Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002336.1 Hibiscus syriacus cultivar Beakdansim tig00004773_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: 54211
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Found at i:2792 original size:14 final size:15
Alignment explanation
Indices: 2769--2905 Score: 94
Period size: 16 Copynumber: 9.3 Consensus size: 15
2759 ATTTCGCTTG
*
2769 AAGAAGAAAT-AAAA
1 AAGAAAAAATGAAAA
*
2783 GAGAAAAAATGAAAA
1 AAGAAAAAATGAAAA
2798 AAG-AAAAATGAAAA
1 AAGAAAAAATGAAAA
*
2812 AATGAAAAAATGAGAAG
1 AA-GAAAAAATGA-AAA
2829 AAGAAAAAGA-GAAAAA
1 AAGAAAAA-ATG-AAAA
2845 AATGAGAAAAATG-AAA
1 AA-GA-AAAAATGAAAA
**
2861 AAG--GGAA-GAAAA
1 AAGAAAAAATGAAAA
*
2873 ATG--AAAATGAAAA
1 AAGAAAAAATGAAAA
2886 AAGAGAAAAATGAAAA
1 AAGA-AAAAATGAAAA
2902 AAGA
1 AAGA
2906 GAAATAAAAG
Statistics
Matches: 98, Mismatches: 11, Indels: 26
0.73 0.08 0.19
Matches are distributed among these distances:
11 1 0.01
12 9 0.09
13 7 0.07
14 21 0.21
15 8 0.08
16 38 0.39
17 9 0.09
18 5 0.05
ACGTcount: A:0.73, C:0.00, G:0.20, T:0.07
Consensus pattern (15 bp):
AAGAAAAAATGAAAA
Found at i:2796 original size:8 final size:8
Alignment explanation
Indices: 2785--2903 Score: 99
Period size: 8 Copynumber: 14.9 Consensus size: 8
2775 AAATAAAAGA
2785 GAAAAAAT
1 GAAAAAAT
2793 GAAAAAA-
1 GAAAAAAT
2800 G-AAAAAT
1 GAAAAAAT
2807 GAAAAAAT
1 GAAAAAAT
2815 GAAAAAAT
1 GAAAAAAT
*
2823 GAGAAGAA-
1 GA-AAAAAT
2831 GAAAAAGA-
1 GAAAAA-AT
2839 GAAAAAAAT
1 G-AAAAAAT
2848 GAGAAAAAT
1 GA-AAAAAT
**
2857 GAAAAAGG
1 GAAAAAAT
2865 GAAGAAAAAT
1 G-A-AAAAAT
2875 G--AAAAT
1 GAAAAAAT
2881 GAAAAAA-
1 GAAAAAAT
2888 GAGAAAAAT
1 GA-AAAAAT
2897 GAAAAAA
1 GAAAAAA
2904 GAGAAATAAA
Statistics
Matches: 92, Mismatches: 6, Indels: 26
0.74 0.05 0.21
Matches are distributed among these distances:
6 11 0.12
7 7 0.08
8 48 0.52
9 21 0.23
10 5 0.05
ACGTcount: A:0.73, C:0.00, G:0.19, T:0.08
Consensus pattern (8 bp):
GAAAAAAT
Found at i:2836 original size:25 final size:25
Alignment explanation
Indices: 2786--2862 Score: 83
Period size: 25 Copynumber: 3.2 Consensus size: 25
2776 AATAAAAGAG
2786 AAAAAATGAAAAAA-GA-AAAATG-
1 AAAAAATGAAAAAATGAGAAAATGA
2808 AAAAAATGAAAAAATGAGAAGAA-GA
1 AAAAAATGAAAAAATGAGAA-AATGA
*
2833 AAAAGA-GAAAAAAATGAGAAAAATGA
1 AAAAAATG-AAAAAATGAG-AAAATGA
2859 AAAA
1 AAAA
2863 GGGAAGAAAA
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
22 14 0.30
23 2 0.04
24 4 0.09
25 19 0.40
26 8 0.17
ACGTcount: A:0.75, C:0.00, G:0.17, T:0.08
Consensus pattern (25 bp):
AAAAAATGAAAAAATGAGAAAATGA
Found at i:2885 original size:50 final size:49
Alignment explanation
Indices: 2799--2903 Score: 126
Period size: 50 Copynumber: 2.1 Consensus size: 49
2789 AAATGAAAAA
*
2799 AGAAAAATGAAAAAATGAAAAAATGAGAAGAAGAAAAAGAGAAAAAAATG
1 AGAAAAATGAAAAAAGGAAAAAATGAGAAGAAGAAAAA-AGAAAAAAATG
* * *
2849 AGAAAAATGAAAAAGGGAAGAAAAATGA-AA-ATGAAAAAAGAGAAAAATG
1 AGAAAAATGAAAAAAGG-A-AAAAATGAGAAGAAGAAAAAAGAAAAAAATG
2898 A-AAAAA
1 AGAAAAA
2904 GAGAAATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
48 5 0.10
49 11 0.22
50 22 0.45
51 3 0.06
52 8 0.16
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (49 bp):
AGAAAAATGAAAAAAGGAAAAAATGAGAAGAAGAAAAAAGAAAAAAATG
Found at i:2909 original size:25 final size:24
Alignment explanation
Indices: 2794--2903 Score: 88
Period size: 25 Copynumber: 4.5 Consensus size: 24
2784 AGAAAAAATG
2794 AAAAA-AGAAAAATGAAAAA-ATGA
1 AAAAAGAGAAAAATGAAAAAGA-GA
*
2817 AAAAATGAGAAGAA-GAAAAAGAGAA
1 AAAAA-GAGAAAAATGAAAAAGAG-A
*
2842 AAAAATGAGAAAAATGAAAAAGGGA
1 AAAAA-GAGAAAAATGAAAAAGAGA
2867 AGAAAA-ATG-AAAATGAAAAAAGAGA
1 A-AAAAGA-GAAAAATG-AAAAAGAGA
*
2892 AAAATGA-AAAAA
1 AAAAAGAGAAAAA
2904 GAGAAATAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
23 5 0.07
24 21 0.29
25 34 0.47
26 12 0.17
ACGTcount: A:0.74, C:0.00, G:0.19, T:0.07
Consensus pattern (24 bp):
AAAAAGAGAAAAATGAAAAAGAGA
Found at i:8132 original size:9 final size:8
Alignment explanation
Indices: 8118--8164 Score: 55
Period size: 8 Copynumber: 6.0 Consensus size: 8
8108 TAAAAACAAC
8118 AAATAAAA
1 AAATAAAA
8126 TAAATAAAA
1 -AAATAAAA
8135 AACA-AAAA
1 AA-ATAAAA
8143 AAAT-AAA
1 AAATAAAA
8150 AAATAAAA
1 AAATAAAA
8158 AAA-AAAA
1 AAATAAAA
8165 CCAATTGCCT
Statistics
Matches: 35, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
7 12 0.34
8 14 0.40
9 9 0.26
ACGTcount: A:0.87, C:0.02, G:0.00, T:0.11
Consensus pattern (8 bp):
AAATAAAA
Found at i:8135 original size:23 final size:23
Alignment explanation
Indices: 8103--8164 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
8093 AAACATAATT
*
8103 AAAAAT-AAAAACAACAAATAA-A
1 AAAAATAAAAAACAA-AAAAAATA
*
8125 ATAAATAAAAAACAAAAAAAATA
1 AAAAATAAAAAACAAAAAAAATA
8148 AAAAATAAAAAA-AAAAA
1 AAAAATAAAAAACAAAAA
8165 CCAATTGCCT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (23 bp):
AAAAATAAAAAACAAAAAAAATA
Found at i:8140 original size:20 final size:22
Alignment explanation
Indices: 8105--8164 Score: 67
Period size: 20 Copynumber: 3.0 Consensus size: 22
8095 ACATAATTAA
*
8105 AAATAAAAACAACAAATAAAAT
1 AAATAAAAACAACAAAAAAAAT
8127 AAAT-AAAA-AACAAAAAAAAT
1 AAATAAAAACAACAAAAAAAAT
*
8147 AAA-AAATA-AA-AAAAAAAA
1 AAATAAAAACAACAAAAAAAA
8165 CCAATTGCCT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
19 8 0.23
20 19 0.54
21 4 0.11
22 4 0.11
ACGTcount: A:0.85, C:0.05, G:0.00, T:0.10
Consensus pattern (22 bp):
AAATAAAAACAACAAAAAAAAT
Found at i:8146 original size:16 final size:16
Alignment explanation
Indices: 8122--8161 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
8112 AACAACAAAT
*
8122 AAAATAAATAAAAAAC
1 AAAAAAAATAAAAAAC
*
8138 AAAAAAAATAAAAAAT
1 AAAAAAAATAAAAAAC
8154 AAAAAAAA
1 AAAAAAAA
8162 AAACCAATTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.88, C:0.03, G:0.00, T:0.10
Consensus pattern (16 bp):
AAAAAAAATAAAAAAC
Found at i:8379 original size:22 final size:20
Alignment explanation
Indices: 8343--8396 Score: 74
Period size: 22 Copynumber: 2.6 Consensus size: 20
8333 CAAAATGCAA
8343 AAATTAAAATAACAGT-AGCT
1 AAATTAAAATAACAGTGA-CT
8363 AAATTAGAAACTAACAGTGACT
1 AAATTA-AAA-TAACAGTGACT
8385 AAATTAAAATAA
1 AAATTAAAATAA
8397 ACAAAACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 9 0.29
21 6 0.19
22 15 0.48
23 1 0.03
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.24
Consensus pattern (20 bp):
AAATTAAAATAACAGTGACT
Found at i:9817 original size:2 final size:2
Alignment explanation
Indices: 9812--9849 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
9802 AAAAAAGTGT
9812 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9850 TAATATTGCT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11248 original size:21 final size:21
Alignment explanation
Indices: 11223--11265 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
11213 ATTTTATAAC
11223 TCGACTTGAATTTGATTTTTT
1 TCGACTTGAATTTGATTTTTT
*
11244 TCGACTTGAATTTTATTTTTT
1 TCGACTTGAATTTGATTTTTT
11265 T
1 T
11266 AGTTACGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.19, C:0.09, G:0.12, T:0.60
Consensus pattern (21 bp):
TCGACTTGAATTTGATTTTTT
Found at i:13622 original size:14 final size:14
Alignment explanation
Indices: 13605--13641 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
13595 AAAAAGATAG
13605 AAAATTAAAGCAAT
1 AAAATTAAAGCAAT
* *
13619 AAAATTAAAGGACT
1 AAAATTAAAGCAAT
13633 AAAATTAAA
1 AAAATTAAA
13642 TAAATAAAGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.65, C:0.05, G:0.08, T:0.22
Consensus pattern (14 bp):
AAAATTAAAGCAAT
Found at i:13649 original size:14 final size:14
Alignment explanation
Indices: 13605--13649 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
13595 AAAAAGATAG
*
13605 AAAATTAAAGCAAT
1 AAAATTAAAGAAAT
* *
13619 AAAATTAAAGGACT
1 AAAATTAAAGAAAT
*
13633 AAAATTAAATAAAT
1 AAAATTAAAGAAAT
13647 AAA
1 AAA
13650 GTAAAGGCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (14 bp):
AAAATTAAAGAAAT
Found at i:14168 original size:29 final size:29
Alignment explanation
Indices: 14107--14168 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
14097 GTTAGAGTGT
* ** *
14107 AATAAAATAAAAGTTAGTGGTTAATATGC
1 AATAAAATAAAAATTAGTAATTAATATGA
14136 AATAAAATAAAAATTAGTAATTAAT-TCGA
1 AATAAAATAAAAATTAGTAATTAATAT-GA
14165 AATA
1 AATA
14169 TAAAAGCATG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.31
Consensus pattern (29 bp):
AATAAAATAAAAATTAGTAATTAATATGA
Found at i:15017 original size:15 final size:16
Alignment explanation
Indices: 14997--15026 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
14987 ATATAGTGAC
14997 AAATTTT-GTAACTAA
1 AAATTTTAGTAACTAA
15012 AAATTTTAGTAACTA
1 AAATTTTAGTAACTA
15027 TAACAGAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.47, C:0.07, G:0.07, T:0.40
Consensus pattern (16 bp):
AAATTTTAGTAACTAA
Found at i:15387 original size:182 final size:179
Alignment explanation
Indices: 15092--15423 Score: 386
Period size: 182 Copynumber: 1.8 Consensus size: 179
15082 TTGTTTGTGA
* * *
15092 TTATATATTTTAATTATAGAGATAAAATGTATAGTCACAAATGATTATATCCAATTTTTAGTACA
1 TTATATATTTTAATTATAGAGACAAAATATATAGTCACAAATAATTATATCCAATTTTTA-TACA
*
15157 AAAACAAAATCATATAGTGACATGATTTGTAACTATAAGCTATAATTATTATTACAAAAAAATTG
65 AAAACAAAATCATATAGTGACATAATTTGTAACTATAAGCTATAATTATTA-TA-AAAAAAATTG
* *
15222 TCAGAACAAATAATGAGATTCAAATTTTTTCGTAAAAAAACAGTGTCTTCCG
128 TCACAAAAAATAATGAGATTCAAATTTTTTCGTAAAAAAACAGTGTCTTCCG
* * * * *
15274 TTATATGTTTTAATTATAGTGACAAAATATATTGTCACAAA-AATTTTCCTCCATATTTTT-TAC
1 TTATATATTTTAATTATAGAGACAAAATATATAGTCACAAATAATTAT-ATCCA-ATTTTTATAC
* * * * * *
15337 -ACAA-AAAATTATATAGTGACA-AATTTTGTAATTATAAGTTTTAGTAATTATTATAGAAAACA
64 AAAAACAAAATCATATAGTGACATAA-TTTGTAACTATAAG--CTA-TAATTATTATAAAAAAAA
*
15399 TTGTCACAAAAAATAATGATATTCA
125 TTGTCACAAAAAATAATGAGATTCA
15424 CGTTTTTTTG
Statistics
Matches: 126, Mismatches: 18, Indels: 14
0.80 0.11 0.09
Matches are distributed among these distances:
178 1 0.01
179 29 0.23
180 30 0.24
181 11 0.09
182 49 0.39
183 6 0.05
ACGTcount: A:0.43, C:0.10, G:0.09, T:0.37
Consensus pattern (179 bp):
TTATATATTTTAATTATAGAGACAAAATATATAGTCACAAATAATTATATCCAATTTTTATACAA
AAACAAAATCATATAGTGACATAATTTGTAACTATAAGCTATAATTATTATAAAAAAAATTGTCA
CAAAAAATAATGAGATTCAAATTTTTTCGTAAAAAAACAGTGTCTTCCG
Found at i:16110 original size:415 final size:411
Alignment explanation
Indices: 15288--16116 Score: 1069
Period size: 415 Copynumber: 2.0 Consensus size: 411
15278 ATGTTTTAAT
* * *
15288 TATAGTGACAAAATATATTGTCACAAAAATTTTCCTCCATATTTTTTACACAAAAAATTATATAG
1 TATAGTAACAAAATATATTGTCACAAAAAATTTCCTCCATATTTTTTACACAAAAAATTATATAA
* * * * *
15353 TGACAAATTTTGTAATTATAAGTTTTAGTAATTATTATAGAAAACATTGTCACAAAAAATAATGA
66 TAACAAATTTTATAACTATAAGTTTTAGTAATTATTACAGAAAACATTGTCACAAAAAATAACGA
* * * **
15418 TATTCACGTTTTTTTGACAAATTATATTTGTAGTTATAAAATTAACTATAGTGATAGTATATATT
131 TATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAAATTAACTATAGTGATAACATATATT
* * * * * *
15483 GTCTTAATTATTTTTCTTCACTTTTTTGTTTTAAAAGTTATATTGATAATTTTTATAATTATAAT
196 GTCATAAATATTTTTCTCCACTTTTTTGTTTAAAAAGTTATATTCATAAGTTTTATAATTATAAT
* *
15548 TTATAGTTATTGTTATAGAAAAAATTATCATATCAAATAATAAAATTCAGATTTTTTATAATCAA
261 TTATAGTTATTGTTATA-AAAAAATTATCACATCAAATAATAAAATTCAGAATTTTTATAATCAA
* * * **
15613 TTACTTTTTTACCTATATATTTTAATTATTATGAAAAATTATACTATTAGAATTATTTATCCCTA
325 TTACTTTTTTACCTATATATTTTAATCATTATGAAAAATTAAACTATCAGAAGCATTTATCCCTA
* *
15678 TTTTTTAGTGTCAAAAATATTA
390 TATTTTAGTGCCAAAAATATTA
* * * *
15700 TATAGTAACAAAATATATTGTCATAAAAAATTTCCTCTATATTTTATTGCGCCAAAAAAATTATA
1 TATAGTAACAAAATATATTGTCACAAAAAATTTCCTCCATATTTT-TTAC-AC-AAAAAATTATA
* *
15765 TAATAACAAATTTTATAACTATAAGTGTTTA-TAATTATTACA-AAAATATTTTCACAAAAAAAT
63 TAATAACAAATTTTATAACTATAAGT-TTTAGTAATTATTACAGAAAACATTGTCAC-AAAAAAT
* * *
15828 AACGGTATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAATTTTAATTATAGTGATAACA
126 AACGATATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAA-ATTAACTATAGTGATAACA
* * *
15893 TATATTGTGATAAATGTTTTT-TCCACTTTTTTTGTTTCAAAAAGTTATATTCATAAGTTTTGTA
190 TATATTGTCATAAATATTTTTCTCCAC-TTTTTTGTTT-AAAAAGTTATATTCATAAGTTTTATA
15957 ATTATAATTTATAGTTATTGTTAT-AAAAAATTATCACATCAGAA-AATAAAATTCA-AATTTTT
253 ATTATAATTTATAGTTATTGTTATAAAAAAATTATCACATCA-AATAATAAAATTCAGAATTTTT
** * *
16019 AGTAATCAATTA-TTTTTGTAGTTATATATTTTAATCATTATGTAAAATTAAACTATCATAAGCA
317 A-TAATCAATTACTTTTT-TACCTATATATTTTAATCATTATGAAAAATTAAACTATCAGAAGCA
* * * *
16083 TTTCTCCGTATATTTTGGTGCCAAAAATGTTA
380 TTTATCCCTATATTTTAGTGCCAAAAATATTA
16115 TA
1 TA
16117 GTAAAAGTTT
Statistics
Matches: 358, Mismatches: 48, Indels: 19
0.84 0.11 0.04
Matches are distributed among these distances:
412 41 0.11
413 3 0.01
414 24 0.07
415 196 0.55
416 48 0.13
417 46 0.13
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.44
Consensus pattern (411 bp):
TATAGTAACAAAATATATTGTCACAAAAAATTTCCTCCATATTTTTTACACAAAAAATTATATAA
TAACAAATTTTATAACTATAAGTTTTAGTAATTATTACAGAAAACATTGTCACAAAAAATAACGA
TATTCACATTTTTGTGACAAATTATACTTGTAGTTATAAAATTAACTATAGTGATAACATATATT
GTCATAAATATTTTTCTCCACTTTTTTGTTTAAAAAGTTATATTCATAAGTTTTATAATTATAAT
TTATAGTTATTGTTATAAAAAAATTATCACATCAAATAATAAAATTCAGAATTTTTATAATCAAT
TACTTTTTTACCTATATATTTTAATCATTATGAAAAATTAAACTATCAGAAGCATTTATCCCTAT
ATTTTAGTGCCAAAAATATTA
Found at i:16306 original size:2 final size:2
Alignment explanation
Indices: 16301--16372 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
16291 AATTTCTGTG
16301 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
16343 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
16373 CAATGACATT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21275 original size:28 final size:28
Alignment explanation
Indices: 21244--21346 Score: 93
Period size: 28 Copynumber: 3.7 Consensus size: 28
21234 TTTACACCTT
*
21244 TATCACCCTTTAAAAAAATTTACAAAAA
1 TATCACCTTTTAAAAAAATTTACAAAAA
* *
21272 TATCACCTTTTTCAAAATAA-TTACTAAAA
1 TATCACC-TTTT-AAAAAAATTTACAAAAA
** * * **
21301 TATCAATTTTTTAAAAAATTTACGAATT
1 TATCACCTTTTAAAAAAATTTACAAAAA
21329 TATCA-CTTTTAAAAAAAT
1 TATCACCTTTTAAAAAAAT
21347 AGCACCATTT
Statistics
Matches: 60, Mismatches: 12, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
27 16 0.27
28 22 0.37
29 16 0.27
30 6 0.10
ACGTcount: A:0.48, C:0.14, G:0.01, T:0.38
Consensus pattern (28 bp):
TATCACCTTTTAAAAAAATTTACAAAAA
Found at i:21311 original size:29 final size:27
Alignment explanation
Indices: 21256--21346 Score: 76
Period size: 29 Copynumber: 3.3 Consensus size: 27
21246 TCACCCTTTA
*
21256 AAAAAATTTACAAAAATATCACCTTTTT
1 AAAAAA-TTACAAAAATATCAACTTTTT
* *
21284 CAAAATAATTACTAAAATATCAATTTTTT
1 -AAAA-AATTACAAAAATATCAACTTTTT
* ** *
21313 AAAAAATTTACGAATTTATC-ACTTTTA
1 AAAAAA-TTACAAAAATATCAACTTTTT
21340 AAAAAAT
1 AAAAAAT
21347 AGCACCATTT
Statistics
Matches: 52, Mismatches: 8, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
26 1 0.02
27 13 0.25
28 14 0.27
29 22 0.42
30 2 0.04
ACGTcount: A:0.51, C:0.11, G:0.01, T:0.37
Consensus pattern (27 bp):
AAAAAATTACAAAAATATCAACTTTTT
Found at i:21375 original size:29 final size:29
Alignment explanation
Indices: 21342--21410 Score: 120
Period size: 29 Copynumber: 2.4 Consensus size: 29
21332 CACTTTTAAA
*
21342 AAAATAGCACCATTTTCAAAATAATTACC
1 AAAATATCACCATTTTCAAAATAATTACC
*
21371 AAAATATCACCATTTTCAAAATAATTACT
1 AAAATATCACCATTTTCAAAATAATTACC
21400 AAAATATCACC
1 AAAATATCACC
21411 CGGTCAACAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.49, C:0.20, G:0.01, T:0.29
Consensus pattern (29 bp):
AAAATATCACCATTTTCAAAATAATTACC
Found at i:27753 original size:29 final size:29
Alignment explanation
Indices: 27716--27873 Score: 137
Period size: 29 Copynumber: 5.6 Consensus size: 29
27706 TGAAAAAATT
* *
27716 TTACAAAAATATCACCCTTTTCAAAATAA
1 TTACTAAAATATCACCCTTTTTAAAATAA
** *
27745 TTACTAAAATATCACTTTTTTTAAAAAAA
1 TTACTAAAATATCACCCTTTTTAAAATAA
* * *
27774 TTA--AGAAT-TTACACTTTTTAAAA-AA
1 TTACTAAAATATCACCCTTTTTAAAATAA
* * * * *
27799 TTACGAAAATAACATCATTTTCAAAATAA
1 TTACTAAAATATCACCCTTTTTAAAATAA
*
27828 TTA-TAAAAATATCACCATTTTTAAAATAA
1 TTACT-AAAATATCACCCTTTTTAAAATAA
*
27857 TTATTAAAATATCACCC
1 TTACTAAAATATCACCC
27874 GGTCAACAGT
Statistics
Matches: 102, Mismatches: 21, Indels: 12
0.76 0.16 0.09
Matches are distributed among these distances:
25 5 0.05
26 12 0.12
27 8 0.08
28 9 0.09
29 67 0.66
30 1 0.01
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.36
Consensus pattern (29 bp):
TTACTAAAATATCACCCTTTTTAAAATAA
Found at i:31994 original size:23 final size:23
Alignment explanation
Indices: 31947--32001 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
31937 GATTTTAATC
31947 AAAATATTAATTATTAAAATATTT
1 AAAATA-TAATTATTAAAATATTT
* * *
31971 AAAATATATTTATTAATATTTTT
1 AAAATATAATTATTAAAATATTT
31994 AATAATAT
1 AA-AATAT
32002 TATATTGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
23 16 0.59
24 11 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
AAAATATAATTATTAAAATATTT
Found at i:31997 original size:21 final size:23
Alignment explanation
Indices: 31949--32016 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 23
31939 TTTTAATCAA
* *
31949 AATATTAATTATTAAAATATTTAA-
1 AATATT-A-TATTAATATTTTTAAT
*
31973 AATATATTTATTAATATTTTTAAT
1 AATAT-TATATTAATATTTTTAAT
*
31997 AATATTATATT-GTATTTTTA
1 AATATTATATTAATATTTTTA
32017 GTATTATAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
22 8 0.22
23 18 0.49
24 10 0.27
25 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.54
Consensus pattern (23 bp):
AATATTATATTAATATTTTTAAT
Found at i:32173 original size:27 final size:29
Alignment explanation
Indices: 32126--32195 Score: 83
Period size: 27 Copynumber: 2.5 Consensus size: 29
32116 AATTTCATAG
32126 AAATAATATTA-TTAAATTA-TTAATAAT
1 AAATAATATTATTTAAATTATTTAATAAT
* * *
32153 GAATAATATTATTTATA-TATTTAATATT
1 AAATAATATTATTTAAATTATTTAATAAT
32181 AATATAATATTATTT
1 AA-ATAATATTATTT
32196 TAATAAATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
27 12 0.33
28 12 0.33
29 12 0.33
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (29 bp):
AAATAATATTATTTAAATTATTTAATAAT
Found at i:32208 original size:14 final size:16
Alignment explanation
Indices: 32155--32209 Score: 50
Period size: 16 Copynumber: 3.8 Consensus size: 16
32145 TTAATAATGA
32155 ATAATATTA-TTT-AT
1 ATAATATTATTTTAAT
*
32169 AT-AT-TTAATATTAAT
1 ATAATATT-ATTTTAAT
32184 ATAATATTATTTTAAT
1 ATAATATTATTTTAAT
32200 A-AATA-TATTT
1 ATAATATTATTT
32210 AAAATATACT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
12 2 0.06
13 3 0.09
14 9 0.26
15 8 0.24
16 10 0.29
17 2 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (16 bp):
ATAATATTATTTTAAT
Found at i:32227 original size:23 final size:23
Alignment explanation
Indices: 32196--32240 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
32186 AATATTATTT
32196 TAATAAATATATTTAAAATATAC
1 TAATAAATATATTTAAAATATAC
* *
32219 TAATTAATATTTTTAAAATATA
1 TAATAAATATATTTAAAATATA
32241 ATATTATTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.44
Consensus pattern (23 bp):
TAATAAATATATTTAAAATATAC
Found at i:34245 original size:23 final size:23
Alignment explanation
Indices: 34218--34269 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
34208 TTCTTATGGA
*
34218 CAATTTTAAATGGCACTACGGTG
1 CAATTTTAAACGGCACTACGGTG
* * *
34241 CAATTCTATACGGCACTTCGGTG
1 CAATTTTAAACGGCACTACGGTG
34264 CAATTT
1 CAATTT
34270 ATATGTTGTG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (23 bp):
CAATTTTAAACGGCACTACGGTG
Found at i:41650 original size:21 final size:21
Alignment explanation
Indices: 41624--41670 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
41614 ACAAAGCCAA
*
41624 AATGCCAAAATTCTTGATCAT
1 AATGCCAAAATTCTTGATCAG
41645 AATGCCAAAATTCTTGATCAG
1 AATGCCAAAATTCTTGATCAG
41666 AATGC
1 AATGC
41671 AACAATCAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.30
Consensus pattern (21 bp):
AATGCCAAAATTCTTGATCAG
Found at i:42102 original size:23 final size:22
Alignment explanation
Indices: 42076--42119 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 22
42066 ATGATAATTT
42076 ATTTAGACAAAATAACAAATTAA
1 ATTTAGACAAAATAA-AAATTAA
**
42099 ATTTAGTTAAAATAAAAATTA
1 ATTTAGACAAAATAAAAATTA
42120 TGTCAAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 6 0.32
23 13 0.68
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.32
Consensus pattern (22 bp):
ATTTAGACAAAATAAAAATTAA
Found at i:42163 original size:98 final size:99
Alignment explanation
Indices: 42061--42388 Score: 250
Period size: 98 Copynumber: 3.3 Consensus size: 99
42051 TAACATAAAG
* *
42061 AAATTATGA-TAATTTATTTAGACAAAATAACAAATTAAATTTAGTTAAAATAAAAATTATGTCA
1 AAATTATGACTAATTTATTTAGTCAAAATAACAAATTAAATTTAGTTAAAATAAAAATTATGTAA
42125 AATTTATTTAGTCAAAATATTTTCTCAAAATAAC
66 AATTTATTTAGTCAAAATATTTTCTCAAAATAAC
* ** * * * ** * *
42159 AAATTAGGACTAATTTAAATAGT-TATATAACAAATTATAATAAATA-TTAATTTCACAA-TAT-
1 AAATTATGACTAATTTATTTAGTCAAAATAACAAATTA-AAT--TTAGTTAAAATAAAAATTATG
* * * *
42220 AAAAATTTA--T-GACAAACAATATGTTTTTCACAATAATC
63 TAAAATTTATTTAGTC-AA-AATAT-TTTCTCAAAATAA-C
* * * * * *
42258 -AATTATAAC-AAGTTTATTTAGTCACAATAACATATTAAATTTAGTCAAGATAAAAATTATGTT
1 AAATTATGACTAA-TTTATTTAGTCAAAATAACAAATTAAATTTAGTTAAAATAAAAATTATGTA
42321 AAATTTATTTCA-TCAAAATA-TTTCTCAAAATAAC
65 AAATTTATTT-AGTCAAAATATTTTCTCAAAATAAC
* * *
42355 AACCTT-TGACAAATTTATTTAGTCATAATAACAA
1 AA-ATTATGACTAATTTATTTAGTCAAAATAACAA
42389 TTTATAACAA
Statistics
Matches: 171, Mismatches: 39, Indels: 40
0.68 0.16 0.16
Matches are distributed among these distances:
95 2 0.01
96 5 0.03
97 15 0.09
98 93 0.54
99 38 0.22
100 12 0.07
101 5 0.03
102 1 0.01
ACGTcount: A:0.48, C:0.09, G:0.05, T:0.37
Consensus pattern (99 bp):
AAATTATGACTAATTTATTTAGTCAAAATAACAAATTAAATTTAGTTAAAATAAAAATTATGTAA
AATTTATTTAGTCAAAATATTTTCTCAAAATAAC
Found at i:42388 original size:197 final size:195
Alignment explanation
Indices: 42071--42860 Score: 753
Period size: 193 Copynumber: 4.1 Consensus size: 195
42061 AAATTATGAT
* * * *
42071 AATTTATTTAGACAAAATAACAAATTAAATTTAGTTAAAATAAAAATTATGTCAAATTTATTT-A
1 AATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAATTATGTCAAATTTATTTCA
* * * ** * * *
42135 GTCAAAATATTTTCTCAAAATAACAAATTAGGACTAATTTAAATAGT-TATATAACAAATTATAA
66 -TCAAAATA-TTTATCAAAATAA-AAATTATGACAAATTTATTTAATCAAAATAACAAATTATAA
* * * * * *
42199 TAAATATTAATTTCACAATATAAAAATTTATGACAAACAATATGTTTTTCACAATAATCAATTAT
128 CAAATATTAATTTCTCAATATAAAAAATTATGACAAATAATAT-TCTTTCACAATAATCAATTGT
42264 AACA
192 AACA
* * *
42268 AGTTTATTTAGTCACAATAACATATTAAATTTAGTCAAGATAAAAATTATGTTAAATTTATTTCA
1 AATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAATTATGTCAAATTTATTTCA
* * * * *
42333 TCAAAATATTTCTCAAAATAACAACCTT-TGACAAATTTATTTAGTCATAATAACAATTTATAAC
66 TCAAAATATTTATCAAAATAA-AA-ATTATGACAAATTTATTTAATCAAAATAACAAATTATAAC
* * * * *
42397 AAATTTTAATTCCTCAAAATAAAAAATTATGACAAATACTATTCTTTCACAAT-A-CAAAGTGTA
129 AAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAATC-AATTGTA
42460 ACA
193 ACA
* * * * **
42463 AATTTATTTAGTTACAATAACATAGTAAATTTAGTTAAAAT-AAAATTTTGTCAAATTTATTTTG
1 AATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAATTATGTCAAATTTATTTCA
* * * *
42527 TCACAATAATTTATCAAAATAAAAATGTA--ACAAATTTA-TTAATCAAAATAATAATTTATAAA
66 TCAAAAT-ATTTATCAAAATAAAAAT-TATGACAAATTTATTTAATCAAAATAACAAATTATAAC
* * ** * * *
42589 AAATAATAATTTCTCATTATAAAAAATCGTGACAATTAATATTCTTTCACAGTAATAAATTGTAA
129 AAATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAATCAATTGTAA
42654 CA
194 CA
* * ** * * *
42656 AAATGATTTAGTCACAATAACACGTT-AAGTTA-TCATAGTAAAAAGTTATGTCAAATTTATTTC
1 AATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAA-TTATGTCAAATTTATTTC
* ** * * * * *
42719 GTCCTAAT-TTTATCAAAATGAAATTTGTGACACATTTATTTAATCAAAATAACAAACTATAACA
65 ATCAAAATATTTATCAAAATAAAAATTATGACAAATTTATTTAATCAAAATAACAAATTATAACA
* * * *
42783 AATATTAATTTCTCATTATAAAAAAATTGTGACAAATAATAAT-TATCACAATAA-CAAATTGTA
130 AATATTAATTTCTCAATAT-AAAAAATTATGACAAATAATATTCTTTCACAATAATC-AATTGTA
*
42846 AAA
193 ACA
*
42849 AAATTATTTAGT
1 AATTTATTTAGT
42861 TATAGTAAAA
Statistics
Matches: 491, Mismatches: 86, Indels: 36
0.80 0.14 0.06
Matches are distributed among these distances:
190 1 0.00
191 19 0.04
192 80 0.16
193 130 0.26
194 49 0.10
195 58 0.12
196 39 0.08
197 114 0.23
198 1 0.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.37
Consensus pattern (195 bp):
AATTTATTTAGTCACAATAACATATTAAATTTAGTCAAAATAAAAATTATGTCAAATTTATTTCA
TCAAAATATTTATCAAAATAAAAATTATGACAAATTTATTTAATCAAAATAACAAATTATAACAA
ATATTAATTTCTCAATATAAAAAATTATGACAAATAATATTCTTTCACAATAATCAATTGTAACA
Found at i:47251 original size:3 final size:3
Alignment explanation
Indices: 47243--47282 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
47233 ATGTAAATTA
*
47243 AAT AAT AAT AAT AAT AAT AAT AAT GAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
47283 TTTTTAAGAC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:47886 original size:66 final size:66
Alignment explanation
Indices: 47755--47975 Score: 288
Period size: 66 Copynumber: 3.4 Consensus size: 66
47745 TCTTTAGGGA
* * * * * * *
47755 TTGTTTCAAGAGAAACAAACTCAAAGAT-GATGCTTCAAGAGAAGCTATCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACAATCTCAAAGATGGGTGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAA
47819 T
66 T
* * *
47820 TTGTTTCAAGGGAAACGATCTCAAATATGGGTGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAA
1 TTGTTTCAAGAGAAACAATCTCAAAGATGGGTGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAA
47885 T
66 T
* * *
47886 TCGTTTCAAGGGAAACAATCTCAAAGATGGGT-TTTCAAGAGAAACTGT-TTCAAGGGAGACCAA
1 TTGTTTCAAGAGAAACAATCTCAAAGATGGGTGTTTCAAGAGAAACTGTCTT-AAGGGAGACAAA
47949 AT
65 AT
47951 TTGTTTC-AGAGAAACAATCTCAAAG
1 TTGTTTCAAGAGAAACAATCTCAAAG
47976 TTTGTCAATT
Statistics
Matches: 138, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
64 19 0.14
65 59 0.43
66 60 0.43
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACAATCTCAAAGATGGGTGTTTCAAGAGAAACTGTCTTAAGGGAGACAAAA
T
Found at i:47957 original size:65 final size:66
Alignment explanation
Indices: 47755--47975 Score: 288
Period size: 65 Copynumber: 3.4 Consensus size: 66
47745 TCTTTAGGGA
* * * * * * *
47755 TTGTTTCAAGAGAAACAAACTCAAAGAT-GATGCTTCAAGAGAAGCTATCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACAATCTCAAAGATGGGTGTTTCAAGAGAAACTGTTTCAAGGGAGACAAAA
47819 T
66 T
* * *
47820 TTGTTTCAAGGGAAACGATCTCAAATATGGGTGTTTCAAGAGAAACTGTCTT-AAGGGAGACAAA
1 TTGTTTCAAGAGAAACAATCTCAAAGATGGGTGTTTCAAGAGAAACTGT-TTCAAGGGAGACAAA
47884 AT
65 AT
* * *
47886 TCGTTTCAAGGGAAACAATCTCAAAGATGGGT-TTTCAAGAGAAACTGTTTCAAGGGAGACCAAA
1 TTGTTTCAAGAGAAACAATCTCAAAGATGGGTGTTTCAAGAGAAACTGTTTCAAGGGAGACAAAA
47950 T
66 T
47951 TTGTTTC-AGAGAAACAATCTCAAAG
1 TTGTTTCAAGAGAAACAATCTCAAAG
47976 TTTGTCAATT
Statistics
Matches: 137, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
64 19 0.14
65 59 0.43
66 58 0.42
67 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.21, T:0.25
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACAATCTCAAAGATGGGTGTTTCAAGAGAAACTGTTTCAAGGGAGACAAAA
T
Done.