Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002477.1 Hibiscus syriacus cultivar Beakdansim tig00005060_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: 56880
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:265 original size:18 final size:18
Alignment explanation
Indices: 242--277 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
232 GATAGACTCG
242 TCCATGACTTGGAATTCA
1 TCCATGACTTGGAATTCA
260 TCCATGACTTGGAATTCA
1 TCCATGACTTGGAATTCA
278 GACTCCAACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.33
Consensus pattern (18 bp):
TCCATGACTTGGAATTCA
Found at i:5610 original size:13 final size:14
Alignment explanation
Indices: 5583--5614 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
5573 TTTATGAAAT
5583 ATAAA-GTAAATAA
1 ATAAATGTAAATAA
5596 ATAAATGTAAA-AA
1 ATAAATGTAAATAA
5609 ATAAAT
1 ATAAAT
5615 TTTTACATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.72
14 5 0.28
ACGTcount: A:0.69, C:0.00, G:0.06, T:0.25
Consensus pattern (14 bp):
ATAAATGTAAATAA
Found at i:6739 original size:17 final size:18
Alignment explanation
Indices: 6717--6755 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
6707 GACGTCATCT
6717 AAAATATT-TAAAAATAA
1 AAAATATTATAAAAATAA
6734 AAAATATTATAAAAATAA
1 AAAATATTATAAAAATAA
6752 AAAA
1 AAAA
6756 GAAATAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATATTATAAAAATAA
Found at i:6762 original size:17 final size:18
Alignment explanation
Indices: 6725--6764 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6715 CTAAAATATT
* *
6725 TAAAAATAAAAAATATTA
1 TAAAAATAAAAAAGATAA
6743 TAAAAATAAAAAAGA-AA
1 TAAAAATAAAAAAGATAA
6760 TAAAA
1 TAAAA
6765 TTTTGAGATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.20
Consensus pattern (18 bp):
TAAAAATAAAAAAGATAA
Found at i:14338 original size:31 final size:31
Alignment explanation
Indices: 14277--14359 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 31
14267 CCATAATTAT
* *
14277 AAAATAGTCAATATATTTTATCCAACTGTTAC
1 AAAATAGTCAATA-AATTTATCAAACTGTTAC
* * *
14309 AAAATAGTCATTAAATTTATCAAAGTGTTAT
1 AAAATAGTCAATAAATTTATCAAACTGTTAC
* *
14340 GAAATAGTCACTAAATTTAT
1 AAAATAGTCAATAAATTTAT
14360 TAATATTTTA
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
31 32 0.73
32 12 0.27
ACGTcount: A:0.43, C:0.11, G:0.08, T:0.37
Consensus pattern (31 bp):
AAAATAGTCAATAAATTTATCAAACTGTTAC
Found at i:15647 original size:164 final size:163
Alignment explanation
Indices: 15376--15678 Score: 423
Period size: 164 Copynumber: 1.9 Consensus size: 163
15366 AATAATATAA
** *
15376 TTTAGTGGTGTTTTTATACAAACGACGCTAAAGGTCATACTTTAGTGGCGTTTTAAGCACAAGCG
1 TTTAGTGGTGTTTTTATACAAACGACGCTAAAGGTCATACTTTAGTGGCGTTGCAAGCACAAACG
* * *
15441 CCACTAATTAGACGCTCTTTAGTGGCGTTTTATGCACAAACGCCGCTAATTACACGTACTCTAGT
66 CCACTAATTACACGCTCTTTAGTGGCATTTTACGCACAAACGCCGCT-ATTACACGTACTCTAGT
*
15506 TGCATTTTTATATAAACGTCGAGAAATACTGTAC
130 GGCATTTTTATATAAACGTCGAGAAATACTGTAC
*
15540 TTTAGTGGTGTTTTTATACAAACG-CTGCTAACGGTCATACTTTAGTGGC-TTGGCAAGCACAAA
1 TTTAGTGGTGTTTTTATACAAACGAC-GCTAAAGGTCATACTTTAGTGGCGTT-GCAAGCACAAA
* * * ** *
15603 CGCCGCTAATTACACG-TATTTTTGTGTTATTTTACGCACAAACGCCGCTATTACACGTACTTTA
64 CGCCACTAATTACACGCT-CTTTAGTGGCATTTTACGCACAAACGCCGCTATTACACGTACTCTA
15667 GTGGCATTTTTA
128 GTGGCATTTTTA
15679 AAAAACGCCG
Statistics
Matches: 122, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
163 29 0.24
164 93 0.76
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (163 bp):
TTTAGTGGTGTTTTTATACAAACGACGCTAAAGGTCATACTTTAGTGGCGTTGCAAGCACAAACG
CCACTAATTACACGCTCTTTAGTGGCATTTTACGCACAAACGCCGCTATTACACGTACTCTAGTG
GCATTTTTATATAAACGTCGAGAAATACTGTAC
Found at i:15678 original size:42 final size:41
Alignment explanation
Indices: 15413--15692 Score: 159
Period size: 42 Copynumber: 6.8 Consensus size: 41
15403 CTAAAGGTCA
* * * *
15413 TACTTTAGTGGCGTTTTAAGCACAAGCGCCACTAATTAGACG
1 TACTTTAGTGGC-TTTTTAGCACAAACGCCGCTAATTACACG
*
15455 CT-CTTTAGTGGCGTTTTATGCACAAACGCCGCTAATTACACG
1 -TACTTTAGTGGCTTTTTA-GCACAAACGCCGCTAATTACACG
* * * * * ** * *
15497 TACTCTAGTTGCATTTTTA-TATAAACGTCGAGAAATAC-TG
1 TACTTTAGTGGC-TTTTTAGCACAAACGCCGCTAATTACACG
* * * *
15537 TACTTTAGTGGTGTTTTTA-TACAAACGCTGCTAACGGT-CA--
1 TACTTTAGTGG-CTTTTTAGCACAAACGCCGCTAA--TTACACG
***
15577 TACTTTAGTGGCTTGGCAAGCACAAACGCCGCTAATTACACG
1 TACTTTAGTGGCTT-TTTAGCACAAACGCCGCTAATTACACG
* * *
15619 TATTTTTGT-GTTATTTTACGCACAAACGCCGCT-ATTACACG
1 TACTTTAGTGGCT-TTTTA-GCACAAACGCCGCTAATTACACG
*
15660 TACTTTAGTGGCATTTTTA--AAAAACGCCGCTAA
1 TACTTTAGTGGC-TTTTTAGCACAAACGCCGCTAA
15693 AGGTCATCTT
Statistics
Matches: 179, Mismatches: 41, Indels: 37
0.70 0.16 0.14
Matches are distributed among these distances:
39 14 0.08
40 41 0.23
41 50 0.28
42 67 0.37
43 7 0.04
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (41 bp):
TACTTTAGTGGCTTTTTAGCACAAACGCCGCTAATTACACG
Found at i:25369 original size:15 final size:16
Alignment explanation
Indices: 25349--25378 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
25339 AATATATATT
25349 TTAAAATAT-TTTAAC
1 TTAAAATATATTTAAC
25364 TTAAAATATATTTAA
1 TTAAAATATATTTAA
25379 ATATTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (16 bp):
TTAAAATATATTTAAC
Found at i:25413 original size:29 final size:29
Alignment explanation
Indices: 25379--25445 Score: 98
Period size: 29 Copynumber: 2.3 Consensus size: 29
25369 ATATATTTAA
** *
25379 ATATTTTATTCTTATTTTTACTTAAAAAT
1 ATATTTTATTCTTATTTCAAATTAAAAAT
*
25408 ATATTTTATTTTTATTTCAAATTAAAAAT
1 ATATTTTATTCTTATTTCAAATTAAAAAT
25437 ATATTTTAT
1 ATATTTTAT
25446 CATTATCTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.58
Consensus pattern (29 bp):
ATATTTTATTCTTATTTCAAATTAAAAAT
Found at i:25467 original size:31 final size:29
Alignment explanation
Indices: 25400--25472 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 29
25390 TTATTTTTAC
** *
25400 TTAAAAATATATTTTATTTTTATTTCAAA
1 TTAAAAATATATTTTATCATTATCTCAAA
25429 TTAAAAATATATTTTATCATTATCT-AAA
1 TTAAAAATATATTTTATCATTATCTCAAA
25457 TTTTTAAAAATATATT
1 ---TTAAAAATATATT
25473 AAAATATCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 3 0.08
29 22 0.58
31 13 0.34
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (29 bp):
TTAAAAATATATTTTATCATTATCTCAAA
Found at i:25510 original size:18 final size:18
Alignment explanation
Indices: 25477--25511 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
25467 TATATTAAAA
*
25477 TATCTTAACTTCAAAATG
1 TATCTTAACTTAAAAATG
*
25495 TATCTTAATTTAAAAAT
1 TATCTTAACTTAAAAAT
25512 AAAATATAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.11, G:0.03, T:0.43
Consensus pattern (18 bp):
TATCTTAACTTAAAAATG
Found at i:25674 original size:59 final size:59
Alignment explanation
Indices: 25611--25737 Score: 179
Period size: 59 Copynumber: 2.2 Consensus size: 59
25601 AAATATTTAA
* * *
25611 ATATATTTTAAGTTAAGGTATTTTTTCAAATA-A-A-TTTTAATTGATGATAAAGATAAAAT
1 ATATATTTTAAGTTAA---ATATTTTAAAATATATATTTTTAAGTGATGATAAAGATAAAAT
25670 ATATATTTTAAGTTAAATATTTTAAAATATATATTTTTAAGTGATGATAAAGATAAAAT
1 ATATATTTTAAGTTAAATATTTTAAAATATATATTTTTAAGTGATGATAAAGATAAAAT
25729 ATATATTTT
1 ATATATTTT
25738 TATATTAAAA
Statistics
Matches: 62, Mismatches: 3, Indels: 6
0.87 0.04 0.08
Matches are distributed among these distances:
56 11 0.18
57 1 0.02
58 1 0.02
59 49 0.79
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.46
Consensus pattern (59 bp):
ATATATTTTAAGTTAAATATTTTAAAATATATATTTTTAAGTGATGATAAAGATAAAAT
Found at i:25703 original size:14 final size:14
Alignment explanation
Indices: 25664--25706 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
25654 ATGATAAAGA
25664 TAAAATATATATTT
1 TAAAATATATATTT
** *
25678 TAAGTTAAATATTT
1 TAAAATATATATTT
25692 TAAAATATATATTT
1 TAAAATATATATTT
25706 T
1 T
25707 TAAGTGATGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (14 bp):
TAAAATATATATTT
Found at i:25730 original size:29 final size:30
Alignment explanation
Indices: 25644--25737 Score: 111
Period size: 30 Copynumber: 3.2 Consensus size: 30
25634 TTTCAAATAA
*
25644 ATTTTAATTGATGATAAAGATAAAATATAT
1 ATTTTAAGTGATGATAAAGATAAAATATAT
* * ***
25674 ATTTTAAGTTA-AAT-ATTTTAAAATATAT
1 ATTTTAAGTGATGATAAAGATAAAATATAT
25702 ATTTTTAAGTGATGATAAAGATAAAATATAT
1 A-TTTTAAGTGATGATAAAGATAAAATATAT
25733 ATTTT
1 ATTTT
25738 TATATTAAAA
Statistics
Matches: 50, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
28 12 0.24
29 11 0.22
30 15 0.30
31 12 0.24
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (30 bp):
ATTTTAAGTGATGATAAAGATAAAATATAT
Found at i:25730 original size:31 final size:31
Alignment explanation
Indices: 25645--25739 Score: 115
Period size: 31 Copynumber: 3.2 Consensus size: 31
25635 TTCAAATAAA
*
25645 TTTTAATTGATGATAAAGATAAAATATATA-
1 TTTTAAGTGATGATAAAGATAAAATATATAT
* * ***
25675 TTTTAAGTTA-AAT-ATTTTAAAATATATAT
1 TTTTAAGTGATGATAAAGATAAAATATATAT
25704 TTTTAAGTGATGATAAAGATAAAATATATAT
1 TTTTAAGTGATGATAAAGATAAAATATATAT
25735 TTTTA
1 TTTTA
25740 TATTAAAATA
Statistics
Matches: 51, Mismatches: 11, Indels: 5
0.76 0.16 0.07
Matches are distributed among these distances:
28 12 0.24
29 11 0.22
30 10 0.20
31 18 0.35
ACGTcount: A:0.46, C:0.00, G:0.08, T:0.45
Consensus pattern (31 bp):
TTTTAAGTGATGATAAAGATAAAATATATAT
Found at i:25751 original size:31 final size:31
Alignment explanation
Indices: 25657--25751 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 31
25647 TTAATTGATG
25657 ATAAAGATAAAATATATA-TTTTAAGTT-AA
1 ATAAAGATAAAATATATATTTTTAAGTTAAA
*** * **
25686 AT-ATTTTAAAATATATATTTTTAAGTGATG
1 ATAAAGATAAAATATATATTTTTAAGTTAAA
25716 ATAAAGATAAAATATATATTTTTATA-TTAAA
1 ATAAAGATAAAATATATATTTTTA-AGTTAAA
25747 ATAAA
1 ATAAA
25752 AGTGAATATA
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
28 12 0.24
29 10 0.20
30 2 0.04
31 25 0.50
32 1 0.02
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (31 bp):
ATAAAGATAAAATATATATTTTTAAGTTAAA
Found at i:25790 original size:30 final size:30
Alignment explanation
Indices: 25756--25817 Score: 81
Period size: 30 Copynumber: 2.1 Consensus size: 30
25746 AATAAAAGTG
25756 AATATATTTAATAAGTT-AAGAAAAAAATAA
1 AATATATTTAATAAGTTAAAG-AAAAAATAA
* * *
25786 AATATGTTTAATTAGTTAAAGCAAAAATAA
1 AATATATTTAATAAGTTAAAGAAAAAATAA
25816 AA
1 AA
25818 CATAATTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.89
31 3 0.11
ACGTcount: A:0.60, C:0.02, G:0.08, T:0.31
Consensus pattern (30 bp):
AATATATTTAATAAGTTAAAGAAAAAATAA
Found at i:26089 original size:11 final size:11
Alignment explanation
Indices: 26073--26101 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
26063 ATAAATCTAT
26073 TAAATTTAAAA
1 TAAATTTAAAA
26084 TAAA-TTAAAA
1 TAAATTTAAAA
26094 TAAATTTA
1 TAAATTTA
26102 GTCATCCAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
10 10 0.59
11 7 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:26140 original size:12 final size:12
Alignment explanation
Indices: 26120--26198 Score: 59
Period size: 12 Copynumber: 5.9 Consensus size: 12
26110 ATCGAATAAA
26120 GACACGTGTCAT
1 GACACGTGTCAT
*
26132 GACAGGTGTCACCAAT
1 GACACGTGT---C-AT
26148 GACACGTGTCAT
1 GACACGTGTCAT
*
26160 GACAGGTGTCACCAAT
1 GACACGTGT---C-AT
26176 GACACGTGTCAT
1 GACACGTGTCAT
*
26188 GACATGTGTCA
1 GACACGTGTCA
26199 CCAATGACAC
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
12 30 0.56
13 2 0.04
15 2 0.04
16 20 0.37
ACGTcount: A:0.28, C:0.24, G:0.25, T:0.23
Consensus pattern (12 bp):
GACACGTGTCAT
Found at i:26151 original size:16 final size:16
Alignment explanation
Indices: 26130--26216 Score: 91
Period size: 16 Copynumber: 5.9 Consensus size: 16
26120 GACACGTGTC
*
26130 ATGACAGGTGTCACCA
1 ATGACACGTGTCACCA
26146 ATGACACGTGT---C-
1 ATGACACGTGTCACCA
*
26158 ATGACAGGTGTCACCA
1 ATGACACGTGTCACCA
26174 ATGACACGTGT---C-
1 ATGACACGTGTCACCA
*
26186 ATGACATGTGTCACCA
1 ATGACACGTGTCACCA
26202 ATGACACGTGTCACC
1 ATGACACGTGTCACC
26217 TCCAGATTCG
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
12 20 0.34
13 2 0.03
15 2 0.03
16 34 0.59
ACGTcount: A:0.29, C:0.26, G:0.23, T:0.22
Consensus pattern (16 bp):
ATGACACGTGTCACCA
Found at i:26152 original size:28 final size:28
Alignment explanation
Indices: 26120--26214 Score: 181
Period size: 28 Copynumber: 3.4 Consensus size: 28
26110 ATCGAATAAA
26120 GACACGTGTCATGACAGGTGTCACCAAT
1 GACACGTGTCATGACAGGTGTCACCAAT
26148 GACACGTGTCATGACAGGTGTCACCAAT
1 GACACGTGTCATGACAGGTGTCACCAAT
*
26176 GACACGTGTCATGACATGTGTCACCAAT
1 GACACGTGTCATGACAGGTGTCACCAAT
26204 GACACGTGTCA
1 GACACGTGTCA
26215 CCTCCAGATT
Statistics
Matches: 66, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.28, C:0.25, G:0.24, T:0.22
Consensus pattern (28 bp):
GACACGTGTCATGACAGGTGTCACCAAT
Found at i:27796 original size:25 final size:25
Alignment explanation
Indices: 27767--27814 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
27757 CAATAAAGAA
* *
27767 TATAAGATAATTTTTTATTTATATT
1 TATAAAATAATTTTTAATTTATATT
*
27792 TATAAAATTATTTTTAATTTATA
1 TATAAAATAATTTTTAATTTATA
27815 AAATAATTAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (25 bp):
TATAAAATAATTTTTAATTTATATT
Found at i:27804 original size:18 final size:19
Alignment explanation
Indices: 27781--27818 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
27771 AGATAATTTT
27781 TTATTTAT-ATTTATAAAA
1 TTATTTATAATTTATAAAA
*
27799 TTATTTTTAATTTATAAAA
1 TTATTTATAATTTATAAAA
27818 T
1 T
27819 AATTATTTGC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATTTATAATTTATAAAA
Found at i:28127 original size:9 final size:9
Alignment explanation
Indices: 28113--28152 Score: 80
Period size: 9 Copynumber: 4.4 Consensus size: 9
28103 TCATATGCAG
28113 TCATTAATA
1 TCATTAATA
28122 TCATTAATA
1 TCATTAATA
28131 TCATTAATA
1 TCATTAATA
28140 TCATTAATA
1 TCATTAATA
28149 TCAT
1 TCAT
28153 ATGCGCGTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 31 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.45
Consensus pattern (9 bp):
TCATTAATA
Found at i:28939 original size:3 final size:3
Alignment explanation
Indices: 28931--28981 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
28921 TATGATAATG
28931 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
28978 TAA T
1 TAA T
28982 TGTTTGTGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 45 0.96
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:31511 original size:2 final size:2
Alignment explanation
Indices: 31504--31553 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
31494 CATATTAAGA
31504 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
31546 AT AT AT AT
1 AT AT AT AT
31554 GGATAAGATC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31587 original size:23 final size:23
Alignment explanation
Indices: 31555--31604 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
31545 TATATATATG
*
31555 GATAAGATCTTATTACACAATGT
1 GATAAAATCTTATTACACAATGT
31578 GATAAAATCTTATTACACAATGT
1 GATAAAATCTTATTACACAATGT
31601 -ATAA
1 GATAA
31605 CTCTTTTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
22 4 0.15
23 22 0.85
ACGTcount: A:0.44, C:0.12, G:0.10, T:0.34
Consensus pattern (23 bp):
GATAAAATCTTATTACACAATGT
Found at i:36999 original size:20 final size:19
Alignment explanation
Indices: 36954--37003 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 19
36944 CCCTTCAAGG
36954 AGTATCGATACTCGGGGTCT
1 AGTATCGATACTCGGGG-CT
*
36974 ATTATCGATACTCAGAGGG-T
1 AGTATCGATACTC-G-GGGCT
36994 AGTATCGATA
1 AGTATCGATA
37004 TTGGTGGCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 22 0.85
21 1 0.04
22 3 0.12
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.30
Consensus pattern (19 bp):
AGTATCGATACTCGGGGCT
Found at i:37705 original size:23 final size:23
Alignment explanation
Indices: 37678--37750 Score: 94
Period size: 23 Copynumber: 3.2 Consensus size: 23
37668 AACTCGTATA
*
37678 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTGCCACATAG
* *
37701 AAATGCACCGAGGTGCCGCATAG
1 AAATGCACCGAAGTGCCACATAG
* *
37724 AAATGCACCGAAGTACCATATA-
1 AAATGCACCGAAGTGCCACATAG
37746 AAATG
1 AAATG
37751 TCTAGAAAGG
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 5 0.12
23 38 0.88
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.15
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:39217 original size:19 final size:19
Alignment explanation
Indices: 39193--39238 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
39183 GTTCCGGAAC
*
39193 AATCAACGAATTAGGATCG
1 AATCAAAGAATTAGGATCG
*
39212 AATCAAAGCATTAGGATCG
1 AATCAAAGAATTAGGATCG
39231 AATCAAAG
1 AATCAAAG
39239 CAAGGCTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (19 bp):
AATCAAAGAATTAGGATCG
Found at i:39239 original size:19 final size:19
Alignment explanation
Indices: 39202--39240 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
39192 CAATCAACGA
39202 ATTAGGATCGAATCAAAGC
1 ATTAGGATCGAATCAAAGC
39221 ATTAGGATCGAATCAAAGC
1 ATTAGGATCGAATCAAAGC
39240 A
1 A
39241 AGGCTAAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (19 bp):
ATTAGGATCGAATCAAAGC
Found at i:40497 original size:19 final size:19
Alignment explanation
Indices: 40459--40497 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
40449 GGTATCAGTA
*
40459 CCCTTAGTATCGATACTCC
1 CCCTTAGTATCAATACTCC
40478 CCCTTAGGTATCAATA-TCC
1 CCCTTA-GTATCAATACTCC
40497 C
1 C
40498 ATGAAGATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.23, C:0.36, G:0.10, T:0.31
Consensus pattern (19 bp):
CCCTTAGTATCAATACTCC
Found at i:48015 original size:19 final size:19
Alignment explanation
Indices: 47988--48031 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
47978 CGGAACAATA
*
47988 AAAGAATTAGGATCGAATC
1 AAAGCATTAGGATCGAATC
48007 AAAGCATTAGGATCGAATC
1 AAAGCATTAGGATCGAATC
48026 AAAGCA
1 AAAGCA
48032 AGGCTAAAGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.48, C:0.14, G:0.20, T:0.18
Consensus pattern (19 bp):
AAAGCATTAGGATCGAATC
Found at i:48725 original size:37 final size:37
Alignment explanation
Indices: 48675--48772 Score: 151
Period size: 37 Copynumber: 2.6 Consensus size: 37
48665 GAGTCGAGGG
*
48675 TTACCTATGTTCTTCGGGATATATGGACAGTTACAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGTTACAGA
* * *
48712 TTACCTATGTTCTTCGAGACATATGGACATTTATAGA
1 TTACCTATGTTCTTCGGGACATATGGACAGTTACAGA
*
48749 TTACCTATGTTCTTTGGGACATAT
1 TTACCTATGTTCTTCGGGACATAT
48773 TGACTGATTA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 55 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (37 bp):
TTACCTATGTTCTTCGGGACATATGGACAGTTACAGA
Found at i:49453 original size:21 final size:21
Alignment explanation
Indices: 49427--49468 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
49417 GGCCGGAATT
49427 ACTGTAGCAAGGTATCGATAC
1 ACTGTAGCAAGGTATCGATAC
** *
49448 ACTGTATTAGGGTATCGATAC
1 ACTGTAGCAAGGTATCGATAC
49469 CCCTATAGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.17, G:0.24, T:0.29
Consensus pattern (21 bp):
ACTGTAGCAAGGTATCGATAC
Found at i:49824 original size:10 final size:10
Alignment explanation
Indices: 49789--49831 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
49779 AATTAAAATA
49789 ATTTCAAAAC
1 ATTTCAAAAC
49799 AATTTTACAAAAC
1 -A-TTT-CAAAAC
*
49812 ATTTCAAACC
1 ATTTCAAAAC
49822 ATTTCAAAAC
1 ATTTCAAAAC
49832 CAAAAATTCC
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
10 14 0.50
11 4 0.14
12 4 0.14
13 6 0.21
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (10 bp):
ATTTCAAAAC
Found at i:52577 original size:16 final size:16
Alignment explanation
Indices: 52556--52587 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
52546 GATGAAGCAT
52556 TAGAAAAATTCATCAC
1 TAGAAAAATTCATCAC
52572 TAGAAAAATTCATCAC
1 TAGAAAAATTCATCAC
52588 GTTTTTAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.06, T:0.25
Consensus pattern (16 bp):
TAGAAAAATTCATCAC
Found at i:55244 original size:20 final size:20
Alignment explanation
Indices: 55187--55244 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 20
55177 TTTGGTGCAG
*
55187 AGGGAATCGATATCCCCTTGA
1 AGGGAATCGATA-CCCCCTGA
* * *
55208 AGGAGAACCGATTCCCCCTGT
1 AGG-GAATCGATACCCCCTGA
55229 AGGGAATCGATACCCC
1 AGGGAATCGATACCCC
55245 TGGAGGTTCT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
20 11 0.37
21 12 0.40
22 7 0.23
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (20 bp):
AGGGAATCGATACCCCCTGA
Done.