Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008915.1 Hibiscus syriacus cultivar Beakdansim tig00112219_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: 65679
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:14370 original size:32 final size:31
Alignment explanation
Indices: 14334--14407 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 31
14324 CGGGGCCGTG
*
14334 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
14366 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
14397 GAGCCTACCTA
1 GGGCCTACCTA
14408 TGAGTCACAT
Statistics
Matches: 34, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
31 21 0.62
32 13 0.38
ACGTcount: A:0.26, C:0.32, G:0.27, T:0.15
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:14403 original size:63 final size:63
Alignment explanation
Indices: 14287--14407 Score: 147
Period size: 63 Copynumber: 1.9 Consensus size: 63
14277 CCCTAAGGGA
* * ** *
14287 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
14350 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTA
14408 TGAGTCACAT
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
62 2 0.04
63 47 0.96
ACGTcount: A:0.25, C:0.30, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:15291 original size:7 final size:7
Alignment explanation
Indices: 15279--15328 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
15269 GTCAAAGAAA
15279 GTCAACG
1 GTCAACG
15286 GTCAACG
1 GTCAACG
15293 GTCAACG
1 GTCAACG
15300 GTC-ACG
1 GTCAACG
15306 GTCAACG
1 GTCAACG
15313 GTC-ACG
1 GTCAACG
15319 GTCAACG
1 GTCAACG
15326 GTC
1 GTC
15329 GGGTCGGGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.29
7 29 0.71
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:15308 original size:13 final size:13
Alignment explanation
Indices: 15279--15328 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
15269 GTCAAAGAAA
15279 GTCAACGGTCAACG
1 GTCAACGGTC-ACG
15293 GTCAACGGTCACG
1 GTCAACGGTCACG
15306 GTCAACGGTCACG
1 GTCAACGGTCACG
15319 GTCAACGGTC
1 GTCAACGGTC
15329 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 26 0.72
14 10 0.28
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (13 bp):
GTCAACGGTCACG
Found at i:15308 original size:20 final size:21
Alignment explanation
Indices: 15279--15328 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
15269 GTCAAAGAAA
15279 GTCAACGGTCAACGGTCAACG
1 GTCAACGGTCAACGGTCAACG
15300 GTC-ACGGTCAACGGTC-ACG
1 GTCAACGGTCAACGGTCAACG
15319 GTCAACGGTC
1 GTCAACGGTC
15329 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.21
20 19 0.68
21 3 0.11
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (21 bp):
GTCAACGGTCAACGGTCAACG
Found at i:15356 original size:16 final size:16
Alignment explanation
Indices: 15317--15376 Score: 93
Period size: 16 Copynumber: 3.7 Consensus size: 16
15307 TCAACGGTCA
15317 CGGTCAACGGTCGGGT
1 CGGTCAACGGTCGGGT
* *
15333 CGGGTCAACAGTCAGGT
1 C-GGTCAACGGTCGGGT
15350 CGGTCAACGGTCGGGT
1 CGGTCAACGGTCGGGT
15366 CGGTCAACGGT
1 CGGTCAACGGT
15377 TCAAAACTGG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
16 25 0.64
17 14 0.36
ACGTcount: A:0.17, C:0.25, G:0.40, T:0.18
Consensus pattern (16 bp):
CGGTCAACGGTCGGGT
Found at i:21686 original size:32 final size:31
Alignment explanation
Indices: 21650--21726 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 31
21640 CGGGGCCGTG
*
21650 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
21682 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
21713 GAGCCTACCTAAGA
1 GGGCCTACCTAAGA
21727 GTCACATTAG
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
31 24 0.65
32 13 0.35
ACGTcount: A:0.27, C:0.31, G:0.27, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:21709 original size:63 final size:63
Alignment explanation
Indices: 21603--21726 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
21593 CCCTAAGGGA
* * ** *
21603 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
21666 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAGA
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAGA
21727 GTCACATTAG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:22607 original size:7 final size:7
Alignment explanation
Indices: 22595--22644 Score: 86
Period size: 7 Copynumber: 7.4 Consensus size: 7
22585 GTCAAAGAAA
22595 GTCAACG
1 GTCAACG
22602 GTCAACG
1 GTCAACG
22609 GTCAACG
1 GTCAACG
22616 GTC-ACG
1 GTCAACG
22622 GTCAACG
1 GTCAACG
22629 GTC-ACG
1 GTCAACG
22635 GTCAACG
1 GTCAACG
22642 GTC
1 GTC
22645 GGGTCGGGTC
Statistics
Matches: 41, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
6 12 0.29
7 29 0.71
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:22624 original size:13 final size:13
Alignment explanation
Indices: 22595--22644 Score: 91
Period size: 13 Copynumber: 3.8 Consensus size: 13
22585 GTCAAAGAAA
22595 GTCAACGGTCAACG
1 GTCAACGGTC-ACG
22609 GTCAACGGTCACG
1 GTCAACGGTCACG
22622 GTCAACGGTCACG
1 GTCAACGGTCACG
22635 GTCAACGGTC
1 GTCAACGGTC
22645 GGGTCGGGTC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
13 26 0.72
14 10 0.28
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (13 bp):
GTCAACGGTCACG
Found at i:22624 original size:20 final size:21
Alignment explanation
Indices: 22595--22644 Score: 86
Period size: 20 Copynumber: 2.5 Consensus size: 21
22585 GTCAAAGAAA
22595 GTCAACGGTCAACGGTCAACG
1 GTCAACGGTCAACGGTCAACG
22616 GTC-ACGGTCAACGGTC-ACG
1 GTCAACGGTCAACGGTCAACG
22635 GTCAACGGTC
1 GTCAACGGTC
22645 GGGTCGGGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.21
20 19 0.68
21 3 0.11
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (21 bp):
GTCAACGGTCAACGGTCAACG
Found at i:22656 original size:17 final size:17
Alignment explanation
Indices: 22634--22674 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
22624 CAACGGTCAC
*
22634 GGTCAACGGTCGGGTCG
1 GGTCAACAGTCGGGTCG
22651 GGTCAACAGTCGGGTCG
1 GGTCAACAGTCGGGTCG
22668 GGTCAAC
1 GGTCAAC
22675 CCGGTTCAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.17, C:0.24, G:0.41, T:0.17
Consensus pattern (17 bp):
GGTCAACAGTCGGGTCG
Found at i:22692 original size:19 final size:19
Alignment explanation
Indices: 22668--22718 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
22658 AGTCGGGTCG
*
22668 GGTCAACCCGGTTC-AGACC
1 GGTCAAACCGGTTCGA-ACC
22687 GGTCAAACCGGTTCGAACC
1 GGTCAAACCGGTTCGAACC
22706 GGTCAAACCGGTT
1 GGTCAAACCGGTT
22719 TTCCAGCAGC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 29 0.97
20 1 0.03
ACGTcount: A:0.24, C:0.31, G:0.27, T:0.18
Consensus pattern (19 bp):
GGTCAAACCGGTTCGAACC
Found at i:22705 original size:10 final size:10
Alignment explanation
Indices: 22670--22718 Score: 57
Period size: 9 Copynumber: 5.1 Consensus size: 10
22660 TCGGGTCGGG
*
22670 TCAACCCGGT
1 TCAAACCGGT
*
22680 TCAGACCGG-
1 TCAAACCGGT
22689 TCAAACCGGT
1 TCAAACCGGT
*
22699 TCGAACCGG-
1 TCAAACCGGT
22708 TCAAACCGGT
1 TCAAACCGGT
22718 T
1 T
22719 TTCCAGCAGC
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
9 16 0.50
10 16 0.50
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.18
Consensus pattern (10 bp):
TCAAACCGGT
Found at i:30439 original size:19 final size:19
Alignment explanation
Indices: 30417--30495 Score: 90
Period size: 19 Copynumber: 4.2 Consensus size: 19
30407 GACCGGTTCC
*
30417 GACCGGTTCGAACCAGTTT
1 GACCGGTTCGAACCGGTTT
* *
30436 GACCGGTTTG-ACCGGTTCC
1 GACCGGTTCGAACCGGTT-T
30455 GACCGGTTCGAACCGGTTT
1 GACCGGTTCGAACCGGTTT
* *
30474 GACCGGTTTG-ACCGGTCT
1 GACCGGTTCGAACCGGTTT
30492 GACC
1 GACC
30496 CGACCCGACT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
18 17 0.33
19 27 0.53
20 7 0.14
ACGTcount: A:0.15, C:0.29, G:0.30, T:0.25
Consensus pattern (19 bp):
GACCGGTTCGAACCGGTTT
Found at i:30446 original size:9 final size:9
Alignment explanation
Indices: 30402--30495 Score: 98
Period size: 9 Copynumber: 10.0 Consensus size: 9
30392 CTGGAAAATT
30402 GGTTTGACC
1 GGTTTGACC
*
30411 GGTTCCGACC
1 GGTT-TGACC
*
30421 GGTTCGAACC
1 GGTTTG-ACC
*
30431 AGTTTGACC
1 GGTTTGACC
30440 GGTTTGACC
1 GGTTTGACC
*
30449 GGTTCCGACC
1 GGTT-TGACC
*
30459 GGTTCGAACC
1 GGTTTG-ACC
30469 GGTTTGACC
1 GGTTTGACC
30478 GGTTTGACC
1 GGTTTGACC
*
30487 GGTCTGACC
1 GGTTTGACC
30496 CGACCCGACT
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
9 43 0.58
10 31 0.42
ACGTcount: A:0.14, C:0.29, G:0.31, T:0.27
Consensus pattern (9 bp):
GGTTTGACC
Found at i:30453 original size:38 final size:38
Alignment explanation
Indices: 30402--30489 Score: 167
Period size: 38 Copynumber: 2.3 Consensus size: 38
30392 CTGGAAAATT
30402 GGTTTGACCGGTTCCGACCGGTTCGAACCAGTTTGACC
1 GGTTTGACCGGTTCCGACCGGTTCGAACCAGTTTGACC
*
30440 GGTTTGACCGGTTCCGACCGGTTCGAACCGGTTTGACC
1 GGTTTGACCGGTTCCGACCGGTTCGAACCAGTTTGACC
30478 GGTTTGACCGGT
1 GGTTTGACCGGT
30490 CTGACCCGAC
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.14, C:0.27, G:0.32, T:0.27
Consensus pattern (38 bp):
GGTTTGACCGGTTCCGACCGGTTCGAACCAGTTTGACC
Found at i:30543 original size:17 final size:17
Alignment explanation
Indices: 30521--30557 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
30511 GACCCGACCC
*
30521 GACCCGACCTGACCGTT
1 GACCCGACCCGACCGTT
*
30538 GACCCGACCCGTCCGTT
1 GACCCGACCCGACCGTT
30555 GAC
1 GAC
30558 TTCCTTTGAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.16, C:0.43, G:0.24, T:0.16
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:37699 original size:10 final size:10
Alignment explanation
Indices: 37686--37786 Score: 122
Period size: 10 Copynumber: 10.6 Consensus size: 10
37676 ACCGATTCCG
*
37686 ACCGGTTCGA
1 ACCGGTTTGA
37696 ACCGGTTTG-
1 ACCGGTTTGA
*
37705 ACCGGTTCGA
1 ACCGGTTTGA
37715 ACCGGTTTG-
1 ACCGGTTTGA
*
37724 ACCGGTATGA
1 ACCGGTTTGA
37734 ACCGGTTTG-
1 ACCGGTTTGA
*
37743 ACCGGTATGA
1 ACCGGTTTGA
37753 ACCGGTTTG-
1 ACCGGTTTGA
*
37762 ACCGGTATGA
1 ACCGGTTTGA
37772 ACCGGTTTG-
1 ACCGGTTTGA
37781 ACCGGT
1 ACCGGT
37787 CTGACCCGAC
Statistics
Matches: 78, Mismatches: 9, Indels: 9
0.81 0.09 0.09
Matches are distributed among these distances:
9 38 0.49
10 40 0.51
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.26
Consensus pattern (10 bp):
ACCGGTTTGA
Found at i:37707 original size:19 final size:19
Alignment explanation
Indices: 37685--37786 Score: 172
Period size: 19 Copynumber: 5.4 Consensus size: 19
37675 GACCGATTCC
37685 GACCGGT-TCGAACCGGTTT
1 GACCGGTAT-GAACCGGTTT
37704 GACCGGT-TCGAACCGGTTT
1 GACCGGTAT-GAACCGGTTT
37723 GACCGGTATGAACCGGTTT
1 GACCGGTATGAACCGGTTT
37742 GACCGGTATGAACCGGTTT
1 GACCGGTATGAACCGGTTT
37761 GACCGGTATGAACCGGTTT
1 GACCGGTATGAACCGGTTT
37780 GACCGGT
1 GACCGGT
37787 CTGACCCGAC
Statistics
Matches: 82, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
19 81 0.99
20 1 0.01
ACGTcount: A:0.19, C:0.24, G:0.32, T:0.25
Consensus pattern (19 bp):
GACCGGTATGAACCGGTTT
Found at i:37708 original size:29 final size:27
Alignment explanation
Indices: 37666--37792 Score: 116
Period size: 29 Copynumber: 4.5 Consensus size: 27
37656 GCTGTTGGAA
*
37666 AACCGGTTTGACCGATTCCGACCGGTTCG
1 AACCGGTTTGACCGGTT-CGACCGGTT-G
37695 AACCGGTTTGACCGGTTCGAACCGGTTTG
1 AACCGGTTTGACCGGTTCG-ACCGG-TTG
* *
37724 -ACCGGTATGAACCGGTTTGACCGGTATG
1 AACCGGTTTG-ACCGGTTCGACCGGT-TG
37752 AACCGGTTTGACCGGTAT-GAACCGGTTTG
1 AACCGGTTTGACCGGT-TCG-ACCGG-TTG
*
37781 -ACCGGTCTGACC
1 AACCGGTTTGACC
37793 CGACCCAACC
Statistics
Matches: 85, Mismatches: 5, Indels: 17
0.79 0.05 0.16
Matches are distributed among these distances:
27 1 0.01
28 35 0.41
29 46 0.54
30 3 0.04
ACGTcount: A:0.19, C:0.26, G:0.30, T:0.25
Consensus pattern (27 bp):
AACCGGTTTGACCGGTTCGACCGGTTG
Found at i:44856 original size:9 final size:9
Alignment explanation
Indices: 44842--44910 Score: 57
Period size: 9 Copynumber: 7.3 Consensus size: 9
44832 CTGCTGGAAA
44842 ACCGGTTTG
1 ACCGGTTTG
44851 ACCGGTTTTG
1 ACCGG-TTTG
*
44861 ACCGGTTCG
1 ACCGGTTTG
* *
44870 AATCGGTTTA
1 -ACCGGTTTG
*
44880 ACCGGTCTG
1 ACCGGTTTG
*
44889 AACTGGTTTG
1 -ACCGGTTTG
*
44899 ACCGGTCTG
1 ACCGGTTTG
44908 ACC
1 ACC
44911 CGACCCGACC
Statistics
Matches: 46, Mismatches: 11, Indels: 6
0.73 0.17 0.10
Matches are distributed among these distances:
9 24 0.52
10 22 0.48
ACGTcount: A:0.16, C:0.25, G:0.29, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:47107 original size:5 final size:5
Alignment explanation
Indices: 47097--47145 Score: 57
Period size: 5 Copynumber: 9.8 Consensus size: 5
47087 AACGGTCAAC
*
47097 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTC- GGTC- GGTCG GGTC
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTCG GGTCG GGTC
47146 AGACCGGTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 8 0.21
5 27 0.69
7 4 0.10
ACGTcount: A:0.04, C:0.22, G:0.53, T:0.20
Consensus pattern (5 bp):
GGTCG
Found at i:47115 original size:22 final size:22
Alignment explanation
Indices: 47090--47134 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
47080 GAAAGTCAAC
47090 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
47112 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
47134 G
1 G
47135 TCGGTCGGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.09, C:0.22, G:0.51, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:47189 original size:19 final size:19
Alignment explanation
Indices: 47142--47191 Score: 66
Period size: 19 Copynumber: 2.6 Consensus size: 19
47132 CGGTCGGTCG
*
47142 GGTCAGACCGGTCAAATCT
1 GGTCAGACCGGTCAAATCC
*
47161 GTTCAGACCGGTCAAA-CC
1 GGTCAGACCGGTCAAATCC
47179 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
47192 TGAACCGGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.26, C:0.28, G:0.28, T:0.18
Consensus pattern (19 bp):
GGTCAGACCGGTCAAATCC
Found at i:60012 original size:22 final size:22
Alignment explanation
Indices: 59987--60030 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
59977 GTCAAAGAAA
*
59987 GTCAACGGTCGGGTCGGGTCGG
1 GTCAACGGTCGGGTCAGGTCGG
60009 GTCAACGGTCGGGTCAGGTCGG
1 GTCAACGGTCGGGTCAGGTCGG
60031 TCGGTCGGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.11, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GTCAACGGTCGGGTCAGGTCGG
Found at i:60020 original size:12 final size:12
Alignment explanation
Indices: 59987--60024 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
59977 GTCAAAGAAA
59987 GTCAACGGTCGG
1 GTCAACGGTCGG
*
59999 GTC--GGGTCGG
1 GTCAACGGTCGG
60009 GTCAACGGTCGG
1 GTCAACGGTCGG
60021 GTCA
1 GTCA
60025 GGTCGGTCGG
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 9 0.41
12 13 0.59
ACGTcount: A:0.13, C:0.24, G:0.45, T:0.18
Consensus pattern (12 bp):
GTCAACGGTCGG
Found at i:60037 original size:18 final size:18
Alignment explanation
Indices: 59992--60043 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 18
59982 AGAAAGTCAA
*
59992 CGGTCGGGTCGGGTCGGGT
1 CGGTC-GGTCGGGTCAGGT
**
60011 C-AACGGTCGGGTCAGGT
1 CGGTCGGTCGGGTCAGGT
60028 CGGTCGGTCGGGTCAG
1 CGGTCGGTCGGGTCAG
60044 ACCGGTCAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 13 0.48
18 13 0.48
19 1 0.04
ACGTcount: A:0.08, C:0.23, G:0.50, T:0.19
Consensus pattern (18 bp):
CGGTCGGTCGGGTCAGGT
Found at i:60049 original size:18 final size:18
Alignment explanation
Indices: 60014--60050 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
60004 GTCGGGTCAA
**
60014 CGGTCGGGTCAGGTCGGT
1 CGGTCGGGTCAGACCGGT
60032 CGGTCGGGTCAGACCGGT
1 CGGTCGGGTCAGACCGGT
60050 C
1 C
60051 AAACCGGTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.27, G:0.46, T:0.19
Consensus pattern (18 bp):
CGGTCGGGTCAGACCGGT
Found at i:60050 original size:9 final size:9
Alignment explanation
Indices: 60038--60097 Score: 66
Period size: 10 Copynumber: 6.3 Consensus size: 9
60028 CGGTCGGTCG
*
60038 GGTCAGACC
1 GGTCAAACC
60047 GGTCAAACC
1 GGTCAAACC
*
60056 GGTTCGAACC
1 GG-TCAAACC
60066 GGTCGAAACC
1 GGTC-AAACC
*
60076 AGTCAAACC
1 GGTCAAACC
60085 GGTCAGAACC
1 GGTCA-AACC
60095 GGT
1 GGT
60098 TGAACCGGTT
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
9 21 0.49
10 22 0.51
ACGTcount: A:0.28, C:0.30, G:0.28, T:0.13
Consensus pattern (9 bp):
GGTCAAACC
Found at i:60067 original size:10 final size:9
Alignment explanation
Indices: 60044--60106 Score: 63
Period size: 9 Copynumber: 6.7 Consensus size: 9
60034 GTCGGGTCAG
*
60044 ACCGGTCAA
1 ACCGGTCGA
60053 ACCGGTTCGA
1 ACCGG-TCGA
60063 ACCGGTCGAA
1 ACCGGTCG-A
* *
60073 ACCAGTCAA
1 ACCGGTCGA
60082 ACCGGTCAGA
1 ACCGGTC-GA
*
60092 ACCGGTTGA
1 ACCGGTCGA
60101 ACCGGT
1 ACCGGT
60107 TTCCAGCAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
9 23 0.51
10 22 0.49
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (9 bp):
ACCGGTCGA
Found at i:60068 original size:19 final size:19
Alignment explanation
Indices: 60044--60106 Score: 76
Period size: 19 Copynumber: 3.3 Consensus size: 19
60034 GTCGGGTCAG
60044 ACCGGTCAAACCGGTTCGA
1 ACCGGTCAAACCGGTTCGA
* *
60063 ACCGGTCGAAACCAG-TCAA
1 ACCGGTC-AAACCGGTTCGA
60082 ACCGGTCAGAACCGGTT-GA
1 ACCGGTCA-AACCGGTTCGA
60101 ACCGGT
1 ACCGGT
60107 TTCCAGCAGC
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
18 1 0.03
19 29 0.78
20 7 0.19
ACGTcount: A:0.29, C:0.30, G:0.27, T:0.14
Consensus pattern (19 bp):
ACCGGTCAAACCGGTTCGA
Done.