Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008810.1 Hibiscus syriacus cultivar Beakdansim tig00111964_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: 34030
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:121 original size:19 final size:19
Alignment explanation
Indices: 79--147 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
69 ATCTATTTGT
*
79 TATTATTA-TTATTTTACTA
1 TATTATTATTTATATTA-TA
98 T-TTATTATTTATATTATA
1 TATTATTATTTATATTATA
*
116 TATTATTATTTAT-TAATAA
1 TATTATTATTTATATTAT-A
135 TATTA-TATTTATA
1 TATTATTATTTATA
148 GACCCAAAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 19 0.43
19 25 0.57
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATTATTTATATTATA
Found at i:137 original size:26 final size:25
Alignment explanation
Indices: 85--146 Score: 81
Period size: 26 Copynumber: 2.5 Consensus size: 25
75 TTGTTATTAT
* * *
85 TATTAT-TTTACTATTTATTATTTA
1 TATTATATTTATTATTTATTAATAA
109 TATTATATATTATTATTTATTAATAA
1 TATTATAT-TTATTATTTATTAATAA
135 TATTATATTTAT
1 TATTATATTTAT
147 AGACCCAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
24 6 0.18
25 5 0.15
26 22 0.67
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (25 bp):
TATTATATTTATTATTTATTAATAA
Found at i:1569 original size:140 final size:138
Alignment explanation
Indices: 1372--1622 Score: 323
Period size: 141 Copynumber: 1.8 Consensus size: 138
1362 TTATGTTTTC
* *
1372 ATATTTATTTTTCAATATTAAGAAAGGGCAGTCTTAAAGAAACTAGATGTCCATTTTT-TAATAT
1 ATATTTATTTTTAAATATTAAGAAAGGGCAGTCTTAAAGAAACTAGAAGTCCATTTTTCTAATAT
* * *
1436 TTTTAAATAAATAAATATTTTATCTTACTTTTATAAATTATATATATTTTAATTATTTTTAGATA
66 TTCTAAATAAATAAATATCTTAT-TTA-TATT-TAAATTA-ATATATTTTAATTATTTTTAGATA
1501 AATGTTTTATTA
127 AATGTTTTATTA
** * *
1513 ATATTT-TTTTTAAATATTAAGAAAGGAGTTGTCTTAAAG-CACTTAGAAG-CTC-TTTTTCTGA
1 ATATTTATTTTTAAATATTAAGAAAGG-GCAGTCTTAAAGAAAC-TAGAAGTC-CATTTTTCTAA
1574 TATTTCTAAATAAATAAATATCTTATTTATATTTAAATTAATATATTTT
63 TATTTCTAAATAAATAAATATCTTATTTATATTTAAATTAATATATTTT
1623 CATAAAATTA
Statistics
Matches: 97, Mismatches: 9, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
137 9 0.09
138 7 0.07
139 3 0.03
140 30 0.31
141 48 0.49
ACGTcount: A:0.38, C:0.06, G:0.08, T:0.48
Consensus pattern (138 bp):
ATATTTATTTTTAAATATTAAGAAAGGGCAGTCTTAAAGAAACTAGAAGTCCATTTTTCTAATAT
TTCTAAATAAATAAATATCTTATTTATATTTAAATTAATATATTTTAATTATTTTTAGATAAATG
TTTTATTA
Found at i:7140 original size:11 final size:11
Alignment explanation
Indices: 7125--7164 Score: 62
Period size: 11 Copynumber: 3.5 Consensus size: 11
7115 TTTTTACAAA
7125 CTTTTTTTTTT
1 CTTTTTTTTTT
*
7136 TTTTTTTTTTT
1 CTTTTTTTTTT
7147 GCTTTTTTTTTT
1 -CTTTTTTTTTT
7159 CTTTTT
1 CTTTTT
7165 ACTGTTGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.00, C:0.07, G:0.03, T:0.90
Consensus pattern (11 bp):
CTTTTTTTTTT
Found at i:7176 original size:1 final size:1
Alignment explanation
Indices: 7126--7164 Score: 51
Period size: 1 Copynumber: 39.0 Consensus size: 1
7116 TTTTACAAAC
** *
7126 TTTTTTTTTTTTTTTTTTTTTGCTTTTTTTTTTCTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7165 ACTGTTGTTT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
1 33 1.00
ACGTcount: A:0.00, C:0.05, G:0.03, T:0.92
Consensus pattern (1 bp):
T
Found at i:7631 original size:3 final size:3
Alignment explanation
Indices: 7614--7665 Score: 72
Period size: 3 Copynumber: 18.0 Consensus size: 3
7604 CAAATTTAAA
* *
7614 AAT AAA AAT -AT AAT AAT AAT AAT AAT AAT AAT AA- GAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
7660 AAT AAT
1 AAT AAT
7666 GGGACGAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
2 3 0.07
3 40 0.93
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:7641 original size:23 final size:23
Alignment explanation
Indices: 7614--7664 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
7604 CAAATTTAAA
7614 AATAAAAATATA-ATAATAATAAT
1 AATAAAAATA-AGATAATAATAAT
*
7637 AATAATAATAAGATAATAATAAT
1 AATAAAAATAAGATAATAATAAT
7660 AATAA
1 AATAA
7665 TGGGACGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 1 0.04
23 25 0.96
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (23 bp):
AATAAAAATAAGATAATAATAAT
Found at i:8136 original size:42 final size:41
Alignment explanation
Indices: 8066--8147 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 41
8056 AGGTCTTTTG
* * *
8066 GATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCTTACA
1 GATGACCCGAATGACTTATCATCATGCTCGAAAGACTTACA
*
8107 GATGACCCGAATGATTTAATCATCATGCTCGAAAGACTTAC
1 GATGACCCGAATGACTT-ATCATCATGCTCGAAAGACTTAC
8148 TAATTGTCGA
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 15 0.42
42 21 0.58
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.27
Consensus pattern (41 bp):
GATGACCCGAATGACTTATCATCATGCTCGAAAGACTTACA
Found at i:8329 original size:232 final size:233
Alignment explanation
Indices: 7916--8718 Score: 1148
Period size: 232 Copynumber: 3.5 Consensus size: 233
7906 AGGTCTTATA
* *
7916 GATGGCCCGAAGGACTTATAAATTTTGGAAATAGTTTACTGGGTAAGAAACCTTTCTTACTTTTC
1 GATGGACCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTC
* * *
7981 AGAAATTTCAAATTTCATATTTAAATGAGAAACATTTCTCATATTTCGATAGACATGTGAAAACA
66 AAAAATTTCAATTTTCAAATTTAAATGAGAAACATTTCTCATATTTCGATAGACATGTGAAAACA
* * *
8046 TCCTACCCGAAGGTCTTTTGGATGGCCCGAATGACTTATCATCTTGCTCGAAAGGCTTACAGATG
131 TCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTACAGATG
*
8111 ACCCGAATGATTTAATCATCATGCTCGAAAGACTTACT
196 ACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACT
* * * *
8149 AATTG-TCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACTTTTCTTACTTTTC
1 GATGGACCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTC
* * * *
8213 AAAGATTTCAATTTTCAAATATAAATGAGAAACATTTCTCATATTTCGATATACATATGAAAACA
66 AAAAATTTCAATTTTCAAATTTAAATGAGAAACATTTCTCATATTTCGATAGACATGTGAAAACA
** *
8278 TCCTACCCAAAGGTCTTATGGATGGCTTGAAGGACTTATCATCTTGCTCGAAAGACTTACAGATG
131 TCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTACAGATG
* * ** *
8343 ACCCAAAGGATTTAAGCATCATGCTTAAAAAACTTAC-
196 ACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACT
* * * *
8380 GATGGACCGAATGACTTATAATTTTTTGAAATAGTTTACTGGGTAAGAAACCTTTCTTACTTTTC
1 GATGGACCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTC
* * * * *
8445 AAAAACTTCAATTTTCAGATTTAAATGAGAAACTTTTCTCATATTTCAATAGACATGTGAAAATA
66 AAAAATTTCAATTTTCAAATTTAAATGAGAAACATTTCTCATATTTCGATAGACATGTGAAAACA
* * * *
8510 TCCTGCCCAAAGGTCTTATAGATGTCCCGAAGGACTTATAATCTTGCTTC-AAAGGCTTACAGAT
131 TCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGC-TCGAAAGGCTTACAGAT
* *
8574 GACTCGAATGATTTAAGCACCATGCTCGAAAGACTTACT
195 GACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACT
* * *
8613 GATGGCCCGAAGGAC-CA-ACAATTTTGGAAATAGTTTACTATGTAAGAAACCTTTCTTACTTTT
1 GATGGACCGAAGGACTTATA-AATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTT
* *
8676 CAAAAATTTCAATTTTCAAATTTGAATGAGAAACCTTTCTCAT
65 CAAAAATTTCAATTTTCAAATTTAAATGAGAAACATTTCTCAT
8719 TTCATTTTTT
Statistics
Matches: 500, Mismatches: 66, Indels: 9
0.87 0.11 0.02
Matches are distributed among these distances:
231 4 0.01
232 478 0.96
233 18 0.04
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.33
Consensus pattern (233 bp):
GATGGACCGAAGGACTTATAAATTTTGGAAATAGTTTACTAGGTAAGAAACCTTTCTTACTTTTC
AAAAATTTCAATTTTCAAATTTAAATGAGAAACATTTCTCATATTTCGATAGACATGTGAAAACA
TCCTACCCAAAGGTCTTATGGATGGCCCGAAGGACTTATCATCTTGCTCGAAAGGCTTACAGATG
ACCCGAATGATTTAAGCATCATGCTCGAAAGACTTACT
Found at i:17347 original size:6 final size:6
Alignment explanation
Indices: 17336--17362 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
17326 CTAGCATGCC
17336 AAAATT AAAATT AAAATT AAAATT AAA
1 AAAATT AAAATT AAAATT AAAATT AAA
17363 TATACTAGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:18767 original size:3 final size:3
Alignment explanation
Indices: 18742--18792 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
18732 CAAAATTAAA
* *
18742 AAT AA- AAT -AT ATT AAT TAT AAT AAT AAT AA- AGAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
18785 AAT AAT AA
1 AAT AAT AA
18793 CGGGACAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
2 5 0.12
3 34 0.85
4 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:22383 original size:19 final size:20
Alignment explanation
Indices: 22340--22385 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
22330 CGATATACCA
22340 GGTAAAAATATGATAAAACC
1 GGTAAAAATATGATAAAACC
22360 GGTAACAAA-ATGATAAAA-C
1 GGTAA-AAATATGATAAAACC
22379 GGTAAAA
1 GGTAAAA
22386 TTAAAGTGTC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.08
19 6 0.24
20 14 0.56
21 3 0.12
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (20 bp):
GGTAAAAATATGATAAAACC
Found at i:22528 original size:20 final size:19
Alignment explanation
Indices: 22505--22550 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 19
22495 CGATATAACA
*
22505 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAAAC
*
22525 GGTATCAAAATGATAAAAAC
1 GGTA-AAAAATGATAAAAAC
22545 GGTAAA
1 GGTAAA
22551 TGATACCGGA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 1 0.05
20 18 0.82
21 3 0.14
ACGTcount: A:0.54, C:0.09, G:0.17, T:0.20
Consensus pattern (19 bp):
GGTAAAAAATGATAAAAAC
Found at i:24881 original size:33 final size:33
Alignment explanation
Indices: 24839--24904 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
24829 AAATAGATGG
*
24839 AGTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
***
24872 AGTGGTGAAAGAAGTTTCGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
24905 TATTAAGATG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.29, C:0.02, G:0.45, T:0.24
Consensus pattern (33 bp):
AGTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
Found at i:26692 original size:19 final size:19
Alignment explanation
Indices: 26668--26706 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
26658 AATGTCGAGT
26668 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
26687 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
26706 T
1 T
26707 TTTTTATGTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.33, C:0.03, G:0.10, T:0.54
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:26734 original size:17 final size:17
Alignment explanation
Indices: 26712--26746 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
26702 TTTATTTTTT
26712 ATGTGAATATAATTATG
1 ATGTGAATATAATTATG
26729 ATGTGAATATAATTATG
1 ATGTGAATATAATTATG
26746 A
1 A
26747 ATGAGATGAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.17, T:0.40
Consensus pattern (17 bp):
ATGTGAATATAATTATG
Found at i:27717 original size:193 final size:197
Alignment explanation
Indices: 26805--28762 Score: 3203
Period size: 196 Copynumber: 10.1 Consensus size: 197
26795 TTAAGGGTCA
* *
26805 TGTCGATACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAATT--AAA-AAGGTGCATC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
26867 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
26932 T-ATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
26996 AATG
194 AATG
*
27000 TGTCGACACTAATATAGTTTTGTGTCGATATTTTTTTCCAG-ATGAATTAAAAACAAGGTGCATC
1 TGTCGACACTAATATAG-TTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
27064 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAA-CCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
27128 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
130 TAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAAT
27193 AA--
194 AATG
*
27195 TGTCGACACTAATATAG-TTGTGTCGATATTTTTTTCCAG-ATGAATTAAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
27258 ATAAAAGTGTCGATCCATATA-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
66 AT-AAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
27322 TAATATGT-ATTTTTAATCTAACC-GTACAATTATACCGGTTTTAT--GAGAATAAGTCTAAATA
130 TAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
27383 ATG
195 ATG
27386 TGTCGACACTAA-ATAGTTTGTGT-GATATTTTTTT-CAGAATGAATTAAAAACAAGGTGCACCA
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
27448 AT-AAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
66 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
27512 AATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAA
131 AATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAA
27577 TG
196 TG
27579 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCA-CC
27644 AAT-AAGTGTCGATCCATATAT-AAAAGTGTCGATCCC-AAATCATCGAACCC-AAAGTAT-ATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
27704 TAATATGTAATTTTTCAATCTAACCGGTACAATTATACCGGTTTTAT-AGAGAATAAGTTCTAAA
130 TAATATGTAATTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAG-TCTAAA
27768 TAATG
193 TAATG
27773 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCCAGAATGAATTAAAAACAA-G-GCAC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTT-CCAGAATGAATTAAAAACAAGGTGCAC
*
27836 CCATAAAGTGTCGATCCCATATATAAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
64 CAATAAAGTGTCGAT-CCATATAT-AAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATA
27901 ATGTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
127 ATGTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTA
27966 AATAATG
191 AATAATG
27973 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCCAGAATGAA-T-AAAACAAGGTGCAC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTT-CCAGAATGAATTAAAAACAAGGTGCAC
28036 CAATAAAGTGTCGATCC--ATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
64 CAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAAT
28099 GTAATATGTAATTTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
129 GTAATATGTAA-TTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
28164 TAAT-
193 TAATG
28168 TGTCGACACTAAT-T-G-TT-TGTCGATATTTTTTTCCCAGAATGAATTAAAAAC-AGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACC
28228 -ATAAAGTGTCGATCCATATAT--AAA--GTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
28288 TAATATGTAATTTTTAATCTAA-C-GTACAATTATACCGGTTTTAT--GAG-A-AAGTCTAAATA
130 TAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
28347 ATG
195 ATG
28350 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTTCCAGAATGAA-TAAAAA-AAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATA-TTTTTTTCCAGAATGAATTAAAAACAAGGTGCACC
*
28413 CATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCC--AATCATCG-ACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
28475 TAATATGTAA-TTTCAATCTAACCGGTACAA-T-TACCGGTTTTATGAGAGAAT-AGTCTAAATA
130 TAATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATA
28536 ATG
195 ATG
28539 TGTCGACACTAATATAGTTTGTGTCGAT-TTTTTTTCCCAGAATGAATT-AAAACAAGGTGCACC
1 TGTCGACACTAATATAGTTTGTGTCGATATTTTTTT-CCAGAATGAATTAAAAACAAGGTGCACC
*
28602 -ATAAAGTGTCGATCCATATA-AAAACGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
65 AATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATG
*
28665 TAATATGTAATTTTTTCAATCTAACCGGTACAATAATACCGGTTTTATGAGAGAAT-AGTCTAAA
130 TAATATGTAA-TTTTT-AATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAA
28729 TAATG
193 TAATG
*
28734 TGTCGACACTAATATATTTTGTGTCGATA
1 TGTCGACACTAATATAGTTTGTGTCGATA
28763 CTAATTTAAA
Statistics
Matches: 1682, Mismatches: 11, Indels: 139
0.92 0.01 0.08
Matches are distributed among these distances:
181 13 0.01
182 14 0.01
183 4 0.00
184 1 0.00
185 38 0.02
186 62 0.04
187 69 0.04
188 117 0.07
189 133 0.08
190 126 0.07
191 78 0.05
192 23 0.01
193 161 0.10
194 150 0.09
195 158 0.09
196 206 0.12
197 161 0.10
198 21 0.01
199 11 0.01
200 121 0.07
201 15 0.01
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (197 bp):
TGTCGACACTAATATAGTTTGTGTCGATATTTTTTTCCAGAATGAATTAAAAACAAGGTGCACCA
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCAAAATCATCGAACCCAAAAGTATAATGT
AATATGTAATTTTTAATCTAACCGGTACAATTATACCGGTTTTATGAGAGAATAAGTCTAAATAA
TG
Found at i:30223 original size:12 final size:12
Alignment explanation
Indices: 30206--30296 Score: 67
Period size: 12 Copynumber: 7.4 Consensus size: 12
30196 GGTCGCAGAA
*
30206 GATGAAGCTGAC
1 GATGAAGATGAC
30218 GATGAAGATGAC
1 GATGAAGATGAC
30230 GATGATGATGATGAC
1 GATGA--A-GATGAC
* *
30245 GATG-AGCTGGC
1 GATGAAGATGAC
*
30256 GATGAAGATGAT
1 GATGAAGATGAC
* * *
30268 GACGATGATGAT
1 GATGAAGATGAC
* *
30280 GATGATGATGAA
1 GATGAAGATGAC
30292 GATGA
1 GATGA
30297 TGATCCAAAG
Statistics
Matches: 65, Mismatches: 10, Indels: 8
0.78 0.12 0.10
Matches are distributed among these distances:
11 8 0.12
12 46 0.71
14 1 0.02
15 10 0.15
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.22
Consensus pattern (12 bp):
GATGAAGATGAC
Found at i:30238 original size:3 final size:3
Alignment explanation
Indices: 30218--30300 Score: 78
Period size: 3 Copynumber: 28.0 Consensus size: 3
30208 TGAAGCTGAC
* * * * ** *
30218 GAT GAA GAT GAC GAT GAT GAT GAT GAC GAT GA- GCT GGC GAT GAA GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
* *
30265 GAT GAC GAT GAT GAT GAT GAT GAT GAA GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
30301 CCAAAGTATA
Statistics
Matches: 62, Mismatches: 17, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
2 1 0.02
3 61 0.98
ACGTcount: A:0.35, C:0.06, G:0.35, T:0.24
Consensus pattern (3 bp):
GAT
Found at i:32160 original size:181 final size:182
Alignment explanation
Indices: 31644--32472 Score: 1447
Period size: 181 Copynumber: 4.6 Consensus size: 182
31634 TTTCAACATA
*
31644 TAATAAATAATATTTGTAATA-AACCGGTATAAATATACC-GTCTTAT--GCGAATAGGTCTACA
1 TAATAGATAAT-TTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACA
31705 ACCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTC
65 ACCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTC
31769 GATACG-TTTAAAAAAGTGTCGACATTTTACACATCGGAACCCAAATTATAATG
130 GATACGATTTAAAAAAG-GTCGACATTTTACACATCGGAACCCAAATTATAATG
31822 TAATAGATAA-TTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAAT-GGTCTACAA
1 TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAA
31885 CCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCG
66 CCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCG
*
31950 ATACAATTTAAAAAAGTGTCGACATTTTACACATCGGAACCCATAATTATAATG
131 ATACGATTTAAAAAAG-GTCGACATTTTACACATCGGAACCCA-AATTATAATG
32004 TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAA
1 TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAA
32069 -CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCG
66 CCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCG
32133 ATACGATTTAAAAAA-GTCGACATTTTACACATCGGAACCCATAATTATAATG
131 ATACGATTTAAAAAAGGTCGACATTTTACACATCGGAACCCA-AATTATAATG
32185 TAATAGATAATTTTGTAATATAACCGGTAT-AATATACCGGTCTTATGCGCGAATAGGTCTACAA
1 TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAA
32249 CCTATATCGACACTTTTTAATATT-TGTCGGTACTTTATGTCCATATTGGAAGAAAAA-GTGTCG
66 CCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCG
32312 ATACGATTTAAAAAAGTGTCGACATTTTACACATCGGAACCC--ATTATAATG
131 ATACGATTTAAAAAAG-GTCGACATTTTACACATCGGAACCCAAATTATAATG
* *
32363 TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAA
1 TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAA
*
32428 CCTATATCGACACTTTATAATA-TGTGTCGGTACTTTATGTCCATA
66 CCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
32473 CCATTTAAAA
Statistics
Matches: 631, Mismatches: 6, Indels: 27
0.95 0.01 0.04
Matches are distributed among these distances:
176 9 0.01
177 18 0.03
178 56 0.09
179 117 0.19
180 128 0.20
181 152 0.24
182 20 0.03
183 122 0.19
184 9 0.01
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (182 bp):
TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAA
CCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCG
ATACGATTTAAAAAAGGTCGACATTTTACACATCGGAACCCAAATTATAATG
Found at i:32279 original size:363 final size:358
Alignment explanation
Indices: 31644--32472 Score: 1451
Period size: 363 Copynumber: 2.3 Consensus size: 358
31634 TTTCAACATA
*
31644 TAATAAATAATATTTGTAATA-AACCGGTATAAATATACC-GTCTTAT-GCGAATAGGTCTACAA
1 TAATAGATAAT-TTTGTAATATAACCGGTATAAATATACCGGTCTTATGGCGAATAGGTCTACAA
31706 CCTATATCGACAC-TTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCG
65 CCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCG
31770 ATACGTTTAAAAAAGTGTCGACATTTTACACATCGGAACCCAAATTATAATGTAATAGATAATTT
130 ATACGTTTAAAAAAG-GTCGACATTTTACACATCGGAACCCAAATTATAATGTAATAGATAATTT
31835 GTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATGGTCTACAACCTATATCGACACTT
194 GTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATGGTCTACAACCTATATCGACACTT
31900 TTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGATACAATTTAAAAAA
259 TTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAA-GTGTCGATACAATTTAAAAAA
31965 GTGTCGACATTTTACACATCGGAACCCATAATTATAATG
323 GTGTCGACATTTTACACATCGGAACCC---ATTATAATG
32004 TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAATAGGTCTACAA
1 TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATG-GCGAATAGGTCTACAA
32069 -CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCG
65 CCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCG
32133 ATACGATTTAAAAAA-GTCGACATTTTACACATCGGAACCCATAATTATAATGTAATAGATAATT
130 ATACG-TTTAAAAAAGGTCGACATTTTACACATCGGAACCCA-AATTATAATGTAATAGATAA-T
32197 TTGTAATATAACCGGTAT-AATATACCGGTCTTATGCGCGAATAGGTCTACAACCTATATCGACA
192 TTGTAATATAACCGGTATAAATATACCGGTCTTATGCGCGAAT-GGTCTACAACCTATATCGACA
*
32261 CTTTTTAATATT-TGTCGGTACTTTATGTCCATATTGGAAGAAAAAGTGTCGATACGATTTAAAA
256 CTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAAGTGTCGATACAATTTAAAA
32325 AAGTGTCGACATTTTACACATCGGAACCCATTATAATG
321 AAGTGTCGACATTTTACACATCGGAACCCATTATAATG
*
32363 TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAA
1 TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATG-GCGAATAGGTCTACAA
*
32428 CCTATATCGACACTTTATAATA-TGTGTCGGTACTTTATGTCCATA
65 CCTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATA
32473 CCATTTAAAA
Statistics
Matches: 454, Mismatches: 5, Indels: 21
0.95 0.01 0.04
Matches are distributed among these distances:
359 104 0.23
360 48 0.11
361 7 0.02
362 85 0.19
363 149 0.33
364 61 0.13
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (358 bp):
TAATAGATAATTTTGTAATATAACCGGTATAAATATACCGGTCTTATGGCGAATAGGTCTACAAC
CTATATCGACACTTTTTAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAATGTGTCGA
TACGTTTAAAAAAGGTCGACATTTTACACATCGGAACCCAAATTATAATGTAATAGATAATTTGT
AATATAACCGGTATAAATATACCGGTCTTATGCGCGAATGGTCTACAACCTATATCGACACTTTT
TAATATTGTGTCGGTACTTTATGTCCATATTGGAAGAAAAAGTGTCGATACAATTTAAAAAAGTG
TCGACATTTTACACATCGGAACCCATTATAATG
Done.