Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 94 of 131
Found at i:31464151 original size:71 final size:77
Alignment explanation
Indices: 31464066--31464231 Score: 272
Period size: 71 Copynumber: 2.2 Consensus size: 77
31464056 ATACATAGCA
31464066 TACATAACTTACATAATACAAAACTTACATAACTTAAATATCTT-AC-A-TTACATAA-C-C-TA
1 TACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTAACAACTTACATAACCACATA
31464125 ATACATTTAACT
66 ATACATTTAACT
31464137 TACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTACACAACTTACATAACCTACA
1 TACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTA-ACAACTTACATAACC-ACA
31464202 TAATACATTTAACT
64 TAATACATTTAACT
31464216 TACATAACTTACATAA
1 TACATAACTTACATAA
31464232 CTTACATAAT
Statistics
Matches: 87, Mismatches: 0, Indels: 8
0.92 0.00 0.08
Matches are distributed among these distances:
71 44 0.51
73 2 0.02
74 1 0.01
75 8 0.09
76 1 0.01
78 1 0.01
79 30 0.34
ACGTcount: A:0.47, C:0.20, G:0.00, T:0.33
Consensus pattern (77 bp):
TACATAACTTACATAATACAAAACTTACATAACTTAAATATCTTAACAACTTACATAACCACATA
ATACATTTAACT
Found at i:31464254 original size:19 final size:20
Alignment explanation
Indices: 31464219--31464259 Score: 66
Period size: 19 Copynumber: 2.0 Consensus size: 20
31464209 TTTAACTTAC
31464219 ATAACTTACATAACTTACATA
1 ATAACTTACA-AACTTACATA
31464240 ATAACTTAC-AACTTACATA
1 ATAACTTACAAACTTACATA
31464259 A
1 A
31464260 CATACATTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.55
21 9 0.45
ACGTcount: A:0.49, C:0.20, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAACTTACAAACTTACATA
Found at i:31464257 original size:28 final size:29
Alignment explanation
Indices: 31464185--31464266 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 29
31464175 TATCTTACAC
* *
31464185 AACTTACATAACCTACAT-A-ATACAT-TT
1 AACTTACA-AACTTACATAACATACATAAT
*
31464212 AACTTACATAACTTACATAACTTACATAAT
1 AACTTACA-AACTTACATAACATACATAAT
31464242 AACTTAC-AACTTACATAACATACAT
1 AACTTACAAACTTACATAACATACAT
31464267 TACTTTGACA
Statistics
Matches: 48, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
27 17 0.35
28 18 0.38
29 5 0.10
30 8 0.17
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (29 bp):
AACTTACAAACTTACATAACATACATAAT
Found at i:31469815 original size:21 final size:21
Alignment explanation
Indices: 31469790--31469840 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
31469780 CTACAACTTA
31469790 AAGCAGAGGAGACAACGAGGG
1 AAGCAGAGGAGACAACGAGGG
** * *
31469811 AAGCAGAGGCTATAGCGAGGG
1 AAGCAGAGGAGACAACGAGGG
31469832 AAGCAGAGG
1 AAGCAGAGG
31469841 TTGCAGTGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.43, T:0.04
Consensus pattern (21 bp):
AAGCAGAGGAGACAACGAGGG
Found at i:31469855 original size:21 final size:21
Alignment explanation
Indices: 31469805--31469878 Score: 94
Period size: 21 Copynumber: 3.5 Consensus size: 21
31469795 GAGGAGACAA
* **
31469805 CGAGGGAAGCAGAGGCTATAG
1 CGAGAGAAGCAGAGGCTGCAG
* *
31469826 CGAGGGAAGCAGAGGTTGCAG
1 CGAGAGAAGCAGAGGCTGCAG
*
31469847 TGAGAGAAGCAGAGGCTGCAG
1 CGAGAGAAGCAGAGGCTGCAG
31469868 CGAGAGAAGCA
1 CGAGAGAAGCA
31469879 ACTAGAGAAG
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.34, C:0.15, G:0.43, T:0.08
Consensus pattern (21 bp):
CGAGAGAAGCAGAGGCTGCAG
Found at i:31470406 original size:43 final size:41
Alignment explanation
Indices: 31470328--31470582 Score: 251
Period size: 42 Copynumber: 5.9 Consensus size: 41
31470318 TTTGTGAAGA
* * * * *
31470328 AAGCGTCGCTAAAGAACAT-TTCTTTTCGCGTCGTTTGTGAATT
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTT-T-ATTT
*
31470371 AAGCGCCGCTAATGAACATGATCTTTAGCGGCGTTTTTATTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTATTT
* * *
31470413 AAGCACCGCTAAAGAACATGATCTTGATCTTTAGCGGCATCTTTTTTT
1 AAGCGCCGCTAAAGAAC---A---TGATCTTTAGCGGCGT-TTTATTT
* *
31470461 AAGCGCCGCTAAAGAACATGATCTTTAACGGCGTCTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTATTT
* *
31470503 AAGCGCCACTAAAGAACATGATCTTTAGCGGCGTCTTTTTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCG--TTTTATTT
*
31470546 AAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTT
31470583 TTTTCTGTAA
Statistics
Matches: 184, Mismatches: 17, Indels: 24
0.82 0.08 0.11
Matches are distributed among these distances:
41 4 0.02
42 71 0.39
43 64 0.35
44 6 0.03
45 2 0.01
47 1 0.01
48 36 0.20
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (41 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTATTT
Found at i:31470445 original size:48 final size:42
Alignment explanation
Indices: 31470369--31470586 Score: 296
Period size: 42 Copynumber: 5.0 Consensus size: 42
31470359 CGTTTGTGAA
*
31470369 TTAAGCGCCGCTAATGAACATGATCTTTAGCGGCGT-TTTTAT
1 TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTT-T
* *
31470411 TTAAGCACCGCTAAAGAACATGATCTTGATCTTTAGCGGCATCTTTTT
1 TTAAGCGCCGCTAAAGAAC---A---TGATCTTTAGCGGCGTCTTTTT
*
31470459 TTAAGCGCCGCTAAAGAACATGATCTTTAACGGCGTCTTTTT
1 TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTT
*
31470501 TTAAGCGCCACTAAAGAACATGATCTTTAGCGGCGTCTTTTTT
1 TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTC-TTTTT
*
31470544 TTAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGT-TTTTT
1 TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTT
31470585 TT
1 TT
31470587 CTGTAAACGC
Statistics
Matches: 158, Mismatches: 10, Indels: 17
0.85 0.05 0.09
Matches are distributed among these distances:
41 7 0.04
42 72 0.46
43 39 0.25
45 2 0.01
48 34 0.22
49 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (42 bp):
TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTCTTTTT
Found at i:31470471 original size:90 final size:84
Alignment explanation
Indices: 31470369--31470586 Score: 303
Period size: 90 Copynumber: 2.5 Consensus size: 84
31470359 CGTTTGTGAA
* *
31470369 TTAAGCGCCGCTAATGAACATGATCTTTAGCGGCGTTTTTATTTAAGCACCGCTAAAGAACATGA
1 TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TTTAAGCACCACTAAAGAAC---A
31470434 TCTTGATCTTTAGCGGCATC-TTTTT
62 ---TGATCTTTAGCGGCATCTTTTTT
* *
31470459 TTAAGCGCCGCTAAAGAACATGATCTTTAACGGCGTCTTTTTTTAAGCGCCACTAAAGAACATGA
1 TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGT-TTTTTTTAAGCACCACTAAAGAACATGA
*
31470524 TCTTTAGCGGCGTCTTTTTT
65 TCTTTAGCGGCATCTTTTTT
*
31470544 TTAAGCGCCGCTAAAGAACATGACCTTTAGCGGCGTTTTTTTT
1 TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTT
31470587 CTGTAAACGC
Statistics
Matches: 119, Mismatches: 7, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
84 23 0.19
85 39 0.33
87 1 0.01
90 52 0.44
91 4 0.03
ACGTcount: A:0.25, C:0.21, G:0.19, T:0.35
Consensus pattern (84 bp):
TTAAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTAAGCACCACTAAAGAACATGAT
CTTTAGCGGCATCTTTTTT
Found at i:31472228 original size:28 final size:28
Alignment explanation
Indices: 31472184--31472499 Score: 199
Period size: 29 Copynumber: 11.0 Consensus size: 28
31472174 TTGATTACAA
**
31472184 TTTGAAAAAGGAAACCTTTGTGG-TGATC
1 TTTGAAAAAGGATGCCTTTGTGGCT-ATC
* *
31472212 TTTGAAAAAGGATACCTTTATGGCTATC
1 TTTGAAAAAGGATGCCTTTGTGGCTATC
* * * *
31472240 TCTGTTAAAAA-GATGTCTTTATGGCGATC
1 T-T-TGAAAAAGGATGCCTTTGTGGCTATC
*
31472269 TCTGAAAAAGGATGCCTTTGTGGCTATC
1 TTTGAAAAAGGATGCCTTTGTGGCTATC
* *
31472297 TCTGTTAAAAGGATGCCTTTGTGGCTATC
1 TTTG-AAAAAGGATGCCTTTGTGGCTATC
** * *
31472326 TCAGTTAAAAGGATGACTTTGTGGCTATC
1 TTTG-AAAAAGGATGCCTTTGTGGCTATC
* *
31472355 TCTAT-TAAAAGGATGCATTTGTGGCTATC
1 T-T-TGAAAAAGGATGCCTTTGTGGCTATC
* * * * *
31472384 TCTAT-TAAAATGAAGTCTTTGTGGCGATC
1 T-T-TGAAAAAGGATGCCTTTGTGGCTATC
* * * *
31472413 TCTGAAAAAAGAAGCCTTTATGGCTATC
1 TTTGAAAAAGGATGCCTTTGTGGCTATC
* * ** *
31472441 TCTGTTAAAAGGATGCCTTTACGGTTATC
1 TTTG-AAAAAGGATGCCTTTGTGGCTATC
* * *
31472470 TCTGTTAAAAGGATGCCTTTGTGACTATC
1 TTTG-AAAAAGGATGCCTTTGTGGCTATC
31472499 T
1 T
31472500 CAGTTAAAGG
Statistics
Matches: 241, Mismatches: 38, Indels: 17
0.81 0.13 0.06
Matches are distributed among these distances:
27 7 0.03
28 67 0.28
29 161 0.67
30 6 0.02
ACGTcount: A:0.28, C:0.15, G:0.22, T:0.36
Consensus pattern (28 bp):
TTTGAAAAAGGATGCCTTTGTGGCTATC
Found at i:31472259 original size:29 final size:29
Alignment explanation
Indices: 31472217--31472541 Score: 370
Period size: 29 Copynumber: 11.3 Consensus size: 29
31472207 TGATCTTTGA
* *
31472217 AAAAGGATACCTTTATGGCTATCTCTGTT
1 AAAAGGATGCCTTTGTGGCTATCTCTGTT
* * * * *
31472246 AAAAAGATGTCTTTATGGCGATCTCTG-A
1 AAAAGGATGCCTTTGTGGCTATCTCTGTT
31472274 AAAAGGATGCCTTTGTGGCTATCTCTGTT
1 AAAAGGATGCCTTTGTGGCTATCTCTGTT
*
31472303 AAAAGGATGCCTTTGTGGCTATCTCAGTT
1 AAAAGGATGCCTTTGTGGCTATCTCTGTT
* *
31472332 AAAAGGATGACTTTGTGGCTATCTCTATT
1 AAAAGGATGCCTTTGTGGCTATCTCTGTT
* *
31472361 AAAAGGATGCATTTGTGGCTATCTCTATT
1 AAAAGGATGCCTTTGTGGCTATCTCTGTT
* * * * *
31472390 AAAATGAAGTCTTTGTGGCGATCTCTG-A
1 AAAAGGATGCCTTTGTGGCTATCTCTGTT
* * *
31472418 AAAAAGAAGCCTTTATGGCTATCTCTGTT
1 AAAAGGATGCCTTTGTGGCTATCTCTGTT
** *
31472447 AAAAGGATGCCTTTACGGTTATCTCTGTT
1 AAAAGGATGCCTTTGTGGCTATCTCTGTT
* *
31472476 AAAAGGATGCCTTTGTGACTATCTCAGTT
1 AAAAGGATGCCTTTGTGGCTATCTCTGTT
*
31472505 -AAAGGAATTCC-TTGTGGCTATCTCTGTT
1 AAAAGG-ATGCCTTTGTGGCTATCTCTGTT
31472533 AAAAAGGAT
1 -AAAAGGAT
31472542 ATCTTCATGG
Statistics
Matches: 251, Mismatches: 40, Indels: 10
0.83 0.13 0.03
Matches are distributed among these distances:
28 66 0.26
29 180 0.72
30 5 0.02
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (29 bp):
AAAAGGATGCCTTTGTGGCTATCTCTGTT
Found at i:31472409 original size:144 final size:143
Alignment explanation
Indices: 31472217--31472564 Score: 441
Period size: 144 Copynumber: 2.4 Consensus size: 143
31472207 TGATCTTTGA
* * * *
31472217 AAAAGGATACCTTTATGGCTATCTCTGTTAAAAAGATGTCTTTATGGCGATCTCTGAAAAAGGAT
1 AAAAGGATA-CTTTGTGGCTATCTCTGTTAAAAAGAAGTCTTTATGGCGATCTCTGAAAAAAGAA
* **
31472282 GCCTTTGTGGCTATCTCTGTTAAAAGGATGCCTTTGTGGCTATCTCAGTTAAAAGGATGACTTTG
65 GCCTTTATGGCTATCTCTGTTAAAAGGATGCCTTTACGGCTATCTCAGTTAAAAGGATGACTTTG
*
31472347 TGGCTATCTCTA-TT
130 TGACTATCTC-AGTT
* * * *
31472361 AAAAGGATGCATTTGTGGCTATCTCTATTAAAATGAAGTCTTTGTGGCGATCTCTGAAAAAAGAA
1 AAAAGGATAC-TTTGTGGCTATCTCTGTTAAAAAGAAGTCTTTATGGCGATCTCTGAAAAAAGAA
* * *
31472426 GCCTTTATGGCTATCTCTGTTAAAAGGATGCCTTTACGGTTATCTCTGTTAAAAGGATGCCTTTG
65 GCCTTTATGGCTATCTCTGTTAAAAGGATGCCTTTACGGCTATCTCAGTTAAAAGGATGACTTTG
31472491 TGACTATCTCAGTT
130 TGACTATCTCAGTT
* * * *
31472505 -AAAGGAATTCCTTGTGGCTATCTCTGTTAAAAAGGATA-TCTTCATGGCGAGACTCTGAAA
1 AAAAGG-ATACTTTGTGGCTATCTCTGTTAAAAA-GA-AGTCTTTATGGCGA-TCTCTGAAA
31472565 GGAAAACTTT
Statistics
Matches: 176, Mismatches: 22, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
143 27 0.15
144 140 0.80
145 9 0.05
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (143 bp):
AAAAGGATACTTTGTGGCTATCTCTGTTAAAAAGAAGTCTTTATGGCGATCTCTGAAAAAAGAAG
CCTTTATGGCTATCTCTGTTAAAAGGATGCCTTTACGGCTATCTCAGTTAAAAGGATGACTTTGT
GACTATCTCAGTT
Found at i:31472523 original size:86 final size:87
Alignment explanation
Indices: 31472217--31472541 Score: 338
Period size: 86 Copynumber: 3.8 Consensus size: 87
31472207 TGATCTTTGA
* * * * * * *
31472217 AAAAGGATACCTTTATGGCTATCTCTGTTAAA-AAGATGTCTTTATGGCGATCTCTG-AAAAAGG
1 AAAAGGATGCCTTTGTGGCTATCTCAGTTAAAGGA-ATGTCCTTATGGCTATCTCTGTTAAAAGG
31472280 ATGCCTTTGTGGCTATCTCTGTT
65 ATGCCTTTGTGGCTATCTCTGTT
* * * *
31472303 AAAAGGATGCCTTTGTGGCTATCTCAGTTAAAAGG-ATGACTTTGTGGCTATCTCTATTAAAAGG
1 AAAAGGATGCCTTTGTGGCTATCTCAGTT-AAAGGAATGTCCTTATGGCTATCTCTGTTAAAAGG
* *
31472367 ATGCATTTGTGGCTATCTCTATT
65 ATGCCTTTGTGGCTATCTCTGTT
* * * * * ** *
31472390 AAAATGAAGTCTTTGTGGCGATCTCTGAAAAAAGAA-G-CCTTTATGGCTATCTCTGTTAAAAGG
1 AAAAGGATGCCTTTGTGGCTATCTCAGTTAAAGGAATGTCC-TTATGGCTATCTCTGTTAAAAGG
** *
31472453 ATGCCTTTACGGTTATCTCTGTT
65 ATGCCTTTGTGGCTATCTCTGTT
* *
31472476 AAAAGGATGCCTTTGTGACTATCTCAGTTAAAGGAAT-TCCTTGTGGCTATCTCTGTTAAAAAGG
1 AAAAGGATGCCTTTGTGGCTATCTCAGTTAAAGGAATGTCCTTATGGCTATCTCTGTT-AAAAGG
31472540 AT
65 AT
31472542 ATCTTCATGG
Statistics
Matches: 194, Mismatches: 37, Indels: 15
0.79 0.15 0.06
Matches are distributed among these distances:
85 1 0.01
86 130 0.67
87 63 0.32
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (87 bp):
AAAAGGATGCCTTTGTGGCTATCTCAGTTAAAGGAATGTCCTTATGGCTATCTCTGTTAAAAGGA
TGCCTTTGTGGCTATCTCTGTT
Found at i:31472785 original size:163 final size:164
Alignment explanation
Indices: 31472509--31472840 Score: 468
Period size: 163 Copynumber: 2.0 Consensus size: 164
31472499 TCAGTTAAAG
* * * * *
31472509 GAATTCCTTGTGGCTATCTCTGTTAAAAAGGATATCTTCATGGCGAGACTCTGAAAGGAAAACTT
1 GAATGCCTTGTGGCAAACTCTGTTAAAAAGGATATCTTCATGGCGAGACTCTAAAAGGAAAACCT
* * *
31472574 TTGTACCTATCTTTGGAAATGAATGCCTTCGTGACAGAATCTGAAGAACGGTTCTCATGATGACC
66 TTGTACCTATCTTTGGAAAGGAACGCCTTCGTGACAGAATCTGAAGAACGGATCTCATGATGACC
* * *
31472639 ATTTGAAGACAACGCCTTTGGGCGGACACCAAAT
131 ATTTAAAGACAACACCTTTAGGCGGACACCAAAT
* * *
31472673 GAATGCCTTGTGGCAAACTCTGTT-AAAAGGATGTCTTCGTGGCGAGACTCTAAAAGGAAAGCCT
1 GAATGCCTTGTGGCAAACTCTGTTAAAAAGGATATCTTCATGGCGAGACTCTAAAAGGAAAACCT
* ***
31472737 TTGTAGCTATCTTTGGAAAGGAACGCCTTCGTGGTGGAATCTGAAGAACGGATCTCATGATGACC
66 TTGTACCTATCTTTGGAAAGGAACGCCTTCGTGACAGAATCTGAAGAACGGATCTCATGATGACC
** *
31472802 ATTTAAAGACAACATTTTTAGGTGGACACCAAAT
131 ATTTAAAGACAACACCTTTAGGCGGACACCAAAT
31472836 GAATG
1 GAATG
31472841 ATGAGCCTCG
Statistics
Matches: 147, Mismatches: 21, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
163 126 0.86
164 21 0.14
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (164 bp):
GAATGCCTTGTGGCAAACTCTGTTAAAAAGGATATCTTCATGGCGAGACTCTAAAAGGAAAACCT
TTGTACCTATCTTTGGAAAGGAACGCCTTCGTGACAGAATCTGAAGAACGGATCTCATGATGACC
ATTTAAAGACAACACCTTTAGGCGGACACCAAAT
Found at i:31478911 original size:20 final size:20
Alignment explanation
Indices: 31478817--31478926 Score: 78
Period size: 20 Copynumber: 5.3 Consensus size: 20
31478807 AATTTTTTAT
* * *
31478817 CCCAAACCCAGAACCTTGAAT
1 CCCAAACCCCGAACC-TCAAA
* *
31478838 CCTAAACCCCGAACCCCAAA
1 CCCAAACCCCGAACCTCAAA
**
31478858 CCCCAAACCATGAACC-CAAA
1 -CCCAAACCCCGAACCTCAAA
* * * *
31478878 TCTCGAATCTCGAACCTCAAA
1 -CCCAAACCCCGAACCTCAAA
31478899 CCCAAACCCCGAACCTCAAA
1 CCCAAACCCCGAACCTCAAA
31478919 CCCTAAAC
1 CCC-AAAC
31478927 TCAAACCCTA
Statistics
Matches: 68, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
20 35 0.51
21 33 0.49
ACGTcount: A:0.39, C:0.44, G:0.06, T:0.11
Consensus pattern (20 bp):
CCCAAACCCCGAACCTCAAA
Found at i:31478911 original size:27 final size:27
Alignment explanation
Indices: 31478817--31478934 Score: 85
Period size: 27 Copynumber: 4.3 Consensus size: 27
31478807 AATTTTTTAT
* ** *
31478817 CCCAAACCCAGAACCTTGAATCCTAAA
1 CCCAAACCCCGAACCTCAAACCCTAAA
* * * * *
31478844 CCCCGAACCCCAAACCCCAAACCATGAA
1 -CCCAAACCCCGAACCTCAAACCCTAAA
* * * *
31478872 CCCAAATCTCGAATCTCGAA-CCTCAAA
1 CCCAAACCCCGAACCTCAAACCCT-AAA
31478899 CCCAAACCCCGAACCTCAAACCCTAAA
1 CCCAAACCCCGAACCTCAAACCCTAAA
*
31478926 CTCAAACCC
1 CCCAAACCC
31478935 TATGTAATAT
Statistics
Matches: 65, Mismatches: 23, Indels: 5
0.70 0.25 0.05
Matches are distributed among these distances:
26 2 0.03
27 42 0.65
28 21 0.32
ACGTcount: A:0.39, C:0.44, G:0.06, T:0.11
Consensus pattern (27 bp):
CCCAAACCCCGAACCTCAAACCCTAAA
Found at i:31482088 original size:7 final size:7
Alignment explanation
Indices: 31482076--31482113 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
31482066 AACCCTGAAC
31482076 AAGGTTT
1 AAGGTTT
31482083 AAGGTTT
1 AAGGTTT
*
31482090 AAAGTTT
1 AAGGTTT
*
31482097 GAGGTTT
1 AAGGTTT
31482104 AAGGTTT
1 AAGGTTT
31482111 AAG
1 AAG
31482114 ATTTGGGATT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.32, C:0.00, G:0.29, T:0.39
Consensus pattern (7 bp):
AAGGTTT
Found at i:31482863 original size:19 final size:20
Alignment explanation
Indices: 31482826--31482871 Score: 58
Period size: 19 Copynumber: 2.3 Consensus size: 20
31482816 ACCACTTAAC
31482826 TTAAATTATTAATAATATTA-
1 TTAAA-TATTAATAATATTAT
* *
31482846 TTAAATATTTATATTATTAT
1 TTAAATATTAATAATATTAT
31482866 TTAAAT
1 TTAAAT
31482872 TTTTTCCTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 12 0.52
20 11 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTAAATATTAATAATATTAT
Found at i:31486848 original size:10 final size:10
Alignment explanation
Indices: 31486833--31486870 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
31486823 ATATTTTTAA
31486833 ATAAAAACAT
1 ATAAAAACAT
31486843 A-AAAAA-ATT
1 ATAAAAACA-T
31486852 ATAAAAACAT
1 ATAAAAACAT
31486862 ATAAAAACA
1 ATAAAAACA
31486871 CTTCAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 1 0.04
9 7 0.28
10 16 0.64
11 1 0.04
ACGTcount: A:0.74, C:0.08, G:0.00, T:0.18
Consensus pattern (10 bp):
ATAAAAACAT
Found at i:31487574 original size:21 final size:22
Alignment explanation
Indices: 31487548--31487594 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
31487538 GGTTCAAAGC
*
31487548 AAATAAATTATTAAAAA-TAAA
1 AAATAAAATATTAAAAAGTAAA
*
31487569 AAATAAAATATTAAAAAGTATA
1 AAATAAAATATTAAAAAGTAAA
31487591 AAAT
1 AAAT
31487595 TTGGTTCAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (22 bp):
AAATAAAATATTAAAAAGTAAA
Found at i:31487776 original size:15 final size:15
Alignment explanation
Indices: 31487752--31487784 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
31487742 AATTTTTATA
31487752 TTTTTAAAAAATATT
1 TTTTTAAAAAATATT
*
31487767 TTTTTGAAAAATATT
1 TTTTTAAAAAATATT
31487782 TTT
1 TTT
31487785 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
TTTTTAAAAAATATT
Found at i:31487791 original size:23 final size:23
Alignment explanation
Indices: 31487765--31487815 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
31487755 TTAAAAAATA
*
31487765 TTTT-TTTGAAAAATATTTTTATT
1 TTTTATTTGAAAAAT-TTTTTACT
* *
31487788 TTTTATTTTAAATATTTTTTACT
1 TTTTATTTGAAAAATTTTTTACT
31487811 TTTTA
1 TTTTA
31487816 AAGAATATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (23 bp):
TTTTATTTGAAAAATTTTTTACT
Found at i:31488389 original size:3 final size:3
Alignment explanation
Indices: 31488381--31488410 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
31488371 CAAAAAGAAA
31488381 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
31488411 GAGAAATACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
CAT
Found at i:31489891 original size:30 final size:30
Alignment explanation
Indices: 31489852--31489915 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
31489842 TTAATGATAT
*
31489852 ATAAAATAT-TTTAAAAA-CAAATATAATA
1 ATAAATTATATTTAAAAATCAAATATAATA
** *
31489880 ATAAATTATATTTAAAAATTTAATATAATG
1 ATAAATTATATTTAAAAATCAAATATAATA
31489910 ATAAAT
1 ATAAAT
31489916 GATANNNNNN
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 8 0.27
29 8 0.27
30 14 0.47
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (30 bp):
ATAAATTATATTTAAAAATCAAATATAATA
Found at i:31495504 original size:16 final size:15
Alignment explanation
Indices: 31495469--31495514 Score: 65
Period size: 15 Copynumber: 2.9 Consensus size: 15
31495459 TAAATGTTAA
*
31495469 AATAATAACAAAAGT
1 AATAATAATAAAAGT
31495484 AATAATAATAAAAGTT
1 AATAATAATAAAAG-T
31495500 AATAATAATAGAAAG
1 AATAATAATA-AAAG
31495515 GCATGCAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
15 13 0.46
16 11 0.39
17 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.09, T:0.24
Consensus pattern (15 bp):
AATAATAATAAAAGT
Found at i:31499395 original size:22 final size:22
Alignment explanation
Indices: 31499354--31499396 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
31499344 ATTTTTTAGA
*
31499354 TTATATATTTTTTCTGATTTTT
1 TTATATATTTTTTCTCATTTTT
31499376 TTATATATTTATTT-TCATTTT
1 TTATATATTT-TTTCTCATTTT
31499397 CATTTTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (22 bp):
TTATATATTTTTTCTCATTTTT
Found at i:31499408 original size:7 final size:7
Alignment explanation
Indices: 31499387--31499467 Score: 137
Period size: 7 Copynumber: 11.7 Consensus size: 7
31499377 TATATATTTA
31499387 TTTTCA-
1 TTTTCAT
31499393 TTTTCAT
1 TTTTCAT
*
31499400 TTTTTAT
1 TTTTCAT
*
31499407 TTTTTAT
1 TTTTCAT
31499414 TTTTCAT
1 TTTTCAT
31499421 TTTTCAT
1 TTTTCAT
31499428 TTTTCAT
1 TTTTCAT
31499435 TTTTCAT
1 TTTTCAT
31499442 TTTTCAT
1 TTTTCAT
31499449 TTTTCAT
1 TTTTCAT
31499456 TTTTCAT
1 TTTTCAT
31499463 TTTTC
1 TTTTC
31499468 TAAATGTATA
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
6 6 0.08
7 66 0.92
ACGTcount: A:0.14, C:0.12, G:0.00, T:0.74
Consensus pattern (7 bp):
TTTTCAT
Found at i:31501944 original size:44 final size:44
Alignment explanation
Indices: 31501895--31501999 Score: 160
Period size: 44 Copynumber: 2.4 Consensus size: 44
31501885 CATGAACATG
31501895 GTTGCTTTCACGTTGCATTGTCTT-CTCACATCATTGATTTAATA
1 GTTGCTTTCACGTTGCATTGTCTTGC-CACATCATTGATTTAATA
* *
31501939 GTTGC-TTCTACGTTGCATTGTCTTGCCACATCATTGATTTGATG
1 GTTGCTTTC-ACGTTGCATTGTCTTGCCACATCATTGATTTAATA
31501983 GTTGCTTTCACGTTGCA
1 GTTGCTTTCACGTTGCA
31502000 ATTTTTTTGT
Statistics
Matches: 56, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
43 3 0.05
44 49 0.88
45 4 0.07
ACGTcount: A:0.17, C:0.21, G:0.18, T:0.44
Consensus pattern (44 bp):
GTTGCTTTCACGTTGCATTGTCTTGCCACATCATTGATTTAATA
Found at i:31502493 original size:17 final size:17
Alignment explanation
Indices: 31502471--31502503 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31502461 TAAAACATTT
31502471 ACAAATTTTTTCTTCTA
1 ACAAATTTTTTCTTCTA
31502488 ACAAATTTTTTCTTCT
1 ACAAATTTTTTCTTCT
31502504 TATTATAACC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (17 bp):
ACAAATTTTTTCTTCTA
Found at i:31503574 original size:12 final size:12
Alignment explanation
Indices: 31503557--31503581 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31503547 AGAACTAATA
31503557 TGTGGATATAGT
1 TGTGGATATAGT
31503569 TGTGGATATAGT
1 TGTGGATATAGT
31503581 T
1 T
31503582 CAGGAAAATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.32, T:0.44
Consensus pattern (12 bp):
TGTGGATATAGT
Found at i:31508788 original size:6 final size:6
Alignment explanation
Indices: 31508779--31508811 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
31508769 ATTTCGACAA
31508779 TTTCTT TTTCTTT TTTCTT TTTCTT TTTCTT TT
1 TTTCTT TTTC-TT TTTCTT TTTCTT TTTCTT TT
31508812 AACACGACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 20 0.77
7 6 0.23
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (6 bp):
TTTCTT
Found at i:31518368 original size:18 final size:19
Alignment explanation
Indices: 31518327--31518369 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
31518317 TTAAAATATT
* *
31518327 TTTTAATAATGTTTTACAAT
1 TTTTAATAA-GTTATACAAA
31518347 TTTTAATAA-TTATACAAA
1 TTTTAATAAGTTATACAAA
31518365 TTTTA
1 TTTTA
31518370 GTAGTTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 12 0.57
20 9 0.43
ACGTcount: A:0.40, C:0.05, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTAATAAGTTATACAAA
Found at i:31518396 original size:19 final size:18
Alignment explanation
Indices: 31518374--31518462 Score: 58
Period size: 19 Copynumber: 4.8 Consensus size: 18
31518364 ATTTTAGTAG
31518374 TTTTTAATTATTTTTACAA
1 TTTTTAATTATTTTT-CAA
*
31518393 TTTTTAATT-CTTTTCAA
1 TTTTTAATTATTTTTCAA
* **
31518410 ATTTT-ATTAAATTTTTGTA
1 TTTTTAATT--ATTTTTCAA
*
31518429 TATTTAATT-TTTTTACAA
1 TTTTTAATTATTTTT-CAA
*
31518447 TTTTTTAATAATTTTT
1 -TTTTTAATTATTTTT
31518463 TAATATTTTT
Statistics
Matches: 52, Mismatches: 11, Indels: 13
0.68 0.14 0.17
Matches are distributed among these distances:
16 3 0.06
17 12 0.23
18 5 0.10
19 24 0.46
20 8 0.15
ACGTcount: A:0.29, C:0.04, G:0.01, T:0.65
Consensus pattern (18 bp):
TTTTTAATTATTTTTCAA
Found at i:31518460 original size:37 final size:36
Alignment explanation
Indices: 31518395--31518470 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
31518385 TTTTACAATT
31518395 TTTAATTCTTTTCAAATTTTATTAAATTTTTGT-ATA
1 TTTAATTCTTTTCAAATTTTATTAAATTTTT-TAATA
*
31518431 TTTAATT-TTTTTACAATTTT-TTAATAATTTTTTAATA
1 TTTAATTCTTTTCA-AATTTTATT-A-AATTTTTTAATA
31518468 TTT
1 TTT
31518471 TTAAAAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
35 7 0.20
36 15 0.43
37 13 0.37
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (36 bp):
TTTAATTCTTTTCAAATTTTATTAAATTTTTTAATA
Found at i:31518466 original size:11 final size:11
Alignment explanation
Indices: 31518433--31518486 Score: 58
Period size: 11 Copynumber: 5.1 Consensus size: 11
31518423 TTTGTATATT
*
31518433 TAATTTTTTTA
1 TAATTTTTTAA
*
31518444 CAATTTTTTAA
1 TAATTTTTTAA
31518455 TAATTTTTTAA
1 TAATTTTTTAA
31518466 T-A-TTTTTAA
1 TAATTTTTTAA
* *
31518475 AAATATTTTAA
1 TAATTTTTTAA
31518486 T
1 T
31518487 TTAGTTAATA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 7 0.20
10 2 0.06
11 26 0.74
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (11 bp):
TAATTTTTTAA
Found at i:31518470 original size:10 final size:10
Alignment explanation
Indices: 31518431--31518499 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
31518421 TTTTTGTATA
31518431 TTTAAT-TTT
1 TTTAATATTT
31518440 TTTACA-ATTT
1 TTTA-ATATTT
31518450 TTTAATAATTT
1 TTTAAT-ATTT
31518461 TTTAATATTT
1 TTTAATATTT
* * *
31518471 TTAAAAATAT
1 TTTAATATTT
*
31518481 TTTAAT-TTA
1 TTTAATATTT
*
31518490 GTTAATATTT
1 TTTAATATTT
31518500 GGTCAATGAC
Statistics
Matches: 46, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
9 11 0.24
10 25 0.54
11 10 0.22
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (10 bp):
TTTAATATTT
Found at i:31518471 original size:20 final size:20
Alignment explanation
Indices: 31518448--31518486 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31518438 TTTTTACAAT
* *
31518448 TTTTTAATAATTTTTTAATA
1 TTTTTAAAAATATTTTAATA
31518468 TTTTTAAAAATATTTTAAT
1 TTTTTAAAAATATTTTAAT
31518487 TTAGTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTTTAAAAATATTTTAATA
Found at i:31519159 original size:55 final size:54
Alignment explanation
Indices: 31519090--31519193 Score: 154
Period size: 55 Copynumber: 1.9 Consensus size: 54
31519080 TTGTTATTAA
* **
31519090 ATTTTAATAGAATTATTATTAAATATAATTTAATAAAAATAAATAATTTAATCAT
1 ATTTTAATAGAATTATTATTAAATACAATACAATAAAAATAAA-AATTTAATCAT
* *
31519145 ATTTTAATATAATTATTATTCAATACAATACAATAAAAATAAAAATTTA
1 ATTTTAATAGAATTATTATTAAATACAATACAATAAAAATAAAAATTTA
31519194 TATTTTAATC
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
54 6 0.14
55 38 0.86
ACGTcount: A:0.54, C:0.04, G:0.01, T:0.41
Consensus pattern (54 bp):
ATTTTAATAGAATTATTATTAAATACAATACAATAAAAATAAAAATTTAATCAT
Found at i:31523774 original size:24 final size:24
Alignment explanation
Indices: 31523742--31524156 Score: 291
Period size: 24 Copynumber: 17.2 Consensus size: 24
31523732 ATTCGATTCA
*
31523742 TGTCAAATTTTGATGTATAAATGC
1 TGTCCAATTTTGATGTATAAATGC
* *
31523766 TG-CCTAATTTTG-TGTCTATATGC
1 TGTCC-AATTTTGATGTATAAATGC
* * *
31523789 AGTCCAATTTTGGTGTAAAAATGC
1 TGTCCAATTTTGATGTATAAATGC
* *
31523813 TGTCCAATTTAATATATATATATATATGC
1 TGTCCAATTT--T-GATGTATA-A-ATGC
* * *
31523842 TGCCCAA-ATTGATGTATAAATCC
1 TGTCCAATTTTGATGTATAAATGC
*
31523865 TGTACAATTTT-AGTGTATAAATGC
1 TGTCCAATTTTGA-TGTATAAATGC
31523889 TGTCCAATTTTGATGTATAAATGC
1 TGTCCAATTTTGATGTATAAATGC
* * * *
31523913 T-ACCTAA-TTTGGTGTCTATATGC
1 TGTCC-AATTTTGATGTATAAATGC
* * * *
31523936 AGTCCAATTTTGGTGTAAAAATGT
1 TGTCCAATTTTGATGTATAAATGC
* *
31523960 TGTCCAA-TTTGATATATATATGC
1 TGTCCAATTTTGATGTATAAATGC
* *
31523983 TGCCCAA-ATTGATGTATAAATGC
1 TGTCCAATTTTGATGTATAAATGC
31524006 TGTCCAATTTT-AGTGTATAAATGC
1 TGTCCAATTTTGA-TGTATAAATGC
*
31524030 -GATTCAATTTTGATGTATAAATGC
1 TG-TCCAATTTTGATGTATAAATGC
* * *
31524054 TG-CCTAA-TTTGGTGTCTATATGC
1 TGTCC-AATTTTGATGTATAAATGC
* *
31524077 AGTCCAATTTTGATGTAAAAATGC
1 TGTCCAATTTTGATGTATAAATGC
*
31524101 TGTCCAA-TTTGATATATATATATATGC
1 TGTCCAATTTTG--ATGTATA-A-ATGC
* * *
31524128 TGCCCAA-ATTGGTGTATAAATGC
1 TGTCCAATTTTGATGTATAAATGC
31524151 TGTCCA
1 TGTCCA
31524157 NNNNNNNNNN
Statistics
Matches: 303, Mismatches: 62, Indels: 53
0.72 0.15 0.13
Matches are distributed among these distances:
23 112 0.37
24 140 0.46
25 19 0.06
26 3 0.01
27 17 0.06
28 2 0.01
29 10 0.03
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (24 bp):
TGTCCAATTTTGATGTATAAATGC
Found at i:31523822 original size:47 final size:47
Alignment explanation
Indices: 31523747--31524110 Score: 319
Period size: 47 Copynumber: 7.6 Consensus size: 47
31523737 ATTCATGTCA
*
31523747 AATTTTGATGTATAAATGCTG-CCTAATTTTGTGTCTATATGCAGTCC
1 AATTTTGATGTATAAATGCTGTCC-AATTTTGTGTATATATGCAGTCC
* * * * * *
31523794 AATTTTGGTGTAAAAATGCTGTCCAATTTAATATATATATATATATGCTGCCC
1 AATTTTGATGTATAAATGCTGTCCAA--T--T-T-TGTGTATATATGCAGTCC
* * * * *
31523847 AA-ATTGATGTATAAATCCTGTACAATTTTAGTGTATAAATGCTGTCC
1 AATTTTGATGTATAAATGCTGTCCAATTTT-GTGTATATATGCAGTCC
* * *
31523894 AATTTTGATGTATAAATGCT-ACCTAATTTGGTGTCTATATGCAGTCC
1 AATTTTGATGTATAAATGCTGTCC-AATTTTGTGTATATATGCAGTCC
* * * * * *
31523941 AATTTTGGTGTAAAAATGTTGTCCAA-TTTGATATATATATGCTGCCC
1 AATTTTGATGTATAAATGCTGTCCAATTTTG-TGTATATATGCAGTCC
* * *
31523988 AA-ATTGATGTATAAATGCTGTCCAATTTTAGTGTATAAATGC-GATTC
1 AATTTTGATGTATAAATGCTGTCCAATTTT-GTGTATATATGCAG-TCC
* *
31524035 AATTTTGATGTATAAATGCTG-CCTAATTTGGTGTCTATATGCAGTCC
1 AATTTTGATGTATAAATGCTGTCC-AATTTTGTGTATATATGCAGTCC
*
31524082 AATTTTGATGTAAAAATGCTGTCCAATTT
1 AATTTTGATGTATAAATGCTGTCCAATTT
31524111 GATATATATA
Statistics
Matches: 251, Mismatches: 47, Indels: 38
0.75 0.14 0.11
Matches are distributed among these distances:
46 24 0.10
47 139 0.55
48 51 0.20
49 1 0.00
50 1 0.00
51 1 0.00
52 19 0.08
53 15 0.06
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.40
Consensus pattern (47 bp):
AATTTTGATGTATAAATGCTGTCCAATTTTGTGTATATATGCAGTCC
Found at i:31524060 original size:141 final size:141
Alignment explanation
Indices: 31523742--31524156 Score: 634
Period size: 141 Copynumber: 2.9 Consensus size: 141
31523732 ATTCGATTCA
* *
31523742 TGTCAAATTTTGATGTATAAATGCTGCCTAATTTTGTGTCTATATGCAGTCCAATTTTGGTGTAA
1 TGTCCAATTTTGATGTATAAATGCTGCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAA
* * *
31523807 AAATGCTGTCCAATTTAATATATATATATATATGCTGCCCAAATTGATGTATAAATCCTGTACAA
66 AAATGCTGTCCAA--T--T-T-GATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAA
31523872 TTTTAGTGTATAAATGC
125 TTTTAGTGTATAAATGC
*
31523889 TGTCCAATTTTGATGTATAAATGCTACCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAA
1 TGTCCAATTTTGATGTATAAATGCTGCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAA
*
31523954 AAATGTTGTCCAATTTGATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAG
66 AAATGCTGTCCAATTTGATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAG
31524019 TGTATAAATGC
131 TGTATAAATGC
* *
31524030 -GATTCAATTTTGATGTATAAATGCTGCCTAATTTGGTGTCTATATGCAGTCCAATTTTGATGTA
1 TG-TCCAATTTTGATGTATAAATGCTGCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTA
*
31524094 AAAATGCTGTCCAATTTGATATATATATATATGCTGCCCAAATTGGTGTATAAATGCTGTCCA
65 AAAATGCTGTCCAATTTG----ATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCA
31524157 NNNNNNNNNN
Statistics
Matches: 251, Mismatches: 12, Indels: 12
0.91 0.04 0.04
Matches are distributed among these distances:
140 1 0.00
141 133 0.53
142 1 0.00
143 1 0.00
145 41 0.16
147 74 0.29
ACGTcount: A:0.31, C:0.13, G:0.16, T:0.40
Consensus pattern (141 bp):
TGTCCAATTTTGATGTATAAATGCTGCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAA
AAATGCTGTCCAATTTGATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAG
TGTATAAATGC
Found at i:31529545 original size:24 final size:23
Alignment explanation
Indices: 31529513--31529576 Score: 83
Period size: 24 Copynumber: 2.7 Consensus size: 23
31529503 NNNNNNNNNN
31529513 CAATTTGGTGTATATATGCTGTC
1 CAATTTGGTGTATATATGCTGTC
* * *
31529536 CAATTTTGGTGTAAAAATGTTGTC
1 CAA-TTTGGTGTATATATGCTGTC
*
31529560 CAATTTGGTTTATATAT
1 CAATTTGGTGTATATAT
31529577 ATGCTGCCCA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 14 0.41
24 20 0.59
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (23 bp):
CAATTTGGTGTATATATGCTGTC
Found at i:31536898 original size:24 final size:23
Alignment explanation
Indices: 31536841--31536959 Score: 148
Period size: 23 Copynumber: 5.1 Consensus size: 23
31536831 GATTCAAGTG
* *
31536841 AATTTAGTGTATATATGCTGTCC
1 AATTTGGTGTATAAATGCTGTCC
31536864 AATTTGGTGTATAAATGCTGTCC
1 AATTTGGTGTATAAATGCTGTCC
*
31536887 AATTTTGGTGTATAAATGTTGTCC
1 AA-TTTGGTGTATAAATGCTGTCC
** * *
31536911 AATTTGGAATATATATGCTGCCC
1 AATTTGGTGTATAAATGCTGTCC
* *
31536934 AATTTGGTATATAAATGCTATCC
1 AATTTGGTGTATAAATGCTGTCC
31536957 AAT
1 AAT
31536960 CTGCCCAAAT
Statistics
Matches: 83, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
23 61 0.73
24 22 0.27
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (23 bp):
AATTTGGTGTATAAATGCTGTCC
Found at i:31536910 original size:47 final size:47
Alignment explanation
Indices: 31536847--31537419 Score: 485
Period size: 47 Copynumber: 11.9 Consensus size: 47
31536837 AGTGAATTTA
*
31536847 GTGTATATATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTG
1 GTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTG
* ** * *
31536894 GTGTATAAATGTTGTCCAATTTGGAATATATATGCTGCCCAA-TTTG
1 GTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTG
* * * *
31536940 GTATATAAATGCTATCCAATCTGCCCAAATTGATGTATAAATGCTGTCCAATTTTA
1 GTGTATAAATGCTGTCCAA--T-------TTGGTGTATAAATGCTGTCCAATTTTG
*
31536996 GTGTATAAATGCTGTCCAATTTTGATGTATAAATGCTG-CCTAA-TTTG
1 GTGTATAAATGCTGTCCAA-TTTGGTGTATAAATGCTGTCC-AATTTTG
* * * * ** *
31537043 GTGTCTATATGCAGTCCAATTTTGGTGTAAAAATATTGTCTAA-TTTG
1 GTGTATAAATGCTGTCCAA-TTTGGTGTATAAATGCTGTCCAATTTTG
* * * * * *
31537090 ATATATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTTA
1 --GTGTATA-A-ATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTG
** * *
31537141 GTGTATAAATGGGGTTCAATTTTGATGTATAAATGCT-TCCTAA-TTTG
1 GTGTATAAATGCTGTCCAA-TTTGGTGTATAAATGCTGTCC-AATTTTG
* * * *
31537188 GTGTCTATATGCAGTCCAATTTTGGTGTAAAAATGCTGTCCAA-TTTG
1 GTGTATAAATGCTGTCCAA-TTTGGTGTATAAATGCTGTCCAATTTTG
* * * * *
31537235 ATATATATATGCTGCCCAAATTGGTGTATAAATGCTGTCCAATTTTG
1 GTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTG
* * *
31537282 GTGTATAAATGTTGTCTAATTTGGTGTATATATGCTGTCCAATTTTG
1 GTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTG
* *
31537329 ATGTATAAATGCTGTCCAATTTGGTGTATATATGCTGTCCAATTTTG
1 GTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTG
* * * * *
31537376 GTGTAAAAACGTTGTCCAATTTGGTTTATATATATGCTGCCCAA
1 GTGTATAAATGCTGTCCAATTTGGTGTATA-A-ATGCTGTCCAA
31537420 CCTATGTTGT
Statistics
Matches: 423, Mismatches: 80, Indels: 44
0.77 0.15 0.08
Matches are distributed among these distances:
46 41 0.10
47 253 0.60
48 43 0.10
49 19 0.04
50 17 0.04
51 12 0.03
55 18 0.04
56 20 0.05
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (47 bp):
GTGTATAAATGCTGTCCAATTTGGTGTATAAATGCTGTCCAATTTTG
Found at i:31536979 original size:32 final size:32
Alignment explanation
Indices: 31536928--31536991 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
31536918 AATATATATG
* *
31536928 CTGCCCAATTTGGTATATAAATGCTATCCAAT
1 CTGCCCAAATTGATATATAAATGCTATCCAAT
* *
31536960 CTGCCCAAATTGATGTATAAATGCTGTCCAAT
1 CTGCCCAAATTGATATATAAATGCTATCCAAT
31536992 TTTAGTGTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.31, C:0.22, G:0.14, T:0.33
Consensus pattern (32 bp):
CTGCCCAAATTGATATATAAATGCTATCCAAT
Found at i:31537000 original size:24 final size:24
Alignment explanation
Indices: 31536973--31537419 Score: 403
Period size: 24 Copynumber: 18.8 Consensus size: 24
31536963 CCCAAATTGA
*
31536973 TGTATAAATGCTGTCCAATTTTAG
1 TGTATAAATGCTGTCCAATTTTGG
*
31536997 TGTATAAATGCTGTCCAATTTTGA
1 TGTATAAATGCTGTCCAATTTTGG
31537021 TGTATAAATGCTG-CCTAA-TTTGG
1 TGTATAAATGCTGTCC-AATTTTGG
* * *
31537044 TGTCTATATGCAGTCCAATTTTGG
1 TGTATAAATGCTGTCCAATTTTGG
* ** * *
31537068 TGTAAAAATATTGTCTAA-TTTGATA
1 TGTATAAATGCTGTCCAATTTTG--G
* * * *
31537093 TATATATATATGCTGCCCAA-ATTGA
1 TGTATA-A-ATGCTGTCCAATTTTGG
*
31537118 TGTATAAATGCTGTCCAATTTTAG
1 TGTATAAATGCTGTCCAATTTTGG
** * *
31537142 TGTATAAATGGGGTTCAATTTTGA
1 TGTATAAATGCTGTCCAATTTTGG
31537166 TGTATAAATGCT-TCCTAA-TTTGG
1 TGTATAAATGCTGTCC-AATTTTGG
* * *
31537189 TGTCTATATGCAGTCCAATTTTGG
1 TGTATAAATGCTGTCCAATTTTGG
* *
31537213 TGTAAAAATGCTGTCCAA-TTTGA
1 TGTATAAATGCTGTCCAATTTTGG
* * * *
31537236 TATATATATGCTGCCCAA-ATTGG
1 TGTATAAATGCTGTCCAATTTTGG
31537259 TGTATAAATGCTGTCCAATTTTGG
1 TGTATAAATGCTGTCCAATTTTGG
* *
31537283 TGTATAAATGTTGTCTAA-TTTGG
1 TGTATAAATGCTGTCCAATTTTGG
* *
31537306 TGTATATATGCTGTCCAATTTTGA
1 TGTATAAATGCTGTCCAATTTTGG
31537330 TGTATAAATGCTGTCCAA-TTTGG
1 TGTATAAATGCTGTCCAATTTTGG
*
31537353 TGTATATATGCTGTCCAATTTTGG
1 TGTATAAATGCTGTCCAATTTTGG
* * *
31537377 TGTAAAAACGTTGTCCAA-TTTGG
1 TGTATAAATGCTGTCCAATTTTGG
* *
31537400 TTTATATATATGCTGCCCAA
1 TGTATA-A-ATGCTGTCCAA
31537420 CCTATGTTGT
Statistics
Matches: 336, Mismatches: 71, Indels: 31
0.77 0.16 0.07
Matches are distributed among these distances:
23 135 0.40
24 172 0.51
25 18 0.05
26 1 0.00
27 10 0.03
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (24 bp):
TGTATAAATGCTGTCCAATTTTGG
Found at i:31537146 original size:145 final size:141
Alignment explanation
Indices: 31536960--31537373 Score: 573
Period size: 145 Copynumber: 2.9 Consensus size: 141
31536950 GCTATCCAAT
31536960 CTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAGTGTATAAATGCTGTCCAATTTTGATGTA
1 CTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAGTGTATAAATGCTGTCCAATTTTGATGTA
* *
31537025 TAAATGCTGCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAATATTGTCTAATTTG
66 TAAATGCTGCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAATACTGTCCAATTTG
31537090 ATATATATATATATG
131 ----ATATATATATG
** *
31537105 CTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAGTGTATAAATGGGGTTCAATTTTGATGTA
1 CTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAGTGTATAAATGCTGTCCAATTTTGATGTA
* *
31537170 TAAATGCTTCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAATGCTGTCCAATTTG
66 TAAATGCTGCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAATACTGTCCAATTTG
31537235 ATATATATATG
131 ATATATATATG
* * * * *
31537246 CTGCCCAAATTGGTGTATAAATGCTGTCCAATTTTGGTGTATAAATGTTGTCTAA-TTTGGTGTA
1 CTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAGTGTATAAATGCTGTCCAATTTTGATGTA
* * * * * * * *
31537310 TATATGCTGTCC-AATTTTGATGTATAAATGCTGTCCAA-TTTGGTGTATATATGCTGTCCAATT
66 TAAATGCTG-CCTAA-TTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAATACTGTCCAATT
31537373 T
129 T
31537374 TGGTGTAAAA
Statistics
Matches: 245, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
140 41 0.17
141 81 0.33
145 123 0.50
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (141 bp):
CTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAGTGTATAAATGCTGTCCAATTTTGATGTA
TAAATGCTGCCTAATTTGGTGTCTATATGCAGTCCAATTTTGGTGTAAAAATACTGTCCAATTTG
ATATATATATG
Found at i:31537280 original size:117 final size:118
Alignment explanation
Indices: 31536969--31537397 Score: 411
Period size: 117 Copynumber: 3.6 Consensus size: 118
31536959 TCTGCCCAAA
* * * *
31536969 TTGATGTATAAATGCTGTCCAATTTTAGTGTATAAATGCTGTCCAATTTTGATGTATAAATGCTG
1 TTGATGTAAAAATGCTGTCCAATTTGA-TGTATATATGCTGTCCAATTTTGGTGTATAAATGCTG
* * * ** * * *** *
31537034 -CCTAA-TTTGGTGTCTATATGCAGTCC-AATTTTGGTGTAAAAATATTGTCTAA-T
65 TCC-AATTTTGATGTATAAATGTTG-CCTAA-TTTGGTGTATATATGCAGTCCAATT
* * * * *
31537087 TTGATATATATATATATGCTGCCCAAATTGATGTATAAATGCTGTCCAATTTTAGTGTATAAATG
1 TTGATGTA-A-A-A-ATGCTGTCCAATTTGATGTATATATGCTGTCCAATTTTGGTGTATAAATG
** * *
31537152 GGGTTCAATTTTGATGTATAAATGCTT-CCTAATTTGGTGTCTATATGCAGTCCAATT
62 CTGTCCAATTTTGATGTATAAATG-TTGCCTAATTTGGTGTATATATGCAGTCCAATT
* * * *
31537209 TTGGTGTAAAAATGCTGTCCAATTTGATATATATATGCTGCCCAA-ATTGGTGTATAAATGCTGT
1 TTGATGTAAAAATGCTGTCCAATTTGATGTATATATGCTGTCCAATTTTGGTGTATAAATGCTGT
* * *
31537273 CCAATTTTGGTGTATAAATGTTGTCTAATTTGGTGTATATATGCTGTCCAATT
66 CCAATTTTGATGTATAAATGTTGCCTAATTTGGTGTATATATGCAGTCCAATT
* * * * *
31537326 TTGATGTATAAATGCTGTCCAATTTGGTGTATATATGCTGTCCAATTTTGGTGTAAAAACGTTGT
1 TTGATGTAAAAATGCTGTCCAATTTGATGTATATATGCTGTCCAATTTTGGTGTATAAATGCTGT
31537391 CCAATTT
66 CCAATTT
31537398 GGTTTATATA
Statistics
Matches: 253, Mismatches: 47, Indels: 22
0.79 0.15 0.07
Matches are distributed among these distances:
116 2 0.01
117 100 0.40
118 58 0.23
119 1 0.00
120 2 0.01
121 55 0.22
122 35 0.14
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.41
Consensus pattern (118 bp):
TTGATGTAAAAATGCTGTCCAATTTGATGTATATATGCTGTCCAATTTTGGTGTATAAATGCTGT
CCAATTTTGATGTATAAATGTTGCCTAATTTGGTGTATATATGCAGTCCAATT
Found at i:31539286 original size:5 final size:5
Alignment explanation
Indices: 31539271--31539303 Score: 50
Period size: 5 Copynumber: 6.6 Consensus size: 5
31539261 TATCTACTTA
31539271 TTTATT TTTAT TTTAT TTTA- TTTAT TTTAT TTT
1 TTTA-T TTTAT TTTAT TTTAT TTTAT TTTAT TTT
31539304 TGTTTGTTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 4 0.15
5 18 0.69
6 4 0.15
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:31539296 original size:14 final size:14
Alignment explanation
Indices: 31539277--31539303 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
31539267 CTTATTTATT
31539277 TTTATTTTATTTTA
1 TTTATTTTATTTTA
31539291 TTTATTTTATTTT
1 TTTATTTTATTTT
31539304 TGTTTGTTTC
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:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:31540307 original size:9 final size:9
Alignment explanation
Indices: 31540295--31540342 Score: 51
Period size: 9 Copynumber: 5.3 Consensus size: 9
31540285 TCTTATCTTC
31540295 ATTATTACT
1 ATTATTACT
*
31540304 ATTATTATT
1 ATTATTACT
* *
31540313 AATATTATT
1 ATTATTACT
* *
31540322 AATATTAAT
1 ATTATTACT
31540331 ATTATTACT
1 ATTATTACT
31540340 ATT
1 ATT
31540343 GTTATTATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTATTACT
Found at i:31540350 original size:15 final size:15
Alignment explanation
Indices: 31540303--31540342 Score: 62
Period size: 15 Copynumber: 2.7 Consensus size: 15
31540293 TCATTATTAC
*
31540303 TATTATTATTAATAT
1 TATTAATATTAATAT
31540318 TATTAATATTAATAT
1 TATTAATATTAATAT
*
31540333 TATTACTATT
1 TATTAATATT
31540343 GTTATTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (15 bp):
TATTAATATTAATAT
Found at i:31552021 original size:12 final size:12
Alignment explanation
Indices: 31552004--31552028 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
31551994 AAATTGAGAT
31552004 TATCCCTTCAGA
1 TATCCCTTCAGA
31552016 TATCCCTTCAGA
1 TATCCCTTCAGA
31552028 T
1 T
31552029 TTTTTTTGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (12 bp):
TATCCCTTCAGA
Found at i:31552911 original size:46 final size:46
Alignment explanation
Indices: 31552844--31553022 Score: 272
Period size: 46 Copynumber: 3.9 Consensus size: 46
31552834 TGCAGGGGAA
* *
31552844 TAGATTAAAGCTGAAGG-CAGCGAATCTCATTTCTATGGCGTCGTAC
1 TAGATTAAAGCTG-AGGTCAGCGAATCTCATTTCCATGGCGTCGTAG
*
31552890 TAGATTAAAGTTGAGGTCAGCGAATCTCATTTCCATGGCGTCGTAG
1 TAGATTAAAGCTGAGGTCAGCGAATCTCATTTCCATGGCGTCGTAG
* *
31552936 TAGATTAAAGCTGAGGGCAGCGAATCTCATTTCCATGACGTCGTAG
1 TAGATTAAAGCTGAGGTCAGCGAATCTCATTTCCATGGCGTCGTAG
*
31552982 TAGATTAAAGCTGAGGGT-AGCGAATCTCATTTCCTTGGCGT
1 TAGATTAAAGCTGA-GGTCAGCGAATCTCATTTCCATGGCGT
31553023 TGCAGTGGAA
Statistics
Matches: 122, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
45 3 0.02
46 117 0.96
47 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.29
Consensus pattern (46 bp):
TAGATTAAAGCTGAGGTCAGCGAATCTCATTTCCATGGCGTCGTAG
Found at i:31553083 original size:97 final size:96
Alignment explanation
Indices: 31552819--31553083 Score: 317
Period size: 92 Copynumber: 2.8 Consensus size: 96
31552809 GACACCAATA
* * * *
31552819 TCATTTCCTTGGCTTTGCAGGGGAATAGATTAAAGCTGAAGGCAGCGAATCTCATTTCTATGGCG
1 TCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTGAGGGCAGCGAATCTCATTTCCAT-GCG
* *
31552884 TCGTACTAGATTAAAGTTGAGGTCAGCGAATC
65 TCGTAGTAGATTAAAGCTGAGGTCAGCGAATC
* *
31552916 TCATTTCCATGGCG-T-C-GT--AGTAGATTAAAGCTGAGGGCAGCGAATCTCATTTCCATGACG
1 TCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTGAGGGCAGCGAATCTCATTTCCATG-CG
31552976 TCGTAGTAGATTAAAGCTGAGGGT-AGCGAATC
65 TCGTAGTAGATTAAAGCTGA-GGTCAGCGAATC
* * * * * *
31553008 TCATTTCCTTGGCGTTGCAGTGGAATAAATTGAAGCTGAGGGCAACGAATTTTATTTCCCTAGCG
1 TCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTGAGGGCAGCGAATCTCATTTCCAT-GCG
*
31553073 TCATAGTAGAT
65 TCGTAGTAGAT
31553084 AGCAGCGAAT
Statistics
Matches: 143, Mismatches: 17, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
91 1 0.01
92 76 0.53
93 4 0.03
94 2 0.01
95 3 0.02
96 1 0.01
97 55 0.38
98 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.26, T:0.30
Consensus pattern (96 bp):
TCATTTCCTTGGCGTTGCAGTGGAATAGATTAAAGCTGAGGGCAGCGAATCTCATTTCCATGCGT
CGTAGTAGATTAAAGCTGAGGTCAGCGAATC
Found at i:31553224 original size:50 final size:50
Alignment explanation
Indices: 31553118--31553463 Score: 250
Period size: 50 Copynumber: 7.0 Consensus size: 50
31553108 ATTACAGTGG
* * ** * * *
31553118 AACAA-ATTAAAGCTAAAGACAGCGAATCTTGTTTCCCAGACGTTACAGTTA
1 AACAAGATTGAAGCTACA-ACAGCGAATCTTACTTCTCTGACGTTGCAG-TA
* * *
31553169 AATAAGATTGAAGCTACAACAACGAATCTTACTTCTCTGATGTTGCAGTA
1 AACAAGATTGAAGCTACAACAGCGAATCTTACTTCTCTGACGTTGCAGTA
* * * *
31553219 AATAAGATTCAAG-TGACAACAGCGAATCTTACTTCTCTGACATTACAGTA
1 AACAAGATTGAAGCT-ACAACAGCGAATCTTACTTCTCTGACGTTGCAGTA
**
31553269 AAGC-AGATTGAAGCTACAACAGCGAATCTTACTTCTCCAACG-T----T-
1 AA-CAAGATTGAAGCTACAACAGCGAATCTTACTTCTCTGACGTTGCAGTA
* * * *
31553313 -ACAA-ATTGAAGCTATAACGGCGAATCTTACTTCCCCGACGTTGCAGTGA
1 AACAAGATTGAAGCTACAACAGCGAATCTTACTTCTCTGACGTTGCAGT-A
* * * *
31553362 AGCAAG-TTAAAGCTACAACAGCAAATTTTACTTCTCTGACGTTGCAG-A
1 AACAAGATTGAAGCTACAACAGCGAATCTTACTTCTCTGACGTTGCAGTA
* * * * * * *
31553410 AAAATAGATTAAAGCTAAAGACAACGAATCTTATTTCCTCTGAAGATGCAGTA
1 AACA-AGATTGAAGCTACA-ACAGCGAATCTTACTT-CTCTGACGTTGCAGTA
31553463 A
1 A
31553464 GTGGAATGAG
Statistics
Matches: 235, Mismatches: 41, Indels: 36
0.75 0.13 0.12
Matches are distributed among these distances:
42 33 0.14
43 3 0.01
45 1 0.00
47 1 0.00
48 3 0.01
49 4 0.02
50 126 0.54
51 40 0.17
52 22 0.09
53 2 0.01
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (50 bp):
AACAAGATTGAAGCTACAACAGCGAATCTTACTTCTCTGACGTTGCAGTA
Found at i:31553336 original size:42 final size:42
Alignment explanation
Indices: 31553275--31553354 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
31553265 AGTAAAGCAG
*
31553275 ATTGAAGCTACAACAGCGAATCTTACTTCTCCAACGTTACAA
1 ATTGAAGCTACAACAGCGAATCTTACTTCCCCAACGTTACAA
* * *
31553317 ATTGAAGCTATAACGGCGAATCTTACTTCCCCGACGTT
1 ATTGAAGCTACAACAGCGAATCTTACTTCCCCAACGTT
31553355 GCAGTGAAGC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (42 bp):
ATTGAAGCTACAACAGCGAATCTTACTTCCCCAACGTTACAA
Found at i:31553393 original size:142 final size:143
Alignment explanation
Indices: 31553175--31553442 Score: 326
Period size: 142 Copynumber: 1.9 Consensus size: 143
31553165 GTTAAATAAG
* * * * *
31553175 ATTGAAGCTACAACAACGAATCTTACTTCTCTGATGTTGCAGTAAATAAGATTCAAGTGACAACA
1 ATTGAAGCTACAACAACGAATCTTACTTCCCCGACGTTGCAGTAAACAAGATTAAAGTGACAACA
* * * * * *
31553240 GCGAATCTTACTTCTCTGACATTACAGTAAAGCAGATTGAAGCTACA-ACAGCGAATCTTACTTC
66 GCAAATCTTACTTCTCTGACATTACAGAAAAACAGATTAAAGCTAAAGACAACGAATCTTACTTC
31553304 TCCAACGTTACAA
131 TCCAACGTTACAA
* ** *
31553317 ATTGAAGCTATAACGGCGAATCTTACTTCCCCGACGTTGCAGTGAAGCAAG-TTAAAGCT-ACAA
1 ATTGAAGCTACAACAACGAATCTTACTTCCCCGACGTTGCAGT-AAACAAGATTAAAG-TGACAA
* * * *
31553380 CAGCAAATTTTACTTCTCTGACGTTGCAGAAAAATAGATTAAAGCTAAAGACAACGAATCTTA
64 CAGCAAATCTTACTTCTCTGACATTACAGAAAAACAGATTAAAGCTAAAGACAACGAATCTTA
31553443 TTTCCTCTGA
Statistics
Matches: 104, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
142 86 0.83
143 18 0.17
ACGTcount: A:0.37, C:0.21, G:0.16, T:0.26
Consensus pattern (143 bp):
ATTGAAGCTACAACAACGAATCTTACTTCCCCGACGTTGCAGTAAACAAGATTAAAGTGACAACA
GCAAATCTTACTTCTCTGACATTACAGAAAAACAGATTAAAGCTAAAGACAACGAATCTTACTTC
TCCAACGTTACAA
Found at i:31553733 original size:11 final size:11
Alignment explanation
Indices: 31553717--31553743 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
31553707 CCTAGCCCAC
31553717 AAAAAAAACAA
1 AAAAAAAACAA
31553728 AAAAAAAACAA
1 AAAAAAAACAA
31553739 AAAAA
1 AAAAA
31553744 CCCTAAGCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:31555035 original size:3 final size:3
Alignment explanation
Indices: 31555027--31555112 Score: 68
Period size: 3 Copynumber: 29.0 Consensus size: 3
31555017 ATATTCGCTG
* * * * *
31555027 TTA TTA TTA TCA TTC TTA TCT- TCA TTA TTA CTA TTA CTA TTA TTA
1 TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
31555072 ATA TTA TTA TTA TTA TTA CTA TTG TTA TTA -TA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31555113 CAATTTATCT
Statistics
Matches: 62, Mismatches: 18, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
2 2 0.03
3 59 0.95
4 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.01, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:31556732 original size:3 final size:3
Alignment explanation
Indices: 31556724--31556768 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
31556714 NNNNNNNNNN
* *
31556724 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TGT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31556769 ATTTTTATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:31564259 original size:21 final size:21
Alignment explanation
Indices: 31564207--31564260 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
31564197 TGTGTTTACT
31564207 TTTC-GTTTAACTCTCATGAG
1 TTTCAGTTTAACTCTCATGAG
*
31564227 CTTCAG-TTAACTCAT-ATGAG
1 TTTCAGTTTAACTC-TCATGAG
31564247 TTTCAGTTTAACTC
1 TTTCAGTTTAACTC
31564261 CATTGGGTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
20 20 0.69
21 9 0.31
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (21 bp):
TTTCAGTTTAACTCTCATGAG
Found at i:31564270 original size:21 final size:21
Alignment explanation
Indices: 31564207--31564270 Score: 64
Period size: 20 Copynumber: 3.1 Consensus size: 21
31564197 TGTGTTTACT
31564207 TTTC-GTTTAACTCTCA-TGAG
1 TTTCAGTTTAACTC-CATTGAG
*
31564227 CTTCAG-TTAACT-CATATGAG
1 TTTCAGTTTAACTCCAT-TGAG
*
31564247 TTTCAGTTTAACTCCATTGGG
1 TTTCAGTTTAACTCCATTGAG
31564268 TTT
1 TTT
31564271 TCATTCAGCT
Statistics
Matches: 36, Mismatches: 3, Indels: 9
0.75 0.06 0.19
Matches are distributed among these distances:
18 2 0.06
20 18 0.50
21 13 0.36
22 3 0.08
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.44
Consensus pattern (21 bp):
TTTCAGTTTAACTCCATTGAG
Found at i:31564310 original size:42 final size:42
Alignment explanation
Indices: 31564264--31564355 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
31564254 TTAACTCCAT
* * * *
31564264 TGGGTTTTCATTCAGCTCTTTTGAGCTTCAATTTAACCCTTA
1 TGGGTTTCCATTCAGCTCTTATGAGCTTCAATTCAACCCTAA
*
31564306 TGGGTTTCCCTTCAGCTCTTATGAGCTTCAATTCAACCCTAA
1 TGGGTTTCCATTCAGCTCTTATGAGCTTCAATTCAACCCTAA
*
31564348 CGGGTTTC
1 TGGGTTTC
31564356 TGTTTAGCAC
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.18, C:0.25, G:0.16, T:0.40
Consensus pattern (42 bp):
TGGGTTTCCATTCAGCTCTTATGAGCTTCAATTCAACCCTAA
Found at i:31564340 original size:21 final size:21
Alignment explanation
Indices: 31564273--31564340 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
31564263 TTGGGTTTTC
*
31564273 ATTCAGCTCTTTTGAGCTTCA
1 ATTCAGCTCTTATGAGCTTCA
* * * * * *
31564294 ATTTAACCCTTATGGGTTTCC
1 ATTCAGCTCTTATGAGCTTCA
*
31564315 CTTCAGCTCTTATGAGCTTCA
1 ATTCAGCTCTTATGAGCTTCA
31564336 ATTCA
1 ATTCA
31564341 ACCCTAACGG
Statistics
Matches: 32, Mismatches: 15, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.25, G:0.13, T:0.41
Consensus pattern (21 bp):
ATTCAGCTCTTATGAGCTTCA
Found at i:31564369 original size:42 final size:42
Alignment explanation
Indices: 31564265--31564370 Score: 113
Period size: 42 Copynumber: 2.5 Consensus size: 42
31564255 TAACTCCATT
* * * * * * *
31564265 GGGTTTTCATTCAGCTCTTTTGAGCTTCAATTTAACCCTTAT
1 GGGTTTCCCTTCAGCACTTATGAGCTTCAATTCAACCCTAAC
*
31564307 GGGTTTCCCTTCAGCTCTTATGAGCTTCAATTCAACCCTAAC
1 GGGTTTCCCTTCAGCACTTATGAGCTTCAATTCAACCCTAAC
** *
31564349 GGGTTTCTGTTTAGCACTTATG
1 GGGTTTCCCTTCAGCACTTATG
31564371 TGCTCCTGTG
Statistics
Matches: 54, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 54 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.41
Consensus pattern (42 bp):
GGGTTTCCCTTCAGCACTTATGAGCTTCAATTCAACCCTAAC
Found at i:31566246 original size:20 final size:20
Alignment explanation
Indices: 31566208--31566246 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31566198 TGACTTCACT
*
31566208 AAATAAAATAATATTTTTTA
1 AAATAAAATAATATATTTTA
31566228 AAATAAAA-AATATCATTTT
1 AAATAAAATAATAT-ATTTT
31566247 TAATTTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (20 bp):
AAATAAAATAATATATTTTA
Found at i:31567544 original size:6 final size:6
Alignment explanation
Indices: 31567494--31567528 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
31567484 ACTTTTAGCC
31567494 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
1 TTTAGT TTTAGT TTTAGT TTTAGT TTTAGT TTTAG
31567529 AATTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.66
Consensus pattern (6 bp):
TTTAGT
Found at i:31568275 original size:14 final size:16
Alignment explanation
Indices: 31568245--31568277 Score: 52
Period size: 14 Copynumber: 2.2 Consensus size: 16
31568235 AAAGTATTAT
31568245 TTTCTATTTTTATATA
1 TTTCTATTTTTATATA
31568261 TTTCT-TTTTTA-ATA
1 TTTCTATTTTTATATA
31568275 TTT
1 TTT
31568278 TTTCTTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 6 0.35
16 5 0.29
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTCTATTTTTATATA
Found at i:31583631 original size:12 final size:12
Alignment explanation
Indices: 31583614--31583640 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31583604 CACAAATCAT
31583614 TGAAGAAGAAGA
1 TGAAGAAGAAGA
31583626 TGAAGAAGAAGA
1 TGAAGAAGAAGA
31583638 TGA
1 TGA
31583641 TGATGATGAC
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:0.56, C:0.00, G:0.33, T:0.11
Consensus pattern (12 bp):
TGAAGAAGAAGA
Found at i:31588066 original size:30 final size:27
Alignment explanation
Indices: 31588003--31588076 Score: 69
Period size: 30 Copynumber: 2.6 Consensus size: 27
31587993 CAATTAGATT
* *
31588003 TATTTAAAATA-AAAAAATTAAATTTA
1 TATTTAAAAAATAAAAAATTAAATTAA
31588029 TATTTTAAAAAATAAAAAATATAATATTAA
1 TA-TTTAAAAAATAAAAAAT-TAA-ATTAA
* *
31588059 GTATTTAAATATTAAAAA
1 -TATTTAAAAAATAAAAA
31588077 TATTTNNNNN
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 2 0.05
27 8 0.21
28 7 0.18
29 3 0.08
30 17 0.44
31 2 0.05
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (27 bp):
TATTTAAAAAATAAAAAATTAAATTAA
Found at i:31588584 original size:27 final size:26
Alignment explanation
Indices: 31588554--31588617 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 26
31588544 TTTATCGAGG
* *
31588554 TTATTAGTTTATCGGTAAATAAATATT
1 TTATTAATTTATCGATAAATAAATA-T
* *
31588581 TTATTAATTTATTGATAAATTAATAT
1 TTATTAATTTATCGATAAATAAATAT
31588607 TTATTAATTTA
1 TTATTAATTTA
31588618 GAAAATATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
26 12 0.36
27 21 0.64
ACGTcount: A:0.39, C:0.02, G:0.06, T:0.53
Consensus pattern (26 bp):
TTATTAATTTATCGATAAATAAATAT
Found at i:31588739 original size:36 final size:38
Alignment explanation
Indices: 31588695--31588769 Score: 127
Period size: 36 Copynumber: 2.0 Consensus size: 38
31588685 TGAATCGGAG
*
31588695 TTAATTGGTTCATGTAA-CAAAAA-AAGAAAGAGTTAA
1 TTAATTGGTTCATGTAACCAAAAAGAAAAAAGAGTTAA
31588731 TTAATTGGTTCATGTAACCAAAAAGAAAAAAGAGTTAA
1 TTAATTGGTTCATGTAACCAAAAAGAAAAAAGAGTTAA
31588769 T
1 T
31588770 GGTTTCAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 17 0.47
37 6 0.17
38 13 0.36
ACGTcount: A:0.49, C:0.07, G:0.16, T:0.28
Consensus pattern (38 bp):
TTAATTGGTTCATGTAACCAAAAAGAAAAAAGAGTTAA
Found at i:31590632 original size:17 final size:17
Alignment explanation
Indices: 31590610--31590654 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
31590600 CCGAAAAAAA
31590610 ATTATT-ATTTAATCGAG
1 ATTATTAATTT-ATCGAG
31590627 ATTATTAATTTATCGA-
1 ATTATTAATTTATCGAG
*
31590643 A-TATTCATTTAT
1 ATTATTAATTTAT
31590655 TGAGGTTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
15 10 0.38
16 1 0.04
17 11 0.42
18 4 0.15
ACGTcount: A:0.36, C:0.07, G:0.07, T:0.51
Consensus pattern (17 bp):
ATTATTAATTTATCGAG
Found at i:31595271 original size:29 final size:29
Alignment explanation
Indices: 31595181--31595272 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 29
31595171 TTGAATAATG
* * * *
31595181 GAATATGACAGCATCGATGTGCATATTCA
1 GAATAGGACAACACCGAAGTGCATATTCA
* * * *
31595210 GAACAAGACAACACTGAA-TGCGTATTCA
1 GAATAGGACAACACCGAAGTGCATATTCA
*
31595238 GAATAGGATAACACCGAAGTGCATATTCA
1 GAATAGGACAACACCGAAGTGCATATTCA
*
31595267 AAATAG
1 GAATAG
31595273 AGAGAGCGCT
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
28 23 0.47
29 26 0.53
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (29 bp):
GAATAGGACAACACCGAAGTGCATATTCA
Found at i:31600146 original size:23 final size:23
Alignment explanation
Indices: 31600134--31600190 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 23
31600124 TTGTCGTTTG
*
31600134 TAATGTTGTTTCACTATTGCTTT
1 TAATGTTGTTTCACTATCGCTTT
* **
31600157 TAATGTTGTTTCGCTGCCGCTTT
1 TAATGTTGTTTCACTATCGCTTT
*
31600180 TAATATTGTTT
1 TAATGTTGTTT
31600191 GGATATTGTA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (23 bp):
TAATGTTGTTTCACTATCGCTTT
Found at i:31602611 original size:21 final size:22
Alignment explanation
Indices: 31602571--31602615 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
31602561 ATTATACTTG
* *
31602571 TTTATTATTGTTATTTATTATT
1 TTTAATATTGTTAATTATTATT
31602593 TTTAATATTG-TAATTATTATT
1 TTTAATATTGTTAATTATTATT
31602614 TT
1 TT
31602616 CGTGTACATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTAATATTGTTAATTATTATT
Found at i:31606840 original size:19 final size:18
Alignment explanation
Indices: 31606812--31606851 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
31606802 GCAAATGTTC
31606812 TTTCACTCTTTACGATTTT
1 TTTCACTCTTT-CGATTTT
* *
31606831 TTTCATTCTTTTGATTTT
1 TTTCACTCTTTCGATTTT
31606849 TTT
1 TTT
31606852 TCTGCCAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.12, C:0.15, G:0.05, T:0.68
Consensus pattern (18 bp):
TTTCACTCTTTCGATTTT
Found at i:31606909 original size:46 final size:46
Alignment explanation
Indices: 31606835--31606968 Score: 243
Period size: 46 Copynumber: 2.9 Consensus size: 46
31606825 GATTTTTTTC
31606835 ATTCTTTTGA-TTTTTTTTCTGCCAAACCATTCATTCATTCATATT
1 ATTCTTTTGATTTTTTTTTCTGCCAAACCATTCATTCATTCATATT
*
31606880 ATTCTTTTGATTTTTTTTTCTGCAAAACCATTCATTCATTCATATT
1 ATTCTTTTGATTTTTTTTTCTGCCAAACCATTCATTCATTCATATT
*
31606926 ATTCCTTTGATTTTTTTTTCTGCCAAACCATTCATTCATTCAT
1 ATTCTTTTGATTTTTTTTTCTGCCAAACCATTCATTCATTCAT
31606969 TCATATTATT
Statistics
Matches: 85, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
45 10 0.12
46 75 0.88
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (46 bp):
ATTCTTTTGATTTTTTTTTCTGCCAAACCATTCATTCATTCATATT
Found at i:31607875 original size:16 final size:16
Alignment explanation
Indices: 31607854--31607923 Score: 71
Period size: 14 Copynumber: 4.8 Consensus size: 16
31607844 TTGAGTCGTT
**
31607854 AAAAAATGATGAAGTG
1 AAAAAATGAAAAAGTG
31607870 AAAAAATGAAAAAGTG
1 AAAAAATGAAAAAGTG
*
31607886 --AAAAGGAAAAA-TG
1 AAAAAATGAAAAAGTG
31607899 -AAAAATGAAAAA-TG
1 AAAAAATGAAAAAGTG
31607913 AAAAAA-GAAAA
1 AAAAAATGAAAA
31607924 TGGAGAGGCT
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.04
14 27 0.56
15 5 0.10
16 14 0.29
ACGTcount: A:0.70, C:0.00, G:0.19, T:0.11
Consensus pattern (16 bp):
AAAAAATGAAAAAGTG
Found at i:31607889 original size:7 final size:7
Alignment explanation
Indices: 31607871--31607923 Score: 72
Period size: 7 Copynumber: 7.6 Consensus size: 7
31607861 GATGAAGTGA
31607871 AAAAATG
1 AAAAATG
31607878 AAAAAGTG
1 AAAAA-TG
*
31607886 -AAAAGG
1 AAAAATG
31607892 AAAAATG
1 AAAAATG
31607899 AAAAATG
1 AAAAATG
31607906 AAAAATG
1 AAAAATG
*
31607913 AAAAAAG
1 AAAAATG
31607920 AAAA
1 AAAA
31607924 TGGAGAGGCT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
6 1 0.02
7 38 0.93
8 2 0.05
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (7 bp):
AAAAATG
Found at i:31609665 original size:44 final size:44
Alignment explanation
Indices: 31609597--31609787 Score: 258
Period size: 44 Copynumber: 4.3 Consensus size: 44
31609587 NNNNNNNNNN
*
31609597 AAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
1 AAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
* *
31609641 AAGATAGCAGATCTTATCTTCATGTATTGACGTGAAGTAGATCA
1 AAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
*** * * * *
31609685 AAGATAGCAGATCTTGTCTTCCCATACTGGTGGCGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCA
*
31609730 AAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCC
1 AAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
*
31609774 AAGATA-CAAATCTT
1 AAGATAGCAGATCTT
31609788 ATCCCCCTGA
Statistics
Matches: 126, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
43 7 0.06
44 82 0.65
45 37 0.29
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (44 bp):
AAGATAGCAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCA
Found at i:31620626 original size:22 final size:20
Alignment explanation
Indices: 31620586--31620623 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
31620576 TATATATATT
31620586 TTTAAAACAATATTGATAAA
1 TTTAAAACAATATTGATAAA
31620606 TTTAAAAC-ATATTGATAA
1 TTTAAAACAATATTGATAA
31620624 TAATTTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (20 bp):
TTTAAAACAATATTGATAAA
Found at i:31620631 original size:22 final size:21
Alignment explanation
Indices: 31620585--31620638 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
31620575 TTATATATAT
31620585 TTTTAAAACAATATTGATAAA
1 TTTTAAAACAATATTGATAAA
31620606 -TTTAAAAC-ATATTGATAATAA
1 TTTTAAAACAATATTGAT-A-AA
31620627 TTTTAAAA-AATA
1 TTTTAAAACAATA
31620639 ATGTATTATG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 8 0.28
20 9 0.31
21 2 0.07
22 10 0.34
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.39
Consensus pattern (21 bp):
TTTTAAAACAATATTGATAAA
Found at i:31629021 original size:3 final size:3
Alignment explanation
Indices: 31629013--31629037 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31629003 TATGTATATC
31629013 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
31629038 GAAAAAAAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:31632018 original size:13 final size:13
Alignment explanation
Indices: 31632000--31632024 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31631990 AAAGCATTGA
31632000 GCCCATTACCACG
1 GCCCATTACCACG
31632013 GCCCATTACCAC
1 GCCCATTACCAC
31632025 TGTTTGAGAG
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:0.24, C:0.48, G:0.12, T:0.16
Consensus pattern (13 bp):
GCCCATTACCACG
Found at i:31637366 original size:21 final size:21
Alignment explanation
Indices: 31637345--31637386 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31637335 CTTCACCAAA
*
31637345 TAAAATATTAATTTTTAAAAAT
1 TAAAAT-TTAATTTTAAAAAAT
*
31637367 TTAAATTTAATTTTAAAAAA
1 TAAAATTTAATTTTAAAAAA
31637387 CGTCTGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAAAATTTAATTTTAAAAAAT
Found at i:31637461 original size:29 final size:28
Alignment explanation
Indices: 31637401--31637476 Score: 84
Period size: 29 Copynumber: 2.6 Consensus size: 28
31637391 TGAATATCTT
* *
31637401 TAAAATTA-ATTTAAAAATTAATAATTTA
1 TAAAATTATATTT-AAAATTAAAAAATTA
31637429 TAAAAATTATATTTAAAATTAAAAAAATT-
1 T-AAAATTATATTTAAAATT-AAAAAATTA
31637458 TAAAATATATATTTAAAAT
1 TAAAAT-TATATTTAAAAT
31637477 ATTATNNNNN
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
28 6 0.14
29 26 0.62
30 10 0.24
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (28 bp):
TAAAATTATATTTAAAATTAAAAAATTA
Found at i:31637739 original size:25 final size:24
Alignment explanation
Indices: 31637711--31637777 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 24
31637701 AAGTCAATAA
31637711 TAAACAATGAAAAATAAAAAAAACT
1 TAAA-AATGAAAAATAAAAAAAACT
*
31637736 TAAAAAATG-TAAATAAATAAAAACT
1 T-AAAAATGAAAAATAAA-AAAAACT
31637761 TAAAAA-GAAAAA-AAAAA
1 TAAAAATGAAAAATAAAAA
31637778 GAAAAAGGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
22 2 0.05
23 4 0.11
24 15 0.41
25 13 0.35
26 3 0.08
ACGTcount: A:0.75, C:0.04, G:0.04, T:0.16
Consensus pattern (24 bp):
TAAAAATGAAAAATAAAAAAAACT
Found at i:31637782 original size:25 final size:24
Alignment explanation
Indices: 31637711--31637783 Score: 67
Period size: 25 Copynumber: 2.9 Consensus size: 24
31637701 AAGTCAATAA
*
31637711 TAAACAATGAAAAATAAAAAAAACT
1 TAAAAAAT-AAAAATAAAAAAAACT
**
31637736 TAAAAAATGTAAATAAATAAAAACT
1 TAAAAAATAAAAATAAA-AAAAACT
*
31637761 TAAAAAGA-AAAAAAAAAGAAAAA
1 TAAAAA-ATAAAAATAAA-AAAAA
31637784 GGACAAATAG
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
24 7 0.18
25 31 0.79
26 1 0.03
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.15
Consensus pattern (24 bp):
TAAAAAATAAAAATAAAAAAAACT
Found at i:31644482 original size:83 final size:83
Alignment explanation
Indices: 31644395--31644717 Score: 301
Period size: 83 Copynumber: 4.0 Consensus size: 83
31644385 TATGTCTTTG
**
31644395 TTTGGAAACAAAATAATATTGAATAAAATCTTGTCAAACGGCGGGAATAAAT-TCCGAAACAAAT
1 TTTGGAAACAAAATAA-ATAAAATAAAATCTTGTCAAACGGCGGGAATAAATCT-CGAAACAAAT
31644459 TTTA-TTAATTCAATTCGAA
64 TTTATTTAATTCAATTCGAA
* * * *
31644478 TTTGGAAACAAAATCAAATAAAATAAAATCTTGTTAAATGGCGGGAATGAATCTCGAAACAGATT
1 TTTGGAAACAAAAT-AAATAAAATAAAATCTTGTCAAACGGCGGGAATAAATCTCGAAACAAATT
* *
31644543 TTATTTAATTCTATTCTAA
65 TTATTTAATTCAATTCGAA
* * * *
31644562 TTTGGAAAC---A-AAAT-AAAT----TCTTGTTAAACGGGGGGAATAAATCCCGAAATAAATTT
1 TTTGGAAACAAAATAAATAAAATAAAATCTTGTCAAACGGCGGGAATAAATCTCGAAACAAATTT
* * *
31644618 TATTTAATTTAATTTCTCATT
66 TATTTAATTCAA-TTC-GA-A
* * * * * *
31644639 TTTGGCAACAAAATCAAATCAAAT-AAATCTTATTAAACAGTGGGAATAAATCTCGAAACAAATT
1 TTTGGAAACAAAAT-AAATAAAATAAAATCTTGTCAAACGGCGGGAATAAATCTCGAAACAAATT
*
31644703 TTATTTAATTTAATT
65 TTATTTAATTCAATT
31644718 TCTAGTTTTT
Statistics
Matches: 201, Mismatches: 24, Indels: 28
0.79 0.09 0.11
Matches are distributed among these distances:
74 42 0.21
75 3 0.01
76 1 0.00
77 8 0.04
78 4 0.02
79 4 0.02
80 1 0.00
81 1 0.00
82 4 0.02
83 61 0.30
84 25 0.12
85 2 0.01
86 45 0.22
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (83 bp):
TTTGGAAACAAAATAAATAAAATAAAATCTTGTCAAACGGCGGGAATAAATCTCGAAACAAATTT
TATTTAATTCAATTCGAA
Found at i:31644739 original size:86 final size:87
Alignment explanation
Indices: 31644572--31644742 Score: 249
Period size: 86 Copynumber: 2.0 Consensus size: 87
31644562 TTTGGAAACA
* * *
31644572 AAATAAATTCTTGTTAAACGGGGGGAATAAATCCCGAAATAAATTTTATTTAATTTAATTTCTCA
1 AAATAAATTCTTATTAAACAGGGGGAATAAATCCCGAAACAAATTTTATTTAATTTAATTTCTCA
31644637 TTTTTGGCAACAAAATCAAATC
66 TTTTTGGCAACAAAATCAAATC
* *
31644659 AAATAAA-TCTTATTAAACAGTGGGAATAAATCTCGAAACAAATTTTATTTAATTTAATTTCT-A
1 AAATAAATTCTTATTAAACAGGGGGAATAAATCCCGAAACAAATTTTATTTAATTTAATTTCTCA
*
31644722 GTTTTTTTGCAAC-AAATCAAA
66 --TTTTTGGCAACAAAATCAAA
31644743 ATGTAGTAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
85 1 0.01
86 58 0.76
87 17 0.22
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (87 bp):
AAATAAATTCTTATTAAACAGGGGGAATAAATCCCGAAACAAATTTTATTTAATTTAATTTCTCA
TTTTTGGCAACAAAATCAAATC
Found at i:31644770 original size:86 final size:86
Alignment explanation
Indices: 31644572--31644789 Score: 221
Period size: 86 Copynumber: 2.5 Consensus size: 86
31644562 TTTGGAAACA
* ** *
31644572 AAATAAATTCTTGTTAAACGGGGGGAATAAATCCCGAAATAAATTTTATTTAATTTAATTTCTCA
1 AAATAAA-TCTCGTTAAACGACGGGAATAAATCCCGAAACAAATTTTATTTAATTTAATTTCTCA
31644637 TTTTTGGCAACAAAATCAAATC
65 TTTTTGGCAACAAAATCAAATC
** * *
31644659 AAATAAATCTTATTAAAC-AGTGGGAATAAATCTCGAAACAAATTTTATTTAATTTAATTTCT-A
1 AAATAAATCTCGTTAAACGA-CGGGAATAAATCCCGAAACAAATTTTATTTAATTTAATTTCTCA
* *
31644722 GTTTTTTTGCAAC-AAATCAAAATG
65 --TTTTTGGCAACAAAATC-AAATC
* * * * *
31644746 TAGTAAATC-CGTTAAACGACGGGAATCAATCGCG-AACGAATTTT
1 AAATAAATCTCGTTAAACGACGGGAATAAATCCCGAAACAAATTTT
31644790 GTTTTACTCG
Statistics
Matches: 111, Mismatches: 15, Indels: 12
0.80 0.11 0.09
Matches are distributed among these distances:
85 10 0.09
86 72 0.65
87 29 0.26
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (86 bp):
AAATAAATCTCGTTAAACGACGGGAATAAATCCCGAAACAAATTTTATTTAATTTAATTTCTCAT
TTTTGGCAACAAAATCAAATC
Found at i:31644960 original size:89 final size:86
Alignment explanation
Indices: 31644806--31644972 Score: 219
Period size: 89 Copynumber: 1.9 Consensus size: 86
31644796 CTCGTTTTTA
* * * *
31644806 GAAATAAAATAAAATTTGGAATAAAATCGTTAAACGATGAGAATCAATCTCGAAACGAATTTTAT
1 GAAATAAAATAAAATATGGAATAAAATCGTTAAACGACGAGAATAAATCCCGAAACGAATTTTAT
31644871 TTACCTTTAATTTCCCGTTTG
66 TTACCTTTAATTTCCCGTTTG
* * *
31644892 GAAATAAAATCAAAATAATGGAATAAAATCCGTTGAACGGCGAGAATAAATCCCGAAATGGAA-T
1 GAAATAAAAT-AAAAT-ATGGAATAAAAT-CGTTAAACGACGAGAATAAATCCCGAAA-CGAATT
*
31644956 TTATTTACTTTTAATTT
62 TTATTTACCTTTAATTT
31644973 TGGAAACAAA
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
86 10 0.14
87 5 0.07
88 11 0.16
89 40 0.58
90 3 0.04
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.32
Consensus pattern (86 bp):
GAAATAAAATAAAATATGGAATAAAATCGTTAAACGACGAGAATAAATCCCGAAACGAATTTTAT
TTACCTTTAATTTCCCGTTTG
Found at i:31661699 original size:43 final size:43
Alignment explanation
Indices: 31661652--31661739 Score: 113
Period size: 43 Copynumber: 2.0 Consensus size: 43
31661642 TGCCATATCT
* * * *
31661652 CAGATATGGTATTACATGTTATCACATATCGATGCCACTGTCC
1 CAGATAGGGTATTACACGTAATCACATATCGATGCCAATGTCC
* * *
31661695 CAGATAGGGTCTTACACGTAATCTCATATCGATGCTAATGTCC
1 CAGATAGGGTATTACACGTAATCACATATCGATGCCAATGTCC
31661738 CA
1 CA
31661740 AACATGATCT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (43 bp):
CAGATAGGGTATTACACGTAATCACATATCGATGCCAATGTCC
Found at i:31661751 original size:43 final size:41
Alignment explanation
Indices: 31661676--31661763 Score: 104
Period size: 43 Copynumber: 2.1 Consensus size: 41
31661666 CATGTTATCA
* * * *
31661676 CATATCGATGCCACTGTCCCAGATAGGGTCTTACACGTAATCT
1 CATATCGATGCCAATGTCCCAAACAGGATCTTACACG-AAT-T
* *
31661719 CATATCGATGCTAATGTCCCAAACATGATCTTACACGAATT
1 CATATCGATGCCAATGTCCCAAACAGGATCTTACACGAATT
31661760 CATA
1 CATA
31661764 CCTCGAAAAT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
41 5 0.13
42 3 0.08
43 31 0.79
ACGTcount: A:0.31, C:0.26, G:0.15, T:0.28
Consensus pattern (41 bp):
CATATCGATGCCAATGTCCCAAACAGGATCTTACACGAATT
Found at i:31668216 original size:42 final size:42
Alignment explanation
Indices: 31668167--31668265 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
31668157 TATATGAACA
31668167 GCACTAAGTGTGCGAAACTAAAAT-GACGAGGTTGAATAAAGG
1 GCACTAAGTGTGCGAAACTAAAATGGA-GAGGTTGAATAAAGG
* * * *
31668209 GCACTAAGTGTGCAAAATTAAAATGGAGATGTTGAATAACGG
1 GCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGAATAAAGG
31668251 GCACTAAGTGTGCGA
1 GCACTAAGTGTGCGA
31668266 TACAGAGAGC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 49 0.96
43 2 0.04
ACGTcount: A:0.38, C:0.12, G:0.28, T:0.21
Consensus pattern (42 bp):
GCACTAAGTGTGCGAAACTAAAATGGAGAGGTTGAATAAAGG
Found at i:31671128 original size:13 final size:13
Alignment explanation
Indices: 31671112--31671136 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31671102 ATTGACTCTA
31671112 CTACTTGAATTTG
1 CTACTTGAATTTG
31671125 CTACTTGAATTT
1 CTACTTGAATTT
31671137 TAACTTTGCT
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:0.24, C:0.16, G:0.12, T:0.48
Consensus pattern (13 bp):
CTACTTGAATTTG
Found at i:31676327 original size:23 final size:25
Alignment explanation
Indices: 31676283--31676341 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
31676273 TAAAGTAGGT
*
31676283 TATA-TATTATTTTTATCAAATT-A
1 TATATTATAATTTTTATCAAATTCA
*
31676306 TATATTATAATTTTTAT-TAATTCA
1 TATATTATAATTTTTATCAAATTCA
*
31676330 TATTTTAATAAT
1 TATATT-ATAAT
31676342 AATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 8 0.27
24 17 0.57
25 5 0.17
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (25 bp):
TATATTATAATTTTTATCAAATTCA
Found at i:31679652 original size:24 final size:25
Alignment explanation
Indices: 31679610--31679664 Score: 67
Period size: 24 Copynumber: 2.2 Consensus size: 25
31679600 TAGTGGGGGA
**
31679610 GAGGGAGAGGGTCGAAGTA-GGGCG
1 GAGGGAGAGAATCGAAGTAGGGGCG
* *
31679634 GAGGGAGAGAATCGGAGTAGGGGGG
1 GAGGGAGAGAATCGAAGTAGGGGCG
31679659 GAGGGA
1 GAGGGA
31679665 TGGTGGGGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.27, C:0.05, G:0.60, T:0.07
Consensus pattern (25 bp):
GAGGGAGAGAATCGAAGTAGGGGCG
Found at i:31683970 original size:39 final size:41
Alignment explanation
Indices: 31683893--31684021 Score: 120
Period size: 39 Copynumber: 3.2 Consensus size: 41
31683883 TCCACGTAAG
** * * *
31683893 CGCGATTTGCTTCCACGTCATC-AAATCGCGCTTACGTGGA
1 CGCGATTTGCTGACACGTCAACTGAATCGCGCTGACGTGGA
* * * *
31683933 CGCGATTTGTTGCCACGT-AAGT-AATCGCGCTGGCGTGGA
1 CGCGATTTGCTGACACGTCAACTGAATCGCGCTGACGTGGA
* **
31683972 CACGATTTGCTGACACGTCCCCTGACATCGCGCTGACGTGGA
1 CGCGATTTGCTGACACGTCAACTGA-ATCGCGCTGACGTGGA
31684014 CGCGATTT
1 CGCGATTT
31684022 CGGGGAAAAT
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
39 31 0.44
40 17 0.24
41 1 0.01
42 22 0.31
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.26
Consensus pattern (41 bp):
CGCGATTTGCTGACACGTCAACTGAATCGCGCTGACGTGGA
Found at i:31695364 original size:987 final size:985
Alignment explanation
Indices: 31693378--31695367 Score: 2736
Period size: 987 Copynumber: 2.0 Consensus size: 985
31693368 AAAATGTTAT
* * * * * *
31693378 TGTCGACTTAAAAATGAAACGAAAATTGGAGTCATCACTGATCCTTTATTGGGGTGTGATCGGCT
1 TGTCAACTTAAAAATAAAACGAAAATTGGAGTCACCACCGATCCTTTATTGAGGTGTGATCCGCT
*
31693443 CACCTTAAAGACAATTTTGGTCTGCAAAATTTTGAGAAAACAGGTTCGGGAGTCGGTTACGCACG
66 CACCTTAAAGACAATTTTGGTCTGCAAAATTTTGAGAAAACAGGTTCGGAAGTCGGTTACGCACG
** * *
31693508 AGGAAGGGTTAGTGCCCTCGTAACTCCCAAAATTGGTACCGAATTGGTTAATTAAGGTCTTAATT
131 AGGAAGGGTTAGCACCCTCGTAACGCCCAAAATTGGTACCGAATTGATTAATTAAGGTCTTAATT
* *
31693573 CCGACTATCGAAAATCCGTGAAGAATTTAAAAAATACAATCCTCCCTTTTATTAATGTTAATTTT
196 CCGACTATCAAAAATCCGTGAAGAATTTAAAAAATACAATCCTCCCTTTTATTAATGATAATTTT
* * * *
31693638 ATAAAATATGCTTGGATAAATCGAGGCAAATGCTGAAGACCTTCTCATCTCAGAGTAATAAAATG
261 ATAAAAGATGCTTGGATAAATAGAGGCAAATGCTAAAGACCTTCTCATCTCAAAGTAATAAAATG
*
31693703 TCACACCCAATACATTAGGACACGACATTTTTAGTCCTTGAGAATAAGCTTGTCTTTTGACTTTC
326 TCACACCCAATACATTAGGACACGACATTTTTAGTCCTCGAGAATAAGCTTGTCTTTTGACTTTC
* * * * ** *
31693768 AAAACTCGTGCGGTGAAGTTGAAAAGGGATATCCAATTGCTATAAGTCAGATGAAAAATTGAAGC
391 AAAACTCGTGCGGCGAAGTTCAAAAAGGATATCCAATTACTATAAGTCAGATGAAAAATCAAAAC
* * **
31693833 CCAATACGTTAGGGCACAATTTCTCAAAATTCCGAGCATTGAATATTGCCCTTATTATTTTTCGA
456 CCAATACGTTAGGGCACAATTTCTCAAAATTCCGAGCATTGAATATAGCCATTATTATTTTTAAA
* * * * * * *
31693898 AATATTCTTGTCTCGAGGAATCAACATGTCATGTCCAATACATTAGGACAACGTATCAAATTCCT
521 AATATTCATGTCTCAAGAAAACAACATGTCATATCCAATACATTAGGACAACATATCAAATTCCC
* * * * *
31693963 GAGAGTGAGCTTTTTGTTTATATTTTGATTAAAGCATATCCTCGATTATTTAGATTCAACAAGGA
586 AAGAATGAGCTTTTTATTTATATTTTGATTAAAGAAAATCCTCGATTATTTAGATTCAACAAGGA
* * *
31694028 AAATTAGAACCCAATACGTTAGAGCTCAATCTTTTCGAAGATCCTAAATGCCGAGCTTTGCGTTA
651 AAATTAGAACCCAATACGTTAGAGCTCAATCTTCTCGAAGATCCTAAATGCCGAGCTTTACATTA
* * * * *
31694093 TCTTGGAAGTTTTTGAATAAATTGGTTTTGACACTTAAACGATATTAGACGTGACCTTTTAAACG
716 TCTTGAAAGCTTTTGAATAAATTGATTTTGACACTTAAACAATATTAGACGTAACCTTTTAAACG
* * *
31694158 AATAAAGTGTGATGGAGTGATAACGTACAATGCGAAAAGATAATTCGAGATTAAAATGTACACTA
781 AATAAAGTGTGATGGAGTGATAACGTACAATGCAAAAAGATAATTCGAGACTAAAACGTACACTA
31694223 ATGGATAATGAATAATCAATAAATAAATTTAAACAAGCATAGCAATAATTATCTCAACCATATAT
846 ATGGATAATGAATAATCAATAAATAAATTTAAACAAGCATAGCAATAATTATCTCAACCATATAT
* * * * * * **
31694288 CATACAAATACCAACATTGACAAGGGGACAAGTGTATGGTGATTATCGAAACCATTTTTTAAAAC
911 CATACAAATACCAACATTGACAA-GGGACAAGTGTAAGCTAATTAACCAAACAATTTTACAAAAC
*** *
31694353 AAAAATGTTAT
975 AAAAATAAAAA
* * *
31694364 TGTCGACTTAAAAATAAAACGAAAATTGGAGTCGCCACCGATCCTTTATTGAGGTGTGATCCGTT
1 TGTCAACTTAAAAATAAAACGAAAATTGGAGTCACCACCGATCCTTTATTGAGGTGTGATCCGCT
* *
31694429 CACCTTAAAGACAATTTTGGTCTGCGAAATTTTGAGAAAACAGGTTTGGAAGTCGGTTACGCACG
66 CACCTTAAAGACAATTTTGGTCTGCAAAATTTTGAGAAAACAGGTTCGGAAGTCGGTTACGCACG
**
31694494 AGGAAGGGTTAGCACCCTCGTAACGCTGAAAATTGGTACCGAATTGATTAATTAAGGTCTTAATT
131 AGGAAGGGTTAGCACCCTCGTAACGCCCAAAATTGGTACCGAATTGATTAATTAAGGTCTTAA-T
* * ***
31694559 TCGGA-TATCAAAAATTCGTGAAGAATTTTTGAAATACAATCCT-CCTTTT-TTAATGATAATTT
195 TCCGACTATCAAAAATCCGTGAAGAATTTAAAAAATACAATCCTCCCTTTTATTAATGATAATTT
* * *
31694621 TATAAAAGATGGTTGGATAAATAGAGGCGAATGCTAAAGACCTTCTCGTCTCAAAGTAATAAAAT
260 TATAAAAGATGCTTGGATAAATAGAGGCAAATGCTAAAGACCTTCTCATCTCAAAGTAATAAAAT
* * *
31694686 GTCATACCCAATACATTAGGACACGACATTTTTAGTCCTCGAGAATAAGTTTGTCTTTTGATTTT
325 GTCACACCCAATACATTAGGACACGACATTTTTAGTCCTCGAGAATAAGCTTGTCTTTTGACTTT
*
31694751 CAAAACTC-TCGCGGCGAAGTTCAAAAAGGATATTCC-ATTACTTTAAGTCAGATGAAAAATCAA
390 CAAAACTCGT-GCGGCGAAGTTCAAAAAGGATA-TCCAATTACTATAAGTCAGATGAAAAATCAA
31694814 AACCCAATACGTTAGGGCACAATTTCTCAAAATTCCGAGCATTGAATATAGCCATTATTATTTTT
453 AACCCAATACGTTAGGGCACAATTTCTCAAAATTCCGAGCATTGAATATAGCCATTATTA-TTTT
* *
31694879 TAAAAATATTCAT-T-TCAAGAAAACGACATGTCATATCCAATACATTAGGACACGACATATCGA
517 TAAAAATATTCATGTCTCAAGAAAACAACATGTCATATCCAATACATTAGGACA--ACATATCAA
* **
31694942 ATTCCCAAGAATGAGCTTTTTATTTATGTGTTTTGATTAAAGAAAATTTTCGATTATTTAGATTC
580 ATTCCCAAGAATGAGCTTTTTATTTA--TATTTTGATTAAAGAAAATCCTCGATTATTTAGATTC
* * * * *
31695007 AACGAGGAAAGTTGGAACCCAATACGTTAGGGCTCAAT-TCTCTCGAGGATTCC-AAAT-CTCGA
643 AACAAGGAAAATTAGAACCCAATACGTTAGAGCTCAATCT-TCTCGAAGA-TCCTAAATGC-CGA
* * *
31695069 G-TATTACATTATTTTGAAAGCTTTTGGATGAAA-TGATTTTGATACTTAAACAATATTAGACGT
705 GCT-TTACATTATCTTGAAAGCTTTTGAAT-AAATTGATTTTGACACTTAAACAATATTAGACGT
* *
31695132 AATCTTTTGAACGAATAAAGTGTGATGGAGTGATAACGTACAATGCAAAAAGATAATTCGAGACT
768 AACCTTTTAAACGAATAAAGTGTGATGGAGTGATAACGTACAATGCAAAAAGATAATTCGAGACT
31695197 AAAACGTACACTAATGGATAATGAATAATCAATAAATAAATTTAAACAAGCATAGCAATAATTAT
833 AAAACGTACACTAATGGATAATGAATAATCAATAAATAAATTTAAACAAGCATAGCAATAATTAT
* * *
31695262 CTCAACCATATATCATACAATTATCAACATTGACAA-GTA-ATAG-G-AAGCTAATTGAAACCAA
898 CTCAACCATATATCATACAAATACCAACATTGACAAGGGACA-AGTGTAAGCTAATT--AACCAA
* * *
31695323 GCAATTTTACATGAACATAAATAAAACA
960 ACAATTTTACA-AAACAAAAATAAAA-A
*
31695351 TG-CAAATTTAAAAATAA
1 TGTC-AACTTAAAAATAA
31695368 TTTAAGAAAT
Statistics
Matches: 881, Mismatches: 104, Indels: 37
0.86 0.10 0.04
Matches are distributed among these distances:
983 40 0.05
984 241 0.27
985 67 0.08
986 223 0.25
987 304 0.35
988 6 0.01
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.31
Consensus pattern (985 bp):
TGTCAACTTAAAAATAAAACGAAAATTGGAGTCACCACCGATCCTTTATTGAGGTGTGATCCGCT
CACCTTAAAGACAATTTTGGTCTGCAAAATTTTGAGAAAACAGGTTCGGAAGTCGGTTACGCACG
AGGAAGGGTTAGCACCCTCGTAACGCCCAAAATTGGTACCGAATTGATTAATTAAGGTCTTAATT
CCGACTATCAAAAATCCGTGAAGAATTTAAAAAATACAATCCTCCCTTTTATTAATGATAATTTT
ATAAAAGATGCTTGGATAAATAGAGGCAAATGCTAAAGACCTTCTCATCTCAAAGTAATAAAATG
TCACACCCAATACATTAGGACACGACATTTTTAGTCCTCGAGAATAAGCTTGTCTTTTGACTTTC
AAAACTCGTGCGGCGAAGTTCAAAAAGGATATCCAATTACTATAAGTCAGATGAAAAATCAAAAC
CCAATACGTTAGGGCACAATTTCTCAAAATTCCGAGCATTGAATATAGCCATTATTATTTTTAAA
AATATTCATGTCTCAAGAAAACAACATGTCATATCCAATACATTAGGACAACATATCAAATTCCC
AAGAATGAGCTTTTTATTTATATTTTGATTAAAGAAAATCCTCGATTATTTAGATTCAACAAGGA
AAATTAGAACCCAATACGTTAGAGCTCAATCTTCTCGAAGATCCTAAATGCCGAGCTTTACATTA
TCTTGAAAGCTTTTGAATAAATTGATTTTGACACTTAAACAATATTAGACGTAACCTTTTAAACG
AATAAAGTGTGATGGAGTGATAACGTACAATGCAAAAAGATAATTCGAGACTAAAACGTACACTA
ATGGATAATGAATAATCAATAAATAAATTTAAACAAGCATAGCAATAATTATCTCAACCATATAT
CATACAAATACCAACATTGACAAGGGACAAGTGTAAGCTAATTAACCAAACAATTTTACAAAACA
AAAATAAAAA
Found at i:31695769 original size:16 final size:18
Alignment explanation
Indices: 31695750--31695789 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
31695740 ATAGGTAAAT
31695750 ATAAT-CAAAT-ATAATA
1 ATAATACAAATAATAATA
31695766 ATAATAGCAAATAATAATA
1 ATAATA-CAAATAATAATA
31695785 ATAAT
1 ATAAT
31695790 TAAGTGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.24
18 5 0.24
19 11 0.52
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.30
Consensus pattern (18 bp):
ATAATACAAATAATAATA
Found at i:31696435 original size:16 final size:17
Alignment explanation
Indices: 31696414--31696445 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
31696404 AAATAATAAT
31696414 AAAGAAAAAA-GCAGAA
1 AAAGAAAAAACGCAGAA
31696430 AAAGAAAAAACGCAGA
1 AAAGAAAAAACGCAGA
31696446 GAGAAAAAGA
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:0.72, C:0.09, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAACGCAGAA
Found at i:31702416 original size:15 final size:16
Alignment explanation
Indices: 31702396--31702425 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
31702386 AAGGGATCTC
31702396 CCAGCATTAG-TGGAT
1 CCAGCATTAGATGGAT
31702411 CCAGCATTAGATGGA
1 CCAGCATTAGATGGA
31702426 GATTTCGATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.23
Consensus pattern (16 bp):
CCAGCATTAGATGGAT
Found at i:31706646 original size:3 final size:3
Alignment explanation
Indices: 31706633--31706676 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
31706623 TGAATGCAAC
31706633 AAT ACAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
31706677 GAAATGAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:31718400 original size:45 final size:45
Alignment explanation
Indices: 31718336--31718423 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
31718326 ATTGGGAGAT
*
31718336 GTATCTACCTTTGATTGAATTTGCTTACAATAACAGTTATCAGAG
1 GTATCTACCTTTGATTGAATTTGCTTACAATAACAATTATCAGAG
*
31718381 GTATCTACCTTTGATTGAATTTGCTTACGATAACAATTATCAG
1 GTATCTACCTTTGATTGAATTTGCTTACAATAACAATTATCAG
31718424 TCCAGTATTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.39
Consensus pattern (45 bp):
GTATCTACCTTTGATTGAATTTGCTTACAATAACAATTATCAGAG
Found at i:31722523 original size:22 final size:22
Alignment explanation
Indices: 31722498--31722558 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
31722488 GAATTAGTGT
31722498 GCATCGAAGTGCAAATCAATAG
1 GCATCGAAGTGCAAATCAATAG
* * *
31722520 GCATCGTAGTGCGAATCAGTAG
1 GCATCGAAGTGCAAATCAATAG
*
31722542 GCA-CTATAGTGCAAATC
1 GCATCGA-AGTGCAAATC
31722559 CCGTACAAGC
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
21 1 0.03
22 31 0.97
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (22 bp):
GCATCGAAGTGCAAATCAATAG
Found at i:31728123 original size:39 final size:39
Alignment explanation
Indices: 31728069--31728188 Score: 165
Period size: 39 Copynumber: 3.1 Consensus size: 39
31728059 GATTTGGGTG
31728069 TTAATTTACTCATCATTTTATTAACATTCACTGAGCTTT
1 TTAATTTACTCATCATTTTATTAACATTCACTGAGCTTT
* * * *
31728108 TTAATTTACTCATCATTTTATTAAGCA-TGATTTG-G-GTG
1 TTAATTTACTCATCATTTTATTAA-CATTCA-CTGAGCTTT
31728146 TTAATTTACTCATCATTTTATTAACATTCACTGAGCTTT
1 TTAATTTACTCATCATTTTATTAACATTCACTGAGCTTT
31728185 TTAA
1 TTAA
31728189 GCTCACACCC
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
37 4 0.06
38 28 0.41
39 32 0.47
40 4 0.06
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.48
Consensus pattern (39 bp):
TTAATTTACTCATCATTTTATTAACATTCACTGAGCTTT
Found at i:31728159 original size:38 final size:38
Alignment explanation
Indices: 31728051--31728169 Score: 161
Period size: 38 Copynumber: 3.1 Consensus size: 38
31728041 TGATTTCGAT
31728051 TTAAGCATGATTTGGGTGTTAATTTACTCATCATTTTA
1 TTAAGCATGATTTGGGTGTTAATTTACTCATCATTTTA
* * * *
31728089 TTAA-CATTCA-CTGAGCTTTTTAATTTACTCATCATTTTA
1 TTAAGCA-TGATTTG-G-GTGTTAATTTACTCATCATTTTA
31728128 TTAAGCATGATTTGGGTGTTAATTTACTCATCATTTTA
1 TTAAGCATGATTTGGGTGTTAATTTACTCATCATTTTA
31728166 TTAA
1 TTAA
31728170 CATTCACTGA
Statistics
Matches: 68, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
37 4 0.06
38 32 0.47
39 28 0.41
40 4 0.06
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.48
Consensus pattern (38 bp):
TTAAGCATGATTTGGGTGTTAATTTACTCATCATTTTA
Found at i:31730021 original size:82 final size:81
Alignment explanation
Indices: 31729923--31730177 Score: 349
Period size: 82 Copynumber: 3.2 Consensus size: 81
31729913 TTGAATAAAA
* * *
31729923 TCTATTTTGGGATTTATTCCCGTCGTTTAATAGATTTTATTCCATTTTGATTTTATTTCCAAATG
1 TCTATTTTGGGATTTATTCCCGTCGTTTAACAGATTTTATT-CATTTTGATTTTGTTTCCAAATA
* * *
31729988 AGAATTATTTGAATAAT
65 AGATTTAATTAAATAAT
* *
31730005 TCTATTTCGGGATTTATTCTCGTCGTTTAACAGA--TT-TT-A-TTTGATTTTGTTTCCAAATAA
1 TCTATTTTGGGATTTATTCCCGTCGTTTAACAGATTTTATTCATTTTGATTTTGTTTCCAAATAA
31730065 GATTTAATTAAATAAT
66 GATTTAATTAAATAAT
* * *
31730081 TCTATTTTGGGATTTATTCCCGCCGTTTAACAAATTTTATTCGATTTTGATTTTGTTTCCAAACA
1 TCTATTTTGGGATTTATTCCCGTCGTTTAACAGATTTTATTC-ATTTTGATTTTGTTTCCAAATA
31730146 AGATTTAATTAAATAAT
65 AGATTTAATTAAATAAT
*
31730163 TTTATTTTGGGATTT
1 TCTATTTTGGGATTT
31730178 CATCCTATCG
Statistics
Matches: 153, Mismatches: 14, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
76 62 0.41
77 1 0.01
78 2 0.01
79 4 0.03
80 2 0.01
81 1 0.01
82 81 0.53
ACGTcount: A:0.27, C:0.11, G:0.12, T:0.49
Consensus pattern (81 bp):
TCTATTTTGGGATTTATTCCCGTCGTTTAACAGATTTTATTCATTTTGATTTTGTTTCCAAATAA
GATTTAATTAAATAAT
Found at i:31730094 original size:76 final size:80
Alignment explanation
Indices: 31729923--31730221 Score: 344
Period size: 82 Copynumber: 3.8 Consensus size: 80
31729913 TTGAATAAAA
* * *
31729923 TCTATTTTGGGATTTATTCCCGTCGTTTAATAGATTTTATTCCATTTTGATTTTATTTCCAAATG
1 TCTATTTTGGGATTTATTCCCGTCGTTTAACAGA-TTTATT-CATTTTGATTTTGTTTCCAAATA
* * *
31729988 AGAATTATTTGAATAAT
64 AGATTTAATTAAATAAT
* *
31730005 TCTATTTCGGGATTTATTCTCGTCGTTTAACAGA-TT-TT-A-TTTGATTTTGTTTCCAAATAAG
1 TCTATTTTGGGATTTATTCCCGTCGTTTAACAGATTTATTCATTTTGATTTTGTTTCCAAATAAG
31730066 ATTTAATTAAATAAT
66 ATTTAATTAAATAAT
* * *
31730081 TCTATTTTGGGATTTATTCCCGCCGTTTAACAAATTTTATTCGATTTTGATTTTGTTTCCAAACA
1 TCTATTTTGGGATTTATTCCCGTCGTTTAACAGA-TTTATTC-ATTTTGATTTTGTTTCCAAATA
31730146 AGATTTAATTAAATAAT
64 AGATTTAATTAAATAAT
* ** * * *
31730163 TTTATTTTGGGATTTCA-TCCTATCGTTCAACAGA---ATTGATTTTGATTTTGTTTCAAAAT
1 TCTATTTTGGGATTT-ATTCCCGTCGTTTAACAGATTTATTCATTTTGATTTTGTTTCCAAAT
31730222 TTTAATTCTG
Statistics
Matches: 188, Mismatches: 22, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
76 62 0.33
77 20 0.11
78 5 0.03
79 4 0.02
80 2 0.01
81 1 0.01
82 93 0.49
83 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (80 bp):
TCTATTTTGGGATTTATTCCCGTCGTTTAACAGATTTATTCATTTTGATTTTGTTTCCAAATAAG
ATTTAATTAAATAAT
Found at i:31730119 original size:158 final size:159
Alignment explanation
Indices: 31729923--31730221 Score: 413
Period size: 158 Copynumber: 1.9 Consensus size: 159
31729913 TTGAATAAAA
* * * **
31729923 TCTATTTTGGGATTTATTCCCGTCGTTTAATAGATTTTATTCCATTTTGATTTTATTTCCAAATG
1 TCTATTTTGGGATTTATTCCCGCCGTTTAACAAATTTTATTCCATTTTGATTTTATTTCCAAACA
* * * * * * *
31729988 AGAATTATTTGAATAATTCTATTTCGGGATTT-ATTCTCGTCGTTTAACAGATTTTA-TTTGATT
66 AGAATTAATTAAATAATTCTATTTCGGGATTTCATCCT-ATCGTTCAACAGAATTGATTTTGATT
*
31730051 TTGTTTCCAAATAAGATTTAATTAAATAAT
130 TTGTTTCAAAATAAGATTTAATTAAATAAT
* *
31730081 TCTATTTTGGGATTTATTCCCGCCGTTTAACAAATTTTATTCGATTTTGATTTTGTTTCCAAACA
1 TCTATTTTGGGATTTATTCCCGCCGTTTAACAAATTTTATTCCATTTTGATTTTATTTCCAAACA
* * *
31730146 AGATTTAATTAAATAATTTTATTTTGGGATTTCATCCTATCGTTCAACAGAATTGATTTTGATTT
66 AGAATTAATTAAATAATTCTATTTCGGGATTTCATCCTATCGTTCAACAGAATTGATTTTGATTT
31730211 TGTTTCAAAAT
131 TGTTTCAAAAT
31730222 TTTAATTCTG
Statistics
Matches: 121, Mismatches: 18, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
158 99 0.82
159 22 0.18
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (159 bp):
TCTATTTTGGGATTTATTCCCGCCGTTTAACAAATTTTATTCCATTTTGATTTTATTTCCAAACA
AGAATTAATTAAATAATTCTATTTCGGGATTTCATCCTATCGTTCAACAGAATTGATTTTGATTT
TGTTTCAAAATAAGATTTAATTAAATAAT
Found at i:31733639 original size:25 final size:25
Alignment explanation
Indices: 31733605--31733677 Score: 83
Period size: 25 Copynumber: 2.9 Consensus size: 25
31733595 CAACTCGTAT
* * *
31733605 GAGCTTACCGGTTTATAGCTCATGA
1 GAGCATACCGATTTACAGCTCATGA
* *
31733630 GATCATACCGATTTACAGCTCGTGA
1 GAGCATACCGATTTACAGCTCATGA
* *
31733655 GGGCATACCGATTCACAGCTCAT
1 GAGCATACCGATTTACAGCTCAT
31733678 ATAAGCATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.22, T:0.27
Consensus pattern (25 bp):
GAGCATACCGATTTACAGCTCATGA
Found at i:31733869 original size:31 final size:30
Alignment explanation
Indices: 31733834--31733892 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
31733824 TTTACATGAA
*
31733834 ATACATGGAAAT-GATTTTACATGATATATAG
1 ATACAT-GAAATGGATGTTACATG-TATATAG
*
31733865 ATACATGATATGGATGTTACATGTATAT
1 ATACATGAAATGGATGTTACATGTATAT
31733893 GGAAACTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 9 0.36
31 16 0.64
ACGTcount: A:0.39, C:0.07, G:0.17, T:0.37
Consensus pattern (30 bp):
ATACATGAAATGGATGTTACATGTATATAG
Found at i:31738031 original size:25 final size:25
Alignment explanation
Indices: 31738003--31738120 Score: 82
Period size: 24 Copynumber: 4.8 Consensus size: 25
31737993 GCGCTCTCTC
31738003 GAGCCATATAACGGGAAGCTCATGT
1 GAGCCATATAACGGGAAGCTCATGT
* * *
31738028 GAGCCAT-GAACGGGAAGCTTATCT
1 GAGCCATATAACGGGAAGCTCATGT
** **
31738052 -AGGCTTTATAACGGGAAGCTCATAA
1 GA-GCCATATAACGGGAAGCTCATGT
* * * *
31738077 GAGCCATAT-TCAGAAAGCTCATGC
1 GAGCCATATAACGGGAAGCTCATGT
* *
31738101 GAGCCA-ATATCGGGTAGCTC
1 GAGCCATATAACGGGAAGCTC
31738121 TGAAGAGTCA
Statistics
Matches: 70, Mismatches: 19, Indels: 9
0.71 0.19 0.09
Matches are distributed among these distances:
23 3 0.04
24 41 0.59
25 25 0.36
26 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.26, T:0.21
Consensus pattern (25 bp):
GAGCCATATAACGGGAAGCTCATGT
Found at i:31738339 original size:25 final size:25
Alignment explanation
Indices: 31738311--31738374 Score: 110
Period size: 25 Copynumber: 2.6 Consensus size: 25
31738301 GAAGAGCTAT
31738311 TAACGGGAAGCTCGCAAGAACAATA
1 TAACGGGAAGCTCGCAAGAACAATA
*
31738336 TAACGAGAAGCTCGCAAGAACAATA
1 TAACGGGAAGCTCGCAAGAACAATA
*
31738361 TAATGGGAAGCTCG
1 TAACGGGAAGCTCG
31738375 AGATAGATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.42, C:0.19, G:0.25, T:0.14
Consensus pattern (25 bp):
TAACGGGAAGCTCGCAAGAACAATA
Found at i:31743730 original size:18 final size:18
Alignment explanation
Indices: 31743704--31743739 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31743694 TATTATAGTT
*
31743704 CAAACCATCAAAATATAC
1 CAAAACATCAAAATATAC
*
31743722 CAAAACATCAACATATAC
1 CAAAACATCAAAATATAC
31743740 ATTAAACCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.17
Consensus pattern (18 bp):
CAAAACATCAAAATATAC
Found at i:31744244 original size:28 final size:30
Alignment explanation
Indices: 31744191--31744255 Score: 98
Period size: 28 Copynumber: 2.2 Consensus size: 30
31744181 TTTTTTTTAA
*
31744191 TTTTAAAAATTCAAAAATTATAAAAA-CTAT
1 TTTTAAAAATT-AAAAATTATAAAAATATAT
31744221 TTTTAAAAATT-AAAATTATAAAAATATAT
1 TTTTAAAAATTAAAAATTATAAAAATATAT
31744250 TTTTAA
1 TTTTAA
31744256 TTTTTTTTAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 13 0.39
29 9 0.27
30 11 0.33
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (30 bp):
TTTTAAAAATTAAAAATTATAAAAATATAT
Found at i:31745788 original size:77 final size:75
Alignment explanation
Indices: 31745662--31745856 Score: 302
Period size: 75 Copynumber: 2.6 Consensus size: 75
31745652 TATCCGTTAT
* *
31745662 CGGTGGATTCAGCACTTAG-ATCCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTTCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCC-TTTCA
31745726 CATTCAAAAATA
65 CATT-AAAAATA
*
31745738 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
* *
31745803 ATTTAAGATA
66 ATTAAAAATA
* *
31745813 CGGTGGGATCAGCCCTTAGCAACCACCAATGATTCGGGGAATCA
1 CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCA
31745857 NNNNNNNNNN
Statistics
Matches: 110, Mismatches: 8, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
75 46 0.42
76 27 0.25
77 37 0.34
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGATTCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTAAAAATA
Found at i:31749002 original size:19 final size:19
Alignment explanation
Indices: 31748978--31749017 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
31748968 AAAAGAGAAA
31748978 TAGATATTGCATGTATTAC
1 TAGATATTGCATGTATTAC
31748997 TAGATATTGCATGTATTAC
1 TAGATATTGCATGTATTAC
31749016 TA
1 TA
31749018 TTCGTAGTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (19 bp):
TAGATATTGCATGTATTAC
Done.