Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002302.1 Hibiscus syriacus cultivar Beakdansim tig00004689_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: 184125
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.34
Found at i:4696 original size:20 final size:21
Alignment explanation
Indices: 4657--4696 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
4647 TAATACTACA
4657 ATGTTGGAATTTATAATTTGG
1 ATGTTGGAATTTATAATTTGG
4678 ATGTT-GAATTT-TAAGTTTG
1 ATGTTGGAATTTATAA-TTTG
4697 AGTTTTTAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 3 0.17
20 10 0.56
21 5 0.28
ACGTcount: A:0.28, C:0.00, G:0.23, T:0.50
Consensus pattern (21 bp):
ATGTTGGAATTTATAATTTGG
Found at i:5499 original size:19 final size:21
Alignment explanation
Indices: 5475--5517 Score: 63
Period size: 19 Copynumber: 2.1 Consensus size: 21
5465 AATCTAAATT
*
5475 TTTAATGA-TTAAATAT-TTA
1 TTTAATGATTTAAAAATGTTA
5494 TTTAATGATTTAAAAATGTTA
1 TTTAATGATTTAAAAATGTTA
5515 TTT
1 TTT
5518 GATTTCTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.38
20 7 0.33
21 6 0.29
ACGTcount: A:0.40, C:0.00, G:0.07, T:0.53
Consensus pattern (21 bp):
TTTAATGATTTAAAAATGTTA
Found at i:7224 original size:27 final size:27
Alignment explanation
Indices: 7181--7255 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
7171 TAAGTACATA
7181 ATTTAAGTATTAAGTTTTTTTATACAAAT
1 ATTTAA-T-TTAAGTTTTTTTATACAAAT
*
7210 ATTTGATTTAAGTTTTTTTATACAAAT
1 ATTTAATTTAAGTTTTTTTATACAAAT
* *
7237 GTTTAATTTAAGTTATTTT
1 ATTTAATTTAAGTTTTTTT
7256 GAATGATATA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 36 0.86
28 1 0.02
29 5 0.12
ACGTcount: A:0.33, C:0.03, G:0.08, T:0.56
Consensus pattern (27 bp):
ATTTAATTTAAGTTTTTTTATACAAAT
Found at i:12829 original size:59 final size:59
Alignment explanation
Indices: 12745--12864 Score: 163
Period size: 59 Copynumber: 2.0 Consensus size: 59
12735 TACATATTCA
* * * *
12745 GGATTGCACTAAATGATACCTAGTGCATATGGTG-GACATGACCTTATGTGTCATATTTG
1 GGATTGCACTAAATGATAACTAGTGCATAGGGTGAG-CACGACCTCATGTGTCATATTTG
*
12804 GGATTGTACTAAA-GTATAACTAGTGCATAGGGTGAGCACGACCTCATGTGTCATATTTG
1 GGATTGCACTAAATG-ATAACTAGTGCATAGGGTGAGCACGACCTCATGTGTCATATTTG
12863 GG
1 GG
12865 TTAGATCTAC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
58 1 0.02
59 52 0.96
60 1 0.02
ACGTcount: A:0.28, C:0.15, G:0.26, T:0.32
Consensus pattern (59 bp):
GGATTGCACTAAATGATAACTAGTGCATAGGGTGAGCACGACCTCATGTGTCATATTTG
Found at i:33059 original size:263 final size:261
Alignment explanation
Indices: 32580--33189 Score: 766
Period size: 263 Copynumber: 2.3 Consensus size: 261
32570 TCTTATATAA
* * * * **
32580 ATTCATAAGATTTTCAAGTTTTAAATTATTTTCTTATCGTGGGAAAATTTAAGGCTCCATCATAT
1 ATTCATAACATTTTC-AGTTTTAACTTATTTTCTTATCGTGAGAAAATTCAAGGCTCCATCAGCT
* * ** *
32645 TAAACTCTGAGAACATTTTAGGCACACTCATTTTAGTATTAAAAATATTAAGATTTCATATTGCA
65 TAAACTCTGATAACATTTTAGGCACACCCATTGCAGTATTAAAAATATTAAGATTTCAGATTGCA
* *
32710 ACATGATTTCTTAGTGAACCAGACATTCTTAGGTCCAACCTATTTTATTAATAAAAATATTAACA
130 ACATGATTTCTTAGTGAACCAGACATACTTAGGGCCAACCTATTTTATTAATAAAAATATTAACA
* *
32775 TTACATGTCACAACATATTTCTTAGCGAATCATGACATTATTGGGCGAAA-CGACATTTATTATA
195 TTACATGTCACAACATATTTCTTAGCGAACCATAACATTATTGGGCGAAATCG-CATTTATTATA
32839 CAT
259 CAT
* **
32842 ATTCATAACAATTTCAGCTTTTAACTTATTTTCTTATCGTGCTAAAATTCAAGGCTCCATCAGCT
1 ATTCATAACATTTTCAG-TTTTAACTTATTTTCTTATCGTGAGAAAATTCAAGGCTCCATCAGCT
* * * *
32907 TAAACTCTGATAACATTTTAGGCCCAACCCATTGCATTATTAAAAATATTAATA-TTCTAGATTT
65 TAAACTCTGATAACATTTTAGGCAC-ACCCATTGCAGTATTAAAAATATTAAGATTTC-AGATTG
* *
32971 CAACTTGATTTCTTAGTGAACCAGACATACTT-GGGCATAACCTATTTTATTAATAAAAATATTA
128 CAACATGATTTCTTAGTGAACCAGACATACTTAGGGC-CAACCTATTTTATTAATAAAAATATTA
* * * *
33035 GCATTACATGAT-ACAACCTATTTCTTAGCGAACCATAACATTATTGGGCGAAATCGTATTTCTT
192 ACATTACATG-TCACAACATATTTCTTAGCGAACCATAACATTATTGGGCGAAATCGCATTTATT
*
33099 ATATAT
256 ATACAT
* * **
33105 ATTCATAACATTTTTAATTTTTAACTTATTTTCTTAT--TGAGGGAATGTCTAAGGC-CCTATCA
1 ATTCATAACA-TTTTCAGTTTTAACTTATTTTCTTATCGTGAGAAAAT-TC-AAGGCTCC-ATCA
*
33167 GCTTAAACTCTGATAACCTTTTA
62 GCTTAAACTCTGATAACATTTTA
33190 CGTGCAACCT
Statistics
Matches: 302, Mismatches: 36, Indels: 19
0.85 0.10 0.05
Matches are distributed among these distances:
261 7 0.02
262 87 0.29
263 201 0.67
264 7 0.02
ACGTcount: A:0.34, C:0.17, G:0.11, T:0.38
Consensus pattern (261 bp):
ATTCATAACATTTTCAGTTTTAACTTATTTTCTTATCGTGAGAAAATTCAAGGCTCCATCAGCTT
AAACTCTGATAACATTTTAGGCACACCCATTGCAGTATTAAAAATATTAAGATTTCAGATTGCAA
CATGATTTCTTAGTGAACCAGACATACTTAGGGCCAACCTATTTTATTAATAAAAATATTAACAT
TACATGTCACAACATATTTCTTAGCGAACCATAACATTATTGGGCGAAATCGCATTTATTATACA
T
Found at i:38870 original size:2 final size:2
Alignment explanation
Indices: 38863--38888 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
38853 AATCAAGTTC
38863 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
38889 CTGTTGAGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40406 original size:2 final size:2
Alignment explanation
Indices: 40399--40456 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
40389 CATCAAGTTC
40399 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
40441 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
40457 CTGTTGAGAA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:47256 original size:36 final size:36
Alignment explanation
Indices: 47208--47359 Score: 126
Period size: 36 Copynumber: 4.0 Consensus size: 36
47198 AAAATGCTAA
*
47208 AGTGTACTGATACACCCTACAGTGTATCCATACACT
1 AGTGTACCGATACACCCTACAGTGTATCCATACACT
* * * * *
47244 AGTGTACCGATACA-CCTATGACTGCTCAAACACCGAATATAATT
1 AGTGTACCGATACACCCTA-CAGTG-T---A-TCC--ATA-CACT
*
47288 AGTGTACCGATACACCCTGCAGTGTATCCATACACT
1 AGTGTACCGATACACCCTACAGTGTATCCATACACT
* **
47324 AGTGTATCGATACACCCTGTAGTGTATCCATACACT
1 AGTGTACCGATACACCCTACAGTGTATCCATACACT
47360 CTCTGCAACG
Statistics
Matches: 92, Mismatches: 14, Indels: 20
0.73 0.11 0.16
Matches are distributed among these distances:
35 4 0.04
36 52 0.57
37 4 0.04
39 2 0.02
40 2 0.02
41 2 0.02
43 4 0.04
44 19 0.21
45 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (36 bp):
AGTGTACCGATACACCCTACAGTGTATCCATACACT
Found at i:47313 original size:20 final size:19
Alignment explanation
Indices: 47288--47358 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
47278 GAATATAATT
47288 AGTGTA-CCGATACACCCTG
1 AGTGTATCC-ATACACCCTG
47307 CAGTGTATCCATACA--CT-
1 -AGTGTATCCATACACCCTG
*
47324 AGTGTATCGATACACCCTG
1 AGTGTATCCATACACCCTG
47343 TAGTGTATCCATACAC
1 -AGTGTATCCATACAC
47359 TCTCTGCAAC
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
16 13 0.30
18 4 0.09
20 25 0.57
21 2 0.05
ACGTcount: A:0.28, C:0.28, G:0.17, T:0.27
Consensus pattern (19 bp):
AGTGTATCCATACACCCTG
Found at i:47329 original size:16 final size:16
Alignment explanation
Indices: 47308--47359 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 16
47298 TACACCCTGC
47308 AGTGTATCCATACACT
1 AGTGTATCCATACACT
*
47324 AGTGTATCGATACACCCTGT
1 AGTGTATCCATACA--C--T
47344 AGTGTATCCATACACT
1 AGTGTATCCATACACT
47360 CTCTGCAACG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
16 14 0.47
18 2 0.07
20 14 0.47
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.31
Consensus pattern (16 bp):
AGTGTATCCATACACT
Found at i:47754 original size:33 final size:33
Alignment explanation
Indices: 47707--47779 Score: 119
Period size: 33 Copynumber: 2.2 Consensus size: 33
47697 TTTCATTGTA
*
47707 TAGGAGAAAGGTTCTAGTTGATCCCGTGAAAAAC
1 TAGG-GAAAGGTTCTAGTTGAGCCCGTGAAAAAC
*
47741 TAGGGAAAGGTTCTAGTTTAGCCCGTGAAAAAC
1 TAGGGAAAGGTTCTAGTTGAGCCCGTGAAAAAC
47774 TAGGGA
1 TAGGGA
47780 GTTTGTAAAG
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
33 33 0.89
34 4 0.11
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (33 bp):
TAGGGAAAGGTTCTAGTTGAGCCCGTGAAAAAC
Found at i:50017 original size:20 final size:20
Alignment explanation
Indices: 49992--50099 Score: 85
Period size: 20 Copynumber: 5.8 Consensus size: 20
49982 AAAATGCTAA
49992 AGTGTA-CCGATACACCCTGC
1 AGTGTATCC-ATACACCCTGC
*
50012 AGTGTATCCTTACA--CTGC
1 AGTGTATCCATACACCCTGC
50030 --TGTA-CCGATACACCCTGC
1 AGTGTATCC-ATACACCCTGC
*
50048 AGTGTATCCTTACA--CTG-
1 AGTGTATCCATACACCCTGC
*
50065 -GTGTA-CCGATACACCCTGT
1 AGTGTATCC-ATACACCCTGC
50084 AGTGTATCCATACACC
1 AGTGTATCCATACACC
50100 TATGATTGCT
Statistics
Matches: 71, Mismatches: 4, Indels: 26
0.70 0.04 0.26
Matches are distributed among these distances:
15 4 0.06
16 17 0.24
18 14 0.20
20 30 0.42
21 6 0.08
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (20 bp):
AGTGTATCCATACACCCTGC
Found at i:50041 original size:36 final size:36
Alignment explanation
Indices: 49994--50098 Score: 183
Period size: 36 Copynumber: 2.9 Consensus size: 36
49984 AATGCTAAAG
49994 TGTACCGATACACCCTGCAGTGTATCCTTACACTGC
1 TGTACCGATACACCCTGCAGTGTATCCTTACACTGC
*
50030 TGTACCGATACACCCTGCAGTGTATCCTTACACTGG
1 TGTACCGATACACCCTGCAGTGTATCCTTACACTGC
* *
50066 TGTACCGATACACCCTGTAGTGTATCCATACAC
1 TGTACCGATACACCCTGCAGTGTATCCTTACAC
50099 CTATGATTGC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.24, C:0.31, G:0.17, T:0.28
Consensus pattern (36 bp):
TGTACCGATACACCCTGCAGTGTATCCTTACACTGC
Found at i:50047 original size:18 final size:19
Alignment explanation
Indices: 49994--50082 Score: 59
Period size: 16 Copynumber: 4.9 Consensus size: 19
49984 AATGCTAAAG
49994 TGTACCGATACACCCTGCA
1 TGTACCGATACACCCTGCA
*
50013 GTGTATCC-TTACA--CTGC-
1 -TGTA-CCGATACACCCTGCA
50030 TGTACCGATACACCCTGCA
1 TGTACCGATACACCCTGCA
* *
50049 GTGTATCC-TTACA--CTG-G
1 -TGTA-CCGATACACCCTGCA
50066 TGTACCGATACACCCTG
1 TGTACCGATACACCCTG
50083 TAGTGTATCC
Statistics
Matches: 54, Mismatches: 5, Indels: 22
0.67 0.06 0.27
Matches are distributed among these distances:
15 4 0.07
16 16 0.30
18 14 0.26
20 16 0.30
21 4 0.07
ACGTcount: A:0.22, C:0.33, G:0.18, T:0.27
Consensus pattern (19 bp):
TGTACCGATACACCCTGCA
Found at i:50596 original size:33 final size:33
Alignment explanation
Indices: 50528--50597 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
50518 CATTGTAAAG
* * *
50528 GGGAAAGGTTCTAGCTAATCCCGTGAAAAGCTA
1 GGGAAAGGTTCTAGCTAAGCCCATGAAAAACTA
* * *
50561 GGGAAAGGTTCTAGTTTAGCCCATGAAAAATTA
1 GGGAAAGGTTCTAGCTAAGCCCATGAAAAACTA
50594 GGGA
1 GGGA
50598 GTTTGTAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (33 bp):
GGGAAAGGTTCTAGCTAAGCCCATGAAAAACTA
Found at i:56623 original size:23 final size:23
Alignment explanation
Indices: 56593--56636 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
56583 ATCTTATATG
56593 GCACTTCGGTGCATTTCTACGCA
1 GCACTTCGGTGCATTTCTACGCA
56616 GCACTTCGGTGCATTTCTACG
1 GCACTTCGGTGCATTTCTACG
56637 AGCTGTGCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.16, C:0.30, G:0.23, T:0.32
Consensus pattern (23 bp):
GCACTTCGGTGCATTTCTACGCA
Found at i:61994 original size:21 final size:21
Alignment explanation
Indices: 61970--62011 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
61960 AGTTTATTTT
61970 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
*
61991 TAAACTTTGTTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
62012 AACTTGGAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.31, C:0.14, G:0.07, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:62048 original size:33 final size:33
Alignment explanation
Indices: 62006--62109 Score: 183
Period size: 33 Copynumber: 3.2 Consensus size: 33
61996 TTTGTTTCAA
62006 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
62039 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
* *
62072 TTATCGAACTTGGAAGTATTTAAGTATTTCAA-
1 TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
62104 TTATCG
1 TTATCG
62110 TAAACTTTGT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
32 6 0.09
33 63 0.91
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (33 bp):
TTATCGAACTTGGAAGTTTTTAAGTATTTGAAT
Found at i:65708 original size:204 final size:206
Alignment explanation
Indices: 65337--65733 Score: 547
Period size: 204 Copynumber: 1.9 Consensus size: 206
65327 AAATATCGAT
*
65337 ACATTTTCAGCTTCTAACTTATTTTCTTTCAATTTTTAAAAGTATCGATCATTACTCCACAAGTA
1 ACATTTTCAGCTTCTAACTTATTTTCTTTAAATTTTTAAAAGTATCGATCATTACTCCACAAGTA
* *
65402 TCGATATTTTAACTTTTGATCTTATCTTCAACTTTTTCAATATGTAAAAGTATCGATAATAATAT
66 TCAATATTTTAACTTTTGATCTTATCTTCAACTTTTTCAATATGTAAAAGTATCAATAATAATAT
* * ** *
65467 ATATTAATTGTTGATATTTAAAATTTTGAT-TTTTTTTTATTTTTTTGGGAGCAATCATATTTAT
131 ATATTAAGTATCAATATTTAAAATTTAGATGTTTTTTTTATTTTTTTGGGAGCAA-CATATTTAT
65531 TATATATGAATA
195 TATATATGAATA
* *
65543 ACATTTTCAGCTT-TAACTTATTTTCTTTAAATTTTT-AAATTATC-AGTCATTAC-CGCATAAG
1 ACATTTTCAGCTTCTAACTTATTTTCTTTAAATTTTTAAAAGTATCGA-TCATTACTC-CACAAG
* * *
65604 TATCAATATTTTAACTTTTGGTCTTATCTTCAACTTTTTTAATATTTAAAAGTATCAATAATAAT
64 TATCAATATTTTAACTTTTGATCTTATCTTCAACTTTTTCAATATGTAAAAGTATCAATAATAAT
* * * *
65669 AT-T-TTCAGTATCAATATTTACAATTTAGAACTGTTTTTTTTATTTTTTTGGGTGCAACCTATT
129 ATATATTAAGTATCAATATTTAAAATTTAG-A-TGTTTTTTTTATTTTTTTGGGAGCAACATATT
65732 TA
192 TA
65734 ATAATAAAAA
Statistics
Matches: 169, Mismatches: 17, Indels: 12
0.85 0.09 0.06
Matches are distributed among these distances:
202 18 0.11
203 4 0.02
204 89 0.53
205 45 0.27
206 13 0.08
ACGTcount: A:0.31, C:0.12, G:0.08, T:0.49
Consensus pattern (206 bp):
ACATTTTCAGCTTCTAACTTATTTTCTTTAAATTTTTAAAAGTATCGATCATTACTCCACAAGTA
TCAATATTTTAACTTTTGATCTTATCTTCAACTTTTTCAATATGTAAAAGTATCAATAATAATAT
ATATTAAGTATCAATATTTAAAATTTAGATGTTTTTTTTATTTTTTTGGGAGCAACATATTTATT
ATATATGAATA
Found at i:66358 original size:237 final size:237
Alignment explanation
Indices: 65918--66372 Score: 587
Period size: 237 Copynumber: 1.9 Consensus size: 237
65908 AACTTTATAG
* * * *
65918 ATCACAACCTATTGCTTAGTAAACCATGACATTATTGGACGAAACCCTATTTCTTATATATATTC
1 ATCACAACCTATTGCTTAGCAAACCATGACATTATTGGACAAAACCCTATTTATTATACATATTC
* * * * *
65983 ATACGATTTTCAGGTTTTAAATTATTTTCTTATCGTGGGAAAATTTAAGGCTCCATCATATTAAA
66 ATACGATTTTCAGCTTTTAAATTATTTTCTTATCGTGCGAAAATTTAAGACTACATCAGATTAAA
* ** *
66048 CTCTGAGAACATTTTAGGCACAACTCATTTTAGTATTAAAAATATTAAGATTTCATATTGCAACA
131 CTCTGAGAACATTTTAGGCACAACCCATTGCAGTATTAAAAATATTAAGATTTCAGATTGCAACA
66113 TAATTTCTTAGTGAACCAGACATTCTTAGGTCCAACCTACAT
196 TAATTTCTTAGTGAACCAGACATTCTTAGGTCCAACCTACAT
* * *
66155 ATCACAACCTATTTCTTAGCGAACCATGACATTATTAGG-CAAAACTGC-ATTTATTATACATAT
1 ATCACAACCTATTGCTTAGCAAACCATGACATTATT-GGACAAAAC-CCTATTTATTATACATAT
* * * *
66218 TTATAAC-ATTTTCAGCTTTTAACTTATTTTCTTATCGTGCTAAAATTTAAGACTACATCAGCTT
64 TCAT-ACGATTTTCAGCTTTTAAATTATTTTCTTATCGTGCGAAAATTTAAGACTACATCAGATT
** * * *
66282 AAACTCTGATTACATTTTAGGCCCAACCCATTGCATTATTAAAAATATTAATA-TTCTAGATT-C
128 AAACTCTGAGAACATTTTAGGCACAACCCATTGCAGTATTAAAAATATTAAGATTTC-AGATTGC
* *
66345 TAACCTGATTTCTTAGTGAACCAGACAT
192 -AACATAATTTCTTAGTGAACCAGACAT
66373 ACTTGGGCAT
Statistics
Matches: 186, Mismatches: 27, Indels: 10
0.83 0.12 0.04
Matches are distributed among these distances:
236 4 0.02
237 177 0.95
238 5 0.03
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.37
Consensus pattern (237 bp):
ATCACAACCTATTGCTTAGCAAACCATGACATTATTGGACAAAACCCTATTTATTATACATATTC
ATACGATTTTCAGCTTTTAAATTATTTTCTTATCGTGCGAAAATTTAAGACTACATCAGATTAAA
CTCTGAGAACATTTTAGGCACAACCCATTGCAGTATTAAAAATATTAAGATTTCAGATTGCAACA
TAATTTCTTAGTGAACCAGACATTCTTAGGTCCAACCTACAT
Found at i:69085 original size:220 final size:216
Alignment explanation
Indices: 68694--69330 Score: 868
Period size: 220 Copynumber: 2.9 Consensus size: 216
68684 TTTACCTGTT
* *
68694 ATATTGTT-ATGTAATAGGTAGCGCCTATTTTCTTAGCGTTTACATTATTAACAACCTTCAAAAA
1 ATATT-TTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAACAACCTTCAAAAA
* * *
68758 AACCGGTAGGTATTTTAATATAATAGGTAGCGCCAATTTTTTTAGTGTTTACATTATTAACAACC
65 AACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACTGTTTACATTATTAACAACC
*
68823 TTAAAAAAAACCAGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTA
130 TTAAAAAAAA-CGGTA-GTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTA
68888 TTAACAACCTTAAAAAAAAACCGATACG
193 TTAACAACCTT---AAAAAACCGATA-G
*
68916 -TATTTTAATGTAATAGGTAGCGCCT-TTTTTTTACCGTTTACATTATTAATAACCTTCAAAAAA
1 ATATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAACAACCTTCAAAAAA
*
68979 ACCGGTAGGTATTTTAATGTAATAGGTAGTGCCTATTTTTTTACTGTTTACATTATTAACAACCT
66 ACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACTGTTTACATTATTAACAACCT
* *
69044 TCAAAAAAATCGGTAGATATTTTAACGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTAT
131 T-AAAAAAAACGGTAG-TATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTAT
* *
69109 TAACAATCTTAAAAAACCGGTAG
194 TAACAACCTTAAAAAACCGATAG
* * * * * * * *
69132 ATATTTTAAAGTAATAGCTAG-GCCTATTTTATTTAATCGTTTACATTATCAGCAATCTTTAAAC
1 ATATTTTAATGTAATAGGTAGCGCCTATTTT-TTT-ACCGTTTACATTATTAACAACCTTCAAAA
* * *
69196 AAACCGGTAGGTATTTTAATGTAATAGGTAGCACCTATTTTTTTTACCGTTTACATTATTAGCAA
64 AAACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTA-TTTTTTTACTGTTTACATTATTAACAA
* * * **
69261 CCTTAAAAAAAACTGGTATGTAGTTTAATATAATAAGTAAAGCCTATTTTTTTTACCGTTTACAT
128 CCTTAAAAAAAAC-GGTA-GTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACAT
69326 TATTA
191 TATTA
69331 GCCGTTTTTA
Statistics
Matches: 373, Mismatches: 32, Indels: 22
0.87 0.07 0.05
Matches are distributed among these distances:
216 5 0.01
217 33 0.09
218 3 0.01
219 66 0.18
220 236 0.63
221 30 0.08
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (216 bp):
ATATTTTAATGTAATAGGTAGCGCCTATTTTTTTACCGTTTACATTATTAACAACCTTCAAAAAA
ACCGGTAGGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTACTGTTTACATTATTAACAACCT
TAAAAAAAACGGTAGTATTTTAATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTA
ACAACCTTAAAAAACCGATAG
Found at i:69332 original size:74 final size:74
Alignment explanation
Indices: 68702--69330 Score: 842
Period size: 73 Copynumber: 8.6 Consensus size: 74
68692 TTATATTGTT
* * *
68702 ATGTAATAGGTAGCGCCTA-TTTTCTTAGCGTTTACATTATTAACAACCTTCAAAAAAACCGGTA
1 ATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAAACCGGTA
68766 GGTATTTTA
66 GGTATTTTA
* * ** *
68775 ATATAATAGGTAGCGCC-AATTTTTTTAGTGTTTACATTATTAACAACCTTAAAAAAAACCAGTA
1 ATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAAACCGGTA
68839 GGTATTTTA
66 GGTATTTTA
*
68848 ATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAAAACCGAT
1 ATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTT-AAAAAAAACCGGT
*
68913 ACGTATTTTA
65 AGGTATTTTA
* *
68923 ATGTAATAGGTAGCGCC--TTTTTTTTACCGTTTACATTATTAATAACCTTCAAAAAAACCGGTA
1 ATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAAACCGGTA
68986 GGTATTTTA
66 GGTATTTTA
* * * *
68995 ATGTAATAGGTAGTGCCTA-TTTTTTTACTGTTTACATTATTAACAACCTTCAAAAAAATCGGTA
1 ATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAAACCGGTA
*
69059 GATATTTTA
66 GGTATTTTA
* *
69068 ACGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAATCTT--AAAAAACCGGTA
1 ATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAAACCGGTA
*
69131 GATATTTTA
66 GGTATTTTA
* * * * * * * * *
69140 AAGTAATAGCTAG-GCCTATTTTATTTAATCGTTTACATTATCAGCAATCTTTAAACAAACCGGT
1 ATGTAATAGGTAGCGCCTATTTT-TTTTACCGTTTACATTATTAACAACCTTAAAAAAAACCGGT
69204 AGGTATTTTA
65 AGGTATTTTA
* * *
69214 ATGTAATAGGTAGCACCTATTTTTTTTACCGTTTACATTATTAGCAACCTTAAAAAAAACTGGTA
1 ATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAAACCGGTA
* *
69279 TGTAGTTTA
66 GGTATTTTA
* * **
69288 ATATAATAAGTAAAGCCTATTTTTTTTACCGTTTACATTATTA
1 ATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTA
69331 GCCGTTTTTA
Statistics
Matches: 495, Mismatches: 51, Indels: 19
0.88 0.09 0.03
Matches are distributed among these distances:
71 9 0.02
72 92 0.19
73 180 0.36
74 169 0.34
75 45 0.09
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (74 bp):
ATGTAATAGGTAGCGCCTATTTTTTTTACCGTTTACATTATTAACAACCTTAAAAAAAACCGGTA
GGTATTTTA
Found at i:71880 original size:2 final size:2
Alignment explanation
Indices: 71873--71952 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
71863 TGATCAACTC
71873 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
71915 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
71953 TGAGTAGGGT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73363 original size:46 final size:45
Alignment explanation
Indices: 73310--73443 Score: 196
Period size: 46 Copynumber: 2.9 Consensus size: 45
73300 ACCACTATGC
* * *
73310 ATTTTCATTTGTGGTATCCTTTCATGCAGATTAAGCACTGTTATAA
1 ATTTTCATTTATGGCATCCTTTCATGCA-ATTATGCACTGTTATAA
73356 ATTTTCATTTATGGCATCCTTTCATGCCAATTATGCACTGTTATAA
1 ATTTTCATTTATGGCATCCTTTCATG-CAATTATGCACTGTTATAA
* *
73402 ATTTTCTTTTATGGCATCCTTTCATACCAATTATGCACTGTT
1 ATTTTCATTTATGGCATCCTTTCAT-GCAATTATGCACTGTT
73444 CTTCATATAA
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
46 79 0.98
47 2 0.02
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.45
Consensus pattern (45 bp):
ATTTTCATTTATGGCATCCTTTCATGCAATTATGCACTGTTATAA
Found at i:73865 original size:112 final size:111
Alignment explanation
Indices: 73688--73897 Score: 269
Period size: 112 Copynumber: 1.9 Consensus size: 111
73678 TACAGTGATT
* * *
73688 CATAAACATATTATGAATTTCTTAATTTTGCACACACTGTGCCCATACGGAGATTCATAAACTTA
1 CATAAACATATTATGAATTTCTTAATTTTGCACACACAGTGCCCATACAGAAATTCATAAACTTA
** *
73753 TTATGAATTTCTTAG-TTCTGCACACACAGTGCCCATACGGAAATC
66 TTAAAAATTTCTTAGCTTCTGCACACAAAGTGCCCATACGGAAATC
* * * * * *
73798 CATAAACTTATTATGAATTTCTTATCTTTTTGCACATAGAGTGTCCATACAGAAATTTATAAACT
1 CATAAACATATTATGAATTTCTTA--ATTTTGCACACACAGTGCCCATACAGAAATTCATAAACT
*
73863 TATTAAAAATTTCTTAGCTTTTTGCACACAAAGTG
64 TATTAAAAATTTCTTAGC-TTCTGCACACAAAGTG
73898 TGTTGAAAAC
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
110 23 0.28
112 46 0.55
114 14 0.17
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (111 bp):
CATAAACATATTATGAATTTCTTAATTTTGCACACACAGTGCCCATACAGAAATTCATAAACTTA
TTAAAAATTTCTTAGCTTCTGCACACAAAGTGCCCATACGGAAATC
Found at i:73898 original size:57 final size:57
Alignment explanation
Indices: 73685--73897 Score: 263
Period size: 55 Copynumber: 3.8 Consensus size: 57
73675 CAATACAGTG
* * * *
73685 ATTCATAAACATATTATGAATTTCTTA--ATTTTGCACACACTGTGCCCATACGGAG
1 ATTCATAAACTTATTATGAATTTCTTAGCTTTTTGCACACACAGTGCCCATACGGAA
*
73740 ATTCATAAACTTATTATGAATTTCTTAG--TTCTGCACACACAGTGCCCATACGGAA
1 ATTCATAAACTTATTATGAATTTCTTAGCTTTTTGCACACACAGTGCCCATACGGAA
* * * * * *
73795 ATCCATAAACTTATTATGAATTTCTTATCTTTTTGCACATAGAGTGTCCATACAGAA
1 ATTCATAAACTTATTATGAATTTCTTAGCTTTTTGCACACACAGTGCCCATACGGAA
* ** *
73852 ATTTATAAACTTATTAAAAATTTCTTAGCTTTTTGCACACAAAGTG
1 ATTCATAAACTTATTATGAATTTCTTAGCTTTTTGCACACACAGTG
73898 TGTTGAAAAC
Statistics
Matches: 137, Mismatches: 18, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
55 76 0.55
57 61 0.45
ACGTcount: A:0.34, C:0.18, G:0.11, T:0.37
Consensus pattern (57 bp):
ATTCATAAACTTATTATGAATTTCTTAGCTTTTTGCACACACAGTGCCCATACGGAA
Found at i:74348 original size:64 final size:63
Alignment explanation
Indices: 74214--74351 Score: 149
Period size: 64 Copynumber: 2.2 Consensus size: 63
74204 GCTTTTGTGT
* *
74214 ACCGATGCACATACCATGCATCGATGCACTCCATATATATTAAAACATCGAATTGATTTTATGT
1 ACCGATGCACATACCATGCATCGATGCACTCCATATATATTAAAACATAGAA-TGATTTTATGC
* *
74278 ACCGATGCACA-AGCCATGCATCGATGCAC-CCAGTCT-TTTTCAAAACATAGAA-GCATATTTA
1 ACCGATGCACATA-CCATGCATCGATGCACTCCA-TATATATT-AAAACATAGAATG-AT-TTTA
74339 TGC
61 TGC
*
74342 ATCGATGCAC
1 ACCGATGCAC
74352 TATCAGTGTA
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
62 1 0.02
63 9 0.14
64 54 0.84
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (63 bp):
ACCGATGCACATACCATGCATCGATGCACTCCATATATATTAAAACATAGAATGATTTTATGC
Found at i:80205 original size:45 final size:44
Alignment explanation
Indices: 80142--80239 Score: 112
Period size: 45 Copynumber: 2.2 Consensus size: 44
80132 TTGTGCATAA
* * *
80142 TGCATCGATACACTATGAA-AGTGCATCGATGCA-TCCATTTTAATG
1 TGCATCGATACACTATGAAGA-TGCACCAATGCACTCC--TTGAATG
80187 TGCATCGATACAAC-ATGAAGATGCACCAATGCACTCCTTGAATG
1 TGCATCGATAC-ACTATGAAGATGCACCAATGCACTCCTTGAATG
80231 TGCATCGAT
1 TGCATCGAT
80240 GCACAGGGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 7
0.82 0.05 0.12
Matches are distributed among these distances:
44 15 0.32
45 26 0.55
46 6 0.13
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.28
Consensus pattern (44 bp):
TGCATCGATACACTATGAAGATGCACCAATGCACTCCTTGAATG
Found at i:83832 original size:57 final size:57
Alignment explanation
Indices: 83764--84104 Score: 580
Period size: 57 Copynumber: 6.0 Consensus size: 57
83754 TATTAACTCA
83764 ACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTT-TATAGCTTTTTGCAC
1 ACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCT-TAGCTTTTTGCAC
* * *
83821 ACAAAGTGCCCATATGGAAATTCATAAACTTATTATGAATTTCTTAGGTTTTTGCAC
1 ACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTTGCAC
83878 ACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTTGCAC
1 ACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTTGCAC
**
83935 ACAAAGTGGTCATACGGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTTGCAC
1 ACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTTGCAC
* *
83992 ACAAAGTGCCCATATGGAAATTCATAAACTCATTATGAATTTC-TATGCTTCTTGCAC
1 ACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTA-GCTTTTTGCAC
84049 ACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAG-TTTTTGCAC
1 ACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTTGCAC
84105 TCACAGTGTC
Statistics
Matches: 267, Mismatches: 14, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
56 10 0.04
57 254 0.95
58 3 0.01
ACGTcount: A:0.34, C:0.19, G:0.13, T:0.34
Consensus pattern (57 bp):
ACAAAGTGCCCATACGGAAATTCATAAACTCATTATGAATTTCTTAGCTTTTTGCAC
Found at i:84466 original size:20 final size:20
Alignment explanation
Indices: 84438--84485 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
84428 TCTCAATAGT
*
84438 ATCGGTACCCCTACCATGGC
1 ATCGATACCCCTACCATGGC
84458 ATCGATACCCCTACCATGGC
1 ATCGATACCCCTACCATGGC
84478 ATCGATAC
1 ATCGATAC
84486 TTCTATAATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.25, C:0.38, G:0.17, T:0.21
Consensus pattern (20 bp):
ATCGATACCCCTACCATGGC
Found at i:92745 original size:22 final size:22
Alignment explanation
Indices: 92719--92765 Score: 85
Period size: 22 Copynumber: 2.1 Consensus size: 22
92709 CAACACTATT
92719 AGATCAAACCAAAGATCTTTAA
1 AGATCAAACCAAAGATCTTTAA
*
92741 AGATCAGACCAAAGATCTTTAA
1 AGATCAAACCAAAGATCTTTAA
92763 AGA
1 AGA
92766 AAAGATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.49, C:0.17, G:0.13, T:0.21
Consensus pattern (22 bp):
AGATCAAACCAAAGATCTTTAA
Found at i:92776 original size:22 final size:22
Alignment explanation
Indices: 92729--92778 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
92719 AGATCAAACC
** *
92729 AAAGATCTTTAAAGATCAGACC
1 AAAGATCTTTAAAGAAAAGACA
*
92751 AAAGATCTTTAAAGAAAAGATA
1 AAAGATCTTTAAAGAAAAGACA
92773 AAAGAT
1 AAAGAT
92779 TGAAGAGATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.14, T:0.22
Consensus pattern (22 bp):
AAAGATCTTTAAAGAAAAGACA
Found at i:102165 original size:27 final size:26
Alignment explanation
Indices: 102117--102169 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 26
102107 TTTACTTTCA
* *
102117 TTTCCTTACCTTAAAACTTTTCCTTCT
1 TTTCATTACCTTAAAACCTTT-CTTCT
* *
102144 TTTCATTACCTTGAATCCTTTCTTCT
1 TTTCATTACCTTAAAACCTTTCTTCT
102170 ACCTTTCCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
26 5 0.23
27 17 0.77
ACGTcount: A:0.17, C:0.28, G:0.02, T:0.53
Consensus pattern (26 bp):
TTTCATTACCTTAAAACCTTTCTTCT
Found at i:111415 original size:2 final size:2
Alignment explanation
Indices: 111408--111432 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
111398 GCCTATTTTA
111408 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
111433 ACCATCCTCT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:122737 original size:21 final size:21
Alignment explanation
Indices: 122704--122758 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
122694 GATTTACATA
* *
122704 TTCGCATTACGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
*
122725 TTCGCGTTGCGATAGTCGAAG
1 TTCGCGTTGCGATAGTCCAAG
*
122746 TTCGAGTTGCGAT
1 TTCGCGTTGCGAT
122759 TTATTACAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.22, C:0.20, G:0.27, T:0.31
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:122797 original size:21 final size:21
Alignment explanation
Indices: 122751--122800 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
122741 CGAAGTTCGA
*
122751 GTTGCGATTTATTACAAATTC
1 GTTGTGATTTATTACAAATTC
*
122772 GTTGTGATTTATTCCAAATTC
1 GTTGTGATTTATTACAAATTC
122793 GTTGTGAT
1 GTTGTGAT
122801 AGTCCAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.24, C:0.12, G:0.18, T:0.46
Consensus pattern (21 bp):
GTTGTGATTTATTACAAATTC
Found at i:122808 original size:19 final size:20
Alignment explanation
Indices: 122765--122808 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
122755 CGATTTATTA
*
122765 CAAATTCGTTGTGATTTATTC
1 CAAATTCGTTGTGA-TTAGTC
122786 CAAATTCGTTGTGA-TAGTC
1 CAAATTCGTTGTGATTAGTC
122805 CAAA
1 CAAA
122809 ATCGCAACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 8 0.36
21 14 0.64
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.39
Consensus pattern (20 bp):
CAAATTCGTTGTGATTAGTC
Found at i:123724 original size:42 final size:42
Alignment explanation
Indices: 123662--123784 Score: 210
Period size: 42 Copynumber: 2.9 Consensus size: 42
123652 TGCGATTTTG
*
123662 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
* *
123704 GACTATCACAACGAACTTGGAATAAATCACAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
*
123746 GACTATTGCAACGAACTTGGAATAAATCGCAACGCGAAC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAAC
123785 ATGGAATAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 75 1.00
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:123796 original size:65 final size:65
Alignment explanation
Indices: 123715--123840 Score: 207
Period size: 65 Copynumber: 1.9 Consensus size: 65
123705 ACTATCACAA
* *
123715 CGAACTTGGAATAAATCACAACGCGAACTTCGACTATTGCAACGAACTTGGAATAAATCGCAACG
1 CGAACATGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACG
* * *
123780 CGAACATGGAATAAATCGCAACGCGAACTTGGACTATCGCAACGAATTTGGAATAAATCGC
1 CGAACATGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGC
123841 CTCGCAACAA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (65 bp):
CGAACATGGAATAAATCACAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACG
Found at i:123890 original size:21 final size:21
Alignment explanation
Indices: 123861--123913 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
123851 ATTTGGAAAA
*
123861 TCGCATTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCGAAGT
* *
123882 TCGCGTTGCGATAGTTGATGT
1 TCGCGTTGCGATAGTCGAAGT
123903 TCGCGTTGCGA
1 TCGCGTTGCGA
123914 ATCTGGAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.17, C:0.19, G:0.32, T:0.32
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCGAAGT
Found at i:124613 original size:40 final size:40
Alignment explanation
Indices: 124563--124839 Score: 174
Period size: 40 Copynumber: 6.9 Consensus size: 40
124553 ATATTATACA
124563 AGATACACACCTAAATAC-GAAAGTGGTGATGTATTGCAAG
1 AGATACACACCTAAATACAGAAA-TGGTGATGTATTGCAAG
* * * * * *
124603 GGATATACACCCAATTACAAGAAAT-GCGATGTATTGCACG
1 AGATACACACCTAAATAC-AGAAATGGTGATGTATTGCAAG
* * *
124643 AGCTACACACCTAAATAC-GAGAGTGGTGATGTTTTGCATA-
1 AGATACACACCTAAATACAGA-AATGGTGATGTATTGCA-AG
* * *
124683 AGATACATACCTAATTACAAGAAA-GGTGATGTATTGTACA-
1 AGATACACACCTAAATAC-AGAAATGGTGATGTATTGCA-AG
* * * *
124723 AGATACACACCCAATTACAAGAAA-GGTAATGTATTGCATG
1 AGATACACACCTAAATAC-AGAAATGGTGATGTATTGCAAG
* * * ** *
124763 GGATACACACCTAAATA-TGAGAGTGGTGATGTATTATACG
1 AGATACACACCTAAATACAGA-AATGGTGATGTATTGCAAG
* * * * *
124803 GGATACACACCCAAAAACAAGGAATGATGATGTATTG
1 AGATACACACCTAAATAC-AGAAATGGTGATGTATTG
124840 TACAAGGTGC
Statistics
Matches: 182, Mismatches: 43, Indels: 23
0.73 0.17 0.09
Matches are distributed among these distances:
38 4 0.02
39 3 0.02
40 154 0.85
41 14 0.08
42 7 0.04
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (40 bp):
AGATACACACCTAAATACAGAAATGGTGATGTATTGCAAG
Found at i:124668 original size:80 final size:80
Alignment explanation
Indices: 124533--124773 Score: 277
Period size: 80 Copynumber: 3.0 Consensus size: 80
124523 TGTACTGATA
* * * *
124533 CCAATTACAAGTAATGTGATATATTATACAAGATACACACCTAAATACGAAAGTGGTGATGTATT
1 CCAATTACAAGAAATGTGATGTATTGTACAAGATACACACCTAAATACGAGAGTGGTGATGTATT
*
124598 GCAAGGGATATACAC
66 GCAAGGGATACACAC
* * * * *
124613 CCAATTACAAGAAATGCGATGTATTGCACGAGCTACACACCTAAATACGAGAGTGGTGATGTTTT
1 CCAATTACAAGAAATGTGATGTATTGTACAAGATACACACCTAAATACGAGAGTGGTGATGTATT
* *
124678 GCATA-AGATACATAC
66 GCA-AGGGATACACAC
* * * * * ** *
124693 CTAATTACAAGAAAGGTGATGTATTGTACAAGATACACACCCAATTACAAGAAAGGTAATGTATT
1 CCAATTACAAGAAATGTGATGTATTGTACAAGATACACACCTAAATACGAGAGTGGTGATGTATT
*
124758 GCATGGGATACACAC
66 GCAAGGGATACACAC
124773 C
1 C
124774 TAAATATGAG
Statistics
Matches: 131, Mismatches: 28, Indels: 4
0.80 0.17 0.02
Matches are distributed among these distances:
80 130 0.99
81 1 0.01
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.25
Consensus pattern (80 bp):
CCAATTACAAGAAATGTGATGTATTGTACAAGATACACACCTAAATACGAGAGTGGTGATGTATT
GCAAGGGATACACAC
Found at i:124775 original size:80 final size:79
Alignment explanation
Indices: 124535--124817 Score: 253
Period size: 80 Copynumber: 3.5 Consensus size: 79
124525 TACTGATACC
* * * *
124535 AATTACAAGTAATGTGATATATTATACAAGATACACACCTAAATAC-GAAAGTGGTGATGTATTG
1 AATTACAAGAAAGGTGATGTATTATACAAGATACACACCCAAATACAGAAA--GGTGATGTATTG
* * *
124599 CAAGGGATATACACCC
64 CATGGGATACACACCT
* * ** * * * ** *
124615 AATTACAAGAAATGCGATGTATTGCACGAGCTACACACCTAAATACGAGAGTGGTGATGTTTTGC
1 AATTACAAGAAAGGTGATGTATTATACAAGATACACACCCAAATAC-AGAAAGGTGATGTATTGC
** *
124680 ATAAGATACATACCT
65 ATGGGATACACACCT
* * *
124695 AATTACAAGAAAGGTGATGTATTGTACAAGATACACACCCAATTACAAGAAAGGTAATGTATTGC
1 AATTACAAGAAAGGTGATGTATTATACAAGATACACACCCAAATAC-AGAAAGGTGATGTATTGC
124760 ATGGGATACACACCT
65 ATGGGATACACACCT
* ** ** **
124775 AAATATGAGAGTGGTGATGTATTATACGGGATACACACCCAAA
1 AATTACAAGAAAGGTGATGTATTATACAAGATACACACCCAAA
124818 AACAAGGAAT
Statistics
Matches: 161, Mismatches: 40, Indels: 4
0.79 0.20 0.02
Matches are distributed among these distances:
80 159 0.99
82 2 0.01
ACGTcount: A:0.40, C:0.16, G:0.19, T:0.25
Consensus pattern (79 bp):
AATTACAAGAAAGGTGATGTATTATACAAGATACACACCCAAATACAGAAAGGTGATGTATTGCA
TGGGATACACACCT
Found at i:124808 original size:120 final size:119
Alignment explanation
Indices: 124548--124854 Score: 327
Period size: 120 Copynumber: 2.5 Consensus size: 119
124538 TACAAGTAAT
* *
124548 GTGATATATTATACAAGATACACACCTAAATAC--GAAAGTGGTGATGTATTG--CAAGGGATAT
1 GTGATGTATTATAC-AGATACACACCTAAATACAAGAAA--GGTGATGTATTGTACAA--GATAC
* * *
124609 ACACCCAATTACAAGAAATGCGATGTATTGCACGAGCTACACACCTAAATACGAGAGTG
61 ACACCCAATTACAAGAAAGGCAATGTATTGCACGAGATACACACCTAAATACGAGAGTG
* * *
124668 GTGATGTTTTGCATA-AGATACATACCTAATTACAAGAAAGGTGATGTATTGTACAAGATACACA
1 GTGATGTATT--ATACAGATACACACCTAAATACAAGAAAGGTGATGTATTGTACAAGATACACA
* * * *
124732 CCCAATTACAAGAAAGGTAATGTATTGCATGGGATACACACCTAAATATGAGAGTG
64 CCCAATTACAAGAAAGGCAATGTATTGCACGAGATACACACCTAAATACGAGAGTG
* * * * * * *
124788 GTGATGTATTATACGGGATACACACCCAAAAACAAGGAATGATGATGTATTGTACAAGGTGCACA
1 GTGATGTATTATAC-AGATACACACCTAAATACAA-GAAAGGTGATGTATTGTACAAGATACACA
124853 CC
64 CC
124855 TAACTATAAG
Statistics
Matches: 156, Mismatches: 22, Indels: 17
0.80 0.11 0.09
Matches are distributed among these distances:
118 3 0.02
120 116 0.74
121 27 0.17
122 10 0.06
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.24
Consensus pattern (119 bp):
GTGATGTATTATACAGATACACACCTAAATACAAGAAAGGTGATGTATTGTACAAGATACACACC
CAATTACAAGAAAGGCAATGTATTGCACGAGATACACACCTAAATACGAGAGTG
Found at i:129628 original size:20 final size:19
Alignment explanation
Indices: 129585--129628 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
129575 TTTATGTTTT
* *
129585 AAATTTATGTTAGAGTGTT
1 AAATTTATGTTAGAATGTG
*
129604 CAATTTGATGTTAGAATGTG
1 AAATTT-ATGTTAGAATGTG
129624 AAATT
1 AAATT
129629 GGGTTATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
19 5 0.25
20 15 0.75
ACGTcount: A:0.34, C:0.02, G:0.20, T:0.43
Consensus pattern (19 bp):
AAATTTATGTTAGAATGTG
Found at i:136255 original size:21 final size:21
Alignment explanation
Indices: 136229--136268 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
136219 CCCCCTTTGA
*
136229 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
136250 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
136269 GGGGTTCTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:140202 original size:21 final size:21
Alignment explanation
Indices: 140170--140238 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
140160 GGTGTCATAA
*
140170 AACCCT-ACGGGCTGGGCATGT
1 AACCCTGA-GGGCTGGGAATGT
* * *
140191 AACCTTGTGGGCTGGGTATGT
1 AACCCTGAGGGCTGGGAATGT
* *
140212 ACCCCTGAGGGCTAGGAATGT
1 AACCCTGAGGGCTGGGAATGT
140233 AACCCT
1 AACCCT
140239 ACGGAGATGA
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.20, C:0.25, G:0.32, T:0.23
Consensus pattern (21 bp):
AACCCTGAGGGCTGGGAATGT
Found at i:140898 original size:17 final size:17
Alignment explanation
Indices: 140876--140911 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
140866 AGACTGAAAC
140876 ATAAATAT-ATAATTCTA
1 ATAAATATAAT-ATTCTA
140893 ATAAATATAATATTCTA
1 ATAAATATAATATTCTA
140910 AT
1 AT
140912 TATATCAAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 16 0.89
18 2 0.11
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (17 bp):
ATAAATATAATATTCTA
Found at i:141889 original size:28 final size:25
Alignment explanation
Indices: 141842--141905 Score: 69
Period size: 26 Copynumber: 2.5 Consensus size: 25
141832 TCATTTTCCT
*
141842 AATTAATAAAAATTCCAAAAATTTAA
1 AATTAATATAAATTCCAAAAATTT-A
141868 AATTAATATAAATT-CATGAAAACTTTA
1 AATTAATATAAATTCCA--AAAA-TTTA
141895 AATTAA-ATAAA
1 AATTAATATAAA
141906 ATATTAAACA
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
25 2 0.06
26 18 0.53
27 11 0.32
28 3 0.09
ACGTcount: A:0.59, C:0.06, G:0.02, T:0.33
Consensus pattern (25 bp):
AATTAATATAAATTCCAAAAATTTA
Found at i:142083 original size:25 final size:24
Alignment explanation
Indices: 142039--142085 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 24
142029 TAATTAGCAC
142039 AAATAATAATTAATTAATAAATTT
1 AAATAATAATTAATTAATAAATTT
142063 AAATAAATAA-TAATTATATAAAT
1 AAAT-AATAATTAATTA-ATAAAT
142086 ATTATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATAATAATTAATTAATAAATTT
Found at i:143813 original size:2 final size:2
Alignment explanation
Indices: 143778--143802 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
143768 CTCTTGCACT
143778 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
143803 TACACTATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:144219 original size:15 final size:16
Alignment explanation
Indices: 144182--144219 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
144172 TGTTTAATTT
*
144182 TAAAATAAATAAAGTCT
1 TAAAA-AAATAAAGTCA
144199 TAAAAAAATAAA-TCA
1 TAAAAAAATAAAGTCA
144214 TAAAAA
1 TAAAAA
144220 CTAAGAGATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 7 0.35
17 5 0.25
ACGTcount: A:0.68, C:0.05, G:0.03, T:0.24
Consensus pattern (16 bp):
TAAAAAAATAAAGTCA
Found at i:144623 original size:45 final size:42
Alignment explanation
Indices: 144567--144681 Score: 117
Period size: 45 Copynumber: 2.7 Consensus size: 42
144557 CACACGCACA
*
144567 CACACACATTAGGGTAAATTACGCGTTTAGTACACACACTCAATG
1 CACACATATTAGGGTAAATTACGCGTTTAGT--ACACACTC-ATG
* * * * *
144612 CACACATATTAGGATAAATTACACGTTTACTGCACATTCATG
1 CACACATATTAGGGTAAATTACGCGTTTAGTACACACTCATG
* *
144654 --CACATATTAGGGTAAATTATGAGTTTAG
1 CACACATATTAGGGTAAATTACGCGTTTAG
144682 AACTTAACTA
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
40 23 0.39
42 3 0.05
43 6 0.10
45 27 0.46
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.30
Consensus pattern (42 bp):
CACACATATTAGGGTAAATTACGCGTTTAGTACACACTCATG
Found at i:150160 original size:19 final size:19
Alignment explanation
Indices: 150130--150182 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
150120 TTAGCATTTT
*
150130 AAAAGAAAAGTAAAA-TAA
1 AAAATAAAAGTAAAAGTAA
* *
150148 AAAATTGAAAGTAAAAGTTA
1 AAAA-TAAAAGTAAAAGTAA
150168 AAAATAAAAGTAAAA
1 AAAATAAAAGTAAAA
150183 CTTTTATAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 4 0.14
19 19 0.66
20 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.11, T:0.17
Consensus pattern (19 bp):
AAAATAAAAGTAAAAGTAA
Found at i:150325 original size:22 final size:24
Alignment explanation
Indices: 150297--150351 Score: 96
Period size: 22 Copynumber: 2.4 Consensus size: 24
150287 AAATCCTAAG
150297 AGATAATTCCTAATAAA-TG-AAA
1 AGATAATTCCTAATAAATTGCAAA
150319 AGATAATTCCTAATAAATTGCAAA
1 AGATAATTCCTAATAAATTGCAAA
150343 AGATAATTC
1 AGATAATTC
150352 TCTTAATTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 17 0.55
23 2 0.06
24 12 0.39
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (24 bp):
AGATAATTCCTAATAAATTGCAAA
Found at i:150611 original size:22 final size:22
Alignment explanation
Indices: 150583--150627 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
150573 CGTAGAAAAT
*
150583 AACAGAAAACACTCAACTTAGC
1 AACAGAAAACACCCAACTTAGC
150605 AACAGAAAACACCCAACTTAGC
1 AACAGAAAACACCCAACTTAGC
150627 A
1 A
150628 GCATAAACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.51, C:0.29, G:0.09, T:0.11
Consensus pattern (22 bp):
AACAGAAAACACCCAACTTAGC
Found at i:150699 original size:41 final size:42
Alignment explanation
Indices: 150650--150736 Score: 126
Period size: 41 Copynumber: 2.1 Consensus size: 42
150640 AGTTGATCCT
*
150650 AGTT-TAAGTTTGCCTCTGGTGGAGTGGAAAT-TGTTGAGTG-
1 AGTTCTAAGTTTGCCTCTGGTGGAGTGG-AATCTATTGAGTGA
*
150690 AGTTCTAAGTTTGCCTTTGGTGGAGTGGAATCTATTGAGTGA
1 AGTTCTAAGTTTGCCTCTGGTGGAGTGGAATCTATTGAGTGA
150732 AGTTC
1 AGTTC
150737 ATTTGAGTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 7 0.17
41 30 0.71
42 5 0.12
ACGTcount: A:0.21, C:0.09, G:0.32, T:0.38
Consensus pattern (42 bp):
AGTTCTAAGTTTGCCTCTGGTGGAGTGGAATCTATTGAGTGA
Found at i:152057 original size:78 final size:78
Alignment explanation
Indices: 151928--152081 Score: 272
Period size: 78 Copynumber: 2.0 Consensus size: 78
151918 ATTAGTATTT
* *
151928 ATTTCATAATGCTTGCATGTGAACCAAGCACAGGCACCTTCAGCTGGTCATATAAACGGAAATAC
1 ATTTCATAAGGCTTGCATGTGAACCAAGCACAGGCACCTTCAGCTGGTCATATAAACCGAAATAC
*
151993 GCTGGAGGGAGAG
66 ACTGGAGGGAGAG
*
152006 ATTTCATAAGGCTTGCATGTGAACCATGCACAGGCACCTTCAGCTGGTCATATAAACCGAAATAC
1 ATTTCATAAGGCTTGCATGTGAACCAAGCACAGGCACCTTCAGCTGGTCATATAAACCGAAATAC
152071 ACTGGAGGGAG
66 ACTGGAGGGAG
152082 GGAGAGAGAG
Statistics
Matches: 72, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (78 bp):
ATTTCATAAGGCTTGCATGTGAACCAAGCACAGGCACCTTCAGCTGGTCATATAAACCGAAATAC
ACTGGAGGGAGAG
Found at i:155938 original size:15 final size:15
Alignment explanation
Indices: 155918--155947 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
155908 CCCACCAACC
155918 CCTCTTTCCATAATG
1 CCTCTTTCCATAATG
155933 CCTCTTTCCATAATG
1 CCTCTTTCCATAATG
155948 ATGAAGGTAT
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:0.20, C:0.33, G:0.07, T:0.40
Consensus pattern (15 bp):
CCTCTTTCCATAATG
Found at i:156999 original size:27 final size:28
Alignment explanation
Indices: 156963--157018 Score: 80
Period size: 27 Copynumber: 2.0 Consensus size: 28
156953 TTAAATTTAT
*
156963 TAATAATTTATTATTATTATT-ATAATTA
1 TAATAATTTATTAATA-TATTAATAATTA
156991 TAAT-ATTTATTAATATATTAATAATTA
1 TAATAATTTATTAATATATTAATAATTA
157018 T
1 T
157019 TGCTTAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 18 0.69
28 4 0.15
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (28 bp):
TAATAATTTATTAATATATTAATAATTA
Found at i:157012 original size:18 final size:18
Alignment explanation
Indices: 156953--157019 Score: 50
Period size: 21 Copynumber: 3.7 Consensus size: 18
156943 CATTTTAAAT
156953 TTAA-ATTTATTAATA-A
1 TTAATATTTATTAATATA
* *
156969 TTTAT-TATTATTATTATAA
1 TTAATAT-TTATTAATAT-A
156988 TTATAATATTTATTAATATA
1 -T-TAATATTTATTAATATA
*
157008 TTAATAATTATT
1 TTAATATTTATT
157020 GCTTAAATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
16 4 0.10
17 8 0.21
18 10 0.26
19 2 0.05
20 2 0.05
21 12 0.31
22 1 0.03
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTAATATTTATTAATATA
Found at i:158583 original size:129 final size:127
Alignment explanation
Indices: 158446--158707 Score: 404
Period size: 130 Copynumber: 2.1 Consensus size: 127
158436 ATTTATTTTT
* *
158446 TTATTTTTTTATATAAATGTTTT-AATATTTATTTATTTTTT-ATATCGAAGAAAAGAGCTGTCT
1 TTATTTTTTAAGA-AAATGTTTTGAATATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCT
*
158509 TAAGGCACCTAGAAGCCCTTTTCTGATATTTTTAAATAAATAAATATCTTATTATATTAAAATAA
65 TAAGGCACCTAGAAGCCCTTTTCTGATATTTCTAAATAAATAAATATCTTATTA-A-T-AAATAA
158574 A
127 A
**
158575 TTATTTTTTAAGAAAATGTTTTGGTTATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTT
1 TTATTTTTTAAGAAAATGTTTTGAATATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTT
* *
158640 AAGGCACCTAGAAGTCCTTTTCTGATATTTCTAAATAAATAAATATTTTATTAATAAATAAA
66 AAGGCACCTAGAAGCCCTTTTCTGATATTTCTAAATAAATAAATATCTTATTAATAAATAAA
158702 -TATTTT
1 TTATTTT
158708 AATAAATTTT
Statistics
Matches: 124, Mismatches: 7, Indels: 7
0.90 0.05 0.05
Matches are distributed among these distances:
126 6 0.05
127 7 0.06
128 10 0.08
129 28 0.23
130 73 0.59
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.46
Consensus pattern (127 bp):
TTATTTTTTAAGAAAATGTTTTGAATATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTT
AAGGCACCTAGAAGCCCTTTTCTGATATTTCTAAATAAATAAATATCTTATTAATAAATAAA
Found at i:158711 original size:16 final size:18
Alignment explanation
Indices: 158673--158714 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
158663 GATATTTCTA
158673 AATAAATAAATATTTTATT
1 AATAAATAAATA-TTTATT
158692 AATAAATAAATA-TT-TT
1 AATAAATAAATATTTATT
158708 AATAAAT
1 AATAAAT
158715 TTTCTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.39
17 2 0.09
19 12 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAATAAATATTTATT
Found at i:161332 original size:7 final size:7
Alignment explanation
Indices: 161297--161338 Score: 59
Period size: 7 Copynumber: 6.0 Consensus size: 7
161287 TTTTCATATA
161297 TGCATTT
1 TGCATTT
161304 T-CATTT
1 TGCATTT
161310 TGCATCTT
1 TGCAT-TT
161318 TGCATTT
1 TGCATTT
*
161325 TTCATTT
1 TGCATTT
161332 TGCATTT
1 TGCATTT
161339 ATACTTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.19
7 18 0.58
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.10, T:0.60
Consensus pattern (7 bp):
TGCATTT
Found at i:164202 original size:1 final size:1
Alignment explanation
Indices: 164196--164278 Score: 58
Period size: 1 Copynumber: 83.0 Consensus size: 1
164186 ATTATACTTG
* * * * * * * * *
164196 AAAAAAACAAAAAGAAAAAAGAAAGAAAAAAGAAAAAAAGAAAAGAAAAAAAGAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
164261 GAAAAAGAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAA
164279 GGGAGAAATT
Statistics
Matches: 58, Mismatches: 24, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 58 1.00
ACGTcount: A:0.86, C:0.01, G:0.13, T:0.00
Consensus pattern (1 bp):
A
Found at i:164215 original size:13 final size:13
Alignment explanation
Indices: 164204--164279 Score: 95
Period size: 13 Copynumber: 5.8 Consensus size: 13
164194 TGAAAAAAAC
164204 AAAAAGAAAA-AA
1 AAAAAGAAAAGAA
164216 GAAAGAA-AAAAGAA
1 -AAA-AAGAAAAGAA
164230 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
164243 AAAAAGAAAAGAA
1 AAAAAGAAAAGAA
164256 AAAAAGAAAAAGAA
1 AAAAAG-AAAAGAA
*
164270 AGAAA-AAAAG
1 AAAAAGAAAAG
164280 GGAGAAATTG
Statistics
Matches: 58, Mismatches: 1, Indels: 9
0.85 0.01 0.13
Matches are distributed among these distances:
12 7 0.12
13 36 0.62
14 15 0.26
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAGAA
Found at i:164233 original size:26 final size:26
Alignment explanation
Indices: 164195--164277 Score: 111
Period size: 26 Copynumber: 3.3 Consensus size: 26
164185 TATTATACTT
*
164195 GAAAAAA-ACAAAAAGAAAAAAGAAA
1 GAAAAAAGAAAAAAAGAAAAAAGAAA
164220 GAAAAAAGAAAAAAAGAAAAGAA-AAA
1 GAAAAAAGAAAAAAAGAAAA-AAGAAA
164246 -AAGAAAAGAAAAAAAG-AAAAAGAAA
1 GAA-AAAAGAAAAAAAGAAAAAAGAAA
164271 GAAAAAA
1 GAAAAAA
164278 AGGGAGAAAT
Statistics
Matches: 52, Mismatches: 1, Indels: 10
0.83 0.02 0.16
Matches are distributed among these distances:
24 2 0.04
25 19 0.37
26 29 0.56
27 2 0.04
ACGTcount: A:0.84, C:0.01, G:0.14, T:0.00
Consensus pattern (26 bp):
GAAAAAAGAAAAAAAGAAAAAAGAAA
Found at i:164278 original size:26 final size:26
Alignment explanation
Indices: 164195--164279 Score: 113
Period size: 24 Copynumber: 3.3 Consensus size: 26
164185 TATTATACTT
* *
164195 GAAAAAAACAAAAAGA-AAAAAGAAA
1 GAAAAAAAGAAAAAAAGAAAAAGAAA
164220 G-AAAAAAGAAAAAAAG-AAAAGAAA
1 GAAAAAAAGAAAAAAAGAAAAAGAAA
*
164244 AAAAGAAAAGAAAAAAAGAAAAAGAAA
1 GAAA-AAAAGAAAAAAAGAAAAAGAAA
164271 GAAAAAAAG
1 GAAAAAAAG
164280 GGAGAAATTG
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
24 20 0.38
25 3 0.06
26 18 0.35
27 11 0.21
ACGTcount: A:0.84, C:0.01, G:0.15, T:0.00
Consensus pattern (26 bp):
GAAAAAAAGAAAAAAAGAAAAAGAAA
Found at i:164279 original size:18 final size:18
Alignment explanation
Indices: 164204--164279 Score: 97
Period size: 18 Copynumber: 4.3 Consensus size: 18
164194 TGAAAAAAAC
164204 AAAAAGAAAAAAGAAAG-A
1 AAAAAG-AAAAAGAAAGAA
164222 AAAAAG-AAAA-AAAGAA
1 AAAAAGAAAAAGAAAGAA
*
164238 AAGAA-AAAAAGAAAAGAA
1 AAAAAGAAAAAG-AAAGAA
164256 AAAAAGAAAAAGAAAGAA
1 AAAAAGAAAAAGAAAGAA
164274 AAAAAG
1 AAAAAG
164280 GGAGAAATTG
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
15 4 0.08
16 13 0.25
18 28 0.55
19 6 0.12
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (18 bp):
AAAAAGAAAAAGAAAGAA
Found at i:166637 original size:114 final size:114
Alignment explanation
Indices: 166436--166661 Score: 389
Period size: 114 Copynumber: 2.0 Consensus size: 114
166426 GTGCCATGTT
*
166436 CTCGTAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCGTAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTGATCTG
* *
166501 ATTTGGTATGAACCCCAAAACCAATCATTGGATTTGAAAGATGAATTTG
66 ATTTGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTG
* *
166550 CTCGTAGTAGAAATAAGGAGCCCCAATAGCATCTTCTGGAAGTATTCTTTGAGTTATCTGATCTG
1 CTCGTAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTGATCTG
* *
166615 GTTTGGTAGGAACCCCAGAACCAATCATTGGAATTGAAAGATGAATT
66 ATTTGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATT
166662 GCATGATCGT
Statistics
Matches: 105, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
114 105 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (114 bp):
CTCGTAGTAGAAATAAGGAGACCCAATAGCATCTTCTAGAAGTATTCTTTGAGTTATCTGATCTG
ATTTGGTAGGAACCCCAAAACCAATCATTGGAATTGAAAGATGAATTTG
Found at i:167750 original size:74 final size:75
Alignment explanation
Indices: 167611--167789 Score: 193
Period size: 75 Copynumber: 2.4 Consensus size: 75
167601 ATTAACAAGA
* * * *
167611 AGCAAAT-ATTGGGGCATGCTGAAAACCCTTTTTCAATCAGAATCAAAAATGTTGAAATATTCTG
1 AGCAAATGA-TGGGGCATGCTGAAAGCCC-ATTTCAATCAGAATCAAAAATGTTGAAACATCCTG
*
167675 AATA-TT-TATC
64 AACACTTGTATC
* * **
167685 AGCAAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGAATTGTTGATGCATCCTGA
1 AGC-AAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAAAATGTTGAAACATCCTGA
*
167750 ACACTTGTATT
65 ACACTTGTATC
* * *
167761 AGCCAATGTTGGGGCATGCTGAAGGCCCA
1 AGCAAATGATGGGGCATGCTGAAAGCCCA
167790 CAACATCCTG
Statistics
Matches: 88, Mismatches: 13, Indels: 7
0.81 0.12 0.06
Matches are distributed among these distances:
74 34 0.39
75 47 0.53
76 7 0.08
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.28
Consensus pattern (75 bp):
AGCAAATGATGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAAAATGTTGAAACATCCTGAA
CACTTGTATC
Found at i:169046 original size:22 final size:22
Alignment explanation
Indices: 169017--169071 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
169007 ATCTACACTC
169017 TTCAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
*
169039 TTTAAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
169061 TTCAAAGATGA
1 TTCAAAGATGA
169072 AAGCTTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:169892 original size:166 final size:167
Alignment explanation
Indices: 169586--169911 Score: 514
Period size: 167 Copynumber: 2.0 Consensus size: 167
169576 AAAATGAGCA
169586 TTATCTTGAGATTGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAAAATGAGAAAACGA
1 TTATCTTGAGATTGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAAAATGAGAAAACGA
* ** * *
169651 TTTTCATAGTTTCTCATTTTATCTTTTCTAAAATGAAATTGTTGAAAAGTAAGAAAACGATTTTC
66 TTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAAAAAACGATTTCC
* *
169716 TT-AGTTTTTTTACTTAGTAAACTATTTCCAACAGCC
131 TTAATTTTTTTTACTTAATAAACTATTTCCAACAGCC
** *
169752 TTATCTTGAGATTGGGGCATGTTACCCAATCAACATGTTATTT-TGAAAA-ATAATGAGAAAACG
1 TTATCTTGAGATT-GGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAAAATGAGAAAACG
*
169815 ATTTCCATAGTTTCTCATTCAATCTTTTCTAAAAATGAAATTGTTGAAAAGTAAAAAAATGATTT
65 ATTTCCATAGTTTCTCATTCAATCTTTTCT-AAAATGAAATTGTTGAAAAGTAAAAAAACGATTT
169880 CCTTAATTTTTTTTACTTAATAAACTATTTCC
129 CCTTAATTTTTTTTACTTAATAAACTATTTCC
169912 CACATCTGTA
Statistics
Matches: 146, Mismatches: 11, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
165 40 0.27
166 52 0.36
167 54 0.37
ACGTcount: A:0.36, C:0.14, G:0.12, T:0.39
Consensus pattern (167 bp):
TTATCTTGAGATTGGGCATGTTACCCAATCAACATGTTATTTCAAAAAACAAAATGAGAAAACGA
TTTCCATAGTTTCTCATTCAATCTTTTCTAAAATGAAATTGTTGAAAAGTAAAAAAACGATTTCC
TTAATTTTTTTTACTTAATAAACTATTTCCAACAGCC
Found at i:169996 original size:76 final size:76
Alignment explanation
Indices: 169914--170404 Score: 849
Period size: 76 Copynumber: 6.5 Consensus size: 76
169904 CTATTTCCCA
* *
169914 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
169979 AGCCTTAGGGT
66 AGCCTTAGGGT
169990 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
170055 ATCCTTAGGGT
66 AGCCTTAGGGT
170066 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
170131 AGCCTTAGGGT
66 AGCCTTAGGGT
*
170142 CATCTGTAAGTCCTGTAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
170207 AGCCATAGGGT
66 AGCCTTAGGGT
* *
170218 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGATATTTT-AA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
170282 AGCCTTAGGGT
66 AGCCTTAGGGT
*
170293 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC-A
* *
170358 AAACCTTCGGGT
65 AAGCCTTAGGGT
* * *
170370 CATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAA
1 CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAA
170405 CATTTTCATC
Statistics
Matches: 395, Mismatches: 18, Indels: 3
0.95 0.04 0.01
Matches are distributed among these distances:
75 71 0.18
76 281 0.71
77 43 0.11
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTGCAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:170546 original size:3 final size:3
Alignment explanation
Indices: 170538--170598 Score: 79
Period size: 3 Copynumber: 20.0 Consensus size: 3
170528 AAATTTAAAT
*
170538 TTA TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA -TA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
*
170583 TTA TTTA TTA ATA TTA
1 TTA -TTA TTA TTA TTA
170599 CAAAACCTAT
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
2 2 0.04
3 43 0.84
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:172201 original size:128 final size:125
Alignment explanation
Indices: 172034--172268 Score: 364
Period size: 128 Copynumber: 1.9 Consensus size: 125
172024 AACATTTTAA
* *
172034 TATTTATGTATTTTTTATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAACCCTTTTCTGAT
1 TATTTATGTATTTTTTATATCGAAGAAAAGAGCTGTCTTAAAGCACCTAGAAACACTTTTCTGAT
*
172099 ATTTTTAAATAAATAAATATCTTATTATATTAAAATAAA-ATTTTTTAAGAAAATGTTTTGAT
66 ATTTCTAAATAAATAAATATCTTATTA-A-T-AAATAAATATTTTTTAAGAAAATGTTTTGAT
* **
172161 TATTTATTTATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAAGCACCTAGAAGTACTTTTCTGA
1 TATTTATGTATTTTTT-ATATCGAAGAAAAGAGCTGTCTTAAAGCACCTAGAAACACTTTTCTGA
*
172226 TATTTCTAAATAAATAAATATTTTATTAATAAATAAATATTTT
65 TATTTCTAAATAAATAAATATCTTATTAATAAATAAATATTTT
172269 AATAAATTTT
Statistics
Matches: 99, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
125 7 0.07
126 6 0.06
127 16 0.16
128 70 0.71
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (125 bp):
TATTTATGTATTTTTTATATCGAAGAAAAGAGCTGTCTTAAAGCACCTAGAAACACTTTTCTGAT
ATTTCTAAATAAATAAATATCTTATTAATAAATAAATATTTTTTAAGAAAATGTTTTGAT
Found at i:172272 original size:16 final size:18
Alignment explanation
Indices: 172234--172275 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 18
172224 GATATTTCTA
172234 AATAAATAAATATTTTATT
1 AATAAATAAATA-TTTATT
172253 AATAAATAAATA-TT-TT
1 AATAAATAAATATTTATT
172269 AATAAAT
1 AATAAAT
172276 TTTCTTTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 9 0.39
17 2 0.09
19 12 0.52
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (18 bp):
AATAAATAAATATTTATT
Found at i:178432 original size:66 final size:66
Alignment explanation
Indices: 178352--178546 Score: 228
Period size: 66 Copynumber: 2.9 Consensus size: 66
178342 AATTGATAAT
* ** * *
178352 CTTTGAGATTGTTTCTCTTGAAACAAATTTTGTCCCGTTTAAGACAGTTTTTCTTGAAATATAAA
1 CTTTGAGATTGTTTCTCTTGAAACAAATTTTATCCCACTTAAGACAATTTTTCTTGAAACATAAA
178417 C
66 C
* *
178418 CTTTGAGATTGTTTCTCTTGAAACAAATTTTATCTCACTTGAGACAATTTTTCTTGAAACATAAA
1 CTTTGAGATTGTTTCTCTTGAAACAAATTTTATCCCACTTAAGACAATTTTTCTTGAAACATAAA
178483 C
66 C
* * * ** ** * *
178484 CATTGAGATTGTTTATCTCGAAACAAAGTTTCGTTTCGCTTAAGACAATTTTCCCTTGAAACA
1 CTTTGAGATTGTTTCTCTTGAAACAAA-TTTTATCCCACTTAAGACAATTTT-TCTTGAAACA
178547 CAAATTTTGA
Statistics
Matches: 111, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
66 83 0.75
67 19 0.17
68 9 0.08
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (66 bp):
CTTTGAGATTGTTTCTCTTGAAACAAATTTTATCCCACTTAAGACAATTTTTCTTGAAACATAAA
C
Found at i:178952 original size:139 final size:138
Alignment explanation
Indices: 178701--179606 Score: 858
Period size: 139 Copynumber: 6.5 Consensus size: 138
178691 AATTGGCAGT
* * * * * * *
178701 CGACCAAATCTCCTCAATGCGTAGGACCAGCGTCATCCTCTGGCAATCAGACTTCCTCATCACGT
1 CGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAACCAGACTTCCTCATCACGT
* * *
178766 AGAAAGCGTGTTATCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCATTGCATAGGAACAAT
66 AGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCATT-CATAGGAACAAT
* *
178831 ATCGTCTAC
130 GTCGTCCAC
* * * * * * * *
178840 TGACCATATCTACTCAACGTGTAGGAGTAGTGTCACCCTCAGATAACCAAACTTCCTCATCACGT
1 CGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAACCAGACTTCCTCATCACGT
* *
178905 AGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACAACTAGACGTCCTCA-TCACGTAGGAACAA
66 AGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCATTCA--TAGGAACAA
*
178969 TGTCGTTCAC
129 TGTCGTCCAC
* * * * * *
178979 TGACCAGATCTCCTCAACGCGTATGAGCAGTGTCATCCTCAGGCAATCAGACTTCCTCACCATGT
1 CGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAACCAGACTTCCTCATCACGT
* * * * * *
179044 AGAAACCGTGTTGTCTCCAAAGTATCCCTAAAGACGGCTGGACATCCTTA-TCATGTAGGAACAA
66 AGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCATTCA--TAGGAACAA
*
179108 TGTCATCCAC
129 TGTCGTCCAC
* * ** * * * * *
179118 CGACCAAATCTCCTTAACAAGTAAGAGCAATGTCATCCTTAGAAAACC-GTACTTCCTTATCACG
1 CGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAACCAG-ACTTCCTCATCACG
* * *
179182 TAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACATCTAGACGTCCTCATCGCATAGGAACAA
65 TAGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCAT-TCATAGGAACAA
* *
179247 TGTCATCAAC
129 TGTCGTCCAC
* * * * * *
179257 CGACCAGATCTCCTAAACGCATAGAAGCAGTGTCACCCTCAGATAACCAGACTTCCTAATCACGT
1 CGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAACCAGACTTCCTCATCACGT
* * ** * * *
179322 AGGAACTGTTTTGTCTCCAAATTATTGCTAAATACGGCTAGACGTCCTCA-TCATGTAGGAATAA
66 AGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCATTCA--TAGGAACAA
* *
179386 TATTGTCCAC
129 TGTCGTCCAC
* * * * * * * *
179396 CGACCAGATCTCCTCAACACGTATGAGCAGTGTTATCCTTAGGCAATCAGACTTCGTCACCACGT
1 CGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAACCAGACTTCCTCATCACGT
* * *
179461 AGGAACCGTGTTGTCTCC-AAGTATCCCTAAA-AGC-GACTATACGTCCTCA-TCATATTGGAAT
66 AGGAACCGTGTTGTCTCCAAATTATCCCTAAAGA-CAG-CTAGACGTCCTCATTCATA--GGAAC
* *
179522 AATGTCATCCAT
127 AATGTCGTCCAC
* * ** * * * *
179534 CGACCAGATCTCCTCAACGAGTAGGAGTAACGTCATCCTTAGACAATCAGAATTTCTCATCACGT
1 CGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAACCAGACTTCCTCATCACGT
179599 A-GAACCGT
66 AGGAACCGT
179607 ATTATCACTA
Statistics
Matches: 626, Mismatches: 129, Indels: 26
0.80 0.17 0.03
Matches are distributed among these distances:
136 2 0.00
137 13 0.02
138 95 0.15
139 513 0.82
140 1 0.00
141 2 0.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.25
Consensus pattern (138 bp):
CGACCAGATCTCCTCAACGCGTAGGAGCAGTGTCATCCTCAGACAACCAGACTTCCTCATCACGT
AGGAACCGTGTTGTCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCATTCATAGGAACAATG
TCGTCCAC
Found at i:179205 original size:278 final size:276
Alignment explanation
Indices: 178702--179606 Score: 976
Period size: 278 Copynumber: 3.3 Consensus size: 276
178692 ATTGGCAGTC
* * * * *
178702 GACCAAATCTCCTCAATGCGTAGGACCAGCGTCATCCTCTGGCAATCAGACTTCCTCATCACGTA
1 GACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTA
* * *
178767 GAAAGCGTGTTATCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCAT--TGCATAGGAACAA
66 GAAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCATG--TAGGAACAA
* * * * ** * * * * * *
178830 TATCGTCTACTGACCATATCTACTCAACGTGTAGGAGTAGTGTCACCCTCAGATAACCAAACTTC
129 TATCGTCCACCGACCAAATCTCCTCAACAAGTAAGAGCAGTGTCATCCTTAGAAAACC-GACTTC
*
178895 CTCATCACGTAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACAACTAGACGTCCTCATCACG
193 CTCATCACGTAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACAACTAGACGTCCTCATCACA
178960 TAGGAACAATGTCGTTCACT
258 TAGGAACAATGTC-TTCACT
* * * * *
178980 GACCAGATCTCCTCAACGCGTATGAGCAGTGTCATCCTCAGGCAATCAGACTTCCTCACCATGTA
1 GACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTA
* * * * *
179045 GAAACCGTGTTGTCTCCAAAGTATCCCTAAAGACGGCTGGACATCCTTATCATGTAGGAACAATG
66 GAAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCATGTAGGAACAATA
* * *
179110 TCATCCACCGACCAAATCTCCTTAACAAGTAAGAGCAATGTCATCCTTAGAAAACCGTACTTCCT
131 TCGTCCACCGACCAAATCTCCTCAACAAGTAAGAGCAGTGTCATCCTTAGAAAACCG-ACTTCCT
* * *
179175 TATCACGTAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACATCTAGACGTCCTCATCGCATA
195 CATCACGTAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACAACTAGACGTCCTCATCACATA
* *
179240 GGAACAATGTCATCAACC
260 GGAACAATGTCTTC-ACT
* * * * * * * *
179258 GACCAGATCTCCTAAACGCATAGAAGCAGTGTCACCCTCAGATAACCAGACTTCCTAATCACGTA
1 GACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTA
* * * ** * *
179323 GGAACTGTTTTGTCTCCAAATTATTGCTAAATACGGCTAGACGTCCTCATCATGTAGGAATAATA
66 GAAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCATGTAGGAACAATA
* * * * * * * * *
179388 TTGTCCACCGACCAGATCTCCTCAACACGTATGAGCAGTGTTATCCTTAGGCAATCAGACTTCGT
131 TCGTCCACCGACCAAATCTCCTCAACAAGTAAGAGCAGTGTCATCCTTA-GAAAACCGACTTCCT
* * * * * *
179453 CACCACGTAGGAACCGTGTTGTCTCC-AAGTATCCCTAAA-AGCGACTATACGTCCTCATCATAT
195 CATCACGTAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGA-CAACTAGACGTCCTCATCACAT
* * *
179516 TGGAATAATGTCATC-CAT
259 AGGAACAATGTCTTCAC-T
* * * * * *
179534 CGACCAGATCTCCTCAACGAGTAGGAGTAACGTCATCCTTAGACAATCAGAATTTCTCATCACGT
1 -GACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGT
179599 AG-AACCGT
65 AGAAACCGT
179607 ATTATCACTA
Statistics
Matches: 520, Mismatches: 99, Indels: 18
0.82 0.16 0.03
Matches are distributed among these distances:
275 1 0.00
276 6 0.01
277 95 0.18
278 411 0.79
279 5 0.01
280 2 0.00
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (276 bp):
GACCAGATCTCCTCAACGCGTAGGAGCAGCGTCATCCTCAGACAATCAGACTTCCTCATCACGTA
GAAACCGTGTTGTCTCCAAATTATCCCTAAAGACGGCTAGACGTCCTCATCATGTAGGAACAATA
TCGTCCACCGACCAAATCTCCTCAACAAGTAAGAGCAGTGTCATCCTTAGAAAACCGACTTCCTC
ATCACGTAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACAACTAGACGTCCTCATCACATAG
GAACAATGTCTTCACT
Found at i:179475 original size:417 final size:416
Alignment explanation
Indices: 178751--179623 Score: 1158
Period size: 417 Copynumber: 2.1 Consensus size: 416
178741 TGGCAATCAG
*
178751 ACTTCCTCATCACGTAGAAAGCGTGTTATCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCA
1 ACTTCCTCATCACGTAGAAACCGTGTTATCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCA
* * * * * * ** * *
178816 TTGCATAGGAACAATATCGTCTACTGACCATATCTACTCAACGTGTAGGAGTAGTGTCACCCTCA
66 TCGCATAGGAACAATATCATCAACCGACCAGATCTACTAAACGCATAGAAGCAGTGTCACCCTCA
*
178881 GATAACCAAACTTCCTCATCACGTAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACAACTAG
131 GATAACCAAACTTCCTAATCACGTAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACAACTAG
* * * *
178946 ACGTCCTCATCACGTAGGAACAATGTCGTTCACTGACCAGATCTCCTCAACGCGTATGAGCAGTG
196 ACGTCCTCATCACGTAGGAACAATATCGTCCACCGACCAGATCTCCTCAACACGTATGAGCAGTG
*
179011 TCATCCTCAGGCAATCAGACTTCCTCACCATGTAGAAACCGTGTTGTCTCCAAAGTATCCCT-AA
261 TCATCCTCAGGCAATCAGACTTCCTCACCACGTAGAAACCGTGTTGTCTCC-AAGTATCCCTAAA
* * * * *
179075 AGACGGCTGGACATCCTTATCATGTAGGAACAATGTCATCCACCGACCAAATCTCCTTAACAAGT
325 AG-CGACTAGACATCCTCATCATATAGGAACAATGTCATCCACCGACCAAATCTCCTCAACAAGT
*
179140 AAGAGCAATGTCATCCTTAGAAAACCGT
389 AAGAGCAACGTCATCCTTAGAAAACCGT
* * * * *
179168 ACTTCCTTATCACGTAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACATCTAGACGTCCTCA
1 ACTTCCTCATCACGTAGAAACCGTGTTATCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCA
* *
179233 TCGCATAGGAACAATGTCATCAACCGACCAGATCTCCTAAACGCATAGAAGCAGTGTCACCCTCA
66 TCGCATAGGAACAATATCATCAACCGACCAGATCTACTAAACGCATAGAAGCAGTGTCACCCTCA
* * * * * **
179298 GATAACCAGACTTCCTAATCACGTAGGAACTGTTTTGTCTCCAAATTATTGCTAAATACGGCTAG
131 GATAACCAAACTTCCTAATCACGTAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACAACTAG
* * *
179363 ACGTCCTCATCATGTAGGAATAATATTGTCCACCGACCAGATCTCCTCAACACGTATGAGCAGTG
196 ACGTCCTCATCACGTAGGAACAATATCGTCCACCGACCAGATCTCCTCAACACGTATGAGCAGTG
* * * *
179428 TTATCCTTAGGCAATCAGACTTCGTCACCACGTAGGAACCGTGTTGTCTCCAAGTATCCCTAAAA
261 TCATCCTCAGGCAATCAGACTTCCTCACCACGTAGAAACCGTGTTGTCTCCAAGTATCCCTAAAA
* * * * * * * *
179493 GCGACTATACGTCCTCATCATATTGGAATAATGTCATCCATCGACCAGATCTCCTCAACGAGTAG
326 GCGACTAGACATCCTCATCATATAGGAACAATGTCATCCACCGACCAAATCTCCTCAACAAGTAA
* * *
179558 GAGTAACGTCATCCTTAGACAATCAG-
391 GAGCAACGTCATCCTTAGA-AAACCGT
* * * * *
179584 AATTTCTCATCACGTAG-AACCGTATTATCACTAAATTATC
1 ACTTCCTCATCACGTAGAAACCGTGTTATCTCCAAATTATC
179624 TCTATATTGA
Statistics
Matches: 391, Mismatches: 63, Indels: 6
0.85 0.14 0.01
Matches are distributed among these distances:
415 18 0.05
416 92 0.24
417 281 0.72
ACGTcount: A:0.31, C:0.27, G:0.16, T:0.26
Consensus pattern (416 bp):
ACTTCCTCATCACGTAGAAACCGTGTTATCTCCAAATTATCCCTAAAGACAGCTAGACGTCCTCA
TCGCATAGGAACAATATCATCAACCGACCAGATCTACTAAACGCATAGAAGCAGTGTCACCCTCA
GATAACCAAACTTCCTAATCACGTAGGAACCGTGTTGTCTCCAAATTATTCCTAAAGACAACTAG
ACGTCCTCATCACGTAGGAACAATATCGTCCACCGACCAGATCTCCTCAACACGTATGAGCAGTG
TCATCCTCAGGCAATCAGACTTCCTCACCACGTAGAAACCGTGTTGTCTCCAAGTATCCCTAAAA
GCGACTAGACATCCTCATCATATAGGAACAATGTCATCCACCGACCAAATCTCCTCAACAAGTAA
GAGCAACGTCATCCTTAGAAAACCGT
Found at i:180296 original size:3 final size:3
Alignment explanation
Indices: 180288--180326 Score: 60
Period size: 3 Copynumber: 12.3 Consensus size: 3
180278 AGGTTCTAAT
180288 TTA TTA TTAA CTTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TT-A -TTA TTA TTA TTA TTA TTA TTA TTA TTA T
180327 ATTTTTGCAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 30 0.88
4 2 0.06
5 2 0.06
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:182554 original size:22 final size:21
Alignment explanation
Indices: 182529--182573 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
182519 TTAATTCAAA
* *
182529 TTAATTCAAAATTGTCAATTTT
1 TTAAATCAAAATCGT-AATTTT
*
182551 TTAAATCAAAGTCGTAATTTT
1 TTAAATCAAAATCGTAATTTT
182572 TT
1 TT
182574 TAAACTTAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.36, C:0.09, G:0.07, T:0.49
Consensus pattern (21 bp):
TTAAATCAAAATCGTAATTTT
Done.