, C:0.23, G:0.24, T:0.34
Consensus pattern (38 bp):
GCGGCGTTTTCTGGAAACGCCACTAATGTCTATTTTCA
Found at i:42316828 original size:60 final size:60
Alignment explanation
Indices: 42316730--42316857 Score: 238
Period size: 60 Copynumber: 2.1 Consensus size: 60
42316720 TTTATGCATT
*
42316730 TATGATTGTATTTTTCTTCAAGATTTTTTATTGTCATAGTTATCTTGATGAACATATCTA
1 TATGGTTGTATTTTTCTTCAAGATTTTTTATTGTCATAGTTATCTTGATGAACATATCTA
*
42316790 TATGGTTGTATTTTTCTTCAAGGTTTTTTATTGTCATAGTTATCTTGATGAACATATCTA
1 TATGGTTGTATTTTTCTTCAAGATTTTTTATTGTCATAGTTATCTTGATGAACATATCTA
42316850 TATGGTTG
1 TATGGTTG
42316858 ATACAAGCCC
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.52
Consensus pattern (60 bp):
TATGGTTGTATTTTTCTTCAAGATTTTTTATTGTCATAGTTATCTTGATGAACATATCTA
Found at i:42318527 original size:12 final size:12
Alignment explanation
Indices: 42318494--42318533 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
42318484 TGTTCATTCA
*
42318494 TTCATCAAGTGTT
1 TTCATCAAG-CTT
42318507 TTCCATCAAGCTT
1 TT-CATCAAGCTT
42318520 TTCATCAAGCTT
1 TTCATCAAGCTT
42318532 TT
1 TT
42318534 ATGTCCTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
12 12 0.48
13 6 0.24
14 7 0.28
ACGTcount: A:0.23, C:0.23, G:0.10, T:0.45
Consensus pattern (12 bp):
TTCATCAAGCTT
Found at i:42321097 original size:109 final size:109
Alignment explanation
Indices: 42320906--42321125 Score: 422
Period size: 109 Copynumber: 2.0 Consensus size: 109
42320896 TACCAGTGTA
*
42320906 TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTGCTGCT
1 TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTACTGCT
42320971 GTCCTGGCTGTTTTTTATTCTTACAAGTAAAGAAATGTTTTCTG
66 GTCCTGGCTGTTTTTTATTCTTACAAGTAAAGAAATGTTTTCTG
42321015 TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTACTGCT
1 TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTACTGCT
*
42321080 GTCCTGGCTGTTTTTTATTCTTACAAGTGAAGAAATGTTTTCTG
66 GTCCTGGCTGTTTTTTATTCTTACAAGTAAAGAAATGTTTTCTG
42321124 TT
1 TT
42321126 GGCTGGTCCA
Statistics
Matches: 109, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
109 109 1.00
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.37
Consensus pattern (109 bp):
TTCCTTACCCAAAAGGCTTGGAAGACGGGTTCTAAGTGGTCGAAATGCTTGATGCTTCTACTGCT
GTCCTGGCTGTTTTTTATTCTTACAAGTAAAGAAATGTTTTCTG
Found at i:42324021 original size:41 final size:42
Alignment explanation
Indices: 42323976--42324082 Score: 101
Period size: 41 Copynumber: 2.6 Consensus size: 42
42323966 ATCTATAGTA
* *
42323976 GCGTTTTTATCTGAGCGCCGCTAAT-TCCCCGATCTTTAGGG
1 GCGTTTTTATATGAGCGCCGCTAATATCCCCGATCTTTAGCG
** * * * *
42324017 GCGTTTCCATATGAACGCCGC-AATATCTCTGGTCTTTAGCG
1 GCGTTTTTATATGAGCGCCGCTAATATCCCCGATCTTTAGCG
* * *
42324058 GCGATTTTATTTCAGCGCCGCTAAT
1 GCGTTTTTATATGAGCGCCGCTAAT
42324083 GCTTGCATCT
Statistics
Matches: 50, Mismatches: 14, Indels: 3
0.75 0.21 0.04
Matches are distributed among these distances:
40 3 0.06
41 44 0.88
42 3 0.06
ACGTcount: A:0.18, C:0.26, G:0.22, T:0.34
Consensus pattern (42 bp):
GCGTTTTTATATGAGCGCCGCTAATATCCCCGATCTTTAGCG
Found at i:42324174 original size:41 final size:41
Alignment explanation
Indices: 42324129--42324240 Score: 120
Period size: 41 Copynumber: 2.7 Consensus size: 41
42324119 GCTCTTTGCA
* * *
42324129 TTTAGCGGCGATTTTGTATAAGCGCCGCTAATGCT-CGGAT
1 TTTAGCGGCGATTTTATCTAAGCGCCGCTAATCCTCCGGAT
* * * *
42324169 CTTTAGTGACGTTTTTATCTAAGCGCCAG-TAATCCTCCGGCT
1 -TTTAGCGGCGATTTTATCTAAGCGCC-GCTAATCCTCCGGAT
*
42324211 TTTAGCGGCGGTTTTATCTAAGCGCCGCTA
1 TTTAGCGGCGATTTTATCTAAGCGCCGCTA
42324241 GTTTATTACC
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
40 1 0.02
41 52 0.90
42 5 0.09
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (41 bp):
TTTAGCGGCGATTTTATCTAAGCGCCGCTAATCCTCCGGAT
Found at i:42324236 original size:82 final size:78
Alignment explanation
Indices: 42324051--42324240 Score: 202
Period size: 78 Copynumber: 2.4 Consensus size: 78
42324041 ATCTCTGGTC
* * * *
42324051 TTTAGCGGCGATTTTATTTCAGCGCCGCTAATGCTTGCATCTTTAGTGGTTATTCTGAGCGCCAC
1 TTTAGCGGCGATTTTATATAAGCGCCGCTAATGCTCGCATCTTTAGTGGTTATTCTAAGCGCCAC
* **
42324116 TATGCTCTTTGCA
66 TATCCTCTCGGCA
* * *
42324129 TTTAGCGGCGATTTTGTATAAGCGCCGCTAATGCTCGGATCTTTAGTGACGTTTTTATCTAAGCG
1 TTTAGCGGCGATTTTATATAAGCGCCGCTAATGCTCGCATCTTTAGTG--G-TTAT-TCTAAGCG
* *
42324194 CCAGTAATCCTC-CGGCT
62 CCACT-ATCCTCTCGGCA
* *
42324211 TTTAGCGGCGGTTTTATCTAAGCGCCGCTA
1 TTTAGCGGCGATTTTATATAAGCGCCGCTA
42324241 GTTTATTACC
Statistics
Matches: 92, Mismatches: 15, Indels: 6
0.81 0.13 0.05
Matches are distributed among these distances:
78 43 0.47
80 1 0.01
81 3 0.03
82 40 0.43
83 5 0.05
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (78 bp):
TTTAGCGGCGATTTTATATAAGCGCCGCTAATGCTCGCATCTTTAGTGGTTATTCTAAGCGCCAC
TATCCTCTCGGCA
Found at i:42324789 original size:14 final size:14
Alignment explanation
Indices: 42324769--42324807 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
42324759 TTTAAGGTTA
42324769 ATTTAGGGTTAGAG
1 ATTTAGGGTTAGAG
* *
42324783 GTTTAGGGGTTTGAG
1 ATTTA-GGGTTAGAG
42324798 ATTTAGGGTT
1 ATTTAGGGTT
42324808 TCAACGGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.21, C:0.00, G:0.38, T:0.41
Consensus pattern (14 bp):
ATTTAGGGTTAGAG
Found at i:42324808 original size:14 final size:14
Alignment explanation
Indices: 42324742--42324808 Score: 59
Period size: 14 Copynumber: 4.9 Consensus size: 14
42324732 TACGGGGTAT
* *
42324742 AGATTTAAGGTTTA
1 AGATTTAGGGTTTG
*
42324756 AGATTTAAGG-TT-
1 AGATTTAGGGTTTG
*
42324768 A-ATTTAGGGTTAG
1 AGATTTAGGGTTTG
*
42324781 AGGTTTAGGGGTTTG
1 AGATTTA-GGGTTTG
42324796 AGATTTAGGGTTT
1 AGATTTAGGGTTT
42324809 CAACGGTCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
11 7 0.16
12 2 0.05
13 3 0.07
14 20 0.45
15 12 0.27
ACGTcount: A:0.27, C:0.00, G:0.31, T:0.42
Consensus pattern (14 bp):
AGATTTAGGGTTTG
Found at i:42325959 original size:90 final size:90
Alignment explanation
Indices: 42325847--42326029 Score: 350
Period size: 90 Copynumber: 2.0 Consensus size: 90
42325837 TTAGATTGAT
42325847 TAAATTGATTGGTAATATGAAGATTACAAGGTTAATTTATAATTTGAGACTTGTTAAATGATACA
1 TAAATTGATTGGTAATATGAAGATTACAAGGTTAATTTATAATTTGAGACTTGTTAAATGATACA
42325912 ATATAACTAATATATACTAGTTATA
66 ATATAACTAATATATACTAGTTATA
42325937 TAAATTG-TTGGTTAATATGAAGATTACAAGGTTAATTTATAATTTGAGACTTGTTAAATGATAC
1 TAAATTGATTGG-TAATATGAAGATTACAAGGTTAATTTATAATTTGAGACTTGTTAAATGATAC
42326001 AATATAACTAATATATACTAGTTATA
65 AATATAACTAATATATACTAGTTATA
42326027 TAA
1 TAA
42326030 TTAAAAACAT
Statistics
Matches: 92, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
89 4 0.04
90 88 0.96
ACGTcount: A:0.42, C:0.05, G:0.13, T:0.39
Consensus pattern (90 bp):
TAAATTGATTGGTAATATGAAGATTACAAGGTTAATTTATAATTTGAGACTTGTTAAATGATACA
ATATAACTAATATATACTAGTTATA
Found at i:42326220 original size:27 final size:27
Alignment explanation
Indices: 42326190--42326241 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
42326180 AATAAACAAA
* *
42326190 TAAATAAGTAAGTAATTATTTATTTGT
1 TAAATAAATAAGTAATTAATTATTTGT
**
42326217 TAAATAAATTGGTAATTAATTATTT
1 TAAATAAATAAGTAATTAATTATTT
42326242 AAATGTAAGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.10, T:0.48
Consensus pattern (27 bp):
TAAATAAATAAGTAATTAATTATTTGT
Found at i:42329232 original size:23 final size:23
Alignment explanation
Indices: 42329183--42329233 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
42329173 CATCTTTGAT
* *
42329183 ATATATATTTATATACAGTTTTA
1 ATATATATTTATATAAAATTTTA
42329206 ATATATATTTAT-TAAAATTTTA
1 ATATATATTTATATAAAATTTTA
42329228 CATATA
1 -ATATA
42329234 CTTGAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 8 0.32
23 17 0.68
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATATATTTATATAAAATTTTA
Found at i:42329345 original size:16 final size:16
Alignment explanation
Indices: 42329284--42329362 Score: 74
Period size: 16 Copynumber: 5.0 Consensus size: 16
42329274 ACACATAGCC
* *
42329284 TACATGACTTACTTAA
1 TACATAACTTACATAA
* *
42329300 TACACAACTTAAATAA
1 TACATAACTTACATAA
*
42329316 TTTAAATAACTTACATAA
1 --TACATAACTTACATAA
42329334 TACATAACTTACAT--
1 TACATAACTTACATAA
42329348 T-CATAACTTACATAA
1 TACATAACTTACATAA
42329363 ACTTATATGT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
13 12 0.24
14 1 0.02
16 25 0.49
18 13 0.25
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:42329354 original size:13 final size:15
Alignment explanation
Indices: 42329321--42329361 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 15
42329311 AATAATTTAA
42329321 ATAACTTACATAATAC
1 ATAACTTACAT-ATAC
42329337 ATAACTTACAT-T-C
1 ATAACTTACATATAC
42329350 ATAACTTACATA
1 ATAACTTACATA
42329362 AACTTATATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 12 0.50
14 1 0.04
16 11 0.46
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAACTTACATATAC
Found at i:42329487 original size:27 final size:24
Alignment explanation
Indices: 42329433--42329491 Score: 73
Period size: 27 Copynumber: 2.3 Consensus size: 24
42329423 ATACATAGCA
42329433 TACATAACAAATATAAACAAAACT
1 TACATAACAAATATAAACAAAACT
* *
42329457 TACATAACTTAAATATATTACACAACT
1 TACATAAC--AAATATA-AACAAAACT
42329484 TACATAAC
1 TACATAAC
42329492 CTGGAATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
24 8 0.27
26 7 0.23
27 15 0.50
ACGTcount: A:0.54, C:0.19, G:0.00, T:0.27
Consensus pattern (24 bp):
TACATAACAAATATAAACAAAACT
Found at i:42332439 original size:43 final size:43
Alignment explanation
Indices: 42332392--42332821 Score: 212
Period size: 43 Copynumber: 10.0 Consensus size: 43
42332382 ATTGTGGCGT
* * *
42332392 TTTTTTGCATAAGCGCCGCGAAAGATCCCCGTCTGTAGTGGCA
1 TTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGCA
* * * *
42332435 TTTTTAG-ACTAAGCGCCGCAAAAGAACCCTATCTATCGTGGCA
1 TTTTTTGCA-TAAGCGCCGCGAAAGAACCCCATCTATAGTGGCA
* * * *
42332478 TTTCTTGCATAAGCGCCG-GAAAAGAACCTCATCTATCGTGGCG
1 TTTTTTGCATAAGCGCCGCG-AAAGAACCCCATCTATAGTGGCA
** ** * * *
42332521 TTTCCTATAGAAGCGCCG-GAGAAGAACCCTATCTATAGTGGCG
1 TTTTTTGCATAAGCGCCGCGA-AAGAACCCCATCTATAGTGGCA
* * * *
42332564 TTTCTTGTATAAGCGCCG-GAAAAGAACCCTC-TCTCTAGTGGCG
1 TTTTTTGCATAAGCGCCGCG-AAAGAACCC-CATCTATAGTGGCA
* * * * * * * *
42332607 TTTGTTGTACAAGCGCCGCTATAGAACCCAAGCTATAGTGGCGT
1 TTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGC-A
* * * * * *
42332651 TTTTTTGTATAAGCGCCGCTATAG-ATCACATCTATAGTGGCG
1 TTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGCA
** * * * * * *
42332693 TTTTGAGTATAATCGCC-AGAATAGACCCACCCTCTATAGTGGCG
1 TTTTTTGCATAAGCGCCGCGAA-AGAACC-CCATCTATAGTGGCA
* * * * ** * *
42332737 TTTTTCGGATAAGCGCCGCTAGAGAGGCCGATCTATAGTGGCG
1 TTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGCA
* * *
42332780 TTTTGTATG--TAAGCGCCGCTAAAGAGCCACATCTATAGTGGC
1 TTTT-T-TGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGC
42332822 GCGGCAAAAG
Statistics
Matches: 306, Mismatches: 66, Indels: 30
0.76 0.16 0.07
Matches are distributed among these distances:
41 1 0.00
42 18 0.06
43 230 0.75
44 55 0.18
45 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27
Consensus pattern (43 bp):
TTTTTTGCATAAGCGCCGCGAAAGAACCCCATCTATAGTGGCA
Found at i:42332689 original size:86 final size:84
Alignment explanation
Indices: 42332380--42332822 Score: 293
Period size: 86 Copynumber: 5.1 Consensus size: 84
42332370 AAAACACAGC
* * * * *
42332380 CTATTGTGGCGTTTTTTTGCATAAGCGCCGCGAAAGATCCCCGTCTGTAGTGGCATTTTTAG-AC
1 CTATAGTGGCG-TTTTTTGCATAAGCGCCGCAAAAGAT-CCCATCTATAGTGGCGTTTTT-GTAC
*
42332444 TAAGCGCCGCAAAAGAACCCTAT
63 -AAGCGCCGCAAAAGAACCCAAT
* * * * * * * * *
42332467 CTATCGTGGCATTTCTTGCATAAGCGCCGGAAAAGAACCTCATCTATCGTGGCGTTTCCTATAGA
1 CTATAGTGGCGTTTTTTGCATAAGCGCCGCAAAAGATCC-CATCTATAGTGGCGTTT-TTGTACA
* * *
42332532 AGCGCCGGAGAAGAACCCTAT
64 AGCGCCGCAAAAGAACCCAAT
* * * * * *
42332553 CTATAGTGGCGTTTCTTGTATAAGCGCCGGAAAAGAACCCTCTCTCTAGTGGCGTTTGTTGTACA
1 CTATAGTGGCGTTTTTTGCATAAGCGCCGCAAAAGATCCC-ATCTATAGTGGCGTTT-TTGTACA
* * *
42332618 AGCGCCGCTATAGAACCCAAG
64 AGCGCCGCAAAAGAACCCAAT
* * * * * *
42332639 CTATAGTGGCGTTTTTTTGTATAAGCGCCGCTATAGATCACATCTATAGTGGCGTTTTGAGTATA
1 CTATAGTGGCG-TTTTTTGCATAAGCGCCGCAAAAGATCCCATCTATAGTGGCGTTTT-TGTACA
* * *
42332704 ATCGCCAG-AATAG-ACCCACCCT
64 AGCGCC-GCAAAAGAACCCA--AT
* * * * * * *
42332726 CTATAGTGGCGTTTTTCGGATAAGCGCCGCTAGAGAGGCCGATCTATAGTGGCG-TTTTGTATGT
1 CTATAGTGGCGTTTTTTGCATAAGCGCCGCAAAAGA-TCCCATCTATAGTGGCGTTTTTGTA--C
* *
42332790 AAGCGCCGCTAAAG-AGCCACAT
63 AAGCGCCGCAAAAGAACCCA-AT
42332812 CTATAGTGGCG
1 CTATAGTGGCG
42332823 CGGCAAAAGA
Statistics
Matches: 286, Mismatches: 57, Indels: 27
0.77 0.15 0.07
Matches are distributed among these distances:
85 12 0.04
86 200 0.70
87 74 0.26
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.28
Consensus pattern (84 bp):
CTATAGTGGCGTTTTTTGCATAAGCGCCGCAAAAGATCCCATCTATAGTGGCGTTTTTGTACAAG
CGCCGCAAAAGAACCCAAT
Found at i:42337955 original size:21 final size:21
Alignment explanation
Indices: 42337930--42337985 Score: 103
Period size: 21 Copynumber: 2.7 Consensus size: 21
42337920 AAACGATATA
*
42337930 GTTTTGTCTTTTAATATAATG
1 GTTTTGACTTTTAATATAATG
42337951 GTTTTGACTTTTAATATAATG
1 GTTTTGACTTTTAATATAATG
42337972 GTTTTGACTTTTAA
1 GTTTTGACTTTTAA
42337986 CTTTAAAAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.25, C:0.05, G:0.14, T:0.55
Consensus pattern (21 bp):
GTTTTGACTTTTAATATAATG
Found at i:42343857 original size:87 final size:87
Alignment explanation
Indices: 42343711--42343973 Score: 508
Period size: 87 Copynumber: 3.0 Consensus size: 87
42343701 AAGTACTAGT
42343711 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
1 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
42343776 ATGTTTTTAATGGCTCCTTGAG
66 ATGTTTTTAATGGCTCCTTGAG
42343798 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
1 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
42343863 ATGTTTTTAATGGCTCCTTGAG
66 ATGTTTTTAATGGCTCCTTGAG
42343885 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
1 TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
* *
42343950 ATGTTCTTAACGGCTCCTTGAG
66 ATGTTTTTAATGGCTCCTTGAG
42343972 TC
1 TC
42343974 CCACCACTGT
Statistics
Matches: 174, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
87 174 1.00
ACGTcount: A:0.22, C:0.17, G:0.23, T:0.38
Consensus pattern (87 bp):
TCAAAGTATTATTTGATAGTGTTCCTCTCGTGGTTGCCAACACTGCTAGGTTGAAGTTTCGAGTA
ATGTTTTTAATGGCTCCTTGAG
Found at i:42345661 original size:33 final size:33
Alignment explanation
Indices: 42345619--42345688 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
42345609 GAAAGACATT
42345619 TCTGTTTGAATTTATTTCCAAGTCATTTAGGTA
1 TCTGTTTGAATTTATTTCCAAGTCATTTAGGTA
42345652 TCTGTTTGAATTTATTTCCAAGTCATTTAGGTA
1 TCTGTTTGAATTTATTTCCAAGTCATTTAGGTA
42345685 TCTG
1 TCTG
42345689 CCACATCTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.23, C:0.13, G:0.16, T:0.49
Consensus pattern (33 bp):
TCTGTTTGAATTTATTTCCAAGTCATTTAGGTA
Found at i:42350439 original size:224 final size:225
Alignment explanation
Indices: 42350038--42350488 Score: 895
Period size: 224 Copynumber: 2.0 Consensus size: 225
42350028 TAATTTTTTG
42350038 AATATATAATATCTTTTGATCTTTGAAATGATAGTATTTTTTTTTTGTAATAAATAATGAATTAT
1 AATATATAATATCTTTTGATCTTTGAAATGATAGTATTTTTTTTTTGTAATAAATAATGAATTAT
42350103 TTTCATATGAAGTGATTCAAAAATTTATAAGTTGGATAAAATCTTTATGTTATTCAATATTTCTA
66 TTTCATATGAAGTGATTCAAAAATTTATAAGTTGGATAAAATCTTTATGTTATTCAATATTTCTA
42350168 ATATTATTCATATTCTTTAACATTTTAATTATTATGTTGATTATTTAAGACTTTACAATGATATC
131 ATATTATTCATATTCTTTAACATTTTAATTATTATGTTGATTATTTAAGACTTTACAATGATATC
42350233 CTTTACATGCATTAATGCATGTGAGATAAA
196 CTTTACATGCATTAATGCATGTGAGATAAA
42350263 AATATATAAT-TCTTTTGATCTTTGAAATGATAGTATTTTTTTTTTGTAATAAATAATGAATTAT
1 AATATATAATATCTTTTGATCTTTGAAATGATAGTATTTTTTTTTTGTAATAAATAATGAATTAT
42350327 TTTCATATGAAGTGATTCAAAAATTTATAAGTTGGATAAAATCTTTATGTTATTCAATATTTCTA
66 TTTCATATGAAGTGATTCAAAAATTTATAAGTTGGATAAAATCTTTATGTTATTCAATATTTCTA
42350392 ATATTATTCATATTCTTTAACATTTTAATTATTATGTTGATTATTTAAGACTTTACAATGATATC
131 ATATTATTCATATTCTTTAACATTTTAATTATTATGTTGATTATTTAAGACTTTACAATGATATC
42350457 CTTTACATGCATTAATGCATGTGAGATAAA
196 CTTTACATGCATTAATGCATGTGAGATAAA
42350487 AA
1 AA
42350489 AAAAACTAGT
Statistics
Matches: 226, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
224 216 0.96
225 10 0.04
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.47
Consensus pattern (225 bp):
AATATATAATATCTTTTGATCTTTGAAATGATAGTATTTTTTTTTTGTAATAAATAATGAATTAT
TTTCATATGAAGTGATTCAAAAATTTATAAGTTGGATAAAATCTTTATGTTATTCAATATTTCTA
ATATTATTCATATTCTTTAACATTTTAATTATTATGTTGATTATTTAAGACTTTACAATGATATC
CTTTACATGCATTAATGCATGTGAGATAAA
Found at i:42357408 original size:16 final size:17
Alignment explanation
Indices: 42357387--42357421 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
42357377 GACATGAAAT
42357387 TAATAAAATAAATA-AA
1 TAATAAAATAAATATAA
*
42357403 TAATAATATAAATATAA
1 TAATAAAATAAATATAA
42357420 TA
1 TA
42357422 GCATTCCCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATAAAATAAATATAA
Found at i:42357891 original size:21 final size:22
Alignment explanation
Indices: 42357865--42357909 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
42357855 ATCATAGTAG
*
42357865 AATAATAAT-TTTATTATTTTT
1 AATAATAATATTAATTATTTTT
*
42357886 AATAATACTATTAATTATTTTT
1 AATAATAATATTAATTATTTTT
42357908 AA
1 AA
42357910 GTACAATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
AATAATAATATTAATTATTTTT
Found at i:42366109 original size:47 final size:48
Alignment explanation
Indices: 42365984--42366368 Score: 160
Period size: 49 Copynumber: 8.1 Consensus size: 48
42365974 AAAAAAAAAC
* * * *
42365984 AAAAAAAATTTTTAGTGCTGGCCTGTCAATGGTCGGCACTAGTATATGA
1 AAAAAAAAATTTT-GTGCTGGCCTGTCAATGGTCGGCACCAATATACGA
* * * * *
42366033 AAAAAAAAATTTAGGCGCT-GCCTTATCAATTGTCAGCACCAATATACG-
1 AAAAAAAAATTT-TGTGCTGGCC-TGTCAATGGTCGGCACCAATATACGA
**
42366081 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCACCAGTAC--
1 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAATA-TACGA
** * * **
42366128 --AAAAAAA-TTTGTTTTGG-GTG-C--TGGCCGGCACCAGCAGTACG-
1 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAATA-TACGA
* * * * ** *
42366169 AAAAAAAATTTTATGTGCTGGTCTATCAATGGCCGGCACCACCAGTATGA
1 AAAAAAAAATTT-TGTGCTGGCCTGTCAATGGTCGGCACCAATA-TACGA
** * * ** *
42366219 AAAAAAATTTTTTGGTGCTGCCCTGTCAAT-GTCCGGTACCAGCAGTATG-
1 AAAAAAAAATTTT-GTGCTGGCCTGTCAATGGT-CGGCACCAATA-TACGA
** * * *
42366268 AAAAAAAAATTTTGGGTGCTAACCTGTGAATGGCCGGCACCAAT-T--TA
1 AAAAAAAAATTTT--GTGCTGGCCTGTCAATGGTCGGCACCAATATACGA
* * **
42366315 AAAAAAAAA-TTGGTGTTGGCCTGTCAATGACCGAG-ACCAATATACGA
1 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCG-GCACCAATATACGA
42366362 AAAAAAA
1 AAAAAAA
42366369 TTTAGGTGCT
Statistics
Matches: 261, Mismatches: 52, Indels: 48
0.72 0.14 0.13
Matches are distributed among these distances:
40 17 0.07
42 1 0.00
43 8 0.03
44 32 0.12
45 15 0.06
46 3 0.01
47 38 0.15
48 22 0.08
49 65 0.25
50 59 0.23
51 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.25
Consensus pattern (48 bp):
AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAATATACGA
Found at i:42366134 original size:49 final size:48
Alignment explanation
Indices: 42365984--42366309 Score: 208
Period size: 49 Copynumber: 6.8 Consensus size: 48
42365974 AAAAAAAAAC
* * * *
42365984 AAAAAAAATTTTTAGTGCTGGCCTGTCAATGGTCGGCACTAGTA-TATG
1 AAAAAAAAATTTT-GTGCTGGCCTGTCAATGGTCGGCACCAGCAGTACG
* * * * * **
42366032 AAAAAAAAAATTTAGGCGCT-GCCTTATCAATTGTCAGCACCAATA-TACG
1 -AAAAAAAAATTT-TGTGCTGGCC-TGTCAATGGTCGGCACCAGCAGTACG
*
42366081 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCACCAGTAC-
1 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTACG
** * *
42366128 --AAAAAAA-TTTGTTTTGG-GTG-C--TGGCCGGCACCAGCAGTACG
1 AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTACG
* * * * * *
42366169 AAAAAAAATTTTATGTGCTGGTCTATCAATGGCCGGCACCACCAGTATG
1 AAAAAAAAATTT-TGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTACG
* * * *
42366218 AAAAAAAATTTTTTGGTGCTGCCCTGTCAAT-GTCCGGTACCAGCAGTATG
1 AAAAAAAA-ATTTT-GTGCTGGCCTGTCAATGGT-CGGCACCAGCAGTACG
** * *
42366268 AAAAAAAAATTTTGGGTGCTAACCTGTGAATGGCCGGCACCA
1 AAAAAAAAATTTT--GTGCTGGCCTGTCAATGGTCGGCACCA
42366310 ATTTAAAAAA
Statistics
Matches: 219, Mismatches: 40, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
40 17 0.08
42 1 0.00
43 8 0.04
44 10 0.05
45 13 0.06
46 1 0.00
47 21 0.10
48 21 0.10
49 66 0.30
50 60 0.27
51 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.26
Consensus pattern (48 bp):
AAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCAGCAGTACG
Found at i:42366198 original size:89 final size:87
Alignment explanation
Indices: 42366077--42366238 Score: 236
Period size: 89 Copynumber: 1.8 Consensus size: 87
42366067 AGCACCAATA
* * *
42366077 TACGAAAAAAAAATTTTGTGCTGGCCTGTCAATGGTCGGCACCACCAGTA-CAAAAAAATTTGTT
1 TACGAAAAAAAAATTTTGTGCTGGCCTATCAATGGCCGGCACCACCAGTATCAAAAAAAATT-TT
42366141 TTGGGTGCTGGCCGGCACCAGCAG
65 TT-GGTGCTGGCCGGCACCAGCAG
* * *
42366165 TACGAAAAAAAATTTTATGTGCTGGTCTATCAATGGCCGGCACCACCAGTATGAAAAAAAATTTT
1 TACGAAAAAAAAATTT-TGTGCTGGCCTATCAATGGCCGGCACCACCAGTATCAAAAAAAATTTT
42366230 TTGGTGCTG
65 TTGGTGCTG
42366239 CCCTGTCAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
88 22 0.33
89 35 0.53
90 9 0.14
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.27
Consensus pattern (87 bp):
TACGAAAAAAAAATTTTGTGCTGGCCTATCAATGGCCGGCACCACCAGTATCAAAAAAAATTTTT
TGGTGCTGGCCGGCACCAGCAG
Found at i:42366248 original size:50 final size:50
Alignment explanation
Indices: 42366149--42366309 Score: 198
Period size: 50 Copynumber: 3.2 Consensus size: 50
42366139 TTTTGGGTGC
* * ** *
42366149 TGGCCGGCACCAGCAGTACGAAAAAAAATTTTAT-GTGCTGGTCTATCAA
1 TGGCCGGCACCAGCAGTATGAAAAAAAATTTTTTGGTGCTGACCTGTCAA
* *
42366198 TGGCCGGCACCACCAGTATGAAAAAAAATTTTTTGGTGCTGCCCTGTCAA
1 TGGCCGGCACCAGCAGTATGAAAAAAAATTTTTTGGTGCTGACCTGTCAA
* * * * * *
42366248 TGTCCGGTACCAGCAGTATGAAAAAAAAATTTTGGGTGCTAACCTGTGAA
1 TGGCCGGCACCAGCAGTATGAAAAAAAATTTTTTGGTGCTGACCTGTCAA
42366298 TGGCCGGCACCA
1 TGGCCGGCACCA
42366310 ATTTAAAAAA
Statistics
Matches: 95, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
49 31 0.33
50 64 0.67
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (50 bp):
TGGCCGGCACCAGCAGTATGAAAAAAAATTTTTTGGTGCTGACCTGTCAA
Found at i:42370321 original size:20 final size:21
Alignment explanation
Indices: 42370283--42370345 Score: 67
Period size: 21 Copynumber: 3.0 Consensus size: 21
42370273 TTAAAATATA
42370283 TTTTTTTCAATTTCAATTTAT
1 TTTTTTTCAATTTCAATTTAT
42370304 TTTTTTCTCAA-TTC-ATTTAT
1 TTTTTT-TCAATTTCAATTTAT
* *
42370324 ATTATTTTTTAATTTAAATTTA
1 -TT-TTTTTCAATTTCAATTTA
42370346 AATTTTTCTG
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
20 6 0.17
21 14 0.40
22 10 0.29
23 5 0.14
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTTTTTCAATTTCAATTTAT
Found at i:42370338 original size:43 final size:43
Alignment explanation
Indices: 42370279--42370372 Score: 118
Period size: 43 Copynumber: 2.2 Consensus size: 43
42370269 TCATTTAAAA
* **
42370279 TATATTTTTTTCAATTTCAATTTATTTTTTTCT-CAATTCATT
1 TATATTTTTTTCAATTTAAATTTAAATTTTTCTGCAATTCATT
* *
42370321 TATATTATTTTTTAATTTAAATTTAAATTTTTCTGCACTTCATT
1 TATATT-TTTTTCAATTTAAATTTAAATTTTTCTGCAATTCATT
*
42370365 TAAATTTT
1 TATATTTT
42370373 CTATTTTCAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
42 6 0.14
43 25 0.57
44 13 0.30
ACGTcount: A:0.28, C:0.10, G:0.01, T:0.62
Consensus pattern (43 bp):
TATATTTTTTTCAATTTAAATTTAAATTTTTCTGCAATTCATT
Found at i:42370458 original size:91 final size:90
Alignment explanation
Indices: 42370297--42370461 Score: 210
Period size: 90 Copynumber: 1.8 Consensus size: 90
42370287 TTTCAATTTC
* * *
42370297 AATTTATTTTTTTCTCAATTCATTTATATTATTTTTTAATTTAAATTTAAATTTTTCTGCACTTC
1 AATTTATTTTTATCTCAATTCATTTATATTATTTTCTAATTTAAATTCAAATTTTTCTGCACTTC
42370362 ATTTAAATTTTCTATTTTCAATGCA
66 ATTTAAATTTTCTATTTTCAATGCA
* * * *
42370387 AATTTATTTTTATCTTATTTCATTTTATATTGAATTTTCTATTTTCAATTCAAATTTTTTCT-C-
1 AATTTATTTTTATCTCAATTCA-TTTATATT--ATTTTCTAATTTAAATTCAAA-TTTTTCTGCA
42370450 C-TCATTTAAATT
62 CTTCATTTAAATT
42370462 AAAATTTTCC
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
90 19 0.30
91 19 0.30
92 1 0.02
93 18 0.28
94 7 0.11
ACGTcount: A:0.28, C:0.12, G:0.02, T:0.59
Consensus pattern (90 bp):
AATTTATTTTTATCTCAATTCATTTATATTATTTTCTAATTTAAATTCAAATTTTTCTGCACTTC
ATTTAAATTTTCTATTTTCAATGCA
Found at i:42371200 original size:13 final size:13
Alignment explanation
Indices: 42371182--42371206 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
42371172 TATTTTAATA
42371182 TTATTTTGTGTGT
1 TTATTTTGTGTGT
42371195 TTATTTTGTGTG
1 TTATTTTGTGTG
42371207 CATTTGATTG
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:0.08, C:0.00, G:0.24, T:0.68
Consensus pattern (13 bp):
TTATTTTGTGTGT
Found at i:42373259 original size:41 final size:41
Alignment explanation
Indices: 42373210--42373340 Score: 199
Period size: 41 Copynumber: 3.2 Consensus size: 41
42373200 GACTTTAAGT
**
42373210 CTAGCAGGCTAATTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
42373251 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
* * * **
42373292 CTAGTAGGCTACGTGCCGGTGATCTGACTCAGGCTATAAGT
1 CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
42373333 CTAGCAGG
1 CTAGCAGG
42373341 TTATGTGTCG
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 82 1.00
ACGTcount: A:0.26, C:0.21, G:0.27, T:0.25
Consensus pattern (41 bp):
CTAGCAGGCTACGTGCCGGTGATCTGAATCAGGTTATAAAC
Found at i:42376694 original size:49 final size:49
Alignment explanation
Indices: 42376524--42376925 Score: 390
Period size: 49 Copynumber: 8.2 Consensus size: 49
42376514 CGGCCTAAAA
*** * * * *
42376524 AAAATTTCTTTTTCGTACTGCTGGTGCTATCCATTGACAGTCTAACACTC
1 AAAATTT-TTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* ** * *
42376574 -AAATTTTTTTTCGTA-TACT-GTGTAGGCCATTGACAGGACAACACCC
1 AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* *
42376620 AAAATTCTTTTTCGTA-TACTGGTGCCGGCCATTGACAGGCCAGCACCCC
1 AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCA-CCC
* * *
42376669 AAAA-ATTTTTTCGTACTGTTGGTGCCGGCCATTAACAGGCCAGCACCC
1 AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* *
42376717 AAAATTTTTTTTCGTACTGTTGGTGCCGGCCATTGACAGGCCAGCACCTAT
1 AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACC--C
* ** * **
42376768 AAAATTTTTTTTTCATACTGCTGGTGTGGGCCATTGACAAGCCAGCATGC
1 AAAA-TTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* *
42376818 AAAATTTTTTTTTCGT-CTGGTGGTGCCGACCATTGACAGGCCAGCACCC
1 AAAA-TTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCC
* * * * *
42376867 AAAATTTTTTTTCGTA-TACTGATGCAGGCCATTAACAAGGCCAACACCC
1 AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGAC-AGGCCAGCACCC
42376916 --AATTTTTTTT
1 AAAATTTTTTTT
42376926 GTTTTTTTTA
Statistics
Matches: 297, Mismatches: 45, Indels: 23
0.81 0.12 0.06
Matches are distributed among these distances:
46 19 0.06
47 31 0.10
48 70 0.24
49 121 0.41
50 15 0.05
51 4 0.01
52 37 0.12
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (49 bp):
AAAATTTTTTTTCGTACTGCTGGTGCCGGCCATTGACAGGCCAGCACCC
Found at i:42376908 original size:150 final size:146
Alignment explanation
Indices: 42376524--42376917 Score: 422
Period size: 150 Copynumber: 2.7 Consensus size: 146
42376514 CGGCCTAAAA
* * * * * *
42376524 AAAATTTCTTTTTCGTACTGCTGGTG-CTATCCATTGACAGTCTAACACTC-AAATTTTTTTTCG
1 AAAATTTTTTTTTCGTACTGCTGGTGCCGA-CCATTGACAGGCCAGCACCCAAAATTTTTTTTCG
* * *
42376587 TATACTGTGTAGGCCATTGACAGGACAACACCCAAAATTCTTTTTCGTATACTGGTGCCGGCCAT
65 TATACTGTGCAGGCCATTGACAGGCCAACACCCAAAATTCTTTTTCATATACTGGTGCCGGCCAT
*
42376652 TGACAGGCCAGCACCCC
130 TGACAAGCCAGCACCCC
* * * *
42376669 AAAA--ATTTTTTCGTACTGTTGGTGCCGGCCATTAACAGGCCAGCACCCAAAATTTTTTTTCGT
1 AAAATTTTTTTTTCGTACTGCTGGTGCCGACCATTGACAGGCCAGCACCCAAAATTTTTTTTCGT
** * * * * * **
42376732 ACTGTTGGTGCCGGCCATTGACAGGCCAGCACCTATAAAATTTTTTTTTCATACTGCTGGTGTGG
66 A-TACT-GTGCAGGCCATTGACAGGCCAACACC--CAAAA-TTCTTTTTCATA-TACTGGTGCCG
**
42376797 GCCATTGACAAGCCAGCA-TGC
125 GCCATTGACAAGCCAGCACCCC
*
42376818 AAAATTTTTTTTTCGT-CTGGTGGTGCCGACCATTGACAGGCCAGCACCCAAAATTTTTTTTCGT
1 AAAATTTTTTTTTCGTACTGCTGGTGCCGACCATTGACAGGCCAGCACCCAAAATTTTTTTTCGT
*
42376882 ATACTGATGCAGGCCATTAACAAGGCCAACACCCAA
66 ATACTG-TGCAGGCCATTGAC-AGGCCAACACCCAA
42376918 TTTTTTTTGT
Statistics
Matches: 202, Mismatches: 35, Indels: 21
0.78 0.14 0.08
Matches are distributed among these distances:
143 32 0.16
144 16 0.08
145 6 0.03
146 22 0.11
148 7 0.03
149 29 0.14
150 81 0.40
151 9 0.04
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.31
Consensus pattern (146 bp):
AAAATTTTTTTTTCGTACTGCTGGTGCCGACCATTGACAGGCCAGCACCCAAAATTTTTTTTCGT
ATACTGTGCAGGCCATTGACAGGCCAACACCCAAAATTCTTTTTCATATACTGGTGCCGGCCATT
GACAAGCCAGCACCCC
Found at i:42376931 original size:101 final size:97
Alignment explanation
Indices: 42376524--42376925 Score: 386
Period size: 101 Copynumber: 4.1 Consensus size: 97
42376514 CGGCCTAAAA
*** * * * *
42376524 AAAATTTCTTTTTCGTACTGCTGGTGCTATCCATTGACAGTCTAACACTC-AAATTTTTTTTCGT
1 AAAATTT-TTTTTCGT-CTGCTGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTCGT
* * *
42376588 A-TACT-GTGTAGGCCATTGACAGGACAACACCC
64 ACTACTGGTGCAGGCCATTAACAGGCCAACACCC
* * * *
42376620 AAAATTCTTTTTCGTATACTGGTGCCGGCCATTGACAGGCCAGCACCCCAAAA-ATTTTTTCGTA
1 AAAATTTTTTTTCGTCTGCTGGTGCCGGCCATTGACAGGCCAGCA-CCCAAAATTTTTTTTCGTA
** * *
42376684 CTGTTGGTGCCGGCCATTAACAGGCCAGCACCC
65 CTACTGGTGCAGGCCATTAACAGGCCAACACCC
* *
42376717 AAAATTTTTTTTCGTACTGTTGGTGCCGGCCATTGACAGGCCAGCACCTATAAAATTTTTTTTTC
1 AAAATTTTTTTTCGT-CTGCTGGTGCCGGCCATTGACAGGCCAGCACC--CAAAA-TTTTTTTTC
* * ** * * * **
42376782 ATACTGCTGGTGTGGGCCATTGACAAGCCAGCATGC
62 GTACTACTGGTGCAGGCCATTAACAGGCCAACACCC
* *
42376818 AAAATTTTTTTTTCGTCTGGTGGTGCCGACCATTGACAGGCCAGCACCCAAAATTTTTTTTCGTA
1 AAAA-TTTTTTTTCGTCTGCTGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTCGTA
*
42376883 -TACTGATGCAGGCCATTAACAAGGCCAACACCC
65 CTACTGGTGCAGGCCATTAAC-AGGCCAACACCC
42376916 --AATTTTTTTT
1 AAAATTTTTTTT
42376926 GTTTTTTTTA
Statistics
Matches: 250, Mismatches: 45, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
94 22 0.09
95 28 0.11
96 13 0.05
97 53 0.21
98 46 0.18
99 8 0.03
101 69 0.28
102 11 0.04
ACGTcount: A:0.25, C:0.24, G:0.19, T:0.33
Consensus pattern (97 bp):
AAAATTTTTTTTCGTCTGCTGGTGCCGGCCATTGACAGGCCAGCACCCAAAATTTTTTTTCGTAC
TACTGGTGCAGGCCATTAACAGGCCAACACCC
Found at i:42378528 original size:5 final size:5
Alignment explanation
Indices: 42378518--42378547 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
42378508 CCCATATTTC
42378518 GGCCG GGCCG GGCCG GGCCG GGCCG GGCCG
1 GGCCG GGCCG GGCCG GGCCG GGCCG GGCCG
42378548 CCCGGCCATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.40, G:0.60, T:0.00
Consensus pattern (5 bp):
GGCCG
Found at i:42379745 original size:18 final size:19
Alignment explanation
Indices: 42379699--42379749 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
42379689 TTTCTCATAC
* * *
42379699 AAAATGATTAAAAAATCAT
1 AAAATCATTAAAAAAACAG
*
42379718 AAAATCATTAAAAAAAGAG
1 AAAATCATTAAAAAAACAG
42379737 AAAAT-ATTAAAAA
1 AAAATCATTAAAAA
42379750 TATTAAAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
18 8 0.29
19 20 0.71
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.22
Consensus pattern (19 bp):
AAAATCATTAAAAAAACAG
Found at i:42380136 original size:21 final size:19
Alignment explanation
Indices: 42380085--42380136 Score: 52
Period size: 21 Copynumber: 2.6 Consensus size: 19
42380075 GAATCCTTTA
42380085 AAAATA-ATAAAAAATGTT
1 AAAATATATAAAAAATGTT
* *
42380103 AAAATTTATTAAAAAATATTT
1 AAAATATA-TAAAAAAT-GTT
42380124 AAAATGATATAAA
1 AAAAT-ATATAAA
42380137 GTTATAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
18 5 0.19
19 1 0.04
20 8 0.30
21 11 0.41
22 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.04, T:0.33
Consensus pattern (19 bp):
AAAATATATAAAAAATGTT
Found at i:42380594 original size:9 final size:9
Alignment explanation
Indices: 42380582--42380808 Score: 57
Period size: 9 Copynumber: 23.2 Consensus size: 9
42380572 TTTATGATTT
42380582 TTTTTATAA
1 TTTTTATAA
*
42380591 TTTTTGTAA
1 TTTTTATAA
*
42380600 GTTTATATCAA
1 -TTTTTAT-AA
* *
42380611 TTTTAATAC
1 TTTTTATAA
*
42380620 TTTTTATGA
1 TTTTTATAA
42380629 TTTTTATAGAA
1 TTTTTAT--AA
* * *
42380640 TTATAATATG
1 TTTTTATA-A
42380650 TTTTTATAAAA
1 TTTTTAT--AA
* *
42380661 ATTTTAAATA
1 TTTTTATA-A
42380671 TGTTTTATTAA
1 T-TTTTA-TAA
* *
42380682 TTTCATAAAA
1 TTT-TTATAA
42380692 TTTTTATAA
1 TTTTTATAA
42380701 TTTTATATCAA
1 TTTT-TAT-AA
* *
42380712 CTTTCAT-A
1 TTTTTATAA
42380720 TATTTT-TAA
1 T-TTTTATAA
*
42380729 TATTTAATAA
1 T-TTTTATAA
42380739 TTTTTAT-A
1 TTTTTATAA
* *
42380747 TCTCTTGATTA
1 T-T-TTTATAA
42380758 TTTTTATGATTA
1 TTTTTAT-A--A
42380770 TTTTTATAA
1 TTTTTATAA
42380779 TTTTTATGATA
1 TTTTTAT-A-A
* *
42380790 ATTTTATGA
1 TTTTTATAA
42380799 TTTTT-TAA
1 TTTTTATAA
42380807 TT
1 TT
42380809 ATTTTATGGA
Statistics
Matches: 157, Mismatches: 37, Indels: 49
0.65 0.15 0.20
Matches are distributed among these distances:
8 8 0.05
9 64 0.41
10 38 0.24
11 37 0.24
12 10 0.06
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (9 bp):
TTTTTATAA
Found at i:42380654 original size:22 final size:23
Alignment explanation
Indices: 42380624--42380676 Score: 65
Period size: 22 Copynumber: 2.3 Consensus size: 23
42380614 TAATACTTTT
*
42380624 TATGATTTTTAT-AGAATTAT-AA
1 TATG-TTTTTATAAAAATTATAAA
*
42380646 TATGTTTTTATAAAAATTTTAAA
1 TATGTTTTTATAAAAATTATAAA
42380669 TATGTTTT
1 TATGTTTT
42380677 ATTAATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 7 0.26
22 10 0.37
23 10 0.37
ACGTcount: A:0.38, C:0.00, G:0.08, T:0.55
Consensus pattern (23 bp):
TATGTTTTTATAAAAATTATAAA
Found at i:42380769 original size:12 final size:12
Alignment explanation
Indices: 42380752--42380804 Score: 62
Period size: 12 Copynumber: 4.8 Consensus size: 12
42380742 TTATATCTCT
42380752 TGATTATTTTTA
1 TGATTATTTTTA
42380764 TGATTATTTTTA
1 TGATTATTTTTA
42380776 T-A--ATTTTTA
1 TGATTATTTTTA
*
42380785 TGA-TAATTTTA
1 TGATTATTTTTA
42380796 TGATT-TTTT
1 TGATTATTTT
42380805 AATTATTTTA
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
9 8 0.22
10 1 0.03
11 13 0.36
12 14 0.39
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (12 bp):
TGATTATTTTTA
Done.