Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003668.1 Hibiscus syriacus cultivar Beakdansim tig00007838_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: 76902
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:8420 original size:13 final size:13
Alignment explanation
Indices: 8402--8467 Score: 69
Period size: 14 Copynumber: 4.8 Consensus size: 13
8392 TGACTTTTTA
8402 GTCAAAGTCAATG
1 GTCAAAGTCAATG
8415 GTCAAAGTCAACTG
1 GTCAAAGTCAA-TG
* *
8429 GTCAAAGTAAACG
1 GTCAAAGTCAATG
*
8442 AGTTAAAGTCAATGG
1 -GTCAAAGTCAAT-G
*
8457 GTAAAAGTCAA
1 GTCAAAGTCAA
8468 CGGATTGACT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
13 12 0.27
14 31 0.70
15 1 0.02
ACGTcount: A:0.42, C:0.14, G:0.23, T:0.21
Consensus pattern (13 bp):
GTCAAAGTCAATG
Found at i:12113 original size:20 final size:20
Alignment explanation
Indices: 12088--12129 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
12078 AACTGAAATA
12088 GACCATTGATTGTTG-ACTTT
1 GACCATTGATT-TTGAACTTT
12108 GACCATTGATTTTGAACTTT
1 GACCATTGATTTTGAACTTT
12128 GA
1 GA
12130 ATTTTTTAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 3 0.14
20 18 0.86
ACGTcount: A:0.24, C:0.14, G:0.19, T:0.43
Consensus pattern (20 bp):
GACCATTGATTTTGAACTTT
Found at i:12839 original size:42 final size:40
Alignment explanation
Indices: 12731--12844 Score: 104
Period size: 41 Copynumber: 2.8 Consensus size: 40
12721 CATCTAAATG
* *
12731 GGATCCTCTACGGAGGGCAACATCCCCGTCCTACACTATAT
1 GGATCCTCTACGGAGGGCAACATCCCC-TTCTACACTATAA
* * * ***
12772 GAGATCC-ATACGGAGGGTAATATCCCCATTCTGTTCTATAAA
1 G-GATCCTCTACGGAGGGCAACATCCCC-TTCTACACTAT-AA
*
12814 GGATCCTCTACGGAGGACAACATCCCCTTCT
1 GGATCCTCTACGGAGGGCAACATCCCCTTCT
12845 TGTTTCTGTT
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
41 34 0.60
42 23 0.40
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (40 bp):
GGATCCTCTACGGAGGGCAACATCCCCTTCTACACTATAA
Found at i:17939 original size:13 final size:13
Alignment explanation
Indices: 17921--17945 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
17911 TCGAATATAC
17921 TTAGAAAATCTTT
1 TTAGAAAATCTTT
17934 TTAGAAAATCTT
1 TTAGAAAATCTT
17946 AAAATTCATT
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:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (13 bp):
TTAGAAAATCTTT
Found at i:19457 original size:17 final size:18
Alignment explanation
Indices: 19437--19475 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
19427 AATTTTTATG
* *
19437 AAAACAT-AATTGAATCA
1 AAAACATCAATTAAAACA
19454 AAAACATCAATTAAAACA
1 AAAACATCAATTAAAACA
19472 AAAA
1 AAAA
19476 AATTCGCTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 7 0.37
18 12 0.63
ACGTcount: A:0.67, C:0.13, G:0.03, T:0.18
Consensus pattern (18 bp):
AAAACATCAATTAAAACA
Found at i:22359 original size:14 final size:14
Alignment explanation
Indices: 22323--22375 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
22313 GTATCGCATG
22323 ATTTACATTTTCAT
1 ATTTACATTTTCAT
22337 -TTCTACATTTTCAT
1 ATT-TACATTTTCAT
* * **
22351 ATTTGCATTATCGC
1 ATTTACATTTTCAT
22365 ATTTACATTTT
1 ATTTACATTTT
22376 TTCACATCTA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 2 0.06
14 27 0.87
15 2 0.06
ACGTcount: A:0.25, C:0.17, G:0.04, T:0.55
Consensus pattern (14 bp):
ATTTACATTTTCAT
Found at i:24012 original size:31 final size:31
Alignment explanation
Indices: 23976--24042 Score: 134
Period size: 31 Copynumber: 2.2 Consensus size: 31
23966 TGAGAATTGA
23976 ATCAAATTTGCAATCTTGCAGTTCTTTGAAT
1 ATCAAATTTGCAATCTTGCAGTTCTTTGAAT
24007 ATCAAATTTGCAATCTTGCAGTTCTTTGAAT
1 ATCAAATTTGCAATCTTGCAGTTCTTTGAAT
24038 ATCAA
1 ATCAA
24043 GGTTGAAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.40
Consensus pattern (31 bp):
ATCAAATTTGCAATCTTGCAGTTCTTTGAAT
Found at i:26767 original size:39 final size:39
Alignment explanation
Indices: 26627--26781 Score: 188
Period size: 38 Copynumber: 4.0 Consensus size: 39
26617 TTTCCTAGAT
* * * **
26627 TCAATCCTTGACTTCCTTGTAAAGAGAAATTAATGTTT-
1 TCAATCCTTGACTTCCTCGTAAAGAGAAGTCAACCTTTG
** *
26665 TTTATCCTTGACTTCCTCATAAAGAGAAGTCAACCTTTG
1 TCAATCCTTGACTTCCTCGTAAAGAGAAGTCAACCTTTG
* *
26704 T-TATCCTTGACTTCCTCGTAAAGAGAAGTCAACGTTTG
1 TCAATCCTTGACTTCCTCGTAAAGAGAAGTCAACCTTTG
* *
26742 TCAATACTTGACTTCCTCGTCAAGAGAAGTCAACCTTTG
1 TCAATCCTTGACTTCCTCGTAAAGAGAAGTCAACCTTTG
26781 T
1 T
26782 TATTTCTGAC
Statistics
Matches: 101, Mismatches: 14, Indels: 3
0.86 0.12 0.03
Matches are distributed among these distances:
38 66 0.65
39 35 0.35
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.35
Consensus pattern (39 bp):
TCAATCCTTGACTTCCTCGTAAAGAGAAGTCAACCTTTG
Found at i:26792 original size:77 final size:76
Alignment explanation
Indices: 26630--26784 Score: 220
Period size: 77 Copynumber: 2.0 Consensus size: 76
26620 CCTAGATTCA
* * * * ** *
26630 ATCCTTGACTTCCTTGTAAAGAGAAATTAATGTTTTTTATCCTTGACTTCCTCATAAAGAGAAGT
1 ATCCTTGACTTCCTCGTAAAGAGAAGTCAACGTTTTCAATACTTGACTTCCTCATAAAGAGAAGT
26695 CAACCTTTGTT
66 CAACCTTTGTT
* *
26706 ATCCTTGACTTCCTCGTAAAGAGAAGTCAACGTTTGTCAATACTTGACTTCCTCGTCAAGAGAAG
1 ATCCTTGACTTCCTCGTAAAGAGAAGTCAACGTTT-TCAATACTTGACTTCCTCATAAAGAGAAG
26771 TCAACCTTTGTT
65 TCAACCTTTGTT
26783 AT
1 AT
26785 TTCTGACTCC
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
76 31 0.45
77 38 0.55
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (76 bp):
ATCCTTGACTTCCTCGTAAAGAGAAGTCAACGTTTTCAATACTTGACTTCCTCATAAAGAGAAGT
CAACCTTTGTT
Found at i:27202 original size:37 final size:37
Alignment explanation
Indices: 27102--27476 Score: 410
Period size: 36 Copynumber: 10.3 Consensus size: 37
27092 TAAATCAACT
*
27102 TCAATCTTAAGCATTCACGGA-TGGGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGACT-GGTAGTGAAGCAAA
* *
27139 TCAAT-TTAAGCCTTCACAGACGGGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGACTGGTAGTGAAGCAAA
*
27175 TTAATCTTAAGCCTTCACGGACTGGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGACTGGTAGTGAAGCAAA
* * *
27212 TCAATATTAATCCTTCACGAACTGGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGACTGGTAGTGAAGCAAA
* * *
27249 TCAATC-TAATCCTTCACGAACGGGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGACTGGTAGTGAAGCAAA
* * * *
27285 TCAATC-TAAGCCTGCAAGGACGGGTAGCGAAGCAAA
1 TCAATCTTAAGCCTTCACGGACTGGTAGTGAAGCAAA
* * * *
27321 GCAATC-TAAGCCTTCATGGTCTGGTATTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGACTGGTAGTGAAGCAAA
* **
27357 GT-AATC-TAAGCCTTCTCGGACAAGTAGTGAAGCAAA
1 -TCAATCTTAAGCCTTCACGGACTGGTAGTGAAGCAAA
* * *
27393 TCAATTTTAAGCCTTTACAGAC-GAGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGACTG-GTAGTGAAGCAAA
**
27430 TCAATC-TAAGCCTTCAC-GAAAGTGTAGTGAAGCAAA
1 TCAATCTTAAGCCTTCACGGACTG-GTAGTGAAGCAAA
27466 TCAATCTTAAG
1 TCAATCTTAAG
27477 ATCCATTGAA
Statistics
Matches: 290, Mismatches: 40, Indels: 16
0.84 0.12 0.05
Matches are distributed among these distances:
35 3 0.01
36 181 0.62
37 106 0.37
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (37 bp):
TCAATCTTAAGCCTTCACGGACTGGTAGTGAAGCAAA
Found at i:27263 original size:73 final size:72
Alignment explanation
Indices: 27102--27472 Score: 401
Period size: 73 Copynumber: 5.1 Consensus size: 72
27092 TAAATCAACT
* * *
27102 TCAATCTTAAGCATTCACGGA-TGGGTAGTGAAGCAAATCAATTTAAGCCTTCAC-AGACGGGTA
1 TCAATC-TAAGCCTTCACGGACT-GGTAGTGAAGCAAATCAATCTAAGCCTTCACGA-ACAGGTA
27165 GTGAAGCAAA
63 GTGAAGCAAA
* * * *
27175 TTAATCTTAAGCCTTCACGGACTGGTAGTGAAGCAAATCAATATTAATCCTTCACGAACTGGTAG
1 TCAATC-TAAGCCTTCACGGACTGGTAGTGAAGCAAATCAAT-CTAAGCCTTCACGAACAGGTAG
27240 TGAAGCAAA
64 TGAAGCAAA
* * * * * * * *
27249 TCAATCTAATCCTTCACGAACGGGTAGTGAAGCAAATCAATCTAAGCCTGCAAGGACGGGTAGCG
1 TCAATCTAAGCCTTCACGGACTGGTAGTGAAGCAAATCAATCTAAGCCTTCACGAACAGGTAGTG
27314 AAGCAAA
66 AAGCAAA
* * * * * * *
27321 GCAATCTAAGCCTTCATGGTCTGGTATTGAAGCAAAGT-AATCTAAGCCTTCTCGGACAAGTAGT
1 TCAATCTAAGCCTTCACGGACTGGTAGTGAAGCAAA-TCAATCTAAGCCTTCACGAACAGGTAGT
27385 GAAGCAAA
65 GAAGCAAA
* * *
27393 TCAATTTTAAGCCTTTACAGAC-GAGTAGTGAAGCAAATCAATCTAAGCCTTCACGAA-AGTGTA
1 TCAA-TCTAAGCCTTCACGGACTG-GTAGTGAAGCAAATCAATCTAAGCCTTCACGAACAG-GTA
27456 GTGAAGCAAA
63 GTGAAGCAAA
27466 TCAATCT
1 TCAATCT
27473 TAAGATCCAT
Statistics
Matches: 251, Mismatches: 39, Indels: 17
0.82 0.13 0.06
Matches are distributed among these distances:
72 89 0.35
73 128 0.51
74 33 0.13
75 1 0.00
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.24
Consensus pattern (72 bp):
TCAATCTAAGCCTTCACGGACTGGTAGTGAAGCAAATCAATCTAAGCCTTCACGAACAGGTAGTG
AAGCAAA
Found at i:27436 original size:181 final size:182
Alignment explanation
Indices: 27124--27472 Score: 497
Period size: 181 Copynumber: 1.9 Consensus size: 182
27114 ATTCACGGAT
* * * *
27124 GGGTAGTGAAGCAAATCAATTTAAGCCTTCACAGACGGGTAGTGAAGCAAATTAATCTTAAGCCT
1 GGGTAGCGAAGCAAAGCAATCTAAGCCTTCACAGACGGGTAGTGAAGCAAAGTAATCTTAAGCCT
** *
27189 TCACGGACTGGTAGTGAAGCAAATCAATATTAATCCTTCACGAACTGGTAGTGAAGCAAATCAAT
66 TCACGGACAAGTAGTGAAGCAAATCAATATTAAGCCTTCACGAACTGGTAGTGAAGCAAATCAAT
* *
27254 CTAATCCTTCACGAACGGGTAGTGAAGCAAATCAATCTAAGCCTGCAAGGAC
131 CTAAGCCTTCACGAAAGGGTAGTGAAGCAAATCAATCTAAGCCTGCAAGGAC
** * * *
27306 GGGTAGCGAAGCAAAGCAATCTAAGCCTTCATGGTCTGGTATTGAAGCAAAGTAATC-TAAGCCT
1 GGGTAGCGAAGCAAAGCAATCTAAGCCTTCACAGACGGGTAGTGAAGCAAAGTAATCTTAAGCCT
* * *
27370 TCTCGGACAAGTAGTGAAGCAAATCAATTTTAAGCCTTTAC-AGAC-GAGTAGTGAAGCAAATCA
66 TCACGGACAAGTAGTGAAGCAAATCAATATTAAGCCTTCACGA-ACTG-GTAGTGAAGCAAATCA
*
27433 ATCTAAGCCTTCACGAAAGTGTAGTGAAGCAAATCAATCT
129 ATCTAAGCCTTCACGAAAGGGTAGTGAAGCAAATCAATCT
27473 TAAGATCCAT
Statistics
Matches: 147, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
180 2 0.01
181 97 0.66
182 48 0.33
ACGTcount: A:0.36, C:0.19, G:0.21, T:0.23
Consensus pattern (182 bp):
GGGTAGCGAAGCAAAGCAATCTAAGCCTTCACAGACGGGTAGTGAAGCAAAGTAATCTTAAGCCT
TCACGGACAAGTAGTGAAGCAAATCAATATTAAGCCTTCACGAACTGGTAGTGAAGCAAATCAAT
CTAAGCCTTCACGAAAGGGTAGTGAAGCAAATCAATCTAAGCCTGCAAGGAC
Found at i:27665 original size:55 final size:55
Alignment explanation
Indices: 27604--27742 Score: 206
Period size: 55 Copynumber: 2.5 Consensus size: 55
27594 CCTTGGATTC
* * * *
27604 TATCTCCCTGAAATAAGAATGGAGCAGATCCATTTTATAAAGATTTATCGAGTCT
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCATTTTACAAAGATCTATCGAGTCT
* * *
27659 TATCTCCCTGAAAGAAGAGTGGAGCAAATCCATTTTCCAAAGATCTCTCGAGTCT
1 TATCTCCCTGAAAGAAGAGTGGAGCAGATCCATTTTACAAAGATCTATCGAGTCT
*
27714 TATCTCCCTGAAAGAAGAGTGGAACAGAT
1 TATCTCCCTGAAAGAAGAGTGGAGCAGAT
27743 TCGTCTTCCC
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 75 1.00
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (55 bp):
TATCTCCCTGAAAGAAGAGTGGAGCAGATCCATTTTACAAAGATCTATCGAGTCT
Found at i:28009 original size:3 final size:3
Alignment explanation
Indices: 27997--28044 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
27987 CCCTTTTTTC
*
27997 TTA TTA -TA TTA TTA CTA -TA TTA -TA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
28042 TTA
1 TTA
28045 ATTCAAATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
2 6 0.15
3 35 0.85
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:36076 original size:29 final size:28
Alignment explanation
Indices: 36034--36107 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 28
36024 GTCAAACATT
*
36034 TTACACAAATAGCACCCTTTTTAAAATAA
1 TTAC-CAAATAGCACCCTTTTCAAAATAA
* *
36063 TTACCAATATAGCACCCTTTTCGAATTAA
1 TTACCAA-ATAGCACCCTTTTCAAAATAA
*
36092 TTCCCAAAATAGCACC
1 TTACC-AAATAGCACC
36108 AAAACCAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 34 0.87
30 2 0.05
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.30
Consensus pattern (28 bp):
TTACCAAATAGCACCCTTTTCAAAATAA
Found at i:36159 original size:13 final size:13
Alignment explanation
Indices: 36141--36165 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
36131 AGCACCGGTC
36141 AACGGGTCGGGTT
1 AACGGGTCGGGTT
36154 AACGGGTCGGGT
1 AACGGGTCGGGT
36166 CGGGTCAACG
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:0.16, C:0.16, G:0.48, T:0.20
Consensus pattern (13 bp):
AACGGGTCGGGTT
Found at i:36166 original size:18 final size:18
Alignment explanation
Indices: 36143--36202 Score: 95
Period size: 18 Copynumber: 3.4 Consensus size: 18
36133 CACCGGTCAA
*
36143 CGGGTCGGGTTAACGGGT
1 CGGGTCGGGTCAACGGGT
36161 CGGGTCGGGTCAAC-GGT
1 CGGGTCGGGTCAACGGGT
*
36178 CGAGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
36196 CGGGTCG
1 CGGGTCG
36203 TGACCGGTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
17 16 0.42
18 22 0.58
ACGTcount: A:0.12, C:0.22, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:36184 original size:17 final size:17
Alignment explanation
Indices: 36146--36193 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
36136 CGGTCAACGG
* *
36146 GTCGGGTTAACGGGTCGG
1 GTCGGGTCAAC-GGTCGA
36164 GTCGGGTCAACGGTCGA
1 GTCGGGTCAACGGTCGA
36181 GTCGGGTCAACGG
1 GTCGGGTCAACGG
36194 GTCGGGTCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 18 0.64
18 10 0.36
ACGTcount: A:0.15, C:0.21, G:0.46, T:0.19
Consensus pattern (17 bp):
GTCGGGTCAACGGTCGA
Found at i:39817 original size:20 final size:19
Alignment explanation
Indices: 39772--39820 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
39762 AGTATCAATC
*
39772 AGTATCGATACCAAAGGGG
1 AGTATCGATACCAAAGGGA
**
39791 AGTATCGATACTGAAGGGA
1 AGTATCGATACCAAAGGGA
39810 AGGTATCGATA
1 A-GTATCGATA
39821 TCATCCGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 17 0.65
20 9 0.35
ACGTcount: A:0.37, C:0.12, G:0.31, T:0.20
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:40555 original size:67 final size:67
Alignment explanation
Indices: 40478--40991 Score: 694
Period size: 67 Copynumber: 7.8 Consensus size: 67
40468 AAAAGATTAA
40478 GAGGCCTAACTGTGCATTGACAGTAAA-GTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATTGACAG-AAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
40542 TTT
65 TTT
* *
40545 GAGGCATAACTGTGCATTGATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
40610 TT
66 TT
* *
40612 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGTCAGTTAGATGAAAGGCTAAGTTCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
40677 TT
66 TT
* * ** *
40679 GAGGCCTAACTGTGCATTAATAGAAATATGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
40744 TT
66 TT
* * * * * ** * *
40746 GAGGCCGAATTATGCTTTGA-AAAAATTATGACAATTATGCTAGTTAGAT-AAAGGCTAAGTGCC
1 GAGGCCTAACTGTGCATTGACAGAAA-GGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCC
40809 TTT
65 TTT
40812 GAGGCCTAA------A-T---AGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
40867 TT
66 TT
*
40869 GAGGCCTAACTGTGCATTGACAGAAAGCTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
1 GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
40934 TT
66 TT
* * * * *
40936 GAGACCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGTCACTTAGATGAAAGG
1 GAGGCCTAACTGTGCA-TTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGG
40992 TTAAATACCT
Statistics
Matches: 397, Mismatches: 36, Indels: 27
0.86 0.08 0.06
Matches are distributed among these distances:
56 19 0.05
57 30 0.08
59 1 0.00
63 1 0.00
64 1 0.00
66 32 0.08
67 278 0.70
68 35 0.09
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.29
Consensus pattern (67 bp):
GAGGCCTAACTGTGCATTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCT
TT
Found at i:40916 original size:123 final size:124
Alignment explanation
Indices: 40697--40943 Score: 354
Period size: 123 Copynumber: 2.0 Consensus size: 124
40687 ACTGTGCATT
* * * *
40697 AATAGAAATATGTCAGTTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCGAATTATGCT
1 AATAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCGAACTATGCA
* * *
40762 TTGAAAAAATTATGACAATTATGCTAGTTAGAT-AAAGGCTAAGTGCCTTTGAGGCCTA
66 TTGAAAAAATGATGACAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGACCTA
* * *
40820 AATAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCTAACTGTGCA
1 AATAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCGAACTATGCA
* * *
40885 TTGACAGAAA-GCTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGACCTA
66 TTGA-AAAAATGATGACAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGACCTA
40944 GCTGTGCATT
Statistics
Matches: 109, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
123 81 0.74
124 28 0.26
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (124 bp):
AATAGAAAGATGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGGCCGAACTATGCA
TTGAAAAAATGATGACAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTGAGACCTA
Found at i:41075 original size:81 final size:81
Alignment explanation
Indices: 40940--41094 Score: 238
Period size: 81 Copynumber: 1.9 Consensus size: 81
40930 GCCTTTGAGA
* * * *
40940 CCTAGCTGTGCATTTGACAAAAAGGTGTCAATTATGTCACTTAGATGAAAGGTTAAATACCTTTA
1 CCTAGCTGTGCATTTGACAAAAAAGTGTCAATCATGCCACTTAGATGAAAGGTTAAATACCTCTA
41005 AGTAAAAGATAAATGG
66 AGTAAAAGATAAATGG
* * * *
41021 CCTAGTTGTGCATTTGACAAAAAAGTGTCAATCATGCCAGTTAGATGAAAGGTTAAATGCCTCTG
1 CCTAGCTGTGCATTTGACAAAAAAGTGTCAATCATGCCACTTAGATGAAAGGTTAAATACCTCTA
41086 AGTAAAAGA
66 AGTAAAAGA
41095 CTAGACGTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
81 66 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (81 bp):
CCTAGCTGTGCATTTGACAAAAAAGTGTCAATCATGCCACTTAGATGAAAGGTTAAATACCTCTA
AGTAAAAGATAAATGG
Found at i:41238 original size:45 final size:45
Alignment explanation
Indices: 41124--41342 Score: 271
Period size: 45 Copynumber: 4.9 Consensus size: 45
41114 GAACGTAGTT
* *
41124 TAAAAGGCATGAAATGATGCCATAAATGAAATGTATAATAGTTTA
1 TAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTA
* * * *
41169 -AAAAGGCATGAAATGATGCTATAAACGAAATGTGTAATAGTGTA
1 TAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTA
41213 TAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTA
1 TAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTA
* * * *
41258 TAAAAGGCATAAAAGGATGCCATAAATGAAATGAAT-ATGGGTGCA
1 TAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAAT-AGTGTA
* ** * *
41303 TTATTGGCATGAAAGAATGCCATAAATGAAAATGCATAAT
1 TAAAAGGCATGAAAGGATGCCATAAATG-AAATGTATAAT
41343 GGTGCAATAT
Statistics
Matches: 152, Mismatches: 18, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
44 42 0.28
45 101 0.66
46 7 0.05
47 2 0.01
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (45 bp):
TAAAAGGCATGAAAGGATGCCATAAATGAAATGTATAATAGTGTA
Found at i:41361 original size:46 final size:45
Alignment explanation
Indices: 41130--41368 Score: 150
Period size: 45 Copynumber: 5.3 Consensus size: 45
41120 AGTTTAAAAG
* * **
41130 GCATGAAATG-ATGCCATAAATGAAATGTATAATAGTTTAA-A-AA
1 GCATGAAA-GAATGCCATAAATGAAATGAATAATGGTGCAATATAA
* * ** * * *
41173 GGCATGAAATG-ATGCTATAAACGAAATGTGTAATAGTG-TATAAAA
1 -GCATGAAA-GAATGCCATAAATGAAATGAATAATGGTGCAATATAA
* * * * *
41218 GGCATGAAAGGATGCCATAAATGAAATGTATAATAGTG-TATAAAA
1 -GCATGAAAGAATGCCATAAATGAAATGAATAATGGTGCAATATAA
* * * **
41263 GGCATAAAAGGATGCCATAAATGAAATGAAT-ATGGGTGCATTATTG
1 -GCATGAAAGAATGCCATAAATGAAATGAATAAT-GGTGCAATATAA
*
41309 GCATGAAAGAATGCCATAAATGAAAATGCATAATGGTGCAATATAA
1 GCATGAAAGAATGCCATAAATG-AAATGAATAATGGTGCAATATAA
* *
41355 GTATGAATGAATGC
1 GCATGAAAGAATGC
41369 TCTCAATGAA
Statistics
Matches: 164, Mismatches: 24, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
43 1 0.01
44 37 0.23
45 94 0.57
46 30 0.18
47 2 0.01
ACGTcount: A:0.45, C:0.08, G:0.22, T:0.26
Consensus pattern (45 bp):
GCATGAAAGAATGCCATAAATGAAATGAATAATGGTGCAATATAA
Found at i:46076 original size:21 final size:21
Alignment explanation
Indices: 46043--46083 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
46033 TTTTAAGTCT
* *
46043 TATATTAACTATAATTTATTA
1 TATATGAAATATAATTTATTA
46064 TATATGAAATATAATTTATT
1 TATATGAAATATAATTTATT
46084 TATCAAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (21 bp):
TATATGAAATATAATTTATTA
Found at i:48337 original size:16 final size:16
Alignment explanation
Indices: 48313--48354 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
48303 ACCAAAGATG
48313 TCAACTTTGCCAACTT
1 TCAACTTTGCCAACTT
*
48329 TCAATTTTGCCAACTT
1 TCAACTTTGCCAACTT
48345 TCAACTTTGC
1 TCAACTTTGC
48355 TAATTTTTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.24, C:0.29, G:0.07, T:0.40
Consensus pattern (16 bp):
TCAACTTTGCCAACTT
Found at i:53075 original size:16 final size:16
Alignment explanation
Indices: 53051--53099 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
53041 ACCAAAGATG
53051 TCAACTTTGCCAATTT
1 TCAACTTTGCCAATTT
* * *
53067 TCAATTTTGTCAACTT
1 TCAACTTTGCCAATTT
*
53083 TCAACTTTGCTAATTT
1 TCAACTTTGCCAATTT
53099 T
1 T
53100 TCAAGCCAAA
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.24, C:0.20, G:0.06, T:0.49
Consensus pattern (16 bp):
TCAACTTTGCCAATTT
Found at i:60021 original size:21 final size:20
Alignment explanation
Indices: 59980--60023 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
59970 CTGCGAAAAT
*
59980 TAAAAATGTAATAATACTAA
1 TAAAAATGTAATAATAATAA
* *
60000 TAAAAATGATGATATTAATAA
1 TAAAAATG-TAATAATAATAA
60021 TAA
1 TAA
60024 TAATAAAAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 8 0.40
21 12 0.60
ACGTcount: A:0.59, C:0.02, G:0.07, T:0.32
Consensus pattern (20 bp):
TAAAAATGTAATAATAATAA
Found at i:60459 original size:134 final size:134
Alignment explanation
Indices: 60192--60655 Score: 563
Period size: 134 Copynumber: 3.5 Consensus size: 134
60182 AAAATAGGAT
* * * * * * * *
60192 GAGGGATCTGTTTCGCTT-TTTTTTAGCGAAAATCATATCTTGGGATGTTGATTCATTCCACTGT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTGT
* * *
60256 CACTCAGGGAAGATTAAATAGAGGTAGACTTGTTCCACTGTTACTCT-GGGGATATCAAATCTTG
66 CACTCAGGGAAGATTAAATAGAGGCAGACTTGTTCCACTATTACT-TAGGGAATATCAAATCTTG
60320 GAAGA
130 GAAGA
* * *
60325 GAGGGATATGTTCCACTTCTTCTTGAGGGAAAATGAGATCTGGGGACGTTGATTCATTCCACTTT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTGT
* * * * * * * *
60390 CACTCAGAGAAGATTTAATCGAAGCAGACTTGTTCCACTCTTACTTAGGAAATATCAAATCCTAG
66 CACTCAGGGAAGATTAAATAGAGGCAGACTTGTTCCACTATTACTTAGGGAATATCAAATCTTGG
60455 AAGA
131 AAGA
* * * ** *
60459 GAGGGATCTGTTTCGCTTCTTGTTGAGGGAAAATCAGATCTGATGACGTTGATTCATTCCAGTGT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTGT
* * * *
60524 CACTTAGGGAAGATTGAATTGAGGCAAACTTGTTCCACTATTACTTAGGGAATATCAAATCTTGG
66 CACTCAGGGAAGATTAAATAGAGGCAGACTTGTTCCACTATTACTTAGGGAATATCAAATCTTGG
60589 AAGA
131 AAGA
* * * * * *
60593 TAGAGATATGTTCCGCTTCTCCTTTAGGGAAAATCAGATCTGGGAACGTTGATTCATTTCACT
1 GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACT
60656 CACTTTAAGG
Statistics
Matches: 277, Mismatches: 52, Indels: 3
0.83 0.16 0.01
Matches are distributed among these distances:
133 16 0.06
134 261 0.94
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.33
Consensus pattern (134 bp):
GAGGGATATGTTCCGCTTCTTCTTGAGGGAAAATCAGATCTGGGGACGTTGATTCATTCCACTGT
CACTCAGGGAAGATTAAATAGAGGCAGACTTGTTCCACTATTACTTAGGGAATATCAAATCTTGG
AAGA
Found at i:66262 original size:20 final size:18
Alignment explanation
Indices: 66239--66286 Score: 55
Period size: 20 Copynumber: 2.6 Consensus size: 18
66229 TCAAAAATAG
66239 AATAATCATAATAAAATAAA
1 AATAATCATAA-AAAA-AAA
66259 AATAAATC-TAAAAAAAAA
1 AAT-AATCATAAAAAAAAA
66277 AA-AATCATAA
1 AATAATCATAA
66287 GACTTATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
16 4 0.15
17 3 0.12
18 5 0.19
19 4 0.15
20 6 0.23
21 4 0.15
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (18 bp):
AATAATCATAAAAAAAAA
Found at i:66281 original size:16 final size:17
Alignment explanation
Indices: 66250--66282 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
66240 ATAATCATAA
*
66250 TAAAATAAAAATAAATC
1 TAAAATAAAAAAAAATC
66267 TAAAA-AAAAAAAAATC
1 TAAAATAAAAAAAAATC
66283 ATAAGACTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (17 bp):
TAAAATAAAAAAAAATC
Found at i:70163 original size:19 final size:20
Alignment explanation
Indices: 70139--70180 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
70129 AACATATGTA
70139 AAAAAT-AATAATTAATAAT
1 AAAAATAAATAATTAATAAT
70158 AAAAATAAAAATAATTAATAAT
1 AAAAAT--AAATAATTAATAAT
70180 A
1 A
70181 CATTTTTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
22 14 0.70
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (20 bp):
AAAAATAAATAATTAATAAT
Found at i:73481 original size:29 final size:29
Alignment explanation
Indices: 73439--73500 Score: 115
Period size: 29 Copynumber: 2.1 Consensus size: 29
73429 TTAATGGAAC
73439 CATTCAATGCTGAATGTTGAACCGTTCAA
1 CATTCAATGCTGAATGTTGAACCGTTCAA
*
73468 CATTCAATGCTGAATGTTGAGCCGTTCAA
1 CATTCAATGCTGAATGTTGAACCGTTCAA
73497 CATT
1 CATT
73501 TAACGTGTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (29 bp):
CATTCAATGCTGAATGTTGAACCGTTCAA
Found at i:75462 original size:12 final size:12
Alignment explanation
Indices: 75447--75471 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
75437 AAACTATAAC
75447 TAAAACATTAAA
1 TAAAACATTAAA
75459 TAAAACATTAAA
1 TAAAACATTAAA
75471 T
1 T
75472 TTGAATTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (12 bp):
TAAAACATTAAA
Done.