Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005276.1 Hibiscus syriacus cultivar Beakdansim tig00011933_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: 77155
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:10664 original size:25 final size:28
Alignment explanation
Indices: 10609--10663 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
10599 TTAAGCCTTA
*
10609 TTATTATTATTAGTTAAATAAAAAACTT
1 TTATTATTATTAGGTAAATAAAAAACTT
*
10637 TTATTATTATT-GGTAAA-AAATAACTT
1 TTATTATTATTAGGTAAATAAAAAACTT
10663 T
1 T
10664 AGCTTTGGTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 9 0.36
27 5 0.20
28 11 0.44
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (28 bp):
TTATTATTATTAGGTAAATAAAAAACTT
Found at i:13656 original size:10 final size:10
Alignment explanation
Indices: 13641--13669 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
13631 GGTTTATTTG
13641 TTCATTTTAA
1 TTCATTTTAA
13651 TTCATTTTAA
1 TTCATTTTAA
13661 TTCATTTTA
1 TTCATTTTA
13670 TGTATAGGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.00, T:0.62
Consensus pattern (10 bp):
TTCATTTTAA
Found at i:14014 original size:63 final size:64
Alignment explanation
Indices: 13875--14022 Score: 171
Period size: 63 Copynumber: 2.3 Consensus size: 64
13865 TTTTTATATT
* *
13875 TTATCTTTG-TTTTAGGTATTTTAGTTTAAATAAGTTTTAGTATTTTAATTAGAATTTAGAATA
1 TTATATTTGTTTTTAGGTATTTTAGTTTAAATAAGTTTAAGTATTTTAATTAGAATTTAGAATA
* * *
13938 TTATATTAT-TTTTTAGGTATTTTGGTTTAAAT-AGTTTAAGTGTTTTAATTAGGATTTA-AGAT
1 TTATATT-TGTTTTTAGGTATTTTAGTTTAAATAAGTTTAAGTATTTTAATTAGAATTTAGA-AT
*
14000 G
64 A
*
14001 TT-TAGTTTGTTTTTAGGAATTT
1 TTATA-TTTGTTTTTAGGTATTT
14023 GAAGGCTATA
Statistics
Matches: 73, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
62 4 0.05
63 47 0.64
64 22 0.30
ACGTcount: A:0.28, C:0.01, G:0.16, T:0.55
Consensus pattern (64 bp):
TTATATTTGTTTTTAGGTATTTTAGTTTAAATAAGTTTAAGTATTTTAATTAGAATTTAGAATA
Found at i:14333 original size:161 final size:161
Alignment explanation
Indices: 14161--14483 Score: 574
Period size: 161 Copynumber: 2.0 Consensus size: 161
14151 TTGGTTATGC
* *
14161 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAGCGAAGACTCAATTCTAAACGTGAGAATTGTAA
1 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGACTCAATTCTAAACGTGAAAATTGTAA
*
14226 GGTACTTAAATCGCTTCAGATTTTTCTCTCTGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
66 GGTACTTAAATCGCTTCAGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
*
14291 TTGACATTGATCCGGATATTGTTATGGTTAA
131 TTGACATTGATCCGGATATTGTTACGGTTAA
* *
14322 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGGCTCAATTTTAAACGTGAAAATTGTAA
1 TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGACTCAATTCTAAACGTGAAAATTGTAA
*
14387 GGTACTTAAATCGCTTCGGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
66 GGTACTTAAATCGCTTCAGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
*
14452 TTGACATTGGTCCGGATATTGTTACGGTTAA
131 TTGACATTGATCCGGATATTGTTACGGTTAA
14483 T
1 T
14484 GTTTGAAGAA
Statistics
Matches: 154, Mismatches: 8, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
161 154 1.00
ACGTcount: A:0.29, C:0.16, G:0.17, T:0.37
Consensus pattern (161 bp):
TTAGCTAATTTTCTTTCAAGCCGAAGGCTAAAACGAAGACTCAATTCTAAACGTGAAAATTGTAA
GGTACTTAAATCGCTTCAGATTTTTCTCTATGTTTTCTGAGCTTACTTTTCAAATCAAAACGATT
TTGACATTGATCCGGATATTGTTACGGTTAA
Found at i:14859 original size:16 final size:16
Alignment explanation
Indices: 14817--14877 Score: 54
Period size: 16 Copynumber: 3.8 Consensus size: 16
14807 AAAATCCCCC
*
14817 TTTTATATTTATTACTA
1 TTTTAT-TTTATTATTA
*
14834 -TTAATATTTATTATTA
1 TTTTAT-TTTATTATTA
*
14850 TATTT-TTTTATTTTTA
1 T-TTTATTTTATTATTA
14866 TTTTATTTTATT
1 TTTTATTTTATT
14878 TTAATATATA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
15 3 0.08
16 31 0.84
17 1 0.03
18 2 0.05
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (16 bp):
TTTTATTTTATTATTA
Found at i:14860 original size:10 final size:11
Alignment explanation
Indices: 14837--14891 Score: 60
Period size: 10 Copynumber: 5.0 Consensus size: 11
14827 ATTACTATTA
14837 ATATTTATTATT
1 ATATTTATT-TT
14849 ATATTT-TTTT
1 ATATTTATTTT
*
14859 ATTTTTATTTT
1 ATATTTATTTT
14870 AT-TTTATTTT
1 ATATTTATTTT
*
14880 AATATATATTTT
1 -ATATTTATTTT
14892 CAACTTTGTC
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
10 15 0.39
11 10 0.26
12 13 0.34
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
ATATTTATTTT
Found at i:14878 original size:16 final size:16
Alignment explanation
Indices: 14840--14884 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
14830 ACTATTAATA
*
14840 TTTATTATTATATTTT
1 TTTATTTTTATATTTT
14856 TTTATTTTTAT-TTTAT
1 TTTATTTTTATATTT-T
*
14872 TTTATTTTAATAT
1 TTTATTTTTATAT
14885 ATATTTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 3 0.12
16 21 0.84
17 1 0.04
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (16 bp):
TTTATTTTTATATTTT
Found at i:15307 original size:25 final size:25
Alignment explanation
Indices: 15269--15318 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
15259 TTGTTCTTCT
15269 TTTGGCTCTACTGAGCTAAAGAGAA
1 TTTGGCTCTACTGAGCTAAAGAGAA
*
15294 TTTGGCTCTGCTGAGCTAAAGAGAA
1 TTTGGCTCTACTGAGCTAAAGAGAA
15319 AATGTACAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (25 bp):
TTTGGCTCTACTGAGCTAAAGAGAA
Found at i:16328 original size:127 final size:127
Alignment explanation
Indices: 16100--16328 Score: 307
Period size: 127 Copynumber: 1.8 Consensus size: 127
16090 TCATGGCTGC
* * *
16100 TTCATCACATCTTCATCACGGCTATTGCTCTTCGATTTGGATTTCGATTCTGGTGAGGTTGTTCC
1 TTCATCACATCTTCATCACGGCTATTGCTCTTCGATTTGGACTTCGATTCTAGTGAGATTGTTCC
* * ** * *
16165 AGTATTGTTCTCGATTACATTGGTTTCCTACTTTTTGATCTGGATATTCGATTCCTGATTGT
66 AGTATTGTTCTCGATTAAACTGGCGTACTACATTTTGATCTGGATATTCGATTCCTGATTGT
* *
16227 TTCATCACATCTTTATCACTG-TAGTTGCTCTTCGATTTGGACTTCGATTCTAGTGAGATTGTTC
1 TTCATCACATCTTCATCACGGCTA-TTGCTCTTCGATTTGGACTTCGATTCTAGTGAGATTGTTC
* * * *
16291 TAGTTTTGTTCTCGATTAAACTGGCGTATTGCATTTTG
65 CAGTATTGTTCTCGATTAAACTGGCGTACTACATTTTG
16329 TGCCTTTTTC
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
126 2 0.02
127 84 0.98
ACGTcount: A:0.17, C:0.19, G:0.19, T:0.45
Consensus pattern (127 bp):
TTCATCACATCTTCATCACGGCTATTGCTCTTCGATTTGGACTTCGATTCTAGTGAGATTGTTCC
AGTATTGTTCTCGATTAAACTGGCGTACTACATTTTGATCTGGATATTCGATTCCTGATTGT
Found at i:26859 original size:21 final size:20
Alignment explanation
Indices: 26835--26895 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 20
26825 AACTTTGAAA
26835 AAATGGTTTTCAAAGTTTGAT
1 AAATGGTTTTCAAA-TTTGAT
26856 AAAT-G-TTTC---TTTGA-
1 AAATGGTTTTCAAATTTGAT
*
26870 AAATGATTTTCAAAATTTGAT
1 AAATGGTTTTC-AAATTTGAT
26891 AAATG
1 AAATG
26896 TTTCTTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 14
0.68 0.02 0.30
Matches are distributed among these distances:
14 4 0.12
15 5 0.16
16 4 0.12
19 4 0.12
20 6 0.19
21 9 0.28
ACGTcount: A:0.38, C:0.05, G:0.15, T:0.43
Consensus pattern (20 bp):
AAATGGTTTTCAAATTTGAT
Found at i:26941 original size:36 final size:36
Alignment explanation
Indices: 26827--26948 Score: 158
Period size: 35 Copynumber: 3.4 Consensus size: 36
26817 TGGTAACCAA
*
26827 CTTTGAAAAAATGGTTTTCAAAGTTTGATAAATGTTT
1 CTTTG-AAAAATGATTTTCAAAGTTTGATAAATGTTT
*
26864 CTTTG-AAAATGATTTTCAAAATTTGATAAATGTTT
1 CTTTGAAAAATGATTTTCAAAGTTTGATAAATGTTT
* * *
26899 CTTTGAAAAATAGTTTTTCAAAGTTTGTTAGATGTTT
1 CTTTGAAAAAT-GATTTTCAAAGTTTGATAAATGTTT
*
26936 -GTTGAAAAATGAT
1 CTTTGAAAAATGAT
26949 AATGGGATAA
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
35 35 0.47
36 14 0.19
37 26 0.35
ACGTcount: A:0.35, C:0.05, G:0.16, T:0.44
Consensus pattern (36 bp):
CTTTGAAAAATGATTTTCAAAGTTTGATAAATGTTT
Found at i:31228 original size:31 final size:31
Alignment explanation
Indices: 31140--31234 Score: 93
Period size: 31 Copynumber: 3.1 Consensus size: 31
31130 GAACCTCGGC
* * * *
31140 AACTGTCCATAGGTCCCAAAAAACCTAGGTA
1 AACTGTCCATATGTCTCAAAAGACATAGGTA
***
31171 AACTGTCCATATGT-TCCTTAGAACATAGGTA
1 AACTGTCCATATGTCTCAAAAG-ACATAGGTA
* *
31202 TACTGTCCATATGTCTCGAAAGACATAGGTA
1 AACTGTCCATATGTCTCAAAAGACATAGGTA
31233 AA
1 AA
31235 ACCCTCGACT
Statistics
Matches: 50, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
30 2 0.04
31 44 0.88
32 4 0.08
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCTCAAAAGACATAGGTA
Found at i:31400 original size:17 final size:19
Alignment explanation
Indices: 31368--31403 Score: 58
Period size: 17 Copynumber: 2.0 Consensus size: 19
31358 CATATATCTC
31368 ATATCATATCACATGTATT
1 ATATCATATCACATGTATT
31387 ATAT-ATAT-ACATGTATT
1 ATATCATATCACATGTATT
31404 CATGTAAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.53
18 4 0.24
19 4 0.24
ACGTcount: A:0.39, C:0.11, G:0.06, T:0.44
Consensus pattern (19 bp):
ATATCATATCACATGTATT
Found at i:32000 original size:64 final size:64
Alignment explanation
Indices: 31892--32051 Score: 200
Period size: 64 Copynumber: 2.5 Consensus size: 64
31882 CAATGAAGGT
* *
31892 ATGCATCGATGCACTACTTGTGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTT-AATGGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAAT--G
*
31955 G
64 C
* * *
31956 ATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATTTAAATGC
* *
32020 ATGCATCGATGCACTGCATGTGCATCGATGCA
1 ATGCATCGATGCACTACTTGTGCATCGATGCA
32052 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 5 0.06
64 71 0.85
65 5 0.06
66 3 0.04
ACGTcount: A:0.26, C:0.20, G:0.19, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAATGC
Found at i:34976 original size:31 final size:31
Alignment explanation
Indices: 34938--35032 Score: 111
Period size: 31 Copynumber: 3.1 Consensus size: 31
34928 GAACCTCGGC
* *
34938 AACTGTCCATAGGTCCCAAAGAACCTAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* **
34969 AACTGTCCATATGTTCCTTAGAACATAGGTA
1 AACTGTCCATATGTCCCAAAGAACATAGGTA
* *
35000 TACTGTCCATATGTCTCGAAAG-ACATAGGTA
1 AACTGTCCATATGTC-CCAAAGAACATAGGTA
35031 AA
1 AA
35033 ACCCTCGACT
Statistics
Matches: 52, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
31 49 0.94
32 3 0.06
ACGTcount: A:0.35, C:0.21, G:0.18, T:0.26
Consensus pattern (31 bp):
AACTGTCCATATGTCCCAAAGAACATAGGTA
Found at i:35190 original size:21 final size:21
Alignment explanation
Indices: 35166--35205 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35156 CATATATCTC
35166 ATATCATAT-CACATGTATTAT
1 ATAT-ATATACACATGTATTAT
*
35187 ATATATATATACATGTATT
1 ATATATATACACATGTATT
35206 CATGTAAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.10, G:0.05, T:0.45
Consensus pattern (21 bp):
ATATATATACACATGTATTAT
Found at i:35797 original size:64 final size:64
Alignment explanation
Indices: 35689--35848 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 64
35679 CAATGAAGGT
* * *
35689 ATGCATCGATACACTACTTATGCATCGGTGCATAAAATGCATTCGATGTTTT-TATTT-AATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAAT--G
*
35752 G
64 C
* *
35753 ATGCATCGATGCACTCCTTATGCATCGATGCAT-AAATCCTATTCGATGTTTTCTATTTAAATTC
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAAATCC-ATTCGATGTTTTCTATTTAAATGC
* * *
35817 ATGCATCGATGCACTTCATGTGCATCGATGCA
1 ATGCATCGATGCACTACTTATGCATCGATGCA
35849 CCTTAAACAA
Statistics
Matches: 84, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
63 5 0.06
64 71 0.85
65 5 0.06
66 3 0.04
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAATCCATTCGATGTTTTCTATTTAAATGC
Found at i:35836 original size:17 final size:18
Alignment explanation
Indices: 35814--35849 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
35804 TCTATTTAAA
35814 TTCA-TGCATCGATGCAC
1 TTCAGTGCATCGATGCAC
35831 TTCATGTGCATCGATGCAC
1 TTCA-GTGCATCGATGCAC
35850 CTTAAACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
19 13 0.76
ACGTcount: A:0.22, C:0.28, G:0.19, T:0.31
Consensus pattern (18 bp):
TTCAGTGCATCGATGCAC
Found at i:37618 original size:21 final size:20
Alignment explanation
Indices: 37594--37657 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
37584 AATTTTGAAA
37594 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
37615 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
37629 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
37650 AAATGTTT
1 AAATGTTT
37658 ATTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:37632 original size:35 final size:35
Alignment explanation
Indices: 37586--37707 Score: 165
Period size: 35 Copynumber: 3.4 Consensus size: 35
37576 TGGTAACCAA
37586 TTTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTT
1 TTTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTT
*
37622 TCTTTG-AAAATGGTTTTCAAAGTTTGGTAAATGTT
1 T-TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTT
* *
37657 TATTTGAAAAATAATTTTTCAAAGTTTGGTAGATGTT
1 T-TTTGAAAAATGA-TTTTCAAAGTTTGGTAAATGTT
*
37694 TGTTGAAAAATGAT
1 TTTTGAAAAATGAT
37708 AATGGGATAA
Statistics
Matches: 76, Mismatches: 7, Indels: 7
0.84 0.08 0.08
Matches are distributed among these distances:
35 34 0.45
36 16 0.21
37 26 0.34
ACGTcount: A:0.34, C:0.03, G:0.18, T:0.44
Consensus pattern (35 bp):
TTTTGAAAAATGATTTTCAAAGTTTGGTAAATGTT
Found at i:44682 original size:29 final size:30
Alignment explanation
Indices: 44642--44712 Score: 99
Period size: 29 Copynumber: 2.4 Consensus size: 30
44632 AAAAGAATAT
*
44642 AAAATATATTTTATTCTTATTTTAA-ATTA
1 AAAATATATTTTATTCTTATCTTAACATTA
* *
44671 AAAATATATTTTATTGTTATCTTAACTTTTA
1 AAAATATATTTTATTCTTATCTTAAC-ATTA
44702 AAAATATATTT
1 AAAATATATTT
44713 AAACATCTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
29 23 0.62
31 14 0.38
ACGTcount: A:0.41, C:0.04, G:0.01, T:0.54
Consensus pattern (30 bp):
AAAATATATTTTATTCTTATCTTAACATTA
Found at i:44830 original size:29 final size:28
Alignment explanation
Indices: 44796--44898 Score: 124
Period size: 29 Copynumber: 3.7 Consensus size: 28
44786 TTTATAAAAG
44796 TTAAAATAAGAATAAAATATACTTTTAAT
1 TTAAAATAAGAATAAAATATA-TTTTAAT
44825 TTAAAATAAGAATAAAATATATTTTCAAT
1 TTAAAATAAGAATAAAATATATTTT-AAT
*
44854 TTAAAATAA-AAT---ATATATTTTTAT
1 TTAAAATAAGAATAAAATATATTTTAAT
**
44878 ATTAAAATAATTATAAAATAT
1 -TTAAAATAAGAATAAAATAT
44899 TTTAATATAT
Statistics
Matches: 66, Mismatches: 2, Indels: 12
0.82 0.03 0.15
Matches are distributed among these distances:
24 2 0.03
25 18 0.27
26 2 0.03
28 7 0.11
29 37 0.56
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (28 bp):
TTAAAATAAGAATAAAATATATTTTAAT
Found at i:44832 original size:23 final size:24
Alignment explanation
Indices: 44806--44887 Score: 85
Period size: 25 Copynumber: 3.2 Consensus size: 24
44796 TTAAAATAAG
*
44806 AATAAAATATA-CTTTTAATTTAA
1 AATAAAATATATATTTTAATTTAA
44829 AATAAGAATAAAATATATTTTCAATTTAA
1 AATAA-AAT---ATATATTTT-AATTTAA
*
44858 AATAAAATATATATTTTTATATTAA
1 AATAAAATATATATTTTAAT-TTAA
44883 AATAA
1 AATAA
44888 TTATAAAATA
Statistics
Matches: 50, Mismatches: 2, Indels: 12
0.78 0.03 0.19
Matches are distributed among these distances:
23 5 0.10
24 5 0.10
25 18 0.36
27 3 0.06
28 7 0.14
29 12 0.24
ACGTcount: A:0.55, C:0.02, G:0.01, T:0.41
Consensus pattern (24 bp):
AATAAAATATATATTTTAATTTAA
Found at i:44882 original size:25 final size:23
Alignment explanation
Indices: 44835--44887 Score: 70
Period size: 23 Copynumber: 2.2 Consensus size: 23
44825 TTAAAATAAG
44835 AATAAAATATATTTTCAATTTAA
1 AATAAAATATATTTTCAATTTAA
**
44858 AATAAAATATATATTTTTATATTAA
1 AATAAAATATAT-TTTCAAT-TTAA
44883 AATAA
1 AATAA
44888 TTATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
23 12 0.46
24 5 0.19
25 9 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (23 bp):
AATAAAATATATTTTCAATTTAA
Found at i:45061 original size:28 final size:30
Alignment explanation
Indices: 45001--45063 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 30
44991 ATAAAAAATG
*
45001 TATTTAATAAGTTAAGACAAAATTAAAATA
1 TATTTAATAAGTTAAGACAAAATTAAAAGA
*
45031 TATTTAATAAGTTTA-A-AAAA-TAAAAGGA
1 TATTTAATAAGTTAAGACAAAATTAAAA-GA
45059 TATTT
1 TATTT
45064 TTAAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
27 5 0.17
28 10 0.33
29 1 0.03
30 14 0.47
ACGTcount: A:0.54, C:0.02, G:0.08, T:0.37
Consensus pattern (30 bp):
TATTTAATAAGTTAAGACAAAATTAAAAGA
Found at i:45067 original size:30 final size:29
Alignment explanation
Indices: 44988--45055 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
44978 TTTGTACATT
* *
44988 AAAATAAAAAATGTATTTAATAAGTTAAGAC
1 AAAAT-AAAAATATATTTAATAAGTTTA-AC
*
45019 AAAATTAAAATATATTTAATAAGTTTAA-
1 AAAATAAAAATATATTTAATAAGTTTAAC
45047 AAAATAAAA
1 AAAATAAAA
45056 GGATATTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
28 8 0.24
29 1 0.03
30 19 0.58
31 5 0.15
ACGTcount: A:0.62, C:0.01, G:0.06, T:0.31
Consensus pattern (29 bp):
AAAATAAAAATATATTTAATAAGTTTAAC
Found at i:46461 original size:19 final size:19
Alignment explanation
Indices: 46437--46480 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
46427 GACTGCCACG
46437 TATTTTGTTTAATAATAAA
1 TATTTTGTTTAATAATAAA
46456 TATTTTGTTTAATAATAAA
1 TATTTTGTTTAATAATAAA
46475 TATTTT
1 TATTTT
46481 ATTTTTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (19 bp):
TATTTTGTTTAATAATAAA
Found at i:50067 original size:8 final size:8
Alignment explanation
Indices: 50054--50094 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
50044 CTCATTTTCA
50054 GAGAATTT
1 GAGAATTT
50062 GAGAATTT
1 GAGAATTT
*
50070 -AGAGTTT
1 GAGAATTT
*
50077 GGGAATTT
1 GAGAATTT
50085 GAGAATTT
1 GAGAATTT
50093 GA
1 GA
50095 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:50393 original size:128 final size:128
Alignment explanation
Indices: 50165--50921 Score: 1415
Period size: 128 Copynumber: 5.9 Consensus size: 128
50155 TAATCGGAGT
* *
50165 ACTATTCACATGAAGGCGTGTTCCCGGGGGCACGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
50230 CATTGCCCTATTATGTCATTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
50293 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTGAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
50358 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACATATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
50421 ACTATTCACATGAAGACGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
50486 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
50549 ACTATTCACATGAAGGCGCGTTCCCGGTGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
50614 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
*
50677 ACTATTCACATGAAGGCGCGTTCTCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
*
50742 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
* *
50805 ACTATTCACATGAAGGCGCGTTCCCAGGGGCGCGCCTTCCATTATTTTGTAAGAGAATATGTTAT
1 ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
50870 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
66 CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTA
50922 AATCAGGTAA
Statistics
Matches: 613, Mismatches: 16, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
128 613 1.00
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.33
Consensus pattern (128 bp):
ACTATTCACATGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTAT
CATTGCCCTATTATGTCACTCATGTCCCTCGGGGACACTAGATATATCAGTACCTATTATTTC
Found at i:51297 original size:30 final size:31
Alignment explanation
Indices: 51261--51321 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
51251 TGTGAACTAT
* *
51261 AATTGGAATA-TAACTTTTAATTTCGAATAC
1 AATTGGAATATTAAATTTAAATTTCGAATAC
51291 AATTGGAATATTAAATTTAAATTTCGAATAC
1 AATTGGAATATTAAATTTAAATTTCGAATAC
51322 TATAATCGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
30 10 0.36
31 18 0.64
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (31 bp):
AATTGGAATATTAAATTTAAATTTCGAATAC
Found at i:51373 original size:34 final size:33
Alignment explanation
Indices: 51335--51433 Score: 128
Period size: 34 Copynumber: 3.0 Consensus size: 33
51325 AATCGGAATG
*
51335 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTT-TATTTTAAAT
* * * *
51369 TTAAATTTTGAATAATATTATTTT-TTTTTATT
1 TTAAATTTCGAATAATATAATTTTATTTTAAAT
51401 TTAAATTTCGAATAATATAATTTTTATTTTAAA
1 TTAAATTTCGAATAATATAA-TTTTATTTTAAA
51434 AACATTTATC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
32 24 0.44
33 5 0.09
34 25 0.46
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (33 bp):
TTAAATTTCGAATAATATAATTTTATTTTAAAT
Found at i:51414 original size:32 final size:32
Alignment explanation
Indices: 51335--51432 Score: 124
Period size: 32 Copynumber: 3.0 Consensus size: 32
51325 AATCGGAATG
* *
51335 TTAAATTTCGAATACTATAATTTATATTTTAAAT
1 TTAAATTTCGAATAATATAATTT-T-TTTTTAAT
* * *
51369 TTAAATTTTGAATAATATTATTTTTTTTTATT
1 TTAAATTTCGAATAATATAATTTTTTTTTAAT
51401 TTAAATTTCGAATAATATAATTTTTATTTTAA
1 TTAAATTTCGAATAATATAATTTTT-TTTTAA
51433 AAACATTTAT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
32 29 0.53
33 6 0.11
34 20 0.36
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (32 bp):
TTAAATTTCGAATAATATAATTTTTTTTTAAT
Found at i:51982 original size:21 final size:21
Alignment explanation
Indices: 51958--52040 Score: 71
Period size: 21 Copynumber: 4.0 Consensus size: 21
51948 ATAAAATCCT
*
51958 GCGGGCTAGGCATGTAACCTG
1 GCGGGCTAGGAATGTAACCTG
*
51979 GCGGGCTCGGAATGTAACCCT-
1 GCGGGCTAGGAATGTAA-CCTG
* * *
52000 GCAGGCTCGAAATGTAACCCT-
1 GCGGGCTAGGAATGTAA-CCTG
* *
52021 GCGGGCTCGGAATATAACCT
1 GCGGGCTAGGAATGTAACCT
52041 CGCCGAAAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
20 3 0.06
21 48 0.89
22 3 0.06
ACGTcount: A:0.23, C:0.27, G:0.31, T:0.19
Consensus pattern (21 bp):
GCGGGCTAGGAATGTAACCTG
Found at i:53467 original size:17 final size:16
Alignment explanation
Indices: 53422--53475 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
53412 TACATTATAA
53422 AAAATAAAAATTAATTT
1 AAAATAAAAA-TAATTT
* * *
53439 AAATTCATAATAACTTT
1 AAAATAAAAATAA-TTT
53456 AAAATAAAAATAAATTT
1 AAAATAAAAAT-AATTT
53473 AAA
1 AAA
53476 TATTAACATT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
16 3 0.10
17 24 0.83
18 2 0.07
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (16 bp):
AAAATAAAAATAATTT
Found at i:53679 original size:30 final size:32
Alignment explanation
Indices: 53615--53693 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
53605 TTAATAATTC
*
53615 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAA
*
53649 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATAATTACATAAATATTATTTAA
53679 TATAAAATATAATAA
1 TA-AAAA-ATAATAA
53694 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.15
31 4 0.10
32 8 0.20
33 18 0.45
34 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTTAA
Found at i:53998 original size:50 final size:50
Alignment explanation
Indices: 53904--53999 Score: 131
Period size: 50 Copynumber: 1.9 Consensus size: 50
53894 TGGAAGACGA
* * * *
53904 GTCCCCAGGGATGCGCTTTCCACACGTGGCAGTCGAGCTGGCGAAAGCGC
1 GTCCCCAGGGATGCGCCTTCCACACGTGGCAGTCCAACTAGCGAAAGCGC
*
53954 GTCCCCGGGGATGCGCCTTCCACACGTGGCA-TCCAACTCAGCGAAA
1 GTCCCCAGGGATGCGCCTTCCACACGTGGCAGTCCAACT-AGCGAAA
54000 ACACGGGTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 5 0.12
50 35 0.88
ACGTcount: A:0.20, C:0.34, G:0.30, T:0.16
Consensus pattern (50 bp):
GTCCCCAGGGATGCGCCTTCCACACGTGGCAGTCCAACTAGCGAAAGCGC
Found at i:65432 original size:10 final size:10
Alignment explanation
Indices: 65419--65463 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
65409 GTTTTTTTTA
65419 ATTAAAATAT
1 ATTAAAATAT
65429 ATT-AAAT-T
1 ATTAAAATAT
*
65437 A-TAAAATAG
1 ATTAAAATAT
*
65446 ATAAAAATAT
1 ATTAAAATAT
65456 ATTAAAAT
1 ATTAAAAT
65464 TAGATAAATA
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
7 1 0.04
8 6 0.21
9 5 0.18
10 16 0.57
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:76149 original size:17 final size:18
Alignment explanation
Indices: 76127--76160 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
76117 TCAGCCGGTC
76127 CGGTTC-GAACGGTTCAA
1 CGGTTCTGAACGGTTCAA
*
76144 CGGTTCTGACCGGTTCA
1 CGGTTCTGAACGGTTCA
76161 CTAGTAGCGG
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:0.18, C:0.26, G:0.29, T:0.26
Consensus pattern (18 bp):
CGGTTCTGAACGGTTCAA
Done.