Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D04
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: 56598092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1600000 characters in sequence are not A, C, G, or T
File 2 of 185
Found at i:497256 original size:9 final size:9
Alignment explanation
Indices: 497242--497336 Score: 94
Period size: 9 Copynumber: 11.2 Consensus size: 9
497232 TAAGGGATAT
497242 TTATGTAAG
1 TTATGTAAG
497251 TTATGTAAG
1 TTATGTAAG
497260 TTATGT-A-
1 TTATGTAAG
* *
497267 TTAAGTAAA
1 TTATGTAAG
497276 TTATGTAAG
1 TTATGTAAG
497285 TTATGT-A-
1 TTATGTAAG
* *
497292 TTAAGTAGG
1 TTATGTAAG
*
497301 TTATGTAAT
1 TTATGTAAG
*
497310 TTATGT--C
1 TTATGTAAG
497317 TTATGTAAG
1 TTATGTAAG
497326 TTATGTAAG
1 TTATGTAAG
497335 TT
1 TT
497337 TTTGTTTTTG
Statistics
Matches: 70, Mismatches: 10, Indels: 12
0.76 0.11 0.13
Matches are distributed among these distances:
7 16 0.23
8 3 0.04
9 51 0.73
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:497274 original size:25 final size:25
Alignment explanation
Indices: 497246--497336 Score: 137
Period size: 25 Copynumber: 3.6 Consensus size: 25
497236 GGATATTTAT
497246 GTAAGTTATGTAAGTTATGTATTAA
1 GTAAGTTATGTAAGTTATGTATTAA
*
497271 GTAAATTATGTAAGTTATGTATTAA
1 GTAAGTTATGTAAGTTATGTATTAA
* * * *
497296 GTAGGTTATGTAATTTATGTCTTAT
1 GTAAGTTATGTAAGTTATGTATTAA
497321 GTAAGTTATGTAAGTT
1 GTAAGTTATGTAAGTT
497337 TTTGTTTTTG
Statistics
Matches: 58, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 58 1.00
ACGTcount: A:0.33, C:0.01, G:0.20, T:0.46
Consensus pattern (25 bp):
GTAAGTTATGTAAGTTATGTATTAA
Found at i:497294 original size:16 final size:17
Alignment explanation
Indices: 497242--497332 Score: 82
Period size: 16 Copynumber: 5.4 Consensus size: 17
497232 TAAGGGATAT
497242 TTATGTAAGTTATGTAAG
1 TTATGT-AGTTATGTAAG
* *
497260 TTATGTA-TTAAGTAAA
1 TTATGTAGTTATGTAAG
497276 TTATGTAAGTTATGT-A-
1 TTATGT-AGTTATGTAAG
* *
497292 TTAAGTAGGTTATGTAAT
1 TTATGTA-GTTATGTAAG
*
497310 TTATGT-CTTATGTAAG
1 TTATGTAGTTATGTAAG
497326 TTATGTA
1 TTATGTA
497333 AGTTTTTGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
15 1 0.02
16 39 0.65
17 4 0.07
18 16 0.27
ACGTcount: A:0.33, C:0.01, G:0.19, T:0.47
Consensus pattern (17 bp):
TTATGTAGTTATGTAAG
Found at i:497402 original size:12 final size:12
Alignment explanation
Indices: 497385--497447 Score: 63
Period size: 12 Copynumber: 5.2 Consensus size: 12
497375 TGGTTATGTA
497385 TTATTATGTAAG
1 TTATTATGTAAG
* *
497397 TTATTATTTAGG
1 TTATTATGTAAG
497409 TTATTATGTAAG
1 TTATTATGTAAG
* * *
497421 TCATTATATATG
1 TTATTATGTAAG
*
497433 TTGGTTATGTAAG
1 TT-ATTATGTAAG
497446 TT
1 TT
497448 GTGATATGAT
Statistics
Matches: 39, Mismatches: 11, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
12 30 0.77
13 9 0.23
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (12 bp):
TTATTATGTAAG
Found at i:497413 original size:24 final size:24
Alignment explanation
Indices: 497385--497447 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
497375 TGGTTATGTA
*
497385 TTATTATGTAAGTTATTATTTAGG
1 TTATTATGTAAGTTATTATATAGG
* *
497409 TTATTATGTAAGTCATTATATATG
1 TTATTATGTAAGTTATTATATAGG
*
497433 TTGGTTATGTAAGTT
1 TT-ATTATGTAAGTT
497448 GTGATATGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 23 0.70
25 10 0.30
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.52
Consensus pattern (24 bp):
TTATTATGTAAGTTATTATATAGG
Found at i:497649 original size:29 final size:29
Alignment explanation
Indices: 497616--497690 Score: 132
Period size: 29 Copynumber: 2.6 Consensus size: 29
497606 ACGTAGGCTA
*
497616 TGTATTATGCAAGTTATTTATGTAAGTGG
1 TGTATTATGCAAGTTATTTATGTAAATGG
497645 TGTATTATGCAAGTTATTTATGTAAATGG
1 TGTATTATGCAAGTTATTTATGTAAATGG
*
497674 TGTATTATGTAAGTTAT
1 TGTATTATGCAAGTTAT
497691 GTACGCTATG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.29, C:0.03, G:0.21, T:0.47
Consensus pattern (29 bp):
TGTATTATGCAAGTTATTTATGTAAATGG
Found at i:497693 original size:16 final size:16
Alignment explanation
Indices: 497582--497693 Score: 65
Period size: 16 Copynumber: 7.2 Consensus size: 16
497572 ACGTAAGTGG
497582 TGTATTATGTAAGTTA
1 TGTATTATGTAAGTTA
* * * *
497598 AGTAAGTTACGTAGGCTA
1 TGT-A-TTATGTAAGTTA
*
497616 TGTATTATGCAAGTTA
1 TGTATTATGTAAGTTA
**
497632 --T-TTATGTAAGTGG
1 TGTATTATGTAAGTTA
*
497645 TGTATTATGCAAGTTA
1 TGTATTATGTAAGTTA
* **
497661 --T-TTATGTAAATGG
1 TGTATTATGTAAGTTA
497674 TGTATTATGTAAGTTA
1 TGTATTATGTAAGTTA
497690 TGTA
1 TGTA
497694 CGCTATGTAT
Statistics
Matches: 66, Mismatches: 22, Indels: 16
0.63 0.21 0.15
Matches are distributed among these distances:
13 17 0.26
14 2 0.03
15 2 0.03
16 32 0.48
17 2 0.03
18 11 0.17
ACGTcount: A:0.30, C:0.04, G:0.22, T:0.44
Consensus pattern (16 bp):
TGTATTATGTAAGTTA
Found at i:498480 original size:19 final size:19
Alignment explanation
Indices: 498456--498493 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
498446 ATGTTATTCG
498456 AATTTTAAATATATATATA
1 AATTTTAAATATATATATA
498475 AATTTTAAATATATATATA
1 AATTTTAAATATATATATA
498494 TTAAAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
AATTTTAAATATATATATA
Found at i:498520 original size:23 final size:25
Alignment explanation
Indices: 498474--498520 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
498464 ATATATATAT
* *
498474 AAATTTTAAATATATATATATTAAA
1 AAATTATAAAAATATATATATTAAA
498499 AAATTATAAAAATAT-TAT-TTAA
1 AAATTATAAAAATATATATATTAA
498521 TGTAAGTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 4 0.20
24 3 0.15
25 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AAATTATAAAAATATATATATTAAA
Found at i:499243 original size:29 final size:29
Alignment explanation
Indices: 499117--499244 Score: 111
Period size: 29 Copynumber: 4.6 Consensus size: 29
499107 GCAAATAAAT
* *
499117 CCTCACCGACAAAAAATTATAAATTGAAA
1 CCTCACCGACAAAACATTAAAAATTGAAA
*
499146 CCTCACCGAAAAAACATTAAAAATTGAAA
1 CCTCACCGACAAAACATTAAAAATTGAAA
*** * * * ***
499175 CCTCTGTGA-ATAACATCATAAATTGTCG
1 CCTCACCGACAAAACATTAAAAATTGAAA
*
499203 CTTCA--G-CAAAACATTAAAAATTGAAA
1 CCTCACCGACAAAACATTAAAAATTGAAA
499229 CCTCACCGACAAAACA
1 CCTCACCGACAAAACA
499245 AAAAAGAAAA
Statistics
Matches: 74, Mismatches: 21, Indels: 8
0.72 0.20 0.08
Matches are distributed among these distances:
26 18 0.24
28 17 0.23
29 39 0.53
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.21
Consensus pattern (29 bp):
CCTCACCGACAAAACATTAAAAATTGAAA
Found at i:500011 original size:47 final size:49
Alignment explanation
Indices: 499926--500023 Score: 148
Period size: 47 Copynumber: 2.0 Consensus size: 49
499916 CATAGTTTTG
*
499926 TTAAGTAATATTTATAATATATAGTAGTAAAATTATAAATTTTAGTGTT
1 TTAACTAATATTTATAATATATAGTAGTAAAATTATAAATTTTAGTGTT
*
499975 TTAACTAATATTTATAA-AT-T-TTAGATAAAATTATAAATTTTAGTGTT
1 TTAACTAATATTTATAATATATAGTAG-TAAAATTATAAATTTTAGTGTT
500022 TT
1 TT
500024 TATTTTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
46 3 0.07
47 25 0.54
48 2 0.04
49 16 0.35
ACGTcount: A:0.42, C:0.01, G:0.08, T:0.49
Consensus pattern (49 bp):
TTAACTAATATTTATAATATATAGTAGTAAAATTATAAATTTTAGTGTT
Found at i:501032 original size:24 final size:23
Alignment explanation
Indices: 501005--501051 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
500995 AACTCTAAAT
* *
501005 CCCTAGCTCTTAACCCCATAAACC
1 CCCTAACTCCTAACCCC-TAAACC
501029 CCCTAACTCCTAACCCCTAAACC
1 CCCTAACTCCTAACCCCTAAACC
501052 TTAAACCATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.30, C:0.49, G:0.02, T:0.19
Consensus pattern (23 bp):
CCCTAACTCCTAACCCCTAAACC
Found at i:501331 original size:22 final size:21
Alignment explanation
Indices: 501298--501346 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
501288 CCCTAAACTA
*
501298 TAAATCCTTAGCTCTAAACCCC
1 TAAATCCTTAGCCCT-AACCCC
501320 TAAA-CCTCTAGCCCTAACCCC
1 TAAATCCT-TAGCCCTAACCCC
501341 TAAATC
1 TAAATC
501347 TTAAATCCTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 13 0.54
22 11 0.46
ACGTcount: A:0.33, C:0.39, G:0.04, T:0.24
Consensus pattern (21 bp):
TAAATCCTTAGCCCTAACCCC
Found at i:501503 original size:15 final size:16
Alignment explanation
Indices: 501477--501510 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
501467 CTATACCTCT
501477 AACCCTTAAATCCATA
1 AACCCTTAAATCCATA
501493 AACCC-TAAATCCATA
1 AACCCTTAAATCCATA
501508 AAC
1 AAC
501511 ACCATATTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.47, C:0.32, G:0.00, T:0.21
Consensus pattern (16 bp):
AACCCTTAAATCCATA
Found at i:501856 original size:41 final size:41
Alignment explanation
Indices: 501797--501909 Score: 165
Period size: 41 Copynumber: 2.8 Consensus size: 41
501787 AAAAAAAAAT
* * *
501797 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGATCT-TAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAG-GCTAGAGC
*
501838 ATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAGGCTAGAGC
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCTAGAGC
*
501879 ATTAGCGGCGCTTCTTAAAAAACGCCGCTAA
1 ATTAGCGGCGCTTCTTCAAAAACGCCGCTAA
501910 GGGCCCCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
40 2 0.03
41 63 0.97
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (41 bp):
ATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCTAGAGC
Found at i:502017 original size:39 final size:40
Alignment explanation
Indices: 501951--502084 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
501941 TGGCTTAGGC
*
501951 TTTTT-GCGGCGATTTTCAGAAAA-CGCCGCTAATGCT-AA
1 TTTTTAGCGGCG-TTTTCTGAAAAGCGCCGCTAATGCTCAA
* *
501989 TTTTTAGCGGCGTTTTCTGAAAAGCGCCGTTAATGCTCTA
1 TTTTTAGCGGCGTTTTCTGAAAAGCGCCGCTAATGCTCAA
** * * * *
502029 CCTTTAGCGGTGTTTT-TATAAAAGTGCCGCTAATGCTCGA
1 TTTTTAGCGGCGTTTTCT-GAAAAGCGCCGCTAATGCTCAA
*
502069 TTTTTAGTGGCGTTTT
1 TTTTTAGCGGCGTTTT
502085 TTGTCCAAAC
Statistics
Matches: 78, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
38 15 0.19
39 19 0.24
40 44 0.56
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.38
Consensus pattern (40 bp):
TTTTTAGCGGCGTTTTCTGAAAAGCGCCGCTAATGCTCAA
Found at i:502549 original size:32 final size:32
Alignment explanation
Indices: 502471--502549 Score: 104
Period size: 32 Copynumber: 2.5 Consensus size: 32
502461 ACTTACACGC
* *
502471 TCGTGTGGCCCACACGACCTAATTGGCTCAGA
1 TCGTGTGGCCCACACAACCCAATTGGCTCAGA
* * *
502503 TCGTGCGACCCACACAACCCAATTGGCTTAGA
1 TCGTGTGGCCCACACAACCCAATTGGCTCAGA
*
502535 TCGTGTGGCTCACAC
1 TCGTGTGGCCCACAC
502550 GGCCTGTCAC
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.23, C:0.33, G:0.23, T:0.22
Consensus pattern (32 bp):
TCGTGTGGCCCACACAACCCAATTGGCTCAGA
Found at i:504754 original size:9 final size:9
Alignment explanation
Indices: 504735--504798 Score: 58
Period size: 9 Copynumber: 7.0 Consensus size: 9
504725 AATGTAGTTC
504735 AAAATATTAT
1 AAAA-ATTAT
504745 AAAAATTAT
1 AAAAATTAT
* *
504754 AAAATTTTT
1 AAAAATTAT
** *
504763 AACATGTTGT
1 AA-AAATTAT
504773 AAAAATTAT
1 AAAAATTAT
504782 -AAAATTAT
1 AAAAATTAT
504790 AAAAATTAT
1 AAAAATTAT
504799 CGATTATTAA
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
8 8 0.18
9 26 0.59
10 10 0.23
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (9 bp):
AAAAATTAT
Found at i:504873 original size:21 final size:20
Alignment explanation
Indices: 504820--504870 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
504810 AAAAAAATTC
504820 TAACAAAACA-T-TAAAATA
1 TAACAAAACATTATAAAATA
* *
504838 TGAATAAAATATTATAAAATA
1 T-AACAAAACATTATAAAATA
504859 TAACAAAACATT
1 TAACAAAACATT
504871 TATCCACATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 1 0.04
19 7 0.27
20 10 0.38
21 8 0.31
ACGTcount: A:0.63, C:0.08, G:0.02, T:0.27
Consensus pattern (20 bp):
TAACAAAACATTATAAAATA
Found at i:505144 original size:16 final size:16
Alignment explanation
Indices: 505097--505145 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
505087 TATTTCGGGT
*
505097 TTGGGCTCAAATTTGC
1 TTGGGCTCAAATTTTC
* * *
505113 TCGAGCTCAAACTTTC
1 TTGGGCTCAAATTTTC
*
505129 TTGGGCTCCAATTTTC
1 TTGGGCTCAAATTTTC
505145 T
1 T
505146 CATACTCAAA
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.39
Consensus pattern (16 bp):
TTGGGCTCAAATTTTC
Found at i:505452 original size:17 final size:17
Alignment explanation
Indices: 505378--505456 Score: 54
Period size: 17 Copynumber: 4.5 Consensus size: 17
505368 TGAATTAGTT
*
505378 TTAAATTTAAT-TTATA
1 TTAAATTTAATCATATA
*
505394 TTCTAATTTAATGGCATAT-
1 TT-AAATTTAAT--CATATA
* * *
505413 TAAATATTTAAATCTTATT
1 TTAA-ATTT-AATCATATA
505432 TTAAATTTAATCATATA
1 TTAAATTTAATCATATA
505449 TTAAATTT
1 TTAAATTT
505457 TGAGATAAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 13
0.70 0.12 0.19
Matches are distributed among these distances:
16 2 0.04
17 23 0.48
18 9 0.19
19 8 0.17
20 6 0.12
ACGTcount: A:0.41, C:0.05, G:0.03, T:0.52
Consensus pattern (17 bp):
TTAAATTTAATCATATA
Found at i:517915 original size:78 final size:76
Alignment explanation
Indices: 517665--517926 Score: 329
Period size: 71 Copynumber: 3.5 Consensus size: 76
517655 GTTTTTCAAA
* *
517665 ATCAACTCATATTGCTAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTCAATTTCTG-T
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTT
*
517729 TTT--CAAAAT
66 TTTAAAAAAAT
* ** * *
517738 -TCAACTTATATTGCGA-AAATGAGTTGAGCCTCAAGACACGTTGAGGTATTTTCAATTTCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTT
* *
517801 TTCAAAAAAAAA
66 TT-TAAAAAAAT
* *
517813 ATCAACTTATATTGCGAGAGGTGAGTTGAGCCTC-GGTTCACATGCTGAGGTATTTTCAATTTCT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG---ACACGCTGAGGTATTTTCAATTTCT
517877 GTTTTTAAAAAAAT
63 GTTTTTAAAAAAAT
*
517891 ATCAACTCATATTGCGAGAGGTGAGTTGAGCTTCAG
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAG
517927 ATTACACACT
Statistics
Matches: 160, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
71 40 0.25
72 17 0.11
75 4 0.03
76 17 0.11
77 14 0.09
78 39 0.24
79 29 0.18
ACGTcount: A:0.31, C:0.16, G:0.20, T:0.34
Consensus pattern (76 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTCTGTT
TTTAAAAAAAT
Found at i:518162 original size:72 final size:73
Alignment explanation
Indices: 518081--518222 Score: 232
Period size: 72 Copynumber: 2.0 Consensus size: 73
518071 TCAAAATCAG
* * *
518081 CTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTTG-TGTTTT
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
518145 AATTTCAA
66 AATTTCAA
* *
518153 CTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTTTTTT
1 CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
518218 AATTT
66 AATTT
518223 ATGTTTCAAA
Statistics
Matches: 64, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
72 54 0.84
73 10 0.16
ACGTcount: A:0.22, C:0.15, G:0.24, T:0.39
Consensus pattern (73 bp):
CTCATATTGCAAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAATTTTCGTTGTTTT
AATTTCAA
Found at i:518374 original size:159 final size:151
Alignment explanation
Indices: 518073--518528 Score: 492
Period size: 159 Copynumber: 2.9 Consensus size: 151
518063 CTACTTTTTC
* *
518073 AAAATCAGCTCATATTGCAAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGG-ACGCTGAGGTATTTTCAATTTTT
* **
518138 GTGTTTTAATTTCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
64 GT-TTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTC
* * *
518203 AATTTTCGTTTTTTTAATTTATGTTTCAAAA
128 AA-ATTC-TATTTTT--TTT-T-TATC-AAA
* ** *
518234 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACGCTGAGGTAATTTCAATTTTTGT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACGCTGAGGTATTTTCAATTTTTGT
* *
518299 TTGTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGATATTTTCAA
66 TT-TAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAA
*
518364 ATTCTA-----TTTTTATCGAA
130 ATTCTATTTTTTTTTTATCAAA
* *
518381 AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACATGCTGAGGTATTTTTAATTTTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC--GCTGAGGTATTTTCAA-TTTT
* * *
518446 TCTTTTTAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGTCTCGGGCCACACG-TCGAGGT
63 T-GTTTT-AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG--ACACGCT-GAGGT
**
518510 CCTTTCAAATTCTATTTTT
122 ATTTTCAAATTCTATTTTT
518529 AATTTCTTTT
Statistics
Matches: 253, Mismatches: 27, Indels: 32
0.81 0.09 0.10
Matches are distributed among these distances:
147 40 0.16
148 3 0.01
149 15 0.06
150 9 0.04
151 5 0.02
152 36 0.14
153 1 0.00
154 21 0.08
157 1 0.00
158 5 0.02
159 82 0.32
160 1 0.00
161 34 0.13
ACGTcount: A:0.28, C:0.16, G:0.22, T:0.35
Consensus pattern (151 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGACGCTGAGGTATTTTCAATTTTTGT
TTTAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAA
TTCTATTTTTTTTTTATCAAA
Found at i:518396 original size:77 final size:74
Alignment explanation
Indices: 518232--518488 Score: 319
Period size: 77 Copynumber: 3.5 Consensus size: 74
518222 TATGTTTCAA
* * *
518232 AAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCA--AGACGCTGAGGTAATTTC-AATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAATT
*
518294 TTTGTTTGTC
66 TTT-TTTATC
*
518304 --AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGATATTTTCAAATT
1 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAATT
518367 CTATTTTTATC
66 -T-TTTTTATC
* * * *
518378 GAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGGACATGCTGAGGTATTTT-TAAT
1 -AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAAT
* *
518442 TTTTTCTTTTT
65 TTTTT-TTATC
518453 AAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAG
1 AAAA-AATCAACTCATATTGCGAGAGGTGAGTTGAG
518489 TCTCGGGCCA
Statistics
Matches: 162, Mismatches: 13, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
70 37 0.23
72 15 0.09
73 4 0.02
74 13 0.08
75 36 0.22
76 4 0.02
77 53 0.33
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.33
Consensus pattern (74 bp):
AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCAAATT
TTTTTTATC
Found at i:518746 original size:71 final size:71
Alignment explanation
Indices: 518646--518783 Score: 231
Period size: 71 Copynumber: 1.9 Consensus size: 71
518636 CTGTTTTAAT
* * *
518646 TCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAACCTCAAGTCACATTGAGGTATTTTCAAT
1 TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACATTGAGATATTTTCAAT
518711 TTATCA
66 TTATCA
* *
518717 TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCCGTTGAGATATTTTCAAT
1 TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACATTGAGATATTTTCAAT
518782 TT
66 TT
518784 CTGCTCAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
71 62 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (71 bp):
TCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACACATTGAGATATTTTCAAT
TTATCA
Found at i:518886 original size:155 final size:157
Alignment explanation
Indices: 518555--518907 Score: 434
Period size: 155 Copynumber: 2.2 Consensus size: 157
518545 AATTTATGTG
* * *
518555 TTTCAAAAAAATCAGCTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGGTGTTTTCCA
1 TTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGATATTTTCCA
* ** * *
518620 TTTTTATTTTCAATTTCTGTTTTAATTCAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAACC
65 TATTTATGCTCAATTTATGTTTT-ATTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACC
518685 TCAAGTCACATTGAGGTATTTTCAATTTAT
129 TCAAGTCACA-TGAGGTATTTTCAATTTAT
** *
518715 CATCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACCCGTTGAGATATTTT-C
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGA--CGCTGAGATATTTTCC
* *
518779 A-ATTTCTGCTCAATTTATG-TTT-TTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC
64 ATATTTATGCTCAATTTATGTTTTATTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACC
* *
518840 TCACA-T-GC-TGAGGTGTTTTCAATTTCTATT
129 TCA-AGTCACATGAGGTATTTTCAA-TT-TA-T
518870 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGA
518908 GCCTTGGCTT
Statistics
Matches: 170, Mismatches: 17, Indels: 17
0.83 0.08 0.08
Matches are distributed among these distances:
152 13 0.08
153 2 0.01
154 3 0.02
155 75 0.44
156 4 0.02
158 3 0.02
159 55 0.32
160 4 0.02
161 11 0.06
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (157 bp):
TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTCAAGACGCTGAGATATTTTCCAT
ATTTATGCTCAATTTATGTTTTATTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAACCTC
AAGTCACATGAGGTATTTTCAATTTAT
Found at i:518976 original size:78 final size:75
Alignment explanation
Indices: 518788--519029 Score: 300
Period size: 78 Copynumber: 3.2 Consensus size: 75
518778 CAATTTCTGC
*
518788 TCAATTTATGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-T--C-ACATGC
1 TCAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTACATGC
*
518848 TGAGGTGTTT
66 TGAGGTTTTT
* *
518858 TCAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTTACACG
1 TCAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGC-TACATG
518923 CTGAGGTATTTT
65 CTGAGGT-TTTT
* * * * *
518935 TCAATTTCTGTTTGTCAAAAAAACCAACTCATATTGTGAGAGGTGAGTTGAGTCTCGGCTCACAT
1 TCAATTTCTGTTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCT-ACAT
519000 GCTGAGGTCTTTT
64 GCTGAGGT-TTTT
519013 T-AATTTCT-TCTTTTCAA
1 TCAATTTCTGT-TTTTCAA
519030 TTTCTGTTTT
Statistics
Matches: 149, Mismatches: 13, Indels: 14
0.85 0.07 0.08
Matches are distributed among these distances:
70 14 0.09
71 36 0.24
72 1 0.01
74 1 0.01
76 14 0.09
77 29 0.19
78 54 0.36
ACGTcount: A:0.26, C:0.17, G:0.19, T:0.37
Consensus pattern (75 bp):
TCAATTTCTGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTACATGC
TGAGGTTTTT
Found at i:519043 original size:15 final size:14
Alignment explanation
Indices: 519009--519058 Score: 57
Period size: 14 Copynumber: 3.6 Consensus size: 14
518999 TGCTGAGGTC
519009 TTTTT-AATTTCTT
1 TTTTTCAATTTCTT
*
519022 CTTTTCAATTTCTGT
1 TTTTTCAATTTCT-T
* *
519037 TTTTTCAATTTATA
1 TTTTTCAATTTCTT
519051 TTTTTCAA
1 TTTTTCAA
519059 AAATCAACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
15 12 0.39
ACGTcount: A:0.20, C:0.12, G:0.02, T:0.66
Consensus pattern (14 bp):
TTTTTCAATTTCTT
Found at i:519173 original size:177 final size:181
Alignment explanation
Indices: 518855--519271 Score: 680
Period size: 177 Copynumber: 2.3 Consensus size: 181
518845 TGCTGAGGTG
* * *
518855 TTTTCAATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGCTTAC
1 TTTTCAATTTATATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGC-GAC
* *
518920 ACGCTGAGGTATTTTTCAATTTCTGTTTGTCAAAAAAACCAACTCATATTGTGAGAGGTGAGTTG
64 ACGCTGAGGTATATTTCAATTTCTGTTTGTC-AAAAAACCAACTCATATTGCGAGAGGTGAGTTG
*
518985 AGTCTCGGCTCACATGCTGAGGTCTTTTTAATTTCTTCTTTTCAATTTCT-GTT
128 AGTCTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTAGTT
*
519038 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAAAGGTGAGTTGAGCCTCGG-GACAC
1 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCGACAC
**
519102 GCTGAGGTA-ATTTCAATTTCTGTTTGTC-AAAAATTAACTCATATTGCGAGAGGTGAGTTGAGT
66 GCTGAGGTATATTTCAATTTCTGTTTGTCAAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGT
*
519165 CTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTATTT
131 CTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTAGTT
*
519216 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGATGTGAGTTGAGCCT
1 TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
519272 TGGGTTCACA
Statistics
Matches: 221, Mismatches: 12, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
177 78 0.35
178 56 0.25
179 18 0.08
180 13 0.06
182 38 0.17
183 18 0.08
ACGTcount: A:0.26, C:0.16, G:0.18, T:0.40
Consensus pattern (181 bp):
TTTTCAATTTATATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGCGACAC
GCTGAGGTATATTTCAATTTCTGTTTGTCAAAAAACCAACTCATATTGCGAGAGGTGAGTTGAGT
CTCGGCTCACATGCTGAGGTCTTTTTAATTTCTGCTTTTCAATTTCTAGTT
Found at i:519217 original size:14 final size:14
Alignment explanation
Indices: 519186--519236 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
519176 TGCTGAGGTC
*
519186 TTTTT-AATTTCTG
1 TTTTTCAATTTCTA
*
519199 CTTTTCAATTTCTA
1 TTTTTCAATTTCTA
*
519213 TTTTTTTCAATTTATA
1 --TTTTTCAATTTCTA
519229 TTTTTCAA
1 TTTTTCAA
519237 AAATCAACTC
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
13 4 0.13
14 15 0.48
16 12 0.39
ACGTcount: A:0.22, C:0.12, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTTTCAATTTCTA
Found at i:519221 original size:16 final size:16
Alignment explanation
Indices: 519200--519233 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
519190 TAATTTCTGC
*
519200 TTTTCAATTTCTATTT
1 TTTTCAATTTATATTT
519216 TTTTCAATTTATATTT
1 TTTTCAATTTATATTT
519232 TT
1 TT
519234 CAAAAATCAA
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:0.21, C:0.09, G:0.00, T:0.71
Consensus pattern (16 bp):
TTTTCAATTTATATTT
Found at i:519406 original size:77 final size:76
Alignment explanation
Indices: 519308--519559 Score: 373
Period size: 77 Copynumber: 3.3 Consensus size: 76
519298 AAATCTACTT
*
519308 TTGCGAGAAGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAG
1 TTGCGAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAA-
519373 AATCAACTCATA
65 AATCAACTCATA
**
519385 TTGTAAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAA
1 TTGCGAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTC-AAAA
519450 AATCAACTCATA
65 AATCAACTCATA
** * ** *
519462 TTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGC-GTTTTCAATTTCTGCTTTTC-AAA
1 TTGCGAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGA-GCTATTTTCAATTTCTGCTTTTCAAAA
519525 AATCAACTCATA
65 AATCAACTCATA
*
519537 TTGCGAGATGTGAGTTGAGCCTT
1 TTGCGAGAGGTGAGTTGAGCCTT
519560 GGGTTTACAT
Statistics
Matches: 160, Mismatches: 13, Indels: 6
0.89 0.07 0.03
Matches are distributed among these distances:
75 36 0.22
77 118 0.74
78 6 0.04
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.34
Consensus pattern (76 bp):
TTGCGAGAGGTGAGTTGAGCCTTTGCTCACGTGCTGAGCTATTTTCAATTTCTGCTTTTCAAAAA
ATCAACTCATA
Found at i:520307 original size:30 final size:30
Alignment explanation
Indices: 520271--520445 Score: 228
Period size: 30 Copynumber: 5.8 Consensus size: 30
520261 ACTTTTCTCA
*
520271 ACTAGCCACACCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
* *
520301 ACTAGCCACACCTTTTCCACCACTAACTCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
* *
520331 ACTAGCCACTCCTTTTCCACCACCAACTCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
*
520361 ACTAGCCACACCTTCTCCACCACCAAATCC
1 ACTAGCCACACCTTCTCCACCACCAACTCC
** *
520391 ACTAGCCACA-CTTGCTCCATTACCTACTCC
1 ACTAGCCACACCTT-CTCCACCACCAACTCC
*
520421 ACTAACCACA-CTTGCTCCACCACCA
1 ACTAGCCACACCTT-CTCCACCACCA
520446 CTTGTACCTA
Statistics
Matches: 130, Mismatches: 14, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
29 3 0.02
30 127 0.98
ACGTcount: A:0.27, C:0.48, G:0.04, T:0.21
Consensus pattern (30 bp):
ACTAGCCACACCTTCTCCACCACCAACTCC
Found at i:521120 original size:25 final size:25
Alignment explanation
Indices: 521089--521137 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
521079 ATATATCTTA
*
521089 ACTATATTATGTATATATTTTTAAC
1 ACTATATTATGTACATATTTTTAAC
521114 ACTATATTATGTACATATTTTTAA
1 ACTATATTATGTACATATTTTTAA
521138 TATTATCACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.37, C:0.08, G:0.04, T:0.51
Consensus pattern (25 bp):
ACTATATTATGTACATATTTTTAAC
Found at i:521285 original size:21 final size:21
Alignment explanation
Indices: 521259--521299 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
521249 TTTCTATTTT
*
521259 ATTATTTATTTTTC-AATATTA
1 ATTA-TTATTATTCTAATATTA
521280 ATTATTATTATTCTAATATT
1 ATTATTATTATTCTAATATT
521300 TTGATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTATTATTATTCTAATATTA
Found at i:521312 original size:16 final size:15
Alignment explanation
Indices: 521288--521335 Score: 69
Period size: 16 Copynumber: 3.1 Consensus size: 15
521278 TAATTATTAT
*
521288 TATTCTAATATTTTGA
1 TATTTTAATATTTT-A
521304 TATTTTAATATTTTA
1 TATTTTAATATTTTA
521319 TATTTTATATATTTTA
1 TATTTTA-ATATTTTA
521335 T
1 T
521336 TATTCACATC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:521323 original size:7 final size:8
Alignment explanation
Indices: 521288--521339 Score: 61
Period size: 8 Copynumber: 6.5 Consensus size: 8
521278 TAATTATTAT
*
521288 TATTCTAA
1 TATTTTAA
*
521296 TATTTTGA
1 TATTTTAA
521304 TATTTTAA
1 TATTTTAA
521312 TATTTT-A
1 TATTTTAA
521319 TATTTTATA
1 TATTTTA-A
*
521328 TATTTTAT
1 TATTTTAA
521336 TATT
1 TATT
521340 CACATCATTG
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
7 7 0.18
8 23 0.61
9 8 0.21
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (8 bp):
TATTTTAA
Found at i:522584 original size:2 final size:2
Alignment explanation
Indices: 522577--522604 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
522567 TTATGAAGAA
522577 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
522605 GAATCCAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:530411 original size:27 final size:27
Alignment explanation
Indices: 530380--530440 Score: 65
Period size: 27 Copynumber: 2.3 Consensus size: 27
530370 TAAATCCAAC
*
530380 AAAAAGAG-GGATTAAATTTCTAGAA-AT
1 AAAAAGAGAAGATTAAATTT-TA-AATAT
530407 AAAAATG-GAAGATTAAATTTTAAATAT
1 AAAAA-GAGAAGATTAAATTTTAAATAT
530434 AAAAAGA
1 AAAAAGA
530441 ATATAGGGAC
Statistics
Matches: 29, Mismatches: 1, Indels: 8
0.76 0.03 0.21
Matches are distributed among these distances:
26 3 0.10
27 15 0.52
28 11 0.38
ACGTcount: A:0.57, C:0.02, G:0.15, T:0.26
Consensus pattern (27 bp):
AAAAAGAGAAGATTAAATTTTAAATAT
Found at i:530963 original size:13 final size:12
Alignment explanation
Indices: 530933--530969 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
530923 AGTAATTTTA
530933 ATTAAGTTTAAT
1 ATTAAGTTTAAT
*
530945 AGTAAGTTCTAAT
1 ATTAAGTT-TAAT
530958 ATTAAGTTTAAT
1 ATTAAGTTTAAT
530970 TAAAATTTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.41, C:0.03, G:0.11, T:0.46
Consensus pattern (12 bp):
ATTAAGTTTAAT
Found at i:532956 original size:86 final size:85
Alignment explanation
Indices: 532806--533061 Score: 307
Period size: 86 Copynumber: 3.0 Consensus size: 85
532796 AGATAAAAAC
* ** *
532806 ATTTGTAATTACTGCCACTTGTTGTGAGTGCACAACATGGTTGCAGATTAAACAAACTGCCACTG
1 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAATTGCCACTG
532871 ATTTTTGTGGACAAGCCACGT
66 A-TTTTGTGGACAAGCCACGT
** * * * * *
532892 ATTTGCAATTACTATCACTTGTTGTAAGTTCACAACATATTTTCAAATTAAACAAATTGTCACTG
1 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAATTGCCACT-
* *
532957 GGTTTTGTGGGCAAGCCACGT
65 GATTTTGTGGACAAGCCACGT
* * * *
532978 ATTTACAGTTAATGCCACTTGTGGTGAGTGCACAACATATTTGCAGATTAAAC-AATCTGCCACT
1 ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAAT-TGCCACT
*
533042 AGATTTTATGGACAAGCCAC
65 -GATTTTGTGGACAAGCCAC
533062 CACTTGTATG
Statistics
Matches: 140, Mismatches: 28, Indels: 4
0.81 0.16 0.02
Matches are distributed among these distances:
85 3 0.02
86 136 0.97
87 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.32
Consensus pattern (85 bp):
ATTTGCAATTACTGCCACTTGTTGTGAGTGCACAACATATTTGCAGATTAAACAAATTGCCACTG
ATTTTGTGGACAAGCCACGT
Found at i:540571 original size:22 final size:23
Alignment explanation
Indices: 540530--540576 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
540520 AAATTGACAT
540530 AAACTTATAAAAATTATATAAAA
1 AAACTTATAAAAATTATATAAAA
540553 AAACTTATAAAACATTATA-AAAA
1 AAACTTATAAAA-ATTATATAAAA
540576 A
1 A
540577 TATTAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (23 bp):
AAACTTATAAAAATTATATAAAA
Found at i:540611 original size:19 final size:19
Alignment explanation
Indices: 540546--540709 Score: 68
Period size: 19 Copynumber: 8.4 Consensus size: 19
540536 ATAAAAATTA
*
540546 TATAAAAAAACTTATAAAAC
1 TATAAAAAATC-TATAAAAC
* *
540566 ATTATAAAAAATAT-TAAAAA
1 --TATAAAAAATCTATAAAAC
*
540586 TCT-AAAAATCTATAAAAC
1 TATAAAAAATCTATAAAAC
* *
540604 TATAAAAAATTTATAAAAT
1 TATAAAAAATCTATAAAAC
* * * *
540623 TAATTAAACATATTTAAAA-
1 T-ATAAAAAATCTATAAAAC
* *
540642 TATTTAAAAATTTATAAAAAC
1 TA-TAAAAAATCTAT-AAAAC
* *
540663 GTGTAAAAATTCT-TAAAAC
1 -TATAAAAAATCTATAAAAC
* *
540682 TTATAAAAATTC-ATTAAAAA
1 -TATAAAAAATCTA-TAAAAC
540702 TATAAAAA
1 TATAAAAA
540710 CATTTTATTA
Statistics
Matches: 110, Mismatches: 23, Indels: 21
0.71 0.15 0.14
Matches are distributed among these distances:
17 7 0.06
18 10 0.09
19 47 0.43
20 28 0.25
21 8 0.07
22 10 0.09
ACGTcount: A:0.60, C:0.06, G:0.01, T:0.32
Consensus pattern (19 bp):
TATAAAAAATCTATAAAAC
Found at i:540659 original size:10 final size:10
Alignment explanation
Indices: 540534--540724 Score: 55
Period size: 10 Copynumber: 19.0 Consensus size: 10
540524 TGACATAAAC
540534 TTATAAAAAT
1 TTATAAAAAT
*
540544 TATATAAAAAAAC
1 T-TAT--AAAAAT
540557 TTATAAAACA-
1 TTATAAAA-AT
540567 TTATAAAAA-
1 TTATAAAAAT
*
540576 ATATTAAAAA-
1 TTA-TAAAAAT
*
540586 -TCTAAAAAT
1 TTATAAAAAT
* *
540595 CTATAAAACT
1 TTATAAAAAT
*
540605 ATA-AAAAAT
1 TTATAAAAAT
540614 TTAT-AAAAT
1 TTATAAAAAT
* *
540623 TAATTAAACAT
1 TTA-TAAAAAT
540634 ATT-T-AAAAT
1 -TTATAAAAAT
540643 ATT-TAAAAAT
1 -TTATAAAAAT
*
540653 TTATAAAAAC
1 TTATAAAAAT
* *
540663 GTGTAAAAAT
1 TTATAAAAAT
*
540673 TCT-T-AAAAC
1 T-TATAAAAAT
540682 TTATAAAAAT
1 TTATAAAAAT
*
540692 TCATTAAAAAT
1 TTA-TAAAAAT
*
540703 ATA-AAAACATT
1 TTATAAAA-A-T
540714 TTATTAAAAAT
1 TTA-TAAAAAT
540725 CATAAGAATA
Statistics
Matches: 137, Mismatches: 23, Indels: 41
0.68 0.11 0.20
Matches are distributed among these distances:
8 7 0.05
9 38 0.28
10 56 0.41
11 21 0.15
12 5 0.04
13 10 0.07
ACGTcount: A:0.59, C:0.06, G:0.01, T:0.34
Consensus pattern (10 bp):
TTATAAAAAT
Found at i:541312 original size:15 final size:15
Alignment explanation
Indices: 541292--541322 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
541282 GTTCACCATC
541292 GCACTGTGACCTGAA
1 GCACTGTGACCTGAA
541307 GCACTGTGACCTGAA
1 GCACTGTGACCTGAA
541322 G
1 G
541323 TTCAAAGCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.19
Consensus pattern (15 bp):
GCACTGTGACCTGAA
Found at i:543223 original size:12 final size:12
Alignment explanation
Indices: 543206--543246 Score: 68
Period size: 12 Copynumber: 3.6 Consensus size: 12
543196 ATGAGAGTCA
543206 ATTTTGATAAAT
1 ATTTTGATAAAT
543218 ATTTTGATAAAT
1 ATTTTGATAAAT
543230 A-TTT-ATAAAT
1 ATTTTGATAAAT
543240 ATTTTGA
1 ATTTTGA
543247 ATTTTTTATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
10 7 0.26
11 6 0.22
12 14 0.52
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (12 bp):
ATTTTGATAAAT
Found at i:545957 original size:11 final size:11
Alignment explanation
Indices: 545936--545979 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
545926 TAATAACAAC
*
545936 AAAATAGTAGT
1 AAAATAATAGT
*
545947 AATATAATAGT
1 AAAATAATAGT
*
545958 AAAATAATAGC
1 AAAATAATAGT
*
545969 AAAACAATAGT
1 AAAATAATAGT
545980 GAAACATCAA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 27 1.00
ACGTcount: A:0.59, C:0.05, G:0.11, T:0.25
Consensus pattern (11 bp):
AAAATAATAGT
Found at i:557697 original size:17 final size:17
Alignment explanation
Indices: 557663--557708 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
557653 TTGCATTCTT
* *
557663 ATATT-TTTAAATTGAC
1 ATATTATTTGAATTAAC
*
557679 ATTTTATTTGAATTAAC
1 ATATTATTTGAATTAAC
557696 ATATTATTTGAAT
1 ATATTATTTGAAT
557709 AGGTGAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
16 4 0.16
17 21 0.84
ACGTcount: A:0.37, C:0.04, G:0.07, T:0.52
Consensus pattern (17 bp):
ATATTATTTGAATTAAC
Found at i:567715 original size:20 final size:20
Alignment explanation
Indices: 567690--567729 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
567680 CCAAAAATGA
*
567690 TTTCTGGAAAATAATTTACT
1 TTTCTGAAAAATAATTTACT
*
567710 TTTCTGAAAAATGATTTACT
1 TTTCTGAAAAATAATTTACT
567730 GAAAATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.45
Consensus pattern (20 bp):
TTTCTGAAAAATAATTTACT
Found at i:567807 original size:33 final size:32
Alignment explanation
Indices: 567720--567805 Score: 95
Period size: 33 Copynumber: 2.7 Consensus size: 32
567710 TTTCTGAAAA
*
567720 ATGATTTACTGAAAATATTTTCTGATGTTTGG
1 ATGATTTCCTGAAAATATTTTCTGATGTTTGG
* * *
567752 ATGA-ATCTGTGTAAAATATTTTCTGTTGTTTGG
1 ATGATTTC-CTG-AAAATATTTTCTGATGTTTGG
567785 CA-GATTTCCTGAAAATATTTT
1 -ATGATTTCCTGAAAATATTTT
567806 TCAGAAAAGT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
31 1 0.02
32 16 0.36
33 24 0.55
34 3 0.07
ACGTcount: A:0.28, C:0.08, G:0.17, T:0.47
Consensus pattern (32 bp):
ATGATTTCCTGAAAATATTTTCTGATGTTTGG
Found at i:567852 original size:20 final size:20
Alignment explanation
Indices: 567827--567865 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
567817 GTTTTTACAT
567827 ATATTAATAAATTTATATAC
1 ATATTAATAAATTTATATAC
*
567847 ATATTAATAAATTTTTATA
1 ATATTAATAAATTTATATA
567866 ATTTAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (20 bp):
ATATTAATAAATTTATATAC
Found at i:570210 original size:16 final size:16
Alignment explanation
Indices: 570189--570219 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
570179 AAATTATCAG
570189 TAACTACAGAAAATTT
1 TAACTACAGAAAATTT
570205 TAACTACAGAAAATT
1 TAACTACAGAAAATT
570220 ATAGCAGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.13, G:0.06, T:0.29
Consensus pattern (16 bp):
TAACTACAGAAAATTT
Found at i:573220 original size:12 final size:13
Alignment explanation
Indices: 573197--573225 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
573187 TACAAAATCA
573197 AAATTCACATATT
1 AAATTCACATATT
573210 AAATT-ACATATT
1 AAATTCACATATT
573222 AAAT
1 AAAT
573226 CAAATTTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (13 bp):
AAATTCACATATT
Found at i:576615 original size:3 final size:3
Alignment explanation
Indices: 576607--576632 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
576597 GTAGCAAAAT
576607 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
576633 GTTATACAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:579805 original size:22 final size:20
Alignment explanation
Indices: 579769--579826 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 20
579759 GGCCCAGCCC
579769 ATTT-TTTTAATAAATACCAAAA
1 ATTTATTTTAA-AAATA--AAAA
579791 ATTTATTTTAAAAATTAAAAA
1 ATTTATTTTAAAAA-TAAAAA
*
579812 A-GTATTTTAAAAATA
1 ATTTATTTTAAAAATA
579827 TTTTAAAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 2 0.06
20 11 0.33
21 5 0.15
22 7 0.21
23 8 0.24
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.41
Consensus pattern (20 bp):
ATTTATTTTAAAAATAAAAA
Found at i:579837 original size:30 final size:30
Alignment explanation
Indices: 579794--579871 Score: 131
Period size: 29 Copynumber: 2.6 Consensus size: 30
579784 ACCAAAAATT
579794 TATTTTAAAAATTAAAAAAGTATTTTAAAAA
1 TATTTT-AAAATTAAAAAAGTATTTTAAAAA
579825 TATTTTAAAATT-AAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAGTATTTTAAAAA
*
579854 CATTTTAAAATTAAAAAA
1 TATTTTAAAATTAAAAAA
579872 AATCACAAGC
Statistics
Matches: 45, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
29 28 0.62
30 11 0.24
31 6 0.13
ACGTcount: A:0.58, C:0.01, G:0.03, T:0.38
Consensus pattern (30 bp):
TATTTTAAAATTAAAAAAGTATTTTAAAAA
Found at i:579840 original size:17 final size:18
Alignment explanation
Indices: 579818--579852 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
579808 AAAAAGTATT
579818 TTAAAAA-TATTTTAAAA
1 TTAAAAAGTATTTTAAAA
579835 TTAAAAAGTATTTTAAAA
1 TTAAAAAGTATTTTAAAA
579853 ACATTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (18 bp):
TTAAAAAGTATTTTAAAA
Found at i:579852 original size:12 final size:11
Alignment explanation
Indices: 579808--579863 Score: 50
Period size: 11 Copynumber: 5.4 Consensus size: 11
579798 TTAAAAATTA
579808 AAAAAGTATTTT
1 AAAAA-TATTTT
579820 AAAAATATTTT
1 AAAAATATTTT
579831 --AAA-A--TT
1 AAAAATATTTT
579837 AAAAAGTATTTT
1 AAAAA-TATTTT
*
579849 AAAAACATTTT
1 AAAAATATTTT
579860 AAAA
1 AAAA
579864 TTAAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 13
0.73 0.02 0.25
Matches are distributed among these distances:
6 2 0.05
8 4 0.11
9 3 0.08
10 1 0.03
11 15 0.41
12 12 0.32
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:579966 original size:10 final size:10
Alignment explanation
Indices: 579953--580010 Score: 59
Period size: 11 Copynumber: 5.9 Consensus size: 10
579943 AAAAAAGTAT
*
579953 TTTTAAAATG
1 TTTTAAAATA
579963 TTTT-AAA-A
1 TTTTAAAATA
*
579971 -TTAAAAATA
1 TTTTAAAATA
579980 TTTTAAAAATA
1 TTTT-AAAATA
579991 TTTTAAAAATA
1 TTTT-AAAATA
580002 TTTTAAAAT
1 TTTTAAAAT
580011 TAAAAAATAA
Statistics
Matches: 41, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
7 2 0.05
8 3 0.07
9 4 0.10
10 11 0.27
11 21 0.51
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (10 bp):
TTTTAAAATA
Found at i:579976 original size:16 final size:17
Alignment explanation
Indices: 579957--580016 Score: 66
Period size: 17 Copynumber: 3.2 Consensus size: 17
579947 AAGTATTTTT
*
579957 AAAATGTTTTAAAATTA
1 AAAATATTTTAAAATTA
579974 AAAATATTTTAAAAATATTTTA
1 AAAATATTTT--AAA-A--TTA
579996 AAAATATTTTAAAATTA
1 AAAATATTTTAAAATTA
580013 AAAA
1 AAAA
580017 ATAAAAAAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
17 16 0.43
19 4 0.11
20 4 0.11
22 13 0.35
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AAAATATTTTAAAATTA
Found at i:579985 original size:11 final size:11
Alignment explanation
Indices: 579971--580009 Score: 78
Period size: 11 Copynumber: 3.5 Consensus size: 11
579961 TGTTTTAAAA
579971 TTAAAAATATT
1 TTAAAAATATT
579982 TTAAAAATATT
1 TTAAAAATATT
579993 TTAAAAATATT
1 TTAAAAATATT
580004 TTAAAA
1 TTAAAA
580010 TTAAAAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:579988 original size:28 final size:29
Alignment explanation
Indices: 579929--579998 Score: 88
Period size: 28 Copynumber: 2.3 Consensus size: 29
579919 ACCAAAAATT
*
579929 TATTTTAAAAATTAAAAAAAGTATTTTTAAAA
1 TATTTT-AAAATT--AAAAAGTATTTTAAAAA
*
579961 TGTTTTAAAATTAAAAA-TATTTTAAAAA
1 TATTTTAAAATTAAAAAGTATTTTAAAAA
579989 TATTTTAAAA
1 TATTTTAAAA
579999 ATATTTTAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 19 0.54
29 5 0.14
31 6 0.17
32 5 0.14
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (29 bp):
TATTTTAAAATTAAAAAGTATTTTAAAAA
Found at i:580000 original size:136 final size:136
Alignment explanation
Indices: 579754--579998 Score: 431
Period size: 135 Copynumber: 1.8 Consensus size: 136
579744 CACAAGCCCG
579754 GGCCCGGCCCAGCCCATTTTTTTAATAAATACCAAAAATTTATTTTAAAAATTAAAAAAGTATTT
1 GGCCCGGCCCAGCCCATTTTTTTAATAAATACCAAAAATTTATTTTAAAAATTAAAAAAGTATTT
579819 TAAAAATATTTTAAAATTAAAAAGTATTTTAAAAACATTTTAAAATTAAAAAAAATCACAAGCCA
66 TAAAAATATTTTAAAATTAAAAAGTATTTTAAAAACATTTTAAAATTAAAAAAAATCACAAGCCA
579884 GGGCTC
131 GGGCTC
*
579890 GGCCCGGCCCGGCCCA-TTTTTTAATAAATACCAAAAATTTATTTTAAAAATTAAAAAAAGTATT
1 GGCCCGGCCCAGCCCATTTTTTTAATAAATACCAAAAATTTATTTTAAAAATT-AAAAAAGTATT
* * *
579954 TTTAAAATGTTTTAAAATTAAAAA-TATTTTAAAAATATTTTAAAA
65 TTAAAAATATTTTAAAATTAAAAAGTATTTTAAAAACATTTTAAAA
579999 ATATTTTAAA
Statistics
Matches: 104, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
135 56 0.54
136 48 0.46
ACGTcount: A:0.47, C:0.12, G:0.08, T:0.34
Consensus pattern (136 bp):
GGCCCGGCCCAGCCCATTTTTTTAATAAATACCAAAAATTTATTTTAAAAATTAAAAAAGTATTT
TAAAAATATTTTAAAATTAAAAAGTATTTTAAAAACATTTTAAAATTAAAAAAAATCACAAGCCA
GGGCTC
Found at i:580032 original size:39 final size:38
Alignment explanation
Indices: 579933--580059 Score: 130
Period size: 39 Copynumber: 3.3 Consensus size: 38
579923 AAAATTTATT
* * * *
579933 TTAAAAATTAAAAAAAGTATTTTTAAAATGTTTTAAAA
1 TTAAAAAATAAAAAAAATATTTTAAAAATATTTTAAAA
***
579971 TTAAAAATATTTTAAAAATATTTTAAAAATATTTTAAAA
1 TTAAAAA-ATAAAAAAAATATTTTAAAAATATTTTAAAA
* ***
580010 TTAAAAAATAAAAAAAATTATTTTAAAAGTA-AAAAAAA
1 TTAAAAAATAAAAAAAA-TATTTTAAAAATATTTTAAAA
580048 TTAAAAAATAAA
1 TTAAAAAATAAA
580060 TATATTTATT
Statistics
Matches: 73, Mismatches: 14, Indels: 4
0.80 0.15 0.04
Matches are distributed among these distances:
38 30 0.41
39 43 0.59
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (38 bp):
TTAAAAAATAAAAAAAATATTTTAAAAATATTTTAAAA
Found at i:580053 original size:28 final size:28
Alignment explanation
Indices: 579984--580054 Score: 83
Period size: 28 Copynumber: 2.5 Consensus size: 28
579974 AAAATATTTT
* *
579984 AAAAATATTTTAAAAATATTTTAAAATTA
1 AAAAATA-ATTAAAAATATTTTAAAAGTA
*
580013 AAAAATAA-AAAAAATTATTTTAAAAGTA
1 AAAAATAATTAAAAA-TATTTTAAAAGTA
580041 AAAAA-AATTAAAAA
1 AAAAATAATTAAAAA
580055 ATAAATATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
27 7 0.19
28 22 0.61
29 7 0.19
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (28 bp):
AAAAATAATTAAAAATATTTTAAAAGTA
Found at i:584314 original size:28 final size:28
Alignment explanation
Indices: 584245--584314 Score: 104
Period size: 28 Copynumber: 2.5 Consensus size: 28
584235 ATGTTTGACA
*
584245 AACCCCTATGGTAAACTCGTATTTAGCG
1 AACCCCTATGGTGAACTCGTATTTAGCG
* *
584273 AACCCCTATAGTGAACTCGTATTTGGCG
1 AACCCCTATGGTGAACTCGTATTTAGCG
*
584301 AACCCCTAGGGTGA
1 AACCCCTATGGTGA
584315 TCACAAGTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.27, C:0.26, G:0.21, T:0.26
Consensus pattern (28 bp):
AACCCCTATGGTGAACTCGTATTTAGCG
Found at i:584382 original size:25 final size:26
Alignment explanation
Indices: 584341--584401 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 26
584331 CTTATGTTGA
* *
584341 ACTACTATGGCGTACCC-TATGGAGG
1 ACTACTATGGCGAACCCTTAAGGAGG
* *
584366 ACTACTATGGTGAACCCTTAAGGAGT
1 ACTACTATGGCGAACCCTTAAGGAGG
*
584392 ACTCCTATGG
1 ACTACTATGG
584402 AAAACCCTCT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
25 15 0.50
26 15 0.50
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (26 bp):
ACTACTATGGCGAACCCTTAAGGAGG
Found at i:590722 original size:21 final size:21
Alignment explanation
Indices: 590698--590752 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
590688 CTTTATCTTA
*
590698 AACCCCAAACTTAGAATCTCG
1 AACCCTAAACTTAGAATCTCG
*
590719 AACCTTAAACATT-GAATCTCG
1 AACCCTAAAC-TTAGAATCTCG
590740 AACCCTAAACTTA
1 AACCCTAAACTTA
590753 AAGCCGAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 2 0.07
21 25 0.86
22 2 0.07
ACGTcount: A:0.40, C:0.29, G:0.07, T:0.24
Consensus pattern (21 bp):
AACCCTAAACTTAGAATCTCG
Found at i:592627 original size:18 final size:19
Alignment explanation
Indices: 592589--592638 Score: 59
Period size: 18 Copynumber: 2.6 Consensus size: 19
592579 TTACAAAGAA
*
592589 AAAATT-AAAATATTTTTT
1 AAAATTCAAAATATTTTAT
592607 AAAATTCAAAATA-TTTAT
1 AAAATTCAAAATATTTTAT
592625 AAAAGTTCTAAAAT
1 AAAA-TTC-AAAAT
592639 TCAAAAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 14 0.50
19 9 0.32
20 5 0.18
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
AAAATTCAAAATATTTTAT
Found at i:598400 original size:21 final size:21
Alignment explanation
Indices: 598374--598510 Score: 85
Period size: 21 Copynumber: 6.5 Consensus size: 21
598364 TTGAAGGTTG
*
598374 AACAGAAGCTCATGAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
* * * * *
598395 AACAGAAACCCATAAGGGTTG
1 AACAGAAGCTCATAAGAGCTA
* * *
598416 AACGGAAGCTCTTAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
* * * *
598437 AACAGAAACCCATAAGGGTTA
1 AACAGAAGCTCATAAGAGCTA
* * *
598458 AATAGAAGCTCAAAAGAGCTG
1 AACAGAAGCTCATAAGAGCTA
** * * *
598479 AATGGAAACTCATATGAGTTA
1 AACAGAAGCTCATAAGAGCTA
598500 AACAGAAGCTC
1 AACAGAAGCTC
598511 GTGAGATCTA
Statistics
Matches: 81, Mismatches: 35, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
21 81 1.00
ACGTcount: A:0.43, C:0.18, G:0.23, T:0.17
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:598416 original size:42 final size:42
Alignment explanation
Indices: 598369--598528 Score: 158
Period size: 42 Copynumber: 3.8 Consensus size: 42
598359 GAAGCTTGAA
* *
598369 GGTTGAACAGAAGCTCATGAGAGCTAAACAGAAACCCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * * *
598411 GGTTGAACGGAAGCTCTTAAGAGCTGAACAGAAACCCATAAG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * * ** * *
598453 GGTTAAATAGAAGCTCAAAAGAGCTGAATGGAAACTCATATG
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
* * * * *
598495 AGTTAAACAGAAGCTCGTGAGATCTAAACGGAAA
1 GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAA
598529 GTAAACACGA
Statistics
Matches: 97, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 97 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.17
Consensus pattern (42 bp):
GGTTAAACAGAAGCTCATAAGAGCTAAACAGAAACCCATAAG
Found at i:605079 original size:5 final size:5
Alignment explanation
Indices: 605069--605133 Score: 75
Period size: 5 Copynumber: 13.2 Consensus size: 5
605059 AATTATGTTT
605069 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA -T-TA TTATA
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
605116 TTATTA TTATA TATATA T
1 TTA-TA TTATA T-TATA T
605134 GACAAAGAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
3 4 0.08
4 4 0.08
5 30 0.57
6 15 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:605083 original size:8 final size:8
Alignment explanation
Indices: 605069--605122 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
605059 AATTATGTTT
605069 TTATATTA
1 TTATATTA
605077 -TATTATTA
1 TTA-TATTA
605085 TTA-ATATA
1 TTATAT-TA
605093 TTATATTATA
1 TTATA-T-TA
605103 TTATATTA
1 TTATATTA
605111 TTATATTA
1 TTATATTA
605119 TTAT
1 TTAT
605123 TATATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
8 24 0.59
9 4 0.10
10 9 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATTA
Found at i:605085 original size:3 final size:3
Alignment explanation
Indices: 605072--605125 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
605062 TATGTTTTTA
*
605072 TAT TA- TAT TAT TAT TAA TA- TAT TA- TAT TA- TAT TA- TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
605114 TAT TAT TAT TAT
1 TAT TAT TAT TAT
605126 ATATATATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
2 12 0.27
3 32 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:605101 original size:29 final size:29
Alignment explanation
Indices: 605069--605133 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
605059 AATTATGTTT
605069 TTATATTATATTATTATTAATA-TATTATA
1 TTATATTATATTATTA-TAATATTATTATA
*
605098 TTATATTATATTATTATATTATTATTATA
1 TTATATTATATTATTATAATATTATTATA
605127 TATATAT
1 T-TATAT
605134 GACAAAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 4 0.12
29 24 0.73
30 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TTATATTATATTATTATAATATTATTATA
Found at i:605199 original size:40 final size:40
Alignment explanation
Indices: 605142--605237 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
605132 ATGACAAAGA
605142 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
605183 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
605223 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
605238 GAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:605463 original size:13 final size:13
Alignment explanation
Indices: 605445--605476 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
605435 TTTCCAGCAA
605445 TTATGAATTTATT
1 TTATGAATTTATT
605458 TTATGAATTTATT
1 TTATGAATTTATT
*
605471 TGATGA
1 TTATGA
605477 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:605684 original size:50 final size:50
Alignment explanation
Indices: 605571--605812 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
605561 ATTTGGGTAA
* * *
605571 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
605627 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
605677 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
605727 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
605777 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
605813 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:605760 original size:100 final size:103
Alignment explanation
Indices: 605571--605820 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
605561 ATTTGGGTAA
605571 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
605636 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
605677 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
605739 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
605777 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
605821 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:607823 original size:12 final size:12
Alignment explanation
Indices: 607806--607830 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
607796 CATGTTATGT
607806 GTATATATATAA
1 GTATATATATAA
607818 GTATATATATAA
1 GTATATATATAA
607830 G
1 G
607831 AGTCAAATTT
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:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (12 bp):
GTATATATATAA
Found at i:608276 original size:13 final size:13
Alignment explanation
Indices: 608258--608285 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
608248 TGATCTCTTC
608258 TGGGTATTCTATA
1 TGGGTATTCTATA
608271 TGGGTATTCTATA
1 TGGGTATTCTATA
608284 TG
1 TG
608286 CTCTTTTATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.25, T:0.46
Consensus pattern (13 bp):
TGGGTATTCTATA
Found at i:610233 original size:5 final size:5
Alignment explanation
Indices: 610223--610287 Score: 75
Period size: 5 Copynumber: 13.2 Consensus size: 5
610213 AATTATGTTT
610223 TTATA TTATA TTATTA TTA-A -TATA TTATA TTATA TTATA -T-TA TTATA
1 TTATA TTATA TTA-TA TTATA TTATA TTATA TTATA TTATA TTATA TTATA
610270 TTATTA TTATA TATATA T
1 TTA-TA TTATA T-TATA T
610288 GACAAAGAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 13
0.80 0.00 0.20
Matches are distributed among these distances:
3 4 0.08
4 4 0.08
5 30 0.57
6 15 0.28
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTATA
Found at i:610237 original size:8 final size:8
Alignment explanation
Indices: 610223--610276 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
610213 AATTATGTTT
610223 TTATATTA
1 TTATATTA
610231 -TATTATTA
1 TTA-TATTA
610239 TTA-ATATA
1 TTATAT-TA
610247 TTATATTATA
1 TTATA-T-TA
610257 TTATATTA
1 TTATATTA
610265 TTATATTA
1 TTATATTA
610273 TTAT
1 TTAT
610277 TATATATATA
Statistics
Matches: 41, Mismatches: 0, Indels: 10
0.80 0.00 0.20
Matches are distributed among these distances:
7 4 0.10
8 24 0.59
9 4 0.10
10 9 0.22
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (8 bp):
TTATATTA
Found at i:610239 original size:3 final size:3
Alignment explanation
Indices: 610226--610279 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
610216 TATGTTTTTA
*
610226 TAT TA- TAT TAT TAT TAA TA- TAT TA- TAT TA- TAT TA- TAT TAT TA-
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
610268 TAT TAT TAT TAT
1 TAT TAT TAT TAT
610280 ATATATATGA
Statistics
Matches: 44, Mismatches: 1, Indels: 12
0.77 0.02 0.21
Matches are distributed among these distances:
2 12 0.27
3 32 0.73
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:610255 original size:29 final size:29
Alignment explanation
Indices: 610223--610287 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
610213 AATTATGTTT
610223 TTATATTATATTATTATTAATA-TATTATA
1 TTATATTATATTATTA-TAATATTATTATA
*
610252 TTATATTATATTATTATATTATTATTATA
1 TTATATTATATTATTATAATATTATTATA
610281 TATATAT
1 T-TATAT
610288 GACAAAGAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 4 0.12
29 24 0.73
30 5 0.15
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (29 bp):
TTATATTATATTATTATAATATTATTATA
Found at i:610353 original size:40 final size:40
Alignment explanation
Indices: 610296--610391 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
610286 ATGACAAAGA
610296 AAGAAAGAAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
1 AAGAAAG-AAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
* *
610337 GAGAAAGAAAGAAACAGAGAGCAAAACGAAACAGAGAAGG
1 AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
*
610377 AAGGAAGGAAAGAAA
1 AA-GAAAGAAAGAAA
610392 GAAAGAAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
40 33 0.66
41 17 0.34
ACGTcount: A:0.64, C:0.08, G:0.28, T:0.00
Consensus pattern (40 bp):
AAGAAAGAAAGAAACAGAGAGCAAAACAAAACAGAGAAGG
Found at i:610617 original size:13 final size:13
Alignment explanation
Indices: 610599--610630 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
610589 TTTCCAGCAA
610599 TTATGAATTTATT
1 TTATGAATTTATT
610612 TTATGAATTTATT
1 TTATGAATTTATT
*
610625 TGATGA
1 TTATGA
610631 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:610838 original size:50 final size:50
Alignment explanation
Indices: 610725--610966 Score: 297
Period size: 50 Copynumber: 4.7 Consensus size: 50
610715 ATTTGGGTAA
* * *
610725 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCA-CC--GAGA-C--G
*
610781 AGAGGTCCCCTGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
610831 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
* * *
610881 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
**
610931 AGAACATCCCATGTAAGACCATGTCTGGGACATGGC
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGC
610967 TTTGGCATGT
Statistics
Matches: 166, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
49 1 0.01
50 91 0.55
51 29 0.17
52 1 0.01
53 3 0.02
55 2 0.01
56 39 0.23
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGACG
Found at i:610914 original size:100 final size:103
Alignment explanation
Indices: 610725--610974 Score: 364
Period size: 100 Copynumber: 2.4 Consensus size: 103
610715 ATTTGGGTAA
610725 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCTTAAGATCATGAGAGGTCCC
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCC---AGATCATGAGAGGTCCC
* *
610790 CTGTAAGACCATGTCTGGGACATGGCATGGGCACCGA-GACG
63 CTATAAGACCATGTCTGGGACATGGCATGGGCACC-ATCACG
* * *
610831 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-CC-GA-GATGAGAGGTCCCCTA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
610893 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
66 TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
* *
610931 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCAT
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAT
610975 GTTATTATCA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
99 1 0.01
100 51 0.38
101 39 0.29
105 2 0.02
106 40 0.30
ACGTcount: A:0.26, C:0.24, G:0.29, T:0.21
Consensus pattern (103 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCCAGATCATGAGAGGTCCCCTA
TAAGACCATGTCTGGGACATGGCATGGGCACCATCACG
Found at i:612388 original size:23 final size:23
Alignment explanation
Indices: 612362--612440 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 23
612352 ATACAGTGAG
612362 CAATGGAAATTGTCTGCTGTTTT
1 CAATGGAAATTGTCTGCTGTTTT
* * * * * *
612385 CAATTCAGACAGTTTTTTGATATTATT
1 CAA-T-GGA-AATTGTCTGCTGTT-TT
612412 GCAATGGAAATTGTCTGCTGTTTT
1 -CAATGGAAATTGTCTGCTGTTTT
612436 CAATG
1 CAATG
612441 AAACTGGAAA
Statistics
Matches: 39, Mismatches: 12, Indels: 10
0.64 0.20 0.16
Matches are distributed among these distances:
23 8 0.21
24 3 0.08
25 11 0.28
26 11 0.28
27 3 0.08
28 3 0.08
ACGTcount: A:0.25, C:0.13, G:0.19, T:0.43
Consensus pattern (23 bp):
CAATGGAAATTGTCTGCTGTTTT
Found at i:622998 original size:16 final size:16
Alignment explanation
Indices: 622965--622998 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
622955 GCACCATGTT
* *
622965 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
622981 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
622997 AA
1 AA
622999 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:625825 original size:21 final size:21
Alignment explanation
Indices: 625799--625839 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
625789 AGACGAGCAA
* *
625799 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
625820 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
625840 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:627778 original size:16 final size:16
Alignment explanation
Indices: 627745--627778 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
627735 GAAGATTGTT
* *
627745 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
627761 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
627777 AA
1 AA
627779 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:654106 original size:11 final size:11
Alignment explanation
Indices: 654090--654115 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
654080 TATTTTTTTA
654090 TTTTAAAATAC
1 TTTTAAAATAC
654101 TTTTAAAATAC
1 TTTTAAAATAC
654112 TTTT
1 TTTT
654116 TTTAAATTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:654148 original size:32 final size:32
Alignment explanation
Indices: 654101--654173 Score: 96
Period size: 31 Copynumber: 2.3 Consensus size: 32
654091 TTTAAAATAC
*
654101 TTTT-AAAATACTTTTTTTAAATTT-TTTTAA
1 TTTTAAAAATATTTTTTTTAAATTTGTTTTAA
**
654131 TTTTAAAAATATTTTTTTTATTTTTGTTTTAA
1 TTTTAAAAATATTTTTTTTAAATTTGTTTTAA
*
654163 TTTTTAAAATA
1 TTTTAAAAATA
654174 AATTTTTGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
30 4 0.11
31 17 0.46
32 16 0.43
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.64
Consensus pattern (32 bp):
TTTTAAAAATATTTTTTTTAAATTTGTTTTAA
Found at i:654180 original size:32 final size:31
Alignment explanation
Indices: 654101--654180 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 31
654091 TTTAAAATAC
*
654101 TTTTAAAATACTTTTTTTAAATTTTTTTAAT
1 TTTTAAAATAATTTTTTTAAATTTTTTTAAT
* * **
654132 TTTAAAAATATTTTTTTTATTTTTGTTTTAAT
1 TTTTAAAATAATTTTTTTAAATTT-TTTTAAT
*
654164 TTTTAAAATAAATTTTT
1 TTTTAAAATAATTTTTT
654181 GGTATTTATT
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 20 0.49
32 21 0.51
ACGTcount: A:0.33, C:0.01, G:0.01, T:0.65
Consensus pattern (31 bp):
TTTTAAAATAATTTTTTTAAATTTTTTTAAT
Found at i:661877 original size:9 final size:9
Alignment explanation
Indices: 661851--661918 Score: 52
Period size: 9 Copynumber: 7.7 Consensus size: 9
661841 ATCTAAGATT
661851 TTATT-TAA
1 TTATTATAA
661859 GTTATATATAA
1 -TTAT-TATAA
661870 TTATTATAA
1 TTATTATAA
**
661879 TTATTACCA
1 TTATTATAA
**
661888 TTATTATGG
1 TTATTATAA
661897 TT-TTAT-A
1 TTATTATAA
*
661904 TTATTATTA
1 TTATTATAA
661913 TTATTA
1 TTATTA
661919 AATAAAATAA
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
7 2 0.04
8 8 0.16
9 31 0.63
10 5 0.10
11 3 0.06
ACGTcount: A:0.35, C:0.03, G:0.04, T:0.57
Consensus pattern (9 bp):
TTATTATAA
Found at i:663211 original size:39 final size:40
Alignment explanation
Indices: 663167--663257 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 40
663157 TGAATTATAG
* * *
663167 AATACTGGATATTGTTTTG-AGTACTG-AGTGAATTGTGAA
1 AATACTGAATATTGTTATGTA-TAATGCAGTGAATTGTGAA
*
663206 AATACTGAATATTGTTATGTATAATGCATTGAATTGTGAA
1 AATACTGAATATTGTTATGTATAATGCAGTGAATTGTGAA
*
663246 ATTACTGCAATA
1 AATACTG-AATA
663258 CTGTGAAACT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
39 21 0.48
40 19 0.43
41 4 0.09
ACGTcount: A:0.35, C:0.07, G:0.20, T:0.38
Consensus pattern (40 bp):
AATACTGAATATTGTTATGTATAATGCAGTGAATTGTGAA
Found at i:663514 original size:45 final size:45
Alignment explanation
Indices: 663440--663588 Score: 156
Period size: 45 Copynumber: 3.3 Consensus size: 45
663430 ATGTGCCGAC
** *
663440 TACTGTTACTGTTA-ATTTTCTGCACTTTGTGTGTCAAATATTGT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATATTGT
* * ** * *
663484 TACTGTTACGGTTACCGATTTGGCACTTTGTGTGTCTAATACTGT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATATTGT
** * * **
663529 TACCATTACTATTATAGATTCAGCACTTTGTGTGTTGAATATTGT
1 TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATATTGT
663574 TACTGTTACTGTTAC
1 TACTGTTACTGTTAC
663589 TGCTACCATT
Statistics
Matches: 81, Mismatches: 23, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
44 13 0.16
45 68 0.84
ACGTcount: A:0.21, C:0.15, G:0.17, T:0.46
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCAGCACTTTGTGTGTCAAATATTGT
Found at i:664981 original size:21 final size:20
Alignment explanation
Indices: 664957--665002 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
664947 ATAAAATACT
664957 TATTTTGTATAATAAATTTTA
1 TATTTTGTATAAT-AATTTTA
* * *
664978 TATTTTTTTTACTAATTTTA
1 TATTTTGTATAATAATTTTA
664998 TATTT
1 TATTT
665003 ATTTACATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 12 0.55
21 10 0.45
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (20 bp):
TATTTTGTATAATAATTTTA
Found at i:665016 original size:18 final size:20
Alignment explanation
Indices: 664971--665022 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
664961 TTGTATAATA
*
664971 AATTTTATATTTTTTTTACT
1 AATTTTATATTTTATTTACT
664991 AATTTTATA-TTTATTTAC-
1 AATTTTATATTTTATTTACT
*
665009 ATTTTTATAATTTT
1 AATTTTAT-ATTTT
665023 CTTACGCCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 7 0.25
19 9 0.32
20 12 0.43
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTATATTTTATTTACT
Found at i:665021 original size:19 final size:20
Alignment explanation
Indices: 664971--665021 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
664961 TTGTATAATA
* *
664971 AATTTTATATTTTTTTTACT
1 AATTTTATAATTTATTTACT
664991 AATTTTAT-ATTTATTTAC-
1 AATTTTATAATTTATTTACT
*
665009 ATTTTTATAATTT
1 AATTTTATAATTT
665022 TCTTACGCCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 7 0.26
19 12 0.44
20 8 0.30
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTATAATTTATTTACT
Found at i:665027 original size:19 final size:19
Alignment explanation
Indices: 664971--665027 Score: 55
Period size: 19 Copynumber: 2.9 Consensus size: 19
664961 TTGTATAATA
*
664971 AATTTTATATTTTTTTTACT
1 AATTTTATA-ATTTTTTACT
664991 AATTTTAT-ATTTATTTAC-
1 AATTTTATAATTT-TTTACT
*
665009 ATTTTTATAATTTTCTTAC
1 AATTTTATAATTTT-TTAC
665028 GCCTTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
18 11 0.34
19 13 0.41
20 8 0.25
ACGTcount: A:0.28, C:0.07, G:0.00, T:0.65
Consensus pattern (19 bp):
AATTTTATAATTTTTTACT
Found at i:665123 original size:30 final size:28
Alignment explanation
Indices: 665080--665152 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 28
665070 TTTATAAAAA
* *
665080 ATTTTT-A-ATTTTTAATAAATTTAAAAT
1 ATTTTTAATATTTTTAATAAAATT-TAAT
*
665107 ATTTTTAAATATTTTTATTAAAATTTAAT
1 ATTTTT-AATATTTTTAATAAAATTTAAT
*
665136 ATTTTTTATATTTTTAA
1 ATTTTTAATATTTTTAA
665153 ATTTTTATCA
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
27 6 0.16
28 9 0.24
29 10 0.26
30 13 0.34
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (28 bp):
ATTTTTAATATTTTTAATAAAATTTAAT
Found at i:669566 original size:18 final size:18
Alignment explanation
Indices: 669543--669578 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
669533 AAAGAAAATT
*
669543 ATCTTTGATTACATACTC
1 ATCTTTAATTACATACTC
669561 ATCTTTAATTACATACTC
1 ATCTTTAATTACATACTC
669579 TGTGTGTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.44
Consensus pattern (18 bp):
ATCTTTAATTACATACTC
Found at i:670265 original size:15 final size:15
Alignment explanation
Indices: 670247--670278 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
670237 TAGAAAATAG
*
670247 AATATTATAATATTA
1 AATATTAAAATATTA
670262 AATATTAAAATATTA
1 AATATTAAAATATTA
670277 AA
1 AA
670279 AAATACTTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
AATATTAAAATATTA
Found at i:670271 original size:28 final size:26
Alignment explanation
Indices: 670211--670273 Score: 65
Period size: 26 Copynumber: 2.3 Consensus size: 26
670201 AATTAGGTTC
670211 ATTAAAATAAAACATTAAATTTAAAT
1 ATTAAAATAAAACATTAAATTTAAAT
* * *
670237 -TAGAAAATAGAATATTATAATATTAAAT
1 AT-TAAAATAAAACATTA-AAT-TTAAAT
670265 ATTAAAATA
1 ATTAAAATA
670274 TTAAAAAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
25 1 0.03
26 12 0.41
27 3 0.10
28 12 0.41
29 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.03, T:0.35
Consensus pattern (26 bp):
ATTAAAATAAAACATTAAATTTAAAT
Found at i:670279 original size:8 final size:8
Alignment explanation
Indices: 670247--670279 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
670237 TAGAAAATAG
*
670247 AATATTAT
1 AATATTAA
670255 AATATT-A
1 AATATTAA
670262 AATATTAA
1 AATATTAA
670270 AATATTAA
1 AATATTAA
670278 AA
1 AA
670280 AATACTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (8 bp):
AATATTAA
Found at i:670326 original size:21 final size:21
Alignment explanation
Indices: 670292--670337 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
670282 TACTTAAACT
* *
670292 TTGATAGATTGTTGATCGATG
1 TTGATAGATCGTTGATCGACG
*
670313 TTGATTGATCGTTGATCGACG
1 TTGATAGATCGTTGATCGACG
670334 TTGA
1 TTGA
670338 CTAGCCATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.28, T:0.41
Consensus pattern (21 bp):
TTGATAGATCGTTGATCGACG
Found at i:670448 original size:20 final size:20
Alignment explanation
Indices: 670425--670465 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
670415 ATTATATTGA
670425 TTAAAAA-TATAAAAAATAAT
1 TTAAAAAGT-TAAAAAATAAT
*
670445 TTAAAAAGTTTAAAAATAAT
1 TTAAAAAGTTAAAAAATAAT
670465 T
1 T
670466 ATATTTTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 18 0.95
21 1 0.05
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAAAAAGTTAAAAAATAAT
Found at i:670637 original size:17 final size:17
Alignment explanation
Indices: 670615--670647 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
670605 TATTATTATT
670615 ATTTTTATAATTTTTAC
1 ATTTTTATAATTTTTAC
*
670632 ATTTTTTTAATTTTTA
1 ATTTTTATAATTTTTA
670648 ATAATATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
ATTTTTATAATTTTTAC
Found at i:670753 original size:22 final size:20
Alignment explanation
Indices: 670716--670759 Score: 52
Period size: 22 Copynumber: 2.1 Consensus size: 20
670706 ATTTTAATAA
*
670716 TTTTTTATAATTTATATGTT
1 TTTTTTATAATTTATATATT
*
670736 TTTTTTCTAGATTATATATATT
1 TTTTTTATA-ATT-TATATATT
670758 TT
1 TT
670760 AATTTGTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 3 0.15
22 9 0.45
ACGTcount: A:0.25, C:0.02, G:0.05, T:0.68
Consensus pattern (20 bp):
TTTTTTATAATTTATATATT
Found at i:684421 original size:66 final size:66
Alignment explanation
Indices: 684315--684446 Score: 264
Period size: 66 Copynumber: 2.0 Consensus size: 66
684305 AAGAAAAGGA
684315 AGTCATATGTTAGTTTCTCAAAATGGTTAGGTATTTAAATTATATATAATCACATAACATAATGA
1 AGTCATATGTTAGTTTCTCAAAATGGTTAGGTATTTAAATTATATATAATCACATAACATAATGA
684380 T
66 T
684381 AGTCATATGTTAGTTTCTCAAAATGGTTAGGTATTTAAATTATATATAATCACATAACATAATGA
1 AGTCATATGTTAGTTTCTCAAAATGGTTAGGTATTTAAATTATATATAATCACATAACATAATGA
684446 T
66 T
684447 TGTTGAAATA
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 66 1.00
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.39
Consensus pattern (66 bp):
AGTCATATGTTAGTTTCTCAAAATGGTTAGGTATTTAAATTATATATAATCACATAACATAATGA
T
Found at i:692011 original size:31 final size:31
Alignment explanation
Indices: 691976--692038 Score: 117
Period size: 31 Copynumber: 2.0 Consensus size: 31
691966 ATAAAATTCT
691976 TTTGCATAAACACAAAAAGGACTGGCATATG
1 TTTGCATAAACACAAAAAGGACTGGCATATG
*
692007 TTTGCATAAACACAAAAAGGACTGTCATATG
1 TTTGCATAAACACAAAAAGGACTGGCATATG
692038 T
1 T
692039 AAGAGTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.41, C:0.16, G:0.17, T:0.25
Consensus pattern (31 bp):
TTTGCATAAACACAAAAAGGACTGGCATATG
Found at i:698554 original size:13 final size:13
Alignment explanation
Indices: 698536--698561 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
698526 CAGATGTTCA
698536 TTTAGATTTGTGT
1 TTTAGATTTGTGT
698549 TTTAGATTTGTGT
1 TTTAGATTTGTGT
698562 GACAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.23, T:0.62
Consensus pattern (13 bp):
TTTAGATTTGTGT
Found at i:703458 original size:23 final size:26
Alignment explanation
Indices: 703432--703479 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 26
703422 TTGAAATTTT
*
703432 AAAA-TTATTAAAA-AA-TTATAAAC
1 AAAATTTATAAAAATAAGTTATAAAC
703455 AAAATTTATAAAAATAAGTTATAAA
1 AAAATTTATAAAAATAAGTTATAAA
703480 GATTATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 4 0.19
24 8 0.38
25 2 0.10
26 7 0.33
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.31
Consensus pattern (26 bp):
AAAATTTATAAAAATAAGTTATAAAC
Found at i:703623 original size:8 final size:9
Alignment explanation
Indices: 703596--703677 Score: 83
Period size: 9 Copynumber: 8.1 Consensus size: 9
703586 TAATAAAATA
703596 TTATAATTT
1 TTATAATTT
703605 TTATAATTT
1 TTATAATTT
703614 TTATAATTTTTT
1 TTATAA---TTT
703626 CTTATAAATTTT
1 -TTAT-AA-TTT
703638 GTCTATAATTT
1 -T-TATAATTT
703649 TTATAATTT
1 TTATAATTT
703658 TTATAATTT
1 TTATAATTT
703667 TTAATAATTT
1 TT-ATAATTT
703677 T
1 T
703678 AAAAATTTAA
Statistics
Matches: 65, Mismatches: 1, Indels: 13
0.82 0.01 0.16
Matches are distributed among these distances:
9 34 0.52
10 9 0.14
11 3 0.05
12 10 0.15
13 7 0.11
14 2 0.03
ACGTcount: A:0.32, C:0.02, G:0.01, T:0.65
Consensus pattern (9 bp):
TTATAATTT
Found at i:703678 original size:9 final size:9
Alignment explanation
Indices: 703642--703685 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
703632 AATTTTGTCT
*
703642 ATAATTTTT
1 ATAATTTTA
*
703651 ATAATTTTT
1 ATAATTTTA
703660 ATAATTTTTA
1 ATAA-TTTTA
703670 ATAATTTTA
1 ATAATTTTA
*
703679 AAAATTT
1 ATAATTT
703686 AAAAGGGCTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
9 24 0.75
10 8 0.25
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (9 bp):
ATAATTTTA
Found at i:703684 original size:19 final size:18
Alignment explanation
Indices: 703644--703685 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
703634 TTTTGTCTAT
* *
703644 AATTTTTATAATTTTTAT
1 AATTTTTATAATTTTAAA
703662 AATTTTTAATAATTTTAAA
1 AATTTTT-ATAATTTTAAA
703681 AATTT
1 AATTT
703686 AAAAGGGCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (18 bp):
AATTTTTATAATTTTAAA
Done.