Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009190.1 Hibiscus syriacus cultivar Beakdansim tig00112763_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: 69896
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:720 original size:14 final size:14
Alignment explanation
Indices: 687--720 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
677 TAGGACTTAC
*
687 AAAATAATAATATA
1 AAAATAATAATAAA
*
701 ATAATAATAATAAA
1 AAAATAATAATAAA
715 AAAATA
1 AAAATA
721 TTTTTTTAAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AAAATAATAATAAA
Found at i:7520 original size:28 final size:28
Alignment explanation
Indices: 7463--7615 Score: 115
Period size: 28 Copynumber: 5.5 Consensus size: 28
7453 CTGTCAAATT
** *
7463 TTACACAAATAGCACCCTTTTTAAAATAA
1 TTAC-CAAATAGCACCCTTTTCGAATTAA
7492 TTACCAAATAGCACCCTTTTCGAATTAA
1 TTACCAAATAGCACCCTTTTCGAATTAA
**
7520 TT-CCAAAT-GCACAAATTTT-GAATTAA
1 TTACCAAATAGCAC-CCTTTTCGAATTAA
* * *
7546 TTCCCAGAATATCA--CTTTTC-AA-AAA
1 TTACCA-AATAGCACCCTTTTCGAATTAA
*
7571 TTACCAAAATAGCACCCATTTCGAATTAA
1 TTACC-AAATAGCACCCTTTTCGAATTAA
7600 TT-CTCAGAATAGCACC
1 TTAC-CA-AATAGCACC
7616 AAAACCGAAT
Statistics
Matches: 100, Mismatches: 12, Indels: 24
0.74 0.09 0.18
Matches are distributed among these distances:
25 12 0.12
26 20 0.20
27 18 0.18
28 30 0.30
29 20 0.20
ACGTcount: A:0.40, C:0.23, G:0.07, T:0.31
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTCGAATTAA
Found at i:7682 original size:18 final size:17
Alignment explanation
Indices: 7653--7701 Score: 80
Period size: 18 Copynumber: 2.8 Consensus size: 17
7643 CCGGTCAACG
7653 GTCAACGGTCGGGTCGA
1 GTCAACGGTCGGGTCGA
*
7670 GTCAACGGGTCGGGTCGG
1 GTCAAC-GGTCGGGTCGA
7688 GTCAACGGTCGGGT
1 GTCAACGGTCGGGT
7702 TAACGGGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
17 14 0.47
18 16 0.53
ACGTcount: A:0.14, C:0.22, G:0.45, T:0.18
Consensus pattern (17 bp):
GTCAACGGTCGGGTCGA
Found at i:11449 original size:30 final size:28
Alignment explanation
Indices: 11415--11498 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 28
11405 ATACCTAATG
*
11415 TTTACTTATGTTTCATTTTAGTACCCGACA
1 TTTACTTTTGTTTCATTTTAGTACCC-A-A
*
11445 TTTACTTTTTGTTTCA--TTAGTACCCAT
1 TTTAC-TTTTGTTTCATTTTAGTACCCAA
11472 TGTTAACTTTTGTTTCATTTTAGTACC
1 T-TT-ACTTTTGTTTCATTTTAGTACC
11499 TAAATTTTTA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
27 1 0.02
28 13 0.28
29 11 0.23
30 13 0.28
31 9 0.19
ACGTcount: A:0.20, C:0.18, G:0.10, T:0.52
Consensus pattern (28 bp):
TTTACTTTTGTTTCATTTTAGTACCCAA
Found at i:15352 original size:21 final size:21
Alignment explanation
Indices: 15328--15369 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
15318 TATGAGAAAT
* *
15328 TATTTTAAAATATAAAAATGA
1 TATTTCAAAATAGAAAAATGA
15349 TATTTCAAAATAGAAAAATGA
1 TATTTCAAAATAGAAAAATGA
15370 AAAAATCTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.02, G:0.07, T:0.33
Consensus pattern (21 bp):
TATTTCAAAATAGAAAAATGA
Found at i:19098 original size:21 final size:21
Alignment explanation
Indices: 19072--19128 Score: 60
Period size: 24 Copynumber: 2.6 Consensus size: 21
19062 TTGTGCATAA
19072 TGCATCGATACACTATGAAAG
1 TGCATCGATACACTATGAAAG
* * *
19093 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGAT--A-CACTATGAAAG
19117 TGCATCGATACA
1 TGCATCGATACA
19129 TCATGAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
21 10 0.34
22 1 0.03
23 1 0.03
24 17 0.59
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (21 bp):
TGCATCGATACACTATGAAAG
Found at i:19147 original size:45 final size:44
Alignment explanation
Indices: 19072--19169 Score: 121
Period size: 45 Copynumber: 2.2 Consensus size: 44
19062 TTGTGCATAA
*
19072 TGCATCGATACACTATGAAAGTGCATCGATGCA-TCCCTTTGAATG
1 TGCATCGATACACTATGAAAGTGCACCGATGCACT-CC-TTGAATG
19117 TGCATCGATACA-TCATG-AAGATGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACT-ATGAAAG-TGCACCGATGCACTCCTTGAATG
*
19161 TACATCGAT
1 TGCATCGAT
19170 GCACACTGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
44 19 0.40
45 28 0.58
46 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (44 bp):
TGCATCGATACACTATGAAAGTGCACCGATGCACTCCTTGAATG
Found at i:21376 original size:65 final size:65
Alignment explanation
Indices: 21319--21461 Score: 259
Period size: 65 Copynumber: 2.2 Consensus size: 65
21309 CACTCTCTAT
21319 GCATCGATGCACTCTTGAACAAATAGAAACATCAAATGCATTCAATGCACCGATGCACAAGCCAC
1 GCATCGATGCACTCTTGAACAAATAGAAACATCAAATGCATTCAATGCACCGATGCACAAGCCAC
* *
21384 GCATCGATGCACTCTTGAACAAATAGAAACATCGAATGCATTCAATGCACCGATGCACAAGCCAT
1 GCATCGATGCACTCTTGAACAAATAGAAACATCAAATGCATTCAATGCACCGATGCACAAGCCAC
*
21449 GTATCGATGCACT
1 GCATCGATGCACT
21462 AAGGCTATTT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
65 75 1.00
ACGTcount: A:0.36, C:0.27, G:0.17, T:0.20
Consensus pattern (65 bp):
GCATCGATGCACTCTTGAACAAATAGAAACATCAAATGCATTCAATGCACCGATGCACAAGCCAC
Found at i:24892 original size:20 final size:20
Alignment explanation
Indices: 24862--24946 Score: 66
Period size: 20 Copynumber: 4.0 Consensus size: 20
24852 CAGAACCACA
24862 GGGGGGTATCGATTCCCCTGT
1 GGGGGG-ATCGATTCCCCTGT
*
24883 GGGGGGATCGGTTCCCCT-T
1 GGGGGGATCGATTCCCCTGT
* *
24902 CAAAGGGGGAATCGATT-CCCTCAT
1 ----GGGGGGATCGATTCCCCT-GT
24926 GGGGGGATCGATTCCCTCTGT
1 GGGGGGATCGATTCCC-CTGT
24947 ACCAAAATGC
Statistics
Matches: 51, Mismatches: 5, Indels: 16
0.71 0.07 0.22
Matches are distributed among these distances:
19 1 0.02
20 23 0.45
21 9 0.18
22 6 0.12
23 11 0.22
24 1 0.02
ACGTcount: A:0.14, C:0.25, G:0.35, T:0.26
Consensus pattern (20 bp):
GGGGGGATCGATTCCCCTGT
Found at i:38567 original size:11 final size:11
Alignment explanation
Indices: 38551--38585 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
38541 ATATAAAAAA
38551 GAAGTGCAAGT
1 GAAGTGCAAGT
38562 GAAGTGCAAGT
1 GAAGTGCAAGT
*
38573 G-AGTACAAGT
1 GAAGTGCAAGT
38583 GAA
1 GAA
38586 AGAAAAAGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.40, C:0.09, G:0.34, T:0.17
Consensus pattern (11 bp):
GAAGTGCAAGT
Found at i:39400 original size:10 final size:11
Alignment explanation
Indices: 39382--39418 Score: 58
Period size: 10 Copynumber: 3.4 Consensus size: 11
39372 AAAATTATTA
39382 TATTATATTTAT
1 TATTAT-TTTAT
39394 TATTATTTTAT
1 TATTATTTTAT
39405 T-TTATTTTAT
1 TATTATTTTAT
39415 TATT
1 TATT
39419 TTTGTAGGCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.42
11 8 0.33
12 6 0.25
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TATTATTTTAT
Found at i:39923 original size:31 final size:30
Alignment explanation
Indices: 39870--39937 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 30
39860 TTTTTATTTC
* *
39870 TTTTTACATTTATATATATATA-TATATATT
1 TTTTTATATTAATATATATATATTA-ATATT
39900 TATTTTATATTAATAT-TATTATATTAATATT
1 T-TTTTATATTAATATATA-TATATTAATATT
39931 TTTTTAT
1 TTTTTAT
39938 TATTCTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
30 9 0.27
31 22 0.67
32 2 0.06
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.63
Consensus pattern (30 bp):
TTTTTATATTAATATATATATATTAATATT
Found at i:39938 original size:14 final size:14
Alignment explanation
Indices: 39902--39939 Score: 58
Period size: 14 Copynumber: 2.7 Consensus size: 14
39892 TATATATTTA
39902 TTTTATATTAATAT
1 TTTTATATTAATAT
*
39916 TATTATATTAATAT
1 TTTTATATTAATAT
*
39930 TTTTTTATTA
1 TTTTATATTA
39940 TTCTTTTCTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTTTATATTAATAT
Found at i:40682 original size:17 final size:16
Alignment explanation
Indices: 40641--40712 Score: 81
Period size: 17 Copynumber: 4.2 Consensus size: 16
40631 ATTCATGCAT
40641 CTAGTTCATTGAATAAA
1 CTAGTTCATT-AATAAA
*
40658 GTTAGTTCATTAATTAAA
1 -CTAGTTCATTAA-TAAA
*
40676 CTAGTTCATTCATCAAA
1 CTAGTTCATTAAT-AAA
40693 CTAGTTCATTTAATAAA
1 CTAGTTCA-TTAATAAA
40710 CTA
1 CTA
40713 ACTCTTAATT
Statistics
Matches: 47, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
16 1 0.02
17 29 0.62
18 17 0.36
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (16 bp):
CTAGTTCATTAATAAA
Found at i:41191 original size:25 final size:25
Alignment explanation
Indices: 41115--41194 Score: 142
Period size: 25 Copynumber: 3.2 Consensus size: 25
41105 AAGCATTCAA
41115 GGCTGATTTAATCATCCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
*
41140 GACTGATTTAATCATCCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
*
41165 GGCTGATTTAATCATTCAAACCAAG
1 GGCTGATTTAATCATCCAAACCAAG
41190 GGCTG
1 GGCTG
41195 TTCATATTCT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
25 52 1.00
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.25
Consensus pattern (25 bp):
GGCTGATTTAATCATCCAAACCAAG
Found at i:44067 original size:17 final size:16
Alignment explanation
Indices: 44017--44072 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
44007 TAAAAAATTC
*
44017 AAAATATATTTAATTT
1 AAAATATATTTATTTT
*
44033 ATAATCATA-TTATTTT
1 AAAAT-ATATTTATTTT
44049 AAAATATATTTATTTTT
1 AAAATATATTTA-TTTT
44066 AAAATAT
1 AAAATAT
44073 CAGAAAAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 3 0.09
16 17 0.50
17 14 0.41
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
AAAATATATTTATTTT
Found at i:44244 original size:24 final size:23
Alignment explanation
Indices: 44217--44267 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
44207 TTTCTTCGAT
44217 ATTTA-AAAAATAAATATTAAAATA
1 ATTTATAAAAATAAATA-T-AAATA
*
44241 ATTTATTAAAAATATATATAAATA
1 ATTTA-TAAAAATAAATATAAATA
44265 ATT
1 ATT
44268 ATTTATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 13 0.54
25 1 0.04
26 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATTTATAAAAATAAATATAAATA
Found at i:44252 original size:27 final size:28
Alignment explanation
Indices: 44219--44275 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
44209 TCTTCGATAT
*
44219 TTAAAAAATAAATATTAA-AATAATTTA
1 TTAAAAAATAAATATAAATAATAATTTA
* *
44246 TT-AAAAATATATATAAATAATTATTTA
1 TTAAAAAATAAATATAAATAATAATTTA
44273 TTA
1 TTA
44276 TATATATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TTAAAAAATAAATATAAATAATAATTTA
Found at i:45643 original size:3 final size:3
Alignment explanation
Indices: 45635--45733 Score: 126
Period size: 3 Copynumber: 33.0 Consensus size: 3
45625 TATATATATT
* *
45635 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * * * * *
45683 TAA TTA TAA TAA TTA TAA TAA TAA TAA TTA TTA GAA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
45731 TAA
1 TAA
45734 ATAAATTAAT
Statistics
Matches: 82, Mismatches: 14, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 82 1.00
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (3 bp):
TAA
Found at i:46553 original size:113 final size:114
Alignment explanation
Indices: 46068--46622 Score: 847
Period size: 112 Copynumber: 4.9 Consensus size: 114
46058 ATGCAAAAAT
* * *
46068 TTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* * *
46133 C-TTCTCTGGAAAAGCTGCTCCATCAAGTGATGTATTTGA-GCAAAAGG
66 CTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTCAGGCAAAAGG
* *
46180 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCTTTCTTCAGATGAATTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
46245 C-TTCTCTGGAAAAACTGATCCATCAAGTGAT-GAATTCAGGCAAAAGG
66 CTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTCAGGCAAAAGG
*
46292 TTGAACAAATTCTTCTCATTATGAA-TTTCTTTTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
* *
46356 ACTTTCTCTCTGGAAAAGCTAATCCATCAAGTGAT-GAATTCAGGCAAAAGG
65 AC-TT-TCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTCAGGCAAAAGG
*
46407 TTGAACAAATTCTTCTCATTATGAA-TTTCTTCTTCCTTCTTCAGACGAGTTCTTCTCATTATGA
1 TTGAACAAATTCTTCTCATTATGAACTTT-TTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGA
*
46471 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTGA-GCAAAAGG
65 ACTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTCAGGCAAAAGG
**
46520 TTGAACAAGCTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
1 TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
* *
46585 CTCTCTCTGGAAAAGCTGATCCATCAAGTAATGGATTT
66 CTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTT
46623 AAATCTTTGC
Statistics
Matches: 411, Mismatches: 25, Indels: 13
0.92 0.06 0.03
Matches are distributed among these distances:
111 7 0.02
112 156 0.38
113 130 0.32
114 11 0.03
115 107 0.26
ACGTcount: A:0.28, C:0.20, G:0.15, T:0.38
Consensus pattern (114 bp):
TTGAACAAATTCTTCTCATTATGAACTTTTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA
CTTTCTCTGGAAAAGCTGATCCATCAAGTGATGGATTTCAGGCAAAAGG
Found at i:47521 original size:83 final size:83
Alignment explanation
Indices: 47337--47975 Score: 1065
Period size: 83 Copynumber: 7.7 Consensus size: 83
47327 GTTCCTACCA
*
47337 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTC-AAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATT
*
47401 CAATGATTGGTTCTGTTC
66 CAATGATTGGTTCTGTCC
*
47419 AACCAGATCGGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTTCTAAAT
*
47483 TCAATGATTGGTTCTGTTC
65 TCAATGATTGGTTCTGTCC
*
47502 AACCAGATCGGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTTCTAAAT
47566 TCAATGATTGGTTCTGTCC
65 TCAATGATTGGTTCTGTCC
*
47585 AACCAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATTG-GCAAATTCATCTTCTAAAT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAGCAAATTCATCTTCTAAAT
47649 TCAATGATTGGTTCTGTCC
65 TCAATGATTGGTTCTGTCC
*
47668 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATT
*
47733 CAATGATTGGTTCTGTCA
66 CAATGATTGGTTCTGTCC
* *
47751 AACCAGATCAGATAACTCAAAGAACACTTCAAGAAGATGCTATGAGCACATTCATCTTCTAAATT
1 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATT
47816 CAATGATTGGTTCTG-CC
66 CAATGATTGGTTCTGTCC
* *
47833 AAACCAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTATGAGCACATTCATCTTCTAAAT
1 -AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAAT
47898 TCAATGATTGGTTCTG-CC
65 TCAATGATTGGTTCTGTCC
* *
47916 AAACCAGATCAGATAACTCAAAGAACACTTCCATAAGATGCTATGAGCACATTCATCTTC
1 -AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTC
47976 CAGTTAATGT
Statistics
Matches: 539, Mismatches: 14, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
82 56 0.10
83 483 0.90
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCAAATTCATCTTCTAAATT
CAATGATTGGTTCTGTCC
Found at i:59813 original size:13 final size:13
Alignment explanation
Indices: 59792--59835 Score: 52
Period size: 13 Copynumber: 3.4 Consensus size: 13
59782 ATAAAATGAA
*
59792 ATATTAATAATAT
1 ATATAAATAATAT
*
59805 ATATAAATACTAT
1 ATATAAATAATAT
*
59818 ATAAAAATAATAT
1 ATATAAATAATAT
*
59831 GTATA
1 ATATA
59836 TATATAAAAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (13 bp):
ATATAAATAATAT
Found at i:59830 original size:24 final size:23
Alignment explanation
Indices: 59803--59856 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 23
59793 TATTAATAAT
*
59803 ATATATAAATACTATATAAAAATA
1 ATATATAAATA-TATATAAAAAAA
*
59827 ATATGT--ATATATATAAAAAAA
1 ATATATAAATATATATAAAAAAA
59848 AT-TATAAAT
1 ATATATAAAT
59857 TAAATATATG
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
20 2 0.08
21 13 0.52
22 5 0.20
24 5 0.20
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (23 bp):
ATATATAAATATATATAAAAAAA
Found at i:60328 original size:17 final size:16
Alignment explanation
Indices: 60278--60333 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
60268 TAAAAAATTC
*
60278 AAAATATATTTAATTT
1 AAAATATATTTATTTT
*
60294 ATAATCATA-TTATTTT
1 AAAAT-ATATTTATTTT
60310 AAAATATATTTATTTTT
1 AAAATATATTTA-TTTT
60327 AAAATAT
1 AAAATAT
60334 CAGAAAAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
15 3 0.09
16 17 0.50
17 14 0.41
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (16 bp):
AAAATATATTTATTTT
Found at i:60505 original size:24 final size:23
Alignment explanation
Indices: 60478--60528 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 23
60468 TTTCTTCGAT
60478 ATTTA-AAAAATAAATATTAAAATA
1 ATTTATAAAAATAAATA-T-AAATA
*
60502 ATTTATTAAAAATATATATAAATA
1 ATTTA-TAAAAATAAATATAAATA
60526 ATT
1 ATT
60529 ATTTATTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 13 0.54
25 1 0.04
26 10 0.42
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (23 bp):
ATTTATAAAAATAAATATAAATA
Found at i:60513 original size:27 final size:28
Alignment explanation
Indices: 60480--60536 Score: 73
Period size: 26 Copynumber: 2.1 Consensus size: 28
60470 TCTTCGATAT
*
60480 TTAAAAAATAAATATTAA-AATAATTTA
1 TTAAAAAATAAATATAAATAATAATTTA
* *
60507 TT-AAAAATATATATAAATAATTATTTA
1 TTAAAAAATAAATATAAATAATAATTTA
60534 TTA
1 TTA
60537 TATATATATT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
26 13 0.52
27 12 0.48
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (28 bp):
TTAAAAAATAAATATAAATAATAATTTA
Found at i:61881 original size:3 final size:3
Alignment explanation
Indices: 61873--61947 Score: 82
Period size: 3 Copynumber: 25.0 Consensus size: 3
61863 TATATATATT
*
61873 TAA TAA TAA TAA TAA TAA TAA TAA T-T TAA TATA TAA TTAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA -TAA TAA TAA
* * *
61918 TAA TAA TTA TTA TAA TTA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
61948 ATAAATTAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 8
0.82 0.08 0.11
Matches are distributed among these distances:
2 3 0.05
3 53 0.85
4 6 0.10
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:61946 original size:24 final size:27
Alignment explanation
Indices: 61870--61947 Score: 110
Period size: 24 Copynumber: 3.0 Consensus size: 27
61860 ATATATATAT
*
61870 ATTTAATA-ATAATAATAATAATAATA
1 ATTTAATATATAATTATAATAATAATA
*
61896 ATTTAATATATAATTAAAATAATAATA
1 ATTTAATATATAATTATAATAATAATA
61923 A-TT-AT-TATAATTATAATAATAATA
1 ATTTAATATATAATTATAATAATAATA
61947 A
1 A
61948 ATAAATTAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 4
0.87 0.05 0.07
Matches are distributed among these distances:
24 19 0.40
25 2 0.04
26 10 0.21
27 17 0.35
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
ATTTAATATATAATTATAATAATAATA
Found at i:64821 original size:20 final size:20
Alignment explanation
Indices: 64796--64834 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
64786 TTAACAAAAT
64796 AATAATTT-TTTATATATTAG
1 AATAATTTATTTA-ATATTAG
64816 AATAATTTATTTAATATTA
1 AATAATTTATTTAATATTA
64835 TTTATGTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (20 bp):
AATAATTTATTTAATATTAG
Found at i:67782 original size:24 final size:20
Alignment explanation
Indices: 67731--67788 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
67721 TTCCCATTGA
*
67731 AGTGCATCGGTGCATTCTAC
1 AGTGCATCGATGCATTCTAC
*
67751 AGTACATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
67774 AGGTGCATCGATGCA
1 A-GTGCATCGATGCA
67789 CTACCATGCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.29
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Done.