Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019168470.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_7, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 26282861
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 74000 characters in sequence are not A, C, G, or T
File 95 of 133
Found at i:18505293 original size:8 final size:8
Alignment explanation
Indices: 18505262--18505328 Score: 53
Period size: 8 Copynumber: 8.4 Consensus size: 8
18505252 TATATATATA
*
18505262 TGTATGTA
1 TGTATGTG
* *
18505270 TGGATGTA
1 TGTATGTG
18505278 TGTATGTG
1 TGTATGTG
18505286 TGTATGTG
1 TGTATGTG
*
18505294 TGTGTGTG
1 TGTATGTG
*
18505302 TGTGTGTG
1 TGTATGTG
* **
18505310 CGCGTGTG
1 TGTATGTG
*
18505318 TGTGTGTG
1 TGTATGTG
18505326 TGT
1 TGT
18505329 GTGGATTTGA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
8 51 1.00
ACGTcount: A:0.09, C:0.03, G:0.42, T:0.46
Consensus pattern (8 bp):
TGTATGTG
Found at i:18505295 original size:2 final size:2
Alignment explanation
Indices: 18505282--18505331 Score: 73
Period size: 2 Copynumber: 25.0 Consensus size: 2
18505272 GATGTATGTA
* * *
18505282 TG TG TG TA TG TG TG TG TG TG TG TG TG TG CG CG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
18505324 TG TG TG TG
1 TG TG TG TG
18505332 GATTTGATAT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.02, C:0.04, G:0.48, T:0.46
Consensus pattern (2 bp):
TG
Found at i:18506975 original size:22 final size:22
Alignment explanation
Indices: 18506950--18507004 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
18506940 AAATCTATTA
18506950 GTAATTCATTGATATTTTGTCG
1 GTAATTCATTGATATTTTGTCG
* * *
18506972 GTAATCCATCGATATTTTGTTG
1 GTAATTCATTGATATTTTGTCG
18506994 GT-ATTCCATTG
1 GTAATT-CATTG
18507005 GTAATTCATC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
21 2 0.07
22 25 0.93
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.47
Consensus pattern (22 bp):
GTAATTCATTGATATTTTGTCG
Found at i:18507046 original size:20 final size:20
Alignment explanation
Indices: 18507009--18507071 Score: 99
Period size: 20 Copynumber: 3.1 Consensus size: 20
18506999 CCATTGGTAA
*
18507009 TTCATCGATAATATCTGAAAT
1 TTCATCAATAATA-CTGAAAT
*
18507030 TTCATCAGTAATACTGAAAT
1 TTCATCAATAATACTGAAAT
18507050 TTCATCAATAATACTGAAAT
1 TTCATCAATAATACTGAAAT
18507070 TT
1 TT
18507072 TGTTGCTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
20 28 0.72
21 11 0.28
ACGTcount: A:0.40, C:0.14, G:0.08, T:0.38
Consensus pattern (20 bp):
TTCATCAATAATACTGAAAT
Found at i:18507141 original size:19 final size:19
Alignment explanation
Indices: 18507117--18507162 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
18507107 TAATTCTATA
18507117 TATAATTATTCAAAAAAAC
1 TATAATTATTCAAAAAAAC
* * *
18507136 TATAATTATTTAAGAAACC
1 TATAATTATTCAAAAAAAC
18507155 TATAATTA
1 TATAATTA
18507163 ACAATTAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.52, C:0.09, G:0.02, T:0.37
Consensus pattern (19 bp):
TATAATTATTCAAAAAAAC
Found at i:18507285 original size:20 final size:20
Alignment explanation
Indices: 18507257--18507299 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
18507247 ATAAAATTAT
*
18507257 CATCTATAAAACATCAATAA
1 CATCCATAAAACATCAATAA
*
18507277 CATCCATAAAACATCCATAA
1 CATCCATAAAACATCAATAA
18507297 CAT
1 CAT
18507300 GCATCAAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (20 bp):
CATCCATAAAACATCAATAA
Found at i:18508320 original size:102 final size:102
Alignment explanation
Indices: 18508069--18508320 Score: 333
Period size: 102 Copynumber: 2.5 Consensus size: 102
18508059 ATTACTAGTT
* * * * * *
18508069 ATCGTAATATACTATTAAGATAGTTCATCAACAATTATAATATACAACCATCATTACAATGCAAA
1 ATCGCAATATACTATAAAGATAGTTAATCAACAATCACAATATACAACCATCATCACAATGCAAA
18508134 ACACACAATAGTTTTCACATTTCACAAATGTAATCTC
66 ACACACAATAGTTTTCACATTTCACAAATGTAATCTC
* * * * * ** *
18508171 ATTGCAATATACTATAAAGATAGTTGATTAACAATCACAACACACAACCATTGTCACAATTCAAA
1 ATCGCAATATACTATAAAGATAGTTAATCAACAATCACAATATACAACCATCATCACAATGCAAA
* *
18508236 ATACACAATAGTTTTCACATTTCACAAATGTGATCTC
66 ACACACAATAGTTTTCACATTTCACAAATGTAATCTC
* * *
18508273 ATCGCAATATACTACAAAGATAGTTAAGCAATAATCACAATATACAAC
1 ATCGCAATATACTATAAAGATAGTTAATCAACAATCACAATATACAAC
18508321 TAGAATCACA
Statistics
Matches: 127, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
102 127 1.00
ACGTcount: A:0.44, C:0.20, G:0.07, T:0.29
Consensus pattern (102 bp):
ATCGCAATATACTATAAAGATAGTTAATCAACAATCACAATATACAACCATCATCACAATGCAAA
ACACACAATAGTTTTCACATTTCACAAATGTAATCTC
Found at i:18514505 original size:20 final size:18
Alignment explanation
Indices: 18514482--18514533 Score: 56
Period size: 18 Copynumber: 2.9 Consensus size: 18
18514472 AAAGAAACCT
18514482 AACAAATCTAAAAAATACTC
1 AACAAATCTAAAAAA-A-TC
18514502 AACAAA--TAAAAAAATC
1 AACAAATCTAAAAAAATC
18514518 AAC-AATACTAAAAAAA
1 AACAAAT-CTAAAAAAA
18514534 AAAACAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
15 2 0.07
16 5 0.17
17 1 0.03
18 15 0.52
20 6 0.21
ACGTcount: A:0.69, C:0.15, G:0.00, T:0.15
Consensus pattern (18 bp):
AACAAATCTAAAAAAATC
Found at i:18514519 original size:16 final size:19
Alignment explanation
Indices: 18514489--18514533 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
18514479 CCTAACAAAT
18514489 CTAAAAAATACTCAACAA-A
1 CTAAAAAA-ACTCAACAATA
18514508 -TAAAAAAA-TCAACAATA
1 CTAAAAAAACTCAACAATA
18514525 CTAAAAAAA
1 CTAAAAAAA
18514534 AAAACAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 7 0.29
17 2 0.08
18 15 0.62
ACGTcount: A:0.69, C:0.16, G:0.00, T:0.16
Consensus pattern (19 bp):
CTAAAAAAACTCAACAATA
Found at i:18514531 original size:19 final size:18
Alignment explanation
Indices: 18514482--18514534 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 18
18514472 AAAGAAACCT
*
18514482 AACAAATCTAAAAAATACTC
1 AACAAA-CTAAAAAA-AATC
18514502 AACAAA-T-AAAAAAATC
1 AACAAACTAAAAAAAATC
18514518 AACAATACTAAAAAAAA
1 AACAA-ACTAAAAAAAA
18514535 AAACAAAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
16 8 0.28
17 6 0.21
18 2 0.07
19 7 0.24
20 6 0.21
ACGTcount: A:0.70, C:0.15, G:0.00, T:0.15
Consensus pattern (18 bp):
AACAAACTAAAAAAAATC
Found at i:18514545 original size:30 final size:30
Alignment explanation
Indices: 18514509--18514566 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
18514499 CTCAACAAAT
18514509 AAAAAAATCAACAATACTAAAAAAAAAAAC
1 AAAAAAATCAACAATACTAAAAAAAAAAAC
* * *
18514539 AAAAAAATTAACAATACTCAACAAAAAA
1 AAAAAAATCAACAATACTAAAAAAAAAA
18514567 TCCAACAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.74, C:0.14, G:0.00, T:0.12
Consensus pattern (30 bp):
AAAAAAATCAACAATACTAAAAAAAAAAAC
Found at i:18514665 original size:25 final size:24
Alignment explanation
Indices: 18514619--18514666 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
18514609 ACAAATCTAT
* *
18514619 AACAAAAAACTAAATAATAAACTC
1 AACAAAAAACTAAACAAGAAACTC
*
18514643 AACAAAAATACTAACCAAGAAACT
1 AACAAAAA-ACTAAACAAGAAACT
18514667 TGAAAAAGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 8 0.40
25 12 0.60
ACGTcount: A:0.65, C:0.19, G:0.02, T:0.15
Consensus pattern (24 bp):
AACAAAAAACTAAACAAGAAACTC
Found at i:18517531 original size:53 final size:53
Alignment explanation
Indices: 18517462--18517597 Score: 191
Period size: 53 Copynumber: 2.6 Consensus size: 53
18517452 TTTTGAAGAA
* * * ** *
18517462 TTTAAGGAAAAATTGATAATTCAACTTTTTCCTAAATATTTTTAAATTTTTAT
1 TTTAAGAAAAAATTGATATTTCAACTTTTTCATAAATATTTCCAAAATTTTAT
*
18517515 TTTATGAAAAAATTGATATTTCAACTTTTTCATAAATATTTCCAAAATTTTAT
1 TTTAAGAAAAAATTGATATTTCAACTTTTTCATAAATATTTCCAAAATTTTAT
* *
18517568 TTTAAGGAAAAATTAATATTTCAACTTTTT
1 TTTAAGAAAAAATTGATATTTCAACTTTTT
18517598 TCTTAGCATT
Statistics
Matches: 73, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 73 1.00
ACGTcount: A:0.39, C:0.08, G:0.05, T:0.48
Consensus pattern (53 bp):
TTTAAGAAAAAATTGATATTTCAACTTTTTCATAAATATTTCCAAAATTTTAT
Found at i:18517620 original size:53 final size:53
Alignment explanation
Indices: 18517462--18517622 Score: 177
Period size: 53 Copynumber: 3.0 Consensus size: 53
18517452 TTTTGAAGAA
* * *
18517462 TTTAAGGAAAAATTGATAATTCAAC-TTTTTCCTAAATATTTT-TAAATTTTTAT
1 TTTAAGGAAAAATTGATATTTCAACTTTTTTCTTAAAT-TTTTCCAAA-TTTTAT
* * * *
18517515 TTTATGAAAAAATTGATATTTCAAC-TTTTTCATAAATATTTCCAAAATTTTAT
1 TTTAAGGAAAAATTGATATTTCAACTTTTTTCTTAAATTTTTCC-AAATTTTAT
* *
18517568 TTTAAGGAAAAATTAATATTTCAACTTTTTTCTTAGCATTTTTCCAAA-TTTAT
1 TTTAAGGAAAAATTGATATTTCAACTTTTTTCTTA-AATTTTTCCAAATTTTAT
18517621 TT
1 TT
18517623 AATTTTTTTA
Statistics
Matches: 92, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
52 3 0.03
53 68 0.74
54 14 0.15
55 7 0.08
ACGTcount: A:0.37, C:0.09, G:0.05, T:0.49
Consensus pattern (53 bp):
TTTAAGGAAAAATTGATATTTCAACTTTTTTCTTAAATTTTTCCAAATTTTAT
Found at i:18517697 original size:22 final size:25
Alignment explanation
Indices: 18517653--18517698 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
18517643 TAGAAAAATA
*
18517653 AAATAAAAATATATATAAGAAGTAG
1 AAATAAAAATACATATAAGAAGTAG
18517678 AAATAAAAAT-CATA-AA-AAGTA
1 AAATAAAAATACATATAAGAAGTA
18517699 TAAAAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 5 0.25
23 2 0.10
24 3 0.15
25 10 0.50
ACGTcount: A:0.67, C:0.02, G:0.09, T:0.22
Consensus pattern (25 bp):
AAATAAAAATACATATAAGAAGTAG
Found at i:18518774 original size:6 final size:6
Alignment explanation
Indices: 18518731--18518788 Score: 50
Period size: 6 Copynumber: 9.8 Consensus size: 6
18518721 CTATTTGACT
* * *
18518731 ATTTTG ATTTT- ATTATTA TTTTTA CTTTTA ATTGTTA ATTTTA A-TTTA
1 ATTTTA ATTTTA ATT-TTA ATTTTA ATTTTA ATT-TTA ATTTTA ATTTTA
18518779 A-TTTA ATTTT
1 ATTTTA ATTTT
18518789 TAATGATTAT
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
5 13 0.29
6 24 0.53
7 8 0.18
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (6 bp):
ATTTTA
Found at i:18519336 original size:32 final size:33
Alignment explanation
Indices: 18519149--18519469 Score: 242
Period size: 32 Copynumber: 9.8 Consensus size: 33
18519139 CCTAATTTTG
* * * * *
18519149 AAAAACTCTTCTAACCAAAGGCAATGAGACATT
1 AAAAACTCCTCTAACCAGAGGCTATGACACTTT
* *
18519182 -AAAACTCCTCTAACCAGAGGTTATGTCACTTTT
1 AAAAACTCCTCTAACCAGAGGCTATGACAC-TTT
* *
18519215 AAAAACTCCTCTAACTAGAGGCTATGGCACTTT
1 AAAAACTCCTCTAACCAGAGGCTATGACACTTT
* * * * * *
18519248 AGAAACTCTTTTTACCA-AAGCCAT-AGCACTTT
1 AAAAACTCCTCTAACCAGAGGCTATGA-CACTTT
* *** *
18519280 AAAAAATCCTCTAATTTGATGCTATGACACTTT
1 AAAAACTCCTCTAACCAGAGGCTATGACACTTT
* *
18519313 AAAAACTCCT-TAACCAAAGGCTATGGCACTTT
1 AAAAACTCCTCTAACCAGAGGCTATGACACTTT
* * * *
18519345 AGAAACTCTTCTAACAAGAGGCCAT-AGCA-TTT
1 AAAAACTCCTCTAACCAGAGGCTATGA-CACTTT
* * *
18519377 AAAAACTCCTATAACTAGAGGCCATGACA-TTT
1 AAAAACTCCTCTAACCAGAGGCTATGACACTTT
* * *
18519409 CAAAAACTCCTTTAACTAGAGGCTATGGCACTTT
1 -AAAAACTCCTCTAACCAGAGGCTATGACACTTT
* *
18519443 CAAAAAATCCTCTAACTAGAGGCTATG
1 -AAAAACTCCTCTAACCAGAGGCTATG
18519470 GTACCTGTTT
Statistics
Matches: 228, Mismatches: 50, Indels: 19
0.77 0.17 0.06
Matches are distributed among these distances:
32 96 0.42
33 77 0.34
34 55 0.24
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (33 bp):
AAAAACTCCTCTAACCAGAGGCTATGACACTTT
Found at i:18519342 original size:65 final size:65
Alignment explanation
Indices: 18519182--18519470 Score: 226
Period size: 65 Copynumber: 4.4 Consensus size: 65
18519172 ATGAGACATT
* * * * *
18519182 AAAACTCCTCTAACCAGAGGTTATGTCACTTTTAAAAACTCCTCTAACTAGAGGCTATGGCACTT
1 AAAACTCCT-TAACCAAAGGCTATGGCAC-TTTAAAAAATCCTCTAACTAGAGGCTATGACACTT
18519247 TA
64 TA
* * * * * * * *
18519249 GAAACTCTTTTTACCAAA-GCCATAGCACTTTAAAAAATCCTCTAATTTGATGCTATGACACTTT
1 AAAACTC-CTTAACCAAAGGCTATGGCACTTTAAAAAATCCTCTAACTAGAGGCTATGACACTTT
18519313 A
65 A
* * * * *
18519314 AAAACTCCTTAACCAAAGGCTATGGCACTTTAGAAACTCTTCTAACAAGAGGCCAT-AGCA-TTT
1 AAAACTCCTTAACCAAAGGCTATGGCACTTTAAAAAATCCTCTAACTAGAGGCTATGA-CACTTT
18519377 A
65 A
* * * * * * *
18519378 AAAACTCCTATAACTAGAGGCCATGACA-TTTCAAAAACTCCTTTAACTAGAGGCTATGGCACTT
1 AAAACTCCT-TAACCAAAGGCTATGGCACTTT-AAAAAATCCTCTAACTAGAGGCTATGACACTT
18519442 TCA
64 T-A
* * *
18519445 AAAAATCCTCTAACTAGAGGCTATGG
1 AAAACTCCT-TAACCAAAGGCTATGG
18519471 TACCTGTTTT
Statistics
Matches: 174, Mismatches: 40, Indels: 16
0.76 0.17 0.07
Matches are distributed among these distances:
64 25 0.14
65 104 0.60
66 9 0.05
67 35 0.20
68 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (65 bp):
AAAACTCCTTAACCAAAGGCTATGGCACTTTAAAAAATCCTCTAACTAGAGGCTATGACACTTTA
Found at i:18519378 original size:97 final size:98
Alignment explanation
Indices: 18519151--18519465 Score: 320
Period size: 97 Copynumber: 3.2 Consensus size: 98
18519141 TAATTTTGAA
* * * * * * *
18519151 AAACTCTTCTAACCAA-AGGCAATGAG-ACATT-AAAACTCCTCTAACCAGAGGTTATGTCACTT
1 AAACTCTTCTAA-CAAGAGGCCAT-AGCACTTTAAAAAATCCTATAACTAGAGGCTATGACAC-T
18519213 TTAAAAACTCCTCTAACTAGAGGCTATGGCACTTTAG
63 TTAAAAACTCCT-TAACTAGAGGCTATGGCACTTTAG
* * * * * *
18519250 AAACTCTTTTTACCAA-A-GCCATAGCACTTTAAAAAATCCTCTAATTTGATGCTATGACACTTT
1 AAACTC-TTCTAACAAGAGGCCATAGCACTTTAAAAAATCCTATAACTAGAGGCTATGACACTTT
* *
18519313 AAAAACTCCTTAACCAAAGGCTATGGCACTTTAG
65 AAAAACTCCTTAACTAGAGGCTATGGCACTTTAG
* *
18519347 AAACTCTTCTAACAAGAGGCCATAGCA-TTTAAAAACTCCTATAACTAGAGGCCATGACA-TTTC
1 AAACTCTTCTAACAAGAGGCCATAGCACTTTAAAAAATCCTATAACTAGAGGCTATGACACTTT-
*
18519410 AAAAACTCCTTTAACTAGAGGCTATGGCACTTTCAA
65 AAAAACTCC-TTAACTAGAGGCTATGGCACTTT-AG
* * *
18519446 AAAATCCTCTAACTAGAGGC
1 AAACTCTTCTAACAAGAGGC
18519466 TATGGTACCT
Statistics
Matches: 181, Mismatches: 27, Indels: 16
0.81 0.12 0.07
Matches are distributed among these distances:
96 10 0.06
97 66 0.36
98 51 0.28
99 50 0.28
100 4 0.02
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (98 bp):
AAACTCTTCTAACAAGAGGCCATAGCACTTTAAAAAATCCTATAACTAGAGGCTATGACACTTTA
AAAACTCCTTAACTAGAGGCTATGGCACTTTAG
Found at i:18519656 original size:33 final size:33
Alignment explanation
Indices: 18519618--18519723 Score: 90
Period size: 33 Copynumber: 3.2 Consensus size: 33
18519608 TCCTTTGTGT
* * *
18519618 AGAGGCTTTTAAATTTTAAAAACTTTTCTAACC
1 AGAGGCTTTAAAACTTTAAAAACTTTTCTAAAC
* * * * **
18519651 AGAGGCTATGAGACTTTAAAAACTCCTT-TAATT
1 AGAGGCTTTAAAACTTTAAAAACT-TTTCTAAAC
18519684 AGAGGCTTTAAAACTTTAAAATA-TTTCTCTAAAC
1 AGAGGCTTTAAAACTTTAAAA-ACTTT-TCTAAAC
18519718 AGAGGC
1 AGAGGC
18519724 AATGGTGTTT
Statistics
Matches: 56, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
32 1 0.02
33 43 0.77
34 12 0.21
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.34
Consensus pattern (33 bp):
AGAGGCTTTAAAACTTTAAAAACTTTTCTAAAC
Found at i:18519754 original size:67 final size:66
Alignment explanation
Indices: 18519617--18519755 Score: 147
Period size: 67 Copynumber: 2.1 Consensus size: 66
18519607 ATCCTTTGTG
* * * * *
18519617 TAGAGGCTTTTAAATTTTAAAAACTTTTCTAACCAGAGGCTATGAGACTTTAAAAACTCCTTTAA
1 TAGAGGCTTTAAAACTTTAAAAACTTTTCTAAACAGAGGCAATGAGACTTTAAAAACTCCTCTAA
*
18519682 T
66 C
** * *
18519683 TAGAGGCTTTAAAACTTTAAAATA-TTTCTCTAAACAGAGGCAATG-GTGTTTTAAAGATTCCTC
1 TAGAGGCTTTAAAACTTTAAAA-ACTTT-TCTAAACAGAGGCAATGAG-ACTTTAAAAACTCCTC
18519746 TAAC
63 TAAC
18519750 TAGAGG
1 TAGAGG
18519756 TGATATGTTT
Statistics
Matches: 60, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
66 24 0.40
67 36 0.60
ACGTcount: A:0.36, C:0.14, G:0.15, T:0.35
Consensus pattern (66 bp):
TAGAGGCTTTAAAACTTTAAAAACTTTTCTAAACAGAGGCAATGAGACTTTAAAAACTCCTCTAA
C
Found at i:18519809 original size:33 final size:33
Alignment explanation
Indices: 18519767--18520044 Score: 197
Period size: 33 Copynumber: 8.5 Consensus size: 33
18519757 GATATGTTTA
* * *
18519767 AAAGATTCCTTTAATCAGAGGTCATGAGATTTG
1 AAAGATTCCTCTAATCAAAGGTAATGAGATTTG
* *
18519800 -GAGTATTCCTCTAATCAAAGGTAATGGGATTTG
1 AAAG-ATTCCTCTAATCAAAGGTAATGAGATTTG
* *
18519833 AAAGATTCTTCTAA-CTAAAGGTAATGGGATTTG
1 AAAGATTCCTCTAATC-AAAGGTAATGAGATTTG
* * * * *
18519866 AAAGATTCTTTTAATCAAAGGTCACGAAATTT-
1 AAAGATTCCTCTAATCAAAGGTAATGAGATTTG
* * * * * *
18519898 AGAGTTTTTCTCAAACCAGAGGTAATGAGATTTG
1 AAAG-ATTCCTCTAATCAAAGGTAATGAGATTTG
* **
18519932 AAAGATTCCTCTAAT-TAAGGCCATGAGATTTG
1 AAAGATTCCTCTAATCAAAGGTAATGAGATTTG
* * * *
18519964 -GAGTATTCCTCTAACCAAAGGTAATGGGATTTT
1 AAAG-ATTCCTCTAATCAAAGGTAATGAGATTTG
*** * *
18519997 AAAGATTCCTCTAATTGGAGGAAATGGGATTTG
1 AAAGATTCCTCTAATCAAAGGTAATGAGATTTG
* *
18520030 AAAAATTCTTCTAAT
1 AAAGATTCCTCTAAT
18520045 AAGTCAAATT
Statistics
Matches: 188, Mismatches: 48, Indels: 18
0.74 0.19 0.07
Matches are distributed among these distances:
31 2 0.01
32 29 0.15
33 149 0.79
34 8 0.04
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (33 bp):
AAAGATTCCTCTAATCAAAGGTAATGAGATTTG
Found at i:18519879 original size:99 final size:98
Alignment explanation
Indices: 18519735--18519945 Score: 260
Period size: 99 Copynumber: 2.1 Consensus size: 98
18519725 ATGGTGTTTT
* * * * * * *
18519735 AAAGATTCCTCTAACTAGAGGTGATATGTTTAAAAGATTCCTTTAATCAGAGGTCATGAGATTTG
1 AAAGATTCCTCTAACTAAAGGTAATAGGTTTAAAAGATTCCTTTAATCAAAGGTCACGAAATTTA
* * *
18519800 GAGTATTCCTCTAATCAAAGGTAATGGGATTTG
66 GAGTATTCCTCAAACCAAAGGTAATGAGATTTG
* * * *
18519833 AAAGATTCTTCTAACTAAAGGTAATGGGATTTGAAAGATTCTTTTAATCAAAGGTCACGAAATTT
1 AAAGATTCCTCTAACTAAAGGTAATAGG-TTTAAAAGATTCCTTTAATCAAAGGTCACGAAATTT
* * *
18519898 AGAGTTTTTCTCAAACCAGAGGTAATGAGATTTG
65 AGAGTATTCCTCAAACCAAAGGTAATGAGATTTG
18519932 AAAGATTCCTCTAA
1 AAAGATTCCTCTAA
18519946 TTAAGGCCAT
Statistics
Matches: 94, Mismatches: 18, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
98 23 0.24
99 71 0.76
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (98 bp):
AAAGATTCCTCTAACTAAAGGTAATAGGTTTAAAAGATTCCTTTAATCAAAGGTCACGAAATTTA
GAGTATTCCTCAAACCAAAGGTAATGAGATTTG
Found at i:18519995 original size:65 final size:65
Alignment explanation
Indices: 18519837--18520012 Score: 208
Period size: 65 Copynumber: 2.7 Consensus size: 65
18519827 GATTTGAAAG
* * * * * *
18519837 ATTCTTCTAACTAAAGGTAATGGGATTTGAAAGATTCTTTTAATCAAAGGTCACGAAATTTAGAG
1 ATTCCTCTAACCAAAGGTAATGGGATTTGAAAGATTCCTCTAAT-TAAGGCCACGAAATTTAGAG
18519902 T
65 T
* * * * * * * *
18519903 TTTTCTCAAACCAGAGGTAATGAGATTTGAAAGATTCCTCTAATTAAGGCCATGAGATTTGGAGT
1 ATTCCTCTAACCAAAGGTAATGGGATTTGAAAGATTCCTCTAATTAAGGCCACGAAATTTAGAGT
*
18519968 ATTCCTCTAACCAAAGGTAATGGGATTTTAAAGATTCCTCTAATT
1 ATTCCTCTAACCAAAGGTAATGGGATTTGAAAGATTCCTCTAATT
18520013 GGAGGAAATG
Statistics
Matches: 90, Mismatches: 20, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
65 55 0.61
66 35 0.39
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (65 bp):
ATTCCTCTAACCAAAGGTAATGGGATTTGAAAGATTCCTCTAATTAAGGCCACGAAATTTAGAGT
Found at i:18520186 original size:33 final size:32
Alignment explanation
Indices: 18520091--18520186 Score: 111
Period size: 33 Copynumber: 2.9 Consensus size: 32
18520081 AGGATTCCTT
* * *
18520091 TAACAAAAGGTGATGAGATTTGAAAGATTTCTC
1 TAACCAAAGGTAATGATATTTGAAAGA-TTCTC
* *
18520124 TAACCAAAGGTTATTATATTTGAAAGATTCATC
1 TAACCAAAGGTAATGATATTTGAAAGATTC-TC
* *
18520157 TAACCAGAGGTAATGGTATTTGAAAGATTC
1 TAACCAAAGGTAATGATATTTGAAAGATTC
18520187 CTTTAATTAG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
32 3 0.06
33 51 0.94
ACGTcount: A:0.39, C:0.10, G:0.19, T:0.32
Consensus pattern (32 bp):
TAACCAAAGGTAATGATATTTGAAAGATTCTC
Found at i:18523656 original size:14 final size:14
Alignment explanation
Indices: 18523637--18523672 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
18523627 CCAATAACTA
18523637 AACTAAAAAAAAAG
1 AACTAAAAAAAAAG
**
18523651 AACTAAAAACTAAG
1 AACTAAAAAAAAAG
18523665 AACTAAAA
1 AACTAAAA
18523673 GAGAGAAAAA
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:0.72, C:0.11, G:0.06, T:0.11
Consensus pattern (14 bp):
AACTAAAAAAAAAG
Found at i:18529957 original size:28 final size:27
Alignment explanation
Indices: 18529898--18529957 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 27
18529888 TGGTTTACCC
*
18529898 CTTAGTTTACATAGTTTAGGATAGTTG
1 CTTAGTTTACATAGTTTAGGATAGTAG
18529925 CTTAGTTTACATAGCTTTAGGATAGATAG
1 CTTAGTTTACATAG-TTTAGGATAG-TAG
18529954 -TTAG
1 CTTAG
18529958 ACATAGCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
27 14 0.47
28 14 0.47
29 2 0.07
ACGTcount: A:0.28, C:0.08, G:0.22, T:0.42
Consensus pattern (27 bp):
CTTAGTTTACATAGTTTAGGATAGTAG
Found at i:18532438 original size:27 final size:27
Alignment explanation
Indices: 18532408--18532474 Score: 98
Period size: 27 Copynumber: 2.5 Consensus size: 27
18532398 CTATTTAATA
*
18532408 AATTATTTAAATTTAATATGTTTAGAT
1 AATTATTTAAATTGAATATGTTTAGAT
** *
18532435 AATTACGTAAATTGAATATGTTTGGAT
1 AATTATTTAAATTGAATATGTTTAGAT
18532462 AATTATTTAAATT
1 AATTATTTAAATT
18532475 CAAATCAAAA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.40, C:0.01, G:0.10, T:0.48
Consensus pattern (27 bp):
AATTATTTAAATTGAATATGTTTAGAT
Found at i:18534554 original size:3 final size:3
Alignment explanation
Indices: 18534546--18534582 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
18534536 AGTTCAATCA
18534546 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
18534583 TGGTGTTTTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:18537937 original size:129 final size:129
Alignment explanation
Indices: 18537707--18537950 Score: 319
Period size: 129 Copynumber: 1.9 Consensus size: 129
18537697 CATTTAATGG
* * *
18537707 GAATGTGATCCATGGTAATTCCAAGATCCTTAAATTATTATTTAATCCATAAAACTTGAGTACAA
1 GAATGTGATCCATGGTAATTCCAAAATCCTTAAATTATTATTCAATCCATAAAACTTGAGCACAA
* ** * * * *
18537772 AAACTATCGGCTGCTACATATTCGACTTTGGTTGTGGATTGAGCAACATTGGTTTGCTTCTTAA
66 AAACTACCAACTACTACATATTCGACTTCGATTGTGGATTAAGCAACATTGGTTTGCTTCTTAA
* * * *
18537836 GAATGTGATCCATGGTAATTCCAAAATCCTTTAATTGTTGTTCAATCCATAAGACTTGAGCACAA
1 GAATGTGATCCATGGTAATTCCAAAATCCTTAAATTATTATTCAATCCATAAAACTTGAGCACAA
* * *
18537901 CAACTACCAATTACTACATATTC-ATCTTCGATTGTGGATTAATCAACATT
66 AAACTACCAACTACTACATATTCGA-CTTCGATTGTGGATTAAGCAACATT
18537951 ATTTTGTTTC
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
128 1 0.01
129 96 0.99
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (129 bp):
GAATGTGATCCATGGTAATTCCAAAATCCTTAAATTATTATTCAATCCATAAAACTTGAGCACAA
AAACTACCAACTACTACATATTCGACTTCGATTGTGGATTAAGCAACATTGGTTTGCTTCTTAA
Found at i:18543330 original size:21 final size:21
Alignment explanation
Indices: 18543306--18543366 Score: 72
Period size: 21 Copynumber: 2.9 Consensus size: 21
18543296 CACCTGATTG
18543306 ATCTTTTTATAGGGGTGATCA
1 ATCTTTTTATAGGGGTGATCA
* *
18543327 ATCTTCTCTAT-GGGGTGATCG
1 ATCTT-TTTATAGGGGTGATCA
18543348 ATCTTTTTTATA-GGGTGAT
1 ATC-TTTTTATAGGGGTGAT
18543367 ATATCCCTTC
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 28 0.82
22 6 0.18
ACGTcount: A:0.20, C:0.11, G:0.25, T:0.44
Consensus pattern (21 bp):
ATCTTTTTATAGGGGTGATCA
Found at i:18550898 original size:10 final size:10
Alignment explanation
Indices: 18550874--18550929 Score: 87
Period size: 10 Copynumber: 5.7 Consensus size: 10
18550864 GATTTAGTGA
*
18550874 TTAGTT-TAA
1 TTAGTTATAG
*
18550883 TTAGTTGTAG
1 TTAGTTATAG
18550893 TTAGTTATAG
1 TTAGTTATAG
18550903 TTAGTTATAG
1 TTAGTTATAG
18550913 TTAGTTATAG
1 TTAGTTATAG
18550923 TTAGTTA
1 TTAGTTA
18550930 ATTTGGTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
9 6 0.14
10 38 0.86
ACGTcount: A:0.29, C:0.00, G:0.20, T:0.52
Consensus pattern (10 bp):
TTAGTTATAG
Found at i:18558785 original size:16 final size:16
Alignment explanation
Indices: 18558764--18558806 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
18558754 AAATTTTAAC
*
18558764 TTTTTATTGTTATGAT
1 TTTTTATTGTTATGAA
* *
18558780 TTTTTATTATTATTAA
1 TTTTTATTGTTATGAA
*
18558796 TTTTAATTGTT
1 TTTTTATTGTT
18558807 TTATTTTTAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.07, T:0.70
Consensus pattern (16 bp):
TTTTTATTGTTATGAA
Found at i:18558813 original size:31 final size:31
Alignment explanation
Indices: 18558780--18558839 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
18558770 TTGTTATGAT
18558780 TTTTTATTATT-A-TTAATTTTAATTGTTTTA
1 TTTTTATT-TTAATTTAATTTTAATTGTTTTA
*
18558810 TTTTTATTTTAATTTAATTTTAGTT-TTTTA
1 TTTTTATTTTAATTTAATTTTAATTGTTTTA
18558840 GTGATTATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 2 0.07
30 14 0.52
31 11 0.41
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (31 bp):
TTTTTATTTTAATTTAATTTTAATTGTTTTA
Found at i:18570629 original size:12 final size:12
Alignment explanation
Indices: 18570612--18570640 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18570602 ATAACACATG
18570612 TATGGTGATGAA
1 TATGGTGATGAA
18570624 TATGGTGATGAA
1 TATGGTGATGAA
18570636 T-TGGT
1 TATGGT
18570641 CAACATAACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (12 bp):
TATGGTGATGAA
Found at i:18570843 original size:62 final size:62
Alignment explanation
Indices: 18570706--18570847 Score: 160
Period size: 62 Copynumber: 2.3 Consensus size: 62
18570696 GAATTTATTT
* * * * * *
18570706 TGAAATGGTTAGTGCTGAAAAGCCTGTGAATTATGGTATGGATCAATGGACGAAATTTGTTT
1 TGAAATGGTTAGTGCTAAAAAGCCTGTGAATTACGGCAAGGATCAATGGACGAAACTTGTTC
* * * * * *
18570768 TGGAATTGCTAGTGCTAAAAAGCCTGTGAATTACGGCCAAGTATCAATTGATGAAACTTGTTC
1 TGAAATGGTTAGTGCTAAAAAGCCTGTGAATTACGG-CAAGGATCAATGGACGAAACTTGTTC
18570831 T-AAATGGTTAGTGCTAA
1 TGAAATGGTTAGTGCTAA
18570848 GAAGTTGAAA
Statistics
Matches: 64, Mismatches: 15, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
62 44 0.69
63 20 0.31
ACGTcount: A:0.32, C:0.11, G:0.25, T:0.32
Consensus pattern (62 bp):
TGAAATGGTTAGTGCTAAAAAGCCTGTGAATTACGGCAAGGATCAATGGACGAAACTTGTTC
Found at i:18571245 original size:22 final size:22
Alignment explanation
Indices: 18571196--18571245 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
18571186 CAAGATTGTG
* *
18571196 AATTCTCAAATGAGAATCCTTG
1 AATTTTCAAATGAGAATCCTTA
* *
18571218 AGTTTTCAAATGAGAATCTTTA
1 AATTTTCAAATGAGAATCCTTA
18571240 AATTTT
1 AATTTT
18571246 TATGTTCTCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.40
Consensus pattern (22 bp):
AATTTTCAAATGAGAATCCTTA
Found at i:18571520 original size:31 final size:31
Alignment explanation
Indices: 18571477--18571556 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
18571467 AAATCTTGCA
* *
18571477 AATCTAAATTCTTGT-ATATCTAAAATTTTACG
1 AATC-AAATTCTTGTGA-AACTAAAATTTTAAG
*
18571509 AATCAAATTCTTGTGAAACTGAAATTTTAAG
1 AATCAAATTCTTGTGAAACTAAAATTTTAAG
18571540 AATCAAATT-TTAGTGAA
1 AATCAAATTCTT-GTGAA
18571557 GTCTTACGAA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 2 0.05
31 36 0.84
32 5 0.12
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (31 bp):
AATCAAATTCTTGTGAAACTAAAATTTTAAG
Found at i:18571724 original size:44 final size:44
Alignment explanation
Indices: 18571668--18572028 Score: 383
Period size: 44 Copynumber: 8.2 Consensus size: 44
18571658 AGAAGCCTTG
*
18571668 TTTA-TTTTTCAAAGTCGTTGAGCTTCTGCTTAGAAGAGCTTTA
1 TTTATTTTTTCAAAGTCGTTGAGCCTCTGCTTAGAAGAGCTTTA
* * *
18571711 TTTATTTTTTCAAAGCCGTTGAGCCTCTACTTAGAGGAG-TCTTA
1 TTTATTTTTTCAAAGTCGTTGAGCCTCTGCTTAGAAGAGCT-TTA
* * * * *
18571755 TTTAGTTTTTTCAAAGTCATTAAGCCTTTGC-TCGAAGGAGCCTTA
1 TTTA-TTTTTTCAAAGTCGTTGAGCCTCTGCTTAGAA-GAGCTTTA
* * * * *
18571800 TTTATTTTTCCAAGGTCGTTGAGCCTCTGATTAGAGGAGCTTTG
1 TTTATTTTTTCAAAGTCGTTGAGCCTCTGCTTAGAAGAGCTTTA
* *
18571844 TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTAAAAGAGCTTTA
1 TTTATTTTTTCAAAGTCGTTGAGCCTCTGCTTAGAAGAGCTTTA
* * * *
18571888 TTTA-TTTTTCTAAAGTCATTGGGCCTCTGTTTAAAAGAGCTTTA
1 TTTATTTTTTC-AAAGTCGTTGAGCCTCTGCTTAGAAGAGCTTTA
* * **
18571932 TTTATTTTTCCAAAGTTGTTGAGCCTCTATTTAGAAGAGCTTTA
1 TTTATTTTTTCAAAGTCGTTGAGCCTCTGCTTAGAAGAGCTTTA
* * *
18571976 TTTATTTTTT-AGAAGTCATTGAGCCTCTGTTTAG-AGAAGCCTTA
1 TTTATTTTTTCA-AAGTCGTTGAGCCTCTGCTTAGAAG-AGCTTTA
18572020 TTTATTTTT
1 TTTATTTTT
18572029 AAAAGTTGTG
Statistics
Matches: 267, Mismatches: 41, Indels: 19
0.82 0.13 0.06
Matches are distributed among these distances:
43 14 0.05
44 214 0.80
45 39 0.15
ACGTcount: A:0.24, C:0.15, G:0.18, T:0.44
Consensus pattern (44 bp):
TTTATTTTTTCAAAGTCGTTGAGCCTCTGCTTAGAAGAGCTTTA
Found at i:18571959 original size:132 final size:132
Alignment explanation
Indices: 18571661--18572028 Score: 426
Period size: 132 Copynumber: 2.8 Consensus size: 132
18571651 ATTGTTGAGA
* * *
18571661 AGCCTTGTTTATTTTT-CAAAGTCGTTGAGCTTCTGCTTAGAAGAGCTTTATTTATTTTTTCAAA
1 AGCCTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTATTTATTTTTTCAAA
* * * *
18571725 GCCGTTGAGCCTCT-ACTTAGAGGAG-TCTTATTTAGTTTTTTCAAAGTCATTAAGCCTTTGCTC
66 GTCGTTGAGCCTCTGA-TTAAAAGAGCT-TTATTTA-TTTTTTCAAAGTCATTAAGCCTCTGCTC
* *
18571788 GAAGG
128 AAAAG
* * *
18571793 AGCCTTATTTATTTTTCCAAGGTCGTTGAGCCTCTGATTAGAGGAGCTTTGTTTATTTTTTCAAA
1 AGCCTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTATTTATTTTTTCAAA
** * *
18571858 GTCGTTGAGCCTCTGATTAAAAGAGCTTTATTTA-TTTTTCTAAAGTCATTGGGCCTCTGTTTAA
66 GTCGTTGAGCCTCTGATTAAAAGAGCTTTATTTATTTTTTC-AAAGTCATTAAGCCTCTGCTCAA
18571922 AAG
130 AAG
* *
18571925 AGCTTTATTTATTTTTCCAAAGTTGTTGAGCCTCT-ATTTAGAAGAGCTTTATTTATTTTTT-AG
1 AGCCTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGA-TTAGAAGAGCTTTATTTATTTTTTCA-
* * * *
18571988 AAGTCATTGAGCCTCTG-TTTAGAGAAGCCTTATTTATTTTT
64 AAGTCGTTGAGCCTCTGATTAAAAG-AGCTTTATTTATTTTT
18572029 AAAAGTTGTG
Statistics
Matches: 203, Mismatches: 25, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
131 13 0.06
132 114 0.56
133 74 0.36
134 2 0.01
ACGTcount: A:0.23, C:0.15, G:0.18, T:0.44
Consensus pattern (132 bp):
AGCCTTATTTATTTTTCCAAAGTCGTTGAGCCTCTGATTAGAAGAGCTTTATTTATTTTTTCAAA
GTCGTTGAGCCTCTGATTAAAAGAGCTTTATTTATTTTTTCAAAGTCATTAAGCCTCTGCTCAAA
AG
Found at i:18572047 original size:43 final size:44
Alignment explanation
Indices: 18571668--18572071 Score: 254
Period size: 44 Copynumber: 9.2 Consensus size: 44
18571658 AGAAGCCTTG
* * * *
18571668 TTTATTTTTCAAAGTCGTTGAGCTTCTGCTTAGA-AGAGCTTTA
1 TTTATTTTTAAAAGTTGTTGAGCCTCTGTTTAGAGAGAGCTTTA
* ** **
18571711 TTTATTTTTTCAAAGCCGTTGAGCCTCTACTTAGAG-GAG-TCTTA
1 TTTA-TTTTTAAAAGTTGTTGAGCCTCTGTTTAGAGAGAGCT-TTA
* ** * * * * *
18571755 TTTAGTTTTTTCAAAGTCATTAAGCCTTTG-CTCGA-AGGAGCCTTA
1 TTTA--TTTTTAAAAGTTGTTGAGCCTCTGTTTAGAGA-GAGCTTTA
* * * * *
18571800 TTTATTTTTCCAAGGTCGTTGAGCCTCTGATTAGAG-GAGCTTTG
1 TTTATTTTT-AAAAGTTGTTGAGCCTCTGTTTAGAGAGAGCTTTA
* * * *
18571844 TTTATTTTTTCAAAGTCGTTGAGCCTCTGATTA-AAAGAGCTTTA
1 TTTA-TTTTTAAAAGTTGTTGAGCCTCTGTTTAGAGAGAGCTTTA
* ** * *
18571888 TTTATTTTTCTAAAGTCATTGGGCCTCTGTTTA-AAAGAGCTTTA
1 TTTATTTTT-AAAAGTTGTTGAGCCTCTGTTTAGAGAGAGCTTTA
* *
18571932 TTTATTTTTCCAAAGTTGTTGAGCCTCTATTTAGA-AGAGCTTTA
1 TTTATTTTT-AAAAGTTGTTGAGCCTCTGTTTAGAGAGAGCTTTA
* ** *
18571976 TTTATTTTTTAGAAGTCATTGAGCCTCTGTTTAGAGA-AGCCTTA
1 TTTA-TTTTTAAAAGTTGTTGAGCCTCTGTTTAGAGAGAGCTTTA
* ** *
18572020 TTTATTTTTAAAAGTTGTGGAATCTCTGTTTAGAG-GAGTTTTTA
1 TTTATTTTTAAAAGTTGTTGAGCCTCTGTTTAGAGAGAG-CTTTA
18572064 TGTTATTT
1 T-TTATTT
18572072 AAGGAGTTTG
Statistics
Matches: 297, Mismatches: 45, Indels: 36
0.79 0.12 0.10
Matches are distributed among these distances:
43 43 0.14
44 203 0.68
45 51 0.17
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (44 bp):
TTTATTTTTAAAAGTTGTTGAGCCTCTGTTTAGAGAGAGCTTTA
Found at i:18572064 original size:132 final size:129
Alignment explanation
Indices: 18571668--18572071 Score: 374
Period size: 132 Copynumber: 3.1 Consensus size: 129
18571658 AGAAGCCTTG
* * *
18571668 TTTATTTTT-CAAAGTCGTTGAGCTTCTGCTTAGAAGAGCTTTATTTATTTTTTCAAAGCCGTTG
1 TTTATTTTTCCAAAGTCGTTGAGCCTCT-ATTAGAAGAGCTTTATTTATTTTTTCAAAGTCGTTG
* * * * * *
18571732 AGCCTCT-ACTTAGAGGAGTCTTATTTAGTTTTTTCAAAGTCATT--AAGCCTTTG-CTCGAAGG
65 AGCCTCTGA-TTAGAGAAGCCTTATTTA--TTTTTAAAAGT--TTGGAA-CCTCTGTTTAG-AGG
*
18571793 AGCCTTA
123 AGCTTTA
* * *
18571800 TTTATTTTTCCAAGGTCGTTGAGCCTCTGATTAGAGGAGCTTTGTTTATTTTTTCAAAGTCGTTG
1 TTTATTTTTCCAAAGTCGTTGAGCCTCT-ATTAGAAGAGCTTTATTTATTTTTTCAAAGTCGTTG
* * * * * *
18571865 AGCCTCTGATTA-AAAGAGCTTTATTTATTTTTCTAAAGTCATTGG-GCCTCTGTTTAAAAGAGC
65 AGCCTCTGATTAGAGA-AGCCTTATTTATTTTT-AAAAGT--TTGGAACCTCTGTTTAGAGGAGC
18571928 TTTA
126 TTTA
* *
18571932 TTTATTTTTCCAAAGTTGTTGAGCCTCTATTTAGAAGAGCTTTATTTATTTTTT-AGAAGTCATT
1 TTTATTTTTCCAAAGTCGTTGAGCCTCTA-TTAGAAGAGCTTTATTTATTTTTTCA-AAGTCGTT
* * *
18571996 GAGCCTCTGTTTAGAGAAGCCTTATTTATTTTTAAAAGTTGTGGAATCTCTGTTTAGAGGAGTTT
64 GAGCCTCTGATTAGAGAAGCCTTATTTATTTTTAAAAGTT-TGGAACCTCTGTTTAGAGGAG-CT
18572061 TTA
127 TTA
18572064 TGTTATTT
1 T-TTATTT
18572072 AAGGAGTTTG
Statistics
Matches: 226, Mismatches: 32, Indels: 27
0.79 0.11 0.09
Matches are distributed among these distances:
129 1 0.00
130 3 0.01
131 25 0.11
132 119 0.53
133 77 0.34
134 1 0.00
ACGTcount: A:0.24, C:0.14, G:0.18, T:0.44
Consensus pattern (129 bp):
TTTATTTTTCCAAAGTCGTTGAGCCTCTATTAGAAGAGCTTTATTTATTTTTTCAAAGTCGTTGA
GCCTCTGATTAGAGAAGCCTTATTTATTTTTAAAAGTTTGGAACCTCTGTTTAGAGGAGCTTTA
Found at i:18572572 original size:12 final size:12
Alignment explanation
Indices: 18572555--18572583 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
18572545 ATTGATTGAA
18572555 TTTTCAGTAAAC
1 TTTTCAGTAAAC
18572567 TTTTCAGTAAAC
1 TTTTCAGTAAAC
18572579 TTTTC
1 TTTTC
18572584 GATATCGGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.48
Consensus pattern (12 bp):
TTTTCAGTAAAC
Found at i:18573291 original size:22 final size:22
Alignment explanation
Indices: 18573258--18573307 Score: 59
Period size: 21 Copynumber: 2.3 Consensus size: 22
18573248 ATTTTCAAAC
*
18573258 AAAAAA-ACAAAAAAATA-AGAT
1 AAAAAATA-AAAAAAATATAAAT
*
18573279 AAAAAATAAAAAAAATTTAAAT
1 AAAAAATAAAAAAAATATAAAT
18573301 AAAAAAT
1 AAAAAAT
18573308 TTGAAATTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 14 0.56
22 11 0.44
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.16
Consensus pattern (22 bp):
AAAAAATAAAAAAAATATAAAT
Found at i:18577333 original size:39 final size:39
Alignment explanation
Indices: 18577261--18577336 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 39
18577251 GTTAATTGAG
* *
18577261 GAGTTTGCATATAGTATACTAGGCGTTCGATGAAATGAA
1 GAGTTTGCATATAGTATACTAGACGTTCAATGAAATGAA
18577300 GAGTTTGCATATAGTATACTA-ACTGTTCAATGAAATG
1 GAGTTTGCATATAGTATACTAGAC-GTTCAATGAAATG
18577337 CCTCAATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.34, C:0.11, G:0.22, T:0.33
Consensus pattern (39 bp):
GAGTTTGCATATAGTATACTAGACGTTCAATGAAATGAA
Found at i:18587529 original size:25 final size:25
Alignment explanation
Indices: 18587493--18587540 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
18587483 TCCAATGATG
* *
18587493 AAATTCTTAGAAATTTC-AAATGGT
1 AAATTCTAAGAAATCTCTAAATGGT
18587517 AAATTCCTAAGAAATCTCTAAATG
1 AAATT-CTAAGAAATCTCTAAATG
18587541 AGAAACTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 5 0.25
25 10 0.50
26 5 0.25
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.33
Consensus pattern (25 bp):
AAATTCTAAGAAATCTCTAAATGGT
Found at i:18591757 original size:17 final size:17
Alignment explanation
Indices: 18591728--18591776 Score: 55
Period size: 17 Copynumber: 2.8 Consensus size: 17
18591718 TGGATGGGAC
*
18591728 AAAAAA-GAAAAAAAAG
1 AAAAAATGAAAAAAGAG
*
18591744 AGAAAAATGGAAAAATGAG
1 A-AAAAAT-GAAAAAAGAG
18591763 AAAAAATGAAAAAA
1 AAAAAATGAAAAAA
18591777 AATGAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 1 0.04
17 11 0.41
18 6 0.22
19 9 0.33
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (17 bp):
AAAAAATGAAAAAAGAG
Found at i:18591757 original size:18 final size:18
Alignment explanation
Indices: 18591728--18591786 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
18591718 TGGATGGGAC
*
18591728 AAAAAAGAAAAAAAAGAG
1 AAAAATGAAAAAAAAGAG
* *
18591746 AAAAATG-GAAAAATGAG
1 AAAAATGAAAAAAAAGAG
18591763 AAAAAATGAAAAAAAATGAG
1 -AAAAATGAAAAAAAA-GAG
18591783 AAAA
1 AAAA
18591787 GAAAAACTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
17 8 0.24
18 13 0.39
19 9 0.27
20 3 0.09
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.07
Consensus pattern (18 bp):
AAAAATGAAAAAAAAGAG
Found at i:18591790 original size:17 final size:17
Alignment explanation
Indices: 18591730--18591792 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 17
18591720 GATGGGACAA
18591730 AAAAGAAAAAAAA-GAG
1 AAAAGAAAAAAAATGAG
**
18591746 AAAA-ATGGAAAAATGAG
1 AAAAGA-AAAAAAATGAG
18591763 AAAAAATGAAAAAAAATGAG
1 --AAAA-GAAAAAAAATGAG
18591783 AAAAGAAAAA
1 AAAAGAAAAA
18591793 CTCAAATTGA
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
15 1 0.03
16 9 0.24
17 9 0.24
18 4 0.11
19 4 0.11
20 9 0.24
21 1 0.03
ACGTcount: A:0.76, C:0.00, G:0.17, T:0.06
Consensus pattern (17 bp):
AAAAGAAAAAAAATGAG
Found at i:18593023 original size:46 final size:46
Alignment explanation
Indices: 18592934--18593069 Score: 220
Period size: 47 Copynumber: 2.9 Consensus size: 46
18592924 ATTGTGAATC
*
18592934 TTCAAATGAGAATCTTTGAGTTTTCAAATGAAAATCTTTAAGACATT
1 TTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATCTTTAAGAC-TT
* *
18592981 TTCAAATGAGAACCTTTAAGTTTT-AAATGAGAATCTTTAAGACTT
1 TTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATCTTTAAGACTT
18593026 TTCAAATGAGAATCTTTGAGTTTTTCAAATGAGAATCTTTAAGA
1 TTCAAATGAGAATCTTTGAG-TTTTCAAATGAGAATCTTTAAGA
18593070 AGAACTCAAA
Statistics
Matches: 82, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
45 20 0.24
46 22 0.27
47 40 0.49
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (46 bp):
TTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATCTTTAAGACTT
Found at i:18593051 original size:68 final size:67
Alignment explanation
Indices: 18592937--18593068 Score: 185
Period size: 68 Copynumber: 1.9 Consensus size: 67
18592927 GTGAATCTTC
*
18592937 AAATGAGAATCTTTGAGTTTTCAAATGAAAATCTTTAAGACATTTTCAAATGAGAACCTTTAAGT
1 AAATGAGAATCTTTGACTTTTCAAATGAAAATCTTT-AGACATTTTCAAATGAGAACCTTTAAGT
18593002 TTT
65 TTT
* ** *
18593005 AAATGAGAATCTTTAAGACTTTTCAAATGAGAATCTTT-GAGTTTTTCAAATGAGAATCTTTAAG
1 AAATGAGAATCTTT--GACTTTTCAAATGAAAATCTTTAGACATTTTCAAATGAGAACCTTTAAG
18593069 AAGAACTCAA
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
68 37 0.65
70 20 0.35
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (67 bp):
AAATGAGAATCTTTGACTTTTCAAATGAAAATCTTTAGACATTTTCAAATGAGAACCTTTAAGTT
TT
Found at i:18593249 original size:45 final size:45
Alignment explanation
Indices: 18593198--18593291 Score: 161
Period size: 45 Copynumber: 2.1 Consensus size: 45
18593188 AAAAAGCTTA
* *
18593198 AACTTTTTGGATGTGAACCCTAAATTTGTCAAATGCGAACCTTTG
1 AACTTTTTGGAGGTGAACCCCAAATTTGTCAAATGCGAACCTTTG
*
18593243 AACTTTTTGGAGGTGAACCCCAAATTTGTCAAATGTGAACCTTTG
1 AACTTTTTGGAGGTGAACCCCAAATTTGTCAAATGCGAACCTTTG
18593288 AACT
1 AACT
18593292 CGAATGAGAA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (45 bp):
AACTTTTTGGAGGTGAACCCCAAATTTGTCAAATGCGAACCTTTG
Found at i:18593465 original size:16 final size:16
Alignment explanation
Indices: 18593427--18593468 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
18593417 ACAAATGCAA
18593427 ATAT-TGAAATCTTGC
1 ATATCTGAAATCTTGC
* * *
18593442 AAACCTGAATTCTTGC
1 ATATCTGAAATCTTGC
18593458 ATATCTGAAAT
1 ATATCTGAAAT
18593469 TTTACGAATC
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.36
Consensus pattern (16 bp):
ATATCTGAAATCTTGC
Found at i:18593712 original size:41 final size:40
Alignment explanation
Indices: 18593653--18593888 Score: 181
Period size: 41 Copynumber: 5.7 Consensus size: 40
18593643 ATTGTCGAAA
*
18593653 AGCTTTTATTTTTCAAAGTCGTTGAGCCTCTACTTAGAGG
1 AGCTTTTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGG
* * * *
18593693 AGCCTTTTATTTTTTAAAGTTGTT-ATGCCTATATTTAGAGC
1 AG-CTTTTATTTTTCAAAGTCGTTGA-GCCTCTATTTAGAGG
* * * *
18593734 AGCTTTTAATTTTTTCAAAAGTTGTTGTGCCTTTGTTTAGAGG
1 AGCTTTT-A-TTTTTC-AAAGTCGTTGAGCCTCTATTTAGAGG
* * **
18593777 AGCTTTTATTTTTCAAAGTTGTT-ATGCCTCTATTTAAAAT
1 AGCTTTTATTTTTCAAAGTCGTTGA-GCCTCTATTTAGAGG
** * **
18593817 AGCCTTTTTATTTTTCAAAGTCACTGAGCCAT-TGTTTAGATA
1 AG-C-TTTTATTTTTCAAAGTCGTTGAGCC-TCTATTTAGAGG
* *
18593859 AGCCTTTTATGTTTCAAAGTCATTGAGCCT
1 AG-CTTTTATTTTTCAAAGTCGTTGAGCCT
18593889 TTGCTTAGAT
Statistics
Matches: 160, Mismatches: 25, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
40 30 0.19
41 64 0.40
42 36 0.22
43 30 0.19
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.45
Consensus pattern (40 bp):
AGCTTTTATTTTTCAAAGTCGTTGAGCCTCTATTTAGAGG
Found at i:18593765 original size:43 final size:40
Alignment explanation
Indices: 18593653--18593837 Score: 201
Period size: 41 Copynumber: 4.5 Consensus size: 40
18593643 ATTGTCGAAA
* *
18593653 AGCTTTTATTTTTCAAAGTCGTTGA-GCCTCTACTTAGAGG
1 AGCTTTTATTTTTCAAAGTTGTT-ATGCCTCTATTTAGAGG
* * *
18593693 AGCCTTTTATTTTTTAAAGTTGTTATGCCTATATTTAGAGC
1 AG-CTTTTATTTTTCAAAGTTGTTATGCCTCTATTTAGAGG
* * *
18593734 AGCTTTTAATTTTTTCAAAAGTTGTTGTGCCTTTGTTTAGAGG
1 AGCTTTT-A-TTTTTC-AAAGTTGTTATGCCTCTATTTAGAGG
* **
18593777 AGCTTTTATTTTTCAAAGTTGTTATGCCTCTATTTAAAAT
1 AGCTTTTATTTTTCAAAGTTGTTATGCCTCTATTTAGAGG
18593817 AGCCTTTTTATTTTTCAAAGT
1 AG-C-TTTTATTTTTCAAAGT
18593838 CACTGAGCCA
Statistics
Matches: 122, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
40 30 0.25
41 41 0.34
42 22 0.18
43 29 0.24
ACGTcount: A:0.24, C:0.13, G:0.16, T:0.48
Consensus pattern (40 bp):
AGCTTTTATTTTTCAAAGTTGTTATGCCTCTATTTAGAGG
Found at i:18593795 original size:83 final size:81
Alignment explanation
Indices: 18593653--18593878 Score: 231
Period size: 83 Copynumber: 2.7 Consensus size: 81
18593643 ATTGTCGAAA
*
18593653 AGCTTTTATTTTTCAAAGTCGTTGAGCCTCTACTTAGAGGAGCCTTTTATTTTTTAAAGTTGTTA
1 AGCTTTTATTTTTCAAAGTCGTTGAGCCTCTACTTAGAGGAGCCTTTTATTTTTCAAAGTTGTTA
18593718 TGCCTATATTTAGAGC
66 TGCCTATATTTAGAGC
* * * **
18593734 AGCTTTTAATTTTTTCAAAAGTTGTTGTGCCTTTGTTTAGAGGAG-CTTTTATTTTTCAAAGTTG
1 AGCTTTT-A-TTTTTC-AAAGTCGTTGAGCCTCTACTTAGAGGAGCCTTTTATTTTTCAAAGTTG
* * **
18593798 TTATGCCTCTATTTAAAAT
63 TTATGCCTATATTTAGAGC
** ** ** *
18593817 AGCCTTTTTATTTTTCAAAGTCACTGAGCCAT-TGTTTAGATAAGCCTTTTATGTTTCAAAGT
1 AG-C-TTTTATTTTTCAAAGTCGTTGAGCC-TCTACTTAGAGGAGCCTTTTATTTTTCAAAGT
18593879 CATTGAGCCT
Statistics
Matches: 121, Mismatches: 17, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
81 7 0.06
82 21 0.17
83 64 0.53
84 25 0.21
85 4 0.03
ACGTcount: A:0.24, C:0.14, G:0.16, T:0.46
Consensus pattern (81 bp):
AGCTTTTATTTTTCAAAGTCGTTGAGCCTCTACTTAGAGGAGCCTTTTATTTTTCAAAGTTGTTA
TGCCTATATTTAGAGC
Found at i:18593863 original size:42 final size:42
Alignment explanation
Indices: 18593817--18593919 Score: 127
Period size: 41 Copynumber: 2.5 Consensus size: 42
18593807 TATTTAAAAT
*
18593817 AGCCTTTTTATTTTTCAAAGTCACTGAGCCATTGTTTAGATA
1 AGCCTTTTTATTTTTCAAAGTCACTGAGCCATTGCTTAGATA
* * * *
18593859 AGCC-TTTTATGTTTCAAAGTCATTGAGCCTTTGCTTAGATG
1 AGCCTTTTTATTTTTCAAAGTCACTGAGCCATTGCTTAGATA
* *
18593900 AGCTTTATTTATTTTCCAAA
1 AGCCTT-TTTATTTTTCAAA
18593920 AGCTATGAAC
Statistics
Matches: 51, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
41 35 0.69
42 5 0.10
43 11 0.22
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.44
Consensus pattern (42 bp):
AGCCTTTTTATTTTTCAAAGTCACTGAGCCATTGCTTAGATA
Found at i:18598202 original size:129 final size:129
Alignment explanation
Indices: 18597946--18598195 Score: 340
Period size: 129 Copynumber: 1.9 Consensus size: 129
18597936 ACATTTAATG
* *
18597946 GGAATGTGATCCATGGTAATTCCAAAATCCTCTAATTATTATTTAATCCATAAAACTTGAGTACA
1 GGAATGTGATCCATGGTAATTCCAAAATCCTCTAATTATTATTCAATCCATAAAACTTGAGCACA
* * * * *
18598011 AAAACTATCGACTACTACATATTCGACTTTGGTTGTAGATTAAGCAACATTGTTTTACTTCTTA
66 AAAACTACCAACTACTACATATTCGACTTTGATTATAGATTAAGCAACATTATTTTACTTCTTA
* * * *
18598075 GGAATGTGATCCATGGTAATTCCAAAATCCTTTAATTGTTGTTCAATCCATAAGACTTGAGCACA
1 GGAATGTGATCCATGGTAATTCCAAAATCCTCTAATTATTATTCAATCCATAAAACTTGAGCACA
* * * * *
18598140 ATAACTACCAATTGCTACATATTC-ATCTTTGATTATGGATTAATCAACATTATTTT
66 AAAACTACCAACTACTACATATTCGA-CTTTGATTATAGATTAAGCAACATTATTTT
18598196 GTTTCTTGAA
Statistics
Matches: 104, Mismatches: 16, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
128 1 0.01
129 103 0.99
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (129 bp):
GGAATGTGATCCATGGTAATTCCAAAATCCTCTAATTATTATTCAATCCATAAAACTTGAGCACA
AAAACTACCAACTACTACATATTCGACTTTGATTATAGATTAAGCAACATTATTTTACTTCTTA
Found at i:18611123 original size:19 final size:18
Alignment explanation
Indices: 18611101--18611148 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
18611091 GATTGAGTGA
18611101 TTAGTTTAATTAGTTGTAG
1 TTAGTTTAATTAGTT-TAG
*
18611120 TTAGTTATAGTTAGTTTAG
1 TTAGTT-TAATTAGTTTAG
18611139 TTAG-TTAATT
1 TTAGTTTAATT
18611149 TGGTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 4 0.15
18 1 0.04
19 13 0.50
20 8 0.31
ACGTcount: A:0.27, C:0.00, G:0.19, T:0.54
Consensus pattern (18 bp):
TTAGTTTAATTAGTTTAG
Found at i:18618062 original size:11 final size:13
Alignment explanation
Indices: 18618034--18618060 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
18618024 TTTTAATTTT
18618034 TATTTTTAAAAAA
1 TATTTTTAAAAAA
18618047 TATTTTTAAAAAA
1 TATTTTTAAAAAA
18618060 T
1 T
18618061 TTGATATTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATTTTTAAAAAA
Found at i:18618147 original size:12 final size:12
Alignment explanation
Indices: 18618125--18618163 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
18618115 AAGTTCATAC
18618125 AAAAATA-AAAT
1 AAAAATAGAAAT
18618136 AAAAATAGAAAT
1 AAAAATAGAAAT
18618148 -AAAA-AG-AAT
1 AAAAATAGAAAT
18618157 AAAAATA
1 AAAAATA
18618164 TATAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
9 3 0.12
10 6 0.24
11 12 0.48
12 4 0.16
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.15
Consensus pattern (12 bp):
AAAAATAGAAAT
Found at i:18619057 original size:27 final size:25
Alignment explanation
Indices: 18619019--18619069 Score: 75
Period size: 27 Copynumber: 2.0 Consensus size: 25
18619009 ACTATTATGA
18619019 TTTTATTATTATTATTAATTTTAATTG
1 TTTTATTATTATT-TTAA-TTTAATTG
*
18619046 TTTTATTTTTATTTTAATTTAATT
1 TTTTATTATTATTTTAATTTAATT
18619070 TTAGTTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 4 0.17
27 12 0.52
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTTATTATTATTTTAATTTAATTG
Found at i:18619071 original size:31 final size:32
Alignment explanation
Indices: 18619019--18619080 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
18619009 ACTATTATGA
*
18619019 TTTTATTATTATTATTAATTTTAATTGTTTTAT
1 TTTTATTATTAATATTAATTTTAATT-TTTTAT
*
18619052 TTTTATT-TTAAT-TTAATTTTAGTTTTTTA
1 TTTTATTATTAATATTAATTTTAATTTTTTA
18619081 ATGATTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 5 0.19
31 11 0.41
32 4 0.15
33 7 0.26
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (32 bp):
TTTTATTATTAATATTAATTTTAATTTTTTAT
Found at i:18619283 original size:29 final size:30
Alignment explanation
Indices: 18619229--18619292 Score: 71
Period size: 29 Copynumber: 2.2 Consensus size: 30
18619219 GTTTAAGAGT
*
18619229 TTATTGGGATACAAATTAATGGTTAATGG-C
1 TTATTGGGATACAAATTAATGATTAA-GGAC
*
18619259 TTATTGGG-TGCAAATTAAAT-ATTAAGGAC
1 TTATTGGGATACAAATT-AATGATTAAGGAC
18619288 TTATT
1 TTATT
18619293 TAAATGCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
28 2 0.07
29 17 0.57
30 11 0.37
ACGTcount: A:0.34, C:0.06, G:0.20, T:0.39
Consensus pattern (30 bp):
TTATTGGGATACAAATTAATGATTAAGGAC
Found at i:18619407 original size:2 final size:2
Alignment explanation
Indices: 18619402--18619428 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
18619392 TGATTCGTGG
18619402 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
18619429 AATTAAGTAC
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:18621825 original size:3 final size:3
Alignment explanation
Indices: 18621817--18621868 Score: 79
Period size: 3 Copynumber: 17.3 Consensus size: 3
18621807 AGAAAAGGCA
*
18621817 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAGG AA- CAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA-G AAG AAG
18621862 AAG AAG A
1 AAG AAG A
18621869 TATTTCGAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 1 0.02
3 41 0.91
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:18630394 original size:12 final size:12
Alignment explanation
Indices: 18630345--18630386 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
18630335 TTAATGGATG
*
18630345 AAGAAATTAAAA
1 AAGAAATGAAAA
*
18630357 AA-AAA-CAAAA
1 AAGAAATGAAAA
18630367 AAGAAATGAAAA
1 AAGAAATGAAAA
18630379 AAGAAATG
1 AAGAAATG
18630387 GGAAAAGAGG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 6 0.23
11 6 0.23
12 14 0.54
ACGTcount: A:0.76, C:0.02, G:0.12, T:0.10
Consensus pattern (12 bp):
AAGAAATGAAAA
Found at i:18630441 original size:9 final size:8
Alignment explanation
Indices: 18630397--18630442 Score: 65
Period size: 8 Copynumber: 5.5 Consensus size: 8
18630387 GGAAAAGAGG
18630397 AAAAAATA
1 AAAAAATA
*
18630405 TAAAAGATA
1 -AAAAAATA
18630414 AAAAAATA
1 AAAAAATA
18630422 AAAAAATA
1 AAAAAATA
18630430 AAAAAATGA
1 AAAAAAT-A
18630439 AAAA
1 AAAA
18630443 GAGAGAAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
8 22 0.65
9 12 0.35
ACGTcount: A:0.83, C:0.00, G:0.04, T:0.13
Consensus pattern (8 bp):
AAAAAATA
Found at i:18630991 original size:12 final size:12
Alignment explanation
Indices: 18630974--18631002 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
18630964 ATAACACATG
18630974 TATGGTGATGAA
1 TATGGTGATGAA
18630986 TATGGTGATGAA
1 TATGGTGATGAA
18630998 T-TGGT
1 TATGGT
18631003 CAACATAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.28, C:0.00, G:0.34, T:0.38
Consensus pattern (12 bp):
TATGGTGATGAA
Found at i:18631205 original size:62 final size:62
Alignment explanation
Indices: 18631065--18631209 Score: 159
Period size: 62 Copynumber: 2.3 Consensus size: 62
18631055 ATAGAATTTA
* * * * *
18631065 TTCTGAAATGATTAGTGCTGAAAAGCCTGTGAATTATGGTATGGATCAATGGACGAAATTTG
1 TTCTGAAATGATTAGTGCTAAAAAGCCTGTGAATTACGGCAAGGATCAATGGACGAAACTTG
* * * * * *
18631127 TTTTGGAATTG-CTAGTGCTAAAAAGCCTGTGAATTACGGCCAAGTATCAATTGATGAAACTTG
1 TTCT-GAAATGATTAGTGCTAAAAAGCCTGTGAATTACGG-CAAGGATCAATGGACGAAACTTG
18631190 TTCT-AAATGATTAGTGCTAA
1 TTCTGAAATGATTAGTGCTAA
18631210 GAAGTTGAAA
Statistics
Matches: 66, Mismatches: 14, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
61 4 0.06
62 37 0.56
63 25 0.38
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (62 bp):
TTCTGAAATGATTAGTGCTAAAAAGCCTGTGAATTACGGCAAGGATCAATGGACGAAACTTG
Found at i:18631873 original size:16 final size:16
Alignment explanation
Indices: 18631852--18631882 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
18631842 TAAATGCAAA
18631852 TCTTGCAAATCTAAAT
1 TCTTGCAAATCTAAAT
*
18631868 TCTTGCATATCTAAA
1 TCTTGCAAATCTAAA
18631883 ATTTTATGAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.06, T:0.39
Consensus pattern (16 bp):
TCTTGCAAATCTAAAT
Found at i:18631902 original size:31 final size:31
Alignment explanation
Indices: 18631859--18631930 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
18631849 AAATCTTGCA
* *
18631859 AATCTAAATTCTTG-CATATCTAAAATTTTATG
1 AATC-AAATTCTTGTCA-AACTAAAATTTTAAG
*
18631891 AATCAAATTCTTGTGAAACTAAAATTTTAAG
1 AATCAAATTCTTGTCAAACTAAAATTTTAAG
18631922 AATCAAATT
1 AATCAAATT
18631931 TCAGTGAAGT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 31 0.86
32 5 0.14
ACGTcount: A:0.43, C:0.11, G:0.07, T:0.39
Consensus pattern (31 bp):
AATCAAATTCTTGTCAAACTAAAATTTTAAG
Found at i:18631938 original size:31 final size:31
Alignment explanation
Indices: 18631878--18631938 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
18631868 TCTTGCATAT
* *
18631878 CTAAAATTTTATGAATCAAATTCTTGTGAAA
1 CTAAAATTTTAAGAATCAAATTCTAGTGAAA
18631909 CTAAAATTTTAAGAATCAAATT-TCAGTGAA
1 CTAAAATTTTAAGAATCAAATTCT-AGTGAA
18631939 GTCATATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (31 bp):
CTAAAATTTTAAGAATCAAATTCTAGTGAAA
Found at i:18632235 original size:44 final size:44
Alignment explanation
Indices: 18632062--18632460 Score: 341
Period size: 44 Copynumber: 9.4 Consensus size: 44
18632052 ATTGTTAAGA
* * *
18632062 AGCCTTGTTTA-TTTTTCAAAGTCATTGAGCCTCTGCTTAGAGA
1 AGCCTTATTTATTTTTTCAAAGTCATTGAGCCTCTGATTAGAGG
18632105 AGCCTTATTTATTTTTTCAAA---A-TGAGCCTCT-ACTTAGAGG
1 AGCCTTATTTATTTTTTCAAAGTCATTGAGCCTCTGA-TTAGAGG
* * * * *
18632145 AGTCTTATTTATTTTTTTCAAAGTCATTAAGCCTTTG-CTCGAAGG
1 AGCCTTATTTA-TTTTTTCAAAGTCATTGAGCCTCTGATTAG-AGG
* * *
18632190 AGCCTTATTTATTTTTCCAAGGTCGTTGAGCCTCTGATTAGAGG
1 AGCCTTATTTATTTTTTCAAAGTCATTGAGCCTCTGATTAGAGG
* *
18632234 AGCCTTGTTTATTTTTTTCAAAGTCATTGAGCCTCTAATT--A-G
1 AGCCTTATTTA-TTTTTTCAAAGTCATTGAGCCTCTGATTAGAGG
* * **
18632276 A--C-----TATTTTTCCAAAGTCATTGAGCCTCTGATTAAAAA
1 AGCCTTATTTATTTTTTCAAAGTCATTGAGCCTCTGATTAGAGG
* * * * *
18632313 AGCTTTATTTA-TTTTTCTAAAGTCATTGGGCCTCTGTTTAAAAG
1 AGCCTTATTTATTTTTTC-AAAGTCATTGAGCCTCTGATTAGAGG
* * * *
18632357 AGCTTTATTTATTTTTTCAAAGTCGTTGAGCCTCTGTTTAGAAG
1 AGCCTTATTTATTTTTTCAAAGTCATTGAGCCTCTGATTAGAGG
* * * *
18632401 AGCTTTGTTTATTTTTT-AGAAGTCATTGAGCCTCTGTTTAGAGA
1 AGCCTTATTTATTTTTTCA-AAGTCATTGAGCCTCTGATTAGAGG
18632445 AGCCTTATTTATTTTT
1 AGCCTTATTTATTTTT
18632461 AAAATTTATG
Statistics
Matches: 294, Mismatches: 38, Indels: 47
0.78 0.10 0.12
Matches are distributed among these distances:
34 26 0.09
35 2 0.01
36 1 0.00
37 1 0.00
40 26 0.09
41 11 0.04
42 2 0.01
43 17 0.06
44 156 0.53
45 52 0.18
ACGTcount: A:0.25, C:0.16, G:0.17, T:0.43
Consensus pattern (44 bp):
AGCCTTATTTATTTTTTCAAAGTCATTGAGCCTCTGATTAGAGG
Found at i:18633723 original size:21 final size:20
Alignment explanation
Indices: 18633681--18633728 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
18633671 TTTTCAAACA
*
18633681 AAAAAACAAAAAAATAAGAT
1 AAAAAATAAAAAAATAAGAT
18633701 AAAAAATAAAAAAATTTAA-AT
1 AAAAAATAAAAAAA--TAAGAT
18633722 AAAAAAT
1 AAAAAAT
18633729 TTGAAATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 13 0.52
21 9 0.36
22 3 0.12
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (20 bp):
AAAAAATAAAAAAATAAGAT
Found at i:18633725 original size:13 final size:15
Alignment explanation
Indices: 18633704--18633735 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
18633694 ATAAGATAAA
18633704 AAATAAAAAAATTT-
1 AAATAAAAAAATTTG
18633718 AAAT-AAAAAATTTG
1 AAATAAAAAAATTTG
18633732 AAAT
1 AAAT
18633736 TAAATACAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 9 0.53
14 8 0.47
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (15 bp):
AAATAAAAAAATTTG
Found at i:18639844 original size:18 final size:18
Alignment explanation
Indices: 18639821--18639873 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 18
18639811 TTTGGAAACT
18639821 CATTTATAAGAAAAGTGG
1 CATTTATAAGAAAAGTGG
*
18639839 CA-TT-T-AG-AAACT--
1 CATTTATAAGAAAAGTGG
18639851 CATTTATAAGAAAAGTGG
1 CATTTATAAGAAAAGTGG
18639869 CATTT
1 CATTT
18639874 TGAGACTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 12
0.66 0.05 0.29
Matches are distributed among these distances:
12 2 0.07
13 2 0.07
14 5 0.19
15 4 0.15
16 5 0.19
17 2 0.07
18 7 0.26
ACGTcount: A:0.42, C:0.09, G:0.17, T:0.32
Consensus pattern (18 bp):
CATTTATAAGAAAAGTGG
Found at i:18639851 original size:30 final size:30
Alignment explanation
Indices: 18639815--18639882 Score: 118
Period size: 30 Copynumber: 2.3 Consensus size: 30
18639805 CTTTATTTTG
18639815 GAAACTCATTTATAAGAAAAGTGGCATTTA
1 GAAACTCATTTATAAGAAAAGTGGCATTTA
*
18639845 GAAACTCATTTATAAGAAAAGTGGCATTTT
1 GAAACTCATTTATAAGAAAAGTGGCATTTA
*
18639875 GAGACTCA
1 GAAACTCA
18639883 AAATTCAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (30 bp):
GAAACTCATTTATAAGAAAAGTGGCATTTA
Found at i:18647767 original size:25 final size:26
Alignment explanation
Indices: 18647739--18647804 Score: 66
Period size: 25 Copynumber: 2.6 Consensus size: 26
18647729 ATAAATATCC
*
18647739 AATGATGAAATTCTTAGAAATTTC-A
1 AATGATGAAATTCTTAGAAATCTCTA
* *
18647764 AATGGT-AAATTCCTAAGAAATCTCTA
1 AATGATGAAATT-CTTAGAAATCTCTA
18647790 AATGA-GAAACTTCTT
1 AATGATGAAA-TTCTT
18647805 TAAATTTATC
Statistics
Matches: 32, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
24 5 0.16
25 15 0.47
26 10 0.31
27 2 0.06
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (26 bp):
AATGATGAAATTCTTAGAAATCTCTA
Found at i:18647950 original size:50 final size:49
Alignment explanation
Indices: 18647886--18647980 Score: 120
Period size: 50 Copynumber: 1.9 Consensus size: 49
18647876 TTCTGAAAAC
*
18647886 AAAAAAAAAATCTAAATA-AGCCCAAATGGTGAAAATTTTATAAATTTTG
1 AAAAAAAAAATCTAAATAGA-CCCAAATGGTGAAAATTTTAGAAATTTTG
* * * *
18647935 AAAAAAAAATCTCTAAATTGACCCAAATGGTGGAGATTTTAGAAAT
1 AAAAAAAAA-ATCTAAATAGACCCAAATGGTGAAAATTTTAGAAAT
18647981 CCAACAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
49 9 0.23
50 29 0.74
51 1 0.03
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.27
Consensus pattern (49 bp):
AAAAAAAAAATCTAAATAGACCCAAATGGTGAAAATTTTAGAAATTTTG
Found at i:18651608 original size:16 final size:14
Alignment explanation
Indices: 18651573--18651623 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
18651563 TCAAAGATAG
*
18651573 AAAGTAAAAAAAA-
1 AAAGAAAAAAAAAC
18651586 AAAGAAAAACAAAAC
1 AAAGAAAAA-AAAAC
18651601 AAAGGAAAAAAAAA-
1 AAA-GAAAAAAAAAC
*
18651615 ACAGAAAAA
1 AAAGAAAAA
18651624 TGAATGCCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
13 14 0.42
14 6 0.18
15 7 0.21
16 6 0.18
ACGTcount: A:0.82, C:0.06, G:0.10, T:0.02
Consensus pattern (14 bp):
AAAGAAAAAAAAAC
Found at i:18652006 original size:17 final size:18
Alignment explanation
Indices: 18651991--18652069 Score: 101
Period size: 18 Copynumber: 4.5 Consensus size: 18
18651981 ATGGAAAAAA
18651991 AAAAAAAAATGAAAAAATG
1 AAAAAAAAA-GAAAAAATG
18652010 -AAAAAAAAG-AAAAATG
1 AAAAAAAAAGAAAAAATG
* *
18652026 GAAAAAAGAGAAAAAATG
1 AAAAAAAAAGAAAAAATG
*
18652044 AAAAAAAAAGAGAAAA-G
1 AAAAAAAAAGAAAAAATG
18652061 AAAAAAAAA
1 AAAAAAAAA
18652070 CTCAAATTGA
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
16 7 0.13
17 19 0.35
18 28 0.52
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (18 bp):
AAAAAAAAAGAAAAAATG
Found at i:18652027 original size:42 final size:42
Alignment explanation
Indices: 18651981--18652065 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 42
18651971 TCACTAATGG
18651981 ATGGAAAAAAAAAAAAAAATGAAAAAATGAAA-A-AAAAGAAAA
1 ATGGAAAAAAAAAAAAAAATGAAAAAA--AAAGAGAAAAGAAAA
* *
18652023 ATGGAAAAAAGAGAAAAAATGAAAAAAAAAGAGAAAAGAAAA
1 ATGGAAAAAAAAAAAAAAATGAAAAAAAAAGAGAAAAGAAAA
18652065 A
1 A
18652066 AAAACTCAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
40 3 0.08
41 1 0.03
42 35 0.90
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.06
Consensus pattern (42 bp):
ATGGAAAAAAAAAAAAAAATGAAAAAAAAAGAGAAAAGAAAA
Found at i:18652031 original size:34 final size:34
Alignment explanation
Indices: 18651987--18652068 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
18651977 ATGGATGGAA
*
18651987 AAAAAAAAAAAAATGAAAAAATG-AAAAAAAAGA-
1 AAAAGAAAAAAAA-GAAAAAATGAAAAAAAAAGAG
*
18652020 AAAATGGAAAAAAGAGAAAAAATGAAAAAAAAAGAG
1 AAAA--GAAAAAAAAGAAAAAATGAAAAAAAAAGAG
18652056 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
18652069 ACTCAAATTG
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
33 4 0.10
34 17 0.40
35 17 0.40
36 4 0.10
ACGTcount: A:0.82, C:0.00, G:0.13, T:0.05
Consensus pattern (34 bp):
AAAAGAAAAAAAAGAAAAAATGAAAAAAAAAGAG
Found at i:18652069 original size:18 final size:19
Alignment explanation
Indices: 18651984--18652069 Score: 64
Period size: 17 Copynumber: 4.9 Consensus size: 19
18651974 CTAATGGATG
18651984 GAAAAAA-AAAAAAAAATGA
1 GAAAAAAGAAAAAAAAA-GA
*
18652003 -AAAAATG--AAAAAAA-A
1 GAAAAAAGAAAAAAAAAGA
* *
18652018 GAAAAATG--GAAAAAAGA
1 GAAAAAAGAAAAAAAAAGA
18652035 GAAAAAATGAAAAAAAAAGA
1 GAAAAAA-GAAAAAAAAAGA
18652055 G--AAAAGAAAAAAAAA
1 GAAAAAAGAAAAAAAAA
18652070 CTCAAATTGA
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
15 1 0.02
16 13 0.23
17 24 0.42
18 10 0.18
20 9 0.16
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (19 bp):
GAAAAAAGAAAAAAAAAGA
Found at i:18653265 original size:47 final size:46
Alignment explanation
Indices: 18653212--18653347 Score: 206
Period size: 47 Copynumber: 2.9 Consensus size: 46
18653202 ATTGTGAATC
18653212 TTCAAATGAGAATCTTTGAGTTTTCAAATGA-AAGTCTTTAAGACATT
1 TTCAAATGAGAATCTTTGAGTTTTCAAATGAGAA-TCTTTAAGAC-TT
*
18653259 TTCAAATGAGAA-CTTTTAAGTTTT-AAATGAGAATCTTTAAGACTT
1 TTCAAATGAGAATC-TTTGAGTTTTCAAATGAGAATCTTTAAGACTT
18653304 TTCAAATGAGAATCTTTGAGTTTTTCAAATGAGAATCTTTAAGA
1 TTCAAATGAGAATCTTTGAG-TTTTCAAATGAGAATCTTTAAGA
18653348 AGAACTCAAA
Statistics
Matches: 82, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
45 19 0.23
46 22 0.27
47 41 0.50
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.39
Consensus pattern (46 bp):
TTCAAATGAGAATCTTTGAGTTTTCAAATGAGAATCTTTAAGACTT
Found at i:18653329 original size:68 final size:68
Alignment explanation
Indices: 18653215--18653343 Score: 174
Period size: 68 Copynumber: 1.9 Consensus size: 68
18653205 GTGAATCTTC
*
18653215 AAATGAGAATCTTTGAGTTTTCAAATGAAAGTCTTTAAGACATTTTCAAATGAGAA-CTTTTAAG
1 AAATGAGAATCTTTGACTTTTCAAATGAAAGTCTTT-AGACATTTTCAAATGAGAATCTTTTAAG
18653279 TTTT
65 TTTT
**
18653283 AAATGAGAATCTTTAAGACTTTTCAAATGAGAA-TCTTT-GAGTTTTTCAAATGAGAATCTTT
1 AAATGAGAATCTTT--GACTTTTCAAATGA-AAGTCTTTAGACATTTTCAAATGAGAATCTTT
18653344 AAGAAGAACT
Statistics
Matches: 54, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
68 30 0.56
69 4 0.07
70 18 0.33
71 2 0.04
ACGTcount: A:0.36, C:0.09, G:0.15, T:0.40
Consensus pattern (68 bp):
AAATGAGAATCTTTGACTTTTCAAATGAAAGTCTTTAGACATTTTCAAATGAGAATCTTTTAAGT
TTT
Found at i:18653375 original size:92 final size:91
Alignment explanation
Indices: 18653212--18653403 Score: 212
Period size: 92 Copynumber: 2.1 Consensus size: 91
18653202 ATTGTGAATC
*** *
18653212 TTCAAATGAGAATCTTTGAGTTTTCAAATGAAAGTCTTTAAGACATTTTCAAATGAGAACTTTTA
1 TTCAAATGAGAATCTTTGAGTTTTCAAATGAAAGTCTTTAAGACAAACTCAAATGAGAACTTTGA
* *
18653277 AGTTTTAAATGAGAATCTTTAAGACTT
66 AGTTTTAAATGAGAAACTCTAAGA-TT
* *
18653304 TTCAAATGAGAATCTTTGAGTTTTTCAAATGAGAA-TCTTTAAGA-AGAACTCAAATTA-ACCTT
1 TTCAAATGAGAATCTTTGAG-TTTTCAAATGA-AAGTCTTTAAGACA-AACTCAAATGAGAACTT
* *
18653366 TG-AGATTTTAGATGTGAAACTCTAAGATT
63 TGAAG-TTTTAAATGAGAAACTCTAAGATT
18653395 TGTCAAATG
1 T-TCAAATG
18653404 TAAACCTTTA
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
91 5 0.06
92 51 0.60
93 27 0.32
94 2 0.02
ACGTcount: A:0.37, C:0.10, G:0.15, T:0.38
Consensus pattern (91 bp):
TTCAAATGAGAATCTTTGAGTTTTCAAATGAAAGTCTTTAAGACAAACTCAAATGAGAACTTTGA
AGTTTTAAATGAGAAACTCTAAGATT
Found at i:18653523 original size:39 final size:39
Alignment explanation
Indices: 18653478--18653559 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
18653468 ACAAGCTTAA
* * *
18653478 ACTTTTTGGATGTGAACTCTAAATTTGTCAAATGTGAAC
1 ACTTTTTGGAGGTGAACCCCAAATTTGTCAAATGTGAAC
18653517 ACTTTTTGGAGGTGAACCCCAAATTTGTCAAATGTGAAC
1 ACTTTTTGGAGGTGAACCCCAAATTTGTCAAATGTGAAC
18653556 -CTTT
1 ACTTT
18653560 GAACTCGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
38 4 0.10
39 36 0.90
ACGTcount: A:0.29, C:0.16, G:0.18, T:0.37
Consensus pattern (39 bp):
ACTTTTTGGAGGTGAACCCCAAATTTGTCAAATGTGAAC
Found at i:18653738 original size:16 final size:16
Alignment explanation
Indices: 18653700--18653741 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
18653690 ACAAATGCAA
18653700 ATAT-TGAAATCTTGC
1 ATATCTGAAATCTTGC
* * *
18653715 AAACCTGAAGTCTTGC
1 ATATCTGAAATCTTGC
18653731 ATATCTGAAAT
1 ATATCTGAAAT
18653742 TTTACAAATC
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
15 2 0.10
16 18 0.90
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (16 bp):
ATATCTGAAATCTTGC
Found at i:18654038 original size:43 final size:41
Alignment explanation
Indices: 18653970--18654110 Score: 130
Period size: 43 Copynumber: 3.4 Consensus size: 41
18653960 AGAAGAGCCT
18653970 TTTTATTTTTT-AAAGTTGTTATGCCTATAATTAAAGGAGC
1 TTTTATTTTTTCAAAGTTGTTATGCCTATAATTAAAGGAGC
* * ** *
18654010 TTTTAATTTTTTCACAAGTTGTTCTGCCTTTGTTTAGAGGAGC
1 TTTT-ATTTTTTCA-AAGTTGTTATGCCTATAATTAAAGGAGC
* *
18654053 TTTTA-TTTTTCAAAGTTGTTGTG-CT-TCAATTTAAAAGAGCC
1 TTTTATTTTTTCAAAGTTGTTATGCCTAT-AA-TTAAAGGAG-C
18654094 TTTT-TATTTTTCAAAGT
1 TTTTAT-TTTTTCAAAGT
18654111 CACTGAGCCC
Statistics
Matches: 83, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
38 1 0.01
39 2 0.02
40 21 0.25
41 19 0.23
42 13 0.16
43 27 0.33
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.50
Consensus pattern (41 bp):
TTTTATTTTTTCAAAGTTGTTATGCCTATAATTAAAGGAGC
Found at i:18654211 original size:41 final size:41
Alignment explanation
Indices: 18653927--18654277 Score: 240
Period size: 41 Copynumber: 8.4 Consensus size: 41
18653917 TGTCGAAGAG
* *
18653927 CTTTTATTTTTCAAAGTCGTTGAGCCTCTGCTTAGAAGAGC
1 CTTTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
* * * ** *
18653968 CTTTTTATTTTTTAAAGTTGTT-ATGCCTATAATTAAAGGAG-
1 C-TTTTATTTTTCAAAGTCGTTGA-GCCTCTGTTTAGAGGAGC
* ** *
18654009 CTTTTAATTTTTTCACAAGTTGTTCTGCCTTTGTTTAGAGGAG-
1 CTTTT-A-TTTTTCA-AAGTCGTTGAGCCTCTGTTTAGAGGAGC
* * * ** * *
18654052 CTTTTATTTTTCAAAGTTGTTGTGCTTCAATTTAAAAGAGC
1 CTTTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
** * * **
18654093 CTTTTTATTTTTCAAAGTCACTGAGCCCCTATTTAGATAAGC
1 C-TTTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
** * * * *
18654135 CTTTTATGATTCAAAGTCATTGAGCATTTGCTTAGAGGAGC
1 CTTTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
* * *
18654176 CTTTTATTTTTCAAAGTCATTGAACCTCTGTTTAGAAGAGC
1 CTTTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
* * *
18654217 CTTATTTATTTTTTCAAAGCCGTTGAACCTCTGATTAGAGGAGC
1 C-T-TTTA-TTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
*
18654261 TTTGTTTATTTTTCAAA
1 -CT-TTTATTTTTCAAA
18654278 AGCTATGAAC
Statistics
Matches: 245, Mismatches: 53, Indels: 22
0.77 0.17 0.07
Matches are distributed among these distances:
40 24 0.10
41 77 0.31
42 69 0.28
43 39 0.16
44 36 0.15
ACGTcount: A:0.25, C:0.15, G:0.16, T:0.44
Consensus pattern (41 bp):
CTTTTATTTTTCAAAGTCGTTGAGCCTCTGTTTAGAGGAGC
Found at i:18654287 original size:43 final size:40
Alignment explanation
Indices: 18654166--18654296 Score: 122
Period size: 44 Copynumber: 3.1 Consensus size: 40
18654156 GAGCATTTGC
* *
18654166 TTAGAGGAGCCTTTTATTTTTCAAAG-TCATTGAACCTCTGT
1 TTAGAGGAGCTTTTTATTTTTCAAAGCT-A-TGAACCTCTGA
*
18654207 TTAGAAGAGCCTTATTTATTTTTTCAAAGCCGT-TGAACCTCTGA
1 TTAGAGGAG-CTT-TTTA-TTTTTCAAAG-C-TATGAACCTCTGA
*
18654251 TTAGAGGAGCTTTGTTTATTTTTCAAAAGCTATGAACCTCTTA
1 TTAGAGGAGC-TT-TTTATTTTTC-AAAGCTATGAACCTCTGA
18654294 TTA
1 TTA
18654297 TGGGAGTTTT
Statistics
Matches: 75, Mismatches: 6, Indels: 16
0.77 0.06 0.16
Matches are distributed among these distances:
41 8 0.11
42 3 0.04
43 25 0.33
44 38 0.51
47 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (40 bp):
TTAGAGGAGCTTTTTATTTTTCAAAGCTATGAACCTCTGA
Found at i:18655969 original size:4 final size:4
Alignment explanation
Indices: 18655960--18655985 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
18655950 CATTTTTATT
18655960 TTAA TTAA TTAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA TTAA TTAA TT
18655986 TTTGAAATAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (4 bp):
TTAA
Found at i:18656115 original size:24 final size:25
Alignment explanation
Indices: 18656079--18656125 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
18656069 ATAATTATCC
*
18656079 AATGATGAAATTTTTAGAAAATTCA
1 AATGATGAAATTTCTAGAAAATTCA
*
18656104 AATGAT-AAATTTCTATAAAATT
1 AATGATGAAATTTCTAGAAAATT
18656126 TCTAGGTGAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.49, C:0.04, G:0.09, T:0.38
Consensus pattern (25 bp):
AATGATGAAATTTCTAGAAAATTCA
Found at i:18656230 original size:9 final size:8
Alignment explanation
Indices: 18656213--18656244 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
18656203 GTTTATTCTT
18656213 AATAAAAA
1 AATAAAAA
*
18656221 ACTAAAAA
1 AATAAAAA
18656229 AATAAAAA
1 AATAAAAA
18656237 AATAAAAA
1 AATAAAAA
18656245 TTTTAATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.12
Consensus pattern (8 bp):
AATAAAAA
Found at i:18656729 original size:63 final size:63
Alignment explanation
Indices: 18656662--18656788 Score: 168
Period size: 63 Copynumber: 2.0 Consensus size: 63
18656652 AAAATTCTGA
* *
18656662 AAAAAAGA-AAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAATCCAACA-AAAAAAT
1 AAAAAAGAGAAA-ATTTCTAAATAGACCC-AATGGTGAAAAATTTAGAAATCCAAAAGAAAAAAT
* * * *
18656725 AAAAAAGAGAGAATTTCTAAATAGGCCCATTGGTGAAAAATTTAGAAATTCAAAAGAAAAAAT
1 AAAAAAGAGAAAATTTCTAAATAGACCCAATGGTGAAAAATTTAGAAATCCAAAAGAAAAAAT
18656788 A
1 A
18656789 TTTCTAATTT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
62 24 0.43
63 30 0.54
64 2 0.04
ACGTcount: A:0.56, C:0.09, G:0.13, T:0.22
Consensus pattern (63 bp):
AAAAAAGAGAAAATTTCTAAATAGACCCAATGGTGAAAAATTTAGAAATCCAAAAGAAAAAAT
Found at i:18656822 original size:114 final size:114
Alignment explanation
Indices: 18656602--18656811 Score: 291
Period size: 114 Copynumber: 1.8 Consensus size: 114
18656592 TGTAAAAAAA
*
18656602 AAAAAAAGAAAAAAAGAATTTTCAAATAGGCCTAAATGGTGAAAAATTTAAAAATTCTGAAAAAA
1 AAAAAAAGAAAAAAAGAAATTTCAAATAGGCCTAAATGGTGAAAAATTTAAAAATTC-GAAAAAA
18656667 AGAAAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAATCCAAC
65 AGAAAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAATCCAAC
* * * *
18656717 AAAAAAATAAAAAAGAGAGAATTTCTAAATAGGCC-CATTGGTGAAAAATTTAGAAATTC-AAAA
1 AAAAAAAGAAAAAA-AGA-AATTTC-AAATAGGCCTAAATGGTGAAAAATTTAAAAATTCGAAAA
* * *
18656780 GAA-AAAATATTTCTAATTTGGCCCAAATGGTG
63 AAAGAAAATATTTCTAAATTGACCCAAATGGTG
18656812 GAATAATTAG
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
114 27 0.32
115 19 0.23
116 3 0.04
117 26 0.31
118 9 0.11
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.24
Consensus pattern (114 bp):
AAAAAAAGAAAAAAAGAAATTTCAAATAGGCCTAAATGGTGAAAAATTTAAAAATTCGAAAAAAA
GAAAATATTTCTAAATTGACCCAAATGGTGAAAAATTTAGAAATCCAAC
Found at i:18658801 original size:27 final size:28
Alignment explanation
Indices: 18658769--18658829 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
18658759 TTGCATTATA
*
18658769 ATAAAAA-TTTAATATGATATTTAAATT
1 ATAAAAATTTTAATATAATATTTAAATT
* *
18658796 TTAAAAATTTTTAATATAATATTTGAATT
1 ATAAAAA-TTTTAATATAATATTTAAATT
18658825 ATAAA
1 ATAAA
18658830 TTTATCAACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.21
29 22 0.79
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (28 bp):
ATAAAAATTTTAATATAATATTTAAATT
Found at i:18658972 original size:29 final size:27
Alignment explanation
Indices: 18658925--18658986 Score: 88
Period size: 29 Copynumber: 2.2 Consensus size: 27
18658915 ATTAATCAAG
*
18658925 AAATTTTTAATTTATATATCATATTAA
1 AAATTTTTAATTTAAATATCATATTAA
18658952 AAATTTTTAAAATTTAAATATCATATTAA
1 AAATTTTT--AATTTAAATATCATATTAA
*
18658981 ATATTT
1 AAATTT
18658987 CACTAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
27 8 0.26
29 23 0.74
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (27 bp):
AAATTTTTAATTTAAATATCATATTAA
Found at i:18660932 original size:63 final size:61
Alignment explanation
Indices: 18660859--18660986 Score: 139
Period size: 63 Copynumber: 2.1 Consensus size: 61
18660849 ATTTTTACTA
* * * * * * * *
18660859 ATTTTTTATATTAAAATTTCTTTTAACTAATTCTTTTTTATTATAATACAAAAGATAATAAAT
1 ATTTTGTATATAAAAAATCCTTTTAACTAAATATTTTTTACTATAATA-AAAA-ACAATAAAT
* * *
18660922 ATTTTGTATATAAAAAATCCTTTTAATTAAATATTTTTTACTATGATATAAAACAATAAAT
1 ATTTTGTATATAAAAAATCCTTTTAACTAAATATTTTTTACTATAATAAAAAACAATAAAT
18660983 ATTT
1 ATTT
18660987 ATATTATATC
Statistics
Matches: 54, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 12 0.22
62 3 0.06
63 39 0.72
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.48
Consensus pattern (61 bp):
ATTTTGTATATAAAAAATCCTTTTAACTAAATATTTTTTACTATAATAAAAAACAATAAAT
Found at i:18661620 original size:25 final size:24
Alignment explanation
Indices: 18661591--18661656 Score: 62
Period size: 26 Copynumber: 2.6 Consensus size: 24
18661581 TTAATATAAC
18661591 TATTAAAATATTAAAAATTATTTAT
1 TATTAAAATATTAAAAA-TATTTAT
*
18661616 TATTAAAGTATACTT-AAAATATTTCT
1 TATTAAA--ATA-TTAAAAATATTTAT
*
18661642 AATTAAAACTATTAA
1 TATTAAAA-TATTAA
18661657 TATTCAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
24 3 0.09
25 10 0.29
26 12 0.35
27 7 0.21
28 2 0.06
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.44
Consensus pattern (24 bp):
TATTAAAATATTAAAAATATTTAT
Found at i:18661852 original size:16 final size:16
Alignment explanation
Indices: 18661817--18661855 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
18661807 TTAAAATAGT
18661817 AATATTT-AATATTAA
1 AATATTTAAATATTAA
18661832 AATATTTAAACTATT-A
1 AATATTTAAA-TATTAA
18661848 AATATTTA
1 AATATTTA
18661856 TATTTTATAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.32
16 11 0.50
17 4 0.18
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (16 bp):
AATATTTAAATATTAA
Found at i:18662726 original size:12 final size:11
Alignment explanation
Indices: 18662709--18662738 Score: 51
Period size: 12 Copynumber: 2.6 Consensus size: 11
18662699 AAAAATGGTG
18662709 CTTTTTTTTTT
1 CTTTTTTTTTT
18662720 CCTTTTTTTTTT
1 -CTTTTTTTTTT
18662732 CTTTTTT
1 CTTTTTT
18662739 AATTTATACA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 7 0.39
12 11 0.61
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:18662825 original size:19 final size:20
Alignment explanation
Indices: 18662801--18662843 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 20
18662791 GGCACATCTA
18662801 TTTGGT-TTTCTTTTTTTTT
1 TTTGGTATTTCTTTTTTTTT
18662820 TTTGGTAATTTCTTTTTTTTT
1 TTTGGT-ATTTCTTTTTTTTT
18662841 TTT
1 TTT
18662844 ACTTTTTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
21 16 0.73
ACGTcount: A:0.05, C:0.05, G:0.09, T:0.81
Consensus pattern (20 bp):
TTTGGTATTTCTTTTTTTTT
Found at i:18667475 original size:22 final size:22
Alignment explanation
Indices: 18667445--18667487 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
18667435 TAGACTTAAA
*
18667445 GTGCCAGCTAAACTAGGTTTAG
1 GTGCCAGCTAAACTACGTTTAG
* *
18667467 GTGCTAGCTAATCTACGTTTA
1 GTGCCAGCTAAACTACGTTTA
18667488 AGATTTGATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.33
Consensus pattern (22 bp):
GTGCCAGCTAAACTACGTTTAG
Found at i:18668580 original size:45 final size:45
Alignment explanation
Indices: 18668523--18668612 Score: 162
Period size: 45 Copynumber: 2.0 Consensus size: 45
18668513 TTTCAAAATT
*
18668523 TTTCATTTCTCAATTCTCTTTATTCCTCATCGTCCAACAAATTAA
1 TTTCATTTCTCAATTCTCTTTATTCCTCATCATCCAACAAATTAA
*
18668568 TTTCGTTTCTCAATTCTCTTTATTCCTCATCATCCAACAAATTAA
1 TTTCATTTCTCAATTCTCTTTATTCCTCATCATCCAACAAATTAA
18668613 GTCTTCAACT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.27, G:0.02, T:0.44
Consensus pattern (45 bp):
TTTCATTTCTCAATTCTCTTTATTCCTCATCATCCAACAAATTAA
Found at i:18669213 original size:27 final size:27
Alignment explanation
Indices: 18669162--18669214 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
18669152 TCAATTCATT
*
18669162 CAAGAAGGTTTCACCATTTGCAGGGAC
1 CAAGAAGGTTTCACCATTTGAAGGGAC
*
18669189 CAAGAAGGTTTTACCACTTT-AAGGGA
1 CAAGAAGGTTTCACCA-TTTGAAGGGA
18669215 ACAAAAGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
27 20 0.87
28 3 0.13
ACGTcount: A:0.32, C:0.19, G:0.25, T:0.25
Consensus pattern (27 bp):
CAAGAAGGTTTCACCATTTGAAGGGAC
Found at i:18673002 original size:15 final size:17
Alignment explanation
Indices: 18672963--18673009 Score: 62
Period size: 17 Copynumber: 2.9 Consensus size: 17
18672953 TTACTGAATA
* *
18672963 ATTATTTTTATGTTAAT
1 ATTAATTTTATTTTAAT
18672980 ATTAATTTTATTTTAA-
1 ATTAATTTTATTTTAAT
18672996 A-TAATTTTATTTTA
1 ATTAATTTTATTTTA
18673010 TGTTTTCTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 13 0.46
16 1 0.04
17 14 0.50
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
ATTAATTTTATTTTAAT
Found at i:18679354 original size:8 final size:8
Alignment explanation
Indices: 18679341--18679371 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
18679331 TTAGGGAAGG
18679341 AGAGAAAA
1 AGAGAAAA
18679349 AGAGAAAA
1 AGAGAAAA
18679357 AGAGAAAA
1 AGAGAAAA
18679365 AGA-AAAA
1 AGAGAAAA
18679372 GGAACAAGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 4 0.17
8 19 0.83
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (8 bp):
AGAGAAAA
Found at i:18679380 original size:13 final size:14
Alignment explanation
Indices: 18679341--18679382 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
18679331 TTAGGGAAGG
18679341 AGAGAAAAAGAGAAAA
1 AGAG-AAAA-AGAAAA
18679357 AGAGAAAAAGAAAA
1 AGAGAAAAAGAAAA
*
18679371 AG-GAACAAGAAA
1 AGAGAAAAAGAAA
18679383 CGAAGGCTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 9 0.36
14 8 0.32
15 4 0.16
16 4 0.16
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (14 bp):
AGAGAAAAAGAAAA
Found at i:18681102 original size:30 final size:30
Alignment explanation
Indices: 18681079--18681135 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
18681069 AATTAAGTCC
*
18681079 TTAAACATCTATTTTCACTTAATTGAACCA
1 TTAAACATATATTTTCACTTAATTGAACCA
18681109 TTAAACATATATTTTCA-TTCAATTGAA
1 TTAAACATATATTTTCACTT-AATTGAA
18681136 TTTTCAATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 2 0.08
30 23 0.92
ACGTcount: A:0.39, C:0.16, G:0.04, T:0.42
Consensus pattern (30 bp):
TTAAACATATATTTTCACTTAATTGAACCA
Found at i:18681591 original size:14 final size:14
Alignment explanation
Indices: 18681572--18681598 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
18681562 TTTTGTTTCG
18681572 TGAAAAATGATTTT
1 TGAAAAATGATTTT
18681586 TGAAAAATGATTT
1 TGAAAAATGATTT
18681599 ATGTATTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.41
Consensus pattern (14 bp):
TGAAAAATGATTTT
Found at i:18681681 original size:23 final size:22
Alignment explanation
Indices: 18681640--18681682 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
18681630 AAATAGTTAG
*
18681640 TCAATAAAAAATGACTTATTGA
1 TCAATAAAAAATGAATTATTGA
*
18681662 TCAATGAAAAATGAGATTATT
1 TCAATAAAAAATGA-ATTATT
18681683 TTTCTGAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.49, C:0.07, G:0.12, T:0.33
Consensus pattern (22 bp):
TCAATAAAAAATGAATTATTGA
Found at i:18682097 original size:25 final size:24
Alignment explanation
Indices: 18682061--18682140 Score: 72
Period size: 29 Copynumber: 3.1 Consensus size: 24
18682051 CATTTATTTT
*
18682061 TATTTTGTATATTATTAATCATAAA
1 TATTTTGTATATT-TTAATAATAAA
*
18682086 TATTTT-TAATATTTTTATAATAAA
1 TATTTTGT-ATATTTTAATAATAAA
18682110 TAGTATTATGTTATTATTTTAATAATAAA
1 TA-T-TT-TG-TA-TATTTTAATAATAAA
18682139 TA
1 TA
18682141 ATAATATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
24 12 0.27
25 12 0.27
26 2 0.04
27 1 0.02
28 1 0.02
29 17 0.38
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.54
Consensus pattern (24 bp):
TATTTTGTATATTTTAATAATAAA
Found at i:18682164 original size:40 final size:40
Alignment explanation
Indices: 18682120--18682201 Score: 121
Period size: 40 Copynumber: 2.0 Consensus size: 40
18682110 TAGTATTATG
*
18682120 TTATTATTTTAATAATAAATAAT-AATATATTTAATAATAT
1 TTATTATTTTAATAATAAATAATAAATA-ATATAATAATAT
* *
18682160 TTATTATTTTAATAATTAATATTAAATAATATAATAATAT
1 TTATTATTTTAATAATAAATAATAAATAATATAATAATAT
18682200 TT
1 TT
18682202 TCATAATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 34 0.89
41 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (40 bp):
TTATTATTTTAATAATAAATAATAAATAATATAATAATAT
Found at i:18682170 original size:18 final size:20
Alignment explanation
Indices: 18682120--18682183 Score: 69
Period size: 22 Copynumber: 3.1 Consensus size: 20
18682110 TAGTATTATG
18682120 TTATTATTTTAATAATAAATA
1 TTATTATTTTAATAAT-AATA
* *
18682141 ATAATATATTTAATAAT-AT-
1 TTATTAT-TTTAATAATAATA
18682160 TTATTATTTTAATAATTAATA
1 TTATTATTTTAATAA-TAATA
18682181 TTA
1 TTA
18682184 AATAATATAA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
18 8 0.23
19 6 0.17
20 4 0.11
21 8 0.23
22 9 0.26
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATTATTTTAATAATAATA
Found at i:18682179 original size:22 final size:22
Alignment explanation
Indices: 18682120--18682182 Score: 62
Period size: 19 Copynumber: 3.0 Consensus size: 22
18682110 TAGTATTATG
*
18682120 TTATTATTTTAATAATAAATA-
1 TTATTATTTTAATAATTAATAT
* * *
18682141 ATAATATATT--TAA-TAATAT
1 TTATTATTTTAATAATTAATAT
18682160 TTATTATTTTAATAATTAATAT
1 TTATTATTTTAATAATTAATAT
18682182 T
1 T
18682183 AAATAATATA
Statistics
Matches: 31, Mismatches: 7, Indels: 7
0.69 0.16 0.16
Matches are distributed among these distances:
18 4 0.13
19 10 0.32
21 10 0.32
22 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTATTATTTTAATAATTAATAT
Found at i:18682556 original size:15 final size:16
Alignment explanation
Indices: 18682536--18682569 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
18682526 TATAATTATT
*
18682536 TTTTAATATTA-ATAA
1 TTTTAATAATATATAA
18682551 TTTTAATAATATATAA
1 TTTTAATAATATATAA
18682567 TTT
1 TTT
18682570 CAAAATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
TTTTAATAATATATAA
Found at i:18682912 original size:2 final size:2
Alignment explanation
Indices: 18682905--18682934 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
18682895 AGATTATTCA
*
18682905 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18682935 TTTAGTTAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Done.