Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008105.1 Hibiscus syriacus cultivar Beakdansim tig00110637_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: 5962497
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 17 of 30
Found at i:3159541 original size:2 final size:2
Alignment explanation
Indices: 3159534--3159559 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3159524 AATAAAAGAA
3159534 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
3159560 TGGTCACTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3160539 original size:6 final size:6
Alignment explanation
Indices: 3160524--3160553 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
3160514 ATTACTAACA
*
3160524 GGTTAT GGTTAG GGTTAG GGTTAG GGTTAG
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG
3160554 TGTTTAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.47, T:0.37
Consensus pattern (6 bp):
GGTTAG
Found at i:3164547 original size:14 final size:14
Alignment explanation
Indices: 3164530--3164556 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3164520 CAAAACCATA
3164530 AATTGAAAAACTCG
1 AATTGAAAAACTCG
3164544 AATTGAAAAACTC
1 AATTGAAAAACTC
3164557 AGTCCTAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.11, T:0.22
Consensus pattern (14 bp):
AATTGAAAAACTCG
Found at i:3165809 original size:47 final size:47
Alignment explanation
Indices: 3165757--3165877 Score: 181
Period size: 47 Copynumber: 2.6 Consensus size: 47
3165747 TTCTAAAATA
* ** *
3165757 TCATCCTCCCTCATTCTTCCTAAAACTCTTCTCCTCTTATTTCACTC
1 TCATCCTCCCTCATTCTTCCTAAAACTCGTCTCCTCCCATTTCACAC
3165804 TCATCCTCCC-CTATTCTTCCTAAAACTCGTCTCCTCCCATTTCACAC
1 TCATCCTCCCTC-ATTCTTCCTAAAACTCGTCTCCTCCCATTTCACAC
*
3165851 TCATCCTCCCTTATTCTTCCTAAAACT
1 TCATCCTCCCTCATTCTTCCTAAAACT
3165878 AGGGTTTTAG
Statistics
Matches: 67, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
46 1 0.01
47 66 0.99
ACGTcount: A:0.19, C:0.41, G:0.01, T:0.39
Consensus pattern (47 bp):
TCATCCTCCCTCATTCTTCCTAAAACTCGTCTCCTCCCATTTCACAC
Found at i:3169405 original size:19 final size:19
Alignment explanation
Indices: 3169349--3169408 Score: 75
Period size: 19 Copynumber: 3.2 Consensus size: 19
3169339 GGTCAACTCT
* * *
3169349 GGTCAAAATCAATGGGTCA
1 GGTCAAAGTCAATAGGTCG
*
3169368 GGTCAAAGTTAATAGGTCG
1 GGTCAAAGTCAATAGGTCG
*
3169387 GGTCAAAGTCAAAAGGTCG
1 GGTCAAAGTCAATAGGTCG
3169406 GGT
1 GGT
3169409 TGACTCTGTC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.33, C:0.13, G:0.32, T:0.22
Consensus pattern (19 bp):
GGTCAAAGTCAATAGGTCG
Found at i:3175657 original size:113 final size:113
Alignment explanation
Indices: 3175297--3175969 Score: 802
Period size: 113 Copynumber: 5.9 Consensus size: 113
3175287 TAGCAAAGAT
* * * *
3175297 TTGAATCCATCACTCAATGGATCAGCATTGCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCT
1 TTGAATTCATCACTCGATGGATCAACATTACCAGAGG-A-AGTTCATAATGAGAAGAACTCATCT
3175362 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
* * *
3175412 TTGAATTCGTCACTCGATGGATTAACATTACCAG-GAAGAGTTCATAATGAGAAGAACTCATCT-
1 TTGAATTCATCACTCGATGGATCAACATTACCAGAGGA-AGTTCATAATGAGAAGAACTCATCTG
* *
3175475 AAGGAGGAAGAAGAAGTTTATAATGAGAAGAACTTGTTTAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
* * * * * *
3175524 TTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTTATTATGAGAAGAACTCATCTAA
1 TTGAATTCATCACTCGATGGATCAACATTACCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
*
3175589 AGAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
* * * * *
3175637 TTGAATCCATTACTCAATGGATCAACATTACCATGAAG-AGTTCATAATGAGAAGAACTCGTCTG
1 TTGAATTCATCACTCGATGGATCAACATTACCA-GAGGAAGTTCATAATGAGAAGAACTCATCTG
3175701 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
65 AAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
** * * *
3175750 TTGAATTCATCGTTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
1 TTGAATTCATCACTCGATGGATCAACATTACCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
* * *
3175815 AG-AGGAAGAAGAAGTTTATAATGAGAAGAGCTTGTTCAACC-TTTGC
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
* * * * * * *
3175861 ATG-ACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCATAATGAGAA
1 TTGAATTC-ATCAC---------TCGAT--GGATCAACATTACCAGAGGAAGTTCATAATGAGAA
* * *
3175925 TAACTTATCTG-AGAAGCAAGAAGAAGTTCATAATGAGAAGAACTT
54 GAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTT
3175970 ATCTGAAGAG
Statistics
Matches: 487, Mismatches: 54, Indels: 27
0.86 0.10 0.05
Matches are distributed among these distances:
110 3 0.01
111 10 0.02
112 139 0.29
113 226 0.46
114 4 0.01
115 28 0.06
120 4 0.01
121 2 0.00
122 71 0.15
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (113 bp):
TTGAATTCATCACTCGATGGATCAACATTACCAGAGGAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGC
Found at i:3175827 original size:225 final size:225
Alignment explanation
Indices: 3175297--3175969 Score: 857
Period size: 225 Copynumber: 2.9 Consensus size: 225
3175287 TAGCAAAGAT
* * * *
3175297 TTGAATCCATCACTCAATGGATCAGCATTGCCAGAGGAAGAGTTCATAATGAGAAGAACTCATCT
1 TTGAATTCATCACTCGATGGATCAACATTTCCAGA-GAA-AGTTCATAATGAGAAGAACTCATCT
* *
3175362 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATTCGTCACTC
64 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATCCATCACTC
* * *
3175427 GATGGATTAACATTACCAGGAAGAGTTCATAATGAGAAGAACTCATCTAAGGAGGAAGAAGAAGT
129 AATGGATCAACATTACCAGGAAGAGTTCATAATGAGAAGAACTCATCTAAGAAGGAAGAAGAAGT
*
3175492 TTATAATGAGAAGAACTTGTTTAACCTTTTGC
194 TCATAATGAGAAGAACTTGTTTAACCTTTTGC
* * * * * *
3175524 TTGAATTCATCACTCGATGGATTAACTTTTCCAGAGGAAGTTTATTATGAGAAGAACTCATCTAA
1 TTGAATTCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* *
3175589 AGAAGGGAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATCCATTACTCAA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATCCATCACTCAA
* *
3175654 TGGATCAACATTACCATGAAGAGTTCATAATGAGAAGAACTCGTCTGAAGAAGGAAGAAGAAGTT
131 TGGATCAACATTACCAGGAAGAGTTCATAATGAGAAGAACTCATCT-AAGAAGGAAGAAGAAGTT
3175719 CATAATGAGAAGAACTTGTTTAACCTTTTGC
195 CATAATGAGAAGAACTTGTTTAACCTTTTGC
** *
3175750 TTGAATTCATCGTTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCTGA
1 TTGAATTCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
* * * * * *
3175815 AG-AGGAAGAAGAAGTTTATAATGAGAAGAGCTTGTTCAACC-TTTGCATGACTCTATCACAGAA
66 AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATCCATCAC----
** * * * * * *
3175878 GGAGATAGATCAGCATCAACTTTTCCAGAGAA-AGTTCATAATGAGAATAACTTATCTGAGAAGC
127 TCA-AT-G----G-ATCAACATTACCAG-GAAGAGTTCATAATGAGAAGAACTCATCTAAGAAGG
3175942 AAGAAGAAGTTCATAATGAGAAGAACTT
184 AAGAAGAAGTTCATAATGAGAAGAACTT
3175970 ATCTGAAGAG
Statistics
Matches: 386, Mismatches: 47, Indels: 19
0.85 0.10 0.04
Matches are distributed among these distances:
224 14 0.04
225 162 0.42
226 107 0.28
227 29 0.08
228 1 0.00
229 2 0.01
230 1 0.00
234 34 0.09
235 33 0.09
236 3 0.01
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (225 bp):
TTGAATTCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTTGAATCCATCACTCAA
TGGATCAACATTACCAGGAAGAGTTCATAATGAGAAGAACTCATCTAAGAAGGAAGAAGAAGTTC
ATAATGAGAAGAACTTGTTTAACCTTTTGC
Found at i:3175963 original size:39 final size:39
Alignment explanation
Indices: 3175909--3176004 Score: 158
Period size: 39 Copynumber: 2.5 Consensus size: 39
3175899 TTTCCAGAGA
*
3175909 AAGTTCATAATGAGAATAACTTATCTG-AGAAGCAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAG-AGCAAGAAG
*
3175948 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAG
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGCAAGAAG
3175987 AAGTTCATAATGAGAAGA
1 AAGTTCATAATGAGAAGA
3176005 GCTCGTTCAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
39 52 0.96
40 2 0.04
ACGTcount: A:0.47, C:0.08, G:0.23, T:0.22
Consensus pattern (39 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGCAAGAAG
Found at i:3175964 original size:161 final size:160
Alignment explanation
Indices: 3175787--3176109 Score: 540
Period size: 161 Copynumber: 2.0 Consensus size: 160
3175777 TTTCCAGAGA
* *
3175787 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTTATAATGAGAAGAGCTTGTTC
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTCGTTC
* *
3175852 AACCTTTGCATGACTCTATCACAGAAGGAGATAGATCAGCATCAACTTTTCCAGAGAAAGTTCAT
66 AACCTTTGCATGACTCTATCACAAAAGGAGATAGATCAGCATCAACATTTCCAGA-AAAGTTCAT
*
3175917 AATGAGAATAACTTATCTG-AGAAGCAAGAAG
130 AATGAGAAGAACTTATCTGAAGAAG-AAGAAG
3175948 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTCGTTC
1 AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTCGTTC
* * *
3176013 AACCTTTGCATGATTCTATCACAAAAGGAGATAGATCAGCATCAACATTTCCATAAATGTTCATA
66 AACCTTTGCATGACTCTATCACAAAAGGAGATAGATCAGCATCAACATTTCCAGAAAAGTTCATA
*
3176078 ATGAGAAGAACTTATCTGAAGAAGGAGAAG
131 ATGAGAAGAACTTATCTGAAGAAGAAGAAG
3176108 AA
1 AA
3176110 CTTGTTATAT
Statistics
Matches: 152, Mismatches: 9, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
160 33 0.22
161 119 0.78
ACGTcount: A:0.41, C:0.14, G:0.21, T:0.24
Consensus pattern (160 bp):
AAGTTCATAATGAGAAGAACTTATCTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAGCTCGTTC
AACCTTTGCATGACTCTATCACAAAAGGAGATAGATCAGCATCAACATTTCCAGAAAAGTTCATA
ATGAGAAGAACTTATCTGAAGAAGAAGAAG
Found at i:3176196 original size:3 final size:3
Alignment explanation
Indices: 3176188--3176269 Score: 98
Period size: 3 Copynumber: 27.7 Consensus size: 3
3176178 CATCCATTTG
* *
3176188 TTA TTA TTA TTA TT- TTA TTTA TTA CTA TTA TTA TT- TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
3176232 -TA TTA TTA TTA TTTA TTA ATA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TT
3176270 TACAGACCCA
Statistics
Matches: 68, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
2 6 0.09
3 56 0.82
4 6 0.09
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:3176241 original size:22 final size:23
Alignment explanation
Indices: 3176188--3176266 Score: 105
Period size: 22 Copynumber: 3.6 Consensus size: 23
3176178 CATCCATTTG
3176188 TTATTATTATTATTTTAT--TTA
1 TTATTATTATTATTTTATAATTA
*
3176209 TTACTATTATTATTTTATAATTA
1 TTATTATTATTATTTTATAATTA
3176232 -TATTATTATTA-TTTATTAA-TA
1 TTATTATTATTATTTTA-TAATTA
3176253 TTATTATTATTATT
1 TTATTATTATTATT
3176267 ATTTACAGAC
Statistics
Matches: 51, Mismatches: 2, Indels: 8
0.84 0.03 0.13
Matches are distributed among these distances:
21 23 0.45
22 24 0.47
23 4 0.08
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (23 bp):
TTATTATTATTATTTTATAATTA
Found at i:3177576 original size:19 final size:20
Alignment explanation
Indices: 3177548--3177587 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3177538 ATTTAGCCAC
*
3177548 TAATTTTAATACTT-TTATT
1 TAATTATAATACTTATTATT
*
3177567 TAATTATAATTCTTATTATT
1 TAATTATAATACTTATTATT
3177587 T
1 T
3177588 TTTATATTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
TAATTATAATACTTATTATT
Found at i:3177621 original size:29 final size:29
Alignment explanation
Indices: 3177563--3177621 Score: 68
Period size: 29 Copynumber: 2.0 Consensus size: 29
3177553 TTAATACTTT
**
3177563 TATTTAATTATAATTCTTATTATTTTTTA
1 TATTTAATTATAATTCTTATTATTGGTTA
3177592 TATTTAATGT-TAATT-TTAGTTATTGGTTA
1 TATTTAAT-TATAATTCTTA-TTATTGGTTA
3177621 T
1 T
3177622 TTATATTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
28 3 0.12
29 22 0.85
30 1 0.04
ACGTcount: A:0.29, C:0.02, G:0.07, T:0.63
Consensus pattern (29 bp):
TATTTAATTATAATTCTTATTATTGGTTA
Found at i:3177698 original size:15 final size:16
Alignment explanation
Indices: 3177678--3177707 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3177668 TTAAGTCATG
3177678 TAAAT-ATATTTATCA
1 TAAATAATATTTATCA
3177693 TAAATAATATTTATC
1 TAAATAATATTTATC
3177708 TATTTATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (16 bp):
TAAATAATATTTATCA
Found at i:3181569 original size:29 final size:29
Alignment explanation
Indices: 3181532--3181596 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
3181522 ATGACAATAT
* ***
3181532 AAAAATTAAAAGCCCTAATTGTGAATACA
1 AAAAATTAAAAGACCTAATTAAAAATACA
* *
3181561 AAAAATTAAGAGACCTATTTAAAAATACA
1 AAAAATTAAAAGACCTAATTAAAAATACA
3181590 AAAAATT
1 AAAAATT
3181597 GAGGGCCTCA
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.57, C:0.11, G:0.08, T:0.25
Consensus pattern (29 bp):
AAAAATTAAAAGACCTAATTAAAAATACA
Found at i:3186067 original size:20 final size:21
Alignment explanation
Indices: 3186036--3186090 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 21
3186026 TGTTGGACCC
3186036 AAAGTATT-GAAACTTTA-AAG
1 AAAGT-TTCGAAACTTTACAAG
*
3186056 AAAGTTTCGAAAC--TACATG
1 AAAGTTTCGAAACTTTACAAG
*
3186075 AAAGTTTCAAAACTTT
1 AAAGTTTCGAAACTTT
3186091 TTAGGCTATT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
18 2 0.07
19 16 0.55
20 10 0.34
21 1 0.03
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (21 bp):
AAAGTTTCGAAACTTTACAAG
Found at i:3188630 original size:19 final size:20
Alignment explanation
Indices: 3188593--3188636 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
3188583 ACGTGTGACA
3188593 AGTTTCGATAATCTTAAGG-
1 AGTTTCGATAATCTTAAGGT
*
3188612 AGTTTCGATACT-TTGAAGGT
1 AGTTTCGATAATCTT-AAGGT
3188632 AGTTT
1 AGTTT
3188637 TGAAACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 2 0.09
19 15 0.68
20 5 0.23
ACGTcount: A:0.27, C:0.09, G:0.23, T:0.41
Consensus pattern (20 bp):
AGTTTCGATAATCTTAAGGT
Found at i:3197211 original size:28 final size:28
Alignment explanation
Indices: 3197180--3197244 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
3197170 AGTTCTAAGC
* *
3197180 TTTAGGATTTAGTGTTTG-GGGTTTAAAT
1 TTTAGGATTTA-TGATTGTGGGTTTAAAA
3197208 TTTAGTG-TTTATGATTGTGGGTTTAAAA
1 TTTAG-GATTTATGATTGTGGGTTTAAAA
3197236 TTTAGGATT
1 TTTAGGATT
3197245 AGGGTTTAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
27 6 0.19
28 25 0.78
29 1 0.03
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.51
Consensus pattern (28 bp):
TTTAGGATTTATGATTGTGGGTTTAAAA
Found at i:3202045 original size:53 final size:53
Alignment explanation
Indices: 3201987--3202101 Score: 212
Period size: 53 Copynumber: 2.2 Consensus size: 53
3201977 TAATAATAAA
*
3201987 AAAAACGACGATGGCAGATTTCAAATTCGCAAGACTCGACTCAGATTCAGAAC
1 AAAAACGACGATGGCAGATTTCAAACTCGCAAGACTCGACTCAGATTCAGAAC
*
3202040 AAAAACGACGATGGCAGATTTCAAACTCGCAAGACTCGACTCATATTCAGAAC
1 AAAAACGACGATGGCAGATTTCAAACTCGCAAGACTCGACTCAGATTCAGAAC
3202093 AAAAACGAC
1 AAAAACGAC
3202102 AAGAAAAACG
Statistics
Matches: 60, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
53 60 1.00
ACGTcount: A:0.42, C:0.23, G:0.17, T:0.17
Consensus pattern (53 bp):
AAAAACGACGATGGCAGATTTCAAACTCGCAAGACTCGACTCAGATTCAGAAC
Found at i:3204361 original size:46 final size:45
Alignment explanation
Indices: 3204274--3204377 Score: 129
Period size: 46 Copynumber: 2.3 Consensus size: 45
3204264 TAAGAAAAGT
* * * *
3204274 CTAATTATTAA-TTATTAATTTGCTAATAGATAATAAGAAAGATG
1 CTAATTATTAATTTATTAATTTGCTAATAAACAACAAGAAAGATA
* *
3204318 CTAATTCATTAATTTATTAATTTTCTAATAAACAACAATAAAGATA
1 CTAATT-ATTAATTTATTAATTTGCTAATAAACAACAAGAAAGATA
3204364 CTAAATTATTAATT
1 CT-AATTATTAATT
3204378 AATAATCATA
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
44 6 0.12
45 5 0.10
46 36 0.71
47 4 0.08
ACGTcount: A:0.46, C:0.08, G:0.06, T:0.40
Consensus pattern (45 bp):
CTAATTATTAATTTATTAATTTGCTAATAAACAACAAGAAAGATA
Found at i:3207740 original size:28 final size:28
Alignment explanation
Indices: 3207700--3207760 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
3207690 GTCTACCGAT
3207700 TAATTTTTTAGTAATAAAATATTATTTG
1 TAATTTTTTAGTAATAAAATATTATTTG
*
3207728 TAATTTTTTAGTAATAAAATATTATTTT
1 TAATTTTTTAGTAATAAAATATTATTTG
3207756 TAATT
1 TAATT
3207761 AAAAAAAGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (28 bp):
TAATTTTTTAGTAATAAAATATTATTTG
Found at i:3208559 original size:22 final size:22
Alignment explanation
Indices: 3208534--3208600 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 22
3208524 ATATATATAT
*
3208534 ATATATATATATTAACTTAAAA
1 ATATATTTATATTAACTTAAAA
* * *
3208556 ATATTTTTATATTAATTTATTAA
1 ATATATTTATATTAACTTA-AAA
3208579 ATATATTTTACTATTAACTTAA
1 ATATA-TTTA-TATTAACTTAA
3208601 TTTTAAAAAA
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
22 16 0.46
23 6 0.17
24 4 0.11
25 9 0.26
ACGTcount: A:0.45, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATATTTATATTAACTTAAAA
Found at i:3208801 original size:31 final size:31
Alignment explanation
Indices: 3208766--3208828 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 31
3208756 ACCACGTCTG
*
3208766 AATTAAATAAAAACGAAAGTGACTATATCTT
1 AATTAAATAAAAACGAAAGTAACTATATCTT
**
3208797 AATTAAATAAAATTGAAAGTAACTATATCTT
1 AATTAAATAAAAACGAAAGTAACTATATCTT
3208828 A
1 A
3208829 TGTTTTTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (31 bp):
AATTAAATAAAAACGAAAGTAACTATATCTT
Found at i:3209101 original size:40 final size:40
Alignment explanation
Indices: 3209057--3209142 Score: 111
Period size: 40 Copynumber: 2.1 Consensus size: 40
3209047 ATACACGTGT
*
3209057 GTATAGAGCGACCCCTGGGG-CGCGCCTTAGGCCACGTAGG
1 GTATAGAGCG-CCCCAGGGGCCGCGCCTTAGGCCACGTAGG
* ***
3209097 GTATAGCGCGGGGCAGGGGCCGCGCCTTAGGCCACGTAGG
1 GTATAGAGCGCCCCAGGGGCCGCGCCTTAGGCCACGTAGG
3209137 GTATAG
1 GTATAG
3209143 CGCGGGGCAG
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
39 5 0.12
40 35 0.88
ACGTcount: A:0.17, C:0.27, G:0.41, T:0.15
Consensus pattern (40 bp):
GTATAGAGCGCCCCAGGGGCCGCGCCTTAGGCCACGTAGG
Found at i:3209143 original size:40 final size:39
Alignment explanation
Indices: 3209073--3209165 Score: 159
Period size: 40 Copynumber: 2.3 Consensus size: 39
3209063 AGCGACCCCT
3209073 GGGGCGCGCCTTAGGCCACGTAGGGTATAGCGCGGGGCA
1 GGGGCGCGCCTTAGGCCACGTAGGGTATAGCGCGGGGCA
3209112 GGGGCCGCGCCTTAGGCCACGTAGGGTATAGCGCGGGGCA
1 GGGG-CGCGCCTTAGGCCACGTAGGGTATAGCGCGGGGCA
*
3209152 GGGGTCGAGCCTTA
1 GGGG-CGCGCCTTA
3209166 CCTGTGAATC
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 4 0.08
40 47 0.92
ACGTcount: A:0.15, C:0.26, G:0.45, T:0.14
Consensus pattern (39 bp):
GGGGCGCGCCTTAGGCCACGTAGGGTATAGCGCGGGGCA
Found at i:3209395 original size:21 final size:22
Alignment explanation
Indices: 3209357--3209425 Score: 61
Period size: 26 Copynumber: 3.0 Consensus size: 22
3209347 TCTGTCTAAG
*
3209357 GTATATTTTA-TTATATTTTTAA
1 GTATTTTTTATTTA-ATTTTTAA
3209379 -TATTTTTTATTTAATTTATTTAA
1 GTATTTTTTATTTAA-TT-TTTAA
3209402 GTATTTAATTTATTTAATATTTTA
1 GTATTT--TTTATTTAAT-TTTTA
3209426 CTTAATTAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
21 9 0.23
22 5 0.13
23 5 0.13
24 5 0.13
25 5 0.13
26 10 0.26
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (22 bp):
GTATTTTTTATTTAATTTTTAA
Found at i:3209396 original size:9 final size:9
Alignment explanation
Indices: 3209384--3209419 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3209374 TTTAATATTT
3209384 TTTATTTAA
1 TTTATTTAA
3209393 TTTATTTAA
1 TTTATTTAA
*
3209402 -GTATTTAA
1 TTTATTTAA
3209410 TTTATTTAA
1 TTTATTTAA
3209419 T
1 T
3209420 ATTTTACTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
8 7 0.29
9 17 0.71
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.64
Consensus pattern (9 bp):
TTTATTTAA
Found at i:3209425 original size:17 final size:17
Alignment explanation
Indices: 3209386--3209423 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
3209376 TAATATTTTT
3209386 TATTTAATTTATTTAAG
1 TATTTAATTTATTTAAG
3209403 TATTTAATTTATTTAA-
1 TATTTAATTTATTTAAG
3209419 TATTT
1 TATTT
3209424 TACTTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (17 bp):
TATTTAATTTATTTAAG
Found at i:3210253 original size:44 final size:44
Alignment explanation
Indices: 3210189--3210317 Score: 195
Period size: 44 Copynumber: 2.9 Consensus size: 44
3210179 TTGGCTTTCC
3210189 TGTACAGGGAGATGTGTCGAGCCACTGACTACAGGCGTAATTCA
1 TGTACAGGGAGATGTGTCGAGCCACTGACTACAGGCGTAATTCA
* * *
3210233 TGTACAGGGAGATGTATCGAGCCACTGACTACAAGCGTAATTCC
1 TGTACAGGGAGATGTGTCGAGCCACTGACTACAGGCGTAATTCA
* * * *
3210277 TGTATAGGGAGATATGTCGAGCCAATGACTATAGGCGTAAT
1 TGTACAGGGAGATGTGTCGAGCCACTGACTACAGGCGTAAT
3210318 GTTATCGGCA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 76 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (44 bp):
TGTACAGGGAGATGTGTCGAGCCACTGACTACAGGCGTAATTCA
Found at i:3211295 original size:36 final size:36
Alignment explanation
Indices: 3211248--3211317 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
3211238 TACTAGATGT
*
3211248 CGCCGCCGCCACCTTCACCTG-GTTTTATGACCCCGC
1 CGCCGCCGCCACCTTCA-CAGAGTTTTATGACCCCGC
*
3211284 CGCCGCTGCCACCTTCACAGAGTTTTATGACCCC
1 CGCCGCCGCCACCTTCACAGAGTTTTATGACCCC
3211318 TCTTGGAGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 2 0.06
36 29 0.94
ACGTcount: A:0.14, C:0.44, G:0.19, T:0.23
Consensus pattern (36 bp):
CGCCGCCGCCACCTTCACAGAGTTTTATGACCCCGC
Found at i:3214296 original size:179 final size:179
Alignment explanation
Indices: 3213972--3214306 Score: 500
Period size: 179 Copynumber: 1.9 Consensus size: 179
3213962 AACTCTCCAT
* ** *
3213972 CCTACCCTCGAGACCACGCTTGGAACTATCAGCCATCGAAATTTTCTACAACACAAATAAAGCAA
1 CCTACACTCGAGACCACGCTCAGAACTATCAGCCATCGAAATTTTCTACAACACAAATAAAGAAA
* * * *
3214037 GGAAGAACCATCAAGATTCCAGAATTATACGAGTACTTTCAGTACCTAGAGGCATGTATTCACTG
66 GGAAGAACCATCAAGATTCCAGAACTATACAAGTACTTTCAGTACCAAGAGGCAGGTATTCACTG
3214102 AAACCTTACTAACTGACCACTGGGTCCTATGGGCATGATTTCACTGACA
131 AAACCTTACTAACTGACCACTGGGTCCTATGGGCATGATTTCACTGACA
3214151 CCTACACTCGAGACCACGCTCAGAACTATCAGCCATCGAAAATTTTCTACAACAC-AATAAAGAA
1 CCTACACTCGAGACCACGCTCAGAACTATCAGCCATCG-AAATTTTCTACAACACAAATAAAGAA
*
3214215 AGGAAGCACCATCAAGATTCCAG-ACT-TACAAGTACTTTCAGTACCCAAG-GGCAGGTATTCAC
65 AGGAAGAACCATCAAGATTCCAGAACTATACAAGTACTTTCAGTA-CCAAGAGGCAGGTATTCAC
*
3214277 T-AACACCTTACTATAACTGACCATTGGGTC
129 TGAA-ACCTTAC--TAACTGACCACTGGGTC
3214307 TTAGGACTGA
Statistics
Matches: 141, Mismatches: 10, Indels: 10
0.88 0.06 0.06
Matches are distributed among these distances:
176 2 0.01
177 36 0.26
178 6 0.04
179 81 0.57
180 16 0.11
ACGTcount: A:0.35, C:0.27, G:0.16, T:0.23
Consensus pattern (179 bp):
CCTACACTCGAGACCACGCTCAGAACTATCAGCCATCGAAATTTTCTACAACACAAATAAAGAAA
GGAAGAACCATCAAGATTCCAGAACTATACAAGTACTTTCAGTACCAAGAGGCAGGTATTCACTG
AAACCTTACTAACTGACCACTGGGTCCTATGGGCATGATTTCACTGACA
Found at i:3215054 original size:26 final size:24
Alignment explanation
Indices: 3214994--3215066 Score: 65
Period size: 26 Copynumber: 2.9 Consensus size: 24
3214984 TTTAGTTACT
*
3214994 GAAAAAGACAAAAAGATAATATTAA
1 GAAAAAGA-AAAAAGATAATAATAA
* *
3215019 GACAATAGAAACAAAGGTAATAATATA
1 GA-AAAAGAAA-AAAGATAATAATA-A
* *
3215046 GAAAAAGAATAAAGACAATAA
1 GAAAAAGAAAAAAGATAATAA
3215067 AAAACAAGGG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
25 13 0.34
26 22 0.58
27 3 0.08
ACGTcount: A:0.66, C:0.05, G:0.14, T:0.15
Consensus pattern (24 bp):
GAAAAAGAAAAAAGATAATAATAA
Found at i:3215063 original size:40 final size:40
Alignment explanation
Indices: 3215017--3215092 Score: 109
Period size: 40 Copynumber: 1.9 Consensus size: 40
3215007 AGATAATATT
* *
3215017 AAGACAAT-AGAAACAAAGGTAATAATATAGAAAAAGAATA
1 AAGACAATAAAAAACAAAGGTAATAAT-TAAAAAAAGAATA
*
3215057 AAGACAATAAAAAACAAGGGTAATAATTAAAAAAAG
1 AAGACAATAAAAAACAAAGGTAATAATTAAAAAAAG
3215093 CAACAAAACA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
40 16 0.50
41 16 0.50
ACGTcount: A:0.66, C:0.05, G:0.14, T:0.14
Consensus pattern (40 bp):
AAGACAATAAAAAACAAAGGTAATAATTAAAAAAAGAATA
Found at i:3219939 original size:20 final size:21
Alignment explanation
Indices: 3219914--3219960 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
3219904 GGTTGTGGCT
3219914 GTTTCTAGCCG-TTGGGGATG
1 GTTTCTAGCCGTTTGGGGATG
*
3219934 GTTTCTAGTCGTTTGGGGATG
1 GTTTCTAGCCGTTTGGGGATG
*
3219955 TTTTCT
1 GTTTCT
3219961 CTTTAAAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.09, C:0.13, G:0.34, T:0.45
Consensus pattern (21 bp):
GTTTCTAGCCGTTTGGGGATG
Found at i:3220093 original size:17 final size:18
Alignment explanation
Indices: 3220066--3220099 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3220056 TAGCCGTTGG
*
3220066 GCCTAATGGTATTGATAA
1 GCCTAATGGTATCGATAA
3220084 GCCT-ATGGTATCGATA
1 GCCTAATGGTATCGATA
3220100 CTACTATGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (18 bp):
GCCTAATGGTATCGATAA
Found at i:3221948 original size:32 final size:31
Alignment explanation
Indices: 3221875--3221987 Score: 120
Period size: 32 Copynumber: 3.6 Consensus size: 31
3221865 AGTCAAGGTA
* * * *
3221875 CATTCAGATAATGCACATTATGGTTA-TAGTG
1 CATTCAGATAATGCACAATAT-GTCAGGATTG
*
3221906 CATTCAGATAATGCACAGTATAGTCAGGATTG
1 CATTCAGATAATGCACAATAT-GTCAGGATTG
* *
3221938 TATTCAGATAATGCACAATATGATCAGGTTTG
1 CATTCAGATAATGCACAATATG-TCAGGATTG
*
3221970 CATTCAGATAATACACAA
1 CATTCAGATAATGCACAA
3221988 GAGTATGAGT
Statistics
Matches: 70, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
31 24 0.34
32 46 0.66
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (31 bp):
CATTCAGATAATGCACAATATGTCAGGATTG
Found at i:3223845 original size:27 final size:29
Alignment explanation
Indices: 3223815--3223884 Score: 81
Period size: 27 Copynumber: 2.4 Consensus size: 29
3223805 AATTTATATA
3223815 TATATATATTTACTA-TTTT-TTTTTTAT
1 TATATATATTTACTATTTTTATTTTTTAT
* *
3223842 TATATATATATATTATTTTTACTTTTTTAT
1 TATATATATTTACTATTTTTA-TTTTTTAT
*
3223872 TATTATTTATTTA
1 TA-TATATATTTA
3223885 TTTGATTTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
27 13 0.37
28 4 0.11
30 10 0.29
31 8 0.23
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.69
Consensus pattern (29 bp):
TATATATATTTACTATTTTTATTTTTTAT
Found at i:3223845 original size:33 final size:33
Alignment explanation
Indices: 3223798--3223877 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 33
3223788 TTATTATCAG
*
3223798 TTTTATTAATT-TATATATATATATATTTACTATTT
1 TTTTATT-ATTATATATATATAT-TATTT-CTACTT
* *
3223833 TTTTTTTATTATATATATATATTATTTTTACTT
1 TTTTATTATTATATATATATATTATTTCTACTT
3223866 TTTTATTATTAT
1 TTTTATTATTAT
3223878 TTATTTATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
33 15 0.38
34 8 0.20
35 17 0.43
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.68
Consensus pattern (33 bp):
TTTTATTATTATATATATATATTATTTCTACTT
Found at i:3223875 original size:71 final size:70
Alignment explanation
Indices: 3223746--3223908 Score: 172
Period size: 73 Copynumber: 2.3 Consensus size: 70
3223736 TTTACTTTAG
* *
3223746 TATATATTTTTA-TTTTTTTAGATTATATATATATATTATATTTTATTATCAGTTTTATTAATTT
1 TATATATTTATATTTTTTTTTGATTATATATATATATTATATTTTATTAT-AGTTTTATT-ATTT
3223810 ATATATA
64 ATATATA
* *
3223817 TATATATTTACTATTTTTTTTTTATTATATATATATATTAT-TTTTACTT-T-TTTATTATTATT
1 TATATATTTA-TATTTTTTTTTGATTATATATATATATTATATTTTA-TTATAGTT-TTATTATT
* *
3223879 TATTTATT
63 TATATATA
* *
3223887 TGATTTATTTATATATTTTTTT
1 T-ATATATTTATATTTTTTTTT
3223909 CTTCTTTTTT
Statistics
Matches: 79, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
70 22 0.28
71 22 0.28
72 8 0.10
73 27 0.34
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (70 bp):
TATATATTTATATTTTTTTTTGATTATATATATATATTATATTTTATTATAGTTTTATTATTTAT
ATATA
Found at i:3223883 original size:4 final size:4
Alignment explanation
Indices: 3223799--3223939 Score: 53
Period size: 4 Copynumber: 35.8 Consensus size: 4
3223789 TATTATCAGT
* * * * * *
3223799 TTTA TTAA TTTA TATA TATA TATA TTTA -CTA TTT- TTTT TTTA TTATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA
* * *
3223846 TATA TATA TTATT TTTA CTTT- TTTA -TTA -TTA TTTA TTTA TTTGA TTTA
1 TTTA TTTA TT-TA TTTA -TTTA TTTA TTTA TTTA TTTA TTTA TTT-A TTTA
* * * * * *
3223894 TTTA TATA TTTT TTTC TTCTT TTTT TTTA TTTG TTTA --TA TTTA TTT
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3223940 TACTTACTAT
Statistics
Matches: 107, Mismatches: 19, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
2 2 0.02
3 14 0.13
4 75 0.70
5 16 0.15
ACGTcount: A:0.25, C:0.03, G:0.01, T:0.71
Consensus pattern (4 bp):
TTTA
Found at i:3227130 original size:13 final size:13
Alignment explanation
Indices: 3227100--3227148 Score: 66
Period size: 13 Copynumber: 3.8 Consensus size: 13
3227090 ATCAAAGCAA
3227100 AAAGAGAAAAAAGC
1 AAAGAGAAAAAA-C
3227114 AAAGAGAAAATAA-
1 AAAGAGAAAA-AAC
3227127 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
3227140 AAAG-GAAAA
1 AAAGAGAAAA
3227149 TTAAAGAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.21
13 14 0.42
14 10 0.30
15 2 0.06
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:3227153 original size:26 final size:27
Alignment explanation
Indices: 3227098--3227149 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
3227088 TAATCAAAGC
3227098 AAAAAGAGAAAAAAGCAAAGAGAAAAT
1 AAAAAGAGAAAAAAGCAAAGAGAAAAT
3227125 AAAAAGAGAAAAAA-CAAAG-GAAAAT
1 AAAAAGAGAAAAAAGCAAAGAGAAAAT
3227150 TAAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 6 0.24
26 5 0.20
27 14 0.56
ACGTcount: A:0.75, C:0.04, G:0.17, T:0.04
Consensus pattern (27 bp):
AAAAAGAGAAAAAAGCAAAGAGAAAAT
Found at i:3227339 original size:69 final size:69
Alignment explanation
Indices: 3227221--3227358 Score: 179
Period size: 69 Copynumber: 2.0 Consensus size: 69
3227211 GATTCAAACT
* *
3227221 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTTCACTCGAAGATCATAGAACA
1 ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTCCACTCGAAAATCATAGAACA
3227286 TCAA
66 TCAA
* * * * * * *
3227290 ATGAGATTGATCAAGCATAATCA-TTTCTTAATTATTGAATCACTCCACTCGAAAATCATGGAGC
1 ATGAGATTGATCAAGCACAATCATTTTC-GAATCACTGAACCACTCCACTCGAAAATCATAGAAC
3227354 ATCAA
65 ATCAA
3227359 GAGAGAGACA
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
68 4 0.07
69 55 0.93
ACGTcount: A:0.38, C:0.21, G:0.13, T:0.28
Consensus pattern (69 bp):
ATGAGATTGATCAAGCACAATCATTTTCGAATCACTGAACCACTCCACTCGAAAATCATAGAACA
TCAA
Found at i:3229080 original size:106 final size:106
Alignment explanation
Indices: 3228947--3229164 Score: 283
Period size: 106 Copynumber: 2.1 Consensus size: 106
3228937 GATATCGTGC
* * *
3228947 GACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCC
1 GACTCGAGACAACACAAGCTCAACTTCACAACAAAGGGACGGCTGGCTGTCAACAAACAATTTCC
* * * *
3229012 CAATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTG
66 CAATTCCAGAGCCAATTTCAACTTCAAAACGAAGGATATTG
* * ** *
3229053 GACTCGAGACAGCACAAGCTCAGCTTCACAACAAAGGGGTGGCTGGCTGTCAACAAACAATTTCT
1 GACTCGAGACAACACAAGCTCAACTTCACAACAAAGGGACGGCTGGCTGTCAACAAACAATTTCC
* * * * *
3229118 TAGTTCCATAGCCAATTTTAACTTCAAAACGGAGGATATTG
66 CAATTCCAGAGCCAATTTCAACTTCAAAACGAAGGATATTG
3229159 GACTCG
1 GACTCG
3229165 GAACAATACA
Statistics
Matches: 95, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
106 95 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (106 bp):
GACTCGAGACAACACAAGCTCAACTTCACAACAAAGGGACGGCTGGCTGTCAACAAACAATTTCC
CAATTCCAGAGCCAATTTCAACTTCAAAACGAAGGATATTG
Found at i:3229607 original size:37 final size:37
Alignment explanation
Indices: 3229532--3229622 Score: 94
Period size: 37 Copynumber: 2.4 Consensus size: 37
3229522 ATTGAAAACA
* * * **
3229532 TTTCCCTTGAAAT-AAATTTTATCTCGCTTGGGGTAG
1 TTTCCCTTAAAATAAAATTTTATCTCCCTTGAGACAG
*
3229568 TTTCCCTTAAAATAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTAAAATAAAATTTTATCTCCCTTGAGACAG
*
3229605 TTTCTCTTGAAACATAAA
1 TTTCCCTT-AAA-ATAAA
3229623 CATTGAAAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
36 12 0.27
37 25 0.56
38 3 0.07
39 5 0.11
ACGTcount: A:0.29, C:0.19, G:0.13, T:0.40
Consensus pattern (37 bp):
TTTCCCTTAAAATAAAATTTTATCTCCCTTGAGACAG
Found at i:3229619 original size:87 final size:87
Alignment explanation
Indices: 3229425--3229597 Score: 256
Period size: 87 Copynumber: 2.0 Consensus size: 87
3229415 GTTTCTCTTG
* * * * *
3229425 AAACATAAACACTGAAAATATTTCCCTTGAAATGAATTTTATCTCAATTGAGATAGTTTCCCTTG
1 AAACTTAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCAATTGAGATAGTTTCCCTTA
*
3229490 AAATGAAATTTTGTCTCCCTTA
66 AAATAAAATTTTGTCTCCCTTA
** * *
3229512 AAACTTAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCCCTTA
1 AAACTTAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCAATTGAGATAGTTTCCCTTA
3229577 AAATAAAATTTTGTCTCCCTT
66 AAATAAAATTTTGTCTCCCTT
3229598 GAGACAGTTT
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
87 76 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (87 bp):
AAACTTAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCAATTGAGATAGTTTCCCTTA
AAATAAAATTTTGTCTCCCTTA
Found at i:3229709 original size:37 final size:37
Alignment explanation
Indices: 3229652--3229722 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
3229642 GAAATTAATT
*
3229652 TTTTCTCTCTCTTGAGATAGTTTCCCTTGAAACAAAA
1 TTTTCTCTCCCTTGAGATAGTTTCCCTTGAAACAAAA
* *
3229689 TTTTGTCTCCCTTGAGATAGTTTCTCTTGAAACA
1 TTTTCTCTCCCTTGAGATAGTTTCCCTTGAAACA
3229723 TAAACCTTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (37 bp):
TTTTCTCTCCCTTGAGATAGTTTCCCTTGAAACAAAA
Found at i:3229711 original size:104 final size:102
Alignment explanation
Indices: 3229512--3229749 Score: 350
Period size: 104 Copynumber: 2.3 Consensus size: 102
3229502 GTCTCCCTTA
* * *
3229512 AAACTTAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGGGGTAGTTTCCCTTA
1 AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCCCTTA
*
3229577 AAATAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
66 AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
* * * *
3229614 AAACATAAACATTGAAAACATTTCCTTTGAAATTAATTTTTTCTCTCTCTTGAGATAGTTTCCCT
1 AAACATAAACATTGAAAACATTTCCCTTGAAA-TAA-ATTTTATCTCGCTTGAGATAGTTTCCCT
* *
3229679 TGAAACAAAATTTTGTCTCCCTTGAGATAGTTTCTCTTG
64 TAAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
* *
3229718 AAACATAAACCTTGAAAACGTTTCCCTTGAAA
1 AAACATAAACATTGAAAACATTTCCCTTGAAA
3229750 CACAAAATAT
Statistics
Matches: 121, Mismatches: 13, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
102 30 0.25
103 3 0.02
104 88 0.73
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.38
Consensus pattern (102 bp):
AAACATAAACATTGAAAACATTTCCCTTGAAATAAATTTTATCTCGCTTGAGATAGTTTCCCTTA
AAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTG
Found at i:3229919 original size:37 final size:36
Alignment explanation
Indices: 3229870--3229983 Score: 122
Period size: 37 Copynumber: 3.1 Consensus size: 36
3229860 CTTTTCCTTG
3229870 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTA
1 AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTA
* * * * *
3229906 GAACTAAGTTTCGTCTCTCTTGATATAGTTTCTTTTA
1 AAAC-AAATTTCGTCTCCCTTGAGACAGTTTCTTTTA
** * *
3229943 AAACAAATTTTTTC-CCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTCGTCTCC-CTTGAGACAGTTTCTTTTA
3229979 AAACA
1 AAACA
3229984 CAAAAAAACC
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
35 1 0.02
36 30 0.48
37 31 0.50
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (36 bp):
AAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTA
Found at i:3229972 original size:36 final size:36
Alignment explanation
Indices: 3229870--3229983 Score: 122
Period size: 36 Copynumber: 3.1 Consensus size: 36
3229860 CTTTTCCTTG
3229870 AAACAAATTTCGTCTCC-CTTGAGACAGTTTCTTTTA
1 AAACAAATTTCGTC-CCTCTTGAGACAGTTTCTTTTA
* * * * *
3229906 GAACTAAGTTTCGTCTCTCTTGATATAGTTTCTTTTA
1 AAAC-AAATTTCGTCCCTCTTGAGACAGTTTCTTTTA
** * *
3229943 AAACAAATTTTTTCCCTCTTGAGACAGTTTCTCTTG
1 AAACAAATTTCGTCCCTCTTGAGACAGTTTCTTTTA
3229979 AAACA
1 AAACA
3229984 CAAAAAAACC
Statistics
Matches: 62, Mismatches: 14, Indels: 4
0.77 0.17 0.05
Matches are distributed among these distances:
36 33 0.53
37 29 0.47
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.41
Consensus pattern (36 bp):
AAACAAATTTCGTCCCTCTTGAGACAGTTTCTTTTA
Found at i:3230010 original size:35 final size:35
Alignment explanation
Indices: 3229969--3230058 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 35
3229959 TCTTGAGACA
* *
3229969 GTTTCTCTTGAAACACAAAAAAACCCCTCGAAATT
1 GTTTCTCTTGAAACACAAAAAAAACCCTCGAAAAT
* *
3230004 GTTTCTCTTGAAACACACACAAAAAAAACCTTTGAAAAT
1 GTTTCTCTTG--A-A-ACACAAAAAAAACCCTCGAAAAT
3230043 GTTTCTCTTGAAACAC
1 GTTTCTCTTGAAACAC
3230059 CAAACCCTTG
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
35 14 0.30
36 1 0.02
37 2 0.04
38 1 0.02
39 29 0.62
ACGTcount: A:0.40, C:0.23, G:0.09, T:0.28
Consensus pattern (35 bp):
GTTTCTCTTGAAACACAAAAAAAACCCTCGAAAAT
Found at i:3230046 original size:39 final size:39
Alignment explanation
Indices: 3229981--3230058 Score: 120
Period size: 39 Copynumber: 2.0 Consensus size: 39
3229971 TTCTCTTGAA
* *
3229981 ACACAAAAAAACCCCTCGAAATTGTTTCTCTTGAAACAC
1 ACACAAAAAAAACCCTCGAAAATGTTTCTCTTGAAACAC
* *
3230020 ACACAAAAAAAACCTTTGAAAATGTTTCTCTTGAAACAC
1 ACACAAAAAAAACCCTCGAAAATGTTTCTCTTGAAACAC
3230059 CAAACCCTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.44, C:0.24, G:0.08, T:0.24
Consensus pattern (39 bp):
ACACAAAAAAAACCCTCGAAAATGTTTCTCTTGAAACAC
Found at i:3231217 original size:23 final size:22
Alignment explanation
Indices: 3231191--3231234 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
3231181 TTTTTACTTT
*
3231191 ATTATATATTTTTATTTTTTTAG
1 ATTATATA-TATTATTTTTTTAG
3231214 ATTATATATATTATTTTTTTA
1 ATTATATATATTATTTTTTTA
3231235 TTATCAGTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 12 0.60
23 8 0.40
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (22 bp):
ATTATATATATTATTTTTTTAG
Found at i:3231302 original size:4 final size:4
Alignment explanation
Indices: 3231243--3231477 Score: 51
Period size: 4 Copynumber: 58.2 Consensus size: 4
3231233 TATTATCAGT
* * * * * * * *
3231243 TTTA TTAA TTTA TATA TATA TATA TATA TATA TTTA -CTA TTTT TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
* *
3231290 TTT- TTTA TTTA TTATA TATA TTATT TTTA CTTT- TTTA -TTA -TTA TTTTA
1 TTTA TTTA TTTA TT-TA TTTA TT-TA TTTA -TTTA TTTA TTTA TTTA -TTTA
* * * * *
3231338 TTTA TATA TTTT TTTC TTCTT TTTC TTTA TTT- TTT- TTATA TTTA TTTTA
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TT-TA TTTA -TTTA
* * * * * *
3231387 CTTA -CTA TTT- TATC TTTA CTTTC TTTA TCTTA TCT- TTTA TTTAA TTTA
1 TTTA TTTA TTTA TTTA TTTA -TTTA TTTA T-TTA TTTA TTTA TTT-A TTTA
* * * *
3231435 TTT- TTTC TTCA TTTTA TTTTAA TTAA TTTA TTTA TTTC TTTA T
1 TTTA TTTA TTTA -TTTA -TTT-A TTTA TTTA TTTA TTTA TTTA T
3231478 CTAACATGGT
Statistics
Matches: 174, Mismatches: 36, Indels: 42
0.69 0.14 0.17
Matches are distributed among these distances:
3 28 0.16
4 104 0.60
5 41 0.24
6 1 0.01
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:3231302 original size:26 final size:30
Alignment explanation
Indices: 3231280--3231333 Score: 87
Period size: 29 Copynumber: 1.9 Consensus size: 30
3231270 ATATATTTAC
3231280 TATT-TTTTTA-TTTTTTATTTATTATATA
1 TATTATTTTTACTTTTTTATTTATTATATA
3231308 TATTATTTTTACTTTTTTA-TTATTAT
1 TATTATTTTTACTTTTTTATTTATTAT
3231334 TTTATTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 4 0.17
29 13 0.54
30 7 0.29
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (30 bp):
TATTATTTTTACTTTTTTATTTATTATATA
Found at i:3231315 original size:23 final size:21
Alignment explanation
Indices: 3231287--3231336 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 21
3231277 TACTATTTTT
3231287 TTATTTTTTA-TTTATTATATATA
1 TTATTTTTTACTTT-TT-TAT-TA
3231310 TTA-TTTTTACTTTTTTATTA
1 TTATTTTTTACTTTTTTATTA
3231330 TTATTTT
1 TTATTTT
3231337 ATTTATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 5 0.20
21 6 0.24
22 8 0.32
23 6 0.24
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (21 bp):
TTATTTTTTACTTTTTTATTA
Found at i:3231324 original size:37 final size:37
Alignment explanation
Indices: 3231263--3231389 Score: 115
Period size: 34 Copynumber: 3.5 Consensus size: 37
3231253 TATATATATA
* *
3231263 TATATATATATATTTACTATTTTTTTATTTTTTATTTAT
1 TATATATAT-TATTT-TTACTTTTTTATTTTTTATTTAT
*
3231302 TATATATATTATTTTTACTTTTTTA-TTATTATTTTAT
1 TATATATATTATTTTTACTTTTTTATTTTTTA-TTTAT
* * *
3231339 T-TATATATT-TTTTT-CTTCTTT-TTCTTTATTTTT
1 TATATATATTATTTTTACTTTTTTATTTTTTATTTAT
*
3231372 TTTATAT-TTA-TTTTACTT
1 TATATATATTATTTTTACTT
3231390 ACTATTTTAT
Statistics
Matches: 76, Mismatches: 7, Indels: 15
0.78 0.07 0.15
Matches are distributed among these distances:
33 11 0.14
34 18 0.24
35 5 0.07
36 13 0.17
37 15 0.20
38 5 0.07
39 9 0.12
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (37 bp):
TATATATATTATTTTTACTTTTTTATTTTTTATTTAT
Found at i:3231403 original size:38 final size:35
Alignment explanation
Indices: 3231284--3231414 Score: 92
Period size: 38 Copynumber: 3.6 Consensus size: 35
3231274 ATTTACTATT
* * * *
3231284 TTTTTATTTTTTATTTATTATATATATTATTT-TTAC
1 TTTTTA-TCTTTATTTTTTTTATAT-TTTTTTCTTAC
3231320 TTTTTTAT-TATTATTTTATTTATATATTTTTTTCTT-C
1 -TTTTTATCT-TTATTTT-TTT-TATATTTTTTTCTTAC
3231357 -TTTT-TCTTTATTTTTTTTATATTTATTTTACTTAC
1 TTTTTATCTTTATTTTTTTTATATTT-TTTT-CTTAC
* *
3231392 TATTTTATCTTTACTTTCTTTAT
1 T-TTTTATCTTTATTTTTTTTAT
3231415 CTTATCTTTT
Statistics
Matches: 78, Mismatches: 5, Indels: 21
0.75 0.05 0.20
Matches are distributed among these distances:
32 7 0.09
33 7 0.09
34 11 0.14
35 7 0.09
36 7 0.09
37 18 0.23
38 21 0.27
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (35 bp):
TTTTTATCTTTATTTTTTTTATATTTTTTTCTTAC
Found at i:3232200 original size:39 final size:38
Alignment explanation
Indices: 3232120--3232366 Score: 204
Period size: 36 Copynumber: 7.1 Consensus size: 38
3232110 GGTTTTTCAA
*
3232120 ATATATTATATAGTTTTGAAAACGATTTTTGAGAATAT
1 ATATATTATATAGTTTTGAAAACGATTTTTGAAAATAT
*
3232158 ATATATTATATAGTTTTTGAAAAC-A-TTTTG-AAACAT
1 ATATATTATATAG-TTTTGAAAACGATTTTTGAAAATAT
*
3232194 AT-TA-TATATAGTTTTTG-AAA--A----T--ATATAT
1 ATATATTATATAG-TTTTGAAAACGATTTTTGAAAATAT
3232222 A-ATA-TATAGT--TTTTGAAAAC-ATTTTTGAAAA-AT
1 ATATATTATA-TAGTTTTGAAAACGATTTTTGAAAATAT
*
3232255 ATATATTATATAGTTTTGAAAAC-ATTTTTG-AAATAC
1 ATATATTATATAGTTTTGAAAACGATTTTTGAAAATAT
*
3232291 ATATAATATATAGTTTTGAAAAC-A-TTTTGAAAATAT
1 ATATATTATATAGTTTTGAAAACGATTTTTGAAAATAT
* * *
3232327 ATATAATATATAGTTTTTGAAAA-TATTTTT-ATAATAT
1 ATATATTATATAG-TTTTGAAAACGATTTTTGAAAATAT
3232364 ATA
1 ATA
3232367 ATTCTAAAAA
Statistics
Matches: 180, Mismatches: 9, Indels: 41
0.78 0.04 0.18
Matches are distributed among these distances:
26 5 0.03
27 3 0.02
28 12 0.07
29 2 0.01
32 2 0.01
33 6 0.03
34 19 0.11
35 14 0.08
36 65 0.36
37 24 0.13
38 18 0.10
39 10 0.06
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (38 bp):
ATATATTATATAGTTTTGAAAACGATTTTTGAAAATAT
Found at i:3232218 original size:60 final size:61
Alignment explanation
Indices: 3232145--3232366 Score: 234
Period size: 60 Copynumber: 3.4 Consensus size: 61
3232135 TTGAAAACGA
* * *
3232145 TTTTTGAGAATATATATATTATATAGTTTTTGAAAACATTTTGAAACATAT-TATATATAG
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAAATATATATATATAG
3232205 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTTGAAAAATATATATTATATAG
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA-TTTTGAAAAATATATA-TATATAG
3232268 -TTTTGAAAACATTTTTGAAATACATATAATATATAG-TTTTGAAAACATTTTGAAAATATATAT
1 TTTTTG-AAA-A----T---AT--ATATAATATATAGTTTTTGAAAACATTTTGAAAA-ATATAT
3232331 AATATATAG
54 -ATATATAG
*
3232340 TTTTTGAAAATATTTTTATAATATATA
1 TTTTTGAAAATA--TATATAATATATA
3232367 ATTCTAAAAA
Statistics
Matches: 139, Mismatches: 4, Indels: 34
0.79 0.02 0.19
Matches are distributed among these distances:
60 36 0.26
61 12 0.09
62 7 0.05
63 10 0.07
64 13 0.09
66 1 0.01
67 1 0.01
68 1 0.01
71 12 0.09
72 27 0.19
73 19 0.14
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (61 bp):
TTTTTGAAAATATATATAATATATAGTTTTTGAAAACATTTTGAAAAATATATATATATAG
Found at i:3232226 original size:24 final size:24
Alignment explanation
Indices: 3232183--3232240 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 24
3232173 TTTGAAAACA
3232183 TTTTGAAACATA-T-TATATATAGT
1 TTTTGAAA-ATATTATATATATAGT
3232206 TTTTGAAAATATATATAATATATAGT
1 TTTTGAAAATAT-TAT-ATATATAGT
3232232 TTTTGAAAA
1 TTTTGAAAA
3232241 CATTTTTGAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
22 3 0.10
23 8 0.26
24 1 0.03
25 1 0.03
26 18 0.58
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.47
Consensus pattern (24 bp):
TTTTGAAAATATTATATATATAGT
Found at i:3232266 original size:135 final size:135
Alignment explanation
Indices: 3232120--3232393 Score: 394
Period size: 135 Copynumber: 2.0 Consensus size: 135
3232110 GGTTTTTCAA
* *
3232120 ATATATTATATAGTTTTGAAAACGATTTTTGAGAATATATATATTATATAGTTTTTGAAAACATT
1 ATATATTATATAGTTTTGAAAAC-ATTTTTGA-AATACATATAATATATAG-TTTTGAAAACATT
* * *
3232185 TTG-AAACATAT-T-ATATATAGTTTTTGAAAATA-TATATAATATATAGTTTTTGAAAACATTT
63 TTGAAAACATATATAATATATAGTTTTTGAAAATATTATATAATATATA-ATTCTAAAAACATTT
3232246 TTGAAAAAT
127 TTGAAAAAT
3232255 ATATATTATATAGTTTTGAAAACATTTTTGAAATACATATAATATATAGTTTTGAAAACATTTTG
1 ATATATTATATAGTTTTGAAAACATTTTTGAAATACATATAATATATAGTTTTGAAAACATTTTG
* * *
3232320 AAAATATATATAATATATAGTTTTTGAAAATATTTTTATAATATATAATTCTAAAAACGTTTTTG
66 AAAACATATATAATATATAGTTTTTGAAAATA-TTATATAATATATAATTCTAAAAACATTTTTG
*
3232385 GAAAAT
130 AAAAAT
3232391 ATA
1 ATA
3232394 CAAGGTATAT
Statistics
Matches: 125, Mismatches: 9, Indels: 9
0.87 0.06 0.06
Matches are distributed among these distances:
132 16 0.13
133 23 0.18
134 9 0.07
135 43 0.34
136 22 0.18
137 12 0.10
ACGTcount: A:0.43, C:0.03, G:0.09, T:0.45
Consensus pattern (135 bp):
ATATATTATATAGTTTTGAAAACATTTTTGAAATACATATAATATATAGTTTTGAAAACATTTTG
AAAACATATATAATATATAGTTTTTGAAAATATTATATAATATATAATTCTAAAAACATTTTTGA
AAAAT
Found at i:3232279 original size:36 final size:38
Alignment explanation
Indices: 3232205--3232366 Score: 246
Period size: 36 Copynumber: 4.4 Consensus size: 38
3232195 TTATATATAG
3232205 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
3232243 TTTTTGAAAA-ATATATATTATATAG-TTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
3232279 TTTTTG-AAATACATATAATATATAG-TTTTGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
3232315 -TTTTGAAAATATATATAATATATAGTTTTTGAAAATA
1 TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
*
3232352 TTTTT-ATAATATATA
1 TTTTTGAAAATATATA
3232367 ATTCTAAAAA
Statistics
Matches: 114, Mismatches: 6, Indels: 9
0.88 0.05 0.07
Matches are distributed among these distances:
35 8 0.07
36 59 0.52
37 33 0.29
38 14 0.12
ACGTcount: A:0.44, C:0.02, G:0.07, T:0.46
Consensus pattern (38 bp):
TTTTTGAAAATATATATAATATATAGTTTTTGAAAACA
Found at i:3232349 original size:26 final size:27
Alignment explanation
Indices: 3232315--3232366 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
3232305 TTTGAAAACA
3232315 TTTTGAAAATA-TATATAATATATAGT
1 TTTTGAAAATATTATATAATATATAGT
*
3232341 TTTTGAAAATATTTTTATAATATATA
1 TTTTGAAAATA-TTATATAATATATA
3232367 ATTCTAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 11 0.48
28 12 0.52
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (27 bp):
TTTTGAAAATATTATATAATATATAGT
Found at i:3233679 original size:27 final size:24
Alignment explanation
Indices: 3233635--3233685 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
3233625 TTTTGAAACA
*
3233635 TTTTTTTTATTTTTTTACTTCTTAT
1 TTTTTTTTATTTTATTACTT-TTAT
3233660 TTTTTTTTATATTTCATTACTTTTAT
1 TTTTTTTTAT-TTT-ATTACTTTTAT
3233686 AATTTAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 10 0.43
26 7 0.30
27 6 0.26
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (24 bp):
TTTTTTTTATTTTATTACTTTTAT
Found at i:3233757 original size:3 final size:3
Alignment explanation
Indices: 3233749--3233777 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
3233739 TTTTTAAGTT
3233749 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
3233778 CTCTAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3235369 original size:2 final size:2
Alignment explanation
Indices: 3235362--3235399 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
3235352 TTTTAAAATA
3235362 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3235400 TGTCATAAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3235642 original size:39 final size:38
Alignment explanation
Indices: 3235599--3235679 Score: 135
Period size: 39 Copynumber: 2.1 Consensus size: 38
3235589 GAAATTCAAA
*
3235599 TATTAATATCATAAATGAAAGAAATTTAATTAAAATAAT
1 TATTAATATCATAAATGAAAGAAATATAATT-AAATAAT
*
3235638 TATTAATATCATAAATGAAATAAATATAATTAAATAAT
1 TATTAATATCATAAATGAAAGAAATATAATTAAATAAT
3235676 TATT
1 TATT
3235680 TTTACAAGGC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
38 11 0.28
39 29 0.73
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (38 bp):
TATTAATATCATAAATGAAAGAAATATAATTAAATAAT
Found at i:3237208 original size:22 final size:22
Alignment explanation
Indices: 3237183--3237233 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3237173 TTGTGTTTGG
3237183 TCAAAGGTTTGGCATTTAATGC
1 TCAAAGGTTTGGCATTTAATGC
* *
3237205 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTAATGC
3237227 TCAAAGG
1 TCAAAGG
3237234 ATTGATGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTAATGC
Found at i:3237865 original size:20 final size:20
Alignment explanation
Indices: 3237838--3237901 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
3237828 TTTTTGTCCC
*
3237838 CTTT-TTTTTTATTTTTGTT
1 CTTTCTTTTTTATTCTTGTT
*
3237857 CTTTCTTTTTTGTTCTTGTT
1 CTTTCTTTTTTATTCTTGTT
* *
3237877 TTTTCCTTTTTTGCTTCTT-TT
1 CTTT-CTTTTTT-ATTCTTGTT
3237898 CTTT
1 CTTT
3237902 TTTCTTTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 16 0.43
21 12 0.32
22 5 0.14
ACGTcount: A:0.02, C:0.14, G:0.06, T:0.78
Consensus pattern (20 bp):
CTTTCTTTTTTATTCTTGTT
Found at i:3237912 original size:22 final size:22
Alignment explanation
Indices: 3237858--3237910 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
3237848 ATTTTTGTTC
3237858 TTTCTTTTTTG-TTCTTGTTTT
1 TTTCTTTTTTGCTTCTTGTTTT
* *
3237879 TTCCTTTTTTGCTTCTTTTCTTT
1 TTTCTTTTTTGCTTCTTGT-TTT
3237902 TTTCTTTTT
1 TTTCTTTTT
3237911 GCCCTTTTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
21 10 0.37
22 6 0.22
23 11 0.41
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTGCTTCTTGTTTT
Found at i:3241016 original size:26 final size:27
Alignment explanation
Indices: 3240970--3241030 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 27
3240960 CTAAAAGATG
*
3240970 AATAAAAATATAATTATTAAGT-GCAA
1 AATAAAAATATAATTAATAAGTAGCAA
* *
3240996 AATAATAATAATAA-TAATAAGTAGTAA
1 AATAAAAAT-ATAATTAATAAGTAGCAA
3241023 AATAAAAA
1 AATAAAAA
3241031 AAAACGCAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 15 0.52
27 14 0.48
ACGTcount: A:0.64, C:0.02, G:0.07, T:0.28
Consensus pattern (27 bp):
AATAAAAATATAATTAATAAGTAGCAA
Found at i:3241232 original size:21 final size:21
Alignment explanation
Indices: 3241206--3241252 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
3241196 ATATATATAT
*
3241206 ATAATTATAATAACG-AAAAAA
1 ATAATT-TAATAAAGTAAAAAA
*
3241227 ATAATTTAATAAAGTAAAATA
1 ATAATTTAATAAAGTAAAAAA
3241248 ATAAT
1 ATAAT
3241253 AATGTAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.64, C:0.02, G:0.04, T:0.30
Consensus pattern (21 bp):
ATAATTTAATAAAGTAAAAAA
Found at i:3241254 original size:16 final size:16
Alignment explanation
Indices: 3241233--3241270 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3241223 AAAAATAATT
3241233 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
3241249 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
3241265 T-ATAAA
1 TAATAAA
3241271 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:3241459 original size:12 final size:12
Alignment explanation
Indices: 3241442--3241499 Score: 66
Period size: 12 Copynumber: 4.8 Consensus size: 12
3241432 TAATAGTACA
3241442 ATAATAATAAAT
1 ATAATAATAAAT
3241454 ATAATAATAAAT
1 ATAATAATAAAT
*
3241466 ATAATAAT-TAT
1 ATAATAATAAAT
*
3241477 A-AATATATATAT
1 ATAATA-ATAAAT
3241489 ATATATAATAA
1 ATA-ATAATAA
3241500 CTTTAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 4 0.10
11 5 0.12
12 24 0.60
13 4 0.10
14 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:3241506 original size:27 final size:27
Alignment explanation
Indices: 3241441--3241499 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
3241431 TTAATAGTAC
*
3241441 AATAATAATAAATATAATAATAAATAT
1 AATAATTATAAATATAATAATAAATAT
*
3241468 AATAATTATAAATAT-ATATATATATAT
1 AATAATTATAAATATAATA-ATAAATAT
3241495 AATAA
1 AATAA
3241500 CTTTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AATAATTATAAATATAATAATAAATAT
Found at i:3241563 original size:27 final size:28
Alignment explanation
Indices: 3241443--3241563 Score: 67
Period size: 27 Copynumber: 4.3 Consensus size: 28
3241433 AATAGTACAA
*
3241443 TAATAATAAATATAATA-ATAAATATAA-
1 TAATAAT-AATATAATATATATATATAAT
*
3241470 TAATTATAAATATATATATATATATAATAACTT
1 TAATAAT-AATATA-ATATATATAT-ATAA--T
* * *
3241503 TAA-AA-AACATTAAAATA-ATAT-TAGAA
1 TAATAATAATA-TAATATATATATATA-AT
*
3241529 TAAAAATAAT-TAATATATATATATAAT
1 TAATAATAATATAATATATATATATAAT
3241556 TAATAATA
1 TAATAATA
3241564 CGATTTATCA
Statistics
Matches: 72, Mismatches: 10, Indels: 24
0.68 0.09 0.23
Matches are distributed among these distances:
26 9 0.12
27 29 0.40
28 8 0.11
29 9 0.12
30 11 0.15
31 2 0.03
32 1 0.01
33 3 0.04
ACGTcount: A:0.60, C:0.02, G:0.01, T:0.37
Consensus pattern (28 bp):
TAATAATAATATAATATATATATATAAT
Found at i:3242018 original size:35 final size:37
Alignment explanation
Indices: 3241942--3242042 Score: 109
Period size: 35 Copynumber: 2.8 Consensus size: 37
3241932 GTGCTTGTGG
* * *
3241942 ATCCTATCTTTAG-GAGTTTAAAAACATAGCAAAATTAT
1 ATCCTAT-TTTAGAGAGTTT-GAATCCTAGCAAAATTAT
* *
3241980 ATCCTATTTTAG-GAG-TTGAATCCTAGCAGAATTCT
1 ATCCTATTTTAGAGAGTTTGAATCCTAGCAAAATTAT
*
3242015 ATCCTATTTTTGAGAGTTTGAATCCTAG
1 ATCCTATTTTAGAGAGTTTGAATCCTAG
3242043 TAGGACGAAA
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
35 24 0.44
36 5 0.09
37 19 0.35
38 7 0.13
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.38
Consensus pattern (37 bp):
ATCCTATTTTAGAGAGTTTGAATCCTAGCAAAATTAT
Found at i:3242811 original size:106 final size:103
Alignment explanation
Indices: 3242503--3243004 Score: 516
Period size: 106 Copynumber: 4.9 Consensus size: 103
3242493 AATATTGTTC
* * *
3242503 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCT-GAAATGGGAAA-T-TTTGTTGACA
* * * * *
3242568 GTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
63 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
* * * * * *
3242609 CGAGTCTAATATCATTCGCTGTGAAGATGAAATTGACTCTG-AA--CGAAATCTTGTTGACAATC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATGGGAAATTTTGTTGACAATC
* * * *
3242671 AGCCGTCCCTTCATTATGAAGTTGAACTTATGTTGTCT
66 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
* *
3242709 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA--TGGGAAAT-TTTGTTGACA
* *
3242774 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
63 ATCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
** * * * *
3242815 CGAGTCCAATATCCTTCGCTGTGAAGTTGAGTTTGGCTCTGAAAT-TG----CTTGTCGACATTC
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATGGGAAATTTTGTTGACAATC
* * * *
3242875 AGTCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCT
66 AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
* * * * * *
3242913 TGGGTCCAATATCCTTTGATGTGAAGTTAAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-TGGGAAATT-TTGTTGACAA
* *
3242978 CCAGCCGTCTCTTCGTTGTGAAGTTGA
64 TCAGCCGTCCCTTCGTTGTGAAGTTGA
3243005 GATTGGCTCC
Statistics
Matches: 324, Mismatches: 59, Indels: 27
0.79 0.14 0.07
Matches are distributed among these distances:
98 78 0.24
99 1 0.00
100 78 0.24
101 3 0.01
102 4 0.01
103 1 0.00
104 2 0.01
105 36 0.11
106 121 0.37
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (103 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATGGGAAATTTTGTTGACAATC
AGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCT
Found at i:3242857 original size:206 final size:202
Alignment explanation
Indices: 3242503--3243004 Score: 592
Period size: 206 Copynumber: 2.5 Consensus size: 202
3242493 AATATTGTTC
* * *
3242503 CGAGTCCAATATCCTCCGCTGTGAAGTTGAAATTGGTTCTGGAACTGGGAAATTATTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAA-T-TTTGTTGACA
** * * * * *
3242568 GTCAACCGCCCCTTCGCTGTGAAGTTGAGCTTGTGCTGTCTCGAGTCTAATATCATTCGCTGTGA
64 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCATTCGCTGTGA
* * *
3242633 AGATGAAATTGACTCTGAACGAAAT-CTTGTTGACAATCAGCCGTCCCTTCATTATGAAGTTGAA
129 AGATGAAATTGACTCTG-A--AAATGCTTGTCGACAATCAGCCGCCCCTTCACTATGAAGTTGAA
*
3242697 CTTATGTTGTCT
191 CTTATGCTGTCT
* * *
3242709 CGAGTCCAATATCCTTCGCTGCGAAGTTGAAATTGGCTCTGAAATTTGAGAAATGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAA-CTGGGAAAT-TTTGTTGACA
* *
3242774 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGA
64 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCATTCGCTGTGA
* ** * * * * * * *
3242839 AGTTGAGTTTGGCTCTGAAATTGCTTGTCGACATTCAGTCGCCCCTTCGCTGTGAAGTTGAGCTT
129 AGATGAAATTGACTCTGAAAATGCTTGTCGACAATCAGCCGCCCCTTCACTATGAAGTTGAACTT
*
3242904 GTGCTGTCT
194 ATGCTGTCT
* * * * * *
3242913 TGGGTCCAATATCCTTTGATGTGAAGTTAAAATTGGCCCTGAAACTGGGAAATTATTGTTGACAA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATT-TTGTTGACAA
*
3242978 CCAGCCGTCTCTTCGTTGTGAAGTTGA
65 CCAGCCGTCCCTTCGTTGTGAAGTTGA
3243005 GATTGGCTCC
Statistics
Matches: 252, Mismatches: 41, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
202 1 0.00
203 46 0.18
204 78 0.31
205 1 0.00
206 120 0.48
207 6 0.02
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (202 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAACTGGGAAATTTTGTTGACAAC
CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGCTGTCTCGAGTCCAATATCATTCGCTGTGAAG
ATGAAATTGACTCTGAAAATGCTTGTCGACAATCAGCCGCCCCTTCACTATGAAGTTGAACTTAT
GCTGTCT
Found at i:3243021 original size:160 final size:158
Alignment explanation
Indices: 3242827--3243162 Score: 564
Period size: 160 Copynumber: 2.1 Consensus size: 158
3242817 AGTCCAATAT
* * * *
3242827 CCTTCGCTGTGAAGTTGAGTTTGGCTCTGAAATTGCTTGTCGACATTCAGTCGCCCCTTCGCTGT
1 CCTTCGTTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGTCGCCCCTTCGCTGT
*
3242892 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTTGATGTGAAGTTAAAATTGGCCCTGAAA
66 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGATGTGAAGTT-AAATTGGCCCTGAAA
*
3242957 CTGGGAAATTATTGTTGACAACCAGCCGTC
130 CT-GGAAATTATTGTTGACAACCAACCGTC
* * *
3242987 TCTTCGTTGTGAAGTTGAGATTGGCTCCGAAATTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGT
1 CCTTCGTTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGTCGCCCCTTCGCTGT
*
3243052 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGTTGTGAAGTTAAATTGGCCCTGAAAC
66 GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGATGTGAAGTTAAATTGGCCCTGAAAC
3243117 TGGAAATTATTGTTGACAACCAACCGTC
131 TGGAAATTATTGTTGACAACCAACCGTC
3243145 CCTTCGTTGTGAAGTTGA
1 CCTTCGTTGTGAAGTTGA
3243163 ACTTGTGTTG
Statistics
Matches: 165, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
158 43 0.26
159 17 0.10
160 105 0.64
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.34
Consensus pattern (158 bp):
CCTTCGTTGTGAAGTTGAGATTGGCTCCGAAATTGCTTGTCGACAGTCAGTCGCCCCTTCGCTGT
GAAGTTGAGCTTGTGCTGTCTTGGGTCCAATATCCTTCGATGTGAAGTTAAATTGGCCCTGAAAC
TGGAAATTATTGTTGACAACCAACCGTC
Found at i:3243645 original size:102 final size:103
Alignment explanation
Indices: 3243529--3243753 Score: 249
Period size: 102 Copynumber: 2.2 Consensus size: 103
3243519 TTTTGTTTTA
* * * *
3243529 AGAAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAATTGTCTCACGGGAGATGAAATT
1 AGAAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATT
3243594 -AGTTCCAA-GGAAACATATTCAAAGATGATGCTTCAAG
66 CA-TTCCAAGGGAAACATATTCAAAGATGATGCTTCAAG
* * * ** *
3243631 AGAAAACTGTCTCAAGGGAGACAAAATTTTGTTTTAAGAGAAACTGTCTCAAGAGAGACGAAATT
1 AGAAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATT
* ** * * * * *
3243696 CATTTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAG
66 CATTCCAAGGGAAACATATTCAAAGATGATGCTTCAAG
*
3243734 AG-AAACTATCTCAAGAGAGA
1 AGAAAACTGTCTCAAGAGAGA
3243754 TGAAATTCAT
Statistics
Matches: 101, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
102 76 0.75
103 25 0.25
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (103 bp):
AGAAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCTCAAGAGAGACGAAATT
CATTCCAAGGGAAACATATTCAAAGATGATGCTTCAAG
Found at i:3243764 original size:65 final size:65
Alignment explanation
Indices: 3243660--3243825 Score: 287
Period size: 65 Copynumber: 2.6 Consensus size: 65
3243650 GACAAAATTT
*
3243660 TGTTTTAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
3243725 TGTTTCAAGAGAAACTATCTCAAGAGAGATGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* *
3243790 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATT
3243826 TTGTTTCGAG
Statistics
Matches: 94, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 94 1.00
ACGTcount: A:0.37, C:0.11, G:0.20, T:0.32
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
Found at i:3243841 original size:37 final size:36
Alignment explanation
Indices: 3243790--3244195 Score: 212
Period size: 37 Copynumber: 11.9 Consensus size: 36
3243780 TCAATGTTTA
*
3243790 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTGTCTCAA-GGAGACAAAATTT
* *
3243827 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATTT
** * *
3243863 CATTTCAAGGGAAA-TGTTTTCAA--TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGAGACAAAATTT
*
3243891 ATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GGAGACAAAATTT
*
3243929 TGTTTCAAGGGAAACTATCTC-AGAGAGACAAAA-TT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATTT
** * **
3243964 CATTTCAAGGGAAA-TGTTTC-------CAATGTTT
1 TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATTT
* * **
3243992 AGTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTT
1 TGTTTCAAGGGAAACTGTCTCAA-GGAGACAAAATTT
* *
3244029 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAA-CT
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAAAATTT
** * *
3244065 CATTTCAAGGGAAA-TGTTTTCAA--TG------TTT
1 TGTTTCAAGGGAAACTG-TCTCAAGGAGACAAAATTT
* *
3244093 ATGTTTC-AGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 -TGTTTCAAGGGAAACTGTCTCAA-GGAGACAAAATTT
*
3244130 TGTTTCAAGGGAAACTGTCTCAA-GAGAC-AAAGTT
1 TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATTT
* *
3244164 TGTTTTAAGAGAAACTGTCTCAAGAGAGACAA
1 TGTTTCAAGGGAAACTGTCTCAAG-GAGACAA
3244196 TGGTGAGCAC
Statistics
Matches: 274, Mismatches: 52, Indels: 86
0.67 0.13 0.21
Matches are distributed among these distances:
27 3 0.01
28 27 0.10
29 27 0.10
30 2 0.01
31 1 0.00
32 1 0.00
33 2 0.01
34 30 0.11
35 21 0.08
36 59 0.22
37 98 0.36
38 3 0.01
ACGTcount: A:0.37, C:0.13, G:0.21, T:0.29
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTGTCTCAAGGAGACAAAATTT
Found at i:3244055 original size:101 final size:102
Alignment explanation
Indices: 3243725--3244156 Score: 744
Period size: 101 Copynumber: 4.3 Consensus size: 102
3243715 TCAATGTTTA
* **
3243725 TGTTTCAAGAGAAACTATCTCAAGAGAGATGAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
3243790 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
3243827 TGTTTCGAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
3243892 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
3243929 TGTTTCAAGGGAAACTATCTC-AGAGAGACAAAATTCATTTCAAGGGAAATGTTTCCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
* **
3243993 -GTTTCAAGAGAAACTGTCTCAATGGAGACGGAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
3244029 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAACTCATTTCAAGGGAAATGTTTTCAATGTTTA
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
*
3244094 TGTTTC-AGAGAAACTGTCTCAAGGGAGAAAAAATTT
66 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
*
3244130 TGTTTCAAGGGAAACTGTCTCAAGAGA
1 TGTTTCAAGGGAAACTATCTCAAGAGA
3244157 CAAAGTTTGT
Statistics
Matches: 312, Mismatches: 16, Indels: 5
0.94 0.05 0.02
Matches are distributed among these distances:
100 54 0.17
101 135 0.43
102 123 0.39
ACGTcount: A:0.36, C:0.13, G:0.21, T:0.30
Consensus pattern (102 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGGAAATGTTTTCAATGTTTA
TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
Found at i:3244168 original size:34 final size:34
Alignment explanation
Indices: 3244094--3244190 Score: 124
Period size: 34 Copynumber: 2.8 Consensus size: 34
3244084 TCAATGTTTA
*
3244094 TGTTTC-AGAGAAACTGTCTCAAGGGAGAAAAAATTT
1 TGTTTCAAGAGAAACTGTCTCAA--GAG-AAAAAGTT
* *
3244130 TGTTTCAAGGGAAACTGTCTCAAGAGACAAAGTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAAAAAGTT
*
3244164 TGTTTTAAGAGAAACTGTCTCAAGAGA
1 TGTTTCAAGAGAAACTGTCTCAAGAGA
3244191 GACAATGGTG
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
34 31 0.56
35 3 0.05
36 6 0.11
37 15 0.27
ACGTcount: A:0.37, C:0.12, G:0.23, T:0.28
Consensus pattern (34 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAAAAAGTT
Found at i:3245080 original size:22 final size:22
Alignment explanation
Indices: 3245055--3245105 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
3245045 TTGTGTTTGG
3245055 TCAAAGGTTTGGCATTTAATGC
1 TCAAAGGTTTGGCATTTAATGC
* *
3245077 TCAAAGGTTTGGTATTTGATGC
1 TCAAAGGTTTGGCATTTAATGC
3245099 TCAAAGG
1 TCAAAGG
3245106 ATTGATGGGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.35
Consensus pattern (22 bp):
TCAAAGGTTTGGCATTTAATGC
Found at i:3245757 original size:20 final size:20
Alignment explanation
Indices: 3245714--3245765 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
3245704 TTTTTGTCCC
* *
3245714 TTTT-TTTTTTATTTTTGTT
1 TTTTCTTTTTTGTTCTTGTT
*
3245733 CTTTCTTTTTTGTTCTTGTT
1 TTTTCTTTTTTGTTCTTGTT
3245753 TTTTCCTTTTTTG
1 TTTT-CTTTTTTG
3245766 CTTATTTTCT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
21 8 0.30
ACGTcount: A:0.02, C:0.10, G:0.08, T:0.81
Consensus pattern (20 bp):
TTTTCTTTTTTGTTCTTGTT
Found at i:3249130 original size:21 final size:24
Alignment explanation
Indices: 3249094--3249153 Score: 72
Period size: 22 Copynumber: 2.6 Consensus size: 24
3249084 ATATATATAT
*
3249094 ATAATAATTATAATAACG-AAAA-A
1 ATAATAATT-TAATAAAGTAAAATA
3249117 A-AATAATTTAATAAAGTAAAATA
1 ATAATAATTTAATAAAGTAAAATA
*
3249140 ATAATAATGTAATA
1 ATAATAATTTAATA
3249154 TAATATAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
21 7 0.22
22 11 0.34
23 3 0.09
24 11 0.34
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (24 bp):
ATAATAATTTAATAAAGTAAAATA
Found at i:3249146 original size:16 final size:16
Alignment explanation
Indices: 3249125--3249162 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
3249115 AAAAATAATT
3249125 TAATAAAGTAAAATAA
1 TAATAAAGTAAAATAA
* *
3249141 TAATAATGTAATATAA
1 TAATAAAGTAAAATAA
3249157 T-ATAAA
1 TAATAAA
3249163 TACATGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
15 4 0.21
16 15 0.79
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (16 bp):
TAATAAAGTAAAATAA
Found at i:3249350 original size:12 final size:12
Alignment explanation
Indices: 3249333--3249390 Score: 66
Period size: 12 Copynumber: 4.8 Consensus size: 12
3249323 TAATAGTACA
3249333 ATAATAATAAAT
1 ATAATAATAAAT
3249345 ATAATAATAAAT
1 ATAATAATAAAT
*
3249357 ATAATAAT-TAT
1 ATAATAATAAAT
*
3249368 A-AATATATATAT
1 ATAATA-ATAAAT
3249380 ATATATAATAA
1 ATA-ATAATAA
3249391 CTTTAAAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
10 4 0.10
11 5 0.12
12 24 0.60
13 4 0.10
14 3 0.08
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAATAATAAAT
Found at i:3249397 original size:27 final size:27
Alignment explanation
Indices: 3249332--3249390 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
3249322 TTAATAGTAC
*
3249332 AATAATAATAAATATAATAATAAATAT
1 AATAATTATAAATATAATAATAAATAT
*
3249359 AATAATTATAAATAT-ATATATATATAT
1 AATAATTATAAATATAATA-ATAAATAT
3249386 AATAA
1 AATAA
3249391 CTTTAAAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.10
27 26 0.90
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (27 bp):
AATAATTATAAATATAATAATAAATAT
Found at i:3249908 original size:35 final size:37
Alignment explanation
Indices: 3249836--3249927 Score: 100
Period size: 35 Copynumber: 2.6 Consensus size: 37
3249826 GGATCCTATC
* * * *
3249836 TTTAG-GAGTTTAAAACATAGCAAAATTATATCCTAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTATATCATAT
* *
3249872 TTTAG-GAG-TTGAATCCTAGCAGAATTCTATCATAT
1 TTTAGAGAGTTTGAATCCTAGCAAAATTATATCATAT
*
3249907 TTTTGAGAGTTTGAATCCTAG
1 TTTAGAGAGTTTGAATCCTAG
3249928 TAGGACGAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
35 25 0.53
36 11 0.23
37 11 0.23
ACGTcount: A:0.34, C:0.12, G:0.16, T:0.38
Consensus pattern (37 bp):
TTTAGAGAGTTTGAATCCTAGCAAAATTATATCATAT
Found at i:3250966 original size:12 final size:12
Alignment explanation
Indices: 3250949--3250974 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3250939 TATCAAATAT
3250949 AAAAATATATAA
1 AAAAATATATAA
3250961 AAAAATATATAA
1 AAAAATATATAA
3250973 AA
1 AA
3250975 CATCGCATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (12 bp):
AAAAATATATAA
Found at i:3257856 original size:26 final size:26
Alignment explanation
Indices: 3257822--3257876 Score: 110
Period size: 26 Copynumber: 2.1 Consensus size: 26
3257812 TCCCGTTGCA
3257822 CATAGTGAGGGTTAAAGATCACACTG
1 CATAGTGAGGGTTAAAGATCACACTG
3257848 CATAGTGAGGGTTAAAGATCACACTG
1 CATAGTGAGGGTTAAAGATCACACTG
3257874 CAT
1 CAT
3257877 CTATCTTTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.35, C:0.16, G:0.25, T:0.24
Consensus pattern (26 bp):
CATAGTGAGGGTTAAAGATCACACTG
Found at i:3259606 original size:40 final size:40
Alignment explanation
Indices: 3259562--3259748 Score: 160
Period size: 40 Copynumber: 4.7 Consensus size: 40
3259552 AATATGTAAA
* * * * *
3259562 TCGCAATACAGAAGTCAAATTTATAGCACAATAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCACAACACAAAAGTCAAAT
* *
3259602 TCGCAACGC-GATAGTCAAATTCGCAACACAAAAGTCAAAT
1 TCGCAACACAGA-AGTCAAATTCACAACACAAAAGTCAAAT
* * * ** * * *
3259642 TCGCAGCACAAAAGTCAAATTCGCAATGCGATAGCCAAAT
1 TCGCAACACAGAAGTCAAATTCACAACACAAAAGTCAAAT
* * * *
3259682 TCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAAT
1 TCGCAACACAGAAGTCAAATTCACAACACAAAAGTCAAAT
* * *
3259722 TCGCAACGCAAAAGTCAAATTCGCAAC
1 TCGCAACACAGAAGTCAAATTCACAAC
3259749 TCGAAATATA
Statistics
Matches: 125, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
39 2 0.02
40 122 0.98
41 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.15, T:0.18
Consensus pattern (40 bp):
TCGCAACACAGAAGTCAAATTCACAACACAAAAGTCAAAT
Found at i:3259608 original size:60 final size:59
Alignment explanation
Indices: 3259541--3259748 Score: 238
Period size: 60 Copynumber: 3.5 Consensus size: 59
3259531 AGTTTCCAAT
* * * * *
3259541 TTCGCAACGCGAATATGTAAA-TCGCAATACAGAAGTCAAATTTATAGCACAATAGTCAAA
1 TTCGCAACGCG-ATA-GTAAATTCGCAACACAAAAGTCAAATTCACAGCACAAAAGTCAAA
*
3259601 TTCGCAACGCGATAGTCAAATTCGCAACACAAAAGTCAAATTCGCAGCACAAAAGTCAAA
1 TTCGCAACGCGATAGT-AAATTCGCAACACAAAAGTCAAATTCACAGCACAAAAGTCAAA
* * * * * *
3259661 TTCGCAATGCGATAGCCAAATTCGCAACACAAAAGTCAAATTCGCAACGCGAAAGTCAAA
1 TTCGCAACGCGATAG-TAAATTCGCAACACAAAAGTCAAATTCACAGCACAAAAGTCAAA
* *
3259721 TTCGCAACGCAAAAGTCAAATTCGCAAC
1 TTCGCAACGCGATAGT-AAATTCGCAAC
3259749 TCGAAATATA
Statistics
Matches: 129, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
58 2 0.02
59 6 0.05
60 121 0.94
ACGTcount: A:0.42, C:0.24, G:0.15, T:0.19
Consensus pattern (59 bp):
TTCGCAACGCGATAGTAAATTCGCAACACAAAAGTCAAATTCACAGCACAAAAGTCAAA
Found at i:3259615 original size:20 final size:20
Alignment explanation
Indices: 3259594--3259748 Score: 211
Period size: 20 Copynumber: 7.8 Consensus size: 20
3259584 ATAGCACAAT
* *
3259594 AGTCAAATTCGCAACGCGAT
1 AGTCAAATTCGCAACGCAAA
*
3259614 AGTCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCAAA
* *
3259634 AGTCAAATTCGCAGCACAAA
1 AGTCAAATTCGCAACGCAAA
* * *
3259654 AGTCAAATTCGCAATGCGAT
1 AGTCAAATTCGCAACGCAAA
* *
3259674 AGCCAAATTCGCAACACAAA
1 AGTCAAATTCGCAACGCAAA
*
3259694 AGTCAAATTCGCAACGCGAA
1 AGTCAAATTCGCAACGCAAA
3259714 AGTCAAATTCGCAACGCAAA
1 AGTCAAATTCGCAACGCAAA
3259734 AGTCAAATTCGCAAC
1 AGTCAAATTCGCAAC
3259749 TCGAAATATA
Statistics
Matches: 117, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 117 1.00
ACGTcount: A:0.43, C:0.25, G:0.15, T:0.17
Consensus pattern (20 bp):
AGTCAAATTCGCAACGCAAA
Found at i:3259889 original size:22 final size:22
Alignment explanation
Indices: 3259859--3259914 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
3259849 ACTCTCTACG
*
3259859 GCGACATCCGTCCCCATCTCC-
1 GCGAAATCCGTCCCCATCTCCA
*
3259880 GACGAAATCCGTCCCCATTTCCA
1 G-CGAAATCCGTCCCCATCTCCA
3259903 GCGAAATCCGTC
1 GCGAAATCCGTC
3259915 TATCTCCATC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 1 0.03
22 29 0.94
23 1 0.03
ACGTcount: A:0.21, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
GCGAAATCCGTCCCCATCTCCA
Found at i:3262352 original size:4 final size:4
Alignment explanation
Indices: 3262343--3262389 Score: 67
Period size: 4 Copynumber: 11.8 Consensus size: 4
3262333 TTTTTGCGGC
* * *
3262343 TTTA TTTA TTTA TTTA TTTA TTTA CTAA TTTA TTTA TTAA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
3262390 TCAGCGGCCT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (4 bp):
TTTA
Found at i:3262625 original size:21 final size:21
Alignment explanation
Indices: 3262530--3262652 Score: 74
Period size: 21 Copynumber: 5.9 Consensus size: 21
3262520 GCCCGATGCA
*
3262530 CCTATCATCATTCAAGAGG-T
1 CCTATCATCGTTCAAGAGGCT
* *
3262550 GCCTCAT-ATCGTTTAAGAGGCC
1 -CCT-ATCATCGTTCAAGAGGCT
* * * *
3262572 CCTCTCATC-ATCAAAGAAGCC
1 CCTATCATCGTTC-AAGAGGCT
** *
3262593 CCTCCCACCGTTCAAGAGGCT
1 CCTATCATCGTTCAAGAGGCT
3262614 CCTATCATCGTTCAAGAGG-T
1 CCTATCATCGTTCAAGAGGCT
**
3262634 CCCGTCAGTCGTTCAAGAG
1 CCTATCA-TCGTTCAAGAG
3262653 CCCGATTCAT
Statistics
Matches: 79, Mismatches: 17, Indels: 12
0.73 0.16 0.11
Matches are distributed among these distances:
20 8 0.10
21 67 0.85
22 4 0.05
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (21 bp):
CCTATCATCGTTCAAGAGGCT
Found at i:3264107 original size:66 final size:64
Alignment explanation
Indices: 3263980--3264124 Score: 236
Period size: 66 Copynumber: 2.2 Consensus size: 64
3263970 TTTTACATTG
3263980 AAAGTTGATTTGTTTAATTAATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
1 AAAGTTGATTTGTTTAATTAATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
* * *
3264044 AAAGTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTTGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTAATGAGGAAATAAGAATTA-TTTTTTGCTTGTTTAATTGATTTGT
3264109 A
64 A
*
3264110 AAAGTTTATTTGTTT
1 AAAGTTGATTTGTTT
3264125 TTTTAAATTC
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
64 17 0.23
65 18 0.24
66 40 0.53
ACGTcount: A:0.30, C:0.01, G:0.17, T:0.52
Consensus pattern (64 bp):
AAAGTTGATTTGTTTAATTAATGAGGAAATAAGAATTATTTTTTGCTTGTTTAATTGATTTGTA
Found at i:3264599 original size:18 final size:18
Alignment explanation
Indices: 3264576--3264611 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3264566 AAGCCGGTTG
*
3264576 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3264594 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
3264612 CCTTTTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3266019 original size:25 final size:25
Alignment explanation
Indices: 3265985--3266034 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
3265975 TATTATTTTC
*
3265985 CAAATAATGTACCCATAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
3266010 CAAATAATGTACCCACAACAATGTT
1 CAAATAATGTACCCACAACAATGTT
3266035 TAATTGATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (25 bp):
CAAATAATGTACCCACAACAATGTT
Found at i:3266130 original size:20 final size:21
Alignment explanation
Indices: 3266095--3266134 Score: 64
Period size: 20 Copynumber: 1.9 Consensus size: 21
3266085 AGACATGTTG
3266095 AAGGTAAACTTTCGCAACGCGA
1 AAGGTAAAC-TTCGCAACGCGA
3266117 AAGGTAAA-TTCGCAACGC
1 AAGGTAAACTTCGCAACGC
3266135 AAAATAAGCG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.56
22 8 0.44
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.17
Consensus pattern (21 bp):
AAGGTAAACTTCGCAACGCGA
Found at i:3266175 original size:20 final size:20
Alignment explanation
Indices: 3266152--3266202 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
3266142 GCGTTGCGAT
*
3266152 AGTCAAATTCGCAACACGAA
1 AGTCAAATTCGCAACACAAA
*
3266172 AGTCAAATTCGCAACGCAAA
1 AGTCAAATTCGCAACACAAA
3266192 AGTCAAATTCG
1 AGTCAAATTCG
3266203 AGTTGTGATT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.43, C:0.24, G:0.16, T:0.18
Consensus pattern (20 bp):
AGTCAAATTCGCAACACAAA
Found at i:3266564 original size:18 final size:18
Alignment explanation
Indices: 3266541--3266576 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
3266531 AGCCAGTTTG
*
3266541 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTGATTT
3266559 TGATTGCGATTTTGATTT
1 TGATTGCGATTTTGATTT
3266577 CCTTTTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.03, G:0.25, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTGATTT
Found at i:3268878 original size:24 final size:24
Alignment explanation
Indices: 3268841--3268894 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
3268831 CCATCACATC
*
3268841 ATCAAAATCTGAGTATTAACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
* * *
3268865 ATCAAAGTCCGAGTATTGATCAAG
1 ATCAAAATCCGAGTATTAACCAAG
3268889 ATCAAA
1 ATCAAA
3268895 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.44, C:0.17, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:3269071 original size:19 final size:19
Alignment explanation
Indices: 3269047--3269090 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3269037 ATTGGAAATG
*
3269047 TGGTGAAACAAAAGTTTCT
1 TGGTGAAACAAAAGTTTAT
*
3269066 TGGTGAAACAAAATTTTAT
1 TGGTGAAACAAAAGTTTAT
3269085 TGGTGA
1 TGGTGA
3269091 TGAAATTGTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.36, C:0.07, G:0.23, T:0.34
Consensus pattern (19 bp):
TGGTGAAACAAAAGTTTAT
Found at i:3269672 original size:16 final size:16
Alignment explanation
Indices: 3269651--3269684 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3269641 AAATCATTGA
*
3269651 AAAATTATATAGAAAT
1 AAAATTATATAAAAAT
*
3269667 AAAATTATGTAAAAAT
1 AAAATTATATAAAAAT
3269683 AA
1 AA
3269685 TTAGAGATGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.06, T:0.29
Consensus pattern (16 bp):
AAAATTATATAAAAAT
Found at i:3269903 original size:19 final size:19
Alignment explanation
Indices: 3269863--3269974 Score: 107
Period size: 19 Copynumber: 5.7 Consensus size: 19
3269853 TTAAATTCGT
* *
3269863 GTTGCGAATTCGAAAATCTA
1 GTTGCGAATTTG-AAATTTA
3269883 GTTGCGAATTTGAAATTTA
1 GTTGCGAATTTGAAATTTA
*
3269902 GTTGCGAATTTGAAATTCA
1 GTTGCGAATTTGAAATTTA
* **
3269921 GTTGCAAATTTGAAATTCCGC
1 GTTGCGAATTTGAAATT--TA
** *
3269942 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGAAATTT-A
3269962 GTTGCGAATTTGA
1 GTTGCGAATTTGA
3269975 CTATCACGTT
Statistics
Matches: 78, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
19 40 0.51
20 24 0.31
21 14 0.18
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (19 bp):
GTTGCGAATTTGAAATTTA
Found at i:3269967 original size:20 final size:20
Alignment explanation
Indices: 3269902--3270173 Score: 193
Period size: 20 Copynumber: 13.6 Consensus size: 20
3269892 TTGAAATTTA
** *
3269902 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGACTTTCGC
* * *
3269921 GTTGCAAATTTGAAATTCCGC
1 GTTGCGAATTTG-ACTTTCGC
* *
3269942 GTTGCGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTCGC
* *
3269962 GTTGCGAATTTGACTATCAC
1 GTTGCGAATTTGACTTTCGC
* *
3269982 GTTGCGAATTTGACTATCAC
1 GTTGCGAATTTGACTTTCGC
*
3270002 GTTGCGAATTTGAC-TTCTGT
1 GTTGCGAATTTGACTTTC-GC
*
3270022 GTTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGAC--TTTCGC
* *
3270042 GTTGCAAATTTGACTATCGC
1 GTTGCGAATTTGACTTTCGC
* * *
3270062 GTTACGAATTTGACTTTTGT
1 GTTGCGAATTTGACTTTCGC
*
3270082 GTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGACTTTCGC
*
3270102 GTTGCGAATTTGAC-TTCTGT
1 GTTGCGAATTTGACTTTC-GC
*
3270122 GTTGCG-ATTT-ACAAATTCGC
1 GTTGCGAATTTGAC--TTTCGC
*
3270142 GTTGCGATTTATAGA--TTCGC
1 GTTGCGAATT-T-GACTTTCGC
3270162 GTTGCGAATTTG
1 GTTGCGAATTTG
3270174 GAAAATCGCA
Statistics
Matches: 203, Mismatches: 34, Indels: 33
0.75 0.13 0.12
Matches are distributed among these distances:
18 5 0.02
19 24 0.12
20 147 0.72
21 23 0.11
22 3 0.01
24 1 0.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.39
Consensus pattern (20 bp):
GTTGCGAATTTGACTTTCGC
Found at i:3269985 original size:40 final size:40
Alignment explanation
Indices: 3269939--3270128 Score: 224
Period size: 40 Copynumber: 4.8 Consensus size: 40
3269929 TTTGAAATTC
3269939 CGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTAT
1 CGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTAT
* * ***
3269979 CACGTTGCGAATTTGACTATCACGTTGCGAATTTGACT-T
1 CGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTAT
* * * * *
3270018 CTGTGTTGCG-ATTT-ACAAATTCGCGTTGCAAATTTGACTAT
1 C-GCGTTGCGAATTTGAC--TTTTGTGTTGCGAATTTGACTAT
*
3270059 CGCGTTACGAATTTGACTTTTGTGTTGCGAATTTGACTAT
1 CGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTAT
*
3270099 CGCGTTGCGAATTTGACTTCTGTGTTGCGA
1 CGCGTTGCGAATTTGACTTTTGTGTTGCGA
3270129 TTTACAAATT
Statistics
Matches: 125, Mismatches: 19, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
38 2 0.02
39 6 0.05
40 109 0.87
41 6 0.05
42 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.23, T:0.39
Consensus pattern (40 bp):
CGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTAT
Found at i:3270005 original size:60 final size:60
Alignment explanation
Indices: 3269941--3270116 Score: 266
Period size: 60 Copynumber: 2.9 Consensus size: 60
3269931 TGAAATTCCG
*
3269941 CGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCACGTTGCGAATTTGACTATCA
1 CGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCA
* * * *
3270001 CGTTGCGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCAAATTTGACTATCG
1 CGTTGCGAATTTGACTTTTGTGTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGACTATCA
*
3270061 CGTTACGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT
1 CGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACT
3270117 TCTGTGTTGC
Statistics
Matches: 103, Mismatches: 9, Indels: 8
0.86 0.08 0.07
Matches are distributed among these distances:
58 2 0.02
59 5 0.05
60 89 0.86
61 5 0.05
62 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.22, T:0.40
Consensus pattern (60 bp):
CGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCA
Found at i:3270052 original size:100 final size:100
Alignment explanation
Indices: 3269933--3270146 Score: 329
Period size: 100 Copynumber: 2.1 Consensus size: 100
3269923 TGCAAATTTG
* * * * *
3269933 AAATTCCGCGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTATCACGTTGCGAATTTGACTA
1 AAATT-CGCGTTGCAAATTTGACTATCGCGTTACGAATTTGACTATCACGTTGCGAATTTGACTA
3269998 TCACGTTGCGAATTTGACTTCTGTGTTGCGATTTAC
65 TCACGTTGCGAATTTGACTTCTGTGTTGCGATTTAC
* ***
3270034 AAATTCGCGTTGCAAATTTGACTATCGCGTTACGAATTTGACTTTTGTGTTGCGAATTTGACTAT
1 AAATTCGCGTTGCAAATTTGACTATCGCGTTACGAATTTGACTATCACGTTGCGAATTTGACTAT
*
3270099 CGCGTTGCGAATTTGACTTCTGTGTTGCGATTTAC
66 CACGTTGCGAATTTGACTTCTGTGTTGCGATTTAC
3270134 AAATTCGCGTTGC
1 AAATTCGCGTTGC
3270147 GATTTATAGA
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
100 98 0.95
101 5 0.05
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (100 bp):
AAATTCGCGTTGCAAATTTGACTATCGCGTTACGAATTTGACTATCACGTTGCGAATTTGACTAT
CACGTTGCGAATTTGACTTCTGTGTTGCGATTTAC
Found at i:3270210 original size:21 final size:21
Alignment explanation
Indices: 3270164--3270210 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
3270154 AGATTCGCGT
*
3270164 TGCGAATTTGGAAAATCGCAA
1 TGCGAATTTGGAAAATCACAA
*
3270185 CGCGAATTTGGAAAATCACAA
1 TGCGAATTTGGAAAATCACAA
3270206 TGCGA
1 TGCGA
3270211 TTTACATATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TGCGAATTTGGAAAATCACAA
Found at i:3270267 original size:20 final size:20
Alignment explanation
Indices: 3270224--3270271 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
3270214 ACATATTCGC
*
3270224 GTTGCGAAATTGGAAACTGG
1 GTTGCGAAATTGGAAACCGG
** *
3270244 GTTGCGAAATTGGAGTCCGT
1 GTTGCGAAATTGGAAACCGG
3270264 GTTGCGAA
1 GTTGCGAA
3270272 TTTGTTGGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.27
Consensus pattern (20 bp):
GTTGCGAAATTGGAAACCGG
Found at i:3271619 original size:19 final size:19
Alignment explanation
Indices: 3271577--3271624 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 19
3271567 TTTTAAAGAA
* * *
3271577 AAATTATAGAAAAATTATC
1 AAATTATATAAAAAATAAC
*
3271596 TAATTATATAAAAAATAAC
1 AAATTATATAAAAAATAAC
3271615 AAATTA-ATAA
1 AAATTATATAA
3271625 TTTAGTTACC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (19 bp):
AAATTATATAAAAAATAAC
Found at i:3272296 original size:20 final size:20
Alignment explanation
Indices: 3272271--3272314 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
3272261 TTTAATATTT
3272271 ATATTAAATTCAAAATTAAA
1 ATATTAAATTCAAAATTAAA
3272291 ATATTAAATTCAAAATTAAA
1 ATATTAAATTCAAAATTAAA
3272311 ATAT
1 ATAT
3272315 AATTTTAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATTAAATTCAAAATTAAA
Found at i:3274819 original size:8 final size:8
Alignment explanation
Indices: 3274801--3274831 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
3274791 CTAACATATG
3274801 TATTG-AT
1 TATTGTAT
3274808 TATTGTAT
1 TATTGTAT
3274816 TATTGTAT
1 TATTGTAT
3274824 TATTGTAT
1 TATTGTAT
3274832 GATGATGTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.22
8 18 0.78
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (8 bp):
TATTGTAT
Done.