Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006407.1 Hibiscus syriacus cultivar Beakdansim tig00015452_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 108032
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:488 original size:29 final size:29
Alignment explanation
Indices: 453--534 Score: 128
Period size: 29 Copynumber: 2.8 Consensus size: 29
443 AAACTAAATT
* *
453 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAAGTAAA
*
482 GATGTCATTGCTTACATCATTTAAGTAAT
1 GATGTCATTGCTTACATCATTTAAGTAAA
511 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
535 GTTAGGTGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
29 44 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.11, T:0.41
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAAGTAAA
Found at i:15488 original size:60 final size:58
Alignment explanation
Indices: 15391--15504 Score: 151
Period size: 60 Copynumber: 1.9 Consensus size: 58
15381 ATAAATGACC
15391 CATCGACTATAGTGTTATTTTGTTGAATCCTTCAACTATTAAAAATTATAAAATAGTA
1 CATCGACTATAGTGTTATTTTGTTGAATCCTTCAACTATTAAAAATTATAAAATAGTA
* * *
15449 CATCGATTATAGGATGTTGTTTTGTT-AATTCCATT-AACTATTAAAAGTTATAAAAT
1 CATCGACTATA-G-TGTTATTTTGTTGAA-TCC-TTCAACTATTAAAAATTATAAAAT
15505 GGCCACCAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
58 10 0.20
59 3 0.06
60 34 0.69
61 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (58 bp):
CATCGACTATAGTGTTATTTTGTTGAATCCTTCAACTATTAAAAATTATAAAATAGTA
Found at i:16170 original size:23 final size:22
Alignment explanation
Indices: 16130--16180 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 22
16120 TTAAAAAAAC
* *
16130 TAAAT-AAAAATATTTTTTATG
1 TAAATAAAAAAAATCTTTTATG
16151 TTAAATAAAAAAAATCTTTTATG
1 -TAAATAAAAAAAATCTTTTATG
16174 TAAATAA
1 TAAATAA
16181 TACTAATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 12 0.46
23 14 0.54
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (22 bp):
TAAATAAAAAAAATCTTTTATG
Found at i:20893 original size:61 final size:61
Alignment explanation
Indices: 20795--20916 Score: 201
Period size: 61 Copynumber: 2.0 Consensus size: 61
20785 TTTTTTCGTG
* * *
20795 CTGCTAATTACAGGTAAAGGATTGCAGATGTCTTAATCCGAGTCTTAAGACTTGAATCGAT
1 CTGCTAATTACAGGGAAAGGATTGCAGATGTCTTAATCCGAATCTTAAGACTCGAATCGAT
20856 CTGCTAATTACAGGGAAAGGATTGCAGATGT-TGTAATCCGAATCTTAAGACTCGAATCGAT
1 CTGCTAATTACAGGGAAAGGATTGCAGATGTCT-TAATCCGAATCTTAAGACTCGAATCGAT
20917 GGATGGCGTC
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
60 1 0.02
61 56 0.98
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.30
Consensus pattern (61 bp):
CTGCTAATTACAGGGAAAGGATTGCAGATGTCTTAATCCGAATCTTAAGACTCGAATCGAT
Found at i:28208 original size:553 final size:559
Alignment explanation
Indices: 27153--28219 Score: 1659
Period size: 553 Copynumber: 1.9 Consensus size: 559
27143 GGTTGGTCGG
* * *
27153 GAATCTCATTCCCGGTAATGTTTTATTACCAATAGTAGATTTTTTGGGTATATTACCGAGAATGT
1 GAATCTCATACCCGATAATGTTTTATTACCAAAAGTAGATTTTTTGGGTATATTACCGAGAATGT
* * * *
27218 CATTATCTCCCTTTCCTTAGGTATTATTGGATTACTAGCGTTTTGGATTAAAATGCGCTTAAATT
66 CATTATCTCCCTTCCCTTAGGTATTATTGGATTACGAGCGTTTTGGACTAAAATGCCCTTAAA-T
** * *
27283 TTTTTCTCTCAAAAATATATTTCTTCTGTCATCGAATAATAAAAATTCTACGAAAGTTAAATTAC
130 AATTTCTCTAAAAAATATACTTCTTCTGTCATCGAATAATAAAAATTCTACGAAAGTTAAATTAC
*
27348 AAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAAATCTTTAATTAAAATTTTATATGAAG
195 AAATTTATCCTTAAACTATTTTAGATTTAC-AAAAAAAAATCTATAATTAAAATTTTATATGAAG
27413 TTCACGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAT
259 TTCACGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAT
* * *
27478 ATATATATAAAAATTTTATGAATTTAATTTTTTTTAAAAATATTTATAAATATTTTTCAACTTGT
324 ATATATATAAAAATTTTATGAATTTAA-TATTTTTAAAAAAATATATAAATATTTTTCAACTTGT
* * *
27543 TAAAAAACAAATATATAATAAGGATAATTTGGTCAAATATACATTCCAATAATCTTTTATTCCTT
388 TAAAAAACAAATATATAATAAGGACAATTTCGTCAAATATACATTCCAATAATATTTTATTCCTT
* **
27608 TAACCAAACACAGTAATCTTACATTCCTGTTAAATGAACCAAACACAAAATACAACATTCCAAGT
453 TAACCAAACACAGTAATCTTACATTCATGTTAAACCAACCAAACACAAAATACAACATTCCAAGT
27673 AATCTTATTCCCTAGTAATCTTACATTCCCCCGTTTGGCCGA
518 AATCTTATTCCCTAGTAATCTTACATTCCCCCGTTTGGCCGA
* *
27715 GAATCTCATACCCGATAATGTTTTATTATCAAAAGTAGATTTTTTGGGTATATTACCGGGAATGT
1 GAATCTCATACCCGATAATGTTTTATTACCAAAAGTAGATTTTTTGGGTATATTACCGAGAATGT
* * *
27780 TATTA-CATTCCTTCCCTTAGGTATTGTTGGATTACCGA-CGTTTTGGACTAAAATGCCCTTAAA
66 CATTATC-TCCCTTCCCTTAGGTATTATTGGATTA-CGAGCGTTTTGGACTAAAATGCCCTTAAA
* *
27843 -AATTT-TC-AAAAAATATACTTCTTCTGTCATTGAATAATAAAAATTCTACGAAGGTTAAATTA
129 TAATTTCTCTAAAAAATATACTTCTTCTGTCATCGAATAATAAAAATTCTACGAAAGTTAAATTA
27905 CAAATTTATCCTTAAACTATTTTAGATTTAC-AAAAAAAATCTATAATTAAAATTTTATATGAAG
194 CAAATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAATCTATAATTAAAATTTTATATGAAG
* *
27969 TTCAGGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTTAATTTTGTAAAA-
259 TTCACGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAAT
* *
28033 A-A-ATCATATAAATTTTATGAATTTAA-ATTTTTAAAGAAAATATATAAATATTTTTTAACTTG
324 ATATAT-ATAAAAATTTTATGAATTTAATATTTTTAAA-AAAATATATAAATATTTTTCAACTTG
* *
28095 TTAAAAAACAAATATATAATAAGGACAATTTCGTCAAATATATATTTCAATAATATTTTATTCCT
387 TTAAAAAACAAATATATAATAAGGACAATTTCGTCAAATATACATTCCAATAATATTTTATTCCT
* * * *
28160 TTAATCAAACACAGTAGTTTTACATTCATGTTAAACCAACCAAACACAAAATTCAACATT
452 TTAACCAAACACAGTAATCTTACATTCATGTTAAACCAACCAAACACAAAATACAACATT
28220 GACATTAATT
Statistics
Matches: 463, Mismatches: 38, Indels: 17
0.89 0.07 0.03
Matches are distributed among these distances:
552 8 0.02
553 138 0.30
554 21 0.05
555 1 0.00
556 94 0.20
558 82 0.18
559 2 0.00
560 3 0.01
561 1 0.00
562 111 0.24
563 2 0.00
ACGTcount: A:0.38, C:0.14, G:0.09, T:0.39
Consensus pattern (559 bp):
GAATCTCATACCCGATAATGTTTTATTACCAAAAGTAGATTTTTTGGGTATATTACCGAGAATGT
CATTATCTCCCTTCCCTTAGGTATTATTGGATTACGAGCGTTTTGGACTAAAATGCCCTTAAATA
ATTTCTCTAAAAAATATACTTCTTCTGTCATCGAATAATAAAAATTCTACGAAAGTTAAATTACA
AATTTATCCTTAAACTATTTTAGATTTACAAAAAAAAATCTATAATTAAAATTTTATATGAAGTT
CACGGGTTAAAATAAAATTTTACCCTTTCATTAAACCTTTTTATATTTTCAATTTTGTAAAATAT
ATATATAAAAATTTTATGAATTTAATATTTTTAAAAAAATATATAAATATTTTTCAACTTGTTAA
AAAACAAATATATAATAAGGACAATTTCGTCAAATATACATTCCAATAATATTTTATTCCTTTAA
CCAAACACAGTAATCTTACATTCATGTTAAACCAACCAAACACAAAATACAACATTCCAAGTAAT
CTTATTCCCTAGTAATCTTACATTCCCCCGTTTGGCCGA
Found at i:32798 original size:18 final size:18
Alignment explanation
Indices: 32775--32810 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
32765 GACCTACGAC
32775 GTGGCTCCCGACGAGGAT
1 GTGGCTCCCGACGAGGAT
32793 GTGGCTCCCGACGAGGAT
1 GTGGCTCCCGACGAGGAT
32811 CGTGACGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.39, T:0.17
Consensus pattern (18 bp):
GTGGCTCCCGACGAGGAT
Found at i:32819 original size:12 final size:12
Alignment explanation
Indices: 32802--32826 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
32792 TGTGGCTCCC
32802 GACGAGGATCGT
1 GACGAGGATCGT
32814 GACGAGGATCGT
1 GACGAGGATCGT
32826 G
1 G
32827 TCGTGCATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.16, G:0.44, T:0.16
Consensus pattern (12 bp):
GACGAGGATCGT
Found at i:32918 original size:29 final size:29
Alignment explanation
Indices: 32886--32957 Score: 101
Period size: 29 Copynumber: 2.5 Consensus size: 29
32876 GCAATCTACA
*
32886 AGGTCGCCATGCACTCCC-AGCGACCTTGT
1 AGGTCGCCATGCACTCCCGA-CGACCTTAT
* *
32915 AGGTCGCCAAGCAATCCCGACGACCTTAT
1 AGGTCGCCATGCACTCCCGACGACCTTAT
32944 AGGTCGCCATGCAC
1 AGGTCGCCATGCAC
32958 GCCGACGTCC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 36 0.97
30 1 0.03
ACGTcount: A:0.22, C:0.36, G:0.24, T:0.18
Consensus pattern (29 bp):
AGGTCGCCATGCACTCCCGACGACCTTAT
Found at i:33612 original size:21 final size:21
Alignment explanation
Indices: 33587--33630 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
33577 AATTTAGTTA
33587 ATTAGTTTGTTAGTATAAATT
1 ATTAGTTTGTTAGTATAAATT
* *
33608 ATTAGTTTGTTAGTTTAAGTT
1 ATTAGTTTGTTAGTATAAATT
33629 AT
1 AT
33631 ATTATATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.16, T:0.55
Consensus pattern (21 bp):
ATTAGTTTGTTAGTATAAATT
Found at i:36785 original size:49 final size:49
Alignment explanation
Indices: 36783--37290 Score: 352
Period size: 60 Copynumber: 9.1 Consensus size: 49
36773 TTTGATTGTA
*
36783 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG
1 ATTTGATTGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TG
36837 ATAGTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
1 AT--T--TGA-TT-GTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
* *
36892 ATTTGATAGTAATGATTTAGTAATGAATAGTAATAATGAAATCATTAATAATTTTTAATGATTTG
1 ATTTGATTGTAATGA-TTAGTAAT-AAT-G--A-AAT----T-ATTATTAATTTTT-A--A--TG
36957 ATAATAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG
1 AT--T--TGA-TT-GTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TG
*
37017 ATAGTAATGATTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTG
1 AT--T--TGATT-GTAATGATTAGTAATAATGAAATTATTATTAAT-TTT--T-A-ATG
37076 ATATTAATGATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
1 --ATT--TGA-TT-GTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
*
37131 ATTTGATAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTG
1 ATTTGATTGTAATGATTAGTAATAATGAAATTATTATTAATTTTT-A--A--TG
*
37185 ATAGTAATGATTAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATG
1 AT--T--TGATT-GTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
* * *
37239 ATTTGATAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATG
1 ATTTGATTGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
37287 ATTT
1 ATTT
37291 AGTAATGATT
Statistics
Matches: 394, Mismatches: 16, Indels: 94
0.78 0.03 0.19
Matches are distributed among these distances:
48 24 0.06
49 62 0.16
50 15 0.04
51 9 0.02
52 3 0.01
53 4 0.01
54 11 0.03
55 9 0.02
56 4 0.01
57 2 0.01
58 8 0.02
59 86 0.22
60 118 0.30
61 4 0.01
62 2 0.01
63 1 0.00
65 7 0.02
66 1 0.00
67 1 0.00
68 1 0.00
69 6 0.02
70 9 0.02
71 7 0.02
ACGTcount: A:0.41, C:0.00, G:0.12, T:0.46
Consensus pattern (49 bp):
ATTTGATTGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATG
Found at i:36801 original size:60 final size:59
Alignment explanation
Indices: 36728--37153 Score: 701
Period size: 60 Copynumber: 7.1 Consensus size: 59
36718 TTTATAAGAT
* * * *
36728 TTAGTAATTATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATTGTAATTTGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAA--TGA
36789 -TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
36847 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* * * *
36907 TTTAGTAATGAATAGTAATAATGAAATCATTAATAATTTTTAATGATTTGATAATAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
36967 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
* *
37027 TTAGTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAATGA
1 TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
37086 TTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 -TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
37146 TTAGTAAT
1 TTAGTAAT
37154 AATGAAATTA
Statistics
Matches: 346, Mismatches: 16, Indels: 8
0.94 0.04 0.02
Matches are distributed among these distances:
58 3 0.01
59 65 0.19
60 278 0.80
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (59 bp):
TTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
Found at i:36944 original size:120 final size:119
Alignment explanation
Indices: 36725--37265 Score: 856
Period size: 120 Copynumber: 4.6 Consensus size: 119
36715 GTATTTATAA
* * * *
36725 GATTTAGTAATTATTAGTAATGATGAAATTATTATTAATATTTAATGATTTGATTGTAATTTGA-
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAA--TGAT
*
36789 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
64 TAGTAATGAATAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
36845 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTT
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA-TT
* * *
36910 AGTAATGAATAGTAATAATGAAATCATTAATAATTTTTAATGATTTGATAATAAT
65 AGTAATGAATAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
36965 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
* * *
37030 GTAATGATTAGTAATAATGAAATTATTATTAATATTTAATGATTTGATATTAAT
66 GTAATGAATAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
37084 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGT-A--A-T-
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
37144 G--AT---TAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
66 GTAATGAATAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
*
37193 GA-TTAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
1 GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
37257 GTAAT-AATA
66 GTAATGAATA
37266 ATTTATTATT
Statistics
Matches: 394, Mismatches: 16, Indels: 25
0.91 0.04 0.06
Matches are distributed among these distances:
108 53 0.13
109 47 0.12
111 1 0.00
112 3 0.01
113 1 0.00
114 1 0.00
115 3 0.01
116 1 0.00
117 2 0.01
118 4 0.01
119 109 0.28
120 169 0.43
ACGTcount: A:0.41, C:0.00, G:0.13, T:0.46
Consensus pattern (119 bp):
GATTTAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGATTA
GTAATGAATAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAAT
Found at i:36969 original size:24 final size:24
Alignment explanation
Indices: 36947--37109 Score: 72
Period size: 25 Copynumber: 6.8 Consensus size: 24
36937 TAATAATTTT
*
36947 TAATGATTTGATAATAATGATTTAG
1 TAATGATTAG-TAATAATGATTTAG
* *
36972 TAATGATTAGTAATAATGAAATTAT
1 TAATGATTAGTAATAATG-ATTTAG
* * *
36997 TATTAATT--T-TTAATGATTTGATAG
1 TAATGATTAGTAATAATGA-TT--TAG
* * * *
37021 TAATGATTAGTAATGATTA-GTAA
1 TAATGATTAGTAATAATGATTTAG
* *
37044 TAATGAAATTATTATTAAT-A-TT--
1 TAATG--ATTAGTAATAATGATTTAG
* *
37066 TAATGATTTGATATTAATGATTTAG
1 TAATGATTAG-TAATAATGATTTAG
37091 TAATGATTAGTAATAATGA
1 TAATGATTAGTAATAATGA
37110 AATTATTATT
Statistics
Matches: 101, Mismatches: 23, Indels: 29
0.66 0.15 0.19
Matches are distributed among these distances:
20 3 0.03
21 8 0.08
22 12 0.12
23 10 0.10
24 26 0.26
25 37 0.37
26 1 0.01
27 4 0.04
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (24 bp):
TAATGATTAGTAATAATGATTTAG
Found at i:37031 original size:10 final size:10
Alignment explanation
Indices: 37018--37044 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
37008 AATGATTTGA
37018 TAGTAATGAT
1 TAGTAATGAT
37028 TAGTAATGAT
1 TAGTAATGAT
37038 TAGTAAT
1 TAGTAAT
37045 AATGAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:37071 original size:35 final size:35
Alignment explanation
Indices: 37031--37133 Score: 91
Period size: 35 Copynumber: 3.2 Consensus size: 35
37021 TAATGATTAG
37031 TAATGATTAGTAATAATGAAATTATTATTAATATT
1 TAATGATTAGTAATAATGAAATTATTATTAATATT
* * * *
37066 TAATGATT--TGAT-AT----TAATGATT--TA-G
1 TAATGATTAGTAATAATGAAATTATTATTAATATT
*
37091 TAATGATTAGTAATAATGAAATTATTATTAATTTT
1 TAATGATTAGTAATAATGAAATTATTATTAATATT
37126 TAATGATT
1 TAATGATT
37134 TGATAGTAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 20
0.63 0.12 0.26
Matches are distributed among these distances:
25 8 0.16
26 2 0.04
27 3 0.06
28 8 0.16
32 8 0.16
33 3 0.06
34 1 0.02
35 16 0.33
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.48
Consensus pattern (35 bp):
TAATGATTAGTAATAATGAAATTATTATTAATATT
Found at i:37141 original size:39 final size:45
Alignment explanation
Indices: 37119--37289 Score: 101
Period size: 59 Copynumber: 3.3 Consensus size: 45
37109 AAATTATTAT
37119 TAATTTTTAATGATTTGATAGTAATGATTAGTAATAATGAAATTATTAT
1 TAATTTTTAA-GA-TTGATA-T-ATGATTAGTAATAATGAAATTATTAT
*
37168 TAATTTTTAATGATTTGATAGTAATGATTAGTAATGATTAGTAATAATAAAATTATTAT
1 TAATTTTT-A--A---G--A-T--TGA-TA-T-ATGATTAGTAATAATGAAATTATTAT
*
37227 TAATTTTTAATGATTTGATAGTAATGATTAGTAATAAT-AATTTATTAT
1 TAATTTTTAA-GA-TTGATA-T-ATGATTAGTAATAATGAAATTATTAT
*
37275 TAATATTTAATGATT
1 TAATTTTTAA-GATT
37290 TAGTAATGAT
Statistics
Matches: 107, Mismatches: 5, Indels: 22
0.80 0.04 0.16
Matches are distributed among these distances:
47 2 0.02
48 21 0.20
49 28 0.26
50 4 0.04
52 3 0.03
54 4 0.04
56 3 0.03
58 4 0.04
59 38 0.36
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.48
Consensus pattern (45 bp):
TAATTTTTAAGATTGATATATGATTAGTAATAATGAAATTATTAT
Found at i:37153 original size:24 final size:24
Alignment explanation
Indices: 37126--37206 Score: 72
Period size: 24 Copynumber: 3.3 Consensus size: 24
37116 TATTAATTTT
37126 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
* *** * * * **
37150 TAATAATGAAATTATTATTAATTTT
1 TAATGATTTGA-TAGTAATGATTAG
37175 TAATGATTTGATAGTAATGATTAG
1 TAATGATTTGATAGTAATGATTAG
37199 TAATGATT
1 TAATGATT
37207 AGTAATAATA
Statistics
Matches: 38, Mismatches: 18, Indels: 2
0.66 0.31 0.03
Matches are distributed among these distances:
24 23 0.61
25 15 0.39
ACGTcount: A:0.40, C:0.00, G:0.15, T:0.46
Consensus pattern (24 bp):
TAATGATTTGATAGTAATGATTAG
Found at i:37199 original size:10 final size:10
Alignment explanation
Indices: 37186--37212 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
37176 AATGATTTGA
37186 TAGTAATGAT
1 TAGTAATGAT
37196 TAGTAATGAT
1 TAGTAATGAT
37206 TAGTAAT
1 TAGTAAT
37213 AATAAAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (10 bp):
TAGTAATGAT
Found at i:37200 original size:59 final size:59
Alignment explanation
Indices: 37137--37261 Score: 241
Period size: 59 Copynumber: 2.1 Consensus size: 59
37127 AATGATTTGA
*
37137 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
37196 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
37255 TAGTAAT
1 TAGTAAT
37262 AATAATTTAT
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 65 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.46
Consensus pattern (59 bp):
TAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGATAGTAATGAT
Found at i:37290 original size:48 final size:49
Alignment explanation
Indices: 37088--37290 Score: 255
Period size: 49 Copynumber: 4.0 Consensus size: 49
37078 ATTAATGATT
* *
37088 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
* *
37137 TAGTAATGATTAGTAATAATGAAATTATTATTAATTTTTAATGATTTGATAGTAATGA
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTT-A--A--TGAT--T--TGA
*
37195 TTAGTAATGATTAGTAATAATAAAATTATTATTAATTTTTAATGATTTGA
1 -TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
*
37245 TAGTAATGATTAGTAATAAT-AATTTATTATTAATATTTAATGATTT
1 TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTT
37291 AGTAATGATT
Statistics
Matches: 141, Mismatches: 3, Indels: 21
0.85 0.02 0.13
Matches are distributed among these distances:
48 24 0.17
49 59 0.42
50 4 0.03
52 2 0.01
54 8 0.06
56 2 0.01
58 4 0.03
59 38 0.27
ACGTcount: A:0.41, C:0.00, G:0.11, T:0.47
Consensus pattern (49 bp):
TAGTAATGATTAGTAATAATAAAATTATTATTAATATTTAATGATTTGA
Found at i:37308 original size:49 final size:46
Alignment explanation
Indices: 37189--37310 Score: 140
Period size: 48 Copynumber: 2.6 Consensus size: 46
37179 GATTTGATAG
* * *
37189 TAATGA-TTAGTAATGATTAGTAATAATAAAATTATTATTAATTTT
1 TAATGATTTAGTAATGATTTGTAGTAATAAAATTATTATTAATATT
* * *
37234 TAATGATTTGATAGTAATGATTAGTAATAAT-AATTTATTATTAATATT
1 TAATGA-TT--TAGTAATGATTTGTAGTAATAAAATTATTATTAATATT
37282 TAATGATTTAGTAATGATTTGATAGTAAT
1 TAATGATTTAGTAATGATTTG-TAGTAAT
37311 GTTTTACGAC
Statistics
Matches: 68, Mismatches: 4, Indels: 9
0.84 0.05 0.11
Matches are distributed among these distances:
45 18 0.26
46 6 0.09
47 3 0.04
48 21 0.31
49 20 0.29
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (46 bp):
TAATGATTTAGTAATGATTTGTAGTAATAAAATTATTATTAATATT
Found at i:39623 original size:30 final size:31
Alignment explanation
Indices: 39589--39674 Score: 115
Period size: 30 Copynumber: 2.8 Consensus size: 31
39579 TCCCTTAAAC
*
39589 AACTAATAAATTATTCTTTAATATAACGTT-
1 AACTAATAAATTATTCTTTAATATAACATTA
*
39619 AACTAATAAACTATTCTTTAATAT-ACATTA
1 AACTAATAAATTATTCTTTAATATAACATTA
*
39649 AACTAATAAATGATT-TTTAATTATAA
1 AACTAATAAATTATTCTTTAA-TATAA
39675 TTTACTACTA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
29 9 0.18
30 39 0.80
31 1 0.02
ACGTcount: A:0.47, C:0.09, G:0.02, T:0.42
Consensus pattern (31 bp):
AACTAATAAATTATTCTTTAATATAACATTA
Found at i:39891 original size:21 final size:21
Alignment explanation
Indices: 39867--39906 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
39857 TTTCTATATG
39867 ATATAACTTAAACTAACAATA
1 ATATAACTTAAACTAACAATA
39888 ATATAACTTAAACTAACAA
1 ATATAACTTAAACTAACAA
39907 ACTAATTAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.15, G:0.00, T:0.28
Consensus pattern (21 bp):
ATATAACTTAAACTAACAATA
Found at i:40050 original size:34 final size:35
Alignment explanation
Indices: 40008--40076 Score: 97
Period size: 37 Copynumber: 2.0 Consensus size: 35
39998 TCTTTTATAT
*
40008 AACTT-AA-ACTAATAAACTATTTTTATTATAATAA
1 AACTTAAACACTAATAAACTAATTTT-TTATAATAA
40042 AACTTAAACTACTAATAAACTAATTTTTTATAATA
1 AACTTAAAC-ACTAATAAACTAATTTTTTATAATA
40077 TAAATTCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
34 5 0.16
35 2 0.06
36 8 0.26
37 16 0.52
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (35 bp):
AACTTAAACACTAATAAACTAATTTTTTATAATAA
Found at i:40136 original size:27 final size:29
Alignment explanation
Indices: 40101--40165 Score: 82
Period size: 28 Copynumber: 2.3 Consensus size: 29
40091 AAAATATAAC
*
40101 TTAACTATTTA-ACTAACT-ACAAACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
40128 TTAAATA-TTAGACTAACTAACACACTAA
1 TTAAATATTTAGACTAACTAACAAACTAA
*
40156 TTAATTATTT
1 TTAAATATTT
40166 TTTTAATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 3 0.09
27 13 0.41
28 14 0.44
29 2 0.06
ACGTcount: A:0.46, C:0.15, G:0.02, T:0.37
Consensus pattern (29 bp):
TTAAATATTTAGACTAACTAACAAACTAA
Found at i:40279 original size:9 final size:9
Alignment explanation
Indices: 40247--40284 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
40237 CTAATAAACT
40247 AATAATTTAA
1 AATAA-TTAA
40257 AATAA-TAA
1 AATAATTAA
*
40265 ACTAATTAA
1 AATAATTAA
40274 AATAATTAA
1 AATAATTAA
40283 AA
1 AA
40285 AAAAAACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 13 0.52
10 5 0.20
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATTAA
Found at i:40617 original size:29 final size:28
Alignment explanation
Indices: 40570--40653 Score: 132
Period size: 29 Copynumber: 2.9 Consensus size: 28
40560 AAAGGCATAG
40570 GTCGTTGGGATCCCTTGGCGACCTACAAT
1 GTCGTTGGGATCCC-TGGCGACCTACAAT
*
40599 GTCGCTGGGATGCCCTGGCGACCTACAAT
1 GTCGTTGGGAT-CCCTGGCGACCTACAAT
40628 GTCGTTGGGATTCCCTGGCGACCTAC
1 GTCGTTGGGA-TCCCTGGCGACCTAC
40654 CCACGTTGCA
Statistics
Matches: 51, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
29 47 0.92
30 4 0.08
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (28 bp):
GTCGTTGGGATCCCTGGCGACCTACAAT
Found at i:40725 original size:42 final size:42
Alignment explanation
Indices: 40678--40765 Score: 167
Period size: 42 Copynumber: 2.1 Consensus size: 42
40668 GCCATGCACA
*
40678 GCCATGCAGAGACTCCAATCTCGCCCAGACCCATGCCACGTT
1 GCCATGCAGAGACTCCAACCTCGCCCAGACCCATGCCACGTT
40720 GCCATGCAGAGACTCCAACCTCGCCCAGACCCATGCCACGTT
1 GCCATGCAGAGACTCCAACCTCGCCCAGACCCATGCCACGTT
40762 GCCA
1 GCCA
40766 CCCCGCCATG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.24, C:0.42, G:0.19, T:0.15
Consensus pattern (42 bp):
GCCATGCAGAGACTCCAACCTCGCCCAGACCCATGCCACGTT
Found at i:49844 original size:2 final size:2
Alignment explanation
Indices: 49837--49870 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
49827 TTTATCCAAA
49837 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
49871 TAAATTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:58240 original size:101 final size:98
Alignment explanation
Indices: 58042--58240 Score: 229
Period size: 101 Copynumber: 2.0 Consensus size: 98
58032 TGAACAAAAA
* * * *
58042 TGGACACTTCAACAAACGAAAATATATGAAATCCTACCTAGAGGAAACTTTCCTTGTCCACATAA
1 TGGAAACTCCAACAAACAAAAATATATAAAATCCTACCTAGAGGAAACTTTCCTTGTCCACATAA
* * * *
58107 AAGAAAGATGTCTTCGAAATTTCAATAACAAAT
66 AACAAAGACGACTTCGAAATTACAATAACAAAT
*
58140 TGGAAACTCCAACAAACAAAAATAT-TAAAAATCCTACCTTAGAGGAAATTTTCCTTTTGTCCAC
1 TGGAAACTCCAACAAACAAAAATATAT-AAAATCCTACC-TAGAGGAAACTTTCC--TTGTCCAC
* * ** *
58204 ATAAAACAAAGCCGAGTTCGATGTTACAATAGCAAAT
62 ATAAAACAAAGACGACTTCGAAATTACAATAACAAAT
58241 GCATTAACAA
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
97 1 0.01
98 32 0.39
99 14 0.17
101 36 0.43
ACGTcount: A:0.43, C:0.20, G:0.12, T:0.26
Consensus pattern (98 bp):
TGGAAACTCCAACAAACAAAAATATATAAAATCCTACCTAGAGGAAACTTTCCTTGTCCACATAA
AACAAAGACGACTTCGAAATTACAATAACAAAT
Found at i:63394 original size:55 final size:54
Alignment explanation
Indices: 63337--63890 Score: 311
Period size: 51 Copynumber: 10.6 Consensus size: 54
63327 TGACGAGCCT
* *
63337 GCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAACGTGTCT
1 GCTCCCTATTCATTCAGAG-AGTATAAGACTCGAACAATCTTCATAAAACG-GTCC
* * *
63392 GCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTTAATAAAACGGGTCC
1 GCTCCCTATTCATTCAGAGAGTATAAGACTCGAACAATC-TTCATAAAAC-GGTCC
* * *
63448 GCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGAAAAATCTTCA-ATAAACAGGTCC
1 GCTCCCTATTCATTCAGAGAGTATAAG-ACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
63503 ACTCCCTATTCATTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
63554 GCTCCCTATTCATTCAGAGAGTACAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
63605 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
63656 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
63707 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
63758 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* * * *
63809 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTCA-ACGAACTTGTCC
1 GCTCCCTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCATA-AAAC-GGTCC
* *
63860 GCTCCCTATTCTTTCAGAGAGTATAGGACTC
1 GCTCCCTATTCATTCAGAGAGTATAAGACTC
63891 AATCTTCAAC
Statistics
Matches: 469, Mismatches: 23, Indels: 17
0.92 0.05 0.03
Matches are distributed among these distances:
51 348 0.74
54 1 0.00
55 72 0.15
56 47 0.10
57 1 0.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (54 bp):
GCTCCCTATTCATTCAGAGAGTATAAGACTCGAACAATCTTCATAAAACGGTCC
Found at i:63560 original size:51 final size:51
Alignment explanation
Indices: 63444--63905 Score: 789
Period size: 51 Copynumber: 9.0 Consensus size: 51
63434 AATAAAACGG
* * * ** **
63444 GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAAAATCTTCAATAAACAG
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTC----AATCTTCAACGAACTT
* *
63499 GTCCACTCCCTATTCATTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
* *
63550 GTCCGCTCCCTATTCATTCAGAGAGTACAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
63601 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
63652 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
63703 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
63754 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
63805 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
63856 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
1 GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACT
63906 AATTTGCTTC
Statistics
Matches: 395, Mismatches: 12, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
51 364 0.92
55 31 0.08
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.30
Consensus pattern (51 bp):
GTCCGCTCCCTATTCTTTCAGAGAGTATAGGACTCAATCTTCAACGAACTT
Found at i:65264 original size:29 final size:29
Alignment explanation
Indices: 65222--65305 Score: 73
Period size: 29 Copynumber: 2.9 Consensus size: 29
65212 AACCCTCCTT
* *
65222 TTATTTCTCTTTTTTTCATTTTTCTCTTA
1 TTATTACTTTTTTTTTCATTTTTCTCTTA
* *
65251 TTATTA-TTTTTTTTCCATTTTTTCTCTTCT
1 TTATTACTTTTTTTTTCA-TTTTTCTCTT-A
* *
65281 TTTTTTCTTTTTTTCTTC-TTTTTCT
1 TTATTACTTTTTTT-TTCATTTTTCT
65306 TTCTTTTTGT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
28 9 0.20
29 15 0.34
30 11 0.25
31 7 0.16
32 2 0.05
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.76
Consensus pattern (29 bp):
TTATTACTTTTTTTTTCATTTTTCTCTTA
Found at i:65288 original size:8 final size:8
Alignment explanation
Indices: 65277--65348 Score: 58
Period size: 8 Copynumber: 8.5 Consensus size: 8
65267 ATTTTTTCTC
65277 TTCTTTTT
1 TTCTTTTT
65285 TTCTTTTT
1 TTCTTTTT
65293 TTCTTCTTT
1 TTCTT-TTT
65302 TTCTTTCTT
1 TTCTTT-TT
65311 TT-TGTTTT
1 TTCT-TTTT
*
65319 TTCCATCATTT
1 TT-C-T-TTTT
65330 TTC-TTTT
1 TTCTTTTT
*
65337 TTCTTATT
1 TTCTTTTT
65345 TTCT
1 TTCT
65349 CATTTTTTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 14
0.75 0.06 0.20
Matches are distributed among these distances:
7 6 0.11
8 26 0.49
9 14 0.26
10 1 0.02
11 6 0.11
ACGTcount: A:0.04, C:0.17, G:0.01, T:0.78
Consensus pattern (8 bp):
TTCTTTTT
Found at i:65291 original size:19 final size:21
Alignment explanation
Indices: 65269--65313 Score: 67
Period size: 19 Copynumber: 2.2 Consensus size: 21
65259 TTTTTTCCAT
65269 TTTTTCTCTTC-TTTT-TTTC
1 TTTTTCTCTTCTTTTTCTTTC
*
65288 TTTTTTTCTTCTTTTTCTTTC
1 TTTTTCTCTTCTTTTTCTTTC
65309 TTTTT
1 TTTTT
65314 GTTTTTTCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 10 0.43
20 4 0.17
21 9 0.39
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTCTCTTCTTTTTCTTTC
Found at i:65291 original size:28 final size:28
Alignment explanation
Indices: 65240--65333 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 28
65230 CTTTTTTTCA
*
65240 TTTTTCTCTTATTATTATTTTTTTTCCAT-
1 TTTTTCTCTTCTT-TT-TTTTTTTTCCATC
* *
65269 TTTTTCTCTTCTTTTTTTCTTTTTTTCTTC
1 TTTTTCTCTTC-TTTTTT-TTTTTTCCATC
*
65299 TTTTTCT-TTCTTTTTGTTTTTTCCATC
1 TTTTTCTCTTCTTTTTTTTTTTTCCATC
65326 ATTTTTCT
1 -TTTTTCT
65334 TTTTTCTTAT
Statistics
Matches: 55, Mismatches: 6, Indels: 9
0.79 0.09 0.13
Matches are distributed among these distances:
27 9 0.16
28 14 0.25
29 23 0.42
30 9 0.16
ACGTcount: A:0.06, C:0.17, G:0.01, T:0.76
Consensus pattern (28 bp):
TTTTTCTCTTCTTTTTTTTTTTTCCATC
Found at i:65304 original size:17 final size:17
Alignment explanation
Indices: 65277--65357 Score: 67
Period size: 17 Copynumber: 4.6 Consensus size: 17
65267 ATTTTTTCTC
65277 TTCTTTTTTTCTT-TTT
1 TTCTTTTTTTCTTCTTT
65293 TTCTTCTTTTTCTTTCTTT
1 TTCTT-TTTTTC-TTCTTT
* * *
65312 TTGTTTTTTCCATCATTT
1 TTCTTTTTTTCTTC-TTT
*
65330 TTC-TTTTTTCTTATTT
1 TTCTTTTTTTCTTCTTT
65346 TCTCATTTTTTT
1 T-TC-TTTTTTT
65358 TGTCTTTTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 11
0.74 0.10 0.16
Matches are distributed among these distances:
16 9 0.18
17 17 0.33
18 12 0.24
19 13 0.25
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.78
Consensus pattern (17 bp):
TTCTTTTTTTCTTCTTT
Found at i:65308 original size:21 final size:20
Alignment explanation
Indices: 65258--65313 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 20
65248 TTATTATTAT
65258 TTTTTTTCCATTTTTTCTCTTC
1 TTTTTTT-C-TTTTTTCTCTTC
65280 TTTTTTTCTTTTTT-TCTTC
1 TTTTTTTCTTTTTTCTCTTC
65299 TTTTTCTTTCTTTTT
1 -TTTT-TTTCTTTTT
65314 GTTTTTTCCA
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
19 5 0.16
20 10 0.31
21 10 0.31
22 7 0.22
ACGTcount: A:0.02, C:0.18, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTTCTTTTTTCTCTTC
Found at i:65346 original size:28 final size:26
Alignment explanation
Indices: 65259--65346 Score: 77
Period size: 27 Copynumber: 3.2 Consensus size: 26
65249 TATTATTATT
* *
65259 TTTTTTCCATTTTTTCTCTTCTTTTTTTC
1 TTTTTTCCATCTTTT-TC-T-TTTTTTTA
* * *
65288 TTTTTTTCTTCTTTTTCTTTCTTTTTG
1 TTTTTTCCATCTTTTTCTTT-TTTTTA
65315 TTTTTTCCATCATTTTTCTTTTTTCTTA
1 TTTTTTCCATC-TTTTTCTTTTTT-TTA
65343 TTTT
1 TTTT
65347 CTCATTTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
26 2 0.04
27 18 0.37
28 17 0.35
29 12 0.24
ACGTcount: A:0.05, C:0.17, G:0.01, T:0.77
Consensus pattern (26 bp):
TTTTTTCCATCTTTTTCTTTTTTTTA
Found at i:65358 original size:28 final size:26
Alignment explanation
Indices: 65259--65365 Score: 83
Period size: 29 Copynumber: 3.9 Consensus size: 26
65249 TATTATTATT
65259 TTTTTTCCATTTTTTCTCTTCTTTTTTTC
1 TTTTTTCCATTTTTT-T-TTC-TTTTTTC
* * *
65288 TTTTTTTCTTCTTTTTCTTTC-TTTTTG
1 TTTTTTCCAT-TTTTT-TTTCTTTTTTC
**
65315 TTTTTTCCA-TCATTTTTCTTTTTTC
1 TTTTTTCCATTTTTTTTTCTTTTTTC
65340 TTATTTTCTCATTTTTTTTGTCTTTT
1 TT-TTTTC-CATTTTTTTT-TCTTTT
65366 ATTTCTTCTT
Statistics
Matches: 62, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
24 4 0.06
25 10 0.16
26 5 0.08
27 14 0.23
28 5 0.08
29 17 0.27
30 7 0.11
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.77
Consensus pattern (26 bp):
TTTTTTCCATTTTTTTTTCTTTTTTC
Found at i:65369 original size:24 final size:24
Alignment explanation
Indices: 65281--65355 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
65271 TTTCTCTTCT
*
65281 TTTTTTCTTTTTTTCTTC-TTTTTC
1 TTTTTTCTTATTTTC-TCATTTTTC
* *
65305 TTTCTTTTTGTTTTTTCCATCATTTTTC
1 TTT-TTTCT-TATTTT-C-TCATTTTTC
65333 TTTTTTCTTATTTTCTCATTTTT
1 TTTTTTCTTATTTTCTCATTTTT
65356 TTTGTCTTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
24 11 0.26
25 5 0.12
26 11 0.26
27 7 0.16
28 9 0.21
ACGTcount: A:0.05, C:0.16, G:0.01, T:0.77
Consensus pattern (24 bp):
TTTTTTCTTATTTTCTCATTTTTC
Found at i:75131 original size:46 final size:46
Alignment explanation
Indices: 75035--75167 Score: 216
Period size: 46 Copynumber: 2.9 Consensus size: 46
75025 AAAAGGAAAT
* * *
75035 CCTAACCGCATGATATCTAATTCGCATGC--TTATTCAAAAATTAA
1 CCTAACCGCATGATATCTAGTTCGCATACATTTATTCAAAAATAAA
75079 CCTAACCGCATGATATCTAGTTCGCATACATTTATTCAAAAATAAA
1 CCTAACCGCATGATATCTAGTTCGCATACATTTATTCAAAAATAAA
75125 CCTAACCGCATGATATCTAGTTCGCATACATTTATTCGAAAAA
1 CCTAACCGCATGATATCTAGTTCGCATACATTTATTC-AAAAA
75168 AACGAAAATA
Statistics
Matches: 83, Mismatches: 3, Indels: 3
0.93 0.03 0.03
Matches are distributed among these distances:
44 27 0.33
46 51 0.61
47 5 0.06
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.31
Consensus pattern (46 bp):
CCTAACCGCATGATATCTAGTTCGCATACATTTATTCAAAAATAAA
Found at i:82609 original size:29 final size:29
Alignment explanation
Indices: 82555--82610 Score: 69
Period size: 30 Copynumber: 1.9 Consensus size: 29
82545 AATTAATTTG
* *
82555 ATATTTAAATTTTTATTTTTATAAATAAA
1 ATATTTAAATTTTTATTTGTACAAATAAA
*
82584 ATATTTGACATTTTTATTTGT-CAAATA
1 ATATTT-AAATTTTTATTTGTACAAATA
82611 TCATACTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 11 0.48
30 12 0.52
ACGTcount: A:0.39, C:0.04, G:0.04, T:0.54
Consensus pattern (29 bp):
ATATTTAAATTTTTATTTGTACAAATAAA
Found at i:85726 original size:9 final size:9
Alignment explanation
Indices: 85714--85912 Score: 61
Period size: 9 Copynumber: 22.1 Consensus size: 9
85704 ATATTTATAT
85714 TATATATTA
1 TATATATTA
85723 TATAGTATTTACA
1 TATA-TA-TT--A
85736 TTATATATTA
1 -TATATATTA
*
85746 CAATATATTA
1 -TATATATTA
85756 TATAGTA-TA
1 TATA-TATTA
85765 TATAGTATT-
1 TATA-TATTA
*
85774 TGTATA--A
1 TATATATTA
85781 TATAT-TTA
1 TATATATTA
*
85789 TAGTATTTTA
1 TA-TATATTA
*
85799 TATCT-TTA
1 TATATATTA
85807 TATAATATTA
1 TAT-ATATTA
85817 -ATATATTA
1 TATATATTA
* *
85825 TATATAGTG
1 TATATATTA
85834 TATAGTATT-
1 TATA-TATTA
85843 TATAGT-TTA
1 TATA-TATTA
* *
85852 TATGTAGTA
1 TATATATTA
*
85861 -A-ATA-AA
1 TATATATTA
85867 GTAT-TATTA
1 -TATATATTA
85876 TATA-ATTA
1 TATATATTA
85884 TTTATATATTA
1 --TATATATTA
85895 TAT-TATTA
1 TATATATTA
85903 -ATATTATTA
1 TATA-TATTA
85912 T
1 T
85913 TTTTTGTTTT
Statistics
Matches: 146, Mismatches: 15, Indels: 57
0.67 0.07 0.26
Matches are distributed among these distances:
6 1 0.01
7 8 0.05
8 36 0.25
9 57 0.39
10 29 0.20
11 6 0.04
12 2 0.01
13 3 0.02
14 4 0.03
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (9 bp):
TATATATTA
Found at i:85754 original size:23 final size:22
Alignment explanation
Indices: 85694--85754 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 22
85684 GTATTTATGT
* *
85694 TATATAACATATATTTATATTA
1 TATATTACATATATTTACATTA
*
85716 TATATTATATAGTATTTACATTA
1 TATATTACATA-TATTTACATTA
85739 TATATTACAATATATT
1 TATATTAC-ATATATT
85755 ATATAGTATA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 9 0.27
23 21 0.64
24 3 0.09
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.51
Consensus pattern (22 bp):
TATATTACATATATTTACATTA
Found at i:85754 original size:33 final size:32
Alignment explanation
Indices: 85715--85796 Score: 96
Period size: 33 Copynumber: 2.6 Consensus size: 32
85705 TATTTATATT
*
85715 ATATATTATATAGTATTTACATTATATAT-TACA
1 ATATATTATATAGTATTTACAGTAT-T-TGTACA
* * *
85748 ATATATTATATAGTATATATAGTATTTGTATA
1 ATATATTATATAGTATTTACAGTATTTGTACA
85780 ATATATT-TATAGTATTT
1 ATATATTATATAGTATTT
85797 TATATCTTTA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
31 10 0.23
32 11 0.26
33 22 0.51
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.51
Consensus pattern (32 bp):
ATATATTATATAGTATTTACAGTATTTGTACA
Found at i:85779 original size:22 final size:20
Alignment explanation
Indices: 85713--85832 Score: 84
Period size: 22 Copynumber: 5.8 Consensus size: 20
85703 TATATTTATA
85713 TTATATAT-TATATAGTA-T
1 TTATATATATATATAGTATT
* * * *
85731 TTACATTATATATTACAATATA
1 TTATA-TATATA-TATAGTATT
85753 TTATATAGTATATATAGTATT
1 TTATATA-TATATATAGTATT
*
85774 TGTATAATATATTTATAGTATT
1 T-TAT-ATATATATATAGTATT
* * *
85796 TTATATCTTTATATAATA-T
1 TTATATATATATATAGTATT
*
85815 TAATATATTATATATAGT
1 TTATATA-TATATATAGT
85833 GTATAGTATT
Statistics
Matches: 77, Mismatches: 17, Indels: 14
0.71 0.16 0.13
Matches are distributed among these distances:
18 4 0.05
19 9 0.12
20 20 0.26
21 17 0.22
22 24 0.31
23 3 0.04
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (20 bp):
TTATATATATATATAGTATT
Found at i:85784 original size:42 final size:40
Alignment explanation
Indices: 85709--85786 Score: 111
Period size: 42 Copynumber: 1.9 Consensus size: 40
85699 AACATATATT
*
85709 TATATTATATATTATATAGTATTTACATTATATATTACAA
1 TATATTATATATTATATAGTATTTACATAATATATTACAA
**
85749 TATATTATATAGTATATATAGTATTTGTATAATATATT
1 TATATTATATA-T-TATATAGTATTTACATAATATATT
85787 TATAGTATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
40 11 0.33
41 1 0.03
42 21 0.64
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (40 bp):
TATATTATATATTATATAGTATTTACATAATATATTACAA
Found at i:85822 original size:8 final size:7
Alignment explanation
Indices: 85702--85829 Score: 70
Period size: 7 Copynumber: 17.9 Consensus size: 7
85692 GTTATATAAC
85702 ATATATT
1 ATATATT
85709 -TATATT
1 ATATATT
85715 ATATATT
1 ATATATT
85722 ATATAGTAT
1 ATATA-T-T
* *
85731 TTACATT
1 ATATATT
85738 ATATATT
1 ATATATT
85745 ACAATATATT
1 ---ATATATT
*
85755 ATATAGT
1 ATATATT
85762 ATATA-T
1 ATATATT
85768 AGTAT-TT
1 A-TATATT
* *
85775 GTATAAT
1 ATATATT
85782 ATAT-TT
1 ATATATT
85788 ATAGTATT
1 ATA-TATT
*
85796 TTATATCT
1 ATATAT-T
*
85804 TTATA-T
1 ATATATT
85810 A-ATATT
1 ATATATT
85816 AATATATT
1 -ATATATT
85824 ATATAT
1 ATATAT
85830 AGTGTATAGT
Statistics
Matches: 95, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
5 3 0.03
6 17 0.18
7 47 0.49
8 17 0.18
9 4 0.04
10 7 0.07
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (7 bp):
ATATATT
Found at i:85901 original size:16 final size:17
Alignment explanation
Indices: 85868--85912 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 17
85858 GTAAATAAAG
* *
85868 TATTATTATATAATTATT
1 TATTATTATATTATTA-A
85886 TATATATTATATTATTAA
1 TAT-TATTATATTATTAA
85904 TATTATTAT
1 TATTATTAT
85913 TTTTTGTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 6 0.25
18 6 0.25
19 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATTATATTATTAA
Found at i:86456 original size:15 final size:15
Alignment explanation
Indices: 86436--86492 Score: 69
Period size: 15 Copynumber: 3.7 Consensus size: 15
86426 AACCGGGTAT
*
86436 CGGGTACCAGATTAC
1 CGGGTACCCGATTAC
**
86451 CGGGTACCCGCAAAATC
1 CGGGTACCCG-ATTA-C
86468 CGGGTACCCGATTAC
1 CGGGTACCCGATTAC
86483 CGGGTACCCG
1 CGGGTACCCG
86493 TAACATCCGG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
15 20 0.57
16 4 0.11
17 11 0.31
ACGTcount: A:0.23, C:0.33, G:0.28, T:0.16
Consensus pattern (15 bp):
CGGGTACCCGATTAC
Found at i:86472 original size:17 final size:16
Alignment explanation
Indices: 86450--86504 Score: 58
Period size: 17 Copynumber: 3.4 Consensus size: 16
86440 TACCAGATTA
86450 CCGGGTACCCGCAAAAT
1 CCGGGTACCCG-AAAAT
**
86467 CCGGGTACCCGATTA-
1 CCGGGTACCCGAAAAT
*
86482 CCGGGTACCCGTAACAT
1 CCGGGTACCCG-AAAAT
86499 CCGGGT
1 CCGGGT
86505 CGGGACACGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
15 11 0.34
16 4 0.12
17 17 0.53
ACGTcount: A:0.22, C:0.35, G:0.27, T:0.16
Consensus pattern (16 bp):
CCGGGTACCCGAAAAT
Found at i:86481 original size:32 final size:32
Alignment explanation
Indices: 86436--86504 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
86426 AACCGGGTAT
86436 CGGGTACCAGATTACCGGGTACCCGCAAAATC
1 CGGGTACCAGATTACCGGGTACCCGCAAAATC
* * *
86468 CGGGTACCCGATTACCGGGTACCCGTAACATC
1 CGGGTACCAGATTACCGGGTACCCGCAAAATC
86500 CGGGT
1 CGGGT
86505 CGGGACACGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.23, C:0.32, G:0.28, T:0.17
Consensus pattern (32 bp):
CGGGTACCAGATTACCGGGTACCCGCAAAATC
Found at i:87634 original size:24 final size:24
Alignment explanation
Indices: 87590--87639 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
87580 ATAAATAACC
*
87590 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
87614 AAAATAAAGTTCAAACA-ACCATTA
1 AAAATAAACTT-AAACATACCATTA
87638 AA
1 AA
87640 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 19 0.83
25 4 0.17
ACGTcount: A:0.60, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:95998 original size:48 final size:48
Alignment explanation
Indices: 95922--96013 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
95912 TATAAATCAG
95922 GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
* *
95970 GTCAAGTATCATATCAG-AATCCATGTCAAGTATCAGATCAGAAT
1 GTCAAGTATCATATCAGAAAT-CAGGTCAAGTAACAGATCAGAAT
96014 TCAAATCGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
47 3 0.07
48 38 0.93
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (48 bp):
GTCAAGTATCATATCAGAAATCAGGTCAAGTAACAGATCAGAATCCAA
Found at i:96013 original size:24 final size:24
Alignment explanation
Indices: 95922--96013 Score: 123
Period size: 24 Copynumber: 3.8 Consensus size: 24
95912 TATAAATCAG
* *
95922 GTCAAGTATCATATCAGAAAT-CAG
1 GTCAAGTATCAGATCAG-AATCCAA
*
95946 GTCAAGTAACAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAA
* *
95970 GTCAAGTATCATATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAA
95994 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
96014 TCAAATCGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
23 3 0.05
24 57 0.95
ACGTcount: A:0.41, C:0.18, G:0.16, T:0.24
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAA
Found at i:98515 original size:18 final size:17
Alignment explanation
Indices: 98494--98552 Score: 54
Period size: 18 Copynumber: 3.6 Consensus size: 17
98484 TGCCGATCAA
98494 CGGGTCGGGTCAACAGGT
1 CGGGTCGGGT-AACAGGT
*
98512 CGGGTTGGGTAA-A--T
1 CGGGTCGGGTAACAGGT
*
98526 -GGGTCGGGTAAACGGGT
1 CGGGTCGGGT-AACAGGT
98543 CGGGTCGGGT
1 CGGGTCGGGT
98553 TATAACCGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 10
0.72 0.07 0.22
Matches are distributed among these distances:
13 8 0.24
14 3 0.09
16 1 0.03
17 3 0.09
18 18 0.55
ACGTcount: A:0.15, C:0.15, G:0.49, T:0.20
Consensus pattern (17 bp):
CGGGTCGGGTAACAGGT
Found at i:98529 original size:13 final size:13
Alignment explanation
Indices: 98512--98547 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
98502 GTCAACAGGT
*
98512 CGGGTTGGGTAAA
1 CGGGTCGGGTAAA
*
98525 TGGGTCGGGTAAA
1 CGGGTCGGGTAAA
98538 CGGGTCGGGT
1 CGGGTCGGGT
98548 CGGGTTATAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.17, C:0.11, G:0.50, T:0.22
Consensus pattern (13 bp):
CGGGTCGGGTAAA
Found at i:100645 original size:24 final size:24
Alignment explanation
Indices: 100618--100669 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
100608 AACGGATATA
*
100618 TCAAAAATCAAAACATAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
** * *
100642 TCAAGTATCATATCAGAAATCAGG
1 TCAAAAATCAAAACAGAAATCAGG
100666 TCAA
1 TCAA
100670 GTAATATATC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.50, C:0.17, G:0.12, T:0.21
Consensus pattern (24 bp):
TCAAAAATCAAAACAGAAATCAGG
Found at i:100670 original size:24 final size:24
Alignment explanation
Indices: 100634--100707 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
100624 ATCAAAACAT
100634 AAATCAGGTCAAGTATCATATCAG
1 AAATCAGGTCAAGTATCATATCAG
100658 AAATCAGGTCAAGTAAT-ATATCAG
1 AAATCAGGTCAAGT-ATCATATCAG
* *
100682 -AATCCATGTCAAGTATCAGATCAG
1 AAAT-CAGGTCAAGTATCATATCAG
100706 AA
1 AA
100708 TTCAAATCGA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
23 5 0.11
24 36 0.82
25 3 0.07
ACGTcount: A:0.43, C:0.16, G:0.16, T:0.24
Consensus pattern (24 bp):
AAATCAGGTCAAGTATCATATCAG
Found at i:103238 original size:13 final size:13
Alignment explanation
Indices: 103199--103256 Score: 53
Period size: 13 Copynumber: 4.2 Consensus size: 13
103189 CGGTCAACGA
103199 TCAACGGGTCGGG
1 TCAACGGGTCGGG
103212 TCAACAGGTCGGTCGGG
1 TCAAC--G--GGTCGGG
*
103229 TCAATGGGTCGGG
1 TCAACGGGTCGGG
* *
103242 TAAACGAGTCGGG
1 TCAACGGGTCGGG
103255 TC
1 TC
103257 GGGTCGGGTT
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
13 23 0.64
15 2 0.06
17 11 0.31
ACGTcount: A:0.19, C:0.21, G:0.41, T:0.19
Consensus pattern (13 bp):
TCAACGGGTCGGG
Found at i:103240 original size:30 final size:31
Alignment explanation
Indices: 103199--103261 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
103189 CGGTCAACGA
*
103199 TCAACGGGTCGGGTCAAC-AGGTC-GGTCGGG
1 TCAACGGGTCGGGTAAACGA-GTCGGGTCGGG
*
103229 TCAATGGGTCGGGTAAACGAGTCGGGTCGGG
1 TCAACGGGTCGGGTAAACGAGTCGGGTCGGG
103260 TC
1 TC
103262 GGGTTATGAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
30 19 0.66
31 10 0.34
ACGTcount: A:0.17, C:0.21, G:0.43, T:0.19
Consensus pattern (31 bp):
TCAACGGGTCGGGTAAACGAGTCGGGTCGGG
Done.