Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000015.1 Hibiscus syriacus cultivar Beakdansim tig00000030_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: 75590
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:572 original size:109 final size:110
Alignment explanation
Indices: 418--672 Score: 331
Period size: 109 Copynumber: 2.4 Consensus size: 110
408 GCTTCCCAAT
* * *
418 TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACCCAAGACAACACAAGCTC-ACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACAAAAGATATTGGACCCAAGACAACACAAGCTCAACTTCA
* *
482 CGATGAAGGGGCGGCTGATTGTCAACAAACAACTTTTCAATTTCA
66 CGACGAAGGGGCAGCTGATTGTCAACAAACAACTTTTCAATTTCA
* * * * *
527 TTCAGAGTCAATTTCAACTTCATAACAAAAGATTTTGGACTCAAGATAACACAAGCTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACAAAAGATATTGGACCCAAGACAACACAAGCTCAACTTCA
* * *
592 CGACGAAGGGGCAGCTGATTGTCAACAAACAA-TTTCCCAGTTC-
66 CGACGAAGGGGCAGCTGATTGTCAACAAACAACTTTTCAATTTCA
** *
635 --CAGAGCCAATTTCAACTTCACAACGGAGGATATTGGAC
1 TTCAGAGCCAATTTCAACTTCACAACAAAAGATATTGGAC
673 TCGGAGCAAT
Statistics
Matches: 126, Mismatches: 19, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
106 32 0.25
109 58 0.46
110 36 0.29
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.24
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACAAAAGATATTGGACCCAAGACAACACAAGCTCAACTTCA
CGACGAAGGGGCAGCTGATTGTCAACAAACAACTTTTCAATTTCA
Found at i:1666 original size:3 final size:3
Alignment explanation
Indices: 1638--1687 Score: 54
Period size: 3 Copynumber: 17.3 Consensus size: 3
1628 GTCTACAAAA
1638 TAT T-T TAT TA- TAT TA- TATT TATT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TAT
1682 T-T TAT T
1 TAT TAT T
1688 TTTGTAGGCC
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
2 8 0.19
3 28 0.67
4 6 0.14
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:1778 original size:33 final size:33
Alignment explanation
Indices: 1741--1821 Score: 110
Period size: 33 Copynumber: 2.5 Consensus size: 33
1731 AAAAATAAAT
* **
1741 CAACGTATTTGAGTCTTATTGAAATTCTAAAAC
1 CAACGTATTTGAGTCATATTGAAACACTAAAAC
1774 CAACGTATTTGAGTCATATTGAAACACTAAAAC
1 CAACGTATTTGAGTCATATTGAAACACTAAAAC
*
1807 CGAA-GCATTTGAGTC
1 C-AACGTATTTGAGTC
1822 CAAGTATGAC
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
33 41 0.95
34 2 0.05
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (33 bp):
CAACGTATTTGAGTCATATTGAAACACTAAAAC
Found at i:2319 original size:18 final size:19
Alignment explanation
Indices: 2298--2337 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
2288 TATTTATATA
2298 TTTATTTATTT-TTATT-AT
1 TTTA-TTATTTATTATTCAT
2316 TTTATTATTTATTATTCAT
1 TTTATTATTTATTATTCAT
2335 TTT
1 TTT
2338 TTCCTTTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
17 6 0.30
18 9 0.45
19 5 0.25
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (19 bp):
TTTATTATTTATTATTCAT
Found at i:2328 original size:15 final size:14
Alignment explanation
Indices: 2302--2331 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2292 TATATATTTA
2302 TTTATTTTTATTAT
1 TTTATTTTTATTAT
2316 TTTATTATTTATTAT
1 TTTATT-TTTATTAT
2331 T
1 T
2332 CATTTTTTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTTATTAT
Found at i:2339 original size:21 final size:21
Alignment explanation
Indices: 2299--2339 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2289 ATTTATATAT
*
2299 TTATTTATTTTTATTATTTTA
1 TTATTTATTTTCATTATTTTA
2320 TTATTTATTATTCATT-TTTT
1 TTATTTATT-TTCATTATTTT
2340 CCTTTTTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (21 bp):
TTATTTATTTTCATTATTTTA
Found at i:2850 original size:27 final size:26
Alignment explanation
Indices: 2820--2877 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 26
2810 TTATAATGAG
*
2820 TATACGAAAGTTACACATTTAGTGTCA
1 TATAC-AAAGTTACACATATAGTGTCA
* * *
2847 TATAACCAATTTACACATATAGTGTCG
1 TAT-ACAAAGTTACACATATAGTGTCA
2874 TATA
1 TATA
2878 GAATATACAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
26 1 0.04
27 23 0.88
28 2 0.08
ACGTcount: A:0.38, C:0.16, G:0.12, T:0.34
Consensus pattern (26 bp):
TATACAAAGTTACACATATAGTGTCA
Found at i:7228 original size:13 final size:13
Alignment explanation
Indices: 7210--7236 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
7200 TACTTAATTG
7210 AGTAAAATTTAAA
1 AGTAAAATTTAAA
7223 AGTAAAATTTAAA
1 AGTAAAATTTAAA
7236 A
1 A
7237 AATATTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.30
Consensus pattern (13 bp):
AGTAAAATTTAAA
Found at i:10039 original size:32 final size:32
Alignment explanation
Indices: 10001--10092 Score: 123
Period size: 32 Copynumber: 2.9 Consensus size: 32
9991 CCCACAACGC
*
10001 CAAAAATTGGTACCTAGTTAAAGACCCTATAT
1 CAAAAATTAGTACCTAGTTAAAGACCCTATAT
** *
10033 TTAAAATTAGTACCTAGTCAAAGACCCTATAT
1 CAAAAATTAGTACCTAGTTAAAGACCCTATAT
*
10065 CAAAAATTAGTA-CTCAATTAAAGACCCT
1 CAAAAATTAGTACCT-AGTTAAAGACCCT
10093 CAAAGCATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
31 2 0.04
32 49 0.96
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (32 bp):
CAAAAATTAGTACCTAGTTAAAGACCCTATAT
Found at i:26473 original size:20 final size:20
Alignment explanation
Indices: 26448--26544 Score: 115
Period size: 20 Copynumber: 4.8 Consensus size: 20
26438 GCGGTTTTCC
26448 TAAATCGCAATGCGAATACG
1 TAAATCGCAATGCGAATACG
* *
26468 TAAATCGCAATGCGATTACA
1 TAAATCGCAATGCGAATACG
** *
26488 TAAATCATAATGCGAATTAGG
1 TAAATCGCAATGCGAA-TACG
* *
26509 AAAATCG-AATGCGATTACG
1 TAAATCGCAATGCGAATACG
26528 TAAATCGCAATGCGAAT
1 TAAATCGCAATGCGAAT
26545 TAGGAAAATC
Statistics
Matches: 62, Mismatches: 13, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
19 9 0.15
20 46 0.74
21 7 0.11
ACGTcount: A:0.41, C:0.16, G:0.19, T:0.24
Consensus pattern (20 bp):
TAAATCGCAATGCGAATACG
Found at i:26500 original size:40 final size:39
Alignment explanation
Indices: 26448--26558 Score: 132
Period size: 40 Copynumber: 2.8 Consensus size: 39
26438 GCGGTTTTCC
* *
26448 TAAATCGCAATGCGAATACGTAAATCGCAATGCGATTACA
1 TAAATCACAATGCGAATACGAAAATCG-AATGCGATTACA
* * *
26488 TAAATCATAATGCGAATTAGGAAAATCGAATGCGATTACG
1 TAAATCACAATGCGAA-TACGAAAATCGAATGCGATTACA
* *
26528 TAAATCGCAATGCGAATTAGGAAAATCGAAT
1 TAAATCACAATGCGAA-TACGAAAATCGAAT
26559 TCGCAACTCG
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
40 54 0.86
41 9 0.14
ACGTcount: A:0.42, C:0.15, G:0.19, T:0.23
Consensus pattern (39 bp):
TAAATCACAATGCGAATACGAAAATCGAATGCGATTACA
Found at i:27412 original size:24 final size:24
Alignment explanation
Indices: 27385--27438 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
27375 GTATTCGAAA
27385 TTTGATCTTGGTCAATACCCAGAC
1 TTTGATCTTGGTCAATACCCAGAC
* *
27409 TTTGATCTTGGTCAATACTCAGAT
1 TTTGATCTTGGTCAATACCCAGAC
27433 TTTGAT
1 TTTGAT
27439 GATTTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.17, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCAGAC
Found at i:29998 original size:19 final size:19
Alignment explanation
Indices: 29976--30067 Score: 87
Period size: 19 Copynumber: 5.4 Consensus size: 19
29966 GAAAATTACT
29976 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
29995 ATCGCAA--C--AA-GAGA
1 ATCGCAATGCGAAATGAAA
30009 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
30028 ATCGTAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
30042 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
30061 ATCGCAA
1 ATCGCAA
30068 CGACAAAATC
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 19 0.33
15 3 0.05
16 3 0.05
17 3 0.05
18 3 0.05
19 26 0.46
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:30018 original size:33 final size:33
Alignment explanation
Indices: 29976--30102 Score: 184
Period size: 33 Copynumber: 3.8 Consensus size: 33
29966 GAAAATTACT
*
29976 ATCGCAATGCGAAATGAAAATCGCAACAAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
30009 ATCGCAATGCGAAATGAAAATCGTAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
30042 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
30075 ATCGTAACGCGAAACT-AAAATCGCAACG
1 ATCGCAATGCGAAA-TGAAAATCGCAACG
30103 CGAAACTAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
33 85 0.99
34 1 0.01
ACGTcount: A:0.46, C:0.20, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:30124 original size:19 final size:19
Alignment explanation
Indices: 30041--30117 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 19
30031 GTAACGAGAG
*
30041 AATCGCAATGCGAAA-TGAA
1 AATCGCAACGCGAAACT-AA
30060 AATCGCAA--CG--AC-AA
1 AATCGCAACGCGAAACTAA
*
30074 AATCGTAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
30093 AATCGCAACGCGAAACTAA
1 AATCGCAACGCGAAACTAA
*
30112 ATTCGC
1 AATCGC
30118 GTTGCGATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 12
0.77 0.05 0.19
Matches are distributed among these distances:
14 9 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 2 0.04
19 33 0.67
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAACTAA
Found at i:30135 original size:19 final size:19
Alignment explanation
Indices: 30113--30243 Score: 67
Period size: 19 Copynumber: 7.7 Consensus size: 19
30103 CGAAACTAAA
30113 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
30132 TTCGCTTTGCGA--GTC--
1 TTCGCGTTGCGATTTTCAT
* *
30147 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
30165 TTCGCATTGC-A-ATTC--
1 TTCGCGTTGCGATTTTCAT
*
30180 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
30198 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
30213 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
30231 TTCGCATTGCGAT
1 TTCGCGTTGCGAT
30244 AGTCATTTTT
Statistics
Matches: 78, Mismatches: 19, Indels: 30
0.61 0.15 0.24
Matches are distributed among these distances:
14 24 0.31
15 1 0.01
16 8 0.10
17 8 0.10
18 1 0.01
19 36 0.46
ACGTcount: A:0.12, C:0.24, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:30159 original size:33 final size:33
Alignment explanation
Indices: 30117--30243 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
30107 ACTAAATTCG
* * *
30117 CGTTGCGATTTTCATTTCGCTTTGCGAGTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
30150 CGTTGCGATTTTCATTTCGCATTGCAATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
30183 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
30216 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
30244 AGTCATTTTT
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:30251 original size:19 final size:17
Alignment explanation
Indices: 30160--30243 Score: 63
Period size: 17 Copynumber: 5.1 Consensus size: 17
30150 CGTTGCGATT
*
30160 TTCATTTCGCATTGCAA
1 TTCATTTCGCATTGCGA
*
30177 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
30191 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
*
30210 TTC-TCTCG--TTGCGA
1 TTCATTTCGCATTGCGA
30224 TTTTCATTTCGCATTGCGA
1 --TTCATTTCGCATTGCGA
30243 T
1 T
30244 AGTCATTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 20
0.68 0.06 0.26
Matches are distributed among these distances:
14 11 0.21
16 14 0.27
17 15 0.29
19 12 0.23
ACGTcount: A:0.14, C:0.24, G:0.17, T:0.45
Consensus pattern (17 bp):
TTCATTTCGCATTGCGA
Found at i:30571 original size:20 final size:20
Alignment explanation
Indices: 30546--30586 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
30536 AATAATTCAG
*
30546 TCATTTTCGTGTTACGATTT
1 TCATTTTCATGTTACGATTT
*
30566 TCATTTTCATGTTGCGATTT
1 TCATTTTCATGTTACGATTT
30586 T
1 T
30587 AAGTTTAGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.15, C:0.15, G:0.15, T:0.56
Consensus pattern (20 bp):
TCATTTTCATGTTACGATTT
Found at i:31164 original size:20 final size:20
Alignment explanation
Indices: 31113--31572 Score: 203
Period size: 20 Copynumber: 22.9 Consensus size: 20
31103 ATGGCGCTAT
31113 GTAAATCGCAATGCGAATTA-
1 GTAAATCGCAATGCG-ATTAC
* * *
31133 GGAATATTGCAAAGCGATTAC
1 GTAA-ATCGCAATGCGATTAC
*
31154 GTAAATCGCAATGCGAATAC
1 GTAAATCGCAATGCGATTAC
*
31174 GT-AATCGCATTGCGATTTAC
1 GTAAATCGCAATGCGA-TTAC
* *
31194 GT-AATCGCATTGCGATTTTC
1 GTAAATCGCAATGCGA-TTAC
* * * *
31214 CTAATTCGCATTGCGATTTTC
1 GTAAATCGCAATGCGA-TTAC
* * * *
31235 CTAATTCGCATTGTGATTTAC
1 GTAAATCGCAATGCGA-TTAC
* * * *
31256 --ATAGCGCCATTCGATTTAC
1 GTAAATCGCAATGCGA-TTAC
* **
31275 -TAAATCTCGTTGCGATTTAC
1 GTAAATCGCAATGCGA-TTAC
**
31295 -TAAATCGCAATATGATTAC
1 GTAAATCGCAATGCGATTAC
31314 GTAAATCGCAATGCGATTAC
1 GTAAATCGCAATGCGATTAC
* *
31334 GTAAATCGCAATACGAATAC
1 GTAAATCGCAATGCGATTAC
* *
31354 GT-AATCGCATTGCAATTTAC
1 GTAAATCGCAATGCGA-TTAC
* * *
31374 GT-AATCGCATTGTGATTTTC
1 GTAAATCGCAATGCGA-TTAC
* * *
31394 CTAATTCGCATTGCGATTTAC
1 GTAAATCGCAATGCGA-TTAC
*
31415 GT-AATCGCATTGCGATTTAC
1 GTAAATCGCAATGCGA-TTAC
* *
31435 GT-ATTCGCATTGCGATTTAC
1 GTAAATCGCAATGCGA-TTAC
*
31455 GT-AATCGCATTGCGATTTAC
1 GTAAATCGCAATGCGA-TTAC
* *
31475 GT-ATTCGCATTGCGATTTAC
1 GTAAATCGCAATGCGA-TTAC
* *
31495 GT-AATCGTATTGCGATTTAC
1 GTAAATCGCAATGCGA-TTAC
* * *
31515 GT-ATTCGCATTGCGATTTAA
1 GTAAATCGCAATGCGA-TTAC
* * **
31535 GAAAATCGCAACGCGAATTTG
1 GTAAATCGCAATGCG-ATTAC
*
31556 GGAAATCGCAATGCGAT
1 GTAAATCGCAATGCGAT
31573 AGTCAGAATT
Statistics
Matches: 365, Mismatches: 65, Indels: 20
0.81 0.14 0.04
Matches are distributed among these distances:
19 38 0.10
20 238 0.65
21 88 0.24
22 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (20 bp):
GTAAATCGCAATGCGATTAC
Found at i:31330 original size:40 final size:40
Alignment explanation
Indices: 31284--31533 Score: 310
Period size: 40 Copynumber: 6.2 Consensus size: 40
31274 CTAAATCTCG
* ** *
31284 TTGCGATTTAC-TAAATCGCAATATGA-TTACGTAAATCGCA
1 TTGCGATTTACGT-AATCGCATTGCGATTTACGT-ATTCGCA
* * * * *
31324 ATGCGA-TTACGTAAATCGCAATACGA-ATACGTAATCGCA
1 TTGCGATTTACGT-AATCGCATTGCGATTTACGTATTCGCA
* * * *
31363 TTGCAATTTACGTAATCGCATTGTGATTTTCCTAATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGT-ATTCGCA
31404 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
31444 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
*
31484 TTGCGATTTACGTAATCGTATTGCGATTTACGTATTCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
31524 TTGCGATTTA
1 TTGCGATTTA
31534 AGAAAATCGC
Statistics
Matches: 189, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
39 25 0.13
40 129 0.68
41 35 0.19
ACGTcount: A:0.27, C:0.19, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
Found at i:31453 original size:180 final size:180
Alignment explanation
Indices: 31141--31474 Score: 521
Period size: 180 Copynumber: 1.9 Consensus size: 180
31131 TAGGAATATT
* *
31141 GCAAAGCGATTACGTAAATCGCAATGCGAATACGTAATCGCATTGCGATTTACGTAATCGCATTG
1 GCAAAGCGATTACGTAAATCGCAATACGAATACGTAATCGCATTGCAATTTACGTAATCGCATTG
* *
31206 CGATTTTCCTAATTCGCATTGCGATTTTCCTAATTCGCATTGTGATTTACATAGCGCCATTCGAT
66 CGATTTTCCTAATTCGCATTGCGATTTACCTAATTCGCATTGCGATTTACATAGCGCCATTCGAT
* *
31271 TTAC-TAAATCTCGTTGCGATTTACTAAATCGCAATATGATTACGTAAATC
131 TTACGT-AATCGCATTGCGATTTACTAAATCGCAATATGATTACGTAAATC
*
31321 GCAATGCGATTACGTAAATCGCAATACGAATACGTAATCGCATTGCAATTTACGTAATCGCATTG
1 GCAAAGCGATTACGTAAATCGCAATACGAATACGTAATCGCATTGCAATTTACGTAATCGCATTG
* * * *
31386 TGATTTTCCTAATTCGCATTGCGATTTACGTAA-TCGCATTGCGATTTACGTATTCG-CATTGCG
66 CGATTTTCCTAATTCGCATTGCGATTTACCTAATTCGCATTGCGATTTACATA-GCGCCATT-CG
31449 ATTTACGTAATCGCATTGCGATTTAC
129 ATTTACGTAATCGCATTGCGATTTAC
31475 GTATTCGCAT
Statistics
Matches: 140, Mismatches: 11, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
179 21 0.15
180 118 0.84
181 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.34
Consensus pattern (180 bp):
GCAAAGCGATTACGTAAATCGCAATACGAATACGTAATCGCATTGCAATTTACGTAATCGCATTG
CGATTTTCCTAATTCGCATTGCGATTTACCTAATTCGCATTGCGATTTACATAGCGCCATTCGAT
TTACGTAATCGCATTGCGATTTACTAAATCGCAATATGATTACGTAAATC
Found at i:31511 original size:180 final size:180
Alignment explanation
Indices: 31114--31517 Score: 514
Period size: 180 Copynumber: 2.2 Consensus size: 180
31104 TGGCGCTATG
* * * * *
31114 TAAATCGCAATGCGAATTA-GGAATATTGCAAAGCGATTACGTAAATCGCAATGCGAATACGTAA
1 TAAATCGCAATACG-ATTACGTAA-ATCGCAATGCGATTACGTAAATCGCAATACGAATACGTAA
* *
31178 TCGCATTGCGATTTACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTTCCTAATTCG
64 TCGCATTGCAATTTACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACCTAATTCG
* * *
31243 CATTGTGATTTACATAGCGCCATTCGATTTACTAAATCTCGTTGCGATTTAC
129 CATTGCGATTTACATAGCGCCATTCGATTTACTAAATCGCATTGCGATTTAC
*
31295 TAAATCGCAATATGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATACGAATACGTAATC
1 TAAATCGCAATACGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATACGAATACGTAATC
* *
31360 GCATTGCAATTTACGTAATCGCATTGTGATTTTCCTAATTCGCATTGCGATTTACGTAA-TCGCA
66 GCATTGCAATTTACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACCTAATTCGCA
* *
31424 TTGCGATTTACGTATTCG-CATTGCGATTTACGT-AATCGCATTGCGATTTAC
131 TTGCGATTTACATA-GCGCCATT-CGATTTAC-TAAATCGCATTGCGATTTAC
* * * * *
31475 GT-ATTCGCATTGCGATTTACGT-AATCGTATTGCGATTTACGTA
1 -TAAATCGCAATACGA-TTACGTAAATCGCAATGCGA-TTACGTA
31518 TTCGCATTGC
Statistics
Matches: 195, Mismatches: 21, Indels: 14
0.85 0.09 0.06
Matches are distributed among these distances:
179 21 0.11
180 144 0.74
181 30 0.15
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.34
Consensus pattern (180 bp):
TAAATCGCAATACGATTACGTAAATCGCAATGCGATTACGTAAATCGCAATACGAATACGTAATC
GCATTGCAATTTACGTAATCGCATTGCGATTTTCCTAATTCGCATTGCGATTTACCTAATTCGCA
TTGCGATTTACATAGCGCCATTCGATTTACTAAATCGCATTGCGATTTAC
Found at i:31960 original size:25 final size:25
Alignment explanation
Indices: 31914--31962 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
31904 GCAATGGAAA
* *
31914 GTTAAAATTATCATGTTTCATTAAG
1 GTTAAAATGATAATGTTTCATTAAG
31939 GTTAAAATGATAAT-TTTACATTAA
1 GTTAAAATGATAATGTTT-CATTAA
31963 ATGAAATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 3 0.14
25 18 0.86
ACGTcount: A:0.41, C:0.06, G:0.10, T:0.43
Consensus pattern (25 bp):
GTTAAAATGATAATGTTTCATTAAG
Found at i:34555 original size:76 final size:75
Alignment explanation
Indices: 34473--34620 Score: 235
Period size: 76 Copynumber: 2.0 Consensus size: 75
34463 TAAACTCAAA
34473 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATAATATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
34537 TTTTAATTAAGT
64 TTTTAATTAAGT
* * * *
34549 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
34614 TTAATTA
66 TTAATTA
34621 GGATTTAGAA
Statistics
Matches: 67, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
75 24 0.36
76 43 0.64
ACGTcount: A:0.29, C:0.03, G:0.10, T:0.58
Consensus pattern (75 bp):
TTTAGGATAATATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:34622 original size:19 final size:19
Alignment explanation
Indices: 34594--34656 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
34584 TGTATTTTAG
*
34594 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
* *
34613 TTTAATTAGGATTTAGAAT
1 TTTAATTAGGTTTTAGTAT
* **
34632 ATTATATTATTTTTTAGGTAT
1 TTTA-ATTAGGTTTTA-GTAT
34653 TTTA
1 TTTA
34657 GTTTAAATAG
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 8 0.24
21 6 0.18
ACGTcount: A:0.32, C:0.00, G:0.13, T:0.56
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:35311 original size:21 final size:22
Alignment explanation
Indices: 35285--35325 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
35275 CTTTAATTTG
35285 TTTATTTAATTATT-TTTTTCT
1 TTTATTTAATTATTATTTTTCT
*
35306 TTTATTTAATTCTTATTTTT
1 TTTATTTAATTATTATTTTT
35326 TTAACCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATTTAATTATTATTTTTCT
Found at i:40218 original size:12 final size:12
Alignment explanation
Indices: 40201--40226 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40191 CAAGGACATG
40201 GATGCAATTGGT
1 GATGCAATTGGT
40213 GATGCAATTGGT
1 GATGCAATTGGT
40225 GA
1 GA
40227 AGCTCAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.08, G:0.35, T:0.31
Consensus pattern (12 bp):
GATGCAATTGGT
Found at i:40899 original size:35 final size:35
Alignment explanation
Indices: 40860--40942 Score: 148
Period size: 35 Copynumber: 2.4 Consensus size: 35
40850 TTGGTTCGAA
40860 TAGTGCAGAAAAATACACAGCAGATTCAAACAATG
1 TAGTGCAGAAAAATACACAGCAGATTCAAACAATG
40895 TAGTGCAGAAAAATACACAGCAGATTCAAACAATG
1 TAGTGCAGAAAAATACACAGCAGATTCAAACAATG
* *
40930 CAGTGCAAAAAAA
1 TAGTGCAGAAAAA
40943 ACATATTTGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
35 46 1.00
ACGTcount: A:0.51, C:0.17, G:0.17, T:0.16
Consensus pattern (35 bp):
TAGTGCAGAAAAATACACAGCAGATTCAAACAATG
Found at i:42634 original size:76 final size:75
Alignment explanation
Indices: 42544--42707 Score: 240
Period size: 76 Copynumber: 2.2 Consensus size: 75
42534 TAAACTCAAA
*
42544 TTTAGGATAATATTTTAAACATTATAT-TTTATCTTTGTATTTTAGTTTAAATAGGTTTTTAGTA
1 TTTAGGATATTATTTT-AACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGG-TTTTAGTA
*
42608 TTTTAATTAAGT
64 TTTTAATTAAGG
* * *
42620 TTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
1 TTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
*
42685 TTAATTAGGG
66 TTAATTAAGG
*
42695 TTTAGAATATTAT
1 TTTAGGATATTAT
42708 ATTATTTTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
75 37 0.46
76 43 0.54
ACGTcount: A:0.29, C:0.02, G:0.12, T:0.57
Consensus pattern (75 bp):
TTTAGGATATTATTTTAACATTATATCTTTATCTTTGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGG
Found at i:45797 original size:53 final size:56
Alignment explanation
Indices: 45713--45867 Score: 185
Period size: 53 Copynumber: 2.8 Consensus size: 56
45703 TGTAATCATA
* *
45713 TTTTAGGTTGT-AA-CATGTTTTTAGGTTGTAACCAAATTTTAGGTTACAAACAT-T
1 TTTTAGGTTGTAAACCA-GATTTTAGGTTGTAACCAAATTTTAGGTTACAAAAATAT
* * * * *
45767 TTTT-TGTTGT-AACCATATTTTAGGTTGTAACCAGATTTGAGGTTGCAAAAATAT
1 TTTTAGGTTGTAAACCAGATTTTAGGTTGTAACCAAATTTTAGGTTACAAAAATAT
*
45821 TTTTAGGTTGTAAACCAGATTTTAGGTTATGAACCAAATTTTAGGTT
1 TTTTAGGTTGTAAACCAGATTTTAGGTTGT-AACCAAATTTTAGGTT
45868 GTCAACTAGT
Statistics
Matches: 84, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
53 38 0.45
54 11 0.13
55 5 0.06
56 16 0.19
57 14 0.17
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (56 bp):
TTTTAGGTTGTAAACCAGATTTTAGGTTGTAACCAAATTTTAGGTTACAAAAATAT
Found at i:45843 original size:19 final size:18
Alignment explanation
Indices: 45633--45869 Score: 147
Period size: 18 Copynumber: 13.0 Consensus size: 18
45623 TTGTGTTAAG
45633 AACCAGATTTTAGGTTGT
1 AACCAGATTTTAGGTTGT
** * *
45651 -ATTATGTTTTTAGGTTGCA
1 AACCA-GATTTTAGGTTG-T
* *
45670 AACCTGTTTTTAGGTTGT
1 AACCAGATTTTAGGTTGT
** * *
45688 AACTTGTTTTTAAGTTGT
1 AACCAGATTTTAGGTTGT
* *
45706 AATCATATTTTAGGTTGT
1 AACCAGATTTTAGGTTGT
*
45724 AA-CATGTTTTTAGGTTGT
1 AACCA-GATTTTAGGTTGT
* **
45742 AACCAAATTTTAGGTTAC
1 AACCAGATTTTAGGTTGT
* * **
45760 AAACA-TTTTTTTGTTGT
1 AACCAGATTTTAGGTTGT
*
45777 AACCATATTTTAGGTTGT
1 AACCAGATTTTAGGTTGT
* *
45795 AACCAGATTTGAGGTTGC
1 AACCAGATTTTAGGTTGT
** *
45813 AAAAATATTTTTAGGTTGT
1 AACCAGA-TTTTAGGTTGT
*
45832 AAACCAGATTTTAGGTTAT
1 -AACCAGATTTTAGGTTGT
*
45851 GAACCAAATTTTAGGTTGT
1 -AACCAGATTTTAGGTTGT
45870 CAACTAGTTT
Statistics
Matches: 164, Mismatches: 47, Indels: 15
0.73 0.21 0.07
Matches are distributed among these distances:
17 15 0.09
18 95 0.58
19 49 0.30
20 5 0.03
ACGTcount: A:0.28, C:0.09, G:0.19, T:0.45
Consensus pattern (18 bp):
AACCAGATTTTAGGTTGT
Found at i:46546 original size:19 final size:19
Alignment explanation
Indices: 46524--46581 Score: 57
Period size: 19 Copynumber: 2.9 Consensus size: 19
46514 TATTATAATT
46524 TAAAAATAATAATAATAAA
1 TAAAAATAATAATAATAAA
46543 TAAAAATAGA-AATAGA-AAA
1 TAAAAATA-ATAATA-ATAAA
46562 TAATAAAATAATAAATAATA
1 T-A-AAAATAAT-AATAATA
46582 GTAATAAAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
19 16 0.50
20 4 0.12
21 7 0.22
22 5 0.16
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.24
Consensus pattern (19 bp):
TAAAAATAATAATAATAAA
Found at i:46577 original size:7 final size:7
Alignment explanation
Indices: 46527--46581 Score: 55
Period size: 7 Copynumber: 8.1 Consensus size: 7
46517 TATAATTTAA
46527 AAATAAT
1 AAATAAT
46534 -AATAAT
1 AAATAAT
46540 AAATAA-
1 AAATAAT
*
46546 AAAT-AG
1 AAATAAT
46552 AAATAGA-
1 AAATA-AT
46559 AAATAAT
1 AAATAAT
46566 AAAATAAT
1 -AAATAAT
46574 AAATAAT
1 AAATAAT
46581 A
1 A
46582 GTAATAAAGA
Statistics
Matches: 42, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
5 1 0.02
6 15 0.36
7 18 0.43
8 8 0.19
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.24
Consensus pattern (7 bp):
AAATAAT
Found at i:46643 original size:18 final size:19
Alignment explanation
Indices: 46622--46664 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
46612 TTTATTTTTA
*
46622 AAATAAAAG-ATAAGAATT
1 AAATAAAAGTAAAAGAATT
*
46640 AAAT-AAAGTAAAATAATT
1 AAATAAAAGTAAAAGAATT
46658 AAATAAA
1 AAATAAA
46665 CAAATTAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 4 0.19
18 15 0.71
19 2 0.10
ACGTcount: A:0.70, C:0.00, G:0.07, T:0.23
Consensus pattern (19 bp):
AAATAAAAGTAAAAGAATT
Found at i:47393 original size:75 final size:75
Alignment explanation
Indices: 47270--47484 Score: 301
Period size: 75 Copynumber: 2.9 Consensus size: 75
47260 TAAAACATTA
* * *
47270 TAAATCCTAATTAAAATACTTAAAACTATTTAAACTAAAATACCTAAAACAAAAATAATAT-TTA
1 TAAATCCTAATTAAAATA-TTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
47334 AAATGATAAT-C
65 AAATGAT-ATCC
*
47345 TAAATCCTAATTAAAATATTAAAACATATTTAAACTAAAATACTTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATATTAAAAC-TATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
*
47410 AAATTATATCC
65 AAATGATATCC
* * *
47421 TAAAACTTAATT-AAATAGTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
1 TAAATCCTAATTAAAATATTAAAA-CTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
47485 TGTTTAAAAT
Statistics
Matches: 127, Mismatches: 9, Indels: 8
0.88 0.06 0.06
Matches are distributed among these distances:
74 7 0.06
75 100 0.79
76 20 0.16
ACGTcount: A:0.58, C:0.11, G:0.02, T:0.29
Consensus pattern (75 bp):
TAAATCCTAATTAAAATATTAAAACTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAA
AATGATATCC
Found at i:47403 original size:25 final size:24
Alignment explanation
Indices: 47356--47403 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
47346 AAATCCTAAT
* **
47356 TAAAATATTAAAACATATTTAAAC
1 TAAAATATTAAAACAAAGATAAAC
47380 TAAAATACTTAAAACAAAGATAAA
1 TAAAATA-TTAAAACAAAGATAAA
47404 ATATAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.62, C:0.08, G:0.02, T:0.27
Consensus pattern (24 bp):
TAAAATATTAAAACAAAGATAAAC
Found at i:49448 original size:5 final size:5
Alignment explanation
Indices: 49438--49560 Score: 95
Period size: 5 Copynumber: 23.8 Consensus size: 5
49428 TGTTTAGAGA
* * **
49438 AAAAT AAAAT AAAAT TAATT AAAAT AAAAT AAAAT AAAAT -AAAT TGAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* **** * *
49487 GAAAAT AAAGT TTGCT AAAGAAT AAAAT AAAAAT AAAACA AAAAT GAAAT
1 -AAAAT AAAAT AAAAT -AA-AAT AAAAT -AAAAT AAAA-T AAAAT AAAAT
49537 AAAAT AAAAT AAAAT AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAAT AAAA
49561 AATAGAACGA
Statistics
Matches: 92, Mismatches: 20, Indels: 12
0.74 0.16 0.10
Matches are distributed among these distances:
4 4 0.04
5 73 0.79
6 14 0.15
7 1 0.01
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:49523 original size:11 final size:11
Alignment explanation
Indices: 49502--49561 Score: 79
Period size: 11 Copynumber: 5.5 Consensus size: 11
49492 TAAAGTTTGC
49502 TAAAGAATAAAA
1 TAAA-AATAAAA
49514 TAAAAATAAAA
1 TAAAAATAAAA
* *
49525 CAAAAATGAAA
1 TAAAAATAAAA
49536 T-AAAATAAAA
1 TAAAAATAAAA
49546 T-AAAATAAAA
1 TAAAAATAAAA
49556 TAAAAA
1 TAAAAA
49562 ATAGAACGAA
Statistics
Matches: 43, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
10 19 0.44
11 20 0.47
12 4 0.09
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:55076 original size:14 final size:13
Alignment explanation
Indices: 55057--55138 Score: 62
Period size: 14 Copynumber: 6.2 Consensus size: 13
55047 GATGAAGTTA
55057 AAAATATATATAAT
1 AAAATATA-ATAAT
*
55071 AAAATAAAATAA-
1 AAAATATAATAAT
* * *
55083 ATATTATAAT-TT
1 AAAATATAATAAT
55095 AAAA-ATAATAAT
1 AAAATATAATAAT
55107 AATAATATAATAAT
1 AA-AATATAATAAT
*
55121 AATAATAAAATAAAT
1 AA-AATATAAT-AAT
55136 AAA
1 AAA
55139 TAAAAAGGGA
Statistics
Matches: 54, Mismatches: 9, Indels: 10
0.74 0.12 0.14
Matches are distributed among these distances:
11 5 0.09
12 12 0.22
13 6 0.11
14 26 0.48
15 5 0.09
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAAATATAATAAT
Found at i:55106 original size:3 final size:3
Alignment explanation
Indices: 55098--55133 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
55088 ATAATTTAAA
55098 AAT AAT AAT AAT AAT -AT AAT AAT AAT AAT AA- AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
55134 ATAAATAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:55118 original size:17 final size:17
Alignment explanation
Indices: 55066--55170 Score: 76
Period size: 17 Copynumber: 6.2 Consensus size: 17
55056 AAAAATATAT
55066 ATAATAA-AATAAAATA
1 ATAATAATAATAAAATA
* *
55082 A-ATATTATAATTTAAA-A
1 ATA-ATAATAA-TAAAATA
*
55099 ATAATAATAATAATATA
1 ATAATAATAATAAAATA
55116 ATAATAATAATAAAATAA
1 ATAATAATAATAAAAT-A
* **
55134 ATAAATAAAAAGGGAAATA
1 AT-AATAATAA-TAAAATA
55153 ATAA-AATAAT-AAATA
1 ATAATAATAATAAAATA
55168 ATA
1 ATA
55171 GTAGTGAAGA
Statistics
Matches: 70, Mismatches: 11, Indels: 17
0.71 0.11 0.17
Matches are distributed among these distances:
15 9 0.13
16 7 0.10
17 30 0.43
18 10 0.14
19 10 0.14
20 4 0.06
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (17 bp):
ATAATAATAATAAAATA
Found at i:55159 original size:8 final size:8
Alignment explanation
Indices: 55096--55170 Score: 55
Period size: 9 Copynumber: 9.1 Consensus size: 8
55086 TTATAATTTA
55096 AAAATAAT
1 AAAATAAT
55104 AATAATAAT
1 AA-AATAAT
*
55113 ATAATAAT
1 AAAATAAT
*
55121 AATAATAAA
1 AA-AATAAT
55130 ATAAATAAAT
1 A-AAAT-AAT
**
55140 AAAA-AGG
1 AAAATAAT
*
55147 GAAATAAT
1 AAAATAAT
55155 AAAATAAT
1 AAAATAAT
55163 -AAATAAT
1 AAAATAAT
55170 A
1 A
55171 GTAGTGAAGA
Statistics
Matches: 51, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
7 11 0.22
8 17 0.33
9 19 0.37
10 4 0.08
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (8 bp):
AAAATAAT
Found at i:55234 original size:18 final size:18
Alignment explanation
Indices: 55211--55253 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
55201 TATTTTTTTA
* *
55211 AAATAAATGATAAGAATT
1 AAATAAAGGAAAAGAATT
*
55229 AAATAAAGGAAAATAATT
1 AAATAAAGGAAAAGAATT
55247 AAATAAA
1 AAATAAA
55254 CAAATTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.67, C:0.00, G:0.09, T:0.23
Consensus pattern (18 bp):
AAATAAAGGAAAAGAATT
Found at i:55956 original size:75 final size:76
Alignment explanation
Indices: 55862--56059 Score: 303
Period size: 76 Copynumber: 2.6 Consensus size: 76
55852 TTAAATCCTA
* * * *
55862 ATTAAAA-CTATTTAAACTAAAATACCTAAAACAAAAATAATAT-TTAAAATAATATTC-TAAAT
1 ATTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATA-TCATAAAA
55924 CCTAATTAAAAT
65 CCTAATTAAAAT
55936 ATTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCATAAAAC
1 ATTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCATAAAAC
*
56001 TTAATTAAAAT
66 CTAATTAAAAT
* *
56012 ACTAAAACCTATTTAAACTAAAATAACTAAAACAAAGATAAAATATAA
1 ATTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAA
56060 CGTTTAAAAT
Statistics
Matches: 114, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
74 7 0.06
75 36 0.32
76 71 0.62
ACGTcount: A:0.60, C:0.11, G:0.01, T:0.28
Consensus pattern (76 bp):
ATTAAAACCTATTTAAACTAAAATACCTAAAACAAAGATAAAATATAAAAATAATATCATAAAAC
CTAATTAAAAT
Found at i:59329 original size:6 final size:6
Alignment explanation
Indices: 59318--59352 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
59308 TTACAAACAA
59318 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCTCC
1 CCTCCC CCTCCC CCTCCC CCTCCC CCTCCC CCTCC
59353 ATCATCATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.00, C:0.83, G:0.00, T:0.17
Consensus pattern (6 bp):
CCTCCC
Found at i:60276 original size:24 final size:23
Alignment explanation
Indices: 60244--60297 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
60234 TGTTTATCTG
* * *
60244 AACCTAAAATCTAAATTCCTATT
1 AACCTAAAACCTAAAATCATATT
60267 AACCTTAAAACCTAAAATCATATT
1 AACC-TAAAACCTAAAATCATATT
60291 -ACCTAAA
1 AACCTAAA
60298 TCTTAAATAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.48, C:0.22, G:0.00, T:0.30
Consensus pattern (23 bp):
AACCTAAAACCTAAAATCATATT
Found at i:60877 original size:2 final size:2
Alignment explanation
Indices: 60829--60858 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
60819 TCGACTTTTG
60829 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60859 GGGTTTTCGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61282 original size:18 final size:18
Alignment explanation
Indices: 61261--61298 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
61251 TGAACTGGTT
*
61261 AACTTGTTAAAACTTGTC
1 AACTTCTTAAAACTTGTC
*
61279 AACTTCTTGAAACTTGTC
1 AACTTCTTAAAACTTGTC
61297 AA
1 AA
61299 TAACCTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (18 bp):
AACTTCTTAAAACTTGTC
Found at i:61503 original size:38 final size:37
Alignment explanation
Indices: 61379--61552 Score: 156
Period size: 37 Copynumber: 4.7 Consensus size: 37
61369 AATGTATTCC
* ** *
61379 AATCGAATATAAATTCGT-AATAATATATTCATATTA
1 AATCAAATATAAATTTATAAATAATATATTCATATTT
* * * **
61415 AATTAAATATAAATTCATAAATAACATATTTGTATTT
1 AATCAAATATAAATTTATAAATAATATATTCATATTT
*
61452 AATCAAATATAAATTTATAAATAATATATTCCTATTT
1 AATCAAATATAAATTTATAAATAATATATTCATATTT
* * *
61489 CAATCAAACATAAATTTGT-AATAATATATTCACATTTT
1 -AATCAAATATAAATTTATAAATAATATATTCATA-TTT
** *
61527 AATTGAATATATATCTT-TAAATAATA
1 AATCAAATATAAAT-TTATAAATAATA
61553 GAACATTATC
Statistics
Matches: 113, Mismatches: 20, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
36 15 0.13
37 70 0.62
38 28 0.25
ACGTcount: A:0.48, C:0.08, G:0.03, T:0.41
Consensus pattern (37 bp):
AATCAAATATAAATTTATAAATAATATATTCATATTT
Found at i:64006 original size:15 final size:15
Alignment explanation
Indices: 63986--64022 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
63976 AGGTTATTCA
63986 ATATATAATTTAT-AC
1 ATATATAATTT-TGAC
64001 ATATATAATTTTGAC
1 ATATATAATTTTGAC
64016 ATATATA
1 ATATATA
64023 GTTAGTAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (15 bp):
ATATATAATTTTGAC
Found at i:66255 original size:9 final size:9
Alignment explanation
Indices: 66239--66286 Score: 69
Period size: 9 Copynumber: 5.1 Consensus size: 9
66229 CAGCAACTAG
66239 AGAACAAAA
1 AGAACAAAA
*
66248 ACAACAAAAA
1 AGAAC-AAAA
66258 AGAACAAAA
1 AGAACAAAA
66267 AGAACAAAAA
1 AGAAC-AAAA
66277 AGAACAAAA
1 AGAACAAAA
66286 A
1 A
66287 CAAAAAGGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
9 18 0.51
10 17 0.49
ACGTcount: A:0.79, C:0.12, G:0.08, T:0.00
Consensus pattern (9 bp):
AGAACAAAA
Found at i:66263 original size:10 final size:10
Alignment explanation
Indices: 66239--66286 Score: 73
Period size: 10 Copynumber: 5.0 Consensus size: 10
66229 CAGCAACTAG
66239 AGAAC-AAAA
1 AGAACAAAAA
*
66248 ACAACAAAAA
1 AGAACAAAAA
66258 AGAAC-AAAA
1 AGAACAAAAA
66267 AGAACAAAAA
1 AGAACAAAAA
66277 AGAACAAAAA
1 AGAACAAAAA
66287 CAAAAAGGGA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
9 13 0.37
10 22 0.63
ACGTcount: A:0.79, C:0.12, G:0.08, T:0.00
Consensus pattern (10 bp):
AGAACAAAAA
Found at i:66263 original size:19 final size:19
Alignment explanation
Indices: 66239--66289 Score: 93
Period size: 19 Copynumber: 2.7 Consensus size: 19
66229 CAGCAACTAG
66239 AGAACAAAAACAACAAAAA
1 AGAACAAAAACAACAAAAA
*
66258 AGAACAAAAAGAACAAAAA
1 AGAACAAAAACAACAAAAA
66277 AGAACAAAAACAA
1 AGAACAAAAACAA
66290 AAAGGGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 30 1.00
ACGTcount: A:0.78, C:0.14, G:0.08, T:0.00
Consensus pattern (19 bp):
AGAACAAAAACAACAAAAA
Found at i:75409 original size:8 final size:8
Alignment explanation
Indices: 75396--75421 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
75386 AAAGATTCTC
75396 ATATGTAT
1 ATATGTAT
75404 ATATGTAT
1 ATATGTAT
75412 ATATGTAT
1 ATATGTAT
75420 AT
1 AT
75422 TATCTCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Done.