Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009006.1 Hibiscus syriacus cultivar Beakdansim tig00112390_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: 52364
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:2231 original size:18 final size:18
Alignment explanation
Indices: 2189--2233 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
2179 CTGGAAGAAA
*
2189 GCCTCACCAGCCGTTATT
1 GCCTCATCAGCCGTTATT
*
2207 GCCTCATCAGCTGTTATT
1 GCCTCATCAGCCGTTATT
2225 GCCTCATCA
1 GCCTCATCA
2234 AGCAAGTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.18, C:0.36, G:0.16, T:0.31
Consensus pattern (18 bp):
GCCTCATCAGCCGTTATT
Found at i:7762 original size:21 final size:22
Alignment explanation
Indices: 7724--7765 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
7714 GCAACGTTTA
7724 CTCTTCAAAATAAAAATAAATC
1 CTCTTCAAAATAAAAATAAATC
7746 CTCTTCAAAAT-AAAATAAAT
1 CTCTTCAAAATAAAAATAAAT
7766 AAATTGAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.55, C:0.17, G:0.00, T:0.29
Consensus pattern (22 bp):
CTCTTCAAAATAAAAATAAATC
Found at i:9635 original size:17 final size:18
Alignment explanation
Indices: 9608--9641 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
9598 ACTAACCATT
9608 TTTTCTTTTCTTTTTTTC
1 TTTTCTTTTCTTTTTTTC
9626 TTTT-TTTTCTTTTTTT
1 TTTTCTTTTCTTTTTTT
9642 TCGTTTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (18 bp):
TTTTCTTTTCTTTTTTTC
Found at i:9648 original size:10 final size:9
Alignment explanation
Indices: 9608--9650 Score: 61
Period size: 9 Copynumber: 4.7 Consensus size: 9
9598 ACTAACCATT
9608 TTTTCTTTTC
1 TTTT-TTTTC
9618 -TTTTTTTC
1 TTTTTTTTC
9626 TTTTTTTTC
1 TTTTTTTTC
9635 TTTTTTTTC
1 TTTTTTTTC
9644 GTTTTTT
1 -TTTTTT
9651 CGCATGCTCC
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 5 0.16
9 20 0.65
10 6 0.19
ACGTcount: A:0.00, C:0.12, G:0.02, T:0.86
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:9648 original size:17 final size:17
Alignment explanation
Indices: 9613--9651 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
9603 CCATTTTTTC
*
9613 TTTTCTTTTTTTCTTTT
1 TTTTCTTTTTTTCTGTT
9630 TTTTCTTTTTTT-TCGTT
1 TTTTCTTTTTTTCT-GTT
9647 TTTTC
1 TTTTC
9652 GCATGCTCCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 1 0.05
17 19 0.95
ACGTcount: A:0.00, C:0.13, G:0.03, T:0.85
Consensus pattern (17 bp):
TTTTCTTTTTTTCTGTT
Found at i:12403 original size:18 final size:19
Alignment explanation
Indices: 12370--12409 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
12360 ATTATTAAAG
12370 TTATAAAATAATTATTTGA
1 TTATAAAATAATTATTTGA
* *
12389 TTATAAAA-CATTATTTTA
1 TTATAAAATAATTATTTGA
12407 TTA
1 TTA
12410 AGTCTTTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (19 bp):
TTATAAAATAATTATTTGA
Found at i:15158 original size:76 final size:77
Alignment explanation
Indices: 15014--15162 Score: 219
Period size: 76 Copynumber: 1.9 Consensus size: 77
15004 TAAAAAACTA
* ** * *
15014 TTAAAATATTTAAAATTTTGAAGTTAAAAATAATATGAAACTTTTACAAATTTTTATTAAATTTG
1 TTAAAATATTTAAAATTTTGAAGTTAAAAATAATATGAAACTTGTACAAATTTTTAACAAAATAG
15079 AAAAAAAATATT
66 AAAAAAAATATT
* * *
15091 TTAAAAT-TTTAAAATTTTGAAGTTAAAAATTATATGAAACTTGTAGAATTTTTTAACAAAATAG
1 TTAAAATATTTAAAATTTTGAAGTTAAAAATAATATGAAACTTGTACAAATTTTTAACAAAATAG
15155 AAAAAAAA
66 AAAAAAAA
15163 AACTTACATG
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
76 57 0.89
77 7 0.11
ACGTcount: A:0.52, C:0.03, G:0.07, T:0.39
Consensus pattern (77 bp):
TTAAAATATTTAAAATTTTGAAGTTAAAAATAATATGAAACTTGTACAAATTTTTAACAAAATAG
AAAAAAAATATT
Found at i:20111 original size:13 final size:13
Alignment explanation
Indices: 20095--20127 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
20085 AATACCTTTT
20095 AAAATAATTTTAA
1 AAAATAATTTTAA
20108 AAAATAATTTTAA
1 AAAATAATTTTAA
*
20121 AAGATAA
1 AAAATAA
20128 AAAATGTGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (13 bp):
AAAATAATTTTAA
Found at i:22112 original size:25 final size:23
Alignment explanation
Indices: 22066--22113 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 23
22056 CTTGAAGTTG
* *
22066 GACTTGTTACCCAAATTGGACTT
1 GACTTGTTACCCAAACTAGACTT
22089 GACTTGTTAACCCCAAACTAGACTT
1 GACTTGTT-A-CCCAAACTAGACTT
22114 AGACCACCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 8 0.38
24 1 0.05
25 12 0.57
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (23 bp):
GACTTGTTACCCAAACTAGACTT
Found at i:22218 original size:2 final size:2
Alignment explanation
Indices: 22206--22238 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
22196 AACTATAAAT
22206 TA TA T- TA TA TA TA TA TA TA TA CTA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA T
22239 TTTTTTAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 1 0.03
2 26 0.90
3 2 0.07
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22231 original size:17 final size:17
Alignment explanation
Indices: 22206--22238 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
22196 AACTATAAAT
*
22206 TATATTATATATATATA
1 TATACTATATATATATA
22223 TATACTATATATATAT
1 TATACTATATATATAT
22239 TTTTTTAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (17 bp):
TATACTATATATATATA
Found at i:22274 original size:26 final size:23
Alignment explanation
Indices: 22230--22279 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 23
22220 ATATATACTA
*
22230 TATATATATTTTTTTAAACTATAT
1 TATATATATTTTTTAAAAC-ATAT
22254 TATATATATTTTTTCCAAAACATAT
1 TATATATATTTTTT--AAAACATAT
22279 T
1 T
22280 TTCTAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
24 14 0.61
25 5 0.22
26 4 0.17
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (23 bp):
TATATATATTTTTTAAAACATAT
Found at i:22353 original size:20 final size:20
Alignment explanation
Indices: 22283--22384 Score: 86
Period size: 20 Copynumber: 5.0 Consensus size: 20
22273 ACATATTTTC
22283 TAAAACTATAT-TATATATA
1 TAAAACTATATATATATATA
*
22302 TATATA-TATATATATATATA
1 TA-AAACTATATATATATATA
*
22322 TATATA-TATATATATATATA
1 TA-AAACTATATATATATATA
*
22342 TTCAAAACTATATATATAT-TT
1 -T-AAAACTATATATATATATA
*
22363 TCAAACCTATACTATATATATA
1 T-AAAACTATA-TATATATATA
22385 ACCAAAATAA
Statistics
Matches: 71, Mismatches: 5, Indels: 11
0.82 0.06 0.13
Matches are distributed among these distances:
19 7 0.10
20 40 0.56
21 11 0.15
22 13 0.18
ACGTcount: A:0.48, C:0.07, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAACTATATATATATATA
Found at i:22360 original size:2 final size:2
Alignment explanation
Indices: 22289--22342 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
22279 TTTCTAAAAC
22289 TA TA T- 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
22330 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
22343 TCAAAACTAT
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:24611 original size:3 final size:3
Alignment explanation
Indices: 24605--24634 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
24595 TATAATAATA
24605 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
24635 TGTTCTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:25148 original size:37 final size:37
Alignment explanation
Indices: 25107--25180 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
25097 TTGTAGGTAA
25107 AAAGAAGAATTAGGAAATAAAATACGGAAAAAGAAAT
1 AAAGAAGAATTAGGAAATAAAATACGGAAAAAGAAAT
*
25144 AAAGAAGAATTAGGAAATAAAATACGGAAAAATAAAT
1 AAAGAAGAATTAGGAAATAAAATACGGAAAAAGAAAT
25181 TATTATTCAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.65, C:0.03, G:0.18, T:0.15
Consensus pattern (37 bp):
AAAGAAGAATTAGGAAATAAAATACGGAAAAAGAAAT
Found at i:25162 original size:18 final size:18
Alignment explanation
Indices: 25107--25164 Score: 57
Period size: 18 Copynumber: 3.2 Consensus size: 18
25097 TTGTAGGTAA
25107 AAAGAAGAATTAGGAAAT
1 AAAGAAGAATTAGGAAAT
* *
25125 AAA-ATACGGAA-AAAGAAAT
1 AAAGA-A--GAATTAGGAAAT
25144 AAAGAAGAATTAGGAAAT
1 AAAGAAGAATTAGGAAAT
25162 AAA
1 AAA
25165 ATACGGAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
17 4 0.13
18 13 0.42
19 10 0.32
20 4 0.13
ACGTcount: A:0.66, C:0.02, G:0.19, T:0.14
Consensus pattern (18 bp):
AAAGAAGAATTAGGAAAT
Found at i:25327 original size:15 final size:16
Alignment explanation
Indices: 25297--25329 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
25287 TTTATTTCGT
*
25297 AATAATAATTAAATAA
1 AATAATAATAAAATAA
25313 AATAA-AATAAAATAA
1 AATAATAATAAAATAA
25328 AA
1 AA
25330 ATTTAAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (16 bp):
AATAATAATAAAATAA
Found at i:28608 original size:36 final size:35
Alignment explanation
Indices: 28559--28656 Score: 106
Period size: 36 Copynumber: 2.7 Consensus size: 35
28549 ATCACCGCCA
* * *
28559 CCTCCAGCAATTTACCCTCCTCAATCCCCGCCACC
1 CCTCCACCCATTTACCCTCCTCAATCCCCACCACC
*
28594 TCCTCCACCCATTTACACTCCTCAATCCCCACCACC
1 -CCTCCACCCATTTACCCTCCTCAATCCCCACCACC
* * * *
28630 CGCTTCACCCGTTTACCCCCCACAATC
1 C-CTCCACCCATTTACCCTCCTCAATC
28657 ACCCCCGCCG
Statistics
Matches: 52, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
35 1 0.02
36 51 0.98
ACGTcount: A:0.20, C:0.54, G:0.04, T:0.21
Consensus pattern (35 bp):
CCTCCACCCATTTACCCTCCTCAATCCCCACCACC
Found at i:29010 original size:21 final size:21
Alignment explanation
Indices: 28986--29026 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
28976 TCCAGCACAT
* *
28986 CATTCACCGCCACCTCCACCA
1 CATTCACCACCACCGCCACCA
*
29007 CATTCTCCACCACCGCCACC
1 CATTCACCACCACCGCCACC
29027 GCTACCACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.59, G:0.05, T:0.15
Consensus pattern (21 bp):
CATTCACCACCACCGCCACCA
Found at i:29020 original size:27 final size:27
Alignment explanation
Indices: 28990--29047 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
28980 GCACATCATT
* *
28990 CACCGCCACCTCCACCACATTCTCCAC
1 CACCGCCACCGCCACCACATTCACCAC
* *
29017 CACCGCCACCGCTACCACATTCACCTC
1 CACCGCCACCGCCACCACATTCACCAC
29044 CACC
1 CACC
29048 ACCAATTTAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.22, C:0.59, G:0.05, T:0.14
Consensus pattern (27 bp):
CACCGCCACCGCCACCACATTCACCAC
Found at i:30653 original size:14 final size:14
Alignment explanation
Indices: 30634--30661 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
30624 TCGATTATAT
30634 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
30648 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
30662 ATTTATGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.14, G:0.21, T:0.57
Consensus pattern (14 bp):
GTTCGTTTATGTTC
Found at i:30666 original size:24 final size:24
Alignment explanation
Indices: 30621--30685 Score: 76
Period size: 24 Copynumber: 2.6 Consensus size: 24
30611 CGTTCATGAA
*
30621 CGTTCGATTATATGTTCGTTTATGTT
1 CGTTCG-TT-TATGTTCATTTATGTT
30647 CGTTCGTTTATGTTCATTTATGTT
1 CGTTCGTTTATGTTCATTTATGTT
** *
30671 TATTCATTTATGTTC
1 CGTTCGTTTATGTTC
30686 GAACAAATGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 27 0.77
25 2 0.06
26 6 0.17
ACGTcount: A:0.15, C:0.12, G:0.15, T:0.57
Consensus pattern (24 bp):
CGTTCGTTTATGTTCATTTATGTT
Found at i:33367 original size:5 final size:5
Alignment explanation
Indices: 33357--33453 Score: 86
Period size: 5 Copynumber: 17.8 Consensus size: 5
33347 AACGGTCAAC
* *
33357 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
* *
33406 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
33454 AGACCGGTCA
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
5 60 0.79
7 16 0.21
ACGTcount: A:0.08, C:0.23, G:0.51, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:33382 original size:17 final size:17
Alignment explanation
Indices: 33362--33454 Score: 101
Period size: 17 Copynumber: 5.9 Consensus size: 17
33352 TCAACGGTCG
33362 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
*
33379 GGTCGGGTCGGGTC--G
1 GGTCGGGTCGGGTCAAC
** *
33394 GGTC--AAC-GGTC--G
1 GGTCGGGTCGGGTCAAC
33406 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
33423 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
33440 GGTCGGGTCGGGTCA
1 GGTCGGGTCGGGTCA
33455 GACCGGTCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
12 9 0.14
13 1 0.02
14 1 0.02
15 8 0.12
17 46 0.71
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:33449 original size:22 final size:22
Alignment explanation
Indices: 33350--33436 Score: 174
Period size: 22 Copynumber: 4.0 Consensus size: 22
33340 AACGGTTAAC
33350 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
33372 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
33394 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
33416 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
33437 AACGGTCGGG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 65 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:33468 original size:9 final size:9
Alignment explanation
Indices: 33450--33547 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
33440 GGTCGGGTCG
*
33450 GGTCAGACC
1 GGTCAAACC
33459 GGTCAAACC
1 GGTCAAACC
*
33468 GGTTCAGACC
1 GG-TCAAACC
33478 -GTCAAACC
1 GGTCAAACC
*
33486 GGTTCGAACC
1 GG-TCAAACC
*
33496 GGTTGAAACC
1 GG-TCAAACC
33506 GGTCAAACC
1 GGTCAAACC
33515 GGTCAGAACC
1 GGTCA-AACC
*
33525 GGTTGAAAACC
1 GG-T-CAAACC
*
33536 GGTTAAACC
1 GGTCAAACC
33545 GGT
1 GGT
33548 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
8 6 0.08
9 31 0.42
10 29 0.39
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.28, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:33483 original size:18 final size:19
Alignment explanation
Indices: 33452--33548 Score: 92
Period size: 19 Copynumber: 5.1 Consensus size: 19
33442 TCGGGTCGGG
33452 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
33471 TCAGACC-GTCAAACCGGT
1 TCAGACCGGTCAAACCGGT
*
33489 TC-GAACCGGTTGAAACCGG-
1 TCAG-ACCGG-TCAAACCGGT
*
33508 TCAAACCGGTCAGAACCGGT
1 TCAGACCGGTCA-AACCGGT
* * *
33528 TGAAAACCGGTTAAACCGGT
1 T-CAGACCGGTCAAACCGGT
33548 T
1 T
33549 TCCAGCAGCC
Statistics
Matches: 66, Mismatches: 5, Indels: 13
0.79 0.06 0.15
Matches are distributed among these distances:
17 1 0.02
18 18 0.27
19 21 0.32
20 17 0.26
21 9 0.14
ACGTcount: A:0.29, C:0.28, G:0.26, T:0.18
Consensus pattern (19 bp):
TCAGACCGGTCAAACCGGT
Found at i:33523 original size:29 final size:28
Alignment explanation
Indices: 33451--33547 Score: 92
Period size: 29 Copynumber: 3.4 Consensus size: 28
33441 GTCGGGTCGG
*
33451 GTCAGACCGGTCAAACCGGTTCAG-ACC-
1 GTCAAACCGGTCAAACCGGTT-AGAACCG
*
33478 GTCAAACCGGTTCGAACCGGTT-GAAACCG
1 GTCAAACCGG-TCAAACCGGTTAG-AACCG
*
33507 GTCAAACCGGTCAGAACCGGTTGAAAACCG
1 GTCAAACCGGTCA-AACCGGTT-AGAACCG
*
33537 GTTAAACCGGT
1 GTCAAACCGGT
33548 TTCCAGCAGC
Statistics
Matches: 58, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
26 1 0.02
27 9 0.16
28 15 0.26
29 18 0.31
30 15 0.26
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTTAGAACCG
Found at i:40698 original size:5 final size:5
Alignment explanation
Indices: 40688--40767 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
40678 AACGGTCAAC
* * *
40688 GGTCG GGTCG GGTCG GGTCAAC GATCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
*
40737 GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC--G GGTCG GGTCG GGTC
40768 AACGGTCGGT
Statistics
Matches: 61, Mismatches: 8, Indels: 12
0.75 0.10 0.15
Matches are distributed among these distances:
5 50 0.82
7 11 0.18
ACGTcount: A:0.09, C:0.23, G:0.50, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:40709 original size:22 final size:22
Alignment explanation
Indices: 40681--40767 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
40671 AACGGTTAAC
40681 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
40703 GGTCAACGATCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
40725 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
40747 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
40768 AACGGTCGGT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 63 1.00
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:40735 original size:17 final size:17
Alignment explanation
Indices: 40715--40780 Score: 80
Period size: 17 Copynumber: 3.6 Consensus size: 17
40705 TCAACGATCG
40715 GGTCGGGTCGGGTCAACGGTC
1 GGTCGGGTCGGGTCAA----C
40736 GGGTCGGGTCGGGTCAAC
1 G-GTCGGGTCGGGTCAAC
40754 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
40771 GGTC-GGTCGG
1 GGTCGGGTCGG
40781 TCAGACCGGT
Statistics
Matches: 44, Mismatches: 0, Indels: 7
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.14
17 20 0.45
18 2 0.05
21 1 0.02
22 15 0.34
ACGTcount: A:0.09, C:0.23, G:0.50, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:40738 original size:39 final size:38
Alignment explanation
Indices: 40693--40780 Score: 108
Period size: 39 Copynumber: 2.3 Consensus size: 38
40683 TCAACGGTCG
*
40693 GGTCGGGTCGGGTCAACGATC-GGGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTC--CGATCACGGTCGGGTCGGGTCAAC
* *
40732 GGTCGGGTCGGGTCGGGTCAACGGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCCGATC-ACGGTCGGGTCGGGTCAAC
40771 GGTC-GGTCGG
1 GGTCGGGTCGG
40781 TCAGACCGGT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
37 3 0.07
38 6 0.14
39 35 0.80
ACGTcount: A:0.10, C:0.23, G:0.49, T:0.18
Consensus pattern (38 bp):
GGTCGGGTCGGGTCCGATCACGGTCGGGTCGGGTCAAC
Found at i:40791 original size:17 final size:17
Alignment explanation
Indices: 40737--40780 Score: 81
Period size: 17 Copynumber: 2.6 Consensus size: 17
40727 TCAACGGTCG
40737 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
40754 GGTCGGGTCGGGTCAAC
1 GGTCGGGTCGGGTCAAC
40771 GGTC-GGTCGG
1 GGTCGGGTCGG
40781 TCAGACCGGT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 6 0.22
17 21 0.78
ACGTcount: A:0.09, C:0.23, G:0.50, T:0.18
Consensus pattern (17 bp):
GGTCGGGTCGGGTCAAC
Found at i:40792 original size:9 final size:9
Alignment explanation
Indices: 40778--40874 Score: 86
Period size: 9 Copynumber: 10.4 Consensus size: 9
40768 AACGGTCGGT
*
40778 CGGTCAGAC
1 CGGTCAAAC
40787 CGGTCAAAC
1 CGGTCAAAC
* *
40796 CGTTCAGAC
1 CGGTCAAAC
40805 CGGTCAAAC
1 CGGTCAAAC
* *
40814 CGTTCGAAC
1 CGGTCAAAC
* *
40823 CGTTGAAAC
1 CGGTCAAAC
40832 CGGTCAAAC
1 CGGTCAAAC
40841 CGGTCAGAAC
1 CGGTCA-AAC
*
40851 CGGTTGAAAAC
1 CGG-T-CAAAC
*
40862 CGGTTAAAC
1 CGGTCAAAC
40871 CGGT
1 CGGT
40875 TTCCAGCAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
9 57 0.79
10 7 0.10
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (9 bp):
CGGTCAAAC
Found at i:40810 original size:27 final size:27
Alignment explanation
Indices: 40778--40874 Score: 104
Period size: 27 Copynumber: 3.5 Consensus size: 27
40768 AACGGTCGGT
* *
40778 CGGTCAGACCGGTCAAACCGTTCAGAC
1 CGGTCAAACCGGTCAAACCGTTCAAAC
* * *
40805 CGGTCAAACCGTTCGAACCGTTGAAAC
1 CGGTCAAACCGGTCAAACCGTTCAAAC
*
40832 CGGTCAAACCGGTCAGAACCGGTTGAAAAC
1 CGGTCAAACCGGTCA-AACC-GTT-CAAAC
*
40862 CGGTTAAACCGGT
1 CGGTCAAACCGGT
40875 TTCCAGCAGC
Statistics
Matches: 58, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
27 35 0.60
28 4 0.07
29 3 0.05
30 16 0.28
ACGTcount: A:0.29, C:0.29, G:0.26, T:0.16
Consensus pattern (27 bp):
CGGTCAAACCGGTCAAACCGTTCAAAC
Found at i:40873 original size:20 final size:21
Alignment explanation
Indices: 40837--40875 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
40827 GAAACCGGTC
40837 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
40858 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
40876 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:41794 original size:26 final size:26
Alignment explanation
Indices: 41758--41808 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
41748 GGTTTGAATC
41758 CTGACCTTACTTAAAAGATCTAGTAT
1 CTGACCTTACTTAAAAGATCTAGTAT
* **
41784 CTGATCTTACTTAAGGGATCTAGTA
1 CTGACCTTACTTAAAAGATCTAGTA
41809 CCTCATCCCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (26 bp):
CTGACCTTACTTAAAAGATCTAGTAT
Found at i:44387 original size:20 final size:20
Alignment explanation
Indices: 44362--44423 Score: 115
Period size: 20 Copynumber: 3.1 Consensus size: 20
44352 CTTCTGGATC
*
44362 CTCCCCTATAACCATCGGCT
1 CTCCCCTATATCCATCGGCT
44382 CTCCCCTATATCCATCGGCT
1 CTCCCCTATATCCATCGGCT
44402 CTCCCCTATATCCATCGGCT
1 CTCCCCTATATCCATCGGCT
44422 CT
1 CT
44424 ATTCTCATGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.16, C:0.45, G:0.10, T:0.29
Consensus pattern (20 bp):
CTCCCCTATATCCATCGGCT
Found at i:45972 original size:6 final size:6
Alignment explanation
Indices: 45961--46023 Score: 69
Period size: 6 Copynumber: 10.5 Consensus size: 6
45951 CTATTTTTTC
*
45961 TTAAAT TTAAAT TTAAAT TTAAAAT ATT-TAT TTAAAT TTAAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT TT-AAAT -TTAAAT TTAAAT TTAAAT TTAAAT
46010 ATT--AT TTAAAT TTA
1 -TTAAAT TTAAAT TTA
46024 TTGTAAATCT
Statistics
Matches: 49, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
4 2 0.04
5 4 0.08
6 35 0.71
7 6 0.12
8 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:45993 original size:25 final size:23
Alignment explanation
Indices: 45965--46023 Score: 100
Period size: 25 Copynumber: 2.5 Consensus size: 23
45955 TTTTTCTTAA
45965 ATTTAAATTTAAATTTAAAATATTT
1 ATTTAAATTTAAATTT-AAATA-TT
45990 ATTTAAATTTAAATTTAAATATT
1 ATTTAAATTTAAATTTAAATATT
46013 ATTTAAATTTA
1 ATTTAAATTTA
46024 TTGTAAATCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
23 13 0.38
24 5 0.15
25 16 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
ATTTAAATTTAAATTTAAATATT
Found at i:46018 original size:11 final size:10
Alignment explanation
Indices: 45986--46031 Score: 56
Period size: 11 Copynumber: 4.2 Consensus size: 10
45976 AATTTAAAAT
45986 ATTTATTTAA
1 ATTTATTTAA
45996 ATTTAAATTTAA
1 ATTT--ATTTAA
46008 ATATTATTTAA
1 AT-TTATTTAA
46019 ATTTATTGTAA
1 ATTTATT-TAA
46030 AT
1 AT
46032 CTTTCATTAA
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.28
11 13 0.41
12 8 0.25
13 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (10 bp):
ATTTATTTAA
Found at i:46211 original size:15 final size:14
Alignment explanation
Indices: 46175--46224 Score: 50
Period size: 15 Copynumber: 3.6 Consensus size: 14
46165 AAAATAAATT
46175 TAATATTTTACATAA
1 TAATATTTTA-ATAA
*
46190 T--TATTTTGATAA
1 TAATATTTTAATAA
*
46202 TGAATATTTTAATAC
1 T-AATATTTTAATAA
46217 TAATATTT
1 TAATATTT
46225 AATTTTTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 7
0.74 0.08 0.18
Matches are distributed among these distances:
12 5 0.17
13 6 0.21
14 7 0.24
15 11 0.38
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (14 bp):
TAATATTTTAATAA
Found at i:46593 original size:29 final size:29
Alignment explanation
Indices: 46543--46598 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
46533 AAATTTTGGA
* * *
46543 TAGTGACTAAAATGTAAGCTTTGAAAGTT
1 TAGTGACTAAAATATAAACTTTAAAAGTT
*
46572 TAGTGACTAAAGTATAAACTTTAAAAG
1 TAGTGACTAAAATATAAACTTTAAAAG
46599 ATCAAGGATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.43, C:0.07, G:0.18, T:0.32
Consensus pattern (29 bp):
TAGTGACTAAAATATAAACTTTAAAAGTT
Found at i:47200 original size:20 final size:21
Alignment explanation
Indices: 47158--47205 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
47148 TTTATTTTTA
*
47158 ATTTTTAAAGCTACATGATTG
1 ATTTTTGAAGCTACATGATTG
47179 ATTTTTGAAGCTACATGA-TG
1 ATTTTTGAAGCTACATGATTG
47199 ATTTTTG
1 ATTTTTG
47206 GACTAAGTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 9 0.35
21 17 0.65
ACGTcount: A:0.29, C:0.08, G:0.17, T:0.46
Consensus pattern (21 bp):
ATTTTTGAAGCTACATGATTG
Found at i:51425 original size:20 final size:20
Alignment explanation
Indices: 51400--51437 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
51390 TTTGATTCAC
*
51400 AGAATAGAAGATTACCAGTA
1 AGAATAAAAGATTACCAGTA
51420 AGAATAAAAGATTACCAG
1 AGAATAAAAGATTACCAG
51438 AAAAAGATTA
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:0.53, C:0.11, G:0.18, T:0.18
Consensus pattern (20 bp):
AGAATAAAAGATTACCAGTA
Done.