Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003304.1 Hibiscus syriacus cultivar Beakdansim tig00006950_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: 84212
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2879 original size:36 final size:36
Alignment explanation
Indices: 2832--2907 Score: 145
Period size: 36 Copynumber: 2.1 Consensus size: 36
2822 CTACTTCCCC
2832 TTTA-CCCCATTACATATAGGAATAGTGTCAGCTAA
1 TTTACCCCCATTACATATAGGAATAGTGTCAGCTAA
2867 TTTACCCCCATTACATATAGGAATAGTGTCAGCTAA
1 TTTACCCCCATTACATATAGGAATAGTGTCAGCTAA
2903 TTTAC
1 TTTAC
2908 TAATTTATGT
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
35 4 0.10
36 36 0.90
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (36 bp):
TTTACCCCCATTACATATAGGAATAGTGTCAGCTAA
Found at i:14112 original size:35 final size:36
Alignment explanation
Indices: 14071--14146 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
14061 TTCATGTTCA
*
14071 AAATTCC-AAAACACTTCAATTGCATTCTAAACCCC
1 AAATTCCAAAAACACTTCAATTACATTCTAAACCCC
* * *
14106 AAATTCCAAAAATACTTTAATTACATTCTAAACCCT
1 AAATTCCAAAAACACTTCAATTACATTCTAAACCCC
14142 AAATT
1 AAATT
14147 AAAGTATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 7 0.19
36 29 0.81
ACGTcount: A:0.43, C:0.25, G:0.01, T:0.30
Consensus pattern (36 bp):
AAATTCCAAAAACACTTCAATTACATTCTAAACCCC
Found at i:14190 original size:35 final size:35
Alignment explanation
Indices: 14142--14218 Score: 100
Period size: 35 Copynumber: 2.2 Consensus size: 35
14132 TCTAAACCCT
* * *
14142 AAATTAAAGTATTTTATAATTTAAGGTTTAAAATA
1 AAATTGAATTATTTTAGAATTTAAGGTTTAAAATA
* **
14177 TAATTGAATTATTTTAGAATTTGGGGTTTAAAATA
1 AAATTGAATTATTTTAGAATTTAAGGTTTAAAATA
14212 AAATTGA
1 AAATTGA
14219 GAACTATGTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.44, C:0.00, G:0.13, T:0.43
Consensus pattern (35 bp):
AAATTGAATTATTTTAGAATTTAAGGTTTAAAATA
Found at i:15334 original size:23 final size:23
Alignment explanation
Indices: 15308--15355 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
15298 TATGATCATG
*
15308 ACTTTACTAATTTATAACAACTA
1 ACTTTACTAACTTATAACAACTA
* * *
15331 ACTTTTCTAACTTCTAACTACTA
1 ACTTTACTAACTTATAACAACTA
15354 AC
1 AC
15356 CACTAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.40
Consensus pattern (23 bp):
ACTTTACTAACTTATAACAACTA
Found at i:15641 original size:71 final size:71
Alignment explanation
Indices: 15548--15713 Score: 179
Period size: 71 Copynumber: 2.3 Consensus size: 71
15538 ATTTTCCTTT
* * * * * *
15548 ATTTTATTTTAGTCCATAAAATTACATTACTTTAATTTGCTGCCTTCTATTTATGTCCTTTACTT
1 ATTTAATTTCAGTCC-TTAAATTACATGACTTTAATTTGCTGCCTTCTATTTATCTCCTCTACTT
*
15613 TTCAGTG
65 TTCAGTA
* ** * * * *
15620 ATTTAATTTGAGTCCTTAAATTTTATGATTTTAATTTTCTGCCTTTTATTTCTCTCCTCTACTTT
1 ATTTAATTTCAGTCCTTAAATTACATGACTTTAATTTGCTGCCTTCTATTTATCTCCTCTACTTT
*
15685 TTAGTA
66 TCAGTA
*
15691 ATTTAATTTCAGTCCTTTAATTA
1 ATTTAATTTCAGTCCTTAAATTA
15714 TTGCATTCTA
Statistics
Matches: 77, Mismatches: 17, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
71 64 0.83
72 13 0.17
ACGTcount: A:0.23, C:0.16, G:0.07, T:0.54
Consensus pattern (71 bp):
ATTTAATTTCAGTCCTTAAATTACATGACTTTAATTTGCTGCCTTCTATTTATCTCCTCTACTTT
TCAGTA
Found at i:19034 original size:18 final size:18
Alignment explanation
Indices: 19011--19077 Score: 80
Period size: 18 Copynumber: 3.7 Consensus size: 18
19001 ACTGTATACA
* *
19011 AACCCTGAATCCGACCTG
1 AACCCTAAACCCGACCTG
*
19029 AACCCTAAACCCGATCTG
1 AACCCTAAACCCGACCTG
* **
19047 AACCCTAAAACCGGTCTG
1 AACCCTAAACCCGACCTG
19065 AACCCTAAACCCG
1 AACCCTAAACCCG
19078 GTTTGCAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.33, C:0.39, G:0.13, T:0.15
Consensus pattern (18 bp):
AACCCTAAACCCGACCTG
Found at i:19078 original size:18 final size:18
Alignment explanation
Indices: 19026--19079 Score: 90
Period size: 18 Copynumber: 3.0 Consensus size: 18
19016 TGAATCCGAC
*
19026 CTGAACCCTAAACCCGAT
1 CTGAACCCTAAACCCGGT
*
19044 CTGAACCCTAAAACCGGT
1 CTGAACCCTAAACCCGGT
19062 CTGAACCCTAAACCCGGT
1 CTGAACCCTAAACCCGGT
19080 TTGCAATCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.31, C:0.37, G:0.15, T:0.17
Consensus pattern (18 bp):
CTGAACCCTAAACCCGGT
Found at i:19121 original size:30 final size:30
Alignment explanation
Indices: 19087--19151 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
19077 GGTTTGCAAT
* ** *
19087 CTAAGCCCCTATTTAAACCCGGCCTGAACC
1 CTAAGCCCCGATTTAAACCCAACCTAAACC
*
19117 CTAAG-CCCGGTTTAAACCCAACCTAAACC
1 CTAAGCCCCGATTTAAACCCAACCTAAACC
19146 CTAAGC
1 CTAAGC
19152 TCGGTCTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 24 0.83
30 5 0.17
ACGTcount: A:0.31, C:0.38, G:0.12, T:0.18
Consensus pattern (30 bp):
CTAAGCCCCGATTTAAACCCAACCTAAACC
Found at i:19145 original size:29 final size:29
Alignment explanation
Indices: 19098--19156 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
19088 TAAGCCCCTA
** *
19098 TTTAAACCCGGCCTGAACCCTAAGCCCGG
1 TTTAAACCCAACCTAAACCCTAAGCCCGG
*
19127 TTTAAACCCAACCTAAACCCTAAGCTCGG
1 TTTAAACCCAACCTAAACCCTAAGCCCGG
19156 T
1 T
19157 CTGAACCCTA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.29, C:0.36, G:0.15, T:0.20
Consensus pattern (29 bp):
TTTAAACCCAACCTAAACCCTAAGCCCGG
Found at i:19196 original size:17 final size:17
Alignment explanation
Indices: 19138--19203 Score: 62
Period size: 17 Copynumber: 3.9 Consensus size: 17
19128 TTAAACCCAA
*
19138 CCTAAACCCTAAGCTCGG
1 CCTAAACCCTAAAC-CGG
* * *
19156 TCTGAACCCTAAA-CGA
1 CCTAAACCCTAAACCGG
**
19172 TTTAAACCCTAAACCGG
1 CCTAAACCCTAAACCGG
19189 CCTAAACCCTAAACC
1 CCTAAACCCTAAACC
19204 TAAATCCTAA
Statistics
Matches: 38, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
16 13 0.34
17 15 0.39
18 10 0.26
ACGTcount: A:0.35, C:0.36, G:0.11, T:0.18
Consensus pattern (17 bp):
CCTAAACCCTAAACCGG
Found at i:19207 original size:13 final size:14
Alignment explanation
Indices: 19189--19222 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
19179 CCTAAACCGG
19189 CCTAAACCCTAAA-
1 CCTAAACCCTAAAT
*
19202 CCTAAATCCTAAAT
1 CCTAAACCCTAAAT
19216 CCTAAAC
1 CCTAAAC
19223 AAATTCTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.44, C:0.35, G:0.00, T:0.21
Consensus pattern (14 bp):
CCTAAACCCTAAAT
Found at i:20036 original size:10 final size:10
Alignment explanation
Indices: 20009--20096 Score: 101
Period size: 10 Copynumber: 8.5 Consensus size: 10
19999 ATGGCAGATT
20009 TTAT-TAATA
1 TTATATAATA
20018 TT-T-TAATA
1 TTATATAATA
20026 TTATATAATA
1 TTATATAATA
20036 TTATATTTTAATA
1 TTATA---TAATA
20049 TTATATAATA
1 TTATATAATA
20059 TTATATTTTAATA
1 TTATA---TAATA
20072 TTATATAATA
1 TTATATAATA
20082 TTATATAATA
1 TTATATAATA
20092 TTATA
1 TTATA
20097 ATAAAAAATA
Statistics
Matches: 71, Mismatches: 0, Indels: 15
0.83 0.00 0.17
Matches are distributed among these distances:
8 8 0.11
9 3 0.04
10 40 0.56
13 20 0.28
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (10 bp):
TTATATAATA
Found at i:20042 original size:23 final size:21
Alignment explanation
Indices: 20020--20096 Score: 111
Period size: 23 Copynumber: 3.5 Consensus size: 21
20010 TATTAATATT
20020 TTAATATTATATAATATTATA
1 TTAATATTATATAATATTATA
20041 TTTTAATATTATATAATATTATA
1 --TTAATATTATATAATATTATA
20064 TTTTAATATTATATAATATTATA
1 --TTAATATTATATAATATTATA
20087 -TAATATTATA
1 TTAATATTATA
20097 ATAAAAAATA
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.19
23 44 0.81
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTAATATTATATAATATTATA
Found at i:20047 original size:13 final size:13
Alignment explanation
Indices: 20010--20077 Score: 85
Period size: 13 Copynumber: 5.6 Consensus size: 13
20000 TGGCAGATTT
20010 TATTAATATTTTAA
1 TATT-ATATTTTAA
20024 TATTATA---TAA
1 TATTATATTTTAA
20034 TATTATATTTTAA
1 TATTATATTTTAA
20047 TATTATA---TAA
1 TATTATATTTTAA
20057 TATTATATTTTAA
1 TATTATATTTTAA
20070 TATTATAT
1 TATTATAT
20078 AATATTATAT
Statistics
Matches: 48, Mismatches: 0, Indels: 13
0.79 0.00 0.21
Matches are distributed among these distances:
10 20 0.42
13 24 0.50
14 4 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
TATTATATTTTAA
Found at i:20061 original size:33 final size:32
Alignment explanation
Indices: 20012--20096 Score: 97
Period size: 33 Copynumber: 2.6 Consensus size: 32
20002 GCAGATTTTA
20012 TTAATATT-TTAATATTATATAATATTATATT
1 TTAATATTATTAATATTATATAATATTATATT
20043 TTAATATTATATAATATTATAT--T-TTAATATT
1 TTAATATTAT-TAATATTATATAATATT-ATATT
20074 ATATAATATTATATAATATTATA
1 -T-TAATATTAT-TAATATTATA
20097 ATAAAAAATA
Statistics
Matches: 49, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
30 2 0.04
31 14 0.29
32 2 0.04
33 31 0.63
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
TTAATATTATTAATATTATATAATATTATATT
Found at i:21328 original size:16 final size:16
Alignment explanation
Indices: 21307--21338 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
21297 AAAAGTTTCA
21307 TAAAATATTAAAAAAT
1 TAAAATATTAAAAAAT
*
21323 TAAAATTTTAAAAAAT
1 TAAAATATTAAAAAAT
21339 AATTCAAAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (16 bp):
TAAAATATTAAAAAAT
Found at i:30005 original size:21 final size:21
Alignment explanation
Indices: 29981--30041 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
29971 GGCAACCAAC
29981 TTTGAAAAATGTTTTTCAAAG
1 TTTGAAAAATGTTTTTCAAAG
**
30002 TTTGGTAAATG--TTTC----
1 TTTGAAAAATGTTTTTCAAAG
*
30017 TTTGAAAAATGTTTTTTAAAG
1 TTTGAAAAATGTTTTTCAAAG
30038 TTTG
1 TTTG
30042 GTAGATGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 12
0.63 0.11 0.26
Matches are distributed among these distances:
15 9 0.31
17 3 0.10
19 4 0.14
21 13 0.45
ACGTcount: A:0.31, C:0.03, G:0.16, T:0.49
Consensus pattern (21 bp):
TTTGAAAAATGTTTTTCAAAG
Found at i:30027 original size:36 final size:36
Alignment explanation
Indices: 29980--30061 Score: 130
Period size: 36 Copynumber: 2.3 Consensus size: 36
29970 TGGCAACCAA
29980 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
* *
30016 CTTTGAAAAATGTTTTTTAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
*
30052 -GTTGAAAAAT
1 CTTTGAAAAAT
30062 ACGAATGGGT
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
35 9 0.21
36 34 0.79
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.46
Consensus pattern (36 bp):
CTTTGAAAAATGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:32034 original size:23 final size:23
Alignment explanation
Indices: 32000--32044 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31990 TAATTTAGGC
*
32000 TTTATGGCACATTTTTCTATGCA
1 TTTATGGCACATTTTCCTATGCA
32023 TTTATAGG-ACATTTTCCTATGC
1 TTTAT-GGCACATTTTCCTATGC
32045 CTTTTGACAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 18 0.90
24 2 0.10
ACGTcount: A:0.22, C:0.18, G:0.13, T:0.47
Consensus pattern (23 bp):
TTTATGGCACATTTTCCTATGCA
Found at i:36375 original size:59 final size:59
Alignment explanation
Indices: 36283--36403 Score: 206
Period size: 59 Copynumber: 2.1 Consensus size: 59
36273 GGAGAGTTGG
* * *
36283 TTAGAGTCATATTATCTAGTTTGTCTTTTCATTGCGACTAGGAGGGTTCGATAGAACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAGAACAC
*
36342 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAGGACAC
1 TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAGAACAC
36401 TTA
1 TTA
36404 TCCATCTATT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.36
Consensus pattern (59 bp):
TTAGAGCCATATTATCGAGTTTGCCTTTTCATTGCGACTAGGAGGGTTCGATAGAACAC
Found at i:38407 original size:24 final size:21
Alignment explanation
Indices: 38340--38392 Score: 106
Period size: 21 Copynumber: 2.5 Consensus size: 21
38330 TCAGAGAACA
38340 TTACCAAGGTACTTCATCCTC
1 TTACCAAGGTACTTCATCCTC
38361 TTACCAAGGTACTTCATCCTC
1 TTACCAAGGTACTTCATCCTC
38382 TTACCAAGGTA
1 TTACCAAGGTA
38393 ATCCTTCATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.26, C:0.30, G:0.11, T:0.32
Consensus pattern (21 bp):
TTACCAAGGTACTTCATCCTC
Found at i:43648 original size:25 final size:25
Alignment explanation
Indices: 43614--43677 Score: 121
Period size: 25 Copynumber: 2.6 Consensus size: 25
43604 TCATTTAAAT
43614 TTATTATTATTATTAAATATTATTA
1 TTATTATTATTATTAAATATTATTA
43639 TTATTATTATTATTAAATATTATTA
1 TTATTATTATTATTAAATATTATTA
43664 TTATTATTA-TATTA
1 TTATTATTATTATTA
43678 TTATTAAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 1
0.98 0.00 0.03
Matches are distributed among these distances:
24 5 0.13
25 34 0.87
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTATTATTATTATTAAATATTATTA
Found at i:43691 original size:25 final size:26
Alignment explanation
Indices: 43614--43694 Score: 119
Period size: 25 Copynumber: 3.0 Consensus size: 26
43604 TCATTTAAAT
43614 TTATTATTATTATTAAAT-ATTATTA
1 TTATTATTATTATTAAATAATTATTA
43639 TTATTATTATTATTAAATATTATTATTA
1 TTATTATTATTATTAAATA--ATTATTA
43667 TTATTATATTATTATTAAATAATTATTA
1 TTA-T-TATTATTATTAAATAATTATTA
43695 CAAGCCCAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
25 18 0.35
28 17 0.33
29 1 0.02
30 15 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (26 bp):
TTATTATTATTATTAAATAATTATTA
Found at i:43694 original size:3 final size:3
Alignment explanation
Indices: 43614--43683 Score: 97
Period size: 3 Copynumber: 23.0 Consensus size: 3
43604 TCATTTAAAT
* *
43614 TTA TTA TTA TTA TTAA ATA TTA TTA TTA TTA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
43661 TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
43684 AATAATTATT
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
2 2 0.03
3 54 0.90
4 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:44133 original size:23 final size:21
Alignment explanation
Indices: 44106--44179 Score: 76
Period size: 23 Copynumber: 3.3 Consensus size: 21
44096 CAGAGAGCAG
44106 AGAAAAACAAAAGAAAAAAGAAA
1 AGAAAAA-AAAA-AAAAAAGAAA
* *
44129 AGAAAAAAAAACAGAAAGAGAGA
1 AGAAAAAAAAA-A-AAAAAGAAA
**
44152 AGAAAAAAAAAACGAAAGAAA
1 AGAAAAAAAAAAAAAAAGAAA
44173 AGAAAAA
1 AGAAAAA
44180 CTACCAACGA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
21 12 0.28
22 6 0.14
23 25 0.58
ACGTcount: A:0.80, C:0.04, G:0.16, T:0.00
Consensus pattern (21 bp):
AGAAAAAAAAAAAAAAAGAAA
Found at i:44141 original size:44 final size:43
Alignment explanation
Indices: 44093--44179 Score: 115
Period size: 44 Copynumber: 2.0 Consensus size: 43
44083 CAAGATACAG
*
44093 AAACAGAGAGCAGAGAA-AAACAAAAGAAA-AAAGAAAAGAAAAAA
1 AAACAGAAAG-AGAGAAGAAA-AAAA-AAACAAAGAAAAGAAAAAA
44137 AAACAGAAAGAGAGAAGAAAAAAAAAACGAAAGAAAAGAAAAA
1 AAACAGAAAGAGAGAAGAAAAAAAAAAC-AAAGAAAAGAAAAA
44180 CTACCAACGA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
42 3 0.08
43 10 0.26
44 26 0.67
ACGTcount: A:0.76, C:0.06, G:0.18, T:0.00
Consensus pattern (43 bp):
AAACAGAAAGAGAGAAGAAAAAAAAAACAAAGAAAAGAAAAAA
Found at i:44145 original size:35 final size:35
Alignment explanation
Indices: 44106--44173 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
44096 CAGAGAGCAG
44106 AGAAAAACAAAAGAAAAAAGAAAA-GAAAAAAAAAC
1 AGAAAAACAAAAGAAAAAA-AAAACGAAAAAAAAAC
* * * *
44141 AGAAAGAGAGAAGAAAAAAAAAACGAAAGAAAA
1 AGAAAAACAAAAGAAAAAAAAAACGAAAAAAAA
44174 GAAAAACTAC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
34 4 0.14
35 24 0.86
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.00
Consensus pattern (35 bp):
AGAAAAACAAAAGAAAAAAAAAACGAAAAAAAAAC
Found at i:44147 original size:28 final size:26
Alignment explanation
Indices: 44108--44179 Score: 81
Period size: 28 Copynumber: 2.6 Consensus size: 26
44098 GAGAGCAGAG
44108 AAAAACAAAAGAAAAAAGAAAAGAAAA
1 AAAAACAAAAGAAAAAAGAAAA-AAAA
* *
44135 AAAAACAGAAAGAGAGAAGAAAAAAAA
1 AAAAACA-AAAGAAAAAAGAAAAAAAA
*
44162 AACGAAAGAAAAGAAAAA
1 AA--AAACAAAAGAAAAA
44180 CTACCAACGA
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
27 13 0.35
28 20 0.54
29 4 0.11
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (26 bp):
AAAAACAAAAGAAAAAAGAAAAAAAA
Found at i:45055 original size:11 final size:11
Alignment explanation
Indices: 45036--45085 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
45026 ACTTTTTATA
45036 TTTAGTTTTAAT
1 TTTA-TTTTAAT
45048 TTTATTTTAAT
1 TTTATTTTAAT
* * *
45059 TATAGTTTAAA
1 TTTATTTTAAT
*
45070 TATATTTTAAT
1 TTTATTTTAAT
45081 TTTAT
1 TTTAT
45086 ATGTTTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 28 0.88
12 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (11 bp):
TTTATTTTAAT
Found at i:45127 original size:23 final size:24
Alignment explanation
Indices: 45094--45140 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
45084 ATATGTTTAA
*
45094 TATTTTAATTAGTAT-TATTATTT
1 TATTTTAATTAATATATATTATTT
*
45117 TATTTTTATTAATATATATTATTT
1 TATTTTAATTAATATATATTATTT
45141 GATTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTTTAATTAATATATATTATTT
Found at i:46003 original size:20 final size:21
Alignment explanation
Indices: 45980--46031 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
45970 AGAAATTAAA
45980 AATTCATTTATTT-AATTTTT
1 AATTCATTTATTTAAATTTTT
* *
46000 AATTCTTTTCTTTCAAATTTTT
1 AATTCATTTATTT-AAATTTTT
46022 -ATT-ATTTATT
1 AATTCATTTATT
46032 ATTTTTATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
20 16 0.62
21 3 0.12
22 7 0.27
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (21 bp):
AATTCATTTATTTAAATTTTT
Found at i:50667 original size:4 final size:4
Alignment explanation
Indices: 50658--50705 Score: 57
Period size: 4 Copynumber: 12.8 Consensus size: 4
50648 CTCATCCAGC
* *
50658 AAAG AAAG -AAG AAGG AAAA AAAG AAAG AAA- AAAG AAAG AAA- AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
50703 AAA
1 AAA
50706 AAAATTGAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
3 9 0.24
4 28 0.76
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:50688 original size:11 final size:11
Alignment explanation
Indices: 50658--50709 Score: 70
Period size: 11 Copynumber: 4.7 Consensus size: 11
50648 CTCATCCAGC
*
50658 AAAGAAAGAAG
1 AAAGAAAAAAG
*
50669 AAGGAAAAAAAG
1 AAAG-AAAAAAG
50681 AAAGAAAAAAG
1 AAAGAAAAAAG
50692 AAAGAAAAAAG
1 AAAGAAAAAAG
50703 AAA-AAAA
1 AAAGAAAA
50710 TTGAATCAAG
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
10 4 0.11
11 24 0.65
12 9 0.24
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:53080 original size:114 final size:114
Alignment explanation
Indices: 52880--53102 Score: 340
Period size: 114 Copynumber: 2.0 Consensus size: 114
52870 TTCCATGTGA
* * *
52880 TCATAGTAGAAATAAGAAGACTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATTTGG
1 TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
* * * *
52945 TTTGGTATGAACCCCAAAACCAATCATTGGATTTAAAAGATGAATTTGC
66 TTCGGTAGGAACCCCAAAACCAATCATTGAAATTAAAAGATGAATTTGC
52994 TCATAGTAGAAATAATG-AGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTG
1 TCATAGTAGAAATAA-GAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTG
* * *
53058 GTTCGGTAGGAATCCCATAACCAATCATTGAAATTGAAAGATGAA
65 GTTCGGTAGGAACCCCAAAACCAATCATTGAAATTAAAAGATGAA
53103 CTGCATGATC
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 97 0.99
115 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.19, T:0.32
Consensus pattern (114 bp):
TCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGAAAGTGTTCTTTGAGTTATCTGATCTGG
TTCGGTAGGAACCCCAAAACCAATCATTGAAATTAAAAGATGAATTTGC
Found at i:55158 original size:54 final size:54
Alignment explanation
Indices: 55094--55248 Score: 247
Period size: 54 Copynumber: 2.9 Consensus size: 54
55084 GAAATCATGG
*
55094 CAGAAACCACAGTAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
1 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
*
55148 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAG
1 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
* *** *
55202 CAGAAGCCACAGGAAAGGATGAATGCACTATCAAATGTTTTACGAAC
1 CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAAC
55249 CTGCTATTCT
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 94 1.00
ACGTcount: A:0.39, C:0.16, G:0.22, T:0.23
Consensus pattern (54 bp):
CAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACGAACATCTGAA
Found at i:56443 original size:76 final size:76
Alignment explanation
Indices: 56312--57259 Score: 1700
Period size: 76 Copynumber: 12.5 Consensus size: 76
56302 ACTATTTCCC
* *
56312 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCATTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
* * *
56377 AAACCATAGGG
66 AAGCCTTCGGG
*
56388 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGAAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
56453 AAGCCTTAGGG
66 AAGCCTTCGGG
*
56464 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
56529 AAGCCTTCGGG
66 AAGCCTTCGGG
56540 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
56605 AAGCCTTCGGG
66 AAGCCTTCGGG
56616 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
56681 AAGCCTTCGGG
66 AAGCCTTCGGG
*
56692 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
56757 AA-CCTTAGGG
66 AAGCCTTCGGG
56767 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
* *
56832 AAACCTTAGGG
66 AAGCCTTCGGG
56843 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
56908 AATCCTTCGGG
66 AAGCCTTCGGG
*
56919 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
56984 AAGCCTTCGGG
66 AAGCCTTCGGG
56995 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
57060 AAGCCTTCGGG
66 AAGCCTTCGGG
57071 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
*
57136 AATCCTTCGGG
66 AAGCCTTCGGG
*
57147 TCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-
* *
57212 AAAACCTTTGGG
65 AAAGCCTTCGGG
* *
57224 TCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAA
57260 CATTTCCATC
Statistics
Matches: 846, Mismatches: 24, Indels: 3
0.97 0.03 0.00
Matches are distributed among these distances:
75 73 0.09
76 730 0.86
77 43 0.05
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.35
Consensus pattern (76 bp):
TCATCTGTAAGTCCTTCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCA
AAGCCTTCGGG
Found at i:57416 original size:25 final size:25
Alignment explanation
Indices: 57385--57459 Score: 123
Period size: 25 Copynumber: 2.9 Consensus size: 25
57375 TTCATTTAAA
57385 TTTATTATTATTATTATTAAATATT
1 TTTATTATTATTATTATTAAATATT
57410 TTTATTATTATTATTATTAAATATT
1 TTTATTATTATTATTATTAAATATT
*
57435 ATTATTATTATATTATTATTAAATA
1 TTTATTA-T-TATTATTATTAAATA
57460 ATTATTACAA
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
25 31 0.66
26 1 0.02
27 15 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
TTTATTATTATTATTATTAAATATT
Found at i:57466 original size:3 final size:3
Alignment explanation
Indices: 57386--57455 Score: 88
Period size: 3 Copynumber: 23.0 Consensus size: 3
57376 TCATTTAAAT
* * *
57386 TTA TTA TTA TTA TTA TTAA ATA TTT TTA TTA TTA TTA TTA TTAA ATA
1 TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TT-A TTA
57433 TTA TTA TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA
57456 AATAATTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.03
3 52 0.90
4 4 0.07
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:57906 original size:23 final size:22
Alignment explanation
Indices: 57879--57950 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 22
57869 CAGAGAGCAG
57879 AGAAAAACAAAAGAAAAAAGAAA
1 AGAAAAA-AAAAGAAAAAAGAAA
* * *
57902 AGAAAAAAAAACAGAAAGAGAGA
1 AGAAAAAAAAAGA-AAAAAGAAA
57925 AGAAAAAAAAACGAAAGAAAAGAAA
1 AGAAAAAAAAA-G-AA-AAAAGAAA
57950 A
1 A
57951 ACTACCAACG
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
22 5 0.13
23 25 0.64
24 1 0.03
25 8 0.21
ACGTcount: A:0.79, C:0.04, G:0.17, T:0.00
Consensus pattern (22 bp):
AGAAAAAAAAAGAAAAAAGAAA
Found at i:57920 original size:28 final size:26
Alignment explanation
Indices: 57881--57951 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 26
57871 GAGAGCAGAG
57881 AAAAACAAAAGAAAAAAGAAAAGAAAA
1 AAAAACAAAAGAAAAAAGAAAA-AAAA
* *
57908 AAAAACAGAAAGAGAGAAGAAAAAAAA
1 AAAAACA-AAAGAAAAAAGAAAAAAAA
* *
57935 ACGAAAGAAAAGAAAAA
1 A-AAAACAAAAGAAAAA
57952 CTACCAACGA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
27 19 0.53
28 17 0.47
ACGTcount: A:0.80, C:0.04, G:0.15, T:0.00
Consensus pattern (26 bp):
AAAAACAAAAGAAAAAAGAAAAAAAA
Found at i:57925 original size:43 final size:44
Alignment explanation
Indices: 57866--57951 Score: 115
Period size: 43 Copynumber: 2.0 Consensus size: 44
57856 CAAGATACAG
*
57866 AAACAGAGAGCAGAGAA-AAACAAAAGAA-AAAAGAAAAGAAAAAA
1 AAACAGAAAGCAGAGAAGAAA-AAAA-AACAAAAGAAAAGAAAAAA
*
57910 AAACAGAAAG-AGAGAAGAAAAAAAAACGAAAGAAAAGAAAAA
1 AAACAGAAAGCAGAGAAGAAAAAAAAACAAAAGAAAAGAAAAA
57952 CTACCAACGA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
42 2 0.05
43 24 0.63
44 12 0.32
ACGTcount: A:0.76, C:0.06, G:0.19, T:0.00
Consensus pattern (44 bp):
AAACAGAAAGCAGAGAAGAAAAAAAAACAAAAGAAAAGAAAAAA
Found at i:58826 original size:11 final size:11
Alignment explanation
Indices: 58807--58856 Score: 55
Period size: 11 Copynumber: 4.5 Consensus size: 11
58797 ACTTTTTATA
58807 TTTAGTTTTAAT
1 TTTA-TTTTAAT
58819 TTTATTTTAAT
1 TTTATTTTAAT
* * *
58830 TATAGTTTAAA
1 TTTATTTTAAT
*
58841 TATATTTTAAT
1 TTTATTTTAAT
58852 TTTAT
1 TTTAT
58857 ATGTTTAATA
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
11 28 0.88
12 4 0.12
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (11 bp):
TTTATTTTAAT
Found at i:58898 original size:23 final size:24
Alignment explanation
Indices: 58865--58911 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
58855 ATATGTTTAA
*
58865 TATTTTAATTAGTAT-TATTATTT
1 TATTTTAATTAATATATATTATTT
*
58888 TATTTTTATTAATATATATTATTT
1 TATTTTAATTAATATATATTATTT
58912 GATTAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 13 0.62
24 8 0.38
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (24 bp):
TATTTTAATTAATATATATTATTT
Found at i:64218 original size:14 final size:15
Alignment explanation
Indices: 64194--64236 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
64184 ATTAAGTATT
64194 TAATA-TATTAAATA
1 TAATATTATTAAATA
*
64208 TAA-ATTATTAAAAA
1 TAATATTATTAAATA
64222 TAATATTA-TAAATA
1 TAATATTATTAAATA
64236 T
1 T
64237 CTACTAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
13 1 0.04
14 20 0.80
15 4 0.16
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAATATTATTAAATA
Found at i:67405 original size:19 final size:18
Alignment explanation
Indices: 67365--67398 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
67355 TTAACTTATT
*
67365 TTTTAAAATTAGGATATA
1 TTTTAAAATTAGAATATA
67383 TTTTAAAATTA-AATAT
1 TTTTAAAATTAGAATAT
67399 TAATTTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47
Consensus pattern (18 bp):
TTTTAAAATTAGAATATA
Found at i:68676 original size:93 final size:95
Alignment explanation
Indices: 68565--68781 Score: 352
Period size: 95 Copynumber: 2.3 Consensus size: 95
68555 AAATCAGACA
**
68565 AATTAAAAAAAAAT-AGAAAACA-TACAAAACAAAATAGTAT-TTTATTTATCTAATTTCAATGT
1 AATT-AAAAAAAATCAGAAAA-ATTACAAAACAAAATAGTATGTTTATTTATCTAATTTCAATAC
*
68627 ATTTTTATCTATCTTGC-AATTTATCTACTTG
64 ATTTTTATCTATCTTGCAAATTGATCTACTTG
68658 AATTAAAAAAAATCAGAAAAATTACAAAACAAAATAGTATGTTTATTTATCTAATTTCAATACAT
1 AATTAAAAAAAATCAGAAAAATTACAAAACAAAATAGTATGTTTATTTATCTAATTTCAATACAT
68723 TTTTATCTATCTTGCAAATTGATCTACTTG
66 TTTTATCTATCTTGCAAATTGATCTACTTG
*
68753 AATTTAAAAAAATCAGAAAAATTACAAAA
1 AATTAAAAAAAATCAGAAAAATTACAAAA
68782 AATCAGAAAA
Statistics
Matches: 116, Mismatches: 4, Indels: 6
0.92 0.03 0.05
Matches are distributed among these distances:
92 10 0.09
93 28 0.24
94 37 0.32
95 41 0.35
ACGTcount: A:0.47, C:0.11, G:0.06, T:0.36
Consensus pattern (95 bp):
AATTAAAAAAAATCAGAAAAATTACAAAACAAAATAGTATGTTTATTTATCTAATTTCAATACAT
TTTTATCTATCTTGCAAATTGATCTACTTG
Found at i:68781 original size:19 final size:19
Alignment explanation
Indices: 68759--68802 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
68749 CTTGAATTTA
68759 AAAAAATCAGAAAAATTAC
1 AAAAAATCAGAAAAATTAC
68778 AAAAAATCAGAAAAATTAC
1 AAAAAATCAGAAAAATTAC
68797 AAAAAA
1 AAAAAA
68803 AATTAGTATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.73, C:0.09, G:0.05, T:0.14
Consensus pattern (19 bp):
AAAAAATCAGAAAAATTAC
Found at i:68782 original size:114 final size:114
Alignment explanation
Indices: 68658--68905 Score: 376
Period size: 114 Copynumber: 2.2 Consensus size: 114
68648 TATCTACTTG
*
68658 AATTAAAAAAAATCAGAAAAATTACAAAACAAAA-TAGTATGTTTATTTATCTAATTTCAATACA
1 AATTACAAAAAATCAGAAAAATTACAAAA-AAAATTAGTATGTTTATTTATCTAATTTCAATACA
* * *
68722 TTTTTATCTATCTTGCAAATTGATCTACTTGAATTTAAAAAA-ATCAGAAA
65 TTTTTATCTATCTTGCAAATTAATCTACTTGAATTTAAAAAATA-AAAAAA
* **
68772 AATTACAAAAAATCAGAAAAATTACAAAAAAAATTAGTATGTTTATTTATCTAATTTTAATTTAT
1 AATTACAAAAAATCAGAAAAATTACAAAAAAAATTAGTATGTTTATTTATCTAATTTCAATACAT
*
68837 TTTTATCTATCTTGCAATTTAATCTACTTGAATTTAAAAAATAAAAAAA
66 TTTTATCTATCTTGCAAATTAATCTACTTGAATTTAAAAAATAAAAAAA
*
68886 AATTACAAAAAA-AAGAAAAA
1 AATTACAAAAAATCAGAAAAA
68906 AAAGAAATTA
Statistics
Matches: 123, Mismatches: 9, Indels: 5
0.90 0.07 0.04
Matches are distributed among these distances:
113 11 0.09
114 111 0.90
115 1 0.01
ACGTcount: A:0.51, C:0.09, G:0.05, T:0.35
Consensus pattern (114 bp):
AATTACAAAAAATCAGAAAAATTACAAAAAAAATTAGTATGTTTATTTATCTAATTTCAATACAT
TTTTATCTATCTTGCAAATTAATCTACTTGAATTTAAAAAATAAAAAAA
Found at i:68872 original size:15 final size:17
Alignment explanation
Indices: 68841--68873 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
68831 ATTTATTTTT
68841 ATCTATCTTGCAATTTA
1 ATCTATCTTGCAATTTA
68858 ATCTA-CTTG-AATTTA
1 ATCTATCTTGCAATTTA
68873 A
1 A
68874 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.45
Consensus pattern (17 bp):
ATCTATCTTGCAATTTA
Found at i:73273 original size:2 final size:2
Alignment explanation
Indices: 73266--73315 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
73256 TATTTTTAAC
73266 AT AT AT 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
73308 AT AT AT AT
1 AT AT AT AT
73316 TAAAAAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:74841 original size:202 final size:202
Alignment explanation
Indices: 74495--74872 Score: 756
Period size: 202 Copynumber: 1.9 Consensus size: 202
74485 CTTCTTTCGG
74495 CTTTGGATGGTATGTCCGACGAGTGAAGCTCGGCGGTGACGGAAGCAACACAGGGAGTAAATATT
1 CTTTGGATGGTATGTCCGACGAGTGAAGCTCGGCGGTGACGGAAGCAACACAGGGAGTAAATATT
74560 TTTTACCCCCGGGGCTATCTTCGTCTACCCCAAGGCAGCTTGCGACGAATCTAGTGGTGGCAGTC
66 TTTTACCCCCGGGGCTATCTTCGTCTACCCCAAGGCAGCTTGCGACGAATCTAGTGGTGGCAGTC
74625 CTCGGCCAGTGAGGGAACCACGGTAACGTGCAACTCACACGGGGAGTAAATATTTTTTACCCCCG
131 CTCGGCCAGTGAGGGAACCACGGTAACGTGCAACTCACACGGGGAGTAAATATTTTTTACCCCCG
74690 GGGCTAT
196 GGGCTAT
74697 CTTTGGATGGTATGTCCGACGAGTGAAGCTCGGCGGTGACGGAAGCAACACAGGGAGTAAATATT
1 CTTTGGATGGTATGTCCGACGAGTGAAGCTCGGCGGTGACGGAAGCAACACAGGGAGTAAATATT
74762 TTTTACCCCCGGGGCTATCTTCGTCTACCCCAAGGCAGCTTGCGACGAATCTAGTGGTGGCAGTC
66 TTTTACCCCCGGGGCTATCTTCGTCTACCCCAAGGCAGCTTGCGACGAATCTAGTGGTGGCAGTC
74827 CTCGGCCAGTGAGGGAACCACGGTAACGTGCAACTCACACGGGGAG
131 CTCGGCCAGTGAGGGAACCACGGTAACGTGCAACTCACACGGGGAG
74873 CGCGTGACGT
Statistics
Matches: 176, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
202 176 1.00
ACGTcount: A:0.23, C:0.25, G:0.30, T:0.22
Consensus pattern (202 bp):
CTTTGGATGGTATGTCCGACGAGTGAAGCTCGGCGGTGACGGAAGCAACACAGGGAGTAAATATT
TTTTACCCCCGGGGCTATCTTCGTCTACCCCAAGGCAGCTTGCGACGAATCTAGTGGTGGCAGTC
CTCGGCCAGTGAGGGAACCACGGTAACGTGCAACTCACACGGGGAGTAAATATTTTTTACCCCCG
GGGCTAT
Found at i:75134 original size:16 final size:16
Alignment explanation
Indices: 75095--75147 Score: 61
Period size: 16 Copynumber: 3.2 Consensus size: 16
75085 AATATGTAAT
*
75095 AATAATAAATAATAGTA
1 AATAAT-AATAATATTA
* *
75112 TAATAATAGTAATGTTA
1 -AATAATAATAATATTA
75129 AATAATAATAATATTA
1 AATAATAATAATATTA
75145 AAT
1 AAT
75148 TTGAACACGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
16 17 0.57
17 7 0.23
18 6 0.20
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
AATAATAATAATATTA
Found at i:76932 original size:38 final size:38
Alignment explanation
Indices: 76865--76955 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 38
76855 ATTTTGTTCG
* * *
76865 GGTCGGGTCGAG-TTTTTTAAGTGTGATATTCGGGTC-
1 GGTCGGGTCGGGTTTTTTTAAGCGTAATATTCGGGTCA
*
76901 GATTCGGGTCGGGTTTTTTTAAGCGTAATATTCGGGTCA
1 G-GTCGGGTCGGGTTTTTTTAAGCGTAATATTCGGGTCA
76940 GGTCGGGTTCGGGTTT
1 GGTCGGG-TCGGGTTT
76956 AGGGTGAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
36 1 0.02
37 9 0.20
38 27 0.59
39 9 0.20
ACGTcount: A:0.13, C:0.12, G:0.36, T:0.38
Consensus pattern (38 bp):
GGTCGGGTCGGGTTTTTTTAAGCGTAATATTCGGGTCA
Found at i:81045 original size:2 final size:2
Alignment explanation
Indices: 81038--81072 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
81028 AAATAATGTA
81038 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
81073 ATTTTTTTAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:83407 original size:2 final size:2
Alignment explanation
Indices: 83400--83468 Score: 117
Period size: 2 Copynumber: 36.0 Consensus size: 2
83390 CCCAAACTTG
83400 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- 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
83441 -T AT AT AT AT -T 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
83469 CAAATTTGAT
Statistics
Matches: 64, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
1 3 0.05
2 61 0.95
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.