Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001919.1 Hibiscus syriacus cultivar Beakdansim tig00003882_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: 41453
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:2174 original size:22 final size:22
Alignment explanation
Indices: 2149--2193 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2139 TCGAAATAAC
*
2149 ATTCATGATAAATATAATATAT
1 ATTCATGATAAAAATAATATAT
*
2171 ATTCATGATAAAAATCATATAT
1 ATTCATGATAAAAATAATATAT
2193 A
1 A
2194 ATAACCTGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.07, G:0.04, T:0.38
Consensus pattern (22 bp):
ATTCATGATAAAAATAATATAT
Found at i:6084 original size:30 final size:30
Alignment explanation
Indices: 6050--6267 Score: 142
Period size: 30 Copynumber: 7.3 Consensus size: 30
6040 TAAAGGACCT
* *
6050 AAATAGCAAAAACATAAACTTAAAGGGATA
1 AAATAGCAAAAATAGAAACTTAAAGGGATA
* * *
6080 AAATAGTAAAAATA-AAAATTTAAGGGACTA
1 AAATAGCAAAAATAGAAACTTAAAGGGA-TA
* * *
6110 AAATAGAAAAAATAGAAATTTCAA-GGACTA
1 AAATAGCAAAAATAGAAACTTAAAGGGA-TA
* * * * *
6140 AAATGGTAAAATTAGAAACTTAAAGAGCTA
1 AAATAGCAAAAATAGAAACTTAAAGGGATA
* * *
6170 AAATAGTAAAAATAGAAAC-TAAA-GGCTCT
1 AAATAGCAAAAATAGAAACTTAAAGGGAT-A
* * * * *
6199 AAATAGGAAATACAGACATTTAAA-GGACTA
1 AAATAGCAAAAATAGAAACTTAAAGGGA-TA
* * *
6229 AAATAACAAAAATAAAAACTT-AAGGGACA
1 AAATAGCAAAAATAGAAACTTAAAGGGATA
6258 AAATAGCAAA
1 AAATAGCAAA
6268 TAATTATAAT
Statistics
Matches: 147, Mismatches: 34, Indels: 15
0.75 0.17 0.08
Matches are distributed among these distances:
28 3 0.02
29 41 0.28
30 94 0.64
31 9 0.06
ACGTcount: A:0.59, C:0.08, G:0.14, T:0.19
Consensus pattern (30 bp):
AAATAGCAAAAATAGAAACTTAAAGGGATA
Found at i:6114 original size:60 final size:60
Alignment explanation
Indices: 6037--6263 Score: 194
Period size: 60 Copynumber: 3.8 Consensus size: 60
6027 ATTGTATTCG
* * *
6037 ATTTAAAGGACCT-AAATAGCAAAAACATAAACTTAAAGGGATAAAATAGTAAAAATAAAA
1 ATTTAAAGGACCTAAAATAGCAAAAATAGAAACTTAAA-GGATAAAATAGTAAAAATAGAA
* * * * * *
6097 ATTTAAGGGA-CTAAAATAGAAAAAATAGAAATTTCAAGGACTAAAATGGTAAAATTAGAA
1 ATTTAAAGGACCTAAAATAGCAAAAATAGAAACTTAAAGGA-TAAAATAGTAAAAATAGAA
* * * * * * * * *
6157 ACTTAAA-GAGCTAAAATAGTAAAAATAGAAAC-TAAAGGCTCTAAATAGGAAATACAGAC
1 ATTTAAAGGACCTAAAATAGCAAAAATAGAAACTTAAAGGAT-AAAATAGTAAAAATAGAA
* * * *
6216 ATTTAAAGGA-CTAAAATAACAAAAATAAAAACTTAAGGGACAAAATAG
1 ATTTAAAGGACCTAAAATAGCAAAAATAGAAACTTAAAGGATAAAATAG
6264 CAAATAATTA
Statistics
Matches: 131, Mismatches: 30, Indels: 13
0.75 0.17 0.07
Matches are distributed among these distances:
58 1 0.01
59 54 0.41
60 76 0.58
ACGTcount: A:0.57, C:0.08, G:0.14, T:0.20
Consensus pattern (60 bp):
ATTTAAAGGACCTAAAATAGCAAAAATAGAAACTTAAAGGATAAAATAGTAAAAATAGAA
Found at i:6241 original size:90 final size:90
Alignment explanation
Indices: 6037--6251 Score: 236
Period size: 90 Copynumber: 2.4 Consensus size: 90
6027 ATTGTATTCG
* * * * *
6037 ATTTAAAGGACCT-AAATAGCAAAAACATAAACTTAAAGGGATAAAATAGTAAAAATAAAAATTT
1 ATTTAAAGGA-CTAAAATAGCAAAAATAAAAACTTAAAGAGATAAAATAGTAAAAATAAAAACTA
* *
6101 AAGGGACTAAAATAGAAAAAATAGAA
65 AAGGCACTAAAATAGAAAAAACAGAA
* * * * * * *
6127 ATTTCAAGGACTAAAATGGTAAAATTAGAAACTTAAAGAGCTAAAATAGTAAAAATAGAAACTAA
1 ATTTAAAGGACTAAAATAGCAAAAATAAAAACTTAAAGAGATAAAATAGTAAAAATAAAAACTAA
* * * *
6192 AGGCTCT-AAATAGGAAATACAGAC
66 AGGCACTAAAATAGAAAAAACAGAA
*
6216 ATTTAAAGGACTAAAATAACAAAAATAAAAACTTAA
1 ATTTAAAGGACTAAAATAGCAAAAATAAAAACTTAA
6252 GGGACAAAAT
Statistics
Matches: 101, Mismatches: 23, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
89 45 0.45
90 56 0.55
ACGTcount: A:0.58, C:0.08, G:0.13, T:0.21
Consensus pattern (90 bp):
ATTTAAAGGACTAAAATAGCAAAAATAAAAACTTAAAGAGATAAAATAGTAAAAATAAAAACTAA
AGGCACTAAAATAGAAAAAACAGAA
Found at i:7911 original size:131 final size:131
Alignment explanation
Indices: 7682--7995 Score: 369
Period size: 131 Copynumber: 2.4 Consensus size: 131
7672 TCTAGTCGAT
* * * * * * *
7682 GGATGACACAGTTCCTACGCGATGAGGATGGCAGACCATATTTAGAGAGGGTGATAAAAAT-GTT
1 GGATGACACGGTTCCTACGTGATAAGGAAGGCAGACCATCTTT--A-AGGATGAT-AACATGGTT
** * * *
7746 CCTATATGACGAGGATGGCTGGTTATCTAGGGGTGACACGACTCCTATGCAATGAGAAGGTATGG
62 CCTACGTGAAGAGGATGGCTGGTTATCTAAGGGTGACACGACTCCTATACAATGAGAAGGTATGG
7811 TCGGG
127 TCGGG
* * *
7816 GGATGACACGGTTTCTACGTGATAAGGAAGGCAGTCTATCTTTAAGGATGATAACATGGTTCCTA
1 GGATGACACGGTTCCTACGTGATAAGGAAGGCAGACCATCTTTAAGGATGATAACATGGTTCCTA
* ** * * *
7881 CGTGAAGAGGATGGCTGGTTATCTAAGGGTGACACGGCTCCTATATGATGAGGAGGTCTGGTCTG
66 CGTGAAGAGGATGGCTGGTTATCTAAGGGTGACACGACTCCTATACAATGAGAAGGTATGGTCGG
7946 G
131 G
* * *
7947 GGATGACACGGTTCCTACGTGATGAGGATGGCAGACCATCTTTAGGGAT
1 GGATGACACGGTTCCTACGTGATAAGGAAGGCAGACCATCTTTAAGGAT
7996 AATGTCTCAA
Statistics
Matches: 152, Mismatches: 27, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
130 4 0.03
131 112 0.74
132 1 0.01
134 35 0.23
ACGTcount: A:0.26, C:0.16, G:0.32, T:0.25
Consensus pattern (131 bp):
GGATGACACGGTTCCTACGTGATAAGGAAGGCAGACCATCTTTAAGGATGATAACATGGTTCCTA
CGTGAAGAGGATGGCTGGTTATCTAAGGGTGACACGACTCCTATACAATGAGAAGGTATGGTCGG
G
Found at i:8103 original size:35 final size:35
Alignment explanation
Indices: 8036--8103 Score: 86
Period size: 35 Copynumber: 1.9 Consensus size: 35
8026 ACAAAATTCG
* *
8036 TTTCAAGGGAAACGATCTCAAAGATGTTTGTTTTA
1 TTTCAAGGGAAACGATCCCAAAGATGTGTGTTTTA
8071 TTTCAAGGGAAACAGA-CCCAAAGATAG-GTGTTT
1 TTTCAAGGGAAAC-GATCCCAAAGAT-GTGTGTTT
8104 CAAGAGAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 26 0.90
36 3 0.10
ACGTcount: A:0.34, C:0.13, G:0.22, T:0.31
Consensus pattern (35 bp):
TTTCAAGGGAAACGATCCCAAAGATGTGTGTTTTA
Found at i:8191 original size:63 final size:61
Alignment explanation
Indices: 8101--8257 Score: 185
Period size: 63 Copynumber: 2.6 Consensus size: 61
8091 AAGATAGGTG
* ** * *
8101 TTTCAAGAGAAACAATCTCAAGGGAGACAAAACTTGTTTCAAGAAAAACATACTCAAAGATTT
1 TTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAAAAACAGACTCAAAGA--T
* *
8164 TTTCAAGAAAAACTGTCTCAAGAGAGACAAAACATTGTTTTAAGAGAAACAGACTCAAAGAT
1 TTTCAAGAAAAACTGTCTCAAGAGAGACAAAAC-TTGTTTCAAGAAAAACAGACTCAAAGAT
* *
8226 CTT--A-AAAAATTGTCTCAAGAGAGACAAAACTT
1 TTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTT
8258 TATTTTAAGA
Statistics
Matches: 84, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
58 2 0.02
59 25 0.30
60 1 0.01
62 3 0.04
63 29 0.35
64 24 0.29
ACGTcount: A:0.46, C:0.15, G:0.15, T:0.24
Consensus pattern (61 bp):
TTTCAAGAAAAACTGTCTCAAGAGAGACAAAACTTGTTTCAAGAAAAACAGACTCAAAGAT
Found at i:8251 original size:59 final size:61
Alignment explanation
Indices: 8116--8334 Score: 196
Period size: 59 Copynumber: 3.5 Consensus size: 61
8106 AGAGAAACAA
* * * * *
8116 TCTCAAGGGAGACAAAACTTGTTTCAAGAAAAACATACTCAAAGATTTTTTCAAGAAAAACTG
1 TCTCAAGAGAGACAAAACTTGTTTTAAGAGAAACAGACTCAAAGA-TTCTT-AAGAAAAACTG
*
8179 TCTCAAGAGAGACAAAACATTGTTTTAAGAGAAACAGACTCAAAGA-TCTT-A-AAAAATTG
1 TCTCAAGAGAGACAAAAC-TTGTTTTAAGAGAAACAGACTCAAAGATTCTTAAGAAAAACTG
* * * * * *
8238 TCTCAAGAGAGACAAAACTTTATTTTAAGAGAAATA-ATTTCAAAGTTTGTCTTAAGAAAGACTA
1 TCTCAAGAGAGACAAAAC-TTGTTTTAAGAGAAACAGA-CTCAAAG-AT-TCTTAAGAAAAACTG
** *
8302 TCTCAAGTA-AGACAAAGTTTGTTTTGAGAGAAA
1 TCTCAAG-AGAGACAAAACTTGTTTTAAGAGAAA
8335 TTGTCTTAAC
Statistics
Matches: 130, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
58 1 0.01
59 46 0.35
60 1 0.01
62 7 0.05
63 31 0.24
64 43 0.33
65 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.16, T:0.27
Consensus pattern (61 bp):
TCTCAAGAGAGACAAAACTTGTTTTAAGAGAAACAGACTCAAAGATTCTTAAGAAAAACTG
Found at i:8580 original size:32 final size:33
Alignment explanation
Indices: 8525--8589 Score: 114
Period size: 32 Copynumber: 2.0 Consensus size: 33
8515 TCACTTCAAG
*
8525 ATGTTGAATCTCCTAAAGATGCCCCAACGTTCA
1 ATGTTGAATCTCCTAAAGATGCCCCAACATTCA
8558 ATGTTGAATCTCC-AAAGATGCCCCAACATTCA
1 ATGTTGAATCTCCTAAAGATGCCCCAACATTCA
8590 TCATTTTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.58
33 13 0.42
ACGTcount: A:0.32, C:0.28, G:0.14, T:0.26
Consensus pattern (33 bp):
ATGTTGAATCTCCTAAAGATGCCCCAACATTCA
Found at i:9631 original size:19 final size:19
Alignment explanation
Indices: 9607--9660 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
9597 CTTCTTGTCC
*
9607 TCTTTTTTCTTTGTTTTTT
1 TCTTTTTTCTTTGTTTCTT
* *
9626 TCTTTTCTCTTT-TTCCTT
1 TCTTTTTTCTTTGTTTCTT
*
9644 T-GTTTTTCTTTGTTTCT
1 TCTTTTTTCTTTGTTTCT
9661 CTTTGCCCTT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
17 8 0.29
18 9 0.32
19 11 0.39
ACGTcount: A:0.00, C:0.17, G:0.06, T:0.78
Consensus pattern (19 bp):
TCTTTTTTCTTTGTTTCTT
Found at i:9638 original size:13 final size:12
Alignment explanation
Indices: 9609--9658 Score: 52
Period size: 12 Copynumber: 4.2 Consensus size: 12
9599 TCTTGTCCTC
9609 TTTTTTCTTTGT
1 TTTTTTCTTTGT
9621 TTTTTTCTTT-T
1 TTTTTTCTTTGT
9632 CTCTTTTTCCTTTG-
1 -T-TTTTT-CTTTGT
9646 -TTTTTCTTTGT
1 TTTTTTCTTTGT
9657 TT
1 TT
9659 CTCTTTGCCC
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
10 5 0.16
11 6 0.19
12 12 0.38
13 5 0.16
14 4 0.12
ACGTcount: A:0.00, C:0.14, G:0.06, T:0.80
Consensus pattern (12 bp):
TTTTTTCTTTGT
Found at i:9639 original size:27 final size:27
Alignment explanation
Indices: 9606--9674 Score: 88
Period size: 26 Copynumber: 2.6 Consensus size: 27
9596 GCTTCTTGTC
*
9606 CTCTTTTTTCTTTGTTTTT-TTCT-TTT
1 CTCTTTTTCCTTTGTTTTTCTT-TGTTT
9632 CTCTTTTTCCTTTGTTTTTCTTTGTTT
1 CTCTTTTTCCTTTGTTTTTCTTTGTTT
**
9659 CTCTTTGCCCTTTGTT
1 CTCTTTTTCCTTTGTT
9675 GTTTTTTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 19 0.50
27 19 0.50
ACGTcount: A:0.00, C:0.20, G:0.07, T:0.72
Consensus pattern (27 bp):
CTCTTTTTCCTTTGTTTTTCTTTGTTT
Found at i:17800 original size:3 final size:3
Alignment explanation
Indices: 17788--17852 Score: 69
Period size: 3 Copynumber: 21.3 Consensus size: 3
17778 GTTACCTGGA
* * * *
17788 AAT AAT -AT AAT AAT AAT AAT AAT AGT ATT AAT AAC AAT AAT AGT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
17835 AAT ACAT AATT AAT AAT A
1 AAT A-AT AA-T AAT AAT A
17853 GACGATTAAA
Statistics
Matches: 52, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.85
4 6 0.12
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:25480 original size:18 final size:18
Alignment explanation
Indices: 25459--25497 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
25449 TCTATATTTC
* * *
25459 TATATAGTATTATTCAGA
1 TATATAATAATATTAAGA
25477 TATATAATAATATTAAGA
1 TATATAATAATATTAAGA
25495 TAT
1 TAT
25498 TATTAAGAAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.03, G:0.08, T:0.44
Consensus pattern (18 bp):
TATATAATAATATTAAGA
Found at i:25535 original size:37 final size:37
Alignment explanation
Indices: 25477--25566 Score: 96
Period size: 37 Copynumber: 2.4 Consensus size: 37
25467 ATTATTCAGA
* *
25477 TATATAATAATATTA-AGATATTATTAAGAATA-ATA-T
1 TATATATTATTATTATA-ATATTATT-AGAATATATATT
* *
25513 TATATATTTATTATTATAATATTCTTATAATATATATT
1 TATATA-TTATTATTATAATATTATTAGAATATATATT
25551 TATATATTATTATTAT
1 TATATATTATTATTAT
25567 TGAAATAATA
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
36 11 0.24
37 27 0.59
38 8 0.17
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (37 bp):
TATATATTATTATTATAATATTATTAGAATATATATT
Found at i:25630 original size:22 final size:22
Alignment explanation
Indices: 25602--25645 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
25592 ATTGAAAGAT
25602 TTAAAGTATTATTTATAATTTA
1 TTAAAGTATTATTTATAATTTA
25624 TTAAAGTATTATTTATAATTTA
1 TTAAAGTATTATTTATAATTTA
25646 ATAATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.55
Consensus pattern (22 bp):
TTAAAGTATTATTTATAATTTA
Found at i:28924 original size:16 final size:16
Alignment explanation
Indices: 28886--28925 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28876 GAATGGTGAT
*
28886 ACATGGAACCAATGAC
1 ACATGGTACCAATGAC
**
28902 ATGTGGTACCAATGAC
1 ACATGGTACCAATGAC
28918 ACATGGTA
1 ACATGGTA
28926 TCATTCGATT
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.38, C:0.20, G:0.23, T:0.20
Consensus pattern (16 bp):
ACATGGTACCAATGAC
Found at i:31581 original size:3 final size:3
Alignment explanation
Indices: 31573--31606 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
31563 AGGCAACCAA
31573 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
31607 TATGTCTTCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:32227 original size:2 final size:2
Alignment explanation
Indices: 32220--32281 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
32210 TAGGATAATG
32220 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
32262 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
32282 TTAAAATGGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33389 original size:2 final size:2
Alignment explanation
Indices: 33382--33412 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33372 AACCAAACTA
33382 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33413 ATTTAAATAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35121 original size:59 final size:59
Alignment explanation
Indices: 35029--35437 Score: 640
Period size: 59 Copynumber: 6.9 Consensus size: 59
35019 AAATTACCAA
*
35029 AGGGCACTTTGTGTGCTAAAGTGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
35088 AGGGCACTTTGTGTGCTAAAATGGTAAGAAAATCATACTAAGTGTATGAATTTCCATAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
*
35147 AGAGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * *
35206 AGGGCATTTTGTGTGCTAAAATAGTAAGGAAACCATACTAGGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* *
35265 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATTATACTAAGTGTATTAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * *
35324 AGGGCATTTTGTGTGCAAAAATGGTAAGGAAATCATACTAGGTGTATGAATTTCCAGAT
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
* * * * * *
35383 A-GGCACTTTATGTGCTAAAATGGTAAGAAAATCATATTGATTGTATGAAATTCCA
1 AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCA
35438 ATTAAAATTA
Statistics
Matches: 319, Mismatches: 31, Indels: 1
0.91 0.09 0.00
Matches are distributed among these distances:
58 45 0.14
59 274 0.86
ACGTcount: A:0.35, C:0.11, G:0.22, T:0.32
Consensus pattern (59 bp):
AGGGCACTTTGTGTGCTAAAATGGTAAGGAAATCATACTAAGTGTATGAATTTCCAGAT
Found at i:39467 original size:23 final size:23
Alignment explanation
Indices: 39441--39495 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
39431 AAATGCACCG
39441 AAGTGCCACGTAGAATTACATCA
1 AAGTGCCACGTAGAATTACATCA
* * * *
39464 AAGTGTCGCGTAGAATTGCATCG
1 AAGTGCCACGTAGAATTACATCA
39487 AAGTGCCAC
1 AAGTGCCAC
39496 ATAAATATCC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.22
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTACATCA
Found at i:40004 original size:2 final size:2
Alignment explanation
Indices: 39997--40024 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39987 ACTCGTAGTC
39997 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
40025 CATTTTACCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.