Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 8 of 438
Found at i:2287171 original size:2 final size:2
Alignment explanation
Indices: 2287164--2287200 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
2287154 TCGTTTACCC
* *
2287164 AT AT AT AT AT AT AT AT AT AT AA AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2287201 ATAATTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:2293463 original size:42 final size:42
Alignment explanation
Indices: 2293416--2293499 Score: 159
Period size: 42 Copynumber: 2.0 Consensus size: 42
2293406 AAATAATACT
2293416 GAAAAAACCCAAAATCGAAACTTAAATAATAATCAAATTTTC
1 GAAAAAACCCAAAATCGAAACTTAAATAATAATCAAATTTTC
*
2293458 GAAAAAACCCAAAATCGAAACTTAAATAATAATCGAATTTTC
1 GAAAAAACCCAAAATCGAAACTTAAATAATAATCAAATTTTC
2293500 TTATCACCCG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.54, C:0.17, G:0.06, T:0.24
Consensus pattern (42 bp):
GAAAAAACCCAAAATCGAAACTTAAATAATAATCAAATTTTC
Found at i:2296555 original size:29 final size:31
Alignment explanation
Indices: 2296504--2296564 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 31
2296494 AGTTTATATA
* *
2296504 TTTATAATTTTTAAAGGATTAAATTA-AATT
1 TTTATAATTTTTAAAGGACTAAAGTATAATT
* *
2296534 TTTATAA-TTTTAGAGGGCTAAAGTATAATT
1 TTTATAATTTTTAAAGGACTAAAGTATAATT
2296564 T
1 T
2296565 AATTTTTACT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.39, C:0.02, G:0.11, T:0.48
Consensus pattern (31 bp):
TTTATAATTTTTAAAGGACTAAAGTATAATT
Found at i:2297162 original size:24 final size:25
Alignment explanation
Indices: 2297135--2297188 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
2297125 ATTACGTTAG
*
2297135 TTTTTAATAATATAAAA-TAAATAAT
1 TTTTTAATAA-AAAAAATTAAATAAT
* *
2297160 TTTTTAATAAAAAAAATTAATTTAT
1 TTTTTAATAAAAAAAATTAAATAAT
2297185 TTTT
1 TTTT
2297189 AATCTAATGT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 5 0.20
25 20 0.80
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTTTAATAAAAAAAATTAAATAAT
Found at i:2303544 original size:10 final size:10
Alignment explanation
Indices: 2303529--2303557 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2303519 AGGCCCCCAT
2303529 TGGGCCCTTA
1 TGGGCCCTTA
2303539 TGGGCCCTTA
1 TGGGCCCTTA
2303549 TGGGCCCTT
1 TGGGCCCTT
2303558 TGGCCATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.31, G:0.31, T:0.31
Consensus pattern (10 bp):
TGGGCCCTTA
Found at i:2314257 original size:14 final size:14
Alignment explanation
Indices: 2314238--2314270 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2314228 TTAGTTTTGC
2314238 AGAAAATGACTTCT
1 AGAAAATGACTTCT
2314252 AGAAAATGACTTCT
1 AGAAAATGACTTCT
2314266 AGAAA
1 AGAAA
2314271 CGATGTCCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.48, C:0.12, G:0.15, T:0.24
Consensus pattern (14 bp):
AGAAAATGACTTCT
Found at i:2319093 original size:10 final size:10
Alignment explanation
Indices: 2319086--2319128 Score: 59
Period size: 11 Copynumber: 4.0 Consensus size: 10
2319076 CGAAAAAAGG
2319086 GAAAAAAAAA
1 GAAAAAAAAA
2319096 GAAAAAAAAAGA
1 G-AAAAAAAA-A
2319108 GAAAAAAGAAA
1 GAAAAAA-AAA
2319119 GAAAAAAAAA
1 GAAAAAAAAA
2319129 TACAAGCAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 4 0.13
11 22 0.73
12 4 0.13
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:2319113 original size:23 final size:22
Alignment explanation
Indices: 2319078--2319128 Score: 75
Period size: 23 Copynumber: 2.3 Consensus size: 22
2319068 GGAAATGACG
*
2319078 AAAAAAGGGAAAAAAAAAGAAA
1 AAAAAAGGAAAAAAAAAAGAAA
*
2319100 AAAAAAGAGAAAAAAGAAAGAAA
1 AAAAAAG-GAAAAAAAAAAGAAA
2319123 AAAAAA
1 AAAAAA
2319129 TACAAGCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
22 7 0.27
23 19 0.73
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (22 bp):
AAAAAAGGAAAAAAAAAAGAAA
Found at i:2320766 original size:45 final size:45
Alignment explanation
Indices: 2320716--2320812 Score: 140
Period size: 45 Copynumber: 2.2 Consensus size: 45
2320706 CTTCCTCTGT
** * *
2320716 GATGCTTGCCATCAAAAGATCTTGACCTTGACCTCTTTCTATCCC
1 GATGCTTGCCATCAAAAGATCTTGACCTCAACCGCCTTCTATCCC
**
2320761 GATGCTTGCCATCAGCAGATCTTGACCTCAACCGCCTTCTATCCC
1 GATGCTTGCCATCAAAAGATCTTGACCTCAACCGCCTTCTATCCC
2320806 GATGCTT
1 GATGCTT
2320813 AGATTTCTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.21, C:0.33, G:0.15, T:0.31
Consensus pattern (45 bp):
GATGCTTGCCATCAAAAGATCTTGACCTCAACCGCCTTCTATCCC
Found at i:2321588 original size:42 final size:42
Alignment explanation
Indices: 2321540--2321679 Score: 192
Period size: 42 Copynumber: 3.3 Consensus size: 42
2321530 AGATCTCCTC
2321540 CTTCGCCTATAACTGATTGGTGATCTTGACTTTGACCTTGA-
1 CTTCGCCTATAACTGATTGGTGATCTTGACTTTGACCTTGAT
* *
2321581 CTTTCGCCTATAAATGATTGGTGATCTTGACTTGGACCTTGAT
1 C-TTCGCCTATAACTGATTGGTGATCTTGACTTTGACCTTGAT
* * * *
2321624 CTTCGCCGATAACTAATTGGTGATCTAGACTTTGATCTTGAT
1 CTTCGCCTATAACTGATTGGTGATCTTGACTTTGACCTTGAT
* *
2321666 CTTCTCCGATAACT
1 CTTCGCCTATAACT
2321680 AAGGGGTGAT
Statistics
Matches: 88, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
41 1 0.01
42 86 0.98
43 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.19, T:0.39
Consensus pattern (42 bp):
CTTCGCCTATAACTGATTGGTGATCTTGACTTTGACCTTGAT
Found at i:2321680 original size:42 final size:42
Alignment explanation
Indices: 2321540--2321698 Score: 187
Period size: 42 Copynumber: 3.8 Consensus size: 42
2321530 AGATCTCCTC
* *
2321540 CTTCGCCTATAACTGATTGGTGATCTTGACTTTGACCTTGA-
1 CTTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
* * * *
2321581 CTTTCGCCTATAAATGATTGGTGATCTTGACTTGGACCTTGAT
1 C-TTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
* *
2321624 CTTCGCCGATAACTAATTGGTGATCTAGACTTTGATCTTGAT
1 CTTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
* ** *
2321666 CTTCTCCGATAACTAAGGGGTGATTTTGA-TTTG
1 CTTCGCCGATAACTAATTGGTGATCTTGACTTTG
2321699 GATCTTGACC
Statistics
Matches: 103, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
41 5 0.05
42 97 0.94
43 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.21, T:0.39
Consensus pattern (42 bp):
CTTCGCCGATAACTAATTGGTGATCTTGACTTTGACCTTGAT
Found at i:2326300 original size:29 final size:29
Alignment explanation
Indices: 2326243--2326308 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
2326233 TCACAAAATA
**
2326243 TTGAAAATTTCAATTAAACCTTATTATTT
1 TTGAAAATTTCAATTAAACCTTAAAATTT
2326272 TTGAAAA-TTCATATTAAATCC-TAAAA-TT
1 TTGAAAATTTCA-ATTAAA-CCTTAAAATTT
2326300 TT-AAAATTT
1 TTGAAAATTT
2326309 TAAGTGATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
27 4 0.12
28 10 0.31
29 16 0.50
30 2 0.06
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.45
Consensus pattern (29 bp):
TTGAAAATTTCAATTAAACCTTAAAATTT
Found at i:2327518 original size:20 final size:20
Alignment explanation
Indices: 2327471--2327528 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 20
2327461 AGCATTTTAG
*
2327471 TTTTTTCTTTTATGTTCTTTT
1 TTTTTTCTTTT-TTTTCTTTT
***
2327492 AACTTTCTTTTTTTTCTTTT
1 TTTTTTCTTTTTTTTCTTTT
* *
2327512 TTTTTTCATTCTTTTCT
1 TTTTTTCTTTTTTTTCT
2327529 GTTTCTTCCT
Statistics
Matches: 28, Mismatches: 9, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
20 20 0.71
21 8 0.29
ACGTcount: A:0.07, C:0.14, G:0.02, T:0.78
Consensus pattern (20 bp):
TTTTTTCTTTTTTTTCTTTT
Found at i:2327766 original size:12 final size:12
Alignment explanation
Indices: 2327749--2327773 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2327739 AACGAGAATG
2327749 AAAAAAAAAGAA
1 AAAAAAAAAGAA
2327761 AAAAAAAAAGAA
1 AAAAAAAAAGAA
2327773 A
1 A
2327774 CGTTAAAAGA
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAA
Found at i:2332066 original size:14 final size:15
Alignment explanation
Indices: 2332047--2332075 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2332037 TTTAAGGTAA
2332047 GTTTTTTTTT-TTTT
1 GTTTTTTTTTGTTTT
2332061 GTTTTTTTTTGTTTT
1 GTTTTTTTTTGTTTT
2332076 TTACTGTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (15 bp):
GTTTTTTTTTGTTTT
Found at i:2332067 original size:10 final size:10
Alignment explanation
Indices: 2332048--2332077 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2332038 TTAAGGTAAG
2332048 TTTT-TTTTT
1 TTTTGTTTTT
2332057 TTTTGTTTTT
1 TTTTGTTTTT
2332067 TTTTGTTTTT
1 TTTTGTTTTT
2332077 T
1 T
2332078 ACTGTTGAGC
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 4 0.20
10 16 0.80
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (10 bp):
TTTTGTTTTT
Found at i:2333344 original size:18 final size:20
Alignment explanation
Indices: 2333323--2333367 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
2333313 AATAATAAAA
*
2333323 AAATTTAT-TGTA-ATTTTG
1 AAATTTATATGAATATTTTG
*
2333341 AAATTTTTATGAATATTTTG
1 AAATTTATATGAATATTTTG
2333361 AAATTTA
1 AAATTTA
2333368 AAAAATATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 7 0.32
19 3 0.14
20 12 0.55
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (20 bp):
AAATTTATATGAATATTTTG
Found at i:2340847 original size:18 final size:18
Alignment explanation
Indices: 2340810--2340902 Score: 123
Period size: 18 Copynumber: 5.2 Consensus size: 18
2340800 CCCAACTACT
*
2340810 GTATACGTGAACAGTACC
1 GTATACGTGAATAGTACC
* * *
2340828 GTATTCGTAAATAGTGCC
1 GTATACGTGAATAGTACC
*
2340846 GTATACGTGAATAGTACT
1 GTATACGTGAATAGTACC
* *
2340864 GTATACGTGAATAGTGCT
1 GTATACGTGAATAGTACC
2340882 GTATACGTGAATAGTACC
1 GTATACGTGAATAGTACC
2340900 GTA
1 GTA
2340903 AACGGTCGTA
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 64 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:2340862 original size:36 final size:36
Alignment explanation
Indices: 2340810--2340902 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
2340800 CCCAACTACT
* *
2340810 GTATACGTGAACAGTACCGTATTCGTAAATAGTGCC
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
* * *
2340846 GTATACGTGAATAGTACTGTATACGTGAATAGTGCT
1 GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
2340882 GTATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
2340903 AACGGTCGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.31, C:0.15, G:0.24, T:0.30
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACGTAAATAGTGCC
Found at i:2350265 original size:46 final size:46
Alignment explanation
Indices: 2350215--2350390 Score: 200
Period size: 46 Copynumber: 3.8 Consensus size: 46
2350205 TGGTTGAGCA
2350215 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* * *
2350261 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G
* *
2350306 CATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
* *
2350354 -CCTGAGCTCGTTGAGTTGAGTCCGAGTTCGCTTATGG
1 TCC-GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2350391 GCGGGTTACA
Statistics
Matches: 111, Mismatches: 9, Indels: 20
0.79 0.06 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 5 0.05
46 62 0.56
47 28 0.25
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.20, C:0.20, G:0.30, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATG
Found at i:2350371 original size:93 final size:93
Alignment explanation
Indices: 2350212--2350383 Score: 301
Period size: 93 Copynumber: 1.8 Consensus size: 93
2350202 GGATGGTTGA
*
2350212 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
2350277 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
2350305 GCATCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG-CCTGAGCTCGTTGAG
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC-GAACTCGTTGAG
2350369 TTGAGTCCGAGTTCG
65 TTGAGTCCGAGTTCG
2350384 CTTATGGGCG
Statistics
Matches: 75, Mismatches: 3, Indels: 2
0.94 0.04 0.03
Matches are distributed among these distances:
92 2 0.03
93 73 0.97
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.28
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2357357 original size:48 final size:48
Alignment explanation
Indices: 2357295--2357387 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
2357285 TTAAAAAAAT
*
2357295 TAAAAATTAAAAAAATATA-TTTTTAAAAATTAAAATTATTAAAAAGTA
1 TAAAAATTAAAAAAAGATAGTTTTTAAAAATTAAAATT-TTAAAAAGTA
* ***
2357343 TAAAAATTATAAAAAGATAGTTTTTAATTTTTAAAATTTTAAAAA
1 TAAAAATTAAAAAAAGATAGTTTTTAAAAATTAAAATTTTAAAAA
2357388 ATTAATTAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 24 0.62
49 15 0.38
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (48 bp):
TAAAAATTAAAAAAAGATAGTTTTTAAAAATTAAAATTTTAAAAAGTA
Found at i:2360173 original size:20 final size:20
Alignment explanation
Indices: 2360115--2360173 Score: 57
Period size: 20 Copynumber: 2.9 Consensus size: 20
2360105 ATCTACACAC
*
2360115 CCATGTGAAAGAGATACACGT
1 CCATGTGAAAG-GACACACGT
*
2360136 CCATGTAAAAAGG-CACACGT
1 CCATGT-GAAAGGACACACGT
* *
2360156 CCGTGTGAAAGGAGACAC
1 CCATGTGAAAGGACACAC
2360174 ACGGCTGTGT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 5 0.16
20 15 0.48
21 7 0.23
22 4 0.13
ACGTcount: A:0.37, C:0.22, G:0.25, T:0.15
Consensus pattern (20 bp):
CCATGTGAAAGGACACACGT
Found at i:2360923 original size:16 final size:16
Alignment explanation
Indices: 2360895--2360935 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
2360885 TTCCAAAAAT
2360895 TAAAAAT-TAATAATAA
1 TAAAAATAT-ATAATAA
2360911 -AATAAATATATAATAA
1 TAA-AAATATATAATAA
2360927 TAAAAATAT
1 TAAAAATAT
2360936 TACATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.09
16 17 0.77
17 3 0.14
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
TAAAAATATATAATAA
Found at i:2360930 original size:14 final size:13
Alignment explanation
Indices: 2360897--2360952 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
2360887 CCAAAAATTA
*
2360897 AAAATTAATA-AT
1 AAAATAAATATAT
2360909 AAAATAAATATAT
1 AAAATAAATATAT
*
2360922 AATAATAAAAATAT
1 AA-AATAAATATAT
* * *
2360936 TACATAAATATCT
1 AAAATAAATATAT
2360949 AAAA
1 AAAA
2360953 CACTCATAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 3
0.76 0.18 0.07
Matches are distributed among these distances:
12 9 0.26
13 14 0.41
14 11 0.32
ACGTcount: A:0.66, C:0.04, G:0.00, T:0.30
Consensus pattern (13 bp):
AAAATAAATATAT
Found at i:2363394 original size:46 final size:46
Alignment explanation
Indices: 2363339--2363519 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
2363329 TAGGATGGTT
2363339 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
2363385 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
2363431 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
2363478 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2363520 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:2363500 original size:93 final size:93
Alignment explanation
Indices: 2363341--2363511 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
2363331 GGATGGTTGA
* *
2363341 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2363406 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
2363434 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2363499 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
2363512 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2366514 original size:15 final size:15
Alignment explanation
Indices: 2366475--2366553 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
2366465 GTATCTTGGG
*
2366475 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
2366490 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
2366505 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
2366519 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
2366534 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
2366548 TTTCTT
1 TTTCTT
2366554 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:2366538 original size:29 final size:29
Alignment explanation
Indices: 2366466--2366552 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
2366456 CATAGTATCG
* * * *
2366466 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
2366496 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
2366525 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
2366553 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Found at i:2368982 original size:46 final size:46
Alignment explanation
Indices: 2368927--2369107 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
2368917 TAGGATGGTT
2368927 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
2368973 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
2369019 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
2369066 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2369108 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:2369088 original size:93 final size:93
Alignment explanation
Indices: 2368929--2369099 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
2368919 GGATGGTTGA
* *
2368929 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2368994 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
2369022 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2369087 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
2369100 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2375503 original size:20 final size:19
Alignment explanation
Indices: 2375473--2375528 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
2375463 TATAAATTTA
2375473 TTTTA-TATTTAATTTAAT
1 TTTTAGTATTTAATTTAAT
2375491 GTTTTAGTATTT-ATTTATAT
1 -TTTTAGTATTTAATTTA-AT
* *
2375511 TTTTGGTATTTAAATTAA
1 TTTTAGTATTTAATTTAA
2375529 GAATATGTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
19 21 0.66
20 11 0.34
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.62
Consensus pattern (19 bp):
TTTTAGTATTTAATTTAAT
Found at i:2376334 original size:16 final size:16
Alignment explanation
Indices: 2376310--2376344 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
2376300 CAAAACTTAG
* *
2376310 AATATAAAATAATAAA
1 AATAAAAAATAAAAAA
2376326 AATAAAAAATAAAAAA
1 AATAAAAAATAAAAAA
2376342 AAT
1 AAT
2376345 CAGATTTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (16 bp):
AATAAAAAATAAAAAA
Found at i:2376493 original size:23 final size:22
Alignment explanation
Indices: 2376454--2376504 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
2376444 CCGGAGCTCC
2376454 CTCTCCCTCTCCCCTTTCTTTT
1 CTCTCCCTCTCCCCTTTCTTTT
** *
2376476 CTCTCTCCTCTCTTCTTTTTTTT
1 CTCTC-CCTCTCCCCTTTCTTTT
2376499 CT-TCCC
1 CTCTCCC
2376505 CTTCTCAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 7 0.28
23 16 0.64
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (22 bp):
CTCTCCCTCTCCCCTTTCTTTT
Found at i:2377301 original size:13 final size:11
Alignment explanation
Indices: 2377258--2377312 Score: 53
Period size: 11 Copynumber: 5.1 Consensus size: 11
2377248 TTCTTTTTCA
2377258 TATTAT-TA-T
1 TATTATATATT
* *
2377267 TATAATATATA
1 TATTATATATT
2377278 TATTATATATT
1 TATTATATATT
2377289 TATGTATAT-TAT
1 TAT-TATATAT-T
2377301 TATTATATATT
1 TATTATATATT
2377312 T
1 T
2377313 TTAATGTTAT
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 5 0.14
10 2 0.05
11 20 0.54
12 10 0.27
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (11 bp):
TATTATATATT
Found at i:2377323 original size:31 final size:33
Alignment explanation
Indices: 2377261--2377326 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 33
2377251 TTTTTCATAT
2377261 TATTATTATAATATATATATTATATATTTATGTA
1 TATTATTAT-ATATATATATTATATATTTATGTA
*
2377295 TATTATTAT-TATATAT-TTTTA-ATGTTATGTA
1 TATTATTATATATATATATTATATAT-TTATGTA
2377326 T
1 T
2377327 TGTATATTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
30 2 0.07
31 12 0.40
32 7 0.23
34 9 0.30
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (33 bp):
TATTATTATATATATATATTATATATTTATGTA
Found at i:2377327 original size:23 final size:23
Alignment explanation
Indices: 2377278--2377344 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 23
2377268 ATAATATATA
*
2377278 TATTATATATTTATGT-ATATTAT
1 TATTATATATTTAT-TAATGTTAT
2377301 TATTATATATTT-TTAATGTTAT
1 TATTATATATTTATTAATGTTAT
* * *
2377323 GTATTGTATATTTCTTACTGTT
1 -TATTATATATTTATTAATGTT
2377345 CGTATACTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
21 1 0.03
22 7 0.18
23 23 0.61
24 7 0.18
ACGTcount: A:0.28, C:0.03, G:0.07, T:0.61
Consensus pattern (23 bp):
TATTATATATTTATTAATGTTAT
Found at i:2377349 original size:23 final size:23
Alignment explanation
Indices: 2377301--2377349 Score: 55
Period size: 23 Copynumber: 2.1 Consensus size: 23
2377291 TGTATATTAT
*
2377301 TATTATATATTTTTAATGTTATG
1 TATTATATATTTTTAATGTTACG
* *
2377324 TATTGTATATTTCTTACTGTT-CG
1 TATTATATATTT-TTAATGTTACG
2377347 TAT
1 TAT
2377350 ACTTTACGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 15 0.68
24 7 0.32
ACGTcount: A:0.24, C:0.06, G:0.10, T:0.59
Consensus pattern (23 bp):
TATTATATATTTTTAATGTTACG
Found at i:2377520 original size:2 final size:2
Alignment explanation
Indices: 2377485--2377511 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2377475 TATCTTTAAC
2377485 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
2377512 GGCATATATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2389137 original size:11 final size:10
Alignment explanation
Indices: 2389116--2389141 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
2389106 AAGGGCATCT
2389116 AAAAAATAAA
1 AAAAAATAAA
2389126 AAAAAATAAA
1 AAAAAATAAA
2389136 AAAAAA
1 AAAAAA
2389142 GGGGGATCAG
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:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:2390203 original size:71 final size:71
Alignment explanation
Indices: 2390082--2390215 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
2390072 GTTTTCCAAG
* * *
2390082 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
2390147 GTTTCA
66 GTTTCA
* * *
2390153 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
2390216 CTACTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:2390255 original size:160 final size:160
Alignment explanation
Indices: 2389991--2390694 Score: 1327
Period size: 160 Copynumber: 4.4 Consensus size: 160
2389981 TTGTTTTTTC
*
2389991 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
2390056 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
2390121 GACACGTTGAGGTAATTTCAATTTATGTTT
131 GACACGTTGAGGTAATTTCAATTTATGTTT
2390151 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
*
2390216 CTACTTTTTAATTCATGTTTTTCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
2390281 GACACGTTGAGGTAATTTCAATTTATGTTT
131 GACACGTTGAGGTAATTTCAATTTATGTTT
2390311 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
*
2390376 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
66 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
2390441 GACACGTTGAGGTAATTTCAATTTATGTTT
131 GACACGTTGAGGTAATTTCAATTTATGTTT
2390471 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
* *
2390536 CTGCTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGATGAGTTGAGCCTCAA
66 CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
2390601 GACACGTTGAGGTAATTTCAATTTATGTTT
131 GACACGTTGAGGTAATTTCAATTTATGTTT
* * * *
2390631 CAAAAATCAACTCATATCGCGAGAAGTGAGTTGAACCTCGGGGCACGCTGAGGTAATTTCAATT
1 CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATT
2390695 CCTATTAAAT
Statistics
Matches: 535, Mismatches: 9, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
160 535 1.00
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (160 bp):
CAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
CTACTTTTTAATTCATGTTTTCCAAGAAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAA
GACACGTTGAGGTAATTTCAATTTATGTTT
Found at i:2390363 original size:71 final size:71
Alignment explanation
Indices: 2390242--2390375 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
2390232 GTTTTTCAAG
* * *
2390242 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
2390307 GTTTCA
66 GTTTCA
* * *
2390313 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
2390376 CTGCTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:2390523 original size:71 final size:71
Alignment explanation
Indices: 2390402--2390535 Score: 214
Period size: 71 Copynumber: 1.9 Consensus size: 71
2390392 GTTTTCCAAG
* * *
2390402 AAAATCAGCTCATATTGCGAGAGGTGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATTTAT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
2390467 GTTTCA
66 GTTTCA
* * *
2390473 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCAATTT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTT
2390536 CTGCTTTTTA
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 57 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCAAGACACGCTGAGGTAATTTCAATTTAT
GTTTCA
Found at i:2390683 original size:71 final size:71
Alignment explanation
Indices: 2390562--2390814 Score: 285
Period size: 74 Copynumber: 3.5 Consensus size: 71
2390552 GTTTTCCAAG
* * * *
2390562 AAAATCAGCTCATATTGCGAG-AGATGAGTTGAGCCTCAAGACACGTTGAGGTAATTTCAATT-T
1 AAAATCAACTCATATTGCGAGAAG-TGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTCT
2390625 ATGTTTCA
65 AT-TTTCA
* * *
2390633 AAAATCAACTCATATCGCGAGAAGTGAGTTGAACCTCGGGGCACGCTGAGGTAATTTCAATTCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATT-CT
* *
2390698 ATTAAATCT
65 ATT--TTCA
* * * *
2390707 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTTGCGGCACGCTAAGGTATTTTCAAATTCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTC-AATTCT
2390772 ATTTTCA
65 ATTTTCA
* * * *
2390779 AAAGTTAATTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCT
2390815 TTAATTTTCG
Statistics
Matches: 155, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
71 52 0.34
72 37 0.24
73 3 0.02
74 59 0.38
75 4 0.03
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (71 bp):
AAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGAGGCACGCTGAGGTAATTTCAATTCTA
TTTTCA
Found at i:2390872 original size:67 final size:66
Alignment explanation
Indices: 2390760--2390958 Score: 292
Period size: 67 Copynumber: 3.0 Consensus size: 66
2390750 CGCTAAGGTA
* * *
2390760 TTTTCAAATTCTA-TTTTCAAAAGTTAATTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTC
1 TTTTCAAAATCTACTTTTCAAAA-TTAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTCC
2390824 GT
65 GT
*
2390826 TTTTCAAAATCTACTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTCC
1 TTTTCAAAATCTACTTTTCAAA-ATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTCC
2390891 GT
65 GT
* *
2390893 TTTTCGAAATATACTTTTCAAATTATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTT
1 TTTTCAAAATCTACTTTTCAAA--ATTAACTCATATTGCGAGAGGTGAGTTGAGCC-TTTAATTT
2390958 C
63 C
2390959 TGCTTCTAAT
Statistics
Matches: 121, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
66 12 0.10
67 68 0.56
68 32 0.26
69 9 0.07
ACGTcount: A:0.28, C:0.15, G:0.16, T:0.41
Consensus pattern (66 bp):
TTTTCAAAATCTACTTTTCAAAATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTCCG
T
Found at i:2390980 original size:68 final size:64
Alignment explanation
Indices: 2390761--2391016 Score: 248
Period size: 67 Copynumber: 3.8 Consensus size: 64
2390751 GCTAAGGTAT
* *
2390761 TTTC-AAATTCTA-TTTTCAAAAGTTAATTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTTC
1 TTTCTAAA-TCTACTTTTCAAAA-TCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAA-TTTC
*
2390824 GTT
63 -TG
*
2390827 TTTCAAAATCTACTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTCCG
1 TTTCTAAATCTACTTTTCAAA-ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTT-C-
*
2390892 TT
63 TG
* * *
2390894 TTTCGAAATATACTTTTCAAATTATTAACTCATATTGCGAGAGGTGAGTTGAGCCTTTTAATTTC
1 TTTCTAAATCTACTTTTCAAA--ATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TTTAATTTC
2390959 TG
63 TG
* * * * **
2390961 CTTCTAATTTCTA-TGTTTCAAAAATCAACCCATATTGCGAAAAATGAGTTGAGCCT
1 TTTCTAA-ATCTACT-TTTC-AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
2391017 CAGTTCACCT
Statistics
Matches: 165, Mismatches: 16, Indels: 18
0.83 0.08 0.09
Matches are distributed among these distances:
66 12 0.07
67 102 0.62
68 40 0.24
69 11 0.07
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (64 bp):
TTTCTAAATCTACTTTTCAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTTAATTTCTG
Found at i:2392261 original size:16 final size:17
Alignment explanation
Indices: 2392235--2392270 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
2392225 CAAAACTTAG
*
2392235 AATATAAAAATAATAAA
1 AATATAAAAATAAAAAA
2392252 AATA-AAAAATAAAAAA
1 AATATAAAAATAAAAAA
2392268 AAT
1 AAT
2392271 CAGATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AATATAAAAATAAAAAA
Found at i:2392406 original size:22 final size:23
Alignment explanation
Indices: 2392381--2392425 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 23
2392371 CCGGAGCTCC
2392381 CTCTCCCTCTCCCCT-TTCTTTT
1 CTCTCCCTCTCCCCTCTTCTTTT
*
2392403 CTCTCCCTCTCCTCTCTTCTTTT
1 CTCTCCCTCTCCCCTCTTCTTTT
2392426 TTTTCTTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 14 0.67
23 7 0.33
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (23 bp):
CTCTCCCTCTCCCCTCTTCTTTT
Found at i:2392437 original size:27 final size:28
Alignment explanation
Indices: 2392377--2392435 Score: 77
Period size: 27 Copynumber: 2.2 Consensus size: 28
2392367 CCCACCGGAG
2392377 CTCCCTCTCCCTCTCCCCTTTCTTTTCT
1 CTCCCTCTCCCTCTCCCCTTTCTTTTCT
** *
2392405 CTCCCTCT-CCTCTCTTCTTTTTTTTCT
1 CTCCCTCTCCCTCTCCCCTTTCTTTTCT
2392432 -TCCC
1 CTCCC
2392436 CTTCTCAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 4 0.14
27 16 0.57
28 8 0.29
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (28 bp):
CTCCCTCTCCCTCTCCCCTTTCTTTTCT
Found at i:2393213 original size:20 final size:20
Alignment explanation
Indices: 2393188--2393239 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 20
2393178 TTTCTTTTTC
2393188 ATATTATTATTATAATATAT
1 ATATTATTATTATAATATAT
* *
2393208 ATATTA-TA-TAT-TTATGT
1 ATATTATTATTATAATATAT
2393225 ATATTATTATATATA
1 ATATTATTAT-TATA
2393240 TTTTTAATGT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
17 10 0.38
18 5 0.19
19 2 0.08
20 9 0.35
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (20 bp):
ATATTATTATTATAATATAT
Found at i:2393230 original size:31 final size:30
Alignment explanation
Indices: 2393195--2393256 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 30
2393185 TTCATATTAT
2393195 TATTATAATATATATATTATATAT-TTATGTA
1 TATTATAATATATAT-TTATA-ATGTTATGTA
* *
2393226 TATTATTATATATATTTTTAATGTTATGTA
1 TATTATAATATATATTTATAATGTTATGTA
2393256 T
1 T
2393257 TGTATATTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
29 2 0.07
30 12 0.43
31 14 0.50
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.58
Consensus pattern (30 bp):
TATTATAATATATATTTATAATGTTATGTA
Found at i:2393249 original size:25 final size:24
Alignment explanation
Indices: 2393194--2393263 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 24
2393184 TTTCATATTA
*
2393194 TTAT-TATAATATATATATTATATAT
1 TTATGTATATTAT-TATA-TATATAT
*
2393219 TTATGTATATTATTATATATATTT
1 TTATGTATATTATTATATATATAT
*
2393243 TTAATGT-TATGTATTGTATAT
1 TT-ATGTATAT-TATTATATAT
2393264 TTCTTACTGT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
24 11 0.28
25 21 0.54
26 7 0.18
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.59
Consensus pattern (24 bp):
TTATGTATATTATTATATATATAT
Found at i:2393279 original size:23 final size:23
Alignment explanation
Indices: 2393236--2393279 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
2393226 TATTATTATA
*
2393236 TATATTTTTAATGTTATGTATTG
1 TATATTTTTAATGTTACGTATTG
*
2393259 TATATTTCTTACTGTT-CGTAT
1 TATATTT-TTAATGTTACGTAT
2393280 ACTCTTACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 11 0.61
24 7 0.39
ACGTcount: A:0.23, C:0.07, G:0.11, T:0.59
Consensus pattern (23 bp):
TATATTTTTAATGTTACGTATTG
Found at i:2393456 original size:2 final size:2
Alignment explanation
Indices: 2393417--2393447 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2393407 TATCTTTAAC
2393417 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2393448 GGCATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2399550 original size:19 final size:21
Alignment explanation
Indices: 2399492--2399551 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
2399482 AATTCTTTTT
*
2399492 ATATATTGTTGAAATTTTCATA
1 ATATATT-TTAAAATTTTCATA
* *
2399514 A-ATATTTTATGAATTTTTA-A
1 ATATATTTTA-AAATTTTCATA
2399534 ATATATTTTAAAATTTTC
1 ATATATTTTAAAATTTTC
2399552 TGGTAATTCC
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
20 10 0.32
21 20 0.65
22 1 0.03
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (21 bp):
ATATATTTTAAAATTTTCATA
Found at i:2404278 original size:20 final size:20
Alignment explanation
Indices: 2404253--2404301 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
2404243 TCTTTTTTAA
*
2404253 ACATGTTAATAGGATTTGAG
1 ACATGTTAATAAGATTTGAG
*
2404273 ACATGTTAATAAGATTTTAG
1 ACATGTTAATAAGATTTGAG
*
2404293 ACATATTAA
1 ACATGTTAA
2404302 ATATTAATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.06, G:0.16, T:0.37
Consensus pattern (20 bp):
ACATGTTAATAAGATTTGAG
Found at i:2416890 original size:2 final size:2
Alignment explanation
Indices: 2416883--2416910 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2416873 TATATCTACA
2416883 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2416911 CTTATGGCTA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2418217 original size:29 final size:29
Alignment explanation
Indices: 2418159--2418222 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
2418149 TTAGGTAAGG
*
2418159 ATTAAAATTGTAAAATTAAAAAAATTAAA
1 ATTAAAATTGTAAAATTAAAAAAATAAAA
*
2418188 ATTAAAATT-TATCAAATT-AAAATATAAAA
1 ATTAAAATTGTA--AAATTAAAAAAATAAAA
*
2418217 ACTAAA
1 ATTAAA
2418223 TTCAGAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 2 0.07
29 23 0.77
30 5 0.17
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (29 bp):
ATTAAAATTGTAAAATTAAAAAAATAAAA
Found at i:2423548 original size:27 final size:27
Alignment explanation
Indices: 2423518--2423622 Score: 122
Period size: 27 Copynumber: 3.9 Consensus size: 27
2423508 TTGTGCCTAC
2423518 CTGACAGGCACAACTAGTTGAGCCTGT
1 CTGACAGGCACAACTAGTTGAGCCTGT
* * *
2423545 CTGACAAGCACGACTAGTTGTGCCTGT
1 CTGACAGGCACAACTAGTTGAGCCTGT
* *
2423572 CTGACAGGCACGACTAGTTGTGCCT-T
1 CTGACAGGCACAACTAGTTGAGCCTGT
** *
2423598 CTTGGTAGGCACAACTAGTGGAGCC
1 C-TGACAGGCACAACTAGTTGAGCC
2423623 CACATGCTTA
Statistics
Matches: 68, Mismatches: 9, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
26 2 0.03
27 66 0.97
ACGTcount: A:0.23, C:0.26, G:0.28, T:0.24
Consensus pattern (27 bp):
CTGACAGGCACAACTAGTTGAGCCTGT
Found at i:2426761 original size:22 final size:22
Alignment explanation
Indices: 2426727--2426792 Score: 64
Period size: 22 Copynumber: 3.0 Consensus size: 22
2426717 TCAACATTTT
*
2426727 AATAAATCA-ATAAAAATTATCA
1 AATAAAT-ATATAAAAATTATAA
*
2426749 AATAAATATATAATAA-TATAA
1 AATAAATATATAAAAATTATAA
*
2426770 AATTACATTATATAAAAATTATA
1 AA-TA-AATATATAAAAATTATA
2426793 TTAAAAAATT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 7 0.19
22 15 0.42
23 10 0.28
24 4 0.11
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (22 bp):
AATAAATATATAAAAATTATAA
Found at i:2426787 original size:16 final size:15
Alignment explanation
Indices: 2426764--2426805 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
2426754 ATATATAATA
2426764 ATATAAAATTACATT
1 ATATAAAATTACATT
*
2426779 ATATAAAAATTATATT
1 ATAT-AAAATTACATT
2426795 A-A-AAAATTACA
1 ATATAAAATTACA
2426806 AAACACTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 8 0.33
15 5 0.21
16 11 0.46
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.36
Consensus pattern (15 bp):
ATATAAAATTACATT
Found at i:2427197 original size:112 final size:112
Alignment explanation
Indices: 2426853--2427631 Score: 1235
Period size: 112 Copynumber: 6.9 Consensus size: 112
2426843 ATACTAACAC
* * * * **
2426853 AAAATAACTATAAAATTATTTTTTT-AAATACATTACTAAATAAAAATCACAATACATTAATACA
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACT-AA-AAAAATTACAATACGCTAAT---
2426917 CACTAAACCACTAAACACTAACAA--TATATAACCTAATCTTAAATTACTAAT
61 -ACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
* * *
2426968 AAAATAGCTAT-AAAATATTTTTTTTAAATATATTACTAAAAAAAAATCACAATACACTAATACA
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACT--AAAAAAATTACAATACGCTAAT--A
*
2427032 CTAAACCACTAAACACTAATAATTTATATAACCTAATCTTAAATTACTAAT
62 CTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
2427083 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAATACTAA
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAATACTAA
2427148 ACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
66 ACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
2427195 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAATACTAA
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAATACTAA
2427260 ACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
66 ACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
*
2427307 AAAATAGCTAT-AAAATATTTTTTTAAAATATATTACTAAGAAAATTACAATACGCTAATACTAA
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAATACTAA
2427371 ACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
66 ACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
* *
2427418 AAAATAGCTATAAAATTATTTTTTTAAAATATATTACTAAAACAATTACAATACGCTAATACTAA
1 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAATACTAA
*
2427483 ACCGCTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
66 ACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
* * *
2427530 AAAATAGCTATAAAATTATTTTTTTAAAAATATATTACTAAAAAAATCACAATACACTAATACAC
1 AAAATAGCTATAAAAATATTTTTTT-AAAATATATTACTAAAAAAATTACAATACGCTAAT--AC
* *
2427595 TAAACTACTAAACACTAACAATTTATATAACCAAATC
63 TAAACCACTAAACACTAACAATTTATATAACCTAATC
2427632 AACTATAATT
Statistics
Matches: 635, Mismatches: 20, Indels: 18
0.94 0.03 0.03
Matches are distributed among these distances:
111 110 0.17
112 295 0.46
113 56 0.09
114 32 0.05
115 114 0.18
116 28 0.04
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.33
Consensus pattern (112 bp):
AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAATACTAA
ACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
Found at i:2427384 original size:223 final size:225
Alignment explanation
Indices: 2426853--2427631 Score: 1248
Period size: 223 Copynumber: 3.4 Consensus size: 225
2426843 ATACTAACAC
* * *
2426853 AAAATAACTATAAAATTATTTTTTT-AAATACATTACTAAATAAAAATCACAATACATTAATACA
1 AAAATAGCTATAAAATTATTTTTTTAAAATATATTACT-AA-AAAAATCACAATACACTAAT--A
2426917 CACTAAACCACTAAACACTAACAA--TATATAACCTAATCTTAAATTACTAATAAAATAGCTAT-
62 -ACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATA
* * *
2426979 AAAATATTTTTTTTAAATATATTACTAAAAAAAAATCACAATACACTAATACACTAAACCACTAA
126 AAAATATTTTTTTAAAATATATTACT--AAAAAAATTACAATACGCTAAT--ACTAAACCACTAA
*
2427044 ACACTAATAATTTATATAACCTAATCTTAAATTACTAAT
187 ACACTAACAATTTATATAACCTAATCTTAAATTACTAAT
* * *
2427083 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAAT-ACTA
1 AAAATAGCTATAAAATTATTTTTTTAAAATATATTACTAAAAAAATCACAATACACTAATAACTA
2427147 AACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAAT
66 AACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAAT
2427212 ATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAATACTAAACCACTAAACACTAACA
131 ATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAATACTAAACCACTAAACACTAACA
2427277 ATTTATATAACCTAATCTTAAATTACTAAT
196 ATTTATATAACCTAATCTTAAATTACTAAT
* * *
2427307 AAAATAGCTATAAAA-TATTTTTTTAAAATATATTACTAAGAAAATTACAATACGCTAAT-ACTA
1 AAAATAGCTATAAAATTATTTTTTTAAAATATATTACTAAAAAAATCACAATACACTAATAACTA
*
2427370 AACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAATT
66 AACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAAT
* *
2427435 ATTTTTTTAAAATATATTACTAAAACAATTACAATACGCTAATACTAAACCGCTAAACACTAACA
131 ATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAATACTAAACCACTAAACACTAACA
2427500 ATTTATATAACCTAATCTTAAATTACTAAT
196 ATTTATATAACCTAATCTTAAATTACTAAT
2427530 AAAATAGCTATAAAATTATTTTTTTAAAAATATATTACTAAAAAAATCACAATACACTAATACAC
1 AAAATAGCTATAAAATTATTTTTTT-AAAATATATTACTAAAAAAATCACAATACACTAATA-AC
* *
2427595 TAAACTACTAAACACTAACAATTTATATAACCAAATC
64 TAAACCACTAAACACTAACAATTTATATAACCTAATC
2427632 AACTATAATT
Statistics
Matches: 522, Mismatches: 19, Indels: 19
0.93 0.03 0.03
Matches are distributed among these distances:
223 219 0.42
224 75 0.14
225 55 0.11
226 20 0.04
227 75 0.14
228 25 0.05
229 17 0.03
230 25 0.05
231 11 0.02
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.33
Consensus pattern (225 bp):
AAAATAGCTATAAAATTATTTTTTTAAAATATATTACTAAAAAAATCACAATACACTAATAACTA
AACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAAT
ATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAATACTAAACCACTAAACACTAACA
ATTTATATAACCTAATCTTAAATTACTAAT
Found at i:2427530 original size:335 final size:338
Alignment explanation
Indices: 2426853--2427631 Score: 1291
Period size: 335 Copynumber: 2.3 Consensus size: 338
2426843 ATACTAACAC
* * *
2426853 AAAATAACTATAAAATTATTTTTTT-AAATACATTACTAAATAAAAATCACAATACATTAATACA
1 AAAATAGCTATAAAATTATTTTTTTAAAATATATTACT-AA-AAAAATCACAATACACTAAT--A
2426917 CACTAAACCACTAAACACTAACAA--TATATAACCTAATCTTAAATTACTAATAAAATAGCTATA
62 -ACTAAACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATA
*
2426980 AAATATTTTTTTTAAATATATTACTAAAAAAAAATCACAATACACTAATACACTAAACCACTAAA
126 AAATATTTTTTTAAAATATATTACT-AAAAAAAATCACAATACACTAATA-ACTAAACCACTAAA
*
2427045 CACTAATAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAATATTTTTTTAA
189 CACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAATATTTTTTTAA
2427110 AATATATTACTAAAAAAATTACAATACGCTAATACTAAACCACTAAACACTAACAATTTATATAA
254 AATATATTACTAAAAAAATTACAATACGCTAATACTAAACCACTAAACACTAACAATTTATATAA
2427175 CCTAATCTTAAATTACTAAT
319 CCTAATCTTAAATTACTAAT
* * *
2427195 AAAATAGCTATAAAAATATTTTTTTAAAATATATTACTAAAAAAATTACAATACGCTAAT-ACTA
1 AAAATAGCTATAAAATTATTTTTTTAAAATATATTACTAAAAAAATCACAATACACTAATAACTA
2427259 AACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAATA
66 AACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAATA
* * *
2427324 TTTTTTTAAAATATATTACT-AAGAAAATTACAATACGCTAAT-ACTAAACCACTAAACACTAAC
131 TTTTTTTAAAATATATTACTAAAAAAAATCACAATACACTAATAACTAAACCACTAAACACTAAC
*
2427387 AATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAATTATTTTTTTAAAATATAT
196 AATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAATATTTTTTTAAAATATAT
* *
2427452 TACTAAAACAATTACAATACGCTAATACTAAACCGCTAAACACTAACAATTTATATAACCTAATC
261 TACTAAAAAAATTACAATACGCTAATACTAAACCACTAAACACTAACAATTTATATAACCTAATC
2427517 TTAAATTACTAAT
326 TTAAATTACTAAT
2427530 AAAATAGCTATAAAATTATTTTTTTAAAAATATATTACTAAAAAAATCACAATACACTAATACAC
1 AAAATAGCTATAAAATTATTTTTTT-AAAATATATTACTAAAAAAATCACAATACACTAATA-AC
* *
2427595 TAAACTACTAAACACTAACAATTTATATAACCAAATC
64 TAAACCACTAAACACTAACAATTTATATAACCTAATC
2427632 AACTATAATT
Statistics
Matches: 412, Mismatches: 19, Indels: 16
0.92 0.04 0.04
Matches are distributed among these distances:
335 184 0.45
336 33 0.08
337 42 0.10
338 37 0.09
339 63 0.15
341 17 0.04
342 25 0.06
343 11 0.03
ACGTcount: A:0.51, C:0.15, G:0.02, T:0.33
Consensus pattern (338 bp):
AAAATAGCTATAAAATTATTTTTTTAAAATATATTACTAAAAAAATCACAATACACTAATAACTA
AACCACTAAACACTAACAATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAATA
TTTTTTTAAAATATATTACTAAAAAAAATCACAATACACTAATAACTAAACCACTAAACACTAAC
AATTTATATAACCTAATCTTAAATTACTAATAAAATAGCTATAAAAATATTTTTTTAAAATATAT
TACTAAAAAAATTACAATACGCTAATACTAAACCACTAAACACTAACAATTTATATAACCTAATC
TTAAATTACTAAT
Found at i:2427907 original size:3 final size:3
Alignment explanation
Indices: 2427901--2427961 Score: 59
Period size: 3 Copynumber: 19.3 Consensus size: 3
2427891 ACCTTTTTTT
* **
2427901 TTC TTC TTCC TTC TTC TTC TTTC TTC TTC TTC TCC TTC ACC TTCC TTC
1 TTC TTC TT-C TTC TTC TTC -TTC TTC TTC TTC TTC TTC TTC TT-C TTC
*
2427949 TTC TTC TCC TTC T
1 TTC TTC TTC TTC T
2427962 CCTTTCTCTC
Statistics
Matches: 47, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
3 38 0.81
4 9 0.19
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (3 bp):
TTC
Found at i:2427916 original size:10 final size:10
Alignment explanation
Indices: 2427901--2427954 Score: 55
Period size: 10 Copynumber: 5.9 Consensus size: 10
2427891 ACCTTTTTTT
2427901 TTCTTCTTCC
1 TTCTTCTTCC
2427911 TTCTTCTT-C
1 TTCTTCTTCC
2427920 -T-TTCTT-C
1 TTCTTCTTCC
2427927 TTCTTC-TCC
1 TTCTTCTTCC
**
2427936 TTCACCTTCC
1 TTCTTCTTCC
2427946 TTCTTCTTC
1 TTCTTCTTC
2427955 TCCTTCTCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
7 6 0.17
8 3 0.08
9 9 0.25
10 18 0.50
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:2427977 original size:22 final size:22
Alignment explanation
Indices: 2427901--2427968 Score: 91
Period size: 22 Copynumber: 3.0 Consensus size: 22
2427891 ACCTTTTTTT
* *
2427901 TTCTTCTTCCTTCTTCTTCTTTC
1 TTCTTCTT-CTCCTTCTCCTTTC
* *
2427924 TTCTTCTTCTCCTTCACCTTCC
1 TTCTTCTTCTCCTTCTCCTTTC
2427946 TTCTTCTTCTCCTTCTCCTTTC
1 TTCTTCTTCTCCTTCTCCTTTC
2427968 T
1 T
2427969 CTCCTTTCTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
22 31 0.79
23 8 0.21
ACGTcount: A:0.01, C:0.40, G:0.00, T:0.59
Consensus pattern (22 bp):
TTCTTCTTCTCCTTCTCCTTTC
Found at i:2429898 original size:31 final size:31
Alignment explanation
Indices: 2429874--2429943 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
2429864 TAAAAAATAA
*
2429874 AATATAATAATAGATTATATTTAAATAATTT
1 AATATAATAATAGATGATATTTAAATAATTT
* * *
2429905 AGTATAATCATATATGATATTTAAATAATTT
1 AATATAATAATAGATGATATTTAAATAATTT
2429936 AATATAAT
1 AATATAAT
2429944 GATACATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.50, C:0.01, G:0.04, T:0.44
Consensus pattern (31 bp):
AATATAATAATAGATGATATTTAAATAATTT
Found at i:2429961 original size:31 final size:31
Alignment explanation
Indices: 2429895--2429961 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
2429885 AGATTATATT
* * * * *
2429895 TAAATAATTTAGTATAATCATATATGATATT
1 TAAATAATTTAATATAATCATACATAAAATA
*
2429926 TAAATAATTTAATATAATGATACATAAAATA
1 TAAATAATTTAATATAATCATACATAAAATA
2429957 TAAAT
1 TAAAT
2429962 TAGTCTAACT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.40
Consensus pattern (31 bp):
TAAATAATTTAATATAATCATACATAAAATA
Found at i:2430383 original size:9 final size:10
Alignment explanation
Indices: 2430346--2430375 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
2430336 AATTTTTTTA
2430346 TTTATAATTT
1 TTTATAATTT
2430356 TTTATAATTT
1 TTTATAATTT
2430366 TTTATAATTT
1 TTTATAATTT
2430376 ATTAAATTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTATAATTT
Found at i:2430990 original size:17 final size:15
Alignment explanation
Indices: 2430953--2430992 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
2430943 GTAAAAATAT
2430953 AATTTTATTATTTTA
1 AATTTTATTATTTTA
2430968 ATATTTTATATATTTATA
1 A-ATTTTAT-TATTT-TA
2430986 AATTTTA
1 AATTTTA
2430993 AAAGGTTAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
15 1 0.05
16 7 0.32
17 11 0.50
18 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
AATTTTATTATTTTA
Found at i:2431690 original size:21 final size:21
Alignment explanation
Indices: 2431623--2431682 Score: 93
Period size: 21 Copynumber: 2.9 Consensus size: 21
2431613 AAGCCCTCCC
*
2431623 AAAAAAAAAAACCTAACTAAA
1 AAAAAAAAAAACCTAACCAAA
*
2431644 AAAAAAAAAAACTTAACCAAA
1 AAAAAAAAAAACCTAACCAAA
*
2431665 AAAAAGAAAAACCTAACC
1 AAAAAAAAAAACCTAACC
2431683 CCCAAAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.73, C:0.17, G:0.02, T:0.08
Consensus pattern (21 bp):
AAAAAAAAAAACCTAACCAAA
Found at i:2431930 original size:17 final size:17
Alignment explanation
Indices: 2431908--2431946 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
2431898 CCTAAAGGTG
*
2431908 ATTTTATT-TTCTTTATT
1 ATTTTATTCTTATTT-TT
2431925 ATTTTATTCTTATTTTT
1 ATTTTATTCTTATTTTT
2431942 ATTTT
1 ATTTT
2431947 TACTTTTACT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (17 bp):
ATTTTATTCTTATTTTT
Found at i:2432014 original size:12 final size:13
Alignment explanation
Indices: 2431997--2432047 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 13
2431987 ATATATACAT
2431997 TATAATAAAAA-A
1 TATAATAAAAATA
2432009 TATAATAAAAATA
1 TATAATAAAAATA
* *
2432022 TATATACAAAACAAA
1 TATA-ATAAAA-ATA
2432037 TATAA-AAAAAT
1 TATAATAAAAAT
2432048 TACATTTTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
12 12 0.36
13 9 0.27
14 6 0.18
15 6 0.18
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.25
Consensus pattern (13 bp):
TATAATAAAAATA
Found at i:2432019 original size:13 final size:13
Alignment explanation
Indices: 2431997--2432046 Score: 50
Period size: 13 Copynumber: 3.8 Consensus size: 13
2431987 ATATATACAT
2431997 TATAAT-AAAAAA
1 TATAATAAAAAAA
*
2432009 TATAATAAAAATA
1 TATAATAAAAAAA
*
2432022 TATATACAAAACAAA
1 TATA-ATAAAA-AAA
2432037 TATAA-AAAAA
1 TATAATAAAAA
2432047 TTACATTTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 7 0.22
13 13 0.41
14 6 0.19
15 6 0.19
ACGTcount: A:0.72, C:0.04, G:0.00, T:0.24
Consensus pattern (13 bp):
TATAATAAAAAAA
Found at i:2432230 original size:29 final size:29
Alignment explanation
Indices: 2432174--2432230 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2432164 CTCTTCTTTT
* *
2432174 TTTCATTTATTTTTCGTATTTACCTTAGA
1 TTTCATTTATTTTGCGTATTTAACTTAGA
*
2432203 TTTCATATTATTTTGC-TATTTAATTTAG
1 TTTCAT-TTATTTTGCGTATTTAACTTAG
2432231 CTTTAAATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 16 0.67
30 8 0.33
ACGTcount: A:0.23, C:0.11, G:0.07, T:0.60
Consensus pattern (29 bp):
TTTCATTTATTTTGCGTATTTAACTTAGA
Found at i:2437596 original size:18 final size:18
Alignment explanation
Indices: 2437573--2437610 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
2437563 TATTTAAAAA
2437573 TATAAAT-TTTAGAATTTT
1 TATAAATATTT-GAATTTT
*
2437591 TATAAATATTTTAATTTT
1 TATAAATATTTGAATTTT
2437609 TA
1 TA
2437611 ATTTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TATAAATATTTGAATTTT
Found at i:2437619 original size:15 final size:15
Alignment explanation
Indices: 2437599--2437627 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
2437589 TTTATAAATA
2437599 TTTTAATTTTTAATT
1 TTTTAATTTTTAATT
2437614 TTTTAATTTTTAAT
1 TTTTAATTTTTAAT
2437628 ATTATTTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TTTTAATTTTTAATT
Found at i:2439726 original size:28 final size:31
Alignment explanation
Indices: 2439657--2439730 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 31
2439647 ACTGTATTAC
* *
2439657 TAGTCACTCAATTATTAGTATATTTCTTTTT
1 TAGTCACTTAACTATTAGTATATTTCTTTTT
* *
2439688 TAATCATTTAACTATTAGTA-A-TT-TTTTT
1 TAGTCACTTAACTATTAGTATATTTCTTTTT
2439716 TAGTCACTTAACTAT
1 TAGTCACTTAACTAT
2439731 GAAAAGTCAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
28 18 0.49
29 2 0.05
30 1 0.03
31 16 0.43
ACGTcount: A:0.30, C:0.12, G:0.05, T:0.53
Consensus pattern (31 bp):
TAGTCACTTAACTATTAGTATATTTCTTTTT
Found at i:2439932 original size:17 final size:18
Alignment explanation
Indices: 2439910--2439943 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2439900 TGTGTAATTT
*
2439910 AGTTTT-TTTTTTTTTGC
1 AGTTTTGTTTTTCTTTGC
2439927 AGTTTTGTTTTTCTTTG
1 AGTTTTGTTTTTCTTTG
2439944 TGATCCTTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.06, C:0.06, G:0.15, T:0.74
Consensus pattern (18 bp):
AGTTTTGTTTTTCTTTGC
Found at i:2447457 original size:152 final size:152
Alignment explanation
Indices: 2447181--2447483 Score: 552
Period size: 152 Copynumber: 2.0 Consensus size: 152
2447171 ATTCCTATTG
*
2447181 TTACTATTACAACTCACAATAGAGTTCACTGTTTTGTCTCGGCCTTTAAGTCGATAGTACTAACA
1 TTACTATTACAACTCACAATAGAGCTCACTGTTTTGTCTCGGCCTTTAAGTCGATAGTACTAACA
* * *
2447246 TTTCTTGTCCCTAGTGTTGACATTCTTTGAGCCTCCTTCGACTTATTGAACGCTTGCCTACGGAG
66 TTCCTTGTCCCTAGTGTTAACATTCTTTGAGCCTCCTTCAACTTATTGAACGCTTGCCTACGGAG
2447311 CACGTGGTCCTTTCTGACCCTA
131 CACGTGGTCCTTTCTGACCCTA
2447333 TTACTATTACAACTCACAATAGAGCTCACTGTTTTGTCTCGGCCTTTAAGTCGATAGTACTAACA
1 TTACTATTACAACTCACAATAGAGCTCACTGTTTTGTCTCGGCCTTTAAGTCGATAGTACTAACA
*
2447398 TTCCTTGTCCCTAGTGTTAACATTCTTTGAGCCTCCTTCAACTTATTGAACGCTTGCCTATGGAG
66 TTCCTTGTCCCTAGTGTTAACATTCTTTGAGCCTCCTTCAACTTATTGAACGCTTGCCTACGGAG
*
2447463 CACGTGGTCTTTTCTGACCCT
131 CACGTGGTCCTTTCTGACCCT
2447484 GGGACTAACT
Statistics
Matches: 145, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
152 145 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (152 bp):
TTACTATTACAACTCACAATAGAGCTCACTGTTTTGTCTCGGCCTTTAAGTCGATAGTACTAACA
TTCCTTGTCCCTAGTGTTAACATTCTTTGAGCCTCCTTCAACTTATTGAACGCTTGCCTACGGAG
CACGTGGTCCTTTCTGACCCTA
Found at i:2450117 original size:19 final size:20
Alignment explanation
Indices: 2450083--2450121 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2450073 ATACATACAT
2450083 GTAAACAAAGAAGAAAAAAA
1 GTAAACAAAGAAGAAAAAAA
*
2450103 GTAAAGAAA-AAGAAAAAAA
1 GTAAACAAAGAAGAAAAAAA
2450122 AAAAAAGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.77, C:0.03, G:0.15, T:0.05
Consensus pattern (20 bp):
GTAAACAAAGAAGAAAAAAA
Found at i:2450132 original size:19 final size:22
Alignment explanation
Indices: 2450089--2450132 Score: 65
Period size: 20 Copynumber: 2.1 Consensus size: 22
2450079 ACATGTAAAC
*
2450089 AAAGAAGAAAAAAAGTAAAGAA
1 AAAGAAGAAAAAAAGAAAAGAA
2450111 AAAGAA-AAAAAAA-AAAAGAA
1 AAAGAAGAAAAAAAGAAAAGAA
2450131 AA
1 AA
2450133 CCGATTCGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 7 0.33
22 6 0.29
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAGAAGAAAAAAAGAAAAGAA
Found at i:2451919 original size:29 final size:28
Alignment explanation
Indices: 2451887--2451955 Score: 68
Period size: 29 Copynumber: 2.4 Consensus size: 28
2451877 GTAACGGGTG
** *
2451887 TATTATTTATTTATTAATGAAAATATTTT
1 TATTATTTATAAATTAAAGAAAA-ATTTT
*
2451916 TATT-TTTGATAAATTAAAGTAAAATTTT
1 TATTATTT-ATAAATTAAAGAAAAATTTT
*
2451944 TAATATTTATAA
1 TATTATTTATAA
2451956 CCTTAAATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (28 bp):
TATTATTTATAAATTAAAGAAAAATTTT
Found at i:2458485 original size:11 final size:11
Alignment explanation
Indices: 2458469--2458494 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
2458459 TTTCTTAAAA
2458469 TAATTTTTAAT
1 TAATTTTTAAT
2458480 TAATTTTTAAT
1 TAATTTTTAAT
2458491 TAAT
1 TAAT
2458495 GGTCATACTA
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:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TAATTTTTAAT
Found at i:2459238 original size:38 final size:38
Alignment explanation
Indices: 2459187--2459260 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
2459177 TTTATAATGT
2459187 ACAATTAAAGGGTTAGAATTCATGCACCCACATTAAGG
1 ACAATTAAAGGGTTAGAATTCATGCACCCACATTAAGG
*
2459225 ACAATTAAAGGGTTAGAATTCATGCATCCACATTAA
1 ACAATTAAAGGGTTAGAATTCATGCACCCACATTAA
2459261 AGATATATTC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.26
Consensus pattern (38 bp):
ACAATTAAAGGGTTAGAATTCATGCACCCACATTAAGG
Found at i:2463335 original size:5 final size:5
Alignment explanation
Indices: 2463325--2463354 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
2463315 TGAATAATAG
2463325 AATTA AATTA AATTA AATTA AATT- AATTA A
1 AATTA AATTA AATTA AATTA AATTA AATTA A
2463355 TTCATATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AATTA
Found at i:2463345 original size:15 final size:14
Alignment explanation
Indices: 2463308--2463354 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
2463298 TATTATAAGC
*
2463308 ATTAAATTGAA-TA
1 ATTAAATTAAATTA
2463321 A-TAGAATTAAATTAA
1 ATTA-AATTAAATT-A
2463336 ATTAAATTAAATTA
1 ATTAAATTAAATTA
2463350 ATTAA
1 ATTAA
2463355 TTCATATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
12 2 0.07
13 7 0.24
14 7 0.24
15 11 0.38
16 2 0.07
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.38
Consensus pattern (14 bp):
ATTAAATTAAATTA
Found at i:2465904 original size:25 final size:24
Alignment explanation
Indices: 2465876--2465933 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
2465866 GATTTTATGT
*
2465876 AATTTTATACATAGAATTTTAATTG
1 AATTTAATA-ATAGAATTTTAATTG
*
2465901 AATTTAATATTAGAATTTTAATTG
1 AATTTAATAATAGAATTTTAATTG
*
2465925 GATTTAATA
1 AATTTAATA
2465934 TTCACAAATC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 22 0.73
25 8 0.27
ACGTcount: A:0.41, C:0.02, G:0.09, T:0.48
Consensus pattern (24 bp):
AATTTAATAATAGAATTTTAATTG
Found at i:2465931 original size:24 final size:24
Alignment explanation
Indices: 2465887--2465935 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
2465877 ATTTTATACA
2465887 TAGAATTTTAATTGAATTTAATAT
1 TAGAATTTTAATTGAATTTAATAT
*
2465911 TAGAATTTTAATTGGATTTAATAT
1 TAGAATTTTAATTGAATTTAATAT
2465935 T
1 T
2465936 CACAAATCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (24 bp):
TAGAATTTTAATTGAATTTAATAT
Found at i:2466675 original size:16 final size:16
Alignment explanation
Indices: 2466646--2466685 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
2466636 TTCCAAAAAT
2466646 TAAAAATA-ATAATAA
1 TAAAAATATATAATAA
2466661 -AATAAATATATAATAA
1 TAA-AAATATATAATAA
2466677 TAAAAATAT
1 TAAAAATAT
2466686 TACATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
14 2 0.09
15 5 0.23
16 13 0.59
17 2 0.09
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAAAATATATAATAA
Found at i:2466680 original size:14 final size:13
Alignment explanation
Indices: 2466648--2466702 Score: 51
Period size: 13 Copynumber: 4.3 Consensus size: 13
2466638 CCAAAAATTA
2466648 AAAAT-AATA-AT
1 AAAATAAATATAT
2466659 AAAATAAATATAT
1 AAAATAAATATAT
*
2466672 AATAATAAAAATAT
1 AA-AATAAATATAT
* * *
2466686 TACATAAATATCT
1 AAAATAAATATAT
2466699 AAAA
1 AAAA
2466703 CACTCATAAG
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
11 5 0.15
12 4 0.12
13 14 0.41
14 11 0.32
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (13 bp):
AAAATAAATATAT
Found at i:2466692 original size:16 final size:15
Alignment explanation
Indices: 2466646--2466692 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 15
2466636 TTCCAAAAAT
*
2466646 TAAAAATAATAATAA
1 TAAAAATATTAATAA
2466661 -AATAAATATATAATAA
1 TAA-AAATAT-TAATAA
2466677 TAAAAATATTACATAA
1 TAAAAATATTA-ATAA
2466693 ATATCTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
14 2 0.07
15 7 0.26
16 16 0.59
17 2 0.07
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (15 bp):
TAAAAATATTAATAA
Found at i:2469119 original size:46 final size:46
Alignment explanation
Indices: 2469064--2469244 Score: 233
Period size: 46 Copynumber: 3.9 Consensus size: 46
2469054 TAGGATGGTT
2469064 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * *
2469110 GAGCGTCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
2469156 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
2469203 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2469245 GCGGGTTACA
Statistics
Matches: 116, Mismatches: 12, Indels: 14
0.82 0.08 0.10
Matches are distributed among these distances:
43 4 0.03
45 2 0.02
46 71 0.61
47 33 0.28
48 2 0.02
50 4 0.03
ACGTcount: A:0.21, C:0.22, G:0.30, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:2469225 original size:93 final size:93
Alignment explanation
Indices: 2469066--2469236 Score: 315
Period size: 93 Copynumber: 1.8 Consensus size: 93
2469056 GGATGGTTGA
* *
2469066 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2469131 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
*
2469159 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
2469224 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
2469237 ACTTATGGGC
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.20, C:0.22, G:0.30, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2472236 original size:15 final size:15
Alignment explanation
Indices: 2472197--2472275 Score: 83
Period size: 15 Copynumber: 5.4 Consensus size: 15
2472187 GTATCTTGGG
*
2472197 TTTCTTTATCCTGGA
1 TTTCTTTATTCTGGA
*
2472212 TCTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
2472227 TTTCTTTATTC-GGG
1 TTTCTTTATTCTGGA
*
2472241 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
*
2472256 TTTCTTTATTC-GGT
1 TTTCTTTATTCTGGA
2472270 TTTCTT
1 TTTCTT
2472276 GTTATCTTTG
Statistics
Matches: 53, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
13 2 0.04
14 17 0.32
15 32 0.60
16 2 0.04
ACGTcount: A:0.10, C:0.18, G:0.14, T:0.58
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:2472260 original size:29 final size:29
Alignment explanation
Indices: 2472188--2472274 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
2472178 CATAGTATCG
* * * *
2472188 TATCTTGGGTTTCTTTATCCTGGATCTCTT
1 TATCTTGGATTTCTTTATTC-GGATTTCTC
*
2472218 TAT-TCTGGATTTCTTTATTCGGGTTTCTC
1 TATCT-TGGATTTCTTTATTCGGATTTCTC
*
2472247 TATCTTGGATTTCTTTATTCGGTTTTCT
1 TATCTTGGATTTCTTTATTCGGATTTCT
2472275 TGTTATCTTT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
29 32 0.65
30 17 0.35
ACGTcount: A:0.10, C:0.17, G:0.16, T:0.56
Consensus pattern (29 bp):
TATCTTGGATTTCTTTATTCGGATTTCTC
Found at i:2474709 original size:46 final size:46
Alignment explanation
Indices: 2474654--2474834 Score: 224
Period size: 46 Copynumber: 3.9 Consensus size: 46
2474644 TAGGATGGTT
2474654 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* * * *
2474700 GAGCGTCCGAACTCGTTAAGTTGAGTCCGAGTTC-GTGA--GATGTAAC
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATG---C
*
2474746 TAGGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
1 GA-GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
* ** *
2474793 GAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
2474835 GCGGGTTACA
Statistics
Matches: 114, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
43 4 0.04
45 2 0.02
46 70 0.61
47 32 0.28
48 2 0.02
50 4 0.04
ACGTcount: A:0.22, C:0.22, G:0.29, T:0.28
Consensus pattern (46 bp):
GAGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGC
Found at i:2474815 original size:93 final size:93
Alignment explanation
Indices: 2474656--2474826 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
2474646 GGATGGTTGA
* *
2474656 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCGTCCGAACTCGTTAAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTAAGT
2474721 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* *
2474749 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTAAGT
2474814 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
2474827 ACTTATGGGC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.27
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCGTTAAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:2480051 original size:10 final size:10
Alignment explanation
Indices: 2480015--2480057 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
2480005 ACTTATTAAC
2480015 AAATTGATTTT
1 AAATT-ATTTT
*
2480026 AAATTATAAGTT
1 AAATTAT--TTT
2480038 AAATTATTTT
1 AAATTATTTT
2480048 AAATTATTTT
1 AAATTATTTT
2480058 GTAATTTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 14 0.50
11 5 0.18
12 9 0.32
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (10 bp):
AAATTATTTT
Found at i:2481032 original size:3 final size:3
Alignment explanation
Indices: 2481024--2481053 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2481014 TTATGCTTTA
2481024 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2481054 TATCATCCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:2483202 original size:222 final size:222
Alignment explanation
Indices: 2482816--2483494 Score: 990
Period size: 222 Copynumber: 3.1 Consensus size: 222
2482806 ACCTTACTGA
* * * *
2482816 ATTTCCAGAATTCATTAAAAGACAAGACAAGTTGGGTT--CTCTAGATCTTTCTAACAACCATAT
1 ATTTCCAGAGTTCATCAAAACACAAGACAAGTT-GGTTGACT-TAGATCTTTCTAACAATCATAT
* * * * * *
2482879 CCATGGTTTTGTGCCCAACTGGTTGTGGAAGAGCAATCTTTCATTGGTAGACCTTTCTTTTAATA
64 CCATGGTGTTGTGCCTAATTGGTTGTGGAAGAGCACTCTTTCATGGGTAGACCTTTCTTTCAATA
2482944 TGATTGATTTTCCAAAACAGCTTCCCTTAAGTGATGCAAACTTCTCTTTCCTAATGTTAAAAGAA
129 TGATTGATTTTCCAAAACAGCTTCCCTTAAGTGATGCAAACTTCTCTTTCCTAATGTTAAAAGAA
*
2483009 TTATATTTGGCCTCATGTAACATAGGTTC
194 TTATATTTGGCCTCATGTAACATAAGTTC
2483038 ATTTCCAGAGTTCATCAAAACACAAGACAAGTTGGTTGACTTAGATCTTTCTAACAATCATATCC
1 ATTTCCAGAGTTCATCAAAACACAAGACAAGTTGGTTGACTTAGATCTTTCTAACAATCATATCC
2483103 ATGGTGTTGTGCCTAATTGGTTGTGGAAGAGCACTCTTTCATGGGTAGACCTTTCTTTCAATATG
66 ATGGTGTTGTGCCTAATTGGTTGTGGAAGAGCACTCTTTCATGGGTAGACCTTTCTTTCAATATG
* * * *
2483168 ATTGATTTTCCAAAACAGCTTCCCTTAAGTGATGCTAACTTCTCTTTCCCATTGTTGAAAA-CAT
131 ATTGATTTTCCAAAACAGCTTCCCTTAAGTGATGCAAACTTCTCTTTCCTAATGTT-AAAAGAAT
*
2483232 TATATTTGGCCTCATGTAACATAAGTTT
195 TATATTTGGCCTCATGTAACATAAGTTC
2483260 ATTTCCAGAGTTCATCAAAACACAAGACAAGTTGGTTGACTTAGATCTTTCTAACAATCATATCC
1 ATTTCCAGAGTTCATCAAAACACAAGACAAGTTGGTTGACTTAGATCTTTCTAACAATCATATCC
* * * *
2483325 ATGGCGTTGTGCCTAATTGGTTGTGGAAGAGCAGC-CTTTCAAGGGTAAACCTTTCTTTCAATGT
66 ATGGTGTTGTGCCTAATTGGTTGTGGAAGAGCA-CTCTTTCATGGGTAGACCTTTCTTTCAATAT
** * * **
2483389 GATTGATTTTCCAAAACAGCTTCCCTTAAGTGATTTAAACTTCTCTTT-TTCAATGTTGAGGGAA
130 GATTGATTTTCCAAAACAGCTTCCCTTAAGTGATGCAAACTTCTCTTTCCT-AATGTTAAAAGAA
* * ** * *
2483453 TTGTATCTGGATTCTTGTAACATAAGCTC
194 TTATATTTGGCCTCATGTAACATAAGTTC
2483482 ATTTCCAGAGTTC
1 ATTTCCAGAGTTC
2483495 TTAAAGAGTC
Statistics
Matches: 414, Mismatches: 37, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
221 5 0.01
222 402 0.97
223 7 0.02
ACGTcount: A:0.28, C:0.19, G:0.17, T:0.36
Consensus pattern (222 bp):
ATTTCCAGAGTTCATCAAAACACAAGACAAGTTGGTTGACTTAGATCTTTCTAACAATCATATCC
ATGGTGTTGTGCCTAATTGGTTGTGGAAGAGCACTCTTTCATGGGTAGACCTTTCTTTCAATATG
ATTGATTTTCCAAAACAGCTTCCCTTAAGTGATGCAAACTTCTCTTTCCTAATGTTAAAAGAATT
ATATTTGGCCTCATGTAACATAAGTTC
Found at i:2483790 original size:72 final size:71
Alignment explanation
Indices: 2483674--2483878 Score: 295
Period size: 72 Copynumber: 2.8 Consensus size: 71
2483664 GCTCTTTCTA
* * *
2483674 TTTCGAAGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGGTTATGCAATATGAGTCAAC
1 TTTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTT-GGCAATATGAGTCAAC
*
2483739 -TTAGCGC
65 TTTA-CAC
* * *
2483746 TTTCTATGCATCTTATAACAATTTCAATGGCCCAATTCCAAATTGCTTGGACAATATGAGTCAAC
1 TTTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTGG-CAATATGAGTCAAC
2483811 TTTACAC
65 TTTACAC
*
2483818 TTTCGATGCATTTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTGGGCAATATGAGT
1 TTTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTT-GGCAATATGAGT
2483879 GCTATGAGTT
Statistics
Matches: 119, Mismatches: 11, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
71 1 0.01
72 113 0.95
73 5 0.04
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (71 bp):
TTTCGATGCATCTTATAACAATTTGAGTGGCCCAATTCCAAATTGCTTGGCAATATGAGTCAACT
TTACAC
Found at i:2486000 original size:20 final size:20
Alignment explanation
Indices: 2485972--2486011 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
2485962 CTGAAGAGTA
2485972 AGGAATTTTCTGCATCTCTT
1 AGGAATTTTCTGCATCTCTT
*
2485992 AGGACTTTTCTGCATCTCTT
1 AGGAATTTTCTGCATCTCTT
2486012 CCTTCTCCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.17, C:0.23, G:0.15, T:0.45
Consensus pattern (20 bp):
AGGAATTTTCTGCATCTCTT
Found at i:2488309 original size:31 final size:31
Alignment explanation
Indices: 2488271--2488332 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
2488261 TCCTTGAGAG
2488271 TTAACTTTGTTCCATTGCTACTCACCAAGCT
1 TTAACTTTGTTCCATTGCTACTCACCAAGCT
*
2488302 TTAACTTTGTTCCATTGTTACTCACCAAGCT
1 TTAACTTTGTTCCATTGCTACTCACCAAGCT
2488333 AACATCTCCC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.27, G:0.10, T:0.40
Consensus pattern (31 bp):
TTAACTTTGTTCCATTGCTACTCACCAAGCT
Found at i:2493488 original size:53 final size:53
Alignment explanation
Indices: 2493347--2493497 Score: 214
Period size: 53 Copynumber: 2.8 Consensus size: 53
2493337 ACAAGTGTGC
* **
2493347 CCGTTTAAGACCATAGCTGGGCTATGGCATCGGTGCAATGTGATAATGTGACT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
*
2493400 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGATT
1 CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
* *
2493453 CCGTATAAGACCAT-GTCTGGGATATGGCTTCGGTATGATATGTGA
1 CCGTATAAGACCATAG-CTGGGCTATGGCATCGGTAT-A-ATGTGA
2493498 ACCGTGTAAG
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
52 1 0.01
53 81 0.91
54 1 0.01
55 6 0.07
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (53 bp):
CCGTATAAGACCATAGCTGGGCTATGGCATCGGTATAATGTGATAATGTGACT
Found at i:2496250 original size:42 final size:43
Alignment explanation
Indices: 2496140--2496337 Score: 260
Period size: 43 Copynumber: 4.6 Consensus size: 43
2496130 GTGGAAAAAG
* * * *
2496140 CGCCACTAAAAGACGTGACTTTTAGCGGCGCTTTTACCACAAA
1 CGCCGCTAAAAGCCGTGACTTTTAGCGACGCTTTTCCCACAAA
*
2496183 CGCCGCTAAAAGCCGTGACTTTTAGCGACGCTTTTCCTACAAA
1 CGCCGCTAAAAGCCGTGACTTTTAGCGACGCTTTTCCCACAAA
*
2496226 TGCCGCT-AAAGCCGTGACTTTTAGCGACGCTTTTCCCACAAA
1 CGCCGCTAAAAGCCGTGACTTTTAGCGACGCTTTTCCCACAAA
* *
2496268 CGCCGCTAAAAGTCAC-AG-CTTTTAGC-AGTGCTTTTCCCACAAA
1 CGCCGCTAAAAG-C-CGTGACTTTTAGCGA-CGCTTTTCCCACAAA
*
2496311 TGCCGCTAAAAGCCGTGACTTTTAGCG
1 CGCCGCTAAAAGCCGTGACTTTTAGCG
2496338 GAGTTTTTTT
Statistics
Matches: 136, Mismatches: 12, Indels: 13
0.84 0.07 0.08
Matches are distributed among these distances:
41 1 0.01
42 43 0.32
43 89 0.65
44 2 0.01
45 1 0.01
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (43 bp):
CGCCGCTAAAAGCCGTGACTTTTAGCGACGCTTTTCCCACAAA
Found at i:2496265 original size:85 final size:86
Alignment explanation
Indices: 2496145--2496337 Score: 277
Period size: 85 Copynumber: 2.3 Consensus size: 86
2496135 AAAAGCGCCA
* * *
2496145 CTAAAAGACGTGACTTTTAGCGGCGCTTTTACCACAAACGCCGCTAAAAG-C-CGTGACTTTTAG
1 CTAAAAGCCGTGACTTTTAGCGACGCTTTTACCACAAACGCCGCTAAAAGTCAC-AG-CTTTTAG
*
2496208 C-GACGCTTTTCCTACAAATGCCG
64 CAG-CGCTTTTCCCACAAATGCCG
*
2496231 CT-AAAGCCGTGACTTTTAGCGACGCTTTTCCCACAAACGCCGCTAAAAGTCACAGCTTTTAGCA
1 CTAAAAGCCGTGACTTTTAGCGACGCTTTTACCACAAACGCCGCTAAAAGTCACAGCTTTTAGCA
*
2496295 GTGCTTTTCCCACAAATGCCG
66 GCGCTTTTCCCACAAATGCCG
2496316 CTAAAAGCCGTGACTTTTAGCG
1 CTAAAAGCCGTGACTTTTAGCG
2496338 GAGTTTTTTT
Statistics
Matches: 97, Mismatches: 6, Indels: 8
0.87 0.05 0.07
Matches are distributed among these distances:
85 72 0.74
86 24 0.25
87 1 0.01
ACGTcount: A:0.26, C:0.28, G:0.19, T:0.26
Consensus pattern (86 bp):
CTAAAAGCCGTGACTTTTAGCGACGCTTTTACCACAAACGCCGCTAAAAGTCACAGCTTTTAGCA
GCGCTTTTCCCACAAATGCCG
Found at i:2499985 original size:25 final size:24
Alignment explanation
Indices: 2499939--2499987 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
2499929 AAATACAAAA
*
2499939 TAAAAAAAAAATTATTATAATTTT
1 TAAAAAAAAAATTATTAGAATTTT
2499963 TAAAAAATATAAATT-TTAGAATTTT
1 TAAAAAA-A-AAATTATTAGAATTTT
2499988 ATGAATATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 7 0.32
25 10 0.45
26 5 0.23
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (24 bp):
TAAAAAAAAAATTATTAGAATTTT
Found at i:2500030 original size:21 final size:22
Alignment explanation
Indices: 2500000--2500048 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
2499990 GAATATTTGA
* *
2500000 ATTTTAAAAAATATTTTGAATT
1 ATTTTGAAAAATATTTTAAATT
*
2500022 -TTTTGAAAATTATTTTAAATT
1 ATTTTGAAAAATATTTTAAATT
2500043 ATTTTG
1 ATTTTG
2500049 TAATTTTTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (22 bp):
ATTTTGAAAAATATTTTAAATT
Found at i:2510151 original size:21 final size:22
Alignment explanation
Indices: 2510128--2510169 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
2510118 ATAATAAATA
2510128 TTTTATAGTATA-AAATATGAAT
1 TTTTA-AGTATATAAATATGAAT
*
2510150 TTTTAATTATATAAATATGA
1 TTTTAAGTATATAAATATGA
2510170 GTATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTTTAAGTATATAAATATGAAT
Found at i:2510176 original size:22 final size:21
Alignment explanation
Indices: 2510136--2510176 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
2510126 TATTTTATAG
*
2510136 TATAAAATATGAATTTTTAAT
1 TATAAAATATGAATATTTAAT
*
2510157 TATATAAATATGAGTATTTA
1 TATA-AAATATGAATATTTA
2510177 TTTAAATTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.46
Consensus pattern (21 bp):
TATAAAATATGAATATTTAAT
Found at i:2510378 original size:2 final size:2
Alignment explanation
Indices: 2510371--2510402 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2510361 TTTGTAACAA
*
2510371 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2510403 TGTTTCATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:2510443 original size:14 final size:14
Alignment explanation
Indices: 2510424--2510459 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
2510414 GAAAAACATT
*
2510424 AAGAAAATGATTTC
1 AAGAAAATGACTTC
2510438 AAGAAAATGACTTC
1 AAGAAAATGACTTC
*
2510452 ATGAAAAT
1 AAGAAAAT
2510460 TTGTCAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.53, C:0.08, G:0.14, T:0.25
Consensus pattern (14 bp):
AAGAAAATGACTTC
Found at i:2511031 original size:9 final size:9
Alignment explanation
Indices: 2511017--2511048 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
2511007 CCATGCCAGT
2511017 CACCTGCTC
1 CACCTGCTC
2511026 CACCTGCTC
1 CACCTGCTC
2511035 CACC-GC-C
1 CACCTGCTC
2511042 CACCTGC
1 CACCTGC
2511049 CTGCAAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
7 5 0.23
8 4 0.18
9 13 0.59
ACGTcount: A:0.12, C:0.59, G:0.12, T:0.16
Consensus pattern (9 bp):
CACCTGCTC
Found at i:2512012 original size:3 final size:3
Alignment explanation
Indices: 2512004--2512657 Score: 208
Period size: 3 Copynumber: 217.0 Consensus size: 3
2511994 TAATTAAATA
* * *
2512004 TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT T-T TGT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
2512051 TAC TAT TAT AAT TA- TAT T-T TAT TTT TGT GT-T TATT TACT TAC TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA-T TA-T TAT TAT
* * * *
2512096 T-T TGT TAT TAAT TCAT TAA T-T TAT TAT TAT TAA CA- TAT TAT TAT
1 TAT TAT TAT T-AT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * *
2512140 TCT TAAT GTAT TAT CAT TAC TAT TAT TTT TAT TTT TAT TAC TAT TAT
1 TAT T-AT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * *
2512187 CAT TGT T-T AAAT TAT TGT AAC TAT TAT TAT TAT TAT TAC TAC TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * *
2512232 TAT TATT TGT TAT T-T AAT ATAT TAT AAT TAT TA- TAT TTT TAT TAC
1 TAT TA-T TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * ** *
2512277 TAC TAC TAC GGT TAT TAT TAT TAT TA- TCT TAT T-T TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * * * *
2512323 CAT TTT TGT AAT TAC TAT TAC TAT T-G TAT TAT GAC TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** *
2512369 T-T TCAT ATAT GT-T TAT T-T TCC TAT TAT TCAT CTAT T-T ATATT TCT
1 TAT T-AT -TAT -TAT TAT TAT TAT TAT TAT T-AT -TAT TAT -TA-T TAT
* *
2512414 TAT GTAT T-T ATAT T-T TCAT TAT TAT TAT ATCT TAGG TAT TA- TAT
1 TAT -TAT TAT -TAT TAT T-AT TAT TAT TAT -TAT TA-T TAT TAT TAT
* * * * **
2512458 CTA- TATT TAGG TAT TAA TAT CAT TAT T-T TAC TAT GGT TA- TATT TAT
1 -TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT
*
2512504 CAT GCTAT 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
* * * * * *
2512551 TAT TAT TAT TAT TAT TAC TAT TAG CAC TAT TTT TAT TAC TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
2512598 AAT ATAT TAT TTT TAT TAC TAC CAT TAC TAT TAT TAT TA- TAT TGT
1 TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
2512643 TAT TAT TAC TAT TAT
1 TAT TAT TAT TAT TAT
2512658 ATTGTTGTAT
Statistics
Matches: 471, Mismatches: 130, Indels: 100
0.67 0.19 0.14
Matches are distributed among these distances:
2 41 0.09
3 374 0.79
4 50 0.11
5 6 0.01
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:2512441 original size:17 final size:18
Alignment explanation
Indices: 2512401--2512443 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
2512391 ATTATTCATC
2512401 TATTTATA-TTTCTTATG
1 TATTTATATTTTCTTATG
2512418 TATTTATATTTTCATTAT-
1 TATTTATATTTTC-TTATG
2512436 TA-TTATAT
1 TATTTATAT
2512444 CTTAGGTATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 14 0.58
18 6 0.25
19 4 0.17
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (18 bp):
TATTTATATTTTCTTATG
Found at i:2512469 original size:19 final size:21
Alignment explanation
Indices: 2512431--2512478 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
2512421 TTATATTTTC
*
2512431 ATTATTAT-TATATCTTAGGT
1 ATTAATATCTATATCTTAGGT
2512451 ATT-ATATCTATAT-TTAGGT
1 ATTAATATCTATATCTTAGGT
2512470 ATTAATATC
1 ATTAATATC
2512479 ATTATTTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 12 0.48
20 13 0.52
ACGTcount: A:0.33, C:0.06, G:0.08, T:0.52
Consensus pattern (21 bp):
ATTAATATCTATATCTTAGGT
Found at i:2521471 original size:14 final size:14
Alignment explanation
Indices: 2521452--2521484 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
2521442 TAAAAAAGGA
2521452 TGGCTCCTTGACAG
1 TGGCTCCTTGACAG
2521466 TGGCTCCTTGACAG
1 TGGCTCCTTGACAG
2521480 TGGCT
1 TGGCT
2521485 GCACCAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.27, G:0.30, T:0.30
Consensus pattern (14 bp):
TGGCTCCTTGACAG
Done.