Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006207.1 Hibiscus syriacus cultivar Beakdansim tig00014778_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: 53175
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:34 original size:23 final size:22
Alignment explanation
Indices: 1--58 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 22
1 AGTGCCACATATAATTGCACCGG
1 AGTGCC-CATATAATTGCACCGG
* *
24 AGTGCCGCATAGAA-TGCACCGT
1 AGTGCC-CATATAATTGCACCGG
46 AGTG-CCATATAAT
1 AGTGCCCATATAAT
59 AATGTCCATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 6 0.20
21 1 0.03
22 11 0.37
23 12 0.40
ACGTcount: A:0.31, C:0.24, G:0.22, T:0.22
Consensus pattern (22 bp):
AGTGCCCATATAATTGCACCGG
Found at i:44 original size:22 final size:23
Alignment explanation
Indices: 1--52 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
*
1 AGTGCCACATATAATTGCACCGG
1 AGTGCCACATAGAATTGCACCGG
* *
24 AGTGCCGCATAGAA-TGCACCGT
1 AGTGCCACATAGAATTGCACCGG
46 AGTGCCA
1 AGTGCCA
53 TATAATAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 13 0.52
23 12 0.48
ACGTcount: A:0.29, C:0.27, G:0.25, T:0.19
Consensus pattern (23 bp):
AGTGCCACATAGAATTGCACCGG
Found at i:237 original size:101 final size:102
Alignment explanation
Indices: 68--283 Score: 355
Period size: 101 Copynumber: 2.1 Consensus size: 102
58 TAATGTCCAT
* *
68 AAGGACCACATATCATTCCTTAAGAATCTATACATATACTAGGGATCAAGTATGTGTCTCACCAG
1 AAGGACCACATATCATTCCTTAAGAATCTATACATATACCAAGGATCAAGTATGTGTCTCACCAG
133 ACTTCACACATGTTCCAAAGAATACATATATGT-CCG
66 ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
169 AAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCA-CA
1 AAGGACCACATATCATTCCTTAAGAATC-TATACATATACCAAGGATCAAGTATGTGTCTCACCA
*
233 GACTTCACACATGTTCCAAAGAATGCATATATGTCCCG
65 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
* *
271 AATGACCATATAT
1 AAGGACCACATAT
284 ACCTCGACTC
Statistics
Matches: 107, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
101 63 0.59
102 44 0.41
ACGTcount: A:0.36, C:0.23, G:0.14, T:0.27
Consensus pattern (102 bp):
AAGGACCACATATCATTCCTTAAGAATCTATACATATACCAAGGATCAAGTATGTGTCTCACCAG
ACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:1659 original size:20 final size:21
Alignment explanation
Indices: 1618--1664 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 21
1608 TTCGCTTGAG
1618 GGGTATCGATTCCCCATTGAAT
1 GGGTATCGATT-CCCATTGAAT
*
1640 GGGTATCGATT-CCTTTGAAT
1 GGGTATCGATTCCCATTGAAT
1660 GGGTA
1 GGGTA
1665 CTGTCGTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 13 0.54
22 11 0.46
ACGTcount: A:0.21, C:0.17, G:0.28, T:0.34
Consensus pattern (21 bp):
GGGTATCGATTCCCATTGAAT
Found at i:2359 original size:3 final size:3
Alignment explanation
Indices: 2353--2410 Score: 52
Period size: 3 Copynumber: 20.3 Consensus size: 3
2343 TTATTATATA
* **
2353 AAT AAT AA- AAT AAT AAT AAT GA- AAT AAT AATT AA- AGC AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT AAT
2396 AAT AAT AA- AAT AAT A
1 AAT AAT AAT AAT AAT A
2411 TTGCAAATAA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
2 6 0.13
3 36 0.80
4 3 0.07
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:2382 original size:29 final size:29
Alignment explanation
Indices: 2350--2410 Score: 79
Period size: 29 Copynumber: 2.1 Consensus size: 29
2340 TATTTATTAT
*
2350 ATAAATAATA-AAATAATAATAATGAAATA
1 ATAAATAA-AGAAATAATAATAATAAAATA
* *
2379 ATAATTAAAGCAATAATAATAATAAAATA
1 ATAAATAAAGAAATAATAATAATAAAATA
2408 ATA
1 ATA
2411 TTGCAAATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (29 bp):
ATAAATAAAGAAATAATAATAATAAAATA
Found at i:2419 original size:26 final size:28
Alignment explanation
Indices: 2360--2432 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 28
2350 ATAAATAATA
*
2360 AAATAATAATAATGAAATAATAATTAAAGC
1 AAATAATAATAATAAAATAATAATT--AGC
2390 -AATAATAATAATAAAATAAT-ATT-GC
1 AAATAATAATAATAAAATAATAATTAGC
*
2415 AAATAATGATTAATAAAA
1 AAATAAT-AATAATAAAA
2433 GGAATTAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
25 2 0.05
26 6 0.15
27 9 0.23
28 3 0.08
29 19 0.49
ACGTcount: A:0.63, C:0.03, G:0.05, T:0.29
Consensus pattern (28 bp):
AAATAATAATAATAAAATAATAATTAGC
Found at i:3541 original size:3 final size:3
Alignment explanation
Indices: 3533--3611 Score: 108
Period size: 3 Copynumber: 25.7 Consensus size: 3
3523 GGCTTGTAAT
3533 TAA TAA TAAA TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA TAA TATA
1 TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TA-A
3580 TAA -AA TAA TAA TAA TAA TAAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TA
3612 GAAAATAGAG
Statistics
Matches: 70, Mismatches: 0, Indels: 12
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.06
3 54 0.77
4 12 0.17
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:4292 original size:102 final size:102
Alignment explanation
Indices: 4185--4735 Score: 440
Period size: 124 Copynumber: 5.0 Consensus size: 102
4175 ATAGAGTCAT
* *
4185 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTT
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTT
*
4250 TATCTGGCAATGTTGATCCATCGAATGATGAATTCAA
66 TATCTGGCAATGTTGATCTATCGAATGATGAATTCAA
* * * * *
4287 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTTTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTC-T-TC
* * * *
4352 ATTGTGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTATGAT-AGAGTCAT
64 -TT-T--A---T--CTGGCAA---TG-T--TGATCTATCGA-----ATGATGA-ATTCAA
*
4411 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTT
4476 TATCTGGCAATGTTGATCTATCGAATGATGAATTCAA
66 TATCTGGCAATGTTGATCTATCGAATGATGAATTCAA
* * * * *
4513 GCAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTTTTCAGATGAGTTCTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTC-T-TC
* * * * *
4578 ATTATGAACTATACCTGGAAATTTTGATGATGATCTATCTATTTCTATGAT-AGAGTCAT
64 --T-T----TAT--CTGGCAA---TGTT---GATCTATCGA-----ATGATGA-ATTCAA
* *
4637 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTTTTCTC
1 GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTT
*
4702 TATCTGGCAATGTTGATCCATCGAATGATGAATT
66 TATCTGGCAATGTTGATCTATCGAATGATGAATT
4736 TGAACTTTGC
Statistics
Matches: 357, Mismatches: 44, Indels: 96
0.72 0.09 0.19
Matches are distributed among these distances:
102 125 0.35
103 4 0.01
104 4 0.01
105 2 0.01
106 2 0.01
107 18 0.05
108 1 0.00
109 1 0.00
110 5 0.01
111 4 0.01
113 24 0.07
115 4 0.01
116 5 0.01
117 1 0.00
118 1 0.00
119 18 0.05
120 2 0.01
121 1 0.00
122 4 0.01
123 4 0.01
124 127 0.36
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (102 bp):
GCAAAAGGTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTT
TATCTGGCAATGTTGATCTATCGAATGATGAATTCAA
Found at i:4419 original size:226 final size:226
Alignment explanation
Indices: 3837--4735 Score: 1656
Period size: 226 Copynumber: 4.0 Consensus size: 226
3827 TGTAATTTGG
* *
3837 AAAAGAGTTGAACAAGTTCTTCTCATTATAAACTTCTTTTTCCTTTTTCAGATGAGTTCTTCTCA
1 AAAA-AGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTTTTCAGATGAGTTCTTCTCA
3902 TTATGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTATGATAGAGTCATGCAAAAG
65 TTATGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTATGATAGAGTCATGCAAAAG
* *
3967 GTTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTATTCTCTATCTGG
130 GTTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCTATCTGG
4032 CAATG-TGATCCATCGAATGATGAATTCAAGC
195 CAATGTTGATCCATCGAATGATGAATTCAAGC
* *
4063 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTTTTCAGATGAGTTCTTCTCAT
4128 TATGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTATGATAGAGTCATGCAAAAGG
66 TATGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTATGATAGAGTCATGCAAAAGG
* * *
4193 TTGAACAAGCTCTTCTCATTATGAACTTCTTCTTCATTCTTCAGATGAGTTCTTCTTTATCTGGC
131 TTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCTATCTGGC
4258 AATGTTGATCCATCGAATGATGAATTCAAGC
196 AATGTTGATCCATCGAATGATGAATTCAAGC
4289 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTTTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTTTTCAGATGAGTTCTTCTCAT
*
4354 TGTGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTATGATAGAGTCATGCAAAAGG
66 TATGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTATGATAGAGTCATGCAAAAGG
4419 TTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCTATCTGGC
131 TTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCTATCTGGC
*
4484 AATGTTGATCTATCGAATGATGAATTCAAGC
196 AATGTTGATCCATCGAATGATGAATTCAAGC
4515 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTTTTCAGATGAGTTCTTCTCAT
1 AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTTTTCAGATGAGTTCTTCTCAT
* *
4580 TATGAACTATACCTGGAAATTTTGATGATGATCTATCTATTTCTATGATAGAGTCATGCAAAAGG
66 TATGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTATGATAGAGTCATGCAAAAGG
*
4645 TTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTTTTCTCTATCTGGC
131 TTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCTATCTGGC
4710 AATGTTGATCCATCGAATGATGAATT
196 AATGTTGATCCATCGAATGATGAATT
4736 TGAACTTTGC
Statistics
Matches: 653, Mismatches: 19, Indels: 2
0.97 0.03 0.00
Matches are distributed among these distances:
225 188 0.29
226 465 0.71
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (226 bp):
AAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTTTTCCTTTTTCAGATGAGTTCTTCTCAT
TATGAACTCTACCTGGAAATGTTGATGATGATCTATCTATTTCTATGATAGAGTCATGCAAAAGG
TTGAACAAGCTCTTCTCATTATGAACTTCTTATTCCTTCTTCAGATGAGTTCTTCTCTATCTGGC
AATGTTGATCCATCGAATGATGAATTCAAGC
Found at i:7814 original size:114 final size:114
Alignment explanation
Indices: 7614--7837 Score: 403
Period size: 114 Copynumber: 2.0 Consensus size: 114
7604 GATCATGCAG
* * *
7614 TTCATCTTTCAATTCCAATGATTGGTTCTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
7679 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* *
7728 TTCATCTTTCAAATCTAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
7793 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
7838 AATGTGGCAC
Statistics
Matches: 105, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:10158 original size:11 final size:10
Alignment explanation
Indices: 10133--10157 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
10123 TTCCTTTTCC
10133 TTTTTGTTTT
1 TTTTTGTTTT
10143 TTTTTGTTTT
1 TTTTTGTTTT
10153 TTTTT
1 TTTTT
10158 TCATTTGTCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:13496 original size:14 final size:14
Alignment explanation
Indices: 13458--13511 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
13448 CATAAAAATA
* *
13458 CAAATGCAAAGATG
1 CAAATGTAAATATG
13472 CCAAATGTAAATATG
1 -CAAATGTAAATATG
* *
13487 CAATTGTAAAAATG
1 CAAATGTAAATATG
*
13501 TAAATGTAAAT
1 CAAATGTAAAT
13512 TATTTAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
14 20 0.62
15 12 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (14 bp):
CAAATGTAAATATG
Found at i:13680 original size:13 final size:13
Alignment explanation
Indices: 13662--13697 Score: 72
Period size: 13 Copynumber: 2.8 Consensus size: 13
13652 CGTAAAAATG
13662 TACAAATGCAAAA
1 TACAAATGCAAAA
13675 TACAAATGCAAAA
1 TACAAATGCAAAA
13688 TACAAATGCA
1 TACAAATGCA
13698 TGTATGAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.58, C:0.17, G:0.08, T:0.17
Consensus pattern (13 bp):
TACAAATGCAAAA
Found at i:15973 original size:3 final size:3
Alignment explanation
Indices: 15965--16016 Score: 63
Period size: 3 Copynumber: 17.3 Consensus size: 3
15955 TACTTATATA
*
15965 AAT AAT AAT AAT AAT AAT GAAT AATT AA- AGT AAT AAT AAT AAT AA-
1 AAT AAT AAT AAT AAT AAT -AAT AA-T AAT AAT AAT AAT AAT AAT AAT
16010 AAT AAT A
1 AAT AAT A
16017 TTGCAAATAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
2 3 0.07
3 34 0.79
4 6 0.14
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17198 original size:3 final size:3
Alignment explanation
Indices: 17190--17275 Score: 104
Period size: 3 Copynumber: 27.7 Consensus size: 3
17180 GGCTTGTAAT
17190 TAA TAA TAAA TAA TAA TAA TAAA TAA -AA TAA TAA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
*
17236 TAA TATA TAA -AA TAC TAA TAA TAA TAAA TAAA TAA TAA TA
1 TAA TA-A TAA TAA TAA TAA TAA TAA T-AA T-AA TAA TAA TA
17276 GAAAATGGAG
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
2 4 0.05
3 55 0.73
4 16 0.21
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:17234 original size:30 final size:30
Alignment explanation
Indices: 17190--17273 Score: 123
Period size: 30 Copynumber: 2.7 Consensus size: 30
17180 GGCTTGTAAT
17190 TAATAATAAATAATAATAATAAATAAAATAA
1 TAATAAT-AATAATAATAATAAATAAAATAA
* *
17221 TAATAATAATAATAATAATATATAAAATAC
1 TAATAATAATAATAATAATAAATAAAATAA
17251 TAATAATAATAAATAAATAATAA
1 TAATAATAAT-AAT-AATAATAA
17274 TAGAAAATGG
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
30 31 0.65
31 10 0.21
32 7 0.15
ACGTcount: A:0.68, C:0.01, G:0.00, T:0.31
Consensus pattern (30 bp):
TAATAATAATAATAATAATAAATAAAATAA
Found at i:18248 original size:16 final size:16
Alignment explanation
Indices: 18209--18251 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
18199 AGCATCAGTT
*
18209 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
18225 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
18242 CTTATCAATC
1 CTTATCAATC
18252 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:20904 original size:23 final size:23
Alignment explanation
Indices: 20878--20955 Score: 93
Period size: 23 Copynumber: 3.3 Consensus size: 23
20868 CACCAAAACT
*
20878 CATATAATTGCACCAAAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
* *
20901 CATATAATTGCACCGGAGTGCCG
1 CATATAATTGCACCGAAGTGCCA
* *
20924 CATAGAATTGCACCGTAGTGCCA
1 CATATAATTGCACCGAAGTGCCA
*
20947 TATAATAAT
1 CAT-ATAAT
20956 GTCCATAAAG
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
23 42 0.91
24 4 0.09
ACGTcount: A:0.35, C:0.23, G:0.18, T:0.24
Consensus pattern (23 bp):
CATATAATTGCACCGAAGTGCCA
Found at i:21133 original size:103 final size:103
Alignment explanation
Indices: 20965--21179 Score: 369
Period size: 103 Copynumber: 2.1 Consensus size: 103
20955 TGTCCATAAA
**
20965 GACCACATATCATTCCTTAAGAATCATATACATATATTAGAGATCAAGTATGTGTCTCACCAGAC
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAGAGATCAAGTATGTGTCTCACCAGAC
*
21030 TTCACACATGTTCCAAAGAATACATATATGTCTCGAAG
66 TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
*
21068 GACCACATATCATTCCTTAAGAATCATATACATATGCCA-ATGATCAAGTATGTGTCTCACCAGA
1 GACCACATATCATTCCTTAAGAATCATATACATATACCAGA-GATCAAGTATGTGTCTCACCAGA
21132 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
65 CTTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
*
21171 GACTACATA
1 GACCACATA
21180 GACCCTCGAC
Statistics
Matches: 106, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 1 0.01
103 105 0.99
ACGTcount: A:0.37, C:0.23, G:0.13, T:0.28
Consensus pattern (103 bp):
GACCACATATCATTCCTTAAGAATCATATACATATACCAGAGATCAAGTATGTGTCTCACCAGAC
TTCACACATGTTCCAAAGAATACATATATGTCCCGAAG
Found at i:22577 original size:22 final size:21
Alignment explanation
Indices: 22552--22611 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
22542 TTCGCTTGAG
*
22552 GGGTATCGATTCCCCATTGAAT
1 GGGTACCGATTCCCC-TTGAAT
22574 GGGTACCGATT-CCCTTGAAT
1 GGGTACCGATTCCCCTTGAAT
22594 GGGTACCGATTCCCCTTG
1 GGGTACCGATTCCCCTTG
22612 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 17 0.47
21 9 0.25
22 10 0.28
ACGTcount: A:0.18, C:0.27, G:0.25, T:0.30
Consensus pattern (21 bp):
GGGTACCGATTCCCCTTGAAT
Found at i:23774 original size:42 final size:43
Alignment explanation
Indices: 23720--23803 Score: 118
Period size: 43 Copynumber: 2.0 Consensus size: 43
23710 GCGCCACAAA
*
23720 TTGATACTTTAGCGACGTTTGTTGT-AAAAACGCTGTAATAGAT
1 TTGATACTTTAGCGACGTTT-TTATAAAAAACGCTGTAATAGAT
*
23763 TTGATA-TTTAGCGCCGTTTTTATAAAAAAACGCTGTAATAG
1 TTGATACTTTAGCGACGTTTTTAT-AAAAAACGCTGTAATAG
23804 GGTGGTTTAT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 3 0.08
42 12 0.32
43 22 0.59
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (43 bp):
TTGATACTTTAGCGACGTTTTTATAAAAAACGCTGTAATAGAT
Found at i:23915 original size:82 final size:83
Alignment explanation
Indices: 23829--23988 Score: 225
Period size: 82 Copynumber: 1.9 Consensus size: 83
23819 CGTTTGTTAA
*
23829 AAAATGCCACAATAAAGT-GGTAAATTAGCAGCGTTTATACCACAAACGCCGTAATAGATTA-AC
1 AAAATGCCACAATAAA-TCGGTAAATTAGCAGCGTTTATACCACAAACGCCGCAATAGATTACAC
23892 ATATAGTGGCATTTTAGCC
65 ATATAGTGGCATTTTAGCC
* ** * **
23911 AAAATGTCGTAATAGATCGGTAAATTAGTGGCGTTTATACCACAAACGCCGCAATAGATTACACA
1 AAAATGCCACAATAAATCGGTAAATTAGCAGCGTTTATACCACAAACGCCGCAATAGATTACACA
*
23976 TATAGTGGTATTT
66 TATAGTGGCATTT
23989 ATTTTTAAAA
Statistics
Matches: 68, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
81 1 0.01
82 52 0.76
83 15 0.22
ACGTcount: A:0.38, C:0.17, G:0.18, T:0.28
Consensus pattern (83 bp):
AAAATGCCACAATAAATCGGTAAATTAGCAGCGTTTATACCACAAACGCCGCAATAGATTACACA
TATAGTGGCATTTTAGCC
Found at i:23982 original size:42 final size:41
Alignment explanation
Indices: 23859--23983 Score: 141
Period size: 41 Copynumber: 3.0 Consensus size: 41
23849 TAAATTAGCA
23859 GCGTTTATACCACAAACGCCGTAATAGATTAACATATAGTG
1 GCGTTTATACCACAAACGCCGTAATAGATTAACATATAGTG
* * *
23900 GCATTT-TAGCCA-AAATGTCGTAATAGATCGGTAA-AT-TAGTG
1 GCGTTTATA-CCACAAACGCCGTAATAGAT---TAACATATAGTG
*
23941 GCGTTTATACCACAAACGCCGCAATAGATTACACATATAGTG
1 GCGTTTATACCACAAACGCCGTAATAGATTA-ACATATAGTG
23983 G
1 G
23984 TATTTATTTT
Statistics
Matches: 68, Mismatches: 7, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
39 2 0.03
40 17 0.25
41 23 0.34
42 23 0.34
43 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.19, T:0.27
Consensus pattern (41 bp):
GCGTTTATACCACAAACGCCGTAATAGATTAACATATAGTG
Found at i:23990 original size:42 final size:41
Alignment explanation
Indices: 23862--23990 Score: 140
Period size: 42 Copynumber: 3.1 Consensus size: 41
23852 ATTAGCAGCG
23862 TTTATACCACAAACGCCGTAATAGATTAACATATAGTGGCA
1 TTTATACCACAAACGCCGTAATAGATTAACATATAGTGGCA
* * *
23903 TTT-TAGCCA-AAATGTCGTAATAGATCGGTAA-AT-TAGTGGCG
1 TTTATA-CCACAAACGCCGTAATAGAT---TAACATATAGTGGCA
* *
23944 TTTATACCACAAACGCCGCAATAGATTACACATATAGTGGTA
1 TTTATACCACAAACGCCGTAATAGATTA-ACATATAGTGGCA
23986 TTTAT
1 TTTAT
23991 TTTTAAAACG
Statistics
Matches: 71, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
39 2 0.03
40 17 0.24
41 21 0.30
42 28 0.39
43 3 0.04
ACGTcount: A:0.36, C:0.17, G:0.17, T:0.30
Consensus pattern (41 bp):
TTTATACCACAAACGCCGTAATAGATTAACATATAGTGGCA
Found at i:24072 original size:41 final size:39
Alignment explanation
Indices: 24011--24163 Score: 128
Period size: 41 Copynumber: 3.8 Consensus size: 39
24001 CCGCAATAGT
* *
24011 CGCAATAGTGATAATAAATAATGGCGTTTTTAAATAAACG
1 CGCAATAGTGTTAATCAATAATGGCGTTTTTAAA-AAACG
*
24051 CTGCAATAGTGTTAATCAATAATGGCGTTTTTAGAAAAATG
1 C-GCAATAGTGTTAATCAATAATGGCGTTTTTA-AAAAACG
* * * * * * *
24092 ACGTAATACTTTTAATCAATAGTAGTGTTTTTTAACAAACG
1 -CGCAATAGTGTTAATCAATAATGGCG-TTTTTAAAAAACG
* * *
24133 CCACAATAGTG-TAATCAATAGTGGCATTTTT
1 -CGCAATAGTGTTAATCAATAATGGCGTTTTT
24164 TTGTATAAAC
Statistics
Matches: 90, Mismatches: 19, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
39 5 0.06
40 13 0.14
41 63 0.70
42 9 0.10
ACGTcount: A:0.37, C:0.12, G:0.16, T:0.35
Consensus pattern (39 bp):
CGCAATAGTGTTAATCAATAATGGCGTTTTTAAAAAACG
Found at i:24962 original size:83 final size:83
Alignment explanation
Indices: 24721--25040 Score: 227
Period size: 83 Copynumber: 3.9 Consensus size: 83
24711 CTATAGGTAC
* * * * * * * * * * *
24721 GTACTTTAGTGGCATTTTTATACAAACGCCGCTATAGAATCTTA-CGTTAGTGGCGTTTTTATAC
1 GTACTTTAGCGGCATTTTAATACAAACACCGCTAAAGACTCGTACCCTTAGTAGCATTTTTAAAT
** *
24785 AAACGCCTATATATACTA
66 AAACGCCGCTATAAACTA
* * * * * * * * * * *
24803 ATACTTTAGTGGCGTTTCT-ATACAAACGCCGCTATATACTCATA-CTTTAGTGGCGTTTTGAAT
1 GTACTTTAGCGGCATTT-TAATACAAACACCGCTAAAGACTCGTACCCTTAGTAGCATTTTTAA-
* * * *
24866 CTAAACACTGCTATAAACTC
64 ATAAACGCCGCTATAAACTA
* *
24886 GTACTTTAGCGGCATTTTGAATGA-AAACACCGCTAAAGACTCGTA-CTTTAGTAGCATTTTTAT
1 GTACTTTAGCGGCATTTT-AAT-ACAAACACCGCTAAAGACTCGTACCCTTAGTAGCATTTTTAA
*
24949 ATAAACGCCGCTATAGACTA
64 ATAAACGCCGCTATAAACTA
* * * * * *
24969 GTACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCGTACCCTTAGTGGCGTTTTTAAAT
1 GTACTTTAGCGGCATTTTAATACAAACACCGCTAAAGACTCGTACCCTTAGTAGCATTTTTAAAT
25034 AAACGCC
66 AAACGCC
25041 ACAATAGATA
Statistics
Matches: 191, Mismatches: 40, Indels: 13
0.78 0.16 0.05
Matches are distributed among these distances:
81 1 0.01
82 74 0.39
83 82 0.43
84 33 0.17
85 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.34
Consensus pattern (83 bp):
GTACTTTAGCGGCATTTTAATACAAACACCGCTAAAGACTCGTACCCTTAGTAGCATTTTTAAAT
AAACGCCGCTATAAACTA
Found at i:24993 original size:166 final size:166
Alignment explanation
Indices: 24720--25028 Score: 415
Period size: 166 Copynumber: 1.9 Consensus size: 166
24710 GCTATAGGTA
* * * * * * *
24720 CGTACTTTAGTGGCATTTTTATACAAACGCCGCTATAGAATCTTACGTTAGTGGCGTTTTTATAC
1 CGTACTTTAGCGGCATTTTAATACAAACACCGCTAAAGAATCGTACGTTAGTAGCATTTTTATAC
* * * * *
24785 AAACGCCTATATATACTAATACTTTAGTGGCGTTTCTATACAAACGCCGCTATATACTCATA-CT
66 AAACGCCGATATAGACTAATACTTTAGTGGCATTTCTATACAAACGCCGCTATAGACTCATACCC
24849 TTAGTGGCGTTTTGAATCTAAACACTGCTATAAACT
131 TTAGTGGCGTTTTGAATCTAAACACTGCTATAAACT
* *
24885 CGTACTTTAGCGGCATTTTGAATGA-AAACACCGCTAAAGACTCGTACTTTAGTAGCATTTTTAT
1 CGTACTTTAGCGGCATTTT-AAT-ACAAACACCGCTAAAGAATCGTACGTTAGTAGCATTTTTAT
* * * * *
24949 ATAAACGCCGCTATAGACTAGTACTTTAGTGGCATTTTTATACAAACGCCGCTATAGACTCGTAC
64 ACAAACGCCGATATAGACTAATACTTTAGTGGCATTTCTATACAAACGCCGCTATAGACTCATAC
25014 CCTTAGTGGCGTTTT
129 CCTTAGTGGCGTTTT
25029 TAAATAAACG
Statistics
Matches: 122, Mismatches: 19, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
165 18 0.15
166 89 0.73
167 15 0.12
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (166 bp):
CGTACTTTAGCGGCATTTTAATACAAACACCGCTAAAGAATCGTACGTTAGTAGCATTTTTATAC
AAACGCCGATATAGACTAATACTTTAGTGGCATTTCTATACAAACGCCGCTATAGACTCATACCC
TTAGTGGCGTTTTGAATCTAAACACTGCTATAAACT
Found at i:25038 original size:42 final size:41
Alignment explanation
Indices: 24703--25040 Score: 322
Period size: 41 Copynumber: 8.2 Consensus size: 41
24693 TTGTATCTAG
* * *
24703 AAACGTCGCTATAG-GTACGTACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTATAGACT-CGTACTTTAGTGGCGTTTTTATAC
* * *
24744 AAACGCCGCTATAGAATCTTACGTTAGTGGCGTTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
** * ** *
24785 AAACGCCTATATATACTAATACTTTAGTGGCGTTTCTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
24826 AAACGCCGCTATATACTCATACTTTAGTGGCGTTTTGA-ATC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATA-C
* * * * * *
24867 TAAACACTGCTATAAACTCGTACTTTAGCGGCATTTTGAATGA-
1 -AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTT-TAT-AC
* * * * *
24910 AAACACCGCTAAAGACTCGTACTTTAGTAGCATTTTTATAT
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* *
24951 AAACGCCGCTATAGACTAGTACTTTAGTGGCATTTTTATAC
1 AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
* * *
24992 AAACGCCGCTATAGACTCGTACCCTTAGTGGCGTTTTTAAAT
1 AAACGCCGCTATAGACTCGTA-CTTTAGTGGCGTTTTTATAC
25034 AAACGCC
1 AAACGCC
25041 ACAATAGATA
Statistics
Matches: 248, Mismatches: 41, Indels: 15
0.82 0.13 0.05
Matches are distributed among these distances:
40 2 0.01
41 159 0.64
42 85 0.34
43 1 0.00
45 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (41 bp):
AAACGCCGCTATAGACTCGTACTTTAGTGGCGTTTTTATAC
Found at i:25114 original size:43 final size:41
Alignment explanation
Indices: 25020--25123 Score: 113
Period size: 43 Copynumber: 2.5 Consensus size: 41
25010 GTACCCTTAG
*
25020 TGGCGTTTTTAAATAAACGCCACAATAGATATAATATTTTA
1 TGGCGTTTTTAAATAAACACCACAATAGATATAATATTTTA
* **
25061 TGGCATTTTTTAAGATAAACACCGTAATAGATATAATATTTT-
1 TGGC-GTTTTTAA-ATAAACACCACAATAGATATAATATTTTA
25103 TGCAGCGTTTTTATAA-AAACA
1 TG--GCGTTTTTA-AATAAACA
25124 TCGCTATAGG
Statistics
Matches: 53, Mismatches: 5, Indels: 9
0.79 0.07 0.13
Matches are distributed among these distances:
41 4 0.08
42 14 0.26
43 32 0.60
44 3 0.06
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (41 bp):
TGGCGTTTTTAAATAAACACCACAATAGATATAATATTTTA
Found at i:33599 original size:21 final size:22
Alignment explanation
Indices: 33575--33631 Score: 57
Period size: 21 Copynumber: 2.7 Consensus size: 22
33565 CGGAAAATGA
*
33575 AGCAAGGGAAGCAGA-TAGAGC
1 AGCAAGGGAAGCAGACCAGAGC
**
33596 AGCAACAGAAGCA-ACCAGAGC
1 AGCAAGGGAAGCAGACCAGAGC
33617 AGC-AGCGGAAGCAGA
1 AGCAAG-GGAAGCAGA
33632 GAAAGAAGCA
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 2 0.07
21 25 0.89
22 1 0.04
ACGTcount: A:0.44, C:0.21, G:0.33, T:0.02
Consensus pattern (22 bp):
AGCAAGGGAAGCAGACCAGAGC
Found at i:33659 original size:21 final size:21
Alignment explanation
Indices: 33612--33684 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
33602 AGAAGCAACC
* * *
33612 AGAGCAGCAGCGGAAGCAGAG
1 AGAGAAGCAGCGGCAGCACAG
* *
33633 AAAGAAGCAGCGGCATCACAG
1 AGAGAAGCAGCGGCAGCACAG
* *
33654 AGAGAA-CAACGGCAGCACAT
1 AGAGAAGCAGCGGCAGCACAG
33674 AGAGAAGCAGC
1 AGAGAAGCAGC
33685 ATATCAGCAG
Statistics
Matches: 41, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 17 0.41
21 24 0.59
ACGTcount: A:0.42, C:0.22, G:0.33, T:0.03
Consensus pattern (21 bp):
AGAGAAGCAGCGGCAGCACAG
Found at i:34129 original size:43 final size:42
Alignment explanation
Indices: 34082--34436 Score: 340
Period size: 43 Copynumber: 8.2 Consensus size: 42
34072 AGGCCTGTAC
* * * *
34082 CGGCGTTTTTAGCAGAAACGCCGCAAAACATCAACACCTACTG
1 CGGCGTTTTTAG-ACAAACGCCGCTAAATATCAACACCTATTG
* * *
34125 CGGCGTTTTTTGTTA-AAACGCCGCTAAACATCATA-ACATATTG
1 CGGCGTTTTTAG--ACAAACGCCGCTAAATATCA-ACACCTATTG
* * * * *
34168 CGGCGTTTGTCTA-AGAAACACTGCTAAATATTAACACCTATTA
1 CGGCGTTT-T-TAGACAAACGCCGCTAAATATCAACACCTATTG
*
34211 CGGCGTTTTTATGACAAACGTCGCTAAATATCAACACCTATTG
1 CGGCGTTTTTA-GACAAACGCCGCTAAATATCAACACCTATTG
* * * * *
34254 CGGCGTTTTTATAAAAAAAACACCACTAAATATCAACACCTATTA
1 CGGCG-TTTT-T-AGACAAACGCCGCTAAATATCAACACCTATTG
* * *
34299 CGACGTTTGTT-GAAAAACGCTGCTAAATATCAACACCTATTG
1 CGGCGTTT-TTAGACAAACGCCGCTAAATATCAACACCTATTG
34341 CGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTG
1 CGGCGTTTTTA-GACAAACGCCGCTAAATATCAACACCTATTG
* * *
34384 CGACGTTTTTCACACAAACGCCGCTAAATATCAATACCTATTG
1 CGGCGTTTTT-AGACAAACGCCGCTAAATATCAACACCTATTG
*
34427 CGGCATTTTT
1 CGGCGTTTTT
34437 GTGAAAAAAA
Statistics
Matches: 259, Mismatches: 38, Indels: 30
0.79 0.12 0.09
Matches are distributed among these distances:
41 4 0.02
42 36 0.14
43 174 0.67
44 12 0.05
45 32 0.12
46 1 0.00
ACGTcount: A:0.33, C:0.24, G:0.15, T:0.28
Consensus pattern (42 bp):
CGGCGTTTTTAGACAAACGCCGCTAAATATCAACACCTATTG
Found at i:34346 original size:173 final size:174
Alignment explanation
Indices: 34111--34447 Score: 428
Period size: 173 Copynumber: 1.9 Consensus size: 174
34101 GCCGCAAAAC
* * * *
34111 ATCAACACCTACTGCGGCGTTTTTTGTTAAAACGCCGCTAAACATCATAACATATTGCGGCGTTT
1 ATCAACACCTACTACGACGTTTGTTGTAAAAACGCCGCTAAACATCATAACATATTGCGGCGTTT
* * * * * * *
34176 GTCTAAGAAACACTGCTAAATATTAACACCTATTACGGCGTTTTT-ATGACAAACGTCGCTAAAT
66 GTATAACAAACACCGCTAAATATCAACACCTATTACGACGTTTTTCA-CACAAACGCCGCTAAAT
*
34240 ATCAACACCTATTGCGGCGTTTTTATAAAAAAAACACCACTAAAT
130 ATCAACACCTATTGCGGCATTTTTATAAAAAAAACACCACTAAAT
* * * *
34285 ATCAACACCTATTACGACGTTTGTTG-AAAAACGCTGCTAAATATCA-ACACCTATTGCGGCGTT
1 ATCAACACCTACTACGACGTTTGTTGTAAAAACGCCGCTAAACATCATA-ACATATTGCGGCGTT
* * * *
34348 TTTATGACAAACGCCGCTAAATATCAACACCTATTGCGACGTTTTTCACACAAACGCCGCTAAAT
65 TGTATAACAAACACCGCTAAATATCAACACCTATTACGACGTTTTTCACACAAACGCCGCTAAAT
* * *
34413 ATCAATACCTATTGCGGCATTTTTGTGAAAAAAAC
130 ATCAACACCTATTGCGGCATTTTTATAAAAAAAAC
34448 GCCGTAAACT
Statistics
Matches: 138, Mismatches: 23, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
172 1 0.01
173 114 0.83
174 23 0.17
ACGTcount: A:0.34, C:0.23, G:0.14, T:0.29
Consensus pattern (174 bp):
ATCAACACCTACTACGACGTTTGTTGTAAAAACGCCGCTAAACATCATAACATATTGCGGCGTTT
GTATAACAAACACCGCTAAATATCAACACCTATTACGACGTTTTTCACACAAACGCCGCTAAATA
TCAACACCTATTGCGGCATTTTTATAAAAAAAACACCACTAAAT
Found at i:34350 original size:130 final size:129
Alignment explanation
Indices: 34082--34393 Score: 389
Period size: 130 Copynumber: 2.4 Consensus size: 129
34072 AGGCCTGTAC
* * * * *** *
34082 CGGCGTTTTTA-GCAGAAACGCCGCAAAACATCAACACCTACTGCGGCGTTTTTTGTTAAAACGC
1 CGGCGTTTTTATG-ACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTAAAAAAACAC
* * * *
34146 CGCTAAACATCATAACATATTGCGGCGTTTGTCTAAGAAACACTGCTAAATATTAACACCTATTA
65 CACTAAACATCATAACATATTACGACGTTTGTCTAAGAAACACTGCTAAATATCAACACCTATTA
*
34211 CGGCGTTTTTATGACAAACGTCGCTAAATATCAACACCTATTGCGGCGTTTTTATAAAAAAAACA
1 CGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT-T-AAAAAAACA
* * *
34276 CCACTAAATATCA-ACACCTATTACGACGTTTGT-TGAA-AAACGCTGCTAAATATCAACACCTA
64 CCACTAAACATCATA-ACATATTACGACGTTTGTCT-AAGAAACACTGCTAAATATCAACACCTA
*
34338 TTG
127 TTA
*
34341 CGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCGACGTTTTT
1 CGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTT
34394 CACACAAACG
Statistics
Matches: 159, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
129 46 0.29
130 80 0.50
131 33 0.21
ACGTcount: A:0.33, C:0.23, G:0.15, T:0.29
Consensus pattern (129 bp):
CGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTATTGCGGCGTTTTTTAAAAAAACACC
ACTAAACATCATAACATATTACGACGTTTGTCTAAGAAACACTGCTAAATATCAACACCTATTA
Found at i:36247 original size:12 final size:12
Alignment explanation
Indices: 36232--36257 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
36222 CGTTCTTATT
36232 AACGAGTTGATA
1 AACGAGTTGATA
36244 AACGAGTTGATA
1 AACGAGTTGATA
36256 AA
1 AA
36258 TGAGCCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.08, G:0.23, T:0.23
Consensus pattern (12 bp):
AACGAGTTGATA
Found at i:37390 original size:20 final size:19
Alignment explanation
Indices: 37345--37394 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
37335 ATACCACGTG
*
37345 AACAGTATCGATACTGTTT
1 AACAGTATCGATACTGTAT
* *
37364 ATGCAGTATTGATACTGTAAT
1 A-ACAGTATCGATACTGT-AT
37385 AACAGTATCG
1 AACAGTATCG
37395 GTATTATGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
19 1 0.04
20 21 0.88
21 2 0.08
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (19 bp):
AACAGTATCGATACTGTAT
Found at i:38489 original size:24 final size:26
Alignment explanation
Indices: 38453--38511 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
38443 ATATAATATT
38453 ATATTATT-AAAAA-TATCAATAAAG
1 ATATTATTAAAAAAGTATCAATAAAG
* *
38477 ATATTTTTCAAAAAGTATCAAT-AAG
1 ATATTATTAAAAAAGTATCAATAAAG
38502 TATATTATTA
1 -ATATTATTA
38512 TAATATTAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 7 0.24
25 8 0.28
26 14 0.48
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (26 bp):
ATATTATTAAAAAAGTATCAATAAAG
Found at i:38506 original size:26 final size:25
Alignment explanation
Indices: 38430--38511 Score: 84
Period size: 22 Copynumber: 3.4 Consensus size: 25
38420 AGTATATTAT
* *
38430 TATAATATTAAAAATAT-AAT--AT
1 TATATTATTAAAAATATCAATAAAG
38452 TATATTATTAAAAATATCAATAAAG
1 TATATTATTAAAAATATCAATAAAG
*
38477 -ATATTTTTCAAAAAGTATCAAT-AAG
1 TATATTATT-AAAAA-TATCAATAAAG
38502 TATATTATTA
1 TATATTATTA
38512 TAATATTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
22 16 0.32
23 3 0.06
24 7 0.14
25 10 0.20
26 14 0.28
ACGTcount: A:0.52, C:0.04, G:0.04, T:0.40
Consensus pattern (25 bp):
TATATTATTAAAAATATCAATAAAG
Found at i:45596 original size:60 final size:60
Alignment explanation
Indices: 45532--45664 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
45522 ATTGAATTTC
* *
45532 ATAGTTTTGAGATGAAATTAGAATATTAAAAAGTTCGATG-ACCAATTTAGAATGAGAGTT
1 ATAGTTTGGAGATGAAATTAGAATATTAAAAAGTTCG-TGAACCAATTTAAAATGAGAGTT
* * * * * **
45592 ATAGTTTGGATATGAAATTAGAATGTTTAAAAGTTTGTGAACCAATTTAAAATGATAGCC
1 ATAGTTTGGAGATGAAATTAGAATATTAAAAAGTTCGTGAACCAATTTAAAATGAGAGTT
45652 ATAGTTTGG-GATG
1 ATAGTTTGGAGATG
45665 TGCGGTGAAA
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
59 5 0.08
60 57 0.92
ACGTcount: A:0.39, C:0.05, G:0.21, T:0.35
Consensus pattern (60 bp):
ATAGTTTGGAGATGAAATTAGAATATTAAAAAGTTCGTGAACCAATTTAAAATGAGAGTT
Found at i:46027 original size:151 final size:151
Alignment explanation
Indices: 45753--46054 Score: 595
Period size: 151 Copynumber: 2.0 Consensus size: 151
45743 TTTAGAACAA
45753 GAGCCATAATCTAATGATGAAATTGGAACATTTGAAAGTTTGAGGACTAATTCAAAATAAGACCA
1 GAGCCATAATCTAATGATGAAATTGGAACATTTGAAAGTTTGAGGACTAATTCAAAATAAGACCA
45818 TAATTTTATGGACGAAATTGAAATATTCAAAATTAATTTACAATGGTTGTGAAAATGTCAATCAC
66 TAATTTTATGGACGAAATTGAAATATTCAAAATTAATTTACAATGGTTGTGAAAATGTCAATCAC
45883 CTTACATTGTTTTGAAAATGT
131 CTTACATTGTTTTGAAAATGT
45904 GAGCCATAATCTAATGATGAAATTGGAACATTTGAAAGTTTGAGGACTAATTCAAAATAAGACCA
1 GAGCCATAATCTAATGATGAAATTGGAACATTTGAAAGTTTGAGGACTAATTCAAAATAAGACCA
*
45969 TAATTTTATGGACGAAATTGAAATATTCAAAATTAATTTACAATGTTTGTGAAAATGTCAATCAC
66 TAATTTTATGGACGAAATTGAAATATTCAAAATTAATTTACAATGGTTGTGAAAATGTCAATCAC
46034 CTTACATTGTTTTGAAAATGT
131 CTTACATTGTTTTGAAAATGT
46055 CATTGTTTTG
Statistics
Matches: 150, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
151 150 1.00
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (151 bp):
GAGCCATAATCTAATGATGAAATTGGAACATTTGAAAGTTTGAGGACTAATTCAAAATAAGACCA
TAATTTTATGGACGAAATTGAAATATTCAAAATTAATTTACAATGGTTGTGAAAATGTCAATCAC
CTTACATTGTTTTGAAAATGT
Found at i:47947 original size:21 final size:21
Alignment explanation
Indices: 47918--47959 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
47908 TCACGCCTCT
* *
47918 GGCGTGGACTGGCACTCCTGC
1 GGCGAGGACTGCCACTCCTGC
*
47939 GGCGAGGACTGCCGCTCCTGC
1 GGCGAGGACTGCCACTCCTGC
47960 TCCTACTCCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.10, C:0.36, G:0.38, T:0.17
Consensus pattern (21 bp):
GGCGAGGACTGCCACTCCTGC
Found at i:50923 original size:13 final size:14
Alignment explanation
Indices: 50905--50937 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
50895 AAACAAGACA
50905 TGTAATACTAC-CC
1 TGTAATACTACGCC
50918 TGTAATACTACGCC
1 TGTAATACTACGCC
50932 TG-AATA
1 TGTAATA
50938 TGCTAGGGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.79
14 4 0.21
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.30
Consensus pattern (14 bp):
TGTAATACTACGCC
Done.