Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002693.1 Hibiscus syriacus cultivar Beakdansim tig00005561_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: 122161
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:69 original size:34 final size:36
Alignment explanation
Indices: 7--88 Score: 105
Period size: 34 Copynumber: 2.3 Consensus size: 36
1 AAAAAC
*
7 TATATAATTTTGAAAACGTTTTTAAAAAACATATAA
1 TATATAATTTTGAAAACATTTTTAAAAAACATATAA
* * *
43 TATATAATTTT-AAAATATTTTT-AAAAATATATAT
1 TATATAATTTTGAAAACATTTTTAAAAAACATATAA
77 TATATAGATTTT
1 TATATA-ATTTT
89 TGGAAACTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
34 16 0.39
35 14 0.34
36 11 0.27
ACGTcount: A:0.48, C:0.02, G:0.04, T:0.46
Consensus pattern (36 bp):
TATATAATTTTGAAAACATTTTTAAAAAACATATAA
Found at i:137 original size:10 final size:10
Alignment explanation
Indices: 122--165 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
112 TTACCTTTTG
122 TTATTTATTA
1 TTATTTATTA
132 TTATTTATTA
1 TTATTTATTA
*
142 TTACTTATT-
1 TTATTTATTA
*
151 TT-TTTATTT
1 TTATTTATTA
160 TTATTT
1 TTATTT
166 TGTTGCAGGG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
8 5 0.17
9 4 0.13
10 21 0.70
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (10 bp):
TTATTTATTA
Found at i:6902 original size:165 final size:165
Alignment explanation
Indices: 6622--7202 Score: 788
Period size: 165 Copynumber: 3.5 Consensus size: 165
6612 TTTGCCAGCT
** * * * *
6622 AAAGACCTTCGAGTTCGACTACGCTCAGCTTTGAGGGAACATCATTTACAGCATAACTTAAGTCG
1 AAAGACCCCCGAGTTCGACTACACTCAGCTTTGAGGGCACATCATTTGCAGCATAACTTAAGTCA
* * *
6687 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTTGATTACGCTCAGCTCCAAGGCACATCATT
66 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATT
*
6752 TGCAGTATAGCTTAAGTCGAGAATGGCTATCTGCC
131 TGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCC
*
6787 AAAGACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTGCAGCATAACTTAAGTCA
1 AAAGACCCCCGAGTTCGACTACACTCAGCTTTGAGGGCACATCATTTGCAGCATAACTTAAGTCA
6852 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATT
66 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATT
6917 TGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCC
131 TGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCC
* * * *
6952 AAAGACCCCCGAGTTCGATTACACTCAGCTTAGAGGGCACATCATTTGCAGTATAACTTAAGTCG
1 AAAGACCCCCGAGTTCGACTACACTCAGCTTTGAGGGCACATCATTTGCAGCATAACTTAAGTCA
* * * *
7017 AGAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCAACTACGCTT-AGCTCCAAGGCATATCAT
66 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACG-TTCAGCTCCAAGGCACATCAT
* * * * * *
7081 TTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCC
130 TTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCC
*** * ** * * * *
7117 AATAAAAGACCTTTGAGTTCGACTACGCTCAGC-TCAACGACACATCATTTGCAGCACAGCTTAA
1 ----AAAGACCCCCGAGTTCGACTACACTCAGCTTTGAGGGCACATCATTTGCAGCATAACTTAA
7181 GTCAAGAAGGGTTATCTGCCAA
62 GTCAAGAAGGGTTATCTGCCAA
7203 AGACCCCCGA
Statistics
Matches: 374, Mismatches: 37, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
165 303 0.81
166 2 0.01
168 45 0.12
169 24 0.06
ACGTcount: A:0.30, C:0.24, G:0.21, T:0.25
Consensus pattern (165 bp):
AAAGACCCCCGAGTTCGACTACACTCAGCTTTGAGGGCACATCATTTGCAGCATAACTTAAGTCA
AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATT
TGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCC
Found at i:7083 original size:249 final size:245
Alignment explanation
Indices: 6574--7367 Score: 894
Period size: 249 Copynumber: 3.2 Consensus size: 245
6564 TTTTCTTAAA
* * * * * * * *
6574 CACATCATTTGCAACATAGCTCAAGGCAATAAGGGCTATTTGCCAGCTAAAGACCTTCGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCG
* * * * *
6639 ACTACGCTCAGCTTTGAGGGAACATCATTTACAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA
66 ACTACGCTCAGC--TCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTG-C-
** * * * *
6704 ACAAAAGACCTTCGAGTTTGATTACGCTCAGCTCCA-A-GGCACATCATTTGCAGTATAGCTTAA
127 -C-AAAGACCCCCGAGTTCGATTACACTCAGCT-TAGAGGGCACATCATTTGCAGTATAACTTAA
* * ** * * * ** *
6767 GTCGAGAATGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACACTCAGCTTTGAGGG
189 GTCGAGAAGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCTTAGC-TCCAAGG
*
6824 CACATCATTTGCAGCATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCG
* * *
6889 ACTACGTTCAGCTCCAAGGCACATCATTTGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCCAA
66 ACTACGCTCAGCT-CAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA
6954 AGACCCCCGAGTTCGATTACACTCAGCTTAGAGGGCACATCATTTGCAGTATAACTTAAGTCGAG
130 AGACCCCCGAGTTCGATTACACTCAGCTTAGAGGGCACATCATTTGCAGTATAACTTAAGTCGAG
* *
7019 AAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCAACTACGCTTAGCTCCAAGG
195 AAGGGTTATCTG---ACCAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGG
* * * * * * *
7073 CATATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAATAAAAGACCTTTGAGTTCG
1 CACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCG
* * *
7138 ACTACGCTCAGCTCAACGACACATCATTTGCAGCACAGCTTAAGTCAAGAAGGGTTATCTGCCAA
66 ACTACGCTCAGCTCAA-GGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAA
* * * * *
7203 AGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACA-TCATAACTCAAGGCTA
130 AGACCCCCGAGTTCGATTACACTCAGCTTAGAGGGCACATCATTTGCAGT-ATAACTTAAGTCGA
* *
7267 GAAGGGTTATCTGTGACCAAAAGACATTCGAGTTCGACTACGTTTAGCTCCAAGG
194 GAAGGGTTATC--TGACC-AAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGG
* * * * *
7322 CACATCATTTACAGCATAGCTTAACTCGAGAAAGGCTATCTGCCAA
1 CACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAA
7368 AGACCCCCGA
Statistics
Matches: 467, Mismatches: 65, Indels: 25
0.84 0.12 0.04
Matches are distributed among these distances:
244 1 0.00
245 27 0.06
246 42 0.09
248 9 0.02
249 295 0.63
250 91 0.19
251 2 0.00
ACGTcount: A:0.30, C:0.25, G:0.20, T:0.25
Consensus pattern (245 bp):
CACATCATTTGCAGCATAACTTAAGTCAAGAAGGGCTATCTGCCAACAAAAGACCTTCGAGTTCG
ACTACGCTCAGCTCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAA
GACCCCCGAGTTCGATTACACTCAGCTTAGAGGGCACATCATTTGCAGTATAACTTAAGTCGAGA
AGGGTTATCTGACCAAAGACCTTCGAGTTCGACTACGCTTAGCTCCAAGG
Found at i:7247 original size:165 final size:161
Alignment explanation
Indices: 6622--7402 Score: 767
Period size: 165 Copynumber: 4.7 Consensus size: 161
6612 TTTGCCAGCT
** * *
6622 AAAGACCTTCGAGTTCGACTACGCTCAGCTTTGAGGGAACATCATTTACAGCATAACTTAAGTCG
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCAAGGGCACATCATTTGCAGCATAACTTAAGTCG
*
6687 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTTGATTACGCTCAGCTCCAAGGCACATCATT
65 AGAAGGGTTATCTGCC--C-AAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATCATT
* * *
6752 TGCAGTATAGCTTAAGTCGAGAATGGCTATCTGCC
127 TGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC
** * * ** *
6787 AAAGACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCACATCATTTGCAGCATAACTTAAGTCA
1 AAAGACCTTCGAGTTCGACTACGCTCAGC-TCAAGGGCACATCATTTGCAGCATAACTTAAGTCG
* *
6852 AGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCATT
65 AGAAGGGTTATCTGCC--C-AAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATCATT
* *
6917 TGCAGTATAGCTTAAGTCGAGAAGGGCTATCTGCC
127 TGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC
** * * * *
6952 AAAGACCCCCGAGTTCGATTACACTCAGCTTAGAGGGCACATCATTTGCAGTATAACTTAAGTCG
1 AAAGACCTTCGAGTTCGACTACGCTCAGCTCA-AGGGCACATCATTTGCAGCATAACTTAAGTCG
* * * * *
7017 AGAAGGGTTATCTGCCAACCAAAGGCCTTCGAGTTCAACTACGCTTAGCTCCAAGGCATATCATT
65 AGAAGGGTTATCTG-C--CCAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATCATT
* * * *
7082 TGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCC
127 TGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCC
* * * * *
7117 AATAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGACACATCATTTGCAGCACAGCTTAAG
1 ----AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGGCACATCATTTGCAGCATAACTTAAG
* ** * * *
7182 TCAAGAAGGGTTATCTG-CCAAAGACCCCCGAGTTCGATTACACTCAGCTTCGAGGGCACATCAT
62 TCGAGAAGGGTTATCTGCCCAAAGACCTTCGAGTTCGATTACGCTCAGC-TCCAAGGCACATCAT
* * * * * *
7246 TTACATCATAACTCAAGGCTAGAAGGGTTATCTGTGACC
126 TTGCAGCATAACTTAAGTCGAGAAGGGCTATC--TG-CC
* * * * * *
7285 AAAAGACATTCGAGTTCGACTACGTTTAGCTCCAA-GGCACATCATTTACAGCATAGCTTAACTC
1 -AAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGGCACATCATTTGCAGCATAACTTAAGTC
* * ** * * *
7349 GAGAAAGGCTATCTG-CCAAAGACCCCCGAGTTCGATTACACTCAGATCGAAGGC
64 GAGAAGGGTTATCTGCCCAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGC
7403 CTATCAACCA
Statistics
Matches: 537, Mismatches: 66, Indels: 27
0.85 0.10 0.04
Matches are distributed among these distances:
164 33 0.06
165 428 0.80
166 5 0.01
167 2 0.00
168 43 0.08
169 26 0.05
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.24
Consensus pattern (161 bp):
AAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGGCACATCATTTGCAGCATAACTTAAGTCGA
GAAGGGTTATCTGCCCAAAGACCTTCGAGTTCGATTACGCTCAGCTCCAAGGCACATCATTTGCA
GCATAACTTAAGTCGAGAAGGGCTATCTGCC
Found at i:7733 original size:2 final size:2
Alignment explanation
Indices: 7726--7778 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
7716 TCGTCTCATT
7726 TA TA TA TA TA TA TA TA TA TA 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 TA TA TA TA TA TA
7768 TA TA TA TA TA T
1 TA TA TA TA TA T
7779 TTAAAAATAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7812 original size:37 final size:37
Alignment explanation
Indices: 7761--7950 Score: 151
Period size: 37 Copynumber: 5.2 Consensus size: 37
7751 ATATATATAT
*
7761 ATATATATATATATATATTTAAAAATATTTTTAAAAC
1 ATATATATATATATATATTTAAAAATATTTTGAAAAC
* * * *
7798 CTATATATATATATA-GTTTGAAAACATGTTTGAAAAC
1 ATATATATATATATATATTTAAAAATAT-TTTGAAAAC
* * *
7835 ATTTATATAT-TATATAGTTTTTAAAATATTTTGAAAAT
1 ATATATATATATATATA--TTTAAAAATATTTTGAAAAC
* *
7873 AAATATA-ATATATA-ATTTTTAAAATATTTT-AAAA-
1 ATATATATATATATATA-TTTAAAAATATTTTGAAAAC
* ** * *
7907 AAATATATAT-TATATAGTTTTTAAACATTTTGAAAAT
1 ATATATATATATATATA-TTTAAAAATATTTTGAAAAC
7944 ATATATA
1 ATATATA
7951 GTTTTTAAAA
Statistics
Matches: 127, Mismatches: 17, Indels: 18
0.78 0.10 0.11
Matches are distributed among these distances:
34 11 0.09
35 19 0.15
36 32 0.25
37 39 0.31
38 17 0.13
39 9 0.07
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (37 bp):
ATATATATATATATATATTTAAAAATATTTTGAAAAC
Found at i:7886 original size:36 final size:36
Alignment explanation
Indices: 7759--7950 Score: 185
Period size: 36 Copynumber: 5.2 Consensus size: 36
7749 ATATATATAT
* *
7759 ATATATATATATATATA-TATTTAAAAATATTTTTAAA
1 ATATATATA-ATATATAGT-TTTTAAAATATTTTGAAA
* *
7796 ACCTATATAT-ATATATAG-TTTGAAAACATGTTTGAAAA
1 A--TATATATAATATATAGTTTTTAAAATAT-TTTG-AAA
* *
7834 CATTTATATATTATATAGTTTTTAAAATATTTTGAAA
1 -ATATATATAATATATAGTTTTTAAAATATTTTGAAA
* * *
7871 ATAAATATAATATATAATTTTTAAAATATTTTAAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
* * *
7907 AAATATATATTATATAGTTTTT-AAACATTTTGAAA
1 ATATATATAATATATAGTTTTTAAAATATTTTGAAA
7942 ATATATATA
1 ATATATATA
7951 GTTTTTAAAA
Statistics
Matches: 128, Mismatches: 19, Indels: 18
0.78 0.12 0.11
Matches are distributed among these distances:
35 19 0.15
36 58 0.45
37 20 0.16
38 14 0.11
39 17 0.13
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (36 bp):
ATATATATAATATATAGTTTTTAAAATATTTTGAAA
Found at i:7911 original size:34 final size:34
Alignment explanation
Indices: 7839--8132 Score: 137
Period size: 36 Copynumber: 8.5 Consensus size: 34
7829 GAAAACATTT
* *
7839 ATATATTATATAGTTTTTAAAATATTTTGAAAATAA
1 ATATAATATATAATTTTTAAAATATTTT-AAAA-AA
7875 ATATAATATATAATTTTTAAAATATTTTAAAAAA
1 ATATAATATATAATTTTTAAAATATTTTAAAAAA
* * *
7909 ATATATATTATATAGTTTTT-AAACATTTT--GAAA
1 ATATA-A-TATATAATTTTTAAAATATTTTAAAAAA
* *
7942 ATAT-ATATAGT--TTTTAAAAAACATTTTGAAGAACATA
1 ATATAATATA-TAATTTT-TAAAATATTTT-AA-AA-A-A
* * * * *
7979 TATCTATTATATAGTTTTT-AAATCATTTCAAAAAC
1 -ATATAATATATAATTTTTAAAAT-ATTTTAAAAAA
* * * * *
8014 TTATAATATATAGTTTTAAAAACATTTT---TAA
1 ATATAATATATAATTTTTAAAATATTTTAAAAAA
* * *
8045 A-A-ACTATATAATTTTGAAAACTTTTTTAAAAAAA
1 ATATAATATATAATTTTTAAAA-TATTTT-AAAAAA
* *
8079 CATATAATATATAA-TTTTATAATATTTTTAAAAAT
1 -ATATAATATATAATTTTTAAAATA-TTTTAAAAAA
*
8114 ATATATTATATAGATTTTT
1 ATATAATATATA-ATTTTT
8133 GGAAACTATT
Statistics
Matches: 196, Mismatches: 34, Indels: 56
0.69 0.12 0.20
Matches are distributed among these distances:
29 19 0.10
30 9 0.05
31 12 0.06
33 7 0.04
34 38 0.19
35 25 0.13
36 54 0.28
37 11 0.06
38 9 0.05
39 8 0.04
40 4 0.02
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.46
Consensus pattern (34 bp):
ATATAATATATAATTTTTAAAATATTTTAAAAAA
Found at i:8053 original size:29 final size:29
Alignment explanation
Indices: 8020--8076 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 29
8010 AAACTTATAA
*
8020 TATATAGTTTTAAAAACATTTTTAAAAAC
1 TATATAATTTTAAAAACATTTTTAAAAAC
* *
8049 TATATAATTTTGAAAACTTTTTTAAAAA
1 TATATAATTTTAAAAACATTTTTAAAAA
8077 AACATATAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (29 bp):
TATATAATTTTAAAAACATTTTTAAAAAC
Found at i:8094 original size:37 final size:38
Alignment explanation
Indices: 8049--8145 Score: 110
Period size: 36 Copynumber: 2.6 Consensus size: 38
8039 TTTTAAAAAC
8049 TATATAATTTTGAAAACT-TTTTTAAAAAAACATATAA
1 TATATAATTTTGAAAACTATTTTTAAAAAAACATATAA
* * * *
8086 TATATAATTTT-ATAA-TATTTTTAAAAATATATATTA
1 TATATAATTTTGAAAACTATTTTTAAAAAAACATATAA
* * *
8122 TATAGATTTTTGGAAACTATTTTT
1 TATATAATTTTGAAAACTATTTTT
8146 TTAGTTTATT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
35 1 0.02
36 28 0.57
37 13 0.27
38 7 0.14
ACGTcount: A:0.44, C:0.03, G:0.04, T:0.48
Consensus pattern (38 bp):
TATATAATTTTGAAAACTATTTTTAAAAAAACATATAA
Found at i:8207 original size:23 final size:23
Alignment explanation
Indices: 8179--8222 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
8169 TGTTATTTAT
8179 TTATTTATTATTATTATTATTAC
1 TTATTTATTATTATTATTATTAC
* * *
8202 TTATTTTTTTTTATTTTTATT
1 TTATTTATTATTATTATTATT
8223 TGTTGCAGGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.23, C:0.02, G:0.00, T:0.75
Consensus pattern (23 bp):
TTATTTATTATTATTATTATTAC
Found at i:9462 original size:17 final size:17
Alignment explanation
Indices: 9442--9475 Score: 59
Period size: 17 Copynumber: 1.9 Consensus size: 17
9432 CTTCTCTCTA
9442 TTTTATTTATTTATTTAT
1 TTTTATTT-TTTATTTAT
9460 TTTTATTTTTTATTTA
1 TTTTATTTTTTATTTA
9476 ATGATTTTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTATTTTTTATTTAT
Found at i:12790 original size:19 final size:17
Alignment explanation
Indices: 12772--12806 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
12762 AAAAAAATGA
12772 AAAATCCTACCCCACATG
1 AAAAT-CTACCCCACATG
*
12790 ATAATCTACCCCACATG
1 AAAATCTACCCCACATG
12807 CTTTAATTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.37, C:0.37, G:0.06, T:0.20
Consensus pattern (17 bp):
AAAATCTACCCCACATG
Found at i:14534 original size:10 final size:10
Alignment explanation
Indices: 14519--14551 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
14509 CTATTCCCGT
14519 TGTTTGGATG
1 TGTTTGGATG
14529 TGTTTGGATG
1 TGTTTGGATG
*
14539 TGTTTGGCTG
1 TGTTTGGATG
14549 TGT
1 TGT
14552 ACTTTGACTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.06, C:0.03, G:0.39, T:0.52
Consensus pattern (10 bp):
TGTTTGGATG
Found at i:14952 original size:2 final size:2
Alignment explanation
Indices: 14945--14986 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
14935 ATATAAAATA
14945 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
14987 TTACGATATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14952 original size:14 final size:15
Alignment explanation
Indices: 14910--14985 Score: 63
Period size: 16 Copynumber: 5.2 Consensus size: 15
14900 AACATAATAA
14910 ATAAATAATA-ATA-
1 ATAAATAATATATAT
*
14923 AT-AA-AATATAAAAT
1 ATAAATAATAT-ATAT
14937 ATAAAATAATATATAT
1 AT-AAATAATATATAT
*
14953 ATATAT-ATATATAT
1 ATAAATAATATATAT
*
14967 ATATATATATATATAT
1 ATAAATA-ATATATAT
14983 ATA
1 ATA
14986 TTTACGATAT
Statistics
Matches: 52, Mismatches: 3, Indels: 13
0.76 0.04 0.19
Matches are distributed among these distances:
11 4 0.08
12 2 0.04
13 4 0.08
14 16 0.31
15 3 0.06
16 18 0.35
17 5 0.10
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (15 bp):
ATAAATAATATATAT
Found at i:15033 original size:17 final size:16
Alignment explanation
Indices: 15013--15061 Score: 55
Period size: 16 Copynumber: 3.0 Consensus size: 16
15003 TTAAAAATTG
15013 TTTTTCAAAATAATATA
1 TTTTTCAAAA-AATATA
*
15030 -TTTTCAAAAAATATC
1 TTTTTCAAAAAATATA
*
15045 TTTTTAAAAACAATATA
1 TTTTTCAAAA-AATATA
15062 ATATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 5 0.19
16 17 0.63
17 5 0.19
ACGTcount: A:0.49, C:0.08, G:0.00, T:0.43
Consensus pattern (16 bp):
TTTTTCAAAAAATATA
Found at i:15048 original size:15 final size:15
Alignment explanation
Indices: 15014--15054 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
15004 TAAAAATTGT
15014 TTTTCAAAATAATATA
1 TTTTCAAAA-AATATA
*
15030 TTTTCAAAAAATATC
1 TTTTCAAAAAATATA
*
15045 TTTTTAAAAA
1 TTTTCAAAAA
15055 CAATATAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (15 bp):
TTTTCAAAAAATATA
Found at i:15161 original size:12 final size:12
Alignment explanation
Indices: 15144--15168 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15134 TATATAATAT
15144 ATGTTTTCAAAA
1 ATGTTTTCAAAA
15156 ATGTTTTCAAAA
1 ATGTTTTCAAAA
15168 A
1 A
15169 CTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:15199 original size:36 final size:37
Alignment explanation
Indices: 15045--15256 Score: 181
Period size: 37 Copynumber: 5.7 Consensus size: 37
15035 AAAAAATATC
* *
15045 TTTTTAAAAACAATATAATATATATATGTTTTTTAAAAATG
1 TTTTCAAAAACTATAT-ATATATATATG--TTTT-AAAATG
* *
15086 TTTTAAAAAAC--CATATA-ATATATGTTTTAAAAAATG
1 TTTTCAAAAACTATATATATATATATGTTTT--AAAATG
15122 TTTTCCAAAAAC--TATATA-ATATATGTTTTCAAAAATG
1 TTTT-CAAAAACTATATATATATATATGTTTT--AAAATG
*
15159 TTTTCAAAAACTATATATATATATATGTTTTCAAAT-
1 TTTTCAAAAACTATATATATATATATGTTTTAAAATG
* * * * *
15195 TTTTC-CAAACTATATAATACATATATATTTTGAAATA
1 TTTTCAAAAACTATAT-ATATATATATGTTTTAAAATG
15232 TTTTC-AAAACTATATATATATATAT
1 TTTTCAAAAACTATATATATATATAT
15257 ATATATATAT
Statistics
Matches: 152, Mismatches: 12, Indels: 19
0.83 0.07 0.10
Matches are distributed among these distances:
35 13 0.09
36 49 0.32
37 58 0.38
38 9 0.06
39 13 0.09
41 10 0.07
ACGTcount: A:0.45, C:0.08, G:0.04, T:0.44
Consensus pattern (37 bp):
TTTTCAAAAACTATATATATATATATGTTTTAAAATG
Found at i:15249 original size:2 final size:2
Alignment explanation
Indices: 15242--15280 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
15232 TTTTCAAAAC
15242 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
15281 CAAAACTTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20533 original size:23 final size:23
Alignment explanation
Indices: 20507--20591 Score: 89
Period size: 23 Copynumber: 3.7 Consensus size: 23
20497 GAGTCGAGGG
* *
20507 TTCTATGCGGTCCTTCGGAATAA
1 TTCTACGCGGTCCTTCGGGATAA
* * * *
20530 TTCTACGTGGTCCTTAGGGACAT
1 TTCTACGCGGTCCTTCGGGATAA
20553 TTCTACGCGGTCCTTCGGGATAA
1 TTCTACGCGGTCCTTCGGGATAA
* * *
20576 TACTATGTGGTCCTTC
1 TTCTACGCGGTCCTTC
20592 AGGACGTTTC
Statistics
Matches: 49, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 49 1.00
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (23 bp):
TTCTACGCGGTCCTTCGGGATAA
Found at i:20616 original size:46 final size:46
Alignment explanation
Indices: 20507--20603 Score: 133
Period size: 46 Copynumber: 2.1 Consensus size: 46
20497 GAGTCGAGGG
* *
20507 TTCTATGCGGTCCTTCGGAATAATTCTACGTGGTCCTTAGGGACAT
1 TTCTACGCGGTCCTTCGGAATAATACTACGTGGTCCTTAGGGACAT
* * *
20553 TTCTACGCGGTCCTTCGGGATAATACTATGTGGTCCTTCA-GGACGT
1 TTCTACGCGGTCCTTCGGAATAATACTACGTGGTCCTT-AGGGACAT
20599 TTCTA
1 TTCTA
20604 TGTGGCACTT
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.35
Consensus pattern (46 bp):
TTCTACGCGGTCCTTCGGAATAATACTACGTGGTCCTTAGGGACAT
Found at i:24924 original size:21 final size:21
Alignment explanation
Indices: 24900--24959 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
24890 GCGTAGAATT
24900 TGTCCCGAAGGACCACATAGA
1 TGTCCCGAAGGACCACATAGA
*
24921 TGTCCCGAATGACCAC-T--A
1 TGTCCCGAAGGACCACATAGA
* *
24939 TGTCCCAAAGGACCGCATAGA
1 TGTCCCGAAGGACCACATAGA
24960 CCCTCGACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
18 14 0.44
19 1 0.03
20 1 0.03
21 16 0.50
ACGTcount: A:0.32, C:0.30, G:0.22, T:0.17
Consensus pattern (21 bp):
TGTCCCGAAGGACCACATAGA
Found at i:29730 original size:21 final size:21
Alignment explanation
Indices: 29704--29751 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
29694 GTGTAAATGA
29704 GCCGAGTCGAGCTCGAGTATT
1 GCCGAGTCGAGCTCGAGTATT
*
29725 GCCGAGTCGAGTTCGAGTATT
1 GCCGAGTCGAGCTCGAGTATT
29746 GCCGAG
1 GCCGAG
29752 CTCAACTCGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.19, C:0.23, G:0.35, T:0.23
Consensus pattern (21 bp):
GCCGAGTCGAGCTCGAGTATT
Found at i:29761 original size:21 final size:21
Alignment explanation
Indices: 29704--29761 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
29694 GTGTAAATGA
*
29704 GCCGAGTCGAGCTCGAGTATT
1 GCCGAGTCGAACTCGAGTATT
**
29725 GCCGAGTCGAGTTCGAGTATT
1 GCCGAGTCGAACTCGAGTATT
29746 GCCGAGCTC-AACTCGA
1 GCCGAG-TCGAACTCGA
29762 ATTTGAAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 31 0.94
22 2 0.06
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.22
Consensus pattern (21 bp):
GCCGAGTCGAACTCGAGTATT
Found at i:29882 original size:16 final size:16
Alignment explanation
Indices: 29861--29891 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
29851 TGAAACTCGA
29861 CTCGAACTCAAAAAAG
1 CTCGAACTCAAAAAAG
29877 CTCGAACTCAAAAAA
1 CTCGAACTCAAAAAA
29892 TATTCAAGAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.52, C:0.26, G:0.10, T:0.13
Consensus pattern (16 bp):
CTCGAACTCAAAAAAG
Found at i:30900 original size:7 final size:7
Alignment explanation
Indices: 30888--30968 Score: 54
Period size: 7 Copynumber: 11.6 Consensus size: 7
30878 TCACATAATC
30888 GGGTTTA
1 GGGTTTA
30895 GGGTTTA
1 GGGTTTA
*
30902 GGGCTTA
1 GGGTTTA
* *
30909 TGATTTA
1 GGGTTTA
*
30916 GGATTTA
1 GGGTTTA
*
30923 GGATTTA
1 GGGTTTA
*
30930 AGGTTTA
1 GGGTTTA
*
30937 TGGTTTA
1 GGGTTTA
**
30944 TAGTTTA
1 GGGTTTA
*
30951 GAGTTTA
1 GGGTTTA
**
30958 GAATTTA
1 GGGTTTA
30965 GGGT
1 GGGT
30969 GCAATCTAAT
Statistics
Matches: 61, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 61 1.00
ACGTcount: A:0.23, C:0.01, G:0.31, T:0.44
Consensus pattern (7 bp):
GGGTTTA
Found at i:31050 original size:7 final size:7
Alignment explanation
Indices: 31038--31138 Score: 98
Period size: 7 Copynumber: 14.7 Consensus size: 7
31028 AATTGGATTA
31038 AGGGTTT
1 AGGGTTT
*
31045 AGGGTTA
1 AGGGTTT
* *
31052 AGTGCTT
1 AGGGTTT
*
31059 AAGGTTT
1 AGGGTTT
31066 AGGGTTT
1 AGGGTTT
31073 AGGGTTT
1 AGGGTTT
*
31080 AGAGTTT
1 AGGGTTT
31087 -GGGTTT
1 AGGGTTT
31093 AGGGTTT
1 AGGGTTT
**
31100 AGTATTT
1 AGGGTTT
**
31107 ATAGTTT
1 AGGGTTT
31114 AGGGTTT
1 AGGGTTT
31121 A-GGTTT
1 AGGGTTT
*
31127 AGGATTT
1 AGGGTTT
31134 AGGGT
1 AGGGT
31139 GTATTCTAAC
Statistics
Matches: 73, Mismatches: 19, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
6 11 0.15
7 62 0.85
ACGTcount: A:0.20, C:0.01, G:0.36, T:0.44
Consensus pattern (7 bp):
AGGGTTT
Found at i:31092 original size:20 final size:21
Alignment explanation
Indices: 31062--31138 Score: 97
Period size: 20 Copynumber: 3.8 Consensus size: 21
31052 AGTGCTTAAG
31062 GTTTAGGGTTTAGGGTTTAGA
1 GTTTAGGGTTTAGGGTTTAGA
31083 GTTT-GGGTTTAGGGTTTAGTA
1 GTTTAGGGTTTAGGGTTTAG-A
**
31104 -TTTATAGTTTAGGGTTTAG-
1 GTTTAGGGTTTAGGGTTTAGA
*
31123 GTTTAGGATTTAGGGT
1 GTTTAGGGTTTAGGGT
31139 GTATTCTAAC
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
20 30 0.62
21 18 0.38
ACGTcount: A:0.18, C:0.00, G:0.35, T:0.47
Consensus pattern (21 bp):
GTTTAGGGTTTAGGGTTTAGA
Found at i:31099 original size:27 final size:27
Alignment explanation
Indices: 31061--31135 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
31051 AAGTGCTTAA
*
31061 GGTTTAGGGTTTAGGGTTTAGAGTTTG
1 GGTTTAGGGTTTAGGATTTAGAGTTTG
* *
31088 GGTTTAGGGTTTAGTATTTATAGTTTAG
1 GGTTTAGGGTTTAGGATTTAGAGTTT-G
31116 GGTTTA-GGTTTAGGATTTAG
1 GGTTTAGGGTTTAGGATTTAG
31136 GGTGTATTCT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
27 35 0.83
28 7 0.17
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.47
Consensus pattern (27 bp):
GGTTTAGGGTTTAGGATTTAGAGTTTG
Found at i:31315 original size:14 final size:14
Alignment explanation
Indices: 31296--31336 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
31286 TATAATTATC
31296 AATAATGTATTTTT
1 AATAATGTATTTTT
31310 AATAA--T-TTTTT
1 AATAATGTATTTTT
*
31321 AATAATGTAATTTT
1 AATAATGTATTTTT
31335 AA
1 AA
31337 AAAATCTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:34723 original size:46 final size:46
Alignment explanation
Indices: 34656--34745 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
34646 GAATATCTTT
34656 GATATTAACATTTTCGGTAGAAAAAATAACATTTTAGGTAGCGCCC
1 GATATTAACATTTTCGGTAGAAAAAATAACATTTTAGGTAGCGCCC
* * *
34702 GATATTAATATTTTCGGTAGAAAAAATGACATTTTATGTAGCGC
1 GATATTAACATTTTCGGTAGAAAAAATAACATTTTAGGTAGCGC
34746 TCTACCGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (46 bp):
GATATTAACATTTTCGGTAGAAAAAATAACATTTTAGGTAGCGCCC
Found at i:34997 original size:29 final size:29
Alignment explanation
Indices: 34963--35021 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
34953 CCTAAATTAA
34963 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
34992 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
35021 T
1 T
35022 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:39682 original size:29 final size:29
Alignment explanation
Indices: 39648--39706 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
39638 CCTAAATTAA
* *
39648 TTTGATGTCATTTCTTATATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
39677 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
39706 T
1 T
39707 AGGTGAAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.53
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:49558 original size:24 final size:24
Alignment explanation
Indices: 49531--49606 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 24
49521 TATATCAAAA
49531 ATCAAAACATAAAT-CAGGTCAAGT
1 ATCAAAACA-AAATCCAGGTCAAGT
* * *
49555 ATCATATCAAAATCCATGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
* * * *
49579 ATCAGATCAGAATCCAAGTCAAGT
1 ATCAAAACAAAATCCAGGTCAAGT
49603 ATCA
1 ATCA
49607 GATCAGAATC
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
23 4 0.09
24 41 0.91
ACGTcount: A:0.45, C:0.20, G:0.12, T:0.24
Consensus pattern (24 bp):
ATCAAAACAAAATCCAGGTCAAGT
Found at i:49607 original size:24 final size:24
Alignment explanation
Indices: 49548--49663 Score: 180
Period size: 24 Copynumber: 4.8 Consensus size: 24
49538 CATAAATCAG
* *
49548 GTCAAGTATCATATCAAAATCCAT
1 GTCAAGTATCAGATCAGAATCCAT
*
49572 GTCAAGTATCAGATCAGAATCCAA
1 GTCAAGTATCAGATCAGAATCCAT
*
49596 GTCAAGTATCAGATCAGAATCTAT
1 GTCAAGTATCAGATCAGAATCCAT
49620 GTC-AGATATCAGATCAGAATCCAT
1 GTCAAG-TATCAGATCAGAATCCAT
49644 GTCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
49664 TCAAATCGAA
Statistics
Matches: 84, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
23 2 0.02
24 80 0.95
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.16, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAT
Found at i:49679 original size:48 final size:48
Alignment explanation
Indices: 49579--49681 Score: 138
Period size: 48 Copynumber: 2.1 Consensus size: 48
49569 CATGTCAAGT
** *
49579 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTATGTCAGAT
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
*
49627 ATCAGATCAGAATCCATGTCAAGTATCAGATCAGAAT-TCAAATC-GAAA
1 ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCT-AAATCAG-AA
49675 ATCAGAT
1 ATCAGAT
49682 AAAATATTCA
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
47 2 0.04
48 47 0.96
ACGTcount: A:0.42, C:0.18, G:0.16, T:0.24
Consensus pattern (48 bp):
ATCAGATCAGAATCCAAGTCAAGTATCAGATCAGAATCTAAATCAGAA
Found at i:51761 original size:13 final size:13
Alignment explanation
Indices: 51743--51768 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51733 AACGGTCAAT
51743 GGTCAACGGGTCG
1 GGTCAACGGGTCG
51756 GGTCAACGGGTCG
1 GGTCAACGGGTCG
51769 AATCGGGTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.46, T:0.15
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:51785 original size:31 final size:27
Alignment explanation
Indices: 51727--51790 Score: 83
Period size: 31 Copynumber: 2.2 Consensus size: 27
51717 GTGGTCAACA
51727 CGGGTCAACGGTCAATGGTCAACGGGT
1 CGGGTCAACGGTCAATGGTCAACGGGT
*
51754 CGGGTCAACGGGTCGAATCGGGTTAACGGGT
1 CGGGTCAAC-GGTC-AAT--GGTCAACGGGT
51785 CGGGTC
1 CGGGTC
51791 GGACTGTGAC
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 9 0.28
28 4 0.12
29 3 0.09
31 16 0.50
ACGTcount: A:0.19, C:0.22, G:0.41, T:0.19
Consensus pattern (27 bp):
CGGGTCAACGGTCAATGGTCAACGGGT
Found at i:51792 original size:18 final size:18
Alignment explanation
Indices: 51749--51792 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
51739 CAATGGTCAA
51749 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
** *
51767 CGAATCGGGTTAACGGGT
1 CGGGTCGGGTCAACGGGT
51785 CGGGTCGG
1 CGGGTCGG
51793 ACTGTGACCG
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.18
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:54679 original size:29 final size:29
Alignment explanation
Indices: 54637--54693 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
54627 CCGAGCGAGG
*
54637 GTAGGTCGCCCGGAGTGCATGACGACCTT
1 GTAGGTCGCCCGGAGGGCATGACGACCTT
*
54666 GTAGGTCGCCCGGAGGGCATGGCGACCT
1 GTAGGTCGCCCGGAGGGCATGACGACCT
54694 ACCCTCGCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.16, C:0.28, G:0.39, T:0.18
Consensus pattern (29 bp):
GTAGGTCGCCCGGAGGGCATGACGACCTT
Found at i:54742 original size:14 final size:14
Alignment explanation
Indices: 54720--54752 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
54710 CCTCGCATAG
*
54720 CTCGTTCGGATGGC
1 CTCGGTCGGATGGC
54734 CTCGGTCGGATGGC
1 CTCGGTCGGATGGC
54748 CTCGG
1 CTCGG
54753 ATGCTCTCGG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.30, G:0.39, T:0.24
Consensus pattern (14 bp):
CTCGGTCGGATGGC
Found at i:54764 original size:20 final size:20
Alignment explanation
Indices: 54739--54792 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
54729 ATGGCCTCGG
54739 TCGGATGGCCTCGGATGCTC
1 TCGGATGGCCTCGGATGCTC
*
54759 TCGGATGGCCTCGGATGCTT
1 TCGGATGGCCTCGGATGCTC
54779 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
54793 TCGGATGGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.09, C:0.28, G:0.37, T:0.26
Consensus pattern (20 bp):
TCGGATGGCCTCGGATGCTC
Found at i:54798 original size:14 final size:14
Alignment explanation
Indices: 54779--54806 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
54769 TCGGATGCTT
54779 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
54793 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
54807 ATGCCCAGCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.07, C:0.29, G:0.43, T:0.21
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:54809 original size:10 final size:10
Alignment explanation
Indices: 54739--54792 Score: 67
Period size: 10 Copynumber: 5.4 Consensus size: 10
54729 ATGGCCTCGG
54739 TCGGATGGCC
1 TCGGATGGCC
54749 TCGGAT-GCTC
1 TCGGATGGC-C
54759 TCGGATGGCC
1 TCGGATGGCC
*
54769 TCGGAT-GCTT
1 TCGGATGGC-C
54779 TCGGATGGCC
1 TCGGATGGCC
54789 TCGG
1 TCGG
54793 TCGGATGGCC
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
9 4 0.11
10 30 0.79
11 4 0.11
ACGTcount: A:0.09, C:0.28, G:0.37, T:0.26
Consensus pattern (10 bp):
TCGGATGGCC
Found at i:57047 original size:265 final size:255
Alignment explanation
Indices: 56543--57118 Score: 830
Period size: 265 Copynumber: 2.2 Consensus size: 255
56533 TTTATTTATA
56543 TATTGAATAAAAAT-ATTTTTTTATTATTTCGA---GTCGGGTTTCTAATTCATATATTCGGGTC
1 TATTGAATAAAAATAATTTTTTTATTATTTCGATCGGTCGGGTTTCTAATTCATATATTCGGGTC
** *
56604 GGGTCGGTGAAACTTTATTTTTGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTTGGGTCAGG
66 GGGTCGGTGAAACTTTATTTTTGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCAGATCAGG
*
56669 TCGAGTTCGGGTTTAGGGTGAAAAATACCCGACCCAAAAATATATATAATTTTACCTTATATATT
131 TCGAGTTCGGGTTTAGGGTGAAAAAGACCCGACCCAAAAATATATATAATTTTACCTTATATATT
* *
56734 TAGAAATAATTACAATAATACCCATCTATATATAATTTTTTTCAATTAAGTCATTGTTTT
196 TAGAAATAATTACAATAATACCCATCTATATATAATTTTTTTCAATTAAATCAATGTTTT
*
56794 TATTGAATAAAAATAATTTTTTTTATTATTTCGGATCGGGTCGGATTTCTAATTCATATATTCGG
1 TATTGAATAAAAATAA-TTTTTTTATTATTTC-GATC-GGTCGGGTTTCTAATTCATATATTCGG
56859 GTCGGGTCGGGTGAAACTTTA-TTTTGTTCGGGTCGGGTCGAGTTTTTTTAAGTGTGATATTCAG
63 GTCGGGTC-GGTGAAACTTTATTTTTG-TCGGGTCGGGTCG-GTTTTTTTAAGTGTGATATTCAG
* *
56923 ATCGGGTC-AGGTTCTGGTTTAGGGTGAAAAAAACCGGACCCGACCCGAAAAA-ATATATAATTT
125 ATCAGGTCGA-GTTCGGGTTTAGGGTG--AAAAA---GACCCGACCC-AAAAATATATATAATTT
*
56986 TACCTTATATATTTA-AGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAAT
183 TACCTTATATATTTAGA-AATAATTACAATAATACCCATCTATATATAATTTTTTTCAATTAAAT
57050 CAATGTTTT
247 CAATGTTTT
*
57059 TATTGAATAAAAATAA-TTTTTTATTATTTC-ATGTCGTGTCGGGTTTCTAATTAATATATT
1 TATTGAATAAAAATAATTTTTTTATTATTTCGA--TCG-GTCGGGTTTCTAATTCATATATT
57119 GAATAAAAAT
Statistics
Matches: 292, Mismatches: 12, Indels: 30
0.87 0.04 0.09
Matches are distributed among these distances:
251 14 0.05
252 1 0.00
253 15 0.05
254 2 0.01
258 38 0.13
259 26 0.09
260 42 0.14
261 1 0.00
262 6 0.02
263 37 0.13
264 1 0.00
265 104 0.36
266 5 0.02
ACGTcount: A:0.30, C:0.12, G:0.17, T:0.41
Consensus pattern (255 bp):
TATTGAATAAAAATAATTTTTTTATTATTTCGATCGGTCGGGTTTCTAATTCATATATTCGGGTC
GGGTCGGTGAAACTTTATTTTTGTCGGGTCGGGTCGGTTTTTTTAAGTGTGATATTCAGATCAGG
TCGAGTTCGGGTTTAGGGTGAAAAAGACCCGACCCAAAAATATATATAATTTTACCTTATATATT
TAGAAATAATTACAATAATACCCATCTATATATAATTTTTTTCAATTAAATCAATGTTTT
Found at i:58133 original size:24 final size:25
Alignment explanation
Indices: 58079--58126 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 25
58069 GTAATACCAT
58079 TACCTGAAACTTTTTTTGAGTGAAA
1 TACCTGAAACTTTTTTTGAGTGAAA
58104 TACCTGAAAC-TTTTTTGAGTGAA
1 TACCTGAAACTTTTTTTGAGTGAA
58127 CTTCCTGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 13 0.57
25 10 0.43
ACGTcount: A:0.31, C:0.12, G:0.17, T:0.40
Consensus pattern (25 bp):
TACCTGAAACTTTTTTTGAGTGAAA
Found at i:58143 original size:25 final size:24
Alignment explanation
Indices: 58079--58146 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
58069 GTAATACCAT
*
58079 TACCTGAAACTTTTTTTGAGTGAAA
1 TACCTGAAAC-GTTTTTGAGTGAAA
* *
58104 TACCTGAAACTTTTTTGAGTGAAC
1 TACCTGAAACGTTTTTGAGTGAAA
* *
58128 TTCCTGGAACAGTTTTTGA
1 TACCTGAAAC-GTTTTTGA
58147 ATTGTTGAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
24 21 0.55
25 17 0.45
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.40
Consensus pattern (24 bp):
TACCTGAAACGTTTTTGAGTGAAA
Found at i:61723 original size:35 final size:35
Alignment explanation
Indices: 61649--61723 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
61639 AATGATATCG
* *
61649 TTTTGGTGCGGCTATTGATGGCTAAAACAACATTT
1 TTTTGGTGCGACTATTGATGGCTAAAACAACATTA
* * *
61684 TTTTGGTGTGACTATTTATGGCTAAAA-AGACGTTA
1 TTTTGGTGCGACTATTGATGGCTAAAACA-ACATTA
61719 TTTTG
1 TTTTG
61724 AGGAAGGCTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
34 1 0.03
35 33 0.97
ACGTcount: A:0.25, C:0.11, G:0.23, T:0.41
Consensus pattern (35 bp):
TTTTGGTGCGACTATTGATGGCTAAAACAACATTA
Found at i:62354 original size:29 final size:29
Alignment explanation
Indices: 62321--62379 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
62311 TCAATCAAAC
62321 ACAAAGGCTCAACTTCAGGTTAAGTAAGA
1 ACAAAGGCTCAACTTCAGGTTAAGTAAGA
62350 ACAAAGGCTCAACTTCAGGTTAAGTAAGA
1 ACAAAGGCTCAACTTCAGGTTAAGTAAGA
62379 A
1 A
62380 GCTTACACCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (29 bp):
ACAAAGGCTCAACTTCAGGTTAAGTAAGA
Found at i:67578 original size:22 final size:21
Alignment explanation
Indices: 67553--67595 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
67543 GGTTCACATT
67553 CTATAATTACAGGGTGTATGAC
1 CTAT-ATTACAGGGTGTATGAC
* * *
67575 CTATGTTATAGGGTTTATGAC
1 CTATATTACAGGGTGTATGAC
67596 TAATGGTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.28, C:0.12, G:0.23, T:0.37
Consensus pattern (21 bp):
CTATATTACAGGGTGTATGAC
Found at i:67665 original size:44 final size:44
Alignment explanation
Indices: 67582--67665 Score: 114
Period size: 44 Copynumber: 1.9 Consensus size: 44
67572 GACCTATGTT
* * * **
67582 ATAGGGTTTATGACTAATGGTTTAGGGTTTAAATTTCTTTATCA
1 ATAGGGTTTACGACTAACGATTTAGGGTTTAAACCTCTTTATCA
*
67626 ATAGGGTTTACGACTTACGATTTAGGGTTTAAACCTCTTT
1 ATAGGGTTTACGACTAACGATTTAGGGTTTAAACCTCTTT
67666 TTAGAATTTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.26, C:0.11, G:0.20, T:0.43
Consensus pattern (44 bp):
ATAGGGTTTACGACTAACGATTTAGGGTTTAAACCTCTTTATCA
Found at i:68375 original size:23 final size:23
Alignment explanation
Indices: 68349--68394 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
68339 TGCAAAATTG
68349 TGCATGAATTCCTTTTCATTGAC
1 TGCATGAATTCCTTTTCATTGAC
68372 TGCATGAATTCCTTTTCATTGAC
1 TGCATGAATTCCTTTTCATTGAC
68395 CACCTTGAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.43
Consensus pattern (23 bp):
TGCATGAATTCCTTTTCATTGAC
Found at i:70921 original size:22 final size:21
Alignment explanation
Indices: 70895--70938 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
70885 GGTTCACATT
70895 CCTATAATTACAGGGTGTATGA
1 CCTAT-ATTACAGGGTGTATGA
* * *
70917 CCTATGTTATAGGGTTTATGA
1 CCTATATTACAGGGTGTATGA
70938 C
1 C
70939 TAACGGTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (21 bp):
CCTATATTACAGGGTGTATGA
Found at i:70977 original size:23 final size:23
Alignment explanation
Indices: 70947--71020 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
70937 ACTAACGGTT
70947 TAGGGTTTAAATTTCTTTATCAA
1 TAGGGTTTAAATTTCTTTATCAA
* *
70970 TAGGGTTTACGA---C-TTA-CGATT
1 TAGGGTTTA-AATTTCTTTATC-A-A
70991 TAGGGTTTAAATTTCTTTATCAA
1 TAGGGTTTAAATTTCTTTATCAA
71014 TAGGGTT
1 TAGGGTT
71021 ACGACTTACG
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
19 1 0.03
20 5 0.13
21 10 0.26
23 17 0.44
24 5 0.13
25 1 0.03
ACGTcount: A:0.27, C:0.09, G:0.19, T:0.45
Consensus pattern (23 bp):
TAGGGTTTAAATTTCTTTATCAA
Found at i:71051 original size:43 final size:44
Alignment explanation
Indices: 70925--71044 Score: 206
Period size: 44 Copynumber: 2.8 Consensus size: 44
70915 GACCTATGTT
* * *
70925 ATAGGGTTTATGACTAACGGTTTAGGGTTTAAATTTCTTTATCA
1 ATAGGGTTTACGACTTACGATTTAGGGTTTAAATTTCTTTATCA
70969 ATAGGGTTTACGACTTACGATTTAGGGTTTAAATTTCTTTATCA
1 ATAGGGTTTACGACTTACGATTTAGGGTTTAAATTTCTTTATCA
71013 ATAGGG-TTACGACTTACGATTTAGGGTTTAAA
1 ATAGGGTTTACGACTTACGATTTAGGGTTTAAA
71045 CCTCTTTTTA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
43 26 0.36
44 47 0.64
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (44 bp):
ATAGGGTTTACGACTTACGATTTAGGGTTTAAATTTCTTTATCA
Found at i:85125 original size:12 final size:12
Alignment explanation
Indices: 85105--85136 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
85095 TTGAATGAAA
*
85105 TGCTGGATTCCT
1 TGCTAGATTCCT
85117 TGCTAGATTCCT
1 TGCTAGATTCCT
85129 TGCTAGAT
1 TGCTAGAT
85137 GCAAGGCGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.41
Consensus pattern (12 bp):
TGCTAGATTCCT
Found at i:95517 original size:14 final size:15
Alignment explanation
Indices: 95498--95526 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
95488 GTTTTCAGTC
95498 GAGAG-AAAAATAGA
1 GAGAGAAAAAATAGA
95512 GAGAGAAAAAATAGA
1 GAGAGAAAAAATAGA
95527 AAACCAGAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 5 0.36
15 9 0.64
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.07
Consensus pattern (15 bp):
GAGAGAAAAAATAGA
Found at i:96471 original size:30 final size:30
Alignment explanation
Indices: 96435--96527 Score: 105
Period size: 30 Copynumber: 3.1 Consensus size: 30
96425 TATGTTAGGG
* *
96435 TTTAACTTTCTATTTTTGATATTTTCGTCC
1 TTTAACTTTCTATTTTTGCTATTTTAGTCC
* *
96465 TTTAACTTTCTGTTTTAGCTATTTTAGTCC
1 TTTAACTTTCTATTTTTGCTATTTTAGTCC
* ** * *
96495 CTTAGGTTTCTATTTTTTCTATTTTGGTCC
1 TTTAACTTTCTATTTTTGCTATTTTAGTCC
96525 TTT
1 TTT
96528 GTAATTTCAA
Statistics
Matches: 51, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 51 1.00
ACGTcount: A:0.14, C:0.16, G:0.10, T:0.60
Consensus pattern (30 bp):
TTTAACTTTCTATTTTTGCTATTTTAGTCC
Found at i:96638 original size:22 final size:21
Alignment explanation
Indices: 96613--96656 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 21
96603 ATGTATGTAC
*
96613 ATGTTGTAAATGTTATTATTTT
1 ATGTTGTAAATATT-TTATTTT
96635 ATGTTGTAAATATTTTATTTT
1 ATGTTGTAAATATTTTATTTT
96656 A
1 A
96657 CATCGTATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.30, C:0.00, G:0.11, T:0.59
Consensus pattern (21 bp):
ATGTTGTAAATATTTTATTTT
Found at i:103683 original size:29 final size:29
Alignment explanation
Indices: 103644--103706 Score: 119
Period size: 29 Copynumber: 2.2 Consensus size: 29
103634 CACACTTAAA
103644 TTAA-TTTGATGTCATTGCTTACATCAAT
1 TTAATTTTGATGTCATTGCTTACATCAAT
103672 TTAATTTTGATGTCATTGCTTACATCAAT
1 TTAATTTTGATGTCATTGCTTACATCAAT
103701 TTAATT
1 TTAATT
103707 AGGTGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.12
29 30 0.88
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.49
Consensus pattern (29 bp):
TTAATTTTGATGTCATTGCTTACATCAAT
Found at i:108362 original size:29 final size:28
Alignment explanation
Indices: 108323--108382 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 28
108313 CACACCTAAA
108323 TTAATTTGATGTCATTGCTTACATCAAT
1 TTAATTTGATGTCATTGCTTACATCAAT
108351 TTAATTTTGATGTCATTGCTTACATCAAT
1 TTAA-TTTGATGTCATTGCTTACATCAAT
108380 TTA
1 TTA
108383 GTTAGGTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 4 0.13
29 27 0.87
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.48
Consensus pattern (28 bp):
TTAATTTGATGTCATTGCTTACATCAAT
Found at i:109076 original size:22 final size:22
Alignment explanation
Indices: 109051--109099 Score: 98
Period size: 22 Copynumber: 2.2 Consensus size: 22
109041 AAGTGTATAC
109051 AAGCAGATATGTAGCACAAGAG
1 AAGCAGATATGTAGCACAAGAG
109073 AAGCAGATATGTAGCACAAGAG
1 AAGCAGATATGTAGCACAAGAG
109095 AAGCA
1 AAGCA
109100 AATAAAATAC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.47, C:0.14, G:0.27, T:0.12
Consensus pattern (22 bp):
AAGCAGATATGTAGCACAAGAG
Found at i:112502 original size:7 final size:8
Alignment explanation
Indices: 112489--112521 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
112479 TTGAATTTAT
*
112489 GATTTTAC
1 GATTTAAC
112497 GATTTAAC
1 GATTTAAC
112505 GATTTAAC
1 GATTTAAC
112513 GATTTAAC
1 GATTTAAC
112521 G
1 G
112522 TCCCTGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.39
Consensus pattern (8 bp):
GATTTAAC
Found at i:113672 original size:29 final size:29
Alignment explanation
Indices: 113640--113696 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
113630 GAAGTGTATC
*
113640 AAATTCTCAATTAT-ATACATAATGTTTTA
1 AAATTCTCAATT-TCATACATAATATTTTA
* *
113669 AAATTTTCAGTTTCATACATAATATTTT
1 AAATTCTCAATTTCATACATAATATTTT
113697 CTTTCGTTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 1 0.04
29 23 0.96
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.47
Consensus pattern (29 bp):
AAATTCTCAATTTCATACATAATATTTTA
Done.