Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_D05
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: 63323194
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1953226 characters in sequence are not A, C, G, or T
File 53 of 199
Found at i:20909959 original size:20 final size:20
Alignment explanation
Indices: 20909934--20909986 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
20909924 AGCCTCTCCA
* *
20909934 TTTTTTTATTTTTCATTTTC
1 TTTTTTCATTTTTCATTCTC
*
20909954 TTTTTTCAATTTTCATTCTC
1 TTTTTTCATTTTTCATTCTC
*
20909974 ATTTTTCATTTTT
1 TTTTTTCATTTTT
20909987 TCAGAGTGCC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTTTTCATTTTTCATTCTC
Found at i:20910958 original size:14 final size:14
Alignment explanation
Indices: 20910934--20910980 Score: 60
Period size: 14 Copynumber: 3.4 Consensus size: 14
20910924 TCTTGATTTG
20910934 ATTTTTC-TTTTTT
1 ATTTTTCTTTTTTT
*
20910947 CTTTTTCTTTTTTT
1 ATTTTTCTTTTTTT
**
20910961 ATTTTGATTTTTTT
1 ATTTTTCTTTTTTT
20910975 ATTTTT
1 ATTTTT
20910981 TTCATTTTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
13 6 0.21
14 22 0.79
ACGTcount: A:0.09, C:0.06, G:0.02, T:0.83
Consensus pattern (14 bp):
ATTTTTCTTTTTTT
Found at i:20910965 original size:13 final size:13
Alignment explanation
Indices: 20910936--20910979 Score: 54
Period size: 13 Copynumber: 3.3 Consensus size: 13
20910926 TTGATTTGAT
20910936 TTTTCTTTTTTCT-
1 TTTTCTTTTTT-TA
20910949 TTTTCTTTTTTTA
1 TTTTCTTTTTTTA
*
20910962 TTTTGATTTTTTTA
1 TTTT-CTTTTTTTA
20910976 TTTT
1 TTTT
20910980 TTTCATTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 1 0.04
13 15 0.54
14 12 0.43
ACGTcount: A:0.07, C:0.07, G:0.02, T:0.84
Consensus pattern (13 bp):
TTTTCTTTTTTTA
Found at i:20919312 original size:24 final size:24
Alignment explanation
Indices: 20919262--20919316 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
20919252 GACTGCGCAA
*
20919262 GAAGGAGCTGGTGAGAGCGTTAGT
1 GAAGGAGCTGGTGAGAGCGTGAGT
*
20919286 GAAGGTGCTGGTGAGAGCGCTGA-T
1 GAAGGAGCTGGTGAGAGCG-TGAGT
20919310 GAAGGAG
1 GAAGGAG
20919317 AGAGGAGAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
24 25 0.93
25 2 0.07
ACGTcount: A:0.25, C:0.09, G:0.47, T:0.18
Consensus pattern (24 bp):
GAAGGAGCTGGTGAGAGCGTGAGT
Found at i:20920598 original size:4 final size:4
Alignment explanation
Indices: 20920589--20920613 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
20920579 TAGAGAGTGC
20920589 AAAG AAAG AAAG AAAG AAAG AAAG A
1 AAAG AAAG AAAG AAAG AAAG AAAG A
20920614 GACAGATACT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:20926511 original size:61 final size:61
Alignment explanation
Indices: 20926424--20926569 Score: 154
Period size: 61 Copynumber: 2.4 Consensus size: 61
20926414 TTACATCCTA
* * * * ** *
20926424 TCAATTT-GATCCTAAATATAATAAATTTAATAAATTT-AGCCTTCAATGTGTAC-AAATTTTG
1 TCAATTTAG-TCCTAATTCTAAAAAATTTAATAAATTTGA-CCCTCAACATGTACGAAA-TCTG
* * *
20926485 TCATTTTAGTTCTAATTCTAAAAAATTTAATAAATTTGACCCTCAACATTTACGAAATCTG
1 TCAATTTAGTCCTAATTCTAAAAAATTTAATAAATTTGACCCTCAACATGTACGAAATCTG
20926546 TCAATTTAGTCCTAATTCTAAAAA
1 TCAATTTAGTCCTAATTCTAAAAA
20926570 TTAAAAATTA
Statistics
Matches: 70, Mismatches: 12, Indels: 6
0.80 0.14 0.07
Matches are distributed among these distances:
61 65 0.93
62 5 0.07
ACGTcount: A:0.39, C:0.14, G:0.07, T:0.40
Consensus pattern (61 bp):
TCAATTTAGTCCTAATTCTAAAAAATTTAATAAATTTGACCCTCAACATGTACGAAATCTG
Found at i:20926890 original size:60 final size:58
Alignment explanation
Indices: 20926764--20926890 Score: 137
Period size: 60 Copynumber: 2.1 Consensus size: 58
20926754 ATGATTTTAA
* * * * * *
20926764 AATTTTTAGAGTTAGGACTAAATTGACAGGTTTGTAAGTATTGAGGGCCAAATTTATT
1 AATTTTTAGAATTAGAACTAAAATGACAAGTTTATAAGCATTGAGGGCCAAATTTATT
* * *
20926822 AATCTTTTTAGAATTAGAACTAAAATGACAAATTTTATAAGCATTGAGGGCTAAATTTGTT
1 AA--TTTTTAGAATTAGAACTAAAATGAC-AAGTTTATAAGCATTGAGGGCCAAATTTATT
20926883 GAATTTTT
1 -AATTTTT
20926891 TAAATTTAGG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
58 2 0.04
60 27 0.48
61 25 0.45
62 2 0.04
ACGTcount: A:0.35, C:0.07, G:0.18, T:0.39
Consensus pattern (58 bp):
AATTTTTAGAATTAGAACTAAAATGACAAGTTTATAAGCATTGAGGGCCAAATTTATT
Found at i:20927602 original size:13 final size:13
Alignment explanation
Indices: 20927584--20927608 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20927574 TAAAAATCAT
20927584 AAAATTTATAAAC
1 AAAATTTATAAAC
20927597 AAAATTTATAAA
1 AAAATTTATAAA
20927609 AATTTTAAAA
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATTTATAAAC
Found at i:20930573 original size:14 final size:15
Alignment explanation
Indices: 20930542--20930575 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
20930532 AAGTAAAATT
*
20930542 AAAAAAGAAAAGTTA
1 AAAAAAGAAAAGTAA
20930557 AAAAAAGAAAAG-AA
1 AAAAAAGAAAAGTAA
20930571 AAAAA
1 AAAAA
20930576 TTTAAATTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (15 bp):
AAAAAAGAAAAGTAA
Found at i:20939401 original size:27 final size:28
Alignment explanation
Indices: 20939346--20939423 Score: 122
Period size: 27 Copynumber: 2.8 Consensus size: 28
20939336 GCGTGTCTCC
*
20939346 TATTTTTTAGATTTTATAGTTTTACCCT
1 TATTTTTTAGATTTTACAGTTTTACCCT
*
20939374 TATTTTTTAGATTCTACAGTTTTA-CCT
1 TATTTTTTAGATTTTACAGTTTTACCCT
*
20939401 TGTTTTTTAGATTTTACAGTTTT
1 TATTTTTTAGATTTTACAGTTTT
20939424 GTCTCTTGCT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
27 24 0.52
28 22 0.48
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (28 bp):
TATTTTTTAGATTTTACAGTTTTACCCT
Found at i:20940192 original size:9 final size:9
Alignment explanation
Indices: 20940173--20940227 Score: 50
Period size: 9 Copynumber: 6.8 Consensus size: 9
20940163 AATTATAAAT
20940173 AATTA-TTA
1 AATTATTTA
20940181 AATTATTTA
1 AATTATTTA
20940190 AATT-TTT-
1 AATTATTTA
20940197 --TTATTTA
1 AATTATTTA
*
20940204 AATTA-CTA
1 AATTATTTA
*
20940212 AACTATTTA
1 AATTATTTA
20940221 AATTATT
1 AATTATT
20940228 GTTGTACGGC
Statistics
Matches: 37, Mismatches: 4, Indels: 11
0.71 0.08 0.21
Matches are distributed among these distances:
5 2 0.05
6 3 0.08
8 14 0.38
9 18 0.49
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (9 bp):
AATTATTTA
Found at i:20941057 original size:17 final size:16
Alignment explanation
Indices: 20941023--20941078 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
20941013 AGTATTGAAT
20941023 TATTAATATCTTAATA
1 TATTAATATCTTAATA
20941039 TATTAA-ATCTTTAA-A
1 TATTAATATC-TTAATA
*
20941054 TA-TAATATTTTAAATA
1 TATTAATATCTT-AATA
*
20941070 TTTTAATAT
1 TATTAATAT
20941079 AAAAATTAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 5 0.15
15 10 0.30
16 12 0.36
17 6 0.18
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.52
Consensus pattern (16 bp):
TATTAATATCTTAATA
Found at i:20941066 original size:22 final size:22
Alignment explanation
Indices: 20941034--20941088 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
20941024 ATTAATATCT
*
20941034 TAATATATTAAATCTTTAAATA
1 TAATATATTAAATATTTAAATA
* *
20941056 TAATATTTTAAATATTTTAATA
1 TAATATATTAAATATTTAAATA
*
20941078 TAA-AAATTAAA
1 TAATATATTAAA
20941089 AAATTTTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATATTAAATATTTAAATA
Found at i:20942951 original size:16 final size:16
Alignment explanation
Indices: 20942906--20942952 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
20942896 TGAATTTCAG
*
20942906 TTTATATTTCTTTTTC
1 TTTATATTTATTTTTC
20942922 TTT-TATTTACTTTTATC
1 TTTATATTTA-TTTT-TC
20942939 TTTAT-TTTATTTTT
1 TTTATATTTATTTTT
20942953 TTCCTCTCCA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
15 6 0.22
16 11 0.41
17 9 0.33
18 1 0.04
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTATATTTATTTTTC
Found at i:20948502 original size:23 final size:22
Alignment explanation
Indices: 20948463--20948510 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
20948453 CAGGCTATAA
*
20948463 TTTTTCAATGTTCTA-TTAATGT
1 TTTTTCAAGGTTCTATTTAAT-T
*
20948485 TTTTTTAAGGTTCTTATTTAATT
1 TTTTTCAAGGTTC-TATTTAATT
20948508 TTT
1 TTT
20948511 AATTGTTGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 11 0.50
23 6 0.27
24 5 0.23
ACGTcount: A:0.21, C:0.06, G:0.08, T:0.65
Consensus pattern (22 bp):
TTTTTCAAGGTTCTATTTAATT
Found at i:20948546 original size:23 final size:25
Alignment explanation
Indices: 20948520--20948581 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 25
20948510 TAATTGTTGG
*
20948520 TTTTATTTTTATTTATT-TTC-AAT
1 TTTTATTTTTATCTATTCTTCTAAT
*
20948543 TTTT-TCTTTTATCTCTTCTTCTAAT
1 TTTTAT-TTTTATCTATTCTTCTAAT
20948568 TTTTAATTATTTAT
1 TTTT-ATT-TTTAT
20948582 GTCAAGTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
22 1 0.03
23 13 0.42
24 3 0.10
25 7 0.23
26 1 0.03
27 6 0.19
ACGTcount: A:0.19, C:0.10, G:0.00, T:0.71
Consensus pattern (25 bp):
TTTTATTTTTATCTATTCTTCTAAT
Found at i:20950908 original size:21 final size:19
Alignment explanation
Indices: 20950866--20950909 Score: 52
Period size: 19 Copynumber: 2.2 Consensus size: 19
20950856 AGTTAGATCA
* *
20950866 TGAATCAATACAAACTGAT
1 TGAATCAATAAAAAATGAT
20950885 TGAATCAACTAAAAAATCGAT
1 TGAATCAA-TAAAAAAT-GAT
20950906 TGAA
1 TGAA
20950910 CTAGATCTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 8 0.38
20 6 0.29
21 7 0.33
ACGTcount: A:0.50, C:0.14, G:0.11, T:0.25
Consensus pattern (19 bp):
TGAATCAATAAAAAATGAT
Found at i:20951517 original size:23 final size:23
Alignment explanation
Indices: 20951470--20951542 Score: 80
Period size: 23 Copynumber: 3.2 Consensus size: 23
20951460 AGTATGCCAT
20951470 AAAGACATCACAAGAA-ACG-CAAC
1 AAAGACATCACAA-AATACGAC-AC
*
20951493 AAATACATCACAAAATACGACAC
1 AAAGACATCACAAAATACGACAC
*
20951516 AAAGGCATCACAAAATAC-ACCAC
1 AAAGACATCACAAAATACGA-CAC
20951539 AAAG
1 AAAG
20951543 GTTTTCTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
22 3 0.07
23 40 0.91
24 1 0.02
ACGTcount: A:0.56, C:0.26, G:0.10, T:0.08
Consensus pattern (23 bp):
AAAGACATCACAAAATACGACAC
Found at i:20958964 original size:27 final size:27
Alignment explanation
Indices: 20958924--20958978 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
20958914 TATAATTTCT
*
20958924 ATCAATTAACCATTTCAAACACATACC
1 ATCAATCAACCATTTCAAACACATACC
*
20958951 ATCAATCAATCATTTCAAACACATACC
1 ATCAATCAACCATTTCAAACACATACC
20958978 A
1 A
20958979 AACATAACCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (27 bp):
ATCAATCAACCATTTCAAACACATACC
Found at i:20959873 original size:26 final size:26
Alignment explanation
Indices: 20959844--20959996 Score: 85
Period size: 26 Copynumber: 6.2 Consensus size: 26
20959834 TCCGCTCTCA
20959844 AGCCATATAATAGGAAGCTCACAAAG
1 AGCCATATAATAGGAAGCTCACAAAG
*
20959870 AGCCAT-TAATTGAGAAGCTCACAAAG
1 AGCCATATAATAG-GAAGCTCACAAAG
* *
20959896 AG-C-T-T-ATCAGGAAGCTTATC--TG
1 AGCCATATAAT-AGGAAGCTCA-CAAAG
* *
20959918 -GCTATATAATAGGAAGCTCA-TAAG
1 AGCCATATAATAGGAAGCTCACAAAG
* * *
20959942 AGCCATA-ATTAGGAAGTTCATAAAG
1 AGCCATATAATAGGAAGCTCACAAAG
* * * *
20959967 A-ACTTTTAATCAGGAAGCTCACGAAG
1 AGCCATATAAT-AGGAAGCTCACAAAG
20959993 AGCC
1 AGCC
20959997 TTTAATCAAG
Statistics
Matches: 94, Mismatches: 19, Indels: 27
0.67 0.14 0.19
Matches are distributed among these distances:
21 1 0.01
22 1 0.01
23 10 0.11
24 28 0.30
25 19 0.20
26 34 0.36
27 1 0.01
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.22
Consensus pattern (26 bp):
AGCCATATAATAGGAAGCTCACAAAG
Found at i:20961121 original size:30 final size:30
Alignment explanation
Indices: 20961087--20961241 Score: 151
Period size: 30 Copynumber: 5.2 Consensus size: 30
20961077 TTTTTTTTTG
* *
20961087 CATTTTAACCCCTATACTTTTCAAAATTTA
1 CATTTTGACCCCTAAACTTTTCAAAATTTA
*
20961117 CATTTTAACCCC-AAACTTTTCTAAAATTTA
1 CATTTTGACCCCTAAACTTTTC-AAAATTTA
* *
20961147 CATTTTGACCCCAAAACATTTT-GAAA-TTA
1 CATTTTGACCCCTAAAC-TTTTCAAAATTTA
*
20961176 CA-TTTGACCCCTAGACTTTCTCAAAATTT-
1 CATTTTGACCCCTAAACTTT-TCAAAATTTA
* * *
20961205 CACTTTGACCCCTAAAC-TCTCAAGAAATTA
1 CATTTTGACCCCTAAACTTTTCAA-AATTTA
20961235 CATTTTG
1 CATTTTG
20961242 GCCTATATTT
Statistics
Matches: 106, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
27 3 0.03
28 17 0.16
29 23 0.22
30 55 0.52
31 4 0.04
32 4 0.04
ACGTcount: A:0.34, C:0.25, G:0.05, T:0.37
Consensus pattern (30 bp):
CATTTTGACCCCTAAACTTTTCAAAATTTA
Found at i:20961839 original size:26 final size:25
Alignment explanation
Indices: 20961793--20961867 Score: 68
Period size: 26 Copynumber: 3.1 Consensus size: 25
20961783 TTCAGCCCCG
*
20961793 AAGAGGAAGGAAAAAAAAGAAAGAAA
1 AAGAAGAAGGAAAAAAAAG-AAGAAA
*
20961819 AAGAAGAA-GAAAAATAGAGAAG-AA
1 AAGAAGAAGGAAAAA-AAAGAAGAAA
* *
20961843 AGGAAG--GGAAAAAAAAGAAAAAA
1 AAGAAGAAGGAAAAAAAAGAAGAAA
20961866 AA
1 AA
20961868 TATATTTTTT
Statistics
Matches: 40, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
22 5 0.12
23 9 0.22
24 7 0.17
25 9 0.22
26 10 0.25
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.01
Consensus pattern (25 bp):
AAGAAGAAGGAAAAAAAAGAAGAAA
Found at i:20961989 original size:22 final size:20
Alignment explanation
Indices: 20961958--20961998 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
20961948 CAGCAGCTCA
20961958 AAACAACAGCCCAAAAAAAAAG
1 AAACAACAG--CAAAAAAAAAG
*
20961980 AAACAGCAGCAAAAAAAAA
1 AAACAACAGCAAAAAAAAA
20961999 TAGCAGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.71, C:0.20, G:0.10, T:0.00
Consensus pattern (20 bp):
AAACAACAGCAAAAAAAAAG
Found at i:20961993 original size:16 final size:16
Alignment explanation
Indices: 20961973--20962006 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
20961963 ACAGCCCAAA
20961973 AAAAAAGAAACAGCAGC
1 AAAAAA-AAACAGCAGC
*
20961990 AAAAAAAAATAGCAGC
1 AAAAAAAAACAGCAGC
20962006 A
1 A
20962007 GACCACCCAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.68, C:0.15, G:0.15, T:0.03
Consensus pattern (16 bp):
AAAAAAAAACAGCAGC
Found at i:20962131 original size:18 final size:19
Alignment explanation
Indices: 20962108--20962150 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
20962098 TAAAATCGTG
20962108 TTTCAAAAATTT-TCATGT
1 TTTCAAAAATTTCTCATGT
*
20962126 TTTC-AAAATTTCTCGTGT
1 TTTCAAAAATTTCTCATGT
20962144 TTT-AAAA
1 TTTCAAAA
20962151 TAATAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.49
Consensus pattern (19 bp):
TTTCAAAAATTTCTCATGT
Found at i:20962133 original size:17 final size:18
Alignment explanation
Indices: 20962108--20962151 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
20962098 TAAAATCGTG
20962108 TTTCAAAAATTT-TCATGT
1 TTTC-AAAATTTCTCATGT
*
20962126 TTTCAAAATTTCTCGTGT
1 TTTCAAAATTTCTCATGT
20962144 TTT-AAAAT
1 TTTCAAAAT
20962152 AATAATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.32, C:0.11, G:0.07, T:0.50
Consensus pattern (18 bp):
TTTCAAAATTTCTCATGT
Found at i:20962434 original size:18 final size:17
Alignment explanation
Indices: 20962401--20962585 Score: 76
Period size: 18 Copynumber: 10.6 Consensus size: 17
20962391 AAAATAAATA
20962401 AAAAATTTCATGTTTTC
1 AAAAATTTCATGTTTTC
*
20962418 AAAAATTTCGTGTTTTTC
1 AAAAATTTCATG-TTTTC
* * ****
20962436 AAAATTTTTCTTGTCAAA
1 AAAA-ATTTCATGTTTTC
*
20962454 AAAAATATCTCATG-TATC
1 AAAAAT-T-TCATGTTTTC
*
20962472 GAAAAA-ATCATG-TTTC
1 -AAAAATTTCATGTTTTC
*
20962488 AAAAATTTTCATGTTTTT
1 AAAAA-TTTCATGTTTTC
* **
20962506 AAAAGTTTTCGCGTTTTC
1 AAAA-ATTTCATGTTTTC
**
20962524 AAAAAAATC-TCGTGTTTC
1 AAAAATTTCAT-GT-TTTC
* *
20962542 -AAATTTTCGTGTTTTC
1 AAAAATTTCATGTTTTC
20962558 AAAAATTTC-TCGTATTTC
1 AAAAATTTCAT-GT-TTTC
20962576 AAAAATTTCA
1 AAAAATTTCA
20962586 CTTTTTGCGT
Statistics
Matches: 124, Mismatches: 28, Indels: 30
0.68 0.15 0.16
Matches are distributed among these distances:
15 5 0.04
16 13 0.10
17 37 0.30
18 54 0.44
19 15 0.12
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (17 bp):
AAAAATTTCATGTTTTC
Found at i:20962529 original size:52 final size:51
Alignment explanation
Indices: 20962473--20962580 Score: 121
Period size: 52 Copynumber: 2.1 Consensus size: 51
20962463 TCATGTATCG
* *
20962473 AAAAAA-TCATGTTTCAAAAATTTTCATGTTTTTAAAAGTTTTCGCGT-TTTCA
1 AAAAAACTCATGTTTC--AAATTTTCATGTTTTCAAAA-ATTTCGCGTATTTCA
* * *
20962525 AAAAAATCTCGTGTTTCAAATTTTCGTGTTTTCAAAAATTTCTCGTATTTCA
1 AAAAAA-CTCATGTTTCAAATTTTCATGTTTTCAAAAATTTCGCGTATTTCA
20962577 AAAA
1 AAAA
20962581 TTTCACTTTT
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
51 7 0.15
52 33 0.69
54 8 0.17
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.43
Consensus pattern (51 bp):
AAAAAACTCATGTTTCAAATTTTCATGTTTTCAAAAATTTCGCGTATTTCA
Found at i:20962556 original size:34 final size:34
Alignment explanation
Indices: 20962511--20962578 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
20962501 TTTTTAAAAG
*
20962511 TTTTCGCGTTTTCAAAAAAATCTCGTGTTTCAAA
1 TTTTCGCGTTTTCAAAAAAATCTCGTATTTCAAA
* **
20962545 TTTTCGTGTTTTCAAAAATTTCTCGTATTTCAAA
1 TTTTCGCGTTTTCAAAAAAATCTCGTATTTCAAA
20962579 AATTTCACTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.28, C:0.16, G:0.10, T:0.46
Consensus pattern (34 bp):
TTTTCGCGTTTTCAAAAAAATCTCGTATTTCAAA
Found at i:20962726 original size:34 final size:33
Alignment explanation
Indices: 20962688--20962990 Score: 266
Period size: 34 Copynumber: 8.9 Consensus size: 33
20962678 AAATGTGTCG
*
20962688 TGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCC
1 TGTTTTAAAAATTTTCGTATTTCTAAAATTT-CC
** * * *
20962722 TGTTTTAAAAATTCCCGTATTCCAAAAAATGTT-G
1 TGTTTTAAAAATTTTCGTATTTC-TAAAAT-TTCC
*
20962756 TGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCC
1 TGTTTTAAAAATTTTCGTATTTCTAAAATTT-CC
** * * *
20962790 TGTTTTAAAAATTCCCGTATTCCAAAAATTGTCG
1 TGTTTTAAAAATTTTCGTATTTCTAAAATT-TCC
20962824 TGTTTTAAAAATTTTCGTATTTCTAAAATTTCCC
1 TGTTTTAAAAATTTTCGTATTTCTAAAATTT-CC
** * * * *
20962858 TGTTTTAAAAATTCCCGTATTCCAAAAAAATGTCG
1 TGTTTTAAAAATTTTCGTATTTC--TAAAATTTCC
*
20962893 TGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCC
1 TGTTTTAAAAATTTTCGTATTTCTAAAATTT-CC
* * * * *
20962927 TATTTTAAAAATTCTCGTATTCCAAAAATTGTCG
1 TGTTTTAAAAATTTTCGTATTTCTAAAATT-TCC
* * *
20962961 TGTTTTAAAAATTTTCTTGTTTTTAAAATT
1 TGTTTTAAAAATTTTCGTATTTCTAAAATT
20962991 CTCGTATTTC
Statistics
Matches: 210, Mismatches: 49, Indels: 20
0.75 0.18 0.07
Matches are distributed among these distances:
32 2 0.01
33 12 0.06
34 161 0.77
35 27 0.13
36 8 0.04
ACGTcount: A:0.31, C:0.14, G:0.09, T:0.46
Consensus pattern (33 bp):
TGTTTTAAAAATTTTCGTATTTCTAAAATTTCC
Found at i:20963022 original size:68 final size:68
Alignment explanation
Indices: 20962676--20962990 Score: 540
Period size: 68 Copynumber: 4.6 Consensus size: 68
20962666 TAGTGTTTCA
20962676 AAAAATGTGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTA
1 AAAAAT-TGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTA
20962741 TTCC
65 TTCC
* *
20962745 AAAAAATGTTGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTAT
1 AAAAATTGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTAT
20962810 TCC
66 TCC
*
20962813 AAAAATTGTCGTGTTTTAAAAATTTTCGTATTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTAT
1 AAAAATTGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTAT
20962878 TCC
66 TCC
* * *
20962881 AAAAAAATGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTATTTTAAAAATTCTCGTA
1 -AAAAATTGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTA
20962946 TTCC
65 TTCC
* *
20962950 AAAAATTGTCGTGTTTTAAAAATTTTCTTGTTTTTAAAATT
1 AAAAATTGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATT
20962991 CTCGTATTTC
Statistics
Matches: 233, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
68 164 0.70
69 69 0.30
ACGTcount: A:0.31, C:0.14, G:0.10, T:0.45
Consensus pattern (68 bp):
AAAAATTGTCGTGTTTTAAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTAT
TCC
Found at i:20963052 original size:17 final size:17
Alignment explanation
Indices: 20962668--20963054 Score: 209
Period size: 17 Copynumber: 22.4 Consensus size: 17
20962658 TAAAAAAATA
*
20962668 GTGTTTCAAAAAATGTGTC
1 GTGTTTC-AAAAAT-TTTC
*
20962687 GTGTTTTAAAAATTTTC
1 GTGTTTCAAAAATTTTC
* *
20962704 GTGTTTCTAAAATTTCC
1 GTGTTTCAAAAATTTTC
* * **
20962721 CTGTTTTAAAAATTCCC
1 GTGTTTCAAAAATTTTC
* * *
20962738 GTATTCCAAAAAATGTT-
1 GTGTTTC-AAAAATTTTC
*
20962755 GTGTTTTAAAAATTTTC
1 GTGTTTCAAAAATTTTC
* *
20962772 GTGTTTCTAAAATTTCC
1 GTGTTTCAAAAATTTTC
* * **
20962789 CTGTTTTAAAAATTCCC
1 GTGTTTCAAAAATTTTC
* * *
20962806 GTATTCCAAAAATTGTC
1 GTGTTTCAAAAATTTTC
*
20962823 GTGTTTTAAAAATTTTC
1 GTGTTTCAAAAATTTTC
* * *
20962840 GTATTTCTAAAATTTCC
1 GTGTTTCAAAAATTTTC
* * **
20962857 CTGTTTTAAAAATTCCC
1 GTGTTTCAAAAATTTTC
* * * *
20962874 GTATTCCAAAAAAATGTC
1 GTGTTTC-AAAAATTTTC
*
20962892 GTGTTTTAAAAATTTTC
1 GTGTTTCAAAAATTTTC
* *
20962909 GTGTTTCTAAAATTTCC
1 GTGTTTCAAAAATTTTC
* * * *
20962926 CTATTTTAAAAATTCTC
1 GTGTTTCAAAAATTTTC
* * *
20962943 GTATTCCAAAAATTGTC
1 GTGTTTCAAAAATTTTC
*
20962960 GTGTTTTAAAAATTTTC
1 GTGTTTCAAAAATTTTC
* ** *
20962977 TTGTTTTTAAAATTCTC
1 GTGTTTCAAAAATTTTC
* * *
20962994 GTATTTCAAAAGTTTCC
1 GTGTTTCAAAAATTTTC
* *
20963011 GTGTTTCAAAAAAAAATTCTA
1 GTGTTTC----AAAAATTTTC
*
20963032 GTGTTTCAAAAATTTTT
1 GTGTTTCAAAAATTTTC
20963049 GTGTTT
1 GTGTTT
20963055 TTTTAATTGT
Statistics
Matches: 269, Mismatches: 92, Indels: 16
0.71 0.24 0.04
Matches are distributed among these distances:
16 8 0.03
17 219 0.81
18 23 0.09
19 6 0.02
21 13 0.05
ACGTcount: A:0.31, C:0.14, G:0.11, T:0.45
Consensus pattern (17 bp):
GTGTTTCAAAAATTTTC
Found at i:20969616 original size:78 final size:75
Alignment explanation
Indices: 20969504--20970548 Score: 860
Period size: 74 Copynumber: 13.7 Consensus size: 75
20969494 CACTTTCTGT
*
20969504 TTTTTTTTTCAAATATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 TTTTTTTTT-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
20969569 TTTAATTTATG
65 TTTAATTTATG
20969580 TATTTTTTTTAAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA
1 T-TTTTTTTT--AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA
20969645 -TTTTAATTTATG
63 TTTTTAATTTATG
** * * *
20969657 CCTTTTTTT-AAAATCAACTCATAATACAGAGGTGAGTTGAGTCTTGGGTCACGCTGAGGTGTTT
1 TTTTTTTTTAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
20969721 TTAATTTCA-G
66 TTAATTT-ATG
* *
20969731 TCTTTTTTT-AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGATATTT
1 TTTTTTTTTAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
**
20969795 TTAATTTCGG
66 TTAATTTATG
*
20969805 TCTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 T-TTTTTTTTAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
*
20969870 TTTAAATTCA-G
65 TTT-AATTTATG
*
20969881 TCTTTTTTTT--AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGATGTATT
1 T-TTTTTTTTAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
**
20969944 TTTAATTCCTG
65 TTTAATTTATG
* * *
20969955 TCTTTTTTT--AAATCAACTCATAATATGAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTATT
1 TTTTTTTTTAAAAATCAACTCATAATA-CAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--
*
20970018 TCTTTTAAATTTTTG
63 T-TTTT-AATTTATG
* ** ** * *
20970033 TTTTTTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGG
1 -TTTTTTTTT---AAAAATCAACTCATAAT-ACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG
20970098 TATTTCTTTTAAATTTATG
61 TA--T-TTTT-AATTTATG
** * * * ** *
20970117 --TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGACCATGCTGAGGTATT
1 TTTTTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--
20970180 TCTTTTAAATTTATG
63 T-TTTT-AATTTATG
** * * ** * * *
20970195 --TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGATGTATT
1 TTTTTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--
*
20970258 TCTTTTAAATTTCTG
63 T-TTTT-AATTTATG
*** * * * ** * *
20970273 -TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGGTATT
1 TTTTTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
* **
20970337 TCT--TTTAAA
65 TTTAATTTATG
* * * *
20970346 TTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGAGTCACGCCGAGGT
1 TTT-T-TTTTT-AAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGT
*
20970411 ATTTTTCAATTCATG
62 ATTTTT-AATTTATG
* * * * *
20970426 ---TTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACATG-TCGAGGT
1 TTTTTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCAC--GCT-GAGGT
**
20970486 ATTTTCGA-TT-T-
62 ATTTTTAATTTATG
* ** * * *
20970497 TTGTTTTTCGAAGATCAACTCATAATCCAAGAGGTGAGTTGAGTCTCGGGTC
1 TTTTTTTTTAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTC
20970549 GCACGCCGAG
Statistics
Matches: 854, Mismatches: 78, Indels: 75
0.85 0.08 0.07
Matches are distributed among these distances:
72 1 0.00
73 84 0.10
74 249 0.29
75 25 0.03
76 82 0.10
77 82 0.10
78 198 0.23
79 65 0.08
80 3 0.00
81 5 0.01
84 60 0.07
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (75 bp):
TTTTTTTTTAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
TTAATTTATG
Found at i:20969862 original size:150 final size:149
Alignment explanation
Indices: 20969486--20970548 Score: 820
Period size: 150 Copynumber: 6.9 Consensus size: 149
20969476 CTTTCAAGAA
* *
20969486 ATATTTTTCACTTTCTGTTTTTTTTTTCAAATATCAACTCATAATACAGAGGTGAGTTGAGCCTC
1 ATATTTTT-AATTTCTGTCTTTTTTTT-AAA-ATCAACTCATAATACAGAGGTGAGTTGAGCCTC
*
20969551 GGGTCACGCTGAGGTATTTTTAATTT-ATGTATTTTTTTTAAAAAAATCAACTCATAATACAGAG
63 GGGTCACGCTGAGGTATTTTTAATTTCA-GT-CTTTTTTT---AAAATCAACTCATAATACAGAG
20969615 GTGAGTTGAGCCTCGGGTCACGCTGAG
123 GTGAGTTGAGCCTCGGGTCACGCTGAG
* * * * *
20969642 GTA-TTTTAATTTATG-CCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGTCTTGGG
1 ATATTTTTAATTTCTGTCTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
*
20969705 TCACGCTGAGGTGTTTTTAATTTCAGTCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTG
66 TCACGCTGAGGTATTTTTAATTTCAGTCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTG
20969770 AGCCTCGGGTCACGCTGAG
131 AGCCTCGGGTCACGCTGAG
*
20969789 ATATTTTTAATTTCGGTCTTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
1 ATATTTTTAATTTCTGTC-TTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
* *
20969854 GTCACGCTGAGGTATTTTTAAATTCAGTCTTTTTTTTAAATCAACTCATAATACAGAGGTGAGTT
65 GTCACGCTGAGGTATTTTTAATTTCAGTCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTT
20969919 GAGCCTCGGGTCACGCTGATG
130 GAGCCTCGGGTCACGCTGA-G
* * *
20969940 -TATTTTTAATTCCTGTC-TTTTTTT-AAATCAACTCATAATATGAGAGGTGAGTTGAGCCTCAG
1 ATATTTTTAATTTCTGTCTTTTTTTTAAAATCAACTCATAATA-CAGAGGTGAGTTGAGCCTCGG
** * * **
20970002 GTCACGCTGAGGTATTTCTTTTAAATTTTTGTTTTTTTTTTCAAAAAAATCAACTCATATTGTGA
65 GTCACGCTGAGGTA--T-TTTT-AATTTCAG-TCTTTTTTT----AAAATCAACTCATAAT-ACA
** * *
20970067 GAGGTGAGTTGAGCCTCGGACCATGCCGAGG
120 GAGGTGAGTTGAGCCTCGGGTCACGCTGA-G
* * *** * * *
20970098 TATTTCTTTTAAATTTATG--TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCT
1 -ATAT-TTTT-AATTTCTGTCTTTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCT
** * *** * *
20970161 CGGACCATGCTGAGGTATTTCTTTTAAATTT-ATGT-TTTTCAAAAAATCAACTCATATTGCGAG
62 CGGGTCACGCTGAGGTA--T-TTTT-AATTTCA-GTCTTTTTTTAAAATCAACTCATAATAC-AG
** * *
20970224 AGGTGAGTTGAGCCTCGGACCATGCCGATG
121 AGGTGAGTTGAGCCTCGGGTCACGCTGA-G
* **** * *
20970254 TATTTCTTTTAAATTTCTGT-TTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 -ATAT-TTTT-AATTTCTGTCTTTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCT
* ** * * * ** * *
20970318 TGGACCATGCCGAGGTATTTCTTTTAAATTTC--TATTTTTCAAAAATCAACTCATATTGCGAGA
62 CGGGTCACGCTGAGGTA--T-TTTT-AATTTCAGTCTTTTTTTAAAATCAACTCATAATAC-AGA
* *
20970381 GGTGAGTTGAGCCTCGAGTCACGCCGAG
122 GGTGAGTTGAGCCTCGGGTCACGCTGAG
* * * *
20970409 GTATTTTTCAA-TTCATG----TTTTTCAAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 ATATTTTT-AATTTC-TGTCTTTTTTTTAAA-ATCAACTCATAATAC-AGAGGTGAGTTGAGCCT
* ** * * ** * *
20970469 CAGG-CACATG-TCGAGGTATTTTCGATTT--TTGTTTTTCGAAGATCAACTCATAATCCAAGAG
62 CGGGTCAC--GCT-GAGGTATTTTTAATTTCAGTCTTTTTTTAAAATCAACTCATAATAC-AGAG
*
20970530 GTGAGTTGAGTCTCGGGTC
123 GTGAGTTGAGCCTCGGGTC
20970549 GCACGCCGAG
Statistics
Matches: 783, Mismatches: 90, Indels: 76
0.83 0.09 0.08
Matches are distributed among these distances:
147 67 0.09
148 97 0.12
149 4 0.01
150 155 0.20
151 97 0.12
152 19 0.02
153 23 0.03
154 8 0.01
155 6 0.01
156 117 0.15
157 84 0.11
158 27 0.03
160 6 0.01
161 9 0.01
162 64 0.08
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (149 bp):
ATATTTTTAATTTCTGTCTTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGG
TCACGCTGAGGTATTTTTAATTTCAGTCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTG
AGCCTCGGGTCACGCTGAG
Found at i:20970257 original size:156 final size:153
Alignment explanation
Indices: 20969508--20970469 Score: 783
Period size: 156 Copynumber: 6.3 Consensus size: 153
20969498 TTCTGTTTTT
* * * **
20969508 TTTTTC-AAATATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT-
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTATTTC
* * * * * * **
20969570 TTAATT-TATGTATTTTTTTTAAAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGT
66 TT--TTAAATTTA-TGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGAC
* *
20969633 CACGCTGAGGTA-TTTT-AATTTATG
128 CACGCCGAGGTATTTTTAAATTCATG
** * * * * ** *
20969657 CCTTTTT-TTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGTCTTGGGTCACGCTGAGG--TG
1 --TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTATT
*** * * *
20969718 T-TTTT-AATTTCA-GTCTTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGG
64 TCTTTTAAATTT-ATGT-TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA
* * * * * *
20969779 TCACGCTGAGATATTTTTAATTTCGGTCT
127 CCACGCCGAGGTATTTTTAAATTC-AT-G
*** * * **
20969808 TTTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTATTTC
* **** * * **
20969869 TTTTAAATTCA-GTCTTTTTTTTAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCA
66 TTTTAAATTTATGT-TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCA
* * *
20969932 CGCTGATGTATTTTT-AATTCCTG
130 CGCCGAGGTATTTTTAAATTCATG
*** * ** *
20969955 TCTTTT-TTTAAATCAACTCATAATATGAGAGGTGAGTTGAGCCTCAGG-TCACGCTGAGGTATT
1 T-TTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACCACGCTGAGGTATT
* *
20970018 TCTTTTAAATTTTTGTTTTTTTTTTCAAAAAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCT
64 TCTTTTAAATTTATG-----TTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
* *
20970083 CGGACCATGCCGAGGTATTTCTTTTAAATTTATG
123 CGGACCACGCCGAGGTA--T-TTTTAAATTCATG
* *
20970117 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGACCATGCTGAGGTATTTC
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTATTTC
*
20970182 TTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCAT
66 TTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCAC
*
20970247 GCCGATGTATTTCTTTTAAATTTC-TG
131 GCCGAGGTA--T-TTTTAAA-TTCATG
* * *
20970273 TTTTTCAAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGGTATTT
1 TTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTATTT
* * *
20970338 CTTTTAAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GAGTC
65 CTTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA-CC
*
20970401 ACGCCGAGGTATTTTTCAATTCATG
129 ACGCCGAGGTATTTTTAAATTCATG
*
20970426 TTTTTC-AAAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
1 TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
20970470 AGGCACATGT
Statistics
Matches: 709, Mismatches: 67, Indels: 70
0.84 0.08 0.08
Matches are distributed among these distances:
146 1 0.00
147 79 0.11
148 41 0.06
149 18 0.03
150 122 0.17
151 101 0.14
152 4 0.01
153 14 0.02
154 1 0.00
155 2 0.00
156 124 0.17
157 96 0.14
158 29 0.04
160 1 0.00
161 10 0.01
162 66 0.09
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (153 bp):
TTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCTGAGGTATTTC
TTTTAAATTTATGTTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCAC
GCCGAGGTATTTTTAAATTCATG
Found at i:20970336 original size:79 final size:78
Alignment explanation
Indices: 20969816--20970489 Score: 704
Period size: 78 Copynumber: 8.7 Consensus size: 78
20969806 CTTTTTTTTT
* * ** * *
20969816 AAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA--T-TTTTAAA-
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAAT
* ***
20969876 TTCAGTCTTTTTTT
66 TTCTGT-TTTTCAA
* * * ** * * *
20969890 TAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGATGTA--T-TTTT-AAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAAT
* **
20969950 TCCTGTCTTTT-TT
66 TTCTGT-TTTTCAA
* * ** * * *
20969963 TAAATCAACTCATAATATGAGAGGTGAGTTGAGCCTCAGG-TCACGCTGAGGTATTTCTTTTAAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGACCATGCCGAGGTATTTCTTTTAAA
*
20970027 TTTTTGTTTTTTTTTTCAAA
65 TTTCTG-----TTTTTC-AA
*
20970047 AAAATCAACTCATATTGTGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAAT
*
20970112 TTATGTTTTTCAA
66 TTCTGTTTTTCAA
* *
20970125 AAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGACCATGCTGAGGTATTTCTTTTAAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAAT
*
20970190 TTATGTTTTTCAA
66 TTCTGTTTTTCAA
*
20970203 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGATGTATTTCTTTTAAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAAT
20970268 TTCTGTTTTTCAAA
66 TTCTGTTTTTC-AA
*
20970282 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATGCCGAGGTATTTCTTTTAAAT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAAT
*
20970347 TTCTATTTTTC-A
66 TTCTGTTTTTCAA
* * *
20970359 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GAGTCACGCCGAGGTA--T-TTTTCAA
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGA-CCATGCCGAGGTATTTCTTTTAAA
20970420 -TTCATGTTTTTC-A
65 TTTC-TGTTTTTCAA
* *
20970433 AAGATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGG-CACATGTCGAGGTATTT
1 AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGAC-CATGCCGAGGTATTT
20970490 TCGATTTTTG
Statistics
Matches: 541, Mismatches: 36, Indels: 43
0.87 0.06 0.07
Matches are distributed among these distances:
73 24 0.04
74 144 0.27
75 13 0.02
76 4 0.01
77 53 0.10
78 155 0.29
79 81 0.15
82 4 0.01
83 3 0.01
84 60 0.11
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (78 bp):
AAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGAGGTATTTCTTTTAAAT
TTCTGTTTTTCAA
Found at i:20970818 original size:30 final size:29
Alignment explanation
Indices: 20970755--20970922 Score: 108
Period size: 30 Copynumber: 5.7 Consensus size: 29
20970745 CCACTGTACT
* * * *
20970755 TTTCAAAAATTACATTTTAACCCCAAAAT
1 TTTCTAAAATTACATTTTGACCCCTAAAC
*
20970784 TTTCTAAAATTTACATTTTGACCCCTAGAC
1 TTTCTAAAA-TTACATTTTGACCCCTAAAC
* * *
20970814 TTTCTCAAAATTGCACTTTGACCCCTAAAA
1 TTTCT-AAAATTACATTTTGACCCCTAAAC
* * * **
20970844 TCTCAAGAAATTACATTTTG--GCCTATATT
1 TTTCTA-AAATTACATTTTGACCCCTA-AAC
* *
20970873 TTTGCTAAAATTGCACTTTGACCCCTAAAC
1 TTT-CTAAAATTACATTTTGACCCCTAAAC
*
20970903 TCTT-AAGAAATTACATTTTG
1 T-TTCTA-AAATTACATTTTG
20970923 GCCTATATTT
Statistics
Matches: 104, Mismatches: 26, Indels: 17
0.71 0.18 0.12
Matches are distributed among these distances:
28 4 0.04
29 24 0.23
30 66 0.63
31 10 0.10
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (29 bp):
TTTCTAAAATTACATTTTGACCCCTAAAC
Found at i:20970884 original size:29 final size:29
Alignment explanation
Indices: 20970851--20970952 Score: 91
Period size: 29 Copynumber: 3.4 Consensus size: 29
20970841 AAATCTCAAG
20970851 AAATTACATTTTGGCCTATATTTTTGCTA
1 AAATTACATTTTGGCCTATATTTTTGCTA
* * * * * * *
20970880 AAATTGCACTTTGACCCCTAAACTCTT--AA
1 AAATTACATTTTG--GCCTATATTTTTGCTA
20970909 GAAATTACATTTTGGCCTATATTTTTGCTA
1 -AAATTACATTTTGGCCTATATTTTTGCTA
20970939 AAATTACACTTTTG
1 AAATTACA-TTTTG
20970953 CCCCAAAAGC
Statistics
Matches: 53, Mismatches: 14, Indels: 11
0.68 0.18 0.14
Matches are distributed among these distances:
28 8 0.15
29 20 0.38
30 17 0.32
31 8 0.15
ACGTcount: A:0.30, C:0.18, G:0.10, T:0.42
Consensus pattern (29 bp):
AAATTACATTTTGGCCTATATTTTTGCTA
Found at i:20970893 original size:59 final size:59
Alignment explanation
Indices: 20970820--20970950 Score: 235
Period size: 59 Copynumber: 2.2 Consensus size: 59
20970810 AGACTTTCTC
20970820 AAAATTGCACTTTGACCCCTAAAATCTCAAGAAATTACATTTTGGCCTATATTTTTGCT
1 AAAATTGCACTTTGACCCCTAAAATCTCAAGAAATTACATTTTGGCCTATATTTTTGCT
* *
20970879 AAAATTGCACTTTGACCCCTAAACTCTTAAGAAATTACATTTTGGCCTATATTTTTGCT
1 AAAATTGCACTTTGACCCCTAAAATCTCAAGAAATTACATTTTGGCCTATATTTTTGCT
*
20970938 AAAATTACACTTT
1 AAAATTGCACTTT
20970951 TGCCCCAAAA
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
59 69 1.00
ACGTcount: A:0.33, C:0.20, G:0.09, T:0.38
Consensus pattern (59 bp):
AAAATTGCACTTTGACCCCTAAAATCTCAAGAAATTACATTTTGGCCTATATTTTTGCT
Found at i:20971525 original size:36 final size:36
Alignment explanation
Indices: 20971484--20971606 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
20971474 AAAAAGAAAG
20971484 AAAAAGAAGAAGAAAAGAGAGAAGAAAGGAAGGGAA
1 AAAAAGAAGAAGAAAAGAGAGAAGAAAGGAAGGGAA
* ** **
20971520 AAAAAGAA-AA-AAATATATTTTGAGGAAGGAAAAAAAAGAAAGA
1 AAAAAGAAGAAGAAA-AGA----GA-GAA-G-AAAGGAAGGGA-A
20971563 AAAAAGAAGAAGAAAAGAGAGAAGAAAGGAAGGGAA
1 AAAAAGAAGAAGAAAAGAGAGAAGAAAGGAAGGGAA
20971599 AAAAAGAA
1 AAAAAGAA
20971607 AAAAATATAT
Statistics
Matches: 66, Mismatches: 10, Indels: 22
0.67 0.10 0.22
Matches are distributed among these distances:
34 3 0.05
35 4 0.06
36 17 0.26
37 7 0.11
38 1 0.02
39 5 0.08
40 5 0.08
41 1 0.02
42 7 0.11
43 9 0.14
44 4 0.06
45 3 0.05
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (36 bp):
AAAAAGAAGAAGAAAAGAGAGAAGAAAGGAAGGGAA
Found at i:20971566 original size:13 final size:13
Alignment explanation
Indices: 20971548--20971589 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
20971538 TTTGAGGAAG
20971548 GAAAAAA-AAGAAA
1 GAAAAAAGAAG-AA
20971561 GAAAAAAGAAGAA
1 GAAAAAAGAAGAA
*
20971574 GAAAAGAG-AGAA
1 GAAAAAAGAAGAA
20971586 GAAA
1 GAAA
20971590 GGAAGGGAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 8 0.30
13 16 0.59
14 3 0.11
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (13 bp):
GAAAAAAGAAGAA
Found at i:20971567 original size:11 final size:11
Alignment explanation
Indices: 20971551--20971610 Score: 52
Period size: 11 Copynumber: 5.5 Consensus size: 11
20971541 GAGGAAGGAA
20971551 AAAAAAGAAAG
1 AAAAAAGAAAG
20971562 AAAAAAG-AAG
1 AAAAAAGAAAG
*
20971572 AAGAAAAGAGAG
1 AA-AAAAGAAAG
* *
20971584 AAGAAAGGAAG
1 AAAAAAGAAAG
**
20971595 GGAAAA-AAAG
1 AAAAAAGAAAG
20971605 AAAAAA
1 AAAAAA
20971611 ATATATTTTT
Statistics
Matches: 37, Mismatches: 10, Indels: 5
0.71 0.19 0.10
Matches are distributed among these distances:
10 12 0.32
11 21 0.57
12 4 0.11
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAG
Found at i:20971601 original size:78 final size:78
Alignment explanation
Indices: 20971463--20971619 Score: 305
Period size: 79 Copynumber: 2.0 Consensus size: 78
20971453 TAGCCCCGAA
20971463 GAGGAAGGAAAAAAAAGAAAGAAAAAGAAGAAGAAAAGAGAGAAGAAAGGAAGGGAAAAAAAGAA
1 GAGGAAGGAAAAAAAAGAAAGAAAAAGAAGAAGAAAAGAGAGAAGAAAGGAAGGGAAAAAAAGAA
20971528 AAAAATATATTTT
66 AAAAATATATTTT
20971541 GAGGAAGGAAAAAAAAGAAAGAAAAAAGAAGAAGAAAAGAGAGAAGAAAGGAAGGGAAAAAAAGA
1 GAGGAAGGAAAAAAAAGAAAG-AAAAAGAAGAAGAAAAGAGAGAAGAAAGGAAGGGAAAAAAAGA
20971606 AAAAAATATATTTT
65 AAAAAATATATTTT
20971620 TTAAAACCAG
Statistics
Matches: 78, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 21 0.27
79 57 0.73
ACGTcount: A:0.67, C:0.00, G:0.25, T:0.08
Consensus pattern (78 bp):
GAGGAAGGAAAAAAAAGAAAGAAAAAGAAGAAGAAAAGAGAGAAGAAAGGAAGGGAAAAAAAGAA
AAAAATATATTTT
Found at i:20971727 original size:22 final size:23
Alignment explanation
Indices: 20971702--20971745 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20971692 CAGCAGCCCA
20971702 AAACAACAGC-CCAAAAAAAAAG
1 AAACAACAGCACCAAAAAAAAAG
* *
20971724 AAACAGCAGCAGCAAAAAAAAA
1 AAACAACAGCACCAAAAAAAAA
20971746 CAGCAGCAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.68, C:0.20, G:0.11, T:0.00
Consensus pattern (23 bp):
AAACAACAGCACCAAAAAAAAAG
Found at i:20972417 original size:18 final size:18
Alignment explanation
Indices: 20972388--20972435 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
20972378 ATTTTTAAAA
20972388 TCATGTTTCAAAAATTT-
1 TCATGTTTCAAAAATTTC
20972405 TCATGTCTTC-AAAATTTC
1 TCATGT-TTCAAAAATTTC
*
20972423 TCGTGTTTCAAAA
1 TCATGTTTCAAAA
20972436 TAATAATAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
17 16 0.59
18 11 0.41
ACGTcount: A:0.31, C:0.17, G:0.08, T:0.44
Consensus pattern (18 bp):
TCATGTTTCAAAAATTTC
Found at i:20972651 original size:21 final size:21
Alignment explanation
Indices: 20972627--20972668 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
20972617 TTTCATATTT
*
20972627 TCGTGTTTTCAAAAAAAATTC
1 TCGTGTTTTAAAAAAAAATTC
20972648 TCGTGTTTTAAAAAAAAATTC
1 TCGTGTTTTAAAAAAAAATTC
20972669 ATGTCTTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.12, G:0.10, T:0.38
Consensus pattern (21 bp):
TCGTGTTTTAAAAAAAAATTC
Found at i:20973073 original size:34 final size:34
Alignment explanation
Indices: 20972987--20973179 Score: 185
Period size: 34 Copynumber: 5.7 Consensus size: 34
20972977 TCGTGTTTTA
*
20972987 AAAATTTCCCTGTTTTAAAAATTCCCGTA-TTCC
1 AAAATTTCCCTGTTTTAAAAATTCCCGTATTTCT
* * * **
20973020 AAAAATTGCGTGTTTTAAAAATTTTCGTATTTCT
1 AAAATTTCCCTGTTTTAAAAATTCCCGTATTTCT
* *
20973054 AAAATTTCCCTGTTTTAAAAATTCCCGTATTCCAAA
1 AAAATTTCCCTGTTTTAAAAATTCCCGTATTTC--T
* * * ** *
20973090 AAAATGT-CGTGTTTTAAAATTTTTCGTGTTTCT
1 AAAATTTCCCTGTTTTAAAAATTCCCGTATTTCT
* *
20973123 AAAATTTCCCTGTTTTAAAAATTCCCGTATTCCA
1 AAAATTTCCCTGTTTTAAAAATTCCCGTATTTCT
*
20973157 AAAATTGT-CGTGTTTTAAAAATT
1 AAAATT-TCCCTGTTTTAAAAATT
20973180 TTCCTGTTTT
Statistics
Matches: 125, Mismatches: 30, Indels: 9
0.76 0.18 0.05
Matches are distributed among these distances:
33 30 0.24
34 69 0.55
35 20 0.16
36 6 0.05
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.42
Consensus pattern (34 bp):
AAAATTTCCCTGTTTTAAAAATTCCCGTATTTCT
Found at i:20973130 original size:69 final size:68
Alignment explanation
Indices: 20972968--20973196 Score: 363
Period size: 69 Copynumber: 3.4 Consensus size: 68
20972958 TAGTGTTTCA
*
20972968 AAAAATGTGTCGTGTTT-TAAAAATTTCCCTGTTTTAAAAATTCCCGTATTCCAAAAATTG-CGT
1 AAAAAT-TTTCGTGTTTCT-AAAATTTCCCTGTTTTAAAAATTCCCGTATTCCAAAAATTGTCGT
20973031 GTTTT
64 GTTTT
* *
20973036 AAAAATTTTCGTATTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTATTCCAAAAAAATGTCGTG
1 AAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTATTCC-AAAAATTGTCGTG
20973101 TTTT
65 TTTT
*
20973105 AAAATTTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTATTCCAAAAATTGTCGTGT
1 AAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTATTCCAAAAATTGTCGTGT
20973170 TTT
66 TTT
* *
20973173 AAAAATTTTCCTGTTTTTAAAATT
1 AAAAATTTTCGTGTTTCTAAAATT
20973197 CTCGTATTTC
Statistics
Matches: 149, Mismatches: 9, Indels: 6
0.91 0.05 0.04
Matches are distributed among these distances:
67 41 0.28
68 51 0.34
69 57 0.38
ACGTcount: A:0.31, C:0.15, G:0.10, T:0.44
Consensus pattern (68 bp):
AAAAATTTTCGTGTTTCTAAAATTTCCCTGTTTTAAAAATTCCCGTATTCCAAAAATTGTCGTGT
TTT
Found at i:20973223 original size:17 final size:17
Alignment explanation
Indices: 20972960--20973260 Score: 163
Period size: 17 Copynumber: 17.4 Consensus size: 17
20972950 AAAAAAAATA
*
20972960 GTGTTTCAAAAAATGTGTC
1 GTGTTTC-AAAAAT-TTTC
* *
20972979 GTGTTTTAAAAATTTCC
1 GTGTTTCAAAAATTTTC
* * **
20972996 CTGTTTTAAAAATTCCC
1 GTGTTTCAAAAATTTTC
* * *
20973013 GTATTCCAAAAA-TTGC
1 GTGTTTCAAAAATTTTC
*
20973029 GTGTTTTAAAAATTTTC
1 GTGTTTCAAAAATTTTC
* * *
20973046 GTATTTCTAAAATTTCC
1 GTGTTTCAAAAATTTTC
* * **
20973063 CTGTTTTAAAAATTCCC
1 GTGTTTCAAAAATTTTC
* * * *
20973080 GTATTCCAAAAAAATGTC
1 GTGTTTC-AAAAATTTTC
* *
20973098 GTGTTTTAAAATTTTTC
1 GTGTTTCAAAAATTTTC
* *
20973115 GTGTTTCTAAAATTTCC
1 GTGTTTCAAAAATTTTC
* * **
20973132 CTGTTTTAAAAATTCCC
1 GTGTTTCAAAAATTTTC
* * *
20973149 GTATTCCAAAAATTGTC
1 GTGTTTCAAAAATTTTC
*
20973166 GTGTTTTAAAAATTTTC
1 GTGTTTCAAAAATTTTC
* ** *
20973183 CTGTTTTTAAAATTCTC
1 GTGTTTCAAAAATTTTC
* *
20973200 GTATTTCAAAAGTTTTC
1 GTGTTTCAAAAATTTTC
*
20973217 GTGTTTCAAAAAAAAATTCTC
1 GTGTTTC----AAAAATTTTC
20973238 GTGTTTCAAAAATTTTC
1 GTGTTTCAAAAATTTTC
20973255 GTGTTT
1 GTGTTT
20973261 TTTTAATTGT
Statistics
Matches: 208, Mismatches: 68, Indels: 14
0.72 0.23 0.05
Matches are distributed among these distances:
16 11 0.05
17 159 0.76
18 17 0.08
19 6 0.03
21 15 0.07
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.44
Consensus pattern (17 bp):
GTGTTTCAAAAATTTTC
Found at i:20973318 original size:19 final size:19
Alignment explanation
Indices: 20973277--20973318 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
20973267 TTGTATTTCT
*
20973277 AAAATTCTCGTTTTTTCAA
1 AAAATTCTCGTTTTTTAAA
20973296 AAAATTC-CGTGTTTTTAAA
1 AAAATTCTCGT-TTTTTAAA
20973315 AAAA
1 AAAA
20973319 AATATTGTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 3 0.14
19 18 0.86
ACGTcount: A:0.40, C:0.12, G:0.07, T:0.40
Consensus pattern (19 bp):
AAAATTCTCGTTTTTTAAA
Found at i:20973370 original size:24 final size:23
Alignment explanation
Indices: 20973333--20973377 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
20973323 TTGTGTTTCA
*
20973333 AAATTCTTGCGTTTTCAAAACAAG
1 AAATTCTCGCG-TTTCAAAACAAG
*
20973357 AAATTCTCGTGTTTCAAAACA
1 AAATTCTCGCGTTTCAAAACA
20973378 TTGAATTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (23 bp):
AAATTCTCGCGTTTCAAAACAAG
Found at i:20977808 original size:21 final size:22
Alignment explanation
Indices: 20977774--20977819 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
20977764 CCAGTATTTC
*
20977774 TCTATATTGTCATCCCTATATT
1 TCTATATTGCCATCCCTATATT
20977796 TCTA-ATTGCCATCCCTATATT
1 TCTATATTGCCATCCCTATATT
20977817 TCT
1 TCT
20977820 CTTGTAACTC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.22, C:0.26, G:0.04, T:0.48
Consensus pattern (22 bp):
TCTATATTGCCATCCCTATATT
Found at i:20982326 original size:2 final size:2
Alignment explanation
Indices: 20982276--20982307 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20982266 AAACTGAAAA
20982276 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20982308 CTTACAGATC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20991019 original size:31 final size:31
Alignment explanation
Indices: 20990984--20991065 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
20990974 ATATCGGTAC
* *
20990984 TCAACTAACCAATTTTTCTTACATTTAATCT
1 TCAACTTAGCAATTTTTCTTACATTTAATCT
*
20991015 TCAACTTAGCAATTTTTCTTACATTTGATCT
1 TCAACTTAGCAATTTTTCTTACATTTAATCT
20991046 TCAACTTAGCAATTTTTCTT
1 TCAACTTAGCAATTTTTCTT
20991066 GAAATCTTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 48 1.00
ACGTcount: A:0.28, C:0.21, G:0.04, T:0.48
Consensus pattern (31 bp):
TCAACTTAGCAATTTTTCTTACATTTAATCT
Found at i:20991281 original size:20 final size:20
Alignment explanation
Indices: 20991258--20991302 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
20991248 AATTTAAACT
*
20991258 TTTTTATTATTTTTT-TATAA
1 TTTTTA-TATTTTTTAAATAA
20991278 TTTTTATATTTTTTAAATAA
1 TTTTTATATTTTTTAAATAA
20991298 TTTTT
1 TTTTT
20991303 TTAATTTTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTATATTTTTTAAATAA
Found at i:21008960 original size:81 final size:81
Alignment explanation
Indices: 21008766--21008960 Score: 204
Period size: 81 Copynumber: 2.4 Consensus size: 81
21008756 TCAACAGTAG
* * *
21008766 AAATGGATGTAATTTAAACAAAATAATCAA-TTTGTTTTTTATCTAACATATAGGATTTAATTTA
1 AAATGGATGTATTTTAAACAAAATAATCAAGTTTGTTTTTTATCTAACATAGAGGAATTAATTTA
*
21008830 TCTATTTTTTAATTAA
66 TCCATTTTTTAATTAA
* * * *
21008846 AAATAGATATAATTTTAAACAAAATTATC-AGTTT-TTTTATTAATCTTACATAGA-GAATTAAT
1 AAATGGATGT-ATTTTAAACAAAATAATCAAGTTTGTTTT-TT-ATCTAACATAGAGGAATTAAT
*
21008908 TTGTCCATTTTTTGAA-TAA
63 TTATCCATTTTTT-AATTAA
* *
21008927 AAATGGATGTGATTTTAAATAAAATGA-CAAGTTT
1 AAATGGATGT-ATTTTAAACAAAATAATCAAGTTT
21008961 ACCTTTTGAT
Statistics
Matches: 95, Mismatches: 14, Indels: 11
0.79 0.12 0.09
Matches are distributed among these distances:
80 14 0.15
81 69 0.73
82 12 0.13
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (81 bp):
AAATGGATGTATTTTAAACAAAATAATCAAGTTTGTTTTTTATCTAACATAGAGGAATTAATTTA
TCCATTTTTTAATTAA
Found at i:21015589 original size:2 final size:2
Alignment explanation
Indices: 21015582--21015624 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
21015572 AGGAAAAGAA
21015582 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
21015624 A
1 A
21015625 TTAAACCAAG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:21020255 original size:19 final size:18
Alignment explanation
Indices: 21020231--21020283 Score: 63
Period size: 18 Copynumber: 2.9 Consensus size: 18
21020221 TTATAAATAA
*
21020231 TAAATTTTAGA-AAAATTAT
1 TAAATTTTA-ATAAAAAT-T
21020250 TAAATTTTAATAAAAATT
1 TAAATTTTAATAAAAATT
*
21020268 TAAATTTTACTAAAAA
1 TAAATTTTAATAAAAA
21020284 ATAGAATTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 17 0.55
19 14 0.45
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
TAAATTTTAATAAAAATT
Found at i:21020272 original size:18 final size:19
Alignment explanation
Indices: 21020225--21020283 Score: 68
Period size: 19 Copynumber: 3.2 Consensus size: 19
21020215 AAAAAATTAT
*
21020225 AAATAATAAATTTTAGA-AA
1 AAATATTAAATTTTA-ATAA
*
21020244 AATTATTAAATTTTAATAA
1 AAATATTAAATTTTAATAA
*
21020263 AAAT-TTAAATTTTACTAA
1 AAATATTAAATTTTAATAA
21020281 AAA
1 AAA
21020284 ATAGAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
18 17 0.49
19 18 0.51
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (19 bp):
AAATATTAAATTTTAATAA
Found at i:21020291 original size:18 final size:18
Alignment explanation
Indices: 21020225--21020293 Score: 61
Period size: 18 Copynumber: 3.7 Consensus size: 18
21020215 AAAAAATTAT
21020225 AAATAATAAATTTTAGA-AA
1 AAAT-ATAAATTTTA-ATAA
*
21020244 AATTATTAAATTTTAATAA
1 AAATA-TAAATTTTAATAA
* *
21020263 AAATTTAAATTTTACTAA
1 AAATATAAATTTTAATAA
21020281 AAA-ATAGAATTTT
1 AAATATA-AATTTT
21020294 TTTTATAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
17 2 0.05
18 23 0.55
19 17 0.40
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.41
Consensus pattern (18 bp):
AAATATAAATTTTAATAA
Found at i:21020448 original size:17 final size:18
Alignment explanation
Indices: 21020417--21020450 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
21020407 GCATATGGTG
21020417 AAAATTGATAAAAAAATA
1 AAAATTGATAAAAAAATA
*
21020435 AAAATT-ATAGAAAAAT
1 AAAATTGATAAAAAAAT
21020451 TATAAAATGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (18 bp):
AAAATTGATAAAAAAATA
Found at i:21020506 original size:21 final size:21
Alignment explanation
Indices: 21020480--21020532 Score: 65
Period size: 20 Copynumber: 2.5 Consensus size: 21
21020470 TACGATAATT
21020480 TTTATAATTTTTTT-TACAAAA
1 TTTATAATTTTTTTCTAC-AAA
*
21020501 TTTAT-ATTTTTTTCTACATA
1 TTTATAATTTTTTTCTACAAA
21020521 TTGTATAATTTT
1 TT-TATAATTTT
21020533 CTTATGAGAC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
20 12 0.43
21 11 0.39
22 5 0.18
ACGTcount: A:0.30, C:0.06, G:0.02, T:0.62
Consensus pattern (21 bp):
TTTATAATTTTTTTCTACAAA
Found at i:21022150 original size:17 final size:14
Alignment explanation
Indices: 21022118--21022152 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
21022108 AAATATAAAA
21022118 TTATTTATATAATT
1 TTATTTATATAATT
21022132 TTATTATATATAATT
1 TTATT-TATATAATT
21022147 TT-TTTA
1 TTATTTA
21022153 ATTTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 2 0.10
14 7 0.35
15 11 0.55
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATTTATATAATT
Found at i:21022156 original size:9 final size:9
Alignment explanation
Indices: 21022142--21022166 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
21022132 TTATTATATA
21022142 TAATTTTTT
1 TAATTTTTT
21022151 TAATTTTTT
1 TAATTTTTT
21022160 TAATTTT
1 TAATTTT
21022167 CTATTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TAATTTTTT
Found at i:21028761 original size:158 final size:158
Alignment explanation
Indices: 21028533--21028855 Score: 493
Period size: 158 Copynumber: 2.0 Consensus size: 158
21028523 CAGGATTGCT
* * *
21028533 AACACTAGCTTGGTTCGATGCTACTAACATTAGCTTCAGAGAATTCGCAACATATGTTGGATCTC
1 AACACTAGCTTGGTTCGATGCTACTAACACTAGCTTCAAAGAATCCGCAACATATGTTGGATCTC
21028598 AAGCCATCAAATTAATTCCTGATCACAACACCCATTTATTCATACAAACTGATATACTCAGGCCG
66 AAGCCATCAAATTAATTCCTGATCACAACACCCATTTATTCATACAAACTGATATACTCAGGCCG
21028663 CTAACATTAGCTTCAAATCAAGGTCGCC
131 CTAACATTAGCTTCAAATCAAGGTCGCC
* * * *
21028691 AACACTAGCTTGGTTCGATGTTGCTAACACTAGCTTTAAAGAATCCGCAACATATGTTGGATGTC
1 AACACTAGCTTGGTTCGATGCTACTAACACTAGCTTCAAAGAATCCGCAACATATGTTGGATCTC
* * * * * *
21028756 AAGCCATCGAATTAATTCTTGATCATAACACCCATTTATTCATACAGACTTATATACTCGGGCCG
66 AAGCCATCAAATTAATTCCTGATCACAACACCCATTTATTCATACAAACTGATATACTCAGGCCG
* * * *
21028821 CTAACATTAGCTTCAGATCAATGTTGCT
131 CTAACATTAGCTTCAAATCAAGGTCGCC
21028849 AACACTA
1 AACACTA
21028856 ACTTCAAAGA
Statistics
Matches: 148, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
158 148 1.00
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (158 bp):
AACACTAGCTTGGTTCGATGCTACTAACACTAGCTTCAAAGAATCCGCAACATATGTTGGATCTC
AAGCCATCAAATTAATTCCTGATCACAACACCCATTTATTCATACAAACTGATATACTCAGGCCG
CTAACATTAGCTTCAAATCAAGGTCGCC
Found at i:21029140 original size:33 final size:32
Alignment explanation
Indices: 21029080--21029141 Score: 81
Period size: 33 Copynumber: 1.9 Consensus size: 32
21029070 CCGCCCATAT
**
21029080 TATTTTTTAATTTTTTTAAAATATTTATAATA
1 TATTTTTTAATTTTAATAAAATATTTATAATA
21029112 TATTATTTTAATATTTAATAAAAT-TTTATA
1 TATT-TTTTAAT-TTTAATAAAATATTTATA
21029142 TTTTTCTATC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
32 4 0.15
33 13 0.50
34 9 0.35
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TATTTTTTAATTTTAATAAAATATTTATAATA
Found at i:21031263 original size:6 final size:6
Alignment explanation
Indices: 21031249--21031302 Score: 63
Period size: 6 Copynumber: 8.7 Consensus size: 6
21031239 ATTGCTTAAT
* * *
21031249 AAAATA AAAAGA AAAAGA AAAAGAA AAATAGA AATATA AAAAGA AAAAGA
1 AAAAGA AAAAGA AAAAGA AAAAG-A AAA-AGA AAAAGA AAAAGA AAAAGA
21031299 AAAA
1 AAAA
21031303 AATTGTTTAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
6 32 0.78
7 7 0.17
8 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.11, T:0.07
Consensus pattern (6 bp):
AAAAGA
Found at i:21043007 original size:22 final size:22
Alignment explanation
Indices: 21042979--21043024 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
21042969 GGCTATTTCC
21042979 TTTTTTTTTCTTTTTGTGAACT
1 TTTTTTTTTCTTTTTGTGAACT
21043001 TTTTTTTTTCTTTTTGTGAACT
1 TTTTTTTTTCTTTTTGTGAACT
21043023 TT
1 TT
21043025 GGCACAGAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.09, C:0.09, G:0.09, T:0.74
Consensus pattern (22 bp):
TTTTTTTTTCTTTTTGTGAACT
Found at i:21055064 original size:31 final size:32
Alignment explanation
Indices: 21054999--21055084 Score: 102
Period size: 31 Copynumber: 2.7 Consensus size: 32
21054989 CGTTTTTTTT
* *
21054999 GTACCTGAACTTGATACTTTTTAGTACAATTTG
1 GTACCTGAACTTGACACTTTTTACTA-AATTTG
* *
21055032 GTACTTGAACTTGACACTTTTTCCT-AATTTG
1 GTACCTGAACTTGACACTTTTTACTAAATTTG
* *
21055063 GTACCTAAACTTGACATTTTTT
1 GTACCTGAACTTGACACTTTTT
21055085 TTATTTGATA
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
31 25 0.54
33 21 0.46
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (32 bp):
GTACCTGAACTTGACACTTTTTACTAAATTTG
Found at i:21055128 original size:56 final size:57
Alignment explanation
Indices: 21055060--21055167 Score: 141
Period size: 56 Copynumber: 1.9 Consensus size: 57
21055050 TTTTCCTAAT
* * * *
21055060 TTGGTACCTAAACTTGACAT-TTTTT-TT-ATTTGATACTTCATCTTTTTTTATACAAC
1 TTGGTACATAAACATGAC-TGTTTTTATTAATTTGATACCTAAT-TTTTTTTATACAAC
21055116 TTGGTACATAAACATGACTGTTTTTATTAATTTGATACCTAATTTTTTTTAT
1 TTGGTACATAAACATGACTGTTTTTATTAATTTGATACCTAATTTTTTTTAT
21055168 TAATTTTGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
55 1 0.02
56 21 0.47
57 11 0.24
58 12 0.27
ACGTcount: A:0.27, C:0.13, G:0.08, T:0.52
Consensus pattern (57 bp):
TTGGTACATAAACATGACTGTTTTTATTAATTTGATACCTAATTTTTTTTATACAAC
Found at i:21062940 original size:38 final size:40
Alignment explanation
Indices: 21062898--21062986 Score: 128
Period size: 38 Copynumber: 2.2 Consensus size: 40
21062888 AAAATTTTTA
* * *
21062898 TTTAATATAATCAAATATTTATTATATTTAT-TTGTG-TT
1 TTTAATATAATAAAACATTTATTATATTTATGTAGTGTTT
21062936 TTTAATATAATAAAACATTTATTATATTTATGGTAGTGTTT
1 TTTAATATAATAAAACATTTATTATATTTAT-GTAGTGTTT
21062977 TTTAATATAA
1 TTTAATATAA
21062987 ATATTTTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
38 29 0.64
40 4 0.09
41 12 0.27
ACGTcount: A:0.37, C:0.02, G:0.07, T:0.54
Consensus pattern (40 bp):
TTTAATATAATAAAACATTTATTATATTTATGTAGTGTTT
Found at i:21070140 original size:33 final size:33
Alignment explanation
Indices: 21070098--21070165 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
21070088 AAATATTATA
*
21070098 ATCATAATAATTGGGGCCTACGAGACCCGATAC
1 ATCATAATAATTAGGGCCTACGAGACCCGATAC
21070131 ATCATAATAATTAGGGCCTACGAGACCCGATAC
1 ATCATAATAATTAGGGCCTACGAGACCCGATAC
21070164 AT
1 AT
21070166 ACTCATGTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (33 bp):
ATCATAATAATTAGGGCCTACGAGACCCGATAC
Found at i:21070660 original size:46 final size:46
Alignment explanation
Indices: 21070557--21070708 Score: 247
Period size: 46 Copynumber: 3.4 Consensus size: 46
21070547 TACGTATGAT
* *
21070557 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
21070600 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
21070646 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGTTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
21070692 CACTTATCACTTTGTCA
1 CACTTATCACTTTGTCA
21070709 TTTATCACTG
Statistics
Matches: 102, Mismatches: 4, Indels: 3
0.94 0.04 0.03
Matches are distributed among these distances:
43 10 0.10
44 5 0.05
45 20 0.20
46 67 0.66
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.34
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:21073540 original size:18 final size:17
Alignment explanation
Indices: 21073519--21073552 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
21073509 AAAATATTAT
21073519 ATTAATAAGATTAAAATA
1 ATTAATAA-ATTAAAATA
*
21073537 ATTAATTAATTAAAAT
1 ATTAATAAATTAAAAT
21073553 TTTAAAAATC
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:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
ATTAATAAATTAAAATA
Found at i:21074932 original size:21 final size:21
Alignment explanation
Indices: 21074890--21074937 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
21074880 ATTTTTATGA
* **
21074890 AATTAACATAAAATTTTTAAT
1 AATTAACATAAAACTTCAAAT
*
21074911 AATTAACATATAACTTCAAAT
1 AATTAACATAAAACTTCAAAT
21074932 AATTAA
1 AATTAA
21074938 TTGAAATTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAACATAAAACTTCAAAT
Found at i:21076252 original size:7 final size:7
Alignment explanation
Indices: 21076240--21076274 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
21076230 AATACTATTA
21076240 TGATGGG
1 TGATGGG
21076247 TGATGGG
1 TGATGGG
21076254 TGATGGG
1 TGATGGG
21076261 TGATGGG
1 TGATGGG
21076268 TGATGGG
1 TGATGGG
21076275 CAATGACATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.14, C:0.00, G:0.57, T:0.29
Consensus pattern (7 bp):
TGATGGG
Found at i:21092995 original size:23 final size:23
Alignment explanation
Indices: 21092963--21093006 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
21092953 CCTTTGGGCA
*
21092963 TACCGTTTTCCCA-TTGCCCATCG
1 TACCGGTTT-CCATTTGCCCATCG
21092986 TACCGGTTTCCATTTGCCCAT
1 TACCGGTTTCCATTTGCCCAT
21093007 ATCAGGGTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.14, C:0.36, G:0.14, T:0.36
Consensus pattern (23 bp):
TACCGGTTTCCATTTGCCCATCG
Found at i:21095990 original size:21 final size:24
Alignment explanation
Indices: 21095965--21096007 Score: 65
Period size: 21 Copynumber: 1.9 Consensus size: 24
21095955 AATTTTGAAA
21095965 ATTTAAA-GGGC-TAAA-TAAATT
1 ATTTAAACGGGCTTAAACTAAATT
21095986 ATTTAAACGGGCTTAAACTAAA
1 ATTTAAACGGGCTTAAACTAAA
21096008 GACTTGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 4 0.21
23 4 0.21
24 4 0.21
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (24 bp):
ATTTAAACGGGCTTAAACTAAATT
Found at i:21141891 original size:23 final size:23
Alignment explanation
Indices: 21141856--21141923 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
21141846 AAAAAAAAGA
*
21141856 ATTGCTATCTTTTTTGTTGTTTT
1 ATTGCTATCTTTTTTATTGTTTT
* *
21141879 ATTGCTGTTTTTTTTATTGTTTT
1 ATTGCTATCTTTTTTATTGTTTT
* *
21141902 GA-TGCTAT-TTTCTTATTATTTT
1 -ATTGCTATCTTTTTTATTGTTTT
21141924 CTCATTGTTT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
22 12 0.32
23 25 0.66
24 1 0.03
ACGTcount: A:0.12, C:0.07, G:0.12, T:0.69
Consensus pattern (23 bp):
ATTGCTATCTTTTTTATTGTTTT
Found at i:21145573 original size:21 final size:20
Alignment explanation
Indices: 21145543--21145590 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
21145533 TTTGTGGTGA
* *
21145543 AAATTAATAAATTTTAATAT
1 AAATTAATAAATATAAATAT
*
21145563 ATATTATATAAATATAAATAT
1 AAATTA-ATAAATATAAATAT
21145584 AAATTAA
1 AAATTAA
21145591 AATAATAACA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.26
21 17 0.74
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (20 bp):
AAATTAATAAATATAAATAT
Found at i:21147798 original size:16 final size:16
Alignment explanation
Indices: 21147777--21147812 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
21147767 TTTGGTTCGC
21147777 TGTATTGGATTAAAGG
1 TGTATTGGATTAAAGG
*
21147793 TGTATTGGATTAGAGG
1 TGTATTGGATTAAAGG
21147809 TGTA
1 TGTA
21147813 ATAGCAAATC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.33, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAAAGG
Found at i:21148069 original size:18 final size:17
Alignment explanation
Indices: 21148048--21148082 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21148038 TTATTATTAA
*
21148048 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
21148066 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
21148083 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:21148157 original size:24 final size:25
Alignment explanation
Indices: 21148130--21148187 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
21148120 TAAATATTGT
21148130 TATTGTTATTTAA-T-ATATAATAAA
1 TATTGTTATTTAATTAATATAA-AAA
* *
21148154 TATTGTTA-ATAATTAATATAAAAG
1 TATTGTTATTTAATTAATATAAAAA
21148178 TATTGTTATT
1 TATTGTTATT
21148188 AGCAGAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
23 3 0.11
24 19 0.68
25 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.07, T:0.50
Consensus pattern (25 bp):
TATTGTTATTTAATTAATATAAAAA
Found at i:21148309 original size:16 final size:16
Alignment explanation
Indices: 21148272--21148313 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
21148262 TTAATCATAT
*
21148272 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
21148288 TT-AAATATATTATAA
1 TTAAAATATATTATAA
21148303 TTAAAATATAT
1 TTAAAATATAT
21148314 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:21148320 original size:14 final size:15
Alignment explanation
Indices: 21148281--21148322 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
21148271 TTTAAACATA
*
21148281 ATTATTATTAAATAT
1 ATTATAATTAAATAT
21148296 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
21148310 A-TATAATTTAATA
1 ATTATAATTAAATA
21148323 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:21148409 original size:120 final size:121
Alignment explanation
Indices: 21148270--21148567 Score: 498
Period size: 120 Copynumber: 2.5 Consensus size: 121
21148260 TTTTAATCAT
*
21148270 ATTTAAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
21148335 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTA-AAAT-ATAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATA--GTATAAATGA-AA
21148392 A-TT-AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
21148455 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATAGTATAAATGAAA
66 ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATAGTATAAATGAAA
* * *
21148511 ATTTGAA-ATAATTAATATTAAATATATTTTAATTAAAATATATTATTTAATAAAATT
1 ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
21148568 TAAAATAATT
Statistics
Matches: 169, Mismatches: 3, Indels: 10
0.93 0.02 0.05
Matches are distributed among these distances:
118 3 0.02
119 7 0.04
120 154 0.91
121 4 0.02
122 1 0.01
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (121 bp):
ATTTGAACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATA
ATTAATATTCTTATATGAATTTACTCAAATCATAATATATGATAGTATAAATGAAA
Found at i:21148440 original size:14 final size:15
Alignment explanation
Indices: 21148391--21148442 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
21148381 GTAAAATATA
21148391 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
21148406 TATTAAATATATTAT
1 AATTAAATATATTAT
21148421 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
21148434 AATTTAATA
1 AATTAAATA
21148443 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:21148580 original size:28 final size:27
Alignment explanation
Indices: 21148502--21148580 Score: 65
Period size: 28 Copynumber: 2.9 Consensus size: 27
21148492 TATGATAGTA
*
21148502 TAAATGAAAATTTGAAATAATTA-ATAT
1 TAAAT-AAAATTTAAAATAATTATATAT
* *
21148529 TAAATATATTTTAATTAA-AA-TATATTAT
1 TAAATAAAATTTAA--AATAATTATA-TAT
*
21148557 TTAATAAAATTTAAAATAATTATA
1 TAAATAAAATTTAAAATAATTATA
21148581 ACTAATAAAT
Statistics
Matches: 40, Mismatches: 6, Indels: 11
0.70 0.11 0.19
Matches are distributed among these distances:
26 10 0.25
27 10 0.25
28 20 0.50
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (27 bp):
TAAATAAAATTTAAAATAATTATATAT
Found at i:21148654 original size:24 final size:25
Alignment explanation
Indices: 21148608--21148655 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
21148598 TATGAATTTG
21148608 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
21148634 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
21148656 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:21152228 original size:25 final size:25
Alignment explanation
Indices: 21152173--21152279 Score: 112
Period size: 25 Copynumber: 4.2 Consensus size: 25
21152163 TTTAAATTTC
* * *
21152173 TTTATTAAAATATTAAAATTTCTTGATT
1 TTTAATAAAATATT-AAAGTCCTT-A-T
21152201 TTTAATAAAATATTAAAGTCCTTAT
1 TTTAATAAAATATTAAAGTCCTTAT
* *
21152226 TTTAAT-TATTGATT--AGTCCTTAT
1 TTTAATAAAAT-ATTAAAGTCCTTAT
21152249 TTTAATAAAATATTAAAGTCCTTAT
1 TTTAATAAAATATTAAAGTCCTTAT
21152274 TTTAAT
1 TTTAAT
21152280 TATTGATTAG
Statistics
Matches: 68, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
23 18 0.26
24 4 0.06
25 25 0.37
26 1 0.01
27 7 0.10
28 13 0.19
ACGTcount: A:0.38, C:0.07, G:0.05, T:0.50
Consensus pattern (25 bp):
TTTAATAAAATATTAAAGTCCTTAT
Found at i:21152247 original size:23 final size:23
Alignment explanation
Indices: 21152217--21152309 Score: 134
Period size: 23 Copynumber: 4.0 Consensus size: 23
21152207 AAAATATTAA
21152217 AGTCCTTATTTTAATTATTGATT
1 AGTCCTTATTTTAATTATTGATT
* *
21152240 AGTCCTTATTTTAATAAAAT-ATT
1 AGTCCTTATTTTAAT-TATTGATT
21152263 AAAGTCCTTATTTTAATTATTGATT
1 --AGTCCTTATTTTAATTATTGATT
21152288 AGTCCTTATTTTAATTATTGAT
1 AGTCCTTATTTTAATTATTGAT
21152310 GTAATTTTTA
Statistics
Matches: 62, Mismatches: 4, Indels: 8
0.84 0.05 0.11
Matches are distributed among these distances:
23 40 0.65
24 4 0.06
25 18 0.29
ACGTcount: A:0.31, C:0.09, G:0.08, T:0.53
Consensus pattern (23 bp):
AGTCCTTATTTTAATTATTGATT
Found at i:21152252 original size:48 final size:48
Alignment explanation
Indices: 21152200--21152302 Score: 206
Period size: 48 Copynumber: 2.1 Consensus size: 48
21152190 ATTTCTTGAT
21152200 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
21152248 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
1 TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
21152296 TTTTAAT
1 TTTTAAT
21152303 TATTGATGTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.51
Consensus pattern (48 bp):
TTTTAATAAAATATTAAAGTCCTTATTTTAATTATTGATTAGTCCTTA
Found at i:21152446 original size:16 final size:16
Alignment explanation
Indices: 21152425--21152476 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
21152415 TTTGGTTCGC
21152425 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
21152441 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
* *
21152457 TGTAATGGAATAGAGG
1 TGTATTGGATTAGAGG
21152473 TGTA
1 TGTA
21152477 ATAGCAAATC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.29, C:0.00, G:0.37, T:0.35
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:21152523 original size:45 final size:44
Alignment explanation
Indices: 21152457--21152551 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 44
21152447 GGATTAGAGG
*
21152457 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAA
* ***
21152502 TGTAATGGAATAGAGGCGTAATAGTAATCCTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
21152546 TGTAAT
1 TGTAAT
21152552 AGAGGTGTAA
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
44 22 0.49
45 23 0.51
ACGTcount: A:0.33, C:0.06, G:0.27, T:0.34
Consensus pattern (44 bp):
TGTAATGGAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAA
Found at i:21152732 original size:18 final size:17
Alignment explanation
Indices: 21152711--21152745 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
21152701 TTATTATTAA
*
21152711 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
21152729 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
21152746 TCTTAATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:21161519 original size:14 final size:14
Alignment explanation
Indices: 21161498--21161531 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
21161488 TGGTATGGGT
21161498 TTAT-GGGTTTTGG
1 TTATAGGGTTTTGG
21161511 TTATAGGGTTTTGG
1 TTATAGGGTTTTGG
21161525 TTATAGG
1 TTATAGG
21161532 CAAATAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 4 0.20
14 16 0.80
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (14 bp):
TTATAGGGTTTTGG
Found at i:21161686 original size:24 final size:25
Alignment explanation
Indices: 21161659--21161708 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
21161649 AGAGGAAAGT
21161659 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
21161683 TTAAATTACTTAAAACGAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
21161708 T
1 T
21161709 ATGGGGATCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 12 0.55
25 10 0.45
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.20
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:21163356 original size:36 final size:36
Alignment explanation
Indices: 21163316--21163394 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
21163306 TTTAACCCCA
* *
21163316 AACTTTTCTAC-TCTTTTAAATTTTAAACTGAATTTT
1 AACTTTTCTACGT-TTTAAAAGTTTAAACTGAATTTT
*
21163352 AACTTTTCTACGTTTTAAAAGTTTACACTGAATTTT
1 AACTTTTCTACGTTTTAAAAGTTTAAACTGAATTTT
21163388 AACTTTT
1 AACTTTT
21163395 TTTTTTGCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
36 38 0.97
37 1 0.03
ACGTcount: A:0.30, C:0.14, G:0.05, T:0.51
Consensus pattern (36 bp):
AACTTTTCTACGTTTTAAAAGTTTAAACTGAATTTT
Found at i:21167387 original size:19 final size:20
Alignment explanation
Indices: 21167355--21167393 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
21167345 TATAAACTAT
*
21167355 AAAACAAATATGAAAGATAA
1 AAAAAAAATATGAAAGATAA
*
21167375 AAAAAAAAT-TGAAATATAA
1 AAAAAAAATATGAAAGATAA
21167394 TAAATTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (20 bp):
AAAAAAAATATGAAAGATAA
Found at i:21175351 original size:20 final size:20
Alignment explanation
Indices: 21175314--21175363 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
21175304 TAATACTTAT
* *
21175314 CTTAATACT-ATTTTATTAA
1 CTTAATATTAATTTGATTAA
*
21175333 CTTAATATTAATTTGATTAT
1 CTTAATATTAATTTGATTAA
*
21175353 CTTATTATTAA
1 CTTAATATTAA
21175364 AATTAATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.36, C:0.08, G:0.02, T:0.54
Consensus pattern (20 bp):
CTTAATATTAATTTGATTAA
Found at i:21178394 original size:123 final size:124
Alignment explanation
Indices: 21178170--21178518 Score: 576
Period size: 123 Copynumber: 2.8 Consensus size: 124
21178160 TTATTTCAAG
21178170 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGT
* * *
21178234 GAAATTGCGCCATTGTGGACATGATTTTGCTACAGTAGGTCATGTAAGAAAT-AATTTTT
65 GAAATCGCGCCATCGTGGACACGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
* *
21178293 TTGACGTTTCTGAGCAAATAGTATAAAATCGGCTCTACCAAGATGCTATTTGAGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
* *
21178358 AAATCGCGCCCTCGTGGACACGATTTTGCTATAGTAGGTCATGTAAGAAATAAATTTTT
66 AAATCGCGCCATCGTGGACACGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
*
21178417 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGGGAAGAAATTGTG
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
** *
21178482 AAATCGCGTTATCGTGGACGCGATTTTGCTACAGTAG
66 AAATCGCGCCATCGTGGACACGATTTTGCTACAGTAG
21178519 CAAGTTTGGG
Statistics
Matches: 209, Mismatches: 15, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
123 107 0.51
124 102 0.49
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (124 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTG
AAATCGCGCCATCGTGGACACGATTTTGCTACAGTAGGTCATGTAAGAAATAAATTTTT
Found at i:21181007 original size:29 final size:29
Alignment explanation
Indices: 21180948--21181033 Score: 127
Period size: 29 Copynumber: 2.9 Consensus size: 29
21180938 TATGCAGGCC
* *
21180948 AGGGTTAAGGTTTTTAATTAGGTTGGGGTT
1 AGGGTTAAGGTTTTTAATTAAGTT-AGGTT
* *
21180978 AGGGTTAGGGTTTTTAATTAAATTAGGTT
1 AGGGTTAAGGTTTTTAATTAAGTTAGGTT
21181007 AGGGTTAAGGTTTTTAATTAAGTTAGG
1 AGGGTTAAGGTTTTTAATTAAGTTAGG
21181034 GTTTTTAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
29 29 0.58
30 21 0.42
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.43
Consensus pattern (29 bp):
AGGGTTAAGGTTTTTAATTAAGTTAGGTT
Found at i:21181032 original size:47 final size:47
Alignment explanation
Indices: 21180981--21181080 Score: 173
Period size: 47 Copynumber: 2.1 Consensus size: 47
21180971 TGGGGTTAGG
21180981 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAA
* *
21181028 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAA
*
21181075 ATTAGG
1 GTTAGG
21181081 TTAGGGTTAG
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 50 1.00
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (47 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAA
Found at i:21181036 original size:18 final size:18
Alignment explanation
Indices: 21181010--21181051 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
21181000 TTAGGTTAGG
*
21181010 GTTAAGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
21181028 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
21181046 GTTAGG
1 GTTAGG
21181052 TTAGGGTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.24, T:0.48
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:21181060 original size:29 final size:29
Alignment explanation
Indices: 21181028--21181207 Score: 150
Period size: 29 Copynumber: 5.8 Consensus size: 29
21181018 TTTTAATTAA
*
21181028 GTTAGGGTTTTTAATTAAGTTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
21181057 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
* * * *
21181086 GTTAGGGTTTTTAGGGTTTAGGATTTTTA-ATTAAGTTA
1 GTTAGGGTTTTTA---ATTA--A--ATTAGGTT-AG--G
*
21181124 GGTTAGGGTTAGGGTT-ATT-AATTAGGTTAGG
1 G-TTAGGGTT---TTTAATTAAATTAGGTTAGG
21181155 GTTAGGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGG
*
21181184 GTTAGGGTTTTTAATTAAGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGG
21181208 GTTTTTAATT
Statistics
Matches: 122, Mismatches: 12, Indels: 34
0.73 0.07 0.20
Matches are distributed among these distances:
27 2 0.02
28 3 0.02
29 76 0.62
30 8 0.07
31 1 0.01
32 3 0.02
33 5 0.04
34 3 0.02
35 3 0.02
36 5 0.04
38 3 0.02
39 8 0.07
42 2 0.02
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (29 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGG
Found at i:21181101 original size:15 final size:16
Alignment explanation
Indices: 21181081--21181114 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
21181071 TTAAATTAGG
*
21181081 TTAGGG-TTAGGGTTT
1 TTAGGGTTTAGGATTT
21181096 TTAGGGTTTAGGATTT
1 TTAGGGTTTAGGATTT
21181112 TTA
1 TTA
21181115 ATTAAGTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (16 bp):
TTAGGGTTTAGGATTT
Found at i:21181167 original size:53 final size:52
Alignment explanation
Indices: 21181096--21181257 Score: 235
Period size: 53 Copynumber: 3.2 Consensus size: 52
21181086 GTTAGGGTTT
* *
21181096 TTAGGGTTTAGGATTTTTAATTAAGTTAGGTTAGGGTTAGGGTTATTAATTAGG
1 TTAGGG-TTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTA-G
*
21181150 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTA-
1 TTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAG
21181201 --A--GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAG
1 TTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATT-AG
21181250 TTAGGGTT
1 TTAGGGTT
21181258 TTTAAATAAA
Statistics
Matches: 98, Mismatches: 4, Indels: 13
0.85 0.03 0.11
Matches are distributed among these distances:
47 44 0.45
48 1 0.01
49 1 0.01
51 1 0.01
53 45 0.46
54 6 0.06
ACGTcount: A:0.25, C:0.00, G:0.29, T:0.46
Consensus pattern (52 bp):
TTAGGGTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAG
Found at i:21181184 original size:47 final size:45
Alignment explanation
Indices: 21181057--21181272 Score: 204
Period size: 47 Copynumber: 4.5 Consensus size: 45
21181047 TTAGGTTAGG
* *
21181057 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGT-TT--TTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA-GTTATTAATTA-A
* *
21181101 GTTTAGGATTTTTAATTAAGTTAGGTTAGGGTTAGGGTTATTAATTAGGTTA
1 G-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTA--GTTATTAATTA----A
*
21181153 GGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAA
1 --GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA--GTTATTAATTAA
* *
21181202 GTTAGGGTTTTTAATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTA--GTTATTAATTAA
*
21181249 GTTAGGGTTTTTAAATAAATTAGG
1 GTTAGGGTTTTTAATTAAATTAGG
21181273 GTTTTTATTA
Statistics
Matches: 151, Mismatches: 11, Indels: 17
0.84 0.06 0.09
Matches are distributed among these distances:
44 1 0.01
45 30 0.20
46 3 0.02
47 70 0.46
49 4 0.03
53 42 0.28
54 1 0.01
ACGTcount: A:0.26, C:0.00, G:0.28, T:0.45
Consensus pattern (45 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGTTATTAATTAA
Found at i:21181207 original size:127 final size:120
Alignment explanation
Indices: 21180976--21181207 Score: 347
Period size: 127 Copynumber: 1.9 Consensus size: 120
21180966 TAGGTTGGGG
* *
21180976 TTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAAGTTAGGGTTTTTA
1 TTAGGGTTAGGATTTTTAATTAAATTAGGTTAGGGTTAAGGTTATTAATTAAGTTAGGGTTTTTA
*
21181041 ATTAAGTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT
66 ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT
* *
21181096 TTAGGGTTTAGGATTTTTAATTAAGTTAGGTTAGGGTTAGGGTTATTAATTAGGTTAGGGTTAGG
1 TTAGGG-TTAGGATTTTTAATTAAATTAGGTTAGGGTTAAGGTTATTAATTA----A--GTTAGG
*
21181161 GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTAGG
59 GTTTTTAATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGG
21181208 GTTTTTAATT
Statistics
Matches: 99, Mismatches: 6, Indels: 7
0.88 0.05 0.06
Matches are distributed among these distances:
120 6 0.06
121 41 0.41
125 1 0.01
127 51 0.52
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (120 bp):
TTAGGGTTAGGATTTTTAATTAAATTAGGTTAGGGTTAAGGTTATTAATTAAGTTAGGGTTTTTA
ATTAAATTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAGGGTTT
Found at i:21181227 original size:17 final size:18
Alignment explanation
Indices: 21181184--21181279 Score: 107
Period size: 18 Copynumber: 5.7 Consensus size: 18
21181174 TTAGGTTAGG
21181184 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
21181202 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
**
21181220 GTTA-GG---TT-A--GG
1 GTTAGGGTTTTTAATTAA
21181231 GTTAGGGTTTTTAATTAA
1 GTTAGGGTTTTTAATTAA
*
21181249 GTTAGGGTTTTTAAATAA
1 GTTAGGGTTTTTAATTAA
*
21181267 ATTAGGGTTTTTA
1 GTTAGGGTTTTTA
21181280 TTACATCAAA
Statistics
Matches: 65, Mismatches: 6, Indels: 14
0.76 0.07 0.16
Matches are distributed among these distances:
11 4 0.06
12 2 0.03
13 1 0.02
14 2 0.03
15 2 0.03
16 1 0.02
17 2 0.03
18 51 0.78
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (18 bp):
GTTAGGGTTTTTAATTAA
Found at i:21181327 original size:25 final size:26
Alignment explanation
Indices: 21181275--21181338 Score: 85
Period size: 25 Copynumber: 2.5 Consensus size: 26
21181265 AAATTAGGGT
* *
21181275 TTTTATTACATCAAATTGAACTTCTA
1 TTTTATTACATCAAATTAAACTTATA
* *
21181301 TTTTATTATATTAAA-TAAACTTATA
1 TTTTATTACATCAAATTAAACTTATA
21181326 TTTTATTACATCA
1 TTTTATTACATCA
21181339 GATAATAAAT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
25 19 0.59
26 13 0.41
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.50
Consensus pattern (26 bp):
TTTTATTACATCAAATTAAACTTATA
Found at i:21181774 original size:18 final size:18
Alignment explanation
Indices: 21181747--21181781 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
21181737 CTGAAAAGGA
* *
21181747 TACATGTAAGGGTTAGGG
1 TACATATAAGGGCTAGGG
21181765 TACATATAAGGGCTAGG
1 TACATATAAGGGCTAGG
21181782 AAACACACCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.09, G:0.34, T:0.26
Consensus pattern (18 bp):
TACATATAAGGGCTAGGG
Found at i:21182443 original size:7 final size:7
Alignment explanation
Indices: 21182433--21182457 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
21182423 TTATATACAT
21182433 AATACTA
1 AATACTA
21182440 AATACTA
1 AATACTA
21182447 AATACTA
1 AATACTA
21182454 AATA
1 AATA
21182458 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:21185451 original size:2 final size:2
Alignment explanation
Indices: 21185444--21185472 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21185434 TAATGAAAAT
21185444 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
21185473 GTGTGTATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:21185947 original size:31 final size:30
Alignment explanation
Indices: 21185911--21185976 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
21185901 GCCATTGATG
*
21185911 AAAATA-TAAAAAAATTTAAAATTATTTTTAA
1 AAAATATTAAAAAAA-TTAAAATTA-TTTCAA
21185942 AAAATATTAAAAAAATTAAAATTATTTCAA
1 AAAATATTAAAAAAATTAAAATTATTTCAA
21185972 AAAAT
1 AAAAT
21185977 GAAATTGAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 10 0.30
31 15 0.45
32 8 0.24
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAATATTAAAAAAATTAAAATTATTTCAA
Found at i:21186034 original size:40 final size:40
Alignment explanation
Indices: 21185987--21186075 Score: 151
Period size: 40 Copynumber: 2.2 Consensus size: 40
21185977 GAAATTGAGG
21185987 GGAAATTGAAATTAAATATGGATTTAAGAGAATTTTGGAA
1 GGAAATTGAAATTAAATATGGATTTAAGAGAATTTTGGAA
* * *
21186027 GGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTTGAA
1 GGAAATTGAAATTAAATATGGATTTAAGAGAATTTTGGAA
21186067 GGAAATTGA
1 GGAAATTGA
21186076 GAGGATTAGA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 46 1.00
ACGTcount: A:0.43, C:0.00, G:0.25, T:0.33
Consensus pattern (40 bp):
GGAAATTGAAATTAAATATGGATTTAAGAGAATTTTGGAA
Found at i:21191470 original size:29 final size:29
Alignment explanation
Indices: 21191428--21191485 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
21191418 GAAGAAGAAT
21191428 AACTCAGACAGATTCATATAAAAAAAGGG
1 AACTCAGACAGATTCATATAAAAAAAGGG
21191457 AACTCAGACAGATTCATATAAAAAAAGGG
1 AACTCAGACAGATTCATATAAAAAAAGGG
21191486 TTAGAAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.52, C:0.14, G:0.17, T:0.17
Consensus pattern (29 bp):
AACTCAGACAGATTCATATAAAAAAAGGG
Found at i:21193230 original size:29 final size:29
Alignment explanation
Indices: 21193208--21193263 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
21193198 CTCTGTTTGT
* * *
21193208 TTGAAGCACTTCGGTGCTACTCTATTCAG
1 TTGAAGCACTTCAGTGCCACTCTGTTCAG
*
21193237 TTGAAGCATTTCAGTGCCACTCTGTTC
1 TTGAAGCACTTCAGTGCCACTCTGTTC
21193264 TAATAAAGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.20, C:0.25, G:0.20, T:0.36
Consensus pattern (29 bp):
TTGAAGCACTTCAGTGCCACTCTGTTCAG
Found at i:21194560 original size:28 final size:28
Alignment explanation
Indices: 21194518--21194572 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
21194508 TATGACATTT
* *
21194518 TTGTAGTACGTTTTTTACTCTTGTAGTC
1 TTGTAGTACGATTTTCACTCTTGTAGTC
* *
21194546 TTGTAGTATGATTTTCAGTCTTGTAGT
1 TTGTAGTACGATTTTCACTCTTGTAGT
21194573 ACGCTTTTGC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.16, C:0.11, G:0.20, T:0.53
Consensus pattern (28 bp):
TTGTAGTACGATTTTCACTCTTGTAGTC
Found at i:21194580 original size:20 final size:20
Alignment explanation
Indices: 21194542--21194580 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
21194532 TTACTCTTGT
*
21194542 AGTCTTGTAGTATGATTTTC
1 AGTCTTGTAGTACGATTTTC
*
21194562 AGTCTTGTAGTACGCTTTT
1 AGTCTTGTAGTACGATTTT
21194581 GCGAGTGATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.49
Consensus pattern (20 bp):
AGTCTTGTAGTACGATTTTC
Done.