Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003923.1 Hibiscus syriacus cultivar Beakdansim tig00008481_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: 75714
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2151 original size:20 final size:20
Alignment explanation
Indices: 2123--2191 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
2113 CACTGTTCAT
* *
2123 TACTGTTCACACAGTGTCAG
1 TACTATTCATACAGTGTCAG
* *
2143 TACTATTCATACAATATC-G
1 TACTATTCATACAGTGTCAG
*
2162 ATA-TTTTCATACAGTG-CAG
1 -TACTATTCATACAGTGTCAG
2181 TACTATTCATA
1 TACTATTCATA
2192 AAAACATTTT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
18 3 0.08
19 19 0.50
20 16 0.42
ACGTcount: A:0.32, C:0.20, G:0.12, T:0.36
Consensus pattern (20 bp):
TACTATTCATACAGTGTCAG
Found at i:7336 original size:13 final size:13
Alignment explanation
Indices: 7285--7328 Score: 79
Period size: 13 Copynumber: 3.4 Consensus size: 13
7275 GTCATTAATC
7285 TATGACGCACATT
1 TATGACGCACATT
*
7298 TATGACACACATT
1 TATGACGCACATT
7311 TATGACGCACATT
1 TATGACGCACATT
7324 TATGA
1 TATGA
7329 TGCTCATTGC
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 29 1.00
ACGTcount: A:0.34, C:0.20, G:0.14, T:0.32
Consensus pattern (13 bp):
TATGACGCACATT
Found at i:7428 original size:85 final size:83
Alignment explanation
Indices: 7339--7506 Score: 259
Period size: 85 Copynumber: 2.0 Consensus size: 83
7329 TGCTCATTGC
7339 GCGTCATTGAAGCCACCGTCATAAAT-TAAG-ATGACACACATTTGTGTGTCATAAATTTATGAC
1 GCGTCATTGAAGCCACCGTCATAAATCT--GCATGACACACATTTGTGTGTCATAAATTTATGAC
7402 ACGCATGTATGACTTACATTTA
64 ACGCATGTATGAC--ACATTTA
* * *
7424 GCGTCATTGAAGCCCCCGTCATAAATCTGCTTGACTCACATTTGTGTGTCATAAATTTATGACAC
1 GCGTCATTGAAGCCACCGTCATAAATCTGCATGACACACATTTGTGTGTCATAAATTTATGACAC
7489 GCATGTATGACACATTTA
66 GCATGTATGACACATTTA
7507 AAAACGACAC
Statistics
Matches: 78, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
83 7 0.09
84 1 0.01
85 69 0.88
86 1 0.01
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (83 bp):
GCGTCATTGAAGCCACCGTCATAAATCTGCATGACACACATTTGTGTGTCATAAATTTATGACAC
GCATGTATGACACATTTA
Found at i:7556 original size:2 final size:2
Alignment explanation
Indices: 7549--7587 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
7539 TTTCGTAAAT
7549 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA 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
7588 TGTAGATTGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:8803 original size:16 final size:16
Alignment explanation
Indices: 8782--8829 Score: 96
Period size: 16 Copynumber: 3.0 Consensus size: 16
8772 GCATTTCGTT
8782 AAAATGAACAAAAGCA
1 AAAATGAACAAAAGCA
8798 AAAATGAACAAAAGCA
1 AAAATGAACAAAAGCA
8814 AAAATGAACAAAAGCA
1 AAAATGAACAAAAGCA
8830 TTTCGTTAAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.69, C:0.12, G:0.12, T:0.06
Consensus pattern (16 bp):
AAAATGAACAAAAGCA
Found at i:9685 original size:33 final size:32
Alignment explanation
Indices: 9614--9685 Score: 74
Period size: 33 Copynumber: 2.2 Consensus size: 32
9604 TCAATTTTAC
* * *
9614 ATTTTAAAAATCAATTAAAAATTAATTTTAAA
1 ATTTTAAAAATCAATTAAAAAATAAGTATAAA
*
9646 AGTTTTAAAAATCAATTAAAACTAATAAGTAT-CA
1 A-TTTTAAAAATCAATTAAAA--AATAAGTATAAA
9680 ATTTTA
1 ATTTTA
9686 CATTTTTATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
32 1 0.03
33 24 0.73
34 2 0.06
35 6 0.18
ACGTcount: A:0.53, C:0.06, G:0.03, T:0.39
Consensus pattern (32 bp):
ATTTTAAAAATCAATTAAAAAATAAGTATAAA
Found at i:14340 original size:14 final size:14
Alignment explanation
Indices: 14321--14358 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
14311 CGTATCACAT
14321 TATCACATATATCA
1 TATCACATATATCA
14335 TATCACATATATCA
1 TATCACATATATCA
14349 TATCACATAT
1 TATCACATAT
14359 TTTATCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (14 bp):
TATCACATATATCA
Found at i:14343 original size:7 final size:7
Alignment explanation
Indices: 14313--14358 Score: 51
Period size: 7 Copynumber: 6.4 Consensus size: 7
14303 TTGAGTCTCG
14313 TATCACA
1 TATCACA
14320 TTATCACA
1 -TATCACA
14328 TAT-ATCA
1 TATCA-CA
14335 TATCACA
1 TATCACA
14342 TAT-ATCA
1 TATCA-CA
14349 TATCACA
1 TATCACA
14356 TAT
1 TAT
14359 TTTATCTCTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
6 2 0.06
7 23 0.68
8 9 0.26
ACGTcount: A:0.41, C:0.22, G:0.00, T:0.37
Consensus pattern (7 bp):
TATCACA
Found at i:21878 original size:6 final size:6
Alignment explanation
Indices: 21857--21898 Score: 66
Period size: 6 Copynumber: 6.8 Consensus size: 6
21847 ATTAAATTAA
*
21857 ATAAAT AAATAAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
1 ATAAAT ATA-AAT ATAAAT ATAAAT ATAAAT ATAAAT ATAAA
21899 AAATATATGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
6 28 0.85
7 5 0.15
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (6 bp):
ATAAAT
Found at i:21890 original size:18 final size:19
Alignment explanation
Indices: 21857--21903 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 19
21847 ATTAAATTAA
21857 ATAAATAAATAATATAAAT
1 ATAAATAAATAATATAAAT
*
21876 ATAAATATA-AATATAAAT
1 ATAAATAAATAATATAAAT
21894 ATAAA-AAATA
1 ATAAATAAATA
21904 TATGATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 2 0.08
18 15 0.60
19 8 0.32
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAAATAAATAATATAAAT
Found at i:21902 original size:27 final size:27
Alignment explanation
Indices: 21842--21905 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
21832 TTGGACATGT
21842 TAAAAAT-TAAATTAAATAAATAAATAA
1 TAAAAATATAAATTAAAT-AATAAATAA
*
21869 TATAAATATAAATATAAAT-ATAAAT-A
1 TAAAAATATAAAT-TAAATAATAAATAA
21895 TAAAAAATATA
1 T-AAAAATATA
21906 TGATAAAAAC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
26 2 0.06
27 20 0.62
28 5 0.16
29 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (27 bp):
TAAAAATATAAATTAAATAATAAATAA
Found at i:22003 original size:37 final size:36
Alignment explanation
Indices: 21911--22249 Score: 206
Period size: 37 Copynumber: 8.8 Consensus size: 36
21901 ATATATGATA
* *
21911 AAAACTATATAATATTATATTTTCAAAAATAATATGTTTTC
1 AAAACTATAT-ATA-TATGTTTTC-AAAA-AAT-CGTTTTC
* *
21952 AAAATTATATTATATACGTTTTCAAAAAATCGTTTTC
1 AAAACTATA-TATATATGTTTTCAAAAAATCGTTTTC
*
21989 AAAAACTATATATATATGTTTTCAAAACTATATTATATATGTTTTC
1 -AAAACTATATATATATGTTTTC--AA--A-A--A-AT-CGTTTTC
* * *
22035 AAAACTATATTATATACGTTTTCAAAAAATCATTTTT
1 AAAACTATA-TATATATGTTTTCAAAAAATCGTTTTC
* *
22072 AAAACTATGTATATTATACGTTTTC-AAAAATGAGTTTTC
1 AAAACTA--TATA-TATATGTTTTCAAAAAAT-CGTTTTC
22111 AAAACTATATAATATATGTTTTC-AAAAAT-GTATTTTC
1 AAAACTATAT-ATATATGTTTTCAAAAAATCG--TTTTC
* * * * *
22148 AAAACCATAT-TATGTATTTTC-AAAAATTGATTTTTA
1 AAAACTATATATATATGTTTTCAAAAAATCG--TTTTC
*
22184 AAAACTATATATCATATGCTTTC-AAAAA-CGTTTTC
1 AAAACTATATAT-ATATGTTTTCAAAAAATCGTTTTC
*
22219 TATAAATTATATATTATATGTTTTCAAAAAA
1 -A-AAACTATATA-TATATGTTTTCAAAAAA
22250 AATATCTTCA
Statistics
Matches: 243, Mismatches: 29, Indels: 55
0.74 0.09 0.17
Matches are distributed among these distances:
35 20 0.08
36 15 0.06
37 82 0.34
38 40 0.16
39 31 0.13
40 7 0.03
41 13 0.05
42 3 0.01
44 3 0.01
45 11 0.05
46 18 0.07
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.43
Consensus pattern (36 bp):
AAAACTATATATATATGTTTTCAAAAAATCGTTTTC
Found at i:22013 original size:23 final size:23
Alignment explanation
Indices: 21983--22061 Score: 133
Period size: 23 Copynumber: 3.4 Consensus size: 23
21973 TCAAAAAATC
21983 GTTTTCAAAAACTATA-TATATAT
1 GTTTTC-AAAACTATATTATATAT
22006 GTTTTCAAAACTATATTATATAT
1 GTTTTCAAAACTATATTATATAT
*
22029 GTTTTCAAAACTATATTATATAC
1 GTTTTCAAAACTATATTATATAT
22052 GTTTTCAAAA
1 GTTTTCAAAA
22062 AATCATTTTT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
22 9 0.17
23 45 0.83
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (23 bp):
GTTTTCAAAACTATATTATATAT
Found at i:22032 original size:83 final size:84
Alignment explanation
Indices: 21942--22100 Score: 250
Period size: 83 Copynumber: 1.9 Consensus size: 84
21932 TTCAAAAATA
* *
21942 ATATGTTTTCAAAATTATATTATATACGTTTTCAAAAAATCGTTTTCAAAAACTA-TATA-TATA
1 ATATGTTTTCAAAACTATATTATATACGTTTTCAAAAAATCATTTT-AAAAACTAGTATATTATA
*
22005 TGTTTTCAAAACTATATTAT
65 CGTTTTCAAAACTATATTAT
*
22025 ATATGTTTTCAAAACTATATTATATACGTTTTCAAAAAATCATTTTTAAAACTATGTATATTATA
1 ATATGTTTTCAAAACTATATTATATACGTTTTCAAAAAATCATTTTAAAAACTA-GTATATTATA
22090 CGTTTTCAAAA
65 CGTTTTCAAAA
22101 ATGAGTTTTC
Statistics
Matches: 69, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
82 7 0.10
83 44 0.64
84 4 0.06
85 14 0.20
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (84 bp):
ATATGTTTTCAAAACTATATTATATACGTTTTCAAAAAATCATTTTAAAAACTAGTATATTATAC
GTTTTCAAAACTATATTAT
Found at i:22230 original size:110 final size:110
Alignment explanation
Indices: 22030--22248 Score: 273
Period size: 110 Copynumber: 2.0 Consensus size: 110
22020 ATTATATATG
* * *
22030 TTTTCAAAACTATATTATATACGTTTTCAAAAAATCATTTTTAAAACTATGTATATTATACGTTT
1 TTTTCAAAACCATATTATATAC-TTTTCAAAAAATCATTTTTAAAACTA-GTATATCATACGCTT
22095 TCAAAAATGAGTTTTCAAAACTATATAATATATGTTTTCAAAAATGTA
64 TCAAAAA-GAGTTTTCAAAACTATATAATATATGTTTTCAAAAATGTA
* * * *
22143 TTTTCAAAACCATATTATGTA-TTTTCAAAAATTGATTTTTAAAAACTA-TATATCATATGCTTT
1 TTTTCAAAACCATATTATATACTTTTCAAAAAATCATTTTT-AAAACTAGTATATCATACGCTTT
* * *
22206 CAAAAA-CGTTTTCTATAAATTATATATTATATGTTTTCAAAAA
65 CAAAAAGAGTTTTC-A-AAACTATATAATATATGTTTTCAAAAA
22249 AAATATCTTC
Statistics
Matches: 93, Mismatches: 10, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
108 6 0.06
109 1 0.01
110 43 0.46
111 17 0.18
112 7 0.08
113 19 0.20
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.43
Consensus pattern (110 bp):
TTTTCAAAACCATATTATATACTTTTCAAAAAATCATTTTTAAAACTAGTATATCATACGCTTTC
AAAAAGAGTTTTCAAAACTATATAATATATGTTTTCAAAAATGTA
Found at i:28833 original size:55 final size:55
Alignment explanation
Indices: 28749--28858 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
28739 GGTGGTGACA
28749 CGTGTCACCACCCAATTGAAATGAAAAATTGAAGAACAAATTTGCGCTCCAACAG
1 CGTGTCACCACCCAATTGAAATGAAAAATTGAAGAACAAATTTGCGCTCCAACAG
28804 CGTGTCACCACCCAATTGAAATGAAAAATTGAAGAACAAATTTGCGCTCCAACAG
1 CGTGTCACCACCCAATTGAAATGAAAAATTGAAGAACAAATTTGCGCTCCAACAG
28859 ATTCGAACTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.40, C:0.24, G:0.16, T:0.20
Consensus pattern (55 bp):
CGTGTCACCACCCAATTGAAATGAAAAATTGAAGAACAAATTTGCGCTCCAACAG
Found at i:29335 original size:92 final size:89
Alignment explanation
Indices: 29221--29571 Score: 353
Period size: 95 Copynumber: 3.9 Consensus size: 89
29211 TTAATAATTT
* *
29221 TCAAATAAATTTTGGTTAGATTAACGGTTAAGGAAAAAATAATTTATTTTATTCGGTTAATAATT
1 TCAAAT-AATTTCGGTTAGATTAA-GGTTAA-GAAAAAA-AATTTATTTGATTCGGTTAATAATT
*
29286 TTCAAATAAATTTAGGTTCGATTAACGG
62 TTCAAATAAATTTCGGTTCGATTAACGG
* * *
29314 TAAAATAATTTCGGTTCGATTAATGGTT-A-AATAAAAA---A----ATTCGGTTAATAATTTTC
1 TCAAATAATTTCGGTTAGATTAA-GGTTAAGAAAAAAAATTTATTTGATTCGGTTAATAATTTTC
* *
29370 AAACAAATTTCGGTTTGATTAACGG
65 AAATAAATTTCGGTTCGATTAACGG
*
29395 TCAAATAATTTCGGTTAGATTAATGTTAAAGAAAAAAAATTCGGTTAATTTGATTCGGTTAATAA
1 TCAAATAATTTCGGTTAGATTAAGGTT-AAGAAAAAAAA-T---TT-ATTTGATTCGGTTAATAA
* * *
29460 ATTTCAAATATATTTCGGTTCAATTAACGG
60 TTTTCAAATAAATTTCGGTTCGATTAACGG
* * * *
29490 TCAAATAATTTCGGTTCGATTAATGTTGAA-AAAAAAATCGATTAATTTGGTTCGGTTAATAATT
1 TCAAATAATTTCGGTTAGATTAAGGTT-AAGAAAAAAA---ATTTATTTGATTCGGTTAATAATT
29554 TTCAAATAAATTTCGGTT
62 TTCAAATAAATTTCGGTT
29572 AATTTGGTTC
Statistics
Matches: 217, Mismatches: 23, Indels: 37
0.78 0.08 0.13
Matches are distributed among these distances:
80 3 0.01
81 61 0.28
82 1 0.00
83 7 0.03
85 1 0.00
88 2 0.01
89 5 0.02
91 2 0.01
92 54 0.25
93 6 0.03
94 7 0.03
95 66 0.30
96 1 0.00
97 1 0.00
ACGTcount: A:0.38, C:0.08, G:0.15, T:0.39
Consensus pattern (89 bp):
TCAAATAATTTCGGTTAGATTAAGGTTAAGAAAAAAAATTTATTTGATTCGGTTAATAATTTTCA
AATAAATTTCGGTTCGATTAACGG
Found at i:29365 original size:81 final size:81
Alignment explanation
Indices: 29271--29443 Score: 276
Period size: 81 Copynumber: 2.1 Consensus size: 81
29261 AATTTATTTT
* *
29271 ATTCGGTTAATAATTTTCAAATAAATTTAGGTTCGATTAACGGTAAAATAATTTCGGTTCGATTA
1 ATTCGGTTAATAATTTTCAAACAAATTTAGGTTCGATTAACGGTAAAATAATTTCGGTTAGATTA
*
29336 ATGGTTAAA-TAAAAAA
66 AT-GTTAAAGAAAAAAA
* * *
29352 ATTCGGTTAATAATTTTCAAACAAATTTCGGTTTGATTAACGGTCAAATAATTTCGGTTAGATTA
1 ATTCGGTTAATAATTTTCAAACAAATTTAGGTTCGATTAACGGTAAAATAATTTCGGTTAGATTA
29417 ATGTTAAAGAAAAAAA
66 ATGTTAAAGAAAAAAA
29433 ATTCGGTTAAT
1 ATTCGGTTAAT
29444 TTGATTCGGT
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
80 6 0.07
81 79 0.93
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (81 bp):
ATTCGGTTAATAATTTTCAAACAAATTTAGGTTCGATTAACGGTAAAATAATTTCGGTTAGATTA
ATGTTAAAGAAAAAAA
Found at i:29407 original size:26 final size:26
Alignment explanation
Indices: 29287--29417 Score: 86
Period size: 26 Copynumber: 4.9 Consensus size: 26
29277 TTAATAATTT
*
29287 TCAAATAAATTTAGGTTCGATTAACGG
1 TCAAAT-AATTTCGGTTCGATTAACGG
* *
29314 TAAAATAATTTCGGTTCGATTAATGG
1 TCAAATAATTTCGGTTCGATTAACGG
* * * ***
29340 TTAAATAAAAAAATTCGGTT--AATAATTT
1 TCAAAT----AATTTCGGTTCGATTAACGG
* *
29368 TCAAACAAATTTCGGTTTGATTAACGG
1 TCAAA-TAATTTCGGTTCGATTAACGG
*
29395 TCAAATAATTTCGGTTAGATTAA
1 TCAAATAATTTCGGTTCGATTAA
29418 TGTTAAAGAA
Statistics
Matches: 80, Mismatches: 17, Indels: 15
0.71 0.15 0.13
Matches are distributed among these distances:
25 9 0.11
26 39 0.49
27 14 0.17
28 9 0.11
30 9 0.11
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.37
Consensus pattern (26 bp):
TCAAATAATTTCGGTTCGATTAACGG
Found at i:31315 original size:2 final size:2
Alignment explanation
Indices: 31308--31341 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
31298 GTCCAATTGA
31308 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
31342 TCAACAAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32036 original size:20 final size:21
Alignment explanation
Indices: 32007--32061 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
31997 AAAGAAGGAA
* * *
32007 AAAATTAATATAATA-ATAAT
1 AAAATAAATAAAATAGATAAC
32027 AAAATAAATAAAATAGATAAC
1 AAAATAAATAAAATAGATAAC
32048 AAAGATAAATAAAA
1 AAA-ATAAATAAAA
32062 GTTAGTACAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
20 13 0.43
21 7 0.23
22 10 0.33
ACGTcount: A:0.71, C:0.02, G:0.04, T:0.24
Consensus pattern (21 bp):
AAAATAAATAAAATAGATAAC
Found at i:32052 original size:51 final size:51
Alignment explanation
Indices: 31974--32091 Score: 120
Period size: 51 Copynumber: 2.3 Consensus size: 51
31964 TTGTTAGATT
* * *
31974 ATAAAATAAAAATAAATATGAAAAAAGA-AGGAA-AAAA-TTAATATAATAATA
1 ATAAAATAAATA-AAATATGAAAAAAGATA--AATAAAAGTTAATACAAAAATA
*
32025 ATAAAATAAATAAAATA-GATAACAAAGATAAATAAAAGTTAGTACAAAAATA
1 ATAAAATAAATAAAATATGA-AA-AAAGATAAATAAAAGTTAATACAAAAATA
32077 ATAAAAT-AATAAAAT
1 ATAAAATAAATAAAAT
32092 GAAACTAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 10
0.81 0.06 0.14
Matches are distributed among these distances:
49 2 0.03
50 9 0.16
51 28 0.48
52 19 0.33
ACGTcount: A:0.69, C:0.02, G:0.07, T:0.22
Consensus pattern (51 bp):
ATAAAATAAATAAAATATGAAAAAAGATAAATAAAAGTTAATACAAAAATA
Found at i:32071 original size:22 final size:22
Alignment explanation
Indices: 32006--32088 Score: 70
Period size: 22 Copynumber: 4.0 Consensus size: 22
31996 AAAAGAAGGA
* *
32006 AAAAATTAATATAATA-ATAA-
1 AAAAATAAATAAAATAGATAAC
*
32026 TAAAATAAATAAAATAGATAAC
1 AAAAATAAATAAAATAGATAAC
*
32048 AAAGATAAATAAAAGTTAG-T-AC
1 AAAAATAAATAAAA--TAGATAAC
32070 AAAAAT-AATAAAATA-ATAA
1 AAAAATAAATAAAATAGATAA
32089 AATGAAACTA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
19 3 0.06
20 14 0.27
21 11 0.22
22 19 0.37
23 1 0.02
24 3 0.06
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (22 bp):
AAAAATAAATAAAATAGATAAC
Found at i:33214 original size:37 final size:38
Alignment explanation
Indices: 33140--33221 Score: 121
Period size: 38 Copynumber: 2.2 Consensus size: 38
33130 AAAATGGTCC
* * *
33140 CCCCCCTTTCTCATGGGATCAGAACCAATCAATAAAAT
1 CCCCCCTTTCTCATAGGATCAAAACCAATCAAAAAAAT
*
33178 CCCCCCTTTCTCATATGATCAAAACCAAT-AAAAAAAT
1 CCCCCCTTTCTCATAGGATCAAAACCAATCAAAAAAAT
33215 CCCCCCT
1 CCCCCCT
33222 CCATGGCTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
37 14 0.35
38 26 0.65
ACGTcount: A:0.35, C:0.35, G:0.06, T:0.23
Consensus pattern (38 bp):
CCCCCCTTTCTCATAGGATCAAAACCAATCAAAAAAAT
Found at i:34149 original size:106 final size:106
Alignment explanation
Indices: 33959--34858 Score: 1228
Period size: 106 Copynumber: 8.6 Consensus size: 106
33949 TATTGTTCCA
* ** * * *
33959 AGTCCAATATCCTCCGCCGTGAAGTTGAAATTGGCTCTGGAACTGAGAAATTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
34024 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
34065 AGTCTAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
34130 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
34171 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
34236 CAGCGGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * ** *
34277 AGTCCAATATCATTCGCTGTGAAGTTGAAATTGGCTCTGATATTGGGAAAATGTTTATTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
34342 CAACGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
34383 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
*
34448 CATG-GGTCCCTTCGTCGTGAAGTTGAACATGCGTTGTCTGG
66 CA-GCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* *
34489 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTATTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
* *
34554 CAGCGGTCCCTTCGTCATGAAGTTGAA-TATGCATTGTCTGG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACT-TGCGTTGTCTGG
* * * *
34595 AGTCCAATATCCTT-ATTG-G--CTCTGAAA-----T-TG-----G-GAAGTTATTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGT-TGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
*
34644 CCAGCGGTCCCTTCGCCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * *
34686 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAGAAGTGGA-AAATTGTTTATTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGAGAAGTTGTTTGTTGACAA
34750 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * * * * * *
34792 AGTCTAATTTTCTTCGCTGCGAAGTTGAAATAGACTCTGAATGAAATT-AGAAAGTTGTTTGTTG
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC----TGAAATTGAG-AAGTTGTTTGTTG
34856 ACA
61 ACA
34859 GACAACTTTT
Statistics
Matches: 707, Mismatches: 59, Indels: 52
0.86 0.07 0.06
Matches are distributed among these distances:
91 68 0.10
92 5 0.01
93 1 0.00
94 5 0.01
95 1 0.00
97 1 0.00
98 1 0.00
99 1 0.00
100 1 0.00
101 1 0.00
102 1 0.00
103 5 0.01
104 1 0.00
105 4 0.01
106 591 0.84
108 1 0.00
109 4 0.01
110 15 0.02
ACGTcount: A:0.24, C:0.18, G:0.25, T:0.33
Consensus pattern (106 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:34682 original size:91 final size:92
Alignment explanation
Indices: 34518--34795 Score: 310
Period size: 91 Copynumber: 2.9 Consensus size: 92
34508 TGAAGTTGAA
* * * *
34518 ATTGGCTCTAAAATTGAGAAGTTATTTGTTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAA-T
1 ATTGGCTCTGAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
*
34582 ATGCATTGTCTGGAGTCCAATATCCTT-
66 -TGCGTTGTCTGGAGTCCAATATCCTTC
*
34609 ATTGGCTCTGAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGCCGTGAAGTTGAACT
1 ATTGGCTCTGAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
34674 TGCGTTGTCTGGAGTCCAATATCCTTC
66 TGCGTTGTCTGGAGTCCAATATCCTTC
* * *
34701 GTTGTGAAGT-TGAAATTGGCTCTAGAAGTGGAAAATTGTTTATTGACAACCAGCGGTCCCTTCG
1 ATTG-G--CTCTGAAATTGG-----GAA---G----TTATTTATTGACAACCAGCGGTCCCTTCG
34765 TCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
51 TCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
34796 TAATTTTCTT
Statistics
Matches: 160, Mismatches: 10, Indels: 19
0.85 0.05 0.10
Matches are distributed among these distances:
91 83 0.52
92 4 0.03
93 1 0.01
94 9 0.06
95 1 0.01
99 3 0.02
102 1 0.01
106 58 0.36
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.33
Consensus pattern (92 bp):
ATTGGCTCTGAAATTGGGAAGTTATTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
TGCGTTGTCTGGAGTCCAATATCCTTC
Found at i:34749 original size:197 final size:197
Alignment explanation
Indices: 34412--34795 Score: 612
Period size: 197 Copynumber: 1.9 Consensus size: 197
34402 TGAAGTTGAA
* * *
34412 ATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCATGGGTCCCTTCGTCGTGAAGTTGAACA
1 ATTGGCTCTGAAATTGAGAAGTTATTTATTGACAACCATGGGTCCCTTCGCCGTGAAGTTGAACA
* *
34477 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTA
66 TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATGGAGAAATTA
*
34542 TTTGTTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAA-TATGCATTGTCTGGAGTCCAATATC
131 TTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACT-TGCATTGTCTGGAGTCCAATATC
34606 CTT
195 CTT
*
34609 ATTGGCTCTGAAATTGGGAAGTTATTTATTGACAACCA-GCGGTCCCTTCGCCGTGAAGTTGAAC
1 ATTGGCTCTGAAATTGAGAAGTTATTTATTGACAACCATG-GGTCCCTTCGCCGTGAAGTTGAAC
* *
34673 TTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAGAAGTGGA-AAAT
65 ATGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTA-AAATGGAGAAAT
* * *
34737 TGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTC
129 TATTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTC
34796 TAATTTTCTT
Statistics
Matches: 172, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
196 1 0.01
197 165 0.96
198 6 0.03
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (197 bp):
ATTGGCTCTGAAATTGAGAAGTTATTTATTGACAACCATGGGTCCCTTCGCCGTGAAGTTGAACA
TGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATGGAGAAATTA
TTTATTGACAACCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCATTGTCTGGAGTCCAATATCC
TT
Found at i:37120 original size:31 final size:31
Alignment explanation
Indices: 37082--37235 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
37072 CCCGAAGGAC
* *
37082 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
37113 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
37144 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
37175 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
37206 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
37236 CCCTCGACCC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:37440 original size:23 final size:24
Alignment explanation
Indices: 37414--37460 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
37404 ATATACTTGT
*
37414 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
37437 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
37461 CATGCCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:38003 original size:21 final size:21
Alignment explanation
Indices: 37973--38017 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
37963 ATTCTGTCGT
* *
37973 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
37994 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
38015 TTG
1 TTG
38018 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:40955 original size:31 final size:31
Alignment explanation
Indices: 40917--41070 Score: 256
Period size: 31 Copynumber: 5.0 Consensus size: 31
40907 CCCGAAGGAC
* *
40917 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TTCCGAAGAACATAGGTAAA
* *
40948 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
40979 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
41010 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAAA
41041 CAGTCCATATGTTCCGAAGAACATAGGTAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAA
41071 CCCTCGACCC
Statistics
Matches: 116, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
31 115 0.99
32 1 0.01
ACGTcount: A:0.37, C:0.21, G:0.20, T:0.22
Consensus pattern (31 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAAA
Found at i:41275 original size:23 final size:24
Alignment explanation
Indices: 41249--41295 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 24
41239 ATATACTTGT
*
41249 TTTCACATATATA-TTTCATATCA
1 TTTCACATATACACTTTCATATCA
41272 TTTCACATATACACTTTCATATCA
1 TTTCACATATACACTTTCATATCA
41296 CATGTCATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 12 0.55
24 10 0.45
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTCACATATACACTTTCATATCA
Found at i:41838 original size:21 final size:21
Alignment explanation
Indices: 41808--41852 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
41798 ATTCTGTCGT
* *
41808 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
41829 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
41850 TTG
1 TTG
41853 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:45008 original size:22 final size:22
Alignment explanation
Indices: 44964--45025 Score: 69
Period size: 22 Copynumber: 2.9 Consensus size: 22
44954 TAATAATAAT
44964 AAAATAAATAAAATAGATAACA
1 AAAATAAATAAAATAGATAACA
*
44986 AAGATAAATAAAAGTTAG-T-ACA
1 AAAATAAATAAAA--TAGATAACA
45008 AAAAT-AATAAAATA-ATAA
1 AAAATAAATAAAATAGATAA
45026 AATGAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
19 3 0.09
20 1 0.03
21 7 0.21
22 19 0.56
23 1 0.03
24 3 0.09
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.21
Consensus pattern (22 bp):
AAAATAAATAAAATAGATAACA
Found at i:46131 original size:38 final size:38
Alignment explanation
Indices: 46080--46162 Score: 130
Period size: 38 Copynumber: 2.2 Consensus size: 38
46070 AAAATGGTGC
* ** *
46080 CCCCCCTTTCTCATGGGATCTGAACCAATCAATAAAAT
1 CCCCCCTTTCTCATAGGATCAAAACCAATCAAAAAAAT
46118 CCCCCCTTTCTCATAGGATCAAAACCAATCAAAAAAAT
1 CCCCCCTTTCTCATAGGATCAAAACCAATCAAAAAAAT
46156 CCCCCCT
1 CCCCCCT
46163 CCATGGCTTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.34, C:0.36, G:0.07, T:0.23
Consensus pattern (38 bp):
CCCCCCTTTCTCATAGGATCAAAACCAATCAAAAAAAT
Found at i:46343 original size:23 final size:21
Alignment explanation
Indices: 46317--46373 Score: 71
Period size: 23 Copynumber: 2.6 Consensus size: 21
46307 TCCTATAAAA
*
46317 AATAAAATAAAAAATT-TATT
1 AATAAAATAAAAAATTATAAT
46337 AATAATAATAAATAAATTATAAT
1 AATAA-AATAAA-AAATTATAAT
46360 AATAAAAATAAAAA
1 AAT-AAAATAAAAA
46374 TATAAAATCT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 5 0.16
21 6 0.19
22 7 0.22
23 12 0.38
24 2 0.06
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AATAAAATAAAAAATTATAAT
Found at i:46359 original size:20 final size:22
Alignment explanation
Indices: 46317--46371 Score: 75
Period size: 20 Copynumber: 2.7 Consensus size: 22
46307 TCCTATAAAA
46317 AATAA-AATAAA-AAATTTATT
1 AATAATAATAAATAAATTTATT
46337 AATAATAATAAATAAA-TTA-T
1 AATAATAATAAATAAATTTATT
46357 AATAATAA-AAATAAA
1 AATAATAATAAATAAA
46372 AATATAAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 7 0.21
20 14 0.42
21 9 0.27
22 3 0.09
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AATAATAATAAATAAATTTATT
Found at i:46377 original size:20 final size:20
Alignment explanation
Indices: 46336--46378 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
46326 AAAAATTTAT
*
46336 TAATAATAATAAATAAATTA
1 TAATAATAATAAATAAAATA
46356 TAATAATAA-AAATAAAAATA
1 TAATAATAATAAAT-AAAATA
46376 TAA
1 TAA
46379 AATCTGATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 4 0.19
20 17 0.81
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TAATAATAATAAATAAAATA
Found at i:46520 original size:2 final size:2
Alignment explanation
Indices: 46515--46560 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
46505 ATAAAAAATA
46515 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
46557 AT AT
1 AT AT
46561 TCAAGTTTCC
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48396 original size:21 final size:21
Alignment explanation
Indices: 48372--48437 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
48362 TAATAAACCC
*
48372 TAATCCACAATTACTAAAACA
1 TAATCAACAATTACTAAAACA
* * *
48393 TAATTAACAATGACTAGAACA
1 TAATCAACAATTACTAAAACA
* *
48414 AAATCAACAATTTCTAAAACA
1 TAATCAACAATTACTAAAACA
48435 TAA
1 TAA
48438 ATTAATACCA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.55, C:0.18, G:0.03, T:0.24
Consensus pattern (21 bp):
TAATCAACAATTACTAAAACA
Found at i:48526 original size:25 final size:25
Alignment explanation
Indices: 48437--48546 Score: 105
Period size: 25 Copynumber: 4.2 Consensus size: 25
48427 CTAAAACATA
** *
48437 AATTAATACCAACAATTTCTAACAC
1 AATTAATATTAACAATTACTAACAC
*
48462 ATTATCAATATTTAACAATTACTAACAC
1 A--ATTAATA-TTAACAATTACTAACAC
* *
48490 GTAATTAGTATTGACAATTACTAACAC
1 --AATTAATATTAACAATTACTAACAC
*
48517 AATTAATATTAACAATTACTACCAC
1 AATTAATATTAACAATTACTAACAC
48542 -ATTAA
1 AATTAA
48547 CAATTAATAA
Statistics
Matches: 70, Mismatches: 10, Indels: 11
0.77 0.11 0.12
Matches are distributed among these distances:
24 5 0.07
25 23 0.33
27 22 0.31
28 19 0.27
30 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.03, T:0.33
Consensus pattern (25 bp):
AATTAATATTAACAATTACTAACAC
Found at i:49894 original size:390 final size:392
Alignment explanation
Indices: 49165--49947 Score: 1192
Period size: 390 Copynumber: 2.0 Consensus size: 392
49155 ACGTGATGAG
* * *
49165 GAGATCGGGTCACTTTTAGTAATTCACTTGATGTCAATTCTGATGATGACATTGTTCCTTCGTGT
1 GAGATCGGGTCACTTTTAGTAATTCACTTGATGTCAATTCTGATGATAACATTGCTCCTTCGTAT
* * *
49230 TAAGGAGATATGGTCATAATTGAAAAATGATGGATCTACTAATGACATGGGCTTTCTGGATCCCG
66 TAAGGAGATATGGTCATAATTGAAAAATGATGGATCTACTAATAACATGGGCTTTCTAGATCACG
49295 TTAAAACAAGTAATATGCTATGATTCCATACATGTCATATGCAACATGTCCTAAAGATAATCTAA
131 TTAAAACAAGTAATATGCTATGATTCC--ACATGTCATATGCAACATGTCCTAAAGATAATCTAA
* * * * *
49360 TTCAATTTGATATGATGAATGTTGGATGCAGTTTTGCGTGTTTTAATACGAGAATTGTGACTTTT
194 TTCAATTTGATATGATGAATGTTGGATGCAATTTTGCATGTTTTAATACGAGAATTATGAATTTG
* * *
49425 TCATTTTCAGTGATCGATCTTCAATCATAACATATGAATTTTCCCTTGTTACTCGTGTTTTTGCA
259 TCATTTTCAATGATCGATCTTCAATCATAACATATGAAATTTCCCTTGTTACTCGTGTTTTTACA
* * * **
49490 ATCTTGGCCCCTATACTACTTGGCTACTACTATGTCCATTCCTACCTCGAAAATGCTTCCTCTAA
324 ATCTTGGCCCCTATACTACTTGGCCACCACTATGCCCATTCCTACCTAAAAAATGCTTCCTCTAA
49555 TTTT
389 TTTT
**
49559 GAGATCGGGTCACTTTTAGTAATTCGGTTGATGTCAATTCTGATGATAACATTGCTCCTTCGTAT
1 GAGATCGGGTCACTTTTAGTAATTCACTTGATGTCAATTCTGATGATAACATTGCTCCTTCGTAT
* * * * * *
49624 TGAGGAGATGTGGTCATAATTGAAAGATGATGGTTCTACTAATAATATGGGCTTTCTAGATCATG
66 TAAGGAGATATGGTCATAATTGAAAAATGATGGATCTACTAATAACATGGGCTTTCTAGATCACG
* *
49689 TTAAAACAAGTAATATGTTATGATT-C-CATGTCATATGCAACATGTCCTAAAGATGATCTAATT
131 TTAAAACAAGTAATATGCTATGATTCCACATGTCATATGCAACATGTCCTAAAGATAATCTAATT
* * *
49752 GAATTTGATATGATGAATGTTGGATGCAATTTTGCATGTTTTAATCCGGGAATTATGAATTTGTC
196 CAATTTGATATGATGAATGTTGGATGCAATTTTGCATGTTTTAATACGAGAATTATGAATTTGTC
* *
49817 ATTTTCAATGATCGATCTTCAGTCATAACATATGAAATTTCCCTTGTTACTCGTGTTTTTACGAT
261 ATTTTCAATGATCGATCTTCAATCATAACATATGAAATTTCCCTTGTTACTCGTGTTTTTACAAT
* * * *
49882 CTTGGTCCCTATACTACTTGGCCACCACTCTGCCCATTTCTGCCTAAAAAATGCTTCCTCTAATT
326 CTTGGCCCCTATACTACTTGGCCACCACTATGCCCATTCCTACCTAAAAAATGCTTCCTCTAATT
49947 T
391 T
49948 GATTAGAGAA
Statistics
Matches: 351, Mismatches: 38, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
390 210 0.60
393 1 0.00
394 140 0.40
ACGTcount: A:0.28, C:0.17, G:0.17, T:0.38
Consensus pattern (392 bp):
GAGATCGGGTCACTTTTAGTAATTCACTTGATGTCAATTCTGATGATAACATTGCTCCTTCGTAT
TAAGGAGATATGGTCATAATTGAAAAATGATGGATCTACTAATAACATGGGCTTTCTAGATCACG
TTAAAACAAGTAATATGCTATGATTCCACATGTCATATGCAACATGTCCTAAAGATAATCTAATT
CAATTTGATATGATGAATGTTGGATGCAATTTTGCATGTTTTAATACGAGAATTATGAATTTGTC
ATTTTCAATGATCGATCTTCAATCATAACATATGAAATTTCCCTTGTTACTCGTGTTTTTACAAT
CTTGGCCCCTATACTACTTGGCCACCACTATGCCCATTCCTACCTAAAAAATGCTTCCTCTAATT
TT
Found at i:50672 original size:11 final size:11
Alignment explanation
Indices: 50658--50724 Score: 52
Period size: 12 Copynumber: 6.1 Consensus size: 11
50648 TTAATTACCC
50658 TTTTTTCTTCA
1 TTTTTTCTTCA
*
50669 TTTTTTTCATTTA
1 -TTTTTTC-TTCA
*
50682 TTATTT-TTCA
1 TTTTTTCTTCA
50692 TTTATTT-TTCA
1 TTT-TTTCTTCA
50703 TTTTTCTCTT--
1 TTTTT-TCTTCA
50713 TTTTTTCTTCA
1 TTTTTTCTTCA
50724 T
1 T
50725 GTATAGTATC
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
9 4 0.09
10 12 0.27
11 12 0.27
12 14 0.31
13 3 0.07
ACGTcount: A:0.12, C:0.13, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTTTTCTTCA
Found at i:50688 original size:14 final size:13
Alignment explanation
Indices: 50658--50700 Score: 61
Period size: 14 Copynumber: 3.3 Consensus size: 13
50648 TTAATTACCC
*
50658 TTTTTTC-TTCAT
1 TTTTTTCATTTAT
50670 TTTTTTCATTTAT
1 TTTTTTCATTTAT
50683 TATTTTTCATTTAT
1 T-TTTTTCATTTAT
50697 TTTT
1 TTTT
50701 CATTTTTCTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 7 0.25
13 8 0.29
14 13 0.46
ACGTcount: A:0.14, C:0.09, G:0.00, T:0.77
Consensus pattern (13 bp):
TTTTTTCATTTAT
Found at i:55062 original size:69 final size:69
Alignment explanation
Indices: 54986--55126 Score: 282
Period size: 69 Copynumber: 2.0 Consensus size: 69
54976 CCTCCACTTT
54986 AGTTTTAGTCCTTCCTCCGTCATCAAGAGCATTGACACCTTGATTTTGGTGATTTGGGAGCGGAT
1 AGTTTTAGTCCTTCCTCCGTCATCAAGAGCATTGACACCTTGATTTTGGTGATTTGGGAGCGGAT
55051 TTAC
66 TTAC
55055 AGTTTTAGTCCTTCCTCCGTCATCAAGAGCATTGACACCTTGATTTTGGTGATTTGGGAGCGGAT
1 AGTTTTAGTCCTTCCTCCGTCATCAAGAGCATTGACACCTTGATTTTGGTGATTTGGGAGCGGAT
55120 TTAC
66 TTAC
55124 AGT
1 AGT
55127 CACACAAGGT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
69 72 1.00
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (69 bp):
AGTTTTAGTCCTTCCTCCGTCATCAAGAGCATTGACACCTTGATTTTGGTGATTTGGGAGCGGAT
TTAC
Found at i:62634 original size:2 final size:2
Alignment explanation
Indices: 62627--62811 Score: 208
Period size: 2 Copynumber: 92.5 Consensus size: 2
62617 GCTGAGGATA
* *
62627 AC AC AC AC AC AC AC AC AC AA AC AC AA AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * * * *
62669 AC AC AA AC AC AA AC AC AA AC AC AC AT AC AC AT AC AC AC GC AT
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * *
62711 GC AC AC AC AC AC AC AC AC AC AC AC GC AC AC AC AC GC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
* * * * *
62753 AC AC GC AT GC GC GC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
62795 AC AC AC AC AC AA AC AC A
1 AC AC AC AC AC AC AC AC A
62812 TATAAGTAGT
Statistics
Matches: 151, Mismatches: 32, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 151 1.00
ACGTcount: A:0.49, C:0.44, G:0.04, T:0.02
Consensus pattern (2 bp):
AC
Found at i:63333 original size:17 final size:17
Alignment explanation
Indices: 63311--63351 Score: 82
Period size: 17 Copynumber: 2.4 Consensus size: 17
63301 TGGTTGAGAG
63311 TTATCTTTGAACATATA
1 TTATCTTTGAACATATA
63328 TTATCTTTGAACATATA
1 TTATCTTTGAACATATA
63345 TTATCTT
1 TTATCTT
63352 GTACTTACCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.05, T:0.51
Consensus pattern (17 bp):
TTATCTTTGAACATATA
Found at i:73602 original size:614 final size:614
Alignment explanation
Indices: 72435--73664 Score: 2451
Period size: 614 Copynumber: 2.0 Consensus size: 614
72425 GCCAAGAGGG
72435 CCAAAGACTCTCAAGGGTCATGGAGACCTTCATCTTCTTAGTCTTAGAGGTCGAGACAGGATCTG
1 CCAAAGACTCTCAAGGGTCATGGAGACCTTCATCTTCTTAGTCTTAGAGGTCGAGACAGGATCTG
72500 AGCCATGGATGAAGATCAGAGAGCCGTAGGAGCCACTAGGTTTAGTATATTCTATGAACACCAAT
66 AGCCATGGATGAAGATCAGAGAGCCGTAGGAGCCACTAGGTTTAGTATATTCTATGAACACCAAT
72565 AGTTCAATCAGGACCATGCAACCTTCGACTTGTAGACAATGTGGTAGGAGACACTCAGGTGAGTG
131 AGTTCAATCAGGACCATGCAACCTTCGACTTGTAGACAATGTGGTAGGAGACACTCAGGTGAGTG
72630 CCATAAAGTTTTCAGAGCATGTTATGGATTTGATTATTTGAGAACCTTATTACAGACTATCTTGA
196 CCATAAAGTTTTCAGAGCATGTTATGGATTTGATTATTTGAGAACCTTATTACAGACTATCTTGA
72695 GGCATGGAGTGTAGCTCTGCCAATTGCACAAAGATCAAATCAGACTGTTCATCTTCCGGATAGTA
261 GGCATGGAGTGTAGCTCTGCCAATTGCACAAAGATCAAATCAGACTGTTCATCTTCCGGATAGTA
72760 GAGTAGAGGTATTGCCATATCCGTAGCCGATTTTGAGGCTAGGGTTGCCTTCTGTCAGTATACAG
326 GAGTAGAGGTATTGCCATATCCGTAGCCGATTTTGAGGCTAGGGTTGCCTTCTGTCAGTATACAG
72825 TCAAAGCTCAAGAGGACTATGAGGCTGCTAAAGTCAATTCAAGTATATTTACAATTTTTTGTATG
391 TCAAAGCTCAAGAGGACTATGAGGCTGCTAAAGTCAATTCAAGTATATTTACAATTTTTTGTATG
72890 TCTGTTACTGGTTTGGTATATCCATGGTCAACTCACTCCTATATTTGTTGTGATCTTATCCGAAA
456 TCTGTTACTGGTTTGGTATATCCATGGTCAACTCACTCCTATATTTGTTGTGATCTTATCCGAAA
72955 TATTGGCATCACAGATGAGGACTTAAAAGTCAAGGTTAGAATTTCAAGTCCTTTAGCATTAGATG
521 TATTGGCATCACAGATGAGGACTTAAAAGTCAAGGTTAGAATTTCAAGTCCTTTAGCATTAGATG
73020 TGTTAGTGGATATGGTCCACCATAAGTGC
586 TGTTAGTGGATATGGTCCACCATAAGTGC
73049 CCAAAGACTCTCAAGGGTCATGGAGACCTTCATCTTCTTAGTCTTAGAGGTCGAGACAGGATCTG
1 CCAAAGACTCTCAAGGGTCATGGAGACCTTCATCTTCTTAGTCTTAGAGGTCGAGACAGGATCTG
73114 AGCCATGGATGAAGATCAGAGAGCCGTAGGAGCCACTAGGTTTAGTATATTCTATGAACACCAAT
66 AGCCATGGATGAAGATCAGAGAGCCGTAGGAGCCACTAGGTTTAGTATATTCTATGAACACCAAT
73179 AGTTCAATCAGGACCATGCAACCTTCGACTTGTAGACAATGTGGTAGGAGACACTCAGGTGAGTG
131 AGTTCAATCAGGACCATGCAACCTTCGACTTGTAGACAATGTGGTAGGAGACACTCAGGTGAGTG
73244 CCATAAAGTTTTCAGAGCATGTTATGGATTTGATTATTTGAGAACCTTATTACAGACTATCTTGA
196 CCATAAAGTTTTCAGAGCATGTTATGGATTTGATTATTTGAGAACCTTATTACAGACTATCTTGA
73309 GGCATGGAGTGTAGCTCTGCCAATTGCACAAAGATCAAATCAGACTGTTCATCTTCCGGATAGTA
261 GGCATGGAGTGTAGCTCTGCCAATTGCACAAAGATCAAATCAGACTGTTCATCTTCCGGATAGTA
73374 GAGTAGAGGTATTGCCATATCCGTAGCCGATTTTGAGGCTAGGGTTGCCTTCTGTCAGTATACAG
326 GAGTAGAGGTATTGCCATATCCGTAGCCGATTTTGAGGCTAGGGTTGCCTTCTGTCAGTATACAG
73439 TCAAAGCTCAAGAGGACTATGAGGCTGCTAAAGTCAATTCAAGTATATTTACAATTTTTTGTATG
391 TCAAAGCTCAAGAGGACTATGAGGCTGCTAAAGTCAATTCAAGTATATTTACAATTTTTTGTATG
*
73504 TCTGTTACTGGTTTGGTATATCCATGGTTAACTCACTCCTATATTTGTTGTGATCTTATCCGAAA
456 TCTGTTACTGGTTTGGTATATCCATGGTCAACTCACTCCTATATTTGTTGTGATCTTATCCGAAA
73569 TATTGGCATCACAGATGAGGACTTAAAAGTCAAGGTTAGAATTTCAAGTCCTTTAGCATTAGATG
521 TATTGGCATCACAGATGAGGACTTAAAAGTCAAGGTTAGAATTTCAAGTCCTTTAGCATTAGATG
73634 TGTTAGTGGATATGGTCCACCATAAGTGC
586 TGTTAGTGGATATGGTCCACCATAAGTGC
73663 CC
1 CC
73665 GACAAATATT
Statistics
Matches: 615, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
614 615 1.00
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (614 bp):
CCAAAGACTCTCAAGGGTCATGGAGACCTTCATCTTCTTAGTCTTAGAGGTCGAGACAGGATCTG
AGCCATGGATGAAGATCAGAGAGCCGTAGGAGCCACTAGGTTTAGTATATTCTATGAACACCAAT
AGTTCAATCAGGACCATGCAACCTTCGACTTGTAGACAATGTGGTAGGAGACACTCAGGTGAGTG
CCATAAAGTTTTCAGAGCATGTTATGGATTTGATTATTTGAGAACCTTATTACAGACTATCTTGA
GGCATGGAGTGTAGCTCTGCCAATTGCACAAAGATCAAATCAGACTGTTCATCTTCCGGATAGTA
GAGTAGAGGTATTGCCATATCCGTAGCCGATTTTGAGGCTAGGGTTGCCTTCTGTCAGTATACAG
TCAAAGCTCAAGAGGACTATGAGGCTGCTAAAGTCAATTCAAGTATATTTACAATTTTTTGTATG
TCTGTTACTGGTTTGGTATATCCATGGTCAACTCACTCCTATATTTGTTGTGATCTTATCCGAAA
TATTGGCATCACAGATGAGGACTTAAAAGTCAAGGTTAGAATTTCAAGTCCTTTAGCATTAGATG
TGTTAGTGGATATGGTCCACCATAAGTGC
Done.