Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005065.1 Hibiscus syriacus cultivar Beakdansim tig00011370_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: 48158
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Found at i:8182 original size:60 final size:61
Alignment explanation
Indices: 8081--8207 Score: 152
Period size: 60 Copynumber: 2.1 Consensus size: 61
8071 TTAGGTAAAA
* *
8081 TACACAAATGGTCCTCCGACTATAGGAAATGTTTTTGTTGAGTTC-CCCGACTATT-AAAAGT
1 TACA-AAATGATCCTCCGACTATAGGAAATGTTTCTGTTGAG-TCACCCGACTATTAAAAAGT
* * * *
8142 TACAAAATGATCCTCTGACTATATGATATTGTTTCT-TTGAGTCACTCGACTATTAAAAAGT
1 TACAAAATGATCCTCCGACTATAGGA-AATGTTTCTGTTGAGTCACCCGACTATTAAAAAGT
8203 TACAA
1 TACAA
8208 TATAGTCACC
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
59 2 0.04
60 33 0.58
61 22 0.39
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (61 bp):
TACAAAATGATCCTCCGACTATAGGAAATGTTTCTGTTGAGTCACCCGACTATTAAAAAGT
Found at i:10705 original size:30 final size:31
Alignment explanation
Indices: 10640--10728 Score: 103
Period size: 31 Copynumber: 2.9 Consensus size: 31
10630 AAATTGACAT
*
10640 TTTATCTAAAATTTAATGGCTAAATTAATAC
1 TTTATCTAAAATTTAATGGCTAAACTAATAC
* *
10671 TTTATCTAAATTTTAATGG-TCAAACTGATA-
1 TTTATCTAAAATTTAATGGCT-AAACTAATAC
*
10701 TTTATCTAAAATTT-ATAGGTTAAACTAA
1 TTTATCTAAAATTTAAT-GGCTAAACTAA
10729 AAATTAACCC
Statistics
Matches: 50, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
29 2 0.04
30 22 0.44
31 26 0.52
ACGTcount: A:0.40, C:0.09, G:0.08, T:0.43
Consensus pattern (31 bp):
TTTATCTAAAATTTAATGGCTAAACTAATAC
Found at i:11315 original size:22 final size:23
Alignment explanation
Indices: 11282--11329 Score: 64
Period size: 22 Copynumber: 2.1 Consensus size: 23
11272 TTAATTTATA
11282 AAACGTTAAATTATAAAATA-TT
1 AAACGTTAAATTATAAAATAGTT
*
11304 AAACG-TATAATTATAAATTAGTT
1 AAACGTTA-AATTATAAAATAGTT
11327 AAA
1 AAA
11330 AATCTAAATG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 2 0.09
22 16 0.70
23 5 0.22
ACGTcount: A:0.54, C:0.04, G:0.06, T:0.35
Consensus pattern (23 bp):
AAACGTTAAATTATAAAATAGTT
Found at i:16226 original size:60 final size:59
Alignment explanation
Indices: 16126--16258 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 59
16116 TTATGAATAA
* ** * * *
16126 TATAAAATGATCCTTTGATTATAGACATTATTTTTATTGAGTTTCTAGATTATTAAAAGT
1 TATAAAATGATCATTTGATTATAGACATTAGCTTTATTGAG-TCCCAGACTATTAAAAGT
* *
16186 TATAAAATGAT-ATATTGATTATATGACATT-GCTTTGTTGAGTCCCCGACTATTAAAAGT
1 TATAAAATGATCAT-TTGATTATA-GACATTAGCTTTATTGAGTCCCAGACTATTAAAAGT
*
16245 TACAAAATGATCAT
1 TATAAAATGATCAT
16259 CTAACTATTC
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
59 25 0.41
60 30 0.49
61 6 0.10
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (59 bp):
TATAAAATGATCATTTGATTATAGACATTAGCTTTATTGAGTCCCAGACTATTAAAAGT
Found at i:17527 original size:35 final size:35
Alignment explanation
Indices: 17480--17565 Score: 100
Period size: 35 Copynumber: 2.5 Consensus size: 35
17470 AAAACAGTCA
* * *
17480 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
* * * *
17515 TCAATTTTATTCTAAACCCTAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
*
17550 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
17566 ATACTTCAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 43 1.00
ACGTcount: A:0.41, C:0.21, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCCCAAATTCCAAAATAAT
Found at i:17559 original size:21 final size:21
Alignment explanation
Indices: 17534--17576 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
17524 TTCTAAACCC
17534 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
17555 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
17576 T
1 T
17577 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:17671 original size:18 final size:16
Alignment explanation
Indices: 17629--17660 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
17619 CAACGAATAA
*
17629 AAATATATATTTATAT
1 AAATGTATATTTATAT
17645 AAATGTATATTTATAT
1 AAATGTATATTTATAT
17661 TTAGATGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (16 bp):
AAATGTATATTTATAT
Found at i:17733 original size:16 final size:18
Alignment explanation
Indices: 17701--17734 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
17691 TATTAATGTA
17701 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
17719 TGAAT-ATTT-TATTTTT
1 TGAATCATTTATATTTTT
17735 AATAAGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 4 0.25
18 5 0.31
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.65
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:18405 original size:130 final size:130
Alignment explanation
Indices: 18202--18449 Score: 433
Period size: 130 Copynumber: 1.9 Consensus size: 130
18192 AATTTTCTTC
* *
18202 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
18267 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
18332 TAATTAGGTGGTAACATGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
18397 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
18450 TATATAAATA
Statistics
Matches: 111, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 111 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.36
Consensus pattern (130 bp):
TAATTAGGAGGTAACATGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:21218 original size:13 final size:14
Alignment explanation
Indices: 21159--21220 Score: 51
Period size: 13 Copynumber: 4.5 Consensus size: 14
21149 AAATACTAGT
*
21159 ATAATA-ATGATAC
1 ATAATATATCATAC
21172 ATAATATCATACA-AC
1 ATAATAT-AT-CATAC
21187 ATCAA-ATATCATAC
1 AT-AATATATCATAC
21201 ATAATATAT-ATAC
1 ATAATATATCATAC
*
21214 TTAATAT
1 ATAATAT
21221 CACACGACAT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 20 0.49
14 10 0.24
15 8 0.20
16 3 0.07
ACGTcount: A:0.52, C:0.13, G:0.02, T:0.34
Consensus pattern (14 bp):
ATAATATATCATAC
Found at i:21231 original size:42 final size:42
Alignment explanation
Indices: 21143--21254 Score: 124
Period size: 42 Copynumber: 2.7 Consensus size: 42
21133 TATCTCATCT
*
21143 AACATCAAATACTAGT--ATAATA-ATGATACATAATATCATAC
1 AACATCAAATA-TAGTAAATAATATAT-ATACATAATATCACAC
* *
21184 AACATCAAATATCA-TACATAATATATATACTTAATATCACAC
1 AACATCAAATAT-AGTAAATAATATATATACATAATATCACAC
* *
21226 GACATCAAGTATAGTAAATAATATATATA
1 AACATCAAATATAGTAAATAATATATATA
21255 TATATTTGGC
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
40 2 0.03
41 13 0.21
42 44 0.72
43 2 0.03
ACGTcount: A:0.51, C:0.14, G:0.04, T:0.30
Consensus pattern (42 bp):
AACATCAAATATAGTAAATAATATATATACATAATATCACAC
Found at i:22037 original size:16 final size:16
Alignment explanation
Indices: 22018--22048 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
22008 TTTTAAATTT
*
22018 ATTTGATTTTTTCTTA
1 ATTTGATTTTCTCTTA
22034 ATTTGATTTTCTCTT
1 ATTTGATTTTCTCTT
22049 TTAATTTTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.16, C:0.10, G:0.06, T:0.68
Consensus pattern (16 bp):
ATTTGATTTTCTCTTA
Found at i:26395 original size:33 final size:31
Alignment explanation
Indices: 26358--26424 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 31
26348 GAGCGTTGTC
26358 AAAGAGATTTAGTCGTCGTCCATAAAAGGAAAT
1 AAAGAGATTTAGTCGTCGTCCATAAAA--AAAT
*
26391 AAAGAGATTTAGTCGTTGTCCATAAAAAAAT
1 AAAGAGATTTAGTCGTCGTCCATAAAAAAAT
26422 AAA
1 AAA
26425 AATAATGCAT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
31 7 0.21
33 26 0.79
ACGTcount: A:0.46, C:0.10, G:0.18, T:0.25
Consensus pattern (31 bp):
AAAGAGATTTAGTCGTCGTCCATAAAAAAAT
Found at i:28904 original size:2 final size:2
Alignment explanation
Indices: 28897--28924 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28887 TGAAACATGC
28897 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
28925 TCATGGGACT
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:29370 original size:111 final size:112
Alignment explanation
Indices: 29249--29463 Score: 297
Period size: 111 Copynumber: 1.9 Consensus size: 112
29239 ATAAATAACA
** * * * *
29249 AGTTAGTGGTTAGTGGTTAGTTGTTAACAAAGTCCGAATCATAATAATATAGATCATATCCTGGA
1 AGTTAGTGGTTAGCAGTTAGATGTTAACAAAGTCCGAACCATAATAATATAGATCATACCCCGGA
*
29314 TCGAGTCACCACAAGGTCGGTTCGAATAATAACAATAAATTTTTAGC
66 TCGAGTCACCACAAGGTCAGTTCGAATAATAACAATAAATTTTTAGC
* * * *
29361 AGTT-GTGGTTAGCAGTTAGATGTTAACAGAGTCTGGACCATAATAATATGGATCATACCCCGGA
1 AGTTAGTGGTTAGCAGTTAGATGTTAACAAAGTCCGAACCATAATAATATAGATCATACCCCGGA
* * *
29425 TCGGGTCACCATAAGGTCAGTTCGAATAATATCAATAAA
66 TCGAGTCACCACAAGGTCAGTTCGAATAATAACAATAAA
29464 CAGAAAATAG
Statistics
Matches: 89, Mismatches: 14, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
111 85 0.96
112 4 0.04
ACGTcount: A:0.34, C:0.15, G:0.21, T:0.29
Consensus pattern (112 bp):
AGTTAGTGGTTAGCAGTTAGATGTTAACAAAGTCCGAACCATAATAATATAGATCATACCCCGGA
TCGAGTCACCACAAGGTCAGTTCGAATAATAACAATAAATTTTTAGC
Found at i:31649 original size:102 final size:103
Alignment explanation
Indices: 31526--31761 Score: 305
Period size: 102 Copynumber: 2.3 Consensus size: 103
31516 TTTGTATTCT
* * *
31526 AAGGGAAAACTGTCTCAAGCGAGAAAAAATTGATTTTAAGAAAAACAATCTCAAGTGAGATAAAT
1 AAGGGAAAATTGTCTCAAGCGAGAAAAAATTGATTCTAAGAAAAACAATCTCAAGTAAGATAAAT
* *
31591 CTTGTTTTAAGTGAAACAATTCCAAAAGTTGTGCTT-C
66 CTTGTTTTAAGAGAAACAATTCCAAAAGTTGTGCTTAA
** * * *
31628 AAGGGAAAATTGTCTCAAGCGAGATGAAATTGGTTCTAAGAAAAATAATCTCAAGTAAGATCAAT
1 AAGGGAAAATTGTCTCAAGCGAGAAAAAATTGATTCTAAGAAAAACAATCTCAAGTAAGATAAAT
* * * * *
31693 TTTGTTTTGAGAGAAACAATTTCAAAATTTGTGTTTAA
66 CTTGTTTTAAGAGAAACAATTCCAAAAGTTGTGCTTAA
*
31731 AAGGG-AAATTGTCTCAAGTGAGACAAAAATT
1 AAGGGAAAATTGTCTCAAGCGAGA-AAAAATT
31762 ATGAATGAAA
Statistics
Matches: 114, Mismatches: 18, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
102 104 0.91
103 10 0.09
ACGTcount: A:0.42, C:0.11, G:0.19, T:0.29
Consensus pattern (103 bp):
AAGGGAAAATTGTCTCAAGCGAGAAAAAATTGATTCTAAGAAAAACAATCTCAAGTAAGATAAAT
CTTGTTTTAAGAGAAACAATTCCAAAAGTTGTGCTTAA
Found at i:33836 original size:27 final size:24
Alignment explanation
Indices: 33798--33859 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 24
33788 TTTCATTTTC
33798 TTTTTTC-TTTTTTATTTTCTCCTCA
1 TTTTTTCTTTTTTTA-TTTCTCCT-A
*
33823 TTTTTTCTTATTTTTATTTCTTCTA
1 TTTTTTCTT-TTTTTATTTCTCCTA
33848 TCTTTTTCTTTT
1 T-TTTTTCTTTT
33860 CTTGTTTATC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 11 0.33
26 16 0.48
27 6 0.18
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTTCTTTTTTTATTTCTCCTA
Found at i:33879 original size:17 final size:15
Alignment explanation
Indices: 33857--33904 Score: 51
Period size: 17 Copynumber: 2.9 Consensus size: 15
33847 ATCTTTTTCT
33857 TTTCTTGTTTATCATTA
1 TTTCTT-TTT-TCATTA
*
33874 TTTCTTTTTTCATTCT
1 TTTCTTTTTTCATT-A
33890 TTTACTTTTTTCATT
1 TTT-CTTTTTTCATT
33905 CTTTTTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
15 5 0.18
16 6 0.21
17 17 0.61
ACGTcount: A:0.12, C:0.15, G:0.02, T:0.71
Consensus pattern (15 bp):
TTTCTTTTTTCATTA
Found at i:33905 original size:17 final size:17
Alignment explanation
Indices: 33877--33909 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
33867 ATCATTATTT
33877 CTTTTTTCATTCTTTTA
1 CTTTTTTCATTCTTTTA
33894 CTTTTTTCATTCTTTT
1 CTTTTTTCATTCTTTT
33910 TTCATTTCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.18, G:0.00, T:0.73
Consensus pattern (17 bp):
CTTTTTTCATTCTTTTA
Found at i:33906 original size:28 final size:30
Alignment explanation
Indices: 33875--33930 Score: 89
Period size: 28 Copynumber: 1.9 Consensus size: 30
33865 TTATCATTAT
33875 TTCTTTTTTCA-TTCTTTTACT-TTTTTCA
1 TTCTTTTTTCATTTCTTTTACTCTTTTTCA
*
33903 TTCTTTTTTCATTTCTTTTTCTCTTTTT
1 TTCTTTTTTCATTTCTTTTACTCTTTTT
33931 TTTCTCTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 11 0.44
29 9 0.36
30 5 0.20
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (30 bp):
TTCTTTTTTCATTTCTTTTACTCTTTTTCA
Found at i:33918 original size:12 final size:11
Alignment explanation
Indices: 33875--33934 Score: 53
Period size: 11 Copynumber: 5.9 Consensus size: 11
33865 TTATCATTAT
33875 TTCTTTTTTCA
1 TTCTTTTTTCA
33886 TTC--TTTT-A
1 TTCTTTTTTCA
33894 --CTTTTTTCA
1 TTCTTTTTTCA
33903 TTCTTTTTTCA
1 TTCTTTTTTCA
33914 TTTCTTTTTCTC-
1 -TTCTTTTT-TCA
33926 TT-TTTTTTC
1 TTCTTTTTTC
33935 TCTCTTATTT
Statistics
Matches: 42, Mismatches: 0, Indels: 16
0.72 0.00 0.28
Matches are distributed among these distances:
6 1 0.02
8 5 0.12
9 7 0.17
10 5 0.12
11 14 0.33
12 8 0.19
13 2 0.05
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.75
Consensus pattern (11 bp):
TTCTTTTTTCA
Found at i:33961 original size:12 final size:12
Alignment explanation
Indices: 33903--33963 Score: 50
Period size: 12 Copynumber: 4.8 Consensus size: 12
33893 ACTTTTTTCA
* *
33903 TTCTTTTTTCAT
1 TTCTTTTCTCTT
33915 TTCTTTTTCTCTT
1 TTC-TTTTCTCTT
*
33928 TTTTTTCTCTCTTAT
1 TTCTTT-TCTC-T-T
*
33943 TTTTTTTCTCTT
1 TTCTTTTCTCTT
33955 TTCTTTTCT
1 TTCTTTTCT
33964 TCAAGTGTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
12 15 0.37
13 14 0.34
14 5 0.12
15 7 0.17
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.77
Consensus pattern (12 bp):
TTCTTTTCTCTT
Found at i:33961 original size:16 final size:16
Alignment explanation
Indices: 33914--33961 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
33904 TCTTTTTTCA
*
33914 TTTCTTTTTCTCTTTTT
1 TTTCTCTTT-TCTTTTT
* *
33931 TTTCTCTCTTATTTTT
1 TTTCTCTTTTCTTTTT
33947 TTTCTCTTTTCTTTT
1 TTTCTCTTTTCTTTT
33962 CTTCAAGTGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.02, C:0.19, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTCTCTTTTCTTTTT
Found at i:35418 original size:9 final size:9
Alignment explanation
Indices: 35400--35434 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
35390 AAATGAAATA
*
35400 AAAGATTGT
1 AAAGAATGT
35409 AAAGAATGT
1 AAAGAATGT
35418 AAAGAATGAT
1 AAAGAATG-T
35428 AAAGAAT
1 AAAGAAT
35435 ATGAAAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
9 16 0.67
10 8 0.33
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (9 bp):
AAAGAATGT
Found at i:35448 original size:19 final size:19
Alignment explanation
Indices: 35396--35449 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
35386 TCAAAAATGA
*
35396 AATA-AAAGATTG-TAAAG
1 AATATAAAGAATGATAAAG
*
35413 AATGTAAAGAATGATAAAG
1 AATATAAAGAATGATAAAG
*
35432 AATATGAA-AATGTATAAA
1 AATATAAAGAATG-ATAAA
35450 ATGATTGATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
17 3 0.10
18 11 0.37
19 16 0.53
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (19 bp):
AATATAAAGAATGATAAAG
Found at i:39528 original size:28 final size:28
Alignment explanation
Indices: 39475--39528 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
39465 TAAAAGATTA
* *
39475 AAAATTAAAGCAAATAAAATTTAAGGGT
1 AAAATTAAAGCAAATAAAAATAAAGGGT
*
39503 AAAATTAAA-TAAATAAAAAATAAAGG
1 AAAATTAAAGCAAAT-AAAAATAAAGG
39529 AATAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 4 0.18
28 18 0.82
ACGTcount: A:0.65, C:0.02, G:0.11, T:0.22
Consensus pattern (28 bp):
AAAATTAAAGCAAATAAAAATAAAGGGT
Found at i:39978 original size:33 final size:32
Alignment explanation
Indices: 39925--39993 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 32
39915 TATTCGAAAC
*
39925 AAATAAAATAAAAAGCAGTGACCAAAATATAAT
1 AAATAAAATAAAAA-CAGTGACCAAAATAAAAT
39958 AAATAATAATAATAAA-AGTGACCAAAATAAAAT
1 AAATAA-AATAA-AAACAGTGACCAAAATAAAAT
39991 AAA
1 AAA
39994 AGCAAAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
33 25 0.76
34 5 0.15
35 3 0.09
ACGTcount: A:0.67, C:0.07, G:0.07, T:0.19
Consensus pattern (32 bp):
AAATAAAATAAAAACAGTGACCAAAATAAAAT
Found at i:41361 original size:44 final size:44
Alignment explanation
Indices: 41293--41411 Score: 150
Period size: 44 Copynumber: 2.7 Consensus size: 44
41283 TTATATTCAT
* *
41293 GCTATGTAATATTGATCT-CTGTGATTACATGAATATGTTATACAA
1 GCTATGTGATA-TGATCTAC-GTGATTACATGAATATGTGATACAA
*
41338 GCTATGTGATATGATCTACGTGATTACATGAATATGTGATATAA
1 GCTATGTGATATGATCTACGTGATTACATGAATATGTGATACAA
* * * *
41382 ACCATGTGACATGACCTACGTGATTACATG
1 GCTATGTGATATGATCTACGTGATTACATG
41412 TCTATGTGTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
44 55 0.83
45 11 0.17
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.35
Consensus pattern (44 bp):
GCTATGTGATATGATCTACGTGATTACATGAATATGTGATACAA
Found at i:41559 original size:23 final size:23
Alignment explanation
Indices: 41524--41575 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
41514 GAGTCGAGGG
**
41524 TTCTACGCAGTCCTTTGGGACAA
1 TTCTACGCAGTCCTCCGGGACAA
** *
41547 TTCTACGTGGTCCTCCGGGACAT
1 TTCTACGCAGTCCTCCGGGACAA
41570 TTCTAC
1 TTCTAC
41576 ACGATCCTTC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.17, C:0.29, G:0.21, T:0.33
Consensus pattern (23 bp):
TTCTACGCAGTCCTCCGGGACAA
Found at i:41604 original size:23 final size:23
Alignment explanation
Indices: 41578--41624 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
41568 ATTTCTACAC
41578 GATCCTTCGAGACAATACTATGT
1 GATCCTTCGAGACAATACTATGT
* * * *
41601 GATCTTTCGGGACATTTCTATGT
1 GATCCTTCGAGACAATACTATGT
41624 G
1 G
41625 GTGCTTCAGT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.19, G:0.21, T:0.36
Consensus pattern (23 bp):
GATCCTTCGAGACAATACTATGT
Found at i:44611 original size:2 final size:2
Alignment explanation
Indices: 44604--44650 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
44594 AAAGAAGTAA
44604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
44645 AT AT AT
1 AT AT AT
44651 GTAAAGCTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Done.