Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008301.1 Hibiscus syriacus cultivar Beakdansim tig00110987_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: 3376434
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 18
Found at i:3023866 original size:14 final size:14
Alignment explanation
Indices: 3023849--3023924 Score: 57
Period size: 14 Copynumber: 5.3 Consensus size: 14
3023839 TATTAAAGTA
*
3023849 ATTTATTTAATATT
1 ATTTATTAAATATT
* *
3023863 ATTTGTTTTAATATT
1 ATTT-ATTAAATATT
3023878 A-TTATTAAAATATT
1 ATTTATT-AAATATT
* *
3023892 ATTTATATCAATGTT
1 ATTTAT-TAAATATT
3023907 A-TTATTAAAATATT
1 ATTTATT-AAATATT
3023921 ATTT
1 ATTT
3023925 CTATAATTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 11
0.73 0.10 0.16
Matches are distributed among these distances:
13 3 0.06
14 23 0.47
15 22 0.45
16 1 0.02
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (14 bp):
ATTTATTAAATATT
Found at i:3023889 original size:29 final size:29
Alignment explanation
Indices: 3023857--3023924 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
3023847 TAATTTATTT
* * *
3023857 AATATTATTTGTTTTAATATTATTATTAA
1 AATATTATTTATATCAATATTATTATTAA
*
3023886 AATATTATTTATATCAATGTTATTATTAA
1 AATATTATTTATATCAATATTATTATTAA
3023915 AATATTATTT
1 AATATTATTT
3023925 CTATAATTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (29 bp):
AATATTATTTATATCAATATTATTATTAA
Found at i:3024030 original size:37 final size:36
Alignment explanation
Indices: 3023965--3024043 Score: 99
Period size: 37 Copynumber: 2.2 Consensus size: 36
3023955 TTGAATATTC
3023965 TATTAAAATAAAAATATTATAAATTATTTT-AAACATT
1 TATTAAAATAAAAATATTATAAATTATTTTGAAA-A-T
* *
3024002 TATTAAAATAATAATATTAT-ATTGTATTTTGAAAAT
1 TATTAAAATAAAAATATTATAAAT-TATTTTGAAAAT
3024038 TATTAA
1 TATTAA
3024044 TAAATACATT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
36 9 0.24
37 26 0.68
38 3 0.08
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.46
Consensus pattern (36 bp):
TATTAAAATAAAAATATTATAAATTATTTTGAAAAT
Found at i:3024137 original size:23 final size:23
Alignment explanation
Indices: 3024096--3024177 Score: 75
Period size: 24 Copynumber: 3.6 Consensus size: 23
3024086 AATACATAAA
*
3024096 TAATATTATTCATTATTAATAATT
1 TAATAATATT-ATTATTAATAATT
3024120 TAATAATATTATCT-TTAAGTAA-T
1 TAATAATATTAT-TATTAA-TAATT
3024143 T-ATAA-ATT-TTATTAATAATT
1 TAATAATATTATTATTAATAATT
*
3024163 TATTATATATTATTA
1 TAATA-ATATTATTA
3024178 AAATAAAATT
Statistics
Matches: 48, Mismatches: 2, Indels: 16
0.73 0.03 0.24
Matches are distributed among these distances:
19 4 0.08
20 7 0.15
21 5 0.10
22 5 0.10
23 11 0.23
24 16 0.33
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (23 bp):
TAATAATATTATTATTAATAATT
Found at i:3024213 original size:23 final size:21
Alignment explanation
Indices: 3024187--3024266 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 21
3024177 AAAATAAAAT
*
3024187 TATAAAACTATATATCATTATAA
1 TATAAAA--ATATATTATTATAA
*
3024210 TATAATTAAGTATATTATTATAA
1 TATAA--AAATATATTATTATAA
* * *
3024233 TATCAAAAATATAATATTACAT
1 TAT-AAAAATATATTATTATAA
3024255 TATTAAAAATAT
1 TA-TAAAAATAT
3024267 TAATAAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 9
0.76 0.10 0.15
Matches are distributed among these distances:
22 22 0.47
23 21 0.45
24 2 0.04
25 2 0.04
ACGTcount: A:0.53, C:0.05, G:0.01, T:0.41
Consensus pattern (21 bp):
TATAAAAATATATTATTATAA
Found at i:3026617 original size:12 final size:12
Alignment explanation
Indices: 3026596--3026625 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3026586 TGGTTAAATG
*
3026596 AAATAGAATCAT
1 AAATAAAATCAT
3026608 AAATAAAATCAT
1 AAATAAAATCAT
3026620 AAATAA
1 AAATAA
3026626 CATAAGGACC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.07, G:0.03, T:0.23
Consensus pattern (12 bp):
AAATAAAATCAT
Found at i:3028722 original size:21 final size:21
Alignment explanation
Indices: 3028696--3028753 Score: 55
Period size: 21 Copynumber: 2.8 Consensus size: 21
3028686 GTCGAGGGTT
*
3028696 TTATGTGGTCATTCGGGATAA
1 TTATGTGGTCATTCGGGACAA
* **
3028717 TTATGTAGTTTTTCGGGACAA
1 TTATGTGGTCATTCGGGACAA
*
3028738 ATATGTGG-CACTTCGG
1 TTATGTGGTCA-TTCGG
3028754 TGCAAACCTA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.28, T:0.38
Consensus pattern (21 bp):
TTATGTGGTCATTCGGGACAA
Found at i:3028769 original size:23 final size:23
Alignment explanation
Indices: 3028739--3028872 Score: 175
Period size: 23 Copynumber: 5.9 Consensus size: 23
3028729 TCGGGACAAA
*
3028739 TATGTGGCACTTCGGTGCAAACC
1 TATGTGGCACTCCGGTGCAAACC
3028762 TATGTGGCACTCCGGTGCAAACC
1 TATGTGGCACTCCGGTGCAAACC
*
3028785 TATGCGGCACTCCGGTGCAAACC
1 TATGTGGCACTCCGGTGCAAACC
*
3028808 TATGCGGCACTCCGGTGCAAACC
1 TATGTGGCACTCCGGTGCAAACC
* **
3028831 TATGTGGTCA-TTCGG-G-AAAAT
1 TATGTGG-CACTCCGGTGCAAACC
*
3028852 TATGTGGCACTTCGGTGCAAA
1 TATGTGGCACTCCGGTGCAAA
3028873 TTACGAGCTG
Statistics
Matches: 101, Mismatches: 6, Indels: 8
0.88 0.05 0.07
Matches are distributed among these distances:
20 2 0.02
21 15 0.15
22 2 0.02
23 80 0.79
24 2 0.02
ACGTcount: A:0.23, C:0.26, G:0.27, T:0.24
Consensus pattern (23 bp):
TATGTGGCACTCCGGTGCAAACC
Found at i:3031310 original size:119 final size:116
Alignment explanation
Indices: 3031080--3031312 Score: 277
Period size: 119 Copynumber: 2.0 Consensus size: 116
3031070 AGAGTCAAGG
* *
3031080 AAAAGGGTGAACAAGTTCTTCTCATTATGAACTTCTTCCTCTTCGGATGAGTTCTTCTCATTATG
1 AAAAGGGTGAACAAGTTCTTCTCATTATGAACTTCTTCCTCTTCGGATAAGTTCTTCTAATTATG
* * * ** * * *
3031145 AACCCTTCCATTGGAAATGTTAATATACCTCCTTCTTTTATTGATTTGAGT
66 AACCCTTCCATTAGAAATGTCAATACACCTCCAGCTGTGATGGATTTGAGT
* * * * *
3031196 AAAAGGTTGGACAAGTTTTTCTCATTATGAACTTCTTCTTCCTGCTCGGATAATTTCTTCTAATT
1 AAAAGGGTGAACAAGTTCTTCTCATTATGAACTTCTTCCT-CT--TCGGATAAGTTCTTCTAATT
* * *
3031261 ATGAACCCTTCCATTAGAAATGTCGATCCACCTTCAGCTGTGATGGATTTGA
63 ATGAACCCTTCCATTAGAAATGTCAATACACCTCCAGCTGTGATGGATTTGA
3031313 ACAAAGTGTT
Statistics
Matches: 96, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
116 36 0.38
117 2 0.02
119 58 0.60
ACGTcount: A:0.25, C:0.20, G:0.15, T:0.39
Consensus pattern (116 bp):
AAAAGGGTGAACAAGTTCTTCTCATTATGAACTTCTTCCTCTTCGGATAAGTTCTTCTAATTATG
AACCCTTCCATTAGAAATGTCAATACACCTCCAGCTGTGATGGATTTGAGT
Found at i:3031592 original size:163 final size:163
Alignment explanation
Indices: 3031206--3032436 Score: 1125
Period size: 163 Copynumber: 7.6 Consensus size: 163
3031196 AAAAGGTTGG
* * * * * *
3031206 ACAAGTTTTTCTCATTATGAACTTCTTCTTCCTGC-TCGGATAATTTCTTCTAATTATGAACCCT
1 ACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTTGGATGAGTTCTTCTCATTATGAACCCT
* * * *** * * * * * * *
3031270 TCCATTAGAAATGTCGATCCACCTTCAGCTGTGATGGATTTGAACAAAGTGTTGACGCTGATCTA
65 TCCATTGGAAATGACGATCCACCTCCTTTTATGATGGATTCGATCAAAATGCTGATGTTGATCTA
* ** * * * * *
3031335 CCTCATTCTGTGATAGAATCGAGTAAGATGGTTGA
130 TCTCATTCTACGATAGAGTCGAGCAAAAAGG-GGA
* * *** ** *
3031370 ACAAATTCTTCTCATTATGAACTTCTTCTTCC-TGTTCAAACAAGTTCTTCTCATTATGAACCAT
1 ACAAGTTCTTCTCATTATGAACTTCTTC-TCCTTCTTTGGATGAGTTCTTCTCATTATGAACCCT
* * * *
3031434 TCCATTGGAAATGCCGATCCACATCCTTTTATTATGGATTTGATCAAAATGCTGATGTTGATCTA
65 TCCATTGGAAATGACGATCCACCTCCTTTTATGATGGATTCGATCAAAATGCTGATGTTGATCTA
* * * *
3031499 TCTCCTTCTACGATAGAGTTGACCAAAAAGGAGA
130 TCTCATTCTACGATAGAGTCGAGCAAAAAGGGGA
* **
3031533 ACAAGTTCTTCTTATTATGAACTTCTTCTTATTCTTTGGATGAGTTCTTCTCATTATGAACCCTT
1 ACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTTGGATGAGTTCTTCTCATTATGAACCCTT
* * * * * *
3031598 CTAGTGGAAATGACAATTCACCTCCTTTTATGATTGATTCGATCAAAATGTTGATGTTGATCTAT
66 CCATTGGAAATGACGATCCACCTCCTTTTATGATGGATTCGATCAAAATGCTGATGTTGATCTAT
* * *
3031663 CTCATTCTACGATAGAGTTGAGCAAAATGGTGA
131 CTCATTCTACGATAGAGTCGAGCAAAAAGGGGA
* *
3031696 ACAAGTTCTTCTCATTATGAATTTCTTCTCCTTCTTTGGACGAGTTCTTCTCATTATGAACCCTT
1 ACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTTGGATGAGTTCTTCTCATTATGAACCCTT
* * * * * * * * * *
3031761 CCACTGGAAATTACGATTCACCTCATTCTATGTTAGATTCGATCAAAATGTTGATGCTGATATAT
66 CCATTGGAAATGACGATCCACCTCCTTTTATGATGGATTCGATCAAAATGCTGATGTTGATCTAT
* * * *
3031826 CTCCTTTTGCGATAGAGTCGAGCAAAAGGGGGA
131 CTCATTCTACGATAGAGTCGAGCAAAAAGGGGA
* * *
3031859 ATAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTTGGACGAGTTCTTCTCATTATGAATCCTT
1 ACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTTGGATGAGTTCTTCTCATTATGAACCCTT
* * * * * * *
3031924 CCATTGGAAATGACGATCCACCTCCTTGTGTGATCGATTCGATCAAAATACTTAT-TCTCATCCA
66 CCATTGGAAATGACGATCCACCTCCTTTTATGATGGATTCGATCAAAATGCTGATGT-TGATCTA
* * *
3031988 TCTCATTCTGCGATAGAATCGAGCAAAAAAGGGA
130 TCTCATTCTACGATAGAGTCGAGCAAAAAGGGGA
* * * *
3032022 ACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTTGAATGATTTCTTATCATTACGAA-CCTT
1 ACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTTGGATGAGTTCTTCTCATTATGAACCCTT
* ** * * * * * * *
3032086 CTATTTAAAATGATGATCCTCCTCATTCTGTGATGGATTTGATCAAAATACTGATGTTGATCTAT
66 CCATTGGAAATGACGATCCACCTCCTTTTATGATGGATTCGATCAAAATGCTGATGTTGATCTAT
* * * *
3032151 CTCCTTCTACGATAGAATCGAGTAAAAGGGGGA
131 CTCATTCTACGATAGAGTCGAGCAAAAAGGGGA
* * * * * * * * *
3032184 ACTCA-TTCTTTTCATTATGAATTTCTTTTTCTTC-TTAGATAAGTTCTTCTTATTATGAGCCCT
1 AC-AAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTTGGATGAGTTCTTCTCATTATGAACCCT
* * *
3032247 TCCATTAGAAATGACGATCCACCT-CTTTCTATGATGGATTCGATCAAAATGCTGATGATGATTT
65 TCCATTGGAAATGACGATCCACCTCCTTT-TATGATGGATTCGATCAAAATGCTGATGTTGATCT
** ** * *
3032311 ATCTCATTCTGTGATAGAACCGATC-AAAAGGTTGA
129 ATCTCATTCTACGATAGAGTCGAGCAAAAAGG-GGA
* * * * * * *
3032346 ACAAGTTTTTGTCATTATGAACTTTTTCTCTCTTCTATGGATGA-TTATT-TACGTTATGAA-CT
1 ACAAGTTCTTCTCATTATGAACTTCTTCTC-CTTCTTTGGATGAGTTCTTCT-CATTATGAACCC
** **
3032408 TTCTTTTGGAAATGTTGATCCACCTCCTT
64 TTCCATTGGAAATGACGATCCACCTCCTT
3032437 CTGTGATAGA
Statistics
Matches: 874, Mismatches: 180, Indels: 27
0.81 0.17 0.02
Matches are distributed among these distances:
161 25 0.03
162 227 0.26
163 492 0.56
164 130 0.15
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (163 bp):
ACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTTGGATGAGTTCTTCTCATTATGAACCCTT
CCATTGGAAATGACGATCCACCTCCTTTTATGATGGATTCGATCAAAATGCTGATGTTGATCTAT
CTCATTCTACGATAGAGTCGAGCAAAAAGGGGA
Found at i:3031829 original size:326 final size:326
Alignment explanation
Indices: 3031206--3032381 Score: 1267
Period size: 326 Copynumber: 3.6 Consensus size: 326
3031196 AAAAGGTTGG
* * * * *
3031206 ACAAGTTTTTCTCATTATGAACTTCTTCTTCCTGCTCGGATAATTTCTTCTAATTATGAACCCTT
1 ACAAGTTCTTCTCATTATGAACTTCTTCTT-CTTCTTGGATAAGTTCTTCTCATTATGAACCCTT
* * *** * * * * * * *
3031271 CCATTAGAAATGTCGATCCACCTTCAGCTGTGATGGATTTGAACAAAGTGTTGACGCTGATCTAC
65 CCATTAGAAATGACGATCCACCTCCTTTTATGATGGATTCGATCAAAATGTTGATGTTGATCTAT
* * * *
3031336 CTCATTCTGTGATAGAATCGAGTAAGATGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTC
130 CTCATTCTGCGATAGAATCGAGCAAAATGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-TC
* ** * * * * * *
3031401 C-TGTTCAAACAAGTTCTTCTCATTATGAACCATTCCATTGGAAATGCCGATCCACATCCTTTTA
194 CTTCTTTGAACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGACGATCCACCTCATTCTA
* * *
3031465 T-TATGGATTTGATCAAAATGCTGATGTTGATCTATCTCCTTCTACGATAGAGTTGACCAAAAAG
259 TGT-TGGATTTGATCAAAATGCTGATGTTGATCTATCTCCTTCTACGATAGAGTCGAGCAAAAGG
*
3031529 GAGA
323 GGGA
* * *
3031533 ACAAGTTCTTCTTATTATGAACTTCTTCTTATTCTTTGGATGAGTTCTTCTCATTATGAACCCTT
1 ACAAGTTCTTCTCATTATGAACTTCTTCTTCTTC-TTGGATAAGTTCTTCTCATTATGAACCCTT
* * * * * *
3031598 CTAGTGGAAATGACAATTCACCTCCTTTTATGATTGATTCGATCAAAATGTTGATGTTGATCTAT
65 CCATTAGAAATGACGATCCACCTCCTTTTATGATGGATTCGATCAAAATGTTGATGTTGATCTAT
* * * *
3031663 CTCATTCTACGATAGAGTTGAGCAAAATGG-TGAACAAGTTCTTCTCATTATGAATTTCTTCTCC
130 CTCATTCTGCGATAGAATCGAGCAAAATGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCC
* * * *
3031727 TTCTTTGGACGAGTTCTTCTCATTATGAACCCTTCCACTGGAAATTACGATTCACCTCATTCTAT
195 TTCTTTGAACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGACGATCCACCTCATTCTAT
* * * * * * *
3031792 GTTAGATTCGATCAAAATGTTGATGCTGATATATCTCCTTTTGCGATAGAGTCGAGCAAAAGGGG
260 GTTGGATTTGATCAAAATGCTGATGTTGATCTATCTCCTTCTACGATAGAGTCGAGCAAAAGGGG
3031857 GA
325 GA
* * ** *
3031859 ATAAGTTCTTCTCATTATGAACTTCTTCTCCTTCTTTGGACGAGTTCTTCTCATTATGAATCCTT
1 ACAAGTTCTTCTCATTATGAACTTCTTCTTCTTC-TTGGATAAGTTCTTCTCATTATGAACCCTT
* * * * * * *
3031924 CCATTGGAAATGACGATCCACCTCCTTGTGTGATCGATTCGATCAAAATACTT-AT-TCTCATCC
65 CCATTAGAAATGACGATCCACCTCCTTTTATGATGGATTCGATCAAAAT-GTTGATGT-TGATCT
*
3031987 ATCTCATTCTGCGATAGAATCGAGCAAAAAAGG--GAACAAGTTCTTCTCATTATGAACTTCTTC
128 ATCTCATTCTGCGATAGAATCGAGC-AAAATGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC
* * * * * ** * *
3032050 TCCTTCTTTGAATGATTTCTTATCATTACGAA-CCTTCTATTTAAAATGATGATCCTCCTCATTC
192 TCCTTCTTTGAACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGACGATCCACCTCATTC
* * * * *
3032114 TGTGATGGATTTGATCAAAATACTGATGTTGATCTATCTCCTTCTACGATAGAATCGAGTAAAAG
257 TATGTTGGATTTGATCAAAATGCTGATGTTGATCTATCTCCTTCTACGATAGAGTCGAGCAAAAG
3032179 GGGGA
322 GGGGA
* * * * * * *
3032184 ACTCA-TTCTTTTCATTATGAATTTCTTTTTCTTCTTAGATAAGTTCTTCTTATTATGAGCCCTT
1 AC-AAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTGGATAAGTTCTTCTCATTATGAACCCTT
* * *
3032248 CCATTAGAAATGACGATCCACCT-CTTTCTATGATGGATTCGATCAAAATGCTGATGATGATTTA
65 CCATTAGAAATGACGATCCACCTCCTTT-TATGATGGATTCGATCAAAATGTTGATGTTGATCTA
* * * * * *
3032312 TCTCATTCTGTGATAGAACCGATCAAAA-GGTTGAACAAGTTTTTGTCATTATGAACTTTTTCTC
129 TCTCATTCTGCGATAGAATCGAGCAAAATGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTC
3032376 TCTTCT
194 -CTTCT
3032382 ATGGATGATT
Statistics
Matches: 704, Mismatches: 132, Indels: 28
0.81 0.15 0.03
Matches are distributed among these distances:
322 2 0.00
323 8 0.01
324 121 0.17
325 117 0.17
326 322 0.46
327 134 0.19
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (326 bp):
ACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTTGGATAAGTTCTTCTCATTATGAACCCTTC
CATTAGAAATGACGATCCACCTCCTTTTATGATGGATTCGATCAAAATGTTGATGTTGATCTATC
TCATTCTGCGATAGAATCGAGCAAAATGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCT
TCTTTGAACGAGTTCTTCTCATTATGAACCCTTCCATTGGAAATGACGATCCACCTCATTCTATG
TTGGATTTGATCAAAATGCTGATGTTGATCTATCTCCTTCTACGATAGAGTCGAGCAAAAGGGGG
A
Found at i:3032858 original size:103 final size:103
Alignment explanation
Indices: 3032725--3033055 Score: 448
Period size: 103 Copynumber: 3.2 Consensus size: 103
3032715 TTGAGTGAAT
* * * * * * ** * *
3032725 CAAATTTTATGTTCCAAGGGGAAACTGTCTCAAGCGATACAAAATTGATTTTAAGAAAAACAATC
1 CAAAATTTGTGTTTCAAGGGAAAAATGTCTCAAGCGAGATGAAATTGGTTTTGAGAAAAACAATC
* *
3032790 TCAAGTGAGATCTATTTGGTTTCAGGTGAAACAAATTC
66 TCAAGTAAGATCAATTTGGTTTCAGGTGAAACAAATTC
* *
3032828 CAAATTTTGTGTTTCAAGGGAAAAATGTCTCAAGCGGGATGAAATTGGTTTTGAGAAAAACAATC
1 CAAAATTTGTGTTTCAAGGGAAAAATGTCTCAAGCGAGATGAAATTGGTTTTGAGAAAAACAATC
* *
3032893 TCAAGTTAGATCAATTTGGTTTAAGGTGAAACAAATTC
66 TCAAGTAAGATCAATTTGGTTTCAGGTGAAACAAATTC
* * *
3032931 CAAAATTTGAGTTTCAAGGGAAAATTGTCTCAAGCGAGATGAAATTGGTTTTGAGAAAAATAATC
1 CAAAATTTGTGTTTCAAGGGAAAAATGTCTCAAGCGAGATGAAATTGGTTTTGAGAAAAACAATC
* * *
3032996 TCAAGTAAGATCAATTTTGTTTCAAGTGAAAC-AATTT
66 TCAAGTAAGATCAATTTGGTTTCAGGTGAAACAAATTC
3033033 CAAAATTTGTGTTTCAAAGGGAA
1 CAAAATTTGTGTTTC-AAGGGAA
3033056 CTTTTCTCAA
Statistics
Matches: 203, Mismatches: 24, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
102 18 0.09
103 185 0.91
ACGTcount: A:0.38, C:0.11, G:0.19, T:0.31
Consensus pattern (103 bp):
CAAAATTTGTGTTTCAAGGGAAAAATGTCTCAAGCGAGATGAAATTGGTTTTGAGAAAAACAATC
TCAAGTAAGATCAATTTGGTTTCAGGTGAAACAAATTC
Found at i:3035195 original size:19 final size:18
Alignment explanation
Indices: 3035170--3035217 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
3035160 CCCTCCTTTC
3035170 ATTTTTTTCTCTTTTCTCTT
1 ATTTTTTTCT-TTTTC-CTT
3035190 -TTTTTTTCTTTTTCCTT
1 ATTTTTTTCTTTTTCCTT
3035207 ATTATTTTTCT
1 ATT-TTTTTCT
3035218 ATCATTCTCC
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
17 3 0.12
18 7 0.27
19 16 0.62
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (18 bp):
ATTTTTTTCTTTTTCCTT
Found at i:3036609 original size:8 final size:9
Alignment explanation
Indices: 3036588--3036612 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3036578 TGAAATAATA
3036588 AAAAATGTC
1 AAAAATGTC
3036597 AAAAATGTC
1 AAAAATGTC
3036606 AAAAATG
1 AAAAATG
3036613 AAATAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.60, C:0.08, G:0.12, T:0.20
Consensus pattern (9 bp):
AAAAATGTC
Found at i:3039286 original size:23 final size:23
Alignment explanation
Indices: 3039227--3039326 Score: 114
Period size: 24 Copynumber: 4.3 Consensus size: 23
3039217 CACTGAAATG
3039227 CCACATA--TTTGTCCCGAAGGA
1 CCACATAGTTTTGTCCCGAAGGA
* *
3039248 CCACATAGGTTTTGTCTCGGAGGA
1 CCACATA-GTTTTGTCCCGAAGGA
* *
3039272 CCATATAGTTTTGTCCCGAATGA
1 CCACATAGTTTTGTCCCGAAGGA
* *
3039295 CCACATAGTTTTGTCCTGAAAAGA
1 CCACATAGTTTTGTCCCG-AAGGA
3039319 CCACATAG
1 CCACATAG
3039327 AACCCTCGAC
Statistics
Matches: 66, Mismatches: 9, Indels: 5
0.82 0.11 0.06
Matches are distributed among these distances:
21 7 0.11
23 29 0.44
24 30 0.45
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (23 bp):
CCACATAGTTTTGTCCCGAAGGA
Found at i:3039321 original size:47 final size:47
Alignment explanation
Indices: 3039227--3039326 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 47
3039217 CACTGAAATG
* *
3039227 CCACATA--TTTGTCCCGAAGGACCACATAGGTTTTGTCTCGGAGGA
1 CCACATAGTTTTGTCCCGAAGGACCACATAGGTTTTGTCTCGAAAGA
* *
3039272 CCATATAGTTTTGTCCCGAATGACCACATA-GTTTTGTC-CTGAAAAGA
1 CCACATAGTTTTGTCCCGAAGGACCACATAGGTTTTGTCTC-G-AAAGA
3039319 CCACATAG
1 CCACATAG
3039327 AACCCTCGAC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
45 7 0.15
46 9 0.20
47 30 0.65
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (47 bp):
CCACATAGTTTTGTCCCGAAGGACCACATAGGTTTTGTCTCGAAAGA
Found at i:3039902 original size:22 final size:22
Alignment explanation
Indices: 3039886--3039927 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
3039876 GCGATACTTC
3039886 CCATCGATGGTATCGATACCAA
1 CCATCGATGGTATCGATACCAA
*
3039908 CCATCGATGGTATTGATACC
1 CCATCGATGGTATCGATACC
3039928 CACTTTGGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.26
Consensus pattern (22 bp):
CCATCGATGGTATCGATACCAA
Found at i:3046162 original size:19 final size:20
Alignment explanation
Indices: 3046137--3046188 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
3046127 TTATTAATTT
*
3046137 AGTATCGATACTGA-AGTGG
1 AGTATCGATACTAAGAGTGG
* *
3046156 GGTATCGATACTAAGAGTTG
1 AGTATCGATACTAAGAGTGG
3046176 AGTATCGATACTA
1 AGTATCGATACTA
3046189 TTATTAAGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (20 bp):
AGTATCGATACTAAGAGTGG
Found at i:3048782 original size:39 final size:39
Alignment explanation
Indices: 3048729--3048881 Score: 202
Period size: 39 Copynumber: 4.0 Consensus size: 39
3048719 GTTTTTAAAG
**
3048729 AAGATTTTATCTCGCTTGAGATAAATTCCCTCGAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
*
3048768 AAGATTTTGTCTCGCTTGAGATAGTTTCCCTCGAAACAA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* *
3048807 AAGATTTTATTTCGCTTGAGATAGTTTCCCTTGAAAC-A
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
* * * * *
3048845 AA-ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACA
3048882 TAAACATTGA
Statistics
Matches: 102, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
37 29 0.28
38 3 0.03
39 70 0.69
ACGTcount: A:0.30, C:0.20, G:0.15, T:0.35
Consensus pattern (39 bp):
AAGATTTTATCTCGCTTGAGATAGTTTCCCTCGAAACAA
Found at i:3048964 original size:37 final size:37
Alignment explanation
Indices: 3048897--3048992 Score: 122
Period size: 37 Copynumber: 2.6 Consensus size: 37
3048887 ATTGAAAACA
** * *
3048897 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
3048933 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
* *
3048970 TTTCTCTTGAAACATAAACTTTG
1 TTTCCCTTGAAACA-AAATTTTG
3048993 AAAATGTTTC
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
36 12 0.23
37 33 0.63
38 7 0.13
ACGTcount: A:0.26, C:0.20, G:0.14, T:0.41
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:3048986 original size:102 final size:102
Alignment explanation
Indices: 3048821--3049006 Score: 345
Period size: 102 Copynumber: 1.8 Consensus size: 102
3048811 TTTTATTTCG
3048821 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
3048886 CATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
66 CATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
3048923 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
1 CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
* **
3048988 CTTTGAAAATGTTTCCCTT
66 CATTGAAAACATTTCCCTT
3049007 AAAACACAAA
Statistics
Matches: 81, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
102 81 1.00
ACGTcount: A:0.30, C:0.20, G:0.13, T:0.38
Consensus pattern (102 bp):
CTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACATAAA
CATTGAAAACATTTCCCTTGAAATGAATTTTGTCTCT
Found at i:3050571 original size:28 final size:26
Alignment explanation
Indices: 3050533--3050585 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 26
3050523 TATATATATA
*
3050533 TATTCCTTTTTATATATTTTTTATTC
1 TATTCCTTTTTATATATTTTCTATTC
* *
3050559 TATTCTCTGTTTTTTCTATTTTCTATT
1 TATTC-CT-TTTTATATATTTTCTATT
3050586 TTTATTATTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 5 0.23
27 2 0.09
28 15 0.68
ACGTcount: A:0.15, C:0.13, G:0.02, T:0.70
Consensus pattern (26 bp):
TATTCCTTTTTATATATTTTCTATTC
Found at i:3051457 original size:20 final size:20
Alignment explanation
Indices: 3051432--3051476 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
3051422 GATATATCTA
3051432 TGTATAAATTTGGATTGAAT
1 TGTATAAATTTGGATTGAAT
*
3051452 TGTATAGATTTGGATTGAAT
1 TGTATAAATTTGGATTGAAT
3051472 TGTAT
1 TGTAT
3051477 CAAAGGAATC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (20 bp):
TGTATAAATTTGGATTGAAT
Found at i:3051930 original size:25 final size:25
Alignment explanation
Indices: 3051896--3051945 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
3051886 GGACAATCTT
*
3051896 TGTGGTCCTTCAGGATAAATTTCTA
1 TGTGGTCCTTCAGGACAAATTTCTA
*
3051921 TGTGGTCCTTCGGGACAAATTTCTA
1 TGTGGTCCTTCAGGACAAATTTCTA
3051946 CACGGTACTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.38
Consensus pattern (25 bp):
TGTGGTCCTTCAGGACAAATTTCTA
Found at i:3053434 original size:23 final size:23
Alignment explanation
Indices: 3053379--3053466 Score: 104
Period size: 23 Copynumber: 3.8 Consensus size: 23
3053369 AACATATTTG
*
3053379 TCCCGAATGACCACATAGGTTTTA
1 TCCCGAAGGACCACATA-GTTTTA
* *
3053403 TCCCAAAGGACCACATAGTTTTT
1 TCCCGAAGGACCACATAGTTTTA
* *
3053426 TCCTGAAGGACCACATAGTTTTG
1 TCCCGAAGGACCACATAGTTTTA
* *
3053449 TCCCGAAAGACCATATAG
1 TCCCGAAGGACCACATAG
3053467 AACCCTCGAC
Statistics
Matches: 55, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
23 40 0.73
24 15 0.27
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (23 bp):
TCCCGAAGGACCACATAGTTTTA
Found at i:3057281 original size:2 final size:2
Alignment explanation
Indices: 3057276--3057327 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
3057266 AAAAAAAATC
3057276 AT AT 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 AT AT
3057318 AT AT AT AT AT
1 AT AT AT AT AT
3057328 TCATGGGACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3057405 original size:43 final size:45
Alignment explanation
Indices: 3057352--3057440 Score: 110
Period size: 44 Copynumber: 2.0 Consensus size: 45
3057342 TAAAATAAAC
* * * * * *
3057352 AGAAACTGAAGTGCAATAATAAAAGGAC-TAATATTAAAGTAATG
1 AGAAACTGAAGGGAAAAAATAAAAAGACAAAAAATTAAAGTAATG
3057396 AGAAA-TGAAGGGAAAAAATAAAAAGACAAAAAATTAAAGTAATG
1 AGAAACTGAAGGGAAAAAATAAAAAGACAAAAAATTAAAGTAATG
3057440 A
1 A
3057441 AATTAAAAGA
Statistics
Matches: 38, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
43 18 0.47
44 20 0.53
ACGTcount: A:0.60, C:0.04, G:0.18, T:0.18
Consensus pattern (45 bp):
AGAAACTGAAGGGAAAAAATAAAAAGACAAAAAATTAAAGTAATG
Found at i:3057443 original size:14 final size:13
Alignment explanation
Indices: 3057426--3057461 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 13
3057416 AAAAGACAAA
3057426 AAATTAAAGTAATG
1 AAATTAAAG-AATG
3057440 AAATTAAAAGAATG
1 AAATT-AAAGAATG
3057454 AAATTAAA
1 AAATTAAA
3057462 TAAATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 14 0.67
15 4 0.19
ACGTcount: A:0.64, C:0.00, G:0.11, T:0.25
Consensus pattern (13 bp):
AAATTAAAGAATG
Found at i:3057819 original size:24 final size:22
Alignment explanation
Indices: 3057758--3057819 Score: 56
Period size: 24 Copynumber: 2.6 Consensus size: 22
3057748 AGCAATAAAT
3057758 AAATAAATATAATAGTGGTTAAGA
1 AAATAAATA-AA-AGTGGTTAAGA
3057782 AAATAAA-AAGAAGTGGTTAATTTG-
1 AAATAAATAA-AAGTGGTTAA---GA
3057806 AAATAAATAAAAGT
1 AAATAAATAAAAGT
3057820 ATAATTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
22 10 0.30
23 2 0.06
24 18 0.55
25 3 0.09
ACGTcount: A:0.56, C:0.00, G:0.16, T:0.27
Consensus pattern (22 bp):
AAATAAATAAAAGTGGTTAAGA
Found at i:3060400 original size:17 final size:17
Alignment explanation
Indices: 3060375--3060414 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
3060365 TAAGATCCTT
*
3060375 TTTCTAACATGTTCCCA
1 TTTCAAACATGTTCCCA
3060392 TTTCAAACATGTTCCCA
1 TTTCAAACATGTTCCCA
3060409 TTTCAA
1 TTTCAA
3060415 GTCAAGAGAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.28, C:0.28, G:0.05, T:0.40
Consensus pattern (17 bp):
TTTCAAACATGTTCCCA
Found at i:3065193 original size:26 final size:26
Alignment explanation
Indices: 3065164--3065217 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
3065154 ACTTAGTGCA
* *
3065164 TATGGTGGGCACGACCTTATGTGTAT
1 TATGGTGGCCACGACCTTATATGTAT
*
3065190 TATGGTGGCCATGACCTTATATGTAT
1 TATGGTGGCCACGACCTTATATGTAT
3065216 TA
1 TA
3065218 GCGCTTCGGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.22, C:0.15, G:0.26, T:0.37
Consensus pattern (26 bp):
TATGGTGGCCACGACCTTATATGTAT
Found at i:3066737 original size:26 final size:28
Alignment explanation
Indices: 3066678--3066745 Score: 72
Period size: 26 Copynumber: 2.5 Consensus size: 28
3066668 TGTTCGGTTT
3066678 GTGTTTATTTAAATTTTTAATATTGTGTTC
1 GTGTTTATTT--ATTTTTAATATTGTGTTC
*
3066708 --GTTTATTTATTTTTGA-A-TGTGTTC
1 GTGTTTATTTATTTTTAATATTGTGTTC
*
3066732 GTGTTTGTTTATTT
1 GTGTTTATTTATTT
3066746 ATTGTTCGCG
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
24 7 0.21
25 1 0.03
26 18 0.53
28 8 0.24
ACGTcount: A:0.18, C:0.03, G:0.16, T:0.63
Consensus pattern (28 bp):
GTGTTTATTTATTTTTAATATTGTGTTC
Found at i:3066769 original size:23 final size:23
Alignment explanation
Indices: 3066737--3066800 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
3066727 TGTTCGTGTT
* *
3066737 TGTTTATTTATTGTTCGCGAACA
1 TGTTCATTTATTGTTCACGAACA
* * * *
3066760 TGTTCGTTTAATATTCACGAACT
1 TGTTCATTTATTGTTCACGAACA
3066783 TGTTCATTTATATGTTCA
1 TGTTCATTTAT-TGTTCA
3066801 TAAATGTGTT
Statistics
Matches: 31, Mismatches: 9, Indels: 1
0.76 0.22 0.02
Matches are distributed among these distances:
23 26 0.84
24 5 0.16
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.48
Consensus pattern (23 bp):
TGTTCATTTATTGTTCACGAACA
Found at i:3069293 original size:225 final size:224
Alignment explanation
Indices: 3068897--3069348 Score: 742
Period size: 225 Copynumber: 2.0 Consensus size: 224
3068887 ATGTTGAATG
*
3068897 TAATTAAAAATATTATCTTTATATTAATATTTTTTATTGAATCTAAAATATTACGAATAAGGTCA
1 TAATTAAAAATATTATCTTTATATTAATATTTTCTATTGAATCTAAAATATTACGAATAAGGTCA
* *
3068962 GCCAAAAATGTTATGAATAAAGTATATTTTCAGTTCAACCGAAAATATTAAAAATTTGTAACATT
66 ACCAAAAATGTTATGAAGAAAGTATATTTTCAGTTCAACCGAAAATATTAAAAATTTGTAACATT
* * * **
3069027 TTAAGTTACGCTCAATCTAAAATGTCATGATTTTTATTACATTTTCAGTTACGTCTTAGAATCGC
131 TTAAGTTACACTCAATCTAAAATGTCATGATTTGTATTACATTTTCAGTTACATCCCAGAATCGC
3069092 CGCTTTTAAATCGTAAATTAGACTGTTGT
196 CGCTTTTAAATCGTAAATTAGACTGTTGT
* * *
3069121 TAATTTAAAATATTATCTTTATGTTAATATTTTCTATTGAATCTAAAATATTATGAATAAGGTCA
1 TAATTAAAAATATTATCTTTATATTAATATTTTCTATTGAATCTAAAATATTACGAATAAGGTCA
* *
3069186 ACCAAAAATGTTATGAAGAATGTAATATTTTCGGTTCAACCGAAAATATTAAAAATTTGTAACAT
66 ACCAAAAATGTTATGAAGAAAGT-ATATTTTCAGTTCAACCGAAAATATTAAAAATTTGTAACAT
* *
3069251 TTTAGGTTACACTCAATCTAAAATGTCATGATTTGTATTACATTTTCGGTTACATCCCAGAATCG
130 TTTAAGTTACACTCAATCTAAAATGTCATGATTTGTATTACATTTTCAGTTACATCCCAGAATCG
* *
3069316 CCTCTTTTAAATCTTAAATTAGACTGTTGT
195 CCGCTTTTAAATCGTAAATTAGACTGTTGT
3069346 TAA
1 TAA
3069349 ACTTCTTCCC
Statistics
Matches: 210, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
224 81 0.39
225 129 0.61
ACGTcount: A:0.37, C:0.12, G:0.11, T:0.40
Consensus pattern (224 bp):
TAATTAAAAATATTATCTTTATATTAATATTTTCTATTGAATCTAAAATATTACGAATAAGGTCA
ACCAAAAATGTTATGAAGAAAGTATATTTTCAGTTCAACCGAAAATATTAAAAATTTGTAACATT
TTAAGTTACACTCAATCTAAAATGTCATGATTTGTATTACATTTTCAGTTACATCCCAGAATCGC
CGCTTTTAAATCGTAAATTAGACTGTTGT
Found at i:3069732 original size:3 final size:3
Alignment explanation
Indices: 3069724--3069794 Score: 76
Period size: 3 Copynumber: 24.3 Consensus size: 3
3069714 CATTATATTG
* *
3069724 TAT TAT TA- TAT TAT TAC TAT TAT TAT TGT TAT TAT TAT TAT TAT T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
3069770 TAT TAA T-T TAT ATAT TAT AAT TAT T
1 TAT TAT TAT TAT -TAT TAT TAT TAT T
3069795 TTTGCAAGCC
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
2 5 0.09
3 48 0.86
4 3 0.05
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3069772 original size:26 final size:25
Alignment explanation
Indices: 3069726--3069796 Score: 81
Period size: 26 Copynumber: 2.8 Consensus size: 25
3069716 TTATATTGTA
* *
3069726 TTATTA-TATTATTACTATTATTATT
1 TTATTATTATTATTA-TTTTATTAAT
3069751 GTTATTATTATTATTATTTTATTAAT
1 -TTATTATTATTATTATTTTATTAAT
*
3069777 TTATATATTATAATTATTTT
1 TTAT-TATTATTATTATTTT
3069797 TGCAAGCCCC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
25 4 0.10
26 28 0.70
27 8 0.20
ACGTcount: A:0.32, C:0.01, G:0.01, T:0.65
Consensus pattern (25 bp):
TTATTATTATTATTATTTTATTAAT
Found at i:3071481 original size:64 final size:63
Alignment explanation
Indices: 3071399--3071555 Score: 172
Period size: 64 Copynumber: 2.5 Consensus size: 63
3071389 TTCAGTGTGT
* * * *
3071399 ATCGATGCACAGGAAGTGCATCGATGCACCCATTAAAAATGGAAATATCGAATACAATTAGTGC
1 ATCGATGCATAGGAAGTGCATCGATGCACCCATT-AAAATGAAAACATCGAAGACAATTAGTGC
* *** * *
3071463 ATCGATGCATAAGG-AGTGCATCGATGCACCCCCTTAAAATGAAAACATCGAAGGTGATTTGTGT
1 ATCGATGCAT-AGGAAGTGCATCGATGCA-CCCATTAAAATGAAAACATCGAAGACAATTAGTGC
* *
3071527 ATCGATGCATGGGTAGTGCATCGATGCAC
1 ATCGATGCATAGGAAGTGCATCGATGCAC
3071556 TTCAAGTGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
63 3 0.04
64 68 0.86
65 8 0.10
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.24
Consensus pattern (63 bp):
ATCGATGCATAGGAAGTGCATCGATGCACCCATTAAAATGAAAACATCGAAGACAATTAGTGC
Found at i:3072681 original size:19 final size:21
Alignment explanation
Indices: 3072642--3072682 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
3072632 TGAATACAAG
3072642 TATAGGAAAATGATATATATA
1 TATAGGAAAATGATATATATA
*
3072663 TATAGGAAGATGA-AT-TATA
1 TATAGGAAAATGATATATATA
3072682 T
1 T
3072683 GAATACACAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.17, T:0.34
Consensus pattern (21 bp):
TATAGGAAAATGATATATATA
Found at i:3072736 original size:2 final size:2
Alignment explanation
Indices: 3072729--3072762 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3072719 GAACATGGGA
3072729 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
3072763 GATAAGACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3077347 original size:64 final size:64
Alignment explanation
Indices: 3077162--3077454 Score: 464
Period size: 63 Copynumber: 4.6 Consensus size: 64
3077152 TGCAGCTTTT
* * * *
3077162 AGAGTCAATTTCAACTTCACAGCGAAGGATATTTGACTCAACAAACAACTTTTCAGTTTCATTT
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
3077226 AGAGTCAATTTCAACTTCAC-ACGAAGGATATTGGACTCAACAAATAACTTTCTAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* * * *
3077289 AGAGTCAATTTCGACTTCACAACGAATGATACTAGACTCAACAAACAACTTTCCAGTTTCATTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
* *
3077353 AGAGTCAATTTCAACTTCAGAACGAAGGATATTGGACTCAACAAACAAC-TTCCAGTTTCAATC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
3077416 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
3077455 GAAACAATGC
Statistics
Matches: 209, Mismatches: 19, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
63 107 0.51
64 102 0.49
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (64 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTC
Found at i:3077454 original size:127 final size:127
Alignment explanation
Indices: 3077162--3077454 Score: 462
Period size: 127 Copynumber: 2.3 Consensus size: 127
3077152 TGCAGCTTTT
* * * *
3077162 AGAGTCAATTTCAACTTCACAGCGAAGGATATTTGACTCAACAAACAACTTTTCAGTTTCATTTA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAACAAACAACTTTCCAGTTTCATTCA
* * * *
3077227 GAGTCAATTTCAACTTCACACGAAGGATATTGGACTCAACAAATAACTTTCTAGTTTCATTC
66 GAGTCAATTTCAACTTCAAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCAATC
* * *
3077289 AGAGTCAATTTCGACTTCACAACGAATGATACTAGACTCAACAAACAACTTTCCAGTTTCATTCA
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAACAAACAACTTTCCAGTTTCATTCA
3077354 GAGTCAATTTCAACTTCAGAACGAAGGATATTGGACTCAACAAACAAC-TTCCAGTTTCAATC
66 GAGTCAATTTCAACTTCA-AACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCAATC
*
3077416 AGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTC
1 AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTC
3077455 GAAACAATGC
Statistics
Matches: 150, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
127 123 0.82
128 27 0.18
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (127 bp):
AGAGTCAATTTCAACTTCACAACGAAGGATATTAGACTCAACAAACAACTTTCCAGTTTCATTCA
GAGTCAATTTCAACTTCAAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCAATC
Found at i:3077639 original size:121 final size:121
Alignment explanation
Indices: 3077478--3077940 Score: 592
Period size: 121 Copynumber: 3.8 Consensus size: 121
3077468 TTACACGAGA
* *
3077478 TTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAC
*
3077543 CCACG-TTTCAACTTCAAGACGAAGGATATCGTGCCCACAAACAACAATGCAACCC
66 CCACGATTTCAACTTCAAGACGAAGGATATCGTGCCCACAAGCAACAATGCAACCC
*** *
3077598 TTGGATTTCAACTTTCACGGTGAAATATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCA
1 TTGGATTTCAAC-TTCACAACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCA
* * * * * *
3077663 TCCATGATTTTAACTTCACGACGAAGGATATCATGCCCACAAGCAGCAATGCAACCC
65 CCCACGATTTCAACTTCAAGACGAAGGATATCGTGCCCACAAGCAACAATGCAACCC
* * * *
3077720 TTGGATTTCAACTTCACAATGAAGGATATCCAATTCAAAGCTCAAATTCACAACGAATGAGCAAC
1 TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAC
* * * * * *
3077785 CCACGATTTCAACTTCATGACGATGGATATTGTGCCCACAAGCAAC-ATACATCTCTAGA
66 CCACGATTTCAACTTCAAGACGAAGGATATCGTGCCCACAAGCAACAATGCAAC-C---C
* * *
3077844 TTGGATTTCAACTTCACAACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAA-GAAGTCA
1 TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATG-AGCCA
*
3077908 CCCACGATTTCAACTTCACA-AAGAAGGATATCG
65 CCCACGATTTCAACTTCA-AGACGAAGGATATCG
3077941 GGCTCAATGG
Statistics
Matches: 300, Mismatches: 35, Indels: 12
0.86 0.10 0.03
Matches are distributed among these distances:
120 17 0.06
121 140 0.47
122 57 0.19
123 1 0.00
124 85 0.28
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (121 bp):
TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAC
CCACGATTTCAACTTCAAGACGAAGGATATCGTGCCCACAAGCAACAATGCAACCC
Found at i:3077728 original size:242 final size:243
Alignment explanation
Indices: 3077478--3077939 Score: 626
Period size: 245 Copynumber: 1.9 Consensus size: 243
3077468 TTACACGAGA
* * * *
3077478 TTGGATTTCAACTTCACGACGAAAGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCAT
1 TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAAGCTCAAATTCACAACGAATGAGCAAC
* *
3077543 CCACG-TTTCAACTTCAAGACGAAGGATATCGTGCCCACAAACAACAATGCAAC-C-CTTGGATT
66 CCACGATTTCAACTTCAAGACGAAGGATATCGTGCCCACAAACAAC-ATACAACTCAATTGGATT
*** * * * *
3077605 TCAACTTTCACGGTGAAATATATCCAATTCAAAGCTCAACTTCACAACGAATG-AGCCATCCATG
130 TCAAC-TTCACAACGAAAGATATCCAATTCAAAACTCAACTTCACAACGAA-GAAGCCACCCACG
* * *
3077669 ATTTTAACTTCACGACGAAGGATATCATGCCCACAAGCAGCAATGCAACCC
193 ATTTCAACTTCACAAAGAAGGATATCATGCCCACAAGCAGCAATGCAACCC
* *
3077720 TTGGATTTCAACTTCACAATGAAGGATATCCAATTCAAAGCTCAAATTCACAACGAATGAGCAAC
1 TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAAGCTCAAATTCACAACGAATGAGCAAC
* * * * *
3077785 CCACGATTTCAACTTCATGACGATGGATATTGTGCCCACAAGCAACATACATCTCTAGATTGGAT
66 CCACGATTTCAACTTCAAGACGAAGGATATCGTGCCCACAAACAACATACAACTC-A-ATTGGAT
* *
3077850 TTCAACTTCACAACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAAGAAGTCACCCACGA
129 TTCAACTTCACAACGAAAGATATCCAATTCAAAACTCAACTTCACAACGAAGAAGCCACCCACGA
3077915 TTTCAACTTCACAAAGAAGGATATC
194 TTTCAACTTCACAAAGAAGGATATC
3077940 GGGCTCAATG
Statistics
Matches: 189, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
242 69 0.37
243 37 0.20
244 1 0.01
245 70 0.37
246 12 0.06
ACGTcount: A:0.37, C:0.26, G:0.14, T:0.23
Consensus pattern (243 bp):
TTGGATTTCAACTTCACAACGAAAGATATCCAATTCAAAGCTCAAATTCACAACGAATGAGCAAC
CCACGATTTCAACTTCAAGACGAAGGATATCGTGCCCACAAACAACATACAACTCAATTGGATTT
CAACTTCACAACGAAAGATATCCAATTCAAAACTCAACTTCACAACGAAGAAGCCACCCACGATT
TCAACTTCACAAAGAAGGATATCATGCCCACAAGCAGCAATGCAACCC
Found at i:3078144 original size:3 final size:3
Alignment explanation
Indices: 3078109--3078194 Score: 70
Period size: 3 Copynumber: 29.0 Consensus size: 3
3078099 CTACAAAAAC
* * * *
3078109 ATT A-T ATT A-T ATT ATT ACT ATT AAT ATT GTT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
3078155 GTT ATT ATT ATT ATTT ATT AAT -TT ATAT ATT ATA ATT ATT
1 ATT ATT ATT ATT A-TT ATT ATT ATT AT-T ATT ATT ATT ATT
3078195 TTTGCAGGCC
Statistics
Matches: 64, Mismatches: 14, Indels: 10
0.73 0.16 0.11
Matches are distributed among these distances:
2 5 0.08
3 53 0.83
4 6 0.09
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:3083103 original size:64 final size:64
Alignment explanation
Indices: 3083002--3083295 Score: 453
Period size: 64 Copynumber: 4.6 Consensus size: 64
3082992 AGCTTTTAGG
* *
3083002 GTCAATTTCAACTTCACAGCGAAGGATGTTGGACTCAACAAACAACTTTCCAGTTTCATTCAGA
1 GTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAGA
* *
3083066 GTCAATTTCAACTTCACAGCGAAGGATATTGGACTCAACAAATAACTTTCCAGTTTCATTCAGA
1 GTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAGA
* * * *
3083130 GTCAATTTCAACTTTACAACGAAGGATACTGGACTCAACAAACAACTTTCTAGTTTCATTTAGA
1 GTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAGA
* * *
3083194 GTCCATTTCAACTTCACAACAAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCAATCAGA
1 GTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAGA
** * *
3083258 GTCAATTTCAACTTCACATTGAAGGATAATAGACTCAA
1 GTCAATTTCAACTTCACAACGAAGGATATTGGACTCAA
3083296 AACAATGAAA
Statistics
Matches: 209, Mismatches: 21, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 209 1.00
ACGTcount: A:0.36, C:0.22, G:0.13, T:0.29
Consensus pattern (64 bp):
GTCAATTTCAACTTCACAACGAAGGATATTGGACTCAACAAACAACTTTCCAGTTTCATTCAGA
Found at i:3084957 original size:22 final size:22
Alignment explanation
Indices: 3084903--3084974 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
3084893 AGTCGAGGGT
*
3084903 TTCATAGGTCCTTCGGGAC-CA
1 TTCATAGGTCCTTCGGGACAAA
*
3084924 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
3084946 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
3084968 TTTCATA
1 -TTCATA
3084975 TGCCACTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 18 0.41
22 21 0.48
23 5 0.11
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:3085809 original size:25 final size:23
Alignment explanation
Indices: 3085768--3085816 Score: 55
Period size: 25 Copynumber: 2.0 Consensus size: 23
3085758 TTGGTATGGT
*
3085768 AATGAGTATGTTGTTTTGCTAATAG
1 AATGAGTATGTTATTTT--TAATAG
3085793 AATGA-TATGTTTATTTTTAATAG
1 AATGAGTATG-TTATTTTTAATAG
3085816 A
1 A
3085817 TGTCCGGACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 7 0.32
24 4 0.18
25 11 0.50
ACGTcount: A:0.33, C:0.02, G:0.18, T:0.47
Consensus pattern (23 bp):
AATGAGTATGTTATTTTTAATAG
Found at i:3091845 original size:22 final size:22
Alignment explanation
Indices: 3091791--3091862 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
3091781 AGTCGAGGGT
*
3091791 TTCATAGGTCCTTCGGGAC-CA
1 TTCATAGGTCCTTCGGGACAAA
*
3091812 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
3091834 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
3091856 TTTCATA
1 -TTCATA
3091863 TGCCACTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 18 0.41
22 21 0.48
23 5 0.11
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:3092761 original size:121 final size:121
Alignment explanation
Indices: 3092545--3093049 Score: 744
Period size: 121 Copynumber: 4.2 Consensus size: 121
3092535 GTGTTACACG
* *
3092545 ATTTCATCTTCACGACGAAGGATATCGTGCCCACAAGCAGTAATGCAACCCTTGGATTTCAACTT
1 ATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAACTT
** * * * *
3092610 CACAACGAAAAATATCCACTTCAAAGCTCAACTTCACAATGAAGGAGCCATCCACA
66 CACAACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAATGAGCCATCCACA
3092666 ATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAACTT
1 ATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAACTT
* *
3092731 CACAACGAAGGATATCCAATTCAAAACTCAAATTCACAACGAATGAGCCATCCACG
66 CACAACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAATGAGCCATCCACA
* * * * *
3092787 ATTTTAACTTCACGACGAAGAATATCGTGCCCACAAACAACAATACAACCCTTGGATTTCAACTT
1 ATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAACTT
* * * *
3092852 CACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCACG
66 CACAACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAATGAGCCATCCACA
* * *
3092908 ATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGC-ATCCATCTCTAGATTGGATTTCA
1 ATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAAC-C---CTTGGATTTCA
*
3092972 ACTTCACAACGAAGGATATCCAATTC-AAACTCAACTTCACAACGAATGAGCCACCCACA
62 ACTTCACAACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAATGAGCCATCCACA
*
3093031 ATTTCAACTTCACAACGAA
1 ATTTCAACTTCACGACGAA
3093050 TGAGTCACCC
Statistics
Matches: 348, Mismatches: 32, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
120 5 0.01
121 261 0.75
123 48 0.14
124 34 0.10
ACGTcount: A:0.36, C:0.28, G:0.14, T:0.22
Consensus pattern (121 bp):
ATTTCAACTTCACGACGAAGGATATCGTGCCCACAAGCAGCAATGCAACCCTTGGATTTCAACTT
CACAACGAAGGATATCCAATTCAAAACTCAACTTCACAACGAATGAGCCATCCACA
Found at i:3092798 original size:66 final size:65
Alignment explanation
Indices: 3092720--3092933 Score: 209
Period size: 66 Copynumber: 3.4 Consensus size: 65
3092710 GCAACCCTTG
*
3092720 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAACTCAAATTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTC-AAACTCAAATTCACAACGAATGAGCCATCCA
3092785 C
65 C
* * * * * *
3092786 GATTTTAACTTCACGACGAAGAATAT-C-GTGC---C-CACAA---ACAAC-AAT-A-CAACCCT
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAACTCA-AATTCACAACGAATGAGCCATCC-
**
3092839 TG
64 AC
* *
3092841 GATTTCAACTTCACGATGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCCA
1 GATTTCAACTTCACGACGAAGGATATCCAATTCAAA-CTCAAATTCACAACGAATGAGCCATCCA
3092906 C
65 C
3092907 GATTTCAACTTCACGACGAAGGATATC
1 GATTTCAACTTCACGACGAAGGATATC
3092934 GTGCCCACAA
Statistics
Matches: 113, Mismatches: 20, Indels: 30
0.69 0.12 0.18
Matches are distributed among these distances:
54 4 0.04
55 24 0.21
56 4 0.04
57 7 0.06
59 2 0.02
60 3 0.03
61 2 0.02
62 2 0.02
64 7 0.06
65 4 0.04
66 50 0.44
67 4 0.04
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.22
Consensus pattern (65 bp):
GATTTCAACTTCACGACGAAGGATATCCAATTCAAACTCAAATTCACAACGAATGAGCCATCCAC
Found at i:3093043 original size:32 final size:32
Alignment explanation
Indices: 3093002--3093075 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
3092992 CAATTCAAAC
3093002 TCAACTTCACAACGAATGAGCCACCCACAATT
1 TCAACTTCACAACGAATGAGCCACCCACAATT
*
3093034 TCAACTTCACAACGAATGAGTCACCCACAATT
1 TCAACTTCACAACGAATGAGCCACCCACAATT
3093066 TCAACTTCAC
1 TCAACTTCAC
3093076 GAAGAAGGAT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.36, C:0.34, G:0.08, T:0.22
Consensus pattern (32 bp):
TCAACTTCACAACGAATGAGCCACCCACAATT
Found at i:3093282 original size:3 final size:3
Alignment explanation
Indices: 3093262--3093325 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
3093252 GAAAACAGTA
* * *
3093262 TAT TA- TAT TAT TAC TAT TAT TAT TGT TAT TAT TAT TATT TAT TAA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT
*
3093307 T-T TAT ATAT TAT AAT TAT T
1 TAT TAT -TAT TAT TAT TAT T
3093326 TTTGCAGGCC
Statistics
Matches: 49, Mismatches: 8, Indels: 8
0.75 0.12 0.12
Matches are distributed among these distances:
2 3 0.06
3 40 0.82
4 6 0.12
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:3096976 original size:10 final size:10
Alignment explanation
Indices: 3096961--3096998 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
3096951 TTTTGTGAGG
3096961 TTACTATTTA
1 TTACTATTTA
3096971 TTACTATTTA
1 TTACTATTTA
*
3096981 TTACTATTCA
1 TTACTATTTA
3096991 TTACTATT
1 TTACTATT
3096999 CACGTGAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (10 bp):
TTACTATTTA
Found at i:3102197 original size:21 final size:21
Alignment explanation
Indices: 3102163--3102203 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3102153 ATGTGTTTGA
*
3102163 ATATAAATATAA-TTCTTTAT
1 ATATAAATAAAATTTCTTTAT
3102183 ATATACAATAAAATTTCTTTA
1 ATATA-AATAAAATTTCTTTA
3102204 AAAAAAACTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 6 0.33
22 7 0.39
ACGTcount: A:0.46, C:0.07, G:0.00, T:0.46
Consensus pattern (21 bp):
ATATAAATAAAATTTCTTTAT
Found at i:3103478 original size:50 final size:50
Alignment explanation
Indices: 3103403--3103754 Score: 614
Period size: 50 Copynumber: 7.0 Consensus size: 50
3103393 ATAAAAAAAA
3103403 TTAAGATATTGAACTCATATGGGGCAACTCAAGTCACAAGAGATGAAATC
1 TTAAGATATTGAACTCATATGGGGCAACTCAAGTCACAAGAGATGAAATC
* * *
3103453 TTAAGATATTGATCTCATATGGGGCAACTCAAGACACACGAGATGAAATC
1 TTAAGATATTGAACTCATATGGGGCAACTCAAGTCACAAGAGATGAAATC
*
3103503 TTAAGATATTGAACTCATATTGGGCAACTCAAGTCACAAGAGATGAAATC
1 TTAAGATATTGAACTCATATGGGGCAACTCAAGTCACAAGAGATGAAATC
* *
3103553 TTAAGATATTGATCTCATATGGGGCAACTCAAGACACAAGAGATGAAATC
1 TTAAGATATTGAACTCATATGGGGCAACTCAAGTCACAAGAGATGAAATC
*
3103603 TTAAGATATTGAACTCATATTGGGCAACTCAAGTCACAAGAGATGAAATC
1 TTAAGATATTGAACTCATATGGGGCAACTCAAGTCACAAGAGATGAAATC
* *
3103653 TTAAGATATTGATCTCATATGGGGCAACTCAAGACACAAGAGATGAAATC
1 TTAAGATATTGAACTCATATGGGGCAACTCAAGTCACAAGAGATGAAATC
*
3103703 TTAAGATATTGAACTCATATTGGGCAACTCAAGTCACAAGAGATGAAATC
1 TTAAGATATTGAACTCATATGGGGCAACTCAAGTCACAAGAGATGAAATC
3103753 TT
1 TT
3103755 TACCCAAAAA
Statistics
Matches: 283, Mismatches: 19, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 283 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (50 bp):
TTAAGATATTGAACTCATATGGGGCAACTCAAGTCACAAGAGATGAAATC
Found at i:3103576 original size:100 final size:100
Alignment explanation
Indices: 3103403--3103754 Score: 686
Period size: 100 Copynumber: 3.5 Consensus size: 100
3103393 ATAAAAAAAA
*
3103403 TTAAGATATTGAACTCATATGGGGCAACTCAAGTCACAAGAGATGAAATCTTAAGATATTGATCT
1 TTAAGATATTGAACTCATATTGGGCAACTCAAGTCACAAGAGATGAAATCTTAAGATATTGATCT
*
3103468 CATATGGGGCAACTCAAGACACACGAGATGAAATC
66 CATATGGGGCAACTCAAGACACAAGAGATGAAATC
3103503 TTAAGATATTGAACTCATATTGGGCAACTCAAGTCACAAGAGATGAAATCTTAAGATATTGATCT
1 TTAAGATATTGAACTCATATTGGGCAACTCAAGTCACAAGAGATGAAATCTTAAGATATTGATCT
3103568 CATATGGGGCAACTCAAGACACAAGAGATGAAATC
66 CATATGGGGCAACTCAAGACACAAGAGATGAAATC
3103603 TTAAGATATTGAACTCATATTGGGCAACTCAAGTCACAAGAGATGAAATCTTAAGATATTGATCT
1 TTAAGATATTGAACTCATATTGGGCAACTCAAGTCACAAGAGATGAAATCTTAAGATATTGATCT
3103668 CATATGGGGCAACTCAAGACACAAGAGATGAAATC
66 CATATGGGGCAACTCAAGACACAAGAGATGAAATC
3103703 TTAAGATATTGAACTCATATTGGGCAACTCAAGTCACAAGAGATGAAATCTT
1 TTAAGATATTGAACTCATATTGGGCAACTCAAGTCACAAGAGATGAAATCTT
3103755 TACCCAAAAA
Statistics
Matches: 250, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 250 1.00
ACGTcount: A:0.39, C:0.16, G:0.19, T:0.25
Consensus pattern (100 bp):
TTAAGATATTGAACTCATATTGGGCAACTCAAGTCACAAGAGATGAAATCTTAAGATATTGATCT
CATATGGGGCAACTCAAGACACAAGAGATGAAATC
Found at i:3107102 original size:13 final size:13
Alignment explanation
Indices: 3107084--3107109 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3107074 TATTGCAGTC
3107084 GATGCAGGTACAA
1 GATGCAGGTACAA
3107097 GATGCAGGTACAA
1 GATGCAGGTACAA
3107110 CACTCGTGCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.31, T:0.15
Consensus pattern (13 bp):
GATGCAGGTACAA
Found at i:3108625 original size:2 final size:2
Alignment explanation
Indices: 3108550--3108605 Score: 103
Period size: 2 Copynumber: 27.5 Consensus size: 2
3108540 CTCTTGACTC
3108550 TA TA TGA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3108593 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
3108606 TACATATGAA
Statistics
Matches: 53, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 51 0.96
3 2 0.04
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3121598 original size:23 final size:22
Alignment explanation
Indices: 3121554--3121610 Score: 55
Period size: 21 Copynumber: 2.5 Consensus size: 22
3121544 TTTAATTATA
*
3121554 TTTTTTATTTATTTACTATATT
1 TTTTTTATATATTTACTATATT
3121576 CCTTTTTTATATA-TTA-TATTATT
1 --TTTTTTATATATTTACTA-TATT
*
3121599 TTTATTATATAT
1 TTTTTTATATAT
3121611 ATCTTATATC
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
21 10 0.34
22 2 0.07
23 7 0.24
24 10 0.34
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.68
Consensus pattern (22 bp):
TTTTTTATATATTTACTATATT
Found at i:3121601 original size:20 final size:19
Alignment explanation
Indices: 3121548--3121610 Score: 63
Period size: 20 Copynumber: 3.1 Consensus size: 19
3121538 TATATTTTTA
*
3121548 ATTATATTTTTTATTTATTT
1 ATTATATTTTTT-TTTATAT
* *
3121568 ACTATATTCCTTTTTTATAT
1 ATTATATT-TTTTTTTATAT
3121588 ATTATATTATTTTTATTATAT
1 ATTATATT-TTTTT-TTATAT
3121609 AT
1 AT
3121611 ATCTTATATC
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
20 24 0.69
21 11 0.31
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (19 bp):
ATTATATTTTTTTTTATAT
Found at i:3121617 original size:25 final size:27
Alignment explanation
Indices: 3121583--3121640 Score: 75
Period size: 25 Copynumber: 2.2 Consensus size: 27
3121573 ATTCCTTTTT
* *
3121583 TATATATTATATTATT-TTTAT-TATA
1 TATATATTATATCATTATATATATATA
*
3121608 TATATCTTATATCATTATATATATATA
1 TATATATTATATCATTATATATATATA
3121635 TATATA
1 TATATA
3121641 GACGTATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 14 0.52
26 4 0.15
27 9 0.33
ACGTcount: A:0.40, C:0.03, G:0.00, T:0.57
Consensus pattern (27 bp):
TATATATTATATCATTATATATATATA
Found at i:3121690 original size:12 final size:12
Alignment explanation
Indices: 3121670--3121712 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
3121660 ATTTACTATG
3121670 TATATATTTTCT
1 TATATATTTTCT
*
3121682 TATACATTTT-T
1 TATATATTTTCT
3121693 ATATATATTTTCT
1 -TATATATTTTCT
3121706 TA-ATATT
1 TATATATT
3121713 CTATTTCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
11 6 0.22
12 20 0.74
13 1 0.04
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.63
Consensus pattern (12 bp):
TATATATTTTCT
Found at i:3121764 original size:16 final size:17
Alignment explanation
Indices: 3121728--3121782 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 17
3121718 TCTGTTTTTA
*
3121728 TTTATTTATA-TA-TAT
1 TTTATTTTTACTATTAT
*
3121743 TATATTTTTACT-TTAT
1 TTTATTTTTACTATTAT
*
3121759 TTTATTTTTTCTATTAT
1 TTTATTTTTACTATTAT
3121776 TTT-TTTT
1 TTTATTTT
3121783 CTTAATATCA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
15 8 0.24
16 18 0.55
17 7 0.21
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTATTTTTACTATTAT
Found at i:3121767 original size:17 final size:17
Alignment explanation
Indices: 3121723--3121782 Score: 54
Period size: 17 Copynumber: 3.5 Consensus size: 17
3121713 CTATTTCTGT
*
3121723 TTTTATTTATTTA-TATA
1 TTTTATTT-TTTACTTTA
*
3121740 TATTATATTTTTACTTTA
1 TTTTAT-TTTTTACTTTA
3121758 TTTTATTTTTT-CTATTA
1 TTTTATTTTTTACT-TTA
3121775 TTTT-TTTT
1 TTTTATTTT
3121783 CTTAATATCA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.16
17 21 0.57
18 10 0.27
ACGTcount: A:0.22, C:0.03, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTATTTTTTACTTTA
Found at i:3121773 original size:25 final size:25
Alignment explanation
Indices: 3121716--3121773 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
3121706 TAATATTCTA
*
3121716 TTTCTGTTTTTATTTATTTATATAT
1 TTTCTATTTTTATTTATTTATATAT
* * *
3121741 ATTATATTTTTACTTTATTT-TATTT
1 TTTCTATTTTTA-TTTATTTATATAT
3121766 TTTCTATT
1 TTTCTATT
3121774 ATTTTTTTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
25 19 0.73
26 7 0.27
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.72
Consensus pattern (25 bp):
TTTCTATTTTTATTTATTTATATAT
Found at i:3122010 original size:15 final size:14
Alignment explanation
Indices: 3121978--3122020 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 14
3121968 TTTCAACATT
3121978 TTATTCATTTTGTTTA
1 TTATT-ATTTT-TTTA
*
3121994 TTTTTATTGTTTTTA
1 TTATTATT-TTTTTA
3122009 TTATTATTTTTT
1 TTATTATTTTTT
3122021 ACGTGTTTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
14 4 0.17
15 14 0.58
16 6 0.25
ACGTcount: A:0.16, C:0.02, G:0.05, T:0.77
Consensus pattern (14 bp):
TTATTATTTTTTTA
Found at i:3125699 original size:33 final size:32
Alignment explanation
Indices: 3125656--3125727 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
3125646 CAAAGAAAAG
* ** * *
3125656 AATAATAATAAATTAACGATAACAAGTAAATTA
1 AATAAAAATAAAGAAACGA-AACAAATAAATAA
*
3125689 AATAAAAATAAAGAAACGAAATAAATAAATAA
1 AATAAAAATAAAGAAACGAAACAAATAAATAA
3125721 AATAAAA
1 AATAAAA
3125728 GACATAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 17 0.52
33 16 0.48
ACGTcount: A:0.69, C:0.04, G:0.06, T:0.21
Consensus pattern (32 bp):
AATAAAAATAAAGAAACGAAACAAATAAATAA
Found at i:3125740 original size:22 final size:22
Alignment explanation
Indices: 3125692--3125743 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
3125682 TAAATTAAAT
*
3125692 AAAAAT-AAAGAAACGAAATAA
1 AAAAATAAAAGAAAAGAAATAA
* * *
3125713 ATAAATAAAATAAAAGACATAA
1 AAAAATAAAAGAAAAGAAATAA
3125735 AAAAATAAA
1 AAAAATAAA
3125744 GTCCATAAAG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 5 0.20
22 20 0.80
ACGTcount: A:0.77, C:0.04, G:0.06, T:0.13
Consensus pattern (22 bp):
AAAAATAAAAGAAAAGAAATAA
Found at i:3125938 original size:2 final size:2
Alignment explanation
Indices: 3125933--3125977 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
3125923 AAAATAGTAA
3125933 AT AT 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 AT AT
3125975 AT A
1 AT A
3125978 AATTAATAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3126084 original size:23 final size:24
Alignment explanation
Indices: 3126045--3126090 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
3126035 ATATACTAAA
3126045 GTAAAAAAGAAAATACAT-AAAAT
1 GTAAAAAAGAAAATACATGAAAAT
*
3126068 GTAAAAAA-AATATTACATGAAAA
1 GTAAAAAAGAA-AATACATGAAAA
3126091 AAGAAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 2 0.10
23 14 0.70
24 4 0.20
ACGTcount: A:0.67, C:0.04, G:0.09, T:0.20
Consensus pattern (24 bp):
GTAAAAAAGAAAATACATGAAAAT
Found at i:3127275 original size:36 final size:36
Alignment explanation
Indices: 3127225--3127334 Score: 118
Period size: 36 Copynumber: 3.1 Consensus size: 36
3127215 AAAGATTGAA
3127225 GTTTCAATGA-AAACTGTCTCAAGAGAGACAAAATTT
1 GTTTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTT
* *
3127261 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAA--A
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
* * * * * *
3127295 CTTCCAAAAGAAACTGTCTCAAGGGAGACGAGATTT
1 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
3127331 GTTT
1 GTTT
3127335 AACGTAAAAC
Statistics
Matches: 59, Mismatches: 12, Indels: 6
0.77 0.16 0.08
Matches are distributed among these distances:
34 26 0.44
35 2 0.03
36 31 0.53
ACGTcount: A:0.41, C:0.15, G:0.19, T:0.25
Consensus pattern (36 bp):
GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTT
Found at i:3127307 original size:34 final size:35
Alignment explanation
Indices: 3127235--3127323 Score: 108
Period size: 34 Copynumber: 2.5 Consensus size: 35
3127225 GTTTCAATGA
** * *
3127235 AAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAG
1 AAACTGTCTCAAGAGAGACAAAA-TACTTCCAAAAG
*
3127271 AAACTATCTCAAGAGAGACAAAA-ACTTCCAAAAG
1 AAACTGTCTCAAGAGAGACAAAATACTTCCAAAAG
*
3127305 AAACTGTCTCAAGGGAGAC
1 AAACTGTCTCAAGAGAGAC
3127324 GAGATTTGTT
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
34 24 0.52
36 22 0.48
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.19
Consensus pattern (35 bp):
AAACTGTCTCAAGAGAGACAAAATACTTCCAAAAG
Found at i:3127384 original size:30 final size:30
Alignment explanation
Indices: 3127348--3127406 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 30
3127338 GTAAAACATA
*
3127348 TTCAAAGATTT-TGTTTCATAG-GAAACTGTT
1 TTCAAAG-TTTATGCTTCA-AGAGAAACTGTT
3127378 TTCAAAGTTTATGCTTCAAGAGAAACTGT
1 TTCAAAGTTTATGCTTCAAGAGAAACTGT
3127407 ATCAAGGGAG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
29 5 0.19
30 21 0.81
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.39
Consensus pattern (30 bp):
TTCAAAGTTTATGCTTCAAGAGAAACTGTT
Found at i:3127581 original size:102 final size:102
Alignment explanation
Indices: 3127368--3127729 Score: 419
Period size: 102 Copynumber: 3.6 Consensus size: 102
3127358 TTGTTTCATA
* * * *
3127368 GGAAACTGTTTTCAAAGTTTATGCTTCAAGAGAAACTGTATCAAGGGAGACAAAA-TTTGTTTCA
1 GGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCA
* *
3127432 AGGGAAACTATCTCATGAGTGACAAAATTCATTTCAA-
66 AGGG-AACTATCTCAAGAGAGACAAAATTCATTTCAAG
* * * * *
3127469 GGAAAATGTTTTCAATGTTTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCA
1 GGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCA
*
3127534 AGGGAACTTATCTCAAGAGAGACAAAATTCATCTCAAG
66 AGGGAAC-TATCTCAAGAGAGACAAAATTCATTTCAAG
* * * *
3127572 GGAAA-TGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCA
1 GGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTC-
* * * * * * **
3127636 AAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAG
65 AAGGGAACTATCTCAAGAGAGACAAAATTCATTTCAAG
* *
3127674 GGAAACAG-ATTCAAAGATTT-TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
1 GGAAACTGTTTTCAAAG-TTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
3127730 CATTTCAAGA
Statistics
Matches: 228, Mismatches: 27, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
101 53 0.23
102 161 0.71
103 14 0.06
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (102 bp):
GGAAACTGTTTTCAAAGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCA
AGGGAACTATCTCAAGAGAGACAAAATTCATTTCAAG
Found at i:3127779 original size:64 final size:65
Alignment explanation
Indices: 3127638--3127793 Score: 199
Period size: 64 Copynumber: 2.4 Consensus size: 65
3127628 TAGTTCCAAA
* * ** *
3127638 AGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATTCAAAGATTTTGTTTCAAG
1 AGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGAGAAACAGATTCAAAGATTTTGTTTCAAG
* * * * *
3127703 AGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAA-TGTTTCAATG-TTTATGTTTCAA
1 AGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGAGAAACAGATTCAAAGATTT-TGTTTCAA
3127766 G
65 G
3127767 AGAAACTGTCTCAAGGGAGACAAAATT
1 AGAAACTGTCTCAAGGGAGACAAAATT
3127794 TTGTTTCAAG
Statistics
Matches: 78, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
63 3 0.04
64 41 0.53
65 34 0.44
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (65 bp):
AGAAACTGTCTCAAGGGAGACAAAATTCATTTCAAGAGAAACAGATTCAAAGATTTTGTTTCAAG
Found at i:3127795 original size:268 final size:269
Alignment explanation
Indices: 3127423--3127941 Score: 907
Period size: 268 Copynumber: 1.9 Consensus size: 269
3127413 GGAGACAAAA
* * *
3127423 TTTGTTTCAAGGGAAACTATCTCATGAGTGACAAAATTCATTTCAAGGAAAATGTTTTCAATGTT
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGAAAATGTTTTCAATGTT
*
3127488 TATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACTTATCTCAAGAG
66 TATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATCTCAAGAG
3127553 AGACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAG
131 AGACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAG
*
3127618 AGACAAAACTTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGA
196 AGACAAAACCTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGA
3127683 TTCAAAGAT
261 TTCAAAGAT
3127692 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAA-GAGAAATG-TTTCAATGT
1 TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGA-AAATGTTTTCAATGT
*
3127755 TTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATCTCAAGA
65 TTATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATCTCAAGA
* * * *
3127820 GAGACAAAATTCATTTTAAGGGAAATTTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGA
130 GAGACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGA
* *
3127885 GAGACGAAACCTAGTTCTAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAG
195 GAGACAAAACCTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAG
3127942 AGAGACAAGA
Statistics
Matches: 237, Mismatches: 12, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
268 189 0.80
269 48 0.20
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (269 bp):
TTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGGAAAATGTTTTCAATGTT
TATATTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATCTCAAGAG
AGACAAAATTCATCTCAAGGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAG
AGACAAAACCTAGTTCCAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGA
TTCAAAGAT
Found at i:3127816 original size:37 final size:37
Alignment explanation
Indices: 3127758--3127830 Score: 110
Period size: 37 Copynumber: 2.0 Consensus size: 37
3127748 TCAATGTTTA
* *
3127758 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
* *
3127795 TGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATT
3127831 CATTTTAAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:3127818 original size:166 final size:167
Alignment explanation
Indices: 3127519--3127889 Score: 480
Period size: 166 Copynumber: 2.2 Consensus size: 167
3127509 TCAAGGGAGA
* *
3127519 CAAA-ATTTTGTTTCAAG-GGAACTTATCTCAAGAGAGACAAAATTCATCTCAAGGGAAATGTTT
1 CAAAGATTTTGTTTCAAGAGAAAC-TATCTCAAGAGAGACAAAATTCATCTCAAGAGAAATGTTT
*
3127582 TCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATGT
65 TCAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATAT
* * **
3127647 CTCAAGGGAGACGAAATTTGTTTCAAGGGAAACAGATT
130 CTCAAGAGAGACAAAATTCATTTCAAGGGAAACAGATT
*
3127685 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATG-TTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATCTCAAGAGAAATGTTTT
* * * * * ** **
3127749 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGGGAACCTATC
66 CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATATC
* ****
3127814 TCAAGAGAGACAAAATTCATTTTAAGGGAAATTTTTT
131 TCAAGAGAGACAAAATTCATTTCAAGGGAAACAGATT
* *
3127851 CAATG-TTTATGTTTCAAGAGAAACTGTCTCAAGAGAGAC
1 CAAAGATTT-TGTTTCAAGAGAAACTATCTCAAGAGAGAC
3127890 GAAACCTAGT
Statistics
Matches: 178, Mismatches: 24, Indels: 6
0.86 0.12 0.03
Matches are distributed among these distances:
165 3 0.02
166 123 0.69
167 48 0.27
168 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.29
Consensus pattern (167 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATCTCAAGAGAAATGTTTT
CAATGTTTATGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAAATATC
TCAAGAGAGACAAAATTCATTTCAAGGGAAACAGATT
Found at i:3127824 original size:101 final size:103
Alignment explanation
Indices: 3127685--3127889 Score: 342
Period size: 101 Copynumber: 2.0 Consensus size: 103
3127675 GAAACAGATT
3127685 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAA-TGTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATTGTTT
*
3127749 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGA
66 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
* * * * *
3127787 CAAA-ATTTTGTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCATTTTAAGGGAAATTTTTT
1 CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATTGTTT
3127851 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
66 CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
3127889 C
1 C
3127890 GAAACCTAGT
Statistics
Matches: 96, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 50 0.52
102 46 0.48
ACGTcount: A:0.38, C:0.13, G:0.18, T:0.31
Consensus pattern (103 bp):
CAAAGATTTTGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATTGTTT
CAATGTTTATGTTTCAAGAGAAACTGTCTCAAGAGAGA
Found at i:3127918 original size:102 final size:101
Alignment explanation
Indices: 3127695--3127944 Score: 304
Period size: 102 Copynumber: 2.5 Consensus size: 101
3127685 CAAAGATTTT
* *
3127695 GTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATGTTTCAATGTTTATG
1 GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATGTTTCAATGTTTATG
* ** *
3127760 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
66 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACCTA
** ** * * *
3127796 GTTTCAAGGGAACCTATCTCAAGAGAGACAAAATTCATTTTAAGGGAAATTTTTTCAATGTTTAT
1 GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGAGAAA-TGTTTCAATGTTTAT
*
3127861 GTTTCAAGAGAAACTGTCTCAAGAGAGACGAAACCTA
65 GTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACCTA
* * * **
3127898 G-TTCTAAAAGAAAATGTCTCAAGGGAGACGAAATTTGTTTCAAGAGA
1 GTTTC-AAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGAGA
3127945 GACAAGATTT
Statistics
Matches: 126, Mismatches: 21, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
101 48 0.38
102 78 0.62
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (101 bp):
GTTTCAAAAGAAAATATCTCAAGAGAGACAAAATTCATTTCAAGAGAAATGTTTCAATGTTTATG
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAACCTA
Found at i:3133108 original size:11 final size:11
Alignment explanation
Indices: 3133088--3133121 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3133078 ATAATGGTGA
3133088 AAATAATAAAT
1 AAATAATAAAT
*
3133099 AAATAGTAAAT
1 AAATAATAAAT
3133110 AAATAAATAAAT
1 AAAT-AATAAAT
3133122 GCAAGAGGGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 14 0.70
12 6 0.30
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:3133347 original size:23 final size:22
Alignment explanation
Indices: 3133287--3133353 Score: 59
Period size: 23 Copynumber: 3.0 Consensus size: 22
3133277 ATGTGTAATC
3133287 TAAAAAAATATATATAC-T-AAAG
1 TAAAAAAA-ATAT-TACATAAAAG
*
3133309 TAAAAAAGAA-AATACATAAAATG
1 TAAAAAA-AATATTACATAAAA-G
3133332 TAAAAAAAATATTACATGAAAA
1 TAAAAAAAATATTACAT-AAAA
3133354 AAAAGAAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 3 0.08
21 2 0.05
22 13 0.35
23 15 0.41
24 4 0.11
ACGTcount: A:0.67, C:0.04, G:0.06, T:0.22
Consensus pattern (22 bp):
TAAAAAAAATATTACATAAAAG
Found at i:3143723 original size:23 final size:21
Alignment explanation
Indices: 3143684--3143725 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 21
3143674 TTTAATTATA
*
3143684 TTTTTTTATTTACTATATTCC
1 TTTTTTTATTTAATATATTCC
3143705 TTTTTTTATTTATAATATATT
1 TTTTTTTA-TT-TAATATATT
3143726 ATATTTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 2 0.11
23 8 0.44
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (21 bp):
TTTTTTTATTTAATATATTCC
Found at i:3143734 original size:20 final size:20
Alignment explanation
Indices: 3143709--3143763 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
3143699 TATTCCTTTT
3143709 TTTATT-TATAATATATTATA
1 TTTATTATAT-ATATATTATA
*
3143729 TTTATTATATATATCTTATA
1 TTTATTATATATATATTATA
*
3143749 -TCATTATATATATAT
1 TTTATTATATATATAT
3143764 ATACGTATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 13 0.42
20 15 0.48
21 3 0.10
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (20 bp):
TTTATTATATATATATTATA
Found at i:3143754 original size:19 final size:20
Alignment explanation
Indices: 3143714--3143763 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
3143704 CTTTTTTTAT
*
3143714 TTATA-ATATATTATATTTA
1 TTATATATATATTATATTCA
*
3143733 TTATATATATCTTATA-TCA
1 TTATATATATATTATATTCA
3143752 TTATATATATAT
1 TTATATATATAT
3143764 ATACGTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
19 18 0.67
20 9 0.33
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (20 bp):
TTATATATATATTATATTCA
Found at i:3143901 original size:17 final size:18
Alignment explanation
Indices: 3143876--3143912 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
3143866 TATACATATA
3143876 TTATATTTTTACT-TTATT
1 TTATATTTTT-CTATTATT
3143894 TTAT-TTTTTCTATTATT
1 TTATATTTTTCTATTATT
3143911 TT
1 TT
3143913 TTTCTTAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 2 0.11
17 12 0.67
18 4 0.22
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTATATTTTTCTATTATT
Found at i:3150233 original size:25 final size:24
Alignment explanation
Indices: 3150173--3150252 Score: 142
Period size: 24 Copynumber: 3.3 Consensus size: 24
3150163 GTTTATTATC
3150173 ATTATTTGAAAAAATATTATACTA
1 ATTATTTGAAAAAATATTATACTA
3150197 ATTATTTGAAAAAATATTATACTA
1 ATTATTTGAAAAAATATTATACTA
*
3150221 ATTATTTGAAAAAAATATTATATTA
1 ATTATTTG-AAAAAATATTATACTA
3150246 ATTATTT
1 ATTATTT
3150253 TCAATTAATT
Statistics
Matches: 54, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
24 32 0.59
25 22 0.41
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.45
Consensus pattern (24 bp):
ATTATTTGAAAAAATATTATACTA
Found at i:3152277 original size:111 final size:111
Alignment explanation
Indices: 3152029--3152279 Score: 439
Period size: 111 Copynumber: 2.3 Consensus size: 111
3152019 GTTTTTTGGA
*
3152029 GTTACCGTATCAACAAAGTGTCGAGATATTTAATTCTTAATCTAATAATCATGCATTAAATATAT
1 GTTACCGTATCAACAAAGTGTCGAGATATTTAATTCTTAATCTAATAATCATGCATTAAATAAAT
*
3152094 CAACTAATTATTACTAATAATTTAAATTAAATTAAAACGTTAAAAT
66 CAACTAAATATTACTAATAATTTAAATTAAATTAAAACGTTAAAAT
* * * *
3152140 ATTACCGTATCAGCAAAATATCGAGATATTTAATTCTTAATCTAATAATCATGCATTAAATAAAT
1 GTTACCGTATCAACAAAGTGTCGAGATATTTAATTCTTAATCTAATAATCATGCATTAAATAAAT
3152205 CAACTAAATATTACTAATAATTTAAATTAAATTAAAACGTTAAAAT
66 CAACTAAATATTACTAATAATTTAAATTAAATTAAAACGTTAAAAT
*
3152251 GTTACCGTATCAACAAAGTGTAGAGATAT
1 GTTACCGTATCAACAAAGTGTCGAGATAT
3152280 ATGATTTCCA
Statistics
Matches: 129, Mismatches: 11, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 129 1.00
ACGTcount: A:0.45, C:0.12, G:0.08, T:0.35
Consensus pattern (111 bp):
GTTACCGTATCAACAAAGTGTCGAGATATTTAATTCTTAATCTAATAATCATGCATTAAATAAAT
CAACTAAATATTACTAATAATTTAAATTAAATTAAAACGTTAAAAT
Found at i:3152417 original size:12 final size:10
Alignment explanation
Indices: 3152403--3152442 Score: 55
Period size: 10 Copynumber: 4.0 Consensus size: 10
3152393 ACCTTAAAAA
*
3152403 GAGAGTATTT
1 GAGAGAATTT
3152413 GAGAGAAATTT
1 GAGAG-AATTT
3152424 -AGAGAATTT
1 GAGAGAATTT
3152433 GAGAGAATTT
1 GAGAGAATTT
3152443 AGTGTGATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
9 5 0.19
10 18 0.67
11 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.28, T:0.33
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:3152432 original size:20 final size:19
Alignment explanation
Indices: 3152404--3152444 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 19
3152394 CCTTAAAAAG
*
3152404 AGAGTATTTGAGAGAAATTT
1 AGAGAATTTGAGAG-AATTT
3152424 AGAGAATTTGAGAGAATTT
1 AGAGAATTTGAGAGAATTT
3152443 AG
1 AG
3152445 TGTGATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 7 0.35
20 13 0.65
ACGTcount: A:0.41, C:0.00, G:0.27, T:0.32
Consensus pattern (19 bp):
AGAGAATTTGAGAGAATTT
Found at i:3152681 original size:50 final size:50
Alignment explanation
Indices: 3152564--3152684 Score: 154
Period size: 50 Copynumber: 2.4 Consensus size: 50
3152554 AGATACGCAG
* * *
3152564 GTATAGTGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
1 GTATAGCGCGGATCAGGGGGCACGATATACCCACGTGGCGCCAAATCACC
* ** *
3152614 GTAT-GTCGTGGGGCAGGGGGCACGATATACCCACGTGGCGCCAAATCAGC
1 GTATAG-CGCGGATCAGGGGGCACGATATACCCACGTGGCGCCAAATCACC
*
3152664 GTATAGCGCGGTTCAGGGGGC
1 GTATAGCGCGGATCAGGGGGC
3152685 GTGCTTTACT
Statistics
Matches: 59, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
49 1 0.02
50 57 0.97
51 1 0.02
ACGTcount: A:0.21, C:0.26, G:0.36, T:0.17
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGGGCACGATATACCCACGTGGCGCCAAATCACC
Found at i:3153285 original size:29 final size:30
Alignment explanation
Indices: 3153252--3153324 Score: 87
Period size: 29 Copynumber: 2.4 Consensus size: 30
3153242 CTACTGTATT
3153252 ATTATACCATTGAACTTTTAATTTT-G-TCA
1 ATTATACCATTGAAC-TTTAATTTTAGTTCA
* * *
3153281 ATTATAGCACTGAACTTTGATTTTAGTTTCA
1 ATTATACCATTGAACTTTAATTTTAG-TTCA
3153312 ATTATACCATTGA
1 ATTATACCATTGA
3153325 TTTGTTAAAT
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
28 8 0.22
29 14 0.39
31 14 0.39
ACGTcount: A:0.32, C:0.14, G:0.10, T:0.45
Consensus pattern (30 bp):
ATTATACCATTGAACTTTAATTTTAGTTCA
Found at i:3156645 original size:21 final size:21
Alignment explanation
Indices: 3156619--3156675 Score: 105
Period size: 21 Copynumber: 2.7 Consensus size: 21
3156609 TTTTATACTG
3156619 GGTGTACCGATACCCTTTGAA
1 GGTGTACCGATACCCTTTGAA
*
3156640 GGTGTATCGATACCCTTTGAA
1 GGTGTACCGATACCCTTTGAA
3156661 GGTGTACCGATACCC
1 GGTGTACCGATACCC
3156676 CTACGCTCCC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 34 1.00
ACGTcount: A:0.23, C:0.25, G:0.25, T:0.28
Consensus pattern (21 bp):
GGTGTACCGATACCCTTTGAA
Found at i:3161241 original size:20 final size:20
Alignment explanation
Indices: 3161216--3161258 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
3161206 TCTAAGAGCC
3161216 CATTTAGGACCATATAGATG
1 CATTTAGGACCATATAGATG
* *
3161236 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
3161256 CAT
1 CAT
3161259 GTGGTGGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.21, T:0.33
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:3166196 original size:20 final size:20
Alignment explanation
Indices: 3166171--3166213 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
3166161 TCTAAGAGCC
3166171 CATTTAGAACCATATAGATG
1 CATTTAGAACCATATAGATG
* * *
3166191 CATTTAGGAGCATATAGTTG
1 CATTTAGAACCATATAGATG
3166211 CAT
1 CAT
3166214 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (20 bp):
CATTTAGAACCATATAGATG
Found at i:3171251 original size:13 final size:13
Alignment explanation
Indices: 3171222--3171256 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
3171212 GGGGAGTAAT
*
3171222 TTTTCAAAATTGA
1 TTTTCAAAAATGA
3171235 -TTTCAAAAATGA
1 TTTTCAAAAATGA
3171247 TTTTCAAAAA
1 TTTTCAAAAA
3171257 GAAAATCTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
TTTTCAAAAATGA
Found at i:3171389 original size:19 final size:19
Alignment explanation
Indices: 3171357--3171396 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
3171347 ATTAATGAAT
* *
3171357 TTTAAGATTTTATACTCGA
1 TTTAAAATTATATACTCGA
*
3171376 TTTAAAATTATATATTCGA
1 TTTAAAATTATATACTCGA
3171395 TT
1 TT
3171397 AAATTATTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.35, C:0.07, G:0.07, T:0.50
Consensus pattern (19 bp):
TTTAAAATTATATACTCGA
Found at i:3173515 original size:8 final size:8
Alignment explanation
Indices: 3173502--3173687 Score: 65
Period size: 8 Copynumber: 27.0 Consensus size: 8
3173492 AATGAAATTT
3173502 ATATTTAA
1 ATATTTAA
3173510 ATATTTAA
1 ATATTTAA
3173518 ATA---AA
1 ATATTTAA
3173523 A-A-TTAA
1 ATATTTAA
*
3173529 AGATTT--
1 ATATTTAA
3173535 A-ATTTAA
1 ATATTTAA
*
3173542 ATATTAAA
1 ATATTTAA
3173550 ATATTTAA
1 ATATTTAA
* *
3173558 AAAGATTAA
1 ATA-TTTAA
*
3173567 AGATTT--
1 ATATTTAA
3173573 A-ATTTAA
1 ATATTTAA
3173580 ATATTTAA
1 ATATTTAA
3173588 ATA-TTAA
1 ATATTTAA
3173595 A-A--TAA
1 ATATTTAA
*
3173600 A-ATTTCA
1 ATATTTAA
*
3173607 ATAATTAA
1 ATATTTAA
3173615 A-A--TAA
1 ATATTTAA
*
3173620 A-ATTTCA
1 ATATTTAA
*
3173627 ATAATTAA
1 ATATTTAA
3173635 ATA-TTAA
1 ATATTTAA
3173642 A-A--TAA
1 ATATTTAA
3173647 A-ATTTAA
1 ATATTTAA
3173654 ATA-TTAA
1 ATATTTAA
3173661 ATA-TTAA
1 ATATTTAA
3173668 A-A--TAA
1 ATATTTAA
3173673 A-ATTTAA
1 ATATTTAA
3173680 ATATTTAA
1 ATATTTAA
3173688 TCATTAAATC
Statistics
Matches: 143, Mismatches: 12, Indels: 46
0.71 0.06 0.23
Matches are distributed among these distances:
4 1 0.01
5 31 0.22
6 8 0.06
7 40 0.28
8 57 0.40
9 6 0.04
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.40
Consensus pattern (8 bp):
ATATTTAA
Found at i:3173549 original size:27 final size:27
Alignment explanation
Indices: 3173535--3173695 Score: 129
Period size: 26 Copynumber: 5.8 Consensus size: 27
3173525 TTAAAGATTT
3173535 AATTTAAATATTAAAATATTTAAAAAGATTAA
1 AATTTAAATATT-AAATA-TTAAA-A-A-TAA
*
3173567 AGATTT-AAT-TTAAATATTTAAATATTAA
1 A-ATTTAAATATTAAATA-TTAAA-AATAA
* *
3173595 AA-TAAAAT-TTCAATAATT-AAAATAA
1 AATTTAAATATTAAAT-ATTAAAAATAA
*
3173620 AATTTCAATAATTAAATATT-AAAATAA
1 AATTTAAAT-ATTAAATATTAAAAATAA
3173647 AATTTAAATATTAAATATT-AAAATAA
1 AATTTAAATATTAAATATTAAAAATAA
*
3173673 AATTTAAATATTTAATCATTAAA
1 AATTTAAATATTAAAT-ATTAAA
3173696 TCATTATTAA
Statistics
Matches: 111, Mismatches: 10, Indels: 20
0.79 0.07 0.14
Matches are distributed among these distances:
25 6 0.05
26 39 0.35
27 32 0.29
28 12 0.11
30 12 0.11
31 2 0.02
32 4 0.04
33 4 0.04
ACGTcount: A:0.58, C:0.02, G:0.01, T:0.39
Consensus pattern (27 bp):
AATTTAAATATTAAATATTAAAAATAA
Found at i:3173566 original size:38 final size:38
Alignment explanation
Indices: 3173502--3173688 Score: 150
Period size: 38 Copynumber: 4.9 Consensus size: 38
3173492 AATGAAATTT
3173502 ATATTTAAATATTTAAATAAAAATTAAAGATTTAATTTAA
1 ATATTTAAATATTT-AA-AAAAATTAAAGATTTAATTTAA
* *
3173542 ATATTAAAATATTTAAAAAGATTAAAGATTTAATTTAA
1 ATATTTAAATATTTAAAAAAATTAAAGATTTAATTTAA
* * * * **
3173580 ATATTTAAATATTAAAATAAAATTTCAATAATTAAAATAA
1 ATATTTAAATATTTAAA-AAAA-TTAAAGATTTAATTTAA
* * * **
3173620 A-ATTTCAATAATT--AAATATTAAA-ATAAAATTTAA
1 ATATTTAAATATTTAAAAAAATTAAAGATTTAATTTAA
* *
3173654 ATA-TTAAATATTAAAATAAAATTTAAATATTTAAT
1 ATATTTAAATATTTAAA-AAAA-TTAAAGATTTAAT
3173689 CATTAAATCA
Statistics
Matches: 113, Mismatches: 26, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
34 14 0.12
35 5 0.04
36 4 0.04
37 4 0.04
38 41 0.36
39 19 0.17
40 26 0.23
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (38 bp):
ATATTTAAATATTTAAAAAAATTAAAGATTTAATTTAA
Found at i:3173600 original size:20 final size:20
Alignment explanation
Indices: 3173502--3173684 Score: 90
Period size: 19 Copynumber: 9.7 Consensus size: 20
3173492 AATGAAATTT
*
3173502 ATATTTAAATATTTAAATAA
1 ATATTTAAATATTAAAATAA
* * **
3173522 A-AATTAAAGATTTAATTTAA
1 ATATTTAAATA-TTAAAATAA
* *
3173542 ATATTAAAATATT-TAA-AA
1 ATATTTAAATATTAAAATAA
* * **
3173560 AGA-TTAAAGATTTAATTTAA
1 ATATTTAAATA-TTAAAATAA
3173580 ATATTTAAATATTAAAATAA
1 ATATTTAAATATTAAAATAA
*
3173600 A-ATTTCAATAATTAAAATAA
1 ATATTTAAAT-ATTAAAATAA
* *
3173620 A-ATTT-CA-A-T-AATTAA
1 ATATTTAAATATTAAAATAA
3173635 ATA-TTAAA-A-TAAAATTTAA
1 ATATTTAAATATTAAAA--TAA
3173654 ATA-TTAAATATTAAAATAA
1 ATATTTAAATATTAAAATAA
3173673 A-ATTTAAATATT
1 ATATTTAAATATT
3173685 TAATCATTAA
Statistics
Matches: 122, Mismatches: 26, Indels: 31
0.68 0.15 0.17
Matches are distributed among these distances:
15 8 0.07
16 5 0.04
17 8 0.07
18 7 0.06
19 39 0.32
20 38 0.31
21 17 0.14
ACGTcount: A:0.57, C:0.01, G:0.02, T:0.40
Consensus pattern (20 bp):
ATATTTAAATATTAAAATAA
Found at i:3173642 original size:47 final size:48
Alignment explanation
Indices: 3173573--3173670 Score: 146
Period size: 47 Copynumber: 2.1 Consensus size: 48
3173563 TTAAAGATTT
* *
3173573 AATTTAAATATTTAAATATTAAAATAAAATTTCAATAATTAAA-A-TAA
1 AATTTAAATAATTAAATATTAAAATAAAATTTAAAT-ATTAAATATTAA
*
3173620 AATTTCAATAATTAAATATTAAAATAAAATTTAAATATTAAATATTAA
1 AATTTAAATAATTAAATATTAAAATAAAATTTAAATATTAAATATTAA
3173668 AAT
1 AAT
3173671 AAAATTTAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
46 6 0.13
47 34 0.74
48 6 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (48 bp):
AATTTAAATAATTAAATATTAAAATAAAATTTAAATATTAAATATTAA
Found at i:3173687 original size:20 final size:20
Alignment explanation
Indices: 3173504--3173687 Score: 117
Period size: 20 Copynumber: 9.7 Consensus size: 20
3173494 TGAAATTTAT
3173504 ATTTAAATATTT-AAATAAA
1 ATTTAAATATTTAAAATAAA
* * **
3173523 AATTAAAGATTTAATTTAAA
1 ATTTAAATATTTAAAATAAA
* *
3173543 TATTAAAATATTT-AAA-AAG
1 -ATTTAAATATTTAAAATAAA
* **
3173562 A-TTAAAGATTTAATTTAAA
1 ATTTAAATATTTAAAATAAA
3173581 TATTTAAATA-TTAAAATAAA
1 -ATTTAAATATTTAAAATAAA
* *
3173601 ATTTCAATAATTAAAATAAA
1 ATTTAAATATTTAAAATAAA
* *
3173621 ATTTCAATAATTAAATATTAAA
1 ATTTAAATATTTAAA-A-TAAA
3173643 A--TAAA-ATTT-AAAT---
1 ATTTAAATATTTAAAATAAA
3173656 A-TTAAATA-TTAAAATAAA
1 ATTTAAATATTTAAAATAAA
3173674 ATTTAAATATTTAA
1 ATTTAAATATTTAA
3173688 TCATTAAATC
Statistics
Matches: 127, Mismatches: 21, Indels: 33
0.70 0.12 0.18
Matches are distributed among these distances:
13 1 0.01
14 6 0.05
15 5 0.04
16 1 0.01
17 9 0.07
18 5 0.04
19 32 0.25
20 47 0.37
21 16 0.13
22 5 0.04
ACGTcount: A:0.58, C:0.01, G:0.02, T:0.40
Consensus pattern (20 bp):
ATTTAAATATTTAAAATAAA
Found at i:3173696 original size:26 final size:26
Alignment explanation
Indices: 3173573--3173695 Score: 150
Period size: 26 Copynumber: 4.8 Consensus size: 26
3173563 TTAAAGATTT
3173573 AATTTAAATATTTAAATATTAAAATAA
1 AATTTAAATA-TTAAATATTAAAATAA
*
3173600 AATTT-CA-A-T--A-ATTAAAATAA
1 AATTTAAATATTAAATATTAAAATAA
*
3173620 AATTTCAATAATTAAATATTAAAATAA
1 AATTTAAAT-ATTAAATATTAAAATAA
3173647 AATTTAAATATTAAATATTAAAATAA
1 AATTTAAATATTAAATATTAAAATAA
*
3173673 AATTTAAATATTTAATCATTAAA
1 AATTTAAATATTAAAT-ATTAAA
3173696 TCATTATTAA
Statistics
Matches: 84, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
20 15 0.18
21 2 0.02
23 2 0.02
24 1 0.01
25 1 0.01
26 34 0.40
27 29 0.35
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (26 bp):
AATTTAAATATTAAATATTAAAATAA
Found at i:3173697 original size:8 final size:7
Alignment explanation
Indices: 3173506--3173701 Score: 103
Period size: 6 Copynumber: 28.4 Consensus size: 7
3173496 AAATTTATAT
3173506 TTAAATA
1 TTAAATA
3173513 TTTAAATA
1 -TTAAATA
3173521 --AAA-A
1 TTAAATA
*
3173525 TTAAAGA
1 TTAAATA
*
3173532 TTTAAT-
1 TTAAATA
3173538 TTAAATA
1 TTAAATA
3173545 TTAAAATA
1 TT-AAATA
*
3173553 TTTAAAAAGA
1 -TT--AAATA
*
3173563 TTAAAGA
1 TTAAATA
*
3173570 TTTAAT-
1 TTAAATA
3173576 TTAAATA
1 TTAAATA
3173583 TTTAAATA
1 -TTAAATA
3173591 TTAAA-A
1 TTAAATA
*
3173597 TAAAAT-
1 TTAAATA
*
3173603 TTCAATAA
1 TTAAAT-A
3173611 TTAAA-A
1 TTAAATA
*
3173617 TAAAAT-
1 TTAAATA
*
3173623 TTCAATAA
1 TTAAAT-A
3173631 TTAAATA
1 TTAAATA
3173638 TTAAA-A
1 TTAAATA
*
3173644 TAAAAT-
1 TTAAATA
3173650 TTAAATA
1 TTAAATA
3173657 TTAAATA
1 TTAAATA
3173664 TTAAA-A
1 TTAAATA
*
3173670 TAAAAT-
1 TTAAATA
3173676 TTAAATA
1 TTAAATA
*
3173683 TTTAATCA
1 TTAAAT-A
3173691 TTAAATCA
1 TTAAAT-A
3173699 TTA
1 TTA
3173702 TTAAAACATC
Statistics
Matches: 147, Mismatches: 21, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
4 1 0.01
5 3 0.02
6 51 0.35
7 44 0.30
8 39 0.27
9 4 0.03
10 5 0.03
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.40
Consensus pattern (7 bp):
TTAAATA
Found at i:3173706 original size:11 final size:11
Alignment explanation
Indices: 3173690--3173860 Score: 85
Period size: 11 Copynumber: 13.8 Consensus size: 11
3173680 ATATTTAATC
3173690 ATTAAATCATT
1 ATTAAATCATT
* *
3173701 ATTAAAACATC
1 ATTAAATCATT
* *
3173712 ATTAGTAGTAATT
1 ATTA--AATCATT
3173725 ATTATAATTTCATT
1 ATTA-AA--TCATT
3173739 ATTAGTAATCATT
1 ATTA--AATCATT
*
3173752 ACTAAATCATT
1 ATTAAATCATT
3173763 AGTATGAAATCATT
1 A-T-T-AAATCATT
*
3173777 A-AAAAT-ATTT
1 ATTAAATCA-TT
3173787 AAATTAATAATCATT
1 --ATT-A-AATCATT
3173802 ATTAAATCATT
1 ATTAAATCATT
3173813 ATTAGTAATCATT
1 ATTA--AATCATT
3173826 ATTAAATCATT
1 ATTAAATCATT
3173837 AGTATCAAATCATT
1 A-T-T-AAATCATT
3173851 AATTAAATCA
1 -ATTAAATCA
3173861 ATAGAGTCGT
Statistics
Matches: 127, Mismatches: 12, Indels: 41
0.71 0.07 0.23
Matches are distributed among these distances:
9 1 0.01
10 6 0.05
11 40 0.31
12 11 0.09
13 32 0.25
14 27 0.21
15 9 0.07
16 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.04, T:0.42
Consensus pattern (11 bp):
ATTAAATCATT
Found at i:3173728 original size:24 final size:23
Alignment explanation
Indices: 3173701--3173840 Score: 93
Period size: 24 Copynumber: 5.7 Consensus size: 23
3173691 TTAAATCATT
*
3173701 ATTAAAACATCATTAGTAGTAATT
1 ATTAAAA-ATCATTAGTAGTAATC
** *
3173725 ATTATAATTTCATTATTAGTAATC
1 ATTA-AAAATCATTAGTAGTAATC
* *
3173749 ATTACTAAATCATTAGTATGAAATC
1 ATTA-AAAATCATTAGTA-GTAATC
* *
3173774 ATTAAAAAT-ATTTAAATTAATAATC
1 ATTAAAAATCA-TT--AGTAGTAATC
* *
3173799 ATTATTAAATCATTATTAGTAATC
1 ATTA-AAAATCATTAGTAGTAATC
*
3173823 ATTATTAAATCATTAGTA
1 ATTA-AAAATCATTAGTA
3173841 TCAAATCATT
Statistics
Matches: 92, Mismatches: 17, Indels: 14
0.75 0.14 0.11
Matches are distributed among these distances:
23 1 0.01
24 62 0.67
25 19 0.21
26 9 0.10
27 1 0.01
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (23 bp):
ATTAAAAATCATTAGTAGTAATC
Found at i:3174040 original size:24 final size:24
Alignment explanation
Indices: 3174005--3174067 Score: 90
Period size: 24 Copynumber: 2.6 Consensus size: 24
3173995 ACTGTCAAAT
* **
3174005 GAGTATCAATACTGTTATATAGAG
1 GAGTATCGATACTACTATATAGAG
3174029 GAGTATCGATACTACTATATAGAG
1 GAGTATCGATACTACTATATAGAG
*
3174053 TAGTATCGATACTAC
1 GAGTATCGATACTAC
3174068 ATTATGGTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.32
Consensus pattern (24 bp):
GAGTATCGATACTACTATATAGAG
Found at i:3174409 original size:24 final size:24
Alignment explanation
Indices: 3174382--3174697 Score: 137
Period size: 24 Copynumber: 12.4 Consensus size: 24
3174372 CAAATCATTT
3174382 ATCATTATTAAATCATTATTAGTA
1 ATCATTATTAAATCATTATTAGTA
* *
3174406 ATCATTATTATCAAATCATTAAATATTA
1 ATCATTA-T-T-AAATCATT-ATTAGTA
* * *
3174434 TTAAATTAGT-AATCATTATTA--A
1 AT-CATTATTAAATCATTATTAGTA
* *
3174456 ATCATTATTAGTAATTATTATAATTTGTA
1 ATCATTATTA--AATCA-T-T-ATTAGTA
*
3174485 ATCATTATGAAATCATTATTAGTAA
1 ATCATTATTAAATCATTATTAGT-A
*
3174510 AT-ATTA-TAATTTCATTATTAGTAGTA
1 ATCATTATTAA-ATCATTA-T--TAGTA
3174536 ATCATTATTAAATCATTATTAGTA
1 ATCATTATTAAATCATTATTAGTA
* *
3174560 ATTATTATTAAATCATTAGTA-TCA
1 ATCATTATTAAATCATTATTAGT-A
* *
3174584 ATTCATTA--AATTATTATTATTATTAA
1 A-TCATTATTAA--ATCATTATTAGT-A
* * *
3174610 ATCATTAGT-AATTATTATTAAATCA
1 ATCATTATTAAATCATTATT-AGT-A
*
3174635 TATCACATTGATTAAATCATTACTAGTA
1 -AT--CATT-ATTAAATCATTATTAGTA
* * * *
3174663 ATTATTATTAAATCAATATCATTAA
1 ATCATTATTAAATCATTATTAGT-A
3174688 ATCATTATTA
1 ATCATTATTA
3174698 TTAAATCATT
Statistics
Matches: 223, Mismatches: 35, Indels: 67
0.69 0.11 0.21
Matches are distributed among these distances:
21 5 0.02
22 2 0.01
23 5 0.02
24 77 0.35
25 49 0.22
26 13 0.06
27 32 0.14
28 14 0.06
29 18 0.08
30 8 0.04
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (24 bp):
ATCATTATTAAATCATTATTAGTA
Found at i:3174424 original size:14 final size:13
Alignment explanation
Indices: 3174382--3174426 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
3174372 CAAATCATTT
3174382 ATCATTA-T-TAA
1 ATCATTATTATAA
3174393 ATCATTATTAGT-A
1 ATCATTATTA-TAA
3174406 ATCATTATTATCAA
1 ATCATTATTAT-AA
3174420 ATCATTA
1 ATCATTA
3174427 AATATTATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 7 0.24
12 2 0.07
13 11 0.38
14 9 0.31
ACGTcount: A:0.42, C:0.11, G:0.02, T:0.44
Consensus pattern (13 bp):
ATCATTATTATAA
Found at i:3174434 original size:18 final size:18
Alignment explanation
Indices: 3174411--3174462 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
3174401 TAGTAATCAT
*
3174411 TATTATCAAATCATTAAA
1 TATTATTAAATCATTAAA
* *
3174429 TATTATTAAATTAGT-AA
1 TATTATTAAATCATTAAA
3174446 TCATTATTAAATCATTA
1 T-ATTATTAAATCATTA
3174463 TTAGTAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
17 3 0.11
18 24 0.89
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (18 bp):
TATTATTAAATCATTAAA
Found at i:3174444 original size:39 final size:40
Alignment explanation
Indices: 3174399--3174520 Score: 128
Period size: 40 Copynumber: 3.1 Consensus size: 40
3174389 TTAAATCATT
3174399 ATTAGTAATCATTATTATCAAATCATTA-AAT-ATTATTA-A
1 ATTAGTAATCATTATT-T-AAATCATTATAATAATTATTATA
*
3174438 ATTAGTAATCATTA-TTAAATCATTATTAGTAATTATTATA
1 ATTAGTAATCATTATTTAAATCATTA-TAATAATTATTATA
* * * *
3174478 ATTTGTAATCATTA-TGAAATCATTATTAGTAAATATTATA
1 ATTAGTAATCATTATTTAAATCATTA-TAATAATTATTATA
3174518 ATT
1 ATT
3174521 TCATTATTAG
Statistics
Matches: 75, Mismatches: 4, Indels: 7
0.87 0.05 0.08
Matches are distributed among these distances:
36 9 0.12
37 1 0.01
38 3 0.04
39 21 0.28
40 41 0.55
ACGTcount: A:0.43, C:0.06, G:0.05, T:0.46
Consensus pattern (40 bp):
ATTAGTAATCATTATTTAAATCATTATAATAATTATTATA
Found at i:3174498 original size:40 final size:40
Alignment explanation
Indices: 3174430--3174521 Score: 150
Period size: 40 Copynumber: 2.3 Consensus size: 40
3174420 ATCATTAAAT
* *
3174430 ATTATTA-AATTAGTAATCATTATTAAATCATTATTAGTA
1 ATTATTATAATTTGTAATCATTATGAAATCATTATTAGTA
3174469 ATTATTATAATTTGTAATCATTATGAAATCATTATTAGTA
1 ATTATTATAATTTGTAATCATTATGAAATCATTATTAGTA
*
3174509 AATATTATAATTT
1 ATTATTATAATTT
3174522 CATTATTAGT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
39 7 0.14
40 42 0.86
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.48
Consensus pattern (40 bp):
ATTATTATAATTTGTAATCATTATGAAATCATTATTAGTA
Found at i:3174505 original size:51 final size:52
Alignment explanation
Indices: 3174444--3174556 Score: 133
Period size: 51 Copynumber: 2.2 Consensus size: 52
3174434 TTAAATTAGT
* * * *
3174444 AATCATTATTAAATCATTATTAGTAA-TT-ATTATAATTTGTAATCATTATGA
1 AATCATTATTAAATAAATATTA-TAATTTCATTATAAGTAGTAATCATTATGA
* * *
3174495 AATCATTATT-AGTAAATATTATAATTTCATTATTAGTAGTAATCATTATTA
1 AATCATTATTAAATAAATATTATAATTTCATTATAAGTAGTAATCATTATGA
3174546 AATCATTATTA
1 AATCATTATTA
3174557 GTAATTATTA
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
49 3 0.06
50 10 0.19
51 39 0.75
ACGTcount: A:0.42, C:0.06, G:0.05, T:0.47
Consensus pattern (52 bp):
AATCATTATTAAATAAATATTATAATTTCATTATAAGTAGTAATCATTATGA
Found at i:3174602 original size:25 final size:26
Alignment explanation
Indices: 3174574--3174629 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
3174564 TTATTAAATC
*
3174574 ATTAGTATCAATTCATTA-AATTATT
1 ATTAGTATCAAATCATTAGAATTATT
* *
3174599 ATTATTATTAAATCATTAGTAATTATT
1 ATTAGTATCAAATCATTAG-AATTATT
3174626 ATTA
1 ATTA
3174630 AATCATATCA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
25 15 0.58
27 11 0.42
ACGTcount: A:0.41, C:0.05, G:0.04, T:0.50
Consensus pattern (26 bp):
ATTAGTATCAAATCATTAGAATTATT
Found at i:3174662 original size:154 final size:153
Alignment explanation
Indices: 3174382--3174670 Score: 363
Period size: 154 Copynumber: 1.9 Consensus size: 153
3174372 CAAATCATTT
3174382 ATCATTATTAAATCATTATTAGTAATCATTATTATCAAATCATTAAATATTATTAAATTAGTAAT
1 ATCATTATTAAATCATTATTAGTAA-CATTATTATCAAATCATTAAATATTATTAAATTAGTAAT
* * * * *
3174447 CATTATTAAATCATTATTAGTAATTATTATAATTTGTAATCATTATGAAATCATTATTAGTAAAT
65 CATTATTAAATCATTAGTAATAATTATTATAATATATAATCATTATGAAATCATTACTAGTAAAT
3174512 ATTATAATTTCATTATTAGTAGTA
130 ATTATAATTTCATTATTAGTAGTA
* *
3174536 ATCATTATTAAATCATTATTAGT-A-ATTATTATTAAATCATTAGTATCAATTCATTAAATTA-T
1 ATCATTATTAAATCATTATTAGTAACATTATTATCAAATCATTA-AAT--ATT-ATTAAATTAGT
* * * * *
3174598 TATTATTATTAAATCATTAGTAATTATTATTA-AATCATATCA-CATTGATTAAATCATTACTAG
62 AATCATTATTAAATCATTAGTAATAATTATTATAAT-ATATAATCATT-ATGAAATCATTACTAG
*
3174661 TAATTATTAT
125 TAAATATTAT
3174671 TAAATCAATA
Statistics
Matches: 116, Mismatches: 13, Indels: 12
0.82 0.09 0.09
Matches are distributed among these distances:
151 17 0.15
152 2 0.02
153 8 0.07
154 80 0.69
155 9 0.08
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.46
Consensus pattern (153 bp):
ATCATTATTAAATCATTATTAGTAACATTATTATCAAATCATTAAATATTATTAAATTAGTAATC
ATTATTAAATCATTAGTAATAATTATTATAATATATAATCATTATGAAATCATTACTAGTAAATA
TTATAATTTCATTATTAGTAGTA
Found at i:3174694 original size:22 final size:22
Alignment explanation
Indices: 3174669--3174711 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
3174659 AGTAATTATT
3174669 ATTA-AATCAATATCATTAAATC
1 ATTATAATCAA-ATCATTAAATC
* *
3174691 ATTATTATTAAATCATTAAAT
1 ATTATAATCAAATCATTAAAT
3174712 TCATGAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTATAATCAAATCATTAAATC
Found at i:3176543 original size:2 final size:2
Alignment explanation
Indices: 3176526--3176584 Score: 91
Period size: 2 Copynumber: 29.0 Consensus size: 2
3176516 AATCTATGTG
* *
3176526 AT AT GAT AT AT TT AT AT AT GT 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 AT AT
3176569 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
3176585 GACAATAGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
2 50 0.96
3 2 0.04
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3176876 original size:31 final size:31
Alignment explanation
Indices: 3176837--3176924 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
3176827 AGAGTCGAGG
*
3176837 GTTACCTATGTCTTTCGAGACATATGAACAA
1 GTTACCTATGTCCTTCGAGACATATGAACAA
* * * * *
3176868 TTTACCTATGTCCTTCGGGATATATGGACAG
1 GTTACCTATGTCCTTCGAGACATATGAACAA
*
3176899 GTTACCTATGTTCTTCG-GAACATATG
1 GTTACCTATGTCCTTCGAG-ACATATG
3176925 GATAGGTCCT
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 1 0.02
31 46 0.98
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (31 bp):
GTTACCTATGTCCTTCGAGACATATGAACAA
Found at i:3181736 original size:31 final size:31
Alignment explanation
Indices: 3181697--3181783 Score: 108
Period size: 30 Copynumber: 2.8 Consensus size: 31
3181687 AGAGTCGAGG
3181697 GTTACCTATGTCTTTCGAGACATATGAAC-T
1 GTTACCTATGTCTTTCGAGACATATGAACAT
* *
3181727 GTTTACCTATGTC-TTCGGGACATATGGACAT
1 G-TTACCTATGTCTTTCGAGACATATGAACAT
*
3181758 GTTACCTATGT-TCTTCGAAACATATG
1 GTTACCTATGTCT-TTCGAGACATATG
3181784 GATAGTTCCT
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
30 25 0.51
31 24 0.49
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (31 bp):
GTTACCTATGTCTTTCGAGACATATGAACAT
Done.