Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004606.1 Hibiscus syriacus cultivar Beakdansim tig00010295_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: 70495
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1085 original size:2 final size:2
Alignment explanation
Indices: 1072--1101 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1062 ATTGTTTATT
*
1072 TA TA TA TT 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
1102 ATCATCTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:1087 original size:12 final size:12
Alignment explanation
Indices: 1066--1101 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1056 TTCAACATTG
*
1066 TTTATTTATATA
1 TTTATATATATA
1078 TTTATATATATA
1 TTTATATATATA
*
1090 TATATATATATA
1 TTTATATATATA
1102 ATCATCTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
TTTATATATATA
Found at i:2167 original size:20 final size:22
Alignment explanation
Indices: 2131--2170 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2121 ATTTAATAAT
2131 ATAATATATATTAATTTTTTTA
1 ATAATATATATTAATTTTTTTA
2153 ATAATATA-ATT-ATTTTTT
1 ATAATATATATTAATTTTTT
2171 ATATTATAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 3 0.17
22 8 0.44
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATAATATATATTAATTTTTTTA
Found at i:2168 original size:17 final size:19
Alignment explanation
Indices: 2132--2168 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
2122 TTTAATAATA
*
2132 TAATATATATTAATTTTTT
1 TAATATATATTAATTATTT
2151 TAATA-ATA-TAATTATTT
1 TAATATATATTAATTATTT
2168 T
1 T
2169 TTATATTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 9 0.53
18 3 0.18
19 5 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TAATATATATTAATTATTT
Found at i:2178 original size:18 final size:17
Alignment explanation
Indices: 2132--2179 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
2122 TTTAATAATA
2132 TAATATATATTAATTTTTT
1 TAATA-ATA-TAATTTTTT
2151 TAATAATATAATTATTTT
1 TAATAATATAATT-TTTT
* *
2169 TTATATTATAA
1 TAATAATATAA
2180 CAATATACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 5 0.19
18 16 0.62
19 5 0.19
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATAATATAATTTTTT
Found at i:8606 original size:16 final size:17
Alignment explanation
Indices: 8580--8611 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
8570 CTGTGTTTTC
8580 AAATAAATAAAAAATAA
1 AAATAAATAAAAAATAA
8597 AAAT-AATAAAAAATA
1 AAATAAATAAAAAATA
8612 TATATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (17 bp):
AAATAAATAAAAAATAA
Found at i:9064 original size:4 final size:4
Alignment explanation
Indices: 9055--9081 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
9045 ATTTGATTGG
9055 ATTA ATTA ATTA ATTA ATTA ATTA ATT
1 ATTA ATTA ATTA ATTA ATTA ATTA ATT
9082 TTAATCCGAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (4 bp):
ATTA
Found at i:12155 original size:24 final size:24
Alignment explanation
Indices: 12100--12155 Score: 58
Period size: 24 Copynumber: 2.3 Consensus size: 24
12090 ATTGCATTTG
12100 TTTTTAAATTAAAAATCAATTGAA
1 TTTTTAAATTAAAAATCAATTGAA
**** * *
12124 GAGATAAATTAAAAATTAATTTAA
1 TTTTTAAATTAAAAATCAATTGAA
12148 TTTTTAAA
1 TTTTTAAA
12156 ATCACACTTT
Statistics
Matches: 22, Mismatches: 10, Indels: 0
0.69 0.31 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.52, C:0.02, G:0.05, T:0.41
Consensus pattern (24 bp):
TTTTTAAATTAAAAATCAATTGAA
Found at i:13229 original size:6 final size:6
Alignment explanation
Indices: 13218--13242 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
13208 GGTTGAGCCA
13218 TGGTTT TGGTTT TGGTTT TGGTTT T
1 TGGTTT TGGTTT TGGTTT TGGTTT T
13243 CGGTGGTGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (6 bp):
TGGTTT
Found at i:13855 original size:21 final size:21
Alignment explanation
Indices: 13813--13865 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
13803 TTATTAAAAA
13813 TTTAA-AATAT-ATATATTAT
1 TTTAATAATATAATATATTAT
13832 TTTAATAATATAATATTATT-T
1 TTTAATAATATAATA-TATTAT
*
13853 TTTAATATTATAA
1 TTTAATAATATAA
13866 CAATATACCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 5 0.17
20 5 0.17
21 16 0.53
22 4 0.13
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (21 bp):
TTTAATAATATAATATATTAT
Found at i:13860 original size:18 final size:20
Alignment explanation
Indices: 13813--13853 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
13803 TTATTAAAAA
13813 TTTAA-AATATATATATTAT
1 TTTAATAATATATATATTAT
13832 TTTAATAATATA-ATATTAT
1 TTTAATAATATATATATTAT
13851 TTT
1 TTT
13854 TTAATATTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTAATAATATATATATTAT
Found at i:18541 original size:3 final size:3
Alignment explanation
Indices: 18535--18582 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
18525 AACAAAAATG
* *
18535 TAA TAA TAA TAT TAA TGA T-A TAA TAA TAA TAA TAA TATA TAA TTAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA -TAA
18581 TA
1 TA
18583 TTTATAATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
2 2 0.05
3 31 0.79
4 6 0.15
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:18557 original size:17 final size:17
Alignment explanation
Indices: 18537--18582 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
18527 CAAAAATGTA
* *
18537 ATAATAATATTAATGAT
1 ATAATAATAATAATAAT
18554 ATAATAATAATAATAAT
1 ATAATAATAATAATAAT
18571 AT-ATAATTAATA
1 ATAATAA-TAATA
18583 TTTATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 4 0.15
17 22 0.85
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (17 bp):
ATAATAATAATAATAAT
Found at i:18560 original size:20 final size:19
Alignment explanation
Indices: 18535--18592 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 19
18525 AACAAAAATG
*
18535 TAATAATAATATTAATGATA
1 TAATAATAATAATAAT-ATA
18555 TAATAATAATAATAATATA
1 TAATAATAATAATAATATA
* *
18574 TAATTAATATTTATAATAT
1 TAA-TAATAATAATAATAT
18593 TTTTTTAATC
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 6 0.18
20 28 0.82
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAATAATAATAATAATATA
Found at i:18581 original size:14 final size:14
Alignment explanation
Indices: 18538--18582 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
18528 AAAAATGTAA
18538 TAATAATAT-TAAT
1 TAATAATATATAAT
*
18551 GATATAATA-ATAA-
1 TA-ATAATATATAAT
18564 TAATAATATATAAT
1 TAATAATATATAAT
18578 TAATA
1 TAATA
18583 TTTATAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
12 6 0.23
13 6 0.23
14 14 0.54
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (14 bp):
TAATAATATATAAT
Found at i:18581 original size:23 final size:23
Alignment explanation
Indices: 18535--18591 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
18525 AACAAAAATG
* *
18535 TAATAATAATATTAATGATATAA
1 TAATAATAATAATAATAATATAA
18558 TAATAATAATAATATATAAT-TAA
1 TAATAATAATAATA-ATAATATAA
* *
18581 TATTTATAATA
1 TAATAATAATA
18592 TTTTTTTAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 25 0.86
24 4 0.14
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
TAATAATAATAATAATAATATAA
Found at i:18962 original size:135 final size:135
Alignment explanation
Indices: 18721--19072 Score: 483
Period size: 135 Copynumber: 2.6 Consensus size: 135
18711 TGTTGGATTA
* * * *
18721 AACAAGTTATTCTCATTATGAACTTCTTCTCTCT--TATGGACGAGTTCTTCTCATTATAAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCGT-TGGATGAGTTCTTCTCATTATGAACTC
* * *
18784 TTCACTAAAAATGTTGACCCCTCAAGCAAGGCATCACTGATTCGAAATGTCATGAATCGTGTGAT
65 TTCACTAAAAATATTGATCCCTCAAGCAAGGCATCACTGATTCGAAATGTCATGAATCGAGTGAT
18849 AGGTCG
130 AGGTCG
*
18855 AACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGGGTTCTTCTCATTATGAACTCT
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
* * * * **
18920 TCACTAAAAATATTGATTCCTCAAGCGAGGCGTGACTGATTCGAAATGTTGTGAATCGAGTGATA
66 TCACTAAAAATATTGATCCCTCAAGCAAGGCATCACTGATTCGAAATGTCATGAATCGAGTGATA
18985 GGTCG
131 GGTCG
* * * *
18990 AACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATAAGTTCTTCTCATTATGAACTC
1 AACAAGCTCTTCTCATTATGAACTTCTTCTCTCTC-GTTGGATGAGTTCTTCTCATTATGAACTC
* * *
19055 TCCACTAGAAACATTGAT
65 TTCACTAAAAATATTGAT
19073 GTGAGATCGA
Statistics
Matches: 193, Mismatches: 22, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
134 32 0.17
135 119 0.62
136 42 0.22
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (135 bp):
AACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAACTCT
TCACTAAAAATATTGATCCCTCAAGCAAGGCATCACTGATTCGAAATGTCATGAATCGAGTGATA
GGTCG
Found at i:19097 original size:92 final size:90
Alignment explanation
Indices: 18987--19155 Score: 266
Period size: 92 Copynumber: 1.9 Consensus size: 90
18977 GAGTGATAGG
18987 TCGAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATAAGTTCTTCTCATTATGAA
1 TCGAACAAGCTCTTCTCATTATGAACTTATTCTCCCTC-GTCGGATAAGTTCTTCTCATTATGAA
19052 CTCTCCACTAGAAACATTGATGTGAGA
65 CTCTCCACT-GAAACATTGATGTGAGA
* * * * *
19079 TCGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
1 TCGAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCGTCGGATAAGTTCTTCTCATTATGAAC
*
19144 TCTTCACTGAAA
66 TCTCCACTGAAA
19156 ATGTTGATTC
Statistics
Matches: 71, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
90 4 0.06
91 32 0.45
92 35 0.49
ACGTcount: A:0.25, C:0.24, G:0.14, T:0.37
Consensus pattern (90 bp):
TCGAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCGTCGGATAAGTTCTTCTCATTATGAAC
TCTCCACTGAAACATTGATGTGAGA
Found at i:19249 original size:227 final size:227
Alignment explanation
Indices: 18852--19299 Score: 761
Period size: 227 Copynumber: 2.0 Consensus size: 227
18842 GTGTGATAGG
*
18852 TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGGGTTCTTCTCATTATGAAC
1 TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
**
18917 TCTTCACTAAAAATATTGATTCCTCAAGCGAGGCGTGACTGATTCGAAATGTTGTGAATCGAGTG
66 TCTTCACTAAAAATATTGATTCCTCAAGCGAGGCGTGACTGATTCGAAATGCCGTGAATCGAGTG
*
18982 ATAGGTCGAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATAAGTTCTTCTCATT
131 ATAGGTCAAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATAAGTTCTTCTCATT
19047 ATGAACTCTCCACTAGAAACATTGATGTGAGA
196 ATGAACTCTCCACTAGAAACATTGATGTGAGA
*
19079 TCGAACAAGTTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
1 TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
* * * *
19144 TCTTCACTGAAAATGTTGATTCCTCAAGTGAGGCGTGACTGATTTGAAATGCCGTGAATCGAGTG
66 TCTTCACTAAAAATATTGATTCCTCAAGCGAGGCGTGACTGATTCGAAATGCCGTGAATCGAGTG
* * * *
19209 ATAGGTCAAACAAGCTCTTCTCGTTATGAACTTCTTCTCCCTCTGTCGGATAAGTTTTTCTTATT
131 ATAGGTCAAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATAAGTTCTTCTCATT
* *
19274 ATGAACTCTCCACTGGAAATATTGAT
196 ATGAACTCTCCACTAGAAACATTGAT
19300 CCACCTTCTT
Statistics
Matches: 206, Mismatches: 15, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
227 206 1.00
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (227 bp):
TCGAACAAGCTCTTCTCATTATGAACTTCTTCTCTCTCGTTGGATGAGTTCTTCTCATTATGAAC
TCTTCACTAAAAATATTGATTCCTCAAGCGAGGCGTGACTGATTCGAAATGCCGTGAATCGAGTG
ATAGGTCAAACAAGCTCTTCTCATTATGAACTTATTCTCCCTCTGTCGGATAAGTTCTTCTCATT
ATGAACTCTCCACTAGAAACATTGATGTGAGA
Found at i:35603 original size:25 final size:25
Alignment explanation
Indices: 35569--35631 Score: 90
Period size: 25 Copynumber: 2.5 Consensus size: 25
35559 ACACATATAT
* *
35569 TATATTATATATAGACACACACGCA
1 TATAATATATATAAACACACACGCA
**
35594 TATAATATATATAAACGTACACGCA
1 TATAATATATATAAACACACACGCA
35619 TATAATATATATA
1 TATAATATATATA
35632 TATATATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (25 bp):
TATAATATATATAAACACACACGCA
Found at i:35630 original size:2 final size:2
Alignment explanation
Indices: 35618--35648 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
35608 ACGTACACGC
35618 AT AT A- 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
35649 TAAATAGCCC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:36198 original size:27 final size:27
Alignment explanation
Indices: 36168--36227 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
36158 GTTAATTTAG
36168 TTATTTCAAAACTCAAGGGTATTTCGA
1 TTATTTCAAAACTCAAGGGTATTTCGA
*** * *
36195 TTATTTTGGAGCTCAAGGGTATTTTGA
1 TTATTTCAAAACTCAAGGGTATTTCGA
*
36222 TCATTT
1 TTATTT
36228 TCATAGTTCA
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.18, T:0.43
Consensus pattern (27 bp):
TTATTTCAAAACTCAAGGGTATTTCGA
Found at i:39358 original size:26 final size:26
Alignment explanation
Indices: 39325--39375 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
39315 TATATTTTCA
39325 TTTCCTAAAATTTT-ATAAATTTATAT
1 TTTCCTAAAATTTTGA-AAATTTATAT
39351 TTTCCTAAAATTTTGAAAATTTATA
1 TTTCCTAAAATTTTGAAAATTTATA
39376 CTTCAAACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 23 0.96
27 1 0.04
ACGTcount: A:0.39, C:0.08, G:0.02, T:0.51
Consensus pattern (26 bp):
TTTCCTAAAATTTTGAAAATTTATAT
Found at i:42770 original size:14 final size:15
Alignment explanation
Indices: 42751--42779 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
42741 TGATTTCTAG
42751 CTATCTT-TAAAGGT
1 CTATCTTCTAAAGGT
42765 CTATCTTCTAAAGGT
1 CTATCTTCTAAAGGT
42780 GAAATGTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.28, C:0.17, G:0.14, T:0.41
Consensus pattern (15 bp):
CTATCTTCTAAAGGT
Found at i:47085 original size:21 final size:21
Alignment explanation
Indices: 47059--47098 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
47049 CCCCCTTTGA
*
47059 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
47080 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
47099 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:51575 original size:14 final size:14
Alignment explanation
Indices: 51556--51585 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
51546 AAAAAAATAC
51556 TATTGAATGATTAA
1 TATTGAATGATTAA
*
51570 TATTGAATTATTAA
1 TATTGAATGATTAA
51584 TA
1 TA
51586 GTGAGTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (14 bp):
TATTGAATGATTAA
Found at i:51823 original size:14 final size:14
Alignment explanation
Indices: 51769--51815 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
51759 AAAATTATAG
*
51769 AAATAATATTTTAA-
1 AAATAATA-TTAAAT
*
51783 AAATAATATTGACAT
1 AAATAATATT-AAAT
51798 AAATAATATTAAAT
1 AAATAATATTAAAT
51812 AAAT
1 AAAT
51816 TATTTTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 2 0.07
14 16 0.57
15 10 0.36
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (14 bp):
AAATAATATTAAAT
Found at i:51846 original size:23 final size:23
Alignment explanation
Indices: 51808--51868 Score: 70
Period size: 23 Copynumber: 2.7 Consensus size: 23
51798 AAATAATATT
* *
51808 AAATAAATTATTTTAATATTTTTA
1 AAATAAATAATATTAA-ATTTTTA
*
51832 AAAT-AATAATATTAAGTTTTTA
1 AAATAAATAATATTAAATTTTTA
*
51854 TAATAAATAATATTA
1 AAATAAATAATATTA
51869 TTTAGTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
22 9 0.28
23 19 0.59
24 4 0.12
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AAATAAATAATATTAAATTTTTA
Found at i:52029 original size:15 final size:15
Alignment explanation
Indices: 52006--52038 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
51996 ATGTAATTCA
52006 TTTTACGAAAAATAT
1 TTTTACGAAAAATAT
*
52021 TTTTTCGAAAAATAT
1 TTTTACGAAAAATAT
52036 TTT
1 TTT
52039 CAGTGAAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.39, C:0.06, G:0.06, T:0.48
Consensus pattern (15 bp):
TTTTACGAAAAATAT
Found at i:56172 original size:23 final size:23
Alignment explanation
Indices: 56127--56176 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
56117 TGTTTTTTAG
* *
56127 TATTATAATAATATATTAAATTA
1 TATTACAATAATATATGAAATTA
**
56150 TATTACAATAATATATGGTATTA
1 TATTACAATAATATATGAAATTA
56173 TATT
1 TATT
56177 TTTATTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (23 bp):
TATTACAATAATATATGAAATTA
Found at i:56187 original size:26 final size:25
Alignment explanation
Indices: 56158--56219 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 25
56148 TATATTACAA
* * *
56158 TAATATATGGTATTATATTTTTATTT
1 TAATATAT-ATATGATATTATTATTT
56184 TAATAATATATATGATATTATTATTT
1 TAAT-ATATATATGATATTATTATTT
56210 TAATAT-TATA
1 TAATATATATA
56220 ATTTTTAGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 4 0.12
25 2 0.06
26 22 0.69
27 4 0.12
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (25 bp):
TAATATATATATGATATTATTATTT
Found at i:56221 original size:31 final size:31
Alignment explanation
Indices: 56149--56221 Score: 85
Period size: 31 Copynumber: 2.3 Consensus size: 31
56139 ATATTAAATT
* * *
56149 ATATTACAATAATATATGGTATTATATTTTT
1 ATATTATAATAATATATGATATTATATTTTA
*
56180 ATTTTAATAAT-ATATATGATATTATTATTTTA
1 ATATT-ATAATAATATATGATATTA-TATTTTA
56212 ATATTATAAT
1 ATATTATAAT
56222 TTTTAGTATT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 21 0.60
32 14 0.40
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (31 bp):
ATATTATAATAATATATGATATTATATTTTA
Found at i:56231 original size:15 final size:15
Alignment explanation
Indices: 56198--56236 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
56188 AATATATATG
*
56198 ATATTATTA-TTTTA
1 ATATTATAATTTTTA
56212 ATATTATAATTTTTA
1 ATATTATAATTTTTA
*
56227 GTATTATAAT
1 ATATTATAAT
56237 AATATTTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 8 0.36
15 14 0.64
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
ATATTATAATTTTTA
Found at i:56456 original size:27 final size:26
Alignment explanation
Indices: 56387--56456 Score: 67
Period size: 27 Copynumber: 2.7 Consensus size: 26
56377 CAAATAATAT
*
56387 TAAAT-AAATTATTTCAAT-ATTTTAA
1 TAAATAAAATTATTT-ATTAATTTTAA
*
56412 -AAATAATAA-TATTAATTAATTTCTAA
1 TAAATAA-AATTATTTATTAATTT-TAA
56438 TAAATAAAATTATTTATTA
1 TAAATAAAATTATTTATTA
56457 TACTTGATAT
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
24 6 0.17
25 9 0.25
26 7 0.19
27 14 0.39
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (26 bp):
TAAATAAAATTATTTATTAATTTTAA
Found at i:57816 original size:18 final size:19
Alignment explanation
Indices: 57783--57819 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
57773 ATTATTCTTC
*
57783 TATTTTATTTTTTTAAAAA
1 TATTTTATTTTATTAAAAA
57802 TATTTT-TTTTATTAAAAA
1 TATTTTATTTTATTAAAAA
57820 AATAACTCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTTTATTTTATTAAAAA
Found at i:57820 original size:19 final size:19
Alignment explanation
Indices: 57783--57820 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
57773 ATTATTCTTC
*
57783 TATTTTATTTTTTTAAAAA
1 TATTTTATTTTTTAAAAAA
57802 TATTTT-TTTTATTAAAAAA
1 TATTTTATTTT-TTAAAAAA
57821 ATAACTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTTATTTTTTAAAAAA
Found at i:62457 original size:65 final size:64
Alignment explanation
Indices: 62382--62541 Score: 250
Period size: 65 Copynumber: 2.5 Consensus size: 64
62372 GATTTAATTG
* *
62382 AACATTGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGGTTTTAT-AA
1 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTT-TCAA
* * *
62446 AATCATCGAATGCATATGATGCATCGATGCACATACCATGCATCGATGCACTCATGCTTTTTCAA
1 AA-CATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTTCAA
62511 AACATCGAATGCATTTTATGCATCGATGCAC
1 AACATCGAATGCATTTTATGCATCGATGCAC
62542 TCTTAGTGCA
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
64 30 0.34
65 57 0.66
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (64 bp):
AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTTTTTCAA
Found at i:68925 original size:127 final size:128
Alignment explanation
Indices: 68790--69133 Score: 548
Period size: 128 Copynumber: 2.7 Consensus size: 128
68780 TATATAAAAT
* * *
68790 ATTTATTTATTT-AGAAATATCAGAAAAGGGCTTCTAGGTGCTTTAAGACAACTCTTTTCTTAAT
1 ATTTATTTATTTAAG-AATATCAGAAAAGGACTTCTAGGTGCTTTAAGACAGCTCATTTCTTAAT
* *
68854 A-TAAAAAATAAATAAATATTAAAACATTTATTTAAAAATAGTTATAATTTATAAAAGTAAGAC
65 ATTAAAAAATATATAAATATTAAAACATTTATTTAAAAATAGATATAATTTATAAAAGTAAGAC
* * *
68917 ATTTATTTATTTAAGAATATTAGAAAATGACTTCTAGGTGCTTTAAGACAGCCCATTTCTTAATA
1 ATTTATTTATTTAAGAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACAGCTCATTTCTTAATA
*
68982 TTAAAAAATATATAAATATTAAAACATTTATTTAAAAATAGATATAATTTATAAAAGTAAGAT
66 TTAAAAAATATATAAATATTAAAACATTTATTTAAAAATAGATATAATTTATAAAAGTAAGAC
* * * *
69045 ATTTATTTATTTAAGAATATCAGAAAAGAACTTATAGGTACTTTTAGACAGCTCATTTCTTAATA
1 ATTTATTTATTTAAGAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACAGCTCATTTCTTAATA
69110 TTAAAAAATATATAAATATTAAAA
66 TTAAAAAATATATAAATATTAAAA
69134 TATGATTATT
Statistics
Matches: 199, Mismatches: 16, Indels: 3
0.91 0.07 0.01
Matches are distributed among these distances:
127 56 0.28
128 143 0.72
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (128 bp):
ATTTATTTATTTAAGAATATCAGAAAAGGACTTCTAGGTGCTTTAAGACAGCTCATTTCTTAATA
TTAAAAAATATATAAATATTAAAACATTTATTTAAAAATAGATATAATTTATAAAAGTAAGAC
Found at i:69317 original size:19 final size:19
Alignment explanation
Indices: 69293--69329 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
69283 ATGACCAACA
* *
69293 AAATCGTAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
69312 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
69330 CATTATCGCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.24
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:69419 original size:20 final size:20
Alignment explanation
Indices: 69394--69441 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
69384 CGCATTTTAT
*
69394 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATATA
69414 AATCGCAATGCGAATATATA
1 AATCGCAATGCGAATATATA
69434 AATCGCAA
1 AATCGCAA
69442 CGAGATAACG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.23
Consensus pattern (20 bp):
AATCGCAATGCGAATATATA
Found at i:69480 original size:61 final size:61
Alignment explanation
Indices: 69415--69546 Score: 142
Period size: 61 Copynumber: 2.2 Consensus size: 61
69405 GAATATGTAA
* *
69415 ATCGCAATGCGAATATAT-A-AATCGCAACGAGATAACGCATGATCGCAACGCGATTCTGACT
1 ATCGCAATGCG-AT-TATGACAACCGCAACGAGATAACACATGATCGCAACGCGATTCTGACT
* * * * * * *
69476 ATCGCAACGCGATTCTGACTACCGCAACGCGATAATACGTGATCGCAATGCGATTCTGACT
1 ATCGCAATGCGATTATGACAACCGCAACGAGATAACACATGATCGCAACGCGATTCTGACT
*
69537 ATCACAATGC
1 ATCGCAATGC
69547 TATAATACGT
Statistics
Matches: 58, Mismatches: 11, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
59 2 0.03
60 3 0.05
61 53 0.91
ACGTcount: A:0.33, C:0.26, G:0.20, T:0.22
Consensus pattern (61 bp):
ATCGCAATGCGATTATGACAACCGCAACGAGATAACACATGATCGCAACGCGATTCTGACT
Found at i:69481 original size:20 final size:20
Alignment explanation
Indices: 69456--69603 Score: 122
Period size: 20 Copynumber: 7.3 Consensus size: 20
69446 ATAACGCATG
69456 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
69476 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
* **
69496 ACCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
*
69516 GATCGCAATGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
* * * **
69537 ATCACAATGCTATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
* *
69557 GATCGCAACACGA-TCATGACC
1 -ATCGCAACGCGATTC-TGACT
69578 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
69598 AACGCA
1 ATCGCA
69604 TCACTGAATT
Statistics
Matches: 99, Mismatches: 21, Indels: 16
0.73 0.15 0.12
Matches are distributed among these distances:
19 4 0.04
20 67 0.68
21 24 0.24
22 4 0.04
ACGTcount: A:0.30, C:0.28, G:0.19, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:69521 original size:41 final size:41
Alignment explanation
Indices: 69476--69590 Score: 151
Period size: 41 Copynumber: 2.8 Consensus size: 41
69466 GATTCTGACT
*
69476 ATCGCAACGCGATTCTGACTACCGCAACGCGATAATACGTG
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACGTG
* * * *
69517 ATCGCAATGCGATTCTGACTATCACAATGCTATAATACGTG
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACGTG
* *
69558 ATCGCAACACGA-TCATGACCATCGCAACGCGAT
1 ATCGCAACGCGATTC-TGACTATCGCAACGCGAT
69591 TCTGACTAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 2
0.83 0.15 0.03
Matches are distributed among these distances:
40 2 0.03
41 60 0.97
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.22
Consensus pattern (41 bp):
ATCGCAACGCGATTCTGACTATCGCAACGCGATAATACGTG
Found at i:69528 original size:21 final size:21
Alignment explanation
Indices: 69498--69564 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
69488 TTCTGACTAC
*
69498 CGCAACGCGATAATACGTGAT
1 CGCAATGCGATAATACGTGAT
**
69519 CGCAATGCGATTCTGAC-T-AT
1 CGCAATGCGATAAT-ACGTGAT
* *
69539 CACAATGCTATAATACGTGAT
1 CGCAATGCGATAATACGTGAT
69560 CGCAA
1 CGCAA
69565 CACGATCATG
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
19 2 0.06
20 13 0.37
21 18 0.51
22 2 0.06
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
CGCAATGCGATAATACGTGAT
Found at i:70432 original size:24 final size:24
Alignment explanation
Indices: 70400--70446 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
70390 AGTCGGTATT
70400 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
*
70424 CGAACTTTGATCTTGGTCAATAC
1 CGAAATTTGATCTTGGTCAATAC
70447 TCAGATTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Found at i:70458 original size:24 final size:24
Alignment explanation
Indices: 70405--70451 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
70395 GTATTCGAAA
*
70405 TTTGATCTTGGTCAATACCCGAAC
1 TTTGATCTTGGTCAATACCAGAAC
70429 TTTGATCTTGGTCAATACTCAGA
1 TTTGATCTTGGTCAATAC-CAGA
70452 TTTTGATGAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 18 0.86
25 3 0.14
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAGAAC
Done.