Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr13
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: 91551117
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2824764 characters in sequence are not A, C, G, or T
File 92 of 276
Found at i:28865377 original size:27 final size:26
Alignment explanation
Indices: 28865339--28865479 Score: 124
Period size: 27 Copynumber: 5.3 Consensus size: 26
28865329 CTAATAGATA
28865339 AAAATGACCGTAATACCCCTGTAAGGT
1 AAAATGACCGTAAT-CCCCTGTAAGGT
* * *
28865366 AAAATGATCGTAATGCCTTCGT-AGGAT
1 AAAATGACCGTAATCCCCT-GTAAGG-T
* *
28865393 AAAATGGCCGTAATGCCCCCG-AAGGT
1 AAAATGACCGTAAT-CCCCTGTAAGGT
* * * *
28865419 AAAATAACCATAATGCCCTATAAGGT
1 AAAATGACCGTAATCCCCTGTAAGGT
* *
28865445 AAAATGATCGTAATGCCCCTGTAGGGT
1 AAAATGACCGTAAT-CCCCTGTAAGGT
28865472 AAAATGAC
1 AAAATGAC
28865480 AAGTATGCCC
Statistics
Matches: 87, Mismatches: 21, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
25 3 0.03
26 34 0.39
27 48 0.55
28 2 0.02
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.23
Consensus pattern (26 bp):
AAAATGACCGTAATCCCCTGTAAGGT
Found at i:28865432 original size:26 final size:26
Alignment explanation
Indices: 28865403--28865463 Score: 68
Period size: 26 Copynumber: 2.3 Consensus size: 26
28865393 AAAATGGCCG
*
28865403 TAATGCCCCCGAAGGTAAAATAACCA
1 TAATGCCCCAGAAGGTAAAATAACCA
* * * * *
28865429 TAATGCCCTATAAGGTAAAATGATCG
1 TAATGCCCCAGAAGGTAAAATAACCA
28865455 TAATGCCCC
1 TAATGCCCC
28865464 TGTAGGGTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.38, C:0.25, G:0.16, T:0.21
Consensus pattern (26 bp):
TAATGCCCCAGAAGGTAAAATAACCA
Found at i:28865649 original size:27 final size:27
Alignment explanation
Indices: 28865605--28865709 Score: 124
Period size: 27 Copynumber: 3.9 Consensus size: 27
28865595 ATGGATGGAG
* * *
28865605 TACTG-TACTAGTGACTATGTCAC-AT
1 TACTGATACTGGTGGCTATGCCACAAT
*
28865630 TCACTGATATTGGTGGCTATGCCACAAT
1 T-ACTGATACTGGTGGCTATGCCACAAT
*
28865658 TACTGATACTGGTGGCTTTGCCACAAT
1 TACTGATACTGGTGGCTATGCCACAAT
* *
28865685 TACTAATACTGGTGGCTTTGCCACA
1 TACTGATACTGGTGGCTATGCCACA
28865710 TTCACTGTTT
Statistics
Matches: 70, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
25 1 0.01
26 4 0.06
27 62 0.89
28 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (27 bp):
TACTGATACTGGTGGCTATGCCACAAT
Found at i:28865723 original size:27 final size:27
Alignment explanation
Indices: 28865632--28865709 Score: 129
Period size: 27 Copynumber: 2.9 Consensus size: 27
28865622 TGTCACATTC
* *
28865632 ACTGATATTGGTGGCTATGCCACAATT
1 ACTGATACTGGTGGCTTTGCCACAATT
28865659 ACTGATACTGGTGGCTTTGCCACAATT
1 ACTGATACTGGTGGCTTTGCCACAATT
*
28865686 ACTAATACTGGTGGCTTTGCCACA
1 ACTGATACTGGTGGCTTTGCCACA
28865710 TTCACTGTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (27 bp):
ACTGATACTGGTGGCTTTGCCACAATT
Found at i:28867828 original size:16 final size:17
Alignment explanation
Indices: 28867751--28867844 Score: 60
Period size: 15 Copynumber: 5.9 Consensus size: 17
28867741 ATCTAATATA
28867751 ATAAAATAATA-ATAA-
1 ATAAAATAATATATAAT
** *
28867766 ATAATTTAATA-ATATT
1 ATAAAATAATATATAAT
* * *
28867782 TTAATATAAT-TATTAT
1 ATAAAATAATATATAAT
28867798 -TAAATATAAT-T-TAAT
1 ATAAA-ATAATATATAAT
28867813 A-AAAATAATATATAAT
1 ATAAAATAATATATAAT
28867829 ATTAAAATAATATATA
1 A-TAAAATAATATATA
28867845 GCCTACTTTA
Statistics
Matches: 62, Mismatches: 9, Indels: 13
0.74 0.11 0.15
Matches are distributed among these distances:
14 5 0.08
15 22 0.35
16 22 0.35
18 13 0.21
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAAAATAATATATAAT
Found at i:28867837 original size:18 final size:18
Alignment explanation
Indices: 28867795--28867844 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
28867785 ATATAATTAT
28867795 TATTAAATATAAT-T-TAA
1 TATTAAA-ATAATATATAA
28867812 TA--AAAATAATATATAA
1 TATTAAAATAATATATAA
28867828 TATTAAAATAATATATA
1 TATTAAAATAATATATA
28867845 GCCTACTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 5 0.17
15 4 0.14
16 5 0.17
17 2 0.07
18 13 0.45
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
TATTAAAATAATATATAA
Found at i:28868731 original size:14 final size:14
Alignment explanation
Indices: 28868712--28868741 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
28868702 TTCTCAAGGC
28868712 TAATTCCATCTTTT
1 TAATTCCATCTTTT
28868726 TAATTCCATCTTTT
1 TAATTCCATCTTTT
28868740 TA
1 TA
28868742 GATAATTCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.20, G:0.00, T:0.57
Consensus pattern (14 bp):
TAATTCCATCTTTT
Found at i:28870867 original size:10 final size:9
Alignment explanation
Indices: 28870852--28870904 Score: 52
Period size: 10 Copynumber: 5.4 Consensus size: 9
28870842 GGTATTGTTA
28870852 TTTTTATAGT
1 TTTTTATA-T
28870862 TTTTTATAT
1 TTTTTATAT
28870871 TTTGTTATAAT
1 TTT-TTAT-AT
*
28870882 TTTTATATAC
1 TTTT-TATAT
*
28870892 TTTTAATAT
1 TTTTTATAT
28870901 TTTT
1 TTTT
28870905 AAAATTTTCA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
9 11 0.30
10 18 0.49
11 8 0.22
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.70
Consensus pattern (9 bp):
TTTTTATAT
Found at i:28873138 original size:82 final size:82
Alignment explanation
Indices: 28873001--28873273 Score: 343
Period size: 82 Copynumber: 3.3 Consensus size: 82
28872991 AAAAAATTAA
* * *
28873001 AATTGAATAATTCTGTTTCGGGATTTA-TTCTCACCATTCAACAGATTTTATTCCATTTTTATTT
1 AATTGAATAATTCTGTTTCGAGATTTATTTC-CGCCATTCAACAGATTTTATTCCATTTTAATTT
*
28873065 TCTTTCCAAACGAGAATT
65 TGTTTCCAAACGAGAATT
*
28873083 AATTGAATAATTCTGTTTCGAGATTTATTTCCGCCATTCAACATATTTTATTCCATTTTAATTTT
1 AATTGAATAATTCTGTTTCGAGATTTATTTCCGCCATTCAACAGATTTTATTCCATTTTAATTTT
*
28873148 GTTTCCGAACGAGAATT
66 GTTTCCAAACGAGAATT
* * *** * * *
28873165 AATTGAATAATCCTGTTTC-AGGATTTATTCCCGTTGTTTAACAGATTTTATTCGATTTTGATTT
1 AATTGAATAATTCTGTTTCGA-GATTTATTTCCGCCATTCAACAGATTTTATTCCATTTTAATTT
* **
28873229 TGTTTCCAAACAAGCTTT
65 TGTTTCCAAACGAGAATT
* *
28873247 AATTAAATAATTTTGTTTCGAGATTTA
1 AATTGAATAATTCTGTTTCGAGATTTA
28873274 ATCCTACCGT
Statistics
Matches: 166, Mismatches: 22, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
81 1 0.01
82 161 0.97
83 4 0.02
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (82 bp):
AATTGAATAATTCTGTTTCGAGATTTATTTCCGCCATTCAACAGATTTTATTCCATTTTAATTTT
GTTTCCAAACGAGAATT
Found at i:28878548 original size:3 final size:3
Alignment explanation
Indices: 28878542--28878571 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
28878532 GTTGTTTCAG
28878542 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28878572 CCTATCCATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:28884794 original size:4 final size:5
Alignment explanation
Indices: 28884772--28884814 Score: 63
Period size: 5 Copynumber: 8.8 Consensus size: 5
28884762 GTATTTCACC
28884772 AAAA- AAAAG AAAAG AAAAG -AAAG AAAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG -AAAAG AAAAG AAAAG AAAA
28884815 AATAGACAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
4 8 0.22
5 24 0.67
6 4 0.11
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:28884800 original size:20 final size:20
Alignment explanation
Indices: 28884775--28884813 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
28884765 TTTCACCAAA
28884775 AAAAAGAAAAGAAAAGAAAG
1 AAAAAGAAAAGAAAAGAAAG
28884795 AAAAAGAAAAGAAAAGAAA
1 AAAAAGAAAAGAAAAGAAA
28884814 AAATAGACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAGAAAAGAAAG
Found at i:28885515 original size:16 final size:17
Alignment explanation
Indices: 28885486--28885518 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
28885476 CCTAAGCATT
28885486 AAAAAAGGATCATTCTA
1 AAAAAAGGATCATTCTA
*
28885503 AAAAAATGA-CATTCTA
1 AAAAAAGGATCATTCTA
28885519 TATTCATGCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.55, C:0.12, G:0.09, T:0.24
Consensus pattern (17 bp):
AAAAAAGGATCATTCTA
Found at i:28886204 original size:138 final size:138
Alignment explanation
Indices: 28886043--28886353 Score: 412
Period size: 138 Copynumber: 2.3 Consensus size: 138
28886033 TGCCACAAAT
* * * * *
28886043 CTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGTAACAAGTCTTACACTTTTGAGGTTGCAG
1 CTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGTAACAAGGCCTACACCTCTAAGGTTGCAG
* * *
28886108 TGGGTCG-GATTAAATCTATCATGGAGAATCTTATCTCCCTAAAGTTGCAGTGGGGCAGATTAAA
66 TAGGT-GAGATTAAATCTATCATGGAGAATCTTATATCCCTAAAGTTGCAGTGGAGCAGATTAAA
28886172 GTT-A-TAGAC
130 -TTCATTA-AC
* * * *
28886181 CTTATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGTGACAAGGCCTATACCTCTAAGGTTGTAG
1 CTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGTAACAAGGCCTACACCTCTAAGGTTGCAG
* * *
28886246 TAGGTGAGATTAAATCTATCATGGAGAATCTTATATCCCTGAAGTTGTAGTGGAGCAGATTGAAT
66 TAGGTGAGATTAAATCTATCATGGAGAATCTTATATCCCTAAAGTTGCAGTGGAGCAGATTAAAT
28886311 TCATTAAC
131 TCATTAAC
* * *
28886319 CTTATCTTCTTGAAGTTGTAGTGGAGCAGATTGAA
1 CTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAA
28886354 ACTGTTCACC
Statistics
Matches: 151, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
137 3 0.02
138 146 0.97
139 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (138 bp):
CTTATCTCCCTGAAGTTGTAGTGGAGTAGATTGAAGTAACAAGGCCTACACCTCTAAGGTTGCAG
TAGGTGAGATTAAATCTATCATGGAGAATCTTATATCCCTAAAGTTGCAGTGGAGCAGATTAAAT
TCATTAAC
Found at i:28886634 original size:51 final size:51
Alignment explanation
Indices: 28886558--28886743 Score: 219
Period size: 51 Copynumber: 3.6 Consensus size: 51
28886548 CTTATTTCTC
* *
28886558 TGAAGTTGCAGTGGCACAGATTAAAGCTATAAGCTACAGATCTTATCTCCA
1 TGAAGTTGCAGTGGAACAGATTAAAGCTACAAGCTACAGATCTTATCTCCA
* * * * *
28886609 TGAAGTTGCATTGGAATAGACTAAAGCTACAAGCTACAGATCTTATTTCCC
1 TGAAGTTGCAGTGGAACAGATTAAAGCTACAAGCTACAGATCTTATCTCCA
* * ** * *
28886660 TGAAAGTTGCACTGGAACATATTAATCCTACAAGCTATAGATCTTATCTTCA
1 TG-AAGTTGCAGTGGAACAGATTAAAGCTACAAGCTACAGATCTTATCTCCA
* * *
28886712 TGAAGTTGCAGTGGAGCAGATTGAAGCGACAA
1 TGAAGTTGCAGTGGAACAGATTAAAGCTACAA
28886744 TTCTTATAAC
Statistics
Matches: 110, Mismatches: 24, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
51 69 0.63
52 41 0.37
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (51 bp):
TGAAGTTGCAGTGGAACAGATTAAAGCTACAAGCTACAGATCTTATCTCCA
Found at i:28888267 original size:3 final size:3
Alignment explanation
Indices: 28888261--28888304 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
28888251 TTTCAGTTTT
28888261 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
28888305 TACCTATCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.32, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:28888413 original size:4 final size:4
Alignment explanation
Indices: 28888404--28888442 Score: 60
Period size: 4 Copynumber: 9.8 Consensus size: 4
28888394 TTTCCTCTAT
* *
28888404 TTTA TTTA TTCA TTTA TTTA TGTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
28888443 CCTTGTCATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:28903759 original size:52 final size:50
Alignment explanation
Indices: 28903667--28903766 Score: 114
Period size: 52 Copynumber: 2.0 Consensus size: 50
28903657 ATTTCACCCT
* * *
28903667 ACACGGTTGAGCACACGGGTGTGTGTCTTGACCATTTGTATGTTGTAATTTA
1 ACACGATTGAGCACACGAGTGTGTGTCTCGACCATTTGTA--TTGTAATTTA
*
28903719 ACACGATTGAGCACAC-AGTCGTGTGTCTCGATC-TTGTGTATTGTAATT
1 ACACGATTGAGCACACGAGT-GTGTGTCTCGACCATT-TGTATTGTAATT
28903767 CAGCTATTCA
Statistics
Matches: 42, Mismatches: 4, Indels: 6
0.81 0.08 0.12
Matches are distributed among these distances:
50 8 0.19
51 4 0.10
52 30 0.71
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (50 bp):
ACACGATTGAGCACACGAGTGTGTGTCTCGACCATTTGTATTGTAATTTA
Found at i:28907098 original size:6 final size:6
Alignment explanation
Indices: 28907087--28907152 Score: 123
Period size: 6 Copynumber: 11.0 Consensus size: 6
28907077 TTTAACATAA
28907087 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT
*
28907135 GTATTT ATATTT ATATTT
1 ATATTT ATATTT ATATTT
28907153 TTCGCTAACG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.67
Consensus pattern (6 bp):
ATATTT
Found at i:28907273 original size:28 final size:25
Alignment explanation
Indices: 28907234--28907291 Score: 80
Period size: 28 Copynumber: 2.2 Consensus size: 25
28907224 TAGTTCTTAC
*
28907234 GTTTTTTGTATTTGAGTTTGTTGAG
1 GTTTTTTGTATTTGAATTTGTTGAG
28907259 GCTTTTATTGTTATTTGAATTTGTTGAG
1 G-TTTT-TTG-TATTTGAATTTGTTGAG
28907287 GTTTT
1 GTTTT
28907292 GATTTAGTTG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
25 1 0.03
26 4 0.14
27 7 0.24
28 17 0.59
ACGTcount: A:0.14, C:0.02, G:0.24, T:0.60
Consensus pattern (25 bp):
GTTTTTTGTATTTGAATTTGTTGAG
Found at i:28910093 original size:12 final size:13
Alignment explanation
Indices: 28910071--28910112 Score: 68
Period size: 12 Copynumber: 3.2 Consensus size: 13
28910061 TTCCAAGTCA
28910071 TTTTCATTTTTCAT
1 TTTTC-TTTTTCAT
28910085 TTTTCTTTTTC-T
1 TTTTCTTTTTCAT
28910097 TTTTCTTTTTCAT
1 TTTTCTTTTTCAT
28910110 TTT
1 TTT
28910113 GGAGAAAACC
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.44
13 10 0.37
14 5 0.19
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (13 bp):
TTTTCTTTTTCAT
Found at i:28910099 original size:5 final size:6
Alignment explanation
Indices: 28910071--28910112 Score: 57
Period size: 6 Copynumber: 6.5 Consensus size: 6
28910061 TTCCAAGTCA
28910071 TTTTCAT TTTTCAT TTTTCT TTTTCT TTTTCT TTTTCAT TTT
1 TTTTC-T TTTTC-T TTTTCT TTTTCT TTTTCT TTTTC-T TTT
28910113 GGAGAAAACC
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 18 0.53
7 16 0.47
ACGTcount: A:0.07, C:0.14, G:0.00, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:28930321 original size:93 final size:93
Alignment explanation
Indices: 28930208--28930379 Score: 308
Period size: 93 Copynumber: 1.8 Consensus size: 93
28930198 CGCCCATAAG
* *
28930208 CGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
*
28930273 ACGAGTTTGGATGCCTAGTTACATCTCA
66 ACGAGTTCGGATGCCTAGTTACATCTCA
*
28930301 CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
1 CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
28930366 ACGAGTTCGGATGC
66 ACGAGTTCGGATGC
28930380 TCAACCATCC
Statistics
Matches: 75, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 75 1.00
ACGTcount: A:0.28, C:0.29, G:0.22, T:0.22
Consensus pattern (93 bp):
CGAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCA
Found at i:28930376 original size:46 final size:46
Alignment explanation
Indices: 28930201--28930376 Score: 207
Period size: 46 Copynumber: 3.8 Consensus size: 46
28930191 TGTAACCCGC
* * *
28930201 CCATAAGCGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
* * *
28930247 CCATAAGTGAACTCGGACTCAACTCAACGAGTTTGGATGCCTAGTT-ACAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA---C-A-TTCGCAT
*
28930297 -C-TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
*
28930340 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGA
28930377 TGCTCAACCA
Statistics
Matches: 109, Mismatches: 12, Indels: 18
0.78 0.09 0.13
Matches are distributed among these distances:
42 2 0.02
43 4 0.04
44 2 0.02
45 2 0.02
46 62 0.57
47 28 0.26
48 2 0.02
49 2 0.02
50 3 0.03
51 2 0.02
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (46 bp):
CCATAAGCGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCAT
Found at i:28930888 original size:71 final size:71
Alignment explanation
Indices: 28930781--28930922 Score: 266
Period size: 71 Copynumber: 2.0 Consensus size: 71
28930771 CACATTATCA
*
28930781 AATTGATCCTTAACTCAAATTTTGGCAAAATTACAATTTTGCCCTTAAACTTTTGCATATTTACA
1 AATTGATCCTTAACTCAAATTTTGGCAAAATTACAATTTTGCCCCTAAACTTTTGCATATTTACA
28930846 TTTTTT
66 TTTTTT
*
28930852 AATTGATCCTTAACTCAAATTTTGGCAAAATTACAATTTTTCCCCTAAACTTTTGCATATTTACA
1 AATTGATCCTTAACTCAAATTTTGGCAAAATTACAATTTTGCCCCTAAACTTTTGCATATTTACA
28930917 TTTTTT
66 TTTTTT
28930923 CCCCTAGGCT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 69 1.00
ACGTcount: A:0.31, C:0.18, G:0.06, T:0.45
Consensus pattern (71 bp):
AATTGATCCTTAACTCAAATTTTGGCAAAATTACAATTTTGCCCCTAAACTTTTGCATATTTACA
TTTTTT
Found at i:28932666 original size:15 final size:15
Alignment explanation
Indices: 28932646--28932701 Score: 87
Period size: 15 Copynumber: 3.7 Consensus size: 15
28932636 GTATCTTGGG
28932646 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
28932661 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
28932676 TTTCTCTA-TCTTGGA
1 TTTCTTTATTC-TGGA
28932691 TTTCTTTATTC
1 TTTCTTTATTC
28932702 GGTTTCCTTG
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 2 0.05
15 33 0.89
16 2 0.05
ACGTcount: A:0.12, C:0.16, G:0.11, T:0.61
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:28934175 original size:60 final size:60
Alignment explanation
Indices: 28934095--28934214 Score: 222
Period size: 60 Copynumber: 2.0 Consensus size: 60
28934085 GACAAAATTA
28934095 GGACATGGAAGGAATTTTTGGAAAGTTTAGTAGTAAGGGTATTTTGGTCATTTAGTTATT
1 GGACATGGAAGGAATTTTTGGAAAGTTTAGTAGTAAGGGTATTTTGGTCATTTAGTTATT
* *
28934155 GGACTTGGATGGAATTTTTGGAAAGTTTAGTAGTAAGGGTATTTTGGTCATTTAGTTATT
1 GGACATGGAAGGAATTTTTGGAAAGTTTAGTAGTAAGGGTATTTTGGTCATTTAGTTATT
28934215 AAAATGAATT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
60 58 1.00
ACGTcount: A:0.27, C:0.03, G:0.28, T:0.42
Consensus pattern (60 bp):
GGACATGGAAGGAATTTTTGGAAAGTTTAGTAGTAAGGGTATTTTGGTCATTTAGTTATT
Found at i:28935281 original size:46 final size:46
Alignment explanation
Indices: 28935209--28935429 Score: 293
Period size: 46 Copynumber: 4.8 Consensus size: 46
28935199 AACTAGGCAT
*
28935209 CCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *
28935255 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAATGT
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
* *** * * * *
28935301 CCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTA-AC-TAGGC
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGCGAACGC
*
28935346 ATCCGAGCTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGC
1 --CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
28935394 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
1 CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28935430 GCGGGTTACA
Statistics
Matches: 148, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
45 2 0.01
46 111 0.75
47 32 0.22
48 3 0.02
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
CCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGC
Found at i:28935392 original size:139 final size:139
Alignment explanation
Indices: 28935161--28935429 Score: 538
Period size: 139 Copynumber: 1.9 Consensus size: 139
28935151 TGGTTGAGCA
28935161 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTG
28935226 AGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
66 AGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28935291 ATGCGAATG
131 ATGCGAATG
28935300 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTG
28935365 AGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
66 AGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
28935430 GCGGGTTACA
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
139 130 1.00
ACGTcount: A:0.21, C:0.20, G:0.30, T:0.28
Consensus pattern (139 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCATCCGAGCTCGTTGAGTTG
AGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
ATGCGAATG
Found at i:28936923 original size:46 final size:46
Alignment explanation
Indices: 28936800--28936927 Score: 145
Period size: 46 Copynumber: 2.8 Consensus size: 46
28936790 TAACCCGCCC
28936800 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTTACAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGA--CCTAGTTACAT
* * * * * *
28936848 CTCA-CGAACTTGGACTCAACTCAATGAGTTCGGA-C-ATTTGCAT
1 CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
28936891 CCATAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
1 -C-TAAGTGAACTCGGACTCAACTCAACGAGTTCGGA
28936928 TGCTCAACCA
Statistics
Matches: 67, Mismatches: 10, Indels: 8
0.79 0.12 0.09
Matches are distributed among these distances:
43 6 0.09
44 2 0.03
45 2 0.03
46 27 0.40
47 27 0.40
48 3 0.04
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (46 bp):
CTAAGTGAACTCGGACTCAACTCAACGAGTTCGGACCTAGTTACAT
Found at i:28936946 original size:46 final size:45
Alignment explanation
Indices: 28936803--28936946 Score: 118
Period size: 46 Copynumber: 3.1 Consensus size: 45
28936793 CCCGCCCCTA
28936803 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGC-CTAGTTA-CATCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTC-A---ACCATCT
* * * * * *
28936850 CA-CGAACTTGGACTCAACTCAATGAGTTCGGACAT-TTGCATCCAT-A
1 -AGTGAACTCGGACTCAACTCAACGAGTTCGG--ATGCT-CAACCATCT
28936896 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCCT
1 AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCAT-CT
28936942 AGTGA
1 AGTGA
28936947 CATGTCACTT
Statistics
Matches: 75, Mismatches: 12, Indels: 20
0.70 0.11 0.19
Matches are distributed among these distances:
44 8 0.11
45 2 0.03
46 31 0.41
47 29 0.39
48 1 0.01
49 3 0.04
50 1 0.01
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.24
Consensus pattern (45 bp):
AGTGAACTCGGACTCAACTCAACGAGTTCGGATGCTCAACCATCT
Found at i:28947858 original size:46 final size:46
Alignment explanation
Indices: 28947791--28948576 Score: 1572
Period size: 46 Copynumber: 17.1 Consensus size: 46
28947781 TTGAGTATTT
28947791 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28947837 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28947883 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28947929 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28947975 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948021 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948067 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948113 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948159 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948205 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948251 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948297 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948343 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948389 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948435 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948481 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948527 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
1 TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
28948573 TGTT
1 TGTT
28948577 TATCTCTTTG
Statistics
Matches: 740, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 740 1.00
ACGTcount: A:0.35, C:0.09, G:0.20, T:0.37
Consensus pattern (46 bp):
TGTTATATGTGTCATTTGATTTGCCAAATGAAGGCATGTAAAAATA
Found at i:28963042 original size:18 final size:19
Alignment explanation
Indices: 28963019--28963054 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
28963009 GATTTATGGC
28963019 ATGATAAATGTTG-TATGT
1 ATGATAAATGTTGATATGT
*
28963037 ATGATAGATGTTGATATG
1 ATGATAAATGTTGATATG
28963055 GTACTAGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.33, C:0.00, G:0.25, T:0.42
Consensus pattern (19 bp):
ATGATAAATGTTGATATGT
Found at i:28966777 original size:3 final size:3
Alignment explanation
Indices: 28966769--28966806 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
28966759 CTCTTCATCT
28966769 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
1 TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TCC TC
28966807 TTCTTCTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (3 bp):
TCC
Found at i:28966811 original size:3 final size:3
Alignment explanation
Indices: 28966805--28966843 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
28966795 CTCCTCCTCC
*
28966805 TCT TCT TCT TCT TTT TCT TCT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
28966844 AGGGTTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TCT
Found at i:28967298 original size:8 final size:8
Alignment explanation
Indices: 28967287--28967369 Score: 62
Period size: 8 Copynumber: 10.0 Consensus size: 8
28967277 ATAATTAATT
28967287 TTTTAAAA
1 TTTTAAAA
28967295 TTTTAAAAAA
1 TTTT--AAAA
**
28967305 TTCAAAAAA
1 TT-TTAAAA
*
28967314 ATTTAAAA
1 TTTTAAAA
28967322 -TTTAAAA
1 TTTTAAAA
28967329 -TTTAAAA
1 TTTTAAAA
*
28967336 TTTAAAAA
1 TTTTAAAA
28967344 TTATTAAAA
1 TT-TTAAAA
28967353 TTATTAAAA
1 TT-TTAAAA
*
28967362 ATTTAAAA
1 TTTTAAAA
28967370 AAATTTAAAA
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
7 14 0.23
8 22 0.35
9 20 0.32
10 6 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (8 bp):
TTTTAAAA
Found at i:28967370 original size:8 final size:8
Alignment explanation
Indices: 28967310--28967380 Score: 67
Period size: 7 Copynumber: 8.6 Consensus size: 8
28967300 AAAAATTCAA
28967310 AAAAATTT
1 AAAAATTT
28967318 -AAAATTT
1 AAAAATTT
28967325 -AAAATTT
1 AAAAATTT
28967332 -AAAATTT
1 AAAAATTT
28967339 AAAAATTATT
1 AAAAA-T-TT
*
28967349 AAAATTATT
1 AAAAAT-TT
28967358 AAAAATTT
1 AAAAATTT
28967366 AAAAAAATTT
1 --AAAAATTT
28967376 AAAAA
1 AAAAA
28967381 AACTTTAAAA
Statistics
Matches: 56, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
7 21 0.38
8 11 0.20
9 10 0.18
10 14 0.25
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
AAAAATTT
Found at i:28967380 original size:11 final size:10
Alignment explanation
Indices: 28967358--28967397 Score: 71
Period size: 10 Copynumber: 3.9 Consensus size: 10
28967348 TAAAATTATT
28967358 AAAAATTTAA
1 AAAAATTTAA
28967368 AAAAATTTAA
1 AAAAATTTAA
28967378 AAAAACTTTAA
1 AAAAA-TTTAA
28967389 AAAAATTTA
1 AAAAATTTA
28967398 TTTTTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
10 19 0.66
11 10 0.34
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (10 bp):
AAAAATTTAA
Found at i:28967387 original size:21 final size:20
Alignment explanation
Indices: 28967358--28967397 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
28967348 TAAAATTATT
28967358 AAAAATTTAAAAAAATTTAA
1 AAAAATTTAAAAAAATTTAA
28967378 AAAAACTTTAAAAAAATTTA
1 AAAAA-TTTAAAAAAATTTA
28967398 TTTTTTATTT
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:0.68, C:0.03, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAATTTAAAAAAATTTAA
Found at i:28968832 original size:32 final size:32
Alignment explanation
Indices: 28968796--28968895 Score: 104
Period size: 32 Copynumber: 3.3 Consensus size: 32
28968786 GAAAATTAAA
28968796 TTAGAATTTAGTTTTTCATTAAATTTTATTTC
1 TTAGAATTTAGTTTTTCATTAAATTTTATTTC
* * * **
28968828 TTAGAATTT--TATAT-ATTTAAA-ATTA--AA
1 TTAGAATTTAGTTTTTCA-TTAAATTTTATTTC
28968855 TTAGAATTTAGTTTTTCATTAAATTTTATTTC
1 TTAGAATTTAGTTTTTCATTAAATTTTATTTC
28968887 TTAGAATTT
1 TTAGAATTT
28968896 TATATATTTA
Statistics
Matches: 51, Mismatches: 10, Indels: 14
0.68 0.13 0.19
Matches are distributed among these distances:
27 9 0.18
29 12 0.24
30 12 0.24
32 18 0.35
ACGTcount: A:0.34, C:0.04, G:0.06, T:0.56
Consensus pattern (32 bp):
TTAGAATTTAGTTTTTCATTAAATTTTATTTC
Found at i:28968879 original size:59 final size:59
Alignment explanation
Indices: 28968787--28968912 Score: 252
Period size: 59 Copynumber: 2.1 Consensus size: 59
28968777 GTAAATAAGG
28968787 AAAATTAAATTAGAATTTAGTTTTTCATTAAATTTTATTTCTTAGAATTTTATATATTT
1 AAAATTAAATTAGAATTTAGTTTTTCATTAAATTTTATTTCTTAGAATTTTATATATTT
28968846 AAAATTAAATTAGAATTTAGTTTTTCATTAAATTTTATTTCTTAGAATTTTATATATTT
1 AAAATTAAATTAGAATTTAGTTTTTCATTAAATTTTATTTCTTAGAATTTTATATATTT
28968905 AAAATTAA
1 AAAATTAA
28968913 GAATAATTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 67 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (59 bp):
AAAATTAAATTAGAATTTAGTTTTTCATTAAATTTTATTTCTTAGAATTTTATATATTT
Found at i:28972862 original size:19 final size:20
Alignment explanation
Indices: 28972829--28972868 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
28972819 ATATATGTAT
28972829 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
28972848 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
28972868 A
1 A
28972869 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:28973609 original size:44 final size:45
Alignment explanation
Indices: 28973546--28974428 Score: 1293
Period size: 44 Copynumber: 20.1 Consensus size: 45
28973536 AAGAACACCG
* * * **
28973546 ATCTGT-TATTTTTGATCTGCTCTCTGCCAATACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
** * *
28973590 ATCTGTC-ATCTTTAATCTGCTCTTCGCCACTACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
*
28973634 ATCTGT-TATCTTCGATCTGCTCTCCGCCGCTACAGAAACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
28973678 ATCTG-CTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * *
28973722 ATCT-ACTATTTTCGATCTACTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
28973766 ATCTG-CTATCTTCGATCTGCTCTCCACCGCTACAGAGATGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
*
28973810 ATCTGT-TATCTTCGATCTGCTCTTCGCCGCTACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * * * *
28973854 ATCTGT-TATCTTCGATCTGCTCTCTGCTGCTACAGAAATGTCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
28973898 ATCTG-CTATCTTCGATCTGCTCTCCACCGCTACAGAGACGCAAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
28973942 ATCTGT-TATCTTCGATCTGCTCTTCGCCGCTACAAAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
28973986 ATCTG-CTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
*
28974030 ATCTGT-TATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
*
28974074 ATCT-ACTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
28974118 ATCTGT-TATCTTCGATCTGCTCTTCGCCGCTACAAAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
28974162 ATCTG-CTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
28974206 ATCTGT-TATCTTCGATCTGCTCTTCGCCGCTACAGAGACCCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
*
28974250 ATCTG-CTATCTTCGATCTGTTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
28974294 ATCTG-CTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* * *
28974338 ATCT-ACTATTTTCGATCTACTCTCCGCCGCTACAGAGACGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
* *
28974382 ATCTGT-TATCTTCGACCTGCTCTCCGCCGCTACAGAGATGCCAA
1 ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
28974426 ATC
1 ATC
28974429 ATCTTAGATT
Statistics
Matches: 762, Mismatches: 60, Indels: 34
0.89 0.07 0.04
Matches are distributed among these distances:
44 762 1.00
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.28
Consensus pattern (45 bp):
ATCTGTCTATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAA
Found at i:28974504 original size:88 final size:87
Alignment explanation
Indices: 28974390--28974622 Score: 344
Period size: 88 Copynumber: 2.7 Consensus size: 87
28974380 AAATCTGTTA
* * * *
28974390 TCTTCGACCTGCTCTCCGCC-GCTACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAAC
1 TCTTCGATCTGCTC-CCGCCTGATACAGAGATGCCAAATCATCTTGGATATGCTTCAACGTAAAC
28974454 ACGTGAAAGCCAAATCAGCTATG
65 ACGTGAAAGCCAAATCAGCTATG
* * *
28974477 TCTTCGATCTGCTCCCTGCCTGATACAGAGATGCCAAATTATCTTGGATCTGCTTTAACGTAAAC
1 TCTTCGATCTGCTCCC-GCCTGATACAGAGATGCCAAATCATCTTGGATATGCTTCAACGTAAAC
*
28974542 ACGTGAAAGCCAAATTAGCTATG
65 ACGTGAAAGCCAAATCAGCTATG
*
28974565 TCTTCGATCTACTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATAT-CTTCAAC
1 TCTTCGATCTGCT-CCCGCCTGATACAGAGATGCCAAATCATCTTGGATATGCTTCAAC
28974623 TTGTTGCCCT
Statistics
Matches: 132, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
86 2 0.02
87 22 0.17
88 105 0.80
89 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (87 bp):
TCTTCGATCTGCTCCCGCCTGATACAGAGATGCCAAATCATCTTGGATATGCTTCAACGTAAACA
CGTGAAAGCCAAATCAGCTATG
Found at i:28974821 original size:61 final size:64
Alignment explanation
Indices: 28974709--28974833 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 64
28974699 TCATGTATCC
28974709 ATGCTTATGCCAAATAATTAGGATGCTATAATTGAAATGAATCAAATGCTCCTAACTAAATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATAATTGAAATGAATCAAATGCTCCTAACTAAATGTG
* *
28974773 ATGCTTTATGTCAAATAATTAGGATG-T-T-A-TGAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGC-TTATGCCAAATAATTAGGATGCTATAATTGAAATGAATCAAATGCTCCTAACTAAATGTG
28974834 TTATTATATA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
61 31 0.53
62 1 0.02
63 1 0.02
64 5 0.09
65 20 0.34
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATAATTGAAATGAATCAAATGCTCCTAACTAAATGTG
Found at i:28976784 original size:40 final size:39
Alignment explanation
Indices: 28976740--28976964 Score: 263
Period size: 40 Copynumber: 5.7 Consensus size: 39
28976730 GCCACTAGCT
*
28976740 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
28976780 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
28976819 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * *
28976859 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * * ** * *
28976899 CGAATGCCTTCAGGACTTAGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
28976939 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
28976965 TATCATCCGA
Statistics
Matches: 163, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 40 0.25
40 123 0.75
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:28976838 original size:79 final size:78
Alignment explanation
Indices: 28976740--28976964 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 78
28976730 GCCACTAGCT
*
28976740 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
28976805 TATAATAACTCGCA
65 TATAATAACTCGCA
* * * * *
28976819 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGTACAAACGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
* * *
28976884 ATATAGTAGCTCGTA
65 -TATAATAACTCGCA
* * * ** *
28976899 CGAATGCCTTCAGGACTTAGCCCGGAATTAGCCACTAGCTCAAATG-CTCTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTAGCACAAATGCCT-TCGGGACTTAGCCCG
28976963 GT
64 GT
28976965 TATCATCCGA
Statistics
Matches: 123, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
79 63 0.51
80 60 0.49
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGT
ATAATAACTCGCA
Found at i:28981890 original size:19 final size:19
Alignment explanation
Indices: 28981866--28981913 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
28981856 GGGAAAATCT
28981866 AATGCAAATGATGCAATGC
1 AATGCAAATGATGCAATGC
*
28981885 AATGCACATGATGCAATGC
1 AATGCAAATGATGCAATGC
28981904 AATGCAAATG
1 AATGCAAATG
28981914 CATGGGATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.42, C:0.17, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGCAAATGATGCAATGC
Found at i:28981926 original size:24 final size:24
Alignment explanation
Indices: 28981876--28981929 Score: 65
Period size: 24 Copynumber: 2.2 Consensus size: 24
28981866 AATGCAAATG
*
28981876 ATGCAATGCAATGCACATGATGCA
1 ATGCAATGCAATGCACAGGATGCA
**
28981900 ATGCAATGCAAATGCATGGGATG-A
1 ATGCAATGC-AATGCACAGGATGCA
28981924 ATGCAA
1 ATGCAA
28981930 AGGAAAGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
24 16 0.62
25 10 0.38
ACGTcount: A:0.39, C:0.17, G:0.24, T:0.20
Consensus pattern (24 bp):
ATGCAATGCAATGCACAGGATGCA
Found at i:28983494 original size:19 final size:20
Alignment explanation
Indices: 28983461--28983500 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
28983451 ATATATGTAT
28983461 ATAAAATAAAGAAAAT-AAA
1 ATAAAATAAAGAAAATGAAA
28983480 ATAAAATAACA-AAAATGAAA
1 ATAAAATAA-AGAAAATGAAA
28983500 A
1 A
28983501 ATGAACAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (20 bp):
ATAAAATAAAGAAAATGAAA
Found at i:28988156 original size:25 final size:25
Alignment explanation
Indices: 28988061--28988162 Score: 95
Period size: 25 Copynumber: 4.2 Consensus size: 25
28988051 CCCGTTATTG
* * *
28988061 GCTCACATGAGCTTCTTGAT-TATG
1 GCTCACATGAGCTTCCTGTTATATA
* *
28988085 GCT-ATTATGAGCTTCCTGTTAAATA
1 GCTCA-CATGAGCTTCCTGTTATATA
* *
28988110 GCCCGA-ATAAGCTTCCTGTTATATA
1 GCTC-ACATGAGCTTCCTGTTATATA
28988135 GCTCACATGAGCTTCCTGTTATAT-
1 GCTCACATGAGCTTCCTGTTATATA
28988159 GCTC
1 GCTC
28988163 GAGAGAGTGC
Statistics
Matches: 63, Mismatches: 10, Indels: 10
0.76 0.12 0.12
Matches are distributed among these distances:
23 1 0.02
24 20 0.32
25 41 0.65
27 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.18, T:0.36
Consensus pattern (25 bp):
GCTCACATGAGCTTCCTGTTATATA
Found at i:28990576 original size:37 final size:37
Alignment explanation
Indices: 28990512--28990668 Score: 199
Period size: 37 Copynumber: 4.0 Consensus size: 37
28990502 TACGTATGAT
*
28990512 CACTTATCAC-TTGTCCCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
*
28990548 CACTTATCACTTTGTTTCTTGATCAGATAAGTGTAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
28990585 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGC
1 CACTTATCACTTTGTCTCTTGATCAGATAA--GT-G-T--AGC
*
28990628 TATCACTTATCACTTTGTCTCTTGATCAGATAAGTATAGC
1 ---CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
28990668 C
1 C
28990669 GAAGCTATCA
Statistics
Matches: 107, Mismatches: 4, Indels: 19
0.82 0.03 0.15
Matches are distributed among these distances:
36 10 0.09
37 54 0.50
39 2 0.02
40 4 0.04
41 1 0.01
42 1 0.01
43 3 0.03
44 2 0.02
46 30 0.28
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (37 bp):
CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGC
Found at i:28990638 original size:46 final size:46
Alignment explanation
Indices: 28990585--28990899 Score: 396
Period size: 46 Copynumber: 6.6 Consensus size: 46
28990575 TAAGTGTAGC
* * **
28990585 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
28990631 CACTTATCACTTTGTCTCTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
28990677 CACTTATCACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTAT
1 CACTTATCAC---T---TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
28990729 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* *
28990775 AACTTATCACTTTATCACTTGATCAGATAAGTATAGCCGAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
* * ** *
28990821 TACTTATCACTTTCCACTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCAC--T----TTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
*
28990873 CACTTATCACTTTATCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
28990900 AGTACTCAAA
Statistics
Matches: 241, Mismatches: 16, Indels: 24
0.86 0.06 0.09
Matches are distributed among these distances:
46 155 0.64
48 1 0.00
49 2 0.01
50 1 0.00
52 82 0.34
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTAT
Found at i:28990750 original size:98 final size:98
Alignment explanation
Indices: 28990585--28990893 Score: 396
Period size: 98 Copynumber: 3.1 Consensus size: 98
28990575 TAAGTGTAGC
* * ** *
28990585 CACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTCT
1 CACTTTTCAC-TTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACT
28990650 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
65 TGATCAGATAAGTATAGCCGAAGCTATCACTTAT
28990684 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
*
28990749 GATCAGATAAGTATAGCCGAAGCTATAACTTAT
66 GATCAGATAAGTATAGCCGAAGCTATCACTTAT
* *
28990782 CAC-TTT-A----TCACTTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTG
1 CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCAC--T----TTG
* ** *
28990841 TCACTTGATCAGATAAGTGTAGCTAAAGCTACCACTTAT
60 TCACTTGATCAGATAAGTATAGCCGAAGCTATCACTTAT
28990880 CACTTTATCACTTG
1 CACTTT-TCACTTG
28990894 ATCAGAAGTA
Statistics
Matches: 184, Mismatches: 13, Indels: 20
0.85 0.06 0.09
Matches are distributed among these distances:
92 40 0.22
94 1 0.01
96 1 0.01
97 3 0.02
98 126 0.68
99 11 0.06
100 1 0.01
101 1 0.01
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.35
Consensus pattern (98 bp):
CACTTTTCACTTGTCACTTGATCAGATAAGTGTAGCCGAAGCTATCACTTATCACTTTGTCACTT
GATCAGATAAGTATAGCCGAAGCTATCACTTAT
Found at i:28990845 original size:144 final size:144
Alignment explanation
Indices: 28990584--28990899 Score: 515
Period size: 144 Copynumber: 2.2 Consensus size: 144
28990574 ATAAGTGTAG
* * * * * *
28990584 CCACTTATCACTTTGTCTCTTGATCAGATAAGTGTAGCTAAAGCTATCACTTATCACTTTGTCTC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCAC
*
28990649 TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTTCACTTGTCACTTGATCAGATAAG
66 TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAG
*
28990714 TGTAGCCGAAGCTA
131 TGTAGCCAAAGCTA
* *
28990728 TCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCGAAGCTATAACTTATCACTTTATCAC
1 CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCAC
*
28990793 TTGATCAGATAAGTATAGCCGAAGCTATTACTTATCACTTTCCACTTGTCACTTGATCAGATAAG
66 TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAG
*
28990858 TGTAGCTAAAGCTA
131 TGTAGCCAAAGCTA
*
28990872 CCACTTATCACTTTATCACTTGATCAGA
1 CCACTTATCACTTTGTCACTTGATCAGA
28990900 AGTACTCAAA
Statistics
Matches: 158, Mismatches: 14, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
144 158 1.00
ACGTcount: A:0.29, C:0.22, G:0.14, T:0.34
Consensus pattern (144 bp):
CCACTTATCACTTTGTCACTTGATCAGATAAGTATAGCCAAAGCTATAACTTATCACTTTATCAC
TTGATCAGATAAGTATAGCCGAAGCTATCACTTATCACTTTCCACTTGTCACTTGATCAGATAAG
TGTAGCCAAAGCTA
Found at i:28996973 original size:13 final size:13
Alignment explanation
Indices: 28996955--28996979 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
28996945 TAAAATAAAA
28996955 GAAATAAAGAAAT
1 GAAATAAAGAAAT
28996968 GAAATAAAGAAA
1 GAAATAAAGAAA
28996980 AAGGAAAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:28997044 original size:19 final size:20
Alignment explanation
Indices: 28997011--28997051 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
28997001 GTTAGTAGGG
28997011 AAAGAAAGAAGAAAA-GAGA
1 AAAGAAAGAAGAAAAGGAGA
28997030 AAAGAAA-AAGAAAAAGGAGA
1 AAAGAAAGAAG-AAAAGGAGA
28997050 AA
1 AA
28997052 TTAGGGTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 3 0.15
19 11 0.55
20 6 0.30
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (20 bp):
AAAGAAAGAAGAAAAGGAGA
Found at i:28997669 original size:3 final size:3
Alignment explanation
Indices: 28997661--28997690 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
28997651 GAATGGTAAG
*
28997661 TAT TAT TAT TAT TAT TAT TAT CAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
28997691 GGTATTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:28998288 original size:18 final size:18
Alignment explanation
Indices: 28998245--28998291 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
28998235 GACTGTCTGC
** *
28998245 TACTGAATAATTGACTGT
1 TACTGAATAAACGACTGA
28998263 TA-TAGAATAAACGACTGA
1 TACT-GAATAAACGACTGA
28998281 TACTGAATAAA
1 TACTGAATAAA
28998292 TGAATATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
17 1 0.04
18 22 0.92
19 1 0.04
ACGTcount: A:0.45, C:0.11, G:0.15, T:0.30
Consensus pattern (18 bp):
TACTGAATAAACGACTGA
Found at i:28998987 original size:37 final size:37
Alignment explanation
Indices: 28998945--28999019 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
28998935 ATGATAAGTG
28998945 TTTAAAGTTAAGTATTAGATAATATATAAAATGCGTT
1 TTTAAAGTTAAGTATTAGATAATATATAAAATGCGTT
*
28998982 TTTAAAGTTAAGTATTAGATAATATATAAAATGTGTT
1 TTTAAAGTTAAGTATTAGATAATATATAAAATGCGTT
28999019 T
1 T
28999020 GGATTGGTTT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.43, C:0.01, G:0.13, T:0.43
Consensus pattern (37 bp):
TTTAAAGTTAAGTATTAGATAATATATAAAATGCGTT
Found at i:29000283 original size:33 final size:34
Alignment explanation
Indices: 29000218--29000304 Score: 108
Period size: 33 Copynumber: 2.6 Consensus size: 34
29000208 CAGCCAACTA
* * *
29000218 CCACCTCAGTACTCCAAT-CATCCTGGCTCGTAT
1 CCACCTCAGTACTCCACTCCTTCCTGGCCCGTAT
29000251 CCACCTCAGTACTCCACTCCTTCC-GGCCCGTAT
1 CCACCTCAGTACTCCACTCCTTCCTGGCCCGTAT
*
29000284 CCA-CTACCGTACTCCACTCCT
1 CCACCT-CAGTACTCCACTCCT
29000305 CTCGACTCAA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
32 2 0.04
33 42 0.88
34 4 0.08
ACGTcount: A:0.18, C:0.46, G:0.10, T:0.25
Consensus pattern (34 bp):
CCACCTCAGTACTCCACTCCTTCCTGGCCCGTAT
Found at i:29003871 original size:27 final size:27
Alignment explanation
Indices: 29003818--29003876 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 27
29003808 TTTGCGCATT
* * *
29003818 TGAGATAGGCACAATTAGTCACGCCTC
1 TGAGAAAGGCACAACTAGTCACACCTC
* *
29003845 TGAGAAAGGCTCAACTAGTCGCACCTC
1 TGAGAAAGGCACAACTAGTCACACCTC
*
29003872 AGAGA
1 TGAGA
29003877 TAGACGCAAC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.32, C:0.25, G:0.24, T:0.19
Consensus pattern (27 bp):
TGAGAAAGGCACAACTAGTCACACCTC
Found at i:29004933 original size:30 final size:30
Alignment explanation
Indices: 29004897--29004960 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
29004887 GCCCGCCCCT
29004897 AAATCCATCATTGGTTATAATTAACTATAC
1 AAATCCATCATTGGTTATAATTAACTATAC
29004927 AAATCCATCATTGGTTATAATTAACTATAC
1 AAATCCATCATTGGTTATAATTAACTATAC
29004957 AAAT
1 AAAT
29004961 TTTTAACAGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (30 bp):
AAATCCATCATTGGTTATAATTAACTATAC
Found at i:29010487 original size:3 final size:3
Alignment explanation
Indices: 29010479--29010638 Score: 320
Period size: 3 Copynumber: 53.3 Consensus size: 3
29010469 AACATTCCAC
29010479 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
29010527 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
29010575 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
29010623 AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA A
29010639 TATGTGTCTG
Statistics
Matches: 157, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 157 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:29017640 original size:110 final size:110
Alignment explanation
Indices: 29017393--29017614 Score: 444
Period size: 110 Copynumber: 2.0 Consensus size: 110
29017383 TCTAATAATA
29017393 TTAGAAAATGAAGGAAGAGAAGAAATAATATTAGAATTTGTTGATATGATTTCCAAATGAAATCC
1 TTAGAAAATGAAGGAAGAGAAGAAATAATATTAGAATTTGTTGATATGATTTCCAAATGAAATCC
29017458 CATTCCTATTTATAGGAATTTTCATGTCTCTTCATAGAGACATCT
66 CATTCCTATTTATAGGAATTTTCATGTCTCTTCATAGAGACATCT
29017503 TTAGAAAATGAAGGAAGAGAAGAAATAATATTAGAATTTGTTGATATGATTTCCAAATGAAATCC
1 TTAGAAAATGAAGGAAGAGAAGAAATAATATTAGAATTTGTTGATATGATTTCCAAATGAAATCC
29017568 CATTCCTATTTATAGGAATTTTCATGTCTCTTCATAGAGACATCT
66 CATTCCTATTTATAGGAATTTTCATGTCTCTTCATAGAGACATCT
29017613 TT
1 TT
29017615 CAATAGGTGT
Statistics
Matches: 112, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
110 112 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (110 bp):
TTAGAAAATGAAGGAAGAGAAGAAATAATATTAGAATTTGTTGATATGATTTCCAAATGAAATCC
CATTCCTATTTATAGGAATTTTCATGTCTCTTCATAGAGACATCT
Found at i:29027504 original size:30 final size:32
Alignment explanation
Indices: 29027470--29027532 Score: 94
Period size: 30 Copynumber: 2.0 Consensus size: 32
29027460 TGAGGATGAG
*
29027470 TAATACAAATACTTG-A-AAATTAAGATTGAT
1 TAATACAAACACTTGAAGAAATTAAGATTGAT
*
29027500 TAATACAAACACTTGAAGAAATTGAGATTGAT
1 TAATACAAACACTTGAAGAAATTAAGATTGAT
29027532 T
1 T
29027533 CAAAACTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 14 0.48
31 1 0.03
32 14 0.48
ACGTcount: A:0.48, C:0.08, G:0.13, T:0.32
Consensus pattern (32 bp):
TAATACAAACACTTGAAGAAATTAAGATTGAT
Found at i:29033546 original size:105 final size:105
Alignment explanation
Indices: 29033421--29033630 Score: 402
Period size: 105 Copynumber: 2.0 Consensus size: 105
29033411 TGAGTAAAAT
29033421 GATGAATTAAAGGCTAAATTGATAGAAATTCAAGTTAGAAATAAAATAAGGATTGAATTGTAAAG
1 GATGAATTAAAGGCTAAATTGATAGAAATTCAAGTTAGAAATAAAATAAGGATTGAATTGTAAAG
29033486 TGATTCATAAGTTTTATGCTTTAAGGACTAAATTGAAAGA
66 TGATTCATAAGTTTTATGCTTTAAGGACTAAATTGAAAGA
* *
29033526 GATGAATTAAAGGCTAAATTGATAGAAATTCAAGTTAGAAGTGAAATAAGGATTGAATTGTAAAG
1 GATGAATTAAAGGCTAAATTGATAGAAATTCAAGTTAGAAATAAAATAAGGATTGAATTGTAAAG
29033591 TGATTCATAAGTTTTATGCTTTAAGGACTAAATTGAAAGA
66 TGATTCATAAGTTTTATGCTTTAAGGACTAAATTGAAAGA
29033631 ATTTCGAAAT
Statistics
Matches: 103, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
105 103 1.00
ACGTcount: A:0.44, C:0.05, G:0.20, T:0.31
Consensus pattern (105 bp):
GATGAATTAAAGGCTAAATTGATAGAAATTCAAGTTAGAAATAAAATAAGGATTGAATTGTAAAG
TGATTCATAAGTTTTATGCTTTAAGGACTAAATTGAAAGA
Found at i:29033932 original size:15 final size:15
Alignment explanation
Indices: 29033909--29033956 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
29033899 TATCAAATTT
29033909 ATATTGATTGAAATC
1 ATATTGATTGAAATC
* * *
29033924 ATTTTGATTGAATTT
1 ATATTGATTGAAATC
29033939 ATATTGATTGAAAT-
1 ATATTGATTGAAATC
29033953 ATAT
1 ATAT
29033957 ATTATATATA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (15 bp):
ATATTGATTGAAATC
Found at i:29034612 original size:18 final size:19
Alignment explanation
Indices: 29034591--29034631 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
29034581 AATGAAATGA
29034591 GAAATTGA-AT-TGAGAATT
1 GAAATTGAGATATGAG-ATT
29034609 GAAATTGAGATATGAGATT
1 GAAATTGAGATATGAGATT
29034628 GAAA
1 GAAA
29034632 ACATGAACCA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 9 0.43
20 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.24, T:0.29
Consensus pattern (19 bp):
GAAATTGAGATATGAGATT
Found at i:29040250 original size:15 final size:15
Alignment explanation
Indices: 29040209--29040255 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
29040199 GAATTTATCA
*
29040209 AATTTATATTGATTG
1 AATTTTTATTGATTG
**
29040224 AAATCATT-TTGATTG
1 -AATTTTTATTGATTG
29040239 AATTTTTATTGATTG
1 AATTTTTATTGATTG
29040254 AA
1 AA
29040256 ATATATATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 5 0.20
15 16 0.64
16 4 0.16
ACGTcount: A:0.34, C:0.02, G:0.13, T:0.51
Consensus pattern (15 bp):
AATTTTTATTGATTG
Found at i:29040785 original size:23 final size:23
Alignment explanation
Indices: 29040757--29040814 Score: 116
Period size: 23 Copynumber: 2.5 Consensus size: 23
29040747 TAATATTCCG
29040757 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
29040780 GGTGTGTTTGGGTTGGATATTCT
1 GGTGTGTTTGGGTTGGATATTCT
29040803 GGTGTGTTTGGG
1 GGTGTGTTTGGG
29040815 AGGAATCCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.07, C:0.03, G:0.43, T:0.47
Consensus pattern (23 bp):
GGTGTGTTTGGGTTGGATATTCT
Found at i:29046047 original size:27 final size:27
Alignment explanation
Indices: 29046016--29046193 Score: 214
Period size: 27 Copynumber: 6.6 Consensus size: 27
29046006 TAAATTGTAC
29046016 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
29046043 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29046069 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
29046097 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
*
29046125 AGCACTAAGTGTGCGATTTGATTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
29046152 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
29046179 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
29046194 GACTCGATAT
Statistics
Matches: 131, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
27 108 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:29046130 original size:82 final size:81
Alignment explanation
Indices: 29046017--29046172 Score: 242
Period size: 82 Copynumber: 1.9 Consensus size: 81
29046007 AAATTGTACA
*
29046017 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTA-GCACTAAGTG
29046081 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
29046098 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTG
*
29046163 TGCGAGTTGA
65 TGCGAATTGA
29046173 TTATATAGCA
Statistics
Matches: 68, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 15 0.22
82 52 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:29046184 original size:82 final size:81
Alignment explanation
Indices: 29046013--29046193 Score: 238
Period size: 82 Copynumber: 2.2 Consensus size: 81
29046003 GATTAAATTG
*
29046013 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
29046078 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
29046094 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTATG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGAT-GCACT
* **
29046158 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
29046176 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
29046194 GACTCGATAT
Statistics
Matches: 85, Mismatches: 13, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
81 18 0.21
82 67 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATATGATGCACTAA
GTGTGCGAATTGACCA
Found at i:29048177 original size:41 final size:37
Alignment explanation
Indices: 29048071--29048177 Score: 88
Period size: 38 Copynumber: 2.8 Consensus size: 37
29048061 TCGGATAGTT
* * **
29048071 CGAAGCAAAGTTGACACCCAGTGTCTCATTGGCTTAGC
1 CGAAGTAAAG-TGACACCCAGTGTCTCATCGAATTAGC
** ** *
29048109 CGAAGTAAAGTGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAAAGTGACACCCAGTGTCTCATCGAAT-TAGC
29048147 CGAAGTAAAATAGTGACACCCAGTGTCTCAT
1 CGAAGT--AA-AGTGACACCCAGTGTCTCAT
29048178 AGACTCAAGG
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
37 16 0.31
38 18 0.35
40 2 0.04
41 16 0.31
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (37 bp):
CGAAGTAAAGTGACACCCAGTGTCTCATCGAATTAGC
Found at i:29048983 original size:18 final size:17
Alignment explanation
Indices: 29048960--29048993 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29048950 GTAAATGTTC
29048960 AATATAAGCAAATACATG
1 AATATAAG-AAATACATG
*
29048978 AATATATGAAATACAT
1 AATATAAGAAATACAT
29048994 TGAAATGATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.09, G:0.09, T:0.26
Consensus pattern (17 bp):
AATATAAGAAATACATG
Found at i:29049500 original size:21 final size:21
Alignment explanation
Indices: 29049476--29049519 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29049466 GATTTAAGCT
29049476 AAAGAAAAGAAACTA-AAATGA
1 AAAGAAAAGAAA-TACAAATGA
* *
29049497 AAAGTAATGAAATACAAATGA
1 AAAGAAAAGAAATACAAATGA
29049518 AA
1 AA
29049520 GTAAGAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.68, C:0.05, G:0.14, T:0.14
Consensus pattern (21 bp):
AAAGAAAAGAAATACAAATGA
Found at i:29049529 original size:20 final size:20
Alignment explanation
Indices: 29049482--29049529 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
29049472 AGCTAAAGAA
*
29049482 AAGAAACTAAAATGAAAAGT
1 AAGAAAATAAAATGAAAAGT
29049502 AATG-AAATACAAATG-AAAGT
1 AA-GAAAATA-AAATGAAAAGT
29049522 AAGAAAAT
1 AAGAAAAT
29049530 TTGAAAGGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
19 1 0.04
20 17 0.71
21 6 0.25
ACGTcount: A:0.65, C:0.04, G:0.15, T:0.17
Consensus pattern (20 bp):
AAGAAAATAAAATGAAAAGT
Found at i:29058840 original size:44 final size:44
Alignment explanation
Indices: 29058772--29059648 Score: 1394
Period size: 44 Copynumber: 19.9 Consensus size: 44
29058762 GAGACGCCAA
*
29058772 ATCTGTCGATCTGTTCTCCGCCGCTACAGAGACGCCAAATCTGTT
1 ATCT-TCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * *
29058817 ATCTTCGATCTGCTCTTCGCCGCTACAGAGACCCCAAATCTGCT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
*
29058861 ATCTTCGATCTGTTCTCCGCCGCTACAGAGACGCCAAATCTGTT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * *
29058905 ATCTTCGATCTGCTCTTCGCCGCTACAGAGACCCCAAATCTGCT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
*
29058949 ATCTTCGATCTGTTCTCCGCCGCTACAGAGACGCCAAATCTGTT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
*
29058993 ATCTTCGATCTGCTCTCCGCCGCTACAGAGATGCCAAATCTGTT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
*
29059037 ATCTTCGATCTGCTCTTCGCCGCTACAGAGACGCCAAATCTGTT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * * * * *
29059081 ATCTTCGATCTGCTCTCTGCTGCTACAGAAATGTCAAATCTGCT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* *
29059125 ATCTTCGATCTGCTCTCCACCGCTACAGAGACGCAAAATCTGTT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * *
29059169 ATCTTCGATCTGCTCTTCGCCGCTACAAAGACGCCAAATCTGCT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
29059213 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* **
29059257 ATCTTCGATCTGCTCTCTGCCGCTACAGAGACGCCAAATCTACT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
29059301 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * *
29059345 ATCTTCGATCTGCTCTTCGCCGCTACAAAGACGCCAAATCTGCT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
29059389 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* * *
29059433 ATCTTCGATCTGCTCTTCGCCGCTACAGAGACCCCAAATCTGCT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* *
29059477 ATCTTCGATCTGTTCTCCGCCGCTACAGAGACGCCAAATCTGCT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
**
29059521 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTACT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* *
29059565 ATTTTCGATCTACTCTCCGCCGCTACAGAGACGCCAAATCTGTT
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
* *
29059609 ATCTTCGACCTGCTCTCCGCCGCTACAGAGATGCCAAATC
1 ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATC
29059649 ATCTTAGATT
Statistics
Matches: 761, Mismatches: 71, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
44 757 0.99
45 4 0.01
ACGTcount: A:0.21, C:0.34, G:0.17, T:0.28
Consensus pattern (44 bp):
ATCTTCGATCTGCTCTCCGCCGCTACAGAGACGCCAAATCTGTT
Found at i:29059724 original size:88 final size:87
Alignment explanation
Indices: 29059610--29059842 Score: 344
Period size: 88 Copynumber: 2.7 Consensus size: 87
29059600 AAATCTGTTA
* * * *
29059610 TCTTCGACCTGCTCTCCGCC-GCTACAGAGATGCCAAATCATCTTAGATTTGCTTCAACGTAAAC
1 TCTTCGATCTGCTC-CCGCCTGATACAGAGATGCCAAATCATCTTGGATATGCTTCAACGTAAAC
29059674 ACGTGAAAGCCAAATCAGCTATG
65 ACGTGAAAGCCAAATCAGCTATG
* * *
29059697 TCTTCGATCTGCTCCCTGCCTGATACAGAGATGCCAAATTATCTTGGATCTGCTTTAACGTAAAC
1 TCTTCGATCTGCTCCC-GCCTGATACAGAGATGCCAAATCATCTTGGATATGCTTCAACGTAAAC
*
29059762 ACGTGAAAGCCAAATTAGCTATG
65 ACGTGAAAGCCAAATCAGCTATG
*
29059785 TCTTCGATCTACTCCCCGCCTGATACAGAGATGCCAAATCATCTTGGATAT-CTTCAAC
1 TCTTCGATCTGCT-CCCGCCTGATACAGAGATGCCAAATCATCTTGGATATGCTTCAAC
29059843 TTGTTGCCCT
Statistics
Matches: 132, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
86 2 0.02
87 22 0.17
88 105 0.80
89 3 0.02
ACGTcount: A:0.28, C:0.27, G:0.17, T:0.28
Consensus pattern (87 bp):
TCTTCGATCTGCTCCCGCCTGATACAGAGATGCCAAATCATCTTGGATATGCTTCAACGTAAACA
CGTGAAAGCCAAATCAGCTATG
Found at i:29060041 original size:61 final size:64
Alignment explanation
Indices: 29059929--29060053 Score: 195
Period size: 61 Copynumber: 2.0 Consensus size: 64
29059919 TCATGTATCC
29059929 ATGCTTATGCCAAATAATTAGGATGCTATAATTGAAATGAATCAAATGCTCCTAACTAAATGTG
1 ATGCTTATGCCAAATAATTAGGATGCTATAATTGAAATGAATCAAATGCTCCTAACTAAATGTG
* *
29059993 ATGCTTTATGTCAAATAATTAGGATG-T-T-A-TGAAATGAATCAAATGCTCCTAACTAGATGTG
1 ATGC-TTATGCCAAATAATTAGGATGCTATAATTGAAATGAATCAAATGCTCCTAACTAAATGTG
29060054 TTATTATATA
Statistics
Matches: 58, Mismatches: 2, Indels: 5
0.89 0.03 0.08
Matches are distributed among these distances:
61 31 0.53
62 1 0.02
63 1 0.02
64 5 0.09
65 20 0.34
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.33
Consensus pattern (64 bp):
ATGCTTATGCCAAATAATTAGGATGCTATAATTGAAATGAATCAAATGCTCCTAACTAAATGTG
Found at i:29062004 original size:40 final size:39
Alignment explanation
Indices: 29061960--29062184 Score: 263
Period size: 40 Copynumber: 5.7 Consensus size: 39
29061950 GCCACTAGCT
*
29061960 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
*
29062000 CAAATGCCTTCGGGACTTAGCCCGGTATAATAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
* * *
29062039 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * *
29062079 CAAACGCCTTCGGGACTTAGCCCGGATATAGTAGCTCGTA
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTCGCA
* * * ** * *
29062119 CGAATGCCTTCAGGACTTAGCCCGGAATTAGCCACTAGCT
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCGCA
29062159 CAAATG-CTCTCGGGACTTAGCCCGGT
1 CAAATGCCT-TCGGGACTTAGCCCGGT
29062185 TATCATCCGA
Statistics
Matches: 163, Mismatches: 19, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
39 40 0.25
40 123 0.75
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (39 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTCGCA
Found at i:29062058 original size:79 final size:78
Alignment explanation
Indices: 29061960--29062184 Score: 263
Period size: 79 Copynumber: 2.8 Consensus size: 78
29061950 GCCACTAGCT
*
29061960 CAAATGCCTTCGGGACTTAGCCCGGTTATAGTAACTTGCACAAATGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
29062025 TATAATAACTCGCA
65 TATAATAACTCGCA
* * * * *
29062039 CAAATGCCTTCGGGACTTAGCCCGGATATAATAGCTCGTACAAACGCCTTCGGGACTTAGCCCGG
1 CAAATGCCTTCGGGACTTAGCCCGG-TATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGG
* * *
29062104 ATATAGTAGCTCGTA
65 -TATAATAACTCGCA
* * * ** *
29062119 CGAATGCCTTCAGGACTTAGCCCGGAATTAGCCACTAGCTCAAATG-CTCTCGGGACTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGTA-TAGTAACTAGCACAAATGCCT-TCGGGACTTAGCCCG
29062183 GT
64 GT
29062185 TATCATCCGA
Statistics
Matches: 123, Mismatches: 20, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
79 63 0.51
80 60 0.49
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (78 bp):
CAAATGCCTTCGGGACTTAGCCCGGTATAGTAACTAGCACAAATGCCTTCGGGACTTAGCCCGGT
ATAATAACTCGCA
Found at i:29073407 original size:21 final size:21
Alignment explanation
Indices: 29073381--29073423 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
29073371 ATGACAGAAA
*
29073381 GTGCCGACCTCCATTGTATTG
1 GTGCCGAACTCCATTGTATTG
29073402 GTGCCGAACTCCATTGTATTG
1 GTGCCGAACTCCATTGTATTG
29073423 G
1 G
29073424 GGAGAACTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.26, G:0.26, T:0.33
Consensus pattern (21 bp):
GTGCCGAACTCCATTGTATTG
Found at i:29080810 original size:20 final size:20
Alignment explanation
Indices: 29080774--29080813 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
29080764 AAATTAATAT
*
29080774 ATTAATAAAATATTATATTA
1 ATTAATAAAATAGTATATTA
29080794 ATTAGATAAAA-AGTATATTA
1 ATTA-ATAAAATAGTATATTA
29080814 TAAATTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
ATTAATAAAATAGTATATTA
Found at i:29081859 original size:23 final size:23
Alignment explanation
Indices: 29081828--29081934 Score: 124
Period size: 23 Copynumber: 4.7 Consensus size: 23
29081818 CTTAGTGTCG
* * *
29081828 TTCTAGTGTGTTTGGATGGGTTA
1 TTCTGGTGTGTTTGGGTGGATTA
* *
29081851 TTCTGGTGTGTTTGGGTTGATTG
1 TTCTGGTGTGTTTGGGTGGATTA
* * *
29081874 TTCTGGTATGTTTGGGTTGATCA
1 TTCTGGTGTGTTTGGGTGGATTA
*
29081897 TTCTGGTGTGTTTGGTTGGATTA
1 TTCTGGTGTGTTTGGGTGGATTA
*
29081920 TTTTGGTGTGTTTGG
1 TTCTGGTGTGTTTGG
29081935 TTCGATCCGT
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 71 1.00
ACGTcount: A:0.08, C:0.05, G:0.36, T:0.51
Consensus pattern (23 bp):
TTCTGGTGTGTTTGGGTGGATTA
Found at i:29091741 original size:48 final size:48
Alignment explanation
Indices: 29091679--29091895 Score: 357
Period size: 48 Copynumber: 4.6 Consensus size: 48
29091669 TATATATGTG
* *
29091679 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTAAA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
*
29091727 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATACATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
* *
29091775 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATG--TG
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
* *
29091821 TGCGGTAAAGCCGAATGGCTAGTGTGAAATATGTATGAGATATGTATA
1 TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
29091869 TGTGGTAAAGCCGAATGGCTAGTGTGA
1 TGTGGTAAAGCCGAATGGCTAGTGTGA
29091896 TGTGACAGCC
Statistics
Matches: 156, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
46 42 0.27
48 114 0.73
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.29
Consensus pattern (48 bp):
TGTGGTAAAGCCGAATGGCTAGTGTGAAATATATATGAGATATGTATA
Found at i:29091847 original size:94 final size:95
Alignment explanation
Indices: 29091679--29091895 Score: 373
Period size: 94 Copynumber: 2.3 Consensus size: 95
29091669 TATATATGTG
*
29091679 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTAAATGTGGTAAAGCCGAATG
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGT-AATGCGGTAAAGCCGAATG
29091744 GCTAGTGTGAAATATACATGAGATATGTATA
65 GCTAGTGTGAAATATACATGAGATATGTATA
*
29091775 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGT-GTGCGGTAAAGCCGAATGG
1 TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTAATGCGGTAAAGCCGAATGG
**
29091839 CTAGTGTGAAATATGTATGAGATATGTATA
66 CTAGTGTGAAATATACATGAGATATGTATA
*
29091869 TGTGGTAAAGCCGAATGGCTAGTGTGA
1 TGTGGTAAAGCCGAATGGCTAATGTGA
29091896 TGTGACAGCC
Statistics
Matches: 116, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
94 71 0.61
96 45 0.39
ACGTcount: A:0.35, C:0.08, G:0.29, T:0.29
Consensus pattern (95 bp):
TGTGGTAAAGCCGAATGGCTAATGTGAAATATATATGAGATATGTAATGCGGTAAAGCCGAATGG
CTAGTGTGAAATATACATGAGATATGTATA
Found at i:29094338 original size:47 final size:47
Alignment explanation
Indices: 29094284--29095442 Score: 1872
Period size: 47 Copynumber: 24.6 Consensus size: 47
29094274 TATTTGAATA
* * *
29094284 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
* * *
29094331 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
* * *
29094378 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
* * *
29094425 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
* * *
29094472 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29094519 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29094566 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29094613 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29094660 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29094707 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29094754 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29094801 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29094848 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29094895 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29094942 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29094989 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
* * *
29095036 AATGTGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AA--TGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
* * *
29095085 AATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29095132 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
* * *
29095179 AATGTGAAAGTGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTG--TATATATGTGATAAGGTCTAATAGTCGATGTGATG
* * *
29095228 AATGTGAAA--GTATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
29095273 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
* * * *
29095320 AATGTGAAAGAGTATATATATGTGATAAGGCCTAATGGCCGATGTGATG
1 AATGTG-AA-AGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
* * * * * * * * *
29095369 AATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCAACGTGATG
1 AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
* *
29095416 GATGTGAAAGTGTATAAATGTGATAAG
1 AATGTGAAAGTGTATATATGTGATAAG
29095443 TCCCGAAGGG
Statistics
Matches: 1074, Mismatches: 30, Indels: 16
0.96 0.03 0.01
Matches are distributed among these distances:
45 44 0.04
47 900 0.84
48 4 0.00
49 126 0.12
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.32
Consensus pattern (47 bp):
AATGTGAAAGTGTATATATGTGATAAGGTCTAATAGTCGATGTGATG
Found at i:29096509 original size:48 final size:48
Alignment explanation
Indices: 29096438--29096887 Score: 769
Period size: 48 Copynumber: 9.4 Consensus size: 48
29096428 GGGGTGTTAC
29096438 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
**
29096486 ATGTGAAATATACATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
*
29096534 GTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
**
29096582 ATGTGAAATATACATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
*
29096630 ATGTGAAATATGCATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
*
29096678 GTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
29096726 GTGTGAAATATGTATGAGATATG--TGTGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
*
29096772 ATGTGAAATATATATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
*
29096820 GTGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
1 ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
* *
29096868 GTGTGAAATATGTAGGAGAT
1 ATGTGAAATATGTATGAGAT
29096888 GTGTGTATAT
Statistics
Matches: 382, Mismatches: 18, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
46 43 0.11
48 339 0.89
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (48 bp):
ATGTGAAATATGTATGAGATATGTATATGTGGTAAAGCCGAATGGCTA
Found at i:29107438 original size:85 final size:85
Alignment explanation
Indices: 29107327--29107483 Score: 296
Period size: 85 Copynumber: 1.8 Consensus size: 85
29107317 GTTACAGTAC
* *
29107327 ATCCACTTAGCACCATGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCATCACGT
1 ATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGT
29107392 TACATGTTTAACCGTGGTAT
66 TACATGTTTAACCGTGGTAT
29107412 ATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGT
1 ATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGT
29107477 TACATGT
66 TACATGT
29107484 ATCAATATGT
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 70 1.00
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (85 bp):
ATCCACTTAGCACCACGTTAATGAATCAATATATGTAACCGTGGCATATCCACTTAGCACCACGT
TACATGTTTAACCGTGGTAT
Found at i:29107469 original size:47 final size:48
Alignment explanation
Indices: 29107400--29107522 Score: 194
Period size: 48 Copynumber: 2.6 Consensus size: 48
29107390 GTTACATGTT
29107400 TAACCGTGGTATATCCACTTAGCACCACGTTA-ATGAATCAATATATG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* * *
29107447 TAACCGTGGCATATCCACTTAGCACCACGTTACATGTATCAATATGTG
1 TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
* *
29107495 TAATCGTTGTATATCCACTTAGCACCAC
1 TAACCGTGGTATATCCACTTAGCACCAC
29107523 ATTTTTTCAT
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
47 31 0.45
48 38 0.55
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (48 bp):
TAACCGTGGTATATCCACTTAGCACCACGTTACATGAATCAATATATG
Found at i:29111869 original size:50 final size:50
Alignment explanation
Indices: 29111794--29112019 Score: 253
Period size: 50 Copynumber: 4.5 Consensus size: 50
29111784 TGAGTACACG
* *
29111794 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCACA
* * **
29111844 TGTGTAGTACTAAGTGCAGGCTACTATGCGTACTCAATGACT-TCGA-TCACA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTAC-C-A-GACTGTTAAGTCACA
* * * *
29111895 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGGTGAGGTCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACT-GTTAAGTCACA
* * * * *
29111945 TATGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATTGTT-GGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCACA
29111994 TGTGTAGTACTAAGTGCAGGCTACTA
1 TGTGTAGTACTAAGTGCAGGCTACTA
29112020 TGCGTATCAG
Statistics
Matches: 149, Mismatches: 20, Indels: 15
0.81 0.11 0.08
Matches are distributed among these distances:
47 1 0.01
48 2 0.01
49 32 0.21
50 72 0.48
51 36 0.24
52 3 0.02
53 3 0.02
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.30
Consensus pattern (50 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGACTGTTAAGTCACA
Found at i:29112027 original size:99 final size:99
Alignment explanation
Indices: 29111794--29112031 Score: 284
Period size: 101 Copynumber: 2.4 Consensus size: 99
29111784 TGAGTACACG
* * * * *
29111794 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCATACTGTTAAGTCGCATGTGTAGTACTAAGT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGA-TGTGAAGTCACATATGTAGTACTAAGT
*
29111859 GCAGGCTACTATGCGTACTCAATGACTTCGATCACA
65 GCAGGCTACTACGCGTACTCAATGA-TTCGATCACA
* *
29111895 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGGTGAGGTCACGTATGTAGTACTAAGT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAT-GTGAAGTCACATATGTAGTACTAAGT
* * * *
29111960 GCAGGCTACTACGTGTAC-CGGATTG-TT-GGTCGCA
65 GCAGGCTACTACGCGTACTC--AATGATTCGATCACA
* *
29111994 TGTGTAGTACTAAGTGCAGGCTACTATGCGTATCAGAT
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGAT
29112032 AGCTTCGGCT
Statistics
Matches: 120, Mismatches: 14, Indels: 8
0.85 0.10 0.06
Matches are distributed among these distances:
99 41 0.34
100 4 0.03
101 72 0.60
102 3 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.30
Consensus pattern (99 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTATCAGATGTGAAGTCACATATGTAGTACTAAGTG
CAGGCTACTACGCGTACTCAATGATTCGATCACA
Found at i:29115046 original size:31 final size:31
Alignment explanation
Indices: 29115003--29115066 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
29114993 CCTTTTCATA
*
29115003 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGACCGAAGCCT
* **
29115034 TTTCATATTTCATATTACTGGACCGAAGCCT
1 TTTCATAATTCATAACACTGGACCGAAGCCT
29115065 TT
1 TT
29115067 ACTGTAATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGACCGAAGCCT
Found at i:29115335 original size:23 final size:23
Alignment explanation
Indices: 29115281--29116136 Score: 1676
Period size: 23 Copynumber: 37.1 Consensus size: 23
29115271 CCTAGCCTCT
*
29115281 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115304 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
29115328 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115351 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115374 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115397 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115420 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115443 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115466 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115489 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115512 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115535 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115558 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115581 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115604 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115627 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115650 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115673 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115696 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115719 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115742 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115765 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115788 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115811 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115834 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115857 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115880 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115903 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115926 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115949 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115972 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29115995 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29116018 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29116041 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29116064 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29116087 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
29116110 TTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
29116134 TTT
1 TTT
29116137 TGCATTTCCT
Statistics
Matches: 829, Mismatches: 2, Indels: 3
0.99 0.00 0.00
Matches are distributed among these distances:
23 785 0.95
24 44 0.05
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:29116209 original size:9 final size:9
Alignment explanation
Indices: 29116195--29116251 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
29116185 ATCTCGAGTG
29116195 CATATCATA
1 CATATCATA
*
29116204 CATATCATGTG
1 CATATCA--TA
29116215 CATATCATA
1 CATATCATA
* *
29116224 CATGTCATGTG
1 CATATCA--TA
29116235 CATATCATA
1 CATATCATA
29116244 CATATCAT
1 CATATCAT
29116252 GTCTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:29116215 original size:20 final size:20
Alignment explanation
Indices: 29116192--29116253 Score: 115
Period size: 20 Copynumber: 3.1 Consensus size: 20
29116182 AACATCTCGA
29116192 GTGCATATCATACATATCAT
1 GTGCATATCATACATATCAT
*
29116212 GTGCATATCATACATGTCAT
1 GTGCATATCATACATATCAT
29116232 GTGCATATCATACATATCAT
1 GTGCATATCATACATATCAT
29116252 GT
1 GT
29116254 CTATCAAAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.35
Consensus pattern (20 bp):
GTGCATATCATACATATCAT
Found at i:29116318 original size:25 final size:25
Alignment explanation
Indices: 29116290--29116337 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
29116280 ATATATAATC
* * *
29116290 CCTAGGGGTATAATGGTCATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
29116315 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
29116338 CATGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:29123678 original size:31 final size:31
Alignment explanation
Indices: 29123635--29123698 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
29123625 CCTTTTCATA
29123635 TTTCATAATTCATAACACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
* ***
29123666 TTTCATATTTCATCTTACTGGGCCGAAGCCT
1 TTTCATAATTCATAACACTGGGCCGAAGCCT
29123697 TT
1 TT
29123699 ACTGTAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.23, C:0.25, G:0.16, T:0.36
Consensus pattern (31 bp):
TTTCATAATTCATAACACTGGGCCGAAGCCT
Found at i:29123967 original size:23 final size:23
Alignment explanation
Indices: 29123913--29124699 Score: 1511
Period size: 23 Copynumber: 34.1 Consensus size: 23
29123903 CCTAGCCTCT
*
29123913 TTTAATAACTGGGGCAAAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29123936 TTTTAATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
29123960 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29123983 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124006 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124029 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124052 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124075 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124098 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124121 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124144 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124167 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124190 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124213 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124236 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124259 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124282 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124305 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124328 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124351 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124374 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124397 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124420 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124443 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124466 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124489 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124512 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124535 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124558 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124581 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
29124604 TTTAATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
**
29124627 TTTAATAACTGGGGCATAAGCGT
1 TTTAATAACTGGGGCATAAGCCC
*
29124650 TTTGATAACTGGGGCATAAGCCC
1 TTTAATAACTGGGGCATAAGCCC
*
29124673 TTTTGATAACTGGGGCATAAGCCC
1 -TTTAATAACTGGGGCATAAGCCC
29124697 TTT
1 TTT
29124700 TGCACTTCCT
Statistics
Matches: 756, Mismatches: 6, Indels: 3
0.99 0.01 0.00
Matches are distributed among these distances:
23 711 0.94
24 45 0.06
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.27
Consensus pattern (23 bp):
TTTAATAACTGGGGCATAAGCCC
Found at i:29124772 original size:9 final size:9
Alignment explanation
Indices: 29124758--29124814 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
29124748 ATCTCGTGTG
29124758 CATATCATA
1 CATATCATA
*
29124767 CATATCATGTG
1 CATATCA--TA
29124778 CATATCATA
1 CATATCATA
* *
29124787 CATGTCATGTG
1 CATATCA--TA
29124798 CATATCATA
1 CATATCATA
29124807 CATATCAT
1 CATATCAT
29124815 GTCTATCAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 23 0.61
11 15 0.39
ACGTcount: A:0.35, C:0.21, G:0.09, T:0.35
Consensus pattern (9 bp):
CATATCATA
Found at i:29124777 original size:20 final size:20
Alignment explanation
Indices: 29124754--29124816 Score: 117
Period size: 20 Copynumber: 3.1 Consensus size: 20
29124744 GAACATCTCG
29124754 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
*
29124774 TGTGCATATCATACATGTCA
1 TGTGCATATCATACATATCA
29124794 TGTGCATATCATACATATCA
1 TGTGCATATCATACATATCA
29124814 TGT
1 TGT
29124817 CTATCAAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.37
Consensus pattern (20 bp):
TGTGCATATCATACATATCA
Found at i:29124894 original size:33 final size:33
Alignment explanation
Indices: 29124852--29124916 Score: 121
Period size: 33 Copynumber: 2.0 Consensus size: 33
29124842 CATATATAAT
29124852 CCCTAGGGGTATAATGGTCATTTTTACCTAGGA
1 CCCTAGGGGTATAATGGTCATTTTTACCTAGGA
*
29124885 CCCTAGGGGTATAATGGTTATTTTTACCTAGG
1 CCCTAGGGGTATAATGGTCATTTTTACCTAGG
29124917 GGCAAAACGG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (33 bp):
CCCTAGGGGTATAATGGTCATTTTTACCTAGGA
Found at i:29124932 original size:25 final size:25
Alignment explanation
Indices: 29124886--29124933 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29124876 TACCTAGGAC
* * * *
29124886 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
29124911 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
29124934 CATGTTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:29125411 original size:15 final size:15
Alignment explanation
Indices: 29125387--29125417 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
29125377 CAAAATTTAG
*
29125387 ATTTTGGTTTTATTT
1 ATTTTAGTTTTATTT
29125402 ATTTTAGTTTTATTT
1 ATTTTAGTTTTATTT
29125417 A
1 A
29125418 ATAATTTACT
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:0.19, C:0.00, G:0.10, T:0.71
Consensus pattern (15 bp):
ATTTTAGTTTTATTT
Found at i:29126923 original size:516 final size:516
Alignment explanation
Indices: 29125951--29127500 Score: 3019
Period size: 516 Copynumber: 3.0 Consensus size: 516
29125941 ACTTTATGGG
29125951 GTAATTATAAACCTATACAATTTCCACAAAGTTTATCAAACTTTATAACCATCAACTTATAAATG
1 GTAATTATAAACCTATACAATTTCCACAAAGTTTATCAAACTTTATAACCATCAACTTATAAATG
29126016 AGTAAGTTCATCAATACCACATATATTTTTCATTCCTAACATAACCATCAACTTGTAAAACGTAT
66 AGTAAGTTCATCAATACCACATATATTTTTCATTCCTAACATAACCATCAACTTGTAAAACGTAT
29126081 TACACAATCATTAAGCTTTTCATAATACTATGAACCACTCCATTTACTTACTTTCCATTTCATTT
131 TACACAATCATTAAGCTTTTCATAATACTATGAACCACTCCATTTACTTACTTTCCATTTCATTT
29126146 ACTTAGCATAACTTAAATAACATTATCAATTCATGAATTAGTGCATTTATCCATGACATAGATAA
196 ACTTAGCATAACTTAAATAACATTATCAATTCATGAATTAGTGCATTTATCCATGACATAGATAA
29126211 ATTCGTCCATAACATAAATAGATCTCTCACGCACGAATACGTTATTTAACTCATCAACTTGTTTT
261 ATTCGTCCATAACATAAATAGATCTCTCACGCACGAATACGTTATTTAACTCATCAACTTGTTTT
29126276 TCATCATATTACATCTCAACTCTAAACTTACCGTTTCATTACCTTTTCTTACTTGTTTCATTTTC
326 TCATCATATTACATCTCAACTCTAAACTTACCGTTTCATTACCTTTTCTTACTTGTTTCATTTTC
29126341 ATAATATAAGACATAAGCTTAAACATCACCCACATGATAAACCATTTCATTAGAAAATACATACT
391 ATAATATAAGACATAAGCTTAAACATCACCCACATGATAAACCATTTCATTAGAAAATACATACT
29126406 TTTATTCTTACCACCCTTTCATGAACATAAGCATATTTTCATTTGACACTTACCCTTTCAA
456 TTTATTCTTACCACCCTTTCATGAACATAAGCATATTTTCATTTGACACTTACCCTTTCAA
*
29126467 GTAATTATAAACCTATACAATTTCCACAAAGTTTATCAAACTTTATAATCATCAACTTATAAATG
1 GTAATTATAAACCTATACAATTTCCACAAAGTTTATCAAACTTTATAACCATCAACTTATAAATG
*
29126532 AGTAAGTTCATCAATACCACATATATTTTTCATTCCTAACATAACCATCAACTTGTAAAATGTAT
66 AGTAAGTTCATCAATACCACATATATTTTTCATTCCTAACATAACCATCAACTTGTAAAACGTAT
29126597 TACACAATCATTAAGCTTTTCATAATACTATGAACCACTCCATTTACTTACTTTCCATTTCATTT
131 TACACAATCATTAAGCTTTTCATAATACTATGAACCACTCCATTTACTTACTTTCCATTTCATTT
29126662 ACTTAGCATAACTTAAATAACATTATCAATTCATGAATTAGTGCATTTATCCATGACATAGATAA
196 ACTTAGCATAACTTAAATAACATTATCAATTCATGAATTAGTGCATTTATCCATGACATAGATAA
29126727 ATTCGTCCATAACATAAATAGATCTCTCACGCACGAATACGTTATTTAACTCATCAACTTGTTTT
261 ATTCGTCCATAACATAAATAGATCTCTCACGCACGAATACGTTATTTAACTCATCAACTTGTTTT
29126792 TCATCATATTACATCTCAACTCTAAACTTACCGTTTCATTACCTTTTCTTACTTGTTTCATTTTC
326 TCATCATATTACATCTCAACTCTAAACTTACCGTTTCATTACCTTTTCTTACTTGTTTCATTTTC
29126857 ATAATATAAGACATAAGCTTAAACATCACCCACATGATAAACCATTTCATTAGAAAATACATACT
391 ATAATATAAGACATAAGCTTAAACATCACCCACATGATAAACCATTTCATTAGAAAATACATACT
29126922 TTTATTCTTACCACCCTTTCATGAACATAAGCATATTTTCATTTGACACTTACCCTTTCAA
456 TTTATTCTTACCACCCTTTCATGAACATAAGCATATTTTCATTTGACACTTACCCTTTCAA
29126983 GTAATTATAAACCTATACAATTTCCACAAAGTTTATCAAACTTTATAACCATCAACTTATAAATG
1 GTAATTATAAACCTATACAATTTCCACAAAGTTTATCAAACTTTATAACCATCAACTTATAAATG
29127048 AGTAAGTTCATCAATACCACATATATTTTTCATTCCTAACATAACCATCAACTTGTAAAACGTAT
66 AGTAAGTTCATCAATACCACATATATTTTTCATTCCTAACATAACCATCAACTTGTAAAACGTAT
29127113 TACACAATCATTAAGCTTTTCATAATACTATGAACCACTCCATTTACTTACTTTCCATTTCATTT
131 TACACAATCATTAAGCTTTTCATAATACTATGAACCACTCCATTTACTTACTTTCCATTTCATTT
*
29127178 ACTTAGCATAACTTAAATAACATTATCAATTCATTAATTAGTGCATTTATCCATGACATAGATAA
196 ACTTAGCATAACTTAAATAACATTATCAATTCATGAATTAGTGCATTTATCCATGACATAGATAA
* * * *
29127243 ATTCGTCCATAACATAAATAGATTTCACACGCACGAATACGCTATTTAACTCATCAATCTTTTTT
261 ATTCGTCCATAACATAAATAGATCTCTCACGCACGAATACGTTATTTAACTCATCAA-C-TTGTT
29127308 TTTCATCATATTACATCTCAACTCTAAACTTACCGTTTCATTACCTTTTCTTACTTGTTTCATTT
324 TTTCATCATATTACATCTCAACTCTAAACTTACCGTTTCATTACCTTTTCTTACTTGTTTCATTT
29127373 TCATAATATAAGACATAAGCTTAAACATCACCCACATGATAAACCATTTCATTAGAAAATACATA
389 TCATAATATAAGACATAAGCTTAAACATCACCCACATGATAAACCATTTCATTAGAAAATACATA
29127438 CTTTTATTCTTACCACCCTTTCATGAACATAAGCATATTTTCATTTGACACTTACCCTTTCAA
454 CTTTTATTCTTACCACCCTTTCATGAACATAAGCATATTTTCATTTGACACTTACCCTTTCAA
29127501 TGCATAACTT
Statistics
Matches: 1023, Mismatches: 9, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
516 825 0.81
517 1 0.00
518 197 0.19
ACGTcount: A:0.36, C:0.22, G:0.06, T:0.37
Consensus pattern (516 bp):
GTAATTATAAACCTATACAATTTCCACAAAGTTTATCAAACTTTATAACCATCAACTTATAAATG
AGTAAGTTCATCAATACCACATATATTTTTCATTCCTAACATAACCATCAACTTGTAAAACGTAT
TACACAATCATTAAGCTTTTCATAATACTATGAACCACTCCATTTACTTACTTTCCATTTCATTT
ACTTAGCATAACTTAAATAACATTATCAATTCATGAATTAGTGCATTTATCCATGACATAGATAA
ATTCGTCCATAACATAAATAGATCTCTCACGCACGAATACGTTATTTAACTCATCAACTTGTTTT
TCATCATATTACATCTCAACTCTAAACTTACCGTTTCATTACCTTTTCTTACTTGTTTCATTTTC
ATAATATAAGACATAAGCTTAAACATCACCCACATGATAAACCATTTCATTAGAAAATACATACT
TTTATTCTTACCACCCTTTCATGAACATAAGCATATTTTCATTTGACACTTACCCTTTCAA
Found at i:29140885 original size:21 final size:22
Alignment explanation
Indices: 29140853--29140894 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
29140843 TTCTCTTTGC
29140853 TTTAGTTTAATTAGTTAAATAG
1 TTTAGTTTAATTAGTTAAATAG
*
29140875 TTTAG-TTAATTAGTTTAATA
1 TTTAGTTTAATTAGTTAAATA
29140895 AACAACCCCT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.52
Consensus pattern (22 bp):
TTTAGTTTAATTAGTTAAATAG
Found at i:29141851 original size:47 final size:47
Alignment explanation
Indices: 29141773--29141940 Score: 223
Period size: 47 Copynumber: 3.6 Consensus size: 47
29141763 CCCTTCGGGA
* * * * * *
29141773 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
29141820 CCTGTCACATATATACACTTTCACATTCATCACATCGGGCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29141867 CTTATCACATATAT--ACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
29141912 CTTATCACATATATATACACTTTCACATT
1 CTTATCAC--ATATATACACTTTCACATT
29141941 TATTCAAATA
Statistics
Matches: 105, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
45 38 0.36
47 56 0.53
49 11 0.10
ACGTcount: A:0.28, C:0.30, G:0.09, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29141893 original size:45 final size:45
Alignment explanation
Indices: 29141773--29141926 Score: 191
Period size: 45 Copynumber: 3.3 Consensus size: 45
29141763 CCCTTCGGGA
* * * * * *
29141773 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACA--TATATACTTTCACATTCATCACATCGGCCATTAGGC
* * *
29141820 CCTGTCACATATATACACTTTCACATTCATCACATCGGGCATTAGGC
1 CTTATCACATATAT--ACTTTCACATTCATCACATCGGCCATTAGGC
29141867 CTTATCACATATATACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACTTTCACATTCATCACATCGGCCATTAGGC
29141912 CTTATCACATATATA
1 CTTATCACATATATA
29141927 TACACTTTCA
Statistics
Matches: 93, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
45 49 0.53
47 44 0.47
ACGTcount: A:0.28, C:0.30, G:0.10, T:0.32
Consensus pattern (45 bp):
CTTATCACATATATACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:29143413 original size:13 final size:13
Alignment explanation
Indices: 29143395--29143419 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29143385 TACTAAATTT
29143395 TCATGGATTCAAA
1 TCATGGATTCAAA
29143408 TCATGGATTCAA
1 TCATGGATTCAA
29143420 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAA
Found at i:29146609 original size:32 final size:30
Alignment explanation
Indices: 29146571--29146634 Score: 92
Period size: 32 Copynumber: 2.1 Consensus size: 30
29146561 CTTAACAAGA
29146571 AAATGCCTTTAAAATAATAAAAAAAAATTAAC
1 AAATGCCTTTAAAATAAT--AAAAAAATTAAC
* *
29146603 AAATGCCTTTAAAATAGTAACAAAATTAAC
1 AAATGCCTTTAAAATAATAAAAAAATTAAC
29146633 AA
1 AA
29146635 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 13 0.43
32 17 0.57
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (30 bp):
AAATGCCTTTAAAATAATAAAAAAATTAAC
Found at i:29146689 original size:22 final size:22
Alignment explanation
Indices: 29146664--29146706 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
29146654 TATCCAAACA
29146664 ATAACAACAAAATAGTAGCAAC
1 ATAACAACAAAATAGTAGCAAC
* * *
29146686 ATAATAATAAAATGGTAGCAA
1 ATAACAACAAAATAGTAGCAA
29146707 AATATGAAGA
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:0.58, C:0.12, G:0.12, T:0.19
Consensus pattern (22 bp):
ATAACAACAAAATAGTAGCAAC
Found at i:29146719 original size:22 final size:22
Alignment explanation
Indices: 29146663--29146719 Score: 53
Period size: 22 Copynumber: 2.6 Consensus size: 22
29146653 ATATCCAAAC
* *
29146663 AATAACAACAAAATAGTAGCAA
1 AATAATAAGAAAATAGTAGCAA
* * *
29146685 CATAATAATAAAATGGTAGCAA
1 AATAATAAGAAAATAGTAGCAA
29146707 AAT-ATGAAGAAAA
1 AATAAT-AAGAAAA
29146720 AAACAAGAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
21 2 0.07
22 26 0.93
ACGTcount: A:0.61, C:0.09, G:0.12, T:0.18
Consensus pattern (22 bp):
AATAATAAGAAAATAGTAGCAA
Found at i:29147714 original size:3 final size:3
Alignment explanation
Indices: 29147706--29147751 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
29147696 AAGGTCTTAG
29147706 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA G
29147752 TGTGTTAGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:29161757 original size:32 final size:30
Alignment explanation
Indices: 29161719--29161782 Score: 92
Period size: 32 Copynumber: 2.1 Consensus size: 30
29161709 CTTAACAAGA
29161719 AAATGCCTTTAAAATAATAAAAAAAAATTAAC
1 AAATGCCTTTAAAATAAT--AAAAAAATTAAC
* *
29161751 AAATGCCTTTAAAATAGTAACAAAATTAAC
1 AAATGCCTTTAAAATAATAAAAAAATTAAC
29161781 AA
1 AA
29161783 TAAAATAAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 13 0.43
32 17 0.57
ACGTcount: A:0.59, C:0.11, G:0.05, T:0.25
Consensus pattern (30 bp):
AAATGCCTTTAAAATAATAAAAAAATTAAC
Found at i:29161837 original size:22 final size:22
Alignment explanation
Indices: 29161811--29161859 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
29161801 ATATCCAAAC
29161811 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAGCAA
* * * *
29161833 CATAATAATAAAATGGTAGCAA
1 AATAACAACAAAATAGTAGCAA
29161855 AATAA
1 AATAA
29161860 ATAATAACAA
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.61, C:0.10, G:0.10, T:0.18
Consensus pattern (22 bp):
AATAACAACAAAATAGTAGCAA
Found at i:29161871 original size:96 final size:96
Alignment explanation
Indices: 29161762--29161954 Score: 332
Period size: 96 Copynumber: 2.0 Consensus size: 96
29161752 AATGCCTTTA
* * *
29161762 AAATAGTAACAAAATTAACAATAAAATAAGTTTTATACAATATCCAAACAATAACAACAAAATAG
1 AAATAATAACAAAATTAACAATAAAATAAGGTTTATACAATATCCAAACAATAAAAACAAAATAG
*
29161827 TAGCAACATAATAATAAAATGGTAGCAAAAT
66 TAGCAACATAATAATAAAATGATAGCAAAAT
29161858 AAATAATAACAAAATTAACAATAAAATAAGGTTTATACAATATCCAAACAATAAAAACAAAATAG
1 AAATAATAACAAAATTAACAATAAAATAAGGTTTATACAATATCCAAACAATAAAAACAAAATAG
* *
29161923 TAGCAACATAATAGTAAAATGATAGTAAAAT
66 TAGCAACATAATAATAAAATGATAGCAAAAT
29161954 A
1 A
29161955 GGGAGAAAAC
Statistics
Matches: 91, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
96 91 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.23
Consensus pattern (96 bp):
AAATAATAACAAAATTAACAATAAAATAAGGTTTATACAATATCCAAACAATAAAAACAAAATAG
TAGCAACATAATAATAAAATGATAGCAAAAT
Found at i:29166123 original size:18 final size:19
Alignment explanation
Indices: 29166100--29166135 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
29166090 TGATACCGAA
29166100 GAATA-TAAAAAACAAATG
1 GAATATTAAAAAACAAATG
*
29166118 GAATATTACAAAACAAAT
1 GAATATTAAAAAACAAAT
29166136 AATATTTGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.64, C:0.08, G:0.08, T:0.19
Consensus pattern (19 bp):
GAATATTAAAAAACAAATG
Found at i:29179439 original size:43 final size:43
Alignment explanation
Indices: 29179391--29179767 Score: 488
Period size: 43 Copynumber: 8.5 Consensus size: 43
29179381 TATTATAATT
29179391 GGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTC
1 GGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTC
* *
29179434 GGGCCTTCGTGCCGGTGATGTGTATTCGGGCCTTCGTGCAGGTGATGTGTATTC
1 GGGCCTTCGTGCC--T-A---G----CAGG-CTTCGTGCCGGTGATGTGTATTC
*
29179488 GGGCCTTCGTGCCTA-CTAGGCTTCTTGCCGGTGATGTGTATTC
1 GGGCCTTCGTGCCTAGC-AGGCTTCGTGCCGGTGATGTGTATTC
*
29179531 GGGCCTTCGTGCCTA-CTAGGCTTCTTGCCGGTGATGTGTATTC
1 GGGCCTTCGTGCCTAGC-AGGCTTCGTGCCGGTGATGTGTATTC
* * *
29179574 GGGCCTTCGTGCCTAGCAGGCTTCTTGCCAGCGATGTGTATTC
1 GGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTC
*
29179617 AGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTC
1 GGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTC
* * * * *
29179660 GAGCCTTCGGGCCTAGCAGGCTTCGTGCTGCTGATGTCTATTC
1 GGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTC
*
29179703 GGGCCTTCGTGCCTAGCAGGCTTCGTGTCGGTGATGTGTATTC
1 GGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTC
*
29179746 GGACCTTCGTGCCTAGCAGGCT
1 GGGCCTTCGTGCCTAGCAGGCT
29179768 ATGATGCTGG
Statistics
Matches: 297, Mismatches: 24, Indels: 26
0.86 0.07 0.07
Matches are distributed among these distances:
43 251 0.85
44 3 0.01
45 1 0.00
46 1 0.00
49 1 0.00
51 1 0.00
52 1 0.00
53 3 0.01
54 35 0.12
ACGTcount: A:0.10, C:0.25, G:0.33, T:0.32
Consensus pattern (43 bp):
GGGCCTTCGTGCCTAGCAGGCTTCGTGCCGGTGATGTGTATTC
Done.