Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002276.1 Hibiscus syriacus cultivar Beakdansim tig00004630_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: 831455
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
File 1 of 5
Found at i:7454 original size:19 final size:20
Alignment explanation
Indices: 7426--7468 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
7416 TTTTAACTTT
7426 TTTTTATC-TTCATTATTAA-
1 TTTTTATCTTTCATT-TTAAC
*
7445 TTTTTCTCTTTCATTTTAAC
1 TTTTTATCTTTCATTTTAAC
7465 TTTT
1 TTTT
7469 ACCTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTTATCTTTCATTTTAAC
Found at i:7474 original size:19 final size:20
Alignment explanation
Indices: 7434--7474 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
7424 TTTTTTTATC
*
7434 TTCATTATTAATTTTTCTCT
1 TTCATTATTAATTTTACTCT
7454 TTCATT-TTAACTTTTAC-CT
1 TTCATTATTAA-TTTTACTCT
7473 TT
1 TT
7475 TCTCTTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (20 bp):
TTCATTATTAATTTTACTCT
Found at i:12433 original size:16 final size:16
Alignment explanation
Indices: 12399--12437 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
12389 AATACATATC
*
12399 AATAATATCAAATCTT
1 AATAATATCAAACCTT
12415 AATTAATAT-AAACCTT
1 AA-TAATATCAAACCTT
12431 AATAATA
1 AATAATA
12438 AATATTAACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 5 0.24
16 10 0.48
17 6 0.29
ACGTcount: A:0.54, C:0.10, G:0.00, T:0.36
Consensus pattern (16 bp):
AATAATATCAAACCTT
Found at i:12672 original size:27 final size:27
Alignment explanation
Indices: 12634--12688 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
12624 ACATTGGCGC
* *
12634 GTGGTGTCAACATTTCTATCTACCTAA
1 GTGGTGTCAACATTCCGATCTACCTAA
*
12661 GTGGTGTCAACATTCCGGTCTACCTAA
1 GTGGTGTCAACATTCCGATCTACCTAA
12688 G
1 G
12689 CAAAAGTACC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (27 bp):
GTGGTGTCAACATTCCGATCTACCTAA
Found at i:16280 original size:21 final size:23
Alignment explanation
Indices: 16254--16302 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
16244 CGAATCGGTT
* *
16254 CGACCTGA-CCGTTGA-CCGATC
1 CGACCTGACCCGTTCACCCGACC
16275 CGACCTGACCCGTTCACCCGACC
1 CGACCTGACCCGTTCACCCGACC
16298 CGACC
1 CGACC
16303 CGTTCACCCG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 8 0.33
22 6 0.25
23 10 0.42
ACGTcount: A:0.18, C:0.47, G:0.20, T:0.14
Consensus pattern (23 bp):
CGACCTGACCCGTTCACCCGACC
Found at i:16297 original size:18 final size:18
Alignment explanation
Indices: 16274--16317 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
16264 GTTGACCGAT
*
16274 CCGACCTGACCCGTTCAC
1 CCGACCCGACCCGTTCAC
16292 CCGACCCGACCCGTTCAC
1 CCGACCCGACCCGTTCAC
16310 CCGACCCG
1 CCGACCCG
16318 TTGACCGAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.55, G:0.18, T:0.11
Consensus pattern (18 bp):
CCGACCCGACCCGTTCAC
Found at i:16299 original size:13 final size:13
Alignment explanation
Indices: 16295--16319 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
16285 CGTTCACCCG
16295 ACCCGACCCGTTC
1 ACCCGACCCGTTC
16308 ACCCGACCCGTT
1 ACCCGACCCGTT
16320 GACCGAGTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (13 bp):
ACCCGACCCGTTC
Found at i:16464 original size:29 final size:29
Alignment explanation
Indices: 16324--16464 Score: 143
Period size: 29 Copynumber: 5.0 Consensus size: 29
16314 CCCGTTGACC
* *
16324 GAGTGGTATTTTGGTAATTATTTTGAAAA
1 GAGTGATATTTTCGTAATTATTTTGAAAA
* *
16353 TG-GTTATATTTTAGTAATTATTTTGAAAA
1 -GAGTGATATTTTCGTAATTATTTTGAAAA
*
16382 TGA-TGCTATTTTCGTAATT-TTTT-AAAA
1 -GAGTGATATTTTCGTAATTATTTTGAAAA
* *
16409 -AGTGATAATTTCGT-ATT-TTTTAAAAA
1 GAGTGATATTTTCGTAATTATTTTGAAAA
*
16435 GAGTGATATTTTGGTAATTATTTTGAAAA
1 GAGTGATATTTTCGTAATTATTTTGAAAA
16464 G
1 G
16465 GATTCTTAAA
Statistics
Matches: 94, Mismatches: 11, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
25 8 0.09
26 14 0.15
27 16 0.17
28 7 0.07
29 48 0.51
30 1 0.01
ACGTcount: A:0.33, C:0.02, G:0.17, T:0.48
Consensus pattern (29 bp):
GAGTGATATTTTCGTAATTATTTTGAAAA
Found at i:16818 original size:21 final size:22
Alignment explanation
Indices: 16789--16832 Score: 72
Period size: 21 Copynumber: 2.0 Consensus size: 22
16779 CGGTCCGAAT
*
16789 CGGTTCGACCTGAC-CGTTGAC
1 CGGTCCGACCTGACTCGTTGAC
16810 CGGTCCGACCTGACTCGTTGAC
1 CGGTCCGACCTGACTCGTTGAC
16832 C
1 C
16833 CGACCCGTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.14, C:0.36, G:0.27, T:0.23
Consensus pattern (22 bp):
CGGTCCGACCTGACTCGTTGAC
Found at i:16841 original size:13 final size:13
Alignment explanation
Indices: 16825--16858 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
16815 CGACCTGACT
16825 CGTTGACCCGACC
1 CGTTGACCCGACC
*
16838 CGTTCACCCGACC
1 CGTTGACCCGACC
16851 CGTTGACC
1 CGTTGACC
16859 GAGTGGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.15, C:0.47, G:0.21, T:0.18
Consensus pattern (13 bp):
CGTTGACCCGACC
Found at i:16897 original size:29 final size:28
Alignment explanation
Indices: 16865--17008 Score: 152
Period size: 29 Copynumber: 5.1 Consensus size: 28
16855 GACCGAGTGG
*
16865 TATTTTGGTAATTATTTTGAAAATGGTGA
1 TATTTTCGTAATTATTTTGAAAA-GGTGA
* * *
16894 TATTTTAGTAATTATTTTGAAAATGATGC
1 TATTTTCGTAATTATTTTGAAAA-GGTGA
*
16923 TATTTTCGTAATT-TTTTTAAAA-GTGA
1 TATTTTCGTAATTATTTTGAAAAGGTGA
* *
16949 TAATTTCGT-ATT-TTTTAAAAAGAGTGA
1 TATTTTCGTAATTATTTTGAAAAG-GTGA
*
16976 TATTTTGGTAATTATTTTGAAAAGGATGA
1 TATTTTCGTAATTATTTTGAAAAGG-TGA
17005 TATT
1 TATT
17009 ATGTAAATAT
Statistics
Matches: 98, Mismatches: 12, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
25 11 0.11
26 10 0.10
27 11 0.11
28 12 0.12
29 54 0.55
ACGTcount: A:0.33, C:0.02, G:0.16, T:0.49
Consensus pattern (28 bp):
TATTTTCGTAATTATTTTGAAAAGGTGA
Found at i:17027 original size:29 final size:30
Alignment explanation
Indices: 16960--17033 Score: 82
Period size: 29 Copynumber: 2.5 Consensus size: 30
16950 AATTTCGTAT
* *
16960 TTTTTAAAAAGAGTGATATTTTGGTAATTA
1 TTTTTAAAAAGAGTGATATTATGGTAAATA
* *
16990 TTTTGAAAAGGA-TGATATTAT-GTAAATA
1 TTTTTAAAAAGAGTGATATTATGGTAAATA
17018 TTTCTTAAAAAG-GTGA
1 TTT-TTAAAAAGAGTGA
17034 AAATTTTGTA
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
28 9 0.25
29 17 0.47
30 10 0.28
ACGTcount: A:0.39, C:0.01, G:0.18, T:0.42
Consensus pattern (30 bp):
TTTTTAAAAAGAGTGATATTATGGTAAATA
Found at i:18001 original size:42 final size:41
Alignment explanation
Indices: 17942--18066 Score: 171
Period size: 42 Copynumber: 3.0 Consensus size: 41
17932 GGAAGTATTG
17942 TCAGGT-TCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTC
1 TCAGGTCT-CTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
*
17984 TCAGGTCTCTTTGCTGTGTGCAAAGGTAAGCCTTATAGTTTC
1 TCAGGTCTCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTC
* * *
18026 CCATGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTT
1 TCAGGTCTCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTT
18067 TCCTAGGCTC
Statistics
Matches: 75, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
41 2 0.03
42 72 0.96
43 1 0.01
ACGTcount: A:0.18, C:0.22, G:0.25, T:0.36
Consensus pattern (41 bp):
TCAGGTCTCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTC
Found at i:25857 original size:35 final size:35
Alignment explanation
Indices: 25816--25887 Score: 144
Period size: 35 Copynumber: 2.1 Consensus size: 35
25806 TTTATGGATA
25816 GAGAGAAAATTAGTAAATAGTTTTGGTACATGAAG
1 GAGAGAAAATTAGTAAATAGTTTTGGTACATGAAG
25851 GAGAGAAAATTAGTAAATAGTTTTGGTACATGAAG
1 GAGAGAAAATTAGTAAATAGTTTTGGTACATGAAG
25886 GA
1 GA
25888 CATTTTTTAG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.43, C:0.03, G:0.26, T:0.28
Consensus pattern (35 bp):
GAGAGAAAATTAGTAAATAGTTTTGGTACATGAAG
Found at i:30459 original size:28 final size:29
Alignment explanation
Indices: 30410--30464 Score: 67
Period size: 28 Copynumber: 1.9 Consensus size: 29
30400 TACTGAATCC
**
30410 TTTGATTATAAAAAATTGTAAAATAATTA
1 TTTGATTATAAAAAATAATAAAATAATTA
* *
30439 TTTGATT-TAAAATATAATAAATTAAT
1 TTTGATTATAAAAAATAATAAAATAAT
30465 GATGTATTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 15 0.68
29 7 0.32
ACGTcount: A:0.51, C:0.00, G:0.05, T:0.44
Consensus pattern (29 bp):
TTTGATTATAAAAAATAATAAAATAATTA
Found at i:31088 original size:12 final size:12
Alignment explanation
Indices: 31067--31098 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
31057 ACGACTTACA
*
31067 TCTTCTCCTCTC
1 TCTTCCCCTCTC
31079 TCTTCCCCTCTC
1 TCTTCCCCTCTC
31091 TCTTCCCC
1 TCTTCCCC
31099 ACTTATCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (12 bp):
TCTTCCCCTCTC
Found at i:32399 original size:31 final size:28
Alignment explanation
Indices: 32364--32420 Score: 87
Period size: 31 Copynumber: 1.9 Consensus size: 28
32354 AGTATTGCTG
32364 AGCTCGACTCGACTCGAAAACTCTGAAATGA
1 AGCTCGACTCGACTC--AAACTC-GAAATGA
32395 AGCTCGACTCGACTCAAACTCGAAAT
1 AGCTCGACTCGACTCAAACTCGAAAT
32421 CTTGAACTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 5 0.19
29 6 0.23
31 15 0.58
ACGTcount: A:0.35, C:0.28, G:0.18, T:0.19
Consensus pattern (28 bp):
AGCTCGACTCGACTCAAACTCGAAATGA
Found at i:32432 original size:36 final size:36
Alignment explanation
Indices: 32366--32436 Score: 99
Period size: 36 Copynumber: 2.0 Consensus size: 36
32356 TATTGCTGAG
*
32366 CTCGACTCGACTCGAAAACTCTGAAATGAAGCTCGA
1 CTCGACTCAACTCGAAAACTCTGAAATGAAGCTCGA
* *
32402 CTCGACTCAAACTCGAAATCT-TGAACTGAAGCTCG
1 CTCGACTC-AACTCGAAAACTCTGAAATGAAGCTCG
32437 TTAACAGCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
36 21 0.68
37 10 0.32
ACGTcount: A:0.32, C:0.28, G:0.18, T:0.21
Consensus pattern (36 bp):
CTCGACTCAACTCGAAAACTCTGAAATGAAGCTCGA
Found at i:32597 original size:37 final size:36
Alignment explanation
Indices: 32541--32618 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 36
32531 CTTACTGTAT
32541 TTTTTAAAAAAATACAT-AAATATTAATATTATTAATAA
1 TTTTTAAAAAAATACATAAAATATTAATA-TATT-AT-A
*
32579 TTTTTAAAAATAA-A-ATAAAATCTTAATATATTATA
1 TTTTTAAAAA-AATACATAAAATATTAATATATTATA
32614 TTTTT
1 TTTTT
32619 GAGCTGCTCA
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
35 6 0.16
36 2 0.05
37 6 0.16
38 21 0.57
39 2 0.05
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (36 bp):
TTTTTAAAAAAATACATAAAATATTAATATATTATA
Found at i:33292 original size:44 final size:42
Alignment explanation
Indices: 33237--33341 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 42
33227 TAATTTTAAC
* * * *
33237 TTTATCTTTATAATTGAGACTCTTAAATTTTTTAATCTCGCTTT
1 TTTATCTTTATAATTGAGAC-CTTAAATTTCTCAATATCAC-TT
* * *
33281 TTTATATTTATAAATGATGACCTTAAGTTTCTCAATATCACTT
1 TTTATCTTTATAATTGA-GACCTTAAATTTCTCAATATCACTT
*
33324 TATATCTTTATAATTGAG
1 TTTATCTTTATAATTGAG
33342 TTCCTAGTTT
Statistics
Matches: 50, Mismatches: 10, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
42 1 0.02
43 16 0.32
44 30 0.60
45 3 0.06
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (42 bp):
TTTATCTTTATAATTGAGACCTTAAATTTCTCAATATCACTT
Found at i:38569 original size:2 final size:2
Alignment explanation
Indices: 38562--38640 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
38552 TCTTTTTAAA
38562 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
38604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
38641 CCCCCATCCG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38775 original size:35 final size:35
Alignment explanation
Indices: 38702--38776 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
38692 TGTCACGTCC
**
38702 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
38737 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
38772 AGTAA
1 AGTAA
38777 TCTTCCTCTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:38886 original size:24 final size:22
Alignment explanation
Indices: 38853--38937 Score: 98
Period size: 24 Copynumber: 3.6 Consensus size: 22
38843 ACATAATTCA
38853 AGTCGAGTATCATATCAGAATCC
1 AGTC-AGTATCATATCAGAATCC
*
38876 AGATCATGTATCAGATCAGAATCC
1 AG-TCA-GTATCATATCAGAATCC
*
38900 ATGTCAATATCATATCAGAATCC
1 A-GTCAGTATCATATCAGAATCC
38923 AGGTCAGGTATCATA
1 A-GTCA-GTATCATA
38938 ACATAATTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
23 23 0.43
24 29 0.55
25 1 0.02
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.27
Consensus pattern (22 bp):
AGTCAGTATCATATCAGAATCC
Found at i:57329 original size:3 final size:3
Alignment explanation
Indices: 57321--57351 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
57311 AGAAGTAAAA
*
57321 AAT AAT AAT AAT AAT AAT AAT AAT AAA AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
57352 TCATTATGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:63138 original size:18 final size:18
Alignment explanation
Indices: 63115--63206 Score: 103
Period size: 18 Copynumber: 4.9 Consensus size: 18
63105 ACTATCAAGA
63115 AAAAATCAAAAGCAAAGG
1 AAAAATCAAAAGCAAAGG
* *
63133 AAAAATTAAAAGCAAAGAA
1 AAAAATCAAAAGCAAAG-G
63152 AAAGAATCAAAAGCAAAGG
1 AAA-AATCAAAAGCAAAGG
* *
63171 AAAAATTAAAAGAAAAGG
1 AAAAATCAAAAGCAAAGG
*
63189 AAAAGAATCAAAATCAAA
1 -AAA-AATCAAAAGCAAA
63207 AGCAAAGTAT
Statistics
Matches: 61, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
18 29 0.48
19 9 0.15
20 23 0.38
ACGTcount: A:0.70, C:0.08, G:0.14, T:0.09
Consensus pattern (18 bp):
AAAAATCAAAAGCAAAGG
Found at i:63163 original size:38 final size:38
Alignment explanation
Indices: 63114--63206 Score: 152
Period size: 38 Copynumber: 2.5 Consensus size: 38
63104 GACTATCAAG
*
63114 AAAA-AATCAAAAGCAAAGGAAAAATTAAAAGCAAAGA
1 AAAAGAATCAAAAGCAAAGGAAAAATTAAAAGAAAAGA
*
63151 AAAAGAATCAAAAGCAAAGGAAAAATTAAAAGAAAAGG
1 AAAAGAATCAAAAGCAAAGGAAAAATTAAAAGAAAAGA
*
63189 AAAAGAATCAAAATCAAA
1 AAAAGAATCAAAAGCAAA
63207 AGCAAAGTAT
Statistics
Matches: 52, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 4 0.08
38 48 0.92
ACGTcount: A:0.70, C:0.08, G:0.14, T:0.09
Consensus pattern (38 bp):
AAAAGAATCAAAAGCAAAGGAAAAATTAAAAGAAAAGA
Found at i:64026 original size:37 final size:38
Alignment explanation
Indices: 63985--64076 Score: 123
Period size: 37 Copynumber: 2.4 Consensus size: 38
63975 AATAGACAAG
* *
63985 TTGTTTATAAACATAAATGAACGAGTCGATAAACG-AT
1 TTGTTTATAAACATAAATGAACAAGTCGATAAACGAAC
* * *
64022 TTGTTTGTGAACATAAATGAATAAGTCGATAAACGAAC
1 TTGTTTATAAACATAAATGAACAAGTCGATAAACGAAC
*
64060 TTGTTCATAAACATAAA
1 TTGTTTATAAACATAAA
64077 AAAGATTGTT
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
37 31 0.67
38 15 0.33
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.30
Consensus pattern (38 bp):
TTGTTTATAAACATAAATGAACAAGTCGATAAACGAAC
Found at i:64075 original size:22 final size:23
Alignment explanation
Indices: 64050--64102 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
64040 GAATAAGTCG
*
64050 ATAAACGAA-CTTGTTCATAAAC
1 ATAAACGAAGATTGTTCATAAAC
* *
64072 ATAAA-AAAGATTGTTCGTAAAC
1 ATAAACGAAGATTGTTCATAAAC
64094 ATAAACGAA
1 ATAAACGAA
64103 ATGAAGATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
21 2 0.08
22 21 0.84
23 2 0.08
ACGTcount: A:0.51, C:0.13, G:0.11, T:0.25
Consensus pattern (23 bp):
ATAAACGAAGATTGTTCATAAAC
Found at i:66754 original size:17 final size:18
Alignment explanation
Indices: 66734--66773 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
66724 AAAAAAAATT
*
66734 AAATTA-CTTTTATTAAA
1 AAATTATCTTTTAATAAA
*
66751 AAATTATCTTTTAATATA
1 AAATTATCTTTTAATAAA
66769 AAATT
1 AAATT
66774 TTACGTATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (18 bp):
AAATTATCTTTTAATAAA
Found at i:71828 original size:19 final size:20
Alignment explanation
Indices: 71792--71829 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
71782 CTCTCTTTGT
*
71792 AATATTTATTCTATTAGTGA
1 AATATTTATTCTAGTAGTGA
*
71812 AATA-TTATTTTAGTAGTG
1 AATATTTATTCTAGTAGTG
71830 TTCGAGGACG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.34, C:0.03, G:0.13, T:0.50
Consensus pattern (20 bp):
AATATTTATTCTAGTAGTGA
Found at i:77384 original size:13 final size:13
Alignment explanation
Indices: 77344--77393 Score: 55
Period size: 14 Copynumber: 3.6 Consensus size: 13
77334 TATACATAAC
*
77344 AAACAAGTAAATAA
1 AAACAAATAAA-AA
*
77358 AAACATAAGAAAAA
1 AAACA-AATAAAAA
77372 AATACAAATAAAAA
1 AA-ACAAATAAAAA
77386 AAACAAAT
1 AAACAAAT
77394 GTAAAGATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
13 6 0.19
14 18 0.58
15 7 0.23
ACGTcount: A:0.76, C:0.08, G:0.04, T:0.12
Consensus pattern (13 bp):
AAACAAATAAAAA
Found at i:77435 original size:25 final size:23
Alignment explanation
Indices: 77407--77459 Score: 63
Period size: 23 Copynumber: 2.2 Consensus size: 23
77397 AAGATGATAA
77407 AAAAATAAAGATA-AGGAATAAAAAT
1 AAAAATAAA-ATAGAGG-A-AAAAAT
*
77432 AAAAATGAAATAGAGGAAAAAAT
1 AAAAATAAAATAGAGGAAAAAAT
77455 AAAAA
1 AAAAA
77460 GGTAAATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 11 0.42
24 4 0.15
25 11 0.42
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (23 bp):
AAAAATAAAATAGAGGAAAAAAT
Found at i:77748 original size:3 final size:3
Alignment explanation
Indices: 77742--77814 Score: 61
Period size: 3 Copynumber: 25.7 Consensus size: 3
77732 TGTTTTAAAA
*
77742 AAT AAT AAT AAT AA- AA- AAT AA- AA- AAT AA- AAT -AT AAA AGAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT
77782 AAT AAT AAT AAT AAT AAT GAGA- AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT -A-AT AAT AAT AAT AA
77815 GTAAAGAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 16
0.77 0.03 0.21
Matches are distributed among these distances:
2 13 0.22
3 43 0.72
4 3 0.05
5 1 0.02
ACGTcount: A:0.71, C:0.00, G:0.04, T:0.25
Consensus pattern (3 bp):
AAT
Found at i:77763 original size:7 final size:7
Alignment explanation
Indices: 77737--77783 Score: 58
Period size: 7 Copynumber: 6.4 Consensus size: 7
77727 ATAAATGTTT
77737 TAAAAAA
1 TAAAAAA
77744 TAATAATAA
1 TAA-AA-AA
77753 TAAAAAA
1 TAAAAAA
77760 TAAAAAA
1 TAAAAAA
*
77767 TAAAATA
1 TAAAAAA
*
77774 TAAAAGA
1 TAAAAAA
77781 TAA
1 TAA
77784 TAATAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
7 27 0.75
8 4 0.11
9 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.02, T:0.21
Consensus pattern (7 bp):
TAAAAAA
Found at i:78216 original size:37 final size:37
Alignment explanation
Indices: 78166--78347 Score: 319
Period size: 37 Copynumber: 4.9 Consensus size: 37
78156 TTATGGATCC
*
78166 TATTTTTAGGAGTTTGAATCTTAGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
* *
78203 TATTTTTACGAGTTTGAATCATAGTAAAACTATATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
* *
78240 TATTTTTAGGAGTTTGAATCTTCGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
78277 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
78314 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
78348 ACGTTATGTT
Statistics
Matches: 136, Mismatches: 9, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 136 1.00
ACGTcount: A:0.34, C:0.11, G:0.13, T:0.42
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCA
Found at i:78912 original size:84 final size:84
Alignment explanation
Indices: 78800--79825 Score: 943
Period size: 84 Copynumber: 12.3 Consensus size: 84
78790 TTTGCCTCTA
* * * * *
78800 AGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTATCGACTTAAGTTATAC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
*
78865 TGCAAAAGATGTGCCTTGG
66 TGCAAATGATGTGCCTTGG
* * ** * ** * *
78884 AGCTTAGCGTAGTCAAACTCGAAGGTCTTTTGG-TGATAAATAACTATTCTAGCCTTGAA-TTAT
1 AGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTT-AAGTTAT
* * * * *
78947 GTTGTAAATGATGCGCCGTCGA
64 GCTGCAAATGATGTGCC-TTGG
* * * * * *
78969 AGCTGAGTGTAATCGAACTCG-AGCGTC--T--TTGGAAGATAGCCATTCTCGACTTAAGTTACG
1 AGCTGAGCGTAGTCGAACTCGAAG-GTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* *
79029 TTGCAAATGATGCGCCTTGG
65 CTGCAAATGATGTGCCTTGG
* * ** * * *
79049 AGCTGAGCGTAGTCAAACTCGAAGGCCTTTTGG-TCACAGATAGCCCTTCT-AACATTGAGTTAT
1 AGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGAC-TTAAGTTAT
* * *
79112 GCT-CTAAATGATATGCCCTCGA
64 GCTGC-AAATGATGTG-CCTTGG
* * * * *
79134 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGG-T---AGATATCCCTTCTCGACTTAAGCTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
*
79195 TGTAAATGATGTGCCTTGG
66 TGCAAATGATGTGCCTTGG
*
79214 AGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
*
79279 TGCAAATGATATGCCTTGG
66 TGCAAATGATGTGCCTTGG
** * * *
79298 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TCACAGATAACCCTTCTAGCCTTGAGTTATG
1 AGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * *
79362 CTGTAAATGATGTGCCCTCGA
65 CTGCAAATGATGTG-CCTTGG
* * * * *
79383 ATCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAGCTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
*
79444 TGCAAATGATGTTCCTTGG
66 TGCAAATGATGTGCCTTGG
* * * * * *
79463 AGTTGATCGTAGTCAAACTTGAAGATCTTTGGTTGGCAGATAACCCTTCTCAACTTAAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* *
79528 TACAAAATGATATGCCTTGG
66 TGC-AAATGATGTGCCTTGG
* ** * * * *
79548 AGTTGAGCGTAGTCGAACTCGAAGGTCTTTCGG-TCACCGATAACCCTTCT-AACATTGATTTAT
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GGTTGGCAGATAACCCTTCTCGAC-TTAAGTTAT
* * *
79611 GCT-CTAAATGATGTACCCTCGA
64 GCTGC-AAATGATGT-GCCTTGG
* * *
79633 AGCTGAGTGTAATCGAACTCG-AGGT-TTT--TTGGCAGATAACCCTTCTCGACTTAAGCTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
79694 TGCAAATGATGTGCCTTGG
66 TGCAAATGATGTGCCTTGG
* *
79713 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCATATAACCCTTCTCAACTTAAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
** * *
79778 TTAAAATGATATGCTTTGG
66 TGCAAATGATGTGCCTTGG
*
79797 AGCTGAGCGCAGTCGAACTCGAAGGTCTT
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
79826 GACTGAATGA
Statistics
Matches: 756, Mismatches: 147, Indels: 78
0.77 0.15 0.08
Matches are distributed among these distances:
80 101 0.13
81 142 0.19
82 11 0.01
83 7 0.01
84 320 0.42
85 173 0.23
86 2 0.00
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.31
Consensus pattern (84 bp):
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
TGCAAATGATGTGCCTTGG
Found at i:79266 original size:249 final size:249
Alignment explanation
Indices: 78997--79825 Score: 1289
Period size: 249 Copynumber: 3.3 Consensus size: 249
78987 TCGAGCGTCT
* * * * * * **
78997 TTGGAAGATAGCCATTCTCGACTTAAGTTACGTTGCAAATGATGCGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * * *
79062 CAAACTCGAAGGCCTTTTGGTCACAGATAGCCCTTCTAACATTGAGTTATGCTCTAAATGATATG
66 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAACATTGAGTTATGCTCTAAATGATGTG
* *
79127 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGTAGATATCCCTTCTCGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTA
* *
79192 TGCTGTAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGG
196 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
*
79246 TTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
1 TTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
* * *
79311 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG
66 CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAACATTGAGTTATGCTCTAAATGATGTG
*
79376 CCCTCGAATCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTA
131 CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTA
* * * * * *
79441 TGCTGCAAATGATGTTCCTTGGAGTTGATCGTAGTCAAACTTGAAGATCTTTGG
196 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* *
79495 TTGGCAGATAACCCTTCTCAACTTAAGTTATGCTACAAAATGATATGCCTTGGAGTTGAGCGTAG
1 TTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGC-AAATGATATGCCTTGGAGCTGAGCGTAG
* * *
79560 TCGAACTCGAAGGTCTTTCGGTCACCGATAACCCTTCTAACATTGATTTATGCTCTAAATGATGT
65 TCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAACATTGAGTTATGCTCTAAATGATGT
* * *
79625 ACCCTCGAAGCTGAGTGTAATCGAACTCGAGGTTTTTTGGCAGATAACCCTTCTCGACTTAAGCT
130 GCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCT
79690 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
195 ATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
* ** * *
79745 TTGGCATATAACCCTTCTCAACTTAAGTTATGCTTAAAATGATATGCTTTGGAGCTGAGCGCAGT
1 TTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
79810 CGAACTCGAAGGTCTT
66 CGAACTCGAAGGTCTT
79826 GACTGAATGA
Statistics
Matches: 529, Mismatches: 50, Indels: 2
0.91 0.09 0.00
Matches are distributed among these distances:
249 300 0.57
250 229 0.43
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.31
Consensus pattern (249 bp):
TTGGCAGATAACCCTTCTCAACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGT
CGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAACATTGAGTTATGCTCTAAATGATGTG
CCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTA
TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG
Found at i:79577 original size:414 final size:417
Alignment explanation
Indices: 78771--79742 Score: 1275
Period size: 414 Copynumber: 2.3 Consensus size: 417
78761 TCTTGCCTTG
*
78771 AGCTATGCTGTAAATTTGATTTGCCTCT-AAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTG
1 AGCTATGCTGTAAA--TGATGTGCCT-TGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTG
* * * * * *
78835 GCAGATAGCCCTTATCGACTTAAGTTATACTGCAAAAGATGTGCCTTGGAGCTTAGCGTAGTCAA
63 GCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
* * * * *
78900 ACTCGAAGGTCTTTTGGTGATAAATAACTATTCTAGCCTTGAATTATGTTGTAAATGATGCGCCG
128 ACTCGAAGGTCTTTTGGTCACAAATAACCATTCTAGCCTTGAATTATGCTGTAAATGATGCGCCC
* * *
78965 TCGAAGCTGAGTGTAATCGAACTCGAGCGTCTTTGGAAGATAGCCATTCTCGACTTAAGTTACGT
193 TCGAAGCTGAGTGTAATCGAACTCGAGCGTCTTTGGAAGATAACCATTCTCGACTTAAGCTACGC
* *
79030 TGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGCCTTTTGGTCACAGATAGCCC
258 TGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGACCTTTTGGTCACAGATAACCC
* * * *
79095 TTCTAACATTGAGTTATGCTCTAAATGATATGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGT
323 TTCTAACATTAAGTTATGCTCAAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGT
* *
79160 CTTT-GGT-A-GATATCCCTTCTCGAC-TTA
388 CTTTCGGTCACGATAACCCTTCT-AACATTA
* ** *
79187 AGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCA
1 AGCTATGCTGTAAATGATGTGCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCA
*
79252 GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACT
66 GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
* * * *
79317 CGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCG
131 CGAAGGTCTTTTGGTCACAAATAACCATTCTAGCCTTGAATTATGCTGTAAATGATGCGCCCTCG
* * * * *
79382 AATCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGC
196 AAGCTGAGTGTAATCGAACTCGAGCGTCTTTGGAAGATAACCATTCTCGACTTAAGCTACGCTGC
** * * * * **
79447 AAATGATGTTCCTTGGAGTTGATCGTAGTCAAACTTGAAGATC-TTTGGTTGGCAGATAACCCTT
261 AAATGATGCGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGACCTTTTGG-TCACAGATAACCCTT
* * * *
79511 CTCAAC-TTAAGTTATGCTACAAAATGATATG-CCTTGGAGTTGAGCGTAGTCGAACTCGAAGGT
325 CT-AACATTAAGTTATGCT-CAAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGT
*
79574 CTTTCGGTCACCGATAACCCTTCTAACATTG
388 CTTTCGGTCA-CGATAACCCTTCTAACATTA
** * * *
79605 ATTTATGCTCTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCG-AGGT-TTT--TTGGC
1 AGCTATGCTGTAAATGATGT-GCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGC
*
79666 AGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
65 AGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAAC
79731 TCGAAGGTCTTT
130 TCGAAGGTCTTT
79743 GGTTGGCATA
Statistics
Matches: 485, Mismatches: 61, Indels: 21
0.86 0.11 0.04
Matches are distributed among these distances:
413 6 0.01
414 306 0.63
415 97 0.20
416 15 0.03
417 5 0.01
418 34 0.07
419 22 0.05
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.31
Consensus pattern (417 bp):
AGCTATGCTGTAAATGATGTGCCTTGAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCA
GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACT
CGAAGGTCTTTTGGTCACAAATAACCATTCTAGCCTTGAATTATGCTGTAAATGATGCGCCCTCG
AAGCTGAGTGTAATCGAACTCGAGCGTCTTTGGAAGATAACCATTCTCGACTTAAGCTACGCTGC
AAATGATGCGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGACCTTTTGGTCACAGATAACCCTTC
TAACATTAAGTTATGCTCAAAATGATATGCCCTCGAAGCTGAGCGTAATCGAACTCGAAGGTCTT
TCGGTCACGATAACCCTTCTAACATTA
Found at i:79758 original size:165 final size:164
Alignment explanation
Indices: 78794--79787 Score: 949
Period size: 165 Copynumber: 6.0 Consensus size: 164
78784 ATTTGATTTG
* * *
78794 CCTCTAAGCTGAGTGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAGCCCTTATCGACTTAAG
1 CCTCGAAGCTGAGTGTAATCGAACTCGAAGGT-TTT--TTGGCAGATAACCCTTCTCGACTTAAG
* * * * * *
78859 TTATACTGCAAAAGATGTGCCTTGGAGCTTAGCGTAGTCAAACTCGAAGGTCTTTTGGTGATAAA
63 TTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGA
** * * *
78924 TAACTATTCT-AGCCTTGAA-TTATGTTGTAAATGATG-C
127 TAACCCTTCTCA-ACTT-AAGTTATGCTCTAAATGATGTC
* * * *
78961 GCCGTCGAAGCTGAGTGTAATCGAACTCG-AGCG-TCTTTGGAAGATAGCCATTCTCGACTTAAG
1 -CC-TCGAAGCTGAGTGTAATCGAACTCGAAG-GTTTTTTGGCAGATAACCCTTCTCGACTTAAG
* * * * * *
79024 TTACGTTGCAAATGATGCGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGCCTTTTGGTCACAGA
63 TTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTGACAGA
* * *
79089 TAGCCCTTCT-AACATTGAGTTATGCTCTAAATGATATGC
127 TAACCCTTCTCAAC-TTAAGTTATGCTCTAAATGATGT-C
* * * * *
79128 CCTCGAAGCTGAGTGTAATCGAACTCG-AGGGTCTTTGGTAGATATCCCTTCTCGACTTAAGCTA
1 CCTCGAAGCTGAGTGTAATCGAACTCGAAGGTTTTTTGGCAGATAACCCTTCTCGACTTAAGTTA
* * *
79192 TGCTGTAAATGATGTGCCTTGGAGCTGAGCATAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAA
66 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAA
* * *
79257 CCCTTCTCGACTTAAGTTATGCTGC-AAATGATATG
130 CCCTTCTCAACTTAAGTTATGCT-CTAAATGATGTC
* * * * * * * *
79292 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
1 CCTCGAAGCTGAGTGTAATCGAACTCGAAGGTTTTTTGG---CAGATAACCCTTCTCGACTTAAG
* * * * * * *
79357 TTATGCTGTAAATGATGTGCCCTCGAATCTGAGTGTAATCGAACTCGAGGGTCTTT-G-G-CAGA
63 TTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGA
* * *
79419 TAACCCTTCTCGACTTAAGCTATGCTGC-AAATGATGTT
127 TAACCCTTCTCAACTTAAGTTATGCT-CTAAATGATGTC
* * * * * * * *
79457 CCTTGGAGTTGA-TCGTAGTCAAACTTGAAGATCTTTGGTTGGCAGATAACCCTTCTCAACTTAA
1 CCTCGAAGCTGAGT-GTAATCGAACTCGAAGGT-TTT--TTGGCAGATAACCCTTCTCGACTTAA
* * * * *
79521 GTTATGCTACAAAATGATATGCCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTCGGTCACC
62 GTTATGCTGC-AAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GGTGACA
* *
79586 GATAACCCTTCT-AACATTGATTTATGCTCTAAATGATGTAC
125 GATAACCCTTCTCAAC-TTAAGTTATGCTCTAAATGATGT-C
*
79627 CCTCGAAGCTGAGTGTAATCGAACTCG-AGGTTTTTTGGCAGATAACCCTTCTCGACTTAAGCTA
1 CCTCGAAGCTGAGTGTAATCGAACTCGAAGGTTTTTTGGCAGATAACCCTTCTCGACTTAAGTTA
* *
79691 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCATATAA
66 TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGG-TGACAGATAA
79756 CCCTTCTCAACTTAAGTTATGCT-TAAAATGAT
130 CCCTTCTCAACTTAAGTTATGCTCT-AAATGAT
79788 ATGCTTTGGA
Statistics
Matches: 687, Mismatches: 108, Indels: 65
0.80 0.13 0.08
Matches are distributed among these distances:
164 34 0.05
165 437 0.64
166 53 0.08
167 4 0.01
168 51 0.07
169 88 0.13
170 19 0.03
171 1 0.00
ACGTcount: A:0.26, C:0.20, G:0.23, T:0.31
Consensus pattern (164 bp):
CCTCGAAGCTGAGTGTAATCGAACTCGAAGGTTTTTTGGCAGATAACCCTTCTCGACTTAAGTTA
TGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTGACAGATAAC
CCTTCTCAACTTAAGTTATGCTCTAAATGATGTC
Found at i:81100 original size:83 final size:88
Alignment explanation
Indices: 80969--81195 Score: 259
Period size: 95 Copynumber: 2.6 Consensus size: 88
80959 GGCTAGCTGA
* *
80969 ATCCATAAAGCCGAGGCGTTTAACCAATTGCTCTAGAGGGATAACTCAA-TA-TG-TA-AA-CAC
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATTGTTATAATCAC
* *
81029 CTGTATCAGGTTAGCTGAATCTT
66 CTGTATCAGGCTAGCTGAATATT
* *
81052 ATCCATAAAGCCGGGGAGTTTAACCAATTGC-CTTAGAGGGACAGCTCAAGCTTTATTGTATATT
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTC-TAGAGGGACAACTCAA---TTATTG----TT
*
81116 ATAATCACCTTTATCAGGCTAGCTGAATATT
58 ATAATCACCTGTATCAGGCTAGCTGAATATT
* *
81147 ATCCATAAAACCGGGGCGTTTAACCAGTTGCTCTAGAGGGACAACTCAA
1 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAA
81196 GCTTTATTGT
Statistics
Matches: 119, Mismatches: 11, Indels: 16
0.82 0.08 0.11
Matches are distributed among these distances:
82 1 0.01
83 43 0.36
87 2 0.02
88 2 0.02
93 2 0.02
94 2 0.02
95 66 0.55
96 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (88 bp):
ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAATTATTGTTATAATCAC
CTGTATCAGGCTAGCTGAATATT
Found at i:81189 original size:95 final size:96
Alignment explanation
Indices: 81017--81216 Score: 296
Period size: 95 Copynumber: 2.1 Consensus size: 96
81007 GGATAACTCA
* * * * *
81017 ATATGTAAACACCTGTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGAGTTTAACCAATTG
1 ATATATAATCACCTGTATCAGGCTAGCTGAATATTATCCATAAAACCGGGGAGTTTAACCAATTG
*
81082 CCTTAGAGGGACAGCTCAAGCTTTATTGTAT
66 CCTTAGAGGGACAACTCAAGCTTTATTGTAT
* * *
81113 AT-TATAATCACCTTTATCAGGCTAGCTGAATATTATCCATAAAACCGGGGCGTTTAACCAGTTG
1 ATATATAATCACCTGTATCAGGCTAGCTGAATATTATCCATAAAACCGGGGAGTTTAACCAATTG
81177 -CTCTAGAGGGACAACTCAAGCTTTATTGTAT
66 CCT-TAGAGGGACAACTCAAGCTTTATTGTAT
81208 ATATATAAT
1 ATATATAAT
81217 ATTATAATCT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
94 2 0.02
95 83 0.89
96 8 0.09
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (96 bp):
ATATATAATCACCTGTATCAGGCTAGCTGAATATTATCCATAAAACCGGGGAGTTTAACCAATTG
CCTTAGAGGGACAACTCAAGCTTTATTGTAT
Found at i:85079 original size:34 final size:31
Alignment explanation
Indices: 85020--85085 Score: 89
Period size: 32 Copynumber: 2.0 Consensus size: 31
85010 AACTTGTTAG
85020 ATAAAAAAATGAAAATAAATAGAATAAAGAAA
1 ATAAAAAAATGAAAATAAATAGAATAAA-AAA
85052 ATAAAAAAATGACCAAAATAAAT-GAATAAAAAA
1 ATAAAAAAATG---AAAATAAATAGAATAAAAAA
85085 A
1 A
85086 GAATGAAGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
32 11 0.35
33 4 0.13
34 7 0.23
35 9 0.29
ACGTcount: A:0.74, C:0.03, G:0.08, T:0.15
Consensus pattern (31 bp):
ATAAAAAAATGAAAATAAATAGAATAAAAAA
Found at i:85228 original size:17 final size:19
Alignment explanation
Indices: 85206--85245 Score: 57
Period size: 17 Copynumber: 2.2 Consensus size: 19
85196 AAAACAAATG
*
85206 TAAAGATGAT-AA-AAAAA
1 TAAAGATAATGAATAAAAA
85223 TAAAGATAATGAATAAAAA
1 TAAAGATAATGAATAAAAA
85242 TAAA
1 TAAA
85246 AAAGAAATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 9 0.45
18 2 0.10
19 9 0.45
ACGTcount: A:0.70, C:0.00, G:0.10, T:0.20
Consensus pattern (19 bp):
TAAAGATAATGAATAAAAA
Found at i:85274 original size:10 final size:10
Alignment explanation
Indices: 85237--85294 Score: 53
Period size: 10 Copynumber: 5.3 Consensus size: 10
85227 GATAATGAAT
85237 AAAAATAAAA
1 AAAAATAAAA
85247 AAGAAATATAGGAA
1 AA-AAATA-A--AA
85261 AAAAATAAAA
1 AAAAATAAAA
* *
85271 AAAAGTAAAT
1 AAAAATAAAA
85281 AAAAATAAATA
1 AAAAATAAA-A
85292 AAA
1 AAA
85295 TAGAATAAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
10 20 0.51
11 8 0.21
12 2 0.05
13 5 0.13
14 4 0.10
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (10 bp):
AAAAATAAAA
Found at i:85286 original size:20 final size:20
Alignment explanation
Indices: 85218--85305 Score: 74
Period size: 20 Copynumber: 4.2 Consensus size: 20
85208 AAGATGATAA
* *
85218 AAAAATAAAGATAAT-GAAT
1 AAAAATAAAAAAAATAGAAT
85237 AAAAATAAAAAAGAAATATAGGAA-
1 AAAAAT--AAAA-AAA-ATA-GAAT
85261 AAAAATAAAAAAAAGTA-AAT
1 AAAAATAAAAAAAA-TAGAAT
*
85281 AAAAATAAATAAAATAGAAT
1 AAAAATAAAAAAAATAGAAT
85301 AAAAA
1 AAAAA
85306 GCAGTAAGTA
Statistics
Matches: 57, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
19 10 0.18
20 22 0.39
21 8 0.14
22 6 0.11
23 2 0.04
24 6 0.11
25 3 0.05
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (20 bp):
AAAAATAAAAAAAATAGAAT
Found at i:85301 original size:10 final size:9
Alignment explanation
Indices: 85162--85304 Score: 51
Period size: 9 Copynumber: 15.0 Consensus size: 9
85152 AACAAACAAG
85162 TAAATAAAA
1 TAAATAAAA
85171 -AAATAAGAA
1 TAAATAA-AA
*
85180 GAAAATACAAA
1 -TAAATA-AAA
85191 TAAATAAAA
1 TAAATAAAA
*
85200 CAAATGTAAAGA
1 TAAA--TAAA-A
*
85212 TGATAAAAAAA
1 T-A-AATAAAA
* *
85223 TAAAGATAA
1 TAAATAAAA
*
85232 TGAATAAAA
1 TAAATAAAA
85241 -ATAA-AAAA
1 TA-AATAAAA
* * *
85249 GAAATATAG
1 TAAATAAAA
*
85258 GAAA-AAAA
1 TAAATAAAA
*
85266 TAAAAAAAA
1 TAAATAAAA
85275 GTAAATAAAAA
1 -TAAAT-AAAA
85286 TAAATAAAA
1 TAAATAAAA
85295 TAGAATAAAA
1 TA-AATAAAA
85305 AGCAGTAAGT
Statistics
Matches: 102, Mismatches: 16, Indels: 31
0.68 0.11 0.21
Matches are distributed among these distances:
8 17 0.17
9 38 0.37
10 22 0.22
11 17 0.17
12 5 0.05
13 1 0.01
14 2 0.02
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.17
Consensus pattern (9 bp):
TAAATAAAA
Found at i:85568 original size:17 final size:17
Alignment explanation
Indices: 85548--85676 Score: 66
Period size: 18 Copynumber: 7.2 Consensus size: 17
85538 ATATGCATAT
** *
85548 AAATAAAATATTTTAAA
1 AAATAAAATAAATAAAA
85565 AAATAATAATAAATAAAA
1 AAATAA-AATAAATAAAA
*
85583 AAATAAAAAAAATAAAA
1 AAATAAAATAAATAAAA
* *
85600 TATATAAAAGATAATAATAA
1 -AAATAAAATA-AATAA-AA
* *
85620 TAATAATAATAAAGTATATA
1 AAATAA-AATAAA-TA-AAA
* *
85640 TAATAATAAT-AGTAAAAA
1 AAATAA-AATAAAT-AAAA
85658 AAATAAAAT--ATAAAA
1 AAATAAAATAAATAAAA
85673 AAAT
1 AAAT
85677 TGAATTTTTT
Statistics
Matches: 90, Mismatches: 14, Indels: 18
0.74 0.11 0.15
Matches are distributed among these distances:
15 8 0.09
16 1 0.01
17 19 0.21
18 30 0.33
19 13 0.14
20 18 0.20
21 1 0.01
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (17 bp):
AAATAAAATAAATAAAA
Found at i:85574 original size:3 final size:3
Alignment explanation
Indices: 85566--85650 Score: 61
Period size: 3 Copynumber: 28.3 Consensus size: 3
85556 TATTTTAAAA
* * * *
85566 AAT AAT AAT AAAT AA- AAA AAT AAA AAA AAT AA- AAT ATAT AAA AGAT
1 AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT A-AT
*
85612 AAT AAT AAT AAT AAT AAT AA- AGT -AT ATAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT A
85651 GTAAAAAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
2 6 0.09
3 50 0.75
4 11 0.16
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:85615 original size:43 final size:44
Alignment explanation
Indices: 85548--85632 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 44
85538 ATATGCATAT
*
85548 AAATAAAATATTTTAAAAAATAATAATAAATAA-AAAAATAAAAA
1 AAATAAAATATTATAAAAAATAATAAT-AATAATAAAAATAAAAA
* *
85592 AAATAAAATA-TATAAAAGATAATAATAATAATAATAATAAA
1 AAATAAAATATTATAAAAAATAATAATAATAATAAAAATAAA
85633 GTATATATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
42 5 0.14
43 22 0.59
44 10 0.27
ACGTcount: A:0.73, C:0.00, G:0.01, T:0.26
Consensus pattern (44 bp):
AAATAAAATATTATAAAAAATAATAATAATAATAAAAATAAAAA
Found at i:86066 original size:37 final size:37
Alignment explanation
Indices: 86015--86122 Score: 162
Period size: 37 Copynumber: 2.9 Consensus size: 37
86005 TTATAGATCC
*
86015 TATTTTTAGAAGTTTGAATCTTAATAAAACTCTATCA
1 TATTTTTAGAAGTTTGAATCATAATAAAACTCTATCA
* * * *
86052 TATTTTTAGGAGTTTGAATAATAGTAAAACTCTATTA
1 TATTTTTAGAAGTTTGAATCATAATAAAACTCTATCA
*
86089 TATTTTTAGAAGTTTGAATCCTAATAAAACTCTA
1 TATTTTTAGAAGTTTGAATCATAATAAAACTCTA
86123 ACGTTATGTT
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 62 1.00
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (37 bp):
TATTTTTAGAAGTTTGAATCATAATAAAACTCTATCA
Found at i:90529 original size:14 final size:14
Alignment explanation
Indices: 90510--90537 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
90500 ACACTTGTGC
90510 ATCTTTTACTTTTT
1 ATCTTTTACTTTTT
90524 ATCTTTTACTTTTT
1 ATCTTTTACTTTTT
90538 TACTTGCTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.14, G:0.00, T:0.71
Consensus pattern (14 bp):
ATCTTTTACTTTTT
Found at i:97410 original size:23 final size:23
Alignment explanation
Indices: 97384--97448 Score: 69
Period size: 23 Copynumber: 2.8 Consensus size: 23
97374 CAGCTCGTAT
97384 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATGTAG
* **
97407 AATTGCACC-AGAGTGTCGCGTAG
1 AATTGCACCGA-AGTGCCATGTAG
* *
97430 AATTGCACAGTAGTGCCAT
1 AATTGCACCGAAGTGCCAT
97449 ATAATAATGT
Statistics
Matches: 32, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
22 1 0.03
23 31 0.97
ACGTcount: A:0.29, C:0.22, G:0.26, T:0.23
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAG
Found at i:97634 original size:103 final size:103
Alignment explanation
Indices: 97467--97671 Score: 356
Period size: 103 Copynumber: 2.0 Consensus size: 103
97457 GTCCATAAGG
* * *
97467 ACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATATGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATATGTCTCACCAGACT
97532 TCACACATGTTCCAAAAAATACATATATGTCCCGAAGA
66 TCACACATGTTCCAAAAAATACATATATGTCCCGAAGA
* *
97570 ACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAATATGTGTCTCACCAGACT
1 ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATATGTCTCACCAGACT
*
97635 TCACACATGTTCCAAAGAATACATATATGTCCCGAAG
66 TCACACATGTTCCAAAAAATACATATATGTCCCGAAG
97672 GACCGCGTAG
Statistics
Matches: 96, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 96 1.00
ACGTcount: A:0.38, C:0.24, G:0.11, T:0.27
Consensus pattern (103 bp):
ACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAATATATGTCTCACCAGACT
TCACACATGTTCCAAAAAATACATATATGTCCCGAAGA
Found at i:106583 original size:20 final size:20
Alignment explanation
Indices: 106546--106584 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
106536 GTACATAACT
* * *
106546 TAAACCTTATACCTTAAACA
1 TAAACCCTAAACCCTAAACA
106566 TAAACCCTAAACCCTAAAC
1 TAAACCCTAAACCCTAAAC
106585 CTTATTACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (20 bp):
TAAACCCTAAACCCTAAACA
Found at i:106603 original size:28 final size:27
Alignment explanation
Indices: 106546--106618 Score: 92
Period size: 28 Copynumber: 2.7 Consensus size: 27
106536 GTACATAACT
* *
106546 TAAACCTTATACCTTAAACATAAACCC
1 TAAACCCTAAACCTTAAACATAAACCC
* *
106573 TAAACCCTAAACCTTATTACATAAATCC
1 TAAACCCTAAACCTTA-AACATAAACCC
*
106601 TAAACTCTAAACCTTAAA
1 TAAACCCTAAACCTTAAA
106619 TCCTATCACA
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
27 15 0.38
28 24 0.62
ACGTcount: A:0.45, C:0.27, G:0.00, T:0.27
Consensus pattern (27 bp):
TAAACCCTAAACCTTAAACATAAACCC
Found at i:106672 original size:28 final size:28
Alignment explanation
Indices: 106603--106668 Score: 125
Period size: 28 Copynumber: 2.4 Consensus size: 28
106593 ATAAATCCTA
106603 AACTCTAAACCTTAAATCCTATCACATT
1 AACTCTAAACCTTAAATCCTATCACATT
106631 AACTCTAAACCTTAAATCCTATCACATT
1 AACTCTAAACCTTAAATCCTATCACATT
106659 -ACTCTAAACC
1 AACTCTAAACC
106669 CTTATAAAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 10 0.26
28 28 0.74
ACGTcount: A:0.39, C:0.30, G:0.00, T:0.30
Consensus pattern (28 bp):
AACTCTAAACCTTAAATCCTATCACATT
Found at i:108939 original size:14 final size:14
Alignment explanation
Indices: 108922--108962 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
108912 TTTATTCATC
108922 AATAATGTATTTTT
1 AATAATGTATTTTT
108936 AAT-A--TATTTTT
1 AATAATGTATTTTT
*
108947 AATAATGTAATTTT
1 AATAATGTATTTTT
108961 AA
1 AA
108963 AAAATATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
11 10 0.43
12 1 0.04
13 1 0.04
14 11 0.48
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (14 bp):
AATAATGTATTTTT
Found at i:110294 original size:36 final size:36
Alignment explanation
Indices: 110232--110747 Score: 347
Period size: 36 Copynumber: 14.9 Consensus size: 36
110222 CAAAGGTTGG
*
110232 TGTTTCAAGAGAAAC--TCTCAAGAGAGACAAAACT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
110266 TGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
110303 AGTTCCAAAAGAAACTATCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* **
110339 TGTTTCAAG-GAAAACAGAT-TC-A-A-AG----TTTT
1 TGTTTCAAGAG-AAACTG-TCTCAAGAGAGACAAAATT
* *
110368 TGTTTCAAGGGAAACTGTCTCAAGATAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
110404 TGTTTTAAGAGAAACTATCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * *
110441 AGTTCCAAAAGAAACTGTCTTCAAGGGAGACAAAATA
1 TGTTTCAAGAGAAACTGTC-TCAAGAGAGACAAAATT
* *
110478 TGTTTCAAG-GAAAACAGAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAACTG-TCTCAAGAGAGACAAAATT
*
110507 TGTTTCAAGGGAAACTGTCTCAAGAGAGAC--AATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
110541 TGTTTTAAGAGAAAATGTTTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * * * *
110577 TGTTTTAAAAGAAACTGTCTCAAGGGAAACGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
110613 TGTTTCAAG-GAAAACAGAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAACTG-TCTCAAGAGAGACAAAATT
* * **
110642 TGTTTCAAGGGAAACTTTCTTTAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
110678 TGTTTTAAGAGAAAATGTCTCAAGATAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
110714 TGTTTTAAAAGAAACTGTATCAAGAGAGACAAAA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
110748 CTTTTTTTTG
Statistics
Matches: 372, Mismatches: 72, Indels: 74
0.72 0.14 0.14
Matches are distributed among these distances:
28 3 0.01
29 53 0.14
30 6 0.02
31 3 0.01
32 6 0.02
33 5 0.01
34 43 0.12
35 5 0.01
36 175 0.47
37 58 0.16
38 15 0.04
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.27
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:110552 original size:19 final size:19
Alignment explanation
Indices: 110528--110584 Score: 59
Period size: 15 Copynumber: 3.1 Consensus size: 19
110518 AAACTGTCTC
110528 AAGAGAGACAATTTGTTTT
1 AAGAGAGACAATTTGTTTT
*
110547 AAGAGA-A-AA--TGTTTC
1 AAGAGAGACAATTTGTTTT
110562 AAGAGAGACAAAATTTGTTTT
1 AAGAGAGAC--AATTTGTTTT
110583 AA
1 AA
110585 AAGAAACTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
15 11 0.37
16 1 0.03
17 2 0.07
18 1 0.03
19 8 0.27
21 7 0.23
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (19 bp):
AAGAGAGACAATTTGTTTT
Found at i:110565 original size:15 final size:15
Alignment explanation
Indices: 110507--110567 Score: 50
Period size: 15 Copynumber: 3.8 Consensus size: 15
110497 TCAAAGATTT
* *
110507 TGTTTCAAGGGAAAC
1 TGTTTCAAGAGAAAA
*
110522 TGTCTCAAGAGAGACAA
1 TGTTTCAAGAGA-A-AA
*
110539 TTTGTTTTAAGAGAAAA
1 --TGTTTCAAGAGAAAA
110556 TGTTTCAAGAGA
1 TGTTTCAAGAGA
110568 GACAAAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
15 21 0.58
16 1 0.03
17 3 0.08
18 1 0.03
19 10 0.28
ACGTcount: A:0.38, C:0.10, G:0.23, T:0.30
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:110737 original size:137 final size:138
Alignment explanation
Indices: 110202--110747 Score: 746
Period size: 137 Copynumber: 4.0 Consensus size: 138
110192 AGGTCTTTTG
* * * *
110202 TGTTTCAA-GAGAAACATATTCAAAGGTTGGTGTTTCAAGAGAAAC--TCTCAAGAGAGACAAAA
1 TGTTTCAAGGA-AAACAGATTCAAAGATT-TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* * * * * *
110264 CTTGTTTCAAGGGAAACTGTCTCAAAAGAGACAAAACTTAGTTCCAAAAGAAACTATCTCAAGGG
64 TTTGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGG
110329 AGACAAAATT
129 AGACAAAATT
* *
110339 TGTTTCAAGGAAAACAGATTCAAAGTTTTTGTTTCAAGGGAAACTGTCTCAAGATAGACAAAATT
1 TGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* *
110404 TGTTTTAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTTCAAGGGA
66 TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTC-TCAAGGGA
*
110469 GACAAAATA
130 GACAAAATT
110478 TGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC--AATT
1 TGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * ** *
110541 TGTTTTAAGAGAAAATGTTTCAAGAGAGACAAAA-TTTGTTTTAAAAGAAACTGTCTCAAGGGAA
66 TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAG
*
110605 ACGAAATT
131 ACAAAATT
* **
110613 TGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTTTCTTTAGAGAGACAAAATT
1 TGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
* * ** * *
110678 TGTTTTAAGAGAAAATGTCTCAAGATAGACAAAA-TTTGTTTTAAAAGAAACTGTATCAAGAGAG
66 TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAG
110742 ACAAAA
131 ACAAAA
110748 CTTTTTTTTG
Statistics
Matches: 371, Mismatches: 32, Indels: 12
0.89 0.08 0.03
Matches are distributed among these distances:
135 70 0.19
136 32 0.09
137 126 0.34
138 70 0.19
139 73 0.20
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (138 bp):
TGTTTCAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
TGTTTTAAGAGAAAATGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGGGAG
ACAAAATT
Found at i:112221 original size:95 final size:94
Alignment explanation
Indices: 112041--112302 Score: 346
Period size: 95 Copynumber: 2.7 Consensus size: 94
112031 GGCTAGTTGA
* * * * * *
112041 ATCCATAAAGCCGGGCCTTTAACCAATTGCTCTATAGGGACATCTTAATATCATTGTATAG-ATA
1 ATCCATAAAGCCGGGCGTTTAACCAATTGCTCTAGAGGGACAAC-TCA-AGC-TT-TATTGTATA
* *
112105 TTATAATCGCCTTTATCAGGCTAGCTGAATTTT
62 TTATAATCACCTTTATCAGGCTAGCTGAATCTT
112138 ATCCATAAAGCCGGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
1 ATCCATAAAGCC-GGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTA
112203 TAATCACCTTTATCAGGCTAGCTGAATCTT
65 TAATCACCTTTATCAGGCTAGCTGAATCTT
* * * *
112233 ATCCATAAAGCCAGGGCGTTTAACCAATTGCTTTAGAGGGATAGCTCAAGCTTTATTGTGTATAT
1 ATCCATAAAGCC-GGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATAT-T
112298 ATAAT
64 ATAAT
112303 ATTATAATGT
Statistics
Matches: 149, Mismatches: 13, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
94 4 0.03
95 94 0.63
96 8 0.05
97 14 0.09
98 29 0.19
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (94 bp):
ATCCATAAAGCCGGGCGTTTAACCAATTGCTCTAGAGGGACAACTCAAGCTTTATTGTATATTAT
AATCACCTTTATCAGGCTAGCTGAATCTT
Found at i:115950 original size:12 final size:12
Alignment explanation
Indices: 115933--115963 Score: 53
Period size: 12 Copynumber: 2.5 Consensus size: 12
115923 TATATAAAGT
115933 AAATAAATAAAA
1 AAATAAATAAAA
115945 AAATAAATAAAA
1 AAATAAATAAAA
115957 AGAATAA
1 A-AATAA
115964 GTCAAAAGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 13 0.72
13 5 0.28
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (12 bp):
AAATAAATAAAA
Found at i:117860 original size:18 final size:18
Alignment explanation
Indices: 117833--117884 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
117823 CTGGAATGTT
*
117833 TATGAGGGAATTGGAATC
1 TATGAAGGAATTGGAATC
117851 TATGAAGGAATTGGAATC
1 TATGAAGGAATTGGAATC
*
117869 --TGTAGGAATTGGAATC
1 TATGAAGGAATTGGAATC
117885 CAATTCCATA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
16 15 0.47
18 17 0.53
ACGTcount: A:0.35, C:0.06, G:0.31, T:0.29
Consensus pattern (18 bp):
TATGAAGGAATTGGAATC
Found at i:118520 original size:27 final size:28
Alignment explanation
Indices: 118458--118524 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
118448 CCTAAAACCG
*
118458 AACCCGACCCGAATATCACATTTAAAAA
1 AACCCGACCCGAATATCACACTTAAAAA
118486 AACCCGACCCGAATATCACACTT-AAAA
1 AACCCGACCCGAATATCACACTTAAAAA
118513 AACCCGACCCGA
1 AACCCGACCCGA
118525 CCCGAACAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
27 16 0.42
28 22 0.58
ACGTcount: A:0.43, C:0.34, G:0.09, T:0.13
Consensus pattern (28 bp):
AACCCGACCCGAATATCACACTTAAAAA
Found at i:122881 original size:48 final size:48
Alignment explanation
Indices: 122828--122948 Score: 170
Period size: 48 Copynumber: 2.5 Consensus size: 48
122818 AACATATTAA
* **
122828 ATTAAATCTAACAACTTCTACAAAAAAAATAGTATACACTAGCTCTCC
1 ATTAAATCTAATAACTTCTACAAAAAAAATAGTATACACTAAATCTCC
* * *
122876 ATTAAATCTAATAACTTTTTCCAAAAAAATAGTATACACTAAATCTCC
1 ATTAAATCTAATAACTTCTACAAAAAAAATAGTATACACTAAATCTCC
* *
122924 ATTAAATCTAATAACTGCTCCAAAA
1 ATTAAATCTAATAACTTCTACAAAA
122949 CATAGTATAC
Statistics
Matches: 63, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 63 1.00
ACGTcount: A:0.46, C:0.21, G:0.03, T:0.30
Consensus pattern (48 bp):
ATTAAATCTAATAACTTCTACAAAAAAAATAGTATACACTAAATCTCC
Found at i:124168 original size:23 final size:23
Alignment explanation
Indices: 124141--124209 Score: 66
Period size: 23 Copynumber: 3.0 Consensus size: 23
124131 AGATTAAATT
*
124141 ATAAATTATGTATAATAATAATA
1 ATAAATTATATATAATAATAATA
* * * *
124164 CTAAAGTATAAATACTAATAATA
1 ATAAATTATATATAATAATAATA
* *
124187 ATTAATCATATAATAATAATAAT
1 ATAAATTATAT-ATAATAATAAT
124210 TAAAACATAA
Statistics
Matches: 34, Mismatches: 11, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
23 24 0.71
24 10 0.29
ACGTcount: A:0.57, C:0.04, G:0.03, T:0.36
Consensus pattern (23 bp):
ATAAATTATATATAATAATAATA
Found at i:125412 original size:17 final size:17
Alignment explanation
Indices: 125390--125449 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 17
125380 CTATTTGGAT
125390 CGGGTCTGGGTCTGCAC
1 CGGGTCTGGGTCTGCAC
* *
125407 CGGGTCTAGGTCTGTAC
1 CGGGTCTGGGTCTGCAC
* *
125424 CGGGTCTGGATGTGCAC
1 CGGGTCTGGGTCTGCAC
*
125441 CGGATCTGG
1 CGGGTCTGG
125450 TTGTAATATG
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 36 1.00
ACGTcount: A:0.10, C:0.25, G:0.40, T:0.25
Consensus pattern (17 bp):
CGGGTCTGGGTCTGCAC
Found at i:125555 original size:8 final size:8
Alignment explanation
Indices: 125542--125600 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
125532 AATAATTAGT
125542 TATAATAA
1 TATAATAA
125550 TATAATATTA
1 TATAATA--A
*
125560 TATACTAA
1 TATAATAA
125568 TA-AAGTAA
1 TATAA-TAA
125576 T-T-ATAA
1 TATAATAA
125582 TATAATAA
1 TATAATAA
*
125590 TATAATTA
1 TATAATAA
125598 TAT
1 TAT
125601 TGAAACCAAA
Statistics
Matches: 42, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
6 4 0.10
7 3 0.07
8 28 0.67
10 7 0.17
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.42
Consensus pattern (8 bp):
TATAATAA
Found at i:125580 original size:19 final size:18
Alignment explanation
Indices: 125533--125600 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 18
125523 TAAAATTATA
125533 ATAATTAGT-TATAATAAT
1 ATAATTA-TATATAATAAT
125551 ATAATATTATATACTAATAA-
1 AT-A-ATTATATA-TAATAAT
125571 AGTAATTATAATATAATAAT
1 A-TAATTAT-ATATAATAAT
125591 ATAATTATAT
1 ATAATTATAT
125601 TGAAACCAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
18 4 0.09
19 20 0.47
20 12 0.28
21 7 0.16
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (18 bp):
ATAATTATATATAATAAT
Found at i:125833 original size:36 final size:36
Alignment explanation
Indices: 125794--125925 Score: 192
Period size: 36 Copynumber: 3.7 Consensus size: 36
125784 TTACTTCTTT
* * *
125794 GTGAAGGCTGGATGTGCATTGCTTCACTACTCTTCT
1 GTGAAGGCTGAATGTGCATCGCTTCACTACTCTTCC
* *
125830 GTGAAGGTTGAATGTGCATCACTTCACTACTCTTCC
1 GTGAAGGCTGAATGTGCATCGCTTCACTACTCTTCC
* *
125866 GTGAAGGCTGAATGTGCATCGTTTCATTACTCTTCC
1 GTGAAGGCTGAATGTGCATCGCTTCACTACTCTTCC
*
125902 GTAAAGGCTGAATGTGCATCGCTT
1 GTGAAGGCTGAATGTGCATCGCTT
125926 GAAAGAATCT
Statistics
Matches: 85, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 85 1.00
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.34
Consensus pattern (36 bp):
GTGAAGGCTGAATGTGCATCGCTTCACTACTCTTCC
Found at i:130281 original size:2 final size:2
Alignment explanation
Indices: 130274--130311 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
130264 TAAACAAGAG
130274 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
130312 ATCATGAAAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:135563 original size:24 final size:20
Alignment explanation
Indices: 135506--135563 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
135496 TTCCCCTTGA
*
135506 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
135526 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
135549 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
135564 CTACCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:135638 original size:64 final size:63
Alignment explanation
Indices: 135551--135711 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 63
135541 TCTTTAACAT
* *
135551 GTGCATCGATGCACTACCCATGCATCGATACACCAA-T-CACCTTCGATGTTTTCATTTTAAAGG
1 GTGCATCGATGCACT-CCTATGCATCGATACACCAACTGCA--TTCGATGTTTCCATTTTAAAGG
135614 G
63 G
* * * *
135615 GTGCATCGATGCACTCCTTATGCATCGATGCACTAACTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTCC-TATGCATCGATACACCAACTGCATTCGATGTTTCCATTTTAAAGGG
* *
135679 GTGCATCCATGCACTTCCTGTGCATCGATACAC
1 GTGCATCGATGCAC-TCCTATGCATCGATACAC
135712 ACTGAACAAT
Statistics
Matches: 84, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
63 2 0.02
64 76 0.90
65 4 0.05
66 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.18, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCACTCCTATGCATCGATACACCAACTGCATTCGATGTTTCCATTTTAAAGGG
Found at i:138831 original size:32 final size:33
Alignment explanation
Indices: 138790--138871 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
138780 TCATATATCT
* *
138790 TATAACATATACA-ATAA-TCAT-TAACACACACA
1 TATATCATAT-CATATAATTCATATAACA-AAACA
*
138822 TATATCATATCATATAATTTATATAACAAAACA
1 TATATCATATCATATAATTCATATAACAAAACA
138855 TATATCTATATCATATA
1 TATATC-ATATCATATA
138872 TATTGTATTC
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
31 2 0.05
32 13 0.30
33 13 0.30
34 15 0.35
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (33 bp):
TATATCATATCATATAATTCATATAACAAAACA
Found at i:140190 original size:18 final size:18
Alignment explanation
Indices: 140169--140203 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
140159 TTCTTTAATA
140169 TCTTCTATATCTTTCATT
1 TCTTCTATATCTTTCATT
140187 TCTTCTATATCTTTCAT
1 TCTTCTATATCTTTCAT
140204 CTTGTTGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.23, G:0.00, T:0.60
Consensus pattern (18 bp):
TCTTCTATATCTTTCATT
Found at i:147575 original size:18 final size:18
Alignment explanation
Indices: 147549--147588 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
147539 ATGGACGGGG
* * *
147549 TCAGGGTCATTAGTCTCT
1 TCAGCGTCAGTAGGCTCT
147567 TCAGCGTCAGTAGGCTCT
1 TCAGCGTCAGTAGGCTCT
147585 TCAG
1 TCAG
147589 GTTCAGCAGG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.17, C:0.25, G:0.25, T:0.33
Consensus pattern (18 bp):
TCAGCGTCAGTAGGCTCT
Found at i:147594 original size:18 final size:17
Alignment explanation
Indices: 147553--147600 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 17
147543 ACGGGGTCAG
* *
147553 GGTCATTAGTCTCTTCA
1 GGTCAGTAGGCTCTTCA
147570 GCGTCAGTAGGCTCTTCA
1 G-GTCAGTAGGCTCTTCA
*
147588 GGTTCAGCAGGCT
1 GG-TCAGTAGGCT
147601 GGGGACTCTC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 2 0.08
18 24 0.92
ACGTcount: A:0.17, C:0.25, G:0.27, T:0.31
Consensus pattern (17 bp):
GGTCAGTAGGCTCTTCA
Found at i:148833 original size:18 final size:18
Alignment explanation
Indices: 148807--148845 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
148797 AAGATGAGAG
148807 AAAGTTAAAAGAAAAAGGT
1 AAAGTTAAAAGAAAAA-GT
*
148826 AAAG-TAAAAGTAAAAGT
1 AAAGTTAAAAGAAAAAGT
148843 AAA
1 AAA
148846 ATGAAGATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 10 0.53
19 4 0.21
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (18 bp):
AAAGTTAAAAGAAAAAGT
Found at i:165647 original size:21 final size:19
Alignment explanation
Indices: 165619--165664 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
165609 TCATTGAATC
165619 ATTA-TTCTTAGCTCCTTAAT
1 ATTAGTTCTTAGCT--TTAAT
165639 ATTAGTTCTTAGCTTTAAT
1 ATTAGTTCTTAGCTTTAAT
165658 ACTTAGT
1 A-TTAGT
165665 AGGATTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.26, C:0.15, G:0.09, T:0.50
Consensus pattern (19 bp):
ATTAGTTCTTAGCTTTAAT
Found at i:171248 original size:42 final size:41
Alignment explanation
Indices: 171201--171315 Score: 131
Period size: 42 Copynumber: 2.8 Consensus size: 41
171191 CTATTTCCCA
* *
171201 ATGATGTTTAAATCCTTAGGTTCATCAGTAAGTCTTTCGAGC
1 ATGATG-TTAAATCCTTAGGGTCATCAGTAAGTCTTTCAAGC
* * *
171243 ATGATGCTTAAATCTTTCGGGTCATCTGTAAGTCTTTCAAGC
1 ATGATG-TTAAATCCTTAGGGTCATCAGTAAGTCTTTCAAGC
* * * *
171285 AAGATGTTAAATCCTTCGAGTCATCCGTAAG
1 ATGATGTTAAATCCTTAGGGTCATCAGTAAG
171316 ACATTCGGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
41 22 0.35
42 41 0.65
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (41 bp):
ATGATGTTAAATCCTTAGGGTCATCAGTAAGTCTTTCAAGC
Found at i:171759 original size:220 final size:220
Alignment explanation
Indices: 171251--171771 Score: 717
Period size: 221 Copynumber: 2.4 Consensus size: 220
171241 GCATGATGCT
* * * * *
171251 TAAATCTTTCGGGTCATCTGTAAGTCTTTCAAGCAAGATGTTAAATCCTTCGAGTCATCCGTAAG
1 TAAATCCTTCAGGTCATCTGTAAGTCTTTCAAGCAAGATGTTAAGTCCTTTGAGCCATCCGTAAG
* *
171316 ACATTCGGGTAGGATCTTTACACATGATTTTCACATGAAAATGAGAAAGCGATTACCAAAGTTTC
66 ACCTTCGGGTAGGATCTTTACACATGATTTTCACATGAAAATGAGAAAGCAATTACCAAAGTTTC
* *
171381 TCATTTAATGTTTTGAGAAAATGAAATTTTTGAAAAGTAAGAAAGCGACTTTCAAAGTTTCTTAC
131 TCATTTAATG-TTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGAGACTTTCAAAGTTTCTTAC
* * *
171446 CTAGTAAACTATTTCCTAATGATTTT
195 CTAGTAAACTATTTCCTAATAATATC
* * * *
171472 TAAATCCTT-AGGGTCATCTATAAGTCTTTCAAGCAAGGTGATAAGT-CTTTCATGCCATCCGTA
1 TAAATCCTTCA-GGTCATCTGTAAGTCTTTCAAGCAAGATGTTAAGTCCTTTGA-GCCATCCGTA
* *
171535 AGACCTTCGGGTAGGATGTTTACACATGATTTTCACATGAAAATGATAAAGCAATTACCAAAGTT
64 AGACCTTCGGGTAGGATCTTTACACATGATTTTCACATGAAAATGAGAAAGCAATTACCAAAGTT
** *
171600 TCTCATTTAATG-TTCAGAAAATGATTTTTTTTGAAAAGTAAGAAAGAGATTTTCAAAGTTTCTT
129 TCTCATTTAATGTTTCAGAAAATGA-AATTTTTGAAAAGTAAGAAAGAGACTTTCAAAGTTTCTT
171664 ACCTAGTAAACTATTT-CTCAATAATATC
193 ACCTAGTAAACTATTTCCT-AATAATATC
* * * * * *
171692 TAAATCCTTCAGGTCATTTGTTAGTCTTTCGAGCAATATGTTAAGTCCTTTGGGCCATCTGTAAG
1 TAAATCCTTCAGGTCATCTGTAAGTCTTTCAAGCAAGATGTTAAGTCCTTTGAGCCATCCGTAAG
*
171757 ACCTTCGGGAAGGAT
66 ACCTTCGGGTAGGAT
171772 TTTTTTACTT
Statistics
Matches: 262, Mismatches: 32, Indels: 13
0.85 0.10 0.04
Matches are distributed among these distances:
219 13 0.05
220 123 0.47
221 126 0.48
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (220 bp):
TAAATCCTTCAGGTCATCTGTAAGTCTTTCAAGCAAGATGTTAAGTCCTTTGAGCCATCCGTAAG
ACCTTCGGGTAGGATCTTTACACATGATTTTCACATGAAAATGAGAAAGCAATTACCAAAGTTTC
TCATTTAATGTTTCAGAAAATGAAATTTTTGAAAAGTAAGAAAGAGACTTTCAAAGTTTCTTACC
TAGTAAACTATTTCCTAATAATATC
Found at i:171964 original size:3 final size:3
Alignment explanation
Indices: 171953--171989 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
171943 TTATAAATAA
171953 TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
171990 CAAATAATAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:172028 original size:20 final size:21
Alignment explanation
Indices: 172003--172045 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 21
171993 ATAATATAAT
172003 AAGTCTAGAGGCCCAATT-AC
1 AAGTCTAGAGGCCCAATTGAC
*
172023 AAGTCTGGAGGCCCAATTGAC
1 AAGTCTAGAGGCCCAATTGAC
172044 AA
1 AA
172046 CAAAACTCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.35, C:0.23, G:0.23, T:0.19
Consensus pattern (21 bp):
AAGTCTAGAGGCCCAATTGAC
Found at i:196031 original size:21 final size:20
Alignment explanation
Indices: 195994--196049 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
195984 ATTATGCTTG
*
195994 AGAAAAAAAATGAAAAAATAAA
1 AGAAAAAAAA--AAAAAAGAAA
*
196016 TGAAAAAAGAAAAAAAAGAAA
1 AGAAAAAA-AAAAAAAAGAAA
196037 AGAGAAAAAAAAA
1 AGA-AAAAAAAAA
196050 GGAGGGTTCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 15 0.52
22 12 0.41
23 2 0.07
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.05
Consensus pattern (20 bp):
AGAAAAAAAAAAAAAAGAAA
Found at i:196042 original size:16 final size:17
Alignment explanation
Indices: 196007--196048 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
195997 AAAAAAATGA
196007 AAAAATAAATGAAAAAAG
1 AAAAA-AAATGAAAAAAG
*
196025 AAAAAAAA-GAAAAGAG
1 AAAAAAAATGAAAAAAG
196041 AAAAAAAA
1 AAAAAAAA
196049 AGGAGGGTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 15 0.65
17 3 0.13
18 5 0.22
ACGTcount: A:0.83, C:0.00, G:0.12, T:0.05
Consensus pattern (17 bp):
AAAAAAAATGAAAAAAG
Found at i:197254 original size:91 final size:91
Alignment explanation
Indices: 197094--197272 Score: 322
Period size: 91 Copynumber: 2.0 Consensus size: 91
197084 AGGAGGTGAA
*
197094 TCAACATTTCCAATGGAGATTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
*
197159 ATGAGAAGAGCTTGTTCAACCTTGGT
66 ATGAGAAGAACTTGTTCAACCTTGGT
* *
197185 TCAAGATTTCCAGTGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
1 TCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
197250 ATGAGAAGAACTTGTTCAACCTT
66 ATGAGAAGAACTTGTTCAACCTT
197273 AGTTTGTTTC
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (91 bp):
TCAACATTTCCAATGGAGAGTTCATAATGAGAAGAACTCATCCAACGAGGGAGAAGAAGTTCATA
ATGAGAAGAACTTGTTCAACCTTGGT
Found at i:200703 original size:16 final size:16
Alignment explanation
Indices: 200682--200724 Score: 86
Period size: 16 Copynumber: 2.7 Consensus size: 16
200672 TGCTTGATCA
200682 TTTCTGGATTAGCCAC
1 TTTCTGGATTAGCCAC
200698 TTTCTGGATTAGCCAC
1 TTTCTGGATTAGCCAC
200714 TTTCTGGATTA
1 TTTCTGGATTA
200725 TCGCGATGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.42
Consensus pattern (16 bp):
TTTCTGGATTAGCCAC
Found at i:201415 original size:12 final size:12
Alignment explanation
Indices: 201398--201427 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
201388 TAGGGCCATT
201398 AGTTTTACATCA
1 AGTTTTACATCA
*
201410 AGTTTTACATTA
1 AGTTTTACATCA
201422 AGTTTT
1 AGTTTT
201428 CTTTATTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.50
Consensus pattern (12 bp):
AGTTTTACATCA
Found at i:203512 original size:7 final size:7
Alignment explanation
Indices: 203500--203600 Score: 66
Period size: 7 Copynumber: 14.7 Consensus size: 7
203490 TATGTGATAA
203500 GTTTAGG
1 GTTTAGG
203507 GTTTAGG
1 GTTTAGG
203514 GTTTA-G
1 GTTTAGG
*
203520 GTTTA-T
1 GTTTAGG
*
203526 GTGATAGG
1 GT-TTAGG
203534 GTTTAGG
1 GTTTAGG
*
203541 GTTTAGC
1 GTTTAGG
* *
203548 ATTTAGA
1 GTTTAGG
203555 GTTTAGG
1 GTTTAGG
* *
203562 ATTTA-T
1 GTTTAGG
*
203568 ATGTTAGG
1 GT-TTAGG
* *
203576 GTTAAGA
1 GTTTAGG
203583 G-TTAGG
1 GTTTAGG
203589 GTTTAGG
1 GTTTAGG
203596 GTTTA
1 GTTTA
203601 AGTTATGCAC
Statistics
Matches: 72, Mismatches: 17, Indels: 10
0.73 0.17 0.10
Matches are distributed among these distances:
6 14 0.19
7 55 0.76
8 3 0.04
ACGTcount: A:0.22, C:0.01, G:0.34, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:205314 original size:26 final size:26
Alignment explanation
Indices: 205277--205337 Score: 113
Period size: 26 Copynumber: 2.3 Consensus size: 26
205267 CCTAGTATTG
205277 GTTTTGGTGCTTGGTGCTCTGTCCCTT
1 GTTTT-GTGCTTGGTGCTCTGTCCCTT
205304 GTTTTGTGCTTGGTGCTCTGTCCCTT
1 GTTTTGTGCTTGGTGCTCTGTCCCTT
205330 GTTTTGTG
1 GTTTTGTG
205338 TGTCTGCAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 29 0.85
27 5 0.15
ACGTcount: A:0.00, C:0.20, G:0.30, T:0.51
Consensus pattern (26 bp):
GTTTTGTGCTTGGTGCTCTGTCCCTT
Found at i:205776 original size:24 final size:24
Alignment explanation
Indices: 205709--205779 Score: 117
Period size: 24 Copynumber: 3.0 Consensus size: 24
205699 ATTTGAGTTT
* *
205709 GAGT-TCGAGCTTGAATCGAACTC
1 GAGTCTCGAGCTTCAATCGAGCTC
205732 GAGTCTCGAGCTTCAATCGAGCTC
1 GAGTCTCGAGCTTCAATCGAGCTC
205756 GAGTCTCGAGCTTCAATCGAGCTC
1 GAGTCTCGAGCTTCAATCGAGCTC
205780 CTGAATTTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
23 4 0.09
24 41 0.91
ACGTcount: A:0.23, C:0.27, G:0.25, T:0.25
Consensus pattern (24 bp):
GAGTCTCGAGCTTCAATCGAGCTC
Found at i:207812 original size:18 final size:19
Alignment explanation
Indices: 207789--207826 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
207779 TATTTAAGTG
*
207789 ATAAAAGCGA-TTAAATAA
1 ATAAAAGCAATTTAAATAA
207807 ATAAAAGCAATTTAAATAA
1 ATAAAAGCAATTTAAATAA
207826 A
1 A
207827 AATAAGAGAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.08, T:0.24
Consensus pattern (19 bp):
ATAAAAGCAATTTAAATAA
Found at i:216900 original size:18 final size:19
Alignment explanation
Indices: 216865--216906 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
216855 TTTGAGTTTC
*
216865 TTTTATGTAATATCTAAAG
1 TTTTATGTAATATCTAAAA
* *
216884 TTTT-TGTAATTTTTAAAA
1 TTTTATGTAATATCTAAAA
216902 TTTTA
1 TTTTA
216907 AATGTAGTCA
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.33, C:0.02, G:0.07, T:0.57
Consensus pattern (19 bp):
TTTTATGTAATATCTAAAA
Found at i:217275 original size:30 final size:30
Alignment explanation
Indices: 217241--217302 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
217231 GATAAATTAC
217241 AATTTT-GTACCTAAATTATCATTTTTCTTT
1 AATTTTAGTACCTAAATT-TCATTTTTCTTT
** * *
217271 AATTTTAGTATGTAAATTTTATTTTTTTTT
1 AATTTTAGTACCTAAATTTCATTTTTCTTT
217301 AA
1 AA
217303 ATCATTGAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 18 0.67
31 9 0.33
ACGTcount: A:0.29, C:0.06, G:0.05, T:0.60
Consensus pattern (30 bp):
AATTTTAGTACCTAAATTTCATTTTTCTTT
Found at i:218014 original size:19 final size:17
Alignment explanation
Indices: 217962--218019 Score: 57
Period size: 19 Copynumber: 3.3 Consensus size: 17
217952 TCCGTACAAT
217962 ATTATTTAAAATTAAATAA
1 ATTATTT-AAA-TAAATAA
*
217981 ATAATTT-AA-AAATAA
1 ATTATTTAAATAAATAA
217996 TATTATTTCAAATAAATAA
1 -ATTATTT-AAATAAATAA
218015 ATTAT
1 ATTAT
218020 ATGATTTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
15 6 0.18
16 6 0.18
17 2 0.06
18 7 0.21
19 12 0.36
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTATTTAAATAAATAA
Found at i:218060 original size:26 final size:24
Alignment explanation
Indices: 218001--218060 Score: 59
Period size: 25 Copynumber: 2.4 Consensus size: 24
217991 AATAATATTA
*
218001 TTTCAAATAAATAAATTATATGAT
1 TTTCAAATAAATAAATTAAATGAT
*
218025 TTTAAAAATAAATAAATTTAAAAT-AT
1 TTT-CAAATAAATAAA-TT-AAATGAT
218051 TTTCATAATA
1 TTTCA-AATA
218061 TTATAAATAA
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
24 3 0.10
25 12 0.41
26 11 0.38
27 3 0.10
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (24 bp):
TTTCAAATAAATAAATTAAATGAT
Found at i:220221 original size:14 final size:14
Alignment explanation
Indices: 220202--220250 Score: 75
Period size: 14 Copynumber: 3.6 Consensus size: 14
220192 GAATTTGAAA
220202 ATATTTTGAGATTT
1 ATATTTTGAGATTT
220216 ATATTTTGAGATTT
1 ATATTTTGAGATTT
220230 ATATTTT--GATTT
1 ATATTTTGAGATTT
*
220242 ATCTTTTGA
1 ATATTTTGA
220251 ATATTTTATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
12 11 0.34
14 21 0.66
ACGTcount: A:0.27, C:0.02, G:0.12, T:0.59
Consensus pattern (14 bp):
ATATTTTGAGATTT
Found at i:220242 original size:12 final size:12
Alignment explanation
Indices: 220211--220250 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
220201 AATATTTTGA
220211 GATTTATATTTT
1 GATTTATATTTT
220223 GAGATTTATATTTT
1 --GATTTATATTTT
*
220237 GATTTATCTTTT
1 GATTTATATTTT
220249 GA
1 GA
220251 ATATTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 13 0.52
14 12 0.48
ACGTcount: A:0.25, C:0.03, G:0.12, T:0.60
Consensus pattern (12 bp):
GATTTATATTTT
Found at i:221046 original size:16 final size:15
Alignment explanation
Indices: 221007--221048 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
220997 TGTTTTCAAC
221007 TATTTA-TTTTCATT
1 TATTTATTTTTCATT
*
221021 TTTTTCATTTTTCATT
1 TATTT-ATTTTTCATT
221037 TAATTTATTTTT
1 T-ATTTATTTTT
221049 AAGTCCCTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 4 0.17
15 1 0.04
16 15 0.65
17 3 0.13
ACGTcount: A:0.19, C:0.07, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTATTTTTCATT
Found at i:230801 original size:21 final size:21
Alignment explanation
Indices: 230777--230826 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
230767 GAAGCTTTAA
230777 GATCATCAATTTTATTTTGAT
1 GATCATCAATTTTATTTTGAT
* *
230798 GATCATCAATTTTCTTTTTAT
1 GATCATCAATTTTATTTTGAT
230819 GATCATCA
1 GATCATCA
230827 TTAATTTTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.28, C:0.14, G:0.08, T:0.50
Consensus pattern (21 bp):
GATCATCAATTTTATTTTGAT
Found at i:230827 original size:24 final size:22
Alignment explanation
Indices: 230778--230835 Score: 64
Period size: 24 Copynumber: 2.6 Consensus size: 22
230768 AAGCTTTAAG
*
230778 ATCATCAA-TTTTATTTTGATG
1 ATCATCAATTTTTATTTTGATC
*
230799 ATCATCAATTTTCTTTTTATGATC
1 ATCATCAATTTT-TATTT-TGATC
*
230823 ATCATTAATTTTT
1 ATCATCAATTTTT
230836 GAAAGTAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 8 0.26
22 3 0.10
23 5 0.16
24 15 0.48
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.55
Consensus pattern (22 bp):
ATCATCAATTTTTATTTTGATC
Found at i:235608 original size:18 final size:18
Alignment explanation
Indices: 235582--235617 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
235572 GATCATGGTC
*
235582 CACACAAAAAGAAAAAAT
1 CACAAAAAAAGAAAAAAT
*
235600 CACAAAAAAAGAGAAAAT
1 CACAAAAAAAGAAAAAAT
235618 AGGTTCGAAA
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:0.72, C:0.14, G:0.08, T:0.06
Consensus pattern (18 bp):
CACAAAAAAAGAAAAAAT
Found at i:250582 original size:21 final size:21
Alignment explanation
Indices: 250558--250601 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
250548 GAAATTTTTT
*
250558 AATAAGAATAATTTATTTAAA
1 AATAAGAATAATTTAATTAAA
* **
250579 AATAATAATTTTTTAATTAAA
1 AATAAGAATAATTTAATTAAA
250600 AA
1 AA
250602 AATTCCATCA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (21 bp):
AATAAGAATAATTTAATTAAA
Found at i:250585 original size:18 final size:17
Alignment explanation
Indices: 250550--250594 Score: 63
Period size: 18 Copynumber: 2.6 Consensus size: 17
250540 TAATATTTGA
*
250550 AATTTTTTAATAAGAAT
1 AATTTTTTAAAAAGAAT
*
250567 AATTTATTTAAAAATAAT
1 AATTT-TTTAAAAAGAAT
250585 AATTTTTTAA
1 AATTTTTTAA
250595 TTAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 10 0.40
18 15 0.60
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (17 bp):
AATTTTTTAAAAAGAAT
Found at i:254504 original size:15 final size:14
Alignment explanation
Indices: 254480--254521 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
254470 TGACAGTAAG
*
254480 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
254495 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
254509 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
254522 GTATCTCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:254512 original size:20 final size:20
Alignment explanation
Indices: 254480--254521 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
254470 TGACAGTAAG
*
254480 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
254500 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
254520 TT
1 TT
254522 GTATCTCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:255015 original size:14 final size:14
Alignment explanation
Indices: 254996--255022 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
254986 GTCTGTAATT
254996 ATTTATTTATATAG
1 ATTTATTTATATAG
255010 ATTTATTTATATA
1 ATTTATTTATATA
255023 TATTAATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (14 bp):
ATTTATTTATATAG
Found at i:255039 original size:3 final size:3
Alignment explanation
Indices: 255026--255073 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
255016 TTATATATAT
255026 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
255072 TA
1 TA
255074 TGGGTAAAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:255360 original size:73 final size:72
Alignment explanation
Indices: 255232--255396 Score: 258
Period size: 73 Copynumber: 2.2 Consensus size: 72
255222 TTCAGATGAG
* **
255232 TTCTTCTCATTATGAACTTTCTGCTGGGGATGATGATCCATCAAATGATGAATTCAAGCAAAAGA
1 TTCTTCTCATTATGAAC--TCTCCTGGCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGA
255297 TTGAACAAA
64 TTGAACAAA
*
255306 TTCTTCTCATTATGAACTCTACCTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGAT
1 TTCTTCTCATTATGAACTCT-CCTGGCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGAT
*
255371 TGAACAAG
65 TGAACAAA
255379 TTCTTCTCATTATGAACT
1 TTCTTCTCATTATGAACT
255397 TCTTCTTCCT
Statistics
Matches: 85, Mismatches: 5, Indels: 3
0.91 0.05 0.03
Matches are distributed among these distances:
72 3 0.04
73 65 0.76
74 17 0.20
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (72 bp):
TTCTTCTCATTATGAACTCTCCTGGCAATGATGATCCATCAAATGATGAATTCAAGCAAAAGATT
GAACAAA
Found at i:255510 original size:116 final size:114
Alignment explanation
Indices: 255306--255807 Score: 730
Period size: 116 Copynumber: 4.4 Consensus size: 114
255296 ATTGAACAAA
* *
255306 TTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGA
1 TTCTTCTCATTATGAACTCTACTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGA
*
255370 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGACGAG
66 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGAT---GAG
* *
255422 TTCTTCTCATTATGAACTCTAC-CTGGCAATGTTGATCCATCAAATGATGAATTCAAGCAAAAGA
1 TTCTTCTCATTATGAACTCTACTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGA
*
255486 TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
66 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * * * * *
255535 TTCTTCTCATTATGAAC-CTTCTCTGGAAAAGATAATCCATCAATTTGATGAATTCAGGTAAAAG
1 TTCTTCTCATTATGAACTCTACTCTGGAAAAGTTGATCCATCAA-ATGATGAATTCAAGCAAAAG
*
255599 GTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
65 ATTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* * * * *
255649 TTCTTCTCATTATGAACT-TTCTCTGGAAAAGCTGATCCATCAAATGATG-ATTCAGGTAAAAGG
1 TTCTTCTCATTATGAACTCTACTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGA
255712 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
66 TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
* **
255761 TTCTTCTCATTATGAACT-T-CTCTGGAAAAGCTGATCTTTCAAATGAT
1 TTCTTCTCATTATGAACTCTACTCTGGAAAAGTTGATCCATCAAATGAT
255808 AGATTTGAAT
Statistics
Matches: 368, Mismatches: 15, Indels: 11
0.93 0.04 0.03
Matches are distributed among these distances:
111 26 0.07
112 85 0.23
113 42 0.11
114 105 0.29
116 110 0.30
ACGTcount: A:0.29, C:0.20, G:0.14, T:0.37
Consensus pattern (114 bp):
TTCTTCTCATTATGAACTCTACTCTGGAAAAGTTGATCCATCAAATGATGAATTCAAGCAAAAGA
TTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAG
Found at i:256749 original size:83 final size:83
Alignment explanation
Indices: 256550--257010 Score: 791
Period size: 83 Copynumber: 5.6 Consensus size: 83
256540 CATACCAAAC
* *
256550 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTAGCAAATTCATCTTCTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
* *
256615 G-TTCTGTCCAACCAAAT
66 GATTCTGTCCAATCAGAT
* *
256632 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCCAAATTCAATGCTT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
*
256697 GATTCTGTCCAATCATAT
66 GATTCTGTCCAATCAGAT
256715 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
256780 GATTCTGTCCAATCAGAT
66 GATTCTGTCCAATCAGAT
256798 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
256863 GATTCTGTCCAATCAGAT
66 GATTCTGTCCAATCAGAT
*
256881 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGATT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
* * * *
256946 GGTTCTG-CTAAACCAGGT
66 GATTCTGTC-CAATCAGAT
256964 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
1 CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCAT
257011 TTGTTCTATT
Statistics
Matches: 363, Mismatches: 14, Indels: 3
0.96 0.04 0.01
Matches are distributed among these distances:
82 63 0.17
83 300 0.83
ACGTcount: A:0.36, C:0.23, G:0.13, T:0.28
Consensus pattern (83 bp):
CAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGGCAAATTCATCTTCTAAACTCAATGCTT
GATTCTGTCCAATCAGAT
Found at i:270282 original size:15 final size:14
Alignment explanation
Indices: 270258--270299 Score: 57
Period size: 15 Copynumber: 2.9 Consensus size: 14
270248 TGACAGTAAG
*
270258 TTTCTCTTCTTTCTT
1 TTTCTTTTCTTTC-T
270273 TTTCTTTTCTTTCT
1 TTTCTTTTCTTTCT
270287 TTTCTGTTTCTTT
1 TTTCT-TTTCTTT
270300 GTATCTCTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 6 0.24
15 19 0.76
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (14 bp):
TTTCTTTTCTTTCT
Found at i:270290 original size:20 final size:20
Alignment explanation
Indices: 270258--270299 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
270248 TGACAGTAAG
*
270258 TTTCTCTTCTTTCTTTTTCT
1 TTTCTCTTCTTTCTGTTTCT
270278 TTTCT-TTCTTTTCTGTTTCT
1 TTTCTCTTC-TTTCTGTTTCT
270298 TT
1 TT
270300 GTATCTCTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (20 bp):
TTTCTCTTCTTTCTGTTTCT
Found at i:270333 original size:13 final size:14
Alignment explanation
Indices: 270315--270343 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
270305 TCTCCCTCTG
270315 TCTTCCTCTCC-TT
1 TCTTCCTCTCCGTT
270328 TCTTCCTCTCCGTT
1 TCTTCCTCTCCGTT
270342 TC
1 TC
270344 GAAGAATGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.00, C:0.45, G:0.03, T:0.52
Consensus pattern (14 bp):
TCTTCCTCTCCGTT
Found at i:270747 original size:14 final size:15
Alignment explanation
Indices: 270728--270761 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
270718 GTCTGTAATT
270728 ATTTATTT-ATATAG
1 ATTTATTTAATATAG
*
270742 ATTTATTTAATATAT
1 ATTTATTTAATATAG
270757 ATTTA
1 ATTTA
270762 ATAATAATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (15 bp):
ATTTATTTAATATAG
Found at i:270768 original size:3 final size:3
Alignment explanation
Indices: 270760--270839 Score: 151
Period size: 3 Copynumber: 26.7 Consensus size: 3
270750 AATATATATT
*
270760 TAA TAA TAA TAA TAA TAA TGA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
270808 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
270840 TGGGTAAAAA
Statistics
Matches: 75, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 75 1.00
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:271131 original size:20 final size:20
Alignment explanation
Indices: 271108--271158 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
271098 CATGGAATGT
271108 AAGATTATCAGTGGGAATAA
1 AAGATTATCAGTGGGAATAA
*
271128 AAGATTACCAGTGGGAATAA
1 AAGATTATCAGTGGGAATAA
271148 AAGATTATCAG
1 AAGATTATCAG
271159 GGAATAAGAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.45, C:0.08, G:0.24, T:0.24
Consensus pattern (20 bp):
AAGATTATCAGTGGGAATAA
Found at i:282078 original size:17 final size:18
Alignment explanation
Indices: 282058--282102 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 18
282048 TTCTTATTTT
282058 TTTCTTATTTTTATA-AC
1 TTTCTTATTTTTATATAC
282075 TTTC-TATTTTTATATAC
1 TTTCTTATTTTTATATAC
*
282092 TATTATTATTT
1 T-TTCTTATTT
282103 AATTTCATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 10 0.42
17 7 0.29
18 2 0.08
19 5 0.21
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (18 bp):
TTTCTTATTTTTATATAC
Found at i:282084 original size:16 final size:17
Alignment explanation
Indices: 282058--282119 Score: 53
Period size: 16 Copynumber: 3.9 Consensus size: 17
282048 TTCTTATTTT
*
282058 TTTCTTATTTTTATAAC
1 TTTCATATTTTTATAAC
282075 TTTC-TATTTTTATATAC
1 TTTCATATTTTTATA-AC
* *
282092 TAT--TATTATT-TAA-
1 TTTCATATTTTTATAAC
282105 TTTCATATTTTTATA
1 TTTCATATTTTTATA
282120 TTATATTATG
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
13 2 0.05
14 1 0.03
15 8 0.22
16 18 0.49
17 8 0.22
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTCATATTTTTATAAC
Done.