Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001323.1 Hibiscus syriacus cultivar Beakdansim tig00002577_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: 120708
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:541 original size:2 final size:2
Alignment explanation
Indices: 536--574 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
526 TTCCAATTCC
536 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
575 GAAAATTATC
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:7942 original size:6 final size:6
Alignment explanation
Indices: 7933--7957 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7923 AAGTGGCTTT
7933 GGCTCA GGCTCA GGCTCA GGCTCA G
1 GGCTCA GGCTCA GGCTCA GGCTCA G
7958 TTCATTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.36, T:0.16
Consensus pattern (6 bp):
GGCTCA
Found at i:13276 original size:31 final size:32
Alignment explanation
Indices: 13233--13307 Score: 91
Period size: 32 Copynumber: 2.3 Consensus size: 32
13223 TCATATATCT
13233 AAAAGGTTTTTGAAATGAAGTGA-T-ATACACTG
1 AAAA-GTTTTTGAAATGAAGTGATTGAT-CACTG
* * *
13265 AAAAGTTTTTGAAGTGAAGTTATTGATCAGTG
1 AAAAGTTTTTGAAATGAAGTGATTGATCACTG
13297 AAAAGTTTTTG
1 AAAAGTTTTTG
13308 TCAAAGAGAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
31 16 0.42
32 20 0.53
33 2 0.05
ACGTcount: A:0.37, C:0.04, G:0.23, T:0.36
Consensus pattern (32 bp):
AAAAGTTTTTGAAATGAAGTGATTGATCACTG
Found at i:15393 original size:217 final size:218
Alignment explanation
Indices: 14983--15419 Score: 619
Period size: 217 Copynumber: 2.0 Consensus size: 218
14973 ATTGCACAAG
* *
14983 ATGGTGACAGAAAAATTTTCCCTATTGCCTTTTCCATTGTTAAAAATGATTTATAGGAAACATGA
1 ATGGTGACAGAAAAATTTTCCCTATTGCCTTTTCCATTGTTAAAAATGAGTTAGAGGAAACATGA
15048 AATTTCTTTCTCTCCAACTTGCATTCCTATGTTGTAACTAAAAATGGGATTTGTATGATATCAAA
66 AATTTCTTTCTCTCCAACTTGCATTCCTATGTTGTAACTAAAAATGGGATTTGTATGATATCAAA
*
15113 CTGTTTACCTTGGTTGTTAGCCACGATTGATAGACCGGGAAGTAGATGGTCGCCTCCTCACGCAT
131 CTGTTTACCTTGGTTGTTAGCCACAATTGATAGACCGGGAAGTAGATGGTCGCCTCCTCACGCAT
15178 ATCAGACATATTGTATACATCAT
196 ATCAGACATATTGTATACATCAT
* * * * *
15201 ATGGTGACAGAAACATTTTTCCTATTG-TTTTTCCATTGTTAAAAATGAGTTAGAGGAAACGTGG
1 ATGGTGACAGAAAAATTTTCCCTATTGCCTTTTCCATTGTTAAAAATGAGTTAGAGGAAACATGA
* * * ** *** * *
15265 AGTTTCTTTTTCTCCAATTTGTGTTCCTATGTTGTTGTTCAAGATTGGG-TTTGTATGATATCAA
66 AATTTCTTTCTCTCCAACTTGCATTCCTATGTTGTAACT-AAAAATGGGATTTGTATGATATCAA
* * *
15329 ACTGTTTACC-TGTGTTGTTAGCCACAATTGATAGACTGGGAAGTAGGTGGTCGCCTCTTCACGC
130 ACTGTTTACCTTG-GTTGTTAGCCACAATTGATAGACCGGGAAGTAGATGGTCGCCTCCTCACGC
* * *
15393 ATATCTGGCGTATTGTATACATCAT
194 ATATCAGACATATTGTATACATCAT
15418 AT
1 AT
15420 TGCTTCCAAT
Statistics
Matches: 193, Mismatches: 24, Indels: 5
0.87 0.11 0.02
Matches are distributed among these distances:
216 2 0.01
217 159 0.82
218 32 0.17
ACGTcount: A:0.27, C:0.17, G:0.19, T:0.37
Consensus pattern (218 bp):
ATGGTGACAGAAAAATTTTCCCTATTGCCTTTTCCATTGTTAAAAATGAGTTAGAGGAAACATGA
AATTTCTTTCTCTCCAACTTGCATTCCTATGTTGTAACTAAAAATGGGATTTGTATGATATCAAA
CTGTTTACCTTGGTTGTTAGCCACAATTGATAGACCGGGAAGTAGATGGTCGCCTCCTCACGCAT
ATCAGACATATTGTATACATCAT
Found at i:19512 original size:19 final size:21
Alignment explanation
Indices: 19467--19524 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 21
19457 ACCCTCATGA
19467 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC-TT-AAG
19490 GGGAACCGATTCCCCC-T-AG
1 GGGAACCGATTCCCCCTTAAG
* *
19509 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
19525 CTGGGGTTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 16 0.48
21 1 0.03
23 16 0.48
ACGTcount: A:0.22, C:0.34, G:0.26, T:0.17
Consensus pattern (21 bp):
GGGAACCGATTCCCCCTTAAG
Found at i:19526 original size:20 final size:19
Alignment explanation
Indices: 19488--19530 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
19478 CCCCCTTTGA
*
19488 AGGGGAACCGATTCCCCCT
1 AGGGGAACCGATCCCCCCT
*
19507 AGGGGAATCGATACCCCCCT
1 AGGGGAACCGAT-CCCCCCT
19527 -GGGG
1 AGGGG
19531 TTCTAGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.21, C:0.33, G:0.33, T:0.14
Consensus pattern (19 bp):
AGGGGAACCGATCCCCCCT
Found at i:23921 original size:10 final size:10
Alignment explanation
Indices: 23882--23922 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
23872 TTCATCACAC
*
23882 CAAATTTTCT
1 CAAATTCTCT
23892 CAAATTCTCT
1 CAAATTCTCT
*
23902 CAATTTCTCT
1 CAAATTCTCT
*
23912 CAAATACTCT
1 CAAATTCTCT
23922 C
1 C
23923 TCTGTTTAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.29, C:0.29, G:0.00, T:0.41
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:23999 original size:17 final size:18
Alignment explanation
Indices: 23964--24004 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
23954 ATATTATGTA
*
23964 TTTAATTTATTTAATTAT
1 TTTACTTTATTTAATTAT
23982 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAATTAT
23999 TTTACT
1 TTTACT
24005 AATATAATTC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (18 bp):
TTTACTTTATTTAATTAT
Found at i:26291 original size:35 final size:33
Alignment explanation
Indices: 26252--26336 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 33
26242 ATATTTCAGT
26252 TAATTTTGTT-TATTACCATTTAATATCAGTTATTG
1 TAATTTTGTTATATTACCATTTAAT-TC--TTATTG
*
26287 TAATTTGGTTATCATTTACCATTTAATTCTTATTG
1 TAATTTTGTTAT-A-TTACCATTTAATTCTTATTG
* *
26322 TAAGTTTGTTGTATT
1 TAATTTTGTTATATT
26337 TAAATACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
33 2 0.05
34 1 0.02
35 24 0.56
36 1 0.02
37 3 0.07
38 12 0.28
ACGTcount: A:0.26, C:0.08, G:0.11, T:0.55
Consensus pattern (33 bp):
TAATTTTGTTATATTACCATTTAATTCTTATTG
Found at i:30046 original size:51 final size:51
Alignment explanation
Indices: 29943--30055 Score: 122
Period size: 51 Copynumber: 2.2 Consensus size: 51
29933 CCCCTACGTG
* * **
29943 GCGTATAGCGCGGATCAGGGGGCGCGCTATACACACGTGTAATCCATGTCA
1 GCGTATAGCGCGGATCAGGAGGCGCGCTATACACACGTGGAATCCAAATCA
* **
29994 GCGTATAGCGCGG-TGCAGGAGGCGCGCTATACCTCACGTGGCGT-CAAATCA
1 GCGTATAGCGCGGAT-CAGGAGGCGCGCTATA-CACACGTGGAATCCAAATCA
*
30045 GCATATAGCGC
1 GCGTATAGCGC
30056 AGTTCAGGGG
Statistics
Matches: 52, Mismatches: 8, Indels: 4
0.81 0.12 0.06
Matches are distributed among these distances:
50 1 0.02
51 43 0.83
52 8 0.15
ACGTcount: A:0.23, C:0.27, G:0.32, T:0.19
Consensus pattern (51 bp):
GCGTATAGCGCGGATCAGGAGGCGCGCTATACACACGTGGAATCCAAATCA
Found at i:33566 original size:40 final size:40
Alignment explanation
Indices: 33522--33609 Score: 131
Period size: 40 Copynumber: 2.2 Consensus size: 40
33512 TTATAACTAC
* * **
33522 AATATTAACTCTAGAACAATAAAATCCATAAATAAACTGT
1 AATATTAACTCTAAAACAATAAAATCCATAAACAAACCAT
*
33562 AATATTAAGTCTAAAACAATAAAATCCATAAACAAACCAT
1 AATATTAACTCTAAAACAATAAAATCCATAAACAAACCAT
33602 AATATTAA
1 AATATTAA
33610 AGTGTCAAAT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 43 1.00
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (40 bp):
AATATTAACTCTAAAACAATAAAATCCATAAACAAACCAT
Found at i:33657 original size:17 final size:17
Alignment explanation
Indices: 33635--33693 Score: 86
Period size: 17 Copynumber: 3.6 Consensus size: 17
33625 GACTCAAACC
33635 ACAATATTAAGTCTACA
1 ACAATATTAAGTCTACA
* *
33652 ACAATATTAA-ACAAC-
1 ACAATATTAAGTCTACA
33667 ACAATATTAAGTCTACA
1 ACAATATTAAGTCTACA
33684 ACAATATTAA
1 ACAATATTAA
33694 ACAACACAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
15 10 0.28
16 6 0.17
17 20 0.56
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.27
Consensus pattern (17 bp):
ACAATATTAAGTCTACA
Found at i:33672 original size:15 final size:15
Alignment explanation
Indices: 33652--33702 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
33642 TAAGTCTACA
33652 ACAATATTAAACAAC
1 ACAATATTAAACAAC
* *
33667 ACAATATTAAGTCTAC
1 ACAATATTAA-ACAAC
33683 AACAATATTAAACAAC
1 -ACAATATTAAACAAC
33699 ACAA
1 ACAA
33703 ATCAAACATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 14 0.47
16 6 0.20
17 10 0.33
ACGTcount: A:0.57, C:0.20, G:0.02, T:0.22
Consensus pattern (15 bp):
ACAATATTAAACAAC
Found at i:33673 original size:32 final size:32
Alignment explanation
Indices: 33634--33702 Score: 138
Period size: 32 Copynumber: 2.2 Consensus size: 32
33624 AGACTCAAAC
33634 CACAATATTAAGTCTACAACAATATTAAACAA
1 CACAATATTAAGTCTACAACAATATTAAACAA
33666 CACAATATTAAGTCTACAACAATATTAAACAA
1 CACAATATTAAGTCTACAACAATATTAAACAA
33698 CACAA
1 CACAA
33703 ATCAAACATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.54, C:0.20, G:0.03, T:0.23
Consensus pattern (32 bp):
CACAATATTAAGTCTACAACAATATTAAACAA
Found at i:38148 original size:19 final size:20
Alignment explanation
Indices: 38109--38158 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
38099 AAAATAAATT
*
38109 AATACTTAATATATATTAAA
1 AATATTTAATATATATTAAA
*
38129 AGAT-TTTAATAT-TTTTAAA
1 A-ATATTTAATATATATTAAA
38148 AATATTTAATA
1 AATATTTAATA
38159 GGAACGACAT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
18 2 0.08
19 14 0.54
20 8 0.31
21 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (20 bp):
AATATTTAATATATATTAAA
Found at i:40225 original size:21 final size:21
Alignment explanation
Indices: 40174--40231 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
40164 TTTCTGGGCT
*
40174 AGGGGAATCAGTACCCATTCA
1 AGGGGAATCGGTACCCATTCA
*
40195 ATGGGAATCGGTACCCATTCA
1 AGGGGAATCGGTACCCATTCA
*
40216 AGGGGAATCGATACCC
1 AGGGGAATCGGTACCC
40232 CCTCAACCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.31, C:0.24, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGGTACCCATTCA
Found at i:41816 original size:23 final size:22
Alignment explanation
Indices: 41759--41833 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
41749 ATGAACAACC
* *
41759 TTATATGGCACTTCAGTGC-AT
1 TTATATGGCACTACGGTGCAAT
* *
41780 TTCTACGCGACACTACGGTGCAAT
1 TTATATG-G-CACTACGGTGCAAT
*
41804 TCTATATGGCACTTCGGTGCAAT
1 T-TATATGGCACTACGGTGCAAT
41827 TTATATG
1 TTATATG
41834 AGCTGTGGTG
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
21 5 0.12
22 7 0.16
23 23 0.53
24 4 0.09
25 4 0.09
ACGTcount: A:0.24, C:0.21, G:0.20, T:0.35
Consensus pattern (22 bp):
TTATATGGCACTACGGTGCAAT
Found at i:45181 original size:21 final size:21
Alignment explanation
Indices: 45153--45201 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
45143 TTTCTGGGCT
45153 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGGTACCCATTCA
*
45174 ATGGGAATCGGTACCCATTCA
1 AGGGGAATCGGTACCCATTCA
45195 AGGGGAA
1 AGGGGAA
45202 CCGATTCCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.31, T:0.18
Consensus pattern (21 bp):
AGGGGAATCGGTACCCATTCA
Found at i:45567 original size:18 final size:17
Alignment explanation
Indices: 45544--45577 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
45534 TATTGTGTGA
*
45544 ATATGTTTTGTTCGTATT
1 ATATGTTATGTT-GTATT
45562 ATATGTTATGTTGTAT
1 ATATGTTATGTTGTAT
45578 GAATTTATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.59
Consensus pattern (17 bp):
ATATGTTATGTTGTATT
Found at i:55163 original size:37 final size:37
Alignment explanation
Indices: 55112--55216 Score: 138
Period size: 37 Copynumber: 2.8 Consensus size: 37
55102 CATTTTCGTC
*
55112 CTACTAAGATTCAAACTCCTAAAAATCGGATAAAATT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
55149 TTACTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
55186 CTACTAAGATTTAAATTCCTAAAGATAGGAT
1 CTACTAAGATTCAAACTCCTAAAAATAGGAT
55217 CCACAAGCAC
Statistics
Matches: 58, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.43, C:0.15, G:0.12, T:0.30
Consensus pattern (37 bp):
CTACTAAGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:55612 original size:18 final size:17
Alignment explanation
Indices: 55573--55615 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
55563 ATTATATGGA
55573 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
55589 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
55607 TATTATTAT
1 TATTATTAT
55616 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:55923 original size:21 final size:20
Alignment explanation
Indices: 55869--55924 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 20
55859 ACTTTATAAC
* *
55869 TTTATATTATTTTTTATTAT
1 TTTATATTATTATTCATTAT
* *
55889 TTTCATTTTTTTATTCATTAT
1 TTT-ATATTATTATTCATTAT
55910 TATTATATTATTATT
1 T-TTATATTATTATT
55925 TTTTTTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 3 0.11
21 23 0.82
22 2 0.07
ACGTcount: A:0.25, C:0.04, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATATTATTATTCATTAT
Found at i:56124 original size:2 final size:2
Alignment explanation
Indices: 56117--56150 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56107 TAATACTTTG
56117 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
56151 TTTTTTTTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60140 original size:18 final size:18
Alignment explanation
Indices: 60117--60186 Score: 68
Period size: 18 Copynumber: 3.7 Consensus size: 18
60107 TTCAGTATTC
*
60117 GTCCCGTAGAACCACTAT
1 GTCCCGTAGGACCACTAT
*
60135 GTCCCGAAGGACCACTGTATAT
1 GTCCCGTAGGACCAC----TAT
60157 GTCCCGTAGGACCACTAT
1 GTCCCGTAGGACCACTAT
* *
60175 ATCCCGAAGGAC
1 GTCCCGTAGGAC
60187 TACTCCTTAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
18 26 0.60
22 17 0.40
ACGTcount: A:0.27, C:0.31, G:0.21, T:0.20
Consensus pattern (18 bp):
GTCCCGTAGGACCACTAT
Found at i:60160 original size:22 final size:20
Alignment explanation
Indices: 60132--60186 Score: 69
Period size: 22 Copynumber: 2.8 Consensus size: 20
60122 GTAGAACCAC
60132 TATGTCCCGAAGGACCACTGTA
1 TATGTCCCGAAGGACCAC--TA
*
60154 TATGTCCCGTAGGACCACTA
1 TATGTCCCGAAGGACCACTA
60174 TA--TCCCGAAGGAC
1 TATGTCCCGAAGGAC
60187 TACTCCTTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
18 10 0.32
20 4 0.13
22 17 0.55
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (20 bp):
TATGTCCCGAAGGACCACTA
Found at i:61834 original size:64 final size:64
Alignment explanation
Indices: 61701--61857 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 64
61691 TAATGAAGGT
* * ** *
61701 ATGCATCGATGCAC-CACTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCACTC-CTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAAAGAG
* * *
61765 ATGCATCGATGCACTCCTTATGCATCGATGCATTAATTGCATTCGATGTT-T-TTATCTTAAA-A
1 ATGCATCGATGCACTCCTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTA--TTAAAGA
61827 G
64 G
61828 AGTGCATCGATGCACTACC-AATGCATCGAT
1 A-TGCATCGATGCACT-CCTAATGCATCGAT
61858 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
62 3 0.04
63 3 0.04
64 71 0.89
65 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTCCTAATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAAAGAG
Found at i:65268 original size:22 final size:18
Alignment explanation
Indices: 65225--65294 Score: 86
Period size: 18 Copynumber: 3.7 Consensus size: 18
65215 TTCAGTATTC
*
65225 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
65243 GTCCCGAAGGACCACTGTATAT
1 GTCCCGAAGGACCAC----TAT
*
65265 GTCCCGTAGGACCACTAT
1 GTCCCGAAGGACCACTAT
65283 GTCCCGAAGGAC
1 GTCCCGAAGGAC
65295 TACTCCTTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 8
0.80 0.05 0.14
Matches are distributed among these distances:
18 28 0.62
22 17 0.38
ACGTcount: A:0.24, C:0.31, G:0.24, T:0.20
Consensus pattern (18 bp):
GTCCCGAAGGACCACTAT
Found at i:68872 original size:183 final size:183
Alignment explanation
Indices: 68564--69100 Score: 941
Period size: 183 Copynumber: 2.9 Consensus size: 183
68554 ATTAAATCCG
*
68564 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATATAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
*
68629 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGATGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
68694 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
**
68747 TAAAGCTGAGCTATTCCACTAAGGCAATTAATTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
68812 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
66 ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
* *
68877 TTGTCAGGCCAAAGACTTTGTGATAAGACGAACCCTTCAGTGATTTGTCCCTC
131 TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
* *
68930 TAAAGCTGAGCTATTCCACTAAGGAAATTGGTTATAGAGGAAACTCGAAAGCCCTGTCTTTATGA
1 TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
** * *
68995 ATAGATTACATTCAAA-TCATGACATTGCTCGGACACTTGGCAATTCGGTGTTTACTCCACTGCT
66 ATAGATTATGTTCAAACT-ATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCT
*
69059 TTTGTCAGGTCAAAGACTTTGTGATGAGATGAACCCTTCAGT
130 TTTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGT
69101 TAAACCTGAT
Statistics
Matches: 336, Mismatches: 17, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
182 1 0.00
183 335 1.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (183 bp):
TAAAGCTGAGCTATTCCACTAAGGCAATTGGTTATAGAGGAAACTCGAAAGCCCTGGCTTTATGA
ATAGATTATGTTCAAACTATGACACTGCTCGGACACTTGGCAATTCGGTGTTTGCTCCACTGCTT
TTGTCAGGCCAAAGACTTTGTGATGAGATGAACCCTTCAGTGATTTGTCCCTC
Found at i:70322 original size:36 final size:36
Alignment explanation
Indices: 70282--70398 Score: 108
Period size: 36 Copynumber: 3.1 Consensus size: 36
70272 ATACTTTGTC
70282 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
** * ** * *
70318 TCACTCAAGATTGTTTTTCTTAAAACAAGATTTATC
1 TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
* * *
70354 TCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATT
1 TCACTTGAGACTGTTTT-TCTCGAAAGAA-G-ATTT-ATT
70394 TCACT
1 TCACT
70399 CAAGGCTGTT
Statistics
Matches: 59, Mismatches: 18, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
36 41 0.69
37 7 0.12
38 1 0.02
39 4 0.07
40 6 0.10
ACGTcount: A:0.28, C:0.19, G:0.15, T:0.38
Consensus pattern (36 bp):
TCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATT
Found at i:70333 original size:72 final size:75
Alignment explanation
Indices: 70241--70411 Score: 199
Period size: 72 Copynumber: 2.3 Consensus size: 75
70231 ATGCAAATGA
* * * * * *
70241 TTATCTCACTCAA-ATTTGTTTTTGTTAAAACATA-CTTTGTCTCACTTGAGACTGTTTT-TCTC
1 TTATTTCACTCAAGA-TTGTTTTTCTTAAAACA-AGATTTATCTCACTTGAGACCGTTTTCACTC
70303 GAAAGAA-G-AT
64 GAAAGAAGGCAT
*
70313 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTATCTCGCTTGAGACCGTTTTCACTCGA
1 TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTATCTCACTTGAGACCGTTTTCACTCGA
70378 AAGAAGGCAT
66 AAGAAGGCAT
**
70388 TTCATTTCACTCAAGGCTGTTTTT
1 TT-ATTTCACTCAAGATTGTTTTT
70412 TAAGAAGATT
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
71 1 0.01
72 48 0.57
73 11 0.13
74 1 0.01
75 4 0.05
76 19 0.23
ACGTcount: A:0.27, C:0.18, G:0.13, T:0.42
Consensus pattern (75 bp):
TTATTTCACTCAAGATTGTTTTTCTTAAAACAAGATTTATCTCACTTGAGACCGTTTTCACTCGA
AAGAAGGCAT
Found at i:70421 original size:72 final size:72
Alignment explanation
Indices: 70280--70436 Score: 178
Period size: 73 Copynumber: 2.2 Consensus size: 72
70270 ACATACTTTG
* * * *
70280 TCTCACTTGAGACTGTTTTTCTCGAAAGAAGATTTATTTCACTCAAGATTGTTTTTCTTAAAACA
1 TCTCGCTTGAGACCGTTTTACTCGAAAGAAGATTTATTTCACTCAAGACTGTTTTTCTT-AAACA
70345 AGA-TTTA
65 AGATTTTA
*
70352 TCTCGCTTGAGACCGTTTTCACTCGAAAGAAGGCATTTCATTTCACTCAAGGCTG-TTTT-TT-A
1 TCTCGCTTGAGACCGTTTT-ACTCGAAAGAA-G-ATTT-ATTTCACTCAAGACTGTTTTTCTTAA
*
70414 AGAAGATTTTA
62 ACAAGATTTTA
*
70425 TCTTGCTTGAGA
1 TCTCGCTTGAGA
70437 TAGTTTCCCT
Statistics
Matches: 73, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
72 23 0.32
73 25 0.34
74 3 0.04
75 8 0.11
76 14 0.19
ACGTcount: A:0.27, C:0.17, G:0.16, T:0.39
Consensus pattern (72 bp):
TCTCGCTTGAGACCGTTTTACTCGAAAGAAGATTTATTTCACTCAAGACTGTTTTTCTTAAACAA
GATTTTA
Found at i:70473 original size:39 final size:39
Alignment explanation
Indices: 70430--70582 Score: 110
Period size: 39 Copynumber: 3.6 Consensus size: 39
70420 TTTTATCTTG
*
70430 CTTGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * *
70469 CTTGAGACAGTTTCTCTTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTC
1 CTTGAGACAGTTTCCCTCG-AAACA--------G-AA--AATTTTGTCTC-C
*
70521 C-TGAGATAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
1 CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
* * *
70559 TTTGAGACAGTTTCTCTTGAAACA
1 CTTGAGACAGTTTCCCTCGAAACA
70583 TAAACATTGA
Statistics
Matches: 88, Mismatches: 12, Indels: 28
0.69 0.09 0.22
Matches are distributed among these distances:
38 1 0.01
39 45 0.51
40 5 0.06
41 2 0.02
42 1 0.01
48 1 0.01
49 2 0.02
50 5 0.06
51 24 0.27
52 2 0.02
ACGTcount: A:0.27, C:0.22, G:0.14, T:0.37
Consensus pattern (39 bp):
CTTGAGACAGTTTCCCTCGAAACAGAAAATTTTGTCTCC
Found at i:70651 original size:105 final size:104
Alignment explanation
Indices: 70485--70803 Score: 509
Period size: 105 Copynumber: 3.1 Consensus size: 104
70475 ACAGTTTCTC
* *
70485 TTGAAAACATTTCCCTTGAAATTAATTTTTTCTCTCCTGAGATAGTTTCCCTCGAAACAGAAAAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
*
70550 TTTGTCTCCTTTGAGACAGTTTCTCTTGAAACATAAACA
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
*
70589 TTGAAAACATTTCCCTTGAAATGATTTTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
1 TTGAAAACATTTCCCTTGAAATGA-ATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAA
*
70654 TTTTGTCTCCCTTGAGACAGTTTCCCTTGAAACATAAACA
65 TTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
* * *
70694 TTGAAAACATTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAC-G--AAT
1 TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
** *
70756 TTTGTCTCCCTTGAGACAGTTTCTCTCCAAACATAAACT
66 TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
70795 TTGAAAACA
1 TTGAAAACA
70804 ATTTAACGAA
Statistics
Matches: 201, Mismatches: 13, Indels: 5
0.92 0.06 0.02
Matches are distributed among these distances:
101 47 0.23
103 1 0.00
104 53 0.26
105 100 0.50
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.37
Consensus pattern (104 bp):
TTGAAAACATTTCCCTTGAAATGAATTTTTTCTCTCTTGAGATAGTTTCCCTCGAAACAGAAAAT
TTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
Found at i:70750 original size:36 final size:36
Alignment explanation
Indices: 70703--70778 Score: 116
Period size: 36 Copynumber: 2.1 Consensus size: 36
70693 ATTGAAAACA
* * *
70703 TTTCCCTTGAAATGAATTTTATCTCGCTTGAGATAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
*
70739 TTTCCCTTGAAACGAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
70775 TTTC
1 TTTC
70779 TCTCCAAACA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.16, T:0.41
Consensus pattern (36 bp):
TTTCCCTTGAAACGAATTTTATCTCCCTTGAGACAG
Found at i:71173 original size:105 final size:105
Alignment explanation
Indices: 70978--71608 Score: 909
Period size: 105 Copynumber: 6.0 Consensus size: 105
70968 ATATCGTAAC
* * * * *
70978 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAAC-AACAACTTCTC
71043 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
71084 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTACTTGTAAACAACAACTTCTCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
71149 ATTTCAGAGCCAATTTCAACTTCACAACAAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
71189 ACTTCAGACAACGCAAGTTCAACTTCACGACAAAGGGACCGCTGCTTGTCAACAACAACTTC-CA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTC-
* *
71253 AATCTCAGAGCCAATTTCAACTTCACAACGAATGATATTGG
65 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* *
71294 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTACTTGTCAACAACAACTTCCCA
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
*
71359 ATCTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
*
71399 ACTCCAGACAACGCAAGTTCAACTCCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TT-TC-
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
* *
71460 A-TTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
66 ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
* * * * * * *
71499 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAA-ATAATTTTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACA-ACTTCTC
* * *
71563 -CTGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGG
65 AAT-TT-CAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
71605 ACTC
1 ACTC
71609 GGAACAATGC
Statistics
Matches: 481, Mismatches: 36, Indels: 16
0.90 0.07 0.03
Matches are distributed among these distances:
100 85 0.18
101 2 0.00
102 3 0.01
103 4 0.01
104 3 0.01
105 301 0.63
106 83 0.17
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (105 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAACTTCTCA
ATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
Found at i:72245 original size:37 final size:37
Alignment explanation
Indices: 72151--72247 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
72141 CATTTTCGTC
72151 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * * *
72188 TTGCTAGGATTCAAACTCCTAAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
* * *
72225 CTACTAAGATTTAAATTCCTAAA
1 CTACTAGGATTCAAACTCCTAAA
72248 GATATGATCC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
37 51 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.30
Consensus pattern (37 bp):
CTACTAGGATTCAAACTCCTAAAAATAGGATAAAATT
Found at i:72650 original size:18 final size:17
Alignment explanation
Indices: 72611--72653 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
72601 ATTATAAGGA
72611 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
72627 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
72645 TATTATTAT
1 TATTATTAT
72654 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:72664 original size:2 final size:2
Alignment explanation
Indices: 72651--72776 Score: 127
Period size: 2 Copynumber: 64.5 Consensus size: 2
72641 TTATTATTAT
* * * *
72651 TA TA TG TA TA TA TA TA TA TA TA TA T- TA AA T- TA TT TCA TT TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA
* * * *
72692 TT TT TT TA CTA TA T- TT TA T- TA T- 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
72732 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
72774 TA T
1 TA T
72777 TCTTTAATAT
Statistics
Matches: 106, Mismatches: 11, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
1 5 0.05
2 98 0.92
3 3 0.03
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.56
Consensus pattern (2 bp):
TA
Found at i:73294 original size:20 final size:22
Alignment explanation
Indices: 73266--73305 Score: 57
Period size: 20 Copynumber: 1.9 Consensus size: 22
73256 TATATAATTA
*
73266 TTATTTTAC-TATTT-TTTTTC
1 TTATCTTACTTATTTATTTTTC
73286 TTATCTTACTTATTTATTTT
1 TTATCTTACTTATTTATTTT
73306 ATTTTTCCCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 8 0.47
21 5 0.29
22 4 0.24
ACGTcount: A:0.17, C:0.10, G:0.00, T:0.72
Consensus pattern (22 bp):
TTATCTTACTTATTTATTTTTC
Found at i:78956 original size:24 final size:23
Alignment explanation
Indices: 78915--78983 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 23
78905 CACATAGATA
* *
78915 TGTCCCGAAGGACTACGTAGAAT
1 TGTCCCAAAGGACCACGTAGAAT
78938 T-TGCCCTGAAA-GACCACGTAGAAT
1 TGT-CCC--AAAGGACCACGTAGAAT
78962 TGTCCCAAAGGACCACGTAGAA
1 TGTCCCAAAGGACCACGTAGAA
78984 CCCTCGACTC
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
22 4 0.10
23 16 0.41
24 16 0.41
25 3 0.08
ACGTcount: A:0.33, C:0.25, G:0.23, T:0.19
Consensus pattern (23 bp):
TGTCCCAAAGGACCACGTAGAAT
Found at i:79110 original size:15 final size:15
Alignment explanation
Indices: 79088--79164 Score: 73
Period size: 15 Copynumber: 5.1 Consensus size: 15
79078 GTCTTTTATC
79088 CACATAGAACACTTT
1 CACATAGAACACTTT
* * *
79103 CGCATAGAGCATTTT
1 CACATAGAACACTTT
** *
79118 CATGTAGAACACATT
1 CACATAGAACACTTT
*
79133 CACATAAAACACTTT
1 CACATAGAACACTTT
* *
79148 CACATGGAACACATT
1 CACATAGAACACTTT
79163 CA
1 CA
79165 TATTTTAATA
Statistics
Matches: 46, Mismatches: 16, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
15 46 1.00
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.26
Consensus pattern (15 bp):
CACATAGAACACTTT
Found at i:79149 original size:30 final size:30
Alignment explanation
Indices: 79088--79164 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 30
79078 GTCTTTTATC
* * * * *
79088 CACATAGAACACTTTCGCATAGAGCATTTT
1 CACATAGAACACATTCACATAAAACACTTT
**
79118 CATGTAGAACACATTCACATAAAACACTTT
1 CACATAGAACACATTCACATAAAACACTTT
*
79148 CACATGGAACACATTCA
1 CACATAGAACACATTCA
79165 TATTTTAATA
Statistics
Matches: 37, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.39, C:0.25, G:0.10, T:0.26
Consensus pattern (30 bp):
CACATAGAACACATTCACATAAAACACTTT
Found at i:79681 original size:20 final size:20
Alignment explanation
Indices: 79658--79703 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
79648 CTTACTCTTG
*
79658 GTATTGATAC-CTTCACATCA
1 GTATCGATACACTTCA-ATCA
79678 GTATCGATACTACTTCAATCA
1 GTATCGATAC-ACTTCAATCA
79699 GTATC
1 GTATC
79704 AATATTGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 9 0.39
21 9 0.39
22 5 0.22
ACGTcount: A:0.30, C:0.24, G:0.11, T:0.35
Consensus pattern (20 bp):
GTATCGATACACTTCAATCA
Found at i:85830 original size:24 final size:23
Alignment explanation
Indices: 85803--85864 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 23
85793 ATATGTCCTA
*
85803 AAGGACCGCGTAGAATTTGTCTCG
1 AAGGACCGCGTAGAA-TTGTCCCG
**
85827 AAGGACCATGTAGAATTGTCCCG
1 AAGGACCGCGTAGAATTGTCCCG
85850 AAGGACCGCGTAGAA
1 AAGGACCGCGTAGAA
85865 CCCTCGACTC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
23 20 0.61
24 13 0.39
ACGTcount: A:0.31, C:0.21, G:0.29, T:0.19
Consensus pattern (23 bp):
AAGGACCGCGTAGAATTGTCCCG
Found at i:86007 original size:30 final size:30
Alignment explanation
Indices: 85970--86045 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
85960 TCTTTCATCC
* ** * *
85970 ACATAGAACACTTTGGCATAGAGCATTTTT
1 ACATAGAACACATTCACATAAAGCACTTTT
*
86000 ACGTAGAACACATTCACATAAAGCACTTTT
1 ACATAGAACACATTCACATAAAGCACTTTT
*
86030 ACATAGAACACGTTCA
1 ACATAGAACACATTCA
86046 TATTTTAATA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (30 bp):
ACATAGAACACATTCACATAAAGCACTTTT
Found at i:87898 original size:18 final size:20
Alignment explanation
Indices: 87853--87898 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
87843 CCCCTATGGG
*
87853 GAGTATCGATACTCTACACTT
1 GAGTATCAATACTCTACAC-T
87874 G-GTATCAATACTCT-CA-T
1 GAGTATCAATACTCTACACT
87891 GAGTATCA
1 GAGTATCA
87899 GTACAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 2 0.09
18 6 0.26
19 2 0.09
20 12 0.52
21 1 0.04
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (20 bp):
GAGTATCAATACTCTACACT
Found at i:95881 original size:16 final size:16
Alignment explanation
Indices: 95860--95893 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
95850 CGATGGTTTC
95860 GACTAAGAATAAGAAA
1 GACTAAGAATAAGAAA
*
95876 GACTAAGAGTAAGAAA
1 GACTAAGAATAAGAAA
95892 GA
1 GA
95894 GAGATGGGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.59, C:0.06, G:0.24, T:0.12
Consensus pattern (16 bp):
GACTAAGAATAAGAAA
Found at i:97648 original size:3 final size:3
Alignment explanation
Indices: 97640--97680 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
97630 GTTCTTGAAT
97640 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
97681 GTGGTGTAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:98566 original size:2 final size:2
Alignment explanation
Indices: 98559--98595 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
98549 GTGTAAGTGG
98559 AT AT AT 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 AT AT AT A
98596 GTTAAAATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:98874 original size:2 final size:2
Alignment explanation
Indices: 98827--98864 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
98817 CATTATTTTG
98827 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
98865 TAAAATATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:100525 original size:4 final size:4
Alignment explanation
Indices: 100518--100542 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
100508 ATGAGAGAGA
100518 ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT A
100543 TATATTTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:100828 original size:18 final size:18
Alignment explanation
Indices: 100802--100836 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
100792 GACAAGGGAT
*
100802 GAAAAAGAAGCAGAAAAA
1 GAAAAAGAAGAAGAAAAA
*
100820 GAAAGAGAAGAAGAAAA
1 GAAAAAGAAGAAGAAAA
100837 TTGTACGACC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.71, C:0.03, G:0.26, T:0.00
Consensus pattern (18 bp):
GAAAAAGAAGAAGAAAAA
Found at i:101810 original size:3 final size:3
Alignment explanation
Indices: 101802--101829 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
101792 TTGGTTCTTC
101802 GTT GTT GTT GTT GTT GTT GTT GTT GTT G
1 GTT GTT GTT GTT GTT GTT GTT GTT GTT G
101830 CTGCTGTTTC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (3 bp):
GTT
Found at i:109009 original size:99 final size:96
Alignment explanation
Indices: 108864--109041 Score: 268
Period size: 99 Copynumber: 1.8 Consensus size: 96
108854 GTTTTTAATT
* * * * *
108864 TAAATTATTAACTATTTTTTTTATTTTACATATTAAGTTGTATTTGAGT-AGTTTGGTAAGTTTA
1 TAAATTATTAAATATTATTTTGATTTTACATATTAAATCGTATTTGAGTGA-TTTGGTAAGTTTA
108928 GTTTAAATTATTTTTATTTTTTATTGAGCAATA
65 GTTTAAATT-TTTTTATTTTTTATTGAGCAATA
108961 TAAATTATTGAAATATCTATTTTGATTTTACATATTAAATCGTATTTGAGTGATTTGGTAAGTTT
1 TAAATTATT-AAATAT-TATTTTGATTTTACATATTAAATCGTATTTGAGTGATTTGGTAAGTTT
109026 AGTTTAAATTTTTTTA
64 AGTTTAAATTTTTTTA
109042 ATTGTAAATA
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
97 9 0.12
98 11 0.15
99 52 0.71
100 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.12, T:0.54
Consensus pattern (96 bp):
TAAATTATTAAATATTATTTTGATTTTACATATTAAATCGTATTTGAGTGATTTGGTAAGTTTAG
TTTAAATTTTTTTATTTTTTATTGAGCAATA
Found at i:111854 original size:44 final size:44
Alignment explanation
Indices: 111801--111887 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 44
111791 CAACTCGTAA
*
111801 TTTGCACCGAAGTGCCACATAATTATCCTGAATAACCACATAGG
1 TTTGCACCGAAGTGCCACATAATTATCCCGAATAACCACATAGG
* * *
111845 TTTGCACCGAAGTGCCACATAATTGTCCCGAATGACCATATAG
1 TTTGCACCGAAGTGCCACATAATTATCCCGAATAACCACATAG
111888 ACCCTCGATT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.25
Consensus pattern (44 bp):
TTTGCACCGAAGTGCCACATAATTATCCCGAATAACCACATAGG
Found at i:115068 original size:16 final size:16
Alignment explanation
Indices: 115047--115099 Score: 67
Period size: 16 Copynumber: 3.4 Consensus size: 16
115037 GATATGATCT
115047 ATGTGACCATATGAGA
1 ATGTGACCATATGAGA
*
115063 ATGTGA-C--ATGAGCT
1 ATGTGACCATATGAG-A
115077 ATGTGACCATATGAGA
1 ATGTGACCATATGAGA
115093 ATGTGAC
1 ATGTGAC
115100 ATGAGATTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
13 5 0.16
14 6 0.19
15 2 0.06
16 13 0.42
17 5 0.16
ACGTcount: A:0.34, C:0.13, G:0.26, T:0.26
Consensus pattern (16 bp):
ATGTGACCATATGAGA
Found at i:115081 original size:30 final size:30
Alignment explanation
Indices: 115035--115104 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
115025 TAACAACCAC
* *
115035 GTGATATGATCTATGTGACCATATGAGAAT
1 GTGACATGAGCTATGTGACCATATGAGAAT
115065 GTGACATGAGCTATGTGACCATATGAGAAT
1 GTGACATGAGCTATGTGACCATATGAGAAT
115095 GTGACATGAG
1 GTGACATGAG
115105 ATTATATGCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.33, C:0.11, G:0.27, T:0.29
Consensus pattern (30 bp):
GTGACATGAGCTATGTGACCATATGAGAAT
Found at i:115105 original size:13 final size:13
Alignment explanation
Indices: 115057--115105 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
115047 ATGTGACCAT
115057 ATGAGAATGTGAC
1 ATGAGAATGTGAC
*
115070 ATGAGCTATGTGACC
1 ATGAG-AATGTGA-C
115085 ATATGAGAATGTGAC
1 --ATGAGAATGTGAC
115100 ATGAGA
1 ATGAGA
115106 TTATATGCAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 11 0.37
14 6 0.20
15 2 0.07
16 6 0.20
17 5 0.17
ACGTcount: A:0.37, C:0.10, G:0.29, T:0.24
Consensus pattern (13 bp):
ATGAGAATGTGAC
Found at i:115119 original size:23 final size:21
Alignment explanation
Indices: 115085--115144 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 21
115075 CTATGTGACC
115085 ATATGAGA-ATGTGACATGAGATT
1 ATATGA-ATATGTGACATGA-A-T
* *
115108 ATATGCATATGTGAAATGAAT
1 ATATGAATATGTGACATGAAT
*
115129 ATGTGAATATGTGACA
1 ATATGAATATGTGACA
115145 AACAAAATGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
21 14 0.45
22 2 0.06
23 15 0.48
ACGTcount: A:0.40, C:0.05, G:0.23, T:0.32
Consensus pattern (21 bp):
ATATGAATATGTGACATGAAT
Found at i:118933 original size:23 final size:20
Alignment explanation
Indices: 118890--118965 Score: 84
Period size: 20 Copynumber: 3.8 Consensus size: 20
118880 AATGCAATTA
*
118890 ATGCATCGATGCA-T-AAGG
1 ATGCATCGATGCACTGTAGG
*
118908 ATGCATAGATGCACATGTTAGGG
1 ATGCATCGATGCAC-TG-TA-GG
*
118931 ATGCATCGATGCACTGTAGA
1 ATGCATCGATGCACTGTAGG
118951 ATGCATCGATGCACT
1 ATGCATCGATGCACT
118966 TCAAGGGGAA
Statistics
Matches: 49, Mismatches: 4, Indels: 8
0.80 0.07 0.13
Matches are distributed among these distances:
18 12 0.24
20 17 0.35
21 2 0.04
22 3 0.06
23 15 0.31
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (20 bp):
ATGCATCGATGCACTGTAGG
Found at i:119946 original size:61 final size:64
Alignment explanation
Indices: 119857--120013 Score: 175
Period size: 60 Copynumber: 2.5 Consensus size: 64
119847 CGGTGTACTA
* * *
119857 AGAGTGCATCGATTCAT-GAGTGCATTCGATGTTTGAAAA-ATAGCCTG-GTGCA-CGATGCAT-
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATAT-GCC-GAGTGCATCGATGCATG
119917 G
64 G
** *
119918 -GCTTGCATCGATGCATCAAATGCATTCGATG-TTGAAAATATTCCGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATGCCGAGTGCATCGATGCATGG
* *
119980 AGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTT
120014 CAATTAAATC
Statistics
Matches: 79, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
59 1 0.01
60 27 0.34
61 22 0.28
62 1 0.01
63 27 0.34
64 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (64 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTGAAAATATGCCGAGTGCATCGATGCATGG
Found at i:120008 original size:63 final size:61
Alignment explanation
Indices: 119857--120013 Score: 178
Period size: 63 Copynumber: 2.6 Consensus size: 61
119847 CGGTGTACTA
* *
119857 AGAGTGCATCGATTCATG-AGTGCATTCGATGTTTGAAAAATAGCCTGGTGCACGATGCATG
1 AGAGTGCATCGATGCATGAAATGCATTCGATG-TTGAAAAATAGCCTGGTGCACGATGCATG
** * *
119918 -GCTTGCATCGATGCATCAAATGCATTCGATGTTG-AAAATATTCC-GAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTTGAAAAATA-GCCTG-GTGCA-CGATGCAT-G
*
119980 AGAGTGCATCGGTGCATGAAATGCATTCGATGTT
1 AGAGTGCATCGATGCATGAAATGCATTCGATGTT
120014 CAATTAAATC
Statistics
Matches: 80, Mismatches: 10, Indels: 10
0.80 0.10 0.10
Matches are distributed among these distances:
59 7 0.09
60 23 0.29
61 20 0.25
62 1 0.01
63 29 0.36
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (61 bp):
AGAGTGCATCGATGCATGAAATGCATTCGATGTTGAAAAATAGCCTGGTGCACGATGCATG
Done.