Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002248.1 Hibiscus syriacus cultivar Beakdansim tig00004567_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: 59910
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:3928 original size:2 final size:2
Alignment explanation
Indices: 3923--3982 Score: 99
Period size: 2 Copynumber: 31.5 Consensus size: 2
3913 AAACAAACAA
3923 AT AT AT A- AT -T A- 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
3962 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
3983 CAAAGGTTAG
Statistics
Matches: 55, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.05
2 52 0.95
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5724 original size:15 final size:15
Alignment explanation
Indices: 5704--5734 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
5694 CTTCACGCTT
5704 AATTGAATGGGGATG
1 AATTGAATGGGGATG
5719 AATTGAATGGGGATG
1 AATTGAATGGGGATG
5734 A
1 A
5735 GTACATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.39, T:0.26
Consensus pattern (15 bp):
AATTGAATGGGGATG
Found at i:6855 original size:23 final size:22
Alignment explanation
Indices: 6829--6871 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
6819 ATTTATCTGT
6829 TTTTGTGGCACACTTTTCTATGC
1 TTTTGTGGCAC-CTTTTCTATGC
* *
6852 TTTTTTGGCACGTTTTCTAT
1 TTTTGTGGCACCTTTTCTAT
6872 CTTCTTTATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.12, C:0.19, G:0.16, T:0.53
Consensus pattern (22 bp):
TTTTGTGGCACCTTTTCTATGC
Found at i:6870 original size:22 final size:24
Alignment explanation
Indices: 6828--6871 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
6818 AATTTATCTG
6828 TTTTTGTGGCACACTTTTCTATGC
1 TTTTTGTGGCACACTTTTCTATGC
*
6852 TTTTT-TGGCAC-GTTTTCTAT
1 TTTTTGTGGCACACTTTTCTAT
6872 CTTCTTTATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (24 bp):
TTTTTGTGGCACACTTTTCTATGC
Found at i:9170 original size:29 final size:30
Alignment explanation
Indices: 9071--9192 Score: 158
Period size: 30 Copynumber: 4.1 Consensus size: 30
9061 TAAATGACCC
9071 AAAATAGCAAAAACAAAAACTTAAAGGACT
1 AAAATAGCAAAAACAAAAACTTAAAGGACT
* *
9101 AAACTAGCAAAGACAAAAACTTAAAGGACT
1 AAAATAGCAAAAACAAAAACTTAAAGGACT
* *
9131 -AAATAACAAAAACATAAACTTAAAGGACT
1 AAAATAGCAAAAACAAAAACTTAAAGGACT
* * * *
9160 AAAATAGAAAAAACATAGA-TTAAAGGGCT
1 AAAATAGCAAAAACAAAAACTTAAAGGACT
9189 AAAA
1 AAAA
9193 ATGAAAAAAT
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
29 38 0.47
30 43 0.53
ACGTcount: A:0.61, C:0.12, G:0.11, T:0.15
Consensus pattern (30 bp):
AAAATAGCAAAAACAAAAACTTAAAGGACT
Found at i:9198 original size:29 final size:30
Alignment explanation
Indices: 9071--9201 Score: 144
Period size: 29 Copynumber: 4.4 Consensus size: 30
9061 TAAATGACCC
* *
9071 AAAATAGCAAAAACAAAAACTTAAAGGACT
1 AAAATAGAAAAAACATAAACTTAAAGGACT
* * * *
9101 AAACTAGCAAAGACAAAAACTTAAAGGACT
1 AAAATAGAAAAAACATAAACTTAAAGGACT
9131 -AAATA-ACAAAAACATAAACTTAAAGGACT
1 AAAATAGA-AAAAACATAAACTTAAAGGACT
* *
9160 AAAATAGAAAAAACATAGA-TTAAAGGGCT
1 AAAATAGAAAAAACATAAACTTAAAGGACT
9189 AAAA-ATGAAAAAA
1 AAAATA-GAAAAAA
9202 TAGCGATTTA
Statistics
Matches: 89, Mismatches: 8, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
28 1 0.01
29 44 0.49
30 43 0.48
31 1 0.01
ACGTcount: A:0.63, C:0.11, G:0.11, T:0.15
Consensus pattern (30 bp):
AAAATAGAAAAAACATAAACTTAAAGGACT
Found at i:9201 original size:59 final size:59
Alignment explanation
Indices: 9079--9191 Score: 147
Period size: 59 Copynumber: 1.9 Consensus size: 59
9069 CCAAAATAGC
* * * *
9079 AAAAACAAAAACTTAAAGGACTAAACTAGCAAAGACAAAAACTTAAAGGACTAAATAAC
1 AAAAACAAAAACTTAAAGGACTAAAATAGAAAAAACAAAAACTTAAAGGACTAAATAAA
* * * *
9138 AAAAACATAAACTTAAAGGACTAAAATAGAAAAAACATAGA-TTAAAGGGCTAAA
1 AAAAACAAAAACTTAAAGGACTAAAATAGAAAAAACAAAAACTTAAAGGACTAAA
9192 AATGAAAAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
58 12 0.26
59 35 0.74
ACGTcount: A:0.61, C:0.12, G:0.12, T:0.15
Consensus pattern (59 bp):
AAAAACAAAAACTTAAAGGACTAAAATAGAAAAAACAAAAACTTAAAGGACTAAATAAA
Found at i:9209 original size:29 final size:31
Alignment explanation
Indices: 9057--9226 Score: 93
Period size: 30 Copynumber: 5.6 Consensus size: 31
9047 AATCATATTC
* ** * *
9057 GATTTAAATGACCCAAAATAGCAAAAACAAA
1 GATTTAAAGGACTAAAAATAGAAAAAACAGA
* * * * * *
9088 AACTTAAAGGACT-AAACTAGCAAAGACAAA
1 GATTTAAAGGACTAAAAATAGAAAAAACAGA
* * *
9118 AACTTAAAGGACT--AAATA-ACAAAAACATA
1 GATTTAAAGGACTAAAAATAGA-AAAAACAGA
* * *
9147 AACTTAAAGGACT-AAAATAGAAAAAACATA
1 GATTTAAAGGACTAAAAATAGAAAAAACAGA
* * *
9177 GA-TTAAAGGGCTAAAAAT-GAAAAAATAGC
1 GATTTAAAGGACTAAAAATAGAAAAAACAGA
9206 GATTTAAAGGACTAAACAATA
1 GATTTAAAGGACTAAA-AATA
9227 ATTACAAATA
Statistics
Matches: 116, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
29 43 0.37
30 60 0.52
31 13 0.11
ACGTcount: A:0.58, C:0.12, G:0.12, T:0.17
Consensus pattern (31 bp):
GATTTAAAGGACTAAAAATAGAAAAAACAGA
Found at i:9813 original size:23 final size:24
Alignment explanation
Indices: 9787--9831 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
9777 AATTAAGTTT
9787 TAATCTTA-AAACAATTTCAAAAA
1 TAATCTTACAAACAATTTCAAAAA
* **
9810 TAATTTTACAAAGTATTTCAAA
1 TAATCTTACAAACAATTTCAAA
9832 CCATTTCAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 7 0.39
24 11 0.61
ACGTcount: A:0.51, C:0.11, G:0.02, T:0.36
Consensus pattern (24 bp):
TAATCTTACAAACAATTTCAAAAA
Found at i:15751 original size:20 final size:21
Alignment explanation
Indices: 15726--15788 Score: 74
Period size: 23 Copynumber: 3.0 Consensus size: 21
15716 TTTTGGTGCA
*
15726 GAGGGAATCGA-TCCCCCCAT
1 GAGGGAACCGATTCCCCCCAT
**
15746 GAGGGAACCGATTCCCCCTTT
1 GAGGGAACCGATTCCCCCCAT
15767 GAAGGGGAACCGATTCCCCCCA
1 G-A-GGGAACCGATTCCCCCCA
15789 CAGGGGAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
20 10 0.29
21 8 0.23
22 1 0.03
23 16 0.46
ACGTcount: A:0.24, C:0.35, G:0.25, T:0.16
Consensus pattern (21 bp):
GAGGGAACCGATTCCCCCCAT
Found at i:18121 original size:35 final size:35
Alignment explanation
Indices: 18081--18150 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
18071 GTTTTAAATT
18081 TAAATGATAAATGGGAGAAGTGTTAAAGTAAGGGG
1 TAAATGATAAATGGGAGAAGTGTTAAAGTAAGGGG
*
18116 TAAATGATAAATTGGAGAAGTGTTAAAGTAAGGGG
1 TAAATGATAAATGGGAGAAGTGTTAAAGTAAGGGG
18151 GAGTAATTTC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.43, C:0.00, G:0.33, T:0.24
Consensus pattern (35 bp):
TAAATGATAAATGGGAGAAGTGTTAAAGTAAGGGG
Found at i:20700 original size:18 final size:17
Alignment explanation
Indices: 20655--20690 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
20645 ATTACATTAT
*
20655 TAAAAATATATAAAAAA
1 TAAAAATTTATAAAAAA
20672 TAAAAATTTATAAAAAA
1 TAAAAATTTATAAAAAA
20689 TA
1 TA
20691 CATTATTTAT
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (17 bp):
TAAAAATTTATAAAAAA
Found at i:21100 original size:28 final size:28
Alignment explanation
Indices: 21068--21143 Score: 116
Period size: 28 Copynumber: 2.7 Consensus size: 28
21058 TAAGGTTTAG
* * *
21068 GATTTAGGGTTTATATTTTATGTAATAT
1 GATTTAAGGTTTAGAGTTTATGTAATAT
*
21096 GATTTAAGGTTTAGAGTTTATGTGATAT
1 GATTTAAGGTTTAGAGTTTATGTAATAT
21124 GATTTAAGGTTTAGAGTTTA
1 GATTTAAGGTTTAGAGTTTA
21144 GGGTTTATGT
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 44 1.00
ACGTcount: A:0.29, C:0.00, G:0.22, T:0.49
Consensus pattern (28 bp):
GATTTAAGGTTTAGAGTTTATGTAATAT
Found at i:21152 original size:28 final size:28
Alignment explanation
Indices: 21093--21297 Score: 141
Period size: 28 Copynumber: 7.1 Consensus size: 28
21083 TTTTATGTAA
* *
21093 TATGATTTAAGGTTTAGAGTTTA-TGTGA
1 TATGATTTAAGGTTTAGAGTTTAGGGT-T
21121 TATGATTTAAGGTTTAGAGTTTAGGGTT
1 TATGATTTAAGGTTTAGAGTTTAGGGTT
* * *
21149 TATG-TATTAGGGGTTAGGGTTTAGGGTT
1 TATGAT-TTAAGGTTTAGAGTTTAGGGTT
* * * * *
21177 TAGGGTTT-ATGTAATATGA-TTTAAGGTT
1 TATGATTTAAGGT-TTA-GAGTTTAGGGTT
*
21205 TATGTATTAGGGATTAAGGTTTAGGGTTTAGGGTT
1 TATG-A-T-----TTAAGGTTTAGAGTTTAGGGTT
*
21240 TATGATTTAAGGTTTATAGTTTAGGGTT
1 TATGATTTAAGGTTTAGAGTTTAGGGTT
* *
21268 TAT-ATATTAAGGGTTAGGGTTTAGGGTT
1 TATGAT-TTAAGGTTTAGAGTTTAGGGTT
21296 TA
1 TA
21298 AGTTATGCTC
Statistics
Matches: 139, Mismatches: 23, Indels: 30
0.72 0.12 0.16
Matches are distributed among these distances:
27 4 0.03
28 108 0.78
29 4 0.03
30 1 0.01
33 1 0.01
34 2 0.01
35 16 0.12
36 3 0.02
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (28 bp):
TATGATTTAAGGTTTAGAGTTTAGGGTT
Found at i:21165 original size:7 final size:7
Alignment explanation
Indices: 21126--21297 Score: 93
Period size: 7 Copynumber: 24.6 Consensus size: 7
21116 TGTGATATGA
*
21126 TTTAAGG
1 TTTAGGG
*
21133 TTTAGAG
1 TTTAGGG
21140 TTTAGGG
1 TTTAGGG
*
21147 TTTA-TG
1 TTTAGGG
21153 TATTAGGG
1 T-TTAGGG
*
21161 GTTAGGG
1 TTTAGGG
21168 TTTAGGG
1 TTTAGGG
21175 TTTAGGG
1 TTTAGGG
*
21182 TTTA-TG
1 TTTAGGG
* * *
21188 TAATATGA
1 T-TTAGGG
*
21196 TTTAAGG
1 TTTAGGG
*
21203 TTTA-TG
1 TTTAGGG
21209 TATTAGGG
1 T-TTAGGG
* *
21217 ATTAAGG
1 TTTAGGG
21224 TTTAGGG
1 TTTAGGG
21231 TTTAGGG
1 TTTAGGG
* *
21238 TTTATGA
1 TTTAGGG
*
21245 TTTAAGG
1 TTTAGGG
**
21252 TTTATAG
1 TTTAGGG
21259 TTTAGGG
1 TTTAGGG
**
21266 TTTA-TA
1 TTTAGGG
21272 TATTAAGGG
1 T-TT-AGGG
21281 -TTAGGG
1 TTTAGGG
21287 TTTAGGG
1 TTTAGGG
21294 TTTA
1 TTTA
21298 AGTTATGCTC
Statistics
Matches: 123, Mismatches: 32, Indels: 20
0.70 0.18 0.11
Matches are distributed among these distances:
6 11 0.09
7 108 0.88
8 4 0.03
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:21216 original size:35 final size:35
Alignment explanation
Indices: 21104--21206 Score: 134
Period size: 35 Copynumber: 2.9 Consensus size: 35
21094 ATGATTTAAG
* *
21104 GTTTAGAGTTTATGTGATATGATTTAAGGTTTAGA
1 GTTTAGGGTTTATGTAATATGATTTAAGGTTTAGA
* * ** * *
21139 GTTTAGGGTTTATGTATTAGGGGTTAGGGTTTAGG
1 GTTTAGGGTTTATGTAATATGATTTAAGGTTTAGA
21174 GTTTAGGGTTTATGTAATATGATTTAAGGTTTA
1 GTTTAGGGTTTATGTAATATGATTTAAGGTTTA
21207 TGTATTAGGG
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
35 55 1.00
ACGTcount: A:0.24, C:0.00, G:0.30, T:0.46
Consensus pattern (35 bp):
GTTTAGGGTTTATGTAATATGATTTAAGGTTTAGA
Found at i:21291 original size:56 final size:56
Alignment explanation
Indices: 21121--21297 Score: 178
Period size: 56 Copynumber: 3.0 Consensus size: 56
21111 GTTTATGTGA
* * *
21121 TATGATTTAAGGTTTAGAGTTTAGGGTTTATGTATTAGGGGTTAGGGTTTAGGGTT
1 TATGATTTAAGGTTTATAGTTTAGGGTTTATATATTAAGGGTTAGGGTTTAGGGTT
* * * * * *
21177 TAGGGTTT-ATG-TAATATGATTTAAGGTTTATGTATTAGGGATTAAGGTTTAGGGTTTAGGGTT
1 TATGATTTAAGGTTTATA-G-TTTAGGGTTTA--TA-T----ATTAAGGGTTAGGGTTTAGGGTT
21240 TATGATTTAAGGTTTATAGTTTAGGGTTTATATATTAAGGGTTAGGGTTTAGGGTT
1 TATGATTTAAGGTTTATAGTTTAGGGTTTATATATTAAGGGTTAGGGTTTAGGGTT
21296 TA
1 TA
21298 AGTTATGCTC
Statistics
Matches: 95, Mismatches: 15, Indels: 22
0.72 0.11 0.17
Matches are distributed among these distances:
54 3 0.03
55 3 0.03
56 40 0.42
58 1 0.01
59 1 0.01
60 1 0.01
61 2 0.02
63 37 0.39
64 3 0.03
65 4 0.04
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (56 bp):
TATGATTTAAGGTTTATAGTTTAGGGTTTATATATTAAGGGTTAGGGTTTAGGGTT
Found at i:22661 original size:180 final size:180
Alignment explanation
Indices: 22352--22704 Score: 557
Period size: 180 Copynumber: 2.0 Consensus size: 180
22342 ATAGGAGTGC
* *
22352 GTGTATCTAGATGCATCCTCAATGAAAAGGAAGTAAGACAGTATCTGGAATGCTAGATTGTACTC
1 GTGTATCTAGATGCATCCTCAATGAAAAGGAAATAAGACAGTATCTGGAATGCTAGACTGTACTC
* * *
22417 GATCCATGAGCATAATCATAAAAATAAAAATACCATATTGTCTTTGGAACCTACAGGATCATTTG
66 GATCCATGAGCATAATCATAAAAATAAAAATACCATAGTGTCTTAGCAACCTACAGGATCATTTG
*
22482 CAACTGGATTTTTCTGCTTCGCCTGACTTCCAGAATTCAAGGGAGTGTGT
131 CAACTGGATTTTTCTCCTTCGCCTGACTTCCAGAATTCAAGGGAGTGTGT
* * *
22532 GTGTATGTAGATGCATCCTCAGTGAAAAGGAAATAAGACAGT-TACTGGAATGCTAGACTGTATT
1 GTGTATCTAGATGCATCCTCAATGAAAAGGAAATAAGACAGTAT-CTGGAATGCTAGACTGTACT
*
22596 CGATCCATGAGCATAATCATAAAAATAAAAATACCATAGTGTCCTTAGCAA-CTGCAGGATCATT
65 CGATCCATGAGCATAATCATAAAAATAAAAATACCATAGTGT-CTTAGCAACCTACAGGATCATT
* * *
22660 TGCAACTGGATTTTTCTCCTTTGCTTGACTTCCATAATTCAAGGG
129 TGCAACTGGATTTTTCTCCTTCGCCTGACTTCCAGAATTCAAGGG
22705 TCCTGATGTT
Statistics
Matches: 158, Mismatches: 13, Indels: 4
0.90 0.07 0.02
Matches are distributed among these distances:
179 1 0.01
180 151 0.96
181 6 0.04
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (180 bp):
GTGTATCTAGATGCATCCTCAATGAAAAGGAAATAAGACAGTATCTGGAATGCTAGACTGTACTC
GATCCATGAGCATAATCATAAAAATAAAAATACCATAGTGTCTTAGCAACCTACAGGATCATTTG
CAACTGGATTTTTCTCCTTCGCCTGACTTCCAGAATTCAAGGGAGTGTGT
Found at i:23223 original size:11 final size:11
Alignment explanation
Indices: 23207--23290 Score: 80
Period size: 11 Copynumber: 7.5 Consensus size: 11
23197 TAACTCATCC
23207 TCGAGCTT-AA
1 TCGAGCTTGAA
23217 GTCGAGCTTGAA
1 -TCGAGCTTGAA
* *
23229 TTGAGCTTACAA
1 TCGAGCTT-GAA
23241 TCGAGCTTGAA
1 TCGAGCTTGAA
**
23252 TCGAGCTCACAA
1 TCGAGCT-TGAA
23264 TCGAGCTTGAA
1 TCGAGCTTGAA
* *
23275 TCGAGTTTCAA
1 TCGAGCTTGAA
23286 TCGAG
1 TCGAG
23291 TTCGAGTCTC
Statistics
Matches: 60, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
11 40 0.67
12 20 0.33
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:23247 original size:23 final size:23
Alignment explanation
Indices: 23207--23290 Score: 118
Period size: 23 Copynumber: 3.7 Consensus size: 23
23197 TAACTCATCC
*
23207 TCGAGCTTA-AGTCGAGCTTGAA
1 TCGAGCTTACAATCGAGCTTGAA
*
23229 TTGAGCTTACAATCGAGCTTGAA
1 TCGAGCTTACAATCGAGCTTGAA
*
23252 TCGAGCTCACAATCGAGCTTGAA
1 TCGAGCTTACAATCGAGCTTGAA
*
23275 TCGAG-TTTCAATCGAG
1 TCGAGCTTACAATCGAG
23291 TTCGAGTCTC
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
22 17 0.31
23 38 0.69
ACGTcount: A:0.29, C:0.20, G:0.24, T:0.27
Consensus pattern (23 bp):
TCGAGCTTACAATCGAGCTTGAA
Found at i:25071 original size:17 final size:17
Alignment explanation
Indices: 25049--25089 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
25039 GATTAAGCGT
25049 TGAATGATTCAATGATC
1 TGAATGATTCAATGATC
*
25066 TGAATGATTCAATGCTC
1 TGAATGATTCAATGATC
*
25083 TGTATGA
1 TGAATGA
25090 ATTGACTCTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (17 bp):
TGAATGATTCAATGATC
Found at i:27942 original size:21 final size:20
Alignment explanation
Indices: 27911--27952 Score: 50
Period size: 19 Copynumber: 2.0 Consensus size: 20
27901 CTCGAGAATC
27911 TCACCCAAAAAC-CTTAAAA
1 TCACCCAAAAACTCTTAAAA
*
27930 TCACCCAGCAAAACTTTTAAAA
1 TCACCCA--AAAACTCTTAAAA
27952 T
1 T
27953 TCTTGAACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 7 0.37
21 5 0.26
22 7 0.37
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (20 bp):
TCACCCAAAAACTCTTAAAA
Found at i:28380 original size:177 final size:177
Alignment explanation
Indices: 28084--28413 Score: 572
Period size: 177 Copynumber: 1.9 Consensus size: 177
28074 AGTCAAACTC
*
28084 AAAATGGGTTTTCTTTTTCAATTAATCCAAAGTCTCATTTGTGTCTTTCATAAATTAGGTGACCT
1 AAAATGGGTTTTCTTTCTCAATTAATCCAAAGTCTCATTTGTGTCTTTCATAAATTAGGTGACCT
* *
28149 AATTGTAATCTTAGTGAAAATTGGGTGAAATATTTGTAATCTTACTAATATTTAGATGGCATGTG
66 AATTGTAATCTTAGTAAAAATTAGGTGAAATATTTGTAATCTTACTAATATTTAGATGGCATGTG
28214 CTGTAATTTACC-AAATGAGAAAACAATAAGAAAAAACTCAAAATGAG
131 CTGTAA-TTACCAAAATGAGAAAACAATAAGAAAAAACTCAAAATGAG
* *
28261 AAAATGGGTTTTCTTTCTCAATTAATCCAATGTCTCATTTGTGTCTTTCTTAAATTAGGTGACCT
1 AAAATGGGTTTTCTTTCTCAATTAATCCAAAGTCTCATTTGTGTCTTTCATAAATTAGGTGACCT
** *
28326 AATTGTAATCTTTTTAAAAATTAGGTGAAATATTTGTAATCTTACTAATATTTAGATTGCATGTG
66 AATTGTAATCTTAGTAAAAATTAGGTGAAATATTTGTAATCTTACTAATATTTAGATGGCATGTG
28391 CTGTAATTACCAAAATGAGAAAA
131 CTGTAATTACCAAAATGAGAAAA
28414 TCATCAAGAA
Statistics
Matches: 144, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
176 5 0.03
177 139 0.97
ACGTcount: A:0.35, C:0.12, G:0.15, T:0.38
Consensus pattern (177 bp):
AAAATGGGTTTTCTTTCTCAATTAATCCAAAGTCTCATTTGTGTCTTTCATAAATTAGGTGACCT
AATTGTAATCTTAGTAAAAATTAGGTGAAATATTTGTAATCTTACTAATATTTAGATGGCATGTG
CTGTAATTACCAAAATGAGAAAACAATAAGAAAAAACTCAAAATGAG
Found at i:34194 original size:134 final size:133
Alignment explanation
Indices: 34043--34340 Score: 416
Period size: 134 Copynumber: 2.2 Consensus size: 133
34033 GAACCGAGGT
* * * * * *
34043 TGATTTGCTTCGTTGTTCTTCAGGAAGACCAAATATGAAAGAAGAATAATTTGCTCCACTCTTCT
1 TGATTTGCTTC-ATGTTCTTCAGGAAGACCAAATATGAAAGAAGAAGAATCTGATACACTCTTCC
*** * *
34108 TTAGGGGAGATCAGACTAGACAAATATTTGATCCACTTCATTGTTCTTCAGGGAATATTGAATCA
65 TTAGGGGAGATCAGACTAGACAAATATTTGATCCACTTCACCATTCTTCAGAGAAGATTGAATCA
34173 AACA
130 AACA
* *
34177 TGATTTGCTTCACTGTTCTTTAGGAAGACAAAATATGAAAGAAGAAGAATCTGATACACTCTTCC
1 TGATTTGCTTCA-TGTTCTTCAGGAAGACCAAATATGAAAGAAGAAGAATCTGATACACTCTTCC
* * *
34242 TTAGGGGAGATCAGACTCGAGAAATATTTGATCCACTTCGCCATTCTTCAGAGAAGATTGAATCA
65 TTAGGGGAGATCAGACTAGACAAATATTTGATCCACTTCACCATTCTTCAGAGAAGATTGAATCA
*
34307 AACT
130 AACA
34311 TGATTTGCTTCGATGTTCTTCAGGAAGACC
1 TGATTTGCTTC-ATGTTCTTCAGGAAGACC
34341 TGATCTAAAG
Statistics
Matches: 143, Mismatches: 19, Indels: 4
0.86 0.11 0.02
Matches are distributed among these distances:
134 142 0.99
135 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Consensus pattern (133 bp):
TGATTTGCTTCATGTTCTTCAGGAAGACCAAATATGAAAGAAGAAGAATCTGATACACTCTTCCT
TAGGGGAGATCAGACTAGACAAATATTTGATCCACTTCACCATTCTTCAGAGAAGATTGAATCAA
ACA
Found at i:34437 original size:67 final size:67
Alignment explanation
Indices: 34359--34775 Score: 342
Period size: 67 Copynumber: 6.6 Consensus size: 67
34349 AGGATTCAAT
* *
34359 TCTCTCCACGAGGAAGTCAAGGATTGGTTCCTCTTCAAAAGGGAGTCATGAAAAATAAAGATTGA
1 TCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTCATGAAAAATAAAGATTGA
34424 CC
66 CC
* *
34426 TCTCTTTACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTCAGGAATAAA-AAAGATTG
1 TCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTCATGAA-AAATAAAGATTG
34490 ACC
65 ACC
* * ** *
34493 TCTCTTTACGAGGAAATCAAGGATTGAATCCTCTT--C-A-GGA---AT----AACAAAGATTGA
1 TCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTCATGAAAAATAAAGATTGA
*
34547 CT
66 CC
* * *
34549 TCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTT-ACGAGGGAGTCAAGAATAATAAAGATTGA
1 TCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTCATGAAAAATAAAGATTGA
*
34613 CT
66 CC
** ** * *
34615 TCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTT--C-----A-T--T-AGTAACAAGGATTGA
1 TCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTCATGAAAAATAAAGATTGA
*
34669 CT
66 CC
* * * * * * * *
34671 TCTATTCCCGAGGAAGTCAAGGATTGGTTTCTTTTTCACAAGGGAGTCAGGAATAACAAAAATTG
1 TCTCTTCACGAGGAAGTCAAGGATTGG-TTCCTCTTCACAAGGGAGTCATGAAAAATAAAGATTG
*
34736 ACT
65 ACC
* * **
34739 TCTCTTCACGAAGAAATCAAGGATTGACTCCTCTTCA
1 TCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCA
34776 GGAATAACAA
Statistics
Matches: 287, Mismatches: 39, Indels: 48
0.77 0.10 0.13
Matches are distributed among these distances:
55 2 0.01
56 79 0.28
57 6 0.02
58 1 0.00
59 5 0.02
60 2 0.01
62 1 0.00
63 3 0.01
64 2 0.01
65 3 0.01
66 46 0.16
67 98 0.34
68 39 0.14
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (67 bp):
TCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTCATGAAAAATAAAGATTGA
CC
Found at i:34518 original size:29 final size:29
Alignment explanation
Indices: 34485--34574 Score: 80
Period size: 29 Copynumber: 3.2 Consensus size: 29
34475 GAATAAAAAA
*
34485 GATTGACCTCTCTTTACGAGGAAATCAAG
1 GATTGACATCTCTTTACGAGGAAATCAAG
* *
34514 GATTGA-ATC-CTCTT-C-AGGAATAACAAA
1 GATTGACATCTCT-TTACGAGGAA-ATCAAG
* * *
34541 GATTGACTTCTCTTCACGAGGAAGTCAAG
1 GATTGACATCTCTTTACGAGGAAATCAAG
34570 GATTG
1 GATTG
34575 GTTCCTCTTA
Statistics
Matches: 47, Mismatches: 8, Indels: 12
0.70 0.12 0.18
Matches are distributed among these distances:
26 5 0.11
27 13 0.28
28 7 0.15
29 17 0.36
30 5 0.11
ACGTcount: A:0.32, C:0.19, G:0.21, T:0.28
Consensus pattern (29 bp):
GATTGACATCTCTTTACGAGGAAATCAAG
Found at i:34553 original size:27 final size:27
Alignment explanation
Indices: 34471--34556 Score: 84
Period size: 27 Copynumber: 3.1 Consensus size: 27
34461 CACAAGGGAG
* *
34471 TCAGGAATAAAAAAGATTGACCTCTCTT
1 TCAGGAATAACAAAGATTGACTTCTC-T
* * * *
34499 TACGAGGAA-ATCAAGGATTGAATCCTCT
1 T-C-AGGAATAACAAAGATTGACTTCTCT
34527 TCAGGAATAACAAAGATTGACTTCTCT
1 TCAGGAATAACAAAGATTGACTTCTCT
34554 TCA
1 TCA
34557 CGAGGAAGTC
Statistics
Matches: 45, Mismatches: 10, Indels: 7
0.73 0.16 0.11
Matches are distributed among these distances:
26 5 0.11
27 19 0.42
28 3 0.07
29 13 0.29
30 5 0.11
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (27 bp):
TCAGGAATAACAAAGATTGACTTCTCT
Found at i:34560 original size:56 final size:56
Alignment explanation
Indices: 34471--34815 Score: 294
Period size: 56 Copynumber: 5.8 Consensus size: 56
34461 CACAAGGGAG
* * * * *
34471 TCAGGAATAAAAAAGATTGACCTCTCTTTACGAGGAAATCAAGGATTGAATCCTCT
1 TCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCT
**
34527 TCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCT
1 TCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCT
*
34583 TACGAGGGAGTCAAGAATAATAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTC
1 T-C-----AG----GAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTC
34648 T
56 T
** * * * * *
34649 TCATTAGTAACAAGGATTGACTTCTATTCCCGAGGAAGTCAAGGATTGGTTTCTTTTTCACAAGG
1 TCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATT-G--AC----TC-C----
***
34714 GAG
54 TCT
* * *
34717 TCAGGAATAACAAAAATTGACTTCTCTTCACGAAGAAATCAAGGATTGACTCCTCT
1 TCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCT
*
34773 TCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAACTCAAG
1 TCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAG
34816 TTGAAGCTTC
Statistics
Matches: 231, Mismatches: 36, Indels: 44
0.74 0.12 0.14
Matches are distributed among these distances:
56 128 0.55
57 2 0.01
59 1 0.00
60 2 0.01
61 2 0.01
62 2 0.01
63 2 0.01
64 1 0.00
65 2 0.01
66 50 0.22
67 1 0.00
68 38 0.16
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.28
Consensus pattern (56 bp):
TCAGGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCT
Found at i:34635 original size:122 final size:123
Alignment explanation
Indices: 34415--34815 Score: 599
Period size: 122 Copynumber: 3.3 Consensus size: 123
34405 CATGAAAAAT
* *
34415 AAAGATTGACCTCTCTTTACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTCAGGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTCAGGAATA
* * *
34480 AAAAAGATTGACCTCTCTTTACGAGGAAATCAAGGATTGAATCCTCTTCAGGAATAAC
66 AAAAAGATTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCCTCTTCAGGAATAAC
* *
34538 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTT-ACGAGGGAGTCAAGAATA
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTCAGGAATA
* * ** *
34602 ATAAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGACTCCTCTTCATTAGTAAC
66 AAAAAGATTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCCTCTTCAGGAATAAC
* * * * *
34660 AAGGATTGACTTCTATTCCCGAGGAAGTCAAGGATTGGTTTCTTTTTCACAAGGGAGTCAGGAAT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGG-TTCCTCTTCACAAGGGAGTCAGGAAT
*
34725 AACAAAA-ATTGACTTCTCTTCACGAAGAAATCAAGGATTGACTCCTCTTCAGGAATAAC
65 AA-AAAAGATTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCCTCTTCAGGAATAAC
*
34784 AAAGATTGACTTCTCTTCACGAGGAACTCAAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAG
34816 TTGAAGCTTC
Statistics
Matches: 246, Mismatches: 29, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
122 101 0.41
123 50 0.20
124 92 0.37
125 3 0.01
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (123 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGGATTGGTTCCTCTTCACAAGGGAGTCAGGAATA
AAAAAGATTGACTTCTCTTCACGAGGAAATCAAGGATTGACTCCTCTTCAGGAATAAC
Found at i:34774 original size:29 final size:29
Alignment explanation
Indices: 34732--34815 Score: 100
Period size: 27 Copynumber: 3.0 Consensus size: 29
34722 AATAACAAAA
34732 ATTGACTTCTCTTCACGAAGAAATCAAGG
1 ATTGACTTCTCTTCACGAAGAAATCAAGG
* * * *
34761 ATTGACTCCTCTTCAGGAA-TAA-CAAAG
1 ATTGACTTCTCTTCACGAAGAAATCAAGG
* *
34788 ATTGACTTCTCTTCACGAGGAACTCAAG
1 ATTGACTTCTCTTCACGAAGAAATCAAG
34816 TTGAAGCTTC
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
27 20 0.47
28 3 0.07
29 20 0.47
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (29 bp):
ATTGACTTCTCTTCACGAAGAAATCAAGG
Found at i:34799 original size:27 final size:27
Alignment explanation
Indices: 34717--34802 Score: 109
Period size: 27 Copynumber: 3.1 Consensus size: 27
34707 CACAAGGGAG
*
34717 TCAGGAATAACAAAAATTGACTTCTCT
1 TCAGGAATAACAAAGATTGACTTCTCT
* * * *
34744 TCACGAAGAAATCAAGGATTGACTCCTCT
1 TCAGGAA-TAA-CAAAGATTGACTTCTCT
34773 TCAGGAATAACAAAGATTGACTTCTCT
1 TCAGGAATAACAAAGATTGACTTCTCT
34800 TCA
1 TCA
34803 CGAGGAACTC
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
27 24 0.50
28 4 0.08
29 20 0.42
ACGTcount: A:0.37, C:0.21, G:0.14, T:0.28
Consensus pattern (27 bp):
TCAGGAATAACAAAGATTGACTTCTCT
Found at i:36203 original size:9 final size:9
Alignment explanation
Indices: 36187--36265 Score: 50
Period size: 10 Copynumber: 8.3 Consensus size: 9
36177 CAGCTAGAAA
36187 ACCGGTTTG
1 ACCGGTTTG
*
36196 ATCGGTTTTG
1 ACCGG-TTTG
36206 ACCGGTTTCG
1 ACCGGTTT-G
*
36216 ACCGGTTCG
1 ACCGGTTTG
* *
36225 AATCGGTCTG
1 -ACCGGTTTG
* *
36235 ACCAGTCTG
1 ACCGGTTTG
*
36244 AACTGGTTTG
1 -ACCGGTTTG
*
36254 ACCGGTCTG
1 ACCGGTTTG
36263 ACC
1 ACC
36266 CAACCCGACC
Statistics
Matches: 53, Mismatches: 13, Indels: 8
0.72 0.18 0.11
Matches are distributed among these distances:
9 25 0.47
10 28 0.53
ACGTcount: A:0.15, C:0.25, G:0.29, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:36299 original size:17 final size:17
Alignment explanation
Indices: 36277--36309 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
36267 AACCCGACCG
*
36277 ACCCGACCGGACCGTTA
1 ACCCGACCCGACCGTTA
36294 ACCCGACCCGACCGTT
1 ACCCGACCCGACCGTT
36310 GACCGTGACC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.45, G:0.21, T:0.12
Consensus pattern (17 bp):
ACCCGACCCGACCGTTA
Found at i:43488 original size:9 final size:9
Alignment explanation
Indices: 43474--43545 Score: 54
Period size: 10 Copynumber: 7.4 Consensus size: 9
43464 CAGCTGGAAA
43474 ACCGGTTTG
1 ACCGGTTTG
43483 ACCGGTTTTG
1 ACCGG-TTTG
*
43493 AATCGGTTTTG
1 -ACCGG-TTTG
*
43504 ACCAGTTTG
1 ACCGGTTTG
*
43513 ACCGGTTCG
1 ACCGGTTTG
*
43522 AACCGGTCTG
1 -ACCGGTTTG
*
43532 AACCAGTTTG
1 -ACCGGTTTG
43542 ACCG
1 ACCG
43546 ACCCGACCGA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
9 19 0.38
10 22 0.44
11 9 0.18
ACGTcount: A:0.18, C:0.24, G:0.28, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:43511 original size:10 final size:10
Alignment explanation
Indices: 43474--43519 Score: 51
Period size: 9 Copynumber: 4.7 Consensus size: 10
43464 CAGCTGGAAA
43474 ACCGG-TTTG
1 ACCGGTTTTG
43483 ACCGGTTTTG
1 ACCGGTTTTG
*
43493 AATCGGTTTTG
1 -ACCGGTTTTG
*
43504 ACCAG-TTTG
1 ACCGGTTTTG
43513 ACCGGTT
1 ACCGGTT
43520 CGAACCGGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
9 13 0.43
10 8 0.27
11 9 0.30
ACGTcount: A:0.15, C:0.20, G:0.28, T:0.37
Consensus pattern (10 bp):
ACCGGTTTTG
Found at i:43538 original size:29 final size:31
Alignment explanation
Indices: 43473--43545 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 31
43463 GCAGCTGGAA
* * * *
43473 AACCGGTTTGACCGGTTTTGAATCGGTTTTG
1 AACCAGTTTGACCGGTTTCGAACCGGTTCTG
43504 -ACCAGTTTGACCGG-TTCGAACCGG-TCTG
1 AACCAGTTTGACCGGTTTCGAACCGGTTCTG
43532 AACCAGTTTGACCG
1 AACCAGTTTGACCG
43546 ACCCGACCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 3 0.08
29 21 0.57
30 13 0.35
ACGTcount: A:0.19, C:0.23, G:0.27, T:0.30
Consensus pattern (31 bp):
AACCAGTTTGACCGGTTTCGAACCGGTTCTG
Found at i:43609 original size:6 final size:7
Alignment explanation
Indices: 43564--43615 Score: 61
Period size: 7 Copynumber: 7.6 Consensus size: 7
43554 GACCCGACCC
43564 GACCGTT
1 GACCGTT
43571 GACCGTT
1 GACCGTT
*
43578 GATCGTT
1 GACCGTT
* **
43585 TACTTTT
1 GACCGTT
43592 GACCGTT
1 GACCGTT
43599 GACCG-T
1 GACCGTT
43605 GACCGTT
1 GACCGTT
43612 GACC
1 GACC
43616 TCCTTTTGAC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
6 6 0.17
7 30 0.83
ACGTcount: A:0.15, C:0.27, G:0.25, T:0.33
Consensus pattern (7 bp):
GACCGTT
Found at i:43609 original size:13 final size:13
Alignment explanation
Indices: 43591--43615 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
43581 CGTTTACTTT
43591 TGACCGTTGACCG
1 TGACCGTTGACCG
43604 TGACCGTTGACC
1 TGACCGTTGACC
43616 TCCTTTTGAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.28, T:0.24
Consensus pattern (13 bp):
TGACCGTTGACCG
Found at i:55243 original size:114 final size:114
Alignment explanation
Indices: 55043--55270 Score: 456
Period size: 114 Copynumber: 2.0 Consensus size: 114
55033 TGTATTGTTC
55043 TCTTTGGGAGAGATTGTTCTCAAGAATTTGGGGTATAATTCTTGAGGGATTTGTAAGGTTACTCT
1 TCTTTGGGAGAGATTGTTCTCAAGAATTTGGGGTATAATTCTTGAGGGATTTGTAAGGTTACTCT
55108 TTGTCCTCAAAAGAAAGACAAATTAGTGAATTTGTGGAAAATCCTTATT
66 TTGTCCTCAAAAGAAAGACAAATTAGTGAATTTGTGGAAAATCCTTATT
55157 TCTTTGGGAGAGATTGTTCTCAAGAATTTGGGGTATAATTCTTGAGGGATTTGTAAGGTTACTCT
1 TCTTTGGGAGAGATTGTTCTCAAGAATTTGGGGTATAATTCTTGAGGGATTTGTAAGGTTACTCT
55222 TTGTCCTCAAAAGAAAGACAAATTAGTGAATTTGTGGAAAATCCTTATT
66 TTGTCCTCAAAAGAAAGACAAATTAGTGAATTTGTGGAAAATCCTTATT
55271 GTGGATAGTT
Statistics
Matches: 114, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
114 114 1.00
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.37
Consensus pattern (114 bp):
TCTTTGGGAGAGATTGTTCTCAAGAATTTGGGGTATAATTCTTGAGGGATTTGTAAGGTTACTCT
TTGTCCTCAAAAGAAAGACAAATTAGTGAATTTGTGGAAAATCCTTATT
Found at i:56707 original size:18 final size:20
Alignment explanation
Indices: 56676--56714 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
56666 TTGATTTTTC
*
56676 TTTTCTTTTCATCT-ATCTT
1 TTTTCTTCTCATCTCATCTT
56695 TTTTCTTCT-ATCTCATCTT
1 TTTTCTTCTCATCTCATCTT
56714 T
1 T
56715 ATTAGATGCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.10, C:0.23, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTCTTCTCATCTCATCTT
Done.