Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1114
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: 70086
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4366 original size:13 final size:13
Alignment explanation
Indices: 4348--4384 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
4338 CATTTTTCTT
4348 TGTATCGATACAA
1 TGTATCGATACAA
*
4361 TGTATCGATACAC
1 TGTATCGATACAA
4374 TGTATCGATAC
1 TGTATCGATAC
4385 TGGGGGATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4540 original size:20 final size:20
Alignment explanation
Indices: 4497--4542 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
4487 AAATCTTTTG
4497 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
4518 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
4538 CAAAA
1 CAAAA
4543 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:6005 original size:22 final size:20
Alignment explanation
Indices: 5971--6013 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
5961 TGATTAATGT
5971 TTTGCTTGACTTTGTGTTTA
1 TTTGCTTGACTTTGTGTTTA
5991 TTTGCATTGTACTTTGTGTTTA
1 TTTGC-TTG-ACTTTGTGTTTA
6013 T
1 T
6014 GGAAATGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 5 0.24
21 3 0.14
22 13 0.62
ACGTcount: A:0.12, C:0.09, G:0.19, T:0.60
Consensus pattern (20 bp):
TTTGCTTGACTTTGTGTTTA
Found at i:12317 original size:13 final size:13
Alignment explanation
Indices: 12299--12323 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12289 AATTCAAGTA
12299 TGTATCGATACAT
1 TGTATCGATACAT
12312 TGTATCGATACA
1 TGTATCGATACA
12324 AAGTGAGTTT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:12408 original size:13 final size:13
Alignment explanation
Indices: 12390--12415 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
12380 TACCAAGAAC
12390 ATGTATCGATACA
1 ATGTATCGATACA
12403 ATGTATCGATACA
1 ATGTATCGATACA
12416 TCTGGTTATG
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:19609 original size:13 final size:13
Alignment explanation
Indices: 19591--19616 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19581 TACCAAGAAC
19591 ATGTATCGATACA
1 ATGTATCGATACA
19604 ATGTATCGATACA
1 ATGTATCGATACA
19617 TCTGTGTGTG
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:21173 original size:24 final size:26
Alignment explanation
Indices: 21146--21200 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 26
21136 GGATGTAACA
21146 TTTCTTTATTTT-C-TTATCTTTTTT
1 TTTCTTTATTTTCCATTATCTTTTTT
* *
21170 TTTCTTTTTTTTCCATTTTTCTTTTTT
1 TTTCTTTATTTTCCA-TTATCTTTTTT
21197 TTTC
1 TTTC
21201 ACTTTTTCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
24 11 0.42
25 1 0.04
27 14 0.54
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.80
Consensus pattern (26 bp):
TTTCTTTATTTTCCATTATCTTTTTT
Found at i:21195 original size:18 final size:18
Alignment explanation
Indices: 21168--21210 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
21158 CTTATCTTTT
*
21168 TTTTTCTTTTTTTTCCA-
1 TTTTTCTTTTTTTTTCAC
21185 TTTTTCTTTTTTTTTCAC
1 TTTTTCTTTTTTTTTCAC
21203 TTTTTCTT
1 TTTTTCTT
21211 CATTACATGC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTTCTTTTTTTTTCAC
Found at i:24953 original size:154 final size:154
Alignment explanation
Indices: 24671--25238 Score: 475
Period size: 154 Copynumber: 3.7 Consensus size: 154
24661 CTAGAAAATT
* * * *
24671 AGGATACCTTCGACGTAAAAATATCTGATACCCCTAAAAGACTTAAAAAGGATTTTTAAATGGGA
1 AGGATACCTTCGACGTAAAAGTACCCGATACCCCTAAAGGAC-TAAAAAGGATTTTTAAATGGGA
* * * ***
24736 TGAACCTATCCTAAATATTCACCTTCGGCATAAAAGCGGAGTTAGTGACAACCTAGGAGTTGGTT
65 TGAACCTATCCCAAATATCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGAGTTGGTT
* *
24801 CCAAAAAATTATGAAAATGCCCCTA
130 CCAAAAAATTACGAAAATACCCCTA
*
24826 GAGGATACCTTCGATGTAAAAGTACCCGATACCCCTAAAGGACTAAAAAGGA-TTTTAAGA-GGG
1 -AGGATACCTTCGACGTAAAAGTACCCGATACCCCTAAAGGACTAAAAAGGATTTTTAA-ATGGG
* * ** *
24889 ATGAACCTATCCCAAATATCCACTTTCGGCATAAAATCAGACCCAGTGATGACGTAGGAGTTGGT
64 ATGAACCTATCCCAAATATCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGAGTTGGT
** *
24954 TCTGAAAAATTACGAAAATACCTCTA
129 TCCAAAAAATTACGAAAATACCCCTA
* * * *
24980 AGGGATACCTTCGACGTAAAAGTACTCGATACCCCTCAAGGATTTAAAAA-GA----TAAA-AGG
1 A-GGATACCTTCGACGTAAAAGTACCCGATACCCCTAAAGGA-CTAAAAAGGATTTTTAAATGGG
* * * * * * * * * * ***
25039 ATGAACCAATCCTAAAT-GCACACCTTTGGCATAGAAGCGGACCCGGTGATAACCTAAGACTCAA
64 ATGAACCTATCCCAAATATC-CACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGAGTTGG
* * *
25103 TTCTAAGAAAATTACTAAAATACCTCTA
128 TTCCAA-AAAATTACGAAAATACCCCTA
* * * * * *
25131 GGGAATATCTTCGACATATAAGTACCCAATACCCCTAAAGGGCTTAAAAAGG-----TAAA-GGG
1 AGG-ATACCTTCGACGTAAAAGTACCCGATACCCCTAAAGGAC-TAAAAAGGATTTTTAAATGGG
* * * *
25190 ATGAACCTATCCTAAAT-GCACACCTTTGGCATAAAAGCGGACCCAGTGA
64 ATGAACCTATCCCAAATATC-CACCTTCGGCATAAAAGCAGACCCAGTGA
25239 TAACTTATGA
Statistics
Matches: 347, Mismatches: 57, Indels: 21
0.82 0.13 0.05
Matches are distributed among these distances:
149 1 0.00
150 56 0.16
151 112 0.32
152 1 0.00
153 1 0.00
154 123 0.35
155 16 0.05
156 37 0.11
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.23
Consensus pattern (154 bp):
AGGATACCTTCGACGTAAAAGTACCCGATACCCCTAAAGGACTAAAAAGGATTTTTAAATGGGAT
GAACCTATCCCAAATATCCACCTTCGGCATAAAAGCAGACCCAGTGACAACCTAGGAGTTGGTTC
CAAAAAATTACGAAAATACCCCTA
Found at i:25154 original size:151 final size:149
Alignment explanation
Indices: 24672--25272 Score: 431
Period size: 151 Copynumber: 3.9 Consensus size: 149
24662 TAGAAAATTA
* * * ** * *
24672 GGATACCTTCGACGTAAAAATATCTGATACCCCTAAAAGACTTAAAAAGGATTTTTAAATGGGAT
1 GGATACCTTCGACATAAAAGTACCCAATACCCCTAAAGGACTTAAAAA-GA----TAAA-AGGAT
* *** * *** * * * ***
24737 GAACCTATCCTAAATATTCACCTTCGGCATAAAAGCGGAGTTAGTGACAACCTAGGAGTTGGTTC
60 GAACCAATCCTAAATGCACACCTTTGGCATAAAAGCGGACCCAGTGATAACCTAAGACTCAATT-
* * *
24802 CAAAAAATTA-TGAAAATGCCCCT-AG
124 AAAAAAATTACT-AAAATACCTCTAAG
** * *
24827 AGGATACCTTCGATGTAAAAGTACCCGATACCCCTAAAGGAC-TAAAAAGGATTTTAAGAGGGAT
1 -GGATACCTTCGACATAAAAGTACCCAATACCCCTAAAGGACTTAAAAA-GA---TAA-AAGGAT
* * * * * * * * * ***
24891 GAACCTATCCCAAATATC-CA-CTTTCGGCATAAAATCAGACCCAGTGATGACGTAGGAGTTGGT
60 GAACCAATCCTAAAT-GCACACCTTT-GGCATAAAAGCGGACCCAGTGATAACCTAAGACTCAAT
** *
24954 TCTGAAAAATTACGAAAATACCTCTAAG
123 T-AAAAAAATTACTAAAATACCTCTAAG
* * * * *
24982 GGATACCTTCGACGTAAAAGTACTCGATACCCCTCAAGGATTTAAAAAGATAAAAGGATGAACCA
1 GGATACCTTCGACATAAAAGTACCCAATACCCCTAAAGGACTTAAAAAGATAAAAGGATGAACCA
* * *
25047 ATCCTAAATGCACACCTTTGGCATAGAAGCGGACCCGGTGATAACCTAAGACTCAATTCTAAGAA
66 ATCCTAAATGCACACCTTTGGCATAAAAGCGGACCCAGTGATAACCTAAGACTCAA-T-TAAAAA
25112 AATTACTAAAATACCTCT-AG
129 AATTACTAAAATACCTCTAAG
* * * * *
25132 GGAATATCTTCGACATATAAGTACCCAATACCCCTAAAGGGCTTAAAAAGGTAAAGGGATGAACC
1 GG-ATACCTTCGACATAAAAGTACCCAATACCCCTAAAGGACTTAAAAAGATAAAAGGATGAACC
* * * * *
25197 TATCCTAAATGCACACCTTTGGCATAAAAGCGGACCCAGTGATAACTTATGATTCGATTAAAAAA
65 AATCCTAAATGCACACCTTTGGCATAAAAGCGGACCCAGTGATAACCTAAGACTCAATTAAAAAA
25262 ATTACTAAAAT
130 ATTACTAAAAT
25273 GCCCTTCAAG
Statistics
Matches: 371, Mismatches: 63, Indels: 29
0.80 0.14 0.06
Matches are distributed among these distances:
149 18 0.05
150 51 0.14
151 129 0.35
152 1 0.00
153 3 0.01
154 115 0.31
155 18 0.05
156 36 0.10
ACGTcount: A:0.39, C:0.20, G:0.18, T:0.24
Consensus pattern (149 bp):
GGATACCTTCGACATAAAAGTACCCAATACCCCTAAAGGACTTAAAAAGATAAAAGGATGAACCA
ATCCTAAATGCACACCTTTGGCATAAAAGCGGACCCAGTGATAACCTAAGACTCAATTAAAAAAA
TTACTAAAATACCTCTAAG
Found at i:26681 original size:19 final size:19
Alignment explanation
Indices: 26646--26697 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
26636 TCCTACTATT
26646 TTTCTATTTTTTCTTTTTAC
1 TTTCT-TTTTTTCTTTTTAC
*
26666 TTTCTTTTTTAT-TTTTTTC
1 TTTCTTTTTT-TCTTTTTAC
*
26685 TCTCTTTTTTTCT
1 TTTCTTTTTTTCT
26698 CGAAGTTCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
18 1 0.04
19 21 0.75
20 6 0.21
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTCTTTTTTTCTTTTTAC
Found at i:26855 original size:13 final size:14
Alignment explanation
Indices: 26833--26868 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
26823 TCCATTTTTT
26833 TCATTTTTTTATTG
1 TCATTTTTTTATTG
*
26847 TCATTTTTTTCTTG
1 TCATTTTTTTATTG
26861 TCATTTTT
1 TCATTTTT
26869 GATTGGATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.06, T:0.72
Consensus pattern (14 bp):
TCATTTTTTTATTG
Found at i:37382 original size:202 final size:203
Alignment explanation
Indices: 37103--37503 Score: 608
Period size: 202 Copynumber: 2.0 Consensus size: 203
37093 TTCAAATGAT
*
37103 ATATTGTTAGAAAGCTAACTTAATAAACATTAATTCCAAAACTTATGACTTGCCCAAAAATTCAA
1 ATATTATTAGAAAGCTAACTTAATAAACATTAATTCC-AAACTTATGACTTGCCCAAAAATTCAA
*
37168 ATCAAAGGTGAAAATATTAATGCAAAAAGGTCTAATTATA-GAGCATAATAAACCTAAATGACAA
65 ATCAAAGGTGAAAATATTAATGCAAAAAGGTCTAATTATAGGA-CATAATAAACATAAATGACAA
* *
37232 GTAGAAACCTAGTTTGTTACTTATCCAAATAAACTAGAGAATAGGTAAAACTTACGACATTAGAA
129 GTAGAAACCTAGTTTGTTACTTATCCAAACAAACTAGAGAAAAGGTAAAACTTACGACATTAGAA
37297 AGCTATCTGA
194 AGCTATCTGA
* * *
37307 ATATTATTAGAAAGCTAACTTAATGAACGTTAATTCC-AATTTATGACTTGCCCAAAAATTCAAA
1 ATATTATTAGAAAGCTAACTTAATAAACATTAATTCCAAACTTATGACTTGCCCAAAAATTCAAA
* * * * * * *
37371 TCAAGGGTGAAAATATTAATGCAACAAGGTCTGATTGTAGGACATAGTAGACATATATGACAAGT
66 TCAAAGGTGAAAATATTAATGCAAAAAGGTCTAATTATAGGACATAATAAACATAAATGACAAGT
* * * *
37436 AGAAACCTAGTTTGTTACTTATCCAAACAGACTCGAGAAAAGGTAAAACTTGCGACATTGGAAAG
131 AGAAACCTAGTTTGTTACTTATCCAAACAAACTAGAGAAAAGGTAAAACTTACGACATTAGAAAG
37501 CTA
196 CTA
37504 CTTGAACAAA
Statistics
Matches: 178, Mismatches: 18, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
202 142 0.80
203 2 0.01
204 34 0.19
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.27
Consensus pattern (203 bp):
ATATTATTAGAAAGCTAACTTAATAAACATTAATTCCAAACTTATGACTTGCCCAAAAATTCAAA
TCAAAGGTGAAAATATTAATGCAAAAAGGTCTAATTATAGGACATAATAAACATAAATGACAAGT
AGAAACCTAGTTTGTTACTTATCCAAACAAACTAGAGAAAAGGTAAAACTTACGACATTAGAAAG
CTATCTGA
Found at i:39265 original size:11 final size:11
Alignment explanation
Indices: 39240--39283 Score: 56
Period size: 10 Copynumber: 4.1 Consensus size: 11
39230 AGATTCAACT
39240 AAAATAAAAGA-
1 AAAA-AAAAGAG
39251 AAAAAAAAGAG
1 AAAAAAAAGAG
39262 -AAAAAAAGAG
1 AAAAAAAAGAG
*
39272 AAAGAAAAGAG
1 AAAAAAAAGAG
39283 A
1 A
39284 GAAGAAATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
10 16 0.53
11 14 0.47
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAAAAGAG
Found at i:39281 original size:21 final size:20
Alignment explanation
Indices: 39245--39283 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
39235 CAACTAAAAT
39245 AAAAGAAAAAAAAAGAGAAA
1 AAAAGAAAAAAAAAGAGAAA
*
39265 AAAAGAGAAAGAAAAGAGA
1 AAAAGA-AAAAAAAAGAGA
39284 GAAGAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAGAAAAAAAAAGAGAAA
Found at i:39290 original size:12 final size:12
Alignment explanation
Indices: 39248--39286 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
39238 CTAAAATAAA
*
39248 AGAAAAAAAAAG
1 AGAAAAAAAGAG
39260 AGAAAAAAAGAG
1 AGAAAAAAAGAG
*
39272 A-AAGAAAAGAG
1 AGAAAAAAAGAG
39283 AGAA
1 AGAA
39287 GAAATAGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (12 bp):
AGAAAAAAAGAG
Found at i:41159 original size:97 final size:97
Alignment explanation
Indices: 41011--41238 Score: 368
Period size: 97 Copynumber: 2.4 Consensus size: 97
41001 TTGGGAATAC
*
41011 TCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATCAAAGTTTAAATCTG
1 TCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCACTTTTAAACACATCAAAGTTTAAATCTG
*
41076 ATTCTCACTTAAATTGTCACCATCGGGGACACT
66 ATTCTCACTTAAATTGTCACCATCGAGGACA-T
* * * * *
41109 T-CAACCCCATTCCTCCGAGGGGATACTCCAACCCTACTTTTAAACGCATCAAAGTTTTAATTTT
1 TCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCACTTTTAAACACATCAAAGTTTAAATCTG
*
41173 ATTCTCACTTAAATTGTCATCATCGAGGACAT
66 ATTCTCACTTAAATTGTCACCATCGAGGACAT
41205 TCCAACCCCATTCCTCCGAGGGGATACTCCAACC
1 TCCAACCCCATTCCTCCGAGGGGATACTCCAACC
41239 TCGTTTTTCA
Statistics
Matches: 121, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
96 2 0.02
97 118 0.98
98 1 0.01
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.28
Consensus pattern (97 bp):
TCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCACTTTTAAACACATCAAAGTTTAAATCTG
ATTCTCACTTAAATTGTCACCATCGAGGACAT
Found at i:41275 original size:97 final size:95
Alignment explanation
Indices: 41011--41268 Score: 262
Period size: 97 Copynumber: 2.7 Consensus size: 95
41001 TTGGGAATAC
*
41011 TCCAACCCCATTCCTCCGAGGGGATACTCCAACCCCGCTTTTAAACACATC-AAAGTTTAA--AT
1 TCCAACCCCATTCCTCCGAGGGGATACTCCAA-CCCG-TTTT--TCA-ATCAAAAG-TTAATTAT
* * *
41073 CTGATTCTCACTTAAATTGTCACCATCGGGGACACT
60 TTTATTCTCACTTAAATTGTCACCATCGAGGACACT
* *
41109 T-CAACCCCATTCCTCCGAGGGGATACTCCAACCC-TACTTTTAAACGCATCAAAGTT--TTAAT
1 TCCAACCCCATTCCTCCGAGGGGATACTCCAACCCGT--TTTTCAA-TCA--AAAGTTAATT-AT
*
41170 TTTATTCTCACTTAAATTGTCATCATCGAGGACA-T
60 TTTATTCTCACTTAAATTGTCACCATCGAGGACACT
*
41205 TCCAACCCCATTCCTCCGAGGGGATACTCCAACCTCGTTTTTCAATCAAAAATTAAATTATTTT
1 TCCAACCCCATTCCTCCGAGGGGATACTCCAACC-CGTTTTTCAATCAAAAGTT-AATTATTTT
41269 CTTTCTCTCG
Statistics
Matches: 135, Mismatches: 10, Indels: 32
0.76 0.06 0.18
Matches are distributed among these distances:
93 1 0.01
94 8 0.06
96 17 0.13
97 106 0.79
98 2 0.01
99 1 0.01
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.30
Consensus pattern (95 bp):
TCCAACCCCATTCCTCCGAGGGGATACTCCAACCCGTTTTTCAATCAAAAGTTAATTATTTTATT
CTCACTTAAATTGTCACCATCGAGGACACT
Found at i:43700 original size:334 final size:333
Alignment explanation
Indices: 43149--43771 Score: 813
Period size: 334 Copynumber: 1.9 Consensus size: 333
43139 AATTTTCCTA
* *
43149 TTTTTGAAATATAGAGTTTTCTATTCCGTAATTTTTTTGGGGAGATTTTTCTTGGTTTTTAATTT
1 TTTTTGAAATATAGAGTTTTCTATTCCGTAATTTTTTTGGGCAGATTTTTATTGGTTTTTAATTT
* * *
43214 TTAAAATTCATCAAATACTGTTATTTAATTCATATTAAATTAGTTCTAAAAAATTCATTCATTTT
66 TTAAAATTCATCAAATACTATTATTTAATTCATATTAAATCAGTTCTAAAAAATTCATTCATCTT
* *** *
43279 CAAAAAATGTTTGAAATTTTTCCTTAAAACTCTCATTTTTTTGAAATACAGAGTTTTCTACTCTG
131 CAAAAAATGTTTGAAATTTTTCCTTAAAACTCTCATATTTCCAAAATACAGAGTTTTCTACTCCG
* * * * *
43344 TAATTTTTTTCGGGGAGATTTTTCTTGGTTTTTAATTTTTAAAATTTATCAAATATTATTATGTA
196 TAAATTTTTTCGAGGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAAAATTATTATGTA
*
43409 AATCCTATTAAATCAATTCTCAAAAATTCATTCATTTTCATAAATTTTTGAATATTTTCCTTGAA
261 AATCATATTAAATCAATTCTCAAAAATTCATTCATTTTCATAAATTTTTGAATATTTTCCTTGAA
43474 AATCATTT
326 AATCATTT
* * *
43482 TTTTTCGAAATATGGAGTTTTCTACTT-TGTAAATTTTTTTGGGCA-TTTTTTATTGGTTTTTTA
1 TTTTT-GAAATATAGAGTTTTCTA-TTCCGT-AATTTTTTTGGGCAGATTTTTATTGG-TTTTTA
* * * *
43545 ATTTTTAAAATTCATCAAATATTATTATTTTAA-TCATATTAAATCAGTTTTTAAAAATTCTTTC
62 ATTTTTAAAATTCATCAAATACTATTA-TTTAATTCATATTAAATCAGTTCTAAAAAATTCATTC
** * * * * * * * *
43609 ATCTTC-ATGAGTTTTTGAATTTTTTCCTTGAAATTTTCCTATTTCCAAAATACGGAGTTTTCTA
126 ATCTTCAAAAAATGTTTGAAATTTTTCCTTAAAACTCTCATATTTCCAAAATACAGAGTTTTCTA
*
43673 CTCCGTAAATTTTTTCGAGGAGATTTTTTTTGGTTTTTAATTTTTAAAATTCATAAAAAATTATT
191 CTCCGTAAATTTTTTCGAGGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAAAATTATT
* ** * * *
43738 ATTTATTTCATATTAAATTAGTTTTCAAAAATTC
256 ATGTAAATCATATTAAATCAATTCTCAAAAATTC
43772 TTTTATCTTC
Statistics
Matches: 245, Mismatches: 40, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
333 5 0.02
334 157 0.64
335 78 0.32
336 5 0.02
ACGTcount: A:0.31, C:0.10, G:0.09, T:0.50
Consensus pattern (333 bp):
TTTTTGAAATATAGAGTTTTCTATTCCGTAATTTTTTTGGGCAGATTTTTATTGGTTTTTAATTT
TTAAAATTCATCAAATACTATTATTTAATTCATATTAAATCAGTTCTAAAAAATTCATTCATCTT
CAAAAAATGTTTGAAATTTTTCCTTAAAACTCTCATATTTCCAAAATACAGAGTTTTCTACTCCG
TAAATTTTTTCGAGGAGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAAAATTATTATGTA
AATCATATTAAATCAATTCTCAAAAATTCATTCATTTTCATAAATTTTTGAATATTTTCCTTGAA
AATCATTT
Found at i:43772 original size:167 final size:167
Alignment explanation
Indices: 43139--43905 Score: 726
Period size: 167 Copynumber: 4.6 Consensus size: 167
43129 TTTCTTTTAC
* * * *
43139 AATTTTCCTATTTTTGAAATATAGAGTTTTCTATTCCGT-AATTTTTTTGGGGAGATTTTTCTTG
1 AATTTTCCTATTTTCGAAATACAGAGTTTTCTACTCCGTAAATTTTTTCGGGGAGATTTTTCTTG
* * * * *
43203 GTTTTTAATTTTTAAAATTCATCAAATACTGTTATTTAATTCATATTAAATTAGTTCTAAAAAAT
66 GTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAAATCATATTAAATCAGTTCTCAAAAAT
* * * * *
43268 TCATTCATTTTCAAAAAATGTTTGAAATTTTTCCTTAA
131 TCATTCATCTTC-ATAAATTTTTGAATTTTTTCCTTGA
* * * * * * *
43306 AACTCTCATTTTTTTGAAATACAGAGTTTTCTACTCTGTAATTTTTTTCGGGGAGATTTTTCTTG
1 AATTTTCCTATTTTCGAAATACAGAGTTTTCTACTCCGTAAATTTTTTCGGGGAGATTTTTCTTG
* * * *
43371 GTTTTTAATTTTTAAAATTTATCAAATATTATTATGTAAATCCTATTAAATCAATTCTCAAAAAT
66 GTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAAATCATATTAAATCAGTTCTCAAAAAT
* *
43436 TCATTCATTTTCATAAATTTTTGAATATTTTCCTTGAA
131 TCATTCATCTTCATAAATTTTTGAATTTTTTCCTTG-A
** ** * * * *
43474 AATCATTT--T-TTTTCGAAATATGGAGTTTTCTACTTTGTAAATTTTTTTGGGCA-TTTTTTAT
1 AAT--TTTCCTATTTTCGAAATACAGAGTTTTCTACTCCGTAAATTTTTTCGGGGAGATTTTTCT
* * *
43535 TGGTTTTTTAATTTTTAAAATTCATCAAATATTATTATTTTAATCATATTAAATCAGTTTTTAAA
64 TGG-TTTTTAATTTTTAAAATTCATCAAATATTATTATTTAAATCATATTAAATCAGTTCTCAAA
* * *
43600 AATTCTTTCATCTTCATGAGTTTTTGAATTTTTTCCTTGA
128 AATTCATTCATCTTCATAAATTTTTGAATTTTTTCCTTGA
* * * * *
43640 AATTTTCCTATTTCCAAAATACGGAGTTTTCTACTCCGTAAATTTTTTCGAGGAGATTTTTTTTG
1 AATTTTCCTATTTTCGAAATACAGAGTTTTCTACTCCGTAAATTTTTTCGGGGAGATTTTTCTTG
* * ** * *
43705 GTTTTTAATTTTTAAAATTCATAAAAAATTATTATTTATTTCATATTAAATTAGTTTTCAAAAAT
66 GTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAAATCATATTAAATCAGTTCTCAAAAAT
* * ** * *
43770 TCTTTTATCTTCATTCATTTTT-CATTTTTT-CTTCAA
131 TCATTCATCTTCATAAATTTTTGAATTTTTTCCTT-GA
* * * ** * * * *
43806 AATCTCCCTATTTTTGAAA-ATTTGAGCTTTCTAGTTCGTAAATATTTTT-GGGG-GATTTTTAT
1 AATTTTCCTATTTTCGAAATA-CAGAGTTTTCTACTCCGTAAAT-TTTTTCGGGGAGATTTTTCT
* * ** * * *
43868 CGATTTAAAATTTTTTAAATTCAACTAATATTATTATT
64 TGGTTTTTAATTTTTAAAATTCATCAAATATTATTATT
43906 AAACTCCCAT
Statistics
Matches: 498, Mismatches: 90, Indels: 26
0.81 0.15 0.04
Matches are distributed among these distances:
164 3 0.01
165 41 0.08
166 56 0.11
167 292 0.59
168 104 0.21
170 2 0.00
ACGTcount: A:0.30, C:0.11, G:0.09, T:0.51
Consensus pattern (167 bp):
AATTTTCCTATTTTCGAAATACAGAGTTTTCTACTCCGTAAATTTTTTCGGGGAGATTTTTCTTG
GTTTTTAATTTTTAAAATTCATCAAATATTATTATTTAAATCATATTAAATCAGTTCTCAAAAAT
TCATTCATCTTCATAAATTTTTGAATTTTTTCCTTGA
Found at i:45499 original size:164 final size:163
Alignment explanation
Indices: 45226--45541 Score: 429
Period size: 164 Copynumber: 1.9 Consensus size: 163
45216 TAGTAAAAAT
** * * **
45226 TAAATATTAATCATTTTTTAATCTTTTATATTCTTATGGGGGTCCGTAAAGGTATAAAAGATTTC
1 TAAATATTAATCATTTTTTAATCTTGCATATTCCTATAGGAATCCGTAAAGGTATAAAAGATTTC
** * * * *
45291 AAAAACTTTTTGTATCTTTTAGGGTTTCCATTAAAGTGTGAAATGGTATTTTTCAAAAATAAATA
66 AAAAACTTTTCATATCTTTTACGATTTCCATTAAAGTATGAAATGGCATTTTTCAAAAATAAATA
**
45356 AATTAAATTAAATTAACACTTTCATAATTGAAA
131 AACAAAATTAAATTAACACTTTCATAATTGAAA
*
45389 TAAATATTAATCATTTTTTTAAATCTTGCATATTCCTATAGGAATCCGTAAGGGTATAAAAGATT
1 TAAATATTAATCA-TTTTTT-AATCTTGCATATTCCTATAGGAATCCGTAAAGGTATAAAAGATT
* *
45454 TC-AAAACTTTTCATATCTTTT-CGATTTCTCTTTAAGGTATGAAATGGCATTTTTCAAAAATAA
64 TCAAAAACTTTTCATATCTTTTACGATTTC-CATTAAAGTATGAAATGGCATTTTTCAAAAATAA
*
45517 ATAAACAAAATTAAATTGACACTTT
128 ATAAACAAAATTAAATTAACACTTT
45542 TGTAGACACC
Statistics
Matches: 132, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
163 18 0.14
164 75 0.57
165 39 0.30
ACGTcount: A:0.38, C:0.10, G:0.11, T:0.41
Consensus pattern (163 bp):
TAAATATTAATCATTTTTTAATCTTGCATATTCCTATAGGAATCCGTAAAGGTATAAAAGATTTC
AAAAACTTTTCATATCTTTTACGATTTCCATTAAAGTATGAAATGGCATTTTTCAAAAATAAATA
AACAAAATTAAATTAACACTTTCATAATTGAAA
Found at i:45847 original size:22 final size:21
Alignment explanation
Indices: 45822--45865 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
45812 AATTTTGAAT
* *
45822 TTCAATAATTTGTATTGATACA
1 TTCAATAA-ATGTATCGATACA
*
45844 TTCAGTAAATGTATCGATACA
1 TTCAATAAATGTATCGATACA
45865 T
1 T
45866 AAGTAACGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.41
Consensus pattern (21 bp):
TTCAATAAATGTATCGATACA
Found at i:48373 original size:51 final size:51
Alignment explanation
Indices: 48317--48610 Score: 263
Period size: 52 Copynumber: 5.6 Consensus size: 51
48307 TTAAGTTTCT
48317 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
* * * *
48368 TAATTTTTCACAATCGGGGATACTCTAACCTCGGTTTTATTT-TCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACAC
* * * * *
48419 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTTC-ATAATCGGGGATACTCCAACCCCGGTTTTATTT-CTAAAACAC
* * * * * * *
48472 CAATTTTTCACAATCGGGGATACTTCAACCCC-G-TTAATCATCGGAGATACTC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTAT-TTC-TA-AAACAC
*** ** *
48524 CAACCCCGTT-ATTTTCGAGGGGATACTCCAACCCCCGGTTTTATTTCTAAAACAT
1 CAA--TTTTTCATAATC--GGGGATACTCCAA-CCCCGGTTTTATTTCTAAAACAC
48579 CAATTTTTCATAATCGGGGATACTCCAACCCC
1 CAATTTTTCATAATCGGGGATACTCCAACCCC
48611 ATTATTCTTG
Statistics
Matches: 186, Mismatches: 42, Indels: 30
0.72 0.16 0.12
Matches are distributed among these distances:
50 6 0.03
51 58 0.31
52 66 0.35
53 20 0.11
54 6 0.03
55 18 0.10
56 5 0.03
57 3 0.02
58 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.13, T:0.32
Consensus pattern (51 bp):
CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
Found at i:48458 original size:52 final size:51
Alignment explanation
Indices: 48317--48502 Score: 232
Period size: 51 Copynumber: 3.6 Consensus size: 51
48307 TTAAGTTTCT
* *
48317 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTA-TTTCTAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAA-CCCGGTTTTATTTTCAAAAACAC
* *
48368 TAATTTTTCACAATCGGGGATACTCTAACCTCGGTTTTATTTTC-AAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACC-CGGTTTTATTTTCAAAAACAC
* ** * *
48419 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTTC-ACAATCGGGGATACTCCAAC-CCGGTTTTATTTTCAAAAACAC
*
48472 CAATTTTTCACAATCGGGGATACTTCAACCC
1 CAATTTTTCACAATCGGGGATACTCCAACCC
48503 CGTTAATCAT
Statistics
Matches: 116, Mismatches: 14, Indels: 10
0.83 0.10 0.07
Matches are distributed among these distances:
50 2 0.02
51 49 0.42
52 49 0.42
53 16 0.14
ACGTcount: A:0.30, C:0.25, G:0.11, T:0.34
Consensus pattern (51 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCGGTTTTATTTTCAAAAACAC
Found at i:48555 original size:28 final size:27
Alignment explanation
Indices: 48484--48558 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
48474 ATTTTTCACA
*
48484 ATCGGGGATACTTCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
* *
48511 ATCGGAGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
48537 TTCGAGGGGATACTCCAACCCC
1 ATC--GGGGATACTCCAACCCC
48559 CGGTTTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.10
27 21 0.51
28 16 0.39
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:48602 original size:80 final size:79
Alignment explanation
Indices: 48511--48690 Score: 245
Period size: 79 Copynumber: 2.3 Consensus size: 79
48501 CCCGTTAATC
*
48511 ATCGGAGATACTCCAACCCCGTTATT-TTCGAGGGGATACTCCAACCCCCGGTTTTATTTCTAAA
1 ATCGGGGATACTCCAACCCCGTTATTCTT-GAGGGGATACTCCAA-CCCCGGTTTTATTTCTAAA
* * * *
48575 ACATCAATTTTTCATA
64 ACACCAATTCTCCACA
* **
48591 ATCGGGGATACTCCAACCCCATTATTCTTGAGGGGATACTTGAACCCCGGTTTTATTTCTAAAAC
1 ATCGGGGATACTCCAACCCCGTTATTCTTGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
48656 ACCAATTCTCCACA
66 ACCAATTCTCCACA
* *
48670 ATCGAGGATATTCCAACCCCG
1 ATCGGGGATACTCCAACCCCG
48691 ACTTTATTTC
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
79 49 0.56
80 37 0.42
81 2 0.02
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.29
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTCTTGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAAC
ACCAATTCTCCACA
Found at i:48688 original size:51 final size:51
Alignment explanation
Indices: 48624--48791 Score: 151
Period size: 51 Copynumber: 3.3 Consensus size: 51
48614 ATTCTTGAGG
* *
48624 GGATACTTGAACCCCGGTTTTATTTCTAAAACACCAA-TTCTCCACAATCGA
1 GGATACTTCAACCCCGGCTTTATTTCTAAAACACCAATTTCT-CACAATCGA
* * * *** *
48675 GGATA-TTCCAACCCCGACTTTATTTCCAAAATATTGATTTCTCACAATCGG
1 GGATACTT-CAACCCCGGCTTTATTTCTAAAACACCAATTTCTCACAATCGA
* * *** * *
48726 GGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATCGG
1 GGATACTTCAACCCCGGCTTTATTTCTAAAACACCAATTTCTCACAATCGA
*
48777 GGATACTCCAACCCC
1 GGATACTTCAACCCC
48792 ATTATTTTCA
Statistics
Matches: 100, Mismatches: 14, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
50 2 0.02
51 92 0.92
52 6 0.06
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (51 bp):
GGATACTTCAACCCCGGCTTTATTTCTAAAACACCAATTTCTCACAATCGA
Found at i:48782 original size:181 final size:184
Alignment explanation
Indices: 48542--48901 Score: 469
Period size: 181 Copynumber: 2.0 Consensus size: 184
48532 TTATTTTCGA
** *
48542 GGGGATACTCCAACCCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCCGGCCTTATTTCTAAAACATCAATTTCTCATAATCGGGGATACTCCAA
* ** *
48607 CCCCATTATTCTTGA-GGGGATACTTGAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAA
66 CCCCATTATT-TTCACGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAA
* * *
48671 TCGA-GGATATTCCAACCCCGACT-TTATTTCCAAAATATT-GATTTCTCACAATC
130 TCGAGGGATACTCCAACCCC-ACTATTATCTCCAAAATATTAAATTTCTCACAATC
* * **
48724 GGGGATACTTCAA-CCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATCGGGGATACTCCAA
1 GGGGATACTCCAACCCCCGGCCTTATTTCTAAAACATCAATTTCTCATAATCGGGGATACTCCAA
* * * * * *
48788 CCCCATTATTTTCACGGGGATACTCCAACCCCGATTTTATTTTTAAAACATCGATTTTCTATAAT
66 CCCCATTATTTTCACGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAAT
*
48853 CGAGGGGATACTCCAACCCCATTATTATCTCCAAAATATTAAATTTCTC
131 CGA-GGGATACTCCAACCCCACTATTATCTCCAAAATATTAAATTTCTC
48902 GTAGGGAGAT
Statistics
Matches: 152, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
180 3 0.02
181 99 0.65
182 14 0.09
183 29 0.19
184 7 0.05
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (184 bp):
GGGGATACTCCAACCCCCGGCCTTATTTCTAAAACATCAATTTCTCATAATCGGGGATACTCCAA
CCCCATTATTTTCACGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAAT
CGAGGGATACTCCAACCCCACTATTATCTCCAAAATATTAAATTTCTCACAATC
Found at i:48820 original size:79 final size:80
Alignment explanation
Indices: 48723--48878 Score: 217
Period size: 79 Copynumber: 1.9 Consensus size: 80
48713 TTCTCACAAT
* * * *
48723 CGGGGATACTTCAACCCCGGCCTTATTTCTAAAATATTGA-TTTCTCATAATC-GGGGATACTCC
1 CGGGGATACTCCAACCCCGACCTTATTTCTAAAACATCGATTTTCT-ATAATCAGGGGATACTCC
48786 AACCCCATTATTTTCA
65 AACCCCATTATTTTCA
** *
48802 CGGGGATACTCCAACCCCGATTTTATTTTTAAAACATCGATTTTCTATAATCGAGGGGATACTCC
1 CGGGGATACTCCAACCCCGACCTTATTTCTAAAACATCGATTTTCTATAATC-AGGGGATACTCC
48867 AACCCCATTATT
65 AACCCCATTATT
48879 ATCTCCAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
79 39 0.58
80 5 0.07
81 23 0.34
ACGTcount: A:0.28, C:0.26, G:0.14, T:0.33
Consensus pattern (80 bp):
CGGGGATACTCCAACCCCGACCTTATTTCTAAAACATCGATTTTCTATAATCAGGGGATACTCCA
ACCCCATTATTTTCA
Found at i:50004 original size:3 final size:3
Alignment explanation
Indices: 49996--50029 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
49986 AGAGATTTAA
49996 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
50030 GGGTTTACAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:50840 original size:13 final size:13
Alignment explanation
Indices: 50822--50847 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50812 CATTATTCAA
50822 TGTATCGATACAT
1 TGTATCGATACAT
50835 TGTATCGATACAT
1 TGTATCGATACAT
50848 CGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:50911 original size:20 final size:19
Alignment explanation
Indices: 50885--50992 Score: 84
Period size: 20 Copynumber: 5.8 Consensus size: 19
50875 GTTTACCAAG
50885 ATGTATCGATACATTTTGCA
1 ATGTATCGATACATTTT-CA
*
50905 TTGTATCGATACA--TT--
1 ATGTATCGATACATTTTCA
*
50920 A--TATCGATACATTGCTCA
1 ATGTATCGATACATT-TTCA
*
50938 TTGTATCGATACATTTTACA
1 ATGTATCGATACATTTT-CA
* *
50958 ATGTATCAATATATTTTACA
1 ATGTATCGATACATTTT-CA
*
50978 ATGTATTGATACATT
1 ATGTATCGATACATT
50993 CAGGTATTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
13 10 0.14
16 1 0.01
18 2 0.03
19 1 0.01
20 55 0.80
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:50924 original size:13 final size:13
Alignment explanation
Indices: 50903--50932 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
50893 ATACATTTTG
*
50903 CATTGTATCGATA
1 CATTATATCGATA
50916 CATTATATCGATA
1 CATTATATCGATA
50929 CATT
1 CATT
50933 GCTCATTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:50930 original size:33 final size:33
Alignment explanation
Indices: 50888--50952 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
50878 TACCAAGATG
*
50888 TATCGATACATT-TTGCATTGTATCGATACATTA
1 TATCGATACATTGCT-CATTGTATCGATACATTA
50921 TATCGATACATTGCTCATTGTATCGATACATT
1 TATCGATACATTGCTCATTGTATCGATACATT
50953 TTACAATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (33 bp):
TATCGATACATTGCTCATTGTATCGATACATTA
Found at i:53337 original size:51 final size:51
Alignment explanation
Indices: 53281--53468 Score: 243
Period size: 51 Copynumber: 3.6 Consensus size: 51
53271 TTAAGTTTCT
*
53281 CAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
* * *
53332 TAATTTTTCACAATCGGGGATACTCTAACCTCGGTTTTATTT-TCAAAACAC
1 CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACAC
* ** * * *
53383 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACAC
1 CAATTTTTC-ACAATCGGGGATACTCCAACCCCGGTTTTATTT-CTAAAACAC
*
53436 CAATTTTTCACAATCGGGGATACTTCAACCCCG
1 CAATTTTTCACAATCGGGGATACTCCAACCCCG
53469 TTAATCATCG
Statistics
Matches: 115, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
50 1 0.01
51 52 0.45
52 47 0.41
53 15 0.13
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.34
Consensus pattern (51 bp):
CAATTTTTCACAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACAC
Found at i:53519 original size:28 final size:27
Alignment explanation
Indices: 53448--53522 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
53438 ATTTTTCACA
*
53448 ATCGGGGATACTTCAACCCCGTTAATC
1 ATCGGGGATACTCCAACCCCGTTAATC
* *
53475 ATCGGAGATACTCCAACCCCGTT-ATT
1 ATCGGGGATACTCCAACCCCGTTAATC
*
53501 TTCGAGGGGATACTCCAACCCC
1 ATC--GGGGATACTCCAACCCC
53523 CGGTTTTATT
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
26 4 0.10
27 21 0.51
28 16 0.39
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (27 bp):
ATCGGGGATACTCCAACCCCGTTAATC
Found at i:53564 original size:79 final size:78
Alignment explanation
Indices: 53475--53653 Score: 243
Period size: 79 Copynumber: 2.3 Consensus size: 78
53465 CCCGTTAATC
53475 ATCGGAGATACTCCAACCCCGTTATT-TTCGAGGGGATACTCCAACCCCCGGTTTTATTTCTAAA
1 ATCGG-GATACTCCAACCCCGTTATTCTT-GAGGGGATACTCCAA-CCCCGGTTTTATTTCTAAA
* * * *
53539 ACATCAATTTTTCATA
63 ACACCAATTCTCCACA
* **
53555 ATCGGGATACTCCAACCCCATTATTCTTGAGGGGATACTTGAACCCCGGTTTTATTTCTAAAACA
1 ATCGGGATACTCCAACCCCGTTATTCTTGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
53620 CCAATTCTCCACA
66 CCAATTCTCCACA
*
53633 ATCGAGGATATTCCAACCCCG
1 ATCG-GGATACTCCAACCCCG
53654 ACTTTATTTC
Statistics
Matches: 88, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
78 35 0.40
79 46 0.52
80 7 0.08
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (78 bp):
ATCGGGATACTCCAACCCCGTTATTCTTGAGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
CCAATTCTCCACA
Found at i:53569 original size:51 final size:51
Alignment explanation
Indices: 53280--53573 Score: 233
Period size: 51 Copynumber: 5.6 Consensus size: 51
53270 GTTAAGTTTC
53280 TCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
* * *
53331 -CTAATTTTTCACAATCGGGGATACTCTAACCTCGGTTTTATTT-TCAAAACA
1 TC-AATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCT-AAAACA
* * * * * *
53382 CCAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAAACA
1 TCAATTTTTC-ATAATCGGGGATACTCCAACCCCGGTTTTATTT-CTAAAACA
* * * * * * *
53435 CCAATTTTTCACAATCGGGGATACTTCAACCCC-G-TTAATCATCGGAGATAC-
1 TCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTAT-TTC-TA-AAACA
*** **
53486 TCCAACCCCGTT-ATTTTCGAGGGGATACTCCAACCCCCGGTTTTATTTCTAAAACA
1 T-CAA--TTTTTCATAATC--GGGGATACTCCAA-CCCCGGTTTTATTTCTAAAACA
53542 TCAATTTTTCATAATC-GGGATACTCCAACCCC
1 TCAATTTTTCATAATCGGGGATACTCCAACCCC
53574 ATTATTCTTG
Statistics
Matches: 186, Mismatches: 38, Indels: 39
0.71 0.14 0.15
Matches are distributed among these distances:
50 11 0.06
51 65 0.35
52 53 0.28
53 20 0.11
54 6 0.03
55 18 0.10
56 6 0.03
57 3 0.02
58 4 0.02
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.33
Consensus pattern (51 bp):
TCAATTTTTCATAATCGGGGATACTCCAACCCCGGTTTTATTTCTAAAACA
Found at i:53651 original size:51 final size:50
Alignment explanation
Indices: 53586--53753 Score: 151
Period size: 51 Copynumber: 3.3 Consensus size: 50
53576 TATTCTTGAG
* *
53586 GGGATACTTGAACCCCGGTTTTATTTCTAAAACACCAA-TTCTCCACAATC
1 GGGATACTTCAACCCCGGCTTTATTTCTAAAACACCAATTTCT-CACAATC
* * * ***
53636 GAGGATA-TTCCAACCCCGACTTTATTTCCAAAATATTGATTTCTCACAATC
1 G-GGATACTT-CAACCCCGGCTTTATTTCTAAAACACCAATTTCTCACAATC
* * *** *
53687 GGGATACTTCAACCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATC
1 GGGATACTTCAACCCCGGCTTTATTTCTAAAACACCAATTTCTCACAATC
*
53737 GGGGATACTCCAACCCC
1 -GGGATACTTCAACCCC
53754 ATTATTTTCA
Statistics
Matches: 100, Mismatches: 13, Indels: 9
0.82 0.11 0.07
Matches are distributed among these distances:
50 45 0.45
51 51 0.51
52 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (50 bp):
GGGATACTTCAACCCCGGCTTTATTTCTAAAACACCAATTTCTCACAATC
Found at i:53711 original size:50 final size:50
Alignment explanation
Indices: 53624--53753 Score: 172
Period size: 50 Copynumber: 2.5 Consensus size: 50
53614 AAAACACCAA
*
53624 TTCTCCACAATCGAGGATA-TTCCAACCCCGACTTTATTTCCAAAATATTGAT
1 TTCT-CACAATCG-GGATACTT-CAACCCCGACCTTATTTCCAAAATATTGAT
* *
53676 TTCTCACAATCGGGATACTTCAACCCCGGCCTTATTTCTAAAATATTGAT
1 TTCTCACAATCGGGATACTTCAACCCCGACCTTATTTCCAAAATATTGAT
* *
53726 TTCTCATAATCGGGGATACTCCAACCCC
1 TTCTCACAATC-GGGATACTTCAACCCC
53754 ATTATTTTCA
Statistics
Matches: 71, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
50 42 0.59
51 25 0.35
52 4 0.06
ACGTcount: A:0.28, C:0.28, G:0.12, T:0.32
Consensus pattern (50 bp):
TTCTCACAATCGGGATACTTCAACCCCGACCTTATTTCCAAAATATTGAT
Found at i:53750 original size:180 final size:182
Alignment explanation
Indices: 53507--53863 Score: 454
Period size: 180 Copynumber: 2.0 Consensus size: 182
53497 TATTTTCGAG
** *
53507 GGGATACTCCAACCCCCGGTTTTATTTCTAAAACATCAATTTTTCATAATCGGGATACTCCAACC
1 GGGATACTCCAACCCCCGGCCTTATTTCTAAAACATCAATTTCTCATAATCGGGATACTCCAACC
* ** *
53572 CCATTATTCTTGA-GGGGATACTTGAACCCCGGTTTTATTTCTAAAACACCAATTCTCCACAATC
66 CCATTATT-TTCACGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATC
* * *
53636 GA-GGATATTCCAACCCCGACT-TTATTTCCAAAATATT-GATTTCTCACAATC
130 GAGGGATACTCCAACCCC-ACTATTATCTCCAAAATATTAAATTTCTCACAATC
* * **
53687 GGGATACTTCAA-CCCCGGCCTTATTTCTAAAATATTGATTTCTCATAATCGGGGATACTCCAAC
1 GGGATACTCCAACCCCCGGCCTTATTTCTAAAACATCAATTTCTCATAATC-GGGATACTCCAAC
* * * * * *
53751 CCCATTATTTTCACGGGGATACTCCAACCCCGATTTTATTTTTAAAACATCGATTTTCTATAATC
65 CCCATTATTTTCACGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATC
*
53816 GAGGGGATACTCCAACCCCATTATTATCTCCAAAATATTAAATTTCTC
130 GA-GGGATACTCCAACCCCACTATTATCTCCAAAATATTAAATTTCTC
53864 GTAGGGAGAT
Statistics
Matches: 150, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
179 35 0.23
180 77 0.51
181 2 0.01
182 29 0.19
183 7 0.05
ACGTcount: A:0.29, C:0.26, G:0.12, T:0.33
Consensus pattern (182 bp):
GGGATACTCCAACCCCCGGCCTTATTTCTAAAACATCAATTTCTCATAATCGGGATACTCCAACC
CCATTATTTTCACGGGGATACTCCAACCCCGATTTTATTTCTAAAACACCAATTCTCCACAATCG
AGGGATACTCCAACCCCACTATTATCTCCAAAATATTAAATTTCTCACAATC
Found at i:54966 original size:3 final size:3
Alignment explanation
Indices: 54958--54982 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
54948 AGAGATTTAA
54958 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
54983 GGGTTTACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:55791 original size:13 final size:13
Alignment explanation
Indices: 55773--55798 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
55763 CATTATTCAA
55773 TGTATCGATACAT
1 TGTATCGATACAT
55786 TGTATCGATACAT
1 TGTATCGATACAT
55799 CGATCTTTGT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:55862 original size:20 final size:19
Alignment explanation
Indices: 55836--55943 Score: 84
Period size: 20 Copynumber: 5.8 Consensus size: 19
55826 GTTTACCAAG
55836 ATGTATCGATACATTTTGCA
1 ATGTATCGATACATTTT-CA
*
55856 TTGTATCGATACA--TT--
1 ATGTATCGATACATTTTCA
*
55871 A--TATCGATACATTGCTCA
1 ATGTATCGATACATT-TTCA
*
55889 TTGTATCGATACATTTTACA
1 ATGTATCGATACATTTT-CA
* *
55909 ATGTATCAATATATTTTACA
1 ATGTATCGATACATTTT-CA
*
55929 ATGTATTGATACATT
1 ATGTATCGATACATT
55944 CAGGTATTTT
Statistics
Matches: 69, Mismatches: 11, Indels: 16
0.72 0.11 0.17
Matches are distributed among these distances:
13 10 0.14
16 1 0.01
18 2 0.03
19 1 0.01
20 55 0.80
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (19 bp):
ATGTATCGATACATTTTCA
Found at i:55875 original size:13 final size:13
Alignment explanation
Indices: 55854--55883 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
55844 ATACATTTTG
*
55854 CATTGTATCGATA
1 CATTATATCGATA
55867 CATTATATCGATA
1 CATTATATCGATA
55880 CATT
1 CATT
55884 GCTCATTGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.17, G:0.10, T:0.40
Consensus pattern (13 bp):
CATTATATCGATA
Found at i:55881 original size:33 final size:33
Alignment explanation
Indices: 55839--55903 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
55829 TACCAAGATG
*
55839 TATCGATACATT-TTGCATTGTATCGATACATTA
1 TATCGATACATTGCT-CATTGTATCGATACATTA
55872 TATCGATACATTGCTCATTGTATCGATACATT
1 TATCGATACATTGCTCATTGTATCGATACATT
55904 TTACAATGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
33 29 0.97
34 1 0.03
ACGTcount: A:0.29, C:0.17, G:0.12, T:0.42
Consensus pattern (33 bp):
TATCGATACATTGCTCATTGTATCGATACATTA
Found at i:57881 original size:12 final size:12
Alignment explanation
Indices: 57864--57894 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
57854 ACCTTTTCGT
57864 AAAAAAAAACAA
1 AAAAAAAAACAA
57876 AAAAAAAAACAA
1 AAAAAAAAACAA
57888 AAAAAAA
1 AAAAAAA
57895 GGTATATTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.94, C:0.06, G:0.00, T:0.00
Consensus pattern (12 bp):
AAAAAAAAACAA
Found at i:58402 original size:53 final size:51
Alignment explanation
Indices: 58297--58484 Score: 156
Period size: 53 Copynumber: 3.6 Consensus size: 51
58287 TTTCGTTTCT
* * *
58297 CAATTTTTCATTAATCGGGGATACTC-CACCCCCGGTTTTTTATTTCTC-AAACA
1 CAATTTTTCA-CAATCGGGGATACTCTCAACCTCGG--TTTTATTT-TCAAAACA
*
58350 CTAATTTTTCACAATCGGGGATACTCTTAACCTCGGTTTTAGTTTTCAAAACA
1 C-AATTTTTCACAATCGGGGATACTCTCAACCTCGGTTTTA-TTTTCAAAACA
* * * *
58403 CACTTTCTT--TAATCGGGGATACTCTCCAA-CTCCGATTTTATTTCCAAAAACA
1 CAATTT-TTCACAATCGGGGATACTCT-CAACCT-CGGTTTTATTTTC-AAAACA
58455 CCAA-TTTTCACAATCGGGGATACT-TCAACC
1 -CAATTTTTCACAATCGGGGATACTCTCAACC
58485 CCGTTTAATC
Statistics
Matches: 112, Mismatches: 11, Indels: 25
0.76 0.07 0.17
Matches are distributed among these distances:
51 26 0.23
52 30 0.27
53 41 0.37
54 15 0.13
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (51 bp):
CAATTTTTCACAATCGGGGATACTCTCAACCTCGGTTTTATTTTCAAAACA
Found at i:60899 original size:13 final size:13
Alignment explanation
Indices: 60881--60906 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60871 CATTATTCAA
60881 TGTATCGATACAT
1 TGTATCGATACAT
60894 TGTATCGATACAT
1 TGTATCGATACAT
60907 CGCTCTTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Done.