Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000027.1 Hibiscus syriacus cultivar Beakdansim tig00000046_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: 83287
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5386 original size:32 final size:33
Alignment explanation
Indices: 5339--5401 Score: 85
Period size: 32 Copynumber: 1.9 Consensus size: 33
5329 CATTAAACCT
*
5339 TTTATATTTTCAATTTTGT-AA-AAAATATAAA
1 TTTATATTTTAAATTTTGTAAAGAAAATATAAA
*
5370 TTTATGATTTTAAATTTTTTAAAGAAAATATA
1 TTTAT-ATTTTAAATTTTGTAAAGAAAATATA
5402 TAAATATTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 5 0.19
32 12 0.44
33 2 0.07
34 8 0.30
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (33 bp):
TTTATATTTTAAATTTTGTAAAGAAAATATAAA
Found at i:13321 original size:15 final size:15
Alignment explanation
Indices: 13287--13337 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
13277 TAATTATTAT
13287 TAATCTAATGATTT-G
1 TAAT-TAATGATTTAG
13302 ATAATTAATGATTTAG
1 -TAATTAATGATTTAG
* *
13318 TAATGATATAATTTAG
1 TAATTA-ATGATTTAG
13334 TAAT
1 TAAT
13338 GATTACTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
15 14 0.45
16 17 0.55
ACGTcount: A:0.41, C:0.02, G:0.12, T:0.45
Consensus pattern (15 bp):
TAATTAATGATTTAG
Found at i:13746 original size:15 final size:15
Alignment explanation
Indices: 13726--13754 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
13716 ATTTATTATT
13726 AATATTTAATGATTC
1 AATATTTAATGATTC
13741 AATATTTAATGATT
1 AATATTTAATGATT
13755 TAGTAATGAT
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:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (15 bp):
AATATTTAATGATTC
Found at i:13770 original size:16 final size:16
Alignment explanation
Indices: 13749--13780 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
13739 TCAATATTTA
*
13749 ATGATTTAGTAATGAT
1 ATGATTTAATAATGAT
13765 ATGATTTAATAATGAT
1 ATGATTTAATAATGAT
13781 TACTAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.16, T:0.44
Consensus pattern (16 bp):
ATGATTTAATAATGAT
Found at i:23866 original size:65 final size:65
Alignment explanation
Indices: 23795--23949 Score: 177
Period size: 65 Copynumber: 2.4 Consensus size: 65
23785 TACACTAGGG
* * ** *
23795 GTGCATCGGTACACTAATTACATTCAATGTTTCAAACA-AGCCTGGAGTGCATCGATGCATGGTT
1 GTGCATCGGTACACAAAATACATTCAATGTTTCAAA-ATAGCCAAGAGTGCATCGATGCATGGCT
23859 T
65 T
* ** **
23860 GTGCATCGGTACACAAAATGCATTTGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACAAAATACATTCAATGTTTCAAAATAGCCAAGAGTGCATCGATGCATGGCTT
* * *
23925 GTGTATCGGTACATAAAATGCATTC
1 GTGCATCGGTACACAAAATACATTC
23950 GAAATGGGTG
Statistics
Matches: 76, Mismatches: 13, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
64 1 0.01
65 75 0.99
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATACATTCAATGTTTCAAAATAGCCAAGAGTGCATCGATGCATGGCTT
Found at i:26351 original size:28 final size:28
Alignment explanation
Indices: 26318--26378 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
26308 GAATTAATCA
*
26318 AAAACTAGTCCTAAGTTCAAAAATCAAT
1 AAAACTAGTCATAAGTTCAAAAATCAAT
26346 AAAACTAGTCATAAGTTCAAAAATCAAT
1 AAAACTAGTCATAAGTTCAAAAATCAAT
26374 AAAAC
1 AAAAC
26379 AGGGGTTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.54, C:0.16, G:0.07, T:0.23
Consensus pattern (28 bp):
AAAACTAGTCATAAGTTCAAAAATCAAT
Found at i:26667 original size:23 final size:22
Alignment explanation
Indices: 26641--26718 Score: 77
Period size: 23 Copynumber: 3.5 Consensus size: 22
26631 CAGCAGAGTG
26641 CATCGATGCACATTCAAGGAATA
1 CATCGATGCACATTCAAGG-ATA
* * *
26664 CATCGGTGCACCTTCATGG-TA
1 CATCGATGCACATTCAAGGATA
* * *
26685 TATCGATGAACATTCAAGGGATG
1 CATCGATGCACATTCAA-GGATA
26708 CATCGATGCAC
1 CATCGATGCAC
26719 TGTCTAATGT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
21 14 0.33
22 2 0.05
23 26 0.62
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (22 bp):
CATCGATGCACATTCAAGGATA
Found at i:28855 original size:16 final size:16
Alignment explanation
Indices: 28834--28864 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
28824 ATTTTAAGGT
28834 CAAAATATTGAAAAAC
1 CAAAATATTGAAAAAC
*
28850 CAAAATATTTAAAAA
1 CAAAATATTGAAAAA
28865 ATTGATATCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.10, G:0.03, T:0.23
Consensus pattern (16 bp):
CAAAATATTGAAAAAC
Found at i:30936 original size:65 final size:65
Alignment explanation
Indices: 30860--31016 Score: 190
Period size: 65 Copynumber: 2.4 Consensus size: 65
30850 AACACTAGGG
* * ** * *
30860 GTGCATCGGTACACTAATTACATTCGATGTTTC-AAATAAGCCTGGAGTGCATCGTTGCATGGTT
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAAAAT-AGCCAAGAGTGCATCGATGCATGGCT
30924 T
65 T
* * **
30925 GTGCATCGGTACACAAAATGCATTTGATGTTTCAAAATATTCAAGAGTGCATCGATGCATGGCTT
1 GTGCATCGGTACACAAAATACATTCGATGTTTCAAAATAGCCAAGAGTGCATCGATGCATGGCTT
* *
30990 GTGCATCGGTACATAAAATGCATTCGA
1 GTGCATCGGTACACAAAATACATTCGA
31017 AATGGGTGTG
Statistics
Matches: 79, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
65 75 0.95
66 4 0.05
ACGTcount: A:0.29, C:0.18, G:0.22, T:0.31
Consensus pattern (65 bp):
GTGCATCGGTACACAAAATACATTCGATGTTTCAAAATAGCCAAGAGTGCATCGATGCATGGCTT
Found at i:32535 original size:138 final size:138
Alignment explanation
Indices: 32287--32561 Score: 550
Period size: 138 Copynumber: 2.0 Consensus size: 138
32277 AAAAAAAAAA
32287 ATTCTCCAATAGGAAAAATTAGTTCATATTATAATGAGTTTATATCAATATTTTGATCAAAATAA
1 ATTCTCCAATAGGAAAAATTAGTTCATATTATAATGAGTTTATATCAATATTTTGATCAAAATAA
32352 TAAACAATGTTAATTATTTATTTATGTCAGTTTTCTTTATCTTAGTTTTCTTTTCAAAGTGATTT
66 TAAACAATGTTAATTATTTATTTATGTCAGTTTTCTTTATCTTAGTTTTCTTTTCAAAGTGATTT
32417 TTTTAATG
131 TTTTAATG
32425 ATTCTCCAATAGGAAAAATTAGTTCATATTATAATGAGTTTATATCAATATTTTGATCAAAATAA
1 ATTCTCCAATAGGAAAAATTAGTTCATATTATAATGAGTTTATATCAATATTTTGATCAAAATAA
32490 TAAACAATGTTAATTATTTATTTATGTCAGTTTTCTTTATCTTAGTTTTCTTTTCAAAGTGATTT
66 TAAACAATGTTAATTATTTATTTATGTCAGTTTTCTTTATCTTAGTTTTCTTTTCAAAGTGATTT
32555 TTTTAAT
131 TTTTAAT
32562 TTTTTCAAAG
Statistics
Matches: 137, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
138 137 1.00
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.48
Consensus pattern (138 bp):
ATTCTCCAATAGGAAAAATTAGTTCATATTATAATGAGTTTATATCAATATTTTGATCAAAATAA
TAAACAATGTTAATTATTTATTTATGTCAGTTTTCTTTATCTTAGTTTTCTTTTCAAAGTGATTT
TTTTAATG
Found at i:36147 original size:21 final size:21
Alignment explanation
Indices: 36123--36196 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 21
36113 GGCCTGTTTG
* *
36123 TAATAATATTAATTATTTATT
1 TAATAATATTAATTATTAATA
*
36144 TAATAATAATAA-TA-TAATA
1 TAATAATATTAATTATTAATA
*
36163 TAATAATATT-ATTATTAAAAA
1 TAATAATATTAATTATT-AATA
*
36184 TAATAATAATAAT
1 TAATAATATTAAT
36197 AAATAAAACA
Statistics
Matches: 43, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
18 1 0.02
19 14 0.33
20 3 0.07
21 23 0.53
22 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TAATAATATTAATTATTAATA
Found at i:36152 original size:3 final size:3
Alignment explanation
Indices: 36144--36198 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
36134 ATTATTTATT
* * * *
36144 TAA TAA TAA TAA T-A TAA T-A TAA TAA TAT TAT TAT TAA AAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
36190 TAA TAA TAA
1 TAA TAA TAA
36199 ATAAAACAAA
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
2 4 0.09
3 42 0.91
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:36664 original size:113 final size:113
Alignment explanation
Indices: 36455--37693 Score: 2063
Period size: 113 Copynumber: 11.0 Consensus size: 113
36445 AGAATCATGC
* *
36455 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCC-TCTTCAGATAAGTTCTTCTTAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
** ** * * * * *
36519 TATGAACT-TTCTCTGAAAAAGTTGATCCATCGAGTGATGAATTCGAGCA
65 TATGAACTCGAC-CTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
* * * *
36568 AAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTATTCTTTCTTCATATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * * *
36633 ATGAACTCGCCCTGGCAATGCTGATCCATCGAATGATAAATTCAAACG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
36681 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
36746 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
36794 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
36859 ATGAACTCGACCTGGTAATGCTGATCCATCAAATGATGAATTCAAGTG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
* *
36907 AAAAGTTGAATAAGTTCTTTTCATTATGAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
36971 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
* * *
37019 AAAAGTTAAACAAATTCTTCTCATTATTAACTTCTTCTTCC-TCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
37083 ATGAACTCGACCTGGTAATGTTGATCCATCGAATGTTGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
*
37131 AAAAGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
37196 ATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGTG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
37244 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
37309 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCA
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
*
37357 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* *
37422 ATGAACTCGACCTGGCAATGTTGATCCATCGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
37470 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
**
37535 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGAA
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
*
37583 AAAAGATGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
37648 ATGAACTCGACCTGGTAATGCTGATCCATCAAATGATGAATTCAAG
66 ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAG
37694 TTTGCTTAAC
Statistics
Matches: 1062, Mismatches: 61, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
112 246 0.23
113 815 0.77
114 1 0.00
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Consensus pattern (113 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGTAATGCTGATCCATCGAATGATGAATTCAAGCG
Found at i:38115 original size:54 final size:54
Alignment explanation
Indices: 37963--38118 Score: 204
Period size: 54 Copynumber: 2.9 Consensus size: 54
37953 AGAATAACAG
* * * * * *
37963 GTTCGTAAAACATTTGACAGCGCATTCATCCTTTCCTGTGGCTTCTGCTCAGAT
1 GTTCATAAAACATTTGACAACACATTCATCCTTTCCTTTGGTTTCTGCTCAGAC
* *
38017 GTTCGTAAAACATTTGACAACACATTCATCCTTTTCTTTGGTTTCTGCTCAGAC
1 GTTCATAAAACATTTGACAACACATTCATCCTTTCCTTTGGTTTCTGCTCAGAC
** * *
38071 GTTCATAAAATGTTTGACAACACATTCATCATTTCCTTTCGTTTCTGC
1 GTTCATAAAACATTTGACAACACATTCATCCTTTCCTTTGGTTTCTGC
38119 CAAGATTTCT
Statistics
Matches: 90, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
54 90 1.00
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.38
Consensus pattern (54 bp):
GTTCATAAAACATTTGACAACACATTCATCCTTTCCTTTGGTTTCTGCTCAGAC
Found at i:39129 original size:76 final size:76
Alignment explanation
Indices: 39004--39174 Score: 227
Period size: 76 Copynumber: 2.3 Consensus size: 76
38994 GATGTGGGCC
* * * *
39004 TTCAGCATGCCCCAACA-ATTACTGATATGAACGTTCAAAATACATCAACATTCTTCATTCTGAT
1 TTCAGCATGCCCCAACATTTTACTGATATAAACATTCAAAATACATCAACATTCCTCATTCTGAT
39068 TGAAAAAGGCT
66 TGAAAAAGGCT
* * ** *
39079 TTCAGCATGTCCCAACATTTTGCTGATATAAACATTCAGGATACATCAACATTCCTGATTCTGAT
1 TTCAGCATGCCCCAACATTTTACTGATATAAACATTCAAAATACATCAACATTCCTCATTCTGAT
* *
39144 TGAAAAGGGTT
66 TGAAAAAGGCT
*
39155 TTCAGTATGCCCCAACATTT
1 TTCAGCATGCCCCAACATTT
39175 GCTTCTTGTT
Statistics
Matches: 82, Mismatches: 13, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
75 16 0.20
76 66 0.80
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (76 bp):
TTCAGCATGCCCCAACATTTTACTGATATAAACATTCAAAATACATCAACATTCCTCATTCTGAT
TGAAAAAGGCT
Found at i:40458 original size:114 final size:114
Alignment explanation
Indices: 40258--40477 Score: 359
Period size: 114 Copynumber: 1.9 Consensus size: 114
40248 GATCATGCAG
* * *
40258 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
40323 ATACTTCCAGAAGATGCTATTGGGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAA
* *
40372 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTTATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
*
40437 ACACTTTCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTA
40478 CGAGAACATG
Statistics
Matches: 97, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
114 97 1.00
ACGTcount: A:0.30, C:0.20, G:0.16, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGGCTCCTTATTTCTACTATGAGCAAA
Found at i:42797 original size:23 final size:23
Alignment explanation
Indices: 42741--42815 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 23
42731 CTTGATTCAA
42741 TTTTCCTTTTTTCTTT-TTTTTT
1 TTTTCCTTTTTTCTTTCTTTTTT
42763 TTGGTT--TATTTTTCTTTCTTTTTT
1 TT--TTCCT-TTTTTCTTTCTTTTTT
* *
42787 TTTTCCTTTTTTCCTTCTTCTTTC
1 TTTTCCTTTTTTCTTTCTT-TTTT
42811 TTTTC
1 TTTTC
42816 TGGATAAGTA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
22 5 0.11
23 20 0.45
24 19 0.43
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.79
Consensus pattern (23 bp):
TTTTCCTTTTTTCTTTCTTTTTT
Found at i:47872 original size:19 final size:20
Alignment explanation
Indices: 47848--47888 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
47838 CCGTTACACA
47848 GGGGGGAATCAGTACCC-CT
1 GGGGGGAATCAGTACCCTCT
*
47867 GGGGGGAATCGGTACCCTCT
1 GGGGGGAATCAGTACCCTCT
47887 GG
1 GG
47889 ACATTCTGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (20 bp):
GGGGGGAATCAGTACCCTCT
Found at i:48154 original size:19 final size:20
Alignment explanation
Indices: 48130--48169 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
48120 AATTTAATCA
*
48130 AATATATAAT-TTAAAATTC
1 AATATAAAATCTTAAAATTC
48149 AATATAAAATCTTAAAATTC
1 AATATAAAATCTTAAAATTC
48169 A
1 A
48170 TTAACACTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.55, C:0.07, G:0.00, T:0.38
Consensus pattern (20 bp):
AATATAAAATCTTAAAATTC
Found at i:51324 original size:20 final size:21
Alignment explanation
Indices: 51299--51341 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
51289 CCGTTACACA
51299 GGGA-GGAATCGGTACCCCCT
1 GGGAGGGAATCGGTACCCCCT
*
51319 GGGAGGGAATCGGTACCCTCT
1 GGGAGGGAATCGGTACCCCCT
51340 GG
1 GG
51342 ACATTATGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.19, C:0.26, G:0.40, T:0.16
Consensus pattern (21 bp):
GGGAGGGAATCGGTACCCCCT
Found at i:55810 original size:26 final size:27
Alignment explanation
Indices: 55779--55842 Score: 94
Period size: 26 Copynumber: 2.4 Consensus size: 27
55769 AATTTTTCCT
55779 GAAGGACCACATAGAACAC-ATGTCCC
1 GAAGGACCACATAGAACACAATGTCCC
*
55805 GAAGGACCACGTAGAACACATATGTCCC
1 GAAGGACCACATAGAACACA-ATGTCCC
*
55833 GAAAGACCAC
1 GAAGGACCAC
55843 GTACAACCCT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 18 0.53
28 16 0.47
ACGTcount: A:0.39, C:0.30, G:0.20, T:0.11
Consensus pattern (27 bp):
GAAGGACCACATAGAACACAATGTCCC
Found at i:55840 original size:28 final size:26
Alignment explanation
Indices: 55783--55845 Score: 90
Period size: 28 Copynumber: 2.3 Consensus size: 26
55773 TTTCCTGAAG
* *
55783 GACCACATAGAACACATGTCCCGAAG
1 GACCACGTAGAACACATGTCCCGAAA
55809 GACCACGTAGAACACATATGTCCCGAAA
1 GACCACGTAGAACAC--ATGTCCCGAAA
55837 GACCACGTA
1 GACCACGTA
55846 CAACCCTCGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 14 0.42
28 19 0.58
ACGTcount: A:0.38, C:0.30, G:0.19, T:0.13
Consensus pattern (26 bp):
GACCACGTAGAACACATGTCCCGAAA
Found at i:57504 original size:16 final size:16
Alignment explanation
Indices: 57485--57531 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
57475 TGTAACTTAC
*
57485 AAGTCAGGTAAATATA
1 AAGTCATGTAAATATA
* * *
57501 AAGTCATATAAACATG
1 AAGTCATGTAAATATA
57517 AAGTCATGTAAATAT
1 AAGTCATGTAAATAT
57532 CTGATCAGTT
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.49, C:0.09, G:0.15, T:0.28
Consensus pattern (16 bp):
AAGTCATGTAAATATA
Found at i:63611 original size:26 final size:26
Alignment explanation
Indices: 63544--63618 Score: 80
Period size: 30 Copynumber: 2.8 Consensus size: 26
63534 TTATTATATT
* *
63544 TTAAAAA-TATTTGATAATTTTAGTT
1 TTAAAAATTATTTGATAATTTTACTA
63569 TCTCAAAAAATGTATTTGATAATTTTACTA
1 T-T--AAAAAT-TATTTGATAATTTTACTA
*
63599 TTAAAAATTATTTGGTAATT
1 TTAAAAATTATTTGATAATT
63619 CTAAATAAAT
Statistics
Matches: 42, Mismatches: 3, Indels: 9
0.78 0.06 0.17
Matches are distributed among these distances:
25 1 0.02
26 12 0.29
27 6 0.14
28 5 0.12
29 1 0.02
30 17 0.40
ACGTcount: A:0.40, C:0.04, G:0.08, T:0.48
Consensus pattern (26 bp):
TTAAAAATTATTTGATAATTTTACTA
Found at i:81161 original size:16 final size:16
Alignment explanation
Indices: 81133--81180 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
81123 AATATAATAT
81133 TATTT-ATTATTTATTA
1 TATTTAATT-TTTATTA
81149 TATTTAATTTTTA-TA
1 TATTTAATTTTTATTA
* *
81164 CATATAATTTTTATTA
1 TATTTAATTTTTATTA
81180 T
1 T
81181 TTCAAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 13 0.48
16 11 0.41
17 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (16 bp):
TATTTAATTTTTATTA
Found at i:81281 original size:13 final size:12
Alignment explanation
Indices: 81262--81295 Score: 59
Period size: 13 Copynumber: 2.8 Consensus size: 12
81252 TTTTTTATTT
81262 ATTATATTAATA
1 ATTATATTAATA
81274 ATTAATATTAATA
1 ATT-ATATTAATA
81287 ATTATATTA
1 ATTATATTA
81296 TTATTATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTATATTAATA
Found at i:83166 original size:24 final size:24
Alignment explanation
Indices: 83117--83168 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 24
83107 ATCGTGCCTT
*
83117 AAGAGCAGAGAAAAACGTGTGCTAC
1 AAGAGCAGAGAAAAACATGT-CTAC
*
83142 AAGAGCATAGAAAAATCATGT-TAC
1 AAGAGCAGAGAAAAA-CATGTCTAC
83166 AAG
1 AAG
83169 GACTGAGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 6 0.25
25 14 0.58
26 4 0.17
ACGTcount: A:0.48, C:0.13, G:0.23, T:0.15
Consensus pattern (24 bp):
AAGAGCAGAGAAAAACATGTCTAC
Done.