Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009014.1 Hibiscus syriacus cultivar Beakdansim tig00112402_pilon, 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: 3470424
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 13
Found at i:490187 original size:25 final size:25
Alignment explanation
Indices: 490154--490202 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
490144 GTGAAGAGAC
*
490154 AAGAAAAACAAAGAGAAATGAAGCT
1 AAGAAAAACAAAGAGAAAAGAAGCT
490179 AAGAAAAACAAAGAGAAAAGAAGC
1 AAGAAAAACAAAGAGAAAAGAAGC
490203 AAAAGAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.67, C:0.08, G:0.20, T:0.04
Consensus pattern (25 bp):
AAGAAAAACAAAGAGAAAAGAAGCT
Found at i:490216 original size:21 final size:21
Alignment explanation
Indices: 490183--490241 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
490173 GAAGCTAAGA
*
490183 AAAACAAAG-AGAAAAGAAGC
1 AAAAGAAAGAAGAAAAGAAGC
*
490203 AAAAGAAAGAAGAAAAAAAAGC
1 AAAAGAAAGAAG-AAAAGAAGC
490225 -AAAGAAAGAAAGAAAAG
1 AAAAGAAAG-AAGAAAAG
490242 CAAAATAAAC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
20 8 0.24
21 14 0.42
22 11 0.33
ACGTcount: A:0.75, C:0.05, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAGAAAGAAGAAAAGAAGC
Found at i:490224 original size:22 final size:21
Alignment explanation
Indices: 490188--490284 Score: 74
Period size: 22 Copynumber: 4.4 Consensus size: 21
490178 TAAGAAAAAC
*
490188 AAAGAGAAAAGAAGCAAAAGAA
1 AAAGA-AAAAAAAGCAAAAGAA
490210 AGAAGAAAAAAAAGC-AAAGAAA
1 A-AAGAAAAAAAAGCAAAAG-AA
* *
490232 GAAAGAAAAGCAAAA--TAAACAA
1 -AAAGAAAA--AAAAGCAAAAGAA
*
490254 AAACAAAAACAAAGCAAAAGAA
1 AAAGAAAAA-AAAGCAAAAGAA
490276 AAAGAAAAA
1 AAAGAAAAA
490285 TCAAAGAGAA
Statistics
Matches: 60, Mismatches: 6, Indels: 18
0.71 0.07 0.21
Matches are distributed among these distances:
19 1 0.02
20 3 0.05
21 11 0.18
22 33 0.55
23 8 0.13
24 4 0.07
ACGTcount: A:0.76, C:0.07, G:0.15, T:0.01
Consensus pattern (21 bp):
AAAGAAAAAAAAGCAAAAGAA
Found at i:490235 original size:18 final size:17
Alignment explanation
Indices: 490203--490245 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
490193 GAAAAGAAGC
490203 AAAAG-AAAGAAGAAAA
1 AAAAGCAAAGAAGAAAA
*
490219 AAAAGCAAAGAAAGAAAG
1 AAAAGCAAAG-AAGAAAA
490237 AAAAGCAAA
1 AAAAGCAAA
490246 ATAAACAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 5 0.21
17 4 0.17
18 15 0.62
ACGTcount: A:0.77, C:0.05, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAGCAAAGAAGAAAA
Found at i:490262 original size:40 final size:40
Alignment explanation
Indices: 490199--490276 Score: 97
Period size: 40 Copynumber: 1.9 Consensus size: 40
490189 AAGAGAAAAG
*
490199 AAGCAAAAGAAAGAAGAAAAAAAAGCAAAG-AAAGAAAGAA
1 AAGCAAAAGAAACAAGAAAAAAAA-CAAAGAAAAGAAAGAA
*
490239 AAGCAAAATAAACAA-AAACAAAAACAAAGCAAAAGAAA
1 AAGCAAAAGAAACAAGAAA-AAAAACAAAG-AAAAGAAA
490277 AAGAAAAATC
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
39 8 0.24
40 18 0.55
41 7 0.21
ACGTcount: A:0.76, C:0.09, G:0.14, T:0.01
Consensus pattern (40 bp):
AAGCAAAAGAAACAAGAAAAAAAACAAAGAAAAGAAAGAA
Found at i:490277 original size:16 final size:15
Alignment explanation
Indices: 490179--490278 Score: 55
Period size: 16 Copynumber: 6.5 Consensus size: 15
490169 AAATGAAGCT
*
490179 AAGAAAAACAAAGAGAA
1 AAGAAAAA-AAAG-CAA
** *
490196 AAGAAGCAAAAGAAA
1 AAGAAAAAAAAGCAA
490211 GAAGAAAAAAAAGC-A
1 -AAGAAAAAAAAGCAA
*
490226 AAG-AAAGAAAG-AA
1 AAGAAAAAAAAGCAA
*
490239 AAGCAAAATAAA-CAAA
1 AAG-AAAAAAAAGC-AA
*
490255 AACAAAAACAAAGCAA
1 AAGAAAAA-AAAGCAA
490271 AAGAAAAA
1 AAGAAAAA
490279 GAAAAATCAA
Statistics
Matches: 64, Mismatches: 11, Indels: 17
0.70 0.12 0.18
Matches are distributed among these distances:
13 11 0.17
14 3 0.05
15 13 0.20
16 30 0.47
17 7 0.11
ACGTcount: A:0.76, C:0.08, G:0.15, T:0.01
Consensus pattern (15 bp):
AAGAAAAAAAAGCAA
Found at i:491578 original size:30 final size:29
Alignment explanation
Indices: 491486--491625 Score: 118
Period size: 30 Copynumber: 4.6 Consensus size: 29
491476 ATCCTTTGAC
* *
491486 TTGTTTCTCTTGAAACAAATTTTATCTCTCGAGA
1 TTGTTTCTCTTGAAACAAA----ATCT-TTGAGT
* *
491520 TAGTTTCTTTTGAAACAAAACATCTTTGAGT
1 TTGTTTCTCTTGAAAC-AAA-ATCTTTGAGT
491551 TTGTTTCTCTTGAAACAAAAGTCTTTGAGT
1 TTGTTTCTCTTGAAACAAAA-TCTTTGAGT
* * * **
491581 CTATTTCTTTTGAAACATCATCTTTGAGT
1 TTGTTTCTCTTGAAACAAAATCTTTGAGT
*
491610 TAGTTTCTCTTGAAAC
1 TTGTTTCTCTTGAAAC
491626 CATTATCCCT
Statistics
Matches: 88, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
29 22 0.25
30 27 0.31
31 18 0.20
32 4 0.05
34 14 0.16
35 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.13, T:0.44
Consensus pattern (29 bp):
TTGTTTCTCTTGAAACAAAATCTTTGAGT
Found at i:491616 original size:29 final size:29
Alignment explanation
Indices: 491520--491625 Score: 124
Period size: 29 Copynumber: 3.6 Consensus size: 29
491510 TCTCTCGAGA
*
491520 TAGTTTCTTTTGAAACAAAACATCTTTGAGT
1 TAGTTTCTCTTGAAAC--AACATCTTTGAGT
* *
491551 TTGTTTCTCTTGAAACAAAAGTCTTTGAGT
1 TAGTTTCTCTTGAAACAACA-TCTTTGAGT
* *
491581 CTA-TTTCTTTTGAAACATCATCTTTGAGT
1 -TAGTTTCTCTTGAAACAACATCTTTGAGT
491610 TAGTTTCTCTTGAAAC
1 TAGTTTCTCTTGAAAC
491626 CATTATCCCT
Statistics
Matches: 64, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
28 2 0.03
29 24 0.38
30 23 0.36
31 15 0.23
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.44
Consensus pattern (29 bp):
TAGTTTCTCTTGAAACAACATCTTTGAGT
Found at i:491893 original size:134 final size:133
Alignment explanation
Indices: 491631--492244 Score: 636
Period size: 134 Copynumber: 4.6 Consensus size: 133
491621 GAAACCATTA
* * * * * * *
491631 TCCCTAAAGATGGCC-TATCTCCTCATCATGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTC
1 TCCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTC
* * *
491695 ATCACGT-AGAAGCCGTGTCACCCCTCGATAACCAGCCGTCCTCATCGCGTAAGAA-CTGTGTTA
66 ATCACGTAAG-AGTCGTGTCACCCCTAGATAACCAACCGTCCTCATCGCGTAAGAATC-GTGTTA
491758 TCATCC
129 TCA-CC
* * ** *
491764 TCCCTAAAGATGGCCAGAACTCTTCATCATGTATGAGTCGTGTCATCCCTTGACAAGACCTCCTC
1 TCCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTC
* * * * *
491829 ATCACGTAAGAGTCATGTCACCCTTAGATAACCAACTGTCCTCATCGTGTAGGAATCGTGTTATC
66 ATCACGTAAGAGTCGTGTCACCCCTAGATAACCAACCGTCCTCATCGCGTAAGAATCGTGTTATC
491894 ACCC
131 A-CC
* * * *
491898 TTCCTAAAGATGGCCATAACTCTTCATCACGTATGAGCCGTCTCATCCCCCGACCAAACCTCCTC
1 TCCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTC
* * * ** * *
491963 ATCACGTAGGAGCCGTGTCACCCCTA-ATAATCAGTCGTCCTCATCACGTAAGAATCATGTTATC
66 ATCACGTAAGAGTCGTGTCACCCCTAGATAACCAACCGTCCTCATCGCGTAAGAATCGTGTTATC
*
492027 A-A
131 ACC
* * * * * *
492029 T-CCTAAAGATGG-TATG-TCGT-TCTCATCACGTAAGAACCATGTCATCCCTCGACCAGACCTC
1 TCCCTAAAGATGGCCA-GAAC-TCT-TCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTC
* * * *
492090 CTTATCACAT-AGAAGTCGTGTCACCCCTAGATAACCATCCGTCCTCATCGCGTAGGAATCGTGT
63 CTCATCACGTAAG-AGTCGTGTCACCCCTAGATAACCAACCGTCCTCATCGCGTAAGAATCGTGT
492154 TATCACC
127 TATCACC
* * ** *
492161 CCTCCTAAAGATGGCCGGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCT
1 TC-CCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCT
* *
492226 CATCACGTAGGAGTTGTGT
65 CATCACGTAAGAGTCGTGT
492245 TACCTTTATA
Statistics
Matches: 392, Mismatches: 74, Indels: 29
0.79 0.15 0.06
Matches are distributed among these distances:
129 4 0.01
130 68 0.17
131 34 0.09
133 46 0.12
134 234 0.60
135 6 0.02
ACGTcount: A:0.25, C:0.32, G:0.17, T:0.26
Consensus pattern (133 bp):
TCCCTAAAGATGGCCAGAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTC
ATCACGTAAGAGTCGTGTCACCCCTAGATAACCAACCGTCCTCATCGCGTAAGAATCGTGTTATC
ACC
Found at i:492123 original size:264 final size:266
Alignment explanation
Indices: 491633--492238 Score: 760
Period size: 264 Copynumber: 2.3 Consensus size: 266
491623 AACCATTATC
* * * * * *
491633 CCTAAAGATGGCCTATCTCCTCATCATGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATC
1 CCTAAAGATGGCCTAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTCATC
* * * *
491698 ACGTAGAAGCCGTGTCACCCCTCGATAACCAGCCGTCCTCATCGCGTAAGAACTGTGTTATCATC
66 ACGTAGGAGCCGTGTCACCCCTCAATAACCAGCCGTCCTCATCACGTAAGAACTATGTTATCA-C
* * * ** * *
491763 CTCCCTAAAGATGGCCAGAACTCTTCATCATGTATGAGTCGTGTCATCCCTTGACAAGACCTCCT
130 ATCCCTAAAGATGGCCAGAACTCTTCATCACGTAAGAACCATGTCATCCCTCGACAAGACCTCCT
* * * *
491828 CATCACGTAAGAGTCATGTCACCCTTAGATAACCAACTGTCCTCATCGTGTAGGAATCGTGTTAT
195 CATCACATAAGAGTCATGTCACCCCTAGATAACCAACCGTCCTCATCGCGTAGGAATCGTGTTAT
*
491893 CACCCTT
260 CACCCCT
* *
491900 CCTAAAGATGGCCATAACTCTTCATCACGTATGAGCCGTCTCATCCCCCGACCAAACCTCCTCAT
1 CCTAAAGATGGCC-TAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTCAT
* *
491965 CACGTAGGAGCCGTGTCACCCCT-AATAATCAGTCGTCCTCATCACGTAAGAA-TCATGTTATCA
65 CACGTAGGAGCCGTGTCACCCCTCAATAACCAGCCGTCCTCATCACGTAAGAACT-ATGTTATCA
* * *
492028 -AT-CCTAAAGATGG-TATG-TCGT-TCTCATCACGTAAGAACCATGTCATCCCTCGACCAGACC
129 CATCCCTAAAGATGGCCA-GAAC-TCT-TCATCACGTAAGAACCATGTCATCCCTCGACAAGACC
* * *
492088 TCCTTATCACAT-AGAAGTCGTGTCACCCCTAGATAACCATCCGTCCTCATCGCGTAGGAATCGT
191 TCCTCATCACATAAG-AGTCATGTCACCCCTAGATAACCAACCGTCCTCATCGCGTAGGAATCGT
492152 GTTATCACCCCT
255 GTTATCACCCCT
* ** *
492164 CCTAAAGATGGCCGGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCAT
1 CCTAAAGATGGCC-TAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTCAT
492229 CACGTAGGAG
65 CACGTAGGAG
492239 TTGTGTTACC
Statistics
Matches: 294, Mismatches: 39, Indels: 15
0.84 0.11 0.04
Matches are distributed among these distances:
263 5 0.02
264 176 0.60
265 1 0.00
266 1 0.00
267 46 0.16
268 65 0.22
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (266 bp):
CCTAAAGATGGCCTAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTCATC
ACGTAGGAGCCGTGTCACCCCTCAATAACCAGCCGTCCTCATCACGTAAGAACTATGTTATCACA
TCCCTAAAGATGGCCAGAACTCTTCATCACGTAAGAACCATGTCATCCCTCGACAAGACCTCCTC
ATCACATAAGAGTCATGTCACCCCTAGATAACCAACCGTCCTCATCGCGTAGGAATCGTGTTATC
ACCCCT
Found at i:492451 original size:3 final size:3
Alignment explanation
Indices: 492443--492514 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
492433 TCTACAAAAA
492443 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
492491 TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
492515 GGTAATTTAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:496301 original size:10 final size:10
Alignment explanation
Indices: 496288--496317 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
496278 AAACAAAAAA
496288 TCCCGGTTTT
1 TCCCGGTTTT
496298 TCCCGGTTTT
1 TCCCGGTTTT
*
496308 TTCCGGTTTT
1 TCCCGGTTTT
496318 CAGCCGGTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.20, T:0.53
Consensus pattern (10 bp):
TCCCGGTTTT
Found at i:500663 original size:23 final size:23
Alignment explanation
Indices: 500637--500705 Score: 84
Period size: 23 Copynumber: 3.0 Consensus size: 23
500627 CACCACAGCT
* *
500637 CGTATAAATGCACCGGAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
500660 CGTAGAATTGCACCAAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
500683 CGTAGAAATGCACCGTAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
500706 TATAAGATTT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.30, C:0.26, G:0.26, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:502254 original size:24 final size:20
Alignment explanation
Indices: 502201--502258 Score: 71
Period size: 20 Copynumber: 2.7 Consensus size: 20
502191 TTCCCTTTGA
*
502201 AGTGCATCAATGCATTCTAC
1 AGTGCATCGATGCATTCTAC
502221 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
502244 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
502259 CTACCCATGC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 16 0.48
22 1 0.03
23 3 0.09
24 13 0.39
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:509733 original size:18 final size:18
Alignment explanation
Indices: 509712--509750 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
509702 CTTTAACCTT
*
509712 ACAACACTTACCACGACA
1 ACAACACTTACCACAACA
* *
509730 ACAACATTTGCCACAACA
1 ACAACACTTACCACAACA
509748 ACA
1 ACA
509751 CCATTCATAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.46, C:0.36, G:0.05, T:0.13
Consensus pattern (18 bp):
ACAACACTTACCACAACA
Found at i:517886 original size:15 final size:15
Alignment explanation
Indices: 517864--517942 Score: 122
Period size: 15 Copynumber: 5.3 Consensus size: 15
517854 CACCTTGGCC
* *
517864 TCGAGTTCATCATCT
1 TCGAGTTCGTCTTCT
*
517879 TGGAGTTCGTCTTCT
1 TCGAGTTCGTCTTCT
517894 TCGAGTTCGTCTTCT
1 TCGAGTTCGTCTTCT
517909 TCGAGTTCGTCTTCT
1 TCGAGTTCGTCTTCT
*
517924 TCGAGTTCTTCTTCT
1 TCGAGTTCGTCTTCT
517939 TCGA
1 TCGA
517943 ATGTATCAGG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 59 1.00
ACGTcount: A:0.10, C:0.25, G:0.19, T:0.46
Consensus pattern (15 bp):
TCGAGTTCGTCTTCT
Found at i:520010 original size:23 final size:24
Alignment explanation
Indices: 519964--520021 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
519954 ATAATTAATA
519964 ATATTATGTAAAATGTTTTCGATT
1 ATATTATGTAAAATGTTTTCGATT
519988 ATATTATGTAAAATG-TTTCGATT
1 ATATTATGTAAAATGTTTTCGATT
520011 ATA--ATGTAAAA
1 ATATTATGTAAAA
520022 ATTATAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
21 8 0.24
23 11 0.32
24 15 0.44
ACGTcount: A:0.40, C:0.03, G:0.12, T:0.45
Consensus pattern (24 bp):
ATATTATGTAAAATGTTTTCGATT
Found at i:520019 original size:21 final size:23
Alignment explanation
Indices: 519968--520021 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
519958 TTAATAATAT
519968 TATGTAAAATGTTTTCGATTATA
1 TATGTAAAATGTTTTCGATTATA
519991 TTATGTAAAATG-TTTCGATTATA
1 -TATGTAAAATGTTTTCGATTATA
520014 -ATGTAAAA
1 TATGTAAAA
520022 ATTATAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 8 0.27
23 11 0.37
24 11 0.37
ACGTcount: A:0.39, C:0.04, G:0.13, T:0.44
Consensus pattern (23 bp):
TATGTAAAATGTTTTCGATTATA
Found at i:520045 original size:20 final size:21
Alignment explanation
Indices: 520011--520070 Score: 59
Period size: 23 Copynumber: 2.8 Consensus size: 21
520001 TGTTTCGATT
* *
520011 ATAATGTAAAAATTATAAATA
1 ATAATATAAATATTATAAATA
520032 ATAAT-TAAATATTATATTAAATA
1 ATAATATAAATA-T-TA-TAAATA
*
520055 ATATTATAAATATTAT
1 ATAATATAAATATTAT
520071 TTAGTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
20 5 0.15
21 7 0.21
22 4 0.12
23 11 0.33
24 6 0.18
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (21 bp):
ATAATATAAATATTATAAATA
Found at i:520064 original size:12 final size:12
Alignment explanation
Indices: 520022--520071 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
520012 TAATGTAAAA
520022 ATTATAAATAAT
1 ATTATAAATAAT
* *
520034 AAT-TAAATATT
1 ATTATAAATAAT
520045 A-TATTAAATAAT
1 ATTA-TAAATAAT
*
520057 ATTATAAATATT
1 ATTATAAATAAT
520069 ATT
1 ATT
520072 TAGTATTTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
10 1 0.03
11 8 0.26
12 20 0.65
13 2 0.06
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (12 bp):
ATTATAAATAAT
Found at i:520069 original size:24 final size:23
Alignment explanation
Indices: 520026--520070 Score: 72
Period size: 23 Copynumber: 1.9 Consensus size: 23
520016 GTAAAAATTA
520026 TAAATAATAATTAAATATTATAT
1 TAAATAATAATTAAATATTATAT
*
520049 TAAATAATATTATAAATATTAT
1 TAAATAATAAT-TAAATATTAT
520071 TTAGTATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATAATAATTAAATATTATAT
Found at i:523050 original size:8 final size:8
Alignment explanation
Indices: 523037--523077 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
523027 CTCATTTTCA
523037 GAGAATTT
1 GAGAATTT
523045 GAGAATTT
1 GAGAATTT
*
523053 -AGAGTTT
1 GAGAATTT
*
523060 GGGAATTT
1 GAGAATTT
523068 GAGAATTT
1 GAGAATTT
523076 GA
1 GA
523078 AAGATTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:523662 original size:28 final size:28
Alignment explanation
Indices: 523630--523717 Score: 99
Period size: 28 Copynumber: 3.2 Consensus size: 28
523620 GAAATTAATG
*
523630 TTAAATTTCGAATACTATAATTTATATT
1 TTAAATTTCGAATAATATAATTTATATT
* * *
523658 TTAAATTTTTGAATAAT-TTATTTTTATT
1 TTAAA-TTTCGAATAATATAATTTATATT
* *
523686 TT-TATTTCGAATAATATAATTTGTATT
1 TTAAATTTCGAATAATATAATTTATATT
523713 TTAAA
1 TTAAA
523718 AACATTTATC
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
26 10 0.21
27 12 0.25
28 17 0.35
29 9 0.19
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (28 bp):
TTAAATTTCGAATAATATAATTTATATT
Found at i:524314 original size:21 final size:21
Alignment explanation
Indices: 524227--524319 Score: 120
Period size: 21 Copynumber: 4.5 Consensus size: 21
524217 ATATGGTATA
*
524227 AACCCTGCGGGCTA-GCATGT
1 AACCCTGCGGGCTAGGAATGT
*
524247 AA-CCTGGCGGGCTAGGCATGT
1 AACCCT-GCGGGCTAGGAATGT
524268 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
524289 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
524310 AACCCTGCGG
1 AACCCTGCGG
524320 AGATGGCATA
Statistics
Matches: 68, Mismatches: 2, Indels: 5
0.91 0.03 0.07
Matches are distributed among these distances:
19 3 0.04
20 10 0.15
21 52 0.76
22 3 0.04
ACGTcount: A:0.20, C:0.27, G:0.34, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:526106 original size:33 final size:31
Alignment explanation
Indices: 526068--526152 Score: 93
Period size: 33 Copynumber: 2.7 Consensus size: 31
526058 TTATAATTCT
*
526068 AAATAAATAATAATTATATAAATATTATTTTA
1 AAATAAATAATAATTATATAAATA-TATTATA
*
526100 ATAATAAAATAAT-ATTACATAAATATATTATA
1 A-AAT-AAATAATAATTATATAAATATATTATA
* *
526132 AAA-AAATAATAACTATTTAAA
1 AAATAAATAATAATTATATAAA
526153 AAATACTAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
29 7 0.16
30 7 0.16
31 2 0.04
32 8 0.18
33 14 0.31
34 7 0.16
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (31 bp):
AAATAAATAATAATTATATAAATATATTATA
Found at i:529610 original size:31 final size:32
Alignment explanation
Indices: 529567--529627 Score: 99
Period size: 31 Copynumber: 1.9 Consensus size: 32
529557 TATTAGATAA
529567 AAAATGTAAGAAATAAATAAA-TAAATAAAATT
1 AAAATGTAAGAAA-AAATAAATTAAATAAAATT
529599 AAAATG-AAGAAAAAATAAATTAAATAAAA
1 AAAATGTAAGAAAAAATAAATTAAATAAAA
529628 GATAAGATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
30 7 0.25
31 15 0.54
32 6 0.21
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (32 bp):
AAAATGTAAGAAAAAATAAATTAAATAAAATT
Found at i:529715 original size:44 final size:42
Alignment explanation
Indices: 529666--529773 Score: 103
Period size: 44 Copynumber: 2.5 Consensus size: 42
529656 AGTGAGTAAA
*
529666 ATAAATATAAAAAATAAAAAATAGTAAATAGTAA-ATATATATAT
1 ATAAATATAAAAAATAAAAAATA--AAA-AATAACATATATATAT
* * *
529710 ATAAAT-TAATAAAACAGATAATAAAAAATAACATATATATAT
1 ATAAATATAA-AAAATAAAAAATAAAAAATAACATATATATAT
* *
529752 ATAATCTAAAAAAAATAAAAAA
1 ATAA-ATATAAAAAATAAAAAA
529774 AATATACTAA
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
41 4 0.08
42 17 0.33
43 12 0.24
44 18 0.35
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.27
Consensus pattern (42 bp):
ATAAATATAAAAAATAAAAAATAAAAAATAACATATATATAT
Found at i:530370 original size:37 final size:37
Alignment explanation
Indices: 530318--530425 Score: 189
Period size: 37 Copynumber: 2.9 Consensus size: 37
530308 TTGTGGATCC
* * *
530318 TATTTTTAGGTGTTTGAATCATAGTAGAACTCTATCA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
530355 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
530392 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
530426 ACGTTATGTT
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
37 68 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTATCA
Found at i:531094 original size:84 final size:84
Alignment explanation
Indices: 530998--532446 Score: 1330
Period size: 84 Copynumber: 17.4 Consensus size: 84
530988 AAATTTGGTT
* * * *
530998 TGCCTTTGAGCTGAGCGTAATCGAACTCGAAAGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
*
531063 AGTTATGCTGCAAATAATG
66 AGTTATGCTGCAAATGATG
* * * * * * *
531082 TGCCTTGGAGCTGAGCATAGTCAAACTTGAAGGTCTTT-ATTGGCAGATAACCCTTCTAGCCTTG
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
531146 AGTTATGCTGCAAATGATG
66 AGTTATGCTGCAAATGATG
* * * * * * * * *
531165 TGCCCTCGAAGCTGAGTGTAATCGAACTAGAGGGTC--T--TTAGCAGATAGCCTTTCTCGACTT
1 TG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTT
531226 AAGTTATGCTGCAAATGATG
65 AAGTTATGCTGCAAATGATG
* * *
531246 TGCCTTAGAGCTCAGCGTAGTTGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
*
531311 AGTTATGCTGCAAATGATA
66 AGTTATGCTGCAAATGATG
* * * * * * *
531330 TACCTTGGAACTGAGCGTAGTCGAACTCGAATGTCTTTTGG-TGACATATAACCCTTCTAGCCTT
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTT
* * * *
531394 GAGTTATGTTGTAAATGTTG
65 AAGTTATGCTGCAAATGATG
* * * * * *
531414 TGCCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACT
1 TG--CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACT
* * * *
531475 TAAGCTATGTTGCAAATAATA
64 TAAGTTATGCTGCAAATGATG
* *
531496 TGCCTTGGAGCTGAGCTTAGTCGAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * *
531561 AGTTATGTTGTAAATGATA
66 AGTTATGCTGCAAATGATG
* * ** ** * *
531580 TGCCTTGAAGCTGAGCGGAGTCGAACTCGAACATCTTTTGG-TCACAGATAACCCTTCTAGCCTT
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTT
* * **
531644 GAGTTATACTATAAATGATG
65 AAGTTATGCTGCAAATGATG
* * * * * * ** * * *
531664 TGCCCTCGAAGCTGAGTGTAATCAAACTCGAGGGGGTCT--TTGGCAGATAGCCTTTCTCGACTT
1 TG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTT
* * *
531727 GAGCTATACTGCAAATGATG
65 AAGTTATGCTGCAAATGATG
* * * ** * **
531747 TGCCTTGGAGATGAGCGTAGTCAAACTCGAAGGTCTTT-GTTGGTAGATAATTCTTTTTTACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* *
531811 AGTTATGCTGCAAACGATA
66 AGTTATGCTGCAAATGATG
** * * *
531830 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGG-TCACATATAACCCTTCTAGCCTT
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GGTTGGCAGATAACCCTTCTCGACTT
* * *
531894 GAGTTATGTTGTAAATGATG
65 AAGTTATGCTGCAAATGATG
* * *** * * * *
531914 TGCCCTCGAAGCTGAGTACAATCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCAACTT
1 TG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTT
* * *
531975 AAGCTATGATGTAAATGATG
65 AAGTTATGCTGCAAATGATG
** * * *
531995 TGCCTTGGAGCTGAGTATAGTTGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTC
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* *
532060 CGTTATGCTGCAAATGATA
66 AGTTATGCTGCAAATGATG
* * * * * *
532079 TGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGTTCGTTTGGTT-ACAGATAACCCATCTAGCCTT
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTT
* * *
532143 GAGTTATACTGTAAATGATG
65 AAGTTATGCTGCAAATGATG
* * * * * * * * *
532163 TGCCCTCGAAGCTGAGTGTAATTGAACTCGAGGGTC--T--TTGGAAGATAGCCCTTCTCGAATT
1 TG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTT
*
532224 AAGCTATGCTGCAAATGATG
65 AAGTTATGCTGCAAATGATG
*
532244 TGCCTTGGAGCTGAGCGTAGTCGATCTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
*
532309 AGTTATGCTGCAAATGATA
66 AGTTATGCTGCAAATGATG
* * * * * *
532328 TGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGATC-TTGG-TGGCAGATAGCCCTTCTGGCCTTG
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* **
532391 AGCTATGCTATAAATGATG
66 AGTTATGCTGCAAATGATG
532410 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
532447 GGCTAACAGA
Statistics
Matches: 1083, Mismatches: 249, Indels: 67
0.77 0.18 0.05
Matches are distributed among these distances:
80 105 0.10
81 107 0.10
82 135 0.12
83 151 0.14
84 467 0.43
85 92 0.08
86 26 0.02
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (84 bp):
TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
AGTTATGCTGCAAATGATG
Found at i:531491 original size:250 final size:248
Alignment explanation
Indices: 530998--532446 Score: 2010
Period size: 250 Copynumber: 5.8 Consensus size: 248
530988 AAATTTGGTT
* * * *
530998 TGCCTTTGAGCTGAGCGTAATCGAACTCGAAAGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * * * * *
531063 AGTTATGCTGCAAATAATGTGCCTTGGAGCTGAGCATAGTCAAACTTGAAGGTCTTTAT--TGGC
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA-GTCTTT-TGGTGAC
*
531126 AGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAA
129 AGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAA
* * * *
531191 CTAGAGGGTCTTTAGCAGATAGCCTTTCTCGACTTAAGTTATGCTGCAAATGATG
194 CTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* * *
531246 TGCCTTAGAGCTCAGCGTAGTTGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* *
531311 AGTTATGCTGCAAATGATATACCTTGGAACTGAGCGTAGTCGAACTCGAATGTCTTTTGGTGACA
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA-GTCTTTTGGTGACA
* * *
531376 TATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGTTGTGCCCCTCGAAGCTGAGTGTAATCGAA
130 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG-CCCTCGAAGCTGAGTGTAATCGAA
* * *
531441 CTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATAATA
194 CTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* *
531496 TGCCTTGGAGCTGAGCTTAGTCGAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * * * * *
531561 AGTTATGTTGTAAATGATATGCCTTGAAGCTGAGCGGAGTCGAACTCGAACATCTTTTGGTCACA
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA-GTCTTTTGGTGACA
* * *
531626 GATAACCCTTCTAGCCTTGAGTTATACTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAAC
130 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
* * *
531691 TCGAGGGGGTCTTTGGCAGATAGCCTTTCTCGACTTGAGCTATACTGCAAATGATG
195 TCGA--GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
* * * ** * **
531747 TGCCTTGGAGATGAGCGTAGTCAAACTCGAAGGTCTTT-GTTGGTAGATAATTCTTTTTTACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * *
531811 AGTTATGCTGCAAACGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGGTCACA
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA-GTCTTTTGGTGACA
* * **
531876 TATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTACAATCGAAC
130 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
* * *
531941 TCGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATGATGTAAATGATG
195 TCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
** * * *
531995 TGCCTTGGAGCTGAGTATAGTTGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTC
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * * *
532060 CGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGTTCGTTTGGTTACA
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG-TCTTTTGGTGACA
* * *
532125 GATAACCCATCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATTGAAC
130 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
* *
532190 TCGAGGGTCTTTGGAAGATAGCCCTTCTCGAATTAAGCTATGCTGCAAATGATG
195 TCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
*
532244 TGCCTTGGAGCTGAGCGTAGTCGATCTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* *
532309 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGATC--TTGGTGGCA
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAG-TCTTTTGGTGACA
* * * * * * * *
532372 GATAGCCCTTCTGGCCTTGAGCTATGCTATAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAAC
130 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
*
532436 TCGAAGGTCTT
195 TCGAGGGTCTT
532447 GGCTAACAGA
Statistics
Matches: 1058, Mismatches: 136, Indels: 16
0.87 0.11 0.01
Matches are distributed among these distances:
246 29 0.03
247 42 0.04
248 186 0.18
249 361 0.34
250 362 0.34
251 78 0.07
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (248 bp):
TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGTCTTTTGGTGACAG
ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
Found at i:532132 original size:249 final size:248
Alignment explanation
Indices: 530998--532446 Score: 1990
Period size: 249 Copynumber: 5.8 Consensus size: 248
530988 AAATTTGGTT
* * * *
530998 TGCCTTTGAGCTGAGCGTAATCGAACTCGAAAGTCTTTGGTTGGCAGATAGCCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * * * * * ** **
531063 AGTTATGCTGCAAATAATGTGCCTTGGAGCTGAGCATAGTCAAACTTGAAGGTCTTTATTGGCAG
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTCACAG
*
531128 ATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
131 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
* * * * *
531193 AGAGGGTCTTTAGCAGATAGCCTTTCTCGACTTAAGTTATGCTGCAAATGATG
196 CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATG
* * *
531246 TGCCTTAGAGCTCAGCGTAGTTGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * *
531311 AGTTATGCTGCAAATGATATACCTTGGAACTGAGCGTAGTCGAACTCGAATG-TCTTTTGGTGAC
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAA-GATC-TTTGGTCAC
* * *
531375 ATATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGTTGTGCCCCTCGAAGCTGAGTGTAATCGA
129 AGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTG-CCCTCGAAGCTGAGTGTAATCGA
* * *
531440 ACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGTTGCAAATAATA
193 ACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATG
* *
531496 TGCCTTGGAGCTGAGCTTAGTCGAACTTGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * * * *
531561 AGTTATGTTGTAAATGATATGCCTTGAAGCTGAGCGGAGTCGAACTCGAACATCTTTTGGTCACA
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATC-TTTGGTCACA
* * *
531626 GATAACCCTTCTAGCCTTGAGTTATACTATAAATGATGTGCCCTCGAAGCTGAGTGTAATCAAAC
130 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
* *
531691 TCGAGGGGGTCTTTGGCAGATAGCCTTTCTCGACTTGAGCTAT-ACTGCAAATGATG
195 TCGA--GGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGA-TGCAAATGATG
* * * ** * **
531747 TGCCTTGGAGATGAGCGTAGTCAAACTCGAAGGTCTTT-GTTGGTAGATAATTCTTTTTTACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* *
531811 AGTTATGCTGCAAACGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTAGGTCACA
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTT-GGTCACA
* * **
531876 TATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTGCCCTCGAAGCTGAGTACAATCGAAC
130 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
* *
531941 TCGAGGGTCTTTGGCAGATAGCCCTTCTCAACTTAAGCTATGATGTAAATGATG
195 TCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATG
** * * *
531995 TGCCTTGGAGCTGAGTATAGTTGAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTC
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* * * *
532060 CGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGTTCGTTTGGTTACA
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATC-TTTGGTCACA
* * *
532125 GATAACCCATCTAGCCTTGAGTTATACTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATTGAAC
130 GATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAAC
* * *
532190 TCGAGGGTCTTTGGAAGATAGCCCTTCTCGAATTAAGCTATGCTGCAAATGATG
195 TCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATG
*
532244 TGCCTTGGAGCTGAGCGTAGTCGATCTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
1 TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
* **
532309 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGTGTAGTCGAACTCGAAGATC-TTGGTGGCAG
66 AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTCACAG
* * * * * * * *
532373 ATAGCCCTTCTGGCCTTGAGCTATGCTATAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACT
131 ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
*
532437 CGAAGGTCTT
196 CGAGGGTCTT
532447 GGCTAACAGA
Statistics
Matches: 1059, Mismatches: 131, Indels: 24
0.87 0.11 0.02
Matches are distributed among these distances:
246 29 0.03
247 41 0.04
248 181 0.17
249 368 0.35
250 362 0.34
251 78 0.07
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.31
Consensus pattern (248 bp):
TGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTA
AGTTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGATCTTTGGTCACAG
ATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACT
CGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGATGCAAATGATG
Found at i:536308 original size:22 final size:21
Alignment explanation
Indices: 536270--536353 Score: 100
Period size: 22 Copynumber: 4.0 Consensus size: 21
536260 CCGTTAGACA
*
536270 GGGGGAATC-GATACCCCATGG
1 GGGGGAATCTG-TACCCCCTGG
*
536291 GGGGGAATCTGTTCCCCCTGGG
1 GGGGGAATCTGTACCCCCT-GG
* *
536313 GGGGGAATCGGTACCCCCT-A
1 GGGGGAATCTGTACCCCCTGG
536333 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
536354 ACATTCTGTT
Statistics
Matches: 53, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
20 18 0.34
21 15 0.28
22 20 0.38
ACGTcount: A:0.17, C:0.27, G:0.38, T:0.18
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:537035 original size:20 final size:20
Alignment explanation
Indices: 537010--537047 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
537000 ACTTTATGCA
*
537010 ATATCAATTGTTGAAATTTG
1 ATATCAATTGTTAAAATTTG
537030 ATATCAATTGTTAAAATT
1 ATATCAATTGTTAAAATT
537048 AAGAGCATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (20 bp):
ATATCAATTGTTAAAATTTG
Found at i:537866 original size:19 final size:20
Alignment explanation
Indices: 537823--537870 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
537813 TCTAAATCCT
*
537823 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
537843 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
537862 TTTTCAAAA
1 TTTTCAAAA
537871 GAAAATCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:539204 original size:20 final size:21
Alignment explanation
Indices: 539145--539203 Score: 100
Period size: 21 Copynumber: 2.8 Consensus size: 21
539135 TGTTAGACAA
*
539145 GGGGGAATCGGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
539166 GGGGGAATCTGTACCCCCTGG
1 GGGGGAATCTGTACCCCCTGG
*
539187 GGGGGAATCTGCACCCC
1 GGGGGAATCTGTACCCC
539204 TTGGACAATC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.15, C:0.31, G:0.39, T:0.15
Consensus pattern (21 bp):
GGGGGAATCTGTACCCCCTGG
Found at i:540440 original size:85 final size:86
Alignment explanation
Indices: 540285--540442 Score: 198
Period size: 85 Copynumber: 1.8 Consensus size: 86
540275 GAAAAAGAAG
* * * *
540285 AAATAATATATAAATAAAATAATAATAAAAAGGTAAAAATAATATATATATATATATATATAATA
1 AAATAATATATAAATAAAATAATAATAAAAAGATAAAAAAAATACATATATATATATATATAAAA
540350 AATAAAAACATAAAAAATAGT
66 AATAAAAACATAAAAAATAGT
* * *
540371 AAAT-ATATATATATAAATTAAT-A-AAAAAGATAATAAAAAATAACATATATATATA-ATCTAA
1 AAATAATATATAAATAAAATAATAATAAAAAGATAA-AAAAAAT-ACATATATATATATATATAA
540432 AAATATAAAAA
64 AAA-ATAAAAA
540443 TATATACTAA
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
83 9 0.15
84 14 0.23
85 35 0.56
86 4 0.06
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (86 bp):
AAATAATATATAAATAAAATAATAATAAAAAGATAAAAAAAATACATATATATATATATATAAAA
AATAAAAACATAAAAAATAGT
Found at i:540458 original size:26 final size:25
Alignment explanation
Indices: 540404--540461 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
540394 AAAAAGATAA
*
540404 TAAAAAATAACATATATATATAATC
1 TAAAAAATAACAAATATATATAATC
540429 TAAAAATATAA-AAATATATACTAA-C
1 TAAAAA-ATAACAAATATATA-TAATC
540454 GTAAAAAA
1 -TAAAAAA
540462 AGAAAATGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 16 0.55
26 13 0.45
ACGTcount: A:0.64, C:0.07, G:0.02, T:0.28
Consensus pattern (25 bp):
TAAAAAATAACAAATATATATAATC
Found at i:541021 original size:37 final size:37
Alignment explanation
Indices: 540971--541041 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
540961 TTGTGGATCT
*
540971 TATTTTTAGGAGTTTGAATCATAGTAGAACTCTATCC
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
*
541008 TATTTTTAGGAGTTTGAATCCTAGTAAAACTCTA
1 TATTTTTAGGAGTTTGAATCATAGTAAAACTCTA
541042 ACGTTATGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.31, C:0.13, G:0.15, T:0.41
Consensus pattern (37 bp):
TATTTTTAGGAGTTTGAATCATAGTAAAACTCTATCC
Found at i:543184 original size:15 final size:15
Alignment explanation
Indices: 543164--543213 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
543154 GTCTGAACAT
*
543164 GATGAAATCAAAGAA
1 GATGAAATCGAAGAA
* *
543179 GATGAACTCGATGAA
1 GATGAAATCGAAGAA
* *
543194 GATGAATTCGAAGAT
1 GATGAAATCGAAGAA
543209 GATGA
1 GATGA
543214 TGAACTCGAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.46, C:0.08, G:0.26, T:0.20
Consensus pattern (15 bp):
GATGAAATCGAAGAA
Found at i:543209 original size:18 final size:18
Alignment explanation
Indices: 543176--543222 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
543166 TGAAATCAAA
543176 GAAGATGAACTC---GAT
1 GAAGATGAACTCGAAGAT
*
543191 GAAGATGAATTCGAAGAT
1 GAAGATGAACTCGAAGAT
*
543209 GATGATGAACTCGA
1 GAAGATGAACTCGA
543223 TACCAAGGTG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
15 11 0.42
18 15 0.58
ACGTcount: A:0.40, C:0.11, G:0.28, T:0.21
Consensus pattern (18 bp):
GAAGATGAACTCGAAGAT
Found at i:548686 original size:17 final size:18
Alignment explanation
Indices: 548663--548704 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 18
548653 TTGACCTGAA
548663 CCGTTGACCCGA-CCGAC
1 CCGTTGACCCGACCCGAC
*
548680 TCGTTGACCCGACCCGAC
1 CCGTTGACCCGACCCGAC
548698 CCGTTGA
1 CCGTTGA
548705 TCGTTGATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.17, C:0.43, G:0.24, T:0.17
Consensus pattern (18 bp):
CCGTTGACCCGACCCGAC
Found at i:548756 original size:29 final size:29
Alignment explanation
Indices: 548714--548897 Score: 124
Period size: 28 Copynumber: 6.3 Consensus size: 29
548704 ATCGTTGATC
* ** *
548714 GGTGCTATTATGGGAA-TATATTCGATTTT
1 GGTGCTATTTTGGGAATTA-ATTCGAAATG
548743 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
* * ** * **
548772 GGTGCTATTTTGGCACTTTTTTTTTTGAAAAA
1 GGTGCTATTTTGGGA---ATTAATTCGAAATG
* * *
548804 AGTGATATTTTGGGAATTAATTTGAAAT-
1 GGTGCTATTTTGGGAATTAATTCGAAATG
* *
548832 TGTGCTATTTTGGGAATTAATTC-AAAAG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
* ** *
548860 GGTGCTATTTTGGTAATT-ATTTTAAAAG
1 GGTGCTATTTTGGGAATTAATTCGAAATG
548888 GGTGCTATTT
1 GGTGCTATTT
548898 GTGTAAAATG
Statistics
Matches: 124, Mismatches: 25, Indels: 13
0.77 0.15 0.08
Matches are distributed among these distances:
27 6 0.05
28 51 0.41
29 45 0.36
30 2 0.02
32 20 0.16
ACGTcount: A:0.27, C:0.06, G:0.23, T:0.44
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCGAAATG
Found at i:548849 original size:28 final size:28
Alignment explanation
Indices: 548743--548897 Score: 130
Period size: 28 Copynumber: 5.4 Consensus size: 28
548733 ATTCGATTTT
*
548743 GGTGCTATTTTGGGAATTAATTCGAAATG
1 GGTGCTATTTTGGGAATTAATTTGAAA-G
* * ** *
548772 GGTGCTATTTTGGCACTTTTTTTTTTGAAAAA
1 GGTGCTATTTTGGGA---ATTAATTTG-AAAG
* * *
548804 AGTGATATTTTGGGAATTAATTTGAAAT
1 GGTGCTATTTTGGGAATTAATTTGAAAG
* **
548832 TGTGCTATTTTGGGAATTAATTCAAAAG
1 GGTGCTATTTTGGGAATTAATTTGAAAG
* * *
548860 GGTGCTATTTTGGTAATTATTTTAAAAG
1 GGTGCTATTTTGGGAATTAATTTGAAAG
548888 GGTGCTATTT
1 GGTGCTATTT
548898 GTGTAAAATG
Statistics
Matches: 100, Mismatches: 22, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
28 60 0.60
29 20 0.20
32 17 0.17
33 3 0.03
ACGTcount: A:0.28, C:0.06, G:0.23, T:0.44
Consensus pattern (28 bp):
GGTGCTATTTTGGGAATTAATTTGAAAG
Found at i:549894 original size:42 final size:41
Alignment explanation
Indices: 549835--550126 Score: 431
Period size: 42 Copynumber: 7.0 Consensus size: 41
549825 GAAGTATTAT
549835 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
* * *
549877 CAGGTCTCTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
549919 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
* *
549961 CAGGTCCCTTTGCTGTGTGTAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
* *
550003 CAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAATTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
550045 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
* *
550087 CAGGTCCCTCTGCTGTGTGCAAGGATAAACCTTACAGTTT
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTT
550127 TCCTAGGATC
Statistics
Matches: 227, Mismatches: 17, Indels: 12
0.89 0.07 0.05
Matches are distributed among these distances:
41 8 0.04
42 215 0.95
43 4 0.02
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTAC
Found at i:549976 original size:84 final size:84
Alignment explanation
Indices: 549835--550126 Score: 505
Period size: 84 Copynumber: 3.5 Consensus size: 84
549825 GAAGTATTAT
*
549835 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCTCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
*
549900 GGTAAGCCTTATAGTTTCC
66 GGTAAGCCTTACAGTTTCC
*
549919 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGTAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
549984 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
* *
550003 CAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAATTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
550068 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
* *
550087 CAGGTCCCTCTGCTGTGTGC-AAGGATAAACCTTACAGTTT
1 CAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAGTTT
550127 TCCTAGGATC
Statistics
Matches: 197, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
83 4 0.02
84 193 0.98
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (84 bp):
CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
GGTAAGCCTTACAGTTTCC
Found at i:550149 original size:43 final size:42
Alignment explanation
Indices: 549835--550165 Score: 328
Period size: 42 Copynumber: 7.8 Consensus size: 42
549825 GAAGTATTAT
* * *
549835 CAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAGTTTAC
1 CAGGTCCCTCTACTGTGTGC-AAGGATAAGCCTTACAGTTTCC
* * * * *
549877 CAGGTCTCTTTGCTGTGTGCAAGGGTAAGCCTTATAGTTTCC
1 CAGGTCCCTCTACTGTGTGCAAGGATAAGCCTTACAGTTTCC
* * *
549919 CAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAGTTTAC
1 CAGGTCCCTCTACTGTGTGC-AAGGATAAGCCTTACAGTTTCC
* * * *
549961 CAGGTCCCTTTGCTGTGTGTAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTCTACTGTGTGCAAGGATAAGCCTTACAGTTTCC
* ** * *
550003 CAGGTCCCTTTGTTGTGTGCGAAGG-TAAGCCTTACAATTTAC
1 CAGGTCCCTCTACTGTGTGC-AAGGATAAGCCTTACAGTTTCC
* * *
550045 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTCTACTGTGTGCAAGGATAAGCCTTACAGTTTCC
* *
550087 CAGGTCCCTCTGCTGTGTGCAAGGATAAACCTTACAGTTTTCC
1 CAGGTCCCTCTACTGTGTGCAAGGATAAGCCTTACAG-TTTCC
* * *
550130 TAGGAT-CCTCTACTTTGTGCATAGGTTAAGCCTTAC
1 CAGG-TCCCTCTACTGTGTGCA-AGGATAAGCCTTAC
550166 TGGTGTATAG
Statistics
Matches: 258, Mismatches: 23, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
41 12 0.05
42 204 0.79
43 29 0.11
44 13 0.05
ACGTcount: A:0.19, C:0.24, G:0.24, T:0.33
Consensus pattern (42 bp):
CAGGTCCCTCTACTGTGTGCAAGGATAAGCCTTACAGTTTCC
Found at i:556291 original size:13 final size:14
Alignment explanation
Indices: 556273--556331 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 14
556263 GACCGGTCAC
556273 GACCCGACA-CGTT
1 GACCCGACACCGTT
556286 GACCCGA-ACCGTT
1 GACCCGACACCGTT
556299 GACCCGACCCGACCCGTT
1 GACCCGA--C-A-CCGTT
556317 GACCCGAC-CCGTT
1 GACCCGACACCGTT
556330 GA
1 GA
556332 GCGTTGACAG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
12 1 0.03
13 25 0.62
16 1 0.03
17 1 0.03
18 12 0.30
ACGTcount: A:0.20, C:0.42, G:0.24, T:0.14
Consensus pattern (14 bp):
GACCCGACACCGTT
Found at i:556308 original size:31 final size:31
Alignment explanation
Indices: 556272--556331 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
556262 TGACCGGTCA
556272 CGACCCGACACGTTGACCCGAACCGTTGACC
1 CGACCCGACACGTTGACCCGAACCGTTGACC
* *
556303 CGACCCGACCCGTTGACCCGACCCGTTGA
1 CGACCCGACACGTTGACCCGAACCGTTGA
556332 GCGTTGACAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.20, C:0.43, G:0.23, T:0.13
Consensus pattern (31 bp):
CGACCCGACACGTTGACCCGAACCGTTGACC
Found at i:556309 original size:18 final size:18
Alignment explanation
Indices: 556286--556327 Score: 75
Period size: 18 Copynumber: 2.3 Consensus size: 18
556276 CCGACACGTT
556286 GACCCGAACCGTTGACCC
1 GACCCGAACCGTTGACCC
*
556304 GACCCGACCCGTTGACCC
1 GACCCGAACCGTTGACCC
556322 GACCCG
1 GACCCG
556328 TTGAGCGTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.19, C:0.48, G:0.24, T:0.10
Consensus pattern (18 bp):
GACCCGAACCGTTGACCC
Found at i:556403 original size:29 final size:29
Alignment explanation
Indices: 556371--556525 Score: 141
Period size: 29 Copynumber: 5.3 Consensus size: 29
556361 TTCGATTTTT
* *
556371 GTGCTATTTTGGGAATTAATTTGAAATGG
1 GTGCTATTTTGGGAATTAATTTAAAAAGG
* ** *
556400 GTGCTATTTTGGTAATTTTTTTGAAAAAAAG
1 GTGCTATTTTGGGAATTAATTT--AAAAAGG
* ** * * **
556431 GTGATATTCAGGGAATTAA-TTCAGATTG
1 GTGCTATTTTGGGAATTAATTTAAAAAGG
*
556459 GTGCTATTTTGGGAATTAATTCAAAAAGG
1 GTGCTATTTTGGGAATTAATTTAAAAAGG
* *
556488 GTGCTATTTTGGTAATTATTTTAAAAAGG
1 GTGCTATTTTGGGAATTAATTTAAAAAGG
556517 GTGCTATTT
1 GTGCTATTT
556526 GTGTAAAATG
Statistics
Matches: 96, Mismatches: 27, Indels: 6
0.74 0.21 0.05
Matches are distributed among these distances:
28 19 0.20
29 58 0.60
30 2 0.02
31 17 0.18
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.41
Consensus pattern (29 bp):
GTGCTATTTTGGGAATTAATTTAAAAAGG
Found at i:557507 original size:42 final size:41
Alignment explanation
Indices: 557460--557790 Score: 475
Period size: 42 Copynumber: 7.8 Consensus size: 41
557450 GAAGTATTAT
*
557460 CAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
557502 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
557544 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
557586 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
*
557628 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTATAGTTTAC
1 CAGGTCCCTTTGCTGTGTGC-AAGGTAAGCCTTACAGTTTAC
*
557670 CAGGTCCCTTTGCTGTGTGCAAGGGTAAGCCTTACAGTTTCC
1 CAGGTCCCTTTGCTGTGTGCAA-GGTAAGCCTTACAGTTTAC
* *
557712 CAGGTCCCTTTGCTGTGTGCAAGGATAAACCTTACAGTTTTC
1 CAGGTCCCTTTGCTGTGTGCAAGG-TAAGCCTTACAGTTTAC
* *
557754 CTAGG-CTCCTCTGCTTTGTGCATAGGTTAAGCCTTAC
1 C-AGGTC-CCTTTGCTGTGTGCA-AGG-TAAGCCTTAC
557791 TGGTGTATAG
Statistics
Matches: 266, Mismatches: 14, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
41 8 0.03
42 226 0.85
43 20 0.08
44 12 0.05
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.32
Consensus pattern (41 bp):
CAGGTCCCTTTGCTGTGTGCAAGGTAAGCCTTACAGTTTAC
Found at i:557601 original size:84 final size:84
Alignment explanation
Indices: 557460--557790 Score: 549
Period size: 84 Copynumber: 3.9 Consensus size: 84
557450 GAAGTATTAT
*
557460 CAGGTCCCTTTGTTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
557525 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
557544 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
557609 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
*
557628 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTATAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
1 CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
557693 GGTAAGCCTTACAGTTTCC
66 GGTAAGCCTTACAGTTTCC
* * * *
557712 CAGGTCCCTTTGCTGTGTGC-AAGGATAAACCTTACAGTTTTCCTAGG-CTCCTCTGCTTTGTGC
1 CAGGTCCCTTTGCTGTGTGCGAAGG-TAAGCCTTACAGTTTACC-AGGTC-CCTTTGCTGTGTGC
*
557775 ATAGGTTAAGCCTTAC
63 A-AGGGTAAGCCTTAC
557791 TGGTGTATAG
Statistics
Matches: 235, Mismatches: 8, Indels: 6
0.94 0.03 0.02
Matches are distributed among these distances:
83 4 0.02
84 202 0.86
85 16 0.07
86 13 0.06
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.32
Consensus pattern (84 bp):
CAGGTCCCTTTGCTGTGTGCGAAGGTAAGCCTTACAGTTTACCAGGTCCCTTTGCTGTGTGCAAG
GGTAAGCCTTACAGTTTCC
Found at i:561242 original size:12 final size:12
Alignment explanation
Indices: 561184--561273 Score: 69
Period size: 12 Copynumber: 7.6 Consensus size: 12
561174 ATGGAGATAT
*
561184 CAGAAATCAAAA
1 CAGAAATCAGAA
* *
561196 CAGTATTCAGAA
1 CAGAAATCAGAA
* *
561208 CAGATATCAAAA
1 CAGAAATCAGAA
*
561220 CAG-AATCCAGAT
1 CAGAAAT-CAGAA
561232 CAGAAATCAGAA
1 CAGAAATCAGAA
* *
561244 CA-AAATTCATAT
1 CAGAAA-TCAGAA
561256 CAGAAATCAGAA
1 CAGAAATCAGAA
561268 CA-AAAT
1 CAGAAAT
561274 TCAAATCGGA
Statistics
Matches: 59, Mismatches: 15, Indels: 9
0.71 0.18 0.11
Matches are distributed among these distances:
11 9 0.15
12 44 0.75
13 6 0.10
ACGTcount: A:0.54, C:0.18, G:0.11, T:0.17
Consensus pattern (12 bp):
CAGAAATCAGAA
Found at i:561270 original size:24 final size:24
Alignment explanation
Indices: 561182--561290 Score: 119
Period size: 24 Copynumber: 4.5 Consensus size: 24
561172 AAATGGAGAT
* **
561182 ATCAGAAATCAAAACAGTATTCAG
1 ATCAGAAATCAGAACAAAATTCAG
* * * * *
561206 AACAGATATCAAAACAGAATCCAG
1 ATCAGAAATCAGAACAAAATTCAG
*
561230 ATCAGAAATCAGAACAAAATTCAT
1 ATCAGAAATCAGAACAAAATTCAG
*
561254 ATCAGAAATCAGAACAAAATTCAA
1 ATCAGAAATCAGAACAAAATTCAG
*
561278 ATCGGAAATCAGA
1 ATCAGAAATCAGA
561291 TAAAATATTC
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.53, C:0.17, G:0.12, T:0.17
Consensus pattern (24 bp):
ATCAGAAATCAGAACAAAATTCAG
Found at i:566260 original size:3 final size:3
Alignment explanation
Indices: 566245--566286 Score: 50
Period size: 3 Copynumber: 14.0 Consensus size: 3
566235 TCTACAAAAA
* *
566245 TAT TAT T-T ATAT TAT TAT TAT AAT TAT TAT AAT TAT TAT TAT
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
566287 GGTAATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
2 1 0.03
3 31 0.94
4 1 0.03
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:571639 original size:25 final size:25
Alignment explanation
Indices: 571606--571654 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
571596 GTGAAGAGAC
*
571606 AAGAAAAACAAAGAGAAATGAAGCT
1 AAGAAAAACAAAGAGAAAGGAAGCT
571631 AAGAAAAACAAAGAGAAAGGAAGC
1 AAGAAAAACAAAGAGAAAGGAAGC
571655 AAAAGAAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.65, C:0.08, G:0.22, T:0.04
Consensus pattern (25 bp):
AAGAAAAACAAAGAGAAAGGAAGCT
Found at i:571659 original size:10 final size:10
Alignment explanation
Indices: 571631--571741 Score: 86
Period size: 10 Copynumber: 11.2 Consensus size: 10
571621 AAATGAAGCT
*
571631 AAGAAAAACA
1 AAGAAAAAGA
* *
571641 AAGAGAAAGG
1 AAGAAAAAGA
*
571651 AAGCAAAAGA
1 AAGAAAAAGA
571661 AAGAAAAAGA
1 AAGAAAAAGA
571671 AAGAAAAA-A
1 AAGAAAAAGA
*
571680 AAG-CAAAGA
1 AAGAAAAAGA
*
571689 AAGAAAGA-A
1 AAGAAAAAGA
571698 AAGCAAAAA-A
1 AAG-AAAAAGA
* *
571708 AACAAAAACA
1 AAGAAAAAGA
*
571718 AAGCAAAAGAAA
1 AAG-AAAA-AGA
571730 AAGAAAAAGA
1 AAGAAAAAGA
571740 AA
1 AA
571742 AATCAAAGAG
Statistics
Matches: 80, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
8 3 0.04
9 17 0.21
10 47 0.59
11 8 0.10
12 5 0.06
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:571671 original size:6 final size:6
Alignment explanation
Indices: 571660--571757 Score: 58
Period size: 6 Copynumber: 15.7 Consensus size: 6
571650 GAAGCAAAAG
* *
571660 AAAGAA AAAGAA AGAAAAA AAAG-C AAAGAA AGAA-AGA AAAGCAA AAA-AA
1 AAAGAA AAAGAA A-AAGAA AAAGAA AAAGAA A-AAGA-A AAAG-AA AAAGAA
* * * *
571709 ACAAAAA CAAAGCA AAAGAA AAAGAA AAAGAA AAATCAA AGAGAA AAAG
1 A-AAGAA -AAAGAA AAAGAA AAAGAA AAAGAA AAA-GAA AAAGAA AAAG
571758 GGGACAAGAA
Statistics
Matches: 71, Mismatches: 11, Indels: 20
0.70 0.11 0.20
Matches are distributed among these distances:
5 7 0.10
6 40 0.56
7 22 0.31
8 2 0.03
ACGTcount: A:0.78, C:0.06, G:0.15, T:0.01
Consensus pattern (6 bp):
AAAGAA
Found at i:571743 original size:18 final size:19
Alignment explanation
Indices: 571631--571743 Score: 97
Period size: 20 Copynumber: 5.9 Consensus size: 19
571621 AAATGAAGCT
* *
571631 AAGAAAAACAAAGAGAAAGG
1 AAGAAAAA-AAAGAAAAAGA
*
571651 AAGCAAAAGAAAGAAAAAGA
1 AAG-AAAAAAAAGAAAAAGA
*
571671 AAGAAAAAAAAG-CAAAGA
1 AAGAAAAAAAAGAAAAAGA
*
571689 AAGAAAGAAAAGCAAAAA-A
1 AAGAAAAAAAAG-AAAAAGA
* *
571708 AACAAAAACAAAGCAAAAGA
1 AAGAAAAA-AAAGAAAAAGA
*
571728 AA-AAGAAAAAGAAAAA
1 AAGAAAAAAAAGAAAAA
571744 TCAAAGAGAA
Statistics
Matches: 76, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
18 24 0.32
19 23 0.30
20 25 0.33
21 4 0.05
ACGTcount: A:0.77, C:0.06, G:0.17, T:0.00
Consensus pattern (19 bp):
AAGAAAAAAAAGAAAAAGA
Found at i:572839 original size:32 final size:32
Alignment explanation
Indices: 572797--572865 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 32
572787 TGAAGCAAGA
* * * *
572797 AACATCGAATATTGGGGTATCTTTGGAGATAC
1 AACATAGAATATTAGAGCATCTTTGGAGATAC
* *
572829 AACATAGAATATTAGAGCATCTTTGGGGATTC
1 AACATAGAATATTAGAGCATCTTTGGAGATAC
572861 AACAT
1 AACAT
572866 CCTGATGTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.22, T:0.30
Consensus pattern (32 bp):
AACATAGAATATTAGAGCATCTTTGGAGATAC
Found at i:573072 original size:29 final size:29
Alignment explanation
Indices: 572995--573082 Score: 122
Period size: 29 Copynumber: 3.0 Consensus size: 29
572985 TTTAAAACAA
572995 AAAATCTTTGAGTTTGTTTCTCTTGAAAC
1 AAAATCTTTGAGTTTGTTTCTCTTGAAAC
*
573024 AAAAGTCTTTGAGTTTGTTTCTTTTGAAAC
1 AAAA-TCTTTGAGTTTGTTTCTCTTGAAAC
** **
573054 ATCATCTTTGAGTCAGTTTCTCTTGAAAC
1 AAAATCTTTGAGTTTGTTTCTCTTGAAAC
573083 CATTATCCTT
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
29 26 0.50
30 26 0.50
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (29 bp):
AAAATCTTTGAGTTTGTTTCTCTTGAAAC
Found at i:573375 original size:134 final size:134
Alignment explanation
Indices: 573092--573694 Score: 632
Period size: 134 Copynumber: 4.5 Consensus size: 134
573082 CCATTATCCT
* * * * *
573092 TAAAGATGGCC-TATCTCCTCATCACGTAGGAACCGTGTCATCCCCTAACCAGACCTCCTCATCA
1 TAAAGATGGCCATAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCA
* * * * ** *
573156 CGTAGGAGCTGTG-CCCCCCTCGATAATCAGTCGTCCTCATTGCGTAAGAA-CTGTGTTATCATC
66 CGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAATC-GTGTTATCACC
*
573219 CTCCC
130 CTTCC
* * * *
573224 TAAAGATGGCCAGAACTCTTCATCATGTATGAGTCGTGTCATCCCCTGACAAGACCTCCTCATCA
1 TAAAGATGGCCATAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCA
* * * * * *
573289 CGTAAGAGTCGTGTCACCCTTAGATAACCA-ACTGTCCTCATCATGTAGGAATCGTGTTATCACC
66 CGTAGGAGCCGTGTCACCCCTAGATAACCAGTC-GTCCTCATCACGTAAGAATCGTGTTATCACC
573353 CTTCC
130 CTTCC
* * *
573358 TAAAGATGGCCATAACTCTTCATCACGTATGAGCCGTCTCATCCCCCGACCAAACCTCCTCATCA
1 TAAAGATGGCCATAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCA
* * *
573423 CGTAGGAGCCGTGTCACCCCTA-ATAATCAGTCGTCTTCATCACGTAAGAATCATGTTATCA---
66 CGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAATCGTGTTATCACCC
*
573484 ATCC
131 TTCC
* ** * * * * * * *
573488 TAAAGATGG-TATGTCGTCCTCATCACGTAAGAACCATGTTAT-CCCTCGACCAGACCTTCTTAT
1 TAAAGATGGCCATAAC-TCTTCATCACGTATGAGCCGTGTCATCCCCT-GACCAGACCTCCTCAT
* * * * *
573551 CACATAGAAGCCGTGTCACCCCTAGATAACCATTCGTCCTCATCTCGTAGGAATCGTGTTATCAC
64 CACGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAATCGTGTTATCAC
*
573616 CCCTCC
129 CCTTCC
** ** * *
573622 TAAAGATGGCCGGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCATCA
1 TAAAGATGGCCATAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCA
573687 CGTAGGAG
66 CGTAGGAG
573695 TTGTGTTACC
Statistics
Matches: 378, Mismatches: 80, Indels: 24
0.78 0.17 0.05
Matches are distributed among these distances:
129 6 0.02
130 67 0.18
131 33 0.09
132 11 0.03
133 86 0.23
134 170 0.45
135 5 0.01
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (134 bp):
TAAAGATGGCCATAACTCTTCATCACGTATGAGCCGTGTCATCCCCTGACCAGACCTCCTCATCA
CGTAGGAGCCGTGTCACCCCTAGATAACCAGTCGTCCTCATCACGTAAGAATCGTGTTATCACCC
TTCC
Found at i:573625 original size:264 final size:265
Alignment explanation
Indices: 573092--573694 Score: 704
Period size: 264 Copynumber: 2.3 Consensus size: 265
573082 CCATTATCCT
* * * * **
573092 TAAAGATGGCCTATCTCCTCATCACGTAGGAACCGTGTCATCCCCTAACCAGACCTCCTCATCAC
1 TAAAGATGGCCTAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTCATCAC
* * * ** * *
573157 GTAGGAGCTGTGCCCCCCTCGATAATCAGTCGTCCTCATTGCGTAAGAACTGTGTTATCATCCTC
66 GTAGGAGCCGTGCACCCCTCAATAATCAGTCGTCCTCATCACGTAAGAACTATGTTATCA-CATC
* * * ** *
573222 CCTAAAGATGGCCAGAACTCTTCATCATGTATGAGTCGTGTCATCCCCTGACAAGACCTCCTCAT
130 CCTAAAGATGGCCAGAACTCCTCATCACGTAAGAACCATGTCATCCCCTGACAAGACCTCCTCAT
* * *
573287 CACGTAAGAGTCGTGTCACCCTTAGATAACCAACTGTCCTCATCATGTAGGAATCGTGTTATCAC
195 CACATAAGAGCCGTGTCACCCCTAGATAACCAACTGTCCTCATCATGTAGGAATCGTGTTATCAC
*
573352 CCTTCC
260 CCCTCC
* *
573358 TAAAGATGGCCATAACTCTTCATCACGTATGAGCCGTCTCATCCCCCGACCAAACCTCCTCATCA
1 TAAAGATGGCC-TAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTCATCA
*
573423 CGTAGGAGCCGTGTCACCCCT-AATAATCAGTCGTCTTCATCACGTAAGAA-TCATGTTATCA-A
65 CGTAGGAGCCGTG-CACCCCTCAATAATCAGTCGTCCTCATCACGTAAGAACT-ATGTTATCACA
* * * * *
573485 T-CCTAAAGATGG-TATG-TCGTCCTCATCACGTAAGAACCATGTTAT-CCCTCGACCAGACCTT
128 TCCCTAAAGATGGCCA-GAAC-TCCTCATCACGTAAGAACCATGTCATCCCCT-GACAAGACCTC
* *
573546 CTTATCACAT-AGAAGCCGTGTCACCCCTAGATAACC-ATTCGTCCTCATC-TCGTAGGAATCGT
190 CTCATCACATAAG-AGCCGTGTCACCCCTAGATAACCAACT-GTCCTCATCAT-GTAGGAATCGT
573608 GTTATCACCCCTCC
252 GTTATCACCCCTCC
* ** *
573622 TAAAGATGGCCGGAACTCTTCATCACGTATGAGAAGTGTCATCCCCCGACCAGATCTCCTCATCA
1 TAAAGATGGCC-TAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTCATCA
573687 CGTAGGAG
65 CGTAGGAG
573695 TTGTGTTACC
Statistics
Matches: 288, Mismatches: 40, Indels: 20
0.83 0.11 0.06
Matches are distributed among these distances:
263 11 0.04
264 168 0.58
265 1 0.00
266 12 0.04
267 90 0.31
268 6 0.02
ACGTcount: A:0.26, C:0.31, G:0.17, T:0.26
Consensus pattern (265 bp):
TAAAGATGGCCTAACTCTTCATCACGTATGAGCCGTGTCATCCCCCGACCAGACCTCCTCATCAC
GTAGGAGCCGTGCACCCCTCAATAATCAGTCGTCCTCATCACGTAAGAACTATGTTATCACATCC
CTAAAGATGGCCAGAACTCCTCATCACGTAAGAACCATGTCATCCCCTGACAAGACCTCCTCATC
ACATAAGAGCCGTGTCACCCCTAGATAACCAACTGTCCTCATCATGTAGGAATCGTGTTATCACC
CCTCC
Found at i:573907 original size:3 final size:3
Alignment explanation
Indices: 573899--573963 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
573889 TCTACAAAAA
573899 TAT TAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
573946 TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT
573964 GGTAATTAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
2 2 0.03
3 59 0.97
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:589053 original size:4 final size:4
Alignment explanation
Indices: 589044--589083 Score: 66
Period size: 4 Copynumber: 10.5 Consensus size: 4
589034 TCTAAGCTTT
589044 GGGA GGGA GGGA GGGA GGGA GGGA GGGA -GG- GGGA GGGA GG
1 GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GGGA GG
589084 CAAAACACAA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 4 0.12
4 30 0.88
ACGTcount: A:0.23, C:0.00, G:0.78, T:0.00
Consensus pattern (4 bp):
GGGA
Found at i:589998 original size:17 final size:17
Alignment explanation
Indices: 589976--590008 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
589966 TGAGATCATA
*
589976 ATATTATTTTTTATATT
1 ATATTATATTTTATATT
589993 ATATTATATTTTATAT
1 ATATTATATTTTATAT
590009 AAATAACTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
ATATTATATTTTATATT
Found at i:590783 original size:21 final size:21
Alignment explanation
Indices: 590743--590786 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
590733 CGATAAAAAA
* * *
590743 TTATCTAAAATATTATTATTT
1 TTATCTAAAACATCAATATTT
590764 TTATCTAAAACATCAATATTT
1 TTATCTAAAACATCAATATTT
590785 TT
1 TT
590787 TAATATTTTC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATCTAAAACATCAATATTT
Found at i:593790 original size:33 final size:31
Alignment explanation
Indices: 593728--593803 Score: 80
Period size: 33 Copynumber: 2.4 Consensus size: 31
593718 GACAATATAA
593728 ATTAATAAAATATATCATATCATAAGAAAAAGT
1 ATTAATAAAATATATCATATCATAAG-AAAA-T
* * * **
593761 ATTAATAAAATATGTTATGTCATTGGAAAAT
1 ATTAATAAAATATATCATATCATAAGAAAAT
*
593792 ATTAACAAAATA
1 ATTAATAAAATA
593804 AGTCATCTCA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
31 12 0.32
32 4 0.11
33 21 0.57
ACGTcount: A:0.54, C:0.05, G:0.08, T:0.33
Consensus pattern (31 bp):
ATTAATAAAATATATCATATCATAAGAAAAT
Found at i:595060 original size:30 final size:30
Alignment explanation
Indices: 595024--595139 Score: 205
Period size: 30 Copynumber: 3.9 Consensus size: 30
595014 AAAATGTCAA
*
595024 GTTAGTATTCTGTTAAGTTTTCAACATCAC
1 GTTAGTATTATGTTAAGTTTTCAACATCAC
* *
595054 GTTAGTATTATGTTAAGTTTTTAGCATCAC
1 GTTAGTATTATGTTAAGTTTTCAACATCAC
595084 GTTAGTATTATGTTAAGTTTTCAACATCAC
1 GTTAGTATTATGTTAAGTTTTCAACATCAC
595114 GTTAGTATTATGTTAAGTTTTCAACA
1 GTTAGTATTATGTTAAGTTTTCAACA
595140 GTTGGACATT
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 81 1.00
ACGTcount: A:0.28, C:0.12, G:0.15, T:0.45
Consensus pattern (30 bp):
GTTAGTATTATGTTAAGTTTTCAACATCAC
Found at i:597699 original size:3 final size:3
Alignment explanation
Indices: 597691--597773 Score: 166
Period size: 3 Copynumber: 27.7 Consensus size: 3
597681 TATTTCTAAC
597691 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
597739 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
597774 CAACAACAAC
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 80 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:598820 original size:34 final size:34
Alignment explanation
Indices: 598736--598849 Score: 95
Period size: 34 Copynumber: 3.4 Consensus size: 34
598726 CCTTTTTATT
* * * **
598736 CTAAACGAGCATGTTCACGAACGATAAACGAATGA
1 CTAAACAAACATGTTCACAAACGATAAAC-AAACA
* * * *
598771 -TAAATAAATAAGTTCACAAATGATAAACAAACA
1 CTAAACAAACATGTTCACAAACGATAAACAAACA
* * * *
598804 CTAAACGAACATGTTCACGAACGATAAACGAACG
1 CTAAACAAACATGTTCACAAACGATAAACAAACA
598838 CTAAACAAACAT
1 CTAAACAAACAT
598850 ATAAACAAAC
Statistics
Matches: 60, Mismatches: 18, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
33 3 0.05
34 57 0.95
ACGTcount: A:0.50, C:0.19, G:0.13, T:0.18
Consensus pattern (34 bp):
CTAAACAAACATGTTCACAAACGATAAACAAACA
Found at i:598872 original size:12 final size:12
Alignment explanation
Indices: 598857--598897 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
598847 CATATAAACA
598857 AACATGTTCATG
1 AACATGTTCATG
*
598869 AACAT-TTAAATG
1 AACATGTT-CATG
598881 AACATGTTCATG
1 AACATGTTCATG
598893 AACAT
1 AACAT
598898 TAAACGAACA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
11 2 0.08
12 21 0.84
13 2 0.08
ACGTcount: A:0.41, C:0.15, G:0.12, T:0.32
Consensus pattern (12 bp):
AACATGTTCATG
Found at i:598878 original size:24 final size:24
Alignment explanation
Indices: 598845--598936 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 24
598835 ACGCTAAACA
* *
598845 AACATATAAACAAACATGTTCATG
1 AACATTTAAACGAACATGTTCATG
*
598869 AACATTTAAATGAACATGTTCATG
1 AACATTTAAACGAACATGTTCATG
**
598893 AACA-TTAAACGAACACATTCATG
1 AACATTTAAACGAACATGTTCATG
*
598916 AACGTTAAATAAACGAACATG
1 AACATT---TAAACGAACATG
598937 AACACCTTCA
Statistics
Matches: 55, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
23 19 0.35
24 26 0.47
27 10 0.18
ACGTcount: A:0.48, C:0.16, G:0.11, T:0.25
Consensus pattern (24 bp):
AACATTTAAACGAACATGTTCATG
Found at i:598906 original size:23 final size:23
Alignment explanation
Indices: 598845--598924 Score: 97
Period size: 23 Copynumber: 3.4 Consensus size: 23
598835 ACGCTAAACA
*
598845 AACATATAAACAAACATGTTCATG
1 AACAT-TAAACGAACATGTTCATG
*
598869 AACATTTAAATGAACATGTTCATG
1 AACA-TTAAACGAACATGTTCATG
**
598893 AACATTAAACGAACACATTCATG
1 AACATTAAACGAACATGTTCATG
*
598916 AACGTTAAA
1 AACATTAAA
598925 TAAACGAACA
Statistics
Matches: 49, Mismatches: 6, Indels: 3
0.84 0.10 0.05
Matches are distributed among these distances:
23 24 0.49
24 24 0.49
25 1 0.02
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.26
Consensus pattern (23 bp):
AACATTAAACGAACATGTTCATG
Found at i:601000 original size:31 final size:31
Alignment explanation
Indices: 600965--601040 Score: 109
Period size: 31 Copynumber: 2.5 Consensus size: 31
600955 TTCAACGTTC
600965 AAGTGACCAAAACGT-AATAAAATAATAACAT
1 AAGTGACCAAAAC-TAAATAAAATAATAACAT
* **
600996 AAGTGACCAAAACTAAATAAAATATTAATGT
1 AAGTGACCAAAACTAAATAAAATAATAACAT
601027 AAGTGACCAAAACT
1 AAGTGACCAAAACT
601041 TATGTTTTTT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
30 1 0.02
31 40 0.98
ACGTcount: A:0.55, C:0.13, G:0.11, T:0.21
Consensus pattern (31 bp):
AAGTGACCAAAACTAAATAAAATAATAACAT
Found at i:604721 original size:3 final size:3
Alignment explanation
Indices: 604707--604765 Score: 84
Period size: 3 Copynumber: 19.7 Consensus size: 3
604697 CACTTTCATA
* *
604707 TAT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAA TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
604752 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
604766 AATAAATAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
2 2 0.04
3 46 0.90
4 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:604773 original size:27 final size:27
Alignment explanation
Indices: 604722--604777 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 27
604712 TTGTTATTAT
*
604722 TATTATTATTATTATTATTATAATATA
1 TATTATTATTATTATTAATATAATATA
604749 TATTATTATTATTATTAA-ATAA-ATA
1 TATTATTATTATTATTAATATAATATA
604774 -ATTA
1 TATTA
604778 CAAATCTAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 4 0.14
25 3 0.11
26 4 0.14
27 17 0.61
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (27 bp):
TATTATTATTATTATTAATATAATATA
Found at i:604775 original size:30 final size:30
Alignment explanation
Indices: 604719--604775 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
604709 TTATTGTTAT
* *
604719 TATTATTATTATTATTATTATTATAATATA
1 TATTATTATTATTATTAATATAATAATATA
604749 TATTATTATTATTATTAA-ATAAATAAT
1 TATTATTATTATTATTAATAT-AATAAT
604776 TACAAATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 2 0.08
30 22 0.92
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (30 bp):
TATTATTATTATTATTAATATAATAATATA
Found at i:604777 original size:21 final size:24
Alignment explanation
Indices: 604704--604777 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 24
604694 TTTCACTTTC
*
604704 ATAT-ATTATTGTTATTAT--TAT
1 ATATAATTATTATTATTATAATAT
*
604725 -TATTATTATTATTATTATAATAT
1 ATATAATTATTATTATTATAATAT
*
604748 ATATTATTATTATTATTA-AATA-
1 ATATAATTATTATTATTATAATAT
604770 A-ATAATTA
1 ATATAATTA
604778 CAAATCTAAG
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
20 3 0.06
21 19 0.40
22 1 0.02
23 7 0.15
24 17 0.36
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (24 bp):
ATATAATTATTATTATTATAATAT
Found at i:604777 original size:24 final size:24
Alignment explanation
Indices: 604707--604773 Score: 82
Period size: 24 Copynumber: 2.8 Consensus size: 24
604697 CACTTTCATA
* * * *
604707 TATTATTGTTATTATTATTATTAT
1 TATTATTATTATAATAAATATTAT
*
604731 TATTATTATTATAATATATATTAT
1 TATTATTATTATAATAAATATTAT
604755 TATTATTATTA-AATAAATA
1 TATTATTATTATAATAAATA
604774 ATTACAAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
23 7 0.19
24 30 0.81
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.58
Consensus pattern (24 bp):
TATTATTATTATAATAAATATTAT
Found at i:605264 original size:19 final size:19
Alignment explanation
Indices: 605240--605278 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
605230 AAGAAAGAAG
*
605240 AGAGACAGCCACGGAGAGC
1 AGAGACAGCCACGGACAGC
605259 AGAGACAGCCACGGACAGC
1 AGAGACAGCCACGGACAGC
605278 A
1 A
605279 AGCAACAGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.38, C:0.28, G:0.33, T:0.00
Consensus pattern (19 bp):
AGAGACAGCCACGGACAGC
Found at i:606128 original size:15 final size:15
Alignment explanation
Indices: 606108--606137 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
606098 GGAGCTTTTA
606108 ATTTTAATAATTGAT
1 ATTTTAATAATTGAT
*
606123 ATTTTAATCATTGAT
1 ATTTTAATAATTGAT
606138 TAATAATTAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.37, C:0.03, G:0.07, T:0.53
Consensus pattern (15 bp):
ATTTTAATAATTGAT
Found at i:606320 original size:2 final size:2
Alignment explanation
Indices: 606313--606337 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
606303 TTATTTTTAT
606313 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
606338 TTTGGTTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:606460 original size:19 final size:19
Alignment explanation
Indices: 606425--606462 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
606415 CAATTATATA
*
606425 TATTAATATAATTTTTTAT
1 TATTAATATAATATTTTAT
606444 TATTAGATA-AATATTTTAT
1 TATTA-ATATAATATTTTAT
606463 CAATATTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 14 0.82
20 3 0.18
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (19 bp):
TATTAATATAATATTTTAT
Found at i:609151 original size:8 final size:8
Alignment explanation
Indices: 609140--609169 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
609130 CATGCATTTG
609140 CATTTTTA
1 CATTTTTA
609148 CATTTTTA
1 CATTTTTA
*
609156 CATCTTTA
1 CATTTTTA
609164 CATTTT
1 CATTTT
609170 CATTTATACT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (8 bp):
CATTTTTA
Found at i:609250 original size:12 final size:13
Alignment explanation
Indices: 609233--609261 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
609223 ACATTCACAT
609233 ATTTACATTT-GC
1 ATTTACATTTAGC
609245 ATTTACATTTAGC
1 ATTTACATTTAGC
609258 ATTT
1 ATTT
609262 TTTTCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.52
Consensus pattern (13 bp):
ATTTACATTTAGC
Found at i:615029 original size:268 final size:267
Alignment explanation
Indices: 614620--615239 Score: 989
Period size: 268 Copynumber: 2.3 Consensus size: 267
614610 AACAAGAAGT
*
614620 AAATACTGGGGCATGCTGAAAGCCCCTTTCAAATCAGAATCAGGAATGTTGATTATTTTGAACGT
1 AAATACTGGGGCATGCTGAAAGCCCCTTTCAAATCAGAATCATGAATGTTGATTATTTTGAACGT
614685 TTGTATTAGCAAATGTTGGGGCATATCGAAAGCCCATTTCAGACAGAAATGATTCATGTAGGGCA
66 TTGTATTAGCAAATGTTGGGGCATATCGAAAGCCCATTTCAGACAGAAATGATTCATGTAGGGCA
* *
614750 TTCTAAGGGCCCACGTCAGTATAAATATTTGGGCATTTTGAAAGCTCACTTCAACAAGAAGCAAA
131 TTCTAAGGGCCCACGTCAGTATAAATATTTGGGCATTTTGAAAGCTCACATCAACAAGAAGAAAA
* * *
614815 TGTTGGGGTATGCTGAAACCCTATTTCAATTATAATCAGGAACATTGACGCATTTTGAAAATTCA
196 TATTGGGGTATACTAAAACCCTATTTCAATTATAATCAGGAACATTGACGCATTTTGAAAATTCA
614880 TGTCAAC
261 TGTCAAC
614887 AAATACTGGGGCATGCTGAAAGCCCCTTTCAAATCAGAATCATGAATGTTGATGTATTTTGAACG
1 AAATACTGGGGCATGCTGAAAGCCCCTTTCAAATCAGAATCATGAATGTTGAT-TATTTTGAACG
* * *
614952 TTTGTATTAGCAAATATTGGGGCATATCGAAAGCCCATTTCAGACATAAATGATTCATGTGGGGC
65 TTTGTATTAGCAAATGTTGGGGCATATCGAAAGCCCATTTCAGACAGAAATGATTCATGTAGGGC
* *
615017 ATTCTGAGGGCCCACGTCAGTATGAATATTTGGGCATTTTGAAAGCTCACATCAACAAGAAGAAA
130 ATTCTAAGGGCCCACGTCAGTATAAATATTTGGGCATTTTGAAAGCTCACATCAACAAGAAGAAA
* *
615082 ATATTGGGGTATACTAAAACCCTATTTTAATTATAATCAGGAACATTGACGCATTTTGAATATTC
195 ATATTGGGGTATACTAAAACCCTATTTCAATTATAATCAGGAACATTGACGCATTTTGAAAATTC
615147 ATGTCAAC
260 ATGTCAAC
** * * ** *
615155 AAATGTTGGGGCATGCTGCAAGCCCATTTC-AATC--AAT--TGGAATGTTGACACATTTTGATC
1 AAATACTGGGGCATGCTGAAAGCCCCTTTCAAATCAGAATCAT-GAATGTTGA-TTATTTTGAAC
*
615215 GTTTGTATTAGCCAATGTTGGGGCA
64 GTTTGTATTAGCAAATGTTGGGGCA
615240 CGCTGAAGGC
Statistics
Matches: 328, Mismatches: 22, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
263 1 0.00
264 40 0.12
265 3 0.01
267 56 0.17
268 228 0.70
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (267 bp):
AAATACTGGGGCATGCTGAAAGCCCCTTTCAAATCAGAATCATGAATGTTGATTATTTTGAACGT
TTGTATTAGCAAATGTTGGGGCATATCGAAAGCCCATTTCAGACAGAAATGATTCATGTAGGGCA
TTCTAAGGGCCCACGTCAGTATAAATATTTGGGCATTTTGAAAGCTCACATCAACAAGAAGAAAA
TATTGGGGTATACTAAAACCCTATTTCAATTATAATCAGGAACATTGACGCATTTTGAAAATTCA
TGTCAAC
Found at i:616571 original size:22 final size:22
Alignment explanation
Indices: 616543--616619 Score: 120
Period size: 22 Copynumber: 3.5 Consensus size: 22
616533 ATCTACACTC
616543 TTCAAAGATGATAGATTCTTTT
1 TTCAAAGATGATAGATTCTTTT
*
616565 TTCAAAGATGATAAATTCTATTT
1 TTCAAAGATGATAGATTCT-TTT
*
616588 TT-AAAGATGATAGATTCTATT
1 TTCAAAGATGATAGATTCTTTT
616609 TTCAAAGATGA
1 TTCAAAGATGA
616620 AATCTTTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
21 4 0.08
22 41 0.82
23 5 0.10
ACGTcount: A:0.38, C:0.08, G:0.13, T:0.42
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTTTT
Found at i:617586 original size:76 final size:76
Alignment explanation
Indices: 617297--618848 Score: 2621
Period size: 76 Copynumber: 20.4 Consensus size: 76
617287 CTATTTCCCA
* ** *
617297 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGACATTTTAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
617362 AACCTTAGGGT
66 AGCCTTAGGGT
*
617373 CCTCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTTTTGATGTTTTC
617438 AAAGCCTTAGGGT
64 AAAGCCTTAGGGT
*
617451 CATCTGTAAGTCCT--A-TGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
617513 AGCCTTAGAGT
66 AGCCTTAGGGT
* * *
617524 CATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTATTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
617589 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
617600 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCTTTTGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
*
617665 AAGCCTTAGAGT
65 AAGCCTTAGGGT
* *
617677 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAA-TCTTCTGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
617741 AGCCTTAGGGT
66 AGCCTTAGGGT
* * *
617752 CATTTGTAAGTCATACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTTTGATGTTTTC
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG--CTTTTTGATGTTTTC
617817 AAAGCCTTAGGGT
64 AAAGCCTTAGGGT
617830 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
617895 AGCATTAGGGT
66 AGCCTTAGGGT
*
617906 CATTTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
617971 AAGCCTTAGGGT
65 AAGCCTTAGGGT
617983 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
618048 AGCCTTAGGGT
66 AGCCTTAGGGT
*
618059 CATCTGTAAGTCCTACAGTGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
618124 AGCCTT-GGGT
66 AGCCTTAGGGT
* * *
618134 CTTCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
618199 AGCCTTAGGGT
66 AGCCTTAGGGT
*
618210 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
618275 AAGCCTTAGGGT
65 AAGCCTTAGGGT
618287 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
618352 AGCCTTAGGGT
66 AGCCTTAGGGT
*
618363 CATCTGTAAGTCCTACAGTGCATGATTTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
618428 AAGCCTTAGGGT
65 AAGCCTTAGGGT
* * *
618440 CATCTGTAAGTCCTACAGTCCATGATATTTCCAAAAGGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
618505 AGCCTTAGGGT
66 AGCCTTAGGGT
618516 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
618581 AGCCTTAGGGT
66 AGCCTTAGGGT
*
618592 CTTCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
618657 AGCCTTAGAGT
66 AGCCTTAGGGT
* *
618668 AATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
618733 AACCTTAGGGT
66 AGCCTTAGGGT
* * *
618744 CATCTGTAAGTCTTACAGTGCATGATGTTT-TAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
618808 AACCTTAGGGT
66 AGCCTTAGGGT
* *
618819 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
618849 TTAACATTTC
Statistics
Matches: 1397, Mismatches: 66, Indels: 27
0.94 0.04 0.02
Matches are distributed among these distances:
73 56 0.04
75 218 0.16
76 715 0.51
77 283 0.20
78 125 0.09
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:617707 original size:153 final size:153
Alignment explanation
Indices: 617297--618848 Score: 2631
Period size: 153 Copynumber: 10.2 Consensus size: 153
617287 CTATTTCCCA
* ** *
617297 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGC-TTTTTGACATTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
* *
617361 AAACCTTAGGGTCCTCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTT
617426 TTTGATGTTTTCAAAGCCTTAGGGT
129 TTTGATGTTTTCAAAGCCTTAGGGT
*
617451 CATCTGTAAGTCCT--A-TGCATGATGTTTCCAAAAAGCCTTCGGGAG-ATTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
* * *
617512 AAGCCTTAGAGTCATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTAT
66 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
617577 TGATATTTTCAAAGCCTTAGGGT
131 TGATGTTTTCAAAGCCTTAGGGT
* *
617600 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCTTTTGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
* * *
617665 AAGCCTTAGAGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAA-TCTTCTGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
617729 TGATGTTTTCAAAGCCTTAGGGT
131 TGATGTTTTCAAAGCCTTAGGGT
* * *
617752 CATTTGTAAGTCATACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTTTGATGTTTTC
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG-CTTTTTTGATGTTTTC
617817 AAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
65 AAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
*
617882 TTGATGTTTTCAAAGCATTAGGGT
130 TTGATGTTTTCAAAGCCTTAGGGT
*
617906 CATTTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
617971 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
618036 TGATGTTTTCAAAGCCTTAGGGT
131 TGATGTTTTCAAAGCCTTAGGGT
*
618059 CATCTGTAAGTCCTACAGTGCATGATATTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
* * *
618123 AAGCCTT-GGGTCTTCTATAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
618187 TGATGTTTTCAAAGCCTTAGGGT
131 TGATGTTTTCAAAGCCTTAGGGT
*
618210 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
618275 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
618340 TGATGTTTTCAAAGCCTTAGGGT
131 TGATGTTTTCAAAGCCTTAGGGT
*
618363 CATCTGTAAGTCCTACAGTGCATGATTTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
* * *
618428 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTCCATGATATTTCCAAAAGGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
618493 TGATGTTTTCAAAGCCTTAGGGT
131 TGATGTTTTCAAAGCCTTAGGGT
618516 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
*
618580 AAGCCTTAGGGTCTTCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
618645 TGATGTTTTCAAAGCCTTAGAGT
131 TGATGTTTTCAAAGCCTTAGGGT
* *
618668 AATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATATTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
* * *
618732 AAACCTTAGGGTCATCTGTAAGTCTTACAGTGCATGATGTTT-TAAAAAGCCTTCGGGAGCTTTT
66 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
* *
618796 TGATATTTTCAAAACCTTAGGGT
131 TGATGTTTTCAAAGCCTTAGGGT
* *
618819 CATCTGTAAGCCCTTCAGTGCATGATGTTT
1 CATCTGTAAGTCCTACAGTGCATGATGTTT
618849 TTAACATTTC
Statistics
Matches: 1326, Mismatches: 63, Indels: 21
0.94 0.04 0.01
Matches are distributed among these distances:
149 56 0.04
151 274 0.21
152 350 0.26
153 550 0.41
154 96 0.07
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (153 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTTGATGTTTTCA
AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
TGATGTTTTCAAAGCCTTAGGGT
Found at i:618373 original size:457 final size:457
Alignment explanation
Indices: 617297--618848 Score: 2634
Period size: 457 Copynumber: 3.4 Consensus size: 457
617287 CTATTTCCCA
* * *
617297 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCAGGAGCTTTTTGACATTTTAAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
*
617362 AACCTTAGGGTCCTCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAAAGCCTTCGGGAGCTTT
66 AACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCC--AAAAAGCCTTCGGGAGCTTT
617427 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCT--A-TGCATGATGTTTCCAAAAAGCCT
129 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCT
* * *
617489 TCGGGAG-ATTTTTGATGTTTTCAAAGCCTTAGAGTCATCTGTAAGTCCTACAATGCATGATGTT
194 TCGGGAGCTTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTT
* *
617553 TCCAAAAAGCCTTCGGGAGCTTATTGATATTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAG
259 TCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAG
* * * *
617618 TGCATGATGTTTCCAAAAAGCTTTTGGGAGCTTTTTTGATGTTTTCAAAGCCTTAGAGTCATCTG
324 TGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATGTTTTCAAAGCCTTAGGGTCTTCTG
*
617683 TAAGTCCTACAGTGCATGATGTTTCCAAAAA-TCTTCT-GGAGCTTTTTGATGTTTTCAAAGCCT
388 TAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT-TGGGAGCTTTTTGATGTTTTCAAAGCCT
617746 TAGGGT
452 TAGGGT
* * * *
617752 CATTTGTAAGTCATACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGATTTTTTTGATGTTTTC
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG--CTTTTTGATATTTTC
*
617817 AAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
64 AAAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTT
* *
617882 TTGATGTTTTCAAAGCATTAGGGTCATTTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCT
129 TTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCT
617947 TCGGGAGCTTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTT
194 TCGGGAGCTTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTT
618012 TCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAG
259 TCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAG
* *
618077 TGCATGATATTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTT-GGGTCTTCTAT
324 TGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCTTCTGT
618141 AAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAAGCCTTA
389 AAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAAGCCTTA
618206 GGGT
454 GGGT
* *
618210 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAATCCTTCGGGAGCTTTTTTGATGTTTTCA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGC-TTTTTGATATTTTCA
*
618275 AAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
65 AAACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTT
*
618340 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATTTTTCCAAAAAGCCTT
130 TGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTT
* *
618405 CGGGAGCTTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTCCATGATATTT
195 CGGGAGCTTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTT
*
618470 CCAAAAGGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGT
260 CCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGT
618535 GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCTTCTGTA
325 GCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCTTCTGTA
*
618600 AGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAG
390 AGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAAGCCTTAG
*
618665 AGT
455 GGT
*
618668 AATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
* *
618733 AACCTTAGGGTCATCTGTAAGTCTTACAGTGCATGATGTTT-TAAAAAGCCTTCGGGAGCTTTTT
66 AACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
* * * *
618797 GATATTTTCAAAACCTTAGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTT
131 GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTT
618849 TTAACATTTC
Statistics
Matches: 1039, Mismatches: 48, Indels: 19
0.94 0.04 0.02
Matches are distributed among these distances:
455 101 0.10
456 69 0.07
457 468 0.45
458 256 0.25
459 145 0.14
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (457 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATATTTTCAA
AACCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTT
GATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTC
GGGAGCTTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTGCATGATGTTTC
CAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCATCTGTAAGTCCTACAGTG
CATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAAAGCCTTAGGGTCTTCTGTAA
GTCCTACAGTGCATGATGTTTCCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAAAGCCTTAGG
GT
Found at i:618986 original size:3 final size:3
Alignment explanation
Indices: 618978--619019 Score: 66
Period size: 3 Copynumber: 13.7 Consensus size: 3
618968 CACTTTCATA
*
618978 TAT TAT TAT TAT TAT TAT TAA TAT ATAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT TAT TA
619020 AATAAATAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
3 33 0.92
4 3 0.08
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:620761 original size:24 final size:25
Alignment explanation
Indices: 620714--620762 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
620704 TATAAAAACC
* *
620714 AGAAAAAATATTGTTTTATTTTATT
1 AGAAAAAATATTATTTTATATTATT
*
620739 AGAAAAATTATTATTTT-TATTATT
1 AGAAAAAATATTATTTTATATTATT
620763 TAAATATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (25 bp):
AGAAAAAATATTATTTTATATTATT
Found at i:622322 original size:213 final size:213
Alignment explanation
Indices: 621955--622380 Score: 762
Period size: 213 Copynumber: 2.0 Consensus size: 213
621945 TGATGACAGG
*
621955 CAAGATAATGCCACGACAAAAGAAAAATCCCCACTAGCAGGAGTTGATGACCAAAGGGAAGGTGT
1 CAAGATAATGCCACGACAAAAGAAAAACCCCCACTAGCAGGAGTTGATGACCAAAGGGAAGGTGT
* *
622020 AGAATTCTGCCATAACTATTTTTTAGGCTTTGGTGATTACTTGAAGCTCGATGAAGAAGACGAAG
66 AGAATTCTGCCATAACTATTTTTTAGGCTTTGGTGATTACTTGAAGCTCGATGAAGAAGACAAAC
* *
622085 ATGAGCTTAAGGATATTCCAAAGGAGACGAGTCAGTCTAACTTACTCATAGTTAGACCAGGTATG
131 ATGAGCTTAAGGATATTCCAAAGGAGACGAGACAGTCTAACTTACTCATAGTTAGACCAGGTACG
622150 AAATTTGAACCTTTGGAT
196 AAATTTGAACCTTTGGAT
* * *
622168 CAAGATAATGCCATGACTAAAGACAAACCCCCACTAGCAGGAGTTGATGACCAAAGGGAAGGTGT
1 CAAGATAATGCCACGACAAAAGAAAAACCCCCACTAGCAGGAGTTGATGACCAAAGGGAAGGTGT
*
622233 AGAATTCTGCCATAACTATTTTTTAGGCTTTGGTGATTACTTGAAGCTCGATGAAGAAGGCAAAC
66 AGAATTCTGCCATAACTATTTTTTAGGCTTTGGTGATTACTTGAAGCTCGATGAAGAAGACAAAC
*
622298 ATGAGCTTAAGGATATTCCAAAGGAGACGAGACAGTCTAACTTACTCATAGTTAGACCCGGTACG
131 ATGAGCTTAAGGATATTCCAAAGGAGACGAGACAGTCTAACTTACTCATAGTTAGACCAGGTACG
622363 AAATTTGAACCTTTGGAT
196 AAATTTGAACCTTTGGAT
622381 TTTATTGAAT
Statistics
Matches: 203, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
213 203 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (213 bp):
CAAGATAATGCCACGACAAAAGAAAAACCCCCACTAGCAGGAGTTGATGACCAAAGGGAAGGTGT
AGAATTCTGCCATAACTATTTTTTAGGCTTTGGTGATTACTTGAAGCTCGATGAAGAAGACAAAC
ATGAGCTTAAGGATATTCCAAAGGAGACGAGACAGTCTAACTTACTCATAGTTAGACCAGGTACG
AAATTTGAACCTTTGGAT
Found at i:623979 original size:36 final size:34
Alignment explanation
Indices: 623939--624068 Score: 99
Period size: 36 Copynumber: 3.7 Consensus size: 34
623929 TAGTATTTAC
623939 TAAAACAAATAAAAATAATAAATATATAATACTAAG
1 TAAAACAAATAAAAATAA-AAATATATAATA-TAAG
* *
623975 TAAAACAAGTAAAAAATAAAGATATACATAATATTAAG
1 TAAAACAAAT-AAAAATAAA-A-ATATATAATA-TAAG
*
624013 -AAAA-AAAT-AAAATAAAGTAAAAATATAATAT-A-
1 TAAAACAAATAAAAAT-AA--AAATATATAATATAAG
*
624045 TATAAATAAATAAAAATAAAAATA
1 TA-AAACAAATAAAAATAAAAATA
624069 GAATATTAAG
Statistics
Matches: 77, Mismatches: 7, Indels: 23
0.72 0.07 0.21
Matches are distributed among these distances:
33 6 0.08
34 9 0.12
35 16 0.21
36 19 0.25
37 14 0.18
38 13 0.17
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (34 bp):
TAAAACAAATAAAAATAAAAATATATAATATAAG
Found at i:624022 original size:17 final size:18
Alignment explanation
Indices: 624002--624057 Score: 53
Period size: 17 Copynumber: 3.2 Consensus size: 18
623992 AAAGATATAC
*
624002 ATAATATTAAG-AAAAAA
1 ATAATATAAAGTAAAAAA
* *
624019 ATAAAATAAAGTAAAAAT
1 ATAATATAAAGTAAAAAA
* *
624037 ATAATATATA-TAAATAA
1 ATAATATAAAGTAAAAAA
624054 ATAA
1 ATAA
624058 AAATAAAAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
17 18 0.58
18 13 0.42
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.27
Consensus pattern (18 bp):
ATAATATAAAGTAAAAAA
Found at i:624203 original size:16 final size:16
Alignment explanation
Indices: 624182--624228 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
624172 ATATATATAT
* *
624182 ATATATATGATATAAG
1 ATATATATAATATAAA
624198 ATATATATAATA-AAA
1 ATATATATAATATAAA
624213 ATA-ATATAATATAAA
1 ATATATATAATATAAA
624228 A
1 A
624229 AAAGAGGAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 8 0.29
15 9 0.32
16 11 0.39
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.34
Consensus pattern (16 bp):
ATATATATAATATAAA
Found at i:625741 original size:110 final size:110
Alignment explanation
Indices: 625585--625783 Score: 274
Period size: 110 Copynumber: 1.8 Consensus size: 110
625575 AACTGGGAAA
* * *
625585 TTGTTTGTTGACAGCCAACCGCCCCTTCGTTGTGAAGTTGAGCTTGTGTTGTCTCAAGT-TCAAT
1 TTGTTTGTTGACAACCAACCGCCCATTCGTTATGAAGTTGAGCTTGTGTTGTCTCAAGTCT-AAT
* *
625649 ATCCTTCGCTGTGAAGTTGAAATTGATTCTGAATGAAACTAAAAAG
65 ATCCCTCACTGTGAAGTTGAAATTGATTCTGAATGAAACTAAAAAG
* ** * * **
625695 TTGTTTGTTGACAATCAGTCGCCCATTTGTTATGAATTTGAGCTTGTGTTGTCTTGAGTCTAATA
1 TTGTTTGTTGACAACCAACCGCCCATTCGTTATGAAGTTGAGCTTGTGTTGTCTCAAGTCTAATA
625760 TCCCTCACTGTGAAGTTGAAATTG
66 TCCCTCACTGTGAAGTTGAAATTG
625784 GCTCTGAAAC
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
110 75 0.99
111 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (110 bp):
TTGTTTGTTGACAACCAACCGCCCATTCGTTATGAAGTTGAGCTTGTGTTGTCTCAAGTCTAATA
TCCCTCACTGTGAAGTTGAAATTGATTCTGAATGAAACTAAAAAG
Found at i:626626 original size:67 final size:66
Alignment explanation
Indices: 626508--626670 Score: 206
Period size: 67 Copynumber: 2.5 Consensus size: 66
626498 AAGATATCTG
* * * **
626508 TTGTTTCATGA-AAA-TGGTCTCAAGGGAAACAAAATTTTGTTTTAAGGGAAATAAATTTGAAGA
1 TTGTTTCAAGAGAAACT-GTCTCAAGGGAGACAAAACTTTGTTTTAAGGGAAATAAATTCAAAGA
626571 TT
65 TT
*
626573 TTGTGTCTCAAGAGAAACTGTCTCAAGGGAGAC-AAACTTTGTTTTAGGGGAAATAAATTCAAAG
1 TTGT-T-TCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTTTAAGGGAAATAAATTCAAAG
626637 ATT
64 ATT
* *
626640 TTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGAC
626671 GAAATATTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
65 28 0.33
66 2 0.02
67 39 0.45
68 16 0.19
69 1 0.01
ACGTcount: A:0.36, C:0.10, G:0.22, T:0.31
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAACTTTGTTTTAAGGGAAATAAATTCAAAGAT
T
Found at i:626752 original size:137 final size:138
Alignment explanation
Indices: 626585--626847 Score: 336
Period size: 137 Copynumber: 1.9 Consensus size: 138
626575 GTGTCTCAAG
* ** * * *
626585 AGAAACTGTCTCAAGGGAGACAAACTTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAACTTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
* *
626650 GGAAACTGTCTCAAGAGAGACGAAATATT-TTTC-AAGAGAAACTGTCTCAAGAGTGACAAAACT
66 GGAAACTGTCTCAAGAGAGACAAAAT-TTGTTTCAAAG-GAAACTGTCTCAAGAGAGACAAAACT
626713 TAGTTCCAAA
129 TAGTTCCAAA
** * * *
626723 AGAAACTGTCT-AAGGGAGATGGAA-TTTGTTTCAAATAAAACATATTCAAATAATTTGTTTCAA
1 AGAAACTGTCTCAAGGGAGA-CAAACTTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAA
* *
626786 GGGAAACTGTCTTAAGAGAGACAAAATTTGTTTCAAAGGAAACTGTCTTAAGAGAGACAAAA
65 GGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAA
626848 TTTATTTCAA
Statistics
Matches: 107, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
136 2 0.02
137 89 0.83
138 16 0.15
ACGTcount: A:0.41, C:0.12, G:0.20, T:0.27
Consensus pattern (138 bp):
AGAAACTGTCTCAAGGGAGACAAACTTTGTTTCAAAGAAAACAAATTCAAAGAATTTGTTTCAAG
GGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAAGGAAACTGTCTCAAGAGAGACAAAACTTA
GTTCCAAA
Found at i:626821 original size:36 final size:36
Alignment explanation
Indices: 626774--626863 Score: 153
Period size: 36 Copynumber: 2.5 Consensus size: 36
626764 ATATTCAAAT
*
626774 AATTTGTTTCAAGGGAAACTGTCTTAAGAGAGACAA
1 AATTTGTTTCAAAGGAAACTGTCTTAAGAGAGACAA
626810 AATTTGTTTCAAAGGAAACTGTCTTAAGAGAGACAA
1 AATTTGTTTCAAAGGAAACTGTCTTAAGAGAGACAA
* *
626846 AATTTATTTCAATGGAAA
1 AATTTGTTTCAAAGGAAA
626864 TGTTTTCAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.30
Consensus pattern (36 bp):
AATTTGTTTCAAAGGAAACTGTCTTAAGAGAGACAA
Found at i:626872 original size:101 final size:101
Alignment explanation
Indices: 626679--626950 Score: 264
Period size: 101 Copynumber: 2.7 Consensus size: 101
626669 ACGAAATATT
* * * * *
626679 TTTCAAGAGAAACTGTCTCAAGAGTGACAAAACTTAGTTCCAAAAGAAACTGTC-TAAGGGAGAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTTAAGAGAGAT
** * *
626743 GGAATTTGTTTCAAATAAAACATATTCAAATAATTT-G
66 AAAATTTATTTCAAATAAAACATATTC-AAT-ATTTAA
* * *
626780 TTTCAAGGGAAACTGTCTTAAGAGAGACAAAA-TTTGTTTCAAAGGAAACTGTCTTAAGAGAGAC
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTTAAGAGAGAT
* ** * *
626844 AAAATTTATTTC-AATGGAAATGTTTTCAATGTTTACA
66 AAAATTTATTTCAAAT-AAAACATATTCAATATTTA-A
* * * * * * *
626881 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGGGAAACTATCTCAAGCGAGAT
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTTAAGAGAGAT
626946 AAAAT
66 AAAAT
626951 CATTTTTTTA
Statistics
Matches: 140, Mismatches: 26, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
99 3 0.02
100 24 0.17
101 82 0.59
102 31 0.22
ACGTcount: A:0.40, C:0.12, G:0.18, T:0.30
Consensus pattern (101 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTTTCAAAGGAAACTGTCTTAAGAGAGAT
AAAATTTATTTCAAATAAAACATATTCAATATTTAA
Found at i:628527 original size:69 final size:69
Alignment explanation
Indices: 628411--628548 Score: 222
Period size: 69 Copynumber: 2.0 Consensus size: 69
628401 TGTCTCTCTC
* * * * *
628411 TTGATGCTCTATGATCTTCGAGTGGAGTGATTTAGTGGTTCGGAAATGATTGTGCTTGATCAATC
1 TTGATGATCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
628476 TCAT
66 TCAT
*
628480 TTGATGATCTATGATCTTCGAGTGAAGTGGTTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
1 TTGATGATCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
628545 TCAT
66 TCAT
628549 AGTTTGAATC
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
69 63 1.00
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (69 bp):
TTGATGATCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGAAAATGATTGTGCTTGATCAATC
TCAT
Found at i:628645 original size:21 final size:21
Alignment explanation
Indices: 628621--628690 Score: 97
Period size: 21 Copynumber: 3.3 Consensus size: 21
628611 TTTTCTTTAA
628621 TTTTCT-TTGTTTGTTCTCTTTT
1 TTTTCTCTT-TTT-TTCTCTTTT
628643 TTTTCTCTTTTTTTCTCTTTT
1 TTTTCTCTTTTTTTCTCTTTT
*
628664 TTTTCTCTTTTTTTTTCTTTT
1 TTTTCTCTTTTTTTCTCTTTT
*
628685 TGTTCT
1 TTTTCT
628691 AATTGAATCT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 34 0.76
22 9 0.20
23 2 0.04
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.80
Consensus pattern (21 bp):
TTTTCTCTTTTTTTCTCTTTT
Found at i:628648 original size:11 final size:11
Alignment explanation
Indices: 628624--628690 Score: 93
Period size: 11 Copynumber: 6.1 Consensus size: 11
628614 TCTTTAATTT
628624 TCTTTGTTTGTTC
1 TCTTT-TTT-TTC
628637 TCTTTTTTTTC
1 TCTTTTTTTTC
628648 TC-TTTTTTTC
1 TCTTTTTTTTC
628658 TCTTTTTTTTC
1 TCTTTTTTTTC
628669 TCTTTTTTTT-
1 TCTTTTTTTTC
*
628679 TCTTTTTGTTC
1 TCTTTTTTTTC
628690 T
1 T
628691 AATTGAATCT
Statistics
Matches: 51, Mismatches: 1, Indels: 6
0.88 0.02 0.10
Matches are distributed among these distances:
10 19 0.37
11 24 0.47
12 3 0.06
13 5 0.10
ACGTcount: A:0.00, C:0.16, G:0.04, T:0.79
Consensus pattern (11 bp):
TCTTTTTTTTC
Found at i:628657 original size:32 final size:31
Alignment explanation
Indices: 628609--628690 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 31
628599 TCTTGTTTTC
628609 TTTTTTCTTTAATTTTCT-TTGTTTGTTCTCTTT
1 TTTTTTCTTT--TTTTCTCTT-TTTGTTCTCTTT
*
628642 TTTTTCTCTTTTTTTCTCTTTTTTTTCTCTTT
1 TTTTT-TCTTTTTTTCTCTTTTTGTTCTCTTT
628674 TTTTTTCTTTTTGTTCT
1 TTTTTTCTTTTT-TTCT
628691 AATTGAATCT
Statistics
Matches: 45, Mismatches: 1, Indels: 7
0.85 0.02 0.13
Matches are distributed among these distances:
31 7 0.16
32 26 0.58
33 7 0.16
34 5 0.11
ACGTcount: A:0.02, C:0.15, G:0.04, T:0.79
Consensus pattern (31 bp):
TTTTTTCTTTTTTTCTCTTTTTGTTCTCTTT
Found at i:631763 original size:21 final size:22
Alignment explanation
Indices: 631739--631779 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 22
631729 AAAACACGTA
631739 AAAAAT-AATAAAAT-AATAAT
1 AAAAATAAATAAAATGAATAAT
631759 AAAAATAAATAAAATGAATAA
1 AAAAATAAATAAAATGAATAA
631780 AATGTAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.32
21 8 0.42
22 5 0.26
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAAATAAATAAAATGAATAAT
Found at i:632172 original size:14 final size:14
Alignment explanation
Indices: 632164--632223 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
632154 TATAAGATAT
632164 ATATAATAAAAATA
1 ATATAATAAAAATA
*
632178 ATATAATATAAATA
1 ATATAATAAAAATA
632192 A-ATAAATAAAAAT-
1 ATAT-AATAAAAATA
*
632205 ATA-ATTAAAAATA
1 ATATAATAAAAATA
632218 TATATA
1 -ATATA
632224 TAGGAGACGA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
12 8 0.21
13 3 0.08
14 26 0.68
15 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (14 bp):
ATATAATAAAAATA
Found at i:632181 original size:25 final size:25
Alignment explanation
Indices: 632137--632208 Score: 69
Period size: 25 Copynumber: 3.0 Consensus size: 25
632127 ACACACACAC
* *
632137 ATATATAT-AT-ATAATGATATAAG
1 ATATATATAATAAAAATAATATAAG
*
632160 ATATATATAATAAAAATAATATAAT
1 ATATATATAATAAAAATAATATAAG
* *
632185 ATAAATA-AATAAATAAAAATATAA
1 ATATATATAATAAA-AATAATATAA
632209 TTAAAAATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
23 8 0.20
24 8 0.20
25 25 0.61
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (25 bp):
ATATATATAATAAAAATAATATAAG
Found at i:632186 original size:23 final size:25
Alignment explanation
Indices: 632153--632213 Score: 72
Period size: 25 Copynumber: 2.5 Consensus size: 25
632143 ATATATAATG
* * *
632153 ATATAAGATATATATAATAAA-AATA
1 ATATAATATAAATA-AATAAATAAAA
632178 ATATAATATAAATAAATAAATAAAA
1 ATATAATATAAATAAATAAATAAAA
632203 ATATAAT-TAAA
1 ATATAATATAAA
632214 AATATATATA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 10 0.31
25 22 0.69
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (25 bp):
ATATAATATAAATAAATAAATAAAA
Found at i:640769 original size:78 final size:77
Alignment explanation
Indices: 640638--640785 Score: 185
Period size: 78 Copynumber: 1.9 Consensus size: 77
640628 TTAATAAATT
**
640638 TCTTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATATGAATTACAATC-TTGAAT
1 TCTTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATAAAAATTACAATCTTTGAAT
640702 GTTTATTTAAAA
66 GTTTATTTAAAA
* * *
640714 TCTTATTTAATT-ATTCTGAATTAAATAT-CAATTAAAAGAGTTGTAATAAAAATTACATTCTTT
1 TCTTATTTAATTAATTC--AATTAAATATAC-ATT-AAAGACTTATAATAAAAATTACAATCTTT
*
640777 TAATGTTTA
62 GAATGTTTA
640786 CTTACTATAT
Statistics
Matches: 61, Mismatches: 6, Indels: 7
0.82 0.08 0.09
Matches are distributed among these distances:
75 4 0.07
76 13 0.21
77 13 0.21
78 21 0.34
79 10 0.16
ACGTcount: A:0.42, C:0.07, G:0.06, T:0.45
Consensus pattern (77 bp):
TCTTATTTAATTAATTCAATTAAATATACATTAAAGACTTATAATAAAAATTACAATCTTTGAAT
GTTTATTTAAAA
Found at i:647699 original size:77 final size:78
Alignment explanation
Indices: 647570--647717 Score: 176
Period size: 77 Copynumber: 1.9 Consensus size: 78
647560 TTAATAAATT
* *
647570 TCTTATTTAATTAATTCAAATTAAATATACACTAAAGACTTATAATCTGAATTACAATC-TTTAA
1 TCTTATTTAATTAATTCAAATTAAATATACACTAAAGAATTACAATCTGAATTACAATCTTTTAA
*
647634 TGTTTATTTAAAA
66 TATTTATTTAAAA
* * * * * *
647647 TCTTATTTAATTATTTCGAATTGAATAT-CAATTAAAAGAATTGCAATC-GAATTACATTCTTTT
1 TCTTATTTAATTAATTCAAATTAAATATAC-ACT-AAAGAATTACAATCTGAATTACAATCTTTT
647710 AATATTTA
64 AATATTTA
647718 CTTACTCTAT
Statistics
Matches: 59, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
76 1 0.02
77 37 0.63
78 21 0.36
ACGTcount: A:0.41, C:0.10, G:0.05, T:0.44
Consensus pattern (78 bp):
TCTTATTTAATTAATTCAAATTAAATATACACTAAAGAATTACAATCTGAATTACAATCTTTTAA
TATTTATTTAAAA
Found at i:652560 original size:50 final size:50
Alignment explanation
Indices: 652489--652586 Score: 151
Period size: 50 Copynumber: 2.0 Consensus size: 50
652479 CATCATGTTA
* ** *
652489 GGGCTAACTAGATCTTGATCTTTTAGCTTGAACCAATTTAATGGTGTTCG
1 GGGCCAACTAGATCTCAATCTTTTAGCTCGAACCAATTTAATGGTGTTCG
*
652539 GGGCCAACTAGATCTCAATCTTTTAGCTCGAACCAATTTAATTGTGTT
1 GGGCCAACTAGATCTCAATCTTTTAGCTCGAACCAATTTAATGGTGTT
652587 TGACACTTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.37
Consensus pattern (50 bp):
GGGCCAACTAGATCTCAATCTTTTAGCTCGAACCAATTTAATGGTGTTCG
Found at i:669237 original size:21 final size:21
Alignment explanation
Indices: 669146--669316 Score: 96
Period size: 21 Copynumber: 8.0 Consensus size: 21
669136 TCGAGGGTTC
* *
669146 TATGTGGTCCTTCGGGACATA
1 TATGTGGTCCTTTGGAACATA
* **
669167 TATATAATCCTTTGGAACATA
1 TATGTGGTCCTTTGGAACATA
* * *
669188 TATGCGGTTCTTCGAGACACATA
1 TATGTGGTCCTTTG-GA-ACATA
*
669211 T-T-TGGTCCTTTGGAATATA
1 TATGTGGTCCTTTGGAACATA
** * *
669230 TATGTGGTCC-TTAAAGAGATT
1 TATGTGGTCCTTTGGA-ACATA
* *
669251 TCAATGTGGTCCTTAGGGACATA
1 T--ATGTGGTCCTTTGGAACATA
* *
669274 TATGTGGTCCTTCGGGACATA
1 TATGTGGTCCTTTGGAACATA
*
669295 CCTATGTGGTCCTTTGGTACAT
1 --TATGTGGTCCTTTGGAACAT
669317 TCCATGTGGA
Statistics
Matches: 112, Mismatches: 28, Indels: 18
0.71 0.18 0.11
Matches are distributed among these distances:
19 5 0.04
20 6 0.05
21 60 0.54
22 3 0.03
23 37 0.33
24 1 0.01
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (21 bp):
TATGTGGTCCTTTGGAACATA
Found at i:669302 original size:44 final size:44
Alignment explanation
Indices: 669146--669316 Score: 143
Period size: 44 Copynumber: 4.0 Consensus size: 44
669136 TCGAGGGTTC
* * **
669146 TATGTGGTCCTTCGGGACATA--TATATAATCCTTTGGAACATA
1 TATGTGGTCCTTCGAGACATACCTATGTGGTCCTTTGGAACATA
* * * * *
669188 TATGCGGTTCTTCGAGAC--ACATATTTGGTCCTTTGGAATATA
1 TATGTGGTCCTTCGAGACATACCTATGTGGTCCTTTGGAACATA
** * ** * * *
669230 TATGTGGTCCTTAAAGAGATTTCAATGTGGTCCTTAGGGACATA
1 TATGTGGTCCTTCGAGACATACCTATGTGGTCCTTTGGAACATA
* *
669274 TATGTGGTCCTTCGGGACATACCTATGTGGTCCTTTGGTACAT
1 TATGTGGTCCTTCGAGACATACCTATGTGGTCCTTTGGAACAT
669317 TCCATGTGGA
Statistics
Matches: 96, Mismatches: 29, Indels: 6
0.73 0.22 0.05
Matches are distributed among these distances:
40 1 0.01
42 45 0.47
44 50 0.52
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (44 bp):
TATGTGGTCCTTCGAGACATACCTATGTGGTCCTTTGGAACATA
Found at i:669304 original size:23 final size:23
Alignment explanation
Indices: 669254--669325 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
669244 AGAGATTTCA
669254 ATGTGGTCCTTAGGGACATA--T
1 ATGTGGTCCTTAGGGACATACCT
*
669275 ATGTGGTCCTTCGGGACATACCT
1 ATGTGGTCCTTAGGGACATACCT
* * *
669298 ATGTGGTCCTTTGGTACATTCC-
1 ATGTGGTCCTTAGGGACATACCT
669320 ATGTGG
1 ATGTGG
669326 AACTTTGGTG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
21 19 0.42
22 6 0.13
23 20 0.44
ACGTcount: A:0.18, C:0.19, G:0.28, T:0.35
Consensus pattern (23 bp):
ATGTGGTCCTTAGGGACATACCT
Found at i:670673 original size:138 final size:138
Alignment explanation
Indices: 670306--670988 Score: 517
Period size: 138 Copynumber: 4.9 Consensus size: 138
670296 CACCTGAAGG
* * * * * *
670306 ATTAAGCCTAAAATGTATGCTCTAATATTAA-CTTAATCAAGTTTTTAACAAATTATTGGATT-G
1 ATTAAACCTAAAATGAAGGCTCTAATATTAATC-TAAACAA--TTTTAGCAATTTATTGG-TTCG
* * * * * * **
670369 AATGATTAAAATGGAACCTCA-AGCATAAATGCAA-AGACCAAATAAAAAAGTCTTCTAAATTAA
62 AATAACTAAAATGGAACCT-AGAGCATAAATACAAGA-ACCAAATTAAATATTCCCCTAAATTAA
* * *
670432 AGGAATATGGTGAA
125 AGGACTAAGATGAA
* * * * * * * *
670446 AATAAACCTATATTAAAGGCTCCAATTTTAGTTCTAACCAATTTTAGCAATTTATTGGTTCGAAT
1 ATTAAACCTAAAATGAAGGCTCTAATATTA-ATCTAAACAATTTTAGCAATTTATTGGTTCGAAT
* *
670511 AACTAAAATGGAACCTAGAGCATAAATACGAGAACCAGATTAAATATTCCCCTAAATTAAAGGAC
65 AACTAAAATGGAACCTAGAGCATAAATACAAGAACCAAATTAAATATTCCCCTAAATTAAAGGAC
670576 TAAGATGAA
130 TAAGATGAA
* *
670585 ATTAAACCTAAAATGAAGGCTCTAATATTAATCTAAATAATTTTAGCTATTTATTGGTTCGAATA
1 ATTAAACCTAAAATGAAGGCTCTAATATTAATCTAAACAATTTTAGCAATTTATTGGTTCGAATA
* * * * * *
670650 ACTAAAATGGAGCCTTATA-CATAAATGCAAGGACCAAATTAAATATTCCGCTAAATCAAAGGAC
66 ACTAAAATGGAACC-TAGAGCATAAATACAAGAACCAAATTAAATATTCCCCTAAATTAAAGGAC
670714 TAAGGTGAAATGAA
130 TAA---G--ATGAA
* * *
670728 ATTAAGCCTAAAATGAAGGTTCTAATAATAATCTTAAACAATTTTAGCAATTTATTGGTTCGAAT
1 ATTAAACCTAAAATGAAGGCTCTAATATTAATC-TAAACAATTTTAGCAATTTATTGGTTCGAAT
* * * * * * * * ***
670793 AAGTAAAATGGGACCTCA-AGCACACATGCAAGAACCAAATAAAAAATT-CTCTTTGTTCAAA-G
65 AACTAAAATGGAACCT-AGAGCATAAATACAAGAACCAAATTAAATATTCCCCTAAATT-AAAGG
670855 ACTAA-AGTGAA
128 ACTAAGA-TGAA
* * * * * * ** *
670866 ATTAAACCTAAACTGAAGGTTCTAGTATTAATCCTAACCAATTTTAACAACTTATTGAATCTAAT
1 ATTAAACCTAAAATGAAGGCTCTAATATTAAT-CTAAACAATTTTAGCAATTTATTGGTTCGAAT
* * * * * *
670931 AA-TAAAAATAGAACCTCAGA-CATAAATGCAAGTATCAAA-TAGAATATTCACATAAATT
65 AACT-AAAATGGAACCT-AGAGCATAAATACAAGAACCAAATTA-AATATTCCCCTAAATT
670989 TAAAAAGTTT
Statistics
Matches: 436, Mismatches: 86, Indels: 43
0.77 0.15 0.08
Matches are distributed among these distances:
137 3 0.01
138 180 0.41
139 108 0.25
140 22 0.05
141 7 0.02
142 1 0.00
143 47 0.11
144 68 0.16
ACGTcount: A:0.44, C:0.14, G:0.13, T:0.29
Consensus pattern (138 bp):
ATTAAACCTAAAATGAAGGCTCTAATATTAATCTAAACAATTTTAGCAATTTATTGGTTCGAATA
ACTAAAATGGAACCTAGAGCATAAATACAAGAACCAAATTAAATATTCCCCTAAATTAAAGGACT
AAGATGAA
Found at i:675343 original size:90 final size:90
Alignment explanation
Indices: 675190--675354 Score: 285
Period size: 90 Copynumber: 1.8 Consensus size: 90
675180 AACACAACAT
* *
675190 TTTTATAGCCAAGCTACCCTAATCATATTATGGTTTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGCTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
675255 TTAATTAATTGGAATTTAATAATCC
66 TTAATTAATTGGAATTTAATAATCC
* * *
675280 TTTTATATCCATGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
1 TTTTATAGCCAAGCTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
675345 TTAATTAATT
66 TTAATTAATT
675355 AAAATTAAAT
Statistics
Matches: 70, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 70 1.00
ACGTcount: A:0.35, C:0.12, G:0.06, T:0.47
Consensus pattern (90 bp):
TTTTATAGCCAAGCTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGGAATTTAATAATCC
Found at i:680386 original size:27 final size:27
Alignment explanation
Indices: 680355--680417 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
680345 AAATGAAGGT
* * *
680355 ATAAATGTTATTTTTTGTCTATTTTTG
1 ATAAATCTTAATTTTTGTCGATTTTTG
680382 ATAAATCTTAATTTTTGTCGATTTTTG
1 ATAAATCTTAATTTTTGTCGATTTTTG
*
680409 GTAAA-CTTA
1 ATAAATCTTA
680418 GAAGCTCTCT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 4 0.12
27 28 0.88
ACGTcount: A:0.27, C:0.06, G:0.11, T:0.56
Consensus pattern (27 bp):
ATAAATCTTAATTTTTGTCGATTTTTG
Found at i:686527 original size:17 final size:18
Alignment explanation
Indices: 686493--686529 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
686483 TTTAAGATTT
686493 TATATTCGATTCAAAATTA
1 TATATTCGATTC-AAATTA
686512 TATATTCGATTC-AATTA
1 TATATTCGATTCAAATTA
686529 T
1 T
686530 TCAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 6 0.33
19 12 0.67
ACGTcount: A:0.38, C:0.11, G:0.05, T:0.46
Consensus pattern (18 bp):
TATATTCGATTCAAATTA
Done.