Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004144.1 Hibiscus syriacus cultivar Beakdansim tig00009062_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: 50858
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:8182 original size:31 final size:31
Alignment explanation
Indices: 8144--8283 Score: 194
Period size: 31 Copynumber: 4.5 Consensus size: 31
8134 GAGTCGAGGG
*
8144 TTACCTATGTTCTTCGGGACATATAGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
8175 TTACCTATGTT-TGTCAGGACATATGGACTGT
1 TTACCTATGTTCT-TCGGGACATATGGACTGT
8206 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* * *
8237 TTATCTATGTTCTTCGGGACATATGAATTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
8268 TTATCTA-GATTCTTCG
1 TTACCTATG-TTCTTCG
8284 TAATCTATGA
Statistics
Matches: 100, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
30 2 0.02
31 97 0.97
32 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.20, T:0.41
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:9029 original size:19 final size:21
Alignment explanation
Indices: 9000--9062 Score: 85
Period size: 21 Copynumber: 3.1 Consensus size: 21
8990 TGCAAAAATT
9000 ACTGTAGCAGTGCATCG-TAC
1 ACTGTAGCAGTGCATCGATAC
*
9020 A-TGTAACAGTGCATCGATAC
1 ACTGTAGCAGTGCATCGATAC
* *
9040 ACTATAGCAGTGCATTGATAC
1 ACTGTAGCAGTGCATCGATAC
9061 AC
1 AC
9063 AATTTATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
19 14 0.38
20 5 0.14
21 18 0.49
ACGTcount: A:0.32, C:0.22, G:0.21, T:0.25
Consensus pattern (21 bp):
ACTGTAGCAGTGCATCGATAC
Found at i:9109 original size:21 final size:21
Alignment explanation
Indices: 9083--9124 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
9073 CGATGTTTTT
9083 GTGCATCGGTACACTATAGCA
1 GTGCATCGGTACACTATAGCA
*
9104 GTGCATCGGTACACTGTAGCA
1 GTGCATCGGTACACTATAGCA
9125 CTGTTCATGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (21 bp):
GTGCATCGGTACACTATAGCA
Found at i:17851 original size:36 final size:35
Alignment explanation
Indices: 17797--17865 Score: 111
Period size: 36 Copynumber: 1.9 Consensus size: 35
17787 ATTAATCTTC
*
17797 AATAAGAAAATACCCAAATTTTTTATGAAACCTTT
1 AATAAGAAAATACCCAAATTTCTTATGAAACCTTT
*
17832 AATAAGAAAAATACTCAAATTTCTTATGAAACCT
1 AATAAG-AAAATACCCAAATTTCTTATGAAACCT
17866 AAATCGGTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 6 0.19
36 25 0.81
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (35 bp):
AATAAGAAAATACCCAAATTTCTTATGAAACCTTT
Found at i:19032 original size:29 final size:29
Alignment explanation
Indices: 18987--19044 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
18977 GTGTTGGCCG
18987 TAGGTCGCCATGCCTT-CCGGACGACCTAC
1 TAGGTCGCCATGCCTTCCCGG-CGACCTAC
*
19016 TAGGTCGCCATGTCTTCCCGGCGACCTAC
1 TAGGTCGCCATGCCTTCCCGGCGACCTAC
19045 AAGAGATTGC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 23 0.85
30 4 0.15
ACGTcount: A:0.16, C:0.38, G:0.24, T:0.22
Consensus pattern (29 bp):
TAGGTCGCCATGCCTTCCCGGCGACCTAC
Found at i:19116 original size:20 final size:20
Alignment explanation
Indices: 19091--19145 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
19081 GGGCATCCGA
*
19091 CCGAGGTCATCCGAAAGCAT
1 CCGAGGCCATCCGAAAGCAT
*
19111 CCGAGGCCATCCGAGAGCAT
1 CCGAGGCCATCCGAAAGCAT
19131 CCGAGGCCATCCGAA
1 CCGAGGCCATCCGAA
19146 CGAGCTATGC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.27, C:0.35, G:0.27, T:0.11
Consensus pattern (20 bp):
CCGAGGCCATCCGAAAGCAT
Found at i:19135 original size:10 final size:10
Alignment explanation
Indices: 19098--19178 Score: 58
Period size: 10 Copynumber: 7.8 Consensus size: 10
19088 CGACCGAGGT
*
19098 CATCCGAAAG
1 CATCCGAGAG
19108 CATCCGAG-G
1 CATCCGAGAG
19117 CCATCCGAGAG
1 -CATCCGAGAG
19128 CATCCGAG-G
1 CATCCGAGAG
19137 CCATCCGAACGAG
1 -CATCCG-A-GAG
* *
19150 CTATGCGAGGG
1 C-ATCCGAGAG
*
19161 CATCCGAGGG
1 CATCCGAGAG
*
19171 CAACCGAG
1 CATCCGAG
19179 CGAGCTACCG
Statistics
Matches: 59, Mismatches: 5, Indels: 14
0.76 0.06 0.18
Matches are distributed among these distances:
9 2 0.03
10 44 0.75
11 5 0.08
12 3 0.05
13 5 0.08
ACGTcount: A:0.27, C:0.32, G:0.31, T:0.10
Consensus pattern (10 bp):
CATCCGAGAG
Found at i:19166 original size:33 final size:33
Alignment explanation
Indices: 19122--19185 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
19112 CGAGGCCATC
*
19122 CGAGAGCATCCGAGGCCATCCGAACGAGCTATG
1 CGAGAGCATCCGAGGCCAACCGAACGAGCTATG
* * *
19155 CGAGGGCATCCGAGGGCAACCGAGCGAGCTA
1 CGAGAGCATCCGAGGCCAACCGAACGAGCTA
19186 CCGAGCGAGG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.30, G:0.34, T:0.09
Consensus pattern (33 bp):
CGAGAGCATCCGAGGCCAACCGAACGAGCTATG
Found at i:19248 original size:10 final size:11
Alignment explanation
Indices: 19214--19276 Score: 55
Period size: 10 Copynumber: 6.0 Consensus size: 11
19204 CCCGGAGTGC
19214 ATGGC-CTCGG
1 ATGGCTCTCGG
*
19224 ATAGCTCGGTCGG
1 ATGGCTC--TCGG
19237 ATGGC-CTCGG
1 ATGGCTCTCGG
19247 AT-GCTCTCGG
1 ATGGCTCTCGG
*
19257 AT-GCTTTCGG
1 ATGGCTCTCGG
19267 ATGGC-CTCGG
1 ATGGCTCTCGG
19277 TCGGATGACC
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
9 2 0.05
10 30 0.68
11 3 0.07
12 1 0.02
13 8 0.18
ACGTcount: A:0.11, C:0.27, G:0.37, T:0.25
Consensus pattern (11 bp):
ATGGCTCTCGG
Found at i:19282 original size:14 final size:14
Alignment explanation
Indices: 19263--19304 Score: 66
Period size: 14 Copynumber: 3.0 Consensus size: 14
19253 TCGGATGCTT
19263 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
* *
19277 TCGGATGACCTTGG
1 TCGGATGGCCTCGG
19291 TCGGATGGCCTCGG
1 TCGGATGGCCTCGG
19305 ATGCCCAGCG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.10, C:0.26, G:0.40, T:0.24
Consensus pattern (14 bp):
TCGGATGGCCTCGG
Found at i:29358 original size:23 final size:22
Alignment explanation
Indices: 29312--29384 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 22
29302 AAAATAATTA
*
29312 TGTCTTTAT-A-ACATGTTCTC
1 TGTCTTTATGATACATTTTCTC
29332 TGTCTTTATGATACATTTATCTC
1 TGTCTTTATGATACATTT-TCTC
* * *
29355 TGTCTTTGTGGTACATTTTTCTT
1 TGTCTTTATGATACA-TTTTCTC
29378 TGTCTTT
1 TGTCTTT
29385 TGGTAGCTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
20 9 0.20
21 1 0.02
22 5 0.11
23 27 0.60
24 3 0.07
ACGTcount: A:0.15, C:0.16, G:0.12, T:0.56
Consensus pattern (22 bp):
TGTCTTTATGATACATTTTCTC
Found at i:30824 original size:22 final size:24
Alignment explanation
Indices: 30788--30844 Score: 80
Period size: 25 Copynumber: 2.4 Consensus size: 24
30778 TAGAAATGTT
30788 AAAA-AATATAATTATAATGACGA
1 AAAATAATATAATTATAATGACGA
*
30811 AAAATAATATTTATTATAATGACGA
1 AAAATAATA-TAATTATAATGACGA
*
30836 TAAATAATA
1 AAAATAATA
30845 ACTTCAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
23 4 0.13
24 4 0.13
25 22 0.73
ACGTcount: A:0.58, C:0.04, G:0.07, T:0.32
Consensus pattern (24 bp):
AAAATAATATAATTATAATGACGA
Found at i:31013 original size:33 final size:33
Alignment explanation
Indices: 30967--31032 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
30957 TTTTAATTAG
30967 ATAAAAAAATATTGTTAATATATTAACATTTTT
1 ATAAAAAAATATTGTTAATATATTAACATTTTT
* *
31000 ATAAAAAATTATTGTTAATATATTTACATTTTT
1 ATAAAAAAATATTGTTAATATATTAACATTTTT
31033 GGCAATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (33 bp):
ATAAAAAAATATTGTTAATATATTAACATTTTT
Found at i:31075 original size:23 final size:23
Alignment explanation
Indices: 31049--31093 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31039 GTTTAATAAT
* *
31049 ATTTTAGTAATTAATTTAATTTA
1 ATTTTAATAATAAATTTAATTTA
*
31072 ATTTTAATCATAAATTTAATTT
1 ATTTTAATAATAAATTTAATTT
31094 TTCGTCATTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTTAATAATAAATTTAATTTA
Found at i:31157 original size:47 final size:47
Alignment explanation
Indices: 31106--31200 Score: 163
Period size: 47 Copynumber: 2.0 Consensus size: 47
31096 CGTCATTGGT
*
31106 ATAATTTGATCAACATTTGATTTAGTATTTCTAGTAAAAATGTTAAA
1 ATAATTAGATCAACATTTGATTTAGTATTTCTAGTAAAAATGTTAAA
* *
31153 ATAATTAGATCAACATTTGATTTAGTATTTTTATTAAAAATGTTAAA
1 ATAATTAGATCAACATTTGATTTAGTATTTCTAGTAAAAATGTTAAA
31200 A
1 A
31201 ATATTGTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
47 45 1.00
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.43
Consensus pattern (47 bp):
ATAATTAGATCAACATTTGATTTAGTATTTCTAGTAAAAATGTTAAA
Found at i:31220 original size:30 final size:30
Alignment explanation
Indices: 31186--31248 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
31176 AGTATTTTTA
*
31186 TTAAA-AATGTTAAAAATATTGTTAATATAT
1 TTAAATAATGATAAAAA-ATTGTTAATATAT
**
31216 TTAAATTTTGATAAAAAATTGTTAATATAT
1 TTAAATAATGATAAAAAATTGTTAATATAT
31246 TTA
1 TTA
31249 CATTTTTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.46
Consensus pattern (30 bp):
TTAAATAATGATAAAAAATTGTTAATATAT
Found at i:31257 original size:32 final size:31
Alignment explanation
Indices: 31196--31254 Score: 102
Period size: 30 Copynumber: 1.9 Consensus size: 31
31186 TTAAAAATGT
31196 TAAAAATATTGTTAATATATTTAAATTTTGA
1 TAAAAATATTGTTAATATATTTAAATTTTGA
*
31227 TAAAAA-ATTGTTAATATATTTACATTTT
1 TAAAAATATTGTTAATATATTTAAATTTT
31255 TTGTAACTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 21 0.78
31 6 0.22
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (31 bp):
TAAAAATATTGTTAATATATTTAAATTTTGA
Found at i:31320 original size:23 final size:24
Alignment explanation
Indices: 31294--31341 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
31284 AAATTAATAA
* *
31294 TATTTTAGTAATTAATTT-ATTTT
1 TATTTTAATAATAAATTTAATTTT
*
31317 TATTTTAATCATAAATTTAATTTT
1 TATTTTAATAATAAATTTAATTTT
31341 T
1 T
31342 TGTCATTAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 15 0.71
24 6 0.29
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
TATTTTAATAATAAATTTAATTTT
Found at i:31748 original size:19 final size:20
Alignment explanation
Indices: 31721--31758 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
31711 AAGAAAAATC
31721 TGAGCTAC-AGTTGATGGTT
1 TGAGCTACAAGTTGATGGTT
* *
31740 TGAGGTACAAGTTTATGGT
1 TGAGCTACAAGTTGATGGT
31759 ATGTCTCAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 7 0.44
20 9 0.56
ACGTcount: A:0.24, C:0.08, G:0.32, T:0.37
Consensus pattern (20 bp):
TGAGCTACAAGTTGATGGTT
Found at i:33534 original size:10 final size:10
Alignment explanation
Indices: 33515--33591 Score: 64
Period size: 10 Copynumber: 7.1 Consensus size: 10
33505 TCGTTTATTG
33515 TGTTCGTTTA
1 TGTTCGTTTA
*
33525 TGTTCATTTATTA
1 TGTTC--GT-TTA
*
33538 TGTTCGTTTG
1 TGTTCGTTTA
33548 TGTTCGTTTA
1 TGTTCGTTTA
* *
33558 CGTTCATTTA
1 TGTTCGTTTA
33568 TTACGTTCGTTTA
1 -T--GTTCGTTTA
33581 TGTTCGTTTA
1 TGTTCGTTTA
33591 T
1 T
33592 CATTTAAATG
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
10 34 0.64
11 1 0.02
12 2 0.04
13 16 0.30
ACGTcount: A:0.13, C:0.12, G:0.17, T:0.58
Consensus pattern (10 bp):
TGTTCGTTTA
Found at i:33534 original size:23 final size:23
Alignment explanation
Indices: 33502--33557 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
33492 TTGTTTGTGT
*
33502 TGTTCGTTTATTGTGTTCGTTTA
1 TGTTCGTTTATTATGTTCGTTTA
* *
33525 TGTTCATTTATTATGTTCGTTTG
1 TGTTCGTTTATTATGTTCGTTTA
33548 TGTTCGTTTA
1 TGTTCGTTTA
33558 CGTTCATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.61
Consensus pattern (23 bp):
TGTTCGTTTATTATGTTCGTTTA
Found at i:33553 original size:33 final size:33
Alignment explanation
Indices: 33512--33591 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
33502 TGTTCGTTTA
*
33512 TTGTGTTCGTTTATGTTCATTTATTATGTTCGT
1 TTGTGTTCGTTTATGTTCATTTATTACGTTCGT
*
33545 TTGTGTTCGTTTACGTTCATTTATTACGTTCGT
1 TTGTGTTCGTTTATGTTCATTTATTACGTTCGT
*
33578 TTATGTTCGTTTAT
1 TTGTGTTCGTTTAT
33592 CATTTAAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 43 1.00
ACGTcount: A:0.12, C:0.11, G:0.17, T:0.59
Consensus pattern (33 bp):
TTGTGTTCGTTTATGTTCATTTATTACGTTCGT
Found at i:35034 original size:27 final size:27
Alignment explanation
Indices: 35004--35082 Score: 140
Period size: 27 Copynumber: 2.9 Consensus size: 27
34994 TGTTGATGTT
35004 ATATTTGAATGAATGTGATTAATATCA
1 ATATTTGAATGAATGTGATTAATATCA
*
35031 ATATTTGAATGAATGTGATTTATATCA
1 ATATTTGAATGAATGTGATTAATATCA
*
35058 ATATTTGAATGAATGTGATGAATAT
1 ATATTTGAATGAATGTGATTAATAT
35083 TTTTTGATGT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (27 bp):
ATATTTGAATGAATGTGATTAATATCA
Found at i:37538 original size:105 final size:104
Alignment explanation
Indices: 37218--37716 Score: 466
Period size: 105 Copynumber: 4.7 Consensus size: 104
37208 AAAAATTATT
*
37218 AAATCAAAATAAATAGTCTAATTAATTTATATTTGAAATTAAAACAATAAATAAAACAATAAAAT
1 AAATCAAAATAAATAGTCTAATTAATTTATATTT-AAAAT-AAA-AATAAAT-AAACAATAAAAT
* * *
37283 TTAAACTAAACTTACCAAATCACTCAAATATGGTTTAATCTGTA
62 TTAAACTAAACTTA-CAAATCACCCAAATATAGTTTAATATGTA
* *
37327 AAATCAAAATAAATAGTCTAA-TAATTTATA-TT--ACTCAATAAA-AAATAAA-AA-ATAATTT
1 AAATCAAAATAAATAGTCTAATTAATTTATATTTAAAAT-AA-AAATAAATAAACAATAAAATTT
* * * *
37385 AAACTAAACTTACAAAACCACTCAAATATAGTTTAATCTATA
64 AAACTAAACTTAC-AAATCACCCAAATATAGTTTAATATGTA
*
37427 AAATCAAAATAAATAATCTAATTAATTTATATTTAAAATAAAAA-AAATGAAACAATAAAATTTA
1 AAATCAAAATAAATAGTCTAATTAATTTATATTTAAAATAAAAATAAAT-AAACAATAAAATTTA
* * * * **
37491 CACTAAATTTACAAGATCACCCAAACACAACTTAATATGTA
65 AACTAAACTTACAA-ATCACCCAAATATAGTTTAATATGTA
* * *
37532 AAATCAAAATAAATAGTCTAA-TAA-TTATTATTTAAAATAAAAACAAA-AAATAACTAAAAATT
1 AAATCAAAATAAATAGTCTAATTAATTTA-TATTTAAAATAAAAATAAATAAACAA-TAAAATTT
* * * * *
37594 ATACGAAAATTTA-AACTAACTTACC-AATATAGTTTAATATGTA
64 AAAC-TAAACTTACAAATCAC---CCAAATATAGTTTAATATGTA
* *
37637 AAATCAAAATAAATAATCTAATTAATTTATATTTAAAACAAAAACAATAAATGAAACAATAAAAT
1 AAATCAAAATAAATAGTCTAATTAATTTATATTT-AAA-ATAAA-AATAAAT-AAACAATAAAAT
* *
37702 TTACATTAAACTTAC
62 TTAAACTAAACTTAC
37717 CAGACCACTC
Statistics
Matches: 326, Mismatches: 39, Indels: 49
0.79 0.09 0.12
Matches are distributed among these distances:
99 1 0.00
100 63 0.19
101 11 0.03
102 12 0.04
103 20 0.06
104 42 0.13
105 100 0.31
106 10 0.03
107 8 0.02
108 13 0.04
109 32 0.10
110 9 0.03
111 5 0.02
ACGTcount: A:0.56, C:0.11, G:0.03, T:0.31
Consensus pattern (104 bp):
AAATCAAAATAAATAGTCTAATTAATTTATATTTAAAATAAAAATAAATAAACAATAAAATTTAA
ACTAAACTTACAAATCACCCAAATATAGTTTAATATGTA
Found at i:38123 original size:39 final size:39
Alignment explanation
Indices: 38068--38182 Score: 133
Period size: 39 Copynumber: 2.9 Consensus size: 39
38058 TCTGCATGAC
*
38068 CTGAAGATGTCGTGCACTCCTGGAGTCTTATCCATT-AA
1 CTGAAGATGTCATGCACTCCTGGAGTCTTATCCATTGAA
* * * * **
38106 CATGAAGACGTCTTGCACTCTTAGAGTCTTATCCATTGGT
1 C-TGAAGATGTCATGCACTCCTGGAGTCTTATCCATTGAA
* *
38146 CTAAAGATGTCATGCACTCCTGGAGTATTATCCATTG
1 CTGAAGATGTCATGCACTCCTGGAGTCTTATCCATTG
38183 TCCTGAATAC
Statistics
Matches: 63, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
38 1 0.02
39 61 0.97
40 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (39 bp):
CTGAAGATGTCATGCACTCCTGGAGTCTTATCCATTGAA
Found at i:38432 original size:29 final size:30
Alignment explanation
Indices: 38365--38452 Score: 99
Period size: 29 Copynumber: 3.0 Consensus size: 30
38355 TTTATATAAC
* *
38365 AATAAATATTTAAAATACATTATTTTTTC-
1 AATAAATATTTAAAGTATATTATTTTTTCA
** * *
38394 TTTAAGTATTTAAAGTATATT-TTTATTCA
1 AATAAATATTTAAAGTATATTATTTTTTCA
*
38423 AATAAATATTTAGAGTATATTATTTTTTCA
1 AATAAATATTTAAAGTATATTATTTTTTCA
38453 TTTAGTACCT
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
28 6 0.13
29 33 0.72
30 7 0.15
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.51
Consensus pattern (30 bp):
AATAAATATTTAAAGTATATTATTTTTTCA
Found at i:38522 original size:29 final size:29
Alignment explanation
Indices: 38458--38554 Score: 90
Period size: 29 Copynumber: 3.4 Consensus size: 29
38448 TTTCATTTAG
* * * *
38458 TACCTAAAATTGTTTTTTATAAAAAAATA
1 TACCTAAAGTTATTTTTTATAAAAATAGA
* *
38487 AATCTAAAGTTATTTTTTATAAAAATAGA
1 TACCTAAAGTTATTTTTTATAAAAATAGA
* *
38516 TACCTAAA-CTATTTTTTATCAAAATATG-
1 TACCTAAAGTTATTTTTTATAAAAATA-GA
*
38544 TAACTAAAGTT
1 TACCTAAAGTT
38555 TTTAAATTTC
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
28 23 0.43
29 31 0.57
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.41
Consensus pattern (29 bp):
TACCTAAAGTTATTTTTTATAAAAATAGA
Found at i:38550 original size:28 final size:28
Alignment explanation
Indices: 38470--38551 Score: 80
Period size: 28 Copynumber: 2.9 Consensus size: 28
38460 CCTAAAATTG
*
38470 TTTTTTATAAAAA-A-ATAAATCTAAAGTTA
1 TTTTTTATAAAAATAGAT-AA-CTAAA-CTA
*
38499 TTTTTTATAAAAATAGATACCTAAACTA
1 TTTTTTATAAAAATAGATAACTAAACTA
*
38527 TTTTTTATCAAAATATG-TAACTAAA
1 TTTTTTATAAAAATA-GATAACTAAA
38552 GTTTTTAAAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
28 23 0.50
29 19 0.41
30 2 0.04
31 2 0.04
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (28 bp):
TTTTTTATAAAAATAGATAACTAAACTA
Found at i:38713 original size:30 final size:28
Alignment explanation
Indices: 38678--38768 Score: 94
Period size: 29 Copynumber: 3.1 Consensus size: 28
38668 TTTATGTACC
38678 TATTTTGATTAAAAAATAACTTTAGATACT
1 TATTTT-A-TAAAAAATAACTTTAGATACT
38708 TATTTTAACTAAAAAAT-ACTTTAGATACT
1 TATTTT-A-TAAAAAATAACTTTAGATACT
** * *
38737 TAAATTACAAAAAATATACTTTAAATACT
1 TATTTTATAAAAAATA-ACTTTAGATACT
38766 TAT
1 TAT
38769 ATAAGCTAAT
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
27 7 0.13
28 1 0.02
29 29 0.56
30 15 0.29
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (28 bp):
TATTTTATAAAAAATAACTTTAGATACT
Found at i:38721 original size:29 final size:29
Alignment explanation
Indices: 38688--38770 Score: 107
Period size: 29 Copynumber: 2.9 Consensus size: 29
38678 TATTTTGATT
*
38688 AAAAAATA-ACTTTAGATACTTATTTTAAC
1 AAAAAATATACTTTAGATACTTATATT-AC
* *
38717 TAAAAA-ATACTTTAGATACTTAAATTAC
1 AAAAAATATACTTTAGATACTTATATTAC
*
38745 AAAAAATATACTTTAAATACTTATAT
1 AAAAAATATACTTTAGATACTTATAT
38771 AAGCTAATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
28 8 0.17
29 38 0.83
ACGTcount: A:0.51, C:0.10, G:0.02, T:0.37
Consensus pattern (29 bp):
AAAAAATATACTTTAGATACTTATATTAC
Found at i:40266 original size:131 final size:131
Alignment explanation
Indices: 39883--40344 Score: 621
Period size: 131 Copynumber: 3.5 Consensus size: 131
39873 CATATTATCA
* *
39883 TGTACGTTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTAT--ATA-TA
1 TGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTT
* * * *
39945 CATATATGGAAGTATCGATATTTGTACATTTACGCCTATTTTTATTATACTGGTAGAAACTTTTA
66 TATATAT-G-AGTATCGATATTTGGACATTTACGCCTATTTTCATTATACTGGTAGAAACGTTTA
*
40010 ATG
129 CTG
* * * * *
40013 TGTACATTGTTAATTTATCTATTACTTTAAAGTAATATGTTTCAAAATTATAA--ATCAATATTT
1 TGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTT
* * *
40076 TATATATGAGTATCGATAATTGGACATTTATGCCTATTTTCATTATAAC-AGTAGAAACGTTTAC
66 TATATATGAGTATCGATATTTGGACATTTACGCCTATTTTCATTAT-ACTGGTAGAAACGTTTAC
40140 TG
130 TG
** * * *
40142 TGTGTATTGTTAATTTACTTATTACTTTAAAGTAATATGTTTTGAAATTATAAGTATCGATACTT
1 TGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTT
* * * * *
40207 TGTATATGAGTATTGATATTTGGACATTTACACCTATTTTCATTATACTGGTAAAAACGTTTACC
66 TATATATGAGTATCGATATTTGGACATTTACGCCTATTTTCATTATACTGGTAGAAACGTTTACT
*
40272 A
131 G
40273 TGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTT
1 TGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTT
40338 TATATAT
66 TATATAT
40345 ATGTATCAAT
Statistics
Matches: 289, Mismatches: 36, Indels: 13
0.86 0.11 0.04
Matches are distributed among these distances:
128 2 0.01
129 95 0.33
130 57 0.20
131 135 0.47
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (131 bp):
TGTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTATAAGTATCGATACTT
TATATATGAGTATCGATATTTGGACATTTACGCCTATTTTCATTATACTGGTAGAAACGTTTACT
G
Found at i:40737 original size:199 final size:198
Alignment explanation
Indices: 40392--41207 Score: 1129
Period size: 199 Copynumber: 4.1 Consensus size: 198
40382 GCATACTGGA
* * * * *
40392 ATAAAAGTATGGATACTTGGTATTTACACCTATTATCAATATATTGGTAGACTTTTATCATTTAC
1 ATAAAAGTATTGATACTTGGTATTTACGCCTATTATCATTATATCGGTAGACTTTTACCATTTAC
* * *
40457 ATTTTTTATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATAT
66 ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCAATACTTTATAT
* * * * * *
40522 ATGTGCATCGATACATTTTGCGTGCAAATAGTTTGAGAAGCGTATTGGAATAAAAGTATCCATAT
131 ATGTGTATCAATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATACATA-
40587 CTAT
195 CTAT
* * * *
40591 ATAAAAGTATTGATACATGGTATTTACGCCCATTATCATTATATCGGTAGATTTTTACCGTTTAC
1 ATAAAAGTATTGATACTTGGTATTTACGCCTATTATCATTATATCGGTAGACTTTTACCATTTAC
* *
40656 ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTTCAAGTATCGATACTTTATAT
66 ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCAATACTTTATAT
* *
40721 ATGCGTATCAATACATTTTGCGTGCAAATTGTTTGAGAAACATACTGGAATAAAAGTAT-CGATA
131 ATGTGTATCAATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATAC-ATA
40785 CCTAT
195 -CTAT
*
40790 ATAAAAGTATTGATACTTGGTATTTACGCCTATTATCATTATATCGGTAGACTTTTACCGTTTAC
1 ATAAAAGTATTGATACTTGGTATTTACGCCTATTATCATTATATCGGTAGACTTTTACCATTTAC
* * * *
40855 ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTCAAATTATCAATACTTTATAC
66 ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCAATACTTTATAT
*
40920 A--TGTATGAATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATACATAC
131 ATGTGTATCAATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATACATAC
40983 ATAT
196 -TAT
* * * *
40987 ATAAAGGGTATCGATACTTGGTATTTACGCCTTTTATCATTATA-CTGGTAGATTTTTACCATTT
1 ATAAA-AGTATTGATACTTGGTATTTACGCCTATTATCATTATATC-GGTAGACTTTTACCATTT
* *
41051 ACATTGTTAATTTACCAATTACTTTAAAGTAATATGTTGT-GAAATTCCAAGTATCAATACTTTA
64 ACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTT-TCGAAATTCCAAGTATCAATACTTTA
* * * * * *
41115 TATATGTGTATCGATACATTTTGCATGCAAACTGTTTGAGAATCATATTGGATTAAAAGTATACA
128 TATATGTGTATCAATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATACA
* *
41180 TACCGAC
193 TA-CTAT
*
41187 ATAAGAAGTATCGATACTTGG
1 ATAA-AAGTATTGATACTTGG
41208 ACATTTTCAT
Statistics
Matches: 554, Mismatches: 53, Indels: 19
0.88 0.08 0.03
Matches are distributed among these distances:
196 1 0.00
197 65 0.12
198 113 0.20
199 300 0.54
200 73 0.13
201 2 0.00
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (198 bp):
ATAAAAGTATTGATACTTGGTATTTACGCCTATTATCATTATATCGGTAGACTTTTACCATTTAC
ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCAATACTTTATAT
ATGTGTATCAATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATACATAC
TAT
Found at i:41134 original size:397 final size:397
Alignment explanation
Indices: 40392--41207 Score: 1185
Period size: 397 Copynumber: 2.1 Consensus size: 397
40382 GCATACTGGA
* * *
40392 ATAAAAGTATGGATACTTGGTATTTACACCTATTATCAATATATTGGTAGACTTTTATCATTTAC
1 ATAAAAGTATCGATACTTGGTATTTACACCTATTATCAATATATCGGTAGACTTTTACCATTTAC
* * * * * *
40457 ATTTTTTATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCGATACTTTATAT
66 ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTCAAAGTATCAATACTTTATAC
* * *
40522 ATGTGCATCGATACATTTTGCGTGCAAATAGTTTGAGAAGCGTATTGGAATAAAAGTATCCATAT
131 ATGT-CATCGATACATTTTGCGTGCAAATAGTTTGAGAAGCATACTGGAATAAAAGTATACATAT
* *
40587 CTATATAAAAGTATTGATACATGGTATTTACGCCCATTATCATTATATCGGTAGATTTTTACCGT
195 CTATATAAAAGTATCGATACATGGTATTTACGCCCATTATCATTATATCGGTAGATTTTTACCAT
* * *
40652 TTACATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCGAAATTTCAAGTATCGATACTTT
260 TTACATTGTTAATTTACCAATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCAATACTTT
* *
40717 ATATATGCGTATCAATACATTTTGCGTGCAAATTGTTTGAGAAACATACTGGAATAAAAGTAT-C
325 ATATATGCGTATCAATACATTTTGCATGCAAACTGTTTGAGAAACATACTGGAATAAAAGTATAC
* *
40781 GATACCTAT
390 -ATACCGAC
* * * *
40790 ATAAAAGTATTGATACTTGGTATTTACGCCTATTATCATTATATCGGTAGACTTTTACCGTTTAC
1 ATAAAAGTATCGATACTTGGTATTTACACCTATTATCAATATATCGGTAGACTTTTACCATTTAC
*
40855 ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTCAAATTATCAATACTTTATAC
66 ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTCAAAGTATCAATACTTTATAC
*
40920 ATGT-AT-GAATACATTTTGCGTGCAAATTGTTTGAGAAGCATACTGGAATAAAAGTATACATA-
131 ATGTCATCG-ATACATTTTGCGTGCAAATAGTTTGAGAAGCATACTGGAATAAAAGTATACATAT
* * **
40982 CATATATAAAGGGTATCGATACTTGGTATTTACGCCTTTTATCATTATA-CTGGTAGATTTTTAC
195 C-TATATAAA-AGTATCGATACATGGTATTTACGCCCATTATCATTATATC-GGTAGATTTTTAC
*
41046 CATTTACATTGTTAATTTACCAATTACTTTAAAGTAATATGTTGT-GAAATTCCAAGTATCAATA
257 CATTTACATTGTTAATTTACCAATTACTTTAAAGTAATAGGTT-TCGAAATTCCAAGTATCAATA
* * * * *
41110 CTTTATATATGTGTATCGATACATTTTGCATGCAAACTGTTTGAGAATCATATTGGATTAAAAGT
321 CTTTATATATGCGTATCAATACATTTTGCATGCAAACTGTTTGAGAAACATACTGGAATAAAAGT
41175 ATACATACCGAC
386 ATACATACCGAC
41187 ATAAGAAGTATCGATACTTGG
1 ATAA-AAGTATCGATACTTGG
41208 ACATTTTCAT
Statistics
Matches: 374, Mismatches: 37, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
395 2 0.01
396 61 0.16
397 173 0.46
398 138 0.37
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.39
Consensus pattern (397 bp):
ATAAAAGTATCGATACTTGGTATTTACACCTATTATCAATATATCGGTAGACTTTTACCATTTAC
ATTGTTAATTTACCTATTACTTTAAAGTAATAGGTTTCAAAATTCAAAGTATCAATACTTTATAC
ATGTCATCGATACATTTTGCGTGCAAATAGTTTGAGAAGCATACTGGAATAAAAGTATACATATC
TATATAAAAGTATCGATACATGGTATTTACGCCCATTATCATTATATCGGTAGATTTTTACCATT
TACATTGTTAATTTACCAATTACTTTAAAGTAATAGGTTTCGAAATTCCAAGTATCAATACTTTA
TATATGCGTATCAATACATTTTGCATGCAAACTGTTTGAGAAACATACTGGAATAAAAGTATACA
TACCGAC
Found at i:42587 original size:197 final size:195
Alignment explanation
Indices: 42252--42844 Score: 830
Period size: 197 Copynumber: 3.0 Consensus size: 195
42242 GTAGCGCTTT
42252 ACCGGTTTTGTCAAATTTCAACATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGA
1 ACCGGTTTTGTCAAATTT-AACATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGA
* * * * *
42317 CACTTTATAGACGCTATTATTTCAATTCTTTTAAATTCCTAAAGTACCAATACTTTGGTACATAT
65 TACTTTATAGCCGCTATTATTACAATTCTTTTAAATTCCTAAAGTATCGATACTTTGGTACATAT
* * *
42382 ACTTATAAAAGTATCGATACAAATTTCAACCATTTCGGTAGCTATTTACTGGTTTTGTCAAATTT
130 ACTTATAAAAGTATCGATACAAATTTCAACAATTTCGGTAGCTCTTTAC-GGTTTTGTCAAATTG
42447 AA
194 AA
* * * *
42449 ACCGGTTTTATCATATTTATACTTGTTATATTGTCATGTATTGATACATGTGTCTAAGGTATCGA
1 ACCGGTTTTGTCAAATTTA-ACATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGA
*
42514 TACTTTATAGCCGCTATTATTACAATTTTTTTAAATTCCTAAAGTATCGATACTTTGGTACATAT
65 TACTTTATAGCCGCTATTATTACAATTCTTTTAAATTCCTAAAGTATCGATACTTTGGTACATAT
* * * *
42579 ACTTATAAACA-TAACGATACACATTTCAACAATTAT-GGTAGCTCTGTACGGTTTTGTCAAACT
130 ACTTATAAA-AGTATCGATACAAATTTCAACAATT-TCGGTAGCTCTTTACGGTTTTGTCAAATT
42642 GAA
193 GAA
* * * * * *
42645 ATCGATTTTGTCAAACTTCAACCTGTTATATTGTCATGTATCGATATATGTGTGTAAGGTATCGA
1 ACCGGTTTTGTCAAA-TTTAACATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGA
* * *
42710 TACTTTATAGCTGTTATTATTGCAATTCTTTTAAATTCCTAAAGTATCGATACTTTGGTACATAT
65 TACTTTATAGCCGCTATTATTACAATTCTTTTAAATTCCTAAAGTATCGATACTTTGGTACATAT
* * * * *
42775 ACTTATAAACGTATCGATACAAATTTCAACAATTCCAGTAACTCTTTACCGATTTTGTCAAATTG
130 ACTTATAAAAGTATCGATACAAATTTCAACAATTTCGGTAGCTCTTTA-CGGTTTTGTCAAATTG
42840 AA
194 AA
42842 ACC
1 ACC
42845 TATTTTGCTA
Statistics
Matches: 349, Mismatches: 40, Indels: 14
0.87 0.10 0.03
Matches are distributed among these distances:
196 168 0.48
197 179 0.51
198 2 0.01
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (195 bp):
ACCGGTTTTGTCAAATTTAACATGTTATATTGTCATGTATCGATACATGTGTCTAAGGTATCGAT
ACTTTATAGCCGCTATTATTACAATTCTTTTAAATTCCTAAAGTATCGATACTTTGGTACATATA
CTTATAAAAGTATCGATACAAATTTCAACAATTTCGGTAGCTCTTTACGGTTTTGTCAAATTGAA
Found at i:43724 original size:11 final size:12
Alignment explanation
Indices: 43685--43728 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
43675 TAATAGTTTA
43685 ATTTTTTATATAT
1 ATTTTTTATA-AT
* *
43698 AATTGTTATAAT
1 ATTTTTTATAAT
43710 ATTTTTTATAA-
1 ATTTTTTATAAT
43721 ATTTTTTA
1 ATTTTTTA
43729 ATTATGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 8 0.30
12 11 0.41
13 8 0.30
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (12 bp):
ATTTTTTATAAT
Found at i:49021 original size:29 final size:29
Alignment explanation
Indices: 48979--49067 Score: 128
Period size: 29 Copynumber: 3.0 Consensus size: 29
48969 CCCAAAGACC
*
48979 AGTCCATA-GATCCCGAAGAACCTAGGTAA
1 AGTCCATATG-TCCCGAAGAACATAGGTAA
49008 AGTCCATATGTCCCGAAGAACATAGGTAAA
1 AGTCCATATGTCCCGAAGAACATAGGT-AA
49038 CAGT-CATATGTCCCGAAGAACATAGGTAA
1 -AGTCCATATGTCCCGAAGAACATAGGTAA
49067 A
1 A
49068 CCCTCGACCC
Statistics
Matches: 56, Mismatches: 1, Indels: 7
0.88 0.02 0.11
Matches are distributed among these distances:
28 1 0.02
29 26 0.46
30 26 0.46
31 3 0.05
ACGTcount: A:0.39, C:0.21, G:0.20, T:0.19
Consensus pattern (29 bp):
AGTCCATATGTCCCGAAGAACATAGGTAA
Found at i:49048 original size:30 final size:31
Alignment explanation
Indices: 48978--49068 Score: 136
Period size: 30 Copynumber: 3.0 Consensus size: 31
48968 TCCCAAAGAC
*
48978 CAGTCCATA-GATCCCGAAGAACCTAGGT-AA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
49008 -AGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
49038 CAGT-CATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
49068 C
1 C
49069 CCTCGACCCT
Statistics
Matches: 57, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
29 24 0.42
30 30 0.53
31 3 0.05
ACGTcount: A:0.38, C:0.23, G:0.20, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:49824 original size:62 final size:64
Alignment explanation
Indices: 49678--49828 Score: 157
Period size: 64 Copynumber: 2.4 Consensus size: 64
49668 TAATGAATGT
* * * *
49678 ATCGATGCAC-TACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTAGGATGC
1 ATCGATGCACTTCCTG-TGCATCGATGCATAAAATGCATTCGATGTTGTATTATTACAAAGATGC
* * * * * *
49742 ATCGATGCACTACTTATGCATCGATGCATTAATTGCATTCGATGTATTTATT-TTA-AAAG-TGC
1 ATCGATGCACTTCCTGTGCATCGATGCATAAAATGCATTCGATGT-TGTATTATTACAAAGATGC
*
49804 ATTGATGCACTTCCTGTGCATCGAT
1 ATCGATGCACTTCCTGTGCATCGAT
49829 ACACCTTCAA
Statistics
Matches: 71, Mismatches: 14, Indels: 6
0.78 0.15 0.07
Matches are distributed among these distances:
62 24 0.34
63 2 0.03
64 39 0.55
65 6 0.08
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (64 bp):
ATCGATGCACTTCCTGTGCATCGATGCATAAAATGCATTCGATGTTGTATTATTACAAAGATGC
Done.