Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005388.1 Hibiscus syriacus cultivar Beakdansim tig00012354_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: 67944
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1318 original size:27 final size:27
Alignment explanation
Indices: 1271--1326 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
1261 TTAATCATAA
** *
1271 TTATTATTTTTACCATAAGTTTTTATT
1 TTATTATTTACACCATAAGTTTTAATT
1298 TTATTATTTACACC-TATAGTTTTAATT
1 TTATTATTTACACCATA-AGTTTTAATT
1325 TT
1 TT
1327 CTATATTCTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 2 0.08
27 23 0.92
ACGTcount: A:0.27, C:0.09, G:0.04, T:0.61
Consensus pattern (27 bp):
TTATTATTTACACCATAAGTTTTAATT
Found at i:1665 original size:17 final size:19
Alignment explanation
Indices: 1629--1665 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
1619 CATGAAATAC
1629 AATATTATAATTTTATAAT
1 AATATTATAATTTTATAAT
*
1648 AATATT-TATTTTTA-AAT
1 AATATTATAATTTTATAAT
1665 A
1 A
1666 TCAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATAATTTTATAAT
Found at i:2518 original size:28 final size:26
Alignment explanation
Indices: 2487--2555 Score: 86
Period size: 28 Copynumber: 2.6 Consensus size: 26
2477 TAATTCTTTC
2487 TTTTCAAAATTTTTATATATACTTATT
1 TTTTCAAAATTTTTATATATA-TTATT
* *
2514 ATTTTCATAATATTTATATATATTATT
1 -TTTTCAAAATTTTTATATATATTATT
*
2541 TTTT-AATATTTTTAT
1 TTTTCAAAATTTTTAT
2556 TTTATTTTCA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
25 8 0.22
26 4 0.11
27 5 0.14
28 19 0.53
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTTCAAAATTTTTATATATATTATT
Found at i:2531 original size:24 final size:23
Alignment explanation
Indices: 2504--2566 Score: 76
Period size: 24 Copynumber: 2.7 Consensus size: 23
2494 AATTTTTATA
2504 TATACTTATTATTTTCATAATATT
1 TATA-TTATTATTTTCATAATATT
*
2528 TATATATATTATTTT-TTAATATT
1 TATAT-TATTATTTTCATAATATT
*
2551 TTTATT-TTATTTTCAT
1 TATATTATTATTTTCAT
2567 GTATTTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 7 0.21
22 2 0.06
23 12 0.35
24 13 0.38
ACGTcount: A:0.30, C:0.05, G:0.00, T:0.65
Consensus pattern (23 bp):
TATATTATTATTTTCATAATATT
Found at i:2586 original size:15 final size:16
Alignment explanation
Indices: 2550--2592 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
2540 TTTTTAATAT
2550 TTTTATTTTATTTTCA
1 TTTTATTTTATTTTCA
*
2566 -TGTATTTTA-TTTCA
1 TTTTATTTTATTTTCA
2580 TTTTATTTT-TTTT
1 TTTTATTTTATTTT
2593 TTGTTAGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 5
0.77 0.07 0.17
Matches are distributed among these distances:
14 5 0.22
15 18 0.78
ACGTcount: A:0.16, C:0.05, G:0.02, T:0.77
Consensus pattern (16 bp):
TTTTATTTTATTTTCA
Found at i:3032 original size:8 final size:8
Alignment explanation
Indices: 3019--3047 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3009 CTAACTTGTT
3019 TTTTTTTA
1 TTTTTTTA
3027 TTTTTTTA
1 TTTTTTTA
3035 -TTTTTTA
1 TTTTTTTA
3042 TTTTTT
1 TTTTTT
3048 CTGAATAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.10, C:0.00, G:0.00, T:0.90
Consensus pattern (8 bp):
TTTTTTTA
Found at i:4688 original size:26 final size:27
Alignment explanation
Indices: 4659--4728 Score: 72
Period size: 26 Copynumber: 2.6 Consensus size: 27
4649 CATTTTACAT
4659 CTTTGCATTTTTATTTTGTATT-CATA
1 CTTTGCATTTTTATTTTGTATTGCATA
* * *
4685 CTTT-TATGTTTACTTTTGTCTTGCATA
1 CTTTGCATTTTTA-TTTTGTATTGCATA
* *
4712 GTTTGCATTCTTATTTT
1 CTTTGCATTTTTATTTT
4729 TTTATTTATG
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
25 6 0.18
26 12 0.35
27 11 0.32
28 5 0.15
ACGTcount: A:0.16, C:0.13, G:0.10, T:0.61
Consensus pattern (27 bp):
CTTTGCATTTTTATTTTGTATTGCATA
Found at i:7442 original size:8 final size:8
Alignment explanation
Indices: 7417--7487 Score: 76
Period size: 7 Copynumber: 8.8 Consensus size: 8
7407 ATTATACTTA
7417 AAAAAAGAG
1 AAAAAAG-G
7426 AAAACAAAGG
1 -AAA-AAAGG
7436 AAAAAAGG
1 AAAAAAGG
7444 AAAAAAAGG
1 -AAAAAAGG
7453 -AAAAAGG
1 AAAAAAGG
7460 -AAAAAGG
1 AAAAAAGG
*
7467 AAAAAAAG
1 AAAAAAGG
7475 -AAAAAGG
1 AAAAAAGG
7482 AAAAAA
1 AAAAAA
7488 TTGAACCAAG
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
7 20 0.36
8 16 0.29
9 11 0.20
10 4 0.07
11 4 0.07
ACGTcount: A:0.77, C:0.01, G:0.21, T:0.00
Consensus pattern (8 bp):
AAAAAAGG
Found at i:7487 original size:23 final size:24
Alignment explanation
Indices: 7431--7487 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 24
7421 AAGAGAAAAC
7431 AAAGGAAAAAAGGAAAAAAAGGAA
1 AAAGGAAAAAAGGAAAAAAAGGAA
7455 AAAGG-AAAAAGGAAAAAAA-GAA
1 AAAGGAAAAAAGGAAAAAAAGGAA
7477 AAAGGAAAAAA
1 AAAGGAAAAAA
7488 TTGAACCAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 8 0.25
23 19 0.59
24 5 0.16
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (24 bp):
AAAGGAAAAAAGGAAAAAAAGGAA
Found at i:7976 original size:32 final size:32
Alignment explanation
Indices: 7940--8001 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
7930 GTCAGACACA
*
7940 AGAAGTATCTCTACGAGATGAGCATAACAACG
1 AGAAGTATCTCTACAAGATGAGCATAACAACG
*
7972 AGAAGTGTCTCTACAAGATGAGCATAACAA
1 AGAAGTATCTCTACAAGATGAGCATAACAA
8002 TCATTTCTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.19
Consensus pattern (32 bp):
AGAAGTATCTCTACAAGATGAGCATAACAACG
Found at i:12622 original size:26 final size:26
Alignment explanation
Indices: 12593--12669 Score: 67
Period size: 26 Copynumber: 3.2 Consensus size: 26
12583 ATCTGTAAGC
12593 CCTTCAGTGCATGATGTTATCAAAAA
1 CCTTCAGTGCATGATGTTATCAAAAA
* * * **
12619 CCTTC-G-G-GTCAT-CTAT--AAGC
1 CCTTCAGTGCATGATGTTATCAAAAA
12639 CCTTCAGTGCATGATGTTATCAAAAA
1 CCTTCAGTGCATGATGTTATCAAAAA
12665 CCTTC
1 CCTTC
12670 GGGTCATCTG
Statistics
Matches: 35, Mismatches: 10, Indels: 12
0.61 0.18 0.21
Matches are distributed among these distances:
20 7 0.20
21 1 0.03
22 4 0.11
23 6 0.17
24 4 0.11
25 1 0.03
26 12 0.34
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.31
Consensus pattern (26 bp):
CCTTCAGTGCATGATGTTATCAAAAA
Found at i:12638 original size:46 final size:45
Alignment explanation
Indices: 12490--13171 Score: 1049
Period size: 45 Copynumber: 15.0 Consensus size: 45
12480 CTATTTCCAA
12490 CATCTGTAAGTCCTTCAGTGCATGATGTTTTTCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTTTC-AAAACCTTCGGGT
*
12537 CATCTGTAATTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
12582 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* * *
12628 CATCTATAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
12674 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAATCCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAA-CCTTCGGGT
12720 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
12765 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTCCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* *
12810 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
* * *
12856 CATCTGTAAGTCCTTCAGTGCATGATGTTGTCAACACCTCCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
12901 CATATGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
12947 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTTCGGGT
*
12993 CATCTGTAAGTCCTTCAATGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * * **
13038 CATCTATAAGCCCTTCAGTGCATGATATTTTCAAAATGTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
*
13083 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
* * *
13128 CATCTGTAAGCCCTTCAGTGCATGCTGTTTTTAAAACCTTCGGG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGG
13172 AGCTTTTTGA
Statistics
Matches: 594, Mismatches: 37, Indels: 10
0.93 0.06 0.02
Matches are distributed among these distances:
45 304 0.51
46 264 0.44
47 26 0.04
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (45 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAACCTTCGGGT
Found at i:12646 original size:91 final size:91
Alignment explanation
Indices: 12490--13171 Score: 1048
Period size: 91 Copynumber: 7.5 Consensus size: 91
12480 CTATTTCCAA
* **
12490 CATCTGTAAGTCCTTCAGTGCATGATGTTTTTCAAAAACCTTCGGGTCATCTGTAATTCCTTCAG
1 CATCTGTAAGTCCTTCAGTGCATGATG-TTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAG
12555 TGCATGATGTTTTCAAAACCTTCGGGT
65 TGCATGATGTTTTCAAAACCTTCGGGT
* *
12582 CATCTGTAAGCCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTATAAGCCCTTCAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
12647 GCATGATGTTATCAAAAACCTTCGGGT
66 GCATGATGTTTTC-AAAACCTTCGGGT
* *
12674 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAATCCTTCGGGTCATCTGTAAGTCCTTCAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
12739 GCATGATGTTTTCAAAACCTTCGGGT
66 GCATGATGTTTTCAAAACCTTCGGGT
* *
12765 CATCTGTAAGTCCTTCAGTGCATGATGTTTTC-AAAACCTCCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
12829 GCATGATGTTATCAAAAACCTTCGGGT
66 GCATGATGTTTTC-AAAACCTTCGGGT
* * * *
12856 CATCTGTAAGTCCTTCAGTGCATGATGTTGTC-AACACCTCCGGGTCATATGTAAGCCCTTCAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
*
12920 GCATGATGTTATCAAAAACCTTCGGGT
66 GCATGATGTTTTC-AAAACCTTCGGGT
* *
12947 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAAT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
13012 GCATGATGTTTTCAAAACCTTCGGGT
66 GCATGATGTTTTCAAAACCTTCGGGT
* * * * **
13038 CATCTATAAGCCCTTCAGTGCATGATATTTTC-AAAATGTTCGGGTCATCTGTAAGCCCTTCAGT
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
13102 GCATGATGTTTTCAAAACCTTCGGGT
66 GCATGATGTTTTCAAAACCTTCGGGT
* * **
13128 CATCTGTAAGCCCTTCAGTGCATGCTGTT-TTTAAAACCTTCGGG
1 CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGG
13172 AGCTTTTTGA
Statistics
Matches: 546, Mismatches: 40, Indels: 10
0.92 0.07 0.02
Matches are distributed among these distances:
89 1 0.00
90 131 0.24
91 263 0.48
92 151 0.28
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.33
Consensus pattern (91 bp):
CATCTGTAAGTCCTTCAGTGCATGATGTTATCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGT
GCATGATGTTTTCAAAACCTTCGGGT
Found at i:13388 original size:3 final size:3
Alignment explanation
Indices: 13380--13417 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
13370 TTTTTCACTA
*
13380 TAT TAT TAT TAT TAT TA- TAT ATAT TAT TAA TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
13418 AATTAAATAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 26 0.84
4 3 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:13404 original size:21 final size:21
Alignment explanation
Indices: 13378--13417 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
13368 AATTTTTCAC
*
13378 TATATTATTATTATTATTATA
1 TATATTATTAATATTATTATA
13399 TATATTATTAATATTATTA
1 TATATTATTAATATTATTA
13418 AATTAAATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
TATATTATTAATATTATTATA
Found at i:13418 original size:9 final size:9
Alignment explanation
Indices: 13383--13430 Score: 50
Period size: 9 Copynumber: 5.7 Consensus size: 9
13373 TTCACTATAT
*
13383 TATTATTAT
1 TATTATTAA
13392 TATTA-TATA
1 TATTATTA-A
13401 TATTATTAA
1 TATTATTAA
13410 TATTATTAA
1 TATTATTAA
13419 -ATTA--AA
1 TATTATTAA
13425 TATTAT
1 TATTAT
13431 AAAACCCTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 9
0.77 0.02 0.20
Matches are distributed among these distances:
6 2 0.06
7 4 0.12
8 6 0.18
9 20 0.59
10 2 0.06
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TATTATTAA
Found at i:15041 original size:17 final size:19
Alignment explanation
Indices: 15005--15041 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
14995 CATGAAATAC
15005 AATATTATAATTTTATAAT
1 AATATTATAATTTTATAAT
*
15024 AATATT-TATTTTTA-AAT
1 AATATTATAATTTTATAAT
15041 A
1 A
15042 TCAAAGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 4 0.24
18 7 0.41
19 6 0.35
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
AATATTATAATTTTATAAT
Found at i:25111 original size:108 final size:107
Alignment explanation
Indices: 24913--25180 Score: 365
Period size: 108 Copynumber: 2.5 Consensus size: 107
24903 GATACACATG
* * * * *
24913 TAGTGCCTATACAGTCATTCATAAACATATTATGAATTACGTGGTTCGCACACATAGTCCCTATA
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGTT-GCACACATAGTCCCTATA
* * *
24978 CGGTTGTTCATCAATACATGTTGAATTCTGTGGGTTGCATACT
65 CGGTTGTTCATCAATACATGATGAATTCTATGGGTTGCACACT
* * * *
25021 TAGTGCCTATACGGTCGTTTATCAACCTATGATGAATTTCGTGGGTTGCACACTTAGTGCCTATA
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGT-GGTTGCACACATAGTCCCTATA
* *
25086 CGGTTGTTCATCAATATATGATGAATTCTATGGGTTGTACACT
65 CGGTTGTTCATCAATACATGATGAATTCTATGGGTTGCACACT
* *
25129 TAGTGCCTATACGCTCGTTCATCATCATATGATGAATTTCGTAGGTTGCACA
1 TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGT-GGTTGCACA
25181 GTTAATGTCT
Statistics
Matches: 140, Mismatches: 19, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
108 136 0.97
109 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (107 bp):
TAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGTTGCACACATAGTCCCTATAC
GGTTGTTCATCAATACATGATGAATTCTATGGGTTGCACACT
Found at i:25193 original size:54 final size:54
Alignment explanation
Indices: 24913--25180 Score: 260
Period size: 54 Copynumber: 5.0 Consensus size: 54
24903 GATACACATG
* * * * * * *
24913 TAGTGCCTATACAGTCATTCATAAACATATTATGAATTACGT-GGTTCGCACACA
1 TAGTGCCTATACGGTCGTTCATCATCATATGATGAATTTCGTAGGTT-GCACACT
* * * * * *
24967 TAGTCCCTATACGGTTGTTCATCAAT-ACATGTTGAA-TTCTGTGGGTTGCATACT
1 TAGTGCCTATACGGTCGTTCATC-ATCATATGATGAATTTC-GTAGGTTGCACACT
* * * *
25021 TAGTGCCTATACGGTCGTTTATCAACCTATGATGAATTTCGTGGGTTGCACACT
1 TAGTGCCTATACGGTCGTTCATCATCATATGATGAATTTCGTAGGTTGCACACT
* *
25075 TAGTGCCTATACGGTTGTTCATCAAT-ATATGATGAA-TTC-TATGGGTTGTACACT
1 TAGTGCCTATACGGTCGTTCATC-ATCATATGATGAATTTCGTA--GGTTGCACACT
*
25129 TAGTGCCTATACGCTCGTTCATCATCATATGATGAATTTCGTAGGTTGCACA
1 TAGTGCCTATACGGTCGTTCATCATCATATGATGAATTTCGTAGGTTGCACA
25181 GTTAATGTCT
Statistics
Matches: 174, Mismatches: 29, Indels: 22
0.77 0.13 0.10
Matches are distributed among these distances:
52 1 0.01
53 8 0.05
54 151 0.87
55 12 0.07
56 2 0.01
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.36
Consensus pattern (54 bp):
TAGTGCCTATACGGTCGTTCATCATCATATGATGAATTTCGTAGGTTGCACACT
Found at i:29346 original size:54 final size:54
Alignment explanation
Indices: 29277--29619 Score: 440
Period size: 54 Copynumber: 6.4 Consensus size: 54
29267 TTTGTTGAGA
* * * * * *
29277 TGCACACGTAATGCCTATACGGTCATTCATAAACATATTATGAATTTTGT-GGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* * *
29330 T-CACATACATAGTGCCTATATGGTCGTTCATCAATATATGATGAATTTCGTGGGT
1 TGCAC--ACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* *
29385 TGTACACTTAGTGCCTATACGGTCGTTCATCAACATATGATTAATTAT-GTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATT-TCGTGGGT
* * *
29439 TGCACACTTAGTGCCTATACGGTTGTTCATCAACATATTATGAATTACGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* * * *
29493 TGCACACTTAGTGCCTATACGATTGTTCATCAATATTTGATGAATTTCGTGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
* * * *
29547 TGCACACTTAGTGCCTATACGTTCGTTCATCAATATATGATGAATTCCATGGGT
1 TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
29601 TGCACACTTAGTGCCTATA
1 TGCACACTTAGTGCCTATA
29620 GTACACATAA
Statistics
Matches: 256, Mismatches: 28, Indels: 11
0.87 0.09 0.04
Matches are distributed among these distances:
52 3 0.01
53 1 0.00
54 245 0.96
55 5 0.02
56 2 0.01
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (54 bp):
TGCACACTTAGTGCCTATACGGTCGTTCATCAACATATGATGAATTTCGTGGGT
Found at i:32218 original size:19 final size:19
Alignment explanation
Indices: 32194--32243 Score: 73
Period size: 19 Copynumber: 2.6 Consensus size: 19
32184 TACCATATTT
32194 TAATTTAATAATTTAATAA
1 TAATTTAATAATTTAATAA
* * *
32213 TAATTTGATAATTTATTAT
1 TAATTTAATAATTTAATAA
32232 TAATTTAATAAT
1 TAATTTAATAAT
32244 AAAATTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TAATTTAATAATTTAATAA
Found at i:42424 original size:28 final size:29
Alignment explanation
Indices: 42372--42436 Score: 123
Period size: 28 Copynumber: 2.3 Consensus size: 29
42362 ATCTGGCAAC
42372 CTGATGCGGTAGGGGGTACATAATGCGGT
1 CTGATGCGGTAGGGGGTACATAATGCGGT
42401 CTGATGCGGTA-GGGGTACATAATGCGGT
1 CTGATGCGGTAGGGGGTACATAATGCGGT
42429 CTGATGCG
1 CTGATGCG
42437 ATTATTGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 25 0.69
29 11 0.31
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (29 bp):
CTGATGCGGTAGGGGGTACATAATGCGGT
Found at i:45720 original size:19 final size:19
Alignment explanation
Indices: 45677--45714 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
45667 AAATGACAAT
45677 GACGACAGTCATGATTGTG
1 GACGACAGTCATGATTGTG
*
45696 GACGACGGTCATGATTGTG
1 GACGACAGTCATGATTGTG
45715 ACCGACAAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.24, C:0.16, G:0.34, T:0.26
Consensus pattern (19 bp):
GACGACAGTCATGATTGTG
Found at i:56827 original size:26 final size:26
Alignment explanation
Indices: 56798--56847 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
56788 TAATTATCAA
* *
56798 GTTAGTAGTTTAGTAACATCAGTATG
1 GTTAGAAGTTTAGTAACATAAGTATG
*
56824 GTTAGAAGTTTAGTGACATAAGTA
1 GTTAGAAGTTTAGTAACATAAGTA
56848 ATAATTGTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.06, G:0.24, T:0.36
Consensus pattern (26 bp):
GTTAGAAGTTTAGTAACATAAGTATG
Found at i:57193 original size:22 final size:22
Alignment explanation
Indices: 57168--57214 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
57158 CAAATGACAC
57168 ATTAAGAACTTGTTTTAAAATT
1 ATTAAGAACTTGTTTTAAAATT
57190 ATTAAGAACTTGTTTTAAAATT
1 ATTAAGAACTTGTTTTAAAATT
57212 ATT
1 ATT
57215 CTAAGTATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.40, C:0.04, G:0.09, T:0.47
Consensus pattern (22 bp):
ATTAAGAACTTGTTTTAAAATT
Found at i:64634 original size:42 final size:41
Alignment explanation
Indices: 64539--64680 Score: 142
Period size: 43 Copynumber: 3.4 Consensus size: 41
64529 AGCGGCGTTT
* ** *
64539 AGGTTTGTTATTTAGTGGCATTTTTAGTCAAAACAACTACAAC
1 AGGTTTGTTATTTAGTGGC-TTTTTAGGCAAAACGTC-GCAAC
* *
64582 ATGTTT-TTATTTAGTGGCGTTTTAGGCACAAACGTCGCAAC
1 AGGTTTGTTATTTAGTGGCTTTTTAGGCA-AAACGTCGCAAC
* *
64623 AGGTTTGTTATTTAGCGGAATTTTTAGGCAAAACAGTCGCAAC
1 AGGTTTGTTATTTAGTGG-CTTTTTAGGCAAAAC-GTCGCAAC
* *
64666 AAGTTTATTATTTAG
1 AGGTTTGTTATTTAG
64681 CGGTGTGTTT
Statistics
Matches: 83, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
41 17 0.20
42 31 0.37
43 35 0.42
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.37
Consensus pattern (41 bp):
AGGTTTGTTATTTAGTGGCTTTTTAGGCAAAACGTCGCAAC
Found at i:64879 original size:41 final size:40
Alignment explanation
Indices: 64834--64911 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 40
64824 ACCACCTTAA
* *
64834 ATTTAATTACGATTTGAATTAAGTAATAATATATAAAAACT
1 ATTTAATTACGATTCGAATTAAGTAACAATATA-AAAAACT
*
64875 ATTTATTTACGATTCGAATTAAGTAACAATATAAAAA
1 ATTTAATTACGATTCGAATTAAGTAACAATATAAAAA
64912 CATAAATAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
40 4 0.12
41 30 0.88
ACGTcount: A:0.49, C:0.06, G:0.08, T:0.37
Consensus pattern (40 bp):
ATTTAATTACGATTCGAATTAAGTAACAATATAAAAAACT
Found at i:65374 original size:13 final size:13
Alignment explanation
Indices: 65365--65403 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
65355 AATTTATAAT
65365 GCGCATTTATGAC
1 GCGCATTTATGAC
*
65378 ACGCATTTATGAC
1 GCGCATTTATGAC
65391 GCGCATTTATGAC
1 GCGCATTTATGAC
65404 TTACATGCGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (13 bp):
GCGCATTTATGAC
Found at i:65567 original size:2 final size:2
Alignment explanation
Indices: 65560--65589 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
65550 ATTTATGAAT
65560 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
65590 ATGTAGATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.