Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002763.1 Hibiscus syriacus cultivar Beakdansim tig00005694_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: 175760
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:2092 original size:47 final size:48
Alignment explanation
Indices: 2023--2114 Score: 134
Period size: 47 Copynumber: 1.9 Consensus size: 48
2013 TTGAACATAA
* *
2023 AAACCTAACCTCATGCTATCTAGTTCGCATG-A-TTATTCAAGAAAAAT
1 AAACCTAACCTAATGATATCTAGTTCGCATGCATTTATTC-AGAAAAAT
*
2070 AAACCTAACCTAATGATCTCTAGTTCGCATGCATTTATTCAGAAA
1 AAACCTAACCTAATGATATCTAGTTCGCATGCATTTATTCAGAAA
2115 GCGAATTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
47 28 0.70
48 6 0.15
49 6 0.15
ACGTcount: A:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (48 bp):
AAACCTAACCTAATGATATCTAGTTCGCATGCATTTATTCAGAAAAAT
Found at i:3860 original size:2 final size:2
Alignment explanation
Indices: 3849--3896 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
3839 GTTATCGAAA
3849 AT AT -T 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
3890 AT AT AT A
1 AT AT AT A
3897 AAGTGACGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8218 original size:19 final size:20
Alignment explanation
Indices: 8179--8225 Score: 78
Period size: 19 Copynumber: 2.4 Consensus size: 20
8169 ATAATCCCTT
*
8179 TGAAAATATATGATTTTTAA
1 TGAAAATATATGATCTTTAA
8199 TGAAAATATATGA-CTTTAA
1 TGAAAATATATGATCTTTAA
8218 TGAAAATA
1 TGAAAATA
8226 ATTTCTCTTG
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (20 bp):
TGAAAATATATGATCTTTAA
Found at i:12372 original size:19 final size:20
Alignment explanation
Indices: 12337--12379 Score: 70
Period size: 19 Copynumber: 2.2 Consensus size: 20
12327 TCCTTTTGAC
*
12337 AATATATGATTTTTAATGAA
1 AATATATGATATTTAATGAA
12357 AATATATGA-ATTTAATGAA
1 AATATATGATATTTAATGAA
12376 AATA
1 AATA
12380 CATGCTCTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (20 bp):
AATATATGATATTTAATGAA
Found at i:17644 original size:21 final size:21
Alignment explanation
Indices: 17611--17656 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
17601 TTTAAACGAG
*
17611 TGAATTAAAAAAAATTCAAAA
1 TGAATTAAAAAAAACTCAAAA
17632 TGAA-TAAACAAAAACTCAAAA
1 TGAATTAAA-AAAAACTCAAAA
17653 TGAA
1 TGAA
17657 ATGGAAAATA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.17
21 19 0.83
ACGTcount: A:0.65, C:0.09, G:0.07, T:0.20
Consensus pattern (21 bp):
TGAATTAAAAAAAACTCAAAA
Found at i:18050 original size:101 final size:100
Alignment explanation
Indices: 17755--18180 Score: 394
Period size: 101 Copynumber: 4.2 Consensus size: 100
17745 AAACATTTTC
* * * * *
17755 ATAAGTATAACATTATAGGTAGAGCCTTTTTTACTTATCCAACGTTTACGTTATATGTTTGAAAC
1 ATAAGTATAACATTATAGGTAGTGCATTTTTTAATT-TTCAACGTTTAAGTTATATGTTTGAAAC
*
17820 C-TTTTATATTATGAAAAAAGTAAGACAAAACATGTTT
65 CATTTT-TATTATGAAAAAA-TAAGACAAAACAGGTTT
* * * ** ** * *
17857 ATAAGTATACCATTGTAGGTTGTGCATTCTTTTAA-TTAGAAATTATTAAGATTATTTGTTTCAA
1 ATAAGTATAACATTATAGGTAGTGCATT-TTTTAATTTTCAACGT-TTAAG-TTATATGTTTGAA
* * * * * *
17921 ACCGTTTTTATTATGCAACAATACGACAAAGCAGGTTG
63 ACCATTTTTATTATGAAAAAATAAGACAAAACAGGTTT
* * * *
17959 ATAAGTCTAACCTTTTAGGTAGCGCATTTTTTAATTTTCAACCGTTTAAGTTATATGTTTGAAAC
1 ATAAGTATAACATTATAGGTAGTGCATTTTTTAATTTTCAA-CGTTTAAGTTATATGTTTGAAAC
*
18024 C-TTTTATATTATGAAAAAATAAGACAAAACATGTTT
65 CATTTT-TATTATGAAAAAATAAGACAAAACAGGTTT
* * *
18060 ATAAGTATAACATTATAGG-ATGTGCATTTTTTAATTGTCAACCG-TTAATATTATATTTTTGAA
1 ATAAGTATAACATTATAGGTA-GTGCATTTTTTAATTTTCAA-CGTTTAA-GTTATATGTTTGAA
* * * * * *
18123 ACCATTTTTAGTATGGAACATTTAGACAAAATAGGTTT
63 ACCATTTTTATTATGAAAAAATAAGACAAAACAGGTTT
*
18161 ATAAGTCTAACATTATAGGT
1 ATAAGTATAACATTATAGGT
18181 TGCATCTTTG
Statistics
Matches: 261, Mismatches: 52, Indels: 22
0.78 0.16 0.07
Matches are distributed among these distances:
100 9 0.03
101 141 0.54
102 76 0.29
103 31 0.12
104 4 0.02
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.40
Consensus pattern (100 bp):
ATAAGTATAACATTATAGGTAGTGCATTTTTTAATTTTCAACGTTTAAGTTATATGTTTGAAACC
ATTTTTATTATGAAAAAATAAGACAAAACAGGTTT
Found at i:20360 original size:254 final size:252
Alignment explanation
Indices: 19910--20803 Score: 692
Period size: 254 Copynumber: 3.4 Consensus size: 252
19900 TTATTATATA
* * * *
19910 TATTCATAACATTTTAAGATTTTAACTTATTTTCTTATCGTGGGAAAATCCAACG-TTCCATCAA
1 TATT-ATAACAATTTAAGCTTTTAACTTATTTTCTTATCGTGGGAAACTCTAACGCTT-CATC-A
* * * * * *
19974 GT-TTAAGTGTGATAATATTTTAGGTGCAACCCATTTTTATTATTAAAAATATTAAGATTCATGA
63 -TCTTAACTTTGATAATATTTTAGGTGAAACCCA-TTTTATTATTAAAAATAGTAAAATTCAAGA
* * * *
20038 TTGCAACTTTCTTTCTTCG-AAACCATGACATTCTTAGGTGCAACCTAATTTT-TTAATAAAAAT
126 TTGCAACATGCTTTCTTAGTAAACCATGACATTCTTGGGTGCAACCT-ATTTTATTAATAAAAAT
* * *
20101 ATTAACATCATATATCAAAACCTATTTCTTAATAAACCATGACATTATTGGGCACAACCATAGT
190 ATTAACATCACAAATCAAAACCCATTTCTTAATAAA-CATGACATTATTGGGCACAACCATAGT
* * *
20165 TATTATAACAATTTAAGCTTTTAACTTATTTTCTTATCGTGAGAAACTCTAATGCTTCATCTTCT
1 TATTATAACAATTTAAGCTTTTAACTTATTTTCTTATCGTGGGAAACTCTAACGCTTCATCATCT
* ** *
20230 TAGACTTTTGATAATATTTTAGGTGAAACTCATTTTATTATTAAAAATAGTATTATTGAAGATTG
66 TA-AC-TTTGATAATATTTTAGGTGAAACCCATTTTATTATTAAAAATAGTAAAATTCAAGATTG
* * * * * *
20295 CAACATGCTTTCTTAGTTAACCATAATATTTTTGGGAGCAACCTATTTTATTAA-AAAATTATTA
129 CAACATGCTTTCTTAGTAAACCATGACATTCTTGGGTGCAACCTATTTTATTAATAAAAATATTA
* * * ** * *** ** *
20359 ACAACACAAATCACAACCCATTTCTTATTGGACATGATATTATTGGGTGTAACTGTATT
194 ACATCACAAATCAAAACCCATTTCTTAATAAACATGACATTATTGGGCACAACCATAGT
* * * * *
20418 TATTATACATATTCATGACATTTTAGGCTTTTAATTTATTTTCTCATCATGGGAAACTCTAAGGC
1 TATTAT--A-A--C---A-A-TTTAAGCTTTTAACTTATTTTCTTATCGTGGGAAACTCTAACGC
* * *
20483 TCCATCAGCTTAAACTTTGATAATATTTTAGG-CACAACCCATTTTATTATTAAAAATAGTAAAA
56 TTCATCATCTT-AACTTTGATAATATTTTAGGTGA-AACCCATTTTATTATTAAAAATAGTAAAA
* * * * * * *
20547 TTTC-ATATTGCAACATGATTTCTTAATGAATCATGACATTCATGAGTGCAACCTATTTTATTAA
119 -TTCAAGATTGCAACATGCTTTCTTAGTAAACCATGACATTCTTGGGTGCAACCTATTTTATTAA
* *** * ** * *
20611 TAAAAATATTAACATTACAAATTGCAACCTATTTCTTGTTGAACTATGATATTATTAGGCGCAAC
183 TAAAAATATTAACATCACAAATCAAAACCCATTTCTTAATAAAC-ATGACATTATT-GG-GC-AC
* *
20676 AA-TATTTTTTATAT
244 AACCA-----TA-GT
* * *
20690 ATATTCATAACATTTTAAGCTTTTAACTTATTTTCTTATCGTGGGAAA-T-TAAAAGTCTACATC
1 -TATT-ATAACAATTTAAGCTTTTAACTTATTTTCTTATCGTGGGAAACTCT-AACG-CTTCATC
* * * * * *
20753 AGCTTAAATTGTGATAACATTTTAGGCGCAACCCATTTTATTATTCAAAAT
62 ATCTTAACTT-TGATAATATTTTAGGTGAAACCCATTTTATTATTAAAAAT
20804 TTAAGATTCC
Statistics
Matches: 512, Mismatches: 91, Indels: 63
0.77 0.14 0.09
Matches are distributed among these distances:
252 1 0.00
253 29 0.06
254 128 0.25
255 55 0.11
256 1 0.00
258 1 0.00
261 2 0.00
262 94 0.18
263 93 0.18
264 89 0.17
265 2 0.00
266 3 0.01
267 2 0.00
269 1 0.00
271 3 0.01
272 2 0.00
273 4 0.01
274 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (252 bp):
TATTATAACAATTTAAGCTTTTAACTTATTTTCTTATCGTGGGAAACTCTAACGCTTCATCATCT
TAACTTTGATAATATTTTAGGTGAAACCCATTTTATTATTAAAAATAGTAAAATTCAAGATTGCA
ACATGCTTTCTTAGTAAACCATGACATTCTTGGGTGCAACCTATTTTATTAATAAAAATATTAAC
ATCACAAATCAAAACCCATTTCTTAATAAACATGACATTATTGGGCACAACCATAGT
Found at i:20777 original size:264 final size:260
Alignment explanation
Indices: 19817--20803 Score: 880
Period size: 264 Copynumber: 3.8 Consensus size: 260
19807 TCTTGGGAGT
* * * * * * * * *
19817 AACCTATTTTATTATTTAAATTATT-A-ATTACATATCGCAACTTATTTCTTAGTGAACCATGGC
1 AACCTATTTTATTAATAAAAATATTAACATCACAAATCACAACCTATTTCTTATTGAACCATGAC
* * *
19880 ATTATTGGAAGCCACATTATTTATTATATATATTCATAACATTTTAAGATTTTAACTTATTTTCT
66 ATTATTGG--GCAACAATATTTATTATATATATTCATAACATTTTAAGCTTTTAACTTATTTTCT
* * * * **
19945 TATCGTGGGAAAATCCAACGT-TCCATCAAG-TTTAAGTGTGATAATATTTTAGGTGCAACCCAT
129 TATCGTGGG-AAATTCAAAGTCTCCATC-AGCTTAAATTGTGATAATATTTTAGGCACAACCCA-
* * * * *
20008 TTTTATTATTAAAAATATTAAGA-TTCATGATTGCAACTTTCTTTCTT-CGAAACCATGACATTC
191 TTTTATTATTAAAAATAGTAAAATTTCAT-ATTGCAACATGCTTTCTTATG-AACCATGACATTC
*
20071 TTAGGTGC
254 TGA-GTGC
* * * * *
20079 AACCTAATTTT-TTAATAAAAATATTAACATCATATATCAAAACCTATTTCTTAATAAACCATGA
1 AACCT-ATTTTATTAATAAAAATATTAACATCACAAATCACAACCTATTTCTTATTGAACCATGA
** * *
20143 CATTATTGGGC-AC-A-A-CCA-TA-GT-TATT-ATAACAATTTAAGCTTTTAACTTATTTTCTT
65 CATTATTGGGCAACAATATTTATTATATATATTCATAACATTTTAAGCTTTTAACTTATTTTCTT
* * * * ** * * * *
20200 ATCGTGAGAAACTCTAA-TGCTTCATCTTCTTAGACTTTTGATAATATTTTAGGTGA-AACTCAT
130 ATCGTGGGAAATTCAAAGT-CTCCATCAGCTTA-AATTGTGATAATATTTTAGG-CACAACCCAT
** ** * * * * *
20263 TTTATTATTAAAAATAGTATTATTGAAGATTGCAACATGCTTTCTTAGTTAACCATAATATTTTT
192 TTTATTATTAAAAATAGTAAAATTTCATATTGCAACATGCTTTCTTA-TGAACCATGACA-TTCT
* *
20328 GGGAGC
255 GAGTGC
* * * * *
20334 AACCTATTTTATTAA-AAAATTATTAACAACACAAATCACAACCCATTTCTTATTGGA-CATGAT
1 AACCTATTTTATTAATAAAAATATTAACATCACAAATCACAACCTATTTCTTATTGAACCATGAC
* ** * * * *
20397 ATTATTGGGTGTAACTGTATTTATTATACATATTCATGACATTTTAGGCTTTTAATTTATTTTCT
66 ATTATT-GG-GCAACAATATTTATTATATATATTCATAACATTTTAAGCTTTTAACTTATTTTCT
* * * * *
20462 CATCATGGGAAACTCTAAGGCTCCATCAGCTTAAACTT-TGATAATATTTTAGGCACAACCCATT
129 TATCGTGGGAAATTCAAAGTCTCCATCAGCTTAAA-TTGTGATAATATTTTAGGCACAACCCATT
* *
20526 TTATTATTAAAAATAGTAAAATTTCATATTGCAACATGATTTCTTAATGAATCATGACATTCATG
193 TTATTATTAAAAATAGTAAAATTTCATATTGCAACATGCTTTCTT-ATGAACCATGACATTC-TG
20591 AGTGC
256 AGTGC
* ** * * *
20596 AACCTATTTTATTAATAAAAATATTAACATTACAAATTGCAACCTATTTCTTGTTGAACTATGAT
1 AACCTATTTTATTAATAAAAATATTAACATCACAAATCACAACCTATTTCTTATTGAACCATGAC
*
20661 ATTATTAGGCGCAACAATATTTTTTATATATATTCATAACATTTTAAGCTTTTAACTTATTTTCT
66 ATTATT-GG-GCAACAATATTTATTATATATATTCATAACATTTTAAGCTTTTAACTTATTTTCT
* * * *
20726 TATCGTGGGAAATTAAAAGTCTACATCAGCTTAAATTGTGATAACATTTTAGGCGCAACCCATTT
129 TATCGTGGGAAATTCAAAGTCTCCATCAGCTTAAATTGTGATAATATTTTAGGCACAACCCATTT
*
20791 TATTATTCAAAAT
194 TATTATTAAAAAT
20804 TTAAGATTCC
Statistics
Matches: 574, Mismatches: 120, Indels: 60
0.76 0.16 0.08
Matches are distributed among these distances:
252 1 0.00
253 16 0.03
254 119 0.21
255 49 0.09
256 6 0.01
257 2 0.00
258 2 0.00
259 2 0.00
260 2 0.00
261 5 0.01
262 112 0.20
263 96 0.17
264 162 0.28
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (260 bp):
AACCTATTTTATTAATAAAAATATTAACATCACAAATCACAACCTATTTCTTATTGAACCATGAC
ATTATTGGGCAACAATATTTATTATATATATTCATAACATTTTAAGCTTTTAACTTATTTTCTTA
TCGTGGGAAATTCAAAGTCTCCATCAGCTTAAATTGTGATAATATTTTAGGCACAACCCATTTTA
TTATTAAAAATAGTAAAATTTCATATTGCAACATGCTTTCTTATGAACCATGACATTCTGAGTGC
Found at i:22258 original size:13 final size:13
Alignment explanation
Indices: 22240--22264 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
22230 ATAAACAATT
22240 AAATAAAAAATAA
1 AAATAAAAAATAA
22253 AAATAAAAAATA
1 AAATAAAAAATA
22265 TAATAAATCG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (13 bp):
AAATAAAAAATAA
Found at i:26698 original size:26 final size:26
Alignment explanation
Indices: 26660--26712 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
26650 TGACCCAAGA
*
26660 ATATCATCAAGCTCAGAAATGATTGG
1 ATATCATCAAGCTCAGAAATGAATGG
* * *
26686 ATATCCTCGAGCTCTGAAATGAATGG
1 ATATCATCAAGCTCAGAAATGAATGG
26712 A
1 A
26713 ATAAAACTGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.36, C:0.17, G:0.21, T:0.26
Consensus pattern (26 bp):
ATATCATCAAGCTCAGAAATGAATGG
Found at i:27705 original size:24 final size:24
Alignment explanation
Indices: 27678--27793 Score: 146
Period size: 24 Copynumber: 4.8 Consensus size: 24
27668 TTCGATTTGA
*
27678 ATTCTAATCTGATACTTGACATGG
1 ATTCTGATCTGATACTTGACATGG
27702 ATTCTGATCTGATA-TCTGACATGG
1 ATTCTGATCTGATACT-TGACATGG
*
27726 ATTCTGATCTGATACTTGACTTGG
1 ATTCTGATCTGATACTTGACATGG
* * *
27750 ATTCTGATATGTTACTTGACCT-G
1 ATTCTGATCTGATACTTGACATGG
*
27773 ATTTCTGATATGATACTTGAC
1 A-TTCTGATCTGATACTTGAC
27794 CTGATTTATG
Statistics
Matches: 83, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
23 3 0.04
24 79 0.95
25 1 0.01
ACGTcount: A:0.25, C:0.16, G:0.18, T:0.41
Consensus pattern (24 bp):
ATTCTGATCTGATACTTGACATGG
Found at i:27810 original size:24 final size:24
Alignment explanation
Indices: 27730--27803 Score: 87
Period size: 24 Copynumber: 3.1 Consensus size: 24
27720 ACATGGATTC
* * *
27730 TGATCTGATACTTGACTTGGA-TTC
1 TGATATGATACTTGACCT-GATTTA
* *
27754 TGATATGTTACTTGACCTGATTTC
1 TGATATGATACTTGACCTGATTTA
27778 TGATATGATACTTGACCTGATTTA
1 TGATATGATACTTGACCTGATTTA
27802 TG
1 TG
27804 TTTTGATTTG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
23 2 0.05
24 42 0.95
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (24 bp):
TGATATGATACTTGACCTGATTTA
Found at i:33787 original size:7 final size:7
Alignment explanation
Indices: 33775--33805 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
33765 GTCAAAGAAA
33775 GTCAACG
1 GTCAACG
33782 GTCAACG
1 GTCAACG
33789 GTCAACG
1 GTCAACG
33796 GTCAACG
1 GTCAACG
33803 GTC
1 GTC
33806 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:33812 original size:5 final size:5
Alignment explanation
Indices: 33802--33857 Score: 58
Period size: 5 Copynumber: 10.4 Consensus size: 5
33792 AACGGTCAAC
* *
33802 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
33851 GGTCG GG
1 GGTCG GG
33858 CCTGACCGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 35 0.81
7 8 0.19
ACGTcount: A:0.07, C:0.21, G:0.54, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:33823 original size:22 final size:22
Alignment explanation
Indices: 33795--33857 Score: 126
Period size: 22 Copynumber: 2.9 Consensus size: 22
33785 AACGGTCAAC
33795 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
33817 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
33839 GGTCAACGGTCGGGTCGGG
1 GGTCAACGGTCGGGTCGGG
33858 CCTGACCGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:33883 original size:19 final size:19
Alignment explanation
Indices: 33861--33955 Score: 95
Period size: 19 Copynumber: 4.9 Consensus size: 19
33851 GGTCGGGCCT
33861 GACCGGTCAAACCGGTTCA
1 GACCGGTCAAACCGGTTCA
33880 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
*
33898 GAACCGGTTGAAACCGG-TCA
1 G-ACCGG-TCAAACCGGTTCA
* *
33918 AACCGGTCAGAACCGGTTGAA
1 GACCGGTCA-AACCGGTT-CA
* *
33939 AACCGGTTAAACCGGTT
1 GACCGGTCAAACCGGTT
33956 TCCAGCAGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.05
19 36 0.55
20 17 0.26
21 9 0.14
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.17
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:33886 original size:10 final size:9
Alignment explanation
Indices: 33862--33954 Score: 87
Period size: 9 Copynumber: 9.7 Consensus size: 9
33852 GTCGGGCCTG
33862 ACCGGTCAA
1 ACCGGTCAA
*
33871 ACCGGTTCAG
1 ACCGG-TCAA
33881 ACCGGTCAA
1 ACCGGTCAA
*
33890 ACCGGTTCGA
1 ACCGG-TCAA
*
33900 ACCGGTTGAA
1 ACCGG-TCAA
33910 ACCGGTCAA
1 ACCGGTCAA
33919 ACCGGTCAGA
1 ACCGGTCA-A
*
33929 ACCGGTTGAAA
1 ACCGG-T-CAA
*
33940 ACCGGTTAA
1 ACCGGTCAA
33949 ACCGGT
1 ACCGGT
33955 TTCCAGCAGC
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 32 0.45
10 31 0.44
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:33904 original size:29 final size:28
Alignment explanation
Indices: 33863--33954 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
33853 TCGGGCCTGA
*
33863 CCGGTCAAACCGGTTCAGACCGGTCAAA
1 CCGGTCAAACCGGTTAAGACCGGTCAAA
*
33891 CCGGTTCGAACCGGTTGAA-ACCGGTCAAA
1 CCGG-TCAAACCGGTT-AAGACCGGTCAAA
* *
33920 CCGGTCAGAACCGGTTGAAAACCGGTTAAA
1 CCGGTCA-AACCGGTT-AAGACCGGTCAAA
33950 CCGGT
1 CCGGT
33955 TTCCAGCAGC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.11
29 35 0.62
30 15 0.27
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.16
Consensus pattern (28 bp):
CCGGTCAAACCGGTTAAGACCGGTCAAA
Found at i:41122 original size:5 final size:5
Alignment explanation
Indices: 41112--41167 Score: 58
Period size: 5 Copynumber: 10.4 Consensus size: 5
41102 AACGGTCAAC
* *
41112 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
41161 GGTCG GG
1 GGTCG GG
41168 CCTGACCGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
5 35 0.81
7 8 0.19
ACGTcount: A:0.07, C:0.21, G:0.54, T:0.18
Consensus pattern (5 bp):
GGTCG
Found at i:41130 original size:22 final size:22
Alignment explanation
Indices: 41105--41167 Score: 126
Period size: 22 Copynumber: 2.9 Consensus size: 22
41095 GAAAGTCAAC
41105 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
41127 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
41149 GGTCAACGGTCGGGTCGGG
1 GGTCAACGGTCGGGTCGGG
41168 CCTGACCGGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 41 1.00
ACGTcount: A:0.10, C:0.22, G:0.51, T:0.17
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:41193 original size:19 final size:19
Alignment explanation
Indices: 41171--41265 Score: 95
Period size: 19 Copynumber: 4.9 Consensus size: 19
41161 GGTCGGGCCT
41171 GACCGGTCAAACCGGTTCA
1 GACCGGTCAAACCGGTTCA
41190 GACCGGTCAAACCGGTTC-
1 GACCGGTCAAACCGGTTCA
*
41208 GAACCGGTTGAAACCGG-TCA
1 G-ACCGG-TCAAACCGGTTCA
* *
41228 AACCGGTCAGAACCGGTTGAA
1 GACCGGTCA-AACCGGTT-CA
* *
41249 AACCGGTTAAACCGGTT
1 GACCGGTCAAACCGGTT
41266 TCCAGCAGCC
Statistics
Matches: 65, Mismatches: 5, Indels: 11
0.80 0.06 0.14
Matches are distributed among these distances:
18 3 0.05
19 36 0.55
20 17 0.26
21 9 0.14
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.17
Consensus pattern (19 bp):
GACCGGTCAAACCGGTTCA
Found at i:41196 original size:10 final size:9
Alignment explanation
Indices: 41172--41264 Score: 87
Period size: 9 Copynumber: 9.7 Consensus size: 9
41162 GTCGGGCCTG
41172 ACCGGTCAA
1 ACCGGTCAA
*
41181 ACCGGTTCAG
1 ACCGG-TCAA
41191 ACCGGTCAA
1 ACCGGTCAA
*
41200 ACCGGTTCGA
1 ACCGG-TCAA
*
41210 ACCGGTTGAA
1 ACCGG-TCAA
41220 ACCGGTCAA
1 ACCGGTCAA
41229 ACCGGTCAGA
1 ACCGGTCA-A
*
41239 ACCGGTTGAAA
1 ACCGG-T-CAA
*
41250 ACCGGTTAA
1 ACCGGTCAA
41259 ACCGGT
1 ACCGGT
41265 TTCCAGCAGC
Statistics
Matches: 71, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 32 0.45
10 31 0.44
11 7 0.10
12 1 0.01
ACGTcount: A:0.29, C:0.28, G:0.27, T:0.16
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:41214 original size:29 final size:28
Alignment explanation
Indices: 41173--41264 Score: 105
Period size: 29 Copynumber: 3.2 Consensus size: 28
41163 TCGGGCCTGA
*
41173 CCGGTCAAACCGGTTCAGACCGGTCAAA
1 CCGGTCAAACCGGTTAAGACCGGTCAAA
*
41201 CCGGTTCGAACCGGTTGAA-ACCGGTCAAA
1 CCGG-TCAAACCGGTT-AAGACCGGTCAAA
* *
41230 CCGGTCAGAACCGGTTGAAAACCGGTTAAA
1 CCGGTCA-AACCGGTT-AAGACCGGTCAAA
41260 CCGGT
1 CCGGT
41265 TTCCAGCAGC
Statistics
Matches: 56, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
28 6 0.11
29 35 0.62
30 15 0.27
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.16
Consensus pattern (28 bp):
CCGGTCAAACCGGTTAAGACCGGTCAAA
Found at i:43386 original size:23 final size:23
Alignment explanation
Indices: 43334--43386 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
43324 CCAAATCGTC
* *
43334 GTCGATTGTTTCTTTCGTTTCCT
1 GTCGATTGTTTCCTTCGTTCCCT
*
43357 GTTGATTGTTTCCTTCGATTCCCT
1 GTCGATTGTTTCCTTCG-TTCCCT
43381 -TCGATT
1 GTCGATT
43387 TTGTCGTCGT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.08, C:0.23, G:0.17, T:0.53
Consensus pattern (23 bp):
GTCGATTGTTTCCTTCGTTCCCT
Found at i:43780 original size:20 final size:20
Alignment explanation
Indices: 43757--43811 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
43747 AGAACCGGAC
* *
43757 TGAGTTAACTCGAACCAGAT
1 TGAGTCAACTCGAACCAAAT
*
43777 TGAGTCAACTCAAACCAAAT
1 TGAGTCAACTCGAACCAAAT
*
43797 TGAGTCAACTTGAAC
1 TGAGTCAACTCGAAC
43812 TGGTCAAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.38, C:0.22, G:0.16, T:0.24
Consensus pattern (20 bp):
TGAGTCAACTCGAACCAAAT
Found at i:45950 original size:20 final size:20
Alignment explanation
Indices: 45925--45964 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
45915 TGGCCTTAAT
*
45925 GTGATACCTCGGATCGGATC
1 GTGATACCTAGGATCGGATC
*
45945 GTGATACTTAGGATCGGATC
1 GTGATACCTAGGATCGGATC
45965 AGGTCACCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.23, C:0.20, G:0.30, T:0.28
Consensus pattern (20 bp):
GTGATACCTAGGATCGGATC
Found at i:50098 original size:33 final size:33
Alignment explanation
Indices: 50061--50125 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
50051 AATATCAGGC
*
50061 TGGAACTTCGTTCCACACTAACTATCCTATTGT
1 TGGAACTTCGCTCCACACTAACTATCCTATTGT
*
50094 TGGAACTTCGCTCTACACTAACTATCCTATTG
1 TGGAACTTCGCTCCACACTAACTATCCTATTG
50126 CATTTGGGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (33 bp):
TGGAACTTCGCTCCACACTAACTATCCTATTGT
Found at i:57425 original size:5 final size:5
Alignment explanation
Indices: 57415--57440 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
57405 TATTATTATT
57415 TCGGG TCGGG TCGGG TCGGG TCGGG T
1 TCGGG TCGGG TCGGG TCGGG TCGGG T
57441 TTCTAAGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.58, T:0.23
Consensus pattern (5 bp):
TCGGG
Found at i:58597 original size:21 final size:21
Alignment explanation
Indices: 58572--58617 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
58562 GATGAACGGG
*
58572 GGTGATGAGGAGGATTTGGGT
1 GGTGATGAGGAGGATTTGAGT
58593 GGTGATGAGGAGGATTTGAGT
1 GGTGATGAGGAGGATTTGAGT
58614 GGTG
1 GGTG
58618 GGCTCGGGGC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.20, C:0.00, G:0.52, T:0.28
Consensus pattern (21 bp):
GGTGATGAGGAGGATTTGAGT
Found at i:68095 original size:21 final size:21
Alignment explanation
Indices: 68070--68165 Score: 120
Period size: 21 Copynumber: 4.4 Consensus size: 21
68060 GGCAGGAGAG
68070 GGGATTGAAAATGGGGAATTA
1 GGGATTGAAAATGGGGAATTA
68091 GGGATTGAAAATGGGGAATTA
1 GGGATTGAAAATGGGGAATTA
* ** **
68112 GGGATTGAAGATACGGAAGGAGA
1 GGGATTGAAAATGGGGAA--TTA
68135 GGGGATTGAAAATGGGGAATTA
1 -GGGATTGAAAATGGGGAATTA
68157 GGGATTGAA
1 GGGATTGAA
68166 GATCGAGAAG
Statistics
Matches: 62, Mismatches: 10, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
21 45 0.73
22 1 0.02
23 1 0.02
24 15 0.24
ACGTcount: A:0.38, C:0.01, G:0.41, T:0.21
Consensus pattern (21 bp):
GGGATTGAAAATGGGGAATTA
Found at i:68144 original size:45 final size:45
Alignment explanation
Indices: 68091--68176 Score: 156
Period size: 45 Copynumber: 1.9 Consensus size: 45
68081 TGGGGAATTA
68091 GGGATTGAAAATGGGGAATTAGGGATTGAAGATACG-GAAGGAGAG
1 GGGATTGAAAATGGGGAATTAGGGATTGAAGAT-CGAGAAGGAGAG
68136 GGGATTGAAAATGGGGAATTAGGGATTGAAGATCGAGAAGG
1 GGGATTGAAAATGGGGAATTAGGGATTGAAGATCGAGAAGG
68177 GGAAATGATG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
44 2 0.05
45 38 0.95
ACGTcount: A:0.37, C:0.02, G:0.42, T:0.19
Consensus pattern (45 bp):
GGGATTGAAAATGGGGAATTAGGGATTGAAGATCGAGAAGGAGAG
Found at i:68290 original size:14 final size:14
Alignment explanation
Indices: 68264--68297 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
68254 TAACCCAGAA
68264 CAAGTAGAGTAGCC
1 CAAGTAGAGTAGCC
68278 CAAGTCAGA-TAGCC
1 CAAGT-AGAGTAGCC
68292 CAAGTA
1 CAAGTA
68298 CCTGCAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 1 0.05
14 15 0.79
15 3 0.16
ACGTcount: A:0.38, C:0.24, G:0.24, T:0.15
Consensus pattern (14 bp):
CAAGTAGAGTAGCC
Found at i:74956 original size:21 final size:22
Alignment explanation
Indices: 74923--74967 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
74913 TAGGGATTTT
74923 TATTTTTATATTATT-AAAATA
1 TATTTTTATATTATTAAAAATA
74944 TATTCTTTA-ATTATTAAAAATA
1 TATT-TTTATATTATTAAAAATA
74966 TA
1 TA
74968 AAACATATTA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TATTTTTATATTATTAAAAATA
Found at i:74995 original size:42 final size:41
Alignment explanation
Indices: 74934--75035 Score: 129
Period size: 42 Copynumber: 2.5 Consensus size: 41
74924 ATTTTTATAT
* *
74934 TATTA-AAATATATT-CTTTAATTATTAAAAATATAA-AACA
1 TATTATAAATATATTATTTTAATAATTAAAAATATAATAA-A
*
74973 TATTATATAATATATTATTTTAATAATTTAAAATATAATAAA
1 TATTATA-AATATATTATTTTAATAATTAAAAATATAATAAA
75015 TAATTATAAATATATTATTTT
1 T-ATTATAAATATATTATTTT
75036 TAAAATATTA
Statistics
Matches: 55, Mismatches: 3, Indels: 7
0.85 0.05 0.11
Matches are distributed among these distances:
39 5 0.09
40 1 0.02
41 8 0.15
42 33 0.60
43 8 0.15
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (41 bp):
TATTATAAATATATTATTTTAATAATTAAAAATATAATAAA
Found at i:75037 original size:43 final size:42
Alignment explanation
Indices: 74930--75051 Score: 128
Period size: 42 Copynumber: 2.9 Consensus size: 42
74920 TTTTATTTTT
* *
74930 ATATTATTAAA-ATA-TATTCTTTAATTATTAAAAATATAAAAC
1 ATATTA-TAAATATATTATT-TTTAATAATTTAAAATATAAAAC
74972 ATATTATATAATATATTA-TTTTAATAATTTAAAATATAATAA-
1 ATATTATA-AATATATTATTTTTAATAATTTAAAATATAA-AAC
*
75014 ATAATTATAAATATATTATTTTTAA-AATATTAATATAT
1 AT-ATTATAAATATATTATTTTTAATAAT-TTAAAATAT
75052 TCGGGACGGA
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
41 2 0.03
42 40 0.57
43 26 0.37
44 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (42 bp):
ATATTATAAATATATTATTTTTAATAATTTAAAATATAAAAC
Found at i:77723 original size:20 final size:20
Alignment explanation
Indices: 77638--77724 Score: 63
Period size: 20 Copynumber: 4.2 Consensus size: 20
77628 TCAATATTTA
77638 AATTTT-TTCTTAAATTAT-T
1 AATTTTATT-TTAAATTATGT
*
77657 TATTTTAATTTTAAATTAATAGT
1 AATTTT-ATTTTAAATT-AT-GT
* * *
77680 AATTTTAGTTTATATT-TTT
1 AATTTTATTTTAAATTATGT
*
77699 AAATTTTATTTTAGATTATGT
1 -AATTTTATTTTAAATTATGT
77720 AATTT
1 AATTT
77725 GAATTTATAA
Statistics
Matches: 53, Mismatches: 8, Indels: 13
0.72 0.11 0.18
Matches are distributed among these distances:
19 6 0.11
20 27 0.51
21 6 0.11
22 8 0.15
23 6 0.11
ACGTcount: A:0.33, C:0.01, G:0.05, T:0.61
Consensus pattern (20 bp):
AATTTTATTTTAAATTATGT
Found at i:78292 original size:26 final size:26
Alignment explanation
Indices: 78184--78286 Score: 188
Period size: 26 Copynumber: 4.0 Consensus size: 26
78174 CATTAAACTC
*
78184 GTTAAGATTTTGCTAGACTCGTGCTT
1 GTTAAGATTTTGCTGGACTCGTGCTT
*
78210 GTTAAGATTTTGTTGGACTCGTGCTT
1 GTTAAGATTTTGCTGGACTCGTGCTT
78236 GTTAAGATTTTGCTGGACTCGTGCTT
1 GTTAAGATTTTGCTGGACTCGTGCTT
78262 GTTAAGATTTTGCTGGACTCGTGCT
1 GTTAAGATTTTGCTGGACTCGTGCT
78287 CATTAAAAAA
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.17, C:0.15, G:0.26, T:0.43
Consensus pattern (26 bp):
GTTAAGATTTTGCTGGACTCGTGCTT
Found at i:79536 original size:12 final size:12
Alignment explanation
Indices: 79521--79546 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
79511 ACGGTTATAA
79521 TACATCATATTG
1 TACATCATATTG
79533 TACATCATATTG
1 TACATCATATTG
79545 TA
1 TA
79547 TAAACTCAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.15, G:0.08, T:0.42
Consensus pattern (12 bp):
TACATCATATTG
Found at i:81515 original size:81 final size:81
Alignment explanation
Indices: 81291--82035 Score: 1147
Period size: 81 Copynumber: 9.2 Consensus size: 81
81281 CATTGTTAAA
* * * * * * *
81291 CATTTATTC-TTTCCTCTAAAGGAATTTAACCTTTCGTCTAACTTGCATTATTGACACCTTTATG
1 CATTTAATCTTTTACTC-AAAGGCATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTG
*
81355 CCAAATGCACAGTTTGG
65 CCAAATGCACAGTTAGG
* *
81372 CATTTAATCTTTTACCCAAAGGCATTT-ACCTTTCATTTAACTAGCATGATTGACACCTTTCTGC
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGC
*
81436 CAAATGCACAGTTAGA
66 CAAATGCACAGTTAGG
* * *
81452 CGTTTAATCTTTTACTCAATGACATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGC
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGC
*
81517 CAAATGAACAGTTAGG
66 CAAATGCACAGTTAGG
81533 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGC
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGC
*
81598 CAAATACACAGTTAGG
66 CAAATGCACAGTTAGG
*
81614 CATTTAATCATTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGGA-ACCTTTCTG
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATT-GACACCTTTCTG
81678 CCAAATGCACAGTTAGG
65 CCAAATGCACAGTTAGG
* * **
81695 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGTCACATTTCTTT
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGC
* *
81760 CAAAGGCACAGTTAGA
66 CAAATGCACAGTTAGG
* * *
81776 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATAATTGGCACATTTCTGC
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGC
* *
81841 CAAATGTACAGTTAAG
66 CAAATGCACAGTTAGG
* *
81857 CATTTAATCTTTTACTCAAAGGCATTTAAACTTTCATCTAACTAGCATGATTGTCACCTTTCTGC
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGC
81922 CAAATGCACAGTTAGG
66 CAAATGCACAGTTAGG
* *
81938 CATTTAATCTGTTACTCAAAGACATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGC
1 CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGC
*
82003 C-AATGCACAATTAGG
66 CAAATGCACAGTTAGG
82018 CATTTAATCTTTTACTCA
1 CATTTAATCTTTTACTCA
82036 TAATATAAAT
Statistics
Matches: 608, Mismatches: 52, Indels: 9
0.91 0.08 0.01
Matches are distributed among these distances:
80 100 0.16
81 501 0.82
82 7 0.01
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (81 bp):
CATTTAATCTTTTACTCAAAGGCATTTAACCTTTCATCTAACTAGCATGATTGACACCTTTCTGC
CAAATGCACAGTTAGG
Found at i:82441 original size:22 final size:21
Alignment explanation
Indices: 82399--82453 Score: 67
Period size: 22 Copynumber: 2.6 Consensus size: 21
82389 TGGCTCAATA
82399 GTATCGATAC-CCATACCATG
1 GTATCGATACTCCATACCATG
* *
82419 GTATCGATACTTCTATACTATG
1 GTATCGATAC-TCCATACCATG
*
82441 GTACCGATACTCC
1 GTATCGATACTCC
82454 CTTTCAGTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 10 0.34
21 2 0.07
22 17 0.59
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (21 bp):
GTATCGATACTCCATACCATG
Found at i:84611 original size:18 final size:18
Alignment explanation
Indices: 84588--84624 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
84578 TAATCCCTTG
*
84588 TATTAGTTAGATGCAGTT
1 TATTAGTTAAATGCAGTT
84606 TATTAGTTAAATGCAGTT
1 TATTAGTTAAATGCAGTT
84624 T
1 T
84625 CTGTTCAGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.19, T:0.46
Consensus pattern (18 bp):
TATTAGTTAAATGCAGTT
Found at i:84996 original size:14 final size:14
Alignment explanation
Indices: 84977--85024 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
84967 TTATTATATT
84977 TTTATTTTATTTTA
1 TTTATTTTATTTTA
*
84991 TTTATTCTATTTTTA
1 TTTATTTTA-TTTTA
*
85006 TTATCATTTTATTTCA
1 TT-T-ATTTTATTTTA
85022 TTT
1 TTT
85025 CATGTTCAGA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
14 8 0.29
15 8 0.29
16 7 0.25
17 5 0.18
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (14 bp):
TTTATTTTATTTTA
Found at i:89835 original size:21 final size:21
Alignment explanation
Indices: 89802--89841 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
89792 AATCTTTGAG
*
89802 TTTGTTTCCCTTGAAACAAAT
1 TTTGTCTCCCTTGAAACAAAT
* *
89823 TTTGTCTCTCTTGAGACAA
1 TTTGTCTCCCTTGAAACAA
89842 TTTCTATTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.25, C:0.20, G:0.12, T:0.42
Consensus pattern (21 bp):
TTTGTCTCCCTTGAAACAAAT
Found at i:89853 original size:66 final size:66
Alignment explanation
Indices: 89670--89989 Score: 444
Period size: 66 Copynumber: 4.8 Consensus size: 66
89660 ACATTAAGAT
* * * * * *
89670 TGTTTCCTTTGAAGCAAAATTTTGTCTCTCTTAAGACAGTTTCTCTTTAAAGAAAAATCTTTGAG
1 TGTTTCCCTTGAAAC-AAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAG
89735 TC
65 TC
* *
89737 TATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGAGAATTTCTCTTGAAACAAAAATCTTTGAG
1 TGTTTCCCTTGAAACAAA-TTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAG
*
89802 TT
65 TC
*
89804 TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTATTGAAACAAAAATCTTTGAGT
1 TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAGT
89869 C
66 C
* * *
89870 TGTTTCCCTTGAATCAAATTTTGTCTCTCTTGAGACATTTTCTCTTTAAACAAAAATCTTTGAGT
1 TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAGT
*
89935 A
66 C
* * * *
89936 TGCTTCCCTTAAAACAAATTTTGTCT-TGCTTGAGACCATTTCTCTTCAAACAAA
1 TGTTTCCCTTGAAACAAATTTTGTCTCT-CTTGAGACAATTTCTCTTGAAACAAA
89990 TTATCCCTAA
Statistics
Matches: 227, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
65 1 0.00
66 155 0.68
67 71 0.31
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (66 bp):
TGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAATTTCTCTTGAAACAAAAATCTTTGAGT
C
Found at i:90454 original size:134 final size:133
Alignment explanation
Indices: 89992--90621 Score: 640
Period size: 134 Copynumber: 4.7 Consensus size: 133
89982 CAAACAAATT
* * * *
89992 ATCCCTAAAGATGGCCAACCGTTCTCAT-A-GTATAGGAACCATGTCATCCACCGACCATATCTC
1 ATCCCTAAAGATGGCCAACCATCCTCATCACG--TAGGAACCGTGTCATCCACCGACCAGATCTC
*** * ** * * * * *
90055 CTCATCACGTTTTA-ACAAATCACCCTTAGATAATCAGTCATCCTCATCACGTAGGAACCATGTT
64 CTCATCACGTAGGAGCCGCATCAACCTTAGATAATCA-ACATCCTCATCACATAGGAATCGTGTT
*
90119 ATCAAC
128 ATCATC
* * * * *
90125 ATCTCTAAATATGGCCAGCCATCTTCATCACGTAGGAACCGTGTCATCCACTGACCAGATCTCCT
1 ATCCCTAAAGATGGCCAACCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCT
* * * *
90190 CATCACGTAGGAGCCGCATCATCCTTAGATAACCAACTGTTCTCATCACATAGGAATCGTGTTAT
66 CATCACGTAGGAGCCGCATCAACCTTAGATAATCAAC-ATCCTCATCACATAGGAATCGTGTTAT
90255 C-TC
130 CATC
* * * * ** *
90258 ATCCCTAAAGATGGCTAGCCATCCTCATCAAGTAGGAATCGTGTCATCCATTGACTAGATCTCCT
1 ATCCCTAAAGATGGCCAACCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCT
* ** * * * * * *
90323 CATCACATAGGAGTTGCGTCAACCTTAGATAATCAGCAATTCTCATAACGTGGGAATCGTGTTAT
66 CATCACGTAGGAGCCGCATCAACCTTAGATAATCAAC-ATCCTCATCACATAGGAATCGTGTTAT
90388 CATC
130 CATC
*
90392 ATCCCTAAAGATGGCCAACTATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCT
1 ATCCCTAAAGATGGCCAACCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCT
* * * *
90457 CATAACGTAGGAGCCGCACCAACCTTAGATAATCAACCATCCTCATCACATAGAAATTGTGTTAT
66 CATCACGTAGGAGCCGCATCAACCTTAGATAATCAA-CATCCTCATCACATAGGAATCGTGTTAT
90522 CATC
130 CATC
* * ** * ** * * *
90526 ATCCCTAACGATAGCCAGA-TTTCCTCATCACATAGGAATTGTGTCACCCACCAACCATATCTCC
1 ATCCCTAAAGATGGCCA-ACCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCC
* *
90590 TCATCACGTATGAGCCGCATCATCCTTAGATA
65 TCATCACGTAGGAGCCGCATCAACCTTAGATA
90622 GCCAGACTTC
Statistics
Matches: 412, Mismatches: 78, Indels: 13
0.82 0.16 0.03
Matches are distributed among these distances:
133 174 0.42
134 235 0.57
135 3 0.01
ACGTcount: A:0.30, C:0.30, G:0.15, T:0.26
Consensus pattern (133 bp):
ATCCCTAAAGATGGCCAACCATCCTCATCACGTAGGAACCGTGTCATCCACCGACCAGATCTCCT
CATCACGTAGGAGCCGCATCAACCTTAGATAATCAACATCCTCATCACATAGGAATCGTGTTATC
ATC
Found at i:106693 original size:2 final size:2
Alignment explanation
Indices: 106684--106721 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
106674 TATCATTAAC
106684 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
106722 ATTGATTACT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:110179 original size:39 final size:39
Alignment explanation
Indices: 110119--110247 Score: 168
Period size: 39 Copynumber: 3.3 Consensus size: 39
110109 TCTATGACTT
* * * * *
110119 GTAAGACCTTACCGTAGGCTCCTCTACTTCGTGCACAAG
1 GTAAGTCCTTACCGAATGCTCCTCTGCTTTGTGCACAAG
*
110158 GTAAGTCCTTACCGAATGCTCCTTTGCTTTGTGCACAAG
1 GTAAGTCCTTACCGAATGCTCCTCTGCTTTGTGCACAAG
* * * *
110197 ATAAGCCCTTACCGCATGCTCCTCTGCTTTGTGCACAGG
1 GTAAGTCCTTACCGAATGCTCCTCTGCTTTGTGCACAAG
110236 GTAAGTCCTTAC
1 GTAAGTCCTTAC
110248 AGCAAACCGT
Statistics
Matches: 77, Mismatches: 13, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
39 77 1.00
ACGTcount: A:0.21, C:0.29, G:0.20, T:0.29
Consensus pattern (39 bp):
GTAAGTCCTTACCGAATGCTCCTCTGCTTTGTGCACAAG
Found at i:122871 original size:38 final size:41
Alignment explanation
Indices: 122786--122877 Score: 100
Period size: 43 Copynumber: 2.2 Consensus size: 41
122776 TATAAAATCT
* *
122786 CTTACCATTTATCCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCA-TTAT-TCATAAGCTCGTAAGCTTATTTTAGC-A-ATA
*
122831 CTTTCCATTATTCATAAGCTCGTAAGCTTA-TTT-GC-ATA
1 CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
122869 CTTACCATT
1 CTTACCATT
122878 TATCAACCAA
Statistics
Matches: 43, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
38 11 0.26
41 1 0.02
42 3 0.07
43 18 0.42
44 4 0.09
45 6 0.14
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (41 bp):
CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
Found at i:126045 original size:9 final size:10
Alignment explanation
Indices: 126036--126116 Score: 55
Period size: 9 Copynumber: 8.3 Consensus size: 10
126026 TTTACCCATT
126036 TTATTTA-T-
1 TTATTTATTA
126044 TTATTTATTA
1 TTATTTATTA
126054 TTA-TTATTA
1 TTATTTATTA
**
126063 TTA-TTAAAA
1 TTATTTATTA
*
126072 TTA-TAATTA
1 TTATTTATTA
* *
126081 TTATTAAATA
1 TTATTTATTA
126091 TTATTATATATA
1 TTATT-TAT-TA
126103 TTATATTATTA
1 TTAT-TTATTA
126114 TTA
1 TTA
126117 AATAATTATT
Statistics
Matches: 59, Mismatches: 8, Indels: 9
0.78 0.11 0.12
Matches are distributed among these distances:
8 7 0.12
9 23 0.39
10 13 0.22
11 6 0.10
12 9 0.15
13 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (10 bp):
TTATTTATTA
Found at i:126127 original size:3 final size:3
Alignment explanation
Indices: 126048--126116 Score: 70
Period size: 3 Copynumber: 23.0 Consensus size: 3
126038 ATTTATTTAT
** * *
126048 TTA TTA TTA TTA TTA TTA TTA AAA TTA TAA TTA TTA TTAA ATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
126094 TTA -TA TATA TTA -TA TTA TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA TTA
126117 AATAATTATT
Statistics
Matches: 54, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
2 4 0.07
3 45 0.83
4 5 0.09
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:127148 original size:2 final size:2
Alignment explanation
Indices: 127141--127172 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
127131 CGTTATCAGA
127141 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
127173 TTAGGTAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130139 original size:22 final size:20
Alignment explanation
Indices: 130105--130151 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 20
130095 TAGCAGTTTA
130105 TAACTCCTATAATTAACTCTTG
1 TAACTCCTATAATT-ACT-TTG
* *
130127 TAACTCTTGTAATTACTTTG
1 TAACTCCTATAATTACTTTG
130147 TAACT
1 TAACT
130152 GGTACAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 3 0.13
22 12 0.52
ACGTcount: A:0.30, C:0.19, G:0.06, T:0.45
Consensus pattern (20 bp):
TAACTCCTATAATTACTTTG
Found at i:139882 original size:50 final size:49
Alignment explanation
Indices: 139827--139921 Score: 136
Period size: 50 Copynumber: 1.9 Consensus size: 49
139817 CAGAAAATTC
* * *
139827 TTTTTCTTTTGATCTAACCTACCTTGAAGAAGTAGTAGAGAATATCTCCT
1 TTTTTCTTTTGATATAACCTACCCTGAAG-AGCAGTAGAGAATATCTCCT
* *
139877 TTTTTCTTTTGATATAGCCTACCCTGAAGAGCAGTGGAGAATATC
1 TTTTTCTTTTGATATAACCTACCCTGAAGAGCAGTAGAGAATATC
139922 ATTCTTTAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
49 14 0.35
50 26 0.65
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (49 bp):
TTTTTCTTTTGATATAACCTACCCTGAAGAGCAGTAGAGAATATCTCCT
Found at i:140216 original size:148 final size:149
Alignment explanation
Indices: 139948--140246 Score: 591
Period size: 148 Copynumber: 2.0 Consensus size: 149
139938 CTAAAATTAA
139948 TCTCACAAAAATTTGTGTTTTTTATCTTTCACTATTAGAAAAAACCCCTTTAATGACGTGCAATG
1 TCTCACAAAAATTTGTGTTTTTTATCTTTCACTATTAGAAAAAACCCCTTTAATGACGTGCAATG
140013 CGTGTCATCTATGTGTGTAGATGACACACAAATTCGTGTCATTGAAGCCACCGACATAAATATCA
66 CGTGTCATCTATGTGTGTAGATGACACACAAATTCGTGTCATTGAAGCCACCGACATAAATATCA
140078 GA-TATGCGCAATTGTGCG
131 GATTATGCGCAATTGTGCG
140096 TCTCACAAAAATTTGTGTTTTTTATCTTTCACTATTAGAAAAAACCCCTTTAATGACGTGCAATG
1 TCTCACAAAAATTTGTGTTTTTTATCTTTCACTATTAGAAAAAACCCCTTTAATGACGTGCAATG
140161 CGTGTCATCTATGTGTGTAGATGACACACAAATTCGTGTCATTGAAGCCACCGACATAAATATCA
66 CGTGTCATCTATGTGTGTAGATGACACACAAATTCGTGTCATTGAAGCCACCGACATAAATATCA
140226 GATTATGCGCAATTGTGCG
131 GATTATGCGCAATTGTGCG
140245 TC
1 TC
140247 ATAAATCTAT
Statistics
Matches: 150, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
148 132 0.88
149 18 0.12
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.33
Consensus pattern (149 bp):
TCTCACAAAAATTTGTGTTTTTTATCTTTCACTATTAGAAAAAACCCCTTTAATGACGTGCAATG
CGTGTCATCTATGTGTGTAGATGACACACAAATTCGTGTCATTGAAGCCACCGACATAAATATCA
GATTATGCGCAATTGTGCG
Found at i:144576 original size:23 final size:23
Alignment explanation
Indices: 144550--144601 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 23
144540 ATCTATATTC
144550 TTGTG-ACACATTTTTCTCTACTT
1 TTGTGAACAC-TTTTTCTCTACTT
144573 TTGTAGAACACTTTTTCTCTACTT
1 TTGT-GAACACTTTTTCTCTACTT
144597 TTGTG
1 TTGTG
144602 GCACGTTCCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
23 5 0.19
24 18 0.67
25 4 0.15
ACGTcount: A:0.17, C:0.19, G:0.12, T:0.52
Consensus pattern (23 bp):
TTGTGAACACTTTTTCTCTACTT
Found at i:156874 original size:15 final size:15
Alignment explanation
Indices: 156856--156892 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
156846 AAGGGTTGTT
*
156856 GTTGCCTCTGTTAAA
1 GTTGCCTCGGTTAAA
*
156871 GTTGCCTCGGTTGAA
1 GTTGCCTCGGTTAAA
156886 GTTGCCT
1 GTTGCCT
156893 ACATAATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.14, C:0.22, G:0.27, T:0.38
Consensus pattern (15 bp):
GTTGCCTCGGTTAAA
Found at i:164151 original size:14 final size:14
Alignment explanation
Indices: 164132--164158 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
164122 GTGATGGACT
164132 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
164146 ATGGTGATGGAAA
1 ATGGTGATGGAAA
164159 TAGTATCTTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.41, T:0.22
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:167910 original size:14 final size:15
Alignment explanation
Indices: 167874--167913 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
167864 ATAAGAATAG
* *
167874 ATGAAAGAAAAGGAA
1 ATGAAATAAAAGAAA
167889 ATGAAATAAAAGAAA
1 ATGAAATAAAAGAAA
167904 ATGAATATAA
1 ATGAA-ATAA
167914 CTTACAACTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 18 0.82
16 4 0.18
ACGTcount: A:0.68, C:0.00, G:0.17, T:0.15
Consensus pattern (15 bp):
ATGAAATAAAAGAAA
Found at i:168554 original size:13 final size:13
Alignment explanation
Indices: 168536--168582 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
168526 TAGTCGTGAA
168536 GGTGATGAACTAT
1 GGTGATGAACTAT
*
168549 GGTGATGGACTAT
1 GGTGATGAACTAT
**
168562 GGTGATGGAAAGAT
1 GGTGAT-GAACTAT
168576 GGTGATG
1 GGTGATG
168583 GAAATAATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 19 0.66
14 10 0.34
ACGTcount: A:0.28, C:0.04, G:0.40, T:0.28
Consensus pattern (13 bp):
GGTGATGAACTAT
Found at i:168579 original size:14 final size:14
Alignment explanation
Indices: 168547--168586 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
168537 GTGATGAACT
**
168547 ATGGTGATGG-ACT
1 ATGGTGATGGAAAG
168560 ATGGTGATGGAAAG
1 ATGGTGATGGAAAG
168574 ATGGTGATGGAAA
1 ATGGTGATGGAAA
168587 TAATATCTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 10 0.42
14 14 0.58
ACGTcount: A:0.33, C:0.03, G:0.40, T:0.25
Consensus pattern (14 bp):
ATGGTGATGGAAAG
Found at i:172987 original size:26 final size:26
Alignment explanation
Indices: 172942--173003 Score: 72
Period size: 26 Copynumber: 2.4 Consensus size: 26
172932 TTGGGTTACC
172942 TTGGTCA-TTTACACTCCAAGGACAT
1 TTGGTCATTTTACACTCCAAGGACAT
* * **
172967 TTGGTCATTTTACAGTTCAAGGGTAT
1 TTGGTCATTTTACACTCCAAGGACAT
*
172993 TTAGTCATTTT
1 TTGGTCATTTT
173004 CTTAATTCAA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
25 7 0.23
26 24 0.77
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (26 bp):
TTGGTCATTTTACACTCCAAGGACAT
Done.