Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004141.1 Hibiscus syriacus cultivar Beakdansim tig00009055_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: 143408
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Found at i:9859 original size:24 final size:24
Alignment explanation
Indices: 9823--9874 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
9813 CTGTAATTTT
*
9823 GAAACCTAAGTGAGCGATAAATCC
1 GAAACCTAAGTGACCGATAAATCC
* *
9847 GAAAGCTATGTGACCGATAAATCC
1 GAAACCTAAGTGACCGATAAATCC
9871 GAAA
1 GAAA
9875 AGAAGATGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.17
Consensus pattern (24 bp):
GAAACCTAAGTGACCGATAAATCC
Found at i:16217 original size:2 final size:2
Alignment explanation
Indices: 16210--16236 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16200 TCATATGGAG
16210 TA 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 TA T
16237 TTATCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:16365 original size:21 final size:20
Alignment explanation
Indices: 16332--16380 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
16322 TTTATTTTGT
* *
16332 TTTTTAAACAATTGTTTATTA
1 TTTTTAATCAATT-TTCATTA
*
16353 TTTTTAATTAATTTTCATTA
1 TTTTTAATCAATTTTCATTA
*
16373 GTTTTAAT
1 TTTTTAAT
16381 GAACTAATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 13 0.54
21 11 0.46
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.61
Consensus pattern (20 bp):
TTTTTAATCAATTTTCATTA
Found at i:21831 original size:4 final size:4
Alignment explanation
Indices: 21822--21852 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
21812 ATCCTCTTTT
21822 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTTG TTT
21853 ATTTTTCGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.23, T:0.77
Consensus pattern (4 bp):
TTTG
Found at i:23828 original size:41 final size:41
Alignment explanation
Indices: 23762--23890 Score: 213
Period size: 41 Copynumber: 3.1 Consensus size: 41
23752 CAGTAAACAA
*
23762 AGAATCAAACCAACTCGAATATCGACTAGTTTTTCGAGTAT
1 AGAACCAAACCAACTCGAATATCGACTAGTTTTTCGAGTAT
* **
23803 AGAACCAAACCGACTCGAACGTCGACTAGTTTTTCGAGTAT
1 AGAACCAAACCAACTCGAATATCGACTAGTTTTTCGAGTAT
*
23844 AGAACCAAACCAACTCGAATATCGACTAGTTTTTCGAGTAC
1 AGAACCAAACCAACTCGAATATCGACTAGTTTTTCGAGTAT
23885 AGAACC
1 AGAACC
23891 TTGGATGCTC
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 80 1.00
ACGTcount: A:0.36, C:0.23, G:0.16, T:0.25
Consensus pattern (41 bp):
AGAACCAAACCAACTCGAATATCGACTAGTTTTTCGAGTAT
Found at i:26354 original size:2 final size:2
Alignment explanation
Indices: 26347--26417 Score: 142
Period size: 2 Copynumber: 35.5 Consensus size: 2
26337 TTAGAAAGTA
26347 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
26389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26418 GCTAAAAACC
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27215 original size:21 final size:21
Alignment explanation
Indices: 27191--27232 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
27181 TGGGATAAGG
* * *
27191 AAAGGGTGGGAAGGGAGAGGA
1 AAAGGGAGGAAAGGAAGAGGA
27212 AAAGGGAGGAAAGGAAGAGGA
1 AAAGGGAGGAAAGGAAGAGGA
27233 GGAAGGGGAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.52, T:0.02
Consensus pattern (21 bp):
AAAGGGAGGAAAGGAAGAGGA
Found at i:33042 original size:41 final size:41
Alignment explanation
Indices: 32965--33042 Score: 129
Period size: 41 Copynumber: 1.9 Consensus size: 41
32955 TAAATTTTCA
*
32965 CAAAATTATATACAACGTTTAGTTTTGGTTATTTTTATTTT
1 CAAAATTATATACAACGTTTAGTTTTGGTTAGTTTTATTTT
* *
33006 CAAAATTATATATAACGTTTAGTTTTGGTTCGTTTTA
1 CAAAATTATATACAACGTTTAGTTTTGGTTAGTTTTA
33043 ATATTTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 34 1.00
ACGTcount: A:0.29, C:0.08, G:0.12, T:0.51
Consensus pattern (41 bp):
CAAAATTATATACAACGTTTAGTTTTGGTTAGTTTTATTTT
Found at i:33053 original size:41 final size:40
Alignment explanation
Indices: 32966--33051 Score: 118
Period size: 41 Copynumber: 2.1 Consensus size: 40
32956 AAATTTTCAC
*
32966 AAAATTATATACAACGTTTAGTTTTGGTTATTTTTATTTT
1 AAAATTATATACAACGTTTAGTTTTGGTTATTTTAATTTT
* *
33006 CAAAATTATATATAACGTTTAGTTTTGGTTCGTTTTAATATTT
1 -AAAATTATATACAACGTTTAGTTTTGGTT-ATTTTAAT-TTT
33049 AAA
1 AAA
33052 TTTTTATTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
41 28 0.70
42 9 0.22
43 3 0.08
ACGTcount: A:0.33, C:0.06, G:0.10, T:0.51
Consensus pattern (40 bp):
AAAATTATATACAACGTTTAGTTTTGGTTATTTTAATTTT
Found at i:39250 original size:2 final size:2
Alignment explanation
Indices: 39243--39282 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
39233 GGCTATACCC
39243 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
39283 TGGCAGCTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:39872 original size:208 final size:208
Alignment explanation
Indices: 39497--40028 Score: 737
Period size: 208 Copynumber: 2.5 Consensus size: 208
39487 TTTGATGCAC
* *** * *
39497 TTTCAATTGGTTAGTTGTTTTCTTCTTTTGAATGCACAAAAAAAATCTGGGAAATCTGCATTTTT
1 TTTCAATTTGTTAGTTGTTTTCTTCTTTTGAATGCA-TGCAAAATTCTGGGGAATCTGCATTTTT
* * *
39562 CTGTTTGGGATTGAGGAAAAGTTTTAACTTGAATATCAATTAGCTTGAATCACAATATGTTGCTG
65 -TGTTT-GGATTGAGGAAAAGTCTTAACTTGACTATCAATTAGCTTGAACCACAATATGTTGCTG
* * *
39627 ATTTAGTTGTGTTGTTTTCTGTTGCACGAGGAAAGTTATT-GATTTATAAGTTTAAGTCCCATGC
128 ATTTAGTTGTGTTGTTTTCTGTTACACGAGCAAAGTTATTAG-CTTATAAGTTTAAGTCCCATGC
*
39691 TTGTGTGTGTTGT-TGGT
192 TTGTGTGTGTT-TCTGAT
*
39708 TTTCAATTTGTTGGTTGTTTTCTTCTTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTT
1 TTTCAATTTGTTAGTTGTTTTCTTC-TTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTT
* * ** *
39773 TGTTT-GTTTGAGGGAAAGTCTTAACTTGACTATCAATTTTCTTGAACCACAATATTTTGCTGAT
65 TGTTTGGATTGAGGAAAAGTCTTAACTTGACTATCAATTAGCTTGAACCACAATATGTTGCTGAT
* * *
39837 TTAGTTGTGTTGTTTTCTTTTACATGAGCAAAGTTATTAGCTTATAAGTTTTAGTCCCATGCTTG
130 TTAGTTGTGTTGTTTTCTGTTACACGAGCAAAGTTATTAGCTTATAAGTTTAAGTCCCATGCTTG
39902 TGTGTGTTTCTGAT
195 TGTGTGTTTCTGAT
* * *
39916 TTTCAATTTGTTTGTTGTTTTCTTCTTTTGGATGCATGCAAAATTCTGGGGAATCTGCAATTTTC
1 TTTCAATTTGTTAGTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGC-ATTTTT
*
39981 TGTTTGGGATTGAGGAAAAGTCTTAACTTGACTATCATTTAGCTTGAA
65 TGTTT-GGATTGAGGAAAAGTCTTAACTTGACTATCAATTAGCTTGAA
40029 TCCAACTTAT
Statistics
Matches: 285, Mismatches: 30, Indels: 13
0.87 0.09 0.04
Matches are distributed among these distances:
207 33 0.12
208 153 0.54
209 1 0.00
210 41 0.14
211 46 0.16
212 11 0.04
ACGTcount: A:0.23, C:0.12, G:0.20, T:0.45
Consensus pattern (208 bp):
TTTCAATTTGTTAGTTGTTTTCTTCTTTTGAATGCATGCAAAATTCTGGGGAATCTGCATTTTTT
GTTTGGATTGAGGAAAAGTCTTAACTTGACTATCAATTAGCTTGAACCACAATATGTTGCTGATT
TAGTTGTGTTGTTTTCTGTTACACGAGCAAAGTTATTAGCTTATAAGTTTAAGTCCCATGCTTGT
GTGTGTTTCTGAT
Found at i:40154 original size:4 final size:4
Alignment explanation
Indices: 40147--40185 Score: 78
Period size: 4 Copynumber: 9.8 Consensus size: 4
40137 CCATAATATA
40147 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
40186 ATGATATTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 35 1.00
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:43805 original size:40 final size:40
Alignment explanation
Indices: 43745--43857 Score: 128
Period size: 39 Copynumber: 2.9 Consensus size: 40
43735 TTAGTTTTTT
* *
43745 TTTC-AAAACCGTTTTTTAAAAATATATATATTATAT-TGC
1 TTTCAAAAACCATTTTCTAAAAATATATATATTATATGT-C
*
43784 TTTCAAAAACCATTTTCTAAAAAT-TATATATTATATGTT
1 TTTCAAAAACCATTTTCTAAAAATATATATATTATATGTC
*
43823 TTTCAAAAA-TATTTTC-AAAAATTATACTATATTAT
1 TTTCAAAAACCATTTTCTAAAAA-TATA-TATATTAT
43858 TATATATACT
Statistics
Matches: 65, Mismatches: 4, Indels: 9
0.83 0.05 0.12
Matches are distributed among these distances:
37 5 0.08
38 7 0.11
39 27 0.42
40 26 0.40
ACGTcount: A:0.42, C:0.10, G:0.03, T:0.46
Consensus pattern (40 bp):
TTTCAAAAACCATTTTCTAAAAATATATATATTATATGTC
Found at i:48992 original size:30 final size:29
Alignment explanation
Indices: 48951--49009 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 29
48941 ATTTAAAGTA
*
48951 TTTTTGTCAAAATAGGTATCTAAAATATT
1 TTTTTGTCAAAATAGGTACCTAAAATATT
* *
48980 TTTTTGGTCAAAATTGGTACCTAAAGTATT
1 TTTTT-GTCAAAATAGGTACCTAAAATATT
49010 CAATTTTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.34, C:0.08, G:0.14, T:0.44
Consensus pattern (29 bp):
TTTTTGTCAAAATAGGTACCTAAAATATT
Found at i:49164 original size:31 final size:29
Alignment explanation
Indices: 49101--49186 Score: 84
Period size: 31 Copynumber: 2.9 Consensus size: 29
49091 TTTAGGTTCC
* ** **
49101 TATTTTGA-CATAAAATACTTTAGCCACC
1 TATTTTGACCAAAAAATACTTTAGGTATT
* *
49129 TATTTTGACTAAAAAGATAAGTTTAGGTATT
1 TATTTTGACCAAAAA-AT-ACTTTAGGTATT
49160 TATTTTGACCAAAAAATACTTTAGGTA
1 TATTTTGACCAAAAAATACTTTAGGTA
49187 CTTAAATGAA
Statistics
Matches: 46, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
28 8 0.17
29 13 0.28
30 4 0.09
31 21 0.46
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (29 bp):
TATTTTGACCAAAAAATACTTTAGGTATT
Found at i:57321 original size:21 final size:21
Alignment explanation
Indices: 57292--57344 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
57282 TTCAAATGTG
*
57292 ACAGATGAACTACCACGTCAAC
1 ACAG-TGAACTAACACGTCAAC
57314 ACAGTGAACTAACACGTCAAC
1 ACAGTGAACTAACACGTCAAC
57335 ACAGTGAACT
1 ACAGTGAACT
57345 GTCTTGTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 26 0.87
22 4 0.13
ACGTcount: A:0.42, C:0.28, G:0.15, T:0.15
Consensus pattern (21 bp):
ACAGTGAACTAACACGTCAAC
Found at i:59335 original size:19 final size:18
Alignment explanation
Indices: 59290--59335 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
59280 ATTTGGGTAG
*
59290 TTTATTTATTTTATTTTA
1 TTTATTTAATTTATTTTA
59308 TTT-TATTAATTTATTTTTA
1 TTTAT-TTAATTTA-TTTTA
59327 TTTATTTAA
1 TTTATTTAA
59336 AGATAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 10 0.42
19 12 0.50
20 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (18 bp):
TTTATTTAATTTATTTTA
Found at i:59662 original size:31 final size:32
Alignment explanation
Indices: 59615--59685 Score: 90
Period size: 32 Copynumber: 2.2 Consensus size: 32
59605 TAAGTGGAAA
* * *
59615 TAATCCCTAACGTTATCG-ATTCGTTCGATTT
1 TAATCCCTAACATTATCGAATCCGTTCAATTT
*
59646 TAATTCCTAACATTATCGAATCCGTTCAATTT
1 TAATCCCTAACATTATCGAATCCGTTCAATTT
*
59678 TAGTCCCT
1 TAATCCCT
59686 TAGCCATGTT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
31 16 0.48
32 17 0.52
ACGTcount: A:0.25, C:0.24, G:0.10, T:0.41
Consensus pattern (32 bp):
TAATCCCTAACATTATCGAATCCGTTCAATTT
Found at i:61478 original size:33 final size:34
Alignment explanation
Indices: 61414--61478 Score: 80
Period size: 33 Copynumber: 1.9 Consensus size: 34
61404 TTAATACTAT
*
61414 AATATATAAAATATATTAACTTAAACTATAATGA
1 AATATATAAAATATATTAACATAAACTATAATGA
* *
61448 AATATA-AAAATATGTTAAGAT-AACTCATAAT
1 AATATATAAAATATATTAACATAAACT-ATAAT
61479 AATATTTATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
32 4 0.15
33 17 0.63
34 6 0.22
ACGTcount: A:0.55, C:0.06, G:0.05, T:0.34
Consensus pattern (34 bp):
AATATATAAAATATATTAACATAAACTATAATGA
Found at i:61621 original size:17 final size:17
Alignment explanation
Indices: 61599--61641 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
61589 TAAAGAATAT
61599 TTAAAAAATATTAGTAA
1 TTAAAAAATATTAGTAA
*
61616 TTAAAATAA-ATTATTAA
1 TTAAAA-AATATTAGTAA
*
61633 TTAATAAAT
1 TTAAAAAAT
61642 TATTTTTTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
TTAAAAAATATTAGTAA
Found at i:62370 original size:16 final size:16
Alignment explanation
Indices: 62349--62383 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
62339 TAATGTTTGT
62349 GTCGACACCCAATTTC
1 GTCGACACCCAATTTC
62365 GTCGACACCCAATTTC
1 GTCGACACCCAATTTC
62381 GTC
1 GTC
62384 AGGAGACCGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.23, C:0.37, G:0.14, T:0.26
Consensus pattern (16 bp):
GTCGACACCCAATTTC
Found at i:62427 original size:18 final size:18
Alignment explanation
Indices: 62393--62446 Score: 69
Period size: 18 Copynumber: 3.1 Consensus size: 18
62383 CAGGAGACCG
62393 TTATTA-TTATTCT-TATT
1 TTATTATTTATT-TATATT
62410 TTATTATTTATTTATATT
1 TTATTATTTATTTATATT
62428 TATATT-TTTATTTATATT
1 T-TATTATTTATTTATATT
62446 T
1 T
62447 CATTTTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
17 7 0.21
18 23 0.68
19 4 0.12
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (18 bp):
TTATTATTTATTTATATT
Found at i:62443 original size:12 final size:12
Alignment explanation
Indices: 62408--62446 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
62398 ATTATTCTTA
*
62408 TTTTATTATTTAT
1 TTTTATT-TATAT
*
62421 TTATATTTATAT
1 TTTTATTTATAT
62433 TTTTATTTATAT
1 TTTTATTTATAT
62445 TT
1 TT
62447 CATTTTTTTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
12 17 0.74
13 6 0.26
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTATTTATAT
Found at i:62453 original size:18 final size:17
Alignment explanation
Indices: 62405--62454 Score: 66
Period size: 18 Copynumber: 2.9 Consensus size: 17
62395 ATTATTATTC
*
62405 TTAT-TTTATTATTTAT
1 TTATATTTATTTTTTAT
62421 TTATATTTATATTTTTAT
1 TTATATTTAT-TTTTTAT
62439 TTATATTTCATTTTTT
1 TTATATTT-ATTTTTT
62455 TGCATGCCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 4 0.13
17 5 0.17
18 19 0.63
19 2 0.07
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (17 bp):
TTATATTTATTTTTTAT
Found at i:63416 original size:3 final size:3
Alignment explanation
Indices: 63408--63462 Score: 101
Period size: 3 Copynumber: 18.3 Consensus size: 3
63398 GATAATAGTA
63408 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
63456 GAT AAT A
1 AAT AAT A
63463 GTAACAAAGA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:68279 original size:15 final size:15
Alignment explanation
Indices: 68259--68287 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
68249 ATCGTCCGAT
68259 GATGACGACGACGAC
1 GATGACGACGACGAC
68274 GATGACGACGACGA
1 GATGACGACGACGA
68288 TCATGAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.24, G:0.34, T:0.07
Consensus pattern (15 bp):
GATGACGACGACGAC
Found at i:68293 original size:15 final size:15
Alignment explanation
Indices: 68255--68293 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
68245 CATCATCGTC
*
68255 CGATGATGACGACGA
1 CGATCATGACGACGA
68270 CGA-CGATGACGACGA
1 CGATC-ATGACGACGA
68285 CGATCATGA
1 CGATCATGA
68294 AGAACTCGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 20 0.95
16 1 0.05
ACGTcount: A:0.33, C:0.23, G:0.31, T:0.13
Consensus pattern (15 bp):
CGATCATGACGACGA
Found at i:71765 original size:28 final size:28
Alignment explanation
Indices: 71734--71799 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
71724 AGGGAGAAAA
*
71734 ATAGTTAGTGGTATATCCTCGATCCTTT
1 ATAGTGAGTGGTATATCCTCGATCCTTT
71762 ATAGTGAGTGGTATATCCTCGATCCTTT
1 ATAGTGAGTGGTATATCCTCGATCCTTT
71790 ATAGTGAGTG
1 ATAGTGAGTG
71800 CATTGAGCTC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.23, C:0.15, G:0.23, T:0.39
Consensus pattern (28 bp):
ATAGTGAGTGGTATATCCTCGATCCTTT
Found at i:74436 original size:36 final size:36
Alignment explanation
Indices: 74389--74461 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
74379 TCATGCGTTC
74389 GTTCCGGATTAGTCTAGCCATTAGCTTAAAATTTAG
1 GTTCCGGATTAGTCTAGCCATTAGCTTAAAATTTAG
*
74425 GTTCCTGATTAGTCTAGCCATTAGCTTAAAATTTAG
1 GTTCCGGATTAGTCTAGCCATTAGCTTAAAATTTAG
74461 G
1 G
74462 GTGTTTACAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.37
Consensus pattern (36 bp):
GTTCCGGATTAGTCTAGCCATTAGCTTAAAATTTAG
Found at i:78976 original size:19 final size:19
Alignment explanation
Indices: 78921--78988 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
78911 AGCCCACTCA
*
78921 ATTAAAATAAATTATATTT
1 ATTAAAATAAATTATATTG
* *
78940 A-TAAAATATAA-AAAATTG
1 ATTAAAATA-AATTATATTG
78958 ATTAAAATAAATTATATTG
1 ATTAAAATAAATTATATTG
*
78977 ATAGAAAATAAA
1 AT-TAAAATAAA
78989 ATTTATTTTA
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
18 14 0.36
19 17 0.44
20 8 0.21
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
ATTAAAATAAATTATATTG
Found at i:78986 original size:20 final size:19
Alignment explanation
Indices: 78924--78988 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 19
78914 CCACTCAATT
*
78924 AAAATAAATTATATTTATA
1 AAAATAAATTATATTGATA
* *
78943 AAATATAAA--AAATTGATT
1 AAA-ATAAATTATATTGATA
78961 AAAATAAATTATATTGATA
1 AAAATAAATTATATTGATA
78980 GAAAATAAA
1 -AAAATAAA
78989 ATTTATTTTA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
17 5 0.14
18 9 0.24
19 10 0.27
20 13 0.35
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.34
Consensus pattern (19 bp):
AAAATAAATTATATTGATA
Found at i:85182 original size:2 final size:2
Alignment explanation
Indices: 85175--85205 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
85165 GTCGATAAAT
85175 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
85206 TTTAATTCGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:86913 original size:15 final size:15
Alignment explanation
Indices: 86893--86923 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
86883 ATTCATGATG
86893 TTAGTAAATTATATT
1 TTAGTAAATTATATT
86908 TTAGTAAATTATATT
1 TTAGTAAATTATATT
86923 T
1 T
86924 ATTAATTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
TTAGTAAATTATATT
Found at i:88442 original size:59 final size:60
Alignment explanation
Indices: 88322--88496 Score: 185
Period size: 59 Copynumber: 2.9 Consensus size: 60
88312 CGTCCTCGAT
* * * * * *
88322 CTATGATCCTCATT-TCAAATTAGTACCTAAACTTTTAAATATTTCAATTTCATCCCTAAA
1 CTATGATCTTCATTCT-AAATTAATCCCCAAACTTTTAAACATTTCAATTTCATCCCCAAA
* * * * *
88382 CTATTA-CTATCATTTTAAATTAATCCTCAGACTTTT-AACATTTCATTTTCATCCCCAAA
1 CTATGATCT-TCATTCTAAATTAATCCCCAAACTTTTAAACATTTCAATTTCATCCCCAAA
* *
88441 CTATGATCTTCATTCTAAATTAATCCCCAAACTTTTTGAACATTTCAATTTAATCC
1 CTATGATCTTCATTCTAAATTAATCCCCAAAC-TTTTAAACATTTCAATTTCATCC
88497 TAAATTATAT
Statistics
Matches: 94, Mismatches: 16, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
59 46 0.49
60 31 0.33
61 17 0.18
ACGTcount: A:0.33, C:0.23, G:0.03, T:0.41
Consensus pattern (60 bp):
CTATGATCTTCATTCTAAATTAATCCCCAAACTTTTAAACATTTCAATTTCATCCCCAAA
Found at i:91859 original size:21 final size:22
Alignment explanation
Indices: 91819--91859 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
91809 TAACAATTTG
* *
91819 ATAAGATTTAATATTTATTTAT
1 ATAAGATTTAATAATCATTTAT
91841 ATAA-ATTTAATAATCATTT
1 ATAAGATTTAATAATCATTT
91860 TTGTAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.51
Consensus pattern (22 bp):
ATAAGATTTAATAATCATTTAT
Found at i:94018 original size:255 final size:252
Alignment explanation
Indices: 93516--94024 Score: 707
Period size: 255 Copynumber: 2.0 Consensus size: 252
93506 ATGTCTACAA
* * *
93516 TGTCAACCATTCTCAAAACGATGCCTCTAGTTACATCAAAACACTTCAATATATTATCAGCCTCG
1 TGTCAACCACTCTCAAAACAATGCCTCTAGTTACATCAAAACACTTCAATATATAATCAGCCTCG
*
93581 TAAATCGAGTGAATACAAACACTTAGATGTGCAACAATGTCTGATGATGTTAAAAAACCAGTTTG
66 TAAATCGAGTGAATACAAACACTTAGATGTGCAAC-A-GTCTGAAGATGTTAAAAAACCAGTTTG
* *
93646 CTAGCTAACAATAGGCGGAAATCTGATCAATCCTAACAAACATACAAGAATGCCAAAGTGGTTCC
129 ATAGCTAACAATAGACGGAAATCTGATCAATCCTAACAAACATACAAGAATGCCAAAGTGGTTCC
* *
93711 ATCAGTCCAGAAATCCAAACCAAGTGTCGGATTCAACGGACAAACAAATCGAATTCAAG
194 ATCAGTCCAGAAATCCAAACCAAGTGTCGGACTCAAAGGACAAACAAATCGAATTCAAG
* * *
93770 TGTCAACCACTCTCAAAACAATGTCTCTAG-TAGCATCAAACCATTTCAATATATAATCAGCCTC
1 TGTCAACCACTCTCAAAACAATGCCTCTAGTTA-CATCAAAACACTTCAATATATAATCAGCCTC
* * * * * *
93834 GTAAAATCGAGTGAATACAATCACTTATATGTGTATC-GTCTTAAGATGTTCAAAAACCAGTTTG
65 GT-AAATCGAGTGAATACAAACACTTAGATGTGCAACAGTCTGAAGATGTTAAAAAACCAGTTTG
* * * * * *
93898 ATAGCTAACTATAGATGGAAAATTTGATCAATCCTAACAAACATACATGAATGCTAAAGTGGTTT
129 ATAGCTAACAATAGACGG-AAATCTGATCAATCCTAACAAACATACAAGAATGCCAAAGTGGTTC
** *
93963 CATCAGAGTCCAGAAATTGAATCCAAGTGTCGGACTCAAAGGACAAACAAATCGAATTCAAG
193 CATC--AGTCCAGAAATCCAAACCAAGTGTCGGACTCAAAGGACAAACAAATCGAATTCAAG
94025 CGTCTAGACG
Statistics
Matches: 224, Mismatches: 26, Indels: 9
0.86 0.10 0.03
Matches are distributed among these distances:
252 38 0.17
253 48 0.21
254 57 0.25
255 81 0.36
ACGTcount: A:0.39, C:0.21, G:0.15, T:0.25
Consensus pattern (252 bp):
TGTCAACCACTCTCAAAACAATGCCTCTAGTTACATCAAAACACTTCAATATATAATCAGCCTCG
TAAATCGAGTGAATACAAACACTTAGATGTGCAACAGTCTGAAGATGTTAAAAAACCAGTTTGAT
AGCTAACAATAGACGGAAATCTGATCAATCCTAACAAACATACAAGAATGCCAAAGTGGTTCCAT
CAGTCCAGAAATCCAAACCAAGTGTCGGACTCAAAGGACAAACAAATCGAATTCAAG
Found at i:105100 original size:18 final size:19
Alignment explanation
Indices: 105062--105100 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
105052 GGGTCACGAT
*
105062 AAATTTTCAAACACAAGTA
1 AAATTTTCAAACACAAATA
*
105081 AAATTTT-AAACAGAAATA
1 AAATTTTCAAACACAAATA
105099 AA
1 AA
105101 GTAAATTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.59, C:0.10, G:0.05, T:0.26
Consensus pattern (19 bp):
AAATTTTCAAACACAAATA
Found at i:116923 original size:25 final size:23
Alignment explanation
Indices: 116895--116941 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
116885 CGCTTCAAAA
116895 AATTAATAAAATAATATAAATATTT
1 AATTAAT-AAATAA-ATAAATATTT
**
116920 AATTTCTAAATAAATAAATATT
1 AATTAATAAATAAATAAATATT
116942 CATAGATAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 9 0.45
24 6 0.30
25 5 0.25
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AATTAATAAATAAATAAATATTT
Found at i:117914 original size:16 final size:16
Alignment explanation
Indices: 117890--117933 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
117880 ATCTATTTTA
*
117890 ATTACTATATTTATAT
1 ATTATTATATTTATAT
117906 ATTATTATATTT-TA-
1 ATTATTATATTTATAT
117920 ATTATT-T-TTTATAT
1 ATTATTATATTTATAT
117934 TTAATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
12 3 0.12
13 3 0.12
14 6 0.24
15 2 0.08
16 11 0.44
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTATTATATTTATAT
Found at i:117925 original size:14 final size:14
Alignment explanation
Indices: 117883--117925 Score: 59
Period size: 14 Copynumber: 2.9 Consensus size: 14
117873 ATAAAATATC
*
117883 TATTTTAATTACTA
1 TATTTTAATTATTA
117897 TATTTATATATTATTA
1 TATTT-TA-ATTATTA
117913 TATTTTAATTATT
1 TATTTTAATTATT
117926 TTTTATATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 11 0.42
15 4 0.15
16 11 0.42
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTTAATTATTA
Found at i:118402 original size:21 final size:22
Alignment explanation
Indices: 118361--118413 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 22
118351 ACTCTAAATT
*
118361 ATAAATCAT-AACCCCATAACC
1 ATAAATCTTAAACCCCATAACC
*
118382 ATAAATCTTAAACCCTA-AACC
1 ATAAATCTTAAACCCCATAACC
118403 -TAAAATCTTAA
1 AT-AAATCTTAA
118414 TTTAGGGTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
20 1 0.04
21 21 0.75
22 6 0.21
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (22 bp):
ATAAATCTTAAACCCCATAACC
Found at i:118702 original size:30 final size:30
Alignment explanation
Indices: 118668--118728 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
118658 TTAACGGCCG
118668 AGTGATAAAAAAACTCAATGCATTAAGTTC
1 AGTGATAAAAAAACTCAATGCATTAAGTTC
118698 AGTGATAAAAAAACTCAATGCATTAAGTTC
1 AGTGATAAAAAAACTCAATGCATTAAGTTC
118728 A
1 A
118729 TTGAAGAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (30 bp):
AGTGATAAAAAAACTCAATGCATTAAGTTC
Found at i:122892 original size:2 final size:2
Alignment explanation
Indices: 122887--122931 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
122877 TCTCTCTTGA
* *
122887 AT AT AT AT AC AT AC 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
122929 AT A
1 AT A
122932 CAGATAGAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:123979 original size:17 final size:17
Alignment explanation
Indices: 123957--123990 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
123947 TGGCCACAGC
123957 TTTGAACGGAAAGCGAT
1 TTTGAACGGAAAGCGAT
123974 TTTGAACGGAAAGCGAT
1 TTTGAACGGAAAGCGAT
123991 ACGGGAATAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.35, C:0.12, G:0.29, T:0.24
Consensus pattern (17 bp):
TTTGAACGGAAAGCGAT
Found at i:127285 original size:157 final size:153
Alignment explanation
Indices: 127005--127360 Score: 439
Period size: 157 Copynumber: 2.3 Consensus size: 153
126995 TTAGTCATTG
* * ** *
127005 ATTTTATTA-TTCTTTCAATTCATTCTTTATGTTAAGTCTGTTTTTCCCAAATTTAAACTACATG
1 ATTTT-TTATTTC-TTCAATTCA-TCTTTATTTTAAATCAATTTTTACCAAATTTAAACTACATG
* * *
127069 CTCCTAAACCATCGTAGAATACATATATACTTTTAATTCATCTTTTTGCTAACAATTTTTCTATT
63 CTCCTAAACCATCGTAGAATACATATATACTTTCAATTCACCTTTTTGATAACAATTTTT-TATT
*
127134 TTTCAATCTAGTCCCTCAATTTTTTATA
127 TTTCAATCTAGT-CCTCAATTTTTCATA
* * *
127162 ATTTTCTTATTTCTTCAATTCATCATTTATTTTAAATCAATTTTTACTAAATTTTAACTATATGC
1 ATTTT-TTATTTCTTCAATTCATC-TTTATTTTAAATCAATTTTTACCAAATTTAAACTACATGC
* *
127227 TCCTAAA-CATTGTAGAATACATATGTACTTTCAATTC-CCTTTTTGATAACAATTTTTTTATTT
64 TCCTAAACCATCGTAGAATACATATATACTTTCAATTCACCTTTTTGATAACAA-TTTTTTATTT
* *
127290 TTCAATTTAGTCCTCAATTTTTCATT
128 TTCAATCTAGTCCTCAATTTTTCATA
* * **
127316 ATTCTTTATTTCTTCAATTCATCCTTATTTTAAATCCTTTTTTAC
1 ATTTTTTATTTCTTCAATTCATCTTTATTTTAAATCAATTTTTAC
127361 AAAAAATGAA
Statistics
Matches: 175, Mismatches: 21, Indels: 11
0.85 0.10 0.05
Matches are distributed among these distances:
152 19 0.11
153 18 0.10
154 17 0.10
155 28 0.16
156 34 0.19
157 56 0.32
158 3 0.02
ACGTcount: A:0.28, C:0.17, G:0.04, T:0.51
Consensus pattern (153 bp):
ATTTTTTATTTCTTCAATTCATCTTTATTTTAAATCAATTTTTACCAAATTTAAACTACATGCTC
CTAAACCATCGTAGAATACATATATACTTTCAATTCACCTTTTTGATAACAATTTTTTATTTTTC
AATCTAGTCCTCAATTTTTCATA
Found at i:127422 original size:153 final size:154
Alignment explanation
Indices: 127083--127423 Score: 368
Period size: 152 Copynumber: 2.2 Consensus size: 154
127073 TAAACCATCG
* * *
127083 TAGAATACATATATACTTTTAATTCATCTTTTTGCTAACAATTTTTCTATTTTTCAATCTAGTCC
1 TAGAATACA-ATGTACTTTCAATTCA-CTTTTTGATAACAATTTTTCTATTTTTCAATCTAGTCC
* * * *
127148 CTCAATTTTTTATAATTTTCTTATTTCTTCAATTCATCATTTATTTTAAATCAATTTTTACTAAA
64 CTCAATTTTTCATAATTCTCTTATTTCTTCAATTCATCACTTATTTTAAATCAATTTTTACAAAA
** * * * * ***
127213 TTTTAACTATATGCTCCTAAACATTG
129 AATGAACCACATGCTCATAAACAAAA
* * *
127239 TAGAATACATATGTACTTTCAATTCCCTTTTTGATAACAATTTTTTTATTTTTCAATTTAGT-CC
1 TAGAATACA-ATGTACTTTCAATTCACTTTTTGATAACAATTTTTCTATTTTTCAATCTAGTCCC
* **
127303 TCAATTTTTCATTATTCT-TTATTTCTTCAATTCATC-CTTATTTTAAATCCTTTTTTACAAAAA
65 TCAATTTTTCATAATTCTCTTATTTCTTCAATTCATCACTTATTTTAAATCAATTTTTACAAAAA
*
127366 ATGAACCACATGCTCATATATCAAAA
130 ATGAACCACATGCTCATA-AACAAAA
*
127392 TGGAATAC-ATGTAAC-TTCAATTCTTACTTTTT
1 TAGAATACAATGT-ACTTTCAATTC--ACTTTTT
127424 TACTAAAAAT
Statistics
Matches: 156, Mismatches: 25, Indels: 11
0.81 0.13 0.06
Matches are distributed among these distances:
151 12 0.08
152 37 0.24
153 34 0.22
154 17 0.11
155 33 0.21
156 23 0.15
ACGTcount: A:0.30, C:0.17, G:0.04, T:0.49
Consensus pattern (154 bp):
TAGAATACAATGTACTTTCAATTCACTTTTTGATAACAATTTTTCTATTTTTCAATCTAGTCCCT
CAATTTTTCATAATTCTCTTATTTCTTCAATTCATCACTTATTTTAAATCAATTTTTACAAAAAA
TGAACCACATGCTCATAAACAAAA
Found at i:127581 original size:20 final size:20
Alignment explanation
Indices: 127556--127594 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
127546 TATTCTTATC
127556 AATATTTTACTCCCAAAATT
1 AATATTTTACTCCCAAAATT
*
127576 AATATTTTACTCTCAAAAT
1 AATATTTTACTCCCAAAAT
127595 ACTTTCTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (20 bp):
AATATTTTACTCCCAAAATT
Found at i:129102 original size:4 final size:4
Alignment explanation
Indices: 129093--129126 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
129083 GCAATTTGTA
129093 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
129127 GTGATTTGAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTAT
Found at i:130298 original size:31 final size:31
Alignment explanation
Indices: 130255--130313 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
130245 GTAAATAAGC
*
130255 TAAATTGGTAACTCAAACAAAACAGATGAGT
1 TAAATTGATAACTCAAACAAAACAGATGAGT
**
130286 TAAATTGATAACTCAAACATGACAGATG
1 TAAATTGATAACTCAAACAAAACAGATG
130314 GACTGTCACG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.47, C:0.14, G:0.15, T:0.24
Consensus pattern (31 bp):
TAAATTGATAACTCAAACAAAACAGATGAGT
Found at i:133206 original size:27 final size:27
Alignment explanation
Indices: 133175--133242 Score: 122
Period size: 27 Copynumber: 2.6 Consensus size: 27
133165 TCTATTTACA
133175 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
133202 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATGGTAAC
133229 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
133243 ATTCCTACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 9 0.22
27 32 0.78
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATGGTAAC
Found at i:136971 original size:27 final size:27
Alignment explanation
Indices: 136940--137007 Score: 113
Period size: 27 Copynumber: 2.6 Consensus size: 27
136930 TCTATTTACA
136940 AAATCATATCTCTATAGGAATAGTAAC
1 AAATCATATCTCTATAGGAATAGTAAC
*
136967 AAATCATATCTCTATAGGAATGGTAAC
1 AAATCATATCTCTATAGGAATAGTAAC
136994 AAATC--ATCTCTATA
1 AAATCATATCTCTATA
137008 ATTCCTACAG
Statistics
Matches: 40, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
25 9 0.22
27 31 0.77
ACGTcount: A:0.43, C:0.16, G:0.10, T:0.31
Consensus pattern (27 bp):
AAATCATATCTCTATAGGAATAGTAAC
Found at i:139434 original size:90 final size:91
Alignment explanation
Indices: 139266--139449 Score: 334
Period size: 90 Copynumber: 2.0 Consensus size: 91
139256 ATCTAAACTA
* *
139266 TCAGTTTTGGTCCGTTTTAGTATCTAAACTTTCAATTTTTTTCAAAAATATACCTAATGTTTAGT
1 TCAGTTTTGGTCCGTTTTAGTATCTAAACTTTCAATTTTTTTCAAAAATATACCGAATGTCTAGT
139331 TTTTGTTTTATTTTAGTACCCCATTG
66 TTTTGTTTTATTTTAGTACCCCATTG
*
139357 TCAGTTTTGGTCCGTTTTAGTATCTAAACTTT-TATTTTTTTCAAAAATATACCGAATGTCTAGT
1 TCAGTTTTGGTCCGTTTTAGTATCTAAACTTTCAATTTTTTTCAAAAATATACCGAATGTCTAGT
139421 TTTTGTTTTATTTTAGTACCCCATTG
66 TTTTGTTTTATTTTAGTACCCCATTG
139447 TCA
1 TCA
139450 AAATCTTAAC
Statistics
Matches: 90, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
90 58 0.64
91 32 0.36
ACGTcount: A:0.24, C:0.15, G:0.11, T:0.50
Consensus pattern (91 bp):
TCAGTTTTGGTCCGTTTTAGTATCTAAACTTTCAATTTTTTTCAAAAATATACCGAATGTCTAGT
TTTTGTTTTATTTTAGTACCCCATTG
Found at i:139468 original size:91 final size:91
Alignment explanation
Indices: 139277--139486 Score: 273
Period size: 90 Copynumber: 2.3 Consensus size: 91
139267 CAGTTTTGGT
* * *
139277 CCGTTTTAGTATCTAAACTTTCAATTTTTTTCAAAAATATACCTAATGTTTAGTTTTTGTTTTAT
1 CCGTCTTAGTATCTAAACTTTCAATTTTTTTCAAAAATATACCGAATGTCTAGTTTTTGTTTTAT
* * **
139342 TTTAGTACCCCATTGTCAGTTTTGGT
66 TTTAGTACCCCATTGTCAATCTTGAA
* *
139368 CCGTTTTAGTATCTAAACTTT-TATTTTTTTCAAAAATATACCGAATGTCTAGTTTTTGTTTTAT
1 CCGTCTTAGTATCTAAACTTTCAATTTTTTTCAAAAATATACCGAATGTCTAGTTTTTGTTTTAT
139432 TTTAGTACCCCATTGTCAAAATCTT-AA
66 TTTAGTACCCCATTGTC--AATCTTGAA
* *
139459 CGCG-CTTAGTACCTAAACTATCAATTTT
1 C-CGTCTTAGTATCTAAACTTTCAATTTT
139487 GATCCGTTTT
Statistics
Matches: 104, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
90 57 0.55
91 36 0.35
92 11 0.11
ACGTcount: A:0.27, C:0.16, G:0.10, T:0.47
Consensus pattern (91 bp):
CCGTCTTAGTATCTAAACTTTCAATTTTTTTCAAAAATATACCGAATGTCTAGTTTTTGTTTTAT
TTTAGTACCCCATTGTCAATCTTGAA
Found at i:141116 original size:11 final size:11
Alignment explanation
Indices: 141100--141131 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
141090 TAGCAACACT
141100 AATCAACCAAA
1 AATCAACCAAA
*
141111 AATCAACCACA
1 AATCAACCAAA
141122 AATCAACCAA
1 AATCAACCAA
141132 TGCAACCACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.59, C:0.31, G:0.00, T:0.09
Consensus pattern (11 bp):
AATCAACCAAA
Done.