Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002884.1 Hibiscus syriacus cultivar Beakdansim tig00005965_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: 49234
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:712 original size:12 final size:12
Alignment explanation
Indices: 695--719 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
685 TAGACTTGAT
695 AAGTTGAATTTG
1 AAGTTGAATTTG
707 AAGTTGAATTTG
1 AAGTTGAATTTG
719 A
1 A
720 CTTGTCATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.36, C:0.00, G:0.24, T:0.40
Consensus pattern (12 bp):
AAGTTGAATTTG
Found at i:1990 original size:20 final size:20
Alignment explanation
Indices: 1961--1998 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
1951 TTTCAAAGTG
1961 ATGCACCGATGCACCAATCC
1 ATGCACCGATGCACCAATCC
*
1981 ATGCATCGATGCACCAAT
1 ATGCACCGATGCACCAAT
1999 TAATTTTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.16, T:0.18
Consensus pattern (20 bp):
ATGCACCGATGCACCAATCC
Found at i:2065 original size:45 final size:46
Alignment explanation
Indices: 2016--2107 Score: 159
Period size: 45 Copynumber: 2.0 Consensus size: 46
2006 TCAAACATCG
* *
2016 AATGCATTTTATGCATCGATGCAC-ATACCATGCATCGATGCACTC
1 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
2061 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
1 AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
2107 A
1 A
2108 GGCTTTTTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
45 23 0.52
46 21 0.48
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (46 bp):
AATGCATTTGATGCATCGATGCACAAGACCATGCATCGATGCACTC
Found at i:2406 original size:11 final size:11
Alignment explanation
Indices: 2390--2425 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
2380 ACAAGCAACT
2390 AGAATCAAGAG
1 AGAATCAAGAG
2401 AGAATCAAGAG
1 AGAATCAAGAG
2412 AGAATCAA-AG
1 AGAATCAAGAG
2422 AGAA
1 AGAA
2426 AGCATCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.58, C:0.08, G:0.25, T:0.08
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:10785 original size:26 final size:26
Alignment explanation
Indices: 10755--10807 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
10745 TCAAACATCG
*
10755 AATGCATTTTATGCATAGATGCACTC
1 AATGCATTTGATGCATAGATGCACTC
*
10781 AATGCATTTGATGCATCGATGCACTC
1 AATGCATTTGATGCATAGATGCACTC
10807 A
1 A
10808 GGCTTTTTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (26 bp):
AATGCATTTGATGCATAGATGCACTC
Found at i:12005 original size:20 final size:18
Alignment explanation
Indices: 11977--12020 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 18
11967 TGCAATATCA
*
11977 ATGTTATATGAAATGTGACT
1 ATGTGATATG-AATGTGA-T
*
11997 ATGTGATATGAATTTGAT
1 ATGTGATATGAATGTGAT
12015 ATGTGA
1 ATGTGA
12021 ACATAAGTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 7 0.32
19 6 0.27
20 9 0.41
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (18 bp):
ATGTGATATGAATGTGAT
Found at i:12351 original size:32 final size:32
Alignment explanation
Indices: 12297--12420 Score: 112
Period size: 31 Copynumber: 3.9 Consensus size: 32
12287 AGTCGAGGGT
* * *
12297 TTACTTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTTCGGGACATATGGACAGAA
*
12329 TTACCTATG-TCTTTCGGGACATATGGACAGCA
1 TTACCTATGTTC-TTCGGGACATATGGACAGAA
** * *
12361 -TACCTATGTTCTAAGGAACATATGGACA-AT
1 TTACCTATGTTCTTCGGGACATATGGACAGAA
* *
12391 TTACCTA-GTTTCTTCGGGACCTATGCACAG
1 TTACCTATG-TTCTTCGGGACATATGGACAG
12421 TTGCCGAGGT
Statistics
Matches: 73, Mismatches: 14, Indels: 10
0.75 0.14 0.10
Matches are distributed among these distances:
30 1 0.01
31 45 0.62
32 27 0.37
ACGTcount: A:0.29, C:0.20, G:0.19, T:0.31
Consensus pattern (32 bp):
TTACCTATGTTCTTCGGGACATATGGACAGAA
Found at i:12381 original size:63 final size:62
Alignment explanation
Indices: 12302--12420 Score: 168
Period size: 62 Copynumber: 1.9 Consensus size: 62
12292 AGGGTTTACT
* *
12302 TATGTTCTACGGAACATATGGACAGAATTACCTATGTCT-TTCGGGACATATGGACAGCATACC
1 TATGTTCTAAGGAACATATGGACA-AATTACCTA-GTCTCTTCGGGACATATGCACAGCATACC
* * *
12365 TATGTTCTAAGGAACATATGGACAATTTACCTAGTTTCTTCGGGACCTATGCACAG
1 TATGTTCTAAGGAACATATGGACAAATTACCTAGTCTCTTCGGGACATATGCACAG
12421 TTGCCGAGGT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
61 3 0.06
62 24 0.48
63 23 0.46
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.30
Consensus pattern (62 bp):
TATGTTCTAAGGAACATATGGACAAATTACCTAGTCTCTTCGGGACATATGCACAGCATACC
Found at i:12382 original size:31 final size:32
Alignment explanation
Indices: 12297--12397 Score: 118
Period size: 31 Copynumber: 3.2 Consensus size: 32
12287 AGTCGAGGGT
*
12297 TTACTTATGTTCTACGGAACATATGGACAGAA
1 TTACCTATGTTCTACGGAACATATGGACAGAA
* * *
12329 TTACCTATG-TCTTTCGGGACATATGGACAGCA
1 TTACCTATGTTC-TACGGAACATATGGACAGAA
* *
12361 -TACCTATGTTCTAAGGAACATATGGACA-AT
1 TTACCTATGTTCTACGGAACATATGGACAGAA
12391 TTACCTA
1 TTACCTA
12398 GTTTCTTCGG
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
31 30 0.53
32 27 0.47
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.32
Consensus pattern (32 bp):
TTACCTATGTTCTACGGAACATATGGACAGAA
Found at i:13179 original size:11 final size:11
Alignment explanation
Indices: 13158--13192 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
13148 ATTTTACGAA
*
13158 AGTACTATAGC
1 AGTACTGTAGC
*
13169 AGTATTGTAGC
1 AGTACTGTAGC
13180 AGTACTGTAGC
1 AGTACTGTAGC
13191 AG
1 AG
13193 GGGTATCGGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.26, T:0.29
Consensus pattern (11 bp):
AGTACTGTAGC
Found at i:13210 original size:22 final size:22
Alignment explanation
Indices: 13185--13227 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
13175 GTAGCAGTAC
* *
13185 TGTAGCAGGGGTATCGGTTCCT
1 TGTAGCAGGGGAAACGGTTCCT
*
13207 TGTAGTAGGGGAAACGGTTCC
1 TGTAGCAGGGGAAACGGTTCC
13228 CCTCTGACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.19, C:0.16, G:0.37, T:0.28
Consensus pattern (22 bp):
TGTAGCAGGGGAAACGGTTCCT
Found at i:14766 original size:11 final size:11
Alignment explanation
Indices: 14750--14774 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
14740 GTCTTCTATT
14750 TTTTAAATATA
1 TTTTAAATATA
14761 TTTTAAATATA
1 TTTTAAATATA
14772 TTT
1 TTT
14775 AATTATATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
TTTTAAATATA
Found at i:14799 original size:16 final size:16
Alignment explanation
Indices: 14770--14808 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
14760 ATTTTAAATA
14770 TATTTAATTATATAGTT
1 TATTTAATTATATA-TT
*
14787 TTTTTAA-TATATATT
1 TATTTAATTATATATT
14802 TATTTAA
1 TATTTAA
14809 AATAATTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
15 8 0.40
16 6 0.30
17 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.62
Consensus pattern (16 bp):
TATTTAATTATATATT
Found at i:15048 original size:26 final size:26
Alignment explanation
Indices: 15019--15069 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
15009 TATAAAATAT
*
15019 TTTAAAT-AGAAAGATGGGTAGTTTTG
1 TTTAAATGA-AAAGATAGGTAGTTTTG
*
15045 TTTAAATGAAAAGTTAGGTAGTTTT
1 TTTAAATGAAAAGATAGGTAGTTTT
15070 TCAATAAGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 21 0.95
27 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.24, T:0.41
Consensus pattern (26 bp):
TTTAAATGAAAAGATAGGTAGTTTTG
Found at i:19617 original size:19 final size:19
Alignment explanation
Indices: 19593--19629 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
19583 ATAACCAACA
*
19593 AAATCGTAATGCGATCTCT
1 AAATCGTAACGCGATCTCT
19612 AAATCGTAACGCGATCTC
1 AAATCGTAACGCGATCTC
19630 CATTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.24, G:0.16, T:0.27
Consensus pattern (19 bp):
AAATCGTAACGCGATCTCT
Found at i:19758 original size:41 final size:41
Alignment explanation
Indices: 19713--19851 Score: 242
Period size: 41 Copynumber: 3.4 Consensus size: 41
19703 GCGAATATGT
*
19713 AAATCGTAACGCGATTCTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
*
19754 AAATCGCAATGCGATTCTGACTATCGCAACGCGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
*
19795 AAATCGCAACGCGATTCTGACTATCGCAACACGATAATACA
1 AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
*
19836 AAATCGCAATGCGATT
1 AAATCGCAACGCGATT
19852 TTCAAAGCGC
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 93 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (41 bp):
AAATCGCAACGCGATTCTGACTATCGCAACGCGATAATACA
Found at i:19761 original size:21 final size:21
Alignment explanation
Indices: 19735--19850 Score: 105
Period size: 21 Copynumber: 5.6 Consensus size: 21
19725 GATTCTGACT
19735 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
* ** *
19756 ATCGCAATGCGATTCTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
19776 ATCGCAACGCGATAATACAAA
1 ATCGCAACGCGATAATACAAA
** *
19797 ATCGCAACGCGATTCTGAC--T
1 ATCGCAACGCGATAAT-ACAAA
*
19817 ATCGCAACACGATAATACAAA
1 ATCGCAACGCGATAATACAAA
*
19838 ATCGCAATGCGAT
1 ATCGCAACGCGAT
19851 TTTCAAAGCG
Statistics
Matches: 72, Mismatches: 17, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
19 4 0.06
20 26 0.36
21 38 0.53
22 4 0.06
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGATAATACAAA
Found at i:20468 original size:19 final size:20
Alignment explanation
Indices: 20440--20479 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
20430 CGCAACGCAA
*
20440 TTTTAGTTTCACATTGCGAT
1 TTTTAGTTTCACATTACGAT
*
20460 TTTTA-TTTCGCATTACGAT
1 TTTTAGTTTCACATTACGAT
20479 T
1 T
20480 ATCCCATTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.20, C:0.15, G:0.12, T:0.53
Consensus pattern (20 bp):
TTTTAGTTTCACATTACGAT
Found at i:20523 original size:20 final size:20
Alignment explanation
Indices: 20487--20552 Score: 71
Period size: 20 Copynumber: 3.3 Consensus size: 20
20477 ATTATCCCAT
**
20487 TGCGATAGTCAAATTCGCGA
1 TGCGATAGTCATTTTCGCGA
20507 TGCGATAGTCATTTTCGC-A
1 TGCGATAGTCATTTTCGCGA
* * *
20526 TTTCGATAGTCATTTTCACGT
1 -TGCGATAGTCATTTTCGCGA
20547 TGCGAT
1 TGCGAT
20553 TTTAAGTTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 4
0.79 0.12 0.08
Matches are distributed among these distances:
19 1 0.03
20 37 0.97
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (20 bp):
TGCGATAGTCATTTTCGCGA
Found at i:20562 original size:20 final size:20
Alignment explanation
Indices: 20539--20583 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
20529 CGATAGTCAT
20539 TTTCACGTTGCGATTTTAAG
1 TTTCACGTTGCGATTTTAAG
*
20559 TTTCATGTTGCGATTTTAAG
1 TTTCACGTTGCGATTTTAAG
20579 TTTCA
1 TTTCA
20584 GAAACTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.49
Consensus pattern (20 bp):
TTTCACGTTGCGATTTTAAG
Found at i:21093 original size:21 final size:22
Alignment explanation
Indices: 21069--21128 Score: 61
Period size: 21 Copynumber: 2.8 Consensus size: 22
21059 ATGTCATCGT
21069 TCAAGAGGCCCCTATCATCC-C
1 TCAAGAGGCCCCTATCATCCAC
* ** *
21090 TCAAGAGTCCCCTCCCA-CCAT
1 TCAAGAGGCCCCTATCATCCAC
*
21111 TCAAGAGGCCCCTGTCAT
1 TCAAGAGGCCCCTATCAT
21129 TGTTGAAGAG
Statistics
Matches: 30, Mismatches: 7, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.07
21 28 0.93
ACGTcount: A:0.23, C:0.42, G:0.15, T:0.20
Consensus pattern (22 bp):
TCAAGAGGCCCCTATCATCCAC
Found at i:21138 original size:42 final size:42
Alignment explanation
Indices: 21068--21159 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
21058 CATGTCATCG
21068 TTCAAGAGGCCCCTATCATCCCTCAAGA-GTCCCCTCCCACCA
1 TTCAAGAGGCCCCTATCATCCCTCAAGAGGT-CCCTCCCACCA
* *** *
21110 TTCAAGAGGCCCCTGTCATTGTTGAAGAGGTCCCTCCCACCA
1 TTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCACCA
21152 TTCAAGAG
1 TTCAAGAG
21160 CCCGATTCAC
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 42 0.95
43 2 0.05
ACGTcount: A:0.24, C:0.37, G:0.17, T:0.22
Consensus pattern (42 bp):
TTCAAGAGGCCCCTATCATCCCTCAAGAGGTCCCTCCCACCA
Found at i:21158 original size:21 final size:21
Alignment explanation
Indices: 21090--21159 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
21080 CTATCATCCC
21090 TCAAGA-GTCCCCTCCCACCAT
1 TCAAGAGGT-CCCTCCCACCAT
* ** ***
21111 TCAAGAGGCCCCTGTCATTGT
1 TCAAGAGGTCCCTCCCACCAT
*
21132 TGAAGAGGTCCCTCCCACCAT
1 TCAAGAGGTCCCTCCCACCAT
21153 TCAAGAG
1 TCAAGAG
21160 CCCGATTCAC
Statistics
Matches: 34, Mismatches: 14, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.19, T:0.21
Consensus pattern (21 bp):
TCAAGAGGTCCCTCCCACCAT
Found at i:22342 original size:23 final size:23
Alignment explanation
Indices: 22316--22384 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
22306 CACCACAGCT
*
22316 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
22339 CGTAGAATT-CAACCGGAGTGCCA
1 CGTAGAATTGC-ACCGAAGTGCCA
*
22362 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
22385 TATAATAATG
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
22 1 0.02
23 39 0.95
24 1 0.02
ACGTcount: A:0.29, C:0.26, G:0.25, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:22571 original size:103 final size:103
Alignment explanation
Indices: 22400--22612 Score: 390
Period size: 103 Copynumber: 2.1 Consensus size: 103
22390 TAATGTCCAT
* * *
22400 AAGGAGCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
22465 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
22503 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
22568 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
22606 AAGGACC
1 AAGGACC
22613 GCGTAGACTC
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.36, C:0.23, G:0.15, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:27631 original size:23 final size:23
Alignment explanation
Indices: 27605--27650 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
27595 CACCACAGCT
*
27605 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
27628 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
27651 TATAATAATG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.28, C:0.26, G:0.26, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:27837 original size:103 final size:103
Alignment explanation
Indices: 27666--27878 Score: 390
Period size: 103 Copynumber: 2.1 Consensus size: 103
27656 TAATGTCCAT
* *
27666 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTATCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCA
27731 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
27769 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCA
27834 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
27872 AAGGACC
1 AAGGACC
27879 GCGTAGACCC
Statistics
Matches: 106, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 106 1.00
ACGTcount: A:0.37, C:0.24, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTATCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:31372 original size:19 final size:20
Alignment explanation
Indices: 31282--31384 Score: 111
Period size: 20 Copynumber: 5.2 Consensus size: 20
31272 AAGGTACACT
* * *
31282 TTCGCAACGCTAAACTCAAA
1 TTCGCAATGCGAAAGTCAAA
*
31302 ATCGCAATGCGAAAGTCAAA
1 TTCGCAATGCGAAAGTCAAA
* *
31322 ATCGCAATGCGAAAGCCAAA
1 TTCGCAATGCGAAAGTCAAA
* *
31342 ATCGCAACGCGAAAGTC-AA
1 TTCGCAATGCGAAAGTCAAA
*
31361 TTCGCATTGCGAAAGTC-AA
1 TTCGCAATGCGAAAGTCAAA
31380 TTCGC
1 TTCGC
31385 GTTGCGATAG
Statistics
Matches: 73, Mismatches: 10, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 23 0.32
20 50 0.68
ACGTcount: A:0.39, C:0.25, G:0.18, T:0.17
Consensus pattern (20 bp):
TTCGCAATGCGAAAGTCAAA
Found at i:31513 original size:20 final size:20
Alignment explanation
Indices: 31350--31514 Score: 168
Period size: 20 Copynumber: 8.7 Consensus size: 20
31340 AAATCGCAAC
* *
31350 GCGAAAGTC-AATTCGCATT
1 GCGATAGTCAAATTCGCGTT
*
31369 GCGAAAGTC-AATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
* * *
31388 GCGATAGTCTAATACGCTTT
1 GCGATAGTCAAATTCGCGTT
*
31408 GCGAT--T----TTCTCGTT
1 GCGATAGTCAAATTCGCGTT
31422 GCGATAGTCAAATTTC-CGTT
1 GCGATAGTCAAA-TTCGCGTT
* *
31442 GCGATAATCAAATTCACGTT
1 GCGATAGTCAAATTCGCGTT
31462 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
31482 GCGATAGTCAAATTCGCGTT
1 GCGATAGTCAAATTCGCGTT
*
31502 GCGATATTCAAAT
1 GCGATAGTCAAAT
31515 GAATGTGTAA
Statistics
Matches: 126, Mismatches: 11, Indels: 17
0.82 0.07 0.11
Matches are distributed among these distances:
14 10 0.08
16 1 0.01
18 1 0.01
19 29 0.23
20 82 0.65
21 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (20 bp):
GCGATAGTCAAATTCGCGTT
Found at i:31708 original size:18 final size:18
Alignment explanation
Indices: 31685--31719 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31675 AAGCCGGTTG
*
31685 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
31703 TGATTGCGATTTTGATT
1 TGATTGCGATTTTGATT
31720 GCCTTTTGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.17, C:0.03, G:0.26, T:0.54
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:31875 original size:20 final size:20
Alignment explanation
Indices: 31851--31922 Score: 74
Period size: 21 Copynumber: 3.5 Consensus size: 20
31841 TGACAACAGT
31851 GTTGCGATTTTGACTATCGC
1 GTTGCGATTTTGACTATCGC
* * *
31871 ATTGCGATTTT-CCAAATTCGC
1 GTTGCGATTTTGAC-TA-TCGC
*
31892 GTTGCGATTTTGTATTATCGC
1 GTTGCGATTTTG-ACTATCGC
31913 GTTGCGATTT
1 GTTGCGATTT
31923 ACATATTCGC
Statistics
Matches: 41, Mismatches: 7, Indels: 7
0.75 0.13 0.13
Matches are distributed among these distances:
19 1 0.02
20 11 0.27
21 28 0.68
22 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.22, T:0.43
Consensus pattern (20 bp):
GTTGCGATTTTGACTATCGC
Found at i:31931 original size:41 final size:41
Alignment explanation
Indices: 31851--31932 Score: 112
Period size: 41 Copynumber: 2.0 Consensus size: 41
31841 TGACAACAGT
*
31851 GTTGCGATTTTGACTATCGCATTGCGATTTTCCAAATTCGC
1 GTTGCGATTTTGACTATCGCATTGCGATTTTACAAATTCGC
* * *
31892 GTTGCGATTTTGTATTATCGCGTTGCGA-TTTACATATTCGC
1 GTTGCGATTTTG-ACTATCGCATTGCGATTTTACAAATTCGC
31933 ATTGTGATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
41 23 0.64
42 13 0.36
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (41 bp):
GTTGCGATTTTGACTATCGCATTGCGATTTTACAAATTCGC
Found at i:32009 original size:19 final size:19
Alignment explanation
Indices: 31985--32021 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
31975 TGCGATACTG
*
31985 GAGATCACGTTGCGATTTA
1 GAGATCACATTGCGATTTA
*
32004 GAGATCGCATTGCGATTT
1 GAGATCACATTGCGATTT
32022 TGTTGGTCAT
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:0.24, C:0.16, G:0.27, T:0.32
Consensus pattern (19 bp):
GAGATCACATTGCGATTTA
Found at i:33001 original size:26 final size:24
Alignment explanation
Indices: 32969--33025 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 24
32959 CAATTATTCA
32969 ATAAATATATTTTAAGAAAATT-ATAT
1 ATAAATAT-TTTT-A-AAAATTCATAT
*
32995 TTAAATATTTTTAAAAATTCATAT
1 ATAAATATTTTTAAAAATTCATAT
33019 ATAAATA
1 ATAAATA
33026 ATGAGGGATT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
23 6 0.21
24 11 0.39
25 4 0.14
26 7 0.25
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (24 bp):
ATAAATATTTTTAAAAATTCATAT
Found at i:38459 original size:16 final size:16
Alignment explanation
Indices: 38432--38475 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
38422 AAACTATGAG
*
38432 ACATGCTATATGTGATT
1 ACATGCTATATGTGA-C
38449 ACATG-TATATGTGAC
1 ACATGCTATATGTGAC
*
38464 ACATGTTATATG
1 ACATGCTATATG
38476 ATATGAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 15 0.60
17 5 0.20
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (16 bp):
ACATGCTATATGTGAC
Found at i:38691 original size:31 final size:31
Alignment explanation
Indices: 38602--38697 Score: 113
Period size: 31 Copynumber: 3.1 Consensus size: 31
38592 AAGAGTCGAG
* *
38602 GGTTACCTATGTCTTTC-GAGACATATGAACA
1 GGTTACCTATGTCCTTCGGA-ACATATGGACA
* *
38633 GTTTACCTATGTCCTTCGGGACATATGGACA
1 GGTTACCTATGTCCTTCGGAACATATGGACA
* * *
38664 GGTTACCTCTGTTCTTCGGAACATATGGATA
1 GGTTACCTATGTCCTTCGGAACATATGGACA
38695 GGT
1 GGT
38698 CCTTCGAGAC
Statistics
Matches: 55, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
31 54 0.98
32 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.23, T:0.33
Consensus pattern (31 bp):
GGTTACCTATGTCCTTCGGAACATATGGACA
Found at i:43674 original size:2 final size:2
Alignment explanation
Indices: 43632--43658 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
43622 ATATGTTATG
43632 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
43659 GTTACATGAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:44060 original size:16 final size:16
Alignment explanation
Indices: 44033--44076 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
44023 AAACTATGAG
*
44033 ACATGATATATGTGATT
1 ACATGATATATGTGA-C
44050 ACATG-TATATGTGAC
1 ACATGATATATGTGAC
*
44065 ACATGTTATATG
1 ACATGATATATG
44077 ATATGAGATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 5 0.20
16 15 0.60
17 5 0.20
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.39
Consensus pattern (16 bp):
ACATGATATATGTGAC
Found at i:44243 original size:31 final size:31
Alignment explanation
Indices: 44203--44290 Score: 108
Period size: 31 Copynumber: 2.8 Consensus size: 31
44193 AAGAGTCGAG
44203 GGTTACCTATGTCT-TTCGAGACATATGGACA
1 GGTTACCTATGT-TATTCGAGACATATGGACA
* * *
44234 GTTTACCTATGTTATTCGGGATATATGGACA
1 GGTTACCTATGTTATTCGAGACATATGGACA
*
44265 GGTTACCTATGTTCTTCG-GAACATAT
1 GGTTACCTATGTTATTCGAG-ACATAT
44291 TGATAGGTCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.04
31 47 0.96
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (31 bp):
GGTTACCTATGTTATTCGAGACATATGGACA
Found at i:46494 original size:23 final size:23
Alignment explanation
Indices: 46468--46623 Score: 154
Period size: 23 Copynumber: 6.8 Consensus size: 23
46458 TATAGGATAA
46468 TTCTATGTGGT-CTGTCGGGACAT
1 TTCTATGTGGTCCT-TCGGGACAT
* ** *
46491 TTCTATGCGGTCCTTTTGGACAA
1 TTCTATGTGGTCCTTCGGGACAT
*
46514 TACTATGTGGTCCTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
* * *
46537 TTCTATGCGGCCCTTCTGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
* * ** *
46560 TTCTATGCGGCCCTTCTAGACAA
1 TTCTATGTGGTCCTTCGGGACAT
*
46583 TACTATGTGGTCCTTCGGGACAT
1 TTCTATGTGGTCCTTCGGGACAT
46606 TTCTATGTGG-CACTTCGG
1 TTCTATGTGGTC-CTTCGG
46624 TCCATATTCT
Statistics
Matches: 109, Mismatches: 22, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
22 1 0.01
23 106 0.97
24 2 0.02
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (23 bp):
TTCTATGTGGTCCTTCGGGACAT
Found at i:46559 original size:69 final size:69
Alignment explanation
Indices: 46485--46621 Score: 229
Period size: 69 Copynumber: 2.0 Consensus size: 69
46475 TGGTCTGTCG
* * * *
46485 GGACATTTCTATGCGGTCCTTTTGGACAATACTATGTGGTCCTTCGGGACATTTCTATGCGGCCC
1 GGACATTTCTATGCGGCCCTTCTAGACAATACTATGTGGTCCTTCGGGACATTTCTATGCGGCAC
46550 TTCT
66 TTCT
*
46554 GGACATTTCTATGCGGCCCTTCTAGACAATACTATGTGGTCCTTCGGGACATTTCTATGTGGCAC
1 GGACATTTCTATGCGGCCCTTCTAGACAATACTATGTGGTCCTTCGGGACATTTCTATGCGGCAC
46619 TTC
66 TTC
46622 GGTCCATATT
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.35
Consensus pattern (69 bp):
GGACATTTCTATGCGGCCCTTCTAGACAATACTATGTGGTCCTTCGGGACATTTCTATGCGGCAC
TTCT
Found at i:46566 original size:46 final size:46
Alignment explanation
Indices: 46445--46623 Score: 175
Period size: 46 Copynumber: 3.9 Consensus size: 46
46435 GAGTCGAGTG
* * *
46445 TTCTATGCGGTCCTAT-AGGATAATTCTATGTGGT-CTGTCGGGACAT
1 TTCTATGCGGTCCT-TCTGGACATTTCTATGTGGTCCT-TCGGGACAT
* * *
46491 TTCTATGCGGTCCTTTTGGACAATACTATGTGGTCCTTCGGGACAT
1 TTCTATGCGGTCCTTCTGGACATTTCTATGTGGTCCTTCGGGACAT
* * * ** *
46537 TTCTATGCGGCCCTTCTGGACATTTCTATGCGGCCCTTCTAGACAA
1 TTCTATGCGGTCCTTCTGGACATTTCTATGTGGTCCTTCGGGACAT
* * *
46583 TACTATGTGGTCCTTCGGGACATTTCTATGTGG-CACTTCGG
1 TTCTATGCGGTCCTTCTGGACATTTCTATGTGGTC-CTTCGG
46624 TCCATATTCT
Statistics
Matches: 111, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
45 2 0.02
46 107 0.96
47 2 0.02
ACGTcount: A:0.17, C:0.23, G:0.24, T:0.36
Consensus pattern (46 bp):
TTCTATGCGGTCCTTCTGGACATTTCTATGTGGTCCTTCGGGACAT
Done.