Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004648.1 Hibiscus syriacus cultivar Beakdansim tig00010418_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: 77794
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:912 original size:22 final size:22
Alignment explanation
Indices: 884--925 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
874 ACGTATACGG
884 TTTTAAAATTATAATATATATT
1 TTTTAAAATTATAATATATATT
* *
906 TTTTAAAGTTGTAATATATA
1 TTTTAAAATTATAATATATA
926 GCTTTGAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.05, T:0.52
Consensus pattern (22 bp):
TTTTAAAATTATAATATATATT
Found at i:935 original size:22 final size:22
Alignment explanation
Indices: 895--936 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
885 TTTAAAATTA
** *
895 TAATATATATTTTTTAAAGTTG
1 TAATATATAGCTTTGAAAGTTG
917 TAATATATAGCTTTGAAAGT
1 TAATATATAGCTTTGAAAGT
937 GTGTGTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.02, G:0.12, T:0.48
Consensus pattern (22 bp):
TAATATATAGCTTTGAAAGTTG
Found at i:1085 original size:12 final size:12
Alignment explanation
Indices: 1070--1121 Score: 52
Period size: 12 Copynumber: 4.1 Consensus size: 12
1060 ATATTTGTTA
1070 TTTTTATTTGATTT
1 TTTTTA-TT-ATTT
1084 TTGTTTATTATTT
1 TT-TTTATTATTT
*
1097 TTTTTCTTATTT
1 TTTTTATTATTT
1109 TTTATT-TTATTT
1 TTT-TTATTATTT
1121 T
1 T
1122 GTAGGTCTAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
12 19 0.54
13 8 0.23
14 4 0.11
15 4 0.11
ACGTcount: A:0.13, C:0.02, G:0.04, T:0.81
Consensus pattern (12 bp):
TTTTTATTATTT
Found at i:4884 original size:54 final size:54
Alignment explanation
Indices: 4819--5340 Score: 679
Period size: 54 Copynumber: 9.7 Consensus size: 54
4809 CTATGTGTAT
* * * *
4819 TATCGGCACTAAGTGTGCAATCCATGGAATTTATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* *
4873 TATCGACACTAAGTGTACAACCCATGGAATTCATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * *
4927 TATCGATACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACTG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * * *
4981 TATCGACAATAAATGTGCAACCCACAGAATTCATAATAAGTTTATGAATGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * * * *
5035 TAACGGCACTAAGTGTGCAA-CCACGAAATTCATAATATGTTTATGAACGATCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
** * * *
5088 TATCGGTACTAAGTGAGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * ** *
5142 TATCGGCACTAAGTGTGTAACCCACATAATTCATAATAAG-TCATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
** * * * *
5195 TATCGGTACTAAGTGTGCAACCCACGAAATTCATAATATGTTTATGAATGATCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * * *
5249 TATCTACACTAAGTGTGCAACCTATGGAATTCATAATAAGTTTATGAATGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
*
5303 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATA
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATA
5341 TGAGTATTGG
Statistics
Matches: 410, Mismatches: 56, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
53 91 0.22
54 319 0.78
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (54 bp):
TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
Found at i:4939 original size:27 final size:27
Alignment explanation
Indices: 4855--4940 Score: 68
Period size: 27 Copynumber: 3.2 Consensus size: 27
4845 GAATTTATAA
*
4855 TAAGTTTATGAACGACCGTATCGACAC
1 TAAGTTTATGAACGACCGTATCGATAC
* * * ** * *
4882 TAAGTGTA-CAACCCATGGAATTC-ATAA
1 TAAGTTTATGAA-CGACCGTA-TCGATAC
4909 TAAGTTTATGAACGACCGTATCGATAC
1 TAAGTTTATGAACGACCGTATCGATAC
4936 TAAGT
1 TAAGT
4941 GTGCAACCCA
Statistics
Matches: 40, Mismatches: 15, Indels: 8
0.63 0.24 0.13
Matches are distributed among these distances:
26 4 0.10
27 32 0.80
28 4 0.10
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (27 bp):
TAAGTTTATGAACGACCGTATCGATAC
Found at i:4966 original size:27 final size:27
Alignment explanation
Indices: 4936--5021 Score: 70
Period size: 27 Copynumber: 3.2 Consensus size: 27
4926 GTATCGATAC
4936 TAAGTGTGCAACCCACAGAATTCATAA
1 TAAGTGTGCAACCCACAGAATTCATAA
* * * * *
4963 TAAGTTTATG-AA-CGACTGTA-TCGACAA
1 TAAG--TGTGCAACCCACAGAATTC-ATAA
*
4990 TAAATGTGCAACCCACAGAATTCATAA
1 TAAGTGTGCAACCCACAGAATTCATAA
5017 TAAGT
1 TAAGT
5022 TTATGAATGA
Statistics
Matches: 41, Mismatches: 12, Indels: 12
0.63 0.18 0.18
Matches are distributed among these distances:
25 3 0.07
26 4 0.10
27 27 0.66
28 4 0.10
29 3 0.07
ACGTcount: A:0.41, C:0.19, G:0.15, T:0.26
Consensus pattern (27 bp):
TAAGTGTGCAACCCACAGAATTCATAA
Found at i:5110 original size:161 final size:161
Alignment explanation
Indices: 4819--5340 Score: 733
Period size: 161 Copynumber: 3.2 Consensus size: 161
4809 CTATGTGTAT
* * ** * *
4819 TATCGGCACTAAGTGTGCAATCCATGGAATTTATAATAAGTTTATGAACGACCGTATCGACACTA
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTA
* * * * *
4884 AGTGTACAACCCATGGAATTCATAATAAGTTTATGAACGACCGTATCGATACTAAGTGTGCAACC
66 AGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGATCGTATCGATACTAAGTGTGCAACC
*
4949 CACAGAATTCATAATAAGTTTATGAACGACTG
131 CAC-GAATTCATAATAAGTTTATGAACGACCG
* * * *
4981 TATCGACAATAAATGTGCAACCCACAGAATTCATAATAAGTTTATGAATGACCGTAACGGCACTA
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTA
* *
5046 AGTGTGCAA-CCACGAAATTCATAATATGTTTATGAACGATCGTATCGGTACTAAGTGAGCAACC
66 AGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGATCGTATCGATACTAAGTGTGCAACC
*
5110 CACGAAATTCATAATAAGTTTATGAACGACCA
131 CACG-AATTCATAATAAGTTTATGAACGACCG
* * * * *
5142 TATCGGCACTAAGTGTGTAACCCACATAATTCATAATAAG-TCATGAACGACCGTATCGGTACTA
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTA
* * *
5206 AGTGTGCAACCCACGAAATTCATAATATGTTTATGAATGATCGTATCTACACTAAGTGTGCAACC
66 AGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGATCGTATCGATACTAAGTGTGCAACC
* * *
5271 TATGGAATTCATAATAAGTTTATGAATGACCG
131 CA-CGAATTCATAATAAGTTTATGAACGACCG
5303 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATA
1 TATCGACACTAAGTGTGCAACCCACAGAATTCATAATA
5341 TGAGTATTGG
Statistics
Matches: 317, Mismatches: 40, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
160 30 0.09
161 223 0.70
162 64 0.20
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (161 bp):
TATCGACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTTATGAACGACCGTATCGGCACTA
AGTGTGCAACCCACGAAATTCATAATATGTTTATGAACGATCGTATCGATACTAAGTGTGCAACC
CACGAATTCATAATAAGTTTATGAACGACCG
Found at i:5120 original size:107 final size:108
Alignment explanation
Indices: 4819--5340 Score: 669
Period size: 107 Copynumber: 4.9 Consensus size: 108
4809 CTATGTGTAT
* * * *
4819 TATCGGCACTAAGTGTGCAATCCATGGAATTTATAATAAGTTTATGAACGACCGTATCGACACTA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACACTA
* * *
4884 AGTGTACAACCCATGGAATTCATAATAAGTTTATGAACGACCG
66 AGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
** * *
4927 TATCGATACTAAGTGTGCAACCCAC-AGAATTCATAATAAGTTTATGAACGACTGTATCGACAAT
1 TATCGGCACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCGTATCGACACT
* *
4991 AAATGTGCAACCCAC-AGAATTCATAATAAGTTTATGAATGACCG
65 AAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCG
* * * **
5035 TAACGGCACTAAGTGTGCAA-CCACGAAATTCATAATATGTTTATGAACGATCGTATCGGTACTA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACACTA
* *
5099 AGTGAGCAACCCACGAAATTCATAATAAGTTTATGAACGACCA
66 AGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
* * **
5142 TATCGGCACTAAGTGTGTAACCCAC-ATAATTCATAATAAG-TCATGAACGACCGTATCGGTACT
1 TATCGGCACTAAGTGTGCAACCCACGA-AATTCATAATAAGTTTATGAACGACCGTATCGACACT
* * *
5205 AAGTGTGCAACCCACGAAATTCATAATATGTTTATGAATGATCG
65 AAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
** * * * *
5249 TATCTACACTAAGTGTGCAACCTATGGAATTCATAATAAGTTTATGAATGACCGTATCGACACTA
1 TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACACTA
5314 AGTGTGCAACCCAC-AGAATTCATAATA
66 AGTGTGCAACCCACGA-AATTCATAATA
5341 TGAGTATTGG
Statistics
Matches: 359, Mismatches: 46, Indels: 18
0.85 0.11 0.04
Matches are distributed among these distances:
107 186 0.52
108 173 0.48
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.27
Consensus pattern (108 bp):
TATCGGCACTAAGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCGTATCGACACTA
AGTGTGCAACCCACGAAATTCATAATAAGTTTATGAACGACCG
Found at i:10939 original size:90 final size:89
Alignment explanation
Indices: 10787--10959 Score: 301
Period size: 90 Copynumber: 1.9 Consensus size: 89
10777 ACACACCCTT
*
10787 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTTAAATTAATTAAATCTATATTTA
1 TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
*
10852 ATTAATTGAAATTTAATAATCCTC
66 ATTAATTGAAATTAAATAATCCTC
* *
10876 TTATATCCAAGTTACCCTGATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATATTT
1 TTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATATTT
10941 AATTAATTGAAATTAAATA
65 AATTAATTGAAATTAAATA
10960 TTCAGGATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 29 0.37
90 50 0.63
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (89 bp):
TTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATATTTA
ATTAATTGAAATTAAATAATCCTC
Found at i:20948 original size:20 final size:20
Alignment explanation
Indices: 20923--20992 Score: 113
Period size: 20 Copynumber: 3.5 Consensus size: 20
20913 GATGTAATTA
* *
20923 GTATCAATACTAAGAAGAAT
1 GTATCAATACAAAGAGGAAT
20943 GTATCAATACAAAGAGGAAT
1 GTATCAATACAAAGAGGAAT
20963 GTATCAATACAAAGAGGAAT
1 GTATCAATACAAAGAGGAAT
*
20983 GTATCGATAC
1 GTATCAATAC
20993 CATGGATTCC
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (20 bp):
GTATCAATACAAAGAGGAAT
Found at i:21463 original size:27 final size:27
Alignment explanation
Indices: 21433--21518 Score: 66
Period size: 27 Copynumber: 3.2 Consensus size: 27
21423 AAATTCATAA
21433 TAAGTTTATAAACGACCGTATCGACAC
1 TAAGTTTATAAACGACCGTATCGACAC
* ** * * * * * *
21460 TAAGTGTGCAACCCACGGAATTC-ATAA
1 TAAGTTTATAAACGACCGTA-TCGACAC
*
21487 TAAGTTTATGAACGACCGTATCGACAC
1 TAAGTTTATAAACGACCGTATCGACAC
21514 TAAGT
1 TAAGT
21519 GTGCACCCCA
Statistics
Matches: 38, Mismatches: 19, Indels: 4
0.62 0.31 0.07
Matches are distributed among these distances:
26 2 0.05
27 34 0.89
28 2 0.05
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (27 bp):
TAAGTTTATAAACGACCGTATCGACAC
Found at i:21482 original size:54 final size:54
Alignment explanation
Indices: 21397--21901 Score: 609
Period size: 54 Copynumber: 9.4 Consensus size: 54
21387 CTATGTGTAC
* * * * *
21397 TATCGGCACTAAGTGTGCAATCTACGAAATTCATAATAAGTTTATAAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
21451 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* *
21505 TATCGACACTAAGTGTGCACCCCACGGAATTCATAATAAGTTTATGAACAACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * * * *
21559 TATCGGCAGTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAATGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * * *
21613 TATCGCCACTAATTGTGCAACCCACGAAATTCATAATAAGTTTATGAATGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
** * ** *
21667 TATCGGTACTAAGTGTACAACCCACAAAATTCATAATAAGTTTATGAACGACAG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * * *
21721 TATCGCCACTAAGTGTGCAACCCACGAAATTCATATTAAGTTTATGAATGACCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
* * * * * *
21775 TATCGACACTAAGAGTGCAGCTCA-TGAAGTTCATAATAACTTTATGAACGATCG
1 TATCGACACTAAGTGTGCAACCCACGGAA-TTCATAATAAGTTTATGAACGACCG
* * * * * * * * *
21829 TATTGGCACTAAGGGTGCAATCCACAGAATTCACAATGAGTTTATGAATGATCG
1 TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
21883 TATCGACACTATA-TGTGCA
1 TATCGACACTA-AGTGTGCA
21902 CCCGAAGGAT
Statistics
Matches: 390, Mismatches: 58, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
53 2 0.01
54 384 0.98
55 4 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (54 bp):
TATCGACACTAAGTGTGCAACCCACGGAATTCATAATAAGTTTATGAACGACCG
Found at i:24130 original size:3 final size:3
Alignment explanation
Indices: 24114--24187 Score: 71
Period size: 3 Copynumber: 25.0 Consensus size: 3
24104 ATTTGTTTTT
* *
24114 TTA TTT TTA TTTA TTA TTA TAA TTA TT- TTA TTA -TA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
24158 ATA ATA TTA ATA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
24188 AATAATAAAT
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
2 4 0.07
3 51 0.88
4 3 0.05
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:24166 original size:15 final size:15
Alignment explanation
Indices: 24146--24194 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
24136 TTATTTTATT
24146 ATATTATTATTAATA
1 ATATTATTATTAATA
*
24161 ATATTAATATTAATA
1 ATATTATTATTAATA
*
24176 TTATTATTATTAAATA
1 ATATTATTATT-AATA
24192 ATA
1 ATA
24195 AATAATTACA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
15 23 0.79
16 6 0.21
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (15 bp):
ATATTATTATTAATA
Found at i:25627 original size:3 final size:3
Alignment explanation
Indices: 25619--25653 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
25609 AATATATTTA
*
25619 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
25654 AAATATATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:25889 original size:155 final size:154
Alignment explanation
Indices: 25733--26041 Score: 433
Period size: 155 Copynumber: 2.0 Consensus size: 154
25723 TATAAATTTA
*
25733 ATTTTATATAAATTACTTTTAGGAAAAATAATTATATTTTAATATTTATTTATTTTTTAATATTA
1 ATTTTATATAAATTA-TTTTAGGAAAAAT-ATT-T-TATTAATATTTATTTATTTTTTAATATTA
* * *
25798 AGAAAATGGTTGCCTTAAAGCAACTAGAAGT-TCTTTTCTGATATTTTTAAATAACTAAATATCC
62 AGAAAATGATTGCCTTAAAGCAACTAGAAGTCT-TTTTCTGATATTTCTAAATAAATAAATATCC
**
25862 TATTTTGATAAAT-TATATATATATTAATTT
126 TATTTAAATAAATATATATATATATTAA--T
* *
25892 ATTTTATTTTAATTATTTTAGGAAAAATATTTTATTAATATTTATTTATTTTTTAATATTAAGAA
1 ATTTTATATAAATTATTTTAGGAAAAATATTTTATTAATATTTATTTATTTTTTAATATTAAGAA
* * *
25957 AATGATTGTCTTAAAGCAACTAGAAGTCTTTTTCTGATATTTCTAAGTAAATAAATATCTTATTT
66 AATGATTGCCTTAAAGCAACTAGAAGTCTTTTTCTGATATTTCTAAATAAATAAATATCCTATTT
*
26022 AAATATATATATATATATAT
131 AAATAAATATATATATATAT
26042 ATATATATAT
Statistics
Matches: 136, Mismatches: 12, Indels: 7
0.88 0.08 0.05
Matches are distributed among these distances:
155 94 0.69
156 13 0.10
157 3 0.02
158 13 0.10
159 13 0.10
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.49
Consensus pattern (154 bp):
ATTTTATATAAATTATTTTAGGAAAAATATTTTATTAATATTTATTTATTTTTTAATATTAAGAA
AATGATTGCCTTAAAGCAACTAGAAGTCTTTTTCTGATATTTCTAAATAAATAAATATCCTATTT
AAATAAATATATATATATATTAAT
Found at i:26095 original size:2 final size:2
Alignment explanation
Indices: 26024--26082 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
26014 TCTTATTTAA
26024 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
26066 AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT A
26083 AGTTAATATA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37350 original size:14 final size:14
Alignment explanation
Indices: 37326--37367 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
37316 ATATTATGCT
37326 TGAAGAAGAAAAAAA
1 TGAA-AAGAAAAAAA
37341 T-AATAAG-AAAAAA
1 TGAA-AAGAAAAAAA
37354 TGAAAAGAAAAAAA
1 TGAAAAGAAAAAAA
37368 AACAAAATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
13 10 0.42
14 13 0.54
15 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.14, T:0.10
Consensus pattern (14 bp):
TGAAAAGAAAAAAA
Found at i:38429 original size:20 final size:22
Alignment explanation
Indices: 38362--38437 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
38352 ACATCTATAT
38362 TCTTCAAAGATGATAAATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
38384 TCTTCAAAGATGACAAATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
38406 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAAATTCTC
*
38428 TTTTCAAAGA
1 TCTTCAAAGA
38438 AGAAAGATTT
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.36, C:0.18, G:0.11, T:0.36
Consensus pattern (22 bp):
TCTTCAAAGATGATAAATTCTC
Found at i:39049 original size:123 final size:122
Alignment explanation
Indices: 38830--39162 Score: 463
Period size: 123 Copynumber: 2.7 Consensus size: 122
38820 CATTCGATGG
* *
38830 ATCAACTTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAAAAGTTCATA
1 ATCAACATTTCCA-AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* ** * *
38895 ATGAGAAGAGCTTGTTCAACCTTTTGCATGACTTTATCACAAAAGGATATGGATCAAC
65 ATGAGAAGAACTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAAC
* *
38953 ATCAACATTTCCATAGAAAGTTCATAATAAGAAGAAATTATCTGAAGAGGAAGAAGAAGTTCATA
1 ATCAACATTTCCA-AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATA
* * *
39018 ATGAGAAGAACTTGTTCAACCTTTTGCATGACGCTATCATAGAAGGAGATAGATCAGC
65 ATGAGAAGAACTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAAC
* * **
39076 ATAAACATTTCC-AGAAGTGTTCATAATGAGAAGAACTCGTCTGAAGAAGG-AGAAGAAGTTCAT
1 ATCAACATTTCCAAGAA-AGTTCATAATGAGAAGAACTTATCTGAAG-AGGAAGAAGAAGTTCAT
*
39139 AATGAGAAGAATTTGTTCAACCTT
64 AATGAGAAGAACTTGTTCAACCTT
39163 GCCTTAATTC
Statistics
Matches: 188, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
121 4 0.02
122 60 0.32
123 124 0.66
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (122 bp):
ATCAACATTTCCAAGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAA
TGAGAAGAACTTGTTCAACCTTTTGCATGACGCTATCACAAAAGGAGATAGATCAAC
Found at i:39277 original size:39 final size:38
Alignment explanation
Indices: 39226--39327 Score: 159
Period size: 39 Copynumber: 2.6 Consensus size: 38
39216 CAGCACTTCC
* *
39226 AGAAGGAGTTCATAATGAGAAGAAGTCATCTGAAAAAGA
1 AGAA-GAGTTCATAATGAGAAGAACTCATCTAAAAAAGA
39265 AGAATGAGTTCATAATGAGAAGAACTCATCTAAAAAAGA
1 AGAA-GAGTTCATAATGAGAAGAACTCATCTAAAAAAGA
39304 AGAAGAAGTTCATAATGAGAAGAA
1 AGAAG-AGTTCATAATGAGAAGAA
39328 TCTATTCAAC
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
38 1 0.02
39 58 0.98
ACGTcount: A:0.51, C:0.08, G:0.23, T:0.19
Consensus pattern (38 bp):
AGAAGAGTTCATAATGAGAAGAACTCATCTAAAAAAGA
Found at i:39567 original size:3 final size:3
Alignment explanation
Indices: 39559--39619 Score: 63
Period size: 3 Copynumber: 21.0 Consensus size: 3
39549 TGTTTGTTTT
** * *
39559 TTA TTA TTA TTA AAA TTA TT- TTA TTA -TG TTA TTA TTA TTA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
39605 ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
39620 AATAATAAAT
Statistics
Matches: 46, Mismatches: 10, Indels: 4
0.77 0.17 0.07
Matches are distributed among these distances:
2 3 0.07
3 43 0.93
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:41062 original size:17 final size:19
Alignment explanation
Indices: 41040--41080 Score: 54
Period size: 17 Copynumber: 2.4 Consensus size: 19
41030 TTATTATTAT
41040 TATTATTAT-TATA-AATA
1 TATTATTATATATATAATA
41057 TATTA-TATATATATAATA
1 TATTATTATATATATAATA
41075 T-TTATT
1 TATTATT
41081 TATTTATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 3 0.14
17 12 0.57
18 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTATTATATATATAATA
Found at i:46557 original size:17 final size:17
Alignment explanation
Indices: 46535--46570 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
46525 CCTCACTTTA
*
46535 AATATATCATTTACCCT
1 AATATATCAGTTACCCT
46552 AATATATCAGTTACCCT
1 AATATATCAGTTACCCT
46569 AA
1 AA
46571 CATGTTAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.39, C:0.22, G:0.03, T:0.36
Consensus pattern (17 bp):
AATATATCAGTTACCCT
Found at i:53316 original size:9 final size:8
Alignment explanation
Indices: 53304--53374 Score: 56
Period size: 8 Copynumber: 8.8 Consensus size: 8
53294 CATGTTGCAC
53304 ATTTATAAT
1 ATTTAT-AT
53313 ATTTATAT
1 ATTTATAT
*
53321 ATGTATTAT
1 ATTTA-TAT
* *
53330 ATTGA-AC
1 ATTTATAT
53337 ATATTATAT
1 AT-TTATAT
*
53346 ATATATAT
1 ATTTATAT
*
53354 ATATATAT
1 ATTTATAT
53362 ATTTAT-T
1 ATTTATAT
53369 ATTTAT
1 ATTTAT
53375 TTTATTACAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
7 10 0.20
8 26 0.51
9 15 0.29
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (8 bp):
ATTTATAT
Found at i:53524 original size:15 final size:15
Alignment explanation
Indices: 53504--53538 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
53494 ACCCAGTTCA
53504 AGACCCGAACCGGCC
1 AGACCCGAACCGGCC
*
53519 AGACCCGAATCGGCC
1 AGACCCGAACCGGCC
53534 AGACC
1 AGACC
53539 TTTCACCCGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.43, G:0.26, T:0.03
Consensus pattern (15 bp):
AGACCCGAACCGGCC
Found at i:54111 original size:22 final size:23
Alignment explanation
Indices: 54083--54135 Score: 72
Period size: 24 Copynumber: 2.3 Consensus size: 23
54073 AGCATTCGAT
* *
54083 TCGTTTATA-TTCATGAACTAGC
1 TCGTTTATAGTTCATAAACAAGC
54105 TCGTTTATATGTTCATAAACAAGC
1 TCGTTTATA-GTTCATAAACAAGC
54129 TCGTTTA
1 TCGTTTA
54136 ATTTTTTATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 9 0.33
24 18 0.67
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.42
Consensus pattern (23 bp):
TCGTTTATAGTTCATAAACAAGC
Found at i:54917 original size:11 final size:11
Alignment explanation
Indices: 54896--54955 Score: 75
Period size: 11 Copynumber: 5.5 Consensus size: 11
54886 GACATGTTTG
*
54896 TGAACGTTAAA
1 TGAACGCTAAA
*
54907 CGAACGCTAAA
1 TGAACGCTAAA
*
54918 TGAACGCTTAA
1 TGAACGCTAAA
* *
54929 CGAACGTTAAA
1 TGAACGCTAAA
54940 TGAACGCTAAA
1 TGAACGCTAAA
54951 TGAAC
1 TGAAC
54956 ACGTTCTCAA
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 40 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (11 bp):
TGAACGCTAAA
Found at i:55174 original size:50 final size:50
Alignment explanation
Indices: 55106--55225 Score: 163
Period size: 50 Copynumber: 2.4 Consensus size: 50
55096 CCCTAATTTT
* * *
55106 CATTAAAAGAA-TGCACTTAAAACTATGTCGTTTTCATTAGAGAAAATGA
1 CATTAAAAAAAGTGCACTTAAAACTATATCGTTTTCATCAGAGAAAATGA
* * *
55155 CATTAAAAAAAGTGCACTTAGAACTATATCGTTTTCATCAGGGAAAATGG
1 CATTAAAAAAAGTGCACTTAAAACTATATCGTTTTCATCAGAGAAAATGA
*
55205 CATT-AAAAAAGGGCACTTAAA
1 CATTAAAAAAAGTGCACTTAAA
55226 TTCATCAGAG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
49 25 0.40
50 37 0.60
ACGTcount: A:0.43, C:0.13, G:0.16, T:0.28
Consensus pattern (50 bp):
CATTAAAAAAAGTGCACTTAAAACTATATCGTTTTCATCAGAGAAAATGA
Found at i:56118 original size:23 final size:23
Alignment explanation
Indices: 56088--56165 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
56078 ATATTAAAAT
*
56088 TCTGTCTTTGTGACATGTTTATC
1 TCTGTCTTTGTGACATGTTTACC
* * *
56111 TCTGTCTTTATGGCACGTTTACC
1 TCTGTCTTTGTGACATGTTTACC
* *
56134 TTTG-CATTTGTGACATGTTTTCC
1 TCTGTC-TTTGTGACATGTTTACC
*
56157 TCTTTCTTT
1 TCTGTCTTT
56166 TGTTATTTTT
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
22 1 0.02
23 40 0.95
24 1 0.02
ACGTcount: A:0.12, C:0.21, G:0.15, T:0.53
Consensus pattern (23 bp):
TCTGTCTTTGTGACATGTTTACC
Found at i:59277 original size:18 final size:18
Alignment explanation
Indices: 59254--59297 Score: 88
Period size: 18 Copynumber: 2.4 Consensus size: 18
59244 CTTCTTTATC
59254 ACCACCATGATCATCACA
1 ACCACCATGATCATCACA
59272 ACCACCATGATCATCACA
1 ACCACCATGATCATCACA
59290 ACCACCAT
1 ACCACCAT
59298 CATCGTCGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.39, C:0.41, G:0.05, T:0.16
Consensus pattern (18 bp):
ACCACCATGATCATCACA
Found at i:59299 original size:15 final size:16
Alignment explanation
Indices: 59263--59301 Score: 53
Period size: 18 Copynumber: 2.4 Consensus size: 16
59253 CACCACCATG
59263 ATCATCACAACCACCA
1 ATCATCACAACCACCA
59279 TGATCATCACAACCACC-
1 --ATCATCACAACCACCA
59296 ATCATC
1 ATCATC
59302 GTCGTCGTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.29
18 15 0.71
ACGTcount: A:0.38, C:0.41, G:0.03, T:0.18
Consensus pattern (16 bp):
ATCATCACAACCACCA
Found at i:61290 original size:34 final size:34
Alignment explanation
Indices: 61247--61312 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
61237 AAATTTTCAA
61247 AGGAAATAATACAACTTACCCATAGAGAAAGCTG
1 AGGAAATAATACAACTTACCCATAGAGAAAGCTG
* *
61281 AGGAAATAATACAACTTCCCCATAGAGGAAGC
1 AGGAAATAATACAACTTACCCATAGAGAAAGC
61313 GTAATTACTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 30 1.00
ACGTcount: A:0.45, C:0.20, G:0.18, T:0.17
Consensus pattern (34 bp):
AGGAAATAATACAACTTACCCATAGAGAAAGCTG
Found at i:62799 original size:3 final size:3
Alignment explanation
Indices: 62791--62820 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
62781 TATATTATAC
62791 TTA TTA TTA TTA TTA TTA TTA TTAA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TT-A TTA TT
62821 CTACAATCAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:64315 original size:30 final size:30
Alignment explanation
Indices: 64224--64316 Score: 98
Period size: 30 Copynumber: 3.1 Consensus size: 30
64214 TAATAGCAAG
* * *
64224 TTAGCCTTTTAACTTTATATTTTTGTTATT
1 TTAGCCTTTTAAATTTATGTTTTTGATATT
* * *
64254 TTAGCCTTTTAAGTTTATG-TTTGGACCATT
1 TTAGCCTTTTAAATTTATGTTTTTGA-TATT
* *
64284 TTAGCCCTTTAAATTTCTGTTTTTGATATT
1 TTAGCCTTTTAAATTTATGTTTTTGATATT
64314 TTA
1 TTA
64317 ATTCTTTAAA
Statistics
Matches: 51, Mismatches: 10, Indels: 4
0.78 0.15 0.06
Matches are distributed among these distances:
29 4 0.08
30 42 0.82
31 5 0.10
ACGTcount: A:0.20, C:0.12, G:0.11, T:0.57
Consensus pattern (30 bp):
TTAGCCTTTTAAATTTATGTTTTTGATATT
Found at i:64350 original size:27 final size:26
Alignment explanation
Indices: 64301--64352 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
64291 TTTAAATTTC
*
64301 TGTTTTTGATATTTTAATTCTTTAAA
1 TGTTTTTGATATTTTAATCCTTTAAA
* *
64327 TGTTTTCTGTTATTTTAGTCCTTTAA
1 TGTTTT-TGATATTTTAATCCTTTAA
64353 GTTTCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.21, C:0.08, G:0.10, T:0.62
Consensus pattern (26 bp):
TGTTTTTGATATTTTAATCCTTTAAA
Found at i:68503 original size:16 final size:16
Alignment explanation
Indices: 68462--68516 Score: 65
Period size: 16 Copynumber: 3.4 Consensus size: 16
68452 ACACACGCTT
*
68462 ATACACACACGCACTC
1 ATACACACACGCACAC
* * *
68478 ACACAAACACGCAGAC
1 ATACACACACGCACAC
*
68494 ATGCACACACGCACAC
1 ATACACACACGCACAC
68510 ATACACA
1 ATACACA
68517 TGCAAGCACA
Statistics
Matches: 30, Mismatches: 9, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.44, C:0.40, G:0.09, T:0.07
Consensus pattern (16 bp):
ATACACACACGCACAC
Found at i:68543 original size:18 final size:18
Alignment explanation
Indices: 68501--68543 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
68491 GACATGCACA
* *
68501 CACGCACACATACACATG
1 CACGCACACACACACACG
* *
68519 CAAGCACACACACACGCG
1 CACGCACACACACACACG
68537 CACGCAC
1 CACGCAC
68544 TTGCGTACGT
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.37, C:0.44, G:0.14, T:0.05
Consensus pattern (18 bp):
CACGCACACACACACACG
Done.