Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006255.1 Hibiscus syriacus cultivar Beakdansim tig00014927_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: 146525
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:17356 original size:14 final size:14
Alignment explanation
Indices: 17337--17367 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
17327 AACCAAAAAC
17337 TATCAAGAAAGCTA
1 TATCAAGAAAGCTA
17351 TATCAAGAAAGCTA
1 TATCAAGAAAGCTA
17365 TAT
1 TAT
17368 GTTCCCTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (14 bp):
TATCAAGAAAGCTA
Found at i:19180 original size:19 final size:19
Alignment explanation
Indices: 19158--19196 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
19148 ACATCGAATG
* *
19158 CATTTTATGCATCGATGCA
1 CATTTGATGCACCGATGCA
*
19177 CATTTGGTGCACCGATGCA
1 CATTTGATGCACCGATGCA
19196 C
1 C
19197 TAAGTGTTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (19 bp):
CATTTGATGCACCGATGCA
Found at i:21131 original size:21 final size:21
Alignment explanation
Indices: 21106--21145 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
21096 AAGACTCTAT
21106 TTTCAAAATACAAAAATGATA
1 TTTCAAAATACAAAAATGATA
**
21127 TTTCAAAATTGAAAAATGA
1 TTTCAAAATACAAAAATGA
21146 AAATAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATACAAAAATGATA
Found at i:23118 original size:42 final size:42
Alignment explanation
Indices: 23059--23142 Score: 150
Period size: 42 Copynumber: 2.0 Consensus size: 42
23049 GAAGAGTCTA
23059 TACATGTTGTTTTCGATGATAATCCCCATACAAGGAAGGATT
1 TACATGTTGTTTTCGATGATAATCCCCATACAAGGAAGGATT
* *
23101 TACATGTTGTTTTCGATGATAATCCCCTTACAAGTAAGGATT
1 TACATGTTGTTTTCGATGATAATCCCCATACAAGGAAGGATT
23143 CTTGTGTTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.36
Consensus pattern (42 bp):
TACATGTTGTTTTCGATGATAATCCCCATACAAGGAAGGATT
Found at i:28041 original size:19 final size:19
Alignment explanation
Indices: 28019--28057 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28009 ACATCGAATG
* *
28019 CATTTTATGCATCGATGCA
1 CATTTGATGCACCGATGCA
*
28038 CATTTGGTGCACCGATGCA
1 CATTTGATGCACCGATGCA
28057 C
1 C
28058 TAAGTGTTCC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.31
Consensus pattern (19 bp):
CATTTGATGCACCGATGCA
Found at i:32700 original size:23 final size:23
Alignment explanation
Indices: 32672--32718 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
32662 GAACATATAG
* *
32672 ACGAATATTTTCGCGAACGTTAA
1 ACGAATATGTTCGCGAACGCTAA
*
32695 ACGAATATGTTCGTGAACGCTAA
1 ACGAATATGTTCGCGAACGCTAA
32718 A
1 A
32719 AAAACGAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.17, G:0.19, T:0.28
Consensus pattern (23 bp):
ACGAATATGTTCGCGAACGCTAA
Found at i:33056 original size:31 final size:31
Alignment explanation
Indices: 33021--33093 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
33011 AAAACATAAT
*
33021 ATTTAGTCACTTTCGA-TTTTATTTAATTAAG
1 ATTTAGTCACTTT-GATTTTTATGTAATTAAG
* *
33052 ATTTAATCACTTTTATTTTTATGTAATTAAG
1 ATTTAGTCACTTTGATTTTTATGTAATTAAG
* *
33083 ATGTCGTCACT
1 ATTTAGTCACT
33094 AAGGGTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 1 0.03
31 34 0.97
ACGTcount: A:0.29, C:0.11, G:0.10, T:0.51
Consensus pattern (31 bp):
ATTTAGTCACTTTGATTTTTATGTAATTAAG
Found at i:34180 original size:2 final size:2
Alignment explanation
Indices: 34173--34210 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
34163 TATTCTTCTC
34173 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
34211 TAAATTAATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42733 original size:301 final size:300
Alignment explanation
Indices: 41926--42837 Score: 1445
Period size: 300 Copynumber: 3.0 Consensus size: 300
41916 CGTAACACAG
* * * * * * * *
41926 CTAATG-AAATAAAGGAGAACGGGATGCAAATGAGGAATTTTTTACCTTTGAAATTGTTGAAACC
1 CTAATGAAAATAAAAGAGAACGGAATGCAAACGAGGAATTTTTTACCTCTGAAGTTATTGTATCC
* * *
41990 AATATACAAATATTGGAGCATTGTCAAATTTCCGATTTCTATAGGTATACTTCCTTCCATAGAGT
66 AAGATTCAAATATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTCCTTCCATAGAGT
* *
42055 TGTTCCACAATGATATATGCCTCAACTCTTTGCACTTGTAAAAACTGCTGGGAATGCTACCAGAA
131 TGTTCCACAATGATATATACCTCAACTCTTTGCACTTGTATAAACTGCTGGGAATGCTACCAGAA
* *
42120 ATCTGGTTCTCATCCAACCTTAATACTTGCAATTTAGACATTGTATCAAATATTTCCGACTCTAG
196 ATCTGGTTCCCATCCAACCTTAATCCTTGCAATTTAGACATT-TATCAAATATTTCCGACTCTAG
*
42185 ATGGCCTGCAGTGAGATTATTAATTATAAAACAACTTTTAT
260 ATGGCCTGCAGTGAGATTGTTAATTATAAAACAACTTTTAT
*
42226 TTAATGAAAATAAAAGAGAACGGAATGCAAAC-AGGAATTTTTTACCTCTGAAGTTATTGTATCC
1 CTAATGAAAATAAAAGAGAACGGAATGCAAACGAGGAATTTTTTACCTCTGAAGTTATTGTATCC
*
42290 AAGATAT-AAATATTGGAGCATAGTCAAATTTCCGATTTCTATGGGTATACTTCCTTCCATAGAG
66 AAGAT-TCAAATATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTCCTTCCATAGAG
42354 TTGTTCCACAATGATATATACCTCAACTCTTTGCACTTGTATAAACTGCTGGGAATGCTACCAGA
130 TTGTTCCACAATGATATATACCTCAACTCTTTGCACTTGTATAAACTGCTGGGAATGCTACCAGA
* *
42419 AATCTGGTTCCCATCCAACCTTAATCCTTGTAATTTAGACATATTATCAAATATTCCCGACTCTA
195 AATCTGGTTCCCATCCAACCTTAATCCTTGCAATTTAGACAT-TTATCAAATATTTCCGACTCTA
*
42484 GATGACCTGCAGTGAGATTGTTAATTATAAAACAACTTTTAT
259 GATGGCCTGCAGTGAGATTGTTAATTATAAAACAACTTTTAT
42526 CTAATGAAAATAAAAGAGAACGGAATGCAAACGAGGAATTTTTTACCTCTGAAGTTATTGTATCC
1 CTAATGAAAATAAAAGAGAACGGAATGCAAACGAGGAATTTTTTACCTCTGAAGTTATTGTATCC
*
42591 AAGATTCAAAGATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTCCTTCCATAGAGT
66 AAGATTCAAATATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTCCTTCCATAGAGT
* * * * *
42656 TGTTCCATAGTGATAAATACATCAACTCTTTGCACTTGTATAAACTGCTGGGAATGCTACTAGAA
131 TGTTCCACAATGATATATACCTCAACTCTTTGCACTTGTATAAACTGCTGGGAATGCTACCAGAA
* * *
42721 ATTTGATTCCCATCCAAGCTTAATCCTTGCAATTTAGACATGTTATCAAATATTTCCGACTCTAG
196 ATCTGGTTCCCATCCAACCTTAATCCTTGCAATTTAGACAT-TTATCAAATATTTCCGACTCTAG
* * * * *
42786 ATGGCCTGCAGTGAAATTGTTAGTTATATAA-ATCTTTTAA
260 ATGGCCTGCAGTGAGATTGTTAATTATAAAACAACTTTTAT
42826 CTAATGAAAATA
1 CTAATGAAAATA
42838 CATTCAAGAT
Statistics
Matches: 566, Mismatches: 41, Indels: 10
0.92 0.07 0.02
Matches are distributed among these distances:
300 304 0.54
301 262 0.46
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (300 bp):
CTAATGAAAATAAAAGAGAACGGAATGCAAACGAGGAATTTTTTACCTCTGAAGTTATTGTATCC
AAGATTCAAATATTGGAGCATAGTCAAATTTCCGATTTCTATAGGTATACTTCCTTCCATAGAGT
TGTTCCACAATGATATATACCTCAACTCTTTGCACTTGTATAAACTGCTGGGAATGCTACCAGAA
ATCTGGTTCCCATCCAACCTTAATCCTTGCAATTTAGACATTTATCAAATATTTCCGACTCTAGA
TGGCCTGCAGTGAGATTGTTAATTATAAAACAACTTTTAT
Found at i:55846 original size:2 final size:2
Alignment explanation
Indices: 55839--55868 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55829 AATAAACATG
55839 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
55869 GTTGGGTCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60514 original size:2 final size:2
Alignment explanation
Indices: 60507--60541 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
60497 ATTTTAATTG
60507 AT AT AT AT AT 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 AT AT AT AT AT A
60542 ATAATAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60782 original size:8 final size:8
Alignment explanation
Indices: 60769--60798 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
60759 CTCCCATCTC
60769 CCTCCTCT
1 CCTCCTCT
60777 CCTCCTCT
1 CCTCCTCT
60785 CCTCCTCT
1 CCTCCTCT
60793 CTCTCC
1 C-CTCC
60799 CACTTCAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 17 0.81
9 4 0.19
ACGTcount: A:0.00, C:0.63, G:0.00, T:0.37
Consensus pattern (8 bp):
CCTCCTCT
Found at i:69698 original size:23 final size:23
Alignment explanation
Indices: 69652--69698 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
69642 TATATTTTTA
*
69652 TTAATATTATATTTATAATGTAT
1 TTAATATTATATTTATAATATAT
69675 TTAATATTATATTT-TAAATATAT
1 TTAATATTATATTTAT-AATATAT
69698 T
1 T
69699 GTTTTAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTAATATTATATTTATAATATAT
Found at i:71137 original size:5 final size:5
Alignment explanation
Indices: 71127--71176 Score: 55
Period size: 5 Copynumber: 9.6 Consensus size: 5
71117 TAAAATGCAC
* * *
71127 AAAAT AAAAT AAAAT AAACAA ACAAAC AAAAT AAAGT AAAAT AAAAT AAA
1 AAAAT AAAAT AAAAT AAA-AT A-AAAT AAAAT AAAAT AAAAT AAAAT AAA
71177 GTAAGCACAC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
5 32 0.84
6 4 0.11
7 2 0.05
ACGTcount: A:0.78, C:0.06, G:0.02, T:0.14
Consensus pattern (5 bp):
AAAAT
Found at i:76949 original size:15 final size:17
Alignment explanation
Indices: 76914--76971 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
76904 TAAGTATGTG
*
76914 TTAAATAACGTTATATT
1 TTAAAAAACGTTATATT
76931 TTAAAAAAC-TTAT-TT
1 TTAAAAAACGTTATATT
*
76946 TTAAATATAATGTTATATT
1 TTAAA-A-AACGTTATATT
76965 TTGAAAA
1 TT-AAAA
76972 TCAAACACCA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
15 7 0.21
16 5 0.15
17 10 0.29
18 4 0.12
19 5 0.15
20 3 0.09
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (17 bp):
TTAAAAAACGTTATATT
Found at i:79247 original size:31 final size:31
Alignment explanation
Indices: 79209--79267 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
79199 ATTTATACTA
79209 ATATACAAGCTTAGCTCCTCCCTTCAAATCG
1 ATATACAAGCTTAGCTCCTCCCTTCAAATCG
* *
79240 ATATACAAGCTTAGTTCCTCTCTTCAAA
1 ATATACAAGCTTAGCTCCTCCCTTCAAA
79268 CCTTAAACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.31, C:0.29, G:0.08, T:0.32
Consensus pattern (31 bp):
ATATACAAGCTTAGCTCCTCCCTTCAAATCG
Found at i:86587 original size:17 final size:17
Alignment explanation
Indices: 86567--86618 Score: 54
Period size: 17 Copynumber: 3.1 Consensus size: 17
86557 TATTTATGTG
86567 TTAAATAACGTTATATT
1 TTAAATAACGTTATATT
*
86584 TTAAAAAAC-TTAT-TT
1 TTAAATAACGTTATATT
* *
86599 TAAATATAATGTTATATT
1 TTAA-ATAACGTTATATT
86617 TT
1 TT
86619 GAAAACAAAC
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
15 5 0.19
16 7 0.26
17 12 0.44
18 3 0.11
ACGTcount: A:0.42, C:0.04, G:0.04, T:0.50
Consensus pattern (17 bp):
TTAAATAACGTTATATT
Found at i:86881 original size:19 final size:20
Alignment explanation
Indices: 86849--86902 Score: 67
Period size: 19 Copynumber: 2.8 Consensus size: 20
86839 GGGGTACGTA
86849 ATGCGGTCTGATGCGATCCG
1 ATGCGGTCTGATGCGATCCG
* *
86869 ATGCGGT-TGATGCGGTCTG
1 ATGCGGTCTGATGCGATCCG
86888 ATGCGGATC-GATGCG
1 ATGCGG-TCTGATGCG
86903 TTTAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.15, C:0.20, G:0.39, T:0.26
Consensus pattern (20 bp):
ATGCGGTCTGATGCGATCCG
Found at i:86889 original size:10 final size:10
Alignment explanation
Indices: 86849--86902 Score: 67
Period size: 10 Copynumber: 5.5 Consensus size: 10
86839 GGGGTACGTA
86849 ATGCGGTCTG
1 ATGCGGTCTG
* *
86859 ATGCGATCCG
1 ATGCGGTCTG
86869 ATGCGGT-TG
1 ATGCGGTCTG
86878 ATGCGGTCTG
1 ATGCGGTCTG
86888 ATGCGGATC-G
1 ATGCGG-TCTG
86898 ATGCG
1 ATGCG
86903 TTTAAATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
9 8 0.21
10 28 0.74
11 2 0.05
ACGTcount: A:0.15, C:0.20, G:0.39, T:0.26
Consensus pattern (10 bp):
ATGCGGTCTG
Found at i:94607 original size:18 final size:18
Alignment explanation
Indices: 94584--94619 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
94574 GACTATTCTG
94584 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
94602 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
94620 TCACGAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (18 bp):
GTTGATCATTGTCCACTC
Found at i:96240 original size:7 final size:7
Alignment explanation
Indices: 96228--96264 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
96218 GTCAAAGAAA
96228 GTCAACG
1 GTCAACG
96235 GTCAACG
1 GTCAACG
96242 GTC-ACG
1 GTCAACG
96248 GTCAACG
1 GTCAACG
96255 GTCAACG
1 GTCAACG
96262 GTC
1 GTC
96265 GGGTCAACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:96250 original size:13 final size:14
Alignment explanation
Indices: 96228--96264 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
96218 GTCAAAGAAA
96228 GTCAACGGTCAACG
1 GTCAACGGTCAACG
96242 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
96255 GTCAACGGTC
1 GTCAACGGTC
96265 GGGTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:96303 original size:10 final size:10
Alignment explanation
Indices: 96285--96334 Score: 59
Period size: 10 Copynumber: 5.2 Consensus size: 10
96275 TCGGGTTGGG
*
96285 TCAGCCCGGT
1 TCAGACCGGT
96295 TCAGACCGG-
1 TCAGACCGGT
*
96304 TCAAACCGGT
1 TCAGACCGGT
96314 TCAGACCGG-
1 TCAGACCGGT
*
96323 TCAAACCGGT
1 TCAGACCGGT
96333 TC
1 TC
96335 GAACCGGTCA
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
9 16 0.47
10 18 0.53
ACGTcount: A:0.22, C:0.34, G:0.26, T:0.18
Consensus pattern (10 bp):
TCAGACCGGT
Found at i:96312 original size:19 final size:19
Alignment explanation
Indices: 96290--96372 Score: 114
Period size: 19 Copynumber: 4.3 Consensus size: 19
96280 TTGGGTCAGC
96290 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAGACCGGTCAAA
96309 CCGGTTCAGACCGGTCAAA
1 CCGGTTCAGACCGGTCAAA
96328 CCGGTTC-GAACCGGTCAAA
1 CCGGTTCAG-ACCGGTCAAA
* * *
96347 TCGGTTCAAAACTGGTCAAA
1 CCGGTTC-AGACCGGTCAAA
96367 CCGGTT
1 CCGGTT
96373 TTCCAGCAGC
Statistics
Matches: 57, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
18 1 0.02
19 42 0.74
20 14 0.25
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (19 bp):
CCGGTTCAGACCGGTCAAA
Found at i:96356 original size:10 final size:10
Alignment explanation
Indices: 96290--96372 Score: 84
Period size: 9 Copynumber: 8.6 Consensus size: 10
96280 TTGGGTCAGC
*
96290 CCGGTTCAGA
1 CCGGTTCAAA
96300 CCGG-TCAAA
1 CCGGTTCAAA
*
96309 CCGGTTCAGA
1 CCGGTTCAAA
96319 CCGG-TCAAA
1 CCGGTTCAAA
*
96328 CCGGTTCGAA
1 CCGGTTCAAA
96338 CCGG-TCAAA
1 CCGGTTCAAA
*
96347 TCGGTTCAAAA
1 CCGGTTC-AAA
*
96358 CTGG-TCAAA
1 CCGGTTCAAA
96367 CCGGTT
1 CCGGTT
96373 TTCCAGCAGC
Statistics
Matches: 59, Mismatches: 9, Indels: 10
0.76 0.12 0.13
Matches are distributed among these distances:
9 29 0.49
10 25 0.42
11 5 0.08
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (10 bp):
CCGGTTCAAA
Found at i:103552 original size:7 final size:7
Alignment explanation
Indices: 103540--103576 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
103530 GTCAAAGATA
103540 GTCAACG
1 GTCAACG
103547 GTCAACG
1 GTCAACG
103554 GTC-ACG
1 GTCAACG
103560 GTCAACG
1 GTCAACG
103567 GTCAACG
1 GTCAACG
103574 GTC
1 GTC
103577 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:103562 original size:13 final size:14
Alignment explanation
Indices: 103540--103576 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
103530 GTCAAAGATA
103540 GTCAACGGTCAACG
1 GTCAACGGTCAACG
103554 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
103567 GTCAACGGTC
1 GTCAACGGTC
103577 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:103588 original size:17 final size:17
Alignment explanation
Indices: 103566--103606 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
103556 CACGGTCAAC
*
103566 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
103583 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
103600 GGTCAAC
1 GGTCAAC
103607 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:103634 original size:10 final size:10
Alignment explanation
Indices: 103602--103651 Score: 50
Period size: 9 Copynumber: 5.1 Consensus size: 10
103592 TCGGGTCGGG
*
103602 TCAACCCGGT
1 TCAAACCGGT
*
103612 TCAGACCGG-
1 TCAAACCGGT
103621 TCAAACCGGT
1 TCAAACCGGT
*
103631 TCAAAACTGG-
1 TC-AAACCGGT
103641 TCAAACCGGT
1 TCAAACCGGT
103651 T
1 T
103652 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
9 14 0.44
10 12 0.38
11 6 0.19
ACGTcount: A:0.28, C:0.30, G:0.22, T:0.20
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:103642 original size:20 final size:19
Alignment explanation
Indices: 103600--103651 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
103590 AGTCGGGTCG
* *
103600 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAAACC
*
103619 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AAACC
103639 GGTCAAACCGGTT
1 GGTCAAACCGGTT
103652 TTCCAGCAGC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.27, C:0.29, G:0.25, T:0.19
Consensus pattern (19 bp):
GGTCAAACCGGTTCAAACC
Found at i:105135 original size:2 final size:2
Alignment explanation
Indices: 105128--105188 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
105118 ATTCAGAAAG
105128 TA TA TA TA TA TA TA TA 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 TA TA TA TA TA
105170 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
105189 GACTAATGCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:113238 original size:30 final size:29
Alignment explanation
Indices: 113203--113280 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 29
113193 GCTTTTAGTT
*
113203 AAAGACGCATTGTCTTCCGGCGACTTTTCC
1 AAAGACGCATTGTGTTCCGGCGAC-TTTCC
* * *
113233 GAAGACACACTGTGTTCTCGGCGACTTTCC
1 AAAGACGCATTGTGTTC-CGGCGACTTTCC
113263 AAAGACGCATTGTGTTCC
1 AAAGACGCATTGTGTTCC
113281 CAACGACTTC
Statistics
Matches: 40, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
29 1 0.03
30 32 0.80
31 7 0.17
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (29 bp):
AAAGACGCATTGTGTTCCGGCGACTTTCC
Found at i:114535 original size:21 final size:21
Alignment explanation
Indices: 114498--114541 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
114488 ACTTTCTTAG
*
114498 CATTATCATATATATTATTAT
1 CATTATCATATATATTATCAT
*
114519 CATTATC-TCTATCATTATCAT
1 CATTATCATATAT-ATTATCAT
114540 CA
1 CA
114542 AATTATTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.34, C:0.18, G:0.00, T:0.48
Consensus pattern (21 bp):
CATTATCATATATATTATCAT
Found at i:114816 original size:21 final size:21
Alignment explanation
Indices: 114790--114856 Score: 134
Period size: 21 Copynumber: 3.2 Consensus size: 21
114780 ATAATGTCCA
114790 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
114811 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
114832 TAAGGACCACATATCATTCCT
1 TAAGGACCACATATCATTCCT
114853 TAAG
1 TAAG
114857 AATCATATAC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.34, C:0.27, G:0.10, T:0.28
Consensus pattern (21 bp):
TAAGGACCACATATCATTCCT
Found at i:120123 original size:18 final size:18
Alignment explanation
Indices: 120100--120135 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
120090 GACTATTCTG
120100 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
120118 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
120136 TCACGAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (18 bp):
GTTGATCATTGTCCACTC
Found at i:122918 original size:30 final size:28
Alignment explanation
Indices: 122856--122931 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 28
122846 TACTGCAAAG
122856 GGTGTTAGATCGGGAAATATAGTCTTACC
1 GGTGTTAGATCGGGAAATATAGTC-TACC
*
122885 GGTGTTAGATCGGTAAATATACCGATC-ACC
1 GGTGTTAGATCGGGAAATATA--G-TCTACC
* *
122915 GGTGATATATCGGGAAA
1 GGTGTTAGATCGGGAAA
122932 ATCACCAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 20 0.50
30 17 0.43
31 1 0.03
32 2 0.05
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (28 bp):
GGTGTTAGATCGGGAAATATAGTCTACC
Found at i:125780 original size:18 final size:18
Alignment explanation
Indices: 125757--125792 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
125747 GACTATTCTG
125757 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
125775 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
125793 TCACGAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (18 bp):
GTTGATCATTGTCCACTC
Found at i:126473 original size:2 final size:2
Alignment explanation
Indices: 126468--126514 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
126458 ACACACACAC
126468 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
126510 AT AT A
1 AT AT A
126515 CACACAGAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:127115 original size:2 final size:2
Alignment explanation
Indices: 127110--127145 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
127100 AATAAAAATA
127110 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
127146 TTAAAAAGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:128122 original size:21 final size:22
Alignment explanation
Indices: 128091--128136 Score: 85
Period size: 21 Copynumber: 2.1 Consensus size: 22
128081 TTATTTCATG
128091 TTAATTTACTATTTAAAAATTA
1 TTAATTTACTATTTAAAAATTA
128113 TTAA-TTACTATTTAAAAATTA
1 TTAATTTACTATTTAAAAATTA
128134 TTA
1 TTA
128137 CACATATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (22 bp):
TTAATTTACTATTTAAAAATTA
Found at i:128144 original size:20 final size:21
Alignment explanation
Indices: 128098--128148 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
128088 ATGTTAATTT
*
128098 ACTATTTAAAAATTATTAATT
1 ACTATTTAAAAATTATTAATC
128119 ACTATTTAAAAATTATT-A-C
1 ACTATTTAAAAATTATTAATC
128138 ACATATTTAAA
1 AC-TATTTAAA
128149 TAATAATTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 2 0.07
20 9 0.32
21 17 0.61
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (21 bp):
ACTATTTAAAAATTATTAATC
Found at i:128223 original size:23 final size:23
Alignment explanation
Indices: 128177--128223 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
128167 TATATTTTTA
*
128177 TTAATATTATATTTATAATGTAT
1 TTAATATTATATTTATAATATAT
128200 TTAATATTATATTT-TAAATATAT
1 TTAATATTATATTTAT-AATATAT
128223 T
1 T
128224 GTTTTAATGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 1 0.05
23 21 0.95
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (23 bp):
TTAATATTATATTTATAATATAT
Found at i:129347 original size:134 final size:134
Alignment explanation
Indices: 129183--129449 Score: 507
Period size: 134 Copynumber: 2.0 Consensus size: 134
129173 GATTCAGCTC
129183 GTGTTCTGTCCAAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
1 GTGTTCTGTCCAAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
129248 TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCAGGTTTTCACTCTGTCTCCTCTTTGAACGA
66 TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCAGGTTTTCACTCTGTCTCCTCTTTGAACGA
129313 TTTT
131 TTTT
* *
129317 GTGTTCTGTTCGAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
1 GTGTTCTGTCCAAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
*
129382 TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCGGGTTTTCACTCTGTCTCCTCTTTGAACGA
66 TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCAGGTTTTCACTCTGTCTCCTCTTTGAACGA
129447 TTT
131 TTT
129450 ATTTGGCTTG
Statistics
Matches: 130, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
134 130 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (134 bp):
GTGTTCTGTCCAAGTAAAGCAAAGATTCCGTTCGTGGTGGCAGAATTGGAGGAAAGCAAAGCATG
TCTGCTTTCTTGTTCTCAGATGCTACATAACGGCCAGGTTTTCACTCTGTCTCCTCTTTGAACGA
TTTT
Found at i:136172 original size:24 final size:24
Alignment explanation
Indices: 136140--136189 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
136130 TTAGAATAGC
136140 TAATATTTTGCATTGTTAACCATG
1 TAATATTTTGCATTGTTAACCATG
136164 TAATATTTTGCATTGTTAACCATG
1 TAATATTTTGCATTGTTAACCATG
136188 TA
1 TA
136190 TAATATAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.46
Consensus pattern (24 bp):
TAATATTTTGCATTGTTAACCATG
Found at i:139585 original size:53 final size:53
Alignment explanation
Indices: 139514--139623 Score: 220
Period size: 53 Copynumber: 2.1 Consensus size: 53
139504 ATTTCTGCAC
139514 TTGTCTCTCCTCCGCCGCAGAGCTTCTTCCTTGTCTTTATTCTTAATTTATAG
1 TTGTCTCTCCTCCGCCGCAGAGCTTCTTCCTTGTCTTTATTCTTAATTTATAG
139567 TTGTCTCTCCTCCGCCGCAGAGCTTCTTCCTTGTCTTTATTCTTAATTTATAG
1 TTGTCTCTCCTCCGCCGCAGAGCTTCTTCCTTGTCTTTATTCTTAATTTATAG
139620 TTGT
1 TTGT
139624 TTCATGGGTA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.13, C:0.27, G:0.14, T:0.46
Consensus pattern (53 bp):
TTGTCTCTCCTCCGCCGCAGAGCTTCTTCCTTGTCTTTATTCTTAATTTATAG
Found at i:141353 original size:18 final size:18
Alignment explanation
Indices: 141330--141365 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
141320 TGGACTATTG
141330 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
141348 GTTGATCATTGTCCACTC
1 GTTGATCATTGTCCACTC
141366 TCACGAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.28, G:0.17, T:0.39
Consensus pattern (18 bp):
GTTGATCATTGTCCACTC
Found at i:142042 original size:2 final size:2
Alignment explanation
Indices: 142030--142063 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
142020 ACTCCGATAC
142030 AT AT CAT AT 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 AT AT AT AT A
142064 CAGAGAGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.