Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002870.1 Hibiscus syriacus cultivar Beakdansim tig00005917_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: 81203
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4463 original size:31 final size:30
Alignment explanation
Indices: 4404--4463 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
4394 GATTTAGTTA
* *
4404 GTAACCAAATTATAAGATTTTAAAAGTTTG
1 GTAACCAAAGTATAAGATTTAAAAAGTTTG
4434 GTAACCAAAGTATAA-ACTTTGAAAAAGTTT
1 GTAACCAAAGTATAAGA-TTT-AAAAAGTTT
4464 AGGGACCAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 17 0.65
31 8 0.31
ACGTcount: A:0.45, C:0.08, G:0.13, T:0.33
Consensus pattern (30 bp):
GTAACCAAAGTATAAGATTTAAAAAGTTTG
Found at i:9784 original size:2 final size:2
Alignment explanation
Indices: 9777--9805 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9767 AAATAACTTT
9777 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
9806 TACTTTTATT
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:9904 original size:60 final size:60
Alignment explanation
Indices: 9840--10012 Score: 192
Period size: 60 Copynumber: 2.9 Consensus size: 60
9830 AAATACAGAA
** * * * * **
9840 ACATATTTACAGTAATATAATTATGTGTTTAATTTTAGGTATTAAGATATTGGGAGATTT
1 ACATATTTACACAAATGTAATCATGTGTTTATTTTTAGGTATTAAGATATTGAGAGATAC
* * * * *
9900 ACATACTTATACCAATGTAAGCATGCT-TTTATTTTTAGGTACTAAGATATTGAGAGATAC
1 ACATATTTACACAAATGTAATCATG-TGTTTATTTTTAGGTATTAAGATATTGAGAGATAC
9960 ACATATTTACACAAATGTAATCATGTGTTTATTTTTAGGTA-T-A-ATATTGAGAG
1 ACATATTTACACAAATGTAATCATGTGTTTATTTTTAGGTATTAAGATATTGAGAG
10013 GTGTACATAA
Statistics
Matches: 95, Mismatches: 16, Indels: 7
0.81 0.14 0.06
Matches are distributed among these distances:
57 10 0.11
58 1 0.01
59 2 0.02
60 81 0.85
61 1 0.01
ACGTcount: A:0.35, C:0.08, G:0.16, T:0.41
Consensus pattern (60 bp):
ACATATTTACACAAATGTAATCATGTGTTTATTTTTAGGTATTAAGATATTGAGAGATAC
Found at i:10193 original size:12 final size:12
Alignment explanation
Indices: 10178--10205 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
10168 ATTAATAAAA
10178 AAAATATATTAT
1 AAAATATATTAT
10190 AAAATATATTAT
1 AAAATATATTAT
10202 AAAA
1 AAAA
10206 ATCTTTTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (12 bp):
AAAATATATTAT
Found at i:15926 original size:15 final size:17
Alignment explanation
Indices: 15896--15929 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
15886 ACTCATTAAT
15896 AATATTTTTATATATAA
1 AATATTTTTATATATAA
15913 AATA-TTTTAT-TATAA
1 AATATTTTTATATATAA
15928 AA
1 AA
15930 AATATGTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.41
16 6 0.35
17 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AATATTTTTATATATAA
Found at i:15931 original size:17 final size:18
Alignment explanation
Indices: 15896--15939 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
15886 ACTCATTAAT
*
15896 AATATTTT-TATATATAA
1 AATATTTTATATATAAAA
15913 AATATTTTAT-TATAAAA
1 AATATTTTATATATAAAA
*
15930 AATATGTTAT
1 AATATTTTAT
15940 GAAAAAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 23 0.96
18 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (18 bp):
AATATTTTATATATAAAA
Found at i:17052 original size:196 final size:196
Alignment explanation
Indices: 16716--17297 Score: 1078
Period size: 196 Copynumber: 3.0 Consensus size: 196
16706 AAGACACATT
16716 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
1 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTT-A-ATATA
16781 TATAATATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACCATT
64 TATAATATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACCATT
*
16846 AATCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCAAACTAATTCGATCCGGTTGT
129 AATCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCGAACTAATTCGATCCGGTTGT
16911 GTC
194 GTC
16914 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
1 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
*
16979 TAATATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACTATTAA
66 TAATATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACCATTAA
*
17044 TCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCGAACTAATTCGATCCAGTTGTGT
131 TCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCGAACTAATTCGATCCGGTTGTGT
17109 C
196 C
17110 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
1 TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
*
17175 T-A-ATATTTAATATTTTTGGTTACTTTGATTAGTTAGCCGATTTTAAACCGAATTAACCATTAA
66 TAATATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACCATTAA
* *
17238 TCGAATATTGAAAAAAATAACTATTCCCCAAATGCATTAATCGAACTAATTCGATCCGGT
131 TCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCGAACTAATTCGATCCGGT
17298 CGATTAATTC
Statistics
Matches: 376, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
194 116 0.31
195 1 0.00
196 201 0.53
197 1 0.00
198 57 0.15
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (196 bp):
TTGCTTCATATGATCTGATTTAAGTTTTTAATTGGTTTGAGCTTAAAATATGTATTTAATATATA
TAATATATTTAATATTTTTGGTTACTTTGATTAGTTACCCGATTTTAAACCGAATTAACCATTAA
TCGAATATTGAAAAAAATAACTATTCCCCGAATGAATTAATCGAACTAATTCGATCCGGTTGTGT
C
Found at i:17850 original size:76 final size:76
Alignment explanation
Indices: 17724--17885 Score: 272
Period size: 76 Copynumber: 2.1 Consensus size: 76
17714 TGTGTCTTCA
* *
17724 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGAAGTTTGTAGCAAAATAAGGAATTCATGGG
1 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
17789 AAGAATAATGC
66 AAGAATAATGC
* *
17800 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCATGATA-TTTGCAGGAAAATAAGGAAATCATGG
1 ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGA-AGTTTGCAGCAAAATAAGGAAATCATGG
17864 GAAGAATAATGC
65 GAAGAATAATGC
17876 ACGTGGGGAC
1 ACGTGGGGAC
17886 GGGAATGAGA
Statistics
Matches: 81, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
76 80 0.99
77 1 0.01
ACGTcount: A:0.31, C:0.11, G:0.31, T:0.27
Consensus pattern (76 bp):
ACGTGGGGACCAGCTTTGTTATGTTTGGTAGCAGGAAGTTTGCAGCAAAATAAGGAAATCATGGG
AAGAATAATGC
Found at i:20647 original size:14 final size:14
Alignment explanation
Indices: 20609--20954 Score: 187
Period size: 14 Copynumber: 24.8 Consensus size: 14
20599 ATTACTATTA
* *
20609 TTAAATTATTAAAC
1 TTAAATCATTAAAG
*
20623 TTTAATCATTAAAG
1 TTAAATCATTAAAG
*
20637 TTAAATAATTATTAA-
1 TTAAATCATTA--AAG
20652 -TAAATCATTAAAG
1 TTAAATCATTAAAG
* *
20665 TTTAATTATTAAAG
1 TTAAATCATTAAAG
* * * *
20679 TGAATTAATTATTA-
1 TTAAATCATTA-AAG
20693 TT-AATCATTAAAG
1 TTAAATCATTAAAG
*
20706 TTAAATAATTATTAA-
1 TTAAATCATTA--AAG
20721 -TAAATCATTAAAG
1 TTAAATCATTAAAG
*
20734 TTAAATTATTAAAG
1 TTAAATCATTAAAG
* * * *
20748 TGAAGTAATTATTA-
1 TTAAATCATTA-AAG
20762 TTAAATCATTAAAG
1 TTAAATCATTAAAG
20776 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* * *
20790 TTAAGTAATTATTA-
1 TTAAATCATTA-AAG
* *
20804 TTAAAGT-ATTTAAT
1 TTAAA-TCATTAAAG
20818 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
20832 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
* *
20846 TTAAAGT-ATTTAAT
1 TTAAA-TCATTAAAG
20860 TTAAATCATTAAAG
1 TTAAATCATTAAAG
* *
20874 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
*
20888 TGAAATCATTAAAG
1 TTAAATCATTAAAG
* *
20902 TTAAATAATTATTA-
1 TTAAATCATTA-AAG
*
20916 TTAAATCATTAAAT
1 TTAAATCATTAAAG
* *
20930 TTAAATGATTAAAT
1 TTAAATCATTAAAG
*
20944 TTAAATAATTA
1 TTAAATCATTA
20955 TTATTAAATA
Statistics
Matches: 253, Mismatches: 54, Indels: 50
0.71 0.15 0.14
Matches are distributed among these distances:
12 5 0.02
13 15 0.06
14 221 0.87
15 8 0.03
16 4 0.02
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (14 bp):
TTAAATCATTAAAG
Found at i:20697 original size:69 final size:69
Alignment explanation
Indices: 20624--20786 Score: 290
Period size: 69 Copynumber: 2.3 Consensus size: 69
20614 TTATTAAACT
* *
20624 TTAATCATTAAAGTTAAATAATTATTAATAAATCATTAAAGTTTAATTATTAAAGTGAATTAATT
1 TTAATCATTAAAGTTAAATAATTATTAATAAATCATTAAAGTTAAATTATTAAAGTGAAGTAATT
20689 ATTA
66 ATTA
20693 TTAATCATTAAAGTTAAATAATTATTAATAAATCATTAAAGTTAAATTATTAAAGTGAAGTAATT
1 TTAATCATTAAAGTTAAATAATTATTAATAAATCATTAAAGTTAAATTATTAAAGTGAAGTAATT
20758 ATTA
66 ATTA
*
20762 TTAAATCATTAAAGTTAAATCATTA
1 TT-AATCATTAAAGTTAAATAATTA
20787 AAGTTAAGTA
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
69 69 0.77
70 21 0.23
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (69 bp):
TTAATCATTAAAGTTAAATAATTATTAATAAATCATTAAAGTTAAATTATTAAAGTGAAGTAATT
ATTA
Found at i:20702 original size:27 final size:28
Alignment explanation
Indices: 20666--20744 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 28
20656 TCATTAAAGT
* *
20666 TTAATTATTAAAGTGAATTAATTATT-A
1 TTAATCATTAAAGTGAAATAATTATTAA
*
20693 TTAATCATTAAAGTTAAATAATTATTAA
1 TTAATCATTAAAGTGAAATAATTATTAA
* * *
20721 TAAATCATTAAAGTTAAATTATTA
1 TTAATCATTAAAGTGAAATAATTA
20745 AAGTGAAGTA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 23 0.50
28 23 0.50
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.44
Consensus pattern (28 bp):
TTAATCATTAAAGTGAAATAATTATTAA
Found at i:20921 original size:42 final size:42
Alignment explanation
Indices: 20695--20912 Score: 305
Period size: 42 Copynumber: 5.2 Consensus size: 42
20685 AATTATTATT
*
20695 AATCATTAAAGTTAAATAATTATTAATAAATCATTAAAGTTA
1 AATCATTAAAGTTAAATAATTATTATTAAATCATTAAAGTTA
* * *
20737 AATTATTAAAGTGAAGTAATTATTATTAAATCATTAAAGTTA
1 AATCATTAAAGTTAAATAATTATTATTAAATCATTAAAGTTA
* * *
20779 AATCATTAAAGTTAAGTAATTATTATTAAAGT-ATTTAATTTA
1 AATCATTAAAGTTAAATAATTATTATTAAA-TCATTAAAGTTA
* *
20821 AATCATTAAAGTTAAATAATTATTATTAAAGT-ATTTAATTTA
1 AATCATTAAAGTTAAATAATTATTATTAAA-TCATTAAAGTTA
*
20863 AATCATTAAAGTTAAATAATTATTATGAAATCATTAAAGTTA
1 AATCATTAAAGTTAAATAATTATTATTAAATCATTAAAGTTA
*
20905 AATAATTA
1 AATCATTA
20913 TTATTAAATC
Statistics
Matches: 161, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
41 1 0.01
42 159 0.99
43 1 0.01
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.41
Consensus pattern (42 bp):
AATCATTAAAGTTAAATAATTATTATTAAATCATTAAAGTTA
Found at i:20928 original size:8 final size:7
Alignment explanation
Indices: 20802--20965 Score: 62
Period size: 6 Copynumber: 23.4 Consensus size: 7
20792 AAGTAATTAT
20802 TATTAAA
1 TATTAAA
*
20809 GTATTTAA
1 -TATTAAA
20817 T-TTAAA
1 TATTAAA
20823 TCATTAAA
1 T-ATTAAA
*
20831 -GTTAAA
1 TATTAAA
*
20837 TAATT-AT
1 T-ATTAAA
20844 TATTAAA
1 TATTAAA
*
20851 GTATTTAA
1 -TATTAAA
20859 T-TTAAA
1 TATTAAA
20865 TCATTAAA
1 T-ATTAAA
*
20873 -GTTAAA
1 TATTAAA
*
20879 TAATT-AT
1 T-ATTAAA
*
20886 TATGAAA
1 TATTAAA
20893 TCATTAAA
1 T-ATTAAA
*
20901 -GTTAAA
1 TATTAAA
*
20907 TAATT-AT
1 T-ATTAAA
20914 TATTAAA
1 TATTAAA
20921 TCATTAAA
1 T-ATTAAA
20929 T-TTAAA
1 TATTAAA
20935 TGATTAAA
1 T-ATTAAA
20943 T-TTAAA
1 TATTAAA
*
20949 TAATT-AT
1 T-ATTAAA
20956 TATTAAA
1 TATTAAA
20963 TAT
1 TAT
20966 ATACTCGAGT
Statistics
Matches: 115, Mismatches: 20, Indels: 43
0.65 0.11 0.24
Matches are distributed among these distances:
6 48 0.42
7 19 0.17
8 48 0.42
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.45
Consensus pattern (7 bp):
TATTAAA
Found at i:28698 original size:3 final size:3
Alignment explanation
Indices: 28692--28755 Score: 78
Period size: 3 Copynumber: 21.0 Consensus size: 3
28682 TTTGGTTTTT
*
28692 TTA TTA TTA TTTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
28739 TTAA TT- TTA TTA -TA TTA
1 TT-A TTA TTA TTA TTA TTA
28756 CAGGCCCAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 4 0.07
3 41 0.76
4 9 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:28703 original size:19 final size:19
Alignment explanation
Indices: 28692--28755 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
28682 TTTGGTTTTT
28692 TTATTATTATTTATTATTA
1 TTATTATTATTTATTATTA
*
28711 TTATTATTA-TTAATATTA
1 TTATTATTATTTATTATTA
*
28729 TTATTTATTATTAATT-TTA
1 TTA-TTATTATTTATTATTA
28748 TTA-TATTA
1 TTATTATTA
28756 CAGGCCCAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 5 0.12
18 11 0.28
19 21 0.52
20 3 0.08
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
TTATTATTATTTATTATTA
Found at i:28731 original size:31 final size:31
Alignment explanation
Indices: 28693--28751 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
28683 TTGGTTTTTT
28693 TATTATTATTTATTATT-ATTATTATTATTAA
1 TATTATTATTTATTATTAATT-TTATTATTAA
28724 TATTATTATTTATTATTAATTTTATTAT
1 TATTATTATTTATTATTAATTTTATTAT
28752 ATTACAGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 24 0.89
32 3 0.11
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (31 bp):
TATTATTATTTATTATTAATTTTATTATTAA
Found at i:30440 original size:20 final size:19
Alignment explanation
Indices: 30415--30456 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
30405 ATATTTTATA
30415 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
30435 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
30454 AAT
1 AAT
30457 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:30452 original size:119 final size:119
Alignment explanation
Indices: 30310--30548 Score: 295
Period size: 120 Copynumber: 2.0 Consensus size: 119
30300 TATTTTAATC
* * * *
30310 TTGTTTTAATATTTATTTATTTTTCAATAT-TAAGAAAGGA-CAGTCTTAAAACAACTGGATGTC
1 TTGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
* *
30373 CATTTTCTGATATTTTTAAATAAATAAATATCATATTTTATAAAT-TATATATTAA
66 C-TTTTCTGATATTTCTAAATAAATAAATATCATA-TTTATAAATATATAAATTAA
* ** *** *
30428 TTGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGTTGTCTTAAGGTACCTAGAAGT
1 TTGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT
**
30493 CCTTTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATAAATTAA
65 CCTTTTCTGATATTTCTAAATAAATAAATATCATATTTATAAATATATAAATTAA
30548 T
1 T
30549 ATTTTTTTTA
Statistics
Matches: 102, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 9 0.09
119 29 0.28
120 48 0.47
121 16 0.16
ACGTcount: A:0.38, C:0.07, G:0.08, T:0.46
Consensus pattern (119 bp):
TTGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
CTTTTCTGATATTTCTAAATAAATAAATATCATATTTATAAATATATAAATTAA
Found at i:30542 original size:27 final size:27
Alignment explanation
Indices: 30512--30566 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
30502 ATATTTCTAA
30512 ATAAATAAATATTTTATTTATAAATAT
1 ATAAATAAATATTTTATTTATAAATAT
* * *
30539 ATAAATTAATATTTTTTTTATAATTAT
1 ATAAATAAATATTTTATTTATAAATAT
30566 A
1 A
30567 ATTTTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
ATAAATAAATATTTTATTTATAAATAT
Found at i:35766 original size:2 final size:2
Alignment explanation
Indices: 35759--35786 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
35749 TTATCCTTTA
35759 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
35787 CCTTTGTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36103 original size:18 final size:18
Alignment explanation
Indices: 36080--36124 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
36070 CTCATCCAGC
* * *
36080 AAAGAAAGAAGAAGGAAA
1 AAAGAAAAAAAAAGAAAA
36098 AAAGAAAAAAAAAGAAAA
1 AAAGAAAAAAAAAGAAAA
36116 AAAGGAAAA
1 AAA-GAAAA
36125 GGAAAATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAAAAAAAGAAAA
Found at i:38919 original size:24 final size:24
Alignment explanation
Indices: 38875--38924 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
38865 ATAAAGAACC
*
38875 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
38899 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
38923 AA
1 AA
38925 TCAACTACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:49182 original size:24 final size:24
Alignment explanation
Indices: 49138--49187 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
49128 ATAAAAAACC
*
49138 AAAATAAACTTAAATATACCATTA
1 AAAATAAACTTAAACATACCATTA
*
49162 AAAATAAAGTTTAAACA-ACCATTA
1 AAAATAAA-CTTAAACATACCATTA
49186 AA
1 AA
49188 TCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 17 0.74
25 6 0.26
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (24 bp):
AAAATAAACTTAAACATACCATTA
Found at i:51194 original size:54 final size:54
Alignment explanation
Indices: 51112--51273 Score: 270
Period size: 54 Copynumber: 3.0 Consensus size: 54
51102 CAATGATTGA
*
51112 GAACATCTAAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
*
51166 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAT
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
* * **
51220 GAACATCTGAGCAGAAGCCACAGGAAAGGATGAATGCGCCGTCAAATGTTTTAC
1 GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
51274 AAACCTGCTA
Statistics
Matches: 101, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
54 101 1.00
ACGTcount: A:0.37, C:0.16, G:0.24, T:0.23
Consensus pattern (54 bp):
GAACATCTGAGCAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
Found at i:51668 original size:22 final size:22
Alignment explanation
Indices: 51637--51691 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
51627 ATCTACACTC
*
51637 TTCAAAGATGATAGATTCCCTT
1 TTCAAAGATGACAGATTCCCTT
* *
51659 TTTAAAGATGACAGATTCTCTT
1 TTCAAAGATGACAGATTCCCTT
*
51681 TTCAAATATGA
1 TTCAAAGATGA
51692 AAGCTTTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGACAGATTCCCTT
Found at i:52284 original size:113 final size:113
Alignment explanation
Indices: 52086--52990 Score: 1399
Period size: 113 Copynumber: 8.0 Consensus size: 113
52076 TTTAGAAAAG
* *
52086 TTGAATTCATTATTCGATGGATTAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
52151 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
*
52199 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
*
52264 AGAAGGAAAAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
*
52312 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
52377 AGAAGGAAGAAGGAGTTCATAATGAGAAAAATTTGTTCAACTTTTCGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
52425 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
52490 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
* *
52538 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATAATGAGAAAAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
52603 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
* *
52651 TTGAATTCATCATTCGATGGATCAGCATTACCAGGTCAAGTTCATATTGAGAAGAACTCATCTGA
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
* * * *
52716 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTATTCAACCTTTTTGT
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
* *
52765 TTGAATTCATCATTTGATGGATCAACATTGCCAGGT-AGAGTTCATAATGAGAAGAACTCGTCAT
1 TTGAATTCATCATTCGATGGATCAACATTACCAGGTCA-AGTTCATAATGAGAAGAA--C-TCAT
* * *
52829 CTGAAGAAGAAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTT-GC
62 CTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTTCGC
* * * * * * *
52881 TT-AAATCAATCACTT-GATAGATCAACTTTTCCAGAG-AAAATTCATAATGAGAAGAACTTATC
1 TTGAATTC-ATCA-TTCGATGGATCAACATTACCAG-GTCAAGTTCATAATGAGAAGAACTCATC
* *
52943 TGAAGAA-GAAGAAGAGGTTCATAATGAGAAGAGCTTGTTCAACCTTTT
63 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
52991 GCATAACTCT
Statistics
Matches: 742, Mismatches: 41, Indels: 19
0.93 0.05 0.02
Matches are distributed among these distances:
112 36 0.05
113 549 0.74
114 57 0.08
115 4 0.01
116 41 0.06
117 55 0.07
ACGTcount: A:0.37, C:0.15, G:0.19, T:0.29
Consensus pattern (113 bp):
TTGAATTCATCATTCGATGGATCAACATTACCAGGTCAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTCGC
Found at i:53094 original size:17 final size:17
Alignment explanation
Indices: 53036--53095 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
53026 CAGCATTTCC
* *
53036 AGAAGGAGTTCATAATG
1 AGAAGAAGTTCATAAGG
* *
53053 AGAAGAA-CTCATCTGAAGA
1 AGAAGAAGTTCA--T-AAGG
53072 AGAAGAAGTTCATAAGG
1 AGAAGAAGTTCATAAGG
53089 AGAAGAA
1 AGAAGAA
53096 TTTGTTCAAC
Statistics
Matches: 33, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
16 3 0.09
17 16 0.48
18 2 0.06
19 9 0.27
20 3 0.09
ACGTcount: A:0.48, C:0.08, G:0.27, T:0.17
Consensus pattern (17 bp):
AGAAGAAGTTCATAAGG
Found at i:53146 original size:120 final size:123
Alignment explanation
Indices: 52921--53139 Score: 304
Period size: 120 Copynumber: 1.8 Consensus size: 123
52911 CCAGAGAAAA
* * *
52921 TTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAGGTTCATAATGAGAAGAGCTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAGGTTCATAAGGAGAAGAACTTGTTCAAC
* *
52986 CTTTTGCATAACTCTATCACAGAAGGAGATATATCATCATCAGCATTTCCAGAAGGAG
66 CTTTTGCATAACTCTATCACAGAAGGAAATAAATCATCATCAGCATTTCCAGAAGGAG
*
53044 TTCATAATGAGAAGAACTCATCTGAAGAAGAAG-A-A-GTTCATAAGGAGAAGAATTTGTTCAAC
1 TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAGGTTCATAAGGAGAAGAACTTGTTCAAC
* * *
53106 TTTTTGC-TAGATTAC-ATCACATAAGGAAATAAAT
66 CTTTTGCATA-ACT-CTATCACAGAAGGAAATAAAT
53140 TGTCATCCCC
Statistics
Matches: 85, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
119 2 0.02
120 48 0.56
121 2 0.02
122 1 0.01
123 32 0.38
ACGTcount: A:0.40, C:0.14, G:0.19, T:0.27
Consensus pattern (123 bp):
TTCATAATGAGAAGAACTCATCTGAAGAAGAAGAAGAGGTTCATAAGGAGAAGAACTTGTTCAAC
CTTTTGCATAACTCTATCACAGAAGGAAATAAATCATCATCAGCATTTCCAGAAGGAG
Found at i:53331 original size:3 final size:3
Alignment explanation
Indices: 53325--53381 Score: 73
Period size: 3 Copynumber: 19.0 Consensus size: 3
53315 CATTTGGTTT
*
53325 TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA TTA TTTA TTA TTAA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TT-A TTA
53371 TTA TTA -TA TTA
1 TTA TTA TTA TTA
53382 CAGGCCCAAT
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
2 4 0.08
3 38 0.79
4 6 0.12
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:55060 original size:20 final size:19
Alignment explanation
Indices: 55035--55076 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
55025 CTATTTTATA
55035 AATTATATATTAATTGTTTT
1 AATTATATATTAATT-TTTT
* *
55055 AATTATTTATTTATTTTTT
1 AATTATATATTAATTTTTT
55074 AAT
1 AAT
55077 ATCGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
AATTATATATTAATTTTTT
Found at i:55067 original size:119 final size:119
Alignment explanation
Indices: 54931--55168 Score: 293
Period size: 120 Copynumber: 2.0 Consensus size: 119
54921 ATTTTAATCA
* * * *
54931 TGTTTTAATATTTATTTATTTTTCAATAT-TAAGAAAGGA-CAGTCTTAAAACAACTGGATGTCC
1 TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-C
* * *
54994 ATTTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAAT-TATATATTAAT
65 ATTTTCTGATATTTCTAAACAAATAAATATCCTA-TTTATAAATATATAAATTAAT
* * *** *
55049 TGTTTTAATTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGTACCTAGAAGTC
1 TGTTTTAA-TATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTC
**
55114 ATTTTCTGATATTTCTAAACAAATAAATATTTTATTTATAAATATATAAATTAAT
65 ATTTTCTGATATTTCTAAACAAATAAATATCCTATTTATAAATATATAAATTAAT
55169 ATTTTTTTTA
Statistics
Matches: 101, Mismatches: 15, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
118 8 0.08
119 29 0.29
120 49 0.49
121 15 0.15
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.45
Consensus pattern (119 bp):
TGTTTTAATATTTATTTATTTTTCAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
TTTTCTGATATTTCTAAACAAATAAATATCCTATTTATAAATATATAAATTAAT
Found at i:55169 original size:27 final size:27
Alignment explanation
Indices: 55134--55186 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
55124 ATTTCTAAAC
55134 AAATAAATATTTTATTTATAAATATAT
1 AAATAAATATTTTATTTATAAATATAT
* * *
55161 AAATTAATATTTTTTTTATAATTATA
1 AAATAAATATTTTATTTATAAATATA
55187 ATTTTGAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (27 bp):
AAATAAATATTTTATTTATAAATATAT
Found at i:59906 original size:35 final size:36
Alignment explanation
Indices: 59860--59928 Score: 104
Period size: 35 Copynumber: 1.9 Consensus size: 36
59850 TAGCGGCACA
* *
59860 ATTTCTTGTGGGATTGATT-ATTGTCATTTTCGTCC
1 ATTTCTTGTGGGATTGATTAATTGCCAATTTCGTCC
*
59895 ATTTCTTGTGGGCTTGATTAATTGCCAATTTCGT
1 ATTTCTTGTGGGATTGATTAATTGCCAATTTCGT
59929 TTTTGAGTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
35 18 0.60
36 12 0.40
ACGTcount: A:0.16, C:0.14, G:0.20, T:0.49
Consensus pattern (36 bp):
ATTTCTTGTGGGATTGATTAATTGCCAATTTCGTCC
Found at i:64379 original size:18 final size:18
Alignment explanation
Indices: 64353--64455 Score: 63
Period size: 18 Copynumber: 5.9 Consensus size: 18
64343 GTAAATCAGG
*
64353 TTTTT-GTAATTCTGGAA
1 TTTTTGGTAATTCAGGAA
*
64370 TTTTTGGTAATTC-GGGA
1 TTTTTGGTAATTCAGGAA
* **
64387 GTTTTGTGTAATTTTGG--
1 TTTTTG-GTAATTCAGGAA
** *
64404 -TTTTGGTACCTCAAGAA
1 TTTTTGGTAATTCAGGAA
*
64421 TTTTTGGTAACTCAGGAA
1 TTTTTGGTAATTCAGGAA
**
64439 CATTTGGTAATTCAGGA
1 TTTTTGGTAATTCAGGA
64456 GCTTTGGGGA
Statistics
Matches: 67, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
15 5 0.07
16 5 0.07
17 13 0.19
18 42 0.63
19 2 0.03
ACGTcount: A:0.23, C:0.09, G:0.23, T:0.45
Consensus pattern (18 bp):
TTTTTGGTAATTCAGGAA
Found at i:64786 original size:18 final size:18
Alignment explanation
Indices: 64763--64803 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
64753 TGTTGGAAAC
64763 TCAGGAACCTTAGGCAAT
1 TCAGGAACCTTAGGCAAT
*
64781 TCAGGAACTTTAGGCAAT
1 TCAGGAACCTTAGGCAAT
64799 TCAGG
1 TCAGG
64804 CTTAGGTAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (18 bp):
TCAGGAACCTTAGGCAAT
Found at i:64809 original size:84 final size:83
Alignment explanation
Indices: 64639--64819 Score: 199
Period size: 84 Copynumber: 2.2 Consensus size: 83
64629 TTGGTAATTC
* * * *
64639 AGGAACTTCAGGCTTTGACAATTCTGGCACCTTTGGAAACTCAGGAACCTTAGGCAATTTAAGTT
1 AGGAACTTCAGGCTTTGACAACTCTGACACCTTTGGAAACTCAGGAACCTTAGGCAATTGAACTT
* * *
64704 TTGGTAATTTAGGAACTTT
66 TAGGCAATTCAGG-ACTTT
* *
64723 AGGAACTTCGGGCTTTGGCAACTCTGAC-CCTGTTGGAAACTCAGGAACCTTAGGCAATTCAGGA
1 AGGAACTTCAGGCTTTGACAACTCTGACACCT-TTGGAAACTCAGGAACCTTAGGCAATT---GA
64787 ACTTTAGGCAATTCAGG-C-TT
62 ACTTTAGGCAATTCAGGACTTT
64807 AGGTAAC-TCAGGC
1 AGG-AACTTCAGGC
64820 ATTTTAGGTA
Statistics
Matches: 82, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
83 3 0.04
84 61 0.74
85 4 0.05
87 14 0.17
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.29
Consensus pattern (83 bp):
AGGAACTTCAGGCTTTGACAACTCTGACACCTTTGGAAACTCAGGAACCTTAGGCAATTGAACTT
TAGGCAATTCAGGACTTT
Found at i:64818 original size:33 final size:33
Alignment explanation
Indices: 64771--64836 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
64761 ACTCAGGAAC
*
64771 CTTAGGCAATTCAGGAACTTTAGGCAATTCAGG
1 CTTAGGCAACTCAGGAACTTTAGGCAATTCAGG
* * * * *
64804 CTTAGGTAACTCAGGCATTTTAGGTATTTCAGG
1 CTTAGGCAACTCAGGAACTTTAGGCAATTCAGG
64837 TTTCGGAATT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.17, G:0.24, T:0.32
Consensus pattern (33 bp):
CTTAGGCAACTCAGGAACTTTAGGCAATTCAGG
Found at i:65983 original size:14 final size:14
Alignment explanation
Indices: 65964--66072 Score: 98
Period size: 14 Copynumber: 8.6 Consensus size: 14
65954 GTAATCTGTC
65964 CATTTATGTTCGTT
1 CATTTATGTTCGTT
*
65978 CATTTATGTCCGTT
1 CATTTATGTTCGTT
65992 CATTTATG-TC---
1 CATTTATGTTCGTT
*
66002 CATGTATGTTCGTT
1 CATTTATGTTCGTT
66016 CATTTATGTTCG--
1 CATTTATGTTCGTT
*
66028 --TGTATGTTCGTT
1 CATTTATGTTCGTT
66040 CATTTATGTTCG--
1 CATTTATGTTCGTT
*
66052 --TGTATGTTCGTT
1 CATTTATGTTCGTT
66064 CATTTATGT
1 CATTTATGT
66073 ATGTGTATGT
Statistics
Matches: 75, Mismatches: 8, Indels: 24
0.70 0.07 0.22
Matches are distributed among these distances:
10 25 0.33
11 2 0.03
13 1 0.01
14 47 0.63
ACGTcount: A:0.15, C:0.15, G:0.17, T:0.53
Consensus pattern (14 bp):
CATTTATGTTCGTT
Found at i:66009 original size:24 final size:24
Alignment explanation
Indices: 65982--66087 Score: 169
Period size: 24 Copynumber: 4.4 Consensus size: 24
65972 TTCGTTCATT
* * *
65982 TATGTCCGTTCATTTATGTCCATG
1 TATGTTCGTTCATTTATGTTCGTG
66006 TATGTTCGTTCATTTATGTTCGTG
1 TATGTTCGTTCATTTATGTTCGTG
66030 TATGTTCGTTCATTTATGTTCGTG
1 TATGTTCGTTCATTTATGTTCGTG
66054 TATGTTCGTTCATTTATGTAT-GTG
1 TATGTTCGTTCATTTATGT-TCGTG
66078 TATGTTCGTT
1 TATGTTCGTT
66088 TATATTGAGG
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
24 77 0.99
25 1 0.01
ACGTcount: A:0.14, C:0.13, G:0.20, T:0.53
Consensus pattern (24 bp):
TATGTTCGTTCATTTATGTTCGTG
Found at i:66048 original size:38 final size:38
Alignment explanation
Indices: 65961--66052 Score: 116
Period size: 38 Copynumber: 2.4 Consensus size: 38
65951 TTGGTAATCT
*
65961 GTCCATTTATGTTCGTTCATTTATGTCCGTTCATTTAT
1 GTCCATTTATGTTCGTTCATTTATGTCCGTTCATTTAC
* *
65999 GTCCATGTATGTTCGTTCATTTATGTTCGTGT-ATGTT-C
1 GTCCATTTATGTTCGTTCATTTATGTCCGT-TCAT-TTAC
*
66037 GTTCATTTATGTTCGT
1 GTCCATTTATGTTCGT
66053 GTATGTTCGT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
38 44 0.94
39 3 0.06
ACGTcount: A:0.14, C:0.16, G:0.17, T:0.52
Consensus pattern (38 bp):
GTCCATTTATGTTCGTTCATTTATGTCCGTTCATTTAC
Found at i:69549 original size:33 final size:32
Alignment explanation
Indices: 69460--69552 Score: 96
Period size: 33 Copynumber: 2.8 Consensus size: 32
69450 TTCCTACCTT
69460 ATTAACCTGGCTAGTTCGCGTAGGCTCAGGCAG
1 ATTAACCTGGCTAGTT-GCGTAGGCTCAGGCAG
* * * * *
69493 ATTAACCTGGCTCGCCTGGGTAGGCTCCGGCCG
1 ATTAACCTGGCTAG-TTGCGTAGGCTCAGGCAG
* *
69526 ATTAACCTGGCTTGTGTGTGTAGGCTC
1 ATTAACCTGGCTAGT-TGCGTAGGCTC
69553 TGACCGACTA
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
33 49 0.98
34 1 0.02
ACGTcount: A:0.16, C:0.26, G:0.31, T:0.27
Consensus pattern (32 bp):
ATTAACCTGGCTAGTTGCGTAGGCTCAGGCAG
Found at i:69884 original size:48 final size:48
Alignment explanation
Indices: 69779--69956 Score: 207
Period size: 48 Copynumber: 3.7 Consensus size: 48
69769 CGTTTCCTTG
* * * **
69779 GGCGTTTGCATAAACAGCGTTTGCG-TTCTTTCGGAGGTGGAGGTACC
1 GGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGGAGGCGGAGGCGCC
* **
69826 GGCGGTTGCATAAATAGCGTCTGCGTTTCTTTAAGAGGCGGAGGCGCC
1 GGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGGAGGCGGAGGCGCC
* * * * * *
69874 GGTGGCTGCATAGACAGAGGT-TGCGTTTCTTTCGGAGGCGGATGCGTC
1 GGCGGTTGCATAAACAG-CGTCTGCGTTTCTTTCGGAGGCGGAGGCGCC
69922 GGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGG
1 GGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGG
69957 CGCCGGTGGT
Statistics
Matches: 107, Mismatches: 21, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
47 24 0.22
48 81 0.76
49 2 0.02
ACGTcount: A:0.16, C:0.20, G:0.35, T:0.28
Consensus pattern (48 bp):
GGCGGTTGCATAAACAGCGTCTGCGTTTCTTTCGGAGGCGGAGGCGCC
Found at i:69986 original size:39 final size:38
Alignment explanation
Indices: 69925--70061 Score: 138
Period size: 39 Copynumber: 3.7 Consensus size: 38
69915 ATGCGTCGGC
*
69925 GGTTGCATAAACAGCGTCTGCGTTTCTTTCGGCGCCGGT
1 GGTTGCATAAACAGAGTCTGCGTTTCTTTCGGCG-CGGT
* * * * *
69964 GGTTGCATAAAAAGAGTTTGCGTCTCTTTCGGAG-GCT
1 GGTTGCATAAACAGAGTCTGCGTTTCTTTCGGCGCGGT
* * *
70001 -GTTGCATGAACAGAGT-T-TGTTTCTTTCGGCGGCGGC
1 GGTTGCATAAACAGAGTCTGCGTTTCTTTCGGC-GCGGT
*
70037 GGTTGCATAAACAGCGTCTGCGTTT
1 GGTTGCATAAACAGAGTCTGCGTTT
70062 GAGGCGGCTG
Statistics
Matches: 77, Mismatches: 16, Indels: 10
0.75 0.16 0.10
Matches are distributed among these distances:
34 10 0.13
35 2 0.03
36 15 0.19
37 16 0.21
38 1 0.01
39 33 0.43
ACGTcount: A:0.17, C:0.20, G:0.31, T:0.32
Consensus pattern (38 bp):
GGTTGCATAAACAGAGTCTGCGTTTCTTTCGGCGCGGT
Found at i:73011 original size:3 final size:3
Alignment explanation
Indices: 72996--73061 Score: 57
Period size: 3 Copynumber: 21.3 Consensus size: 3
72986 TTTTACTTTA
*
72996 ATT ATT ACT -TT ATT ATT ATT ATTT ATT ATT ATT -TAT ATAT ATAT ATT
1 ATT ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT AT-T AT-T AT-T ATT
73043 ATT A-T ATGT ATT ATT ATT A
1 ATT ATT AT-T ATT ATT ATT A
73062 AAAATAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 12
0.80 0.03 0.17
Matches are distributed among these distances:
2 4 0.07
3 36 0.65
4 15 0.27
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:73023 original size:10 final size:10
Alignment explanation
Indices: 73008--73060 Score: 63
Period size: 10 Copynumber: 5.1 Consensus size: 10
72998 TATTACTTTA
73008 TTATTATTAT
1 TTATTATTAT
73018 TTATTATTAT
1 TTATTATTAT
73028 TTATATATATAT
1 TTAT-TAT-TAT
73040 ATTATTA-TAT
1 -TTATTATTAT
*
73050 GTATTATTAT
1 TTATTATTAT
73060 T
1 T
73061 AAAAATAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 5 0.14
10 20 0.54
11 3 0.08
12 5 0.14
13 4 0.11
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (10 bp):
TTATTATTAT
Found at i:74592 original size:2 final size:2
Alignment explanation
Indices: 74585--74625 Score: 52
Period size: 2 Copynumber: 22.0 Consensus size: 2
74575 TCATTTAAAC
*
74585 AT AT AT AT AT AT AT AT AT AT AT AT -T AT TT A- AT AT AT A- AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
74624 AT
1 AT
74626 TTATTTTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
1 3 0.09
2 31 0.91
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:74626 original size:14 final size:15
Alignment explanation
Indices: 74585--74629 Score: 58
Period size: 14 Copynumber: 3.1 Consensus size: 15
74575 TCATTTAAAC
*
74585 ATATATAT-ATATAT
1 ATATATATAATATTT
*
74599 ATATATATATTATTT
1 ATATATATAATATTT
74614 A-ATATATAATATTT
1 ATATATATAATATTT
74628 AT
1 AT
74630 TTTTTTCAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
ATATATATAATATTT
Found at i:74629 original size:18 final size:20
Alignment explanation
Indices: 74595--74631 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
74585 ATATATATAT
74595 ATATATATATATATTATTTA
1 ATATATATATATATTATTTA
74615 ATATATA-ATAT-TTATTT
1 ATATATATATATATTATTT
74632 TTTTCAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 4 0.24
20 7 0.41
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATATATATATTATTTA
Found at i:80454 original size:9 final size:9
Alignment explanation
Indices: 80440--80482 Score: 79
Period size: 9 Copynumber: 4.9 Consensus size: 9
80430 TATTATACTT
80440 GGAAAAAAA
1 GGAAAAAAA
80449 GG-AAAAAA
1 GGAAAAAAA
80457 GGAAAAAAA
1 GGAAAAAAA
80466 GGAAAAAAA
1 GGAAAAAAA
80475 GGAAAAAA
1 GGAAAAAA
80483 GTAAAAGGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
8 8 0.24
9 25 0.76
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
GGAAAAAAA
Found at i:80456 original size:8 final size:8
Alignment explanation
Indices: 80443--80517 Score: 86
Period size: 8 Copynumber: 9.6 Consensus size: 8
80433 TATACTTGGA
80443 AAAAAAGG
1 AAAAAAGG
80451 AAAAAAGG
1 AAAAAAGG
80459 AAAAAAAGG
1 -AAAAAAGG
80468 AAAAAAAGG
1 -AAAAAAGG
80477 AAAAAA-G
1 AAAAAAGG
*
80484 -TAAAAGG
1 AAAAAAGG
80491 AAAAAAGG
1 AAAAAAGG
80499 -AAAAA-G
1 AAAAAAGG
*
80505 AAAAAAAG
1 AAAAAAGG
80513 AAAAA
1 AAAAA
80518 GAAAAAATTG
Statistics
Matches: 60, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
6 5 0.08
7 12 0.20
8 26 0.43
9 17 0.28
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (8 bp):
AAAAAAGG
Found at i:80509 original size:6 final size:7
Alignment explanation
Indices: 80443--80524 Score: 67
Period size: 7 Copynumber: 10.9 Consensus size: 7
80433 TATACTTGGA
80443 AAAAAAGG
1 AAAAAA-G
80451 AAAAAAGG
1 AAAAAA-G
80459 AAAAAAAGG
1 -AAAAAA-G
80468 AAAAAAAGG
1 -AAAAAA-G
80477 AAAAAAG
1 AAAAAAG
* *
80484 TAAAAGG
1 AAAAAAG
80491 AAAAAAG
1 AAAAAAG
*
80498 GAAAAAG
1 AAAAAAG
80505 AAAAAA-
1 AAAAAAG
80511 AGAAAAAG
1 A-AAAAAG
80519 AAAAAA
1 AAAAAA
80525 TTGAACCAAG
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
6 1 0.02
7 32 0.49
8 15 0.23
9 17 0.26
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (7 bp):
AAAAAAG
Found at i:80511 original size:9 final size:9
Alignment explanation
Indices: 80442--80524 Score: 51
Period size: 9 Copynumber: 8.6 Consensus size: 9
80432 TTATACTTGG
*
80442 AAAAAAAGG
1 AAAAAAAGA
*
80451 AAAAAAGGA
1 AAAAAAAGA
*
80460 AAAAAAGGA
1 AAAAAAAGA
*
80469 AAAAAAGGA
1 AAAAAAAGA
80478 AAAAAGTAA-A
1 AAAAA--AAGA
80488 AGGAAAAAAGGA
1 A--AAAAAA-GA
*
80500 AAAAGAAAAA
1 AAAA-AAAGA
80510 AAGAAAAAGA
1 AA-AAAAAGA
80520 AAAAA
1 AAAAA
80525 TTGAACCAAG
Statistics
Matches: 61, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
9 33 0.54
10 16 0.26
11 6 0.10
12 6 0.10
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:81007 original size:32 final size:32
Alignment explanation
Indices: 80967--81028 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
80957 TCTGGAAACA
* *
80967 AGAAGTATCTCTACGAGATGAGCCTAACAACG
1 AGAAGTATCTCTACAAGATGAGCATAACAACG
*
80999 AGAAGTATCTCTACAATATGAGCATAACAA
1 AGAAGTATCTCTACAAGATGAGCATAACAA
81029 TCATTTCTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.42, C:0.19, G:0.18, T:0.21
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Done.