Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006994.1 Hibiscus syriacus cultivar Beakdansim tig00018033_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: 104793
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:1305 original size:19 final size:19
Alignment explanation
Indices: 1277--1337 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
1267 TTGTATTTAG
*
1277 TTTAAATAGGTTTTAGTAT
1 TTTAATTAGGTTTTAGTAT
*
1296 TTTAATTAGGATTTAGATAT
1 TTTAATTAGGTTTTAG-TAT
*
1316 TTT-ATTA-TTTTTAGGTAT
1 TTTAATTAGGTTTTA-GTAT
1334 TTTA
1 TTTA
1338 GTTTAAATAG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 10 0.29
19 19 0.54
20 6 0.17
ACGTcount: A:0.30, C:0.00, G:0.13, T:0.57
Consensus pattern (19 bp):
TTTAATTAGGTTTTAGTAT
Found at i:1320 original size:62 final size:63
Alignment explanation
Indices: 1272--1400 Score: 183
Period size: 62 Copynumber: 2.0 Consensus size: 63
1262 TATCTTTGTA
1272 TTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTT-AGATATTTTATTATTTTTAGGTAT
1 TTTAGTTTAAATA-GTTTTAAGTATTTTAATTAGGATTTAAGATATTTTATTATTTTTAGGTAT
* * *
1334 TTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTAAGATGTTTTAGCTTGTTTTTAGG-AT
1 TTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTTTA--TTATTTTTAGGTAT
1398 TTT
1 TTT
1401 GAAGGCTATA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
61 5 0.08
62 31 0.52
63 9 0.15
64 5 0.08
65 10 0.17
ACGTcount: A:0.27, C:0.01, G:0.16, T:0.56
Consensus pattern (63 bp):
TTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAAGATATTTTATTATTTTTAGGTAT
Found at i:1321 original size:75 final size:76
Alignment explanation
Indices: 1157--1328 Score: 221
Period size: 75 Copynumber: 2.3 Consensus size: 76
1147 TTAAACTCAA
* * **
1157 ATTTAGGATAATA-TTTTAAACATTATATTTATCTTTGTATTTTAATTTAAATAGGTTTTTAGTA
1 ATTTAGGATATTATTTTTATATTTTATATTTATCTTTGTATTTTAATTTAAATAGGTTTTTAGTA
1221 TTTTAATTAAG
66 TTTTAATTAAG
* * *
1232 TTTTAGGATATTATTTTTATATTTTATCTTTATCTTTGTA-TTTAGTTTAAATAGG-TTTTAGTA
1 ATTTAGGATATTATTTTTATATTTTATATTTATCTTTGTATTTTAATTTAAATAGGTTTTTAGTA
*
1295 TTTTAATTAGG
66 TTTTAATTAAG
*
1306 ATTTA-GATATT-TTATTAT-TTTTA
1 ATTTAGGATATTATTTTTATATTTTA
1329 GGTATTTTAG
Statistics
Matches: 86, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
71 5 0.06
72 6 0.07
73 6 0.07
74 22 0.26
75 25 0.29
76 22 0.26
ACGTcount: A:0.30, C:0.02, G:0.10, T:0.58
Consensus pattern (76 bp):
ATTTAGGATATTATTTTTATATTTTATATTTATCTTTGTATTTTAATTTAAATAGGTTTTTAGTA
TTTTAATTAAG
Found at i:1979 original size:18 final size:17
Alignment explanation
Indices: 1958--1997 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
1948 CTTTAATTTG
1958 TTTAATTAATTATTATT
1 TTTAATTAATTATTATT
* *
1975 ATTTATTTAATTCTTATT
1 -TTTAATTAATTATTATT
1993 TTTAA
1 TTTAA
1998 CCACAACTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
17 4 0.21
18 15 0.79
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTAATTAATTATTATT
Found at i:13069 original size:38 final size:38
Alignment explanation
Indices: 13026--13104 Score: 149
Period size: 38 Copynumber: 2.1 Consensus size: 38
13016 ATACCGTCTT
13026 ATATTCACTCTAGATAACGGAATCAAAGTTTATTCGAG
1 ATATTCACTCTAGATAACGGAATCAAAGTTTATTCGAG
*
13064 ATATTCACTCTAGATAACGGAATCAATGTTTATTCGAG
1 ATATTCACTCTAGATAACGGAATCAAAGTTTATTCGAG
13102 ATA
1 ATA
13105 GTGGAAGAGG
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 40 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (38 bp):
ATATTCACTCTAGATAACGGAATCAAAGTTTATTCGAG
Found at i:17336 original size:20 final size:19
Alignment explanation
Indices: 17298--17336 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
17288 ACATGCTCGA
*
17298 CAACTTCCTTGGACATGGC
1 CAACTTCCTTGCACATGGC
*
17317 CAACTTCTCTTGCACTTGGC
1 CAACTTC-CTTGCACATGGC
17337 TTCTATTCGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.18, C:0.33, G:0.18, T:0.31
Consensus pattern (19 bp):
CAACTTCCTTGCACATGGC
Found at i:18849 original size:16 final size:16
Alignment explanation
Indices: 18825--18858 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
18815 TATCGCCGAC
*
18825 CAAATTTCACTATTCA
1 CAAAATTCACTATTCA
18841 CAAAATTCACTATTCA
1 CAAAATTCACTATTCA
18857 CA
1 CA
18859 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.41, C:0.26, G:0.00, T:0.32
Consensus pattern (16 bp):
CAAAATTCACTATTCA
Found at i:19487 original size:2 final size:2
Alignment explanation
Indices: 19482--19631 Score: 279
Period size: 2 Copynumber: 76.5 Consensus size: 2
19472 TGTTACTAAT
19482 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
19524 AC AC AC AC AC AC AC AC AC A- AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
19565 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC -C AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
19606 AC AC AC AC AC AC AC AC -C AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC A
19632 TACTTACATA
Statistics
Matches: 145, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
1 3 0.02
2 142 0.98
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:19643 original size:4 final size:4
Alignment explanation
Indices: 19629--19861 Score: 457
Period size: 4 Copynumber: 58.2 Consensus size: 4
19619 CACCACACAC
*
19629 ACAT ACTT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
19677 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
19725 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
19773 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
19821 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
19862 TATGTCTATC
Statistics
Matches: 227, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
4 227 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:22200 original size:24 final size:24
Alignment explanation
Indices: 22147--22200 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
22137 GTGCCCTTGA
* *
22147 TAACCAGGAAATTGCCTGAGCTAC
1 TAACCGGGAAATTGCCTAAGCTAC
22171 TAACCGGGAAATTGCCTAAGCTAC
1 TAACCGGGAAATTGCCTAAGCTAC
*
22195 TCACCG
1 TAACCG
22201 TTGTTGAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.31, C:0.28, G:0.20, T:0.20
Consensus pattern (24 bp):
TAACCGGGAAATTGCCTAAGCTAC
Found at i:23427 original size:57 final size:57
Alignment explanation
Indices: 23354--23582 Score: 316
Period size: 57 Copynumber: 4.0 Consensus size: 57
23344 CAGAACCATA
* * * * *
23354 CAACCCCATCATGAACAATAAGACCCTAAGTACAAAACCGAGGAACTTGCAAGTATT
1 CAACCCCGTCACGAACAATAAGACCCTAAGCACAAAGCCGAGGAACCTGCAAGTATT
* **
23411 CAACCCCGTCACGAACAGTAAGACCCTCGGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAATAAGACCCTAAGCACAAAGCCGAGGAACCTGCAAGTATT
* *
23468 CAACCCCGTCACGAACAATAAGGCCCTTAGCACAAAGCCGAGGAACCTGCAAGTATT
1 CAACCCCGTCACGAACAATAAGACCCTAAGCACAAAGCCGAGGAACCTGCAAGTATT
* * * *
23525 CAACCCCGTCACGAATAGTAAGGCCCTCAA-CACAAAGCCGAGGAACTTGCAAGTATT
1 CAACCCCGTCACGAACAATAAGACCCT-AAGCACAAAGCCGAGGAACCTGCAAGTATT
23582 C
1 C
23583 TTCCTCCAAC
Statistics
Matches: 155, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
57 154 0.99
58 1 0.01
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.15
Consensus pattern (57 bp):
CAACCCCGTCACGAACAATAAGACCCTAAGCACAAAGCCGAGGAACCTGCAAGTATT
Found at i:23559 original size:114 final size:114
Alignment explanation
Indices: 23354--23582 Score: 350
Period size: 114 Copynumber: 2.0 Consensus size: 114
23344 CAGAACCATA
* * *
23354 CAACCCCATCATGAACAATAAGACCCTAAGTACAAAACCGAGGAACTTGCAAGTATTCAACCCCG
1 CAACCCCATCACGAACAATAAGACCCTAAGCACAAAACCGAGGAACCTGCAAGTATTCAACCCCG
**
23419 TCACGAACAGTAAGACCCTCGGCACAAAGCCGAGGAACCTGCAAGTATT
66 TCACGAACAGTAAGACCCTCAACACAAAGCCGAGGAACCTGCAAGTATT
* * * *
23468 CAACCCCGTCACGAACAATAAGGCCCTTAGCACAAAGCCGAGGAACCTGCAAGTATTCAACCCCG
1 CAACCCCATCACGAACAATAAGACCCTAAGCACAAAACCGAGGAACCTGCAAGTATTCAACCCCG
* * *
23533 TCACGAATAGTAAGGCCCTCAACACAAAGCCGAGGAACTTGCAAGTATT
66 TCACGAACAGTAAGACCCTCAACACAAAGCCGAGGAACCTGCAAGTATT
23582 C
1 C
23583 TTCCTCCAAC
Statistics
Matches: 103, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
114 103 1.00
ACGTcount: A:0.36, C:0.31, G:0.18, T:0.15
Consensus pattern (114 bp):
CAACCCCATCACGAACAATAAGACCCTAAGCACAAAACCGAGGAACCTGCAAGTATTCAACCCCG
TCACGAACAGTAAGACCCTCAACACAAAGCCGAGGAACCTGCAAGTATT
Found at i:23676 original size:24 final size:24
Alignment explanation
Indices: 23649--23698 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 24
23639 ATCAAAACAT
*
23649 AATCCATGTCAAGTATCATATCAG
1 AATCCAGGTCAAGTATCATATCAG
* * *
23673 AATCTAGGTCAGGTATTATATCAG
1 AATCCAGGTCAAGTATCATATCAG
23697 AA
1 AA
23699 ATCAAATAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.30
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCATATCAG
Found at i:25581 original size:64 final size:65
Alignment explanation
Indices: 25429--25588 Score: 193
Period size: 65 Copynumber: 2.5 Consensus size: 65
25419 AATTAAATTG
* * *
25429 AACATCGAATGCATTTCATGCATTGATGCA-CATACCATACATCGATGCACTGAGGATTTTATGA
1 AACATCGAATGCATTTAATGCATCGATGCACCATACCATACATCGATGCACTCAGGATTTTAT-A
25493 A
65 A
* * *
25494 AACATCGAATGCATTTAATGCATCGATGCACCA-GCCATGCATCGATGCACTCTGGCTATTTT-T
1 AACATCGAATGCATTTAATGCATCGATGCACCATACCATACATCGATGCACTCAGG--ATTTTAT
25557 -A
64 AA
* *
25558 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTAATGCATCGATGCAC
25589 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
64 30 0.36
65 46 0.55
66 3 0.04
67 5 0.06
ACGTcount: A:0.31, C:0.23, G:0.17, T:0.28
Consensus pattern (65 bp):
AACATCGAATGCATTTAATGCATCGATGCACCATACCATACATCGATGCACTCAGGATTTTATAA
Found at i:32227 original size:35 final size:34
Alignment explanation
Indices: 32155--32228 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 34
32145 CGTCACTAAC
**
32155 AGTAAGGCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCTGAGCACACAGCCGAGGAACCGCCA
*
32189 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGG-CCTGAGCACACAGCCGAGGAACCGCCA
32224 AGTAA
1 AGTAA
32229 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 7 0.19
35 29 0.81
ACGTcount: A:0.34, C:0.28, G:0.28, T:0.09
Consensus pattern (34 bp):
AGTAAGGCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:32366 original size:23 final size:23
Alignment explanation
Indices: 32306--32380 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
32296 CATAATTCAA
*
32306 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
32330 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
32354 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
32377 GTCA
1 GTCA
32381 GGATCATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:32386 original size:23 final size:23
Alignment explanation
Indices: 32310--32395 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
32300 ATTCAAGTCA
*
32310 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
32333 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
32357 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* * *
32380 AGGATCATAACAGAAT
1 AGTATCAGATCAGAAT
32396 TCAAGTCGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 33 0.61
24 21 0.39
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:33378 original size:26 final size:26
Alignment explanation
Indices: 33349--33401 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
33339 TCATTTTTAT
*
33349 TCCATTCATTTCAGAGCTCGATGATA
1 TCCAATCATTTCAGAGCTCGATGATA
* * *
33375 TCCAATCATTTCTGAGCTTGGTGATA
1 TCCAATCATTTCAGAGCTCGATGATA
33401 T
1 T
33402 TCTTGGGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (26 bp):
TCCAATCATTTCAGAGCTCGATGATA
Found at i:33500 original size:18 final size:18
Alignment explanation
Indices: 33479--33514 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
33469 CTTCCATCCG
*
33479 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
33497 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
33515 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:33981 original size:17 final size:18
Alignment explanation
Indices: 33949--33982 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
33939 AACTAACATT
33949 TTTTATGCACATCAATAG
1 TTTTATGCACATCAATAG
*
33967 TTTTA-GCAGATCAATA
1 TTTTATGCACATCAATA
33983 ATTCTTTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (18 bp):
TTTTATGCACATCAATAG
Found at i:34798 original size:10 final size:9
Alignment explanation
Indices: 34785--34825 Score: 50
Period size: 10 Copynumber: 4.6 Consensus size: 9
34775 GTCAAAGTTT
34785 TGGTCAACAG
1 TGGTCAAC-G
34795 TGGTCAACG
1 TGGTCAACG
34804 TGGGTCAACG
1 T-GGTCAACG
34814 -GGTCAACG
1 TGGTCAACG
34822 -GGTC
1 TGGTC
34826 GGGTCAACGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 12 0.40
9 2 0.07
10 16 0.53
ACGTcount: A:0.22, C:0.22, G:0.37, T:0.20
Consensus pattern (9 bp):
TGGTCAACG
Found at i:34818 original size:8 final size:8
Alignment explanation
Indices: 34786--34839 Score: 51
Period size: 8 Copynumber: 6.6 Consensus size: 8
34776 TCAAAGTTTT
34786 GGTCAACAG
1 GGTCAAC-G
34795 TGGTCAACGTG
1 -GGTCAAC--G
34806 GGTCAACG
1 GGTCAACG
34814 GGTCAACG
1 GGTCAACG
34822 GGT---CG
1 GGTCAACG
34827 GGTCAACG
1 GGTCAACG
34835 GGTCA
1 GGTCA
34840 GGTCAGGTCA
Statistics
Matches: 39, Mismatches: 1, Indels: 10
0.78 0.02 0.20
Matches are distributed among these distances:
5 5 0.13
8 19 0.49
10 14 0.36
11 1 0.03
ACGTcount: A:0.22, C:0.22, G:0.39, T:0.17
Consensus pattern (8 bp):
GGTCAACG
Found at i:34830 original size:13 final size:13
Alignment explanation
Indices: 34812--34887 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
34802 CGTGGGTCAA
34812 CGGGTCAACGGGT
1 CGGGTCAACGGGT
34825 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
34838 CAGGTCAGGTCAACTGGT
1 C--G---GGTCAACGGGT
*
34856 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
34869 CGGGTAAACGGGT
1 CGGGTCAACGGGT
34882 CGGGTC
1 CGGGTC
34888 GGGTTATGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
15 1 0.02
16 1 0.02
18 11 0.20
ACGTcount: A:0.18, C:0.21, G:0.43, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:36914 original size:33 final size:34
Alignment explanation
Indices: 36843--36915 Score: 103
Period size: 33 Copynumber: 2.1 Consensus size: 34
36833 CGTCACTAAC
**
36843 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAG-ACACAGCCGAGGAACCGCCA
*
36878 AGTAAGGCCCTGAG-CACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGACACAGCCGAGGAACCGCCA
36911 AGTAA
1 AGTAA
36916 TATACTTCCG
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
33 21 0.60
35 14 0.40
ACGTcount: A:0.33, C:0.29, G:0.29, T:0.10
Consensus pattern (34 bp):
AGTAAGGCCCTGAGACACAGCCGAGGAACCGCCA
Found at i:38020 original size:35 final size:35
Alignment explanation
Indices: 37947--38021 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
37937 CGTCACTAAC
**
37947 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
37982 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
38017 AGTAA
1 AGTAA
38022 TATACTTCCG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:39128 original size:35 final size:35
Alignment explanation
Indices: 39055--39129 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
39045 CGTCACTAAC
**
39055 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
39090 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
39125 AGTAA
1 AGTAA
39130 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:39267 original size:23 final size:23
Alignment explanation
Indices: 39207--39281 Score: 105
Period size: 24 Copynumber: 3.2 Consensus size: 23
39197 CATAATTCAA
*
39207 GTCAAGTATCATATCAGAATCCAG
1 GTCAA-TATCAGATCAGAATCCAG
* *
39231 GTCATGTATCAGATCAGAATCCAT
1 GTCA-ATATCAGATCAGAATCCAG
39255 GTCAATATCAGATCAGAATCCAG
1 GTCAATATCAGATCAGAATCCAG
39278 GTCA
1 GTCA
39282 GGATCATAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
23 21 0.47
24 24 0.53
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.25
Consensus pattern (23 bp):
GTCAATATCAGATCAGAATCCAG
Found at i:39287 original size:23 final size:23
Alignment explanation
Indices: 39211--39296 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
39201 ATTCAAGTCA
*
39211 AGTATCATATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
*
39234 ATGTATCAGATCAGAATCCATGTC
1 A-GTATCAGATCAGAATCCAGGTC
*
39258 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCAGGTC
* * *
39281 AGGATCATAACAGAAT
1 AGTATCAGATCAGAAT
39297 TCAAGTCGAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
23 33 0.61
24 21 0.39
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.24
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCAGGTC
Found at i:40280 original size:26 final size:26
Alignment explanation
Indices: 40251--40303 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
40241 TCATTTTTAT
*
40251 TCCATTCATTTCAGAGCTCGATGATA
1 TCCAATCATTTCAGAGCTCGATGATA
* * *
40277 TCCAATCATTTCTGAGCTTGGTGATA
1 TCCAATCATTTCAGAGCTCGATGATA
40303 T
1 T
40304 TCTTGGGTCA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.25, C:0.21, G:0.17, T:0.38
Consensus pattern (26 bp):
TCCAATCATTTCAGAGCTCGATGATA
Found at i:40402 original size:18 final size:18
Alignment explanation
Indices: 40381--40416 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
40371 CTTCCATCCG
*
40381 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
40399 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
40417 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:41725 original size:7 final size:7
Alignment explanation
Indices: 41713--41751 Score: 60
Period size: 7 Copynumber: 5.3 Consensus size: 7
41703 GGTCAACGTG
41713 GGTCAAC
1 GGTCAAC
41720 GGTCAAC
1 GGTCAAC
41727 GGGTCAAC
1 -GGTCAAC
41735 GGTCAAC
1 GGTCAAC
41742 GGGTCAAC
1 -GGTCAAC
41750 GG
1 GG
41752 GTCGGGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 16 0.53
8 14 0.47
ACGTcount: A:0.26, C:0.26, G:0.36, T:0.13
Consensus pattern (7 bp):
GGTCAAC
Found at i:41732 original size:15 final size:15
Alignment explanation
Indices: 41712--41751 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
41702 TGGTCAACGT
41712 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
41727 GGGTCAACGGTCAAC
1 GGGTCAACGGTCAAC
41742 GGGTCAACGG
1 GGGTCAACGG
41752 GTCGGGTCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.25, C:0.25, G:0.38, T:0.12
Consensus pattern (15 bp):
GGGTCAACGGTCAAC
Found at i:41733 original size:8 final size:8
Alignment explanation
Indices: 41693--41767 Score: 79
Period size: 8 Copynumber: 9.5 Consensus size: 8
41683 TCAAAGTTTT
41693 GGTCAACAG
1 GGTCAAC-G
41702 TGGTCAACGTG
1 -GGTCAAC--G
41713 GGTCAAC-
1 GGTCAACG
41720 GGTCAACG
1 GGTCAACG
41728 GGTCAAC-
1 GGTCAACG
41735 GGTCAACG
1 GGTCAACG
41743 GGTCAACG
1 GGTCAACG
41751 GGT---CG
1 GGTCAACG
41756 GGTCAACG
1 GGTCAACG
41764 GGTC
1 GGTC
41768 GGGTCAGGTC
Statistics
Matches: 58, Mismatches: 1, Indels: 14
0.79 0.01 0.19
Matches are distributed among these distances:
5 5 0.09
7 14 0.24
8 24 0.41
10 14 0.24
11 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.37, T:0.16
Consensus pattern (8 bp):
GGTCAACG
Found at i:41759 original size:13 final size:13
Alignment explanation
Indices: 41741--41816 Score: 80
Period size: 13 Copynumber: 5.5 Consensus size: 13
41731 CAACGGTCAA
41741 CGGGTCAACGGGT
1 CGGGTCAACGGGT
41754 CGGGTCAACGGGT
1 CGGGTCAACGGGT
*
41767 CGGGTCAGGTCAACTGGT
1 C--G---GGTCAACGGGT
*
41785 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
41798 CGGGTAAACGGGT
1 CGGGTCAACGGGT
41811 CGGGTC
1 CGGGTC
41817 GGGTTATGAC
Statistics
Matches: 54, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
13 41 0.76
15 1 0.02
16 1 0.02
18 11 0.20
ACGTcount: A:0.17, C:0.21, G:0.45, T:0.17
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:41772 original size:18 final size:18
Alignment explanation
Indices: 41735--41789 Score: 65
Period size: 18 Copynumber: 2.9 Consensus size: 18
41725 ACGGGTCAAC
*
41735 GGTCAACGGGTCAACGGGTCG
1 GGTCAACGGGT---CGGGTCA
41756 GGTCAACGGGTCGGGTCA
1 GGTCAACGGGTCGGGTCA
*
41774 GGTCAACTGGTCGGGT
1 GGTCAACGGGTCGGGT
41790 AAACGGGTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
18 21 0.66
21 11 0.34
ACGTcount: A:0.16, C:0.22, G:0.44, T:0.18
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCA
Found at i:41786 original size:31 final size:31
Alignment explanation
Indices: 41743--41802 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
41733 ACGGTCAACG
*
41743 GGTCAACGGGTCGGGTCAACGGGTCGGGTCA
1 GGTCAACGGGTCGGGTAAACGGGTCGGGTCA
*
41774 GGTCAACTGGTCGGGTAAACGGGTCGGGT
1 GGTCAACGGGTCGGGTAAACGGGTCGGGT
41803 AAACGGGTCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.17, C:0.20, G:0.45, T:0.18
Consensus pattern (31 bp):
GGTCAACGGGTCGGGTAAACGGGTCGGGTCA
Found at i:43125 original size:21 final size:21
Alignment explanation
Indices: 43099--43143 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
43089 GATTTCTGGG
* *
43099 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
43120 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
43141 CAA
1 CAA
43144 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:44012 original size:32 final size:32
Alignment explanation
Indices: 43971--44066 Score: 126
Period size: 32 Copynumber: 3.0 Consensus size: 32
43961 GAGTCGAGGG
43971 TTTACCTATGTTCTACGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
44003 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
44034 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
44066 T
1 T
44067 ACCGAGGATC
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
31 26 0.47
32 29 0.53
ACGTcount: A:0.29, C:0.18, G:0.19, T:0.34
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:44183 original size:29 final size:30
Alignment explanation
Indices: 44058--44180 Score: 203
Period size: 30 Copynumber: 4.1 Consensus size: 30
44048 AAGGAACATA
44058 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
44088 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
*
44118 TGGACAATTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
44148 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
44177 TGGA
1 TGGA
44181 TAGGTCCTTC
Statistics
Matches: 88, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
29 18 0.20
30 70 0.80
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:44463 original size:2 final size:2
Alignment explanation
Indices: 44453--44496 Score: 61
Period size: 2 Copynumber: 22.0 Consensus size: 2
44443 TGTATGTGTG
* * *
44453 AT AT GT AT AT AT AT AG AT AG 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 AT AT AT AT AT AT
44495 AT
1 AT
44497 GAAAGGTGCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (2 bp):
AT
Found at i:47765 original size:12 final size:13
Alignment explanation
Indices: 47741--47771 Score: 55
Period size: 12 Copynumber: 2.5 Consensus size: 13
47731 TCTTGAAATA
47741 GAATTTATAAGTT
1 GAATTTATAAGTT
47754 GAATTT-TAAGTT
1 GAATTTATAAGTT
47766 GAATTT
1 GAATTT
47772 GACTTGTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 12 0.67
13 6 0.33
ACGTcount: A:0.35, C:0.00, G:0.16, T:0.48
Consensus pattern (13 bp):
GAATTTATAAGTT
Found at i:48034 original size:21 final size:21
Alignment explanation
Indices: 48008--48052 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
47998 GATTTCTGGG
* *
48008 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
48029 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
48050 CAA
1 CAA
48053 ACGACAGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:48122 original size:23 final size:22
Alignment explanation
Indices: 48078--48122 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
48068 AATGCCAGAG
*
48078 GGGAACCGATACCCCCACAGGA
1 GGGAACCGATACCCCCAAAGGA
* *
48100 GGGAATCGATTCCCCCTAAAGGA
1 GGGAACCGATACCCCC-AAAGGA
48123 AAATGTTAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.31, C:0.31, G:0.27, T:0.11
Consensus pattern (22 bp):
GGGAACCGATACCCCCAAAGGA
Found at i:48921 original size:32 final size:32
Alignment explanation
Indices: 48880--48975 Score: 108
Period size: 32 Copynumber: 3.0 Consensus size: 32
48870 GAGTCGAGGG
*
48880 TTTACCTATGTTCTACGGAATATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
* *
48912 TTTACCTATG-TCTTTC-GAGACATATGGATAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
48943 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
48975 T
1 T
48976 ACCGAGGATC
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
31 25 0.48
32 27 0.52
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:48966 original size:31 final size:30
Alignment explanation
Indices: 48881--48978 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
48871 AGTCGAGGGT
* *
48881 TTACCTATGTTCTACGGAATATATGGACAG
1 TTACCTATGTTCTAAGGAACATATGGACAG
*** *
48911 TTTTACCTATG-TCTTTCGAGACATATGGATAG
1 --TTACCTATGTTCTAAGGA-ACATATGGACAG
48943 TATACCTATGTTCTAAGGAACATATGGACAG
1 T-TACCTATGTTCTAAGGAACATATGGACAG
48974 TTACC
1 TTACC
48979 GAGGATCTTT
Statistics
Matches: 54, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
30 5 0.09
31 25 0.46
32 24 0.44
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (30 bp):
TTACCTATGTTCTAAGGAACATATGGACAG
Found at i:49092 original size:29 final size:30
Alignment explanation
Indices: 48967--49089 Score: 212
Period size: 30 Copynumber: 4.1 Consensus size: 30
48957 AAGGAACATA
48967 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
48997 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
49027 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * *
49057 TGGATAGTTACCG-GGGTCTTTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
49086 TGGA
1 TGGA
49090 TAGGTCCTTC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
29 18 0.20
30 72 0.80
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:49347 original size:2 final size:2
Alignment explanation
Indices: 49337--49400 Score: 119
Period size: 2 Copynumber: 32.0 Consensus size: 2
49327 TGTATGTGTG
*
49337 AT AT GT AT AT AT 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 AT AT AT AT AT AT
49379 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
49401 GAAGGTGCAT
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52735 original size:64 final size:63
Alignment explanation
Indices: 52667--52825 Score: 203
Period size: 64 Copynumber: 2.5 Consensus size: 63
52657 AATTAAATTG
* * * * *
52667 AACATCGAATGTATTTCATGCATCGATGCACATACCATGCATTGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCAATGCACAT-CCATGCATCGATGCACTCAGGATATTT-TGA
* * *
52731 AACATCGAATGCATTTGATGCATCCATGCACCATCCATGCATCGATGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCAATGCA-CATCCATGCATCGATGCACTCAGGATATTTTGA
*
52795 AACATCGAATGCACTTGATGCATCAATGCAC
1 AACATCGAATGCATTTGATGCATCAATGCAC
52826 TCTTAGTGCA
Statistics
Matches: 84, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
63 1 0.01
64 77 0.92
65 6 0.07
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCAATGCACATCCATGCATCGATGCACTCAGGATATTTTGA
Found at i:55364 original size:18 final size:18
Alignment explanation
Indices: 55341--55375 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
55331 AAACAATCCC
* *
55341 TTAGTCGACAAGAGAAAG
1 TTAGTCAACAAAAGAAAG
55359 TTAGTCAACAAAAGAAA
1 TTAGTCAACAAAAGAAA
55376 AGAAGTGAGC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.51, C:0.11, G:0.20, T:0.17
Consensus pattern (18 bp):
TTAGTCAACAAAAGAAAG
Found at i:57506 original size:45 final size:45
Alignment explanation
Indices: 57442--57554 Score: 217
Period size: 45 Copynumber: 2.5 Consensus size: 45
57432 TCTTTTATGT
57442 TTGGCTCCTCAACATGATCAGCACTATTTTCTGCCGCTGTATTCC
1 TTGGCTCCTCAACATGATCAGCACTATTTTCTGCCGCTGTATTCC
*
57487 TTGGCTCCTCAACATGATCAGCACTATTTTCTGCCGCTGTCTTCC
1 TTGGCTCCTCAACATGATCAGCACTATTTTCTGCCGCTGTATTCC
57532 TTGGCTCCTCAACATGATCAGCA
1 TTGGCTCCTCAACATGATCAGCA
57555 GTAATATCTT
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 67 1.00
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.34
Consensus pattern (45 bp):
TTGGCTCCTCAACATGATCAGCACTATTTTCTGCCGCTGTATTCC
Found at i:59087 original size:6 final size:6
Alignment explanation
Indices: 59076--59105 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
59066 GCACCTGTCT
59076 TAGCAG TAGCAG TAGCAG TAGCAG TAGCAG
1 TAGCAG TAGCAG TAGCAG TAGCAG TAGCAG
59106 CAGGAGCTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (6 bp):
TAGCAG
Found at i:63760 original size:18 final size:18
Alignment explanation
Indices: 63733--63767 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
63723 GTGCTCTCGT
63733 TCTCTCTCCTTCTCCCGC
1 TCTCTCTCCTTCTCCCGC
*
63751 TCTCTTTCCTTCTCCCG
1 TCTCTCTCCTTCTCCCG
63768 TCGCTCCAAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.00, C:0.51, G:0.06, T:0.43
Consensus pattern (18 bp):
TCTCTCTCCTTCTCCCGC
Found at i:76884 original size:14 final size:14
Alignment explanation
Indices: 76865--76899 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
76855 GTTTAGGATA
76865 ATATTTTAATCATT
1 ATATTTTAATCATT
*
76879 ATATTTT-ATCTTT
1 ATATTTTAATCATT
76892 ATATTTTA
1 ATATTTTA
76900 GTTTAAATAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
13 12 0.63
14 7 0.37
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.63
Consensus pattern (14 bp):
ATATTTTAATCATT
Found at i:76935 original size:75 final size:75
Alignment explanation
Indices: 76856--77073 Score: 209
Period size: 76 Copynumber: 3.0 Consensus size: 75
76846 TAAACTCAAG
76856 TTTAGGATAATATTTTAATCATTATAT-TTTATCTTTA-TATTTTAGTTTAAATAGGTTTTAGTA
1 TTTAGGATAATATTTTAAT-ATTATATCTTTAT-TTTAGTATTTTAGTTTAAATAGGTTTTAGTA
76919 TTTTAATTAAGT
64 TTTTAATTAAGT
* * * * * *
76931 TTTAGGATATTATTTTTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTGT
1 TTTAGGATAATATTTTAATATTATATCTTTATTTTA-GTATTTTAGTTTAAATAGGTTTTAGTAT
* *
76996 TTTAATTAGGA
65 TTTAATTAAGT
* * * * ** *
77007 TTTAGAATATTAGTTTAA-A-TAT-T-ATT-TTTGGGTATTTTAGTTTAAATA-GTTTTAAGTGT
1 TTTAGGATAATATTTTAATATTATATCTTTATTTTAGTATTTTAGTTTAAATAGGTTTT-AGTAT
77066 TTTAATTA
65 TTTAATTA
77074 GGATTTAAGA
Statistics
Matches: 124, Mismatches: 15, Indels: 13
0.82 0.10 0.09
Matches are distributed among these distances:
69 5 0.04
70 30 0.24
71 3 0.02
72 2 0.02
73 1 0.01
74 12 0.10
75 22 0.18
76 49 0.40
ACGTcount: A:0.29, C:0.01, G:0.12, T:0.57
Consensus pattern (75 bp):
TTTAGGATAATATTTTAATATTATATCTTTATTTTAGTATTTTAGTTTAAATAGGTTTTAGTATT
TTAATTAAGT
Found at i:77069 original size:70 final size:75
Alignment explanation
Indices: 76893--77080 Score: 235
Period size: 76 Copynumber: 2.6 Consensus size: 75
76883 TTTATCTTTA
* * * * * *
76893 TATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTATC
1 TATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATTATGTTTATA-TATATC
*
76958 TTTGTTTTAGG
65 TATGTTTTAGG
*
76969 TATTTTAGTTTAAATATGTTTTAGTGTTTTAATTAGGATTTAGAATATTA-GTTTA-A-ATAT-T
1 TATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATTATGTTTATATATATCT
*
77030 AT-TTTTGGG
66 ATGTTTTAGG
77039 TATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 TATTTTAGTTTAAATAGGTTTT-AGTGTTTTAATTAGGATTTA
77081 AGATATTTTT
Statistics
Matches: 102, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
69 5 0.05
70 42 0.41
71 2 0.02
72 3 0.03
74 1 0.01
75 4 0.04
76 45 0.44
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (75 bp):
TATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATTATGTTTATATATATCT
ATGTTTTAGG
Found at i:77087 original size:70 final size:75
Alignment explanation
Indices: 76893--77087 Score: 233
Period size: 70 Copynumber: 2.7 Consensus size: 75
76883 TTTATCTTTA
* * * * * *
76893 TATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTATC
1 TATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAAGATATTATGTTTATA-TATATC
*
76958 TTTGTTTTAGG
65 TATGTTTTAGG
*
76969 TATTTTAGTTTAAATATGTTTTAGTGTTTTAATTAGGATTT-AGAATATTA-GTTTA-A-ATAT-
1 TATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAAG-ATATTATGTTTATATATATC
*
77029 TAT-TTTTGGG
65 TATGTTTTAGG
77039 TATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTAAGATATT
1 TATTTTAGTTTAAATAGGTTTT-AGTGTTTTAATTAGGATTTAAGATATT
77088 TTTGCTTGTT
Statistics
Matches: 107, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
69 5 0.05
70 46 0.43
71 4 0.04
72 3 0.03
74 1 0.01
75 5 0.05
76 43 0.40
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (75 bp):
TATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAAGATATTATGTTTATATATATCT
ATGTTTTAGG
Found at i:77957 original size:17 final size:17
Alignment explanation
Indices: 77935--77970 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
77925 CAACCCGACA
* *
77935 GACCCGGCCTGACCGTT
1 GACCCGACCCGACCGTT
77952 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
77969 GA
1 GA
77971 ACGTTGACCT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.17, C:0.42, G:0.28, T:0.14
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:80049 original size:17 final size:17
Alignment explanation
Indices: 80024--80057 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
80014 CTTTATCTCA
*
80024 ATTTATTTATTTTATTT
1 ATTTATTTATTTAATTT
*
80041 ATTTGTTTATTTAATTT
1 ATTTATTTATTTAATTT
80058 TTATCTCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.74
Consensus pattern (17 bp):
ATTTATTTATTTAATTT
Found at i:83342 original size:21 final size:21
Alignment explanation
Indices: 83328--83377 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
83318 AAAAGTTTAG
83328 CTAAGCATGACAAAAGTCATA
1 CTAAGCATGACAAAAGTCATA
*
83349 CTTAGCATGACAAAAGTCATA
1 CTAAGCATGACAAAAGTCATA
*
83370 CTTAGCAT
1 CTAAGCAT
83378 AAAAATAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (21 bp):
CTAAGCATGACAAAAGTCATA
Found at i:86139 original size:24 final size:24
Alignment explanation
Indices: 86112--86211 Score: 78
Period size: 24 Copynumber: 4.2 Consensus size: 24
86102 GATATCAAAA
*
86112 ATCAAAACATAATTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * *
86136 ATCATAACAGAATCCATG-TTAGGA-
1 ATCAAAACAGAATTCA-GATCA-GAT
* *
86160 ATCAGAACAGATTTCAGATCAGAT
1 ATCAAAACAGAATTCAGATCAGAT
* * * *
86184 GTCAAAACATAATTCAAATCAGAA
1 ATCAAAACAGAATTCAGATCAGAT
86208 ATCA
1 ATCA
86212 GATAAAATAT
Statistics
Matches: 57, Mismatches: 15, Indels: 8
0.71 0.19 0.10
Matches are distributed among these distances:
23 3 0.05
24 51 0.89
25 3 0.05
ACGTcount: A:0.47, C:0.17, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAAAACAGAATTCAGATCAGAT
Found at i:86211 original size:48 final size:48
Alignment explanation
Indices: 86105--86213 Score: 110
Period size: 48 Copynumber: 2.3 Consensus size: 48
86095 AAACGGAGAT
* * * * *
86105 ATCAAAAATCAAAACATAATTCAGATCAGATATCATAACAGAATCCAT
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
* * * * * * *
86153 GTTAGGAATCAGAACAGATTTCAGATCAGATGTCAAAACATAATTCAA
1 ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
86201 ATCAGAAATCAGA
1 ATCAGAAATCAGA
86214 TAAAATATTC
Statistics
Matches: 46, Mismatches: 15, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.49, C:0.17, G:0.12, T:0.23
Consensus pattern (48 bp):
ATCAGAAATCAGAACAGAATTCAGATCAGATATCAAAACAGAATCCAA
Found at i:87375 original size:18 final size:18
Alignment explanation
Indices: 87354--87389 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
87344 CTTCCATCCG
*
87354 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
87372 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
87390 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:88725 original size:13 final size:13
Alignment explanation
Indices: 88707--88761 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
88697 CGCCGGTCAA
88707 CGGGTCAACGGGT
1 CGGGTCAACGGGT
88720 CGGGTCAACGGGT
1 CGGGTCAACGGGT
88733 CGGGT---CGGGT
1 CGGGTCAACGGGT
*
88743 CGGGTAAACGGGT
1 CGGGTCAACGGGT
*
88756 TGGGTC
1 CGGGTC
88762 GGGTTGTGAC
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
10 10 0.27
13 27 0.73
ACGTcount: A:0.13, C:0.20, G:0.49, T:0.18
Consensus pattern (13 bp):
CGGGTCAACGGGT
Found at i:88745 original size:23 final size:23
Alignment explanation
Indices: 88715--88765 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
88705 AACGGGTCAA
*
88715 CGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGGTAAACGGGTCGGGT
*
88738 CGGGTCGGGTAAACGGGTTGGGT
1 CGGGTCGGGTAAACGGGTCGGGT
88761 CGGGT
1 CGGGT
88766 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.10, C:0.18, G:0.53, T:0.20
Consensus pattern (23 bp):
CGGGTCGGGTAAACGGGTCGGGT
Found at i:89831 original size:3 final size:3
Alignment explanation
Indices: 89823--89882 Score: 84
Period size: 3 Copynumber: 19.0 Consensus size: 3
89813 CAGTTTGTTT
*
89823 TTA TTA TTA TTA TTA TTA TTA TTA TACA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA -TTA TTA
89870 TTTA TTA TTA TTA
1 -TTA TTA TTA TTA
89883 ATAAATAAAT
Statistics
Matches: 52, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
3 44 0.85
4 8 0.15
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:89867 original size:13 final size:13
Alignment explanation
Indices: 89822--89882 Score: 76
Period size: 13 Copynumber: 5.0 Consensus size: 13
89812 TCAGTTTGTT
89822 TTTATTATTATTA
1 TTTATTATTATTA
89835 -TTATTATTATTA
1 TTTATTATTATTA
**
89847 TACATTATTATTA
1 TTTATTATTATTA
89860 -TTA-T-TTATTA
1 TTTATTATTATTA
89870 TTTATTATTATTA
1 TTTATTATTATTA
89883 ATAAATAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
10 6 0.15
11 4 0.10
12 14 0.35
13 16 0.40
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.66
Consensus pattern (13 bp):
TTTATTATTATTA
Found at i:91354 original size:37 final size:37
Alignment explanation
Indices: 91286--91394 Score: 97
Period size: 37 Copynumber: 3.0 Consensus size: 37
91276 ATTACAAGTT
*
91286 TTATTTTT-TT-TTA-CATTTTATTATTATTATTTTAA-
1 TTATTTTTATTATTATCATTTT-TAATTA-TATTTTAAC
91321 TT-TTATTTATT-TTAGTCATTGTTTAATTATATTTTAAC
1 TTATT-TTTATTATTA-TCATT-TTTAATTATATTTTAAC
*
91359 TTAATTTTTATTATTATTATTTTTAA-TATATTTTAA
1 TT-ATTTTTATTATTATCATTTTTAATTATATTTTAA
91395 ATCATTACTT
Statistics
Matches: 63, Mismatches: 2, Indels: 16
0.78 0.02 0.20
Matches are distributed among these distances:
34 2 0.03
35 5 0.08
36 5 0.08
37 18 0.29
38 16 0.25
39 12 0.19
40 5 0.08
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (37 bp):
TTATTTTTATTATTATCATTTTTAATTATATTTTAAC
Found at i:91392 original size:25 final size:26
Alignment explanation
Indices: 91364--91453 Score: 62
Period size: 25 Copynumber: 3.4 Consensus size: 26
91354 TTAACTTAAT
*
91364 TTTTATTATTATTATTTTTAA-TA-TA
1 TTTTATTATTATTA-CTTTAATTATTA
* *
91389 TTTTA-AATCATTACTTTAATTATTA
1 TTTTATTATTATTACTTTAATTATTA
91414 TTTTATTA-TATTAGTCTTATAATTATATA
1 TTTTATTATTATTA--CTT-TAATTAT-TA
*
91443 TATTTTTTATT
1 T-TTTATTATT
91454 TATTTAATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
23 5 0.10
24 8 0.16
25 16 0.32
26 1 0.02
27 3 0.06
28 7 0.14
29 3 0.06
30 6 0.12
31 1 0.02
ACGTcount: A:0.32, C:0.03, G:0.01, T:0.63
Consensus pattern (26 bp):
TTTTATTATTATTACTTTAATTATTA
Found at i:91561 original size:22 final size:22
Alignment explanation
Indices: 91536--91581 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
91526 GGTATTTTAA
91536 ATAATTAAATATTATAAAAATT
1 ATAATTAAATATTATAAAAATT
* * **
91558 ATAATTTAATTTTATTTAAATT
1 ATAATTAAATATTATAAAAATT
91580 AT
1 AT
91582 TTTTTAGGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
ATAATTAAATATTATAAAAATT
Done.