Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009094.1 Hibiscus syriacus cultivar Beakdansim tig00112541_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: 58366
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:6363 original size:29 final size:29
Alignment explanation
Indices: 6291--6374 Score: 105
Period size: 29 Copynumber: 2.9 Consensus size: 29
6281 CGCCTATTTA
* * *
6291 GGTCGCCATGCAGGCTGTGCACCATTGTT
1 GGTCGCCATGAAGGCTATGCGCCATTGTT
*
6320 GGTCGCCATGTAGGCTATGCGCCATTGTT
1 GGTCGCCATGAAGGCTATGCGCCATTGTT
* * *
6349 GGTCGCCACGAAGGCCATGCGACATT
1 GGTCGCCATGAAGGCTATGCGCCATT
6375 CTATCAAAAG
Statistics
Matches: 48, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.17, C:0.27, G:0.31, T:0.25
Consensus pattern (29 bp):
GGTCGCCATGAAGGCTATGCGCCATTGTT
Found at i:6541 original size:29 final size:29
Alignment explanation
Indices: 6474--6562 Score: 97
Period size: 29 Copynumber: 3.1 Consensus size: 29
6464 CCCCAACACC
* *
6474 CCTACAAGGTTGCCAAGCACTCCCAGCAA
1 CCTACAAGGTCGCCAAGCACTCCCAGCGA
* *
6503 CCTACAAGGTCTCCATGCACTCCCAGCGA
1 CCTACAAGGTCGCCAAGCACTCCCAGCGA
*** * *
6532 CCTTGTAGGTCGCCAAGCAATCCCGGCGA
1 CCTACAAGGTCGCCAAGCACTCCCAGCGA
6561 CC
1 CC
6563 AAGCTTCACG
Statistics
Matches: 49, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.25, C:0.39, G:0.20, T:0.16
Consensus pattern (29 bp):
CCTACAAGGTCGCCAAGCACTCCCAGCGA
Found at i:7127 original size:47 final size:47
Alignment explanation
Indices: 7089--7178 Score: 123
Period size: 45 Copynumber: 2.0 Consensus size: 47
7079 TTATATAGTT
* * *
7089 AAAAAA-TAATTAATTAGTTTGT-TTTGTT-AATCGTTAGTTATATA
1 AAAAAATTAATTAATTAGTTTGTGGTAGTTAAATAGTTAGTTATATA
*
7133 AAAAAATTATTTAATTAGTTTGTGGTAGTTAAATAGTTAGTTATAT
1 AAAAAATTAATTAATTAGTTTGTGGTAGTTAAATAGTTAGTTATAT
7179 TTGTTTGTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
44 6 0.15
45 15 0.38
46 4 0.10
47 14 0.36
ACGTcount: A:0.39, C:0.01, G:0.13, T:0.47
Consensus pattern (47 bp):
AAAAAATTAATTAATTAGTTTGTGGTAGTTAAATAGTTAGTTATATA
Found at i:7347 original size:8 final size:8
Alignment explanation
Indices: 7334--7368 Score: 61
Period size: 8 Copynumber: 4.4 Consensus size: 8
7324 TTTAAAAAGT
*
7334 TTAGTTTG
1 TTAGTTTA
7342 TTAGTTTA
1 TTAGTTTA
7350 TTAGTTTA
1 TTAGTTTA
7358 TTAGTTTA
1 TTAGTTTA
7366 TTA
1 TTA
7369 TATTAAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (8 bp):
TTAGTTTA
Found at i:9580 original size:25 final size:25
Alignment explanation
Indices: 9552--9600 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
9542 TGTTCAGTCA
*
9552 TAAATCATTACTATCAAATCATTAT
1 TAAATCATTAATATCAAATCATTAT
9577 TAAATCATTAATATCAAATCATTA
1 TAAATCATTAATATCAAATCATTA
9601 AATATTAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.39
Consensus pattern (25 bp):
TAAATCATTAATATCAAATCATTAT
Found at i:9601 original size:14 final size:14
Alignment explanation
Indices: 9553--9601 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
9543 GTTCAGTCAT
*
9553 AAATCATTACTATC
1 AAATCATTAATATC
9567 AAATCATT-AT-T-
1 AAATCATTAATATC
9578 AAATCATTAATATC
1 AAATCATTAATATC
9592 AAATCATTAA
1 AAATCATTAA
9602 ATATTAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
11 8 0.26
12 3 0.10
13 2 0.06
14 18 0.58
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.37
Consensus pattern (14 bp):
AAATCATTAATATC
Found at i:9634 original size:10 final size:10
Alignment explanation
Indices: 9619--9645 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
9609 TAAAATTATT
9619 ATTACTAATC
1 ATTACTAATC
9629 ATTACTAATC
1 ATTACTAATC
9639 ATTACTA
1 ATTACTA
9646 TCAAATCATT
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:0.19, G:0.00, T:0.41
Consensus pattern (10 bp):
ATTACTAATC
Found at i:9684 original size:48 final size:48
Alignment explanation
Indices: 9629--9952 Score: 471
Period size: 48 Copynumber: 6.6 Consensus size: 48
9619 ATTACTAATC
9629 ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
* *
9677 ATTACTAATCATTACTAAATCATTAATACAAATCATTAATATTAATAATAATTTCATT
1 ATTACTAATCATTACT--ATCA--AAT-C--AT--TAAAA-TTAATAATAATTTCATT
9735 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAAT-ATTTCATT
1 ATTACTAATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATT
9783 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATT
9832 ATTACTAAT-ATTACTATCAAATCATTAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
9879 ATTACTAATCATTACTATCAAATCATTAAAAATTAAT-ATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATT
9927 ATTACTAATCATTA-T-T-AAATCATTAA
1 ATTACTAATCATTACTATCAAATCATTAA
9953 TATCAAATCA
Statistics
Matches: 258, Mismatches: 4, Indels: 32
0.88 0.01 0.11
Matches are distributed among these distances:
44 2 0.01
45 8 0.03
46 1 0.00
47 31 0.12
48 123 0.48
49 35 0.14
50 6 0.02
51 2 0.01
52 3 0.01
53 2 0.01
54 3 0.01
55 2 0.01
56 4 0.02
57 3 0.01
58 33 0.13
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATT
Found at i:9689 original size:34 final size:34
Alignment explanation
Indices: 9649--9796 Score: 88
Period size: 34 Copynumber: 4.2 Consensus size: 34
9639 ATTACTATCA
9649 AATCATTAAAATTAATAATAATTTCATTATTACT
1 AATCATTAAAATTAATAATAATTTCATTATTACT
* * ** *
9683 AATCATTACTAAATCATTAATACAAATCATTAATATTAAT
1 AATCATTA--AAATTAATAATA-ATTTCA-T--TATTACT
* ** * * * *
9723 AATAATT-TCATTATTACTAA--TCATTACTATCA
1 AATCATTAAAATTAATAATAATTTCATTATTA-CT
9755 AATCATTAAAAATTAATAAT-ATTTCATTATTACT
1 AATCATT-AAAATTAATAATAATTTCATTATTACT
9789 AATCATTA
1 AATCATTA
9797 CTATCAAATC
Statistics
Matches: 83, Mismatches: 20, Indels: 23
0.66 0.16 0.18
Matches are distributed among these distances:
31 4 0.05
32 6 0.07
33 3 0.04
34 26 0.31
35 8 0.10
36 11 0.13
37 12 0.14
38 1 0.01
40 12 0.14
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (34 bp):
AATCATTAAAATTAATAATAATTTCATTATTACT
Found at i:9690 original size:58 final size:58
Alignment explanation
Indices: 9568--10333 Score: 801
Period size: 58 Copynumber: 14.2 Consensus size: 58
9558 ATTACTATCA
* *
9568 AATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAA-AA-TT-ATTATTACT
1 AATCATTACT-AATCATTACTATCAAATCATTAAA-ATTAATAATAATTTCATTATTACT
9625 AATCATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACT
* *
9683 AATCATTACTAAATCATTAATA-CAAATCATTAATATTAATAATAATTTCATTATTACT
1 AATCATTACT-AATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACT
*
9741 AATCATTACT-ATCA--A--ATC--AT--TAAAAATTAATAAT-ATTTCATTATTACT
1 AATCATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACT
*
9789 AATCATTACT-ATCA--A--ATC--AT--TAAAAATTAATAATAATTTC------A-T
1 AATCATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACT
9831 --T-ATTACTAAT-ATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACT
*
9885 AATCATTACT-ATCA--A--ATC--AT--TAAAAATTAAT-ATAATTTCATTATTACT
1 AATCATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACT
* *
9933 AATCATTATTAAATCATTAATATCAAATCATTAAATATTAAT-A-AATTTCATTATTACT
1 AATCATTACT-AATCATTACTATCAAATCATTAAA-ATTAATAATAATTTCATTATTACT
9991 AATCATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTACT-AATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATTATTACT
*
10051 AATCATTACTAAATCATTACTATCAAATCATT--AA-TATTAATAA--T-ATT-TTA-T
1 AATCATTACT-AATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACT
10102 --T-ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTA-T--T
1 AATCATTACTAATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATTATTACT
10155 -A-C--TA-T--T-ATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT
1 AATCATTACTAATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATTATTACT
10206 AATCATTACTAAATCATTA-TATCAAATCATTAAATATTAATAATAATTTCATTA-TACT
1 AATCATTACT-AATCATTACTATCAAATCATTAAA-ATTAATAATAATTTCATTATTACT
* * *
10264 AATCATTATTAAATCATTACTATC-AATCATTAATATTAATAATAATTTCATCATTACT
1 AATCATTACT-AATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACT
10322 AATCATTACTAA
1 AATCATTACTAA
10334 ATCTTATAAA
Statistics
Matches: 626, Mismatches: 18, Indels: 130
0.81 0.02 0.17
Matches are distributed among these distances:
39 7 0.01
40 3 0.00
41 1 0.00
42 1 0.00
43 4 0.01
45 2 0.00
47 40 0.06
48 120 0.19
49 30 0.05
50 6 0.01
51 15 0.02
52 8 0.01
53 11 0.02
54 10 0.02
55 11 0.02
56 43 0.07
57 40 0.06
58 166 0.27
59 57 0.09
60 51 0.08
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (58 bp):
AATCATTACTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACT
Found at i:9790 original size:96 final size:98
Alignment explanation
Indices: 9687--10332 Score: 641
Period size: 107 Copynumber: 6.2 Consensus size: 98
9677 ATTACTAATC
* *
9687 ATTACTAAATCATTAATA-CAAATCATT-AATATTAATAATAATTTCATTATTACTAATCATTAC
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTAC
9750 TATCAAATCATTAAAAATTAATAAT-ATTTCATT
65 TATCAAATCATTAAAAATTAATAATAATTTCATT
9783 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAAT-ATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
9847 ATCAAATCATT-AAAATTAATAATAATTTCATT
66 ATCAAATCATTAAAAATTAATAATAATTTCATT
9879 ATTACTAATCATTACTATCAAATCATTAAAAATTAAT-ATAATTTCATTATTACTAATCATTATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC---ATT
*
9943 AAATCATTAATATCAAATCATTAAATATTAAT-A-AATTTCATTATTACTAAT
63 --A-C-----TATCAAATCATTAAAAATTAATAATAATTTC------A-T--T
9994 CATTACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
1 -ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTA
* * *
10059 CTAAATCATTACTATCAAATCATTAATATTAATAAT-ATTTTATT
64 CT--ATCA--A--ATC--AT--TAAAAATTAATAATAATTTCATT
*
10103 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACT-ATTATTACT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
10167 ATCAAATCATTAAAAATTAATAATAATTTCATT
66 ATCAAATCATTAAAAATTAATAATAATTTCATT
*
10200 ATTACTAATCATTACTAAATCATTATATCAAATCATTAAATATTAATAATAATTTCATTATACTA
1 ATTACTAATCA-T--T--A-C----TATCAAATCATTAAAAATTAATAATAATTTCATTAT--T-
* *
10265 ATCATTATTAAATCATTACTATC-AATCATT-AATATTAATAATAATTTCATC
53 A-C-----T-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
10316 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
10333 AATCTTATAA
Statistics
Matches: 475, Mismatches: 13, Indels: 114
0.79 0.02 0.19
Matches are distributed among these distances:
95 42 0.09
96 89 0.19
97 47 0.10
98 3 0.01
99 3 0.01
100 4 0.01
101 1 0.00
102 3 0.01
103 1 0.00
104 4 0.01
106 16 0.03
107 98 0.21
108 14 0.03
109 6 0.01
110 2 0.00
111 4 0.01
112 3 0.01
113 6 0.01
115 7 0.01
116 37 0.08
117 48 0.10
118 37 0.08
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (98 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACT
ATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:9925 original size:21 final size:21
Alignment explanation
Indices: 9805--9927 Score: 54
Period size: 21 Copynumber: 5.3 Consensus size: 21
9795 TACTATCAAA
9805 TCATTAAAAATTAATAATAATT
1 TCATTAAAAATTAAT-ATAATT
* *
9827 TCATTATTACTAATATTACTATCAA-A
1 TCATTA--A--AA-ATTAATAT-AATT
9853 TCATT-AAAATTAATAATAATT
1 TCATTAAAAATTAAT-ATAATT
* *
9874 TCATTATTACTAATCATTACTATCAA-A
1 TCATTA--A--AA--ATTAATAT-AATT
9901 TCATTAAAAATTAATATAATT
1 TCATTAAAAATTAATATAATT
9922 TCATTA
1 TCATTA
9928 TTACTAATCA
Statistics
Matches: 76, Mismatches: 8, Indels: 35
0.64 0.07 0.29
Matches are distributed among these distances:
20 9 0.12
21 22 0.29
22 6 0.08
23 3 0.04
24 2 0.03
25 1 0.01
26 11 0.14
27 15 0.20
28 7 0.09
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (21 bp):
TCATTAAAAATTAATATAATT
Found at i:10011 original size:21 final size:21
Alignment explanation
Indices: 9985--10072 Score: 60
Period size: 21 Copynumber: 4.3 Consensus size: 21
9975 AAATTTCATT
9985 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
* * *
10006 ATTACT-ATCAAATCATTAAA-A
1 ATTACTAATC--ATTACTAAATC
* * * *
10027 ATTAATAATAATT--T-CATT
1 ATTACTAATCATTACTAAATC
10045 ATTACTAATCATTACTAAATC
1 ATTACTAATCATTACTAAATC
10066 ATTACTA
1 ATTACTA
10073 TCAAATCATT
Statistics
Matches: 48, Mismatches: 12, Indels: 14
0.65 0.16 0.19
Matches are distributed among these distances:
17 1 0.02
18 12 0.25
20 6 0.12
21 20 0.42
22 9 0.19
ACGTcount: A:0.45, C:0.15, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTACTAATCATTACTAAATC
Found at i:10106 original size:368 final size:368
Alignment explanation
Indices: 9568--10282 Score: 1205
Period size: 368 Copynumber: 1.9 Consensus size: 368
9558 ATTACTATCA
9568 AATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAAAATTATTATTACTAATCATTA
1 AATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAAAATTATTATTACTAATCATTA
9633 CTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC
66 CTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC
9698 ATTAATACAAATCATTAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTA
131 ATTAATACAAATCATTAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTA
9763 AAAATTAATAAT-ATTTCATTATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATT
196 AAAATTAATAATAATTTCATTATTACT-ATCATTACTATCAAATCATTAAAAATTAATAATAATT
9827 TCATTATTACTAAT-A-T-T-A-C-TATCAAATCATTAAA-ATTAATAATAATTTCATTATTACT
260 TCATTATTACTAATCATTATAATCATATCAAATCATTAAATATTAATAATAATTTCATTA-TACT
9885 AATCATTACTATCAAATCATTAAAAATTAATATAATTTCATTATTACT
324 AATCATTA-T-T-AAATCATTAAAAATTAATATAATTTCATTATTACT
*
9933 AATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAAATTTCATTATTACTAATCATT
1 AATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAAAATT-ATTATTACTAATCATT
9998 ACTAAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATCATTACTAA
65 ACT-AATCATTACTATCAAATCATT-AAAATTAATAATAATTTCATTATTACTAATCATTACTAA
* *
10063 ATCATTACTATCAAATCATTAATATTAATAAT-ATTTTATTATTACTAATCATTACTATCAAATC
128 ATCATTAATA-CAAATCATTAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATC
*
10127 ATTAAAAATTAATAATAATTTCATTATTACTATTATTACTATCAAATCATTAAAAATTAATAATA
192 ATTAAAAATTAATAATAATTTCATTATTACTATCATTACTATCAAATCATTAAAAATTAATAATA
10192 ATTTCATTATTACTAATCATTACTAAATCATTATATCAAATCATTAAATATTAATAATAATTTCA
257 ATTTCATTATTACTAATCATTA-T-AATC---ATATCAAATCATTAAATATTAATAATAATTTCA
10257 TTATACTAATCATTATTAAATCATTA
317 TTATACTAATCATTATTAAATCATTA
10283 CTATCAATCA
Statistics
Matches: 329, Mismatches: 4, Indels: 23
0.92 0.01 0.06
Matches are distributed among these distances:
365 47 0.14
366 19 0.06
367 21 0.06
368 145 0.44
369 36 0.11
370 1 0.00
372 1 0.00
374 1 0.00
375 1 0.00
376 9 0.03
377 1 0.00
378 1 0.00
379 27 0.08
380 19 0.06
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (368 bp):
AATCATTATTAAATCATTAATATCAAATCATTAAATATTAATAAAATTATTATTACTAATCATTA
CTAATCATTACTATCAAATCATTAAAATTAATAATAATTTCATTATTACTAATCATTACTAAATC
ATTAATACAAATCATTAATATTAATAATAATTTCATTATTACTAATCATTACTATCAAATCATTA
AAAATTAATAATAATTTCATTATTACTATCATTACTATCAAATCATTAAAAATTAATAATAATTT
CATTATTACTAATCATTATAATCATATCAAATCATTAAATATTAATAATAATTTCATTATACTAA
TCATTATTAAATCATTAAAAATTAATATAATTTCATTATTACT
Found at i:10138 original size:48 final size:49
Alignment explanation
Indices: 10055--10332 Score: 276
Period size: 48 Copynumber: 5.3 Consensus size: 49
10045 ATTACTAATC
* *
10055 ATTACTAAATCATTACTATCAAATCATT-AATATTAATAAT-ATTTTATT
1 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
10103 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
10152 ATTACT-ATTATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
*
10200 ATTACTAATCATTACTAAATCATTATATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCA-T--T--A-C----TATCAAATCATTAAAAATTAATAATAATTTCATT
* * * *
10259 A-TACTAATCATTATTAAATCATTACTATCAATCATTAATATTAATAATAATTTCATC
1 ATTACTAATCATTACT--ATCA--A--ATC-AT--TAAAAATTAATAATAATTTCATT
10316 ATTACTAATCATTACTA
1 ATTACTAATCATTACTA
10333 AATCTTATAA
Statistics
Matches: 198, Mismatches: 9, Indels: 38
0.81 0.04 0.16
Matches are distributed among these distances:
47 21 0.11
48 65 0.33
49 16 0.08
50 5 0.03
52 2 0.01
53 1 0.01
54 4 0.02
55 4 0.02
56 1 0.01
57 23 0.12
58 22 0.11
59 34 0.17
ACGTcount: A:0.45, C:0.12, G:0.00, T:0.43
Consensus pattern (49 bp):
ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
Found at i:10222 original size:24 final size:23
Alignment explanation
Indices: 10195--10340 Score: 60
Period size: 24 Copynumber: 6.3 Consensus size: 23
10185 AATAATAATT
10195 TCATTATTACTAATCATTACTAAA
1 TCATTATTACTAATCATTA-TAAA
*
10219 TCATTA-TATCAAATCA-T-TAAA
1 TCATTATTA-CTAATCATTATAAA
* *
10240 T-ATTAATAATAATTTCATTATACTAA
1 TCATTATTACTAA--TCATTATA--AA
10266 TCATTATTA--AATCATTACTATCAA
1 TCATTATTACTAATCATTA-TA--AA
* * *
10290 TCATTAATATTAAT-A--ATAATT
1 TCATTATTACTAATCATTATAA-A
*
10311 TCATCATTACTAATCATTACTAAA
1 TCATTATTACTAATCATTA-TAAA
10335 TC-TTAT
1 TCATTAT
10341 AAATACATAG
Statistics
Matches: 92, Mismatches: 13, Indels: 35
0.66 0.09 0.25
Matches are distributed among these distances:
20 7 0.08
21 18 0.20
22 6 0.07
23 14 0.15
24 29 0.32
25 6 0.07
26 6 0.07
27 6 0.07
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (23 bp):
TCATTATTACTAATCATTATAAA
Found at i:13854 original size:28 final size:28
Alignment explanation
Indices: 13822--13881 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
13812 AATTTTTATA
13822 TAATATAATATAACTTAAACTAACAAAC
1 TAATATAATATAACTTAAACTAACAAAC
13850 TAATATAATATAACTTAAACTAACAAAC
1 TAATATAATATAACTTAAACTAACAAAC
13878 TAAT
1 TAAT
13882 TAACTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
TAATATAATATAACTTAAACTAACAAAC
Found at i:14513 original size:29 final size:29
Alignment explanation
Indices: 14396--14507 Score: 143
Period size: 29 Copynumber: 3.9 Consensus size: 29
14386 GTCGAGGCTT
*
14396 GGTCGCCGGGATTGCTTGGCGACCTACAA
1 GGTCGCCGGGAGTGCTTGGCGACCTACAA
*
14425 GGTCGCCGGGATTGCTTGGCGACCTACAA
1 GGTCGCCGGGAGTGCTTGGCGACCTACAA
* * ***
14454 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCCGGGAGTGCTTGGCGACCTACAA
* *
14483 GGTCGCTGGGAGTACTTGGCGACCT
1 GGTCGCCGGGAGTGCTTGGCGACCT
14508 TGTAGGGGTG
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.15, C:0.25, G:0.38, T:0.22
Consensus pattern (29 bp):
GGTCGCCGGGAGTGCTTGGCGACCTACAA
Found at i:14533 original size:30 final size:29
Alignment explanation
Indices: 14396--14537 Score: 115
Period size: 29 Copynumber: 4.9 Consensus size: 29
14386 GTCGAGGCTT
* * * ***
14396 GGTCGCCGGGATTGCTTGGCGACCTACAA
1 GGTCGCTGGGAGTGCATGGCGACCTTGTA
* * * ***
14425 GGTCGCCGGGATTGCTTGGCGACCTACAA
1 GGTCGCTGGGAGTGCATGGCGACCTTGTA
14454 GGTCGCTGGGAGTGCATGGCGACCTTGTA
1 GGTCGCTGGGAGTGCATGGCGACCTTGTA
* *
14483 GGTCGCTGGGAGTACTTGGCGACCTTGTA
1 GGTCGCTGGGAGTGCATGGCGACCTTGTA
* *
14512 GGGGT-GTTGGGAATGCATGGCGACCT
1 --GGTCGCTGGGAGTGCATGGCGACCT
14538 ATTGGGGACG
Statistics
Matches: 99, Mismatches: 12, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
29 79 0.80
30 17 0.17
31 3 0.03
ACGTcount: A:0.15, C:0.23, G:0.39, T:0.23
Consensus pattern (29 bp):
GGTCGCTGGGAGTGCATGGCGACCTTGTA
Found at i:14662 original size:29 final size:29
Alignment explanation
Indices: 14628--14724 Score: 167
Period size: 29 Copynumber: 3.3 Consensus size: 29
14618 GCATGGCTTT
*
14628 CATGGCGACCAACAATGGCGCATAGCCTT
1 CATGGCGACCAACAATGGCGCATAGCCTA
*
14657 CGTGGCGACCAACAATGGCGCATAGCCTA
1 CATGGCGACCAACAATGGCGCATAGCCTA
*
14686 CATGGCGACCAACAATGGCGCACAGCCTA
1 CATGGCGACCAACAATGGCGCATAGCCTA
14715 CATGGCGACC
1 CATGGCGACC
14725 TAAATAGGTC
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 64 1.00
ACGTcount: A:0.28, C:0.33, G:0.26, T:0.13
Consensus pattern (29 bp):
CATGGCGACCAACAATGGCGCATAGCCTA
Found at i:14905 original size:5 final size:5
Alignment explanation
Indices: 14903--14930 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
14893 TTAATCAAAT
14903 CAATC CAATC CAATC CAATC CAATC CAA
1 CAATC CAATC CAATC CAATC CAATC CAA
14931 AAGACCTCGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.39, G:0.00, T:0.18
Consensus pattern (5 bp):
CAATC
Found at i:16349 original size:9 final size:9
Alignment explanation
Indices: 16335--16364 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
16325 AACTGATGTC
16335 TATTTTTAT
1 TATTTTTAT
16344 TATTTTTAT
1 TATTTTTAT
*
16353 CATTTTTAT
1 TATTTTTAT
16362 TAT
1 TAT
16365 ATAAAAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (9 bp):
TATTTTTAT
Found at i:35486 original size:46 final size:46
Alignment explanation
Indices: 35436--35578 Score: 130
Period size: 46 Copynumber: 3.0 Consensus size: 46
35426 TTTATCTTTT
35436 ATATTGAAAAGATAGAATTTACATCTCAATATTTATCTTTTAAATA
1 ATATTGAAAAGATAGAATTTACATCTCAATATTTATCTTTTAAATA
** * * * * * *
35482 ATATTGAATCTGACTTAAAATTTA-GT-TCATTAATTGT-TTTCGAGATATA
1 ATATTGAA-AAGA--TAGAATTTACATCTCAATATTTATCTTT-TA-A-ATA
*
35531 ATATTGAAAAGATAGAATTTACATCTCAATATTTATCTTTTATATA
1 ATATTGAAAAGATAGAATTTACATCTCAATATTTATCTTTTAAATA
35577 AT
1 AT
35579 TGTGATTAAA
Statistics
Matches: 71, Mismatches: 17, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
46 24 0.34
47 12 0.17
48 13 0.18
49 22 0.31
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.43
Consensus pattern (46 bp):
ATATTGAAAAGATAGAATTTACATCTCAATATTTATCTTTTAAATA
Found at i:38160 original size:38 final size:38
Alignment explanation
Indices: 38104--38178 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
38094 GCCTCATCCT
* * * *
38104 ACTAAATTAACTAATTATTGGTAAAGTTAATCTTTCTC
1 ACTAAATCAACTAATTATTGATAAAATTAACCTTTCTC
*
38142 ACTAAATCAACTAGTTATTGATAAAATTAACCTTTCT
1 ACTAAATCAACTAATTATTGATAAAATTAACCTTTCT
38179 TTCTTGCAAG
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.40
Consensus pattern (38 bp):
ACTAAATCAACTAATTATTGATAAAATTAACCTTTCTC
Found at i:43565 original size:32 final size:32
Alignment explanation
Indices: 43529--43592 Score: 101
Period size: 32 Copynumber: 2.0 Consensus size: 32
43519 GGTAGATATC
* *
43529 ATGATATGATAGGTGTTATATTCATCTTTGAA
1 ATGATAGGATAGATGTTATATTCATCTTTGAA
*
43561 ATGATAGGATATATGTTATATTCATCTTTGAA
1 ATGATAGGATAGATGTTATATTCATCTTTGAA
43593 TAACACTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.33, C:0.06, G:0.17, T:0.44
Consensus pattern (32 bp):
ATGATAGGATAGATGTTATATTCATCTTTGAA
Found at i:44244 original size:14 final size:13
Alignment explanation
Indices: 44217--44250 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
44207 TCTTTTCACA
44217 TTGCAT-TCGCAT
1 TTGCATCTCGCAT
44229 TTGCATCTCTGCAT
1 TTGCATCTC-GCAT
44243 TTGCATCT
1 TTGCATCT
44251 GTATTGCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 6 0.30
13 2 0.10
14 12 0.60
ACGTcount: A:0.15, C:0.26, G:0.15, T:0.44
Consensus pattern (13 bp):
TTGCATCTCGCAT
Found at i:48944 original size:19 final size:20
Alignment explanation
Indices: 48901--48948 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
48891 TCTAAATCCT
*
48901 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
48921 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
48940 TTTTCAAAA
1 TTTTCAAAA
48949 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:49861 original size:34 final size:32
Alignment explanation
Indices: 49808--49877 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
49798 CCTTACAAAC
* *
49808 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTACAACCTT
*
49840 TCCCTAGATTTTACACGGGCTAAGCTACAACCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTACAACCTT
49874 TCCC
1 TCCC
49878 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTACAACCTT
Found at i:55594 original size:21 final size:20
Alignment explanation
Indices: 55562--55600 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
55552 AAAGTTTAAT
*
55562 TTTTTATATTAAAGTATGCC
1 TTTTTATATTAAAATATGCC
*
55582 TTTTTACTTTTAAAATATG
1 TTTTTA-TATTAAAATATG
55601 TTATGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (20 bp):
TTTTTATATTAAAATATGCC
Found at i:55977 original size:2 final size:2
Alignment explanation
Indices: 55970--55999 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
55960 ATATTATTTG
*
55970 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
56000 AGATAGTACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Done.