Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008026.1 Hibiscus syriacus cultivar Beakdansim tig00110502_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: 525378
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
File 2 of 4
Found at i:162655 original size:60 final size:60
Alignment explanation
Indices: 162591--162729 Score: 242
Period size: 60 Copynumber: 2.3 Consensus size: 60
162581 GATAACCAAT
* *
162591 ATCCAATACTAGTGGGATAACCAGTATCCAATACTAGTGGGATATTGAGTCATTACTAAC
1 ATCCAATACTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACTAAA
*
162651 ATCCAATACTATTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACTAAA
1 ATCCAATACTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACTAAA
*
162711 ATCCAATACTAGTGAGATA
1 ATCCAATACTAGTGGGATA
162730 TTGAGCATTA
Statistics
Matches: 74, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
60 74 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (60 bp):
ATCCAATACTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACTAAA
Found at i:162655 original size:85 final size:85
Alignment explanation
Indices: 162512--162694 Score: 330
Period size: 85 Copynumber: 2.2 Consensus size: 85
162502 CATTAACCAG
*
162512 TACTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTTATTACCAACATCCAATACTA
1 TACTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACCAACATCCAATACTA
162577 GTGGGATAACCAATATCCAA
66 GTGGGATAACCAATATCCAA
* *
162597 TACTAGTGGGATAACCAGTATCCAATACTAGTGGGATATTGAGTCATTACTAACATCCAATACTA
1 TACTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACCAACATCCAATACTA
*
162662 TTGGGATAACCAATATCCAA
66 GTGGGATAACCAATATCCAA
162682 TACTAGTGGGATA
1 TACTAGTGGGATA
162695 TTGAGTCATT
Statistics
Matches: 94, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
85 94 1.00
ACGTcount: A:0.37, C:0.18, G:0.17, T:0.28
Consensus pattern (85 bp):
TACTAGTGGGATAACCAATATCCAATACTAGTGGGATATTGAGTCATTACCAACATCCAATACTA
GTGGGATAACCAATATCCAA
Found at i:162667 original size:35 final size:34
Alignment explanation
Indices: 162616--162739 Score: 131
Period size: 35 Copynumber: 3.9 Consensus size: 34
162606 GATAACCAGT
*
162616 ATCCAATACTAGTGGGATATTGAGTCATTACTAAC
1 ATCCAATACTAGTGGGATATTGAG-CATTACTAAA
* *
162651 ATCCAATACTATTGGGATA---A-C----C-AAT
1 ATCCAATACTAGTGGGATATTGAGCATTACTAAA
162676 ATCCAATACTAGTGGGATATTGAGTCATTACTAAA
1 ATCCAATACTAGTGGGATATTGAG-CATTACTAAA
*
162711 ATCCAATACTAGTGAGATATTGAGCATTA
1 ATCCAATACTAGTGGGATATTGAGCATTA
162740 TCAACATTCC
Statistics
Matches: 74, Mismatches: 5, Indels: 21
0.74 0.05 0.21
Matches are distributed among these distances:
25 20 0.27
26 1 0.01
28 1 0.01
30 2 0.03
32 1 0.01
34 6 0.08
35 43 0.58
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.31
Consensus pattern (34 bp):
ATCCAATACTAGTGGGATATTGAGCATTACTAAA
Found at i:174233 original size:55 final size:55
Alignment explanation
Indices: 174158--174652 Score: 692
Period size: 55 Copynumber: 9.0 Consensus size: 55
174148 ACCTATTACA
* ** * * *
174158 ATACGGAAATTCATAAACTTATTATGAATTTCTT-AGTTTTGCACACAAAGTGCCC
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCC
*
174213 ATACAAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* **
174268 ATA-AAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCTT
1 ATACGA-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* * *
174323 ACACGGAAATTCAACCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* *
174378 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTATACATAAAGTGTCC
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
174433 ATAC-AGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAATGCCC
1 ATACGA-AAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
**
174488 ATATTAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* *
174543 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTACCC
1 ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* * * * * *
174598 ATACGAAAATTCAT-CACCTTAGCATGAATTTATTAATTTTGCACACATAGTGCCC
1 ATACGAAAATTCATCCA-CTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
174653 TTTGGTAATC
Statistics
Matches: 397, Mismatches: 37, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
54 5 0.01
55 389 0.98
56 3 0.01
ACGTcount: A:0.37, C:0.19, G:0.11, T:0.34
Consensus pattern (55 bp):
ATACGAAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
Found at i:180205 original size:55 final size:55
Alignment explanation
Indices: 179821--180200 Score: 593
Period size: 55 Copynumber: 6.9 Consensus size: 55
179811 CCTATTACCA
* ** * * * *
179821 ATACGGAAAATCATAAACTTATTATGAATTTCTT-AGTTTTGCACACAAAGTACCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAG-TTTACACATAAAGTGCCC
*
179876 ATACAGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
* *
179931 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTACTC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
179986 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
180041 ATACGGAAATTCATCCACTTTGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
180096 ATATGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
1 ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
*
180151 ATACGGAAATTCAAT-CACTTAGTATGAATTTCTTAATTTTGCACACATAA
1 ATACGGAAATTC-ATCCACTTAGTATGAATTTCTTAAGTTT--ACACATAA
180201 TGCCCTTTGG
Statistics
Matches: 303, Mismatches: 18, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
55 291 0.96
56 4 0.01
57 8 0.03
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.34
Consensus pattern (55 bp):
ATACGGAAATTCATCCACTTAGTATGAATTTCTTAAGTTTACACATAAAGTGCCC
Found at i:185446 original size:60 final size:58
Alignment explanation
Indices: 185333--185446 Score: 133
Period size: 60 Copynumber: 1.9 Consensus size: 58
185323 GGTAGCACCT
* * *
185333 TAGGTTCATAAGGACTTACTATAGTCGAAGCATAAGAGCCACCTGAGGGGAGTGCCAC
1 TAGGTTCATAAGGACTTACTATAGACAAAGCATAAGAGCCACCTGAGGAGAGTGCCAC
* *
185391 TAGGTTCATAAGGACTTACCT-TAAGCACAAAGCA-AATGAGCCACCTTATGAGAGTG
1 TAGGTTCATAAGGACTTA-CTAT-AG-ACAAAGCATAA-GAGCCACCTGAGGAGAGTG
185447 TCATAGGGTC
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
58 19 0.40
59 6 0.13
60 22 0.47
ACGTcount: A:0.33, C:0.20, G:0.25, T:0.22
Consensus pattern (58 bp):
TAGGTTCATAAGGACTTACTATAGACAAAGCATAAGAGCCACCTGAGGAGAGTGCCAC
Found at i:187371 original size:17 final size:17
Alignment explanation
Indices: 187346--187391 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
187336 TAGCTCAGCT
*
187346 CAATTAGTGGCTCGACTA
1 CAATCAGTGGCTCGAC-A
187364 -AATCAGTGGCTCGACA
1 CAATCAGTGGCTCGACA
187380 CAATCAGTGGCT
1 CAATCAGTGGCT
187392 TGGTTTGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 1 0.04
17 25 0.96
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.24
Consensus pattern (17 bp):
CAATCAGTGGCTCGACA
Found at i:188533 original size:25 final size:23
Alignment explanation
Indices: 188497--188543 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
188487 TAAAGAACCA
*
188497 AAATAAACTTAAATATACCATTAC
1 AAATAAACTTAAACA-ACCATTAC
*
188521 AAATAAAGTTTAAACAACCATTA
1 AAATAAA-CTTAAACAACCATTA
188544 AATCAACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.55, C:0.15, G:0.02, T:0.28
Consensus pattern (23 bp):
AAATAAACTTAAACAACCATTAC
Found at i:189213 original size:18 final size:18
Alignment explanation
Indices: 189192--189238 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
189182 ACACCATAGA
*
189192 CAAACTGCACCTTTCCCT
1 CAAACAGCACCTTTCCCT
*
189210 CAAACAACACCTTTCCCT
1 CAAACAGCACCTTTCCCT
189228 CAAACAGCACC
1 CAAACAGCACC
189239 ATTAAGAAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.32, C:0.45, G:0.04, T:0.19
Consensus pattern (18 bp):
CAAACAGCACCTTTCCCT
Found at i:196411 original size:21 final size:21
Alignment explanation
Indices: 196385--196425 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
196375 GCTATGGCTT
*
196385 TGAAGTAAGGCGCCTTGATTA
1 TGAAGTAAAGCGCCTTGATTA
*
196406 TGAAGTAAAGCTCCTTGATT
1 TGAAGTAAAGCGCCTTGATT
196426 CTTAATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (21 bp):
TGAAGTAAAGCGCCTTGATTA
Found at i:208020 original size:14 final size:14
Alignment explanation
Indices: 208001--208028 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
207991 TGATTTGTCC
208001 TTCCTACATAATAG
1 TTCCTACATAATAG
208015 TTCCTACATAATAG
1 TTCCTACATAATAG
208029 GAAATATATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.07, T:0.36
Consensus pattern (14 bp):
TTCCTACATAATAG
Found at i:208582 original size:78 final size:79
Alignment explanation
Indices: 208484--208633 Score: 214
Period size: 78 Copynumber: 1.9 Consensus size: 79
208474 ATATAATAAG
*
208484 TAAACATTAAAAGAATGTAATTTTGATTACAACTCTTTTAATCGATATTT-AATTCGAAATAATT
1 TAAACATTAAAAGAATGTAATTTAGATTACAACTC-TTTAATCGATATTTAAATTCGAAATAATT
208548 AAATAAGAGTTCAAA
65 AAATAAGAGTTCAAA
* * * * * *
208563 TAAACATT-AAAGATTGTAATTTAGATTATAAGTCTTTAATGGATATTTAAATTTGAATTAATTA
1 TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTAATCGATATTTAAATTCGAAATAATTA
208627 AATAAGA
66 AATAAGA
208634 TTTTTTATTA
Statistics
Matches: 63, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
77 13 0.21
78 42 0.67
79 8 0.13
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (79 bp):
TAAACATTAAAAGAATGTAATTTAGATTACAACTCTTTAATCGATATTTAAATTCGAAATAATTA
AATAAGAGTTCAAA
Found at i:209756 original size:11 final size:10
Alignment explanation
Indices: 209731--209807 Score: 52
Period size: 10 Copynumber: 7.9 Consensus size: 10
209721 GGCTGCTGGA
209731 AACCGG-TTT
1 AACCGGTTTT
209740 AACCGGTTTT
1 AACCGGTTTT
*
209750 CAACCGGTTCT
1 -AACCGGTTTT
*
209761 GACCGG-TTT
1 AACCGGTTTT
* * *
209770 GATCGGTTTC
1 AACCGGTTTT
**
209780 AACCGGTTCG
1 AACCGGTTTT
209790 AACCGG-TTT
1 AACCGGTTTT
*
209799 GACCGGTTT
1 AACCGGTTT
209808 GACCGGTCTG
Statistics
Matches: 52, Mismatches: 12, Indels: 7
0.73 0.17 0.10
Matches are distributed among these distances:
9 19 0.37
10 24 0.46
11 9 0.17
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (10 bp):
AACCGGTTTT
Found at i:209784 original size:19 final size:18
Alignment explanation
Indices: 209732--209814 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 18
209722 GCTGCTGGAA
*
209732 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTAACCGG-TTT-G
*
209752 ACCGGTTCTGACCGGTTTG
1 ACCGGTT-TAACCGGTTTG
* *
209771 ATCGGTTTCAACCGGTTCG
1 ACCGGTTT-AACCGGTTTG
*
209790 AACCGGTTTGACCGGTTTG
1 -ACCGGTTTAACCGGTTTG
209809 ACCGGT
1 ACCGGT
209815 CTGACCCGAC
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
18 7 0.13
19 22 0.42
20 17 0.33
21 6 0.12
ACGTcount: A:0.16, C:0.25, G:0.28, T:0.31
Consensus pattern (18 bp):
ACCGGTTTAACCGGTTTG
Found at i:209794 original size:29 final size:30
Alignment explanation
Indices: 209731--209807 Score: 113
Period size: 29 Copynumber: 2.6 Consensus size: 30
209721 GGCTGCTGGA
*
209731 AACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 AACCGGTTTGACCGG-TTTCAACCGGTTCTG
*
209762 -ACCGGTTTGATCGGTTTCAACCGGTTC-G
1 AACCGGTTTGACCGGTTTCAACCGGTTCTG
209790 AACCGGTTTGACCGGTTT
1 AACCGGTTTGACCGGTTT
209808 GACCGGTCTG
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
28 1 0.02
29 29 0.69
30 12 0.29
ACGTcount: A:0.17, C:0.25, G:0.26, T:0.32
Consensus pattern (30 bp):
AACCGGTTTGACCGGTTTCAACCGGTTCTG
Found at i:209819 original size:9 final size:9
Alignment explanation
Indices: 209732--209820 Score: 79
Period size: 9 Copynumber: 9.3 Consensus size: 9
209722 GCTGCTGGAA
*
209732 ACCGGTTTA
1 ACCGGTTTG
*
209741 ACCGGTTTTCA
1 ACCGG-TTT-G
209752 ACCGGTTCTG
1 ACCGGTT-TG
209762 ACCGGTTTG
1 ACCGGTTTG
* *
209771 ATCGGTTTCA
1 ACCGGTTT-G
*
209781 ACCGGTTCG
1 ACCGGTTTG
209790 AACCGGTTTG
1 -ACCGGTTTG
209800 ACCGGTTTG
1 ACCGGTTTG
*
209809 ACCGGTCTG
1 ACCGGTTTG
209818 ACC
1 ACC
209821 CGACCTGACC
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
9 34 0.51
10 26 0.39
11 7 0.10
ACGTcount: A:0.16, C:0.27, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:209846 original size:5 final size:5
Alignment explanation
Indices: 209834--209896 Score: 54
Period size: 5 Copynumber: 11.8 Consensus size: 5
209824 CCTGACCGTT
* * * *
209834 GACCC GACTC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACTC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC
209883 GACCC GACCC GACC
1 GACCC GACCC GACC
209897 GTTGACCGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 8
0.74 0.13 0.13
Matches are distributed among these distances:
5 39 0.85
7 7 0.15
ACGTcount: A:0.19, C:0.49, G:0.22, T:0.10
Consensus pattern (5 bp):
GACCC
Found at i:209852 original size:22 final size:22
Alignment explanation
Indices: 209817--209903 Score: 147
Period size: 22 Copynumber: 4.0 Consensus size: 22
209807 TGACCGGTCT
*
209817 GACCCGACCTGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
209839 GACTCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
*
209861 GACCCGACCCGACCGTTGACTC
1 GACCCGACCCGACCGTTGACCC
209883 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
209904 GTTGACCGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 60 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:217105 original size:10 final size:9
Alignment explanation
Indices: 217081--217144 Score: 65
Period size: 10 Copynumber: 6.8 Consensus size: 9
217071 GGCTGCTGGA
217081 AACCGGTTT
1 AACCGGTTT
217090 AACCGGTTT
1 AACCGGTTT
*
217099 CAACCGGTTCG
1 -AACCGGTT-T
217110 AACCGGTTT
1 AACCGGTTT
* *
217119 GACCGGTCTG
1 AACCGGT-TT
217129 AACCGGTTT
1 AACCGGTTT
*
217138 GACCGGT
1 AACCGGT
217145 CTGACCCGAC
Statistics
Matches: 45, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
9 22 0.49
10 23 0.51
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.27
Consensus pattern (9 bp):
AACCGGTTT
Found at i:217105 original size:19 final size:18
Alignment explanation
Indices: 217081--217144 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 18
217071 GGCTGCTGGA
*
217081 AACCGGTTTAACCGGTTT
1 AACCGGTTGAACCGGTTT
217099 CAACCGGTTCGAACCGGTTT
1 -AACCGGTT-GAACCGGTTT
*
217119 GACCGGTCTGAACCGGTTT
1 AACCGGT-TGAACCGGTTT
*
217138 GACCGGT
1 AACCGGT
217145 CTGACCCGAC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 31 0.76
20 10 0.24
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.27
Consensus pattern (18 bp):
AACCGGTTGAACCGGTTT
Found at i:217145 original size:19 final size:19
Alignment explanation
Indices: 217090--217148 Score: 84
Period size: 19 Copynumber: 3.1 Consensus size: 19
217080 AAACCGGTTT
*
217090 AACCGGTTTCAACCGGT-TCG
1 AACCGGTTT-GACCGGTCT-G
217110 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
217129 AACCGGTTTGACCGGTCTG
1 AACCGGTTTGACCGGTCTG
217148 A
1 A
217149 CCCGACCCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
19 27 0.73
20 10 0.27
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (19 bp):
AACCGGTTTGACCGGTCTG
Found at i:217149 original size:9 final size:9
Alignment explanation
Indices: 217111--217150 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
217101 ACCGGTTCGA
*
217111 ACCGGTTTG
1 ACCGGTCTG
217120 ACCGGTCTG
1 ACCGGTCTG
*
217129 AACCGGTTTG
1 -ACCGGTCTG
217139 ACCGGTCTG
1 ACCGGTCTG
217148 ACC
1 ACC
217151 CGACCCGACC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
9 19 0.70
10 8 0.30
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.25
Consensus pattern (9 bp):
ACCGGTCTG
Found at i:217168 original size:17 final size:17
Alignment explanation
Indices: 217146--217184 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
217136 TTGACCGGTC
217146 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
217163 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
217180 TGACC
1 TGACC
217185 GTTGACCGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.18, C:0.46, G:0.23, T:0.13
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:229179 original size:24 final size:24
Alignment explanation
Indices: 229160--229206 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
229150 ATTTCTATAT
*
229160 GGTCCTTCGGGACAAATTCTACGC
1 GGTCCTTCGGGACAAATTCTACAC
229184 GGTCCTTCGGGACAAATTTCTAC
1 GGTCCTTCGGGACAAA-TTCTAC
229207 GCGACACTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.21, C:0.28, G:0.23, T:0.28
Consensus pattern (24 bp):
GGTCCTTCGGGACAAATTCTACAC
Found at i:229216 original size:25 final size:24
Alignment explanation
Indices: 229163--229232 Score: 81
Period size: 25 Copynumber: 2.8 Consensus size: 24
229153 TCTATATGGT
*
229163 CCTTCGGGACAAATTCTACGCGGT
1 CCTTCGGGACAAATTCTACGCGGA
229187 CCTTCGGGACAAATTTCTACGC-GA
1 CCTTCGGGACAAA-TTCTACGCGGA
229211 CACTTCGGTG-CAAAATTCTACG
1 C-CTTCGG-GAC-AAATTCTACG
229233 TGGCACTACG
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
24 15 0.37
25 22 0.54
26 4 0.10
ACGTcount: A:0.24, C:0.29, G:0.21, T:0.26
Consensus pattern (24 bp):
CCTTCGGGACAAATTCTACGCGGA
Found at i:229239 original size:25 final size:25
Alignment explanation
Indices: 229173--229248 Score: 84
Period size: 25 Copynumber: 3.0 Consensus size: 25
229163 CCTTCGGGAC
229173 AAATTCTACGCGGTC-CTTCGG-GACA
1 AAATTCTACGCGG-CACTTCGGTG-CA
* *
229198 AATTTCTACGCGACACTTCGGTGCA
1 AAATTCTACGCGGCACTTCGGTGCA
* *
229223 AAATTCTACGTGGCACTACGGTGCA
1 AAATTCTACGCGGCACTTCGGTGCA
229248 A
1 A
229249 TTTATACGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
24 1 0.02
25 41 0.95
26 1 0.02
ACGTcount: A:0.26, C:0.26, G:0.22, T:0.25
Consensus pattern (25 bp):
AAATTCTACGCGGCACTTCGGTGCA
Found at i:234241 original size:25 final size:25
Alignment explanation
Indices: 234180--234263 Score: 93
Period size: 25 Copynumber: 3.4 Consensus size: 25
234170 ATTCTTAAGG
* * *
234180 AATTTCTATGTGGTCCTTCGGGATA
1 AATTTCTACGCGGTCCTTCGGGACA
234205 AA-TTCTACGCGGTCCTTCGGGACA
1 AATTTCTACGCGGTCCTTCGGGACA
234229 AATTTCTACGCGG-CACTTCGGTG-CA
1 AATTTCTACGCGGTC-CTTCGG-GACA
*
234254 AAATTCTACG
1 AATTTCTACG
234264 TGGCCCTACG
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
24 22 0.42
25 29 0.56
26 1 0.02
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.31
Consensus pattern (25 bp):
AATTTCTACGCGGTCCTTCGGGACA
Found at i:234275 original size:25 final size:25
Alignment explanation
Indices: 234204--234279 Score: 91
Period size: 25 Copynumber: 3.0 Consensus size: 25
234194 CCTTCGGGAT
*
234204 AAATTCTACGCGGTCCTTCGG-GACA
1 AAATTCTACGCGGCCCTTCGGTG-CA
* *
234229 AATTTCTACGCGGCACTTCGGTGCA
1 AAATTCTACGCGGCCCTTCGGTGCA
* *
234254 AAATTCTACGTGGCCCTACGGTGCA
1 AAATTCTACGCGGCCCTTCGGTGCA
234279 A
1 A
234280 TTTATACGAG
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
25 42 0.98
26 1 0.02
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.25
Consensus pattern (25 bp):
AAATTCTACGCGGCCCTTCGGTGCA
Found at i:236446 original size:220 final size:219
Alignment explanation
Indices: 236064--236584 Score: 846
Period size: 220 Copynumber: 2.4 Consensus size: 219
236054 TTTTTTATTA
* * * *
236064 TTTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGATCGGGTTTTTTTAAGTTTGATA
1 TTTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGG-TTTTTTAAGTGTGATA
*
236129 TTC-GGTCGGGTCGGGTTCGGATTTAGGTGAAAAAAACCGGACCGACCCGAAAATATATATAATT
65 TTCGGGTCGGGTC-GGTTCGGATTTAGGTGAAAAAAACCAGACCGACCCGAAAATATATATAATT
* * *
236193 CAGGTCGGGTTGGATTAAGTCACTGTTTTTATTAAATAAAATTAATTTTTTATTATTTCGGGTCT
129 CAGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCG
*
236258 GGTCGGGTTGGATTTCTAATTCATAT
194 GGTCGGGTCGGATTTCTAATTCATAT
236284 TTTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATAT
1 TTTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATAT
** * * *
236349 TCGGGTCAAGTCGGTTCGGGTTTAGGGTGAAAAATACCAGATCGACCCGAAAATATATATAATTC
66 TCGGGTCGGGTCGGTTCGGATTTA-GGTGAAAAAAACCAGACCGACCCGAAAATATATATAATTC
*
236414 GGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGG
130 AGGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGG
236479 GTCGGGTCGGATTTCTAATTCATAT
195 GTCGGGTCGGATTTCTAATTCATAT
* * *
236504 ATTCAGGTCGGGTCAGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATAT
1 TTTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATAT
236569 TCGGGTCGGGTCGGTT
66 TCGGGTCGGGTCGGTT
236585 TTTTTAAATG
Statistics
Matches: 279, Mismatches: 20, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
219 29 0.10
220 250 0.90
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (219 bp):
TTTCGGGTCGGGTCGGATGAAACTTTATTTTGTTCGGGTCGGGTCGGGTTTTTTAAGTGTGATAT
TCGGGTCGGGTCGGTTCGGATTTAGGTGAAAAAAACCAGACCGACCCGAAAATATATATAATTCA
GGTCGGGTCGGATTAAGTCACTGTTTTTATTAAATAAAAATAATTTTTTATTATTTCGGGTCGGG
TCGGGTCGGATTTCTAATTCATAT
Found at i:236576 original size:32 final size:32
Alignment explanation
Indices: 236536--236617 Score: 137
Period size: 32 Copynumber: 2.6 Consensus size: 32
236526 CTTTATTTTG
*
236536 TTCGGGTCGGGTCGGGTTTTTTAAGTGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTAAATGTGATA
*
236568 TTCGGGTCGGGTCGGTTTTTTTAAATGTGATA
1 TTCGGGTCGGGTCGGGTTTTTTAAATGTGATA
*
236600 TTCGGGTCAGGTCGGGTT
1 TTCGGGTCGGGTCGGGTT
236618 CGAGTTTAGG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.12, C:0.11, G:0.37, T:0.40
Consensus pattern (32 bp):
TTCGGGTCGGGTCGGGTTTTTTAAATGTGATA
Found at i:240322 original size:18 final size:18
Alignment explanation
Indices: 240292--240369 Score: 81
Period size: 18 Copynumber: 4.4 Consensus size: 18
240282 CATTTCACTA
*
240292 TTATCGGAT-ATTTACAG
1 TTATCAGATGATTTACAG
* *
240309 TTATCGGATGATTTTCAG
1 TTATCAGATGATTTACAG
* *
240327 TTATTAGATGA-TTACAA
1 TTATCAGATGATTTACAG
240344 TTATCAGATG-TTTAACAG
1 TTATCAGATGATTT-ACAG
240362 TTATCAGA
1 TTATCAGA
240370 CATAGATATT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
17 24 0.47
18 27 0.53
ACGTcount: A:0.32, C:0.10, G:0.17, T:0.41
Consensus pattern (18 bp):
TTATCAGATGATTTACAG
Found at i:241710 original size:74 final size:74
Alignment explanation
Indices: 241565--241702 Score: 199
Period size: 74 Copynumber: 1.9 Consensus size: 74
241555 GAGTACAAAT
* ** *
241565 AAAATTTCAGGGTGGGCGTCATCCATAAAATAAGTAACTAATCGAAGAAAACTCAGATTTCACGA
1 AAAATTTCAAGGTGGGCACCATCCATAAAATAAGTAACTAATCGAAGAAAACTCAGATTTCAAGA
241630 TAGGCACAA
66 TAGGCACAA
*
241639 AAAATTTCAAGGTGGGCACCAT-CAGTAAAATAAGTAACTAATCGAAGAAAATTC-GAATTTCAA
1 AAAATTTCAAGGTGGGCACCATCCA-TAAAATAAGTAACTAATCGAAGAAAACTCAG-ATTTCAA
241702 G
64 G
241703 TTGGGCACGT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
73 3 0.05
74 54 0.95
ACGTcount: A:0.43, C:0.16, G:0.18, T:0.22
Consensus pattern (74 bp):
AAAATTTCAAGGTGGGCACCATCCATAAAATAAGTAACTAATCGAAGAAAACTCAGATTTCAAGA
TAGGCACAA
Found at i:241877 original size:88 final size:88
Alignment explanation
Indices: 241718--241886 Score: 230
Period size: 88 Copynumber: 1.9 Consensus size: 88
241708 CACGTGCCCG
* * *
241718 CCCTGACCAAGCTGTGCGTCCGCCACTGATTCGAACCTCTGACATTGTTTAAGGGATATAGTTTC
1 CCCTGACCAAGCTGTGCGTCCGCCACTGATTCAAACCTCTGACATTGCTTAAGGGATATAGTGTC
241783 TCATCCTAGACCAACTGTTCCCA
66 TCATCCTAGACCAACTGTTCCCA
* * * * * * *
241806 CCCTGACCAAGTTGTGGGTCTGCCACTGATTCAAACCTTTGACCTTGCTTAAGTGATCTAGTGTC
1 CCCTGACCAAGCTGTGCGTCCGCCACTGATTCAAACCTCTGACATTGCTTAAGGGATATAGTGTC
* *
241871 TTATCCTATACCAACT
66 TCATCCTAGACCAACT
241887 AGTTTTTGAT
Statistics
Matches: 69, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
88 69 1.00
ACGTcount: A:0.22, C:0.29, G:0.18, T:0.31
Consensus pattern (88 bp):
CCCTGACCAAGCTGTGCGTCCGCCACTGATTCAAACCTCTGACATTGCTTAAGGGATATAGTGTC
TCATCCTAGACCAACTGTTCCCA
Found at i:247990 original size:45 final size:45
Alignment explanation
Indices: 247939--248038 Score: 173
Period size: 45 Copynumber: 2.2 Consensus size: 45
247929 ATTTAAAATA
* * *
247939 ATGAAAGTGATCATATGTGGTTATGTGAAAAGTGATGGAAAAGAT
1 ATGAAAGTGATCATATGTGCTTATGTGAAAAGTAATGAAAAAGAT
247984 ATGAAAGTGATCATATGTGCTTATGTGAAAAGTAATGAAAAAGAT
1 ATGAAAGTGATCATATGTGCTTATGTGAAAAGTAATGAAAAAGAT
248029 ATGAAAGTGA
1 ATGAAAGTGA
248039 GAAATGTATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.28
Consensus pattern (45 bp):
ATGAAAGTGATCATATGTGCTTATGTGAAAAGTAATGAAAAAGAT
Found at i:255930 original size:45 final size:45
Alignment explanation
Indices: 255879--255978 Score: 173
Period size: 45 Copynumber: 2.2 Consensus size: 45
255869 ATGTAAAATA
* * *
255879 ATGAAAGTGATCATATGTGGTTATGTGAAAAGTGATGGAAAAGAT
1 ATGAAAGTGATCATATGTGCTTATGTGAAAAGTAATGAAAAAGAT
255924 ATGAAAGTGATCATATGTGCTTATGTGAAAAGTAATGAAAAAGAT
1 ATGAAAGTGATCATATGTGCTTATGTGAAAAGTAATGAAAAAGAT
255969 ATGAAAGTGA
1 ATGAAAGTGA
255979 GAAATATATT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 52 1.00
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.28
Consensus pattern (45 bp):
ATGAAAGTGATCATATGTGCTTATGTGAAAAGTAATGAAAAAGAT
Found at i:256084 original size:18 final size:18
Alignment explanation
Indices: 256061--256133 Score: 85
Period size: 18 Copynumber: 3.9 Consensus size: 18
256051 AGGGATAATC
*
256061 AGTGGTCCTTCGGGACAT
1 AGTGGTCATTCGGGACAT
* *
256079 AGTGGTTC-TTCGGAATAAT
1 AGTGG-TCATTCGGGA-CAT
256098 CAGTGGTCATTCGGGACAT
1 -AGTGGTCATTCGGGACAT
256117 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
256134 AATATTCAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
18 28 0.60
19 8 0.17
20 11 0.23
ACGTcount: A:0.22, C:0.18, G:0.32, T:0.29
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:256317 original size:18 final size:18
Alignment explanation
Indices: 256294--256346 Score: 106
Period size: 18 Copynumber: 2.9 Consensus size: 18
256284 CGGAATAATC
256294 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
256312 AGTGGTCATTCGGGACAT
1 AGTGGTCATTCGGGACAT
256330 AGTGGTCATTCGGGACA
1 AGTGGTCATTCGGGACA
256347 AATATTCAGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.23, C:0.17, G:0.34, T:0.26
Consensus pattern (18 bp):
AGTGGTCATTCGGGACAT
Found at i:260237 original size:16 final size:15
Alignment explanation
Indices: 260206--260261 Score: 58
Period size: 16 Copynumber: 3.6 Consensus size: 15
260196 TAATTTTCGG
*
260206 TTCGGTTCGGTTGCT
1 TTCGGTTTGGTTGCT
260221 TTCGGTTTGGATTGCT
1 TTCGGTTTGG-TTGCT
* *
260237 TTTGGTTTAGGTTACT
1 TTCGGTTT-GGTTGCT
*
260253 TTCGATTTG
1 TTCGGTTTG
260262 ATTAAATTCA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
15 10 0.29
16 22 0.65
17 2 0.06
ACGTcount: A:0.07, C:0.12, G:0.29, T:0.52
Consensus pattern (15 bp):
TTCGGTTTGGTTGCT
Found at i:260418 original size:13 final size:13
Alignment explanation
Indices: 260400--260425 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
260390 TCATATCTCG
260400 ATTCGAATAATCA
1 ATTCGAATAATCA
260413 ATTCGAATAATCA
1 ATTCGAATAATCA
260426 TGTTCGAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
ATTCGAATAATCA
Found at i:262169 original size:2 final size:2
Alignment explanation
Indices: 262162--262186 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
262152 CCTTAGCTTA
262162 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
262187 CATTATTGCC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:263172 original size:2 final size:2
Alignment explanation
Indices: 263165--263205 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
263155 ATAAATCGAG
263165 AT AT AT AT 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 AT AT AT AT A
263206 CACTACACAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:263392 original size:2 final size:2
Alignment explanation
Indices: 263385--263432 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
263375 ATCGTGACCC
263385 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
263427 AT AT AT
1 AT AT AT
263433 CGGTATAAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:264092 original size:60 final size:60
Alignment explanation
Indices: 263987--264101 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
263977 ATAGTCAGAT
* * * *
263987 GACTATTTTATAACTTTTAATAGTCTGGAGACTCAATAAAGTAATA-TCCTATAATAAGAG
1 GACTATTTTATAACTTTTAATAGTCTAGAAACTCAACAAAATAATACT-CTATAATAAGAG
* *
264047 GACTATTTTATAATTTTTAATAGT-TAAGAAATTCAACAAAATAATACTCTATAAT
1 GACTATTTTATAACTTTTAATAGTCT-AGAAACTCAACAAAATAATACTCTATAAT
264102 TAGGGACCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.02
60 45 0.96
61 1 0.02
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (60 bp):
GACTATTTTATAACTTTTAATAGTCTAGAAACTCAACAAAATAATACTCTATAATAAGAG
Found at i:264947 original size:2 final size:2
Alignment explanation
Indices: 264940--265011 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
264930 TCATTAAACT
264940 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
264982 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
265012 ACTTTATTAA
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:265213 original size:60 final size:60
Alignment explanation
Indices: 265090--265219 Score: 156
Period size: 60 Copynumber: 2.2 Consensus size: 60
265080 TTAATACTCT
* * * *
265090 AATTTCATCCTCAAACTATGATATTCATTCTAAATTAGTCCTAAAATTTTTGAACATTCC
1 AATTTCATCCACAAACTATGATATTCATTCTAAATTACTCCTAAAACTTTTAAACATTCC
* * * *
265150 AATTTCATCCACAAACTATGAT-TCTTATTCTAAATTACTCGTTAAACTTTTAAATC-TTTC
1 AATTTCATCCACAAACTATGATAT-TCATTCTAAATTACTCCTAAAACTTTTAAA-CATTCC
265210 AATTTCATCC
1 AATTTCATCC
265220 CCATATTCAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
59 1 0.02
60 58 0.97
61 1 0.02
ACGTcount: A:0.34, C:0.21, G:0.04, T:0.42
Consensus pattern (60 bp):
AATTTCATCCACAAACTATGATATTCATTCTAAATTACTCCTAAAACTTTTAAACATTCC
Found at i:271417 original size:21 final size:20
Alignment explanation
Indices: 271378--271415 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
271368 CGGTGACTAA
271378 AAATATAAAAGTTAAAAATT
1 AAATATAAAAGTTAAAAATT
271398 AAATGATAAAA-TTAAAAA
1 AAAT-ATAAAAGTTAAAAA
271416 ATGATAAAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.26
Consensus pattern (20 bp):
AAATATAAAAGTTAAAAATT
Found at i:271419 original size:16 final size:16
Alignment explanation
Indices: 271398--271433 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
271388 GTTAAAAATT
271398 AAATGATAAAATTAAA
1 AAATGATAAAATTAAA
* *
271414 AAATGATAAAGTTAAG
1 AAATGATAAAATTAAA
271430 AAAT
1 AAAT
271434 CAAAACAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (16 bp):
AAATGATAAAATTAAA
Found at i:272607 original size:19 final size:19
Alignment explanation
Indices: 272583--272643 Score: 72
Period size: 19 Copynumber: 3.3 Consensus size: 19
272573 AAACTGAAAC
272583 CGGTTTTTTCAATTCGGTT
1 CGGTTTTTTCAATTCGGTT
*
272602 CGGTTTTTTTAA--CGGTT
1 CGGTTTTTTCAATTCGGTT
* **
272619 CGGGTTTTTCGGTTCGGTT
1 CGGTTTTTTCAATTCGGTT
272638 CGGTTT
1 CGGTTT
272644 ATCGGTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
17 13 0.38
19 21 0.62
ACGTcount: A:0.07, C:0.15, G:0.28, T:0.51
Consensus pattern (19 bp):
CGGTTTTTTCAATTCGGTT
Found at i:272642 original size:18 final size:19
Alignment explanation
Indices: 272614--272650 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
272604 GTTTTTTTAA
*
272614 CGGTTCGGGTTTTTCGGTT
1 CGGTTCGGGTTTATCGGTT
272633 CGGTTC-GGTTTATCGGTT
1 CGGTTCGGGTTTATCGGTT
272651 TTTCAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.03, C:0.16, G:0.35, T:0.46
Consensus pattern (19 bp):
CGGTTCGGGTTTATCGGTT
Found at i:272863 original size:9 final size:9
Alignment explanation
Indices: 272825--272867 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
272815 AACCAAACCG
272825 TTTTACTCGA
1 TTTTA-TCGA
*
272835 TTCGTATCGA
1 TT-TTATCGA
272845 TTTT-TCGA
1 TTTTATCGA
272853 TTTTATCGA
1 TTTTATCGA
272862 TTTTAT
1 TTTTAT
272868 TGCTCAGCCC
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
8 8 0.28
9 11 0.38
10 8 0.28
11 2 0.07
ACGTcount: A:0.19, C:0.14, G:0.12, T:0.56
Consensus pattern (9 bp):
TTTTATCGA
Found at i:273452 original size:47 final size:49
Alignment explanation
Indices: 273399--273491 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 49
273389 AAAAAAATGG
273399 TATTGATATATCAAATAAC-TGG-TATATAATTTTTAAAAAATAAATTA
1 TATTGATATATCAAATAACTTGGATATATAATTTTTAAAAAATAAATTA
*
273446 TATTGATATATCAAATAACTTGGTATATATAATTTTTATAAAATAA
1 TATTGATATATCAAATAACTTGG-ATATATAATTTTTAAAAAATAA
273492 TAAAAATATA
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
47 19 0.45
48 3 0.07
50 20 0.48
ACGTcount: A:0.47, C:0.04, G:0.06, T:0.42
Consensus pattern (49 bp):
TATTGATATATCAAATAACTTGGATATATAATTTTTAAAAAATAAATTA
Found at i:273491 original size:50 final size:47
Alignment explanation
Indices: 273383--273491 Score: 157
Period size: 47 Copynumber: 2.3 Consensus size: 47
273373 ATGATTTACC
*
273383 TTTTATAAAA-AAATGGTATTGATATATCAAATAACTGGTATATAAT
1 TTTTATAAAATAAATGATATTGATATATCAAATAACTGGTATATAAT
* *
273429 TTTTAAAAAATAAATTATATTGATATATCAAATAACTTGGTATATATAAT
1 TTTTATAAAATAAATGATATTGATATATCAAATAAC-TGG--TATATAAT
273479 TTTTATAAAATAA
1 TTTTATAAAATAA
273492 TAAAAATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
46 9 0.16
47 23 0.42
48 3 0.05
50 20 0.36
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (47 bp):
TTTTATAAAATAAATGATATTGATATATCAAATAACTGGTATATAAT
Found at i:274913 original size:13 final size:13
Alignment explanation
Indices: 274895--274921 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
274885 TAACGCATAC
274895 GTGTCGTATTTGG
1 GTGTCGTATTTGG
274908 GTGTCGTATTTGG
1 GTGTCGTATTTGG
274921 G
1 G
274922 GATATATCGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.07, C:0.07, G:0.41, T:0.44
Consensus pattern (13 bp):
GTGTCGTATTTGG
Found at i:275666 original size:21 final size:21
Alignment explanation
Indices: 275616--275753 Score: 122
Period size: 21 Copynumber: 6.8 Consensus size: 21
275606 CGTTGTGATT
*
275616 TTAGACTATCGCAA--CGAAT
1 TTAGACTATCGCAACGCGAAC
**
275635 TTAGAAAATCGCAACGCGAAC
1 TTAGACTATCGCAACGCGAAC
* *
275656 TTCGACTATCGCAACGTGAAC
1 TTAGACTATCGCAACGCGAAC
* * *
275677 TTGGACAATCGCAA--CGAAT
1 TTAGACTATCGCAACGCGAAC
** *
275696 TTAGAAAATCGTAACGCGAAC
1 TTAGACTATCGCAACGCGAAC
* *
275717 TTCGACTATCGCAACGTGAAC
1 TTAGACTATCGCAACGCGAAC
*
275738 TTAAACTATCGCAACG
1 TTAGACTATCGCAACG
275754 AATTTGGACT
Statistics
Matches: 93, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
19 26 0.28
21 67 0.72
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (21 bp):
TTAGACTATCGCAACGCGAAC
Found at i:275764 original size:40 final size:39
Alignment explanation
Indices: 275620--275762 Score: 110
Period size: 40 Copynumber: 3.5 Consensus size: 39
275610 GTGATTTTAG
* * * **
275620 ACTATCGCAACGAATTTAGAAAATCGCAACGCGAACTTCG
1 ACTATCGCAACGAACTTGGACAATCGCAACG-GAACTTAA
*
275660 ACTATCGCAACGTGAACTTGGACAATCGCAAC-GAATTTAGA
1 ACTATCGCAAC--GAACTTGGACAATCGCAACGGAACTTA-A
* * * *
275701 A-AATCGTAACGCGAACTTCGACTATCGCAACGTGAACTTAA
1 ACTATCGCAA--CGAACTTGGACAATCGCAACG-GAACTTAA
*
275742 ACTATCGCAACGAATTTGGAC
1 ACTATCGCAACGAACTTGGAC
275763 TAACGTAAAT
Statistics
Matches: 80, Mismatches: 15, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
40 48 0.60
41 3 0.04
42 29 0.36
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.22
Consensus pattern (39 bp):
ACTATCGCAACGAACTTGGACAATCGCAACGGAACTTAA
Found at i:275770 original size:61 final size:61
Alignment explanation
Indices: 275620--275758 Score: 242
Period size: 61 Copynumber: 2.3 Consensus size: 61
275610 GTGATTTTAG
* **
275620 ACTATCGCAACGAATTTAGAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGG
1 ACTATCGCAACGAATTTAGAAAATCGTAACGCGAACTTCGACTATCGCAACGTGAACTTAA
*
275681 ACAATCGCAACGAATTTAGAAAATCGTAACGCGAACTTCGACTATCGCAACGTGAACTTAA
1 ACTATCGCAACGAATTTAGAAAATCGTAACGCGAACTTCGACTATCGCAACGTGAACTTAA
275742 ACTATCGCAACGAATTT
1 ACTATCGCAACGAATTT
275759 GGACTAACGT
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
61 73 1.00
ACGTcount: A:0.37, C:0.24, G:0.17, T:0.22
Consensus pattern (61 bp):
ACTATCGCAACGAATTTAGAAAATCGTAACGCGAACTTCGACTATCGCAACGTGAACTTAA
Found at i:275836 original size:41 final size:41
Alignment explanation
Indices: 275786--275897 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 41
275776 AAAAATCGTG
*
275786 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATCGCA
1 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATAGCA
* *
275827 TTGCGATTTTGTATTATCGCGTTGCAATAGTCAGAATAGCG
1 TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATAGCA
**
275868 TTGCGA-TTTACA-TATTCGCGTTGCGATAGT
1 TTGCGATTTTGTATTA-TCGCGTTGCGATAGT
275898 TAAAATCGTG
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
39 2 0.03
40 18 0.28
41 44 0.69
ACGTcount: A:0.22, C:0.16, G:0.24, T:0.38
Consensus pattern (41 bp):
TTGCGATTTTGTATTATCGCGTTGCGATAGTCAGAATAGCA
Found at i:275851 original size:21 final size:21
Alignment explanation
Indices: 275780--275851 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
275770 AATTTGAAAA
*
275780 ATCGTGTTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
* **
275801 ATCGCGTTGCGA--TAGTCAGA
1 ATCGCGTTGCGATTTTGT-ATT
*
275821 ATCGCATTGCGATTTTGTATT
1 ATCGCGTTGCGATTTTGTATT
275842 ATCGCGTTGC
1 ATCGCGTTGC
275852 AATAGTCAGA
Statistics
Matches: 39, Mismatches: 9, Indels: 6
0.72 0.17 0.11
Matches are distributed among these distances:
19 3 0.08
20 12 0.31
21 21 0.54
22 3 0.08
ACGTcount: A:0.18, C:0.17, G:0.25, T:0.40
Consensus pattern (21 bp):
ATCGCGTTGCGATTTTGTATT
Found at i:275951 original size:20 final size:19
Alignment explanation
Indices: 275928--275973 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
275918 GGAAACTGAT
* *
275928 TTGCGATACTGGAGATCGCG
1 TTGCGAT-CTAGAGATCGCA
*
275948 TTGCGATTTAGAGATCGCA
1 TTGCGATCTAGAGATCGCA
275967 TTGCGAT
1 TTGCGAT
275974 TTTGTTGGTC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.30
Consensus pattern (19 bp):
TTGCGATCTAGAGATCGCA
Found at i:275963 original size:19 final size:19
Alignment explanation
Indices: 275939--275975 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
275929 TGCGATACTG
*
275939 GAGATCGCGTTGCGATTTA
1 GAGATCGCATTGCGATTTA
275958 GAGATCGCATTGCGATTT
1 GAGATCGCATTGCGATTT
275976 TGTTGGTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
GAGATCGCATTGCGATTTA
Found at i:292686 original size:25 final size:25
Alignment explanation
Indices: 292652--292702 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
292642 TGCACTATAA
292652 TAGTTTAGCATCCTAGGCCTTTCGT
1 TAGTTTAGCATCCTAGGCCTTTCGT
292677 TAGTTTAGCATCCTAGGCCTTTCGT
1 TAGTTTAGCATCCTAGGCCTTTCGT
292702 T
1 T
292703 CGGGACATTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.16, C:0.24, G:0.20, T:0.41
Consensus pattern (25 bp):
TAGTTTAGCATCCTAGGCCTTTCGT
Found at i:296037 original size:24 final size:24
Alignment explanation
Indices: 295983--296039 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
295973 TCCGGTTCAA
*
295983 TCTCCGATTTAGCCTCTTGTTTGG
1 TCTCCGGTTTAGCCTCTTGTTTGG
*
296007 TATCCGGTTTAGCCTCTTGTTTGG
1 TCTCCGGTTTAGCCTCTTGTTTGG
296031 TCTCCGGTT
1 TCTCCGGTT
296040 CCGGCATTGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.07, C:0.25, G:0.23, T:0.46
Consensus pattern (24 bp):
TCTCCGGTTTAGCCTCTTGTTTGG
Found at i:296880 original size:34 final size:34
Alignment explanation
Indices: 296782--296884 Score: 86
Period size: 34 Copynumber: 3.0 Consensus size: 34
296772 CCGGGGAGAG
296782 TGGAAATGGGAAAGTCCTTCAAACTTTGTTTATA
1 TGGAAATGGGAAAGTCCTTCAAACTTTGTTTATA
** * ** * * *
296816 TCTAAATCTGGACAA-TTATT--ATCATATGTTTATT
1 TGGAAAT-GGGA-AAGTCCTTCAAAC-TTTGTTTATA
296850 TGGAAATGGGAAAGTCCTTCAAACTTTGTTTATA
1 TGGAAATGGGAAAGTCCTTCAAACTTTGTTTATA
296884 T
1 T
296885 CTAAATCTGG
Statistics
Matches: 47, Mismatches: 16, Indels: 12
0.63 0.21 0.16
Matches are distributed among these distances:
32 2 0.04
33 8 0.17
34 27 0.57
35 8 0.17
36 2 0.04
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (34 bp):
TGGAAATGGGAAAGTCCTTCAAACTTTGTTTATA
Found at i:301322 original size:36 final size:38
Alignment explanation
Indices: 301277--301382 Score: 144
Period size: 36 Copynumber: 2.7 Consensus size: 38
301267 TTTTTAAATA
*
301277 AATTAAATATTAATTTTTTAATATTATA-TA-GATATT
1 AATTTAATATTAATTTTTTAATATTATATTATGATATT
301313 AATTTAATATTAATTTTTTAATATTATATTATGATATT
1 AATTTAATATTAATTTTTTAATATTATATTATGATATT
301351 AATTTTATATATATAATTATTTTATATATTAT
1 AA-TTTA-ATAT-TAATT-TTTTA-ATATTAT
301383 TAAAATTTTA
Statistics
Matches: 62, Mismatches: 1, Indels: 7
0.89 0.01 0.10
Matches are distributed among these distances:
36 27 0.44
37 2 0.03
38 8 0.13
39 4 0.06
40 4 0.06
41 5 0.08
42 5 0.08
43 7 0.11
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (38 bp):
AATTTAATATTAATTTTTTAATATTATATTATGATATT
Found at i:301352 original size:19 final size:19
Alignment explanation
Indices: 301294--301360 Score: 61
Period size: 19 Copynumber: 3.6 Consensus size: 19
301284 TATTAATTTT
301294 TTAATATTATA-TA-GATA
1 TTAATATTATATTATGATA
* *
301311 TTAAT-TTAATATTAAT-TTT
1 TTAATATT-ATATT-ATGATA
301330 TTAATATTATATTATGATA
1 TTAATATTATATTATGATA
*
301349 TTAATTTTATAT
1 TTAATATTATAT
301361 ATATAATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 10
0.72 0.09 0.19
Matches are distributed among these distances:
16 2 0.05
17 8 0.21
18 3 0.08
19 24 0.62
20 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTAATATTATATTATGATA
Found at i:301357 original size:61 final size:56
Alignment explanation
Indices: 301230--301365 Score: 159
Period size: 60 Copynumber: 2.3 Consensus size: 56
301220 GGTTTTATAT
301230 TTAATTTTATAT-TATAGATATTAATTGCTATATTAATTTTTTAAATAAATTAAATA
1 TTAATTTTATATATATAGATATTAATT-CTATATTAATTTTTTAAATAAATTAAATA
* *
301286 TTAATTTTTTAATATTATATAGATATTAATT-TAATATTAATTTTTTAATATTATATTATGATA
1 TTAA--TTTT-ATA-TATATAGATATTAATTCT-ATATTAATTTTTTAA-A-TAAATTA-AATA
301349 TTAATTTTATATATATA
1 TTAATTTTATATATATA
301366 ATTATTTTAT
Statistics
Matches: 69, Mismatches: 2, Indels: 15
0.80 0.02 0.17
Matches are distributed among these distances:
56 4 0.06
58 4 0.06
59 10 0.14
60 19 0.28
61 19 0.28
62 6 0.09
63 7 0.10
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (56 bp):
TTAATTTTATATATATAGATATTAATTCTATATTAATTTTTTAAATAAATTAAATA
Found at i:301406 original size:17 final size:17
Alignment explanation
Indices: 301328--301406 Score: 61
Period size: 17 Copynumber: 4.5 Consensus size: 17
301318 AATATTAATT
*
301328 TTTTAATATTATATTATGA
1 TTTTAATTTTATATT-T-A
* *
301347 TATTAATTTTATATATA
1 TTTTAATTTTATATTTA
*
301364 TAATT-ATTTTATATATTA
1 T-TTTAATTTTATAT-TTA
**
301382 TTAAAATTTTATATTTA
1 TTTTAATTTTATATTTA
301399 TTTTAATT
1 TTTTAATT
301407 ATTTTGATTT
Statistics
Matches: 48, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
17 20 0.42
18 16 0.33
19 12 0.25
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (17 bp):
TTTTAATTTTATATTTA
Found at i:302059 original size:29 final size:30
Alignment explanation
Indices: 302004--302061 Score: 82
Period size: 29 Copynumber: 1.9 Consensus size: 30
301994 TAGTTGTATG
**
302004 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAA-TTCAGTATTACAAAACTAA
302035 AATTATTTAAA-TCAGTATTACAAAACT
1 AATTATTTAAATTCAGTATTACAAAACT
302062 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 14 0.56
31 11 0.44
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.40
Consensus pattern (30 bp):
AATTATTTAAATTCAGTATTACAAAACTAA
Found at i:307131 original size:20 final size:22
Alignment explanation
Indices: 307101--307141 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
307091 TTCTGTCTTG
307101 GAAAGTTTCGAAAC-TCTTGTA
1 GAAAGTTTCGAAACTTCTTGTA
307122 GAAA-TTTCGAAACTTCTTGT
1 GAAAGTTTCGAAACTTCTTGT
307142 CAAAGCTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (22 bp):
GAAAGTTTCGAAACTTCTTGTA
Found at i:307274 original size:11 final size:11
Alignment explanation
Indices: 307258--307292 Score: 61
Period size: 11 Copynumber: 3.2 Consensus size: 11
307248 GACTCATATT
*
307258 AAAGTTTTGAA
1 AAAGTTTAGAA
307269 AAAGTTTAGAA
1 AAAGTTTAGAA
307280 AAAGTTTAGAA
1 AAAGTTTAGAA
307291 AA
1 AA
307293 CATTAAACAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (11 bp):
AAAGTTTAGAA
Found at i:307944 original size:43 final size:43
Alignment explanation
Indices: 307882--307980 Score: 128
Period size: 43 Copynumber: 2.3 Consensus size: 43
307872 TTTAAAGGTT
* *
307882 AAAAGTGAGATTGAAAAAAATTAGGGGCCTAAATTATACAAGTA
1 AAAAATGAGATTGAAAAAAATTAGAGGCCTAAATTATA-AAGTA
* * *
307926 AAAAATGAGATTG-AAAAAATTAGAGGCCTCAGTTATAAAGTT
1 AAAAATGAGATTGAAAAAAATTAGAGGCCTAAATTATAAAGTA
307968 AAAAATAGAGATT
1 AAAAAT-GAGATT
307981 AGGGGTGTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
42 10 0.20
43 27 0.55
44 12 0.24
ACGTcount: A:0.51, C:0.06, G:0.19, T:0.24
Consensus pattern (43 bp):
AAAAATGAGATTGAAAAAAATTAGAGGCCTAAATTATAAAGTA
Found at i:308041 original size:41 final size:44
Alignment explanation
Indices: 307988--308171 Score: 143
Period size: 43 Copynumber: 4.3 Consensus size: 44
307978 ATTAGGGGTG
*
307988 TCAATTGA-AAAGGTAGAAAGTGAGATTGAAAAA-TT-A-GGAGC-
1 TCAATT-ATAAAGGTAAAAAGTGAGATTGAAAAACTTAAGGGA-CA
* * *
308029 TCAATTATAAAGGTACAAAGTGGGATTGAAAAACTTAA-GGTCA
1 TCAATTATAAAGGTAAAAAGTGAGATTGAAAAACTTAAGGGACA
* * * *
308072 TCAATTATAAATGTACAAAAGTGGGATTGAAAAAAATTAAGGG-CC
1 TCAATTATAAAGGTA-AAAAGTGAGATTG-AAAAACTTAAGGGACA
* * * * *
308117 TCAATTATAAAGATAAAAATTAAGATT-ACAAAA-TTTAGGGACT
1 TCAATTATAAAGGTAAAAAGTGAGATTGA-AAAACTTAAGGGACA
308160 TCAATTATAAAG
1 TCAATTATAAAG
308172 ACAAAAATAT
Statistics
Matches: 120, Mismatches: 14, Indels: 16
0.80 0.09 0.11
Matches are distributed among these distances:
40 1 0.01
41 29 0.24
42 10 0.08
43 34 0.28
44 21 0.17
45 23 0.19
46 2 0.02
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (44 bp):
TCAATTATAAAGGTAAAAAGTGAGATTGAAAAACTTAAGGGACA
Found at i:308088 original size:43 final size:42
Alignment explanation
Indices: 307988--308171 Score: 155
Period size: 41 Copynumber: 4.3 Consensus size: 42
307978 ATTAGGGGTG
* *
307988 TCAATTGA-AAAGGTA-GAAAGTGAGATTGAAAAATT-AGGAGC
1 TCAATT-ATAAAGGTACAAAAGTGGGATTGAAAAATTAAGG-GC
*
308029 TCAATTATAAAGGTAC-AAAGTGGGATTGAAAAACTTAAGGTC
1 TCAATTATAAAGGTACAAAAGTGGGATTGAAAAA-TTAAGGGC
*
308071 ATCAATTATAAATGTACAAAAGTGGGATTGAAAAAAATTAAGGGCC
1 -TCAATTATAAAGGTACAAAAGTGGGATTG--AAAAATTAAGGG-C
* * ** *
308117 TCAATTATAAAGATA-AAAATTAAGATT-ACAAAATTTAGGGAC
1 TCAATTATAAAGGTACAAAAGTGGGATTGA-AAAATTAAGGG-C
308159 TTCAATTATAAAG
1 -TCAATTATAAAG
308172 ACAAAAATAT
Statistics
Matches: 121, Mismatches: 11, Indels: 20
0.80 0.07 0.13
Matches are distributed among these distances:
40 1 0.01
41 30 0.25
42 14 0.12
43 30 0.25
44 21 0.17
45 19 0.16
46 6 0.05
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (42 bp):
TCAATTATAAAGGTACAAAAGTGGGATTGAAAAATTAAGGGC
Found at i:308121 original size:45 final size:43
Alignment explanation
Indices: 307988--308128 Score: 164
Period size: 41 Copynumber: 3.3 Consensus size: 43
307978 ATTAGGGGTG
* *
307988 TCAATTGA-AAAGGTAGAAAGTGAGATTG-AAAAATT-AGGAG-C
1 TCAATT-ATAAAGGTACAAAGTGGGATTGAAAAAATTAAGG-GCC
* * *
308029 TCAATTATAAAGGTACAAAGTGGGATTGAAAAACTTAAGGTCA
1 TCAATTATAAAGGTACAAAGTGGGATTGAAAAAATTAAGGGCC
*
308072 TCAATTATAAATGTACAAAAGTGGGATTGAAAAAAATTAAGGGCC
1 TCAATTATAAAGGTAC-AAAGTGGGATTG-AAAAAATTAAGGGCC
308117 TCAATTATAAAG
1 TCAATTATAAAG
308129 ATAAAAATTA
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
40 1 0.01
41 24 0.29
42 6 0.07
43 18 0.21
44 12 0.14
45 23 0.27
ACGTcount: A:0.46, C:0.08, G:0.21, T:0.25
Consensus pattern (43 bp):
TCAATTATAAAGGTACAAAGTGGGATTGAAAAAATTAAGGGCC
Found at i:308769 original size:15 final size:15
Alignment explanation
Indices: 308749--308786 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
308739 TTTATTGAAT
*
308749 AATCGAATCGAATCA
1 AATCGAATCAAATCA
308764 AATCGAATCAAATCA
1 AATCGAATCAAATCA
*
308779 AATTGAAT
1 AATCGAAT
308787 ACACCCCTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.50, C:0.16, G:0.11, T:0.24
Consensus pattern (15 bp):
AATCGAATCAAATCA
Found at i:309449 original size:14 final size:14
Alignment explanation
Indices: 309430--309472 Score: 77
Period size: 14 Copynumber: 3.1 Consensus size: 14
309420 TCGATTATAT
*
309430 GTTCATTTTTGTTC
1 GTTCATTTATGTTC
309444 GTTCATTTATGTTC
1 GTTCATTTATGTTC
309458 GTTCATTTATGTTC
1 GTTCATTTATGTTC
309472 G
1 G
309473 AACAAAGGGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.12, C:0.14, G:0.16, T:0.58
Consensus pattern (14 bp):
GTTCATTTATGTTC
Found at i:309794 original size:14 final size:14
Alignment explanation
Indices: 309726--309794 Score: 61
Period size: 14 Copynumber: 5.1 Consensus size: 14
309716 TTATTTTTTG
*
309726 TGTTTGTGTT-GTT
1 TGTTTATGTTCGTT
* *
309739 CGTTTATGTTCATT
1 TGTTTATGTTCGTT
*
309753 T-ATTATGTTCGTT
1 TGTTTATGTTCGTT
* *
309766 CGTTTTTGTTCGTT
1 TGTTTATGTTCGTT
*
309780 TGTTTGTGTTCGTT
1 TGTTTATGTTCGTT
309794 T
1 T
309795 ATGTTCCTTT
Statistics
Matches: 43, Mismatches: 11, Indels: 3
0.75 0.19 0.05
Matches are distributed among these distances:
13 18 0.42
14 25 0.58
ACGTcount: A:0.06, C:0.09, G:0.22, T:0.64
Consensus pattern (14 bp):
TGTTTATGTTCGTT
Found at i:309862 original size:16 final size:16
Alignment explanation
Indices: 309841--309873 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
309831 AAATTTTTTT
309841 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
309857 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
309873 T
1 T
309874 TTATTATTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:309881 original size:71 final size:71
Alignment explanation
Indices: 309768--309969 Score: 320
Period size: 71 Copynumber: 2.9 Consensus size: 71
309758 TGTTCGTTCG
* * * *
309768 TTTTTGTTC-GTT-TGTTTGTGTTCGTTTATGTTCCTTTATTATTTAAATGAACGAACATGAACA
1 TTTTTGTTCATTTATGTTCGTGTTCATTTATGTTCGTTTATTATTTAAATGAACGAACATGAACA
*
309831 AAATTT
66 AAAATT
309837 TTTTTGTTCATTTATGTTCGTGTTCATTTATGTTCGTTTATTATTTAAATGAACGAACATGAACA
1 TTTTTGTTCATTTATGTTCGTGTTCATTTATGTTCGTTTATTATTTAAATGAACGAACATGAACA
309902 AAAATT
66 AAAATT
*
309908 TTTTTGTTCATTTATGTTCGTGTTCATTTATGTTCGTTTATT-TATTAAATGAATGAACATGA
1 TTTTTGTTCATTTATGTTCGTGTTCATTTATGTTCGTTTATTAT-TTAAATGAACGAACATGA
309970 CATACCTCCG
Statistics
Matches: 124, Mismatches: 6, Indels: 4
0.93 0.04 0.03
Matches are distributed among these distances:
69 9 0.07
70 3 0.02
71 112 0.90
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.50
Consensus pattern (71 bp):
TTTTTGTTCATTTATGTTCGTGTTCATTTATGTTCGTTTATTATTTAAATGAACGAACATGAACA
AAAATT
Found at i:309933 original size:16 final size:16
Alignment explanation
Indices: 309912--309952 Score: 68
Period size: 16 Copynumber: 2.7 Consensus size: 16
309902 AAAATTTTTT
309912 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
309928 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
309944 T-TT-ATTTAT
1 TGTTCATTTAT
309953 TAAATGAATG
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.24
15 2 0.08
16 17 0.68
ACGTcount: A:0.15, C:0.10, G:0.15, T:0.61
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:311199 original size:27 final size:27
Alignment explanation
Indices: 311161--311222 Score: 106
Period size: 27 Copynumber: 2.3 Consensus size: 27
311151 CCAACCAAAT
* *
311161 ACACCCTGAGAAACATAGGGGTGAGGA
1 ACACCCTAAGAAACATAGGGGTGAGAA
311188 ACACCCTAAGAAACATAGGGGTGAGAA
1 ACACCCTAAGAAACATAGGGGTGAGAA
311215 ACACCCTA
1 ACACCCTA
311223 CGATTACTGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (27 bp):
ACACCCTAAGAAACATAGGGGTGAGAA
Found at i:315454 original size:15 final size:15
Alignment explanation
Indices: 315430--315485 Score: 67
Period size: 15 Copynumber: 3.6 Consensus size: 15
315420 CGAATATTAT
315430 GGGTACCCGGTAATC
1 GGGTACCCGGTAATC
* **
315445 GGGTATCCGGATTTTGC
1 GGGTACCCGG-TAAT-C
315462 GGGTACCCGGTAATC
1 GGGTACCCGGTAATC
315477 GGGTACCCG
1 GGGTACCCG
315486 ATACCCGGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
15 19 0.58
16 4 0.12
17 10 0.30
ACGTcount: A:0.16, C:0.25, G:0.36, T:0.23
Consensus pattern (15 bp):
GGGTACCCGGTAATC
Found at i:315529 original size:14 final size:15
Alignment explanation
Indices: 315494--315526 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
315484 CGATACCCGG
*
315494 TTTTT-AATTTTTAA
1 TTTTTAAATTATTAA
315508 TTTTTAAATTATTAA
1 TTTTTAAATTATTAA
315523 TTTT
1 TTTT
315527 AAAAAATATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTTTAAATTATTAA
Found at i:316147 original size:19 final size:18
Alignment explanation
Indices: 316083--316149 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 18
316073 ATTCCTCTAA
* *
316083 ATATTTTTTAATTAAATCT
1 ATATTTTTTTA-TAAATAT
*
316102 ATATTTTTATTAAATAAAAAT
1 ATATTTTT-TT--ATAAATAT
316123 AATATTTTTTTATAAATAT
1 -ATATTTTTTTATAAATAT
316142 ATTATTTT
1 A-TATTTT
316150 GGGTCGGTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
18 1 0.03
19 21 0.54
20 1 0.03
21 7 0.18
22 9 0.23
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTTTTTTATAAATAT
Found at i:317668 original size:75 final size:71
Alignment explanation
Indices: 317589--317879 Score: 268
Period size: 72 Copynumber: 3.9 Consensus size: 71
317579 TGTTTTTTGT
* *
317589 ATTAAAAAATTTAAAAAATATAAAAATATATTGTAAA-TAGTAGTT-TAGAGATAAAAATTAAGA
1 ATTAAAAAA-TT-AAAAATATAAAAA-ATATTATAAATTA-TAGTTATA-AG-TAAAAATTAAAA
317652 ATTATTTCTTCC
60 ATTATTTCTTCC
* * * *
317664 ATTAAAAAATTAAAAATATATAAAAATGTTGTAAACTATAGTTAATAAGT-AAAATTAAAAAAAA
1 ATTAAAAAATTAAAAATATA-AAAAATATTATAAATTATAGTT-ATAAGTAAAAATT--AAAAAT
*
317728 TATCTCTTCC
62 TATTTCTTCC
* * * *
317738 ATTAATAATAATTAAAAATACATAAAAATATTATAAATTAAAGTTAATAAATAAAAATAAAAAAT
1 ATTAA-AA-AATTAAAAATATA-AAAAATATTATAAATTATAGTT-ATAAGTAAAAATTAAAAAT
*
317803 CATTTCTTCC
62 TATTTCTTCC
* *
317813 ATTAACAAAAATT-AAAA-ATAAAAAATATTATAAATTATAATTAATAAGTAAAAATTAAGAATT
1 ATT-A-AAAAATTAAAAATATAAAAAATATTATAAATTATAGTT-ATAAGTAAAAATTAAAAATT
317876 ATTT
63 ATTT
317880 TCTGCATTAA
Statistics
Matches: 184, Mismatches: 21, Indels: 25
0.80 0.09 0.11
Matches are distributed among these distances:
72 47 0.26
73 26 0.14
74 32 0.17
75 33 0.18
76 40 0.22
77 6 0.03
ACGTcount: A:0.57, C:0.05, G:0.04, T:0.34
Consensus pattern (71 bp):
ATTAAAAAATTAAAAATATAAAAAATATTATAAATTATAGTTATAAGTAAAAATTAAAAATTATT
TCTTCC
Found at i:317763 original size:76 final size:74
Alignment explanation
Indices: 317658--317870 Score: 256
Period size: 76 Copynumber: 2.9 Consensus size: 74
317648 AAGAATTATT
* * *
317658 TCTTCCATTAAAAAATTAAAAATATATAAAAATGTTGTAAACTATAGTTAATAAGTAAAATTAAA
1 TCTTCCATTAAAAAATTAAAAATA-ATAAAAATATTATAAATTATAGTTAATAAGTAAAATTAAA
317723 AAAAAT-ATC
65 AAAAATCATC
* *
317732 TCTTCCATTAATAATAATTAAAAATACATAAAAATATTATAAATTAAAGTTAATAAATAAAA--A
1 TCTTCCATTAA-AA-AATTAAAAATA-ATAAAAATATTATAAATTATAGTTAATAAGTAAAATTA
* *
317795 TAAAAAATCATT
63 AAAAAAATCATC
*
317807 TCTTCCATTAACAAAAATTAAAAAT-A-AAAAATATTATAAATTATAATTAATAAGTAAAAATTA
1 TCTTCCATT-A-AAAAATTAAAAATAATAAAAATATTATAAATTATAGTTAATAAGT-AAAATTA
317870 A
63 A
317871 GAATTATTTT
Statistics
Matches: 119, Mismatches: 12, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
72 26 0.22
73 5 0.04
74 19 0.16
75 24 0.20
76 44 0.37
77 1 0.01
ACGTcount: A:0.58, C:0.07, G:0.03, T:0.33
Consensus pattern (74 bp):
TCTTCCATTAAAAAATTAAAAATAATAAAAATATTATAAATTATAGTTAATAAGTAAAATTAAAA
AAAATCATC
Found at i:317857 original size:72 final size:73
Alignment explanation
Indices: 317479--317902 Score: 298
Period size: 75 Copynumber: 5.8 Consensus size: 73
317469 ATATAACTAT
* * * * * * *
317479 TAAATTATAATTAATAGAT-AAAATTAAGAATTATTTATTCAATT-A-AAAAA-TATAAACTATG
1 TAAATTATAATTAATAAATAAAAATAAAAAATTATTTCTTCCATTAATAAAAATTA-AAAATATA
317540 AAAA-A-TA
65 AAAATATTA
* * * * * * ** *
317547 TAAATTATAATTAATAAATAAAAGTCAAGAGTTGTTTTTTGTATTAA-AAAATTTAAAAAATATA
1 TAAATTATAATTAATAAATAAAAATAAAAAATTATTTCTTCCATTAATAAAAATT-AAAAATAT-
*
317611 AAAATATATTG
64 AAAA-ATATTA
* * * * * *
317622 TAAA-TAGTAGTTTAGAGATAAAAATTAAGAATTATTTCTTCCATT-A-AAAAATTAAAAATATA
1 TAAATTA-TAATTAATAAATAAAAATAAAAAATTATTTCTTCCATTAATAAAAATT-AAAA-ATA
* *
317684 TAAAAATGTTG
63 TAAAAATATTA
* * * * * * *
317695 TAAACTATAGTTAATAAGTAAAATTAAAAAAAATATCTCTTCCATTAATAATAATTAAAAATACA
1 TAAATTATAATTAATAAATAAAAAT-AAAAAATTATTTCTTCCATTAATAAAAATTAAAAAT--A
317760 TAAAAATATTA
63 TAAAAATATTA
* *
317771 TAAATTA-AAGTTAATAAATAAAAATAAAAAATCATTTCTTCCATTAACAAAAATTAAAAATA-A
1 TAAATTATAA-TTAATAAATAAAAATAAAAAATTATTTCTTCCATTAATAAAAATTAAAAATATA
317834 AAAATATTA
65 AAAATATTA
* * * * *
317843 TAAATTATAATTAATAAGTAAAAATTAAGAATTATTT-TCTGCATTAATAAAAATTTAAAA
1 TAAATTATAATTAATAAATAAAAATAAAAAATTATTTCT-TCCATTAATAAAAATTAAAAA
317903 CTTAATAAAA
Statistics
Matches: 284, Mismatches: 53, Indels: 34
0.77 0.14 0.09
Matches are distributed among these distances:
68 18 0.06
69 18 0.06
70 5 0.02
71 8 0.03
72 62 0.22
73 26 0.09
74 39 0.14
75 73 0.26
76 35 0.12
ACGTcount: A:0.55, C:0.04, G:0.05, T:0.35
Consensus pattern (73 bp):
TAAATTATAATTAATAAATAAAAATAAAAAATTATTTCTTCCATTAATAAAAATTAAAAATATAA
AAATATTA
Found at i:317924 original size:149 final size:150
Alignment explanation
Indices: 317545--317924 Score: 361
Period size: 149 Copynumber: 2.6 Consensus size: 150
317535 CTATGAAAAA
* * * * * * *
317545 TATAAATTATAATTAATAAATAAAAGTCAAGAGTTGTTTTTTGTATT-A-AAAAATTTAAAAA-A
1 TATAAATTATAATTAATAAGTAAAAATTAAGAATTATTTTCTGCATTAATAAAAATTTAAAAATA
* * * * * * *
317607 TATAAAAATATATTGTAAA-TAGTAGTTTAGAGATAAAAATTAAGAATTATTTCTTCCATTAAAA
66 -AT-AAAATATATTATAAATTAGAAGTTAAGAAATAAAAATAAAAAATCATTTCTTCCATTAAAA
*
317671 AATTAAAAATATATAAAAATGT
129 AATTAAAAATATATAAAAATAT
* * * * ** * * *
317693 TGTAAACTATAGTTAATAAGT-AAAATTAAAAAAAATATCTCTTCCATTAATAATAA-TTAAAAA
1 TATAAATTATAATTAATAAGTAAAAATTAAGAATTAT-TTTC-TGCATTAATAAAAATTTAAAAA
*
317756 TACATAAAA-ATATTATAAATTA-AAGTTAATAAATAAAAATAAAAAATCATTTCTTCCATTAAC
64 TA-ATAAAATATATTATAAATTAGAAGTTAAGAAATAAAAATAAAAAATCATTTCTTCCATT-A-
317819 AAAAATT-AAAA-ATA-AAAAATAT
126 AAAAATTAAAAATATATAAAAATAT
*
317841 TATAAATTATAATTAATAAGTAAAAATTAAGAATTATTTTCTGCATTAATAAAAATTTAAAACTT
1 TATAAATTATAATTAATAAGTAAAAATTAAGAATTATTTTCTGCATTAATAAAAATTTAAAA-AT
317906 AATAAAATTATATT-TAAAT
65 AATAAAA-TATATTATAAAT
317925 ATGTGACTGG
Statistics
Matches: 183, Mismatches: 36, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
147 20 0.11
148 59 0.32
149 66 0.36
150 24 0.13
151 14 0.08
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (150 bp):
TATAAATTATAATTAATAAGTAAAAATTAAGAATTATTTTCTGCATTAATAAAAATTTAAAAATA
ATAAAATATATTATAAATTAGAAGTTAAGAAATAAAAATAAAAAATCATTTCTTCCATTAAAAAA
TTAAAAATATATAAAAATAT
Found at i:320204 original size:32 final size:33
Alignment explanation
Indices: 320146--320211 Score: 98
Period size: 32 Copynumber: 2.0 Consensus size: 33
320136 TAAGCTAAAA
*
320146 TTTTGTTCCATGGGATTACCCAGCGTCTTTAGT
1 TTTTGCTCCATGGGATTACCCAGCGTCTTTAGT
* *
320179 TTTTGCTCCAT-GGATTACTCGGCGTCTTTAGT
1 TTTTGCTCCATGGGATTACCCAGCGTCTTTAGT
320211 T
1 T
320212 AAATTCTTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 20 0.67
33 10 0.33
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
TTTTGCTCCATGGGATTACCCAGCGTCTTTAGT
Found at i:321131 original size:23 final size:24
Alignment explanation
Indices: 321104--321150 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 24
321094 TAACCCTGAA
321104 ATATTTTGA-ATAGATTAA-ATTTT
1 ATATTTTGACATA-ATTAACATTTT
321127 ATATTTTGACATAATTAACATTTT
1 ATATTTTGACATAATTAACATTTT
321151 GTTTTGAAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 14 0.64
24 8 0.36
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.51
Consensus pattern (24 bp):
ATATTTTGACATAATTAACATTTT
Found at i:325306 original size:101 final size:102
Alignment explanation
Indices: 325171--325371 Score: 298
Period size: 101 Copynumber: 2.0 Consensus size: 102
325161 TGCTACACTT
* * *
325171 TTTTATTTACTTACACCGTTGTAAGTATGGATTAAGTGTTACACCTT-TTTATTTTATTCACTTA
1 TTTTATTCACTTACACCGGTGTAAGTATGGATTAAGTGCTACA-CTTGTTTATTTTATTCACTTA
* *
325235 CACCGGTAT-AGTATGTGTTAAGTGTTACATTTTTTTA
65 CACCGGTATAAGTATGTGTTAAATGCTACATTTTTTTA
* * *
325272 TTTTATTCACTTACACCGGTGTAAGTGTGTATTAAGTGCTACATTTGTTTATTTTATTCACTTAC
1 TTTTATTCACTTACACCGGTGTAAGTATGGATTAAGTGCTACACTTGTTTATTTTATTCACTTAC
*
325337 ACCGGTGTAAGTATGTGTTAAATGCTACATTTTTT
66 ACCGGTATAAGTATGTGTTAAATGCTACATTTTTT
325372 GTTGTATAAA
Statistics
Matches: 89, Mismatches: 9, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
100 2 0.02
101 63 0.71
102 24 0.27
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.47
Consensus pattern (102 bp):
TTTTATTCACTTACACCGGTGTAAGTATGGATTAAGTGCTACACTTGTTTATTTTATTCACTTAC
ACCGGTATAAGTATGTGTTAAATGCTACATTTTTTTA
Found at i:325328 original size:51 final size:50
Alignment explanation
Indices: 325171--325371 Score: 269
Period size: 51 Copynumber: 4.0 Consensus size: 50
325161 TGCTACACTT
* * * * *
325171 TTTTATTTACTTACACCGTTGTAAGTATGGATTAAGTGTTACACCTTTTTA
1 TTTTATTCACTTACACCGGTGTAAGTATGTATTAAGTGCTACA-TTTTTTA
* * *
325222 TTTTATTCACTTACACCGGTAT-AGTATGTGTTAAGTGTTACATTTTTTTA
1 TTTTATTCACTTACACCGGTGTAAGTATGTATTAAGTGCTACA-TTTTTTA
*
325272 TTTTATTCACTTACACCGGTGTAAGTGTGTATTAAGTGCTACATTTGTTTA
1 TTTTATTCACTTACACCGGTGTAAGTATGTATTAAGTGCTACATTT-TTTA
* *
325323 TTTTATTCACTTACACCGGTGTAAGTATGTGTTAAATGCTACATTTTTT
1 TTTTATTCACTTACACCGGTGTAAGTATGTATTAAGTGCTACATTTTTT
325372 GTTGTATAAA
Statistics
Matches: 134, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
50 51 0.38
51 83 0.62
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.47
Consensus pattern (50 bp):
TTTTATTCACTTACACCGGTGTAAGTATGTATTAAGTGCTACATTTTTTA
Found at i:331607 original size:21 final size:22
Alignment explanation
Indices: 331560--331656 Score: 101
Period size: 23 Copynumber: 4.5 Consensus size: 22
331550 ACACTACCTA
331560 GTGCATCGATGCATCCCTTGAAT
1 GTGCATCGATGCA-CCCTTGAAT
* * *
331583 GTGCATCGATTCA-CCATGAAG
1 GTGCATCGATGCACCCTTGAAT
*
331604 GTGCACCGATGCACGCCTTGAAT
1 GTGCATCGATGCAC-CCTTGAAT
* *
331627 GTGCATCGATGCACTC-TG-TT
1 GTGCATCGATGCACCCTTGAAT
331647 GTGCATCGAT
1 GTGCATCGAT
331657 ATACCGGTCA
Statistics
Matches: 62, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 19 0.31
22 1 0.02
23 31 0.50
ACGTcount: A:0.22, C:0.26, G:0.25, T:0.28
Consensus pattern (22 bp):
GTGCATCGATGCACCCTTGAAT
Found at i:335176 original size:16 final size:17
Alignment explanation
Indices: 335155--335192 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
335145 TGAACGGATT
* *
335155 TAAATTTATAT-TTTCA
1 TAAATTTAAATATTTAA
335171 TAAATTTAAATATTTAA
1 TAAATTTAAATATTTAA
335188 TAAAT
1 TAAAT
335193 AATAATATCC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 10 0.53
17 9 0.47
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (17 bp):
TAAATTTAAATATTTAA
Found at i:336862 original size:21 final size:22
Alignment explanation
Indices: 336818--336865 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
336808 AATTAATAAG
336818 TTATATTTTATAATTTAAAAATT
1 TTATATTTTATAATTT-AAAATT
*
336841 TTATATTTTGTAATTT-AAATT
1 TTATATTTTATAATTTAAAATT
336862 TTAT
1 TTAT
336866 TTTAGATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 9 0.38
23 15 0.62
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (22 bp):
TTATATTTTATAATTTAAAATT
Found at i:336889 original size:25 final size:26
Alignment explanation
Indices: 336838--336889 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
336828 TAATTTAAAA
* * *
336838 ATTTTATATTTTGTAATTTAAATTTT
1 ATTTTAGATTTTGTAAGTTAAAATTT
336864 ATTTTAGATTTT-TAAGTTAAAATTT
1 ATTTTAGATTTTGTAAGTTAAAATTT
336889 A
1 A
336890 CAAAATTACG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (26 bp):
ATTTTAGATTTTGTAAGTTAAAATTT
Found at i:337236 original size:18 final size:18
Alignment explanation
Indices: 337215--337252 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
337205 TGCTACAATT
337215 AATTATAAAAGTTTAATA
1 AATTATAAAAGTTTAATA
* *
337233 AATTATAATATTTTAATA
1 AATTATAAAAGTTTAATA
337251 AA
1 AA
337253 ATTTAATGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (18 bp):
AATTATAAAAGTTTAATA
Found at i:337580 original size:23 final size:22
Alignment explanation
Indices: 337554--337597 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
337544 TTGTAAATTT
337554 ATAATATTT-TAATAAATTTAATG
1 ATAAT-TTTATAAT-AATTTAATG
337577 ATAATTTTATAATAATTTAAT
1 ATAATTTTATAATAATTTAAT
337598 AATTATAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (22 bp):
ATAATTTTATAATAATTTAATG
Found at i:337582 original size:11 final size:11
Alignment explanation
Indices: 337549--337600 Score: 56
Period size: 11 Copynumber: 5.0 Consensus size: 11
337539 AATTTTTGTA
337549 AATTT-ATAAT
1 AATTTAATAAT
*
337559 ATTTTAAT-A-
1 AATTTAATAAT
*
337568 AATTTAATGAT
1 AATTTAATAAT
*
337579 AATTTTATAAT
1 AATTTAATAAT
337590 AATTTAATAAT
1 AATTTAATAAT
337601 TATAAACGGT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
9 7 0.21
10 6 0.18
11 21 0.62
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (11 bp):
AATTTAATAAT
Found at i:339898 original size:21 final size:21
Alignment explanation
Indices: 339872--339918 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 21
339862 AGAGCCCAAC
339872 AATAACAAAACCGGTAGAAAA-
1 AATAACAAAACCGGTA-AAAAT
339893 AATAACAAAACCGGTAAAAAT
1 AATAACAAAACCGGTAAAAAT
339914 AATAA
1 AATAA
339919 TATTTCAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 4 0.16
21 21 0.84
ACGTcount: A:0.64, C:0.13, G:0.11, T:0.13
Consensus pattern (21 bp):
AATAACAAAACCGGTAAAAAT
Found at i:342414 original size:10 final size:10
Alignment explanation
Indices: 342399--342429 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
342389 GGGATGGGCA
342399 TGGGTCGGGT
1 TGGGTCGGGT
342409 TGGGTCGGGT
1 TGGGTCGGGT
342419 TGGGTCGGGT
1 TGGGTCGGGT
342429 T
1 T
342430 TTTTGTCTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.00, C:0.10, G:0.58, T:0.32
Consensus pattern (10 bp):
TGGGTCGGGT
Found at i:345590 original size:579 final size:579
Alignment explanation
Indices: 344492--345652 Score: 2196
Period size: 579 Copynumber: 2.0 Consensus size: 579
344482 TTGATGCTGG
*
344492 ATAAATCCAGTAATCTTGTCCATATACAATATCTTATGTTTTTGGTTAACTTTTTTATTACCCGT
1 ATAAATCCAGTAATCTTGTCCATATACAATATCTTATGTTTTTGATTAACTTTTTTATTACCCGT
*
344557 CAGTGTAGTTGGGGATCGACAATATTGGTGTTCTTGTATTGCGAGATGTACAATGATTCATTACT
66 CAGTGTAGTTGGGGATCGACAATATTGGCGTTCTTGTATTGCGAGATGTACAATGATTCATTACT
344622 TGTAAATGATGTGTATACGATTGAAATCATTGGATGCACGATATTATTACAATCGTGGGAATGTC
131 TGTAAATGATGTGTATACGATTGAAATCATTGGATGCACGATATTATTACAATCGTGGGAATGTC
*
344687 ACAGAATTCCATGGTTAACACCGATTAGCCGAACTGCAGTTGACTTTCCTCTTACCGGAAGGTAA
196 ACAGAATTCCATGGTTAACACCGATTAGCCGAACTGCAGTTGACTTTCCTCTTACCAGAAGGTAA
344752 TTTTTTATTTAAAATATTTGATCTTAAATTAATTAAAGAATATATTGTAAAGGAAAAATAATTAC
261 TTTTTTATTTAAAATATTTGATCTTAAATTAATTAAAGAATATATTGTAAAGGAAAAATAATTAC
*
344817 AGAATTTTATTTTGATTCGTATACAGATGGAGGCATAAAATAGAAAGAACGGGGTTGATGCACAA
326 AGAATTTTATTTTGATTCGTATACAAATGGAGGCATAAAATAGAAAGAACGGGGTTGATGCACAA
* *
344882 TAACGTGAAAGAGTTTAGGTTTAAGATTGACATCAAATGCAAAGTTGATATATATATATAATTAA
391 TAACGTGAAAGAGTTTAGGTTTAAGATTGACATCAAATGCAAAGTTGAGATATATATAAAATTAA
344947 TTAGCGAATTTATTTTTTATTATGTTTATATTATAATATTGTTGTTTATTTATTTAGTTGAATTT
456 TTAGCGAATTTATTTTTTATTATGTTTATATTATAATATTGTTGTTTATTTATTTAGTTGAATTT
345012 TATAATTATTTAATTAAATAATAACTATATAATTTTGTTTTATAGTTTATTTGGAGGCC
521 TATAATTATTTAATTAAATAATAACTATATAATTTTGTTTTATAGTTTATTTGGAGGCC
345071 ATAAATCCAGTAATCTTGTCCATATACAATATCTTATGTTTTTGATTAACTTTTTTATTACCCGT
1 ATAAATCCAGTAATCTTGTCCATATACAATATCTTATGTTTTTGATTAACTTTTTTATTACCCGT
*
345136 CAGTGTAGTTGGGGATCGACAATATTGGCGTTCTTGTATTGCGAGGTGTACAATGATTCATTACT
66 CAGTGTAGTTGGGGATCGACAATATTGGCGTTCTTGTATTGCGAGATGTACAATGATTCATTACT
*
345201 TGTAAATGATGTGTATACGATTGAAATCGTTGGATGCACGATATTATTACAATCGTGGGAATGTC
131 TGTAAATGATGTGTATACGATTGAAATCATTGGATGCACGATATTATTACAATCGTGGGAATGTC
* *
345266 ACAGAATTCCATGGTTAACACCGATTAGCCGAACTGCAGTTGACTTTTCTCTTACCAGAATGTAA
196 ACAGAATTCCATGGTTAACACCGATTAGCCGAACTGCAGTTGACTTTCCTCTTACCAGAAGGTAA
345331 TTTTTTATTTAAAATATTTGATCTTAAATTAATTAAAGAATATATTGTAAAGGAAAAATAATTAC
261 TTTTTTATTTAAAATATTTGATCTTAAATTAATTAAAGAATATATTGTAAAGGAAAAATAATTAC
*
345396 ATAATTTTATTTTGATTCGTATACAAATGGAGGCATAAAATAGAAAGAACGGGGTTGATGCACAA
326 AGAATTTTATTTTGATTCGTATACAAATGGAGGCATAAAATAGAAAGAACGGGGTTGATGCACAA
* *
345461 TAACGTGAAAGAGTTTAGGTTTAAGATTGACATCAAATGCAAAGTTGAGGTATATATAAAATTTA
391 TAACGTGAAAGAGTTTAGGTTTAAGATTGACATCAAATGCAAAGTTGAGATATATATAAAATTAA
345526 TTAGCGAATTTATTTTTTATTATGTTTATATTATAATATTGTTGTTTATTTATTTAGTTGAATTT
456 TTAGCGAATTTATTTTTTATTATGTTTATATTATAATATTGTTGTTTATTTATTTAGTTGAATTT
*
345591 TATAATTATTTAATTAAATAATAACTATATAATTTTGTTTTATAGTTTATTTGGAGGTC
521 TATAATTATTTAATTAAATAATAACTATATAATTTTGTTTTATAGTTTATTTGGAGGCC
345650 ATA
1 ATA
345653 TGATGATGGA
Statistics
Matches: 568, Mismatches: 14, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
579 568 1.00
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (579 bp):
ATAAATCCAGTAATCTTGTCCATATACAATATCTTATGTTTTTGATTAACTTTTTTATTACCCGT
CAGTGTAGTTGGGGATCGACAATATTGGCGTTCTTGTATTGCGAGATGTACAATGATTCATTACT
TGTAAATGATGTGTATACGATTGAAATCATTGGATGCACGATATTATTACAATCGTGGGAATGTC
ACAGAATTCCATGGTTAACACCGATTAGCCGAACTGCAGTTGACTTTCCTCTTACCAGAAGGTAA
TTTTTTATTTAAAATATTTGATCTTAAATTAATTAAAGAATATATTGTAAAGGAAAAATAATTAC
AGAATTTTATTTTGATTCGTATACAAATGGAGGCATAAAATAGAAAGAACGGGGTTGATGCACAA
TAACGTGAAAGAGTTTAGGTTTAAGATTGACATCAAATGCAAAGTTGAGATATATATAAAATTAA
TTAGCGAATTTATTTTTTATTATGTTTATATTATAATATTGTTGTTTATTTATTTAGTTGAATTT
TATAATTATTTAATTAAATAATAACTATATAATTTTGTTTTATAGTTTATTTGGAGGCC
Found at i:346648 original size:27 final size:28
Alignment explanation
Indices: 346602--346659 Score: 91
Period size: 27 Copynumber: 2.1 Consensus size: 28
346592 AATATTAAAA
*
346602 TAAAAATTAAAGATATAATTTAAATATT
1 TAAAAATTAAAGATAAAATTTAAATATT
*
346630 TAAATATT-AAGATAAAATTTAAATATT
1 TAAAAATTAAAGATAAAATTTAAATATT
346657 TAA
1 TAA
346660 TCATTATTAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
27 21 0.75
28 7 0.25
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (28 bp):
TAAAAATTAAAGATAAAATTTAAATATT
Found at i:346689 original size:24 final size:24
Alignment explanation
Indices: 346653--346737 Score: 100
Period size: 24 Copynumber: 3.5 Consensus size: 24
346643 AAAATTTAAA
*
346653 TATTTAATCATTATTAGTAATAAT
1 TATTAAATCATTATTAGTAATAAT
* *
346677 TATTAAATAATTATTAGTAATTAT
1 TATTAAATCATTATTAGTAATAAT
* * *
346701 TA-TAATTTCATTATTAATAATCAT
1 TATTAA-ATCATTATTAGTAATAAT
346725 TATTAAATCATTA
1 TATTAAATCATTA
346738 AATATCAAAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
23 3 0.06
24 45 0.88
25 3 0.06
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (24 bp):
TATTAAATCATTATTAGTAATAAT
Found at i:346726 original size:13 final size:13
Alignment explanation
Indices: 346657--346867 Score: 96
Period size: 13 Copynumber: 17.0 Consensus size: 13
346647 TTTAAATATT
*
346657 TAATCATTATTAG
1 TAATCATTATTAA
*
346670 TAATAATTATT-A
1 TAATCATTATTAA
* *
346682 -AATAATTATTAG
1 TAATCATTATTAA
*
346694 TAATTATTA-TAA
1 TAATCATTATTAA
*
346706 T-TTCATTATTAA
1 TAATCATTATTAA
346718 TAATCATTATT-A
1 TAATCATTATTAA
*
346730 -AATCATTA-AATA
1 TAATCATTATTA-A
346742 TCAAATCATTAAATTAA
1 T--AATCATT--ATTAA
* *
346759 TAATAATTAGT-A
1 TAATCATTATTAA
*
346771 -AAT-ATTATTAT
1 TAATCATTATTAA
*
346782 TAATCATTATTAG
1 TAATCATTATTAA
346795 TAATCA-TATT-A
1 TAATCATTATTAA
*
346806 T--TCATTAGT-A
1 TAATCATTATTAA
** *
346816 TCAAATCAAAATTGA
1 T--AATCATTATTAA
346831 TAATCATTATT-A
1 TAATCATTATTAA
*
346843 -AATCATTATTAG
1 TAATCATTATTAA
346855 TAATCATTATTAA
1 TAATCATTATTAA
346868 ATTATTAGTA
Statistics
Matches: 151, Mismatches: 24, Indels: 46
0.68 0.11 0.21
Matches are distributed among these distances:
9 3 0.02
10 10 0.07
11 37 0.25
12 18 0.12
13 59 0.39
14 5 0.03
15 15 0.10
17 3 0.02
18 1 0.01
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (13 bp):
TAATCATTATTAA
Found at i:346847 original size:24 final size:24
Alignment explanation
Indices: 346818--346869 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
346808 CATTAGTATC
346818 AAATCAAAATT-GATAATCATTATT
1 AAATCAAAATTAG-TAATCATTATT
**
346842 AAATCATTATTAGTAATCATTATT
1 AAATCAAAATTAGTAATCATTATT
346866 AAAT
1 AAAT
346870 TATTAGTATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 24 0.96
25 1 0.04
ACGTcount: A:0.48, C:0.08, G:0.04, T:0.40
Consensus pattern (24 bp):
AAATCAAAATTAGTAATCATTATT
Found at i:346873 original size:8 final size:8
Alignment explanation
Indices: 346860--346896 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
346850 ATTAGTAATC
346860 ATTATTAA
1 ATTATTAA
346868 ATTATT--
1 ATTATTAA
*
346874 AGTATTAA
1 ATTATTAA
346882 ATTATTAA
1 ATTATTAA
346890 ATTATTA
1 ATTATTA
346897 TTATTTATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
6 5 0.20
8 20 0.80
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (8 bp):
ATTATTAA
Found at i:346896 original size:11 final size:11
Alignment explanation
Indices: 346836--346899 Score: 51
Period size: 11 Copynumber: 5.6 Consensus size: 11
346826 ATTGATAATC
*
346836 ATTATTAAATC
1 ATTATTAAATT
*
346847 ATTATTAGTAATC
1 ATTATTA--AATT
346860 ATTATTAAATT
1 ATTATTAAATT
*
346871 ATTAGT--ATT
1 ATTATTAAATT
346880 AAATTATTAAATT
1 --ATTATTAAATT
346893 ATTATTA
1 ATTATTA
346900 TTTATAATCA
Statistics
Matches: 44, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
9 3 0.07
11 27 0.61
13 14 0.32
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
ATTATTAAATT
Found at i:346901 original size:14 final size:14
Alignment explanation
Indices: 346862--346888 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
346852 TAGTAATCAT
346862 TATTAAATTATTAG
1 TATTAAATTATTAG
346876 TATTAAATTATTA
1 TATTAAATTATTA
346889 AATTATTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (14 bp):
TATTAAATTATTAG
Found at i:347267 original size:13 final size:13
Alignment explanation
Indices: 347214--347272 Score: 50
Period size: 13 Copynumber: 4.5 Consensus size: 13
347204 ATGTTATCAA
*
347214 ATTAATAGTAATC
1 ATTATTAGTAATC
347227 ATTATTA--AATC
1 ATTATTAGTAATC
** *
347238 ATTAAAATTCAAATC
1 ATTATTAGT--AATC
347253 ATTATTAGTAATC
1 ATTATTAGTAATC
347266 ATTATTA
1 ATTATTA
347273 TCAAATCATT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
11 9 0.25
13 17 0.47
15 10 0.28
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.42
Consensus pattern (13 bp):
ATTATTAGTAATC
Found at i:347287 original size:22 final size:22
Alignment explanation
Indices: 347262--347305 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
347252 CATTATTAGT
*
347262 AATCATTATTATCAAATCATTA
1 AATCACTATTATCAAATCATTA
* *
347284 AATCGCTATTATTAAATCATTA
1 AATCACTATTATCAAATCATTA
347306 GTAGTAAATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.02, T:0.41
Consensus pattern (22 bp):
AATCACTATTATCAAATCATTA
Found at i:347319 original size:22 final size:22
Alignment explanation
Indices: 347294--347339 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
347284 AATCGCTATT
*
347294 ATTAAATCATTAGTAGTAAATC
1 ATTAAATCATTAGTAATAAATC
*
347316 ATTAAATCATTATTAATAAATC
1 ATTAAATCATTAGTAATAAATC
347338 AT
1 AT
347340 ATCATTACTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.48, C:0.09, G:0.04, T:0.39
Consensus pattern (22 bp):
ATTAAATCATTAGTAATAAATC
Found at i:349478 original size:60 final size:60
Alignment explanation
Indices: 349410--349526 Score: 173
Period size: 60 Copynumber: 1.9 Consensus size: 60
349400 TCGTTCTCGC
* * *
349410 CCCCACCTATTCACGCATGCAGAGATTCTC-GACCCCCCAACATGCAGCAGGGATCACATT
1 CCCCACCTATTCACACATGCAGAGATTCTCGGA-CCCCAAACATACAGCAGGGATCACATT
* *
349470 CCCCACCTATTCATACATGCAGTGATTCTCGGACCCCAAACATACAGCAGGGATCAC
1 CCCCACCTATTCACACATGCAGAGATTCTCGGACCCCAAACATACAGCAGGGATCAC
349527 GTTCTCGGCC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
60 49 0.96
61 2 0.04
ACGTcount: A:0.28, C:0.37, G:0.16, T:0.19
Consensus pattern (60 bp):
CCCCACCTATTCACACATGCAGAGATTCTCGGACCCCAAACATACAGCAGGGATCACATT
Found at i:351648 original size:26 final size:26
Alignment explanation
Indices: 351614--351673 Score: 84
Period size: 26 Copynumber: 2.3 Consensus size: 26
351604 TTTAACGAGT
*
351614 ACTGTTGAGCACCATTAACGATGAGC
1 ACTGCTGAGCACCATTAACGATGAGC
* *
351640 ACTGCTGAGTACTATTAACGATGAGC
1 ACTGCTGAGCACCATTAACGATGAGC
*
351666 ATTGCTGA
1 ACTGCTGA
351674 ACAAAATTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (26 bp):
ACTGCTGAGCACCATTAACGATGAGC
Found at i:351682 original size:26 final size:26
Alignment explanation
Indices: 351627--351683 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
351617 GTTGAGCACC
** **
351627 ATTAACGATGAGCACTGCTGAGTACT
1 ATTAACGATGAGCACTGCTGAACAAA
*
351653 ATTAACGATGAGCATTGCTGAACAAA
1 ATTAACGATGAGCACTGCTGAACAAA
351679 ATTAA
1 ATTAA
351684 TTTAATTTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.26
Consensus pattern (26 bp):
ATTAACGATGAGCACTGCTGAACAAA
Found at i:353733 original size:11 final size:11
Alignment explanation
Indices: 353717--353741 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
353707 AATTCTACGT
353717 GTAAATAAAGA
1 GTAAATAAAGA
353728 GTAAATAAAGA
1 GTAAATAAAGA
353739 GTA
1 GTA
353742 GACGGTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (11 bp):
GTAAATAAAGA
Found at i:355598 original size:21 final size:21
Alignment explanation
Indices: 355573--355615 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
355563 AAGCAAGGAG
355573 TGTTAAATATTTGAACATCCC
1 TGTTAAATATTTGAACATCCC
355594 TGTTAAATATTTGAACATCCC
1 TGTTAAATATTTGAACATCCC
355615 T
1 T
355616 ATCATTTGTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.40
Consensus pattern (21 bp):
TGTTAAATATTTGAACATCCC
Found at i:359525 original size:22 final size:22
Alignment explanation
Indices: 359500--359578 Score: 77
Period size: 22 Copynumber: 3.6 Consensus size: 22
359490 CAATTTATGG
*
359500 AAGTGCCTTAGCACTGGTATTA
1 AAGTGCCTTAGCACTGATATTA
* * * **
359522 AAGTGTCTCAGTACTGATATGG
1 AAGTGCCTTAGCACTGATATTA
* * *
359544 AAGTGCGTTCGCACTGATACTA
1 AAGTGCCTTAGCACTGATATTA
359566 AAGTGCCTTAGCA
1 AAGTGCCTTAGCA
359579 TTGTAGGCAT
Statistics
Matches: 41, Mismatches: 16, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.28, C:0.19, G:0.24, T:0.29
Consensus pattern (22 bp):
AAGTGCCTTAGCACTGATATTA
Found at i:361367 original size:23 final size:22
Alignment explanation
Indices: 361352--361404 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 22
361342 ATTACACCGA
361352 AGTGCCACGTAGAATTGCACATG
1 AGTGCCACGTAGAATTGCAC-TG
*
361375 AGTGCCGCGTAGAATTGCACTG
1 AGTGCCACGTAGAATTGCACTG
361397 TAGTGCCA
1 -AGTGCCA
361405 TATAATAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.26, C:0.23, G:0.28, T:0.23
Consensus pattern (22 bp):
AGTGCCACGTAGAATTGCACTG
Found at i:361591 original size:103 final size:103
Alignment explanation
Indices: 361424--361628 Score: 374
Period size: 103 Copynumber: 2.0 Consensus size: 103
361414 GTCCATAAGG
* *
361424 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
361489 TCACACATATTCCAAAGAATACATATATGTCCCGAAGA
66 TCACACATATTCCAAAGAATACATATATGTCCCGAAGA
*
361527 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
*
361592 TCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TCACACATATTCCAAAGAATACATATATGTCCCGAAG
361629 GACCGCGTAG
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 98 1.00
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGTGTCTCACCAGACT
TCACACATATTCCAAAGAATACATATATGTCCCGAAGA
Done.