Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008529.1 Hibiscus syriacus cultivar Beakdansim tig00111404_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: 55556
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:649 original size:26 final size:21
Alignment explanation
Indices: 599--655 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
589 ATAAAATTCG
599 ATTTGATTTGATTAATTTTAT
1 ATTTGATTTGATTAATTTTAT
620 ATTTGATTTGATTAATTTTAT
1 ATTTGATTTGATTAATTTTAT
*
641 ATTTAATTTGATTAA
1 ATTTGATTTGATTAA
656 AAAATACTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.09, T:0.60
Consensus pattern (21 bp):
ATTTGATTTGATTAATTTTAT
Found at i:15227 original size:20 final size:21
Alignment explanation
Indices: 15202--15262 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
15192 TTTTGGTGCA
*
15202 GAGGGAATCGA-TCCCCCCCT
1 GAGGGAACCGATTCCCCCCCT
**
15222 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCCT
15243 GAAGGGGAACCGATTCCCCC
1 G-A-GGGAACCGATTCCCCC
15263 ACAGGGGAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
20 10 0.29
21 8 0.23
22 1 0.03
23 16 0.46
ACGTcount: A:0.21, C:0.36, G:0.26, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCCT
Found at i:15270 original size:20 final size:20
Alignment explanation
Indices: 15245--15282 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
15235 CCCCCTTTGA
*
15245 AGGGGAACCGATTCCCCCAC
1 AGGGGAACCGATACCCCCAC
*
15265 AGGGGAATCGATACCCCC
1 AGGGGAACCGATACCCCC
15283 CTGGGGTTCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.37, G:0.26, T:0.11
Consensus pattern (20 bp):
AGGGGAACCGATACCCCCAC
Found at i:22680 original size:28 final size:29
Alignment explanation
Indices: 22639--22698 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
22629 TATCATCTCC
* * *
22639 AATGTTTTCAAGCACTGACTTGATGACAT
1 AATGTTTTCAAGCACTAACTCGACGACAT
22668 AATG-TTTCAAGCACTAACTCGACGACAT
1 AATGTTTTCAAGCACTAACTCGACGACAT
22696 AAT
1 AAT
22699 ATAAACGAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 24 0.86
29 4 0.14
ACGTcount: A:0.35, C:0.20, G:0.15, T:0.30
Consensus pattern (29 bp):
AATGTTTTCAAGCACTAACTCGACGACAT
Found at i:23006 original size:13 final size:13
Alignment explanation
Indices: 22988--23012 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22978 AAATATTAAC
22988 AAATATTTATATT
1 AAATATTTATATT
23001 AAATATTTATAT
1 AAATATTTATAT
23013 AATTAATCTC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AAATATTTATATT
Found at i:23750 original size:23 final size:23
Alignment explanation
Indices: 23724--23769 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
23714 TTGGAACAAA
23724 CTACTATTAATGCTATTAAACCT
1 CTACTATTAATGCTATTAAACCT
*
23747 CTACTATTAATGTTATTAAACCT
1 CTACTATTAATGCTATTAAACCT
23770 TTCATAGGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (23 bp):
CTACTATTAATGCTATTAAACCT
Found at i:24699 original size:6 final size:6
Alignment explanation
Indices: 24688--24718 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
24678 ACAGTTAAAG
*
24688 CTCAAA CTCAAA CTCAAA CTCGAA CTCAAA C
1 CTCAAA CTCAAA CTCAAA CTCAAA CTCAAA C
24719 CTAAATATTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.45, C:0.35, G:0.03, T:0.16
Consensus pattern (6 bp):
CTCAAA
Found at i:27487 original size:53 final size:53
Alignment explanation
Indices: 27407--27510 Score: 154
Period size: 53 Copynumber: 2.0 Consensus size: 53
27397 CAAGCTTTGT
27407 TTTCAATTCCAAAGTAGACGAGGTTGCTACATGATTAGGGAATATGTGCTCGG
1 TTTCAATTCCAAAGTAGACGAGGTTGCTACATGATTAGGGAATATGTGCTCGG
* * * * * *
27460 TTTCAATTCCGAAGTCGACTAGGTTGCTCCATGATTAGGTAGTATGTGCTC
1 TTTCAATTCCAAAGTAGACGAGGTTGCTACATGATTAGGGAATATGTGCTC
27511 TCGGTTTAGC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
53 45 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (53 bp):
TTTCAATTCCAAAGTAGACGAGGTTGCTACATGATTAGGGAATATGTGCTCGG
Found at i:28049 original size:29 final size:25
Alignment explanation
Indices: 28017--28097 Score: 76
Period size: 29 Copynumber: 3.1 Consensus size: 25
28007 TAAGAATATT
28017 TTATATTTTATATTATTAATAAACTAATA
1 TTAT-TTTTATATTATT-A-AAA-TAATA
*
28046 TTATTAATTATATTATTAAAATAATA
1 TTATT-TTTATATTATTAAAATAATA
*
28072 ATATTTTTATATTA--AAATATAATA
1 TTATTTTTATATTATTAAA-ATAATA
28096 TT
1 TT
28098 TTTATTTTAA
Statistics
Matches: 46, Mismatches: 4, Indels: 9
0.78 0.07 0.15
Matches are distributed among these distances:
23 3 0.07
24 7 0.15
25 8 0.17
26 9 0.20
27 3 0.07
28 2 0.04
29 14 0.30
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.52
Consensus pattern (25 bp):
TTATTTTTATATTATTAAAATAATA
Found at i:28095 original size:21 final size:22
Alignment explanation
Indices: 28059--28113 Score: 85
Period size: 21 Copynumber: 2.5 Consensus size: 22
28049 TTAATTATAT
28059 TATTAAAATAATAATATTTTTA
1 TATTAAAATAATAATATTTTTA
28081 TATTAAAAT-ATAATATTTTTA
1 TATTAAAATAATAATATTTTTA
* *
28102 TTTTAATATAAT
1 TATTAAAATAAT
28114 TGAGCATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 19 0.63
22 11 0.37
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTAAAATAATAATATTTTTA
Found at i:28103 original size:19 final size:20
Alignment explanation
Indices: 28058--28113 Score: 69
Period size: 19 Copynumber: 2.8 Consensus size: 20
28048 ATTAATTATA
28058 TTATTAAAATAATAATATTTT
1 TTATTAAAAT-ATAATATTTT
28079 TATATTAAAATATAATA-TTT
1 T-TATTAAAATATAATATTTT
**
28099 TTATTTTAATATAAT
1 TTATTAAAATATAAT
28114 TGAGCATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 12 0.38
20 4 0.12
21 7 0.22
22 9 0.28
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
TTATTAAAATATAATATTTT
Found at i:31083 original size:21 final size:20
Alignment explanation
Indices: 30997--31154 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
30987 AAATGACCAA
**
30997 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
31016 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
31036 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
31056 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
31077 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
31098 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
31118 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
31139 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
31155 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 44 0.43
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:31147 original size:20 final size:20
Alignment explanation
Indices: 31122--31432 Score: 79
Period size: 20 Copynumber: 15.5 Consensus size: 20
31112 GATTTTCAAT
* *
31122 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
31142 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
31162 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
31182 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
31202 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
31222 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
31242 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
31262 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
31283 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
31303 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
31323 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
31343 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* *
31363 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
31383 AATCGCAACGATAATC-CGTA
1 AATCGCAACGCGAA-CACATA
* *
31403 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
31423 AATCGCAACG
1 AATCGCAACG
31433 ATAATCCGTA
Statistics
Matches: 244, Mismatches: 38, Indels: 18
0.81 0.13 0.06
Matches are distributed among these distances:
19 3 0.01
20 224 0.92
21 16 0.07
22 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:31167 original size:40 final size:40
Alignment explanation
Indices: 31122--31511 Score: 439
Period size: 40 Copynumber: 9.7 Consensus size: 40
31112 GATTTTCAAT
* ** * * *
31122 AATCGCAACGCGAATATGAAAATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAAC-CGTA
* *
31162 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
** * * *
31202 AATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
31242 TATCGCAACGCGTATCCGTAAATCGCAACGA-TAATACATAA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGT-A
* *
31283 AATCGCAACGCGTATCCGTAAATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
* * *
31323 AATCGCAACGCGTATCCGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
31363 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
31403 AATCGCAACGCGTATCCGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * *
31443 AATCGCAACGAGAATCTGTAAATCGCAACGA-TAATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGAGTAA-CCGTA
* * * *
31483 AATCGCAACGAGAATCTGTAAATCACAAC
1 AATCGCAACGCGTATCCGTAAATCGCAAC
31512 ACTGAAATTT
Statistics
Matches: 312, Mismatches: 33, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
39 4 0.01
40 272 0.87
41 34 0.11
42 2 0.01
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (40 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGAGTAACCGTA
Found at i:31439 original size:20 final size:19
Alignment explanation
Indices: 31160--31511 Score: 398
Period size: 20 Copynumber: 17.6 Consensus size: 19
31150 CGCGAACACA
31160 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
31180 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
**
31200 TAAATCGCAACGCGTATGGG
1 TAAATCGCAACG-GTATCCG
*
31220 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
31240 TATATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
* * *
31260 TAAATCGCAACGATAATACA
1 TAAATCGCAACGGT-ATCCG
31280 TAAAATCGCAACGCGTATCCG
1 T-AAATCGCAACG-GTATCCG
31301 TAAATCGCAACGTGTATCCG
1 TAAATCGCAACG-GTATCCG
31321 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
31341 TAAATCGCAATGCGTATCCG
1 TAAATCGCAACG-GTATCCG
31361 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
31381 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
31401 TAAATCGCAACGCGTATCCG
1 TAAATCGCAACG-GTATCCG
*
31421 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
31441 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
31461 TAAATCGCAACGATAATCCG
1 TAAATCGCAACGGT-ATCCG
* *
31481 TAAATCGCAACGAGAATCTG
1 TAAATCGCAACG-GTATCCG
*
31501 TAAATCACAAC
1 TAAATCGCAAC
31512 ACTGAAATTT
Statistics
Matches: 290, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.01
20 270 0.93
21 16 0.06
22 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (19 bp):
TAAATCGCAACGGTATCCG
Found at i:32226 original size:24 final size:24
Alignment explanation
Indices: 32187--32233 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
32177 AAATTTGGTC
32187 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
32211 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
32234 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:34734 original size:19 final size:19
Alignment explanation
Indices: 34712--34985 Score: 354
Period size: 19 Copynumber: 15.4 Consensus size: 19
34702 CGGAAAATAC
*
34712 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
34731 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
34745 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
34765 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
34779 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
34798 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
34817 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
34831 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
34850 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
34869 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
34888 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
34907 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
34926 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
34940 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
34959 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
34978 AATCGCAA
1 AATCGCAA
34986 CGAGATAATC
Statistics
Matches: 226, Mismatches: 8, Indels: 42
0.82 0.03 0.15
Matches are distributed among these distances:
14 40 0.18
15 2 0.01
16 11 0.05
17 10 0.04
18 3 0.01
19 147 0.65
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:34914 original size:109 final size:105
Alignment explanation
Indices: 34740--35007 Score: 459
Period size: 109 Copynumber: 2.5 Consensus size: 105
34730 AAATCCCAAC
34740 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGA-GAATCGCAATGCGAAATGAAAATCGC
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGC
*
34804 AATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
65 AATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
*
34845 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAAATGAAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGAT-G-AATCGCAATGCGAAATGAAAAT
34910 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
62 CGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
34954 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAT-AATCGCAATGCGAAAT
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAAT
35008 TATAAACGCA
Statistics
Matches: 155, Mismatches: 3, Indels: 11
0.92 0.02 0.07
Matches are distributed among these distances:
104 32 0.21
105 16 0.10
106 4 0.03
107 5 0.03
108 1 0.01
109 97 0.63
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (105 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATGAATCGCAATGCGAAATGAAAATCGCA
ATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
Found at i:35023 original size:52 final size:52
Alignment explanation
Indices: 34740--35007 Score: 455
Period size: 52 Copynumber: 5.0 Consensus size: 52
34730 AAATCCCAAC
34740 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
34793 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
34845 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
34902 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
34954 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
35006 AT
1 AT
35008 TATAAACGCA
Statistics
Matches: 207, Mismatches: 3, Indels: 11
0.94 0.01 0.05
Matches are distributed among these distances:
52 134 0.65
53 17 0.08
54 4 0.02
55 5 0.02
56 1 0.00
57 46 0.22
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:35104 original size:19 final size:19
Alignment explanation
Indices: 35014--35096 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
35004 AAATTATAAA
35014 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
35033 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
35053 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
35069 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
35086 CGCATTGCGAT
1 CGCATTGCGAT
35097 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:35222 original size:14 final size:14
Alignment explanation
Indices: 35203--35239 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
35193 CATCAATTAC
35203 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
35217 ACAAATCATCTTTT
1 ACAAATCAACTTTT
35231 ACAAATCAA
1 ACAAATCAA
35240 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:37209 original size:14 final size:14
Alignment explanation
Indices: 37190--37246 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
37180 GCGAAATGAA
*
37190 AATCGCAACGACAG
1 AATCGCAACGAAAG
37204 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
37221 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
37237 AATCGCAACG
1 AATCGCAACG
37247 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:37217 original size:33 final size:33
Alignment explanation
Indices: 37171--37263 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
37161 GCGAAACCAA
*
37171 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
37204 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
37237 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
37264 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:37228 original size:19 final size:19
Alignment explanation
Indices: 37134--37268 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
37124 TAGTTTACTT
* *
37134 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
37154 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
37173 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
37192 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
37206 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
37225 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
37239 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
37258 TCGCAATGCGA
1 TCGCAACGCGA
37269 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:37286 original size:19 final size:19
Alignment explanation
Indices: 37264--37392 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
37254 AAAATCGCAA
37264 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
37283 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
37297 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
37316 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
37330 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
37349 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
37368 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
37388 TGCGA
1 TGCGA
37393 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:37306 original size:33 final size:33
Alignment explanation
Indices: 37264--37355 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
37254 AAAATCGCAA
37264 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
37297 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
37330 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
37356 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:37606 original size:92 final size:93
Alignment explanation
Indices: 37436--37814 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
37426 TTGAATGGAT
37436 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
37501 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
37529 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
37593 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
37621 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
37685 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
37713 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
37778 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
37806 AAATTTACT
1 AAATTTACT
37815 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:37765 original size:185 final size:185
Alignment explanation
Indices: 37436--37814 Score: 733
Period size: 185 Copynumber: 2.0 Consensus size: 185
37426 TTGAATGGAT
37436 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
37501 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
37566 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
37621 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
37685 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
37750 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
37806 AAATTTACT
1 AAATTTACT
37815 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 100 0.52
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:39537 original size:14 final size:14
Alignment explanation
Indices: 39518--39607 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
39508 TTGAAATGAA
39518 AATCGCAACGAGAG
1 AATCGCAACGAGAG
39532 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
39549 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
39565 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
39584 AATCGCAACGAGAG
1 AATCGCAACGAGAG
39598 AATCGCAACG
1 AATCGCAACG
39608 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:39555 original size:33 final size:33
Alignment explanation
Indices: 39510--39624 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
39500 TCTTTTGGTT
39510 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
39543 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
39576 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
39609 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
39625 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:39556 original size:19 final size:18
Alignment explanation
Indices: 39517--39629 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
39507 GTTGAAATGA
39517 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
39532 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
39549 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
39565 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
39582 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
39598 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
39615 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
39630 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:39660 original size:14 final size:14
Alignment explanation
Indices: 39641--39695 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
39631 TTTGGTTTCG
39641 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
39655 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
39674 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
39688 CGTTGCGA
1 CGTTGCGA
39696 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:39673 original size:33 final size:33
Alignment explanation
Indices: 39625--39695 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
39615 AAAATCGCAA
**
39625 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
39658 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
39691 TGCGA
1 TGCGA
39696 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:39703 original size:33 final size:33
Alignment explanation
Indices: 39636--39717 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
39626 GCGATTTTGG
***
39636 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
39669 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
39702 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
39718 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:39722 original size:20 final size:20
Alignment explanation
Indices: 39648--39736 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
39638 TCGCGTTGCG
39648 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
39668 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
39681 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
39701 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
39721 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
39737 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:39857 original size:32 final size:33
Alignment explanation
Indices: 39816--39885 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
39806 AATACTAACT
*
39816 TGAAAATCGCAACGAGA-AATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
39848 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
39881 TGAAA
1 TGAAA
39886 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 16 0.47
33 18 0.53
ACGTcount: A:0.49, C:0.19, G:0.21, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:40119 original size:22 final size:22
Alignment explanation
Indices: 40067--40121 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
40057 TGGTTGTGAG
**
40067 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
40089 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
40111 GGATTTCTTCG
1 GGATTTCTTCG
40122 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:40292 original size:20 final size:20
Alignment explanation
Indices: 40267--40459 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
40257 CTTTAAATAT
40267 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
40287 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
40309 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
40328 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
40348 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
40368 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
40388 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
40408 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
40428 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
40448 CGCGTTGCGATT
1 CGCGTTGCGATT
40460 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:40454 original size:60 final size:60
Alignment explanation
Indices: 40267--40459 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
40257 CTTTAAATAT
**
40267 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
40328 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
40388 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
40448 CGCGTTGCGATT
1 CGCGTTGCGATT
40460 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:40939 original size:18 final size:18
Alignment explanation
Indices: 40916--40965 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
40906 TCTCATTCGT
40916 CTTCATCTTCATCCTCCG
1 CTTCATCTTCATCCTCCG
* * * *
40934 CTTCATCATCGTCATCGG
1 CTTCATCTTCATCCTCCG
*
40952 CTTCTTCTTCATCC
1 CTTCATCTTCATCC
40966 AACGGAAGCG
Statistics
Matches: 24, Mismatches: 8, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.12, C:0.40, G:0.08, T:0.40
Consensus pattern (18 bp):
CTTCATCTTCATCCTCCG
Found at i:42014 original size:27 final size:27
Alignment explanation
Indices: 41984--42040 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
41974 GTTGTCAGGA
*
41984 TATTTCACATGTTTTATTTTGTTTATG
1 TATTTCACATGTTTTATTTAGTTTATG
42011 TATTTCACATGTTTTATTTAGTTTATG
1 TATTTCACATGTTTTATTTAGTTTATG
42038 TAT
1 TAT
42041 ATTTTTATCT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.21, C:0.07, G:0.11, T:0.61
Consensus pattern (27 bp):
TATTTCACATGTTTTATTTAGTTTATG
Found at i:42930 original size:49 final size:49
Alignment explanation
Indices: 42876--43071 Score: 329
Period size: 49 Copynumber: 4.0 Consensus size: 49
42866 ATGACTTGAA
42876 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
1 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
*
42925 TTACACAAGCATAGAGAATCTATGTTCATCTTTCTTTTACTCTTGTATG
1 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
* *
42974 TTACACAAGCATAGAGAATCTATGTTCATCTTTCTTTTACTCTTTTATG
1 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
* * * *
43023 TTACACAACCATAGAGTATCTATGTTCATCTGTCTTTTATTCTTATATG
1 TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
43072 AACATCTTCA
Statistics
Matches: 140, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
49 140 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (49 bp):
TTACACAAGCATAGAGAATCTATGTTCATCTGTCTTTTACTCTTGTATG
Found at i:45621 original size:2 final size:2
Alignment explanation
Indices: 45614--45649 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
45604 CGTATTCCCA
* *
45614 CT CT CT CT CT CG CT TT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
45650 TATTCTCAAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.47, G:0.03, T:0.50
Consensus pattern (2 bp):
CT
Found at i:48699 original size:19 final size:19
Alignment explanation
Indices: 48675--48747 Score: 146
Period size: 19 Copynumber: 3.8 Consensus size: 19
48665 ATTAAAACAT
48675 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGCATGGA
48694 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGCATGGA
48713 GAGTGCATCGATGCATGGA
1 GAGTGCATCGATGCATGGA
48732 GAGTGCATCGATGCAT
1 GAGTGCATCGATGCAT
48748 AAACTGCATT
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.26, C:0.16, G:0.36, T:0.22
Consensus pattern (19 bp):
GAGTGCATCGATGCATGGA
Found at i:48704 original size:65 final size:64
Alignment explanation
Indices: 48567--48705 Score: 170
Period size: 64 Copynumber: 2.2 Consensus size: 64
48557 TGCACTAAGT
* * * * * * *
48567 GTGCATCGATGCATAAAATGCATTCGATGTTTTGAATAAGCCTAAGTGCATTGATGCATGGTGT
1 GTGCATCGATACATAAAATGCATTCGATGTTTTCAATAAACATAAGTGCATCGATGCATGGAGA
* * * *
48631 GTGCATCGATACATAAAATGTATTTGATGTTTTCATTAAAACATGAGTGCATCGATGCATGGAGA
1 GTGCATCGATACATAAAATGCATTCGATGTTTTCAAT-AAACATAAGTGCATCGATGCATGGAGA
48696 GTGCATCGAT
1 GTGCATCGAT
48706 GCATGGAGAG
Statistics
Matches: 63, Mismatches: 11, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
64 32 0.51
65 31 0.49
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (64 bp):
GTGCATCGATACATAAAATGCATTCGATGTTTTCAATAAACATAAGTGCATCGATGCATGGAGA
Found at i:48800 original size:20 final size:20
Alignment explanation
Indices: 48775--48812 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
48765 CAATTTATTC
*
48775 ATTGGTGTATCGATGCATGG
1 ATTGGTGCATCGATGCATGG
*
48795 ATTGGTGCATCGGTGCAT
1 ATTGGTGCATCGATGCAT
48813 CCCTTTGAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.34, T:0.34
Consensus pattern (20 bp):
ATTGGTGCATCGATGCATGG
Found at i:51428 original size:23 final size:21
Alignment explanation
Indices: 51402--51444 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
51392 TTGATGCATA
51402 TTCAAGGAGTACATCGATGCACC
1 TTCAAGGAGT--ATCGATGCACC
* *
51425 TTCATGGTGTATCGATGCAC
1 TTCAAGGAGTATCGATGCAC
51445 TGTGAAGTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 10 0.56
23 8 0.44
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (21 bp):
TTCAAGGAGTATCGATGCACC
Done.