Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008389.1 Hibiscus syriacus cultivar Beakdansim tig00111154_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: 140999
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:167 original size:20 final size:20
Alignment explanation
Indices: 137--184 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
127 TAAGTCATAG
*
137 AAAAGAATAAATTGAATTTCC
1 AAAA-AATAAATTGAATCTCC
158 AAAAAATAAATTGAATCTCC
1 AAAAAATAAATTGAATCTCC
*
178 AATAAAT
1 AAAAAAT
185 TGAACTTGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 21 0.84
21 4 0.16
ACGTcount: A:0.56, C:0.10, G:0.06, T:0.27
Consensus pattern (20 bp):
AAAAAATAAATTGAATCTCC
Found at i:518 original size:1 final size:1
Alignment explanation
Indices: 514--553 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
504 TGACCCCCCC
* * *
514 TTTTTTTTTTTTTTTTTTCTTTTTTTTTCTTTTCTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
554 CTTTCTTCAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (1 bp):
T
Found at i:538 original size:15 final size:15
Alignment explanation
Indices: 513--560 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
503 TTGACCCCCC
513 CTTTT-TTTTTTTTT
1 CTTTTCTTTTTTTTT
*
527 TTTTTCTTTTTTTTT
1 CTTTTCTTTTTTTTT
542 CTTTTCTTTTTTCTTT
1 CTTTTCTTTTTT-TTT
558 CTT
1 CTT
561 CAAGCATAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
14 4 0.13
15 20 0.67
16 6 0.20
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (15 bp):
CTTTTCTTTTTTTTT
Found at i:539 original size:22 final size:22
Alignment explanation
Indices: 514--557 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
504 TGACCCCCCC
514 TTTTTTTT-TTTT-TTTTTTCT
1 TTTTTTTTCTTTTCTTTTTTCT
534 TTTTTTTTCTTTTCTTTTTTCT
1 TTTTTTTTCTTTTCTTTTTTCT
556 TT
1 TT
558 CTTCAAGCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
20 8 0.36
21 4 0.18
22 10 0.45
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (22 bp):
TTTTTTTTCTTTTCTTTTTTCT
Found at i:554 original size:12 final size:12
Alignment explanation
Indices: 513--557 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
503 TTGACCCCCC
*
513 CTTTTTTTTTTT
1 CTTTTTTCTTTT
*
525 TTTTTTTC-TTT
1 CTTTTTTCTTTT
536 -TTTTTTCTTTT
1 CTTTTTTCTTTT
547 CTTTTTTCTTT
1 CTTTTTTCTTT
558 CTTCAAGCAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
10 7 0.24
11 6 0.21
12 16 0.55
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (12 bp):
CTTTTTTCTTTT
Found at i:560 original size:11 final size:10
Alignment explanation
Indices: 513--557 Score: 65
Period size: 10 Copynumber: 4.4 Consensus size: 10
503 TTGACCCCCC
513 CTTTTTTTTT
1 CTTTTTTTTT
523 -TTTTTTTTT
1 CTTTTTTTTT
532 CTTTTTTTTT
1 CTTTTTTTTT
542 CTTTTCTTTTTT
1 C-TTT-TTTTTT
554 CTTT
1 CTTT
558 CTTCAAGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 9 0.28
10 10 0.31
11 6 0.19
12 7 0.22
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:12693 original size:20 final size:20
Alignment explanation
Indices: 12668--12706 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
12658 TCTTCTCTGT
12668 TTTTTTTTTCTGTCTCTCTC
1 TTTTTTTTTCTGTCTCTCTC
12688 TTTTTTTTTCTGTCTCTCT
1 TTTTTTTTTCTGTCTCTCT
12707 GTCCCGTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.05, T:0.72
Consensus pattern (20 bp):
TTTTTTTTTCTGTCTCTCTC
Found at i:13189 original size:3 final size:3
Alignment explanation
Indices: 13181--13281 Score: 166
Period size: 3 Copynumber: 33.7 Consensus size: 3
13171 AATATATATT
* *
13181 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
13229 TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAT TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
13277 TAA TA
1 TAA TA
13282 TGGATAAAAA
Statistics
Matches: 90, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 90 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:13426 original size:24 final size:22
Alignment explanation
Indices: 13390--13444 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
13380 AAAACACAAG
*
13390 AATTTTCCAA-AAAAAAAT-TT
1 AATTTTCAAATAAAAAAATGTT
13410 AAATTTTCGAAATAAAAAAATGTT
1 -AATTTTC-AAATAAAAAAATGTT
13434 AATTTTCAAAT
1 AATTTTCAAAT
13445 TATTGTGTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 7 0.23
22 6 0.20
23 15 0.50
24 2 0.07
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (22 bp):
AATTTTCAAATAAAAAAATGTT
Found at i:23706 original size:31 final size:31
Alignment explanation
Indices: 23639--23698 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
23629 CAATTTAAGG
*
23639 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
23670 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
23699 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:28293 original size:12 final size:12
Alignment explanation
Indices: 28254--28293 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
28244 ATCAAATTCT
*
28254 TCCTCAACTTCC
1 TCCTCAGCTTCC
*
28266 TACTCAGCTTCC
1 TCCTCAGCTTCC
*
28278 TCCTCAGCTTCT
1 TCCTCAGCTTCC
28290 TCCT
1 TCCT
28294 GAACATCTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.12, C:0.45, G:0.05, T:0.38
Consensus pattern (12 bp):
TCCTCAGCTTCC
Found at i:38006 original size:223 final size:224
Alignment explanation
Indices: 37585--38155 Score: 961
Period size: 223 Copynumber: 2.6 Consensus size: 224
37575 TTGTCGGTTT
* *
37585 GTGTCGATAATTTAT-AAAATGTATTGATCCATAACAATATAACA-GTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
37648 GGTCTATAAATGACAAAACAGGTAAAACGCTACTGGATATATTAAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
*
37713 AATGTATCGATCCATAACAATCTAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
131 AATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
37778 CAGGTAAAGTGCTACCGGATATATTGAAA
196 CAGGTAAAGTGCTACCGGATATATTGAAA
* * *
37807 GTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAAAATGACAAAAGC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
37872 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
*
37937 AATGTATCGATCCATAACAATATAACATGT-AAAAAATGACAAAACCGGTCTATAAATGACAAAA
131 AATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
38001 CAGGTAAAGTGCTACCGGATATATTGAAA
196 CAGGTAAAGTGCTACCGGATATATTGAAA
* *
38030 GTGTCGATACTTTATAAAAATGTATCAATCTATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
38094 GGTTTATAAATGATAAAACAGGTAAAGCGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTAT
38156 TATAAGTATC
Statistics
Matches: 326, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
222 85 0.26
223 134 0.41
224 107 0.33
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (224 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAAGTGTCGATACTTTATAAA
AATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACCGGTCTATAAATGACAAAA
CAGGTAAAGTGCTACCGGATATATTGAAA
Found at i:38035 original size:111 final size:112
Alignment explanation
Indices: 37585--38155 Score: 943
Period size: 112 Copynumber: 5.1 Consensus size: 112
37575 TTGTCGGTTT
* *
37585 GTGTCGATAATTTAT-AAAATGTATTGATCCATAACAATATAACA-GTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * *
37648 GGTCTATAAATGACAAAACAGGTAAAACGCTACTGGATATATTAAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
37695 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATCTAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
37760 GGTCTATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * *
37807 GTGTCAATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAAAATGACAAAAGC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
37872 GGTCTATAAATGACAAAACAAGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
37919 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACATGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
37983 GGTCTATAAATGACAAAACAGGTAAAGTGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
38030 GTGTCGATACTTTATAAAAATGTATCAATCTATAACAATATAACAGGT-AAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
* * * *
38094 GGTTTATAAATGATAAAACAGGTAAAGCGCTACCGGATATGTTGATA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
38141 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
38156 TATAAGTATC
Statistics
Matches: 432, Mismatches: 27, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
110 14 0.03
111 205 0.47
112 213 0.49
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:38246 original size:66 final size:67
Alignment explanation
Indices: 38140--38288 Score: 255
Period size: 66 Copynumber: 2.2 Consensus size: 67
38130 ATATGTTGAT
38140 AGTGTCGATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGTTATAGCGCT-AT
1 AGTGTCGATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGTTATAGCGCTAAT
38204 AA
66 AA
* * * *
38206 AGTGTCAATATTTTATTATAAGTATCGACATTTTTGGAATTTAAAAGAGAAGTTATAGCGCTAAT
1 AGTGTCGATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGTTATAGCGCTAAT
38271 AA
66 AA
38273 AGTGTCGATACTTTAT
1 AGTGTCGATACTTTAT
38289 AAAAATGTAT
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
66 58 0.76
67 18 0.24
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (67 bp):
AGTGTCGATACTTTATTATAAGTATCGACACTTTTAGAATTTAAAAGAGAAGTTATAGCGCTAAT
AA
Found at i:38991 original size:23 final size:23
Alignment explanation
Indices: 38965--39012 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
38955 AAATAGATCA
* *
38965 ATATAAGCGTTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
38988 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
39011 AT
1 AT
39013 TATATTTGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:47708 original size:9 final size:9
Alignment explanation
Indices: 47694--47718 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
47684 ATTTCTTTTT
47694 GTTTTGCTG
1 GTTTTGCTG
47703 GTTTTGCTG
1 GTTTTGCTG
47712 GTTTTGC
1 GTTTTGC
47719 AGGCACTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.32, T:0.56
Consensus pattern (9 bp):
GTTTTGCTG
Found at i:51214 original size:16 final size:19
Alignment explanation
Indices: 51193--51229 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
51183 AAAATTATAT
51193 TATTTTA-TTT-A-TTTAA
1 TATTTTAGTTTCATTTTAA
51209 TATTTTAGTTTCATTTTAA
1 TATTTTAGTTTCATTTTAA
51228 TA
1 TA
51230 AAAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 1 0.06
19 7 0.39
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TATTTTAGTTTCATTTTAA
Found at i:51664 original size:30 final size:29
Alignment explanation
Indices: 51600--51706 Score: 112
Period size: 30 Copynumber: 3.7 Consensus size: 29
51590 TTTTCAGAAA
* *
51600 ATGTAATTTATTTTAC--AAAAAAAATTT
1 ATGTAATTCATTTTACGTAAAAAAATTTT
*
51627 A-GTAATTCATTTTACGTAAAATAATTTT
1 ATGTAATTCATTTTACGTAAAAAAATTTT
*
51655 CATGTAATTCATTTTACGTAAAACAATTTTT
1 -ATGTAATTCATTTTACGTAAAA-AAATTTT
* * *
51686 AAGTAATCCATTTTATGTAAA
1 ATGTAATTCATTTTACGTAAA
51707 TTATTTCTCA
Statistics
Matches: 67, Mismatches: 8, Indels: 7
0.82 0.10 0.09
Matches are distributed among these distances:
26 13 0.19
27 1 0.01
28 9 0.13
29 1 0.01
30 38 0.57
31 5 0.07
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (29 bp):
ATGTAATTCATTTTACGTAAAAAAATTTT
Found at i:51668 original size:15 final size:14
Alignment explanation
Indices: 51624--51675 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
51614 ACAAAAAAAA
51624 TTTA-GTAATTCAT
1 TTTACGTAATTCAT
* *
51637 TTTACGTAAAATAAT
1 TTTACGT-AATTCAT
*
51652 TTTCATGTAATTCAT
1 TTT-ACGTAATTCAT
51667 TTTACGTAA
1 TTTACGTAA
51676 AACAATTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
13 4 0.13
14 7 0.23
15 16 0.53
16 3 0.10
ACGTcount: A:0.35, C:0.10, G:0.08, T:0.48
Consensus pattern (14 bp):
TTTACGTAATTCAT
Found at i:52636 original size:127 final size:121
Alignment explanation
Indices: 52462--52847 Score: 391
Period size: 127 Copynumber: 3.3 Consensus size: 121
52452 ATTTTCAATA
*
52462 AATTAAGAAAAAAAATAATAAAATATATATTTTTATAGTTAATAATTTAAACATATATTTTAAAT
1 AATTAAG-AAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTT-AA-A-ATATTTTAAAT
52527 ATATATTCTTAACTTAAATAATAAGTTTGGCCTAATTTAAACCAAATATATATATATTATAT
62 ATATATTCTTAACTTAAATAATAA-TTTGGCCTAATTTAAACCAAA-ATATATATATTATAT
* *
52589 ACATTAAGAAAAAAATAATAAAATATATATTTTTATAATTAAGAATTT-AGATATTTTAAATATA
1 A-ATTAAGAAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAAATATTTTAAATATA
* * **
52653 TATTCTTAACTTAAATAAT-A--------AACTTAAACACACACATATAT-T-CGATA-
65 TATTCTTAACTTAAATAATAATTTGGCCTAATTTAAAC-CA-AAATATATATATTATAT
* *
52700 AATTAAGAACATAATAAT-AAATATATATTTTTATAGTTAAGAA-TTAAAATA-TTTAAATATAT
1 AATTAAGAAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAAATATTTTAAATATAT
* * *
52762 ATCCTT-ACTTCAAATAATAATCTTGGCCTACTTTAAACCAAAAAATATATATTCA-AT
66 ATTCTTAACTT-AAATAATAAT-TTGGCCTAATTTAAACCAAAATATATATATT-ATAT
*
52819 AAATT---AAAAAAATAATAAAATGTATATTT
1 -AATTAAGAAAAAAATAATAAAATATATATTT
52848 AAGATTATAC
Statistics
Matches: 217, Mismatches: 21, Indels: 51
0.75 0.07 0.18
Matches are distributed among these distances:
107 4 0.02
108 25 0.12
109 29 0.13
110 15 0.07
111 1 0.00
112 3 0.01
113 9 0.04
114 8 0.04
115 1 0.00
116 6 0.03
117 12 0.06
118 19 0.09
119 1 0.00
120 4 0.02
122 1 0.00
123 33 0.15
125 1 0.00
127 39 0.18
128 6 0.03
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (121 bp):
AATTAAGAAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAAATATTTTAAATATAT
ATTCTTAACTTAAATAATAATTTGGCCTAATTTAAACCAAAATATATATATTATAT
Found at i:57678 original size:9 final size:9
Alignment explanation
Indices: 57664--57688 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
57654 ATTTCTTTTT
57664 GTTTTGCTG
1 GTTTTGCTG
57673 GTTTTGCTG
1 GTTTTGCTG
57682 GTTTTGC
1 GTTTTGC
57689 AGGCACTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.32, T:0.56
Consensus pattern (9 bp):
GTTTTGCTG
Found at i:61184 original size:16 final size:19
Alignment explanation
Indices: 61163--61199 Score: 53
Period size: 16 Copynumber: 2.1 Consensus size: 19
61153 AAAATTATAT
61163 TATTTTA-TTT-A-TTTAA
1 TATTTTAGTTTCATTTTAA
61179 TATTTTAGTTTCATTTTAA
1 TATTTTAGTTTCATTTTAA
61198 TA
1 TA
61200 AAAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 1 0.06
19 7 0.39
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (19 bp):
TATTTTAGTTTCATTTTAA
Found at i:61610 original size:27 final size:29
Alignment explanation
Indices: 61572--61654 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
61562 TTCAGAAAAT
*
61572 GTAATTTATTTTAC-AAAAAAAATTT-AG
1 GTAATTCATTTTACGAAAAAAAATTTCAG
* * *
61599 GTAATTCATTTTACGTAAAATAATTTTCAT
1 GTAATTCATTTTACG-AAAAAAAATTTCAG
* *
61629 GTAATTCATTTTACGTAAAACAATTT
1 GTAATTCATTTTACGAAAAAAAATTT
61655 TTAAGTAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 13 0.29
29 16 0.36
30 16 0.36
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.43
Consensus pattern (29 bp):
GTAATTCATTTTACGAAAAAAAATTTCAG
Found at i:61635 original size:30 final size:29
Alignment explanation
Indices: 61570--61677 Score: 112
Period size: 30 Copynumber: 3.7 Consensus size: 29
61560 TTTTCAGAAA
* *
61570 ATGTAATTTATTTTAC--AAAAAAAATTT
1 ATGTAATTCATTTTACGTAAAAAAATTTT
* *
61597 AGGTAATTCATTTTACGTAAAATAATTTT
1 ATGTAATTCATTTTACGTAAAAAAATTTT
*
61626 CATGTAATTCATTTTACGTAAAACAATTTTT
1 -ATGTAATTCATTTTACGTAAAA-AAATTTT
* * *
61657 AAGTAATCCATTTTATGTAAA
1 ATGTAATTCATTTTACGTAAA
61678 TTATTTCTCA
Statistics
Matches: 67, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
27 14 0.21
29 9 0.13
30 39 0.58
31 5 0.07
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (29 bp):
ATGTAATTCATTTTACGTAAAAAAATTTT
Found at i:61639 original size:15 final size:14
Alignment explanation
Indices: 61594--61646 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
61584 ACAAAAAAAA
*
61594 TTTAGGTAATTCAT
1 TTTACGTAATTCAT
* *
61608 TTTACGTAAAATAAT
1 TTTACGT-AATTCAT
*
61623 TTTCATGTAATTCAT
1 TTT-ACGTAATTCAT
61638 TTTACGTAA
1 TTTACGTAA
61647 AACAATTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 11 0.37
15 16 0.53
16 3 0.10
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (14 bp):
TTTACGTAATTCAT
Found at i:62552 original size:128 final size:121
Alignment explanation
Indices: 62417--62822 Score: 427
Period size: 110 Copynumber: 3.4 Consensus size: 121
62407 ATAAAATTTT
*
62417 AAAATATATTTTCAATAAATTAAGAAAAATAATAATAAAATATATATTTTTATAGTTAATAATTT
1 AAAATATATTTTCAATAAATTAAG-AAAATAATAATAAAATATATATTTTTATAGTTAAGAATTT
62482 AAACATATATTTTAAATATATATTCTTAACTTAAATAATAAGTTTGGTCTAATTTAAACCAA
65 -AA-A-ATATTTTAAATATATATTCTTAACTTAAATAATAA-TTTGG-CTAATTTAAACCAA
* * *
62544 ATATATATATATATT-ATATACATTAAGAAAA-AATAATAAAATATATATTTTTATAATTAAGAA
1 A-A-A-ATATATTTTCA-ATAAATTAAGAAAATAATAATAAAATATATATTTTTATAGTTAAGAA
* *
62607 TTT-AGATATTTTAAATATATATTCTTAACTTAAATAAT-A-------AACTTAAA-CACA
62 TTTAAAATATTTTAAATATATATTCTTAACTTAAATAATAATTTGGCTAATTTAAACCA-A
* * * *
62658 CACATATA--TTCGATAAATTAAGAACATAATAATAAAATATATATTTTTATAGTTAAGAA-TTA
1 AAAATATATTTTCAATAAATTAAGAAAATAATAATAAAATATATATTTTTATAGTTAAGAATTTA
* *
62720 AAATATTTTAAATATATATCCTT-ACTTCAAATAATAATCTTGGCCTACTTTAAACCAA
66 AAATATTTTAAATATATATTCTTAACTT-AAATAATAAT-TTGG-CTAATTTAAACCAA
* *
62778 AAAATATATATTCAATAAATT-A-AAAA-AATAATAAAATGTATATTT
1 AAAATATATTTTCAATAAATTAAGAAAATAATAATAAAATATATATTT
62823 AAGATTATAC
Statistics
Matches: 236, Mismatches: 21, Indels: 52
0.76 0.07 0.17
Matches are distributed among these distances:
109 20 0.08
110 59 0.25
111 6 0.03
113 3 0.01
114 8 0.03
119 18 0.08
120 16 0.07
121 3 0.01
122 10 0.04
123 1 0.00
124 33 0.14
126 1 0.00
127 1 0.00
128 34 0.14
129 6 0.03
130 17 0.07
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (121 bp):
AAAATATATTTTCAATAAATTAAGAAAATAATAATAAAATATATATTTTTATAGTTAAGAATTTA
AAATATTTTAAATATATATTCTTAACTTAAATAATAATTTGGCTAATTTAAACCAA
Found at i:67652 original size:9 final size:9
Alignment explanation
Indices: 67638--67662 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
67628 ATTTCTTTTT
67638 GTTTTGCTG
1 GTTTTGCTG
67647 GTTTTGCTG
1 GTTTTGCTG
67656 GTTTTGC
1 GTTTTGC
67663 AGGCACTGGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.00, C:0.12, G:0.32, T:0.56
Consensus pattern (9 bp):
GTTTTGCTG
Found at i:76976 original size:30 final size:29
Alignment explanation
Indices: 76910--76996 Score: 104
Period size: 30 Copynumber: 3.0 Consensus size: 29
76900 TTTTCAGAAA
* * *
76910 ATGTAATTTATTTTAC-AAAAAAAAATTT
1 ATGTAATTCATTTTACGTAAAAAAATTTT
* *
76938 AGGTAATTCATTTTACGTAAAATAATTTT
1 ATGTAATTCATTTTACGTAAAAAAATTTT
*
76967 CATGTAATTCATTTTACGTAAAACAATTTT
1 -ATGTAATTCATTTTACGTAAAAAAATTTT
76997 TAAGTAATCC
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
28 14 0.28
29 9 0.18
30 27 0.54
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (29 bp):
ATGTAATTCATTTTACGTAAAAAAATTTT
Found at i:76980 original size:15 final size:14
Alignment explanation
Indices: 76935--76987 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
76925 CAAAAAAAAA
*
76935 TTTAGGTAATTCAT
1 TTTACGTAATTCAT
* *
76949 TTTACGTAAAATAAT
1 TTTACGT-AATTCAT
*
76964 TTTCATGTAATTCAT
1 TTT-ACGTAATTCAT
76979 TTTACGTAA
1 TTTACGTAA
76988 AACAATTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 11 0.37
15 16 0.53
16 3 0.10
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (14 bp):
TTTACGTAATTCAT
Found at i:77004 original size:30 final size:30
Alignment explanation
Indices: 76935--77018 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
76925 CAAAAAAAAA
* *
76935 TTTAGGTAATTCATTTTACGTAAAATAATT
1 TTTAAGTAATTCATTTTACGTAAAACAATT
* *
76965 TTCATGTAATTCATTTTACGTAAAACAATT
1 TTTAAGTAATTCATTTTACGTAAAACAATT
* * *
76995 TTTAAGTAATCCATTCTATGTAAA
1 TTTAAGTAATTCATTTTACGTAAA
77019 TTATATCTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (30 bp):
TTTAAGTAATTCATTTTACGTAAAACAATT
Found at i:83540 original size:27 final size:29
Alignment explanation
Indices: 83502--83584 Score: 89
Period size: 29 Copynumber: 2.9 Consensus size: 29
83492 TTCAGAAAAT
*
83502 GTAATTTATTTTAC-AAAAAAAATTT-AG
1 GTAATTCATTTTACGAAAAAAAATTTCAG
* * *
83529 GTAATTCATTTTACGTAAAATAATTTTCAT
1 GTAATTCATTTTACG-AAAAAAAATTTCAG
* *
83559 GTAATTCATTTTACGTAAAACAATTT
1 GTAATTCATTTTACGAAAAAAAATTT
83585 TTAAGTAATC
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
27 13 0.29
29 16 0.36
30 16 0.36
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.43
Consensus pattern (29 bp):
GTAATTCATTTTACGAAAAAAAATTTCAG
Found at i:83565 original size:30 final size:29
Alignment explanation
Indices: 83500--83585 Score: 104
Period size: 30 Copynumber: 3.0 Consensus size: 29
83490 TTTTCAGAAA
* *
83500 ATGTAATTTATTTTAC--AAAAAAAATTT
1 ATGTAATTCATTTTACGTAAAAAAATTTT
* *
83527 AGGTAATTCATTTTACGTAAAATAATTTT
1 ATGTAATTCATTTTACGTAAAAAAATTTT
*
83556 CATGTAATTCATTTTACGTAAAACAATTTT
1 -ATGTAATTCATTTTACGTAAAAAAATTTT
83586 TAAGTAATCC
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
27 14 0.28
29 9 0.18
30 27 0.54
ACGTcount: A:0.41, C:0.08, G:0.07, T:0.44
Consensus pattern (29 bp):
ATGTAATTCATTTTACGTAAAAAAATTTT
Found at i:83569 original size:15 final size:14
Alignment explanation
Indices: 83524--83576 Score: 52
Period size: 15 Copynumber: 3.6 Consensus size: 14
83514 ACAAAAAAAA
*
83524 TTTAGGTAATTCAT
1 TTTACGTAATTCAT
* *
83538 TTTACGTAAAATAAT
1 TTTACGT-AATTCAT
*
83553 TTTCATGTAATTCAT
1 TTT-ACGTAATTCAT
83568 TTTACGTAA
1 TTTACGTAA
83577 AACAATTTTT
Statistics
Matches: 30, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 11 0.37
15 16 0.53
16 3 0.10
ACGTcount: A:0.34, C:0.09, G:0.09, T:0.47
Consensus pattern (14 bp):
TTTACGTAATTCAT
Found at i:83593 original size:30 final size:30
Alignment explanation
Indices: 83524--83607 Score: 105
Period size: 30 Copynumber: 2.8 Consensus size: 30
83514 ACAAAAAAAA
* *
83524 TTTAGGTAATTCATTTTACGTAAAATAATT
1 TTTAAGTAATTCATTTTACGTAAAACAATT
* *
83554 TTCATGTAATTCATTTTACGTAAAACAATT
1 TTTAAGTAATTCATTTTACGTAAAACAATT
* * *
83584 TTTAAGTAATCCATTCTATGTAAA
1 TTTAAGTAATTCATTTTACGTAAA
83608 TTATTTCTCA
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.08, T:0.44
Consensus pattern (30 bp):
TTTAAGTAATTCATTTTACGTAAAACAATT
Found at i:84482 original size:128 final size:123
Alignment explanation
Indices: 84350--84787 Score: 473
Period size: 128 Copynumber: 3.5 Consensus size: 123
84340 AAATTTTAAA
* *
84350 ATATATTTTCAATAAATTAAGAAAAATAATAATAAAATATATATTTTTATAGTTAATAATTTAAA
1 ATATATATTCAATAAATTAAG-AAAA-AATAATAAAATATATATTTTTATAGTTAAGAATTTAAA
84415 CATATATTTTAAATATATATTCTTAACTTAAATAATAAGTTTGGCCTAATTTAAACCAAATAT
64 -A-ATATTTTAAATATATATTCTTAACTTAAATAATAA-TTTGGCCTAATTTAAACCAAATAT
* * *
84478 ATATATATTCTATACATTAAGAAAAAATAATAAAAATATATATTTTTATAATTAAGAATTTAGAT
1 ATATATATTCAATAAATTAAGAAAAAATAAT-AAAATATATATTTTTATAGTTAAGAA-TT---T
* * ** * *
84543 ATTTTAAAATATTTTAAATATATATTCTTAACTTAAATAATAA----ACTTAA-ACACACACATA
61 A----AAAATATTTTAAATATATATTCTTAACTTAAATAATAATTTGGCCTAATTTAAAC-CAAA
84603 TAT
121 TAT
* *
84606 ATATATATTCGATAAATTAAGAACATAATAATAAAATATATATTTTTATAGTTAAGAA-TT-AAA
1 ATATATATTCAATAAATTAAGAA-AAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAAA
* * * * * *
84669 ATATTTTAAATATATATCCTTACCTCAAATAGTAATCTTGGCCTACTTTAAACCAAA-AA
65 ATATTTTAAATATATATTCTTAACTTAAATAATAAT-TTGGCCTAATTTAAACCAAATAT
*
84728 ATATATATTCAATAAATT-A-AAAAAATAATAAAATGTATATTTTTATAGTTAAGAATTTAA
1 ATATATATTCAATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAA
84788 TATTATACTA
Statistics
Matches: 261, Mismatches: 30, Indels: 45
0.78 0.09 0.13
Matches are distributed among these distances:
118 34 0.13
119 32 0.12
120 4 0.02
121 2 0.01
122 18 0.07
123 7 0.03
124 3 0.01
126 7 0.03
127 31 0.12
128 76 0.29
129 7 0.03
131 2 0.01
133 35 0.13
134 1 0.00
135 2 0.01
ACGTcount: A:0.49, C:0.07, G:0.04, T:0.39
Consensus pattern (123 bp):
ATATATATTCAATAAATTAAGAAAAAATAATAAAATATATATTTTTATAGTTAAGAATTTAAAAA
TATTTTAAATATATATTCTTAACTTAAATAATAATTTGGCCTAATTTAAACCAAATAT
Found at i:84678 original size:118 final size:117
Alignment explanation
Indices: 84546--84784 Score: 286
Period size: 118 Copynumber: 2.0 Consensus size: 117
84536 TTTAGATATT
* * * * *
84546 TTAAAATATTTTAAATATATATTCTTAACTTAAATAATAAACTTAAAC-AC-ACA-CATATATAT
1 TTAAAATATTTTAAATATATATCCTTAACTCAAATAATAAACTTAAACTACTAAACCA-AAAAAT
*
84608 ATATATTCGATAAATTAAGAACATAATAATAAAATATATATTTTTATAGTTAAGAA
65 ATATATTCAATAAATTAA-AA-A-AATAATAAAATATATATTTTTATAGTTAAGAA
* * * ***
84664 TTAAAATATTTTAAATATATATCCTTACCTCAAATAGTAATCTTGGCCTACTTTAAACCAAAAAA
1 TTAAAATATTTTAAATATATATCCTTAACTCAAATAATAAACTTAAACTAC--TAAACCAAAAAA
*
84729 TATATATTCAATAAATTAAAAAAATAATAAAATGTATATTTTTATAGTTAAGAA
64 TATATATTCAATAAATTAAAAAAATAATAAAATATATATTTTTATAGTTAAGAA
84783 TT
1 TT
84785 TAATATTATA
Statistics
Matches: 103, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
118 40 0.39
119 35 0.34
120 1 0.01
121 2 0.02
122 23 0.22
123 2 0.02
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (117 bp):
TTAAAATATTTTAAATATATATCCTTAACTCAAATAATAAACTTAAACTACTAAACCAAAAAATA
TATATTCAATAAATTAAAAAAATAATAAAATATATATTTTTATAGTTAAGAA
Found at i:95110 original size:3 final size:3
Alignment explanation
Indices: 95102--95202 Score: 148
Period size: 3 Copynumber: 33.7 Consensus size: 3
95092 TTTTTATCCA
* * *
95102 TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CAT TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
95150 TAT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT TTT TAC TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
95198 TAT TA
1 TAT TA
95203 AATATATTAA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 86 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:95702 original size:18 final size:18
Alignment explanation
Indices: 95672--95706 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
95662 AGAGACAGAA
95672 ACAGAAAACGAAAAAAAT
1 ACAGAAAACGAAAAAAAT
95690 ACAGAGAAA-GAAAAAAA
1 ACAGA-AAACGAAAAAAA
95707 AAAAAACAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.03
Consensus pattern (18 bp):
ACAGAAAACGAAAAAAAT
Found at i:96652 original size:21 final size:22
Alignment explanation
Indices: 96622--96663 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
96612 GATATTTTTG
**
96622 TTTTATTATATTGTTAAATATT
1 TTTTATTATATTCATAAATATT
96644 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
96664 ACATATAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (22 bp):
TTTTATTATATTCATAAATATT
Found at i:108014 original size:1 final size:1
Alignment explanation
Indices: 108008--108125 Score: 74
Period size: 1 Copynumber: 118.0 Consensus size: 1
107998 CTTGAAGAAT
* * * * * * * * *
108008 AAAAAAAAAGAAAAAAAAGAAAAAAAAAAAGAAAAAAGAAAAGAAAAAGAAAAGAAAGAAAAGAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * * * ** ** *
108073 AAAAGAAAAGAAAAAAATAGAAAATGAAAAATGAAAAAAAAAAGAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
108126 GAAAGGGGGT
Statistics
Matches: 83, Mismatches: 34, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 83 1.00
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (1 bp):
A
Found at i:108021 original size:5 final size:5
Alignment explanation
Indices: 108008--108129 Score: 92
Period size: 5 Copynumber: 23.6 Consensus size: 5
107998 CTTGAAGAAT
* *
108008 AAAAA AAAAG AAAA- AAAAG AAAA- AAAA- AAAGAA AAAAG AAAAG AAAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAAG AAA-AG AAAAG AAAAG -AAAAG
108057 AAAAG -AAAG AAAAG AAAAAAG AAAAG AAAA- AAATAG AAAATG AAAAATG
1 AAAAG AAAAG AAAAG --AAAAG AAAAG AAAAG AAA-AG AAAA-G -AAAA-G
* *
108106 AAAAAA AAAAG AAAAA AAAAG AAA
1 -AAAAG AAAAG AAAAG AAAAG AAA
108130 GGGGGTCAAG
Statistics
Matches: 100, Mismatches: 6, Indels: 22
0.78 0.05 0.17
Matches are distributed among these distances:
4 18 0.18
5 54 0.54
6 12 0.12
7 16 0.16
ACGTcount: A:0.84, C:0.00, G:0.13, T:0.02
Consensus pattern (5 bp):
AAAAG
Found at i:108025 original size:12 final size:12
Alignment explanation
Indices: 108008--108125 Score: 114
Period size: 12 Copynumber: 9.4 Consensus size: 12
107998 CTTGAAGAAT
*
108008 AAAAAAA-AAGA
1 AAAAAAAGAAAA
108019 AAAAAAAGAAAA
1 AAAAAAAGAAAA
108031 AAAAAAAGAAAA
1 AAAAAAAGAAAA
*
108043 AAGAAAAGAAAAA
1 AAAAAAAG-AAAA
108056 GAAAAGAAAGAAAA
1 -AAAA-AAAGAAAA
*
108070 GAAAAAAGAAAAGA
1 AAAAAAAG-AAA-A
108084 AAAAAATAGAAAA
1 AAAAAA-AGAAAA
* *
108097 TGAAAAATG-AAA
1 -AAAAAAAGAAAA
108109 AAAAAAAGAAAA
1 AAAAAAAGAAAA
108121 AAAAA
1 AAAAA
108126 GAAAGGGGGT
Statistics
Matches: 89, Mismatches: 9, Indels: 17
0.77 0.08 0.15
Matches are distributed among these distances:
11 13 0.15
12 37 0.42
13 12 0.13
14 21 0.24
15 6 0.07
ACGTcount: A:0.85, C:0.00, G:0.13, T:0.03
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:109208 original size:84 final size:84
Alignment explanation
Indices: 109065--109629 Score: 1058
Period size: 84 Copynumber: 6.7 Consensus size: 84
109055 AACCTTTTAT
* **
109065 ATGTGCCCAATAGCATCTTCTGGAAATGTTCTTTGAGTTATCTGATCTGGTTTTACAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
109130 CATTGAAGTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
*
109149 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
109214 CATTGAAGTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
*
109233 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
109298 CATTGAAGTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
*
109317 ATGTGCTCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
109382 CATTGAAGTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
109401 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
*
109466 CATTGAATTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
109485 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
*
109550 CATTGAATTTAGAAGATGA
66 CATTGAAGTTAGAAGATGA
109569 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAAC
1 ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAAC
109630 TTATAGAACC
Statistics
Matches: 475, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 475 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (84 bp):
ATGTGCCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACCAAT
CATTGAAGTTAGAAGATGA
Found at i:110408 original size:113 final size:113
Alignment explanation
Indices: 110240--110877 Score: 1015
Period size: 113 Copynumber: 5.6 Consensus size: 113
110230 TACAAGGTAG
*
110240 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
110305 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
*
110353 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
110418 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
*
110466 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
110531 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
110579 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *** * * * * * *
110644 AACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTACCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
* * *
110692 GGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAGGTTCATAATGAGAAGAACTTGTTC
1 AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
* *** * * * * * *
110757 AACTTTTTGTTTAAATTCATCATTTGATGGATCAACATTGCCAGAGAA
66 AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
* *
110805 AGTTCATGAATGAAAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT
1 AGTTCAT-AATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTT
110870 CAACCTTT
65 CAACCTTT
110878 GTTTGATATT
Statistics
Matches: 503, Mismatches: 21, Indels: 1
0.96 0.04 0.00
Matches are distributed among these distances:
113 443 0.88
114 60 0.12
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (113 bp):
AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTC
AACCTTTTACCTGAATCCATCATTTGGTGGATCATCTTTTCCAGAGAA
Found at i:111180 original size:3 final size:3
Alignment explanation
Indices: 111172--111272 Score: 132
Period size: 3 Copynumber: 33.7 Consensus size: 3
111162 TTTTTATCCA
* * *
111172 TAT TAT TAT TAT TAT TAT TAT TAA TAT TAT TAT TAT CA- TAT TAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * *
111219 TATT TAT TAT TAT TTT TAT TAT TAT TAT TAT TAT TAT TTT TAC TAT
1 TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
111265 TAT TAT TA
1 TAT TAT TA
111273 AATATATTAA
Statistics
Matches: 84, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
2 1 0.01
3 80 0.95
4 3 0.04
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:111773 original size:18 final size:18
Alignment explanation
Indices: 111743--111777 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
111733 AGAGACAGAA
111743 ACAGAAAACGAAAAAAAT
1 ACAGAAAACGAAAAAAAT
111761 ACAGAGAAA-GAAAAAAA
1 ACAGA-AAACGAAAAAAA
111778 AACAAACTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 13 0.81
19 3 0.19
ACGTcount: A:0.74, C:0.09, G:0.14, T:0.03
Consensus pattern (18 bp):
ACAGAAAACGAAAAAAAT
Found at i:112661 original size:20 final size:21
Alignment explanation
Indices: 112624--112664 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
112614 GATATTTTTG
**
112624 TTTTATTATATTGTTAAATAT
1 TTTTATTATATTCATAAATAT
112645 TTTTA-TATATTCATAAATAT
1 TTTTATTATATTCATAAATAT
112665 ACATATAATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (21 bp):
TTTTATTATATTCATAAATAT
Found at i:115611 original size:19 final size:19
Alignment explanation
Indices: 115584--115639 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
115574 ACCTGATCTG
*
115584 ACCCTTTGACTTTGACCCA
1 ACCCGTTGACTTTGACCCA
**
115603 ACCCGTTGACTTTGACCTG
1 ACCCGTTGACTTTGACCCA
115622 ACCCGTTGACTATTGACC
1 ACCCGTTGACT-TTGACC
115640 GGTCTAAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 27 0.82
20 6 0.18
ACGTcount: A:0.20, C:0.34, G:0.16, T:0.30
Consensus pattern (19 bp):
ACCCGTTGACTTTGACCCA
Found at i:115662 original size:22 final size:23
Alignment explanation
Indices: 115626--115683 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 23
115616 GACCTGACCC
115626 GTTGACTATTGACCGGTCTAAAT
1 GTTGACTATTGACCGGTCTAAAT
* *
115649 GTTGACT-TTGACCGGTCTGACT
1 GTTGACTATTGACCGGTCTAAAT
*
115671 GTTGACAATTGAC
1 GTTGACTATTGAC
115684 TTTGACAAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
22 19 0.61
23 12 0.39
ACGTcount: A:0.22, C:0.19, G:0.24, T:0.34
Consensus pattern (23 bp):
GTTGACTATTGACCGGTCTAAAT
Found at i:121269 original size:35 final size:36
Alignment explanation
Indices: 121230--121311 Score: 107
Period size: 35 Copynumber: 2.4 Consensus size: 36
121220 AATGGATTAT
* * *
121230 GAATTTGGA-GTTGGGCATGTAATTGAAGTATTTTG
1 GAATTTGGAGGTTGAGAATGTAACTGAAGTATTTTG
*
121265 GAATTT-GAGGTTTAGAATGTAACTGAAGTATTTTG
1 GAATTTGGAGGTTGAGAATGTAACTGAAGTATTTTG
121300 GAATTTGG-GGTT
1 GAATTTGGAGGTT
121312 TATAATATAA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
34 2 0.05
35 38 0.93
36 1 0.02
ACGTcount: A:0.27, C:0.02, G:0.30, T:0.40
Consensus pattern (36 bp):
GAATTTGGAGGTTGAGAATGTAACTGAAGTATTTTG
Found at i:121312 original size:35 final size:35
Alignment explanation
Indices: 121246--121313 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
121236 GGAGTTGGGC
*
121246 ATGTAATTGAAGTATTTTGGAATTTGAGGTTTAGA
1 ATGTAACTGAAGTATTTTGGAATTTGAGGTTTAGA
*
121281 ATGTAACTGAAGTATTTTGGAATTTGGGGTTTA
1 ATGTAACTGAAGTATTTTGGAATTTGAGGTTTA
121314 TAATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.29, C:0.01, G:0.26, T:0.43
Consensus pattern (35 bp):
ATGTAACTGAAGTATTTTGGAATTTGAGGTTTAGA
Found at i:121918 original size:21 final size:21
Alignment explanation
Indices: 121894--121933 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
121884 TTTATCTATC
* *
121894 ATTAAATTAGTGAAATAATAT
1 ATTAAATTAATAAAATAATAT
121915 ATTAAATTAATAAAATAAT
1 ATTAAATTAATAAAATAAT
121934 CTCATTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (21 bp):
ATTAAATTAATAAAATAATAT
Found at i:124239 original size:42 final size:41
Alignment explanation
Indices: 124175--124253 Score: 113
Period size: 42 Copynumber: 1.9 Consensus size: 41
124165 CAATCCGTAA
* *
124175 TGATATTCAAGCTTTCATAGATCTCATTCCACCATTGGTGG
1 TGATATTCAAGCTTTCACAGATCCCATTCCACCATTGGTGG
* *
124216 TGATATTCAAAGTTTTCACAGATCCCATTTCACCATTG
1 TGATATTC-AAGCTTTCACAGATCCCATTCCACCATTG
124254 AGGATCTCAT
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
41 8 0.24
42 25 0.76
ACGTcount: A:0.27, C:0.23, G:0.14, T:0.37
Consensus pattern (41 bp):
TGATATTCAAGCTTTCACAGATCCCATTCCACCATTGGTGG
Found at i:125430 original size:20 final size:20
Alignment explanation
Indices: 125407--125444 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
125397 ATCAATACAA
*
125407 GATGCTCGGTATCGAGATTG
1 GATGCTCGATATCGAGATTG
*
125427 GATGCTCGATCTCGAGAT
1 GATGCTCGATATCGAGAT
125445 CACTTGTCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (20 bp):
GATGCTCGATATCGAGATTG
Found at i:125496 original size:20 final size:20
Alignment explanation
Indices: 125471--125523 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
125461 GATGGACTAA
* *
125471 TCTCTATATTGAAGGATTGG
1 TCTCTATATCGAAGGACTGG
*
125491 TCTCTATACCGAAGGACTGG
1 TCTCTATATCGAAGGACTGG
125511 TCTCTATATCGAA
1 TCTCTATATCGAA
125524 TATTGAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (20 bp):
TCTCTATATCGAAGGACTGG
Found at i:127823 original size:18 final size:19
Alignment explanation
Indices: 127800--127838 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
127790 AAAGAAACAC
*
127800 AAAAAATTATTGTTT-TAA
1 AAAAAATCATTGTTTCTAA
*
127818 AAAAAATCATTTTTTCTAA
1 AAAAAATCATTGTTTCTAA
127837 AA
1 AA
127839 TCTTGAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (19 bp):
AAAAAATCATTGTTTCTAA
Found at i:131559 original size:18 final size:19
Alignment explanation
Indices: 131538--131578 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 19
131528 AAAAATTTTA
131538 AAAAATAA-AAAAATATAT
1 AAAAATAATAAAAATATAT
*
131556 -AAAATAATTAAAATATAT
1 AAAAATAATAAAAATATAT
131574 AAAAA
1 AAAAA
131579 AATTGAAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (19 bp):
AAAAATAATAAAAATATAT
Found at i:131582 original size:18 final size:18
Alignment explanation
Indices: 131547--131587 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
131537 AAAAAATAAA
*
131547 AAAATATATAAAATAATT
1 AAAATATATAAAAAAATT
131565 AAAATATATAAAAAAATT
1 AAAATATATAAAAAAATT
*
131583 GAAAT
1 AAAAT
131588 TGTTAGAGAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.29
Consensus pattern (18 bp):
AAAATATATAAAAAAATT
Found at i:132740 original size:26 final size:26
Alignment explanation
Indices: 132670--132746 Score: 75
Period size: 26 Copynumber: 3.0 Consensus size: 26
132660 CTGTGCATCG
* * * *
132670 TATATCAAAACACATCATTGATGTAA
1 TATATCAAAATACATCACTAATATAA
* * * *
132696 CAGATTAAAATACAACACTAATATAA
1 TATATCAAAATACATCACTAATATAA
132722 TATATCAAAATACATCACTAA-ATAA
1 TATATCAAAATACATCACTAATATAA
132747 ATTATTTTTA
Statistics
Matches: 39, Mismatches: 12, Indels: 1
0.75 0.23 0.02
Matches are distributed among these distances:
25 4 0.10
26 35 0.90
ACGTcount: A:0.53, C:0.16, G:0.04, T:0.27
Consensus pattern (26 bp):
TATATCAAAATACATCACTAATATAA
Found at i:136433 original size:32 final size:32
Alignment explanation
Indices: 136366--136436 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
136356 AATCGATATG
* * *
136366 ATATTGACCCGACCCAAAATATAACCGATTAA
1 ATATTGACCCAACCCAAAATACAACCGATCAA
* *
136398 ATATTGACCCAACCCAAAAGT-CAACCGGTCCA
1 ATATTGACCCAACCCAAAA-TACAACCGATCAA
136430 ATATTGA
1 ATATTGA
136437 TCAAAATAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
32 32 0.97
33 1 0.03
ACGTcount: A:0.41, C:0.27, G:0.11, T:0.21
Consensus pattern (32 bp):
ATATTGACCCAACCCAAAATACAACCGATCAA
Done.