Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006121.1 Hibiscus syriacus cultivar Beakdansim tig00014516_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: 67944
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:91 original size:55 final size:55
Alignment explanation
Indices: 22--338 Score: 404
Period size: 55 Copynumber: 5.8 Consensus size: 55
12 AGTGTACTAT
* * * **
22 AGGCACTATATGTGCAAATCCACATAATTTATCATGAGTTGATGAATAGTTGTAC
1 AGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGCCGTAC
* *
77 AGGCACTATGTGTGCAAATCCACAGAATTAATCATGAGTTGATGAATAGCCGTAT
1 AGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGCCGTAC
* * *
132 AGGAACTATGTGTGCAAATCCATCA-AATTCATCATCAGTTGATGAATAACCGTAC
1 AGGCACTATGTGTGCAAATCCA-CAGAATTCATCATGAGTTGATGAATAGCCGTAC
* * * * *
187 ATGCATTATGTGTGCAAATCCACGGAATTCGTCATAAGTTGATGAATAGCCGTAC
1 AGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGCCGTAC
* * * *
242 AGGCACTATGTGTGCAAATCCACGGAA-TCATCATGAGTTCATGAATAGTCGTAT
1 AGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGCCGTAC
* * * *
296 AGGCACTAGGTGTGCAAAACCACGGAATTTATCATGAGTTGAT
1 AGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGAT
339 AATTACCGTA
Statistics
Matches: 230, Mismatches: 29, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
54 48 0.21
55 180 0.78
56 2 0.01
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.28
Consensus pattern (55 bp):
AGGCACTATGTGTGCAAATCCACAGAATTCATCATGAGTTGATGAATAGCCGTAC
Found at i:5071 original size:69 final size:72
Alignment explanation
Indices: 4991--5138 Score: 203
Period size: 76 Copynumber: 2.0 Consensus size: 72
4981 TTTTTAAACA
* *
4991 TTATATTTTATC-TTT-GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGATA
1 TTATATTTTATCTTTTAGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATA
5054 TTAT-TT
66 TTATATT
*
5060 TTATATTTTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAGGATTTA
1 TTATATTTTATC----TTTTA-GTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTA
5125 GAATATTATATT
61 GAATATTATATT
5137 TT
1 TT
5139 TTAGGTATTT
Statistics
Matches: 68, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
69 12 0.18
74 3 0.04
76 49 0.72
77 4 0.06
ACGTcount: A:0.28, C:0.01, G:0.11, T:0.59
Consensus pattern (72 bp):
TTATATTTTATCTTTTAGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGATTTAGAATA
TTATATT
Found at i:9629 original size:23 final size:23
Alignment explanation
Indices: 9594--9662 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
9584 ACATCTTATA
*
9594 TGGCACTTCGGTGCATTTCTAC-
1 TGGCACTTAGGTGCATTTCTACG
*
9616 TCGGCACTTAGGTGCAATTCTACG
1 T-GGCACTTAGGTGCATTTCTACG
* *
9640 TGGCACTTAGATGCATTTATACG
1 TGGCACTTAGGTGCATTTCTACG
9663 AGTTGTGGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
22 1 0.03
23 38 0.95
24 1 0.03
ACGTcount: A:0.20, C:0.23, G:0.23, T:0.33
Consensus pattern (23 bp):
TGGCACTTAGGTGCATTTCTACG
Found at i:14425 original size:5 final size:5
Alignment explanation
Indices: 14417--14518 Score: 82
Period size: 5 Copynumber: 19.8 Consensus size: 5
14407 ATATTTTTGT
* * **
14417 TTTTA TTTTCA TTTTA TTTTTG TTTTA TTTTCA TTTTA TTTTTA GTGAA
1 TTTTA TTTT-A TTTTA -TTTTA TTTTA TTTT-A TTTTA -TTTTA TTTTA
* * *
14466 CTTTA TTTCA TTCTA -TTTA TTTTA TTTTGA -TTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA
14515 TTTT
1 TTTT
14519 TTCTTTGAAC
Statistics
Matches: 77, Mismatches: 13, Indels: 14
0.74 0.12 0.13
Matches are distributed among these distances:
4 4 0.05
5 53 0.69
6 20 0.26
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.73
Consensus pattern (5 bp):
TTTTA
Found at i:14436 original size:22 final size:22
Alignment explanation
Indices: 14408--14459 Score: 95
Period size: 22 Copynumber: 2.3 Consensus size: 22
14398 CATTTCGTTA
14408 TATTTTTGTTTTTATTTTCATTT
1 TATTTTTG-TTTTATTTTCATTT
14431 TATTTTTGTTTTATTTTCATTT
1 TATTTTTGTTTTATTTTCATTT
14453 TATTTTT
1 TATTTTT
14460 AGTGAACTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 21 0.72
23 8 0.28
ACGTcount: A:0.13, C:0.04, G:0.04, T:0.79
Consensus pattern (22 bp):
TATTTTTGTTTTATTTTCATTT
Found at i:16482 original size:62 final size:63
Alignment explanation
Indices: 16401--16520 Score: 199
Period size: 62 Copynumber: 1.9 Consensus size: 63
16391 TTTATATATT
*
16401 TTATCTTTATTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTAATTAGGATTTAGAATA
1 TTATATTTATTTTAGGTATTTTAGTTTAAATA-GTTTTAAGTATTTTAATTAGGATTTAGAATA
*
16464 TTATATTT-TTTTAGGTATTTTAGTTTAAATAGTTTTAAGTGTTTTAATTAGGATTTA
1 TTATATTTATTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTA
16521 ATATGCTTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
61 5 0.09
62 42 0.78
63 7 0.13
ACGTcount: A:0.29, C:0.01, G:0.14, T:0.56
Consensus pattern (63 bp):
TTATATTTATTTTAGGTATTTTAGTTTAAATAGTTTTAAGTATTTTAATTAGGATTTAGAATA
Found at i:16999 original size:28 final size:28
Alignment explanation
Indices: 16967--17022 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
16957 GAAGAATTGT
*
16967 TCTTGCAGTAACCGATGTGAATCTTGAA
1 TCTTGCAGTAACCGACGTGAATCTTGAA
*
16995 TCTTGTAGTAACCGACGTGAATCTTGAA
1 TCTTGCAGTAACCGACGTGAATCTTGAA
17023 GTAAAAATAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.21, T:0.32
Consensus pattern (28 bp):
TCTTGCAGTAACCGACGTGAATCTTGAA
Found at i:17168 original size:19 final size:18
Alignment explanation
Indices: 17117--17165 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
17107 AATCTCTTTA
17117 ATTTGTTTATTTAATTATT
1 ATTT-TTTATTTAATTATT
* *
17136 TTTCTTTTATTTAATTCTT
1 ATT-TTTTATTTAATTATT
17155 ATTTTTTATTT
1 ATTTTTTATTT
17166 TAAAAACAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
18 8 0.31
19 17 0.65
20 1 0.04
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:21227 original size:2 final size:2
Alignment explanation
Indices: 21222--21247 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
21212 TCTGAATTAT
21222 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
21248 ATATGAAGAG
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:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:23468 original size:20 final size:20
Alignment explanation
Indices: 23443--23494 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
23433 TTGGGAAAAC
23443 CGCAATGCGATACTTACTAT
1 CGCAATGCGATACTTACTAT
23463 CGCAATGCGATACTTACTAT
1 CGCAATGCGATACTTACTAT
23483 CGCAATGCGATA
1 CGCAATGCGATA
23495 ATACAAAATC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (20 bp):
CGCAATGCGATACTTACTAT
Found at i:23508 original size:61 final size:61
Alignment explanation
Indices: 23438--23554 Score: 144
Period size: 61 Copynumber: 1.9 Consensus size: 61
23428 GCGAATTGGG
* * * * * *
23438 AAAACCGCAATGCGATACTTACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAACCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
23499 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAACCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGAT
23555 TTACATAGCG
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 46 1.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAACCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:23551 original size:20 final size:20
Alignment explanation
Indices: 23503--23555 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
23493 TAATACAAAA
* *
23503 TCGCAACGAGATACTGACTT
1 TCGCAACGCGATTCTGACTT
23523 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
23543 TCGCAACGCGATT
1 TCGCAACGCGATT
23556 TACATAGCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.25, C:0.28, G:0.21, T:0.26
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:24135 original size:19 final size:19
Alignment explanation
Indices: 24111--24155 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
24101 GCAACGAGAT
*
24111 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
24130 AATCGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
24149 AATCGCA
1 AATCGCA
24156 TTGCGATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.49, C:0.27, G:0.16, T:0.09
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:24186 original size:19 final size:19
Alignment explanation
Indices: 24151--24334 Score: 156
Period size: 19 Copynumber: 10.1 Consensus size: 19
24141 GAAACCAAAA
*
24151 TCGCATTGCGA-TTTCATT
1 TCGCGTTGCGATTTTCATT
24169 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
24188 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
24207 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
* *
24227 TTGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
24243 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
24260 TCGCGTTGCGA--TTC-TC
1 TCGCGTTGCGATTTTCATT
**
24276 TCGC--TGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
24293 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
24313 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
24333 TC
1 TC
24335 AACCAAAAGA
Statistics
Matches: 136, Mismatches: 16, Indels: 27
0.76 0.09 0.15
Matches are distributed among these distances:
14 15 0.11
15 1 0.01
16 8 0.06
17 5 0.04
18 14 0.10
19 48 0.35
20 44 0.32
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:24220 original size:39 final size:38
Alignment explanation
Indices: 24151--24334 Score: 156
Period size: 33 Copynumber: 5.1 Consensus size: 38
24141 GAAACCAAAA
*
24151 TCGCATTGCGA-TTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
24188 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
* * * **
24227 TTGCGTTGCGATTGTC---T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* **
24260 TCGCGTTGCGA--TTC-TCTCGC--TGCGATAGTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
* *
24293 TCCGCGTTGCGATTCTCATTATCTCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCATT
24333 TC
1 TC
24335 AACCAAAAGA
Statistics
Matches: 118, Mismatches: 16, Indels: 24
0.75 0.10 0.15
Matches are distributed among these distances:
31 2 0.02
33 36 0.31
34 11 0.09
35 1 0.01
36 3 0.03
37 11 0.09
38 13 0.11
39 29 0.25
40 12 0.10
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.43
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:24311 original size:20 final size:20
Alignment explanation
Indices: 24288--24334 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
24278 GCTGCGATAG
24288 TCATTTCCGCGTTGCGATTC
1 TCATTTCCGCGTTGCGATTC
* *
24308 TCATTAT-CTCGTTGCGATTT
1 TCATT-TCCGCGTTGCGATTC
24328 TCATTTC
1 TCATTTC
24335 AACCAAAAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
19 1 0.04
20 21 0.91
21 1 0.04
ACGTcount: A:0.13, C:0.26, G:0.15, T:0.47
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATTC
Found at i:26416 original size:42 final size:42
Alignment explanation
Indices: 26336--26458 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
26326 GCCTGATTCG
* * * *
26336 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCC
* * *
26378 CCTATCATTCCTCGAGAGTCCCCTCCCACCATTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCC
** * ** *
26420 ATTGTCATCGTTAAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCATTCAAGAG
26459 CCCGATTCAC
Statistics
Matches: 65, Mismatches: 15, Indels: 2
0.79 0.18 0.02
Matches are distributed among these distances:
42 61 0.94
43 4 0.06
ACGTcount: A:0.24, C:0.36, G:0.16, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCATTCAAGAGGCC
Found at i:26457 original size:21 final size:20
Alignment explanation
Indices: 26398--26458 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 20
26388 CTCGAGAGTC
26398 CCCTCCCACCATTCAAGAGG
1 CCCTCCCACCATTCAAGAGG
* ** * * *
26418 CCATTGTCATCGTTAAAGAGG
1 CC-CTCCCACCATTCAAGAGG
26439 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCATTCAAGAG
26459 CCCGATTCAC
Statistics
Matches: 27, Mismatches: 12, Indels: 3
0.64 0.29 0.07
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.26, C:0.36, G:0.16, T:0.21
Consensus pattern (20 bp):
CCCTCCCACCATTCAAGAGG
Found at i:27836 original size:14 final size:14
Alignment explanation
Indices: 27817--27852 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
27807 ATTGTTTAAT
27817 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
27831 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
27845 TGATTTGT
1 TGATTTGT
27853 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:28037 original size:33 final size:33
Alignment explanation
Indices: 27994--28093 Score: 121
Period size: 33 Copynumber: 3.0 Consensus size: 33
27984 ACTCGAAATT
* *
27994 AAATTTGCGTTGCGATTTTCATTTCGCATTGTG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCG
*
28027 AAATTAGCGTTGTGATTTTCATTTCGCATTGCG
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCG
* ** *
28060 -ATTCTCTCGTTGCGATTTTCATTTCGCATAGCG
1 AAAT-TAGCGTTGCGATTTTCATTTCGCATTGCG
28093 A
1 A
28094 TAGTAATTTC
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.43
Consensus pattern (33 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCG
Found at i:30399 original size:12 final size:12
Alignment explanation
Indices: 30382--30406 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
30372 TCTTCGGGGA
30382 CTTTTTCTTCTT
1 CTTTTTCTTCTT
30394 CTTTTTCTTCTT
1 CTTTTTCTTCTT
30406 C
1 C
30407 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:31738 original size:19 final size:19
Alignment explanation
Indices: 31697--31764 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
31687 CATTTGACTA
31697 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
31713 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
31730 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
31749 TCGCATTACGATTTTC
1 TCGCATTGCGATTTTC
31765 TCGTTGCGAT
Statistics
Matches: 46, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
14 11 0.24
16 3 0.07
17 3 0.07
19 29 0.63
ACGTcount: A:0.15, C:0.22, G:0.16, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:33819 original size:20 final size:19
Alignment explanation
Indices: 33784--33850 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
33774 GAAACTTAAA
33784 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
33803 ATCGCAACGCAGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
33823 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
33842 ATCGCAACG
1 ATCGCAACG
33851 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:33858 original size:14 final size:14
Alignment explanation
Indices: 33839--33896 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
33829 ATGCGAAATG
33839 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
33853 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
33869 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
33885 AAAATCGCAACG
1 AAAATCGCAACG
33897 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:33881 original size:32 final size:33
Alignment explanation
Indices: 33823--33901 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
33813 AGAAATGGCT
33823 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
33856 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
33888 ATCGCAACGCGAAA
1 ATCGCAATGCGAAA
33902 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 29 0.64
33 16 0.36
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:33949 original size:14 final size:14
Alignment explanation
Indices: 33930--33987 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
33920 TTTCATTTCG
33930 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
33944 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
33960 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
33976 TGTTGCGATTTT
1 CGTTGCGATTTT
33988 CATTTCGCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 21 0.57
16 7 0.19
18 9 0.24
ACGTcount: A:0.10, C:0.16, G:0.24, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:33994 original size:33 final size:33
Alignment explanation
Indices: 33913--34003 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
33903 ACAAATCGCA
*
33913 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
33946 TTGCGA-TTTCATTTCGCATTGCGATTTTGTTG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
33978 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
34004 AGCCATTTCC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.18, G:0.22, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:34022 original size:20 final size:19
Alignment explanation
Indices: 33988--34042 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
33978 TTGCGATTTT
*
33988 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
34007 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
34027 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
34043 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:34550 original size:18 final size:18
Alignment explanation
Indices: 34524--34568 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
34514 GTCGATCAGA
*
34524 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
34542 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
34560 TGATGGCTC
1 TGATGGCTC
34569 CTGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:35907 original size:20 final size:20
Alignment explanation
Indices: 35882--35925 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
35872 AATAGTTTCT
35882 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
** *
35902 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACAC
35922 GAAA
1 GAAA
35926 CTAAAATTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.50, C:0.20, G:0.18, T:0.11
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:36471 original size:21 final size:21
Alignment explanation
Indices: 36438--36538 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
36428 TGCGAAAGTA
* * *
36438 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
36459 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
36479 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
36501 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
36522 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
36539 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:36494 original size:20 final size:20
Alignment explanation
Indices: 36400--36494 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
36390 GATTATGTAT
*
36400 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
36420 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGATAGTCAG
* ** * *
36440 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-TAGTCAG
*
36461 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
36481 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
36495 TTTCCCAATT
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 48 0.79
21 13 0.21
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:36513 original size:41 final size:41
Alignment explanation
Indices: 36422--36556 Score: 139
Period size: 41 Copynumber: 3.3 Consensus size: 41
36412 AAAGTCAGTA
* * * ** *
36422 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* *
36462 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
* **
36504 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTCCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGATTTTCCCAAT
36545 TCGCGTTGCGAT
1 TCGCGTTGCGAT
36557 TTACTTATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
40 3 0.04
41 74 0.94
42 2 0.03
ACGTcount: A:0.19, C:0.21, G:0.21, T:0.39
Consensus pattern (41 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCCAAT
Found at i:36548 original size:21 final size:20
Alignment explanation
Indices: 36483--36575 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
36473 ATAGTCAGTA
*
36483 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
36504 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
*
36524 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGA-TTTACCAAT
* **
36545 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACCAAT
36565 TCGCATTGCGA
1 TCGCATTGCGA
36576 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACCAAT
Found at i:36557 original size:41 final size:41
Alignment explanation
Indices: 36483--36575 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
36473 ATAGTCAGTA
36483 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
36524 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
36565 TCGCATTGCGA
1 TCGCATTGCGA
36576 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:37656 original size:2 final size:2
Alignment explanation
Indices: 37649--37681 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
37639 AATTTAGTGT
37649 TA TA TA 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 TA TA TA T
37682 TTTTTTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38550 original size:20 final size:22
Alignment explanation
Indices: 38525--38573 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
38515 TTAATTCTAA
*
38525 ATTTTACAT-TAAATT-TAATT
1 ATTTTAAATATAAATTATAATT
38545 ATTTTAAAATATAAATTATAATT
1 ATTTT-AAATATAAATTATAATT
38568 -TTTTAA
1 ATTTTAA
38574 TTTTTTAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 5 0.20
21 5 0.20
22 10 0.40
23 5 0.20
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
ATTTTAAATATAAATTATAATT
Found at i:38576 original size:28 final size:28
Alignment explanation
Indices: 38508--38577 Score: 72
Period size: 27 Copynumber: 2.5 Consensus size: 28
38498 AAATAGAAAT
* * * *
38508 TAATTTTTTAATTCTAAATTTTACATTA
1 TAATTTTTTAATTTTAAAATATAAATTA
*
38536 -AATTTAATT-ATTTTAAAATATAAATTA
1 TAATTT-TTTAATTTTAAAATATAAATTA
38563 TAATTTTTTAATTTT
1 TAATTTTTTAATTTT
38578 TTAAAAATAT
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
27 21 0.64
28 12 0.36
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (28 bp):
TAATTTTTTAATTTTAAAATATAAATTA
Found at i:41881 original size:20 final size:20
Alignment explanation
Indices: 41845--41891 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
41835 TATTCCCTGG
**
41845 TAATCTTTTATGCCCACTGA
1 TAATCTTTTATGCCCACCAA
**
41865 TAATCTTTTATTTCCACCAA
1 TAATCTTTTATGCCCACCAA
41885 TAATCTT
1 TAATCTT
41892 ACATTCCGTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.28, C:0.23, G:0.04, T:0.45
Consensus pattern (20 bp):
TAATCTTTTATGCCCACCAA
Found at i:42917 original size:2 final size:2
Alignment explanation
Indices: 42854--42905 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
42844 TGATTGAAAG
42854 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
42896 CT CT CT CT CT
1 CT CT CT CT CT
42906 ATTTTCCTCT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:46507 original size:17 final size:17
Alignment explanation
Indices: 46485--46524 Score: 62
Period size: 18 Copynumber: 2.3 Consensus size: 17
46475 TAATATTCGA
*
46485 AAAATTGGATCGAATAT
1 AAAATTGAATCGAATAT
46502 AAAATTTGAATCGAATAT
1 AAAA-TTGAATCGAATAT
46520 AAAAT
1 AAAAT
46525 CTTAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.53, C:0.05, G:0.12, T:0.30
Consensus pattern (17 bp):
AAAATTGAATCGAATAT
Found at i:59262 original size:2 final size:2
Alignment explanation
Indices: 59255--59314 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
59245 TGGTGATAAG
59255 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
59297 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
59315 TGTTCATTAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61209 original size:87 final size:86
Alignment explanation
Indices: 60981--61229 Score: 444
Period size: 86 Copynumber: 2.9 Consensus size: 86
60971 TATGTTATAT
*
60981 TATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATTTAATGTAATAGAT
1 TATTTAA-CGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
61046 AGCGCTTATATAATAAAATAGG
65 AGCGCTTATATAATAAAATAGG
61068 TATTTAACGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGATA
1 TATTTAACGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGATA
61133 GCGCTTATATAATAAAATAGG
66 GCGCTTATATAATAAAATAGG
* * *
61154 TATTTAACGGGAAATATTTTCAAGTACAATAACATATTAGGTAGCGCTTATATAATGTAATAGGT
1 TATTTAAC-GGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGAT
61219 AGCGCTTATAT
65 AGCGCTTATAT
61230 TGACCTATTT
Statistics
Matches: 157, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
86 86 0.55
87 71 0.45
ACGTcount: A:0.41, C:0.10, G:0.15, T:0.34
Consensus pattern (86 bp):
TATTTAACGGAAATATTATCAAGTACAATAACATATTAGGTAACGCTTATATAATGTAATAGATA
GCGCTTATATAATAAAATAGG
Found at i:61719 original size:259 final size:244
Alignment explanation
Indices: 61342--61856 Score: 798
Period size: 259 Copynumber: 2.0 Consensus size: 244
61332 CTTTTTATAA
*
61342 AAGTATCGACACTTTATGCTTGCACCTCGTTGGGCATTAATATTTCATTCTGGACAAAAATTTCG
1 AAGTATCGACACTTTATGCTTGCACCTCGTTGGGCATTAATATTTCATTCTGGACAAAAATATCG
* *
61407 ACACAAACTAAAAAAGTGTCGATACATGATTAGACATATTTTCTCATAAAACCGGTATAATTATA
66 ACACAAACTAAAAAAATGTCGATACATGATTAGACATATTCTCTCATAAAACCGGTATAATTATA
61472 CCGGTTTCATTGACCATTTACCTATTACACTATACTTATGGGTTTCGATGTTTTAGGGATCGATA
131 CCGGTTTCATTG---A---A-C-A-T----TATACTTATGGGTTTCGATGTTTTAGGGATCGATA
*
61537 TTTTTTTAATAAATGTATCGACACTTTTAAGGGTACACCTTTTTTGGCATTCATTCTAGACCGT
183 CTTTTTTAATAAATGTATCGACAC-TTTAAGGGTACACC-TTTTTGGCATTCATTCTAGACCGT
* **
61601 AAGTATCGACACTTTATGCTTGCATCTCGTT-GGTTTTAATATTTCATTCTGGACAAAAATATCG
1 AAGTATCGACACTTTATGCTTGCACCTCGTTGGGCATTAATATTTCATTCTGGACAAAAATATCG
* *
61665 ACACAAACTAAAAAAATGTCGATACCTGATTTAGACCTATTCTCTCATAAAACCGGTATAATTAT
66 ACACAAACTAAAAAAATGTCGATACATGA-TTAGACATATTCTCTCATAAAACCGGTATAATTAT
61730 ACCGGTTTCATTGAACATTATACTTATGGGTTTCGATGTTTTAGGGATCGATACTTTTTTAATAA
130 ACCGGTTTCATTGAACATTATACTTATGGGTTTCGATGTTTTAGGGATCGATACTTTTTTAATAA
61795 ATGTATCGACACTTTAAGGGTACACCTTTTTGGCATTCATTCTAGACCGT
195 ATGTATCGACACTTTAAGGGTACACCTTTTTGGCATTCATTCTAGACCGT
61845 AAGTATCGACAC
1 AAGTATCGACAC
61857 AACTTTAACA
Statistics
Matches: 246, Mismatches: 9, Indels: 17
0.90 0.03 0.06
Matches are distributed among these distances:
244 36 0.15
245 14 0.06
246 58 0.24
250 1 0.00
251 1 0.00
252 1 0.00
253 1 0.00
256 1 0.00
258 57 0.23
259 76 0.31
ACGTcount: A:0.30, C:0.18, G:0.15, T:0.37
Consensus pattern (244 bp):
AAGTATCGACACTTTATGCTTGCACCTCGTTGGGCATTAATATTTCATTCTGGACAAAAATATCG
ACACAAACTAAAAAAATGTCGATACATGATTAGACATATTCTCTCATAAAACCGGTATAATTATA
CCGGTTTCATTGAACATTATACTTATGGGTTTCGATGTTTTAGGGATCGATACTTTTTTAATAAA
TGTATCGACACTTTAAGGGTACACCTTTTTGGCATTCATTCTAGACCGT
Found at i:65136 original size:302 final size:302
Alignment explanation
Indices: 64576--65164 Score: 1056
Period size: 302 Copynumber: 2.0 Consensus size: 302
64566 TTAAAATTAG
*
64576 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* *
64641 ATACCGTTTATATTACAAAATTATCTATTACATTATAATTTTGGGTTCCGATGTGTAAATGTCGA
66 ATACCGTTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTACGATGTGTAAATGTCGA
*
64706 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
131 CACTTTTTGACAAGGTATAGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
64771 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAACCGGTATACTTATACAGGTTATAT
196 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAACCGGTATACTTATACAGGTTATAT
*
64836 TACAAAATTGTCTAGTACATTATAATTATGGACATAAAGTAC
261 TACAAAATTATCTAGTACATTATAATTATGGACATAAAGTAC
*
64878 CGACACAAAATTAAAAAGTGTTGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
64943 ATACCAG-TTATATTACAAAATTATCTATTACATTATAATTCTGGGTTACGATGTGTAAATGTCG
66 ATACC-GTTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTACGATGTGTAAATGTCG
65007 ACACTTTTTGACAAGGTATAGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATAT
130 ACACTTTTTGACAAGGTATAGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATAT
* * *
65072 TAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATAC-GGTTAT
195 TAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAAT-AAACCGGTATACTTATACAGGTTAT
*
65136 ATTACAAAATTATCTATTACATTATAATT
259 ATTACAAAATTATCTAGTACATTATAATT
65165 CTGGGTTCCG
Statistics
Matches: 275, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
302 257 0.93
303 18 0.07
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (302 bp):
CGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACCGTTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTACGATGTGTAAATGTCGA
CACTTTTTGACAAGGTATAGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAACCGGTATACTTATACAGGTTATAT
TACAAAATTATCTAGTACATTATAATTATGGACATAAAGTAC
Found at i:65317 original size:182 final size:183
Alignment explanation
Indices: 64864--65349 Score: 861
Period size: 181 Copynumber: 2.7 Consensus size: 183
64854 ATTATAATTA
* *
64864 TGGACATAAAGTACCGACACAAAATTAAAAAGTGTTGATATAGGTTGTAGACCTATTCGCTCATA
1 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
*
64929 AAACCGGTATATTTATACCAGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTACGA
66 AAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTACGA
*
64994 TGTGTAAATGTCGACACTTTTTGACAAGGTATAGACACATTTTTCTTCCATTC
131 TGTGTAAATGTCGACACTTTTTGACAAGGTATACACACATTTTTCTTCCATTC
65047 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
1 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
*
65112 AAACCGGTATATTTATA-CGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGA
66 AAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTACGA
*
65176 TGTGTAAATGTCGACACTTTTTGACAATGTAT-CACACATTTTTCTTCCATTC
131 TGTGTAAATGTCGACACTTTTTGACAAGGTATACACACATTTTTCTTCCATTC
* *
65228 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATA
1 TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
* *
65293 AAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACA-TATAATTCTGG
66 AAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGG
65350 ACATAAAGTA
Statistics
Matches: 292, Mismatches: 10, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
181 109 0.37
182 103 0.35
183 80 0.27
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (183 bp):
TGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATA
AAACCGGTATATTTATACCGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTACGA
TGTGTAAATGTCGACACTTTTTGACAAGGTATACACACATTTTTCTTCCATTC
Found at i:65394 original size:300 final size:301
Alignment explanation
Indices: 65043--65646 Score: 1088
Period size: 300 Copynumber: 2.0 Consensus size: 301
65033 TTTTTCTTCC
* *
65043 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACT
65108 CATAAAACCGGTATATTTATAC-GGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
66 CATAAAACCGGTATA-TTATACTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTT
*
65172 CCGATGTGTAAATGTCGACACTTTTTGACAATGTATC-ACACATTTTTCTTCCATTCTGGACATA
130 CCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATA
65236 AAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGT
195 AAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGT
65301 ATACTTATACCGGTTATATTACAAAATTATCTAGTACA-TATA
260 ATA-TTATACCGGTTATATTACAAAATTATCTAGTACATTATA
65343 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACT
65408 CATAAAACCGGTATATTATACTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTC
66 CATAAAACCGGTATATTATACTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTC
65473 CGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAA
131 CGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAA
* * *
65538 AGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACTTATTCGCTCATAAAACCGGTA
196 AGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTA
* * *
65603 TATTATGCCGGTTATATTATAAAATTATCTATTACATTATA
261 TATTATACCGGTTATATTACAAAATTATCTAGTACATTATA
65644 ATT
1 ATT
65647 ATGGGTTCCG
Statistics
Matches: 292, Mismatches: 9, Indels: 5
0.95 0.03 0.02
Matches are distributed among these distances:
299 6 0.02
300 187 0.64
301 99 0.34
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (301 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACT
CATAAAACCGGTATATTATACTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTC
CGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAA
AGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTA
TATTATACCGGTTATATTACAAAATTATCTAGTACATTATA
Found at i:65462 original size:119 final size:119
Alignment explanation
Indices: 65224--65468 Score: 420
Period size: 119 Copynumber: 2.1 Consensus size: 119
65214 TTTTTCTTCC
* *
65224 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCACT
65289 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATATA
*
65343 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACT
1 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCACT
* * *
65408 CATAAAACCGGTATA-TTATACTGGTTATATTACAAAATTATCTATTACATTATA
66 AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACA-TATA
65462 ATTCTGG
1 ATTCTGG
65469 GTTCCGATGT
Statistics
Matches: 119, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
118 32 0.27
119 87 0.73
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.32
Consensus pattern (119 bp):
ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGACATAGGTTGTAGACCTATTCACT
AATAAAACCGGTATACTTATACCGGTTATATTACAAAATTATCTAGTACATATA
Found at i:65602 original size:482 final size:484
Alignment explanation
Indices: 64576--65831 Score: 2202
Period size: 482 Copynumber: 2.6 Consensus size: 484
64566 TTAAAATTAG
64576 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* *
64641 ATACCGTTTATATTACAAAATTATCTATTACATTATAATTTTGGGTTCCGATGTGTAAATGTCGA
66 ATA-CGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGA
64706 CACTTTTTGACAAGGTATCGACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
130 CACTTTTTGACAAGGTATC-ACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
*
64771 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAAT-AAACCGGTATACTTATACAGGTTATA
194 AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATA
* *
64835 TTACAAAATTGTCTAGTACATTATAATTATGGACATAAAGTACCGACACAAAATTAAAAAGTGTT
259 TTACAAAATTATCTAGTACATTATAATTATGGACATAAAGTACCGACACAAAATTAAAAAGTGTC
*
64900 GATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTTATACCAGTTATATTACAAAATT
324 GATATAGGTTGTAGACCTATTCACTCATAAAACCGGTATATTTATACCAGTTATATTACAAAATT
64965 ATCTATTACATTATAATTCTGGGTTACGATGTGTAAATGTCGACACTTTTTGACAAGGTATAGAC
389 ATCTATTACATTATAATTCTGGGTTACGATGTGTAAATGTCGACACTTTTTGACAAGGTATAGAC
65030 ACATTTTTCTTCCATTCTGGACATAAAGTAC
454 ACATTTTTCTTCCATTCTGGACATAAAGTAC
65061 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
*
65126 ATACGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGAC
66 ATACGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGAC
*
65191 ACTTTTTGACAATGTATCACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATTAA
131 ACTTTTTGACAAGGTATCACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATTAA
65256 AAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATATT
196 AAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATATT
*
65321 ACAAAATTATCTAGTACA-TATAATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGA
261 ACAAAATTATCTAGTACATTATAATTATGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGA
**
65385 TATAGGTTGTAGACCTATTCACTCATAAAACCGGTATA-TTATACTGGTTATATTACAAAATTAT
326 TATAGGTTGTAGACCTATTCACTCATAAAACCGGTATATTTATACCAGTTATATTACAAAATTAT
* *
65449 CTATTACATTATAATTCTGGGTTCCGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACAC
391 CTATTACATTATAATTCTGGGTTACGATGTGTAAATGTCGACACTTTTTGACAAGGTATAGACAC
65514 ATTTTTCTTCCATTCTGGACATAAAGTAC
456 ATTTTTCTTCCATTCTGGACATAAAGTAC
*
65543 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACTTATTCGCTCATAAAACCGGTATA-TT
1 CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
* *
65607 ATGCCGGTTATATTATAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGA
66 AT-ACGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGA
* *
65672 CACTTTTTGACAAGGTATC-GACATATTTTCTTCCATTCTGCACATAAAGTACC-ACACAATATT
130 CACTTTTTGACAAGGTATCACACAT-TTTTCTTCCATTCTGGACATAAAGTACCGACACAATATT
* * * * *
65735 AAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAATC-GTATATTTATACCGATTAT
194 -AAAAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTAT
*
65799 ATTACAAAATTATCTATTACATTATAATTATGG
258 ATTACAAAATTATCTAGTACATTATAATTATGG
65832 GTTCTGATGT
Statistics
Matches: 740, Mismatches: 26, Indels: 13
0.95 0.03 0.02
Matches are distributed among these distances:
481 55 0.07
482 332 0.45
483 164 0.22
484 121 0.16
485 68 0.09
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Consensus pattern (484 bp):
CGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCTCATAAAACCGGTATATTT
ATACGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTCCGATGTGTAAATGTCGAC
ACTTTTTGACAAGGTATCACACATTTTTCTTCCATTCTGGACATAAAGTACCGACACAATATTAA
AAAGTGTCGACATAGGTTGTAGACCTATTCGCTAATAAAACCGGTATACTTATACCGGTTATATT
ACAAAATTATCTAGTACATTATAATTATGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGA
TATAGGTTGTAGACCTATTCACTCATAAAACCGGTATATTTATACCAGTTATATTACAAAATTAT
CTATTACATTATAATTCTGGGTTACGATGTGTAAATGTCGACACTTTTTGACAAGGTATAGACAC
ATTTTTCTTCCATTCTGGACATAAAGTAC
Found at i:65654 original size:182 final size:182
Alignment explanation
Indices: 65343--65924 Score: 910
Period size: 182 Copynumber: 3.2 Consensus size: 182
65333 AGTACATATA
* *
65343 ATTCTGGACATAAAGTACCGACACAAAATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCACT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
65408 CATAAAACCGGTATATTATACTGGTTATATTACAAAATTATCTATTACATTATAATTCTGGGTTC
66 CATAAAACCGGTATATTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTC
*
65473 CGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACACATTTTTCTTCC
131 CGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACATATTTTTCTTCC
*
65525 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACTTATTCGCT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
* *
65590 CATAAAACCGGTATATTATGCCGGTTATATTATAAAATTATCTATTACATTATAATTATGGGTTC
66 CATAAAACCGGTATATTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTC
65655 CGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACATA-TTTTCTTCC
131 CGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACATATTTTTCTTCC
*
65706 ATTCTGCACATAAAGTACC-ACACAATATTAAAAAAGTGTCGATATAGGTTGTAGACCTATTCGC
1 ATTCTGGACATAAAGTACCGACACAATATT-AAAAAGTGTCGATATAGGTTGTAGACCTATTCGC
* *
65770 TCATAAAATC-GTATATTTATACCGATTATATTACAAAATTATCTATTACATTATAATTATGGGT
65 TCATAAAACCGGTATA-TTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGT
* * * * *
65834 TCTGATGTTTTTTCAA--TCGACACTTATTGAAAAGG-ATCG--ATATTTTTCTTCC
129 TCCGATG---TGTAAATGTCGACACTTTTTGACAAGGTATCGACATATTTTTCTTCC
*
65886 ATTCTAGACATAAAGTACCGACACAATATTAAAAAGTGT
1 ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGT
65925 GAAAACTTTG
Statistics
Matches: 372, Mismatches: 21, Indels: 16
0.91 0.05 0.04
Matches are distributed among these distances:
179 3 0.01
180 50 0.13
181 134 0.36
182 181 0.49
184 4 0.01
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.35
Consensus pattern (182 bp):
ATTCTGGACATAAAGTACCGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCGCT
CATAAAACCGGTATATTATACCGGTTATATTACAAAATTATCTATTACATTATAATTATGGGTTC
CGATGTGTAAATGTCGACACTTTTTGACAAGGTATCGACATATTTTTCTTCC
Found at i:67129 original size:3 final size:3
Alignment explanation
Indices: 67121--67164 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
67111 ACTTGTTTGG
* *
67121 ATC ATC ATC ATC A-C ATC ATC ATC ATC ATC ATC GTC ATC TTC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
67165 GTCACTTCAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
2 2 0.06
3 34 0.94
ACGTcount: A:0.30, C:0.34, G:0.02, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:67165 original size:12 final size:12
Alignment explanation
Indices: 67136--67192 Score: 71
Period size: 12 Copynumber: 4.8 Consensus size: 12
67126 CATCATCACA
* *
67136 TCATCATCATCA
1 TCATCGTCATCT
67148 TCATCGTCATCT
1 TCATCGTCATCT
67160 TCATCGTCA-CT
1 TCATCGTCATCT
*
67171 TCATCGTCAGCT
1 TCATCGTCATCT
*
67183 TCATCTTCAT
1 TCATCGTCAT
67193 TGACCGCTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
11 11 0.28
12 29 0.73
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (12 bp):
TCATCGTCATCT
Found at i:67192 original size:6 final size:6
Alignment explanation
Indices: 67136--67192 Score: 53
Period size: 6 Copynumber: 9.7 Consensus size: 6
67126 CATCATCACA
* * * * * *
67136 TCATCA TCATCA TCATCG TCATCT TCATCG TCA-CT TCATCG TCAGCT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT
67183 TCATCT TCAT
1 TCATCT TCAT
67193 TGACCGCTTG
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
5 4 0.10
6 38 0.90
ACGTcount: A:0.21, C:0.33, G:0.07, T:0.39
Consensus pattern (6 bp):
TCATCT
Done.