Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007624.1 Hibiscus syriacus cultivar Beakdansim tig00023110_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: 55001
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Found at i:826 original size:23 final size:23
Alignment explanation
Indices: 783--825 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
773 AAAATTAAAT
783 AATTTAATAATAATAAGTTTTGA
1 AATTTAATAATAATAAGTTTTGA
806 AATTT-ATGAATAAT-AGTTTT
1 AATTTAAT-AATAATAAGTTTT
826 TATTGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (23 bp):
AATTTAATAATAATAAGTTTTGA
Found at i:951 original size:11 final size:11
Alignment explanation
Indices: 935--964 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
925 ATATTTAATA
935 ATTAAAATTTT
1 ATTAAAATTTT
946 ATTAAAATTTT
1 ATTAAAATTTT
*
957 AATAAAAT
1 ATTAAAAT
965 GTATAATAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTAAAATTTT
Found at i:4030 original size:18 final size:18
Alignment explanation
Indices: 4009--4061 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
3999 TTTTATTGAA
4009 AAATCATTAT-ATATTATT
1 AAATCATTATAATATTA-T
* **
4027 AAATAAAAATAATATTAT
1 AAATCATTATAATATTAT
*
4045 ATATCATTATAATATTA
1 AAATCATTATAATATTA
4062 AAGAATATAA
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
18 21 0.78
19 6 0.22
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATCATTATAATATTAT
Found at i:4127 original size:11 final size:11
Alignment explanation
Indices: 4111--4140 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
4101 TAATTTAATA
4111 ATTAAAATTTT
1 ATTAAAATTTT
4122 ATTAAAATTTT
1 ATTAAAATTTT
*
4133 AATAAAAT
1 ATTAAAAT
4141 AGTATAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATTAAAATTTT
Found at i:5765 original size:2 final size:2
Alignment explanation
Indices: 5760--5801 Score: 68
Period size: 2 Copynumber: 21.5 Consensus size: 2
5750 AAAAATATCG
*
5760 TA TA TA TA TA TA TA TA TA T- TA TA TA AA 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
5801 T
1 T
5802 CCAAGAAATA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5776 original size:19 final size:19
Alignment explanation
Indices: 5754--5801 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
5744 TTATAAAAAA
* *
5754 ATATCGTATATATATATAT
1 ATATAGTATATAAATATAT
*
5773 ATATATTATATAAATATAT
1 ATATAGTATATAAATATAT
5792 ATATA-TATAT
1 ATATAGTATAT
5802 CCAAGAAATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
18 5 0.19
19 21 0.81
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
ATATAGTATATAAATATAT
Found at i:5778 original size:21 final size:21
Alignment explanation
Indices: 5754--5799 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
5744 TTATAAAAAA
* *
5754 ATATCGTATATATATATATAT
1 ATATCATATAAATATATATAT
*
5775 ATATTATATAAATATATATAT
1 ATATCATATAAATATATATAT
5796 ATAT
1 ATAT
5800 ATCCAAGAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (21 bp):
ATATCATATAAATATATATAT
Found at i:5810 original size:23 final size:23
Alignment explanation
Indices: 5763--5813 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 23
5753 AATATCGTAT
* *
5763 ATATATATATATATATTATATAA
1 ATATATATATATATATCATAGAA
5786 ATATATATATATATATCCA-AGAA
1 ATATATATATATATAT-CATAGAA
5809 ATATA
1 ATATA
5814 AAATATTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 24 0.96
24 1 0.04
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (23 bp):
ATATATATATATATATCATAGAA
Found at i:7567 original size:2 final size:2
Alignment explanation
Indices: 7560--7618 Score: 111
Period size: 2 Copynumber: 30.0 Consensus size: 2
7550 TTAATTCTTG
7560 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
7601 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
7619 TTTTTTTTTA
Statistics
Matches: 56, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 55 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:10773 original size:2 final size:2
Alignment explanation
Indices: 10766--10803 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
10756 TTAATTCTTG
10766 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
10804 TATTTTTTCT
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:19998 original size:24 final size:24
Alignment explanation
Indices: 19966--20097 Score: 149
Period size: 24 Copynumber: 5.5 Consensus size: 24
19956 TATATCAAAA
* * *
19966 ATCAAATCATAATTCATGTCAAGT
1 ATCATATCAGAATCCATGTCAAGT
* * *
19990 TTCATATCAAAATCCAGGTCAAGT
1 ATCATATCAGAATCCATGTCAAGT
* *
20014 ATCATATCAGAATCCAAGTTAAGT
1 ATCATATCAGAATCCATGTCAAGT
* *
20038 ATCAGATCAGAATCCATATC-AGAT
1 ATCATATCAGAATCCATGTCAAG-T
20062 ATCATATCAGAATCCATGTCAAGT
1 ATCATATCAGAATCCATGTCAAGT
*
20086 ATCAGATCAGAA
1 ATCATATCAGAA
20098 ATCAAATCGA
Statistics
Matches: 90, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
23 2 0.02
24 86 0.96
25 2 0.02
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (24 bp):
ATCATATCAGAATCCATGTCAAGT
Found at i:20060 original size:12 final size:12
Alignment explanation
Indices: 20043--20078 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
20033 TAAGTATCAG
20043 ATCAGAATCCAT
1 ATCAGAATCCAT
20055 ATCAGATAT-CAT
1 ATCAGA-ATCCAT
20067 ATCAGAATCCAT
1 ATCAGAATCCAT
20079 GTCAAGTATC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
11 2 0.09
12 18 0.82
13 2 0.09
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (12 bp):
ATCAGAATCCAT
Found at i:29464 original size:2 final size:2
Alignment explanation
Indices: 29457--29496 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
29447 TTTATTCTTG
29457 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
29497 TATTTTTTCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33973 original size:23 final size:22
Alignment explanation
Indices: 33929--33970 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
33919 ATAATCCTAT
33929 TATTTCAAAATATATTAATTTA
1 TATTTCAAAATATATTAATTTA
33951 TATTT-AAAATAT-TT-ATTTA
1 TATTTCAAAATATATTAATTTA
33970 T
1 T
33971 TTAGAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 7 0.35
22 5 0.25
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
TATTTCAAAATATATTAATTTA
Found at i:34618 original size:13 final size:13
Alignment explanation
Indices: 34600--34624 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
34590 AAATTATAAT
34600 AAAACTGAATTAG
1 AAAACTGAATTAG
34613 AAAACTGAATTA
1 AAAACTGAATTA
34625 CAAGGCTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
AAAACTGAATTAG
Found at i:35662 original size:3 final size:3
Alignment explanation
Indices: 35642--35700 Score: 61
Period size: 3 Copynumber: 20.3 Consensus size: 3
35632 TAATTTATTT
* * *
35642 ATA ATA TATA ACA ATA ATA ATA ATA ATA AT- ATA ATA ATA ACA ATT
1 ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
35687 A-A ATA ATA A-A ATA A
1 ATA ATA ATA ATA ATA A
35701 AAGTAAACTG
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.11
3 38 0.83
4 3 0.07
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:35677 original size:14 final size:14
Alignment explanation
Indices: 35641--35699 Score: 68
Period size: 14 Copynumber: 4.1 Consensus size: 14
35631 TTAATTTATT
35641 TATAATATATAACAA
1 TATAATA-ATAACAA
*
35656 TAATAATAATAATAA
1 T-ATAATAATAACAA
35671 TATAATAATAACAA
1 TATAATAATAACAA
35685 T-TAAATAATAA-AA
1 TAT-AATAATAACAA
35698 TA
1 TA
35700 AAAGTAAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
13 4 0.10
14 21 0.54
15 8 0.21
16 6 0.15
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (14 bp):
TATAATAATAACAA
Found at i:35677 original size:17 final size:17
Alignment explanation
Indices: 35654--35700 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
35644 AATATATAAC
35654 AATAATAATAATAA-TA
1 AATAATAATAATAATTA
*
35670 ATATAATAATAACAATTA
1 A-ATAATAATAATAATTA
35688 AATAATAA-AATAA
1 AATAATAATAATAA
35701 AAGTAAACTG
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
16 5 0.19
17 19 0.70
18 3 0.11
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AATAATAATAATAATTA
Found at i:35691 original size:25 final size:23
Alignment explanation
Indices: 35642--35700 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
35632 TAATTTATTT
*
35642 ATAAT-ATATAACAATAATAATA
1 ATAATAATATAACAATAACAATA
*
35664 ATAATAATATAATAATAACAATTAA
1 ATAATAATATAACAATAACAA-T-A
*
35689 ATAATAAAATAA
1 ATAATAATATAA
35701 AAGTAAACTG
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.16
23 13 0.42
24 1 0.03
25 12 0.39
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (23 bp):
ATAATAATATAACAATAACAATA
Found at i:35978 original size:76 final size:76
Alignment explanation
Indices: 35827--36392 Score: 958
Period size: 76 Copynumber: 7.5 Consensus size: 76
35817 GATGAAAATG
* * * * *
35827 TTTGAAAACATCATGCACTGAAGGGCTTACAGATGACCCGAAGGTTTTTGAAAACATCAAAAAGC
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGG-CTTTGAAAACATCAAAAAGC
35892 TCCCGAAGGCTT
65 TCCCGAAGGCTT
35904 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
35969 CCTGAAGGCTT
66 CCCGAAGGCTT
*
35980 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGTT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
36045 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
36056 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
36120 CCCGAAGGCTT
66 CCCGAAGGCTT
* *
36131 TTTGGAAACATTATGCACTGTAGGACTTACAGATGACCCGAAGGC-TTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
*
36195 CCCAAAGGCTT
66 CCCGAAGGCTT
*
36206 TTTGGAAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
36271 CCCGAAGGCTTT
66 CCCGAAGGC-TT
*
36283 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGTTTTGAAAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
36347 CCCGAAGGCTT
66 CCCGAAGGCTT
*
36358 TTTGGAAACATCATGCACTGCAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGTAGGACTTACAGATG
36393 TGGGAAATAG
Statistics
Matches: 466, Mismatches: 21, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
75 179 0.38
76 190 0.41
77 97 0.21
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGTAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:37261 original size:22 final size:22
Alignment explanation
Indices: 37236--37290 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
37226 CATAAAGCTT
* *
37236 TCATCTTTGAAAAGAGAATGTA
1 TCATCTTTGAAAAGAAAATCTA
* *
37258 TCATATTTAAAAAGAAAATCTA
1 TCATCTTTGAAAAGAAAATCTA
37280 TCATCTTTGAA
1 TCATCTTTGAA
37291 GAGTGTAGAT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.11, T:0.35
Consensus pattern (22 bp):
TCATCTTTGAAAAGAAAATCTA
Found at i:39990 original size:114 final size:114
Alignment explanation
Indices: 39823--40042 Score: 377
Period size: 114 Copynumber: 1.9 Consensus size: 114
39813 GATCATGCAG
* * * *
39823 TTCATCTTTCAATTCCAATGATTGGTTTTGGGGTTCCTACCGAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
39888 ACACTTCCAGAAGATTCTATTCGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTATGAGCAAA
*
39937 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCAAATCAGATAACTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
*
40002 ACACTTCCAGAAGATACTATTGGGTCTCCTTATTTCTACTA
66 ACACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTA
40043 CGAGAACGTG
Statistics
Matches: 99, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 99 1.00
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAAATCAGATAACTCAAAGA
ACACTTCCAGAAGATACTATTCGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:44222 original size:14 final size:15
Alignment explanation
Indices: 44205--44237 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
44195 TAAAAGTATG
44205 AATGCAAA-ATGAAA
1 AATGCAAAGATGAAA
*
44219 AATGCAAAGATGCAA
1 AATGCAAAGATGAAA
44234 AATG
1 AATG
44238 AAATGCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.58, C:0.09, G:0.18, T:0.15
Consensus pattern (15 bp):
AATGCAAAGATGAAA
Found at i:46626 original size:21 final size:20
Alignment explanation
Indices: 46600--46641 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
46590 TATGAAATCA
46600 TAAAAATTGAAAGAAAAT-AAT
1 TAAAAATT-AAA-AAAATGAAT
46621 TAAAAATTAAAAAAATGAAT
1 TAAAAATTAAAAAAATGAAT
46641 T
1 T
46642 TTTAATTTCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 7 0.35
21 8 0.40
ACGTcount: A:0.67, C:0.00, G:0.07, T:0.26
Consensus pattern (20 bp):
TAAAAATTAAAAAAATGAAT
Found at i:47097 original size:31 final size:32
Alignment explanation
Indices: 47036--47100 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 32
47026 AAATTTAAAA
**
47036 TTCAAAGATATATTTAATTATAATCCTATTAT
1 TTCAAAGATATATTTAATTATAATAATATTAT
*
47068 TTCAAA-ATATATTTTATATATAA-AATATTAT
1 TTCAAAGATATATTTAAT-TATAATAATATTAT
47099 TT
1 TT
47101 ATTTAGAAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
31 18 0.62
32 11 0.38
ACGTcount: A:0.43, C:0.06, G:0.02, T:0.49
Consensus pattern (32 bp):
TTCAAAGATATATTTAATTATAATAATATTAT
Found at i:47197 original size:30 final size:29
Alignment explanation
Indices: 47162--47224 Score: 76
Period size: 29 Copynumber: 2.1 Consensus size: 29
47152 TTCGATATTA
*
47162 AAAAATAAATAAATAA-TTAAACAT-TTTTAT
1 AAAAAT-AAT-AATAATTTAAA-ATAATTTAT
47192 AAAAATAATAATAATTTAAAATAATTTAT
1 AAAAATAATAATAATTTAAAATAATTTAT
47221 AAAA
1 AAAA
47225 TAGGATATTA
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
28 7 0.23
29 17 0.57
30 6 0.20
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (29 bp):
AAAAATAATAATAATTTAAAATAATTTAT
Found at i:47750 original size:13 final size:13
Alignment explanation
Indices: 47732--47756 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
47722 TAAATTATAT
47732 AAAACTGAATTAG
1 AAAACTGAATTAG
47745 AAAACTGAATTA
1 AAAACTGAATTA
47757 CAAGGCTCAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.12, T:0.24
Consensus pattern (13 bp):
AAAACTGAATTAG
Found at i:48767 original size:3 final size:3
Alignment explanation
Indices: 48761--48809 Score: 55
Period size: 3 Copynumber: 16.0 Consensus size: 3
48751 AATTTATTAT
* *
48761 TAA TAA TATA TAA CAA TAA TAA TAA T-A TTA TAA TAA TAA TAAA TAA
1 TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA
48807 TAA
1 TAA
48810 ATAAAAGTAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
2 2 0.05
3 32 0.80
4 6 0.15
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:48795 original size:17 final size:17
Alignment explanation
Indices: 48761--48806 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
48751 AATTTATTAT
48761 TAATAAT-ATATAACAA
1 TAATAATAATATAACAA
* *
48777 TAATAATAATATTATAA
1 TAATAATAATATAACAA
48794 TAATAATAA-ATAA
1 TAATAATAATATAA
48807 TAAATAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 10 0.38
17 16 0.62
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (17 bp):
TAATAATAATATAACAA
Found at i:48812 original size:17 final size:17
Alignment explanation
Indices: 48761--48813 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 17
48751 AATTTATTAT
* *
48761 TAATAATATATAA-CAA
1 TAATAATAAATAATAAA
*
48777 TAATAAT-AATATTATAA
1 TAATAATAAATAATA-AA
48794 TAATAATAAATAATAAA
1 TAATAATAAATAATAAA
48811 TAA
1 TAA
48814 AAGTAAACTG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.10
16 7 0.23
17 14 0.47
18 6 0.20
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (17 bp):
TAATAATAAATAATAAA
Found at i:48813 original size:14 final size:13
Alignment explanation
Indices: 48762--48809 Score: 53
Period size: 13 Copynumber: 3.6 Consensus size: 13
48752 ATTTATTATT
*
48762 AATAATATATAA-C
1 AATAATA-ATAATA
48775 AATAATAATAATA
1 AATAATAATAATA
*
48788 TTATAATAATAATA
1 -AATAATAATAATA
48802 AATAATAA
1 AATAATAA
48810 ATAAAAGTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
12 4 0.13
13 14 0.47
14 12 0.40
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (13 bp):
AATAATAATAATA
Found at i:51138 original size:64 final size:65
Alignment explanation
Indices: 51067--51215 Score: 167
Period size: 65 Copynumber: 2.3 Consensus size: 65
51057 CTAGGGGTGC
* * *
51067 ATCGGTACACTAATTACATTCGATGTTTC-AAAGAGCCATGAGTGCATCGATGCATGG-TATGTG
1 ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCT-TGTG
51130 A
65 A
** * * ** * *
51131 ATCGGTACACAAAATGTATTTGATGTTTCAAAATATTCAAGAGTGCATCGATGCTTGGCTTGTGC
1 ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTTGTGA
*
51196 ATCGGTACACAAAATGCATT
1 ATCGGTACACAAAATACATT
51216 AGATATGGGT
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
64 24 0.34
65 46 0.65
66 1 0.01
ACGTcount: A:0.31, C:0.17, G:0.21, T:0.31
Consensus pattern (65 bp):
ATCGGTACACAAAATACATTCGATGTTTCAAAAGAGCCAAGAGTGCATCGATGCATGGCTTGTGA
Found at i:51577 original size:12 final size:13
Alignment explanation
Indices: 51551--51585 Score: 54
Period size: 13 Copynumber: 2.7 Consensus size: 13
51541 TAAGATTTTC
51551 TTTGAAAATCAAT
1 TTTGAAAATCAAT
51564 TTTGAAAA-CAAT
1 TTTGAAAATCAAT
51576 TTTGCAAAAT
1 TTTG-AAAAT
51586 TACTCCCCCT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (13 bp):
TTTGAAAATCAAT
Done.