Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011131.1 Kokia drynarioides strain JFW-HI SEQ_126104, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 545426
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 70 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:3298 original size:24 final size:23
Alignment explanation
Indices: 3241--3303 Score: 65
Period size: 24 Copynumber: 2.7 Consensus size: 23
3231 AAGCGGTTAC
* *
3241 AAGAAGACGAAATGTGAAGAGTT
1 AAGAAGATGAAAGGTGAAGAGTT
*
3264 AAGGAATATGAAAGGTGAA-AGGTT
1 AA-GAAGATGAAAGGTGAAGA-GTT
3288 GAAGAAGATGAAAGGT
1 -AAGAAGATGAAAGGT
3304 TGAATATCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
23 3 0.09
24 28 0.85
25 2 0.06
ACGTcount: A:0.48, C:0.02, G:0.33, T:0.17
Consensus pattern (23 bp):
AAGAAGATGAAAGGTGAAGAGTT
Found at i:7765 original size:17 final size:18
Alignment explanation
Indices: 7727--7767 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
7717 CTTTACTTTT
* *
7727 ATTTTATTTTACCACTGA
1 ATTTTATTTTAACACAGA
7745 ATTTTATTTTAACA-AGA
1 ATTTTATTTTAACACAGA
7762 ATTTTA
1 ATTTTA
7768 GTCACCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.34, C:0.10, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTTATTTTAACACAGA
Found at i:27579 original size:6 final size:6
Alignment explanation
Indices: 27570--27599 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
27560 TATATTATCA
*
27570 TGAGAT TGAGAT TGAGAT TGAGAC TGAGAT
1 TGAGAT TGAGAT TGAGAT TGAGAT TGAGAT
27600 ATACAAGTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.33, C:0.03, G:0.33, T:0.30
Consensus pattern (6 bp):
TGAGAT
Found at i:45117 original size:15 final size:15
Alignment explanation
Indices: 45083--45120 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
45073 CGAAAGTAAC
*
45083 TAAAATAT-AATATT
1 TAAAATATAAATAAT
*
45097 TCAAATATAAATAAT
1 TAAAATATAAATAAT
45112 TAAAATATA
1 TAAAATATA
45121 TCTTGAGCTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (15 bp):
TAAAATATAAATAAT
Found at i:46662 original size:20 final size:20
Alignment explanation
Indices: 46637--46677 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
46627 ATGGGTATAA
46637 CCTCGTCCGCCCCGTCGCAT
1 CCTCGTCCGCCCCGTCGCAT
46657 CCTCGTCCGCCCCGTCGCAT
1 CCTCGTCCGCCCCGTCGCAT
46677 C
1 C
46678 TCTGCCCACC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.05, C:0.56, G:0.20, T:0.20
Consensus pattern (20 bp):
CCTCGTCCGCCCCGTCGCAT
Found at i:48453 original size:52 final size:52
Alignment explanation
Indices: 48383--48569 Score: 286
Period size: 52 Copynumber: 3.6 Consensus size: 52
48373 TCGTAAAGGA
* *
48383 ATTCATGTACTCACGATGACACTTAGTCATCGGACCTCACAATCTGTAAAAG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTCATAATCTGTAAAAG
* *
48435 ATTCATTTACTCACGATGACACTTAGTCATCAGACCTCATAATCTGTAAAGG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTCATAATCTGTAAAAG
* *
48487 ATTCATTTACTCACGATGATACTTAGTCATCGGACCTCATAATCCGT-AAAG
1 ATTCATTTACTCACGATGACACTTAGTCATCGGACCTCATAATCTGTAAAAG
* *
48538 AATTCATATACTCACGATGACACTTATTCATC
1 -ATTCATTTACTCACGATGACACTTAGTCATC
48570 AAACCCTTTT
Statistics
Matches: 123, Mismatches: 11, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
51 3 0.02
52 120 0.98
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (52 bp):
ATTCATTTACTCACGATGACACTTAGTCATCGGACCTCATAATCTGTAAAAG
Found at i:48519 original size:104 final size:105
Alignment explanation
Indices: 48354--48570 Score: 323
Period size: 104 Copynumber: 2.1 Consensus size: 105
48344 GGTGGCATAA
* *
48354 AGTCATCAGACCTCTTATTTCGTAAAGGAATTCATGTACTCACGATGACACTTAGTCATCGGACC
1 AGTCATCAGACCTCTAATCTCGTAAAGGAATTCATGTACTCACGATGACACTTAGTCATCGGACC
* *
48419 TCACAATCTGTAAA-AGATTCATTTACTCACGATGACACTT
66 TCACAATCCGTAAAGA-ATTCATATACTCACGATGACACTT
* *
48459 AGTCATCAGACCTCATAATCT-GTAAAGG-ATTCATTTACTCACGATGATACTTAGTCATCGGAC
1 AGTCATCAGACCTC-TAATCTCGTAAAGGAATTCATGTACTCACGATGACACTTAGTCATCGGAC
*
48522 CTCATAATCCGTAAAGAATTCATATACTCACGATGACACTT
65 CTCACAATCCGTAAAGAATTCATATACTCACGATGACACTT
*
48563 ATTCATCA
1 AGTCATCA
48571 AACCCTTTTT
Statistics
Matches: 102, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
104 76 0.75
105 22 0.22
106 4 0.04
ACGTcount: A:0.33, C:0.24, G:0.13, T:0.30
Consensus pattern (105 bp):
AGTCATCAGACCTCTAATCTCGTAAAGGAATTCATGTACTCACGATGACACTTAGTCATCGGACC
TCACAATCCGTAAAGAATTCATATACTCACGATGACACTT
Found at i:55730 original size:52 final size:52
Alignment explanation
Indices: 55612--55844 Score: 245
Period size: 52 Copynumber: 4.5 Consensus size: 52
55602 TTCATTTAAC
* * ** *
55612 ACTCATGATGACA-TAAAGTCATTGGACCTCTTGTTCCGTAAAGGAATTCATGT
1 ACTCATGATGACACT-AAGTCATTGAACCTCATAATCCGTAAAGG-ATTCATTT
* * *
55665 ACTCATGATGACACTAAATCATTGAACCTCACAATCCATAAAGGATTCATTT
1 ACTCATGATGACACTAAGTCATTGAACCTCATAATCCGTAAAGGATTCATTT
* * * *
55717 ACTCATGATGACACCT-AGTCATCGGACCTTATAATCCGCAAAGGATTCATTT
1 ACTCATGATGACA-CTAAGTCATTGAACCTCATAATCCGTAAAGGATTCATTT
* * * * * * *
55769 CCACACGATGACACTTAGTCATCGAACCTCATAATCTGTAAAGGATTCATAT
1 ACTCATGATGACACTAAGTCATTGAACCTCATAATCCGTAAAGGATTCATTT
*
55821 ACTCATGATGACACTTAGTCATTG
1 ACTCATGATGACACTAAGTCATTG
55845 TGCCCTTTTT
Statistics
Matches: 150, Mismatches: 27, Indels: 7
0.82 0.15 0.04
Matches are distributed among these distances:
51 2 0.01
52 110 0.73
53 37 0.25
54 1 0.01
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.30
Consensus pattern (52 bp):
ACTCATGATGACACTAAGTCATTGAACCTCATAATCCGTAAAGGATTCATTT
Found at i:61322 original size:24 final size:26
Alignment explanation
Indices: 61295--61345 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
61285 ATAATTCAAA
61295 ATATTTAT-AAAAA-ATTCAAAATTT
1 ATATTTATGAAAAAGATTCAAAATTT
* *
61319 ATATTTTTGAAAAAGCTTCAAAATTT
1 ATATTTATGAAAAAGATTCAAAATTT
61345 A
1 A
61346 AAAATAATCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 7 0.30
25 5 0.22
26 11 0.48
ACGTcount: A:0.49, C:0.06, G:0.04, T:0.41
Consensus pattern (26 bp):
ATATTTATGAAAAAGATTCAAAATTT
Found at i:63152 original size:38 final size:38
Alignment explanation
Indices: 63088--63328 Score: 220
Period size: 38 Copynumber: 6.3 Consensus size: 38
63078 TGGAATGCTG
*
63088 ATTATACTT-AATGCTTGCTCAGACGAGCAAATCCACTA
1 ATTATA-TTGAATGCTTGCTCAAACGAGCAAATCCACTA
* * * *
63126 ATTATATTGAATTCTTTCTCAAACGAGCGAATCTACTA
1 ATTATATTGAATGCTTGCTCAAACGAGCAAATCCACTA
** *
63164 ATTATATTGAATGCTTGCTCAGGCGAGCGAATCCACTGA
1 ATTATATTGAATGCTTGCTCAAACGAGCAAATCCACT-A
* * *
63203 A-TATACTGAATGCTTGCTC-AACGAGGAAACCCACTA
1 ATTATATTGAATGCTTGCTCAAACGAGCAAATCCACTA
* * * * * *
63239 ATTTTACTGAATGTTTGTTCAAACGAGCTATAA-CTACTG
1 ATTATATTGAATGCTTGCTCAAACGAGC-A-AATCCACTA
* * * *
63278 ATTATATTGAATGCTCGCTCAAATGAGCATTATCCACTG
1 ATTATATTGAATGCTTGCTCAAACGAGCA-AATCCACTA
63317 ATTATATTGAAT
1 ATTATATTGAAT
63329 AAGATTTTTC
Statistics
Matches: 166, Mismatches: 30, Indels: 13
0.79 0.14 0.06
Matches are distributed among these distances:
36 2 0.01
37 28 0.17
38 88 0.53
39 46 0.28
40 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.15, T:0.32
Consensus pattern (38 bp):
ATTATATTGAATGCTTGCTCAAACGAGCAAATCCACTA
Found at i:63290 original size:114 final size:114
Alignment explanation
Indices: 63085--63298 Score: 290
Period size: 114 Copynumber: 1.9 Consensus size: 114
63075 AAGTGGAATG
* * * *
63085 CTGATTATACTTAATGCTTGCTCAGACGAGCAAATCCACTAATTATATTGAATTCTTTCTCAAAC
1 CTGAATATACTGAATGCTTGCTCAGACGAGCAAACCCACTAATTATACTGAATTCTTTCTCAAAC
* *
63150 GAGCGAATCTACTAATTATATTGAATGCTTGCTCAGGCGAGCGAATCCA
66 GAGCGAAACTACTAATTATATTGAATGCTCGCTCAGGCGAGCGAATCCA
* *
63199 CTGAATATACTGAATGCTTGCTCA-ACGAGGAAACCCACTAATTTTACTGAATGT-TTGT-TCAA
1 CTGAATATACTGAATGCTTGCTCAGACGAGCAAACCCACTAATTATACTGAAT-TCTT-TCTCAA
* *
63261 ACGAGCTATAACTACTGATTATATTGAATGCTCGCTCA
64 ACGAGCGA-AACTACTAATTATATTGAATGCTCGCTCA
63299 AATGAGCATT
Statistics
Matches: 87, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
113 37 0.43
114 50 0.57
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.32
Consensus pattern (114 bp):
CTGAATATACTGAATGCTTGCTCAGACGAGCAAACCCACTAATTATACTGAATTCTTTCTCAAAC
GAGCGAAACTACTAATTATATTGAATGCTCGCTCAGGCGAGCGAATCCA
Found at i:64897 original size:42 final size:42
Alignment explanation
Indices: 64823--65302 Score: 579
Period size: 42 Copynumber: 11.4 Consensus size: 42
64813 CAAGTTAGGT
* * * * *
64823 TTGTTTGTTGTTTTAAATCAATTATGTACTTATTTGAATAGA
1 TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTTGAATCGA
* * *
64865 TTGTTTGTTGTTTAAAATTGATTCTTTGCTTATTTCAATC-A
1 TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTTGAATCGA
** *
64906 TTTGTTTGTTGTTTTAAATAAATTCTTTGCTTATTTGAATAGA
1 -TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTTGAATCGA
* * * *
64949 TTGTTTGTTGTTTTAAATCGATTATTTGTTTCTTTGAATTGA
1 TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTTGAATCGA
* * * *
64991 TTGTTTGTTGTTTTAAATTGATTCATTCCTTATTTCAATCGA
1 TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTTGAATCGA
* * *
65033 TTGTTTGTTGCTTTAAATCGATCCTTTGCTTATTTGAACCTG-
1 TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTTGAATC-GA
* * *
65075 TTGTTTGTTGTTTTAAATAGATTATTTGCTTATTTTAATCGA
1 TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTTGAATCGA
* *
65117 TTGTTTGTTGTTTTAAATCGATCCTTTGCTTATTTTAATCGA
1 TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTTGAATCGA
* *
65159 TTGTTTGTTGTTTTAAATAGATTATTTGCTTATTTCG-ATCGA
1 TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTT-GAATCGA
* * *
65201 TTGTTTGTTGTTTTAAATTGATTCTTTGCTTCTTGGAATCGA
1 TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTTGAATCGA
** * *
65243 TTGTTTACTGTTTTAAATCGATTCTTTGTTTATTTCAATCGA
1 TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTTGAATCGA
*
65285 TTTTTTGTTGTTTTAAAT
1 TTGTTTGTTGTTTTAAAT
65303 TAGTTCTTTT
Statistics
Matches: 371, Mismatches: 61, Indels: 12
0.84 0.14 0.03
Matches are distributed among these distances:
41 3 0.01
42 366 0.99
43 2 0.01
ACGTcount: A:0.21, C:0.09, G:0.15, T:0.56
Consensus pattern (42 bp):
TTGTTTGTTGTTTTAAATCGATTCTTTGCTTATTTGAATCGA
Found at i:65244 original size:21 final size:21
Alignment explanation
Indices: 65111--65270 Score: 76
Period size: 21 Copynumber: 7.6 Consensus size: 21
65101 TGCTTATTTT
* * *
65111 AATCGATTGTTTGTTGTTTTA
1 AATCGATTCTTTGCTGTTTGA
* **
65132 AATCGATCCTTTGCT-TATTTT
1 AATCGATTCTTTGCTGT-TTGA
* * *
65153 AATCGATTGTTTGTTGTTTTA
1 AATCGATTCTTTGCTGTTTGA
* * *
65174 AATAGATTATTTGCTTATTTCG-
1 AATCGATTCTTTGC-TGTTT-GA
* * *
65196 -ATCGATTGTTTGTTGTTTTA
1 AATCGATTCTTTGCTGTTTGA
* *
65216 AATTGATTCTTTGCT-TCTTGG
1 AATCGATTCTTTGCTGT-TTGA
* * *
65237 AATCGATTGTTTACTGTTTTA
1 AATCGATTCTTTGCTGTTTGA
65258 AATCGATTCTTTG
1 AATCGATTCTTTG
65271 TTTATTTCAA
Statistics
Matches: 101, Mismatches: 30, Indels: 16
0.69 0.20 0.11
Matches are distributed among these distances:
20 6 0.06
21 89 0.88
22 6 0.06
ACGTcount: A:0.20, C:0.10, G:0.16, T:0.54
Consensus pattern (21 bp):
AATCGATTCTTTGCTGTTTGA
Found at i:65428 original size:16 final size:16
Alignment explanation
Indices: 65403--65436 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
65393 CATATTCATT
65403 TGGTAAGAAATATATA
1 TGGTAAGAAATATATA
*
65419 TGGTAGGAAATATATA
1 TGGTAAGAAATATATA
65435 TG
1 TG
65437 AAGAGACAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.24, T:0.32
Consensus pattern (16 bp):
TGGTAAGAAATATATA
Found at i:70265 original size:4 final size:4
Alignment explanation
Indices: 70256--70337 Score: 74
Period size: 4 Copynumber: 20.5 Consensus size: 4
70246 TTTTAAGATG
* * * * * *
70256 TAAA TAAA TAAC TAAA TAAG TAAG TAAG TAAG TAAA TAAA TAAC TAAA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA
* * * *
70304 TAAG TAAG TAAG TAAG TAAA TAAA TAAA TAAA TA
1 TAAA TAAA TAAA TAAA TAAA TAAA TAAA TAAA TA
70338 TATATATATA
Statistics
Matches: 70, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 70 1.00
ACGTcount: A:0.62, C:0.02, G:0.10, T:0.26
Consensus pattern (4 bp):
TAAA
Found at i:70296 original size:32 final size:32
Alignment explanation
Indices: 70255--70337 Score: 157
Period size: 32 Copynumber: 2.6 Consensus size: 32
70245 ATTTTAAGAT
70255 GTAAATAAATAACTAAATAAGTAAGTAAGTAA
1 GTAAATAAATAACTAAATAAGTAAGTAAGTAA
70287 GTAAATAAATAACTAAATAAGTAAGTAAGTAA
1 GTAAATAAATAACTAAATAAGTAAGTAAGTAA
*
70319 GTAAATAAATAAATAAATA
1 GTAAATAAATAACTAAATA
70338 TATATATATA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.61, C:0.02, G:0.11, T:0.25
Consensus pattern (32 bp):
GTAAATAAATAACTAAATAAGTAAGTAAGTAA
Found at i:70470 original size:30 final size:31
Alignment explanation
Indices: 70435--70511 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 31
70425 AGTTTTCCCC
*
70435 AAAAACAACATATATCCCTAAATAATT-T-TA
1 AAAAACAACATATAT-CCTAAATAATTATAAA
* *
70465 AAAAACAATTCA-AAATCCTAATTAATTATAAA
1 AAAAACAA--CATATATCCTAAATAATTATAAA
70497 AAAAACAACATATAT
1 AAAAACAACATATAT
70512 GCCTTATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
30 20 0.53
31 7 0.18
32 11 0.29
ACGTcount: A:0.58, C:0.14, G:0.00, T:0.27
Consensus pattern (31 bp):
AAAAACAACATATATCCTAAATAATTATAAA
Found at i:70732 original size:24 final size:24
Alignment explanation
Indices: 70704--70751 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
70694 GTTCACAAAC
* * *
70704 AAGCTCGTTTATTGGCTCGTTTAT
1 AAGCTCATTTATTGACTCATTTAT
*
70728 AAGCTTATTTATTGACTCATTTAT
1 AAGCTCATTTATTGACTCATTTAT
70752 TTATTAATGA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.48
Consensus pattern (24 bp):
AAGCTCATTTATTGACTCATTTAT
Found at i:70905 original size:23 final size:23
Alignment explanation
Indices: 70842--70923 Score: 85
Period size: 23 Copynumber: 3.5 Consensus size: 23
70832 ACATTGTTTG
*
70842 TGAACATGTTCAATTATATGTTAA
1 TGAACATGTTCGATTA-ATGTTAA
* ** *
70866 TGAACATTTTCTTTTAATGTTCA
1 TGAACATGTTCGATTAATGTTAA
70889 TGAACATGTTCGATTAA-GTTAAA
1 TGAACATGTTCGATTAATGTT-AA
*
70912 TGAACATATTCG
1 TGAACATGTTCG
70924 TGAGCATTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
22 3 0.06
23 32 0.67
24 13 0.27
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.41
Consensus pattern (23 bp):
TGAACATGTTCGATTAATGTTAA
Found at i:78031 original size:24 final size:22
Alignment explanation
Indices: 78002--78045 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
77992 TTTTTTAAAA
78002 TTTATTATTAGTATATATTTTTAT
1 TTTATTA-TA-TATATATTTTTAT
*
78026 TTTATTATATATATTTTTTT
1 TTTATTATATATATATTTTT
78046 TAAAAAAGTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 2 0.11
24 7 0.37
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTATTATATATATATTTTTAT
Found at i:78036 original size:18 final size:19
Alignment explanation
Indices: 78002--78047 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
77992 TTTTTTAAAA
78002 TTTATTATTAGTATATAT-T
1 TTTATT-TTAGTATATATAT
*
78021 TTTATTTTATTATATATAT
1 TTTATTTTAGTATATATAT
78040 TTT-TTTTA
1 TTTATTTTA
78048 AAAAAGTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
18 15 0.60
19 10 0.40
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTATTTTAGTATATATAT
Found at i:83268 original size:22 final size:22
Alignment explanation
Indices: 83242--83294 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
83232 TGGACATGCC
83242 ACCATTGATTTGCATATAAATT
1 ACCATTGATTTGCATATAAATT
*
83264 GCCATTGATTTGCATATAAATT
1 ACCATTGATTTGCATATAAATT
*
83286 ACCACTGAT
1 ACCATTGAT
83295 AACATTGATG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (22 bp):
ACCATTGATTTGCATATAAATT
Found at i:84289 original size:5 final size:6
Alignment explanation
Indices: 84274--84298 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
84264 ACAAGAAGAA
84274 AAAAAG AAAAAG AAAAAG AAAAAG A
1 AAAAAG AAAAAG AAAAAG AAAAAG A
84299 GGATTTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:89863 original size:15 final size:17
Alignment explanation
Indices: 89836--89870 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
89826 ATAATATTTT
89836 AAATGTTATAAAG-ATA
1 AAATGTTATAAAGAATA
89852 AAATGTTA-AAAGAATA
1 AAATGTTATAAAGAATA
89868 AAA
1 AAA
89871 AAATTGAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.63, C:0.00, G:0.11, T:0.26
Consensus pattern (17 bp):
AAATGTTATAAAGAATA
Found at i:95272 original size:52 final size:52
Alignment explanation
Indices: 95173--95272 Score: 173
Period size: 52 Copynumber: 1.9 Consensus size: 52
95163 ACTTGTTTTA
* *
95173 GACTCCCCCTAATGGTAACATTACATTACATCTTTGGGTCGACGTATTGAAT
1 GACTCCCCCTAATGGTAACATTACATTACATCTTTGAGTCAACGTATTGAAT
*
95225 GACTCCCCCTAATGGTAACATTACATTACATCTTTGAGTCAATGTATT
1 GACTCCCCCTAATGGTAACATTACATTACATCTTTGAGTCAACGTATT
95273 CAATCTTGTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (52 bp):
GACTCCCCCTAATGGTAACATTACATTACATCTTTGAGTCAACGTATTGAAT
Found at i:105807 original size:18 final size:18
Alignment explanation
Indices: 105779--105826 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
105769 ATCATGATCA
*
105779 TATGCAGTCACATGCTCAG
1 TATGCAATCACATGCTC-G
*
105798 -ATGTAATCACATGCTCG
1 TATGCAATCACATGCTCG
105815 TATGCAATCACA
1 TATGCAATCACA
105827 GCAAACTGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 1 0.04
18 24 0.96
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (18 bp):
TATGCAATCACATGCTCG
Found at i:118189 original size:25 final size:24
Alignment explanation
Indices: 118132--118190 Score: 66
Period size: 25 Copynumber: 2.4 Consensus size: 24
118122 GAAAATGTGC
118132 AAAAAAAAGAAAAAATACAGAAAA
1 AAAAAAAAGAAAAAATACAGAAAA
* *
118156 AAGTAAAAAGAAAAAGTACA-AAACA
1 AA-AAAAAAGAAAAAATACAGAAA-A
118181 AAAACAAAAG
1 AAAA-AAAAG
118191 CAATGTGACT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 6 0.21
25 23 0.79
ACGTcount: A:0.78, C:0.07, G:0.10, T:0.05
Consensus pattern (24 bp):
AAAAAAAAGAAAAAATACAGAAAA
Found at i:119393 original size:63 final size:62
Alignment explanation
Indices: 119333--119484 Score: 193
Period size: 62 Copynumber: 2.5 Consensus size: 62
119323 GGATTTAGGT
* *
119333 TTTAAAAATTTAGGGATTTTTGGGACTTTTAG-GGTTGTTGGGTTTGGGGAATTTGGTTTAG
1 TTTAAAAATTTAGGGATTTTTGGGACTTTTAGAGGTTGTTAGGCTTGGGGAATTTGGTTTAG
* * * *
119394 ATTTAAGAAATTTGGGGA-TTTT-GGAATTTTTGAGGTTGTTAGGCTTGGGGATTTTGGTTTAAG
1 -TTTAA-AAATTTAGGGATTTTTGGGACTTTTAGAGGTTGTTAGGCTTGGGGAATTTGGTTT-AG
*
119457 TTTAAAAATTTAGGGATTTTCGGGACTT
1 TTTAAAAATTTAGGGATTTTTGGGACTT
119485 AGGATTCAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
61 18 0.24
62 41 0.54
63 17 0.22
ACGTcount: A:0.22, C:0.03, G:0.30, T:0.45
Consensus pattern (62 bp):
TTTAAAAATTTAGGGATTTTTGGGACTTTTAGAGGTTGTTAGGCTTGGGGAATTTGGTTTAG
Found at i:124119 original size:3 final size:3
Alignment explanation
Indices: 124111--124200 Score: 173
Period size: 3 Copynumber: 30.3 Consensus size: 3
124101 CTATGTGCTA
124111 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
124159 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-T TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
124201 TTGGTTGAAC
Statistics
Matches: 86, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 84 0.98
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:135377 original size:21 final size:21
Alignment explanation
Indices: 135351--135401 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
135341 TGGACAAGCC
135351 ACCACATATTTGCCAATAATG
1 ACCACATATTTGCCAATAATG
* *
135372 GCCACATATTTTCCAATAATG
1 ACCACATATTTGCCAATAATG
135393 ACCACATAT
1 ACCACATAT
135402 CTTCCACCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.37, C:0.25, G:0.08, T:0.29
Consensus pattern (21 bp):
ACCACATATTTGCCAATAATG
Found at i:135406 original size:21 final size:20
Alignment explanation
Indices: 135351--135407 Score: 78
Period size: 21 Copynumber: 2.7 Consensus size: 20
135341 TGGACAAGCC
135351 ACCACATATTTGCCAATAATG
1 ACCACATATTT-CCAATAATG
*
135372 GCCACATATTTTCCAATAATG
1 ACCACATA-TTTCCAATAATG
135393 ACCACATATCTTCCA
1 ACCACATAT-TTCCA
135408 CCTTTCACAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 1 0.03
21 28 0.88
22 3 0.09
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (20 bp):
ACCACATATTTCCAATAATG
Found at i:140947 original size:21 final size:23
Alignment explanation
Indices: 140894--140951 Score: 66
Period size: 21 Copynumber: 2.6 Consensus size: 23
140884 TAGTTATTTT
*
140894 ATATTTTTATAATATAAAAAAAT
1 ATATTTTTATAATATAAAAAAAG
*
140917 ATAATCTTTATAA-A-AAAAAAAG
1 AT-ATTTTTATAATATAAAAAAAG
*
140939 CTATTTTTATAAT
1 ATATTTTTATAAT
140952 CTTTTAGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
21 9 0.31
22 8 0.28
23 3 0.10
24 9 0.31
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATTTTTATAATATAAAAAAAG
Found at i:142094 original size:30 final size:30
Alignment explanation
Indices: 142060--142134 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 30
142050 ATTACATTTA
*
142060 ACAAAACAGTCACTCAAC-T-TTGAAAATGTG
1 ACAAAACAATCACT-AACATATTGAAAA-GTG
142090 ACAAAACAATCACTAACATTATTGAAAAGTG
1 ACAAAACAATCACTAACA-TATTGAAAAGTG
142121 ACAAAACAATCACT
1 ACAAAACAATCACT
142135 GTTTAATCCA
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
29 3 0.07
30 13 0.32
31 18 0.44
32 7 0.17
ACGTcount: A:0.49, C:0.20, G:0.09, T:0.21
Consensus pattern (30 bp):
ACAAAACAATCACTAACATATTGAAAAGTG
Found at i:143793 original size:19 final size:20
Alignment explanation
Indices: 143771--143810 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
143761 TAAAAAATAA
143771 TGAA-AGAATTTGAAA-ATTT
1 TGAATAGAATTT-AAATATTT
143790 TGAATAGAATTTAAATATTT
1 TGAATAGAATTTAAATATTT
143810 T
1 T
143811 CTCAATACAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.45, C:0.00, G:0.12, T:0.42
Consensus pattern (20 bp):
TGAATAGAATTTAAATATTT
Found at i:144497 original size:33 final size:33
Alignment explanation
Indices: 144455--144523 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
144445 AAAAGTAATG
144455 AATCAAGTGGAAAGGAGAAGTTCAATTTGGACA
1 AATCAAGTGGAAAGGAGAAGTTCAATTTGGACA
144488 AATCAAGTGGAAAGGAGAAGTTCAATTTGGACA
1 AATCAAGTGGAAAGGAGAAGTTCAATTTGGACA
144521 AAT
1 AAT
144524 TGCCGCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.22
Consensus pattern (33 bp):
AATCAAGTGGAAAGGAGAAGTTCAATTTGGACA
Found at i:146857 original size:51 final size:51
Alignment explanation
Indices: 146798--146955 Score: 207
Period size: 51 Copynumber: 3.1 Consensus size: 51
146788 TACGCCACAT
146798 AGGCTTTACAAGTGACTCACCATAAAGGCTTCCCCAAATAAATTGCA-ACGA
1 AGGCTTTACAAGTGACTCACCATAAAGGCTTCCCCAAATAAATT-CACACGA
** *
146849 AGGCTTTACAAGTGACTTGCCATAAAGGCTTCCCAAAATAAA-TCATCACGA
1 AGGCTTTACAAGTGACTCACCATAAAGGCTTCCCCAAATAAATTCA-CACGA
* *
146900 AGGCTTTACAGGTGACTCACCATAAAGGCTT-CCCAAATTAAA-TCATCACAA
1 AGGCTTTACAAGTGACTCACCATAAAGGCTTCCCCAAA-TAAATTCA-CACGA
146951 AGGCT
1 AGGCT
146956 AGGTCTGGTT
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
49 2 0.02
50 6 0.06
51 88 0.92
ACGTcount: A:0.37, C:0.25, G:0.16, T:0.23
Consensus pattern (51 bp):
AGGCTTTACAAGTGACTCACCATAAAGGCTTCCCCAAATAAATTCACACGA
Found at i:146876 original size:25 final size:25
Alignment explanation
Indices: 146798--146879 Score: 65
Period size: 25 Copynumber: 3.2 Consensus size: 25
146788 TACGCCACAT
**
146798 AGGCTTTACAAGTGACTCACCATAA
1 AGGCTTTACAAGTGACTTGCCATAA
** * * * * **
146823 AGGCTTCCCCAAATAAATTGCAACGA
1 AGGCTT-TACAAGTGACTTGCCATAA
146849 AGGCTTTACAAGTGACTTGCCATAA
1 AGGCTTTACAAGTGACTTGCCATAA
146874 AGGCTT
1 AGGCTT
146880 CCCAAAATAA
Statistics
Matches: 38, Mismatches: 18, Indels: 2
0.66 0.31 0.03
Matches are distributed among these distances:
25 23 0.61
26 15 0.39
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.24
Consensus pattern (25 bp):
AGGCTTTACAAGTGACTTGCCATAA
Found at i:146955 original size:26 final size:26
Alignment explanation
Indices: 146872--146955 Score: 71
Period size: 26 Copynumber: 3.3 Consensus size: 26
146862 GACTTGCCAT
146872 AAAGGCTTCCCAAAATAAATCATCAC
1 AAAGGCTTCCCAAAATAAATCATCAC
* ** ** * * * *
146898 GAAGGCTTTAC-AGGTGACTCACCAT
1 AAAGGCTTCCCAAAATAAATCATCAC
*
146923 AAAGGCTTCCCAAATTAAATCATCAC
1 AAAGGCTTCCCAAAATAAATCATCAC
146949 AAAGGCT
1 AAAGGCT
146956 AGGTCTGGTT
Statistics
Matches: 39, Mismatches: 18, Indels: 2
0.66 0.31 0.03
Matches are distributed among these distances:
25 16 0.41
26 23 0.59
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.21
Consensus pattern (26 bp):
AAAGGCTTCCCAAAATAAATCATCAC
Found at i:151617 original size:37 final size:37
Alignment explanation
Indices: 151576--151650 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
151566 AATAGAGTCG
*
151576 TTGCAGCCATTAAAACTAACATTAAATGTAGAGCCCA
1 TTGCAGCCATTAAAACTAACATTAAATGTAGAACCCA
151613 TTGCAGCCATTAAAACTAACATTAAATGTAGAACCCA
1 TTGCAGCCATTAAAACTAACATTAAATGTAGAACCCA
151650 T
1 T
151651 CAGAGTATCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.25
Consensus pattern (37 bp):
TTGCAGCCATTAAAACTAACATTAAATGTAGAACCCA
Found at i:173789 original size:42 final size:42
Alignment explanation
Indices: 173693--173831 Score: 120
Period size: 42 Copynumber: 3.3 Consensus size: 42
173683 ACAGTTTTAC
* * * * *
173693 AAGTCTTCCTTTAAA-ACAATTTTATGCTC-TACCAAGTCAT
1 AAGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCAT
* * *
173733 AAGTCTTCCTTTTAAACATAATCTGATGCTCATTCTGAGTCAT
1 AAGTCTTCC-TTTAAACATAATCTCATGCTCATCCCGAGTCAT
* * * * * *
173776 TAGTCTTCCTTTAATCGTATTCTCATTCTCATCCCGAGACAT
1 AAGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCAT
*
173818 GAGTCTTCCTTTAA
1 AAGTCTTCCTTTAA
173832 TATATCCTCA
Statistics
Matches: 80, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
40 9 0.11
41 6 0.08
42 49 0.61
43 16 0.20
ACGTcount: A:0.27, C:0.24, G:0.10, T:0.40
Consensus pattern (42 bp):
AAGTCTTCCTTTAAACATAATCTCATGCTCATCCCGAGTCAT
Found at i:178705 original size:18 final size:19
Alignment explanation
Indices: 178675--178710 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
178665 ATTATCCTCA
*
178675 AAATTACAAGTCTTAAAAC
1 AAATTACAAGTCTCAAAAC
178694 AAATTA-AAGTCTCAAAA
1 AAATTACAAGTCTCAAAA
178711 TTATTAAAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.56, C:0.14, G:0.06, T:0.25
Consensus pattern (19 bp):
AAATTACAAGTCTCAAAAC
Found at i:181592 original size:71 final size:71
Alignment explanation
Indices: 181441--181592 Score: 205
Period size: 71 Copynumber: 2.1 Consensus size: 71
181431 TGACTTGTTT
* * * *
181441 GTCGCAACACACAGGAGCTATGTTGCGACAACGCCTGTAGAATGATGCTTCACATGGAGATTGAT
1 GTCGCGACACACAGGAGCTATGTCGCGACAACGCCTGTAGAATGATGCTTCACATGGAGACTAAT
*
181506 GCCCAT
66 GCCCAG
* * * *
181512 GTCGTGACACATAGGAGCTATGTCGCGACAACGCCTGTAGGATGATGTTTCACATGGAGACTAAT
1 GTCGCGACACACAGGAGCTATGTCGCGACAACGCCTGTAGAATGATGCTTCACATGGAGACTAAT
* *
181577 TCCTAG
66 GCCCAG
181583 GTCGCGACAC
1 GTCGCGACAC
181593 TGGACCTGGT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.27, C:0.24, G:0.26, T:0.23
Consensus pattern (71 bp):
GTCGCGACACACAGGAGCTATGTCGCGACAACGCCTGTAGAATGATGCTTCACATGGAGACTAAT
GCCCAG
Found at i:199035 original size:17 final size:18
Alignment explanation
Indices: 199004--199037 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
198994 TTTCTAAAAA
199004 AAATAGAAATAACTAAAG
1 AAATAGAAATAACTAAAG
*
199022 AAATA-AAATGACTAAA
1 AAATAGAAATAACTAAA
199038 CCTAAATTAC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.68, C:0.06, G:0.09, T:0.18
Consensus pattern (18 bp):
AAATAGAAATAACTAAAG
Found at i:200784 original size:22 final size:22
Alignment explanation
Indices: 200756--200809 Score: 108
Period size: 22 Copynumber: 2.5 Consensus size: 22
200746 CTGGTCACTT
200756 CGTCACAACATAGGATATTCCA
1 CGTCACAACATAGGATATTCCA
200778 CGTCACAACATAGGATATTCCA
1 CGTCACAACATAGGATATTCCA
200800 CGTCACAACA
1 CGTCACAACA
200810 AAGGGACCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.37, C:0.30, G:0.13, T:0.20
Consensus pattern (22 bp):
CGTCACAACATAGGATATTCCA
Found at i:237186 original size:22 final size:22
Alignment explanation
Indices: 237157--237199 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
237147 AAAGAAATAA
237157 AATTAACCC-AATTAATTAATT
1 AATTAACCCAAATTAATTAATT
*
237178 AATTGAACCCAAATTATTTAAT
1 AATT-AACCCAAATTAATTAAT
237200 GAAATATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 5 0.26
23 10 0.53
ACGTcount: A:0.47, C:0.14, G:0.02, T:0.37
Consensus pattern (22 bp):
AATTAACCCAAATTAATTAATT
Found at i:243099 original size:21 final size:21
Alignment explanation
Indices: 243051--243093 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
243041 GAAATAGGGT
243051 AGATGATTCCTGTATCTAACC
1 AGATGATTCCTGTATCTAACC
243072 AGATGATTCCTGTATCTAACC
1 AGATGATTCCTGTATCTAACC
243093 A
1 A
243094 TTTGATCACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (21 bp):
AGATGATTCCTGTATCTAACC
Found at i:247046 original size:12 final size:12
Alignment explanation
Indices: 247029--247069 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
247019 GCCCATGGTT
*
247029 GAGAAAGAGAAG
1 GAGAAAGAAAAG
*
247041 GAGAAAGAAAAA
1 GAGAAAGAAAAG
*
247053 GAGAAGGAAAAG
1 GAGAAAGAAAAG
247065 GAGAA
1 GAGAA
247070 GACGCCATTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.63, C:0.00, G:0.37, T:0.00
Consensus pattern (12 bp):
GAGAAAGAAAAG
Found at i:273981 original size:392 final size:392
Alignment explanation
Indices: 273252--274430 Score: 1770
Period size: 392 Copynumber: 3.0 Consensus size: 392
273242 GCGACATACT
*
273252 TATCAATTTTGGTTTTTAAGCATTCTGACCCCTTGGTTGCTACATAAAAGAGGGTATGTCGCGTC
1 TATCAATTTTGGTTTTTAAGCATTCTGACCCCTTGGTTGCTACATAGAAGAGGGTATGTCGCGTC
* *
273317 ATAGCATACCTGGGTGTCTTTGGAGCAATCTGGTTTCTTTGTCACGACGTGGCCTATCTGTGTCG
66 ATAGCATGCCTGGGTGTCTTTGGAGCAATCTGGTTGCTTTGTCACGACGTGGCCTATCTGTGTCG
* *
273382 CGACAAATATATCAGATTTAAAAGAAATACCTGAAACGGATGAGATGTGATTACGTTAGTATGTT
131 CGACAAACATATCAGATTTAAAAGAAATACCTGAAACGGATGAGATGTGATTACATTAGTATGTT
*
273447 AGTGACTAAAATATAAAATTAAGGGTTAGTTCTTGTCAGAATGGTTTGACAAGAGTGTTAGGGTG
196 AGTGACTAAAATATAAAATTAAGGGTTAGTTCTTGTCAGAATAGTTTGACAAGAGTGTTAGGGTG
* * * * * * *
273512 CACTGGAGTTGGTCTATTTTATTGTTTTTTGTCCACCAGTCATTGTGCCAAACTATTTTCTGAAG
261 CACTGCAGTCGGTCTATTTTATTGTTGTTTGTCCAACAGCCATTGTGCCAAGCTATTTTCTGGAG
* * *
273577 TTTATCTCTTTCTCGAAGTTTTCCTTTTCTTCCTGCGTAGATTACCTCCAGTTCCTTTCGTCGAT
326 TTTATCTCTTTCTCGAAGTTTTCCTTTTCTTCCTGTGTAGATTACCGCCAGTTCCTTTCGCCGAT
273642 CA
391 CA
* * *
273644 TATCGATTTTGGTTTTTAAGCATTTTGACCCCTTGGTTGCTACATAGAAGAGGGTATGTCGCATC
1 TATCAATTTTGGTTTTTAAGCATTCTGACCCCTTGGTTGCTACATAGAAGAGGGTATGTCGCGTC
* * * * * *
273709 ATAGCATGCCTGGGTGTCTTTGGAGTAGTCTAGTTGCTTTGTCACGACATGGCTTATCTGTGTCA
66 ATAGCATGCCTGGGTGTCTTTGGAGCAATCTGGTTGCTTTGTCACGACGTGGCCTATCTGTGTCG
*
273774 CGACAAACATATCAGATTTAAAAGAAATACTTGAAACGGATGAGATGTGATTACATTAGTATGTT
131 CGACAAACATATCAGATTTAAAAGAAATACCTGAAACGGATGAGATGTGATTACATTAGTATGTT
* *
273839 AGTGACTTAAATATAAAATTAAGGGTTAGTTCTTGTCAAAATAGTTTGACAAGAGTGTTAGGGTG
196 AGTGACTAAAATATAAAATTAAGGGTTAGTTCTTGTCAGAATAGTTTGACAAGAGTGTTAGGGTG
* * * *
273904 CATTGCAGTCGGTCTATTTTATTGTTGTTTGTCTAGCAGCCGTTGTGCCAAGCTATTTTCTGGAG
261 CACTGCAGTCGGTCTATTTTATTGTTGTTTGTCCAACAGCCATTGTGCCAAGCTATTTTCTGGAG
* * * *
273969 TTTGTCTCTTTCTCGAAGCTTTCCTTTTCTTCCTGTGTAAATTACCGCCAGTTCCTTTTGCCGAT
326 TTTATCTCTTTCTCGAAGTTTTCCTTTTCTTCCTGTGTAGATTACCGCCAGTTCCTTTCGCCGAT
274034 CA
391 CA
* *
274036 TATCAATTTTGGTTTTTAAGCATTCTGACCCCTTGGTTGCTACATAGAAGAGGGTATGTCACGTT
1 TATCAATTTTGGTTTTTAAGCATTCTGACCCCTTGGTTGCTACATAGAAGAGGGTATGTCGCGTC
** * * *
274101 ATAGCATG-CTTAG-GTCTTTGGAGCAATTTGGTTGCTTTGTCGCGACGTGGCCTATCTGTGTTG
66 ATAGCATGCCTGGGTGTCTTTGGAGCAATCTGGTTGCTTTGTCACGACGTGGCCTATCTGTGTCG
* * *
274164 CGACGAACCTATCAGATTTAAAAGAAATACCCTGAAACGGATGAGATGTGATTACATTAGTACGT
131 CGACAAACATATCAGATTTAAAAGAAATA-CCTGAAACGGATGAGATGTGATTACATTAGTATGT
** * * *
274229 TAGTGACTAAAATATAAAATTAAGGGTTAGTTCACGTCAGAATTGTCTGACATGAGTGTTAGGGT
195 TAGTGACTAAAATATAAAATTAAGGGTTAGTTCTTGTCAGAATAGTTTGACAAGAGTGTTAGGGT
* * * * * *
274294 GCACTGTAGTCGTTTTATTTTATCGTTGTTCGTCCAACAGCCATTATGCCAAGCTATTTTCTGGA
260 GCACTGCAGTCGGTCTATTTTATTGTTGTTTGTCCAACAGCCATTGTGCCAAGCTATTTTCTGGA
* * * *
274359 GTTTATCTCTTTCTTGAAATTTT-CTTTCTCTTCCTATGTAGATTACCGCCAGTTCCTTTCACCG
325 GTTTATCTCTTTCTCGAAGTTTTCCTTT-TCTTCCTGTGTAGATTACCGCCAGTTCCTTTCGCCG
274423 ATCA
389 ATCA
274427 TATC
1 TATC
274431 GATTGATAAC
Statistics
Matches: 705, Mismatches: 80, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
390 72 0.10
391 208 0.30
392 425 0.60
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.37
Consensus pattern (392 bp):
TATCAATTTTGGTTTTTAAGCATTCTGACCCCTTGGTTGCTACATAGAAGAGGGTATGTCGCGTC
ATAGCATGCCTGGGTGTCTTTGGAGCAATCTGGTTGCTTTGTCACGACGTGGCCTATCTGTGTCG
CGACAAACATATCAGATTTAAAAGAAATACCTGAAACGGATGAGATGTGATTACATTAGTATGTT
AGTGACTAAAATATAAAATTAAGGGTTAGTTCTTGTCAGAATAGTTTGACAAGAGTGTTAGGGTG
CACTGCAGTCGGTCTATTTTATTGTTGTTTGTCCAACAGCCATTGTGCCAAGCTATTTTCTGGAG
TTTATCTCTTTCTCGAAGTTTTCCTTTTCTTCCTGTGTAGATTACCGCCAGTTCCTTTCGCCGAT
CA
Found at i:275775 original size:14 final size:15
Alignment explanation
Indices: 275751--275780 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
275741 AAGTTGTTTG
275751 AAAGTATAAAAATAA
1 AAAGTATAAAAATAA
275766 AAAG-ATAAAAATAA
1 AAAGTATAAAAATAA
275780 A
1 A
275781 TTAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.17
Consensus pattern (15 bp):
AAAGTATAAAAATAA
Found at i:282680 original size:73 final size:73
Alignment explanation
Indices: 282557--282724 Score: 282
Period size: 73 Copynumber: 2.3 Consensus size: 73
282547 CGAACAGTAG
* * *
282557 GGACGTCGATCTGCCTATTCCTTTTGAATGAAAATTATCTAAGTATGGAAGATCCATTACATCCG
1 GGACGTCGATCCGCCTATTCCTTTTGAAAGAAAATTATCCAAGTATGGAAGATCCATTACATCCG
282622 AATGGTAA
66 AATGGTAA
* *
282630 GGATGTCGATCCACCTATTCCTTTTGAAAGAAAATTATCCAAGTATGGAAGATCCATTACATCCG
1 GGACGTCGATCCGCCTATTCCTTTTGAAAGAAAATTATCCAAGTATGGAAGATCCATTACATCCG
*
282695 AATGGTAG
66 AATGGTAA
282703 GGACGTCGATCCGCCTATTCCT
1 GGACGTCGATCCGCCTATTCCT
282725 CGTGTGATAG
Statistics
Matches: 87, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
73 87 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.30
Consensus pattern (73 bp):
GGACGTCGATCCGCCTATTCCTTTTGAAAGAAAATTATCCAAGTATGGAAGATCCATTACATCCG
AATGGTAA
Found at i:285541 original size:24 final size:24
Alignment explanation
Indices: 285500--285546 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
285490 GTTAAGAGTA
* *
285500 AAAATTGTCAGTGCAAATGTAATAT
1 AAAATTGTCAGAGAAAAT-TAATAT
285525 AAAA-TGTCAGAGAAAATTAATA
1 AAAATTGTCAGAGAAAATTAATA
285547 AAAGATGAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 5 0.25
24 11 0.55
25 4 0.20
ACGTcount: A:0.51, C:0.06, G:0.15, T:0.28
Consensus pattern (24 bp):
AAAATTGTCAGAGAAAATTAATAT
Found at i:288523 original size:3 final size:3
Alignment explanation
Indices: 288515--288539 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
288505 GAGCTGAAAG
288515 GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA G
288540 GCAGTCAACT
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:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:292315 original size:51 final size:51
Alignment explanation
Indices: 292209--292318 Score: 127
Period size: 51 Copynumber: 2.2 Consensus size: 51
292199 AACAAAATCA
* * * *
292209 ATTAAATAAATATTTATTTTATATAAAATATCAGATTTAAACAAATCACTT
1 ATTAAATAAATATTTATTTTATATAAAACATCAGATTGAAACAAATAAATT
* *
292260 -TTAAATAAATATTTATATTTATTTAAAACATCATATCTGAAA-AAA-AAATT
1 ATTAAATAAATATTTAT-TTTATATAAAACATCAGAT-TGAAACAAATAAATT
292310 ATTAAATAA
1 ATTAAATAA
292319 GATCTAAAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 6
0.81 0.10 0.10
Matches are distributed among these distances:
50 19 0.38
51 27 0.54
52 4 0.08
ACGTcount: A:0.52, C:0.06, G:0.02, T:0.40
Consensus pattern (51 bp):
ATTAAATAAATATTTATTTTATATAAAACATCAGATTGAAACAAATAAATT
Found at i:300735 original size:24 final size:24
Alignment explanation
Indices: 300707--300758 Score: 95
Period size: 24 Copynumber: 2.2 Consensus size: 24
300697 TAAGAGGTTG
*
300707 ATTGAAACAAATAAACAAAGTTTA
1 ATTGAAACAAATAAACAAAGTTCA
300731 ATTGAAACAAATAAACAAAGTTCA
1 ATTGAAACAAATAAACAAAGTTCA
300755 ATTG
1 ATTG
300759 GAAGATTACT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.56, C:0.10, G:0.10, T:0.25
Consensus pattern (24 bp):
ATTGAAACAAATAAACAAAGTTCA
Found at i:302666 original size:24 final size:24
Alignment explanation
Indices: 302649--302696 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
302639 AGTTTGTCTG
302649 AAACAAATAAGAAGAGTTTAATTA
1 AAACAAATAAGAAGAGTTTAATTA
* *
302673 AAACAAATAAGCAGAGTTCAATTA
1 AAACAAATAAGAAGAGTTTAATTA
302697 GAAGATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.23
Consensus pattern (24 bp):
AAACAAATAAGAAGAGTTTAATTA
Found at i:306867 original size:27 final size:27
Alignment explanation
Indices: 306750--306849 Score: 168
Period size: 27 Copynumber: 3.8 Consensus size: 27
306740 TTAGAAAATA
*
306750 AAGCCTTTGTGGCAATCTATGAAATGA
1 AAGCCTTTGTGGCAATCTATGAAATGG
*
306777 AAGCC--TGTGGAAATCTATGAAATGG
1 AAGCCTTTGTGGCAATCTATGAAATGG
306802 AAGCCTTTGTGGCAATCTATGAAATGG
1 AAGCCTTTGTGGCAATCTATGAAATGG
306829 AAGCCTTTGTGGCAATCTATG
1 AAGCCTTTGTGGCAATCTATG
306850 GAATAGAATT
Statistics
Matches: 68, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
25 23 0.34
27 45 0.66
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (27 bp):
AAGCCTTTGTGGCAATCTATGAAATGG
Found at i:307326 original size:158 final size:158
Alignment explanation
Indices: 307037--307371 Score: 557
Period size: 158 Copynumber: 2.1 Consensus size: 158
307027 AATATGTAAA
*
307037 GCAAACTCTGAAGGAACTGAAGAATAATAGACATTGAAGGAAGAACCGTTGTGGCATAACTTGTT
1 GCAAACTCTGAAGGAACTGAAGAATAATAGACATTGAAGGAAGAACCGTTCTGGCATAACTTGTT
* *
307102 ATACCTCCAAAAAGGGTATTTTAATGATTTCCTTCATGGTGACTCATGAAAAGAAATGCCCTTGT
66 ATACCTCCAAAAAGGGTATTTTAATGATTTCCTTCATGGCGACTCATGAAAAGAAATGCCCCTGT
*
307167 GGCGTAATATGAAAGAAAATCCTCTATG
131 GGCATAATATGAAAGAAAATCCTCTATG
* *
307195 GCAAACTCTGAAGGAAC-GAAAGAATAATAGACTTTGAAGGAAGAATCGTTCTGGCATAACTTGT
1 GCAAACTCTGAAGGAACTG-AAGAATAATAGACATTGAAGGAAGAACCGTTCTGGCATAACTTGT
*
307259 TATACCTCCAAAAAGGGTATTTTAATGATTTCC-TCTGTGGCGACTCATGAAAAGAAATGCCCCT
65 TATACCTCCAAAAAGGGTATTTTAATGATTTCCTTC-ATGGCGACTCATGAAAAGAAATGCCCCT
307323 GTGGCATAATATGAAAGAAAATCCTCTATG
129 GTGGCATAATATGAAAGAAAATCCTCTATG
* *
307353 GCGAACTCTGAAGAAACTG
1 GCAAACTCTGAAGGAACTG
307372 CATCATGACG
Statistics
Matches: 165, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
157 3 0.02
158 161 0.98
159 1 0.01
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (158 bp):
GCAAACTCTGAAGGAACTGAAGAATAATAGACATTGAAGGAAGAACCGTTCTGGCATAACTTGTT
ATACCTCCAAAAAGGGTATTTTAATGATTTCCTTCATGGCGACTCATGAAAAGAAATGCCCCTGT
GGCATAATATGAAAGAAAATCCTCTATG
Found at i:309909 original size:46 final size:46
Alignment explanation
Indices: 309842--309933 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
309832 GTTGAAGTTA
309842 ACCTAAATTTTGTAAGATTCAAATTGATTATATCACACCTATCCAT
1 ACCTAAATTTTGTAAGATTCAAATTGATTATATCACACCTATCCAT
309888 ACCTAAATTTTGTAAGATTCAAATTGATTATATCACACCTATCCAT
1 ACCTAAATTTTGTAAGATTCAAATTGATTATATCACACCTATCCAT
309934 TTGTTTTATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.37, C:0.20, G:0.07, T:0.37
Consensus pattern (46 bp):
ACCTAAATTTTGTAAGATTCAAATTGATTATATCACACCTATCCAT
Found at i:310439 original size:22 final size:21
Alignment explanation
Indices: 310411--310464 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
310401 AAAATTCTTA
310411 AATTTTACTTTAACTA-AAATAT
1 AATTTTA-TTT-ACTATAAATAT
310433 AATTTTATTTACTATAAAT-T
1 AATTTTATTTACTATAAATAT
*
310453 ATATTCTATTTA
1 A-ATTTTATTTA
310465 AATTATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 6 0.21
21 16 0.55
22 7 0.24
ACGTcount: A:0.41, C:0.07, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTTTATTTACTATAAATAT
Found at i:312011 original size:14 final size:15
Alignment explanation
Indices: 311988--312033 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 15
311978 AAAAAACCAA
*
311988 AAAAATTAAATTCAT
1 AAAAATAAAATTCAT
*
312003 AAAAATAAAAAT-AT
1 AAAAATAAAATTCAT
*
312017 AAAAATGAAATTC-T
1 AAAAATAAAATTCAT
312031 AAA
1 AAA
312034 TTTATAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
14 16 0.62
15 10 0.38
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.26
Consensus pattern (15 bp):
AAAAATAAAATTCAT
Found at i:312042 original size:29 final size:29
Alignment explanation
Indices: 311988--312051 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 29
311978 AAAAAACCAA
* *
311988 AAAAATTAAATTCATAAAAATAAAAATAT
1 AAAAATGAAATTCATAAAAATAAAAAAAT
**
312017 AAAAATGAAATTC-TAAATTTATAAAAAAT
1 AAAAATGAAATTCATAAAAATA-AAAAAAT
312046 ACAAAA
1 A-AAAA
312052 ATTTCTAACA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 6 0.21
29 19 0.66
30 4 0.14
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.27
Consensus pattern (29 bp):
AAAAATGAAATTCATAAAAATAAAAAAAT
Found at i:316209 original size:23 final size:26
Alignment explanation
Indices: 316170--316229 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 26
316160 AAATAAACAA
*
316170 ATAAATTATATTA-TTGAAT-T-AAAT
1 ATAAAATATA-TACTTGAATGTGAAAT
*
316194 GTAAAA-ATATACTTGAATGTGAAAT
1 ATAAAATATATACTTGAATGTGAAAT
316219 ATAAAATATAT
1 ATAAAATATAT
316230 TAGTAATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 2 0.07
23 9 0.31
24 5 0.17
25 9 0.31
26 4 0.14
ACGTcount: A:0.52, C:0.02, G:0.08, T:0.38
Consensus pattern (26 bp):
ATAAAATATATACTTGAATGTGAAAT
Found at i:316313 original size:13 final size:13
Alignment explanation
Indices: 316295--316327 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
316285 ATTAAGAAAA
*
316295 AATAATTTTTTAT
1 AATAATTTTTAAT
316308 AATAATTTTTAAT
1 AATAATTTTTAAT
316321 AA-AATTT
1 AATAATTT
316328 GTTGCTAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
AATAATTTTTAAT
Found at i:324115 original size:133 final size:136
Alignment explanation
Indices: 323930--324172 Score: 393
Period size: 133 Copynumber: 1.8 Consensus size: 136
323920 CAAAATAGAA
* *
323930 TGTTGATTTAATAATAATAATTAAAGAAAAGCACCTATAGTTGATGACATAATAATAATCTTATG
1 TGTTGATTTAATAATAAAAATTAAAGAAAAGCACCTATAGTTGATGACATAATAATAATCTTATA
** *
323995 TATACACACCTAATGTGACTAATGC-ATA-AGAATATTACAAGATGGATTAATCTCAAATTTAAT
66 TATACACACCTAACATGACTAATACAATATAGAATATTACAAGATGGATTAATCTCAAATTTAAT
324058 AAATTT
131 AAATTT
* *
324064 TGTTGATTTAATAATAAAAATTAAA-AGAAGCACCTATAGTTGATGGCATAATAATAATCTTATA
1 TGTTGATTTAATAATAAAAATTAAAGAAAAGCACCTATAGTTGATGACATAATAATAATCTTATA
*
324128 TATACACACCTAACATGACTAGTACAATATAGAATATTACAAGAT
66 TATACACACCTAACATGACTAATACAATATAGAATATTACAAGAT
324173 AAAATGAGAA
Statistics
Matches: 99, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
133 57 0.58
134 27 0.27
135 15 0.15
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.33
Consensus pattern (136 bp):
TGTTGATTTAATAATAAAAATTAAAGAAAAGCACCTATAGTTGATGACATAATAATAATCTTATA
TATACACACCTAACATGACTAATACAATATAGAATATTACAAGATGGATTAATCTCAAATTTAAT
AAATTT
Found at i:327912 original size:20 final size:21
Alignment explanation
Indices: 327883--327934 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
327873 TTGGAGCTAT
*
327883 GGTATAGATACCTGAT-AAAA
1 GGTATCGATACCTGATGAAAA
* **
327903 GGTATCGATACTTTTTGAAAA
1 GGTATCGATACCTGATGAAAA
327924 GGTATCGATAC
1 GGTATCGATAC
327935 TTTTTTTCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.37, C:0.12, G:0.21, T:0.31
Consensus pattern (21 bp):
GGTATCGATACCTGATGAAAA
Found at i:327925 original size:21 final size:21
Alignment explanation
Indices: 327899--327939 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
327889 GATACCTGAT
327899 AAAAGGTATCGATACTTTTTG
1 AAAAGGTATCGATACTTTTTG
327920 AAAAGGTATCGATACTTTTT
1 AAAAGGTATCGATACTTTTT
327940 TTCATTGTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.34, C:0.10, G:0.17, T:0.39
Consensus pattern (21 bp):
AAAAGGTATCGATACTTTTTG
Found at i:331610 original size:58 final size:58
Alignment explanation
Indices: 331528--331647 Score: 195
Period size: 58 Copynumber: 2.1 Consensus size: 58
331518 AAAAGGAGTT
* *
331528 GTTTATGAGTGTTATTTAGGAATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTA
1 GTTTATGAATGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTA
* * *
331586 GTTTATGAATGTTTTTTAATAATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTA
1 GTTTATGAATGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTA
331644 GTTT
1 GTTT
331648 GTTGATGGGT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.17, T:0.49
Consensus pattern (58 bp):
GTTTATGAATGTTATTTAAGAATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTA
Found at i:331661 original size:58 final size:58
Alignment explanation
Indices: 331548--331662 Score: 178
Period size: 58 Copynumber: 2.0 Consensus size: 58
331538 GTTATTTAGG
**
331548 AATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTAGTTTATGAATGTTTTTTAAT
1 AATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTAGTTTATGAATGGGTTTTAAT
* *
331606 AATAAAATTATATTTGGGTTTAAAAATATTTGGGTTTAGTTTGTTG-ATGGGTTTTAA
1 AATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTAGTTT-ATGAATGGGTTTTAA
331663 ATATTAGGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
58 50 0.96
59 2 0.04
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.49
Consensus pattern (58 bp):
AATAAAATTATATTTGAGTTTAAAAATATTTGGGTTTAGTTTATGAATGGGTTTTAAT
Found at i:334475 original size:16 final size:16
Alignment explanation
Indices: 334454--334497 Score: 63
Period size: 16 Copynumber: 2.8 Consensus size: 16
334444 TGCATATAGT
334454 TATAAATGTT-TCTTAG
1 TATAAAT-TTGTCTTAG
*
334470 TATAAATTTGTTTTAG
1 TATAAATTTGTCTTAG
334486 TATAAATTTGTC
1 TATAAATTTGTC
334498 AATACTAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.32, C:0.05, G:0.11, T:0.52
Consensus pattern (16 bp):
TATAAATTTGTCTTAG
Found at i:336739 original size:16 final size:16
Alignment explanation
Indices: 336718--336749 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
336708 GGTAATTTTT
*
336718 ATGTTAAAGGATTAAA
1 ATGTTAAAGAATTAAA
336734 ATGTTAAAGAATTAAA
1 ATGTTAAAGAATTAAA
336750 TTTATAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.16, T:0.31
Consensus pattern (16 bp):
ATGTTAAAGAATTAAA
Found at i:337207 original size:27 final size:27
Alignment explanation
Indices: 337171--337272 Score: 123
Period size: 27 Copynumber: 3.7 Consensus size: 27
337161 AGGAGTAATT
* * *
337171 TGATTTTGGCTCAAAATAGCGTTATTT
1 TGATTCTGGCTCAAAAGAGCGTTATTC
*
337198 TGATTCTGGCTCGAAAGAGCGTTATTC
1 TGATTCTGGCTCAAAAGAGCGTTATTC
* *
337225 TGATTCTGGCTCGAAAGAGCATTATTC
1 TGATTCTGGCTCAAAAGAGCGTTATTC
* *
337252 TAATTCTGGACTCATAAGAGC
1 TGATTCTGG-CTCAAAAGAGC
337273 TAACCATTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
27 57 0.86
28 9 0.14
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.35
Consensus pattern (27 bp):
TGATTCTGGCTCAAAAGAGCGTTATTC
Found at i:337293 original size:24 final size:24
Alignment explanation
Indices: 337254--337371 Score: 130
Period size: 24 Copynumber: 4.9 Consensus size: 24
337244 CATTATTCTA
* *
337254 ATTCTGGACTCATAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
337278 ATTTTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
* *
337302 ATTCTGGGCTCATGAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
* * * *
337326 ATTTTGGGCTAGTGAGATCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
*
337350 -TATCTGGGCTCGTATGAGCTAA
1 AT-TCTGGGCTCGTAAGAGCTAA
337372 TTTTGTCTGG
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
23 1 0.01
24 77 0.99
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:337314 original size:48 final size:48
Alignment explanation
Indices: 337254--337371 Score: 157
Period size: 48 Copynumber: 2.5 Consensus size: 48
337244 CATTATTCTA
* *
337254 ATTCTGGACTCATAAGAGCTAACCATTTTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCATAAGAGCTAACCATTTTGGGCTAGTAAGAGCTAACC
* * *
337302 ATTCTGGGCTCATGAGAGCTAACCATTTTGGGCTAGTGAGATCTAACC
1 ATTCTGGGCTCATAAGAGCTAACCATTTTGGGCTAGTAAGAGCTAACC
* *
337350 -TATCTGGGCTCGTATGAGCTAA
1 AT-TCTGGGCTCATAAGAGCTAA
337372 TTTTGTCTGG
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
47 1 0.02
48 60 0.98
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (48 bp):
ATTCTGGGCTCATAAGAGCTAACCATTTTGGGCTAGTAAGAGCTAACC
Found at i:338718 original size:20 final size:20
Alignment explanation
Indices: 338672--338711 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
338662 TTATTAGTTT
338672 TACAAATATATGATGGTAAA
1 TACAAATATATGATGGTAAA
338692 TACAAATATATGATGGTAAA
1 TACAAATATATGATGGTAAA
338712 GTCAAATGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.05, G:0.15, T:0.30
Consensus pattern (20 bp):
TACAAATATATGATGGTAAA
Found at i:347401 original size:16 final size:16
Alignment explanation
Indices: 347380--347410 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
347370 TGTTATTTTC
*
347380 TTATATATTATGAAAT
1 TTATATAATATGAAAT
347396 TTATATAATATGAAA
1 TTATATAATATGAAA
347411 ATTAAATGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (16 bp):
TTATATAATATGAAAT
Found at i:348680 original size:21 final size:21
Alignment explanation
Indices: 348656--348720 Score: 94
Period size: 21 Copynumber: 3.0 Consensus size: 21
348646 GTTAGTAACC
348656 TAACTCTCCTCATAATGTTTG
1 TAACTCTCCTCATAATGTTTG
* *
348677 TAACTTTCCTCATAATGTTTTA
1 TAACTCTCCTCATAATG-TTTG
*
348699 TAACTCTCCTCATTATGTTTG
1 TAACTCTCCTCATAATGTTTG
348720 T
1 T
348721 TTTAAATTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
21 20 0.53
22 18 0.47
ACGTcount: A:0.23, C:0.22, G:0.08, T:0.48
Consensus pattern (21 bp):
TAACTCTCCTCATAATGTTTG
Found at i:348708 original size:22 final size:22
Alignment explanation
Indices: 348656--348718 Score: 92
Period size: 22 Copynumber: 2.9 Consensus size: 22
348646 GTTAGTAACC
*
348656 TAACTCTCCTCATAATG-TTTG
1 TAACTCTCCTCATAATGTTTTA
*
348677 TAACTTTCCTCATAATGTTTTA
1 TAACTCTCCTCATAATGTTTTA
*
348699 TAACTCTCCTCATTATGTTT
1 TAACTCTCCTCATAATGTTT
348719 GTTTTAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
21 16 0.43
22 21 0.57
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (22 bp):
TAACTCTCCTCATAATGTTTTA
Found at i:353186 original size:15 final size:16
Alignment explanation
Indices: 353166--353200 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
353156 TTATCATAAA
353166 TTCTTTTGCTT-CTTT
1 TTCTTTTGCTTCCTTT
*
353181 TTCTTTTTCTTCCTTT
1 TTCTTTTGCTTCCTTT
353197 TTCT
1 TTCT
353201 CATTTTTCCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (16 bp):
TTCTTTTGCTTCCTTT
Found at i:353196 original size:16 final size:16
Alignment explanation
Indices: 353166--353213 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
353156 TTATCATAAA
*
353166 TTCTTTTGCTT-CTTT
1 TTCTTTTTCTTCCTTT
353181 TTCTTTTTCTTCCTTT
1 TTCTTTTTCTTCCTTT
*
353197 TTCTCATTT-TTCCTTT
1 TTCT-TTTTCTTCCTTT
353213 T
1 T
353214 CAAGTGACTG
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.34
16 16 0.55
17 3 0.10
ACGTcount: A:0.02, C:0.23, G:0.02, T:0.73
Consensus pattern (16 bp):
TTCTTTTTCTTCCTTT
Found at i:353813 original size:19 final size:20
Alignment explanation
Indices: 353768--353819 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
353758 ATGGAAATGC
**
353768 AATAAAAATGCAACTAACTT
1 AATAAAAATGCAACTAACAA
* *
353788 AACAAAAATGCAA-TGACAA
1 AATAAAAATGCAACTAACAA
353807 AATAAAAATGCAA
1 AATAAAAATGCAA
353820 GAAAACTATC
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.62, C:0.13, G:0.08, T:0.17
Consensus pattern (20 bp):
AATAAAAATGCAACTAACAA
Found at i:364904 original size:17 final size:18
Alignment explanation
Indices: 364872--364909 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
364862 GTTCTTTGTT
*
364872 TTTAAATTTATTTTTACA
1 TTTAAATTTATATTTACA
*
364890 TTTAAA-TTATATTTATA
1 TTTAAATTTATATTTACA
364907 TTT
1 TTT
364910 TTCATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (18 bp):
TTTAAATTTATATTTACA
Found at i:365703 original size:18 final size:18
Alignment explanation
Indices: 365658--365704 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
365648 TTCAAAAGGA
* *
365658 GGAGGTGGTAGGGGTGGT
1 GGAGGAGGTGGGGGTGGT
*
365676 GGAGGCGGTGGGGGTGGT
1 GGAGGAGGTGGGGGTGGT
365694 GGAGGAGGTGG
1 GGAGGAGGTGG
365705 ACAAGGATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.11, C:0.02, G:0.70, T:0.17
Consensus pattern (18 bp):
GGAGGAGGTGGGGGTGGT
Found at i:365774 original size:15 final size:15
Alignment explanation
Indices: 365754--365786 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
365744 TGAGAATGGG
*
365754 GGAGGCGGTGGTGGC
1 GGAGGCGGAGGTGGC
365769 GGAGGCGGAGGTGGC
1 GGAGGCGGAGGTGGC
365784 GGA
1 GGA
365787 AGTTCTGGAG
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:0.12, C:0.12, G:0.67, T:0.09
Consensus pattern (15 bp):
GGAGGCGGAGGTGGC
Found at i:367475 original size:16 final size:16
Alignment explanation
Indices: 367454--367484 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
367444 TATAATACTC
*
367454 TATATTATGTTATTTT
1 TATATTATGTAATTTT
367470 TATATTATGTAATTT
1 TATATTATGTAATTT
367485 AAAACACGTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (16 bp):
TATATTATGTAATTTT
Found at i:371624 original size:36 final size:36
Alignment explanation
Indices: 371544--371624 Score: 119
Period size: 36 Copynumber: 2.2 Consensus size: 36
371534 TTGTTGTGAA
371544 AGTGAATATGTGGGTATGTTATTCATGCCATGAGAC
1 AGTGAATATGTGGGTATGTTATTCATGCCATGAGAC
** *
371580 AGAAAATATGTGGGTATGTTATTCATGTCAT-ATGAC
1 AGTGAATATGTGGGTATGTTATTCATGCCATGA-GAC
371616 AGTGAATAT
1 AGTGAATAT
371625 ATTGTGTTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
35 1 0.03
36 38 0.97
ACGTcount: A:0.32, C:0.09, G:0.25, T:0.35
Consensus pattern (36 bp):
AGTGAATATGTGGGTATGTTATTCATGCCATGAGAC
Found at i:372092 original size:59 final size:59
Alignment explanation
Indices: 372014--372205 Score: 204
Period size: 59 Copynumber: 3.1 Consensus size: 59
372004 CTATCATTAA
* * *
372014 ATGTGAATAAATGTCACTAAATGTTATTAATATGTGATTTGATAAATGCTGAAATATTC
1 ATGTGAATAAATGTGACTAAATGTAATTAATATGTGATGTGATAAATGCTGAAATATTC
* * * *
372073 ATGTGAGTAAATATGACTAAATGTAATTAATATGAGATGTGATAAATGCTAAAAGATTCATGTGA
1 ATGTGAATAAATGTGACTAAATGTAATTAATATGTGATGTGATAAATGCT-GAA-A-T-AT-T--
372138 C
59 C
* * **
372139 TAATGTGATTAAATGTGACTAAATATAATTAATATGTGATGTGATAAATATTGAAATATTC
1 --ATGTGAATAAATGTGACTAAATGTAATTAATATGTGATGTGATAAATGCTGAAATATTC
372200 ATGTGA
1 ATGTGA
372206 CCAATGTGAT
Statistics
Matches: 110, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
59 50 0.45
60 2 0.02
61 2 0.02
62 1 0.01
63 3 0.03
64 3 0.03
65 1 0.01
66 2 0.02
67 2 0.02
68 44 0.40
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.36
Consensus pattern (59 bp):
ATGTGAATAAATGTGACTAAATGTAATTAATATGTGATGTGATAAATGCTGAAATATTC
Found at i:372158 original size:68 final size:68
Alignment explanation
Indices: 372073--372216 Score: 207
Period size: 68 Copynumber: 2.1 Consensus size: 68
372063 TGAAATATTC
* * *
372073 ATGTGAGTAAATATGACTAAATGTAATTAATATGAGATGTGATAAATGCTAAAAGATTCATGTGA
1 ATGTGATTAAATATGACTAAATATAATTAATATGAGATGTGATAAATACTAAAAGATTCATGTGA
*
372138 CTA
66 CCA
* * * * *
372141 ATGTGATTAAATGTGACTAAATATAATTAATATGTGATGTGATAAATATTGAAATATTCATGTGA
1 ATGTGATTAAATATGACTAAATATAATTAATATGAGATGTGATAAATACTAAAAGATTCATGTGA
372206 CCA
66 CCA
372209 ATGTGATT
1 ATGTGATT
372217 TGTGCTTAAA
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (68 bp):
ATGTGATTAAATATGACTAAATATAATTAATATGAGATGTGATAAATACTAAAAGATTCATGTGA
CCA
Found at i:372457 original size:23 final size:23
Alignment explanation
Indices: 372208--372447 Score: 318
Period size: 23 Copynumber: 10.4 Consensus size: 23
372198 TCATGTGACC
372208 AATGTGATTTGTGCTTAAATATT
1 AATGTGATTTGTGCTTAAATATT
* * *
372231 AATGTGATTTATGCTTAAGTTTT
1 AATGTGATTTGTGCTTAAATATT
* * *
372254 AATATGATTTATGCTTAAAAATT
1 AATGTGATTTGTGCTTAAATATT
372277 AATGTGATTTGTGCTTAAATATT
1 AATGTGATTTGTGCTTAAATATT
* *
372300 AATGTGATTTGTACTTAAATTTT
1 AATGTGATTTGTGCTTAAATATT
*
372323 AATGTGATTTGTGTTTAAATATT
1 AATGTGATTTGTGCTTAAATATT
372346 AATGTGATTTGTGCTTAAATATT
1 AATGTGATTTGTGCTTAAATATT
372369 AATGTGATTTGTGCTTAAATATT
1 AATGTGATTTGTGCTTAAATATT
* ** * *
372392 AAAGTGATTCATGGTTAAATGTT
1 AATGTGATTTGTGCTTAAATATT
* * * *
372415 AATATGATTTATACTAAAATATT
1 AATGTGATTTGTGCTTAAATATT
372438 AATGTGATTT
1 AATGTGATTT
372448 ATGTGTAAAT
Statistics
Matches: 188, Mismatches: 29, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 188 1.00
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.47
Consensus pattern (23 bp):
AATGTGATTTGTGCTTAAATATT
Found at i:373551 original size:14 final size:15
Alignment explanation
Indices: 373516--373552 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
373506 AAAAGAAAAA
373516 AGAA-AAGAAAGGAG
1 AGAAGAAGAAAGGAG
*
373530 AAAAGAAGAAAGG-G
1 AGAAGAAGAAAGGAG
373544 AGAAGAAGA
1 AGAAGAAGA
373553 GATGTGTGGC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (15 bp):
AGAAGAAGAAAGGAG
Found at i:374082 original size:71 final size:69
Alignment explanation
Indices: 373994--374159 Score: 185
Period size: 71 Copynumber: 2.4 Consensus size: 69
373984 TTCTTCATCA
* * *
373994 TTTCTATTAAAATGTTAATTTCAATCCCACAT-TGACTAGAAAATACTCT-TTTAGCTCAATTCT
1 TTTC-ATTAAAAAGTTAATTTTAATCCCACATGT-ACTAGAAAATACTCTCATT-GCTCAATTCT
* *
374057 TTACTAT
63 TCACGAT
* * * *
374064 TTTCATTATAAAAAGTTAATTTTAAACTCACATGTACTAGAAAATACTCTCATTGTTCACTTCTT
1 TTTCA-T-TAAAAAGTTAATTTTAATCCCACATGTACTAGAAAATACTCTCATTGCTCAATTCTT
374129 CACGAT
64 CACGAT
374135 TTTCATTAAAAA-TTAATTTTAATCC
1 TTTCATTAAAAAGTTAATTTTAATCC
374160 TTACGTTGGC
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
68 11 0.14
69 7 0.09
70 6 0.07
71 54 0.67
72 3 0.04
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.42
Consensus pattern (69 bp):
TTTCATTAAAAAGTTAATTTTAATCCCACATGTACTAGAAAATACTCTCATTGCTCAATTCTTCA
CGAT
Found at i:374282 original size:6 final size:6
Alignment explanation
Indices: 374271--374302 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
374261 ATTTTTACTA
374271 AAAATT AAAATT AAAATT AAAATT AAAATT AA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AA
374303 CTAAATCTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
AAAATT
Found at i:374405 original size:68 final size:70
Alignment explanation
Indices: 374289--374447 Score: 200
Period size: 68 Copynumber: 2.3 Consensus size: 70
374279 AATTAAAATT
* * * * * *
374289 AAAATTA-AAATTAACTAAAT-CTTAGTATATGCACTTAAATTATAGTATGTGTAAATACTTTAT
1 AAAATTATGAATTAATTAAATATTTAGTATACGCACTTAAACTATAGTATGTGAAAATACTTTAT
374352 ATATA
66 ATATA
*
374357 AAAATTATGAATTAATTAAATATTTA-TATACGCAC-TAAACTATAGTATGTGAAAATATTTTAT
1 AAAATTATGAATTAATTAAATATTTAGTATACGCACTTAAACTATAGTATGTGAAAATACTTTAT
374420 ATATA
66 ATATA
** *
374425 AAAAACATGAATTGATTAAATAT
1 AAAATTATGAATTAATTAAATAT
374448 ATTTTTTTTG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
68 57 0.72
69 19 0.24
70 3 0.04
ACGTcount: A:0.48, C:0.06, G:0.08, T:0.38
Consensus pattern (70 bp):
AAAATTATGAATTAATTAAATATTTAGTATACGCACTTAAACTATAGTATGTGAAAATACTTTAT
ATATA
Found at i:374463 original size:19 final size:20
Alignment explanation
Indices: 374436--374473 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
374426 AAAACATGAA
* *
374436 TTGATTAAATATA-TTTTTT
1 TTGAATAAAGATACTTTTTT
374455 TTGAATAAAGATACTTTTT
1 TTGAATAAAGATACTTTTT
374474 GAATCAATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 11 0.69
20 5 0.31
ACGTcount: A:0.34, C:0.03, G:0.08, T:0.55
Consensus pattern (20 bp):
TTGAATAAAGATACTTTTTT
Found at i:380155 original size:47 final size:47
Alignment explanation
Indices: 380086--380178 Score: 150
Period size: 47 Copynumber: 2.0 Consensus size: 47
380076 GATATCGAAT
* * *
380086 TTCTTCTTAGTCTTCCATAAGCATTTAAGTTGTGCCCGTAGACTATA
1 TTCTTCTTAGTCTTCCATAAGCACTTAAGTTGCGCCCGCAGACTATA
*
380133 TTCTTCTTGGTCTTCCATAAGCACTTAAGTTGCGCCCGCAGACTAT
1 TTCTTCTTAGTCTTCCATAAGCACTTAAGTTGCGCCCGCAGACTAT
380179 CCGGATTGTA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 42 1.00
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.38
Consensus pattern (47 bp):
TTCTTCTTAGTCTTCCATAAGCACTTAAGTTGCGCCCGCAGACTATA
Found at i:380957 original size:21 final size:21
Alignment explanation
Indices: 380931--380973 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
380921 AAATATCGTT
380931 AAAAACATATTTAACAGTTTA
1 AAAAACATATTTAACAGTTTA
*
380952 AAAAACATATTTAATAGTTTA
1 AAAAACATATTTAACAGTTTA
380973 A
1 A
380974 GATATTGTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACATATTTAACAGTTTA
Found at i:383803 original size:33 final size:32
Alignment explanation
Indices: 383756--383833 Score: 102
Period size: 33 Copynumber: 2.4 Consensus size: 32
383746 AGTTTATATA
383756 GATGTAAGACCATAGCTAGGCTATGACATTCT
1 GATGTAAGACCATAGCTAGGCTATGACATTCT
* * *
383788 GATGATAAGATCATAGTTGGGCTATGACATTCT
1 GATG-TAAGACCATAGCTAGGCTATGACATTCT
* *
383821 AACGTAAGACCAT
1 GATGTAAGACCAT
383834 GGTTGGACCA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
32 12 0.31
33 27 0.69
ACGTcount: A:0.33, C:0.17, G:0.22, T:0.28
Consensus pattern (32 bp):
GATGTAAGACCATAGCTAGGCTATGACATTCT
Found at i:383872 original size:69 final size:69
Alignment explanation
Indices: 383788--383979 Score: 303
Period size: 69 Copynumber: 2.8 Consensus size: 69
383778 ATGACATTCT
* * * *
383788 GATGATAAGATCATAGTTGGGCTATGACATTCTAACGTAAGACCATGGTTGGACCATGGTAGTGT
1 GATG-TAAGACCATAGTTGGGCTATGGCATTCTGATGTAAGACCATGGTTGGACCATGGTAGTGT
383853 ATATA
65 ATATA
*
383858 GATGTAAGACCATAGTTGGGCTATGGCATTTTGATGTAAGACCATGGTTGGACCATGGTAGTGTA
1 GATGTAAGACCATAGTTGGGCTATGGCATTCTGATGTAAGACCATGGTTGGACCATGGTAGTGTA
383923 TATA
66 TATA
* *
383927 GATGTAAGACCATAGTTGGGTTATGGCATTCTGATGATAAGACCATAGTTGGA
1 GATGTAAGACCATAGTTGGGCTATGGCATTCTGATG-TAAGACCATGGTTGGA
383980 TTATGGCATT
Statistics
Matches: 113, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
69 94 0.83
70 19 0.17
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.31
Consensus pattern (69 bp):
GATGTAAGACCATAGTTGGGCTATGGCATTCTGATGTAAGACCATGGTTGGACCATGGTAGTGTA
TATA
Found at i:383876 original size:37 final size:37
Alignment explanation
Indices: 383824--383945 Score: 164
Period size: 37 Copynumber: 3.4 Consensus size: 37
383814 ACATTCTAAC
*
383824 GTAAGACCATGGTTGGACCATGGTAGTGTATATAGAT
1 GTAAGACCATAGTTGGACCATGGTAGTGTATATAGAT
* * *
383861 GTAAGACCATAGTTGGGCTATGGCA-T-T-T-T-GAT
1 GTAAGACCATAGTTGGACCATGGTAGTGTATATAGAT
*
383893 GTAAGACCATGGTTGGACCATGGTAGTGTATATAGAT
1 GTAAGACCATAGTTGGACCATGGTAGTGTATATAGAT
383930 GTAAGACCATAGTTGG
1 GTAAGACCATAGTTGG
383946 GTTATGGCAT
Statistics
Matches: 71, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
32 24 0.34
33 2 0.03
34 2 0.03
35 2 0.03
36 2 0.03
37 39 0.55
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (37 bp):
GTAAGACCATAGTTGGACCATGGTAGTGTATATAGAT
Found at i:383893 original size:102 final size:101
Alignment explanation
Indices: 383713--383908 Score: 293
Period size: 102 Copynumber: 1.9 Consensus size: 101
383703 AGACAAGCTG
* * *
383713 CATTCTGACGTAAGACCATGGTTGGATCATGGCAGTTTATATAGATGTAAGACCATAGCTAGGCT
1 CATTCTAACGTAAGACCATGGTTGGACCATGGCAGTGTATATAGATGTAAGACCATAGCTAGGCT
*
383778 ATGACATTCTGATGATAAGATCATAGTTGGGCTATGA
66 ATGACATTCTGATG-TAAGACCATAGTTGGGCTATGA
* * *
383815 CATTCTAACGTAAGACCATGGTTGGACCATGGTAGTGTATATAGATGTAAGACCATAGTTGGGCT
1 CATTCTAACGTAAGACCATGGTTGGACCATGGCAGTGTATATAGATGTAAGACCATAGCTAGGCT
* * *
383880 ATGGCATTTTGATGTAAGACCATGGTTGG
66 ATGACATTCTGATGTAAGACCATAGTTGG
383909 ACCATGGTAG
Statistics
Matches: 84, Mismatches: 10, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
101 13 0.15
102 71 0.85
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (101 bp):
CATTCTAACGTAAGACCATGGTTGGACCATGGCAGTGTATATAGATGTAAGACCATAGCTAGGCT
ATGACATTCTGATGTAAGACCATAGTTGGGCTATGA
Found at i:384017 original size:33 final size:32
Alignment explanation
Indices: 383945--384022 Score: 93
Period size: 33 Copynumber: 2.4 Consensus size: 32
383935 ACCATAGTTG
***
383945 GGTTATGGCATTCTGATGATAAGACCATAGTT
1 GGTTATGGCATTCTGATGATAAGACCATAACC
* *
383977 GGATTATGGCATTTTGATGTTAAGACCATAACC
1 GG-TTATGGCATTCTGATGATAAGACCATAACC
384010 GAGTTATGGCATT
1 G-GTTATGGCATT
384023 ATGAATGTAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
32 2 0.05
33 36 0.92
34 1 0.03
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (32 bp):
GGTTATGGCATTCTGATGATAAGACCATAACC
Found at i:385730 original size:21 final size:22
Alignment explanation
Indices: 385682--385735 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
385672 ACAGTCATTT
*
385682 GAAAACATTT-GTTTATTTTAGTA
1 GAAAAC-TTTAGTCTATTTTAG-A
385705 GAAAACTTTAGTCTATTTTA-A
1 GAAAACTTTAGTCTATTTTAGA
*
385726 GAAAAGTTTA
1 GAAAACTTTA
385736 CGAGTTTATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 10 0.36
22 3 0.11
23 15 0.54
ACGTcount: A:0.39, C:0.06, G:0.13, T:0.43
Consensus pattern (22 bp):
GAAAACTTTAGTCTATTTTAGA
Found at i:386426 original size:43 final size:43
Alignment explanation
Indices: 386365--386458 Score: 179
Period size: 43 Copynumber: 2.2 Consensus size: 43
386355 AGTTAACAAA
386365 GAGCTAAGAAGAGTATTTTTCAAGTCAAGGATCGATCCAATAT
1 GAGCTAAGAAGAGTATTTTTCAAGTCAAGGATCGATCCAATAT
386408 GAGCTAAGAAGAGTATTTTTCAAGTCAAGGATCGATCCAATAT
1 GAGCTAAGAAGAGTATTTTTCAAGTCAAGGATCGATCCAATAT
386451 GAAGCTAA
1 G-AGCTAA
386459 ATTATGCTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 44 0.88
44 6 0.12
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (43 bp):
GAGCTAAGAAGAGTATTTTTCAAGTCAAGGATCGATCCAATAT
Found at i:387149 original size:12 final size:12
Alignment explanation
Indices: 387132--387157 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
387122 TGTTATCATG
387132 ATGAATGCTATT
1 ATGAATGCTATT
387144 ATGAATGCTATT
1 ATGAATGCTATT
387156 AT
1 AT
387158 TTCTTTAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATGAATGCTATT
Found at i:388458 original size:21 final size:19
Alignment explanation
Indices: 388434--388486 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
388424 CACCACGTTA
388434 TGGATAAACCACTTACCATTG
1 TGGATAAACCACTT--CATTG
**
388455 TGGACGAACCAC-TCATTG
1 TGGATAAACCACTTCATTG
388473 TGGATAAACCACTT
1 TGGATAAACCACTT
388487 GTAACAACTC
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 15 0.56
19 1 0.04
20 1 0.04
21 10 0.37
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (19 bp):
TGGATAAACCACTTCATTG
Found at i:389697 original size:28 final size:28
Alignment explanation
Indices: 389614--389745 Score: 88
Period size: 28 Copynumber: 4.7 Consensus size: 28
389604 ATGAATGAAC
* * * *
389614 AATCTATATTTGGCTCGAAAAGAGCAATG
1 AATCTGTATCTGGCTCG-AATGAGCAATA
**
389643 AATCTGTATCTATCTCGAATGAGCAATA
1 AATCTGTATCTGGCTCGAATGAGCAATA
* *
389671 AATTTGTATCTGGCTCGAATG-GACAATT
1 AATCTGTATCTGGCTCGAATGAG-CAATA
* * * * *
389699 AGTCTATTTCTGGCTTGAATGAGTAAT-
1 AATCTGTATCTGGCTCGAATGAGCAATA
* * *
389726 ATTTTGTATTTGGCTCGAAT
1 AATCTGTATCTGGCTCGAAT
389746 AAGCCATATT
Statistics
Matches: 79, Mismatches: 22, Indels: 6
0.74 0.21 0.06
Matches are distributed among these distances:
27 15 0.19
28 50 0.63
29 14 0.18
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (28 bp):
AATCTGTATCTGGCTCGAATGAGCAATA
Found at i:389745 original size:27 final size:27
Alignment explanation
Indices: 389656--389802 Score: 82
Period size: 27 Copynumber: 5.4 Consensus size: 27
389646 CTGTATCTAT
* * *
389656 CTCGAATGAGCAATAAATTTGTATCTGG
1 CTCGAATGAGAAAT-ATTTTGTATTTGG
** *
389684 CTCGAATG-GACAAT-TAGTCTATTTCTGG
1 CTCGAATGAGA-AATATTTTGTA-TT-TGG
* *
389712 CTTGAATGAGTAATATTTTGTATTTGG
1 CTCGAATGAGAAATATTTTGTATTTGG
* ** * * * *
389739 CTCGAATAAGCCATATTCTGCATCTAG
1 CTCGAATGAGAAATATTTTGTATTTGG
* *
389766 CTCAAATGAAAAATATTTTGTATTTGG
1 CTCGAATGAGAAATATTTTGTATTTGG
*
389793 CTGGAATGAG
1 CTCGAATGAG
389803 CCACTTTCTG
Statistics
Matches: 83, Mismatches: 31, Indels: 11
0.66 0.25 0.09
Matches are distributed among these distances:
26 3 0.04
27 49 0.59
28 26 0.31
29 5 0.06
ACGTcount: A:0.30, C:0.14, G:0.20, T:0.36
Consensus pattern (27 bp):
CTCGAATGAGAAATATTTTGTATTTGG
Found at i:392598 original size:11 final size:10
Alignment explanation
Indices: 392578--392603 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
392568 TATATGCATA
392578 TTTTTATTTT
1 TTTTTATTTT
392588 TTTTTATTTT
1 TTTTTATTTT
392598 TTTTTA
1 TTTTTA
392604 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (10 bp):
TTTTTATTTT
Found at i:394356 original size:18 final size:18
Alignment explanation
Indices: 394335--394376 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
394325 CTCCACCGCT
394335 TAAACCTCCTGGT-CCACC
1 TAAACCTCC-GGTCCCACC
394353 TAAACCTCCGGTCCCACC
1 TAAACCTCCGGTCCCACC
394371 TAAACC
1 TAAACC
394377 GCCGAGACCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 3 0.13
18 20 0.87
ACGTcount: A:0.26, C:0.45, G:0.10, T:0.19
Consensus pattern (18 bp):
TAAACCTCCGGTCCCACC
Found at i:397596 original size:23 final size:22
Alignment explanation
Indices: 397569--397619 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 22
397559 TTTACAATAC
*
397569 TTTTAGATAATTAAG-TTTATTT
1 TTTTA-ATAATTAAGAGTTATTT
397591 TCTTT-ATAATTAAGAGTTATTT
1 T-TTTAATAATTAAGAGTTATTT
397613 TTTTAAT
1 TTTTAAT
397620 TTCATGTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 12 0.48
22 10 0.40
23 3 0.12
ACGTcount: A:0.31, C:0.02, G:0.08, T:0.59
Consensus pattern (22 bp):
TTTTAATAATTAAGAGTTATTT
Found at i:410237 original size:34 final size:34
Alignment explanation
Indices: 410198--410311 Score: 126
Period size: 34 Copynumber: 3.4 Consensus size: 34
410188 TTTAACAAAA
*
410198 CAATACAGTAGC-AATAAATATGCTTATAAGAGAT
1 CAATACAGTAGCAAAT-AATATGCTTATAACAGAT
* * *
410232 CAATACTA-TAACAAATTATATGCTTATAACAAAT
1 CAATAC-AGTAGCAAATAATATGCTTATAACAGAT
* *
410266 CAATACAGTAGAAAATAATATACTTATAACAGAT
1 CAATACAGTAGCAAATAATATGCTTATAACAGAT
410300 CAA-ATCAGTAGC
1 CAATA-CAGTAGC
410312 TAAAAGTCAT
Statistics
Matches: 66, Mismatches: 10, Indels: 8
0.79 0.12 0.10
Matches are distributed among these distances:
33 2 0.03
34 60 0.91
35 4 0.06
ACGTcount: A:0.49, C:0.14, G:0.10, T:0.27
Consensus pattern (34 bp):
CAATACAGTAGCAAATAATATGCTTATAACAGAT
Found at i:424502 original size:21 final size:22
Alignment explanation
Indices: 424476--424532 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 22
424466 AAATAGTGCA
424476 AACTTCTATCGATACAAGT-AT
1 AACTTCTATCGATACAAGTCAT
* *
424497 AACTTCTACCGAAACAAGTCAT
1 AACTTCTATCGATACAAGTCAT
*
424519 -GCTTCTATCGATAC
1 AACTTCTATCGATAC
424533 TAACAACTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 28 0.93
22 2 0.07
ACGTcount: A:0.35, C:0.25, G:0.11, T:0.30
Consensus pattern (22 bp):
AACTTCTATCGATACAAGTCAT
Found at i:425296 original size:42 final size:42
Alignment explanation
Indices: 425238--425509 Score: 278
Period size: 42 Copynumber: 6.4 Consensus size: 42
425228 CAGAGGCATA
425238 AGTCTTCCTTTCAAACATAATCTCATGCTCATTCCGAGACATG
1 AGTCTTCCTTT-AAACATAATCTCATGCTCATTCCGAGACATG
* *
425281 AGTCTTCCTTTAAACATAATCTCATTCTCATTCCAAGACATG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATTCCGAGACATG
* * *
425323 AGTTTTCCTTTAAACATAAT-TCATTCTCA-CCTCGAGACATG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATTC-CGAGACATG
* * * * *
425364 AGTCTTCCTTTTTAAACATATTCTCATGCTTATTCTGAGTCACG
1 AGTCTTCC--TTTAAACATAATCTCATGCTCATTCCGAGACATG
* * * ** *
425408 AGTCTTCCTTTAAACTTATTCTCATGCTAATTTTGATACATG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATTCCGAGACATG
* ** * * *
425450 AGTCTTCCTTTAAACATACTCTTGTGCTCATCCCGAGTCACG
1 AGTCTTCCTTTAAACATAATCTCATGCTCATTCCGAGACATG
*
425492 AGTCTTCCATTTATACAT
1 AGTCTTCC-TTTAAACAT
425510 CAAGTGTTTC
Statistics
Matches: 192, Mismatches: 31, Indels: 12
0.82 0.13 0.05
Matches are distributed among these distances:
40 1 0.01
41 24 0.12
42 115 0.60
43 30 0.16
44 21 0.11
45 1 0.01
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.38
Consensus pattern (42 bp):
AGTCTTCCTTTAAACATAATCTCATGCTCATTCCGAGACATG
Found at i:425389 original size:85 final size:84
Alignment explanation
Indices: 425238--425509 Score: 269
Period size: 85 Copynumber: 3.2 Consensus size: 84
425228 CAGAGGCATA
*
425238 AGTCTTCCTTTCAAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATAATCT
1 AGTCTTCCTTT-AAACATAATCTCATGCTCACTCCGAGACATGAGTCTTCCTTTAAACATAATCT
* *
425303 CATTCTCATTCCAAGACATG
65 CATGCTCATTCCAAGACACG
* * *
425323 AGTTTTCCTTTAAACATAAT-TCATTCTCAC-CTCGAGACATGAGTCTTCCTTTTTAAACATATT
1 AGTCTTCCTTTAAACATAATCTCATGCTCACTC-CGAGACATGAGTCTTCC--TTTAAACATAAT
* ** *
425386 CTCATGCTTATTCTGAGTCACG
63 CTCATGCTCATTCCAAGACACG
* * * * ** * * *
425408 AGTCTTCCTTTAAACTTATTCTCATGCTAATTTTGATACATGAGTCTTCCTTTAAACATACTCTT
1 AGTCTTCCTTTAAACATAATCTCATGCTCACTCCGAGACATGAGTCTTCCTTTAAACATAATCTC
* * * *
425473 GTGCTCATCCCGAGTCACG
66 ATGCTCATTCCAAGACACG
*
425492 AGTCTTCCATTTATACAT
1 AGTCTTCC-TTTAAACAT
425510 CAAGTGTTTC
Statistics
Matches: 154, Mismatches: 27, Indels: 12
0.80 0.14 0.06
Matches are distributed among these distances:
82 1 0.01
83 25 0.16
84 45 0.29
85 61 0.40
86 22 0.14
ACGTcount: A:0.26, C:0.25, G:0.10, T:0.38
Consensus pattern (84 bp):
AGTCTTCCTTTAAACATAATCTCATGCTCACTCCGAGACATGAGTCTTCCTTTAAACATAATCTC
ATGCTCATTCCAAGACACG
Found at i:425411 original size:127 final size:126
Alignment explanation
Indices: 425238--425467 Score: 316
Period size: 127 Copynumber: 1.8 Consensus size: 126
425228 CAGAGGCATA
*
425238 AGTCTTCCTTTCAAACATAATCTCATGCTCATTCCGAGACATGAGTCTTCCTTTAAACATAATCT
1 AGTCTTCCTTTCAAACATAATCTCATGCTCATTCCGAGACACGAGTCTTCCTTTAAACATAATCT
* * *
425303 CATTCTCATTCCAAGACATGAGTTTTCCTTTAAACATAATTCATTCTCACCTCGAGACATG
66 CATGCTAATTCCAAGACATGAGTCTTCCTTTAAACATAATTCATTCTCACCTCGAGACATG
* * * * * * *
425364 AGTCTTCCTTTTTAAACATATTCTCATGCTTATTCTGAGTCACGAGTCTTCCTTTAAACTTATTC
1 AGTCTTCC-TTTCAAACATAATCTCATGCTCATTCCGAGACACGAGTCTTCCTTTAAACATAATC
*** *
425429 TCATGCTAATTTTGATACATGAGTCTTCCTTTAAACATA
65 TCATGCTAATTCCAAGACATGAGTCTTCCTTTAAACATA
425468 CTCTTGTGCT
Statistics
Matches: 88, Mismatches: 15, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
126 8 0.09
127 80 0.91
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.39
Consensus pattern (126 bp):
AGTCTTCCTTTCAAACATAATCTCATGCTCATTCCGAGACACGAGTCTTCCTTTAAACATAATCT
CATGCTAATTCCAAGACATGAGTCTTCCTTTAAACATAATTCATTCTCACCTCGAGACATG
Found at i:433830 original size:34 final size:34
Alignment explanation
Indices: 433753--433817 Score: 94
Period size: 34 Copynumber: 1.9 Consensus size: 34
433743 TTTAATAGAA
* * * *
433753 CAATACAATAGCAATTAATATGTTTATAATAGTT
1 CAATACAGTAGCAAATAATATGCTTATAACAGTT
433787 CAATACAGTAGCAAATAATATGCTTATAACA
1 CAATACAGTAGCAAATAATATGCTTATAACA
433818 TATCAACTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
34 27 1.00
ACGTcount: A:0.46, C:0.12, G:0.09, T:0.32
Consensus pattern (34 bp):
CAATACAGTAGCAAATAATATGCTTATAACAGTT
Found at i:434105 original size:29 final size:28
Alignment explanation
Indices: 434073--434158 Score: 100
Period size: 28 Copynumber: 3.0 Consensus size: 28
434063 AATTCTAGGT
* *
434073 AAAACTGTAAAATTTGTAAAATAGGGGAC
1 AAAACTGTAAAATTTGAAAAATAAGGG-C
* *
434102 AAAACTGTAAAATCTAAAAAATAAGGGC
1 AAAACTGTAAAATTTGAAAAATAAGGGC
* * *
434130 AAAACTATAAAACTTGAAAAATAAAGGC
1 AAAACTGTAAAATTTGAAAAATAAGGGC
434158 A
1 A
434159 CATGATCTTG
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
28 25 0.52
29 23 0.48
ACGTcount: A:0.56, C:0.09, G:0.15, T:0.20
Consensus pattern (28 bp):
AAAACTGTAAAATTTGAAAAATAAGGGC
Found at i:437192 original size:4 final size:4
Alignment explanation
Indices: 437185--437227 Score: 68
Period size: 4 Copynumber: 10.8 Consensus size: 4
437175 ATTTTTATAT
* *
437185 ATAC ATAC ATAT ATAC ATAC ATAC AAAC ATAC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
437228 TATTTTTTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.53, C:0.21, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:438381 original size:5 final size:5
Alignment explanation
Indices: 438371--438421 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
438361 GAATCCTATT
* *
438371 TTTTA TTTTA TTTCTT TTTTA -TTTA TTTAATA TTTTA TTTTA TATTA
1 TTTTA TTTTA TTT-TA TTTTA TTTTA TTT--TA TTTTA TTTTA TTTTA
438418 TTTT
1 TTTT
438422 TAAATAGTGT
Statistics
Matches: 38, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
4 4 0.11
5 25 0.66
6 4 0.11
7 5 0.13
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:438390 original size:16 final size:17
Alignment explanation
Indices: 438368--438422 Score: 62
Period size: 16 Copynumber: 3.4 Consensus size: 17
438358 ATTGAATCCT
438368 ATTTTTTATTTTATTT-
1 ATTTTTTATTTTATTTA
*
438384 CTTTTTTA-TTTATTTA
1 ATTTTTTATTTTATTTA
*
438400 ATATTTTATTTTATATT-
1 ATTTTTTATTTTAT-TTA
438417 ATTTTT
1 ATTTTT
438423 AAATAGTGTT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 7 0.22
16 13 0.41
17 10 0.31
18 2 0.06
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (17 bp):
ATTTTTTATTTTATTTA
Found at i:438423 original size:16 final size:15
Alignment explanation
Indices: 438370--438423 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 15
438360 TGAATCCTAT
*
438370 TTTTTATTTTATTTC
1 TTTTTATTTTATTTA
438385 TTTTT-TATTTATTTAA
1 TTTTTAT-TTTATTT-A
438401 TATTTTATTTTATATTA
1 T-TTTTATTTTAT-TTA
438418 TTTTTA
1 TTTTTA
438424 AATAGTGTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
14 1 0.03
15 12 0.36
16 6 0.18
17 11 0.33
18 3 0.09
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTTATTTTATTTA
Done.