Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004952.1 Hibiscus syriacus cultivar Beakdansim tig00011138_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: 88059
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:4334 original size:39 final size:39
Alignment explanation
Indices: 4272--4367 Score: 124
Period size: 39 Copynumber: 2.5 Consensus size: 39
4262 AAGTTTTGGG
* *
4272 ATTTGTTCATCAATGGAAGATAGTGG-GAAAAGC-TCTAAA
1 ATTTATTCATCAATGGAAAATAGTGGAG-AAAGCTTC-AAA
* *
4311 ATTTATTCATCAATGTAAAATAGTGGAGAAATCTTCAAA
1 ATTTATTCATCAATGGAAAATAGTGGAGAAAGCTTCAAA
4350 ATTTATTCATCAATGGAA
1 ATTTATTCATCAATGGAA
4368 GATAACGTTG
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
39 47 0.94
40 3 0.06
ACGTcount: A:0.41, C:0.10, G:0.17, T:0.32
Consensus pattern (39 bp):
ATTTATTCATCAATGGAAAATAGTGGAGAAAGCTTCAAA
Found at i:14411 original size:22 final size:22
Alignment explanation
Indices: 14383--14428 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
14373 GTAGTGACCA
14383 TTCCTCTATTGTTTTTCATATC
1 TTCCTCTATTGTTTTTCATATC
*
14405 TTCCTCTATTGTTTTTCATTTC
1 TTCCTCTATTGTTTTTCATATC
14427 TT
1 TT
14429 GCGGAATATG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.11, C:0.22, G:0.04, T:0.63
Consensus pattern (22 bp):
TTCCTCTATTGTTTTTCATATC
Found at i:14984 original size:20 final size:22
Alignment explanation
Indices: 14945--14986 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
14935 TGATAATTTC
14945 TTTTTCAAAAACCCATTTATTA
1 TTTTTCAAAAACCCATTTATTA
*
14967 TTTTT-AAAACCCCA-TTATTA
1 TTTTTCAAAAACCCATTTATTA
14987 ATTGAGAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTTTCAAAAACCCATTTATTA
Found at i:21565 original size:24 final size:24
Alignment explanation
Indices: 21538--21584 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
21528 AGAAGGCCGG
21538 TTGATTTTCAAACTAAGGGGCTGA
1 TTGATTTTCAAACTAAGGGGCTGA
*
21562 TTGATTTTCAAATTAAGGGGCTG
1 TTGATTTTCAAACTAAGGGGCTG
21585 CTTTGAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.36
Consensus pattern (24 bp):
TTGATTTTCAAACTAAGGGGCTGA
Found at i:21595 original size:24 final size:24
Alignment explanation
Indices: 21538--21597 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
21528 AGAAGGCCGG
*
21538 TTGATTTTCAAACTAAGGGGCTGA
1 TTGATATTCAAACTAAGGGGCTGA
* * *
21562 TTGATTTTCAAATTAAGGGGCTGCT
1 TTGATATTCAAACTAAGGGGCTG-A
21587 TTGA-ATTCAAA
1 TTGATATTCAAA
21598 ATAGGGTGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 28 0.88
25 4 0.12
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.37
Consensus pattern (24 bp):
TTGATATTCAAACTAAGGGGCTGA
Found at i:22047 original size:16 final size:17
Alignment explanation
Indices: 22026--22060 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
22016 TACTATTCAC
22026 GTGAAT-AGTAAATTTT
1 GTGAATAAGTAAATTTT
*
22042 GTGAATAATTAAATTTT
1 GTGAATAAGTAAATTTT
22059 GT
1 GT
22061 TGGCGATACG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.37, C:0.00, G:0.17, T:0.46
Consensus pattern (17 bp):
GTGAATAAGTAAATTTT
Found at i:23942 original size:24 final size:24
Alignment explanation
Indices: 23915--23963 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
23905 CTAGAAGGCC
23915 GGTTGATTTTCAAACTAAGGGGCT
1 GGTTGATTTTCAAACTAAGGGGCT
*
23939 GGTTGATTTTCAAATTAAGGGGCT
1 GGTTGATTTTCAAACTAAGGGGCT
23963 G
1 G
23964 CTTTGAATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.10, G:0.31, T:0.35
Consensus pattern (24 bp):
GGTTGATTTTCAAACTAAGGGGCT
Found at i:23974 original size:24 final size:24
Alignment explanation
Indices: 23915--23976 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
23905 CTAGAAGGCC
*
23915 GGTTGATTTTCAAACTAAGGGGCT
1 GGTTGATATTCAAACTAAGGGGCT
* *
23939 GGTTGATTTTCAAATTAAGGGGCT
1 GGTTGATATTCAAACTAAGGGGCT
*
23963 GCTTTGA-ATTCAAA
1 G-GTTGATATTCAAA
23977 ATAGGGTGGT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
24 30 0.88
25 4 0.12
ACGTcount: A:0.27, C:0.11, G:0.26, T:0.35
Consensus pattern (24 bp):
GGTTGATATTCAAACTAAGGGGCT
Found at i:25319 original size:5 final size:5
Alignment explanation
Indices: 25309--25335 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
25299 GAGTGAGACA
25309 CATAG CATAG CATAG CATAG CATAG CA
1 CATAG CATAG CATAG CATAG CATAG CA
25336 GTTAAACTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.19
Consensus pattern (5 bp):
CATAG
Found at i:32582 original size:73 final size:73
Alignment explanation
Indices: 32456--32637 Score: 193
Period size: 73 Copynumber: 2.4 Consensus size: 73
32446 AAATGACTAG
* * * * * * * * *
32456 GGGTATCGGTACCTCTAAGGGGGTATCGATATCCATAGGGCATTATGTTTTTCTCGGAGCCAAGA
1 GGGTATCGGTACCTATTA-GGGGTATCGGTACCCATAGGACAATATGTTTTTCTCAGAACCAAAA
*
32521 TTTACATAA
65 TTGACATAA
* * *
32530 GGGTATCAGTACCTATTAGGGGTATCGGTACCCATTGGACAATCTGTTTTTCTCAGAACCAAAAT
1 GGGTATCGGTACCTATTAGGGGTATCGGTACCCATAGGACAATATGTTTTTCTCAGAACCAAAAT
* *
32595 TGGCATAG
66 TGACATAA
32603 GGGTATCGGTACACCATATTAGGGGTATCGGTACC
1 GGGTATCGGT--ACC-TATTAGGGGTATCGGTACC
32638 TCCCTATTTA
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
73 52 0.58
74 15 0.17
75 3 0.03
76 19 0.21
ACGTcount: A:0.26, C:0.19, G:0.26, T:0.30
Consensus pattern (73 bp):
GGGTATCGGTACCTATTAGGGGTATCGGTACCCATAGGACAATATGTTTTTCTCAGAACCAAAAT
TGACATAA
Found at i:33317 original size:20 final size:20
Alignment explanation
Indices: 33269--33320 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
33259 ATTCAAGTTC
*
33269 AAACATCCAAA-CATCCATA
1 AAACATCAAAATCATCCATA
33288 AAACATTCAAAATCAATCCA-A
1 AAACA-TCAAAATC-ATCCATA
33309 AAACATCAAAAT
1 AAACATCAAAAT
33321 GTTTAACAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.17
20 12 0.41
21 7 0.24
22 5 0.17
ACGTcount: A:0.58, C:0.25, G:0.00, T:0.17
Consensus pattern (20 bp):
AAACATCAAAATCATCCATA
Found at i:34864 original size:23 final size:23
Alignment explanation
Indices: 34836--34895 Score: 120
Period size: 23 Copynumber: 2.6 Consensus size: 23
34826 TACCTTTATG
34836 GGGGTATCGATACACATTCAAAT
1 GGGGTATCGATACACATTCAAAT
34859 GGGGTATCGATACACATTCAAAT
1 GGGGTATCGATACACATTCAAAT
34882 GGGGTATCGATACA
1 GGGGTATCGATACA
34896 TGTTAAAGGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.33, C:0.17, G:0.25, T:0.25
Consensus pattern (23 bp):
GGGGTATCGATACACATTCAAAT
Found at i:39950 original size:74 final size:74
Alignment explanation
Indices: 39821--39964 Score: 207
Period size: 74 Copynumber: 1.9 Consensus size: 74
39811 GTTAAATGAC
* * * * * *
39821 TAGGGGTATCGGTACCCATAGGACATTCTGTTTTTCTCGGAGCCAAGATTTGCATAGGGGTATCG
1 TAGGGGTATCGATACCCATAGGACAATCTGTTTTTCTCAGAACCAAAATTAGCATAGGGGTATCG
39886 GTACCCTAT
66 GTACCCTAT
* * *
39895 TAGGGGTATCGATACCCATTGGGCAATCTGTTTTTCTTAGAACCAAAATTAGCATAGGGGTATCG
1 TAGGGGTATCGATACCCATAGGACAATCTGTTTTTCTCAGAACCAAAATTAGCATAGGGGTATCG
39960 GTACC
66 GTACC
39965 TCCCTATTTA
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
74 61 1.00
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (74 bp):
TAGGGGTATCGATACCCATAGGACAATCTGTTTTTCTCAGAACCAAAATTAGCATAGGGGTATCG
GTACCCTAT
Found at i:41394 original size:17 final size:16
Alignment explanation
Indices: 41373--41437 Score: 51
Period size: 17 Copynumber: 3.7 Consensus size: 16
41363 AAAATTTGAT
41373 AAATAAATAAATAATA
1 AAATAAATAAATAATA
41389 ATAATATAACCT-AATATATA
1 A-AATA-AA--TAAATA-ATA
*
41409 AAATAATATAAATAACA
1 AAATAA-ATAAATAATA
41426 AAATGAAATAAA
1 AAAT-AAATAAA
41438 AAAGAAAAAT
Statistics
Matches: 40, Mismatches: 1, Indels: 15
0.71 0.02 0.27
Matches are distributed among these distances:
16 1 0.03
17 16 0.40
18 9 0.22
19 9 0.22
20 5 0.12
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.26
Consensus pattern (16 bp):
AAATAAATAAATAATA
Found at i:41553 original size:35 final size:35
Alignment explanation
Indices: 41511--41916 Score: 138
Period size: 35 Copynumber: 11.6 Consensus size: 35
41501 AAAAACTATT
* *
41511 TTTAAAAACTATATTA-TATATGCTTTCAAAACCGG
1 TTTAAAAACTATA-TACTATACGCTTTCAAAACCAG
* * *
41546 TTTAAAAACTATATACTATACGTTTTCAAAACTAT
1 TTTAAAAACTATATACTATACGCTTTCAAAACCAG
* * ** *
41581 TTTAAAAACTATTTTAAAAACTATTTACGTTTTCAAAATTAT
1 TTTAAAAACTA---T--ATACTA--TACGCTTTCAAAACCAG
* ** *
41623 TTTAAAAACTATATAC-AT----TTTTAAAATTAT
1 TTTAAAAACTATATACTATACGCTTTCAAAACCAG
* * ** *
41653 TTTAAAAACTATAT--TATATGTTTTCAAAATTAT
1 TTTAAAAACTATATACTATACGCTTTCAAAACCAG
** * * ** *
41686 TTTAAAAACGGTAT--TATATGTTTTCAAAATTAT
1 TTTAAAAACTATATACTATACGCTTTCAAAACCAG
* * * ** *
41719 TTTAAAAATTATATTCTAT--GTTTTCAAAATTAT
1 TTTAAAAACTATATACTATACGCTTTCAAAACCAG
* *
41752 TTTAAAAAACTATATACTATATGTTTTCAAAACC-G
1 TTT-AAAAACTATATACTATACGCTTTCAAAACCAG
* * * * *
41787 TTTAAAAACTATATATTATATGTTTTCAAAACTATTT
1 TTTAAAAACTATATACTATACGCTTTCAAAACCA--G
* ** * **
41824 TTTAAAAACTATATATTATTTGTTTTCAAAATTA-
1 TTTAAAAACTATATACTATACGCTTTCAAAACCAG
* * * **
41858 TCTTAAAAACTATATGCTATATGTTTTCAAAAATAG
1 T-TTAAAAACTATATACTATACGCTTTCAAAACCAG
*
41894 TTTTAAAAACTATATATTATACG
1 -TTTAAAAACTATATACTATACG
41917 TTTTTTAAAA
Statistics
Matches: 315, Mismatches: 32, Indels: 47
0.80 0.08 0.12
Matches are distributed among these distances:
29 2 0.01
30 25 0.08
33 70 0.22
34 46 0.15
35 73 0.23
36 29 0.09
37 36 0.11
38 1 0.00
39 1 0.00
40 5 0.02
42 27 0.09
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.44
Consensus pattern (35 bp):
TTTAAAAACTATATACTATACGCTTTCAAAACCAG
Found at i:41625 original size:12 final size:12
Alignment explanation
Indices: 41568--41606 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
41558 ATACTATACG
*
41568 TTTTCAAAACTA
1 TTTTAAAAACTA
41580 TTTTAAAAACTA
1 TTTTAAAAACTA
41592 TTTTAAAAACTA
1 TTTTAAAAACTA
41604 TTT
1 TTT
41607 ACGTTTTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.44, C:0.10, G:0.00, T:0.46
Consensus pattern (12 bp):
TTTTAAAAACTA
Found at i:41687 original size:33 final size:33
Alignment explanation
Indices: 41580--41908 Score: 366
Period size: 33 Copynumber: 9.8 Consensus size: 33
41570 TTCAAAACTA
* * *
41580 TTTTAAAAACTATTTTAAAAAC--TATT-TACG
1 TTTTCAAAATTATTTTAAAAACTATATTATATG
*
41610 TTTTCAAAATTATTTTAAAAACTATA-TACAT-
1 TTTTCAAAATTATTTTAAAAACTATATTATATG
41641 TTTT-AAAATTATTTTAAAAACTATATTATATG
1 TTTTCAAAATTATTTTAAAAACTATATTATATG
**
41673 TTTTCAAAATTATTTTAAAAACGGTATTATATG
1 TTTTCAAAATTATTTTAAAAACTATATTATATG
* *
41706 TTTTCAAAATTATTTTAAAAATTATATTCTATG
1 TTTTCAAAATTATTTTAAAAACTATATTATATG
41739 TTTTCAAAATTATTTTAAAAAACTATATACTATATG
1 TTTTCAAAATTATTTT-AAAAACTATAT--TATATG
***
41775 TTTTCAAAA-CCGTTTAAAAACTATATATTATATG
1 TTTTCAAAATTATTTTAAAAAC--TATATTATATG
* *
41809 TTTTCAAAACTATTTTTTAAAAACTATATATTATTTG
1 TTTTCAAAA-T-TATTTTAAAAAC--TATATTATATG
*
41846 TTTTCAAAATTATCTTAAAAACTATATGCTATATG
1 TTTTCAAAATTATTTTAAAAACTATAT--TATATG
*
41881 TTTTCAAAAATAGTTTTAAAAACTATAT
1 TTTTCAAAATTA-TTTTAAAAACTATAT
41909 ATTATACGTT
Statistics
Matches: 257, Mismatches: 25, Indels: 28
0.83 0.08 0.09
Matches are distributed among these distances:
30 41 0.16
31 9 0.04
32 7 0.03
33 76 0.30
34 31 0.12
35 29 0.11
36 34 0.13
37 30 0.12
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (33 bp):
TTTTCAAAATTATTTTAAAAACTATATTATATG
Found at i:44206 original size:29 final size:29
Alignment explanation
Indices: 44134--44249 Score: 189
Period size: 29 Copynumber: 4.0 Consensus size: 29
44124 AAAATGTTTT
* *
44134 TGGGTGTCCAATCACACCCTAATTAAAGA
1 TGGGTGCCCAATCACACCCTAATCAAAGA
44163 T-GGTGCCCAATCACACCCTAATCAAAGA
1 TGGGTGCCCAATCACACCCTAATCAAAGA
*
44191 TGGGTGTCCAATCACACCCTAATCAAAGA
1 TGGGTGCCCAATCACACCCTAATCAAAGA
*
44220 TGTGTGCCCAATCACACCCTAATCAAAGA
1 TGGGTGCCCAATCACACCCTAATCAAAGA
44249 T
1 T
44250 TGATGGCGAC
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
28 26 0.32
29 55 0.68
ACGTcount: A:0.34, C:0.28, G:0.16, T:0.22
Consensus pattern (29 bp):
TGGGTGCCCAATCACACCCTAATCAAAGA
Found at i:45649 original size:63 final size:63
Alignment explanation
Indices: 45550--45680 Score: 262
Period size: 63 Copynumber: 2.1 Consensus size: 63
45540 AAAGGAAAAA
45550 TATCAACTATTACTTCAAGTACACAATGTGACATTTTAAGTCCATCATATTGTATTTGAGGTG
1 TATCAACTATTACTTCAAGTACACAATGTGACATTTTAAGTCCATCATATTGTATTTGAGGTG
45613 TATCAACTATTACTTCAAGTACACAATGTGACATTTTAAGTCCATCATATTGTATTTGAGGTG
1 TATCAACTATTACTTCAAGTACACAATGTGACATTTTAAGTCCATCATATTGTATTTGAGGTG
45676 TATCA
1 TATCA
45681 GTCTTAATAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
63 68 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (63 bp):
TATCAACTATTACTTCAAGTACACAATGTGACATTTTAAGTCCATCATATTGTATTTGAGGTG
Found at i:64096 original size:15 final size:15
Alignment explanation
Indices: 64076--64105 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
64066 TATCACAATC
64076 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
64091 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
64106 AGCACCGTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.27, G:0.47, T:0.13
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:70322 original size:25 final size:25
Alignment explanation
Indices: 70294--70343 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
70284 TAAAGTAGTT
70294 GCCCCAAGTTGAATGTTGGTATAAC
1 GCCCCAAGTTGAATGTTGGTATAAC
70319 GCCCCAAGTTGAATGTTGGTATAAC
1 GCCCCAAGTTGAATGTTGGTATAAC
70344 ACCAACTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (25 bp):
GCCCCAAGTTGAATGTTGGTATAAC
Found at i:74314 original size:34 final size:36
Alignment explanation
Indices: 74255--74363 Score: 159
Period size: 34 Copynumber: 3.0 Consensus size: 36
74245 TGGCAACCAA
*
74255 CTTTGAAACAAATGGATTTCAAAGTTTGGTAAATGTTT
1 CTTTG-AA-AAATGGTTTTCAAAGTTTGGTAAATGTTT
74293 CTTTG-AAAATGG-TTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
74327 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
74364 GTTGATTTTT
Statistics
Matches: 67, Mismatches: 1, Indels: 7
0.89 0.01 0.09
Matches are distributed among these distances:
34 27 0.40
35 13 0.19
36 1 0.01
37 21 0.31
38 5 0.07
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.43
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:76087 original size:21 final size:21
Alignment explanation
Indices: 76062--76121 Score: 62
Period size: 21 Copynumber: 3.2 Consensus size: 21
76052 CAACTTTTAA
76062 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
*
76083 AAAT-G-TTTC----TTT-GA
1 AAATGGTTTTCAAAGTTTGGT
76097 AAATGGTTTTCAAAGTTTGGT
1 AAATGGTTTTCAAAGTTTGGT
76118 AAAT
1 AAAT
76122 ATTTCTTTGA
Statistics
Matches: 30, Mismatches: 2, Indels: 14
0.65 0.04 0.30
Matches are distributed among these distances:
14 5 0.17
15 4 0.13
16 4 0.13
19 4 0.13
20 4 0.13
21 9 0.30
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (21 bp):
AAATGGTTTTCAAAGTTTGGT
Found at i:76105 original size:35 final size:36
Alignment explanation
Indices: 76055--76162 Score: 173
Period size: 35 Copynumber: 3.0 Consensus size: 36
76045 TGGCAACCAA
*
76055 CTTTTAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
76091 CTTTG-AAAATGGTTTTCAAAGTTTGGTAAATATTT
1 CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
*
76126 CTTTGAAAAATGGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGG-TTTTCAAAGTTTGGTAAATGTTT
76163 GTTGATTTTT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
35 34 0.52
36 11 0.17
37 21 0.32
ACGTcount: A:0.30, C:0.06, G:0.19, T:0.46
Consensus pattern (36 bp):
CTTTGAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:81706 original size:23 final size:23
Alignment explanation
Indices: 81675--81730 Score: 94
Period size: 23 Copynumber: 2.4 Consensus size: 23
81665 GGAACCGATT
81675 ACCACCTCGCGAAAGAGACGTCC
1 ACCACCTCGCGAAAGAGACGTCC
* *
81698 ACCGCCTCGCGAAAGAGACGTCT
1 ACCACCTCGCGAAAGAGACGTCC
81721 ACCACCTCGC
1 ACCACCTCGC
81731 TGAGCAGGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.27, C:0.41, G:0.21, T:0.11
Consensus pattern (23 bp):
ACCACCTCGCGAAAGAGACGTCC
Found at i:81908 original size:3 final size:3
Alignment explanation
Indices: 81900--81991 Score: 98
Period size: 3 Copynumber: 31.0 Consensus size: 3
81890 ATTTGGTTTT
* * *
81900 TTA TTA TTA -TA TTTA TTA TTT TTA TTT TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
81945 TTA TTT TTA TTA ATA TTA TTA ATA TTA TTA ATA TTA TTA TT- TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
81992 CAGATACAAC
Statistics
Matches: 72, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
2 4 0.06
3 66 0.92
4 2 0.03
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:83968 original size:149 final size:146
Alignment explanation
Indices: 83807--84075 Score: 425
Period size: 149 Copynumber: 1.8 Consensus size: 146
83797 AAAATAATCA
* *
83807 TATTTTAATATTTATTTATTTTTTAATATTAAGAAATGGGCTGTCTTAAAACACCTAGAAGTCCT
1 TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAAACACCTAGAAGTCCT
*
83872 TTTATGATA-TTCTTAAATAAATAAATATCATATT-TTTATAAATTATATATATATTAATTTATT
66 TTTATGATATTTC-TAAATAAATAAATAT--T-TTATTTATAAA-TATATATAAATTAATTTATT
83935 TAATTATTTTTAGAAAGATGT
126 TAATTATTTTTAGAAAGATGT
**
83956 TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCCT
1 TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAAACACCTAGAAGTCCT
*
84021 TTTCTGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATTAAT
66 TTTATGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATTAAT
84076 AGATTTTCTT
Statistics
Matches: 112, Mismatches: 6, Indels: 7
0.90 0.05 0.06
Matches are distributed among these distances:
146 16 0.14
147 9 0.08
149 84 0.75
150 3 0.03
ACGTcount: A:0.39, C:0.07, G:0.07, T:0.47
Consensus pattern (146 bp):
TATTTTAATATTTATTTATTTTTTAATATTAAGAAAAGAGCTGTCTTAAAACACCTAGAAGTCCT
TTTATGATATTTCTAAATAAATAAATATTTTATTTATAAATATATATAAATTAATTTATTTAATT
ATTTTTAGAAAGATGT
Found at i:84622 original size:13 final size:14
Alignment explanation
Indices: 84598--84636 Score: 55
Period size: 13 Copynumber: 2.9 Consensus size: 14
84588 TATTATTTTT
84598 ATATTATTTTATTA
1 ATATTATTTTATTA
*
84612 ATATT-TTTTATTT
1 ATATTATTTTATTA
84625 AT-TTATTTTATT
1 ATATTATTTTATT
84637 CAAGTATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 2 0.09
13 16 0.70
14 5 0.22
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (14 bp):
ATATTATTTTATTA
Done.