Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005283.1 Hibiscus syriacus cultivar Beakdansim tig00011946_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: 108076
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:8418 original size:22 final size:20
Alignment explanation
Indices: 8393--8433 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
8383 TCAAGGAAAT
8393 AAGATTAGAATAAAATAAAAAA
1 AAGATTA-AA-AAAATAAAAAA
8415 AAGATTAAAAAAATGAAAA
1 AAGATTAAAAAAAT-AAAA
8434 TAAATAAGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (20 bp):
AAGATTAAAAAAATAAAAAA
Found at i:8433 original size:20 final size:22
Alignment explanation
Indices: 8393--8433 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 22
8383 TCAAGGAAAT
8393 AAGATTAGAATAAAATAAAAAA
1 AAGATTAGAATAAAATAAAAAA
*
8415 AAGATTA-AA-AAAATGAAAA
1 AAGATTAGAATAAAATAAAAA
8434 TAAATAAGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 2 0.11
22 7 0.39
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (22 bp):
AAGATTAGAATAAAATAAAAAA
Found at i:14013 original size:19 final size:21
Alignment explanation
Indices: 13976--14018 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
13966 TCCTTTCTTG
13976 AAAGGGATCAATCCTTTTG-A
1 AAAGGGATCAATCCTTTTGCA
**
13996 AAAGGGATTGATCC-TTTGCA
1 AAAGGGATCAATCCTTTTGCA
14016 AAA
1 AAA
14019 CAGAAACTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 4 0.20
20 16 0.80
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.28
Consensus pattern (21 bp):
AAAGGGATCAATCCTTTTGCA
Found at i:15625 original size:19 final size:19
Alignment explanation
Indices: 15593--15629 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
15583 TTTTCAATAT
*
15593 ATATCAATTTGTTTAATTG
1 ATATCAATTGGTTTAATTG
*
15612 ATATCCATTGGTTTAATT
1 ATATCAATTGGTTTAATT
15630 AGCCCAACGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (19 bp):
ATATCAATTGGTTTAATTG
Found at i:20419 original size:32 final size:31
Alignment explanation
Indices: 20373--20494 Score: 104
Period size: 32 Copynumber: 3.8 Consensus size: 31
20363 CCTAAGGTGA
*
20373 CCCTCGGGTAGGCTCTTAAGCCCCGAGATGTT
1 CCCTTGGGTAGGCTC-TAAGCCCCGAGATGTT
* * *
20405 CCCTTGGGTAGGCTCTTAGGCCCTA-ATGTACT
1 CCCTTGGGTAGGCTCTAAGCCCCGAGATGT--T
* * * **
20437 CACTTGGGTGGGCTCTAAGGCCCCAAGACATT
1 CCCTTGGGTAGGCTCTAA-GCCCCGAGATGTT
20469 -CCTTGGGTAGGCTCTAAGACCCCGAG
1 CCCTTGGGTAGGCTCTAAG-CCCCGAG
20495 GCATTTTTTA
Statistics
Matches: 71, Mismatches: 14, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
30 5 0.07
31 28 0.39
32 31 0.44
33 5 0.07
34 2 0.03
ACGTcount: A:0.18, C:0.30, G:0.28, T:0.25
Consensus pattern (31 bp):
CCCTTGGGTAGGCTCTAAGCCCCGAGATGTT
Found at i:22486 original size:54 final size:54
Alignment explanation
Indices: 22425--22608 Score: 242
Period size: 54 Copynumber: 3.4 Consensus size: 54
22415 TTCTGTGGTT
* * * * *
22425 TTGCACACATAGTGTCGATACAGTAATTCACAAACTCATTGTGAATTACGTAGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
* *
22479 TTGCACACGTAATGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
* * * *
22533 TTGCACATATAGTGCCAATATGGTAATTCCCAGACTCATTATGAATTACTTAGG
1 TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
* * *
22587 TTTCATACATAGTTCCAATACG
1 TTGCACACATAGTGCCAATACG
22609 ATAAAATTCA
Statistics
Matches: 112, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 112 1.00
ACGTcount: A:0.33, C:0.20, G:0.16, T:0.32
Consensus pattern (54 bp):
TTGCACACATAGTGCCAATACGGTAATTCACAAACTCATTATGAATTACTTAGG
Found at i:22685 original size:20 final size:21
Alignment explanation
Indices: 22642--22685 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
22632 AAAGTAACTT
** *
22642 ACATCCATAAATCTCCTTATA
1 ACATCCATAAATCTCCAAAGA
22663 ACATCCA-AAATCTCCAAAGA
1 ACATCCATAAATCTCCAAAGA
22683 ACA
1 ACA
22686 CTAAAAACTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.45, C:0.30, G:0.02, T:0.23
Consensus pattern (21 bp):
ACATCCATAAATCTCCAAAGA
Found at i:23042 original size:16 final size:17
Alignment explanation
Indices: 23023--23060 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
23013 AATTTTTCAG
23023 CTTTTA-CCATTTTTCC
1 CTTTTACCCATTTTTCC
23039 CTTTTACCCATTTTTCC
1 CTTTTACCCATTTTTCC
23056 CTTTT
1 CTTTT
23061 CAACCTTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 6 0.29
17 15 0.71
ACGTcount: A:0.11, C:0.32, G:0.00, T:0.58
Consensus pattern (17 bp):
CTTTTACCCATTTTTCC
Found at i:35768 original size:11 final size:12
Alignment explanation
Indices: 35731--35771 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 12
35721 AAGCTTTCTC
35731 TTTTTACTTTTCA
1 TTTTT-CTTTTCA
*
35744 -TGTTCTTTTCA
1 TTTTTCTTTTCA
35755 TTTTTCTTTT-A
1 TTTTTCTTTTCA
35766 TTTTTC
1 TTTTTC
35772 AAGCTTTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.10, C:0.15, G:0.02, T:0.73
Consensus pattern (12 bp):
TTTTTCTTTTCA
Found at i:47630 original size:32 final size:32
Alignment explanation
Indices: 47559--47630 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
47549 AACATAAGGG
* * *
47559 AGTACCTCGGGACCTTAGAGCCTACCCAAGAT
1 AGTACCTTGGGACCTAAGAACCTACCCAAGAT
*
47591 AGTACCTTGGGGCCTAAGAACCTACCCAATGA-
1 AGTACCTTGGGACCTAAGAACCTACCCAA-GAT
47623 AGTACCTT
1 AGTACCTT
47631 AGGTGTGTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
32 33 0.94
33 2 0.06
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.21
Consensus pattern (32 bp):
AGTACCTTGGGACCTAAGAACCTACCCAAGAT
Found at i:63753 original size:17 final size:20
Alignment explanation
Indices: 63719--63755 Score: 53
Period size: 17 Copynumber: 2.0 Consensus size: 20
63709 ATGGTGATAC
63719 TGTAGTATTGGTTGCTTGTG
1 TGTAGTATTGGTTGCTTGTG
63739 TGTA-TATT-GTT-CTTGTG
1 TGTAGTATTGGTTGCTTGTG
63756 AATGATAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
17 6 0.35
18 3 0.18
19 4 0.24
20 4 0.24
ACGTcount: A:0.11, C:0.05, G:0.30, T:0.54
Consensus pattern (20 bp):
TGTAGTATTGGTTGCTTGTG
Found at i:69627 original size:28 final size:29
Alignment explanation
Indices: 69595--69652 Score: 73
Period size: 28 Copynumber: 2.0 Consensus size: 29
69585 AATATAAAAT
69595 AAAATAAAAATAAATA-ACAAAAATATAA
1 AAAATAAAAATAAATATACAAAAATATAA
** * *
69623 AAAATAGCAATAAATATATAAATATATAA
1 AAAATAAAAATAAATATACAAAAATATAA
69652 A
1 A
69653 TATATACAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
28 14 0.56
29 11 0.44
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.22
Consensus pattern (29 bp):
AAAATAAAAATAAATATACAAAAATATAA
Found at i:69639 original size:19 final size:19
Alignment explanation
Indices: 69595--69640 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
69585 AATATAAAAT
*
69595 AAAATAAAAATAAATAACA
1 AAAATATAAATAAATAACA
*
69614 AAAATATAAA-AAATAGCA
1 AAAATATAAATAAATAACA
69632 ATAAATATA
1 A-AAATATA
69641 TAAATATATA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.74, C:0.04, G:0.02, T:0.20
Consensus pattern (19 bp):
AAAATATAAATAAATAACA
Found at i:69643 original size:8 final size:8
Alignment explanation
Indices: 69632--69658 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
69622 AAAAATAGCA
69632 ATAAATAT
1 ATAAATAT
69640 ATAAATAT
1 ATAAATAT
69648 ATAAATAT
1 ATAAATAT
69656 ATA
1 ATA
69659 CAAGTAGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (8 bp):
ATAAATAT
Found at i:69726 original size:17 final size:16
Alignment explanation
Indices: 69706--69739 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
69696 GAAAAACACC
69706 ATAATAAAAAAAGTAAT
1 ATAAT-AAAAAAGTAAT
*
69723 ATAATATAAAAGTAAT
1 ATAATAAAAAAGTAAT
69739 A
1 A
69740 AAGGTAAATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
ATAATAAAAAAGTAAT
Found at i:69758 original size:16 final size:17
Alignment explanation
Indices: 69739--69772 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
69729 TAAAAGTAAT
*
69739 AAAGGTAAATAA-AAAA
1 AAAGGAAAATAATAAAA
69755 AAAGGAAAATAATAAAA
1 AAAGGAAAATAATAAAA
69772 A
1 A
69773 TAATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.12, T:0.12
Consensus pattern (17 bp):
AAAGGAAAATAATAAAA
Found at i:70936 original size:9 final size:9
Alignment explanation
Indices: 70914--70951 Score: 51
Period size: 9 Copynumber: 4.3 Consensus size: 9
70904 TATCTATACA
70914 ATATAT-AT
1 ATATATGAT
*
70922 ACATATGAT
1 ATATATGAT
70931 ATATATGAT
1 ATATATGAT
*
70940 ATATATAAT
1 ATATATGAT
70949 ATA
1 ATA
70952 AATATATTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
8 5 0.19
9 21 0.81
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (9 bp):
ATATATGAT
Found at i:71720 original size:106 final size:103
Alignment explanation
Indices: 71580--71949 Score: 411
Period size: 106 Copynumber: 3.6 Consensus size: 103
71570 GTTATGGAAC
** * *
71580 TGGGAAATTATTTGTTGTA-AGTCAGCCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCGA
1 TGGGAAATTATTTGTTG-ACAACCAGCCGCCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGA
* *
71644 GTCCAATATCATTCACTGGGAAATTGAAATTGGCTCTAAAAT
65 GTCCAATATCCTTC-CTGTG-AATTGAAATT-GCTCTAAAAT
* *
71686 TGGGAAATTATTTGTTGACAACCAGTCGTCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAG
1 TGGGAAATTATTTGTTGACAACCAGCCGCCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAG
71751 TCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTAAAAT
66 TCCAATATCCTTC-CTGTGAA-TTGAAATTG-CTCTAAAAT
* * * * **
71792 TGGGAAGTTGTTTGATGACAACGAGCCGCCCCTTCATTGTGAAGTTGAGA-TTGTGTTGTCTTAA
1 TGGGAAATTATTTGTTGACAACCAGCCGCCCCTTCATTGTGAAGTTGA-ACTTGTGTTGTCTCGA
* *
71856 GTCCAATATCCGTCGT-TG---TG-AA-T--T-TAAAAT
65 GTCCAATATCCTTCCTGTGAATTGAAATTGCTCTAAAAT
* * * *
71886 TGGGAAATTGTTTGTTGACAACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTATTGTCTCGA
1 TGGGAAATTATTTGTTGACAACCAGCCGCCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGA
71950 ATGGCACAAT
Statistics
Matches: 232, Mismatches: 27, Indels: 22
0.83 0.10 0.08
Matches are distributed among these distances:
93 1 0.00
94 60 0.26
95 1 0.00
98 1 0.00
99 2 0.01
100 2 0.01
104 2 0.01
105 5 0.02
106 157 0.68
107 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.35
Consensus pattern (103 bp):
TGGGAAATTATTTGTTGACAACCAGCCGCCCCTTCATTGTGAAGTTGAACTTGTGTTGTCTCGAG
TCCAATATCCTTCCTGTGAATTGAAATTGCTCTAAAAT
Found at i:72344 original size:14 final size:14
Alignment explanation
Indices: 72325--72351 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
72315 TAGTTTCTTG
72325 TCTGGAATCTTGAT
1 TCTGGAATCTTGAT
72339 TCTGGAATCTTGA
1 TCTGGAATCTTGA
72352 AGTTTAGATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.15, G:0.22, T:0.41
Consensus pattern (14 bp):
TCTGGAATCTTGAT
Found at i:81614 original size:19 final size:19
Alignment explanation
Indices: 81590--81633 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
81580 CAACCGGAAA
81590 TTACCTTAGCCTGACACAC
1 TTACCTTAGCCTGACACAC
81609 TTACCTTAGCCTGACACAC
1 TTACCTTAGCCTGACACAC
81628 TTACCT
1 TTACCT
81634 ATCTCCCCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.25, C:0.36, G:0.09, T:0.30
Consensus pattern (19 bp):
TTACCTTAGCCTGACACAC
Found at i:82072 original size:25 final size:25
Alignment explanation
Indices: 82018--82075 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
82008 ATGTAATGGG
*
82018 ATAAATAACATAAAAGAGTAAACAT
1 ATAAATAACATAAAAGAATAAACAT
*
82043 GTAAATATACAT-AAAGAATAAA-AGT
1 ATAAATA-ACATAAAAGAATAAACA-T
82068 ATAAATAA
1 ATAAATAA
82076 GAATATAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 2 0.07
25 22 0.79
26 4 0.14
ACGTcount: A:0.64, C:0.05, G:0.09, T:0.22
Consensus pattern (25 bp):
ATAAATAACATAAAAGAATAAACAT
Found at i:82227 original size:7 final size:7
Alignment explanation
Indices: 82215--82255 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
82205 AAAGAAACCG
82215 AAAATAT
1 AAAATAT
82222 AAAATA-
1 AAAATAT
82228 AAAATA-
1 AAAATAT
82234 AATAA-AT
1 AA-AATAT
82241 AAAATAT
1 AAAATAT
82248 AAAATAT
1 AAAATAT
82255 A
1 A
82256 TAAAAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
6 11 0.35
7 20 0.65
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (7 bp):
AAAATAT
Found at i:82249 original size:21 final size:21
Alignment explanation
Indices: 82216--82284 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 21
82206 AAGAAACCGA
*
82216 AAATATAAA-ATAAAAATAAAT
1 AAATA-AAATATAAAAATATAT
82237 AAATAAAATAT-AAAATATAT
1 AAATAAAATATAAAAATATAT
* *
82257 AAAAAAAATAGCAATAAATATAT
1 AAATAAAATA-TAA-AAATATAT
82280 AAATA
1 AAATA
82285 CATACAAGTA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 20 0.50
21 7 0.17
22 1 0.03
23 12 0.30
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (21 bp):
AAATAAAATATAAAAATATAT
Found at i:82253 original size:20 final size:19
Alignment explanation
Indices: 82220--82282 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
82210 AACCGAAAAT
82220 ATAAAATAAAAATAAATAA
1 ATAAAATAAAAATAAATAA
*
82239 ATAAAATATAAAATATATAA
1 ATAAAATA-AAAATAAATAA
* ** *
82259 AAAAAATAGCAATAAATAT
1 ATAAAATAAAAATAAATAA
82278 ATAAA
1 ATAAA
82283 TACATACAAG
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 19 0.53
20 17 0.47
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.24
Consensus pattern (19 bp):
ATAAAATAAAAATAAATAA
Found at i:92180 original size:18 final size:18
Alignment explanation
Indices: 92157--92202 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
92147 CATTGATGCC
92157 GAGGATAATGATGAGATA
1 GAGGATAATGATGAGATA
92175 GAGGATAATGATGAGATA
1 GAGGATAATGATGAGATA
*
92193 GAAGATAATG
1 GAGGATAATG
92203 TGGCTGATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.33, T:0.22
Consensus pattern (18 bp):
GAGGATAATGATGAGATA
Found at i:94031 original size:130 final size:130
Alignment explanation
Indices: 93788--94032 Score: 391
Period size: 130 Copynumber: 1.9 Consensus size: 130
93778 ATTAAAAATC
* * *
93788 TGTTTGTTTTATGATATTAATCTGTGGCATTATTGTTAGCTTCATGCATGTTGCTTCTTGAGCAC
1 TGTTAGTTTTATGATATTAATCTGTGGCAATATTGTTAGCTTCATGCATGTTGCTTCTTAAGCAC
* * *
93853 AAGCAAATACTTAGGTTTTGGAGGTCTGATAACTATTTCAAAGGGTTATCATATCATATCAGTTT
66 AAGCAAATACTTAGGTTTGGGAGGTCTGATAACTATCTCAAAGAGTTATCATATCATATCAGTTT
* *
93918 TGTTAGTTTTATGATATTAATTTGTGGCAATATTGTTAGCTTCATGCATGTTGCTTCTTAAGCGC
1 TGTTAGTTTTATGATATTAATCTGTGGCAATATTGTTAGCTTCATGCATGTTGCTTCTTAAGCAC
* * *
93983 AAGCAAATACTTAGGTTTGGGGGGTCTGATAACTCTCTGAAAGAGTTATC
66 AAGCAAATACTTAGGTTTGGGAGGTCTGATAACTATCTCAAAGAGTTATC
94033 TTTTAGGATC
Statistics
Matches: 104, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
130 104 1.00
ACGTcount: A:0.25, C:0.13, G:0.21, T:0.41
Consensus pattern (130 bp):
TGTTAGTTTTATGATATTAATCTGTGGCAATATTGTTAGCTTCATGCATGTTGCTTCTTAAGCAC
AAGCAAATACTTAGGTTTGGGAGGTCTGATAACTATCTCAAAGAGTTATCATATCATATCAGTTT
Found at i:99214 original size:40 final size:39
Alignment explanation
Indices: 99155--99235 Score: 135
Period size: 40 Copynumber: 2.1 Consensus size: 39
99145 GTCGAATTTG
* *
99155 GAAAGTCGTATTAAGACTTATCCCTCACGTAACCATTTTT
1 GAAAGTCGTATTAAAACTTATCCCTCACGT-ACCACTTTT
99195 GAAAGTCGTATTAAAACTTATCCCTCACGTACCACTTTT
1 GAAAGTCGTATTAAAACTTATCCCTCACGTACCACTTTT
99234 GA
1 GA
99236 TTTTAAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
39 10 0.26
40 29 0.74
ACGTcount: A:0.31, C:0.23, G:0.12, T:0.33
Consensus pattern (39 bp):
GAAAGTCGTATTAAAACTTATCCCTCACGTACCACTTTT
Found at i:99919 original size:32 final size:32
Alignment explanation
Indices: 99882--99942 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
99872 AATGACATAC
* *
99882 ATATCCCAATAGCATATATCCGAATAACATTT
1 ATATCCCAATAACACATATCCGAATAACATTT
* *
99914 ATATCCGAATAACGCATATCCGAATAACA
1 ATATCCCAATAACACATATCCGAATAACA
99943 CATATCATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.43, C:0.23, G:0.08, T:0.26
Consensus pattern (32 bp):
ATATCCCAATAACACATATCCGAATAACATTT
Found at i:99934 original size:15 final size:15
Alignment explanation
Indices: 99880--99948 Score: 75
Period size: 15 Copynumber: 4.5 Consensus size: 15
99870 AGAATGACAT
* *
99880 ACATATCCCAATAGC
1 ACATATCCGAATAAC
*
99895 ATATATCCGAATAAC
1 ACATATCCGAATAAC
*
99910 ATTTATATCCGAATAAC
1 A--CATATCCGAATAAC
*
99927 GCATATCCGAATAAC
1 ACATATCCGAATAAC
99942 ACATATC
1 ACATATC
99949 ATATTAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
15 32 0.70
17 14 0.30
ACGTcount: A:0.42, C:0.25, G:0.07, T:0.26
Consensus pattern (15 bp):
ACATATCCGAATAAC
Found at i:100617 original size:21 final size:21
Alignment explanation
Indices: 100591--100638 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
100581 TAGACCGCCC
*
100591 AGGGTGCTGCCCAGCTGCACA
1 AGGGTGCTGCCCAACTGCACA
* *
100612 AGGGTGCTGTCCAACTGCACC
1 AGGGTGCTGCCCAACTGCACA
100633 AGGGTG
1 AGGGTG
100639 TTATTTGACG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.19, C:0.29, G:0.35, T:0.17
Consensus pattern (21 bp):
AGGGTGCTGCCCAACTGCACA
Found at i:103208 original size:25 final size:22
Alignment explanation
Indices: 103167--103213 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
103157 GCCAGCCGTT
*
103167 CCTCTACTCCAATTGCTCTGCCG
1 CCTCTACTCCAACTGCTC-GCCG
103190 CCTCTACTCTACAACTGCTCGCCG
1 CCTCTACTC--CAACTGCTCGCCG
103214 TCATGTTCCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 9 0.43
24 4 0.19
25 8 0.38
ACGTcount: A:0.15, C:0.45, G:0.13, T:0.28
Consensus pattern (22 bp):
CCTCTACTCCAACTGCTCGCCG
Found at i:103364 original size:13 final size:13
Alignment explanation
Indices: 103346--103373 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
103336 GAACAAACAC
103346 ATTTTGAAGGCCT
1 ATTTTGAAGGCCT
103359 ATTTTGAAGGCCT
1 ATTTTGAAGGCCT
103372 AT
1 AT
103374 AAAAGGCCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.21, T:0.39
Consensus pattern (13 bp):
ATTTTGAAGGCCT
Found at i:105183 original size:26 final size:27
Alignment explanation
Indices: 105135--105195 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 27
105125 CTTTTAAAAA
105135 ATTTTATATATACTTATTATTTTTAAT
1 ATTTTATATATACTTATTATTTTTAAT
*
105162 ATTTATATATATA-TTATTTTTTTATTAAT
1 ATTT-TATATATACTTA-TTATTT-TTAAT
105191 ATTTT
1 ATTTT
105196 TATTTTATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
27 7 0.23
28 14 0.47
29 9 0.30
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (27 bp):
ATTTTATATATACTTATTATTTTTAAT
Found at i:105201 original size:17 final size:18
Alignment explanation
Indices: 105148--105204 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 18
105138 TTATATATAC
105148 TTAT-TATTTTTAATATTTA
1 TTATATATTTTT-AT-TTTA
105167 TATATATATTATTT-TTTTA
1 T-TATATATT-TTTATTTTA
105186 TTA-ATATTTTTATTTTA
1 TTATATATTTTTATTTTA
105203 TT
1 TT
105205 TTCAAGTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.09
17 12 0.35
18 2 0.06
19 6 0.18
20 4 0.12
21 4 0.12
22 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TTATATATTTTTATTTTA
Found at i:106738 original size:21 final size:20
Alignment explanation
Indices: 106710--106753 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
106700 GAGTAACACC
106710 TTTTCATACATGCATTTGCA
1 TTTTCATACATGCATTTGCA
** *
106730 TTTTGCATATTTGCATTTTCA
1 TTTT-CATACATGCATTTGCA
106751 TTT
1 TTT
106754 ATACTTTTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (20 bp):
TTTTCATACATGCATTTGCA
Done.