Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 83 of 226
Found at i:29697279 original size:24 final size:25
Alignment explanation
Indices: 29697233--29697279 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29697223 CAATCATATC
* * *
29697233 AATTTTTAACAGTACAAATGGATAA
1 AATTTTTAACAGAAAAAAAGGATAA
29697258 AATTTTTAACA-AAAAAAAGGAT
1 AATTTTTAACAGAAAAAAAGGAT
29697280 TAATTTGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 8 0.42
25 11 0.58
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.30
Consensus pattern (25 bp):
AATTTTTAACAGAAAAAAAGGATAA
Found at i:29697423 original size:22 final size:20
Alignment explanation
Indices: 29697391--29697434 Score: 54
Period size: 19 Copynumber: 2.1 Consensus size: 20
29697381 TTTACGGTGC
29697391 AAATTATATATTAACATATCAAA
1 AAATTATATA-TAA-ATAT-AAA
29697414 AAATT-TATATAAATATAAA
1 AAATTATATATAAATATAAA
29697433 AA
1 AA
29697435 TACGATACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
19 5 0.24
20 4 0.19
21 3 0.14
22 4 0.19
23 5 0.24
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
AAATTATATATAAATATAAA
Found at i:29699477 original size:14 final size:14
Alignment explanation
Indices: 29699454--29699487 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29699444 TACAATATCT
29699454 AAATAATAACAATA
1 AAATAATAACAATA
*
29699468 AAATAGTAACAATA
1 AAATAATAACAATA
*
29699482 TAATAA
1 AAATAA
29699488 CGAAATGACA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (14 bp):
AAATAATAACAATA
Found at i:29699514 original size:11 final size:11
Alignment explanation
Indices: 29699498--29699536 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
29699488 CGAAATGACA
29699498 ACAAAACAATG
1 ACAAAACAATG
29699509 ACAAAACAA-G
1 ACAAAACAATG
29699519 AGCAAAACAATG
1 A-CAAAACAATG
*
29699531 GCAAAA
1 ACAAAA
29699537 TAGAATTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
10 2 0.08
11 22 0.88
12 1 0.04
ACGTcount: A:0.64, C:0.18, G:0.13, T:0.05
Consensus pattern (11 bp):
ACAAAACAATG
Found at i:29700473 original size:15 final size:16
Alignment explanation
Indices: 29700418--29700474 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
29700408 ACAATTGGAT
29700418 GAAGAAAAAAAGGAAAA
1 GAAGAAAAAAA-GAAAA
29700435 -AAGAACAAAAAGAAATA
1 GAAGAA-AAAAAGAAA-A
* *
29700452 GATGAAAAAAA-TAAA
1 GAAGAAAAAAAGAAAA
29700467 GAAGAAAA
1 GAAGAAAA
29700475 GGAAAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 8 0.24
16 11 0.32
17 11 0.32
18 4 0.12
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.05
Consensus pattern (16 bp):
GAAGAAAAAAAGAAAA
Found at i:29704854 original size:32 final size:32
Alignment explanation
Indices: 29704813--29704879 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
29704803 CTCACAAAAT
29704813 TTATTATATCTCATGATTTACAATTCTGTTAC
1 TTATTATATCTCATGATTTACAATTCTGTTAC
29704845 TTATTATATCTCATGATTTACAATTCTGTTAC
1 TTATTATATCTCATGATTTACAATTCTGTTAC
29704877 TTA
1 TTA
29704880 CACCGTTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.28, C:0.15, G:0.06, T:0.51
Consensus pattern (32 bp):
TTATTATATCTCATGATTTACAATTCTGTTAC
Found at i:29707853 original size:40 final size:40
Alignment explanation
Indices: 29707794--29707872 Score: 106
Period size: 40 Copynumber: 2.0 Consensus size: 40
29707784 TAACCTATTT
*
29707794 GTACTTCAGTACCTCTGATTGCACATACGTGCCCTTGTTC
1 GTACTTCAGTACCTCTGATTGCACATACGTGCCCCTGTTC
* * *
29707834 GTACTTCCGTATCCT-TGATTGCACTTATGTGCCCCTGTT
1 GTACTTCAGTA-CCTCTGATTGCACATACGTGCCCCTGTT
29707873 TACATTTTCG
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 31 0.91
41 3 0.09
ACGTcount: A:0.15, C:0.29, G:0.18, T:0.38
Consensus pattern (40 bp):
GTACTTCAGTACCTCTGATTGCACATACGTGCCCCTGTTC
Found at i:29709259 original size:14 final size:15
Alignment explanation
Indices: 29709222--29709259 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
29709212 GATTCAATTG
29709222 AATAAAT-TATTAAA
1 AATAAATATATTAAA
*
29709236 AATAAAAATATTTAAA
1 AATAAATATA-TTAAA
29709252 AATAAATA
1 AATAAATA
29709260 AAATCAATTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 6 0.30
15 2 0.10
16 12 0.60
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAAATATATTAAA
Found at i:29711875 original size:5 final size:5
Alignment explanation
Indices: 29711865--29711915 Score: 102
Period size: 5 Copynumber: 10.2 Consensus size: 5
29711855 AGACATATTT
29711865 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
1 TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA TATCA
29711915 T
1 T
29711916 GTCCTACTCC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 46 1.00
ACGTcount: A:0.39, C:0.20, G:0.00, T:0.41
Consensus pattern (5 bp):
TATCA
Found at i:29712698 original size:33 final size:31
Alignment explanation
Indices: 29712661--29712734 Score: 82
Period size: 28 Copynumber: 2.4 Consensus size: 31
29712651 GAGCCCTATT
29712661 CAGTAACAGTACAGTGAGGGCCTTAGCCAAATA
1 CAGTAACAGTACAGT--GGGCCTTAGCCAAATA
*
29712694 CAGTAACAGT---GTGGGCCTTAGCCCAATA
1 CAGTAACAGTACAGTGGGCCTTAGCCAAATA
* *
29712722 CTGTATCAGTACA
1 CAGTAACAGTACA
29712735 ATGTAATAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
28 23 0.66
30 2 0.06
33 10 0.29
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.22
Consensus pattern (31 bp):
CAGTAACAGTACAGTGGGCCTTAGCCAAATA
Found at i:29712709 original size:28 final size:28
Alignment explanation
Indices: 29712666--29712731 Score: 89
Period size: 28 Copynumber: 2.4 Consensus size: 28
29712656 CTATTCAGTA
29712666 ACAGT-ACAGTGAGGGCCTTAGCCAAAT
1 ACAGTAACAGTGAGGGCCTTAGCCAAAT
* *
29712693 ACAGTAACAGTGTGGGCCTTAGCCCAAT
1 ACAGTAACAGTGAGGGCCTTAGCCAAAT
* *
29712721 ACTGTATCAGT
1 ACAGTAACAGT
29712732 ACAATGTAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 5 0.15
28 29 0.85
ACGTcount: A:0.30, C:0.23, G:0.24, T:0.23
Consensus pattern (28 bp):
ACAGTAACAGTGAGGGCCTTAGCCAAAT
Found at i:29712895 original size:26 final size:26
Alignment explanation
Indices: 29712861--29712940 Score: 115
Period size: 26 Copynumber: 3.1 Consensus size: 26
29712851 CAGAAGTAGC
* *
29712861 ATCGCAGCAAAGCTGCTAGTAACAGT
1 ATCGAAGCAAAGCTGCCAGTAACAGT
*
29712887 ATTGAAGCAAAGCTGCCAGTAACAGT
1 ATCGAAGCAAAGCTGCCAGTAACAGT
* *
29712913 ATCGCAGCAAAGTTGCCAGTAACAGT
1 ATCGAAGCAAAGCTGCCAGTAACAGT
29712939 AT
1 AT
29712941 ACTCCCTCCA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.36, C:0.21, G:0.23, T:0.20
Consensus pattern (26 bp):
ATCGAAGCAAAGCTGCCAGTAACAGT
Found at i:29713122 original size:27 final size:27
Alignment explanation
Indices: 29713074--29713220 Score: 160
Period size: 27 Copynumber: 5.5 Consensus size: 27
29713064 AAGGCCATAA
* **
29713074 CAGTCATTTTGACTCT-TAGGGGTATAA
1 CAGTCATTTT-ACCCTATAGGGGTATTT
*
29713101 CAGTCATTTTACCCTATGGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
* *
29713128 C-GATCATTGTACCCTATGGGGGTATTT
1 CAG-TCATTTTACCCTATAGGGGTATTT
*
29713155 CAGACATTTTACCCTAT-GGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
*
29713181 TAGTCATTTTACCCTATAGGGGTATTT
1 CAGTCATTTTACCCTATAGGGGTATTT
29713208 C-GATCA-TTTACCC
1 CAG-TCATTTTACCC
29713221 AGAAATGGCA
Statistics
Matches: 105, Mismatches: 10, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
26 37 0.35
27 67 0.64
28 1 0.01
ACGTcount: A:0.22, C:0.19, G:0.20, T:0.39
Consensus pattern (27 bp):
CAGTCATTTTACCCTATAGGGGTATTT
Found at i:29713151 original size:54 final size:53
Alignment explanation
Indices: 29713090--29713205 Score: 153
Period size: 53 Copynumber: 2.2 Consensus size: 53
29713080 TTTTGACTCT
*
29713090 TAGGGGTATAACAGTCATTTTACCCTATGGGGGTATTTCGA-TCATTGTACCCTA
1 TAGGGGTATAACAGACATTTTACCCTAT-GGGGTATTT-GAGTCATTGTACCCTA
* ** * *
29713144 TGGGGGTATTTCAGACATTTTACCCTATGGGGTATTTTAGTCATTTTACCCTA
1 TAGGGGTATAACAGACATTTTACCCTATGGGGTATTTGAGTCATTGTACCCTA
29713197 TAGGGGTAT
1 TAGGGGTAT
29713206 TTCGATCATT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
52 1 0.02
53 29 0.54
54 24 0.44
ACGTcount: A:0.22, C:0.16, G:0.23, T:0.38
Consensus pattern (53 bp):
TAGGGGTATAACAGACATTTTACCCTATGGGGTATTTGAGTCATTGTACCCTA
Found at i:29713217 original size:26 final size:27
Alignment explanation
Indices: 29713104--29713220 Score: 161
Period size: 27 Copynumber: 4.4 Consensus size: 27
29713094 GGTATAACAG
29713104 TCATTTTACCCTATGGGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCGA
*
29713131 TCATTGTACCCTATGGGGGTATTTCAGA
1 TCATTTTACCCTATGGGGGTATTTC-GA
*
29713159 -CATTTTACCCTAT-GGGGTATTT-TA
1 TCATTTTACCCTATGGGGGTATTTCGA
*
29713183 GTCATTTTACCCTATAGGGGTATTTCGA
1 -TCATTTTACCCTATGGGGGTATTTCGA
29713211 TCA-TTTACCC
1 TCATTTTACCC
29713221 AGAAATGGCA
Statistics
Matches: 81, Mismatches: 4, Indels: 11
0.84 0.04 0.11
Matches are distributed among these distances:
24 1 0.01
26 29 0.36
27 48 0.59
28 3 0.04
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.40
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCGA
Found at i:29715581 original size:5 final size:5
Alignment explanation
Indices: 29715571--29715595 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
29715561 TTGATAGACT
29715571 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
29715596 ATAGCAAGTT
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:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:29717297 original size:19 final size:20
Alignment explanation
Indices: 29717273--29717310 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
29717263 TAGATCAAAA
29717273 TTTATTAAAT-ATATAATTT
1 TTTATTAAATGATATAATTT
*
29717292 TTTATTATATGATATAATT
1 TTTATTAAATGATATAATT
29717311 AGTGACTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (20 bp):
TTTATTAAATGATATAATTT
Found at i:29717639 original size:26 final size:27
Alignment explanation
Indices: 29717589--29717640 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 27
29717579 TTAAAATATG
* *
29717589 TTTTTTATGTTTTATAATTTTTAATAC
1 TTTTTTATGTTTTATAATATATAATAC
*
29717616 TTTTTTAT-TTTTTTAATATATAATA
1 TTTTTTATGTTTTATAATATATAATA
29717641 AAATAATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (27 bp):
TTTTTTATGTTTTATAATATATAATAC
Found at i:29724360 original size:9 final size:9
Alignment explanation
Indices: 29724324--29724360 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
29724314 ATATGTTTGA
29724324 ATTATTTAT
1 ATTATTTAT
29724333 A-T-TTTAT
1 ATTATTTAT
*
29724340 ATAATTTAT
1 ATTATTTAT
29724349 ATTATTTAT
1 ATTATTTAT
29724358 ATT
1 ATT
29724361 TAGGCGAGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
7 6 0.25
8 1 0.04
9 17 0.71
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTATTTAT
Found at i:29724666 original size:21 final size:21
Alignment explanation
Indices: 29724625--29724668 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29724615 GAATTTGAAA
*
29724625 TTAAAACTTTTAATATTTATT
1 TTAAAACTTTTAATATATATT
*
29724646 TTAAAA-TTTTGATATAATATT
1 TTAAAACTTTTAATAT-ATATT
29724667 TT
1 TT
29724669 TAATTTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
TTAAAACTTTTAATATATATT
Found at i:29731289 original size:13 final size:13
Alignment explanation
Indices: 29731271--29731299 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
29731261 TACAGATGCC
29731271 GCTAATTCATCAG
1 GCTAATTCATCAG
29731284 GCTAATTCATCAG
1 GCTAATTCATCAG
29731297 GCT
1 GCT
29731300 GCGTCTAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (13 bp):
GCTAATTCATCAG
Found at i:29732257 original size:20 final size:20
Alignment explanation
Indices: 29732225--29732262 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29732215 TTGAAACATG
*
29732225 TTTAAAATAAAAATTATCGT
1 TTTAAAATAAAAAGTATCGT
29732245 TTTATAAAT-AAAAGTATC
1 TTTA-AAATAAAAAGTATC
29732263 ATGAAAACCG
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 12 0.75
21 4 0.25
ACGTcount: A:0.50, C:0.05, G:0.05, T:0.39
Consensus pattern (20 bp):
TTTAAAATAAAAAGTATCGT
Found at i:29738628 original size:17 final size:16
Alignment explanation
Indices: 29738586--29738641 Score: 62
Period size: 17 Copynumber: 3.5 Consensus size: 16
29738576 TTATACTACA
29738586 AAATATTTATTATTAAT
1 AAATATTTATTA-TAAT
* *
29738603 ACATTTTTAATTATAAT
1 AAATATTT-ATTATAAT
29738620 AAATATTTATTAT--T
1 AAATATTTATTATAAT
29738634 AAATATTT
1 AAATATTT
29738642 TAGAAGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
14 9 0.26
16 5 0.15
17 16 0.47
18 4 0.12
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATATTTATTATAAT
Found at i:29739461 original size:38 final size:40
Alignment explanation
Indices: 29739414--29739499 Score: 108
Period size: 38 Copynumber: 2.2 Consensus size: 40
29739404 AAACTAAAGA
* *
29739414 TATTGAAAATATATTTTTAT-A-TTTTAT-ACTTTTTAATT
1 TATTAAAAATAT-TTTTTATAATTTTTATAACTTTTTAAAT
*
29739452 TATTAAAAATATTTTTTATAATTTTTTTAACTTTTTAAAT
1 TATTAAAAATATTTTTTATAATTTTTATAACTTTTTAAAT
29739492 T-TTAAAAA
1 TATTAAAAA
29739500 ATGAATTATT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
37 7 0.17
38 12 0.29
39 12 0.29
40 11 0.26
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (40 bp):
TATTAAAAATATTTTTTATAATTTTTATAACTTTTTAAAT
Found at i:29739500 original size:40 final size:38
Alignment explanation
Indices: 29739419--29739501 Score: 98
Period size: 40 Copynumber: 2.1 Consensus size: 38
29739409 AAAGATATTG
*
29739419 AAAATATATTTTTATATTTTATACTTTTTAATTTATTA
1 AAAATATATTTTTATATTTTATACTTTTTAATTTATAA
*
29739457 AAAATAT-TTTTTATAATTTTTTTAACTTTTTAAATTT-TAA
1 AAAATATATTTTTAT-A-TTTTAT-ACTTTTT-AATTTATAA
29739497 AAAAT
1 AAAAT
29739502 GAATTATTTG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
37 7 0.18
38 8 0.21
39 5 0.13
40 14 0.36
41 5 0.13
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (38 bp):
AAAATATATTTTTATATTTTATACTTTTTAATTTATAA
Found at i:29741631 original size:16 final size:16
Alignment explanation
Indices: 29741595--29741637 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
29741585 GTGAAAAATC
29741595 TAATAATA-ATATGAA
1 TAATAATATATATGAA
*
29741610 TGATAATATATAT-ACA
1 TAATAATATATATGA-A
29741626 TAATAATATATA
1 TAATAATATATA
29741638 ANNNNNNNNN
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 8 0.33
16 16 0.67
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (16 bp):
TAATAATATATATGAA
Found at i:29742895 original size:28 final size:27
Alignment explanation
Indices: 29742845--29742897 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
29742835 TACATGATGA
* *
29742845 AATTAAATAATAATATATGATAAAAAG
1 AATTAAATAATAATACATAATAAAAAG
*
29742872 AATTAAAATAATAGTACATAATAAAA
1 AATT-AAATAATAATACATAATAAAA
29742898 TAAAATAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.64, C:0.02, G:0.06, T:0.28
Consensus pattern (27 bp):
AATTAAATAATAATACATAATAAAAAG
Found at i:29742905 original size:23 final size:21
Alignment explanation
Indices: 29742875--29742918 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
29742865 TAAAAAGAAT
29742875 TAAAATAATAGTACATAATAAAA
1 TAAAATAAT-GTACAT-ATAAAA
*
29742898 TAAAATAATGTATATATAAAA
1 TAAAATAATGTACATATAAAA
29742919 AGGTAAACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 5 0.25
23 9 0.45
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAAATAATGTACATATAAAA
Found at i:29742953 original size:3 final size:3
Alignment explanation
Indices: 29742945--29743015 Score: 54
Period size: 3 Copynumber: 22.7 Consensus size: 3
29742935 AAACTAATAC
* * * * *
29742945 AAT AAT AAT ACCT -AT AAT AAT AAC AAC AAC AAT AAT AAT AGT AAT
1 AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
29742990 AAT AAT AAT AATT AATT AATT AAT AA
1 AAT AAT AAT AA-T AA-T AA-T AAT AA
29743016 AAAAACCAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
2 1 0.02
3 46 0.78
4 12 0.20
ACGTcount: A:0.61, C:0.07, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:29743076 original size:30 final size:30
Alignment explanation
Indices: 29743040--29743100 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
29743030 AAAAAGGATT
29743040 AAATCGCAATTAAAACTGAATTAACAGGAA
1 AAATCGCAATTAAAACTGAATTAACAGGAA
29743070 AAATCGCAATTAAAACTGAATTAACAGGAA
1 AAATCGCAATTAAAACTGAATTAACAGGAA
29743100 A
1 A
29743101 CAAATAAAAT
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:0.54, C:0.13, G:0.13, T:0.20
Consensus pattern (30 bp):
AAATCGCAATTAAAACTGAATTAACAGGAA
Found at i:29746830 original size:27 final size:27
Alignment explanation
Indices: 29746792--29746852 Score: 122
Period size: 27 Copynumber: 2.3 Consensus size: 27
29746782 CACATTGCTA
29746792 ACATTTACCCAATAGAAAGAAGAGTTC
1 ACATTTACCCAATAGAAAGAAGAGTTC
29746819 ACATTTACCCAATAGAAAGAAGAGTTC
1 ACATTTACCCAATAGAAAGAAGAGTTC
29746846 ACATTTA
1 ACATTTA
29746853 TGAAAGTACG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.44, C:0.18, G:0.13, T:0.25
Consensus pattern (27 bp):
ACATTTACCCAATAGAAAGAAGAGTTC
Found at i:29746857 original size:21 final size:23
Alignment explanation
Indices: 29746803--29746858 Score: 62
Period size: 27 Copynumber: 2.3 Consensus size: 23
29746793 CATTTACCCA
29746803 ATAGAAAGAAGAGTTCACATTTACCC
1 ATAGAAAGAAGAGTTCACATTT---C
29746829 AATAGAAAGAAGAGTTCACATTT-
1 -ATAGAAAGAAGAGTTCACATTTC
29746852 AT-GAAAG
1 ATAGAAAG
29746859 TACGCAGACC
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
21 5 0.17
22 2 0.07
27 22 0.76
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.23
Consensus pattern (23 bp):
ATAGAAAGAAGAGTTCACATTTC
Found at i:29749511 original size:119 final size:119
Alignment explanation
Indices: 29749298--29749637 Score: 619
Period size: 119 Copynumber: 2.8 Consensus size: 119
29749288 TTAATCATAT
*
29749298 TTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTT-ATAAAATTCTTAATATT
29749363 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
29749418 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTATAAAATTCTTAATATTA
1 TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTATAAAATTCTTAATATTA
29749483 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
66 AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
* * *
29749537 TTTAAAATAACTATTATCAAATATAATTTAATAAAAAACATATAA-TTATAAAATTCTTAATATT
1 TTTAAAATAATTATTATTAAATATAATTTAAT-AAAAATATATAATTTATAAAATTCTTAATATT
29749601 AAATATTCTTATATGAATTTACTAAAATCATAATATA
65 AAATATTCTTATATGAATTTACTAAAATCATAATATA
29749638 NNNNNNNNNN
Statistics
Matches: 215, Mismatches: 4, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
119 158 0.73
120 57 0.27
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (119 bp):
TTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTATAAAATTCTTAATATTA
AATATTCTTATATGAATTTACTAAAATCATAATATATAATACTATAAAATATAA
Found at i:29749798 original size:16 final size:17
Alignment explanation
Indices: 29749767--29749798 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
29749757 ATTATTATCA
29749767 ATATAATTTAATAAAAC
1 ATATAATTTAATAAAAC
29749784 ATATAATTT-ATAAAA
1 ATATAATTTAATAAAA
29749799 TTCTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAATTTAATAAAAC
Found at i:29750042 original size:17 final size:17
Alignment explanation
Indices: 29750002--29750035 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29749992 ATTATTATTA
29750002 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29750019 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
29750036 TCTTAATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:29750044 original size:22 final size:19
Alignment explanation
Indices: 29749998--29750036 Score: 64
Period size: 17 Copynumber: 2.2 Consensus size: 19
29749988 AATAATTATT
29749998 ATTAATATAATTTAATAAA
1 ATTAATATAATTTAATAAA
29750017 A-T-ATATAATTTAATAAA
1 ATTAATATAATTTAATAAA
29750034 ATT
1 ATT
29750037 CTTAATATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 16 0.84
18 2 0.11
19 1 0.05
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTAATATAATTTAATAAA
Found at i:29750069 original size:119 final size:118
Alignment explanation
Indices: 29749738--29750101 Score: 619
Period size: 118 Copynumber: 3.1 Consensus size: 118
29749728 NNNNNNNNNN
* *
29749738 TAAAATATAATTTAAAATAATTATTATCAATATAATTTAATAAAACATATAATTT-ATAAAATTC
1 TAAAATATAATTTAAAATAATTATTATTAATATAATTTAATAAAATATATAATTTAATAAAATTC
29749802 TTAATATTAAATATTCTTATATGAATTTACT-AAATCATAATATATAATACTA
66 TTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
*
29749854 TAAAATAT-ATTTAAAATAATTATTATTAAATATAATTTAAAAAATATATATAATTTAATAAAAT
1 TAAAATATAATTTAAAATAATTATTATT-AATATAATTTAATAAA-ATATATAATTTAATAAAAT
29749918 TCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
64 TCTTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
*
29749973 TAAAATATAATCTAAAATAATTATTATTAATATAATTTAATAAAATATATAATTTAATAAAATTC
1 TAAAATATAATTTAAAATAATTATTATTAATATAATTTAATAAAATATATAATTTAATAAAATTC
* *
29750038 TTAATATTAAATATTCTTATATGAGTTTTACTAAAATCATAATATATAATAATA
66 TTAATATTAAATATTCTTATATGA-ATTTACTAAAATCATAATATATAATACTA
29750092 TAAAA-ATAAT
1 TAAAATATAAT
29750102 ATATAATCTA
Statistics
Matches: 235, Mismatches: 7, Indels: 10
0.93 0.03 0.04
Matches are distributed among these distances:
115 18 0.08
116 23 0.10
117 10 0.04
118 90 0.38
119 76 0.32
120 18 0.08
ACGTcount: A:0.52, C:0.05, G:0.01, T:0.42
Consensus pattern (118 bp):
TAAAATATAATTTAAAATAATTATTATTAATATAATTTAATAAAATATATAATTTAATAAAATTC
TTAATATTAAATATTCTTATATGAATTTACTAAAATCATAATATATAATACTA
Found at i:29751549 original size:49 final size:49
Alignment explanation
Indices: 29751492--29751595 Score: 181
Period size: 49 Copynumber: 2.1 Consensus size: 49
29751482 AGAAAAAAAC
* * *
29751492 AAATTAAAATTAAGTTTAATATCATGAATCAAAAGGTGAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
29751541 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
1 AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
29751590 AAATTA
1 AAATTA
29751596 TAACACATGA
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.50, C:0.11, G:0.08, T:0.32
Consensus pattern (49 bp):
AAATTAAAATTAAGTTCAATATCATGAATCAAAAGCTCAACACTTTATA
Found at i:29754140 original size:16 final size:16
Alignment explanation
Indices: 29754101--29754134 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
29754091 AATAAATTAG
29754101 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
29754117 AATATTAAAAATAAAA
1 AATATTAAAAATAAAA
29754133 AA
1 AA
29754135 ATTTAATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATATTAAAAATAAAA
Found at i:29754429 original size:13 final size:13
Alignment explanation
Indices: 29754411--29754438 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
29754401 TAACCATTAC
29754411 AATAGTCACTCAA
1 AATAGTCACTCAA
29754424 AATAGTCACTCAA
1 AATAGTCACTCAA
29754437 AA
1 AA
29754439 CTGATTTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.50, C:0.21, G:0.07, T:0.21
Consensus pattern (13 bp):
AATAGTCACTCAA
Found at i:29755884 original size:19 final size:20
Alignment explanation
Indices: 29755841--29755883 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
29755831 ACACAAACGG
*
29755841 AAAACATCAACTTAATACAA
1 AAAACATAAACTTAATACAA
29755861 AAAACATAAACTTAATACAA
1 AAAACATAAACTTAATACAA
29755881 AAA
1 AAA
29755884 CCAAAACATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.65, C:0.16, G:0.00, T:0.19
Consensus pattern (20 bp):
AAAACATAAACTTAATACAA
Found at i:29762369 original size:50 final size:50
Alignment explanation
Indices: 29762313--29762441 Score: 159
Period size: 50 Copynumber: 2.6 Consensus size: 50
29762303 GGTCTCATGG
* ** *
29762313 AAGACCATATTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCCGA
1 AAGACCATATTTGGGACATGGCATTGGCACCGAGATGAGAACTCCCACGA
* * * * *
29762363 AAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACTCCCATGT
1 AAGACCATATTTGGGACATGGCATTGGCACCGAGATGAGAACTCCCACGA
* *
29762413 AAGACCATATCTGGGATATGGCATTGGCA
1 AAGACCATATTTGGGACATGGCATTGGCA
29762442 GTACAAGAAA
Statistics
Matches: 66, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 66 1.00
ACGTcount: A:0.28, C:0.22, G:0.29, T:0.21
Consensus pattern (50 bp):
AAGACCATATTTGGGACATGGCATTGGCACCGAGATGAGAACTCCCACGA
Found at i:29763156 original size:16 final size:17
Alignment explanation
Indices: 29763135--29763169 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
29763125 AGACGAAAAA
*
29763135 GAAAG-AAAGAAAAGGG
1 GAAAGAAAAGAAAAAGG
29763151 GAAAGAAAAGAAAAAGG
1 GAAAGAAAAGAAAAAGG
29763168 GA
1 GA
29763170 GAATTAGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 5 0.29
17 12 0.71
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GAAAGAAAAGAAAAAGG
Found at i:29763940 original size:6 final size:6
Alignment explanation
Indices: 29763929--29763960 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
29763919 GGATTGAATG
29763929 AAAATA AAAATA AAAATA AAAATA AAAATA AA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AA
29763961 TAAACATGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAATA
Found at i:29764055 original size:2 final size:2
Alignment explanation
Indices: 29764050--29764089 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29764040 TATATATATA
29764050 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG 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
29764090 AATTGAGTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:29764698 original size:39 final size:38
Alignment explanation
Indices: 29764618--29764745 Score: 123
Period size: 45 Copynumber: 3.2 Consensus size: 38
29764608 ACTTGTCGGC
* *
29764618 TTACTGATCAGGCAC-TTATGTGCCGACTACTGTTACTG
1 TTACTGATC-GGCACTTTGTGTGCCGAATACTGTTACTG
*
29764656 TTACTGATTCGGCACTTTGTGTGTCGAGTACTGTTACTGTTACTG
1 TTACTGA-TCGGCACTTTGTGTGCCGA--A----TACTGTTACTG
* *
29764701 TTACCGACTCGGCACTTTGTGTGCCGAATACTGTTACCG
1 TTACTGA-TCGGCACTTTGTGTGCCGAATACTGTTACTG
29764740 TTACTG
1 TTACTG
29764746 TTACAGGTTC
Statistics
Matches: 74, Mismatches: 8, Indels: 15
0.76 0.08 0.15
Matches are distributed among these distances:
38 12 0.16
39 26 0.35
43 1 0.01
45 35 0.47
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.37
Consensus pattern (38 bp):
TTACTGATCGGCACTTTGTGTGCCGAATACTGTTACTG
Found at i:29764713 original size:45 final size:45
Alignment explanation
Indices: 29764645--29764790 Score: 193
Period size: 45 Copynumber: 3.2 Consensus size: 45
29764635 ATGTGCCGAC
* *
29764645 TACTGTTACTGTTACTGATTCGGCACTTTGTGTGTCGAGTACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
* * *
29764690 TACTGTTACTGTTACCGACTCGGCACTTTGTGTGCCGAATACTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
* * * * * *
29764735 TACCGTTACTGTTACAGGTTCAGTACTTTGTGTGTTGAATATTGT
1 TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
29764780 TACTGTTACTG
1 TACTGTTACTG
29764791 CTACTGTTAC
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 87 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (45 bp):
TACTGTTACTGTTACAGATTCGGCACTTTGTGTGTCGAATACTGT
Found at i:29764809 original size:7 final size:6
Alignment explanation
Indices: 29764777--29764816 Score: 53
Period size: 6 Copynumber: 6.3 Consensus size: 6
29764767 TGTTGAATAT
*
29764777 TGTTAC TGTTAC TGCTAC TGTTAC TGATTAC TGTTTAC TG
1 TGTTAC TGTTAC TGTTAC TGTTAC TG-TTAC TG-TTAC TG
29764817 GTGTGTTTGG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
6 18 0.60
7 12 0.40
ACGTcount: A:0.17, C:0.17, G:0.17, T:0.47
Consensus pattern (6 bp):
TGTTAC
Found at i:29770746 original size:24 final size:24
Alignment explanation
Indices: 29770699--29770748 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
29770689 CACTAAAAAT
* *
29770699 ATTAAAATAAATGTTTTCCATTAA
1 ATTAAAATAAATATTTTACATTAA
29770723 ATTAAAATAAATATTTATAC-TTAA
1 ATTAAAATAAATATTT-TACATTAA
29770747 AT
1 AT
29770749 AACACTAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (24 bp):
ATTAAAATAAATATTTTACATTAA
Found at i:29778143 original size:4 final size:4
Alignment explanation
Indices: 29778119--29778181 Score: 90
Period size: 4 Copynumber: 15.8 Consensus size: 4
29778109 AGGTGCTCGT
* *
29778119 ATAC ATGC ATAC ATGC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
* *
29778167 ACAC ATAC ATGC ATA
1 ATAC ATAC ATAC ATA
29778182 AAAAGCATGC
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 51 1.00
ACGTcount: A:0.46, C:0.25, G:0.05, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:29782279 original size:23 final size:23
Alignment explanation
Indices: 29782253--29782328 Score: 125
Period size: 23 Copynumber: 3.3 Consensus size: 23
29782243 ATAAGTGCAA
29782253 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
29782276 CACTGTTATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
29782299 CACTGTTATATAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
29782322 CACTGAT
1 CACTGAT
29782329 CAATAACACT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.25
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:29782580 original size:18 final size:17
Alignment explanation
Indices: 29782554--29782592 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 17
29782544 ATTTTCCTTC
29782554 CACATTC-AATATTAATT
1 CACATTCAAATA-TAATT
29782571 CACATATCAAATATAATT
1 CACAT-TCAAATATAATT
29782589 CACA
1 CACA
29782593 ATTTATAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.25
18 11 0.55
19 4 0.20
ACGTcount: A:0.46, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
CACATTCAAATATAATT
Found at i:29783754 original size:2 final size:2
Alignment explanation
Indices: 29783747--29783778 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29783737 TTAGATATGG
29783747 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29783779 TGAGTTGAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29804697 original size:30 final size:30
Alignment explanation
Indices: 29804663--29804753 Score: 146
Period size: 30 Copynumber: 3.0 Consensus size: 30
29804653 TTCCTTATCT
29804663 TGAACTTCGACGCTATTCGTTTCCTTGCCA
1 TGAACTTCGACGCTATTCGTTTCCTTGCCA
29804693 TGAACTTCGACGCTATTCGTTTCCTTGCCA
1 TGAACTTCGACGCTATTCGTTTCCTTGCCA
* * * *
29804723 TGAACTTCAACACTGTTTGTTTCCTTGCCA
1 TGAACTTCGACGCTATTCGTTTCCTTGCCA
29804753 T
1 T
29804754 TTGTTTCCTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 57 1.00
ACGTcount: A:0.18, C:0.29, G:0.15, T:0.38
Consensus pattern (30 bp):
TGAACTTCGACGCTATTCGTTTCCTTGCCA
Found at i:29819782 original size:11 final size:10
Alignment explanation
Indices: 29819757--29819791 Score: 61
Period size: 10 Copynumber: 3.4 Consensus size: 10
29819747 ATTATTTTAA
29819757 TTTTTAGAAT
1 TTTTTAGAAT
29819767 TTTTTAGAAT
1 TTTTTAGAAT
29819777 TCTTTTAGAAT
1 T-TTTTAGAAT
29819788 TTTT
1 TTTT
29819792 ATAAATATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
10 14 0.58
11 10 0.42
ACGTcount: A:0.26, C:0.03, G:0.09, T:0.63
Consensus pattern (10 bp):
TTTTTAGAAT
Found at i:29819820 original size:17 final size:18
Alignment explanation
Indices: 29819788--29819826 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
29819778 CTTTTAGAAT
*
29819788 TTTTATAAATATATTTAA
1 TTTTATAAAAATATTTAA
*
29819806 TTTTA-AAAAATATTTTA
1 TTTTATAAAAATATTTAA
29819823 TTTT
1 TTTT
29819827 TTGTAATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (18 bp):
TTTTATAAAAATATTTAA
Found at i:29828116 original size:2 final size:2
Alignment explanation
Indices: 29828109--29828139 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
29828099 TAAGTTAGGA
29828109 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29828140 AACTATTATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29831686 original size:17 final size:18
Alignment explanation
Indices: 29831643--29831689 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
29831633 CCTCATATTA
29831643 TCACAATTTACAAAAAAT
1 TCACAATTTACAAAAAAT
* *
29831661 TATACCAATTT-CAAAATAT
1 T-CA-CAATTTACAAAAAAT
29831680 TCACAATTTA
1 TCACAATTTA
29831690 ATCCCTAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 6
0.72 0.09 0.19
Matches are distributed among these distances:
17 6 0.26
18 2 0.09
19 9 0.39
20 6 0.26
ACGTcount: A:0.49, C:0.17, G:0.00, T:0.34
Consensus pattern (18 bp):
TCACAATTTACAAAAAAT
Found at i:29836826 original size:63 final size:63
Alignment explanation
Indices: 29836747--29836875 Score: 222
Period size: 63 Copynumber: 2.0 Consensus size: 63
29836737 AATCTTGATT
* *
29836747 TATAACTTCAATTTGGTAATTCAAACTATATTAAGATGCACCTCATTCTTGATGTGATAAGAA
1 TATAACTTAAATTTGGTAATTCAAACTATATTAAGATGCACCTCATTCCTGATGTGATAAGAA
* *
29836810 TATAACTTAAATTTGGTAATTCAAACTCTATTAAGATGCGCCTCATTCCTGATGTGATAAGAA
1 TATAACTTAAATTTGGTAATTCAAACTATATTAAGATGCACCTCATTCCTGATGTGATAAGAA
29836873 TAT
1 TAT
29836876 CTCCATGTGA
Statistics
Matches: 62, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 62 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (63 bp):
TATAACTTAAATTTGGTAATTCAAACTATATTAAGATGCACCTCATTCCTGATGTGATAAGAA
Found at i:29837259 original size:12 final size:12
Alignment explanation
Indices: 29837242--29837266 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29837232 TGTTTTTGTG
29837242 TGTGTATATATA
1 TGTGTATATATA
29837254 TGTGTATATATA
1 TGTGTATATATA
29837266 T
1 T
29837267 CTAAAGGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (12 bp):
TGTGTATATATA
Found at i:29840346 original size:31 final size:31
Alignment explanation
Indices: 29840307--29840401 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 31
29840297 TATGTGTTTG
29840307 AGGATTAAATTGATAGAATTTATAAATATGA
1 AGGATTAAATTGATAGAATTTATAAATATGA
* * * * *
29840338 AGGGTTAAATTTATTGAATTATTTAAA-ATTA
1 AGGATTAAATTGATAGAATT-TATAAATATGA
* * *
29840369 A-GATCAAATTGATAGAATGTATAAGTATTGA
1 AGGATTAAATTGATAGAATTTATAAATA-TGA
29840400 AG
1 AG
29840402 ACTCAATGTG
Statistics
Matches: 47, Mismatches: 13, Indels: 7
0.70 0.19 0.10
Matches are distributed among these distances:
29 4 0.09
30 14 0.30
31 24 0.51
32 5 0.11
ACGTcount: A:0.45, C:0.01, G:0.17, T:0.37
Consensus pattern (31 bp):
AGGATTAAATTGATAGAATTTATAAATATGA
Found at i:29847368 original size:24 final size:24
Alignment explanation
Indices: 29847336--29847384 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
29847326 TTTTGATAAA
29847336 TATCTTACACAAATGTGTATCTGC
1 TATCTTACACAAATGTGTATCTGC
*
29847360 TATCTTACACAAATGTGTATTTGC
1 TATCTTACACAAATGTGTATCTGC
29847384 T
1 T
29847385 TCGGTGGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (24 bp):
TATCTTACACAAATGTGTATCTGC
Found at i:29859795 original size:20 final size:19
Alignment explanation
Indices: 29859769--29859823 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
29859759 AATATATATA
*
29859769 CTTTAATTAATTCATTAAT
1 CTTTAATTAATTAATTAAT
29859788 CATTTAATTAATCTAATTAAT
1 C-TTTAATTAAT-TAATTAAT
29859809 CTTTAATTAATTAAT
1 CTTTAATTAATTAAT
29859824 CTTAATCTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
19 5 0.15
20 20 0.61
21 8 0.24
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (19 bp):
CTTTAATTAATTAATTAAT
Found at i:29859799 original size:24 final size:22
Alignment explanation
Indices: 29859771--29859831 Score: 67
Period size: 21 Copynumber: 2.8 Consensus size: 22
29859761 TATATATACT
29859771 TTAATTAATTCATTAATCATTTAA
1 TTAATTAA-TCATTAATC-TTTAA
29859795 TTAATCT-A--ATTAATCTTTAA
1 TTAAT-TAATCATTAATCTTTAA
29859815 TTAATTAATC-TTAATCT
1 TTAATTAATCATTAATCT
29859832 CAATAAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
19 1 0.03
20 11 0.33
21 14 0.42
24 6 0.18
25 1 0.03
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (22 bp):
TTAATTAATCATTAATCTTTAA
Found at i:29859821 original size:15 final size:16
Alignment explanation
Indices: 29859795--29859831 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
29859785 AATCATTTAA
29859795 TTAATCTAATTAATCT
1 TTAATCTAATTAATCT
29859811 TTAAT-TAATTAATC-
1 TTAATCTAATTAATCT
29859825 TTAATCT
1 TTAATCT
29859832 CAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 5 0.25
15 10 0.50
16 5 0.25
ACGTcount: A:0.38, C:0.11, G:0.00, T:0.51
Consensus pattern (16 bp):
TTAATCTAATTAATCT
Found at i:29860587 original size:16 final size:15
Alignment explanation
Indices: 29860566--29860611 Score: 56
Period size: 16 Copynumber: 2.9 Consensus size: 15
29860556 CATTAAATTT
*
29860566 TATTAATTGATATAAA
1 TATTAATTAAT-TAAA
29860582 TATTAATTAATTAAA
1 TATTAATTAATTAAA
*
29860597 GATTAATTAGATTAA
1 TATTAATTA-ATTAA
29860612 TTAAATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
15 12 0.44
16 15 0.56
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (15 bp):
TATTAATTAATTAAA
Found at i:29860610 original size:20 final size:19
Alignment explanation
Indices: 29860583--29860637 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 19
29860573 TGATATAAAT
29860583 ATTAATTAATTAAAGATTA
1 ATTAATTAATTAAAGATTA
*
29860602 ATTAGATTAATTAAATTATTA
1 ATTA-ATTAATTAAA-GATTA
*
29860623 ATGAATTAATTAAAG
1 ATTAATTAATTAAAG
29860638 TATATATTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 20 0.65
21 7 0.23
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (19 bp):
ATTAATTAATTAAAGATTA
Found at i:29863425 original size:70 final size:71
Alignment explanation
Indices: 29863351--29863496 Score: 195
Period size: 71 Copynumber: 2.1 Consensus size: 71
29863341 ACCCATCAGA
* * * * * *
29863351 GTATCGATAGAAGTG-CAGGGATGTTGAACTTTGGCTACTAATTTGACTTGTTTCGATAGAAGTC
1 GTATCGATAAAAGTGTAAGAGATGCTGAACTTTGGCTACTAACTTGACTTGTTTCGATAAAAGTC
29863415 CTCAAG
66 CTCAAG
* * * *
29863421 GTATCGGTAAAAGTGTAAGAGATGCTGATCTTTGGCTACTAACTTGACTTGTTTTGGTAAAAGTC
1 GTATCGATAAAAGTGTAAGAGATGCTGAACTTTGGCTACTAACTTGACTTGTTTCGATAAAAGTC
29863486 CTCAAG
66 CTCAAG
29863492 GTATC
1 GTATC
29863497 AGTAGCACTT
Statistics
Matches: 65, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
70 13 0.20
71 52 0.80
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (71 bp):
GTATCGATAAAAGTGTAAGAGATGCTGAACTTTGGCTACTAACTTGACTTGTTTCGATAAAAGTC
CTCAAG
Found at i:29871782 original size:10 final size:10
Alignment explanation
Indices: 29871767--29871799 Score: 57
Period size: 10 Copynumber: 3.2 Consensus size: 10
29871757 GTAGAGTTGT
29871767 TTTCTTGAAA
1 TTTCTTGAAA
29871777 TTTCTTGAAA
1 TTTCTTGAAA
29871787 TTTCTTGAGAA
1 TTTCTTGA-AA
29871798 TT
1 TT
29871800 GATCAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 18 0.82
11 4 0.18
ACGTcount: A:0.27, C:0.09, G:0.12, T:0.52
Consensus pattern (10 bp):
TTTCTTGAAA
Found at i:29872735 original size:20 final size:23
Alignment explanation
Indices: 29872710--29872757 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
29872700 TCAAATTCAG
*
29872710 TAAAATTATT-CA-A-GTTAAAT
1 TAAAATTATTACACATGTCAAAT
29872730 TAAAA-TATTACACATGTCAAAT
1 TAAAATTATTACACATGTCAAAT
29872752 TAAAAT
1 TAAAAT
29872758 ATGGTTACAG
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
19 4 0.17
20 7 0.30
21 1 0.04
22 11 0.48
ACGTcount: A:0.52, C:0.08, G:0.04, T:0.35
Consensus pattern (23 bp):
TAAAATTATTACACATGTCAAAT
Found at i:29873027 original size:37 final size:37
Alignment explanation
Indices: 29872953--29873027 Score: 96
Period size: 37 Copynumber: 2.0 Consensus size: 37
29872943 TTATATATTC
* * * *
29872953 TTTAGAATTTTTTATTATTTTTTTAAAAAATATAAAT
1 TTTAGAATTTTTTATAAATATTTTAAAAAATAAAAAT
* *
29872990 TTTAGAATTTTTTATAAATATTTTAAATATTAAAAAT
1 TTTAGAATTTTTTATAAATATTTTAAAAAATAAAAAT
29873027 T
1 T
29873028 ATTTTGTAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.55
Consensus pattern (37 bp):
TTTAGAATTTTTTATAAATATTTTAAAAAATAAAAAT
Found at i:29873339 original size:127 final size:127
Alignment explanation
Indices: 29873107--29873348 Score: 430
Period size: 127 Copynumber: 1.9 Consensus size: 127
29873097 TACACCAATG
*
29873107 TATTATTTGAATTATTCGAATCATTTAAATTGTAAAATTCAACTCGACTCGAACTCGAAACTTGA
1 TATTATTTGAATTATTCGAATCATTTAAATTGTAAAATTCAACTCGACTCGAACTCGAAACTCGA
*
29873172 ATTACTTATTCGAGTTGGCTCAAATAACTCGATTCGATTAACTTAAAATTTAAATTTTAATA
66 ATTACTTATTCAAGTTGGCTCAAATAACTCGATTCGATTAACTTAAAATTTAAATTTTAATA
* *
29873234 TATTATTTGAATTATTCGAGTCATTTAAATTGTAAAATTCAACTCGACTCGAATTCGAAACTCGA
1 TATTATTTGAATTATTCGAATCATTTAAATTGTAAAATTCAACTCGACTCGAACTCGAAACTCGA
* *
29873299 ATTACTTATTCAAGTTGGCTCAAATAACTCGGTTCTATTAACTTAAAATT
66 ATTACTTATTCAAGTTGGCTCAAATAACTCGATTCGATTAACTTAAAATT
29873349 CGAAAAAAAA
Statistics
Matches: 109, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
127 109 1.00
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (127 bp):
TATTATTTGAATTATTCGAATCATTTAAATTGTAAAATTCAACTCGACTCGAACTCGAAACTCGA
ATTACTTATTCAAGTTGGCTCAAATAACTCGATTCGATTAACTTAAAATTTAAATTTTAATA
Found at i:29877100 original size:12 final size:11
Alignment explanation
Indices: 29877082--29877135 Score: 56
Period size: 12 Copynumber: 4.6 Consensus size: 11
29877072 TAAAAAGGAG
29877082 TAATAAATAAA
1 TAATAAATAAA
*
29877093 TGAATAAACGAAA
1 T-AATAAA-TAAA
29877106 TAAT-AATAAA
1 TAATAAATAAA
29877116 TAATAAAATAAA
1 TAAT-AAATAAA
29877128 TAAATAAA
1 T-AATAAA
29877136 CCAAGGCTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
10 7 0.19
11 3 0.08
12 19 0.53
13 7 0.19
ACGTcount: A:0.70, C:0.02, G:0.04, T:0.24
Consensus pattern (11 bp):
TAATAAATAAA
Found at i:29878821 original size:34 final size:35
Alignment explanation
Indices: 29878777--29878843 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
29878767 CAGTAAAATA
29878777 TTTTCCGTAAAATGATTT-CGGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
29878811 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
29878844 TTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:29879962 original size:22 final size:20
Alignment explanation
Indices: 29879937--29879979 Score: 50
Period size: 20 Copynumber: 2.0 Consensus size: 20
29879927 AAACACAATA
29879937 ACAAGTCAATATTCTAATATTC
1 ACAA-TCAA-ATTCTAATATTC
* *
29879959 ACAATCAAATTTTATTATTC
1 ACAATCAAATTCTAATATTC
29879979 A
1 A
29879980 TTCCTGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 11 0.58
21 4 0.21
22 4 0.21
ACGTcount: A:0.42, C:0.16, G:0.02, T:0.40
Consensus pattern (20 bp):
ACAATCAAATTCTAATATTC
Found at i:29885691 original size:16 final size:15
Alignment explanation
Indices: 29885663--29885698 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
29885653 TTATACATAT
29885663 TATTTTAATATTTTA
1 TATTTTAATATTTTA
*
29885678 TATTTTATATATTTTT
1 TATTTTA-ATATTTTA
29885694 TATTT
1 TATTT
29885699 ATAGTCATCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTTAATATTTTA
Found at i:29886152 original size:11 final size:11
Alignment explanation
Indices: 29886131--29886232 Score: 90
Period size: 11 Copynumber: 9.5 Consensus size: 11
29886121 ATAAATCCTT
29886131 TCTCTAATTTCC
1 TCTC-AATTTCC
29886143 TCTCAATTTCC
1 TCTCAATTTCC
29886154 TCTCAAATTT-C
1 TCTC-AATTTCC
29886165 TCTCAAATTT-C
1 TCTC-AATTTCC
*
29886176 TCTCAAATT-C
1 TCTCAATTTCC
**
29886186 -CT--ATTTAG
1 TCTCAATTTCC
*
29886194 TCTCAATTTGC
1 TCTCAATTTCC
29886205 TCTCAATTTCC
1 TCTCAATTTCC
*
29886216 TCTCAAGTTCC
1 TCTCAATTTCC
29886227 TCTCAA
1 TCTCAA
29886233 ATCCCTATTT
Statistics
Matches: 78, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
7 3 0.04
9 4 0.05
10 5 0.06
11 57 0.73
12 9 0.12
ACGTcount: A:0.23, C:0.30, G:0.03, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:29886208 original size:51 final size:51
Alignment explanation
Indices: 29886143--29886243 Score: 150
Period size: 51 Copynumber: 2.0 Consensus size: 51
29886133 TCTAATTTCC
* *
29886143 TCTCAATTTCCTCTCAAATTT-CTCTCAAATTTCTCTCAAATTCCTATTTAG
1 TCTCAATTTCCTCTC-AATTTCCTCTCAAATTCCTCTCAAATCCCTATTTAG
* *
29886194 TCTCAATTTGCTCTCAATTTCCTCTCAAGTTCCTCTCAAATCCCTATTTA
1 TCTCAATTTCCTCTCAATTTCCTCTCAAATTCCTCTCAAATCCCTATTTA
29886244 AAAGAGCTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
50 5 0.11
51 40 0.89
ACGTcount: A:0.24, C:0.30, G:0.03, T:0.44
Consensus pattern (51 bp):
TCTCAATTTCCTCTCAATTTCCTCTCAAATTCCTCTCAAATCCCTATTTAG
Found at i:29886430 original size:18 final size:18
Alignment explanation
Indices: 29886407--29886468 Score: 51
Period size: 18 Copynumber: 3.5 Consensus size: 18
29886397 TAAGTGTTAA
29886407 ATTTAATTTTTAAATATT
1 ATTTAATTTTTAAATATT
*
29886425 ATTTAAGATTTTT-TAT-TT
1 ATTT-A-ATTTTTAAATATT
*
29886443 ATGTAA-TTTTAAATAATT
1 ATTTAATTTTTAAAT-ATT
29886461 A-TTAATTT
1 ATTTAATTT
29886469 ATTATTTGTT
Statistics
Matches: 34, Mismatches: 4, Indels: 12
0.68 0.08 0.24
Matches are distributed among these distances:
15 4 0.12
16 3 0.09
17 4 0.12
18 14 0.41
19 3 0.09
20 6 0.18
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
ATTTAATTTTTAAATATT
Found at i:29887193 original size:16 final size:17
Alignment explanation
Indices: 29887169--29887211 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
29887159 CTCGAGTAAA
*
29887169 CCACCCATAT-ACATTC
1 CCACTCATATGACATTC
29887185 CCACTCATAATGACATTC
1 CCACTCAT-ATGACATTC
29887203 CCACTCATA
1 CCACTCATA
29887212 ACGAGGTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 7 0.29
17 3 0.12
18 14 0.58
ACGTcount: A:0.33, C:0.40, G:0.02, T:0.26
Consensus pattern (17 bp):
CCACTCATATGACATTC
Found at i:29888550 original size:126 final size:126
Alignment explanation
Indices: 29888324--29888625 Score: 455
Period size: 126 Copynumber: 2.4 Consensus size: 126
29888314 CACGTGGGAG
* ** * **
29888324 ATTTTTTCAGGAGTTAC-GTAGTAAAAGCGCATCCACGTGGGAGCTTCTTTCAGTACTTATGTTG
1 ATTTTTTCAGGAGCTACTGTAAAAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTATGCAG
*
29888388 ACTAAGCATCCTGCTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATT
66 ACAAAGCATCCTGCTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATT
* * * * * *
29888449 ATTTTTTCAAGAGCTACTGTAACAAAAGCGTGTCCACGTGGAAGCTTTTTTCAGTACTTCTGCAG
1 ATTTTTTCAGGAGCTACTGTAAAAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTATGCAG
29888514 ACAAAGCATCCTGCTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATT
66 ACAAAGCATCCTGCTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATT
*
29888575 ATTTTCTT-AGGAGCCACTGTAAAAAAAGCGCGTCCACGTGGGAGCTTCTTT
1 ATTTT-TTCAGGAGCTACTGTAAAAAAAGCGCGTCCACGTGGGAGCTTCTTT
29888626 AAATTAACAA
Statistics
Matches: 157, Mismatches: 18, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
125 15 0.10
126 140 0.89
127 2 0.01
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.33
Consensus pattern (126 bp):
ATTTTTTCAGGAGCTACTGTAAAAAAAGCGCGTCCACGTGGGAGCTTCTTTCAGTACTTATGCAG
ACAAAGCATCCTGCTTAAAGCGTTTTTGACACTGTTTGCTCAGAAACGTCTACTCGAAATT
Found at i:29888876 original size:94 final size:96
Alignment explanation
Indices: 29888658--29888886 Score: 275
Period size: 94 Copynumber: 2.4 Consensus size: 96
29888648 GGTAACCGTA
* *
29888658 AACCCCAAACCCTAATTTATTTGAGTTTTTACTTAAAAACCCTAAACACTAAACCCTAAACTAAT
1 AACCCTAAACCCTAATTTAATTGA-TTTTTACTTAAAAACCCTAAACACTAAACCCTAAACTAAT
* *
29888723 TTATTATAAATTTATAATTCATTTACTCAAGT
65 TTATTATAAATTTATAATTAAATTACTCAAGT
* * * * * * *
29888755 AACCCTGAACCTTAATTTAATTAATTTTTCCTTAAAAACCCCT-AACTCTAAATCCTAATCTAAT
1 AACCCTAAACCCTAATTTAATTGATTTTTACTTAAAAA-CCCTAAACACTAAACCCTAAACTAAT
** *
29888819 TT-TTA-ATTTTTTTAATTAAATTACTCAAGT
65 TTATTATAAATTTATAATTAAATTACTCAAGT
* *
29888849 AACTCTAAACCCTAATTTAATTGATTTTTTCTTAAAAA
1 AACCCTAAACCCTAATTTAATTGATTTTTACTTAAAAA
29888887 ATAATAAACA
Statistics
Matches: 112, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
94 53 0.47
95 3 0.03
96 33 0.29
97 23 0.21
ACGTcount: A:0.38, C:0.19, G:0.03, T:0.40
Consensus pattern (96 bp):
AACCCTAAACCCTAATTTAATTGATTTTTACTTAAAAACCCTAAACACTAAACCCTAAACTAATT
TATTATAAATTTATAATTAAATTACTCAAGT
Found at i:29893034 original size:28 final size:29
Alignment explanation
Indices: 29892974--29893035 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
29892964 AAAGCCCTTT
* *
29892974 TTTTTTCAATATTTATCGAAATGGGCCGG
1 TTTTTTCAATATTTACCGAAATGGGCCGA
*
29893003 TTTTTT-AATTATTTACCGAAATGGTCC-A
1 TTTTTTCAA-TATTTACCGAAATGGGCCGA
29893031 TTTTT
1 TTTTT
29893036 CGCGAAATCG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
28 7 0.24
29 22 0.76
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (29 bp):
TTTTTTCAATATTTACCGAAATGGGCCGA
Found at i:29918135 original size:43 final size:43
Alignment explanation
Indices: 29918082--29918171 Score: 126
Period size: 43 Copynumber: 2.1 Consensus size: 43
29918072 TTATGTGGAA
* * **
29918082 AAACGCCGCTATAGAACATGACCTTTAGCAGTGCTTTCCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCAGCACTTTCCCCAC
**
29918125 AAACACCGCTAAAGAACATGACCTTTAGTGGCACTTTCCCCAC
1 AAACACCGCTAAAGAACATGACCTTTAGCAGCACTTTCCCCAC
29918168 AAAC
1 AAAC
29918172 GCCACTAACT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.21
Consensus pattern (43 bp):
AAACACCGCTAAAGAACATGACCTTTAGCAGCACTTTCCCCAC
Found at i:29918500 original size:34 final size:34
Alignment explanation
Indices: 29918457--29918525 Score: 129
Period size: 34 Copynumber: 2.0 Consensus size: 34
29918447 TTTCATCATA
*
29918457 TTCTGAAGCTGTAGTTGAAGTTTGTCATATTTTC
1 TTCTGAAGCTGTAGTTGAAGTTCGTCATATTTTC
29918491 TTCTGAAGCTGTAGTTGAAGTTCGTCATATTTTC
1 TTCTGAAGCTGTAGTTGAAGTTCGTCATATTTTC
29918525 T
1 T
29918526 GCTTGCCCCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.46
Consensus pattern (34 bp):
TTCTGAAGCTGTAGTTGAAGTTCGTCATATTTTC
Found at i:29919023 original size:13 final size:14
Alignment explanation
Indices: 29918997--29919025 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
29918987 ACAAATGACG
29918997 AATTAAACCATTAT
1 AATTAAACCATTAT
29919011 AATTAAA-CATTAT
1 AATTAAACCATTAT
29919024 AA
1 AA
29919026 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:29923313 original size:27 final size:27
Alignment explanation
Indices: 29923283--29923387 Score: 115
Period size: 27 Copynumber: 4.3 Consensus size: 27
29923273 GATCTAAAGT
29923283 TTTATGTAAGTTATGATATGATATATA
1 TTTATGTAAGTTATGATATGATATATA
29923310 TTTA--T--G-TAT--TATG-T--A-A
1 TTTATGTAAGTTATGATATGATATATA
*
29923326 GTTATGTAAGTTATGATATGATATATA
1 TTTATGTAAGTTATGATATGATATATA
*
29923353 TTTATGTAAGTTATGATATGGTATATA
1 TTTATGTAAGTTATGATATGATATATA
29923380 TTTATGTA
1 TTTATGTA
29923388 TTATGTAAGT
Statistics
Matches: 64, Mismatches: 3, Indels: 22
0.72 0.03 0.25
Matches are distributed among these distances:
16 4 0.06
17 1 0.02
18 1 0.02
19 1 0.02
20 5 0.08
21 3 0.05
22 3 0.05
23 5 0.08
24 1 0.02
25 1 0.02
26 1 0.02
27 38 0.59
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (27 bp):
TTTATGTAAGTTATGATATGATATATA
Found at i:29923475 original size:13 final size:13
Alignment explanation
Indices: 29923457--29923483 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29923447 TGATTATCAT
29923457 CTTTAAATTTTAA
1 CTTTAAATTTTAA
29923470 CTTTAAATTTTAA
1 CTTTAAATTTTAA
29923483 C
1 C
29923484 CCTTTAATTA
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:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (13 bp):
CTTTAAATTTTAA
Found at i:29925780 original size:25 final size:25
Alignment explanation
Indices: 29925727--29925781 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
29925717 GTGATGCAGT
*
29925727 AGAGGAGTGTCAACGGCGATGCGAT
1 AGAGGAGTGTCAACGGCGATGCGAC
* * *
29925752 AGAGGAGTGTCGACGGCGATGTGGC
1 AGAGGAGTGTCAACGGCGATGCGAC
29925777 AGAGG
1 AGAGG
29925782 GGACAATCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.25, C:0.15, G:0.45, T:0.15
Consensus pattern (25 bp):
AGAGGAGTGTCAACGGCGATGCGAC
Found at i:29937488 original size:17 final size:17
Alignment explanation
Indices: 29937466--29937499 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
29937456 GTTCTATAAC
29937466 TTAGTGAACTAGGTAGA
1 TTAGTGAACTAGGTAGA
29937483 TTAGTGAACTAGGTAGA
1 TTAGTGAACTAGGTAGA
29937500 CTTACTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.06, G:0.29, T:0.29
Consensus pattern (17 bp):
TTAGTGAACTAGGTAGA
Found at i:29937621 original size:22 final size:22
Alignment explanation
Indices: 29937593--29937636 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29937583 AGCAATATAA
29937593 TACTATAACTTAGTGAACTTTT
1 TACTATAACTTAGTGAACTTTT
29937615 TACTATAACTTAGTGAACTTTT
1 TACTATAACTTAGTGAACTTTT
29937637 ATGGTTTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.09, T:0.45
Consensus pattern (22 bp):
TACTATAACTTAGTGAACTTTT
Found at i:29939433 original size:19 final size:19
Alignment explanation
Indices: 29939409--29939448 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
29939399 ACAAATACAT
*
29939409 TACCAACTTAATTCAGATG
1 TACCAACTTAATTCAAATG
*
29939428 TACCAACTTAGTTCAAATG
1 TACCAACTTAATTCAAATG
29939447 TA
1 TA
29939449 ACTAAGTAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.10, T:0.33
Consensus pattern (19 bp):
TACCAACTTAATTCAAATG
Found at i:29940409 original size:101 final size:98
Alignment explanation
Indices: 29940223--29940421 Score: 317
Period size: 101 Copynumber: 2.0 Consensus size: 98
29940213 ACTAGGCTCC
* *
29940223 TATAGGTTGATTCATTAACCTTCTCAAAAACACATTGGCTATGCTTTTCTCCAAAACCAACTGGA
1 TATAGGTTGATTCATTAACCTTCTCAAAAACACATTGGCTATGCGTTTCTCCAAAACCAAATGGA
29940288 GTACTAGTTGCTTTGCAATTTGGCATGGGGAAT
66 GTACTAGTTGCTTTGCAATTTGGCATGGGGAAT
*
29940321 TATAGGTTGATTCATTAACCTTCTCAAAAACACCTTGGCTTGATAGCGTTTCTCCAAAACCAAAT
1 TATAGGTTGATTCATTAACCTTCTCAAAAACACATTGGC-T-AT-GCGTTTCTCCAAAACCAAAT
* * *
29940386 GGAGTACTAGTTGCTTTGTAATTTTGCATTGGGAAT
63 GGAGTACTAGTTGCTTTGCAATTTGGCATGGGGAAT
29940422 CTGTTTAGGA
Statistics
Matches: 92, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
98 38 0.41
99 1 0.01
100 2 0.02
101 51 0.55
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.35
Consensus pattern (98 bp):
TATAGGTTGATTCATTAACCTTCTCAAAAACACATTGGCTATGCGTTTCTCCAAAACCAAATGGA
GTACTAGTTGCTTTGCAATTTGGCATGGGGAAT
Found at i:29953345 original size:86 final size:84
Alignment explanation
Indices: 29953062--29953607 Score: 516
Period size: 86 Copynumber: 6.5 Consensus size: 84
29953052 GATTAAGTCT
* * * * *
29953062 TCGTTTGGAAACAAAATTAAGATCGAATAAAACCTGTTAAA-CGGCGGGAATAAATCCCAAAATA
1 TCGTTTGGAAACAAAATAAAAATGGAATAAAATCTGTTAAATC-GCGGGAATAAATCCCGAAATA
*
29953126 GA-TTATTCAA-TTTAATAC
65 GATTTATTTAATTTTAATAC
** * * * *
29953144 TAATTTGGAAACAAAATTACAAAT-GACTAAAATATGTTAAA-CGACTGGAATAAATCCCGAAAT
1 TCGTTTGGAAACAAAA-TAAAAATGGAATAAAATCTGTTAAATCG-CGGGAATAAATCCCGAAAT
**
29953207 AGA-TTATTTAA-TTTAATTT
64 AGATTTATTTAATTTTAATAC
** ** * * *
29953226 TAATTTGGAAACAAAA-ATAAAATAAAATAAAATCTGTTAAATAGCGGGAATAAATCCCGACACA
1 TCGTTTGGAAACAAAATA-AAAATGGAATAAAATCTGTTAAATCGCGGGAATAAATCCCGAAATA
* *
29953290 GATTTTATTTAATTTTAGTTTC
65 GA-TTTATTTAATTTTA-ATAC
* *
29953312 TCGTTTGGCAACAAAATAAAAATGGAATAAAATCTGTTAAATGGCGGGAATAAATCCCGAAATAG
1 TCGTTTGGAAACAAAATAAAAATGGAATAAAATCTGTTAAATCGCGGGAATAAATCCCGAAATAG
29953377 ATTTTATTTAATTTTAATAC
66 A-TTTATTTAATTTTAATAC
* * * * * ** *
29953397 TCGTTTGGAAACAAGATCAAAATTGGAATAAAATCTATTGAACCGCGGGAATAAATCTTGAAACA
1 TCGTTTGGAAACAAAAT-AAAAATGGAATAAAATCTGTTAAATCGCGGGAATAAATCCCGAAATA
*
29953462 TATTTTATTTAATTTTAATAC
65 GA-TTTATTTAATTTTAATAC
* * * * *
29953483 TCGTTCTGGAAATAAAATCAAAATTGGAATAAAATCTGTTGAAT-GAGGGAATAAATCCCAAAAT
1 TCGTT-TGGAAACAAAAT-AAAAATGGAATAAAATCTGTTAAATCGCGGGAATAAATCCCGAAAT
29953547 AGATTTATTTAATTTTAATAC
64 AGATTTATTTAATTTTAATAC
* * * * *
29953568 TCTTTTTAGAAATAAAATAAAAAATTGAATAAAATTTGTT
1 TC-GTTTGGAAACAAAAT-AAAAATGGAATAAAATCTGTT
29953608 GAAGAACGAG
Statistics
Matches: 391, Mismatches: 60, Indels: 23
0.82 0.13 0.05
Matches are distributed among these distances:
80 1 0.00
81 5 0.01
82 111 0.28
83 5 0.01
84 8 0.02
85 70 0.18
86 156 0.40
87 35 0.09
ACGTcount: A:0.44, C:0.10, G:0.13, T:0.32
Consensus pattern (84 bp):
TCGTTTGGAAACAAAATAAAAATGGAATAAAATCTGTTAAATCGCGGGAATAAATCCCGAAATAG
ATTTATTTAATTTTAATAC
Found at i:29954458 original size:20 final size:20
Alignment explanation
Indices: 29954415--29954463 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
29954405 AGGGGTAGTT
* *
29954415 AAATCAATTTGATTAAAATC
1 AAATCAAATTGATTAAAATA
*
29954435 AAATCAAATTGATTAGAATA
1 AAATCAAATTGATTAAAATA
*
29954455 AAATAAAAT
1 AAATCAAAT
29954464 CAGGGTATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.06, G:0.06, T:0.31
Consensus pattern (20 bp):
AAATCAAATTGATTAAAATA
Found at i:29961029 original size:27 final size:28
Alignment explanation
Indices: 29960970--29961030 Score: 72
Period size: 27 Copynumber: 2.2 Consensus size: 28
29960960 TGCCATATCA
* *
29960970 ATAGGC-GACACCAGTGACCCCTCTTTG
1 ATAGGCAGACACCAGTGACCCCTATTCG
**
29960997 GCAGGCAG-CACCAGTGACCCCTATTCG
1 ATAGGCAGACACCAGTGACCCCTATTCG
29961024 ATAGGCA
1 ATAGGCA
29961031 ATACAGGAGA
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.25, C:0.33, G:0.25, T:0.18
Consensus pattern (28 bp):
ATAGGCAGACACCAGTGACCCCTATTCG
Found at i:29967519 original size:25 final size:25
Alignment explanation
Indices: 29967491--29967547 Score: 98
Period size: 25 Copynumber: 2.3 Consensus size: 25
29967481 GAAAATTTTA
29967491 GAGAAAATCATCACCATTTTGAGCT
1 GAGAAAATCATCACCATTTTGAGCT
*
29967516 GAGAAAATCATCACCATTTTTAGCT
1 GAGAAAATCATCACCATTTTGAGCT
29967541 GA-AAAAT
1 GAGAAAAT
29967548 AGCCATTGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 5 0.16
25 26 0.84
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.28
Consensus pattern (25 bp):
GAGAAAATCATCACCATTTTGAGCT
Found at i:29972618 original size:15 final size:15
Alignment explanation
Indices: 29972598--29972629 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
29972588 AGTATTATGT
29972598 AATATATGGCTATAA
1 AATATATGGCTATAA
29972613 AATATATGGCTATAA
1 AATATATGGCTATAA
29972628 AA
1 AA
29972630 GGCATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.06, G:0.12, T:0.31
Consensus pattern (15 bp):
AATATATGGCTATAA
Found at i:29973540 original size:26 final size:25
Alignment explanation
Indices: 29973510--29973602 Score: 66
Period size: 26 Copynumber: 3.4 Consensus size: 25
29973500 CCTTTGCCTA
29973510 TTTATTATTGTCATTATTATTTTATT
1 TTTATTATT-TCATTATTATTTTATT
*
29973536 TTTA-TATTT-ATTCTAGTTATCTTATCT
1 TTTATTATTTCA-T-TA-TTATTTTAT-T
29973563 ATTTATTATTACTCCCATTATTATTTTATT
1 -TTTATTATT--T--CATTATTATTTTATT
29973593 TTTA-TATTTC
1 TTTATTATTTC
29973603 TTCTAGTTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 24
0.68 0.03 0.30
Matches are distributed among these distances:
23 1 0.02
24 3 0.06
25 6 0.11
26 13 0.24
27 1 0.02
28 8 0.15
29 8 0.15
30 1 0.02
31 9 0.17
32 2 0.04
33 1 0.02
34 1 0.02
ACGTcount: A:0.24, C:0.10, G:0.02, T:0.65
Consensus pattern (25 bp):
TTTATTATTTCATTATTATTTTATT
Found at i:29973612 original size:26 final size:26
Alignment explanation
Indices: 29973526--29973618 Score: 80
Period size: 26 Copynumber: 3.4 Consensus size: 26
29973516 ATTGTCATTA
* *
29973526 TTATTTTATTTTTATATTTATTCTAG
1 TTATCTTATTTTTATATTTCTTCTAG
* *
29973552 TTATCTTATCTATTTATTATTACTCCCATTA-
1 TTATCTTAT-T-TTTA-TATTTCT-TC--TAG
*
29973583 TTATTTTATTTTTATATTTCTTCTAG
1 TTATCTTATTTTTATATTTCTTCTAG
29973609 TTATCTTATT
1 TTATCTTATT
29973619 ATTTCTTTTA
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
25 2 0.04
26 17 0.33
27 2 0.04
28 10 0.19
29 9 0.17
30 2 0.04
31 8 0.15
32 2 0.04
ACGTcount: A:0.23, C:0.11, G:0.02, T:0.65
Consensus pattern (26 bp):
TTATCTTATTTTTATATTTCTTCTAG
Found at i:29976025 original size:13 final size:13
Alignment explanation
Indices: 29976009--29976034 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
29975999 AATTTACGTA
29976009 AACAAATGGTTTT
1 AACAAATGGTTTT
29976022 AACAAATGGTTTT
1 AACAAATGGTTTT
29976035 TGGAAACATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.38
Consensus pattern (13 bp):
AACAAATGGTTTT
Found at i:29978364 original size:30 final size:30
Alignment explanation
Indices: 29978284--29978393 Score: 123
Period size: 30 Copynumber: 3.7 Consensus size: 30
29978274 GGTGATAACC
* *
29978284 ATCAAATTATG-AAAAGGAATGGCTTCGACT
1 ATCAAATTATGAAAAAGG-ATAGCTTCGGCT
* *
29978314 ATAAAATTATGAAAAGGGATAGCTTCGGCT
1 ATCAAATTATGAAAAAGGATAGCTTCGGCT
* * * *
29978344 ATCAAACTATGAAAAAGGATAACTTTGGTT
1 ATCAAATTATGAAAAAGGATAGCTTCGGCT
*
29978374 ATCGAATTATGAAAAAGGAT
1 ATCAAATTATGAAAAAGGAT
29978394 GTGTCAACCA
Statistics
Matches: 67, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
30 62 0.93
31 5 0.07
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.27
Consensus pattern (30 bp):
ATCAAATTATGAAAAAGGATAGCTTCGGCT
Found at i:29980518 original size:15 final size:15
Alignment explanation
Indices: 29980498--29980534 Score: 74
Period size: 15 Copynumber: 2.5 Consensus size: 15
29980488 ATCATAAAAC
29980498 CAAGGCATAAGCCAT
1 CAAGGCATAAGCCAT
29980513 CAAGGCATAAGCCAT
1 CAAGGCATAAGCCAT
29980528 CAAGGCA
1 CAAGGCA
29980535 AAACACACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.41, C:0.27, G:0.22, T:0.11
Consensus pattern (15 bp):
CAAGGCATAAGCCAT
Found at i:29981236 original size:4 final size:4
Alignment explanation
Indices: 29981227--29981251 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
29981217 AGGATGTTAG
29981227 AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT A
29981252 TGAAAGTTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:29992755 original size:31 final size:31
Alignment explanation
Indices: 29992717--29992776 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
29992707 TTAATTAAAG
*
29992717 TTCAGAGACTAATTTGTAAAAGCCTAATCGT
1 TTCAGAGACTAAATTGTAAAAGCCTAATCGT
*
29992748 TTCAGAGACTAAATTGTAAAAGTCTAATC
1 TTCAGAGACTAAATTGTAAAAGCCTAATC
29992777 ACTATTGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (31 bp):
TTCAGAGACTAAATTGTAAAAGCCTAATCGT
Found at i:29993006 original size:143 final size:142
Alignment explanation
Indices: 29992749--29993036 Score: 450
Period size: 143 Copynumber: 2.0 Consensus size: 142
29992739 CCTAATCGTT
* * *
29992749 TCAGAGACTAAATTGTAAAAGTCTAATCACTATTGATTTTTATATTGGAAAATTTCGATGACCTA
1 TCAGAAACTAAATTGTAAAAGTCCAATCACTATTGAATTTTATATTGGAAAATTTCGATGACCTA
* *
29992814 ATCGATAATTAACCAAGGGACCTAAATGGCAATTAACTCATTGTTTCTTATAAGATAGTGGATGA
66 ATCGATAATTAACCAAGGGACCTAAATAGCAATTAACTCATTGTTTCTTATAAGATAATGGATGA
29992879 TAACGATGATAG
131 TAACGATGATAG
* * *
29992891 TCAGAAACTAAATTGTAAAAGTCCATTCGCTATTGAATTTTATATTGGAAAATGTTTGATGACCT
1 TCAGAAACTAAATTGTAAAAGTCCAATCACTATTGAATTTTATATTGGAAAAT-TTCGATGACCT
* * **
29992956 AATTGGTAATTAACCAAGGGACCTAAATAGTTATTAACTCATTGTTTCTTATAAGATAATGGATG
65 AATCGATAATTAACCAAGGGACCTAAATAGCAATTAACTCATTGTTTCTTATAAGATAATGGATG
*
29993021 ATAATGATGATAG
130 ATAACGATGATAG
29993034 TCA
1 TCA
29993037 TTTAACTTTG
Statistics
Matches: 132, Mismatches: 13, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
142 48 0.36
143 84 0.64
ACGTcount: A:0.37, C:0.12, G:0.17, T:0.34
Consensus pattern (142 bp):
TCAGAAACTAAATTGTAAAAGTCCAATCACTATTGAATTTTATATTGGAAAATTTCGATGACCTA
ATCGATAATTAACCAAGGGACCTAAATAGCAATTAACTCATTGTTTCTTATAAGATAATGGATGA
TAACGATGATAG
Found at i:29993136 original size:2 final size:2
Alignment explanation
Indices: 29993129--29993158 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
29993119 ATCTAAATAA
29993129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29993159 CAAATAGTGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29999132 original size:29 final size:29
Alignment explanation
Indices: 29999095--29999150 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
29999085 ATTAAGTTTG
* * *
29999095 AAAGTTTAATTAAATTTTTAAAAAAAATA
1 AAAGCTTAATAAAATATTTAAAAAAAATA
29999124 AAAGCTTAATAAAATATTTAAAAAAAA
1 AAAGCTTAATAAAATATTTAAAAAAAA
29999151 CTTGATTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (29 bp):
AAAGCTTAATAAAATATTTAAAAAAAATA
Found at i:30000569 original size:20 final size:20
Alignment explanation
Indices: 30000544--30000581 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
30000534 ATAAAAAAAT
30000544 TTATTTTCTTCTCCTTTCAC
1 TTATTTTCTTCTCCTTTCAC
* *
30000564 TTATTTTTTTTTCCTTTC
1 TTATTTTCTTCTCCTTTC
30000582 TCCTTTCTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.08, C:0.24, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTTCTTCTCCTTTCAC
Found at i:30000717 original size:2 final size:2
Alignment explanation
Indices: 30000710--30000735 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
30000700 CATATAATTG
30000710 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
30000736 GCTGAAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30010954 original size:2 final size:2
Alignment explanation
Indices: 30010949--30010975 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30010939 TGTGTGTGTG
30010949 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
30010976 GAGTGTTCTT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30014972 original size:11 final size:11
Alignment explanation
Indices: 30014956--30014982 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
30014946 ATTTTATAAT
30014956 ACATATTCATA
1 ACATATTCATA
30014967 ACATATTCATA
1 ACATATTCATA
30014978 ACATA
1 ACATA
30014983 CCACTACCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.48, C:0.19, G:0.00, T:0.33
Consensus pattern (11 bp):
ACATATTCATA
Found at i:30016151 original size:23 final size:23
Alignment explanation
Indices: 30016117--30016170 Score: 99
Period size: 23 Copynumber: 2.3 Consensus size: 23
30016107 ATTCTGGAAA
30016117 ACACAAAATAAGGTTTGGGTCATT
1 ACAC-AAATAAGGTTTGGGTCATT
30016141 ACACAAATAAGGTTTGGGTCATT
1 ACACAAATAAGGTTTGGGTCATT
30016164 ACACAAA
1 ACACAAA
30016171 GTAGTCTTAT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 26 0.87
24 4 0.13
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.26
Consensus pattern (23 bp):
ACACAAATAAGGTTTGGGTCATT
Found at i:30019357 original size:23 final size:26
Alignment explanation
Indices: 30019312--30019364 Score: 76
Period size: 23 Copynumber: 2.2 Consensus size: 26
30019302 GAAAAGTTTA
30019312 AATAATTATGTGATAAAATTTAAAAT
1 AATAATTATGTGATAAAATTTAAAAT
*
30019338 AATAA-TATGTTAT-AAA-TTAAAAT
1 AATAATTATGTGATAAAATTTAAAAT
30019361 AATA
1 AATA
30019365 TTGATGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 11 0.42
24 3 0.12
25 7 0.27
26 5 0.19
ACGTcount: A:0.57, C:0.00, G:0.06, T:0.38
Consensus pattern (26 bp):
AATAATTATGTGATAAAATTTAAAAT
Found at i:30019379 original size:22 final size:23
Alignment explanation
Indices: 30019300--30019389 Score: 64
Period size: 23 Copynumber: 4.0 Consensus size: 23
30019290 ATAATAATAC
* *
30019300 ATGAAAAGTTTAAATAATTATGTG
1 ATGAAAAGTTAAAATAA-TATATG
*
30019324 AT-AAAATTTAAAATAATAATATG
1 ATGAAAAGTTAAAATAAT-ATATG
*
30019347 -TTATAAA-TTAAAATAATAT-TG
1 ATGA-AAAGTTAAAATAATATATG
*
30019368 ATGATAAGTTAAGAA-AATATAT
1 ATGAAAAGTTAA-AATAATATAT
30019390 TAAGTTTAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
21 4 0.07
22 15 0.28
23 30 0.56
24 5 0.09
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (23 bp):
ATGAAAAGTTAAAATAATATATG
Found at i:30019406 original size:22 final size:22
Alignment explanation
Indices: 30019381--30019430 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
30019371 ATAAGTTAAG
* *
30019381 AAAATATAT-TAAGTTTAAACAT
1 AAAATATATGTAAATTTAAA-AA
30019403 AAAATA-ATGTAAATTTAAAAA
1 AAAATATATGTAAATTTAAAAA
30019424 AAAATAT
1 AAAATAT
30019431 CCAAAAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.32
Consensus pattern (22 bp):
AAAATATATGTAAATTTAAAAA
Found at i:30023797 original size:20 final size:21
Alignment explanation
Indices: 30023754--30023796 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
30023744 ATAAAAACAC
30023754 AAATATACATAAATAGTTTAA
1 AAATATACATAAATAGTTTAA
*
30023775 AAATATA-ATAAAT-TTTTAA
1 AAATATACATAAATAGTTTAA
30023794 AAA
1 AAA
30023797 ACCATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.35
Consensus pattern (21 bp):
AAATATACATAAATAGTTTAA
Found at i:30024669 original size:17 final size:17
Alignment explanation
Indices: 30024640--30024685 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
30024630 TTATTATAAT
*
30024640 TTTTAATATATTTGTGTA
1 TTTTAATA-ATTTGTATA
*
30024658 TTTTAATAATTTTTATA
1 TTTTAATAATTTGTATA
*
30024675 TTTTAAGAATT
1 TTTTAATAATT
30024686 AGGATCAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
17 17 0.68
18 8 0.32
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.61
Consensus pattern (17 bp):
TTTTAATAATTTGTATA
Found at i:30025173 original size:31 final size:31
Alignment explanation
Indices: 30025135--30025201 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
30025125 TTAATATAAT
* * ** *
30025135 ATTTGATATTTGAATATGATTTTTTTTTTTA
1 ATTTGATACTCGAATATGACATTTTTTCTTA
*
30025166 ATTTGATACTCGAATTTGACATTTTTTCTTA
1 ATTTGATACTCGAATATGACATTTTTTCTTA
30025197 ATTTG
1 ATTTG
30025202 GTACCTAATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.06, G:0.10, T:0.58
Consensus pattern (31 bp):
ATTTGATACTCGAATATGACATTTTTTCTTA
Found at i:30025212 original size:30 final size:31
Alignment explanation
Indices: 30025156--30025214 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
30025146 GAATATGATT
*
30025156 TTTTTTTTTAATTTGATACTCGAATTTGACA
1 TTTTTTCTTAATTTGATACTCGAATTTGACA
* *
30025187 TTTTTTCTTAATTTGGTAC-CTAATTTGA
1 TTTTTTCTTAATTTGATACTCGAATTTGA
30025215 TACTTGAATT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 8 0.32
31 17 0.68
ACGTcount: A:0.24, C:0.10, G:0.10, T:0.56
Consensus pattern (31 bp):
TTTTTTCTTAATTTGATACTCGAATTTGACA
Done.