Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold446
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: 3567220
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 22
Found at i:287248 original size:20 final size:20
Alignment explanation
Indices: 287223--287293 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
287213 TGACAGAATA
287223 TATCGATACATTAAAAAATG
1 TATCGATACATTAAAAAATG
** * *
287243 TATCGATACATGCATACATG
1 TATCGATACATTAAAAAATG
* * *
287263 TATCGATATATTGAAAGATG
1 TATCGATACATTAAAAAATG
287283 TATCGATACAT
1 TATCGATACAT
287294 CTGGGTAAAA
Statistics
Matches: 41, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.41, C:0.13, G:0.14, T:0.32
Consensus pattern (20 bp):
TATCGATACATTAAAAAATG
Found at i:288011 original size:32 final size:29
Alignment explanation
Indices: 287939--288013 Score: 78
Period size: 32 Copynumber: 2.5 Consensus size: 29
287929 GCTTTAGACC
*
287939 TCCATGTTTTTCTTAGCTTTTTCTCTTTT
1 TCCAAGTTTTTCTTAGCTTTTTCTCTTTT
* *
287968 TCCAAGCTTTTCTTCAGTCTTTTTTTCTTCTT
1 TCCAAGTTTTTCTT-AG-CTTTTTCTCTT-TT
**
288000 TCTTAGTTTTTCTT
1 TCCAAGTTTTTCTT
288014 TGTTGAAATT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 12 0.32
30 2 0.05
31 10 0.27
32 13 0.35
ACGTcount: A:0.08, C:0.21, G:0.07, T:0.64
Consensus pattern (29 bp):
TCCAAGTTTTTCTTAGCTTTTTCTCTTTT
Found at i:289222 original size:21 final size:20
Alignment explanation
Indices: 289198--289240 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
289188 ATTTGTATTA
*
289198 ATACAAACAGTAAATGTATCG
1 ATACAAA-AGCAAATGTATCG
* *
289219 ATACATAAGCGAATGTATCG
1 ATACAAAAGCAAATGTATCG
289239 AT
1 AT
289241 GGATGCCTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.44, C:0.14, G:0.16, T:0.26
Consensus pattern (20 bp):
ATACAAAAGCAAATGTATCG
Found at i:291149 original size:13 final size:13
Alignment explanation
Indices: 291131--291155 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
291121 GCATAAGTGT
291131 TGTATCGATACAA
1 TGTATCGATACAA
291144 TGTATCGATACA
1 TGTATCGATACA
291156 TAAGTTTTTT
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:291151 original size:32 final size:32
Alignment explanation
Indices: 291110--291182 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
291100 ACAAATCGTA
*
291110 AATGTATCGATGCATAAGTGTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
* *
291142 AATGTATCGATACATAAGTTTTTTATCGATAC
1 AATGTATCGATACATAAGTGTTGTATCGATAC
291174 AATGTATCG
1 AATGTATCG
291183 CTATGAAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTGTATCGATAC
Found at i:291225 original size:21 final size:21
Alignment explanation
Indices: 291199--291240 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
291189 AGCTACTGCC
291199 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
291220 AAGGAAATGTATCGATACATT
1 AAGGAAATGTATCGATACATT
291241 GTATCGATAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.19, T:0.29
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:291245 original size:13 final size:13
Alignment explanation
Indices: 291227--291252 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
291217 ATTAAGGAAA
291227 TGTATCGATACAT
1 TGTATCGATACAT
291240 TGTATCGATACAT
1 TGTATCGATACAT
291253 CTATCTTTGT
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:293751 original size:79 final size:79
Alignment explanation
Indices: 293616--293870 Score: 375
Period size: 79 Copynumber: 3.2 Consensus size: 79
293606 TTTTCATCTC
* ** * * *** *
293616 GGGGATACTCCAACCTCGATTTTATTTCTAAAACACCAATTTTTCACAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
* * *
293681 CCCGTCACTTCCGA
66 CCCGTTATTTTCGA
*
293695 GGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGATTTCTCACAATCAGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
293760 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
* *
293774 GGGGATACTCCAACCCTGGCTTTATTCCTAAAATATTGATTTCTCGCAATCGGGGATACTCCAAC
1 GGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
293839 CCCGTTATTTTCGA
66 CCCGTTATTTTCGA
293853 GGGGATACTCCAACCCCG
1 GGGGATACTCCAACCCCG
293871 TTATTATCTC
Statistics
Matches: 159, Mismatches: 17, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 159 1.00
ACGTcount: A:0.26, C:0.29, G:0.16, T:0.29
Consensus pattern (79 bp):
GGGGATACTCCAACCCCGGCTTTATTCCTAAAATATTGATTTCTCACAATCGGGGATACTCCAAC
CCCGTTATTTTCGA
Found at i:306254 original size:1 final size:1
Alignment explanation
Indices: 306250--306302 Score: 61
Period size: 1 Copynumber: 53.0 Consensus size: 1
306240 TTCTTTTTTC
* * * * *
306250 AAAAAACAAAAAAAAAAACAAAAAAATAAAAAAAAACAAAAAAAAAAGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
306303 GAAGAATCTG
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
1 42 1.00
ACGTcount: A:0.91, C:0.06, G:0.02, T:0.02
Consensus pattern (1 bp):
A
Found at i:307436 original size:61 final size:60
Alignment explanation
Indices: 307274--308594 Score: 1282
Period size: 61 Copynumber: 22.4 Consensus size: 60
307264 TCTTCTTCAC
* * * *
307274 TTTTCAGTCCTCAAAGAGCATGATGCCTTTTCCTTT-TAAAGCCCACACTAGTTGGCT-GCA
1 TTTTCAGTCCTCAAAGAGCAGGACGCC-TTTCCTTTGCAAAGCCCACACAAGTTGG-TGGCA
** * **
307334 CTTCCCAGTCCTCAAAGAGCAGGATGCC--T--TTT--AAAGCCCACACAAGCCGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* * * *
307389 CTTTCAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTGCAAAGCCCACAAAAGCTAGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACGCCTT-TCCTTTGCAAAGCCCACACAAGTTGGTGGCA
** * *
307450 CCTTCAGTCCTCAAAGAGCAGGACGCATTTCCTTTTCAAAGCCCACACAAGTTGGTGGCA
1 TTTTCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* *
307510 TTTTCCAGTCTTCAAAGAGCAGGA-----TGCCTTT-CAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* *
307565 TTTTCCAGTCCTCAAAGAGCAAGATG-CTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACGCCTTTC-CTTTGCAAAGCCCACACAAGTTGGTGGCA
* * * * * *
307626 CCTTCCAGTTCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGCTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* *
307687 TTTTTCAGTCCTCAAAGAGTAGGATG-CTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACGCCTTTC-CTTTGCAAAGCCCACACAAGTTGGTGGCA
* * * * **
307748 CCTTCCAGTCTTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACAGGAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* * *
307809 TTTTCCAGTCCTCAAAGAGCAAGATG-CTTTCTCTATGCAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACGCCTTTC-CTTTGCAAAGCCCACACAAGTTGGTGGCA
* * * *
307870 CCTTCCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
*
307931 TTTTCCAGTCCTCAAAGAGCAGGACG-----CCTTT-CAAAGCCTACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* * * *
307986 TTTTCCAGCCCTCAAAGAGCATGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
*
308047 TTTTCCAGTCCTCAAAGAGCAGGACG-----CCTTT-CAAAGCCTACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* * *
308102 TTTTTCAGCCCTCAAAGAGCATGACG-----CCTTT-CAAAGCCCACACAAGTGGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* * * *
308157 TTTTCCAGTCCTCAAAGAGCAGGATGCTTTTTCTTTGCAAAGCCCACACAGGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* * * * * ** *
308218 CCTTCCAATCCTCAAAGAGCAGGGCACCTTTCCTTTTTAAAGCCCACACGAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* *
308279 TTTTTCAGTCCTCAAAGAGCAGGA-----TGCCTTT-CAAAGCCCACACCAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
308334 TTTTCCAGTCCTCAAAGAGCAGGACG-----CCTTT-CAAAGCCCACACAAGTTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* * * *
308389 TTTTCCAGTCCTCAAAGAGCAGGATGTC-TTCTCTTTGCAAAGCCCATACAAATTGGTGGCA
1 TTTT-CAGTCCTCAAAGAGCAGGACGCCTTTC-CTTTGCAAAGCCCACACAAGTTGGTGGCA
* * * * * *
308450 CCTTCCAGTCCTCAAAGAGTAGGACGCATTTCCTTTGCAAAGCCCATACTAGTTGGTGGCA
1 -TTTTCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* * * * * * ** *
308511 CCTTCCAATCCTCAAAAAGCAGGACGCCTTTCCTTTTCAAAGCCCGCATGAGTT-GTGCCA
1 -TTTTCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
* *
308571 CTTTTTAGTCCTCAAAGAGTAGGA
1 -TTTTCAGTCCTCAAAGAGCAGGA
308595 TGTACTTTAT
Statistics
Matches: 1072, Mismatches: 138, Indels: 101
0.82 0.11 0.08
Matches are distributed among these distances:
54 32 0.03
55 290 0.27
56 29 0.03
57 1 0.00
58 1 0.00
59 6 0.01
60 83 0.08
61 604 0.56
62 26 0.02
ACGTcount: A:0.26, C:0.28, G:0.21, T:0.25
Consensus pattern (60 bp):
TTTTCAGTCCTCAAAGAGCAGGACGCCTTTCCTTTGCAAAGCCCACACAAGTTGGTGGCA
Found at i:307718 original size:122 final size:122
Alignment explanation
Indices: 307278--308555 Score: 1529
Period size: 122 Copynumber: 10.8 Consensus size: 122
307268 CTTCACTTTT
* * * * *
307278 CAGTCCTCAAAGAGCATGATGCCTTTTCCTTTT-AAAGCCCACACTAGTTGGCT-GCACTTCCCA
1 CAGTCCTCAAAGAGCAGGACGCC-TTTCCTTTTCAAAGCCCACACGAGTTGG-TGGCATTTTCCA
** *
307341 GTCCTCAAAGAGCAGGATGC---CT-TTT--AAAGCCCACACAAGCCGGTGGCA-CTTT
64 GTCCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
* ** * * **
307393 CAGTCCTCAAAGAGCAGGACGCCTTCTCCTTTGCAAAGCCCACAAAAGCTAGTGGCACCTT-CAG
1 CAGTCCTCAAAGAGCAGGACGCCTT-TCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAG
* * **
307457 TCCTCAAAGAGCAGGACGCATTTC-CTTTTCAAAGCCCACACAAGTTGGTGGCATTTTC
65 TCCTCAAAGAGCAGGATGC-TTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
307515 CAGTCTTCAAAGAGCAGGA-----TGCC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
*
307574 CCTCAAAGAGCAAGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
66 CCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
* * *
307631 CAGTTCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGCTGGTGGCATTTTTCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
*
307696 CCTCAAAGAGTAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
66 CCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
* *
307753 CAGTCTTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACAGGAGTTGGTGGCATTTTCCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
* *
307818 CCTCAAAGAGCAAGATGCTTTCTCTATGCAAAGCCCACACAAGTTGGTGGCACCTTC
66 CCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
307875 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
* * **
307940 CCTCAAAGAGCAGGA--C--GC-CTTT-CAAAGCCTACACAAGTTGGTGGCATTTTC
66 CCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
* *
307991 CAGCCCTCAAAGAGCATGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
* * ** *
308056 CCTCAAAGAGCAGGA--C--GC-CTTT-CAAAGCCTACACAAGTTGGTGGCATTTTT
66 CCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
* * * *
308107 CAGCCCTCAAAGAGCATGACG-----CC-TTTCAAAGCCCACACAAGTGGGTGGCATTTTCCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
* *
308166 CCTCAAAGAGCAGGATGCTTTTTCTTTGCAAAGCCCACACAGGTTGGTGGCACCTTC
66 CCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
* * * * *
308223 CAATCCTCAAAGAGCAGGGCACCTTTCCTTTTTAAAGCCCACACGAGTTGGTGGCATTTTTCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
* **
308288 CCTCAAAGAGCAGGATG----C-CTTT-CAAAGCCCACACCAGTTGGTGGCATTTTC
66 CCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
*
308339 CAGTCCTCAAAGAGCAGGACG-----CC-TTTCAAAGCCCACACAAGTTGGTGGCATTTTCCAGT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
* *
308398 CCTCAAAGAGCAGGATG-TCTTCTCTTTGCAAAGCCCATACAAATTGGTGGCACCTTC
66 CCTCAAAGAGCAGGATGCT-TTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
* * * * * ** *
308455 CAGTCCTCAAAGAGTAGGACGCATTTCCTTTGCAAAGCCCATACTAGTTGGTGGCACCTTCCAAT
1 CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
* * *
308520 CCTCAAAAAGCAGGACGCCTTTC-CTTTTCAAAGCCC
66 CCTCAAAGAGCAGGATG-CTTTCTCTTTGCAAAGCCC
308556 GCATGAGTTG
Statistics
Matches: 1020, Mismatches: 98, Indels: 83
0.85 0.08 0.07
Matches are distributed among these distances:
110 99 0.10
111 4 0.00
112 1 0.00
114 3 0.00
115 86 0.08
116 376 0.37
117 8 0.01
118 1 0.00
119 4 0.00
120 1 0.00
121 28 0.03
122 405 0.40
123 3 0.00
124 1 0.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.25
Consensus pattern (122 bp):
CAGTCCTCAAAGAGCAGGACGCCTTTCCTTTTCAAAGCCCACACGAGTTGGTGGCATTTTCCAGT
CCTCAAAGAGCAGGATGCTTTCTCTTTGCAAAGCCCACACAAGTTGGTGGCACCTTC
Found at i:308951 original size:32 final size:32
Alignment explanation
Indices: 308910--308982 Score: 119
Period size: 32 Copynumber: 2.3 Consensus size: 32
308900 ACAAATCATA
*
308910 AATGTATCGATACATAAGTGTTCTATTGATAC
1 AATGTATCGATACATAAGTGTTCTATCGATAC
* *
308942 AATGTATCGATACATAAGTTTTGTATCGATAC
1 AATGTATCGATACATAAGTGTTCTATCGATAC
308974 AATGTATCG
1 AATGTATCG
308983 CTACGAAGCT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.37
Consensus pattern (32 bp):
AATGTATCGATACATAAGTGTTCTATCGATAC
Found at i:309025 original size:21 final size:21
Alignment explanation
Indices: 308999--309040 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
308989 AGCTACTACC
308999 AAGGAAATGAATCGATACATT
1 AAGGAAATGAATCGATACATT
*
309020 AAGGAAATGTATCGATACATT
1 AAGGAAATGAATCGATACATT
309041 GTATCGATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.45, C:0.10, G:0.19, T:0.26
Consensus pattern (21 bp):
AAGGAAATGAATCGATACATT
Found at i:309045 original size:13 final size:13
Alignment explanation
Indices: 309027--309052 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
309017 ATTAAGGAAA
309027 TGTATCGATACAT
1 TGTATCGATACAT
309040 TGTATCGATACAT
1 TGTATCGATACAT
309053 CTATCTTTAT
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:312142 original size:52 final size:52
Alignment explanation
Indices: 312064--312192 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
312054 CGAAATATGA
* * * *
312064 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATATATCGATACATATGGGC
*
312116 AAATTTGCCTGCATGTATCGATACATTTTATAATATATCGATACATATGGGC
1 AAATTTGCCTGCATGTATCGATACATTTAATAATATATCGATACATATGGGC
312168 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
312193 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTAATAATATATCGATACATATGGGC
Found at i:312207 original size:52 final size:51
Alignment explanation
Indices: 312064--312212 Score: 201
Period size: 52 Copynumber: 2.9 Consensus size: 51
312054 CGAAATATGA
* *
312064 AAATTTACCTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATATGGGC
* * *
312116 AAATTTGCCTGCATGTATCGATACATTTTATAATATATCGATACATATGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTAATAGTGTATCGATACATATGGGC
*
312168 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTA-AT-AGTGTATCGATACA
312213 ATGTATCGAT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 2 0.02
52 84 0.98
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTAATAGTGTATCGATACATATGGGC
Found at i:312219 original size:13 final size:13
Alignment explanation
Indices: 312201--312225 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312191 CAAAGATCAG
312201 TGTATCGATACAA
1 TGTATCGATACAA
312214 TGTATCGATACA
1 TGTATCGATACA
312226 TTTGAGTAAT
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:312303 original size:33 final size:33
Alignment explanation
Indices: 312266--312332 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
312256 AGTAGCTTAA
312266 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
312299 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
312332 A
1 A
312333 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:312306 original size:13 final size:13
Alignment explanation
Indices: 312288--312312 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
312278 CAAAAAAATA
312288 TGTATCGATACAT
1 TGTATCGATACAT
312301 TGTATCGATACA
1 TGTATCGATACA
312313 ACACTTTATG
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:313283 original size:55 final size:51
Alignment explanation
Indices: 313223--313337 Score: 126
Period size: 49 Copynumber: 2.2 Consensus size: 51
313213 CGATATTGGG
* * * *
313223 CTTAAAGATGAGAAAAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAA
1 CTTAAAGATGAG---AAGG-TGCCAATATGCTGATTCAACGCCAGCGACATTGAA
* *
313278 CTTAAAGAT--GAAGGTGCCAATATGCTGATTCAACGCCAGCGATATTGGA
1 CTTAAAGATGAGAAGGTGCCAATATGCTGATTCAACGCCAGCGACATTGAA
313327 CTTAAAGATGA
1 CTTAAAGATGA
313338 TGATGAATAG
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
49 38 0.73
50 4 0.08
53 1 0.02
55 9 0.17
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (51 bp):
CTTAAAGATGAGAAGGTGCCAATATGCTGATTCAACGCCAGCGACATTGAA
Found at i:313521 original size:169 final size:170
Alignment explanation
Indices: 313113--313674 Score: 722
Period size: 169 Copynumber: 3.3 Consensus size: 170
313103 TTTTAGAGAT
*
313113 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGATGATGAGAAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGATGAGAAAA
* *
313178 GTGATAAAGATGCCAATATATTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
*** * * * *
313243 TGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TAAAAAAGTCCTGATGC-AGGCCAGCGACATTGAACTTAAA
* * *
313284 GATGAAGGTGCCAATATGCTGATTCAACGCCAGCGATATTGGACTTAAAGATGATGAT--GAATA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGATGAGAAAA
* * * *
313347 GTGATAAA-AGGACCAATACGTTGATTCACGGCCAACGATATTGGGTTTAAAAATGAGAAAAAGG
66 GTGATAAAGATG-CCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGG
* * *
313411 ATAAAAAAG-CCAAT-ATGC-GGCTAGCGATATTGGACTTAAA
130 ATAAAAAAGTCC--TGATGCAGGCCAGCGACATTGAACTTAAA
* * *
313451 GATAAAGGTGCCAATGTGCTGATTCAAGGCCAGTGATATTGGACTTAAAGATGAAGATGAGAAAA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGATGAGAAAA
*
313516 GTGATAAAGATGCCAATATGTTGATTCACAGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
66 GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
*** * * * *
313581 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
131 TAAAAAAGTCCTGATGC-AGGCCAGCGACATTGAACTTAAA
*
313622 GATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAG
1 GAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAG
313675 GTGGAAAAGG
Statistics
Matches: 334, Mismatches: 44, Indels: 23
0.83 0.11 0.06
Matches are distributed among these distances:
167 71 0.21
168 4 0.01
169 135 0.40
170 4 0.01
171 76 0.23
174 44 0.13
ACGTcount: A:0.38, C:0.14, G:0.24, T:0.24
Consensus pattern (170 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTTAAAGATGATGATGAGAAAA
GTGATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGA
TAAAAAAGTCCTGATGCAGGCCAGCGACATTGAACTTAAA
Found at i:313740 original size:43 final size:44
Alignment explanation
Indices: 313679--314089 Score: 454
Period size: 43 Copynumber: 8.9 Consensus size: 44
313669 TTAAAGGTGG
*
313679 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGAC-T
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
313722 AAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
313766 AAAGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTT
1 --A-A--AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
313815 -AGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
*
313858 AAAGAAGAAGGTGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT
1 ----AA-AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* * *
313907 -AAAGGTGCCAATGTGCTGATTCAATGCCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
313950 AAAGATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
1 AAA-A--G-----GTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
* *
314002 -AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTT
1 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
314045 AAAGATGATGGTGCCAATATGCTGATTCAAGGCCA-CTGATATTGG
1 -AA-A--A-GGTGCCAATATGCTGATTCAAGGCCAGCT-ATATTGG
314090 GGTTAGAAGG
Statistics
Matches: 315, Mismatches: 25, Indels: 50
0.81 0.06 0.13
Matches are distributed among these distances:
43 152 0.48
44 4 0.01
45 3 0.01
46 2 0.01
47 2 0.01
48 5 0.02
49 108 0.34
50 1 0.00
51 2 0.01
52 36 0.11
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (44 bp):
AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT
Found at i:313825 original size:92 final size:92
Alignment explanation
Indices: 313628--314089 Score: 746
Period size: 92 Copynumber: 5.0 Consensus size: 92
313618 TAAAGATGGA
* * *
313628 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGGTGGAAAAGGTGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
* *
313693 TGCTGATTCAAGGCCAGCGATATTGGACTA
63 TGCTGATTCAAGGCCAGCTATATTGGACTT
313723 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
313788 TGATTCAAGGCCAGCTATATTGGGCTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
313815 AGAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAAGAAGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
*
313880 TGATTCAAGGCCAGCGATATTGGACTT
66 TGATTCAAGGCCAGCTATATTGGACTT
* *
313907 AAAGGTGCCAATGTGCTGATTCAATGCCAGCTACATTGGACTTAAAGATGGAAAATGTGCCAATA
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATA
313972 TGCTGATTCAAGGCCAGCTATATTGGACTT
63 TGCTGATTCAAGGCCAGCTATATTGGACTT
*
314002 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGATGGTGCCAATATGC
1 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
314067 TGATTCAAGGCCA-CTGATATTGG
66 TGATTCAAGGCCAGCT-ATATTGG
314090 GGTTAGAAGG
Statistics
Matches: 345, Mismatches: 18, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
91 2 0.01
92 206 0.60
93 1 0.00
94 2 0.01
95 134 0.39
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (92 bp):
AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGC
TGATTCAAGGCCAGCTATATTGGACTT
Found at i:314135 original size:32 final size:31
Alignment explanation
Indices: 314092--314161 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 31
314082 GATATTGGGG
314092 TTAGAAGGGTTGCCACCGACTTGTGTGGGCT
1 TTAGAAGGGTTGCCACCGACTTGTGTGGGCT
314123 TTGAGAAGGGTTGCCACCGACTTGTGTGGGCT
1 TT-AGAAGGGTTGCCACCGACTTGTGTGGGCT
314155 TTAGAAG
1 TTAGAAG
314162 AAGGTTGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
31 7 0.18
32 31 0.82
ACGTcount: A:0.19, C:0.17, G:0.36, T:0.29
Consensus pattern (31 bp):
TTAGAAGGGTTGCCACCGACTTGTGTGGGCT
Found at i:314251 original size:34 final size:34
Alignment explanation
Indices: 314169--314730 Score: 477
Period size: 34 Copynumber: 17.1 Consensus size: 34
314159 AAGAAGGTTG
* **
314169 AAAGA-TGCCACGAAGTTGTGAACTTAAAAGGAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG-AA
* *
314203 AAATAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
314238 AAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
314274 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAA-G--
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
314306 ---G-GTGCCACGGAGTTGTGGACTT-------A
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * *
314329 AAATAGTGCCACAGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * *
314363 AAAGAGTGTCATGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
314397 AAAGAGTGCCACGGAGTTGTGGGCTT------AA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * * *
314425 AATG-GTGCCACAGAGTTGTGGACTTAGACGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
*
314458 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* *
314492 AAAGAGTGCCACGGAGTTGTGAGCTT------AC
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * * *
314520 AATG-GTGCCACAGAGTTGTGGACTTAGAAGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
* * ** *
314553 AAAG-GTGCCACGGGGTTGTGGACTTTGATGGAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
**
314586 AAAGAGTGCCACGGAGTTGTGAACTTAAAAGGAAA
1 AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGG-AA
*
314621 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
*
314656 AAAG-GTGCCACGGAATTGTGGGCTTTGAAAAGGGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TT-AAAA-GGAA
*
314692 AAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
1 AAAGAGTGCCACGGAGTTGTGGGC-TTAAAAGGAA
314727 AAAG
1 AAAG
314731 GCTCCATGAT
Statistics
Matches: 444, Mismatches: 48, Indels: 71
0.79 0.09 0.13
Matches are distributed among these distances:
27 59 0.13
28 27 0.06
29 1 0.00
33 38 0.09
34 175 0.39
35 65 0.15
36 36 0.08
37 43 0.10
ACGTcount: A:0.34, C:0.12, G:0.33, T:0.21
Consensus pattern (34 bp):
AAAGAGTGCCACGGAGTTGTGGGCTTAAAAGGAA
Found at i:314424 original size:95 final size:94
Alignment explanation
Indices: 314169--314722 Score: 526
Period size: 95 Copynumber: 5.7 Consensus size: 94
314159 AAGAAGGTTG
* * ** * *
314169 AAAGATGCCACGAAGTTGTGAACTTAAAAGGAAAAAATAGTGCCACGGAGTTGTGGGCTTTAAAA
1 AAAGGTGCCACGGAGTTGTGGGCTTAGAAGG-AAAAAGAGTGCCACGGAGTTGTGGGC-TT----
* * * *
314234 AGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
60 A-AAATA-GTGCCACAGAGTTGTGGAC-TT-AGAA-GGAA
* * *
314274 AAAGAGTGCCACGGAGTTGTGGGCTT------TAAAAGGGTGCCACGGAGTTGTGGACTTAAAAT
1 AAAG-GTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAT
314333 AGTGCCACAGAGTTGTGGACTTAGAAGGAA
65 AGTGCCACAGAGTTGTGGACTTAGAAGGAA
* *
314363 AAAGAGTGTCATGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAT
1 AAAG-GTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAT
* *
314428 GGTGCCACAGAGTTGTGGACTTAGACGGAA
65 AGTGCCACAGAGTTGTGGACTTAGAAGGAA
* *
314458 AAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGAGCTTACAAT
1 AAAG-GTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAT
*
314523 GGTGCCACAGAGTTGTGGACTTAGAAGGAA
65 AGTGCCACAGAGTTGTGGACTTAGAAGGAA
* * * * **
314553 AAAGGTGCCACGGGGTTGTGGACTTTGATGGAAAAAGAGTGCCACGGAGTTGTGAACTTAAAAGG
1 AAAGGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT------
* * * * *
314618 AAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGAA
60 --AAAATAGTGCCACAGAGTTGTGGAC-TTAGAAGGAA
* *
314656 AAAGGTGCCACGGAATTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA
1 AAAGGTGCCACGGAGTTGTGGGC-TT-AGAA-GGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAA
314721 AA
62 AA
314723 AGAAAAAGGC
Statistics
Matches: 385, Mismatches: 44, Indels: 46
0.81 0.09 0.10
Matches are distributed among these distances:
89 28 0.07
90 3 0.01
91 2 0.01
92 17 0.04
93 4 0.01
94 51 0.13
95 152 0.39
98 2 0.01
99 26 0.07
102 20 0.05
103 28 0.07
104 2 0.01
105 5 0.01
106 43 0.11
107 2 0.01
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (94 bp):
AAAGGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAATA
GTGCCACAGAGTTGTGGACTTAGAAGGAA
Found at i:314727 original size:71 final size:69
Alignment explanation
Indices: 314523--314731 Score: 253
Period size: 71 Copynumber: 3.0 Consensus size: 69
314513 AGCTTACAAT
* * * * * * * **
314523 GGTGCCACAGAGTTGTGGACTTAGAA-GGAAAAAG-GTGCCACGGGGTTGTGGACTTT-GATGGA
1 GGTGCCACGGAATTGTGAACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGA
314585 AAAA
66 AAAA
* *
314589 GAGTGCCACGGAGTTGTGAACTTAAAAGGAAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG
1 G-GTGCCACGGAATTGTGAACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAG
314654 AAAAA
65 AAAAA
**
314659 GGTGCCACGGAATTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA
1 GGTGCCACGGAATTGTGAAC-TT-AAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAA
314724 GAAAAA
64 GAAAAA
314730 GG
1 GG
314732 CTCCATGATT
Statistics
Matches: 124, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
66 1 0.01
67 22 0.18
68 7 0.06
69 36 0.29
70 10 0.08
71 48 0.39
ACGTcount: A:0.35, C:0.11, G:0.34, T:0.20
Consensus pattern (69 bp):
GGTGCCACGGAATTGTGAACTTAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAAGA
AAAA
Found at i:318695 original size:47 final size:46
Alignment explanation
Indices: 318608--318735 Score: 134
Period size: 47 Copynumber: 2.7 Consensus size: 46
318598 TGTACTAGAT
* * *
318608 GGTTTGCAATTTTA-TCTATGCAAAAGTTATAAGTTATTTGTGAGGAA-
1 GGTTTGTAACTTTATTC-ATGCAAAAGTTATAAG-CATTTGTGA-GAAG
318655 GGTTTGTAACTTTATTCATGCAAAAGTTATAAGCAGTTTGTGAGAAG
1 GGTTTGTAACTTTATTCATGCAAAAGTTATAAGCA-TTTGTGAGAAG
* * * * *
318702 GGCTTATAGCTTTATTCATACAAAAGTTACAAGC
1 GGTTTGTAACTTTATTCATGCAAAAGTTATAAGC
318736 TGTGTTGGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
46 4 0.06
47 64 0.91
48 2 0.03
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (46 bp):
GGTTTGTAACTTTATTCATGCAAAAGTTATAAGCATTTGTGAGAAG
Found at i:319734 original size:19 final size:17
Alignment explanation
Indices: 319701--319739 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 17
319691 CACAAAATTG
*
319701 CTTTTTTTTTCCTTTGT
1 CTTTTTTTTTCCTTTCT
319718 CTTTTTCTTTTCTCTTTCT
1 CTTTTT-TTTTC-CTTTCT
319737 CTT
1 CTT
319740 GCTTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 5 0.26
19 8 0.42
ACGTcount: A:0.00, C:0.23, G:0.03, T:0.74
Consensus pattern (17 bp):
CTTTTTTTTTCCTTTCT
Found at i:320428 original size:22 final size:22
Alignment explanation
Indices: 320385--320425 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
320375 TACATAAAAA
320385 TTTAATTTAAATAATTAAAATT
1 TTTAATTTAAATAATTAAAATT
*
320407 TTTAATTTATA-AATTAAAA
1 TTTAATTTAAATAATTAAAA
320426 ATTAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
TTTAATTTAAATAATTAAAATT
Found at i:324634 original size:5 final size:5
Alignment explanation
Indices: 324624--324648 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
324614 GGTACCAAAA
324624 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
324649 GTGACTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:324816 original size:29 final size:30
Alignment explanation
Indices: 324784--324846 Score: 76
Period size: 31 Copynumber: 2.1 Consensus size: 30
324774 AAACATCATA
* *
324784 AATTATTTTAA-A-AATTATTAAAATTTTTT
1 AATTATTATAATATAATTA-TAAAATTTTAT
324813 AATTATTATAATTATAATTATAAAATTTTAT
1 AATTATTATAA-TATAATTATAAAATTTTAT
324844 AAT
1 AAT
324847 AAATTATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 10 0.34
31 14 0.48
32 5 0.17
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (30 bp):
AATTATTATAATATAATTATAAAATTTTAT
Found at i:325269 original size:19 final size:20
Alignment explanation
Indices: 325230--325269 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
325220 GAATAAACAT
*
325230 ATAATTATTAAGATCCTGAA
1 ATAAATATTAAGATCCTGAA
325250 ATAAATATTAAGAT-CTGAA
1 ATAAATATTAAGATCCTGAA
325269 A
1 A
325270 ACATTGTAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (20 bp):
ATAAATATTAAGATCCTGAA
Found at i:325390 original size:30 final size:30
Alignment explanation
Indices: 325354--325437 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 30
325344 TAACAATTAT
325354 TTATTTTGTATTTATATAATTTTATT-TAAA
1 TTATTTT-TATTTATATAATTTTATTATAAA
* *
325384 TTATTTTATATTTACA-AATTTTTTTATAAA
1 TTATTTT-TATTTATATAATTTTATTATAAA
*
325414 TTAATATTTATATTAT-TAATTTTA
1 TT-ATTTTTAT-TTATATAATTTTA
325438 AAATATTTAT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
29 8 0.18
30 23 0.52
31 13 0.30
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.62
Consensus pattern (30 bp):
TTATTTTTATTTATATAATTTTATTATAAA
Found at i:325449 original size:27 final size:26
Alignment explanation
Indices: 325418--325511 Score: 77
Period size: 27 Copynumber: 3.5 Consensus size: 26
325408 TATAAATTAA
325418 TATTTATATTATTAATTTTAAAATATT
1 TATTTATATTATTAATTTT-AAATATT
* *
325445 TATTTAT-TCATATTATATTTTTATTA-T
1 TATTTATAT--TATTA-ATTTTAAATATT
325472 T-TTTATATTATATAATAATTTAAATATT
1 TATTTATATTAT-TAAT--TTTAAATATT
*
325500 TTTTTATATTAT
1 TATTTATATTAT
325512 ATTTATATTA
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
25 5 0.09
26 8 0.15
27 16 0.30
28 10 0.19
29 15 0.28
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (26 bp):
TATTTATATTATTAATTTTAAATATT
Found at i:325509 original size:51 final size:53
Alignment explanation
Indices: 325420--325521 Score: 133
Period size: 51 Copynumber: 2.0 Consensus size: 53
325410 TAAATTAATA
*
325420 TTTATATTATTAATTTTAAAATATTTATTTATTCATATTATATTTTTATTATT
1 TTTATATTATTAATTTTAAAATATTTATTTATTCATATTATATTTATATTATT
325473 TTTATATTATATAATAATTT-AAATA-TT-TTT-TT-ATATTATATTTATATTA
1 TTTATATTAT-TAAT--TTTAAAATATTTATTTATTCATATTATATTTATATTA
325522 AGTTTAAAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
51 16 0.36
52 2 0.04
53 13 0.29
54 6 0.13
55 5 0.11
56 3 0.07
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (53 bp):
TTTATATTATTAATTTTAAAATATTTATTTATTCATATTATATTTATATTATT
Found at i:325527 original size:11 final size:11
Alignment explanation
Indices: 325445--325521 Score: 51
Period size: 11 Copynumber: 7.5 Consensus size: 11
325435 TTAAAATATT
*
325445 TATT-TATTCA
1 TATTATATTTA
*
325455 TATTATATTTT
1 TATTATATTTA
*
325466 TATTATTTTTA
1 TATTATATTTA
325477 TATTATA--TA
1 TATTATATTTA
325486 -A-TA-ATTTAAA
1 TATTATATTT--A
*
325496 TATT-TTTTTA
1 TATTATATTTA
325506 TATTATATTTA
1 TATTATATTTA
325517 TATTA
1 TATTA
325522 AGTTTAAAAT
Statistics
Matches: 51, Mismatches: 7, Indels: 17
0.68 0.09 0.23
Matches are distributed among these distances:
6 1 0.02
7 2 0.04
8 2 0.04
9 2 0.04
10 10 0.20
11 30 0.59
12 4 0.08
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (11 bp):
TATTATATTTA
Found at i:326043 original size:25 final size:26
Alignment explanation
Indices: 325995--326043 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 26
325985 AAAATAAATA
* * *
325995 AATAAAATATTTTAATTTATATTATT
1 AATAAAATATTATAATTAAGATTATT
326021 AATAAAAT-TTATAATTAAGATTA
1 AATAAAATATTATAATTAAGATTA
326044 GTATCACTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 12 0.60
26 8 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
AATAAAATATTATAATTAAGATTATT
Found at i:326176 original size:18 final size:18
Alignment explanation
Indices: 326153--326208 Score: 64
Period size: 18 Copynumber: 3.3 Consensus size: 18
326143 ATCATTTTAA
326153 ATTTTTAAATTTTAAGTC
1 ATTTTTAAATTTTAAGTC
*
326171 ATTTTTAAATTTGAA-TC
1 ATTTTTAAATTTTAAGTC
* *
326188 -GTTTT-AATTTTAAGTT
1 ATTTTTAAATTTTAAGTC
326204 ATTTT
1 ATTTT
326209 GAATTTAGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
15 7 0.23
16 5 0.16
17 5 0.16
18 14 0.45
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (18 bp):
ATTTTTAAATTTTAAGTC
Found at i:326360 original size:15 final size:15
Alignment explanation
Indices: 326340--326421 Score: 53
Period size: 15 Copynumber: 5.3 Consensus size: 15
326330 CAATTCAAAT
*
326340 TTTAATTATTTTAAA
1 TTTAATCATTTTAAA
326355 TTTAAT--TTATCTAAA
1 TTTAATCATT-T-TAAA
*
326370 TTCATATCA-TTTAAA
1 TTTA-ATCATTTTAAA
* *
326385 TTCGAATCATTTTATA
1 TT-TAATCATTTTAAA
*
326401 TTAAGATCATTTTAAA
1 TTTA-ATCATTTTAAA
326417 TTTAA
1 TTTAA
326422 ATTAAATTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 16
0.71 0.08 0.21
Matches are distributed among these distances:
13 2 0.04
14 1 0.02
15 25 0.47
16 24 0.45
17 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.02, T:0.51
Consensus pattern (15 bp):
TTTAATCATTTTAAA
Found at i:326422 original size:6 final size:6
Alignment explanation
Indices: 326411--326443 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
326401 TTAAGATCAT
326411 TTTAAA TTTAAA -TTAAA -TTAAA TTTAAA TTTAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAA
326444 GTGAATTGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 10 0.38
6 16 0.62
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (6 bp):
TTTAAA
Found at i:327087 original size:33 final size:34
Alignment explanation
Indices: 327048--327135 Score: 94
Period size: 32 Copynumber: 2.7 Consensus size: 34
327038 AAAATATGAC
* *
327048 ATAATATATATACATTAAT-ATTTTAAAATTTAT
1 ATAATATATATACATTAATCATATCAAAATTTAT
*
327081 ATAATATATATTC-TT-ATCATATCAAAATTTAT
1 ATAATATATATACATTAATCATATCAAAATTTAT
* *
327113 A-AATATAAAATACATTAAACATA
1 ATAATAT-ATATACATTAATCATA
327136 ATTATAATAC
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
31 7 0.16
32 19 0.42
33 14 0.31
34 5 0.11
ACGTcount: A:0.51, C:0.07, G:0.00, T:0.42
Consensus pattern (34 bp):
ATAATATATATACATTAATCATATCAAAATTTAT
Found at i:330094 original size:18 final size:18
Alignment explanation
Indices: 330071--330123 Score: 70
Period size: 18 Copynumber: 2.9 Consensus size: 18
330061 GCACCACTTT
330071 CCTCTGATTCTTCTTCTC
1 CCTCTGATTCTTCTTCTC
*
330089 CCTCTGATTCTTCTGCTC
1 CCTCTGATTCTTCTTCTC
* * *
330107 CTTCGGATGCTTCTTCT
1 CCTCTGATTCTTCTTCT
330124 TCTCCTTCTG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.06, C:0.36, G:0.11, T:0.47
Consensus pattern (18 bp):
CCTCTGATTCTTCTTCTC
Found at i:330120 original size:21 final size:21
Alignment explanation
Indices: 330096--330138 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
330086 CTCCCTCTGA
330096 TTCTTCTGCTCCTTCGGATGC
1 TTCTTCTGCTCCTTCGGATGC
* *
330117 TTCTTCTTCTCCTTCTGATGC
1 TTCTTCTGCTCCTTCGGATGC
330138 T
1 T
330139 CCTGATTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.05, C:0.33, G:0.14, T:0.49
Consensus pattern (21 bp):
TTCTTCTGCTCCTTCGGATGC
Found at i:330147 original size:21 final size:21
Alignment explanation
Indices: 330104--330147 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
330094 GATTCTTCTG
* **
330104 CTCCTTCGGATGCTTCTTCTT
1 CTCCTTCGGATGCTCCTGATT
*
330125 CTCCTTCTGATGCTCCTGATT
1 CTCCTTCGGATGCTCCTGATT
330146 CT
1 CT
330148 TCCTCTTCCT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.07, C:0.34, G:0.14, T:0.45
Consensus pattern (21 bp):
CTCCTTCGGATGCTCCTGATT
Found at i:330343 original size:2 final size:2
Alignment explanation
Indices: 330336--330365 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
330326 CAGTCTTTTC
330336 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
330366 TACTTTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:330610 original size:23 final size:24
Alignment explanation
Indices: 330584--330631 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 24
330574 GTAAAAGTAG
330584 ATTATTTTT-AATATT-TTTTATTA
1 ATTATTTTTAAAT-TTATTTTATTA
330607 ATTATTTTTAAATTTATTTTATTA
1 ATTATTTTTAAATTTATTTTATTA
330631 A
1 A
330632 AATTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 11 0.48
24 12 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
ATTATTTTTAAATTTATTTTATTA
Found at i:330638 original size:26 final size:23
Alignment explanation
Indices: 330584--330631 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 23
330574 GTAAAAGTAG
330584 ATTATTTTTAATATTTTTTATTA
1 ATTATTTTTAATATTTTTTATTA
330607 ATTATTTTTAA-ATTTATTTTATTA
1 ATTATTTTTAATA-TT-TTTTATTA
330631 A
1 A
330632 AATTATTAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 1 0.04
23 13 0.57
24 9 0.39
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
ATTATTTTTAATATTTTTTATTA
Found at i:330891 original size:24 final size:23
Alignment explanation
Indices: 330831--330920 Score: 83
Period size: 23 Copynumber: 3.8 Consensus size: 23
330821 TAAAAAGATT
*
330831 AGTAGTTTTTTCGAATAAAAAATGTG
1 AGTAGTTTTTT-TAAT--AAAATGTG
**
330857 AAAAGTTTTTTTATATAAAATGTG
1 AGTAGTTTTTTTA-ATAAAATGTG
* **
330881 AGTAG-TCTTTTAATAAAAAATG
1 AGTAGTTTTTTTAATAAAATGTG
330903 AGTAGTTTTTTTAATAAA
1 AGTAGTTTTTTTAATAAA
330921 TGGGTAATTA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
22 13 0.25
23 17 0.32
24 11 0.21
25 1 0.02
26 11 0.21
ACGTcount: A:0.41, C:0.02, G:0.14, T:0.42
Consensus pattern (23 bp):
AGTAGTTTTTTTAATAAAATGTG
Found at i:333745 original size:23 final size:23
Alignment explanation
Indices: 333719--333769 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
333709 GCTAAAAATA
** * *
333719 GTAAGGCATTTGAATGTCATGGT
1 GTAAGGCATGCGAATGCCATGGG
333742 GTAAGGCATGCGAATGCCATGGG
1 GTAAGGCATGCGAATGCCATGGG
333765 GTAAG
1 GTAAG
333770 TTATTCAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.25
Consensus pattern (23 bp):
GTAAGGCATGCGAATGCCATGGG
Found at i:337184 original size:22 final size:23
Alignment explanation
Indices: 337136--337190 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
337126 TGAAAAGTAA
* **
337136 TTTTATATTAATATTTATATATTT
1 TTTTA-ATTAATATTTAAATAAAT
337160 TTTTAATTAA-ATTTAAATAAAT
1 TTTTAATTAATATTTAAATAAAT
*
337182 TTTTTATTA
1 TTTTAATTA
337191 TTAAATAATA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
22 17 0.63
23 5 0.19
24 5 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
TTTTAATTAATATTTAAATAAAT
Found at i:339189 original size:24 final size:24
Alignment explanation
Indices: 339160--339231 Score: 81
Period size: 24 Copynumber: 2.9 Consensus size: 24
339150 AATAAAAATT
* *
339160 AGCCACCAATTTTGACAAATAACA
1 AGCCACCATTTTTGACAAATAAAA
* *
339184 AGCCACCTTTTTTGACAAACAAAA
1 AGCCACCATTTTTGACAAATAAAA
339208 AGGAACCACCATTTTTGACAAATA
1 A-G--CCACCATTTTTGACAAATA
339232 CAAATAGTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
24 21 0.54
25 1 0.03
27 17 0.44
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (24 bp):
AGCCACCATTTTTGACAAATAAAA
Found at i:343612 original size:24 final size:24
Alignment explanation
Indices: 343583--343659 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
343573 AATAAAAATT
* * *
343583 AGCCACCAATTTTGACAAATAACA
1 AGCCACCATTTTTGACAAACAAAA
*
343607 AGCCACCATTTTTTACAAACAAAA
1 AGCCACCATTTTTGACAAACAAAA
*
343631 AGGAACCACCATTTTTGACAAACACAA
1 A-G--CCACCATTTTTGACAAACAAAA
343658 AG
1 AG
343660 GGTGGCTTTT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
24 21 0.48
25 1 0.02
26 1 0.02
27 21 0.48
ACGTcount: A:0.45, C:0.25, G:0.09, T:0.21
Consensus pattern (24 bp):
AGCCACCATTTTTGACAAACAAAA
Found at i:343644 original size:27 final size:27
Alignment explanation
Indices: 343585--343660 Score: 86
Period size: 27 Copynumber: 2.9 Consensus size: 27
343575 TAAAAATTAG
* * *
343585 CCACCAATTTTGACAAATAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
*
343609 CCACCATTTTTTACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
*
343636 CCACCATTTTTGACAAACACAAAGG
1 CCACCATTTTTGACAAACAAAAAGG
343661 GTGGCTTTTG
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
24 19 0.44
25 1 0.02
27 23 0.53
ACGTcount: A:0.45, C:0.25, G:0.09, T:0.21
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:349228 original size:50 final size:50
Alignment explanation
Indices: 349171--349376 Score: 250
Period size: 50 Copynumber: 4.1 Consensus size: 50
349161 GCAAAATGAT
* * *
349171 TTGACTATTCATCACCAACCTTTGACAATCGAGAAAGGTGACCATATTTG
1 TTGACTATTCTTCACCAACCTTTGACAATTGAGAAAGGTGACCATAATTG
* * *
349221 TTAACTATTCTTCACCAACCTTTGACAATTGAGAGAGGTGGCCATAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATTGAGAAAGGTGACCATAATTG
* * * * ** *
349271 TTGACTATTCTTAACCAATCATTGACAATTGAGAGAGGTGGTCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATTGAGAAAGGTGACCATAATTG
* * * **
349321 TTGATTATTCTTCACCAACCTTTAATAATAAAGAAAGGTGACCATAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATTGAGAAAGGTGACCATAATTG
349371 TTGACT
1 TTGACT
349377 CTAAGCATCT
Statistics
Matches: 131, Mismatches: 25, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
50 131 1.00
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATTGAGAAAGGTGACCATAATTG
Found at i:351184 original size:42 final size:42
Alignment explanation
Indices: 351093--351185 Score: 168
Period size: 42 Copynumber: 2.2 Consensus size: 42
351083 ATTGTGTTTT
**
351093 AAGTAAGCAAAATAGATTGAAGTTCAGCACATCTAATGCTAG
1 AAGTAAGTGAAATAGATTGAAGTTCAGCACATCTAATGCTAG
351135 AAGTAAGTGAAATAGATTGAAGTTCAGCACATCTAATGCTAG
1 AAGTAAGTGAAATAGATTGAAGTTCAGCACATCTAATGCTAG
351177 AAGTAAGTG
1 AAGTAAGTG
351186 CATTCTAGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 49 1.00
ACGTcount: A:0.42, C:0.12, G:0.22, T:0.25
Consensus pattern (42 bp):
AAGTAAGTGAAATAGATTGAAGTTCAGCACATCTAATGCTAG
Found at i:352967 original size:3 final size:3
Alignment explanation
Indices: 352959--353025 Score: 118
Period size: 3 Copynumber: 22.7 Consensus size: 3
352949 TTTTATTTAT
*
352959 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
353007 TTA TTA TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TTA TTA TT
353026 TTCTTTGCTT
Statistics
Matches: 61, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.30, C:0.00, G:0.01, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:353456 original size:17 final size:17
Alignment explanation
Indices: 353436--353469 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
353426 TCCAAATAAG
353436 TTTTATCTATTT-ATATT
1 TTTTAT-TATTTAATATT
353453 TTTTATTATTTAATATT
1 TTTTATTATTTAATATT
353470 AAAAAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATTATTTAATATT
Found at i:353923 original size:12 final size:11
Alignment explanation
Indices: 353902--353947 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
353892 ATATTTTAAA
353902 ATTAATTTTAT
1 ATTAATTTTAT
353913 ATTAATATTTAT
1 ATTAAT-TTTAT
353925 A-T-ATTTTAT
1 ATTAATTTTAT
353934 AATTAAATTTTAT
1 -ATT-AATTTTAT
353947 A
1 A
353948 AGCTTAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 8 0.27
12 7 0.23
13 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTAATTTTAT
Found at i:353923 original size:33 final size:33
Alignment explanation
Indices: 353868--353947 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
353858 ATCCAAGTCG
353868 AATTAAGTTTTAT-TTAAAATTTAAATATTTTAA
1 AATTAA-TTTTATATTAAAATTTAAATATTTTAA
* * *
353901 AATTAATTTTATATTAATATTTATATATTTTAT
1 AATTAATTTTATATTAAAATTTAAATATTTTAA
353934 AATTAAATTTTATA
1 AATT-AATTTTATA
353948 AGCTTAAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 6 0.14
33 27 0.64
34 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (33 bp):
AATTAATTTTATATTAAAATTTAAATATTTTAA
Found at i:353945 original size:22 final size:21
Alignment explanation
Indices: 353906--353947 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
353896 TTTAAAATTA
353906 ATTTTATATTAATATTTATAT
1 ATTTTATATTAATATTTATAT
353927 ATTTTATAATTAA-ATTT-TAT
1 ATTTTAT-ATTAATATTTATAT
353947 A
1 A
353948 AGCTTAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTATATTAATATTTATAT
Found at i:361733 original size:3 final size:3
Alignment explanation
Indices: 361725--361759 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
361715 AACCTCTTGT
*
361725 TCA TCA TCA TCA TCA TCA TCA TCA TTA TCA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TC
361760 CTCTTTGCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.31, C:0.31, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:363690 original size:166 final size:163
Alignment explanation
Indices: 363501--364254 Score: 683
Period size: 164 Copynumber: 4.6 Consensus size: 163
363491 TGAGCAATTG
* *
363501 ATTTTCTTTTGAAATTCCTCATGTTTTCAAATTACGAGGTTTTCTTTTTCGTAAATTTTTTCGGG
1 ATTTT-TTTTGAAATT-CTCATGTTTTCAAAATACGAGGTTTTCTTTTCCGTAAATTTTTTCGGG
* ** * *
363566 AGGATTTTCATGGGTTTAAAATTTTTAAAATTCATCAAATACTATTATTTGA-TTCATATTAAAT
64 AGGATTTTC-TTGGTTTTTAATTTTTAAAATTCATAAAATACTATTATTT-ATTTCATAATAAAT
*
363630 TCATTTTTAAAATTTCATTCATTTTCATGAGTTTTTGA
127 T-ATTTTTAAAAATTCATTCATTTTCATGAGTTTTTGA
** * *
363668 ATTTTTTCTTGAAATTCTCATG-TTTCTAAAATAC-AGAGTTTTCTACTCTGTAAATTTTTTTGA
1 ATTTTTT-TTGAAATTCTCATGTTTTC-AAAATACGAG-GTTTTCTTTTCCGTAAATTTTTTCG-
* * * *
363731 GG-GGATTTTTGTTAGTTTTTAATTTTTAAAATTCATAAAATATTATTACTTATTTCATAATAAA
62 GGAGGA-TTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTATTATTTATTTCATAATAAA
* *
363795 TTATTTTTGAAAAATTCATTCATTTTCATGAGTATTTAA
126 TTATTTTT-AAAAATTCATTCATTTTCATGAGTTTTTGA
* ** * * * * *
363834 ATTTTTTTCTTGAAATTTTTTTGTTTTTAAAA-ATTGA-GTTTTCTATTCCATAAATTTTTTCGA
1 A-TTTTTT-TTGAAATTCTCATGTTTTCAAAATA-CGAGGTTTTCTTTTCCGTAAATTTTTTCGG
* * * * *
363897 AAGGATTGTT-TT-GTTTTTAATTATTAAAATTTATCAAATATTATTATTTATTTCATAATAAAT
63 GAGGATT-TTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTATTATTTATTTCATAATAAAT
* *
363960 TATTCTTAAAAATTCATTCATTTTCATGAGTTTTTTA
127 TATTTTTAAAAATTCATTCATTTTCATGAGTTTTTGA
* * * ** **
363997 TTTTTTTTTGAAATTCTCTTGTTTTCCAAAA-ATG-GAGTTTTCTACTCCGTAAATTTTTTTAGG
1 ATTTTTTTTGAAATTCTCATGTTTT-CAAAATACGAG-GTTTTCTTTTCCGTAAATTTTTTCGGG
* * * * *
364060 AGGATTTTTCTTGGTTTTTAATTTTTTAAATCCATAAAATACTATTATTTATTTCATATTATATC
64 AGGA-TTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTATTATTTATTTCATAATAAATT
* * *
364125 AGTTTTTAGAAATTCATTCATTTTCAAGAG-TTTTGG
128 A-TTTTTAAAAATTCATTCATTTTCATGAGTTTTTGA
* * ** *
364161 ATTTTTTTT-AAA-TCTTCATTTTTTCAAAAAAATCGA-GTTTT-TTATTCCAAAAATATTTTCG
1 ATTTTTTTTGAAATTC-TCATGTTTTC-AAAATA-CGAGGTTTTCTT-TTCCGTAAATTTTTTCG
* **
364222 GGAGGATTTTCTTTGGTATAAAATTTTTAAAAT
62 GGAGGATTTTC-TTGGTTTTTAATTTTTAAAAT
364255 AAATCTAATA
Statistics
Matches: 485, Mismatches: 75, Indels: 57
0.79 0.12 0.09
Matches are distributed among these distances:
161 18 0.04
162 41 0.08
163 52 0.11
164 149 0.31
165 43 0.09
166 137 0.28
167 41 0.08
168 4 0.01
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (163 bp):
ATTTTTTTTGAAATTCTCATGTTTTCAAAATACGAGGTTTTCTTTTCCGTAAATTTTTTCGGGAG
GATTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTATTATTTATTTCATAATAAATTATT
TTTAAAAATTCATTCATTTTCATGAGTTTTTGA
Found at i:364169 original size:164 final size:165
Alignment explanation
Indices: 363550--364168 Score: 700
Period size: 166 Copynumber: 3.8 Consensus size: 165
363540 TTTTCTTTTT
** * ** *
363550 CGTAAATTTTTTCGGGAGGA-TTTTCATGGGTTTAAAATTTTTAAAATTCATCAAATACTATTAT
1 CGTAAATTTTTTTAGGAGGATTTTTC-TTGGTTTTTAATTTTTAAAATTCATAAAATACTATTAT
* *
363614 TTGA-TTCATATTAAATTCATTTTTAAAATTTCATTCATTTTCATGAGTTTTTGAA-TTTTTTCT
65 TT-ATTTCATAATAAA-TCATTTTTAAAAATTCATTCATTTTCATGAG-TTTTGAATTTTTTTCT
* *
363677 TGAAATTCTCATG-TTTCTAAAATACAGAGTTTTCTACTC
127 TGAAATTCTCTTGTTTTCTAAAA-ATAGAGTTTTCTACTC
* * * * *
363716 TGTAAATTTTTTTGAGG-GGATTTTTGTTAGTTTTTAATTTTTAAAATTCATAAAATATTATTAC
1 CGTAAATTTTTTT-AGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTATTAT
* *
363780 TTATTTCATAATAAATTATTTTTGAAAAATTCATTCATTTTCATGAGTATTTAAATTTTTTTCTT
65 TTATTTCATAATAAATCATTTTT-AAAAATTCATTCATTTTCATGAGT-TTTGAATTTTTTTCTT
* * * *
363845 GAAATTTTTTTGTTTT-TAAAAATTGAGTTTTCTATTC
128 GAAATTCTCTTGTTTTCTAAAAATAGAGTTTTCTACTC
* * * * * * * *
363882 CATAAA-TTTTTTCGAAAGGATTGTT-TT-GTTTTTAATTATTAAAATTTATCAAATATTATTAT
1 CGTAAATTTTTTTAG-GAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTATTAT
* * **
363944 TTATTTCATAATAAATTATTCTTAAAAATTCATTCATTTTCATGAGTTTTTTATTTTTTT-TTGA
65 TTATTTCATAATAAATCATTTTTAAAAATTCATTCATTTTCATGAGTTTTGAATTTTTTTCTTGA
* *
364008 AATTCTCTTGTTTTCCAAAAATGGAGTTTTCTACTC
130 AATTCTCTTGTTTTCTAAAAATAGAGTTTTCTACTC
* *
364044 CGTAAATTTTTTTAGGAGGATTTTTCTTGGTTTTTAATTTTTTAAATCCATAAAATACTATTATT
1 CGTAAATTTTTTTAGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTATTATT
* * * * *
364109 TATTTCATATTATATCAGTTTTTAGAAATTCATTCATTTTCAAGAGTTTTGGATTTTTTT
66 TATTTCATAATAAATCA-TTTTTAAAAATTCATTCATTTTCATGAGTTTTGAATTTTTTT
364169 TAAATCTTCA
Statistics
Matches: 383, Mismatches: 56, Indels: 29
0.82 0.12 0.06
Matches are distributed among these distances:
161 16 0.04
162 42 0.11
163 33 0.09
164 98 0.26
165 54 0.14
166 108 0.28
167 29 0.08
168 3 0.01
ACGTcount: A:0.30, C:0.09, G:0.09, T:0.52
Consensus pattern (165 bp):
CGTAAATTTTTTTAGGAGGATTTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATACTATTATT
TATTTCATAATAAATCATTTTTAAAAATTCATTCATTTTCATGAGTTTTGAATTTTTTTCTTGAA
ATTCTCTTGTTTTCTAAAAATAGAGTTTTCTACTC
Found at i:364332 original size:328 final size:328
Alignment explanation
Indices: 363638--364332 Score: 730
Period size: 328 Copynumber: 2.1 Consensus size: 328
363628 ATTCATTTTT
* * *
363638 AAAATTTCATTCATTTTCATGAGTTTTTGAATTTTTTCTTGAAATTCTCATGTTTCTAAAATACA
1 AAAAATTCATTCATTTTCATGAGATTTTGAATTTTTT-TTGAAATTCTCATGTTTCCAAAATACA
* * *
363703 GAGTTTTCTACTCTGTAAATTTTTTTGAGGGGATTTTTGTTAGTTTTTAATTTTTAAAATTCATA
65 GAGTTTTCTACTCCGTAAATTTTTTTGAGGGGATTTTTCTTAGTTTTTAATTTTTAAAATCCATA
* * *
363768 AAATATTATTACTTATTTCATAATAAATTATTTTTGAAAAATTCATTCATTTTCATGAGTATTTA
130 AAATACTATTACTTATTTCATAATAAATCATTTTTGAAAAATTCATTCATTTTCAAGAGTATTTA
*** * * *
363833 AATTTTTTTCTTGAAATTTTTTTGTTTTTAAAAATTGAGTTTTCTATTCCATAAATTTTTTCGAA
195 AATTTTTTTCTTGAAATTTTTTTGTTCAAAAAAATCGAGTTTTCTATTCCAAAAATATTTTCGAA
* ** ** * * ** *
363898 AGGATTGTTTTGTTTTTAATTATTAAAATTTATCAAATATTATTATTTATTTCATAATAAATTAT
260 AGGATTGTTTTGTATAAAATTATTAAAATAAATCAAATAGTATTATTAATCCCATAATAAAGTAT
*
363963 TCTT
325 TCTG
* * * * **
363967 AAAAATTCATTCATTTTCATGAGTTTTTTATTTTTTTTTGAAATTCTCTTGTTTTCCAAAA-ATG
1 AAAAATTCATTCATTTTCATGAGATTTTGAATTTTTTTTGAAATTCTCATG-TTTCCAAAATACA
* *
364031 GAGTTTTCTACTCCGTAAATTTTTTT-AGGAGGATTTTTCTTGGTTTTTAATTTTTTAAATCCAT
65 GAGTTTTCTACTCCGTAAATTTTTTTGAGG-GGATTTTTCTTAGTTTTTAATTTTTAAAATCCAT
* * * *
364095 AAAATACTATTATTTATTTCATATTATATCAGTTTTT-AGAAATTCATTCATTTTCAAGAGT-TT
129 AAAATACTATTACTTATTTCATAATAAATCA-TTTTTGAAAAATTCATTCATTTTCAAGAGTATT
** *
364158 TGGA-TTTTTT-TT-AAATCTTCATTTT-TTCAAAAAAATCGAGTTTTTTATTCCAAAAATATTT
193 TAAATTTTTTTCTTGAAAT-TT--TTTTGTTCAAAAAAATCGAGTTTTCTATTCCAAAAATATTT
** * * * *
364219 TCGGGAGGATTTTCTTTGGTATAAAATTTTTAAAATAAATCTAATAGTGTTATTGAACTCCCATT
255 TCGAAAGGATTGT-TTT-GTATAAAATTATTAAAATAAATCAAATAGTATTATT-AA-TCCCA-T
**
364284 AATGCAGT-TT-TG
315 AATAAAGTATTCTG
* *
364296 AAAAATTCAATTTATTTT-TTGA-ATTTTGAATTTTTTT
1 AAAAATTC-ATTCATTTTCATGAGATTTTGAATTTTTTT
364333 GTATATATCA
Statistics
Matches: 302, Mismatches: 52, Indels: 25
0.80 0.14 0.07
Matches are distributed among these distances:
324 4 0.01
325 4 0.01
326 45 0.15
327 14 0.05
328 156 0.52
329 60 0.20
330 13 0.04
331 6 0.02
ACGTcount: A:0.31, C:0.09, G:0.09, T:0.52
Consensus pattern (328 bp):
AAAAATTCATTCATTTTCATGAGATTTTGAATTTTTTTTGAAATTCTCATGTTTCCAAAATACAG
AGTTTTCTACTCCGTAAATTTTTTTGAGGGGATTTTTCTTAGTTTTTAATTTTTAAAATCCATAA
AATACTATTACTTATTTCATAATAAATCATTTTTGAAAAATTCATTCATTTTCAAGAGTATTTAA
ATTTTTTTCTTGAAATTTTTTTGTTCAAAAAAATCGAGTTTTCTATTCCAAAAATATTTTCGAAA
GGATTGTTTTGTATAAAATTATTAAAATAAATCAAATAGTATTATTAATCCCATAATAAAGTATT
CTG
Found at i:364843 original size:12 final size:12
Alignment explanation
Indices: 364820--364870 Score: 68
Period size: 12 Copynumber: 4.2 Consensus size: 12
364810 AATTCAACTG
364820 AAGGAGGAGAAAA
1 AAGGA-GAGAAAA
364833 AAGGAGAGAAAA
1 AAGGAGAGAAAA
* *
364845 AAAGAAAGAAAA
1 AAGGAGAGAAAA
364857 AA-GAGAGAAAA
1 AAGGAGAGAAAA
364868 AAG
1 AAG
364871 ATAAATATAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 10 0.29
12 19 0.56
13 5 0.15
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (12 bp):
AAGGAGAGAAAA
Found at i:364856 original size:11 final size:11
Alignment explanation
Indices: 364826--364871 Score: 65
Period size: 11 Copynumber: 4.0 Consensus size: 11
364816 ACTGAAGGAG
364826 GAGAAAAAAGGA
1 GAGAAAAAA-GA
364838 GAGAAAAAAAGA
1 GAG-AAAAAAGA
*
364850 AAGAAAAAAGA
1 GAGAAAAAAGA
364861 GAGAAAAAAGA
1 GAGAAAAAAGA
364872 TAAATATAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 18 0.58
12 7 0.23
13 6 0.19
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
GAGAAAAAAGA
Found at i:369155 original size:26 final size:26
Alignment explanation
Indices: 369119--369168 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
369109 CTGAGATAAA
* *
369119 ATCTTTTAAATCTTTTTAAGAATTCT
1 ATCTTCTAAATCTTCTTAAGAATTCT
369145 ATCTTCTAAATCTTCTTAAGAATT
1 ATCTTCTAAATCTTCTTAAGAATT
369169 TTATTCAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.32, C:0.14, G:0.04, T:0.50
Consensus pattern (26 bp):
ATCTTCTAAATCTTCTTAAGAATTCT
Found at i:370526 original size:14 final size:15
Alignment explanation
Indices: 370506--370539 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
370496 ATAATAACTC
370506 AAAAAAA-TATAAAAT
1 AAAAAAAGTA-AAAAT
370521 AAAAAAAGTAAAAAT
1 AAAAAAAGTAAAAAT
370536 AAAA
1 AAAA
370540 TCATTTGAGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 16 0.89
16 2 0.11
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (15 bp):
AAAAAAAGTAAAAAT
Found at i:370756 original size:23 final size:23
Alignment explanation
Indices: 370726--370776 Score: 75
Period size: 23 Copynumber: 2.2 Consensus size: 23
370716 GCTAGAAATA
* *
370726 GTAAGGCATTTGAATGCCATGGT
1 GTAAGGCATGTGAATGCCATGGG
*
370749 GTAAGGCATGTGAATGCGATGGG
1 GTAAGGCATGTGAATGCCATGGG
370772 GTAAG
1 GTAAG
370777 ATATTCAATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.27, C:0.10, G:0.37, T:0.25
Consensus pattern (23 bp):
GTAAGGCATGTGAATGCCATGGG
Found at i:373097 original size:2 final size:2
Alignment explanation
Indices: 373090--373133 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
373080 TTTTATAGAT
373090 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
373132 TA
1 TA
373134 AAATTTATTA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:373868 original size:2 final size:2
Alignment explanation
Indices: 373861--373886 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
373851 TTTATTTTAA
373861 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
373887 GGAGCATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:373940 original size:29 final size:28
Alignment explanation
Indices: 373886--373943 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 28
373876 TATATATATA
373886 TGGAGCATATTCTTTGCAGTATATTCTT
1 TGGAGCATATTCTTTGCAGTATATTCTT
* *
373914 TGGAGTATATTCTTTTGGAGTATATTCTT
1 TGGAGCATATTC-TTTGCAGTATATTCTT
373943 T
1 T
373944 TGTTTATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 11 0.41
29 16 0.59
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.50
Consensus pattern (28 bp):
TGGAGCATATTCTTTGCAGTATATTCTT
Found at i:373945 original size:15 final size:14
Alignment explanation
Indices: 373886--373943 Score: 89
Period size: 14 Copynumber: 4.1 Consensus size: 14
373876 TATATATATA
*
373886 TGGAGCATATTCTT
1 TGGAGTATATTCTT
*
373900 TGCAGTATATTCTT
1 TGGAGTATATTCTT
373914 TGGAGTATATTCTTT
1 TGGAGTATATTC-TT
373929 TGGAGTATATTCTT
1 TGGAGTATATTCTT
373943 T
1 T
373944 TGTTTATTTG
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
14 26 0.65
15 14 0.35
ACGTcount: A:0.21, C:0.10, G:0.19, T:0.50
Consensus pattern (14 bp):
TGGAGTATATTCTT
Found at i:374724 original size:21 final size:23
Alignment explanation
Indices: 374677--374730 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
374667 TGAAAAGTAA
* *
374677 TTTTATATTAATATTTATATATT
1 TTTTATATTAATATTTAAATAAT
374700 TTTTA-ATTAA-ATTTAAATAAT
1 TTTTATATTAATATTTAAATAAT
*
374721 TTTTTTATTA
1 TTTTATATTA
374731 TTAAATAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 13 0.48
22 9 0.33
23 5 0.19
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (23 bp):
TTTTATATTAATATTTAAATAAT
Found at i:374733 original size:25 final size:22
Alignment explanation
Indices: 374677--374736 Score: 68
Period size: 23 Copynumber: 2.6 Consensus size: 22
374667 TGAAAAGTAA
*
374677 TTTTATATTAATATTTATATATT
1 TTTTATATTAA-ATTTAAATATT
374700 TTTTA-ATTAAATTTAAATAATTT
1 TTTTATATTAAATTTAAAT-A-TT
374723 TTTTATTATTAAAT
1 TTTTA-TATTAAAT
374737 AATAATTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
21 7 0.22
22 6 0.19
23 12 0.38
25 7 0.22
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTATATTAAATTTAAATATT
Found at i:378617 original size:33 final size:33
Alignment explanation
Indices: 378580--378646 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
378570 TTCAACGATT
378580 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
378613 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
378646 T
1 T
378647 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:378618 original size:13 final size:13
Alignment explanation
Indices: 378600--378624 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
378590 CATAAAATGT
378600 TGTATCGATACAA
1 TGTATCGATACAA
378613 TGTATCGATACA
1 TGTATCGATACA
378625 TATTTTTTTG
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:378705 original size:13 final size:13
Alignment explanation
Indices: 378687--378711 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
378677 ATTACTCACA
378687 TGTATCGATACAT
1 TGTATCGATACAT
378700 TGTATCGATACA
1 TGTATCGATACA
378712 CTGATTTTTG
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:378848 original size:52 final size:52
Alignment explanation
Indices: 378700--378840 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
378690 ATCGATACAT
**
378700 TGTATCGATACACTGATT-TTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
378752 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
378804 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATTAAATGTATCGATACATGCAG
378841 ATAAATTTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:387206 original size:28 final size:28
Alignment explanation
Indices: 387114--387206 Score: 96
Period size: 28 Copynumber: 3.1 Consensus size: 28
387104 GCACTTTTTC
387114 TTTAAAGCCCACAATTCCGTGGCACTTT
1 TTTAAAGCCCACAATTCCGTGGCACTTT
* * **
387142 TTTCATCTTTAAGTCCACAACTCCGTGGCACCCT
1 TTT-A-----AAGCCCACAATTCCGTGGCACTTT
387176 TTTAAAGCCCACAATTCCGTGGCACTTT
1 TTTAAAGCCCACAATTCCGTGGCACTTT
387204 TTT
1 TTT
387207 CATCTTTAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
28 26 0.51
29 1 0.02
33 1 0.02
34 23 0.45
ACGTcount: A:0.23, C:0.30, G:0.13, T:0.34
Consensus pattern (28 bp):
TTTAAAGCCCACAATTCCGTGGCACTTT
Found at i:387324 original size:70 final size:70
Alignment explanation
Indices: 387084--387941 Score: 971
Period size: 70 Copynumber: 12.4 Consensus size: 70
387074 GCATTTTGTC
* * * *
387084 TCAAAGTCCACGACTCAGTGGCAC-TTTTTC-TTTAAAGCCCACAATTCCGTGGCACT-TTTTT-
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
*
387145 CATCTT
66 CCT-TT
* * *
387151 T--AAGTCCACAACTCCGTGGCAC-----CCTTTTAAAGCCCACAATTCCGTGGCACT-TTTTT-
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
*
387207 CATCTT
66 CCT-TT
*
387213 T--AAGTCCACAACTCCGTGGCACCTTTTTT-TGTTTAAAGCCCACAACTCCGTGGCACTCTTTT
1 TCAAAGCCCACAACTCCGTGGCA-CTTTTTTCT-TTTAAAGCCCACAACTCCGTGGCACTCTTTT
387275 TCCCTTT
64 TCCCTTT
*
387282 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
387347 CCTTT
66 CCTTT
* ** * * *
387352 T--AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAAC-C
1 TCAAAGCCCACAACTCCGTGGCA-CTTT-TTTCTT-TTAAAG-CC-CACAACTCCGTGGC-ACTC
*
387414 TTCTT--CTTT
60 TTTTTCCCTTT
* * ** *
387423 TCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTT
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
387488 CCTTT
66 CCTTT
* * *
387493 TTAAAGCCCACAACTCCGTGGCACCTTTTTTCGTTTAAAGCCCACAACTCTGTGGCACTCTTTTT
1 TCAAAGCCCACAACTCCGTGGCA-CTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
387558 CCCTTT
65 CCCTTT
387564 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
387629 CCTTT
66 CCTTT
* ** * * *
387634 T--AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAAC-C
1 TCAAAGCCCACAACTCCGTGGCA-CTTT-TTTCTT-TTAAAG-CC-CACAACTCCGTGGC-ACTC
*
387696 TTCTT--CTTT
60 TTTTTCCCTTT
* * ** *
387705 TCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTT
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
387770 CCTTT
66 CCTTT
* * *
387775 TTAAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
1 TCAAAGCCCACAACTCCGTGGCA-CTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTT
387840 CCCTTT
65 CCCTTT
387846 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
1 TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
387911 CCTTT
66 CCTTT
*
387916 T--AAGTCCACAACTCCGTGGCATCTTT
1 TCAAAGCCCACAACTCCGTGGCA-CTTT
387942 CTCCCTTCCC
Statistics
Matches: 690, Mismatches: 63, Indels: 74
0.83 0.08 0.09
Matches are distributed among these distances:
61 1 0.00
62 58 0.08
63 1 0.00
65 19 0.03
67 6 0.01
68 114 0.17
69 24 0.03
70 209 0.30
71 172 0.25
72 10 0.01
73 72 0.10
74 4 0.01
ACGTcount: A:0.21, C:0.33, G:0.13, T:0.34
Consensus pattern (70 bp):
TCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
CCTTT
Found at i:387722 original size:282 final size:282
Alignment explanation
Indices: 387156--387979 Score: 1486
Period size: 282 Copynumber: 3.0 Consensus size: 282
387146 ATCTTTAAGT
* * *
387156 CCACAACTCCGTGGCA-C--C--CTTTTAAAGCCCACAA-TTCCGTGGCA--CTTTTTTCATCTT
1 CCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTT-TGTGGCACTCTTTTTTCCTTTT
* *
387213 T-AAGTCCACAACTCCGTGGCACCTTTTTTTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
65 TAAAGCCCACAACTCCGTGGCACCTTTTTTCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTC
*
387277 CCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCT
130 CCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCT
387342 TTTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGT
195 TTTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGT
387407 GGCAACCTTCTTCTTTTCAAAGC
260 GGCAACCTTCTTCTTTTCAAAGC
387430 CCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTTT
1 CCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTTT
*
387495 AAAGCCCACAACTCCGTGGCACCTTTTTTCGTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCC
66 AAAGCCCACAACTCCGTGGCACCTTTTTTCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
387560 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
131 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
387625 TTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTG
196 TTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTG
387690 GCAACCTTCTTCTTTTCAAAGC
261 GCAACCTTCTTCTTTTCAAAGC
387712 CCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTTT
1 CCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTTT
*
387777 AAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
66 AAAGCCCACAACTCCGTGGCACCTTTTTTCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
387842 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
131 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
* *
387907 TTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCCAAAGCCCACACAAGTTGGTG
196 TTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTG
387972 GCAACCTT
261 GCAACCTT
387980 TCTCCAAAGC
Statistics
Matches: 530, Mismatches: 11, Indels: 10
0.96 0.02 0.02
Matches are distributed among these distances:
274 16 0.03
275 1 0.00
277 1 0.00
279 22 0.04
280 2 0.00
281 12 0.02
282 476 0.90
ACGTcount: A:0.20, C:0.34, G:0.13, T:0.33
Consensus pattern (282 bp):
CCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCTTTTT
AAAGCCCACAACTCCGTGGCACCTTTTTTCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
TTTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTG
GCAACCTTCTTCTTTTCAAAGC
Found at i:387961 original size:141 final size:138
Alignment explanation
Indices: 387087--387948 Score: 1065
Period size: 141 Copynumber: 6.2 Consensus size: 138
387077 TTTTGTCTCA
* * * * *
387087 AAGTCCACGACTCAGTGGCA-CTTT-T-TCTTTAAAGCCCACAATTCCGTGGCACT-TTTTTCAT
1 AAGTCCACAACTCCGTGGCACCTTTCTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
* * *
387148 CTTT--AAGTCCACAACTCCGTGGCAC-----CCTTTTAAAGCCCACAATTCCGTGGCACT-TTT
66 -TTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
*
387205 TT-CATCTTT
130 TTCCCT-TTT
* ***
387214 AAGTCCACAACTCCGTGGCACCTTTTTTTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 AAGTCCACAACTCCGTGGCACCTTTCTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-CC
*
387279 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCTGTGGCACTCTTT
65 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
387344 TTCCCTTTT
130 TTCCCTTTT
* * * *
387353 AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAAC-CTTC
1 AAGTCCACAACTCCGTGGCACCTTTCTCCCTT--TAAAG-CC-CACAACTCCGTGGC-ACTCTTT
* * **
387417 TT-CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACT
61 TTCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACT
*
387481 CTTTTTTCCTTTTT
126 C-TTTTTCCCTTTT
* * * * *
387495 AAAGCCCACAACTCCGTGGCACCTTTTTTCGTTTAAAGCCCACAACTCTGTGGCACTCTTTTTCC
1 -AAGTCCACAACTCCGTGGCACCTTTCTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-C
387560 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
64 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
387625 TTTCCCTTTT
129 TTTCCCTTTT
* * * *
387635 AAGTCCACAACTCCGTGGCATCTTTCTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAAC-CTTC
1 AAGTCCACAACTCCGTGGCACCTTTCTCCCTT--TAAAG-CC-CACAACTCCGTGGC-ACTCTTT
* * **
387699 TT-CTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTTAAAGCCCACAACTTTGTGGCACT
61 TTCCTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACT
*
387763 CTTTTTTCCTTTTT
126 C-TTTTTCCCTTTT
* * *
387777 AAAGCCCACAACTCCGTGGCACCTTTTTCCGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCC
1 -AAGTCCACAACTCCGTGGCACCTTTCTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTTT-C
387842 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
64 CTTTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTT
387907 TTTCCCTTTT
129 TTTCCCTTTT
*
387917 AAGTCCACAACTCCGTGGCATCTTTCTCCCTT
1 AAGTCCACAACTCCGTGGCACCTTTCTCCCTT
387949 CCCAAAGCCC
Statistics
Matches: 637, Mismatches: 64, Indels: 56
0.84 0.08 0.07
Matches are distributed among these distances:
127 18 0.03
128 4 0.01
129 1 0.00
130 26 0.04
131 8 0.01
132 2 0.00
133 20 0.03
138 30 0.05
139 124 0.19
140 28 0.04
141 257 0.40
142 26 0.04
143 89 0.14
144 4 0.01
ACGTcount: A:0.20, C:0.33, G:0.13, T:0.34
Consensus pattern (138 bp):
AAGTCCACAACTCCGTGGCACCTTTCTCCCTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCT
TTTCAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
TCCCTTTT
Found at i:387994 original size:104 final size:103
Alignment explanation
Indices: 387176--387961 Score: 499
Period size: 104 Copynumber: 7.5 Consensus size: 103
387166 GTGGCACCCT
* * * * *
387176 TTTAAAGCCCACAATTCCGTGGCACT-TTTTTCATCTT---TAAGTCCACAACTCCGTGGCACCT
1 TTTAAAGCCCACAACTCCGTGGCACTCTTTCTC-CCTTCCCAAAGCCCACAACTCCGTGGCA-CT
* * **
387237 TTTTTTGTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
64 CTTTCT-TCCAAAGCCCACAACTCCGTGGCAC-CTTTTTCCC
* ** *
387279 TTTTCAAAGCCCACAACTCCGTGGCACT-TTT-T-TCTT-TTAAAGCCCACAACTCTGTGGCACT
1 -TTT-AAAGCCCACAACTCCGTGGCACTCTTTCTCCCTTCCCAAAGCCCACAACTCCGTGGCACT
* * * *
387340 CTTT-TTCCCTTTTAAGTCCACAACTCCGTGGCATCTTTCTCCC
64 CTTTCTT-CC---AAAGCCCACAACTCCGTGGCACCTTTTTCCC
* * * **
387383 TTCCTAAAGCCCACACAAGTCGGTGGCAAC-C-TTCT-TCTTTTCAAAGCCCACAACTCCGTGGC
1 TT--TAAAG-CC-CACAACTCCGTGGC-ACTCTTTCTCCCTTCCCAAAGCCCACAACTCCGTGGC
** ** *
387445 AC-CTTCTTCTTTTAAAGCCCACAACTTTGTGGCACTCTTTTTTCCTT
61 ACTC-T-TTCTTCCAAAGCCCACAACTCCGTGGCAC-C-TTTTTCC-C
* * * * *
387492 TTTAAAGCCCACAACTCCGTGGCAC-CTTTTTTCGTT--TAAAGCCCACAACTCTGTGGCACTCT
1 TTTAAAGCCCACAACTCCGTGGCACTCTTTCTCCCTTCCCAAAGCCCACAACTCCGTGGCACTC-
* * *
387554 TTTTCCCTTTTCAAAGCCCACAACTCCGTGGCA-CTTTTTTCT
65 -TTT--C-TTCCAAAGCCCACAACTCCGTGGCACCTTTTTCCC
* ** *
387596 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTT--TTAAGTCCACAACTCCGTGGCA-TCT
1 TTTAAAGCCCACAACTCCGTGGCACTCTTTCTCCCTTCCCAAAGCCCACAACTCCGTGGCACTC-
* * * *
387658 TTCTCCCTTCCTAAAGCCCACACAAGTCGGTGGCAACCTTCTT-CT
65 TT-T--CTTCC-AAAG-CC-CACAACTCCGTGGC-ACCTTTTTCCC
* ** **
387703 TTTCAAAGCCCACAACTCCGTGGCAC-C-TTCT-TCTT-TTAAAGCCCACAACTTTGTGGCACTC
1 TTT-AAAGCCCACAACTCCGTGGCACTCTTTCTCCCTTCCCAAAGCCCACAACTCCGTGGCACTC
* *
387764 TTTTTTCCTTTTTAAAGCCCACAACTCCGTGGCACCTTTTTCCG
65 TTTCTTCC-----AAAGCCCACAACTCCGTGGCACCTTTTTCCC
* ** *
387808 TTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACTTT
1 TTTAAAGCCCACAACTCCGTGGCACTCTTTCTCCCTTCCCAAAGCCCACAACTCCGTGGCAC-TC
**
387873 TTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
65 TTTCTTCCAAAGCCCACAACTCCGTGGCAC-CTTTTTCCC
* *
387913 TTTTAAGTCCACAACTCCGTGGCA-TCTTTCTCCCTTCCCAAAGCCCACA
1 TTTAAAGCCCACAACTCCGTGGCACTCTTTCTCCCTTCCCAAAGCCCACA
387962 CAAGTTGGTG
Statistics
Matches: 563, Mismatches: 70, Indels: 98
0.77 0.10 0.13
Matches are distributed among these distances:
101 1 0.00
102 5 0.01
103 17 0.03
104 167 0.30
105 152 0.27
106 78 0.14
107 32 0.06
108 99 0.18
109 10 0.02
110 2 0.00
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.34
Consensus pattern (103 bp):
TTTAAAGCCCACAACTCCGTGGCACTCTTTCTCCCTTCCCAAAGCCCACAACTCCGTGGCACTCT
TTCTTCCAAAGCCCACAACTCCGTGGCACCTTTTTCCC
Found at i:388131 original size:49 final size:49
Alignment explanation
Indices: 388015--388803 Score: 1024
Period size: 49 Copynumber: 15.8 Consensus size: 49
388005 GCAACCCCTC
* * *
388015 TAAGCCCAATATAGCTGGCCTTGAATTAGCATATTGGCACATTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAC--CTT-CATCTT
* * *
388067 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
388116 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* * *
388168 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
388217 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
388266 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTG
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
*
388315 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
388364 TAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
388413 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
388462 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACTTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * * * *
388511 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCA-CTTGCACCAT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTT-CATCTT
*
388560 TAAGTCC-ATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* * *
388608 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
* *
388657 TCAGTCCAATATAGCTGGCCTTGAATCAGCATATCGGCACCTTTTCCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACC--TT-CATCTT
* * * *
388709 TAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGACATCCTTTTTCATCATCTT
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA-CC----T--TCATCTT
* * * * *
388765 TAAGCCCAATATCGTTGGCCATGAATCAACATATTGGCA
1 TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCA
388804 TCTTTATCAC
Statistics
Matches: 651, Mismatches: 72, Indels: 24
0.87 0.10 0.03
Matches are distributed among these distances:
48 40 0.06
49 443 0.68
50 4 0.01
51 4 0.01
52 118 0.18
53 2 0.00
55 3 0.00
56 36 0.06
57 1 0.00
ACGTcount: A:0.25, C:0.26, G:0.17, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTT
Found at i:389712 original size:33 final size:33
Alignment explanation
Indices: 389675--389741 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
389665 TTCAACGATT
389675 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
389708 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
389741 T
1 T
389742 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:389713 original size:13 final size:13
Alignment explanation
Indices: 389695--389719 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
389685 CATAAAATGT
389695 TGTATCGATACAA
1 TGTATCGATACAA
389708 TGTATCGATACA
1 TGTATCGATACA
389720 TATTTTTTTG
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:389800 original size:13 final size:13
Alignment explanation
Indices: 389782--389806 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
389772 ATTACTCACA
389782 TGTATCGATACAT
1 TGTATCGATACAT
389795 TGTATCGATACA
1 TGTATCGATACA
389807 CTGATTTTTG
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:389943 original size:52 final size:52
Alignment explanation
Indices: 389795--389935 Score: 230
Period size: 52 Copynumber: 2.7 Consensus size: 52
389785 ATCGATACAT
**
389795 TGTATCGATACACTGATT-TTTGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACT-ATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
* *
389847 TGTATCGATACATTATAAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
1 TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
389899 TGTATCGATACACTATTAAATGTATCGATACATGCAG
1 TGTATCGATACACTATTAAATGTATCGATACATGCAG
389936 ATAAATTTTC
Statistics
Matches: 82, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 2 0.02
52 80 0.98
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (52 bp):
TGTATCGATACACTATTAAATGTATCGATACATGCAGGCAAATTTGCCCAGA
Found at i:395849 original size:24 final size:25
Alignment explanation
Indices: 395822--395893 Score: 83
Period size: 27 Copynumber: 2.8 Consensus size: 25
395812 TAATAAAATT
* * *
395822 AGCCACCAATTTTGACAAA-TAACA
1 AGCCACCATTTTTGACAAACAAAAA
*
395846 AGCCACCATTTTTTACAAACAAAAA
1 AGCCACCATTTTTGACAAACAAAAA
395871 AGAACCACCATTTTTGACAAACA
1 AG--CCACCATTTTTGACAAACA
395894 CAAAGGGTGG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
24 17 0.43
25 5 0.12
27 18 0.45
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (25 bp):
AGCCACCATTTTTGACAAACAAAAA
Found at i:397198 original size:15 final size:15
Alignment explanation
Indices: 397137--397200 Score: 53
Period size: 14 Copynumber: 4.4 Consensus size: 15
397127 AAATTTTAGA
397137 AAAATTAAA-TTATC
1 AAAATTAAATTTATC
*
397151 AAAACTACAATTTATC
1 AAAATTA-AATTTATC
*** *
397167 -TTTTTTAATTT-TC
1 AAAATTAAATTTATC
397180 AAAATTAAATTTATC
1 AAAATTAAATTTATC
397195 AAAATT
1 AAAATT
397201 CATAATTCCG
Statistics
Matches: 36, Mismatches: 10, Indels: 7
0.68 0.19 0.13
Matches are distributed among these distances:
13 2 0.06
14 18 0.50
15 11 0.31
16 5 0.14
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (15 bp):
AAAATTAAATTTATC
Found at i:401483 original size:50 final size:50
Alignment explanation
Indices: 401405--401610 Score: 205
Period size: 50 Copynumber: 4.1 Consensus size: 50
401395 GCAAAATGAT
* * * *
401405 TTGACTATTCATCACTAACCTTTGACAATCGAGAAAGGTGACCATATTTG
1 TTGACTATTCTTCACCAAACTTTGACAATCGAGAAAGGTGACCATAATTG
* * * * *
401455 TTAACAATTCTTCACCAAACTTTGACAATCGAGAGAGGTGGCCATAATTA
1 TTGACTATTCTTCACCAAACTTTGACAATCGAGAAAGGTGACCATAATTG
* * * * * ** *
401505 TTGACTATTCTTAACCAATCATTGACAATTGAGAGAGGTGGTCGTAATTG
1 TTGACTATTCTTCACCAAACTTTGACAATCGAGAAAGGTGACCATAATTG
* * * * **
401555 TTGATTATTCTTCACCAACCTTTAATAATAAAGAAAGGTGACCATAATTG
1 TTGACTATTCTTCACCAAACTTTGACAATCGAGAAAGGTGACCATAATTG
401605 TTGACT
1 TTGACT
401611 CTAAGCATCT
Statistics
Matches: 125, Mismatches: 31, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 125 1.00
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (50 bp):
TTGACTATTCTTCACCAAACTTTGACAATCGAGAAAGGTGACCATAATTG
Found at i:406021 original size:50 final size:50
Alignment explanation
Indices: 405941--406179 Score: 307
Period size: 50 Copynumber: 4.8 Consensus size: 50
405931 GCAAAGTGAT
* *
405941 TTGACTATTCTTTACCAACATTTGACAATCGAGAGAGGTGGTCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * *
405991 TTGACTATTCTTCACCAACTTTTGAAAATCGAGAGAGGTGGTCATAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * * * * * *
406041 TTGACTATTCTTTACCAACTTTTGACAATCAATAGAGGTAGCCGTAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * * *
406091 TTGACTATTCTTCACCAACCTTTGACAATCGAAATAAGTGGTTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * *
406141 TTGATTATTCTTCACCAACCTTTGACAATAGAGAAAGGT
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGT
406180 AACCCATAAT
Statistics
Matches: 162, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 162 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
Found at i:407607 original size:3 final size:3
Alignment explanation
Indices: 407599--407650 Score: 88
Period size: 3 Copynumber: 17.7 Consensus size: 3
407589 TTTTATTTAT
*
407599 TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TT-
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
407646 TTA TT
1 TTA TT
407651 TTCTTTGCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 44 0.96
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:408079 original size:17 final size:17
Alignment explanation
Indices: 408059--408092 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
408049 TCCAAATAAG
408059 TTTTATCTATTT-ATATT
1 TTTTAT-TATTTAATATT
408076 TTTTATTATTTAATATT
1 TTTTATTATTTAATATT
408093 AAAAAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATTATTTAATATT
Found at i:408542 original size:12 final size:11
Alignment explanation
Indices: 408521--408566 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
408511 ATATTTTAAA
408521 ATTAATTTTAT
1 ATTAATTTTAT
408532 ATTAATATTTAT
1 ATTAAT-TTTAT
408544 A-T-ATTTTAT
1 ATTAATTTTAT
408553 AATTAAATTTTAT
1 -ATT-AATTTTAT
408566 A
1 A
408567 AGCTTAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 8 0.27
12 7 0.23
13 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTAATTTTAT
Found at i:408542 original size:33 final size:33
Alignment explanation
Indices: 408487--408566 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
408477 ATCCAAGTCG
408487 AATTAAGTTTTAT-TTAAAATTTAAATATTTTAA
1 AATTAA-TTTTATATTAAAATTTAAATATTTTAA
* * *
408520 AATTAATTTTATATTAATATTTATATATTTTAT
1 AATTAATTTTATATTAAAATTTAAATATTTTAA
408553 AATTAAATTTTATA
1 AATT-AATTTTATA
408567 AGCTTAAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 6 0.14
33 27 0.64
34 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (33 bp):
AATTAATTTTATATTAAAATTTAAATATTTTAA
Found at i:408564 original size:22 final size:21
Alignment explanation
Indices: 408525--408566 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
408515 TTTAAAATTA
408525 ATTTTATATTAATATTTATAT
1 ATTTTATATTAATATTTATAT
408546 ATTTTATAATTAA-ATTT-TAT
1 ATTTTAT-ATTAATATTTATAT
408566 A
1 A
408567 AGCTTAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTATATTAATATTTATAT
Found at i:415506 original size:50 final size:50
Alignment explanation
Indices: 415426--415664 Score: 307
Period size: 50 Copynumber: 4.8 Consensus size: 50
415416 GCAAAGTGAT
* *
415426 TTGACTATTCTTTACCAACATTTGACAATCGAGAGAGGTGGTCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * *
415476 TTGACTATTCTTCACCAACTTTTGAAAATCGAGAGAGGTGGTCATAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * * * * * *
415526 TTGACTATTCTTTACCAACTTTTGACAATCAATAGAGGTAGCCGTAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * * *
415576 TTGACTATTCTTCACCAACCTTTGACAATCGAAATAAGTGGTTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * *
415626 TTGATTATTCTTCACCAACCTTTGACAATAGAGAAAGGT
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGT
415665 AACCCATAAT
Statistics
Matches: 162, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 162 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
Found at i:417097 original size:3 final size:3
Alignment explanation
Indices: 417082--417142 Score: 97
Period size: 3 Copynumber: 20.7 Consensus size: 3
417072 TTTTATTTAT
* *
417082 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
417130 TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TT
417143 TTCTTTGCTT
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:417571 original size:17 final size:17
Alignment explanation
Indices: 417551--417584 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
417541 TCCAAATAAG
417551 TTTTATCTATTT-ATATT
1 TTTTAT-TATTTAATATT
417568 TTTTATTATTTAATATT
1 TTTTATTATTTAATATT
417585 AAAAAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATTATTTAATATT
Found at i:418034 original size:12 final size:11
Alignment explanation
Indices: 418013--418058 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
418003 ATATTTTAAA
418013 ATTAATTTTAT
1 ATTAATTTTAT
418024 ATTAATATTTAT
1 ATTAAT-TTTAT
418036 A-T-ATTTTAT
1 ATTAATTTTAT
418045 AATTAAATTTTAT
1 -ATT-AATTTTAT
418058 A
1 A
418059 AGCTTAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 8 0.27
12 7 0.23
13 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTAATTTTAT
Found at i:418034 original size:33 final size:33
Alignment explanation
Indices: 417979--418058 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
417969 ATCCAAGTCG
417979 AATTAAGTTTTAT-TTAAAATTTAAATATTTTAA
1 AATTAA-TTTTATATTAAAATTTAAATATTTTAA
* * *
418012 AATTAATTTTATATTAATATTTATATATTTTAT
1 AATTAATTTTATATTAAAATTTAAATATTTTAA
418045 AATTAAATTTTATA
1 AATT-AATTTTATA
418059 AGCTTAAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 6 0.14
33 27 0.64
34 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (33 bp):
AATTAATTTTATATTAAAATTTAAATATTTTAA
Found at i:418056 original size:22 final size:21
Alignment explanation
Indices: 418017--418058 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
418007 TTTAAAATTA
418017 ATTTTATATTAATATTTATAT
1 ATTTTATATTAATATTTATAT
418038 ATTTTATAATTAA-ATTT-TAT
1 ATTTTAT-ATTAATATTTATAT
418058 A
1 A
418059 AGCTTAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTATATTAATATTTATAT
Found at i:424991 original size:50 final size:50
Alignment explanation
Indices: 424911--425149 Score: 307
Period size: 50 Copynumber: 4.8 Consensus size: 50
424901 GCAAAGTGAT
* *
424911 TTGACTATTCTTTACCAACATTTGACAATCGAGAGAGGTGGTCGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * *
424961 TTGACTATTCTTCACCAACTTTTGAAAATCGAGAGAGGTGGTCATAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * * * * * *
425011 TTGACTATTCTTTACCAACTTTTGACAATCAATAGAGGTAGCCGTAATTA
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * * *
425061 TTGACTATTCTTCACCAACCTTTGACAATCGAAATAAGTGGTTGTAATTG
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
* * *
425111 TTGATTATTCTTCACCAACCTTTGACAATAGAGAAAGGT
1 TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGT
425150 AACCCATAAT
Statistics
Matches: 162, Mismatches: 27, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
50 162 1.00
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.35
Consensus pattern (50 bp):
TTGACTATTCTTCACCAACCTTTGACAATCGAGAGAGGTGGTCGTAATTG
Found at i:426577 original size:3 final size:3
Alignment explanation
Indices: 426569--426629 Score: 106
Period size: 3 Copynumber: 20.7 Consensus size: 3
426559 TTTTATTTAT
*
426569 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
426617 TTA TTA TT- TTA TT
1 TTA TTA TTA TTA TT
426630 TTCTTTGCTT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
2 2 0.04
3 53 0.96
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:427058 original size:17 final size:17
Alignment explanation
Indices: 427038--427071 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
427028 TCCAAATAAG
427038 TTTTATCTATTT-ATATT
1 TTTTAT-TATTTAATATT
427055 TTTTATTATTTAATATT
1 TTTTATTATTTAATATT
427072 AAAAAAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTATTATTTAATATT
Found at i:427520 original size:12 final size:11
Alignment explanation
Indices: 427499--427544 Score: 51
Period size: 11 Copynumber: 4.1 Consensus size: 11
427489 ATATTTTAAA
427499 ATTAATTTTAT
1 ATTAATTTTAT
427510 ATTAATATTTAT
1 ATTAAT-TTTAT
427522 A-T-ATTTTAT
1 ATTAATTTTAT
427531 AATTAAATTTTAT
1 -ATT-AATTTTAT
427544 A
1 A
427545 AGCTTAAAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
9 5 0.17
10 3 0.10
11 8 0.27
12 7 0.23
13 7 0.23
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (11 bp):
ATTAATTTTAT
Found at i:427520 original size:33 final size:33
Alignment explanation
Indices: 427465--427544 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
427455 ATCCAAGTCG
427465 AATTAAGTTTTAT-TTAAAATTTAAATATTTTAA
1 AATTAA-TTTTATATTAAAATTTAAATATTTTAA
* * *
427498 AATTAATTTTATATTAATATTTATATATTTTAT
1 AATTAATTTTATATTAAAATTTAAATATTTTAA
427531 AATTAAATTTTATA
1 AATT-AATTTTATA
427545 AGCTTAAAGT
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
32 6 0.14
33 27 0.64
34 9 0.21
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (33 bp):
AATTAATTTTATATTAAAATTTAAATATTTTAA
Found at i:427542 original size:22 final size:21
Alignment explanation
Indices: 427503--427544 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
427493 TTTAAAATTA
427503 ATTTTATATTAATATTTATAT
1 ATTTTATATTAATATTTATAT
427524 ATTTTATAATTAA-ATTT-TAT
1 ATTTTAT-ATTAATATTTATAT
427544 A
1 A
427545 AGCTTAAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTATATTAATATTTATAT
Found at i:437336 original size:166 final size:162
Alignment explanation
Indices: 437147--437835 Score: 612
Period size: 166 Copynumber: 4.2 Consensus size: 162
437137 TGAGCAATTG
* * * *
437147 ATTTTCTTTTGAAATTCCTCATGTTTTCAAATTACGAGGTTTTCTTTTTCGTAAATTTTTTCGGG
1 ATTTT-TTTTGAAATT-CTCATGTTTTCAAATTACGAGGTTTTCTATTCCATAAATTTTTTCGAG
* ** * * *
437212 AGGATTTTCATGGGTTTAAAATTTTTAAAATTCATCAAATACTATTATTTGA-TTCATATTAAAT
64 AGGATTTTC-TTGGTTTTTAATTTTTAAAATTCATAAAATATTATTATTT-ATTTCATAATAAAT
437276 TCATTTTTAAAATTTCATTCATTTTCATGAGTTTTTGA
127 T-ATTTTTAAAA-TTCATTCATTTTCATGAGTTTTTGA
* * * ** ** *
437314 ATTTTTTCTTGAAATTCTCATG-TTTCTAAAATACAAAGTTTTCTGCTCTGTAAATTTTTTTGAG
1 ATTTTTT-TTGAAATTCTCATGTTTTC-AAATTACGAGGTTTTCTATTCCATAAATTTTTTCGAG
* * * *
437378 AGGATTTTTGTTAGTTTTTAATTTTTAAAATTCATAAAATGTTATTACTTATTTCATAATAAATT
64 AGGA-TTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATTATTATTTATTTCATAATAAATT
* *
437443 ATTTTTGAAACATTCATTCATTTTCATGAGTATTTAA
128 ATTTTT-AAA-ATTCATTCATTTTCATGAGTTTTTGA
* ** *
437480 ATTTTTTTCTTGAAATTTTTTTGTTTTTAAAAATT--GA-GTTTTCTATTCCATAAATTTTTTCG
1 A-TTTTTT-TTGAAATTCTCATG-TTTT-CAAATTACGAGGTTTTCTATTCCATAAATTTTTTCG
* * * * *
437542 AAAGGATTTT-TTTGTTTTTAATTATTAAAATTTATCAAATATTATTATTTATTTCATAATAAAT
62 AGAGGATTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATTATTATTTATTTCATAATAAAT
* * *
437606 TATTCTTAAAAATTCATTCATTTTCATTCA-TTTTTTA
127 TATT-TTTAAAATTCATTCATTTTCA-TGAGTTTTTGA
* * * * * *
437643 TTTTTTTTTTGAAATTCTCTTGTTTTCCAAA-AATG-GAGTTTTCTACTCCATAAACTTTTTTAG
1 -ATTTTTTTTGAAATTCTCATGTTTT-CAAATTACGAG-GTTTTCTATTCCATAAA-TTTTTTCG
* * * *
437706 -GAGGATTTTTCTTGGTTTTTAATTTTTTAAATCCATAAAATATTATTATTTATTTCATATTATA
62 AGAGGA-TTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATTATTATTTATTTCATAATAAA
* * *
437770 TCAGTTTTTAGAAATTCATTCATTTTCAAGAG-TTTTGG
126 TTA-TTTTTA-AAATTCATTCATTTTCATGAGTTTTTGA
*
437808 ATTTTTTTT-AAA-TCTTCATTTTTTCAAA
1 ATTTTTTTTGAAATTC-TCATGTTTTCAAA
437836 AAAAAATCGA
Statistics
Matches: 429, Mismatches: 69, Indels: 53
0.78 0.13 0.10
Matches are distributed among these distances:
161 7 0.02
162 19 0.04
163 56 0.13
164 76 0.18
165 72 0.17
166 155 0.36
167 37 0.09
169 7 0.02
ACGTcount: A:0.29, C:0.09, G:0.08, T:0.53
Consensus pattern (162 bp):
ATTTTTTTTGAAATTCTCATGTTTTCAAATTACGAGGTTTTCTATTCCATAAATTTTTTCGAGAG
GATTTTCTTGGTTTTTAATTTTTAAAATTCATAAAATATTATTATTTATTTCATAATAAATTATT
TTTAAAATTCATTCATTTTCATGAGTTTTTGA
Found at i:438353 original size:22 final size:22
Alignment explanation
Indices: 438328--438370 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
438318 AAAAATGCCT
*
438328 AAAAA-AATAGAAAAAGGTAAGG
1 AAAAATAAAAGAAAAA-GTAAGG
438350 AAAAATAAAAGAAAAAGTAAG
1 AAAAATAAAAGAAAAAGTAAG
438371 ATATTAGCGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (22 bp):
AAAAATAAAAGAAAAAGTAAGG
Found at i:438491 original size:12 final size:12
Alignment explanation
Indices: 438474--438518 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
438464 CTGAAAGAAG
438474 GAGAAAAAAGGA
1 GAGAAAAAAGGA
*
438486 GAGAAAAAAAGA
1 GAGAAAAAAGGA
*
438498 AAGAAAAAA-GA
1 GAGAAAAAAGGA
438509 GAGAAAAAAG
1 GAGAAAAAAG
438519 ATAAATATAG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAGAAAAAAGGA
Found at i:438504 original size:11 final size:11
Alignment explanation
Indices: 438474--438519 Score: 65
Period size: 11 Copynumber: 4.0 Consensus size: 11
438464 CTGAAAGAAG
438474 GAGAAAAAAGGA
1 GAGAAAAAA-GA
438486 GAGAAAAAAAGA
1 GAG-AAAAAAGA
*
438498 AAGAAAAAAGA
1 GAGAAAAAAGA
438509 GAGAAAAAAGA
1 GAGAAAAAAGA
438520 TAAATATAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
11 18 0.58
12 7 0.23
13 6 0.19
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
GAGAAAAAAGA
Found at i:442156 original size:26 final size:26
Alignment explanation
Indices: 442120--442169 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
442110 CTGAGATAGA
* *
442120 ATCTTTTAAATCTTTTTAAAAATTCT
1 ATCTTCTAAATCTTCTTAAAAATTCT
*
442146 ATCTTCTAAATCTTCTTAAGAATT
1 ATCTTCTAAATCTTCTTAAAAATT
442170 TTATTCAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.34, C:0.14, G:0.02, T:0.50
Consensus pattern (26 bp):
ATCTTCTAAATCTTCTTAAAAATTCT
Found at i:444782 original size:39 final size:37
Alignment explanation
Indices: 444739--444814 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
444729 AAAAATTTTA
*
444739 TTAATTAAAAATTATTTAA-GTAATAAATATTTTTTTAAT
1 TTAATTAAAAA-TA-TTAACATAA-AAATATTTTTTTAAT
*
444778 TTAATTATAAATATTAACATAAAAATATTTTTTTAAT
1 TTAATTAAAAATATTAACATAAAAATATTTTTTTAAT
444815 ATTATTTTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 19 0.56
38 5 0.15
39 10 0.29
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (37 bp):
TTAATTAAAAATATTAACATAAAAATATTTTTTTAAT
Found at i:444804 original size:37 final size:37
Alignment explanation
Indices: 444763--444836 Score: 105
Period size: 37 Copynumber: 2.0 Consensus size: 37
444753 TTTAAGTAAT
* *
444763 AAATATTTTTTTAAT-TTAATTATAAATATTAACATAA
1 AAATATTTTTTTAATATT-ATTATAAATAATAAAATAA
*
444800 AAATATTTTTTTAATATTATTTTAAATAATAAAATAA
1 AAATATTTTTTTAATATTATTATAAATAATAAAATAA
444837 TCTGAACTTA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
37 31 0.94
38 2 0.06
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (37 bp):
AAATATTTTTTTAATATTATTATAAATAATAAAATAA
Found at i:445374 original size:23 final size:23
Alignment explanation
Indices: 445344--445394 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
445334 GCTAGAAATA
** * *
445344 GTAAGGCATTTGAATGTCATGGT
1 GTAAGGCATGCGAATGCCATGGG
445367 GTAAGGCATGCGAATGCCATGGG
1 GTAAGGCATGCGAATGCCATGGG
445390 GTAAG
1 GTAAG
445395 ATATTCAATG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.27, C:0.12, G:0.35, T:0.25
Consensus pattern (23 bp):
GTAAGGCATGCGAATGCCATGGG
Found at i:447731 original size:2 final size:2
Alignment explanation
Indices: 447724--447749 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
447714 TAATAACTTT
447724 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
447750 ATAAGCTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Done.