Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000429.1 Hibiscus syriacus cultivar Beakdansim tig00000788_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: 59532
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:1103 original size:17 final size:16
Alignment explanation
Indices: 1072--1105 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
1062 CACGTGAGGA
1072 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
1088 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
1105 T
1 T
1106 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:10454 original size:17 final size:16
Alignment explanation
Indices: 10423--10456 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
10413 CACGTGAGGA
10423 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
10439 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
10456 T
1 T
10457 ACTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:17906 original size:138 final size:140
Alignment explanation
Indices: 17658--17924 Score: 389
Period size: 138 Copynumber: 1.9 Consensus size: 140
17648 ACCGAAGTGC
* * *
17658 CGAAATGGAAATTCACAAACTCATTATGAATTCCATGGATGCAAACATAGTGCCGAAAGTACACT
1 CGAAATGGAAATTCACAAACTCATTATGAATACCATAGATGCAAACATAGTGCCGAAAGTACACA
* *
17723 TAGTACTGATACAAAAATGCACCGTTATGCATTAAACAAAATCAATCGATAACT-TT-CATACAT
66 TAGTACTGATACAAAAATGCACCATTATGCATTAAACAAAATCAATCAATAACTATTACATACAT
17786 AATTGTATAT
131 AATTGTATAT
* *
17796 CGAAATGGTAATTCACAAACTCATTATGAATACCATAGTTG-AATATC-TAGTGCCGAAAGTACA
1 CGAAATGGAAATTCACAAACTCATTATGAATACCATAGATGCAA-A-CATAGTGCCGAAAGTACA
* * * *
17859 CATAGTACTGATACGAAAATGCACCATTATGTATTACAGAAAATCAATCAATAACTATTACATAC
64 CATAGTACTGATACAAAAATGCACCATTATGCATTAAACAAAATCAATCAATAACTATTACATAC
17924 A
129 A
17925 ATTTCTGTCG
Statistics
Matches: 114, Mismatches: 11, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
137 2 0.02
138 103 0.90
139 3 0.03
140 6 0.05
ACGTcount: A:0.42, C:0.18, G:0.13, T:0.27
Consensus pattern (140 bp):
CGAAATGGAAATTCACAAACTCATTATGAATACCATAGATGCAAACATAGTGCCGAAAGTACACA
TAGTACTGATACAAAAATGCACCATTATGCATTAAACAAAATCAATCAATAACTATTACATACAT
AATTGTATAT
Found at i:22603 original size:19 final size:20
Alignment explanation
Indices: 22562--22612 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
22552 GAAACCCCTT
*
22562 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
22582 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
22601 TGAAGATACATG
1 TGAAAATACATG
22613 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:23562 original size:30 final size:30
Alignment explanation
Indices: 23527--23583 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
23517 CTGCCATGAT
**
23527 ATCTAAATGAAATGAAAACATAATAAATTA
1 ATCTAAAACAAATGAAAACATAATAAATTA
* *
23557 ATCTAAAACATATGTAAACATAATAAA
1 ATCTAAAACAAATGAAAACATAATAAA
23584 AAGATGTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.26
Consensus pattern (30 bp):
ATCTAAAACAAATGAAAACATAATAAATTA
Found at i:27369 original size:16 final size:16
Alignment explanation
Indices: 27348--27382 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
27338 TTTTATTAAA
27348 TTTTTAAATTTAATTT
1 TTTTTAAATTTAATTT
*
27364 TTTTTAATTTTAATTT
1 TTTTTAAATTTAATTT
27380 TTT
1 TTT
27383 ATATTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTAAATTTAATTT
Found at i:30516 original size:29 final size:29
Alignment explanation
Indices: 30474--30532 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
30464 TTTTTCACCT
30474 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
30503 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
30532 A
1 A
30533 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:32734 original size:15 final size:15
Alignment explanation
Indices: 32714--32742 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32704 AAGTTGCAGT
32714 CCTCATTGCTTCAGC
1 CCTCATTGCTTCAGC
32729 CCTCATTGCTTCAG
1 CCTCATTGCTTCAG
32743 GCCAAAACCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.14, C:0.38, G:0.14, T:0.34
Consensus pattern (15 bp):
CCTCATTGCTTCAGC
Found at i:34931 original size:29 final size:29
Alignment explanation
Indices: 34889--34947 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
34879 TTTTTCACCT
*
34889 AACTAAATTGATGTAAGCAACT-ACATCAA
1 AACTAAATTAATGTAAGCAA-TGACATCAA
34918 AACTAAATTAATGTAAGCAATGACATCAA
1 AACTAAATTAATGTAAGCAATGACATCAA
34947 A
1 A
34948 TTAATTTAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.51, C:0.15, G:0.10, T:0.24
Consensus pattern (29 bp):
AACTAAATTAATGTAAGCAATGACATCAA
Found at i:36127 original size:29 final size:31
Alignment explanation
Indices: 36085--36142 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
36075 AAATAAGTAA
*
36085 TAAGGAATTAAAATAATAAATATAACAAATT
1 TAAGGAATTAAAATAATAAAAATAACAAATT
*
36116 TAAGG-ATT-AAATTATAAAAATAACAAA
1 TAAGGAATTAAAATAATAAAAATAACAAA
36143 AGATCAAGGC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 17 0.68
30 3 0.12
31 5 0.20
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (31 bp):
TAAGGAATTAAAATAATAAAAATAACAAATT
Found at i:37733 original size:80 final size:81
Alignment explanation
Indices: 37585--37856 Score: 253
Period size: 82 Copynumber: 3.4 Consensus size: 81
37575 GGGAAATATG
* * * *
37585 CTCCACTCTTCTTTCAGGGAGATAGGACTTGATCTGTATCTCTTTTTCAGGTAGTCATATCACTT
1 CTCCACTCTTCTTTCAGGGAGATAAGACTTGATCTGTATCTCTTTTACAGGTAGTCAGATCAATT
37650 TTGGAAAACAAGTCCA
66 TTGGAAAACAAGTCCA
* *
37666 CTCCACTCTTTTTTTCAGGGAGATAAGATTTGATCTGT-T-TCTTTTACAGGTAGTCAGATCAAT
1 CTCCACTC-TTCTTTCAGGGAGATAAGACTTGATCTGTATCTCTTTTACAGGTAGTCAGATCAAT
** **
37729 TTTGGAAAACGTGTCTG
65 TTTGGAAAACAAGTCCA
** * ** * * * * * *
37746 CTCCACTAATCATTCAGGGAAGACCAGACATGATTTGTACCTCTTTTTCGGGTAGTCATATCAAT
1 CTCCACTCTTCTTTCAGGG-AGATAAGACTTGATCTGTATCTCTTTTACAGGTAGTCAGATCAAT
* ** **
37811 TTT-GAATGACGTGTCTG
65 TTTGGAA-AACAAGTCCA
*
37828 CTCCACTATTCTTTCAGGGAGATAAGACT
1 CTCCACTCTTCTTTCAGGGAGATAAGACT
37857 CGAGAAATCT
Statistics
Matches: 157, Mismatches: 29, Indels: 10
0.80 0.15 0.05
Matches are distributed among these distances:
79 8 0.05
80 54 0.34
81 19 0.12
82 76 0.48
ACGTcount: A:0.25, C:0.20, G:0.19, T:0.36
Consensus pattern (81 bp):
CTCCACTCTTCTTTCAGGGAGATAAGACTTGATCTGTATCTCTTTTACAGGTAGTCAGATCAATT
TTGGAAAACAAGTCCA
Found at i:38010 original size:55 final size:55
Alignment explanation
Indices: 37928--38112 Score: 181
Period size: 55 Copynumber: 3.5 Consensus size: 55
37918 AAGATGAATT
* * *
37928 TGCTCCACTCTTTTTTTCA-AGGAGATAAGACTCGAGAAATCTTTATAAAACGGACC
1 TGCTCCACTC-TTCTTTCAGA-GAGATAAGACTCGAGAAATCTTTGTAAAACGGATC
* * * * *
37984 TGCTCCACTCTTCTTTCAGAGAGATAA-AATC--CAAA-----GGAATACGAATC
1 TGCTCCACTCTTCTTTCAGAGAGATAAGACTCGAGAAATCTTTGTAAAACGGATC
* *
38031 TGCTCCACTCTTCTTTTAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGATC
1 TGCTCCACTCTTCTTTCAGAGAGATAAGACTCGAGAAATCTTTGTAAAACGGATC
* *
38086 TGCCCCACTCTTCTTTCAGGGAGATAA
1 TGCTCCACTCTTCTTTCAGAGAGATAA
38113 AATCCAAGGG
Statistics
Matches: 103, Mismatches: 17, Indels: 19
0.74 0.12 0.14
Matches are distributed among these distances:
47 32 0.31
48 3 0.03
50 3 0.03
52 3 0.03
54 3 0.03
55 48 0.47
56 11 0.11
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.29
Consensus pattern (55 bp):
TGCTCCACTCTTCTTTCAGAGAGATAAGACTCGAGAAATCTTTGTAAAACGGATC
Found at i:38037 original size:47 final size:47
Alignment explanation
Indices: 37974--38361 Score: 209
Period size: 47 Copynumber: 7.7 Consensus size: 47
37964 AAATCTTTAT
* * *
37974 AAAACGGACCTGCTCCACTCTTCTTTCAGAGAGATAAAATCCAAAGG
1 AAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAAATCCAAAGG
* * * * *
38021 AATACGAATCTGCTCCACTCTTCTTTTAGGGAGATAAGACTCGAGAAATCTTTGT
1 AAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAA-AATC--CAAA-----GG
* * *
38076 AAAACGGATCTGCCCCACTCTTCTTTCAGGGAGATAAAATCCAAGGG
1 AAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAAATCCAAAGG
* ** * * * *
38123 AAGATAAATCTGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAATTCTTTGT
1 AAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAA-AATCCA-AA------GG
* * * * * *
38178 AAAATGGATATGCTCCACTCTTCTTTCAGGGATATAAAATACAAGGG
1 AAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAAATCCAAAGG
* * * * * ** *
38225 AAGATGAATCTTCTCCGCTCTTCTTTCAGGGAGATAATACTTGAGAAATCTTTGT
1 AAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAA-A-AT-CCAAA-----GG
* *
38280 AAAACGAACCTGCTCCACTCTTCTTTCAGGGAGATAAAATCCAAGGG
1 AAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAAATCCAAAGG
* * * * *
38327 AAGACGAATCTGTTCCACTTTTATTTCAAGGAGAT
1 AAAACGAATCTGCTCCACTCTTCTTTCAGGGAGAT
38362 CAGACTTGAT
Statistics
Matches: 254, Mismatches: 63, Indels: 48
0.70 0.17 0.13
Matches are distributed among these distances:
47 126 0.50
48 8 0.03
49 2 0.01
50 6 0.02
52 4 0.02
53 2 0.01
54 7 0.03
55 99 0.39
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.29
Consensus pattern (47 bp):
AAAACGAATCTGCTCCACTCTTCTTTCAGGGAGATAAAATCCAAAGG
Found at i:38094 original size:102 final size:102
Alignment explanation
Indices: 37824--38367 Score: 755
Period size: 102 Copynumber: 5.3 Consensus size: 102
37814 GAATGACGTG
* * * *
37824 TCTGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAATGGATATGCTCCAA
1 TCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGATCTGCTCCAC
* *
37889 TATTCTTTCAAGGAGATAAAATCCAAGGGAAGATGAA
66 TCTTCTTTCAGGGAGATAAAATCCAAGGGAAGATGAA
* * * * *
37926 TTTGCTCCACTCTTTTTTTCAAGGAGATAAGACTCGAGAAATCTTTATAAAACGGACCTGCTCCA
1 TCTGCTCCACTC-TTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGATCTGCTCCA
* * * *
37991 CTCTTCTTTCAGAGAGATAAAATCCAAAGGAATACGAA
65 CTCTTCTTTCAGGGAGATAAAATCCAAGGGAAGATGAA
* *
38029 TCTGCTCCACTCTTCTTTTAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGATCTGCCCCAC
1 TCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGATCTGCTCCAC
*
38094 TCTTCTTTCAGGGAGATAAAATCCAAGGGAAGATAAA
66 TCTTCTTTCAGGGAGATAAAATCCAAGGGAAGATGAA
* * * *
38131 TCTGCTCCACTATTCTTTCAGGGAGATAAGACTCGAGAATTCTTTGTAAAATGGATATGCTCCAC
1 TCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGATCTGCTCCAC
* *
38196 TCTTCTTTCAGGGATATAAAATACAAGGGAAGATGAA
66 TCTTCTTTCAGGGAGATAAAATCCAAGGGAAGATGAA
* * * * * *
38233 TCTTCTCCGCTCTTCTTTCAGGGAGATAATACTTGAGAAATCTTTGTAAAACGAACCTGCTCCAC
1 TCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGATCTGCTCCAC
*
38298 TCTTCTTTCAGGGAGATAAAATCCAAGGGAAGACGAA
66 TCTTCTTTCAGGGAGATAAAATCCAAGGGAAGATGAA
* * * * *
38335 TCTGTTCCACTTTTATTTCAAGGAGATCAGACT
1 TCTGCTCCACTCTTCTTTCAGGGAGATAAGACT
38368 TGATATGATT
Statistics
Matches: 384, Mismatches: 57, Indels: 2
0.87 0.13 0.00
Matches are distributed among these distances:
102 296 0.77
103 88 0.23
ACGTcount: A:0.32, C:0.20, G:0.18, T:0.29
Consensus pattern (102 bp):
TCTGCTCCACTCTTCTTTCAGGGAGATAAGACTCGAGAAATCTTTGTAAAACGGATCTGCTCCAC
TCTTCTTTCAGGGAGATAAAATCCAAGGGAAGATGAA
Found at i:38574 original size:62 final size:62
Alignment explanation
Indices: 38508--38647 Score: 226
Period size: 62 Copynumber: 2.3 Consensus size: 62
38498 TGCAATATTT
* * *
38508 ACTTCTCTTCACGAGGAAGTAAATGATTGACTCTATTGGGGAGTCAAAAATAACAAAGATTG
1 ACTTCTCTTCACGAGGAAGTAAAGGATTGACTATATTGGGGAGTCAAAAATAACAAAGATCG
* *
38570 ACTTCTCTTCACAAGGAAGTAAAGGATTGACTATATTGGGGAGTCATAAATAACAAAGATCG
1 ACTTCTCTTCACGAGGAAGTAAAGGATTGACTATATTGGGGAGTCAAAAATAACAAAGATCG
*
38632 ACTTTTCTTCACGAGG
1 ACTTCTCTTCACGAGG
38648 CAGTCAATAA
Statistics
Matches: 71, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 71 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.28
Consensus pattern (62 bp):
ACTTCTCTTCACGAGGAAGTAAAGGATTGACTATATTGGGGAGTCAAAAATAACAAAGATCG
Found at i:38662 original size:38 final size:40
Alignment explanation
Indices: 38618--38704 Score: 108
Period size: 40 Copynumber: 2.2 Consensus size: 40
38608 GGGAGTCATA
* *
38618 AATAACAAAGA-TCGACTT-T-TCTTCACGAGGCAGTCAAT
1 AATAACAAAGACT-GACTTCTCTCTTCACAAGGAAGTCAAT
* *
38656 AATAACAAATACTGACTTCTCTTTTCACAAGGAAGTCAAT
1 AATAACAAAGACTGACTTCTCTCTTCACAAGGAAGTCAAT
38696 AATAACAAA
1 AATAACAAA
38705 TAGTAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
38 15 0.36
39 2 0.05
40 25 0.60
ACGTcount: A:0.43, C:0.20, G:0.11, T:0.26
Consensus pattern (40 bp):
AATAACAAAGACTGACTTCTCTCTTCACAAGGAAGTCAAT
Found at i:39170 original size:247 final size:247
Alignment explanation
Indices: 38710--39453 Score: 979
Period size: 250 Copynumber: 3.0 Consensus size: 247
38700 ACAAATAGTA
* * * * **
38710 AAAATATCCTACCCTAAGGTCTTACGGATGGCCCAAAGGAATTATCATCTTCCTCAAAAGACTGG
1 AAAACATCCTACCCGAAGGTCTTACGGATGGCCCAAAGG-ACTATCATCTTACTCAAAAGACTAA
* ** * * *
38775 CAGATAACTTGAAGGATTTAATCATCATGCTCAAAAGACTTATTGATGGCCCGAAGAACTTACAA
65 CAGATGAC-CAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
* * *
38840 ATTTTGGGAAATAATTTACTGGGTAAGAAACTTTGGCAATCACTTTCTTACTTTTCAATAATTTC
129 ATTTT-GGAAATAATTTACTAGGTAAGAAACTTTGGTAATCACTTTCTTACTTTTCAAGAATTTC
* * *
38905 ATTTTCTGAGAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
193 ATATTATGA-AGCATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
* * *
38961 -AAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAGGACTATCATCTTGCTCAAAAGACTTAC
1 AAAACATCCTACCCGAAGGTCTTACGGATGGCCCAAAGGACTATCATCTTACTCAAAAGACTAAC
* *
39025 AGATGACCAAAGTATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCAAAGGACTTACAAAT
66 AGATGACCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAAT
*
39090 TTTGGAAATATTTTACTAGGTAAGAAACTTTGGTAATCACTTTCTTACTTTTCAAGAATTTCATA
131 TTTGGAAATAATTTACTAGGTAAGAAACTTTGGTAATCACTTTCTTACTTTTCAAGAATTTCATA
* * *
39155 TTATGCAAGCATTAAATGAAAAACATCGGTAATCGCTTTCTCATTTTCATGTG
196 TTATG-AAGCATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
* * * **
39208 AAAATATCCTACCTGAAGGTCTTACGAATATCCCAAAGGACTTATCATCTTACTCAAAAGACTAA
1 AAAACATCCTACCCGAAGGTCTTACGGATGGCCCAAAGGAC-TATCATCTTACTCAAAAGACTAA
* * * * *
39273 CAAATGGCCCAAAGGATTTAAGCATCATGCTCGAAAGACTTACTAATGACCCGAAGGACTTACAA
65 CAGAT-GACCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAA
* *
39338 ATTTTGGAAATAATTTACTAAGTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAAGAATTTCA
129 ATTTTGGAAATAATTTACTAGGTAAGAAACTTTGGTAATCACTTTCTTACTTTTCAAGAATTTCA
* ** * * **
39403 TATCACAAAAAG-ATGAAATGAGAAACTTTAGTAATCATTTTCTCATTTTCA
194 TAT--TATGAAGCATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCA
39454 AAACAACTTA
Statistics
Matches: 434, Mismatches: 53, Indels: 13
0.87 0.11 0.03
Matches are distributed among these distances:
247 103 0.24
248 89 0.21
249 53 0.12
250 185 0.43
251 3 0.01
252 1 0.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.32
Consensus pattern (247 bp):
AAAACATCCTACCCGAAGGTCTTACGGATGGCCCAAAGGACTATCATCTTACTCAAAAGACTAAC
AGATGACCAAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTACAAAT
TTTGGAAATAATTTACTAGGTAAGAAACTTTGGTAATCACTTTCTTACTTTTCAAGAATTTCATA
TTATGAAGCATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTCATGTG
Found at i:40744 original size:40 final size:40
Alignment explanation
Indices: 40676--40780 Score: 115
Period size: 40 Copynumber: 2.6 Consensus size: 40
40666 TGGCTCATAT
* *
40676 GGGCCTTCAAAAATACCCTCAACA-TTATTTCATAATGGTAC
1 GGGCCTTC-AAAATGCCCT-AACATTTATTTCATAATGATAC
* * *
40717 GGGCCTTCAAAATGCCCTAACATTTATTTCTTACTGATAT
1 GGGCCTTCAAAATGCCCTAACATTTATTTCATAATGATAC
*
40757 GAGCCTTCAAAATGGCCC-AACATT
1 GGGCCTTCAAAAT-GCCCTAACATT
40781 CCAAGTTGCA
Statistics
Matches: 56, Mismatches: 6, Indels: 5
0.84 0.09 0.07
Matches are distributed among these distances:
39 4 0.07
40 40 0.71
41 12 0.21
ACGTcount: A:0.31, C:0.25, G:0.13, T:0.30
Consensus pattern (40 bp):
GGGCCTTCAAAATGCCCTAACATTTATTTCATAATGATAC
Found at i:48933 original size:15 final size:15
Alignment explanation
Indices: 48915--48946 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
48905 TTAATAGTTT
48915 TAATAATGATAATAA
1 TAATAATGATAATAA
48930 TAATAATGATAATAA
1 TAATAATGATAATAA
48945 TA
1 TA
48947 TAAGTAAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.34
Consensus pattern (15 bp):
TAATAATGATAATAA
Found at i:50451 original size:23 final size:23
Alignment explanation
Indices: 50417--50462 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
50407 GAGAATTTCT
*
50417 TATGTTTCTCTTGTTATGGTCTA
1 TATGTTTCTCTTGGTATGGTCTA
*
50440 TATGTTTGTCTTGGTATGGTCTA
1 TATGTTTCTCTTGGTATGGTCTA
50463 AATTATAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.13, C:0.11, G:0.22, T:0.54
Consensus pattern (23 bp):
TATGTTTCTCTTGGTATGGTCTA
Found at i:55336 original size:15 final size:16
Alignment explanation
Indices: 55308--55340 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
55298 AAAATCTTTC
55308 TTTCCCGTTCTGGATT
1 TTTCCCGTTCTGGATT
55324 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTGGATT
55339 TT
1 TT
55341 GATCTGCCAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.06, C:0.24, G:0.18, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTGGATT
Found at i:56111 original size:16 final size:16
Alignment explanation
Indices: 56087--56120 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
56077 TATCGTCGAC
* *
56087 CGAATTTCAGTATTCA
1 CGAAATTCACTATTCA
56103 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
56119 CG
1 CG
56121 CGAATAGTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:57392 original size:27 final size:27
Alignment explanation
Indices: 57362--57415 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
57352 TCGCGAGCTT
*
57362 GGCTTTGAGGGTCATTCCTTCCGTGGA
1 GGCTTTGAGGGACATTCCTTCCGTGGA
57389 GGCTTTGAGGGACATTCCTTCCGTGGA
1 GGCTTTGAGGGACATTCCTTCCGTGGA
57416 TTCGGTATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.13, C:0.22, G:0.33, T:0.31
Consensus pattern (27 bp):
GGCTTTGAGGGACATTCCTTCCGTGGA
Done.