Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008147.1 Hibiscus syriacus cultivar Beakdansim tig00110711_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: 85812
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Found at i:10821 original size:2 final size:2
Alignment explanation
Indices: 10781--10806 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
10771 AATAATATGG
10781 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
10807 GTATTTTAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10941 original size:21 final size:20
Alignment explanation
Indices: 10915--10954 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 20
10905 AACTTATTTA
10915 ATTT-AATTTATTATTATTTTT
1 ATTTAAATTT-TTA-TATTTTT
10936 ATTTAAATTTTTATATTTT
1 ATTTAAATTTTTATATTTT
10955 ATTCTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
21 7 0.39
22 5 0.28
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
ATTTAAATTTTTATATTTTT
Found at i:11025 original size:29 final size:29
Alignment explanation
Indices: 10947--11015 Score: 111
Period size: 29 Copynumber: 2.4 Consensus size: 29
10937 TTTAAATTTT
*
10947 TATATTTTATTCTTATATGAACTTAAAAA
1 TATATTTTATTCTTATATTAACTTAAAAA
* *
10976 TACATTTTATTCTTATTTTAACTTAAAAA
1 TATATTTTATTCTTATATTAACTTAAAAA
11005 TATATTTTATT
1 TATATTTTATT
11016 TTTGTCTTAA
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:0.38, C:0.07, G:0.01, T:0.54
Consensus pattern (29 bp):
TATATTTTATTCTTATATTAACTTAAAAA
Found at i:11052 original size:28 final size:30
Alignment explanation
Indices: 11002--11059 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
10992 TTTAACTTAA
* **
11002 AAATATATTTTATTTTTGTCTT-AAATTTT
1 AAATATATTATATTTTAATCTTAAAATTTT
11031 AAATATA-TATATTTTAATCTTAAAATTTT
1 AAATATATTATATTTTAATCTTAAAATTTT
11060 TGGACTTTAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (30 bp):
AAATATATTATATTTTAATCTTAAAATTTT
Found at i:15800 original size:43 final size:43
Alignment explanation
Indices: 15739--15824 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
15729 CATACTTTTA
15739 ACCTTCATCCTCAATATTGATACACACTCTCAAACAGAAAATT
1 ACCTTCATCCTCAATATTGATACACACTCTCAAACAGAAAATT
15782 ACCTTCATCCTCAATATTGATACACACTCTCAAACAGAAAATT
1 ACCTTCATCCTCAATATTGATACACACTCTCAAACAGAAAATT
15825 GGTCGTGATT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.40, C:0.28, G:0.05, T:0.28
Consensus pattern (43 bp):
ACCTTCATCCTCAATATTGATACACACTCTCAAACAGAAAATT
Found at i:19424 original size:45 final size:44
Alignment explanation
Indices: 19319--19416 Score: 133
Period size: 45 Copynumber: 2.2 Consensus size: 44
19309 TGACGTTGTC
* * *
19319 CTTTAAAATGTAATACCTAGCGTGGGTTCAAATCTCGACGTTTG
1 CTTTAAAATATAATACCTAGCGTGGGTTCAAATCTCAACATTTG
* * *
19363 CTTTAAAACTATAATACCTAGTGTGGGTTCGAATCTCAACATTTT
1 CTTTAAAA-TATAATACCTAGCGTGGGTTCAAATCTCAACATTTG
19408 CTTTAAAAT
1 CTTTAAAAT
19417 TTTAATACAT
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
44 9 0.19
45 38 0.81
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (44 bp):
CTTTAAAATATAATACCTAGCGTGGGTTCAAATCTCAACATTTG
Found at i:22103 original size:51 final size:51
Alignment explanation
Indices: 22012--22114 Score: 116
Period size: 51 Copynumber: 2.0 Consensus size: 51
22002 TTTTTTGGGT
* * * * *
22012 TTTATTAAAATTTCACCGTTCAACAGAAGTTAGTTCTGTTTCGAGATTTAA
1 TTTATTAAAATCTCACCATTCAACAAAAATTAGTTATGTTTCGAGATTTAA
** * * *
22063 TTTATTAAAATCTCGTCATTCAACAAAAATTGGTTATGTTTTGGGATTTAA
1 TTTATTAAAATCTCACCATTCAACAAAAATTAGTTATGTTTCGAGATTTAA
22114 T
1 T
22115 CTCGTTGTCC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.43
Consensus pattern (51 bp):
TTTATTAAAATCTCACCATTCAACAAAAATTAGTTATGTTTCGAGATTTAA
Found at i:24012 original size:21 final size:21
Alignment explanation
Indices: 23957--24013 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
23947 AGATTAGATT
*
23957 CTTTAATCAAAAGGATAAGTC
1 CTTTAATCAAAAGGTTAAGTC
23978 CTTTAATCAAAAGGTTAAGTC
1 CTTTAATCAAAAGGTTAAGTC
*
23999 CTTTCATCAAAAGGT
1 CTTTAATCAAAAGGT
24014 CTTAACCCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (21 bp):
CTTTAATCAAAAGGTTAAGTC
Found at i:29599 original size:10 final size:9
Alignment explanation
Indices: 29546--29658 Score: 73
Period size: 10 Copynumber: 11.8 Consensus size: 9
29536 GGCTGCTGGA
29546 AACCGGTTT
1 AACCGGTTT
29555 AACCGGTTTT
1 AACCGG-TTT
*
29565 CAACAGGTTCT
1 -AACCGGTT-T
* *
29576 GACTGGTTT
1 AACCGGTTT
*
29585 GACCGGTTT
1 AACCGGTTT
*
29594 CAACCGGTTCG
1 -AACCGGTT-T
29605 AACCGGTTT
1 AACCGGTTT
* *
29614 GACCGGTCTG
1 AACCGGT-TT
29624 AACCGGTTT
1 AACCGGTTT
* *
29633 GACCGGTCTA
1 AACCGGT-TT
29643 AACCGGTTT
1 AACCGGTTT
*
29652 GACCGGT
1 AACCGGT
29659 CTGACCCGAC
Statistics
Matches: 81, Mismatches: 16, Indels: 14
0.73 0.14 0.13
Matches are distributed among these distances:
9 35 0.43
10 40 0.49
11 6 0.07
ACGTcount: A:0.19, C:0.25, G:0.27, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:29602 original size:19 final size:19
Alignment explanation
Indices: 29562--29658 Score: 81
Period size: 19 Copynumber: 5.1 Consensus size: 19
29552 TTTAACCGGT
* *
29562 TTTCAACAGGTTCTGACTGG
1 TTTCAACCGGTT-TGACCGG
* *
29582 TTT-GACCGGTTTCAACCGG
1 TTTCAACCGGTTT-GACCGG
29601 -TTCGAACCGGTTTGACCGG
1 TTTC-AACCGGTTTGACCGG
* *
29620 TCTGAACCGGTTTGACCGG
1 TTTCAACCGGTTTGACCGG
* *
29639 TCTAAACCGGTTTGACCGG
1 TTTCAACCGGTTTGACCGG
29658 T
1 T
29659 CTGACCCGAC
Statistics
Matches: 64, Mismatches: 9, Indels: 9
0.78 0.11 0.11
Matches are distributed among these distances:
18 3 0.05
19 49 0.77
20 12 0.19
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.30
Consensus pattern (19 bp):
TTTCAACCGGTTTGACCGG
Found at i:29612 original size:29 final size:28
Alignment explanation
Indices: 29547--29639 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
29537 GCTGCTGGAA
* *
29547 ACCGGTTTAACCGGTTTTCAACAGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
*
29577 ACTGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
29605 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
29634 ACCGGT
1 ACCGGT
29640 CTAAACCGGT
Statistics
Matches: 55, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 7 0.13
29 36 0.65
30 12 0.22
ACGTcount: A:0.17, C:0.25, G:0.28, T:0.30
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:29659 original size:19 final size:19
Alignment explanation
Indices: 29605--29660 Score: 103
Period size: 19 Copynumber: 2.9 Consensus size: 19
29595 AACCGGTTCG
*
29605 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTA
29624 AACCGGTTTGACCGGTCTA
1 AACCGGTTTGACCGGTCTA
29643 AACCGGTTTGACCGGTCT
1 AACCGGTTTGACCGGTCT
29661 GACCCGACTG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.18, C:0.27, G:0.29, T:0.27
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTA
Found at i:29663 original size:9 final size:9
Alignment explanation
Indices: 29606--29664 Score: 64
Period size: 9 Copynumber: 6.3 Consensus size: 9
29596 ACCGGTTCGA
*
29606 ACCGGTTTG
1 ACCGGTCTG
29615 ACCGGTCTG
1 ACCGGTCTG
*
29624 AACCGGTTTG
1 -ACCGGTCTG
*
29634 ACCGGTCTAA
1 ACCGGTCT-G
*
29644 ACCGGTTTG
1 ACCGGTCTG
29653 ACCGGTCTG
1 ACCGGTCTG
29662 ACC
1 ACC
29665 CGACTGTTGA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
9 26 0.63
10 15 0.37
ACGTcount: A:0.17, C:0.29, G:0.29, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:29695 original size:22 final size:22
Alignment explanation
Indices: 29661--29722 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
29651 TGACCGGTCT
* *
29661 GACCCGACTGTTGACCCGACCC
1 GACCCAACCGTTGACCCGACCC
29683 GACCCAACCGTTGACCCGACCC
1 GACCCAACCGTTGACCCGACCC
*
29705 GACCGTTAACCGTTGACC
1 GACC--CAACCGTTGACC
29723 GTTGACCGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 24 0.69
24 11 0.31
ACGTcount: A:0.21, C:0.44, G:0.21, T:0.15
Consensus pattern (22 bp):
GACCCAACCGTTGACCCGACCC
Found at i:29698 original size:17 final size:17
Alignment explanation
Indices: 29678--29711 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
29668 CTGTTGACCC
29678 GACCCGACCCAACCGTT
1 GACCCGACCCAACCGTT
*
29695 GACCCGACCCGACCGTT
1 GACCCGACCCAACCGTT
29712 AACCGTTGAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.47, G:0.21, T:0.12
Consensus pattern (17 bp):
GACCCGACCCAACCGTT
Found at i:29718 original size:7 final size:7
Alignment explanation
Indices: 29705--29735 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
29695 GACCCGACCC
29705 GACCGTT
1 GACCGTT
*
29712 AACCGTT
1 GACCGTT
29719 GACCGTT
1 GACCGTT
29726 GACCGTT
1 GACCGTT
29733 GAC
1 GAC
29736 TTTCTTTGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.19, C:0.29, G:0.26, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:31624 original size:21 final size:21
Alignment explanation
Indices: 31569--31625 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
31559 AGATTAGATT
*
31569 CTTTAATCAAAAGGATAAGTC
1 CTTTAATCAAAAGGTTAAGTC
31590 CTTTAATCAAAAGGTTAAGTC
1 CTTTAATCAAAAGGTTAAGTC
*
31611 CTTTCATCAAAAGGT
1 CTTTAATCAAAAGGT
31626 CTTAACCCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (21 bp):
CTTTAATCAAAAGGTTAAGTC
Found at i:50650 original size:15 final size:16
Alignment explanation
Indices: 50630--50659 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
50620 ATTAAAAATA
50630 TTAAATATA-ATTATT
1 TTAAATATATATTATT
50645 TTAAATATATATTAT
1 TTAAATATATATTAT
50660 AAAACCCTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTAAATATATATTATT
Found at i:56075 original size:29 final size:29
Alignment explanation
Indices: 56043--56170 Score: 93
Period size: 29 Copynumber: 4.5 Consensus size: 29
56033 CATTTTACAG
*
56043 AAATAACACCCTTTTTAAAATAATTACCA
1 AAATAACACCATTTTTAAAATAATTACCA
* * * *
56072 AAATAGCA-CATTTTTCGAATTAATTCCCA
1 AAATAACACCATTTTT-AAAATAATTACCA
* * * * *
56101 AAATAGCACCAATTTCAAATTAATTCCCA
1 AAATAACACCATTTTTAAAATAATTACCA
* * *
56130 GAATATCA-C-TTTTTGAAA-AATTACCA
1 AAATAACACCATTTTTAAAATAATTACCA
56156 AAATAACACCTATTT
1 AAATAACACC-ATTT
56171 CGAATTAATT
Statistics
Matches: 77, Mismatches: 17, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
26 13 0.17
27 6 0.08
28 7 0.09
29 46 0.60
30 5 0.06
ACGTcount: A:0.44, C:0.20, G:0.04, T:0.32
Consensus pattern (29 bp):
AAATAACACCATTTTTAAAATAATTACCA
Found at i:56171 original size:55 final size:58
Alignment explanation
Indices: 56043--56193 Score: 175
Period size: 55 Copynumber: 2.7 Consensus size: 58
56033 CATTTTACAG
* * * * * *
56043 AAATAACACCCT-TTTTAAAATAATTACCAAAATAGCACATTTTTCGAATTAATTCCCA
1 AAATAACA-CCTATTTCAAATTAATTCCCAGAATAGCACATTTTTCGAATAAATTACCA
* * *
56101 AAATAGCACCAATTTCAAATTAATTCCCAGAATATCAC-TTTTT-GAA-AAATTACCA
1 AAATAACACCTATTTCAAATTAATTCCCAGAATAGCACATTTTTCGAATAAATTACCA
*
56156 AAATAACACCTATTTCGAATTAATTCCCAGAATAGCAC
1 AAATAACACCTATTTCAAATTAATTCCCAGAATAGCAC
56194 CAAAATCGAA
Statistics
Matches: 79, Mismatches: 13, Indels: 5
0.81 0.13 0.05
Matches are distributed among these distances:
55 41 0.52
56 3 0.04
57 7 0.09
58 28 0.35
ACGTcount: A:0.43, C:0.21, G:0.05, T:0.30
Consensus pattern (58 bp):
AAATAACACCTATTTCAAATTAATTCCCAGAATAGCACATTTTTCGAATAAATTACCA
Found at i:56172 original size:84 final size:85
Alignment explanation
Indices: 56053--56218 Score: 253
Period size: 84 Copynumber: 2.0 Consensus size: 85
56043 AAATAACACC
* * **
56053 CTTTTTAAAATAATTACCAAAATAGCACATTTTTCGAATTAATTCCCAAAATAGCACCAATTTCA
1 CTTTTTAAAATAATTACCAAAATAACACATATTTCGAATTAATTCCCAAAATAGCACCAAAATCA
56118 AATTAATTCCCAGAATATCA
66 AATTAATTCCCAGAATATCA
* * * *
56138 CTTTTTGAAA-AATTACCAAAATAACACCTATTTCGAATTAATTCCCAGAATAGCACCAAAATCG
1 CTTTTTAAAATAATTACCAAAATAACACATATTTCGAATTAATTCCCAAAATAGCACCAAAATCA
56202 AATTAATTCCCAGAATA
66 AATTAATTCCCAGAATA
56219 GCACCGGTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
84 64 0.88
85 9 0.12
ACGTcount: A:0.43, C:0.20, G:0.06, T:0.31
Consensus pattern (85 bp):
CTTTTTAAAATAATTACCAAAATAACACATATTTCGAATTAATTCCCAAAATAGCACCAAAATCA
AATTAATTCCCAGAATATCA
Found at i:56194 original size:29 final size:29
Alignment explanation
Indices: 56063--56223 Score: 157
Period size: 29 Copynumber: 5.7 Consensus size: 29
56053 CTTTTTAAAA
* * *
56063 TAATTACCAAAATAGCACATTTTTCGAAT
1 TAATTCCCAAAATAGCACCTATTTCGAAT
* *
56092 TAATTCCCAAAATAGCACCAATTTCAAAT
1 TAATTCCCAAAATAGCACCTATTTCGAAT
* * *
56121 TAATTCCCAGAATATCA-CT-TTTTGAA-
1 TAATTCCCAAAATAGCACCTATTTCGAAT
* * *
56147 AAATTACCAAAATAACACCTATTTCGAAT
1 TAATTCCCAAAATAGCACCTATTTCGAAT
* * **
56176 TAATTCCCAGAATAGCACCAAAATCGAAT
1 TAATTCCCAAAATAGCACCTATTTCGAAT
*
56205 TAATTCCCAGAATAGCACC
1 TAATTCCCAAAATAGCACC
56224 GGTCAACGGT
Statistics
Matches: 107, Mismatches: 22, Indels: 6
0.79 0.16 0.04
Matches are distributed among these distances:
26 13 0.12
27 7 0.07
28 7 0.07
29 80 0.75
ACGTcount: A:0.42, C:0.22, G:0.07, T:0.29
Consensus pattern (29 bp):
TAATTCCCAAAATAGCACCTATTTCGAAT
Found at i:63344 original size:29 final size:28
Alignment explanation
Indices: 63312--63444 Score: 99
Period size: 29 Copynumber: 4.6 Consensus size: 28
63302 TTTTTTTAAA
63312 TAATTACCAAAATAGCACCCTTTTCGAAT
1 TAATT-CCAAAATAGCACCCTTTTCGAAT
* *
63341 TAATTCCTAAAAT--CACCATTTTCAAAT
1 TAATTCC-AAAATAGCACCCTTTTCGAAT
* * * * * *
63368 TAGTTCTTAGAATATCACCTTTTTCGAAA
1 TAATTC-CAAAATAGCACCCTTTTCGAAT
* * *
63397 AAATTACCAATATAGCACCCATTTCGAAT
1 TAATT-CCAAAATAGCACCCTTTTCGAAT
*
63426 TAATTCCCAGAATAGCACC
1 TAATT-CCAAAATAGCACC
63445 AAAGAATTAA
Statistics
Matches: 78, Mismatches: 21, Indels: 10
0.72 0.19 0.09
Matches are distributed among these distances:
27 21 0.27
28 2 0.03
29 54 0.69
30 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.32
Consensus pattern (28 bp):
TAATTCCAAAATAGCACCCTTTTCGAAT
Found at i:66173 original size:44 final size:46
Alignment explanation
Indices: 66124--66215 Score: 125
Period size: 44 Copynumber: 2.0 Consensus size: 46
66114 GTGCCACATA
* *
66124 AAATGTCCCAAAAGACCACATAG-ATT-TCCCGAATGATCGCGTAG
1 AAATGTCCCAAAAGACCACATAGAATTATCCCAAATGACCGCGTAG
* * *
66168 AAATGTCCCGAAGGACCACGTAGAATTATCCCAAATGACCGCGTAG
1 AAATGTCCCAAAAGACCACATAGAATTATCCCAAATGACCGCGTAG
66214 AA
1 AA
66216 CCCTCGACTC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
44 20 0.49
45 3 0.07
46 18 0.44
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (46 bp):
AAATGTCCCAAAAGACCACATAGAATTATCCCAAATGACCGCGTAG
Found at i:66176 original size:23 final size:23
Alignment explanation
Indices: 66150--66215 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 23
66140 CACATAGATT
* *
66150 TCCCGAATGATCGCGTAGAAATG
1 TCCCGAATGACCGCGTAGAAATA
* * *
66173 TCCCGAAGGACCACGTAGAATTA
1 TCCCGAATGACCGCGTAGAAATA
*
66196 TCCCAAATGACCGCGTAGAA
1 TCCCGAATGACCGCGTAGAA
66216 CCCTCGACTC
Statistics
Matches: 35, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (23 bp):
TCCCGAATGACCGCGTAGAAATA
Found at i:80217 original size:23 final size:24
Alignment explanation
Indices: 80184--80233 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
80174 TCAAAGATAG
80184 TTTTTTAGATGAG-TTTTGAACAT
1 TTTTTTAGATGAGTTTTTGAACAT
*
80207 TTTTTTGGATGAGTTTTTGAACAT
1 TTTTTTAGATGAGTTTTTGAACAT
80231 TTT
1 TTT
80234 CCTTGTATAG
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
23 12 0.48
24 13 0.52
ACGTcount: A:0.22, C:0.04, G:0.18, T:0.56
Consensus pattern (24 bp):
TTTTTTAGATGAGTTTTTGAACAT
Found at i:85171 original size:21 final size:22
Alignment explanation
Indices: 85146--85196 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 22
85136 ATAACTTTTT
85146 ATTAAATATTTAACTA-CATAA
1 ATTAAATATTTAACTACCATAA
85167 ATT-AAT-TTT-ACTACCATAA
1 ATTAAATATTTAACTACCATAA
*
85186 ACTAAA-ATTTA
1 ATTAAATATTTA
85197 CTAGGGTACG
Statistics
Matches: 25, Mismatches: 1, Indels: 8
0.74 0.03 0.24
Matches are distributed among these distances:
18 4 0.16
19 10 0.40
20 8 0.32
21 3 0.12
ACGTcount: A:0.49, C:0.12, G:0.00, T:0.39
Consensus pattern (22 bp):
ATTAAATATTTAACTACCATAA
Done.