Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004316.1 Hibiscus syriacus cultivar Beakdansim tig00009467_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: 93393
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:39 original size:31 final size:31
Alignment explanation
Indices: 1--82 Score: 139
Period size: 30 Copynumber: 2.7 Consensus size: 31
1 TTCCGAAGAACATAGGTAAACAGTCCATATG
1 TTCCGAAGAACATAGGTAAACAGTCCATATG
32 TTCCGAAGAACATAGGT-AACAGTCCATATG
1 TTCCGAAGAACATAGGTAAACAGTCCATATG
* *
62 TCCCGAAGAACCTAGGTAAAC
1 TTCCGAAGAACATAGGTAAAC
83 CCTCGACCCT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
30 28 0.58
31 20 0.42
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
TTCCGAAGAACATAGGTAAACAGTCCATATG
Found at i:2120 original size:13 final size:14
Alignment explanation
Indices: 2089--2121 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
2079 AAAATATATT
2089 ATAAAATACAATAA
1 ATAAAATACAATAA
*
2103 CTAAAATA-AATAA
1 ATAAAATACAATAA
2116 ATAAAA
1 ATAAAA
2122 AACTCAAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 10 0.59
14 7 0.41
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (14 bp):
ATAAAATACAATAA
Found at i:5622 original size:2 final size:2
Alignment explanation
Indices: 5615--5665 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
5605 TGAATTTAAC
5615 AT AT 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 AT AT
5657 AT AT AT AT A
1 AT AT AT AT A
5666 GAAATCATAT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6453 original size:15 final size:15
Alignment explanation
Indices: 6413--6444 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
6403 TGATAAAATT
6413 AAGTGATTAAATTAA
1 AAGTGATTAAATTAA
6428 AAGTGATTAAATTAA
1 AAGTGATTAAATTAA
6443 AA
1 AA
6445 AGTTTTAAAG
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:0.56, C:0.00, G:0.12, T:0.31
Consensus pattern (15 bp):
AAGTGATTAAATTAA
Found at i:13434 original size:27 final size:29
Alignment explanation
Indices: 13372--13445 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 29
13362 TAAACCCTAG
13372 GAAACCCTGGGTACATTTTTTTCAGAAAAGT
1 GAAACCCTGGGTACATTTTTTT-A-AAAAGT
* *
13403 GAAACCCTGGGTACGTTTTTTT-TAAA-T
1 GAAACCCTGGGTACATTTTTTTAAAAAGT
13430 GAAACCCTGGGTACAT
1 GAAACCCTGGGTACAT
13446 ATATACAAGT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
27 16 0.40
28 3 0.08
31 21 0.52
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.32
Consensus pattern (29 bp):
GAAACCCTGGGTACATTTTTTTAAAAAGT
Found at i:16872 original size:2 final size:2
Alignment explanation
Indices: 16860--16891 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
16850 CATCCCAAAC
*
16860 TA TA CA 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
16892 CTAATCACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:22343 original size:20 final size:20
Alignment explanation
Indices: 22314--22359 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
22304 CATCAAATTT
*
22314 TTAAAATTA-TAAATTTATTA
1 TTAAATTTATTAAA-TTATTA
22334 TTAAATTTATTAAATTATTA
1 TTAAATTTATTAAATTATTA
*
22354 TAAAAT
1 TTAAAT
22360 AATCAGTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
TTAAATTTATTAAATTATTA
Found at i:22500 original size:20 final size:20
Alignment explanation
Indices: 22440--22494 Score: 101
Period size: 20 Copynumber: 2.8 Consensus size: 20
22430 AATTTGATAT
*
22440 AATTTAGTGGTTATTTAATA
1 AATTTAGTGATTATTTAATA
22460 AATTTAGTGATTATTTAATA
1 AATTTAGTGATTATTTAATA
22480 AATTTAGTGATTATT
1 AATTTAGTGATTATT
22495 ATATAATTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (20 bp):
AATTTAGTGATTATTTAATA
Found at i:22501 original size:23 final size:22
Alignment explanation
Indices: 22440--22501 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 22
22430 AATTTGATAT
*
22440 AATTTAGTGGTTA-T-TTAATA
1 AATTTAGTGATTATTATTAATA
22460 AATTTAGTGATTA-T-TTAATA
1 AATTTAGTGATTATTATTAATA
22480 AATTTAGTGATTATTATATAAT
1 AATTTAGTGATTATTAT-TAAT
22502 TTTTAAACTT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
20 32 0.84
21 1 0.03
22 1 0.03
23 4 0.11
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
AATTTAGTGATTATTATTAATA
Found at i:24082 original size:41 final size:41
Alignment explanation
Indices: 24037--24196 Score: 286
Period size: 41 Copynumber: 3.9 Consensus size: 41
24027 TAAGGTTTAG
24037 ATTTGGAATTATCATATTAGTGAGCTAATGCTTAGTTTGAA
1 ATTTGGAATTATCATATTAGTGAGCTAATGCTTAGTTTGAA
24078 ATTTGGAATTATCATATTAGTGAGCTAATGCATT-GTTTGAA
1 ATTTGGAATTATCATATTAGTGAGCTAATGC-TTAGTTTGAA
*
24119 ATTTGGAATGATCATATTAGTGAGCTAATGCTTAGTTTGAA
1 ATTTGGAATTATCATATTAGTGAGCTAATGCTTAGTTTGAA
*
24160 ATTTGGAATTATCAAATTAGTGAGCTAATGCTTAGTT
1 ATTTGGAATTATCATATTAGTGAGCTAATGCTTAGTT
24197 CAAAATATTA
Statistics
Matches: 114, Mismatches: 3, Indels: 4
0.94 0.02 0.03
Matches are distributed among these distances:
40 2 0.02
41 110 0.96
42 2 0.02
ACGTcount: A:0.32, C:0.07, G:0.20, T:0.41
Consensus pattern (41 bp):
ATTTGGAATTATCATATTAGTGAGCTAATGCTTAGTTTGAA
Found at i:38104 original size:28 final size:28
Alignment explanation
Indices: 38063--38149 Score: 70
Period size: 31 Copynumber: 2.9 Consensus size: 28
38053 ACTTTTAAAC
38063 TTATAAAAGT-ATTAAATTTATCAAATTA
1 TTATAAAA-TAATTAAATTTATCAAATTA
*
38091 TTATAAAATAATTATTGGATTCTAT-AAATTA
1 TTATAAAATAATTA---AATT-TATCAAATTA
*
38122 TTACAAAATGATCATTAAATTTATCAAA
1 TTATAAAAT-A--ATTAAATTTATCAAA
38150 CTTGTATAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
27 1 0.02
28 12 0.26
30 3 0.06
31 23 0.49
32 4 0.09
34 4 0.09
ACGTcount: A:0.48, C:0.06, G:0.05, T:0.41
Consensus pattern (28 bp):
TTATAAAATAATTAAATTTATCAAATTA
Found at i:39298 original size:38 final size:37
Alignment explanation
Indices: 39228--39325 Score: 99
Period size: 38 Copynumber: 2.6 Consensus size: 37
39218 AGTAAATCAA
* * * *
39228 CTTGTTATGAATAGAAATGAACAAGTTGATAAACGTG
1 CTTGTTATGAACATAAATGAACAAGTTGATAAAAGAG
*
39265 CTTGTTCATGAACATAAATGAACGAGTCT-ATAAAAGAG
1 CTTGTT-ATGAACATAAATGAACAAGT-TGATAAAAGAG
* *
39303 TTTATTAGTGAACATAAATGAAC
1 CTTGTTA-TGAACATAAATGAAC
39326 TGAATACACC
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
37 7 0.14
38 43 0.84
39 1 0.02
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (37 bp):
CTTGTTATGAACATAAATGAACAAGTTGATAAAAGAG
Found at i:39955 original size:15 final size:15
Alignment explanation
Indices: 39935--39986 Score: 95
Period size: 15 Copynumber: 3.5 Consensus size: 15
39925 TTACCCATTA
*
39935 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
39950 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
39965 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
39980 CCCGCCC
1 CCCGCCC
39987 AGTAAAATAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
15 36 1.00
ACGTcount: A:0.10, C:0.69, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:41345 original size:3 final size:3
Alignment explanation
Indices: 41339--41363 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41329 TATTTTTTTA
41339 ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT A
41364 ATGTTAATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:41987 original size:23 final size:21
Alignment explanation
Indices: 41948--41996 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
41938 TAAAAGTATT
* *
41948 TTAAATTTATAAAATTTTTAAG
1 TTAAATTAATAAAA-TTTTAAA
*
41970 TTAAATATAATAACATTTTAAA
1 TTAAAT-TAATAAAATTTTAAA
41992 TTAAA
1 TTAAA
41997 ATCATCTTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
TTAAATTAATAAAATTTTAAA
Found at i:42369 original size:33 final size:33
Alignment explanation
Indices: 42332--42424 Score: 105
Period size: 40 Copynumber: 2.6 Consensus size: 33
42322 CTACATGGCA
42332 CATGCACGTCCCCAACACCCCAACACAGGTCAC
1 CATGCACGTCCCCAACACCCCAACACAGGTCAC
*
42365 CATGCACGTCCCCAGCACCCAACACCCCAACACAGGTCGC
1 CATGCACGT------C-CCCAACACCCCAACACAGGTCAC
*
42405 CATGCACGTCCCCAGCACCC
1 CATGCACGTCCCCAACACCC
42425 AACGTCCCTA
Statistics
Matches: 51, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
33 18 0.35
34 1 0.02
39 1 0.02
40 31 0.61
ACGTcount: A:0.27, C:0.51, G:0.14, T:0.09
Consensus pattern (33 bp):
CATGCACGTCCCCAACACCCCAACACAGGTCAC
Found at i:42397 original size:40 final size:40
Alignment explanation
Indices: 42342--42427 Score: 163
Period size: 40 Copynumber: 2.1 Consensus size: 40
42332 CATGCACGTC
42342 CCCAACACCCCAACACAGGTCACCATGCACGTCCCCAGCA
1 CCCAACACCCCAACACAGGTCACCATGCACGTCCCCAGCA
*
42382 CCCAACACCCCAACACAGGTCGCCATGCACGTCCCCAGCA
1 CCCAACACCCCAACACAGGTCACCATGCACGTCCCCAGCA
42422 CCCAAC
1 CCCAAC
42428 GTCCCTAGCA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.29, C:0.51, G:0.13, T:0.07
Consensus pattern (40 bp):
CCCAACACCCCAACACAGGTCACCATGCACGTCCCCAGCA
Found at i:42431 original size:16 final size:16
Alignment explanation
Indices: 42410--42443 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42400 GTCGCCATGC
42410 ACGTCCCCAGCACCCA
1 ACGTCCCCAGCACCCA
*
42426 ACGTCCCTAGCACCCA
1 ACGTCCCCAGCACCCA
42442 AC
1 AC
42444 ACCCAACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.26, C:0.53, G:0.12, T:0.09
Consensus pattern (16 bp):
ACGTCCCCAGCACCCA
Found at i:42485 original size:23 final size:23
Alignment explanation
Indices: 42455--42500 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
42445 CCCAACACAG
42455 CTACAAGGTCGCCATGCACTCCC
1 CTACAAGGTCGCCATGCACTCCC
*
42478 CTACAAGGTCTCCATGCACTCCC
1 CTACAAGGTCGCCATGCACTCCC
42501 AGCGACCTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.43, G:0.15, T:0.20
Consensus pattern (23 bp):
CTACAAGGTCGCCATGCACTCCC
Found at i:42521 original size:29 final size:29
Alignment explanation
Indices: 42455--42565 Score: 108
Period size: 29 Copynumber: 4.0 Consensus size: 29
42445 CCCAACACAG
42455 CTACAAGGTCGCCATGCACT--C--C--C
1 CTACAAGGTCGCCATGCACTCCCAGCGAC
*
42478 CTACAAGGTCTCCATGCACTCCCAGCGAC
1 CTACAAGGTCGCCATGCACTCCCAGCGAC
*
42507 CTACAAGGTCGCCATGTACTCCCAGCGAC
1 CTACAAGGTCGCCATGCACTCCCAGCGAC
*** * * *
42536 CTTGTAGGTCGCCAAGCAATCCCGGCGAC
1 CTACAAGGTCGCCATGCACTCCCAGCGAC
42565 C
1 C
42566 AAGCCTCGAC
Statistics
Matches: 72, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
23 19 0.26
25 1 0.01
27 1 0.01
29 51 0.71
ACGTcount: A:0.23, C:0.40, G:0.21, T:0.17
Consensus pattern (29 bp):
CTACAAGGTCGCCATGCACTCCCAGCGAC
Found at i:44792 original size:2 final size:2
Alignment explanation
Indices: 44785--44809 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
44775 AATTTTGAAA
44785 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
44810 AATTTTATGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:45635 original size:22 final size:23
Alignment explanation
Indices: 45610--45655 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
45600 AAATATACTA
* *
45610 AATTGAGAACTTTTTA-AAAGTT
1 AATTAAGAACTTTCTATAAAGTT
*
45632 AATTAAGTACTTTCTATAAAGTT
1 AATTAAGAACTTTCTATAAAGTT
45655 A
1 A
45656 CTTTCTCTCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 13 0.65
23 7 0.35
ACGTcount: A:0.41, C:0.07, G:0.11, T:0.41
Consensus pattern (23 bp):
AATTAAGAACTTTCTATAAAGTT
Found at i:45790 original size:60 final size:62
Alignment explanation
Indices: 45711--45836 Score: 238
Period size: 61 Copynumber: 2.1 Consensus size: 62
45701 ATTTGTTCTT
45711 ATTCCTCTTGAAATTTGGTTTA-TTTTATTAGAATATTTAATTAATATTA-TTTATTTGCAC
1 ATTCCTCTTGAAATTTGGTTTATTTTTATTAGAATATTTAATTAATATTATTTTATTTGCAC
45771 ATTCCTCTTGAAATTTGGTTTATTTTTATTAGAATATTTAATTAATATTATTTTATTTGCAC
1 ATTCCTCTTGAAATTTGGTTTATTTTTATTAGAATATTTAATTAATATTATTTTATTTGCAC
45833 ATTC
1 ATTC
45837 TTTGTTCCAC
Statistics
Matches: 64, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
60 22 0.34
61 27 0.42
62 15 0.23
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.54
Consensus pattern (62 bp):
ATTCCTCTTGAAATTTGGTTTATTTTTATTAGAATATTTAATTAATATTATTTTATTTGCAC
Found at i:51661 original size:5 final size:5
Alignment explanation
Indices: 51651--51675 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
51641 GAGTATCGTG
51651 AATAA AATAA AATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA
51676 TTATCTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AATAA
Found at i:67217 original size:51 final size:51
Alignment explanation
Indices: 67152--67257 Score: 133
Period size: 51 Copynumber: 2.1 Consensus size: 51
67142 TGAAAGATTC
** * * *
67152 AAAAGTTTGGGGACTTATTTAGAAAGAGGGTCATAGTTTAG-GGATAAAATT
1 AAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATAATTT-GTGGATAAAATT
* *
67203 AAAAGTTTAAGGACTAATTTAGAATGAGAGTCATAATTTGTGGATGAAATT
1 AAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATAATTTGTGGATAAAATT
67254 AAAA
1 AAAA
67258 TATTCAAAAG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
50 1 0.02
51 46 0.98
ACGTcount: A:0.42, C:0.04, G:0.24, T:0.31
Consensus pattern (51 bp):
AAAAGTTTAAGGACTAATTTAGAAAGAGAGTCATAATTTGTGGATAAAATT
Found at i:79138 original size:84 final size:81
Alignment explanation
Indices: 78976--79141 Score: 251
Period size: 84 Copynumber: 2.0 Consensus size: 81
78966 ACAATTCTTC
* *
78976 AAAATGAAATACACTAGAGACGAAAACTCGAAGTCTCGCAGAGTTCGAATTCAAATATCTACAAC
1 AAAATGAAATACACTAGAGAAGAAAACTCGAAGTCTCGCAGAGTTCGAATTCAAACATCTACAAC
*
79041 CCCATCCTCTTCATCT
66 CCCATCATCTTCATCT
* * *
79057 AAAATGAAAATAATCACTCGAGAAGAAAACTCGAAGTCTCGCAGAGTTCGAATTCCAACATCTGC
1 AAAATG-AAAT-A-CACTAGAGAAGAAAACTCGAAGTCTCGCAGAGTTCGAATTCAAACATCTAC
79122 AACCCCATCATCTTCATCT
63 AACCCCATCATCTTCATCT
79141 A
1 A
79142 TTCTTAACAG
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 6 0.08
82 4 0.05
83 1 0.01
84 65 0.86
ACGTcount: A:0.39, C:0.26, G:0.13, T:0.23
Consensus pattern (81 bp):
AAAATGAAATACACTAGAGAAGAAAACTCGAAGTCTCGCAGAGTTCGAATTCAAACATCTACAAC
CCCATCATCTTCATCT
Found at i:81523 original size:55 final size:55
Alignment explanation
Indices: 81433--81543 Score: 177
Period size: 55 Copynumber: 2.0 Consensus size: 55
81423 ATAGCGGTGG
* * * *
81433 CGGCTGAAACTACTGTTATCGAAAGTTACATTGTAAAGTGGATTTACACCAATAA
1 CGGCTGAAACCACTATTATCGAAAGTTACAGTGTAAAGTGGATTCACACCAATAA
*
81488 CGGCTGAAACCACTATTATCGAAAGTTGCAGTGTAAAGTGGATTCACACCAATAA
1 CGGCTGAAACCACTATTATCGAAAGTTACAGTGTAAAGTGGATTCACACCAATAA
81543 C
1 C
81544 AGTGGAGCAC
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 51 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (55 bp):
CGGCTGAAACCACTATTATCGAAAGTTACAGTGTAAAGTGGATTCACACCAATAA
Found at i:83360 original size:32 final size:31
Alignment explanation
Indices: 83278--83367 Score: 99
Period size: 32 Copynumber: 2.8 Consensus size: 31
83268 ATTAATCATT
*
83278 TTTTTAACAATTCGATAAAATTTAATGAGCA
1 TTTTTAACAATTCGATAAAATTTAATGACCA
* * *
83309 TTTTATAATAGTTCGATAAAGTTTAATGACCA
1 TTTT-TAACAATTCGATAAAATTTAATGACCA
* * *
83341 CTTTTTAACGATTCAATAAAACTTAAT
1 -TTTTTAACAATTCGATAAAATTTAAT
83368 AATCATCTCA
Statistics
Matches: 47, Mismatches: 10, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
31 4 0.09
32 39 0.83
33 4 0.09
ACGTcount: A:0.40, C:0.11, G:0.09, T:0.40
Consensus pattern (31 bp):
TTTTTAACAATTCGATAAAATTTAATGACCA
Found at i:83381 original size:64 final size:63
Alignment explanation
Indices: 83278--83397 Score: 150
Period size: 64 Copynumber: 1.9 Consensus size: 63
83268 ATTAATCATT
* * * * * * *
83278 TTTTTAACAATTCGATAAAATTTAATGAGCATTTTATAATAGTTCGATAAAGTTTAATGACCAC
1 TTTTTAACAATTCAATAAAACTTAATAAGCATCTCATAATAATTCAATAAA-TTTAATGACCAC
* *
83342 TTTTTAACGATTCAATAAAACTTAATAATCATCTCATAATAATTCAATAAATTTAA
1 TTTTTAACAATTCAATAAAACTTAATAAGCATCTCATAATAATTCAATAAATTTAA
83398 AGATGATTAC
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
63 5 0.11
64 42 0.89
ACGTcount: A:0.42, C:0.12, G:0.07, T:0.39
Consensus pattern (63 bp):
TTTTTAACAATTCAATAAAACTTAATAAGCATCTCATAATAATTCAATAAATTTAATGACCAC
Found at i:83697 original size:65 final size:66
Alignment explanation
Indices: 83600--83729 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 66
83590 AAGGCGTGTG
* *
83600 TAACATTACTTTTAAAAAGATATTTTAAAATTAAAATGAT-AAGTTATATTATATTTTTCTTAAA
1 TAACATTACTTTTAAAAAAATATTTTAAAATTAAAATGATAAAG-TATATTATATTTTCCTTAAA
83664 AT
65 AT
83666 TAACATTAC-TTTAAAAAAATATTTTAAAATTAAAATGATAAAGTATATTATATTTTCCTTAAAA
1 TAACATTACTTTTAAAAAAATATTTTAAAATTAAAATGATAAAGTATATTATATTTTCCTTAAAA
83730 CAATTTAAAT
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
65 49 0.80
66 12 0.20
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (66 bp):
TAACATTACTTTTAAAAAAATATTTTAAAATTAAAATGATAAAGTATATTATATTTTCCTTAAAA
T
Found at i:83776 original size:23 final size:24
Alignment explanation
Indices: 83756--83805 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
83746 GAGAATGATT
* *
83756 AAAAACTCTGACTATAAATGAATA
1 AAAAACTCTAAATATAAATGAATA
*
83780 AAAAACTCTAAATATAAA-CAATA
1 AAAAACTCTAAATATAAATGAATA
83803 AAA
1 AAA
83806 TATATTGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 7 0.30
24 16 0.70
ACGTcount: A:0.62, C:0.12, G:0.04, T:0.22
Consensus pattern (24 bp):
AAAAACTCTAAATATAAATGAATA
Found at i:87703 original size:38 final size:38
Alignment explanation
Indices: 87645--87721 Score: 109
Period size: 38 Copynumber: 2.0 Consensus size: 38
87635 TAAGGTGTTG
87645 GTGGTGACCGGAACAAAGAGTTAATAACTAGCGGATTA
1 GTGGTGACCGGAACAAAGAGTTAATAACTAGCGGATTA
* * * * *
87683 GTGGTGACCGTAATAGAGAGTTCATAACTAGTGGATTA
1 GTGGTGACCGGAACAAAGAGTTAATAACTAGCGGATTA
87721 G
1 G
87722 GGGGAGATGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.34, C:0.12, G:0.30, T:0.25
Consensus pattern (38 bp):
GTGGTGACCGGAACAAAGAGTTAATAACTAGCGGATTA
Done.