Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001173.1 Hibiscus syriacus cultivar Beakdansim tig00002337_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: 131951
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:701 original size:21 final size:21
Alignment explanation
Indices: 653--701 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
643 GTATCATTTT
*
653 ACCGG-TTTTATCATTTTGTT
1 ACCGGTTTTTATCATTTTGTA
673 ACCGGTTTTTATCATATTT-TA
1 ACCGGTTTTTATCAT-TTTGTA
*
694 ACCTGTTT
1 ACCGGTTT
702 ATCGTTGTGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 5 0.20
21 17 0.68
22 3 0.12
ACGTcount: A:0.18, C:0.16, G:0.12, T:0.53
Consensus pattern (21 bp):
ACCGGTTTTTATCATTTTGTA
Found at i:858 original size:19 final size:18
Alignment explanation
Indices: 815--858 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 18
805 CACTTTTAAA
815 TTTACCGGTTTTATCATTT
1 TTTA-CGGTTTTATCATTT
834 TGTTACGGTTTTATCATATT
1 T-TTACGGTTTTATCAT-TT
854 TTTAC
1 TTTAC
859 CTGGTATATC
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.18, C:0.14, G:0.11, T:0.57
Consensus pattern (18 bp):
TTTACGGTTTTATCATTT
Found at i:1987 original size:15 final size:15
Alignment explanation
Indices: 1961--2000 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
1951 TGATAATATT
*
1961 TATTTATTTTTTAAA
1 TATTTTTTTTTTAAA
1976 TATTTTTATTTTTAATA
1 TATTTTT-TTTTTAA-A
1993 TATTTTTT
1 TATTTTTT
2001 ATTAAATAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 6 0.27
16 8 0.36
17 8 0.36
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTTTTTTTTTAAA
Found at i:1989 original size:16 final size:18
Alignment explanation
Indices: 1954--1999 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
1944 TACCCATTGA
1954 TAATAT-TTATTTATTTTT
1 TAATATATT-TTTATTTTT
1972 TAA-ATATTTTTA-TTTT
1 TAATATATTTTTATTTTT
1988 TAATATATTTTT
1 TAATATATTTTT
2000 TATTAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
16 7 0.27
17 14 0.54
18 5 0.19
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (18 bp):
TAATATATTTTTATTTTT
Found at i:2008 original size:16 final size:15
Alignment explanation
Indices: 1967--2008 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
1957 TATTTATTTA
1967 TTTTTTAAATAT-TT
1 TTTTTTAAATATATT
*
1981 TTATTTTTAATATATT
1 TT-TTTTAAATATATT
1997 TTTTATTAAATA
1 TTTT-TTAAATA
2009 ATAAAAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTTTAAATATATT
Found at i:4785 original size:3 final size:3
Alignment explanation
Indices: 4770--4824 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
4760 AGTTAAAAAA
* * *
4770 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT TAG
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4817 TAT TAT TA
1 TAT TAT TA
4825 AGTGTATTTA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
2 1 0.02
3 44 0.98
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:6025 original size:50 final size:50
Alignment explanation
Indices: 5970--6069 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
5960 AGAATAGCCA
5970 TATTTTATTTGTTTAACGTATAGCTTAGTTGGATATATATATATATATAT
1 TATTTTATTTGTTTAACGTATAGCTTAGTTGGATATATATATATATATAT
*
6020 TATTTTATTTGTTTAACGTATAGTTTAGTTGGATATATATATATATATAT
1 TATTTTATTTGTTTAACGTATAGCTTAGTTGGATATATATATATATATAT
6070 ATATATATAT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (50 bp):
TATTTTATTTGTTTAACGTATAGCTTAGTTGGATATATATATATATATAT
Found at i:6130 original size:2 final size:2
Alignment explanation
Indices: 6052--6111 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
6042 GTTTAGTTGG
6052 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
6094 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
6112 TAAATTAGTG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6533 original size:68 final size:68
Alignment explanation
Indices: 6456--6592 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
6446 TAAATAATGC
6456 ATATAATTTTTGTATTAGAATGTCATGGTAATTTTCATGAGTTAAATAATCATTTATTTTATTTA
1 ATATAATTTTTGTATTAGAATGTCATGGTAATTTTCATGAGTTAAATAATCATTTATTTTATTTA
6521 ATT
66 ATT
* *
6524 ATATAATTTTTGTATTAGAATGTCATGGTAATTTTCATGAGTTGAATAATCATTTGTTTTATTTA
1 ATATAATTTTTGTATTAGAATGTCATGGTAATTTTCATGAGTTAAATAATCATTTATTTTATTTA
6589 ATT
66 ATT
6592 A
1 A
6593 ATTTTTGTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (68 bp):
ATATAATTTTTGTATTAGAATGTCATGGTAATTTTCATGAGTTAAATAATCATTTATTTTATTTA
ATT
Found at i:18024 original size:8 final size:8
Alignment explanation
Indices: 18011--18105 Score: 89
Period size: 7 Copynumber: 12.5 Consensus size: 8
18001 TATGCTTGAA
*
18011 AAAAAAGG
1 AAAAAATG
18019 AAAAAAT-
1 AAAAAATG
18026 AAAAAGATG
1 AAAAA-ATG
18035 AAAAAATG
1 AAAAAATG
18043 -AAAAATG
1 AAAAAATG
18050 -AAAAATG
1 AAAAAATG
18057 AAAAAAAATG
1 --AAAAAATG
18067 -AAAAAT-
1 AAAAAATG
18073 AAAAAATG
1 AAAAAATG
18081 -AAAAA--
1 AAAAAATG
*
18086 AAGAAATG
1 AAAAAATG
18094 AAAAAATG
1 AAAAAATG
18102 AAAA
1 AAAA
18106 GAGAAAAATG
Statistics
Matches: 74, Mismatches: 3, Indels: 20
0.76 0.03 0.21
Matches are distributed among these distances:
6 4 0.05
7 36 0.49
8 22 0.30
9 5 0.07
10 7 0.09
ACGTcount: A:0.77, C:0.00, G:0.13, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:18045 original size:24 final size:23
Alignment explanation
Indices: 18011--18114 Score: 94
Period size: 24 Copynumber: 4.6 Consensus size: 23
18001 TATGCTTGAA
*
18011 AAAAAAGGAAAAAATAAAAAGATG
1 AAAAAATG-AAAAATAAAAAGATG
*
18035 AAAAAATGAAAAATGAAAAATGA-A
1 AAAAAATGAAAAAT-AAAAA-GATG
18059 AAAAAATGAAAAATAAAAA-ATG
1 AAAAAATGAAAAATAAAAAGATG
*
18081 AAAAAA--AGAAATGAAAAA-ATG
1 AAAAAATGAAAAAT-AAAAAGATG
*
18102 AAAAGA-GAAAAAT
1 AAAAAATGAAAAAT
18115 GAGGGTTTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
20 5 0.07
21 14 0.20
22 11 0.16
23 11 0.16
24 26 0.38
25 2 0.03
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (23 bp):
AAAAAATGAAAAATAAAAAGATG
Found at i:19236 original size:91 final size:90
Alignment explanation
Indices: 19120--19287 Score: 284
Period size: 92 Copynumber: 1.9 Consensus size: 90
19110 TGAGGGATTG
19120 ACATTTTCAGGAGAGTTCATAATGAGAAGAACTCATCCAAC-GAGGAAGAAGAAGTTCATAATGA
1 ACATTTTCAGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGA
19184 GAAGAACTTGTTCAACTTCGCATCA
66 GAAGAACTTGTTCAACTTCGCATCA
* *
19209 ACATTTTCAATGGAGAGTTCATAATGAGAAGAACTCATCCGACAGAGGGAGAAGAAGTTCATAAT
1 ACATTTTC-A-GGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAAT
*
19274 GAGAAGAGCTTGTT
64 GAGAAGAACTTGTT
19288 TGACCTATCA
Statistics
Matches: 73, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
89 8 0.11
90 1 0.01
91 31 0.42
92 33 0.45
ACGTcount: A:0.39, C:0.15, G:0.23, T:0.24
Consensus pattern (90 bp):
ACATTTTCAGGAGAGTTCATAATGAGAAGAACTCATCCAACAGAGGAAGAAGAAGTTCATAATGA
GAAGAACTTGTTCAACTTCGCATCA
Found at i:19559 original size:105 final size:105
Alignment explanation
Indices: 19339--19593 Score: 323
Period size: 105 Copynumber: 2.4 Consensus size: 105
19329 CTCGCTTGAG
* *
19339 GGATCGACATTTCCAATGAAGAGTTCATAATGAAAAGAACTCATCATAAAGGAGAAAGTTCATAA
1 GGATCAACATTTCC-A-GAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
* * * * *
19404 TAAGAAGAACTTGTTCCTTTCAAATTCACCACAGATGGAGGT
64 TAAGAAAAACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
* * * * *
19446 GAACCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
1 GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATA
* * **
19511 AGAAAAACATGTT-CTTTCTAAGTCCACCGCAAAAGGATTT
66 AGAAAAACATGTTCCTTTC-AAATCCACCACAAAAGGAGGT
*
19551 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATC
1 GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATC
19594 CACGAGAAAG
Statistics
Matches: 127, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
104 5 0.04
105 110 0.87
106 1 0.01
107 11 0.09
ACGTcount: A:0.40, C:0.17, G:0.18, T:0.24
Consensus pattern (105 bp):
GGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATA
AGAAAAACATGTTCCTTTCAAATCCACCACAAAAGGAGGT
Found at i:19774 original size:3 final size:3
Alignment explanation
Indices: 19759--19822 Score: 103
Period size: 3 Copynumber: 21.7 Consensus size: 3
19749 GGTTAAAAAA
*
19759 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
19806 TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TA
19823 AGTGTGTTTA
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
2 1 0.02
3 55 0.98
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:20939 original size:47 final size:49
Alignment explanation
Indices: 20846--20943 Score: 164
Period size: 49 Copynumber: 2.0 Consensus size: 49
20836 GTACACATAC
*
20846 CTTGGAAATTGATTCTTTGTTCATATATATATATATTCGTTTAACGTGT
1 CTTGGAAACTGATTCTTTGTTCATATATATATATATTCGTTTAACGTGT
*
20895 CTTGGAAACTGATTTTTTGTTCATATATATATAT-TT-GTTTAACGTGT
1 CTTGGAAACTGATTCTTTGTTCATATATATATATATTCGTTTAACGTGT
20942 CT
1 CT
20944 GAGGAATAAT
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
47 13 0.28
48 2 0.04
49 32 0.68
ACGTcount: A:0.26, C:0.10, G:0.14, T:0.50
Consensus pattern (49 bp):
CTTGGAAACTGATTCTTTGTTCATATATATATATATTCGTTTAACGTGT
Found at i:21039 original size:65 final size:65
Alignment explanation
Indices: 20962--21085 Score: 239
Period size: 65 Copynumber: 1.9 Consensus size: 65
20952 ATAGCCATAT
20962 TTTATTTGTTTAACGTATAGCTTAGTTGGATATATATATATATATATATATATATATATGTATTA
1 TTTATTTGTTTAACGTATAGCTTAGTTGGATATATATATATATATATATATATATATATGTATTA
*
21027 TTTATTTGTTTAACGTATAGTTTAGTTGGATATATATATATATATATATATATATATAT
1 TTTATTTGTTTAACGTATAGCTTAGTTGGATATATATATATATATATATATATATATAT
21086 TAAATTAGTG
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 58 1.00
ACGTcount: A:0.35, C:0.02, G:0.10, T:0.52
Consensus pattern (65 bp):
TTTATTTGTTTAACGTATAGCTTAGTTGGATATATATATATATATATATATATATATATGTATTA
Found at i:21104 original size:2 final size:2
Alignment explanation
Indices: 20991--21085 Score: 61
Period size: 2 Copynumber: 48.0 Consensus size: 2
20981 GCTTAGTTGG
* *
20991 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT -T AT TT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * **
21032 TT GT TT A- AC GT AT AGT TT AGT -T GG AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT A-T AT A-T AT AT AT AT AT AT AT AT AT AT AT
21074 AT AT AT AT AT AT
1 AT AT AT AT AT AT
21086 TAAATTAGTG
Statistics
Matches: 72, Mismatches: 16, Indels: 10
0.73 0.16 0.10
Matches are distributed among these distances:
1 3 0.04
2 67 0.93
3 2 0.03
ACGTcount: A:0.40, C:0.01, G:0.07, T:0.52
Consensus pattern (2 bp):
AT
Found at i:21507 original size:68 final size:68
Alignment explanation
Indices: 21430--21566 Score: 256
Period size: 68 Copynumber: 2.0 Consensus size: 68
21420 AAATAAATGC
21430 ATATAATTTTTGTATTAGAATGTCATGGTAATTTTCATGAGTTAAATAATCATTTATTTTATTTA
1 ATATAATTTTTGTATTAGAATGTCATGGTAATTTTCATGAGTTAAATAATCATTTATTTTATTTA
21495 ATT
66 ATT
* *
21498 ATATAATTTTTGTATTAGAATGTCATGGTAATTTTCATGAGTTGAATAATCATTTGTTTTATTTA
1 ATATAATTTTTGTATTAGAATGTCATGGTAATTTTCATGAGTTAAATAATCATTTATTTTATTTA
21563 ATT
66 ATT
21566 A
1 A
21567 ATTTTTGTAT
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
68 67 1.00
ACGTcount: A:0.33, C:0.04, G:0.12, T:0.51
Consensus pattern (68 bp):
ATATAATTTTTGTATTAGAATGTCATGGTAATTTTCATGAGTTAAATAATCATTTATTTTATTTA
ATT
Found at i:22701 original size:20 final size:20
Alignment explanation
Indices: 22676--22722 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
22666 ACCAACAAAT
*
22676 TCGCAACGCTAATCTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
22696 TCGCAACGCGAATTTGTAAA
1 TCGCAACGCGAATCTGTAAA
*
22716 TTGCAAC
1 TCGCAAC
22723 ACAGAAGTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGAATCTGTAAA
Found at i:22740 original size:40 final size:41
Alignment explanation
Indices: 22696--22874 Score: 196
Period size: 40 Copynumber: 4.5 Consensus size: 41
22686 AATCTGTAAA
*
22696 TCGCAACGCGAATTTGT-AAATT-GCAACACAGAAGTCAAAT
1 TCGCAACGCGAA-TAGTCAAATTCGCAACACAGAAGTCAAAT
* * *
22736 TCGCAACGTG-ATAGTCAAATTCGCAACGC-GATAGTGAAAT
1 TCGCAACGCGAATAGTCAAATTCGCAACACAGA-AGTCAAAT
* * *
22776 TCGCAATGC-AATAGTCAAATTCGCAACACAAAATTC-AAT
1 TCGCAACGCGAATAGTCAAATTCGCAACACAGAAGTCAAAT
*
22815 TCGCAACGCGAATTTGT-AAA-TCGCAACACAGAAGTCAAAT
1 TCGCAACGCGAA-TAGTCAAATTCGCAACACAGAAGTCAAAT
22855 TCGCAACGCGAA-AGTCAAAT
1 TCGCAACGCGAATAGTCAAAT
22875 GTTTTTACGC
Statistics
Matches: 114, Mismatches: 15, Indels: 20
0.77 0.10 0.13
Matches are distributed among these distances:
38 5 0.04
39 36 0.32
40 69 0.61
41 4 0.04
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.21
Consensus pattern (41 bp):
TCGCAACGCGAATAGTCAAATTCGCAACACAGAAGTCAAAT
Found at i:22741 original size:20 final size:20
Alignment explanation
Indices: 22713--22874 Score: 126
Period size: 20 Copynumber: 8.2 Consensus size: 20
22703 GCGAATTTGT
*
22713 AAATT-GCAACACAGAAGTC
1 AAATTCGCAACGCAGAAGTC
*
22732 AAATTCGCAACG-TGATAGTC
1 AAATTCGCAACGCAGA-AGTC
*
22752 AAATTCGCAACGC-GATAGTG
1 AAATTCGCAACGCAGA-AGTC
*
22772 AAATTCGCAATGCA-ATAGTC
1 AAATTCGCAACGCAGA-AGTC
* * *
22792 AAATTCGCAACACAAAATTC
1 AAATTCGCAACGCAGAAGTC
22812 -AATTCGCAACGC-GAATTTGT-
1 AAATTCGCAACGCAGAA---GTC
*
22832 AAA-TCGCAACACAGAAGTC
1 AAATTCGCAACGCAGAAGTC
22851 AAATTCGCAACGC-GAAAGTC
1 AAATTCGCAACGCAG-AAGTC
22871 AAAT
1 AAAT
22875 GTTTTTACGC
Statistics
Matches: 117, Mismatches: 13, Indels: 25
0.75 0.08 0.16
Matches are distributed among these distances:
18 4 0.03
19 22 0.19
20 84 0.72
21 7 0.06
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (20 bp):
AAATTCGCAACGCAGAAGTC
Found at i:25591 original size:20 final size:20
Alignment explanation
Indices: 25507--25622 Score: 101
Period size: 21 Copynumber: 5.7 Consensus size: 20
25497 CTTATAATTA
*
25507 TTCAAGAGGCACCTCTTATCG
1 TTCAAGAGGC-CCTCTCATCG
25528 TTCAAGAGGTCCCTCTCATC-
1 TTCAAGAGG-CCCTCTCATCG
* * *
25548 ATCGAAGAAGCCCCTCTCACCG
1 TTC-AAG-AGGCCCTCTCATCG
*
25570 TTCAAGAGGCCCTATCATCG
1 TTCAAGAGGCCCTCTCATCG
* * *
25590 TTCAAGAGGTCCTGCCCACCG
1 TTCAAGAGGCCCT-CTCATCG
25611 TTCAAGA-GCCCT
1 TTCAAGAGGCCCT
25623 ATTCACATGG
Statistics
Matches: 77, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
20 29 0.38
21 43 0.56
22 5 0.06
ACGTcount: A:0.23, C:0.34, G:0.19, T:0.23
Consensus pattern (20 bp):
TTCAAGAGGCCCTCTCATCG
Found at i:26257 original size:63 final size:64
Alignment explanation
Indices: 26155--26295 Score: 207
Period size: 64 Copynumber: 2.2 Consensus size: 64
26145 ATTTACATTG
*
26155 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGATTTA-TTTTTT-ATTGATTAATTGATTTGT-
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGATTG-TTAATTGATTTGTA
* * *
26217 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTATTTTTTTGATTGTTAATTGATTTGTA
26282 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
26296 GTTTCTAAAA
Statistics
Matches: 71, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
62 17 0.24
63 18 0.25
64 19 0.27
65 17 0.24
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.51
Consensus pattern (64 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTTGATTGTTAATTGATTTGTA
Found at i:26379 original size:20 final size:20
Alignment explanation
Indices: 26354--26391 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
26344 GTTGAAGGTA
26354 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
26374 CAAATTCGCAACGCGAAA
1 CAAATTCGCAACGCGAAA
26392 TAAGCATTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.42, C:0.26, G:0.18, T:0.13
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:26708 original size:38 final size:39
Alignment explanation
Indices: 26630--26715 Score: 129
Period size: 39 Copynumber: 2.2 Consensus size: 39
26620 TCAAGTTGTA
* *
26630 GATTTTGATTTCCTTTTACTTGGCACCATATGAGATTTG
1 GATTTTGATTTCCTTTTACTTGGAACCATATGAGACTTG
* *
26669 GATTTTGATTTCTTTTTGCTTGGAACCATATGAG-CTTG
1 GATTTTGATTTCCTTTTACTTGGAACCATATGAGACTTG
26707 GATTTTGAT
1 GATTTTGAT
26716 GAGCATCGGA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
38 12 0.28
39 31 0.72
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.48
Consensus pattern (39 bp):
GATTTTGATTTCCTTTTACTTGGAACCATATGAGACTTG
Found at i:30216 original size:24 final size:24
Alignment explanation
Indices: 30189--30242 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
30179 CCATCACATC
*
30189 ATCAAAATCCGAGTATTCCCCAAG
1 ATCAAAATCCGAGTATTCACCAAG
* * *
30213 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTCACCAAG
30237 ATCAAA
1 ATCAAA
30243 TTTCGAATAC
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:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTCACCAAG
Found at i:30389 original size:12 final size:12
Alignment explanation
Indices: 30368--30401 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
30358 GGTTGTGGGT
*
30368 TTTGAGATTGTG
1 TTTGATATTGTG
30380 TTTGATATTGTG
1 TTTGATATTGTG
*
30392 TTTGGTATTG
1 TTTGATATTG
30402 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:30976 original size:16 final size:15
Alignment explanation
Indices: 30954--30992 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
30944 GAAATCATTG
30954 AAAAATTATATAGAAA
1 AAAAATTATATA-AAA
* *
30970 TAAAATTATGTAAAA
1 AAAAATTATATAAAA
30985 AAAAATTA
1 AAAAATTA
30993 GAGATGGGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.67, C:0.00, G:0.05, T:0.28
Consensus pattern (15 bp):
AAAAATTATATAAAA
Found at i:31213 original size:21 final size:19
Alignment explanation
Indices: 31149--31220 Score: 99
Period size: 19 Copynumber: 3.7 Consensus size: 19
31139 ACTAAAACCT
* *
31149 GTTGTGAATTTAAAATTCA
1 GTTGCGAATTTGAAATTCA
31168 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTCA
*
31187 GTTGCGAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT-C-A
31208 GTTGCGAATTTGA
1 GTTGCGAATTTGA
31221 CTATCGTGTT
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
19 34 0.71
20 1 0.02
21 13 0.27
ACGTcount: A:0.29, C:0.11, G:0.22, T:0.38
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTCA
Found at i:31291 original size:20 final size:19
Alignment explanation
Indices: 31241--31295 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
31231 GCGATTTACA
31241 GATTCGCGTTGCGAAATTG
1 GATTCGCGTTGCGAAATTG
** *
31260 GAAACTGGGTTGCGAAATTG
1 GATTC-GCGTTGCGAAATTG
31280 GAGTTCGCGTTGCGAA
1 GA-TTCGCGTTGCGAA
31296 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.11
20 24 0.86
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.27
Consensus pattern (19 bp):
GATTCGCGTTGCGAAATTG
Found at i:32165 original size:5 final size:5
Alignment explanation
Indices: 32155--32179 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
32145 CAGGGACTTA
32155 GAAAT GAAAT GAAAT GAAAT GAAAT
1 GAAAT GAAAT GAAAT GAAAT GAAAT
32180 TTAGGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (5 bp):
GAAAT
Found at i:38151 original size:20 final size:20
Alignment explanation
Indices: 38122--38168 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
38112 TATTAGCAGA
*
38122 AAAATGATTGATTATTTAAG
1 AAAATAATTGATTATTTAAG
38142 AAAATAATTGATTATTTAAG
1 AAAATAATTGATTATTTAAG
38162 AAAATAA
1 AAAATAA
38169 AACTCTATCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (20 bp):
AAAATAATTGATTATTTAAG
Found at i:48367 original size:20 final size:20
Alignment explanation
Indices: 48342--48388 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
48332 TACGCGATTT
48342 TGAAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
*
48362 T-TAAAATGTGTTGCGATAG
1 TGAAAAATGTGTTGCGATAG
48381 TGAAAAAT
1 TGAAAAAT
48389 CCAAAATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.38, C:0.04, G:0.26, T:0.32
Consensus pattern (20 bp):
TGAAAAATGTGTTGCGATAG
Found at i:48645 original size:6 final size:5
Alignment explanation
Indices: 48616--48649 Score: 50
Period size: 5 Copynumber: 6.4 Consensus size: 5
48606 CCGTCCCGTC
48616 TCGGG TCGGG TCGGG TCGGG TCGTGG TCGTGG TC
1 TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TC
48650 ATACGTGTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 18 0.64
6 10 0.36
ACGTcount: A:0.00, C:0.21, G:0.53, T:0.26
Consensus pattern (5 bp):
TCGGG
Found at i:48760 original size:21 final size:21
Alignment explanation
Indices: 48734--48774 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
48724 CAGTCGTTGC
48734 GAACTTCGACTATCACAACGT
1 GAACTTCGACTATCACAACGT
* *
48755 GAACTTGGACTATCGCAACG
1 GAACTTCGACTATCACAACG
48775 AATTTGGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (21 bp):
GAACTTCGACTATCACAACGT
Found at i:48911 original size:20 final size:19
Alignment explanation
Indices: 48888--48933 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
48878 GGAAACTGAT
* *
48888 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
48908 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
48927 TTGCGAT
1 TTGCGAT
48934 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:48923 original size:19 final size:19
Alignment explanation
Indices: 48899--48935 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
48889 TGCGATACTG
*
48899 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
48918 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
48936 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:49073 original size:22 final size:22
Alignment explanation
Indices: 49032--49097 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
49022 TTTAAATCAT
* *
49032 TTTAAAATTTAAATATAAAAATA
1 TTTAAAAATAAAATA-AAAAATA
*
49055 TTTAAAAATAAAATAAAAAACA
1 TTTAAAAATAAAATAAAAAATA
*
49077 -ATAAAAATAAAAATAAAAAAT
1 TTTAAAAAT-AAAATAAAAAAT
49098 TAAATTACTA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
21 7 0.19
22 17 0.46
23 13 0.35
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (22 bp):
TTTAAAAATAAAATAAAAAATA
Found at i:49124 original size:15 final size:15
Alignment explanation
Indices: 49035--49128 Score: 74
Period size: 16 Copynumber: 6.4 Consensus size: 15
49025 AAATCATTTT
*
49035 AAAATTTAAAT-ATA
1 AAAAATTAAATAATA
49049 AAAATATTTAAA-AATA
1 AAAA-A-TTAAATAATA
* *
49065 AAATAA-AAAACAAT-
1 AAA-AATTAAATAATA
49079 AAAAA-TAAA-AATA
1 AAAAATTAAATAATA
*
49092 AAAAATTAAATTACTA
1 AAAAATTAAA-TAATA
49108 AAAAATTAAATAATA
1 AAAAATTAAATAATA
49123 AAAAAT
1 AAAAAT
49129 CATTTTAACT
Statistics
Matches: 66, Mismatches: 5, Indels: 17
0.75 0.06 0.19
Matches are distributed among these distances:
12 3 0.05
13 10 0.15
14 14 0.21
15 13 0.20
16 25 0.38
17 1 0.02
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (15 bp):
AAAAATTAAATAATA
Found at i:55835 original size:30 final size:31
Alignment explanation
Indices: 55776--55835 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
55766 GATTAAATTA
*
55776 ATATTTTATCTAAAATTTATTGGTTAAAATG
1 ATATTTTATCTAAAATTTATAGGTTAAAATG
*
55807 ATATTTTATCT-AATTTTA-AGGTTTAAAAT
1 ATATTTTATCTAAAATTTATAGG-TTAAAAT
55836 AAACATTAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 2 0.08
30 13 0.50
31 11 0.42
ACGTcount: A:0.38, C:0.03, G:0.08, T:0.50
Consensus pattern (31 bp):
ATATTTTATCTAAAATTTATAGGTTAAAATG
Found at i:62482 original size:17 final size:18
Alignment explanation
Indices: 62446--62486 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
62436 ATATTATGTA
*
62446 TTTAATTTATTTAAACAT
1 TTTACTTTATTTAAACAT
*
62464 TTTACTTTATTT-AATAT
1 TTTACTTTATTTAAACAT
62481 TTTACT
1 TTTACT
62487 AATATAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.32, C:0.07, G:0.00, T:0.61
Consensus pattern (18 bp):
TTTACTTTATTTAAACAT
Found at i:68507 original size:50 final size:52
Alignment explanation
Indices: 68405--68518 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 52
68395 CACCTACGTG
* **
68405 GCGTATAGCGC-GTATCAGGGGGCGCGTTATACCCACGTGTATGCCATGTCA
1 GCGTATAGCGCGGTATCAGGGGGCGCGTTATACCCACGTGTACGCCAAATCA
*
68456 GCGTATAGCGCGGTA-CA-GGGGCGC-TCTATACCCTACGTG-GCGCCAAATCA
1 GCGTATAGCGCGGTATCAGGGGGCGCGT-TATACCC-ACGTGTACGCCAAATCA
*
68506 GCATATAGCGCGG
1 GCGTATAGCGCGG
68519 GGGCAGGGAG
Statistics
Matches: 55, Mismatches: 5, Indels: 7
0.82 0.07 0.10
Matches are distributed among these distances:
49 1 0.02
50 33 0.60
51 18 0.33
52 3 0.05
ACGTcount: A:0.21, C:0.27, G:0.32, T:0.20
Consensus pattern (52 bp):
GCGTATAGCGCGGTATCAGGGGGCGCGTTATACCCACGTGTACGCCAAATCA
Found at i:79211 original size:22 final size:22
Alignment explanation
Indices: 79180--79222 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
79170 GAGCCTAACT
*
79180 TTTTATGTTG-AATAAAGAAATA
1 TTTTAGGTTGAAATAAA-AAATA
79202 TTTTAGGTTGAAATAAAAAAT
1 TTTTAGGTTGAAATAAAAAAT
79223 TTTACATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 13 0.68
23 6 0.32
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.40
Consensus pattern (22 bp):
TTTTAGGTTGAAATAAAAAATA
Found at i:84173 original size:2 final size:2
Alignment explanation
Indices: 84166--84190 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
84156 GTCCCTGACA
84166 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 A
84191 ATGATTTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:85325 original size:32 final size:32
Alignment explanation
Indices: 85279--85352 Score: 130
Period size: 32 Copynumber: 2.3 Consensus size: 32
85269 TTCTGCTTTC
* *
85279 TTTCGGATGCACCCATAATTAGTCCTTGATCA
1 TTTCGAATGAACCCATAATTAGTCCTTGATCA
85311 TTTCGAATGAACCCATAATTAGTCCTTGATCA
1 TTTCGAATGAACCCATAATTAGTCCTTGATCA
85343 TTTCGAATGA
1 TTTCGAATGA
85353 GAACCCCTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 40 1.00
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.35
Consensus pattern (32 bp):
TTTCGAATGAACCCATAATTAGTCCTTGATCA
Found at i:87661 original size:14 final size:14
Alignment explanation
Indices: 87642--87706 Score: 112
Period size: 14 Copynumber: 4.6 Consensus size: 14
87632 CAACCCAAAT
87642 TGAGTCAACTTATC
1 TGAGTCAACTTATC
87656 TGAGTCAACTTATC
1 TGAGTCAACTTATC
87670 TGAGTCAACTTATC
1 TGAGTCAACTTATC
*
87684 CGAGTCAACTTATC
1 TGAGTCAACTTATC
*
87698 CGAGTCAAC
1 TGAGTCAAC
87707 CTATTAACTT
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
14 50 1.00
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (14 bp):
TGAGTCAACTTATC
Found at i:89081 original size:23 final size:22
Alignment explanation
Indices: 89018--89112 Score: 88
Period size: 23 Copynumber: 4.3 Consensus size: 22
89008 CACCACATCT
* *
89018 CACATAATTTGCACTGAAGTG-T
1 CACATAATTTGCCCTGAAG-GAC
* *
89040 CACAT-ATTTGTCCTAAAGGAC
1 CACATAATTTGCCCTGAAGGAC
89061 CACATAAGTTTGCCCTGAAGGAC
1 CACATAA-TTTGCCCTGAAGGAC
*
89084 CACATAATTTTGTCCC-GAATGAC
1 CACATAA-TTTG-CCCTGAAGGAC
89107 CACATA
1 CACATA
89113 GAACCCTCGA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
20 1 0.02
21 15 0.25
22 6 0.10
23 36 0.59
24 3 0.05
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (22 bp):
CACATAATTTGCCCTGAAGGAC
Found at i:89088 original size:44 final size:45
Alignment explanation
Indices: 89018--89112 Score: 106
Period size: 46 Copynumber: 2.1 Consensus size: 45
89008 CACCACATCT
* *
89018 CACATAATTTGCACTGAAGTGTCACAT-A-TTTGTCCTAAAGGAC
1 CACATAATTTGCACTGAAGTGCCACATAATTTTGTCCCAAAGGAC
* * *
89061 CACATAAGTTTGCCCTGAAG-GACCACATAATTTTGTCCCGAATGAC
1 CACATAA-TTTGCACTGAAGTG-CCACATAATTTTGTCCCAAAGGAC
89107 CACATA
1 CACATA
89113 GAACCCTCGA
Statistics
Matches: 43, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
43 8 0.19
44 16 0.37
45 1 0.02
46 18 0.42
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (45 bp):
CACATAATTTGCACTGAAGTGCCACATAATTTTGTCCCAAAGGAC
Found at i:93960 original size:103 final size:103
Alignment explanation
Indices: 93632--93952 Score: 606
Period size: 103 Copynumber: 3.1 Consensus size: 103
93622 GTCGAGGGTC
*
93632 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTATGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
93697 TTGATCCCTAGTATATGTATATGTTTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
93735 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACATATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
93800 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
*
93838 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTAGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
93903 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
93941 TATGTGGTCCTT
1 TATGTGGTCCTT
93953 ATGGACATTA
Statistics
Matches: 213, Mismatches: 5, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
103 213 1.00
ACGTcount: A:0.27, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:94036 original size:23 final size:23
Alignment explanation
Indices: 93968--94028 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
93958 CATTATTATA
*
93968 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
*
93991 CGGCACTACGGTGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
94014 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
94029 TTTATATGAG
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.20, C:0.26, G:0.28, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:99008 original size:103 final size:103
Alignment explanation
Indices: 98829--99157 Score: 633
Period size: 103 Copynumber: 3.2 Consensus size: 103
98819 GTCGAGGGTC
98829 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
*
98894 TTGATCCCTAGTATATGTATATGATTCTTAAGAAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
98932 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
98997 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
99035 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
99100 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
66 TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
99138 TATGTGGTCCTT-GTGGACAT
1 TATGTGGTCCTTCG-GGACAT
99158 TATTATATGG
Statistics
Matches: 224, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
102 1 0.00
103 223 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGTATATGTATATGATTCTTAAGGAATGA
Found at i:99233 original size:23 final size:23
Alignment explanation
Indices: 99165--99225 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
99155 CATTATTATA
*
99165 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTATG
* *
99188 CGGCACTACGATGCAATTCTATG
1 TGGCACTACGGTGCAATTCTATG
*
99211 TGGCACTTCGGTGCA
1 TGGCACTACGGTGCA
99226 TTTATATGAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTATG
Found at i:106903 original size:14 final size:15
Alignment explanation
Indices: 106884--106914 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
106874 AGTAGAAGGG
106884 TTTCTTTTCTT-ATT
1 TTTCTTTTCTTCATT
106898 TTTCTTTTCTTCATT
1 TTTCTTTTCTTCATT
106913 TT
1 TT
106915 AGAGAATAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.69
15 5 0.31
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTCTTTTCTTCATT
Found at i:107290 original size:22 final size:24
Alignment explanation
Indices: 107265--107316 Score: 72
Period size: 25 Copynumber: 2.2 Consensus size: 24
107255 TCATTAGTAA
107265 TAAAAGA-TAA-TATTATTCCTCT
1 TAAAAGATTAACTATTATTCCTCT
*
107287 TAAAATATTTAACTATTATTCCTCT
1 TAAAAGA-TTAACTATTATTCCTCT
107312 TAAAA
1 TAAAA
107317 AATTTAATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 6 0.23
24 3 0.12
25 17 0.65
ACGTcount: A:0.42, C:0.13, G:0.02, T:0.42
Consensus pattern (24 bp):
TAAAAGATTAACTATTATTCCTCT
Found at i:107308 original size:25 final size:25
Alignment explanation
Indices: 107275--107323 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
107265 TAAAAGATAA
*
107275 TATTATTCCTCTTAAAATATTTAAC
1 TATTATTCCTCTTAAAAAATTTAAC
107300 TATTATTCCTCTTAAAAAATTTAA
1 TATTATTCCTCTTAAAAAATTTAA
107324 TTTAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.39, C:0.14, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTATTCCTCTTAAAAAATTTAAC
Found at i:109044 original size:13 final size:12
Alignment explanation
Indices: 109013--109046 Score: 52
Period size: 11 Copynumber: 2.8 Consensus size: 12
109003 TATTATAGAT
109013 ATTTTTTT-ATA
1 ATTTTTTTAATA
109024 ATTTTTTTAATA
1 ATTTTTTTAATA
109036 ATTTATTTTAA
1 ATTT-TTTTAA
109047 CTTTTAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 8 0.38
12 7 0.33
13 6 0.29
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
ATTTTTTTAATA
Found at i:113860 original size:22 final size:22
Alignment explanation
Indices: 113811--113862 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
113801 ATTTCAGGCG
113811 AAATTTAATATAAAATATTAAT
1 AAATTTAATATAAAATATTAAT
**
113833 TTATTTAATATAAAA-ATTATAT
1 AAATTTAATATAAAATATTA-AT
113855 AAATTTAA
1 AAATTTAA
113863 AACATTTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 4 0.16
22 21 0.84
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
AAATTTAATATAAAATATTAAT
Found at i:113911 original size:26 final size:26
Alignment explanation
Indices: 113864--113929 Score: 78
Period size: 26 Copynumber: 2.5 Consensus size: 26
113854 TAAATTTAAA
* *
113864 ACATTTTCAATTAAAATTAAAAATATT
1 ACATTTT-AGTTATAATTAAAAATATT
* *
113891 ATATTTTAGTTATAATTAAAAATGTT
1 ACATTTTAGTTATAATTAAAAATATT
*
113917 ACGTTTTAGTTAT
1 ACATTTTAGTTAT
113930 TTTAATGTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 27 0.82
27 6 0.18
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (26 bp):
ACATTTTAGTTATAATTAAAAATATT
Found at i:127932 original size:32 final size:32
Alignment explanation
Indices: 127895--127959 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
127885 CCAGAACAAG
127895 GTTTCCTGGAAATTGCAACAGATGAACAACCA
1 GTTTCCTGGAAATTGCAACAGATGAACAACCA
127927 GTTTCCTGGAAATTGCAACAGATGAACAACCA
1 GTTTCCTGGAAATTGCAACAGATGAACAACCA
127959 G
1 G
127960 CATAAAACCA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (32 bp):
GTTTCCTGGAAATTGCAACAGATGAACAACCA
Done.