Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003387.1 Hibiscus syriacus cultivar Beakdansim tig00007129_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: 119994
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:4756 original size:19 final size:20
Alignment explanation
Indices: 4696--4766 Score: 126
Period size: 20 Copynumber: 3.6 Consensus size: 20
4686 TAGTTGGAAA
4696 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
*
4716 TCGCGTTGCGATTTTTCATT
1 TCGCGTTGCGATTTTCCATT
4736 TCGCGTTGCGA-TTTCCATT
1 TCGCGTTGCGATTTTCCATT
4755 TCGCGTTGCGAT
1 TCGCGTTGCGAT
4767 AGTCTACAGT
Statistics
Matches: 48, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 18 0.38
20 30 0.62
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.44
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:4924 original size:17 final size:17
Alignment explanation
Indices: 4902--4934 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
4892 CGTATTACCA
4902 CGACCACGACCACGACC
1 CGACCACGACCACGACC
*
4919 CGACCACGACGACGAC
1 CGACCACGACCACGAC
4935 GGCGGCGGCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.30, C:0.48, G:0.21, T:0.00
Consensus pattern (17 bp):
CGACCACGACCACGACC
Found at i:4935 original size:6 final size:6
Alignment explanation
Indices: 4898--4934 Score: 58
Period size: 6 Copynumber: 6.3 Consensus size: 6
4888 GACACGTATT
*
4898 ACCACG ACCACG ACCACG ACC-CG ACCACG ACGACG AC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG AC
4935 GGCGGCGGCG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.32, C:0.49, G:0.19, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:5445 original size:6 final size:6
Alignment explanation
Indices: 5416--5474 Score: 72
Period size: 6 Copynumber: 10.5 Consensus size: 6
5406 TCGTCTCGTC
*
5416 TCGT-G TCGT-G TCGT-G TCATGG TCGTGG TCGTGG TCGTGG -CGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
*
5460 TCATGG TCGTGG TCG
1 TCGTGG TCGTGG TCG
5475 AAACGTGTTC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
5 18 0.38
6 30 0.62
ACGTcount: A:0.03, C:0.19, G:0.44, T:0.34
Consensus pattern (6 bp):
TCGTGG
Found at i:5447 original size:17 final size:18
Alignment explanation
Indices: 5434--5474 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
5424 TGTCGTGTCA
*
5434 TGGTCGTGGTCGTGGTCG
1 TGGTCGTGGTCATGGTCG
5452 TGG-CGTGGTCATGGTCG
1 TGGTCGTGGTCATGGTCG
5469 TGGTCG
1 TGGTCG
5475 AAACGTGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.02, C:0.17, G:0.49, T:0.32
Consensus pattern (18 bp):
TGGTCGTGGTCATGGTCG
Found at i:5453 original size:23 final size:23
Alignment explanation
Indices: 5416--5474 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
5406 TCGTCTCGTC
*
5416 TCGT-GTCGT-GTCGTGTCATGG
1 TCGTGGTCGTGGTCGTGGCATGG
*
5437 TCGTGGTCGTGGTCGTGGCGTGG
1 TCGTGGTCGTGGTCGTGGCATGG
*
5460 TCATGGTCGTGGTCG
1 TCGTGGTCGTGGTCG
5475 AAACGTGTTC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 4 0.12
22 5 0.15
23 24 0.73
ACGTcount: A:0.03, C:0.19, G:0.44, T:0.34
Consensus pattern (23 bp):
TCGTGGTCGTGGTCGTGGCATGG
Found at i:5481 original size:23 final size:23
Alignment explanation
Indices: 5434--5481 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
5424 TGTCGTGTCA
* ***
5434 TGGTCGTGGTCGTGGTCGTGGCG
1 TGGTCATGGTCGTGGTCGAAACG
5457 TGGTCATGGTCGTGGTCGAAACG
1 TGGTCATGGTCGTGGTCGAAACG
5480 TG
1 TG
5482 TTCAGTGGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.08, C:0.17, G:0.46, T:0.29
Consensus pattern (23 bp):
TGGTCATGGTCGTGGTCGAAACG
Found at i:7910 original size:26 final size:27
Alignment explanation
Indices: 7880--7930 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
7870 AGGTGTAGAC
*
7880 TGTTAAAG-AACATGCACGTGTATTGT
1 TGTTAAAGAAACATGCACATGTATTGT
*
7906 TGTTAAAGAAATATGCACATGTATT
1 TGTTAAAGAAACATGCACATGTATT
7931 AAGCAGTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.35, C:0.10, G:0.20, T:0.35
Consensus pattern (27 bp):
TGTTAAAGAAACATGCACATGTATTGT
Found at i:9565 original size:36 final size:36
Alignment explanation
Indices: 9518--9730 Score: 331
Period size: 36 Copynumber: 5.9 Consensus size: 36
9508 TGAATAAGAA
*
9518 GAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
*
9554 GAACGAAAGGAAGCATCGGCACTTTCGATTC-AAGAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAG-T
9590 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
* * *
9626 GAACGGAAGGAAGCATCCGCACTTTCGATTC-AAGAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAG-T
9662 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
* *
9698 GAACGGAAGGAAGCATCCGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCGGCACTTTCGATTCAA
9731 TTGTTCATCT
Statistics
Matches: 162, Mismatches: 11, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
35 6 0.04
36 150 0.93
37 6 0.04
ACGTcount: A:0.37, C:0.21, G:0.24, T:0.18
Consensus pattern (36 bp):
GAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGT
Found at i:9630 original size:72 final size:72
Alignment explanation
Indices: 9513--9730 Score: 409
Period size: 72 Copynumber: 3.0 Consensus size: 72
9503 GAAGGTGAAT
* * *
9513 AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGAAAGGAAGCATCGGCACTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
9578 TCGATTC
66 TCGATTC
9585 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
9650 TCGATTC
66 TCGATTC
9657 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
1 AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
9722 TCGATTC
66 TCGATTC
9729 AA
1 AA
9731 TTGTTCATCT
Statistics
Matches: 143, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
72 143 1.00
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (72 bp):
AAGAAGAACGAAAGGAAGCATCGGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
TCGATTC
Found at i:9828 original size:26 final size:26
Alignment explanation
Indices: 9780--9830 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
9770 GAATGTTAGA
*
9780 CTGTTAAAGAACATGCACGTGTATTG
1 CTGTTAAAGAACATGCACATGTATTG
*
9806 CTGTTAAAGAAATATG-ACATGTATT
1 CTGTTAAAG-AACATGCACATGTATT
9831 AAGCAGTTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.33
Consensus pattern (26 bp):
CTGTTAAAGAACATGCACATGTATTG
Found at i:13370 original size:10 final size:10
Alignment explanation
Indices: 13342--13385 Score: 58
Period size: 10 Copynumber: 4.7 Consensus size: 10
13332 ACACAAACTC
*
13342 AAAGCAAAAG
1 AAAGGAAAAG
13352 AAA--AAAAG
1 AAAGGAAAAG
13360 AAAGGAAAAG
1 AAAGGAAAAG
13370 AAAGGAAAA-
1 AAAGGAAAAG
13379 AAAGGAA
1 AAAGGAA
13386 GTCATGGTAG
Statistics
Matches: 32, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.25
9 7 0.22
10 17 0.53
ACGTcount: A:0.75, C:0.02, G:0.23, T:0.00
Consensus pattern (10 bp):
AAAGGAAAAG
Found at i:13685 original size:18 final size:19
Alignment explanation
Indices: 13657--13698 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
13647 AATATTATTT
13657 TAATAGATTTATAATTT-AA
1 TAATAGATTTAT-ATTTAAA
13676 TAAT-GATTTATATTTAAA
1 TAATAGATTTATATTTAAA
13694 TAATA
1 TAATA
13699 ATTAATTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
17 4 0.19
18 13 0.62
19 4 0.19
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (19 bp):
TAATAGATTTATATTTAAA
Found at i:13733 original size:29 final size:31
Alignment explanation
Indices: 13679--13736 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
13669 AATTTAATAA
13679 TGATTTATATTTAAATAATAATTAATTTTAG
1 TGATTTATATTTAAATAATAATTAATTTTAG
**
13710 TGATTTA-ATTTATTTAA-AATTAATTTT
1 TGATTTATATTTAAATAATAATTAATTTT
13737 TTTAAATTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 10 0.40
30 8 0.32
31 7 0.28
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (31 bp):
TGATTTATATTTAAATAATAATTAATTTTAG
Found at i:14727 original size:3 final size:3
Alignment explanation
Indices: 14711--14764 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
14701 GCTTCGTTCG
* *
14711 ATT A-T ATT -TT ATT ATT AAT ATT ATT ATT AAT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
14757 ATT ATT AT
1 ATT ATT AT
14765 CTCGGATTAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
2 4 0.09
3 41 0.91
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:15587 original size:81 final size:79
Alignment explanation
Indices: 15466--15634 Score: 248
Period size: 81 Copynumber: 2.1 Consensus size: 79
15456 ACTGAACCAA
* * *
15466 ATTAACCGATTTTGTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAAA
1 ATTAACCGATTTTGTTATTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCAAA
15531 TTTATTTGAAAATT
66 TTTATTTGAAAATT
* ** **
15545 ATTAACCGATTTTTTTTATTTAACCATTAATCGAACCAAAATTATTTTTCCGTTAATTGAACCCA
1 ATTAACCGA-TTTTGTTATTTAA-CATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCA
15610 AATTTATTTGAAAATT
64 AATTTATTTGAAAATT
15626 ATTAACCGA
1 ATTAACCGA
15635 ATTAACCGAA
Statistics
Matches: 80, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
79 9 0.11
80 11 0.14
81 60 0.75
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (79 bp):
ATTAACCGATTTTGTTATTTAACATTAATCGAACCAAAATTATTTGACCGTTAATCAAACCCAAA
TTTATTTGAAAATT
Found at i:15777 original size:95 final size:94
Alignment explanation
Indices: 15667--15853 Score: 261
Period size: 95 Copynumber: 2.0 Consensus size: 94
15657 TTTTTTAACC
* *
15667 GTTAATCGAACCGAAATTTATTTCAAAATTATTAACCGAA-ACAAATCAACCGATTATTTTTCTT
1 GTTAATCGAACCGAAATTTATTTCAAAATTATTAACCGAATA-AAAT-AAACGATT-TTTTTCCT
*
15731 TAACCATTAATCGAACTGAAA-TTATTTGACT
63 TAACCATTAATCGAACCGAAATTTATTTGACT
* * **
15762 GTTAATCGAATCGAAATTTATTTGAAAATTATTAACCGAATAAAATAAATTATTTTTTTCCTTAA
1 GTTAATCGAACCGAAATTTATTTCAAAATTATTAACCGAATAAAATAAACGATTTTTTTCCTTAA
*
15827 CCGTTAATCGAACCGAAATTTATTTGA
66 CCATTAATCGAACCGAAATTTATTTGA
15854 AAATTATTAA
Statistics
Matches: 82, Mismatches: 8, Indels: 5
0.86 0.08 0.05
Matches are distributed among these distances:
93 26 0.32
94 13 0.16
95 42 0.51
96 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.37
Consensus pattern (94 bp):
GTTAATCGAACCGAAATTTATTTCAAAATTATTAACCGAATAAAATAAACGATTTTTTTCCTTAA
CCATTAATCGAACCGAAATTTATTTGACT
Found at i:15779 original size:247 final size:239
Alignment explanation
Indices: 15355--16056 Score: 680
Period size: 247 Copynumber: 2.8 Consensus size: 239
15345 TTTTCTTTAA
* * * *
15355 CCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCAAAATTATTTGA
1 CCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCAAACCAAATAAAACAAAATTATTTAA
* * * * * *
15420 TCGTTAATTGAACCAAAATTTATTTGAAAATTATTAACTGAACCAAATTAACCGATTTTGTTCTT
66 CCGTTAATCGAACCAAAATTTATTTCAAAATTATTAACCGAAACAAATCAACCGATTTTGTTCTT
15485 TAACATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAAATTTATTTGAAAATTATTAA
131 TAACATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAAATTTATTTGAAAATTATTAA
15550 CCGATTTTTTTTATTTAACCATTAATCGAACCAAAATTATTTTT
196 CCGATTTTTTTTATTTAACCATTAATCGAACCAAAATTATTTTT
* * *
15594 CCGTTAATTGAACCCAAATTTATTTGAAAATTATTAACCGAATTAACCGAATAAAATAAATTATT
1 CCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACC--A--AACCAAATAAAACAAA--ATT
* *
15659 TTTTAACCGTTAATCGAACCGAAATTTATTTCAAAATTATTAACCGAAACAAATCAACCGATTAT
60 ATTTAACCGTTAATCGAACCAAAATTTATTTCAAAATTATTAACCGAAACAAATCAACCGATT-T
* * * * *
15724 TTTTCTTTAACCATTAATCGAACTGAAATTATTTGACTGTTAATCGAATCGAAATTTATTTGAAA
124 TGTTCTTTAA-CATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAAATTTATTTGAAA
* * * **
15789 ATTATTAACCGAATAAAATAAATTATTTTTTTCCTTAACCGTTAATCGAACCGAAATTTATTTGA
188 ATTATTAACCG------AT---TT-TTTTTAT--TTAACCATTAATCGAACC-AAAATTATTTTT
*** * * * ** ** * *
15854 AAATT-AT-TAA-CCAAATTGAATT-AACCGAATT-TTTTCTTTAACCATTAATCGAACCAAAAT
1 CCGTTAATCGAACCCAAATTTATTTGAA---AATTATTAAC-CAAACCA--AAT-AAAACAAAAT
* * * * *
15914 TATTTGACCGTTAATCTAACCAAAATGTATTTGAAAATTATTAACC-AAACCAAATTAACCGAAT
59 TATTTAACCGTTAATCGAACCAAAATTTATTTCAAAATTATTAACCGAAA-CAAATCAACCG-AT
* *
15978 TTT-TTCTTTAACATTAATCAAACCGAAATTATTTGACCGTTAATCGAACCGAAATTTATTTGAA
122 TTTGTTCTTTAACATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAAATTTATTTGAA
*
16042 AATTATTAATCGATT
187 AATTATTAACCGATT
16057 AATGATTAAT
Statistics
Matches: 382, Mismatches: 51, Indels: 54
0.78 0.10 0.11
Matches are distributed among these distances:
239 37 0.10
241 1 0.00
243 12 0.03
245 58 0.15
246 10 0.03
247 61 0.16
248 2 0.01
253 2 0.01
254 60 0.16
255 15 0.04
256 58 0.15
257 22 0.06
258 10 0.03
259 23 0.06
260 11 0.03
ACGTcount: A:0.40, C:0.15, G:0.08, T:0.37
Consensus pattern (239 bp):
CCGTTAATCGAACCCAAATTTATTTGAAAATTATTAACCAAACCAAATAAAACAAAATTATTTAA
CCGTTAATCGAACCAAAATTTATTTCAAAATTATTAACCGAAACAAATCAACCGATTTTGTTCTT
TAACATTAATCGAACCGAAATTATTTGACCGTTAATCAAACCGAAATTTATTTGAAAATTATTAA
CCGATTTTTTTTATTTAACCATTAATCGAACCAAAATTATTTTT
Found at i:15844 original size:67 final size:68
Alignment explanation
Indices: 15762--15920 Score: 205
Period size: 67 Copynumber: 2.4 Consensus size: 68
15752 TTATTTGACT
* * ** *
15762 GTTAATCGAATCGAAATTTATTTGAAAATTATTAACCGAA-TAAAATAAATTATTTTTTTCCTTA
1 GTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAATTAAAATAAACGAATTTTTTCCTTA
15826 ACC
66 ACC
* * * *
15829 GTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAATTGAATTAACCGAATTTTTTCTTTA
1 GTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAATTAAAATAAACGAATTTTTTCCTTA
15894 ACC
66 ACC
* *
15897 ATTAATCGAACC-AAAATTATTTGA
1 GTTAATCGAACCGAAATTTATTTGA
15921 CCGTTAATCT
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
67 49 0.61
68 31 0.39
ACGTcount: A:0.40, C:0.13, G:0.08, T:0.38
Consensus pattern (68 bp):
GTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAATTAAAATAAACGAATTTTTTCCTTA
ACC
Found at i:15929 original size:161 final size:163
Alignment explanation
Indices: 15545--15959 Score: 561
Period size: 166 Copynumber: 2.5 Consensus size: 163
15535 TTTGAAAATT
* ** * *
15545 ATTAACCGATTTTTTTTATTTAACCATTAATCGAACCAAAATTATTTTTCCGTTAATTGAACCCA
1 ATTAACCGA-TTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAA
15610 AATTTATTTGAAAATTATTAACCGAATTAACCGAATAAAATAAATTATTTTTTAACCGTTAATCG
65 AATTTATTTGAAAATTATTAACCGAATTAA-C-AATAAAATAAATTATTTTTTAACCGTTAATCG
15675 AACCGAAATTTATTTCAAAATTATTAACCGAAACAA
128 AACCGAAATTTATTTCAAAATTATTAACCGAAACAA
* ** * * *
15711 ATCAACCGATTATTTTTCTTTAACCATTAATCGAACTGAAATTATTTGACTGTTAATCGAATCGA
1 ATTAACCGATT-TTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAA
* *
15776 AATTTATTTGAAAATTATTAACCGAA-TAA-AAT-AAAT-TATTTTTTTCCTTAACCGTTAATCG
65 AATTTATTTGAAAATTATTAACCGAATTAACAATAAAATAAATTATTTT--TTAACCGTTAATCG
* **
15837 AACCGAAATTTATTTGAAAATTATTAACC-AAATTGA
128 AACCGAAATTTATTTCAAAATTATTAACCGAAA-CAA
* *
15873 ATTAACCGAATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCTAACCAAA
1 ATTAACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAAA
*
15938 ATGTATTTGAAAATTATTAACC
66 ATTTATTTGAAAATTATTAACC
15960 AAACCAAATT
Statistics
Matches: 221, Mismatches: 24, Indels: 13
0.86 0.09 0.05
Matches are distributed among these distances:
160 7 0.03
161 76 0.34
162 55 0.25
165 5 0.02
166 78 0.35
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (163 bp):
ATTAACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCGAACCAAA
ATTTATTTGAAAATTATTAACCGAATTAACAATAAAATAAATTATTTTTTAACCGTTAATCGAAC
CGAAATTTATTTCAAAATTATTAACCGAAACAA
Found at i:16004 original size:161 final size:162
Alignment explanation
Indices: 15545--16013 Score: 554
Period size: 161 Copynumber: 2.9 Consensus size: 162
15535 TTTGAAAATT
* ** *
15545 ATTAACCGATTTTTTTTATTTAACCATTAATCGAACCAAAATTATTTTTCCGTTAAT-TGAACCC
1 ATTAACCGA-TTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCT-AACCA
* * *
15609 AAATTTATTTGAAAATTATTAACCGAATTAACCGAATAAAATAAATTATTT-TTTAACCGTTAAT
64 AAATTTATTTGAAAATTATTAACC--A--AACCAAATTAAATAAATTTTTTCTTTAACCGTTAAT
*
15673 CGAACCGAAATTTATTTCAAAATTATTAACCGAAACAA
125 CGAACCGAAATTTATTTGAAAATTATTAACCGAAACAA
* ** * * * *
15711 ATCAACCGATTATTTTTCTTTAACCATTAATCGAACTGAAATTATTTGACTGTTAATCGAATCGA
1 ATTAACCGATT-TTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCTAACCAA
* * * * * *
15776 AATTTATTTGAAAATTATTAACCGAA-TAAAATAAATTATTTTTTTCCTTAACCGTTAATCGAAC
65 AATTTATTTGAAAATTATTAACCAAACCAAATTAAATAAATTTTTTCTTTAACCGTTAATCGAAC
**
15840 CGAAATTTATTTGAAAATTATTAACC-AAATTGA
130 CGAAATTTATTTGAAAATTATTAACCGAAA-CAA
*
15873 ATTAACCGAATTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCTAACCAAA
1 ATTAACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCTAACCAAA
* *** * *
15938 ATGTATTTGAAAATTATTAACCAAACCAAATTAACCGAATTTTTTCTTTAA-CATTAATCAAACC
66 ATTTATTTGAAAATTATTAACCAAACCAAATTAAATAAATTTTTTCTTTAACCGTTAATCGAACC
16002 GAAA-TTATTTGA
131 GAAATTTATTTGA
16014 CCGTTAATCG
Statistics
Matches: 257, Mismatches: 41, Indels: 16
0.82 0.13 0.05
Matches are distributed among these distances:
160 8 0.03
161 101 0.39
162 72 0.28
165 2 0.01
166 74 0.29
ACGTcount: A:0.40, C:0.15, G:0.07, T:0.38
Consensus pattern (162 bp):
ATTAACCGATTTTTTTCTTTAACCATTAATCGAACCAAAATTATTTGACCGTTAATCTAACCAAA
ATTTATTTGAAAATTATTAACCAAACCAAATTAAATAAATTTTTTCTTTAACCGTTAATCGAACC
GAAATTTATTTGAAAATTATTAACCGAAACAA
Found at i:16043 original size:93 final size:94
Alignment explanation
Indices: 15826--16050 Score: 371
Period size: 94 Copynumber: 2.4 Consensus size: 94
15816 TTTTTCCTTA
***
15826 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAATTGAATTAACCGAATTTTTTCT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCGAATTTTTTCT
*
15891 TTAACCATTAATCGAACCAAAATTATTTG
66 TTAACCATTAATCAAACCAAAATTATTTG
* * *
15920 ACCGTTAATCTAACCAAAATGTATTTGAAAATTATTAACCAAACCAAATTAACCGAATTTTTTCT
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCGAATTTTTTCT
*
15985 TTAA-CATTAATCAAACCGAAATTATTTG
66 TTAACCATTAATCAAACCAAAATTATTTG
16013 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAA
1 ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAA
16051 TCGATTAATG
Statistics
Matches: 120, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
93 57 0.47
94 63 0.52
ACGTcount: A:0.41, C:0.16, G:0.08, T:0.35
Consensus pattern (94 bp):
ACCGTTAATCGAACCGAAATTTATTTGAAAATTATTAACCAAACCAAATTAACCGAATTTTTTCT
TTAACCATTAATCAAACCAAAATTATTTG
Found at i:20688 original size:21 final size:21
Alignment explanation
Indices: 20652--20709 Score: 57
Period size: 21 Copynumber: 2.8 Consensus size: 21
20642 TGAGGTATCT
* *
20652 AATATTTAAAAATATTAAAA-
1 AATATTTAATATTATTAAAAG
20672 ATATATTTAATATTATTTAAAAG
1 A-ATATTTAATATTA-TTAAAAG
*
20695 AAT-TTTATTATTATT
1 AATATTTAATATTATT
20710 TTTTAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
20 3 0.09
21 20 0.62
22 8 0.25
23 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (21 bp):
AATATTTAATATTATTAAAAG
Found at i:22422 original size:18 final size:18
Alignment explanation
Indices: 22399--22434 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
22389 ATTTGGCATT
* *
22399 GACATTTTCATTTGCCAC
1 GACATTTCCATCTGCCAC
22417 GACATTTCCATCTGCCAC
1 GACATTTCCATCTGCCAC
22435 ATTGAAATCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.33, G:0.11, T:0.33
Consensus pattern (18 bp):
GACATTTCCATCTGCCAC
Found at i:32145 original size:20 final size:21
Alignment explanation
Indices: 32107--32159 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 21
32097 ATATTCAAGC
32107 GATGATTGCAGTAAAAAAAAG
1 GATGATTGCAGTAAAAAAAAG
* *
32128 GATGATTACAGT-AAAAAATG
1 GATGATTGCAGTAAAAAAAAG
*
32148 AATGATTGCAGT
1 GATGATTGCAGT
32160 GATGTGATTC
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.47, C:0.06, G:0.23, T:0.25
Consensus pattern (21 bp):
GATGATTGCAGTAAAAAAAAG
Found at i:40375 original size:30 final size:30
Alignment explanation
Indices: 40330--40405 Score: 89
Period size: 30 Copynumber: 2.5 Consensus size: 30
40320 TCTTTCAACA
* * * *
40330 TAAAATTTGAATCAATTAAGTATTCAAATC
1 TAAAAATTAAATCAATTAAATATGCAAATC
* *
40360 TAACAATTAAATCAATTAAATATGCGAATC
1 TAAAAATTAAATCAATTAAATATGCAAATC
*
40390 TAAAAATTGAATCAAT
1 TAAAAATTAAATCAAT
40406 CAAGCTCTCG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 38 1.00
ACGTcount: A:0.50, C:0.11, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAAAATTAAATCAATTAAATATGCAAATC
Found at i:41029 original size:13 final size:13
Alignment explanation
Indices: 41011--41041 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
41001 TTTTAAAAAT
41011 AAAATATTTTTTA
1 AAAATATTTTTTA
41024 AAAATATTTTTTA
1 AAAATATTTTTTA
41037 AAAAT
1 AAAAT
41042 CTGGACGTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
AAAATATTTTTTA
Found at i:42806 original size:34 final size:36
Alignment explanation
Indices: 42763--42864 Score: 156
Period size: 34 Copynumber: 2.9 Consensus size: 36
42753 TTTCGTCCTA
*
42763 TTAGGATTCAAACTCCTAAAAATATGATAGA-A-TT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGACATTT
42797 TTAGGATTCAAACTCCTAAAAATAGGATA-ACATTT
1 TTAGGATTCAAACTCCTAAAAATAGGATAGACATTT
42832 TGCTAGGATTCAAACTCCTAAAAATAGGATAGA
1 T--TAGGATTCAAACTCCTAAAAATAGGATAGA
42865 GTTCTACTAA
Statistics
Matches: 62, Mismatches: 1, Indels: 6
0.90 0.01 0.09
Matches are distributed among these distances:
33 1 0.02
34 29 0.47
35 3 0.05
37 28 0.45
38 1 0.02
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (36 bp):
TTAGGATTCAAACTCCTAAAAATAGGATAGACATTT
Found at i:43294 original size:18 final size:17
Alignment explanation
Indices: 43255--43297 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
43245 ATTATATGGA
43255 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
43271 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
43289 TATTATTAT
1 TATTATTAT
43298 ATGTGTATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:43600 original size:25 final size:25
Alignment explanation
Indices: 43555--43602 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
43545 TATATATATA
* *
43555 TTATTATTATTTTCGTTTTTTTTAT
1 TTATTATTATTATCATTTTTTTTAT
43580 TTATTATTATTAT-ATTATTTTTT
1 TTATTATTATTATCATT-TTTTTT
43603 TAAAAACCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 2 0.10
25 18 0.90
ACGTcount: A:0.21, C:0.02, G:0.02, T:0.75
Consensus pattern (25 bp):
TTATTATTATTATCATTTTTTTTAT
Found at i:43777 original size:38 final size:40
Alignment explanation
Indices: 43726--43805 Score: 112
Period size: 40 Copynumber: 2.0 Consensus size: 40
43716 AGTGAGAGGG
*
43726 TAGCTTTTCTATTTT-TAAATA-TTTGGTGTATATATATA
1 TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
*
43764 TAGCTTATT-TATTTTATTAATACTTTGATGTATATATATA
1 TAGCTT-TTCTATTTTATAAATACTTTGATGTATATATATA
43804 TA
1 TA
43806 TATATTTTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 12 0.32
39 7 0.19
40 18 0.49
ACGTcount: A:0.31, C:0.05, G:0.09, T:0.55
Consensus pattern (40 bp):
TAGCTTTTCTATTTTATAAATACTTTGATGTATATATATA
Found at i:43879 original size:29 final size:29
Alignment explanation
Indices: 43862--43940 Score: 140
Period size: 29 Copynumber: 2.7 Consensus size: 29
43852 CTTTACTATT
43862 TTTTTCCTTTATCTTATTTATTTATTTTA
1 TTTTTCCTTTATCTTATTTATTTATTTTA
43891 TTTTTCCTTTATCTTATTTATTTATTTTA
1 TTTTTCCTTTATCTTATTTATTTATTTTA
43920 TTTTTCCCTTTTATCTTATTT
1 TTTTT-CC-TTTATCTTATTT
43941 GTTTTCTTTA
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 34 0.71
30 2 0.04
31 12 0.25
ACGTcount: A:0.15, C:0.13, G:0.00, T:0.72
Consensus pattern (29 bp):
TTTTTCCTTTATCTTATTTATTTATTTTA
Found at i:43891 original size:13 final size:13
Alignment explanation
Indices: 43869--43922 Score: 54
Period size: 13 Copynumber: 3.9 Consensus size: 13
43859 ATTTTTTTCC
43869 TTTATCTTATTTA
1 TTTATCTTATTTA
* *
43882 TTTATTTTATTTTTCC
1 TTTATCTTA--TTT-A
43898 TTTATCTTATTTA
1 TTTATCTTATTTA
*
43911 TTTATTTTATTT
1 TTTATCTTATTT
43923 TTCCCTTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
13 19 0.58
14 3 0.09
15 3 0.09
16 8 0.24
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (13 bp):
TTTATCTTATTTA
Found at i:46999 original size:16 final size:17
Alignment explanation
Indices: 46952--46999 Score: 50
Period size: 16 Copynumber: 2.9 Consensus size: 17
46942 AGAAAAAAGA
46952 AAAGAAACAAA-A-AAAC
1 AAAGAAA-AAAGAGAAAC
46968 AAAGAAAAAAGAGAAAC
1 AAAGAAAAAAGAGAAAC
46985 -AAGAACAAAAG-GAAA
1 AAAGAA-AAAAGAGAAA
47000 AAACAAGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
15 3 0.10
16 17 0.59
17 9 0.31
ACGTcount: A:0.77, C:0.08, G:0.15, T:0.00
Consensus pattern (17 bp):
AAAGAAAAAAGAGAAAC
Found at i:47003 original size:19 final size:17
Alignment explanation
Indices: 46961--47013 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 17
46951 AAAAGAAACA
46961 AAAAAACAAAGAAAAAAG
1 AAAAAAC-AAGAAAAAAG
*
46979 -AGAAACAAGAACAAAAGG
1 AAAAAACAAGAA-AAAA-G
46997 AAAAAACAAGAATAAAA
1 AAAAAACAAGAA-AAAA
47014 AAGAAAGAGG
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
16 5 0.17
17 9 0.31
18 1 0.03
19 14 0.48
ACGTcount: A:0.77, C:0.08, G:0.13, T:0.02
Consensus pattern (17 bp):
AAAAAACAAGAAAAAAG
Found at i:48123 original size:18 final size:18
Alignment explanation
Indices: 48100--48135 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
48090 TCAACATCAA
* *
48100 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATATTTGG
48118 ATATTGAGGCATATTTGG
1 ATATTGAGGCATATTTGG
48136 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.22, C:0.06, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGAGGCATATTTGG
Found at i:48555 original size:36 final size:36
Alignment explanation
Indices: 48515--48583 Score: 84
Period size: 36 Copynumber: 1.9 Consensus size: 36
48505 AGACTTTGTC
* *
48515 TCACTTAGGACTGTTTTACTCAAAAGAAGATTTATT
1 TCACTCAGGACTGTTTTACTCAAAACAAGATTTATT
* * * *
48551 TCACTCATGATTGTTTTTCTTAAAACAAGATTT
1 TCACTCAGGACTGTTTTACTCAAAACAAGATTT
48584 GTCTCGCTTG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 27 1.00
ACGTcount: A:0.32, C:0.14, G:0.12, T:0.42
Consensus pattern (36 bp):
TCACTCAGGACTGTTTTACTCAAAACAAGATTTATT
Found at i:48603 original size:36 final size:36
Alignment explanation
Indices: 48563--48684 Score: 106
Period size: 36 Copynumber: 3.4 Consensus size: 36
48553 ACTCATGATT
* * *
48563 GTTTTTCTTAAAACAAGATTTGTCTCGCTTGAGACC
1 GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
* * * * *
48599 GTTT-TCACTAGAA-TAGTTTTGTCTCTCTTGAGACA
1 GTTTCTC-TTAAAACAAGATTTGTCTCCCTTGAGACA
* *
48634 GTTTCCCTTGAAACAA-ATTTTGTCTCCCTTGAGACA
1 GTTTCTCTTAAAACAAGA-TTTGTCTCCCTTGAGACA
*
48670 GTTTCTCTTGAAACA
1 GTTTCTCTTAAAACA
48685 TAAACATTGA
Statistics
Matches: 68, Mismatches: 14, Indels: 8
0.76 0.16 0.09
Matches are distributed among these distances:
35 27 0.40
36 41 0.60
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (36 bp):
GTTTCTCTTAAAACAAGATTTGTCTCCCTTGAGACA
Found at i:48747 original size:36 final size:36
Alignment explanation
Indices: 48700--48962 Score: 245
Period size: 36 Copynumber: 7.4 Consensus size: 36
48690 ATTGAAAACA
* * *
48700 TTTCCCTTGAAATAAATTTCGTCTCCCTTGAGATAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
*
48736 TTTCCCTTGAAACAAAATTTTGTCTCTCTTGAGACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* * *
48773 TTTCCCTTGAAATAAATTTTGTATCTCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
* * *
48809 TTTCCCTTGAAACAAA------ATAT-TTGA-ATATG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA-G
* * * *
48838 TTTTCTTTGAAACAAATTTCGTCTCCCTTAAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
** * * * *
48874 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAAACAG
1 TTTCCCTTGAAAC-AAATTTCGTCTCTCTTGAGACAG
* *
48911 TTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAG
1 TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
48947 TTTCCCTTGAAACAAA
1 TTTCCCTTGAAACAAA
48963 ATCTTTGAAT
Statistics
Matches: 185, Mismatches: 31, Indels: 22
0.78 0.13 0.09
Matches are distributed among these distances:
28 2 0.01
29 19 0.10
30 3 0.02
35 1 0.01
36 97 0.52
37 63 0.34
ACGTcount: A:0.28, C:0.19, G:0.13, T:0.40
Consensus pattern (36 bp):
TTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACAG
Found at i:48769 original size:138 final size:137
Alignment explanation
Indices: 48615--49025 Score: 534
Period size: 138 Copynumber: 3.0 Consensus size: 137
48605 ACTAGAATAG
* *
48615 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * *
48680 AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTCGTCTCCCTTGAGATAGTTTCCCTTG
66 AAACA-AAACATTGAATATATTTCCCTTGAAAAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTG
48745 AAACAAAA
130 AAACAAAA
* *
48753 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAATAAATTTTGTATCTCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * * * *
48818 AAACAAAATATTTGAATATGTTTTCTTTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCTTTTG
66 AAACAAAACA-TTGAATATATTTCCCTTGAAAAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTG
* * *
48883 GAACTAAG
130 AAACAAAA
* * * *
48891 TTTTGTCTCTCTTGAAACAGTTTCTCTTGAAACAAATTTCGTCTATCTTGAGACAGTTTCCCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
* * * * * *
48956 AAACAAAATCTTTGAATTTATTTCCCCTAAAAAAAATTTTGTCTCCCTTGAGACAGTTACTCTTG
66 AAACAAAA-CATTGAATATATTTCCCTTGAAAAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTG
49021 AAACA
130 AAACA
49026 CAAAATCTTC
Statistics
Matches: 232, Mismatches: 39, Indels: 4
0.84 0.14 0.01
Matches are distributed among these distances:
137 4 0.02
138 228 0.98
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (137 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTG
AAACAAAACATTGAATATATTTCCCTTGAAAAAAATTTCGTCTCCCTTGAGACAGTTTCTCTTGA
AACAAAA
Found at i:48848 original size:102 final size:102
Alignment explanation
Indices: 48742--48926 Score: 264
Period size: 102 Copynumber: 1.8 Consensus size: 102
48732 ATAGTTTCCC
* * * *
48742 TTGAAACAAAATTTTGTCTCTCTTGAGACAGTTTCCCTT-GAAATAAATTTTGTATCTCTTGAGA
1 TTGAAAC-AAATTTCGTCTCCCTTAAGACAGTTTCCCTTGGAAATAAATTTTGTATCTCTTGAAA
48806 CAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
65 CAGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
** * * *
48844 TTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAAAC
1 TTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCCCTTGGAAATAAATTTTGTATCTCTTGAAAC
*
48909 AGTTTCTCTTGAAACAAA
66 AGTTTCCCTTGAAACAAA
48927 TTTCGTCTAT
Statistics
Matches: 72, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
101 26 0.36
102 46 0.64
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.40
Consensus pattern (102 bp):
TTGAAACAAATTTCGTCTCCCTTAAGACAGTTTCCCTTGGAAATAAATTTTGTATCTCTTGAAAC
AGTTTCCCTTGAAACAAAATATTTGAATATGTTTTCT
Found at i:49054 original size:67 final size:68
Alignment explanation
Indices: 48920--49093 Score: 212
Period size: 68 Copynumber: 2.6 Consensus size: 68
48910 GTTTCTCTTG
* ** * **
48920 AAAC-AAATTTCGTCTATCTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTTCCC
1 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCC
48982 CTA
66 CTA
*
48985 AAA-AAAATTTTGTCTCCCTTGAGACAGTTACTCTTGAAACACAAAATCTTCAAATTTATTTCCC
1 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCC
*
49049 TTA
66 CTA
* * * *
49052 AAACATAATTTTGTTTCCCTTGAGACCGTTTCTCATGAAACA
1 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
49094 ACAGATATCT
Statistics
Matches: 92, Mismatches: 13, Indels: 5
0.84 0.12 0.05
Matches are distributed among these distances:
65 30 0.33
66 2 0.02
67 27 0.29
68 33 0.36
ACGTcount: A:0.33, C:0.21, G:0.09, T:0.36
Consensus pattern (68 bp):
AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACACAAAATCTTCAAATTTATTTCCC
CTA
Found at i:49930 original size:105 final size:105
Alignment explanation
Indices: 49698--50254 Score: 768
Period size: 105 Copynumber: 5.3 Consensus size: 105
49688 GCCATCCGCG
* * * * *
49698 ATTTCAACTCCACGACGGAGGATATCGTGGCAC-TCGAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTTC-AGACAACGCAAGTTCAACTTCACGACGA
* *
49762 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
62 AGGGACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
49807 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
49872 ACCGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
66 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
49912 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
49977 ACCGCTGCTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
50017 ATTTCAACTTCACAATGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* **
50082 ACGGCTGCTTGTCAACAA-AA-TT-TC-A-TTCAGATTCA
66 ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
* *
50117 ATTTCAACTTCACAACGAAGGATATTGGAC-TCGAGACAACACAAGTTCAACTTCACAACGAAGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTTC-AGACAACGCAAGTTCAACTTCACGACGAAGG
* * ** *
50181 GACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAGAGCCA
65 GACGGCTGCTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
* *
50223 ATTTCAACTTCACGACGGAGGATATTGGACTT
1 ATTTCAACTTCACAACGAAGGATATTGGACTT
50255 GGAACAATGC
Statistics
Matches: 409, Mismatches: 30, Indels: 20
0.89 0.07 0.04
Matches are distributed among these distances:
99 1 0.00
100 81 0.20
101 3 0.01
102 3 0.01
103 4 0.01
104 3 0.01
105 205 0.50
106 81 0.20
107 6 0.01
109 22 0.05
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACGGCTGCTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:50889 original size:37 final size:35
Alignment explanation
Indices: 50801--50936 Score: 150
Period size: 37 Copynumber: 3.8 Consensus size: 35
50791 TTTCGTCCTA
50801 CTAGGATTCAAACTCCTAAAAATAGGATATAATTT
1 CTAGGATTCAAACTCCTAAAAATAGGATATAATTT
*
50836 -TAAGATTCAAACTCCTAAAAATAGGATA-ACATTTT
1 CTAGGATTCAAACTCCTAAAAATAGGATATA-A-TTT
* *
50871 GCTAGGATTCAAACTCCTAAAAATAGGATAGAGTTCT
1 -CTAGGATTCAAACTCCTAAAAATAGGATATAATT-T
* * * *
50908 ACTAAGATTTAAATTCCTAAAGATAGGAT
1 -CTAGGATTCAAACTCCTAAAAATAGGAT
50937 CCACAAGCAC
Statistics
Matches: 87, Mismatches: 8, Indels: 10
0.83 0.08 0.10
Matches are distributed among these distances:
33 1 0.01
34 28 0.32
35 3 0.03
36 2 0.02
37 52 0.60
38 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.13, T:0.30
Consensus pattern (35 bp):
CTAGGATTCAAACTCCTAAAAATAGGATATAATTT
Found at i:51332 original size:18 final size:17
Alignment explanation
Indices: 51293--51335 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
51283 ATTATATGGA
51293 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
51309 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
51327 TATTATTAT
1 TATTATTAT
51336 ATGTATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:51390 original size:3 final size:3
Alignment explanation
Indices: 51378--51409 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
51368 TCTTTTACTA
51378 TAT T-T TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
51410 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 26 0.93
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TAT
Found at i:51414 original size:2 final size:2
Alignment explanation
Indices: 51407--51441 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
51397 TTATTATTAT
51407 TA 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 TA T
51442 CTTTAATATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54219 original size:31 final size:31
Alignment explanation
Indices: 54175--54241 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
54165 GGGGGAATGG
** *
54175 TCCCTAATGTTATCAATCCATTCGATTTTAA
1 TCCCTAACATTATCAATCCATTCAATTTTAA
* * *
54206 TCCCTAACATTATCGATCTATTCAATTTTAG
1 TCCCTAACATTATCAATCCATTCAATTTTAA
54237 TCCCT
1 TCCCT
54242 CAGCCATATC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.25, G:0.06, T:0.42
Consensus pattern (31 bp):
TCCCTAACATTATCAATCCATTCAATTTTAA
Found at i:70993 original size:21 final size:21
Alignment explanation
Indices: 70967--71036 Score: 70
Period size: 21 Copynumber: 3.3 Consensus size: 21
70957 AACTATTGTT
70967 GTTGTTTATGGGTGGTTTAGG
1 GTTGTTTATGGGTGGTTTAGG
* * * ** *
70988 GTTGTTTCTTGTTTATTT-GTT
1 GTTGTTTATGGGTGGTTTAG-G
71009 GTTGTTTATGGGTGGTTTAGG
1 GTTGTTTATGGGTGGTTTAGG
71030 GTTGTTT
1 GTTGTTT
71037 CTTGTTTATT
Statistics
Matches: 35, Mismatches: 12, Indels: 4
0.69 0.24 0.08
Matches are distributed among these distances:
20 1 0.03
21 33 0.94
22 1 0.03
ACGTcount: A:0.07, C:0.01, G:0.34, T:0.57
Consensus pattern (21 bp):
GTTGTTTATGGGTGGTTTAGG
Found at i:71021 original size:42 final size:42
Alignment explanation
Indices: 70962--71056 Score: 181
Period size: 42 Copynumber: 2.3 Consensus size: 42
70952 GGTTGAACTA
70962 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
1 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
71004 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
1 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
*
71046 TTGTTTTTGTT
1 TTGTTGTTGTT
71057 CAGGGTGTTT
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.06, C:0.02, G:0.29, T:0.62
Consensus pattern (42 bp):
TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
Found at i:71075 original size:42 final size:42
Alignment explanation
Indices: 70962--71081 Score: 154
Period size: 42 Copynumber: 2.9 Consensus size: 42
70952 GGTTGAACTA
* *
70962 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
1 TTGTTGTTGTTCATGGGTGGTTTAAGGTTGTTTCTTGTTTAT
* *
71004 TTGTTGTTGTTTATGGGTGGTTTAGGGTTGTTTCTTGTTTAT
1 TTGTTGTTGTTCATGGGTGGTTTAAGGTTGTTTCTTGTTTAT
* *
71046 TTGTTTTTGTTCA-GGGT-GTTTACCAGGTTGTATCTT
1 TTGTTGTTGTTCATGGGTGGTTTA--AGGTTGTTTCTT
71082 ATGTAATTTC
Statistics
Matches: 72, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
40 5 0.07
41 4 0.06
42 63 0.88
ACGTcount: A:0.08, C:0.05, G:0.29, T:0.57
Consensus pattern (42 bp):
TTGTTGTTGTTCATGGGTGGTTTAAGGTTGTTTCTTGTTTAT
Found at i:75549 original size:70 final size:70
Alignment explanation
Indices: 75460--75602 Score: 250
Period size: 70 Copynumber: 2.0 Consensus size: 70
75450 ATATAGCGGC
* *
75460 GTTTGTTGAACAAATGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTATCAGAAATACGCCGCAA
1 GTTTGTTGAACAAACGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTATCAGAAAAACGCCGCAA
75525 TAGGT
66 TAGGT
* *
75530 GTTTGTTGAACAAACGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTGTCAGAAAAATGCCGCAA
1 GTTTGTTGAACAAACGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTATCAGAAAAACGCCGCAA
75595 TAGGT
66 TAGGT
75600 GTT
1 GTT
75603 GATGTTTAGT
Statistics
Matches: 69, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
70 69 1.00
ACGTcount: A:0.27, C:0.14, G:0.25, T:0.34
Consensus pattern (70 bp):
GTTTGTTGAACAAACGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTATCAGAAAAACGCCGCAA
TAGGT
Found at i:75578 original size:43 final size:43
Alignment explanation
Indices: 75541--75705 Score: 116
Period size: 43 Copynumber: 3.8 Consensus size: 43
75531 TTTGTTGAAC
* * *
75541 AAACGTCGCAATAGGTTTTGTTATTTAGCGGCGTTTGTCAGAA
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAGAA
* * * ** *
75584 AAATGCCGCAATAGGTGTTGATGTTTAGTGGCGTTT-TACTTAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGT-CAGAA
* * * * * * ** *
75627 GAACGCCGTAGTAGGTGTTGATATTTTGCGGTGTTTTTCCCAC
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAGAA
* * * *
75670 AAACGCCGCAGTATGTGATGATTTTTAGCGGCGTTT
1 AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTT
75706 CTAGTATACA
Statistics
Matches: 94, Mismatches: 26, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
42 1 0.01
43 92 0.98
44 1 0.01
ACGTcount: A:0.22, C:0.16, G:0.27, T:0.36
Consensus pattern (43 bp):
AAACGCCGCAATAGGTGTTGATATTTAGCGGCGTTTGTCAGAA
Found at i:75755 original size:44 final size:44
Alignment explanation
Indices: 75701--75857 Score: 214
Period size: 44 Copynumber: 3.6 Consensus size: 44
75691 TTTTTAGCGG
75701 CGTTTCTAGTATACAAACGCCGCTAAATGT-TCGGTATATTGCGA
1 CGTTTCTAGTATACAAACGCCGCTAAATGTAT-GGTATATTGCGA
* *
75745 CGTTTCTAGTATACAAACGCCGCTAAATATATGGTATATTGTGA
1 CGTTTCTAGTATACAAACGCCGCTAAATGTATGGTATATTGCGA
* * *
75789 CGTTTCTAGTATACAAACGCTGTTAAATGTATGGTATATTGCGG
1 CGTTTCTAGTATACAAACGCCGCTAAATGTATGGTATATTGCGA
* *
75833 CATTT-T--TTTACAAACGCCGCTAAAT
1 CGTTTCTAGTATACAAACGCCGCTAAAT
75858 AACACATAAT
Statistics
Matches: 101, Mismatches: 11, Indels: 5
0.86 0.09 0.04
Matches are distributed among these distances:
41 16 0.16
43 1 0.01
44 83 0.82
45 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.34
Consensus pattern (44 bp):
CGTTTCTAGTATACAAACGCCGCTAAATGTATGGTATATTGCGA
Found at i:76217 original size:21 final size:21
Alignment explanation
Indices: 76173--76243 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
76163 TTGTTGATAT
* *
76173 GCTGCTTCTCTCTGTACTGT-C
1 GCTGCTTCTCTCTATGCT-TCC
* *
76194 GCTGCTTCTTTCTCTGCTTCC
1 GCTGCTTCTCTCTATGCTTCC
* *
76215 GCTACTGCTCTCTATGCTTCC
1 GCTGCTTCTCTCTATGCTTCC
76236 -CTTGCTTC
1 GC-TGCTTC
76244 ATTTTCCGCT
Statistics
Matches: 39, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
20 2 0.05
21 37 0.95
ACGTcount: A:0.04, C:0.37, G:0.15, T:0.44
Consensus pattern (21 bp):
GCTGCTTCTCTCTATGCTTCC
Found at i:80462 original size:16 final size:17
Alignment explanation
Indices: 80441--80475 Score: 63
Period size: 16 Copynumber: 2.1 Consensus size: 17
80431 TTACTATTCA
80441 CGTGAATAGTG-AATTT
1 CGTGAATAGTGAAATTT
80457 CGTGAATAGTGAAATTT
1 CGTGAATAGTGAAATTT
80474 CG
1 CG
80476 GTCGGCGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.31, C:0.09, G:0.26, T:0.34
Consensus pattern (17 bp):
CGTGAATAGTGAAATTT
Found at i:81243 original size:15 final size:16
Alignment explanation
Indices: 81225--81257 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
81215 GTGGCAGATC
81225 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
81240 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
81256 AA
1 AA
81258 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:81809 original size:609 final size:609
Alignment explanation
Indices: 80678--81896 Score: 2438
Period size: 609 Copynumber: 2.0 Consensus size: 609
80668 AAAAATCTTT
80678 ATCAACCTCTCTCAGGAAAGCAACCAGAGGGCATGAAGAATGAAGACTGGGCTCTTCTCGACCGA
1 ATCAACCTCTCTCAGGAAAGCAACCAGAGGGCATGAAGAATGAAGACTGGGCTCTTCTCGACCGA
80743 CAAGCCCTTGGAGTCATCCGACTGACGTTGTCCCGAAATGTTGCTTTCAACATAGCAAAGGAAAA
66 CAAGCCCTTGGAGTCATCCGACTGACGTTGTCCCGAAATGTTGCTTTCAACATAGCAAAGGAAAA
80808 GACCACAGCGGGTCTTATGGCGGCTCTCTCCAGTATGTATGAGAAGCCATCGGCCTCAAACAAAG
131 GACCACAGCGGGTCTTATGGCGGCTCTCTCCAGTATGTATGAGAAGCCATCGGCCTCAAACAAAG
80873 TTCATTTGATGAGGCGATTATTCAATTTGCGGATGACGGAAGGGGCATCGGTGGCACAACACCTA
196 TTCATTTGATGAGGCGATTATTCAATTTGCGGATGACGGAAGGGGCATCGGTGGCACAACACCTA
80938 AATGAACTCAACACAATCACAACCCAGTTGAGTTCAGTGGAAATTGAGTTCGATGATGAAGTTCG
261 AATGAACTCAACACAATCACAACCCAGTTGAGTTCAGTGGAAATTGAGTTCGATGATGAAGTTCG
81003 AGCTTTAATTCTCTTATCATCTCTACCAGACAGTTGGAATGCTACTGTTACAGCAGTCAGCAGTT
326 AGCTTTAATTCTCTTATCATCTCTACCAGACAGTTGGAATGCTACTGTTACAGCAGTCAGCAGTT
81068 CGTCGGGAAACAGCAAATTAAAATTCGACGATGTTCGAGATCTGGTACTGAGTGAAGAAATTCGA
391 CGTCGGGAAACAGCAAATTAAAATTCGACGATGTTCGAGATCTGGTACTGAGTGAAGAAATTCGA
81133 CGGAGAGAATCGGGTGAAGCATCAACCTCCTCAGCCTTGCACACGGAGTCTAGAGGAAGAACTTC
456 CGGAGAGAATCGGGTGAAGCATCAACCTCCTCAGCCTTGCACACGGAGTCTAGAGGAAGAACTTC
81198 AGAAAGATATTCAAATCGTGGCAGATCAAAATCCAGACGGGAAAAATCTAGAACGGGAAAGAAAG
521 AGAAAGATATTCAAATCGTGGCAGATCAAAATCCAGACGGGAAAAATCTAGAACGGGAAAGAAAG
81263 ATTTTACCTGTTATAATTGTGGCA
586 ATTTTACCTGTTATAATTGTGGCA
81287 ATCAACCTCTCTCAGGAAAGCAACCAGAGGGCATGAAGAATGAAGACTGGGCTCTTCTCGACCGA
1 ATCAACCTCTCTCAGGAAAGCAACCAGAGGGCATGAAGAATGAAGACTGGGCTCTTCTCGACCGA
81352 CAAGCCCTTGGAGTCATCCGACTGACGTTGTCCCGAAATGTTGCTTTCAACATAGCAAAGGAAAA
66 CAAGCCCTTGGAGTCATCCGACTGACGTTGTCCCGAAATGTTGCTTTCAACATAGCAAAGGAAAA
81417 GACCACAGCGGGTCTTATGGCGGCTCTCTCCAGTATGTATGAGAAGCCATCGGCCTCAAACAAAG
131 GACCACAGCGGGTCTTATGGCGGCTCTCTCCAGTATGTATGAGAAGCCATCGGCCTCAAACAAAG
81482 TTCATTTGATGAGGCGATTATTCAATTTGCGGATGACGGAAGGGGCATCGGTGGCACAACACCTA
196 TTCATTTGATGAGGCGATTATTCAATTTGCGGATGACGGAAGGGGCATCGGTGGCACAACACCTA
81547 AATGAACTCAACACAATCACAACCCAGTTGAGTTCAGTGGAAATTGAGTTCGATGATGAAGTTCG
261 AATGAACTCAACACAATCACAACCCAGTTGAGTTCAGTGGAAATTGAGTTCGATGATGAAGTTCG
81612 AGCTTTAATTCTCTTATCATCTCTACCAGACAGTTGGAATGCTACTGTTACAGCAGTCAGCAGTT
326 AGCTTTAATTCTCTTATCATCTCTACCAGACAGTTGGAATGCTACTGTTACAGCAGTCAGCAGTT
81677 CGTCGGGAAACAGCAAATTAAAATTCGACGATGTTCGAGATCTGGTACTGAGTGAAGAAATTCGA
391 CGTCGGGAAACAGCAAATTAAAATTCGACGATGTTCGAGATCTGGTACTGAGTGAAGAAATTCGA
81742 CGGAGAGAATCGGGTGAAGCATCAACCTCCTCAGCCTTGCACACGGAGTCTAGAGGAAGAACTTC
456 CGGAGAGAATCGGGTGAAGCATCAACCTCCTCAGCCTTGCACACGGAGTCTAGAGGAAGAACTTC
81807 AGAAAGATATTCAAATCGTGGCAGATCAAAATCCAGACGGGAAAAATCTAGAACGGGAAAGAAAG
521 AGAAAGATATTCAAATCGTGGCAGATCAAAATCCAGACGGGAAAAATCTAGAACGGGAAAGAAAG
81872 ATTTTACCTGTTATAATTGTGGCA
586 ATTTTACCTGTTATAATTGTGGCA
81896 A
1 A
81897 GAAAGGTCAC
Statistics
Matches: 610, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
609 610 1.00
ACGTcount: A:0.32, C:0.21, G:0.24, T:0.23
Consensus pattern (609 bp):
ATCAACCTCTCTCAGGAAAGCAACCAGAGGGCATGAAGAATGAAGACTGGGCTCTTCTCGACCGA
CAAGCCCTTGGAGTCATCCGACTGACGTTGTCCCGAAATGTTGCTTTCAACATAGCAAAGGAAAA
GACCACAGCGGGTCTTATGGCGGCTCTCTCCAGTATGTATGAGAAGCCATCGGCCTCAAACAAAG
TTCATTTGATGAGGCGATTATTCAATTTGCGGATGACGGAAGGGGCATCGGTGGCACAACACCTA
AATGAACTCAACACAATCACAACCCAGTTGAGTTCAGTGGAAATTGAGTTCGATGATGAAGTTCG
AGCTTTAATTCTCTTATCATCTCTACCAGACAGTTGGAATGCTACTGTTACAGCAGTCAGCAGTT
CGTCGGGAAACAGCAAATTAAAATTCGACGATGTTCGAGATCTGGTACTGAGTGAAGAAATTCGA
CGGAGAGAATCGGGTGAAGCATCAACCTCCTCAGCCTTGCACACGGAGTCTAGAGGAAGAACTTC
AGAAAGATATTCAAATCGTGGCAGATCAAAATCCAGACGGGAAAAATCTAGAACGGGAAAGAAAG
ATTTTACCTGTTATAATTGTGGCA
Found at i:81852 original size:15 final size:16
Alignment explanation
Indices: 81834--81866 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
81824 GTGGCAGATC
81834 AAAATCCAG-ACGGGA
1 AAAATCCAGAACGGGA
*
81849 AAAATCTAGAACGGGA
1 AAAATCCAGAACGGGA
81865 AA
1 AA
81867 GAAAGATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.52, C:0.15, G:0.24, T:0.09
Consensus pattern (16 bp):
AAAATCCAGAACGGGA
Found at i:92862 original size:29 final size:29
Alignment explanation
Indices: 92817--92881 Score: 103
Period size: 29 Copynumber: 2.2 Consensus size: 29
92807 CTAAAATAAA
*
92817 ACAAAAACTAAAGCTTTTAACGACATGGT
1 ACAAAAACTAAAACTTTTAACGACATGGT
*
92846 ACAAAAACTAAAACTTTTAACGATATGGT
1 ACAAAAACTAAAACTTTTAACGACATGGT
*
92875 ACTAAAA
1 ACAAAAA
92882 TGAAATAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.49, C:0.15, G:0.11, T:0.25
Consensus pattern (29 bp):
ACAAAAACTAAAACTTTTAACGACATGGT
Found at i:93304 original size:19 final size:19
Alignment explanation
Indices: 93280--93332 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
93270 TGAAATATGA
93280 ATTTTTAAATAAATAAAAT
1 ATTTTTAAATAAATAAAAT
* *
93299 ATTTTT-ATTATAATGAAAT
1 ATTTTTAAATA-AATAAAAT
93318 -TTTATTAAATAAATA
1 ATTT-TTAAATAAATA
93333 TAAACCGTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
18 6 0.22
19 18 0.67
20 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (19 bp):
ATTTTTAAATAAATAAAAT
Found at i:98059 original size:29 final size:27
Alignment explanation
Indices: 98001--98076 Score: 82
Period size: 29 Copynumber: 2.7 Consensus size: 27
97991 AATTTCATTA
* *
98001 CTTTAATTTTCTATTTTATATTTTTTC
1 CTTTAATTTTCTACTTTATATTTTGTC
98028 CTTTAATTTTCATAACTTTA-ATTTTAGTC
1 CTTTAATTTTC-T-ACTTTATATTTT-GTC
*
98057 CTTTAATTATCGTACTTTAT
1 CTTTAATTTTC-TACTTTAT
98077 TTCATGTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
27 11 0.27
28 12 0.29
29 18 0.44
ACGTcount: A:0.24, C:0.13, G:0.03, T:0.61
Consensus pattern (27 bp):
CTTTAATTTTCTACTTTATATTTTGTC
Found at i:101145 original size:31 final size:31
Alignment explanation
Indices: 101107--101165 Score: 102
Period size: 32 Copynumber: 1.9 Consensus size: 31
101097 ATTATTATTA
101107 TTGAT-AAATTTAATGATTATTTTATAATTGT
1 TTGATAAAATTTAATGATTA-TTTATAATTGT
101138 TTGATAAAATTTAATGATTATTTATAAT
1 TTGATAAAATTTAATGATTATTTATAAT
101166 AAATAGATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 13 0.48
32 14 0.52
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (31 bp):
TTGATAAAATTTAATGATTATTTATAATTGT
Found at i:101175 original size:31 final size:32
Alignment explanation
Indices: 101112--101181 Score: 97
Period size: 31 Copynumber: 2.2 Consensus size: 32
101102 TATTATTGAT
*** *
101112 AAATTTAATGATTATTTTATAATTGTTTGATA
1 AAATTTAATGATTATTTTATAATAAATAGATA
101144 AAATTTAATGATTA-TTTATAATAAATAGATA
1 AAATTTAATGATTATTTTATAATAAATAGATA
101175 AAATTTA
1 AAATTTA
101182 GGGTAAACTA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 20 0.59
32 14 0.41
ACGTcount: A:0.46, C:0.00, G:0.07, T:0.47
Consensus pattern (32 bp):
AAATTTAATGATTATTTTATAATAAATAGATA
Found at i:101460 original size:25 final size:27
Alignment explanation
Indices: 101410--101475 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 27
101400 TCTTTCTATT
*
101410 TGATCATAGTTTTAATAAATTAAAAT-A
1 TGAT-ATATTTTTAATAAATTAAAATAA
* *
101437 T-ATTTATTTTTAAT-TATTATAAATAA
1 TGATATATTTTTAATAAATTA-AAATAA
101463 TGATATATTTTTA
1 TGATATATTTTTA
101476 TACAAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
24 4 0.12
25 13 0.41
26 4 0.12
27 11 0.34
ACGTcount: A:0.42, C:0.02, G:0.05, T:0.52
Consensus pattern (27 bp):
TGATATATTTTTAATAAATTAAAATAA
Found at i:102909 original size:28 final size:30
Alignment explanation
Indices: 102859--102929 Score: 85
Period size: 28 Copynumber: 2.4 Consensus size: 30
102849 AATATCGCAC
* *
102859 TATTAATATAATATAACATATCATATTAAAA
1 TATTAATATAATAT-ACACATCATATAAAAA
102890 TATTAATAT-ATAT-CACATCATATAAAAA
1 TATTAATATAATATACACATCATATAAAAA
*
102918 TAATAATA-AATA
1 TATTAATATAATA
102930 ATTTGTCATT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 23 0.64
30 4 0.11
31 9 0.25
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (30 bp):
TATTAATATAATATACACATCATATAAAAA
Found at i:104158 original size:23 final size:23
Alignment explanation
Indices: 104127--104171 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
104117 CACCACAGCT
* *
104127 CGTATAATTGCATCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
*
104150 CGTAGAATTGCACCGGAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
104172 GTAAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:104425 original size:23 final size:27
Alignment explanation
Indices: 104397--104455 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 27
104387 CTTTCACAAT
104397 TCACATAAT-T-T-GTAT-AATTCATG
1 TCACATAATATATAGTATGAATTCATG
104420 TCACATAATGCATATAGTATGAATTCATG
1 TCACATAAT--ATATAGTATGAATTCATG
104449 TCACATA
1 TCACATA
104456 TCATAATATG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
23 9 0.30
26 1 0.03
27 1 0.03
28 4 0.13
29 15 0.50
ACGTcount: A:0.37, C:0.15, G:0.10, T:0.37
Consensus pattern (27 bp):
TCACATAATATATAGTATGAATTCATG
Found at i:113649 original size:19 final size:19
Alignment explanation
Indices: 113625--113670 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
113615 AAATGGGTAC
113625 CGATACCACTCAAGAGTAT
1 CGATACCACTCAAGAGTAT
113644 CGATACCACTCAAGAGTAT
1 CGATACCACTCAAGAGTAT
113663 CGATACCA
1 CGATACCA
113671 TAGTGCAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.37, C:0.28, G:0.15, T:0.20
Consensus pattern (19 bp):
CGATACCACTCAAGAGTAT
Found at i:116853 original size:94 final size:96
Alignment explanation
Indices: 116740--116932 Score: 284
Period size: 104 Copynumber: 2.0 Consensus size: 96
116730 AATTAATTTC
*
116740 TAATGAAAAGGGGGAGCTGAACATTTTCATATATTTTCCAACAATT-G-G-TATCTTTTTCATTA
1 TAATGAAAAGGGGAAGCTGAACATTTTCATATATTTTCCAACAATTGGAGATATCTTTTTCATTA
116802 AACATTTCATTAAGGGGGAGTTTTTGCTTCT
66 AACATTTCATTAAGGGGGAGTTTTTGCTTCT
116833 TAATGAAAAAGGGGAAGCTGAACATTTTCATATATTTTCCAACAATTGGTAACAATTGATATCTT
1 TAATG-AAAAGGGGAAGCTGAACATTTTCATATATTTTCCAACAATTGG-----A--GATATCTT
116898 TTTCATTAAACATTTCATTAAGGGGGAGTTTTTGC
58 TTTCATTAAACATTTCATTAAGGGGGAGTTTTTGC
116933 CAAAAAAAAA
Statistics
Matches: 88, Mismatches: 1, Indels: 11
0.88 0.01 0.11
Matches are distributed among these distances:
93 5 0.06
94 40 0.45
95 1 0.01
103 1 0.01
104 41 0.47
ACGTcount: A:0.32, C:0.12, G:0.18, T:0.38
Consensus pattern (96 bp):
TAATGAAAAGGGGAAGCTGAACATTTTCATATATTTTCCAACAATTGGAGATATCTTTTTCATTA
AACATTTCATTAAGGGGGAGTTTTTGCTTCT
Found at i:118666 original size:17 final size:17
Alignment explanation
Indices: 118633--118667 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
118623 TGTTAAAAGA
*
118633 AGAAGAAAAAGATGAAG
1 AGAAGAAAAAGAAGAAG
*
118650 AGAAGAAAAATAAGAAG
1 AGAAGAAAAAGAAGAAG
118667 A
1 A
118668 AAAGGAGGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.69, C:0.00, G:0.26, T:0.06
Consensus pattern (17 bp):
AGAAGAAAAAGAAGAAG
Found at i:119811 original size:18 final size:18
Alignment explanation
Indices: 119788--119826 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
119778 TGCAAATGAC
119788 ATCTCTCTAACAATTGAT
1 ATCTCTCTAACAATTGAT
*
119806 ATCTCTCTAATAATTGAT
1 ATCTCTCTAACAATTGAT
119824 ATC
1 ATC
119827 AACTTTTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.41
Consensus pattern (18 bp):
ATCTCTCTAACAATTGAT
Done.