Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002858.1 Hibiscus syriacus cultivar Beakdansim tig00005893_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: 125628
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:3745 original size:24 final size:24
Alignment explanation
Indices: 3718--3771 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3708 GGTTGGTTCT
* *
3718 TCTTCATCGGCTGGCTGGTGAACC
1 TCTTCATCGGCGGGCTGGTGAACA
* *
3742 TCTTCATTGGCGGGCTGGTGAGCA
1 TCTTCATCGGCGGGCTGGTGAACA
3766 TCTTCA
1 TCTTCA
3772 GATGCTTTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.13, C:0.26, G:0.30, T:0.31
Consensus pattern (24 bp):
TCTTCATCGGCGGGCTGGTGAACA
Found at i:4959 original size:27 final size:26
Alignment explanation
Indices: 4910--4963 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 26
4900 GGGAAGAAGA
4910 GAAGAGATAAAACAAAGTGAAAAAGT
1 GAAGAGATAAAACAAAGTGAAAAAGT
*
4936 GAAGAAGATAAGAACAAAGTAAAAAAGT
1 GAAG-AGATAA-AACAAAGTGAAAAAGT
4964 AGGGGTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.16
27 6 0.24
28 15 0.60
ACGTcount: A:0.63, C:0.04, G:0.22, T:0.11
Consensus pattern (26 bp):
GAAGAGATAAAACAAAGTGAAAAAGT
Found at i:11567 original size:19 final size:19
Alignment explanation
Indices: 11543--11594 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
11533 AATGCATTTT
11543 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
11562 ATGCATCGATGCACATACC
1 ATGCATCGATGCACATACC
11581 ATGCATCGATGCAC
1 ATGCATCGATGCAC
11595 TCAGGTTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
ATGCATCGATGCACATACC
Found at i:11640 original size:65 final size:64
Alignment explanation
Indices: 11561--11704 Score: 184
Period size: 65 Copynumber: 2.2 Consensus size: 64
11551 ATGCACATAC
* * *
11561 CATGCATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATGAAAACATCGAATGCAT
1 CATGCATCGATGCACA-AGCCATGCATCGATACACTCAGGCTTGTT-TG-AAACATCGAATGCAC
11624 TT
63 TT
* * *
11626 GATGCATTGATGCACAAGCCATGCATCGATACACTCGGGCTTGTTTGAAACATCGAATGCACTT
1 CATGCATCGATGCACAAGCCATGCATCGATACACTCAGGCTTGTTTGAAACATCGAATGCACTT
*
11690 CATGCATCGGTGCAC
1 CATGCATCGATGCAC
11705 TCTTAGTGCA
Statistics
Matches: 68, Mismatches: 9, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
64 29 0.43
65 35 0.51
66 4 0.06
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACAAGCCATGCATCGATACACTCAGGCTTGTTTGAAACATCGAATGCACTT
Found at i:13667 original size:21 final size:21
Alignment explanation
Indices: 13643--13682 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13633 AAGAAATTGT
13643 TTTTAAAATAT-AAAAATGATA
1 TTTTAAAAT-TGAAAAATGATA
*
13664 TTTTGAAATTGAAAAATGA
1 TTTTAAAATTGAAAAATGA
13683 AAACAATCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.38
Consensus pattern (21 bp):
TTTTAAAATTGAAAAATGATA
Found at i:17874 original size:12 final size:12
Alignment explanation
Indices: 17857--17886 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17847 TTCTATGATG
17857 AACATTATATCA
1 AACATTATATCA
17869 AACATTATATCA
1 AACATTATATCA
*
17881 AGCATT
1 AACATT
17887 GATTGTTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.17, G:0.03, T:0.33
Consensus pattern (12 bp):
AACATTATATCA
Found at i:19584 original size:2 final size:2
Alignment explanation
Indices: 19577--19638 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
19567 TTAAATCTTA
19577 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
19619 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
19639 GTTTGGTTTG
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20350 original size:64 final size:63
Alignment explanation
Indices: 20262--20420 Score: 207
Period size: 64 Copynumber: 2.5 Consensus size: 63
20252 GAATAAATTG
* *
20262 AACATCGAATGCATTATATACATCGATGCACATA-CCATGCATCGATGCACTCAGG-TTTTTATG
1 AACATCGAATGCATT-TATGCATCGATGCACA-AGCCATGCATCGATGCACTCAGGCTTGTT-TG
20325 AA
63 -A
*
20327 AACATCGAATG-ATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCGGGCTTGTTTGA
1 AACATCGAATGCATTT-ATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTTGTTTGA
*
20390 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCA-TTTATGCATCGATGCAC
20421 TCTTAGTGCA
Statistics
Matches: 85, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
63 14 0.16
64 54 0.64
65 17 0.20
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTTGTTTGA
Found at i:23348 original size:19 final size:19
Alignment explanation
Indices: 23288--23348 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 19
23278 TTATATAAAA
*
23288 TATATTTTTATTATAATTA
1 TATATTTTTATTATAATTT
* *
23307 TAT-TTTTTCATTTGTATTTT
1 TATATTTTT-A-TTATAATTT
*
23327 TATATTTTTGTTATAATTT
1 TATATTTTTATTATAATTT
23346 TAT
1 TAT
23349 TAGAGAGAGT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
18 5 0.15
19 14 0.42
20 9 0.27
21 5 0.15
ACGTcount: A:0.26, C:0.02, G:0.03, T:0.69
Consensus pattern (19 bp):
TATATTTTTATTATAATTT
Found at i:24973 original size:22 final size:22
Alignment explanation
Indices: 24945--25000 Score: 112
Period size: 22 Copynumber: 2.5 Consensus size: 22
24935 GGACTATTAT
24945 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
24967 GTCCCGAAGGACCACTGGATAC
1 GTCCCGAAGGACCACTGGATAC
24989 GTCCCGAAGGAC
1 GTCCCGAAGGAC
25001 TAATATACCC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.27, C:0.32, G:0.29, T:0.12
Consensus pattern (22 bp):
GTCCCGAAGGACCACTGGATAC
Found at i:28993 original size:21 final size:21
Alignment explanation
Indices: 28968--29007 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
28958 AGATAAACGA
28968 AAACAACATG-AAAAAAATCGT
1 AAACAACA-GCAAAAAAATCGT
28989 AAACAACAGCAAAAAAATC
1 AAACAACAGCAAAAAAATC
29008 ATAAGTTACC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.65, C:0.17, G:0.07, T:0.10
Consensus pattern (21 bp):
AAACAACAGCAAAAAAATCGT
Found at i:30208 original size:2 final size:2
Alignment explanation
Indices: 30201--30228 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30191 ATCATATAAG
30201 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
30229 TAATTTTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30411 original size:16 final size:17
Alignment explanation
Indices: 30382--30424 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
30372 TGAGATTTAA
30382 AAAATTACAATAGAA-AT
1 AAAATTA-AATAGAATAT
*
30399 CAAATTAAATAGAATAT
1 AAAATTAAATAGAATAT
30416 AAAATTAAA
1 AAAATTAAA
30425 AGACTAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 7 0.30
17 16 0.70
ACGTcount: A:0.65, C:0.05, G:0.05, T:0.26
Consensus pattern (17 bp):
AAAATTAAATAGAATAT
Found at i:32405 original size:20 final size:20
Alignment explanation
Indices: 32377--32417 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
32367 GGTGCCAAAA
32377 TGAAAGCACATGATGCATGG
1 TGAAAGCACATGATGCATGG
* *
32397 TGAAGGCACATGATGCTTGG
1 TGAAAGCACATGATGCATGG
32417 T
1 T
32418 AGCAAGGATG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (20 bp):
TGAAAGCACATGATGCATGG
Found at i:44788 original size:32 final size:30
Alignment explanation
Indices: 44705--44798 Score: 116
Period size: 30 Copynumber: 3.1 Consensus size: 30
44695 CCGAAGGACC
* *
44705 ACTATCCATATGTTCCAAAGAACATAGGTA
1 ACTATCCATATGTCCCAAAGGACATAGGTA
**
44735 ACTATCCATACATCCCAAAGGACATAGGTA
1 ACTATCCATATGTCCCAAAGGACATAGGTA
* *
44765 ATCCTGTCCATATGTCCCGAAGGACATAGGTA
1 A--CTATCCATATGTCCCAAAGGACATAGGTA
44797 AC
1 AC
44799 CCTCGACTCT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 28 0.52
32 26 0.48
ACGTcount: A:0.36, C:0.24, G:0.16, T:0.23
Consensus pattern (30 bp):
ACTATCCATATGTCCCAAAGGACATAGGTA
Found at i:47070 original size:15 final size:16
Alignment explanation
Indices: 47050--47079 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
47040 ATGCCTACAA
47050 TAAATAAAG-AAAACT
1 TAAATAAAGTAAAACT
47065 TAAATAAAGTAAAAC
1 TAAATAAAGTAAAAC
47080 AGATAATGGG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.20
Consensus pattern (16 bp):
TAAATAAAGTAAAACT
Found at i:53142 original size:10 final size:10
Alignment explanation
Indices: 53098--53144 Score: 76
Period size: 10 Copynumber: 4.7 Consensus size: 10
53088 TGTTTTATTT
*
53098 TTCTCTTTTC
1 TTCTTTTTTC
*
53108 TTCTCTTTTC
1 TTCTTTTTTC
53118 TTCTTTTTTC
1 TTCTTTTTTC
53128 TTCTTTTTTC
1 TTCTTTTTTC
53138 TTCTTTT
1 TTCTTTT
53145 GACACTTCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 36 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTCTTTTTTC
Found at i:59638 original size:53 final size:52
Alignment explanation
Indices: 59581--59681 Score: 125
Period size: 53 Copynumber: 1.9 Consensus size: 52
59571 TTGATTTCTC
* *
59581 TGTG-TTTTTCTTCTT-TCTGTGTATTTTCTGTCTCTCTTTGTCTCTGTCTCTGT
1 TGTGTTTTTTCTTCTTCTCT-TGT-TCTTCTCTCTCTCTTT-TCTCTGTCTCTGT
* *
59634 TGTGTTTTTTTTTCTTCTCTTGTTCTTCTCTCTGTCTTTTCTCTGTCT
1 TGTGTTTTTTCTTCTTCTCTTGTTCTTCTCTCTCTCTTTTCTCTGTCT
59682 TTTTTTTTTC
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
52 9 0.21
53 17 0.40
54 13 0.31
55 3 0.07
ACGTcount: A:0.01, C:0.22, G:0.13, T:0.64
Consensus pattern (52 bp):
TGTGTTTTTTCTTCTTCTCTTGTTCTTCTCTCTCTCTTTTCTCTGTCTCTGT
Found at i:59998 original size:9 final size:10
Alignment explanation
Indices: 59965--60003 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
59955 TGGGCTTGTA
59965 ATTTAATATT
1 ATTTAATATT
59975 ATTTATATATGT
1 ATTTA-ATAT-T
59987 ATTTAATA-T
1 ATTTAATATT
59996 ATTTAATA
1 ATTTAATA
60004 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 5 0.19
11 7 0.26
12 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:60007 original size:3 final size:3
Alignment explanation
Indices: 59999--60096 Score: 169
Period size: 3 Copynumber: 32.7 Consensus size: 3
59989 TTAATATATT
*
59999 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
60047 TAA TAA TAA TAA TAA TAG TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
60095 TA
1 TA
60097 TTTATAATAT
Statistics
Matches: 89, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 89 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:60681 original size:113 final size:113
Alignment explanation
Indices: 60443--60982 Score: 895
Period size: 113 Copynumber: 4.8 Consensus size: 113
60433 GTTAAATAAG
*
60443 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAAC-TTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * * * * *
60507 GAAAAGCTGCTCCATCAAGTGATGGATT-TGAGCAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGAATTCAG-GTAAAAGGTTGAACAAA
* *
60555 TTCTTCTTATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* *
60620 GAAAAGCTGCTCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAA
60668 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
60733 GAAAAGATGATCCATCAAATGATGGATTCAGGTAAAAGGTTGAACAAA
66 GAAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAA
60781 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
* * *
60846 GAAAAGATAATCCATCAATTGATGAATTCAGGTAAAAGGGTTGAACAAG
66 GAAAAGATGATCCATCAAATGATGAATTCAGGTAAAA-GGTTGAACAAA
*
60895 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTTATTATGAACTTTCTCTG
1 TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
*
60960 GAAAAGATAATCCATCAAATGAT
66 GAAAAGATGATCCATCAAATGAT
60983 AGATTTGAAT
Statistics
Matches: 409, Mismatches: 16, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
112 56 0.14
113 256 0.63
114 97 0.24
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (113 bp):
TTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATTATGAACTTTCTCTG
GAAAAGATGATCCATCAAATGATGAATTCAGGTAAAAGGTTGAACAAA
Found at i:62121 original size:83 final size:83
Alignment explanation
Indices: 61788--62119 Score: 610
Period size: 83 Copynumber: 4.0 Consensus size: 83
61778 CTACTATGAG
* *
61788 CAAATTCATCTTCCAAATTCAATGATTGGTTATGCCAAATCAGATCAGATAACTCAAAGAACACT
1 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACT
* *
61853 TCCAGAATATGCTATTAG
66 TCCAGAAGATGCTATTAA
61871 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACT
1 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACT
61936 TCCAGAAGATGCTATTAA
66 TCCAGAAGATGCTATTAA
61954 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACT
1 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACT
62019 TCCAGAAGATGCTATTAA
66 TCCAGAAGATGCTATTAA
* *
62037 TAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGGTAACTCAAAGAACACT
1 CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACT
62102 TCCAGAAGATGCTATTAA
66 TCCAGAAGATGCTATTAA
62120 TACATTACAT
Statistics
Matches: 243, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 243 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.27
Consensus pattern (83 bp):
CAAATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTAA
Found at i:73964 original size:25 final size:23
Alignment explanation
Indices: 73936--73998 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 23
73926 TAAAATGAAA
73936 TATAAATAATATATAAAAAAATAT
1 TATAAATAATATATAAAAAAA-AT
*
73960 GTATATAT-ATATATAAAAAAAAT
1 -TATAAATAATATATAAAAAAAAT
73983 TATAAATTAAATATAT
1 TATAAA-T-AATATAT
73999 GAATTTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
22 5 0.15
23 3 0.09
24 13 0.39
25 12 0.36
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (23 bp):
TATAAATAATATATAAAAAAAAT
Found at i:75900 original size:16 final size:16
Alignment explanation
Indices: 75875--75911 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
75865 GGACGTGGCA
75875 GCGG-TGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
75890 GCGGCTGGAGGCAGAG
1 GCGGCTGGAGGCAGAG
75906 GCGGCT
1 GCGGCT
75912 AGGGATTAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 4 0.19
16 17 0.81
ACGTcount: A:0.16, C:0.19, G:0.57, T:0.08
Consensus pattern (16 bp):
GCGGCTGGAGGCAGAG
Found at i:76030 original size:9 final size:10
Alignment explanation
Indices: 75997--76035 Score: 53
Period size: 9 Copynumber: 3.8 Consensus size: 10
75987 TGGGCTTGTA
75997 ATTTAATATT
1 ATTTAATATT
76007 ATTTATATATGT
1 ATTTA-ATAT-T
76019 ATTTAATA-T
1 ATTTAATATT
76028 ATTTAATA
1 ATTTAATA
76036 ATAATAATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
9 9 0.33
10 5 0.19
11 7 0.26
12 6 0.22
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (10 bp):
ATTTAATATT
Found at i:76039 original size:3 final size:3
Alignment explanation
Indices: 76031--76110 Score: 124
Period size: 3 Copynumber: 26.7 Consensus size: 3
76021 TTAATATATT
* * *
76031 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TTA TAG
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
76079 TAA TAA TAA TAA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
76111 TTTATAATAT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:76606 original size:43 final size:42
Alignment explanation
Indices: 76545--76778 Score: 204
Period size: 43 Copynumber: 5.5 Consensus size: 42
76535 ATAATAAGTA
* *
76545 TTGATATTTAGCGACGTTTGTGTGACAAACGCCGCAATAGATG
1 TTGATATTTAGCGGCGTTTGT-TGACAAACGCCGCAATAGGTG
* * *
76588 TTGATATTTAGCGGCGTTTGTCAT-AAAAACGCCACAATATGTG
1 TTGATATTTAGCGGCGTTTGT--TGACAAACGCCGCAATAGGTG
* * *
76631 TTGATATTTAGTGGCGTTTGTTATAAAAACGCCGCAATAGGTG
1 TTGATATTTAGCGGCGTTTGTT-GACAAACGCCGCAATAGGTG
* ** *
76674 TTAATATTTAGCAACGTTT-TTCAGACAAACGTCGCAATAGGT-
1 TTGATATTTAGCGGCGTTTGTT--GACAAACGCCGCAATAGGTG
* * * * *
76716 TATGATGTTTAGCGGCGTTTTTTTCACAAACGCCGCAGTAGGTA
1 T-TGATATTTAGCGGCG-TTTGTTGACAAACGCCGCAATAGGTG
* *
76760 TTGATGTTTTGCGGCGTTT
1 TTGATATTTAGCGGCGTTT
76779 CTGCTAAAAA
Statistics
Matches: 159, Mismatches: 24, Indels: 17
0.80 0.12 0.09
Matches are distributed among these distances:
41 1 0.01
42 6 0.04
43 145 0.91
44 5 0.03
45 2 0.01
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (42 bp):
TTGATATTTAGCGGCGTTTGTTGACAAACGCCGCAATAGGTG
Found at i:76778 original size:86 final size:85
Alignment explanation
Indices: 76545--76778 Score: 236
Period size: 86 Copynumber: 2.7 Consensus size: 85
76535 ATAATAAGTA
* * * *
76545 TTGATATTTAGCGACGTTTGTGTGACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTGTC
1 TTGATATTTAGCGGCGTTTTTAT-ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTC
* *
76610 ATAAAAACGCCACAATATGTG
65 AGAAAAACGCCACAATAGGTG
* * * ** *
76631 TTGATATTTAGTGGCGTTTGTTATAAAAACGCCGCAATAGGTGTTAATATTTAGCAACGTTTTTC
1 TTGATATTTAGCGGCGTTT-TTATACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTC
* * *
76696 AGACAAACGTCGCAATAGGT-
65 AGAAAAACGCCACAATAGGTG
* * * * * *
76716 TATGATGTTTAGCGGCGTTTTTTTCACAAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTT
1 T-TGATATTTAGCGGCGTTTTTAT-ACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
76779 CTGCTAAAAA
Statistics
Matches: 119, Mismatches: 26, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
85 4 0.03
86 113 0.95
87 2 0.02
ACGTcount: A:0.26, C:0.15, G:0.24, T:0.35
Consensus pattern (85 bp):
TTGATATTTAGCGGCGTTTTTATACAAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCA
GAAAAACGCCACAATAGGTG
Found at i:76778 original size:129 final size:129
Alignment explanation
Indices: 76548--76793 Score: 280
Period size: 129 Copynumber: 1.9 Consensus size: 129
76538 ATAAGTATTG
* **
76548 ATATTTAGCGACGTTTGTGTGACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTGTCATA
1 ATATTTAGCAACGTTTGTCAGACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTGTCATA
* * * * *
76613 AAAACGCCACAATATGTGTTGATATTTAGTGGCGTTTGTTATAAAAACGCCGCAATAGGTGTTA
66 AAAACGCCACAATAGGTATTGATATTTAGCGGCGTTTCTGATAAAAACGCCGCAATAGGTGTTA
* * * * **
76677 ATATTTAGCAACGTTTTTCAGACAAACGTCGCAATAGGT-TATGATGTTTAGCGGCGTTT-TTTT
1 ATATTTAGCAACGTTTGTCAGACAAACGCCGCAATAGATGT-TGATATTTAGCGGCGTTTGTCAT
* * * * * *
76740 CACAAACGCCGCAGTAGGTATTGATGTTTTGCGGCGTTTCTGCTAAAAACGCCG
65 -AAAAACGCCACAATAGGTATTGATATTTAGCGGCGTTTCTGATAAAAACGCCG
76794 GTACAGGTCT
Statistics
Matches: 95, Mismatches: 20, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
128 3 0.03
129 92 0.97
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.33
Consensus pattern (129 bp):
ATATTTAGCAACGTTTGTCAGACAAACGCCGCAATAGATGTTGATATTTAGCGGCGTTTGTCATA
AAAACGCCACAATAGGTATTGATATTTAGCGGCGTTTCTGATAAAAACGCCGCAATAGGTGTTA
Found at i:77204 original size:21 final size:20
Alignment explanation
Indices: 77179--77249 Score: 70
Period size: 21 Copynumber: 3.4 Consensus size: 20
77169 ATTCTTCACA
77179 TCTCTGCTGATATGCTGCTTC
1 TCTCTG-TGATATGCTGCTTC
* **
77200 TCTCTGTGTTGCCGCTGCTTC
1 TCTCTGTGAT-ATGCTGCTTC
* *
77221 TCTCTGTGCTGTCGCTGCTTC
1 TCTCTGTGATAT-GCTGCTTC
77242 TCTCTGTG
1 TCTCTGTG
77250 TTGTCGTTGC
Statistics
Matches: 42, Mismatches: 6, Indels: 4
0.81 0.12 0.08
Matches are distributed among these distances:
20 3 0.07
21 39 0.93
ACGTcount: A:0.03, C:0.31, G:0.23, T:0.44
Consensus pattern (20 bp):
TCTCTGTGATATGCTGCTTC
Found at i:77238 original size:42 final size:42
Alignment explanation
Indices: 77192--77281 Score: 128
Period size: 42 Copynumber: 2.1 Consensus size: 42
77182 CTGCTGATAT
*
77192 GCTGCTTCTCTCTGTGTTGCCGCTGCTTCTCTCTGTGCTGT-C
1 GCTGCTTCTCTCTGTGTTGCCGCTGCTTCTCTCTCTGCT-TCC
* * *
77234 GCTGCTTCTCTCTGTGTTGTCGTTGCTTCTTTCTCTGCTTCC
1 GCTGCTTCTCTCTGTGTTGCCGCTGCTTCTCTCTCTGCTTCC
77276 GCTGCT
1 GCTGCT
77282 GCTTTGGTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
41 1 0.02
42 42 0.98
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (42 bp):
GCTGCTTCTCTCTGTGTTGCCGCTGCTTCTCTCTCTGCTTCC
Found at i:77254 original size:21 final size:21
Alignment explanation
Indices: 77192--77263 Score: 117
Period size: 21 Copynumber: 3.4 Consensus size: 21
77182 CTGCTGATAT
*
77192 GCTGCTTCTCTCTGTGTTGCC
1 GCTGCTTCTCTCTGTGTTGTC
*
77213 GCTGCTTCTCTCTGTGCTGTC
1 GCTGCTTCTCTCTGTGTTGTC
77234 GCTGCTTCTCTCTGTGTTGTC
1 GCTGCTTCTCTCTGTGTTGTC
*
77255 GTTGCTTCT
1 GCTGCTTCT
77264 TTCTCTGCTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.00, C:0.31, G:0.24, T:0.46
Consensus pattern (21 bp):
GCTGCTTCTCTCTGTGTTGTC
Found at i:77281 original size:21 final size:21
Alignment explanation
Indices: 77192--77281 Score: 96
Period size: 21 Copynumber: 4.3 Consensus size: 21
77182 CTGCTGATAT
77192 GCTGCTTCTCTCTGTG-TTGCC
1 GCTGCTTCTCTCTGTGCTT-CC
77213 GCTGCTTCTCTCTGTGCTGT-C
1 GCTGCTTCTCTCTGTGCT-TCC
*
77234 GCTGCTTCTCTCTGTG-TTGTC
1 GCTGCTTCTCTCTGTGCTT-CC
* * *
77255 GTTGCTTCTTTCTCTGCTTCC
1 GCTGCTTCTCTCTGTGCTTCC
77276 GCTGCT
1 GCTGCT
77282 GCTTTGGTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 10
0.80 0.07 0.14
Matches are distributed among these distances:
19 1 0.02
20 1 0.02
21 53 0.90
22 3 0.05
23 1 0.02
ACGTcount: A:0.00, C:0.32, G:0.22, T:0.46
Consensus pattern (21 bp):
GCTGCTTCTCTCTGTGCTTCC
Found at i:77286 original size:21 final size:21
Alignment explanation
Indices: 77257--77317 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
77247 GTGTTGTCGT
*
77257 TGCTTCTTTCTCTGCTTCCGC
1 TGCTGCTTTCTCTGCTTCCGC
* * *
77278 TGCTGCTTTGGT-TGCTTCTGT
1 TGCTGCTTT-CTCTGCTTCCGC
*
77299 TGCTGCTCTCTCTGCTTCC
1 TGCTGCTTTCTCTGCTTCC
77318 CTTGCTTCAT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.00, C:0.33, G:0.20, T:0.48
Consensus pattern (21 bp):
TGCTGCTTTCTCTGCTTCCGC
Found at i:82169 original size:21 final size:21
Alignment explanation
Indices: 82128--82171 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
82118 ATTGGGCTTG
* *
82128 TATATATTTTTTATTATTATT
1 TATATATTATTTAATATTATT
82149 TATATATGTATTTAATA-TATT
1 TATATAT-TATTTAATATTATT
82170 TA
1 TA
82172 ATCATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TATATATTATTTAATATTATT
Found at i:82183 original size:3 final size:3
Alignment explanation
Indices: 82170--82246 Score: 64
Period size: 3 Copynumber: 25.7 Consensus size: 3
82160 TTAATATATT
* * * * * * * *
82170 TAA TCA TAA TAA TAA TAA TAA TAA TTA TTA TTA TTA TTA TTA TAG TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
* *
82218 TAA TAA TTA TTA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
82247 TTTATAATAT
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 66 1.00
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (3 bp):
TAA
Found at i:82820 original size:113 final size:113
Alignment explanation
Indices: 82560--83025 Score: 812
Period size: 113 Copynumber: 4.1 Consensus size: 113
82550 ATCTCCTTCT
* * * *
82560 GTGATAGAATT-ATGTAAAAAGTTGAACAAGTTCTTCTTATTATGAACTTCTTCTTCCTTCTTTA
1 GTGAT-GAATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
82624 GATGAGTTCTTCTCATTATGAAC-TTCTCTGGAAAAGCT-ACTCCATCAA
65 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGA-TCCATCAA
82672 GTGATGAATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
82737 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
66 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
82785 GTGATGAATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
82850 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
66 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
*
82898 GTGATGAATTCAGGTAAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
1 GTGATGAATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
* * *
82963 ATGAGTTCTTCTCATTATGAACCTTCTCTGGAAAAGATAATCCATCAA
66 ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
*
83011 TTGATGAATTCAGGT
1 GTGATGAATTCAGGT
83026 CTTTGCTAAA
Statistics
Matches: 342, Mismatches: 9, Indels: 5
0.96 0.03 0.01
Matches are distributed among these distances:
111 5 0.01
112 77 0.23
113 259 0.76
114 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.38
Consensus pattern (113 bp):
GTGATGAATTCAGGTAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAG
ATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGCTGATCCATCAA
Found at i:83910 original size:83 final size:83
Alignment explanation
Indices: 83807--84401 Score: 942
Period size: 83 Copynumber: 7.1 Consensus size: 83
83797 TTTATTTCTA
*
83807 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
83872 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
83890 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
83955 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* *
83973 TTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
84038 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * * * *
84056 CTATTAAGTCACCTTTATCTT-TACTATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTC
1 CTA-TGAG-CACATTCATCTTCCA-AATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTC
84120 AAAGAACACTTCCAGAAGATG
63 AAAGAACACTTCCAGAAGATG
* * *
84141 CTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
84206 GAACACTTCCAGAAGATG
66 GAACACTTCCAGAAGATG
* * * *
84224 CTATTGAGCCACTTTTATCTT-TACTATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTC
1 CTA-TGAG-CACATTCATCTTCCA-AATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTC
84288 AAAGAACACTTCCAGAAGATG
63 AAAGAACACTTCCAGAAGATG
* * *
84309 CTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
*
84374 GAACACTTCTAGAAGATG
66 GAACACTTCCAGAAGATG
84392 CTATTGAGCA
1 CTA-TGAGCA
84402 TATGGCATTT
Statistics
Matches: 470, Mismatches: 33, Indels: 17
0.90 0.06 0.03
Matches are distributed among these distances:
83 304 0.65
84 24 0.05
85 142 0.30
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (83 bp):
CTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATG
Found at i:84158 original size:168 final size:167
Alignment explanation
Indices: 83807--84401 Score: 1032
Period size: 168 Copynumber: 3.6 Consensus size: 167
83797 TTTATTTCTA
* * *
83807 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
1 CTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
* * *
83872 GAACACTTCCAGAAGATGCTA-TGAGCACATTCATC-TTCCAAATTCAATGATTGGTTCTGTCAA
66 GAACACTTCCAGAAGATGCTATTGAGCACATTTATCTTTAC-TATTCAATGATTGGTTCTGTCAA
83935 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
130 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* * *
83973 TTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
* *
84038 GAACACTTCCAGAAGATGCTATTAAGTCACCTTTATCTTTACTATTCAATGATTGGTTCTGTCAA
66 GAACACTTCCAGAAGATGCTATTGAG-CACATTTATCTTTACTATTCAATGATTGGTTCTGTCAA
84103 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
130 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
84141 CTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
*
84206 GAACACTTCCAGAAGATGCTATTGAGCCACTTTTATCTTTACTATTCAATGATTGGTTCTGTCAA
66 GAACACTTCCAGAAGATGCTATTGAG-CACATTTATCTTTACTATTCAATGATTGGTTCTGTCAA
84271 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
130 ACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
84309 CTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
*
84374 GAACACTTCTAGAAGATGCTATTGAGCA
66 GAACACTTCCAGAAGATGCTATTGAGCA
84402 TATGGCATTT
Statistics
Matches: 411, Mismatches: 15, Indels: 5
0.95 0.03 0.01
Matches are distributed among these distances:
166 83 0.20
167 5 0.01
168 320 0.78
169 3 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (167 bp):
CTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATTGAGCACATTTATCTTTACTATTCAATGATTGGTTCTGTCAAA
CCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:84338 original size:251 final size:249
Alignment explanation
Indices: 83807--84404 Score: 948
Period size: 251 Copynumber: 2.4 Consensus size: 249
83797 TTTATTTCTA
83807 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
* * *
83872 GAACACTTCCAGAAGATGCTATGAGCACATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAAC
66 GAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAAC
* *
83937 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATGAGCACATTCATCTTCCAAATTCAA
131 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTACAAATTCAA
84002 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
196 TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* ** * * *
84056 CTATTAAGTCACCTTTATCTT-TACTATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTC
1 CTA-TGAG-CAAATTCATCTTCCA-AATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTC
84120 AAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCA
63 AAAGAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCA
* * *
84185 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCCACTTTTATCTTTAC-T
128 AACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGAG-CACATTCATC-TTACAA
*
84249 ATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
190 ATTCAATGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
* * *
84309 CTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAACCAGATCAGATAACTCAAA
1 CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
*
84374 GAACACTTCTAGAAGATGCTATTGAGCATAT
66 GAACACTTCCAGAAGATGCTA-TGAGCATAT
84405 GGCATTTGTT
Statistics
Matches: 317, Mismatches: 24, Indels: 13
0.90 0.07 0.04
Matches are distributed among these distances:
249 3 0.01
250 4 0.01
251 220 0.69
252 17 0.05
253 70 0.22
254 3 0.01
ACGTcount: A:0.36, C:0.22, G:0.14, T:0.28
Consensus pattern (249 bp):
CTATGAGCAAATTCATCTTCCAAATTCAATGATTGGTTCTGTCAAACCAGATCAGATAACTCAAA
GAACACTTCCAGAAGATGCTATGAGCATATTCATCTTCCAAATTCAATGATTAGTTCTGCCAAAC
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAGCACATTCATCTTACAAATTCAA
TGATTGGTTCTGCCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATG
Found at i:98401 original size:21 final size:21
Alignment explanation
Indices: 98360--98403 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
98350 ATTGGGCTTG
* *
98360 TATATATTTTTTATTATTATT
1 TATATATTATTTAATATTATT
98381 TATATATGTATTTAATA-TATT
1 TATATAT-TATTTAATATTATT
98402 TA
1 TA
98404 ATAATAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (21 bp):
TATATATTATTTAATATTATT
Found at i:98408 original size:12 final size:10
Alignment explanation
Indices: 98392--98463 Score: 68
Period size: 9 Copynumber: 7.9 Consensus size: 10
98382 ATATATGTAT
*
98392 TTAAT-ATAT
1 TTAATAATAA
98401 TTAATAATAA
1 TTAATAATAA
98411 -TAATAATAA
1 TTAATAATAA
*
98420 -TGATAATAA
1 TTAATAATAA
98429 -TAATAATAA
1 TTAATAATAA
98438 -TAATAATAA
1 TTAATAATAA
98447 -TAATAAT-A
1 TTAATAATAA
*
98455 TTTATAATA
1 TTAATAATA
98464 TGGGTAAAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
8 1 0.02
9 52 0.93
10 3 0.05
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.40
Consensus pattern (10 bp):
TTAATAATAA
Found at i:98410 original size:3 final size:3
Alignment explanation
Indices: 98402--98454 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
98392 TTAATATATT
*
98402 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
98450 TAA TA
1 TAA TA
98455 TTTATAATAT
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:99153 original size:13 final size:13
Alignment explanation
Indices: 99135--99160 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
99125 ATGATTGAAA
99135 AACAATGTAACTT
1 AACAATGTAACTT
99148 AACAATGTAACTT
1 AACAATGTAACTT
99161 GGCTCAACTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
AACAATGTAACTT
Found at i:99873 original size:41 final size:41
Alignment explanation
Indices: 99828--100213 Score: 384
Period size: 41 Copynumber: 9.4 Consensus size: 41
99818 ATATATTATA
* * * *
99828 TCTATTGCGGCGTTTATCTAAAAATGCCACTAAAGTACGAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* * *
99869 TCTATAGCGGCATTTGTATAAAAGCGCCACTAAAGTATGAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* * ** * *
99910 TCTATAGCGGCGTTTATATAAAAATGCTGCCAAAGTACGTG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* *
99951 TCTTTAGCGGCGTTT-TCATTCAAAACGCCACTAAAGTACGAG
1 TCTATAGCGGCGTTTGT-A-TAAAAACGCCACTAAAGTACGAG
* * * * *
99993 TTTATAGCGACGTTTAG-ATTCAAAATGCCACTAAAGTATGAG
1 TCTATAGCGGCGTTT-GTA-TAAAAACGCCACTAAAGTACGAG
* * * *
100035 TATATAGCGGTGTTTGTATAGAAACGCCACTAAAGTACTAG
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* * *
100076 TATATAGCGGCGTTTGTATAAAAACGCCACTAACGTACGATT
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGA-G
* * * *
100118 TTTATAGTGGCGTTTGTATAAAAATGCCACTAAAGTACGAT
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
* *
100159 TCTATAGAGGCGTTTGTAT-AAAACACCACTAAAGTACGTA-
1 TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACG-AG
*
100199 CCTATAGCGGCGTTT
1 TCTATAGCGGCGTTT
100214 ATTGGAAAAC
Statistics
Matches: 287, Mismatches: 51, Indels: 15
0.81 0.14 0.04
Matches are distributed among these distances:
40 31 0.11
41 155 0.54
42 101 0.35
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.30
Consensus pattern (41 bp):
TCTATAGCGGCGTTTGTATAAAAACGCCACTAAAGTACGAG
Found at i:100008 original size:83 final size:81
Alignment explanation
Indices: 99834--100213 Score: 381
Period size: 83 Copynumber: 4.6 Consensus size: 81
99824 TATATCTATT
* *
99834 GCGGCGTTTATCTAAAAATGCCACTAAAGTACGAGTCTATAGCGGCATTTGTATAAAAGCGCCAC
1 GCGGCGTTTATATAAAAATGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAA-CGCCAC
* *
99899 TAAAGTATGAGTCTATA
65 TAAAGTACGAGTATATA
** * * *
99916 GCGGCGTTTATATAAAAATGCTGCCAAAGTACGTGTCTTTAGCGGCGTTT-TCATTCAAAACGCC
1 GCGGCGTTTATATAAAAATGCCACTAAAGTACGAGTCTATAGCGGCGTTTGT-A-T-AAAACGCC
*
99980 ACTAAAGTACGAGTTTATA
63 ACTAAAGTACGAGTATATA
* * * * * *
99999 GCGACGTTTAGATTCAAAATGCCACTAAAGTATGAGTATATAGCGGTGTTTGTATAGAAACGCCA
1 GCGGCGTTTATA-TAAAAATGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATA-AAACGCCA
*
100064 CTAAAGTACTAGTATATA
64 CTAAAGTACGAGTATATA
* * * * * * *
100082 GCGGCGTTTGTATAAAAACGCCACTAACGTACGATTTTTATAGTGGCGTTTGTATAAAAATGCCA
1 GCGGCGTTTATATAAAAATGCCACTAAAGTACGA-GTCTATAGCGGCGTTTGTAT-AAAACGCCA
* *
100147 CTAAAGTACGATTCTATA
64 CTAAAGTACGAGTATATA
* * *
100165 GAGGCGTTTGTATAAAACA--CCACTAAAGTACGTA-CCTATAGCGGCGTTT
1 GCGGCGTTTATATAAAA-ATGCCACTAAAGTACG-AGTCTATAGCGGCGTTT
100214 ATTGGAAAAC
Statistics
Matches: 246, Mismatches: 42, Indels: 21
0.80 0.14 0.07
Matches are distributed among these distances:
81 13 0.05
82 75 0.30
83 121 0.49
84 36 0.15
85 1 0.00
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (81 bp):
GCGGCGTTTATATAAAAATGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAACGCCACT
AAAGTACGAGTATATA
Found at i:101714 original size:41 final size:41
Alignment explanation
Indices: 101607--101716 Score: 134
Period size: 41 Copynumber: 2.7 Consensus size: 41
101597 TTTATACCCA
* *
101607 AAAAATACCACTATTGATTAAAACTATTGCGGCATTTTTCT
1 AAAAATGCCACTATTGATTAACACTATTGCGGCATTTTTCT
*
101648 AAAAACGCCACTATTGATTAACACTATTGC-G-ATGTTTATCT
1 AAAAATGCCACTATTGATTAACACTATTGCGGCAT-TTT-TCT
* * *
101689 AGAAATGCCACTATTTATTATCACTATT
1 AAAAATGCCACTATTGATTAACACTATT
101717 CTGACGTTTT
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
39 2 0.03
40 4 0.07
41 54 0.90
ACGTcount: A:0.35, C:0.18, G:0.10, T:0.36
Consensus pattern (41 bp):
AAAAATGCCACTATTGATTAACACTATTGCGGCATTTTTCT
Found at i:101777 original size:42 final size:41
Alignment explanation
Indices: 101731--101925 Score: 127
Period size: 41 Copynumber: 4.7 Consensus size: 41
101721 CGTTTTAAGA
* * *
101731 ATAAATGCCACTATATGTGTAATCTATTGTGGCGTTTGTGGT
1 ATAAATGCCGCTATATGT-TAATCTATTGCGGCATTTGTGGT
** *
101773 ATAAACACCGCTA-AT-TTACCGATTTATTGCGGCATTT-TGGCT
1 ATAAATGCCGCTATATGTTA---ATCTATTGCGGCATTTGTGG-T
* *
101815 A-AAATGCCACTATATGTTAATCTATTACGGCATTTGTGGT
1 ATAAATGCCGCTATATGTTAATCTATTGCGGCATTTGTGGT
* * *
101855 ATAAACGCCGCTA-AT-TTACCACTCTATTGTGGCGTTTGT--T
1 ATAAATGCCGCTATATGTTA--A-TCTATTGCGGCATTTGTGGT
* *
101895 AAAAAATGCCGCTATATGTCAAATCTATTGC
1 -ATAAATGCCGCTATATGT-TAATCTATTGC
101926 AGCGTTTTTA
Statistics
Matches: 118, Mismatches: 20, Indels: 31
0.70 0.12 0.18
Matches are distributed among these distances:
39 5 0.04
40 20 0.17
41 44 0.37
42 44 0.37
43 4 0.03
44 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (41 bp):
ATAAATGCCGCTATATGTTAATCTATTGCGGCATTTGTGGT
Found at i:101901 original size:82 final size:83
Alignment explanation
Indices: 101733--101923 Score: 228
Period size: 82 Copynumber: 2.3 Consensus size: 83
101723 TTTTAAGAAT
* ** * *
101733 AAATGCCACTATATGTGTAATCTATTGTGGCGTTTGTGGTATAAACACCGCTAATTTACCGATTT
1 AAATGCCACTATATGTCTAATCTATTACGGCATTTGTGGTATAAACACCGCTAATTTACCGATCT
*
101798 ATTGCGGCATTTTGGCTA
66 ATTGCGGCAGTTTGGCTA
*
101816 AAATGCCACTATATGT-TAATCTATTACGGCATTTGTGGTATAAACGCCGCTAATTTACC-ACTC
1 AAATGCCACTATATGTCTAATCTATTACGGCATTTGTGGTATAAACACCGCTAATTTACCGA-TC
* *
101879 TATTGTGGC-GTTT-GTTAAA
65 TATTGCGGCAGTTTGGCT--A
* *
101898 AAATGCCGCTATATGTCAAATCTATT
1 AAATGCCACTATATGTCTAATCTATT
101924 GCAGCGTTTT
Statistics
Matches: 94, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
80 2 0.02
81 4 0.04
82 64 0.68
83 24 0.26
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (83 bp):
AAATGCCACTATATGTCTAATCTATTACGGCATTTGTGGTATAAACACCGCTAATTTACCGATCT
ATTGCGGCAGTTTGGCTA
Found at i:103767 original size:11 final size:11
Alignment explanation
Indices: 103753--103777 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
103743 ATTAACATAC
103753 TTTATTTTATA
1 TTTATTTTATA
103764 TTTATTTTATA
1 TTTATTTTATA
103775 TTT
1 TTT
103778 CATTATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTATTTTATA
Found at i:119191 original size:20 final size:20
Alignment explanation
Indices: 119153--119191 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
119143 GTTGAAATTA
*
119153 AATGTTAGAATGATGATTTT
1 AATGTTAGAATGATAATTTT
*
119173 AATGTTAGAATGTTAATTT
1 AATGTTAGAATGATAATTT
119192 GGATTGATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.18, T:0.46
Consensus pattern (20 bp):
AATGTTAGAATGATAATTTT
Found at i:120849 original size:2 final size:2
Alignment explanation
Indices: 120842--120906 Score: 116
Period size: 2 Copynumber: 33.5 Consensus size: 2
120832 ATAGTTTTTA
120842 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
120884 AT AT AT AT AT -T AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
120907 AATAGTAGTA
Statistics
Matches: 61, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
1 2 0.03
2 59 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:124508 original size:3 final size:3
Alignment explanation
Indices: 124500--124559 Score: 88
Period size: 3 Copynumber: 20.7 Consensus size: 3
124490 ATAAAATATT
* *
124500 TAA TAA TAA T-A TAA TAA TAA TTA TAA TTA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
124547 TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TA
124560 TAAAAATATT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
2 4 0.08
3 47 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:124515 original size:18 final size:17
Alignment explanation
Indices: 124500--124567 Score: 88
Period size: 15 Copynumber: 4.1 Consensus size: 17
124490 ATAAAATATT
124500 TAATAATAATATAATAA
1 TAATAATAATATAATAA
*
124517 TAATTATAAT-T-ATAA
1 TAATAATAATATAATAA
124532 TAATAATAATAATAATAA
1 TAATAATAAT-ATAATAA
*
124550 TAATAA-AATATAAAAA
1 TAATAATAATATAATAA
124566 TA
1 TA
124568 TTCAAATGAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
15 13 0.29
16 9 0.20
17 13 0.29
18 10 0.22
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATAATAATATAATAA
Found at i:124609 original size:2 final size:2
Alignment explanation
Indices: 124602--124643 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
124592 TTAGTTTTTA
124602 AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
124643 A
1 A
124644 ATAGGAGTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:124834 original size:23 final size:22
Alignment explanation
Indices: 124807--124850 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
124797 ACTTTTTATG
124807 TTTACGCGATTAACTAGTTTTGT
1 TTTACGCG-TTAACTAGTTTTGT
124830 TTTACGCGTTAACTAGTTTTG
1 TTTACGCGTTAACTAGTTTTG
124851 GTGAAAAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.20, C:0.14, G:0.18, T:0.48
Consensus pattern (22 bp):
TTTACGCGTTAACTAGTTTTGT
Done.