Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003104.1 Hibiscus syriacus cultivar Beakdansim tig00006481_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: 72624
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2057 original size:21 final size:21
Alignment explanation
Indices: 2031--2085 Score: 85
Period size: 21 Copynumber: 2.6 Consensus size: 21
2021 AAATTACCTT
2031 AGTATCAATACTCCTACGAGA
1 AGTATCAATACTCCTACGAGA
*
2052 AGTATCAATACTCCTACGGGA
1 AGTATCAATACTCCTACGAGA
2073 AGTAT-AGATACTC
1 AGTATCA-ATACTC
2086 TGGGAGTACC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 1 0.03
21 31 0.97
ACGTcount: A:0.36, C:0.22, G:0.16, T:0.25
Consensus pattern (21 bp):
AGTATCAATACTCCTACGAGA
Found at i:5116 original size:18 final size:18
Alignment explanation
Indices: 5093--5127 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
5083 TACTAGATTC
5093 TGTTTGGGTTAAAATGGG
1 TGTTTGGGTTAAAATGGG
5111 TGTTTGGGTTAAAATGG
1 TGTTTGGGTTAAAATGG
5128 TATTTAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.37, T:0.40
Consensus pattern (18 bp):
TGTTTGGGTTAAAATGGG
Found at i:15858 original size:182 final size:181
Alignment explanation
Indices: 15551--16224 Score: 901
Period size: 182 Copynumber: 3.7 Consensus size: 181
15541 TGGCGGTTTA
* *
15551 TGTCGATACTTTATAA-AACTGTATCGATCCACATCAATATAACATGTAAAAATATGACAAAATC
1 TGTCGATACTTTATAACAA-TGTATCGATCCACATCAATATAACAGGTAAAAATATGACAAAACC
* *
15615 GGTCTTGAAAAGACAAAACCGGTAAAACGGTA-TCGGATATATTGAAAGTGTCGATACTTTAATA
65 GGTCTCGAAAAGACAAAACCGGTAAAAC-GTACT-GGATATATTGAAAGTGTTGATACTTTAATA
* *
15679 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTCAGAGCCTATAAAG
128 TAAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
*
15733 TGTCGATACTTTATAA-AACTGAATCGATCCACATCAATATAACAGGTAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAA-TGTATCGATCCACATCAATATAACAGGTAAAAATATGACAAAACC
**
15797 GGTCTCGAAAAGACAAAATAGGTAAAACGATACTGGATATATTGAAAGTGTTGATACTTTAATAT
65 GGTCTCGAAAAGACAAAACCGGTAAAACG-TACTGGATATATTGAAAGTGTTGATACTTTAATAT
* * *
15862 AAGTATCGACACTTTGTAAATTTAAAAGAGAACCAGTTTTAGCGCTTATAAAG
129 AAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
** ** *
15915 TGTCGATACTTTATAACAATGTATCGATCCACATTGATATAACATATAAAAATATGACAAAATCG
1 TGTCGATACTTTATAACAATGTATCGATCCACATCAATATAACAGGTAAAAATATGACAAAACCG
* * * ***
15980 GTCTCTAAAGGACAAAACCGGTATAGAGCG-ACCAAATATATTGAAAGTGTTGATACTTTAATAT
66 GTCTCGAAAAGACAAAACCGGTA-A-AACGTACTGGATATATTGAAAGTGTTGATACTTTAATAT
* * *
16044 AAGTATCGACACTTCGTGAATTTAAAAGTGAAACAGTTTTAGCGCCCATAAAG
129 AAGTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
**
16097 TGTCGATACTTTATAACAATGTATCGATCCA-AAAAGATATAACAGGTAAAAATATGACAAAACC
1 TGTCGATACTTTATAACAATGTATCGATCCACATCA-ATATAACAGGTAAAAATATGACAAAACC
* * * * * * *
16161 AGTCTCGAAATGACAAAACCGGTATAGAGCG-ACCGAATATATTTAAAGTGTCGATACTTTAATA
65 GGTCTCGAAAAGACAAAACCGGTA-A-AACGTACTGGATATATTGAAAGTGTTGATACTTTAATA
16225 AGTACGCGTA
Statistics
Matches: 442, Mismatches: 44, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
181 2 0.00
182 433 0.98
183 4 0.01
184 3 0.01
ACGTcount: A:0.42, C:0.15, G:0.16, T:0.28
Consensus pattern (181 bp):
TGTCGATACTTTATAACAATGTATCGATCCACATCAATATAACAGGTAAAAATATGACAAAACCG
GTCTCGAAAAGACAAAACCGGTAAAACGTACTGGATATATTGAAAGTGTTGATACTTTAATATAA
GTATCGACACTTTGTGAATTTAAAAGAGAAACAGTTTTAGCGCCTATAAAG
Found at i:20051 original size:19 final size:19
Alignment explanation
Indices: 20029--20074 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
20019 GTTAATATTT
20029 TATAAGATTTATAATTTTG
1 TATAAGATTTATAATTTTG
*
20048 TATACGATTTATAATTTTG
1 TATAAGATTTATAATTTTG
*
20067 TATGAGAT
1 TATAAGAT
20075 GAGAAAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.35, C:0.02, G:0.13, T:0.50
Consensus pattern (19 bp):
TATAAGATTTATAATTTTG
Found at i:20756 original size:199 final size:197
Alignment explanation
Indices: 20402--21557 Score: 1407
Period size: 199 Copynumber: 5.8 Consensus size: 197
20392 GTAAGCAGAT
*
20402 GTGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
* * *
20467 GGTAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGTGAGAACAGGTCTACATAATGT
66 GGTAATTTT-TAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACATAATGT
* * * *
20532 ATCGACACTTTCGAAATTGGTGTCGATACTTTTTTTCCATAATAAATCCCAAAATGGTGAACACA
130 ATCGACACTTT-GAAATTTGTGTCGATACTTTTTGTCCAGAATAAATCCCAAAATGGTGCACACA
20597 TAAA
194 TAAA
*
20601 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACTTCGAAACCCATAATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
*
20666 GGTAATTTTTCAACGTAACCGGTA-AAACTATACCAGTTTTATGAGAGAATAGGTCTACATAATG
66 GGTAATTTTT-AATGTAACCGGTATAAA-TATACCAGTTTTATGAGAGAATAGGTCTACATAATG
* * * ** *
20730 TATCGACACTTATGGAATTTGTGTCGATACTGTTTGTCTAGAAGGAATGCCCAAAAGGGTGCACA
129 TATCGACACTT-TGAAATTTGTGTCGATACTTTTTGTCCAGAATAAAT-CCCAAAATGGTGCACA
*
20795 AATAAA
192 CATAAA
* * *
20801 GAGTCGATACATTTTTTAAAAGTGA-CGATCCCA-AAGACATCGAAACCCATAATTATAATGTAA
1 GTGTCGATACATTTATAAAAAGT-ATCGATCCCAGAA-ACATCGAAACCCATAATTATAATGTAA
*
20864 TAGGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTAT-ATGAGAATAGGTCTACATAA
64 TAGGTAATTTT-TAATGTAACCGGTATAAATATACCAGTTTTATGA-GAGAATAGGTCTACATAA
* * * * *
20928 TGTATCGACACATTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATTCCAAAATGGTGAAT
127 TGTATCGACAC-TTTGAAATTTGTGTCGATACTTTTTGTCCAGAATAAATCCCAAAATGGTGCAC
*
20993 GCATAAA
191 ACATAAA
* * * *
21000 GTGTCAATACATTTTTAAAAAGTGTCAATCCCAGAGAA-ATCG-AACCCATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGA-AACATCGAAACCCATAATTATAATGTAAT
* *
21063 AGGTATTTTTGTAATGTAACCGGTATAAATATACC-GTTTTTATGTGAGAATAGGTCTACATAAT
65 AGGTAATTTT-TAATGTAACCGGTATAAATATACCAG-TTTTATGAGAGAATAGGTCTACATAAT
** * *
21127 GTATCGACACTTTTTAATTATGTGTCGATACATTTTT-TCTAGAATAAATGCCTAAAAAATGGTG
128 GTATCGACACTTTGAAATT-TGTGTCGATAC-TTTTTGTCCAGAATAAAT-CC--CAAAATGGTG
*
21191 CACGCATAAA
188 CACACATAAA
* * *
21201 CTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATTGAAACCCATGATTATAATGTAATA
1 GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
** * * * * *
21266 GGTAATTTTTCAATGTAACCGGTATAAATATACTGGTTTTATGCGAGAATATGTATAGAAAATGT
66 GGTAATTTTT-AATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACATAATGT
* * * * * *
21331 ATCGACACTTCTGGAATTTGTTTCGATACTTTTTGTCCAGAATTAATGCCAAAAGGGTGCACCCA
130 ATCGACACTT-TGAAATTTGTGTCGATACTTTTTGTCCAGAATAAATCCCAAAATGGTGCACACA
*
21396 TTAA
194 TAAA
* * * * *
21400 GTGTCGATACATTT-TTAAAAGTGTCGATCCCTA-AAAGATCAAAACCAATAATTATAATGTAAT
1 GTGTCGATACATTTATAAAAAGTATCGATCCC-AGAAACATCGAAACCCATAATTATAATGTAAT
* * * * *
21463 AGGTAAATTATTAATGTAACCAGTATAAATATA-CATGTTTTATGAGAAAATAGGTCAACATAAA
65 AGGT-AATTTTTAATGTAACCGGTATAAATATACCA-GTTTTATGAGAGAATAGGTCTACATAAT
* *
21527 GTATCGACAATTGTTAAATTTGTGTCGATAC
128 GTATCGACACTT-TGAAATTTGTGTCGATAC
21558 CATTTTAAAA
Statistics
Matches: 829, Mismatches: 99, Indels: 59
0.84 0.10 0.06
Matches are distributed among these distances:
197 8 0.01
198 224 0.27
199 247 0.30
200 174 0.21
201 65 0.08
202 105 0.13
203 6 0.01
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.32
Consensus pattern (197 bp):
GTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTAATA
GGTAATTTTTAATGTAACCGGTATAAATATACCAGTTTTATGAGAGAATAGGTCTACATAATGTA
TCGACACTTTGAAATTTGTGTCGATACTTTTTGTCCAGAATAAATCCCAAAATGGTGCACACATA
AA
Found at i:21316 original size:400 final size:396
Alignment explanation
Indices: 20403--21563 Score: 1507
Period size: 400 Copynumber: 2.9 Consensus size: 396
20393 TAAGCAGATG
20403 TGTCGATACATTTATAAAAAGTATCGATCCCAAAAACATCGAAACCCATAATTATAATGTAATAG
1 TGTCGATACATTTATAAAAAGTATCGATCCC-AAAACATCGAAACCCATAATTATAATGTAATAG
* * *
20468 GTAATTTTGTAATATAACCGGTATAAATATACCAGTTTTATGTGAGAACAGGTCTACATAATGTA
65 GTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGTA
* *
20533 TCGACACTTTCGAAATTGGTGTCGATACTTTTTTTCCATAATAAATCCCAAAATGGTGAACACAT
130 TCGACACTTT-GAAATTGGTGTCGATACTTTTTGTCCAGAATAAATCCCAAAATGGTGAACACAT
* * *
20598 AAAGTGTCGATACATTTATAAAAAGTATCGATCCCAGAAACTTCGAAACCCATAATTATAATGTA
194 AAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCG-AACCCATAATTATAATGTA
* *
20663 ATAGGTAATTTTTCAACGTAACCGGTA-AAACTATACCAG-TTTTATGAGAGAATAGGTCTACAT
258 ATAGGTAATTTTTTAATGTAACCGGTATAAA-TATACC-GTTTTTATGAGAGAATAGGTCTACAT
** * *
20726 AATGTATCGACACTTATGGAATTTGTGTCGATAC-TGTTTGTCTAGAAGGAATGCCCAAAAGGGT
321 AATGTATCGACACTTATTAAATTTGTGTCGATACAT-TTTGTCTAGAAGAAATGCCAAAAAGGGT
*
20790 GCACAAATAAAG
385 GCACAAATAAAC
* * *
20802 AGTCGATACATTTTTTAAAAGTGA-CGATCCCAAAGACATCGAAACCCATAATTATAATGTAATA
1 TGTCGATACATTTATAAAAAGT-ATCGATCCCAAA-ACATCGAAACCCATAATTATAATGTAATA
*
20866 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATATGAGAATAGGTCTACATAATGT
64 GGTAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * **
20931 ATCGACACATTTGAAATTGGTGTCGATACTTTTTGTCCAGAATGAATTCCAAAATGGTGAATGCA
129 ATCGACAC-TTTGAAATTGGTGTCGATACTTTTTGTCCAGAATAAATCCCAAAATGGTGAACACA
* *
20996 TAAAGTGTCAATACATTTTTAAAAAGTGTCAATCCCAGAGAA-ATCGAACCCATAATTATAATGT
193 TAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGA-AACATCGAACCCATAATTATAATGT
*
21060 AATAGGT-ATTTTTGTAATGTAACCGGTATAAATATACCGTTTTTATGTGAGAATAGGTCTACAT
257 AATAGGTAATTTTT-TAATGTAACCGGTATAAATATACCGTTTTTATGAGAGAATAGGTCTACAT
* * * *
21124 AATGTATCGACACTT-TTTAATTATGTGTCGATACATTTTTTCTAGAATAAATGCCTAAAAAATG
321 AATGTATCGACACTTATTAAATT-TGTGTCGATACATTTTGTCTAGAAGAAATGCC--AAAAAGG
**
21188 GTGCACGCATAAAC
383 GTGCACAAATAAAC
* *
21202 TGTCGATACATTTATAAAAAGTATCGATCCCAGAAACATTGAAACCCATGATTATAATGTAATAG
1 TGTCGATACATTTATAAAAAGTATCGATCCCA-AAACATCGAAACCCATAATTATAATGTAATAG
* * * * * *
21267 GTAATTTT-TCAATGTAACCGGTATAAATATACTGGTTTTATGCGAGAATATGTATAGAAAATGT
65 GTAATTTTGT-AATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGT
* * * * * * * *
21331 ATCGACACTTCTGGAATTTGTTTCGATACTTTTTGTCCAGAATTAATGCCAAAAGGGTGCACCCA
129 ATCGACACTT-TGAAATTGGTGTCGATACTTTTTGTCCAGAATAAATCCCAAAATGGTGAACACA
* * * *
21396 TTAAGTGTCGATACATTTTT-AAAAGTGTCGATCCCTA-AAAGATCAAAACCAATAATTATAATG
193 TAAAGTGTCGATACATTTTTAAAAAGTGTCGATCCC-AGAAACATC-GAACCCATAATTATAATG
* * * * * *
21459 TAATAGGTAAATTATTAATGTAACCAGTATAAATATA-CATGTTTTATGAGAAAATAGGTCAACA
256 TAATAGGTAATTTTTTAATGTAACCGGTATAAATATACCGT-TTTTATGAGAGAATAGGTCTACA
* * *
21523 TAAAGTATCGACAATTGTTAAATTTGTGTCGATACCATTTT
320 TAATGTATCGACACTTATTAAATTTGTGTCGATA-CATTTT
21564 AAAAATTGCG
Statistics
Matches: 673, Mismatches: 67, Indels: 42
0.86 0.09 0.05
Matches are distributed among these distances:
397 12 0.02
398 113 0.17
399 237 0.35
400 293 0.44
401 18 0.03
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (396 bp):
TGTCGATACATTTATAAAAAGTATCGATCCCAAAACATCGAAACCCATAATTATAATGTAATAGG
TAATTTTGTAATGTAACCGGTATAAATATACCGGTTTTATGTGAGAATAGGTCTACATAATGTAT
CGACACTTTGAAATTGGTGTCGATACTTTTTGTCCAGAATAAATCCCAAAATGGTGAACACATAA
AGTGTCGATACATTTTTAAAAAGTGTCGATCCCAGAAACATCGAACCCATAATTATAATGTAATA
GGTAATTTTTTAATGTAACCGGTATAAATATACCGTTTTTATGAGAGAATAGGTCTACATAATGT
ATCGACACTTATTAAATTTGTGTCGATACATTTTGTCTAGAAGAAATGCCAAAAAGGGTGCACAA
ATAAAC
Found at i:25603 original size:199 final size:198
Alignment explanation
Indices: 24705--26059 Score: 1556
Period size: 200 Copynumber: 6.8 Consensus size: 198
24695 AGTTTCCCAT
* * * *
24705 AAAGCGTCGATACATGTTTAAAAAGTATCGATCCCAAAAACATCTAAACCGAAAATTATAATGTA
1 AAAGTGTCGATACAT-TTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* * *
24770 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTTTGAGAAAATAGAT-ATACATA
65 ATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCA-ACATA
** * * * * *
24834 ATGTAT---CA--TGGA-ATTTGTGTCGATATTTTTTATCCAAAATGAATGCCAAACATGGTGCA
129 ATGTATCGACACTTTTAGATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGGTTCA
* *
24893 CGCAT
194 AGCAA
* *
24898 ACAGTGTCGATACATTTTAAAAAAGTATCGATCCCAAAAACATCGAAACTC-ATAATTATAATGT
1 AAAGTGTCGATACA-TTTGAAAAAGTATCGATCCCAAAAACATCGAAAC-CGATAATTATAATGT
* * ** * * * * * * *
24962 AATAGGCAATTTTGTAATATAATCGATAAAAATATACCAGTTTTATGTGAGAATAGGTCTACATA
64 AATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACATA
* * * * *
25027 ATGTATCTAAACTTTTTA-ATTTTGTCTCGATACTTTTTGTCCAGAATGAATGCCCAAA-AT-GA
129 ATGTATCGACAC-TTTTAGA-TTTGTGTCGATACTTTTTGTCCAGAATGAATG-CCAAACGTGGT
* *
25089 TGAACGCAT
191 TCAA-GCAA
* * * *
25098 AAAGTGTCAATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTT-GAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
** * * *
25163 ATAGGTAAATTTACAATGTAACC-AGTATAGCTATACCGGTTTTATGTGAGAATAGGTCTACATA
65 ATAGGTAAATTTACAATGTAACCGA-TATAAATATACCGGTTTTATGAGAAAATAGGTCAACATA
* * * *
25227 ATGTATCGACACTTATGGAATTTGTGTCGATACTTTTTGTCTAAAATGAATGCCAGAA-G-GGTT
129 ATGTATCGACACTTTTAG-ATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCA-AACGTGGTT
* *
25290 GCACGCAT
192 -CAAGCAA
* *
25298 AAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACTGATAATTATAATGTA
1 AAAGTGTCGATACA-TTTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* * * * * *
25363 ATAGGTAAATTTACAATGTAACCGGTAGAAATTTACCGGTTTTATAAGAAAATAGGTGAACATAT
65 ATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAA
* * * *
25428 TCTATCGACACGTTTTAGATTTGAGTCGATACATTTTGTCCAGAATGAATGCCAAACGTTGTTCA
130 TGTATCGACAC-TTTTAGATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGGTTCA
25493 AGCAA
194 AGCAA
** * *
25498 AAAGTGTCGATACATTTGAAATTGTATCGATCCAAAAAACATCAAAACCGATAATTATAATGTAA
1 AAAGTGTCGATACATTTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
* * * *
25563 TTGGTAAATTTACAATGTAACCGATATAAATTTACCGGTTTTATAAGAAAATAGGTGAACATAAT
66 TAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAAT
* * * * * *
25628 ATATCGAAACGTTTTAGATTTGTGTCGATACATTTTGTCCTGAATGAATGCCAAACGTTGTTCAG
131 GTATCGACAC-TTTTAGATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGGTTCAA
25693 GCAA
195 GCAA
** * *
25697 AAAGTGTCGATACATTTGAAATTGTATTGAT-CCAAAAACATCAAAACCGATAATTATAATGTAA
1 AAAGTGTCGATACATTTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
* * ** *
25761 TAGGTAAATTTACAATGTAACCGGTATAAATTTACTAGTTTTATGAGAAAATAGGTGAACATAAT
66 TAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAAT
* *
25826 GTATAGACACATTTTAGATTTGTGTCGATA-TATTTTGTCCAGAATGAATGCCAAACGTGGTGCA
131 GTATCGACAC-TTTTAGATTTGTGTCGATACT-TTTTGTCCAGAATGAATGCCAAACGTGGTTCA
*
25890 AGAAA
194 AGCAA
** *
25895 AAAGTGTCGATACATTTGAAATTGTATCGATCCCAAAAACATCGAAACC-ATTAATTATAACGTA
1 AAAGTGTCGATACATTTGAAAAAGTATCGATCCCAAAAACATCGAAACCGA-TAATTATAATGTA
* *
25959 ATAGGTAAATTTACAATGTAACCGATATAAATATACTGGTTTTATGAGAGAATAGGTCAACATAA
65 ATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAA
* *
26024 TGTATCGACACTTTTAAATTTTTGTCGATACTTTTT
130 TGTATCGACACTTTTAGATTTGTGTCGATACTTTTT
26060 AAATAACGTG
Statistics
Matches: 1010, Mismatches: 123, Indels: 53
0.85 0.10 0.04
Matches are distributed among these distances:
193 111 0.11
194 2 0.00
196 1 0.00
198 202 0.20
199 317 0.31
200 360 0.36
201 17 0.02
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (198 bp):
AAAGTGTCGATACATTTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
TAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAAT
GTATCGACACTTTTAGATTTGTGTCGATACTTTTTGTCCAGAATGAATGCCAAACGTGGTTCAAG
CAA
Found at i:25880 original size:397 final size:398
Alignment explanation
Indices: 24705--26059 Score: 1641
Period size: 397 Copynumber: 3.4 Consensus size: 398
24695 AGTTTCCCAT
* * * *
24705 AAAGCGTCGATACATGTTTAAAAAGTATCGATCCCAAAAACATCTAAACCGAAAATTATAATGTA
1 AAAGTGTCGATACAT-TTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
* * *
24770 ATAGGTAAATTTACAATGTAACCGGTATAAATATACCGGTTTTTTGAGAAAATAGAT-ATACATA
65 ATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCA-ACATA
** * * * * *
24834 ATGTAT---CA--TGGA-ATTTGTGTCGATATTTTTTATCCAAAATGAATGCCAAACATGGTGCA
129 ATGTATCGACACTTTTAGATTTGTGTCGATACTTTTTGTCCTAAATGAATGCCAAACGTGGTTCA
*
24893 CGCATACAGTGTCGATACATTTTAAAAAAGTATCGATCCCAAAAACATCGAAACTC-ATAATTAT
194 CGCATAAAGTGTCGATACATTTTAAAAAAGTATCGATCCCAAAAACATCGAAAC-CGATAATTAT
* * ** * * * * * * **
24957 AATGTAATAGGCAATTTTGTAATATAATCGATAAAAATATACCAGTTTTATGTGAGAATAGGTCT
258 AATGTAATAGGTAAATTTACAATGTAACCGGTAAAAATTTACCAGTTTTATGAGAAAATAGGTGA
* * * *
25022 ACATAATGTATCTAAACTTTTTA-ATTTTGTCTCGATACT-TTTTGTCCAGAATGAATGCCCAAA
323 ACATAATGTATCGACACATTTTAGA-TTTGTGTCGATA-TATTTTGTCCAGAATGAATG-CCAAA
* * * *
25085 --ATGATGAACGCAT
385 CGTTGTTCAA-GCAA
* * * *
25098 AAAGTGTCAATACATTTATAAAAAGTATCGATCCCAGAAACATCGAAACCCATAATTATAATGTA
1 AAAGTGTCGATACATTT-GAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTA
** * * *
25163 ATAGGTAAATTTACAATGTAACC-AGTATAGCTATACCGGTTTTATGTGAGAATAGGTCTACATA
65 ATAGGTAAATTTACAATGTAACCGA-TATAAATATACCGGTTTTATGAGAAAATAGGTCAACATA
* *
25227 ATGTATCGACACTTATGGAATTTGTGTCGATACTTTTTGT-CTAAAATGAATGCCAGAA-G-GGT
129 ATGTATCGACACTTTTAG-ATTTGTGTCGATACTTTTTGTCCT-AAATGAATGCCA-AACGTGGT
* *
25289 TGCACGCATAAAGTGTCGATACATTTTTAAAAAGTATCGATCCCAAAAACATCGAAACTGATAAT
191 T-CACGCATAAAGTGTCGATACATTTTAAAAAAGTATCGATCCCAAAAACATCGAAACCGATAAT
* * *
25354 TATAATGTAATAGGTAAATTTACAATGTAACCGGTAGAAATTTACCGGTTTTATAAGAAAATAGG
255 TATAATGTAATAGGTAAATTTACAATGTAACCGGTAAAAATTTACCAGTTTTATGAGAAAATAGG
* * * * *
25419 TGAACATATTCTATCGACACGTTTTAGATTTGAGTCGATACATTTTGTCCAGAATGAATGCCAAA
320 TGAACATAATGTATCGACACATTTTAGATTTGTGTCGATATATTTTGTCCAGAATGAATGCCAAA
25484 CGTTGTTCAAGCAA
385 CGTTGTTCAAGCAA
** * *
25498 AAAGTGTCGATACATTTGAAATTGTATCGATCCAAAAAACATCAAAACCGATAATTATAATGTAA
1 AAAGTGTCGATACATTTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
* * * *
25563 TTGGTAAATTTACAATGTAACCGATATAAATTTACCGGTTTTATAAGAAAATAGGTGAACATAAT
66 TAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAAT
* * * * * *
25628 ATATCGAAACGTTTTAGATTTGTGTCGATACATTTTGTCCTGAATGAATGCCAAACGTTGTTCAG
131 GTATCGACAC-TTTTAGATTTGTGTCGATACTTTTTGTCCTAAATGAATGCCAAACGTGGTTCAC
* * ** * *
25693 GCAAAAAGTGTCGATACA-TTTGAAATTGTATTGAT-CCAAAAACATCAAAACCGATAATTATAA
195 GCATAAAGTGTCGATACATTTTAAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAA
* *
25756 TGTAATAGGTAAATTTACAATGTAACCGGTATAAATTTACTAGTTTTATGAGAAAATAGGTGAAC
260 TGTAATAGGTAAATTTACAATGTAACCGGTAAAAATTTACCAGTTTTATGAGAAAATAGGTGAAC
* *
25821 ATAATGTATAGACACATTTTAGATTTGTGTCGATATATTTTGTCCAGAATGAATGCCAAACGTGG
325 ATAATGTATCGACACATTTTAGATTTGTGTCGATATATTTTGTCCAGAATGAATGCCAAACGTTG
* *
25886 TGCAAGAAA
390 TTCAAGCAA
** *
25895 AAAGTGTCGATACATTTGAAATTGTATCGATCCCAAAAACATCGAAACC-ATTAATTATAACGTA
1 AAAGTGTCGATACATTTGAAAAAGTATCGATCCCAAAAACATCGAAACCGA-TAATTATAATGTA
* *
25959 ATAGGTAAATTTACAATGTAACCGATATAAATATACTGGTTTTATGAGAGAATAGGTCAACATAA
65 ATAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAA
* *
26024 TGTATCGACACTTTTAAATTTTTGTCGATACTTTTT
130 TGTATCGACACTTTTAGATTTGTGTCGATACTTTTT
26060 AAATAACGTG
Statistics
Matches: 827, Mismatches: 111, Indels: 45
0.84 0.11 0.05
Matches are distributed among these distances:
392 2 0.00
393 116 0.14
396 25 0.03
397 279 0.34
398 16 0.02
399 163 0.20
400 218 0.26
401 8 0.01
ACGTcount: A:0.39, C:0.14, G:0.16, T:0.32
Consensus pattern (398 bp):
AAAGTGTCGATACATTTGAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAATGTAA
TAGGTAAATTTACAATGTAACCGATATAAATATACCGGTTTTATGAGAAAATAGGTCAACATAAT
GTATCGACACTTTTAGATTTGTGTCGATACTTTTTGTCCTAAATGAATGCCAAACGTGGTTCACG
CATAAAGTGTCGATACATTTTAAAAAAGTATCGATCCCAAAAACATCGAAACCGATAATTATAAT
GTAATAGGTAAATTTACAATGTAACCGGTAAAAATTTACCAGTTTTATGAGAAAATAGGTGAACA
TAATGTATCGACACATTTTAGATTTGTGTCGATATATTTTGTCCAGAATGAATGCCAAACGTTGT
TCAAGCAA
Found at i:30819 original size:198 final size:198
Alignment explanation
Indices: 30319--30838 Score: 631
Period size: 200 Copynumber: 2.6 Consensus size: 198
30309 TGTCCAGAAT
* * *
30319 ATAAAGTGTCGATACATTTATTAAAAGTATCGATCTCAATAACATCGAAAACAATAATTATAATG
1 ATAAAGTGTCGATACATTTA-TAAAAGTATCGATC-CAAAAACATCGAAACCGATAATTATAATG
* * * * ** * * *
30384 TAATATGTACATTTATAATGTAACTGGTAAAAATATACTGGTTTTATAAGAAAATAGGTTAGCAT
64 TAATAGGTAAATTTACAATGTTACCAGTAAAAATATACCGGTTTTATAAGAAAATAGATTAGAAT
* *
30449 AAAGTATCGACACTATTTAAATTTGTGTCGATACGTTTTGTTCATAATGAATGCCAAATGGAGTG
129 AAAGTATCGACACTATTTAAATTTGTGTCGATACGTTTTGTTCAAAATGAATGCCAAACGGAGTG
30514 CACGC
194 CACGC
* * *
30519 ATAAAGTGTCGATACATTTATTAAAAGTATCGATACCACAAACATTGAAACCGATAATTACAATG
1 ATAAAGTGTCGATACATTTA-TAAAAGTATCGAT-CCAAAAACATCGAAACCGATAATTATAATG
* * * *
30584 TGATAGGTAAATTTACAATG-TACCCGATAGAAATATACCGGTTTTATGAGAAAATAGATATA-A
64 TAATAGGTAAATTTACAATGTTACCAG-TAAAAATATACCGGTTTTATAAGAAAATAGAT-TAGA
* * * *
30647 ATAATGTATCGACACTTTTTAAGTTTGTGTCGATAC-TTTT-TTCCAAAATGAATGCCCAAC-GA
127 ATAAAGTATCGACACTATTTAAATTTGTGTCGATACGTTTTGTT-CAAAATGAATGCCAAACGGA
*
30709 GGTGCATGC
191 -GTGCACGC
*
30718 ATAAAGTGTCGATACATTTA-AAATTGTATCGATCCAAAAAACATCGAAACCGATAATTATAATG
1 ATAAAGTGTCGATACATTTATAAA-AGTATCGATCC-AAAAACATCGAAACCGATAATTATAATG
* *
30782 TAATAGGTAAATTTACAATGTTACCAGTATAAATATACCGG-TTTACTTAGAAAATAG
64 TAATAGGTAAATTTACAATGTTACCAGTAAAAATATACCGGTTTTA-TAAGAAAATAG
30839 GTCGATATAA
Statistics
Matches: 278, Mismatches: 33, Indels: 20
0.84 0.10 0.06
Matches are distributed among these distances:
197 9 0.03
198 79 0.28
199 53 0.19
200 134 0.48
201 3 0.01
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.32
Consensus pattern (198 bp):
ATAAAGTGTCGATACATTTATAAAAGTATCGATCCAAAAACATCGAAACCGATAATTATAATGTA
ATAGGTAAATTTACAATGTTACCAGTAAAAATATACCGGTTTTATAAGAAAATAGATTAGAATAA
AGTATCGACACTATTTAAATTTGTGTCGATACGTTTTGTTCAAAATGAATGCCAAACGGAGTGCA
CGC
Found at i:30913 original size:23 final size:23
Alignment explanation
Indices: 30843--30904 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
30833 AAATAGGTCG
30843 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
30866 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTATTACATT
30889 ATATAAGCGCTACCTA
1 ATATAAGCGCTACCTA
30905 ATATGTTATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.35, C:0.23, G:0.10, T:0.32
Consensus pattern (23 bp):
ATATAAGCGCTACCTATTACATT
Found at i:30954 original size:87 final size:87
Alignment explanation
Indices: 30863--31028 Score: 305
Period size: 87 Copynumber: 1.9 Consensus size: 87
30853 TACCTATTAC
*
30863 ATTATATAAGCGCTACCTATTACATTATATAAGCGCTACCTAATATGTTATTGTACTTGATAATA
1 ATTATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATA
30928 TTTCCGGTTAAATGTCTATTTT
66 TTTCCGGTTAAATGTCTATTTT
*
30950 ATTATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTCTTGTACTTGATAATA
1 ATTATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATA
*
31015 TTTTCGGTTAAATG
66 TTTCCGGTTAAATG
31029 ATATAACATA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (87 bp):
ATTATATAAGCGCTACCTATTACATTATATAAGAGCTACCTAATATGTTATTGTACTTGATAATA
TTTCCGGTTAAATGTCTATTTT
Found at i:33505 original size:157 final size:157
Alignment explanation
Indices: 33219--33532 Score: 583
Period size: 157 Copynumber: 2.0 Consensus size: 157
33209 CATGTTTAGG
** *
33219 GTTTATCTTTGATTTCATGATTCAACCATGTTTTAAGCGTTAAAAATGTGTTTTTAAGACACCTT
1 GTTTATCTTTGATTTCATGATTCAACCAAATTTTAAGCGTTAAAAATGTATTTTTAAGACACCTT
33284 AAGACCCTAAACAACTCACTAAAACTTCAGAACAAGATTAGAAACCAACCCAAGTCATTTAGGAT
66 AAGACCCTAAACAACTCACTAAAACTTCAGAACAAGATTAGAAACCAACCCAAGTCATTTAGGAT
*
33349 AATTTTAGGTGTTTTCTTGAGCCTAAA
131 AATTTTAGGTGTTTTCTCGAGCCTAAA
33376 GTTTATCTTTGATTTCATGATTCAACCAAATTTTAAGCGTTAAAAATGTATTTTTAAGACACCTT
1 GTTTATCTTTGATTTCATGATTCAACCAAATTTTAAGCGTTAAAAATGTATTTTTAAGACACCTT
*
33441 AAGACCCTAAATAACTCACTAAAACTTCAGAACAAGATTAGAAACCAACCCAAGTCATTTAGGAT
66 AAGACCCTAAACAACTCACTAAAACTTCAGAACAAGATTAGAAACCAACCCAAGTCATTTAGGAT
33506 AATTTTAGGTGTTTTCTCGAGCCTAAA
131 AATTTTAGGTGTTTTCTCGAGCCTAAA
33533 ATATCAGTTT
Statistics
Matches: 152, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 152 1.00
ACGTcount: A:0.36, C:0.18, G:0.13, T:0.33
Consensus pattern (157 bp):
GTTTATCTTTGATTTCATGATTCAACCAAATTTTAAGCGTTAAAAATGTATTTTTAAGACACCTT
AAGACCCTAAACAACTCACTAAAACTTCAGAACAAGATTAGAAACCAACCCAAGTCATTTAGGAT
AATTTTAGGTGTTTTCTCGAGCCTAAA
Found at i:53675 original size:21 final size:22
Alignment explanation
Indices: 53634--53683 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
53624 TGAATAGTAC
53634 CGATACCATATGGAAGAGGTAT
1 CGATACCATATGGAAGAGGTAT
*
53656 CGATACC-TAT-GAGGAGGGTAT
1 CGATACCATATGGAAGA-GGTAT
53677 CGATACC
1 CGATACC
53684 CAGAAAACTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 4 0.15
21 15 0.58
22 7 0.27
ACGTcount: A:0.32, C:0.18, G:0.28, T:0.22
Consensus pattern (22 bp):
CGATACCATATGGAAGAGGTAT
Found at i:54608 original size:32 final size:30
Alignment explanation
Indices: 54567--54655 Score: 124
Period size: 32 Copynumber: 2.9 Consensus size: 30
54557 GAGTCGAGGG
*
54567 TTACCTATGTCCTTTGGGACATATGGACAGTA
1 TTACCTATGTCCTTCGGGACATATGGACA--A
*
54599 TTACCTATGTCCTTCAGGACATATGGACAA
1 TTACCTATGTCCTTCGGGACATATGGACAA
* *
54629 TTACCTATGTTCTTCGGAACATATGGA
1 TTACCTATGTCCTTCGGGACATATGGA
54656 TAGGTCCTTC
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
30 25 0.48
32 27 0.52
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (30 bp):
TTACCTATGTCCTTCGGGACATATGGACAA
Found at i:59214 original size:20 final size:19
Alignment explanation
Indices: 59175--59213 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
59165 TTATTTTAAA
59175 TATTTAATTCTTTAAATTT
1 TATTTAATTCTTTAAATTT
59194 TATTATAATT-TTTAAATTT
1 TATT-TAATTCTTTAAATTT
59213 T
1 T
59214 TTAATTGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (19 bp):
TATTTAATTCTTTAAATTT
Found at i:62121 original size:20 final size:20
Alignment explanation
Indices: 62085--62122 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
62075 ATCCTATTCC
**
62085 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
62105 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
62123 GCGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:66496 original size:21 final size:21
Alignment explanation
Indices: 66472--66531 Score: 84
Period size: 21 Copynumber: 2.9 Consensus size: 21
66462 CAGAACCCCA
*
66472 GGGGGTATCAATTCCCCTATG
1 GGGGGAATCAATTCCCCTATG
*
66493 GGGGGAATCGATTCCCCTATG
1 GGGGGAATCAATTCCCCTATG
**
66514 GGGGGAATCGGTTCCCCT
1 GGGGGAATCAATTCCCCT
66532 TCAAAAGGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.17, C:0.25, G:0.33, T:0.25
Consensus pattern (21 bp):
GGGGGAATCAATTCCCCTATG
Found at i:66613 original size:29 final size:29
Alignment explanation
Indices: 66580--66649 Score: 140
Period size: 29 Copynumber: 2.4 Consensus size: 29
66570 CCCTCTGCAC
66580 CAAAATGCTAAAATCCGATTTTAAACACT
1 CAAAATGCTAAAATCCGATTTTAAACACT
66609 CAAAATGCTAAAATCCGATTTTAAACACT
1 CAAAATGCTAAAATCCGATTTTAAACACT
66638 CAAAATGCTAAA
1 CAAAATGCTAAA
66650 TTAATTTCCT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.47, C:0.20, G:0.07, T:0.26
Consensus pattern (29 bp):
CAAAATGCTAAAATCCGATTTTAAACACT
Done.