Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004724.1 Hibiscus syriacus cultivar Beakdansim tig00010651_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: 76372
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1860 original size:18 final size:18
Alignment explanation
Indices: 1837--1889 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
1827 GTTCTTAAGG
1837 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
1855 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCGGGACAT
*
1873 AGTGGTCCTACGGGACA
1 AGTGGTCCTTCGGGACA
1890 AATTCTATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.19, C:0.23, G:0.34, T:0.25
Consensus pattern (18 bp):
AGTGGTCCTTCGGGACAT
Found at i:3611 original size:18 final size:17
Alignment explanation
Indices: 3588--3621 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
3578 ACATGGGCAT
3588 TATCATTTGTTCATTTCA
1 TATCATTTGTTC-TTTCA
3606 TATCATTTGTTCTTTC
1 TATCATTTGTTCTTTC
3622 TCTTCTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.18, C:0.18, G:0.06, T:0.59
Consensus pattern (17 bp):
TATCATTTGTTCTTTCA
Found at i:3798 original size:2 final size:2
Alignment explanation
Indices: 3791--3832 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3781 ACATATGTTC
3791 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
3833 GTCACATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9171 original size:17 final size:17
Alignment explanation
Indices: 9126--9198 Score: 62
Period size: 18 Copynumber: 4.2 Consensus size: 17
9116 TACATATATA
*
9126 ATTATCTTATTACTTATC
1 ATTATCATATTA-TTATC
*
9144 ATTATCCTATTATTATC
1 ATTATCATATTATTATC
9161 ATTAAT-ATATT-TTATC
1 ATT-ATCATATTATTATC
9177 ATATTATCATA-TACTTATC
1 --ATTATCATATTA-TTATC
9196 ATT
1 ATT
9199 TATACCCATC
Statistics
Matches: 47, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
16 5 0.11
17 18 0.38
18 19 0.40
19 5 0.11
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTATCATATTATTATC
Found at i:9514 original size:21 final size:21
Alignment explanation
Indices: 9461--9517 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
9451 CATATGAAAT
*
9461 TTGTCCTGAACGACCACTGAA
1 TTGTCCTGAAGGACCACTGAA
*
9482 TTGTCCTGAAGGACCACTGTA
1 TTGTCCTGAAGGACCACTGAA
*
9503 TTGTCCTTAAGGACC
1 TTGTCCTGAAGGACC
9518 TATGAAACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (21 bp):
TTGTCCTGAAGGACCACTGAA
Found at i:9795 original size:2 final size:2
Alignment explanation
Indices: 9788--9817 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9778 ACATATGTTC
9788 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
9818 GTCACATATA
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:12991 original size:21 final size:22
Alignment explanation
Indices: 12967--13041 Score: 107
Period size: 23 Copynumber: 3.4 Consensus size: 22
12957 CACCAAAGTG
*
12967 CCACATA-TTTGTCCCGAATGA
1 CCACATAGTTTATCCCGAATGA
12988 CCACATAGTTTTATCCCGAATGA
1 CCACATAG-TTTATCCCGAATGA
*
13011 CCACATAGTTTTATCCCGAAGGA
1 CCACATAG-TTTATCCCGAATGA
13034 CCACATAG
1 CCACATAG
13042 AACCCTCGAC
Statistics
Matches: 50, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
21 7 0.14
23 43 0.86
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.27
Consensus pattern (22 bp):
CCACATAGTTTATCCCGAATGA
Found at i:13007 original size:23 final size:23
Alignment explanation
Indices: 12978--13041 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
12968 CACATATTTG
12978 TCCCGAATGACCACATAGTTTTA
1 TCCCGAATGACCACATAGTTTTA
13001 TCCCGAATGACCACATAGTTTTA
1 TCCCGAATGACCACATAGTTTTA
*
13024 TCCCGAAGGACCACATAG
1 TCCCGAATGACCACATAG
13042 AACCCTCGAC
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (23 bp):
TCCCGAATGACCACATAGTTTTA
Found at i:17996 original size:24 final size:24
Alignment explanation
Indices: 17969--18032 Score: 101
Period size: 24 Copynumber: 2.7 Consensus size: 24
17959 TTCTATTATA
*
17969 ATACCTGACCTGGATTCTGATCGG
1 ATACTTGACCTGGATTCTGATCGG
* *
17993 ATACTTGACCTGGATTTTGATCTG
1 ATACTTGACCTGGATTCTGATCGG
18017 ATACTTGACCTGGATT
1 ATACTTGACCTGGATT
18033 ATGTTTTGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (24 bp):
ATACTTGACCTGGATTCTGATCGG
Found at i:19687 original size:24 final size:24
Alignment explanation
Indices: 19660--19720 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
19650 CCGTTATAAT
* * *
19660 CTTGACATGGATTCTGGTCGGATA
1 CTTGACCTGGATTCTGATAGGATA
* *
19684 CTTGACCTGGATTTTGATATGATA
1 CTTGACCTGGATTCTGATAGGATA
19708 CTTGACCTGGATT
1 CTTGACCTGGATT
19721 ATGTTTTGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.21, C:0.16, G:0.25, T:0.38
Consensus pattern (24 bp):
CTTGACCTGGATTCTGATAGGATA
Found at i:21627 original size:25 final size:26
Alignment explanation
Indices: 21577--21626 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
21567 CTGGACACAT
21577 TTTATTGAAAATATTTTTTATTTTTA
1 TTTATTGAAAATATTTTTTATTTTTA
*
21603 TTTATT-AAACATGTTTTTTATTTT
1 TTTATTGAAA-ATATTTTTTATTTT
21627 AAAAATTGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 3 0.14
26 19 0.86
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (26 bp):
TTTATTGAAAATATTTTTTATTTTTA
Found at i:24416 original size:2 final size:2
Alignment explanation
Indices: 24409--24434 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
24399 AAATTAATAA
24409 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
24435 GGATTATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25608 original size:41 final size:43
Alignment explanation
Indices: 25537--25629 Score: 97
Period size: 41 Copynumber: 2.3 Consensus size: 43
25527 TTATATTGTC
* ** *
25537 AAAATATATT-CTTTAATTATTAAAATTATAA-AAA-ATATTTT
1 AAAATATATTAATTTAACAATTAAAATTATAATAAACA-ATTAT
*
25578 AAAATATATTAATTTAACAATTTAAA-TATAATAAACAATTAT
1 AAAATATATTAATTTAACAATTAAAATTATAATAAACAATTAT
25620 -AAATATATTA
1 AAAATATATTA
25630 TTATAAAATA
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
41 25 0.57
42 18 0.41
43 1 0.02
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (43 bp):
AAAATATATTAATTTAACAATTAAAATTATAATAAACAATTAT
Found at i:25632 original size:14 final size:15
Alignment explanation
Indices: 25615--25646 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
25605 ATAATAAACA
25615 ATTAT-AAATATATT
1 ATTATAAAATATATT
25629 ATTATAAAATATATT
1 ATTATAAAATATATT
25644 ATT
1 ATT
25647 TTAATTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:28404 original size:16 final size:16
Alignment explanation
Indices: 28383--28413 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
28373 TAATATTGAA
28383 ACTTGAACTCAAAAAG
1 ACTTGAACTCAAAAAG
28399 ACTTGAACTCAAAAA
1 ACTTGAACTCAAAAA
28414 AAAATTAGAA
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:0.19, G:0.10, T:0.19
Consensus pattern (16 bp):
ACTTGAACTCAAAAAG
Found at i:38794 original size:19 final size:19
Alignment explanation
Indices: 38770--38818 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
38760 CAACTAAATC
38770 GCAATGCGATCGATAATTT
1 GCAATGCGATCGATAATTT
38789 GCAATGCGATCGATAATTT
1 GCAATGCGATCGATAATTT
*
38808 GCAACGCGATC
1 GCAATGCGATC
38819 TCCGGTATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (19 bp):
GCAATGCGATCGATAATTT
Found at i:38936 original size:20 final size:20
Alignment explanation
Indices: 38911--39058 Score: 260
Period size: 20 Copynumber: 7.4 Consensus size: 20
38901 TCCTAATTCA
*
38911 CAATGCAAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
38931 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
38951 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
*
38971 CAATGCGAATACGTAAATCA
1 CAATGCGAATACGTAAATCG
38991 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
* *
39011 CAATGAGAATACGTAAATCA
1 CAATGCGAATACGTAAATCG
39031 CAATGCGAATACGTAAATCG
1 CAATGCGAATACGTAAATCG
39051 CAATGCGA
1 CAATGCGA
39059 TTTACATAGC
Statistics
Matches: 121, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 121 1.00
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.20
Consensus pattern (20 bp):
CAATGCGAATACGTAAATCG
Found at i:39263 original size:22 final size:22
Alignment explanation
Indices: 39238--39324 Score: 129
Period size: 22 Copynumber: 4.0 Consensus size: 22
39228 GCGACATCCA
39238 TCCCCATCTCCGACGAAATCAG
1 TCCCCATCTCCGACGAAATCAG
*
39260 TCCCCATCTCCGATGAAATCAG
1 TCCCCATCTCCGACGAAATCAG
*
39282 TCCCCATCTCCGACGATATCAG
1 TCCCCATCTCCGACGAAATCAG
* * *
39304 TCTCTATCTCCGGCGAAATCA
1 TCCCCATCTCCGACGAAATCA
39325 TTCACGGTCA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 58 1.00
ACGTcount: A:0.25, C:0.38, G:0.14, T:0.23
Consensus pattern (22 bp):
TCCCCATCTCCGACGAAATCAG
Found at i:39721 original size:20 final size:20
Alignment explanation
Indices: 39692--39741 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
39682 TGCGATTCTT
*
39692 GCGTTACGATAGTCAAATTC
1 GCGTTGCGATAGTCAAATTC
**
39712 GCGTTGCGATAGTCATTTTC
1 GCGTTGCGATAGTCAAATTC
*
39732 GTGTTGCGAT
1 GCGTTGCGAT
39742 TTTCATTTTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.26, T:0.36
Consensus pattern (20 bp):
GCGTTGCGATAGTCAAATTC
Found at i:39747 original size:20 final size:20
Alignment explanation
Indices: 39709--39764 Score: 85
Period size: 20 Copynumber: 2.8 Consensus size: 20
39699 GATAGTCAAA
* **
39709 TTCGCGTTGCGATAGTCATT
1 TTCGTGTTGCGATTTTCATT
39729 TTCGTGTTGCGATTTTCATT
1 TTCGTGTTGCGATTTTCATT
39749 TTCGTGTTGCGATTTT
1 TTCGTGTTGCGATTTT
39765 AAGTTTCAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.50
Consensus pattern (20 bp):
TTCGTGTTGCGATTTTCATT
Found at i:39771 original size:20 final size:20
Alignment explanation
Indices: 39728--39771 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
39718 CGATAGTCAT
* *
39728 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTTAAG
39748 TTTCGTGTTGCGATTTTAAG
1 TTTCGTGTTGCGATTTTAAG
39768 TTTC
1 TTTC
39772 AGAAACTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.14, G:0.20, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTTAAG
Found at i:41683 original size:20 final size:20
Alignment explanation
Indices: 41658--41709 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
41648 AGAATAGTTT
* *
41658 ACTATCACAATGCGAAAATG
1 ACTATCGCAATGCGAAAATA
*
41678 ACTATCGCAACGCGAAAATA
1 ACTATCGCAATGCGAAAATA
41698 ACTATCGCAATG
1 ACTATCGCAATG
41710 AGAGAATCGC
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATA
Found at i:41773 original size:20 final size:20
Alignment explanation
Indices: 41748--41816 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
41738 CAACAACAAA
41748 ATCGCAACGCAAAAATGACT
1 ATCGCAACGCAAAAATGACT
*
41768 ATCGCAATGCAAAAATGACT
1 ATCGCAACGCAAAAATGACT
* * **
41788 ATCGCAATGCGAATTTGACT
1 ATCGCAACGCAAAAATGACT
41808 ATCGCAACG
1 ATCGCAACG
41817 AAAGAATCGC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.39, C:0.23, G:0.17, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCAAAAATGACT
Found at i:41904 original size:20 final size:20
Alignment explanation
Indices: 41859--41927 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
41849 GCGATTCTCT
* **
41859 CGTTGCGATAGTTAAATTCG
1 CGTTGCGATAGTCATTTTCG
* *
41879 CATTGCGATAGTCATTTTCT
1 CGTTGCGATAGTCATTTTCG
41899 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
41919 CGTTGCGAT
1 CGTTGCGAT
41928 TTTAAGTTTC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:42451 original size:18 final size:19
Alignment explanation
Indices: 42412--42453 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
42402 CTTACCTGTC
42412 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
42433 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
42451 ATC
1 ATC
42454 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:42507 original size:42 final size:42
Alignment explanation
Indices: 42435--42517 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 42
42425 CCTCCCCTAT
42435 CGTTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCAC
1 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGT-CCCTCCCAC
* ** *
42477 CGTTCAAGAGGCCACC-GTCATCTTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCC-CCTATCATCCCTCAAGAGGTCCCTCCCA
42518 ATATTCTAGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
42 31 0.89
43 4 0.11
ACGTcount: A:0.22, C:0.40, G:0.18, T:0.20
Consensus pattern (42 bp):
CGTTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:43922 original size:14 final size:14
Alignment explanation
Indices: 43903--43938 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
43893 ATTGTTTAAT
43903 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
43917 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
43931 TGATTTGT
1 TGATTTGT
43939 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:44094 original size:33 final size:33
Alignment explanation
Indices: 44044--44124 Score: 117
Period size: 33 Copynumber: 2.4 Consensus size: 33
44034 AAAACAGACT
* ** *
44044 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCACAACGAGAGA
44078 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCACAACGAGAGA
44111 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
44125 ACGAGAGAAT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 34 0.79
34 9 0.21
ACGTcount: A:0.43, C:0.21, G:0.23, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCACAACGAGAGA
Found at i:44157 original size:20 final size:22
Alignment explanation
Indices: 44102--44166 Score: 98
Period size: 22 Copynumber: 3.0 Consensus size: 22
44092 TGAAAATCAC
44102 AACGAGAGAATCGCAATGCGAA
1 AACGAGAGAATCGCAATGCGAA
44124 AACGAGAGAATCGCAATGCGAA
1 AACGAGAGAATCGCAATGCGAA
* *
44146 AATGA-A-AATCGCAACGCGAA
1 AACGAGAGAATCGCAATGCGAA
44166 A
1 A
44167 CTAAATTCGC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 14 0.34
21 1 0.02
22 26 0.63
ACGTcount: A:0.48, C:0.18, G:0.25, T:0.09
Consensus pattern (22 bp):
AACGAGAGAATCGCAATGCGAA
Found at i:44208 original size:14 final size:14
Alignment explanation
Indices: 44189--44223 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
44179 TGCGATTTTC
44189 ATTTTCACATTGTG
1 ATTTTCACATTGTG
* *
44203 ATTTTCTCGTTGTG
1 ATTTTCACATTGTG
44217 ATTTTCA
1 ATTTTCA
44224 TTTCGCATTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.54
Consensus pattern (14 bp):
ATTTTCACATTGTG
Found at i:44244 original size:33 final size:33
Alignment explanation
Indices: 44176--44271 Score: 111
Period size: 33 Copynumber: 2.8 Consensus size: 33
44166 ACTAAATTCG
* * *
44176 CGTTGCGATTTTCATTTTCACATTGTGATTTTCT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCTCT
*
44210 CGTTGTGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
** *
44243 CGTTGCGATAGTCATTTCCGCGTTGCGAT
1 CGTTGCGATTTTCATTT-CGCATTGCGAT
44272 AGTCATTTCT
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
33 30 0.57
34 23 0.43
ACGTcount: A:0.14, C:0.21, G:0.20, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:44268 original size:20 final size:20
Alignment explanation
Indices: 44243--44311 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
44233 GCGATTCTCT
44243 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
44263 CGTTGCGATAGTCATTTCTG
1 CGTTGCGATAGTCATTTCCG
* *
44283 TGTTACGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
*
44303 TGTTGCGAT
1 CGTTGCGAT
44312 TTTCGCGTTG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
20 41 0.95
21 2 0.05
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.39
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:47646 original size:20 final size:20
Alignment explanation
Indices: 47622--47748 Score: 200
Period size: 20 Copynumber: 6.3 Consensus size: 20
47612 AAATTCAGTA
*
47622 TTGCGATAGTCAGAATCGCA
1 TTGCGATAGTCAGAATCGCG
47642 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
47662 TTGCGATAGTCAGAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
47682 TTGCGATAGTCAGAATCTCA
1 TTGCGATAGTCAGAATCGCG
*
47702 TTGCGATAGTCATAATCGCG
1 TTGCGATAGTCAGAATCGCG
* *
47722 TTACGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
47742 TTGCGAT
1 TTGCGAT
47749 TTACGTATTC
Statistics
Matches: 97, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 97 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.28
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:47758 original size:20 final size:20
Alignment explanation
Indices: 47735--47787 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
47725 CGATAGTCAG
*
47735 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
47755 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
47775 ATTCGCATTGCGA
1 ATTCGCATTGCGA
47788 ATTAGAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:47808 original size:21 final size:21
Alignment explanation
Indices: 47784--47829 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
47774 TATTCGCATT
*
47784 GCGAATTAGAAAAATCGCAAC
1 GCGAATTAGAAAAATCACAAC
* * *
47805 GCGAATTTGGAAAATCACAAT
1 GCGAATTAGAAAAATCACAAC
47826 GCGA
1 GCGA
47830 TAGTCAGAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.17, G:0.22, T:0.17
Consensus pattern (21 bp):
GCGAATTAGAAAAATCACAAC
Found at i:50130 original size:5 final size:5
Alignment explanation
Indices: 50120--50156 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
50110 AGCGCTGATT
* *
50120 TTTTA TTTTA TTTTA TATAA TTTTA TTTTA TTTTA TT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TT
50157 GTAGATGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (5 bp):
TTTTA
Found at i:51345 original size:31 final size:32
Alignment explanation
Indices: 51307--51378 Score: 98
Period size: 31 Copynumber: 2.4 Consensus size: 32
51297 TGAAGAAATA
51307 AATGAAAAATAAT-TTAATAGAAAACTTTAAT
1 AATGAAAAATAATATTAATAGAAAACTTTAAT
* *
51338 AATGAAAAA-GATATTAATTGAAAACTTTAAT
1 AATGAAAAATAATATTAATAGAAAACTTTAAT
51369 AA--AAAAATAA
1 AATGAAAAATAA
51379 AAAGACATCA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 5 0.14
30 3 0.08
31 28 0.78
ACGTcount: A:0.61, C:0.03, G:0.07, T:0.29
Consensus pattern (32 bp):
AATGAAAAATAATATTAATAGAAAACTTTAAT
Found at i:51925 original size:60 final size:60
Alignment explanation
Indices: 51754--51937 Score: 176
Period size: 60 Copynumber: 3.0 Consensus size: 60
51744 CAATCCTTTG
* * * * *
51754 GGAATGAAATTAGAACATCTAAAAGTTTGAGGACCAATATAGAATGAGAGTCATAGTTTA
1 GGAATGAAATTAGAATATTTAAAAGTTTGAGGAACAATTTAGAATAAGAGTCATAGTTTA
* * * ** * *
51814 GGGATGAATTTAGAATATTCAAAAGTTTGATTAATAATTTA-ACA-AGTGAGTC-TGAGTTTA
1 GGAATGAAATTAGAATATTTAAAAGTTTGAGGAACAATTTAGA-ATA-AGAGTCAT-AGTTTA
* * *
51874 GGAATGAAATCAAAATATTTAAAAGTTTAAGGAACAATTTAGAATAAGAGTCATAGTTTGA
1 GGAATGAAATTAGAATATTTAAAAGTTTGAGGAACAATTTAGAATAAGAGTCATAGTTT-A
51935 GGA
1 GGA
51938 TGTACAATAC
Statistics
Matches: 95, Mismatches: 22, Indels: 13
0.73 0.17 0.10
Matches are distributed among these distances:
59 2 0.02
60 86 0.91
61 7 0.07
ACGTcount: A:0.43, C:0.06, G:0.21, T:0.30
Consensus pattern (60 bp):
GGAATGAAATTAGAATATTTAAAAGTTTGAGGAACAATTTAGAATAAGAGTCATAGTTTA
Found at i:62524 original size:1 final size:1
Alignment explanation
Indices: 62520--62920 Score: 604
Period size: 1 Copynumber: 401.0 Consensus size: 1
62510 AAACTAAAGG
* * ** * * * *
62520 TTTTTTTTATTTTTTATTTTTTAATTTTTTTTTTTATTTTATTTTTTTTTTATTTTTTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
62585 TTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
62650 TTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
62715 TTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* *
62780 TTTTTTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * * * *
62845 TTTTTTTTTATTTTTTTTTTTTTTTATTTTTTTTTTTTTATTTTTTTATTTTTTTTTTTATTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
62910 TATTTTTTTTT
1 TTTTTTTTTTT
62921 GTAGCAAATG
Statistics
Matches: 358, Mismatches: 42, Indels: 0
0.89 0.10 0.00
Matches are distributed among these distances:
1 358 1.00
ACGTcount: A:0.05, C:0.00, G:0.00, T:0.95
Consensus pattern (1 bp):
T
Found at i:75488 original size:2 final size:2
Alignment explanation
Indices: 75481--75513 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
75471 ATGTAACTTT
*
75481 TA TA TA TA TA TA TC 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 TA TA T
75514 CCCTAAACAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.