Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167882.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_15, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22478863
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 61000 characters in sequence are not A, C, G, or T
File 20 of 106
Found at i:3475269 original size:133 final size:132
Alignment explanation
Indices: 3475021--3475280 Score: 369
Period size: 133 Copynumber: 2.0 Consensus size: 132
3475011 AATCTACGAG
* * *
3475021 CATGATTTCTAAGACCTCTAAGCATAATTTCGATTCGCGGTGTTATCCCGATCGATTCTTTATTT
1 CATGATTTCTAAGACCTCTAAGCATAATCTCGATTCACGGTGTTATCCCGATCGATTCTTTATCT
* * *
3475086 TTTAACTTGTAATGTTATCATAGTCAATTCTGTAAGACCTTCAGACATGATTCTCTAAGACCTGC
66 TTCAACTTGTAATGTTATCATAATCAATTCTGTAAGACCTCCAGACATGATT-TCTAAGACCTGC
3475151 AGA
130 AGA
* *
3475154 CATGATTTTTAAGACCT-TCGAGCATAATCTCGATTCACGGTGTTATCCCGATCGATTCTTTATC
1 CATGATTTCTAAGACCTCT-AAGCATAATCTCGATTCACGGTGTTATCCCGATCGATTCTTTATC
* * * * **
3475218 TTTCGACTTGTGATGTTATCATAATCGATTCTGTAAGACCTCCGGGTATGATTTCTAAGACCT
65 TTTCAACTTGTAATGTTATCATAATCAATTCTGTAAGACCTCCAGACATGATTTCTAAGACCT
3475281 CCGAACATAA
Statistics
Matches: 112, Mismatches: 14, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
132 11 0.10
133 101 0.90
ACGTcount: A:0.25, C:0.21, G:0.16, T:0.38
Consensus pattern (132 bp):
CATGATTTCTAAGACCTCTAAGCATAATCTCGATTCACGGTGTTATCCCGATCGATTCTTTATCT
TTCAACTTGTAATGTTATCATAATCAATTCTGTAAGACCTCCAGACATGATTTCTAAGACCTGCA
GA
Found at i:3475327 original size:110 final size:110
Alignment explanation
Indices: 3475134--3475393 Score: 351
Period size: 110 Copynumber: 2.4 Consensus size: 110
3475124 CTTCAGACAT
* * * * * *
3475134 GATTCTCTAAGACCTGCAGACATGATTTTTAAGACCTTCGAGCATAATCTCGATTCACGGTGTTA
1 GATTCTGTAAGACCTCCAGACATGATTTCTAAGACCTCCGAACATAATCTCGATTCACGATGTTA
* *
3475199 TCCCGATCGATTCTTTATCTTTCGACTTGTGATGTTATCATAATC
66 TCCCGATCGATTCTTTATCTTTCAACTTGTGATGTTATCACAATC
* **
3475244 GATTCTGTAAGACCTCCGGGTATGATTTCTAAGACCTCCGAACATAAAT-TCGATTCACGATGTT
1 GATTCTGTAAGACCTCCAGACATGATTTCTAAGACCTCCGAACAT-AATCTCGATTCACGATGTT
* * * *
3475308 ATCCCGATCGATTTTTTATCTTTCAACTTGTGGTGTTATCCCAGTC
65 ATCCCGATCGATTCTTTATCTTTCAACTTGTGATGTTATCACAATC
*
3475354 GATTCTGTAAGACCTCCAGACATGATTTTGTAAGACCTCC
1 GATTCTGTAAGACCTCCAGACATGA-TTTCTAAGACCTCC
3475394 AGGCATGATT
Statistics
Matches: 129, Mismatches: 19, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
110 113 0.88
111 16 0.12
ACGTcount: A:0.25, C:0.23, G:0.17, T:0.36
Consensus pattern (110 bp):
GATTCTGTAAGACCTCCAGACATGATTTCTAAGACCTCCGAACATAATCTCGATTCACGATGTTA
TCCCGATCGATTCTTTATCTTTCAACTTGTGATGTTATCACAATC
Found at i:3475380 original size:23 final size:22
Alignment explanation
Indices: 3475354--3475415 Score: 88
Period size: 23 Copynumber: 2.7 Consensus size: 22
3475344 TATCCCAGTC
3475354 GATTCTGTAAGACCTCCAGACAT
1 GATT-TGTAAGACCTCCAGACAT
*
3475377 GATTTTGTAAGACCTCCAGGCAT
1 GA-TTTGTAAGACCTCCAGACAT
*
3475400 GATTTCTAAGACCTCC
1 GATTTGTAAGACCTCC
3475416 GGGTATAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
22 13 0.36
23 21 0.58
24 2 0.06
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (22 bp):
GATTTGTAAGACCTCCAGACAT
Found at i:3475390 original size:133 final size:133
Alignment explanation
Indices: 3475244--3475952 Score: 736
Period size: 133 Copynumber: 5.3 Consensus size: 133
3475234 TATCATAATC
* * * *
3475244 GATTCTGTAAGACCTCCGGGTATGATTTCTAAGACCTCCGAACATAAATTCGATTCACGATGTTA
1 GATTTTGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGAGCATAAATTCGATTCGCGATGTTA
* *
3475309 TCCCGATCGATTTTTTATCTTTCAACTTGTGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAGA
66 TCCCGATCGATTCTTTATCTTTCAACTTATGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAGA
3475374 CAT
131 CAT
* * * * *
3475377 GATTTTGTAAGACCTCCAGGCATGATTTCTAAGACCTCCGGGTATAATTTTGATTCGCGATGTTA
1 GATTTTGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGAGCATAAATTCGATTCGCGATGTTA
* * * ** * * *
3475442 TCCTGATCTATTTTTTATCTTTTGACTTACGGTGTTATCCCAGTTGATTCTGTAAGACCT-TAGG
66 TCCCGATCGATTCTTTATCTTTCAACTTATGGTGTTATCCCAGTCGATTCTGTAAGACCTCCA-G
*
3475506 ATAT
130 ACAT
* *
3475510 GATTTTGTAAGACCTCCGGGCATGATTTCTAAGACTTCC-AGGCAT-AATCTCAATTCGCGATGT
1 GATTTTGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGA-GCATAAAT-TCGATTCGCGATGT
* * * * *
3475573 TATCCTGATCAATTCTTTATCTTTCAACTTATGGTGTTATCCCAATTGATTTTGTAAGACCTCCA
64 TATCCCGATCGATTCTTTATCTTTCAACTTATGGTGTTATCCCAGTCGATTCTGTAAGACCTCCA
*
3475638 GACAC
129 GACAT
* * *
3475643 G-TTTCTGTAAGACCTTCGAGCATGATTTCTAAGACCTCCGAGCAT-AATCTCGATTCGCGGTGT
1 GATTT-TGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGAGCATAAAT-TCGATTCGCGATGT
* * * *
3475706 TATCCCGATCGATTCTTTATTTTTCAACTTATGGTGTTATCTCAATCAATTCTGTAAGACCTCC-
64 TATCCCGATCGATTCTTTATCTTTCAACTTATGGTGTTATCCCAGTCGATTCTGTAAGACCTCCA
3475770 GAACA-
129 G-ACAT
* * * * * * *
3475775 CATTTTTGTAAAACCTCCGAGCATGCTTTCTAAGACCTCCGAGCATAATTTCGATTTG-TAGTGT
1 GA-TTTTGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGAGCATAAATTCGATTCGCGA-TGT
* * ** * ** * * *
3475839 TATCCCAATTGATTCTTTAT-TTTTGACTTGTGGTGTTATTTC-GATCAATTCTGTAAGACTTTC
64 TATCCCGATCGATTCTTTATCTTTCAACTTATGGTGTTATCCCAG-TCGATTCTGTAAGACCTCC
*
3475902 GGACAT
128 AGACAT
* * * ** *
3475908 GATTCTCTAAGATCTCAAGGCATGATTTTTAAGACCTCCGAGCAT
1 GATTTTGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGAGCAT
3475953 GATTTCTAAG
Statistics
Matches: 488, Mismatches: 74, Indels: 29
0.83 0.13 0.05
Matches are distributed among these distances:
132 79 0.16
133 402 0.82
134 7 0.01
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.37
Consensus pattern (133 bp):
GATTTTGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGAGCATAAATTCGATTCGCGATGTTA
TCCCGATCGATTCTTTATCTTTCAACTTATGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAGA
CAT
Found at i:3475426 original size:22 final size:22
Alignment explanation
Indices: 3475361--3475426 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
3475351 GTCGATTCTG
* * *
3475361 TAAGACCTCCAGACATGATTTTG
1 TAAGACCTCCAGGCAT-AATTTC
*
3475384 TAAGACCTCCAGGCATGATTTC
1 TAAGACCTCCAGGCATAATTTC
* *
3475406 TAAGACCTCCGGGTATAATTT
1 TAAGACCTCCAGGCATAATTT
3475427 TGATTCGCGA
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
22 21 0.58
23 15 0.42
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.30
Consensus pattern (22 bp):
TAAGACCTCCAGGCATAATTTC
Found at i:3475553 original size:22 final size:23
Alignment explanation
Indices: 3475508--3475554 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
3475498 ACCTTAGGAT
* *
3475508 ATGATTTTGTAAGACCTCCGGGC
1 ATGATTTTCTAAGACCTCCAGGC
*
3475531 ATGA-TTTCTAAGACTTCCAGGC
1 ATGATTTTCTAAGACCTCCAGGC
3475553 AT
1 AT
3475555 AATCTCAATT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (23 bp):
ATGATTTTCTAAGACCTCCAGGC
Found at i:3475614 original size:266 final size:266
Alignment explanation
Indices: 3475244--3476318 Score: 1087
Period size: 266 Copynumber: 4.0 Consensus size: 266
3475234 TATCATAATC
* * * * *
3475244 GATTCTGTAAGACCTCCGGGTATGATTTCTAAGACCTCCGAACATAAATTCGATTCACGATGTTA
1 GATTTTGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGAGCATAATTTCGATTCGCGATGTTA
* *
3475309 TCCCGATCGATTTTTTATCTTTCAACTTGTGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAGA
66 TCCCAATCGATTCTTTATCTTTCAACTTGTGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAGA
* * *
3475374 CATGATTTTGTAAGACCTCC-AGGCATGATTTCTAAGACCTCCGGGTATAATTTTGATTCGCGAT
131 CATGATTTTGTAAGACCTCCGA-GCATGATTTCTAAGACCTCCGAGCATAATTTCGATTCGCGAT
* * * * * *
3475438 GTTATCCTGATCTATTTTTTATCTTTTGACTTACGGTGTTATCCCAGTTGATTCTGTAAGACCTT
195 GTTATCCTGATCGATTCTTTATCTTTCGACTTATGGTGTTATCCCAGTCGATTCTGTAAGACCTC
* *
3475503 AGGATAT
260 CGGACAT
* * *
3475510 GATTTTGTAAGACCTCCGGGCATGATTTCTAAGACTTCC-AGGCATAATCTCAATTCGCGATGTT
1 GATTTTGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGA-GCATAATTTCGATTCGCGATGTT
** * * * * *
3475574 ATCCTGATCAATTCTTTATCTTTCAACTTATGGTGTTATCCCAATTGATTTTGTAAGACCTCCAG
65 ATCCCAATCGATTCTTTATCTTTCAACTTGTGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAG
* * * *
3475639 ACACG-TTTCTGTAAGACCTTCGAGCATGATTTCTAAGACCTCCGAGCATAATCTCGATTCGCGG
130 ACATGATTT-TGTAAGACCTCCGAGCATGATTTCTAAGACCTCCGAGCATAATTTCGATTCGCGA
* * * * * *
3475703 TGTTATCCCGATCGATTCTTTATTTTTCAACTTATGGTGTTATCTCAATCAATTCTGTAAGACCT
194 TGTTATCCTGATCGATTCTTTATCTTTCGACTTATGGTGTTATCCCAGTCGATTCTGTAAGACCT
*
3475768 CCGAACA-
259 CCGGACAT
* * * * * *
3475775 CATTTTTGTAAAACCTCCGAGCATGCTTTCTAAGACCTCCGAGCATAATTTCGATTTG-TAGTGT
1 GA-TTTTGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGAGCATAATTTCGATTCGCGA-TGT
* ** ** *
3475839 TATCCCAATTGATTCTTTAT-TTTTGACTTGTGGTGTTATTTC-GATCAATTCTGTAAGACTTTC
64 TATCCCAATCGATTCTTTATCTTTCAACTTGTGGTGTTATCCCAG-TCGATTCTGTAAGA----C
* *
3475902 GGACATGATTCTCTAAGATCTCAAGGCATGATTTTTAAGACCTCCGAGCATGATTTCTAAGACCT
124 ---C-----TC-C--AGA---C-ATG-AT--TTTGTAAGACCTCCGAGCATGATTTCTAAGACCT
* * *
3475967 TCGAGCATAATTTCGATTCGC-AGTGTTATCCTGATAC-ATTCTTTATCTTTCGACTTGTGGTAT
171 CCGAGCATAATTTCGATTCGCGA-TGTTATCCTGAT-CGATTCTTTATCTTTCGACTTATGGTGT
* *
3476030 TATCCTAGTCGATTCTGTAAGACCTCCGGGCAT
234 TATCCCAGTCGATTCTGTAAGACCTCCGGACAT
* * *
3476063 GATTTTGTAAGACCTCTGGGCATGATTTCTAAGATCT-CTAGGCATAATTTCGATTCGCGATGTT
1 GATTTTGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGA-GCATAATTTCGATTCGCGATGTT
* * *
3476127 ATCCCAATCGATTTTTTATCTTTCGACTTGTGGTGTTATCCCAGTCGATTCTGTAAGACCTCCGG
65 ATCCCAATCGATTCTTTATCTTTCAACTTGTGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAG
* * * * *
3476192 GCATGATTCTATAAGACCTTCG-GACATGATTTCTAAGACCTCC-AGGCATAATTT-TATTCGCG
130 ACATGATTTTGTAAGACCTCCGAG-CATGATTTCTAAGACCTCCGA-GCATAATTTCGATTCGCG
* * * * * *
3476254 GTATTATCCTAATCGATTCTTTATCTTTCGACTTATGGTGTTATCCTAGTCGATTTTATAAGACC
193 ATGTTATCCTGATCGATTCTTTATCTTTCGACTTATGGTGTTATCCCAGTCGATTCTGTAAGACC
3476319 CTATGCATGA
Statistics
Matches: 662, Mismatches: 106, Indels: 83
0.78 0.12 0.10
Matches are distributed among these distances:
264 1 0.00
265 98 0.15
266 324 0.49
267 2 0.00
268 2 0.00
269 3 0.00
270 1 0.00
272 1 0.00
273 1 0.00
275 1 0.00
276 2 0.00
277 2 0.00
278 1 0.00
280 3 0.00
281 1 0.00
283 1 0.00
284 3 0.00
286 3 0.00
287 174 0.26
288 37 0.06
289 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (266 bp):
GATTTTGTAAGACCTCCGGGCATGATTTCTAAGACCTCCGAGCATAATTTCGATTCGCGATGTTA
TCCCAATCGATTCTTTATCTTTCAACTTGTGGTGTTATCCCAGTCGATTCTGTAAGACCTCCAGA
CATGATTTTGTAAGACCTCCGAGCATGATTTCTAAGACCTCCGAGCATAATTTCGATTCGCGATG
TTATCCTGATCGATTCTTTATCTTTCGACTTATGGTGTTATCCCAGTCGATTCTGTAAGACCTCC
GGACAT
Found at i:3475826 original size:22 final size:22
Alignment explanation
Indices: 3475760--3475826 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
3475750 ATCAATTCTG
* * * *
3475760 TAAGACCTCCGAACACATTTTTG
1 TAAGACCTCCGAGCATA-ATTTC
* **
3475783 TAAAACCTCCGAGCATGCTTTC
1 TAAGACCTCCGAGCATAATTTC
3475805 TAAGACCTCCGAGCATAATTTC
1 TAAGACCTCCGAGCATAATTTC
3475827 GATTTGTAGT
Statistics
Matches: 35, Mismatches: 9, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
22 22 0.63
23 13 0.37
ACGTcount: A:0.30, C:0.28, G:0.13, T:0.28
Consensus pattern (22 bp):
TAAGACCTCCGAGCATAATTTC
Found at i:3475952 original size:22 final size:22
Alignment explanation
Indices: 3475905--3475980 Score: 82
Period size: 22 Copynumber: 3.4 Consensus size: 22
3475895 GACTTTCGGA
* *
3475905 CATGATTCTCTAAGATCT-CAAGG
1 CATGATT-TCTAAGACCTCCGA-G
*
3475928 CATGATTTTTAAGACCTCCGAG
1 CATGATTTCTAAGACCTCCGAG
*
3475950 CATGATTTCTAAGACCTTCGAG
1 CATGATTTCTAAGACCTCCGAG
*
3475972 CATAATTTC
1 CATGATTTC
3475981 GATTCGCAGT
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
22 37 0.80
23 9 0.20
ACGTcount: A:0.29, C:0.22, G:0.16, T:0.33
Consensus pattern (22 bp):
CATGATTTCTAAGACCTCCGAG
Found at i:3475972 original size:154 final size:155
Alignment explanation
Indices: 3475778--3476096 Score: 399
Period size: 154 Copynumber: 2.1 Consensus size: 155
3475768 CCGAACACAT
* * * *
3475778 TTTTGTAAAACCTCCGAGCATGCTTTCTAAGACCTCCGAGCATAATTTCGATTTGTAGTGTTATC
1 TTTT-TAAGACCTCCGAGCATGATTTCTAAGACCTCCGAGCATAATTTCGATTCGCAGTGTTATC
** * * * * *
3475843 CCAATTGATTCTTTAT-TTTTGACTTGTGGTGTTATTTCGA-TCAATTCTGTAAGACTTTCGGAC
65 CCAATACATTCTTTATCTTTCGACTTGTGGTATTA-TCCGAGTCAATTCTGTAAGACCTCCGGAC
*
3475906 ATGATTCTCTAAGATCTCAAGGCATGA
129 ATGATTCTCTAAGACCTCAAGGCATGA
*
3475933 TTTTTAAGACCTCCGAGCATGATTTCTAAGACCTTCGAGCATAATTTCGATTCGCAGTGTTATCC
1 TTTTTAAGACCTCCGAGCATGATTTCTAAGACCTCCGAGCATAATTTCGATTCGCAGTGTTATCC
** * * *
3475998 TGATACATTCTTTATCTTTCGACTTGTGGTATTATCCTAGTCGATTCTGTAAGACCTCCGGGCAT
66 CAATACATTCTTTATCTTTCGACTTGTGGTATTATCCGAGTCAATTCTGTAAGACCTCCGGACAT
* * **
3476063 GATTTTGTAAGACCTCTGGGCATGA
131 GATTCTCTAAGACCTCAAGGCATGA
*
3476088 TTTCTAAGA
1 TTTTTAAGA
3476097 TCTCTAGGCA
Statistics
Matches: 139, Mismatches: 23, Indels: 4
0.84 0.14 0.02
Matches are distributed among these distances:
154 70 0.50
155 69 0.50
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (155 bp):
TTTTTAAGACCTCCGAGCATGATTTCTAAGACCTCCGAGCATAATTTCGATTCGCAGTGTTATCC
CAATACATTCTTTATCTTTCGACTTGTGGTATTATCCGAGTCAATTCTGTAAGACCTCCGGACAT
GATTCTCTAAGACCTCAAGGCATGA
Found at i:3476071 original size:23 final size:23
Alignment explanation
Indices: 3476040--3476090 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
3476030 TATCCTAGTC
*
3476040 GATTCTGTAAGACCTCCGGGCAT
1 GATTTTGTAAGACCTCCGGGCAT
*
3476063 GATTTTGTAAGACCTCTGGGCAT
1 GATTTTGTAAGACCTCCGGGCAT
3476086 GATTT
1 GATTT
3476091 CTAAGATCTC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.33
Consensus pattern (23 bp):
GATTTTGTAAGACCTCCGGGCAT
Found at i:3476101 original size:22 final size:22
Alignment explanation
Indices: 3476047--3476113 Score: 80
Period size: 22 Copynumber: 3.0 Consensus size: 22
3476037 GTCGATTCTG
* *
3476047 TAAGACCTCCGGGCATGATTTTG
1 TAAGACCTCTGGGCATGA-TTTC
3476070 TAAGACCTCTGGGCATGATTTC
1 TAAGACCTCTGGGCATGATTTC
* * *
3476092 TAAGATCTCTAGGCATAATTTC
1 TAAGACCTCTGGGCATGATTTC
3476114 GATTCGCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
22 22 0.56
23 17 0.44
ACGTcount: A:0.25, C:0.21, G:0.21, T:0.33
Consensus pattern (22 bp):
TAAGACCTCTGGGCATGATTTC
Found at i:3476108 original size:133 final size:131
Alignment explanation
Indices: 3475908--3476318 Score: 533
Period size: 133 Copynumber: 3.1 Consensus size: 131
3475898 TTTCGGACAT
* * ** * * *
3475908 GATTCTCTAAGATCTCAAGGCATGATTTTTAAGACCTCCGAGCATGATTTCTAAGACCT-TCGAG
1 GATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTCTGGGCATGATTTCTAAGACCTCTAG-G
* *
3475972 CATAATTTCGATTCGCAGTGTTATCCTGATAC-ATTCTTTATCTTTCGACTTGTGGTATTATCCT
65 CATAATTTCGATTCGC-GTGTTATCCTAAT-CGATTCTTTATCTTTCGACTTGTGGTGTTATCCT
3476036 AGTC
128 AGTC
*
3476040 GATTCTGTAAGACCTCCGGGCATGATTTTGTAAGACCTCTGGGCATGATTTCTAAGATCTCTAGG
1 GATTCTGTAAGACCTCCGGGCATGATTTT-TAAGACCTCTGGGCATGATTTCTAAGACCTCTAGG
* * *
3476105 CATAATTTCGATTCGCGATGTTATCCCAATCGATTTTTTATCTTTCGACTTGTGGTGTTATCCCA
65 CATAATTTCGATTCGCG-TGTTATCCTAATCGATTCTTTATCTTTCGACTTGTGGTGTTATCCTA
3476170 GTC
129 GTC
* * *
3476173 GATTCTGTAAGACCTCCGGGCATGATTCTATAAGACCT-TCGGACATGATTTCTAAGACCTCCAG
1 GATTCTGTAAGACCTCCGGGCATGATT-TTTAAGACCTCT-GGGCATGATTTCTAAGACCTCTAG
* * *
3476237 GCATAATTT-TATTCGCGGTATTATCCTAATCGATTCTTTATCTTTCGACTTATGGTGTTATCCT
64 GCATAATTTCGATTCGC-GTGTTATCCTAATCGATTCTTTATCTTTCGACTTGTGGTGTTATCCT
3476301 AGTC
128 AGTC
* *
3476305 GATTTTATAAGACC
1 GATTCTGTAAGACC
3476319 CTATGCATGA
Statistics
Matches: 247, Mismatches: 25, Indels: 14
0.86 0.09 0.05
Matches are distributed among these distances:
132 91 0.37
133 153 0.62
134 3 0.01
ACGTcount: A:0.23, C:0.21, G:0.18, T:0.37
Consensus pattern (131 bp):
GATTCTGTAAGACCTCCGGGCATGATTTTTAAGACCTCTGGGCATGATTTCTAAGACCTCTAGGC
ATAATTTCGATTCGCGTGTTATCCTAATCGATTCTTTATCTTTCGACTTGTGGTGTTATCCTAGT
C
Found at i:3476113 original size:155 final size:154
Alignment explanation
Indices: 3475787--3476113 Score: 370
Period size: 155 Copynumber: 2.1 Consensus size: 154
3475777 TTTTTGTAAA
* ** * * **
3475787 ACCTCCGAGCATGCTTTCTAAGACCTCCGAGCATAATTTCGATTTGTAGTGTTATCCCAATTGAT
1 ACCTCAGAGCATAATTTCTAAGACCTCCGAGCATAATTTCGATTCGCAGTGTTATCCCAATACAT
* * * * * *
3475852 TCTTTATTTTTGACTTGTGGTGTTATTTCGATCAATTCTGTAAGACTTTCGGACATGATTCTCTA
66 TCTTTATTTTCGACTTGTGGTATTATCTAGATCAATTCTGTAAGACCTCCGGACATGATTCTCTA
* *
3475917 AGATCTCAAGGCATGATTTTTAAG
131 AGACCTCAAGGCATGATTTCTAAG
* * * **
3475941 ACCTCCGAGCATGATTTCTAAGACCTTCGAGCATAATTTCGATTCGCAGTGTTATCCTGATACAT
1 ACCTCAGAGCATAATTTCTAAGACCTCCGAGCATAATTTCGATTCGCAGTGTTATCCCAATACAT
* * * *
3476006 TCTTTATCTTTCGACTTGTGGTATTATCCTAG-TCGATTCTGTAAGACCTCCGGGCATGATTTTG
66 TCTTTAT-TTTCGACTTGTGGTATTAT-CTAGATCAATTCTGTAAGACCTCCGGACATGATTCTC
**
3476070 TAAGACCTCTGGGCATGATTTCTAAG
129 TAAGACCTCAAGGCATGATTTCTAAG
*
3476096 ATCTCTAG-GCATAATTTC
1 ACCTC-AGAGCATAATTTC
3476114 GATTCGCGAT
Statistics
Matches: 145, Mismatches: 25, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
154 64 0.44
155 78 0.54
156 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.18, T:0.38
Consensus pattern (154 bp):
ACCTCAGAGCATAATTTCTAAGACCTCCGAGCATAATTTCGATTCGCAGTGTTATCCCAATACAT
TCTTTATTTTCGACTTGTGGTATTATCTAGATCAATTCTGTAAGACCTCCGGACATGATTCTCTA
AGACCTCAAGGCATGATTTCTAAG
Found at i:3476206 original size:23 final size:23
Alignment explanation
Indices: 3476173--3476240 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
3476163 TATCCCAGTC
*
3476173 GATTCTGTAAGACCTCCGGGCAT
1 GATTCTATAAGACCTCCGGGCAT
* *
3476196 GATTCTATAAGACCTTCGGACAT
1 GATTCTATAAGACCTCCGGGCAT
* *
3476219 GATT-TCTAAGACCTCCAGGCAT
1 GATTCTATAAGACCTCCGGGCAT
3476241 AATTTTATTC
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
22 14 0.37
23 24 0.63
ACGTcount: A:0.26, C:0.25, G:0.21, T:0.28
Consensus pattern (23 bp):
GATTCTATAAGACCTCCGGGCAT
Found at i:3476245 original size:22 final size:21
Alignment explanation
Indices: 3476180--3476245 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 21
3476170 GTCGATTCTG
3476180 TAAGACCTCCGGGCATGATTCTA
1 TAAGACCTCC-GGCATGATT-TA
* *
3476203 TAAGACCTTCGGACATGATTTC
1 TAAGACCTCCGG-CATGATTTA
*
3476225 TAAGACCTCCAGGCATAATTT
1 TAAGACCTCC-GGCATGATTT
3476246 TATTCGCGGT
Statistics
Matches: 37, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
22 19 0.51
23 18 0.49
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (21 bp):
TAAGACCTCCGGCATGATTTA
Found at i:3476296 original size:420 final size:421
Alignment explanation
Indices: 3475508--3476297 Score: 1017
Period size: 420 Copynumber: 1.9 Consensus size: 421
3475498 ACCTTAGGAT
*
3475508 ATGATTTTGTAAGACCTCCGGGCATGATTTCTAAGACTTCCAGGCATAATCTCAATTCGCGATGT
1 ATGATTTTGTAAGACCTCCGAGCATGATTTCTAAGACTTCCAGGCATAATCTCAATTCGCGATGT
* * *
3475573 TATCCTGATCAATTCTTTATCTTTCAACTTATGGTGTTATCCCAATTGATTTTGTAAGACCTCCA
66 TATCCTGATCAATTCTTTATCTTTCAACTTATGGTATTATCCCAATCGATTCTGTAAGACCTCCA
* *
3475638 GACACGTTTCTGTAAGACCTTCGAGCATGATTTCTAAGACCTCCGAGCATAATCTCGATTCGCGG
131 GACACGTTTCTGTAAGACCTTCGAGCATGATTTCTAAGACCTCAGAGCATAATCTCGATTCGCGA
* * *
3475703 TGTTATCCCGATCGATTCTTTATTTTTCAACTTATGGTGTTATCTCAATCAATTCTGTAAGACCT
196 TGTTATCCCAATCGATTCTTTATCTTTCAACTTATGGTGTTATCCCAATCAATTCTGTAAGACCT
* * * *
3475768 CCGAACACATTTTTGTAAAACCTCCGAGCATGCTTTCTAAGACCTCCGAGCATAATTTCGATTTG
261 CCGAACACATTTCTATAAAACCTCCGAGCATGATTTCTAAGACCTCCGAGCATAATTTCGATTCG
* * * * *
3475833 TAGTGTTATCCCAATTGATTCTTTATTTTTGACTTGTGGTGTTATTTCGATCAATTCTGTAAGAC
326 CAGTATTATCCCAATCGATTCTTTATTTTCGACTTATGGTGTTATTTCGATCAATTCTGTAAGAC
3475898 TTTCGGACATGATTCTCTAAGATCTCAAGGC
391 TTTCGGACATGATTCTCTAAGATCTCAAGGC
* * *
3475929 ATGATTTT-TAAGACCTCCGAGCATGATTTCTAAGACCTTCGA-GCATAATTTCGATTCGC-AGT
1 ATGATTTTGTAAGACCTCCGAGCATGATTTCTAAGA-CTTCCAGGCATAATCTCAATTCGCGA-T
* * * *
3475991 GTTATCCTGAT-ACATTCTTTATCTTTCGACTTGTGGTATTATCCTAGTCGATTCTGTAAGACCT
64 GTTATCCTGATCA-ATTCTTTATCTTTCAACTTATGGTATTATCCCAATCGATTCTGTAAGACCT
* * * * * *
3476055 CCGGGCATGATTT-TGTAAGACC-TCTGGGCATGATTTCTAAGATCTCTAG-GCATAATTTCGAT
128 CCAGACACG-TTTCTGTAAGACCTTC-GAGCATGATTTCTAAGACCTC-AGAGCATAATCTCGAT
* * * * *
3476117 TCGCGATGTTATCCCAATCGATTTTTTATCTTTCGACTTGTGGTGTTATCCCAGTCGATTCTGTA
190 TCGCGATGTTATCCCAATCGATTCTTTATCTTTCAACTTATGGTGTTATCCCAATCAATTCTGTA
** * * *
3476182 AGACCTCCGGGCATGA-TTCTATAAGACCTTCG-GACATGATTTCTAAGACCTCC-AGGCATAAT
255 AGACCTCCGAACA-CATTTCTATAAAACCTCCGAG-CATGATTTCTAAGACCTCCGA-GCATAAT
* * *
3476244 TT-TATTCGCGGTATTATCCTAATCGATTCTTTATCTTTCGACTTATGGTGTTAT
317 TTCGATTCGCAGTATTATCCCAATCGATTCTTTAT-TTTCGACTTATGGTGTTAT
3476298 CCTAGTCGAT
Statistics
Matches: 315, Mismatches: 44, Indels: 21
0.83 0.12 0.06
Matches are distributed among these distances:
419 31 0.10
420 266 0.84
421 18 0.06
ACGTcount: A:0.24, C:0.21, G:0.17, T:0.38
Consensus pattern (421 bp):
ATGATTTTGTAAGACCTCCGAGCATGATTTCTAAGACTTCCAGGCATAATCTCAATTCGCGATGT
TATCCTGATCAATTCTTTATCTTTCAACTTATGGTATTATCCCAATCGATTCTGTAAGACCTCCA
GACACGTTTCTGTAAGACCTTCGAGCATGATTTCTAAGACCTCAGAGCATAATCTCGATTCGCGA
TGTTATCCCAATCGATTCTTTATCTTTCAACTTATGGTGTTATCCCAATCAATTCTGTAAGACCT
CCGAACACATTTCTATAAAACCTCCGAGCATGATTTCTAAGACCTCCGAGCATAATTTCGATTCG
CAGTATTATCCCAATCGATTCTTTATTTTCGACTTATGGTGTTATTTCGATCAATTCTGTAAGAC
TTTCGGACATGATTCTCTAAGATCTCAAGGC
Found at i:3476519 original size:110 final size:110
Alignment explanation
Indices: 3476323--3476523 Score: 271
Period size: 110 Copynumber: 1.8 Consensus size: 110
3476313 AAGACCCTAT
* * *
3476323 GCATGATGTCTAAGACCTCCGAGCATAAATTCAATTCGTGATGTTATCCTGATCGATTCCTTATT
1 GCATGATGTCTAAGACCTCCAAGCATAAATTCAATTCGTGATGTTATCCTGATCAATTCATTATT
* *
3476388 TTTTAACTTGCAGTATTATCCCAATCAATTCTGTAAGACCTCCGG
66 TTTTAACTTACAGTATCATCCCAATCAATTCTGTAAGACCTCCGG
* * *
3476433 GCATGATTTGTAAGACCTTCAAGCATAAATTCAATTCGT-ATTGTTAT-CTCGATCAATTCATTA
1 GCATGATGTCTAAGACCTCCAAGCATAAATTCAATTCGTGA-TGTTATCCT-GATCAATTCATTA
* * *
3476496 TTTTTTGACTTACGGTGTCATCCCAATC
64 TTTTTTAACTTACAGTATCATCCCAATC
3476524 GTTTTGTGTT
Statistics
Matches: 78, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
109 3 0.04
110 75 0.96
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.37
Consensus pattern (110 bp):
GCATGATGTCTAAGACCTCCAAGCATAAATTCAATTCGTGATGTTATCCTGATCAATTCATTATT
TTTTAACTTACAGTATCATCCCAATCAATTCTGTAAGACCTCCGG
Found at i:3476687 original size:9 final size:9
Alignment explanation
Indices: 3476669--3476719 Score: 59
Period size: 9 Copynumber: 5.8 Consensus size: 9
3476659 TCGTTTTACT
3476669 ATAATATTA
1 ATAATATTA
*
3476678 ATAATTTTA
1 ATAATATTA
*
3476687 ATAATAATA
1 ATAATATTA
*
3476696 ATAATAATA
1 ATAATATTA
3476705 ATAAT-TTA
1 ATAATATTA
*
3476713 AAAATAT
1 ATAATAT
3476720 AATTATTAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
8 6 0.17
9 30 0.83
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (9 bp):
ATAATATTA
Found at i:3476691 original size:3 final size:3
Alignment explanation
Indices: 3476669--3476709 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
3476659 TCGTTTTACT
* * *
3476669 ATA ATA TTA ATA ATT TTA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
3476710 TTAAAAATAT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (3 bp):
ATA
Found at i:3478231 original size:16 final size:16
Alignment explanation
Indices: 3478221--3478319 Score: 76
Period size: 16 Copynumber: 6.1 Consensus size: 16
3478211 AAAACTCCTG
3478221 AAATCCGAAACCCCTA
1 AAATCCGAAACCCCTA
*
3478237 AAATCCTAAACCCCTAA
1 AAATCCGAAACCCCT-A
* * *
3478254 AAATCCAAAATCCCTT
1 AAATCCGAAACCCCTA
* *
3478270 AAAT-CTAAACCCTTAA
1 AAATCCGAAACCCCT-A
*
3478286 AAATCCAAAACCCCCTA
1 AAATCCGAAA-CCCCTA
* *
3478303 AAATTC-AAACCCGTA
1 AAATCCGAAACCCCTA
3478318 AA
1 AA
3478320 TCAAAACCAC
Statistics
Matches: 67, Mismatches: 12, Indels: 9
0.76 0.14 0.10
Matches are distributed among these distances:
15 14 0.21
16 25 0.37
17 24 0.36
18 4 0.06
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.18
Consensus pattern (16 bp):
AAATCCGAAACCCCTA
Found at i:3478258 original size:33 final size:32
Alignment explanation
Indices: 3478221--3478319 Score: 119
Period size: 33 Copynumber: 3.0 Consensus size: 32
3478211 AAAACTCCTG
*
3478221 AAATCCGAAACCCCTAAAATCCTAAACCCCTAA
1 AAATCCAAAACCCCTAAAAT-CTAAACCCCTAA
* * *
3478254 AAATCCAAAATCCCTTAAATCTAAACCCTTAA
1 AAATCCAAAACCCCTAAAATCTAAACCCCTAA
*
3478286 AAATCCAAAACCCCCTAAAAT-TCAAACCCGTAA
1 AAATCCAAAA-CCCCTAAAATCT-AAACCCCTAA
3478319 A
1 A
3478320 TCAAAACCAC
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
32 22 0.39
33 35 0.61
ACGTcount: A:0.47, C:0.32, G:0.02, T:0.18
Consensus pattern (32 bp):
AAATCCAAAACCCCTAAAATCTAAACCCCTAA
Found at i:3478287 original size:32 final size:33
Alignment explanation
Indices: 3478221--3478304 Score: 116
Period size: 32 Copynumber: 2.6 Consensus size: 33
3478211 AAAACTCCTG
* *
3478221 AAATCCGAAACCCCTAAAATCCTAAACCCCTAA
1 AAATCCAAAACCCCTTAAATCCTAAACCCCTAA
* *
3478254 AAATCCAAAATCCCTTAAAT-CTAAACCCTTAA
1 AAATCCAAAACCCCTTAAATCCTAAACCCCTAA
*
3478286 AAATCCAAAACCCCCTAAA
1 AAATCCAAAACCCCTTAAA
3478305 ATTCAAACCC
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
32 28 0.62
33 17 0.38
ACGTcount: A:0.48, C:0.33, G:0.01, T:0.18
Consensus pattern (33 bp):
AAATCCAAAACCCCTTAAATCCTAAACCCCTAA
Found at i:3478370 original size:37 final size:38
Alignment explanation
Indices: 3478344--3478429 Score: 133
Period size: 37 Copynumber: 2.3 Consensus size: 38
3478334 CTTAAATTTT
3478344 AAAA-CCGAAACCCTAAAATCTTCAAA-CTCTAAAATC
1 AAAACCCGAAACCCTAAAATCTTCAAACCTCTAAAATC
*
3478380 AAAACCCTAAACCCTAAAATCTTCAAA-CTCTAAAATC
1 AAAACCCGAAACCCTAAAATCTTCAAACCTCTAAAATC
*
3478417 AAAACCCTAAACC
1 AAAACCCGAAACC
3478430 TTCCATACCC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
36 4 0.08
37 44 0.92
ACGTcount: A:0.50, C:0.30, G:0.01, T:0.19
Consensus pattern (38 bp):
AAAACCCGAAACCCTAAAATCTTCAAACCTCTAAAATC
Found at i:3478375 original size:16 final size:16
Alignment explanation
Indices: 3478351--3478446 Score: 54
Period size: 16 Copynumber: 5.8 Consensus size: 16
3478341 TTTAAAACCG
3478351 AAACCCTAAAATCTTC
1 AAACCCTAAAATCTTC
* **
3478367 AAACTCTAAAATCAAAACCC
1 AAACCCTAAAATC----TTC
3478387 TAAACCCTAAAATCTTC
1 -AAACCCTAAAATCTTC
* *
3478404 AAACTCTAAAATC--A
1 AAACCCTAAAATCTTC
*
3478418 AAACCCT-AAACCTTCC
1 AAACCCTAAAATCTT-C
*
3478434 ATACCCTAAAATC
1 AAACCCTAAAATC
3478447 CAAGCCTTAA
Statistics
Matches: 58, Mismatches: 13, Indels: 17
0.66 0.15 0.19
Matches are distributed among these distances:
13 4 0.07
14 6 0.10
16 30 0.52
17 5 0.09
20 1 0.02
21 12 0.21
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (16 bp):
AAACCCTAAAATCTTC
Found at i:3495268 original size:19 final size:21
Alignment explanation
Indices: 3495230--3495269 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
3495220 TTCTTAAAAT
3495230 AAATCTAAAATTTGAGTTTAA
1 AAATCTAAAATTTGAGTTTAA
3495251 AAATC-AAAATTTGA-TTTAA
1 AAATCTAAAATTTGAGTTTAA
3495270 TAAACGGATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.26
20 9 0.47
21 5 0.26
ACGTcount: A:0.50, C:0.05, G:0.07, T:0.38
Consensus pattern (21 bp):
AAATCTAAAATTTGAGTTTAA
Found at i:3496268 original size:15 final size:16
Alignment explanation
Indices: 3496245--3496278 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
3496235 TTATTCAATT
3496245 AAATATTTA-ATTTTA
1 AAATATTTATATTTTA
*
3496260 AAATTTTTATATTTTA
1 AAATATTTATATTTTA
3496276 AAA
1 AAA
3496279 AATTAAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
AAATATTTATATTTTA
Found at i:3497553 original size:22 final size:22
Alignment explanation
Indices: 3497525--3497572 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
3497515 AATTTAGGCT
3497525 TTTATTATATTGTTTATATGAC
1 TTTATTATATTGTTTATATGAC
* * *
3497547 TTTATTATATTTTTTATTTGGC
1 TTTATTATATTGTTTATATGAC
3497569 TTTA
1 TTTA
3497573 AGGTTGGAAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.23, C:0.04, G:0.08, T:0.65
Consensus pattern (22 bp):
TTTATTATATTGTTTATATGAC
Found at i:3499245 original size:10 final size:10
Alignment explanation
Indices: 3499232--3499257 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
3499222 TAAAACGTAC
3499232 AAAAATAATA
1 AAAAATAATA
3499242 AAAAATAATA
1 AAAAATAATA
3499252 AAAAAT
1 AAAAAT
3499258 GTGAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (10 bp):
AAAAATAATA
Found at i:3500584 original size:7 final size:7
Alignment explanation
Indices: 3500572--3500600 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
3500562 ATATATTATG
3500572 TATGATT
1 TATGATT
3500579 TATGATT
1 TATGATT
3500586 TATGATT
1 TATGATT
3500593 TATGATT
1 TATGATT
3500600 T
1 T
3500601 TTCATAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.28, C:0.00, G:0.14, T:0.59
Consensus pattern (7 bp):
TATGATT
Found at i:3500708 original size:25 final size:24
Alignment explanation
Indices: 3500678--3500734 Score: 78
Period size: 25 Copynumber: 2.3 Consensus size: 24
3500668 ATTTTCTCTC
3500678 AATTTAAATTTACACACATATCTTT
1 AATTTAAATTTACACACATATC-TT
* * *
3500703 AATTTAGATTTATACACATCTCTT
1 AATTTAAATTTACACACATATCTT
3500727 AATTTAAA
1 AATTTAAA
3500735 ATTAAACAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.44
Consensus pattern (24 bp):
AATTTAAATTTACACACATATCTT
Found at i:3502869 original size:4 final size:4
Alignment explanation
Indices: 3502860--3502905 Score: 83
Period size: 4 Copynumber: 11.5 Consensus size: 4
3502850 GTCTACTTTT
*
3502860 TATG TATG TATG TATA TATG TATG TATG TATG TATG TATG TATG TA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TA
3502906 CATATTCTTG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 40 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.50
Consensus pattern (4 bp):
TATG
Found at i:3505090 original size:18 final size:17
Alignment explanation
Indices: 3505067--3505106 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3505057 AGAAGAATTG
*
3505067 AAAAATTCCATAAAAACC
1 AAAAATT-CAAAAAAACC
*
3505085 AAAAATTGAAAAAAACC
1 AAAAATTCAAAAAAACC
3505102 AAAAA
1 AAAAA
3505107 GAGAAAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.70, C:0.15, G:0.03, T:0.12
Consensus pattern (17 bp):
AAAAATTCAAAAAAACC
Found at i:3505112 original size:17 final size:17
Alignment explanation
Indices: 3505078--3505113 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3505068 AAAATTCCAT
**
3505078 AAAAACCAAAAATTGAA
1 AAAAACCAAAAAGAGAA
3505095 AAAAACCAAAAAGAGAA
1 AAAAACCAAAAAGAGAA
3505112 AA
1 AA
3505114 CTAAAACATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.75, C:0.11, G:0.08, T:0.06
Consensus pattern (17 bp):
AAAAACCAAAAAGAGAA
Found at i:3505119 original size:23 final size:23
Alignment explanation
Indices: 3505093--3505137 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
3505083 CCAAAAATTG
*
3505093 AAAAAAACCAAAAAGAGAAAACT
1 AAAAAAACCAAAAAGAAAAAACT
* * *
3505116 AAAACATCCAAAATGAAAAAAC
1 AAAAAAACCAAAAAGAAAAAAC
3505138 CATAAAGGAG
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.71, C:0.16, G:0.07, T:0.07
Consensus pattern (23 bp):
AAAAAAACCAAAAAGAAAAAACT
Found at i:3509359 original size:25 final size:25
Alignment explanation
Indices: 3509309--3509359 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
3509299 GAAAAAAATG
*
3509309 AAAATCCAAAAAATCTAAATATAAA
1 AAAATCCAAAAAATCTAAAGATAAA
*
3509334 AAAATCCAAAAAAATTTAAAGA-AAA
1 AAAATCC-AAAAAATCTAAAGATAAA
3509359 A
1 A
3509360 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 11 0.48
26 12 0.52
ACGTcount: A:0.71, C:0.10, G:0.02, T:0.18
Consensus pattern (25 bp):
AAAATCCAAAAAATCTAAAGATAAA
Found at i:3515842 original size:3 final size:3
Alignment explanation
Indices: 3515829--3515866 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
3515819 AGTATAAGAA
* *
3515829 GAT GAT AAT GAT GAT GAT GAT GAT GAT GAT GAC GAT GA
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GA
3515867 AAAGGAAGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.37, C:0.03, G:0.32, T:0.29
Consensus pattern (3 bp):
GAT
Found at i:3518719 original size:21 final size:21
Alignment explanation
Indices: 3518693--3518748 Score: 58
Period size: 21 Copynumber: 2.7 Consensus size: 21
3518683 AAAATTTAGA
3518693 TTTTACTGACAAAATTCTCAC
1 TTTTACTGACAAAATTCTCAC
* ***
3518714 TTTTACTTATGGAATTCTCAC
1 TTTTACTGACAAAATTCTCAC
* *
3518735 TTTCATTGACAAAA
1 TTTTACTGACAAAA
3518749 ATCAACTTTT
Statistics
Matches: 25, Mismatches: 10, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.32, C:0.20, G:0.07, T:0.41
Consensus pattern (21 bp):
TTTTACTGACAAAATTCTCAC
Found at i:3519395 original size:26 final size:26
Alignment explanation
Indices: 3519366--3519415 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
3519356 ACAATTTTTC
**
3519366 TAAATTCCTTCTATATATATATATAT
1 TAAATTCCACCTATATATATATATAT
3519392 TAAATTCCACCTATATATATATAT
1 TAAATTCCACCTATATATATATAT
3519416 TGAGGAATTA
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:0.40, C:0.14, G:0.00, T:0.46
Consensus pattern (26 bp):
TAAATTCCACCTATATATATATATAT
Found at i:3520356 original size:24 final size:22
Alignment explanation
Indices: 3520309--3520366 Score: 66
Period size: 24 Copynumber: 2.6 Consensus size: 22
3520299 CTAAACATGC
*
3520309 ATAAGAATAAATAAACTAGTAA
1 ATAAGAATAAATAAACTAGAAA
3520331 ATAAGCAAGTAAATAAA-TAGAAAA
1 ATAAG-AA-TAAATAAACTAG-AAA
3520355 ATAA-AATAAATA
1 ATAAGAATAAATA
3520367 GATTAAAAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
21 6 0.19
22 7 0.22
23 5 0.16
24 14 0.44
ACGTcount: A:0.67, C:0.03, G:0.09, T:0.21
Consensus pattern (22 bp):
ATAAGAATAAATAAACTAGAAA
Found at i:3526984 original size:24 final size:23
Alignment explanation
Indices: 3526932--3526984 Score: 54
Period size: 24 Copynumber: 2.3 Consensus size: 23
3526922 GGTTTAAGGC
*
3526932 TGGGTT-TTTTTTGTAGTTTTTT
1 TGGGTTCTTTCTTGTAGTTTTTT
** *
3526954 TTTGTTCTTTCTTGTTGTATTTTT
1 TGGGTTCTTTCTTGTAGT-TTTTT
3526978 TGGGTTC
1 TGGGTTC
3526985 AAAGGGCTAT
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
22 4 0.17
23 9 0.39
24 10 0.43
ACGTcount: A:0.04, C:0.06, G:0.21, T:0.70
Consensus pattern (23 bp):
TGGGTTCTTTCTTGTAGTTTTTT
Found at i:3528310 original size:16 final size:15
Alignment explanation
Indices: 3528286--3528321 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
3528276 TTATTTTTCC
3528286 TTTTTTGTAATTTAA
1 TTTTTTGTAATTTAA
3528301 TTTTTGTGTAATTTAA
1 TTTTT-TGTAATTTAA
3528317 TTTTT
1 TTTTT
3528322 AATTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.22, C:0.00, G:0.08, T:0.69
Consensus pattern (15 bp):
TTTTTTGTAATTTAA
Found at i:3528641 original size:6 final size:6
Alignment explanation
Indices: 3528632--3528726 Score: 95
Period size: 6 Copynumber: 15.0 Consensus size: 6
3528622 TTTGATCTTG
*
3528632 GTTTTT GTTTTT GGTTTTT GTTGTTT -TTTTT -TTTCTT GATTTTT GTTGTT
1 GTTTTT GTTTTT -GTTTTT GTT-TTT GTTTTT GTTT-TT G-TTTTT GTTTTT
*
3528682 GTTGTT GTCTTTT GTTTTTT GTTTTTT GTTTTT GTTTTT GTTTTT
1 GTTTTT GT-TTTT G-TTTTT G-TTTTT GTTTTT GTTTTT GTTTTT
3528727 TGTTAATTAA
Statistics
Matches: 80, Mismatches: 2, Indels: 14
0.83 0.02 0.15
Matches are distributed among these distances:
5 6 0.08
6 42 0.52
7 28 0.35
8 4 0.05
ACGTcount: A:0.01, C:0.02, G:0.18, T:0.79
Consensus pattern (6 bp):
GTTTTT
Found at i:3528643 original size:7 final size:7
Alignment explanation
Indices: 3528633--3528730 Score: 87
Period size: 7 Copynumber: 14.1 Consensus size: 7
3528623 TTGATCTTGG
3528633 TTTTTGT
1 TTTTTGT
*
3528640 TTTTGGTT
1 TTTTTG-T
3528648 TTTGTTGT
1 TTT-TTGT
*
3528656 TTTTTTT
1 TTTTTGT
*
3528663 TTTCTTGA
1 TTT-TTGT
3528671 TTTTTG-
1 TTTTTGT
*
3528677 TTGTTG-
1 TTTTTGT
*
3528683 TTGTTGT
1 TTTTTGT
*
3528690 CTTTTGT
1 TTTTTGT
3528697 TTTTTGT
1 TTTTTGT
3528704 TTTTTG-
1 TTTTTGT
3528710 TTTTTG-
1 TTTTTGT
3528716 TTTTTGT
1 TTTTTGT
3528723 TTTTTGT
1 TTTTTGT
3528730 T
1 T
3528731 AATTAATAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
6 23 0.30
7 39 0.51
8 13 0.17
9 2 0.03
ACGTcount: A:0.01, C:0.02, G:0.17, T:0.80
Consensus pattern (7 bp):
TTTTTGT
Found at i:3528645 original size:13 final size:13
Alignment explanation
Indices: 3528629--3528730 Score: 95
Period size: 13 Copynumber: 7.9 Consensus size: 13
3528619 TATTTTGATC
3528629 TTGGTTTTTGTTT
1 TTGGTTTTTGTTT
3528642 TTGGTTTTTGTTGT
1 TTGGTTTTTGTT-T
3528656 TT--TTTTT-TTT
1 TTGGTTTTTGTTT
* *
3528666 CTTGATTTTTGTTG
1 -TTGGTTTTTGTTT
*
3528680 TT-GTTGTTGTCTT
1 TTGGTTTTTGT-TT
*
3528693 TTGTTTTTTGTTT
1 TTGGTTTTTGTTT
*
3528706 TTTGTTTTTGTTT
1 TTGGTTTTTGTTT
*
3528719 TTGTTTTTTGTT
1 TTGGTTTTTGTT
3528731 AATTAATAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 14
0.75 0.10 0.15
Matches are distributed among these distances:
10 1 0.01
11 4 0.06
12 11 0.15
13 45 0.62
14 11 0.15
ACGTcount: A:0.01, C:0.02, G:0.19, T:0.78
Consensus pattern (13 bp):
TTGGTTTTTGTTT
Found at i:3528671 original size:44 final size:42
Alignment explanation
Indices: 3528611--3528708 Score: 108
Period size: 44 Copynumber: 2.3 Consensus size: 42
3528601 ATTGAATTGA
* * *
3528611 TTTTTTTTTATTTTGATCTTGGTTTTTGTTTTTGGT-TTTTGT
1 TTTTTTTTTTTTTTGATCTTGGTTGTTGTTGTT-GTCTTTTGT
* *
3528653 TGTTTTTTTTTTTCTTGATTTTTGTTGTTGTTGTTGTCTTTTGT
1 T-TTTTTTTTTTT-TTGATCTTGGTTGTTGTTGTTGTCTTTTGT
*
3528697 TTTTTGTTTTTT
1 TTTTTTTTTTTT
3528709 GTTTTTGTTT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
42 1 0.02
43 22 0.47
44 24 0.51
ACGTcount: A:0.03, C:0.03, G:0.16, T:0.78
Consensus pattern (42 bp):
TTTTTTTTTTTTTTGATCTTGGTTGTTGTTGTTGTCTTTTGT
Found at i:3529114 original size:125 final size:125
Alignment explanation
Indices: 3528886--3529415 Score: 512
Period size: 126 Copynumber: 4.2 Consensus size: 125
3528876 TGACTTAGAG
* * * * * *
3528886 ATTATG-CTCAGAGATCTTAAAGATTGTGTCCAAAGGTCTTA-AAGATCTTAAAATCTTTTAATG
1 ATTATGCCT-AGAGGTCTTAGAGATTATGCCCAAAGGTCTTACAA-ATCTCAAAATCTTTGAATG
* * * * *
3528949 CTCTTCACACATTAAAGGCATTGAAACTTTAAAAATTTAAAATGTTTAGCCCGAAGGTCTTAAA
64 CTCCTCATA-A-TAGAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCTCGAAGGTCTTAAA
* * * * *
3529013 GGTTAGGCTTAGAGGTCTTAGAGATTAT-CCCAAAGGTCTTACCAATCTCAAAATTTTTGAATGC
1 -ATTATGCCTAGAGGTCTTAGAGATTATGCCCAAAGGTCTTACAAATCTCAAAATCTTTGAATGC
* **
3529077 TCCTCATAGTAGAGGCATTGAAACTTTGCAAATTTAAAATGTTTTGCTCGAAGGTCTTGAAA
65 TCCTCATAATAGAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCTCGAAGGTCTT-AAA
* ** * * * * * *
3529139 ATTATTCCCGGAAGTATTAGAAATTATGACCCGAA-GTCTGACAAATATCAAAATCTTTGAATGC
1 ATTATGCCTAGAGGTCTTAGAGATTATG-CCCAAAGGTCTTACAAATCTCAAAATCTTTGAATGC
* ** * * *
3529203 TCCTCGTAATAGAGGTGTTGAAACTTTAAAAATTTAAAATGTTTTGCTTGGAGGTTTTAAAA
65 TCCTCATAATAGAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCTCGAAGGTCTT-AAA
* * * *
3529265 ATGATGCCTAAAGGTCTTAGAGATTATGCCCAAAGGTTTTACAAATCCCAAAATCTTTGAATGCT
1 ATTATGCCTAGAGGTCTTAGAGATTATGCCCAAAGGTCTTACAAATCTCAAAATCTTTGAATGCT
** * * * **
3529330 CCTCATAATAGAGGTGTTGAAACTTTGAAATTTTAAAATGTTTTGCT-TAGAGGTCTTGGA
66 CCTCATAATAGAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCTCGA-AGGTCTTAAA
* * *
3529390 ATTGTGCCTAAAGGTCTTAAAGATTA
1 ATTATGCCTAGAGGTCTTAGAGATTA
3529416 CAAAATCTTT
Statistics
Matches: 328, Mismatches: 67, Indels: 17
0.80 0.16 0.04
Matches are distributed among these distances:
125 91 0.28
126 176 0.54
127 40 0.12
128 20 0.06
129 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.18, T:0.34
Consensus pattern (125 bp):
ATTATGCCTAGAGGTCTTAGAGATTATGCCCAAAGGTCTTACAAATCTCAAAATCTTTGAATGCT
CCTCATAATAGAGGCATTGAAACTTTAAAAATTTAAAATGTTTTGCTCGAAGGTCTTAAA
Found at i:3529728 original size:8 final size:9
Alignment explanation
Indices: 3529712--3529739 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
3529702 TTTTTCTCTC
3529712 TCTTTTTTT
1 TCTTTTTTT
3529721 TCTTTTTTT
1 TCTTTTTTT
3529730 TCTTTTTTT
1 TCTTTTTTT
3529739 T
1 T
3529740 TTACAAAGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TCTTTTTTT
Found at i:3531406 original size:17 final size:18
Alignment explanation
Indices: 3531377--3531410 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
3531367 CATGTCTCTC
3531377 TCTTTTTTGCTCTTTTTT
1 TCTTTTTTGCTCTTTTTT
3531395 TCTTTTTT-CTCTTTTT
1 TCTTTTTTGCTCTTTTT
3531411 CGTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (18 bp):
TCTTTTTTGCTCTTTTTT
Found at i:3531411 original size:8 final size:9
Alignment explanation
Indices: 3531375--3531410 Score: 56
Period size: 10 Copynumber: 4.0 Consensus size: 9
3531365 TACATGTCTC
3531375 TCTCTTTTT
1 TCTCTTTTT
3531384 TGCTCTTTTT
1 T-CTCTTTTT
3531394 T-TCTTTTT
1 TCTCTTTTT
3531402 TCTCTTTTT
1 TCTCTTTTT
3531411 CGTTCATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
8 8 0.32
9 8 0.32
10 9 0.36
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (9 bp):
TCTCTTTTT
Found at i:3534458 original size:171 final size:171
Alignment explanation
Indices: 3534168--3534482 Score: 438
Period size: 171 Copynumber: 1.8 Consensus size: 171
3534158 GAACCCAAGT
** * * * * *
3534168 GAACATATGGATATGTGAACCCTGGTGGACATAATGGCACTTCAATTGCTATTTCCTCCCTTACT
1 GAACATATGGATATGTGAACCCAAGTAGACACAATGGCACTTCAACTACTATTTCCTCCCTGACT
* *
3534233 CCATGTGTTTCAATGATTCCTTTTCTTTTTATCCAACCTACTAGCATCTGTCTTAATCCTGCTAA
66 CCATGTGTTTCAATGATTCCTTTTCTTTTTATCCAACCTACTAACATCTGTCTTAATCCTACTAA
3534298 CTATCTATACATATTCTATTACATTCCTATAACTATTTCTC
131 CTATCTATACATATTCTATTACATTCCTATAACTATTTCTC
* * *
3534339 GAACATATGGATATGTGAACCCAATTAGACACAATGGCACTTCAACTACTATTTCTTCCCTCGCC
1 GAACATATGGATATGTGAACCCAAGTAGACACAATGGCACTTCAACTACTATTTCCTCCCT-GAC
* * * *
3534404 T-CATGTGTTTCAATGATTCCTTTT-TCTTTTGTCC-ACCTTGCTAACATTTGTCTTAATTCTAC
65 TCCATGTGTTTCAATGATTCCTTTTCT-TTTTATCCAACC-TACTAACATCTGTCTTAATCCTAC
3534466 TAACTATCTATACATAT
128 TAACTATCTATACATAT
3534483 CTGTCTATAC
Statistics
Matches: 125, Mismatches: 16, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
170 4 0.03
171 119 0.95
172 2 0.02
ACGTcount: A:0.26, C:0.24, G:0.10, T:0.39
Consensus pattern (171 bp):
GAACATATGGATATGTGAACCCAAGTAGACACAATGGCACTTCAACTACTATTTCCTCCCTGACT
CCATGTGTTTCAATGATTCCTTTTCTTTTTATCCAACCTACTAACATCTGTCTTAATCCTACTAA
CTATCTATACATATTCTATTACATTCCTATAACTATTTCTC
Found at i:3534491 original size:14 final size:14
Alignment explanation
Indices: 3534472--3534498 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3534462 CTACTAACTA
3534472 TCTATACATATCTG
1 TCTATACATATCTG
3534486 TCTATACATATCT
1 TCTATACATATCT
3534499 ATTACATTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.30, C:0.22, G:0.04, T:0.44
Consensus pattern (14 bp):
TCTATACATATCTG
Found at i:3540974 original size:20 final size:19
Alignment explanation
Indices: 3540949--3540992 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
3540939 CCTTCTTGTC
*
3540949 TTTTTTTTTTATAATTTAAA
1 TTTTTTTTATATAATTT-AA
*
3540969 TTTTTTTTATGTAATTTAA
1 TTTTTTTTATATAATTTAA
3540988 TTTTT
1 TTTTT
3540993 GTAATTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTTTTATATAATTTAA
Found at i:3541001 original size:18 final size:20
Alignment explanation
Indices: 3540960--3541003 Score: 56
Period size: 19 Copynumber: 2.3 Consensus size: 20
3540950 TTTTTTTTTA
* *
3540960 TAATTTAAATTTTTTTTATG
1 TAATTTAAATTTTTGTAATG
3540980 TAATTT-AATTTTTGTAAT-
1 TAATTTAAATTTTTGTAATG
3540998 TAATTT
1 TAATTT
3541004 TTATTTTATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 6 0.27
19 10 0.45
20 6 0.27
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.64
Consensus pattern (20 bp):
TAATTTAAATTTTTGTAATG
Found at i:3541002 original size:13 final size:14
Alignment explanation
Indices: 3540973--3541005 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
3540963 TTTAAATTTT
3540973 TTTTATGTAATTTAA
1 TTTT-TGTAATTTAA
3540988 TTTTTGTAA-TTAA
1 TTTTTGTAATTTAA
3541001 TTTTT
1 TTTTT
3541006 ATTTTATATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 5 0.28
15 4 0.22
ACGTcount: A:0.27, C:0.00, G:0.06, T:0.67
Consensus pattern (14 bp):
TTTTTGTAATTTAA
Found at i:3541636 original size:20 final size:20
Alignment explanation
Indices: 3541564--3541664 Score: 69
Period size: 20 Copynumber: 4.9 Consensus size: 20
3541554 CATTATTCAT
3541564 ACAAACCCCTAAACCTAAACCC
1 ACAAA-CCCT-AACCTAAACCC
* * * *
3541586 TCAAACCCCAAACTGAACCC
1 ACAAACCCTAACCTAAACCC
* * *
3541606 ATAAACTCTAACCTAAATCC
1 ACAAACCCTAACCTAAACCC
**
3541626 ACAAACCCTAAATTTAAACCC
1 ACAAACCCT-AACCTAAACCC
*
3541647 -CAAGCCCTAAACCTAAAC
1 ACAAACCCT-AACCTAAAC
3541665 TAAACCCTCA
Statistics
Matches: 59, Mismatches: 19, Indels: 4
0.72 0.23 0.05
Matches are distributed among these distances:
20 44 0.75
21 11 0.19
22 4 0.07
ACGTcount: A:0.45, C:0.39, G:0.02, T:0.15
Consensus pattern (20 bp):
ACAAACCCTAACCTAAACCC
Found at i:3541682 original size:20 final size:18
Alignment explanation
Indices: 3541651--3541701 Score: 68
Period size: 20 Copynumber: 2.8 Consensus size: 18
3541641 AAACCCCAAG
3541651 CCCTAAACCTAAACTAAA
1 CCCTAAACCTAAACTAAA
3541669 CCCTCAAACTCTAAACTAAA
1 CCCT-AAAC-CTAAACTAAA
*
3541689 TCCT-AACCTAAAC
1 CCCTAAACCTAAAC
3541702 CCTAAGCTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
17 6 0.20
18 7 0.23
19 4 0.13
20 13 0.43
ACGTcount: A:0.45, C:0.35, G:0.00, T:0.20
Consensus pattern (18 bp):
CCCTAAACCTAAACTAAA
Found at i:3541688 original size:31 final size:30
Alignment explanation
Indices: 3541653--3541722 Score: 86
Period size: 32 Copynumber: 2.2 Consensus size: 30
3541643 ACCCCAAGCC
3541653 CTAAACCTAAACTAAACCCTCAAACTCTAAA
1 CTAAACCTAAACTAAACCCT-AAACTCTAAA
* * *
3541684 CTAAATCCTAACCTAAACCCTAAGCTTTAAA
1 CTAAA-CCTAAACTAAACCCTAAACTCTAAA
3541715 CTTAAACC
1 C-TAAACC
3541723 GCAAGTCTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
31 16 0.47
32 18 0.53
ACGTcount: A:0.44, C:0.31, G:0.01, T:0.23
Consensus pattern (30 bp):
CTAAACCTAAACTAAACCCTAAACTCTAAA
Found at i:3541705 original size:7 final size:7
Alignment explanation
Indices: 3541570--3541706 Score: 50
Period size: 7 Copynumber: 20.9 Consensus size: 7
3541560 TCATACAAAC
3541570 CCCTAAA
1 CCCTAAA
3541577 -CCTAAA
1 CCCTAAA
3541583 CCCTCAAA
1 CCCT-AAA
*
3541591 CCCCAAA
1 CCCTAAA
*
3541598 --CTGAA
1 CCCTAAA
3541603 CCCATAAA
1 CCC-TAAA
*
3541611 CTCT-AA
1 CCCTAAA
3541617 -CCTAAA
1 CCCTAAA
3541623 TCCAC-AAA
1 -CC-CTAAA
3541631 CCCTAAA
1 CCCTAAA
**
3541638 -TTTAAA
1 CCCTAAA
* *
3541644 CCCCAAG
1 CCCTAAA
3541651 CCCTAAA
1 CCCTAAA
3541658 -CCTAAA
1 CCCTAAA
3541664 --CTAAA
1 CCCTAAA
3541669 CCCTCAAA
1 CCCT-AAA
*
3541677 CTCTAAA
1 CCCTAAA
3541684 --CTAAA
1 CCCTAAA
*
3541689 TCCT-AA
1 CCCTAAA
3541695 -CCTAAA
1 CCCTAAA
3541701 CCCTAA
1 CCCTAA
3541707 GCTTTAAACT
Statistics
Matches: 97, Mismatches: 15, Indels: 36
0.66 0.10 0.24
Matches are distributed among these distances:
5 18 0.19
6 25 0.26
7 32 0.33
8 21 0.22
9 1 0.01
ACGTcount: A:0.44, C:0.37, G:0.01, T:0.18
Consensus pattern (7 bp):
CCCTAAA
Found at i:3542925 original size:18 final size:18
Alignment explanation
Indices: 3542885--3542929 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
3542875 CATCATTACT
*
3542885 ATTATTTTTAATTTTATC
1 ATTATTATTAATTTTATC
*
3542903 ATTATTATTATTTTTAATC
1 ATTATTATTAATTTT-ATC
3542922 -TTATTATT
1 ATTATTATT
3542930 GATCAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 21 0.88
19 3 0.12
ACGTcount: A:0.29, C:0.04, G:0.00, T:0.67
Consensus pattern (18 bp):
ATTATTATTAATTTTATC
Found at i:3542925 original size:24 final size:24
Alignment explanation
Indices: 3542869--3542925 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
3542859 CTATAACAAC
*
3542869 TAATCTCATCATTACTATTATTTT
1 TAATCTTATCATTACTATTATTTT
* *
3542893 TAATTTTATCATTATTATTATTTT
1 TAATCTTATCATTACTATTATTTT
3542917 TAATCTTAT
1 TAATCTTAT
3542926 TATTGATCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.11, G:0.00, T:0.60
Consensus pattern (24 bp):
TAATCTTATCATTACTATTATTTT
Found at i:3543416 original size:18 final size:19
Alignment explanation
Indices: 3543385--3543422 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
3543375 AAATATTATT
3543385 TTTAAAATAATATT-TAAA
1 TTTAAAATAATATTCTAAA
**
3543403 TTTAAAATTTTATTCTAAA
1 TTTAAAATAATATTCTAAA
3543422 T
1 T
3543423 ATATGCAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTAAAATAATATTCTAAA
Found at i:3544325 original size:17 final size:17
Alignment explanation
Indices: 3544297--3544334 Score: 60
Period size: 17 Copynumber: 2.2 Consensus size: 17
3544287 TCTTTTTATG
3544297 TTTTCAATTTTTTTCTCA
1 TTTTCAATTTTTTTCT-A
3544315 TTTTCAA-TTTTTTCTA
1 TTTTCAATTTTTTTCTA
3544331 TTTT
1 TTTT
3544335 TATATATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.25
17 8 0.40
18 7 0.35
ACGTcount: A:0.16, C:0.13, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTTCAATTTTTTTCTA
Found at i:3547123 original size:195 final size:197
Alignment explanation
Indices: 3546731--3547123 Score: 607
Period size: 195 Copynumber: 2.0 Consensus size: 197
3546721 TTGCATTGCA
* * * *
3546731 TACATGACATAATTTTTTACGAAAAGTAAATTTAGACCTCCCAAAGATGAGATTTTAAAAGTATT
1 TACATGACAT-ATTTCTTACGAAAAATAAATTGAGACCTCCCAAAGATGAGATTCTAAAAGTATT
3546796 CCGAGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACATACT
65 CCGAGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACATACT
* * * * *
3546861 GGAACATTTTAAGAATTATTTCAATAAGAAGGTTTTAATTTATTTTTCTCGAGAATAAATTTTTT
130 AGAACATTTTAAGAATTATTTCAATAAAAAAGTTTTAATTTATTTTTCTAGAGAATAAATATTTT
3546926 TTT
195 TTT
*
3546929 TACATGACAT-TTTCTTACGAAAAATAAATTCGAG-CCT-CCGAAGATGAGATTCTAAAAGTATT
1 TACATGACATATTTCTTACGAAAAATAAATT-GAGACCTCCCAAAGATGAGATTCTAAAAGTATT
* *
3546991 CCGAGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTATCAACGTACT
65 CCGAGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACATACT
3547056 AGAACATTTTAAGAATTATTTCAATAAAAAAGTTTTAATTTATTTTTTCTTAG-GAATAAA-ATT
130 AGAACATTTTAAGAATTATTTCAATAAAAAAGTTTTAATTTA-TTTTTC-TAGAGAATAAATATT
3547119 TTTTT
193 TTTTT
3547124 AAATAAATAA
Statistics
Matches: 180, Mismatches: 12, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
195 132 0.73
196 34 0.19
197 4 0.02
198 10 0.06
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (197 bp):
TACATGACATATTTCTTACGAAAAATAAATTGAGACCTCCCAAAGATGAGATTCTAAAAGTATTC
CGAGTAGAGATGCTTTAAGAAATCTCTAGGTGAGAAAGAGTTCTTTTAATGTTACCAACATACTA
GAACATTTTAAGAATTATTTCAATAAAAAAGTTTTAATTTATTTTTCTAGAGAATAAATATTTTT
TT
Found at i:3548491 original size:29 final size:29
Alignment explanation
Indices: 3548449--3548507 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3548439 TCAAATGGGG
3548449 AGAGGGACTTGATCTCAATTCTTCTAAGA
1 AGAGGGACTTGATCTCAATTCTTCTAAGA
3548478 AGAGGGACTTGATCTCAATTCTTCTAAGA
1 AGAGGGACTTGATCTCAATTCTTCTAAGA
3548507 A
1 A
3548508 TCATATCTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.31
Consensus pattern (29 bp):
AGAGGGACTTGATCTCAATTCTTCTAAGA
Found at i:3550967 original size:2 final size:2
Alignment explanation
Indices: 3550960--3550993 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3550950 GTAACCTCTA
3550960 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3550994 TCATTGGCAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3551116 original size:111 final size:112
Alignment explanation
Indices: 3550975--3551201 Score: 393
Period size: 111 Copynumber: 2.0 Consensus size: 112
3550965 TATATATATA
* * **
3550975 TATATATATATATATATATTCATTGGCAGTTACAGAATAGTTGTTGCAAGCTCTTGAGCAAAAGT
1 TATATATATATATATATATTCATAGACAGTTACAGAATAGTTGTAACAAGCTCTTGAGCAAAAGT
3551040 CCATGATCTTTTGTACGAAATAAAATGGTTTATCTTTTAAATAGTAC
66 CCATGATCTTTTGTACGAAATAAAATGGTTTATCTTTTAAATAGTAC
*
3551087 TATATATAT-TATATATATTCATAGACAGTTATAGAATAGTTGTAACAAGCTCTTGAGCAAAAGT
1 TATATATATATATATATATTCATAGACAGTTACAGAATAGTTGTAACAAGCTCTTGAGCAAAAGT
*
3551151 CCATGATCTTTTGTATGAAATAAAATGGTTTATCTTTTAAATAGTAC
66 CCATGATCTTTTGTACGAAATAAAATGGTTTATCTTTTAAATAGTAC
3551198 TATA
1 TATA
3551202 ATTTAAGCTG
Statistics
Matches: 109, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
111 100 0.92
112 9 0.08
ACGTcount: A:0.37, C:0.11, G:0.14, T:0.39
Consensus pattern (112 bp):
TATATATATATATATATATTCATAGACAGTTACAGAATAGTTGTAACAAGCTCTTGAGCAAAAGT
CCATGATCTTTTGTACGAAATAAAATGGTTTATCTTTTAAATAGTAC
Found at i:3556404 original size:23 final size:23
Alignment explanation
Indices: 3556378--3556424 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3556368 TTGTTAGTAG
*
3556378 ATTGGTCTAGATTTAGAGAGAGA
1 ATTGGTCTAGATTTAGAGAAAGA
* * *
3556401 ATTGGTTTGGTTTTAGAGAAAGA
1 ATTGGTCTAGATTTAGAGAAAGA
3556424 A
1 A
3556425 AAAGTATGAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.34
Consensus pattern (23 bp):
ATTGGTCTAGATTTAGAGAAAGA
Found at i:3556464 original size:18 final size:19
Alignment explanation
Indices: 3556438--3556481 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
3556428 GTATGAATTC
* *
3556438 AAATGAAAA-AAATATAAA
1 AAATAAAAAGAAATAGAAA
3556456 AAATAAAAAGAAATAGAAA
1 AAATAAAAAGAAATAGAAA
*
3556475 AAGTAAA
1 AAATAAA
3556482 GATTTTGGGT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 8 0.36
19 14 0.64
ACGTcount: A:0.77, C:0.00, G:0.09, T:0.14
Consensus pattern (19 bp):
AAATAAAAAGAAATAGAAA
Found at i:3557131 original size:129 final size:128
Alignment explanation
Indices: 3556974--3557222 Score: 313
Period size: 129 Copynumber: 1.9 Consensus size: 128
3556964 AAGCAACGAC
* * ** * *
3556974 ATTGAAAAATGTTGCAAATACAACAAGTTTTTGTAACAAT-A-TCTTTATCATTATAAATATAAT
1 ATTGAAAAATGTTGCAAATAAAAAAAGTTTTCATAACAATAATTCTTTATCATTACAAATATAAC
** * * *
3557037 AAAAATTTTTGTAATAATTTTTTTGTCGTTGTATAAAATATTAAAAAAATAAATTAACCAACCAT
66 AAAAA-TTTCATAATAACTTTTTTATCATTGTATAAAATATT-AAAAAATAAATTAACCAACCAT
* * * * *
3557102 ATTGAAAATTTGTTGTAAATAAAAAAAGTTTTCATAACAATAATTTTTTATCGTTACAAATATGA
1 ATTGAAAA-ATGTTGCAAATAAAAAAAGTTTTCATAACAATAATTCTTTATCATTACAAATATAA
3557167 CAAAAATTTCATAATAACTTTTTTATCATTGTATAAAATATTAAAAAATAAATTAA
65 CAAAAATTTCATAATAACTTTTTTATCATTGTATAAAATATTAAAAAATAAATTAA
3557223 GTAATGAAAT
Statistics
Matches: 102, Mismatches: 16, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
128 8 0.08
129 40 0.39
130 32 0.31
131 22 0.22
ACGTcount: A:0.47, C:0.08, G:0.06, T:0.39
Consensus pattern (128 bp):
ATTGAAAAATGTTGCAAATAAAAAAAGTTTTCATAACAATAATTCTTTATCATTACAAATATAAC
AAAAATTTCATAATAACTTTTTTATCATTGTATAAAATATTAAAAAATAAATTAACCAACCAT
Found at i:3563408 original size:22 final size:22
Alignment explanation
Indices: 3563383--3563425 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
3563373 AAAAGGTACC
*
3563383 TGAAAGTTTTAAAGATTATACT
1 TGAAAGTTTTAAAGATAATACT
* *
3563405 TGAAGGTTTTATAGATAATAC
1 TGAAAGTTTTAAAGATAATAC
3563426 CTAGAAGACT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.40, C:0.05, G:0.16, T:0.40
Consensus pattern (22 bp):
TGAAAGTTTTAAAGATAATACT
Found at i:3564719 original size:19 final size:19
Alignment explanation
Indices: 3564675--3564719 Score: 63
Period size: 19 Copynumber: 2.4 Consensus size: 19
3564665 AATAATCAAA
* *
3564675 CAAACAATAATTATTCATG
1 CAAAAAATAATTAATCATG
*
3564694 CATAAAATAATTAATCATG
1 CAAAAAATAATTAATCATG
3564713 CAAAAAA
1 CAAAAAA
3564720 AATCATAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.56, C:0.13, G:0.04, T:0.27
Consensus pattern (19 bp):
CAAAAAATAATTAATCATG
Found at i:3564740 original size:2 final size:2
Alignment explanation
Indices: 3564735--3564785 Score: 52
Period size: 2 Copynumber: 26.5 Consensus size: 2
3564725 TAATAAACTG
* * * *
3564735 TA TA TA TA AA AA TA TA TA TA TG CA TA TA -A 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
3564776 TA TA T- TA TA T
1 TA TA TA TA TA T
3564786 GAAATGAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:3564778 original size:17 final size:17
Alignment explanation
Indices: 3564735--3564785 Score: 59
Period size: 17 Copynumber: 3.1 Consensus size: 17
3564725 TAATAAACTG
*
3564735 TATATATA-AAAATATA
1 TATATATATATAATATA
**
3564751 TATATGCATATAATATA
1 TATATATATATAATATA
*
3564768 TATATATATATATTATA
1 TATATATATATAATATA
3564785 T
1 T
3564786 GAAATGAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
16 6 0.21
17 22 0.79
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (17 bp):
TATATATATATAATATA
Found at i:3566202 original size:6 final size:6
Alignment explanation
Indices: 3566191--3566263 Score: 56
Period size: 6 Copynumber: 11.8 Consensus size: 6
3566181 TTAAAAAAAT
* * * * **
3566191 AAATTA AAATTAA AAACTA AATTTA AAATTA AGACTA AAATTA AAACCCA
1 AAATTA AAATT-A AAATTA AAATTA AAATTA AAATTA AAATTA AAA-TTA
* *
3566241 AAACTA AAATCA AAATTA AAATT
1 AAATTA AAATTA AAATTA AAATT
3566264 GTAGGCTTTT
Statistics
Matches: 51, Mismatches: 14, Indels: 4
0.74 0.20 0.06
Matches are distributed among these distances:
6 42 0.82
7 9 0.18
ACGTcount: A:0.63, C:0.10, G:0.01, T:0.26
Consensus pattern (6 bp):
AAATTA
Found at i:3566231 original size:19 final size:18
Alignment explanation
Indices: 3566184--3566261 Score: 68
Period size: 19 Copynumber: 4.2 Consensus size: 18
3566174 TTGACTCTTA
*
3566184 AAAAAATAAATTAAAATT
1 AAAAACTAAATTAAAATT
3566202 AAAAACTAAATTTAAAATT
1 AAAAACTAAA-TTAAAATT
* **
3566221 -AAGACTAAAATTAAAACC
1 AAAAACT-AAATTAAAATT
* *
3566239 CAAAACTAAAATCAAAATT
1 AAAAACT-AAATTAAAATT
3566258 AAAA
1 AAAA
3566262 TTGTAGGCTT
Statistics
Matches: 48, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
18 20 0.42
19 28 0.58
ACGTcount: A:0.67, C:0.09, G:0.01, T:0.23
Consensus pattern (18 bp):
AAAAACTAAATTAAAATT
Found at i:3572302 original size:17 final size:16
Alignment explanation
Indices: 3572280--3572329 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
3572270 TTTTAGATTT
3572280 GTAACTTTCTATTTTTA
1 GTAACTTTC-ATTTTTA
* *
3572297 GTAACTGTCCTTTTTA
1 GTAACTTTCATTTTTA
* *
3572313 GTAAATTTCCTTTTTA
1 GTAACTTTCATTTTTA
3572329 G
1 G
3572330 GTCTTTCATT
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
16 21 0.72
17 8 0.28
ACGTcount: A:0.22, C:0.14, G:0.10, T:0.54
Consensus pattern (16 bp):
GTAACTTTCATTTTTA
Found at i:3572326 original size:15 final size:16
Alignment explanation
Indices: 3572291--3572329 Score: 60
Period size: 16 Copynumber: 2.4 Consensus size: 16
3572281 TAACTTTCTA
*
3572291 TTTTTAGTAACTGTCC
1 TTTTTAGTAAATGTCC
*
3572307 TTTTTAGTAAATTTCC
1 TTTTTAGTAAATGTCC
3572323 TTTTTAG
1 TTTTTAG
3572330 GTCTTTCATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.13, G:0.10, T:0.56
Consensus pattern (16 bp):
TTTTTAGTAAATGTCC
Found at i:3575753 original size:26 final size:24
Alignment explanation
Indices: 3575708--3575755 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
3575698 GGTAACCTAA
*
3575708 GTTTTCTTTTTTATTTGTTTATGT
1 GTTTTCTTTTTTATGTGTTTATGT
3575732 GTTTTCTTTATGTTATGTGTTTAT
1 GTTTTCTTT-T-TTATGTGTTTAT
3575756 TTTTCTCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.43
25 1 0.05
26 11 0.52
ACGTcount: A:0.10, C:0.04, G:0.15, T:0.71
Consensus pattern (24 bp):
GTTTTCTTTTTTATGTGTTTATGT
Found at i:3578798 original size:263 final size:263
Alignment explanation
Indices: 3578315--3578844 Score: 900
Period size: 263 Copynumber: 2.0 Consensus size: 263
3578305 TTTCTTTTAA
*
3578315 TTTTTTGTTCTATTTTAGGGGTTTTGGTTTATGTTTGCATTCTGTTTTAGTGTTCCTAAATGGAT
1 TTTTGTGTTCTATTTTAGGGGTTTTGGTTTATGTTTGCATTCTGTTTTAGTGTTCCTAAATGGAT
3578380 GAAAATGTTAGTTGAATGATGTTTATAACTTGTTCGTTGAAATAGCTTAGTTATGGATTTGGTTT
66 GAAAATGTTAGTTGAATGATGTTTATAACTTGTTCGTTGAAATAGCTTAGTTATGGATTTGGTTT
* * *
3578445 CCAGGCTTTTTCCATGCATTTTTCCTTTCTAGTTTTCAAAACTATTTTGCATCCATTTTCGGTTC
131 CCAAGCTTTTTCCATGCATTTTTCCTTACTAGTTTTCAAAACTATTTTGCATCCATTTTCGATTC
* *
3578510 TGTTTTGGAGGTAATATTCTGCATCTTGTTCATCCATTTTTATGTCTATCTTAACATTCTAATCT
196 TGTTTTGGAGGTAAAATTCTGCATCTTGTTCATCCACTTTTATGTCTATCTTAACATTCTAATCT
3578575 TGG
261 TGG
*
3578578 TTTTGTGTTCTATTTTAGGGGTTTTGGTTTATGTTTGCATTC-GATTTTAGTGTTCCTGAATGGA
1 TTTTGTGTTCTATTTTAGGGGTTTTGGTTTATGTTTGCATTCTG-TTTTAGTGTTCCTAAATGGA
* * * * *
3578642 TGAAAATGTTGGTTGAATGATGTTTATGACTTGTTTGTTGAAATAGCTTAGTTATTGCTTTGGTT
65 TGAAAATGTTAGTTGAATGATGTTTATAACTTGTTCGTTGAAATAGCTTAGTTATGGATTTGGTT
3578707 TCCAAGCTTTTTCCATGCATTTTTCCTTACTAGTTTTCAAAACTATTTTGCATCCATTTTCGATT
130 TCCAAGCTTTTTCCATGCATTTTTCCTTACTAGTTTTCAAAACTATTTTGCATCCATTTTCGATT
* * * *
3578772 TTGTTTTGGAGGTAAAATTTTGCATCTTGTTTATCCACTTTTATGTCTATCTTAACGTTCTAATC
195 CTGTTTTGGAGGTAAAATTCTGCATCTTGTTCATCCACTTTTATGTCTATCTTAACATTCTAATC
3578837 TTGG
260 TTGG
3578841 TTTT
1 TTTT
3578845 CATGCTGCAT
Statistics
Matches: 250, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
262 1 0.00
263 249 1.00
ACGTcount: A:0.20, C:0.13, G:0.18, T:0.50
Consensus pattern (263 bp):
TTTTGTGTTCTATTTTAGGGGTTTTGGTTTATGTTTGCATTCTGTTTTAGTGTTCCTAAATGGAT
GAAAATGTTAGTTGAATGATGTTTATAACTTGTTCGTTGAAATAGCTTAGTTATGGATTTGGTTT
CCAAGCTTTTTCCATGCATTTTTCCTTACTAGTTTTCAAAACTATTTTGCATCCATTTTCGATTC
TGTTTTGGAGGTAAAATTCTGCATCTTGTTCATCCACTTTTATGTCTATCTTAACATTCTAATCT
TGG
Found at i:3583352 original size:13 final size:13
Alignment explanation
Indices: 3583336--3583360 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3583326 TAGAGTAAAT
3583336 TTAATATTAAAAA
1 TTAATATTAAAAA
3583349 TTAATATTAAAA
1 TTAATATTAAAA
3583361 TTACTCTAAT
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:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
TTAATATTAAAAA
Found at i:3583805 original size:96 final size:95
Alignment explanation
Indices: 3583610--3583849 Score: 254
Period size: 96 Copynumber: 2.5 Consensus size: 95
3583600 AGAAAGAATC
* * * *
3583610 ATTAAATCTTCCAATAGTTTGGTAAGATTTAACTTA-AGATTTAAATCTTCCAATAGTTTCGTAG
1 ATTAAATCTTCCAATAGTTTGGTAAGAATTAATTTAGAGATTTAAATCTTCCAATAGCTTAGTAG
* *** * * * *
3583674 GATTGAAAATTTTATTTTTTCATAAAAGCTC
66 GATTAAAAAAAATATTATTACACAAAA-CTA
* * **
3583705 ATTAAGTCTGCCAATAGTTTGGTAAGACGTAATTTAGAGATTTAAATCTTCCAATAGCTTAGTAG
1 ATTAAATCTTCCAATAGTTTGGTAAGAATTAATTTAGAGATTTAAATCTTCCAATAGCTTAGTAG
3583770 GATTAAAAACAAAAATATTATTAC-CAAAA-TA
66 GATT--AAA-AAAAATATTATTACACAAAACTA
* *
3583801 ATTAAAACTTTCAATAGTTTGGTAAGAATTAATTT-GAGATTTAAATCTT
1 ATTAAATCTTCCAATAGTTTGGTAAGAATTAATTTAGAGATTTAAATCTT
3583850 TTAATAGTTT
Statistics
Matches: 120, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
95 45 0.38
96 60 0.50
98 6 0.05
99 9 0.08
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.38
Consensus pattern (95 bp):
ATTAAATCTTCCAATAGTTTGGTAAGAATTAATTTAGAGATTTAAATCTTCCAATAGCTTAGTAG
GATTAAAAAAAATATTATTACACAAAACTA
Found at i:3583904 original size:18 final size:19
Alignment explanation
Indices: 3583867--3583904 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
3583857 TTTGATAAGA
**
3583867 TTAAAAAGATTTTATTTTC
1 TTAAAAAGATTTTAAATTC
3583886 TTAAAAAGA-TTTAAATTC
1 TTAAAAAGATTTTAAATTC
3583904 T
1 T
3583905 CCAATAATGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.47
Consensus pattern (19 bp):
TTAAAAAGATTTTAAATTC
Found at i:3596109 original size:9 final size:9
Alignment explanation
Indices: 3596097--3596122 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
3596087 ACTACTACTA
3596097 CTGCTGCTG
1 CTGCTGCTG
3596106 CTGCTGCTG
1 CTGCTGCTG
3596115 CTGCTGCT
1 CTGCTGCT
3596123 ACTACTACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.00, C:0.35, G:0.31, T:0.35
Consensus pattern (9 bp):
CTGCTGCTG
Found at i:3603351 original size:26 final size:26
Alignment explanation
Indices: 3603315--3603365 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
3603305 AGTTGAACGG
3603315 AAGTCGAATGGGTGTTCTTAGAAAAT
1 AAGTCGAATGGGTGTTCTTAGAAAAT
* *
3603341 AAGTTGAATGGGTGTTCTTGGAAAA
1 AAGTCGAATGGGTGTTCTTAGAAAA
3603366 GATTATGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.33, C:0.06, G:0.29, T:0.31
Consensus pattern (26 bp):
AAGTCGAATGGGTGTTCTTAGAAAAT
Found at i:3605676 original size:52 final size:52
Alignment explanation
Indices: 3605611--3605715 Score: 147
Period size: 52 Copynumber: 2.0 Consensus size: 52
3605601 TATAACCATA
* * * * *
3605611 CAAACTTATTTATTAAAAATTTCTTTTGTCTTATAATTCTTTTTCTGGAAGT
1 CAAACTTACTTATTAAAAATTTCTTTTCTCTTAGAATTCTTCTTCTGCAAGT
* *
3605663 CAAACTTACTTATTAAGAATTTTTTTTCTCTTAGAATTCTTCTTCTGCAAGT
1 CAAACTTACTTATTAAAAATTTCTTTTCTCTTAGAATTCTTCTTCTGCAAGT
3605715 C
1 C
3605716 TTCTTGTCCA
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
52 46 1.00
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.50
Consensus pattern (52 bp):
CAAACTTACTTATTAAAAATTTCTTTTCTCTTAGAATTCTTCTTCTGCAAGT
Found at i:3606964 original size:19 final size:20
Alignment explanation
Indices: 3606940--3606986 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3606930 TTTGACAGTG
3606940 ATTAAAAAGCT-GCAAACAT
1 ATTAAAAAGCTAGCAAACAT
** *
3606959 ATTAAAAATTTATCAAACAT
1 ATTAAAAAGCTAGCAAACAT
3606979 ATTAAAAA
1 ATTAAAAA
3606987 AATAAAATTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.57, C:0.11, G:0.04, T:0.28
Consensus pattern (20 bp):
ATTAAAAAGCTAGCAAACAT
Found at i:3619356 original size:18 final size:16
Alignment explanation
Indices: 3619324--3619357 Score: 50
Period size: 18 Copynumber: 2.0 Consensus size: 16
3619314 AGTGCAAACA
3619324 TTCTTCTTGTATTTGT
1 TTCTTCTTGTATTTGT
3619340 TTCTCTCTTGATATTTGT
1 TTCT-TCTTG-TATTTGT
3619358 AGACATCCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.25
17 5 0.31
18 7 0.44
ACGTcount: A:0.09, C:0.15, G:0.12, T:0.65
Consensus pattern (16 bp):
TTCTTCTTGTATTTGT
Found at i:3630659 original size:43 final size:42
Alignment explanation
Indices: 3630607--3630913 Score: 236
Period size: 43 Copynumber: 6.7 Consensus size: 42
3630597 TTTAAAGGTA
* *
3630607 TTTATTTATTTTTCAAAAGTTATTAAGCCTCTATTTAGAAGAGC
1 TTTA-TTATTTTTCAAAAGTT-GTAAGCCTCTATTTAGAGGAGC
*
3630651 TTTATTATTTTTTTTTAAAAGTTGTTAAGCCTCTATTTAGAGGAGC
1 TTTATTA---TTTTTCAAAAGTTG-TAAGCCTCTATTTAGAGGAGC
* *
3630697 TTTATTTATTTATTTATTTTTCAAAAGTTGTGAGCCTCTATTTAGAGGAAC
1 --------TTTA-TTATTTTTCAAAAGTTGTAAGCCTCTATTTAGAGGAGC
** *
3630748 TTTATTATTTTTCAAAAGTTGTTGTGCTTCTATTTAGAGGAGC
1 TTTATTATTTTTCAAAAGTTG-TAAGCCTCTATTTAGAGGAGC
* *
3630791 TTTATTTATTTATTTATTTTTTAAAAGTTGTGAGCCTCTATTTAGAGGAGC
1 --------TTTA-TTATTTTTCAAAAGTTGTAAGCCTCTATTTAGAGGAGC
* *
3630842 TTTATTATTTTTCAAAAGTTGTAGAGCTTCTATTTAGAAGAGC
1 TTTATTATTTTTCAAAAGTTGTA-AGCCTCTATTTAGAGGAGC
* * *
3630885 CTTATATATTTTCCAAAAGTTGTGAGCCT
1 TTTAT-TATTTTTCAAAAGTTGTAAGCCT
3630914 TTGTTTAAAG
Statistics
Matches: 218, Mismatches: 20, Indels: 51
0.75 0.07 0.18
Matches are distributed among these distances:
42 34 0.16
43 54 0.25
44 20 0.09
46 32 0.15
51 42 0.19
52 29 0.13
54 4 0.02
55 3 0.01
ACGTcount: A:0.27, C:0.10, G:0.15, T:0.48
Consensus pattern (42 bp):
TTTATTATTTTTCAAAAGTTGTAAGCCTCTATTTAGAGGAGC
Found at i:3630733 original size:51 final size:50
Alignment explanation
Indices: 3630605--3630851 Score: 286
Period size: 51 Copynumber: 5.1 Consensus size: 50
3630595 TGTTTAAAGG
* * *
3630605 TATTTATTTATTTTTCAAAAGTTATTAAGCCTCTATTTAGAAGAGCTTTAT
1 TATTTATTTATTTTTCAAAAGTT-GTGAGCCTCTATTTAGAGGAGCTTTAT
*
3630656 TA--T-TTT-TTTTT-AAAAGTTGTTAAGCCTCTATTTAGAGGAGCTTTATT
1 TATTTATTTATTTTTCAAAAGTTG-TGAGCCTCTATTTAGAGGAGCTTTA-T
3630703 TATTTATTTATTTTTCAAAAGTTGTGAGCCTCTATTTAGAGGA-----A-
1 TATTTATTTATTTTTCAAAAGTTGTGAGCCTCTATTTAGAGGAGCTTTAT
* * *
3630747 -CTTTA-TTATTTTTCAAAAGTTGTTGTGCTTCTATTTAGAGGAGCTTTATT
1 TATTTATTTATTTTTCAAAAGTTG-TGAGCCTCTATTTAGAGGAGCTTTA-T
*
3630797 TATTTATTTATTTTTTAAAAGTTGTGAGCCTCTATTTAGAGGAGCTTTAT
1 TATTTATTTATTTTTCAAAAGTTGTGAGCCTCTATTTAGAGGAGCTTTAT
3630847 TATTT
1 TATTT
3630852 TTCAAAAGTT
Statistics
Matches: 169, Mismatches: 10, Indels: 35
0.79 0.05 0.16
Matches are distributed among these distances:
42 17 0.10
43 21 0.12
46 32 0.19
47 8 0.05
48 4 0.02
49 2 0.01
50 9 0.05
51 52 0.31
52 24 0.14
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.50
Consensus pattern (50 bp):
TATTTATTTATTTTTCAAAAGTTGTGAGCCTCTATTTAGAGGAGCTTTAT
Found at i:3630765 original size:94 final size:94
Alignment explanation
Indices: 3630605--3630895 Score: 422
Period size: 94 Copynumber: 3.1 Consensus size: 94
3630595 TGTTTAAAGG
* * * *
3630605 TATTTATTTATTTTTCAAAAGTTATTAAGCCTCTATTTAGAAGAGCTTTATTATTTTTTTTTAAA
1 TATTTATTTATTTTTCAAAAGTT-GTGAGCCTCTATTTAGAGGAGCTTTATTA---TTTTTCAAA
*
3630670 AGTTGTTAAGCCTCTATTTAGAGGAGCTTTATT
62 AGTTGTTAAGCTTCTATTTAGAGGAGCTTTATT
*
3630703 TATTTATTTATTTTTCAAAAGTTGTGAGCCTCTATTTAGAGGAACTTTATTATTTTTCAAAAGTT
1 TATTTATTTATTTTTCAAAAGTTGTGAGCCTCTATTTAGAGGAGCTTTATTATTTTTCAAAAGTT
**
3630768 GTTGTGCTTCTATTTAGAGGAGCTTTATT
66 GTTAAGCTTCTATTTAGAGGAGCTTTATT
*
3630797 TATTTATTTATTTTTTAAAAGTTGTGAGCCTCTATTTAGAGGAGCTTTATTATTTTTCAAAAGTT
1 TATTTATTTATTTTTCAAAAGTTGTGAGCCTCTATTTAGAGGAGCTTTATTATTTTTCAAAAGTT
* * *
3630862 G-TAGAGCTTCTATTTAGAAGAGCCTTATA
66 GTTA-AGCTTCTATTTAGAGGAGCTTTATT
3630891 TATTT
1 TATTT
3630896 TCCAAAAGTT
Statistics
Matches: 177, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
93 1 0.01
94 128 0.72
97 25 0.14
98 23 0.13
ACGTcount: A:0.27, C:0.09, G:0.14, T:0.49
Consensus pattern (94 bp):
TATTTATTTATTTTTCAAAAGTTGTGAGCCTCTATTTAGAGGAGCTTTATTATTTTTCAAAAGTT
GTTAAGCTTCTATTTAGAGGAGCTTTATT
Found at i:3631949 original size:9 final size:9
Alignment explanation
Indices: 3631937--3631983 Score: 51
Period size: 9 Copynumber: 4.9 Consensus size: 9
3631927 TGGTATTTGT
3631937 TTTATTTTA
1 TTTATTTTA
3631946 TTTATGTATTTA
1 TTTA--T-TTTA
3631958 TTTATTTTA
1 TTTATTTTA
3631967 TTT-TGTTTA
1 TTTAT-TTTA
3631976 TTTATTTT
1 TTTATTTT
3631984 TAAAGTATTT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
8 1 0.03
9 21 0.64
10 2 0.06
11 1 0.03
12 8 0.24
ACGTcount: A:0.19, C:0.00, G:0.04, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:3631966 original size:26 final size:26
Alignment explanation
Indices: 3631930--3631982 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
3631920 CCTATTTTGG
*
3631930 TATTTGTTTTATTTTATTTATGTATT
1 TATTTATTTTATTTTATTTATGTATT
* *
3631956 TATTTATTTTATTTTGTTTATTTATT
1 TATTTATTTTATTTTATTTATGTATT
3631982 T
1 T
3631983 TTAAAGTATT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (26 bp):
TATTTATTTTATTTTATTTATGTATT
Found at i:3634144 original size:19 final size:19
Alignment explanation
Indices: 3634120--3634157 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
3634110 GATATAATAA
*
3634120 TTTTTTCATGAAAATAAAT
1 TTTTTTCATAAAAATAAAT
3634139 TTTTTTCATAAAAATAAAT
1 TTTTTTCATAAAAATAAAT
3634158 AAAAATATAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (19 bp):
TTTTTTCATAAAAATAAAT
Found at i:3634960 original size:21 final size:21
Alignment explanation
Indices: 3634922--3634966 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
3634912 ATAGAACAAC
3634922 CCAAACAAAAGAAACAGAATAG
1 CCAAACAAAAGAAACAGAA-AG
**
3634944 CCAAAC-AAAGATTCAGAAAG
1 CCAAACAAAAGAAACAGAAAG
3634964 CCA
1 CCA
3634967 CAGGATCTCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 10 0.48
22 6 0.29
ACGTcount: A:0.58, C:0.22, G:0.13, T:0.07
Consensus pattern (21 bp):
CCAAACAAAAGAAACAGAAAG
Found at i:3635693 original size:13 final size:13
Alignment explanation
Indices: 3635675--3635699 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3635665 TTATCTGCTC
3635675 AATCTTAATTTTT
1 AATCTTAATTTTT
3635688 AATCTTAATTTT
1 AATCTTAATTTT
3635700 GTATCACAAT
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:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
AATCTTAATTTTT
Found at i:3636185 original size:21 final size:21
Alignment explanation
Indices: 3636159--3636319 Score: 65
Period size: 21 Copynumber: 7.5 Consensus size: 21
3636149 GCAATCATAC
3636159 AATCATGCAAAATATATAATA
1 AATCATGCAAAATATATAATA
3636180 AATCATGCAAACATTATCATGCAATAA
1 AATCATGCAAA-A-TAT-AT--AAT-A
*
3636207 AAACAT-CATACAATAATATAA-A
1 AATCATGCA-A-AATA-TATAATA
3636229 ATATCATGCAAAA-A-AT--T-
1 A-ATCATGCAAAATATATAATA
* *
3636246 -GTCATGCAATAATATAAAAT-
1 AATCATGCAA-AATATATAATA
* * *
3636266 TATCATGTAAAA-ATATCATACA
1 AATCATGCAAAATATAT-A-ATA
3636288 AAT-ACTGCAAAATATATAATA
1 AATCA-TGCAAAATATATAATA
3636309 AATCATGCAAA
1 AATCATGCAAA
3636320 CATTATCATG
Statistics
Matches: 105, Mismatches: 11, Indels: 48
0.64 0.07 0.29
Matches are distributed among these distances:
15 8 0.08
16 2 0.02
17 1 0.01
18 1 0.01
19 5 0.05
20 4 0.04
21 32 0.30
22 15 0.14
23 12 0.11
24 6 0.06
26 9 0.09
27 9 0.09
28 1 0.01
ACGTcount: A:0.54, C:0.13, G:0.06, T:0.27
Consensus pattern (21 bp):
AATCATGCAAAATATATAATA
Found at i:3636230 original size:59 final size:59
Alignment explanation
Indices: 3636152--3636361 Score: 199
Period size: 59 Copynumber: 3.4 Consensus size: 59
3636142 ATATCATGCA
* *
3636152 ATCATACAATCATGCAAAATATATAATAAATCATGCAAACATTATCATGCAATAAAAAC
1 ATCATACAATAATACAAAATATATAATAAATCATGCAAACATTATCATGCAATAAAAAC
* * * *
3636211 ATCATACAATAATATAAAATATCATGCAAAAAATTGTCATGCAATA-ATATAAAATTAT-CATGT
1 ATCATACAATAATACAAAATAT-AT--AATAAA---TCATGCAA-ACAT-T---ATCATGCA-AT
*
3636274 AAAAAT
54 AAAAAC
* *
3636280 ATCATACAAATACTGCAAAATATATAATAAATCATGCAAACATTATCATGCAATAAAAAC
1 ATCATAC-AATAATACAAAATATATAATAAATCATGCAAACATTATCATGCAATAAAAAC
*
3636340 ATCATACAATAATATAAAATAT
1 ATCATACAATAATACAAAATAT
3636362 CATGCAAAAA
Statistics
Matches: 119, Mismatches: 17, Indels: 30
0.72 0.10 0.18
Matches are distributed among these distances:
59 31 0.26
60 19 0.16
61 2 0.02
62 5 0.04
63 2 0.02
64 10 0.08
65 10 0.08
66 2 0.02
67 5 0.04
68 2 0.02
69 19 0.16
70 12 0.10
ACGTcount: A:0.54, C:0.14, G:0.05, T:0.28
Consensus pattern (59 bp):
ATCATACAATAATACAAAATATATAATAAATCATGCAAACATTATCATGCAATAAAAAC
Found at i:3636270 original size:36 final size:36
Alignment explanation
Indices: 3636192--3636278 Score: 113
Period size: 36 Copynumber: 2.4 Consensus size: 36
3636182 TCATGCAAAC
3636192 ATTATCATGCAATAAAAACATCATACAATAATATAAA
1 ATTATCATGCAA-AAAAACATCATACAATAATATAAA
*** *
3636229 A-TATCATGCAAAAAATTGTCATGCAATAATATAAA
1 ATTATCATGCAAAAAAACATCATACAATAATATAAA
*
3636264 ATTATCATGTAAAAA
1 ATTATCATGCAAAAA
3636279 TATCATACAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
35 21 0.48
36 22 0.50
37 1 0.02
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (36 bp):
ATTATCATGCAAAAAAACATCATACAATAATATAAA
Found at i:3636305 original size:129 final size:129
Alignment explanation
Indices: 3636152--3636431 Score: 519
Period size: 129 Copynumber: 2.2 Consensus size: 129
3636142 ATATCATGCA
3636152 ATCATAC-AAT-CATGCAAAATATATAATAAATCATGCAAACATTATCATGCAATAAAAACATCA
1 ATCATACAAATAC-TGCAAAATATATAATAAATCATGCAAACATTATCATGCAATAAAAACATCA
3636215 TACAATAATATAAAATATCATGCAAAAAATTGTCATGCAATAATATAAAATTATCATGTAAAAAT
65 TACAATAATATAAAATATCATGCAAAAAATTGTCATGCAATAATATAAAATTATCATGTAAAAAT
3636280 ATCATACAAATACTGCAAAATATATAATAAATCATGCAAACATTATCATGCAATAAAAACATCAT
1 ATCATACAAATACTGCAAAATATATAATAAATCATGCAAACATTATCATGCAATAAAAACATCAT
3636345 ACAATAATATAAAATATCATGCAAAAAATTGTCATGCAATAATATAAAATTATCATGTAAAAAT
66 ACAATAATATAAAATATCATGCAAAAAATTGTCATGCAATAATATAAAATTATCATGTAAAAAT
**
3636409 ATCATACAAATACTATAAAATAT
1 ATCATACAAATACTGCAAAATAT
3636432 CATGCAAAAA
Statistics
Matches: 148, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
128 7 0.05
129 140 0.95
130 1 0.01
ACGTcount: A:0.54, C:0.13, G:0.05, T:0.28
Consensus pattern (129 bp):
ATCATACAAATACTGCAAAATATATAATAAATCATGCAAACATTATCATGCAATAAAAACATCAT
ACAATAATATAAAATATCATGCAAAAAATTGTCATGCAATAATATAAAATTATCATGTAAAAAT
Found at i:3636395 original size:21 final size:21
Alignment explanation
Indices: 3636369--3636410 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3636359 TATCATGCAA
* *
3636369 AAAATTGTCATGCAATAATAT
1 AAAATTATCATGCAAAAATAT
*
3636390 AAAATTATCATGTAAAAATAT
1 AAAATTATCATGCAAAAATAT
3636411 CATACAAATA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (21 bp):
AAAATTATCATGCAAAAATAT
Found at i:3636444 original size:35 final size:34
Alignment explanation
Indices: 3636323--3636445 Score: 149
Period size: 35 Copynumber: 3.5 Consensus size: 34
3636313 ATGCAAACAT
*
3636323 TATCATGCAATAAAAACATCATACAATAATATAAAA
1 TATCATGC-A-AAAAATATCATACAATAATATAAAA
* *
3636359 TATCATGCAAAAAATTGTCATGCAATAATATAAAA
1 TATCATGCAAAAAA-TATCATACAATAATATAAAA
* *
3636394 TTATCATG-TAAAAATATCATACAAATACTATAAAA
1 -TATCATGCAAAAAATATCATAC-AATAATATAAAA
3636429 TATCATGCAAAAAATAT
1 TATCATGCAAAAAATAT
3636446 TATGCAAATA
Statistics
Matches: 75, Mismatches: 8, Indels: 9
0.82 0.09 0.10
Matches are distributed among these distances:
34 18 0.24
35 42 0.56
36 15 0.20
ACGTcount: A:0.54, C:0.12, G:0.05, T:0.28
Consensus pattern (34 bp):
TATCATGCAAAAAATATCATACAATAATATAAAA
Found at i:3636460 original size:15 final size:14
Alignment explanation
Indices: 3636425--3636461 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3636415 CAAATACTAT
*
3636425 AAAATATCATGCAA
1 AAAATATTATGCAA
3636439 AAAATATTATGCAA
1 AAAATATTATGCAA
3636453 ATAAATATT
1 A-AAATATT
3636462 TAATAAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 14 0.67
15 7 0.33
ACGTcount: A:0.57, C:0.08, G:0.05, T:0.30
Consensus pattern (14 bp):
AAAATATTATGCAA
Found at i:3636501 original size:24 final size:24
Alignment explanation
Indices: 3636447--3636503 Score: 71
Period size: 24 Copynumber: 2.4 Consensus size: 24
3636437 AAAAAATATT
*
3636447 ATGCAAATAAATATTTAATAAATG
1 ATGCAAATAAATATTTAATAAATC
**
3636471 ACACAAATAAATATATTAAT-AATC
1 ATGCAAATAAATAT-TTAATAAATC
3636495 ATGCAAATA
1 ATGCAAATA
3636504 TATTAATATA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 22 0.81
25 5 0.19
ACGTcount: A:0.56, C:0.09, G:0.05, T:0.30
Consensus pattern (24 bp):
ATGCAAATAAATATTTAATAAATC
Found at i:3636504 original size:20 final size:19
Alignment explanation
Indices: 3636479--3636556 Score: 68
Period size: 19 Copynumber: 3.9 Consensus size: 19
3636469 TGACACAAAT
3636479 AAATATATTAATAATCATGC
1 AAATA-ATTAATAATCATGC
**
3636499 AAATATATTAATATATCACAC
1 AAATA-ATTAATA-ATCATGC
*
3636520 AAAGAA-TAATTAATCATGC
1 AAATAATTAA-TAATCATGC
* *
3636539 AATTAAGTAATAATCATG
1 AAATAATTAATAATCATG
3636557 TAATCACACA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
19 20 0.42
20 19 0.40
21 9 0.19
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.32
Consensus pattern (19 bp):
AAATAATTAATAATCATGC
Found at i:3636795 original size:10 final size:9
Alignment explanation
Indices: 3636782--3636831 Score: 50
Period size: 9 Copynumber: 5.6 Consensus size: 9
3636772 ATAAAAAGAG
*
3636782 AAAAAATTT
1 AAAAAAATT
*
3636791 AAAAAAAGGT
1 AAAAAAA-TT
3636801 AAAAAAATT
1 AAAAAAATT
3636810 AAAAAAA--
1 AAAAAAATT
3636817 AAAGAAAATT
1 AAA-AAAATT
3636827 AAAAA
1 AAAAA
3636832 CTTATCATTC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
7 3 0.09
8 4 0.12
9 16 0.47
10 11 0.32
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (9 bp):
AAAAAAATT
Found at i:3636824 original size:19 final size:18
Alignment explanation
Indices: 3636774--3636831 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 18
3636764 AATAAATAAT
* *
3636774 AAAAAGAGAAAAAATTTA
1 AAAAAAAGAAAAAATTAA
*
3636792 AAAAAAGGTAAAAAAATTAA
1 AAAAAAAG--AAAAAATTAA
*
3636812 AAAAAAA-AGAAAATTAA
1 AAAAAAAGAAAAAATTAA
3636829 AAA
1 AAA
3636832 CTTATCATTC
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
17 12 0.36
18 6 0.18
20 15 0.45
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAAAAAGAAAAAATTAA
Found at i:3637845 original size:6 final size:6
Alignment explanation
Indices: 3637834--3637899 Score: 62
Period size: 6 Copynumber: 11.0 Consensus size: 6
3637824 TTTACCAAAA
** * * *
3637834 AAAATT AAAATT AAAAACC AAAATC CAAATT AAAATT AAAATC AAAATT
1 AAAATT AAAATT -AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT
*
3637883 AAAATT -GAATT AAAATT
1 AAAATT AAAATT AAAATT
3637900 TTTGGGCTTT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
5 4 0.08
6 40 0.83
7 4 0.08
ACGTcount: A:0.64, C:0.08, G:0.02, T:0.27
Consensus pattern (6 bp):
AAAATT
Found at i:3641692 original size:3 final size:3
Alignment explanation
Indices: 3641684--3641779 Score: 81
Period size: 3 Copynumber: 32.7 Consensus size: 3
3641674 ATGGTATCTT
* * * *
3641684 TTA TTA TTA GTA -TA TTA -TA TTA -AA TTA CTA TTA TTA TTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
3641729 TTA CTA TTA TTTA CTA TTA TTA TTA CTA TTA CTA TTA TTA TTA TTA
1 TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3641775 CTA TT
1 TTA TT
3641780 TATGTTTTTT
Statistics
Matches: 72, Mismatches: 17, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
2 5 0.07
3 64 0.89
4 3 0.04
ACGTcount: A:0.34, C:0.07, G:0.01, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:3642187 original size:10 final size:10
Alignment explanation
Indices: 3642172--3642205 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
3642162 GATTTAGAGC
3642172 TTTTTGGGAT
1 TTTTTGGGAT
* *
3642182 TTTTTGGAAC
1 TTTTTGGGAT
3642192 TTTTTGGGAT
1 TTTTTGGGAT
3642202 TTTT
1 TTTT
3642206 CTAGGTTTGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.12, C:0.03, G:0.24, T:0.62
Consensus pattern (10 bp):
TTTTTGGGAT
Found at i:3642705 original size:14 final size:14
Alignment explanation
Indices: 3642625--3642713 Score: 56
Period size: 14 Copynumber: 6.1 Consensus size: 14
3642615 CCTTTTCCAA
3642625 TTTATTTTTATTTTT
1 TTTA-TTTTATTTTT
* *
3642640 ATTT-TTTGATTTGAT
1 -TTTATTTTATTT-TT
3642655 TTTATTTTATTTTT
1 TTTATTTTATTTTT
***
3642669 AACCCATTTTA-TTTT
1 --TTTATTTTATTTTT
*
3642684 ATTATTTTATTTTT
1 TTTATTTTATTTTT
*
3642698 TTTGTTTTATTTTT
1 TTTATTTTATTTTT
3642712 TT
1 TT
3642714 AAAAAAATAT
Statistics
Matches: 56, Mismatches: 12, Indels: 12
0.70 0.15 0.15
Matches are distributed among these distances:
13 6 0.11
14 29 0.52
15 12 0.21
16 9 0.16
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.76
Consensus pattern (14 bp):
TTTATTTTATTTTT
Found at i:3642712 original size:13 final size:13
Alignment explanation
Indices: 3642625--3642714 Score: 56
Period size: 13 Copynumber: 6.3 Consensus size: 13
3642615 CCTTTTCCAA
3642625 TTTATTTTTATTTT
1 TTTA-TTTTATTTT
3642639 TATT-TTTTGATTTGAT
1 T-TTATTTT-ATTT--T
3642655 TTTATTTTATTTT
1 TTTATTTTATTTT
**
3642668 TAACCCATTTTATTTT
1 T---TTATTTTATTTT
*
3642684 ATTATTTTATTTTT
1 TTTATTTTA-TTTT
*
3642698 TTTGTTTTATTTT
1 TTTATTTTATTTT
3642711 TTTA
1 TTTA
3642715 AAAAAATATT
Statistics
Matches: 59, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
13 19 0.32
14 16 0.27
15 8 0.14
16 16 0.27
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.76
Consensus pattern (13 bp):
TTTATTTTATTTT
Found at i:3642807 original size:27 final size:27
Alignment explanation
Indices: 3642777--3642828 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
3642767 AAATGATTCA
3642777 ATAAAAAAAATCTTTTCAAATAAAAAT
1 ATAAAAAAAATCTTTTCAAATAAAAAT
* *
3642804 ATAACAAACATCTTTTCAAATAAAA
1 ATAAAAAAAATCTTTTCAAATAAAA
3642829 GTTTTCAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.29
Consensus pattern (27 bp):
ATAAAAAAAATCTTTTCAAATAAAAAT
Found at i:3643178 original size:18 final size:18
Alignment explanation
Indices: 3643155--3643191 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
3643145 GAATGTGATA
3643155 CTAGTCTCTATGAATACT
1 CTAGTCTCTATGAATACT
*
3643173 CTAGTCTTTATGAATACT
1 CTAGTCTCTATGAATACT
3643191 C
1 C
3643192 CTGAGGTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.22, G:0.11, T:0.41
Consensus pattern (18 bp):
CTAGTCTCTATGAATACT
Found at i:3652244 original size:115 final size:116
Alignment explanation
Indices: 3651988--3652263 Score: 338
Period size: 115 Copynumber: 2.4 Consensus size: 116
3651978 TCATTTATCC
* * * * * * *
3651988 GATCTTGGCTCAATCCAGATCATTTTATATGATTCCTGATTTCATCCCAGTCATTTTCAACCTTG
1 GATCTTGGCTCAGTCTAGATCATTTCATATGATTCATGGTTTCGTCCCAATCATTTTCAACCTTG
* * * * *
3652053 ACTCGGTCTAGGTCACTTTTATTTTGACTCGTGTTTTTATTCTGATCATTT
66 ACTCGATCTAGGTCACTTTTATTTTGACTCGTGATTTCATCCCGATCATTT
* * * * ** *
3652104 TATCTTGGCTTAGTCTCGATCATTTCATATGATTCATGGTTTCGTCTCAATCATTTTTTATCTTG
1 GATCTTGGCTCAGTCTAGATCATTTCATATGATTCATGGTTTCGTCCCAATCATTTTCAACCTTG
* *
3652169 ACTCGATCTAGGTCAC-TTTATTTTGACTTGTGATTTCATCCCGGTCATTT
66 ACTCGATCTAGGTCACTTTTATTTTGACTCGTGATTTCATCCCGATCATTT
* *
3652219 GATTTTGGCTCAGTCTAGATCATTTCATATGATTCGTGGTTTCGT
1 GATCTTGGCTCAGTCTAGATCATTTCATATGATTCATGGTTTCGT
3652264 TCCGGTAATT
Statistics
Matches: 134, Mismatches: 26, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
115 68 0.51
116 66 0.49
ACGTcount: A:0.19, C:0.20, G:0.16, T:0.46
Consensus pattern (116 bp):
GATCTTGGCTCAGTCTAGATCATTTCATATGATTCATGGTTTCGTCCCAATCATTTTCAACCTTG
ACTCGATCTAGGTCACTTTTATTTTGACTCGTGATTTCATCCCGATCATTT
Found at i:3653162 original size:10 final size:10
Alignment explanation
Indices: 3653147--3653192 Score: 67
Period size: 10 Copynumber: 4.6 Consensus size: 10
3653137 ATTTAGAGCT
3653147 TTTTTTAGGA
1 TTTTTTAGGA
3653157 TTTTTT-GGAA
1 TTTTTTAGG-A
*
3653167 TTTTCTAGGA
1 TTTTTTAGGA
3653177 TTTTTTAGGA
1 TTTTTTAGGA
3653187 TTTTTT
1 TTTTTT
3653193 TTTGGTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 2 0.06
10 28 0.88
11 2 0.06
ACGTcount: A:0.17, C:0.02, G:0.17, T:0.63
Consensus pattern (10 bp):
TTTTTTAGGA
Found at i:3653689 original size:18 final size:18
Alignment explanation
Indices: 3653666--3653703 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
3653656 ATTTTTAACC
3653666 TATTTTA-TTTTATTATTT
1 TATTTTAGTTTTATT-TTT
3653684 TATTTTAGTTTTATTTTT
1 TATTTTAGTTTTATTTTT
3653702 TA
1 TA
3653704 AAAAAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 12 0.63
19 7 0.37
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.76
Consensus pattern (18 bp):
TATTTTAGTTTTATTTTT
Found at i:3653811 original size:26 final size:27
Alignment explanation
Indices: 3653760--3653812 Score: 97
Period size: 27 Copynumber: 2.0 Consensus size: 27
3653750 AAATGATTCA
3653760 ATAAAAAAAATCTTTTCAAATAAAAAT
1 ATAAAAAAAATCTTTTCAAATAAAAAT
*
3653787 ATAAAAAACATCTTTTCAAATAAAAA
1 ATAAAAAAAATCTTTTCAAATAAAAA
3653813 GTTTTCAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.28
Consensus pattern (27 bp):
ATAAAAAAAATCTTTTCAAATAAAAAT
Found at i:3653866 original size:14 final size:15
Alignment explanation
Indices: 3653842--3653872 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
3653832 AAATTCTTTT
3653842 AAGTAAAAAAAAAAA
1 AAGTAAAAAAAAAAA
3653857 AAGTAAAAAAAAAAA
1 AAGTAAAAAAAAAAA
3653872 A
1 A
3653873 TCTTTTTTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.87, C:0.00, G:0.06, T:0.06
Consensus pattern (15 bp):
AAGTAAAAAAAAAAA
Found at i:3654469 original size:32 final size:32
Alignment explanation
Indices: 3654425--3654519 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 32
3654415 ATTAATGACA
* *
3654425 ACTTCTCTTACACCTATCTAGCTATAAGTCCG
1 ACTTCTCCTACACATATCTAGCTATAAGTCCG
*
3654457 ACTTCTCCTACACATATCTAGCTATAAATCCG
1 ACTTCTCCTACACATATCTAGCTATAAGTCCG
3654489 ACTTCTCCTACACATATCTAGCTATAAGTCC
1 ACTTCTCCTACACATATCTAGCTATAAGTCC
3654520 TGTGATGACA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.28, C:0.32, G:0.07, T:0.33
Consensus pattern (32 bp):
ACTTCTCCTACACATATCTAGCTATAAGTCCG
Done.