Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001056.1 Hibiscus syriacus cultivar Beakdansim tig00002091_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: 77503
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Found at i:14139 original size:21 final size:23
Alignment explanation
Indices: 14114--14252 Score: 123
Period size: 23 Copynumber: 6.3 Consensus size: 23
14104 CACCAAAGTG
*
14114 CCACATAATTAT-C-CCGAAGGA
1 CCACATAGTTATGCACCGAAGGA
* *
14135 CCACATAGGTT-TGCACCTAAGTA
1 CCACATA-GTTATGCACCGAAGGA
* *
14158 CCACATAGTTTTGCACCGAAGTA
1 CCACATAGTTATGCACCGAAGGA
* *
14181 CCACATAGTTTTGCACCGAAGTA
1 CCACATAGTTATGCACCGAAGGA
*
14204 CCACATA-TT-TGTC-CCAAAGGA
1 CCACATAGTTATG-CACCGAAGGA
*
14225 CCACATAATTAT-C-CCGAAGGA
1 CCACATAGTTATGCACCGAAGGA
14246 CCACATA
1 CCACATA
14253 TAACCCTCGA
Statistics
Matches: 104, Mismatches: 7, Indels: 14
0.83 0.06 0.11
Matches are distributed among these distances:
21 38 0.37
22 11 0.11
23 55 0.53
ACGTcount: A:0.34, C:0.28, G:0.15, T:0.23
Consensus pattern (23 bp):
CCACATAGTTATGCACCGAAGGA
Found at i:14164 original size:23 final size:23
Alignment explanation
Indices: 14100--14210 Score: 145
Period size: 23 Copynumber: 4.9 Consensus size: 23
14090 CAGCTCGTAA
* * *
14100 TTTGCACCAAAGTGCCACATAAT
1 TTTGCACCGAAGTACCACATAGT
* * *
14123 TAT-C-CCGAAGGACCACATAGG
1 TTTGCACCGAAGTACCACATAGT
*
14144 TTTGCACCTAAGTACCACATAGT
1 TTTGCACCGAAGTACCACATAGT
14167 TTTGCACCGAAGTACCACATAGT
1 TTTGCACCGAAGTACCACATAGT
14190 TTTGCACCGAAGTACCACATA
1 TTTGCACCGAAGTACCACATA
14211 TTTGTCCCAA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
21 14 0.19
22 2 0.03
23 59 0.79
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (23 bp):
TTTGCACCGAAGTACCACATAGT
Found at i:14188 original size:46 final size:44
Alignment explanation
Indices: 14100--14231 Score: 156
Period size: 46 Copynumber: 3.0 Consensus size: 44
14090 CAGCTCGTAA
*
14100 TTTGCACCAAAGTGCCACATAATTATCCCGAAGGACCACATAGG
1 TTTGCACCAAAGTACCACATAATTATCCCGAAGGACCACATAGG
* * * * *
14144 TTTGCACCTAAGTACCACATAGTTTTGCACCGAAGTACCACATAGT
1 TTTGCACCAAAGTACCACATAATTAT-C-CCGAAGGACCACATAGG
* * * *
14190 TTTGCACCGAAGTACCACATATTTGTCCCAAAGGACCACATA
1 TTTGCACCAAAGTACCACATAATTATCCCGAAGGACCACATA
14232 ATTATCCCGA
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
44 35 0.47
45 2 0.03
46 38 0.51
ACGTcount: A:0.33, C:0.27, G:0.16, T:0.24
Consensus pattern (44 bp):
TTTGCACCAAAGTACCACATAATTATCCCGAAGGACCACATAGG
Found at i:21590 original size:32 final size:34
Alignment explanation
Indices: 21549--21621 Score: 105
Period size: 34 Copynumber: 2.2 Consensus size: 34
21539 TTTTCTAACT
* *
21549 TACTGACATTCTAAC-TTTTA-TTTTACTGTTTA
1 TACTAACATTCTAACTTTTTATTTTTACTGTTCA
*
21581 TACTAACATTCTAACTTTTTATTTTTATTGTTCA
1 TACTAACATTCTAACTTTTTATTTTTACTGTTCA
21615 TACTAAC
1 TACTAAC
21622 TTTTTATTTT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 14 0.39
33 5 0.14
34 17 0.47
ACGTcount: A:0.27, C:0.16, G:0.04, T:0.52
Consensus pattern (34 bp):
TACTAACATTCTAACTTTTTATTTTTACTGTTCA
Found at i:21625 original size:26 final size:26
Alignment explanation
Indices: 21591--21649 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
21581 TACTAACATT
*
21591 CTAACTTTTTATTTTTATTGTTCATA
1 CTAACTTTTTATTTTTATTGCTCATA
*
21617 CTAACTTTTTATTTTTATTGCTCTTA
1 CTAACTTTTTATTTTTATTGCTCATA
21643 CTAACTT
1 CTAACTT
21650 ACTAACATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.22, C:0.15, G:0.03, T:0.59
Consensus pattern (26 bp):
CTAACTTTTTATTTTTATTGCTCATA
Found at i:22130 original size:17 final size:17
Alignment explanation
Indices: 22108--22203 Score: 183
Period size: 17 Copynumber: 5.6 Consensus size: 17
22098 TTATAAAGTT
*
22108 TTCATGTTAGTCTCTTG
1 TTCATGTTAGTCCCTTG
22125 TTCATGTTAGTCCCTTG
1 TTCATGTTAGTCCCTTG
22142 TTCATGTTAGTCCCTTG
1 TTCATGTTAGTCCCTTG
22159 TTCATGTTAGTCCCTTG
1 TTCATGTTAGTCCCTTG
22176 TTCATGTTAGTCCCTTG
1 TTCATGTTAGTCCCTTG
22193 TTCATGTTAGT
1 TTCATGTTAGT
22204 AGACTATCGA
Statistics
Matches: 78, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
17 78 1.00
ACGTcount: A:0.12, C:0.21, G:0.18, T:0.49
Consensus pattern (17 bp):
TTCATGTTAGTCCCTTG
Found at i:26172 original size:26 final size:25
Alignment explanation
Indices: 26132--26214 Score: 82
Period size: 26 Copynumber: 3.3 Consensus size: 25
26122 TGCAAAGTGT
*
26132 AAAGATAAAATAAAAGCAAAGGAAAA
1 AAAGA-AAAAAAAAAGCAAAGGAAAA
26158 AAAGAAAAAACAAAAAGCAAA-GAAAA
1 AAAG-AAAAA-AAAAAGCAAAGGAAAA
* *
26184 AAAGAAGAAAAAAAG--AAGAAAAA
1 AAAGAAAAAAAAAAGCAAAGGAAAA
26207 ATAAGAAA
1 A-AAGAAA
26215 TAGAGGAAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
22 2 0.04
23 5 0.10
24 11 0.22
25 4 0.08
26 17 0.35
27 10 0.20
ACGTcount: A:0.78, C:0.04, G:0.14, T:0.04
Consensus pattern (25 bp):
AAAGAAAAAAAAAAGCAAAGGAAAA
Found at i:26184 original size:27 final size:25
Alignment explanation
Indices: 26132--26197 Score: 87
Period size: 26 Copynumber: 2.6 Consensus size: 25
26122 TGCAAAGTGT
* *
26132 AAAGATAAAATAAAAGCAAAGGAAAA
1 AAAGAAAAAAAAAAAGCAAA-GAAAA
26158 AAAGAAAAAACAAAAAGCAAAGAAAA
1 AAAGAAAAAA-AAAAAGCAAAGAAAA
*
26184 AAAGAAGAAAAAAA
1 AAAGAAAAAAAAAA
26198 GAAGAAAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.11
26 23 0.64
27 9 0.25
ACGTcount: A:0.79, C:0.05, G:0.14, T:0.03
Consensus pattern (25 bp):
AAAGAAAAAAAAAAAGCAAAGAAAA
Found at i:26191 original size:11 final size:12
Alignment explanation
Indices: 26143--26207 Score: 71
Period size: 11 Copynumber: 5.2 Consensus size: 12
26133 AAGATAAAAT
26143 AAAAGCAAAGGAAA
1 AAAAG-AAA-GAAA
*
26157 AAAAGAAAAAACA
1 AAAAGAAAGAA-A
26170 AAAAGCAAAGAAA
1 AAAAG-AAAGAAA
26183 AAAAG-AAGAAA
1 AAAAGAAAGAAA
26194 AAAAG-AAGAAA
1 AAAAGAAAGAAA
26205 AAA
1 AAA
26208 TAAGAAATAG
Statistics
Matches: 47, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
11 20 0.43
12 2 0.04
13 15 0.32
14 10 0.21
ACGTcount: A:0.80, C:0.05, G:0.15, T:0.00
Consensus pattern (12 bp):
AAAAGAAAGAAA
Found at i:26194 original size:10 final size:10
Alignment explanation
Indices: 26181--26214 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
26171 AAAGCAAAGA
26181 AAAAAAGAAG
1 AAAAAAGAAG
26191 AAAAAAAGAAG
1 -AAAAAAGAAG
*
26202 AAAAAATAAG
1 AAAAAAGAAG
26212 AAA
1 AAA
26215 TAGAGGAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.82, C:0.00, G:0.15, T:0.03
Consensus pattern (10 bp):
AAAAAAGAAG
Found at i:29848 original size:122 final size:122
Alignment explanation
Indices: 29634--30139 Score: 527
Period size: 122 Copynumber: 4.1 Consensus size: 122
29624 GAAAGTTCCC
* * * * *
29634 AGAAATCTTCAACATGGATGAGCAGTGTCATCTTTAACACCAAATTATCTCCAGATTGACCCGAC
1 AGAACTCTTCAACATGGATGAGCAGAGTCATCTTCAACACCAATTTATCTCCAGATTGACCCGAT
* * * *
29699 TTCCTTAACAAGAAGGAATATCATCATCTTCAGCAAATAATTTACCTGAAAGC-AGCT
66 TTCCTCAACAAGAAGGAACAACATCATCTTCAGCAAACAATTTACCTGAAAGCGA-CT
** *
29756 AGAACTCTTCAACATGGATGAGCAGAGTTGTCTTTAACACCAATTTATCTCCAGATTGACCCGAC
1 AGAACTCTTCAACATGGATGAGCAGAGTCATCTTCAACACCAATTTATCTCCAGATTGACCCGA-
* * * * *
29821 TTT-CTTAACAAGAATGAACAACTTCATCTTCAGAAAACAATTTACCTGAAAGCGTCT
65 TTTCCTCAACAAGAAGGAACAACATCATCTTCAGCAAACAATTTACCTGAAAGCGACT
* * * ** *
29878 AGAACTCTTCAATACGGATGAGCAGAGTCGTCTTCAACA-CTGTATTATCTCCAGATTGACCTGA
1 AGAACTCTTCAACATGGATGAGCAGAGTCATCTTCAACACCAAT-TTATCTCCAGATTGACCCGA
** * * * *
29942 TTTCCTCAA-AGAGAAGGAACAATGTCATCTTCAACAAACAATTTATCTGAAAACAACT
65 TTTCCTCAACA-AGAAGGAACAACATCATCTTCAGCAAACAATTTACCTGAAAGCGACT
* * * * * *
30000 ATATATATCTTCAACATGGATGAGTAGAGTCATCATCAACACCGAA-TTATCTCTAGATTGACTC
1 AGA-A-CTCTTCAACATGGATGAGCAGAGTCATCTTCAACACC-AATTTATCTCCAGATTGACCC
* * * * * * *
30064 GATTTCCCCAACAAGAAGGAACATCATCATCTTTAGCAAGCAATTTATCTGAATGCGACC
63 GATTTCCTCAACAAGAAGGAACAACATCATCTTCAGCAAACAATTTACCTGAAAGCGACT
*
30124 AGATCTCTTCAACATG
1 AGAACTCTTCAACATG
30140 TGTTGAGTTA
Statistics
Matches: 318, Mismatches: 56, Indels: 20
0.81 0.14 0.05
Matches are distributed among these distances:
121 6 0.02
122 214 0.67
123 3 0.01
124 93 0.29
125 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (122 bp):
AGAACTCTTCAACATGGATGAGCAGAGTCATCTTCAACACCAATTTATCTCCAGATTGACCCGAT
TTCCTCAACAAGAAGGAACAACATCATCTTCAGCAAACAATTTACCTGAAAGCGACT
Found at i:30110 original size:246 final size:244
Alignment explanation
Indices: 29632--30137 Score: 561
Period size: 246 Copynumber: 2.1 Consensus size: 244
29622 ATGAAAGTTC
* * * *
29632 CCAGAAATCTTCAACATGGATGAGCAGTGTCATCTTTAACACCAAATTATCTCCAGATTGACCCG
1 CCAGAACTCTTCAACACGGATGAGCAGAGTCATCTTCAACACCAAATTATCTCCAGATTGACCCG
* * * * * * *
29697 ACTTCCTTAACAAGAAGGAATATCATCATCTTCAGCAAATAATTTACCTGAAAGCAGCTAGAACT
66 ACTTCCTCAACAAGAAGGAAAATCATCATCTTCAACAAACAATTTACCTGAAAACAACTAGAAAT
** * * **
29762 CTTCAACATGGATGAGCAGAGTTGTCTTTAACACCAATTTATCTCCAGATTGACCCGACTTTCTT
131 CTTCAACATGGATGAGCAGAGTCATCATCAACACCAATTTATCTCCAGATTGACCCGACTTTCCC
* * *
29827 AACAAGAATGAACAACTTCATCTTCAGAAAACAATTTACCTGAAAGCGT
196 AACAAGAAGGAACAACATCATCTTCAGAAAACAATTTACCTGAAAGCGA
* * * *** *
29876 CTAGAACTCTTCAATACGGATGAGCAGAGTCGTCTTCAACACTGTATTATCTCCAGATTGACCTG
1 CCAGAACTCTTCAACACGGATGAGCAGAGTCATCTTCAACACCAAATTATCTCCAGATTGACCCG
* * * *
29941 ATTTCCTCAA-AGAGAAGGAACAAT-GTCATCTTCAACAAACAATTTATCTGAAAACAACTATAT
66 ACTTCCTCAACA-AGAAGGAA-AATCATCATCTTCAACAAACAATTTACCTGAAAACAACTAGA-
* * *
30004 ATATCTTCAACATGGATGAGTAGAGTCATCATCAACACCGAA-TTATCTCTAGATTGACTCGA-T
128 A-ATCTTCAACATGGATGAGCAGAGTCATCATCAACACC-AATTTATCTCCAGATTGACCCGACT
* * * * * *
30067 TTCCCCAACAAGAAGGAACATCATCATCTTTAGCAAGCAATTTATCTGAATGCGA
191 TT-CCCAACAAGAAGGAACAACATCATCTTCAGAAAACAATTTACCTGAAAGCGA
*
30122 CCAGATCTCTTCAACA
1 CCAGAACTCTTCAACA
30138 TGTGTTGAGT
Statistics
Matches: 213, Mismatches: 43, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
243 1 0.00
244 101 0.47
245 6 0.03
246 103 0.48
247 2 0.01
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (244 bp):
CCAGAACTCTTCAACACGGATGAGCAGAGTCATCTTCAACACCAAATTATCTCCAGATTGACCCG
ACTTCCTCAACAAGAAGGAAAATCATCATCTTCAACAAACAATTTACCTGAAAACAACTAGAAAT
CTTCAACATGGATGAGCAGAGTCATCATCAACACCAATTTATCTCCAGATTGACCCGACTTTCCC
AACAAGAAGGAACAACATCATCTTCAGAAAACAATTTACCTGAAAGCGA
Found at i:33558 original size:21 final size:21
Alignment explanation
Indices: 33532--33571 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33522 CAGAACCCCA
*
33532 GGGGGGTATCGATTCCCCTGT
1 GGGGGGAATCGATTCCCCTGT
*
33553 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGATTCCCCT
33572 TCAAAGGGGG
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:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (21 bp):
GGGGGGAATCGATTCCCCTGT
Found at i:33606 original size:20 final size:21
Alignment explanation
Indices: 33552--33614 Score: 65
Period size: 20 Copynumber: 2.9 Consensus size: 21
33542 GATTCCCCTG
33552 TGGGGGGAATCGGTTCCCCTTCAA
1 TGGGGGG-ATCGGTT-CCC-TCAA
* *
33576 AGGGGGAATCGGTTCCCTC-A
1 TGGGGGGATCGGTTCCCTCAA
*
33596 TGGGGGGATCGATTCCCTC
1 TGGGGGGATCGGTTCCCTC
33615 TGCACAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
20 17 0.50
21 2 0.06
22 3 0.09
23 7 0.21
24 5 0.15
ACGTcount: A:0.16, C:0.25, G:0.35, T:0.24
Consensus pattern (21 bp):
TGGGGGGATCGGTTCCCTCAA
Found at i:40408 original size:16 final size:15
Alignment explanation
Indices: 40385--40414 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
40375 TATTATAACC
40385 ATTTTTTATTTATTG
1 ATTTTTTATTTATTG
40400 ATTTGTTTATTTATT
1 ATTT-TTTATTTATT
40415 TTTTCTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (15 bp):
ATTTTTTATTTATTG
Found at i:40502 original size:10 final size:10
Alignment explanation
Indices: 40487--40524 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
40477 CTCCTAAATT
40487 TTTATTATTA
1 TTTATTATTA
40497 TTTATTATTA
1 TTTATTATTA
40507 TTT-TT-TTGA
1 TTTATTATT-A
40516 TTTATTATT
1 TTTATTATT
40525 TGACCTTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.08
9 6 0.24
10 15 0.60
11 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTATTATTA
Found at i:40506 original size:13 final size:12
Alignment explanation
Indices: 40484--40525 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
40474 TAACTCCTAA
40484 ATTTTTATTATT
1 ATTTTTATTATT
40496 ATTTATTATTATT
1 ATTT-TTATTATT
40509 -TTTTTGATTTATT
1 ATTTTT-A-TTATT
40522 ATTT
1 ATTT
40526 GACCTTGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 8 0.31
13 13 0.50
14 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:40701 original size:26 final size:26
Alignment explanation
Indices: 40628--40711 Score: 93
Period size: 26 Copynumber: 3.3 Consensus size: 26
40618 TACTAACATT
*
40628 CTAAC-TTTTA-TTTTATTGTTTATA
1 CTAACTTTTTATTTTTATTGTTCATA
* *
40652 CTAACATTCTAACTTTTT-TTGTTCATA
1 CTAAC-TTTTTA-TTTTTATTGTTCATA
*
40679 CTAACTTTTTATTTTTATTGTTCTTA
1 CTAACTTTTTATTTTTATTGTTCATA
40705 CTAACTT
1 CTAACTT
40712 ACTAACATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
24 5 0.10
25 5 0.10
26 22 0.45
27 13 0.27
28 4 0.08
ACGTcount: A:0.24, C:0.14, G:0.04, T:0.58
Consensus pattern (26 bp):
CTAACTTTTTATTTTTATTGTTCATA
Found at i:40741 original size:33 final size:34
Alignment explanation
Indices: 40677--40742 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
40667 TTTTTGTTCA
* * **
40677 TACTAACTTTTTATTTTTATTGTTCTTACTAACT
1 TACTAACATTTTATTTTTATTGTACAAACTAACT
40711 TACTAACATTTTA-TTTTATTGTACAAACTAAC
1 TACTAACATTTTATTTTTATTGTACAAACTAAC
40743 CCGCTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (34 bp):
TACTAACATTTTATTTTTATTGTACAAACTAACT
Found at i:44895 original size:22 final size:21
Alignment explanation
Indices: 44853--44892 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
44843 GAGTTTGTTT
*
44853 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
44874 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
44893 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:47840 original size:16 final size:15
Alignment explanation
Indices: 47817--47846 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
47807 TATTATAACC
47817 ATTTTTTATTTATTG
1 ATTTTTTATTTATTG
47832 ATTTGTTTATTTATT
1 ATTT-TTTATTTATT
47847 TTTTCTCATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.00, G:0.07, T:0.73
Consensus pattern (15 bp):
ATTTTTTATTTATTG
Found at i:47934 original size:10 final size:10
Alignment explanation
Indices: 47919--47956 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
47909 CTCCTAAATT
47919 TTTATTATTA
1 TTTATTATTA
47929 TTTATTATTA
1 TTTATTATTA
47939 TTT-TT-TTGA
1 TTTATTATT-A
47948 TTTATTATT
1 TTTATTATT
47957 TGACCTTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 2 0.08
9 6 0.24
10 15 0.60
11 2 0.08
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (10 bp):
TTTATTATTA
Found at i:47938 original size:13 final size:12
Alignment explanation
Indices: 47916--47957 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 12
47906 TAACTCCTAA
47916 ATTTTTATTATT
1 ATTTTTATTATT
47928 ATTTATTATTATT
1 ATTT-TTATTATT
47941 -TTTTTGATTTATT
1 ATTTTT-A-TTATT
47954 ATTT
1 ATTT
47958 GACCTTGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 2 0.08
12 8 0.31
13 13 0.50
14 3 0.12
ACGTcount: A:0.24, C:0.00, G:0.02, T:0.74
Consensus pattern (12 bp):
ATTTTTATTATT
Found at i:48086 original size:32 final size:30
Alignment explanation
Indices: 48050--48165 Score: 95
Period size: 32 Copynumber: 3.9 Consensus size: 30
48040 TTTTCTAACT
48050 TACTAACATTCTAACTTTTATTTTATTGTTTA
1 TACTAAC-TTCTAACTTTT-TTTTATTGTTTA
*
48082 TACTAACATTCTAAC--TTTTTT-TTGTTCA
1 TACTAAC-TTCTAACTTTTTTTTATTGTTTA
*
48110 TACTAACTT-T---TTATTTTTATTGTTCT-
1 TACTAACTTCTAACTTTTTTTTATTGTT-TA
48136 TACTAACTTACTAACATTTTATTTTATTGT
1 TACTAACTT-CTAAC-TTTT-TTTTATTGT
48166 ACAAACTAAC
Statistics
Matches: 69, Mismatches: 4, Indels: 21
0.73 0.04 0.22
Matches are distributed among these distances:
25 5 0.07
26 15 0.22
27 2 0.03
28 14 0.20
29 4 0.06
30 2 0.03
32 18 0.26
33 9 0.13
ACGTcount: A:0.26, C:0.14, G:0.03, T:0.57
Consensus pattern (30 bp):
TACTAACTTCTAACTTTTTTTTATTGTTTA
Found at i:48112 original size:28 final size:28
Alignment explanation
Indices: 48050--48160 Score: 84
Period size: 26 Copynumber: 3.8 Consensus size: 28
48040 TTTTCTAACT
*
48050 TACTAACATTCTAACTTTTATTTTATTGTTTA
1 TACTAAC-TTCTAAC-TTT-TTTT-TTGTTCA
48082 TACTAACATTCTAAC-TTTTTTTTGTTCA
1 TACTAAC-TTCTAACTTTTTTTTTGTTCA
* * * *
48110 TACTAACTTTTTA--TTTTTATTGTTCT
1 TACTAACTTCTAACTTTTTTTTTGTTCA
*
48136 TACTAACTTACTAACATTTTATTTT
1 TACTAACTT-CTAAC-TTTTTTTTT
48161 ATTGTACAAA
Statistics
Matches: 66, Mismatches: 9, Indels: 10
0.78 0.11 0.12
Matches are distributed among these distances:
26 20 0.30
27 6 0.09
28 13 0.20
29 4 0.06
30 8 0.12
32 15 0.23
ACGTcount: A:0.26, C:0.14, G:0.03, T:0.57
Consensus pattern (28 bp):
TACTAACTTCTAACTTTTTTTTTGTTCA
Found at i:48133 original size:26 final size:26
Alignment explanation
Indices: 48060--48144 Score: 93
Period size: 26 Copynumber: 3.3 Consensus size: 26
48050 TACTAACATT
*
48060 CTAAC-TTTTA-TTTTATTGTTTATA
1 CTAACTTTTTATTTTTATTGTTCATA
* * *
48084 CTAACATTCTAACTTTTTTTTGTTCATA
1 CTAAC-TTTTTA-TTTTTATTGTTCATA
*
48112 CTAACTTTTTATTTTTATTGTTCTTA
1 CTAACTTTTTATTTTTATTGTTCATA
48138 CTAACTT
1 CTAACTT
48145 ACTAACATTT
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
24 5 0.10
26 23 0.47
27 4 0.08
28 17 0.35
ACGTcount: A:0.24, C:0.14, G:0.04, T:0.59
Consensus pattern (26 bp):
CTAACTTTTTATTTTTATTGTTCATA
Found at i:48174 original size:33 final size:34
Alignment explanation
Indices: 48110--48175 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 34
48100 TTTTTGTTCA
* * **
48110 TACTAACTTTTTATTTTTATTGTTCTTACTAACT
1 TACTAACATTTTATTTTTATTGTACAAACTAACT
48144 TACTAACATTTTA-TTTTATTGTACAAACTAAC
1 TACTAACATTTTATTTTTATTGTACAAACTAAC
48176 CCGCTAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 16 0.57
34 12 0.43
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (34 bp):
TACTAACATTTTATTTTTATTGTACAAACTAACT
Found at i:56013 original size:19 final size:20
Alignment explanation
Indices: 55979--56017 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
55969 ATTTCTTAAT
*
55979 AACATAACATTTTAATATAA
1 AACAAAACATTTTAATATAA
55999 AACAAAACA-TTTAATATAA
1 AACAAAACATTTTAATATAA
56018 CTATTATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.59, C:0.10, G:0.00, T:0.31
Consensus pattern (20 bp):
AACAAAACATTTTAATATAA
Found at i:56485 original size:46 final size:46
Alignment explanation
Indices: 56435--56706 Score: 400
Period size: 46 Copynumber: 5.9 Consensus size: 46
56425 TATGGTCTCT
* * * * * *
56435 TTTCATACATTAATACATCCATTCATACTTTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
*
56481 TTTCATGCCTTAATGCATCCTTTCATGGATTTTCAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTT-AATTATGGCATCC
**
56528 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGAAATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
* * *
56574 TTTCATGACTTAATGCATCCTTTCATGCATTTTAATTACGGTATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
*
56620 TTTCATGCCTTAATGCATTCTTTCATGCATTTTAATTATGGCATCC
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
* *
56666 TTTCACGCCTTAATGCATCATTTCATGCATTTTAATTATGG
1 TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGG
56707 ATTCGATTTA
Statistics
Matches: 204, Mismatches: 21, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
46 159 0.78
47 45 0.22
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.44
Consensus pattern (46 bp):
TTTCATGCCTTAATGCATCCTTTCATGCATTTTAATTATGGCATCC
Found at i:56500 original size:20 final size:20
Alignment explanation
Indices: 56475--56693 Score: 114
Period size: 20 Copynumber: 9.7 Consensus size: 20
56465 TTTAATTATG
56475 GCATCCTTTCATGCCTTAAT
1 GCATCCTTTCATGCCTTAAT
**
56495 GCATCCTTTCATGGATTTTCAATTAT
1 GCATCCTTTCAT-G-CCTT--A--AT
56521 GGCATCCTTTCATGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
56542 GCATCCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
* *
56567 GAAATCCTTTCATGACTTAAT
1 G-CATCCTTTCATGCCTTAAT
*
56588 GCATCCTTTCATGCATTTTAATT
1 GCATCCTTTCATGC--CTTAA-T
*
56611 ACGGTATCCTTTCATGCCTTAAT
1 ---GCATCCTTTCATGCCTTAAT
* *
56634 GCATTCTTTCATGCATTTTAATTAT
1 GCATCCTTTCATGC--CTT-A--AT
*
56659 GGCATCCTTTCACGCCTTAAT
1 -GCATCCTTTCATGCCTTAAT
*
56680 GCATCATTTCATGC
1 GCATCCTTTCATGC
56694 ATTTTAATTA
Statistics
Matches: 153, Mismatches: 21, Indels: 50
0.68 0.09 0.22
Matches are distributed among these distances:
20 61 0.40
21 8 0.05
22 10 0.07
23 7 0.05
24 9 0.06
25 7 0.05
26 39 0.25
27 12 0.08
ACGTcount: A:0.23, C:0.24, G:0.11, T:0.42
Consensus pattern (20 bp):
GCATCCTTTCATGCCTTAAT
Found at i:57304 original size:20 final size:19
Alignment explanation
Indices: 57279--57330 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 19
57269 GTCTTGGAAT
57279 GGTATCGATATCTTCCCT-TC
1 GGTATCGATA-C-TCCCTCTC
57299 GGTATCGATACTCCCTCGTC
1 GGTATCGATACTCCCTC-TC
57319 GGTATCGATACT
1 GGTATCGATACT
57331 GATTCAATCA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 5 0.17
19 1 0.03
20 24 0.80
ACGTcount: A:0.17, C:0.29, G:0.19, T:0.35
Consensus pattern (19 bp):
GGTATCGATACTCCCTCTC
Found at i:57889 original size:3 final size:3
Alignment explanation
Indices: 57881--57910 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
57871 ACACCAACGT
57881 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
57911 TAGGGAATGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:59320 original size:29 final size:30
Alignment explanation
Indices: 59287--59343 Score: 73
Period size: 29 Copynumber: 1.9 Consensus size: 30
59277 CAAATTTTGG
*
59287 TTAGTGACC-AAAATATAAA-TTTTGAAAGT
1 TTAGTG-CCTAAAATATAAAGTTTAGAAAGT
*
59316 TTAGTGCCTAAATTATAAAGTTTAGAAA
1 TTAGTGCCTAAAATATAAAGTTTAGAAA
59344 AATTCAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.08
29 15 0.62
30 7 0.29
ACGTcount: A:0.44, C:0.07, G:0.14, T:0.35
Consensus pattern (30 bp):
TTAGTGCCTAAAATATAAAGTTTAGAAAGT
Found at i:62436 original size:21 final size:21
Alignment explanation
Indices: 62410--62484 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
62400 ATATAGAATG
62410 TCCCGAAGGACCACATATATA
1 TCCCGAAGGACCACATATATA
* * * *
62431 TCCCGAATGACCGCTTAGAATTA
1 TCCCGAAGGACCACATA-TA-TA
** *
62454 TCCCGAAATACCACATATATG
1 TCCCGAAGGACCACATATATA
*
62475 TCTCGAAGGA
1 TCCCGAAGGA
62485 TCGTGGAGAA
Statistics
Matches: 39, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
21 22 0.56
22 2 0.05
23 15 0.38
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.23
Consensus pattern (21 bp):
TCCCGAAGGACCACATATATA
Found at i:69661 original size:21 final size:21
Alignment explanation
Indices: 69637--69706 Score: 104
Period size: 21 Copynumber: 3.2 Consensus size: 21
69627 AAAAGTCCTG
69637 AAGGACCACATATATGTCCCA
1 AAGGACCACATATATGTCCCA
* *
69658 AAGGACCACGTAGAATTGTCCCA
1 AAGGACCACATA-TA-TGTCCCA
69681 AAGGACCACATATATGTCCCA
1 AAGGACCACATATATGTCCCA
69702 AAGGA
1 AAGGA
69707 TCGCTTAGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
21 23 0.53
22 2 0.05
23 18 0.42
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.17
Consensus pattern (21 bp):
AAGGACCACATATATGTCCCA
Found at i:71994 original size:39 final size:38
Alignment explanation
Indices: 71915--71996 Score: 112
Period size: 39 Copynumber: 2.1 Consensus size: 38
71905 AAAAATAATA
* *
71915 TGATATGACTATTATATGATATTTGTTTATCATTGCTT
1 TGATATGACTATTATATGATATTTATTTATCATGGCTT
*
71953 TGATATGACTATTATGTATGATA-TTATTTATCATGGTTT
1 TGATATGACTATTA--TATGATATTTATTTATCATGGCTT
71992 TGATA
1 TGATA
71997 AAATCATGAG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 14 0.36
39 18 0.46
40 7 0.18
ACGTcount: A:0.28, C:0.06, G:0.15, T:0.51
Consensus pattern (38 bp):
TGATATGACTATTATATGATATTTATTTATCATGGCTT
Done.