Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008771.1 Hibiscus syriacus cultivar Beakdansim tig00111876_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: 169649
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:5784 original size:19 final size:19
Alignment explanation
Indices: 5760--5810 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
5750 GAAAAAATTC
5760 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
5779 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
5798 A-A-TGCATTCGATG
1 AGAGTGCA-TCGATG
5811 TTCAATTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
17 4 0.14
18 6 0.21
19 19 0.66
ACGTcount: A:0.25, C:0.16, G:0.35, T:0.24
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:5795 original size:65 final size:65
Alignment explanation
Indices: 5653--5812 Score: 200
Period size: 65 Copynumber: 2.5 Consensus size: 65
5643 TGCACCAAGT
* ***
5653 GTGCATCGATGCATGAAATGCATTCGATG-TTTAAGAAATAGCCTGATGCATCGATGCATGGCTT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTAAGAAATAGCCAGATGCATCGATGCATGGAGA
* **
5717 GTGCATCGATGCATCAAATGCATTCGATGTTTTGAA-AAA-ATTCAGAGTGCATCGATGCATGGA
1 GTGCATCGATGCATGAAATGCATTCGATGTTTT-AAGAAATAGCCAGA-TGCATCGATGCATGGA
5780 GA
64 GA
* *
5782 GTGCATCGGTGCATGGAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
5813 CAATTAATTC
Statistics
Matches: 83, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
64 32 0.39
65 49 0.59
66 2 0.02
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTAAGAAATAGCCAGATGCATCGATGCATGGAGA
Found at i:6385 original size:18 final size:20
Alignment explanation
Indices: 6364--6403 Score: 57
Period size: 18 Copynumber: 2.1 Consensus size: 20
6354 ATTTAATCAA
*
6364 TTTGTCACA-TTTAACC-GT
1 TTTGTCAAATTTTAACCTGT
6382 TTTGTCAAATTTTAACCTGT
1 TTTGTCAAATTTTAACCTGT
6402 TT
1 TT
6404 AGAAATTCTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 8 0.42
19 7 0.37
20 4 0.21
ACGTcount: A:0.23, C:0.17, G:0.10, T:0.50
Consensus pattern (20 bp):
TTTGTCAAATTTTAACCTGT
Found at i:10882 original size:229 final size:229
Alignment explanation
Indices: 10473--10887 Score: 620
Period size: 229 Copynumber: 1.8 Consensus size: 229
10463 ATAGTAAAAT
* * *
10473 GGTTTCCTTCAATGGAATCGGAATACTCTCTACTACAAGTATCGGTACATTTATACAACCTATAA
1 GGTTTCCGTCAATGGAATCGGAATACTCTCTACTACAAGTATCAGTACATTTATACAACCTACAA
* *
10538 TATCATTTTCTACCTATAATATTATATACAAGTATCGATATTTATTTTCTACCCATAATATCACT
66 TATCATTTTCTACCTATAATATTATATAAAAGTATCGATATTTATTTTCTACCCAGAATATCACT
* * * *
10603 TTCTAACTCTAATCGGTCCCAAATCCTTCTTTGTTTTAAATCCTCAAACCCATAAACCCTAATCC
131 TTCTAACTCTAATCGGTCCCAAATCCTTCTTTCTTTGAAAACCCCAAACCCATAAACCCTAATCC
10668 CTATTTCTAAATACTATAATACTAAAAAAACTAG
196 CTATTTCTAAATACTATAATACTAAAAAAACTAG
* **
10702 GGTTTCCGTCAAAT-GAATGGGAATACTCTCTACTACAAGTATCAGTACATTTATACAATGTACA
1 GGTTTCCGTC-AATGGAATCGGAATACTCTCTACTACAAGTATCAGTACATTTATACAACCTACA
*
10766 ATATCATTTTCTACCTATAATATTATATAAAAGTATCGATATTTATTTTCTA-CCAGAATATTAC
65 ATATCATTTTCTACCTATAATATTATATAAAAGTATCGATATTTATTTTCTACCCAGAATATCAC
* * * * *
10830 TTTCT-ACATGTCATCGGTCTCAAATGCTTTTTTACTTTGAAAACCCCAAACCCATAAA
130 TTTCTAAC-TCTAATCGGTCCCAAATCCTTCTTT-CTTTGAAAACCCCAAACCCATAAA
10888 ACCTCTATTT
Statistics
Matches: 165, Mismatches: 18, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
227 2 0.01
228 35 0.21
229 125 0.76
230 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.36
Consensus pattern (229 bp):
GGTTTCCGTCAATGGAATCGGAATACTCTCTACTACAAGTATCAGTACATTTATACAACCTACAA
TATCATTTTCTACCTATAATATTATATAAAAGTATCGATATTTATTTTCTACCCAGAATATCACT
TTCTAACTCTAATCGGTCCCAAATCCTTCTTTCTTTGAAAACCCCAAACCCATAAACCCTAATCC
CTATTTCTAAATACTATAATACTAAAAAAACTAG
Found at i:23511 original size:16 final size:18
Alignment explanation
Indices: 23490--23522 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
23480 CCTAAATTGA
23490 GAAAAG-GAA-AAAAGAG
1 GAAAAGAGAATAAAAGAG
23506 GAAAAGAGAATAAAAGA
1 GAAAAGAGAATAAAAGA
23523 AGAGAAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 3 0.20
18 6 0.40
ACGTcount: A:0.70, C:0.00, G:0.27, T:0.03
Consensus pattern (18 bp):
GAAAAGAGAATAAAAGAG
Found at i:24454 original size:105 final size:105
Alignment explanation
Indices: 24272--24919 Score: 974
Period size: 105 Copynumber: 6.2 Consensus size: 105
24262 AGGTTTTACC
* * *
24272 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACGCAAGTTCAACTTCGCG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
24337 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
24377 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
24442 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
24482 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
24547 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
24587 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCCGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* * *
24652 ACGAAGGGACCGCTGGTTGTCAATAAACATTTCCCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
24692 CAGAGCCAATTTCAACTTCGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
24757 ACGAAGGGA------GTTGTCAACAAACATCTCTC-AATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT-T
* * * * * * *
24791 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCAAGACAGCACAAGCTCGACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
24856 ACGAAGGGA-CGACTGACTGTCAACGAATA-ATTTCTC-AATT
66 ACGAAGGGACCG-CTGGTTGTCAAC-AA-ACATTTCTCAAATT
* *
24896 CCATAGCCAATTCCAACTTCACAA
1 -CAGAGCCAATTTCAACTTCACAA
24920 ACAGATTGAC
Statistics
Matches: 503, Mismatches: 30, Indels: 19
0.91 0.05 0.03
Matches are distributed among these distances:
98 2 0.00
99 84 0.17
105 385 0.77
106 31 0.06
107 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:26445 original size:17 final size:15
Alignment explanation
Indices: 26425--26498 Score: 60
Period size: 15 Copynumber: 4.6 Consensus size: 15
26415 ATTTTCATTA
26425 TTATTATATTTTACTCC
1 TTATTATATTTTA-T-C
*
26442 TTATTTATATATATATC
1 TTA-TTATAT-TTTATC
*
26459 TTATGTATATTTTATT
1 TTAT-TATATTTTATC
*
26475 TTATTATATTATAT-
1 TTATTATATTTTATC
26489 TTATGTATAT
1 TTAT-TATAT
26499 ATGCACCCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
14 4 0.08
15 14 0.29
16 9 0.18
17 12 0.24
18 7 0.14
19 3 0.06
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (15 bp):
TTATTATATTTTATC
Found at i:26497 original size:15 final size:15
Alignment explanation
Indices: 26442--26498 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
26432 ATTTTACTCC
*
26442 TTATTTATATATATAT
1 TTATGTATAT-TATAT
*
26458 CTTATGTATATTTTATT
1 -TTATGTATATTATA-T
26475 TTAT-TATATTATAT
1 TTATGTATATTATAT
26489 TTATGTATAT
1 TTATGTATAT
26499 ATGCACCCAT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
14 5 0.14
15 13 0.37
16 7 0.20
17 10 0.29
ACGTcount: A:0.32, C:0.02, G:0.04, T:0.63
Consensus pattern (15 bp):
TTATGTATATTATAT
Found at i:26512 original size:2 final size:2
Alignment explanation
Indices: 26507--26533 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
26497 ATATGCACCC
26507 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 A
26534 CATAACCATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26629 original size:26 final size:26
Alignment explanation
Indices: 26580--26629 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
26570 TGATGGCGTA
* **
26580 TATAAATGTATATTTTTTTCTTTTAT
1 TATAAATGTATATTCTTTAATTTTAT
*
26606 TATATATGTATATTCTTTAATTTT
1 TATAAATGTATATTCTTTAATTTT
26630 TTTCATTTAC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.28, C:0.04, G:0.04, T:0.64
Consensus pattern (26 bp):
TATAAATGTATATTCTTTAATTTTAT
Found at i:27567 original size:193 final size:194
Alignment explanation
Indices: 27237--27617 Score: 548
Period size: 193 Copynumber: 2.0 Consensus size: 194
27227 TTACGACACC
* * * *
27237 TTCAACATATCCGGTAGCTCTTTACTAGATTTGTCATATTGAAACCTATTTTGTCATATTTTAAC
1 TTCAACATATCCGATAGCTCTTTACTAGATTTGTCATATGGAAACCGATTTTCTCATATTTTAAC
* * *
27302 CTGTTATGTTGTTATGTATCGATACATGTTTATAAAATATCGATACTTTATAAGCGCTATTATTG
66 ATGTTATGTTGTTATGTATCAATACATGTTTATAAAATATCGATACTTTATAAGAGCTATTATTG
* *
27367 CAATTCTTTTAAATTCTTAAAGTATCGATAATATGATACATATACTTATAAAAGTATCAATATT
131 CAATTCTTTTAAATTCATAAAGTATCGATAATATGATACATATACTTAGAAAAGTATCAATATT
* * * *
27431 TTCAACATATCCGATAGTTCTTTACTGGTTTTGTCATATGGAAACCGATTTTCTTATATTTTAAC
1 TTCAACATATCCGATAGCTCTTTACTAGATTTGTCATATGGAAACCGATTTTCTCATATTTTAAC
* * ** * * * *
27496 AT-TTATGTTGTTATGTATTAATACATGTTTCTAATGTCTCTATACTTTATAGGAGTTATTATTG
66 ATGTTATGTTGTTATGTATCAATACATGTTTATAAAATATCGATACTTTATAAGAGCTATTATTG
* *
27560 CAATTCTTTTAAATTCATAAAGTATCGATAATTTGATGCATATACTTAGAAAAGTATC
131 CAATTCTTTTAAATTCATAAAGTATCGATAATATGATACATATACTTAGAAAAGTATC
27618 GATACAAATT
Statistics
Matches: 164, Mismatches: 23, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
193 106 0.65
194 58 0.35
ACGTcount: A:0.32, C:0.13, G:0.12, T:0.44
Consensus pattern (194 bp):
TTCAACATATCCGATAGCTCTTTACTAGATTTGTCATATGGAAACCGATTTTCTCATATTTTAAC
ATGTTATGTTGTTATGTATCAATACATGTTTATAAAATATCGATACTTTATAAGAGCTATTATTG
CAATTCTTTTAAATTCATAAAGTATCGATAATATGATACATATACTTAGAAAAGTATCAATATT
Found at i:28338 original size:22 final size:22
Alignment explanation
Indices: 28310--28362 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
28300 ATTGGTATAA
28310 TTACACATTTTATCCTCAATAT
1 TTACACATTTTATCCTCAATAT
*
28332 TTACACATTTTATCCTCGATAT
1 TTACACATTTTATCCTCAATAT
*
28354 TTATACATT
1 TTACACATT
28363 CTTTCAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.30, C:0.21, G:0.02, T:0.47
Consensus pattern (22 bp):
TTACACATTTTATCCTCAATAT
Found at i:30831 original size:114 final size:114
Alignment explanation
Indices: 30631--30859 Score: 431
Period size: 114 Copynumber: 2.0 Consensus size: 114
30621 ATAGTTAATG
*
30631 CTTTTTGATCCTTTATCTGCTTCCAGTTCGTGTGACTCAGGGTCGTCTTATGAGTTTGTAAGTAT
1 CTTTTTGATCCTTTATCTGCTTCCAGTTCGTGTGACTCAGGGTCGTCTTATGAGTTTGTAACTAT
30696 TTTTTGGCACCTCAATGACCTTTAAAGGGAAAGTAGTTCAAAGGAACAA
66 TTTTTGGCACCTCAATGACCTTTAAAGGGAAAGTAGTTCAAAGGAACAA
* *
30745 CTTTTTGATCCTTTATCTGCTTCCCGTTCGTGTGGCTCAGGGTCGTCTTATGAGTTTGTAACTAT
1 CTTTTTGATCCTTTATCTGCTTCCAGTTCGTGTGACTCAGGGTCGTCTTATGAGTTTGTAACTAT
30810 TTTTTGGCACCTCAATGACCTTTAAAGGGAAAGTAGTTCAAAGGAACAA
66 TTTTTGGCACCTCAATGACCTTTAAAGGGAAAGTAGTTCAAAGGAACAA
30859 C
1 C
30860 CTGCAATAGT
Statistics
Matches: 112, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
114 112 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.37
Consensus pattern (114 bp):
CTTTTTGATCCTTTATCTGCTTCCAGTTCGTGTGACTCAGGGTCGTCTTATGAGTTTGTAACTAT
TTTTTGGCACCTCAATGACCTTTAAAGGGAAAGTAGTTCAAAGGAACAA
Found at i:32859 original size:25 final size:25
Alignment explanation
Indices: 32813--32860 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
32803 AATTTTTTTA
* *
32813 AAATTTTTTAATTTATATAAAAATT
1 AAATTTTTTAATTCATAAAAAAATT
32838 AAATGTTTTTAATTCA-AAAAAAA
1 AAAT-TTTTTAATTCATAAAAAAA
32861 GTTTATAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
25 10 0.50
26 10 0.50
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (25 bp):
AAATTTTTTAATTCATAAAAAAATT
Found at i:33098 original size:40 final size:37
Alignment explanation
Indices: 33013--33099 Score: 86
Period size: 40 Copynumber: 2.2 Consensus size: 37
33003 ATATTATATA
* *
33013 ATAT-ATTTAATAATTTTTAATTAAAAAAAACAGTTT
1 ATATAATTTAATAATATATAATTAAAAAAAACAGTTT
* *
33049 ACAATTAATTTAAATAATATATAATTATAAAATAAACATTTT
1 A-TA-TAATTT-AATAATATATAATTA-AAAA-AAACAGTTT
33091 ATATAATTT
1 ATATAATTT
33100 TTTTAATTAA
Statistics
Matches: 40, Mismatches: 5, Indels: 8
0.75 0.09 0.15
Matches are distributed among these distances:
36 1 0.03
37 1 0.03
38 1 0.03
39 4 0.10
40 19 0.47
41 5 0.12
42 9 0.22
ACGTcount: A:0.52, C:0.03, G:0.01, T:0.44
Consensus pattern (37 bp):
ATATAATTTAATAATATATAATTAAAAAAAACAGTTT
Found at i:33195 original size:183 final size:185
Alignment explanation
Indices: 32826--33209 Score: 537
Period size: 184 Copynumber: 2.1 Consensus size: 185
32816 TTTTTTAATT
* * * *
32826 TATATAAAA-ATTAAAT-GTTTTTAATTCAAAAAAAAGTTTATAATTAATTTAAATAATATATAA
1 TATATAAAATATTTAATAATTTTTAATTAAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
* *
32889 TTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTGATTTATGTTTAAAAATTAT
66 TTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAATTAT
* *
32954 TAGACCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTTAGCTCATATA-T-
131 TAGACCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTAACCTCATATATTA
*
33007 TATATAATATATTTAATAATTTTTAATTAAAAAAAACAGTTTACAATTAATTTAAATAATATATA
1 TATATAAAATATTTAATAATTTTTAATTAAAAAAAA-AGTTTACAATTAATTTAAATAATATATA
* * * *
33072 ATTATAAAATAAACATTTTATATAATTTTTTTAATTAATTAATATTAATTTAAGTTT-AAAATTA
65 ATTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAATTA
* * ** * *
33136 TTTGATCTTAAATTATTAATTGTGTTTTAAATTGTTTGGGCTGAACCT-ATATGTTA
130 TTAGACCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCT-AACCTCATATATTA
33192 TATATAAAATATTTAATA
1 TATATAAAATATTTAATA
33210 TTTAAAATTT
Statistics
Matches: 177, Mismatches: 20, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
181 8 0.05
182 6 0.03
183 64 0.36
184 82 0.46
185 17 0.10
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (185 bp):
TATATAAAATATTTAATAATTTTTAATTAAAAAAAAAGTTTACAATTAATTTAAATAATATATAA
TTATAAAATAAAAATTTCAGATAAATTTTTTAATTAATTAATATTAATTTAAGTTTAAAAATTAT
TAGACCTTAAATTATTAATTAAGTTTTAAATGGTTTGGGCTAACCTCATATATTA
Found at i:39867 original size:58 final size:59
Alignment explanation
Indices: 39766--39878 Score: 138
Period size: 58 Copynumber: 1.9 Consensus size: 59
39756 ACGCGAGAGA
* * * * **
39766 CCCCCAATTATGATCCTATTTTAAATTGGTCCATACATTTTAAAACATTATGTATAGAT
1 CCCCAAATTATGATCATATTTTAAATTAGTCCATAAACATTAAAACATTATGTATAGAT
* * *
39825 CCCCAAATTATGAT-ATATTTTAAATTAGTCCCTAAACATTAAACCATTTTGTAT
1 CCCCAAATTATGATCATATTTTAAATTAGTCCATAAACATTAAAACATTATGTAT
39879 CAATCATCAA
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
58 32 0.71
59 13 0.29
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (59 bp):
CCCCAAATTATGATCATATTTTAAATTAGTCCATAAACATTAAAACATTATGTATAGAT
Found at i:45098 original size:15 final size:16
Alignment explanation
Indices: 45078--45119 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
45068 TATCTAGATT
45078 TTTAAAAAAAT-ATTA
1 TTTAAAAAAATAATTA
* *
45093 TTTAAAAATATAATTT
1 TTTAAAAAAATAATTA
*
45109 TTTGAAAAAAT
1 TTTAAAAAAAT
45120 CTTTACGTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (16 bp):
TTTAAAAAAATAATTA
Found at i:45707 original size:28 final size:28
Alignment explanation
Indices: 45675--45731 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
45665 CTCTCTGTTT
*
45675 ACATTATATCGTTGAACTAGTGTTTGAA
1 ACATTATATCGTTGAACTAATGTTTGAA
*
45703 ACATTATATCGTTGAGCTAATGTTTGAA
1 ACATTATATCGTTGAACTAATGTTTGAA
45731 A
1 A
45732 GCAACGACGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.33, C:0.11, G:0.18, T:0.39
Consensus pattern (28 bp):
ACATTATATCGTTGAACTAATGTTTGAA
Found at i:48738 original size:65 final size:65
Alignment explanation
Indices: 48605--48764 Score: 218
Period size: 65 Copynumber: 2.5 Consensus size: 65
48595 TGCACTAAGA
* * *
48605 GTGCATTGATGCATGAAAGGCATTCGATG-TTTCAAAATAACCAGAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAACCAGAGTGCATCGATGCATAGCTG
* * *
48669 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAA-AACTCTGAGTGCATCGATGCATAG-T
1 GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAAC-CAGAGTGCATCGATGCATAGCT
*
48732 AT
65 -G
48734 GTGCATCGATGCATGAAATGCATTCGATGTT
1 GTGCATCGATGCATGAAATGCATTCGATGTT
48765 CAATTTATTC
Statistics
Matches: 85, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
64 30 0.35
65 55 0.65
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.30
Consensus pattern (65 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTTCAAAATAACCAGAGTGCATCGATGCATAGCTG
Found at i:48803 original size:65 final size:64
Alignment explanation
Indices: 48605--48812 Score: 212
Period size: 65 Copynumber: 3.2 Consensus size: 64
48595 TGCACTAAGA
* * * *
48605 GTGCATTGATGCATGAAAGGCATTCGATGTTTCAAAATAACCA-GAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTC-AATTAACCATGAGTGCATCGATGCATGGTTG
* * *
48669 GTGCATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTC-TGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAAT-TAAC-CATGAGTGCATCGATGCATGGT
48732 AT-
63 -TG
* *
48734 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATG-GTGCATCGATACATGGAT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTA-ACCATGAGTGCATCGATGCATGG-T
48797 TG
63 TG
*
48799 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
48813 CACTTTGAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 21
0.78 0.08 0.14
Matches are distributed among these distances:
63 4 0.03
64 47 0.39
65 68 0.57
66 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAACCATGAGTGCATCGATGCATGGTTG
Found at i:51474 original size:23 final size:23
Alignment explanation
Indices: 51429--51509 Score: 87
Period size: 23 Copynumber: 3.6 Consensus size: 23
51419 ACCCGATGGA
*
51429 TGCATCGATGCACATTTAAGGTG
1 TGCATCGATGCACATTCAAGGTG
* * *
51452 TGCATCGGTGCACCTTCATGGTG
1 TGCATCGATGCACATTCAAGGTG
51475 T--ATCGATGCACATTCAAAGG-G
1 TGCATCGATGCACATTC-AAGGTG
51496 ATGCATCGATGCAC
1 -TGCATCGATGCAC
51510 TGTTAAGTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
21 13 0.28
22 4 0.09
23 20 0.43
24 10 0.21
ACGTcount: A:0.25, C:0.22, G:0.26, T:0.27
Consensus pattern (23 bp):
TGCATCGATGCACATTCAAGGTG
Found at i:57185 original size:73 final size:72
Alignment explanation
Indices: 57036--57185 Score: 189
Period size: 73 Copynumber: 2.1 Consensus size: 72
57026 GCACTAAGAG
* * *
57036 TGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGGCTGGT
1 TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGAGGCATAGCTGGT
*
57101 GCATCGG
66 GCATCGA
*
57108 TGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-A-CTCTGAGTGCATCGAGGCATAG-T
1 TGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGC-CAGAGTGCATCGAGGCATAGCT
*
57170 ATGTGCATCGA
63 -GGTGCATCGA
57181 TGCAT
1 TGCAT
57186 GAAATACATT
Statistics
Matches: 68, Mismatches: 6, Indels: 7
0.84 0.07 0.09
Matches are distributed among these distances:
72 29 0.43
73 36 0.53
74 3 0.04
ACGTcount: A:0.27, C:0.19, G:0.25, T:0.29
Consensus pattern (72 bp):
TGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGAGGCATAGCTGGT
GCATCGA
Found at i:57554 original size:24 final size:19
Alignment explanation
Indices: 57516--57564 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 19
57506 ATTTTATTAT
57516 TATAATTATATTAATATAATA
1 TATAATTATATT-A-ATAATA
57537 TATAATTATTATGCTAATAATA
1 TATAATTA-TAT--TAATAATA
57559 TATAAT
1 TATAAT
57565 AAACTATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
21 8 0.32
22 15 0.60
23 1 0.04
24 1 0.04
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (19 bp):
TATAATTATATTAATAATA
Found at i:57654 original size:16 final size:17
Alignment explanation
Indices: 57633--57664 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
57623 TTGAATATTT
57633 AATAT-ATATTTTTTAA
1 AATATAATATTTTTTAA
57649 AATATAATATTTTTTA
1 AATATAATATTTTTTA
57665 TTTTAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
AATATAATATTTTTTAA
Found at i:57671 original size:15 final size:16
Alignment explanation
Indices: 57653--57691 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
57643 TTTTAAAATA
*
57653 TAATATTTTTTA-TTT
1 TAATATTTTTAATTTT
57668 TAATA-TTTTAATTTT
1 TAATATTTTTAATTTT
57683 TAATATTTT
1 TAATATTTT
57692 AATAATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 5 0.24
15 13 0.62
16 3 0.14
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (16 bp):
TAATATTTTTAATTTT
Found at i:57683 original size:7 final size:8
Alignment explanation
Indices: 57653--57695 Score: 63
Period size: 8 Copynumber: 5.6 Consensus size: 8
57643 TTTTAAAATA
57653 TAATATTT
1 TAATATTT
*
57661 T-TTATTT
1 TAATATTT
57668 TAATATTT
1 TAATATTT
57676 TAAT-TTT
1 TAATATTT
57683 TAATATTT
1 TAATATTT
57691 TAATA
1 TAATA
57696 ATAATATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
7 13 0.42
8 18 0.58
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TAATATTT
Found at i:57692 original size:15 final size:15
Alignment explanation
Indices: 57665--57694 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
57655 ATATTTTTTA
57665 TTTTAATATTTTAAT
1 TTTTAATATTTTAAT
57680 TTTTAATATTTTAAT
1 TTTTAATATTTTAAT
57695 AATAATATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTTAATATTTTAAT
Found at i:57782 original size:20 final size:20
Alignment explanation
Indices: 57692--57783 Score: 80
Period size: 21 Copynumber: 4.4 Consensus size: 20
57682 TTAATATTTT
* *
57692 AATAATAATATTAATTTATTA
1 AATATTAATA-TAATTTATAA
57713 AATAATTAATATAA-TTAGTAA
1 AAT-ATTAATATAATTTA-TAA
* *
57734 TATATTATTATAATTT-TAATA
1 AATATTAATATAATTTAT-A-A
57755 AATAATTAATATAATTTATAA
1 AAT-ATTAATATAATTTATAA
57776 AATATTAA
1 AATATTAA
57784 ATGAGTTATT
Statistics
Matches: 58, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
19 1 0.02
20 18 0.31
21 19 0.33
22 19 0.33
23 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.01, T:0.46
Consensus pattern (20 bp):
AATATTAATATAATTTATAA
Found at i:58412 original size:26 final size:26
Alignment explanation
Indices: 58361--58412 Score: 61
Period size: 26 Copynumber: 2.0 Consensus size: 26
58351 TTGTTTGGTT
**
58361 TGTTTGACATGAATAATAGATTACAA
1 TGTTTGACATGAATAATAGAAGACAA
*
58387 TGTTTGA-ATGAATGAATATAAGACAA
1 TGTTTGACATGAAT-AATAGAAGACAA
58413 GGAAAATGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 6 0.27
26 16 0.73
ACGTcount: A:0.44, C:0.06, G:0.17, T:0.33
Consensus pattern (26 bp):
TGTTTGACATGAATAATAGAAGACAA
Found at i:58835 original size:30 final size:30
Alignment explanation
Indices: 58769--58836 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 30
58759 GCAGTGCAAC
*
58769 CCATAAAATAGGTTGCAACTTAAAATGACAG
1 CCAT-AAATAGGTTGCAACTTAAAATGACAA
*
58800 CCATAAATAGGTTGCAACTTAAAATGGCAA
1 CCATAAATAGGTTGCAACTTAAAATGACAA
*
58830 TCATAAA
1 CCATAAA
58837 AAAGGGTAGT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 30 0.88
31 4 0.12
ACGTcount: A:0.46, C:0.16, G:0.15, T:0.24
Consensus pattern (30 bp):
CCATAAATAGGTTGCAACTTAAAATGACAA
Found at i:63835 original size:20 final size:20
Alignment explanation
Indices: 63798--63852 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 20
63788 CTCAAAATCA
***
63798 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCAAATTTTG
63818 TTTTTCAAAATCAAATTTTG
1 TTTTTCAAAATCAAATTTTG
*
63838 -CTTTCAAAATCAAAT
1 TTTTTCAAAATCAAAT
63853 CATTTTTTGA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 14 0.45
20 17 0.55
ACGTcount: A:0.35, C:0.13, G:0.04, T:0.49
Consensus pattern (20 bp):
TTTTTCAAAATCAAATTTTG
Found at i:64327 original size:6 final size:6
Alignment explanation
Indices: 64316--64365 Score: 57
Period size: 6 Copynumber: 8.2 Consensus size: 6
64306 TTGAAACCTC
* *
64316 TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT CTTCTT ATTCATT CTTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTC-TT -TTTCTT
64365 T
1 T
64366 GGAGCTTCAC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
5 4 0.11
6 27 0.71
7 4 0.11
8 3 0.08
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTCTT
Found at i:64349 original size:17 final size:17
Alignment explanation
Indices: 64316--64364 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
64306 TTGAAACCTC
*
64316 TTTCTTTTTCTTTTTCTT
1 TTTCTTTTT-TTCTTCTT
64334 TTTCTTTTTTTCTTCTT
1 TTTCTTTTTTTCTTCTT
* * *
64351 ATTCATTCTTTCTT
1 TTTCTTTTTTTCTT
64365 TGGAGCTTCA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
17 18 0.67
18 9 0.33
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (17 bp):
TTTCTTTTTTTCTTCTT
Found at i:67544 original size:13 final size:13
Alignment explanation
Indices: 67513--67538 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
67503 AAGGTAATTC
67513 AACAATAAATGTA
1 AACAATAAATGTA
67526 AACAATAAATGTA
1 AACAATAAATGTA
67539 TTCAATGCAT
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:0.62, C:0.08, G:0.08, T:0.23
Consensus pattern (13 bp):
AACAATAAATGTA
Found at i:68065 original size:16 final size:16
Alignment explanation
Indices: 68044--68076 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
68034 GTAAAACAGT
68044 AAATAA-AAGATAAATA
1 AAATAAGAAGA-AAATA
68060 AAATAAGAAGAAAATA
1 AAATAAGAAGAAAATA
68076 A
1 A
68077 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAGAAGAAAATA
Found at i:78172 original size:17 final size:16
Alignment explanation
Indices: 78150--78183 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
78140 TAAAAACAGT
78150 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
78167 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
78183 A
1 A
78184 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:79717 original size:22 final size:22
Alignment explanation
Indices: 79692--79734 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
79682 GCCCACCATA
*
79692 TGCACTAGGTATCCTTTAGTGT
1 TGCAATAGGTATCCTTTAGTGT
79714 TGCAATAGGTATCCTTTAGTG
1 TGCAATAGGTATCCTTTAGTG
79735 CTAAATCAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.21, C:0.16, G:0.23, T:0.40
Consensus pattern (22 bp):
TGCAATAGGTATCCTTTAGTGT
Found at i:83572 original size:21 final size:20
Alignment explanation
Indices: 83528--83579 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
83518 TCTCTGACTC
*
83528 AAAGGATCAATCCCTTAGCA
1 AAAGGATCGATCCCTTAGCA
* *
83548 AAAGAATCGATCCCTTTGACA
1 AAAGGATCGATCCCTTAG-CA
83569 AAAGGATCGAT
1 AAAGGATCGAT
83580 ATCCTTGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAGGATCGATCCCTTAGCA
Found at i:83659 original size:20 final size:21
Alignment explanation
Indices: 83621--83671 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 21
83611 AGTGAGTTTG
* *
83621 GGATCGATTCTTTGAC-AAAA
1 GGATCGATCCTTTCACAAAAA
*
83641 GGATCGATCCTTTCCCAAAAA
1 GGATCGATCCTTTCACAAAAA
*
83662 GGATTGATCC
1 GGATCGATCC
83672 CTTTGGTATA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 13 0.50
21 13 0.50
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (21 bp):
GGATCGATCCTTTCACAAAAA
Found at i:84452 original size:19 final size:20
Alignment explanation
Indices: 84428--84466 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
84418 CAAAATAATC
*
84428 CAATTTC-ACATTCTAACAT
1 CAATTTCAACACTCTAACAT
84447 CAATTTCAACACTCTAACAT
1 CAATTTCAACACTCTAACAT
84467 TACTTTCCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.33
Consensus pattern (20 bp):
CAATTTCAACACTCTAACAT
Found at i:89823 original size:20 final size:21
Alignment explanation
Indices: 89793--89832 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 21
89783 AGCCGTTGGG
89793 GCCTGATGGTATCGATACTAT
1 GCCTGATGGTATCGATACTAT
89814 GCCT-ATGGTATCGATACTA
1 GCCTGATGGTATCGATACTA
89833 CTATACATAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.33
Consensus pattern (21 bp):
GCCTGATGGTATCGATACTAT
Found at i:94651 original size:27 final size:27
Alignment explanation
Indices: 94596--94659 Score: 76
Period size: 27 Copynumber: 2.4 Consensus size: 27
94586 TATTAACTTA
*
94596 TTAAATATATTTTATTATTATCTTAAT
1 TTAAAAATATTTTATTATTATCTTAAT
* * *
94623 TTAAACATATTTTATT-TCTATTTTTAT
1 TTAAAAATATTTTATTAT-TATCTTAAT
94650 TTAAAAATAT
1 TTAAAAATAT
94660 ATAATTTATT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
26 1 0.03
27 31 0.97
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.58
Consensus pattern (27 bp):
TTAAAAATATTTTATTATTATCTTAAT
Found at i:109538 original size:17 final size:17
Alignment explanation
Indices: 109513--109546 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
109503 CTCAATATCA
*
109513 CTAGGGATATTTCCTTG
1 CTAGAGATATTTCCTTG
109530 CTAGAGATATTTCCTTG
1 CTAGAGATATTTCCTTG
109547 TGGGCGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (17 bp):
CTAGAGATATTTCCTTG
Found at i:109733 original size:20 final size:21
Alignment explanation
Indices: 109695--109733 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
109685 CATCAAGGTC
109695 TTTGTTGAGGCCATGAAATCT
1 TTTGTTGAGGCCATGAAATCT
109716 TTTGTTGAGGCCAT-AAAT
1 TTTGTTGAGGCCATGAAAT
109734 TCCTGCAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.38
Consensus pattern (21 bp):
TTTGTTGAGGCCATGAAATCT
Found at i:120897 original size:29 final size:29
Alignment explanation
Indices: 120862--120943 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
120852 AAACTAAATT
*
120862 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
120891 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
120920 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
120944 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:125668 original size:29 final size:29
Alignment explanation
Indices: 125633--125714 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
125623 AAACTAAATT
*
125633 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
125662 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
125691 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
125715 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:128332 original size:2 final size:2
Alignment explanation
Indices: 128325--128367 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
128315 ATCCTAACCT
128325 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
128367 T
1 T
128368 GCATGGTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:129332 original size:17 final size:17
Alignment explanation
Indices: 129310--129342 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
129300 TGAATTCTTT
*
129310 AATTCGGAATGAATCAA
1 AATTCGGAACGAATCAA
129327 AATTCGGAACGAATCA
1 AATTCGGAACGAATCA
129343 TATCTCTTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.15, G:0.18, T:0.21
Consensus pattern (17 bp):
AATTCGGAACGAATCAA
Found at i:129939 original size:3 final size:3
Alignment explanation
Indices: 129931--130006 Score: 152
Period size: 3 Copynumber: 25.3 Consensus size: 3
129921 TTTCATGTCA
129931 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
129979 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
130007 TGCTTTAACT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 73 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:133413 original size:35 final size:35
Alignment explanation
Indices: 133366--133440 Score: 132
Period size: 35 Copynumber: 2.1 Consensus size: 35
133356 CGTCACGAAC
* *
133366 AGTAAGGTCCTGAGCACAAAGCCGAGGAGCCTGCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
133401 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
1 AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
133436 AGTAA
1 AGTAA
133441 TCTTCCTCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.33, C:0.27, G:0.29, T:0.11
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACAAAGCCGAGGAGCCTCCA
Found at i:133551 original size:24 final size:23
Alignment explanation
Indices: 133523--133609 Score: 93
Period size: 24 Copynumber: 3.7 Consensus size: 23
133513 ATTCAAGTCA
* *
133523 AGTATCATATCAGAATCCATATC
1 AGTATCAGATCAGAATCCATGTC
*
133546 ATGTATCAGATTAGAATCCATGTC
1 A-GTATCAGATCAGAATCCATGTC
* *
133570 AATATCAGATCAGAATCCAGGTC
1 AGTATCAGATCAGAATCCATGTC
* *
133593 AGGTATCATAACAGAAT
1 A-GTATCAGATCAGAAT
133610 TCAAATTTGA
Statistics
Matches: 53, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
23 21 0.40
24 32 0.60
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (23 bp):
AGTATCAGATCAGAATCCATGTC
Found at i:133609 original size:47 final size:48
Alignment explanation
Indices: 133519--133609 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 48
133509 CATAATTCAA
* * * **
133519 GTCAAGTATCATATCAGAATCCATATCATGTATCAGATTAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAATCCAT
* *
133567 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAAT
133610 TCAAATTTGA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
47 31 0.86
48 5 0.14
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGATCAGGTATCAGAACAGAATCCAT
Found at i:136131 original size:12 final size:12
Alignment explanation
Indices: 136100--136139 Score: 71
Period size: 12 Copynumber: 3.2 Consensus size: 12
136090 CAACGGTCAA
136100 CGGTCAACGGGT
1 CGGTCAACGGGT
136112 CGGGTCAACGGGT
1 C-GGTCAACGGGT
136125 CGGTCAACGGGT
1 CGGTCAACGGGT
136137 CGG
1 CGG
136140 GTCGGGTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 15 0.56
13 12 0.44
ACGTcount: A:0.15, C:0.25, G:0.45, T:0.15
Consensus pattern (12 bp):
CGGTCAACGGGT
Found at i:136153 original size:18 final size:18
Alignment explanation
Indices: 136120--136195 Score: 92
Period size: 18 Copynumber: 4.6 Consensus size: 18
136110 GTCGGGTCAA
*
136120 CGGGTC-GGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
136137 CGGGTCGGGTAAA-----
1 CGGGTCGGGTAAACGGGT
136150 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
136168 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTAAACGGGT
136186 CGGGTCGGGT
1 CGGGTCGGGT
136196 TGTGACCGGT
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
13 13 0.25
17 6 0.12
18 32 0.63
ACGTcount: A:0.13, C:0.20, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:136168 original size:31 final size:31
Alignment explanation
Indices: 136107--136190 Score: 143
Period size: 31 Copynumber: 2.7 Consensus size: 31
136097 CAACGGTCAA
*
136107 CGGGTCGGGTCAACGGGTC-GGTCAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTAAACGGGT
*
136137 CGGGTCGGGTAAACGGGTCGGGTAAACGGGT
1 CGGGTCGGGTCAACGGGTCGGGTAAACGGGT
136168 CGGGTCGGGTCAACGGGTCGGGT
1 CGGGTCGGGTCAACGGGTCGGGT
136191 CGGGTTGTGA
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
30 18 0.36
31 32 0.64
ACGTcount: A:0.14, C:0.20, G:0.49, T:0.17
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCGGGTAAACGGGT
Found at i:136191 original size:13 final size:13
Alignment explanation
Indices: 136101--136173 Score: 85
Period size: 13 Copynumber: 5.3 Consensus size: 13
136091 AACGGTCAAC
136101 GGTCAACGGGTCG
1 GGTCAACGGGTCG
136114 GGTCAACGGGTC-
1 GGTCAACGGGTCG
136126 GGTCAACGGGTCG
1 GGTCAACGGGTCG
136139 GGTCGGGTAAACGGGTCG
1 GGTC-----AACGGGTCG
*
136157 GGTAAACGGGTCG
1 GGTCAACGGGTCG
136170 GGTC
1 GGTC
136174 GGGTCAACGG
Statistics
Matches: 52, Mismatches: 2, Indels: 12
0.79 0.03 0.18
Matches are distributed among these distances:
12 12 0.23
13 28 0.54
18 12 0.23
ACGTcount: A:0.16, C:0.21, G:0.47, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:141258 original size:11 final size:11
Alignment explanation
Indices: 141244--141271 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
141234 GAAAAGATAG
141244 AAAAAATATTA
1 AAAAAATATTA
141255 AAAAAATATTA
1 AAAAAATATTA
141266 AAAAAA
1 AAAAAA
141272 CCCAAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (11 bp):
AAAAAATATTA
Found at i:141470 original size:15 final size:16
Alignment explanation
Indices: 141450--141480 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
141440 ACAAAAAAAC
141450 ATGACTAAAA-TAATA
1 ATGACTAAAACTAATA
141465 ATGACTAAAACTAATA
1 ATGACTAAAACTAATA
141481 GCTTAAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.58, C:0.10, G:0.06, T:0.26
Consensus pattern (16 bp):
ATGACTAAAACTAATA
Found at i:142554 original size:7 final size:7
Alignment explanation
Indices: 142542--142593 Score: 56
Period size: 7 Copynumber: 7.9 Consensus size: 7
142532 AAAATGATTA
142542 AATAAAT
1 AATAAAT
142549 AATAAA-
1 AATAAAT
*
142555 AACAAA-
1 AATAAAT
*
142561 AGTAAAT
1 AATAAAT
142568 AATAAAT
1 AATAAAT
142575 AATAAAT
1 AATAAAT
*
142582 AA-AAAG
1 AATAAAT
142588 AATAAA
1 AATAAA
142594 ATACTATATG
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
6 14 0.37
7 24 0.63
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (7 bp):
AATAAAT
Found at i:142592 original size:23 final size:25
Alignment explanation
Indices: 142542--142589 Score: 71
Period size: 26 Copynumber: 1.9 Consensus size: 25
142532 AAAATGATTA
142542 AATAAATAATAAAAACAAAAGTAAAT
1 AATAAATAATAAAAACAAAAG-AAAT
*
142568 AATAAATAATAAATA-AAAAGAA
1 AATAAATAATAAAAACAAAAGAA
142590 TAAAATACTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 2 0.10
25 5 0.24
26 14 0.67
ACGTcount: A:0.75, C:0.02, G:0.04, T:0.19
Consensus pattern (25 bp):
AATAAATAATAAAAACAAAAGAAAT
Found at i:142805 original size:35 final size:34
Alignment explanation
Indices: 142617--142946 Score: 215
Period size: 35 Copynumber: 9.3 Consensus size: 34
142607 TATAACGAAA
* * * *
142617 AAAAAGTTTTAAAACTTTATATAATATATATTTC
1 AAAATGTTTTAAAACTATATATTATATAAATTTC
* * * *
142651 AAAGATATTTTCAAAACCATATATTATATAATTTTA
1 AAA-ATGTTTT-AAAACTATATATTATATAAATTTC
* *
142687 AAAATGTTTTCAAACTATATGTTATAGT---TTTC
1 AAAATGTTTTAAAACTATATATTATA-TAAATTTC
* *
142719 AAAAACGTTTTAAAAC--TATATTATAT--GTTTC
1 -AAAATGTTTTAAAACTATATATTATATAAATTTC
142750 AAAAATGTTTTTAAAGACTATATATTATATAAATTTC
1 -AAAATG-TTTTAAA-ACTATATATTATATAAATTTC
* *
142787 AAAATGATCTTAAAACTATATATTATATAAGCTTTC
1 AAAATG-TTTTAAAACTATATATTATATAA-ATTTC
* **
142823 AAAATGGTTTTAAAAATTATATATTATATATGCTTTC
1 AAAAT-GTTTT-AAAACTATATATTATATA-AATTTC
* * **
142860 TAAAAATGTTTTAAAAATTACATATTATATAGTTTTC
1 --AAAATGTTTT-AAAACTATATATTATATAAATTTC
* *
142897 AAAGGTATTTTTTTTAAAACTATATATTATATACATTTCC
1 AAA---A--TGTTTTAAAACTATATATTATATAAATTT-C
142937 AAAATGTTTT
1 AAAATGTTTT
142947 TTTAAAAAAA
Statistics
Matches: 241, Mismatches: 32, Indels: 45
0.76 0.10 0.14
Matches are distributed among these distances:
30 1 0.00
31 18 0.07
32 10 0.04
33 15 0.06
34 16 0.07
35 46 0.19
36 45 0.19
37 33 0.14
38 24 0.10
39 24 0.10
40 9 0.04
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (34 bp):
AAAATGTTTTAAAACTATATATTATATAAATTTC
Found at i:142949 original size:39 final size:35
Alignment explanation
Indices: 142617--142946 Score: 193
Period size: 36 Copynumber: 9.3 Consensus size: 35
142607 TATAACGAAA
* * * *
142617 AAAAAGTTTT-AAAACTTTATATAATATATATTTC
1 AAAATGTTTTAAAAACTATATATTATATACATTTC
* * * *
142651 AAAGATATTTTCAAAACCATATATTATATA-ATTTTA
1 AAA-ATGTTTTAAAAACTATATATTATATACA-TTTC
* *
142687 AAAATGTTTT-CAAACTATATGTTATAGT---TTTC
1 AAAATGTTTTAAAAACTATATATTATA-TACATTTC
* *
142719 AAAAACGTTTT-AAAAC--TATATTATAT--GTTTC
1 -AAAATGTTTTAAAAACTATATATTATATACATTTC
* *
142750 AAAAATGTTTTTAAAGACTATATATTATATAAATTTC
1 -AAAATG-TTTTAAAAACTATATATTATATACATTTC
*
142787 AAAATGATCTT-AAAACTATATATTATATA-AGCTTTC
1 AAAATG-TTTTAAAAACTATATATTATATACA--TTTC
*
142823 AAAATGGTTTTAAAAATTATATATTATATATGC-TTTC
1 AAAAT-GTTTTAAAAACTATATATTATATA--CATTTC
* * **
142860 TAAAAATGTTTTAAAAATTACATATTATATAGTTTTC
1 --AAAATGTTTTAAAAACTATATATTATATACATTTC
* *
142897 AAAGGTATTTTTTTTAAAACTATATATTATATACATTTCC
1 AAA---A-TGTTTTAAAAACTATATATTATATACATTT-C
142937 AAAATGTTTT
1 AAAATGTTTT
142947 TTTAAAAAAA
Statistics
Matches: 238, Mismatches: 31, Indels: 52
0.74 0.10 0.16
Matches are distributed among these distances:
30 1 0.00
31 18 0.08
32 7 0.03
33 17 0.07
34 17 0.07
35 43 0.18
36 47 0.20
37 31 0.13
38 24 0.10
39 29 0.12
40 4 0.02
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (35 bp):
AAAATGTTTTAAAAACTATATATTATATACATTTC
Found at i:144255 original size:90 final size:90
Alignment explanation
Indices: 144102--144274 Score: 303
Period size: 90 Copynumber: 1.9 Consensus size: 90
144092 ATATATAAAC
* * *
144102 ACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
144167 ACAACTCAAGCTTTATTGAATAATT
66 ACAACTCAAGCTTTATTGAATAATT
144192 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT-TAGAGG
144256 GACAACTCAAGCTTTATTG
65 GACAACTCAAGCTTTATTG
144275 TATATATATA
Statistics
Matches: 79, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
89 2 0.03
90 77 0.97
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (90 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGAATAATT
Found at i:146735 original size:16 final size:16
Alignment explanation
Indices: 146691--146736 Score: 83
Period size: 16 Copynumber: 2.9 Consensus size: 16
146681 ATGAAAAATC
*
146691 CTACCCCACATGATAT
1 CTACCCCACATGCTAT
146707 CTACCCCACATGCTAT
1 CTACCCCACATGCTAT
146723 CTACCCCACATGCT
1 CTACCCCACATGCT
146737 TTAATTCCTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.26, C:0.43, G:0.07, T:0.24
Consensus pattern (16 bp):
CTACCCCACATGCTAT
Found at i:147808 original size:32 final size:36
Alignment explanation
Indices: 147717--147812 Score: 94
Period size: 34 Copynumber: 2.7 Consensus size: 36
147707 AAACGATAAT
*
147717 TAAAAATAATAATAAAATAAATGAAATAGAGATGAAA
1 TAAAAATAAAAATAAAATAAAT-AAATAGAGATGAAA
* *
147754 TAAAAAGAGAAAA-AATGGATAAATAAAT-GA-A-G-AA
1 TAAAAATA-AAAATAA--AATAAATAAATAGAGATGAAA
147788 TAAAAATAAAAATAAAATAAATAAA
1 TAAAAATAAAAATAAAATAAATAAA
147813 ATAAATAAAA
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
32 9 0.18
33 4 0.08
34 11 0.22
35 1 0.02
36 1 0.02
37 11 0.22
38 7 0.14
39 6 0.12
ACGTcount: A:0.71, C:0.00, G:0.10, T:0.19
Consensus pattern (36 bp):
TAAAAATAAAAATAAAATAAATAAATAGAGATGAAA
Found at i:147811 original size:9 final size:9
Alignment explanation
Indices: 147774--147822 Score: 57
Period size: 9 Copynumber: 5.3 Consensus size: 9
147764 AAAAATGGAT
147774 AAATAAATGA
1 AAATAAAT-A
147784 AGAATAAA-A
1 A-AATAAATA
147793 ATAA-AAATA
1 A-AATAAATA
147802 AAATAAATA
1 AAATAAATA
147811 AAATAAATA
1 AAATAAATA
147820 AAA
1 AAA
147823 GGCTTAATAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
8 5 0.14
9 23 0.66
10 1 0.03
11 6 0.17
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.18
Consensus pattern (9 bp):
AAATAAATA
Found at i:148076 original size:15 final size:16
Alignment explanation
Indices: 148056--148085 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
148046 CATAAAAACT
148056 TGACTAAAA-TAATAA
1 TGACTAAAACTAATAA
148071 TGACTAAAACTAATA
1 TGACTAAAACTAATA
148086 GCTTAAATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.10, G:0.07, T:0.27
Consensus pattern (16 bp):
TGACTAAAACTAATAA
Found at i:149176 original size:7 final size:7
Alignment explanation
Indices: 149164--149215 Score: 58
Period size: 7 Copynumber: 7.9 Consensus size: 7
149154 AAAATGATTA
149164 AATAAAT
1 AATAAAT
149171 AAT-AA-
1 AATAAAT
149176 AATCAAA-
1 AAT-AAAT
149183 AATAAAT
1 AATAAAT
149190 AATAAAT
1 AATAAAT
149197 AATAAAT
1 AATAAAT
*
149204 AA-AAAG
1 AATAAAT
149210 AATAAA
1 AATAAA
149216 ATACTATATG
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
5 3 0.08
6 10 0.25
7 27 0.68
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.21
Consensus pattern (7 bp):
AATAAAT
Found at i:149183 original size:30 final size:30
Alignment explanation
Indices: 149147--149207 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
149137 CTTGACAAAC
*
149147 ATCAAAAA-AAATGATTAAATAA-ATAATAAA
1 ATCAAAAATAAAT-AATAAATAATA-AATAAA
149177 ATCAAAAATAAATAATAAATAATAAATAAA
1 ATCAAAAATAAATAATAAATAATAAATAAA
149207 A
1 A
149208 AGAATAAAAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 23 0.82
31 5 0.18
ACGTcount: A:0.72, C:0.03, G:0.02, T:0.23
Consensus pattern (30 bp):
ATCAAAAATAAATAATAAATAATAAATAAA
Found at i:149218 original size:14 final size:14
Alignment explanation
Indices: 149183--149215 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
149173 TAAAATCAAA
*
149183 AATAAATAATAAAT
1 AATAAATAATAAAG
149197 AATAAATAA-AAAG
1 AATAAATAATAAAG
149210 AATAAA
1 AATAAA
149216 ATACTATATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (14 bp):
AATAAATAATAAAG
Found at i:149796 original size:66 final size:64
Alignment explanation
Indices: 149659--149860 Score: 198
Period size: 65 Copynumber: 3.1 Consensus size: 64
149649 TTTTTCAGAG
* * * *
149659 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAATTA-AATTG-AACATCGAATGC
1 TGATGCATCGATGCACCAA-CCATGCACCGATGCACTCA-G-GTTATTA-TGAAACATCGAATGC
149721 ATT
62 ATT
* *
149724 TCATGCATCGATGCA-CATACCATGCACCCGATGCACTGAGGATT-TTATGAAAACATCGAATGC
1 TGATGCATCGATGCACCA-ACCATGCA-CCGATGCACTCAGG-TTATTATG-AAACATCGAATGC
149787 ATT
62 ATT
* * * * *
149790 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGTTATTTTGAAACATCGAATGCACT
1 TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGTTATTATGAAACATCGAATGCATT
149854 TGATGCA
1 TGATGCA
149861 CTCTTAGTGC
Statistics
Matches: 115, Mismatches: 13, Indels: 19
0.78 0.09 0.13
Matches are distributed among these distances:
64 35 0.30
65 41 0.36
66 37 0.32
67 2 0.02
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCACCGATGCACTCAGGTTATTATGAAACATCGAATGCATT
Found at i:155316 original size:42 final size:44
Alignment explanation
Indices: 155269--155363 Score: 124
Period size: 44 Copynumber: 2.2 Consensus size: 44
155259 TTGTGCTTAA
* *
155269 TGCATCGATATACC-T-AACAGTGCATCGATGCA-TCCTTGAATG
1 TGCATCGATATACCATGAA-AGTGCACCGATGCACGCCTTGAATG
*
155311 TGCATCGATATACCATGAAGGTGCACCGATGCACGCCTTGAATG
1 TGCATCGATATACCATGAAAGTGCACCGATGCACGCCTTGAATG
*
155355 TGTATCGAT
1 TGCATCGAT
155364 GCACAAGACC
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
42 14 0.30
43 13 0.28
44 19 0.41
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.27
Consensus pattern (44 bp):
TGCATCGATATACCATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:155334 original size:21 final size:20
Alignment explanation
Indices: 155269--155340 Score: 58
Period size: 21 Copynumber: 3.5 Consensus size: 20
155259 TTGTGCTTAA
155269 TGCATCGATATACCT-AACAG
1 TGCATCGATATACCTGAA-AG
*
155289 TGCATCGATGCAT-CCTTGAATG
1 TGCATCGAT--ATACC-TGAAAG
*
155311 TGCATCGATATACCATGAAGG
1 TGCATCGATATACC-TGAAAG
*
155332 TGCACCGAT
1 TGCATCGAT
155341 GCACGCCTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
20 11 0.26
21 17 0.40
22 13 0.30
23 2 0.05
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (20 bp):
TGCATCGATATACCTGAAAG
Found at i:156951 original size:21 final size:21
Alignment explanation
Indices: 156925--156973 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
156915 CCGAGAGCTG
*
156925 GCTCTTCACGAGCTGCTCCTA
1 GCTCTTCACGAGATGCTCCTA
156946 GCTCTTCACGAGATGCTCCTA
1 GCTCTTCACGAGATGCTCCTA
*
156967 GATCTTC
1 GCTCTTC
156974 TCGTGCTCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.16, C:0.35, G:0.18, T:0.31
Consensus pattern (21 bp):
GCTCTTCACGAGATGCTCCTA
Found at i:158964 original size:37 final size:36
Alignment explanation
Indices: 158918--159087 Score: 146
Period size: 38 Copynumber: 4.5 Consensus size: 36
158908 AAATGATCTT
* *
158918 AAAACTATATTTTATATAAGCTTTCAAAATGGTTTTA
1 AAAATTATATATTATATAAGCTTTCAAAAT-GTTTTA
* *
158955 AAAGTTATATATTATATATGCTTTCTATAAATGTTTTA
1 AAAATTATATATTATATAAGCTTTC-A-AAATGTTTTA
* * *
158993 AAAATTATATATTATAT-AGTTTTCAAAGGTATTTTTTT
1 AAAATTATATATTATATAAGCTTTCAAA---ATGTTTTA
* *
159031 AAAACTATATATTATATACA-TTTTCAAAATGTTTTTTAA
1 AAAATTATATATTATATA-AGCTTTCAAAATG--TTTT-A
*
159070 AAAATCATATATTATATA
1 AAAATTATATATTATATA
159088 CGTATTTTTC
Statistics
Matches: 109, Mismatches: 14, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
35 2 0.02
36 3 0.03
37 26 0.24
38 49 0.45
39 28 0.26
40 1 0.01
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (36 bp):
AAAATTATATATTATATAAGCTTTCAAAATGTTTTA
Found at i:159055 original size:39 final size:38
Alignment explanation
Indices: 158988--159102 Score: 124
Period size: 38 Copynumber: 2.9 Consensus size: 38
158978 TCTATAAATG
* * *
158988 TTTTAAAAATTATATATTATATA-GTTTTCAAAGGTATT
1 TTTTAAAAAATATATATTATATACATTTTCAAA-ATATT
* * *
159026 TTTTTAAAACTATATATTATATACATTTTCAAAATGTT
1 TTTTAAAAAATATATATTATATACATTTTCAAAATATT
159064 TTTTAAAAAATCATATATTATATACGTATTTTTCAAAAT
1 TTTTAAAAAAT-ATATATTATATAC--A-TTTTCAAAAT
159103 CCATTTTGCG
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
38 33 0.51
39 21 0.32
41 1 0.02
42 10 0.15
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (38 bp):
TTTTAAAAAATATATATTATATACATTTTCAAAATATT
Done.