Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007613.1 Hibiscus syriacus cultivar Beakdansim tig00022665_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: 95908
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Found at i:2785 original size:2 final size:2
Alignment explanation
Indices: 2778--2802 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2768 AAAAGTATCT
2778 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 T
2803 TCCAAGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4595 original size:13 final size:13
Alignment explanation
Indices: 4577--4601 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4567 TTAATTCTTG
4577 ATATATATATATA
1 ATATATATATATA
4590 ATATATATATAT
1 ATATATATATAT
4602 TTTTTTCTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATATATATATATA
Found at i:5958 original size:2 final size:2
Alignment explanation
Indices: 5951--5981 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
5941 AAAAGTATCT
*
5951 TA TA TA TA TA TA TC TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5982 TTCCAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:13706 original size:19 final size:19
Alignment explanation
Indices: 13682--13738 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 19
13672 TTTTTATTGA
13682 AAAATCATTATATATTATT
1 AAAATCATTATATATTATT
* *
13701 AAAATCA-AAGTATAATATT
1 AAAATCATTA-TATATTATT
*
13720 ATATATCATTATAATATTA
1 A-AAATCATTAT-ATATTA
13739 AAGAATATAA
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
18 1 0.03
19 16 0.55
20 6 0.21
21 6 0.21
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (19 bp):
AAAATCATTATATATTATT
Found at i:14181 original size:2 final size:2
Alignment explanation
Indices: 14174--14211 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
14164 TTAATTCTTG
14174 AT AT 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 AT AT
14212 TATTTTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15965 original size:25 final size:24
Alignment explanation
Indices: 15901--15969 Score: 66
Period size: 25 Copynumber: 2.8 Consensus size: 24
15891 ACTCCACTTG
15901 CAAACTCGTATATAAATCAGATTT
1 CAAACTCGTATATAAATCAGATTT
* * *** *
15925 CACTATTTAAAAATAAATCAGATTTT
1 CA-AACTCGTATATAAATCAGA-TTT
15951 CAAACTCGTATATAAATCA
1 CAAACTCGTATATAAATCA
15970 AAATACAATT
Statistics
Matches: 31, Mismatches: 12, Indels: 3
0.67 0.26 0.07
Matches are distributed among these distances:
24 2 0.06
25 24 0.77
26 5 0.16
ACGTcount: A:0.45, C:0.16, G:0.06, T:0.33
Consensus pattern (24 bp):
CAAACTCGTATATAAATCAGATTT
Found at i:16615 original size:24 final size:24
Alignment explanation
Indices: 16588--16702 Score: 126
Period size: 24 Copynumber: 4.8 Consensus size: 24
16578 CATAATTCAT
* * *
16588 GTCAAGTTTCATATCAAAATCCAG
1 GTCAAGTATCATATCAGAATCCAA
16612 GTCAAGTATCATATCAGAATCCAA
1 GTCAAGTATCATATCAGAATCCAA
* *
16636 GTTAAGTATCAGATCAGAATCCATA
1 GTCAAGTATCATATCAGAATCCA-A
* *
16661 -TC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCATATCAGAATCCAA
*
16684 GTCAAGTATCAGATCAGAA
1 GTCAAGTATCATATCAGAA
16703 ATCAAATCGA
Statistics
Matches: 80, Mismatches: 7, Indels: 8
0.84 0.07 0.08
Matches are distributed among these distances:
23 2 0.03
24 75 0.94
25 3 0.04
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCATATCAGAATCCAA
Found at i:27958 original size:23 final size:22
Alignment explanation
Indices: 27914--27955 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
27904 ATAATCCTAT
27914 TATTTCAAAATATATTAATTTA
1 TATTTCAAAATATATTAATTTA
27936 TATTT-AAAATAT-TT-ATTTA
1 TATTTCAAAATATATTAATTTA
27955 T
1 T
27956 TTAGAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 7 0.35
22 5 0.25
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTCAAAATATATTAATTTA
Found at i:29669 original size:3 final size:3
Alignment explanation
Indices: 29649--29709 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
29639 ATTTATTTAT
* *
29649 TAA TAA TATA TAA CAA TAA TAA TAA TAA TAA T-A TAA TAA TAA CAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
29694 TTA -AA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
29710 AAGTAAACTG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:29700 original size:25 final size:23
Alignment explanation
Indices: 29649--29709 Score: 70
Period size: 23 Copynumber: 2.6 Consensus size: 23
29639 ATTTATTTAT
*
29649 TAATAAT-ATATAACAATAATAA
1 TAATAATAATATAACAATAACAA
*
29671 TAATAATAATATAATAATAACAA
1 TAATAATAATATAACAATAACAA
*
29694 TTAAATAATAAAATAA
1 -T-AATAATAATATAA
29710 AAGTAAACTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 7 0.21
23 13 0.39
24 1 0.03
25 12 0.36
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (23 bp):
TAATAATAATATAACAATAACAA
Found at i:29987 original size:76 final size:76
Alignment explanation
Indices: 29836--30402 Score: 976
Period size: 76 Copynumber: 7.5 Consensus size: 76
29826 GATGAAAATG
* * * * *
29836 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
29901 TCCCGAAGGCTT
65 TCCCGAAGGCTT
29913 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
29978 CCTGAAGGCTT
66 CCCGAAGGCTT
*
29989 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGTT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
30054 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
30065 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
30129 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
30140 TTTGGAAACATTATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
30204 CCCAAAGGCTT
66 CCCGAAGGCTT
30215 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
30280 CCCGAAGGCTTT
66 CCCGAAGGC-TT
*
30292 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
30357 CCCGAAGGCTT
66 CCCGAAGGCTT
*
30368 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
30403 TGGGAAATAG
Statistics
Matches: 469, Mismatches: 19, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
75 144 0.31
76 210 0.45
77 115 0.25
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:31271 original size:22 final size:22
Alignment explanation
Indices: 31246--31300 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
31236 CATAAAGCTT
* *
31246 TCATATTTGAAAAGAGAATGTA
1 TCATATTTGAAAAGAAAATCTA
*
31268 TCATATTTAAAAAGAAAATCTA
1 TCATATTTGAAAAGAAAATCTA
*
31290 TCATCTTTGAA
1 TCATATTTGAA
31301 GAGTGTAGAT
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:0.45, C:0.09, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATATTTGAAAAGAAAATCTA
Found at i:34003 original size:114 final size:114
Alignment explanation
Indices: 33836--34055 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
33826 GATCATGCAG
* * * *
33836 TTCATCTTTCAATTCCAATGATTGGTTTTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
33901 ACACTTCCAGAAGATTCTATTCGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTATGAGCAAA
*
33950 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
34015 ACACTTCCAGAAGATACTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTA
34056 CGAGAACGTG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:38247 original size:14 final size:14
Alignment explanation
Indices: 38230--38268 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
38220 TAAAAGTATG
38230 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
38244 AATGCAAAGATGCAA
1 AATGCAAA-ATGAAA
38259 AATG-AAAATG
1 AATGCAAAATG
38269 CATATATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.59, C:0.08, G:0.18, T:0.15
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:40679 original size:20 final size:21
Alignment explanation
Indices: 40629--40679 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
40619 TAAATATTAT
* *
40629 GAAAATCATAAAAAATTGAAA
1 GAAAATAATTAAAAATTGAAA
40650 GAAAATAATTAAAAATT-AAA
1 GAAAATAATTAAAAATTGAAA
40670 -AAAATGAATT
1 GAAAAT-AATT
40680 TTTAATTTCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 5 0.19
20 7 0.26
21 15 0.56
ACGTcount: A:0.67, C:0.02, G:0.08, T:0.24
Consensus pattern (21 bp):
GAAAATAATTAAAAATTGAAA
Found at i:41348 original size:145 final size:145
Alignment explanation
Indices: 41120--41380 Score: 341
Period size: 145 Copynumber: 1.8 Consensus size: 145
41110 ATTATTTCAA
* * * *
41120 AATATATTAATTTATATATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTTCTAGGTGC
1 AATATATTAATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGC
* *
41185 CTTAAGACAGCTCTTTTCTTCGATATTAAAAAAATAAATAAATA-A-TTAAAACATTTTTATAAA
66 CTTAAGACAGCTCCTTTCTT-AATATT-AAAAAATAAATAAATATATTTAAAACATTTTTATAAA
41248 AATAATAATAATATATT
129 AATAATAATAATATATT
** * *
41265 AATATA-TAATTTATAAAATAGGATATTTATTTATTTAAAAATATCAGAAAATGGGCATCCAGTT
1 AATATATTAATTTAT-AAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACATCCAGGT
* * *
41329 GCTTTAAGACTG-TCCTTTCTTAATATTGAAAAATAAATAAATATATTTAAAA
64 GCCTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATATATTTAAAA
41381 AATTATTACT
Statistics
Matches: 99, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
143 15 0.15
144 14 0.14
145 52 0.53
146 18 0.18
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (145 bp):
AATATATTAATTTATAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATCCAGGTGC
CTTAAGACAGCTCCTTTCTTAATATTAAAAAATAAATAAATATATTTAAAACATTTTTATAAAAA
TAATAATAATATATT
Found at i:42868 original size:3 final size:3
Alignment explanation
Indices: 42848--42902 Score: 53
Period size: 3 Copynumber: 19.0 Consensus size: 3
42838 ATTTATTTAT
* * *
42848 TAA TAA TATA TAA CAA TAA TAA TAA T-A TTA TAA TAA TAA TTA -AA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42892 TAA TAA -AA TAA
1 TAA TAA TAA TAA
42903 AAGTAAACTG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
2 5 0.12
3 35 0.81
4 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42893 original size:11 final size:12
Alignment explanation
Indices: 42848--42897 Score: 54
Period size: 11 Copynumber: 4.5 Consensus size: 12
42838 ATTTATTTAT
42848 TAATAA-TAT-A
1 TAATAATTATAA
* *
42858 TAACAATAATAA
1 TAATAATTATAA
42870 TAAT-ATTATAA
1 TAATAATTATAA
42881 TAATAATTA-AA
1 TAATAATTATAA
42892 TAATAA
1 TAATAA
42898 AATAAAAGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
10 5 0.15
11 20 0.61
12 8 0.24
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (12 bp):
TAATAATTATAA
Found at i:42894 original size:14 final size:15
Alignment explanation
Indices: 42848--42897 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 15
42838 ATTTATTTAT
*
42848 TAATAATATATAACAA
1 TAATAATA-ATTACAA
**
42864 TAATAATAA-TATTA
1 TAATAATAATTACAA
42878 TAATAATAATTA-AA
1 TAATAATAATTACAA
42892 TAATAA
1 TAATAA
42898 AATAAAAGTA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 18 0.62
15 3 0.10
16 8 0.28
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
TAATAATAATTACAA
Found at i:45263 original size:64 final size:65
Alignment explanation
Indices: 45192--45340 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 65
45182 CTAGGGGTGT
* * *
45192 ATCGGTACACTAATTACATTCGATGTTTC-AAAGAGCCATGAGTGCATCGATGCATGG-TATGTG
1 ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCT-TGTG
45255 A
65 A
** * * ** * *
45256 ATCGGTACACAAAATGTATTTGATGTTTCAAAATATTCAAGAGTGCATCGATGCTTGGCTTGTGC
1 ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTTGTGA
*
45321 ATCGGTACACAAAATGCATT
1 ATCGGTACACAAAATACATT
45341 AGATATGGGT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 24 0.34
65 46 0.65
66 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (65 bp):
ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTTGTGA
Found at i:45706 original size:12 final size:13
Alignment explanation
Indices: 45680--45714 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
45670 TAAGATTTTC
45680 TTTGAAAATCAAT
1 TTTGAAAATCAAT
45693 TTTGAAAA-CAAT
1 TTTGAAAATCAAT
45705 TTTGCAAAAT
1 TTTG-AAAAT
45715 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (13 bp):
TTTGAAAATCAAT
Found at i:50116 original size:2 final size:2
Alignment explanation
Indices: 50109--50140 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
50099 TTAATTCTTG
50109 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
50141 TATTTTTATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:51484 original size:2 final size:2
Alignment explanation
Indices: 51479--51529 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
51469 AAAAATATCT
51479 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
51521 TA TA TA TA T
1 TA TA TA TA T
51530 TCCAAGAAAT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:52654 original size:20 final size:22
Alignment explanation
Indices: 52611--52655 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
52601 TTAAGATTAT
*
52611 TAAATTTTATTGAAACTTTGAA
1 TAAATTATATTGAAACTTTGAA
*
52633 TAAATTATATT-AAA-TTTTAA
1 TAAATTATATTGAAACTTTGAA
52653 TAA
1 TAA
52656 TAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAATTATATTGAAACTTTGAA
Found at i:55847 original size:12 final size:12
Alignment explanation
Indices: 55820--55912 Score: 55
Period size: 12 Copynumber: 7.8 Consensus size: 12
55810 ACAGAGATGT
* *
55820 CAGAAATCAAAA
1 CAGAATTCAGAA
*
55832 CAGAATTCAGAT
1 CAGAATTCAGAA
55844 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* * *
55856 CAAAATCCAGAT
1 CAGAATTCAGAA
*
55868 CAGAAATCAGAA
1 CAGAATTCAGAA
* *
55880 CAGGATTCATATA
1 CAGAATTCAGA-A
* *
55893 -AGAAATCATAA
1 CAGAATTCAGAA
55904 CAGAATTCA
1 CAGAATTCA
55913 AATCGAAAAT
Statistics
Matches: 60, Mismatches: 17, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
11 3 0.05
12 54 0.90
13 3 0.05
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.18
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:55847 original size:24 final size:24
Alignment explanation
Indices: 55819--55926 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
55809 CACAGAGATG
*
55819 TCAGAAATCAAAACAGAATTCAGA
1 TCAGAAATCAGAACAGAATTCAGA
* * *
55843 TCAGATATCAGAACAAAATCCAGA
1 TCAGAAATCAGAACAGAATTCAGA
* *
55867 TCAGAAATCAGAACAGGATTCATA
1 TCAGAAATCAGAACAGAATTCAGA
* * *
55891 TAAGAAATCATAACAGAATTCAAA
1 TCAGAAATCAGAACAGAATTCAGA
55915 TC-GAAAATCAGA
1 TCAG-AAATCAGA
55927 TAAAACATTC
Statistics
Matches: 68, Mismatches: 15, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
23 1 0.01
24 67 0.99
ACGTcount: A:0.52, C:0.17, G:0.13, T:0.19
Consensus pattern (24 bp):
TCAGAAATCAGAACAGAATTCAGA
Found at i:64815 original size:2 final size:2
Alignment explanation
Indices: 64808--64839 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
64798 AATTCCTGAC
64808 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
64840 TTTTATGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67370 original size:20 final size:22
Alignment explanation
Indices: 67327--67371 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
67317 TTAAGATTAT
*
67327 TAAATTTTATTGAAACTTTGAA
1 TAAATTATATTGAAACTTTGAA
*
67349 TAAATTATATT-AAA-TTTTAA
1 TAAATTATATTGAAACTTTGAA
67369 TAA
1 TAA
67372 TAATAATAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 8 0.38
21 3 0.14
22 10 0.48
ACGTcount: A:0.47, C:0.02, G:0.04, T:0.47
Consensus pattern (22 bp):
TAAATTATATTGAAACTTTGAA
Found at i:67606 original size:18 final size:18
Alignment explanation
Indices: 67583--67640 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
67573 AAAATAAAAG
67583 TATAATATTATATATAAT
1 TATAATATTATATATAAT
67601 TATAATATTACATAATATAA-
1 TATAATATT--AT-ATATAAT
* *
67621 TATCATATTAT-TAGAAT
1 TATAATATTATATATAAT
67638 TAT
1 TAT
67641 GAGTAAATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
16 4 0.12
17 3 0.09
18 11 0.32
20 10 0.29
21 6 0.18
ACGTcount: A:0.48, C:0.03, G:0.02, T:0.47
Consensus pattern (18 bp):
TATAATATTATATATAAT
Found at i:68053 original size:2 final size:2
Alignment explanation
Indices: 68046--68083 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
68036 TTAATTCTTG
68046 AT AT 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 AT AT
68084 TATTTTTTCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76407 original size:21 final size:22
Alignment explanation
Indices: 76357--76407 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
76347 AATATTAAGA
*
76357 TTATTAAATTTTATTGAAACTT
1 TTATTAAATTATATTGAAACTT
* **
76379 TTAATAAATTATATT-AATTTT
1 TTATTAAATTATATTGAAACTT
76400 TTATTAAA
1 TTATTAAA
76408 ATAATAATGA
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (22 bp):
TTATTAAATTATATTGAAACTT
Found at i:76668 original size:23 final size:24
Alignment explanation
Indices: 76625--76676 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 24
76615 AAAGTATAAT
*
76625 ATTATATATCATTATAATATTA-A
1 ATTATATATCATCATAATATTAGA
*
76648 ATTATATAAT-ATCATATTATTAGA
1 ATTATAT-ATCATCATAATATTAGA
76672 ATTAT
1 ATTAT
76677 GAGTTTATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 17 0.68
24 8 0.32
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (24 bp):
ATTATATATCATCATAATATTAGA
Found at i:78228 original size:2 final size:2
Alignment explanation
Indices: 78221--78251 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
78211 AAAAATATCT
*
78221 TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
78252 TTCAAAGAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:80435 original size:22 final size:21
Alignment explanation
Indices: 80406--80450 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
80396 ATTAATTTTT
80406 ATTTGGGTGCTA-TTTGTGTAA
1 ATTTGGGTGCTAGTTT-TGTAA
*
80427 ATTTCGGGTGTTAGTTTTGTAA
1 ATTT-GGGTGCTAGTTTTGTAA
80449 AT
1 AT
80451 AATTGTATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 4 0.19
22 14 0.67
23 3 0.14
ACGTcount: A:0.20, C:0.04, G:0.27, T:0.49
Consensus pattern (21 bp):
ATTTGGGTGCTAGTTTTGTAA
Found at i:83367 original size:43 final size:43
Alignment explanation
Indices: 83305--83401 Score: 176
Period size: 43 Copynumber: 2.3 Consensus size: 43
83295 ACCATTACAA
* *
83305 CAGGTCCCTTTGTTGTGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCC
83348 CAGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCC
1 CAGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCC
83391 CAGGTCCCTTT
1 CAGGTCCCTTT
83402 ATCTAACTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 52 1.00
ACGTcount: A:0.16, C:0.28, G:0.24, T:0.32
Consensus pattern (43 bp):
CAGGTCCCTTTGCTATGTGCAAGGGTAAGCCTTACAGTTTCCC
Found at i:86213 original size:2 final size:2
Alignment explanation
Indices: 86206--86242 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
86196 AAAAATATCT
86206 TA TA TA TA 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 TA TA TA TA T
86243 TTCCAAGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:87508 original size:23 final size:21
Alignment explanation
Indices: 87480--87557 Score: 70
Period size: 21 Copynumber: 3.6 Consensus size: 21
87470 ATAATATATA
87480 TAATTTAATAATAATACATTATT
1 TAATTTAA-AATAAT-CATTATT
*
87503 TAATTTATGAATAAT-ATTATT
1 TAATTTA-AAATAATCATTATT
* * *
87524 TTATTGAAAA-AATCATTATA
1 TAATTTAAAATAATCATTATT
87544 TAATATTAAAATAA
1 TAAT-TTAAAATAA
87558 AAGAATAATA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
19 3 0.07
20 10 0.23
21 16 0.36
22 2 0.05
23 13 0.30
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (21 bp):
TAATTTAAAATAATCATTATT
Found at i:90333 original size:64 final size:64
Alignment explanation
Indices: 90231--90388 Score: 178
Period size: 64 Copynumber: 2.5 Consensus size: 64
90221 AATTAAATTG
* * * *
90231 AACATCGAATGTATTTCACGCATCGATGCA-CATACCATGCACCGATGCACTGAGGAT-TTTATG
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATACACT-AGGATATTT-TG
90294 A
64 A
* * ** *
90295 AACATCGAATGCATTTGATGCATCGATGCACCA-GCCATGCATCGATACACTCTGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATACACTAGGATATTTTGA
**
90358 AACATCGAATGCACATGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
90389 TCTTAGTGCA
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 34 0.42
64 45 0.56
65 2 0.02
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACCATACCATGCACCGATACACTAGGATATTTTGA
Done.