Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A11
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: 113101708
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2797742 characters in sequence are not A, C, G, or T
File 75 of 352
Found at i:23474021 original size:5 final size:5
Alignment explanation
Indices: 23474011--23474035 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
23474001 TGTTTAAAGG
23474011 GTTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT
23474036 TAAGTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:23477719 original size:20 final size:20
Alignment explanation
Indices: 23477681--23477728 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
23477671 TAATTTTTAA
* **
23477681 AAAGATAAATACATTTAATT
1 AAAGATAAATAAAGATAATT
23477701 AAAGATAAATAAAGATAATT
1 AAAGATAAATAAAGATAATT
23477721 AAA-ATAAA
1 AAAGATAAA
23477729 ATCCTAAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
19 5 0.20
20 20 0.80
ACGTcount: A:0.65, C:0.02, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAGATAAATAAAGATAATT
Found at i:23478506 original size:16 final size:17
Alignment explanation
Indices: 23478469--23478510 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
23478459 CTTATATCAA
*
23478469 TAAAA-TAAAATAATTT
1 TAAAATTAAAATAACTT
23478485 TAAAAATTAAAAT-ACTT
1 T-AAAATTAAAATAACTT
23478502 TAAAATTAA
1 TAAAATTAA
23478511 CTTAATTGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
16 9 0.39
17 8 0.35
18 6 0.26
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
TAAAATTAAAATAACTT
Found at i:23480376 original size:24 final size:24
Alignment explanation
Indices: 23480349--23480399 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
23480339 GACAGCGGTG
*
23480349 GAGATGAATATGAATATGAGG-GTC
1 GAGATGAACATGAATATG-GGAGTC
23480373 GAGATGAACATGAATATGGGAGTC
1 GAGATGAACATGAATATGGGAGTC
23480397 GAG
1 GAG
23480400 GTGCTAGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.37, C:0.06, G:0.35, T:0.22
Consensus pattern (24 bp):
GAGATGAACATGAATATGGGAGTC
Found at i:23482272 original size:19 final size:19
Alignment explanation
Indices: 23482248--23482345 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
23482238 AATCTTTAAG
23482248 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23482267 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23482286 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23482303 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23482322 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
23482343 GAT
1 GAT
23482346 CTTGTAATAT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:23482278 original size:36 final size:35
Alignment explanation
Indices: 23482238--23482345 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 35
23482228 ATGGAAATAT
23482238 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
23482274 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
*
23482310 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
23482346 CTTGTAATAT
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 28 0.46
37 1 0.02
38 7 0.11
40 10 0.16
41 6 0.10
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Found at i:23484936 original size:14 final size:14
Alignment explanation
Indices: 23484917--23484969 Score: 56
Period size: 14 Copynumber: 3.7 Consensus size: 14
23484907 ATCTATACCT
23484917 TTTGCATTCATGCA
1 TTTGCATTCATGCA
*
23484931 TTTGCATCTCATAGTA
1 TTTGCAT-TCAT-GCA
23484947 TTT-CATTGCAT-CA
1 TTTGCATT-CATGCA
23484960 TTTGCATTCA
1 TTTGCATTCA
23484970 AAATTATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
13 6 0.18
14 12 0.36
15 10 0.30
16 5 0.15
ACGTcount: A:0.23, C:0.21, G:0.11, T:0.45
Consensus pattern (14 bp):
TTTGCATTCATGCA
Found at i:23488624 original size:132 final size:132
Alignment explanation
Indices: 23488387--23489101 Score: 1207
Period size: 132 Copynumber: 5.4 Consensus size: 132
23488377 CAGAGAAACA
* * * * *
23488387 AGATTTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGAAGATCTGACACTCTTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
* * *
23488452 ACAGCGAAGCAGATCGAAGATTTTAGCATGGCATCCCTGTGTTTATATGGAGCAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
23488517 GC
131 GC
** * *
23488519 AGATTTTTCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGTAGATCTAACACTT-CTGTGAT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACA-TTCCTGTGAT
*
23488583 TACAGCGAAGCAGATTGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAT
65 TACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAT
23488648 AGC
130 AGC
* * *
23488651 AGATTTAGCATCCCTGTATTTATAAGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
*
23488716 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
23488781 GC
131 GC
* *
23488783 AGATTTGGCATCCTTGTGTTTATAGGGAACAAAACGAAGATAGCAGATCTGACATTCCTGTGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
*
23488848 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAGA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
23488913 GC
131 GC
23488915 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
*
23488980 ACAGCAAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
23489045 GC
131 GC
* *
23489047 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAACAAATCTGACAT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACAT
23489102 CTCCATTTCG
Statistics
Matches: 550, Mismatches: 31, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
131 2 0.00
132 547 0.99
133 1 0.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGATT
ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GC
Found at i:23489697 original size:19 final size:19
Alignment explanation
Indices: 23489673--23489784 Score: 156
Period size: 19 Copynumber: 5.8 Consensus size: 19
23489663 AATCTTTAAA
23489673 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23489692 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23489711 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
23489728 GATATACAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23489747 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
* *
23489768 GATCTTGTAATCTTAGA
1 GAT-ATGCAATCTTAGA
23489785 GATTTAATTT
Statistics
Matches: 85, Mismatches: 3, Indels: 9
0.88 0.03 0.09
Matches are distributed among these distances:
17 17 0.20
19 48 0.56
20 3 0.04
21 9 0.11
22 8 0.09
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:23489703 original size:36 final size:35
Alignment explanation
Indices: 23489663--23489770 Score: 117
Period size: 36 Copynumber: 2.9 Consensus size: 35
23489653 ATGGAAATAT
*
23489663 AATCTTTAAAGATATGCAATCTTAGATATGATATGC
1 AATC-TTAAAGATATGCAATCTTAGATATGATATAC
* * *
23489699 AATCTTAGATATGATACAATCTTAGATATGATATAC
1 AATCTTAAAGAT-ATGCAATCTTAGATATGATATAC
23489735 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTTA-A-A-GATATGCAATCTT--AGATATGAT
23489771 CTTGTAATCT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
35 6 0.10
36 32 0.54
38 10 0.17
39 2 0.03
40 9 0.15
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (35 bp):
AATCTTAAAGATATGCAATCTTAGATATGATATAC
Found at i:23492332 original size:17 final size:19
Alignment explanation
Indices: 23492290--23492333 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
23492280 CCTAAACAAA
23492290 AAAAAACTCTAACCCTCTT
1 AAAAAACTCTAACCCTCTT
*
23492309 AACAAACTCTAA-CC-CTT
1 AAAAAACTCTAACCCTCTT
23492326 AAAAAACT
1 AAAAAACT
23492334 ATAAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 10 0.43
18 2 0.09
19 11 0.48
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.23
Consensus pattern (19 bp):
AAAAAACTCTAACCCTCTT
Found at i:23497436 original size:312 final size:312
Alignment explanation
Indices: 23496871--23497499 Score: 1258
Period size: 312 Copynumber: 2.0 Consensus size: 312
23496861 GATGAGCAAG
23496871 ATTGTGAATAGTAATCTCATTTTATGATTGGCTAGGGACATTATTGCTCGGCTGTCTTTCTTTAC
1 ATTGTGAATAGTAATCTCATTTTATGATTGGCTAGGGACATTATTGCTCGGCTGTCTTTCTTTAC
23496936 ACCATTCATTCTTTTTGTCATTTTTTGTCATCTCAAGTTTTTCATGACCAAAAACAGAAAGAATA
66 ACCATTCATTCTTTTTGTCATTTTTTGTCATCTCAAGTTTTTCATGACCAAAAACAGAAAGAATA
23497001 AATGTGTAGTAAGATCACCAATGAAGTGATTGTTTCGTGGGATTTAACTTCAAATCCATTTCCAG
131 AATGTGTAGTAAGATCACCAATGAAGTGATTGTTTCGTGGGATTTAACTTCAAATCCATTTCCAG
23497066 ATTTGGTGCCAAAAATCAAATCTGAAAATTTCTACATTTATAAATTATCTACAACAGGGTTGGAC
196 ATTTGGTGCCAAAAATCAAATCTGAAAATTTCTACATTTATAAATTATCTACAACAGGGTTGGAC
23497131 ATTTAGAGGATACCATAACTACAATCAAAACCAGGGATGCCATGTTGGATCC
261 ATTTAGAGGATACCATAACTACAATCAAAACCAGGGATGCCATGTTGGATCC
23497183 ATTGTGAATAGTAATCTCATTTTATGATTGGCTAGGGACATTATTGCTCGGCTGTCTTTCTTTAC
1 ATTGTGAATAGTAATCTCATTTTATGATTGGCTAGGGACATTATTGCTCGGCTGTCTTTCTTTAC
23497248 ACCATTCATTCTTTTTGTCATTTTTTGTCATCTCAAGTTTTTCATGACCAAAAACAGAAAGAATA
66 ACCATTCATTCTTTTTGTCATTTTTTGTCATCTCAAGTTTTTCATGACCAAAAACAGAAAGAATA
23497313 AATGTGTAGTAAGATCACCAATGAAGTGATTGTTTCGTGGGATTTAACTTCAAATCCATTTCCAG
131 AATGTGTAGTAAGATCACCAATGAAGTGATTGTTTCGTGGGATTTAACTTCAAATCCATTTCCAG
23497378 ATTTGGTGCCAAAAATCAAATCTGAAAATTTCTACATTTATAAATTATCTACAACAGGGTTGGAC
196 ATTTGGTGCCAAAAATCAAATCTGAAAATTTCTACATTTATAAATTATCTACAACAGGGTTGGAC
23497443 ATTTAGAGGATACCATAACTACAATCAAAACCAGGGATGCCATGTTGGATCC
261 ATTTAGAGGATACCATAACTACAATCAAAACCAGGGATGCCATGTTGGATCC
23497495 ATTGT
1 ATTGT
23497500 ACATAAATTT
Statistics
Matches: 317, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
312 317 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (312 bp):
ATTGTGAATAGTAATCTCATTTTATGATTGGCTAGGGACATTATTGCTCGGCTGTCTTTCTTTAC
ACCATTCATTCTTTTTGTCATTTTTTGTCATCTCAAGTTTTTCATGACCAAAAACAGAAAGAATA
AATGTGTAGTAAGATCACCAATGAAGTGATTGTTTCGTGGGATTTAACTTCAAATCCATTTCCAG
ATTTGGTGCCAAAAATCAAATCTGAAAATTTCTACATTTATAAATTATCTACAACAGGGTTGGAC
ATTTAGAGGATACCATAACTACAATCAAAACCAGGGATGCCATGTTGGATCC
Found at i:23517263 original size:20 final size:19
Alignment explanation
Indices: 23517207--23517277 Score: 83
Period size: 19 Copynumber: 3.7 Consensus size: 19
23517197 AAAAAAATAA
23517207 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTA-AAATT
* *
23517227 ATTTTAAATTTTAAAAATT
1 ATTTTGAATTTTTAAAATT
23517246 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAATT
23517266 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
23517278 TTTTTGTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 3 0.07
19 25 0.56
20 17 0.38
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:23517278 original size:20 final size:20
Alignment explanation
Indices: 23517207--23517277 Score: 85
Period size: 20 Copynumber: 3.6 Consensus size: 20
23517197 AAAAAAATAA
*
23517207 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTAAAAATT
*
23517227 ATTTT-AAATTTTAAAAATT
1 ATTTTGAATTTTTAAAAATT
*
23517246 ATTTTGAATTTTTGAAAATT
1 ATTTTGAATTTTTAAAAATT
23517266 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
23517278 TTTTTGTAAT
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
18 10 0.22
19 12 0.27
20 23 0.51
ACGTcount: A:0.37, C:0.00, G:0.06, T:0.58
Consensus pattern (20 bp):
ATTTTGAATTTTTAAAAATT
Found at i:23521229 original size:16 final size:16
Alignment explanation
Indices: 23521196--23521229 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23521186 ACCCCGTGTT
* *
23521196 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
23521212 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
23521228 AA
1 AA
23521230 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:23524052 original size:21 final size:21
Alignment explanation
Indices: 23524026--23524066 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
23524016 AGACGAGCAA
* *
23524026 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
23524047 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
23524067 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:23526004 original size:16 final size:16
Alignment explanation
Indices: 23525971--23526004 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
23525961 GGAGATTGTT
* *
23525971 AACATTAATGGGAGAC
1 AACATTAATGGCAAAC
23525987 AACATTAATGGCAAAC
1 AACATTAATGGCAAAC
23526003 AA
1 AA
23526005 TACAAAGTGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.15, G:0.18, T:0.18
Consensus pattern (16 bp):
AACATTAATGGCAAAC
Found at i:23531336 original size:27 final size:27
Alignment explanation
Indices: 23531306--23531361 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
23531296 ACTTATAACA
23531306 CATAGCATGAAAATTGATCATTCCCAT
1 CATAGCATGAAAATTGATCATTCCCAT
23531333 CATAGCATGAAAATTGATCATTCCCAT
1 CATAGCATGAAAATTGATCATTCCCAT
23531360 CA
1 CA
23531362 CCTTTATTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.23, G:0.11, T:0.29
Consensus pattern (27 bp):
CATAGCATGAAAATTGATCATTCCCAT
Found at i:23531872 original size:3 final size:3
Alignment explanation
Indices: 23531864--23531895 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
23531854 CACCAGTTGC
*
23531864 TCT TCT TCT TCT TCT TCT TCT TCT TCT ACT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
23531896 CTCAAGCTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.03, C:0.34, G:0.00, T:0.62
Consensus pattern (3 bp):
TCT
Found at i:23533379 original size:17 final size:18
Alignment explanation
Indices: 23533357--23533394 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
23533347 ATATAAATAT
* *
23533357 ATTTTTTAATATT-ATTA
1 ATTTTTAAAAATTAATTA
23533374 ATTTTTAAAAATTAATTA
1 ATTTTTAAAAATTAATTA
23533392 ATT
1 ATT
23533395 GTAAATATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
ATTTTTAAAAATTAATTA
Found at i:23535051 original size:15 final size:15
Alignment explanation
Indices: 23535033--23535063 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
23535023 TTTTAGGGGA
23535033 TTTCATTTTAGTCAC
1 TTTCATTTTAGTCAC
*
23535048 TTTCATTTTGGTCAC
1 TTTCATTTTAGTCAC
23535063 T
1 T
23535064 CAGTTTTTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.16, C:0.19, G:0.10, T:0.55
Consensus pattern (15 bp):
TTTCATTTTAGTCAC
Found at i:23547183 original size:22 final size:21
Alignment explanation
Indices: 23547134--23547184 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
23547124 ATATAACCAA
*
23547134 AAATAAATAAAAATTGAAAAT
1 AAATAAATAAAAATTAAAAAT
** *
23547155 ACTTAAATCAATAATTAAAAAT
1 AAATAAAT-AAAAATTAAAAAT
23547177 AAATAAAT
1 AAATAAAT
23547185 GATAAAAAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 6 0.26
22 17 0.74
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATAAATAAAAATTAAAAAT
Found at i:23550035 original size:30 final size:30
Alignment explanation
Indices: 23549999--23550059 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
23549989 TACACCCCAT
23549999 TTAGTATGTACCACCTTATTCTGGTCCGTA
1 TTAGTATGTACCACCTTATTCTGGTCCGTA
23550029 TTAGTATGTACCACCTTATTCTGGTCCGTA
1 TTAGTATGTACCACCTTATTCTGGTCCGTA
23550059 T
1 T
23550060 CCTAGCCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.41
Consensus pattern (30 bp):
TTAGTATGTACCACCTTATTCTGGTCCGTA
Found at i:23553674 original size:21 final size:21
Alignment explanation
Indices: 23553612--23553676 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
23553602 CCTGATCAGA
*
23553612 ATACGACACATAAAGTGCCTA
1 ATACGACACATAAAGTGCCTG
* ** *
23553633 AAACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTG
23553654 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
23553675 AT
1 AT
23553677 CAGTAAAGCC
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.38, C:0.25, G:0.20, T:0.17
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:23554604 original size:22 final size:21
Alignment explanation
Indices: 23554579--23554619 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
23554569 TTTCTTTCTT
23554579 TTCTTTGATTCCTTTTATTTCA
1 TTCTTTGATT-CTTTTATTTCA
*
23554601 TTCTTTTATTCTTTTATTT
1 TTCTTTGATTCTTTTATTT
23554620 ACTTTGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.12, C:0.15, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCTTTGATTCTTTTATTTCA
Found at i:23554844 original size:23 final size:23
Alignment explanation
Indices: 23554817--23554873 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
23554807 AAATTAGTTA
*
23554817 TTTTATTACAAGTGTA-C-ATAT
1 TTTTATTACAAATGTACCAATAT
23554838 CTATTTATTACAAATGTACCAATAT
1 -T-TTTATTACAAATGTACCAATAT
23554863 TTTTATTACAA
1 TTTTATTACAA
23554874 TTGTCATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 1 0.03
23 24 0.77
24 2 0.06
25 4 0.13
ACGTcount: A:0.37, C:0.12, G:0.05, T:0.46
Consensus pattern (23 bp):
TTTTATTACAAATGTACCAATAT
Found at i:23555114 original size:3 final size:3
Alignment explanation
Indices: 23555106--23555167 Score: 58
Period size: 3 Copynumber: 21.3 Consensus size: 3
23555096 TAATGAAACC
* ** *
23555106 ATA ATA ATA ATA ATA ATA ATA ATA AT- TTA AT- ATA A-A ACC ATA CTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
23555151 ATA ATTA ATA ATA ATA A
1 ATA A-TA ATA ATA ATA A
23555168 AATCTTAGAA
Statistics
Matches: 48, Mismatches: 7, Indels: 8
0.76 0.11 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:23562164 original size:20 final size:20
Alignment explanation
Indices: 23562126--23562164 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23562116 ATTTCAAATA
*
23562126 TAAGGAAATAAAATGTAACC
1 TAAGGAAATAAAATATAACC
23562146 TAAGGTAAATAAAA-ATAAC
1 TAAGG-AAATAAAATATAAC
23562165 TATTTTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.59, C:0.08, G:0.13, T:0.21
Consensus pattern (20 bp):
TAAGGAAATAAAATATAACC
Found at i:23564115 original size:16 final size:16
Alignment explanation
Indices: 23564094--23564124 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
23564084 CGACGTGTTG
23564094 CTATAAATCACAAACT
1 CTATAAATCACAAACT
23564110 CTATAAATCACAAAC
1 CTATAAATCACAAAC
23564125 CAACACTGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.00, T:0.23
Consensus pattern (16 bp):
CTATAAATCACAAACT
Found at i:23569199 original size:29 final size:28
Alignment explanation
Indices: 23569150--23569205 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
23569140 CTTGTCATTT
23569150 ATTTCACATTTCAACCTCTAAATTTTCAC
1 ATTTCACATTTCAACCTCT-AATTTTCAC
23569179 ATTTCACAATTT-AATCC-CTAATTTTCA
1 ATTTCAC-ATTTCAA-CCTCTAATTTTCA
23569206 TTTTTACCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
28 8 0.32
29 11 0.44
30 6 0.24
ACGTcount: A:0.32, C:0.25, G:0.00, T:0.43
Consensus pattern (28 bp):
ATTTCACATTTCAACCTCTAATTTTCAC
Found at i:23580816 original size:17 final size:17
Alignment explanation
Indices: 23580794--23580827 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
23580784 ATTGACAATG
23580794 TTATAAAAAATAATTAA
1 TTATAAAAAATAATTAA
*
23580811 TTATAAAAAGTAATTAA
1 TTATAAAAAATAATTAA
23580828 AAATAATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (17 bp):
TTATAAAAAATAATTAA
Found at i:23580849 original size:33 final size:33
Alignment explanation
Indices: 23580803--23580869 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
23580793 GTTATAAAAA
*
23580803 ATAATTAATTATAA-AAAGTAATTAAAAATAATT
1 ATAATTAATTATAATAAA-TAATTAAAAACAATT
*
23580836 ATAATTTAA-TATAATAAATAATTTAAAACAATT
1 ATAA-TTAATTATAATAAATAATTAAAAACAATT
23580869 A
1 A
23580870 ATTAAAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 23 0.77
34 7 0.23
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.37
Consensus pattern (33 bp):
ATAATTAATTATAATAAATAATTAAAAACAATT
Found at i:23584630 original size:12 final size:11
Alignment explanation
Indices: 23584602--23584646 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
23584592 TCATTAATAA
23584602 ATAAACGAGTC
1 ATAAACGAGTC
*
23584613 ATAAACGAGCTT
1 ATAAACGAG-TC
23584625 ATAAACGAGTC
1 ATAAACGAGTC
*
23584636 AATAAATGAGT
1 -ATAAACGAGT
23584647 TTGCTCGTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.47, C:0.13, G:0.18, T:0.22
Consensus pattern (11 bp):
ATAAACGAGTC
Found at i:23585904 original size:40 final size:42
Alignment explanation
Indices: 23585788--23585904 Score: 107
Period size: 41 Copynumber: 2.8 Consensus size: 42
23585778 GTTTTTTTTT
*
23585788 AAAACGCTTCCACGTAGACGCGTTTTCAAG--TGTAAATCAGA
1 AAAACGCTTCCACGTAGACGCGTTTTC-AGTTTGTTAATCAGA
* ** * * * *
23585829 AAAATGCTTTTAGGTGGACGCGTTTTTAGTGTTGTTAA-CTG-
1 AAAACGCTTCCACGTAGACGCGTTTTCAGT-TTGTTAATCAGA
*
23585870 AAAACGCTTCCACGTAGACGTGTTTTCAGTTTGTT
1 AAAACGCTTCCACGTAGACGCGTTTTCAGTTTGTT
23585905 GTTAGGAAAA
Statistics
Matches: 58, Mismatches: 15, Indels: 7
0.73 0.19 0.09
Matches are distributed among these distances:
40 7 0.12
41 44 0.76
42 2 0.03
43 5 0.09
ACGTcount: A:0.26, C:0.17, G:0.22, T:0.34
Consensus pattern (42 bp):
AAAACGCTTCCACGTAGACGCGTTTTCAGTTTGTTAATCAGA
Found at i:23591156 original size:211 final size:211
Alignment explanation
Indices: 23590788--23591215 Score: 840
Period size: 211 Copynumber: 2.0 Consensus size: 211
23590778 GTGTCTTAAG
23590788 CCTA-ATGGCAGCTCCTTTTTGGATCCTAAGCTCCTGTACTGAAAGTAGATTGAAATTAATGCTT
1 CCTAGATGGCAGCTCCTTTTTGGATCCTAAGCTCCTGTACTGAAAGTAGATTGAAATTAATGCTT
23590852 GGCTTAAAAGTTGACCCTTTATTTAACAAAACAAATACTTAAATTCTTTGGCTTACTAAGAAGAA
66 GGCTTAAAAGTTGACCCTTTATTTAACAAAACAAATACTTAAATTCTTTGGCTTACTAAGAAGAA
*
23590917 TATTTTTCAAAAAATTACGTTAAATTAAACTCCTAGGAAAGACTGGAGAGGTCACAGATGGTCCC
131 TATTTTTCAAAAAATTACGTTAAATTAAACTCCTAGGAAAGACTGGAGAGGTCACAGATGCTCCC
23590982 GTTTAAGTCTCAATCT
196 GTTTAAGTCTCAATCT
23590998 CCTAGATGGCAGCTCCTTTTTGGATCCTAAGCTCCTGTACTGAAAGTAGATTGAAATTAATGCTT
1 CCTAGATGGCAGCTCCTTTTTGGATCCTAAGCTCCTGTACTGAAAGTAGATTGAAATTAATGCTT
23591063 GGCTTAAAAGTTGACCCTTTATTTAACAAAACAAATACTTAAATTCTTTGGCTTACTAAGAAGAA
66 GGCTTAAAAGTTGACCCTTTATTTAACAAAACAAATACTTAAATTCTTTGGCTTACTAAGAAGAA
23591128 TATTTTTCAAAAAATTACGTTAAATTAAACTCCTAGGAAAGACTGGAGAGGTCACAGATGCTCCC
131 TATTTTTCAAAAAATTACGTTAAATTAAACTCCTAGGAAAGACTGGAGAGGTCACAGATGCTCCC
23591193 GTTTAAGTCTCAATCT
196 GTTTAAGTCTCAATCT
23591209 CCTAGAT
1 CCTAGAT
23591216 AGAGTTTTAA
Statistics
Matches: 216, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
210 4 0.02
211 212 0.98
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (211 bp):
CCTAGATGGCAGCTCCTTTTTGGATCCTAAGCTCCTGTACTGAAAGTAGATTGAAATTAATGCTT
GGCTTAAAAGTTGACCCTTTATTTAACAAAACAAATACTTAAATTCTTTGGCTTACTAAGAAGAA
TATTTTTCAAAAAATTACGTTAAATTAAACTCCTAGGAAAGACTGGAGAGGTCACAGATGCTCCC
GTTTAAGTCTCAATCT
Found at i:23594152 original size:34 final size:34
Alignment explanation
Indices: 23594109--23594177 Score: 138
Period size: 34 Copynumber: 2.0 Consensus size: 34
23594099 GACATAATTG
23594109 TGTTAGATTAATTACATTTCTTAACTTAGAAATA
1 TGTTAGATTAATTACATTTCTTAACTTAGAAATA
23594143 TGTTAGATTAATTACATTTCTTAACTTAGAAATA
1 TGTTAGATTAATTACATTTCTTAACTTAGAAATA
23594177 T
1 T
23594178 TAAGCCCATT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (34 bp):
TGTTAGATTAATTACATTTCTTAACTTAGAAATA
Found at i:23599125 original size:45 final size:45
Alignment explanation
Indices: 23599075--23599162 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
23599065 AGTGGAATTT
23599075 GACATAAATAGCCTTATATTTGATGTTTTAAATGTTTATAAACTA
1 GACATAAATAGCCTTATATTTGATGTTTTAAATGTTTATAAACTA
*
23599120 GACATAAATGGCCTTATATTTGATGTTTTAAATGTTTATAAAC
1 GACATAAATAGCCTTATATTTGATGTTTTAAATGTTTATAAAC
23599163 CAAGGTTAAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.36, C:0.09, G:0.12, T:0.42
Consensus pattern (45 bp):
GACATAAATAGCCTTATATTTGATGTTTTAAATGTTTATAAACTA
Found at i:23600038 original size:43 final size:42
Alignment explanation
Indices: 23599966--23600068 Score: 116
Period size: 43 Copynumber: 2.4 Consensus size: 42
23599956 TATCAAGATG
* * ** ** *
23599966 TGATTACATGTAAGACCATGTGTGGGACATTGGTATTGTATTA
1 TGATTACGTGTAAGACCATGTCTAAGACATTGACATTGT-TAA
23600009 TGATTACGTGTAAGACCATGTCTAAGACATTGACATTGTTAA
1 TGATTACGTGTAAGACCATGTCTAAGACATTGACATTGTTAA
*
23600051 TCGATTATGTGTAAGACC
1 T-GATTACGTGTAAGACC
23600069 TATCTTGGAT
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
42 3 0.06
43 48 0.94
ACGTcount: A:0.30, C:0.13, G:0.22, T:0.35
Consensus pattern (42 bp):
TGATTACGTGTAAGACCATGTCTAAGACATTGACATTGTTAA
Found at i:23605798 original size:43 final size:43
Alignment explanation
Indices: 23605750--23605855 Score: 176
Period size: 43 Copynumber: 2.5 Consensus size: 43
23605740 TTTTTTTTAA
*
23605750 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCACTTTTCCCAC
*
23605793 AAACGCCGCTAAAGGTCATAGCCTTTAGCGGCACTTTTCCCAC
1 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCACTTTTCCCAC
* *
23605836 AAACGCAGTTAAAGGTCATG
1 AAACGCCGCTAAAGGTCATG
23605856 AAATTTAAAA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
43 58 1.00
ACGTcount: A:0.26, C:0.29, G:0.22, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAGGTCATGGCCTTTAGCGGCACTTTTCCCAC
Found at i:23606150 original size:19 final size:20
Alignment explanation
Indices: 23606104--23606150 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
23606094 TAAATATTAA
*
23606104 AATAAAAAATAAAAATATAG
1 AATAAAAAATAAAAATAAAG
* * *
23606124 AATCAAAACT-AAAATAAAT
1 AATAAAAAATAAAAATAAAG
23606143 AATAAAAA
1 AATAAAAA
23606151 TTAGATTAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.19
Consensus pattern (20 bp):
AATAAAAAATAAAAATAAAG
Found at i:23611190 original size:14 final size:14
Alignment explanation
Indices: 23611170--23611214 Score: 81
Period size: 14 Copynumber: 3.2 Consensus size: 14
23611160 CACTAAAAAT
23611170 TAAACCCTAAACTA
1 TAAACCCTAAACTA
*
23611184 TACACCCTAAACTA
1 TAAACCCTAAACTA
23611198 TAAACCCTAAACTA
1 TAAACCCTAAACTA
23611212 TAA
1 TAA
23611215 TGATAATTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 29 1.00
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:23611802 original size:21 final size:21
Alignment explanation
Indices: 23611776--23611858 Score: 76
Period size: 21 Copynumber: 3.6 Consensus size: 21
23611766 CTCTTAAACC
*
23611776 TAAACCCTAAACCGTATATCT
1 TAAACCCTAAACCATATATCT
* *
23611797 TAAACCATAGTTAACTCATAAACCTACT
1 TAAACCCTA---AAC-CATATA--T-CT
23611825 TAAACCCTAAACCATATATCT
1 TAAACCCTAAACCATATATCT
23611846 TAAACCCTAAACC
1 TAAACCCTAAACC
23611859 TTAAACTGTA
Statistics
Matches: 50, Mismatches: 5, Indels: 14
0.72 0.07 0.20
Matches are distributed among these distances:
21 23 0.46
22 1 0.02
24 8 0.16
25 7 0.14
27 1 0.02
28 10 0.20
ACGTcount: A:0.42, C:0.29, G:0.02, T:0.27
Consensus pattern (21 bp):
TAAACCCTAAACCATATATCT
Found at i:23611808 original size:45 final size:48
Alignment explanation
Indices: 23611759--23611851 Score: 138
Period size: 49 Copynumber: 2.0 Consensus size: 48
23611749 CTTCAAATAC
* *
23611759 TAGTTAACTCTTAAA-C-C-TAAACCCTAAACCGTATATCTTAAACCA
1 TAGTTAACTCATAAACCACTTAAACCCTAAACCATATATCTTAAACCA
23611804 TAGTTAACTCATAAACCTACTTAAACCCTAAACCATATATCTTAAACC
1 TAGTTAACTCATAAACC-ACTTAAACCCTAAACCATATATCTTAAACC
23611852 CTAAACCTTA
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
45 14 0.33
46 1 0.02
48 1 0.02
49 26 0.62
ACGTcount: A:0.41, C:0.27, G:0.03, T:0.29
Consensus pattern (48 bp):
TAGTTAACTCATAAACCACTTAAACCCTAAACCATATATCTTAAACCA
Found at i:23612275 original size:41 final size:41
Alignment explanation
Indices: 23612026--23612268 Score: 357
Period size: 41 Copynumber: 6.0 Consensus size: 41
23612016 GTTATATGAC
* *
23612026 TTTTAGCGGCGTTTTACTAAAAGCGCCGCTAATGCTTTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
23612067 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
23612108 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
23612149 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCT-GT
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
** * ** *
23612189 TTTTAGCGGCGTTTTAGTAAAAAAG-GCCTCTGTTGCT-TTGT
1 TTTTAGCGGCGTTTTA--CCAAAAGCGCCGCTAATGCTCTGGT
* *
23612230 TTTTAGCGGCGTTTTACCAAAAACGCCGCTATTGCTCTG
1 TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTG
23612269 TATTTTAAAA
Statistics
Matches: 184, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
39 4 0.02
40 29 0.16
41 146 0.79
42 5 0.03
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTACCAAAAGCGCCGCTAATGCTCTGGT
Found at i:23612913 original size:21 final size:20
Alignment explanation
Indices: 23612882--23612921 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
23612872 ACAAAACTTG
23612882 CATAACTATCATTAAACATT
1 CATAACTATCATTAAACATT
23612902 CATAATCTATCATTAAACAT
1 CATAA-CTATCATTAAACAT
23612922 CAAAATACTC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (20 bp):
CATAACTATCATTAAACATT
Found at i:23613732 original size:33 final size:33
Alignment explanation
Indices: 23613690--23613755 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
23613680 ACACGAGAAT
*
23613690 AAGACGATACATACTAACTAGTGGGTGGTGCAA
1 AAGACGATACATACTAACTAGTGGGGGGTGCAA
*
23613723 AAGACGATACATACTGACTAGTGGGGGGTGCAA
1 AAGACGATACATACTAACTAGTGGGGGGTGCAA
23613756 TCATTGATGG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.35, C:0.15, G:0.30, T:0.20
Consensus pattern (33 bp):
AAGACGATACATACTAACTAGTGGGGGGTGCAA
Found at i:23625646 original size:16 final size:17
Alignment explanation
Indices: 23625596--23625646 Score: 59
Period size: 19 Copynumber: 2.9 Consensus size: 17
23625586 ATGGAAATAT
*
23625596 AATCTTTAAGGATATGC
1 AATCTTGAAGGATATGC
*
23625613 AATCTTAGATATGATATGC
1 AATCTT-GA-AGGATATGC
23625632 AATCTTGAA-GATATG
1 AATCTTGAAGGATATG
23625647 ATCTTGTAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
16 6 0.20
17 7 0.23
18 3 0.10
19 14 0.47
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (17 bp):
AATCTTGAAGGATATGC
Found at i:23625665 original size:22 final size:21
Alignment explanation
Indices: 23625606--23625648 Score: 72
Period size: 19 Copynumber: 2.1 Consensus size: 21
23625596 AATCTTTAAG
23625606 GATATGCAATCTT--AGATAT
1 GATATGCAATCTTGAAGATAT
23625625 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTTGAAGATAT
23625646 GAT
1 GAT
23625649 CTTGTAATCT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 13 0.59
21 9 0.41
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (21 bp):
GATATGCAATCTTGAAGATAT
Found at i:23625890 original size:32 final size:32
Alignment explanation
Indices: 23625865--23625932 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 32
23625855 TTTTTTCTTA
23625865 TTTTATTCTTCGTCTATCTTAG-TTTTTCAACC
1 TTTTATTCTTCGTCTATCTTAGTTTTTTCAA-C
23625897 TTTTATTCTTCGTCTATCTTAG-TTTTTCAACC
1 TTTTATTCTTCGTCTATCTTAGTTTTTTCAA-C
23625929 TTTT
1 TTTT
23625933 TTTTATTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.15, C:0.21, G:0.06, T:0.59
Consensus pattern (32 bp):
TTTTATTCTTCGTCTATCTTAGTTTTTTCAAC
Found at i:23632247 original size:132 final size:132
Alignment explanation
Indices: 23632008--23633207 Score: 2006
Period size: 132 Copynumber: 9.1 Consensus size: 132
23631998 CAAAGAAACT
* * *
23632008 AGATTTGGCAT-CCTGTGTTTATAGGGAAACAGATCGAAGATAGCAGATCTGACACTCATGTGCT
1 AGATTTGGCATCCCTGTGTTTATAGGG-AACAAATCGAAGATAGCAGATCTGACATTCCTGTGCT
* *
23632072 TACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCGCAGTGTTTATAGGGAACAAGTTGAAGAT
65 TACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGAT
23632137 AGC
130 AGC
* * *
23632140 AGATTTGGAATCCCTGTGTTTATAGGGAACAAATCAAAGATAGCAGATCTGACATTCCTATGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
23632205 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
*
23632270 AC
131 GC
23632272 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
*
23632337 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTAAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
23632402 GC
131 GC
* * * * * *
23632404 AGATTTTGCATCCCTATTTTTATAGGGAATAAATCGAAGATAGTAGATCTGATATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* *
23632469 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATATGGAACAAGTTAAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
23632534 GC
131 GC
23632536 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
*
23632601 ACAGCGAAGCAGATCAAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
23632666 GC
131 GC
*
23632668 AGATTTGGCATCCCTGTGTTTATAGGGAATAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* * *
23632733 ACAGCGAAGAAGATCGAAGATTTCAGCATGGCATCCCTGTTTTTATAGAGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
23632798 GC
131 GC
*
23632800 AGATTTGGCATCCCTGTGTTTATAGGGAATAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* ** * * * *
23632865 ATAGCGAAATAGATCAAAGATTTTAACATGGCATCCCTATGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
*
23632930 GT
131 GC
*
23632932 AGATTTGGCATCCCTGTGTTTATAGGGAATAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
*
23632997 ACAGCGAAGCAGGTCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
23633062 GC
131 GC
* * * * *
23633064 AGATTTGGCATCCCTATGTTTATAGGGAACAAATCGAAAATAACAAATCTAACATTCCTGTGCTT
1 AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
* *
23633129 ACAGTGAAGCAGATCGAAGATTTCAGCATGGTATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
66 ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
*
23633194 GT
131 GC
23633196 AGATTTGGCATC
1 AGATTTGGCATC
23633208 TCCGTATTCG
Statistics
Matches: 1003, Mismatches: 64, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
132 988 0.99
133 15 0.01
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (132 bp):
AGATTTGGCATCCCTGTGTTTATAGGGAACAAATCGAAGATAGCAGATCTGACATTCCTGTGCTT
ACAGCGAAGCAGATCGAAGATTTCAGCATGGCATCCCTGTGTTTATAGGGAACAAGTTGAAGATA
GC
Found at i:23633716 original size:14 final size:15
Alignment explanation
Indices: 23633697--23633753 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 15
23633687 CATCTTTAAG
23633697 GATATG-CAATCTTA
1 GATATGACAATCTTA
23633711 GATATGATACAATCTTA
1 GATATG--ACAATCTTA
23633728 GATATGATATGCAATCTTA
1 GATATG--A--CAATCTTA
23633747 GATATGA
1 GATATGA
23633754 TATGCAATCT
Statistics
Matches: 38, Mismatches: 0, Indels: 7
0.84 0.00 0.16
Matches are distributed among these distances:
14 6 0.16
17 18 0.47
19 14 0.37
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (15 bp):
GATATGACAATCTTA
Found at i:23633737 original size:36 final size:38
Alignment explanation
Indices: 23633697--23633775 Score: 126
Period size: 36 Copynumber: 2.1 Consensus size: 38
23633687 CATCTTTAAG
23633697 GATATGCAATCTTAGATATGATA-CAATCTT-AGATAT
1 GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
23633733 GATATGCAATCTTAGATATGATATGCAATCTTGAAGATAT
1 GATATGCAATCTTAGATATGATA-GCAATCTT-AAGATAT
23633773 GAT
1 GAT
23633776 CTTGTAATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 23 0.59
38 7 0.18
40 9 0.23
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (38 bp):
GATATGCAATCTTAGATATGATAGCAATCTTAAGATAT
Found at i:23633744 original size:19 final size:19
Alignment explanation
Indices: 23633697--23633775 Score: 126
Period size: 19 Copynumber: 4.2 Consensus size: 19
23633687 CATCTTTAAG
23633697 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23633716 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23633733 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
23633752 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
23633773 GAT
1 GAT
23633776 CTTGTAATCT
Statistics
Matches: 56, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.30
19 30 0.54
21 9 0.16
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:23638911 original size:17 final size:16
Alignment explanation
Indices: 23638846--23638914 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
23638836 ATGCTAACTG
* *
23638846 CAAACTGCGAGTTCAC
1 CAAATTGCGAGCTCAC
*
23638862 CAAATGTGCAAGCTCAC
1 CAAAT-TGCGAGCTCAC
* *
23638879 CAAAAAATGTGAGCTCAC
1 C--AAATTGCGAGCTCAC
23638897 CAAGATTGCGAGCTCAC
1 CAA-ATTGCGAGCTCAC
23638914 C
1 C
23638915 TGCGAACTGC
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
16 6 0.15
17 22 0.54
18 10 0.24
19 3 0.07
ACGTcount: A:0.35, C:0.29, G:0.19, T:0.17
Consensus pattern (16 bp):
CAAATTGCGAGCTCAC
Found at i:23642419 original size:93 final size:93
Alignment explanation
Indices: 23642308--23642489 Score: 319
Period size: 93 Copynumber: 2.0 Consensus size: 93
23642298 GAGAAGATTC
*
23642308 AAGAAAACACTCAAAAAACACCATCGAAACTAACTTAAAAACGGATCTCCATCAAGATCGAAGGT
1 AAGAAAACACTCAAAAAACACCATCGAAACTAACTTAAAAACGGATCTCCATCAAGATCGAAGAT
*
23642373 CTCCTTTTAATTTATTTTGAAGTTATTG
66 CTCCTTTTAATCTATTTTGAAGTTATTG
* * *
23642401 AAGAAAACACTTAAAAAACACCATCGAAACTAACTTAGAAGCGGATCTCCATCAAGATCGAAGAT
1 AAGAAAACACTCAAAAAACACCATCGAAACTAACTTAAAAACGGATCTCCATCAAGATCGAAGAT
23642466 CTCCTTTTAATCTATTTTGAAGTT
66 CTCCTTTTAATCTATTTTGAAGTT
23642490 TTATTGAGTT
Statistics
Matches: 84, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 84 1.00
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (93 bp):
AAGAAAACACTCAAAAAACACCATCGAAACTAACTTAAAAACGGATCTCCATCAAGATCGAAGAT
CTCCTTTTAATCTATTTTGAAGTTATTG
Found at i:23643971 original size:28 final size:28
Alignment explanation
Indices: 23643939--23643992 Score: 108
Period size: 28 Copynumber: 1.9 Consensus size: 28
23643929 ACTTATCACC
23643939 AACCTCGATTCAAATGGTCTTACATACT
1 AACCTCGATTCAAATGGTCTTACATACT
23643967 AACCTCGATTCAAATGGTCTTACATA
1 AACCTCGATTCAAATGGTCTTACATA
23643993 TCCTAAGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.33, C:0.24, G:0.11, T:0.31
Consensus pattern (28 bp):
AACCTCGATTCAAATGGTCTTACATACT
Found at i:23644350 original size:69 final size:69
Alignment explanation
Indices: 23644269--23644461 Score: 176
Period size: 69 Copynumber: 2.8 Consensus size: 69
23644259 AGCTGTTTCA
* * * *
23644269 AAGGTTGTGATCATAAACCTGTG-AGCCTTTATGATATCAGTTAGG-AACGTGGGTTCGCAAGCC
1 AAGGTTGCGATCATAAACCTG-GAAGCCTTTATAATATCAGTT-GGAAACGTAGGTCCGCAAGCC
23644332 GTATTG
64 GTATTG
* * * * *
23644338 GAGGTTGCGATCACAAA-CTGGCAAGCCTTTGTAATATCAGTTGGAAACGTAGGTCCGCGAGCTG
1 AAGGTTGCGATCATAAACCTGG-AAGCCTTTATAATATCAGTTGGAAACGTAGGTCCGCAAGCCG
*
23644402 TGTTG
65 TATTG
* *** * * * *
23644407 AAGGCTGCGATCATAAACCAACAAGCCTTTGTAATATCAATTGGGAACATAGGTC
1 AAGGTTGCGATCATAAACCTGGAAGCCTTTATAATATCAGTTGGAAACGTAGGTC
23644462 TGCGAGCTGC
Statistics
Matches: 101, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
67 1 0.01
68 5 0.05
69 94 0.93
70 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.27
Consensus pattern (69 bp):
AAGGTTGCGATCATAAACCTGGAAGCCTTTATAATATCAGTTGGAAACGTAGGTCCGCAAGCCGT
ATTG
Found at i:23644521 original size:69 final size:68
Alignment explanation
Indices: 23644338--23644522 Score: 219
Period size: 69 Copynumber: 2.7 Consensus size: 68
23644328 AGCCGTATTG
* * * * * *
23644338 GAGGTTGCGATCACAAACTGGCAAGCCTTTGTAATATCAGTTGGAAACGTAGGTCCGCGAGCTGT
1 GAGGCTGCGATCATAAACTGACAAGCCTTTGTAATATCAGTTGGGAACATAGGTCCGCGAGCTGC
*
23644403 GTT
66 GTA
** * *
23644406 GAAGGCTGCGATCATAAACCAACAAGCCTTTGTAATATCAATTGGGAACATAGGTCTGCGAGCTG
1 G-AGGCTGCGATCATAAACTGACAAGCCTTTGTAATATCAGTTGGGAACATAGGTCCGCGAGCTG
23644471 CGCTA
65 CG-TA
* *
23644476 GAGGCTGCGATCATAAACTGACAAG-CTTGTATAATATCAGCTGGGAA
1 GAGGCTGCGATCATAAACTGACAAGCCTT-TGTAATATCAGTTGGGAA
23644523 TGTAAGTTCA
Statistics
Matches: 98, Mismatches: 16, Indels: 5
0.82 0.13 0.04
Matches are distributed among these distances:
68 4 0.04
69 92 0.94
70 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.24
Consensus pattern (68 bp):
GAGGCTGCGATCATAAACTGACAAGCCTTTGTAATATCAGTTGGGAACATAGGTCCGCGAGCTGC
GTA
Found at i:23646631 original size:13 final size:13
Alignment explanation
Indices: 23646613--23646639 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
23646603 TTTTAAGTTC
23646613 ATAAAACATTTAT
1 ATAAAACATTTAT
23646626 ATAAAACATTTAT
1 ATAAAACATTTAT
23646639 A
1 A
23646640 GCATAGTATT
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:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (13 bp):
ATAAAACATTTAT
Found at i:23652829 original size:24 final size:24
Alignment explanation
Indices: 23652802--23652854 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
23652792 TGGTTACTGG
23652802 CCTTTACATGTCACATTTCATTAT
1 CCTTTACATGTCACATTTCATTAT
***
23652826 CCTTTTGTTGTCACATTTCATTAT
1 CCTTTACATGTCACATTTCATTAT
23652850 CCTTT
1 CCTTT
23652855 TGTCTTTTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.19, C:0.25, G:0.06, T:0.51
Consensus pattern (24 bp):
CCTTTACATGTCACATTTCATTAT
Found at i:23652855 original size:24 final size:24
Alignment explanation
Indices: 23652810--23652857 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
23652800 GGCCTTTACA
23652810 TGTCACATTTCATTATCCTTTTGT
1 TGTCACATTTCATTATCCTTTTGT
23652834 TGTCACATTTCATTATCCTTTTGT
1 TGTCACATTTCATTATCCTTTTGT
23652858 CTTTTTTGCG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.17, C:0.21, G:0.08, T:0.54
Consensus pattern (24 bp):
TGTCACATTTCATTATCCTTTTGT
Found at i:23654636 original size:17 final size:17
Alignment explanation
Indices: 23654614--23654649 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
23654604 ACTCCTCCAA
23654614 CTTTTAACCTTTATACT
1 CTTTTAACCTTTATACT
*
23654631 CTTTTAACCTTTATTCT
1 CTTTTAACCTTTATACT
23654648 CT
1 CT
23654650 GTAACCTCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (17 bp):
CTTTTAACCTTTATACT
Found at i:23657637 original size:26 final size:27
Alignment explanation
Indices: 23657590--23657640 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
23657580 CACGAAATAT
**
23657590 AGATAGTCCATCAGGGTAGTAAACACA
1 AGATAGTCCATCAGGACAGTAAACACA
23657617 AGATAGTCCA-CAGGACAGTAAACA
1 AGATAGTCCATCAGGACAGTAAACA
23657641 TGAGGTAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 12 0.55
27 10 0.45
ACGTcount: A:0.43, C:0.20, G:0.22, T:0.16
Consensus pattern (27 bp):
AGATAGTCCATCAGGACAGTAAACACA
Found at i:23659451 original size:28 final size:28
Alignment explanation
Indices: 23659383--23659458 Score: 98
Period size: 28 Copynumber: 2.7 Consensus size: 28
23659373 AAAATTGACA
*
23659383 TACAACTCATGTGAGTAAATTCAAATAT
1 TACAACTCATGTGAGCAAATTCAAATAT
* * *
23659411 CACAGCTCATGTGAGCAAATTCGAATAT
1 TACAACTCATGTGAGCAAATTCAAATAT
**
23659439 TACAACTTGTGTGAGCAAAT
1 TACAACTCATGTGAGCAAAT
23659459 CGGTCACGTT
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 40 1.00
ACGTcount: A:0.38, C:0.17, G:0.16, T:0.29
Consensus pattern (28 bp):
TACAACTCATGTGAGCAAATTCAAATAT
Found at i:23661195 original size:47 final size:47
Alignment explanation
Indices: 23661126--23661218 Score: 177
Period size: 47 Copynumber: 2.0 Consensus size: 47
23661116 TGAAAGTGAG
*
23661126 TAAAAGAAATTTCTTTTAAAAGACTACAACTTGAGTTATAAAACATT
1 TAAAAGAAATTTCTTTTAAAAGACTACAACTCGAGTTATAAAACATT
23661173 TAAAAGAAATTTCTTTTAAAAGACTACAACTCGAGTTATAAAACAT
1 TAAAAGAAATTTCTTTTAAAAGACTACAACTCGAGTTATAAAACAT
23661219 GAAACCAAGA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.47, C:0.12, G:0.09, T:0.32
Consensus pattern (47 bp):
TAAAAGAAATTTCTTTTAAAAGACTACAACTCGAGTTATAAAACATT
Found at i:23672896 original size:30 final size:30
Alignment explanation
Indices: 23672861--23672918 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
23672851 CACGGCCATG
*
23672861 ACACACGAGCGTGTGG-TCTACCCGTGTGTC
1 ACACACGAGCATGTGGATC-ACCCGTGTGTC
*
23672891 ACACACGGGCATGTGGATCACCCGTGTG
1 ACACACGAGCATGTGGATCACCCGTGTG
23672919 GAAATGCCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 23 0.92
31 2 0.08
ACGTcount: A:0.19, C:0.29, G:0.31, T:0.21
Consensus pattern (30 bp):
ACACACGAGCATGTGGATCACCCGTGTGTC
Found at i:23673497 original size:100 final size:100
Alignment explanation
Indices: 23673324--23673523 Score: 364
Period size: 100 Copynumber: 2.0 Consensus size: 100
23673314 CCACTGGCTC
*
23673324 GCAATGTTGCTCATACAAGATGTAGAAAATCCATAACAAATGTAGGATCTCAGCCATCTCTACGA
1 GCAATGTTGCTCACACAAGATGTAGAAAATCCATAACAAATGTAGGATCTCAGCCATCTCTACGA
*
23673389 TTTGTATCACTAGCTCAAGGCCTGATAGTCAATAT
66 TCTGTATCACTAGCTCAAGGCCTGATAGTCAATAT
* *
23673424 GCAATGTTTCTCACACAAGATGTAGAAAATCCATAACAAATGTAGGATCTCAGCCATCTCTACGG
1 GCAATGTTGCTCACACAAGATGTAGAAAATCCATAACAAATGTAGGATCTCAGCCATCTCTACGA
23673489 TCTGTATCACTAGCTCAAGGCCTGATAGTCAATAT
66 TCTGTATCACTAGCTCAAGGCCTGATAGTCAATAT
23673524 CCATTTTCAT
Statistics
Matches: 96, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
100 96 1.00
ACGTcount: A:0.34, C:0.22, G:0.17, T:0.28
Consensus pattern (100 bp):
GCAATGTTGCTCACACAAGATGTAGAAAATCCATAACAAATGTAGGATCTCAGCCATCTCTACGA
TCTGTATCACTAGCTCAAGGCCTGATAGTCAATAT
Found at i:23679809 original size:18 final size:19
Alignment explanation
Indices: 23679778--23679823 Score: 76
Period size: 18 Copynumber: 2.5 Consensus size: 19
23679768 TTTGTCATGC
23679778 TTTTAGGATAACACTTCAT
1 TTTTAGGATAACACTTCAT
*
23679797 TTTTAGGA-CACACTTCAT
1 TTTTAGGATAACACTTCAT
23679815 TTTTAGGAT
1 TTTTAGGAT
23679824 TGTTCTTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (19 bp):
TTTTAGGATAACACTTCAT
Found at i:23682935 original size:23 final size:23
Alignment explanation
Indices: 23682905--23682986 Score: 103
Period size: 23 Copynumber: 3.6 Consensus size: 23
23682895 AGCACGCTTG
23682905 TGAATTTAGCACTTCGGTGCTCC
1 TGAATTTAGCACTTCGGTGCTCC
* *
23682928 TGAATTTAGCATTTCAGTGCTCC
1 TGAATTTAGCACTTCGGTGCTCC
* * *
23682951 CGAACTTAGCATTTCGGTGCTCC
1 TGAATTTAGCACTTCGGTGCTCC
*
23682974 T-AATTTAGAACTT
1 TGAATTTAGCACTT
23682987 ATGTGATCGT
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 9 0.18
23 41 0.82
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.37
Consensus pattern (23 bp):
TGAATTTAGCACTTCGGTGCTCC
Found at i:23685147 original size:18 final size:19
Alignment explanation
Indices: 23685115--23685159 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
23685105 TTAAGAATGA
* * *
23685115 TTAACTAATTAAATTTGAT
1 TTAATTAATTAAATTTAAC
23685134 TTAATTAATT-AATTTAAC
1 TTAATTAATTAAATTTAAC
23685152 TTAATTAA
1 TTAATTAA
23685160 AGGTTAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.49
Consensus pattern (19 bp):
TTAATTAATTAAATTTAAC
Found at i:23687266 original size:22 final size:22
Alignment explanation
Indices: 23687234--23687276 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
23687224 ACAGAGAATC
* *
23687234 ATGTCGTGACGAAGGACTCTCA
1 ATGTCGCGACGAAGAACTCTCA
*
23687256 ATGTCGCGACGACGAACTCTC
1 ATGTCGCGACGAAGAACTCTC
23687277 TACATCACGA
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:0.28, G:0.26, T:0.21
Consensus pattern (22 bp):
ATGTCGCGACGAAGAACTCTCA
Found at i:23692677 original size:28 final size:28
Alignment explanation
Indices: 23692635--23692689 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
23692625 GCTTAACAGG
*
23692635 AACTTTTTATTAAGAAGTGAGCATAAGC
1 AACTTTTTATCAAGAAGTGAGCATAAGC
23692663 AACTTTTTATCAAGAAGTGAGCATAAG
1 AACTTTTTATCAAGAAGTGAGCATAAG
23692690 ATATAAAAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.40, C:0.11, G:0.18, T:0.31
Consensus pattern (28 bp):
AACTTTTTATCAAGAAGTGAGCATAAGC
Found at i:23694604 original size:14 final size:15
Alignment explanation
Indices: 23694587--23694626 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
23694577 ATGTTTTCCA
23694587 GAAAATGATTTC-TG
1 GAAAATGATTTCTTG
*
23694601 GAAAATAATTTCTTG
1 GAAAATGATTTCTTG
23694616 GAAAATGATTT
1 GAAAATGATTT
23694627 ACTTTTCTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.40, C:0.05, G:0.17, T:0.38
Consensus pattern (15 bp):
GAAAATGATTTCTTG
Found at i:23695110 original size:22 final size:22
Alignment explanation
Indices: 23695085--23695133 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
23695075 ATCCAAGTGC
* *
23695085 ATAACTAATATTACACTATATG
1 ATAACTAATATTACACCACATG
23695107 ATAACTAATATTACACCACATG
1 ATAACTAATATTACACCACATG
23695129 ATAAC
1 ATAAC
23695134 AACAATAGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.47, C:0.18, G:0.04, T:0.31
Consensus pattern (22 bp):
ATAACTAATATTACACCACATG
Found at i:23696182 original size:27 final size:30
Alignment explanation
Indices: 23696116--23696188 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 30
23696106 GTCAATCATT
*
23696116 TCAATATCCAACAAGCTTAAAACATAATAAAC
1 TCAATATCTAACAAGCTTAAAAC--AATAAAC
*
23696148 TCAATATCTAACAAGCTTGAAAC-AT-AA-
1 TCAATATCTAACAAGCTTAAAACAATAAAC
23696175 TCAATATCTAACAA
1 TCAATATCTAACAA
23696189 AATCAAGACA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
27 14 0.36
28 2 0.05
29 2 0.05
32 21 0.54
ACGTcount: A:0.51, C:0.21, G:0.04, T:0.25
Consensus pattern (30 bp):
TCAATATCTAACAAGCTTAAAACAATAAAC
Found at i:23696271 original size:30 final size:31
Alignment explanation
Indices: 23696203--23696271 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
23696193 AAGACATAAT
* **
23696203 AATTTCAGAATCCAACAAATATAATAAACTAA
1 AATTTTAGAATCCAAC-AATATAATAAAAAAA
23696235 AATTTTAGAATCCAAC-AT-TAATAAAAAAA
1 AATTTTAGAATCCAACAATATAATAAAAAAA
23696264 CAATTTTA
1 -AATTTTA
23696272 ATACTAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
29 9 0.27
30 9 0.27
32 15 0.45
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (31 bp):
AATTTTAGAATCCAACAATATAATAAAAAAA
Found at i:23698338 original size:3 final size:3
Alignment explanation
Indices: 23698330--23698363 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
23698320 TAAGGTTGAG
23698330 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
23698364 TTTTATAATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.00, C:0.32, G:0.00, T:0.68
Consensus pattern (3 bp):
TCT
Found at i:23700587 original size:35 final size:36
Alignment explanation
Indices: 23700538--23700606 Score: 95
Period size: 35 Copynumber: 1.9 Consensus size: 36
23700528 ATTAAGGAAA
* *
23700538 ATGGAAGAGATTTGAAGAACGAAAGAAGAAGAAGAC
1 ATGGAAGAAATTTGAAGAACGAAAGAAAAAGAAGAC
* *
23700574 ATGGAA-AAATTTGAAGAATGGAAGAAAAAGAAG
1 ATGGAAGAAATTTGAAGAACGAAAGAAAAAGAAG
23700607 GCAGAACGGA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 23 0.79
36 6 0.21
ACGTcount: A:0.55, C:0.03, G:0.29, T:0.13
Consensus pattern (36 bp):
ATGGAAGAAATTTGAAGAACGAAAGAAAAAGAAGAC
Found at i:23704804 original size:42 final size:42
Alignment explanation
Indices: 23704741--23704867 Score: 154
Period size: 42 Copynumber: 3.0 Consensus size: 42
23704731 CTTCGTTTTC
* * *
23704741 TCGATGCCATAGTTCAACTATGGTCTTACACATCTTCACATAA
1 TCGATGCCATAGTCCAGCTATGGTCTTACACATATTCACAT-A
* *
23704784 T-GATGCCATAGTCCAGCTATGATCTTACACATATTCATATA
1 TCGATGCCATAGTCCAGCTATGGTCTTACACATATTCACATA
23704825 TCGATGCCATAG-CCTAGCTATGGTCTTACACGA-A-TCACATA
1 TCGATGCCATAGTCC-AGCTATGGTCTTACAC-ATATTCACATA
23704866 TC
1 TC
23704868 TCACTGATGC
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
41 12 0.16
42 60 0.81
43 2 0.03
ACGTcount: A:0.30, C:0.25, G:0.13, T:0.31
Consensus pattern (42 bp):
TCGATGCCATAGTCCAGCTATGGTCTTACACATATTCACATA
Found at i:23704893 original size:46 final size:46
Alignment explanation
Indices: 23704826--23704945 Score: 125
Period size: 47 Copynumber: 2.6 Consensus size: 46
23704816 ATTCATATAT
* * * *
23704826 CGATGCCATAGCCTAGCTATGGTCTTACACGAAT-CACATATCTCAC
1 CGATGCCATATCCCAGATATGGTCTTACAC-AATGCACATATCACAC
* * * *
23704872 TGATGCCATATCCCAGATATGGTCTTATACAGTGGCATATATCACAC
1 CGATGCCATATCCCAGATATGGTCTTACACAAT-GCACATATCACAC
* *
23704919 CAATTCCATATCCCAGATATGGTCTTA
1 CGATGCCATATCCCAGATATGGTCTTA
23704946 TACGGAAATC
Statistics
Matches: 61, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
45 2 0.03
46 25 0.41
47 34 0.56
ACGTcount: A:0.29, C:0.27, G:0.15, T:0.29
Consensus pattern (46 bp):
CGATGCCATATCCCAGATATGGTCTTACACAATGCACATATCACAC
Found at i:23705009 original size:31 final size:31
Alignment explanation
Indices: 23704974--23705122 Score: 244
Period size: 31 Copynumber: 4.8 Consensus size: 31
23704964 CTTGTCACTT
*
23704974 GTAGCCGAAGCTACCACTATTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
* *
23705005 GTAGCCGGAGCTACCATTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
23705036 GTAGCCGGAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
23705067 GTAGCAGAAGCTACCACTTTTCACTGATCAG
1 GTAGCCGAAGCTACCACTTTTCACTGATCAG
*
23705098 GTAGCTGAAGCTACCACTTTTCACT
1 GTAGCCGAAGCTACCACTTTTCACT
23705123 TGTCATTTGT
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 111 1.00
ACGTcount: A:0.26, C:0.28, G:0.20, T:0.27
Consensus pattern (31 bp):
GTAGCCGAAGCTACCACTTTTCACTGATCAG
Found at i:23705204 original size:50 final size:51
Alignment explanation
Indices: 23705098--23705226 Score: 199
Period size: 50 Copynumber: 2.5 Consensus size: 51
23705088 CACTGATCAG
* * *
23705098 GTAGCTGAAGCTACCACTTTTCACTTGTCATTTGTCATTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
*
23705149 GTAGCCGAAGCTATCACTTATCACTT-TCACTTT-TCCTTGATCAGATAAGT
1 GTAGCCGAAGCTATCACTTATCACTTGTCA-TTTGTCATTGATCAGATAAGT
23705199 GTAGCCGAAGCTATCACTTATCACTTGT
1 GTAGCCGAAGCTATCACTTATCACTTGT
23705227 TGCCATGGTC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
50 45 0.62
51 27 0.38
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (51 bp):
GTAGCCGAAGCTATCACTTATCACTTGTCATTTGTCATTGATCAGATAAGT
Found at i:23707843 original size:22 final size:21
Alignment explanation
Indices: 23707792--23707848 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
23707782 CAAGAGCCTA
23707792 AGGTCTCGAGACATATTTGTAT
1 AGGTCTCGAGACA-ATTTGTAT
* *
23707814 A-GTCTCGAGACAATTGTTTCT
1 AGGTCTCGAGACAATT-TGTAT
*
23707835 AGGTCTCGACACAA
1 AGGTCTCGAGACAA
23707849 GTAACCTTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
20 3 0.10
21 15 0.50
22 12 0.40
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (21 bp):
AGGTCTCGAGACAATTTGTAT
Found at i:23707940 original size:21 final size:21
Alignment explanation
Indices: 23707914--23707960 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
23707904 TCAAGTTTCG
* *
23707914 AGACAAGAATCCCTTGTCTTA
1 AGACAAGAATCCCTTCTCTCA
*
23707935 AGACAAGAATCCTTTCTCTCA
1 AGACAAGAATCCCTTCTCTCA
23707956 AGACA
1 AGACA
23707961 TTCAAACATC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.26, G:0.13, T:0.26
Consensus pattern (21 bp):
AGACAAGAATCCCTTCTCTCA
Found at i:23712280 original size:46 final size:46
Alignment explanation
Indices: 23712230--23712405 Score: 182
Period size: 46 Copynumber: 3.8 Consensus size: 46
23712220 TGGTTGAGCA
23712230 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
* *
23712276 TCCGAACTCGTTGAGTTGAGTCCGAG--CTC-GA-GAGATGT-AACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATG-GATGTGAA-T--G
* * * *
23712321 CATCCGAGCTTGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
* * *
23712369 CCCGAGCTCTTTGAGTTGAGTCCGAGTTCACTTATGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
23712406 GCGGGTTACA
Statistics
Matches: 108, Mismatches: 11, Indels: 22
0.77 0.08 0.16
Matches are distributed among these distances:
42 3 0.03
43 7 0.06
44 2 0.02
45 1 0.01
46 60 0.56
47 24 0.22
48 1 0.01
49 2 0.02
50 5 0.05
51 3 0.03
ACGTcount: A:0.21, C:0.20, G:0.29, T:0.30
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAATG
Found at i:23718398 original size:40 final size:40
Alignment explanation
Indices: 23718333--23718517 Score: 181
Period size: 40 Copynumber: 4.6 Consensus size: 40
23718323 CGATATATCG
* * * * * * * *
23718333 CACACTAAGTGTCGTACATACCCGAAACTATCTCAAATCT
1 CACACTAAGTGCCATATATAGCCGAAGCTATATCGAATCA
* * *
23718373 CACACTAAGTGCCATATATAGCCGAAGCTATGTCGAACCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATATCGAATCA
* *
23718413 CACACTAAGTGGCATATATAGCTGAAGCTATATCGAATCA
1 CACACTAAGTGCCATATATAGCCGAAGCTATATCGAATCA
* * * * *
23718453 CACACTAAGGGCCATATATAGCCGAAGATATGTCGTATCG
1 CACACTAAGTGCCATATATAGCCGAAGCTATATCGAATCA
* * *
23718493 CACACTAAGTTCCATAAATAACCGA
1 CACACTAAGTGCCATATATAGCCGA
23718518 TTTTTTGTCG
Statistics
Matches: 120, Mismatches: 25, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 120 1.00
ACGTcount: A:0.36, C:0.25, G:0.16, T:0.23
Consensus pattern (40 bp):
CACACTAAGTGCCATATATAGCCGAAGCTATATCGAATCA
Found at i:23718467 original size:80 final size:80
Alignment explanation
Indices: 23718331--23718502 Score: 227
Period size: 80 Copynumber: 2.1 Consensus size: 80
23718321 CTCGATATAT
* * * * *
23718331 CGCACACTAAGTGTCGTACATACCCGAAACTATCTCAAATCTCACACTAAGTGCCATATATAGCC
1 CGCACACTAAGTGGCATACATACCCGAAACTATATCAAATCACACACTAAGGGCCATATATAGCC
*
23718396 GAAGCTATGTCGAAC
66 GAAGATATGTCGAAC
* * * * *
23718411 CGCACACTAAGTGGCATATATAGCTGAAGCTATATCGAATCACACACTAAGGGCCATATATAGCC
1 CGCACACTAAGTGGCATACATACCCGAAACTATATCAAATCACACACTAAGGGCCATATATAGCC
* *
23718476 GAAGATATGTCGTAT
66 GAAGATATGTCGAAC
23718491 CGCACACTAAGT
1 CGCACACTAAGT
23718503 TCCATAAATA
Statistics
Matches: 79, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
80 79 1.00
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (80 bp):
CGCACACTAAGTGGCATACATACCCGAAACTATATCAAATCACACACTAAGGGCCATATATAGCC
GAAGATATGTCGAAC
Found at i:23721860 original size:20 final size:20
Alignment explanation
Indices: 23721824--23721865 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
23721814 AAAAACTCAA
*
23721824 ATAATTTTTAATTAAATTTTT
1 ATAATTTTTAA-TAAATATTT
23721845 ATAATTTTATAA-AAATATTT
1 ATAATTTT-TAATAAATATTT
23721865 A
1 A
23721866 AAGCTCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 8 0.42
21 8 0.42
22 3 0.16
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
ATAATTTTTAATAAATATTT
Found at i:23724904 original size:18 final size:19
Alignment explanation
Indices: 23724883--23724920 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
23724873 AATATGAAAT
23724883 TAAATTAT-ATTGTATTAA
1 TAAATTATAATTGTATTAA
* *
23724901 TAAATTTTAATTGTTTTAA
1 TAAATTATAATTGTATTAA
23724920 T
1 T
23724921 TTCGTAGCTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TAAATTATAATTGTATTAA
Found at i:23725150 original size:24 final size:24
Alignment explanation
Indices: 23725106--23725152 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
23725096 ATTTAAATGG
23725106 ATTGATTTAGTATGTGATGAATTT
1 ATTGATTTAGTATGTGATGAATTT
23725130 ATTGAATTTA-TAT-TGATTGAATT
1 ATTG-ATTTAGTATGTGA-TGAATT
23725153 GGCATATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 13 0.62
25 5 0.24
ACGTcount: A:0.32, C:0.00, G:0.17, T:0.51
Consensus pattern (24 bp):
ATTGATTTAGTATGTGATGAATTT
Found at i:23726212 original size:46 final size:46
Alignment explanation
Indices: 23726151--23726314 Score: 192
Period size: 46 Copynumber: 3.5 Consensus size: 46
23726141 GTCTCGTTCC
23726151 GAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTT
1 GAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTT
* * *
23726197 GAGTTGAGTCCGAGTTC-GTGA--GATG-TAACTAGGCATCCGAACTCGTT
1 GAGTTGAGTCCGAGTTCACTTATGGATGCGAA-T--G--TCCGAACTCGTT
* * *
23726244 GAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTT
1 GAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTT
*
23726290 GAGTTGAGTCCGAGTTCGCTTATGG
1 GAGTTGAGTCCGAGTTCACTTATGG
23726315 GCGGGTTACA
Statistics
Matches: 99, Mismatches: 10, Indels: 18
0.78 0.08 0.14
Matches are distributed among these distances:
42 2 0.02
43 5 0.05
45 3 0.03
46 51 0.52
47 29 0.29
48 3 0.03
50 4 0.04
51 2 0.02
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.29
Consensus pattern (46 bp):
GAGTTGAGTCCGAGTTCACTTATGGATGCGAATGTCCGAACTCGTT
Found at i:23733269 original size:35 final size:36
Alignment explanation
Indices: 23733230--23733316 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 36
23733220 TGGTTGAGCA
23733230 TCCGAACTCGT-CGAGTTCACTTATGGATGCGAATG
1 TCCGAACTCGTCCGAGTTCACTTATGGATGCGAATG
23733265 TCCGAACTCGTTGAGTCCGAGTTCACTTATGGATGCGAATG
1 TCCGAACTC-----GTCCGAGTTCACTTATGGATGCGAATG
23733306 TCCGAACTCGT
1 TCCGAACTCGT
23733317 TAAGTTGAGT
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
35 9 0.20
36 2 0.04
40 2 0.04
41 33 0.72
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (36 bp):
TCCGAACTCGTCCGAGTTCACTTATGGATGCGAATG
Found at i:23733327 original size:46 final size:46
Alignment explanation
Indices: 23733241--23733435 Score: 210
Period size: 46 Copynumber: 4.3 Consensus size: 46
23733231 CCGAACTCGT
23733241 CGAGTTCACTTATGGATGCGAATGTCCGAACTC-----GTTGAGTC
1 CGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGAGTC
*
23733282 CGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTAAGTTGAGTC
1 CGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGAGTC
* * *
23733328 CGAGTTC-GTGA--GATG-TAACTAGGCATCCGAACTCGTTGAGTTGAGTC
1 CGAGTTCACTTATGGATGCGAA-T--G--TCCGAACTCGTTGAGTTGAGTC
* * *
23733375 CGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGAGTC
1 CGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGAGTC
*
23733421 CGAGTTCGCTTATGG
1 CGAGTTCACTTATGG
23733436 GCGGGTTACA
Statistics
Matches: 129, Mismatches: 11, Indels: 23
0.79 0.07 0.14
Matches are distributed among these distances:
41 33 0.26
42 2 0.02
43 5 0.04
45 3 0.02
46 49 0.38
47 28 0.22
48 3 0.02
50 4 0.03
51 2 0.02
ACGTcount: A:0.22, C:0.21, G:0.29, T:0.29
Consensus pattern (46 bp):
CGAGTTCACTTATGGATGCGAATGTCCGAACTCGTTGAGTTGAGTC
Found at i:23735909 original size:28 final size:28
Alignment explanation
Indices: 23735850--23735978 Score: 97
Period size: 28 Copynumber: 4.6 Consensus size: 28
23735840 ATGTGGCAAA
** *
23735850 AAAAATATAAAAAA-A-TAAAAATCAAT
1 AAAAATATAAAAAATATTAAATTTTAAT
*
23735876 AAAAAATTATAAAAACTATTAAATTTTAAT
1 -AAAAA-TATAAAAAATATTAAATTTTAAT
*
23735906 AAAAATATAAAAGAAT-TTAAATTTTATT
1 AAAAATATAAAA-AATATTAAATTTTAAT
* * *
23735934 AAAATTA-AAAAAATTATAAAAATTGTAA-
1 AAAAATATAAAAAA-TAT-TAAATTTTAAT
*
23735962 AAAAATATAAAATATAT
1 AAAAATATAAAAAATAT
23735979 AGAAATATAG
Statistics
Matches: 82, Mismatches: 12, Indels: 15
0.75 0.11 0.14
Matches are distributed among these distances:
26 2 0.02
27 10 0.12
28 42 0.51
29 20 0.24
30 8 0.10
ACGTcount: A:0.66, C:0.02, G:0.02, T:0.31
Consensus pattern (28 bp):
AAAAATATAAAAAATATTAAATTTTAAT
Found at i:23735937 original size:27 final size:27
Alignment explanation
Indices: 23735877--23735953 Score: 84
Period size: 27 Copynumber: 2.7 Consensus size: 27
23735867 AAAATCAATA
*
23735877 AAAAATTATAAAAACTATTAAATTTTAAT
1 AAAAATTA-AAAAAAT-TTAAATTTTAAT
*
23735906 AAAAATATAAAAGAATTTAAATTTT-AT
1 AAAAAT-TAAAAAAATTTAAATTTTAAT
*
23735933 TAAAATTAAAAAAATTATAAA
1 AAAAATTAAAAAAATT-TAAA
23735954 AATTGTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
26 9 0.21
27 11 0.26
28 9 0.21
29 11 0.26
30 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (27 bp):
AAAAATTAAAAAAATTTAAATTTTAAT
Found at i:23735994 original size:56 final size:52
Alignment explanation
Indices: 23735848--23735995 Score: 116
Period size: 56 Copynumber: 2.6 Consensus size: 52
23735838 ACATGTGGCA
* * * *
23735848 AAAAAAATATAAAAAAATAAAAATCAATAAAAAATTATAAAAACTATTAAATTTT
1 AAAAAAATATAAAAATAT-AAAAT--ATAAAAAATTAAAAAAACTATAAAATTGT
* * * * *
23735903 AATAAAAATATAAAAGAATTTAAATTTTATTAAAATTAAAAAAATTATAAAAATTGT
1 AA-AAAAATAT-AAA-AATATAAAATATA-AAAAATTAAAAAAACTAT-AAAATTGT
23735960 AAAAAAATATAAAATATATAGAAATATAGAAAAATT
1 AAAAAAATATAAAA-ATATA-AAATATA-AAAAATT
23735996 TCTAAGATTT
Statistics
Matches: 72, Mismatches: 14, Indels: 13
0.73 0.14 0.13
Matches are distributed among these distances:
54 1 0.01
55 11 0.15
56 42 0.58
57 15 0.21
58 3 0.04
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (52 bp):
AAAAAAATATAAAAATATAAAATATAAAAAATTAAAAAAACTATAAAATTGT
Found at i:23736239 original size:20 final size:20
Alignment explanation
Indices: 23736216--23736254 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
23736206 TTAAAGAGCA
23736216 TTTTTAATGCA-TTTTATAAC
1 TTTTTAATG-ATTTTTATAAC
*
23736236 TTTTTTATGATTTTTATAA
1 TTTTTAATGATTTTTATAA
23736255 AATTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.28, C:0.05, G:0.05, T:0.62
Consensus pattern (20 bp):
TTTTTAATGATTTTTATAAC
Found at i:23736249 original size:9 final size:9
Alignment explanation
Indices: 23736227--23736346 Score: 64
Period size: 9 Copynumber: 12.7 Consensus size: 9
23736217 TTTTAATGCA
23736227 TTTTATAACTT
1 TTTTATAA--T
*
23736238 TTTTATGAT
1 TTTTATAAT
*
23736247 TTTTATAAAA
1 TTTTAT-AAT
23736257 TTTTATAAT
1 TTTTATAAT
**
23736266 TTTTACGAT
1 TTTTATAAT
*
23736275 ATTTATAATT
1 TTTTATAA-T
23736285 TATTTATAAT
1 T-TTTATAAT
*
23736295 TTTTAATAAG
1 TTTT-ATAAT
*
23736305 ATTTA-AATT
1 TTTTATAA-T
*
23736314 TTTTATATT
1 TTTTATAAT
*
23736323 TTATTA-AAA
1 TT-TTATAAT
*
23736332 TTTAATAAT
1 TTTTATAAT
23736341 TTTTAT
1 TTTTAT
23736347 TGATTTTAAT
Statistics
Matches: 81, Mismatches: 20, Indels: 18
0.68 0.17 0.15
Matches are distributed among these distances:
8 4 0.05
9 42 0.52
10 21 0.26
11 14 0.17
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:23736260 original size:30 final size:28
Alignment explanation
Indices: 23736226--23736299 Score: 85
Period size: 28 Copynumber: 2.5 Consensus size: 28
23736216 TTTTTAATGC
* *
23736226 ATTTTATAACTTTTTTATGATTTTTATAAA
1 ATTTTATAA--TTTTTACGATATTTATAAA
*
23736256 ATTTTATAATTTTTACGATATTTATAAT
1 ATTTTATAATTTTTACGATATTTATAAA
*
23736284 TTATTTATAATTTTTA
1 AT-TTTATAATTTTTA
23736300 ATAAGATTTA
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
28 17 0.44
29 13 0.33
30 9 0.23
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (28 bp):
ATTTTATAATTTTTACGATATTTATAAA
Found at i:23736313 original size:29 final size:28
Alignment explanation
Indices: 23736248--23736344 Score: 83
Period size: 28 Copynumber: 3.4 Consensus size: 28
23736238 TTTTATGATT
** * *
23736248 TTTATAAAATTTTATAATTTTTACGATA
1 TTTATAATTTTTTATAATTTTTACAAGA
*
23736276 TTTATAATTTATTTATAATTTTTAATAAGA
1 TTTATAATTT-TTTATAATTTTT-ACAAGA
*
23736306 TTTA-AATTTTTTATATTTTATTA-AA-A
1 TTTATAATTTTTTATAATTT-TTACAAGA
23736332 TTTAATAATTTTT
1 TTT-ATAATTTTT
23736345 ATTGATTTTA
Statistics
Matches: 58, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
26 4 0.07
27 3 0.05
28 25 0.43
29 19 0.33
30 7 0.12
ACGTcount: A:0.38, C:0.01, G:0.02, T:0.59
Consensus pattern (28 bp):
TTTATAATTTTTTATAATTTTTACAAGA
Found at i:23737401 original size:14 final size:14
Alignment explanation
Indices: 23737382--23737410 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
23737372 ATAAGAGTGT
23737382 TATAAACATGGTAA
1 TATAAACATGGTAA
23737396 TATAAACATGGTAA
1 TATAAACATGGTAA
23737410 T
1 T
23737411 TAATATCTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.48, C:0.07, G:0.14, T:0.31
Consensus pattern (14 bp):
TATAAACATGGTAA
Found at i:23738661 original size:40 final size:40
Alignment explanation
Indices: 23738601--23738736 Score: 148
Period size: 40 Copynumber: 3.4 Consensus size: 40
23738591 TCGAGAATAT
* *
23738601 AAAGTGGATAGGATTCGTTCCTGATTCACTATAATACCTC
1 AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
** * *
23738641 AAAGTGGATAGGATTTGTTCCTGATTCACTATGGTAATTT
1 AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
* * ** *
23738681 AAA-TGAATAGGATTTATTCCTGATTCACTATGGTAACTT
1 AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
* *
23738720 AAGGCGGATAGGATTTG
1 AAAGTGGATAGGATTTG
23738737 ACCTGAAAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
39 35 0.43
40 47 0.57
ACGTcount: A:0.30, C:0.13, G:0.21, T:0.35
Consensus pattern (40 bp):
AAAGTGGATAGGATTTGTTCCTGATTCACTATAATAACTC
Found at i:23738742 original size:39 final size:38
Alignment explanation
Indices: 23738646--23738742 Score: 106
Period size: 39 Copynumber: 2.5 Consensus size: 38
23738636 ACCTCAAAGT
* * *
23738646 GGATAGGATTTGTTCCTGATTCACTATGGTAATTTAAAT
1 GGATAGGATTTG-ACCTGATTCACTATGGTAACTTAAAC
* *
23738685 GAATAGGATTT-ATTCCTGATTCACTATGGTAACTTAAGGC
1 GGATAGGATTTGA--CCTGATTCACTATGGTAACTTAA-AC
23738725 GGATAGGATTTGACCTGA
1 GGATAGGATTTGACCTGA
23738743 AAATGTAATA
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
39 37 0.77
40 10 0.21
41 1 0.02
ACGTcount: A:0.29, C:0.12, G:0.23, T:0.36
Consensus pattern (38 bp):
GGATAGGATTTGACCTGATTCACTATGGTAACTTAAAC
Found at i:23738791 original size:78 final size:78
Alignment explanation
Indices: 23738701--23738852 Score: 259
Period size: 78 Copynumber: 1.9 Consensus size: 78
23738691 GATTTATTCC
* *
23738701 TGATTCACTATGGTAACTTAAGGCGGATAGGATTTGACCTGAAAATGTAATACTGATTCACTACA
1 TGATTCACTATGGTAACCTAAGGCGGATAGGATTTGACCTGAAAAGGTAATACTGATTCACTACA
23738766 GTTACATGATATA
66 GTTACATGATATA
* * *
23738779 TGATTCATTATGGTAACCTAAGGTGGATAGGATTTGACCTGAAAAGGTAATCCTGATTCACTACA
1 TGATTCACTATGGTAACCTAAGGCGGATAGGATTTGACCTGAAAAGGTAATACTGATTCACTACA
23738844 GTTACATGA
66 GTTACATGA
23738853 GATGTGACTC
Statistics
Matches: 69, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 69 1.00
ACGTcount: A:0.34, C:0.14, G:0.20, T:0.32
Consensus pattern (78 bp):
TGATTCACTATGGTAACCTAAGGCGGATAGGATTTGACCTGAAAAGGTAATACTGATTCACTACA
GTTACATGATATA
Found at i:23761459 original size:17 final size:17
Alignment explanation
Indices: 23761427--23761460 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
23761417 AGAAATTAAT
* *
23761427 ATAATAATATATTAAAG
1 ATAATAATAAAATAAAG
23761444 ATAATAATAAAATAAAG
1 ATAATAATAAAATAAAG
23761461 CACATAATTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (17 bp):
ATAATAATAAAATAAAG
Found at i:23761500 original size:17 final size:17
Alignment explanation
Indices: 23761439--23761501 Score: 58
Period size: 17 Copynumber: 3.7 Consensus size: 17
23761429 AATAATATAT
23761439 TAAAGATAAT-AATAAAA
1 TAAAGA-AATAAATAAAA
* *
23761456 TAAAGCACATAATTAAAA
1 TAAAG-AAATAAATAAAA
* *
23761474 CATA-AAATAAATAAAA
1 TAAAGAAATAAATAAAA
23761490 TAAAGAAATAAA
1 TAAAGAAATAAA
23761502 GAAACAATTG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
16 12 0.34
17 14 0.40
18 9 0.26
ACGTcount: A:0.70, C:0.05, G:0.05, T:0.21
Consensus pattern (17 bp):
TAAAGAAATAAATAAAA
Found at i:23765838 original size:39 final size:39
Alignment explanation
Indices: 23765792--23765892 Score: 148
Period size: 39 Copynumber: 2.6 Consensus size: 39
23765782 GCTCTGGTGA
* **
23765792 GCTTCAGTTAGCCTTTGGGCTTCCGTTTGGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAACACTTATGT
23765831 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAACACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAACACTTATGT
* **
23765870 GCTTCAATTAGATTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
23765893 AGATCACGAT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.14, C:0.24, G:0.23, T:0.40
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAACACTTATGT
Found at i:23768417 original size:621 final size:614
Alignment explanation
Indices: 23767100--23768948 Score: 2478
Period size: 621 Copynumber: 3.0 Consensus size: 614
23767090 ACCATACATT
* * *
23767100 ATTTATTTTACTTTTAGTGGGAAAATAAATCTCTCTTCAATAGAAACCA-GTAGAATTGTTATTC
1 ATTTATTTTACTTTCAGTGAGAAAAAAAATCTCTCTTCAATAGAAACCAGGTAGAATTGTTATTC
* * * * *
23767164 TGGAAAATAGAATTTGTACTTAGAAAATAAATTCTAACAATTTTTGGGCAGAATAACAATATTTT
66 TAGAAAATAGAATTTATACTTAGAAAATAAATTCTAACAATTTTTGGGCAGAAGAACAATATCTC
* * * * * *
23767229 AAGGTTATGTATTCAATCCTACTGGTGCCATCTA-TTAGCAAGGAGAAGAAGTGAAACACTTGTT
131 AAAGTTGTGTATTTAACCCTACTGGTGCCATCTATTTA-TAGGGAGAAGAAGTGAAACACTTGTT
*
23767293 GAATTAGTAGAAGTCTATTTCTATAGATAAACAAAATCCTAGTCTAACTAGGAT---GGAGGGGG
195 GAATTAGTAGAAGTCTATTTCAATAGA-AAACAAAATCCTAGTCTAACTAGGATGGGGGAGGGGG
***
23767355 GCGATTGCCCTAGTTAAATATACTAAGGTTTGCCTGTTGGAAAATTAGATTTGGAAACGCAGTGA
259 GCGACAACCCTAGTTAAATATACTAAGGTTTGCCTGTTGGAAAATTAGATTTGGAAACGCAGTGA
* *
23767420 AAATTAAGTTTAAGAGAAAAACCAGAGCTTTAAAAAAAATCAAAACAAGAACTTAGTTGTGATAT
324 AAATTAAGTTTAAGGGAAAAACCAGAG-TTTAAAAAAAATTAAAACAAGAACTTAGTTGTGATAT
* * *
23767485 CTAAAGTAATAAACACTTAATCAAAATTATAAATTTTCAATTCGTCTAGAATGAACGCTTTGACC
388 CTAAAGTAATAAACACTTAATCAAAATTATACATTTTCGATTCGTCTAGGATGAACGCTTTGACC
* * * * *
23767550 GAGTAGTCTTCTCCTTATCCTCAAGTTCACGTCTGTCGAGTGTGGTCTCGCTTCGAATAAAAAAA
453 AAGTAGTCTTCTCCCTATCCTTAAGTTCACGTCTGCCGAGTGTGGGCTCGCTTCGAAT-AAAAAA
* * *
23767615 AATT-CACAAAATTACTAGTGGAGTAATTTCACAATTACTCTAAACTTCTGGGTCAAGTTGTAAA
517 ATTTCCACAAAATTACTAGTGGAGTAATTTCACAATTTCTCTAAACTTCTGGGTCAAGTTATAAA
*
23767679 TAAGAAAAATATCTCTAGACATCTTCTAAAATA
582 TAAGAAAAATATCTCTAGAAATCTTCTAAAATA
* *
23767712 ATTTATTTTACTTTCAAT-AGAAAAAAAAATCTCTCTTCAATAGAAATC-GGTAGAATTGTTATT
1 ATTTATTTTACTTTCAGTGAG-AAAAAAAATCTCTCTTCAATAGAAACCAGGTAGAATTGTTATT
* * *
23767775 CTTGAAGATAGAATTTATACTTAGAAAATAAATTCTAACAATTTTTGGGCATAAGAACAATATCT
65 CTAGAAAATAGAATTTATACTTAGAAAATAAATTCTAACAATTTTTGGGCAGAAGAACAATATCT
* *
23767840 CAAAGTTGTGTATTTAGCCCTACTGGTGCCATCTATTTATAGGGAGAAGAAGTGTAACACTTGTT
130 CAAAGTTGTGTATTTAACCCTACTGGTGCCATCTATTTATAGGGAGAAGAAGTGAAACACTTGTT
* *
23767905 GAATTAGTAGAAATCTATTCCAATAGAAAAACAAAATCCTAGTCTAACTAGGATTTGGGGGAGGG
195 GAATTAGTAGAAGTCTATTTCAATAG-AAAACAAAATCCTAGTCTAACTAGGA--TGGGGGAGGG
* * * * **
23767970 GTGGCGACAACACTAGTTAAATATAATAGGGTTTGCCTATTGGAAAATCGGATTTGGAAACGCAG
257 G-GGCGACAACCCTAGTTAAATATACTAAGGTTTGCCTGTTGGAAAATTAGATTTGGAAACGCAG
* * *
23768035 TGAAAATTAAGTTGAAGGGAAAAACCAGAGTTTAAAAAAAAAATTTAAATAAGAACTTAGTTGTG
321 TGAAAATTAAGTTTAAGGGAAAAACCAGAGTTT--AAAAAAAATTAAAACAAGAACTTAGTTGTG
23768100 ATATCTAAAGTAATAAACACTTAATCAAAATTATACATTTTCGATTCGTCTAGGATGAACGCTTT
384 ATATCTAAAGTAATAAACACTTAATCAAAATTATACATTTTCGATTCGTCTAGGATGAACGCTTT
* * * *
23768165 GACCAAGTAGTATTCTCCGCCATCCTTAAGTTCACATCTGCCAAGTGTGGGCTCGCTTCGAATCA
449 GACCAAGTAGTCTTCTCC-CTATCCTTAAGTTCACGTCTGCCGAGTGTGGGCTCGCTTCGAAT-A
* * * *
23768230 ACAAAATTTCCTCAAAATTACTAGTGGAGTAATTTCACAATTTCTCTAAACTTCCGGGTCATGTT
512 AAAAAATTTCCACAAAATTACTAGTGGAGTAATTTCACAATTTCTCTAAACTTCTGGGTCAAGTT
*
23768295 TTAAATAAGAAAAATATCTCTAGAAATCTTCTAAAATA
577 ATAAATAAGAAAAATATCTCTAGAAATCTTCTAAAATA
* * * *
23768333 ATTTATTTTACTTTCAGTGAGAAAACAAATCTTTATTCAATCGAAA-CAGGTAGAATTGTTATTC
1 ATTTATTTTACTTTCAGTGAGAAAAAAAATCTCTCTTCAATAGAAACCAGGTAGAATTGTTATTC
* * *
23768397 TAGAAAATAAAATTTATACTTAGAAAATAAATTCTAACAATTTTCGGGCAGAAGAATAATATCTC
66 TAGAAAATAGAATTTATACTTAGAAAATAAATTCTAACAATTTTTGGGCAGAAGAACAATATCTC
* *
23768462 AAAGTTGTGTATTTAACCCTACCGGTACCATCTATTTATAGGGAGAAGAAGTGAAACACTTGTTG
131 AAAGTTGTGTATTTAACCCTACTGGTGCCATCTATTTATAGGGAGAAGAAGTGAAACACTTGTTG
* *** * * *****
23768527 AATTAGTAGAAGTCTATTTCAATAG----GATTTTTCT--TTTTTGGGGGA-GGGGGA-GGGGGC
196 AATTAGTAGAAGTCTATTTCAATAGAAAACAAAATCCTAGTCTAACTAGGATGGGGGAGGGGGGC
* * * * *
23768584 GACAACCCTAGTTAGATATACTATGGTTGGCCTGTTGGAAAATTAGATTTAGAAAATGCAGTGAA
261 GACAACCCTAGTTAAATATACTAAGGTTTGCCTGTTGGAAAATTAGATTT-GGAAACGCAGTGAA
* * * * *
23768649 AAATAAGTTTAAGGGAAAAACTAAAGTTTAAAAAAAATTCAAAACAAGAACTTGGTGGTGATATC
325 AATTAAGTTTAAGGGAAAAACCAGAGTTTAAAAAAAATT-AAAACAAGAACTTAGTTGTGATATC
* * * *
23768714 TAAAGTAATAAATACTTAATCAAAATTATACATTTTTGATTTGTCTAGGATGAACGCTTTGATCG
389 TAAAGTAATAAACACTTAATCAAAATTATACATTTTCGATTCGTCTAGGATGAACGCTTTGA-CC
* *
23768779 AA-TAGTCTTCTCTCCTAT-CTTCAAGTTCATGTCTGCCGAGTGTGAGCTCGCTTCGAATAAAAA
453 AAGTAGTCTTCTC-CCTATCCTT-AAGTTCACGTCTGCCGAGTGTGGGCTCGCTTCGAATAAAAA
* * * *
23768842 AATTTCCACATAATTACTAGTGG-GATAATTTCACAATTTCTTTAAACTTCTAGGTCAAATTATA
516 AATTTCCACAAAATTACTAGTGGAG-TAATTTCACAATTTCTCTAAACTTCTGGGTCAAGTTATA
* *
23768906 AATAAGAAAAATATTTCTAGAAATCTTTTAAAATA
580 AATAAGAAAAATATCTCTAGAAATCTTCTAAAATA
23768941 ATTTATTT
1 ATTTATTT
23768949 AGAAAACTTT
Statistics
Matches: 1090, Mismatches: 125, Indels: 48
0.86 0.10 0.04
Matches are distributed among these distances:
607 1 0.00
608 112 0.10
609 169 0.16
610 44 0.04
611 7 0.01
612 214 0.20
613 4 0.00
614 6 0.01
616 4 0.00
617 10 0.01
618 82 0.08
619 105 0.10
620 46 0.04
621 284 0.26
622 2 0.00
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (614 bp):
ATTTATTTTACTTTCAGTGAGAAAAAAAATCTCTCTTCAATAGAAACCAGGTAGAATTGTTATTC
TAGAAAATAGAATTTATACTTAGAAAATAAATTCTAACAATTTTTGGGCAGAAGAACAATATCTC
AAAGTTGTGTATTTAACCCTACTGGTGCCATCTATTTATAGGGAGAAGAAGTGAAACACTTGTTG
AATTAGTAGAAGTCTATTTCAATAGAAAACAAAATCCTAGTCTAACTAGGATGGGGGAGGGGGGC
GACAACCCTAGTTAAATATACTAAGGTTTGCCTGTTGGAAAATTAGATTTGGAAACGCAGTGAAA
ATTAAGTTTAAGGGAAAAACCAGAGTTTAAAAAAAATTAAAACAAGAACTTAGTTGTGATATCTA
AAGTAATAAACACTTAATCAAAATTATACATTTTCGATTCGTCTAGGATGAACGCTTTGACCAAG
TAGTCTTCTCCCTATCCTTAAGTTCACGTCTGCCGAGTGTGGGCTCGCTTCGAATAAAAAAATTT
CCACAAAATTACTAGTGGAGTAATTTCACAATTTCTCTAAACTTCTGGGTCAAGTTATAAATAAG
AAAAATATCTCTAGAAATCTTCTAAAATA
Found at i:23773559 original size:33 final size:33
Alignment explanation
Indices: 23773517--23773586 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
23773507 ACTGAAAATG
23773517 ACTTCTAGAAAATAATTTCTGGAAAAATGACTT
1 ACTTCTAGAAAATAATTTCTGGAAAAATGACTT
23773550 ACTTCTAGAAAATAATTTCTGGAAAAATGACTT
1 ACTTCTAGAAAATAATTTCTGGAAAAATGACTT
23773583 ACTT
1 ACTT
23773587 TTTTGAAAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.41, C:0.13, G:0.11, T:0.34
Consensus pattern (33 bp):
ACTTCTAGAAAATAATTTCTGGAAAAATGACTT
Found at i:23776971 original size:31 final size:31
Alignment explanation
Indices: 23776935--23777002 Score: 120
Period size: 30 Copynumber: 2.2 Consensus size: 31
23776925 ACATAAGGTG
23776935 TACTGGTTTTTCTAATACGGATCAGTTTAAC
1 TACTGGTTTTTCTAATACGGATCAGTTTAAC
*
23776966 TACTGG-TTTTCTAATACGGATCAGTTTATC
1 TACTGGTTTTTCTAATACGGATCAGTTTAAC
23776996 TACTGGT
1 TACTGGT
23777003 CTAGTTCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
30 29 0.83
31 6 0.17
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.43
Consensus pattern (31 bp):
TACTGGTTTTTCTAATACGGATCAGTTTAAC
Found at i:23778495 original size:40 final size:40
Alignment explanation
Indices: 23778421--23778588 Score: 151
Period size: 41 Copynumber: 4.1 Consensus size: 40
23778411 GCAAAAATTG
* ** *
23778421 TAAAACACATAGCAATAGCGGCG-TTTTACCAAAAACGCCAC
1 TAAAA-ACAGAGCAATAGCGGCGCTTTT-GGAAAAACGCCGC
* * *
23778462 TAAAAACAGAACAATAGCGGCG-TTTTAGTAAAAAATGCCGC
1 TAAAAACAGAGCAATAGCGGCGCTTTT-G-GAAAAACGCCGC
* * * * *
23778503 AAAAAATAGAGCATTAGCGGCGCTTCTGGCAAAACGCCGC
1 TAAAAACAGAGCAATAGCGGCGCTTTTGGAAAAACGCCGC
* *
23778543 TAAAAACCAGAGCATTAGCGGCGCTTTTGGAAAAATGCCGC
1 TAAAAA-CAGAGCAATAGCGGCGCTTTTGGAAAAACGCCGC
23778584 TAAAA
1 TAAAA
23778589 GTCATATAAC
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
40 34 0.32
41 68 0.65
42 3 0.03
ACGTcount: A:0.40, C:0.22, G:0.20, T:0.18
Consensus pattern (40 bp):
TAAAAACAGAGCAATAGCGGCGCTTTTGGAAAAACGCCGC
Found at i:23778770 original size:21 final size:21
Alignment explanation
Indices: 23778745--23778831 Score: 84
Period size: 21 Copynumber: 4.0 Consensus size: 21
23778735 TAATTATCAT
*
23778745 TATATGGTTTATGGTTTAAGA
1 TATATGGTTTAGGGTTTAAGA
* *
23778766 TATATGGTTTAGGGTTTAGGG
1 TATATGGTTTAGGGTTTAAGA
* **
23778787 TTTATGAGTTAACTATAGTTTAAGA
1 TATATG-GTT---TAGGGTTTAAGA
23778812 TATATGGTTTAGGGTTTAAG
1 TATATGGTTTAGGGTTTAAG
23778832 GTTTAGAAGT
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
21 32 0.63
22 3 0.06
24 3 0.06
25 13 0.25
ACGTcount: A:0.28, C:0.01, G:0.26, T:0.45
Consensus pattern (21 bp):
TATATGGTTTAGGGTTTAAGA
Found at i:23778825 original size:46 final size:46
Alignment explanation
Indices: 23778758--23778847 Score: 155
Period size: 46 Copynumber: 2.0 Consensus size: 46
23778748 ATGGTTTATG
*
23778758 GTTTAAGATATATGGTTTAGGGTTTAGGGTTTATG-AGTTAACTATA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTA-GAAGTTAACTATA
23778804 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGAAGTTAACTA
1 GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGAAGTTAACTA
23778848 GTATTTGAAG
Statistics
Matches: 42, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
45 1 0.02
46 41 0.98
ACGTcount: A:0.30, C:0.02, G:0.26, T:0.42
Consensus pattern (46 bp):
GTTTAAGATATATGGTTTAGGGTTTAAGGTTTAGAAGTTAACTATA
Found at i:23778903 original size:7 final size:7
Alignment explanation
Indices: 23778891--23778992 Score: 73
Period size: 7 Copynumber: 14.7 Consensus size: 7
23778881 GAGATTATGA
23778891 TTTAGGG
1 TTTAGGG
23778898 TTTAGGG
1 TTTAGGG
*
23778905 GTTA-GG
1 TTTAGGG
* *
23778911 ATTAGAG
1 TTTAGGG
*
23778918 TTTAAGG
1 TTTAGGG
*
23778925 TGTAAGGG
1 T-TTAGGG
*
23778933 TTTGGGG
1 TTTAGGG
* *
23778940 TTAAGTG
1 TTTAGGG
* *
23778947 TTAATGG
1 TTTAGGG
*
23778954 TTTAGAG
1 TTTAGGG
*
23778961 TTTA-GT
1 TTTAGGG
23778967 TTTAGGG
1 TTTAGGG
23778974 TTTAGGG
1 TTTAGGG
23778981 TTTAGGG
1 TTTAGGG
23778988 TTTAG
1 TTTAG
23778993 TGGCATTTTT
Statistics
Matches: 71, Mismatches: 21, Indels: 6
0.72 0.21 0.06
Matches are distributed among these distances:
6 9 0.13
7 57 0.80
8 5 0.07
ACGTcount: A:0.21, C:0.00, G:0.37, T:0.42
Consensus pattern (7 bp):
TTTAGGG
Found at i:23778913 original size:21 final size:20
Alignment explanation
Indices: 23778869--23778921 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 20
23778859 TTTATGATGA
*
23778869 ATTATGGGTTTAGAGATTATG
1 ATTA-GGGTTTAGAGATTAGG
* *
23778890 ATTTAGGGTTTAGGGGTTAGG
1 A-TTAGGGTTTAGAGATTAGG
*
23778911 ATTAGAGTTTA
1 ATTAGGGTTTA
23778922 AGGTGTAAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 9 0.33
21 15 0.56
22 3 0.11
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (20 bp):
ATTAGGGTTTAGAGATTAGG
Found at i:23779288 original size:14 final size:14
Alignment explanation
Indices: 23779265--23779309 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
23779255 TTAATTATCA
23779265 TTATAGTTTAGGGT
1 TTATAGTTTAGGGT
23779279 TTAT-GATTTAGGGT
1 TTATAG-TTTAGGGT
*
23779293 ATATAGTTTAGGGT
1 TTATAGTTTAGGGT
23779307 TTA
1 TTA
23779310 AGGTGTAGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
13 1 0.04
14 25 0.93
15 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.27, T:0.49
Consensus pattern (14 bp):
TTATAGTTTAGGGT
Found at i:23780942 original size:25 final size:25
Alignment explanation
Indices: 23780905--23780969 Score: 103
Period size: 25 Copynumber: 2.6 Consensus size: 25
23780895 CTCATCGTTG
23780905 TTCGCCGTCGTCTCTTCTGCGTCCC
1 TTCGCCGTCGTCTCTTCTGCGTCCC
*
23780930 TTCGCCGTTGTCTCTTCTGCGTCCC
1 TTCGCCGTCGTCTCTTCTGCGTCCC
*
23780955 TTCACCGTCGCTCTC
1 TTCGCCGTCG-TCTC
23780970 CGCTTCCGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
25 32 0.89
26 4 0.11
ACGTcount: A:0.02, C:0.43, G:0.18, T:0.37
Consensus pattern (25 bp):
TTCGCCGTCGTCTCTTCTGCGTCCC
Found at i:23784452 original size:31 final size:31
Alignment explanation
Indices: 23784386--23784444 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
23784376 TGGTTGTATT
* *
23784386 TTTTATGTTAAATTTGCTGTTTTTGGTTACA
1 TTTTATATTAAATTTGCTGTATTTGGTTACA
* *
23784417 TTTTATATTATATTTGTTGTATTTGGTT
1 TTTTATATTAAATTTGCTGTATTTGGTT
23784445 GGATTTTAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.19, C:0.03, G:0.15, T:0.63
Consensus pattern (31 bp):
TTTTATATTAAATTTGCTGTATTTGGTTACA
Found at i:23796137 original size:44 final size:44
Alignment explanation
Indices: 23796072--23796267 Score: 141
Period size: 44 Copynumber: 4.5 Consensus size: 44
23796062 CTGGCCGTTA
* * * *
23796072 CCCTACTGCATAGGGGTTTAAGGCCCATCACCTCTGATCTGTTT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCATCTCTGATCTGTTT
** * * *
23796116 CCCTACTGCTTAGGGGGTTAAGATCCTTCGTCTTTGATCTG-CT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCATCTCTGATCTGTTT
* * * * ** * * *
23796159 CCACTATTGTTTAGGGTGATAA-GATCTGCAAT-TCAG-TCTGTTA
1 CC-CTACTGCTTAGGGGGTTAAGGCCCTTC-ATCTCTGATCTGTTT
* * *
23796202 CCTTACTGCTTAGGGGTTTAAGGCCCTTCGTCT-TCGATCTGTTT
1 CCCTACTGCTTAGGGGGTTAAGGCCCTTCATCTCT-GATCTGTTT
23796246 CCCTACTGCTTAGGGGGTTAAG
1 CCCTACTGCTTAGGGGGTTAAG
23796268 ATCTGTAAAT
Statistics
Matches: 109, Mismatches: 36, Indels: 14
0.69 0.23 0.09
Matches are distributed among these distances:
42 18 0.17
43 16 0.15
44 75 0.69
ACGTcount: A:0.17, C:0.24, G:0.23, T:0.36
Consensus pattern (44 bp):
CCCTACTGCTTAGGGGGTTAAGGCCCTTCATCTCTGATCTGTTT
Found at i:23796312 original size:87 final size:87
Alignment explanation
Indices: 23796110--23796742 Score: 727
Period size: 87 Copynumber: 7.3 Consensus size: 87
23796100 CACCTCTGAT
* * ** * * * * *
23796110 CTGTTTCCCTACTGCTTAGGGGGTTAAGATCCTTCGTCTTTGATCTG-CTCCACTATTGTTTAGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGCCTTCGATCTGTTTCC-CTACTGCTTAGG
* * * *
23796174 GTGATAAGATCTG-CAATTCAGT
65 GGGTTAAGATCTGTAAATTCAGC
* *
23796196 CTGTTACCTTACTGCTTAGGGGTTTAAGGCCCTTCGTCTTCGATCTGTTTCCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGCCTTCGATCTGTTTCCCTACTGCTTAGGG
23796261 GGTTAAGATCTGTAAATTCAGC
66 GGTTAAGATCTGTAAATTCAGC
* * ** * * * *
23796283 CTATTACCTTACTATTTAGGGGGTTAAGG-CTTGTCACCTTCGATCTGTTTCCCTACTGCTTAGC
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCT-TCGCCTTCGATCTGTTTCCCTACTGCTTAGG
* * *
23796347 GTGATGAGATCTGTAAATTCAGC
65 GGGTTAAGATCTGTAAATTCAGC
* * *
23796370 CTGTTACCTTACTACTTAGGGGTTTAAGGCCCTTCACCTTCGATCTGTTTCCCTACTGCTTAGGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGCCTTCGATCTGTTTCCCTACTGCTTAGGG
*
23796435 GGTTAAGATCTGTAAATTTAGC
66 GGTTAAGATCTGTAAATTCAGC
* * * * ** *
23796457 CTATTACCCTATTGCTTAGGGGTTTAAGGCCATTCGTCTTCGATCT-ACTCCACTACTGCTTAGA
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGCCTTCGATCTGTTTCC-CTACTGCTTAGG
* * * * *
23796521 GAGATCAGATCTGTAAATTTAAC
65 GGGTTAAGATCTGTAAATTCAGC
* * * * * *
23796544 CTATTACCCTACTGCTTAGGGGTTTAAGGTCCATCGCCTTCGATCTGTTTTCGTACTACTTAGGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGCCTTCGATCTGTTTCCCTACTGCTTAGGG
23796609 GGTTAAGATCTGTAAATTCAGC
66 GGTTAAGATCTGTAAATTCAGC
* *
23796631 CTGTTACCCCACTGCTTAGGGGTTTAAGG-CCTGTCGCCTTCGATCTATTTCCCTACTGCTTAGG
1 CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCT-TCGCCTTCGATCTGTTTCCCTACTGCTTAGG
*
23796695 GGGTTAAGATCTGTAAATTTAGC
65 GGGTTAAGATCTGTAAATTCAGC
23796718 CTGTTACCCTACTGCTTAAGGGGTT
1 CTGTTACCCTACTGCTT-AGGGGTT
23796743 ATGGCTTGTG
Statistics
Matches: 467, Mismatches: 72, Indels: 14
0.84 0.13 0.03
Matches are distributed among these distances:
86 69 0.15
87 387 0.83
88 11 0.02
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (87 bp):
CTGTTACCCTACTGCTTAGGGGTTTAAGGCCCTTCGCCTTCGATCTGTTTCCCTACTGCTTAGGG
GGTTAAGATCTGTAAATTCAGC
Done.