Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003716.1 Hibiscus syriacus cultivar Beakdansim tig00007946_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: 68459
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:1053 original size:36 final size:35
Alignment explanation
Indices: 997--1187 Score: 112
Period size: 36 Copynumber: 5.7 Consensus size: 35
987 GAAACACAAA
*
997 CTTTGAGATCATTTTC-CTTGAAACGAATTTTGTCT
1 CTTTGAGATCAGTTTCTCTTGAAAC-AATTTTGTCT
1032 CTATTGAGA-CAGTTTCTCTTGAAAC-A-----TCAT
1 CT-TTGAGATCAGTTTCTCTTGAAACAATTTTGTC-T
*
1062 CTTTGAGATC-GTTTCCCTTGAAACAAATTTTGTCT
1 CTTTGAGATCAGTTTCTCTTGAAAC-AATTTTGTCT
* **
1097 CTCTAGAGA-CAGTTTCTCTTGAAAC-A---TCAC-
1 CT-TTGAGATCAGTTTCTCTTGAAACAATTTTGTCT
* *
1127 CTTTAAGATC-GTTTCTCTTAAAACGAATTTT-TCCT
1 CTTTGAGATCAGTTTCTCTTGAAAC-AATTTTGT-CT
*
1162 CTCTTGAG-GCAGTTTCTCTTGAAACA
1 CT-TTGAGATCAGTTTCTCTTGAAACA
1188 TCATCTTTGA
Statistics
Matches: 120, Mismatches: 13, Indels: 46
0.67 0.07 0.26
Matches are distributed among these distances:
29 38 0.32
30 7 0.06
31 4 0.03
34 4 0.03
35 16 0.13
36 51 0.43
ACGTcount: A:0.26, C:0.21, G:0.14, T:0.40
Consensus pattern (35 bp):
CTTTGAGATCAGTTTCTCTTGAAACAATTTTGTCT
Found at i:1069 original size:65 final size:64
Alignment explanation
Indices: 979--1198 Score: 282
Period size: 65 Copynumber: 3.4 Consensus size: 64
969 TTGGAAATTA
* * *
979 TTTCACTTGAAACA-CAAACTTTGAGATCATTTTCCTTGAAACGAATTTTGTCTCTATTGAGACA
1 TTTCTCTTGAAACATC-ATCTTTGAGATC-TTTTCCTTGAAACGAATTTTGTCTCTCTTGAGACA
1043 G
64 G
* * *
1044 TTTCTCTTGAAACATCATCTTTGAGATCGTTTCCCTTGAAACAAATTTTGTCTCTCTAGAGACAG
1 TTTCTCTTGAAACATCATCTTTGAGATC-TTTTCCTTGAAACGAATTTTGTCTCTCTTGAGACAG
* * * * *
1109 TTTCTCTTGAAACATCACCTTTAAGATCGTTTCTCTTAAAACGAATTTT-TCCTCTCTTGAGGCA
1 TTTCTCTTGAAACATCATCTTTGAGATCTTTTC-CTTGAAACGAATTTTGT-CTCTCTTGAGACA
1173 G
64 G
1174 TTTCTCTTGAAACATCATCTTTGAG
1 TTTCTCTTGAAACATCATCTTTGAG
1199 TTGAAACAAA
Statistics
Matches: 135, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
64 4 0.03
65 130 0.96
66 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (64 bp):
TTTCTCTTGAAACATCATCTTTGAGATCTTTTCCTTGAAACGAATTTTGTCTCTCTTGAGACAG
Found at i:1488 original size:134 final size:133
Alignment explanation
Indices: 1246--1509 Score: 305
Period size: 134 Copynumber: 2.0 Consensus size: 133
1236 TGAAACTATT
* * * **
1246 ATCCCTAAAGATGGCCAGCCGTCTTCATCACCTAGGAACCGTGTCATCCACTGACCATATCTCCT
1 ATCCCTAAAGATGGCCAACCATCTTCATCACCTAGGAACCGAGTCATCCACCAACCATATCTCCT
* ** * * * *
1311 CATCACGTAGGAGTTGCATCAACCTTTGATAACTAGCCGTCCTCATCGCGTAGGAACCATGTTAT
66 CATAACGTAGGAGCCGCATCAACCTTAGATAACCAGACGTCCTCA-CACGTAGGAACCATGTTAT
1376 CATC
130 CATC
* * *
1380 ATCCCTAAAGATGGTCAATCATCCTT-ATCACGTAGGAACCGAGTCATCCACCAACCATATCTCC
1 ATCCCTAAAGATGGCCAACCAT-CTTCATCACCTAGGAACCGAGTCATCCACCAACCATATCTCC
** * * * * *
1444 TCATAACGTAGGAGCCGTGTCACCCTTAGATAGCCAGACTTCCTCACATGTATGAACCATGTTAT
65 TCATAACGTAGGAGCCGCATCAACCTTAGATAACCAGACGTCCTCACACGTAGGAACCATGTTAT
1509 C
130 C
1510 TCCAAATTTA
Statistics
Matches: 107, Mismatches: 22, Indels: 3
0.81 0.17 0.02
Matches are distributed among these distances:
133 17 0.16
134 87 0.81
135 3 0.03
ACGTcount: A:0.27, C:0.31, G:0.16, T:0.26
Consensus pattern (133 bp):
ATCCCTAAAGATGGCCAACCATCTTCATCACCTAGGAACCGAGTCATCCACCAACCATATCTCCT
CATAACGTAGGAGCCGCATCAACCTTAGATAACCAGACGTCCTCACACGTAGGAACCATGTTATC
ATC
Found at i:1709 original size:3 final size:3
Alignment explanation
Indices: 1701--1735 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
1691 GGGCTCTACA
1701 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1736 CATTACAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:3192 original size:64 final size:65
Alignment explanation
Indices: 3118--3253 Score: 213
Period size: 65 Copynumber: 2.1 Consensus size: 65
3108 ACACCCTAAT
* *
3118 TCGAATGCATTTTGTGTACCGATGCACAG-CCATGCATCGATGCACTCC-AGATTTTATTGAAAC
1 TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTAGATCTT-TTGAAAC
3181 A
65 A
* *
3182 TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTGGCTCTTTTGAAACA
1 TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTAGATCTTTTGAAACA
3247 TCGAATG
1 TCGAATG
3254 TAATTAGTGT
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
64 28 0.42
65 34 0.52
66 4 0.06
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (65 bp):
TCGAATGCATTTTATGTACCGATGCACAGACCATGCATCGATGCACTCCTAGATCTTTTGAAACA
Found at i:6476 original size:17 final size:18
Alignment explanation
Indices: 6443--6476 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
6433 GAATTTGTCC
*
6443 CGAATGACCACTATATCT
1 CGAAGGACCACTATATCT
6461 CGAAGGACCA-TATATC
1 CGAAGGACCACTATATC
6477 ACATATGTCC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.35, C:0.26, G:0.15, T:0.24
Consensus pattern (18 bp):
CGAAGGACCACTATATCT
Found at i:6503 original size:18 final size:18
Alignment explanation
Indices: 6480--6515 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
6470 ATATATCACA
6480 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
6498 TATGTCCCGAAGGACCAC
1 TATGTCCCGAAGGACCAC
6516 ATAGAACCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.17
Consensus pattern (18 bp):
TATGTCCCGAAGGACCAC
Found at i:15364 original size:44 final size:44
Alignment explanation
Indices: 15301--15407 Score: 151
Period size: 44 Copynumber: 2.4 Consensus size: 44
15291 TTTTGTTCAC
* *
15301 TATGCATCAATACACTATGAAAGTGTAACGATGCATCCCTTAAA
1 TATGCATCGATACACTATGAAAGTGCAACGATGCATCCCTTAAA
* * * *
15345 TATGCATCGATACACTATGAAGGTGCACCGATGCATGCCTTGAA
1 TATGCATCGATACACTATGAAAGTGCAACGATGCATCCCTTAAA
*
15389 TGTGCATCGATACACTATG
1 TATGCATCGATACACTATG
15408 CAGTGCATTG
Statistics
Matches: 56, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 56 1.00
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (44 bp):
TATGCATCGATACACTATGAAAGTGCAACGATGCATCCCTTAAA
Found at i:15941 original size:13 final size:13
Alignment explanation
Indices: 15912--15948 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
15902 CATACTATGA
*
15912 TTTTTCAAACATTG
1 TTTTTCAAA-ATAG
15926 TTTTTCAAAATAG
1 TTTTTCAAAATAG
15939 TTTTTCAAAA
1 TTTTTCAAAA
15949 ATTTGCCCAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.35, C:0.11, G:0.05, T:0.49
Consensus pattern (13 bp):
TTTTTCAAAATAG
Found at i:17758 original size:12 final size:14
Alignment explanation
Indices: 17731--17765 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
17721 AGGGGAAGTA
17731 ATTTTCAAAAATTG
1 ATTTTCAAAAATTG
17745 A-TTTCAAAAA-TG
1 ATTTTCAAAAATTG
17757 ATTTTCAAA
1 ATTTTCAAA
17766 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 3 0.15
13 16 0.80
14 1 0.05
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (14 bp):
ATTTTCAAAAATTG
Found at i:18251 original size:65 final size:64
Alignment explanation
Indices: 18099--18254 Score: 201
Period size: 65 Copynumber: 2.4 Consensus size: 64
18089 ACACCCTAAT
* * *
18099 TCGAATGCATTTTGTGTACCAATGCACAACCATGCATCGATGCACTCCTGATTTTATTGAAACA
1 TCGAATGCATTTAGTGTACCGATGCACAACCATGCATCGATGCACTCCTGATCTTATTGAAACA
* * *
18163 TCGAATCCATTTTA-TGTATCGATGCACAGACCATGCATCGATGCACTCCTGGCTCTT-TTGAAA
1 TCGAATGCA-TTTAGTGTACCGATGCACA-ACCATGCATCGATGCACTCCT-GATCTTATTGAAA
18226 CA
63 CA
18228 TCGAATGTCA-TTAGTGTACCGATGCAC
1 TCGAATG-CATTTAGTGTACCGATGCAC
18255 CCCAAGTGTA
Statistics
Matches: 79, Mismatches: 8, Indels: 9
0.82 0.08 0.09
Matches are distributed among these distances:
64 23 0.29
65 50 0.63
66 6 0.08
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (64 bp):
TCGAATGCATTTAGTGTACCGATGCACAACCATGCATCGATGCACTCCTGATCTTATTGAAACA
Found at i:20791 original size:21 final size:19
Alignment explanation
Indices: 20728--20798 Score: 106
Period size: 19 Copynumber: 3.6 Consensus size: 19
20718 CGGCCAAGAG
20728 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
20747 CATGTATCTTCATTAAAAT
1 CATGTATCTTCATTAAAAT
*
20766 CATGTATTTTCATTTAAAAGT
1 CATGTATCTTCA-TTAAAA-T
*
20787 CATGTATTTTCA
1 CATGTATCTTCA
20799 AAGGGGTTTC
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
19 30 0.61
20 6 0.12
21 13 0.27
ACGTcount: A:0.34, C:0.14, G:0.07, T:0.45
Consensus pattern (19 bp):
CATGTATCTTCATTAAAAT
Found at i:21525 original size:14 final size:12
Alignment explanation
Indices: 21502--21566 Score: 69
Period size: 14 Copynumber: 5.0 Consensus size: 12
21492 GTACAAAAAG
21502 AAAGAAAAGACAA
1 AAAGAAAAGA-AA
21515 AAAGAAAA-AGAA
1 AAAGAAAAGA-AA
21527 AAAGAAAAGAAGAA
1 AAAGAAAAG-A-AA
21541 AAAGAAAAGAAGA
1 AAAGAAAAGAA-A
21554 AAAGAAAAAGAAA
1 AAAG-AAAAGAAA
21567 TTCAAAAAGA
Statistics
Matches: 47, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
12 12 0.26
13 15 0.32
14 20 0.43
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:21526 original size:19 final size:18
Alignment explanation
Indices: 21502--21566 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 18
21492 GTACAAAAAG
21502 AAAGAAAAGACAAAAAGAA
1 AAAGAAAAGA-AAAAAGAA
21521 AAAGAAAAAGAAAAGAAGAA
1 AAAG-AAAAGAAAA-AAGAA
21541 AAAGAAAAGAAGAAAAGAA
1 AAAGAAAAGAA-AAAAGAA
21560 AAAGAAA
1 AAAGAAA
21567 TTCAAAAAGA
Statistics
Matches: 43, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
19 26 0.60
20 17 0.40
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAGAAAAGAAAAAAGAA
Found at i:24967 original size:19 final size:21
Alignment explanation
Indices: 24943--24994 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
24933 CGGCCAAGAG
*
24943 CATGTATCTTCA-TTAAAA-T
1 CATGTATTTTCATTTAAAAGT
24962 CATGTATTTTCATTTAAAAGT
1 CATGTATTTTCATTTAAAAGT
24983 CATGTATTTTCA
1 CATGTATTTTCA
24995 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 6 0.20
21 13 0.43
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAGT
Found at i:45703 original size:20 final size:20
Alignment explanation
Indices: 45678--45727 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
45668 CTTTAAGGAG
*
45678 TATCGATACTC-GAGGTTCGA
1 TATCGATACTCAGAGGAT-GA
*
45698 TATCGATACTCAGAGGATGG
1 TATCGATACTCAGAGGATGA
45718 TATCGATACT
1 TATCGATACT
45728 AATGACAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
20 22 0.81
21 5 0.19
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (20 bp):
TATCGATACTCAGAGGATGA
Found at i:45887 original size:18 final size:21
Alignment explanation
Indices: 45866--45915 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
45856 TAAAATTGGC
45866 ATCGATACT-A-AGGC-CAGT
1 ATCGATACTGACAGGCTCAGT
45884 ATCGATACTGACAGGCTCAGT
1 ATCGATACTGACAGGCTCAGT
*
45905 ATCGGTACTGA
1 ATCGATACTGA
45916 TGTCCTGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 9 0.32
19 1 0.04
20 4 0.14
21 14 0.50
ACGTcount: A:0.30, C:0.22, G:0.24, T:0.24
Consensus pattern (21 bp):
ATCGATACTGACAGGCTCAGT
Found at i:46206 original size:22 final size:22
Alignment explanation
Indices: 46178--46246 Score: 66
Period size: 22 Copynumber: 3.1 Consensus size: 22
46168 GGTGTTACAA
* * *
46178 CACTTTTTTATCAGTGCAAATG
1 CACTTTTGTACCAGTGCAAAGG
*
46200 CACTTTTGTACCAGTGCTAAGG
1 CACTTTTGTACCAGTGCAAAGG
* ** *
46222 CACTTTAGTATTAGTGCTAAGG
1 CACTTTTGTACCAGTGCAAAGG
46244 CAC
1 CAC
46247 CTCCTTGATT
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (22 bp):
CACTTTTGTACCAGTGCAAAGG
Found at i:54155 original size:23 final size:23
Alignment explanation
Indices: 54112--54161 Score: 91
Period size: 23 Copynumber: 2.2 Consensus size: 23
54102 TATGTGTTTG
*
54112 TTGATATATTTTTTATATTAATT
1 TTGATATATTTTTTATATTAATA
54135 TTGATATATTTTTTATATTAATA
1 TTGATATATTTTTTATATTAATA
54158 TTGA
1 TTGA
54162 AATGGTTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (23 bp):
TTGATATATTTTTTATATTAATA
Found at i:54895 original size:25 final size:25
Alignment explanation
Indices: 54857--54924 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
54847 AGTTTTTGAA
54857 ATAT-TTTTTAAAAATATATATAAT
1 ATATATTTTTAAAAATATATATAAT
*
54881 ATATATTTTTGAAAATATATATAAT
1 ATATATTTTTAAAAATATATATAAT
* *
54906 ATATAGTTTCAAAAA-ATAT
1 ATATATTTTTAAAAATATAT
54925 TTTTCGAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 8 0.21
25 31 0.79
ACGTcount: A:0.50, C:0.01, G:0.03, T:0.46
Consensus pattern (25 bp):
ATATATTTTTAAAAATATATATAAT
Found at i:54910 original size:36 final size:37
Alignment explanation
Indices: 54770--55074 Score: 208
Period size: 38 Copynumber: 8.4 Consensus size: 37
54760 TCCAGAGTTT
* *
54770 TATTTTT-AAAACATTTTTCAAAAAAAATATATAATATA
1 TATTTTTGAAAATATTTTT--AAAAATATATATAATATA
54808 TAATTTTTGAAACAT-TTTTTAAAAATATATATAATATA
1 T-ATTTTTGAAA-ATATTTTTAAAAATATATATAATATA
54846 TAGTTTTTG-AAATATTTTTTAAAAATATATATAATATA
1 TA-TTTTTGAAAATA-TTTTTAAAAATATATATAATATA
54884 TATTTTTGAAAATA----T----ATATA-AT-ATATA
1 TATTTTTGAAAATATTTTTAAAAATATATATAATATA
* *** * ** *
54911 -GTTTCAAAAAATATTTTTCGAAAACGTAAATAATATA
1 TATTTTTGAAAATATTTTT-AAAAATATATATAATATA
* *
54948 TAGTTTTAGAAAACATTTTTTAAAAATATATATAATATA
1 TA-TTTTTGAAAATA-TTTTTAAAAATATATATAATATA
* *** *
54987 TAGTTTTGAAAA-CGCTTTGAAAATATATATAATATA
1 TATTTTTGAAAATATTTTTAAAAATATATATAATATA
* * * * *
55023 TAGTTTAGAAAATATTTTTGAAAACATACATAATATA
1 TATTTTTGAAAATATTTTTAAAAATATATATAATATA
* *
55060 TAGTTTTAAAAATAT
1 TATTTTTGAAAATAT
55075 ATAATATATA
Statistics
Matches: 215, Mismatches: 30, Indels: 45
0.74 0.10 0.16
Matches are distributed among these distances:
26 9 0.04
27 5 0.02
28 2 0.01
29 5 0.02
30 1 0.00
33 1 0.00
35 3 0.01
36 35 0.16
37 46 0.21
38 63 0.29
39 31 0.14
40 13 0.06
41 1 0.00
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.43
Consensus pattern (37 bp):
TATTTTTGAAAATATTTTTAAAAATATATATAATATA
Found at i:54928 original size:63 final size:65
Alignment explanation
Indices: 54823--54960 Score: 165
Period size: 63 Copynumber: 2.2 Consensus size: 65
54813 TTTGAAACAT
* *** * *
54823 TTTTTAAAAATATATATAATATATAGTTTTTGAAATATTTTTT-AAAAATATATATAATATATA-
1 TTTTTGAAAATATATATAATATATAGTTTAAAAAATATTTTTTCAAAAACATAAATAATATATAG
* *
54886 TTTTTGAAAATATATATAATATATAGTTTCAAAAAATA-TTTTTCGAAAACGTAAATAATATATA
1 TTTTTGAAAATATATATAATATATAGTTT-AAAAAATATTTTTTCAAAAACATAAATAATATATA
54950 G
65 G
*
54951 TTTTAGAAAA
1 TTTTTGAAAA
54961 CATTTTTTAA
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
63 33 0.52
64 21 0.33
65 9 0.14
ACGTcount: A:0.48, C:0.02, G:0.06, T:0.44
Consensus pattern (65 bp):
TTTTTGAAAATATATATAATATATAGTTTAAAAAATATTTTTTCAAAAACATAAATAATATATAG
Found at i:55072 original size:37 final size:37
Alignment explanation
Indices: 54883--55074 Score: 217
Period size: 39 Copynumber: 5.1 Consensus size: 37
54873 TATATAATAT
*
54883 ATATTTTTGAAAATATATATAATATATAGTTTCAAAAA
1 ATATTTTTGAAAATATATATAATATATAGTTT-TAAAA
** *
54921 ATATTTTTCGAAAACGTAAATAATATATAGTTTTAGAAA
1 ATATTTTT-GAAAATATATATAATATATAGTTTTA-AAA
* * *
54960 ACATTTTTTAAAAATATATATAATATATAGTTTTGAAA
1 ATA-TTTTTGAAAATATATATAATATATAGTTTTAAAA
***
54998 A-CGCTTTGAAAATATATATAATATATAG-TTTAGAAA
1 ATATTTTTGAAAATATATATAATATATAGTTTTA-AAA
* *
55034 ATATTTTTGAAAACATACATAATATATAGTTTTAAAA
1 ATATTTTTGAAAATATATATAATATATAGTTTTAAAA
55071 ATAT
1 ATAT
55075 ATAATATATA
Statistics
Matches: 128, Mismatches: 20, Indels: 13
0.80 0.12 0.08
Matches are distributed among these distances:
35 3 0.02
36 27 0.21
37 29 0.23
38 17 0.13
39 47 0.37
40 5 0.04
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (37 bp):
ATATTTTTGAAAATATATATAATATATAGTTTTAAAA
Found at i:55078 original size:23 final size:25
Alignment explanation
Indices: 55038--55097 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 25
55028 TAGAAAATAT
55038 TTTTGAAAACATACATAATATATAG
1 TTTTGAAAACATACATAATATATAG
* *
55063 TTTT-AAAA-ATATATAATATATAA
1 TTTTGAAAACATACATAATATATAG
*
55086 TTTAGAAAACAT
1 TTTTGAAAACAT
55098 TTTTGAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 16 0.53
24 8 0.27
25 6 0.20
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (25 bp):
TTTTGAAAACATACATAATATATAG
Found at i:55080 original size:60 final size:61
Alignment explanation
Indices: 55006--55120 Score: 187
Period size: 60 Copynumber: 1.9 Consensus size: 61
54996 AAACGCTTTG
* *
55006 AAAATATATATAATATATAGTTTAGAAAATATTTTTGAAAACATACATAATATATAGTTTT
1 AAAATATATATAATATATAATTTAGAAAACATTTTTGAAAACATACATAATATATAGTTTT
* *
55067 AAAA-ATATATAATATATAATTTAGAAAACATTTTTGAAAATATATATAATATAT
1 AAAATATATATAATATATAATTTAGAAAACATTTTTGAAAACATACATAATATAT
55121 GATTTTGAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
60 46 0.92
61 4 0.08
ACGTcount: A:0.52, C:0.03, G:0.05, T:0.40
Consensus pattern (61 bp):
AAAATATATATAATATATAATTTAGAAAACATTTTTGAAAACATACATAATATATAGTTTT
Found at i:55117 original size:37 final size:35
Alignment explanation
Indices: 55063--55156 Score: 125
Period size: 37 Copynumber: 2.5 Consensus size: 35
55053 TAATATATAG
55063 TTTTAAAAATATATAATATATAATTTAGAAAACAT
1 TTTTAAAAATATATAATATATAATTTAGAAAACAT
* *
55098 TTTTGAAAATATATATAATATATGATTTTGAAAACAT
1 TTTT-AAAA-ATATATAATATATAATTTAGAAAACAT
55135 TTTTCCAAAAAATATATAATAT
1 TTTT---AAAAATATATAATAT
55157 TAGTTTTTTA
Statistics
Matches: 52, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
35 4 0.08
36 4 0.08
37 29 0.56
38 11 0.21
39 4 0.08
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.41
Consensus pattern (35 bp):
TTTTAAAAATATATAATATATAATTTAGAAAACAT
Found at i:62757 original size:37 final size:38
Alignment explanation
Indices: 62697--62925 Score: 308
Period size: 39 Copynumber: 6.1 Consensus size: 38
62687 CGGAGTTTTA
* *
62697 TTTTTGAAACA-TTTTT-AATATATATAT-A-ATATAG
1 TTTTGGAAACATTTTTTGAAAATATATATAATATATAG
*
62731 TTTTGGAAACATTTTTTTTAAAATATATATAATATATAG
1 TTTTGGAAACA-TTTTTTGAAAATATATATAATATATAG
*
62770 TTTTTGAAACATTTTTTGAAAATATATATAATATATAG
1 TTTTGGAAACATTTTTTGAAAATATATATAATATATAG
*
62808 TTTTGAAAACA-TTTTTGAAAATATATATAATATATAG
1 TTTTGGAAACATTTTTTGAAAATATATATAATATATAG
* **
62845 TTTTGGAAAACATTTTTCGAAAACGTATATAATATATAG
1 TTTTGG-AAACATTTTTTGAAAATATATATAATATATAG
*
62884 TTTTGGAAAACATTTTTTGAGAATATATATAATAT-TAG
1 TTTTGG-AAACATTTTTTGAAAATATATATAATATATAG
62922 TTTT
1 TTTT
62926 TAAAAAATAT
Statistics
Matches: 174, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
34 10 0.06
36 5 0.03
37 41 0.24
38 48 0.28
39 70 0.40
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.46
Consensus pattern (38 bp):
TTTTGGAAACATTTTTTGAAAATATATATAATATATAG
Found at i:62985 original size:28 final size:28
Alignment explanation
Indices: 62954--63008 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
62944 TTACATTATA
62954 TTTATTT-TTTATTTAATTATTC-ATTTTG
1 TTTATTTCTTTATTT--TTATTCTATTTTG
62982 TTTATTTCTTTATTTTTATTCTATTTT
1 TTTATTTCTTTATTTTTATTCTATTTT
63009 TTCTTTTTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 6 0.24
28 12 0.48
29 7 0.28
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (28 bp):
TTTATTTCTTTATTTTTATTCTATTTTG
Done.