Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003108.1 Hibiscus syriacus cultivar Beakdansim tig00006492_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: 126883
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:15074 original size:2 final size:2
Alignment explanation
Indices: 15067--15099 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
15057 AACAAAATGC
15067 AT AT AT AT 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 AT AT AT AT A
15100 AATGGTGGCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15152 original size:22 final size:22
Alignment explanation
Indices: 15127--15205 Score: 70
Period size: 22 Copynumber: 3.6 Consensus size: 22
15117 CGGTTAATAG
15127 AAGTGCCTTAGCACTGGTCCTA
1 AAGTGCCTTAGCACTGGTCCTA
* * **
15149 AAGTGCCTCAGCACT-GACACGG
1 AAGTGCCTTAGCACTGGTC-CTA
* * *
15171 AAGTGCATTAGCACTGATACTA
1 AAGTGCCTTAGCACTGGTCCTA
*
15193 AAGTACCTTAGCA
1 AAGTGCCTTAGCA
15206 TTGTTGGGGA
Statistics
Matches: 42, Mismatches: 13, Indels: 4
0.71 0.22 0.07
Matches are distributed among these distances:
21 2 0.05
22 40 0.95
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (22 bp):
AAGTGCCTTAGCACTGGTCCTA
Found at i:21089 original size:27 final size:27
Alignment explanation
Indices: 21051--21109 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
21041 CATGTCTGTT
21051 ATGCCAAGGCAATCATCACGAGAGTGA
1 ATGCCAAGGCAATCATCACGAGAGTGA
21078 ATGCCAAGGCAATCATCACGAGAGTGA
1 ATGCCAAGGCAATCATCACGAGAGTGA
21105 ATGCC
1 ATGCC
21110 TGACAAACCA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.36, C:0.24, G:0.25, T:0.15
Consensus pattern (27 bp):
ATGCCAAGGCAATCATCACGAGAGTGA
Found at i:21817 original size:23 final size:23
Alignment explanation
Indices: 21790--21848 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
21780 TAAATTAATG
*
21790 CACCGAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAGAAATA
* *
21813 CACCGAAGTGCCGCGTAGAAATG
1 CACCGAAGTGCCACGTAGAAATA
21836 CACCGAAGTGCCA
1 CACCGAAGTGCCA
21849 TATAAGATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.32, C:0.29, G:0.25, T:0.14
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAAATA
Found at i:30451 original size:23 final size:23
Alignment explanation
Indices: 30414--30503 Score: 101
Period size: 23 Copynumber: 3.9 Consensus size: 23
30404 TACCACAGCT
* * *
30414 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATACACCGAAGTGCCG
* *
30437 CGTAGAATTGA-ACCGAAGTACCG
1 CGTAGAAAT-ACACCGAAGTGCCG
*
30460 CATAGAAATACACCGAAGTGCCG
1 CGTAGAAATACACCGAAGTGCCG
*
30483 CGTAGAAATACACCAAAGTGC
1 CGTAGAAATACACCGAAGTGC
30504 ATATAAGATG
Statistics
Matches: 55, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
22 1 0.02
23 54 0.98
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (23 bp):
CGTAGAAATACACCGAAGTGCCG
Found at i:38580 original size:19 final size:19
Alignment explanation
Indices: 38554--38594 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
38544 TTCTTTTTGA
38554 TTTATTCCTTTATTTTA-T
1 TTTATTCCTTTATTTTACT
*
38572 TTTATTTCCTTTTTTTTACT
1 TTTA-TTCCTTTATTTTACT
38592 TTT
1 TTT
38595 CTCTCTCCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 12 0.60
20 4 0.20
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTATTCCTTTATTTTACT
Found at i:38726 original size:26 final size:22
Alignment explanation
Indices: 38669--38723 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
38659 CCCATTTACC
38669 CCATCCACTCATTTCTTTTCAA
1 CCATCCACTCATTTCTTTTCAA
*
38691 CCGTCCACTCATTTCTTTTCAA
1 CCATCCACTCATTTCTTTTCAA
38713 CCATCCACTCA
1 CCATCCACTCA
38724 CTCCACCTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.22, C:0.40, G:0.02, T:0.36
Consensus pattern (22 bp):
CCATCCACTCATTTCTTTTCAA
Found at i:43165 original size:18 final size:18
Alignment explanation
Indices: 43144--43275 Score: 93
Period size: 19 Copynumber: 7.6 Consensus size: 18
43134 TATACATTAC
43144 ATATATATAATTTTGAAA
1 ATATATATAATTTTGAAA
* *
43162 ATATATAAAATTTT-ATGA
1 ATATATATAATTTTGA-AA
*
43180 ATATATATAGTATTTGAAA
1 ATATATATAAT-TTTGAAA
43199 ATATATATAACTTTT---A
1 ATATATATAA-TTTTGAAA
* *
43215 ATATATAT-A-TAT-ATA
1 ATATATATAATTTTGAAA
*
43230 CTATATAT-A-TTTGAAA
1 ATATATATAATTTTGAAA
* *
43246 ATAAATATAGTTTTGAAAA
1 ATATATATAATTTTG-AAA
43265 ATATATATAAT
1 ATATATATAAT
43276 ATATTATATA
Statistics
Matches: 89, Mismatches: 15, Indels: 19
0.72 0.12 0.15
Matches are distributed among these distances:
13 2 0.02
15 12 0.13
16 17 0.19
17 1 0.01
18 27 0.30
19 28 0.31
20 2 0.02
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (18 bp):
ATATATATAATTTTGAAA
Found at i:43225 original size:37 final size:35
Alignment explanation
Indices: 43144--43223 Score: 108
Period size: 37 Copynumber: 2.3 Consensus size: 35
43134 TATACATTAC
43144 ATATATATAATTTTGAAAATATATAAAATTTTATGA
1 ATATATATAATTTTGAAAATATATAAAATTTTAT-A
* * *
43180 ATATATATAGTATTTGAAAATATATATAACTTT-TA
1 ATATATATAAT-TTTGAAAATATATAAAATTTTATA
43215 ATATATATA
1 ATATATATA
43224 TATATACTAT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
35 10 0.25
36 11 0.28
37 19 0.47
ACGTcount: A:0.49, C:0.01, G:0.05, T:0.45
Consensus pattern (35 bp):
ATATATATAATTTTGAAAATATATAAAATTTTATA
Found at i:43246 original size:47 final size:48
Alignment explanation
Indices: 43183--43287 Score: 133
Period size: 47 Copynumber: 2.2 Consensus size: 48
43173 TTTATGAATA
* *
43183 TATATAGTATTTGAAAATATATATAACTTTT-AATATATATAT-ATATAC
1 TATATA-TATTTGAAAATAAATAT-ACTTTTAAAAATATATATAATATAC
* *
43231 TATATATATTTGAAAATAAATATAGTTTTGAAAAATATATATAATATAT
1 TATATATATTTGAAAATAAATATACTTTT-AAAAATATATATAATATAC
43280 TATATATA
1 TATATATA
43288 GTGTATATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
46 5 0.10
47 16 0.32
48 16 0.32
49 13 0.26
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.45
Consensus pattern (48 bp):
TATATATATTTGAAAATAAATATACTTTTAAAAATATATATAATATAC
Found at i:43307 original size:23 final size:25
Alignment explanation
Indices: 43266--43312 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
43256 TTTTGAAAAA
*
43266 TATATATAATATATTATATATAGTG
1 TATATATAATATATCATATATAGTG
43291 TATAT-TAATATA-CATATATAGT
1 TATATATAATATATCATATATAGT
43313 TTCTTAAAGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 9 0.43
24 7 0.33
25 5 0.24
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (25 bp):
TATATATAATATATCATATATAGTG
Found at i:46662 original size:39 final size:39
Alignment explanation
Indices: 46606--46739 Score: 128
Period size: 39 Copynumber: 3.4 Consensus size: 39
46596 ACATAAGAGC
* * *
46606 CTACGGTAAAGAGTTACCATGTTCACAAAGCAAATGAGT
1 CTACGGTAAGGACTTACCATGTGCACAAAGCAAATGAGT
*
46645 CTACGGTAAGGACTTACCATGTGGC-CAAAG-AATAGGAGT
1 CTACGGTAAGGACTTACCATGT-GCACAAAGCAA-ATGAGT
* ** * * * *
46684 TTGGGGTAAGGATTTACCCTGTGAACAAAGCAAATGAGC
1 CTACGGTAAGGACTTACCATGTGCACAAAGCAAATGAGT
*
46723 CTACAGTAAGGACTTAC
1 CTACGGTAAGGACTTAC
46740 AAGTCATATA
Statistics
Matches: 74, Mismatches: 17, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
38 3 0.04
39 68 0.92
40 3 0.04
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (39 bp):
CTACGGTAAGGACTTACCATGTGCACAAAGCAAATGAGT
Found at i:47660 original size:27 final size:27
Alignment explanation
Indices: 47616--47698 Score: 94
Period size: 28 Copynumber: 3.0 Consensus size: 27
47606 CATTCCAACG
** *
47616 AGGGTATTTCAGTCATTTTAAAGCTCG
1 AGGGTATTTTGGTCATTTTAAAGCTCA
* * *
47643 ATGGTATTTTGGTTATTTTTAAATCTCA
1 AGGGTATTTTGGTCA-TTTTAAAGCTCA
*
47671 AGGGTATTTTGGTCATTTTAAAGTTCA
1 AGGGTATTTTGGTCATTTTAAAGCTCA
47698 A
1 A
47699 TCATAGAGTA
Statistics
Matches: 45, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
27 22 0.49
28 23 0.51
ACGTcount: A:0.27, C:0.10, G:0.19, T:0.45
Consensus pattern (27 bp):
AGGGTATTTTGGTCATTTTAAAGCTCA
Found at i:48739 original size:15 final size:15
Alignment explanation
Indices: 48719--48755 Score: 65
Period size: 15 Copynumber: 2.5 Consensus size: 15
48709 TTTTATATAG
48719 GAGAGAAAAAATAAA
1 GAGAGAAAAAATAAA
*
48734 GAGAGAAAAAATAGA
1 GAGAGAAAAAATAAA
48749 GAGAGAA
1 GAGAGAA
48756 TTATAAACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.05
Consensus pattern (15 bp):
GAGAGAAAAAATAAA
Found at i:50198 original size:21 final size:19
Alignment explanation
Indices: 50160--50205 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
50150 AATTAATCCT
50160 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
50180 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
50201 A-TAAT
1 ACTAAT
50206 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:53163 original size:18 final size:18
Alignment explanation
Indices: 53130--53193 Score: 74
Period size: 18 Copynumber: 3.4 Consensus size: 18
53120 ATTTTATTTT
**
53130 CAAAAAAACTAAAAAAAAA
1 CAAAAAAAC-AAAAAAAGC
*
53149 CAAAAAGAGCCAAAAAAAGC
1 CAAAAA-A-ACAAAAAAAGC
53169 CAAAAAAACAAAAAAAGC
1 CAAAAAAACAAAAAAAGC
53187 CAAAAAA
1 CAAAAAA
53194 GCCAAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
18 17 0.44
19 7 0.18
20 14 0.36
21 1 0.03
ACGTcount: A:0.77, C:0.16, G:0.06, T:0.02
Consensus pattern (18 bp):
CAAAAAAACAAAAAAAGC
Found at i:53190 original size:10 final size:10
Alignment explanation
Indices: 53130--53200 Score: 78
Period size: 10 Copynumber: 7.5 Consensus size: 10
53120 ATTTTATTTT
53130 CAAAAAAA-C
1 CAAAAAAAGC
* **
53139 TAAAAAAAAA
1 CAAAAAAAGC
*
53149 CAAAAAGAGC
1 CAAAAAAAGC
53159 CAAAAAAAGC
1 CAAAAAAAGC
53169 CAAAAAAA--
1 CAAAAAAAGC
53177 CAAAAAAAGC
1 CAAAAAAAGC
53187 C-AAAAAAGC
1 CAAAAAAAGC
53196 CAAAA
1 CAAAA
53201 TTTAAAAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
8 8 0.16
9 16 0.31
10 27 0.53
ACGTcount: A:0.75, C:0.17, G:0.07, T:0.01
Consensus pattern (10 bp):
CAAAAAAAGC
Found at i:53191 original size:9 final size:9
Alignment explanation
Indices: 53149--53200 Score: 68
Period size: 9 Copynumber: 5.6 Consensus size: 9
53139 TAAAAAAAAA
53149 CAAAAAGAGC
1 CAAAAA-AGC
53159 CAAAAAAAGC
1 C-AAAAAAGC
*
53169 CAAAAAAAC
1 CAAAAAAGC
*
53178 AAAAAAAGC
1 CAAAAAAGC
53187 CAAAAAAGC
1 CAAAAAAGC
53196 CAAAA
1 CAAAA
53201 TTTAAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
9 27 0.73
10 5 0.14
11 5 0.14
ACGTcount: A:0.71, C:0.19, G:0.10, T:0.00
Consensus pattern (9 bp):
CAAAAAAGC
Found at i:53217 original size:27 final size:27
Alignment explanation
Indices: 53142--53200 Score: 100
Period size: 28 Copynumber: 2.1 Consensus size: 27
53132 AAAAAACTAA
*
53142 AAAAAAACAAAAAGAGCCAAAAAAAGCC
1 AAAAAAACAAAAAAAGCC-AAAAAAGCC
53170 AAAAAAACAAAAAAAGCCAAAAAAGCC
1 AAAAAAACAAAAAAAGCCAAAAAAGCC
53197 AAAA
1 AAAA
53201 TTTAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 13 0.43
28 17 0.57
ACGTcount: A:0.75, C:0.17, G:0.08, T:0.00
Consensus pattern (27 bp):
AAAAAAACAAAAAAAGCCAAAAAAGCC
Found at i:61763 original size:12 final size:12
Alignment explanation
Indices: 61745--61796 Score: 63
Period size: 12 Copynumber: 4.5 Consensus size: 12
61735 ATTTTTTGAA
*
61745 ATTTTGGCTTTT
1 ATTTTGCCTTTT
* *
61757 TTTTTG-GTTTT
1 ATTTTGCCTTTT
61768 -TTTTGCCTTTT
1 ATTTTGCCTTTT
61779 ATTTTGCCTTTT
1 ATTTTGCCTTTT
61791 ATTTTG
1 ATTTTG
61797 TTTTCTTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
10 5 0.14
11 8 0.23
12 22 0.63
ACGTcount: A:0.06, C:0.10, G:0.13, T:0.71
Consensus pattern (12 bp):
ATTTTGCCTTTT
Found at i:61771 original size:22 final size:22
Alignment explanation
Indices: 61746--61813 Score: 61
Period size: 22 Copynumber: 3.1 Consensus size: 22
61736 TTTTTTGAAA
*
61746 TTTTGGCTTTTTTTTTGGTTTT
1 TTTTGGCTTTTATTTTGGTTTT
* *
61768 TTTTGCCTTTTATTTTGCCTTTT
1 TTTTGGCTTTTATTTTG-GTTTT
*
61791 ATTTT-G-TTTTCTTTT-GTTTT
1 -TTTTGGCTTTTATTTTGGTTTT
61811 TTT
1 TTT
61814 GAAAAAAAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
19 3 0.08
20 4 0.11
22 23 0.61
23 4 0.11
24 4 0.11
ACGTcount: A:0.03, C:0.09, G:0.12, T:0.76
Consensus pattern (22 bp):
TTTTGGCTTTTATTTTGGTTTT
Found at i:65815 original size:12 final size:12
Alignment explanation
Indices: 65800--65863 Score: 65
Period size: 12 Copynumber: 5.3 Consensus size: 12
65790 TTGGGGTGGC
65800 TTTTTTTTTGTT
1 TTTTTTTTTGTT
**
65812 TTTTTTTTTGCC
1 TTTTTTTTTGTT
* **
65824 TTTTGTTTTGCC
1 TTTTTTTTTGTT
* *
65836 TTTTGTTGTGTT
1 TTTTTTTTTGTT
65848 TTTTTTTTTGTT
1 TTTTTTTTTGTT
65860 TTTT
1 TTTT
65864 GAAAAAAAAT
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 44 1.00
ACGTcount: A:0.00, C:0.06, G:0.12, T:0.81
Consensus pattern (12 bp):
TTTTTTTTTGTT
Found at i:71890 original size:22 final size:21
Alignment explanation
Indices: 71865--71910 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 21
71855 TTTTTGGAAA
*
71865 TTTTGGCTTTTTTTTTTTTGTT
1 TTTTGGCTTTTTTTGTTTT-TT
71887 TTTTGGCTTTTTTTGTTTTTT
1 TTTTGGCTTTTTTTGTTTTTT
71908 TTT
1 TTT
71911 GTTTTTTTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.00, C:0.04, G:0.13, T:0.83
Consensus pattern (21 bp):
TTTTGGCTTTTTTTGTTTTTT
Found at i:85974 original size:390 final size:386
Alignment explanation
Indices: 85255--86034 Score: 1088
Period size: 389 Copynumber: 2.0 Consensus size: 386
85245 CACTCCAATT
85255 TGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGTGTTTGCCTTTTCATTGCG
1 TGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGTGTTTGCCTTTTCATTGCG
* * *
85320 ACTAGGAGGGCTTGATAGGATATTATCCATCGATTTTCCACATCCATCCACGCCATCAATCATCT
66 ACTAGGAGGGCTCGATAGGACATTATCCATCGATTTTCCACATCCATCCACACCATCAATCATCT
* * *
85385 TTACCGTTCACTTTCATAAAGGGAGATCTTTGATTTCTTGGTTATTTTCTCTATTCTTAATTCCT
131 TTACCGTTCACCTTCATAAAGGGAGATCTTTGATTTCTTGATTATTTTCTCTATTCTTAATTCAT
* * * * ** *
85450 TTATCTTTTGTTTATCTTATTTTAATCTTATTTGTTTTCTTGTTTTTAGCACTAAAAGAAACCCT
196 TTATCTTTTGTTTATCTTATTCTAATC---TGTGTTGTCTTGATTACAGCACTAAAAGAAACCAT
* * * * *
85515 AAAGAATCCTAGCTATTGTCGCCACCTTCCTCATTCATTCCTTATTGTTCTTCATCGAGTCTAGA
258 AAACAATCCTAGCGACTGCCGCCACCTTCCTCATTCATTCATTATTGTTCTTCATCGAGTCTAGA
**
85580 GCTTTTCTAGGTTTGATTCTTCAACAAGAGCAACGTTCATCAATCCGCCACCGTTTCCCTATCAA
323 GC-TTTCTAGGTTTGATTCTTCAACAAGAGCAACGTTCATCAATCCGCCACCACTTCCCTATCAA
*
85645 TGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCAT-TTATCGTGTTTGTCTTTTCATTGCG
1 TGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGTGTTTGCCTTTTCATTGCG
* **
85709 ACTAGGAGGGCTCGATAGGACACTTATCCATCTATTTTCCACAAATCCATCTGCACCATCAATCA
66 ACTAGGAGGGCTCGATAGGACA-TTATCCATCGATTTTCCAC--ATCCATCCACACCATCAATCA
* * * *
85774 TCTTTACCGTTCACCTTCAT-AAGGGAGATCTTTTGATTTCTTTATTATCTTATTTC-ATTTTTC
128 TCTTTACCGTTCACCTTCATAAAGGGAGATC-TTTGATTTCTTGATTAT-TT-TCTCTATTCTTA
* *
85837 ATTTATTTATCTTTTGTTTATTTTATTCTAATC-GTGTTGTCTTGATTACAGCACATAAAAGAAA
190 ATTCATTTATCTTTTGTTTATCTTATTCTAATCTGTGTTGTCTTGATTACAGCAC-TAAAAGAAA
*
85901 CCATAAACAATCCTAGCGACTGCCGCCACCTTCC-CATATTCA-TCATCT-TTGTTCTTCATCGG
254 CCATAAACAATCCTAGCGACTGCCGCCACCTTCCTC--ATTCATTCAT-TATTGTTCTTCATCGA
* *
85963 GTCTAGAGCTTTCTAGGTTTGATTCTTCAACAAGGGCAATGTTCATCAATCCGCCACCACTTCCC
316 GTCTAGAGCTTTCTAGGTTTGATTCTTCAACAAGAGCAACGTTCATCAATCCGCCACCACTTCCC
86028 TATCAA
381 TATCAA
86034 T
1 T
86035 TGGTATCAGA
Statistics
Matches: 347, Mismatches: 33, Indels: 21
0.87 0.08 0.05
Matches are distributed among these distances:
389 120 0.35
390 120 0.35
391 16 0.05
392 52 0.15
393 36 0.10
394 3 0.01
ACGTcount: A:0.23, C:0.23, G:0.15, T:0.39
Consensus pattern (386 bp):
TGCCTTTTCATCGCGACTAGGAGGGTTGGTTAGAGCCATATTATCGTGTTTGCCTTTTCATTGCG
ACTAGGAGGGCTCGATAGGACATTATCCATCGATTTTCCACATCCATCCACACCATCAATCATCT
TTACCGTTCACCTTCATAAAGGGAGATCTTTGATTTCTTGATTATTTTCTCTATTCTTAATTCAT
TTATCTTTTGTTTATCTTATTCTAATCTGTGTTGTCTTGATTACAGCACTAAAAGAAACCATAAA
CAATCCTAGCGACTGCCGCCACCTTCCTCATTCATTCATTATTGTTCTTCATCGAGTCTAGAGCT
TTCTAGGTTTGATTCTTCAACAAGAGCAACGTTCATCAATCCGCCACCACTTCCCTATCAA
Found at i:86238 original size:10 final size:10
Alignment explanation
Indices: 86195--86231 Score: 74
Period size: 10 Copynumber: 3.7 Consensus size: 10
86185 TATTTTTTTC
86195 AAAAAAACAA
1 AAAAAAACAA
86205 AAAAAAACAA
1 AAAAAAACAA
86215 AAAAAAACAA
1 AAAAAAACAA
86225 AAAAAAA
1 AAAAAAA
86232 GCCAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:87615 original size:10 final size:10
Alignment explanation
Indices: 87600--87636 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
87590 TATTTTTTTC
87600 AAAAAAACAA
1 AAAAAAACAA
87610 AAAAAAACAA
1 AAAAAAACAA
**
87620 AAAAAGGCAA
1 AAAAAAACAA
87630 AAAAAAA
1 AAAAAAA
87637 GCCAAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.86, C:0.08, G:0.05, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:92054 original size:8 final size:8
Alignment explanation
Indices: 92041--92104 Score: 60
Period size: 8 Copynumber: 8.0 Consensus size: 8
92031 CTATTGTTTT
92041 CAAAAAAA
1 CAAAAAAA
92049 CAAAAAAA
1 CAAAAAAA
92057 -AAACAAAA
1 CAAA-AAAA
* *
92065 -AAATAAG
1 CAAAAAAA
92072 CAAAAAAA
1 CAAAAAAA
* *
92080 TAAAAAAGG
1 CAAAAAA-A
92089 CAAAAAAA
1 CAAAAAAA
92097 CAAAAAAA
1 CAAAAAAA
92105 AGCCAAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
7 5 0.11
8 34 0.76
9 6 0.13
ACGTcount: A:0.83, C:0.09, G:0.05, T:0.03
Consensus pattern (8 bp):
CAAAAAAA
Found at i:92076 original size:17 final size:15
Alignment explanation
Indices: 92041--92103 Score: 58
Period size: 17 Copynumber: 3.9 Consensus size: 15
92031 CTATTGTTTT
92041 CAAAAAAACAAAAAA-
1 CAAAAAAA-AAAAAAG
92056 -AAAACAAAAAAATAAG
1 CAAAA-AAAAAAA-AAG
92072 CAAAAAAATAAAAAAGG
1 CAAAAAAA-AAAAAA-G
92089 CAAAAAAACAAAAAA
1 CAAAAAAA-AAAAAA
92104 AAGCCAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
14 8 0.20
15 5 0.12
16 5 0.12
17 23 0.56
ACGTcount: A:0.83, C:0.10, G:0.05, T:0.03
Consensus pattern (15 bp):
CAAAAAAAAAAAAAG
Found at i:92106 original size:19 final size:19
Alignment explanation
Indices: 92053--92112 Score: 70
Period size: 19 Copynumber: 3.2 Consensus size: 19
92043 AAAAAACAAA
*
92053 AAAAAAACAAAAAAATAAGC
1 AAAAAAACAAAAAAA-AGGC
*
92073 -AAAAAA-ATAAAAAAGGC
1 AAAAAAACAAAAAAAAGGC
*
92090 AAAAAAACAAAAAAAAGCC
1 AAAAAAACAAAAAAAAGGC
92109 AAAA
1 AAAA
92113 TTTCAAAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
17 3 0.09
18 12 0.35
19 19 0.56
ACGTcount: A:0.80, C:0.10, G:0.07, T:0.03
Consensus pattern (19 bp):
AAAAAAACAAAAAAAAGGC
Found at i:96707 original size:11 final size:11
Alignment explanation
Indices: 96663--96700 Score: 60
Period size: 11 Copynumber: 3.5 Consensus size: 11
96653 TTCAAAAAAT
96663 AAAAAAAA-AA
1 AAAAAAAACAA
*
96673 CAAAAAAACAA
1 AAAAAAAACAA
96684 AAAAAAAACAA
1 AAAAAAAACAA
96695 AAAAAA
1 AAAAAA
96701 GCCAAAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 7 0.28
11 18 0.72
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAA
Found at i:96707 original size:19 final size:19
Alignment explanation
Indices: 96656--96699 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
96646 TTTTTTTTTC
*
96656 AAAAAATAAAAAAAAAACA
1 AAAAAACAAAAAAAAAACA
96675 AAAAAACAAAAAAAAAACA
1 AAAAAACAAAAAAAAAACA
96694 AAAAAA
1 AAAAAA
96700 AGCCAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.91, C:0.07, G:0.00, T:0.02
Consensus pattern (19 bp):
AAAAAACAAAAAAAAAACA
Found at i:96717 original size:1 final size:1
Alignment explanation
Indices: 96656--96700 Score: 54
Period size: 1 Copynumber: 45.0 Consensus size: 1
96646 TTTTTTTTTC
* * * *
96656 AAAAAATAAAAAAAAAACAAAAAAACAAAAAAAAAACAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
96701 GCCAAAATTT
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:0.91, C:0.07, G:0.00, T:0.02
Consensus pattern (1 bp):
A
Found at i:99105 original size:10 final size:10
Alignment explanation
Indices: 99068--99106 Score: 69
Period size: 10 Copynumber: 3.8 Consensus size: 10
99058 TTGGCTTCTT
99068 TTTTTTTTGCC
1 TTTTTTTTG-C
99079 TTTTTTTTGC
1 TTTTTTTTGC
99089 TTTTTTTTGC
1 TTTTTTTTGC
99099 TTTTTTTT
1 TTTTTTTT
99107 TTTGTTTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
10 19 0.68
11 9 0.32
ACGTcount: A:0.00, C:0.10, G:0.08, T:0.82
Consensus pattern (10 bp):
TTTTTTTTGC
Found at i:99114 original size:11 final size:11
Alignment explanation
Indices: 99066--99116 Score: 50
Period size: 11 Copynumber: 4.5 Consensus size: 11
99056 TTTTGGCTTC
99066 TTTTTTTTTTG
1 TTTTTTTTTTG
**
99077 CCTTTTTTTTG
1 TTTTTTTTTTG
*
99088 -CTTTTTTTTG
1 TTTTTTTTTTG
99098 CTTTTTTTTTTTG
1 --TTTTTTTTTTG
99111 TTTTTT
1 TTTTTT
99117 GAAAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
10 10 0.29
11 15 0.44
13 9 0.26
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (11 bp):
TTTTTTTTTTG
Found at i:99115 original size:13 final size:13
Alignment explanation
Indices: 99066--99116 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 13
99056 TTTTGGCTTC
99066 TTTTTTTTTTGC-
1 TTTTTTTTTTGCT
*
99078 -CTTTTTTTTGC-
1 TTTTTTTTTTGCT
99089 --TTTTTTTTGCT
1 TTTTTTTTTTGCT
99100 TTTTTTTTTTG-T
1 TTTTTTTTTTGCT
99112 TTTTT
1 TTTTT
99117 GAAAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
10 10 0.29
11 10 0.29
12 6 0.17
13 9 0.26
ACGTcount: A:0.00, C:0.08, G:0.08, T:0.84
Consensus pattern (13 bp):
TTTTTTTTTTGCT
Found at i:99116 original size:10 final size:11
Alignment explanation
Indices: 99067--99107 Score: 66
Period size: 11 Copynumber: 3.8 Consensus size: 11
99057 TTTGGCTTCT
99067 TTTTTTTTTGC
1 TTTTTTTTTGC
*
99078 CTTTTTTTTGC
1 TTTTTTTTTGC
99089 -TTTTTTTTGC
1 TTTTTTTTTGC
99099 TTTTTTTTT
1 TTTTTTTTT
99108 TTGTTTTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
10 10 0.36
11 18 0.64
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.83
Consensus pattern (11 bp):
TTTTTTTTTGC
Found at i:99116 original size:21 final size:21
Alignment explanation
Indices: 99068--99107 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
99058 TTGGCTTCTT
99068 TTTTTTTTGCCTTTTTTTTGC
1 TTTTTTTTGCCTTTTTTTTGC
*
99089 TTTTTTTTGCTTTTTTTTT
1 TTTTTTTTGCCTTTTTTTT
99108 TTGTTTTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.00, C:0.10, G:0.07, T:0.82
Consensus pattern (21 bp):
TTTTTTTTGCCTTTTTTTTGC
Found at i:99508 original size:25 final size:25
Alignment explanation
Indices: 99469--99516 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
99459 CGATTAGAAT
99469 AAAATAAAATAAAGATAAATAAATGA
1 AAAATAAAATAAAGAT-AATAAATGA
*
99495 AAAATGAAAT-AAGATAATAAAT
1 AAAATAAAATAAAGATAATAAAT
99517 AAATCAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.33
25 5 0.24
26 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.08, T:0.21
Consensus pattern (25 bp):
AAAATAAAATAAAGATAATAAATGA
Found at i:112408 original size:21 final size:20
Alignment explanation
Indices: 112384--112436 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 20
112374 AGCAGAGAAA
*
112384 GGATCGATCCTTTCTTTCAAG
1 GGATCGATCCTTTCTGT-AAG
112405 GGATCGATCCTTTTCTGTAAG
1 GGATCGATCC-TTTCTGTAAG
*
112426 GGATAGATCCT
1 GGATCGATCCT
112437 CAGTTGGATA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 1 0.03
21 22 0.76
22 6 0.21
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
GGATCGATCCTTTCTGTAAG
Found at i:124829 original size:4 final size:4
Alignment explanation
Indices: 124820--124878 Score: 109
Period size: 4 Copynumber: 14.8 Consensus size: 4
124810 AATATTGAAT
*
124820 ATAC ATAC ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
124868 ATAC ATAC ATA
1 ATAC ATAC ATA
124879 TGGTGGCATT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 53 1.00
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (4 bp):
ATAC
Found at i:124929 original size:22 final size:22
Alignment explanation
Indices: 124904--124973 Score: 61
Period size: 22 Copynumber: 3.2 Consensus size: 22
124894 TTGTTAACGG
*
124904 AAGTACCTTAGCACTGGTACTA
1 AAGTACCTTAGCACTGATACTA
* * * *
124926 AAGTGCCTCAACACTAATA-TA
1 AAGTACCTTAGCACTGATACTA
* *
124947 GAAGTTCATTAGCACTGATACTA
1 -AAGTACCTTAGCACTGATACTA
124970 AAGT
1 AAGT
124974 GCCATAGAAC
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.37, C:0.20, G:0.16, T:0.27
Consensus pattern (22 bp):
AAGTACCTTAGCACTGATACTA
Found at i:125741 original size:20 final size:20
Alignment explanation
Indices: 125718--125803 Score: 113
Period size: 20 Copynumber: 4.3 Consensus size: 20
125708 CTCAGTATAC
* *
125718 ATACTCTAGGGAAAGTATTG
1 ATACTCTTGGGAAAGTATCG
125738 ATACTCTTGGGAAAGTATCG
1 ATACTCTTGGGAAAGTATCG
* *
125758 ATAATCTTGTGGAAAATAT--
1 ATACTCTTG-GGAAAGTATCG
125777 ATACTCTTGGGAAAGTATCG
1 ATACTCTTGGGAAAGTATCG
125797 ATACTCT
1 ATACTCT
125804 CATCTAGAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 6
0.83 0.09 0.09
Matches are distributed among these distances:
18 8 0.14
19 8 0.14
20 33 0.58
21 8 0.14
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.33
Consensus pattern (20 bp):
ATACTCTTGGGAAAGTATCG
Done.