Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1876
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: 62953
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:174 original size:42 final size:43
Alignment explanation
Indices: 113--234 Score: 140
Period size: 42 Copynumber: 2.8 Consensus size: 43
103 CTTTTTTTCC
*
113 CTTTTGTCCCCAAAAAGCAGGACGCACTTTATTTTCC-TCTTT
1 CTTTTGTCCTCAAAAAGCAGGACGCACTTTATTTTCCTTCTTT
* * *
155 CTTTTGTCCTCAAAGAGCAGGATGCA-TTTCATTTTCCTTTTTTT
1 CTTTTGTCCTCAAAAAGCAGGACGCACTTT-ATTTTCC-TTCTTT
* * * *
199 CCTTTATCCTCAAAAAGCAGGACGTACTTTTTTTTC
1 CTTTTGTCCTCAAAAAGCAGGACGCACTTTATTTTC
235 GCTTTGTCTT
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
41 3 0.05
42 30 0.45
44 30 0.45
45 3 0.05
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (43 bp):
CTTTTGTCCTCAAAAAGCAGGACGCACTTTATTTTCCTTCTTT
Found at i:187 original size:87 final size:86
Alignment explanation
Indices: 70--234 Score: 215
Period size: 86 Copynumber: 1.9 Consensus size: 86
60 CCTTTTCTCC
* *
70 TTTGTCCTCAAAGAGTAGCACACACTTCA-TTCCCTTTTTTTCCCTTTTGTCCCCAAAAAGCAGG
1 TTTGTCCTCAAAGAGCAGCACACACTTCATTTCCCTTTTTTT-CC-TTTATCCCCAAAAAGCAGG
134 ACGCACTTTATTTTCCTCTTTCT
64 ACGCACTTTATTTTCCTCTTTCT
* ** * * *
157 TTTGTCCTCAAAGAGCAGGATGCATTTCATTTTCCTTTTTTTCCTTTATCCTCAAAAAGCAGGAC
1 TTTGTCCTCAAAGAGCAGCACACACTTCATTTCCCTTTTTTTCCTTTATCCCCAAAAAGCAGGAC
* *
222 GTACTTTTTTTTC
66 GCACTTTATTTTC
235 GCTTTGTCTT
Statistics
Matches: 67, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
86 30 0.45
87 26 0.39
88 11 0.16
ACGTcount: A:0.21, C:0.26, G:0.12, T:0.41
Consensus pattern (86 bp):
TTTGTCCTCAAAGAGCAGCACACACTTCATTTCCCTTTTTTTCCTTTATCCCCAAAAAGCAGGAC
GCACTTTATTTTCCTCTTTCT
Found at i:3363 original size:51 final size:51
Alignment explanation
Indices: 3306--3411 Score: 126
Period size: 51 Copynumber: 2.1 Consensus size: 51
3296 TCTCGGGAAA
* **
3306 ACTCCAA-TCCCGGTTCCATTTCCAAAACA-TCAATTTTTCTTAATCGGGGAT
1 ACTCCAACT-CCGATTCCATTTCCAAAACACT-AATTTTTCACAATCGGGGAT
** *
3357 ACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATTGGGGAT
1 ACTCCAACTCCGATTCCATTTCCAAAACACTAATTTTTCACAATCGGGGAT
3408 ACTC
1 ACTC
3412 AAACCTCGTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
51 45 0.96
52 2 0.04
ACGTcount: A:0.29, C:0.26, G:0.10, T:0.34
Consensus pattern (51 bp):
ACTCCAACTCCGATTCCATTTCCAAAACACTAATTTTTCACAATCGGGGAT
Found at i:3464 original size:28 final size:29
Alignment explanation
Indices: 3402--3470 Score: 81
Period size: 28 Copynumber: 2.4 Consensus size: 29
3392 TTTCACAATT
*
3402 GGGGATACT-CAAACCTCGTTATTTCATC
1 GGGGATACTCCAAACCTCGTTATTTCATA
* *
3430 GGAGATACTCCAATCCT-GTTATTTC-TGA
1 GGGGATACTCCAAACCTCGTTATTTCAT-A
3458 GGGGATACTCCAA
1 GGGGATACTCCAA
3471 CCCCGGCTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 1 0.03
28 28 0.80
29 6 0.17
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.30
Consensus pattern (29 bp):
GGGGATACTCCAAACCTCGTTATTTCATA
Found at i:3588 original size:106 final size:106
Alignment explanation
Indices: 3351--3624 Score: 338
Period size: 106 Copynumber: 2.6 Consensus size: 106
3341 TTTCTTAATC
* * * *
3351 GGGGATACTCCAACTCCGATTTTATTTCCAAAACACTAATTTTTCACAATTGGGGATACTCAAAC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATA-TAATTTTTCACAATCGGGGATACTCAAAC
* **
3416 CTCGTTATTTCATCGGAGATACTCCAATCCTGTTATTTCTGA
65 CCCGTTATTTCATCGGAGATACTCCAATCCCATTATTTCTGA
** * * * * *
3458 GGGGATACTCCAACCCCGGCTTTATATCTGAAATATTGAA-TTTTCATAATCGGGGGTACTCTAA
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATA-T-AATTTTTCACAATCGGGGATACTCAAA
*
3522 CCCCGTTATGTT-ATCGG-GATACTCCAATCCCATTATTTTTGA
64 CCCCGTTAT-TTCATCGGAGATACTCCAATCCCATTATTTCTGA
*
3564 GGGGATACTCCAACCCCGATTTTATTTCTAAAATACCAATTTTTCACAATCGGGGATACTC
1 GGGGATACTCCAACCCCGATTTTATTTCTAAAATA-TAATTTTTCACAATCGGGGATACTC
3625 CAACTCCGAT
Statistics
Matches: 140, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
105 2 0.01
106 72 0.51
107 62 0.44
108 4 0.03
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.34
Consensus pattern (106 bp):
GGGGATACTCCAACCCCGATTTTATTTCTAAAATATAATTTTTCACAATCGGGGATACTCAAACC
CCGTTATTTCATCGGAGATACTCCAATCCCATTATTTCTGA
Found at i:3626 original size:51 final size:51
Alignment explanation
Indices: 3564--3681 Score: 159
Period size: 51 Copynumber: 2.3 Consensus size: 51
3554 TTATTTTTGA
*
3564 GGGGATACTCCAACCCCGATTTTA-TTTCTAAAATACCAATTTT-TCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACCAATTTTCT-ACAATC
* *
3615 GGGGATACTCCAACTCCGATTTTATTTTCAAAACACCAATTTTCTATAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTACAATC
**
3666 AAGGATACTCCAACCC
1 GGGGATACTCCAACCC
3682 TGTTATTTCG
Statistics
Matches: 59, Mismatches: 6, Indels: 4
0.86 0.09 0.06
Matches are distributed among these distances:
51 54 0.92
52 5 0.08
ACGTcount: A:0.32, C:0.26, G:0.10, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACCAATTTTCTACAATC
Found at i:3846 original size:79 final size:80
Alignment explanation
Indices: 3615--3835 Score: 306
Period size: 79 Copynumber: 2.8 Consensus size: 80
3605 TTTCACAATC
* * *
3615 GGGGATACTCCAACTCC-GATTTTATTTTCAAAACACCAATTTTCTATAATCAAGGATACTCCAA
1 GGGGATACTCCAAC-CCTGATTTTACTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAA
3679 CCCTGTTA-TTTCGAA
65 CCCTGTTATTTTCGAA
* * * * *
3694 AGAGATACTCCAACCCTGATTTTAGTTTCAAAATACCGATTTTCTATAATCAGGGATATTCCAAC
1 GGGGATACTCCAACCCTGATTTTACTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAAC
3759 CCTGTTATTTTCG-A
66 CCTGTTATTTTCGAA
* *
3773 GGGGATACTCCAACCCTGATTTTACTTCCAAAACACCGATTTT-TCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCTGATTTTACTTTCAAAACACCGATTTTCT-ATAATCAGGGATACTCCA
3836 GTCCCGTTAT
Statistics
Matches: 125, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
78 3 0.02
79 117 0.94
80 5 0.04
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (80 bp):
GGGGATACTCCAACCCTGATTTTACTTTCAAAACACCGATTTTCTATAATCAGGGATACTCCAAC
CCTGTTATTTTCGAA
Found at i:6301 original size:28 final size:28
Alignment explanation
Indices: 6270--6351 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
6260 TCTTATAAGG
* *
6270 TAATTTCA-TATTTATTTTTTTATTTTTT
1 TAATTTCAGTA-TTATTTTTTTAATTTGT
*
6298 TAATTTTAGTATTATTTTTTTAATTTGT
1 TAATTTCAGTATTATTTTTTTAATTTGT
* *
6326 TAAAATTTTGATTATTATTTTTTTAA
1 T--AA-TTTCAGTATTATTTTTTTAA
6352 CAGTAAATCC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
28 23 0.51
29 2 0.04
30 2 0.04
31 18 0.40
ACGTcount: A:0.27, C:0.01, G:0.04, T:0.68
Consensus pattern (28 bp):
TAATTTCAGTATTATTTTTTTAATTTGT
Found at i:10601 original size:20 final size:20
Alignment explanation
Indices: 10576--10628 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
10566 TTTTCACAAT
*
10576 TTGTATCGATACATTGTTCA
1 TTGTATCGATACATTATTCA
10596 TTGTATCGATACATTATTCA
1 TTGTATCGATACATTATTCA
10616 TTGTATCGATACA
1 TTGTATCGATACA
10629 ATGTATCGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.43
Consensus pattern (20 bp):
TTGTATCGATACATTATTCA
Found at i:10635 original size:13 final size:13
Alignment explanation
Indices: 10617--10641 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10607 CATTATTCAT
10617 TGTATCGATACAA
1 TGTATCGATACAA
10630 TGTATCGATACA
1 TGTATCGATACA
10642 TTCTGGGTTT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:13080 original size:79 final size:79
Alignment explanation
Indices: 12985--13211 Score: 278
Period size: 79 Copynumber: 2.9 Consensus size: 79
12975 TTTTTCATCT
* * * **
12985 CGGGGATACTCCAACCCCGGTTTTATTTATAAAATATTGATTTCTCATAATCAGGGATACTCCAA
1 CGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTTTCATAATTGGGGATACTCCAA
**
13050 CCCCGTTATTTTGG
66 CCCCGTTATTTTCA
* * * * *
13064 CGGGGACACTCCAACCCCGGCCTTATTTCTAAAGCT-TCGATTTTTCACAATTGGGGATACTCCA
1 CGGGGATACTCCAACCCCGGCTTTATTTCTAAA-ATATTGATTTTTCATAATTGGGGATACTCCA
13128 ACCCCGTTATTTTCA
65 ACCCCGTTATTTTCA
* ** * *
13143 AGGGGATACTTAAACCCCGGCTTTATTTCTAAAATATTGATTTTTTAT-CTTGGGGATACTCCAA
1 CGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTTTCATAATTGGGGATACTCCAA
13207 CCCCG
66 CCCCG
13212 GTTTTATTTT
Statistics
Matches: 124, Mismatches: 22, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
78 21 0.17
79 102 0.82
80 1 0.01
ACGTcount: A:0.25, C:0.25, G:0.17, T:0.33
Consensus pattern (79 bp):
CGGGGATACTCCAACCCCGGCTTTATTTCTAAAATATTGATTTTTCATAATTGGGGATACTCCAA
CCCCGTTATTTTCA
Found at i:13204 original size:129 final size:127
Alignment explanation
Indices: 13065--13337 Score: 329
Period size: 129 Copynumber: 2.1 Consensus size: 127
13055 TTATTTTGGC
* * * * *
13065 GGGGACACTCCAACCCCGGCCTTA-TTTCTAAAGCTTCGATTTTTCACAATTGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGCCTTATTTTC-AAAACATCAATTTTTCACAATCGGGGATACTCCAA
* * * *
13129 CCCCGTTATTTT-CAAGGGGATACTTAAACC-CCGGCTTTATTTCTAAAATATTGATTTTTTATC
65 CCCCGTTATTTTCCAAGGGGATAC-T---CCTCCAGCTTTATTTCTAAAATATTAATTTCTCA-C
13192 -TT
125 ATT
** * *
13194 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACATCAATTTTTCATAATCGGGGATACTCCAAT
1 GGGGATACTCCAACCCCGGCCTTATTTTCAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
*
13259 CCCGTTATTTTCCGAGGGGATACTCCTCCAGCTTTATTTCTAAAATATTAATTTCTCACAATT
66 CCCGTTATTTTCCAAGGGGATACTCCTCCAGCTTTATTTCTAAAATATTAATTTCTCAC-ATT
13322 GGGGATACTCCAACCC
1 GGGGATACTCCAACCC
13338 TGTTATTTTG
Statistics
Matches: 125, Mismatches: 14, Indels: 11
0.83 0.09 0.07
Matches are distributed among these distances:
126 3 0.02
127 27 0.22
128 18 0.14
129 63 0.50
130 14 0.11
ACGTcount: A:0.26, C:0.25, G:0.15, T:0.34
Consensus pattern (127 bp):
GGGGATACTCCAACCCCGGCCTTATTTTCAAAACATCAATTTTTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCCAAGGGGATACTCCTCCAGCTTTATTTCTAAAATATTAATTTCTCACATT
Found at i:13236 original size:50 final size:51
Alignment explanation
Indices: 13144--13262 Score: 125
Period size: 50 Copynumber: 2.4 Consensus size: 51
13134 TTATTTTCAA
** * ** * * *
13144 GGGGATACTTAAACCCCGGCTTTATTTCTAAAATATTGATTTTTTAT-CTT
1 GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCATAATC
*
13194 GGGGATACTCCAACCCCGGTTTTATTT-TCAAAACATCAATTTTTCATAATC
1 GGGGATACTCCAACCCCGGCTTTATTTCT-AAAACATCAATTTTTCATAATC
*
13245 GGGGATACTCCAATCCCG
1 GGGGATACTCCAACCCCG
13263 TTATTTTCCG
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
49 1 0.02
50 38 0.67
51 18 0.32
ACGTcount: A:0.27, C:0.22, G:0.15, T:0.36
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGCTTTATTTCTAAAACATCAATTTTTCATAATC
Found at i:13367 original size:206 final size:207
Alignment explanation
Indices: 12974--13381 Score: 527
Period size: 206 Copynumber: 2.0 Consensus size: 207
12964 AAATTTCTAT
* **
12974 ATTTTTCATCTCGGGGATACTCCAACCCCGGTTTTATTTATAAAATATTGATTTCTCATAATCAG
1 ATTTTTCATCTCGGGGATACTCCAACCCCGGTTTTATTTATAAAACATCAATTTCTCATAATCAG
* * * * *
13039 GGATACTCCAACCCCGTTATTTTGGCGGGGACACTCCAACCCCGGCCTTATTTCTAAAGCTTCGA
66 GGATACTCCAACCCCGTTATTTTCGAGGGGACACTCC-ACCCCAGCCTTATTTCTAAAGATTCAA
* * *
13104 TTTTTCACAATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTTAAACCCCGGCTTTAT
130 TTTCTCACAATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCAAACCCCGGCCTTAT
13169 TTCTAAAATATTG
195 TTCTAAAATATTG
* * * *
13182 ATTTTTTATCTTGGGGATACTCCAACCCCGGTTTTATTT-TCAAAACATCAATTTTTCATAATCG
1 ATTTTTCATCTCGGGGATACTCCAACCCCGGTTTTATTTAT-AAAACATCAATTTCTCATAATCA
* * * * *
13246 GGGATACTCCAATCCCGTTATTTTCCGAGGGGATACT-C-CTCCAGCTTTATTTCTAAA-ATATT
65 GGGATACTCCAACCCCGTTATTTT-CGAGGGGACACTCCACCCCAGCCTTATTTCTAAAGAT-TC
* *** *
13308 AATTTCTCACAATTGGGGATACTCCAACCCTGTTATTTTGGCGGGGATACTCCAACCCCGGCCTT
128 AATTTCTCACAATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCAAACCCCGGCCTT
13373 ATTTCTAAA
193 ATTTCTAAA
13382 GCTTCGATTT
Statistics
Matches: 172, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
205 1 0.01
206 82 0.48
207 1 0.01
208 79 0.46
209 9 0.05
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.35
Consensus pattern (207 bp):
ATTTTTCATCTCGGGGATACTCCAACCCCGGTTTTATTTATAAAACATCAATTTCTCATAATCAG
GGATACTCCAACCCCGTTATTTTCGAGGGGACACTCCACCCCAGCCTTATTTCTAAAGATTCAAT
TTCTCACAATTGGGGATACTCCAACCCCGTTATTTTCAAGGGGATACTCAAACCCCGGCCTTATT
TCTAAAATATTG
Found at i:13530 original size:79 final size:77
Alignment explanation
Indices: 13194--13570 Score: 318
Period size: 79 Copynumber: 4.8 Consensus size: 77
13184 TTTTTATCTT
*
13194 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACATCAATTTT-TCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCGGTTTTA-TTTCAAAACAT-GATTTTCTCATAATCGGGGATACTCCAA
13258 TCCCGTTATTTTCCGA
64 -CCCGTTATTTT-CGA
* * * * * * * *
13274 GGGGATACT-C--CTCCAGCTTTATTTCTAAAATATTAATTTCTCACAATTGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGTTTTATTTC-AAAACATGATTTTCTCATAATCGGGGATACTCCAAC
* *
13336 CCTGTTATTTTGGC
65 CC-GTTATTTTCGA
** * * * *
13350 GGGGATACTCCAACCCCGGCCTTATTTCTAAAGCTTCGATTTTC-CACAATCGGGGATACTCTAA
1 GGGGATACTCCAACCCCGGTTTTATTTC-AAAACAT-GATTTTCTCATAATCGGGGATACTCCAA
*
13414 CTCCGTTATTTTCAA
64 C-CCGTTATTTTCGA
* * * * *
13429 AGGGATACTCAAACCCCGATTTTATTTTCAAAACACTGATTTTCT-ATAATCAGGGATGCTCCAA
1 GGGGATACTCCAACCCCGGTTTTA-TTTCAAAACA-TGATTTTCTCATAATCGGGGATACTCCAA
13493 CCCTGTTATTTTCGA
64 CCC-GTTATTTTCGA
* ** * * *
13508 GGGGATACTCCAACCTCAATTTTAATTCCAGAACACCGATTTT-TCATAATCGGGGATACTCCA
1 GGGGATACTCCAACCCCGGTTTT-ATTTCAAAACA-TGATTTTCTCATAATCGGGGATACTCCA
13571 GCCCCATTGT
Statistics
Matches: 239, Mismatches: 44, Indels: 29
0.77 0.14 0.09
Matches are distributed among these distances:
76 21 0.09
77 42 0.18
78 3 0.01
79 151 0.63
80 22 0.09
ACGTcount: A:0.27, C:0.25, G:0.15, T:0.33
Consensus pattern (77 bp):
GGGGATACTCCAACCCCGGTTTTATTTCAAAACATGATTTTCTCATAATCGGGGATACTCCAACC
CGTTATTTTCGA
Found at i:27179 original size:61 final size:61
Alignment explanation
Indices: 27059--27247 Score: 256
Period size: 61 Copynumber: 3.1 Consensus size: 61
27049 GAGCAGGATG
* * *
27059 CCTTTTAAAGCCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAGAGCAAGATGCCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCAC-CTTCTAGTCCTCAAAGAGCAGGATGCCTTCT
* * * * *
27121 CCTTTTAAAGCACACACAAGTTAGTGACACCTTCCAGTCCTCAAAGAGTAGGATGCCTTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTCT
*
27182 CCTCTTAAAGCCCACACAAGTTGGTGGCA-CTTCTTAGTCCTCAAAGAGCAGGATG-CTCTCT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTC-TAGTCCTCAAAGAGCAGGATGCCT-TCT
27243 CCTTT
1 CCTTT
27248 CACCCTTTAG
Statistics
Matches: 110, Mismatches: 15, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
60 6 0.05
61 77 0.70
62 27 0.25
ACGTcount: A:0.26, C:0.28, G:0.17, T:0.29
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTCTAGTCCTCAAAGAGCAGGATGCCTTCT
Found at i:27327 original size:55 final size:55
Alignment explanation
Indices: 27256--27567 Score: 234
Period size: 55 Copynumber: 5.3 Consensus size: 55
27246 TTCACCCTTT
* * *
27256 AGTCCTCAAAGTGCAGGACGCCTTTCAAAGCCCACACTAA-TTGGTGGCATTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACAC-AAGTTGGTGGCACTTTCC
* *
27311 AGTCCTTAAAGAGCAGGACACCTTTTAAAGCCCACACAAGTTGGTGGCACTTTCC
1 AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
* * *
27366 AGTCCTCAAAGAGTAGGACACCTTTTCCTTTTAAAGCCCACACAAGCTGGTGGCACCTT-C
1 AGTCCTCAAAGAGCAGGACACC-TTT-C----AAAGCCCACACAAGTTGGTGGCACTTTCC
* * * * * *
27426 AGTCCTTAAAGAGTAAGATGCATTTTCCTTTTAAAACCCACACAAGTTGGTGGCACTTTTCT
1 AGTCCTCAAAGAGCAGGA--CA----CCTTTCAAAGCCCACACAAGTTGGTGGCAC-TTTCC
* * ** *
27488 AGTCCTCAAAAAGCAGGATACCTTTTTCTTTTCAAAGCCCACATGAGTTGGTGGCACCTTT-T
1 AGTCCTCAAAGAGCAGGACA-C-----C-TTTCAAAGCCCACACAAGTTGGTGGCA-CTTTCC
27550 AGTCCTCAAAGAGCAGGA
1 AGTCCTCAAAGAGCAGGA
27568 TGCCTTTTCT
Statistics
Matches: 207, Mismatches: 28, Indels: 37
0.76 0.10 0.14
Matches are distributed among these distances:
54 2 0.01
55 67 0.32
56 3 0.01
57 1 0.00
60 40 0.19
61 27 0.13
62 35 0.17
63 26 0.13
64 1 0.00
65 3 0.01
66 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (55 bp):
AGTCCTCAAAGAGCAGGACACCTTTCAAAGCCCACACAAGTTGGTGGCACTTTCC
Found at i:27597 original size:61 final size:61
Alignment explanation
Indices: 27331--27622 Score: 329
Period size: 61 Copynumber: 4.8 Consensus size: 61
27321 GAGCAGGACA
* * *
27331 CCTTTTAAAGCCCACACAAGTTGGTGGCA-CTTTCCAGTCCTCAAAGAGTAGGACACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAGGATACCTTTT
* * * * * * *
27392 CCTTTTAAAGCCCACACAAGCTGGTGGCACC-TTCAGTCCTTAAAGAGTAAGATGCATTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATACCTTTT
* * *
27452 CCTTTTAAAACCCACACAAGTTGGTGGCACTTTTCTAGTCCTCAAAAAGCAGGATACCTTTT
1 CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTT-TAGTCCTCAAAGAGCAGGATACCTTTT
* ** *
27514 TCTTTTCAAAGCCCACATGAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATGCCTTTT
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATACCTTTT
* ** * *
27576 -CTTTTCAAAGTCCACATGAGTTAGTGGCACTTTTTAGTCCTCAAAGA
1 CCTTTT-AAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGA
27623 ATAGGACACC
Statistics
Matches: 201, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
60 50 0.25
61 76 0.38
62 51 0.25
63 24 0.12
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (61 bp):
CCTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGATACCTTTT
Found at i:27805 original size:85 final size:87
Alignment explanation
Indices: 27661--27932 Score: 272
Period size: 85 Copynumber: 3.2 Consensus size: 87
27651 GTAGGACGCC
* * * *
27661 TTTTCCTTTTTTCCTTTGTCCTCAAAAAGTAGGACACATTTCATTTCCTTCTTTTCCCTT-TTGT
1 TTTTTCTTTTTTCCTTTATCCTCAAAAAGTAGGACACACTTCATTTCCTTCTTTTCCCTTCTAGT
* * *
27725 CCTCGAAGAGCATGATGC-CTT
66 CCTCAAAGAGCAGGACGCACTT
** *
27746 TTTTTCTTTTTTCCTTTATCCTCAAGGAGTAGGACGCACTTCATTTCCTTCTTTTCCCTTCTAGT
1 TTTTTCTTTTTTCCTTTATCCTCAAAAAGTAGGACACACTTCATTTCCTTCTTTTCCCTTCTAGT
* *
27811 TCTCAAAGAGTAGGACGCACTT
66 CCTCAAAGAGCAGGACGCACTT
* * * * * *
27833 TATTCTCCTTTTTCCTTTATCCTCAAAAAGCAGGACACATTTAATTTCC-TGTTTT--CTT-T-G
1 T-TTTTCTTTTTTCCTTTATCCTCAAAAAGTAGGACACACTTCATTTCCTTCTTTTCCCTTCTAG
* * *
27893 TCTTCAAAGGGCAGGATGCA-TT
65 TCCTCAAAGAGCAGGACGCACTT
27915 TTATTTCTTTTTTTCCTT
1 TT-TTTC-TTTTTTCCTT
27933 AGTCCCCAAA
Statistics
Matches: 154, Mismatches: 28, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
81 1 0.01
82 6 0.04
83 25 0.16
84 1 0.01
85 57 0.37
86 16 0.10
87 9 0.06
88 39 0.25
ACGTcount: A:0.19, C:0.24, G:0.12, T:0.45
Consensus pattern (87 bp):
TTTTTCTTTTTTCCTTTATCCTCAAAAAGTAGGACACACTTCATTTCCTTCTTTTCCCTTCTAGT
CCTCAAAGAGCAGGACGCACTT
Found at i:27868 original size:88 final size:85
Alignment explanation
Indices: 27649--27882 Score: 292
Period size: 85 Copynumber: 2.7 Consensus size: 85
27639 TTGCCCTCTT
*
27649 GAGTAGGACGCC-TTTTC-CTTTTTTCCTTTGTCCTCAAAAAGTAGGACACATTTCATTTCCTTC
1 GAGTAGGACGCCTTTTTCTCTTTTTTCCTTTATCCTCAAAAAGTAGGACACATTTCATTTCCTTC
* *
27712 TTTTCCCTTTTGTCCTCGAA
66 TTTTCCCTTTAGTCCTCAAA
* * * * ** * *
27732 GAGCATGATGCCTTTTTTTCTTTTTTCCTTTATCCTCAAGGAGTAGGACGCACTTCATTTCCTTC
1 GAGTAGGACGCCTTTTTCTCTTTTTTCCTTTATCCTCAAAAAGTAGGACACATTTCATTTCCTTC
*
27797 TTTTCCCTTCTAGTTCTCAAA
66 TTTTCCCTT-TAGTCCTCAAA
* * *
27818 GAGTAGGACGCACTTTATTCTCCTTTTTCCTTTATCCTCAAAAAGCAGGACACATTTAATTTCCT
1 GAGTAGGACGC-CTTT-TTCTCTTTTTTCCTTTATCCTCAAAAAGTAGGACACATTTCATTTCCT
27883 GTTTTCTTTG
Statistics
Matches: 123, Mismatches: 23, Indels: 5
0.81 0.15 0.03
Matches are distributed among these distances:
83 9 0.07
84 4 0.03
85 50 0.41
86 16 0.13
87 4 0.03
88 40 0.33
ACGTcount: A:0.20, C:0.26, G:0.13, T:0.41
Consensus pattern (85 bp):
GAGTAGGACGCCTTTTTCTCTTTTTTCCTTTATCCTCAAAAAGTAGGACACATTTCATTTCCTTC
TTTTCCCTTTAGTCCTCAAA
Found at i:27888 original size:42 final size:42
Alignment explanation
Indices: 27662--27988 Score: 229
Period size: 41 Copynumber: 7.7 Consensus size: 42
27652 TAGGACGCCT
* * * *
27662 TTTCCTTTTTTCCTTTGTCCTCAAAAAGTAGGACACATTTCA
1 TTTCCTTTTTTCCTTTATCCTCAAAGAGCAGGACGCATTTCA
* * * * *
27704 TTTCCTTCTTTTCCCTTTTGTCCTCGAAGAGCATGATGCCTTT--
1 TTTCCTT-TTTT-CC-TTTATCCTCAAAGAGCAGGACGCATTTCA
* * * *
27747 TTTTCTTTTTTCCTTTATCCTCAAGGAGTAGGACGCACTTCA
1 TTTCCTTTTTTCCTTTATCCTCAAAGAGCAGGACGCATTTCA
* *
27789 TTTCCTTCTTTTCCCTTCTAGTTCTCAAAGAGTAGGACGCACTTT-A
1 TTTCCTT-TTTT-CCTT-TA-TCCTCAAAGAGCAGGACGCA-TTTCA
* * *
27835 TTCTCC-TTTTTCCTTTATCCTCAAAAAGCAGGACACATTTAA
1 TT-TCCTTTTTTCCTTTATCCTCAAAGAGCAGGACGCATTTCA
* * * * * *
27877 TTTCCTGTTTT-CTTTGTCTTCAAAGGGCAGGATGCATTTTA
1 TTTCCTTTTTTCCTTTATCCTCAAAGAGCAGGACGCATTTCA
* * * *
27918 TTTCTTTTTTTCC-TTAGTCCCCAAAGAACAGGACCCATTTCA
1 TTTCCTTTTTTCCTTTA-TCCTCAAAGAGCAGGACGCATTTCA
* *
27960 -TT-CTCTTTTTCCTTAATCCTCGAAGAGCA
1 TTTCCT-TTTTTCCTTTATCCTCAAAGAGCA
27989 AGATGCTCCC
Statistics
Matches: 221, Mismatches: 47, Indels: 35
0.73 0.16 0.12
Matches are distributed among these distances:
40 20 0.09
41 61 0.28
42 61 0.28
43 16 0.07
44 10 0.05
45 26 0.12
46 22 0.10
47 5 0.02
ACGTcount: A:0.20, C:0.25, G:0.12, T:0.42
Consensus pattern (42 bp):
TTTCCTTTTTTCCTTTATCCTCAAAGAGCAGGACGCATTTCA
Found at i:28657 original size:20 final size:20
Alignment explanation
Indices: 28632--28670 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
28622 TACCCAAATG
*
28632 TATCGATACATTGTTCATTA
1 TATCGATACATTATTCATTA
28652 TATCGATACATTATTCATT
1 TATCGATACATTATTCATT
28671 GTATTGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.15, G:0.08, T:0.46
Consensus pattern (20 bp):
TATCGATACATTATTCATTA
Found at i:28730 original size:74 final size:75
Alignment explanation
Indices: 28598--28737 Score: 203
Period size: 74 Copynumber: 1.9 Consensus size: 75
28588 TACATTGTTC
* *
28598 ATTGTATCGATGCATTCTGGGTTTTACCCAAATGTATCGATACATTGTTCATTATATCGATACAT
1 ATTGTATCGATACATTCTGGGTTTTACCCAAATGTATCGATACATTGTTCAATATATCGATACAT
28663 TATTCATTGT
66 TATTCATTGT
* * * *
28673 ATTGTATCGATACATTTTGGG-TTTA-CCAAGATGTATCGATATATTTTTCAATGTATCGATACA
1 ATTGTATCGATACATTCTGGGTTTTACCCAA-ATGTATCGATACATTGTTCAATATATCGATACA
28736 TT
65 TT
28738 CAGGCATTTT
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
73 4 0.07
74 35 0.60
75 19 0.33
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.43
Consensus pattern (75 bp):
ATTGTATCGATACATTCTGGGTTTTACCCAAATGTATCGATACATTGTTCAATATATCGATACAT
TATTCATTGT
Found at i:33107 original size:27 final size:27
Alignment explanation
Indices: 33070--33127 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
33060 CCATATTTTT
* *
33070 CTACTCAACCTCTATACCCGTCATATC
1 CTACTCAACCTCCATACCCATCATATC
* *
33097 CTACTTAACCTCCATACCCATTATATC
1 CTACTCAACCTCCATACCCATCATATC
33124 CTAC
1 CTAC
33128 CACGACCCAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.28, C:0.40, G:0.02, T:0.31
Consensus pattern (27 bp):
CTACTCAACCTCCATACCCATCATATC
Found at i:33961 original size:34 final size:32
Alignment explanation
Indices: 33897--33961 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
33887 TAGCCAAACT
**
33897 TGTATCGATACACAAAGTATGTATCAATACAA
1 TGTATCGATACACAAAAAATGTATCAATACAA
*
33929 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCAATACA
33962 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
32 13 0.46
33 4 0.14
34 11 0.39
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCAATACAA
Found at i:36195 original size:21 final size:21
Alignment explanation
Indices: 36162--36211 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
36152 TTGCAAGTTG
*
36162 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
36184 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
36205 AAATAAA
1 AAATAAA
36212 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:38029 original size:15 final size:15
Alignment explanation
Indices: 38009--38039 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
37999 TAAAAATGTC
*
38009 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
38024 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
38039 C
1 C
38040 CAAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:40403 original size:13 final size:13
Alignment explanation
Indices: 40385--40410 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
40375 TACAGCAAGT
40385 ATGTATCGATACA
1 ATGTATCGATACA
40398 ATGTATCGATACA
1 ATGTATCGATACA
40411 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:40932 original size:34 final size:35
Alignment explanation
Indices: 40869--40935 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
40859 CTAAGTGATT
40869 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
40905 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
40936 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:45857 original size:13 final size:13
Alignment explanation
Indices: 45839--45864 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
45829 TACAGCAAGT
45839 ATGTATCGATACA
1 ATGTATCGATACA
45852 ATGTATCGATACA
1 ATGTATCGATACA
45865 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:46386 original size:34 final size:35
Alignment explanation
Indices: 46323--46389 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
46313 CTAAGTGATT
46323 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
46359 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
46390 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:47889 original size:28 final size:28
Alignment explanation
Indices: 47858--47922 Score: 103
Period size: 28 Copynumber: 2.3 Consensus size: 28
47848 ACGGTGTTAT
** *
47858 AGTATCCCCTTGAAAATGATAGGTTTGG
1 AGTATCCCCTCAAAAATGATAGGGTTGG
47886 AGTATCCCCTCAAAAATGATAGGGTTGG
1 AGTATCCCCTCAAAAATGATAGGGTTGG
47914 AGTATCCCC
1 AGTATCCCC
47923 GATGGTGAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.29, C:0.20, G:0.23, T:0.28
Consensus pattern (28 bp):
AGTATCCCCTCAAAAATGATAGGGTTGG
Found at i:47973 original size:79 final size:79
Alignment explanation
Indices: 47882--48433 Score: 561
Period size: 79 Copynumber: 6.8 Consensus size: 79
47872 AATGATAGGT
* *
47882 TTGGAGTATCCCCTCAAAAATGATAGGGTTGGAGTATCCCCGATGGTGAAAAATCAATA-TTTGG
1 TTGGAGTATCCCCTCAGAAATGATAGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTGG
* *
47946 TAAATACAAATGGGG
66 -AAATAAAAACGGGG
* *
47961 TTGGAGTATCCCCTCAGAAATGATGGGGTTGGAGTATCCCTAATGGTGAAAAATCAATATTTTGG
1 TTGGAGTATCCCCTCAGAAATGATAGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTGG
48026 AAATAAAAACGGGG
66 AAATAAAAACGGGG
* ** * ** *
48040 TTGAAGTATCCCCTCAGAAATGATAGGGTTAAAGTATCCCCGATGGTGAAAAATTGATATTTTGA
1 TTGGAGTATCCCCTCAGAAATGATAGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTGG
*
48105 AAATAAAAATGGGG
66 AAATAAAAACGGGG
* * * * *
48119 TTGGAGTATCCTCTGACCTCTTCGGATATGATGGGGTTGGAGTA-CCCCTAATGATGGAAAATTT
1 TTGGAGTA---TC---CC-C-TCAGAAATGATAGGGTTGGAGTATCCCC-AATGGT-GAAAA-AT
** * *
48183 TGATATTTTGGAATTAAAAACGAGG
55 CAATATTTTGGAAATAAAAACGGGG
* * * * * * *
48208 TTAGAGTATCCCCTCAGATATGATGGGGTTGAAGTATCCTCAATAGTAAAAAATCAATATTTTGG
1 TTGGAGTATCCCCTCAGAAATGATAGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTGG
* **
48273 AAATAAAAATGGCA
66 AAATAAAAACGGGG
* * ** *
48287 TCGGAGTATCCCTTTGGAAATGATAGGGTTGGAGTATCCCCAATGGTGAAAAATCGATATTTTGG
1 TTGGAGTATCCCCTCAGAAATGATAGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTGG
48352 AAATAAAAACGGGG
66 AAATAAAAACGGGG
* * * * * *
48366 TTGGAGTATCCCTTCAGAAATAAT-GAAGTTGGAGTATCCTCGATGGTGAAAAATCGATACTTTT
1 TTGGAGTATCCCCTCAGAAATGATAG-GGTTGGAGTATCCCCAATGGTGAAAAATCAATA-TTTT
48430 GGAA
64 GGAA
48434 GGAGAAATTT
Statistics
Matches: 392, Mismatches: 66, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
78 1 0.00
79 276 0.70
80 17 0.04
81 25 0.06
82 6 0.02
83 2 0.01
85 2 0.01
86 7 0.02
87 22 0.06
88 5 0.01
89 29 0.07
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.29
Consensus pattern (79 bp):
TTGGAGTATCCCCTCAGAAATGATAGGGTTGGAGTATCCCCAATGGTGAAAAATCAATATTTTGG
AAATAAAAACGGGG
Found at i:48973 original size:51 final size:53
Alignment explanation
Indices: 48839--48993 Score: 219
Period size: 51 Copynumber: 3.0 Consensus size: 53
48829 GGTTCGAAAT
* * *
48839 GGTCAAAATAGCCTGAATGTATCGATACAATGAAGAATGTATC-AGTACA-TTGA
1 GGTCAAAA-ACCCAGAATGTATCGATACAATGAAAAATGTATCGA-TACATTTGA
*
48892 GGTCAAAAACCCAGAATGTATCGATACAATGAATAATGTATCGATACATTTG-
1 GGTCAAAAACCCAGAATGTATCGATACAATGAAAAATGTATCGATACATTTGA
*
48944 GGTC-AAAACCTAGAATGTATCGATACAATGAAAAATGTATCGATACATTT
1 GGTCAAAAACCCAGAATGTATCGATACAATGAAAAATGTATCGATACATTT
48994 TCTTTCTAGA
Statistics
Matches: 95, Mismatches: 5, Indels: 6
0.90 0.05 0.06
Matches are distributed among these distances:
51 44 0.46
52 39 0.41
53 12 0.13
ACGTcount: A:0.41, C:0.14, G:0.18, T:0.27
Consensus pattern (53 bp):
GGTCAAAAACCCAGAATGTATCGATACAATGAAAAATGTATCGATACATTTGA
Found at i:50029 original size:66 final size:65
Alignment explanation
Indices: 49780--50261 Score: 503
Period size: 66 Copynumber: 7.4 Consensus size: 65
49770 CACTAATTTA
** *
49780 TGTGGGCTTTAAAAGAAAAA-AAA-GCATTTTGCACTTTGAGGACTAAAAGGTGCCACCAACTTG
1 TGTGGGCTTTAAAAGAAAAAGAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTG
** * * * * **
49843 TGTGGGCTTTAAAAGAAAAAGAAAAACGTCTTACTCTATGAGGACTAAAAGGTTTCACCAACTTG
1 TGTGGGCTTTAAAAGAAAAAGAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTG
** * * *
49908 TGTAAGCTTTTTAAAG---GA-AAAGGCATCCTACTCTTTGAGGACTAAAAGGTGCCACCAACTT
1 TGTGGGC-TTTAAAAGAAAAAGAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTT
*
49969 A
65 G
* ** ** * * *
49970 TGTGAGCTTTAAAAGGAAAAAGTTAGGTGTCCTGCTCTTTAAGGACTAAAAGGTACCACCAATTT
1 TGTGGGCTTTAAAA-GAAAAAGAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTT
50035 G
65 G
*
50036 TGTGGGCTTTAAAAAGAAAAGGAGAA-GCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACT
1 TGTGGGCTTT-AAAAGAAAAAGA-AAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACT
50100 TG
64 TG
* * *
50102 TGTGAGCTTTAAAAGAAAAAGGAAAGGCATCTTGCTCTTTGAGGACTATAAA-GTGCCACCACCT
1 TGTGGGCTTTAAAAGAAAAA-GAAAGGCATCCTGCTCTTTGAGGACTA-AAAGGTGCCACCAACT
50166 TG
64 TG
* * * * *
50168 TGTGGGTTTTAAGAAAAAAAAGAAGAAGCGTCCTGCTCTTTGAGGACTAAAAGGTGCCACTAACT
1 TGTGGGCTTTAA-AAGAAAAAGAA-AGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACT
50233 TG
64 TG
* *
50235 TATGGGCTTTAAAAGGAAAAGGAAAGG
1 TGTGGGCTTTAAAA-GAAAAAGAAAGG
50262 TGTTTTACTT
Statistics
Matches: 344, Mismatches: 58, Indels: 31
0.79 0.13 0.07
Matches are distributed among these distances:
61 6 0.02
62 43 0.12
63 21 0.06
64 3 0.01
65 49 0.14
66 157 0.46
67 65 0.19
ACGTcount: A:0.35, C:0.16, G:0.23, T:0.26
Consensus pattern (65 bp):
TGTGGGCTTTAAAAGAAAAAGAAAGGCATCCTGCTCTTTGAGGACTAAAAGGTGCCACCAACTTG
Found at i:54016 original size:25 final size:24
Alignment explanation
Indices: 53984--54051 Score: 93
Period size: 23 Copynumber: 2.8 Consensus size: 24
53974 TGAAAATCCA
53984 TTTAATATTGACTAAACTTTCCTAT
1 TTTAATATTGACTAAA-TTTCCTAT
* *
54009 TTTAATATTAAC-AATTTTCCTAT
1 TTTAATATTGACTAAATTTCCTAT
*
54032 TTTAATATTGAGTAAATTTC
1 TTTAATATTGACTAAATTTC
54052 AACCGTTGCT
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.49
24 8 0.22
25 11 0.30
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.50
Consensus pattern (24 bp):
TTTAATATTGACTAAATTTCCTAT
Found at i:54194 original size:12 final size:10
Alignment explanation
Indices: 54171--54199 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
54161 CTTGCTTCGA
54171 TTCTTCTCTT
1 TTCTTCTCTT
54181 TTCTTCTCTT
1 TTCTTCTCTT
54191 TT-TTCTCTT
1 TTCTTCTCTT
54200 GTTGTTTCGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 7 0.37
10 12 0.63
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (10 bp):
TTCTTCTCTT
Found at i:54583 original size:23 final size:24
Alignment explanation
Indices: 54553--54606 Score: 83
Period size: 23 Copynumber: 2.2 Consensus size: 24
54543 CGTTTCTGAG
54553 TTCAGCAGCTTAATTG-TAGCTGT
1 TTCAGCAGCTTAATTGATAGCTGT
54576 TTCAGCAGCTTAATTGCAATAGCTGT
1 TTCAGCAGCTTAATTG--ATAGCTGT
54602 TTCAG
1 TTCAG
54607 TTTTTATTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
23 16 0.57
26 12 0.43
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (24 bp):
TTCAGCAGCTTAATTGATAGCTGT
Found at i:54687 original size:30 final size:30
Alignment explanation
Indices: 54652--54718 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
54642 TTCTTTGCTG
* **
54652 CTTGATTCATTTTTGTCTTCATTGTAGCAT
1 CTTGATTCATTTTTGTCTTCAGTACAGCAT
*
54682 CTTGATTCGTTTTTGTCTTCAGTACAGCAT
1 CTTGATTCATTTTTGTCTTCAGTACAGCAT
54712 CTTGATT
1 CTTGATT
54719 GCTTTAATTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.16, C:0.18, G:0.15, T:0.51
Consensus pattern (30 bp):
CTTGATTCATTTTTGTCTTCAGTACAGCAT
Found at i:54805 original size:12 final size:12
Alignment explanation
Indices: 54790--54831 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
54780 ACTTTATCGT
54790 TTGCTTTCTTCA
1 TTGCTTTCTTCA
54802 TTGCATTTGCTTCA
1 TTGC-TTT-CTTCA
*
54816 TTGGTTTCTTCA
1 TTGCTTTCTTCA
54828 TTGC
1 TTGC
54832 ACCTTGATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
12 12 0.46
13 6 0.23
14 8 0.31
ACGTcount: A:0.10, C:0.21, G:0.14, T:0.55
Consensus pattern (12 bp):
TTGCTTTCTTCA
Found at i:55544 original size:42 final size:42
Alignment explanation
Indices: 55485--55658 Score: 165
Period size: 42 Copynumber: 4.2 Consensus size: 42
55475 AAATGACCCA
** * **
55485 GACAGGCAGACTAAGGGTTAGAAAGTCTCCAAAGTCAAAGCC
1 GACAGGCAGACCGAGGGTAAGAAAGTCTCCAGGGTCAAAGCC
* *
55527 GACAGGCAGACCGAGGGTAAGAAAGTCTCTAGGGTCAAAGCT
1 GACAGGCAGACCGAGGGTAAGAAAGTCTCCAGGGTCAAAGCC
* * * ** * **
55569 GACAGGTAGACTTGA-GGTGAGGCAGTCTCTAGGGTCAAAGGT
1 GACAGGCAGAC-CGAGGGTAAGAAAGTCTCCAGGGTCAAAGCC
* *
55611 GATAGGCAGA-CTAGGGTAAGAAAGTCTCCAGGGTCAAAG-C
1 GACAGGCAGACCGAGGGTAAGAAAGTCTCCAGGGTCAAAGCC
55651 GACAGGCA
1 GACAGGCA
55659 CACTTGAGAA
Statistics
Matches: 107, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
40 8 0.07
41 21 0.20
42 76 0.71
43 2 0.02
ACGTcount: A:0.33, C:0.18, G:0.33, T:0.16
Consensus pattern (42 bp):
GACAGGCAGACCGAGGGTAAGAAAGTCTCCAGGGTCAAAGCC
Found at i:56075 original size:134 final size:131
Alignment explanation
Indices: 55910--56150 Score: 313
Period size: 134 Copynumber: 1.8 Consensus size: 131
55900 AAAAAAGGTG
* * *
55910 GATTTAACTAGGATGGTAACCATACGTCAAATCAGAAT-GAAATGAATCTGACTAGAGTGGTAAC
1 GATTTAACTAGGATGGTAACCATACATCAAATCAAAATAGAAA-AAAT-TGACTAGAGTGGTAAC
* * *
55974 CATACATCAGACCGAAATGAGAAAAGTTTGACTAGGGTGGTAACTAATACAATTAAATAAAACAG
64 CATACAT--GACCAAAATGAGAAAAATTTGACCAGGGTGGTAACTAATACAATTAAATAAAACAG
56039 AGGCA
127 AGGCA
* * * *
56044 GATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAAAATTGATTAGGGTGGTAACC
1 GATTTAACTAGGATGGTAACCATACATCAAATCAAAAT-AGAAAAAATTGACTAGAGTGGTAACC
* * *
56109 ATACGTTATCAAAATGAGAAAAATTTGACCAGGGTGGTAACT
65 ATACATGACCAAAATGAGAAAAATTTGACCAGGGTGGTAACT
56151 GTATGTCAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
132 31 0.34
134 54 0.59
135 3 0.03
136 4 0.04
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.24
Consensus pattern (131 bp):
GATTTAACTAGGATGGTAACCATACATCAAATCAAAATAGAAAAAATTGACTAGAGTGGTAACCA
TACATGACCAAAATGAGAAAAATTTGACCAGGGTGGTAACTAATACAATTAAATAAAACAGAGGC
A
Found at i:56109 original size:44 final size:44
Alignment explanation
Indices: 55911--56149 Score: 191
Period size: 44 Copynumber: 5.4 Consensus size: 44
55901 AAAAAGGTGG
* * * *
55911 ATTTAACTAGGATGGTAACCATACGTCAAATCAGAAT--GAAATGA
1 ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAA--A
* * * * * *
55955 ATCTGACTAGAGTGGTAACCATACATCAGACCGAAATGAGAAAA
1 ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAA
* * * * ** *
55999 GTTTGACTAGGGTGGTAACTAATACAATTAAAT-AAAACAGAGGCAG
1 ATTTGACTAGGGTGGTAAC-CATAC-ATCAAATCAAAATA-AGAAAA
56045 ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAA
1 ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAA
* * * * *
56089 AATTGATTAGGGTGGTAACCATACGT--TATCAAAATGAGAAAA
1 ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAA
*
56131 ATTTGACCAGGGTGGTAAC
1 ATTTGACTAGGGTGGTAAC
56150 TGTATGTCAA
Statistics
Matches: 152, Mismatches: 37, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
42 30 0.20
44 77 0.51
45 16 0.11
46 29 0.19
ACGTcount: A:0.42, C:0.13, G:0.21, T:0.23
Consensus pattern (44 bp):
ATTTGACTAGGGTGGTAACCATACATCAAATCAAAATAAGAAAA
Found at i:57144 original size:88 final size:88
Alignment explanation
Indices: 56926--57158 Score: 238
Period size: 88 Copynumber: 2.7 Consensus size: 88
56916 AACATGCATG
* * ** *
56926 AAACAATGCAAATACAAGCATCAGTAAAGTGGCAAATGCATATGAAAATGATGCAAATGTCAATG
1 AAACAATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAAATGATGCAAATACCAATA
* *
56991 TTATTTGAATGCAAATGCATGTA
66 TTATTTAAATGCAAATGCAGGTA
** * * * ** * *
57014 AAATGATACAAATGCAAGCATCAACAAAGGGGCAAACACATATG-TAATGATGCAAATACCACTA
1 AAACAATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAAATGATGCAAATACCAATA
* * *
57078 TTATTTAAAATGTAAATGTAGGTG
66 TTATTT-AAATGCAAATGCAGGTA
* *
57102 AGACAATGCAAATGCAATCATCAATAGAA-TGGCAAATGCATATGAAAAT-ATGCAAAT
1 AAACAATGCAAATGCAAGCATCAATA-AAGTGGCAAATGCATATGAAAATGATGCAAAT
57159 GCTAATGCAG
Statistics
Matches: 113, Mismatches: 29, Indels: 6
0.76 0.20 0.04
Matches are distributed among these distances:
87 21 0.19
88 87 0.77
89 5 0.04
ACGTcount: A:0.46, C:0.13, G:0.17, T:0.24
Consensus pattern (88 bp):
AAACAATGCAAATGCAAGCATCAATAAAGTGGCAAATGCATATGAAAATGATGCAAATACCAATA
TTATTTAAATGCAAATGCAGGTA
Done.