Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold3834.1
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: 99286
ACGTcount: A:0.32, C:0.21, G:0.14, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:5748 original size:27 final size:27
Alignment explanation
Indices: 5718--5895 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
5708 ATATTGAGTC
* * * *
5718 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
5745 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
5772 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
5800 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
5827 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
5854 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
5881 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
5896 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:5857 original size:82 final size:81
Alignment explanation
Indices: 5739--5894 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
5729 TGCTATATAA
* *
5739 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
5804 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
5821 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
5885 CACTTAGTGC
65 CACTTAGTGC
5895 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:12387 original size:30 final size:30
Alignment explanation
Indices: 12351--12410 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
12341 TTCACAAAGG
12351 AGCGCATCTCATAAAATGGTTTGGCTACTT
1 AGCGCATCTCATAAAATGGTTTGGCTACTT
*
12381 AGCGCATCTCATAGAATGGTTTGGCTACTT
1 AGCGCATCTCATAAAATGGTTTGGCTACTT
12411 CCCTTTGTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (30 bp):
AGCGCATCTCATAAAATGGTTTGGCTACTT
Found at i:13199 original size:21 final size:21
Alignment explanation
Indices: 13154--13196 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
13144 CGGGATTACC
13154 ATAATTCAAATTATAAACATA
1 ATAATTCAAATTATAAACATA
*
13175 ATAA-TCATATTATTAAATCATA
1 ATAATTCAAATTA-TAAA-CATA
13197 TAACTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 8 0.42
22 4 0.21
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAATTCAAATTATAAACATA
Found at i:13210 original size:4 final size:4
Alignment explanation
Indices: 13201--13232 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
13191 ATCATATAAC
13201 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
13233 CTAAACCAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:14193 original size:23 final size:22
Alignment explanation
Indices: 14146--14193 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
14136 ATATTTAATC
14146 CTAACTAAATTCACTTACTTTT
1 CTAACTAAATTCACTTACTTTT
*
14168 CTAACTGAATTCATACTT-CTTTT
1 CTAACTAAATTC--ACTTACTTTT
14191 CTA
1 CTA
14194 CTTAATTTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
22 11 0.48
23 8 0.35
24 4 0.17
ACGTcount: A:0.29, C:0.23, G:0.02, T:0.46
Consensus pattern (22 bp):
CTAACTAAATTCACTTACTTTT
Found at i:20872 original size:40 final size:39
Alignment explanation
Indices: 20798--20875 Score: 95
Period size: 40 Copynumber: 1.9 Consensus size: 39
20788 TGCTGAACCA
*
20798 AGACTCTGAACACCTATTAATTTGCATACCGAAACAACTG
1 AGACTCTGAACACCTATTAATATGCA-ACCGAAACAACTG
* *
20838 AGACTTTGAACACCTATTAACCTATGC-ACGGAAACAAC
1 AGACTCTGAACACCTATTAA--TATGCAACCGAAACAAC
20876 CGTACATTGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 29 0.88
42 4 0.12
ACGTcount: A:0.38, C:0.26, G:0.13, T:0.23
Consensus pattern (39 bp):
AGACTCTGAACACCTATTAATATGCAACCGAAACAACTG
Found at i:20956 original size:21 final size:21
Alignment explanation
Indices: 20911--20953 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
20901 TGGTATTTTC
20911 ATAATTCAAATTATAAACATA
1 ATAATTCAAATTATAAACATA
*
20932 ATAA-TCATATTATTAAATCATA
1 ATAATTCAAATTA-TAAA-CATA
20954 TAACTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 8 0.42
22 4 0.21
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAATTCAAATTATAAACATA
Found at i:22313 original size:38 final size:38
Alignment explanation
Indices: 22271--22345 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
22261 TGTAGTTTTT
* * * * *
22271 CCGTTTTCTTTTCTTTTTCTCCGTTCTTTCTTTCTTTC
1 CCGTTTGCTATTCTGTTTCTTCCTTCTTTCTTTCTTTC
*
22309 CCGTTTGCTATTCTGTTTCTTCCTTCTTTGTTTCTTT
1 CCGTTTGCTATTCTGTTTCTTCCTTCTTTCTTTCTTT
22346 TCTTTTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.01, C:0.27, G:0.08, T:0.64
Consensus pattern (38 bp):
CCGTTTGCTATTCTGTTTCTTCCTTCTTTCTTTCTTTC
Found at i:22757 original size:54 final size:54
Alignment explanation
Indices: 22692--22800 Score: 191
Period size: 54 Copynumber: 2.0 Consensus size: 54
22682 AATTAAATAA
* *
22692 AAAATATCACAAATTTATATATTTCTATTAATTCACTTGTATTAAATCACTACC
1 AAAATATCACAAATGTATATATTTCTATTAATACACTTGTATTAAATCACTACC
*
22746 AAAATTTCACAAATGTATATATTTCTATTAATACACTTGTATTAAATCACTACC
1 AAAATATCACAAATGTATATATTTCTATTAATACACTTGTATTAAATCACTACC
22800 A
1 A
22801 TACATTTGTC
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.41, C:0.17, G:0.03, T:0.39
Consensus pattern (54 bp):
AAAATATCACAAATGTATATATTTCTATTAATACACTTGTATTAAATCACTACC
Found at i:28719 original size:21 final size:21
Alignment explanation
Indices: 28674--28716 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
28664 TGGTATTTTC
28674 ATAATTCAAATTATAAACATA
1 ATAATTCAAATTATAAACATA
*
28695 ATAA-TCATATTATTAAATCATA
1 ATAATTCAAATTA-TAAA-CATA
28717 TAACTTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 7 0.37
21 8 0.42
22 4 0.21
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.37
Consensus pattern (21 bp):
ATAATTCAAATTATAAACATA
Found at i:30076 original size:38 final size:38
Alignment explanation
Indices: 30034--30108 Score: 96
Period size: 38 Copynumber: 2.0 Consensus size: 38
30024 TGTAGTTTTT
* * * * *
30034 CCGTTTTCTTTTCTTTTTCTCCGTTCTTTCTTTCTTTC
1 CCGTTTGCTATTCTGTTTCTTCCTTCTTTCTTTCTTTC
*
30072 CCGTTTGCTATTCTGTTTCTTCCTTCTTTGTTTCTTT
1 CCGTTTGCTATTCTGTTTCTTCCTTCTTTCTTTCTTT
30109 TCTTTTATTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.01, C:0.27, G:0.08, T:0.64
Consensus pattern (38 bp):
CCGTTTGCTATTCTGTTTCTTCCTTCTTTCTTTCTTTC
Found at i:31600 original size:54 final size:55
Alignment explanation
Indices: 31493--31607 Score: 128
Period size: 54 Copynumber: 2.1 Consensus size: 55
31483 CCGTATGACT
* *
31493 CACACGACTAAGTCACATGCCCATGTCTCAGACCGTGTAACCTTTGAACTAGGGA
1 CACACGACCAAGTCACATGCCCATGTCTCAGACCGTGTAACCCTTGAACTAGGGA
* * * * *
31548 CACACGACCATGTCTCA-GCCCATGTCTTCA-CCCGTGTAACTCCTTG-AGTAGGGT
1 CACACGACCAAGTCACATGCCCATGTC-TCAGACCGTGTAAC-CCTTGAACTAGGGA
31602 CACACG
1 CACACG
31608 CCCGTGTGCT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
54 30 0.59
55 21 0.41
ACGTcount: A:0.25, C:0.32, G:0.20, T:0.23
Consensus pattern (55 bp):
CACACGACCAAGTCACATGCCCATGTCTCAGACCGTGTAACCCTTGAACTAGGGA
Found at i:33065 original size:26 final size:26
Alignment explanation
Indices: 33033--33085 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
33023 GAGTAATGTA
33033 TGTATTAAATGAGCTAGATTCAGTAT
1 TGTATTAAATGAGCTAGATTCAGTAT
33059 TGTATTAAATGAGCTAGATTCAGTAT
1 TGTATTAAATGAGCTAGATTCAGTAT
33085 T
1 T
33086 ATAGATCAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.34, C:0.08, G:0.19, T:0.40
Consensus pattern (26 bp):
TGTATTAAATGAGCTAGATTCAGTAT
Found at i:34465 original size:30 final size:30
Alignment explanation
Indices: 34429--34499 Score: 124
Period size: 30 Copynumber: 2.4 Consensus size: 30
34419 CACACGGGTA
**
34429 GACACACGGGCGTGTGTCTGGACCGTGTGT
1 GACACACGGGCGTGTGTCTAAACCGTGTGT
34459 GACACACGGGCGTGTGTCTAAACCGTGTGT
1 GACACACGGGCGTGTGTCTAAACCGTGTGT
34489 GACACACGGGC
1 GACACACGGGC
34500 AGCCATACGG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.18, C:0.25, G:0.37, T:0.20
Consensus pattern (30 bp):
GACACACGGGCGTGTGTCTAAACCGTGTGT
Found at i:45105 original size:47 final size:47
Alignment explanation
Indices: 45036--45310 Score: 251
Period size: 47 Copynumber: 5.9 Consensus size: 47
45026 GGGTATAATA
* *
45036 TCGATGCCATATCCCAGACATGGTCTTGCACTGGCTCTCACGTTAAG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACGTTAAG
* * **
45083 TCGATGCCATGTCCTAGACATGGTCTTACACTGACTCTCACGTATCCG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACGT-TAAG
* * * * *
45131 TTCTGACGCCATGTCCCAGACATGGTCTTATACTGACACATCATG-T-AG
1 -TC-GATGCCATGTCCCAGACATGGTCTTACACTGGCTC-TCACGTTAAG
* *** *
45179 TCGATG-CATGTCCCAGACAT-GTCTTACACTGGCTTTCATCAAGAGG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA-CGTTAAG
* *
45225 CCGATG-CATGTCCCAGACAT-GTCTTACACTAGCTCT--CGTATCAATG
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACGT-T-AA-G
*
45271 CCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA
1 TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCA
45311 TAATGTGGTT
Statistics
Matches: 185, Mismatches: 29, Indels: 25
0.77 0.12 0.10
Matches are distributed among these distances:
43 4 0.02
44 11 0.06
45 15 0.08
46 44 0.24
47 55 0.30
48 18 0.10
49 3 0.02
50 31 0.17
51 4 0.02
ACGTcount: A:0.23, C:0.30, G:0.20, T:0.28
Consensus pattern (47 bp):
TCGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCACGTTAAG
Found at i:45235 original size:46 final size:46
Alignment explanation
Indices: 45180--45348 Score: 200
Period size: 46 Copynumber: 3.6 Consensus size: 46
45170 ATCATGTAGT
*
45180 CGATGCATGTCCCAGACATGTCTTACACTGGCTTTCATCAAGAGGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCAAGAGGC
* *
45226 CGATGCATGTCCCAGACATGTCTTACACTAGCTCTCGTATC-A-ATGC
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCTC--ATCAAGAGGC
* *
45272 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCAT-AATGTGGT
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATCAA-GAGGC
* * *
45320 TGATGGATGTCCTAGACATGTCTTACACT
1 CGATGCATGTCCCAGACATGTCTTACACT
45349 AGCACACAAA
Statistics
Matches: 106, Mismatches: 10, Indels: 14
0.82 0.08 0.11
Matches are distributed among these distances:
46 55 0.52
47 27 0.25
48 24 0.23
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (46 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATCAAGAGGC
Found at i:45297 original size:94 final size:92
Alignment explanation
Indices: 45180--45351 Score: 256
Period size: 94 Copynumber: 1.8 Consensus size: 92
45170 ATCATGTAGT
*
45180 CGATGCATGTCCCAGACATGTCTTACACTGGCTTTCATCAA-GAGGCCGATGCATGTCCCAGACA
1 CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCAT-AATGAGGCCGATGCATGTCCCAGACA
45244 TGTCTTACACTAGCTCTCGTATCAATGC
65 TGTCTTACACTAGCTCTCGTATCAATGC
* ** * *
45272 CGATGCCATGTCCCAGACATGGTCTTACACTGGCTCTCATAATGTGGTTGATGGATGTCCTAGAC
1 CGATG-CATGTCCCAGACAT-GTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAGAC
45337 ATGTCTTACACTAGC
64 ATGTCTTACACTAGC
45352 ACACAAACAT
Statistics
Matches: 71, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
92 5 0.07
93 16 0.23
94 50 0.70
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.28
Consensus pattern (92 bp):
CGATGCATGTCCCAGACATGTCTTACACTGGCTCTCATAATGAGGCCGATGCATGTCCCAGACAT
GTCTTACACTAGCTCTCGTATCAATGC
Found at i:45340 original size:140 final size:141
Alignment explanation
Indices: 45084--45348 Score: 340
Period size: 140 Copynumber: 1.9 Consensus size: 141
45074 CACGTTAAGT
* ** * *
45084 CGATGCCATGTCCTAGACATGGTCTTACACTGACTCTCACGTATCCGTTCTGACGCCATGTCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGACTCT-ACGTATCAATGCCGACGCCATGTCCCA
* *
45149 GACATGGTCTTATACTGACACATCATGTAGTCGATGCATGTCCCAGACATGTCTTACACTGGCTT
65 GACATGGTCTTACACTGACACATAATGTAGTCGATGCATGTCCCAGACATGTCTTACACTGGCTT
45214 TCATCAAGAGGC
130 TCATCAAGAGGC
*
45226 CGATG-CATGTCCCAGACAT-GTCTTACACT-AGCTCT-CGTATCAATGCCGATGCCATGTCCCA
1 CGATGCCATGTCCCAGACATGGTCTTACACTGA-CTCTACGTATCAATGCCGACGCCATGTCCCA
* * * * * *
45287 GACATGGTCTTACACTGGCTCTCATAATGTGGTTGATGGATGTCCTAGACATGTCTTACACT
65 GACATGGTCTTACACT-G-ACACATAATGTAGTCGATGCATGTCCCAGACATGTCTTACACT
45349 AGCACACAAA
Statistics
Matches: 106, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
138 36 0.34
139 2 0.02
140 50 0.47
141 13 0.12
142 5 0.05
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (141 bp):
CGATGCCATGTCCCAGACATGGTCTTACACTGACTCTACGTATCAATGCCGACGCCATGTCCCAG
ACATGGTCTTACACTGACACATAATGTAGTCGATGCATGTCCCAGACATGTCTTACACTGGCTTT
CATCAAGAGGC
Found at i:50369 original size:29 final size:29
Alignment explanation
Indices: 50336--50394 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
50326 AACTATAATT
50336 TAATTCAATTATTTATTCCT-AATATCAAC
1 TAATTCAATTATTTATT-CTAAATATCAAC
*
50365 TAATTCAATTATTTATTGTAAATATCAAC
1 TAATTCAATTATTTATTCTAAATATCAAC
50394 T
1 T
50395 GTAAGTGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.39, C:0.14, G:0.02, T:0.46
Consensus pattern (29 bp):
TAATTCAATTATTTATTCTAAATATCAAC
Found at i:51559 original size:26 final size:26
Alignment explanation
Indices: 51513--51565 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
51503 TCAAACATGC
*
51513 ATTTAGGTCAATTTAACCCTATGGGT
1 ATTTAGGTCAATTTAACCCTAGGGGT
* *
51539 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAAC-CCTAGGGGT
51565 A
1 A
51566 AAACTGTAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.25, C:0.15, G:0.21, T:0.40
Consensus pattern (26 bp):
ATTTAGGTCAATTTAACCCTAGGGGT
Found at i:53078 original size:26 final size:26
Alignment explanation
Indices: 53048--53155 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
53038 TGAAATGCCC
*
53048 ATCATGGAACATTTACCTGACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
53074 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
53100 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
53126 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
53152 ATCA
1 ATCA
53156 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.35, C:0.26, G:0.07, T:0.31
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:53839 original size:18 final size:18
Alignment explanation
Indices: 53816--53850 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
53806 CAAAGGTAGC
*
53816 TTTTTATTTTTTTTTTCT
1 TTTTTATTTTTGTTTTCT
53834 TTTTTATTTTTGTTTTC
1 TTTTTATTTTTGTTTTC
53851 ATTTCAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.06, C:0.06, G:0.03, T:0.86
Consensus pattern (18 bp):
TTTTTATTTTTGTTTTCT
Found at i:54720 original size:3 final size:3
Alignment explanation
Indices: 54707--54766 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
54697 CACATTTATC
** * * *
54707 TTA TT- TTA TTA TTA -TA TTA TTA TTA TTA AAA TCA TCA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
54753 TTA ATA TTA TTA TT
1 TTA TTA TTA TTA TT
54767 CTTAAATTTT
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:54860 original size:15 final size:15
Alignment explanation
Indices: 54833--54866 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54823 AAATTTTTAG
54833 TTTGTTATTCTTATT
1 TTTGTTATTCTTATT
54848 ATTTGTT-TTCTTATT
1 -TTTGTTATTCTTATT
54863 TTTG
1 TTTG
54867 GCTTGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 4 0.22
15 8 0.44
16 6 0.33
ACGTcount: A:0.12, C:0.06, G:0.09, T:0.74
Consensus pattern (15 bp):
TTTGTTATTCTTATT
Found at i:57658 original size:37 final size:37
Alignment explanation
Indices: 57600--57707 Score: 171
Period size: 37 Copynumber: 2.9 Consensus size: 37
57590 GCTCAGACGC
* * *
57600 AATCTCCACACGAAGTTATCGGGTCTTACCTGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
57637 ACTCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
*
57674 AATCTCCACACGTAGTCATCGGGTCTCACCCGGA
1 AATCTCCACACGTAGTCATCGGGTCTTACCCGGA
57708 ATATATTTCC
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 65 1.00
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
AATCTCCACACGTAGTCATCGGGTCTTACCCGGACAT
Found at i:57823 original size:48 final size:48
Alignment explanation
Indices: 57752--59095 Score: 2391
Period size: 48 Copynumber: 28.0 Consensus size: 48
57742 TGTTACAACA
57752 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
57800 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
57848 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
57896 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
57944 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
57992 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58040 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58088 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58136 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58184 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58232 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58280 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58328 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58376 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58424 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58472 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58520 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
58568 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * *
58616 TTCACATTAGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * * *
58664 TTCACATTCGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * * *
58712 TTCACATTCGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * * *
58760 TTCACATTCGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * * *
58808 TTCACATTCGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * * *
58856 TTCACATTCGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * * *
58904 TTCACATTCGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
* * * *
58952 TTCACATTCGCCATTCGGCTTTACCACATATACATATCTCATACATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
59000 TTCACATTCGCCATTCGGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
*
59048 TTCACATTAGCCATTCAGCTTTACCACATATACATATCACACATATAT
1 TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
59096 ATATTTATCT
Statistics
Matches: 1287, Mismatches: 9, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
48 1287 1.00
ACGTcount: A:0.32, C:0.28, G:0.06, T:0.34
Consensus pattern (48 bp):
TTCACATTAGCCATTCGGCTTTACCACATATACATATCACACATATAT
Found at i:59649 original size:29 final size:29
Alignment explanation
Indices: 59614--59671 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
59604 TTTGCTTCCA
59614 CGGTCTCTTTTATAAGAAACTAGACCAAC
1 CGGTCTCTTTTATAAGAAACTAGACCAAC
59643 CGGTCTCTTTTATAAGAAACTAGACCAAC
1 CGGTCTCTTTTATAAGAAACTAGACCAAC
59672 TAAGCTTTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (29 bp):
CGGTCTCTTTTATAAGAAACTAGACCAAC
Found at i:61991 original size:245 final size:245
Alignment explanation
Indices: 61556--62048 Score: 968
Period size: 245 Copynumber: 2.0 Consensus size: 245
61546 TTGACATGCA
61556 AGTCCACCCCTTTGATTACATGCACTAATAGATCCTTATAGATTAACCTATCACATTTCAAAAGT
1 AGTCCACCCCTTTGATTACATGCACTAATAGATCCTTATAGATTAACCTATCACATTTCAAAAGT
61621 GTCACACATAAGTCCTATTGACTAAATTCACATGCAATTTACTAAATCGAAGCTTAAAACTTTCA
66 GTCACACATAAGTCCTATTGACTAAATTCACATGCAATTTACTAAATCGAAGCTTAAAACTTTCA
*
61686 CACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAATATTTTGGTGACTCGGTTTA
131 CACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAATAATTTGGTGACTCGGTTTA
61751 GCGGTCCCGAAACCGCTTTCCGACTAGGGTCACTTTAGGGCTGTCACATG
196 GCGGTCCCGAAACCGCTTTCCGACTAGGGTCACTTTAGGGCTGTCACATG
*
61801 AGTCTACCCCTTTGATTACATGCACTAATAGATCCTTATAGATTAACCTATCACATTTCAAAAGT
1 AGTCCACCCCTTTGATTACATGCACTAATAGATCCTTATAGATTAACCTATCACATTTCAAAAGT
61866 GTCACACATAAGTCCTATTGACTAAATTCACATGCAATTTACTAAATCGAAGCTTAAAACTTTCA
66 GTCACACATAAGTCCTATTGACTAAATTCACATGCAATTTACTAAATCGAAGCTTAAAACTTTCA
61931 CACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAATAATTTGGTGACTCGGTTTA
131 CACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAATAATTTGGTGACTCGGTTTA
61996 GCGGTCCCGAAACCGCTTTCCGACTAGGGTCACTTTAGGGCTGTCACATG
196 GCGGTCCCGAAACCGCTTTCCGACTAGGGTCACTTTAGGGCTGTCACATG
62046 AGT
1 AGT
62049 TTTCGCAAAA
Statistics
Matches: 246, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
245 246 1.00
ACGTcount: A:0.33, C:0.22, G:0.13, T:0.32
Consensus pattern (245 bp):
AGTCCACCCCTTTGATTACATGCACTAATAGATCCTTATAGATTAACCTATCACATTTCAAAAGT
GTCACACATAAGTCCTATTGACTAAATTCACATGCAATTTACTAAATCGAAGCTTAAAACTTTCA
CACATTCATAATCACATATTTTAGACAATAAATATCATATTCAAATAATTTGGTGACTCGGTTTA
GCGGTCCCGAAACCGCTTTCCGACTAGGGTCACTTTAGGGCTGTCACATG
Found at i:62810 original size:29 final size:29
Alignment explanation
Indices: 62744--62890 Score: 133
Period size: 29 Copynumber: 5.2 Consensus size: 29
62734 TACATCCATG
* *
62744 CATATGGCCCA-CTAGGCCTAA-TCTCATT
1 CATATGGCCCATC-AGGCCCAATTCACATT
* * * *
62772 TATATGGCCCATCCGGCCGAATTCACGTT
1 CATATGGCCCATCAGGCCCAATTCACATT
62801 CATATGGCCCATCAGGCCCAATTCACATT
1 CATATGGCCCATCAGGCCCAATTCACATT
* *
62830 CCTATGGCCCATTAGGCCCAATCTC-C-TT
1 CATATGGCCCATCAGGCCCAAT-TCACATT
* * * *
62858 TATATGGCCTATCTGGCCCAAATCACATT
1 CATATGGCCCATCAGGCCCAATTCACATT
62887 -ATAT
1 CATAT
62891 TCATGCTCAC
Statistics
Matches: 97, Mismatches: 17, Indels: 10
0.78 0.14 0.08
Matches are distributed among these distances:
27 2 0.02
28 39 0.40
29 54 0.56
30 2 0.02
ACGTcount: A:0.24, C:0.32, G:0.15, T:0.29
Consensus pattern (29 bp):
CATATGGCCCATCAGGCCCAATTCACATT
Found at i:70611 original size:29 final size:29
Alignment explanation
Indices: 70578--70677 Score: 107
Period size: 29 Copynumber: 3.5 Consensus size: 29
70568 CAATCCGCCT
*
70578 AATTCACGTTCATATGGCCCATCAGGCCC
1 AATTCACATTCATATGGCCCATCAGGCCC
*
70607 AATTCACATTCATATGGCCCATTAGGCCC
1 AATTCACATTCATATGGCCCATCAGGCCC
* * * *
70636 AA-T-ATCTTTTATATGGCCTATCTGGCCC
1 AATTCA-CATTCATATGGCCCATCAGGCCC
*
70664 AAATCACATT-ATAT
1 AATTCACATTCATAT
70678 TCATGCTCAC
Statistics
Matches: 60, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
27 1 0.02
28 25 0.42
29 33 0.55
30 1 0.02
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.31
Consensus pattern (29 bp):
AATTCACATTCATATGGCCCATCAGGCCC
Found at i:70675 original size:28 final size:28
Alignment explanation
Indices: 70589--70677 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 28
70579 ATTCACGTTC
* *
70589 ATATGGCCCATCAGGCCCAATTCACATT
1 ATATGGCCCATCTGGCCCAAATCACATT
**
70617 CATATGGCCCAT-TAGGCCCAATATC-TTTT
1 -ATATGGCCCATCT-GGCCCAA-ATCACATT
*
70646 ATATGGCCTATCTGGCCCAAATCACATT
1 ATATGGCCCATCTGGCCCAAATCACATT
70674 ATAT
1 ATAT
70678 TCATGCTCAC
Statistics
Matches: 49, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
27 3 0.06
28 23 0.47
29 21 0.43
30 2 0.04
ACGTcount: A:0.28, C:0.28, G:0.13, T:0.30
Consensus pattern (28 bp):
ATATGGCCCATCTGGCCCAAATCACATT
Found at i:73767 original size:31 final size:31
Alignment explanation
Indices: 73732--73793 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
73722 ATAAACATAG
*
73732 CATAATGCAACTCAATTTGAATCTAAAAGCC
1 CATAATGCAACTCAATTTGAATCCAAAAGCC
73763 CATAATGCAACTCAATTTGAATCCAAAAGCC
1 CATAATGCAACTCAATTTGAATCCAAAAGCC
73794 TAACACATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.42, C:0.24, G:0.10, T:0.24
Consensus pattern (31 bp):
CATAATGCAACTCAATTTGAATCCAAAAGCC
Found at i:74661 original size:29 final size:30
Alignment explanation
Indices: 74596--74650 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
74586 CATAGCAGCC
74596 CATAATTTTCATTATTTCACACATTTACCA
1 CATAATTTTCATTATTTCACACATTTACCA
*
74626 CATAATTTTCATT-TTTCTCA-ATTTA
1 CATAATTTTCATTATTTCACACATTTA
74651 AACCCCTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 5 0.21
29 6 0.25
30 13 0.54
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (30 bp):
CATAATTTTCATTATTTCACACATTTACCA
Found at i:76533 original size:28 final size:28
Alignment explanation
Indices: 76479--76537 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
76469 CTTTTGGTTG
* **
76479 TTTGGTCACTTTGGCCCTTTATGTTTTT
1 TTTGGTCACTTTGGCCCTCTAACTTTTT
76507 TTTGGATCACTTTGGCCC-CTAACTTTTT
1 TTTGG-TCACTTTGGCCCTCTAACTTTTT
76535 TTT
1 TTT
76538 TATCAAATTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.10, C:0.20, G:0.15, T:0.54
Consensus pattern (28 bp):
TTTGGTCACTTTGGCCCTCTAACTTTTT
Found at i:76534 original size:29 final size:28
Alignment explanation
Indices: 76479--76538 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
76469 CTTTTGGTTG
* *
76479 TTTGGTCACTTTGGCCCTTTATGTTTTT
1 TTTGGTCACTTTGGCCCCTAATGTTTTT
76507 TTTGGATCACTTTGGCCCCTAACT-TTTTT
1 TTTGG-TCACTTTGGCCCCTAA-TGTTTTT
76536 TTT
1 TTT
76539 ATCAAATTGG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 5 0.18
29 22 0.79
30 1 0.04
ACGTcount: A:0.10, C:0.20, G:0.15, T:0.55
Consensus pattern (28 bp):
TTTGGTCACTTTGGCCCCTAATGTTTTT
Found at i:76701 original size:9 final size:9
Alignment explanation
Indices: 76687--76753 Score: 62
Period size: 9 Copynumber: 6.9 Consensus size: 9
76677 AATGAATTTG
76687 AAATTATTA
1 AAATTATTA
76696 AAATTATTTTA
1 AAATTA--TTA
*
76707 AAATAATTTA
1 AAATTA-TTA
76717 AAATTATTA
1 AAATTATTA
*
76726 AAATGATTTTA
1 AAAT--TATTA
*
76737 AAATAATTA
1 AAATTATTA
76746 AAATTATT
1 AAATTATT
76754 TTAAAAAAAG
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
9 23 0.48
10 9 0.19
11 16 0.33
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (9 bp):
AAATTATTA
Found at i:76707 original size:11 final size:11
Alignment explanation
Indices: 76693--76759 Score: 72
Period size: 11 Copynumber: 6.5 Consensus size: 11
76683 TTTGAAATTA
76693 TTAAAATTATT
1 TTAAAATTATT
*
76704 TTAAAA-TAAT
1 TTAAAATTATT
76714 TTAAAATTA--
1 TTAAAATTATT
*
76723 TTAAAATGATT
1 TTAAAATTATT
*
76734 TTAAAA-TA-A
1 TTAAAATTATT
76743 TTAAAATTATT
1 TTAAAATTATT
76754 TTAAAA
1 TTAAAA
76760 AAAGCCTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 10
0.75 0.08 0.16
Matches are distributed among these distances:
9 14 0.30
10 12 0.26
11 20 0.43
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (11 bp):
TTAAAATTATT
Found at i:76710 original size:20 final size:20
Alignment explanation
Indices: 76693--76759 Score: 82
Period size: 20 Copynumber: 3.3 Consensus size: 20
76683 TTTGAAATTA
*
76693 TTAAAATTATTTTAAAA-TAAT
1 TTAAAATTA--TTAAAATTATT
*
76714 TTAAAATTATTAAAATGATT
1 TTAAAATTATTAAAATTATT
*
76734 TTAAAATAATTAAAATTATT
1 TTAAAATTATTAAAATTATT
76754 TTAAAA
1 TTAAAA
76760 AAAGCCTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
19 6 0.15
20 26 0.63
21 9 0.22
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (20 bp):
TTAAAATTATTAAAATTATT
Found at i:76721 original size:30 final size:30
Alignment explanation
Indices: 76676--76753 Score: 122
Period size: 30 Copynumber: 2.6 Consensus size: 30
76666 CCACATCAAC
* *
76676 AAATGAATTTGAAATTATTAAAATTATTTTA
1 AAAT-AATTTAAAATTATTAAAATGATTTTA
76707 AAATAATTTAAAATTATTAAAATGATTTTA
1 AAATAATTTAAAATTATTAAAATGATTTTA
76737 AAATAA-TTAAAATTATT
1 AAATAATTTAAAATTATT
76754 TTAAAAAAAG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
29 11 0.24
30 30 0.67
31 4 0.09
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (30 bp):
AAATAATTTAAAATTATTAAAATGATTTTA
Found at i:77419 original size:29 final size:28
Alignment explanation
Indices: 77359--77433 Score: 69
Period size: 29 Copynumber: 2.6 Consensus size: 28
77349 GAGCAATCCC
* * *
77359 CAAAATCTCAAAAATCAAAAACCTTAAA
1 CAAAATCCCCAAAGTCAAAAACCTTAAA
* * **
77387 CAAAAATTCCCAAAGTCAAAACCCTTACC
1 C-AAAATCCCCAAAGTCAAAAACCTTAAA
*
77416 CAAAATCCCCAAATTCAA
1 CAAAATCCCCAAAGTCAA
77434 CCACCCAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
28 16 0.43
29 21 0.57
ACGTcount: A:0.52, C:0.29, G:0.01, T:0.17
Consensus pattern (28 bp):
CAAAATCCCCAAAGTCAAAAACCTTAAA
Found at i:77481 original size:23 final size:23
Alignment explanation
Indices: 77414--77485 Score: 110
Period size: 23 Copynumber: 3.1 Consensus size: 23
77404 AAAACCCTTA
*
77414 CCCAAAATCCCCAAATTCAACCA-
1 CCCAAAATCCCCAAATTCGA-CAG
77437 CCCAAAATCCCCAAATTCGACAG
1 CCCAAAATCCCCAAATTCGACAG
*
77460 CCCAAAATCCCCAAATTTGACAG
1 CCCAAAATCCCCAAATTCGACAG
77483 CCC
1 CCC
77486 TAAACAATTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
22 2 0.04
23 44 0.96
ACGTcount: A:0.39, C:0.42, G:0.06, T:0.14
Consensus pattern (23 bp):
CCCAAAATCCCCAAATTCGACAG
Found at i:84930 original size:49 final size:48
Alignment explanation
Indices: 84858--85169 Score: 190
Period size: 49 Copynumber: 6.6 Consensus size: 48
84848 GTGAGGTGTT
84858 GATGCCATGTCCCAGACATGGTCTTACACTGACGATCATCATCGAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACGATCATCATCGA-GCC
* * *
84907 GATGCCATGTCCTAGACATGGTCTTACACT-A-GCTCTGTAT-ATCCGTGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACGATC---ATCAT-CGAGCC
* *
84956 GATGCCATGTCCCAAACATGGTCTTACACTGAC-A-CATC-TCGCAGTC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACGATCATCATCG-AGCC
* * * *
85002 GATG-CATGTTCCAGACAT-GTCTTACACTGGC-TTACATCCT-GAGGCC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACGAT-CATCATCGA-GCC
* * * * * * **
85048 GAT-ACATGTGCCAGACAT-GTCTTACGCTGGC-ACTCGTC-TCAATAC
1 GATGCCATGTCCCAGACATGGTCTTACACTGACGA-TCATCATCGAGCC
** * ** * *
85093 GAATGCCATGTCCCAGACATGGTCTTACGTTGGCTCTCATAAT-GTGGCC
1 G-ATGCCATGTCCCAGACATGGTCTTACACTGACGATCATCATCG-AGCC
85142 GATG-CATGTCCCAGACAT-GTCTTACACT
1 GATGCCATGTCCCAGACATGGTCTTACACT
85170 AGCTCACACA
Statistics
Matches: 210, Mismatches: 32, Indels: 45
0.73 0.11 0.16
Matches are distributed among these distances:
44 12 0.06
45 18 0.09
46 58 0.28
47 32 0.15
48 19 0.09
49 66 0.31
50 5 0.02
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (48 bp):
GATGCCATGTCCCAGACATGGTCTTACACTGACGATCATCATCGAGCC
Found at i:88418 original size:47 final size:47
Alignment explanation
Indices: 88365--88775 Score: 750
Period size: 47 Copynumber: 8.7 Consensus size: 47
88355 TTAGGATTCT
88365 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
88412 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
88459 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
88506 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
88553 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
88600 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
88647 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * * * *
88694 ATGTGATGAATGTGAAAGTGTATATATGTGACAGGGCCGAGTGGCCA
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
* * *
88741 ACGTGATGGATGTGAAAGTGTATAAATGTGATAAG
1 ATGTGATGAATGTGAAAGTGTATATATGTGATAAG
88776 TCCCGAAGGG
Statistics
Matches: 354, Mismatches: 10, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
47 354 1.00
ACGTcount: A:0.32, C:0.08, G:0.30, T:0.29
Consensus pattern (47 bp):
ATGTGATGAATGTGAAAGTGTATATATGTGATAAGGCCTAATGGCCG
Found at i:88950 original size:37 final size:37
Alignment explanation
Indices: 88894--88972 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 37
88884 CCGAGCTCTA
* * *
88894 AAGACCCGATGACTACGTGTGGGGATTTTGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
*
88931 AAGACCCGATAACTTCGTGTGGAGATTATGTCCGGGT
1 AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
88968 AAGAC
1 AAGAC
88973 TTCGTAATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.25
Consensus pattern (37 bp):
AAGACCCGATAACTACGTGTGGAGATTATGTCCGGGT
Found at i:92920 original size:46 final size:46
Alignment explanation
Indices: 92853--93024 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
92843 AACCCGCCCC
*
92853 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
92899 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGATGCCTAGTT-ACAT-C-
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG--G-C--GTTCGCATCCA
* * * *
92947 TCA-CGAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
*
92992 TAGGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
93025 ATGCTCAACC
Statistics
Matches: 107, Mismatches: 10, Indels: 18
0.79 0.07 0.13
Matches are distributed among these distances:
42 2 0.02
43 3 0.03
44 2 0.02
45 1 0.01
46 60 0.56
47 28 0.26
48 3 0.03
49 2 0.02
50 3 0.03
51 3 0.03
ACGTcount: A:0.28, C:0.28, G:0.22, T:0.22
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGTTCGGGCGTTCGCATCCA
Found at i:92965 original size:93 final size:93
Alignment explanation
Indices: 92858--93028 Score: 306
Period size: 93 Copynumber: 1.8 Consensus size: 93
92848 GCCCCTAAGT
* *
92858 GAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCATAAGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
92923 CGAGTTCGGATGCCTAGTTACATCTCAC
66 CGAGTTCGGATGCCTAGTTACATCTCAC
* *
92951 GAACTCGGACTCAACTCAACGAGTTCGGACATTCGCATCCATAGGTGAACTCGGACTCAACTCAA
1 GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
93016 CGAGTTCGGATGC
66 CGAGTTCGGATGC
93029 TCAACCATCC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 74 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.21
Consensus pattern (93 bp):
GAACTCGGACTCAACTCAACGAGCTCGGACATTCGCATCCATAAGTGAACTCGGACTCAACTCAA
CGAGTTCGGATGCCTAGTTACATCTCAC
Found at i:93480 original size:30 final size:30
Alignment explanation
Indices: 93446--93505 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
93436 ATTTAATACG
93446 AACTTTGGAAAAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
* * *
93476 AACTTTTGCATAATTACACTTTTGCCCCTA
1 AACTTTGGAAAAATTACACTTTTGCCCCTA
93506 GGCTCGGGAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.30, C:0.25, G:0.08, T:0.37
Consensus pattern (30 bp):
AACTTTGGAAAAATTACACTTTTGCCCCTA
Done.