Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002430.1 Hibiscus syriacus cultivar Beakdansim tig00004970_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: 67629
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:474 original size:11 final size:12
Alignment explanation
Indices: 451--484 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
441 AACACCTCAA
451 GTGAAGAAGAGG
1 GTGAAGAAGAGG
463 GTGAAG-AGAGG
1 GTGAAGAAGAGG
474 GT-AAGAAGAGG
1 GTGAAGAAGAGG
485 AAATTGTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 3 0.14
11 12 0.57
12 6 0.29
ACGTcount: A:0.41, C:0.00, G:0.50, T:0.09
Consensus pattern (12 bp):
GTGAAGAAGAGG
Found at i:2048 original size:19 final size:20
Alignment explanation
Indices: 2010--2049 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
2000 TTTAACCAGA
2010 AGTTTCGAAACTTCTACAAG
1 AGTTTCGAAACTTCTACAAG
2030 AGTTTCGAAACTT-TACAAG
1 AGTTTCGAAACTTCTACAAG
2049 A
1 A
2050 CAATTTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (20 bp):
AGTTTCGAAACTTCTACAAG
Found at i:2088 original size:19 final size:19
Alignment explanation
Indices: 2064--2115 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
2054 TTCTCAAAAT
* *
2064 GTTTCGATACTTTTTAAGA
1 GTTTCGAAACTTTCTAAGA
* *
2083 GTTTCGAAACTATCTCAGA
1 GTTTCGAAACTTTCTAAGA
2102 GTTTCGAAACTTTC
1 GTTTCGAAACTTTC
2116 CCTAAAATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.27, C:0.17, G:0.15, T:0.40
Consensus pattern (19 bp):
GTTTCGAAACTTTCTAAGA
Found at i:2582 original size:64 final size:65
Alignment explanation
Indices: 2508--2636 Score: 217
Period size: 65 Copynumber: 2.0 Consensus size: 65
2498 TTTAAATGTT
* *
2508 ACTCTTGATCCTTG-AAAAAGAAAGAAC-AATTAGTGGATTTGTTGGAAAATCCTAAGTGAGGAG
1 ACTCTTGATCCTTGAAAAAAGAAAGAACAAATTAGTAGA-TTGTTGGAAAATCCTAAGTAAGGAG
2571 C
65 C
2572 ACTCTTGATCCTTGAAAAAAGAAAGAACAAATTAGTAGATTGTTGGAAAATCCTAAGTAAGGAGC
1 ACTCTTGATCCTTGAAAAAAGAAAGAACAAATTAGTAGATTGTTGGAAAATCCTAAGTAAGGAGC
2637 TTAGGTAGTG
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
64 14 0.23
65 38 0.62
66 9 0.15
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.26
Consensus pattern (65 bp):
ACTCTTGATCCTTGAAAAAAGAAAGAACAAATTAGTAGATTGTTGGAAAATCCTAAGTAAGGAGC
Found at i:3056 original size:16 final size:17
Alignment explanation
Indices: 3018--3056 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
3008 AGGTAGAGAA
3018 AAAAAAGGAAGAAAAAG
1 AAAAAAGGAAGAAAAAG
* *
3035 GAAAAA-GATGAAAAAG
1 AAAAAAGGAAGAAAAAG
3051 AAAAAA
1 AAAAAA
3057 TAATTTTTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.03
Consensus pattern (17 bp):
AAAAAAGGAAGAAAAAG
Found at i:5585 original size:20 final size:20
Alignment explanation
Indices: 5560--5599 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
5550 TTATGCTTGA
5560 ATGTGGTTGCTTTTATATGT
1 ATGTGGTTGCTTTTATATGT
5580 ATGTGGTTGCTTTTATATGT
1 ATGTGGTTGCTTTTATATGT
5600 GAAAGAGTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.15, C:0.05, G:0.25, T:0.55
Consensus pattern (20 bp):
ATGTGGTTGCTTTTATATGT
Found at i:6941 original size:31 final size:31
Alignment explanation
Indices: 6903--6967 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
6893 TTTTGGGACA
*
6903 AAAGTCCCCTTCATAGATGGAAATCATTAGT
1 AAAGTCCCCTCCATAGATGGAAATCATTAGT
*
6934 AAAGTCCCCTCCATAGATGGAAATCATTTGT
1 AAAGTCCCCTCCATAGATGGAAATCATTAGT
6965 AAA
1 AAA
6968 TAAATGGTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (31 bp):
AAAGTCCCCTCCATAGATGGAAATCATTAGT
Found at i:16965 original size:23 final size:23
Alignment explanation
Indices: 16939--16983 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
16929 TATTTAGATA
16939 GAATGCATCATTATTAGTGTATG
1 GAATGCATCATTATTAGTGTATG
*
16962 GAATGGATCATTATTAGTGTAT
1 GAATGCATCATTATTAGTGTAT
16984 ACGGTATATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.31, C:0.07, G:0.22, T:0.40
Consensus pattern (23 bp):
GAATGCATCATTATTAGTGTATG
Found at i:23189 original size:2 final size:2
Alignment explanation
Indices: 23182--23232 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
23172 TCTTAGAAAC
23182 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
23224 TA TA TA TA T
1 TA TA TA TA T
23233 CAATTGGCTA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23475 original size:18 final size:18
Alignment explanation
Indices: 23452--23489 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
23442 TTTTAAGATT
23452 TTATATTCGATTTAAATA
1 TTATATTCGATTTAAATA
*
23470 TTATATTCGATTTAATTA
1 TTATATTCGATTTAAATA
23488 TT
1 TT
23490 CGAATATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.55
Consensus pattern (18 bp):
TTATATTCGATTTAAATA
Found at i:29699 original size:17 final size:20
Alignment explanation
Indices: 29651--29699 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
29641 CTTGCTAGGA
29651 ATCGATACTACTAGCATAGT
1 ATCGATACTACTAGCATAGT
29671 ATCGATACTACTAGCATAGT
1 ATCGATACTACTAGCATAGT
*
29691 ATCAATACT
1 ATCGATACT
29700 TATTTCATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.12, T:0.31
Consensus pattern (20 bp):
ATCGATACTACTAGCATAGT
Found at i:30320 original size:12 final size:13
Alignment explanation
Indices: 30293--30325 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
30283 ATTATAAAAT
*
30293 TTTTCAAACTTAG
1 TTTTCAAACATAG
30306 TTTTCAAA-ATAG
1 TTTTCAAACATAG
30318 TTTTCAAA
1 TTTTCAAA
30326 TTTGCCTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.36, C:0.12, G:0.06, T:0.45
Consensus pattern (13 bp):
TTTTCAAACATAG
Found at i:32005 original size:21 final size:21
Alignment explanation
Indices: 31979--32021 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
31969 TTTTCGGGCT
* *
31979 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
32000 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
32021 A
1 A
32022 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:32075 original size:65 final size:67
Alignment explanation
Indices: 32001--32150 Score: 223
Period size: 66 Copynumber: 2.3 Consensus size: 67
31991 ACCCATTCAA
* *
32001 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
32065 -G
66 GG
* * *
32066 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
32131 GGG
66 -GG
*
32134 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
32151 ATGAGAAAAA
Statistics
Matches: 76, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
65 26 0.34
66 33 0.43
68 17 0.22
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (67 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GG
Found at i:32490 original size:29 final size:29
Alignment explanation
Indices: 32456--32524 Score: 102
Period size: 29 Copynumber: 2.4 Consensus size: 29
32446 ATTATGATAT
* *
32456 ATGACATGAATTTATATTAAATGTATTAC
1 ATGACATGAATTCATATGAAATGTATTAC
* *
32485 ATGACATGAATTCATATGATATGTATTGC
1 ATGACATGAATTCATATGAAATGTATTAC
32514 ATGACATGAAT
1 ATGACATGAAT
32525 ATGCAGAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.38
Consensus pattern (29 bp):
ATGACATGAATTCATATGAAATGTATTAC
Found at i:32581 original size:30 final size:30
Alignment explanation
Indices: 32539--32615 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
32529 AGAAAAAGTT
* *
32539 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
32570 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
32600 ATATGACTACGTGATA
1 ATATGACTATGTGATA
32616 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:32914 original size:23 final size:22
Alignment explanation
Indices: 32826--32906 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
32816 ATCATTATAT
*
32826 GGCACTACGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
*
32848 GGCACTTCGGTGTAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
32870 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
32893 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
32907 TTTATACGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 40 0.73
23 15 0.27
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.26
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:38977 original size:21 final size:21
Alignment explanation
Indices: 38951--38993 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
38941 TTTTTGGGCT
* *
38951 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCATTCA
*
38972 AGGGGAACCGATACCCCTTCA
1 AGGGGAACCGATACCCATTCA
38993 A
1 A
38994 CGAATATGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (21 bp):
AGGGGAACCGATACCCATTCA
Found at i:39053 original size:66 final size:68
Alignment explanation
Indices: 38973--39123 Score: 234
Period size: 67 Copynumber: 2.2 Consensus size: 68
38963 ACCCATTCAA
* *
38973 GGGGAACCGATACCCCTTCAACGAATATG-ATTTCCAGAATGCTAGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
39037 -GG
66 GGG
* * *
39039 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGAATGCTTGAGGGGAATCGATACCCCCA
1 GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
39104 GGG
66 GGG
*
39107 GGGGAACCGATTCCCCC
1 GGGGAACCGATACCCCC
39124 ATGAGAAAAA
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
66 26 0.34
67 33 0.43
68 18 0.23
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.18
Consensus pattern (68 bp):
GGGGAACCGATACCCCCTCAACGAATATGAAATTCCAGAATGCTAGAGGGGAATCGATACCCCCA
GGG
Found at i:39460 original size:29 final size:29
Alignment explanation
Indices: 39426--39497 Score: 108
Period size: 29 Copynumber: 2.5 Consensus size: 29
39416 CATATTATGA
* *
39426 TACATGACATGAATTTATATTAAATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
39455 TACATGACATGAATTCATATGATATGTAT
1 TACATGACATGAATTCATATGAAATGTAT
*
39484 TGCATGACATGAAT
1 TACATGACATGAAT
39498 ATGCAGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.39, C:0.10, G:0.14, T:0.38
Consensus pattern (29 bp):
TACATGACATGAATTCATATGAAATGTAT
Found at i:39554 original size:30 final size:30
Alignment explanation
Indices: 39512--39588 Score: 118
Period size: 30 Copynumber: 2.5 Consensus size: 30
39502 AGAAAAAGTT
* *
39512 ATATGAGCTATGTGATAAAGGTATGTAAATG
1 ATATGA-CTATGTGATAAAGGTATGGAAATA
39543 ATATGACTATGTGATAAAGGTATGGAAATA
1 ATATGACTATGTGATAAAGGTATGGAAATA
*
39573 ATATGACTACGTGATA
1 ATATGACTATGTGATA
39589 TGAACTACGG
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 37 0.86
31 6 0.14
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.31
Consensus pattern (30 bp):
ATATGACTATGTGATAAAGGTATGGAAATA
Found at i:39831 original size:22 final size:22
Alignment explanation
Indices: 39799--39879 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
39789 ATCATTATAT
* *
39799 GGCACTACGGTGCAATTCTACA
1 GGCACTTCGGTGCAATTCTACG
39821 GGCACTTCGGTGCAATTCTACG
1 GGCACTTCGGTGCAATTCTACG
39843 GGCACTTCGGTGCAATTCTACGG
1 GGCACTTCGGTGCAATTCTAC-G
39866 GGCACTTCGGTGCA
1 GGCACTTCGGTGCA
39880 TTTATACGAG
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
22 41 0.73
23 15 0.27
ACGTcount: A:0.20, C:0.27, G:0.28, T:0.25
Consensus pattern (22 bp):
GGCACTTCGGTGCAATTCTACG
Found at i:41002 original size:18 final size:18
Alignment explanation
Indices: 40979--41016 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
40969 TTTTAAGATT
*
40979 TTATATTTGATTTAAATA
1 TTATATTCGATTTAAATA
*
40997 TTATATTCGATTTAATTA
1 TTATATTCGATTTAAATA
41015 TT
1 TT
41017 CGAATATTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.03, G:0.05, T:0.58
Consensus pattern (18 bp):
TTATATTCGATTTAAATA
Found at i:41460 original size:22 final size:22
Alignment explanation
Indices: 41432--41488 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
41422 TTATACAGGT
41432 AGTACCGATACCCCTATGAAGG
1 AGTACCGATACCCCTATGAAGG
41454 AGTACCGATACCCCTATGAAGG
1 AGTACCGATACCCCTATGAAGG
41476 AGTACCGATACCC
1 AGTACCGATACCC
41489 ATACGCTCCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.32, C:0.30, G:0.21, T:0.18
Consensus pattern (22 bp):
AGTACCGATACCCCTATGAAGG
Found at i:42686 original size:20 final size:20
Alignment explanation
Indices: 42661--42703 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
42651 AATAATATGT
42661 TAAGTAATGTAACATTCTGG
1 TAAGTAATGTAACATTCTGG
42681 TAAGTAATGTAACATTCTGG
1 TAAGTAATGTAACATTCTGG
42701 TAA
1 TAA
42704 TGTCATTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.09, G:0.19, T:0.35
Consensus pattern (20 bp):
TAAGTAATGTAACATTCTGG
Found at i:48295 original size:24 final size:24
Alignment explanation
Indices: 48268--48315 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
48258 GGATCATGTC
48268 GTTCAAATTTGGTTAAAAATAGAA
1 GTTCAAATTTGGTTAAAAATAGAA
48292 GTTCAAATTTGGTTAAAAATAGAA
1 GTTCAAATTTGGTTAAAAATAGAA
48316 TTAAAATGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.17, T:0.33
Consensus pattern (24 bp):
GTTCAAATTTGGTTAAAAATAGAA
Found at i:51205 original size:20 final size:19
Alignment explanation
Indices: 51162--51220 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 19
51152 ATTTTGCCTC
*
51162 AAAGGATCAAT-CCTTTAA
1 AAAGGATCAATCCCTTGAA
51180 CTAAAGGATCAATCCCCTTGAA
1 --AAAGGATCAAT-CCCTTGAA
*
51202 AAAGGATCGATCCCTTGAA
1 AAAGGATCAATCCCTTGAA
51221 TTCTAGTATC
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 8 0.23
20 21 0.60
22 6 0.17
ACGTcount: A:0.39, C:0.22, G:0.15, T:0.24
Consensus pattern (19 bp):
AAAGGATCAATCCCTTGAA
Found at i:52670 original size:21 final size:20
Alignment explanation
Indices: 52650--52767 Score: 101
Period size: 20 Copynumber: 5.8 Consensus size: 20
52640 ATTCGCGTTG
*
52650 CATTTCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-GTTC
* ** *
52671 AAAATCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGAT-GTTC
* ** *
52692 AAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATGTTC
*
52712 CATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATGTTC
* *
52732 CATCTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATGTTC
*
52752 CATTTTGCGTTGCGAT
1 CATTTCGCGTTGCGAT
52768 AGTCTACAGT
Statistics
Matches: 86, Mismatches: 11, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
20 52 0.60
21 34 0.40
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (20 bp):
CATTTCGCGTTGCGATGTTC
Found at i:52721 original size:20 final size:20
Alignment explanation
Indices: 52696--52767 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
52686 TAGTTGAAAA
52696 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
52716 TCGCGTTGCGATTTTCCATC
1 TCGCGTTGCGATTTTCCATT
52736 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
52756 TTGCGTTGCGAT
1 TCGCGTTGCGAT
52768 AGTCTACAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.10, C:0.25, G:0.22, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:52941 original size:41 final size:41
Alignment explanation
Indices: 52884--53031 Score: 260
Period size: 41 Copynumber: 3.6 Consensus size: 41
52874 CACGACCACG
* * *
52884 ATTTTCAACTATCGCAACGCGAAATGGAAAATCACAACACT
1 ATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCA
52925 ATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCA
1 ATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCA
*
52966 ATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCG
1 ATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCA
53007 ATTTTCAACTATCGCAACGCGAAAT
1 ATTTTCAACTATCGCAACGCGAAAT
53032 AGAACACGAA
Statistics
Matches: 103, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 103 1.00
ACGTcount: A:0.39, C:0.24, G:0.16, T:0.22
Consensus pattern (41 bp):
ATTTTCAACTATCGCAACGCGAAATGGAAAATCGCAACGCA
Found at i:52960 original size:20 final size:20
Alignment explanation
Indices: 52894--53007 Score: 86
Period size: 20 Copynumber: 5.6 Consensus size: 20
52884 ATTTTCAACT
52894 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* * * ** ** *
52914 ATCACAACACTATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
52935 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* ** *
52955 ATCGCAACGC-AATTTTCAACT
1 ATCGCAACGCGAA-ATGGAA-A
52976 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
52996 ATCGCAACGCGA
1 ATCGCAACGCGA
53008 TTTTCAACTA
Statistics
Matches: 66, Mismatches: 24, Indels: 8
0.67 0.24 0.08
Matches are distributed among these distances:
19 2 0.03
20 37 0.56
21 25 0.38
22 2 0.03
ACGTcount: A:0.40, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:61883 original size:266 final size:266
Alignment explanation
Indices: 61409--61941 Score: 1030
Period size: 266 Copynumber: 2.0 Consensus size: 266
61399 ATTTGATATT
* *
61409 CTAGTAGGATATTTGATATTTTGTTTGTAGTAATGTATTATATTCGAACTTAAACTACTATGTGA
1 CTAGTAGGATATTTGATATTTTGTTTGTAGTAATGTATTATATTCGAACTTAAACAACTATATGA
*
61474 TGAACTTTAACATTGTTTTACACACTAGTAGTTAAGGAACATTTCAATATTATATTATTAAATTG
66 TGAACTTAAACATTGTTTTACACACTAGTAGTTAAGGAACATTTCAATATTATATTATTAAATTG
*
61539 TTTTATTTAAAGAAACAAAATTTTAGTGGTTTTCAAATACGAAAATATTTTAAAAGATATGTGAC
131 TTTTATTTAAAGAAACAAAATTTTAGTGATTTTCAAATACGAAAATATTTTAAAAGATATGTGAC
61604 ACCTATGAGTTGTGTACGGGGGCATATACGAAAAATGGTTGTTACAAAAATGGTCTCCAGTTATG
196 ACCTATGAGTTGTGTACGGGGGCATATACGAAAAATGGTTGTTACAAAAATGGTCTCCAGTTATG
61669 CATTTC
261 CATTTC
61675 CTAGTAGGATATTTGATATTTTGTTTGTAGTAATGTATTATATTCGAACTTAAACAACTATATGA
1 CTAGTAGGATATTTGATATTTTGTTTGTAGTAATGTATTATATTCGAACTTAAACAACTATATGA
61740 TGAACTTAAACATTGTTTTACACACTAGTAGTTAAGGAACATTTCAATATTATATTATTAAATTG
66 TGAACTTAAACATTGTTTTACACACTAGTAGTTAAGGAACATTTCAATATTATATTATTAAATTG
61805 TTTTATTTAAAGAAACAAAATTTTAGTGATTTTCAAATACGAAAATATTTTAAAAGATATGTGAC
131 TTTTATTTAAAGAAACAAAATTTTAGTGATTTTCAAATACGAAAATATTTTAAAAGATATGTGAC
61870 ACCTATGAGTTGTGTACGGGGGCATATACGAAAAATGGTTGTTACAAAAATGGTCTCCAGTTATG
196 ACCTATGAGTTGTGTACGGGGGCATATACGAAAAATGGTTGTTACAAAAATGGTCTCCAGTTATG
61935 CATTTC
261 CATTTC
61941 C
1 C
61942 ATGATTCCAT
Statistics
Matches: 263, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
266 263 1.00
ACGTcount: A:0.36, C:0.10, G:0.16, T:0.38
Consensus pattern (266 bp):
CTAGTAGGATATTTGATATTTTGTTTGTAGTAATGTATTATATTCGAACTTAAACAACTATATGA
TGAACTTAAACATTGTTTTACACACTAGTAGTTAAGGAACATTTCAATATTATATTATTAAATTG
TTTTATTTAAAGAAACAAAATTTTAGTGATTTTCAAATACGAAAATATTTTAAAAGATATGTGAC
ACCTATGAGTTGTGTACGGGGGCATATACGAAAAATGGTTGTTACAAAAATGGTCTCCAGTTATG
CATTTC
Found at i:62375 original size:16 final size:16
Alignment explanation
Indices: 62351--62389 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
62341 TTATTATTAT
*
62351 TATTATTTTCTTTTCA
1 TATTTTTTTCTTTTCA
62367 TATTTTTTTCTTTTCA
1 TATTTTTTTCTTTTCA
62383 TATTTTT
1 TATTTTT
62390 CTTTTTAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (16 bp):
TATTTTTTTCTTTTCA
Found at i:62388 original size:14 final size:15
Alignment explanation
Indices: 62351--62394 Score: 63
Period size: 16 Copynumber: 2.9 Consensus size: 15
62341 TTATTATTAT
62351 TATTATTTTCTTTTCA
1 TATT-TTTTCTTTTCA
62367 TATTTTTTTCTTTTCA
1 TA-TTTTTTCTTTTCA
62383 TA-TTTTTCTTTT
1 TATTTTTTCTTTT
62395 TAATTGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
14 10 0.37
16 15 0.56
17 2 0.07
ACGTcount: A:0.14, C:0.11, G:0.00, T:0.75
Consensus pattern (15 bp):
TATTTTTTCTTTTCA
Found at i:63654 original size:2 final size:2
Alignment explanation
Indices: 63643--63680 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
63633 TGAATAAAAC
*
63643 TA TA -A TA TA TA TA TA T- TA TA TA TA TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63681 CTGTTAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Done.