Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003623.1 Hibiscus syriacus cultivar Beakdansim tig00007664_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: 113888
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.34
Found at i:569 original size:63 final size:64
Alignment explanation
Indices: 502--663 Score: 161
Period size: 64 Copynumber: 2.5 Consensus size: 64
492 ATTGTTCAAG
* * *
502 GTGTATCGATGCACATGAAGTGCATCGATGCA-CTCCTTTAAATAAAAACATCGAATGCCATCA
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCCTTAAATAAAAACATCGAATGCCATCA
* * * ** * *
565 GTGTATCGATGTACAAGTAGTGCGTCGATGCACCCCCCTTAAATGCAAACATCGAATAG-GATTT
1 GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCCTTAAATAAAAACATCGAAT-GCCA-TC
629 A
64 A
* *
630 -TGTATCGATGTA-TAGATAGTGCATCGATGCACCC
1 GTGTATCGATGCACAAGA-AGTGCATCGATGCACCC
664 GTTAAGGGAT
Statistics
Matches: 82, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
63 30 0.37
64 49 0.60
65 3 0.04
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (64 bp):
GTGTATCGATGCACAAGAAGTGCATCGATGCACCCCCCTTAAATAAAAACATCGAATGCCATCA
Found at i:10781 original size:17 final size:18
Alignment explanation
Indices: 10749--10782 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
10739 TAGTAAAATG
10749 TGTTTATCCTAATTTTAC
1 TGTTTATCCTAATTTTAC
*
10767 TGTTTTTCC-AATTTTA
1 TGTTTATCCTAATTTTA
10783 ATTTTAGTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.21, C:0.15, G:0.06, T:0.59
Consensus pattern (18 bp):
TGTTTATCCTAATTTTAC
Found at i:24487 original size:80 final size:79
Alignment explanation
Indices: 24291--24538 Score: 352
Period size: 85 Copynumber: 3.0 Consensus size: 79
24281 TATCAGCTAT
24291 ATTTTTTTAATCTTTTACGTTTACAGTTTTGATCAATTTAACTGTTAATATTTAAAAATAAATAA
1 ATTTTTTTAATCTTTTACGTTTACAGTTTTGATCAATTTAACTGTTAATATTTAAAAA-AAAT-A
24356 ATAAATAGTTGTACAATATA
64 AT--A-A-TTGTACAATATA
* * *
24376 ATTTTTTTAATCTTTTACGTTTACAGTTTTGATAAATTTAACTGTTAATATTTTAAAAAAATAGT
1 ATTTTTTTAATCTTTTACGTTTACAGTTTTGATCAATTTAACTGTTAATATTTAAAAAAAATAAT
24441 AATTGTACAATATA
66 AATTGTACAATATA
* *
24455 ATTTTTTTTAATCTTTTACGTTTACAATTTTGATCAATTTAACTGTTTATATTTAAAAATAAAAA
1 A-TTTTTTTAATCTTTTACGTTTACAGTTTTGATCAATTTAACTGTTAATATTT--AAA-AAAAA
*
24520 AAATAATTGTACAATATA
62 TAATAATTGTACAATATA
24538 A
1 A
24539 AATTTTAATA
Statistics
Matches: 150, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
79 13 0.09
80 50 0.33
81 1 0.01
82 2 0.01
83 24 0.16
84 4 0.03
85 56 0.37
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (79 bp):
ATTTTTTTAATCTTTTACGTTTACAGTTTTGATCAATTTAACTGTTAATATTTAAAAAAAATAAT
AATTGTACAATATA
Found at i:24562 original size:80 final size:82
Alignment explanation
Indices: 24291--24538 Score: 367
Period size: 80 Copynumber: 3.0 Consensus size: 82
24281 TATCAGCTAT
*
24291 ATTTTTTTAATCTTTTACGTTTACAGTTTTGATCAATTTAACTGTTAATATTTAAAAATAAATAA
1 ATTTTTTTAATCTTTTACGTTTACAATTTTGATCAATTTAACTGTTAATATTTAAAAAT-AA-AA
*
24356 ATAAATAGTTGTACAATATA
64 A-AAATAATTGTACAATATA
* * * *
24376 ATTTTTTTAATCTTTTACGTTTACAGTTTTGATAAATTTAACTGTTAATATTT--TAA-AAAAAT
1 ATTTTTTTAATCTTTTACGTTTACAATTTTGATCAATTTAACTGTTAATATTTAAAAATAAAAAA
*
24438 AGTAATTGTACAATATA
66 AATAATTGTACAATATA
*
24455 ATTTTTTTTAATCTTTTACGTTTACAATTTTGATCAATTTAACTGTTTATATTTAAAAATAAAAA
1 A-TTTTTTTAATCTTTTACGTTTACAATTTTGATCAATTTAACTGTTAATATTTAAAAATAAAAA
24520 AAATAATTGTACAATATA
65 AAATAATTGTACAATATA
24538 A
1 A
24539 AATTTTAATA
Statistics
Matches: 148, Mismatches: 11, Indels: 10
0.88 0.07 0.06
Matches are distributed among these distances:
79 16 0.11
80 52 0.35
81 2 0.01
82 2 0.01
83 24 0.16
85 52 0.35
ACGTcount: A:0.40, C:0.07, G:0.06, T:0.47
Consensus pattern (82 bp):
ATTTTTTTAATCTTTTACGTTTACAATTTTGATCAATTTAACTGTTAATATTTAAAAATAAAAAA
AATAATTGTACAATATA
Found at i:33360 original size:15 final size:15
Alignment explanation
Indices: 33340--33378 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
33330 TTACTTTTAT
33340 ATTTAATTATAAATC
1 ATTTAATTATAAATC
* *
33355 ATTTAACTA-AAATT
1 ATTTAATTATAAATC
33369 ATTTAATTAT
1 ATTTAATTAT
33379 GTTATTATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTAATTATAAATC
Found at i:35195 original size:23 final size:23
Alignment explanation
Indices: 35149--35197 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
35139 AAAAACAATT
*
35149 TAAAAATAAAAATAAATTACTAA
1 TAAAAATAAAAATAAATTAATAA
*
35172 TAAAAA-ATAAATAAATTATATAA
1 TAAAAATAAAAATAAATTA-ATAA
35195 TAA
1 TAA
35198 TTTAAAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 11 0.48
23 12 0.52
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (23 bp):
TAAAAATAAAAATAAATTAATAA
Found at i:43412 original size:36 final size:37
Alignment explanation
Indices: 43371--43440 Score: 99
Period size: 36 Copynumber: 1.9 Consensus size: 37
43361 TTATGAATTT
43371 AATATTAATAAAATAT-TTTAATATCATTT-TAATCAA
1 AATATTAATAAAATATATTTAATAT-ATTTCTAATCAA
* *
43407 AATATTATTAAAATATATTTATTATATTTCTAAT
1 AATATTAATAAAATATATTTAATATATTTCTAAT
43441 AATATAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
36 19 0.63
37 11 0.37
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (37 bp):
AATATTAATAAAATATATTTAATATATTTCTAATCAA
Found at i:43450 original size:26 final size:26
Alignment explanation
Indices: 43421--43528 Score: 82
Period size: 26 Copynumber: 4.1 Consensus size: 26
43411 TTATTAAAAT
*
43421 ATATTTATTATATTTCTAATAATATA
1 ATATTTATTATATTTATAATAATATA
* *
43447 ATATTATATTTTTAATATTATAATAAAATA
1 ATATT-TA-TTAT-AT-TTATAATAATATA
43477 ATCA---ATTATA-TTATAATAATATA
1 AT-ATTTATTATATTTATAATAATATA
* *
43500 ATATATATTTTTATTT-TAATAATATA
1 ATATTTA-TTATATTTATAATAATATA
43526 ATA
1 ATA
43529 AATTATTAAT
Statistics
Matches: 66, Mismatches: 6, Indels: 20
0.72 0.07 0.22
Matches are distributed among these distances:
22 1 0.02
23 14 0.21
25 2 0.03
26 25 0.38
27 5 0.08
28 3 0.05
29 2 0.03
30 13 0.20
31 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (26 bp):
ATATTTATTATATTTATAATAATATA
Found at i:43451 original size:22 final size:22
Alignment explanation
Indices: 43426--43471 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
43416 AAAATATATT
43426 TATTATATTTCTAATAATATAA
1 TATTATATTTCTAATAATATAA
* *
43448 TATTATATTTTTAATATTATAA
1 TATTATATTTCTAATAATATAA
43470 TA
1 TA
43472 AAATAATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.54
Consensus pattern (22 bp):
TATTATATTTCTAATAATATAA
Found at i:43452 original size:36 final size:36
Alignment explanation
Indices: 43379--43464 Score: 90
Period size: 36 Copynumber: 2.4 Consensus size: 36
43369 TTAATATTAA
*
43379 TAAAATATTTTAATATCATTTTAATCAAAATATTAT
1 TAAAATATTTTAATATCATTTTAATCAAAATAATAT
* *
43415 TAAAATATATTTATTAT-ATTTCTAAT-AATATAATAT
1 TAAAATAT-TTTAATATCATTT-TAATCAAAATAATAT
*
43451 T-ATAT-TTTTAATAT
1 TAAAATATTTTAATAT
43465 TATAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
33 7 0.16
34 1 0.02
35 3 0.07
36 21 0.49
37 11 0.26
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.51
Consensus pattern (36 bp):
TAAAATATTTTAATATCATTTTAATCAAAATAATAT
Found at i:43466 original size:53 final size:51
Alignment explanation
Indices: 43407--43534 Score: 145
Period size: 53 Copynumber: 2.5 Consensus size: 51
43397 TTTTAATCAA
** *
43407 AATATTAT-TAAAATATATTTATTATATTTCTAATAATATAATATTATATTTTT
1 AATATTATATAAAATA-ATCAATTATA-TTATAATAATATAATA-TATATTTTT
43460 AATATTATAATAAAATAATCAATTATATTATAATAATATAATATATATTTTT
1 AATATTAT-ATAAAATAATCAATTATATTATAATAATATAATATATATTTTT
* * *
43512 -ATTTTA-ATAATATAATAAATTAT
1 AATATTATATAAAATAATCAATTAT
43535 TAATAAAATT
Statistics
Matches: 67, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
49 15 0.22
51 5 0.07
52 9 0.13
53 23 0.34
54 8 0.12
55 7 0.10
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (51 bp):
AATATTATATAAAATAATCAATTATATTATAATAATATAATATATATTTTT
Found at i:43664 original size:23 final size:23
Alignment explanation
Indices: 43638--43682 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
43628 AATAATATTT
43638 TAATAAAGATATTTAAAATATAC
1 TAATAAAGATATTTAAAATATAC
* * *
43661 TAATTAATATTTTTAAAATATA
1 TAATAAAGATATTTAAAATATA
43683 ATATAACACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAAAGATATTTAAAATATAC
Found at i:43814 original size:26 final size:27
Alignment explanation
Indices: 43785--43835 Score: 70
Period size: 27 Copynumber: 1.9 Consensus size: 27
43775 ATTATAAAAA
*
43785 TAATA-TTTAATAATAAATAA-ATTATT
1 TAATATTTTAAAAAT-AATAATATTATT
43811 TAATATTTTAAAAATAATAATATTA
1 TAATATTTTAAAAATAATAATATTA
43836 AGTTTTATGA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
26 10 0.45
27 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (27 bp):
TAATATTTTAAAAATAATAATATTATT
Found at i:44060 original size:15 final size:15
Alignment explanation
Indices: 44042--44111 Score: 58
Period size: 15 Copynumber: 4.9 Consensus size: 15
44032 TCATTTTCCA
44042 TAATTCAAATTTCAG
1 TAATTCAAATTTCAG
* *
44057 TAATT-TATTTTCCAG
1 TAATTCAAATTT-CAG
44072 -AATTCAAATTTCAG
1 TAATTCAAATTTCAG
* **
44086 TAATTTATTTTTCAG
1 TAATTCAAATTTCAG
44101 -AATTC-AATTTC
1 TAATTCAAATTTC
44112 CAGAAAACCA
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
13 4 0.10
14 15 0.36
15 23 0.55
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (15 bp):
TAATTCAAATTTCAG
Found at i:44069 original size:29 final size:29
Alignment explanation
Indices: 44027--44111 Score: 136
Period size: 29 Copynumber: 3.0 Consensus size: 29
44017 TTCCAGAAAT
* *
44027 GTAATTCATTTTCCATAATTCAAATTTCA
1 GTAATTTATTTTCCAGAATTCAAATTTCA
44056 GTAATTTATTTTCCAGAATTCAAATTTCA
1 GTAATTTATTTTCCAGAATTCAAATTTCA
*
44085 GTAATTTATTTTTCAGAATTC-AATTTC
1 GTAATTTATTTTCCAGAATTCAAATTTC
44112 CAGAAAACCA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
28 6 0.11
29 47 0.89
ACGTcount: A:0.33, C:0.14, G:0.06, T:0.47
Consensus pattern (29 bp):
GTAATTTATTTTCCAGAATTCAAATTTCA
Found at i:44115 original size:14 final size:14
Alignment explanation
Indices: 44029--44116 Score: 63
Period size: 14 Copynumber: 6.1 Consensus size: 14
44019 CCAGAAATGT
* *
44029 AATTCATTTTCCAT
1 AATTCAATTTCCAG
44043 AATTCAAATTT-CAG
1 AATTC-AATTTCCAG
* *
44057 TAATTTATTTTCCAG
1 -AATTCAATTTCCAG
44072 AATTCAAATTT-CAG
1 AATTC-AATTTCCAG
* * *
44086 TAATTTATTTTTCAG
1 -AATTCAATTTCCAG
44101 AATTCAATTTCCAG
1 AATTCAATTTCCAG
44115 AA
1 AA
44117 AACCAATTAC
Statistics
Matches: 57, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
14 35 0.61
15 22 0.39
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (14 bp):
AATTCAATTTCCAG
Found at i:49296 original size:15 final size:15
Alignment explanation
Indices: 49276--49308 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
49266 ATTTTTTTTC
49276 AAAAAAAAAAG-CAA
1 AAAAAAAAAAGCCAA
49290 AAAAAAAAAAGCCAA
1 AAAAAAAAAAGCCAA
49305 AAAA
1 AAAA
49309 GCCAAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.85, C:0.09, G:0.06, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAGCCAA
Found at i:50958 original size:75 final size:75
Alignment explanation
Indices: 50825--51033 Score: 258
Period size: 75 Copynumber: 2.8 Consensus size: 75
50815 CAAAGTCAAA
* * * * * **
50825 AATTCCAGATTGCTCAGAGGAAACCGATTCCCCTCCATAGGAGGAATCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCC-CCATAGGAGGAACCGATTCCCCCCTAAACAG
50890 TTTGGCTCCGAG
64 TTTGGCTCCGAG
*
50902 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
* *
50967 TTGTTCCGAG
66 TGGCTCCGAG
* * * *
50977 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCCA-AGGGGGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGAT-TCCCCCATAGGAGGAACCGATTCCCCCCT
51034 TGTACAACGG
Statistics
Matches: 116, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
75 82 0.71
76 9 0.08
77 25 0.22
ACGTcount: A:0.24, C:0.31, G:0.23, T:0.22
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:63894 original size:31 final size:30
Alignment explanation
Indices: 63859--63958 Score: 85
Period size: 31 Copynumber: 3.2 Consensus size: 30
63849 AGGTTCGTTT
63859 TTAATTTGACTATTGAACTTTAGATAAAATA
1 TTAATTTGACT-TTGAACTTTAGATAAAATA
* * * *
63890 TTAATTTAACCTTTAAACTTTCA-TTAGAATA
1 TTAATTTGA-CTTTGAACTTT-AGATAAAATA
* * * *
63921 TCAATTTGTCCTTTGATCATTAGATAAAATA
1 TTAATTTG-ACTTTGAACTTTAGATAAAATA
63952 TTAATTT
1 TTAATTT
63959 ATTCTATGAA
Statistics
Matches: 52, Mismatches: 13, Indels: 8
0.71 0.18 0.11
Matches are distributed among these distances:
30 1 0.02
31 48 0.92
32 3 0.06
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (30 bp):
TTAATTTGACTTTGAACTTTAGATAAAATA
Found at i:83849 original size:2 final size:2
Alignment explanation
Indices: 83842--83866 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
83832 TCAGTCTACA
83842 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 A
83867 ATTTACGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:85348 original size:36 final size:36
Alignment explanation
Indices: 85279--85388 Score: 106
Period size: 36 Copynumber: 3.2 Consensus size: 36
85269 ATTAACTTTC
* *
85279 CTAATTATATATTAAATATTAGAT--TT-AATATTTAT
1 CTAATTATCT-TTAAAT-TTAGATGATTAAATATTTAA
85314 CTAATTATCTTTAAATTTAGATGATTAAATATTTAA
1 CTAATTATCTTTAAATTTAGATGATTAAATATTTAA
* * * *
85350 CTAATTACCGTTAAAATTAGAGGATT--A-ATTTAA
1 CTAATTATCTTTAAATTTAGATGATTAAATATTTAA
85383 CTAATT
1 CTAATT
85389 TTGTAAATGT
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
33 18 0.27
34 7 0.11
35 11 0.17
36 30 0.45
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.45
Consensus pattern (36 bp):
CTAATTATCTTTAAATTTAGATGATTAAATATTTAA
Found at i:91016 original size:59 final size:60
Alignment explanation
Indices: 90898--91025 Score: 145
Period size: 59 Copynumber: 2.1 Consensus size: 60
90888 AGTCGATAAT
* * * * *
90898 CATTTTATAACTTTTAATAGTTGAGAGACTCAACAAAATAATACCCTATTGTCGGGAGAC
1 CATTTTGTAACTTTTAATAGTTCAAAGACTCAACAAAATAACACCCTATTGTCGAGAGAC
* *
90958 CATTTTGTAACTTTTAATCG-TCAAAGACTCAAC-AAATCAACACTCTATAT-TCGAGAGAC
1 CATTTTGTAACTTTTAATAGTTCAAAGACTCAACAAAAT-AACACCCTAT-TGTCGAGAGAC
*
91017 CATTGTGTA
1 CATTTTGTA
91026 TTTTACCCTA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
58 4 0.07
59 35 0.60
60 19 0.33
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGTTCAAAGACTCAACAAAATAACACCCTATTGTCGAGAGAC
Found at i:91888 original size:29 final size:30
Alignment explanation
Indices: 91851--91916 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
91841 ATATAATTTA
*
91851 TATAATATTTT-TAAATA-ATCATGTCGTAT
1 TATATTATTTTCT-AATACATCATGTCGTAT
* *
91880 TATATTATTTTCTAATACATCATTTCTTAT
1 TATATTATTTTCTAATACATCATGTCGTAT
91910 TCATATT
1 T-ATATT
91917 TTCATGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
29 14 0.45
30 12 0.39
31 5 0.16
ACGTcount: A:0.33, C:0.11, G:0.03, T:0.53
Consensus pattern (30 bp):
TATATTATTTTCTAATACATCATGTCGTAT
Found at i:103559 original size:29 final size:29
Alignment explanation
Indices: 103526--103593 Score: 136
Period size: 29 Copynumber: 2.3 Consensus size: 29
103516 GATTTGCAAT
103526 CAAATATATACATCAATTGCTCCAAAATA
1 CAAATATATACATCAATTGCTCCAAAATA
103555 CAAATATATACATCAATTGCTCCAAAATA
1 CAAATATATACATCAATTGCTCCAAAATA
103584 CAAATATATA
1 CAAATATATA
103594 GACAGAAAAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.50, C:0.19, G:0.03, T:0.28
Consensus pattern (29 bp):
CAAATATATACATCAATTGCTCCAAAATA
Found at i:104957 original size:28 final size:29
Alignment explanation
Indices: 104860--104932 Score: 137
Period size: 29 Copynumber: 2.5 Consensus size: 29
104850 TGGCTCAGGG
104860 CCCTCAATTTTTATATTTGTAATGGGTATC
1 CCCT-AATTTTTATATTTGTAATGGGTATC
104890 CCCTAATTTTTATATTTGTAATGGGTATC
1 CCCTAATTTTTATATTTGTAATGGGTATC
104919 CCCTAATTTTTATA
1 CCCTAATTTTTATA
104933 CCTATAATTG
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 39 0.91
30 4 0.09
ACGTcount: A:0.25, C:0.16, G:0.11, T:0.48
Consensus pattern (29 bp):
CCCTAATTTTTATATTTGTAATGGGTATC
Found at i:105579 original size:25 final size:26
Alignment explanation
Indices: 105546--105608 Score: 92
Period size: 26 Copynumber: 2.5 Consensus size: 26
105536 ATTTCATATA
*
105546 AGAATGGATTTTTCC-CTTTTTTATT
1 AGAATGGATTTTGCCTCTTTTTTATT
* *
105571 AGAAGGGATTTTGCCTTTTTTTTATT
1 AGAATGGATTTTGCCTCTTTTTTATT
105597 AGAATGGATTTT
1 AGAATGGATTTT
105609 ATTTTGAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
25 13 0.39
26 20 0.61
ACGTcount: A:0.22, C:0.08, G:0.17, T:0.52
Consensus pattern (26 bp):
AGAATGGATTTTGCCTCTTTTTTATT
Found at i:109931 original size:12 final size:13
Alignment explanation
Indices: 109901--109932 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
109891 GGCTTTCATT
109901 AGTTTTTACATCA
1 AGTTTTTACATCA
109914 AG-TTTTACATC-
1 AGTTTTTACATCA
109925 AGTTTTTA
1 AGTTTTTA
109933 TCTTTATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 2 0.11
12 14 0.78
13 2 0.11
ACGTcount: A:0.28, C:0.12, G:0.09, T:0.50
Consensus pattern (13 bp):
AGTTTTTACATCA
Done.