Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002764.1 Hibiscus syriacus cultivar Beakdansim tig00005701_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: 80270
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.33
Found at i:1428 original size:23 final size:23
Alignment explanation
Indices: 1389--1458 Score: 101
Period size: 21 Copynumber: 3.2 Consensus size: 23
1379 ATAGGTAAAA
*
1389 ATATGATGT-ATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
1411 ATATAATGTAATAGGTAGCG-TT
1 ATATAATGTAATAGGTAGCGCTT
*
1433 -TATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1455 ATAT
1 ATAT
1459 TGTAAAGTAT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
21 18 0.42
22 12 0.28
23 13 0.30
ACGTcount: A:0.33, C:0.06, G:0.23, T:0.39
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1918 original size:23 final size:22
Alignment explanation
Indices: 1865--1934 Score: 92
Period size: 20 Copynumber: 3.3 Consensus size: 22
1855 GGTAAAAATG
1865 ATGTAATAGGTAGCGCTTATAT
1 ATGTAATAGGTAGCGCTTATAT
*
1887 A--TAATAGGTAGCGTTTATAT
1 ATGTAATAGGTAGCGCTTATAT
*
1907 AATGTAATAGGTAGTGCTTATAT
1 -ATGTAATAGGTAGCGCTTATAT
1930 -TGTAA
1 ATGTAA
1935 AGTATCTATC
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
20 18 0.43
21 6 0.14
22 1 0.02
23 17 0.40
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (22 bp):
ATGTAATAGGTAGCGCTTATAT
Found at i:2362 original size:23 final size:23
Alignment explanation
Indices: 2331--2403 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2321 ATAGATAAAA
* *
2331 ATATGATGTAATAGGTAGCACTT
1 ATATAATGTAATAGGTAGCGCTT
*
2354 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
2377 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
2400 ATAT
1 ATAT
2404 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2840 original size:23 final size:23
Alignment explanation
Indices: 2809--2881 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
2799 ATAGGTAAAA
* *
2809 ATATGATGTAATATGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
2832 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
*
2855 ATATAATGTAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
2878 ATAT
1 ATAT
2882 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.40
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:2843 original size:478 final size:478
Alignment explanation
Indices: 1177--3281 Score: 3643
Period size: 474 Copynumber: 4.4 Consensus size: 478
1167 GGTGCACGCA
*
1177 TAATATTGTTAAATTTCAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
1 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
* * * *
1242 TGTGTAAATGAAATTATTAAATTAATATTTTAGGCGGAAAACATGAAATACTATTAAAAAATAAA
66 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAA-AAT
1307 TGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTT
130 TGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTT
1372 CAATATAATAGGTAAAAATATGATGT-ATAGGTAGCGCTTATATAATGTAATAGGTAGCG-TT-T
195 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTAT
*
1434 ATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATTCTTTTTATAAAAGTGTCCATACTTT
260 ATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTT
1499 TTTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTC
325 TTTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTC
1564 TAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATA-
390 TAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATAT
1628 TACATA-TTATTATTATCTTTGGT
455 TACATATTTATTATTATCTTTGGT
*
1651 TAATATTATTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
1 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
1716 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
66 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
* *
1781 GAAACATAAATTGCATAACTTTAAAAAAAATATCGATCATTTTTATAAAAAGTATGGACACTTTC
131 GAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTC
1846 AATATAATAGGT-AAAA-ATGATGTAATAGGTAGCGCTTATAT-A--TAATAGGTAGCGTTTATA
196 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATA
1906 TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTT
261 TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTT
1971 TTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
326 TTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
2036 AATGATTTA-TTTTTACGTTACGGTATATATTATTATTAAATT-AAAACAATAAAC--ATATATT
391 AATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATT
2097 ACATATTTATTATTATCTTTGGT
456 ACATATTTATTATTATCTTTGGT
*
2120 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAAAAATCAAATAATTTTT
1 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAA-TTTT
2185 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
65 TTGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAAT
* *
2250 TGAAACATAAATTACATAACTTTAAAAAAAGTATCAATCCTTTTTATAAAAA-TATGGACACTTT
130 TGAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTT
* *
2314 CAATATAATAGATAAAAATATGATGTAATAGGTAGCACTTATATAATGTAATAGGTAGCGTTTAT
195 CAATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTAT
*
2379 ATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCAATACTTT
260 ATAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTT
*
2444 TTTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAAATATTAATTTAGTAATTATAGGCGTC
325 TTTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTC
2509 TAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATAT
390 TAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATAT
2574 TACATATTTATTATTATCTTTGGT
455 TACATATTTATTATTATCTTTGGT
*
2598 TAATATTATTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
1 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
*
2663 TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
66 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
* * *
2728 GAAACATAAATTGCATAACTTTAAAAAAAGTATCGATCTTTTTTATAAAAAGTATGAACACTTTC
131 GAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTC
*
2793 AATATAATAGGTAAAAATATGATGTAATATGTAGCGCTTATATAATGTAATAGGTAGCGTTTATA
196 AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATA
*
2858 TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCATTTTTATAAAAGTGTCCATACTTTT
261 TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTT
* *
2923 TTCAATGTGGAAAACATTAATTTAAGGTTATCTTTTGAGTGAGTTTTAAGATATCAATTTAGTAA
326 TTCACTGTGGAAAACATTAATTTAAGG--------T---T-AGTTTTAAGATATTAATTTAGTAA
**** * *
2988 TTATATATATCTAATGA-TTATTTTTTATGTTACGGTATATATTATCATTAAATTAAAAACAATA
379 TTATAGGCGTCTAATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATA
*
3052 AACATATATATTACATATTTATTATTATCTTTAGT
444 AACATATATATTACATATTTATTATTATCTTTGGT
*
3087 TAATATTGTTAAATTTAAATTCTAAATATTATTTTATAAAATATCAAAACAATCAAATAATTTTT
1 TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
* *
3152 TGTGCAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAATACTATT--AAAAAATT
66 TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
3215 GAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTC
131 GAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTC
3280 AA
196 AA
3282 CATATTATAA
Statistics
Matches: 1556, Mismatches: 47, Indels: 43
0.95 0.03 0.03
Matches are distributed among these distances:
467 5 0.00
468 6 0.00
469 123 0.08
470 156 0.10
471 172 0.11
472 22 0.01
473 78 0.05
474 276 0.18
475 33 0.02
476 12 0.01
477 117 0.08
478 251 0.16
486 1 0.00
487 72 0.05
489 197 0.13
490 35 0.02
ACGTcount: A:0.42, C:0.08, G:0.11, T:0.40
Consensus pattern (478 bp):
TAATATTGTTAAATTTAAATTCTAAATAATATTTTATAAAATATCAAAACAATCAAATAATTTTT
TGTGTAAATGAAATTATTAAATTAATATTGTAGGTGGAAAACATGAAACACTATTAAAAAAAATT
GAAACATAAATTACATAACTTTAAAAAAAGTATCGATCATTTTTATAAAAAGTATGGACACTTTC
AATATAATAGGTAAAAATATGATGTAATAGGTAGCGCTTATATAATGTAATAGGTAGCGTTTATA
TAATGTAATAGGTAGTGCTTATATTGTAAAGTATCTATCCTTTTTATAAAAGTGTCCATACTTTT
TTCACTGTGGAAAACATTAATTTAAGGTTAGTTTTAAGATATTAATTTAGTAATTATAGGCGTCT
AATGATTTATTTTTTACGTTACGGTATATATTATTATTAAATTAAAAACAATAAACATATATATT
ACATATTTATTATTATCTTTGGT
Found at i:8946 original size:11 final size:11
Alignment explanation
Indices: 8930--9046 Score: 71
Period size: 11 Copynumber: 10.1 Consensus size: 11
8920 AGATCCAATC
8930 AGAAAAAAAGA
1 AGAAAAAAAGA
8941 AGAAAAAAAGGA
1 AGAAAAAAA-GA
*
8953 AAAAAAAAAGA
1 AGAAAAAAAGA
8964 A-AAAGAAATAG-
1 AGAAA-AAA-AGA
8975 AGCAAAAAAAGA
1 AG-AAAAAAAGA
* *
8987 GAAAAGAAAAAAA
1 -AGAA-AAAAAGA
*
9000 AGAAATTAAAGCAA
1 AGAAA-AAAAG--A
9014 AGAAAAAAAG-
1 AGAAAAAAAGA
*
9024 AGCAAAAAAGA
1 AGAAAAAAAGA
9035 A-AAGAAAAAGA
1 AGAA-AAAAAGA
9046 A
1 A
9047 AAAGGGACGA
Statistics
Matches: 84, Mismatches: 9, Indels: 26
0.71 0.08 0.22
Matches are distributed among these distances:
10 13 0.15
11 28 0.33
12 23 0.27
13 14 0.17
14 6 0.07
ACGTcount: A:0.78, C:0.03, G:0.17, T:0.03
Consensus pattern (11 bp):
AGAAAAAAAGA
Found at i:8962 original size:23 final size:22
Alignment explanation
Indices: 8932--9048 Score: 74
Period size: 23 Copynumber: 4.8 Consensus size: 22
8922 ATCCAATCAG
8932 AAAAAAAGAAGAAAAAAAGGAAA
1 AAAAAAAGAA-AAAAAAAGGAAA
8955 AAAAAAAGAAAAAGAAATAGAGCAAA
1 AAAAAAAGAAAAA-AAA-AG-G-AAA
*
8981 AAAAGAGAA-AAGAAAAAAAAGAAA
1 AAAA-A-AAGAA-AAAAAAAGGAAA
* * *
9005 TTAAAGCAAAGAAAAAAAGAGCAAA
1 --AAA-AAAAGAAAAAAAAAGGAAA
9030 AAAGAAAAGAAAAAGAAAA
1 AAA-AAAAGAAAAA-AAAA
9049 AGGGACGATA
Statistics
Matches: 75, Mismatches: 7, Indels: 23
0.71 0.07 0.22
Matches are distributed among these distances:
22 3 0.04
23 26 0.35
24 8 0.11
25 13 0.17
26 14 0.19
27 6 0.08
28 5 0.07
ACGTcount: A:0.79, C:0.03, G:0.16, T:0.03
Consensus pattern (22 bp):
AAAAAAAGAAAAAAAAAGGAAA
Found at i:9013 original size:34 final size:35
Alignment explanation
Indices: 8943--9047 Score: 97
Period size: 34 Copynumber: 2.8 Consensus size: 35
8933 AAAAAAGAAG
*
8943 AAAAAAAGGAAAAAAAAAAGAAAAAGAAATAGAGC
1 AAAAAAAGGAAAAAAAAAAGAAAAAGAAATAAAGC
* *
8978 AAAAAAA-GAGAAAAGAAA-AAAAAGAAATTAAAGC
1 AAAAAAAGGAAAAAAAAAAGAAAAAGAAA-TAAAGC
9012 AAAGAAAAAAAGAGCAAAAAAGAAAAGAAAAAGAAA
1 ----AAAAAAAG-G-AAAAAA-AAAAGAAAAAGAAA
9048 AAGGGACGAT
Statistics
Matches: 55, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
33 9 0.16
34 14 0.25
35 7 0.13
38 7 0.13
40 1 0.02
41 5 0.09
42 3 0.05
43 9 0.16
ACGTcount: A:0.78, C:0.03, G:0.16, T:0.03
Consensus pattern (35 bp):
AAAAAAAGGAAAAAAAAAAGAAAAAGAAATAAAGC
Found at i:9029 original size:15 final size:15
Alignment explanation
Indices: 9009--9049 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
8999 AAGAAATTAA
9009 AGCAAAGAAAAAAAG
1 AGCAAAGAAAAAAAG
9024 AGCAAA-AAAGAAAAG
1 AGCAAAGAAA-AAAAG
*
9039 A-AAAAGAAAAA
1 AGCAAAGAAAAA
9050 GGGACGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
14 8 0.35
15 15 0.65
ACGTcount: A:0.78, C:0.05, G:0.17, T:0.00
Consensus pattern (15 bp):
AGCAAAGAAAAAAAG
Found at i:9031 original size:33 final size:32
Alignment explanation
Indices: 8963--9036 Score: 80
Period size: 33 Copynumber: 2.3 Consensus size: 32
8953 AAAAAAAAAG
*
8963 AAAAAGAAATAGAGCAAAAAAAGAGAAAAGAAA
1 AAAAAGAAATAAAGCAAAAAAAGAGAAAAG-AA
* *
8996 AAAAAGAAATTAAAGCAAAGAAAA-A-AAGAGCA
1 AAAAAGAAA-TAAAGCAAA-AAAAGAGAAAAGAA
9028 AAAAAGAAA
1 AAAAAGAAA
9037 AGAAAAAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
32 10 0.28
33 13 0.36
34 9 0.25
35 4 0.11
ACGTcount: A:0.76, C:0.04, G:0.16, T:0.04
Consensus pattern (32 bp):
AAAAAGAAATAAAGCAAAAAAAGAGAAAAGAA
Found at i:10108 original size:32 final size:32
Alignment explanation
Indices: 10072--10142 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 32
10062 AGGAACAATA
* *
10072 GGGCATCGTTAAAGATTCAACAACAAATGTTG
1 GGGCATAGTTAAAGATTCAACAACAAATATTG
* ** * *
10104 GGGCATATTTGGAGATTCAACATCGAATATTG
1 GGGCATAGTTAAAGATTCAACAACAAATATTG
10136 GGGCATA
1 GGGCATA
10143 TTTGGGAATT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.14, G:0.25, T:0.27
Consensus pattern (32 bp):
GGGCATAGTTAAAGATTCAACAACAAATATTG
Found at i:10143 original size:32 final size:32
Alignment explanation
Indices: 10084--10159 Score: 109
Period size: 32 Copynumber: 2.4 Consensus size: 32
10074 GCATCGTTAA
* *
10084 AGATTCAACAACAAATGTTGGGGCATATTTGG
1 AGATTCAACATCAAATATTGGGGCATATTTGG
*
10116 AGATTCAACATCGAATATTGGGGCATATTTGG
1 AGATTCAACATCAAATATTGGGGCATATTTGG
10148 -GAATTCAACATC
1 AG-ATTCAACATC
10160 TTGATGCAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
31 1 0.03
32 39 0.98
ACGTcount: A:0.34, C:0.14, G:0.22, T:0.29
Consensus pattern (32 bp):
AGATTCAACATCAAATATTGGGGCATATTTGG
Found at i:10641 original size:43 final size:43
Alignment explanation
Indices: 10550--10678 Score: 149
Period size: 43 Copynumber: 3.0 Consensus size: 43
10540 ATGAAGGGGC
*
10550 CATCCACGATTTCAACTCCACGACGGAGGATATCGTAC-CA-A
1 CATCCACGATTTCAATTCCACGACGGAGGATATCGTACACACA
* *
10591 CGGATCCATGATTTCAATTCCACGACGGAGGATATCGTGCACACA
1 C--ATCCACGATTTCAATTCCACGACGGAGGATATCGTACACACA
* *
10636 CATCCACGGTTTCAACTT-CACGACGAAGGGA-ATCGTACACACA
1 CATCCACGATTTCAA-TTCCACGACGGA-GGATATCGTACACACA
10679 AGCAGTATCT
Statistics
Matches: 75, Mismatches: 7, Indels: 10
0.82 0.08 0.11
Matches are distributed among these distances:
41 1 0.01
43 65 0.87
44 7 0.09
45 2 0.03
ACGTcount: A:0.31, C:0.29, G:0.19, T:0.20
Consensus pattern (43 bp):
CATCCACGATTTCAATTCCACGACGGAGGATATCGTACACACA
Found at i:10914 original size:43 final size:43
Alignment explanation
Indices: 10852--10961 Score: 157
Period size: 43 Copynumber: 2.6 Consensus size: 43
10842 CGAAGGGGGC
* *
10852 CATCCACGATTTCAACTCCATGACAGAGGATATCGTACCAACG
1 CATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAACA
* * *
10895 GATCCACGATTTCAACTCCACGACAGAGGATATCGTGCCCACA
1 CATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAACA
* *
10938 CATCCACGGTTTCAACTTCACGAC
1 CATCCACGATTTCAACTCCACGAC
10962 GAAGGGAATC
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 59 1.00
ACGTcount: A:0.30, C:0.33, G:0.16, T:0.21
Consensus pattern (43 bp):
CATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAACA
Found at i:11092 original size:302 final size:302
Alignment explanation
Indices: 10529--11148 Score: 1019
Period size: 302 Copynumber: 2.1 Consensus size: 302
10519 AAGTCAAGGC
*
10529 TCAACTTCACGATGAA-GGGGCCATCCACGATTTCAACTCCACGACGGAGGATATCGTACCAACG
1 TCAACTTCACGATGAAGGGGGCCATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAACG
* * *
10593 GATCCATGATTTCAATTCCACGACGGAGGATATCGTGCACACACATCCACGGTTTCAACTTCACG
66 GATCCACGATTTCAACTCCACGACAGAGGATATCGTGCACACACATCCACGGTTTCAACTTCACG
* * * **
10658 ACGAAGGGAATCGTACACACAAGCAGTATCTATCTCTAGATTGGATTTCAACTTCACGTAGAATT
131 ACGAAGGGAATCGTACACACAAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACGTAAAAGG
*
10723 ATATCCAACTCAAAGAAAGAGTGTATGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCATCTTC
196 ATATCCAACTCAAAGAAAGAGTGTATGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTC
* *
10788 ACGACGAATGATATTGGACTCGAAACAACACAAGCTTGGATT
261 ACGACGAAGGATATTAGACTCGAAACAACACAAGCTTGGATT
* *
10830 TCAACTTCACGACGAAGGGGGCCATCCACGATTTCAACTCCATGACAGAGGATATCGTACCAACG
1 TCAACTTCACGATGAAGGGGGCCATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAACG
*
10895 GATCCACGATTTCAACTCCACGACAGAGGATATCGTGCCCACACATCCACGGTTTCAACTTCACG
66 GATCCACGATTTCAACTCCACGACAGAGGATATCGTGCACACACATCCACGGTTTCAACTTCACG
*
10960 ACGAAGGGAATCGTACACACAAGTAGCATCCATCTCTAGATTGGATTTCAACTTCACG-ACAAAG
131 ACGAAGGGAATCGTACACACAAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACGTA-AAAG
* * *
11024 GATATCCTACTCAAAGAAGGAGTGTCTGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTT
195 GATATCCAACTCAAAGAAAGAGTGTATGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTT
* **
11089 CACGGCGAAGGATATTAGACTCGAAACAGTACAAGCTTGGATT
260 CACGACGAAGGATATTAGACTCGAAACAACACAAGCTTGGATT
11132 TCAACTTCACGATGAAG
1 TCAACTTCACGATGAAG
11149 CATATTCAAG
Statistics
Matches: 294, Mismatches: 23, Indels: 3
0.92 0.07 0.01
Matches are distributed among these distances:
301 16 0.05
302 278 0.95
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (302 bp):
TCAACTTCACGATGAAGGGGGCCATCCACGATTTCAACTCCACGACAGAGGATATCGTACCAACG
GATCCACGATTTCAACTCCACGACAGAGGATATCGTGCACACACATCCACGGTTTCAACTTCACG
ACGAAGGGAATCGTACACACAAGCAGCATCCATCTCTAGATTGGATTTCAACTTCACGTAAAAGG
ATATCCAACTCAAAGAAAGAGTGTATGTCAATAAACTTTCCAGTTTCAGAGCCAATTTCAACTTC
ACGACGAAGGATATTAGACTCGAAACAACACAAGCTTGGATT
Found at i:11243 original size:42 final size:42
Alignment explanation
Indices: 11184--11343 Score: 266
Period size: 42 Copynumber: 3.8 Consensus size: 42
11174 AGTGAAACAA
11184 GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
1 GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
*
11226 GTCATCAGTAAGTCTTCCGAGCATAATGCTTAAATCCTTCGG
1 GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
*
11268 ATCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
1 GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
* * * *
11310 GTCATCTGTAAGCCTTTCGAGCATGATACTTAAA
1 GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAA
11344 ATTTTTGGGA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 110 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.31
Consensus pattern (42 bp):
GTCATCAGTAAGTCTTCCGAGCATGATGCTTAAATCCTTCGG
Found at i:11820 original size:109 final size:109
Alignment explanation
Indices: 11581--12171 Score: 737
Period size: 111 Copynumber: 5.3 Consensus size: 109
11571 TGAAGCAAAT
* * *
11581 CCAGATATGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTTTTCCAAGATTTGATATTCCCT
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTC-TTT-CAAGATTTGATATTCCC-
** * *
11646 TCAGAGT-A-AATGGAACAAGTCTTGCCAC-GATTCAATGGATCAACTCTC
63 T--GAGTGACAGCGGAACAAGTC-TACC-CTGATTCAATGAATCAACTCTC
* * * *
11694 CCATATCTGATATTCCCTCAGAGGAAGCGGAACAGGTCTCTCTTTCAAGATTTGATATTTCCTTA
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGA
* * * *
11759 GTAACAGCGGAACAAGTCTACTCTGATTCAAAGAATCAACTTTC
66 GTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTCTC
* *
11803 CCAGATCTGATATTCCCTCAGAGGAAGTGGAACCGATCTCTCTTTTTCAAGATTTGATATTCCCT
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTC--TTTCAAGATTTGATATTCCCT
* * * *
11868 GAGTGACAGCGGAACAAATATGTCCC-GATTCAATGGATCAACTCTC
64 GAGTGACAGCGGAACAAGTCT-ACCCTGATTCAATGAATCAACTCTC
* * *
11914 CCATATCTGATATTCCCTTAAAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGA
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGA
* *
11979 GTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAAATTTC
66 GTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTCTC
* *
12023 CCAGATCTGATATTCCCTCAGAGGAAACGGAACAGATCCATCTTTTTCAAGATTTGATATTCCCT
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGAT-C-TCTCTTTCAAGATTTGATATTCCCT
*
12088 GAGTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACAAC-C
64 GAGTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAAC-TCTC
12134 CCAGATCTGATATTCCCT--GAGTGACAGCGGAACAGATC
1 CCAGATCTGATATTCCCTCAGAG-GA-AGCGGAACAGATC
12172 CCTCATCATA
Statistics
Matches: 418, Mismatches: 48, Indels: 27
0.85 0.10 0.05
Matches are distributed among these distances:
108 7 0.02
109 151 0.36
110 16 0.04
111 202 0.48
112 5 0.01
113 37 0.09
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (109 bp):
CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGA
GTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACTCTC
Found at i:11972 original size:220 final size:218
Alignment explanation
Indices: 11581--12151 Score: 815
Period size: 220 Copynumber: 2.6 Consensus size: 218
11571 TGAAGCAAAT
* * *
11581 CCAGATATGATATTCCCTCAGAAGAAGCGGAACAGATCCCTCTTTTCCAAGATTTGATATTCCCT
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGAT-CCTCTTTTTCAAGATTTGATATTCCC-
**
11646 TCAGAGT-A-AATGGAACAAGTCTTGCCACGATTCAATGGATCAACTCTCCCATATCTGATATTC
64 T--GAGTGACAGCGGAACAAGTCTT-CC-CGATTCAATGGATCAACTCTCCCATATCTGATATTC
* * * *
11709 CCTCAGAGGAAGCGGAACAGGTCTCTCTTTCAAGATTTGATATTTCCTTAGTAACAGCGGAACAA
125 CCTCAAAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACAA
* *
11774 GTCTACTCTGATTCAAAGAATCAACTTTC
190 GTCTACCCTGATTCAAAGAATCAAATTTC
* *
11803 CCAGATCTGATATTCCCTCAGAGGAAGTGGAACCGATCTCTCTTTTTCAAGATTTGATATTCCCT
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATC-CTCTTTTTCAAGATTTGATATTCCCT
* * *
11868 GAGTGACAGCGGAACAAATATGTCCCGATTCAATGGATCAACTCTCCCATATCTGATATTCCCTT
65 GAGTGACAGCGGAACAAGTCT-TCCCGATTCAATGGATCAACTCTCCCATATCTGATATTCCCTC
*
11933 AAAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGAGTGACAGCGGAACAAGTCT
129 AAAGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACAAGTCT
*
11998 ACCCTGATTCAATGAATCAAATTTC
194 ACCCTGATTCAAAGAATCAAATTTC
*
12023 CCAGATCTGATATTCCCTCAGAGGAAACGGAACAGATCCATCTTTTTCAAGATTTGATATTCCCT
1 CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCC-TCTTTTTCAAGATTTGATATTCCCT
* * * *
12088 GAGTGACAGCGGAACAAGTCTACCCTGATTCAATGAATCAACAAC-CCCAGATCTGATATTCCCT
65 GAGTGACAGCGGAACAAGTCTTCCC-GATTCAATGGATCAAC-TCTCCCATATCTGATATTCCCT
12152 GAGTGACAGC
Statistics
Matches: 315, Mismatches: 27, Indels: 16
0.88 0.08 0.04
Matches are distributed among these distances:
219 8 0.03
220 234 0.74
221 15 0.05
222 58 0.18
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.28
Consensus pattern (218 bp):
CCAGATCTGATATTCCCTCAGAGGAAGCGGAACAGATCCTCTTTTTCAAGATTTGATATTCCCTG
AGTGACAGCGGAACAAGTCTTCCCGATTCAATGGATCAACTCTCCCATATCTGATATTCCCTCAA
AGGAAGCGGAACAGATCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGCGGAACAAGTCTAC
CCTGATTCAAAGAATCAAATTTC
Found at i:16853 original size:13 final size:13
Alignment explanation
Indices: 16837--16861 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16827 TCCGTTTTCT
16837 GTTTCTGTCTCTG
1 GTTTCTGTCTCTG
16850 GTTTCTGTCTCT
1 GTTTCTGTCTCT
16862 TTCTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.20, T:0.56
Consensus pattern (13 bp):
GTTTCTGTCTCTG
Found at i:17355 original size:3 final size:3
Alignment explanation
Indices: 17347--17411 Score: 121
Period size: 3 Copynumber: 21.7 Consensus size: 3
17337 AATATAAATT
*
17347 TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
17395 TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TA
17412 TGGATAAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:17887 original size:114 final size:113
Alignment explanation
Indices: 17547--18186 Score: 809
Period size: 114 Copynumber: 5.6 Consensus size: 113
17537 ATTGAATAAA
* * ** * *
17547 TTCTTC-TCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGAAAAGATAATCCATC
*
17611 AAATGATGAATTCA-AGCAAAAGATTGAACAAATTCTTCTCATTATGAAC
65 AAATGATGAATTCAGA-CAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* * * * *
17660 TTCTTCTTCCTTCTTCAGATGACGAGTTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCC
1 TTCTTCTTCCTTCTTCAGAT---GAGTTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCC
* *
17724 ATCAAATGATGAATTCA-AGCAAAAGATTGAACAAGTTCTTCTCATTATGAAC
62 ATCAAATGATGAATTCAGA-CAAAAGGTTGAACAAATTCTTCTCATTATGAAC
17776 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
* *
17841 ATTTGATGAATTCAGAAAAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-ATGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
**
17890 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCCCCA
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
*
17955 ATTTGATGAATTCAGGA-AAAAGGTTGAACAAATTCTTCTCATTATGAAC
66 A-ATGATGAATTCA-GACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
18004 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAA--TTGAC-CT--AACAATGCTGATCC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTT--CTCTGGAA-AA-GATAATCC
* * * *
18064 ATCAAGTGATAGAATT-AGGCAGAAGGTTGAACAAATTCTTCTCATTATGAAT
62 ATCAAATGAT-GAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
* *
18116 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTGGAAATG-TCAATCCATC
1 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGAT-AATCCATC
18180 AAATGAT
65 AAATGAT
18187 AGATTTGAAT
Statistics
Matches: 477, Mismatches: 29, Indels: 42
0.87 0.05 0.08
Matches are distributed among these distances:
111 3 0.01
112 83 0.17
113 75 0.16
114 205 0.43
115 5 0.01
116 84 0.18
117 20 0.04
118 2 0.00
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (113 bp):
TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCA
AATGATGAATTCAGACAAAAGGTTGAACAAATTCTTCTCATTATGAAC
Found at i:18180 original size:340 final size:341
Alignment explanation
Indices: 17547--18181 Score: 958
Period size: 340 Copynumber: 1.9 Consensus size: 341
17537 ATTGAATAAA
* * ** * * *
17547 TTCTTCTCTTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATCA
1 TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTGCTGGAAAAGATAATCCACCA
*
17612 AATGATGAATTCAAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
66 AATGATGAATTCAAGAAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
** *
17677 GATGACGAGTTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAA
131 GAT-A-GAGTTCTTCTCATTATGAACTCTACCTAACAATGCTGATCCATCAAATGATGAATTCAA
*
17742 GCAAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
194 GCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTC
17807 ATTATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGAAAAAAGGTTGAACAA
259 ATTATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGAAAAAAGGTTGAACAA
17872 ATTCTTCTCATTATGAAC
324 ATTCTTCTCATTATGAAC
*
17890 TTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCT-CTGGAAAAGATAATCCCCC
1 TTCTTC-TCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTGCTGGAAAAGATAATCCACC
* * *
17954 AATTTGATGAATTCAGGAAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT
65 AA-ATGATGAATTCAAGAAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTT
*
18019 CAGAT-GAGTTCTTCTCATTATGAA-T-TGACCTAACAATGCTGATCCATCAAGTGATAGAATT-
129 CAGATAGAGTTCTTCTCATTATGAACTCT-ACCTAACAATGCTGATCCATCAAATGAT-GAATTC
* * * *
18080 AGGCAGAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCAGATGAGTTCTTC
192 AAGCAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTC
* *
18145 TCATTATGAACTTTCTCTGGAAATG-TCAATCCATCAA
257 TCATTATGAACCTTCTCTGGAAAAGAT-AATCCATCAA
18182 ATGATAGATT
Statistics
Matches: 264, Mismatches: 23, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
339 2 0.01
340 118 0.45
341 24 0.09
343 21 0.08
344 99 0.38
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (341 bp):
TTCTTCTCCTTCTTCAGATGAGTTCTTCTCATTATGAACCTTCTGCTGGAAAAGATAATCCACCA
AATGATGAATTCAAGAAAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
GATAGAGTTCTTCTCATTATGAACTCTACCTAACAATGCTGATCCATCAAATGATGAATTCAAGC
AAAAGATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
TATGAACCTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGAAAAAAGGTTGAACAAAT
TCTTCTCATTATGAAC
Found at i:18862 original size:13 final size:13
Alignment explanation
Indices: 18846--18870 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18836 TCCGTTTTCT
18846 GTTTCTGTCTCTG
1 GTTTCTGTCTCTG
18859 GTTTCTGTCTCT
1 GTTTCTGTCTCT
18871 TTCTTTTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.00, C:0.24, G:0.20, T:0.56
Consensus pattern (13 bp):
GTTTCTGTCTCTG
Found at i:19362 original size:3 final size:3
Alignment explanation
Indices: 19354--19438 Score: 145
Period size: 3 Copynumber: 28.7 Consensus size: 3
19344 AATATAAATT
* *
19354 TAA TAA TAA TAA TAA TGA TGA T-A TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
19401 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
19439 TGGATAAAAA
Statistics
Matches: 80, Mismatches: 1, Indels: 2
0.96 0.01 0.02
Matches are distributed among these distances:
2 2 0.03
3 78 0.98
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:21401 original size:59 final size:59
Alignment explanation
Indices: 21254--21402 Score: 137
Period size: 59 Copynumber: 2.5 Consensus size: 59
21244 TTAGTCATTA
* * * *
21254 AACTTTTAAATATTAT-AATTTCATCCCTAAATTGTGACTATCATTCTAAAGTAGTCCTC
1 AACTTTTAAACATT-TCCATTTCATCCCAAAATTGTCACTATCATTCTAAAGTAGTCCTC
* * *
21313 AACTTTTAAACATTTCGATTTCATCCCCAAAATATGTCA-T-TCATTCTAAATTGGTCC-C
1 AACTTTTAAACATTTCCATTTCAT-CCCAAAAT-TGTCACTATCATTCTAAAGTAGTCCTC
*
21371 TAACATTTTGAACA-TTCCATTTTCATCCCAAA
1 -AAC-TTTTAAACATTTCCA-TTTCATCCCAAA
21403 TTATAAGTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
58 2 0.03
59 48 0.63
60 22 0.29
61 4 0.05
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (59 bp):
AACTTTTAAACATTTCCATTTCATCCCAAAATTGTCACTATCATTCTAAAGTAGTCCTC
Found at i:21654 original size:60 final size:57
Alignment explanation
Indices: 21528--21689 Score: 175
Period size: 60 Copynumber: 2.8 Consensus size: 57
21518 TTTGCATGCT
* ** * *
21528 TTTACGGATGAAATTAAATATTC-AAAGTTTGGGGACCAATTTAGAAATAGTCATAG
1 TTTAGGGATGAAATTAAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGTCATAG
* *
21584 TTTAGGGATGAAATTAAAATGTTCAAAAGTTTAACGACTAATTTAGAATGAGAGTCATAG
1 TTTAGGGATGAAATT-AAATATTCAAAAGTTTAAGGACTAATTTAGAA--AGAGTCATAG
* * *
21644 TTT-GGAGATGAAATTGGAATCTTTAAAAGTTTAAGGACTAATTTAG
1 TTTAGG-GATGAAATT-AAATATTCAAAAGTTTAAGGACTAATTTAG
21690 GGACATATGA
Statistics
Matches: 89, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
56 14 0.16
57 7 0.08
58 19 0.21
59 2 0.02
60 47 0.53
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (57 bp):
TTTAGGGATGAAATTAAATATTCAAAAGTTTAAGGACTAATTTAGAAAGAGTCATAG
Found at i:21721 original size:2 final size:2
Alignment explanation
Indices: 21714--21766 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
21704 ATTAACGTAA
21714 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
21756 AT AT AT AT AT A
1 AT AT AT AT AT A
21767 CTTGGTAAAC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:22897 original size:2 final size:2
Alignment explanation
Indices: 22890--22915 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
22880 TTTAACCATA
22890 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
22916 TCATATTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31092 original size:2 final size:2
Alignment explanation
Indices: 30995--31074 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
30985 GTAATAGGAT
30995 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31037 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31075 ATTGGAGTTG
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33248 original size:18 final size:18
Alignment explanation
Indices: 33227--33261 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
33217 CTTTAACCGA
*
33227 GTTTTTTATTATTATTTT
1 GTTTTTAATTATTATTTT
*
33245 GTTTTTAATTGTTATTT
1 GTTTTTAATTATTATTT
33262 CGAGACTAAT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.09, T:0.74
Consensus pattern (18 bp):
GTTTTTAATTATTATTTT
Found at i:39751 original size:7 final size:7
Alignment explanation
Indices: 39687--39761 Score: 53
Period size: 7 Copynumber: 10.3 Consensus size: 7
39677 CCCGGTCCAA
39687 CATTGAC
1 CATTGAC
*
39694 CATTTGGC
1 CA-TTGAC
39702 CATTGAC
1 CATTGAC
*
39709 CGTTTGA-
1 C-ATTGAC
*
39716 CATTGAT
1 CATTGAC
*
39723 CGTTGAC
1 CATTGAC
*
39730 CGTTTGAC
1 C-ATTGAC
39738 CATTTGAC
1 CA-TTGAC
*
39746 CATTGAT
1 CATTGAC
39753 CATTGAC
1 CATTGAC
39760 CA
1 CA
39762 AAAAGTCAAA
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
6 4 0.08
7 26 0.49
8 23 0.43
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (7 bp):
CATTGAC
Found at i:39752 original size:30 final size:29
Alignment explanation
Indices: 39704--39760 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
39694 CATTTGGCCA
* *
39704 TTGACCGTTTGACATTGATCGTTGACCGT
1 TTGACCATTTGACATTGATCATTGACCGT
39733 TTGACCATTTGACCATTGATCATTGACC
1 TTGACCATTTGA-CATTGATCATTGACC
39761 AAAAAGTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.21, C:0.23, G:0.19, T:0.37
Consensus pattern (29 bp):
TTGACCATTTGACATTGATCATTGACCGT
Found at i:40981 original size:21 final size:21
Alignment explanation
Indices: 40957--41007 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
40947 TACGAGTTAA
*
40957 ACTTTTATAGTTAATTATTTT
1 ACTTTTATAGTTAATTATCTT
40978 ACTTTTATAGTTAATTATCTT
1 ACTTTTATAGTTAATTATCTT
40999 ACTTTTATA
1 ACTTTTATA
41008 AATGTTAATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.59
Consensus pattern (21 bp):
ACTTTTATAGTTAATTATCTT
Found at i:46151 original size:16 final size:17
Alignment explanation
Indices: 46130--46162 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
46120 TCGAAAAACA
46130 TAAAA-TATGACTTTTT
1 TAAAATTATGACTTTTT
*
46146 TAAAATTTTGACTTTTT
1 TAAAATTATGACTTTTT
46163 GGTCAACGGT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.33, C:0.06, G:0.06, T:0.55
Consensus pattern (17 bp):
TAAAATTATGACTTTTT
Found at i:46178 original size:8 final size:8
Alignment explanation
Indices: 46163--46215 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
46153 TTGACTTTTT
46163 GGTC-AAC
1 GGTCAAAC
46170 GGTCAAAC
1 GGTCAAAC
*
46178 GATCAAAC
1 GGTCAAAC
46186 GGTCAAAAC
1 GGTC-AAAC
*
46195 AGTCAAA-
1 GGTCAAAC
*
46202 TGTCAAAC
1 GGTCAAAC
46210 GGTCAA
1 GGTCAA
46216 TGTTAGAACG
Statistics
Matches: 38, Mismatches: 5, Indels: 5
0.79 0.10 0.10
Matches are distributed among these distances:
7 10 0.26
8 21 0.55
9 7 0.18
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.15
Consensus pattern (8 bp):
GGTCAAAC
Found at i:47152 original size:8 final size:8
Alignment explanation
Indices: 47126--47184 Score: 61
Period size: 8 Copynumber: 7.8 Consensus size: 8
47116 CGGTCCAACG
47126 TTGACCGT
1 TTGACCGT
*
47134 TTGTCCG-
1 TTGACCGT
47141 TTGACCGT
1 TTGACCGT
*
47149 TTGA-TGT
1 TTGACCGT
47156 TTGACCGT
1 TTGACCGT
* *
47164 TTGATCAT
1 TTGACCGT
47172 TTGACCG-
1 TTGACCGT
47179 TTGACC
1 TTGACC
47185 AAAAAGTCAA
Statistics
Matches: 41, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
7 18 0.44
8 23 0.56
ACGTcount: A:0.14, C:0.22, G:0.24, T:0.41
Consensus pattern (8 bp):
TTGACCGT
Found at i:47159 original size:15 final size:16
Alignment explanation
Indices: 47126--47180 Score: 69
Period size: 15 Copynumber: 3.6 Consensus size: 16
47116 CGGTCCAACG
**
47126 TTGACCGTTTG-TCCG
1 TTGACCGTTTGATCAT
*
47141 TTGACCGTTTGAT-GT
1 TTGACCGTTTGATCAT
47156 TTGACCGTTTGATCAT
1 TTGACCGTTTGATCAT
47172 TTGACCGTT
1 TTGACCGTT
47181 GACCAAAAAG
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
15 24 0.69
16 11 0.31
ACGTcount: A:0.13, C:0.20, G:0.24, T:0.44
Consensus pattern (16 bp):
TTGACCGTTTGATCAT
Found at i:48843 original size:22 final size:22
Alignment explanation
Indices: 48796--48843 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
48786 TAATATTCAA
* *
48796 TTTTTTAATTTATTGTATTATG
1 TTTTTTAATTTATTGAATTATC
*
48818 TTTTTATAATTTATT-AATTTTC
1 TTTTT-TAATTTATTGAATTATC
48840 TTTT
1 TTTT
48844 CTTTATTTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (22 bp):
TTTTTTAATTTATTGAATTATC
Found at i:50691 original size:15 final size:15
Alignment explanation
Indices: 50664--50728 Score: 60
Period size: 15 Copynumber: 4.3 Consensus size: 15
50654 CCCGGTCCAA
*
50664 CATTGACCATTTGAC
1 CATTGACCGTTTGAC
*
50679 CATTGGCCGTTTGAC
1 CATTGACCGTTTGAC
* *
50694 TATTGATCG-TTGATC
1 CATTGACCGTTTGA-C
**
50709 GTTTGACCGTTTGAC
1 CATTGACCGTTTGAC
50724 CATTG
1 CATTG
50729 GTACCAAAAA
Statistics
Matches: 38, Mismatches: 10, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
14 4 0.11
15 30 0.79
16 4 0.11
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (15 bp):
CATTGACCGTTTGAC
Found at i:57133 original size:8 final size:8
Alignment explanation
Indices: 57122--57193 Score: 67
Period size: 8 Copynumber: 9.2 Consensus size: 8
57112 TTGGTCAACT
57122 GTCAAACG
1 GTCAAACG
*
57130 GTCAAATG
1 GTCAAACG
* *
57138 ATCAAACA
1 GTCAAACG
57146 GTCAAACG
1 GTCAAACG
*
57154 GTCAAACA
1 GTCAAACG
* *
57162 ATCAAA-A
1 GTCAAACG
57169 GTCAAACG
1 GTCAAACG
57177 GTC-AACG
1 GTCAAACG
*
57184 GACAAACG
1 GTCAAACG
57192 GT
1 GT
57194 TAACGTTGGA
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
7 12 0.24
8 38 0.76
ACGTcount: A:0.44, C:0.22, G:0.19, T:0.14
Consensus pattern (8 bp):
GTCAAACG
Found at i:57134 original size:15 final size:15
Alignment explanation
Indices: 57114--57198 Score: 62
Period size: 15 Copynumber: 5.5 Consensus size: 15
57104 TTGACTTTTT
*
57114 GGTCAACTGTCAAAC
1 GGTCAACGGTCAAAC
* *
57129 GGTCAAATGATCAAAC
1 GGTC-AACGGTCAAAC
*
57145 AGTCAAACGGTCAAAC
1 GGTC-AACGGTCAAAC
** **
57161 AATCAAAAGTCAAAC
1 GGTCAACGGTCAAAC
*
57176 GGTCAACGGACAAAC
1 GGTCAACGGTCAAAC
*
57191 GGTTAACG
1 GGTCAACG
57199 TTGGACCGGG
Statistics
Matches: 54, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
15 30 0.56
16 24 0.44
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAAAC
Found at i:57144 original size:16 final size:15
Alignment explanation
Indices: 57114--57181 Score: 64
Period size: 16 Copynumber: 4.4 Consensus size: 15
57104 TTGACTTTTT
*
57114 GGTCAACTGTCAAAC
1 GGTCAAATGTCAAAC
57129 GGTCAAATGATCAAAC
1 GGTCAAATG-TCAAAC
* *
57145 AGTCAAACGGTCAAAC
1 GGTCAAA-TGTCAAAC
** *
57161 AATCAAAAGTCAAAC
1 GGTCAAATGTCAAAC
57176 GGTCAA
1 GGTCAA
57182 CGGACAAACG
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 19 0.43
16 24 0.55
17 1 0.02
ACGTcount: A:0.44, C:0.22, G:0.18, T:0.16
Consensus pattern (15 bp):
GGTCAAATGTCAAAC
Found at i:57149 original size:24 final size:23
Alignment explanation
Indices: 57122--57181 Score: 93
Period size: 24 Copynumber: 2.6 Consensus size: 23
57112 TTGGTCAACT
**
57122 GTCAAACGGTCAAATGATCAAACA
1 GTCAAACGGTCAAACAATCAAA-A
57146 GTCAAACGGTCAAACAATCAAAA
1 GTCAAACGGTCAAACAATCAAAA
57169 GTCAAACGGTCAA
1 GTCAAACGGTCAA
57182 CGGACAAACG
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
23 14 0.41
24 20 0.59
ACGTcount: A:0.47, C:0.22, G:0.17, T:0.15
Consensus pattern (23 bp):
GTCAAACGGTCAAACAATCAAAA
Found at i:58237 original size:15 final size:15
Alignment explanation
Indices: 58195--58234 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
58185 CATTTGTCCG
58195 TTGACCGTTTGACAT
1 TTGACCGTTTGACAT
*
58210 TCGACCGTTTGACAGT
1 TTGACCGTTTGACA-T
58226 TTGACCGTT
1 TTGACCGTT
58235 GACCAAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (15 bp):
TTGACCGTTTGACAT
Found at i:59350 original size:8 final size:8
Alignment explanation
Indices: 59327--59386 Score: 70
Period size: 8 Copynumber: 7.8 Consensus size: 8
59317 CGGTCCAACG
59327 TTGACCGT
1 TTGACCGT
59335 TTGA-CGT
1 TTGACCGT
59342 TTGACCGT
1 TTGACCGT
*
59350 TTAACCGT
1 TTGACCGT
*
59358 TTGACTGT
1 TTGACCGT
*
59366 TTGATCGT
1 TTGACCGT
*
59374 TTTACCG-
1 TTGACCGT
59381 TTGACC
1 TTGACC
59387 AAAAAGTTAA
Statistics
Matches: 43, Mismatches: 8, Indels: 3
0.80 0.15 0.06
Matches are distributed among these distances:
7 12 0.28
8 31 0.72
ACGTcount: A:0.15, C:0.22, G:0.22, T:0.42
Consensus pattern (8 bp):
TTGACCGT
Found at i:59374 original size:24 final size:23
Alignment explanation
Indices: 59330--59382 Score: 79
Period size: 24 Copynumber: 2.3 Consensus size: 23
59320 TCCAACGTTG
59330 ACCGTTTGACGTTTGACCGTTTA
1 ACCGTTTGACGTTTGACCGTTTA
* *
59353 ACCGTTTGACTGTTTGATCGTTTT
1 ACCGTTTGAC-GTTTGACCGTTTA
59377 ACCGTT
1 ACCGTT
59383 GACCAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 10 0.37
24 17 0.63
ACGTcount: A:0.15, C:0.21, G:0.21, T:0.43
Consensus pattern (23 bp):
ACCGTTTGACGTTTGACCGTTTA
Found at i:60529 original size:8 final size:8
Alignment explanation
Indices: 60516--60717 Score: 395
Period size: 8 Copynumber: 25.2 Consensus size: 8
60506 TTTTAAGATG
*
60516 ATACATAC
1 ATACATGC
60524 ATACATGC
1 ATACATGC
60532 ATACATGC
1 ATACATGC
60540 ATACATGC
1 ATACATGC
60548 ATACATGC
1 ATACATGC
60556 ATACATGC
1 ATACATGC
60564 ATACATGC
1 ATACATGC
60572 ATACATGC
1 ATACATGC
60580 ATACATGC
1 ATACATGC
60588 ATACATGC
1 ATACATGC
60596 ATACATGC
1 ATACATGC
60604 ATACATGC
1 ATACATGC
60612 ATACATGC
1 ATACATGC
60620 ATACATGC
1 ATACATGC
60628 ATACATGC
1 ATACATGC
60636 ATACATGC
1 ATACATGC
60644 ATACATGC
1 ATACATGC
60652 ATACATGC
1 ATACATGC
60660 ATACATGC
1 ATACATGC
60668 ATACATGC
1 ATACATGC
60676 ATACATGC
1 ATACATGC
60684 ATACATGC
1 ATACATGC
60692 ATACATGC
1 ATACATGC
60700 ATACATGC
1 ATACATGC
60708 ATACATGC
1 ATACATGC
60716 AT
1 AT
60718 GGCTTAACTT
Statistics
Matches: 193, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
8 193 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (8 bp):
ATACATGC
Found at i:61624 original size:30 final size:30
Alignment explanation
Indices: 61588--61647 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
61578 AAAAGCTCCC
*
61588 CCTTTTTCATTAC-TGAAATTGAATTTTTCA
1 CCTTTTTCATT-CTTGAAATTGAATATTTCA
61618 CCTTTTTCATTCTTGAAATTGAATATTTCA
1 CCTTTTTCATTCTTGAAATTGAATATTTCA
61648 AACCATATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.27, C:0.17, G:0.07, T:0.50
Consensus pattern (30 bp):
CCTTTTTCATTCTTGAAATTGAATATTTCA
Found at i:64698 original size:21 final size:21
Alignment explanation
Indices: 64673--64729 Score: 96
Period size: 21 Copynumber: 2.7 Consensus size: 21
64663 CATGATGAAC
64673 AGTATCGATACTGATGTAAGT
1 AGTATCGATACTGATGTAAGT
*
64694 AGTATCGATACTAATGTAAGT
1 AGTATCGATACTGATGTAAGT
*
64715 AGCATCGATACTGAT
1 AGTATCGATACTGAT
64730 ATGGGGTATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.12, G:0.21, T:0.32
Consensus pattern (21 bp):
AGTATCGATACTGATGTAAGT
Found at i:73194 original size:21 final size:22
Alignment explanation
Indices: 73165--73206 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
73155 TATTATATTA
**
73165 AAATGTTTTATTTTTTAGAAAC
1 AAATGTTTTATGGTTTAGAAAC
73187 AAAT-TTTTATGGTTTAGAAA
1 AAATGTTTTATGGTTTAGAAA
73207 TAAGGAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (22 bp):
AAATGTTTTATGGTTTAGAAAC
Done.