Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008677.1 Hibiscus syriacus cultivar Beakdansim tig00111694_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: 103999
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:19002 original size:36 final size:36
Alignment explanation
Indices: 18942--19021 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
18932 TTTGGTAAAT
* *
18942 GAACTTATAAATGAGCCAACAAATGAGATTTCAAAC
1 GAACTTATAAACGAACCAACAAATGAGATTTCAAAC
* * *
18978 GAACTTATAAACGAATCAATAAATGAGCTTTCAAAC
1 GAACTTATAAACGAACCAACAAATGAGATTTCAAAC
*
19014 GAGCTTAT
1 GAACTTAT
19022 TTGTGAACAT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.45, C:0.16, G:0.14, T:0.25
Consensus pattern (36 bp):
GAACTTATAAACGAACCAACAAATGAGATTTCAAAC
Found at i:25468 original size:20 final size:20
Alignment explanation
Indices: 25443--25491 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
25433 GTAAAGACTA
25443 TAGAGAAAGGGGAAGAAATG
1 TAGAGAAAGGGGAAGAAATG
25463 TAGAGAAAGGGGAAGAAATG
1 TAGAGAAAGGGGAAGAAATG
*
25483 TGGAGAAAG
1 TAGAGAAAG
25492 AAGAAAGGAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.00, G:0.41, T:0.10
Consensus pattern (20 bp):
TAGAGAAAGGGGAAGAAATG
Found at i:30403 original size:28 final size:28
Alignment explanation
Indices: 30369--30464 Score: 174
Period size: 28 Copynumber: 3.4 Consensus size: 28
30359 TGAAATATAA
*
30369 CAAATTGAATTTTATGTGAAATAAATAT
1 CAAATTGAAATTTATGTGAAATAAATAT
30397 CAAATTGAAATTTATGTGAAATAAATAT
1 CAAATTGAAATTTATGTGAAATAAATAT
30425 CAAATTGAAATTTATGTGAAATAAATAT
1 CAAATTGAAATTTATGTGAAATAAATAT
*
30453 CAAATTCAAATT
1 CAAATTGAAATT
30465 CAAGAGATTA
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 66 1.00
ACGTcount: A:0.49, C:0.05, G:0.09, T:0.36
Consensus pattern (28 bp):
CAAATTGAAATTTATGTGAAATAAATAT
Found at i:30862 original size:21 final size:21
Alignment explanation
Indices: 30831--31025 Score: 132
Period size: 21 Copynumber: 9.3 Consensus size: 21
30821 CGATTTACAT
*
30831 ATTCGCATTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* *
30852 GTTCGCGTTGCGATAGTCGAA
1 ATTCGCGTTGCGATAGTCCAA
* **
30873 GTTCGCGTTGCGATTTTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* *
30894 ATTCTCGTTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TAGTCCAA
* *
30917 ATT--TGTTGCAATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
* * *
30936 GTTCGCGTTGCGATTTATTACAA
1 ATTCGCGTTGCGA--TAGTCCAA
*
30959 ATT--CGTTGCGATAGTCGAA
1 ATTCGCGTTGCGATAGTCCAA
* * *
30978 GTTCGCATTGCGATTTATTCCAA
1 ATTCGCGTTGCGA--TAGTCCAA
31001 ATT--CGTTGCGATAGTCCAA
1 ATTCGCGTTGCGATAGTCCAA
*
31020 AATCGC
1 ATTCGC
31026 AACGACTGGT
Statistics
Matches: 133, Mismatches: 29, Indels: 24
0.72 0.16 0.13
Matches are distributed among these distances:
19 25 0.19
21 82 0.62
23 26 0.20
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (21 bp):
ATTCGCGTTGCGATAGTCCAA
Found at i:30941 original size:84 final size:83
Alignment explanation
Indices: 30813--31019 Score: 226
Period size: 84 Copynumber: 2.5 Consensus size: 83
30803 ACTTCGACTA
*
30813 TCGCATTGCGATTTA---CATATTCGCATTGCGATAGTCCAAGTTCGCGTTGCGA-TAGT-CGAA
1 TCGCATTGCGATTTATTCCAAATTCG--TTGCGATAGTCCAAGTTCGCGTTGCGATTAGTAC-AA
* **
30873 GTTCGCGTTGCGATTTTCCAAAT
63 ATT--CGTTGCGATAGTCCAAAT
* * * * *
30896 TCTCGTTGCGATTTATTCCAAATTTGTTGCAATAGTCCAAGTTCGCGTTGCGATTTATTACAAAT
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGA-TTAGTACAAAT
* *
30961 TCGTTGCGATAGTCGAAGT
65 TCGTTGCGATAGTCCAAAT
30980 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAA
31020 AATCGCAACG
Statistics
Matches: 103, Mismatches: 15, Indels: 11
0.80 0.12 0.09
Matches are distributed among these distances:
83 13 0.13
84 76 0.74
86 13 0.13
87 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.36
Consensus pattern (83 bp):
TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTAGTACAAATT
CGTTGCGATAGTCCAAAT
Found at i:31026 original size:42 final size:42
Alignment explanation
Indices: 30813--31026 Score: 195
Period size: 42 Copynumber: 5.1 Consensus size: 42
30803 ACTTCGACTA
* *
30813 TCGCATTGCGATTTA---CATATTCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATTTATTCCAAATTCG--TTGCGATAGTCCAAAT
* * * * **
30854 TCGCGTTGCGA--TAGTCGAAGTTCGCGTTGCGATTTTCCAAAT
1 TCGCATTGCGATTTATTCCAAATT--CGTTGCGATAGTCCAAAT
* * * * *
30896 TCTCGTTGCGATTTATTCCAAATTTGTTGCAATAGTCCAAGT
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAT
* * * *
30938 TCGCGTTGCGATTTATTACAAATTCGTTGCGATAGTCGAAGT
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAT
*
30980 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAA
1 TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAT
31022 TCGCA
1 TCGCA
31027 ACGACTGGTG
Statistics
Matches: 140, Mismatches: 26, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
39 2 0.01
41 10 0.07
42 118 0.84
44 10 0.07
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.35
Consensus pattern (42 bp):
TCGCATTGCGATTTATTCCAAATTCGTTGCGATAGTCCAAAT
Found at i:31120 original size:6 final size:6
Alignment explanation
Indices: 31109--31141 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
31099 GACACGTATT
31109 ACCACG ACCACG ACCACG ACCACG ACC-CG ACCA
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCA
31142 GAGACGAGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.33, C:0.52, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:31915 original size:21 final size:22
Alignment explanation
Indices: 31882--32106 Score: 145
Period size: 21 Copynumber: 10.5 Consensus size: 22
31872 ACTACCATAA
31882 CGAATAAATCGCAACGCGAACTT
1 CGAAT-AATCGCAACGCGAACTT
*
31905 CGACT-ATCGCAA--CGAACTT
1 CGAATAATCGCAACGCGAACTT
*
31924 GGAATAAATCGCAACGCGAACTT
1 CGAAT-AATCGCAACGCGAACTT
*
31947 CGACT-ATCGCAA--CGAACTT
1 CGAATAATCGCAACGCGAACTT
*
31966 -GAAATAAATCGCAACGTGAACTT
1 CG-AAT-AATCGCAACGCGAACTT
* * *
31989 CGACT-ATCGCAACACGAATTT
1 CGAATAATCGCAACGCGAACTT
* * *
32010 GGAATAAATCGTAA--CGAATTT
1 CGAAT-AATCGCAACGCGAACTT
*
32031 GGAATAAATCGCAACGCGAACTT
1 CGAAT-AATCGCAACGCGAACTT
* *
32054 CGACT-ATCGCAA--TGAACTT
1 CGAATAATCGCAACGCGAACTT
* *
32073 GGAATAAATCGCAACGCGAATTT
1 CGAAT-AATCGCAACGCGAACTT
*
32096 GGAA-AATCGCA
1 CGAATAATCGCA
32107 TTGCGATAGT
Statistics
Matches: 161, Mismatches: 23, Indels: 38
0.73 0.10 0.17
Matches are distributed among these distances:
18 1 0.01
19 28 0.17
21 85 0.53
23 46 0.29
24 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.21
Consensus pattern (22 bp):
CGAATAATCGCAACGCGAACTT
Found at i:31942 original size:42 final size:42
Alignment explanation
Indices: 31883--32025 Score: 232
Period size: 42 Copynumber: 3.4 Consensus size: 42
31873 CTACCATAAC
31883 GAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTG
1 GAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTG
31925 GAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTG
1 GAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTG
* * *
31967 AAATAAATCGCAACGTGAACTTCGACTATCGCAACACGAATTTG
1 GAATAAATCGCAACGCGAACTTCGACTATCGC-A-ACGAACTTG
*
32011 GAATAAATCGTAACG
1 GAATAAATCGCAACG
32026 AATTTGGAAT
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
42 72 0.77
43 1 0.01
44 21 0.22
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (42 bp):
GAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTG
Found at i:32037 original size:65 final size:63
Alignment explanation
Indices: 31952--32106 Score: 206
Period size: 65 Copynumber: 2.4 Consensus size: 63
31942 AACTTCGACT
* * * *
31952 ATCGCAACGAACTTGAAATAAATCGCAACGTGAACTTCGACTATCGCAACACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGC-A-ACGAACTTGGAATAA
* *
32017 ATCGTAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGAACTTGGAATAA
1 ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
32080 ATCGCAACGCGAATTTGG-A-AAATCGCA
1 ATCGCAA--CGAATTTGGAATAAATCGCA
32107 TTGCGATAGT
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
63 27 0.33
64 2 0.02
65 52 0.64
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.22
Consensus pattern (63 bp):
ATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAA
Found at i:32105 original size:107 final size:107
Alignment explanation
Indices: 31910--32106 Score: 313
Period size: 107 Copynumber: 1.8 Consensus size: 107
31900 AACTTCGACT
31910 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGAAATAAAT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGAAATAAAT
* **
31975 CGCAACGTGAACTTCGACTATCGCAACACGAATTTGGAATAA
66 CGCAACGCGAACTTCGAAAATCGCAACACGAATTTGGAATAA
* * * *
32017 ATCGTAACGAATTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAATGAACTTGGAATAAAT
1 ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGAAATAAAT
* *
32082 CGCAACGCGAATTTGGAAAATCGCA
66 CGCAACGCGAACTTCGAAAATCGCA
32107 TTGCGATAGT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
107 81 1.00
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (107 bp):
ATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACGAACTTGAAATAAAT
CGCAACGCGAACTTCGAAAATCGCAACACGAATTTGGAATAA
Found at i:32151 original size:21 final size:21
Alignment explanation
Indices: 32102--32154 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
32092 ATTTGGAAAA
*
32102 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
*
32123 TCGCGTTGCGATAGTCGATGT
1 TCGCGTTGCGATAGTCGAAGT
*
32144 TCGTGTTGCGA
1 TCGCGTTGCGA
32155 ATCTGAAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:32752 original size:29 final size:31
Alignment explanation
Indices: 32699--32758 Score: 106
Period size: 30 Copynumber: 2.0 Consensus size: 31
32689 CAATCTAAGG
32699 CAAAATGGTTTTTGGATTTGAATTGAATTTA
1 CAAAATGGTTTTTGGATTTGAATTGAATTTA
32730 CAAAAT-GTTTTTGGATTT-AATTGAATTTA
1 CAAAATGGTTTTTGGATTTGAATTGAATTTA
32759 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 12 0.41
31 6 0.21
ACGTcount: A:0.33, C:0.03, G:0.17, T:0.47
Consensus pattern (31 bp):
CAAAATGGTTTTTGGATTTGAATTGAATTTA
Found at i:32853 original size:8 final size:8
Alignment explanation
Indices: 32840--32926 Score: 51
Period size: 8 Copynumber: 11.0 Consensus size: 8
32830 GGTGTCAAAG
32840 TGCATCCA
1 TGCATCCA
32848 TGCATCCA
1 TGCATCCA
*
32856 TGCATCCC
1 TGCATCCA
*
32864 TGCA---G
1 TGCATCCA
32869 TGCATCCA
1 TGCATCCA
32877 TGCAT-C-
1 TGCATCCA
*
32883 TGCA-CTAA
1 TGCATC-CA
*
32891 TGCATCGA
1 TGCATCCA
32899 TGCATCAGGCAA
1 TGCATC---C-A
32911 TGCATCCA
1 TGCATCCA
32919 TGCATCCA
1 TGCATCCA
32927 AACATCGAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 22
0.69 0.07 0.24
Matches are distributed among these distances:
5 4 0.06
6 4 0.06
7 1 0.02
8 44 0.71
9 2 0.03
12 7 0.11
ACGTcount: A:0.25, C:0.33, G:0.17, T:0.24
Consensus pattern (8 bp):
TGCATCCA
Found at i:32986 original size:20 final size:21
Alignment explanation
Indices: 32945--32999 Score: 85
Period size: 20 Copynumber: 2.7 Consensus size: 21
32935 ATGCAATTAG
32945 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
*
32966 TGTATCGATGCATCC-TGCCA
1 TGCATCGATGCATCCTTGCCA
*
32986 TGCATCCATGCATC
1 TGCATCGATGCATC
33000 AAGGCTACAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.20, C:0.33, G:0.18, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:33402 original size:34 final size:32
Alignment explanation
Indices: 33363--33432 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
33353 TTTTGTAAAG
* *
33363 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAATGTTCTAGCTTAGCCCG-G-AAAAACTA
*
33397 GGGAAATGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
33429 GGGA
1 GGGA
33433 GTTGTAAGGT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 11 0.33
33 1 0.03
34 21 0.64
ACGTcount: A:0.31, C:0.16, G:0.27, T:0.26
Consensus pattern (32 bp):
GGGAAATGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:33972 original size:21 final size:23
Alignment explanation
Indices: 33933--33981 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
33923 AAAAATTGAC
33933 TTTATATTCTTTTTGTATTGAAT
1 TTTATATTCTTTTTGTATTGAAT
*
33956 TTTA-ATTCTTTTT-TATTGATT
1 TTTATATTCTTTTTGTATTGAAT
33977 TTTAT
1 TTTAT
33982 TGATTTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
22 9 0.38
23 4 0.17
ACGTcount: A:0.20, C:0.04, G:0.06, T:0.69
Consensus pattern (23 bp):
TTTATATTCTTTTTGTATTGAAT
Found at i:33978 original size:10 final size:10
Alignment explanation
Indices: 33965--33990 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
33955 TTTTAATTCT
33965 TTTTTATTGA
1 TTTTTATTGA
33975 TTTTTATTGA
1 TTTTTATTGA
33985 TTTTTA
1 TTTTTA
33991 AAAAAAGTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (10 bp):
TTTTTATTGA
Found at i:33988 original size:21 final size:22
Alignment explanation
Indices: 33933--33989 Score: 55
Period size: 21 Copynumber: 2.6 Consensus size: 22
33923 AAAAATTGAC
*
33933 TTTATATTCTTTTTGTATTGAAT
1 TTTA-ATTATTTTTGTATTGAAT
*
33956 TTTAATTCTTTTT-TATTG-AT
1 TTTAATTATTTTTGTATTGAAT
*
33976 TTTTATTGATTTTT
1 TTTAATT-ATTTTT
33990 AAAAAAAGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.26
21 10 0.32
22 9 0.29
23 4 0.13
ACGTcount: A:0.19, C:0.04, G:0.07, T:0.70
Consensus pattern (22 bp):
TTTAATTATTTTTGTATTGAAT
Found at i:34302 original size:32 final size:30
Alignment explanation
Indices: 34242--34311 Score: 88
Period size: 30 Copynumber: 2.2 Consensus size: 30
34232 TATAAATTAT
34242 AATTAAAAGTATAAAAATGCAATAAAAAAG
1 AATTAAAAGTATAAAAATGCAATAAAAAAG
*
34272 AATTAAAAGTGA-ATAAAATTCAATACAAAAAG
1 AATTAAAAGT-ATA-AAAATGCAATA-AAAAAG
34304 AATATAAA
1 AAT-TAAA
34312 GTCAATTTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
30 11 0.31
31 11 0.31
32 9 0.26
33 4 0.11
ACGTcount: A:0.66, C:0.04, G:0.09, T:0.21
Consensus pattern (30 bp):
AATTAAAAGTATAAAAATGCAATAAAAAAG
Found at i:34357 original size:26 final size:28
Alignment explanation
Indices: 34320--34371 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
34310 AAGTCAATTT
*
34320 TTTTTTGAAATTATATAAA-ATTTATAA
1 TTTTTTGAAATTATAAAAATATTTATAA
34347 TTTTTT-AAATTATAAAAATATTTAT
1 TTTTTTGAAATTATAAAAATATTTAT
34372 TATAATCATC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TTTTTTGAAATTATAAAAATATTTATAA
Found at i:38618 original size:31 final size:31
Alignment explanation
Indices: 38581--38642 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
38571 CCGGCCACAG
38581 AAAAGATATGCAGAAGTCCAAGCCTGTAGAT
1 AAAAGATATGCAGAAGTCCAAGCCTGTAGAT
38612 AAAAGATATGCAGAAGTCCAAGCCTGTAGAT
1 AAAAGATATGCAGAAGTCCAAGCCTGTAGAT
38643 GGCAAAGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.16, G:0.23, T:0.19
Consensus pattern (31 bp):
AAAAGATATGCAGAAGTCCAAGCCTGTAGAT
Found at i:55429 original size:14 final size:14
Alignment explanation
Indices: 55407--55440 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
55397 ATAATTTTAA
55407 TTAAAATTAAAACG
1 TTAAAATTAAAACG
* *
55421 TTAATATTAAAATG
1 TTAAAATTAAAACG
55435 TTAAAA
1 TTAAAA
55441 AATATAGGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.56, C:0.03, G:0.06, T:0.35
Consensus pattern (14 bp):
TTAAAATTAAAACG
Found at i:56702 original size:526 final size:516
Alignment explanation
Indices: 55711--56743 Score: 1834
Period size: 526 Copynumber: 2.0 Consensus size: 516
55701 GTTTCTGAGT
55711 CTGATCCCAAATTTCCACCGAAAGATTAGATTAGGGCTTTCACTCGATTCTCAATGGAAAGAATC
1 CTGATCCCAAATTTCCACCGAAAGATTAGATTAGGGCTTTCACTCGATTCTCAATGGAAAGAATC
*
55776 AGAAGAGCTTCTCATGCAGGATCTTGGTACACTGATAACCGTAAGTCCTTTAAAGCTGTTTTTCT
66 AGAAGAGCTTCTCATGCAGGATCTTGGTACACTGATAACCGTAAGTCCTTTAAAGCTGTTTTGCT
* *
55841 TCTCCAAACCCTTAACGATTCTAGTAACTAATTCCGATTCATGTTTTTTGCTTACCTTTGTGCGA
131 TCTCCAAACCCTTAACGATTCTAGTAACTAATTCCGATTCATGCTATTTGCTTACCTTTGTGCGA
* *
55906 ATTACTACTCGAGGCAAAAAAATCGTTTATTTCGAGAAAATTAATCAATGTGGATTGAGGAGCTA
196 ATTACTACTCGAGGCAAAAAAATCATTTATTTCGAGAAAATTAATCAATGTGGATTGAGGAACTA
*
55971 AGCTAAGTAATTTCGAAGAGTCAATTAAGATAGTGTTGTTTCTGTAATGAATTAGTATTCTGTTA
261 AGCTAAGTAATTTCGAAGAGTCAATTAAGATAGTGTTGTTTCTGGAATGAATTAGTATTCTGTTA
*
56036 AGTAAAGCTGGAAGAAATTAAATTCGTTTAATTGTTTCAAGTGTTGAATTTGTAATTCCACTGAA
326 AGTAAAGCTGGAAGAAATTAAATTCGTTTAATAGTTTCAAGTGTTGAATTTGTAATTCCACTGAA
* * *
56101 CTAATCTTCTGAAGTTGAAAACATTGATGGTTTTAACTTGTACTGGAAGGCTTTAGGTAATTCGT
391 CTAATCTTCTGAAGTGGAAAACATGGATGGTTTTAACTTGTACTGGAAGGCTTTAGGTAATTCAT
*
56166 TATTCGTGCCTTAGGTGTAGCTAATTACATCTGTAATTCAAACTTCTAAGAATCAGAAGAG
456 TATCCGTGCCTTAGGTGTAGCTAATTACATCTGTAATTCAAACTTCTAAGAATCAGAAGAG
*
56227 CTGATCCCAAATTTCCACCGAAAGATTAGATTAGGGCTTTCACTCGATTCTCGATGGAAAGAATC
1 CTGATCCCAAATTTCCACCGAAAGATTAGATTAGGGCTTTCACTCGATTCTCAATGGAAAGAATC
56292 AGAAGAGCTTCTCATGCAGGATCTTGGTACACTGATAACCGTAAGTCCTTTAATA-CTGTTTTGC
66 AGAAGAGCTTCTCATGCAGGATCTTGGTACACTGATAACCGTAAGTCCTTTAA-AGCTGTTTTGC
56356 TTCCTCCAAACCCTTAACGATTCTAGTAACTAATTCCGATTCATGCTATTTGCTTACCTTTGTGC
130 TT-CTCCAAACCCTTAACGATTCTAGTAACTAATTCCGATTCATGCTATTTGCTTACCTTTGTGC
56421 GAATTATCTACTCGAGGCAAAAAAATCATTTATTTCGAGAAAATTAATCAATTAATCAATGTGGA
194 GAATTA-CTACTCGAGGCAAAAAAATCATTTATTTCGAG------AA--AATTAATCAATGTGGA
56486 TTGAGGAACTAAGCTAAGTAATTTCGAAGAGTCAATTAAGATAGTGTTGTTTCTGGAATGAATTA
250 TTGAGGAACTAAGCTAAGTAATTTCGAAGAGTCAATTAAGATAGTGTTGTTTCTGGAATGAATTA
* *
56551 GTCTTCTGTTAAGTAAAGCTGGAAGAAATTAAATTCGTTTAATAGTTTTAAGTGTTGAATTTGTA
315 GTATTCTGTTAAGTAAAGCTGGAAGAAATTAAATTCGTTTAATAGTTTCAAGTGTTGAATTTGTA
56616 ATTCCACTGAACTAATCTTCTGAAGTGGAAAACATGGATGGTTTTAACTTGTACTGGAAGGCTTT
380 ATTCCACTGAACTAATCTTCTGAAGTGGAAAACATGGATGGTTTTAACTTGTACTGGAAGGCTTT
56681 AGGTAATTCATTATCCGTGCCTTAGGTGTAGCTAATTACATCTGTAATTCAAACTTCTAAGAA
445 AGGTAATTCATTATCCGTGCCTTAGGTGTAGCTAATTACATCTGTAATTCAAACTTCTAAGAA
56744 AACAACATAA
Statistics
Matches: 492, Mismatches: 14, Indels: 12
0.95 0.03 0.02
Matches are distributed among these distances:
516 127 0.26
517 67 0.14
518 31 0.06
524 2 0.00
526 265 0.54
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (516 bp):
CTGATCCCAAATTTCCACCGAAAGATTAGATTAGGGCTTTCACTCGATTCTCAATGGAAAGAATC
AGAAGAGCTTCTCATGCAGGATCTTGGTACACTGATAACCGTAAGTCCTTTAAAGCTGTTTTGCT
TCTCCAAACCCTTAACGATTCTAGTAACTAATTCCGATTCATGCTATTTGCTTACCTTTGTGCGA
ATTACTACTCGAGGCAAAAAAATCATTTATTTCGAGAAAATTAATCAATGTGGATTGAGGAACTA
AGCTAAGTAATTTCGAAGAGTCAATTAAGATAGTGTTGTTTCTGGAATGAATTAGTATTCTGTTA
AGTAAAGCTGGAAGAAATTAAATTCGTTTAATAGTTTCAAGTGTTGAATTTGTAATTCCACTGAA
CTAATCTTCTGAAGTGGAAAACATGGATGGTTTTAACTTGTACTGGAAGGCTTTAGGTAATTCAT
TATCCGTGCCTTAGGTGTAGCTAATTACATCTGTAATTCAAACTTCTAAGAATCAGAAGAG
Found at i:57186 original size:32 final size:32
Alignment explanation
Indices: 57146--57210 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
57136 CTTCTCCTCT
57146 TTGATTGCTATAGTTTAATATCATATAATGTA
1 TTGATTGCTATAGTTTAATATCATATAATGTA
57178 TTGATTGCTATAGTTTAATATCATATAATGTA
1 TTGATTGCTATAGTTTAATATCATATAATGTA
57210 T
1 T
57211 CTCAATTCCC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.12, T:0.48
Consensus pattern (32 bp):
TTGATTGCTATAGTTTAATATCATATAATGTA
Found at i:59336 original size:2 final size:2
Alignment explanation
Indices: 59329--59379 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
59319 AACGTCATGG
59329 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
59371 TA TA TA TA T
1 TA TA TA TA T
59380 TCACTTGATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60468 original size:37 final size:32
Alignment explanation
Indices: 60397--60460 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
60387 TCGAATTACA
60397 TAGTCCAACAACCAAACATAATTAAAAAATGT
1 TAGTCCAACAACCAAACATAATTAAAAAATGT
*
60429 TAGTCCAACATCCAAACATAATTAAAAAATGT
1 TAGTCCAACAACCAAACATAATTAAAAAATGT
60461 CATGTTAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.52, C:0.19, G:0.06, T:0.23
Consensus pattern (32 bp):
TAGTCCAACAACCAAACATAATTAAAAAATGT
Found at i:61113 original size:66 final size:65
Alignment explanation
Indices: 61007--61140 Score: 207
Period size: 66 Copynumber: 2.0 Consensus size: 65
60997 CTATAAAAAA
* *
61007 ATAATATATAGTGACCAAAGAGGTAGTTTACCTAAATAATAATCGAGTGACCAAAATA-AATTAG
1 ATAATATATAGTGACCAAAGAGGCAGTTTACCTAAATAATAATCAAGTGACCAAAATATAATTAG
* *
61071 ATAATATATAAGTGACCAAATAGGCAGTTTGCTCTAAATAATAATCAAGTGACCAAAATATAATT
1 ATAATATAT-AGTGACCAAAGAGGCAGTTTAC-CTAAATAATAATCAAGTGACCAAAATATAATT
61136 AG
64 AG
61138 ATA
1 ATA
61141 CCAAATATAT
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
64 9 0.14
65 19 0.30
66 26 0.41
67 9 0.14
ACGTcount: A:0.47, C:0.11, G:0.14, T:0.28
Consensus pattern (65 bp):
ATAATATATAGTGACCAAAGAGGCAGTTTACCTAAATAATAATCAAGTGACCAAAATATAATTAG
Found at i:62256 original size:36 final size:34
Alignment explanation
Indices: 62189--62494 Score: 157
Period size: 36 Copynumber: 8.9 Consensus size: 34
62179 TATACATAAT
* *
62189 TTTTGAAAACATTTT-GAAATGTATATAATATATAG
1 TTTTAAAAACATTTTAGAAA-ATATAT-ATATATAG
* * *
62224 TTTTAAAAATATTTGTTGAAACTATAT-TATATAG
1 TTTTAAAAACATTT-TAGAAAATATATATATATAG
*
62258 TTTTTAAAACATTTTAGAAAATATATATATATAG
1 TTTTAAAAACATTTTAGAAAATATATATATATAG
* *
62292 TTTTTTAAAATCATTTT-GAAAATATA-ATATATTG
1 --TTTTAAAAACATTTTAGAAAATATATATATATAG
* *** * * * *
62326 TTTT-GAATTTTTTTAAAAAACATTTAAATATATAAT
1 TTTTAAAAACATTTT-AGAAA-ATATATATATAT-AG
*
62362 TTTTGAAAAACATTTTA-AAATATATATAATATATAA
1 TTTT-AAAAACATTTTAGAAA-ATATAT-ATATATAG
* * * *
62398 TTTTTAAACCGTTTCT-GAAAATATAT-TATA-AA
1 TTTTAAAAACATTT-TAGAAAATATATATATATAG
* * * *
62430 TTTTTAAAACGTTTTA-AAAACATGTATAATATAG
1 TTTTAAAAACATTTTAGAAAATATATAT-ATATAG
* *
62464 TTTTTAAAAAGCATTTT-GGAAATTTATATAT
1 -TTTTAAAAA-CATTTTAGAAAATATATATAT
62495 TATATTTCGA
Statistics
Matches: 211, Mismatches: 38, Indels: 44
0.72 0.13 0.15
Matches are distributed among these distances:
31 15 0.07
32 20 0.09
33 20 0.09
34 38 0.18
35 50 0.24
36 51 0.24
37 11 0.05
38 6 0.03
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (34 bp):
TTTTAAAAACATTTTAGAAAATATATATATATAG
Found at i:62260 original size:34 final size:33
Alignment explanation
Indices: 62211--62329 Score: 141
Period size: 34 Copynumber: 3.5 Consensus size: 33
62201 TTTGAAATGT
*
62211 ATATAATATATAGTTTTAAAAATATTTGTTGAAA
1 ATATAATATATAGTTTTTAAAATATTT-TTGAAA
* * * *
62245 CTATATTATATAGTTTTTAAAACATTTTAGAAA
1 ATATAATATATAGTTTTTAAAATATTTTTGAAA
62278 ATATATATATATAGTTTTTTAAAATCA-TTTTGAAA
1 ATATA-ATATATAG-TTTTTAAAAT-ATTTTTGAAA
*
62313 ATATAATATATTGTTTT
1 ATATAATATATAGTTTT
62330 GAATTTTTTT
Statistics
Matches: 72, Mismatches: 10, Indels: 7
0.81 0.11 0.08
Matches are distributed among these distances:
33 13 0.18
34 37 0.51
35 21 0.29
36 1 0.01
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.48
Consensus pattern (33 bp):
ATATAATATATAGTTTTTAAAATATTTTTGAAA
Found at i:62323 original size:68 final size:67
Alignment explanation
Indices: 62174--62494 Score: 179
Period size: 69 Copynumber: 4.6 Consensus size: 67
62164 TGAAAATACT
* * *
62174 TATAATATACATAATTTTTGAAAACATTTTGAAATGTATATAATATATAG-TTTTAAAAAT-ATT
1 TATAATAT--ATAGTTTTT-AAAACATTTTGAAA-ATATAT-ATATATAGTTTTTTAAAATCA-T
* *
62237 TGTTGAAAC
60 T-TTAAAAA
* *
62246 TATATTATATAGTTTTTAAAACATTTTAGAAAATATATATATATAGTTTTTTAAAATCATTTTGA
1 TATAATATATAGTTTTTAAAACATTTT-GAAAATATATATATATAGTTTTTTAAAATCATTTTAA
62311 AAA
65 AAA
* * *** * * * * * *
62314 TATAATATATTG-TTTTGAATTTTTTTAAAAAACATTTAAATATATAATTTTTGAAAAACATTTT
1 TATAATATATAGTTTTTAAAACATTTT--GAAA-ATATATATATATAGTTTTTTAAAATCATTTT
62378 AAAATATA
63 -AAA-A-A
* * * * *
62386 TATAATATATAATTTTTAAACCGTTTCTGAAAATATAT-TATA-A-ATTTTTAAAA-CGTTTTAA
1 TATAATATATAGTTTTTAAAACATTT-TGAAAATATATATATATAGTTTTTTAAAATCATTTTAA
62447 AAA
65 AAA
* * * *
62450 CATGTATAATATAGTTTTTAAAAAGCATTTTGGAAATTTATATAT
1 TAT-AAT-ATATAGTTTTT-AAAA-CATTTTGAAAATATATATAT
62495 TATATTTCGA
Statistics
Matches: 197, Mismatches: 37, Indels: 34
0.74 0.14 0.13
Matches are distributed among these distances:
64 3 0.02
65 3 0.02
66 13 0.07
67 27 0.14
68 43 0.22
69 53 0.27
70 19 0.10
71 5 0.03
72 21 0.11
73 9 0.05
74 1 0.01
ACGTcount: A:0.44, C:0.04, G:0.07, T:0.45
Consensus pattern (67 bp):
TATAATATATAGTTTTTAAAACATTTTGAAAATATATATATATAGTTTTTTAAAATCATTTTAAA
AA
Found at i:62370 original size:26 final size:28
Alignment explanation
Indices: 62335--62387 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 28
62325 GTTTTGAATT
62335 TTTTTAAAAAACA-TTT-AAATATATAA
1 TTTTTAAAAAACATTTTAAAATATATAA
*
62361 TTTTTGAAAAACATTTTAAAATATATA
1 TTTTTAAAAAACATTTTAAAATATATA
62388 TAATATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 12 0.50
27 3 0.12
28 9 0.38
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (28 bp):
TTTTTAAAAAACATTTTAAAATATATAA
Found at i:62445 original size:105 final size:104
Alignment explanation
Indices: 62251--62499 Score: 251
Period size: 105 Copynumber: 2.4 Consensus size: 104
62241 GAAACTATAT
* *
62251 TATATAGTTTTT-AAAACATTTTAGAAA-ATATAT-ATATATAGTTTTTTAAAATCATTTTGAAA
1 TATATAGTTTTTAAAAACATTTTA-AAATATATATAATATATAGATTTTTAAAACCATTTTGAAA
* * *** *
62313 ATATAATATATTGTTTTGAATTTTTTTAAAAAACATTTAAA
65 ATATAATATAATGTTTTAAAACGTTTT-AAAAACATGTAAA
* *
62354 TATATAATTTTTGAAAAACATTTTAAAATATATATAATATATA-ATTTTT-AAACCGTTTCTGAA
1 TATATAGTTTTT-AAAAACATTTTAAAATATATATAATATATAGATTTTTAAAACCATTT-TGAA
* *
62417 AATATATTATAAAT-TTTTAAAACGTTTTAAAAACATGTATA
64 AATATAATAT-AATGTTTTAAAACGTTTTAAAAACATGTAAA
* * *
62458 -ATATAGTTTTTAAAAAGCATTTTGGAAATTTATATATTATAT
1 TATATAGTTTTTAAAAA-CATTTT-AAAATATATATAATATAT
62500 TTCGAAAATA
Statistics
Matches: 122, Mismatches: 16, Indels: 15
0.80 0.10 0.10
Matches are distributed among these distances:
102 5 0.04
103 27 0.22
104 36 0.30
105 45 0.37
106 9 0.07
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (104 bp):
TATATAGTTTTTAAAAACATTTTAAAATATATATAATATATAGATTTTTAAAACCATTTTGAAAA
TATAATATAATGTTTTAAAACGTTTTAAAAACATGTAAA
Found at i:62512 original size:2 final size:2
Alignment explanation
Indices: 62507--62532 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
62497 TATTTCGAAA
62507 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
62533 TATTATTATT
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:69088 original size:164 final size:164
Alignment explanation
Indices: 68815--69751 Score: 1442
Period size: 165 Copynumber: 5.7 Consensus size: 164
68805 TTTTAAACAA
* * *
68815 ATCATTTACAGCATAAATCAAGGCTAGAAGGGTTATCTGTTAGAAAAGACCTTCGAGTTCGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTA
*
68880 CGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGAC
66 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGAC
*** * *
68945 CCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
131 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
*
68979 AACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTA
*
69044 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
66 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGAC
* *
69109 CCCCGAGTTCGATTACGCTCAGCTTCGAGGGCGC
131 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * * ** *
69143 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAATCAAAGACCTTTGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TTAGCAAAGACCTTTGAGTTCGACT
*
69208 ACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGA
65 ACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGA
*** * *
69273 CCCTTAAGTTCGATTACACTCAGCTTCAAGGGCAT
130 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
*
69308 AACATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTA
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTA
*
69373 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGAC
66 CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGAC
* *
69438 CCCCGAGTTCGATTACGCTCAGCTTCGAGGGCGC
131 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * * * ** *
69472 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAATCAAAGACCTTTGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTG-TTAGCAAAGACCTTTGAGTTCGACT
* * * *
69537 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCCATCTGCCAAAGA
65 ACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGA
69602 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
130 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * *
69637 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTCGAGTTCGACT
1 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGC-AAAGACCTTTGAGTTCGACT
*
69702 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGA
65 ACGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGA
69752 AGACCTGGTT
Statistics
Matches: 700, Mismatches: 70, Indels: 5
0.90 0.09 0.01
Matches are distributed among these distances:
164 334 0.48
165 366 0.52
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (164 bp):
ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTA
CGCTCAGCTCCAAGGCACATCATTTGCAGAATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGAC
CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
Found at i:69457 original size:329 final size:329
Alignment explanation
Indices: 68815--69750 Score: 1642
Period size: 329 Copynumber: 2.8 Consensus size: 329
68805 TTTTAAACAA
* * * * * ** *
68815 ATCATTTACAGCATAAATCAAGGCTAGAAGGGTTATCTGTTAGA--AAAGACCTTCGAGTTCGAC
1 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCA-ATCAAAGACCTTTGAGTTCGAC
68878 TACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAG
65 TACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAG
68943 ACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAA
130 ACCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAA
69008 GGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
195 GGGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
69073 AATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACGCTCAGCTTCGAG
260 AATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACGCTCAGCTTCGAG
69138 GGCGC
325 GGCGC
69143 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAATCAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAATCAAAGACCTTTGAGTTCGACT
69208 ACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGA
69273 CCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAG
131 CCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAG
69338 GGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGA
196 GGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGA
69403 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACGCTCAGCTTCGAGG
261 ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACGCTCAGCTTCGAGG
69468 GCGC
326 GCGC
69472 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAATCAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAATCAAAGACCTTTGAGTTCGACT
* * * *
69537 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCAAGAAGGGCCATCTGCCAAAGA
66 ACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGA
*** * * *
69602 CCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAGAAG
131 CCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAG
* * *
69667 GGTTATCTGTGACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
196 GGTTATCTGTTAGC-AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAG
*
69732 CATAGCTTAAGTCGAGAAG
260 AATAGCTTAAGTCGAGAAG
69751 AAGACCTGGT
Statistics
Matches: 583, Mismatches: 22, Indels: 4
0.96 0.04 0.01
Matches are distributed among these distances:
327 1 0.00
328 35 0.06
329 480 0.82
330 67 0.11
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.24
Consensus pattern (329 bp):
ATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAATCAAAGACCTTTGAGTTCGACT
ACGCTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGAGCTATCTGCCAAAGA
CCCTTAAGTTCGATTACACTCAGCTTCAAGGGCATAACATTTACAGCATAACTCAAGGCTAGAAG
GGTTATCTGTTAGCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGA
ATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTACGCTCAGCTTCGAGG
GCGC
Found at i:70317 original size:38 final size:37
Alignment explanation
Indices: 70275--70610 Score: 187
Period size: 37 Copynumber: 9.1 Consensus size: 37
70265 TGAAAATACT
* *
70275 TATAATATACATAATTTTGAAAACA-TTTTGAAAATGTA
1 TATAATATA-ATAGTTTTTAAAACATTTTTGAAAAT-TA
* * *
70313 TATAATAT-ATAGTTTTAAAAATATTTGTTG-AAACTA
1 TATAATATAATAGTTTTTAAAACATTT-TTGAAAATTA
* *
70349 TATATTAT-ATAGTTTTTAAAACATTTTAGAAAATATA
1 TATAATATAATAGTTTTTAAAACATTTTTGAAAAT-TA
70386 TATAATAT-ATAGTTTTTAAAATCATTTTTGAAAAATTA
1 TATAATATAATAGTTTTTAAAA-CATTTTTG-AAAATTA
* * ** * **
70424 TATAATAT-ATTG-TTTT-GAATTTTTTTAAAAAACA
1 TATAATATAATAGTTTTTAAAACATTTTTGAAAATTA
* * *
70458 TTTAAATATTATATAATTTTGAAAAACA-TTTT-AAAATATA
1 TAT-AATA-TA-ATAGTTTT-TAAAACATTTTTGAAAAT-TA
* * * *
70498 TATAATAT-ATAATTTTTAAACCGTTTCTGAAAA-TA
1 TATAATATAATAGTTTTTAAAACATTTTTGAAAATTA
* * * * * *
70533 TATATTATAA-AATTTTTAAAACGTTTTTAAAAACATG
1 TATAATATAATAGTTTTTAAAACATTTTTGAAAA-TTA
* * *
70570 TATAATAT-ATAGTTTTAAAAAGCATTTTGGAAATTTA
1 TATAATATAATAGTTTTTAAAA-CATTTTTGAAAATTA
70607 TATA
1 TATA
70611 TTACATATTT
Statistics
Matches: 231, Mismatches: 46, Indels: 43
0.72 0.14 0.13
Matches are distributed among these distances:
34 7 0.03
35 44 0.19
36 56 0.24
37 57 0.25
38 42 0.18
39 16 0.07
40 7 0.03
41 2 0.01
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (37 bp):
TATAATATAATAGTTTTTAAAACATTTTTGAAAATTA
Found at i:70388 original size:37 final size:36
Alignment explanation
Indices: 70263--70621 Score: 196
Period size: 36 Copynumber: 9.8 Consensus size: 36
70253 GCAAACGGTC
* * *
70263 TTTGAAAATACT-TATAATATACATAATTTTGAAAACAT
1 TTTGAAAATA-TATAT-AT-TATATAGTTTTTAAAACAT
* * * *
70301 TTTGAAAATGTATATAATATATAGTTTTAAAAATATT
1 TTTGAAAATATATATATTATATAGTTTTTAAAACA-T
*
70338 TGTTG-AAA-CTATATATTATATAGTTTTTAAAACAT
1 T-TTGAAAATATATATATTATATAGTTTTTAAAACAT
*
70373 TTTAGAAAATATATATAATATATAGTTTTTAAAATCATT
1 TTT-GAAAATATATATATTATATAGTTTTTAAAA-CA-T
* * * ***
70412 TTTGAAAA-AT-TATATAATATATTGTTTTGAATTTT
1 TTTGAAAATATATATATTATATAGT-TTTTAAAACAT
* * * * *
70447 TTTAAAAAACATTTAAATATTATATAATTTTGAAAAACAT
1 TTT--GAAA-ATATATATATTATATAGTTTT-TAAAACAT
* * * *
70487 TTT-AAAATATATATAATATATAATTTTTAAACCGT
1 TTTGAAAATATATATATTATATAGTTTTTAAAACAT
* * *
70522 TTCTG-AAA-ATATATATTATAAAATTTTTAAAACGTT
1 TT-TGAAAATATATATATTATATAGTTTTTAAAAC-AT
* * * * *
70558 TTTAAAAACATGTATAATATATAGTTTTAAAAAGCAT
1 TTTGAAAATATATATATTATATAGTTTTTAAAA-CAT
* * *
70595 TTTGGAAATTTATATATTACATA-TTTT
1 TTTGAAAATATATATATTATATAGTTTT
70622 CGAAAATATT
Statistics
Matches: 247, Mismatches: 53, Indels: 44
0.72 0.15 0.13
Matches are distributed among these distances:
34 2 0.01
35 37 0.15
36 81 0.33
37 79 0.32
38 24 0.10
39 8 0.03
40 16 0.06
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TTTGAAAATATATATATTATATAGTTTTTAAAACAT
Found at i:70484 original size:28 final size:29
Alignment explanation
Indices: 70446--70503 Score: 84
Period size: 28 Copynumber: 2.0 Consensus size: 29
70436 TTTTGAATTT
70446 TTTTAAAAAACA-TTT-AAATATTATATAA
1 TTTTAAAAAACATTTTAAAATA-TATATAA
*
70474 TTTTGAAAAACATTTTAAAATATATATAA
1 TTTTAAAAAACATTTTAAAATATATATAA
70503 T
1 T
70504 ATATAATTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 11 0.41
29 11 0.41
30 5 0.19
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (29 bp):
TTTTAAAAAACATTTTAAAATATATATAA
Found at i:70512 original size:36 final size:36
Alignment explanation
Indices: 70267--70597 Score: 201
Period size: 38 Copynumber: 9.0 Consensus size: 36
70257 ACGGTCTTTG
* * *
70267 AAAATACT-TATAATATACATAATTTTGAAAACATTTTG
1 AAAATA-TATATAATAT--ATAGTTTTAAAAACATTTTA
* * *
70305 AAAATGTATATAATATATAGTTTTAAAAATATTTGTTG
1 AAAATATATATAATATATAGTTTTAAAAACA-TT-TTA
* *
70343 AAACTATATAT--TATATAGTTTTTAAAACATTTTA
1 AAAATATATATAATATATAGTTTTAAAAACATTTTA
*
70377 GAAAATATATATAATATATAGTTTTTAAAATCATTTTTGA
1 -AAAATATATATAATATATAG-TTTTAAAAACA-TTTT-A
* * ***
70417 AAAAT-TATATAATATATTGTTTT-GAATTTTTTTAAA
1 AAAATATATATAATATATAGTTTTAAAAACATTTT--A
* * * *
70453 AAACATTTAAATATTATATAATTTTGAAAAACATTTT-
1 AAA-ATATATATAATATATAGTTTT-AAAAACATTTTA
* * * * *
70490 AAAATATATATAATATATAATTTTTAAACCGTTTCTG
1 AAAATATATATAATATATAGTTTTAAAAACATTT-TA
* * * *
70527 AAAATATATAT--TATAAAATTTTTAAAACGTTTTTA
1 AAAATATATATAATATATAGTTTTAAAAAC-ATTTTA
* *
70562 AAAACATGTATAATATATAGTTTTAAAAAGCATTTT
1 AAAATATATATAATATATAGTTTTAAAAA-CATTTT
70598 GGAAATTTAT
Statistics
Matches: 232, Mismatches: 41, Indels: 41
0.74 0.13 0.13
Matches are distributed among these distances:
34 2 0.01
35 48 0.21
36 57 0.25
37 47 0.20
38 62 0.27
39 9 0.04
40 7 0.03
ACGTcount: A:0.46, C:0.04, G:0.06, T:0.44
Consensus pattern (36 bp):
AAAATATATATAATATATAGTTTTAAAAACATTTTA
Found at i:74189 original size:15 final size:15
Alignment explanation
Indices: 74169--74232 Score: 65
Period size: 15 Copynumber: 4.3 Consensus size: 15
74159 TGGCAGTGGA
*
74169 GATGAGGATGATGAT
1 GATGAGGATGACGAT
*
74184 GATGAGGATGACGGT
1 GATGAGGATGACGAT
* *
74199 GGTGATGATGACGAT
1 GATGAGGATGACGAT
* **
74214 GATGACGACAACGAT
1 GATGAGGATGACGAT
74229 GATG
1 GATG
74233 GCGAAGAAGA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.31, C:0.08, G:0.39, T:0.22
Consensus pattern (15 bp):
GATGAGGATGACGAT
Found at i:74256 original size:9 final size:9
Alignment explanation
Indices: 74238--74270 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
74228 TGATGGCGAA
74238 GAAGAGGAG
1 GAAGAGGAG
*
74247 GAAGAAGAG
1 GAAGAGGAG
74256 GAAGAGGAG
1 GAAGAGGAG
74265 GAAGAG
1 GAAGAG
74271 CTTCAGCCAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (9 bp):
GAAGAGGAG
Found at i:78503 original size:5 final size:5
Alignment explanation
Indices: 78493--78550 Score: 53
Period size: 5 Copynumber: 10.8 Consensus size: 5
78483 AACGGTCAAC
* * *
78493 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTAG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
78542 GGTCG GGTC
1 GGTCG GGTC
78551 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
5 35 0.81
7 8 0.19
ACGTcount: A:0.09, C:0.21, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:78514 original size:22 final size:22
Alignment explanation
Indices: 78486--78550 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
78476 AACGGTCAAC
78486 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
78508 GGTCAACGGTCGGGTCGGGTAG
1 GGTCAACGGTCGGGTCGGGTCG
78530 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
78551 AGACCGGTCA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.11, C:0.22, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:78602 original size:10 final size:10
Alignment explanation
Indices: 78553--78645 Score: 90
Period size: 9 Copynumber: 9.7 Consensus size: 10
78543 GTCGGGTCAG
78553 ACCGG-TCAA
1 ACCGGTTCAA
78562 ACCGGTT-AA
1 ACCGGTTCAA
78571 ACCGG-TCAA
1 ACCGGTTCAA
* *
78580 ATCGGTTCGA
1 ACCGGTTCAA
*
78590 ACCGGTTGAA
1 ACCGGTTCAA
78600 ACCGG-TCAA
1 ACCGGTTCAA
78609 ACCGG-TCAGA
1 ACCGGTTCA-A
*
78619 ACCGGTTGAAA
1 ACCGGTT-CAA
78630 ACCGGTT-AA
1 ACCGGTTCAA
78639 ACCGGTT
1 ACCGGTT
78646 TCCAGCAGCC
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
8 1 0.01
9 38 0.54
10 22 0.31
11 9 0.13
12 1 0.01
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.18
Consensus pattern (10 bp):
ACCGGTTCAA
Found at i:78605 original size:29 final size:30
Alignment explanation
Indices: 78553--78644 Score: 61
Period size: 29 Copynumber: 3.2 Consensus size: 30
78543 GTCGGGTCAG
*
78553 ACCGGTCAAACCGGTT-A-AACCGG-TCAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAA
* * * *
78580 ATCGGTTCGAACCGGTTGA-AACCGG-TCAA
1 ACCGG-TCAAACCGGTTCAGAACCGGTTGAA
* *
78609 ACCGGTCAGAACCGGTTGAAAACCGGTT-AA
1 ACCGGTCA-AACCGGTTCAGAACCGGTTGAA
78639 ACCGGT
1 ACCGGT
78645 TTCCAGCAGC
Statistics
Matches: 56, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
27 4 0.07
28 12 0.21
29 25 0.45
30 14 0.25
31 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (30 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAA
Found at i:85800 original size:22 final size:22
Alignment explanation
Indices: 85775--85817 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
85765 GAAAGTCAAC
85775 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
85797 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
85818 AGACCGGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:85863 original size:20 final size:21
Alignment explanation
Indices: 85827--85865 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
85817 CAGACCGGTC
*
85827 AAACCGGTTCGAACCGGTTGA
1 AAACCGGTTCAAACCGGTTGA
85848 AAACCGGTT-AAACCGGTT
1 AAACCGGTTCAAACCGGTT
85866 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.21
Consensus pattern (21 bp):
AAACCGGTTCAAACCGGTTGA
Found at i:87328 original size:18 final size:18
Alignment explanation
Indices: 87302--87336 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
87292 CGAAAATAAA
* *
87302 TAGAGTATTGTTTTGTTG
1 TAGAATATTATTTTGTTG
87320 TAGAATATTATTTTGTT
1 TAGAATATTATTTTGTT
87337 AAGTCTATCG
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:0.23, C:0.00, G:0.20, T:0.57
Consensus pattern (18 bp):
TAGAATATTATTTTGTTG
Found at i:102652 original size:3 final size:3
Alignment explanation
Indices: 102644--102672 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
102634 GTTGAACATC
102644 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
102673 CACGCGAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:103534 original size:20 final size:20
Alignment explanation
Indices: 103497--103542 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
103487 GAGAGAAAGT
103497 AACAAAGAGGCTAGAAGGAGG
1 AACAAAGAGGCTAGAAGGA-G
*
103518 AACAAAGA-GCTATAAGGAG
1 AACAAAGAGGCTAGAAGGAG
103537 AACAAA
1 AACAAA
103543 TCGGGTTGGG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
20 9 0.38
21 8 0.33
ACGTcount: A:0.54, C:0.11, G:0.28, T:0.07
Consensus pattern (20 bp):
AACAAAGAGGCTAGAAGGAG
Done.