Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008756.1 Hibiscus syriacus cultivar Beakdansim tig00111848_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: 4584045
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 21 of 21
Found at i:4457181 original size:20 final size:20
Alignment explanation
Indices: 4457156--4457209 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
4457146 GATTTTGTAT
4457156 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
4457176 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
4457196 TATCGCATTGCGAT
1 TATCGCATTGCGAT
4457210 TTTCCCAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:4457198 original size:61 final size:61
Alignment explanation
Indices: 4457096--4457212 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
4457086 CGCTATGTAA
* * * * * *
4457096 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTATT
* * *
4457157 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTAAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT
4457213 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTGTATT
Found at i:4457228 original size:61 final size:61
Alignment explanation
Indices: 4457096--4457230 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
4457086 CGCTATGTAA
* * * * * * ** *
4457096 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTCCAAT
* * *
4457157 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTT-CCAAT
4457219 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
4457231 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:4457341 original size:21 final size:21
Alignment explanation
Indices: 4457280--4457333 Score: 108
Period size: 21 Copynumber: 2.6 Consensus size: 21
4457270 ACTGTATACC
4457280 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
4457301 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGATTTCCAACT
4457322 ATCGCAACGCGA
1 ATCGCAACGCGA
4457334 AATGCAACGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.30, C:0.33, G:0.17, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATTTCCAACT
Found at i:4459070 original size:15 final size:15
Alignment explanation
Indices: 4459050--4459079 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
4459040 AATTTACATT
4459050 GAAACAGAGCAACCA
1 GAAACAGAGCAACCA
4459065 GAAACAGAGCAACCA
1 GAAACAGAGCAACCA
4459080 TCTTCATTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.27, G:0.20, T:0.00
Consensus pattern (15 bp):
GAAACAGAGCAACCA
Found at i:4465052 original size:19 final size:19
Alignment explanation
Indices: 4465028--4465064 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
4465018 CTTGATTCGA
4465028 TATAAATTATTAATTTAAG
1 TATAAATTATTAATTTAAG
4465047 TATAAATTATTAATTTAA
1 TATAAATTATTAATTTAA
4465065 CCTTTTATAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (19 bp):
TATAAATTATTAATTTAAG
Found at i:4465161 original size:22 final size:19
Alignment explanation
Indices: 4465135--4465189 Score: 101
Period size: 19 Copynumber: 2.8 Consensus size: 19
4465125 TATATTATAT
4465135 AATTATTAAAAATATAATA
1 AATTATTAAAAATATAATA
4465154 AATTATTAAAAATATAATA
1 AATTATTAAAAATATAATA
4465173 AATTATTATAAAATATA
1 AATTATTA-AAAATATA
4465190 TTATTTTAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 27 0.77
20 8 0.23
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
AATTATTAAAAATATAATA
Found at i:4474053 original size:22 final size:22
Alignment explanation
Indices: 4474026--4474071 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
4474016 ATGAATGACA
*
4474026 ACAATTCAATCGAATGAGGAAG
1 ACAATTCAATCGAAGGAGGAAG
* *
4474048 ACAATTTAATCGTAGGAGGAAG
1 ACAATTCAATCGAAGGAGGAAG
4474070 AC
1 AC
4474072 GAAACAGAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.20
Consensus pattern (22 bp):
ACAATTCAATCGAAGGAGGAAG
Found at i:4485042 original size:61 final size:62
Alignment explanation
Indices: 4484946--4485069 Score: 241
Period size: 61 Copynumber: 2.0 Consensus size: 62
4484936 TCTTCATTGG
4484946 ATCGCTCGCTCAAAAGGCCCAAAAGGGTAACCGGACTTGACCGGGGAAGGTATGTTCAGTCA
1 ATCGCTCGCTCAAAAGGCCCAAAAGGGTAACCGGACTTGACCGGGGAAGGTATGTTCAGTCA
4485008 ATCGCTCGCTCAAAA-GCCCAAAAGGGTAACCGGACTTGACCGGGGAAGGTATGTTCAGTCA
1 ATCGCTCGCTCAAAAGGCCCAAAAGGGTAACCGGACTTGACCGGGGAAGGTATGTTCAGTCA
4485069 A
1 A
4485070 ATGAGTCGAC
Statistics
Matches: 62, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
61 47 0.76
62 15 0.24
ACGTcount: A:0.30, C:0.24, G:0.28, T:0.18
Consensus pattern (62 bp):
ATCGCTCGCTCAAAAGGCCCAAAAGGGTAACCGGACTTGACCGGGGAAGGTATGTTCAGTCA
Found at i:4487572 original size:11 final size:11
Alignment explanation
Indices: 4487556--4487581 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4487546 GGAGATTTTC
4487556 TTTTGATACCG
1 TTTTGATACCG
4487567 TTTTGATACCG
1 TTTTGATACCG
4487578 TTTT
1 TTTT
4487582 CTGGACCGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.54
Consensus pattern (11 bp):
TTTTGATACCG
Found at i:4492695 original size:21 final size:21
Alignment explanation
Indices: 4492669--4492713 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
4492659 TGTATTTACC
4492669 ATAGATTTGTCAAAAAAATCA
1 ATAGATTTGTCAAAAAAATCA
4492690 ATAGATTTGTCAAAAAAATCA
1 ATAGATTTGTCAAAAAAATCA
4492711 ATA
1 ATA
4492714 ATTAGTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (21 bp):
ATAGATTTGTCAAAAAAATCA
Found at i:4495274 original size:21 final size:21
Alignment explanation
Indices: 4495248--4495288 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
4495238 TTCTCTGTTG
4495248 TTTTTTTTTTCTGTCTCTCTC
1 TTTTTTTTTTCTGTCTCTCTC
*
4495269 TTTTTTTTTTCTGTTTCTCT
1 TTTTTTTTTTCTGTCTCTCT
4495289 GTCCCGTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.00, C:0.20, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTTTTTTTTCTGTCTCTCTC
Found at i:4495764 original size:3 final size:3
Alignment explanation
Indices: 4495756--4495871 Score: 184
Period size: 3 Copynumber: 39.7 Consensus size: 3
4495746 TTAATATATT
*
4495756 TAA TAA TAA TAA TAA TAA TGA T-A TAA TAA T-A TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4495802 TAA TAG TAA TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4495849 TAA TAA TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
4495872 TGGATAAAAA
Statistics
Matches: 105, Mismatches: 5, Indels: 6
0.91 0.04 0.05
Matches are distributed among these distances:
2 6 0.06
3 99 0.94
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:4496407 original size:113 final size:113
Alignment explanation
Indices: 4496189--4496729 Score: 783
Period size: 113 Copynumber: 4.8 Consensus size: 113
4496179 ATAGAATTAT
* * * *
4496189 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTTCTTCTTCAGATGACGAGTTCTT
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAGTTCTT
* * * *
4496254 CTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAA
63 CTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAA
4496305 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
4496370 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAA
*
4496418 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* *
4496483 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGGATTCAG
66 ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAA
* *
4496531 GTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTTTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
* * *
4496596 ATTATGAACTTTCTCTGGCAAAA-ATAATCCATCAAGTGATGAATTC-A
66 ATTATGAACTTTCTCTGG-AAAAGCTGATCCATCAAATGATGAATTCAA
4496643 GACAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCC-T-TTCAGATGATGAGTTCT
1 G-CAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTC--A-GATGAGTTCT
4496706 TCTCATTATGAAC---CTCTGGAAAAG
62 TCTCATTATGAACTTTCTCTGGAAAAG
4496730 ATAATCTATC
Statistics
Matches: 400, Mismatches: 18, Indels: 19
0.92 0.04 0.04
Matches are distributed among these distances:
110 4 0.01
111 9 0.02
112 4 0.01
113 306 0.76
114 27 0.07
116 50 0.12
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
GCAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
ATTATGAACTTTCTCTGGAAAAGCTGATCCATCAAATGATGAATTCAA
Found at i:4497662 original size:84 final size:84
Alignment explanation
Indices: 4497492--4497804 Score: 583
Period size: 84 Copynumber: 3.7 Consensus size: 84
4497482 GTAATTTTTA
* * * *
4497492 CCAAACCAGATTAGATAACTCAAAGAACACTTTCAAAAGATGCTATTG-GCAAATTCATCTTCCA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
4497556 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
4497575 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
4497640 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
4497659 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
4497724 AATTCAATGATTGGTTCTG
66 AATTCAATGATTGGTTCTG
4497743 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTT
1 CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTT
4497805 TCAGTTAATG
Statistics
Matches: 225, Mismatches: 4, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
83 44 0.20
84 181 0.80
ACGTcount: A:0.38, C:0.21, G:0.14, T:0.27
Consensus pattern (84 bp):
CCAAATCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCAAATTCATCTTCCA
AATTCAATGATTGGTTCTG
Found at i:4498596 original size:19 final size:20
Alignment explanation
Indices: 4498572--4498613 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
4498562 AATAGAAAAG
*
4498572 AATAAATTGAATTTCCAA-A
1 AATAAATTGAATCTCCAATA
4498591 AATAAATTGAATCTCCAATA
1 AATAAATTGAATCTCCAATA
4498611 AAT
1 AAT
4498614 TGAACTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (20 bp):
AATAAATTGAATCTCCAATA
Found at i:4498962 original size:11 final size:10
Alignment explanation
Indices: 4498957--4499010 Score: 72
Period size: 11 Copynumber: 5.0 Consensus size: 10
4498947 CTTTTTCTCT
4498957 TTTTTTTTTC
1 TTTTTTTTTC
4498967 TTTTCTTTTTC
1 TTTT-TTTTTC
4498978 TTTTCTTTTTC
1 TTTT-TTTTTC
4498989 TTTTTTTTTTC
1 -TTTTTTTTTC
4499000 TTTTTTCTTTC
1 TTTTTT-TTTC
4499011 CTCTTCAAGC
Statistics
Matches: 41, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.24
11 27 0.66
12 4 0.10
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (10 bp):
TTTTTTTTTC
Found at i:4498981 original size:29 final size:30
Alignment explanation
Indices: 4498949--4499015 Score: 95
Period size: 29 Copynumber: 2.3 Consensus size: 30
4498939 GACCCCCCCT
4498949 TTTTCTCTTTT-TTTTTTCTTTTC-TTTTTC
1 TTTTCTCTTTTCTTTTTT-TTTTCTTTTTTC
4498978 TTTTCT-TTTTCTTTTTTTTTTCTTTTTTC
1 TTTTCTCTTTTCTTTTTTTTTTCTTTTTTC
*
4499007 TTTCCTCTT
1 TTTTCTCTT
4499016 CAAGCATAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
28 9 0.26
29 23 0.68
30 2 0.06
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (30 bp):
TTTTCTCTTTTCTTTTTTTTTTCTTTTTTC
Found at i:4498986 original size:22 final size:22
Alignment explanation
Indices: 4498949--4499003 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
4498939 GACCCCCCCT
*
4498949 TTTTCTCTTTTTTTTTTCTTTTC
1 TTTT-TCTTTTCTTTTTCTTTTC
*
4498972 TTTTTCTTTTCTTTTTCTTTTT
1 TTTTTCTTTTCTTTTTCTTTTC
4498994 TTTTTCTTTT
1 TTTTTCTTTT
4499004 TTCTTTCCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (22 bp):
TTTTTCTTTTCTTTTTCTTTTC
Found at i:4499010 original size:22 final size:21
Alignment explanation
Indices: 4498948--4499010 Score: 81
Period size: 22 Copynumber: 2.9 Consensus size: 21
4498938 TGACCCCCCC
*
4498948 TTTTTCTCTTTTTTTTTTCTTT
1 TTTTTTTC-TTTTTTTTTCTTT
*
4498970 TCTTTTTCTTTTCTTTTTCTTT
1 TTTTTTTCTTTT-TTTTTCTTT
4498992 TTTTTTTCTTTTTTCTTTC
1 TTTTTTTCTTTTTT-TTTC
4499011 CTCTTCAAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 6 0.17
22 30 0.83
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTTTTCTTTTTTTTTCTTT
Found at i:4511300 original size:20 final size:20
Alignment explanation
Indices: 4511275--4511313 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
4511265 TCTCTGTTGT
4511275 TTTTTTTTTCTGTCTCTCTC
1 TTTTTTTTTCTGTCTCTCTC
*
4511295 TTTTTTTTTCTGTTTCTCT
1 TTTTTTTTTCTGTCTCTCT
4511314 GTCCGTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.05, T:0.74
Consensus pattern (20 bp):
TTTTTTTTTCTGTCTCTCTC
Found at i:4511793 original size:3 final size:3
Alignment explanation
Indices: 4511785--4511896 Score: 172
Period size: 3 Copynumber: 37.7 Consensus size: 3
4511775 AATATATATT
*
4511785 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* * *
4511833 TAA TAA TAG T-A TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAT TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
4511880 TAT TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
4511897 TGGATAAAAA
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
2 1 0.01
3 97 0.99
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:4514406 original size:18 final size:18
Alignment explanation
Indices: 4514383--4514418 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
4514373 TGAGGGCACA
*
4514383 TGTACTTATCTTGAAATT
1 TGTACTTATCTTAAAATT
*
4514401 TGTACTTGTCTTAAAATT
1 TGTACTTATCTTAAAATT
4514419 CAAATTTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (18 bp):
TGTACTTATCTTAAAATT
Found at i:4516928 original size:42 final size:42
Alignment explanation
Indices: 4516877--4517102 Score: 362
Period size: 42 Copynumber: 5.3 Consensus size: 42
4516867 CATATTCACA
4516877 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* * *
4516919 TTGCGATAGTCGAAGTTCGTGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
* *
4516961 TTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
4517005 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
4517047 TTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
*
4517089 TTGCAATAGTCCAA
1 TTGCGATAGTCCAA
4517103 AATCGCAACG
Statistics
Matches: 170, Mismatches: 12, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
42 131 0.77
44 39 0.23
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
Found at i:4516981 original size:86 final size:84
Alignment explanation
Indices: 4516877--4517099 Score: 374
Period size: 86 Copynumber: 2.6 Consensus size: 84
4516867 CATATTCACA
*
4516877 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGTGTT
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
4516942 GCGATTTATTCCAAATTCG
66 GCGATTTATTCCAAATTCG
* *
4516961 TTGCGATTTATTCCAAGTTCGCGTTGCGATTTATTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 TTGCGA--TAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
*
4517026 TTGCGATTTATTCCAAGTTCG
64 TTGCGATTTATTCCAAATTCG
* *
4517047 TTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCAATAGTC
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTC
4517100 CAAAATCGCA
Statistics
Matches: 129, Mismatches: 8, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
84 49 0.38
86 80 0.62
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.37
Consensus pattern (84 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTT
GCGATTTATTCCAAATTCG
Found at i:4517850 original size:20 final size:20
Alignment explanation
Indices: 4517825--4517870 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
4517815 ACTATCGCAA
*
4517825 TGCGATTTATATATTTGCAT
1 TGCGATTTACATATTTGCAT
4517845 TGCGATTTACATATTTGCAT
1 TGCGATTTACATATTTGCAT
*
4517865 TTCGAT
1 TGCGAT
4517871 AGTCCAAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (20 bp):
TGCGATTTACATATTTGCAT
Found at i:4517885 original size:21 final size:21
Alignment explanation
Indices: 4517861--4517932 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
4517851 TTACATATTT
*
4517861 GCATTTCGATAGTCCAAGTTC
1 GCATTGCGATAGTCCAAGTTC
4517882 GCATTGCGATAGTCCAAGTTC
1 GCATTGCGATAGTCCAAGTTC
* *
4517903 GCGTTGCGATAGTCGAAGTTC
1 GCATTGCGATAGTCCAAGTTC
*
4517924 GCGTTGCGA
1 GCATTGCGA
4517933 ATCTGGAAAC
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.21, C:0.22, G:0.28, T:0.29
Consensus pattern (21 bp):
GCATTGCGATAGTCCAAGTTC
Found at i:4519299 original size:2 final size:2
Alignment explanation
Indices: 4519294--4519322 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4519284 AAAAAAATCT
4519294 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
4519323 TAAATGACCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4520490 original size:18 final size:16
Alignment explanation
Indices: 4520449--4520479 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
4520439 TAATTTATTG
4520449 ATAATATTTTTAAAAT
1 ATAATATTTTTAAAAT
4520465 ATAATATTTTTAAAA
1 ATAATATTTTTAAAA
4520480 ATGTTAATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATTTTTAAAAT
Found at i:4524884 original size:66 final size:66
Alignment explanation
Indices: 4524778--4524911 Score: 268
Period size: 66 Copynumber: 2.0 Consensus size: 66
4524768 TGCACAACGG
4524778 TTCATTAAGTTTTTAACGGAGGGGAAATTAAAGTTTTAAACAAATAATACTTAAATAATTTATAT
1 TTCATTAAGTTTTTAACGGAGGGGAAATTAAAGTTTTAAACAAATAATACTTAAATAATTTATAT
4524843 A
66 A
4524844 TTCATTAAGTTTTTAACGGAGGGGAAATTAAAGTTTTAAACAAATAATACTTAAATAATTTATAT
1 TTCATTAAGTTTTTAACGGAGGGGAAATTAAAGTTTTAAACAAATAATACTTAAATAATTTATAT
4524909 A
66 A
4524910 TT
1 TT
4524912 TATAAAGTGT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 68 1.00
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (66 bp):
TTCATTAAGTTTTTAACGGAGGGGAAATTAAAGTTTTAAACAAATAATACTTAAATAATTTATAT
A
Found at i:4528116 original size:24 final size:25
Alignment explanation
Indices: 4528059--4528126 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 25
4528049 AATGTAATCC
4528059 TTGAATTATTTTTTAATAATTTAATTT
1 TTGAA-TA-TTTTTAATAATTTAATTT
4528086 TAT-AATATTTTT-AT-ATTTAATTT
1 T-TGAATATTTTTAATAATTTAATTT
*
4528109 ATTGAATA-TCTTAATAAT
1 -TTGAATATTTTTAATAAT
4528127 CATTTATATT
Statistics
Matches: 35, Mismatches: 1, Indels: 12
0.73 0.02 0.25
Matches are distributed among these distances:
23 13 0.37
24 9 0.26
25 7 0.20
26 2 0.06
27 3 0.09
28 1 0.03
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (25 bp):
TTGAATATTTTTAATAATTTAATTT
Found at i:4539608 original size:19 final size:18
Alignment explanation
Indices: 4539586--4539646 Score: 56
Period size: 18 Copynumber: 3.4 Consensus size: 18
4539576 TGAAATATGA
4539586 ATATATTATTTATAAATGT
1 ATATATTATTTATAAAT-T
*
4539605 ATAT-TTGATTAAATAAA-T
1 ATATATT-ATT-TATAAATT
*
4539623 ATATATTATTTATGAATT
1 ATATATTATTTATAAATT
4539641 -TATATT
1 ATATATT
4539647 CAATTAAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
17 10 0.29
18 11 0.31
19 9 0.26
20 5 0.14
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (18 bp):
ATATATTATTTATAAATT
Found at i:4539609 original size:17 final size:17
Alignment explanation
Indices: 4539586--4539646 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
4539576 TGAAATATGA
4539586 ATATATTATTTATAAAT
1 ATATATTATTTATAAAT
* *
4539603 GTATATTTGATTAAATAAAT
1 ATATA-TT-ATT-TATAAAT
*
4539623 ATATATTATTTATGAAT
1 ATATATTATTTATAAAT
*
4539640 TTATATT
1 ATATATT
4539647 CAATTAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
17 15 0.43
18 5 0.14
19 5 0.14
20 10 0.29
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (17 bp):
ATATATTATTTATAAAT
Found at i:4539628 original size:37 final size:37
Alignment explanation
Indices: 4539549--4539667 Score: 127
Period size: 37 Copynumber: 3.2 Consensus size: 37
4539539 ATTTAATGTG
* *
4539549 AATATATTA-TTACAAATTATATTCGATTGAAATATG
1 AATATATTATTTATAAATTATATTCGATTGAAATATA
*
4539585 AATATATTATTTATAAATGTATATTTGATT-AAATA-A
1 AATATATTATTTATAAAT-TATATTCGATTGAAATATA
* * * *
4539621 ATATATATTATTTATGAATTTATATTCAATTAAAATACA
1 A-ATATATTATTTAT-AAATTATATTCGATTGAAATATA
4539660 AATATATT
1 AATATATT
4539668 GTTACAAGTT
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
36 10 0.14
37 34 0.48
38 25 0.35
39 2 0.03
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.45
Consensus pattern (37 bp):
AATATATTATTTATAAATTATATTCGATTGAAATATA
Found at i:4553254 original size:16 final size:17
Alignment explanation
Indices: 4553233--4553278 Score: 51
Period size: 16 Copynumber: 2.7 Consensus size: 17
4553223 ATTTATTTAC
4553233 TTTTTAAATATT-AAAT
1 TTTTTAAATATTGAAAT
*
4553249 TTTTTAAACT-TTGAGAT
1 TTTTTAAA-TATTGAAAT
4553266 TATTTTAAATATT
1 T-TTTTAAATATT
4553279 TAAAAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
16 10 0.40
17 6 0.24
18 9 0.36
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (17 bp):
TTTTTAAATATTGAAAT
Found at i:4563170 original size:14 final size:14
Alignment explanation
Indices: 4563151--4563178 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4563141 TCAAAATAAA
4563151 TATACAATTTACGT
1 TATACAATTTACGT
4563165 TATACAATTTACGT
1 TATACAATTTACGT
4563179 GATCGGTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.14, G:0.07, T:0.43
Consensus pattern (14 bp):
TATACAATTTACGT
Found at i:4565260 original size:2 final size:2
Alignment explanation
Indices: 4565253--4565286 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
4565243 CAAATAAAGA
4565253 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
4565287 TCACTTTTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4567732 original size:23 final size:23
Alignment explanation
Indices: 4567677--4567733 Score: 78
Period size: 23 Copynumber: 2.5 Consensus size: 23
4567667 CTCATATAAA
*
4567677 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
4567700 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
*
4567723 TGCACTGTAGT
1 TGCACCGTAGT
4567734 ACCATATAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.26, C:0.25, G:0.26, T:0.23
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:4567924 original size:103 final size:103
Alignment explanation
Indices: 4567753--4568073 Score: 597
Period size: 103 Copynumber: 3.1 Consensus size: 103
4567743 TAATGTCCAA
* * *
4567753 AAGGACTACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
4567818 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
4567856 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
4567921 GACTTCAAACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
4567959 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
4568024 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
4568062 AAGGACCACATA
1 AAGGACCACATA
4568074 GACCCTCGAC
Statistics
Matches: 211, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 211 1.00
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:4573046 original size:23 final size:23
Alignment explanation
Indices: 4573020--4573080 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
4573010 CTCATATAAA
*
4573020 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGTAGTGCCACATAGAAT
* *
4573043 TGCACCGTAGTGCCGCGTAGAAT
1 TGCACCGTAGTGCCACATAGAAT
4573066 TGCACCGTAGTGCCA
1 TGCACCGTAGTGCCA
4573081 TATAATAATG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.26, C:0.28, G:0.26, T:0.20
Consensus pattern (23 bp):
TGCACCGTAGTGCCACATAGAAT
Found at i:4577995 original size:23 final size:23
Alignment explanation
Indices: 4577969--4578029 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
4577959 CTCATATAAA
4577969 TGCACCGAAGTGCCACATAGAAT
1 TGCACCGAAGTGCCACATAGAAT
* *
4577992 TGCACC-ATAGTGCCGCGTAGAAT
1 TGCACCGA-AGTGCCACATAGAAT
*
4578015 TGCACCGTAGTGCCA
1 TGCACCGAAGTGCCA
4578030 TATAATAATG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.28, C:0.28, G:0.25, T:0.20
Consensus pattern (23 bp):
TGCACCGAAGTGCCACATAGAAT
Found at i:4578160 original size:21 final size:20
Alignment explanation
Indices: 4578120--4578160 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
4578110 GACTTCACAC
*
4578120 ATGTTCCAAAGAATACATAT
1 ATGTTCCAAAGAACACATAT
*
4578140 ATGTTCCAAAGGACCACATAT
1 ATGTTCCAAA-GAACACATAT
4578161 CATTCCTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (20 bp):
ATGTTCCAAAGAACACATAT
Found at i:4578366 original size:103 final size:102
Alignment explanation
Indices: 4578052--4578369 Score: 510
Period size: 103 Copynumber: 3.0 Consensus size: 102
4578042 AAAAAGGACT
* *
4578052 ACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
* *
4578117 CACATGTTCCAAAGAATACATATATGTTCCAAAGGACC
66 CACATGTTCCAAAGAATACATATATGTCCCGAA-GACC
*
4578155 ACATATCATTCCTTAAGAATCATATACATATATATGCCAATGATCAAGTATGTGTCTCACCAGAC
1 ACATATCATTCCTTAAGAATCATATAC--ATATA--CCAAGGATCAAGTATGTGTCTCACCAGAC
* *
4578220 TTCAAACATGTTCCAAAGAATACATATATGTCCTGAATGACC
62 TTCACACATGTTCCAAAGAATACATATATGTCCCGAA-GACC
4578262 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
1 ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
4578327 CACATGTTCCAAAGAATACATATATGTCCCGAAGAACC
66 CACATGTTCCAAAGAATACATATATGTCCCGAAG-ACC
4578365 ACATA
1 ACATA
4578370 GACCCTCGAC
Statistics
Matches: 199, Mismatches: 11, Indels: 10
0.90 0.05 0.05
Matches are distributed among these distances:
102 1 0.01
103 98 0.49
105 10 0.05
107 90 0.45
ACGTcount: A:0.38, C:0.23, G:0.12, T:0.28
Consensus pattern (102 bp):
ACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACTTCA
CACATGTTCCAAAGAATACATATATGTCCCGAAGACC
Done.