Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008457.1 Hibiscus syriacus cultivar Beakdansim tig00111270_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: 73366
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:8894 original size:39 final size:39
Alignment explanation
Indices: 8812--8895 Score: 96
Period size: 39 Copynumber: 2.2 Consensus size: 39
8802 GCGGTAAAGA
* * * *
8812 CTTACCCTGTGCACAAAGCATAGGAACCTGTGGTCAGGG
1 CTTACACTGTGCACAAAGCAGAGGAACCTATGGTAAGGG
* * * *
8851 CTTACACTGTGCACAAAGCAGATGAGCTTATGGTAAGGT
1 CTTACACTGTGCACAAAGCAGAGGAACCTATGGTAAGGG
8890 CTTACA
1 CTTACA
8896 ACTCATAGAC
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.29, C:0.23, G:0.25, T:0.24
Consensus pattern (39 bp):
CTTACACTGTGCACAAAGCAGAGGAACCTATGGTAAGGG
Found at i:10453 original size:13 final size:13
Alignment explanation
Indices: 10437--10471 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
10427 CGGCTTGGTA
10437 GCTCGACTCAGTG
1 GCTCGACTCAGTG
*
10450 GCTCGAGTCAGTG
1 GCTCGACTCAGTG
*
10463 GCTCAACTC
1 GCTCGACTC
10472 GACTCAGCTC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23
Consensus pattern (13 bp):
GCTCGACTCAGTG
Found at i:10960 original size:23 final size:23
Alignment explanation
Indices: 10925--10983 Score: 91
Period size: 23 Copynumber: 2.6 Consensus size: 23
10915 ATCAAGCACA
* *
10925 ATAACATATTAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
10948 ATAATATAATAGGTAGCGCTTAT
1 ATAATATAATAGGTAGCGCTTAT
*
10971 ATAATAAAATAGG
1 ATAATATAATAGG
10984 CATTAACCGA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.42, C:0.08, G:0.17, T:0.32
Consensus pattern (23 bp):
ATAATATAATAGGTAGCGCTTAT
Found at i:12140 original size:18 final size:18
Alignment explanation
Indices: 12119--12168 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
12109 ACCTTTTCTA
12119 GTTTTGTCATTTTTTCCG
1 GTTTTGTCATTTTTTCCG
*
12137 GTTTTGTCATTTTTTTCG
1 GTTTTGTCATTTTTTCCG
12155 GTTTTGTCATTTTT
1 GTTTTGTCATTTTT
12169 AGACCAGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.06, C:0.12, G:0.16, T:0.66
Consensus pattern (18 bp):
GTTTTGTCATTTTTTCCG
Found at i:14600 original size:23 final size:23
Alignment explanation
Indices: 14574--14621 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
14564 ATAAAGTACA
*
14574 ATAACATACTAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
**
14597 ATAATGTAATAGGTAGCGCTTAT
1 ATAACATAATAGGTAGCGCTTAT
14620 AT
1 AT
14622 TTACCTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.12, G:0.19, T:0.33
Consensus pattern (23 bp):
ATAACATAATAGGTAGCGCTTAT
Found at i:15035 original size:23 final size:23
Alignment explanation
Indices: 15009--15070 Score: 81
Period size: 22 Copynumber: 2.7 Consensus size: 23
14999 ATATAACCAT
15009 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
15032 TACCTATTACA-TATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
15054 TACCTATTACATCATAT
1 TACCTATTACATTATAT
15071 GTTTACCTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
22 19 0.56
23 15 0.44
ACGTcount: A:0.39, C:0.19, G:0.06, T:0.35
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:15431 original size:427 final size:427
Alignment explanation
Indices: 14733--15597 Score: 1657
Period size: 427 Copynumber: 2.0 Consensus size: 427
14723 GGATCGATAC
14733 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
14798 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATACCGT
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATACCGT
14863 AACGTAAAAAATAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAGA
131 AACGTAAAAAATAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAGA
14928 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
196 TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
14993 TTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACA-TATATAAGGGCTAC
261 TTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTAC
15057 CTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA
326 CTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA
15122 C-TTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
391 CTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
15158 TTTAACAGTGTTTCATG-TTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
1 TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
15222 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAA-TTTTAATTTAATAATAATATATACC
66 ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAAT-A-ATATACC
15286 GTAACGTAAAAAATAAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAA
129 GTAACGTAAAAAAT-AATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTC-A
15351 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
192 AAGATAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAG
*
15416 ACACTTTACAATATAATCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
257 ACACTTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGG
15481 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
322 CTACCTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATC
15546 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
387 GATACTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
15587 TTTAACAGTGT
1 TTTAACAGTGT
15598 ACTGCGAATT
Statistics
Matches: 433, Mismatches: 1, Indels: 8
0.98 0.00 0.02
Matches are distributed among these distances:
423 15 0.03
424 87 0.20
425 38 0.09
426 48 0.11
427 119 0.27
428 80 0.18
429 46 0.11
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.40
Consensus pattern (427 bp):
TTTAACAGTGTTTCATGTTTTCCACCTACAATATTGATTTAATAATTTCATTTGCACAAAAAATT
ATTTGATTGTTTTGATATTTTATAAAATATTATTTAGAATTTTTAATTTAATAATAATATACCGT
AACGTAAAAAATAATCATTAGACGCCTATAATTACTAAATTAATATCTTAAAACTCACTCAAAGA
TAACCTTAAATTAATGTTTTCCACAGTGAAAAAAGTATGGACACTTTTATAAAAAGGATAGACAC
TTTACAATATAACCATTACCTATTACATTATATAAACGATACCTATTACATTATATAAGGGCTAC
CTATTACATCATATGTTTACCTATTATATTGAAAGTGTCCATACTTTTTATAAAAAGGATCGATA
CTTTTTTTAAAACTTATGTAATTTATGTTTCAATTTT
Found at i:15462 original size:23 final size:23
Alignment explanation
Indices: 15436--15498 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
15426 ATATAATCAT
15436 TACCTATTACATTATATAAACGA
1 TACCTATTACATTATATAAACGA
** *
15459 TACCTATTACATTATATAAGGGC
1 TACCTATTACATTATATAAACGA
*
15482 TACCTATTACATCATAT
1 TACCTATTACATTATAT
15499 GTTTACCTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 36 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.37
Consensus pattern (23 bp):
TACCTATTACATTATATAAACGA
Found at i:18618 original size:183 final size:184
Alignment explanation
Indices: 18045--18709 Score: 1236
Period size: 183 Copynumber: 3.7 Consensus size: 184
18035 TTTTAAATGG
*
18045 TATGGACATAAAGTACCGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
*
18109 TAAAACCGGTATATTTATACCGGTTATATTACAAAATTATCTA-TACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
18173 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACA-TTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
18226 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
18291 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTAT-A--ATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
18353 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
18407 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
18472 TAAGACCGGTATA-TTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
*
18536 GATGTGTAAAATGTCGACACTTTTTTAAATCGTATCGACACATTTTTCTTCCAA
131 GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
18590 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
1 TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
**
18655 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTTTATTATAAT
66 TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAAT
18710 ATGTTGAAAG
Statistics
Matches: 472, Mismatches: 5, Indels: 11
0.97 0.01 0.02
Matches are distributed among these distances:
180 89 0.19
181 118 0.25
182 78 0.17
183 148 0.31
184 39 0.08
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.35
Consensus pattern (184 bp):
TATGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCGCA
TAAGACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCC
GATGTGTAAAATGTCGACACTTTTTTAAATTGTATCGACACATTTTTCTTCCAA
Found at i:20072 original size:3 final size:3
Alignment explanation
Indices: 20064--20114 Score: 66
Period size: 3 Copynumber: 17.0 Consensus size: 3
20054 ACTTGTTTGG
* * * *
20064 ATC ATC ATC TTC ATC ATC ATC GTC ATC ATC ATC ATC ATC GTC ATC TTC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
20112 ATC
1 ATC
20115 GTCAGCTTCA
Statistics
Matches: 40, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.25, C:0.33, G:0.04, T:0.37
Consensus pattern (3 bp):
ATC
Found at i:20081 original size:12 final size:12
Alignment explanation
Indices: 20064--20126 Score: 81
Period size: 12 Copynumber: 5.2 Consensus size: 12
20054 ACTTGTTTGG
20064 ATCATCATCTTC
1 ATCATCATCTTC
*
20076 ATCATCATCGTC
1 ATCATCATCTTC
*
20088 ATCATCATCATC
1 ATCATCATCTTC
*
20100 ATCGTCATCTTC
1 ATCATCATCTTC
* *
20112 ATCGTCAGCTTC
1 ATCATCATCTTC
20124 ATC
1 ATC
20127 TTCTGCGACC
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 46 1.00
ACGTcount: A:0.24, C:0.33, G:0.06, T:0.37
Consensus pattern (12 bp):
ATCATCATCTTC
Found at i:20125 original size:18 final size:18
Alignment explanation
Indices: 20068--20129 Score: 88
Period size: 18 Copynumber: 3.4 Consensus size: 18
20058 GTTTGGATCA
20068 TCATCTTCATCATCATCG
1 TCATCTTCATCATCATCG
*
20086 TCATCATCATCATCATCG
1 TCATCTTCATCATCATCG
* * *
20104 TCATCTTCATCGTCAGCT
1 TCATCTTCATCATCATCG
20122 TCATCTTC
1 TCATCTTC
20130 TGCGACCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (18 bp):
TCATCTTCATCATCATCG
Found at i:20129 original size:6 final size:6
Alignment explanation
Indices: 20068--20129 Score: 61
Period size: 6 Copynumber: 10.3 Consensus size: 6
20058 GTTTGGATCA
* * * * * *
20068 TCATCT TCATCA TCATCG TCATCA TCATCA TCATCG TCATCT TCATCG
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
*
20116 TCAGCT TCATCT TC
1 TCATCT TCATCT TC
20130 TGCGACCGAT
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
6 47 1.00
ACGTcount: A:0.21, C:0.34, G:0.06, T:0.39
Consensus pattern (6 bp):
TCATCT
Found at i:22157 original size:197 final size:196
Alignment explanation
Indices: 21585--22591 Score: 1744
Period size: 197 Copynumber: 5.1 Consensus size: 196
21575 TTTAAATTAG
*
21585 TATCGACACAAA--ATATTAGTGTCGACACATTATTTAGACATATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
21648 ATTGTA-CGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
*
21712 GACACTTTTTATATATGGATCGACACTTTATTGATTCACCTTGTAAAAATTCATTCTGG-AAAAA
131 GACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAAA
21776 A
196 A
21777 TATCGACACAAACTATA-TAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
21841 ATTGTACCGGTTAGATTAAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* *
21906 CGACACTTTTTATATATGGATCGACACTTTATTGATTCACCTCGTAAAAATTCATTCTGGAAAAA
130 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGG-AAAA
21971 AAA
194 AAA
21974 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
22039 ATTGTA-CGGTTAGATTGAAAAATTACATATTACATTATAC-TTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * ***
22102 CGACACTTTTTATATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
130 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCT-GGAAA
22167 AAAA
193 AAAA
22171 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
22236 ATTGTACCGGTTAGATTGAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
66 ATTGTACCGGTTAGATT-AAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGAT
* * *** *
22301 CGACACTTTTT-TATATGGATCGACACTTTATGGGTGCACCTTGTTTTTAATTCATTCTGGGAAA
130 CGACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTG-TAAAAATTCATTCTGGAAAA
22365 AAA
194 AAA
22368 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACC-GTATA
1 TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
22432 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
66 ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
22497 GACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAAA
131 GACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAAA
22562 A
196 A
*
22563 TATCGACACAAACTATATTAGTATCGACA
1 TATCGACACAAACTATATTAGTGTCGACA
22592 TGACCCTTAA
Statistics
Matches: 785, Mismatches: 18, Indels: 21
0.95 0.02 0.03
Matches are distributed among these distances:
192 12 0.02
193 52 0.07
194 13 0.02
195 211 0.27
196 115 0.15
197 212 0.27
198 136 0.17
199 34 0.04
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.37
Consensus pattern (196 bp):
TATCGACACAAACTATATTAGTGTCGACACATTATTTAGACTTATTCTCTCATAAAACCGGTATA
ATTGTACCGGTTAGATTAAAAATTACATATTACATTATACTTTTGGGTTCGATGATTTTGGGATC
GACACTTTTTATATATGGATCGACACTTTATTGATGCACCTTGTAAAAATTCATTCTGGAAAAAA
A
Found at i:22700 original size:19 final size:19
Alignment explanation
Indices: 22676--22733 Score: 107
Period size: 19 Copynumber: 3.1 Consensus size: 19
22666 CACATAAAAA
22676 ATAAATCGTATACAAAATT
1 ATAAATCGTATACAAAATT
22695 ATAAATCGTATACAAAATT
1 ATAAATCGTATACAAAATT
*
22714 ATAAATCTTATACAAAATT
1 ATAAATCGTATACAAAATT
22733 A
1 A
22734 ACTCGACATT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.33
Consensus pattern (19 bp):
ATAAATCGTATACAAAATT
Found at i:24548 original size:33 final size:33
Alignment explanation
Indices: 24511--24576 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
24501 CATCTTAATA
*
24511 TCACCCCTTAACACCGAAACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
***
24544 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCGAAACTTCTTTCACCACT
24577 CCATCTATTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.24, C:0.45, G:0.02, T:0.29
Consensus pattern (33 bp):
TCACCCCTCAACACCGAAACTTCTTTCACCACT
Found at i:26711 original size:24 final size:23
Alignment explanation
Indices: 26674--26725 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 23
26664 CCGTTCTATC
26674 TATTTTCAGAGGATAT-TTAGCTTA
1 TATTTTCAGAGGATATGTTA--TTA
**
26698 TATTTTCATCGGATATGTTATTA
1 TATTTTCAGAGGATATGTTATTA
26721 TATTT
1 TATTT
26726 AATCGATACA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
23 8 0.32
24 14 0.56
25 3 0.12
ACGTcount: A:0.27, C:0.08, G:0.13, T:0.52
Consensus pattern (23 bp):
TATTTTCAGAGGATATGTTATTA
Found at i:28123 original size:22 final size:22
Alignment explanation
Indices: 28085--28126 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
28075 ATATTAAAAG
*
28085 CGGAATATAAAATGTTATAAGA
1 CGGAATATAAAAAGTTATAAGA
28107 CGGAAT-TAGAAAAGTTATAA
1 CGGAATATA-AAAAGTTATAA
28127 ATATAATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 2 0.11
22 16 0.89
ACGTcount: A:0.50, C:0.05, G:0.19, T:0.26
Consensus pattern (22 bp):
CGGAATATAAAAAGTTATAAGA
Found at i:28552 original size:77 final size:77
Alignment explanation
Indices: 28342--28671 Score: 233
Period size: 77 Copynumber: 4.3 Consensus size: 77
28332 TGCGCCTAAA
* * * * *
28342 AATGTCATGGTTCACAAAGAAATA-GATTGTGATGTAGAATATTAATATTTTTATTAATAAAATG
1 AATGTCATGGTTCACTAAGAAATATG-TTGTGATATAGAATGTCAAAATTTTTATTAATAAAATG
* *
28406 AGTTGCGCTCAAG
65 GGTAGCGCTCAAG
* * * * * *
28419 AATGTAATGATTCACTAAGACATATGTTGCGA-CTAGAATG-CTAATATTTTTTATTAATAAAAT
1 AATGTCATGGTTCACTAAGAAATATGTTGTGATATAGAATGTC-AA-AATTTTTATTAATAAAAT
28482 GGGTAGCGAC-CAAG
64 GGGTAGCG-CTCAAG
* * ** * *
28496 AATGTCATGGTTTATTAAGAAATATGTTGTGATATAGAATGTCAACGTTTTAATTAAAAAAATGG
1 AATGTCATGGTTCACTAAGAAATATGTTGTGATATAGAATGTCAAAATTTTTATTAATAAAATGG
* ** * *
28561 ATTTCACCCAAG
66 GTAGCGCTCAAG
* * * * * * *
28573 AATGTTACGGTTCACAAAAAAATA-GATTGCGATAT-GAAATGTTAATATTTTTATTAATAAAAT
1 AATGTCATGGTTCACTAAGAAATATG-TTGTGATATAG-AATGTCAAAATTTTTATTAATAAAAT
* *
28636 GGGTTGCGC-CAAAA
64 GGGTAGCGCTC-AAG
* *
28650 AATGTTATGGTTCATTAAGAAA
1 AATGTCATGGTTCACTAAGAAA
28672 GTAAGATGGG
Statistics
Matches: 196, Mismatches: 47, Indels: 20
0.75 0.18 0.08
Matches are distributed among these distances:
76 12 0.06
77 172 0.88
78 11 0.06
79 1 0.01
ACGTcount: A:0.39, C:0.09, G:0.18, T:0.34
Consensus pattern (77 bp):
AATGTCATGGTTCACTAAGAAATATGTTGTGATATAGAATGTCAAAATTTTTATTAATAAAATGG
GTAGCGCTCAAG
Found at i:34942 original size:52 final size:53
Alignment explanation
Indices: 34862--34970 Score: 184
Period size: 52 Copynumber: 2.1 Consensus size: 53
34852 ACACAAGATG
*
34862 AGGCACATAGAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATTACA
1 AGGCACATA-AAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACA
*
34916 AGGCACAT-AAATAGGAGACTAGCCTAGAGTTAGGGGATTACAACTAATCACA
1 AGGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACA
34968 AGG
1 AGG
34971 ATGTGCCTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
52 45 0.85
54 8 0.15
ACGTcount: A:0.41, C:0.16, G:0.24, T:0.19
Consensus pattern (53 bp):
AGGCACATAAAATAGGAAACTAGCCTAGAGTTAGGGGATTACAACTAATCACA
Found at i:51503 original size:22 final size:19
Alignment explanation
Indices: 51480--51524 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
51470 CTCTAAATAT
*
51480 TATTATTTTA-TATATTTAA
1 TATTATTATATTAT-TTTAA
*
51499 TATTAATATATTATTTTAA
1 TATTATTATATTATTTTAA
51518 TATTATT
1 TATTATT
51525 TTAAAAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 19 0.86
20 3 0.14
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TATTATTATATTATTTTAA
Found at i:51712 original size:27 final size:28
Alignment explanation
Indices: 51657--51713 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 28
51647 TAAAATAAAT
* * *
51657 TTTTAATAAAATTAATATTATTTATTTA
1 TTTTAATAAAAATAATATTATTGAATTA
51685 TTTT-ATAAAAATAATATTATTGAATTA
1 TTTTAATAAAAATAATATTATTGAATTA
51712 TT
1 TT
51714 GAATATTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
27 22 0.85
28 4 0.15
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (28 bp):
TTTTAATAAAAATAATATTATTGAATTA
Found at i:55276 original size:95 final size:93
Alignment explanation
Indices: 55104--55490 Score: 491
Period size: 95 Copynumber: 4.3 Consensus size: 93
55094 AAAACAATAT
* * *
55104 TTTATTTGAAAATTATTAATCAAACCAAATTAACCGATTTTTTTCTTTAACATTAATCGAACCGA
1 TTTATTTGAAAATTATTAACCGAACCAAATTAACTGATTTTTTTCTTTAACATTAATCGAACCGA
55169 AATTATTTGACCGTTAATCGAACAGAAA
66 AATTATTTGACCGTTAATCGAACAGAAA
55197 TTTATTTGAAAATTATTAACCGAACCAAATTAACTGATTTTTTTTTCTTTAACATTAATCGAACC
1 TTTATTTGAAAATTATTAACCGAACCAAATTAACTGA--TTTTTTTCTTTAACATTAATCGAACC
* *
55262 AAAATTATTTGACCGTTAATCGAACCGAAA
64 GAAATTATTTGACCGTTAATCGAACAGAAA
55292 GTTT-TTTGAAAATTATTAACCG----------A---ATTTTTTTCTTTAATCATTAATCGAACC
1 -TTTATTTGAAAATTATTAACCGAACCAAATTAACTGATTTTTTTCTTTAA-CATTAATCGAACC
55343 GAAATTATTTGACCGTTAATCGAACCA-AAA
64 GAAATTATTTGACCGTTAATCGAA-CAGAAA
* * *
55373 TTTATTTGTAAATTATTAACCGAACCAAATCAACTGATTTTTTTCTTTAACCATTAATCGAACTG
1 TTTATTTGAAAATTATTAACCGAACCAAATTAACTGATTTTTTTCTTTAA-CATTAATCGAACCG
* *
55438 AAATTATTTAACCGTTAATCG-ACTCGAAA
65 AAATTATTTGACCGTTAATCGAAC-AGAAA
* *
55467 TTTATTTAAAAAATATTAACCGAA
1 TTTATTTGAAAATTATTAACCGAA
55491 TAAAATAAAA
Statistics
Matches: 258, Mismatches: 15, Indels: 41
0.82 0.05 0.13
Matches are distributed among these distances:
80 16 0.06
81 56 0.22
82 2 0.01
85 1 0.00
91 1 0.00
92 1 0.00
93 35 0.14
94 71 0.28
95 72 0.28
96 3 0.01
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (93 bp):
TTTATTTGAAAATTATTAACCGAACCAAATTAACTGATTTTTTTCTTTAACATTAATCGAACCGA
AATTATTTGACCGTTAATCGAACAGAAA
Found at i:55355 original size:81 final size:80
Alignment explanation
Indices: 55236--55396 Score: 270
Period size: 81 Copynumber: 2.0 Consensus size: 80
55226 TTAACTGATT
*
55236 TTTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCGAAAGTTT-TTTG
1 TTTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACC-AAAATTTATTTG
55300 AAAATTATTAACCGAA
65 AAAATTATTAACCGAA
*
55316 TTTTTTTCTTTAATCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAAATTTATTTG
1 TTTTTTTCTTTAA-CATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAAAATTTATTTG
*
55381 TAAATTATTAACCGAA
65 AAAATTATTAACCGAA
55397 CCAAATCAAC
Statistics
Matches: 76, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
80 19 0.25
81 57 0.75
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (80 bp):
TTTTTTTCTTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAAAATTTATTTGA
AAATTATTAACCGAA
Found at i:55447 original size:26 final size:27
Alignment explanation
Indices: 55418--55475 Score: 84
Period size: 26 Copynumber: 2.2 Consensus size: 27
55408 GATTTTTTTC
55418 TTTAACCATTAATCGAACT-GAAA-TTA
1 TTTAACCATTAATCG-ACTCGAAATTTA
*
55444 TTTAACCGTTAATCGACTCGAAATTTA
1 TTTAACCATTAATCGACTCGAAATTTA
55471 TTTAA
1 TTTAA
55476 AAAATATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 3 0.10
26 18 0.62
27 8 0.28
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (27 bp):
TTTAACCATTAATCGACTCGAAATTTA
Found at i:55454 original size:175 final size:174
Alignment explanation
Indices: 55132--55491 Score: 568
Period size: 176 Copynumber: 2.1 Consensus size: 174
55122 ATCAAACCAA
55132 ATTAACCG-ATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACAGAA
1 ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACAGAA
*
55196 ATTTATTTGAAAATTATTAACCGAACCAAATTAACTGATTTTTTTTTCTTTAACATTAATCGAAC
66 ATTTATTTGAAAATTATTAACCGAACCAAATCAACTGA-TTTTTTTTCTTTAACATTAATCGAAC
* * *
55261 CAAAATTATTTGACCGTTAATCGAAC-CGAAAGTTT-TTTGAAAATT
130 CAAAATTATTTAACCGTTAATCG-ACTCGAAA-TTTATTTAAAAAAT
55306 ATTAACCGAATTTTTTTCTTTAATCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCA-
1 ATTAACCGAATTTTTTTCTTTAA-CATTAATCGAACCGAAATTATTTGACCGTTAATCGAA-CAG
*
55370 AAATTTATTTGTAAATTATTAACCGAACCAAATCAACTGA-TTTTTTTCTTTAACCATTAATCGA
64 AAATTTATTTGAAAATTATTAACCGAACCAAATCAACTGATTTTTTTTCTTTAA-CATTAATCGA
**
55434 ACTGAAATTATTTAACCGTTAATCGACTCGAAATTTATTTAAAAAAT
128 ACCAAAATTATTTAACCGTTAATCGACTCGAAATTTATTTAAAAAAT
55481 ATTAACCGAAT
1 ATTAACCGAAT
55492 AAAATAAAAT
Statistics
Matches: 173, Mismatches: 7, Indels: 11
0.91 0.04 0.06
Matches are distributed among these distances:
174 26 0.15
175 70 0.40
176 75 0.43
177 2 0.01
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (174 bp):
ATTAACCGAATTTTTTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCGAACAGAA
ATTTATTTGAAAATTATTAACCGAACCAAATCAACTGATTTTTTTTCTTTAACATTAATCGAACC
AAAATTATTTAACCGTTAATCGACTCGAAATTTATTTAAAAAAT
Found at i:55484 original size:94 final size:94
Alignment explanation
Indices: 55315--55490 Score: 273
Period size: 94 Copynumber: 1.9 Consensus size: 94
55305 TATTAACCGA
* *
55315 ATTTTTTTCTTTAATCATTAATCGAACCGAAATTATTTGACCGTTAATCGAACCAAAATTTATTT
1 ATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTAACCGTTAATCGAACCAAAATTTATTT
** *
55380 GTAAATTATTAACCGAACCAAATCAACTG
66 AAAAAATATTAACCGAACCAAATCAACTG
* *
55409 ATTTTTTTCTTTAACCATTAATCGAACTGAAATTATTTAACCGTTAATCG-ACTCGAAATTTATT
1 ATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTAACCGTTAATCGAAC-CAAAATTTATT
55473 TAAAAAATATTAACCGAA
65 TAAAAAATATTAACCGAA
55491 TAAAATAAAA
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
93 2 0.03
94 72 0.97
ACGTcount: A:0.38, C:0.16, G:0.08, T:0.38
Consensus pattern (94 bp):
ATTTTTTTCTTTAACCATTAATCGAACCGAAATTATTTAACCGTTAATCGAACCAAAATTTATTT
AAAAAATATTAACCGAACCAAATCAACTG
Found at i:55860 original size:22 final size:22
Alignment explanation
Indices: 55835--55913 Score: 63
Period size: 22 Copynumber: 3.4 Consensus size: 22
55825 CATGTCATGT
55835 TTTAATTGGATAGTTAAATTTC
1 TTTAATTGGATAGTTAAATTTC
*
55857 TTTAATT-GA-ATTTAAATAGTGTC
1 TTTAATTGGATAGTTAAAT--T-TC
*
55880 ATGTTCTAATTGGATAGTCAAATTTC
1 ---TT-TAATTGGATAGTTAAATTTC
55906 TTTAATTG
1 TTTAATTG
55914 AATTAAAATA
Statistics
Matches: 45, Mismatches: 3, Indels: 18
0.68 0.05 0.27
Matches are distributed among these distances:
20 7 0.16
21 2 0.04
22 14 0.31
23 4 0.09
26 4 0.09
27 6 0.13
28 2 0.04
29 6 0.13
ACGTcount: A:0.32, C:0.06, G:0.14, T:0.48
Consensus pattern (22 bp):
TTTAATTGGATAGTTAAATTTC
Found at i:55880 original size:49 final size:49
Alignment explanation
Indices: 55827--55923 Score: 167
Period size: 49 Copynumber: 2.0 Consensus size: 49
55817 TATTGACACA
* * *
55827 TGTCATGTTTTAATTGGATAGTTAAATTTCTTTAATTGAATTTAAATAG
1 TGTCATGTTCTAATTGGATAGTCAAATTTCTTTAATTGAATTAAAATAG
55876 TGTCATGTTCTAATTGGATAGTCAAATTTCTTTAATTGAATTAAAATA
1 TGTCATGTTCTAATTGGATAGTCAAATTTCTTTAATTGAATTAAAATA
55924 ATGACTAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
49 45 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.46
Consensus pattern (49 bp):
TGTCATGTTCTAATTGGATAGTCAAATTTCTTTAATTGAATTAAAATAG
Found at i:58538 original size:2 final size:2
Alignment explanation
Indices: 58531--58556 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
58521 CAAATTGTGA
58531 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
58557 TTATTTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62885 original size:2 final size:2
Alignment explanation
Indices: 62878--62911 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
62868 AAATATGTTT
62878 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
62912 TAAATCCATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:63069 original size:11 final size:11
Alignment explanation
Indices: 63047--63079 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
63037 AGTTAATCTA
63047 ATTAAAAAATT
1 ATTAAAAAATT
63058 A-TAAAAATATT
1 ATTAAAAA-ATT
63069 ATTAAAAAATT
1 ATTAAAAAATT
63080 TGGTTAGTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.30
11 8 0.40
12 6 0.30
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
ATTAAAAAATT
Found at i:63348 original size:3 final size:3
Alignment explanation
Indices: 63340--63373 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
63330 TATCTAATTG
63340 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
63374 AATATGCTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:63943 original size:24 final size:22
Alignment explanation
Indices: 63904--63948 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
63894 AGAAAACCAG
*
63904 AAAAAAAAACAGAGGATAGAGA
1 AAAAAAAAACAGAGGAAAGAGA
*
63926 AAAAAAAAAGAGAAAGGAAAGAG
1 AAAAAAAAACAG--AGGAAAGAG
63949 GAGAGAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.71, C:0.02, G:0.24, T:0.02
Consensus pattern (22 bp):
AAAAAAAAACAGAGGAAAGAGA
Found at i:64510 original size:19 final size:19
Alignment explanation
Indices: 64464--64510 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 19
64454 CAGTAATTTG
*
64464 TATATTATGTTTGCTGATAT
1 TATATT-TGGTTGCTGATAT
64484 TATAATTTGGTTG-TGATATT
1 TAT-ATTTGGTTGCTGATA-T
64504 TATATTT
1 TATATTT
64511 ATTTCGTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 9 0.38
20 12 0.50
21 3 0.12
ACGTcount: A:0.26, C:0.02, G:0.15, T:0.57
Consensus pattern (19 bp):
TATATTTGGTTGCTGATAT
Found at i:66967 original size:31 final size:32
Alignment explanation
Indices: 66931--66992 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
66921 TATTTACATG
66931 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
66962 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
1 TACTAACTTATTTCTTCTCTTTTGTTTGTGT
66993 CATTTTGTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.43
32 17 0.57
ACGTcount: A:0.15, C:0.15, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTCTCTTTTGTTTGTGTA
Found at i:68427 original size:26 final size:25
Alignment explanation
Indices: 68396--68475 Score: 80
Period size: 26 Copynumber: 3.3 Consensus size: 25
68386 CCAATTTTTG
68396 ACATTCTATCTCTTTGAGACCTTG-A
1 ACATTCT-TCTCTTTGAGACCTTGAA
* *
68421 A-A-TATTCT-TTT-CGACCTTGAA
1 ACATTCTTCTCTTTGAGACCTTGAA
*
68442 ACATTCCCTCTCTTTGAGACCTTGAA
1 ACATT-CTTCTCTTTGAGACCTTGAA
68468 ACATTCTT
1 ACATTCTT
68476 TCCACCTTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
20 7 0.16
21 5 0.12
22 4 0.09
23 3 0.07
24 4 0.09
25 6 0.14
26 14 0.33
ACGTcount: A:0.25, C:0.25, G:0.10, T:0.40
Consensus pattern (25 bp):
ACATTCTTCTCTTTGAGACCTTGAA
Found at i:69117 original size:14 final size:14
Alignment explanation
Indices: 69098--69138 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
69088 GAGAAAAGAA
69098 AAACAAAGAGAAAG
1 AAACAAAGAGAAAG
69112 AAACAAAGA-AAA-
1 AAACAAAGAGAAAG
*
69124 AAAAAGAAGAGAAAG
1 AAACA-AAGAGAAAG
69139 TGGACAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
12 4 0.17
13 7 0.30
14 12 0.52
ACGTcount: A:0.76, C:0.05, G:0.20, T:0.00
Consensus pattern (14 bp):
AAACAAAGAGAAAG
Found at i:69119 original size:24 final size:23
Alignment explanation
Indices: 69092--69137 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
69082 AGCGAAGAGA
69092 AAAGAAAAACAAAGAGAA-AGAAAC
1 AAAGAAAAA-AAA-AGAAGAGAAAC
69116 AAAGAAAAAAAAAGAAGAGAAA
1 AAAGAAAAAAAAAGAAGAGAAA
69138 GTGGACAAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 4 0.19
23 8 0.38
24 9 0.43
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.00
Consensus pattern (23 bp):
AAAGAAAAAAAAAGAAGAGAAAC
Found at i:70326 original size:4 final size:4
Alignment explanation
Indices: 70317--70348 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
70307 AAAAGTATAC
70317 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
70349 GTACATAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:71026 original size:36 final size:36
Alignment explanation
Indices: 70981--71065 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
70971 ACAAAGTTGA
**
70981 TCTCACTTGAGATCGTTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAGA-CAATTTCTCTAAAAACAAACTTTG
* *
71017 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
*
71053 TCTCATTTGAGAC
1 TCTCACTTGAGAC
71066 TATATCTTAA
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.31, C:0.21, G:0.12, T:0.36
Consensus pattern (36 bp):
TCTCACTTGAGACAATTTCTCTAAAAACAAACTTTG
Found at i:71421 original size:29 final size:29
Alignment explanation
Indices: 71343--71448 Score: 137
Period size: 31 Copynumber: 3.7 Consensus size: 29
71333 ACAGTTTCTC
71343 TTGAAAAAAAAT-TTTGAGTTTGTTCCTT
1 TTGAAAAAAAATCTTTGAGTTTGTTCCTT
*
71371 TTGAACAAAAAAATCTTGGAGTTTGTTCCTT
1 TTG-A-AAAAAAATCTTTGAGTTTGTTCCTT
* *
71402 TTGAATAAAAATCTTTGAG-TTGTTTCTT
1 TTGAAAAAAAATCTTTGAGTTTGTTCCTT
*
71430 TTG-GAAAAAATCTTTGAGT
1 TTGAAAAAAAATCTTTGAGT
71449 CTATTTATTT
Statistics
Matches: 68, Mismatches: 6, Indels: 8
0.83 0.07 0.10
Matches are distributed among these distances:
27 13 0.19
28 14 0.21
29 14 0.21
30 9 0.13
31 18 0.26
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.43
Consensus pattern (29 bp):
TTGAAAAAAAATCTTTGAGTTTGTTCCTT
Found at i:71463 original size:27 final size:27
Alignment explanation
Indices: 71408--71460 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
71398 CCTTTTGAAT
* *
71408 AAAAATCTTTGAGTTGTTTCTTTTGGA
1 AAAAATCTTTGAGTTATTTATTTTGGA
71435 AAAAATCTTTGAGTCTATTTATTTTG
1 AAAAATCTTTGAGT-TATTTATTTTG
71461 AAACAAAGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 14 0.61
28 9 0.39
ACGTcount: A:0.28, C:0.08, G:0.15, T:0.49
Consensus pattern (27 bp):
AAAAATCTTTGAGTTATTTATTTTGGA
Found at i:71549 original size:50 final size:52
Alignment explanation
Indices: 71459--71560 Score: 145
Period size: 52 Copynumber: 2.0 Consensus size: 52
71449 CTATTTATTT
*
71459 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTG-CTCTCTTGAGACAATTTCGCGAAAAAATCTTTGAGTC
* *
71511 TGAAACAAAGTTTTG-TCTCTTGAGGCAATTTTGCGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGCTCTCTTGAGACAATTTCGCG-AAAAAATCTTTGAG
71561 ATTGTTTCAT
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
50 17 0.38
52 28 0.62
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (52 bp):
TGAAACAAAGTTTTGCTCTCTTGAGACAATTTCGCGAAAAAATCTTTGAGTC
Found at i:71612 original size:29 final size:29
Alignment explanation
Indices: 71546--71626 Score: 114
Period size: 30 Copynumber: 2.8 Consensus size: 29
71536 CAATTTTGCG
71546 AAAAAAATCTTTGAGAT-TGTTTCATTTGA
1 AAAAAAATCTTTGAG-TCTGTTTCATTTGA
71575 AACAAAAATCTTTGAGTCTGTTTC-TTTGGA
1 AA-AAAAATCTTTGAGTCTGTTTCATTT-GA
71605 AAAAAAATCTTTGAGTC-GTTTC
1 AAAAAAATCTTTGAGTCTGTTTC
71627 CCTTCAAACG
Statistics
Matches: 49, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
28 5 0.10
29 21 0.43
30 23 0.47
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (29 bp):
AAAAAAATCTTTGAGTCTGTTTCATTTGA
Found at i:72408 original size:31 final size:31
Alignment explanation
Indices: 72370--72524 Score: 206
Period size: 31 Copynumber: 5.0 Consensus size: 31
72360 CCCGAAGGAC
* * *
72370 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
72401 CAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* * *
72432 CAGTCCGTATGTTCCGAAGAACATAGGTAAT
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
72463 CAGTCCA-ATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
72493 CAGTCCATATGTCCAGAATAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
72524 C
1 C
72525 CCTCGACCCT
Statistics
Matches: 109, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
30 28 0.26
31 80 0.73
32 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:72504 original size:61 final size:62
Alignment explanation
Indices: 72370--72522 Score: 231
Period size: 61 Copynumber: 2.5 Consensus size: 62
72360 CCCGAAGGAC
* *
72370 CAGTCCATA-GATTCCGAAGAACCTAGGTAATCAGTCCATATGTCCCGAAGGACATAGGTAAA
1 CAGTCCATATG-TTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
*
72432 CAGTCCGTATGTTCCGAAGAACATAGGTAATCAGTCCA-ATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
*
72493 CAGTCCATATG-TCCAGAATAACATAGGTAA
1 CAGTCCATATGTTCC-GAAGAACATAGGTAA
72523 ACCCTCGACC
Statistics
Matches: 84, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
60 3 0.04
61 46 0.55
62 34 0.40
63 1 0.01
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.22
Consensus pattern (62 bp):
CAGTCCATATGTTCCGAAGAACATAGGTAATCAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:72743 original size:24 final size:22
Alignment explanation
Indices: 72698--72743 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
72688 ATATACTTGT
*
72698 TTTCACATATATATTCATATCA
1 TTTCACATATACATTCATATCA
72720 TTTCACATATACACTTTCATATCA
1 TTTCACATATACA--TTCATATCA
72744 CATGCCATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.57
24 9 0.43
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (22 bp):
TTTCACATATACATTCATATCA
Found at i:73310 original size:20 final size:21
Alignment explanation
Indices: 73270--73313 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
73260 ATTCTGTCGT
*
73270 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTATCGATTCCCC
*
73291 TTGAATGGGTA-CGATTCCCC
1 TTGAAGGGGTATCGATTCCCC
73311 TTG
1 TTG
73314 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.16, C:0.23, G:0.30, T:0.32
Consensus pattern (21 bp):
TTGAAGGGGTATCGATTCCCC
Done.